BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780143|ref|YP_003064556.1| DNA-directed RNA polymerase
subunit beta [Candidatus Liberibacter asiaticus str. psy62]
         (1386 letters)

Database: nr 
           13,984,884 sequences; 4,792,584,752 total letters

Searching..................................................done



>gi|298291428|ref|YP_003693367.1| DNA-directed RNA polymerase subunit beta [Starkeya novella DSM 506]
 gi|296927939|gb|ADH88748.1| DNA-directed RNA polymerase, beta subunit [Starkeya novella DSM 506]
          Length = 1376

 Score = 1783 bits (4618), Expect = 0.0,   Method: Composition-based stats.
 Identities = 909/1366 (66%), Positives = 1114/1366 (81%), Gaps = 5/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  RVRKFFGK  E+ ++P+LIEVQKASYD FL ++     R ++G+QA FKSV
Sbjct: 1    MAQTFTGRKRVRKFFGKITEVAEMPNLIEVQKASYDQFLQIDEPKGGRADDGIQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ FSGAAMLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFDVD  TG+KS+
Sbjct: 61   FPISDFSGAAMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTGSKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTSNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS L ALG+D EEIL+TFY  I +++  
Sbjct: 181  RIIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLFALGLDGEEILNTFYETIAFTRTK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P      M G K  + LVD DTGE VIE+GKK+T    + L EKG+K L I+ + 
Sbjct: 241  DGWRMPFDP-KRMKGYKAVADLVDADTGEVVIEAGKKVTVRQARQLAEKGLKALKISDEE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G YVAED+VN  TGEIY+EAG+ + EK L+++      ++PIL +D VN  AYIRNTL
Sbjct: 300  MVGQYVAEDLVNPSTGEIYVEAGEEVTEKMLKQLAELGYDELPILDIDHVNVGAYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   A++MF+ LFFDS++YDLS VGRVKMNMRL+L
Sbjct: 360  AIDKNLTREDALFDIYRVMRPGEPPTLDSAQAMFHSLFFDSERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D VR +R+EDI+A+IK LV+LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 420  DAEDTVRVLRREDILAVIKTLVELRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPQDLINAKPVAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIEAPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D +V ++VVYLSAMEE   Y+AQAN  LD +G FTE+L+ CR AG+ +LV  +++D
Sbjct: 600  RRVKDSQVQDEVVYLSAMEEGKYYVAQANIPLDAEGRFTEDLIVCRHAGDVLLVTPDRVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGMESVVA+ 
Sbjct: 660  FMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMESVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R GI++QVDA RIVIR+ E + DPS SGVDIYRL KFQRSNQ+TC+NQRPLV
Sbjct: 720  SGAAIAARRTGIIDQVDATRIVIRATEEN-DPSKSGVDIYRLQKFQRSNQSTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V++ DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L+SE +   DVF+SI
Sbjct: 779  RVGDRVKKGDIIADGPSTDLGDLALGRNILVAFMPWNGYNFEDSILLSENISKGDVFSSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKITPKG
Sbjct: 839  HIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQAGDILCGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GTVV+VR+FNRHG+DK+ER+ ++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKAADVRDTSLRVPPGVTGTVVEVRVFNRHGVDKDERAQAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN++ RL E+L G+  V+GPKGFKK T ++  +++EYPRSQWW
Sbjct: 959  EIERLAKDRDDEQAILDRNVFGRLAEMLDGKTGVAGPKGFKKDTAITRSVLAEYPRSQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            QFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVF+A+KR
Sbjct: 1019 QFAVADDQLMGELEAIRNQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFIAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTPVDMVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC GLG+ I   I  Y+   D++PL+    K+ G     E I+  D+D ++ +    + 
Sbjct: 1139 WACAGLGRVIDRAIESYRQTNDVAPLKDAFGKIYGKD---ETIASLDEDGLVELGSNLRR 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I  ML +A LD S QS L+DG TGE FDR VTVGYIYMLKL+H+
Sbjct: 1196 GVPIATPVFDGAREADIEHMLELAGLDSSAQSTLFDGRTGEQFDRKVTVGYIYMLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L NS+T
Sbjct: 1316 AGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELMNSKT 1361


>gi|161619199|ref|YP_001593086.1| DNA-directed RNA polymerase subunit beta [Brucella canis ATCC 23365]
 gi|260566231|ref|ZP_05836701.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 4 str.
            40]
 gi|189043848|sp|A9M5R0|RPOB_BRUC2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|161336010|gb|ABX62315.1| DNA-directed RNA polymerase, beta subunit [Brucella canis ATCC 23365]
 gi|260155749|gb|EEW90829.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 4 str.
            40]
          Length = 1377

 Score = 1780 bits (4609), Expect = 0.0,   Method: Composition-based stats.
 Identities = 944/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    IAQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSIAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|256113798|ref|ZP_05454598.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 3
            str. Ether]
 gi|265995155|ref|ZP_06107712.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 3
            str. Ether]
 gi|262766268|gb|EEZ12057.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 3
            str. Ether]
          Length = 1377

 Score = 1780 bits (4609), Expect = 0.0,   Method: Composition-based stats.
 Identities = 943/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|306840291|ref|ZP_07473064.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. BO2]
 gi|306289746|gb|EFM60932.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. BO2]
          Length = 1377

 Score = 1779 bits (4608), Expect = 0.0,   Method: Composition-based stats.
 Identities = 944/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  I Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYNTITYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|256061322|ref|ZP_05451470.1| DNA-directed RNA polymerase subunit beta [Brucella neotomae 5K33]
 gi|261325327|ref|ZP_05964524.1| DNA-directed RNA polymerase subunit beta [Brucella neotomae 5K33]
 gi|261301307|gb|EEY04804.1| DNA-directed RNA polymerase subunit beta [Brucella neotomae 5K33]
          Length = 1377

 Score = 1779 bits (4607), Expect = 0.0,   Method: Composition-based stats.
 Identities = 943/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERVSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|17987032|ref|NP_539666.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. 16M]
 gi|62290154|ref|YP_221947.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 1 str.
            9-941]
 gi|82700076|ref|YP_414650.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis biovar
            Abortus 2308]
 gi|148559302|ref|YP_001259162.1| DNA-directed RNA polymerase subunit beta [Brucella ovis ATCC 25840]
 gi|163843508|ref|YP_001627912.1| DNA-directed RNA polymerase subunit beta [Brucella suis ATCC 23445]
 gi|189024390|ref|YP_001935158.1| DNA-directed RNA polymerase beta subunit [Brucella abortus S19]
 gi|237815661|ref|ZP_04594658.1| DNA-directed RNA polymerase, beta subunit [Brucella abortus str. 2308
            A]
 gi|254693945|ref|ZP_05155773.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 3 str.
            Tulya]
 gi|254701982|ref|ZP_05163810.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 5 str.
            513]
 gi|254710311|ref|ZP_05172122.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            B2/94]
 gi|254714308|ref|ZP_05176119.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M644/93/1]
 gi|254717745|ref|ZP_05179556.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M13/05/1]
 gi|254730489|ref|ZP_05189067.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 4 str.
            292]
 gi|256031805|ref|ZP_05445419.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M292/94/1]
 gi|256044890|ref|ZP_05447794.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. Rev.1]
 gi|256159978|ref|ZP_05457693.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M490/95/1]
 gi|256255206|ref|ZP_05460742.1| DNA-directed RNA polymerase subunit beta [Brucella ceti B1/94]
 gi|256369666|ref|YP_003107176.1| DNA-directed RNA polymerase beta subunit [Brucella microti CCM 4915]
 gi|260546699|ref|ZP_05822438.1| DNA-directed RNA polymerase subunit beta [Brucella abortus NCTC 8038]
 gi|260565508|ref|ZP_05835992.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. 16M]
 gi|260758200|ref|ZP_05870548.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 4 str.
            292]
 gi|261214238|ref|ZP_05928519.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 3 str.
            Tulya]
 gi|261219589|ref|ZP_05933870.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M13/05/1]
 gi|261222402|ref|ZP_05936683.1| DNA-directed RNA polymerase subunit beta [Brucella ceti B1/94]
 gi|261317875|ref|ZP_05957072.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            B2/94]
 gi|261322084|ref|ZP_05961281.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M644/93/1]
 gi|261752550|ref|ZP_05996259.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 5 str.
            513]
 gi|265988904|ref|ZP_06101461.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M292/94/1]
 gi|265991318|ref|ZP_06103875.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. Rev.1]
 gi|265998368|ref|ZP_06110925.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M490/95/1]
 gi|306844147|ref|ZP_07476741.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. BO1]
 gi|41017775|sp|Q8YHP8|RPOB_BRUME RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|75496674|sp|Q57CP8|RPOB_BRUAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88909124|sp|Q2YM15|RPOB_BRUA2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229285|sp|A5VR15|RPOB_BRUO2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189043849|sp|B0CH41|RPOB_BRUSI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699377|sp|B2S687|RPOB_BRUA1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|17982686|gb|AAL51930.1| DNA-directed RNA polymerase beta chain [Brucella melitensis bv. 1
            str. 16M]
 gi|62196286|gb|AAX74586.1| RpoB, DNA-directed RNA polymerase [Brucella abortus bv. 1 str. 9-941]
 gi|82616177|emb|CAJ11220.1| RNA polymerase Rpb2, domain 6:RNA polymerase, beta subunit:RNA
            polymerase Rpb2, domain 7:RNA polymerase Rpb2, domain
            2:RNA po [Brucella melitensis biovar Abortus 2308]
 gi|148370559|gb|ABQ60538.1| DNA-directed RNA polymerase, beta subunit [Brucella ovis ATCC 25840]
 gi|163674231|gb|ABY38342.1| DNA-directed RNA polymerase, beta subunit [Brucella suis ATCC 23445]
 gi|189019962|gb|ACD72684.1| DNA-directed RNA polymerase beta subunit [Brucella abortus S19]
 gi|237788959|gb|EEP63170.1| DNA-directed RNA polymerase, beta subunit [Brucella abortus str. 2308
            A]
 gi|255999828|gb|ACU48227.1| DNA-directed RNA polymerase beta subunit [Brucella microti CCM 4915]
 gi|260095749|gb|EEW79626.1| DNA-directed RNA polymerase subunit beta [Brucella abortus NCTC 8038]
 gi|260151576|gb|EEW86670.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. 16M]
 gi|260668518|gb|EEX55458.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 4 str.
            292]
 gi|260915845|gb|EEX82706.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 3 str.
            Tulya]
 gi|260920986|gb|EEX87639.1| DNA-directed RNA polymerase subunit beta [Brucella ceti B1/94]
 gi|260924678|gb|EEX91246.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M13/05/1]
 gi|261294774|gb|EEX98270.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M644/93/1]
 gi|261297098|gb|EEY00595.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            B2/94]
 gi|261742303|gb|EEY30229.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 5 str.
            513]
 gi|262552836|gb|EEZ08826.1| DNA-directed RNA polymerase subunit beta [Brucella ceti M490/95/1]
 gi|263002102|gb|EEZ14677.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 1
            str. Rev.1]
 gi|264661101|gb|EEZ31362.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M292/94/1]
 gi|306275590|gb|EFM57322.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. BO1]
          Length = 1377

 Score = 1779 bits (4607), Expect = 0.0,   Method: Composition-based stats.
 Identities = 943/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|254689460|ref|ZP_05152714.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 6 str.
            870]
 gi|256257706|ref|ZP_05463242.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 9 str.
            C68]
 gi|260754984|ref|ZP_05867332.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 6 str.
            870]
 gi|260883992|ref|ZP_05895606.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 9 str.
            C68]
 gi|297248548|ref|ZP_06932266.1| DNA-directed RNA polymerase, beta subunit [Brucella abortus bv. 5
            str. B3196]
 gi|260675092|gb|EEX61913.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 6 str.
            870]
 gi|260873520|gb|EEX80589.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 9 str.
            C68]
 gi|297175717|gb|EFH35064.1| DNA-directed RNA polymerase, beta subunit [Brucella abortus bv. 5
            str. B3196]
          Length = 1377

 Score = 1779 bits (4607), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTG+ V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGKVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|254704525|ref|ZP_05166353.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 3 str.
            686]
 gi|261755209|ref|ZP_05998918.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 3 str.
            686]
 gi|261744962|gb|EEY32888.1| DNA-directed RNA polymerase subunit beta [Brucella suis bv. 3 str.
            686]
          Length = 1377

 Score = 1778 bits (4606), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDV++C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVNECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|254719298|ref|ZP_05181109.1| DNA-directed RNA polymerase subunit beta [Brucella sp. 83/13]
 gi|265984299|ref|ZP_06097034.1| DNA-directed RNA polymerase subunit beta [Brucella sp. 83/13]
 gi|306838942|ref|ZP_07471767.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. NF 2653]
 gi|264662891|gb|EEZ33152.1| DNA-directed RNA polymerase subunit beta [Brucella sp. 83/13]
 gi|306405975|gb|EFM62229.1| DNA-directed RNA polymerase, beta subunit [Brucella sp. NF 2653]
          Length = 1377

 Score = 1778 bits (4606), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1136/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+L +LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLEELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|23502120|ref|NP_698247.1| DNA-directed RNA polymerase subunit beta [Brucella suis 1330]
 gi|41017741|sp|Q8G069|RPOB_BRUSU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|23348081|gb|AAN30162.1| DNA-directed RNA polymerase, beta subunit [Brucella suis 1330]
          Length = 1377

 Score = 1778 bits (4605), Expect = 0.0,   Method: Composition-based stats.
 Identities = 943/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEAVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|225852740|ref|YP_002732973.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis ATCC
            23457]
 gi|256263773|ref|ZP_05466305.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 2
            str. 63/9]
 gi|254765276|sp|C0RJL1|RPOB_BRUMB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|225641105|gb|ACO01019.1| DNA-directed RNA polymerase, beta subunit [Brucella melitensis ATCC
            23457]
 gi|263093884|gb|EEZ17835.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis bv. 2
            str. 63/9]
 gi|326409265|gb|ADZ66330.1| DNA-directed RNA polymerase subunit beta [Brucella melitensis M28]
 gi|326538972|gb|ADZ87187.1| DNA-directed RNA polymerase, beta subunit [Brucella melitensis M5-90]
          Length = 1377

 Score = 1776 bits (4601), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1137/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQ N  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL++++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLVDMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|294852579|ref|ZP_06793252.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
 gi|294821168|gb|EFG38167.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
          Length = 1377

 Score = 1775 bits (4598), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1376 (68%), Positives = 1135/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+ LRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVALRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P  A     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYFAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFA++DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAIEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|225627712|ref|ZP_03785749.1| DNA-directed RNA polymerase, beta subunit [Brucella ceti str. Cudo]
 gi|260168939|ref|ZP_05755750.1| DNA-directed RNA polymerase subunit beta [Brucella sp. F5/99]
 gi|261758432|ref|ZP_06002141.1| DNA-directed RNA polymerase subunit beta [Brucella sp. F5/99]
 gi|225617717|gb|EEH14762.1| DNA-directed RNA polymerase, beta subunit [Brucella ceti str. Cudo]
 gi|261738416|gb|EEY26412.1| DNA-directed RNA polymerase subunit beta [Brucella sp. F5/99]
          Length = 1377

 Score = 1774 bits (4595), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1136/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGV SRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVLSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1374


>gi|153009277|ref|YP_001370492.1| DNA-directed RNA polymerase subunit beta [Ochrobactrum anthropi ATCC
            49188]
 gi|166229296|sp|A6X0A9|RPOB_OCHA4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|151561165|gb|ABS14663.1| DNA-directed RNA polymerase, beta subunit [Ochrobactrum anthropi ATCC
            49188]
          Length = 1377

 Score = 1774 bits (4595), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1138/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRSDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFD PKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDAPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD E+ILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEDILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA D   G K+ S L+D DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSA-DRFKGMKIISDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D +N   YIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHINIGGYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDERGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIAARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD +++ DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDPIQKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK + ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGSTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVDDEKLQGELEALRGQYDESKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  LI+ Y+   +I PLR  LE +       E +  YDDDSVL +A Q 
Sbjct: 1139 LGWACAGMGKKIGELIDVYRKTANIEPLRDTLEHIYPDNDRNEPVRSYDDDSVLMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R +    + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTRDEQQQALPD 1374


>gi|110634169|ref|YP_674377.1| DNA-directed RNA polymerase subunit beta [Mesorhizobium sp. BNC1]
 gi|122965927|sp|Q11HB3|RPOB_MESSB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110285153|gb|ABG63212.1| DNA-directed RNA polymerase subunit beta [Chelativorans sp. BNC1]
          Length = 1379

 Score = 1773 bits (4593), Expect = 0.0,   Method: Composition-based stats.
 Identities = 934/1372 (68%), Positives = 1141/1372 (83%), Gaps = 2/1372 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTQTFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPQGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+G AMLEFV YEF+ PKFD ++C  RDLTYA PLK+TLRLIVFD+DE TG+K
Sbjct: 61   SVFPISDFAGTAMLEFVKYEFEAPKFDTEECRQRDLTYAAPLKVTLRLIVFDIDEDTGSK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEILSTFY K+ + +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILSTFYNKLTFIR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K ++ ++D DTGE V+E+GKK+T+ + + L +KG+K +  T 
Sbjct: 241  DGDNWRVPFSAE-RFRGMKATADIIDADTGEVVLEAGKKMTARMARQLADKGLKAIRATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN +TGEI++EAGD IDEK+L+ +  +   ++  L +D VN   YIRN
Sbjct: 300  DDLLGNYLAEDIVNMKTGEIFLEAGDEIDEKTLKILLETAGNEVKFLDIDHVNIGGYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLV DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLVADKNESRQDALFDIYRVMRPGEPPTLETAEAMFHSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD VR +R ED++A+++ LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  ELDCPDTVRVLRSEDMVAVVRTLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT +VVYLSAMEE   Y+AQAN+++DE+G F +E V CR AGE I+ PRE 
Sbjct: 600  PYRKIVDGKVTEEVVYLSAMEEAKHYVAQANATIDENGGFADEFVVCRHAGEVIMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  +D S SGVDIYRL KFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIAARRTGVVDQVDATRIVIRATED-VDASQSGVDIYRLQKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V +D+FT
Sbjct: 779  LVRVGDLINKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVRDDIFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL E+L G+ A++GPKGFKK   L+ +L+ EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQSILDRNVYARLSEMLIGKEAIAGPKGFKKGGALTKELLGEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK+ L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQSELEALRAQYDESKNALQQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKMQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI+ YK  GDI PLR+ +E +I      E +  YDD+SV+R++EQ 
Sbjct: 1139 LGWACAGMGRQIGELIDAYKEAGDIKPLRAKIESLIPDNDRNEPVRQYDDESVVRLSEQL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A L+ SGQ  LYDG TGE FDR VTVGYIYMLKL+
Sbjct: 1199 RRGVSIATPVFDGAHESDINEMLEEAGLNSSGQVTLYDGRTGEEFDRKVTVGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++LENS   ++ 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENSSRFDTP 1370


>gi|254706579|ref|ZP_05168407.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M163/99/10]
 gi|261314038|ref|ZP_05953235.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M163/99/10]
 gi|261303064|gb|EEY06561.1| DNA-directed RNA polymerase subunit beta [Brucella pinnipedialis
            M163/99/10]
          Length = 1377

 Score = 1773 bits (4592), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1376 (68%), Positives = 1136/1376 (82%), Gaps = 2/1376 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTHSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFV YEFDPPKFDVD+C  RDL Y+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLIYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++
Sbjct: 181  AARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T 
Sbjct: 241  DGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  DDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITP
Sbjct: 839  SIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q 
Sbjct: 1139 LGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQV 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 KRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTRKAEQPALPD 1374


>gi|150396199|ref|YP_001326666.1| DNA-directed RNA polymerase subunit beta [Sinorhizobium medicae
            WSM419]
 gi|166229307|sp|A6U851|RPOB_SINMW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|150027714|gb|ABR59831.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium medicae
            WSM419]
          Length = 1380

 Score = 1773 bits (4591), Expect = 0.0,   Method: Composition-based stats.
 Identities = 967/1382 (69%), Positives = 1158/1382 (83%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPQGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYQR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P    D + G K  + L+D DTGE V+E GKKLT  LL+ L++KG+K L  T 
Sbjct: 241  DGEGWRVPFQP-DALKGQKALADLIDADTGEVVVEGGKKLTPRLLRQLQDKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDIDHINIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT+DVVYLSAMEE   ++AQANS LDEDGSF+EE V CR AGE +L PR+ 
Sbjct: 600  PYRKIVDGKVTSDVVYLSAMEEAKYHVAQANSVLDEDGSFSEEFVVCRHAGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V +DVFT
Sbjct: 779  LVTVGDVLNKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVRDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL+++L G  AV+GPKGFKK T LS+ +ISEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLVDMLRGHVAVAGPKGFKKGTELSNAVISEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA++DEK Q  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAIEDEKAQGEIEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD+S++R+AEQ 
Sbjct: 1139 LGWACAGMGKKIGAMLDAYKAGADIQPLRDTIDSVIGSGPKGEPIKQYDDESIVRLAEQT 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 RRGVSIATPVFDGAVEADVNEMLEQAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+        ++PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKVDEVGASAQLPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|15965101|ref|NP_385454.1| DNA-directed RNA polymerase subunit beta [Sinorhizobium meliloti
            1021]
 gi|307314836|ref|ZP_07594429.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium meliloti
            BL225C]
 gi|307322135|ref|ZP_07601509.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium meliloti
            AK83]
 gi|41018106|sp|Q92QH7|RPOB_RHIME RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|15074281|emb|CAC45927.1| Probable DNA-directed RNA polymerase beta chain [Sinorhizobium
            meliloti 1021]
 gi|306892220|gb|EFN23032.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium meliloti
            AK83]
 gi|306898950|gb|EFN29597.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium meliloti
            BL225C]
          Length = 1380

 Score = 1771 bits (4587), Expect = 0.0,   Method: Composition-based stats.
 Identities = 968/1382 (70%), Positives = 1160/1382 (83%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPQGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYQR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P    D + G K  + ++D DTGE V+ESGKKLT  LL+ L+EKG+K L  T 
Sbjct: 241  DGEGWRVPFQP-DALKGQKTLADMIDADTGEVVVESGKKLTPRLLRQLQEKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDIDHINIGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVTNDVVYLSAMEE   ++AQANS LD+DGSF+EE V CR AGE +L PR+ 
Sbjct: 600  PYRKIVDGKVTNDVVYLSAMEEAKYHVAQANSVLDDDGSFSEEFVVCRHAGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIAARRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V +DVFT
Sbjct: 779  LVTVGDVINKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVRDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL+++L G  AV+GPKGFKK T LS+ +ISEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLVDMLRGHVAVAGPKGFKKGTELSNVVISEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA++DEK Q  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAIEDEKAQGEIEALRAQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD+S++R+AEQ 
Sbjct: 1139 LGWACAGMGKKIGAMLDAYKAGADIQPLRDTIDSVIGSGPKGEPIKQYDDESIVRLAEQT 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 RRGVSIATPVFDGAVEADVNEMLEQAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+  +     ++PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKVDDVGSTAQLPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|27380521|ref|NP_772050.1| DNA-directed RNA polymerase subunit beta [Bradyrhizobium japonicum
            USDA 110]
 gi|41017724|sp|Q89J74|RPOB_BRAJA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|27353685|dbj|BAC50675.1| DNA-directed RNA polymerase beta chain [Bradyrhizobium japonicum USDA
            110]
          Length = 1372

 Score = 1769 bits (4583), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1378 (65%), Positives = 1122/1378 (81%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPQGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++P+L +D VN  AYIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEQGYKELPLLDIDHVNVGAYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE + V  +K
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRYTVAQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDIVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL E+L G+  ++GPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYNRLAELLEGRQGIAGPKGFKKDTKITRAVLEEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I   ++ Y +  DI PL+  L+KV G     E I   +D+ ++ +    
Sbjct: 1138 LGWACAGLGKRIGQTVDAYLSKQDIKPLKETLKKVYGED---ETIKSLNDNELIELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKMGPAPTSEAAE 1372


>gi|220921892|ref|YP_002497193.1| DNA-directed RNA polymerase subunit beta [Methylobacterium nodulans
            ORS 2060]
 gi|254765296|sp|B8IS78|RPOB_METNO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219946498|gb|ACL56890.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium nodulans
            ORS 2060]
          Length = 1374

 Score = 1769 bits (4581), Expect = 0.0,   Method: Composition-based stats.
 Identities = 899/1382 (65%), Positives = 1124/1382 (81%), Gaps = 8/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM++     RP+EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIREVAEMPNLIEVQKASYDQFLMVDEPEGGRPDEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAK
Sbjct: 59   SVFPISDFSSTALLEFVKYTFEAPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT++GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTENGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI++ RIDR+RK+PVTS L ALG+D EEILSTFY +I Y++
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVYARIDRKRKIPVTSLLFALGLDGEEILSTFYNRISYTR 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G K S+ L+D D+GE V+E+GKKLT+   + + EKGV  L  T 
Sbjct: 239  DGADWRVPYDAERL-KGFKASTDLIDADSGEVVLEAGKKLTARSARQIAEKGVTALRATD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAGD I EK L+ +    I +IP+L +D VN   YIRN
Sbjct: 298  EDLIGQYIAEDMVNYKTGEIYAEAGDEISEKLLKGLADVGIEEIPVLDIDHVNVGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN +R+ AL DIYRVMRPG+  T   AE+MF+ LFFD+++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSNREGALFDIYRVMRPGEPPTLDTAEAMFHSLFFDAERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD +R +R++D++A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAPDTMRTLRRDDMLAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 478  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V +G VT++VVYLSAMEE   Y+AQA++++DE+   TE+LV CR AGE I+V  ++
Sbjct: 598  PFRRVKNGVVTDEVVYLSAMEEARYYVAQASAAMDENRRLTEDLVVCRRAGEVIVVAPDR 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGMESVVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMESVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+GIV+QVDA RIVIR+ E   DP+  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRSGIVDQVDATRIVIRATEET-DPTKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG++V + DIIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEQVGKGDIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+ GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL ++L GQ  V+GPKGFKK TVL+ + +++YPRSQ
Sbjct: 957  REEIERLAKDRDDEQAILDRNTYARLADVLVGQAPVAGPKGFKKDTVLTREGLADYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVVDDRLMTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+++   ++ Y  + D +PLR  + ++         +    D  +  +    
Sbjct: 1137 LGWAAAGLGRQVAQAVDAYLRSHDATPLREQMRRIYSEAE----LDGLSDQDLAEIGNNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I +ML MA LD SGQS LYDG TGEPFDR VTVGYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIEAMLEMAGLDRSGQSTLYDGRTGEPFDRKVTVGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +S+   + ++E  P+ 
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELISSKRAANDQLEAPPEA 1372

Query: 1381 NK 1382
             +
Sbjct: 1373 AE 1374


>gi|222085668|ref|YP_002544198.1| DNA-directed RNA polymerase, beta subunit [Agrobacterium radiobacter
            K84]
 gi|254765265|sp|B9JDS1|RPOB_AGRRK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|221723116|gb|ACM26272.1| DNA-directed RNA polymerase, beta subunit [Agrobacterium radiobacter
            K84]
          Length = 1380

 Score = 1768 bits (4580), Expect = 0.0,   Method: Composition-based stats.
 Identities = 969/1382 (70%), Positives = 1166/1382 (84%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQ+ FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQSVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEILSTFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILSTFYTKSLYER 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P +A  L  GAK  + ++D DTGE V+E GKKLT  LL+ L++KG+K L  T 
Sbjct: 241  SGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVEGGKKLTPRLLRQLQDKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L GL++AEDIVN +TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  EDLYGLFLAEDIVNFQTGEIYLEAGDEIDEKTLPVILKAGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L+  D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLEVADTVRVLRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVT DV+YLSAMEE   Y+AQAN+ LD +GSF EE V CR AGE +L PR+ 
Sbjct: 600  PYRRIIDGKVTTDVLYLSAMEEAKYYVAQANAELDAEGSFIEEFVVCRHAGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLMKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + DI+ADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDFVNKGDILADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+E+L GQ A++GPK FKK T LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIEMLRGQVALAGPKNFKKGTELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQGELEALRGQYDESKSHLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI  YKANG+I PLR  ++ V+G G  ++ + +YDD SVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIEAYKANGNIEPLRKTIDMVVGDGPKSDDVHNYDDASVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  +N ML MA L E+GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGAGEADVNEMLAMAGLKETGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+  +     ++PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKVDDLQAAGQLPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|227821748|ref|YP_002825718.1| DNA-directed RNA polymerase subunit beta [Sinorhizobium fredii
            NGR234]
 gi|254765299|sp|C3MAX2|RPOB_RHISN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|227340747|gb|ACP24965.1| DNA-directed RNA polymerase, beta subunit [Sinorhizobium fredii
            NGR234]
          Length = 1380

 Score = 1768 bits (4579), Expect = 0.0,   Method: Composition-based stats.
 Identities = 963/1382 (69%), Positives = 1161/1382 (84%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPAGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEILSTFY + +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILSTFYTQSLYQR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL+ L+EKG+K L  T 
Sbjct: 241  DGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRQLQEKGLKALKSTD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLS+  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSRFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DG VT+DVVYLSAME+   ++AQANS L++DGSF EE V CR AGE +L PR+ 
Sbjct: 600  PYRKIVDGNVTSDVVYLSAMEDAKYHVAQANSVLNDDGSFAEEFVVCRHAGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGMESVVA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMESVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIAARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V +DVFT
Sbjct: 779  LVTVGDLVNKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVRDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL+++L G  AV+GPKGFKK T LS+ +ISEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLIDMLRGHVAVAGPKGFKKGTELSNAVISEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEK Q  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKAQGEIEALRAQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI ++++ Y  +GDI PLR+ ++ VIG+G   E I  YDD+S++R+AEQ 
Sbjct: 1139 LGWACAGMGKKIGAMLDAYHESGDIKPLRTTIDDVIGSGPKGEPIKQYDDESIVRLAEQT 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKLN
Sbjct: 1199 RRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+  +     ++PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKVDDLGTTAQLPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|316933512|ref|YP_004108494.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            DX-1]
 gi|315601226|gb|ADU43761.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            DX-1]
          Length = 1374

 Score = 1768 bits (4579), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1380 (65%), Positives = 1117/1380 (80%), Gaps = 8/1380 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+   P  RP+EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVAEPPGGRPDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS A+MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNASMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARIIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEEILSTFYNKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              D W  P    +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKDGWRVPFDV-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I +K+L+ +     +++P+L +D VN   YIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIYAEAGEEITDKALKMLNEQGYKELPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLNVDKNMTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+A+IK LV LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTHRTLRKEDILAVIKTLVGLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYR+V DG VT++VVYLSAMEE    +AQAN  LD  G FT++L+ CR     + +L+P 
Sbjct: 599  PYRRVKDGHVTDEVVYLSAMEEGRYAVAQANVPLDAKGRFTDDLIVCRAGGTRDVVLIPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DQVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R GI++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGIIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 778  RPLVKVGDHVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEE+TRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEVTRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L G+  ++GPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLDGRQGIAGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFAAPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   I+ Y  + D+ PLR  L K+ G     E I   DD  +L +  
Sbjct: 1138 THLGWACAGLGKRIGQTIDTYYQSQDLKPLRETLRKIYGED---ETIKSLDDGELLELGR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVFDGA E  I  ML++A  D SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLRHGVPIATPVFDGAKEADIEEMLKLAGFDASGQSTVYDGRTGDQFDRRVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+  N+   E   
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGNTPPAEAAE 1374


>gi|158422511|ref|YP_001523803.1| DNA-directed RNA polymerase subunit beta [Azorhizobium caulinodans
            ORS 571]
 gi|182676552|sp|A8HTY8|RPOB_AZOC5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158329400|dbj|BAF86885.1| DNA-directed RNA polymerase beta subunit [Azorhizobium caulinodans
            ORS 571]
          Length = 1376

 Score = 1768 bits (4578), Expect = 0.0,   Method: Composition-based stats.
 Identities = 907/1382 (65%), Positives = 1115/1382 (80%), Gaps = 6/1382 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RKFFGK  E+ ++P+LIEVQKASYD FL +      R ++GLQA FKSV
Sbjct: 1    MAQTFTGRKRIRKFFGKIKEVAEMPNLIEVQKASYDQFLQIEEPKGGRADDGLQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ FSGAAMLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAKS+
Sbjct: 61   FPISDFSGAAMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +Y GD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYTGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS L ALG+DSEEIL+TFY KI+Y++  
Sbjct: 181  RIIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLFALGLDSEEILNTFYEKILYTRAK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P      M G K  + L+D DTGE V+E+GKKLT    + L EKG+K L I+ D 
Sbjct: 241  DGWRMPFDP-KRMKGYKAVADLIDADTGEVVVEAGKKLTVRAARQLVEKGLKALKISDDE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y+ EDIVN  TGEIY EAG+ I EK L+ +  +   +IP+L +D +N  AYIRNTL
Sbjct: 300  MVGQYIGEDIVNVHTGEIYAEAGEEITEKVLKTLGDAGFDEIPVLDIDHINTGAYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R++AL DIYRVMRPG+  T   A++MF+ LFFD+++YDLS VGRVKMNMRL+L
Sbjct: 360  SADKNSSREEALFDIYRVMRPGEPPTLDSAQAMFHSLFFDAERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D VR +R+EDI+A+IK LV+LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 420  DAEDTVRILRREDILAVIKTLVELRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPQDLINAKPVAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIEAPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG+VT++VVYLSAMEE   Y+AQAN  LD DG F E+LV CR AG+ ++V  +++D
Sbjct: 600  RRVVDGRVTDEVVYLSAMEEGKYYVAQANVPLDTDGRFQEDLVICRHAGDVLVVSPDRVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VVA+ 
Sbjct: 660  FMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRSQAPLVGTGMEAVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+RAG+++QVDA RIVIR+  G+ DPS SGVDIYRLMKFQRSNQ+TC+NQRPLV
Sbjct: 720  SGAAIAARRAGVIDQVDATRIVIRAT-GETDPSKSGVDIYRLMKFQRSNQSTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V++ DIIADGPST+LG+LALGRN+LVAFMPW+GYN+EDS+L+SE +V EDVFTSI
Sbjct: 779  RVGDVVKKGDIIADGPSTELGELALGRNVLVAFMPWNGYNYEDSILLSENIVKEDVFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFE MARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKG
Sbjct: 839  HIEEFEAMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P G +GT+V+VR+FNRHG+DK+ER++++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKAADVRDTSLRLPPGTTGTIVEVRVFNRHGVDKDERALAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN+Y RL E+L G+ A++GPK FKK T ++ D + EYPRSQWW
Sbjct: 959  EIERLAKDRDDEQAILDRNVYGRLSEMLVGKVAIAGPKAFKKDTEITKDALGEYPRSQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             FAV D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1019 LFAVADDALMSELEAIRAQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTNVDIVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC GLG+++ + ++ Y  + D   LR+ L KV G     + I   D+  +  + E  + 
Sbjct: 1139 WACAGLGRQVAAAVDAYYGSKDQQVLRNALVKVYG----PDDIEVLDEKQITELGENLRK 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I   L  A L+ SGQS L+DG TGEPFDR VTVGYIYMLKL+H+
Sbjct: 1195 GVPMATPVFDGAHEADIEEHLEKAGLNPSGQSTLFDGRTGEPFDRKVTVGYIYMLKLHHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             GRT+VYE+IV G DTFE+G PESFNVLVKEM++LGL+++L NS+T          +   
Sbjct: 1315 AGRTKVYEAIVRGEDTFESGIPESFNVLVKEMRSLGLNVELLNSKTGRQTNPGTRENLPA 1374

Query: 1383 CE 1384
             E
Sbjct: 1375 AE 1376


>gi|148256402|ref|YP_001240987.1| DNA-directed RNA polymerase subunit beta [Bradyrhizobium sp. BTAi1]
 gi|158513289|sp|A5ELN7|RPOB_BRASB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146408575|gb|ABQ37081.1| DNA-directed RNA polymerase subunit beta [Bradyrhizobium sp. BTAi1]
          Length = 1372

 Score = 1767 bits (4577), Expect = 0.0,   Method: Composition-based stats.
 Identities = 907/1378 (65%), Positives = 1120/1378 (81%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     RP+EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRPDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY K++Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEQILSTFYKKLIYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRTARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I +K  + +     +D+P+L +D VN   YIRN
Sbjct: 299  EELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKVLNEQGYKDLPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTQRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE + +  +K
Sbjct: 599  PYRKVRDGRVTDEVVYLSAMEEGRYRVAQANVPLDAKGRFTEDLVVCRHAGEVVPMTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+V+Q+DA R+VIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVVDQIDATRVVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDIVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+YSRL ++L G+  +SGPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYSRLADMLDGRQGISGPKGFKKDTKITRAVLDEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFASANDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I   ++ Y +  D+ PL+  L+++ G     E I   +D+ +L +    
Sbjct: 1138 LGWACAGLGKRIAQTVDAYLSKQDVKPLKETLKRIYGED---ETIKSLNDNELLELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML++A +D SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKEADIEEMLKLAGMDASGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGPAPTSEAAE 1372


>gi|163759407|ref|ZP_02166493.1| DNA-directed RNA polymerase beta subunit [Hoeflea phototrophica
            DFL-43]
 gi|162283811|gb|EDQ34096.1| DNA-directed RNA polymerase beta subunit [Hoeflea phototrophica
            DFL-43]
          Length = 1380

 Score = 1767 bits (4576), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1382 (67%), Positives = 1146/1382 (82%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRK FGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKIFGKIPEVAEMPNLIEVQKASYDQFLMVEEPQGGRTDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG+AMLEFVSYEF+ PKFDV++C  RDLTY+ PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPISDFSGSAMLEFVSYEFEHPKFDVEECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PV+S LMALGMD+EEILSTFY   VYS+
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVSSLLMALGMDAEEILSTFYTHSVYSR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  G K    ++D D+ E V+E+GKKLT  LL+ L EKGVK +  T 
Sbjct: 241  DGEGWRIPFQPETL-KGQKTIVDMIDADSNEVVVEAGKKLTPRLLRQLTEKGVKSIKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN ETGE+++EAGD IDEK+L  +  + + +IP+L +D +N  AYIRN
Sbjct: 300  EDLYGSYLAEDIVNPETGEVFLEAGDEIDEKTLPVLAEAGLDEIPVLDIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAADKNESRQDALFDIYRVMRPGEPPTMESAEAMFQSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RK+DI+A++K LV LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDAEDTVRVLRKDDILAVVKTLVSLRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT +VVYLSAMEE   ++AQAN+ L EDGS  +E +  R AG+ ++ PRE 
Sbjct: 600  PYRKIKDGKVTEEVVYLSAMEEAKYHVAQANAELSEDGSLVDEFIVSRHAGDVMMTPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ID +D SP+Q+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  IDLMDVSPRQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E   + S SGVDIYRL KFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIAARRGGVVDQVDATRIVIRATEDM-EASRSGVDIYRLQKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+VS+DVFT
Sbjct: 779  LVTVGDVINKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+EFEVMARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIDEFEVMARDTKLGPEEITRDIPNVSEEALRNLDEAGIVYIGAEVAPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL ++L G+ A++GPKGFKK   ++ + I+EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLSDMLKGKAAIAGPKGFKKGAEVTEEAIAEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKLQGEIEALRAQYDDSKKLLESRFMDKVEKVQRGDELPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILPCEDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRILPCEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GK+I  +++ Y A G+I PLR  ++ VIGTG   E    YDD S++R+AEQ 
Sbjct: 1139 LGWACAGMGKQIGEMLDAYNAGGEIQPLRDTIDSVIGTGPKGEPTKQYDDPSIVRLAEQT 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A L+ SGQS LYDG TGE FDRPVTVGYIYMLKLN
Sbjct: 1199 RRGVSIATPVFDGAVEADINIMLEQAGLNVSGQSTLYDGRTGETFDRPVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++LE+++    A  +E+PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELESAKIDGIADQDELPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|36333357|gb|AAP75736.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 1372

 Score = 1767 bits (4576), Expect = 0.0,   Method: Composition-based stats.
 Identities = 904/1378 (65%), Positives = 1121/1378 (81%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPAGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN  AYIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDIDHVNVGAYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE + V  +K
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRYTVAQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDIVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL E+L G+  ++GPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYNRLAELLEGRQGIAGPKGFKKDTKITRAVLEEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I   ++ Y +  DI PL+  L+KV G     E I   +D+ ++ +    
Sbjct: 1138 LGWACAGLGKRIGQTVDAYLSKQDIKPLKETLKKVYGED---ETIKTLNDNELIELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+ FDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDAFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKVGPAPTSEAAE 1372


>gi|146340046|ref|YP_001205094.1| DNA-directed RNA polymerase subunit beta [Bradyrhizobium sp. ORS278]
 gi|158514299|sp|A4YSI1|RPOB_BRASO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146192852|emb|CAL76857.1| RNA polymerase, beta subunit [Bradyrhizobium sp. ORS278]
          Length = 1372

 Score = 1766 bits (4574), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1378 (65%), Positives = 1120/1378 (81%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     RP+EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRPDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+IL+TFY K++Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMFALGLDGEQILATFYKKLIYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I +K  + +     +D+P+L +D VN   YIRN
Sbjct: 299  EELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKVLNEQGYKDLPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTQRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE + +  +K
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRYRVAQANVPLDAKGRFTEDLVVCRHAGEVVPMTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDIVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+YSRL ++L G+  +SGPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYSRLADMLDGRQGISGPKGFKKDTKITRAVLDEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFAASNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I   ++ Y +  D+ PL+  L+++ G     E I   +D+ +L +    
Sbjct: 1138 LGWACAGLGKRIAQTVDAYLSKQDVKPLKETLKRIYGED---ETIKTLNDNELLELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML++A +D SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKESDIEEMLKLAGMDASGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGPAPTSEAAE 1372


>gi|71390282|gb|AAZ31528.1| DNA-dependent RNA polymerase beta chain [Brucella suis]
 gi|71390288|gb|AAZ31531.1| DNA-dependent RNA polymerase beta chain [Brucella canis]
          Length = 1364

 Score = 1766 bits (4574), Expect = 0.0,   Method: Composition-based stats.
 Identities = 941/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    IAQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSIAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|36333341|gb|AAP75728.1| RNA polymerase beta subunit [Afipia broomeae ATCC 49717]
          Length = 1372

 Score = 1766 bits (4573), Expect = 0.0,   Method: Composition-based stats.
 Identities = 907/1378 (65%), Positives = 1116/1378 (80%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              D W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKDGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRSARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G+Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++P+L +D VN   YIRN
Sbjct: 299  DELVGMYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPLLDIDHVNIGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLAADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT+DVVYLSAMEE    +AQAN  LD  G FT++LV CR AGE + +  +K
Sbjct: 599  PYRKVKDGRVTDDVVYLSAMEEGRYRVAQANVPLDNKGRFTDDLVICRHAGEVLQITPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD+VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 778  LVKVGDQVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN++ RL ++L  +  ++GPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVFGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWQFASPNDKLMAEIEAMRXQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I      Y +  D+ PL+  L+KV G     E I   +D  +L +A   
Sbjct: 1138 LGWACAGLGKRIGQAAEAYWSKQDLKPLKETLKKVYGDD---ETIKSLNDSELLELARNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA E+ I  ML +A +++SGQS++YDG TG+ FDR VTVGYIYMLKL+
Sbjct: 1195 KPGVPIATPVFDGAKEKDIEDMLELAGMNKSGQSVVYDGRTGDQFDRNVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGPTPTSEAAE 1372


>gi|46982188|gb|AAT08134.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
 gi|71390276|gb|AAZ31525.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1765 bits (4572), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|71390300|gb|AAZ31537.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
          Length = 1364

 Score = 1765 bits (4571), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEIDVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|71390290|gb|AAZ31532.1| DNA-dependent RNA polymerase beta chain [Brucella neotomae]
          Length = 1364

 Score = 1765 bits (4571), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERVSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|49089813|gb|AAT51864.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|49089815|gb|AAT51865.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390270|gb|AAZ31522.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
 gi|71390272|gb|AAZ31523.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
 gi|71390278|gb|AAZ31526.1| DNA-dependent RNA polymerase beta chain [Brucella suis ATCC 23445]
 gi|71390284|gb|AAZ31529.1| DNA-dependent RNA polymerase beta chain [Brucella suis]
 gi|71390286|gb|AAZ31530.1| DNA-dependent RNA polymerase beta chain [Brucella ovis]
 gi|71390292|gb|AAZ31533.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390294|gb|AAZ31534.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390296|gb|AAZ31535.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390298|gb|AAZ31536.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390302|gb|AAZ31538.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390308|gb|AAZ31541.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
          Length = 1364

 Score = 1765 bits (4571), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|86357297|ref|YP_469189.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli CFN 42]
 gi|123512272|sp|Q2K9M4|RPOB_RHIEC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|86281399|gb|ABC90462.1| DNA-directed RNA polymerase beta chain protein [Rhizobium etli CFN
            42]
          Length = 1379

 Score = 1765 bits (4571), Expect = 0.0,   Method: Composition-based stats.
 Identities = 958/1375 (69%), Positives = 1155/1375 (84%), Gaps = 2/1375 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAGD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLAVILANGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLSVEDTVRTLRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVTNDV+YLSAMEE   Y+AQAN+ L+ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGKVTNDVLYLSAMEEAKYYVAQANAELNADGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDVVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+++L GQ +++GPKGFKK T LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIDMLRGQVSIAGPKGFKKGTELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI  YKANG+I PLR  +  V+G G   E++ ++DD+SVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIEAYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDESVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEGDVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   +   +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDEAQATQ 1373


>gi|71390304|gb|AAZ31539.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390306|gb|AAZ31540.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
 gi|71390310|gb|AAZ31542.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
          Length = 1364

 Score = 1764 bits (4570), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTG+ V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGKVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|71390280|gb|AAZ31527.1| DNA-dependent RNA polymerase beta chain [Brucella suis]
          Length = 1364

 Score = 1764 bits (4570), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDV++C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVNECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|154253170|ref|YP_001413994.1| DNA-directed RNA polymerase subunit beta [Parvibaculum
            lavamentivorans DS-1]
 gi|171769622|sp|A7HWQ4|RPOB_PARL1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|154157120|gb|ABS64337.1| DNA-directed RNA polymerase, beta subunit [Parvibaculum
            lavamentivorans DS-1]
          Length = 1362

 Score = 1764 bits (4570), Expect = 0.0,   Method: Composition-based stats.
 Identities = 876/1363 (64%), Positives = 1084/1363 (79%), Gaps = 5/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  RVRK FG  P+I ++P+LIEVQK SYD FL ++     R  +GLQA FKSV
Sbjct: 1    MTQSFTGRKRVRKVFGHIPQIAEMPNLIEVQKYSYDQFLQVDEPTGGREEQGLQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ FS ++ LEFV+YEF+ PK+DV++C  R +T+A PLK+TLRLIVF+VDE TGAKS+
Sbjct: 61   FPISDFSESSTLEFVNYEFETPKYDVEECQQRGMTFAAPLKVTLRLIVFEVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDMPLMTENGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI+ VRIDRRRK+PVT+ L ALG+DSEEILSTFY  + +++  
Sbjct: 181  RVIPYRGSWLDFEFDAKDIVFVRIDRRRKLPVTTLLYALGLDSEEILSTFYNSVTFTKVK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P +A D   GAK    L+D  TG+ V+E+G+K+T  L K L E+G+K L +  + 
Sbjct: 241  QGWRVPFNA-DRYRGAKPERDLIDAKTGKVVVEAGRKVTPRLAKKLAEEGLKELLVQDED 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +   Y+A++IVN ETGEI+ EAGD I  + LE +  +   DI  L +D VN  A+IRNTL
Sbjct: 300  IHTRYLAQEIVNMETGEIFAEAGDEITPELLEALVEAGHTDIITLDIDHVNTGAFIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DK  +R+ AL+DIYRVMRPG+  T   AE++F  LFFD+++YDLS VGRVKMNMRL+L
Sbjct: 360  AVDKCTNREQALIDIYRVMRPGEPPTADTAEALFKSLFFDAERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D VR +RKEDI+A+IK LV LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 420  DVSDTVRVLRKEDILAVIKTLVGLRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V  GK+ +D+VYLSAMEE    IAQAN ++ + G    ELV CR  G+  +VP +++D
Sbjct: 600  RRVKGGKLADDIVYLSAMEESRYRIAQANVAIGKKGEIEGELVNCRIDGDFEMVPPDQVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAP VGTGME VVA+ 
Sbjct: 660  FVDVSPKQIVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRSEAPLVGTGMEEVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+V+QVDA RIVIR+ E   D S SGVDIY L KFQRSNQNTC+NQRPLV
Sbjct: 720  SGAAIGARRTGVVDQVDATRIVIRATEEV-DSSKSGVDIYNLRKFQRSNQNTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD+V++ DIIADGPST+LGDLALGRN+LVAFMPW+GYNFEDS+LISER+V +DVFTSI
Sbjct: 779  RVGDQVKKGDIIADGPSTELGDLALGRNVLVAFMPWNGYNFEDSILISERIVRDDVFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNV EE LKN+DE GI+ +GAEVNPGDIL GKITPKG
Sbjct: 839  HIEEFEVMARDTKLGPEEITRDIPNVGEEALKNLDEAGIVYIGAEVNPGDILCGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV GTVV+VR+FNRHGIDK+ER++++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVQGTVVEVRVFNRHGIDKDERAMAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDE  ILDRN+Y RL EIL G+   SGPKG +    ++   + +    QWW
Sbjct: 959  EIERLAKDRDDEFGILDRNVYGRLSEILLGKQIASGPKGMEADAKVTQANLDDLSHGQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A+++EK Q  +E+LK QY+ SK  LE RF +K++K+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1019 QIALKNEKAQSEIEALKKQYDESKERLEARFADKVDKLQRGDELPPGVMKMVKVFVAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q+GDKMAGRHGNKG++SRI+P EDMP+L DG PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KLQTGDKMAGRHGNKGVISRIVPMEDMPYLDDGQPVDIVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC GLGKKI+  ++ Y        L+  ++++ G       ++  D++ ++ +A    +
Sbjct: 1139 WACAGLGKKIEVALDAYHRENKPKELKDLVKQIYGDD---PTVASLDEEQLVEMAGNLTN 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I  ML +A LD SGQ  L+DG TGEPFDR VTVGYIYMLKL+H+
Sbjct: 1196 GVPIATPVFDGAREPEIVEMLELAGLDRSGQVTLHDGRTGEPFDRKVTVGYIYMLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L  
Sbjct: 1316 AGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELLT 1358


>gi|52082903|gb|AAU26031.1| RNA polymerase beta subunit [Afipia sp. SP3302452]
          Length = 1372

 Score = 1764 bits (4568), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1378 (65%), Positives = 1117/1378 (81%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPQGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKEGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRTARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G+Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++P+L +D VN   YIRN
Sbjct: 299  DELVGMYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPLLDIDHVNIGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT+DVVYLSAMEE    +AQAN  LD  G FT++LV CR AGE + +P ++
Sbjct: 599  PYRKVKDGRVTDDVVYLSAMEEGRYRVAQANVPLDNKGRFTDDLVICRHAGEVLQLPPDR 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD+V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 778  LVKVGDQVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+SQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPKSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWQFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I      Y +  D+ PL+  L+KV G     E I   +D  +L +A   
Sbjct: 1138 LGWACAGLGKRIGQAAEAYWSKQDLKPLKETLKKVYGDD---ETIKTLNDQELLELARNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA E+ I  ML +A +++SGQS++YDG TG+ FDR VTVGYIYMLKL+
Sbjct: 1195 KPGVPIATPVFDGAKEKDIEDMLDLAGMNKSGQSVVYDGRTGDQFDRNVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGPTPTSEAAE 1372


>gi|46982198|gb|AAT08139.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1764 bits (4568), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ     N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMNQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETLEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|46982196|gb|AAT08138.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1763 bits (4567), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ     N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMGQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETLEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|46982204|gb|AAT08142.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1763 bits (4567), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL ALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLLALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|154247292|ref|YP_001418250.1| DNA-directed RNA polymerase subunit beta [Xanthobacter autotrophicus
            Py2]
 gi|226699461|sp|A7IKQ0|RPOB_XANP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|154161377|gb|ABS68593.1| DNA-directed RNA polymerase, beta subunit [Xanthobacter autotrophicus
            Py2]
          Length = 1358

 Score = 1763 bits (4567), Expect = 0.0,   Method: Composition-based stats.
 Identities = 903/1364 (66%), Positives = 1114/1364 (81%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RKFFGK  E+ ++P+LIEVQKASYD FL +      R ++GLQA FKSV
Sbjct: 1    MAQTFTGRKRIRKFFGKIKEVAEMPNLIEVQKASYDQFLQIEEPKGGRDDDGLQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ FSGA+MLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAKS+
Sbjct: 61   FPISDFSGASMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPETGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +Y GD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYTGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+DIEFD+KDI+  RIDRRRK+PVTS L ALG+D+EEILSTFY KI +++  
Sbjct: 181  RIIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLLYALGLDNEEILSTFYEKIPFTREK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P      M G K  + L+D DTGE V+E+GKKLT    + L EKG+K L I+ + 
Sbjct: 241  GGWRMPFDP-KRMKGYKAVADLIDADTGEVVLEAGKKLTVRAGRQLAEKGLKALKISDEE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y+AED+V+  +GEI+ EAG+ I EK+L+ +  +   +IP+L +D VN  AYIRNTL
Sbjct: 300  MIGQYIAEDLVDLTSGEIHAEAGEEITEKTLKLLEETGYNEIPVLDIDHVNTGAYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   A++MF+ LFFDS++YDLS VGRVKMNMRL+L
Sbjct: 360  TADKNVTREDALFDIYRVMRPGEPPTLDSAQAMFHSLFFDSERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D PD VR +R++DI+++I+ LV+LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 420  DCPDTVRVLRRDDILSVIRTLVELRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPQDLINAKPVAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIEAPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D KVT++VVYLSAMEE   Y+AQAN  LD+DG F E+L+ CR AG+ +LV  +++D
Sbjct: 600  RRVVDSKVTDEVVYLSAMEEGKYYVAQANIPLDKDGRFEEDLIVCRHAGDVLLVAPDRVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VVA+ 
Sbjct: 660  FMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRSQAPLVGTGMEAVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+++QVDA RIVIR+ E   DPS SGVDIYRLMKFQRSNQ+TC+NQRPLV
Sbjct: 720  SGAAIAARRTGVIDQVDATRIVIRATEEA-DPSKSGVDIYRLMKFQRSNQSTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD+V++ DIIADGPST+LG+LALGRN+LVAFMPW+GYNFEDS+L+SE +  EDVFTSI
Sbjct: 779  RVGDQVKKGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILLSENIAKEDVFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFE MARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKG
Sbjct: 839  HIEEFEAMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P G +GT+V+VR+FNRHG+DK+ER++++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKAADVRDTSLRLPPGTTGTIVEVRVFNRHGVDKDERALAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN+Y RL+EIL G+ A++GPKGF+K TV++ ++++EYPRSQWW
Sbjct: 959  EIERLAKDRDDEQAILDRNVYGRLIEILDGKTAIAGPKGFRKETVVTREILTEYPRSQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             FAV D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1019 LFAVADDAIMAELEAIRAQYDDSKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTNVDIVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC GLG+++ + +  Y    D+ PLR  LE + G     ++I    D  +  + E  + 
Sbjct: 1139 WACAGLGRQVAAAMEAYYGKQDLKPLRDRLETIYG----KDEIEQLKDGELPELGENLRK 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I   L  A LD SGQS LYDG TGEPFDR VTVGYIYMLKL+H+
Sbjct: 1195 GVPMATPVFDGAHEADIEQQLEKAGLDASGQSTLYDGRTGEPFDRKVTVGYIYMLKLHHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT+VYE+IV G DTFE+G PESFNVLVKEM++LGL++DLENS
Sbjct: 1315 AGRTKVYEAIVRGEDTFESGIPESFNVLVKEMRSLGLNVDLENS 1358


>gi|71390274|gb|AAZ31524.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1763 bits (4566), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQ N  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL++++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLVDMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|209548927|ref|YP_002280844.1| DNA-directed RNA polymerase subunit beta [Rhizobium leguminosarum bv.
            trifolii WSM2304]
 gi|226699436|sp|B5ZYS7|RPOB_RHILW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|209534683|gb|ACI54618.1| DNA-directed RNA polymerase, beta subunit [Rhizobium leguminosarum
            bv. trifolii WSM2304]
          Length = 1379

 Score = 1763 bits (4565), Expect = 0.0,   Method: Composition-based stats.
 Identities = 957/1370 (69%), Positives = 1154/1370 (84%), Gaps = 2/1370 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAAD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLTVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DG+VT+DV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGRVTSDVLYLSAMEEAKYYVAQANAEMNADGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGDEV R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDEVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+E+L GQ +++GPKGFKK T LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIEMLRGQASIAGPKGFKKGTELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI+ YKANG+I PLR  +  V+G G   E++ D+DDDSVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIDAYKANGNIEPLRKTIGDVVGDGPKAEQVQDFDDDSVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEADVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDE 1368


>gi|46982202|gb|AAT08141.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1762 bits (4564), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT+ RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITYKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|46982200|gb|AAT08140.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1762 bits (4564), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT  RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITLKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|46982192|gb|AAT08136.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1762 bits (4564), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ     N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMYQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|49089817|gb|AAT51866.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
          Length = 1364

 Score = 1762 bits (4563), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1131/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT+ RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITYKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|46982194|gb|AAT08137.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1762 bits (4563), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1129/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ     N LS ITH R LSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMNQTNPLSEITHKRSLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|36333353|gb|AAP75734.1| RNA polymerase beta subunit [Afipia sp. B-91-007287]
          Length = 1372

 Score = 1762 bits (4563), Expect = 0.0,   Method: Composition-based stats.
 Identities = 908/1378 (65%), Positives = 1115/1378 (80%), Gaps = 6/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG+  E+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQQ-TFTGRKRVRKFFGQIKEVAEMPNLIEVQKASYDQFLMVEEPAGGRPDEGLQAVFK 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNTSMLEFVRYEFEAPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMYALGLDGEEILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  AA    G    + LVD DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDAA-RFRGYTTINDLVDADTGKVVLEAGKKLTVRTARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G ++AED+VN +TGEI+ EAGD I EKSL+ +     +++PIL +D VN   YIRN
Sbjct: 299  EELVGNFLAEDLVNPKTGEIHAEAGDEITEKSLKVLNEIGYKELPILDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +R+EDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTHRTLRREDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE   Y+AQAN  LD  G FTE+LV  R AG+ + V  +K
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRHYVAQANVPLDAKGRFTEDLVVARHAGDVLQVTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQTVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL E+L  ++ ++GPKGFKK T ++  ++ EYPRSQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYGRLAELLNNRDGLAGPKGFKKDTRITKAVLEEYPRSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFATSNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLG++I   ++ Y +  D  PLR  L+KV G     E I    +  ++ +    
Sbjct: 1138 LGWACAGLGRRIAQTVDAYYSKQDSKPLREMLKKVYGED---ETIKSLGEGELVELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML +A +D SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKETDIEEMLTLAGVDGSGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+  ++   E   
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGSTPPAEAAD 1372


>gi|36333355|gb|AAP75735.1| RNA polymerase beta subunit [Afipia genosp. 2]
          Length = 1373

 Score = 1761 bits (4562), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1367 (66%), Positives = 1111/1367 (81%), Gaps = 6/1367 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG+  E+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQQ-TFTGRKRVRKFFGQIKEVAEMPNLIEVQKASYDQFLMVEEPAGGRPDEGLQAVFK 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNTSMLEFVRYEFEAPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMYALGLDGEEILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  AA    G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDAA-RFRGYTTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G ++AED+VN +TGEI+ EAGD I EKSL+ +     +++PIL +D VN   YIRN
Sbjct: 299  EELVGNFLAEDLVNPKTGEIHAEAGDEITEKSLKALNEIGYKELPILDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLAADKNMTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +R+EDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTHRTLRREDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG+VT++VVYLSAMEE   Y+AQAN  LD  G FTE+LV  R AG+ + V  +K
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRHYVAQANVPLDAKGRFTEDLVVARHAGDVLQVTPDK 658

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA
Sbjct: 659  VDYMDVSPKQTVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVA 718

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRP
Sbjct: 719  RDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRP 777

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFT
Sbjct: 778  LVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFT 837

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITP
Sbjct: 838  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITP 897

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++E
Sbjct: 898  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIE 957

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL E+L  +  ++GPKGFKK T ++  ++ EYPRSQ
Sbjct: 958  REEIERLAKDRDDEQAILDRNVYGRLAELLNNREGIAGPKGFKKDTRITKAVLEEYPRSQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1018 WWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLG++I   ++ Y +  D  PLR  L+KV G     E I    +  ++ +    
Sbjct: 1138 LGWACAGLGRRIAQTVDAYYSKQDSKPLREMLKKVYGED---ETIKSLGEGELVELGHNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML +A +D SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 1195 SRGVPIATPVFDGAKETDIEEMLTLAGVDGSGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1315 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1361


>gi|46982206|gb|AAT08143.1| DNA-dependent RNA polymerase beta chain [Brucella abortus]
          Length = 1364

 Score = 1761 bits (4562), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ     N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMYQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|36333345|gb|AAP75730.1| RNA polymerase beta subunit [Afipia felis ATCC 53690]
          Length = 1378

 Score = 1761 bits (4562), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1383 (65%), Positives = 1111/1383 (80%), Gaps = 10/1383 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPQGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEAPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS ++ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMLALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  D W  P SA D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L ++
Sbjct: 241  RTKDGWRVPFSA-DRFRGYSAVTDLIDADSGKVVLEAGKKLTVRQARLLQEKGLKALRMS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               L G ++AED+VN +TGEIY EAG+ I EKSL+ +     +D+PIL +D VN   YIR
Sbjct: 300  DADLVGTFLAEDLVNPKTGEIYAEAGEEITEKSLKALIEQGYKDLPILDIDHVNVGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMR
Sbjct: 360  NTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDAERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE I +  +
Sbjct: 600  TPYRKVKDGRVTDEVVYLSAMEEGRYRVAQANVPLDNKGRFTEDLVICRHAGEVIQLTPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  RVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYPRS
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPRS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWAFASPNDKLMGEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKI----KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            HLGWAC GLGK+I     + +       D   L+  L++V G     E +   +D+ +L 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYLAKGDGKSDTKALKGTLKEVYGDD---EVVKSLNDNELLE 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +    K GVP++TPVFDGA E  I  ML +A +D+SGQS +YDG TG+ FDR VTVGYIY
Sbjct: 1196 LGRNLKPGVPIATPVFDGAKEADIEQMLELAGVDKSGQSTVYDGRTGDQFDRKVTVGYIY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E
Sbjct: 1316 TVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKMGPAPTSE 1375

Query: 1376 EIP 1378
               
Sbjct: 1376 AAE 1378


>gi|241204157|ref|YP_002975253.1| DNA-directed RNA polymerase subunit beta [Rhizobium leguminosarum bv.
            trifolii WSM1325]
 gi|240858047|gb|ACS55714.1| DNA-directed RNA polymerase, beta subunit [Rhizobium leguminosarum
            bv. trifolii WSM1325]
          Length = 1379

 Score = 1761 bits (4562), Expect = 0.0,   Method: Composition-based stats.
 Identities = 957/1370 (69%), Positives = 1154/1370 (84%), Gaps = 2/1370 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL++L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRTLSDKGLKALKAAD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLTVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVT+DV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGKVTSDVLYLSAMEEAKYYVAQANAEMNADGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGDEV R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDEVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+E+L GQ +++GPKGFKK   LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIEMLRGQASIAGPKGFKKGAELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI+ YKANG+I PLR  +  V+G G   E++ ++DDDSVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIDAYKANGNIEPLRKTIGDVVGDGPKAEQVHEFDDDSVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L +SGQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEADVNDMLRLAGLKDSGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDE 1368


>gi|299135268|ref|ZP_07028459.1| DNA-directed RNA polymerase, beta subunit [Afipia sp. 1NLS2]
 gi|50982576|gb|AAP75731.2| RNA polymerase beta subunit [Afipia felis genospecies A]
 gi|298590245|gb|EFI50449.1| DNA-directed RNA polymerase, beta subunit [Afipia sp. 1NLS2]
          Length = 1378

 Score = 1761 bits (4561), Expect = 0.0,   Method: Composition-based stats.
 Identities = 908/1383 (65%), Positives = 1114/1383 (80%), Gaps = 10/1383 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPQGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEAPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS ++ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMLALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  D W  P SA D   G   ++ LVD D+G+ V+E+GKKLT    + L+EKG+K L ++
Sbjct: 241  RAKDGWRVPFSA-DRFRGYSAATDLVDADSGKVVLEAGKKLTVRQARLLQEKGLKALRMS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               L G ++AED+VN +TGEIY EAG+ I EKSL+ +     +D+PIL +D VN   YIR
Sbjct: 300  DADLVGTFLAEDLVNPKTGEIYAEAGEEITEKSLKALIEQGYKDLPILDIDHVNVGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMR
Sbjct: 360  NTLSADKNVTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDSERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTHRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE I +  +
Sbjct: 600  TPYRKVKDGRVTDEVVYLSAMEEGRYRVAQANVPLDNRGRFTEDLVICRHAGEVIQLTPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  RVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYPRS
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPRS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWAFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKI----KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            HLGWAC GLGK+I     + +       D   L+S L++V G     E +   +D+ +L 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYLAKGDGKSDTKALKSTLKEVYGDD---EVVKSLNDNELLE 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +    K GVP++TPVFDGA E+ I  ML +A +D+SGQS +YDG TG+ FDR VTVGYIY
Sbjct: 1196 LGRNLKPGVPIATPVFDGAKEKDIEDMLELAGVDKSGQSTVYDGRTGDQFDRKVTVGYIY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E
Sbjct: 1316 TVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKMGPAPTSE 1375

Query: 1376 EIP 1378
               
Sbjct: 1376 AAE 1378


>gi|116251532|ref|YP_767370.1| DNA-directed RNA polymerase subunit beta [Rhizobium leguminosarum bv.
            viciae 3841]
 gi|158564213|sp|Q1MIE9|RPOB_RHIL3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115256180|emb|CAK07261.1| putative DNA-directed RNA polymerase beta chain [Rhizobium
            leguminosarum bv. viciae 3841]
          Length = 1379

 Score = 1761 bits (4561), Expect = 0.0,   Method: Composition-based stats.
 Identities = 957/1370 (69%), Positives = 1154/1370 (84%), Gaps = 2/1370 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL++L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRTLSDKGLKALKAAD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLTVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVT+DV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGKVTSDVLYLSAMEEAKYYVAQANAEMNADGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGDEV R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDEVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+E+L GQ +++GPKGFKK + LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIEMLRGQASIAGPKGFKKGSELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI  YKANG+I PLR  +  V+G G   E++ ++DDDSVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIEAYKANGNIEPLRKTIGDVVGDGPKAEQVHEFDDDSVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L +SGQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEADVNDMLRLAGLKDSGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDE 1368


>gi|46982190|gb|AAT08135.1| DNA-dependent RNA polymerase beta chain [Brucella melitensis]
          Length = 1364

 Score = 1760 bits (4559), Expect = 0.0,   Method: Composition-based stats.
 Identities = 939/1365 (68%), Positives = 1130/1365 (82%), Gaps = 2/1365 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            NG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPI  
Sbjct: 1    NGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQD 60

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            FSGA+MLEFV YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKE
Sbjct: 61   FSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKE 120

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF++ G +R++ SQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 121  QDVYMGDMPLMTDNGTFIVNGTERVIFSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 180

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  
Sbjct: 181  RGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRI 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y
Sbjct: 241  PYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSY 299

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN
Sbjct: 300  LAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDKN 359

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D 
Sbjct: 360  ESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDT 419

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IK
Sbjct: 420  VRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK 479

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG G
Sbjct: 480  ERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPG 539

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV D
Sbjct: 540  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVD 599

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKVTNDVVYLSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D S
Sbjct: 600  GKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 659

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI
Sbjct: 660  PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAI 719

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD 
Sbjct: 720  AARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDR 778

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEF
Sbjct: 779  IHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEF 838

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 839  EVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 898

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE L
Sbjct: 899  PEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERL 958

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+
Sbjct: 959  AKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVE 1018

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ G
Sbjct: 1019 DEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPG 1078

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G
Sbjct: 1079 DKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAG 1138

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +GKKI  L++ Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++
Sbjct: 1139 MGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIA 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK+
Sbjct: 1199 TPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTIGYIYMLKLHHLVDDKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+
Sbjct: 1259 HARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R     
Sbjct: 1319 VYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQP 1363


>gi|39936331|ref|NP_948607.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            CGA009]
 gi|192292057|ref|YP_001992662.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            TIE-1]
 gi|81562131|sp|Q6N4R9|RPOB_RHOPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699438|sp|B3QC00|RPOB_RHOPT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|39650186|emb|CAE28709.1| RNA polymerase beta subunit [Rhodopseudomonas palustris CGA009]
 gi|192285806|gb|ACF02187.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            TIE-1]
          Length = 1374

 Score = 1760 bits (4559), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1369 (66%), Positives = 1114/1369 (81%), Gaps = 8/1369 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+   P  RP+EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVAEPPGGRPDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS A+MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNASMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARIIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEEILSTFYNKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P    +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDV-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I +K+L+ +     +++P+L +D VN   YIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIYAEAGEEITDKTLKMLNEQGYKELPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLNADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+A+IK LV LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTHRTLRKEDILAVIKTLVGLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYRKV +G+VT++VVYLSAMEE    +AQAN SLD  G FT++LV CR     + + +P 
Sbjct: 599  PYRKVKEGRVTDEVVYLSAMEEGRYAVAQANVSLDAKGKFTDDLVVCRAGGTRDVVPMPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DQVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R GI++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGIIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 778  RPLVKVGDHVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L G+  ++GPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLDGRQGIAGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFAAPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   I+ Y  + D+ PLR  L K+ G     E I   DD  +L +  
Sbjct: 1138 THLGWACAGLGKRIGETIDAYYQSQDLKPLRETLRKIYGED---ETIKSLDDGELLELGR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML++A  D SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLSHGVPIATPVFDGAKEADIEEMLKLAGFDASGQSTVYDGRTGDQFDRRVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1363


>gi|327194525|gb|EGE61383.1| DNA-directed RNA polymerase protein, beta subunit [Rhizobium etli
            CNPAF512]
          Length = 1379

 Score = 1760 bits (4559), Expect = 0.0,   Method: Composition-based stats.
 Identities = 957/1375 (69%), Positives = 1155/1375 (84%), Gaps = 2/1375 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAGD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILSNGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLTVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVTNDV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGKVTNDVLYLSAMEEAKYYVAQANAEMNPDGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDVVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+++L GQ +++GPKGFKK T LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIDMLRGQVSIAGPKGFKKGTELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI  YKANG+I PLR  +  V+G G   E++ ++DD+SVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIEAYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDESVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEGDVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   +   +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDEAQATQ 1373


>gi|190891347|ref|YP_001977889.1| DNA-directed RNA polymerase protein, beta subunit [Rhizobium etli
            CIAT 652]
 gi|226699435|sp|B3PW59|RPOB_RHIE6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|190696626|gb|ACE90711.1| DNA-directed RNA polymerase protein, beta subunit [Rhizobium etli
            CIAT 652]
          Length = 1379

 Score = 1760 bits (4558), Expect = 0.0,   Method: Composition-based stats.
 Identities = 958/1375 (69%), Positives = 1155/1375 (84%), Gaps = 2/1375 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    
Sbjct: 241  DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAGD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  DDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILSNGFDEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLTVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR++ DGKVTNDV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+ 
Sbjct: 600  PYRRIVDGKVTNDVLYLSAMEEAKYYVAQANAEMNPDGSFVDEFVVCRHAGEVMLAPRDS 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VVA
Sbjct: 660  MNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVTVGDVVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+++L GQ +++GPKGFKK T LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIDMLRGQVSIAGPKGFKKGTELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G++I  LI  YKANG+I PLR  +  V+G G   E++ ++DDDSVLR+A+QW
Sbjct: 1139 LGWACAGMGRQIGELIEAYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDDSVLRLADQW 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLN
Sbjct: 1199 KRGVSIATPVFDGANEGDVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LEN++   +   +
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENTKLDEAQANQ 1373


>gi|36333349|gb|AAP75732.1| RNA polymerase beta subunit [Afipia genosp. 3]
          Length = 1372

 Score = 1758 bits (4553), Expect = 0.0,   Method: Composition-based stats.
 Identities = 902/1366 (66%), Positives = 1111/1366 (81%), Gaps = 6/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+SV
Sbjct: 2    GQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRLDEGLQAVFRSV 61

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+G +MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGAKS+
Sbjct: 62   FPISDFAGTSMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAKSV 121

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 122  KDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 181

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y Q  
Sbjct: 182  RVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMYALGLDGEEILSTFYQKIIYKQIK 241

Query: 243  D-FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            +  W  P   +    G    + L+D DTG+  +E+GKKLT    + L EKG+K L +T +
Sbjct: 242  EGGWRVPFDPS-RFRGYSTVNDLIDADTGKVALEAGKKLTVRAARQLAEKGLKALQLTDE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G Y+A+D+VN +TGEIY EAG+ I EK L+ +     +++P+L +D VN  AYIRNT
Sbjct: 301  DLIGSYLADDLVNAKTGEIYAEAGEEITEKLLKALDEEGYKELPLLDIDHVNIGAYIRNT 360

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL 
Sbjct: 361  LAADKNVTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDAERYDLSAVGRVKMNMRLE 420

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLLR
Sbjct: 421  LDAPDTHRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGLLR 480

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 481  MERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 540

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ETP
Sbjct: 541  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETP 600

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +G+VT++VVYLSAMEE    +AQAN  LD  G FT+E+V CR AG+ + +P +K+
Sbjct: 601  YRKVKEGRVTDEVVYLSAMEEGRYSVAQANVPLDAKGHFTDEMVICRHAGDVMPLPADKV 660

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+
Sbjct: 661  DYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVAR 720

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRPL
Sbjct: 721  DSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRPL 779

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VKVGD VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDVFTS
Sbjct: 780  VKVGDVVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDVFTS 839

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPK
Sbjct: 840  IHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKITPK 899

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++ER
Sbjct: 900  GESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAIER 959

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK + ++  ++ E PRSQW
Sbjct: 960  EEIERLAKDRDDEQAILDRNVYGRLADLLENKVGIAGPKGFKKDSKITRAVLDENPRSQW 1019

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            W FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+K
Sbjct: 1020 WMFATANDKLMTEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVK 1079

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1080 RKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHL 1139

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC G+GKKI   I+ +    D+ PLR  L+ V G     E I   +DD ++ +A   K
Sbjct: 1140 GWACAGMGKKIGETIDAFYQRQDLKPLRETLKNVYGDD---EVIKSLNDDELIELARNLK 1196

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I  ML++A  D+SGQS +YDG TG+ FDR VTVGYIYMLKL+H
Sbjct: 1197 PGVPIATPVFDGAKEADIEDMLKLAGFDKSGQSTVYDGRTGDQFDRKVTVGYIYMLKLHH 1256

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1257 LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1316

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1317 VAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1362


>gi|36333359|gb|AAP75737.1| RNA polymerase beta subunit [Bradyrhizobium liaoningense]
          Length = 1374

 Score = 1758 bits (4553), Expect = 0.0,   Method: Composition-based stats.
 Identities = 900/1380 (65%), Positives = 1118/1380 (81%), Gaps = 8/1380 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++  P  R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPPGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAK
Sbjct: 60   SVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAK 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L +  
Sbjct: 240  TKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMAD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN   YIRN
Sbjct: 299  EELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKELPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLESAQAMFQSLFFDAERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYRK+ DG+VT++VVYLSAMEE    +AQAN  +D  G FTE+LV CR +   + + +  
Sbjct: 599  PYRKIKDGRVTDEVVYLSAMEEGRYSVAQANVPVDAKGRFTEDLVVCRSSGTRDVVPMTP 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 778  RPLVKVGDIVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y+RL E+L G+  ++GPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYNRLAELLEGRQGIAGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ Q + SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFASPNDKLMAEIEAMRKQSDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   ++ Y +  DI PL+  L+KV G     E I   +D+ +L +  
Sbjct: 1138 THLGWACAGLGKRIGQTVDAYLSKQDIKPLKETLKKVYGED---ETIKSLNDNELLELGH 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+PFDR VTVGYIYMLK
Sbjct: 1195 NLSRGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDPFDRKVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E   
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKMGPAPTSEAAE 1374


>gi|323137105|ref|ZP_08072184.1| DNA-directed RNA polymerase, beta subunit [Methylocystis sp. ATCC
            49242]
 gi|322397463|gb|EFX99985.1| DNA-directed RNA polymerase, beta subunit [Methylocystis sp. ATCC
            49242]
          Length = 1383

 Score = 1757 bits (4551), Expect = 0.0,   Method: Composition-based stats.
 Identities = 893/1378 (64%), Positives = 1114/1378 (80%), Gaps = 7/1378 (0%)

Query: 1    MAKGVV--FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     F G  R RKFFG   E   +P+LIEVQKASYD FL+++     RP+EGLQ+ 
Sbjct: 1    MAQTSARKFTGRKRTRKFFGHIREAAAMPNLIEVQKASYDQFLLVDEPKGGRPDEGLQSV 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            FKSVFPI+ FS  A+LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  T 
Sbjct: 61   FKSVFPISDFSQVALLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTQ 120

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            AKS+KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKL
Sbjct: 121  AKSVKDIKEQDVYMGDMPFMTSNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKL 180

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L+A RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS L ALG+D EEIL+TFY  I Y
Sbjct: 181  LFAARIIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLFALGLDGEEILTTFYKTITY 240

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  G+ W  P  A  L  G K  + ++D DTG+ ++E+GKKL     + L +KGVK + +
Sbjct: 241  TADGENWRMPFDAERL-KGLKAVADMIDADTGDVILEAGKKLAVRAARQLADKGVKAIRV 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            +++ L G Y+A+D+ + +TGEI+ EAGD I  K+L  +      ++PIL +D +N   YI
Sbjct: 300  SAEDLYGQYLAQDLYDPKTGEIFAEAGDEITAKTLPLLLEKGFDELPILDIDHINVGPYI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN +R++AL DIYRVMRPG+  T   AE+MF+ LFFD+++YDLS VGRVKMNM
Sbjct: 360  RNTLAVDKNSNREEALFDIYRVMRPGEPPTMDTAEAMFHSLFFDAERYDLSAVGRVKMNM 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD PD  R +R+EDI+A++K LVDLR+G+G IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 420  RLDLDAPDTTRTLRREDILAVVKALVDLRDGRGEIDDIDHLGNRRVRSVGELMENQYRLG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH 
Sbjct: 480  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E PYR+V DGKVTN+V YLSAMEE   ++AQAN+ +D DG+ TE+LV CR AG+ +LVPR
Sbjct: 600  EAPYRRVRDGKVTNEVAYLSAMEEAKYHVAQANAPIDADGNLTEDLVLCRHAGDVMLVPR 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            EK+D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KA+AP VGTGME+V
Sbjct: 660  EKVDAMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLVGTGMEAV 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGAAI A+R G+V+Q+DA RIVIR+ E  LDP+  GVDIYRLMKFQRSNQ+TC+NQ
Sbjct: 720  VAADSGAAISARRTGVVDQIDATRIVIRATEE-LDPAKPGVDIYRLMKFQRSNQSTCINQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLV+VGD V++ DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L++ER+V EDV
Sbjct: 779  KPLVRVGDIVKKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLNERIVKEDV 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHI+EFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 839  FTSIHIDEFEVMARDTKLGPEEITRDIPNVSEETLKNLDEAGIVYIGAEVQAGDILVGKI 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG++K+ER+ +
Sbjct: 899  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVEKDERAQA 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDE  ILDRN+Y+RL E L G+ A++GPK FKK  VL+  ++ EYPR
Sbjct: 959  IEREEIERLAKDRDDELAILDRNVYARLSETLIGKKAIAGPKSFKKEQVLTQAILDEYPR 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW F ++D+ +  ++E+++ QY+ SK  LE+RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1019 SQWWTFVIEDDALMSSIEAVRKQYDESKKGLENRFLDKVEKLQRGDELPPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGTPVDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AVKRKIQPGDKMAGRHGNKGVVSRIVPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK++   ++ Y  + D +P+R+ L+ V G     E+I + D+ +++ + +
Sbjct: 1139 THLGWACAGLGKQVGKAVDAYMKSRDTTPIRAALKDVYG---PDEEIDNLDETTLVEIGK 1195

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K GVP++TPVFDGA E+ I  ML  A L  SGQ  L+DG TGE FDR VTVGYIYMLK
Sbjct: 1196 DLKRGVPIATPVFDGAREKDIVDMLTKAGLSSSGQVTLFDGRTGEAFDRKVTVGYIYMLK 1255

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1256 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1315

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            SDDV GRT+VYESIV G+DTFE+G PESFNVL+KEM++L L+++L N+      +  E
Sbjct: 1316 SDDVAGRTKVYESIVRGDDTFESGIPESFNVLIKEMRSLALNVELTNAEPPEGHEEIE 1373


>gi|209884799|ref|YP_002288656.1| DNA-directed RNA polymerase, beta subunit [Oligotropha
            carboxidovorans OM5]
 gi|209872995|gb|ACI92791.1| DNA-directed RNA polymerase, beta subunit [Oligotropha
            carboxidovorans OM5]
          Length = 1377

 Score = 1757 bits (4551), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1372 (66%), Positives = 1114/1372 (81%), Gaps = 10/1372 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+      R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVEEPEGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI+ FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPISDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS ++ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMLALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  + W  P SA D   G   ++ L+D D+G+ V+E+GKKLT    + L+EKG+K L ++
Sbjct: 241  RAKEGWRVPFSA-DRFRGYSAATDLIDADSGKVVLEAGKKLTVRQARQLQEKGLKALRMS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               L G+++AED+VN +TGEIY EAG+ I EKSL+ +     +D+PIL +D VN   YIR
Sbjct: 300  DADLVGMFLAEDLVNLKTGEIYAEAGEEITEKSLKALIEQGYKDLPILDIDHVNVGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMR
Sbjct: 360  NTLSADKNVTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDSERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT++VVYLSAMEE    +AQAN  LD  G FTE+LV CR AGE I +  +
Sbjct: 600  TPYRKVKDGRVTDEVVYLSAMEEGRYRVAQANVPLDNRGRFTEDLVVCRHAGEVIQLTPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  RVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R+G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRSGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYPRS
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLDEYPRS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWAFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKI----KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            HLGWAC GLGK+I     + +       D   L+S L++V G     E +   +D+ +L 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYLAKGDGKSDTKALKSTLKEVYGDD---EVVKSLNDNELLE 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +    K GVP++TPVFDGA E  I  ML +A +D+SGQS++YDG TG+ FDR VTVGYIY
Sbjct: 1196 LGRNLKPGVPIATPVFDGAKEGDIEQMLELAGVDKSGQSVVYDGRTGDRFDRKVTVGYIY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            T+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1316 TVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1367


>gi|36333343|gb|AAP75729.1| RNA polymerase beta subunit [Afipia clevelandensis ATCC 49720]
          Length = 1376

 Score = 1757 bits (4550), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1381 (65%), Positives = 1113/1381 (80%), Gaps = 8/1381 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPAGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  D W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L  +
Sbjct: 241  RIKDGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRTARQLQEKGLKALRFS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             + L G Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++PIL +D VN   YIR
Sbjct: 300  DEELVGSYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPILDIDHVNIGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMR
Sbjct: 360  NTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT+DVVYLSAMEE   Y+AQAN  LD  G FT++LV CR AGE + +  +
Sbjct: 600  TPYRKVKDGRVTDDVVYLSAMEEGRHYVAQANVPLDNKGRFTDDLVICRHAGEVLQLSPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            K+D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  KVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD+VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDQVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+S
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPKS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWWQFA  ++K+   +E++  QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWQFASPNDKLMAEIEAMHKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKIKSLINDYK--ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            HLGWAC GLGK+I   ++ Y      DI PL+S L++V G     E I   +D  ++ + 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKSTLKEVYGDD---EVIKTLNDQELMELG 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++GVP++TPVFDGA E  I  ML +A  ++SGQS +YDG TG+ FDR VTVGYIYML
Sbjct: 1196 RNLRAGVPIATPVFDGAKEADIEQMLELAGQNKSGQSTVYDGRTGDQFDRNVTVGYIYML 1255

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1256 KLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1315

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E  
Sbjct: 1316 KSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKMGPAPTSEAA 1375

Query: 1378 P 1378
             
Sbjct: 1376 E 1376


>gi|182678330|ref|YP_001832476.1| DNA-directed RNA polymerase subunit beta [Beijerinckia indica subsp.
            indica ATCC 9039]
 gi|182634213|gb|ACB94987.1| DNA-directed RNA polymerase, beta subunit [Beijerinckia indica subsp.
            indica ATCC 9039]
          Length = 1387

 Score = 1756 bits (4548), Expect = 0.0,   Method: Composition-based stats.
 Identities = 898/1365 (65%), Positives = 1110/1365 (81%), Gaps = 5/1365 (0%)

Query: 1    MAKGV--VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+ +   F G  RVRKFFG   E+ ++P+LIEVQKASYD FL+++     RP+EGLQ+ 
Sbjct: 1    MAQSLAQTFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLLVDEPKGGRPDEGLQSV 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            FKSVFPI+ FSG A+LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TG
Sbjct: 61   FKSVFPISDFSGTALLEFVKYEFELPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTG 120

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            AKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKL
Sbjct: 121  AKSVKDIKEQDVYMGDMPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKL 180

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L+A RIIP +G W+DIEFD+KDI++ RIDRRRK+P TS L ALGMD EEILSTFY  IVY
Sbjct: 181  LFAARIIPYRGSWLDIEFDAKDIVYARIDRRRKIPATSVLYALGMDGEEILSTFYKTIVY 240

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            ++  D W  P  A   M G K +  L+D ++GE V+E+GKKLT    + L E+G+KF+  
Sbjct: 241  TRDKDGWRIPFDAE-RMKGMKAAIDLIDAESGEVVLEAGKKLTVRTARQLAERGLKFIKA 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              + L G Y+A D+ N +TGEI+ EAG+ I  K+L  +  S   +IP+L +D +N   YI
Sbjct: 300  QDEDLHGQYIASDLYNPQTGEIFAEAGEEISAKTLTTLVDSGFEEIPVLDIDHINIGPYI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF+ LFFD ++YDLS VGRVKMNM
Sbjct: 360  RNTLAVDKNNSREDALFDIYRVMRPGEPPTLETAEAMFHSLFFDPERYDLSAVGRVKMNM 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R++LD  D VR +RK DI+A+++ LVDLR+G+G IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 420  RMDLDAADTVRILRKADIVAVMRALVDLRDGRGEIDDIDHLGNRRVRSVGELMENQYRLG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  ++V EFF SSQLSQ  +  N LS ITH 
Sbjct: 480  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAASVREFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E PYR+V D  VT+DVVYLSAMEE   Y+AQA++ +D D    E+L+ CR AG+ I+VPR
Sbjct: 600  EAPYRRVRDNHVTDDVVYLSAMEESKYYVAQADAKVDADRGLVEDLIVCRHAGDVIMVPR 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KA+AP VGTGME+V
Sbjct: 660  ERVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLVGTGMEAV 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G ++Q+DA RIVIR+ E   D    GVDIYRLMKFQRSNQ+TCVNQ
Sbjct: 720  VARDSGAAIAARRTGYIDQIDATRIVIRATEET-DAGKPGVDIYRLMKFQRSNQSTCVNQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLV+VGD VR+ DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L++ER+V +DV
Sbjct: 779  KPLVRVGDFVRKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLNERIVKDDV 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHI+EFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 839  FTSIHIDEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQAGDILVGKI 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ +
Sbjct: 899  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQA 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDE  ILDRN+Y+RL+++L G+ A++GPKGFKK TVLS  +I EYPR
Sbjct: 959  IEREEIERLAKDRDDELAILDRNVYTRLIDLLDGKKAIAGPKGFKKETVLSRSVIEEYPR 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA++ +++   +E+++ QY+ +K  LE+RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1019 SQWWTFAIESDQLMAEIEAMRKQYDEAKKGLENRFLDKVEKLQRGDELPPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL DG PVDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AIKRKIQPGDKMAGRHGNKGVVSKIVPQEDMPFLADGQPVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK++   +N Y    D  P+R  L ++ G G   E+IS  D+++++ V E
Sbjct: 1139 THLGWACAGLGKQVSEAVNAYLRQQDTQPIRDKLIEIYGEGQ-REQISALDEETLVEVGE 1197

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVFDGA E+ I +ML  A LD SGQ  LYDG +GE FDR VTVGYIYMLK
Sbjct: 1198 NLRRGVPIATPVFDGAREKDIVAMLEEAGLDHSGQVTLYDGRSGEAFDRKVTVGYIYMLK 1257

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1258 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1317

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GRT+VYESIV G+D FE+G PESFNVLVKEM++LGL+++L
Sbjct: 1318 SDDVAGRTKVYESIVRGDDAFESGIPESFNVLVKEMRSLGLNVEL 1362


>gi|170738710|ref|YP_001767365.1| DNA-directed RNA polymerase subunit beta [Methylobacterium sp. 4-46]
 gi|226699423|sp|B0UHX6|RPOB_METS4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|168192984|gb|ACA14931.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium sp. 4-46]
          Length = 1374

 Score = 1756 bits (4547), Expect = 0.0,   Method: Composition-based stats.
 Identities = 897/1382 (64%), Positives = 1122/1382 (81%), Gaps = 8/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM++     RP+EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIREVAEMPNLIEVQKASYDQFLMVDEPEGGRPDEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAK
Sbjct: 59   SVFPISDFSSTALLEFVKYTFEAPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT++GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTENGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI++ RIDR+RK+PVTS L ALG+D EEILSTFY +I Y++
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVYARIDRKRKIPVTSLLFALGLDGEEILSTFYNRITYAR 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G K ++ L+D D+GE V+E+GKKLT+   + + EKG K L  T 
Sbjct: 239  DGRDWRVPYDAERL-KGFKATTDLIDADSGEVVLEAGKKLTARAARQIAEKGTKALRATD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAGD I EK L+ +    I +IP+L +D VN   YIRN
Sbjct: 298  EDLVGQYIAEDMVNYKTGEIYAEAGDEISEKLLKGLSDVGIEEIPVLDIDHVNVGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+ AL DIYRVMRPG+  T   AE+MF+ LFFD+++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSAREGALFDIYRVMRPGEPPTLDTAEAMFHSLFFDAERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD +R +R+ED++A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAPDTMRTLRREDMLAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 478  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V  G VT++VVYLSAMEE   Y+AQA++++D +   TE+LV CR AGE I+V  ++
Sbjct: 598  PFRRVRGGVVTDEVVYLSAMEEAKYYVAQASAAMDAERRLTEDLVVCRRAGEVIVVAPDR 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+RAG+++QVDA RIVIR+ E   DP+  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRAGVIDQVDATRIVIRATEET-DPTKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG+ V++ DIIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEVVKKGDIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+ GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL ++L GQ+ V+GPKGFKK T+L+ +++++YPRSQ
Sbjct: 957  REEIERLAKDRDDEQAILDRNTYARLADVLVGQSPVAGPKGFKKDTLLTREVLADYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVVDDRMMTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+++   ++ Y  N D  PLR  + ++         +    D  +  V    
Sbjct: 1137 LGWAAAGLGRQVAQAVDAYLRNQDAQPLREQMSRIYSPSE----LEGLSDRELAEVGNNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I +ML MA LD SGQS LYDG TGEPFDR VTVGYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIEAMLEMAGLDRSGQSTLYDGRTGEPFDRKVTVGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +S+   + ++E  P+ 
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELISSKRAANDQLEAPPEA 1372

Query: 1381 NK 1382
             +
Sbjct: 1373 AE 1374


>gi|115525596|ref|YP_782507.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            BisA53]
 gi|122295399|sp|Q07KK7|RPOB_RHOP5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115519543|gb|ABJ07527.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            BisA53]
          Length = 1373

 Score = 1756 bits (4547), Expect = 0.0,   Method: Composition-based stats.
 Identities = 904/1369 (66%), Positives = 1110/1369 (81%), Gaps = 8/1369 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+      R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVEEPVGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  +MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNTSMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMFALGLDGEEILSTFYKKIIYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G   ++ ++D DTG+ V+E+GKKLT    + L+EKG+K L +T 
Sbjct: 240  TKEGWRVPFDA-NRFRGYTTTNDVIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRMTD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +D+ +L +D VN   YIRN
Sbjct: 299  EDIVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEQGYKDLTLLDIDHVNIGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLAADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +RKEDI+A+IK LV LR+G+G IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTHRTLRKEDILAVIKTLVGLRDGRGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYR+V DG+VT++VVYLSAMEE    +AQAN  LD  G F E+L+ CR     + +L+P 
Sbjct: 599  PYRRVKDGRVTDEVVYLSAMEEGRYAVAQANVQLDPKGRFVEDLIVCRDGGTRDVVLIPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DKVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G+V+Q+DA RIVIR+ E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGVVDQIDATRIVIRATED-LDPTKSGVDIYRLMKFQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD+V + DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DV
Sbjct: 778  RPLVKVGDQVAKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLDNRQGIAGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWMFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   I+ Y    D+ P+R  L+K+ G     E I   +D  ++ +A 
Sbjct: 1138 THLGWACAGLGKRIGQTIDAYYQKQDLKPMRETLKKIYGDD---ETIKSLNDAELIELAR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K GVP++TPVFDGA E  I  ML +A LD SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLKPGVPIATPVFDGAKEADIEEMLHLAGLDASGQSTVYDGRTGDSFDRKVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1363


>gi|328543349|ref|YP_004303458.1| DNA-directed RNA polymerase subunit beta [Polymorphum gilvum
            SL003B-26A1]
 gi|326413094|gb|ADZ70157.1| DNA-directed RNA polymerase subunit beta [Polymorphum gilvum
            SL003B-26A1]
          Length = 1378

 Score = 1755 bits (4546), Expect = 0.0,   Method: Composition-based stats.
 Identities = 914/1376 (66%), Positives = 1127/1376 (81%), Gaps = 1/1376 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                FNG  RVRKFFG   ++  +P+LIEVQKASYD FL ++     R +EGLQA F+SV
Sbjct: 1    MTHTFNGRKRVRKFFGSIRDVTAMPNLIEVQKASYDQFLQVDEPKGGRSDEGLQAVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+G A+LEFV +EF+ PK+DV++C  R +TYA PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPISDFAGTALLEFVRFEFEAPKYDVEECRQRGMTYAAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDMPFMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALG+D EEIL+TFY +I YS+ G
Sbjct: 181  RVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGLDGEEILNTFYKRIEYSRSG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                      D + G K S  LVD D+GE VIE+G+K+T+  +K L EKGVK L +T + 
Sbjct: 241  KGAWRMPFDGDRLKGTKASYDLVDADSGEVVIEAGRKITARTIKQLTEKGVKALKVTDED 300

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+AED+V+  TGEIY EAGD I+ K L+E+      DI +L +D VN  AYIRNTL
Sbjct: 301  LHGQYLAEDMVDPSTGEIYAEAGDEINAKILDELVQRGYEDISVLDIDHVNTGAYIRNTL 360

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNMRL+L
Sbjct: 361  AVDKNESREDALFDIYRVMRPGEPPTIDSAEAMFQSLFFDAERYDLSAVGRVKMNMRLDL 420

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  D VR +RKEDI+A+I++L++LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 421  ECEDTVRTLRKEDILAVIRLLLELRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLLRM 480

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 481  ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLS 540

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 541  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 600

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG V+N+VVYLSAMEE   Y+AQ+N+ +DE G F E+LV CR AGE +LVP +++D
Sbjct: 601  RKVKDGVVSNEVVYLSAMEEAKHYVAQSNAEMDESGRFVEDLVTCRHAGENMLVPSDRVD 660

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 661  LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARD 720

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRLMKFQRSNQNTC+NQRPLV
Sbjct: 721  SGAAIAARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLMKFQRSNQNTCINQRPLV 779

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFTSI
Sbjct: 780  RVGDVISKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLSERIVRDDVFTSI 839

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H+EEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAE+ PGDILVGKITPKG
Sbjct: 840  HLEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAELKPGDILVGKITPKG 899

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHG++K+ER++++ERE
Sbjct: 900  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVTGTVVEVRVFNRHGVEKDERAMAIERE 959

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN+Y RL E+L G+ A+ GPKG KK  V+S D+++E+PRSQWW
Sbjct: 960  EIERLAKDRDDEQAILDRNVYGRLAEMLIGKTAIGGPKGSKKDVVISGDVLNEFPRSQWW 1019

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            QFA  DEK    VE+L+ QY+ S+  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1020 QFAADDEKFMSEVEALRGQYDESRKRLEQRFIDKVEKLQRGDELPPGVMKMVKVFVAVKR 1079

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS+I P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1080 KIQPGDKMAGRHGNKGVVSKINPNEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLG 1139

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC G+G+KI  L + Y+ +G+IS L+  + ++ G     + + ++DD+S++R+A+Q K 
Sbjct: 1140 WACAGMGRKIGELYDQYRKSGEISALKGQIVEIYGDNLKGDPVKEFDDESIVRLADQLKK 1199

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GV ++TPVFDGA E  I  ML++ADLD SGQS+LYDG TGEPFDR VTVGYIYMLKL+H+
Sbjct: 1200 GVSIATPVFDGAHEPDIVDMLKVADLDPSGQSVLYDGRTGEPFDRKVTVGYIYMLKLHHL 1259

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1260 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1319

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+ +            
Sbjct: 1320 AGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELQQTEVPQITDEPAAD 1375


>gi|217979965|ref|YP_002364112.1| DNA-directed RNA polymerase subunit beta [Methylocella silvestris
            BL2]
 gi|217505341|gb|ACK52750.1| DNA-directed RNA polymerase, beta subunit [Methylocella silvestris
            BL2]
          Length = 1376

 Score = 1755 bits (4545), Expect = 0.0,   Method: Composition-based stats.
 Identities = 892/1370 (65%), Positives = 1108/1370 (80%), Gaps = 7/1370 (0%)

Query: 1    MAK--GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     FNG  R+RKFFG   E+ ++P+LIEVQKASYD FL+++     RP+EGLQ+ 
Sbjct: 1    MAQFSAQTFNGRKRIRKFFGHIREVAEMPNLIEVQKASYDQFLLVDEPQGGRPDEGLQSV 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            FKSVFPI+ FS  A+LEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFDVD  T 
Sbjct: 61   FKSVFPISDFSNTALLEFVKYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTA 120

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            A+S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKL
Sbjct: 121  ARSVKDIKEQDVYMGDMPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKL 180

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L+A RIIP +G W+DIEFD+KDI++ RIDRRRK+P TS L ALGMD EEILSTFY  I+ 
Sbjct: 181  LFAARIIPYRGSWLDIEFDAKDIVYARIDRRRKIPATSVLYALGMDGEEILSTFYKTILV 240

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            ++  + W  P  A  L  G K    L+D +TGE V+E+GKKLT    + L E+G+KFL +
Sbjct: 241  TRDKEGWRQPFDAERL-KGLKAVVDLLDAETGEVVLEAGKKLTVRTARQLAERGLKFLRM 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              + L G Y+A D+ +  TGEI+ EAG+ I  K+L  +  +   ++P+L +D +N   YI
Sbjct: 300  QDEDLHGQYIATDLYDSATGEIFAEAGEEITVKTLPLLIEAGFDELPLLDIDHINIGPYI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKNK R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNM
Sbjct: 360  RNTLHVDKNKAREEALFDIYRVMRPGEPPTLDSAEAMFHSLFFDSERYDLSAVGRVKMNM 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R++LD  D VR +RKEDIIA+++ LVDLR+G+G IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 420  RMDLDAADTVRTLRKEDIIAVMRALVDLRDGRGEIDDIDHLGNRRVRSVGELMENQYRLG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  ++V EFF SSQLSQ  +  N LS ITH 
Sbjct: 480  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAASVREFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E PYR+V +  V+++VVYLSAMEE   Y+AQAN+ LD D   TE+LV CR AG+ ++VPR
Sbjct: 600  EAPYRRVKENHVSDEVVYLSAMEESKYYVAQANAPLDADSRLTEDLVVCRHAGDVVMVPR 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+AP VGTGME+V
Sbjct: 660  ERVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPLVGTGMEAV 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G ++Q+DA RIV+R+ E   D S  GVDIYRLMKFQRSNQ+TCVNQ
Sbjct: 720  VARDSGAAIAARRTGYIDQIDATRIVVRATEES-DASKPGVDIYRLMKFQRSNQSTCVNQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLV+VGD VR+ DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L++ER+V +DV
Sbjct: 779  KPLVRVGDFVRKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLNERIVKDDV 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHI+EFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 839  FTSIHIDEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQAGDILVGKI 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG++K+ER+ +
Sbjct: 899  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVEKDERAQA 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDE  ILDRN+Y+RL+++L G+ A++GPKGFKK TVL+ ++I EYPR
Sbjct: 959  IEREEIERLAKDRDDELAILDRNVYARLLDVLAGKKAIAGPKGFKKDTVLTREIIEEYPR 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA+++++    +E+++ QY+ SK  LE RF +K+EK+Q GD++ PGV+++VKVFV
Sbjct: 1019 SQWWIFAIENDQTMAELEAMRKQYDESKKGLESRFLDKVEKLQRGDELSPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL DGTPVDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AVKRKIQPGDKMAGRHGNKGVVSKIVPQEDMPFLADGTPVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLG+++   +N Y  N D  PLR  L ++        +I   DD+ V+ + E
Sbjct: 1139 THLGWACAGLGRQVAETVNAYMRNQDSGPLREKLGQIYDA---KAEIDALDDNVVVEIGE 1195

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVFDGA E  I  ML  A LD SGQS +YDG TGE FDR VTVGYIYMLK
Sbjct: 1196 NLRRGVPIATPVFDGAHEADIVVMLEQAGLDPSGQSTVYDGRTGEAFDRKVTVGYIYMLK 1255

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1256 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1315

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            SDDV GRT+VYESIV G+D FE+G PESFNVLVKEM++L L+++L  S  
Sbjct: 1316 SDDVAGRTKVYESIVRGDDAFESGIPESFNVLVKEMRSLCLNVELTMSNK 1365


>gi|91977663|ref|YP_570322.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            BisB5]
 gi|123721725|sp|Q134R8|RPOB_RHOPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91684119|gb|ABE40421.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            BisB5]
          Length = 1374

 Score = 1754 bits (4544), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1369 (66%), Positives = 1112/1369 (81%), Gaps = 8/1369 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+   P  R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVAEPPGGRDDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS A+MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNASMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN   YIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEEGYKELPLLDIDHVNIGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+A+IK LV LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTHRTLRKEDILAVIKTLVGLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYRKV +G+VT++VVYLSAMEE    +AQAN SLD  G FT++L+ CR     + +L+P 
Sbjct: 599  PYRKVKEGRVTDEVVYLSAMEEGRYAVAQANISLDAKGRFTDDLIVCRAGGTRDVVLIPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DQVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V + DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 778  RPLVKVGDSVAKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  VSGPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLDNRQGVSGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFAAPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+GKKI   I+ Y    D+ PLR  L+K+ G     E I   +D  ++ +  
Sbjct: 1138 THLGWACAGMGKKIGQTIDAYYQRQDLKPLRETLKKIYGDD---ETIKSLNDGELIELGR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML++A  D SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLSHGVPIATPVFDGAKEADIEEMLKLAGFDASGQSTVYDGRTGDEFDRKVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1363


>gi|36333339|gb|AAP75727.1| RNA polymerase beta subunit [Afipia birgiae]
          Length = 1376

 Score = 1754 bits (4543), Expect = 0.0,   Method: Composition-based stats.
 Identities = 904/1370 (65%), Positives = 1111/1370 (81%), Gaps = 8/1370 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  + W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L  +
Sbjct: 241  RIKEGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRTARQLQEKGLKALRFS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             D L G Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++P+L +D VN   YIR
Sbjct: 300  DDELVGNYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPLLDIDHVNIGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMR
Sbjct: 360  NTLNADKNMTREDALFDIYRVMRPGEPPTIDSAQAMFQSLFFDSERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT+DVVYLSAMEE    +AQAN  LD  G FT++LV CR AGE + +  +
Sbjct: 600  TPYRKVKDGRVTDDVVYLSAMEEGRYRVAQANVPLDNKGRFTDDLVICRHAGEVLQITPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            K+D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  KVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD+V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDQVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL E+L  +  ++GPKGFKK T ++  ++ EYP+S
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLAELLENRQGIAGPKGFKKDTKITRAVLEEYPKS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWWQFA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWQFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKIKSLINDYK--ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            HLGWAC GLGK+I   ++ Y      DI PL+  L+KV G     E I   +D  ++ + 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKETLKKVYGDD---EVIKTLNDTELMELG 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++GVP++TPVFDGA E  I  ML +A +++SGQS +YDG TG+ FDR VTVGYIYML
Sbjct: 1196 RNLRAGVPIATPVFDGAKEADIEQMLELAGMNKSGQSTVYDGRTGDQFDRNVTVGYIYML 1255

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1256 KLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1315

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1316 KSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1365


>gi|260469682|ref|ZP_05813844.1| DNA-directed RNA polymerase, beta subunit [Mesorhizobium
            opportunistum WSM2075]
 gi|259028541|gb|EEW29855.1| DNA-directed RNA polymerase, beta subunit [Mesorhizobium
            opportunistum WSM2075]
          Length = 1378

 Score = 1754 bits (4542), Expect = 0.0,   Method: Composition-based stats.
 Identities = 940/1374 (68%), Positives = 1142/1374 (83%), Gaps = 2/1374 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGLQA FK
Sbjct: 1    MAQTQTFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGMD EEILSTFY KI Y +
Sbjct: 181  AARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGMDGEEILSTFYNKITYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P +      G K    LVD DTGE V+E+GKK+T+   ++L EKG+K +  T 
Sbjct: 241  AGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITARQARALGEKGLKAIKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  EDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLGTGENEIKVLDIDHVNVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  ELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGK+TNDVVYLSAMEE   ++AQAN+ LD++G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKIVDGKLTNDVVYLSAMEEAKHHVAQANAELDKNGGFVDEFVICRSAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQMVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDP  SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGARRGGIVDQVDATRIVIRATED-LDPGKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV++GD V + DIIADGPST+LGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVRMGDRVNKGDIIADGPSTELGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ A++GPKGFKK + LS D + EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLSDVLVGKEAIAGPKGFKKGSTLSKDTLDEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV++EK+Q  +E+L+ QY+ SK  LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVENEKLQSELEALRGQYDDSKKALEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G+KI  LI+ YKA GDI PLR  LE  +      E + +YDD+S++R++EQ 
Sbjct: 1139 LGWACAGMGRKIGELIDTYKAAGDIKPLRKTLESFMPANDRNEPVREYDDESIVRLSEQM 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 RRGVSIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++LEN++  ++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENTKLDDNPIR 1372


>gi|159184990|ref|NP_354931.2| DNA-directed RNA polymerase subunit beta [Agrobacterium tumefaciens
            str. C58]
 gi|41017768|sp|Q8UE08|RPOB_AGRT5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|159140264|gb|AAK87716.2| DNA-directed RNA polymerase beta chain [Agrobacterium tumefaciens
            str. C58]
          Length = 1378

 Score = 1754 bits (4542), Expect = 0.0,   Method: Composition-based stats.
 Identities = 950/1382 (68%), Positives = 1155/1382 (83%), Gaps = 4/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGL A FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLNAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEILSTFY K  Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGEEILSTFYTKATYER 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P     L   AKV + ++D DTGE V+E GKKLT  L++ L +KG+K L  T 
Sbjct: 241  SGDGWRIPFQPEAL-KNAKVITDMIDADTGEVVVEGGKKLTPRLIRQLVDKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  S   +IP+L +D VN  AYIRN
Sbjct: 300  EDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGLILQSGFDEIPVLNIDHVNVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDAEDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT DV+YLSAMEE   Y+AQAN+ LD +G+FTEE V CR +GE +L PR+ 
Sbjct: 600  PYRKIIDGKVTTDVIYLSAMEEAKYYVAQANAELDGEGAFTEEFVVCRHSGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME +VA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+VS+DVFT
Sbjct: 779  LVSVGDAISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILMSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+++L G  +++GPKGFKK   LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIDMLRGHVSIAGPKGFKKGVELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEK Q  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKAQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDI LNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDICLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            L WAC G+GKKI  ++ +Y+   DIS LRS L ++  + ++ E +  +DDDS++++AE+ 
Sbjct: 1139 LAWACAGMGKKIGEMLEEYRKTMDISELRSELTEIYASEANDE-VQRFDDDSLVKLAEEA 1197

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  + +ML+ A L ESGQS+LYDG TGEPFDR VTVGY+YM+KLN
Sbjct: 1198 KRGVSIATPVFDGAHEPDVAAMLKKAGLHESGQSVLYDGRTGEPFDRKVTVGYMYMIKLN 1257

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1258 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1317

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+ +N ++ +++PD 
Sbjct: 1318 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKIENQSE-DQLPDA 1376

Query: 1381 NK 1382
             +
Sbjct: 1377 AE 1378


>gi|319783308|ref|YP_004142784.1| DNA-directed RNA polymerase, subunit beta [Mesorhizobium ciceri
            biovar biserrulae WSM1271]
 gi|317169196|gb|ADV12734.1| DNA-directed RNA polymerase, beta subunit [Mesorhizobium ciceri
            biovar biserrulae WSM1271]
          Length = 1378

 Score = 1754 bits (4542), Expect = 0.0,   Method: Composition-based stats.
 Identities = 942/1374 (68%), Positives = 1141/1374 (83%), Gaps = 2/1374 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1    MAQTQTFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVAEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGMD EEILSTFY KI Y +
Sbjct: 181  AARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGMDGEEILSTFYNKITYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P +      G K    LVD DTGE V+E+GKK+T+   ++L EKG+K +  T 
Sbjct: 241  AGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITARQARALGEKGLKAIKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +I +L +D VN  AYIRN
Sbjct: 300  EDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLGTGEEEIKVLDIDHVNVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  ELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGK+TNDVVYLSAMEE   ++AQAN+ LD++G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKIVDGKLTNDVVYLSAMEEAKHHVAQANAELDKNGGFVDEFVICRSAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQMVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDP  SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGARRGGIVDQVDATRIVIRATED-LDPGKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV++GD V + DIIADGPST+LGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVRMGDRVNKGDIIADGPSTELGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ A++GPKGFKK + LS D + EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLSDVLVGKEAIAGPKGFKKGSTLSKDTLDEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV++EK+Q  +E+L+ QY+ SK  LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVENEKLQSELEALRGQYDDSKKALEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G+KI  LI+ YKA GDI PLR  LE  I      E + DYDD+S++R++EQ 
Sbjct: 1139 LGWACAGMGRKIGELIDTYKAAGDIKPLRKTLESFIPANDRNEPVRDYDDESIVRLSEQM 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 RRGVSIATPVFDGAHEADINIMLEQAGLHSSGQSQLYDGRTGEPFDRKVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++LEN++  ++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENTKLDDNPVR 1372


>gi|222148357|ref|YP_002549314.1| DNA-directed RNA polymerase subunit beta [Agrobacterium vitis S4]
 gi|254765266|sp|B9JVM8|RPOB_AGRVS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|221735345|gb|ACM36308.1| DNA-directed RNA polymerase beta subunit [Agrobacterium vitis S4]
          Length = 1379

 Score = 1753 bits (4541), Expect = 0.0,   Method: Composition-based stats.
 Identities = 950/1382 (68%), Positives = 1152/1382 (83%), Gaps = 3/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGLQ  FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPEGGRPDEGLQTVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGA+
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAR 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEILSTFY K  Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILSTFYSKSDYKR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G+K    +VD D+GE V+E+GKKLT  LL+ L++KG+K L  T 
Sbjct: 241  DGKGWRVPFQAETL-KGSKTLVDMVDADSGEVVVEAGKKLTPRLLRQLQDKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300  EDLYGNYLAEDIVNFATGEIYLEAGDEIDEKTLPIILDAGFEEIPVLGIDHINVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +L+  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLEVADTVRVLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DG VT DV+YLSAMEE   Y+AQAN+ L+ +G F EE V CR AGE +L PR+ 
Sbjct: 600  PYRKIIDGVVTKDVIYLSAMEEAKYYVAQANAELNAEGKFVEEFVVCRHAGEVMLSPRDT 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME +VA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIGARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+VSEDVFT
Sbjct: 779  LVAVGDILNKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILMSERIVSEDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALRNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTIVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL++ L GQ +++GPKGFKK   L++ +ISEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLLDTLRGQVSIAGPKGFKKGVELNNAVISEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            L WAC G+G+KI  ++ DY+ + DI+ LR+ L  +  + SH E ++ +DD+S+LR+A+Q 
Sbjct: 1139 LAWACAGMGRKIGQMLEDYQKHLDITELRTELVDLYASESHDE-VARFDDESLLRLADQA 1197

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            KSG+ ++TPVFDGA E  ++ ML  A L  SGQS+LYDG TGE FDR VTVGY+YM+KLN
Sbjct: 1198 KSGLSIATPVFDGAHESDVSEMLTRAGLHTSGQSVLYDGRTGETFDRKVTVGYMYMIKLN 1257

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1258 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1317

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+ + +  +  +PD 
Sbjct: 1318 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKLETADTVNPLPDA 1377

Query: 1381 NK 1382
             +
Sbjct: 1378 AE 1379


>gi|114704476|ref|ZP_01437384.1| DNA-directed RNA polymerase beta subunit [Fulvimarina pelagi
            HTCC2506]
 gi|114539261|gb|EAU42381.1| DNA-directed RNA polymerase beta subunit [Fulvimarina pelagi
            HTCC2506]
          Length = 1380

 Score = 1753 bits (4541), Expect = 0.0,   Method: Composition-based stats.
 Identities = 912/1382 (65%), Positives = 1123/1382 (81%), Gaps = 2/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M++   F+G  RVRK FG  PE+ ++P+LIEVQKASYD FLM+      R ++GLQA FK
Sbjct: 1    MSQTTTFSGRRRVRKVFGHIPEVAEMPNLIEVQKASYDQFLMIEEPEGGRTDDGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  FSG AMLEFV YEF+PPKFDV++C  RDLTYAVPLK+TLRLIVFDVDE TG+K
Sbjct: 61   SVFPIQDFSGQAMLEFVKYEFEPPKFDVEECRQRDLTYAVPLKVTLRLIVFDVDEDTGSK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+P+MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPVMTGNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KD++H RIDRRRK+P TS LMALGMD EEILSTFY  + + +
Sbjct: 181  AGRVIPYRGSWLDIEFDAKDVVHARIDRRRKIPATSLLMALGMDGEEILSTFYNFVEFKK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P S    +    + + LVD D+GE ++E+GKK+T+   + L E+GVK   ++ 
Sbjct: 241  DKKGWRAPFSVE-RVRNQGMITDLVDADSGEVLVEAGKKVTARQARKLAEQGVKAFRVSE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G Y+AEDIVN ETGE+Y+EAGD +DEK+L+ +  +      +L VD VN  +YIRN
Sbjct: 300  EDIYGNYLAEDIVNFETGEVYLEAGDELDEKTLQVLIDAGYESFQVLDVDHVNIGSYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLAVDKNESRQDALFDIYRVMRPGEPPTMETAEAMFQSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   D VR +RKEDIIA++K LVDLR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DVQAEDTVRTLRKEDIIAVVKTLVDLRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR+V +GKVTN+VVYLSAMEE   ++AQAN+ L +D +F  E V CR AG+  + PRE 
Sbjct: 600  PYRRVVEGKVTNEVVYLSAMEESKHHVAQANAILTDDNTFQNEFVVCRHAGDVFMTPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  L+   SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGARRTGIVDQVDATRIVIRATED-LEAGKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + DI+ADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+VS+DVFT
Sbjct: 779  LVAVGDRVEKGDILADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALRNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSSRMPPGTYGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+E+L G+  ++GPKGFK+ T ++ +++ EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLVEMLSGKQGIAGPKGFKRGTEINQEVMEEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEK+Q  +E L+  Y+ +K  LE RF +K+EK+Q GD++PPGV++ VKVFVA+
Sbjct: 1019 WWMFAVEDEKLQGELEDLRKVYDEAKKTLEARFMDKVEKVQRGDELPPGVMKQVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPF +DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFTEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI +++  Y+ N D++PLR  +  ++G     EK+ DYDDDSV+ +A+Q 
Sbjct: 1139 LGWACSGMGKKIGAMLEAYQENNDVAPLRQEISGLLGDNDRNEKVKDYDDDSVITLAKQM 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GV ++TPVFDGA+E+ I   L  A L+ SGQ  LYDG TGEPFDR VTVGYIYMLKL+
Sbjct: 1199 SKGVSIATPVFDGANEKDIVEWLEGAGLNGSGQVTLYDGRTGEPFDRQVTVGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+D FE+G PESFNVLVKEM++LGL +DL N+       +EE+PD 
Sbjct: 1319 DVAGRTKVYEAIVRGDDAFESGIPESFNVLVKEMRSLGLDVDLANNPENAGGGVEELPDA 1378

Query: 1381 NK 1382
             +
Sbjct: 1379 AE 1380


>gi|13470542|ref|NP_102110.1| DNA-directed RNA polymerase subunit beta [Mesorhizobium loti
            MAFF303099]
 gi|41017783|sp|Q98N66|RPOB_RHILO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|14021283|dbj|BAB47896.1| RNA polymerase beta subunit [Mesorhizobium loti MAFF303099]
          Length = 1378

 Score = 1753 bits (4540), Expect = 0.0,   Method: Composition-based stats.
 Identities = 944/1374 (68%), Positives = 1142/1374 (83%), Gaps = 2/1374 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGLQA FK
Sbjct: 1    MAQTQTFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGMD EEILSTFY KI Y +
Sbjct: 181  AARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGMDGEEILSTFYNKITYVR 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P +      G K    LVD DTGE V+E+GKK+T+   + L EKG+K +  T 
Sbjct: 241  AGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEAGKKITARQARQLGEKGLKAIKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +  ++I +L +D VN  AYIRN
Sbjct: 300  EDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLGTGEQEIKVLDIDHVNVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS++YDLS VGRVKMNMRL
Sbjct: 360  TLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDSERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L   D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  ELKAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGK+TNDVVYLSAMEE   ++AQAN+ LD++G F +E V CR AGE ++ PRE 
Sbjct: 600  PYRKIVDGKLTNDVVYLSAMEEAKHHVAQANAELDKNGGFVDEFVICRSAGEVMMAPREN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQMVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R GIV+QVDA RIVIR+ E  LDP  SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGARRGGIVDQVDATRIVIRATED-LDPGKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV++GD V + DIIADGPST+LGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 779  LVRMGDRVNKGDIIADGPSTELGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ A++GPKGFKK + LS D + EYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYARLSDVLVGKEAIAGPKGFKKGSTLSKDTLDEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV++EK+Q  +E+L+ QY+ SK  LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWQFAVENEKLQSELEALRGQYDDSKKALEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  LI+ YKA GDI PLR  LE  +      E I +YDD+S++R++EQ 
Sbjct: 1139 LGWACAGMGKKIGELIDTYKAAGDIKPLRKTLESFMPANDRNEPIREYDDESIVRLSEQM 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1199 RRGVSIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++LEN++  ++   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENTKLDDAPVR 1372


>gi|85715144|ref|ZP_01046128.1| DNA-directed RNA polymerase beta subunit [Nitrobacter sp. Nb-311A]
 gi|85698059|gb|EAQ35932.1| DNA-directed RNA polymerase beta subunit [Nitrobacter sp. Nb-311A]
          Length = 1380

 Score = 1753 bits (4539), Expect = 0.0,   Method: Composition-based stats.
 Identities = 907/1371 (66%), Positives = 1108/1371 (80%), Gaps = 12/1371 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F G  RVRKFFG   E+  +P+LIEVQKASYD FLM++     R +EGLQA FKSVF
Sbjct: 3    QQTFTGRKRVRKFFGHIREVAAMPNLIEVQKASYDQFLMVDEPEGGRLDEGLQAVFKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI  FSG + LEFV YEF+ PK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGAKS+K
Sbjct: 63   PINDFSGTSQLEFVRYEFEAPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAKSVK 122

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R
Sbjct: 123  DIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAAR 182

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG- 242
            +IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+DSEEILSTFY KIVY +   
Sbjct: 183  VIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDSEEILSTFYKKIVYKRAKS 242

Query: 243  ----DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                D W  P        G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L +
Sbjct: 243  GGHSDGWRVPYDPV-RFRGYSTLNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRM 301

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            + + L G+Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN   YI
Sbjct: 302  SDEELVGMYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEEGYKELPLLDIDHVNVGPYI 361

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNM
Sbjct: 362  RNTLAADKNMTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDAERYDLSAVGRVKMNM 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+G
Sbjct: 422  RLDLDAPDTYRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVG 481

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH 
Sbjct: 482  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 541

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+
Sbjct: 542  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFV 601

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV DG+VT++VVYLSAMEE   ++AQAN  LD  G FTE+LV CR AGE + V  
Sbjct: 602  ETPYRKVKDGRVTDEVVYLSAMEEGRYHVAQANLPLDNRGRFTEDLVVCRHAGEVLPVTP 661

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 662  DKVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 721

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 722  VARDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 780

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 781  RPLVKVGDTVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 840

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 841  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 900

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 901  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 960

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+
Sbjct: 961  IEREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRSVLEEYPK 1020

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1021 SQWWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1080

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1081 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1140

Query: 1139 THLGWACVGLGKKIKSLINDY--KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            THLGWAC GLG++I   ++ Y      +  PL+  L+KV G     E I   +D  ++ +
Sbjct: 1141 THLGWACAGLGRRIGQAVDAYLASTKQETKPLKETLKKVYGDN---ETIKSLNDHELVEL 1197

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                  GVP++TPVFDGA E  I  ML +A +D SGQS +YDG TG+PFDR VTVGYIYM
Sbjct: 1198 GRNLSRGVPIATPVFDGAKETDIEQMLELAGMDRSGQSTVYDGRTGDPFDRKVTVGYIYM 1257

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1258 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1317

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            +KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1318 VKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1368


>gi|325293346|ref|YP_004279210.1| DNA-directed RNA polymerase beta chain protein [Agrobacterium sp.
            H13-3]
 gi|325061199|gb|ADY64890.1| DNA-directed RNA polymerase beta chain protein [Agrobacterium sp.
            H13-3]
          Length = 1378

 Score = 1752 bits (4537), Expect = 0.0,   Method: Composition-based stats.
 Identities = 949/1382 (68%), Positives = 1152/1382 (83%), Gaps = 4/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM++     RP+EGL A FK
Sbjct: 1    MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLNAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61   SVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEILSTFY K  Y +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGEEILSTFYSKASYER 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P     L   AKV + ++D DTGE V+E GKKLT  L++ L +KG+K L  T 
Sbjct: 241  SGDGWRIPFQPETL-KNAKVITDMIDADTGEVVVEGGKKLTPRLIRQLVDKGLKALKATD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G ++AEDIVN  TGEIY+EAGD IDEK+L  I  S   +IP+L +D VN  AYIRN
Sbjct: 300  EDLYGNFLAEDIVNYSTGEIYLEAGDEIDEKTLGLILQSGFDEIPVLNIDHVNVGAYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLHADKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420  DLDAEDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480  RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT DV+YLSAMEE   Y+AQAN+ LD +G+FTEE V CR +GE +L PR+ 
Sbjct: 600  PYRKIIDGKVTTDVIYLSAMEEAKYYVAQANAELDGEGAFTEEFVVCRHSGEVMLAPRDN 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME +VA
Sbjct: 660  INLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL KFQRSNQNTCVNQRP
Sbjct: 720  RDSGAAIAARRGGVVDQVDATRIVIRATEE-LDAGKSGVDIYRLQKFQRSNQNTCVNQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+VS+DVFT
Sbjct: 779  LVAVGDIISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILMSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITP
Sbjct: 839  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL+++L G  +++GPKGFKK   LS+ ++SEYPRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLIDMLRGHVSIAGPKGFKKGVELSNAVVSEYPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW FAV+DEK Q  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1019 WWMFAVEDEKAQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDI LNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDICLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            L WAC G+GKKI  ++ +Y+   DIS LR+ L ++  + SH E +  +DD+S++++AE+ 
Sbjct: 1139 LAWACAGMGKKIGEMLEEYRKTMDISELRTELTEIYASESHDE-VKRFDDESLVKLAEEA 1197

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  + +ML+ A L ESGQS+LYDG TGEPFDR VTVGY+YM+KLN
Sbjct: 1198 KRGVSIATPVFDGAHEPDVAAMLKKAGLHESGQSVLYDGRTGEPFDRKVTVGYMYMIKLN 1257

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1258 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1317

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGLS++LENS+   +   +++PD 
Sbjct: 1318 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLSVELENSKV-ETQPEDQLPDA 1376

Query: 1381 NK 1382
             +
Sbjct: 1377 AE 1378


>gi|36333337|gb|AAP75726.1| RNA polymerase beta subunit [Afipia massiliensis]
          Length = 1375

 Score = 1751 bits (4535), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1370 (66%), Positives = 1113/1370 (81%), Gaps = 8/1370 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPTGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  + W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L ++
Sbjct: 241  RIKEGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRTARQLQEKGLKALRLS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             D L   Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++PIL +D VN   YIR
Sbjct: 300  DDELITNYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPILDIDHVNIGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMR
Sbjct: 360  NTLNADKNMTREDALFDIYRVMRPGEPPTIDSAQAMFQSLFFDSERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT+DVVYLSAMEE    +AQAN  LD  G FT++LV CR AGE + +  +
Sbjct: 600  TPYRKVKDGRVTDDVVYLSAMEEGRYRVAQANVPLDNKGRFTDDLVICRHAGEVLQITPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            K+D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  KVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD+VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDQVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL E+L  +  ++GPKGFKK T ++  ++ EYP+S
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLAELLENRQGIAGPKGFKKDTKITRAVLEEYPKS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWWQFA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWQFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKIKSLINDYK--ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            HLGWAC GLGK+I   ++ Y      DI PL+  L+KV G     E I   +D  ++ + 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKETLKKVYGDD---EVIKTLNDAELMELG 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            +  ++GVP++TPVFDGA E+ I  ML +A +++SGQS +YDG TG+ FDR VTVGYIYML
Sbjct: 1196 KNLRAGVPIATPVFDGAKEKDIEDMLELAGMNKSGQSTVYDGRTGDQFDRNVTVGYIYML 1255

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1256 KLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1315

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1316 KSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1365


>gi|52082901|gb|AAU26030.1| RNA polymerase beta subunit [Afipia sp. SP17]
          Length = 1376

 Score = 1751 bits (4535), Expect = 0.0,   Method: Composition-based stats.
 Identities = 902/1381 (65%), Positives = 1111/1381 (80%), Gaps = 8/1381 (0%)

Query: 1    MAKGV-VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA+    F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F
Sbjct: 1    MAQSQQTFTGRKRVRKFFGHIKEVAEMPNLIEVQKASYDQFLMVDEPAGGRLDEGLQAVF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  FSG + LEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGA
Sbjct: 61   RSVFPINDFSGTSQLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL
Sbjct: 121  KSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y 
Sbjct: 181  FAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYK 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +  + W  P  A D   G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L  +
Sbjct: 241  RIKEGWRVPFVA-DRFRGYSTINDLIDADSGKVVLEAGKKLTVRTARQLQEKGLKALRFS 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             + +   Y+AED+VN +TGEI+ EAG+ I EK L+ +     +++PIL +D VN   YIR
Sbjct: 300  DEEVVSNYLAEDLVNPKTGEIHAEAGEEITEKLLKALNEQGYKELPILDIDHVNIGPYIR 359

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNMR
Sbjct: 360  NTLSADKNMTREDALFDIYRVMRPGEPPTIDSAQAMFQSLFFDAERYDLSAVGRVKMNMR 419

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD +R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 420  LELDAPDTMRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGL 479

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 480  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 539

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+E
Sbjct: 540  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVE 599

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYRKV DG+VT+DVVYLSAMEE    +AQAN  LD  G FT++LV CR AGE + +P +
Sbjct: 600  TPYRKVKDGRVTDDVVYLSAMEEGRYRVAQANVPLDAKGRFTDDLVICRHAGEVLQLPPD 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VV
Sbjct: 660  RVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQR
Sbjct: 720  ARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVF
Sbjct: 779  PLVKVGDSVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDIL GKIT
Sbjct: 839  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILCGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER++++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+S
Sbjct: 959  EREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLEEYPKS 1018

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWWQFA  ++K+   +E++  QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1019 QWWQFASPNDKLMAEIEAMHKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFVA 1078

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1079 VKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1138

Query: 1140 HLGWACVGLGKKIKSLINDYK--ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            HLGWAC GLGK+I   ++ Y      DI PL+  L+KV G     E I   +D  ++ + 
Sbjct: 1139 HLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKETLKKVYGDD---EVIKTLNDTELMELG 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++GVP++TPVFDGA E  I  ML MA +++SGQS +YDG TG+ FDR VTVGYIYML
Sbjct: 1196 RNLRAGVPIATPVFDGAKEADIEQMLEMAGMNKSGQSTVYDGRTGDQFDRNVTVGYIYML 1255

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1256 KLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1315

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+   +   E  
Sbjct: 1316 KSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSKLGPTPTSEAA 1375

Query: 1378 P 1378
             
Sbjct: 1376 E 1376


>gi|188583688|ref|YP_001927133.1| DNA-directed RNA polymerase subunit beta [Methylobacterium populi
            BJ001]
 gi|226699421|sp|B1ZGS0|RPOB_METPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|179347186|gb|ACB82598.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium populi
            BJ001]
          Length = 1375

 Score = 1751 bits (4535), Expect = 0.0,   Method: Composition-based stats.
 Identities = 898/1378 (65%), Positives = 1114/1378 (80%), Gaps = 8/1378 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM++     R +EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIREVAEMPNLIEVQKASYDQFLMVDEPEGGRADEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAK
Sbjct: 59   SVFPISDFASTALLEFVRYTFEQPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI+HVRIDR+RK+PVTS L ALG+D EEILSTFY ++ Y +
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVHVRIDRKRKLPVTSLLFALGLDGEEILSTFYNRVSYER 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G K S  L+D D+GE V+E+GKKL +   + + EKG KFL  T 
Sbjct: 239  DGADWRVPFDAERL-KGFKASVDLIDADSGEVVLEAGKKLNARNARLIGEKGTKFLKATD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEI+ EAGD I EK L+ +    + +IP+L +D VN   YIRN
Sbjct: 298  EDLVGQYIAEDLVNAKTGEIWAEAGDEISEKLLKALDDVGVTEIPVLDIDHVNVGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+ AL DIYRVMRPG+  T   AE+MF+ LFFD+++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSAREGALFDIYRVMRPGEPPTLDTAEAMFHSLFFDAERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +R+ED++A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAADTVRTLRREDMLAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 478  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V DG VT++V YLSAMEE   Y+AQAN+ +D     T++LV CR AGE I+V  ++
Sbjct: 598  PFRRVKDGVVTDEVAYLSAMEEAKYYVAQANAGMDAARKLTDDLVVCRRAGEVIVVAPDR 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+GIV+QVDA RIVIR+ E   DP+  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRSGIVDQVDATRIVIRATEET-DPTKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG+ V++ +IIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEPVKKGEIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+ GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL E+L GQ+ ++GPKGF+K T L+ + ISEYPRSQ
Sbjct: 957  REEIERLAKDRDDEQTILDRNTYARLAEVLIGQSPIAGPKGFRKDTTLTREGISEYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVVDDRLMTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+K+   ++ Y  N DI+PLR+ +E +         +    D+++       
Sbjct: 1137 LGWAAAGLGRKVSKAVDAYLKNQDIAPLRAEMEAIYSPSE----LEGLSDEALAEAGNNV 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I +ML MA LD S QS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIETMLEMAGLDRSAQSTLYDGRTGEPFDRKVTMGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L NS+ + +    E P
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELTNSKQQAANDQIEPP 1370


>gi|163853415|ref|YP_001641458.1| DNA-directed RNA polymerase subunit beta [Methylobacterium extorquens
            PA1]
 gi|218532274|ref|YP_002423090.1| DNA-directed RNA polymerase subunit beta [Methylobacterium
            chloromethanicum CM4]
 gi|254563344|ref|YP_003070439.1| RNA polymerase subunit beta [Methylobacterium extorquens DM4]
 gi|226699419|sp|A9W8N8|RPOB_METEP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765295|sp|B7KN45|RPOB_METC4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|163665020|gb|ABY32387.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium
            extorquens PA1]
 gi|218524577|gb|ACK85162.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium
            chloromethanicum CM4]
 gi|254270622|emb|CAX26625.1| RNA polymerase, beta subunit [Methylobacterium extorquens DM4]
          Length = 1376

 Score = 1749 bits (4531), Expect = 0.0,   Method: Composition-based stats.
 Identities = 898/1384 (64%), Positives = 1118/1384 (80%), Gaps = 8/1384 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM++     R +EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIREVAEMPNLIEVQKASYDQFLMVDEPEGGRADEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAK
Sbjct: 59   SVFPISDFASTALLEFVRYTFEQPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI+HVRIDR+RK+PVTS L ALG+D EEILSTFY ++ Y +
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVHVRIDRKRKLPVTSLLFALGLDGEEILSTFYNRVAYQR 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G K S  L+D D+GE V+E+GKKL +   + + EKG KFL    
Sbjct: 239  DGADWRVPFDAERL-KGFKASVDLIDADSGEVVLEAGKKLNARNARLIGEKGTKFLRAAD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEI+ EAGD I EK L+ +    + ++P+L +D VN   YIRN
Sbjct: 298  EDLIGQYIAEDLVNMKTGEIWAEAGDEISEKLLKSLDDVGVTELPVLDIDHVNVGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+ AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSAREGALFDIYRVMRPGEPPTLDTAEAMFHSLFFDSERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +R+ED++A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAADTVRTLRREDMLAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 478  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V DG VT++V YLSAMEE   Y+AQAN+ +DE    T++LV CR AGE I+V  ++
Sbjct: 598  PFRRVKDGVVTDEVAYLSAMEEAKYYVAQANAGMDEGRKLTDDLVVCRRAGEVIVVAPDR 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+GIV+QVDA RIVIR+ E   DP+  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRSGIVDQVDATRIVIRASEET-DPTKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG+ V++ +IIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEPVKKGEIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+ GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL E+L GQ+ ++GPKGF+K T L+ ++ISEYPRSQ
Sbjct: 957  REEIERLAKDRDDEQTILDRNTYARLAEVLIGQSPIAGPKGFRKDTTLTREIISEYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVVDDRMMTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+K+   ++ Y  N DI+PLR+ +E +         +    D+++       
Sbjct: 1137 LGWAAAGLGRKVSKAVDAYLKNQDIAPLRAEMEAIYSPSE----LEGLSDEALAEAGNNV 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I +ML MA LD S QS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIETMLEMAGLDRSAQSTLYDGRTGEPFDRKVTMGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +S+ + +A  +  P  
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELTSSKQQQAANDQIEPPA 1372

Query: 1381 NKCE 1384
            +  E
Sbjct: 1373 DAAE 1376


>gi|75675542|ref|YP_317963.1| DNA-directed RNA polymerase subunit beta [Nitrobacter winogradskyi
            Nb-255]
 gi|88909623|sp|Q3SSY0|RPOB_NITWN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|74420412|gb|ABA04611.1| DNA-directed RNA polymerase subunit beta [Nitrobacter winogradskyi
            Nb-255]
          Length = 1380

 Score = 1749 bits (4530), Expect = 0.0,   Method: Composition-based stats.
 Identities = 906/1371 (66%), Positives = 1112/1371 (81%), Gaps = 12/1371 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA FKSVF
Sbjct: 3    QQTFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVDEPEGGRLDEGLQAVFKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI  FSGA+ LEFV YEF+ PK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGAKS+K
Sbjct: 63   PINDFSGASQLEFVRYEFEAPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAKSVK 122

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R
Sbjct: 123  DIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAAR 182

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG- 242
            +IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +   
Sbjct: 183  VIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIIYKRAKS 242

Query: 243  ----DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                D W  P        G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L +
Sbjct: 243  GGGSDGWRVPYDPV-RFRGYSTLNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRM 301

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            + + L G+Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN   YI
Sbjct: 302  SDEELVGMYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEEGYKELPLLDIDHVNVGPYI 361

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRVKMNM
Sbjct: 362  RNTLAADKNMTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDAERYDLSAVGRVKMNM 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+G
Sbjct: 422  RLDLDAPDTYRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVG 481

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH 
Sbjct: 482  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 541

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+
Sbjct: 542  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFV 601

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV DG+VT++VVYLSAMEE   ++AQAN  LD  G FTE+LV CR AGE + V  
Sbjct: 602  ETPYRKVKDGRVTDEVVYLSAMEEGRYHVAQANLPLDARGRFTEDLVVCRHAGEVLPVTP 661

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 662  DKVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 721

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R+G+++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 722  VARDSGAAIAARRSGVIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 780

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 781  RPLVKVGDIVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 840

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LK++DE GI+ +GAEV  GDILVGKI
Sbjct: 841  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKSLDEAGIVYIGAEVRAGDILVGKI 900

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 901  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 960

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  ++ EYP+
Sbjct: 961  IEREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVLDEYPK 1020

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1021 SQWWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1080

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1081 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1140

Query: 1139 THLGWACVGLGKKIKSLINDY--KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            THLGWAC GLG++I   ++ Y   A  +  PL+  L+KV G     E I   +D  ++ +
Sbjct: 1141 THLGWACAGLGRRIGQAVDAYLASAKQETKPLKETLKKVYGDN---ETIKSLEDHELVEL 1197

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                + GVP++TPVFDGA E  I  ML +A +D+SGQS +YDG TG+PFDR VTVGYIYM
Sbjct: 1198 GRNLRRGVPIATPVFDGAKEADIEQMLELAGMDKSGQSTVYDGRTGDPFDRKVTVGYIYM 1257

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1258 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1317

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            +KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1318 VKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1368


>gi|288957413|ref|YP_003447754.1| DNA-directed RNA polymerase subunit beta [Azospirillum sp. B510]
 gi|288909721|dbj|BAI71210.1| DNA-directed RNA polymerase subunit beta [Azospirillum sp. B510]
          Length = 1397

 Score = 1748 bits (4527), Expect = 0.0,   Method: Composition-based stats.
 Identities = 853/1394 (61%), Positives = 1070/1394 (76%), Gaps = 35/1394 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  RVRK FG+ PE+  +P+LIEVQ++SYDHFL M++AP++R N GLQ  FKSV
Sbjct: 1    MAKSFTGRKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVAPEKRANLGLQEVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS  A+L+FV YE + PK+DV++C  R +T+A PLK+TLRL VFDV+E TG +SI
Sbjct: 61   FPIKDFSDRAVLDFVKYELEQPKYDVEECQQRGMTFAAPLKVTLRLSVFDVEEDTGLRSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A 
Sbjct: 121  RDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHASGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--------------------- 221
            R+IP +G W+D EFD+KD+++VRIDRRRK+P T+ L AL                     
Sbjct: 181  RVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALDGADTEALRAERKANRKDLLP 240

Query: 222  ----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
                GM  EEIL+ FY  I YS+    W  P SA   M G K+ S LVD  TG  V E+G
Sbjct: 241  YEAQGMSKEEILNYFYDTITYSRSAGGWKTPFSAE-RMKGVKLVSDLVDAATGAIVAEAG 299

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             K+T   +K L E G+    ++++ L G Y+A DI+N  TGE+  EAGD +    L+++ 
Sbjct: 300  AKMTPRAIKKLVEAGLTEQQVSTEELTGRYLAVDIINERTGEVLFEAGDELSASDLDKLE 359

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
             + + ++P+L +D +N  AYIRNT+  D+N  R+DAL+DIYRVMRPG+  T   AE++F+
Sbjct: 360  KTGVDELPVLAIDHLNVGAYIRNTMNADRNASREDALIDIYRVMRPGEPPTLESAEALFS 419

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             LFFDS++YDLS VGRVKMN RLN  T D +R +RKEDI+ I+K+LV+L++G+G IDDID
Sbjct: 420  GLFFDSERYDLSAVGRVKMNARLNFQTDDQMRVLRKEDILEILKVLVNLKDGRGEIDDID 479

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            +LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+SSV+ID+VMP DLINAKP  +AV EFF
Sbjct: 480  HLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFF 539

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG
Sbjct: 540  GSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEG 599

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL ++ARVN YGFIE+PYRKV DGKVTN+VVYLSAMEE    +AQAN+ L+ D
Sbjct: 600  PNIGLINSLATYARVNQYGFIESPYRKVIDGKVTNEVVYLSAMEEGRYVVAQANAELNPD 659

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              F  +LV CR  GE ++   E ID ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQ
Sbjct: 660  NGFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQ 719

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVPL+KA+AP VGTGME+ VA+ SG  IVAKR+GIV+QVDA RIV+R+ +   D +  
Sbjct: 720  RQAVPLVKADAPLVGTGMEATVARDSGVTIVAKRSGIVDQVDATRIVVRATD-SSDSTAP 778

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+KFQRSNQNTC+ QRPLVKVGD V   DI+ADGPSTDLG+LALGRN+LVAFMP
Sbjct: 779  GVDIYNLLKFQRSNQNTCITQRPLVKVGDRVNAGDIVADGPSTDLGELALGRNVLVAFMP 838

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYNFEDS+LI+ER+V +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE LKN+D
Sbjct: 839  WNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALKNLD 898

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV PGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV G
Sbjct: 899  EAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVVG 958

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            T+V+VR+F+R G+DK+ER++++ER +IE LA+D+DDE+ IL+R+ Y+RL E+L GQ A S
Sbjct: 959  TIVEVRVFSRRGVDKDERALAIERAEIEKLAKDRDDERGILERSFYTRLKEVLIGQTAQS 1018

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            GPKG K  TVL+ ++++   +  W Q A+ DE+V   VE+L   ++ S   L+DRF+NK+
Sbjct: 1019 GPKGMKGGTVLTDEVLAGLSKGLWRQIAIADEQVMETVENLAKVFDDSIKALQDRFENKV 1078

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSRI+P EDMP+L+DGTP
Sbjct: 1079 DKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRIIPQEDMPYLEDGTP 1138

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK--------ANGDISPLR 1169
            VD+VLNPLGVPSRMNVGQI ETHLGWA  GLGK+I   ++ Y+            +  LR
Sbjct: 1139 VDLVLNPLGVPSRMNVGQILETHLGWAASGLGKQIGRAVDQYRLAIRQKAEGAPQLEALR 1198

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L+   G  ++ E I+D  D  +L +    + GVP +TPVFDGA EE I   L  A  D
Sbjct: 1199 GTLKSAYGEVTYNEDIADMTDGELLELGGNLRKGVPFATPVFDGAREEDICVHLERAGFD 1258

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
             SGQS L DG TGE FDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  
Sbjct: 1259 RSGQSTLVDGRTGETFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1318

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D FE G PESFNV
Sbjct: 1319 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNV 1378

Query: 1350 LVKEMQALGLSIDL 1363
            LVKE+++LGL+++L
Sbjct: 1379 LVKELRSLGLNVEL 1392


>gi|90417770|ref|ZP_01225682.1| DNA-directed RNA polymerase beta chain [Aurantimonas manganoxydans
            SI85-9A1]
 gi|90337442|gb|EAS51093.1| DNA-directed RNA polymerase beta chain [Aurantimonas manganoxydans
            SI85-9A1]
          Length = 1389

 Score = 1747 bits (4525), Expect = 0.0,   Method: Composition-based stats.
 Identities = 919/1392 (66%), Positives = 1118/1392 (80%), Gaps = 13/1392 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M++   F+G  RVRKFFG  PE+ ++P+LIEVQKASYD FLM++   + R +EGLQA FK
Sbjct: 1    MSQTTTFSGRRRVRKFFGSIPEVAEMPNLIEVQKASYDQFLMVDEPVNGRLDEGLQAVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG AMLEFV YEF+ PKFDV++C  RDLTYA PLK+TLRLIVFDVDE TG+K
Sbjct: 61   SVFPISDFSGQAMLEFVKYEFEQPKFDVEECRQRDLTYAAPLKVTLRLIVFDVDEDTGSK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121  SIKDIKEQDVYMGDMPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KD++H RIDRRRK+PVTS LMALGMD EEILSTFY  + + +
Sbjct: 181  AARVIPYRGSWLDIEFDAKDVVHARIDRRRKIPVTSLLMALGMDGEEILSTFYGTVKFEK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P S    + G      L+D D+GE ++E+GKK+T+   + ++EKGVK L  T 
Sbjct: 241  DKNGWRVPFSVE-RVRGQGAVVDLIDADSGEVLVEAGKKVTARQARQMQEKGVKALRATE 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDV----------IDEKSLEEIFHSEIRDIPILYVD 350
            D L G Y+AEDIVN ETGEIY+EAG              + SL ++ ++   +  +L +D
Sbjct: 300  DDLVGSYIAEDIVNPETGEIYLEAGQELEMTVDAKTGERKGSLIDLINAGYDEFTVLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             VN   YIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFDS++YDLS 
Sbjct: 360  HVNVGGYIRNTLAVDKNEGRQDALFDIYRVMRPGEPPTMETAEAMFQSLFFDSERYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRL++D  D VR +RKEDI+A+++ LVDLR+GKG IDDIDNLGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLDVDAEDTVRVLRKEDILAVVRTLVDLRDGKGEIDDIDNLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FA
Sbjct: 540  PLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIE+PYRKV DG VT+DVVYLSAMEE   ++AQAN+ L +D  F  E V CR  
Sbjct: 600  RVNKYGFIESPYRKVVDGVVTHDVVYLSAMEESKHHVAQANAILTDDNQFQNEFVVCRHQ 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  + PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPF
Sbjct: 660  GDVFMTPRDNVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPF 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTGME +VA+ SGAAI A+R GIV+QVDA RIVIR+ E  L+   SGVDIYRLMKFQRS
Sbjct: 720  VGTGMEPIVARDSGAAIGARRTGIVDQVDATRIVIRATED-LEAGKSGVDIYRLMKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRPLV VGD V + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+S
Sbjct: 779  NQNTCINQRPLVAVGDRVEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+V++DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV P
Sbjct: 839  ERIVADDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTS R+P G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSNRMPPGAYGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++++ERE+IE LA+D+DDEQ ILDRN+Y RL+E+L G+ AV+ PKGFKK +V+++
Sbjct: 959  EKDERAMAIEREEIERLAKDRDDEQAILDRNVYGRLVEMLDGKAAVAAPKGFKKGSVITA 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + EYPRSQWW FAV+DEK Q  +E L+  Y+ +K  LE RF +K+EK+Q GD++PPGV
Sbjct: 1019 EAMGEYPRSQWWMFAVEDEKTQAALEDLRNVYDEAKKTLEQRFMDKVEKVQRGDELPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            ++ VKVFVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPF  DGT VDIVLNPLGVPSR
Sbjct: 1079 MKQVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFNADGTHVDIVLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETHLGWAC G+G+KI  ++  Y+ + D+SPLR  +  ++G     EK+  YDD
Sbjct: 1139 MNVGQILETHLGWACAGMGRKIGDMLEAYQTSQDVSPLRDEIAGLLGDSDRNEKVKTYDD 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
             SVL +A+Q K GV ++TPVFDGA E+ I  ML  A L+ SGQ  LYDG TGE FDR VT
Sbjct: 1199 ASVLTLAKQMKRGVSIATPVFDGAVEQDIVEMLERAGLNGSGQVTLYDGRTGEAFDRQVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G+D FE+G PESFNVLVKEM++LGL +DL NS    
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVRGDDAFESGIPESFNVLVKEMRSLGLDVDLANS-AAE 1377

Query: 1371 SAKMEEIPDFNK 1382
                 ++PD  +
Sbjct: 1378 LPAPADLPDAAE 1389


>gi|36333363|gb|AAP75739.1| RNA polymerase beta subunit [Bosea minatitlanensis]
          Length = 1373

 Score = 1746 bits (4523), Expect = 0.0,   Method: Composition-based stats.
 Identities = 895/1365 (65%), Positives = 1103/1365 (80%), Gaps = 5/1365 (0%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            G  RVRKFFGK  E+ ++P+LIEVQKASYD FLM++     RP+EGLQ+ FKSVFPI  F
Sbjct: 7    GRRRVRKFFGKLKEVAEMPNLIEVQKASYDQFLMVDEPKGGRPDEGLQSVFKSVFPIGDF 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            SGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+KDIKEQ
Sbjct: 67   SGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSVKDIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +
Sbjct: 127  DVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARIIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEILS FY  I Y++    W  P
Sbjct: 187  GSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILSRFYNTITYTKDAKGWRVP 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              A   M G K +  L+D DTGE V+E+GKKL +   + L EKG+KFL    + L   Y+
Sbjct: 247  YDAE-RMKGFKATEDLIDADTGEVVVEAGKKLVARTARQLAEKGLKFLRAQDEDLYTQYI 305

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AED+VN  TGE+Y EAG+ I EK L+++      +IP+L +D +    YIRNTL  DKN 
Sbjct: 306  AEDLVNPATGEVYAEAGEEITEKLLKQLVDDGFDEIPVLDIDHITVGPYIRNTLNVDKNS 365

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             R++AL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKMNMRL+LD  D V
Sbjct: 366  RREEALFDIYRVMRPGEPPTLETAENMFQSLFFDPERYDLSAVGRVKMNMRLDLDAEDTV 425

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLLRMER+IKE
Sbjct: 426  RILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLLRMERAIKE 485

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 486  RMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 545

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++ DG
Sbjct: 546  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIRDG 605

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            KVT++V+YLSAMEE    +AQAN+++D+DG  T++LV CR AGE ++ P +K+DF D SP
Sbjct: 606  KVTDEVIYLSAMEEAKYNVAQANAAVDKDGRLTDDLVVCRRAGEVVVTPVDKVDFQDVSP 665

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA+ SGAAI 
Sbjct: 666  KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVARDSGAAIA 725

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRPLVKVGD V
Sbjct: 726  ARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRPLVKVGDSV 784

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFTSIHIEEFE
Sbjct: 785  KKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFTSIHIEEFE 844

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            VMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKGESPMTP
Sbjct: 845  VMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKITPKGESPMTP 904

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE+IE LA
Sbjct: 905  EEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIEREEIERLA 964

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW FA  +
Sbjct: 965  KDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWWLFATAE 1024

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            + +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR IQ GD
Sbjct: 1025 DSLMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKRKIQPGD 1084

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GL
Sbjct: 1085 KMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGL 1144

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK+I + ++ YK   D   L++  + V       E I+  D++ ++ + +  + GVPV+T
Sbjct: 1145 GKQIGAALDAYKKTNDFKALKASFDAVYEDN---EIIASMDENELVEMGQNLRRGVPVAT 1201

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            PVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++
Sbjct: 1202 PVFNGAKEADIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIH 1261

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+V
Sbjct: 1262 ARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKV 1321

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            YESIV G D FE G PESFNVLVKEM++LGL+++L N++ K    
Sbjct: 1322 YESIVRGEDNFEAGIPESFNVLVKEMRSLGLNVELVNNKVKPGEL 1366


>gi|92117084|ref|YP_576813.1| DNA-directed RNA polymerase subunit beta [Nitrobacter hamburgensis
            X14]
 gi|122418099|sp|Q1QN44|RPOB_NITHX RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91799978|gb|ABE62353.1| DNA-directed RNA polymerase subunit beta [Nitrobacter hamburgensis
            X14]
          Length = 1380

 Score = 1746 bits (4523), Expect = 0.0,   Method: Composition-based stats.
 Identities = 905/1371 (66%), Positives = 1108/1371 (80%), Gaps = 12/1371 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA FKSVF
Sbjct: 3    QQTFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVDEPEGGRLDEGLQAVFKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI  FSG + LEFV YEF+ PK+DVD+C  R +TYA PLK+TLRLIVFD+DE T AKS+K
Sbjct: 63   PINDFSGTSQLEFVRYEFEAPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETAAKSVK 122

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R
Sbjct: 123  DIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAAR 182

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG- 242
            +IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +   
Sbjct: 183  VIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIIYKRAKS 242

Query: 243  ----DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                D W  P        G    + L+D D+G+ V+E+GKKLT    + L+EKG+K L +
Sbjct: 243  GSNADGWRVPYDPV-RFRGYSTLNDLIDADSGKVVLEAGKKLTVRAARQLQEKGLKALRM 301

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            + + L G+Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN   YI
Sbjct: 302  SDEELVGMYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEHGYKELPLLDIDHVNVGPYI 361

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNM
Sbjct: 362  RNTLSADKNLTREDALFDIYRVMRPGEPPTLESAQNMFQSLFFDSERYDLSAVGRVKMNM 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+G
Sbjct: 422  RLDLDAPDTYRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVG 481

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH 
Sbjct: 482  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 541

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+
Sbjct: 542  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFV 601

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV DG+VT++VVYLSAMEE   ++AQAN  LD  G FTE+LV CR AGE + V  
Sbjct: 602  ETPYRKVKDGRVTDEVVYLSAMEEGRYHVAQANLPLDNRGRFTEDLVVCRHAGEVLPVTS 661

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 662  DKVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 721

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R+GI++Q+DA R+VIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 722  VARDSGAAIAARRSGIIDQIDATRVVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 780

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 781  RPLVKVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 840

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 841  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 900

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 901  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 960

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  +I EYP+
Sbjct: 961  IEREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRSVIEEYPK 1020

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1021 SQWWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1080

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1081 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1140

Query: 1139 THLGWACVGLGKKIKSLINDY--KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            THLGWAC GLG++I   ++ Y   A  +  PL+  L+KV G     E I   +D  ++ +
Sbjct: 1141 THLGWACAGLGRRIGQAVDAYLASAKQETKPLKETLKKVYGDN---ETIKSLNDHELVEL 1197

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                  GVP++TPVFDGA E  I  ML +A +D+SGQS +YDG TG+ FDR VTVGYIYM
Sbjct: 1198 GRNLSRGVPIATPVFDGAKEADIEQMLELAGMDKSGQSTVYDGRTGDTFDRKVTVGYIYM 1257

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1258 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1317

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            +KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1318 VKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1368


>gi|296444412|ref|ZP_06886377.1| DNA-directed RNA polymerase, beta subunit [Methylosinus trichosporium
            OB3b]
 gi|296258059|gb|EFH05121.1| DNA-directed RNA polymerase, beta subunit [Methylosinus trichosporium
            OB3b]
          Length = 1383

 Score = 1746 bits (4521), Expect = 0.0,   Method: Composition-based stats.
 Identities = 892/1375 (64%), Positives = 1111/1375 (80%), Gaps = 7/1375 (0%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     F+G  RVRKFFG   E  ++P+LIEVQKASYD FL+++     RP+EGLQ+ 
Sbjct: 1    MAQTSAQTFSGRKRVRKFFGHIREAAEMPNLIEVQKASYDQFLLVDEPQGGRPDEGLQSV 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            FKSVFPI+ FS  ++LEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFDVD  T 
Sbjct: 61   FKSVFPISDFSQVSLLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDVDPDTQ 120

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            AKS+KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKL
Sbjct: 121  AKSVKDIKEQDVYMGDMPFMTANGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKL 180

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L+A RIIP +G W+DIEFD+KDI++ RIDRRRK+PVTS L ALG+D EEILSTFY  +VY
Sbjct: 181  LFAARIIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLFALGLDGEEILSTFYKTVVY 240

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
               GD W  P     L  G K  + +VD D+GE ++E+GKKLT    + L EKGVK + +
Sbjct: 241  KASGDSWRQPFDPERL-KGVKAVNDIVDADSGEVLVEAGKKLTVRAARQLAEKGVKAIKV 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             S+ L G Y+A+D+ +  TGEI+ EAGD I  K+L  +      ++PIL +D +N   YI
Sbjct: 300  QSEDLYGQYLAQDLYDPSTGEIFAEAGDEITIKTLPMLVEKGFDELPILDIDHINIGPYI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNM
Sbjct: 360  RNTLAIDKNSSREDALFDIYRVMRPGEPPTMDTAEAMFHSLFFDSERYDLSAVGRVKMNM 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD PD +R +R+EDI+A+++ LVDLR+G+G IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 420  RLDLDAPDTMRVLRREDIVAVVRALVDLRDGRGEIDDIDHLGNRRVRSVGELMENQYRLG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH 
Sbjct: 480  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E PYR+V DGKVT++V YLSAMEE+  ++AQAN+ +D +G+ TE+LV CR AG+ +LVPR
Sbjct: 600  EGPYRRVRDGKVTDEVAYLSAMEEQKYHVAQANAPIDAEGNLTEDLVLCRHAGDVVLVPR 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KA+APFVGTGME +
Sbjct: 660  ERVDAMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPFVGTGMEPI 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGAAI A+R G+V+Q+DA RIV+R+ E   DP+  GVDIYRLMKFQRSNQ+TC+NQ
Sbjct: 720  VAADSGAAIAARRTGVVDQIDATRIVVRATEEQ-DPAKPGVDIYRLMKFQRSNQSTCINQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLVKVGD VR+ DIIADGPSTD+GDLALGRN+LVAFMPW+GYNFEDS+L++ER+V EDV
Sbjct: 779  KPLVKVGDFVRKGDIIADGPSTDMGDLALGRNVLVAFMPWNGYNFEDSILLNERIVKEDV 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHI+EFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 839  FTSIHIDEFEVMARDTKLGPEEITRDIPNVSEETLKNLDEAGIVYIGAEVQAGDILVGKI 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG++K+ER+ +
Sbjct: 899  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVEKDERAQA 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDE  ILDRN+Y+RL E+L G+ A++GPK FKK   L+  ++ EYPR
Sbjct: 959  IEREEIERLAKDRDDELAILDRNVYARLHEMLLGKVAIAGPKSFKKDQPLTQAILDEYPR 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW F V+D+ +   +E+++ QY+ SK  LE+RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1019 SQWWTFVVEDDNLMAGIEAVRKQYDESKKGLENRFLDKVEKLQRGDELPPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGTPVDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AVKRKIQPGDKMAGRHGNKGVVSRIVPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK++ + ++ Y    + +PL+  L ++ G     E +   D+ ++L V +
Sbjct: 1139 THLGWACAGLGKQVSAAVDAYMRTKNAAPLKEKLVEIYG---PNESLESLDEPTLLEVGK 1195

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVFDGA E+ I  ML  A L  SGQ  L+DG TGEPFDR VTVGYIY+LK
Sbjct: 1196 NLRRGVPIATPVFDGAREKDICDMLGRAGLASSGQVTLFDGRTGEPFDRKVTVGYIYILK 1255

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1256 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1315

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            SDDV GRT+VYESIV G+DTFE+G PESFNVL+KEM++L L+++L  +      +
Sbjct: 1316 SDDVAGRTKVYESIVRGDDTFESGIPESFNVLIKEMRSLALNVELTTAEEGEDEE 1370


>gi|240140835|ref|YP_002965315.1| RNA polymerase, beta subunit [Methylobacterium extorquens AM1]
 gi|240010812|gb|ACS42038.1| RNA polymerase, beta subunit [Methylobacterium extorquens AM1]
          Length = 1376

 Score = 1744 bits (4517), Expect = 0.0,   Method: Composition-based stats.
 Identities = 896/1384 (64%), Positives = 1117/1384 (80%), Gaps = 8/1384 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM+      R +EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIREVAEMPNLIEVQKASYDQFLMVGEPEGGRADEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  TGAK
Sbjct: 59   SVFPISDFASTALLEFVRYTFEQPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI+HVRIDR+RK+PVTS L ALG+D EEILSTFY ++ Y +
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVHVRIDRKRKLPVTSLLFALGLDGEEILSTFYNRVAYQR 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A  L  G K S  L+D D+GE V+E+GKKL +   + + EKG KFL    
Sbjct: 239  DGADWRVPFDAERL-KGFKASVDLIDADSGEVVLEAGKKLNARNARLIGEKGTKFLRAAD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEI+ EAGD I EK L+ +    + ++P+L +D VN   YIRN
Sbjct: 298  EDLIGQYIAEDLVNMKTGEIWAEAGDEISEKLLKSLDDVGVTELPVLDIDHVNVGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+ AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSAREGALFDIYRVMRPGEPPTLDTAEAMFHSLFFDSERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +R+ED++A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAADTVRTLRREDMLAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLS+  +  N LS +TH RR
Sbjct: 478  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSRFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V DG VT++V YLSAMEE   Y+AQAN+ +DE    T++LV CR AGE I+V  ++
Sbjct: 598  PFRRVKDGVVTDEVAYLSAMEEAKYYVAQANAGMDEGRKLTDDLVVCRRAGEVIVVAPDR 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+R+GIV+QVDA RIVIR+ E   DP+  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRSGIVDQVDATRIVIRASEET-DPTKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG+ V++ +IIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEPVKKGEIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+ GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL E+L GQ+ ++GPKGF+K T L+ ++ISEYPRSQ
Sbjct: 957  REEIERLAKDRDDEQTILDRNTYARLAEVLIGQSPIAGPKGFRKDTTLTREIISEYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVVDDRMMTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR I+ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIRPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+K+   ++ Y  N DI+PLR+ +E +         +    D+++       
Sbjct: 1137 LGWAAAGLGRKVSKAVDAYLKNQDIAPLRAEMEAIYSPSE----LEGLSDEALAEAGNNV 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I +ML MA LD S QS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIETMLEMAGLDRSAQSTLYDGRTGEPFDRKVTMGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +S+ + +A  +  P  
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELTSSKQQQAANDQIEPPA 1372

Query: 1381 NKCE 1384
            +  E
Sbjct: 1373 DAAE 1376


>gi|36333365|gb|AAP75740.1| RNA polymerase beta subunit [Bosea vestrisii]
          Length = 1372

 Score = 1744 bits (4517), Expect = 0.0,   Method: Composition-based stats.
 Identities = 898/1374 (65%), Positives = 1106/1374 (80%), Gaps = 5/1374 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                  G  RVRKFFGK  E+ ++P+LIEVQKASYD FLM+      R +EGLQ+ FKSV
Sbjct: 1    MVTSLQGRRRVRKFFGKLKEVAEMPNLIEVQKASYDQFLMVEEPKGGRSDEGLQSVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FSGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+
Sbjct: 61   FPIGDFSGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGEMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEIL+ FY  + Y +  
Sbjct: 181  RIIPYRGSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILARFYNHLSYVRDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P  A   M G K +  ++D DTGE VIE+GKKL +   + L EKG+KFL  T + 
Sbjct: 241  DGWRVPYDAE-RMKGFKATVDMIDADTGEVVIEAGKKLVARTARQLAEKGLKFLRATDED 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+AED+VN  TGE++ EAGD IDEKSL+ +  +   ++P+L +D +    YIRNTL
Sbjct: 300  LYGQYIAEDLVNPATGEVFAEAGDEIDEKSLKALLDAGFDELPVLDIDHITVGPYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R++AL DIYRVMRPG+  T   AE+MF  LFFDS++YDLS VGRVKMNMRL+L
Sbjct: 360  KVDKNSRREEALFDIYRVMRPGEPPTLETAENMFQSLFFDSERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D VR +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLLRM
Sbjct: 420  DAADTVRILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHTTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ DGK T++++YLSAMEE    +AQAN+++D++G  T++L+ CR AGE I+VP +K+D
Sbjct: 600  RRIRDGKQTDEIIYLSAMEEAKYNVAQANAAVDKEGRLTDDLIVCRRAGEVIVVPVDKVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA+ 
Sbjct: 660  FMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+++Q+DA RIVIR++E  LDP+ SGVDIYRLMKFQRSNQ+TC+NQRPLV
Sbjct: 720  SGAAIAARRTGVIDQIDATRIVIRALED-LDPTKSGVDIYRLMKFQRSNQSTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD V++ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFTSI
Sbjct: 779  KVGDVVKKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKG
Sbjct: 839  HIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW
Sbjct: 959  EIERLAKDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             FA  D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1019 LFATADDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KIQPGDKMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGK+I   I+ Y+   D   LR+  + V       E I+  DD  ++ + +  + 
Sbjct: 1139 WAAAGLGKQIGKAIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDAELIEMGQNLRR 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+
Sbjct: 1196 GVPIATPVFNGAKESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             GRT+VYESIV G D FE G PESFNVLVKEM++LGL+++L N++ K      E
Sbjct: 1316 AGRTKVYESIVRGEDNFEAGIPESFNVLVKEMRSLGLNVELVNTKPKQGDVPAE 1369


>gi|86749405|ref|YP_485901.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            HaA2]
 gi|123292712|sp|Q2IXS0|RPOB_RHOP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|86572433|gb|ABD06990.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            HaA2]
          Length = 1390

 Score = 1744 bits (4516), Expect = 0.0,   Method: Composition-based stats.
 Identities = 902/1385 (65%), Positives = 1110/1385 (80%), Gaps = 24/1385 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+   P  R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVAEPPGGRDDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS A+MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNASMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYNKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A+    G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDAS-RFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE----------------EIFHSEIRDI 344
              L G Y+AED+VN +TGEI+ EAGD +  K ++                 I     +++
Sbjct: 299  SELVGNYLAEDLVNPKTGEIFAEAGDELTGKPIKGDDKEIELFVGATPMKAILEQGYKEL 358

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD++
Sbjct: 359  PLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDAE 418

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YDLS VGRVKMNMRL+LD PD  R +RKEDI+A+IK LV LR+GKG IDDID+LGNRRV
Sbjct: 419  RYDLSAVGRVKMNMRLDLDAPDTHRTLRKEDILAVIKTLVGLRDGKGEIDDIDHLGNRRV 478

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            RSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ
Sbjct: 479  RSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQ 538

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++
Sbjct: 539  FMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIN 598

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL +FARVN YGF+ETPYRKV +G+VT++VVYLSAMEE    +AQAN SLD  G FT++L
Sbjct: 599  SLATFARVNKYGFVETPYRKVKEGRVTDEVVYLSAMEEGRYAVAQANISLDAKGRFTDDL 658

Query: 645  VFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            + CR     + +L+P +++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVP
Sbjct: 659  IVCRAGGTRDVVLIPADQVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVP 718

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            L++AEAPFVGTGME VVA+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIY
Sbjct: 719  LVRAEAPFVGTGMEGVVARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIY 777

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            RLMK+QRSNQ+TC+NQRPLVKVGD+V + DIIADGPSTDLG+LALGRN+LVAFMPW+GYN
Sbjct: 778  RLMKYQRSNQSTCINQRPLVKVGDKVAKGDIIADGPSTDLGELALGRNVLVAFMPWNGYN 837

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+L+SER+V EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+
Sbjct: 838  FEDSILLSERIVKEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIV 897

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+V
Sbjct: 898  YIGAEVRAGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEV 957

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            R+FNRHG+DK+ER++++ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  V+GPKGF
Sbjct: 958  RVFNRHGVDKDERALAIEREEIERLAKDRDDEQAILDRNVYGRLADLLDNRQGVAGPKGF 1017

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK T ++  ++ EYP+SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q 
Sbjct: 1018 KKDTKITRAVLEEYPKSQWWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQR 1077

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV+++VKVFVA+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVL
Sbjct: 1078 GDELPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVL 1137

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMNVGQI ETHLGWAC G+GKKI   I+ Y    D+ PLR  L+K+ G     
Sbjct: 1138 NPLGVPSRMNVGQILETHLGWACAGMGKKIGQTIDAYYQRQDLKPLRETLKKIYGDD--- 1194

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
            E I   DD  ++ +      GVP++TPVFDGA E  I  ML++A  D SGQS +YDG TG
Sbjct: 1195 ETIKSLDDGELIELGRNLSHGVPIATPVFDGAKEADIEEMLKLAGFDASGQSTVYDGRTG 1254

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            + FDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1255 DEFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1314

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++D
Sbjct: 1315 EAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVD 1374

Query: 1363 LENSR 1367
            L NS+
Sbjct: 1375 LHNSK 1379


>gi|240850292|ref|YP_002971685.1| DNA-directed RNA polymerase subunit beta [Bartonella grahamii as4aup]
 gi|240267415|gb|ACS51003.1| DNA-directed RNA polymerase subunit beta [Bartonella grahamii as4aup]
          Length = 1382

 Score = 1744 bits (4516), Expect = 0.0,   Method: Composition-based stats.
 Identities = 935/1367 (68%), Positives = 1130/1367 (82%), Gaps = 2/1367 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKS
Sbjct: 6    AMMSQFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFKS 65

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFDVDE TG+K 
Sbjct: 66   VFPISDFSGTAMLEFVGYEFDLPKFDVEECRQRDLTYAAPLKVILRLIVFDVDEDTGSKD 125

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            IKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+A
Sbjct: 126  IKDIKEQGVYMGDMPLMTTNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFA 185

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+DIEFD+KDII+ RIDRRRK+PVTS LMALGMD+ +ILSTFY K+ Y + 
Sbjct: 186  ARVIPYRGSWLDIEFDAKDIIYARIDRRRKIPVTSLLMALGMDASDILSTFYDKVTYERD 245

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            G+ W  P S  D   G K+ S L+D D+GE V E+GKKLT    KSL EKG+K + ++ D
Sbjct: 246  GEGWRVPYSV-DRFKGMKLISDLIDADSGEVVAEAGKKLTVRTAKSLAEKGLKAVKVSED 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G Y+AEDIVN ETGEIY+EAGD IDEK L+ +       I IL +D +N  AYIRNT
Sbjct: 305  DLLGCYLAEDIVNYETGEIYLEAGDEIDEKVLKVLLDVSADQINILDIDHMNIGAYIRNT 364

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFFD ++YDLS VGRVKMN+R++
Sbjct: 365  LKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMD 424

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLR
Sbjct: 425  LDCPDTVRILRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLR 484

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 485  MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 544

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 545  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 604

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 605  YRKIVDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHV 664

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+
Sbjct: 665  DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVAR 724

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPL
Sbjct: 725  DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPL 783

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD V + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTS
Sbjct: 784  VHVGDRVEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTS 843

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITPK
Sbjct: 844  IHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPK 903

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ER
Sbjct: 904  GESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIER 963

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ AV GPKGF  S  L S ++  YPRSQW
Sbjct: 964  EEIERLAKDRDDEQSILDRNVYARLTDMLTGKVAVEGPKGFSGSKKLDSTVMGHYPRSQW 1023

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            WQFAV+DEK+Q  +E+L+ QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+K
Sbjct: 1024 WQFAVEDEKLQNEIEALRKQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKVFVAVK 1083

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1084 RKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHL 1143

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC G+GKKI  L+  Y+  GDI PLR  +E ++   +  E +  YD++S+ ++A Q K
Sbjct: 1144 GWACAGMGKKIGDLLELYQETGDILPLRQRIENLMPDDNQNEPVRQYDNESLYKLALQMK 1203

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYMLKL+H
Sbjct: 1204 KGVSIATPVFDGAHESDINIMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYMLKLHH 1263

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1264 LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1323

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            V GRT+VYE+IV G+DTFE G PESFNVLVKEM++L L+++L+++R 
Sbjct: 1324 VAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLALNVELDDARE 1370


>gi|170750237|ref|YP_001756497.1| DNA-directed RNA polymerase subunit beta [Methylobacterium
            radiotolerans JCM 2831]
 gi|226699422|sp|B1LY43|RPOB_METRJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|170656759|gb|ACB25814.1| DNA-directed RNA polymerase, beta subunit [Methylobacterium
            radiotolerans JCM 2831]
          Length = 1374

 Score = 1743 bits (4514), Expect = 0.0,   Method: Composition-based stats.
 Identities = 894/1382 (64%), Positives = 1114/1382 (80%), Gaps = 8/1382 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +V  G  R+RKFFGK  E+ ++P+LIEVQKASYD FLM++     R +EGLQ+ FK
Sbjct: 1    MANTLV--GRKRIRKFFGKIKEVAEMPNLIEVQKASYDQFLMVDEPEGGRADEGLQSVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+  A+LEFV Y F+ PK+DVD+C  R +T+A PLK+TLRLIVFDVD  T AK
Sbjct: 59   SVFPISDFASTALLEFVRYTFEAPKYDVDECRQRGITFAAPLKVTLRLIVFDVDPDTQAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT++GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTENGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D+EFD+KDI+HVRIDR+RK+P TS L ALG+D EEILSTFY K+VY +
Sbjct: 179  AARIIPYRGSWLDVEFDAKDIVHVRIDRKRKLPATSLLYALGLDGEEILSTFYNKVVYDR 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G  W  P  A   M G K +  L+D D+GE V+E+GKKL +   + + EKG KFL  T 
Sbjct: 239  DGADWRVPFDAE-RMKGMKATVDLIDADSGEVVLEAGKKLNARNARQITEKGTKFLKATD 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G YVAED+VN +TGEI+ EAG+ + +K L+ +    I ++P+L +D VN   YIRN
Sbjct: 298  EDLVGQYVAEDLVNAQTGEIWAEAGEEVTDKLLKSLEEVGITELPVLDIDHVNIGPYIRN 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN +R+ AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL
Sbjct: 358  TLAVDKNSNREGALFDIYRVMRPGEPPTLETAEAMFHSLFFDSERYDLSAVGRVKMNMRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD  D VR +RKED++A++K LV+LR+GKG +DDID+LGNRRVRSVGE+++NQYRLGLL
Sbjct: 418  DLDAADTVRTLRKEDMLAVVKALVELRDGKGEVDDIDHLGNRRVRSVGELMENQYRLGLL 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+I+ER+S VDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 478  RMERAIRERMSQVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIET
Sbjct: 538  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIET 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            P+R+V DG VT++V YLSAMEE   Y+AQAN+ +DE+   TE+LV CR AGE I+V  E+
Sbjct: 598  PFRRVRDGVVTDEVAYLSAMEEAKYYVAQANAQMDENRKLTEDLVVCRRAGEVIVVGPER 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA
Sbjct: 658  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+RAGI++QVDA RIVIR+ E   D +  GVDIYRL KFQRSNQ+TC+ Q+P
Sbjct: 718  RDSGAAIAARRAGIIDQVDATRIVIRATEEA-DANKPGVDIYRLQKFQRSNQSTCITQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VG+ V++ +IIADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DVFT
Sbjct: 777  LVRVGEFVKKGEIIADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEVN GDILVGKITP
Sbjct: 837  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVNAGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV+GT+V+VR+FNRHG+DK+ER+ ++E
Sbjct: 897  KGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVTGTIVEVRVFNRHGVDKDERAQAIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN Y+RL ++L GQ  V+GPKGFKK T L+ +LI++YPRSQ
Sbjct: 957  REEIERLAKDRDDEQAILDRNTYARLADVLIGQAPVAGPKGFKKDTTLTRELINDYPRSQ 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAV D+++   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1017 WWQFAVIDDRLMTEMEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG+K+   ++ Y    DI+PLR  ++ +   G     +    D+ +       
Sbjct: 1137 LGWAAAGLGRKVSKAVDAYLKTQDIAPLREEMKAIYSPGE----LDGLTDEELAEAGNNV 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVF+GA E  I  ML MA LD S QS LYDG TGEPFDR VT+GYIYMLKL+
Sbjct: 1193 RRGVPMATPVFNGAKEADIEQMLEMAGLDRSAQSTLYDGRTGEPFDRKVTMGYIYMLKLH 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +S+   + ++E   D 
Sbjct: 1313 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELTSSKKAANDQLEPPADA 1372

Query: 1381 NK 1382
             +
Sbjct: 1373 AE 1374


>gi|90424947|ref|YP_533317.1| DNA-directed RNA polymerase subunit beta [Rhodopseudomonas palustris
            BisB18]
 gi|122475728|sp|Q211D8|RPOB_RHOPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|90106961|gb|ABD88998.1| DNA-directed RNA polymerase, beta subunit [Rhodopseudomonas palustris
            BisB18]
          Length = 1373

 Score = 1743 bits (4514), Expect = 0.0,   Method: Composition-based stats.
 Identities = 903/1369 (65%), Positives = 1109/1369 (81%), Gaps = 8/1369 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM++     R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVDEPVGGRLDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS  +MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNTSMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKIQYKK 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  + +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  IKEGWRVPFDS-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN  AYIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKGLNEQGYKELPLLDIDHVNIGAYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLAADKNMTREDALFDIYRVMRPGEPPTIDSAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD PD  R +RKEDI+A+IK LV LR+G+G IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  ELDAPDTHRTLRKEDILAVIKTLVGLRDGRGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYR+  DG+VT++VVYLSAMEE    +AQAN  LD  G F E+L+ CR     + +L+P 
Sbjct: 599  PYRRCKDGRVTDEVVYLSAMEEGRYSVAQANVQLDPKGRFVEDLIVCRDGGTRDVVLIPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF+D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DKVDFMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G+++Q+DA RIVIR+ +  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGVIDQIDATRIVIRATDD-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD V + DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V +DV
Sbjct: 778  RPLVKVGDMVAKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKDDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L  +  ++GPKGFKK T ++  +I EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLENRQGIAGPKGFKKDTKITRAVIEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFASPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   I+ Y    D+ P+R  L K+ G     E I   +D  +L +A 
Sbjct: 1138 THLGWACAGLGKRIGQTIDAYYQKQDLKPMRETLRKIYGED---ETIKSLNDAELLELAR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLKPGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDTFDRKVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            SDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL NS+
Sbjct: 1315 SDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVDLHNSK 1363


>gi|49475398|ref|YP_033439.1| DNA-directed RNA polymerase subunit beta [Bartonella henselae str.
            Houston-1]
 gi|41017805|sp|Q9KJG4|RPOB_BARHE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|9309387|gb|AAF87049.1|AF171070_1 RNA polymerase beta subunit [Bartonella henselae str. Houston-1]
 gi|49238204|emb|CAF27414.1| DNA-directed RNA polymerase beta chain [Bartonella henselae str.
            Houston-1]
          Length = 1383

 Score = 1743 bits (4513), Expect = 0.0,   Method: Composition-based stats.
 Identities = 929/1368 (67%), Positives = 1131/1368 (82%), Gaps = 2/1368 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 5    LAMTSQFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPKGGRPDEGLQAVFK 64

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG AMLEFV Y+FD PKFDV++C  RDLTYA PLK+ LRLIVFDVDE TG+K
Sbjct: 65   SVFPISDFSGTAMLEFVGYQFDSPKFDVEECRQRDLTYAAPLKVILRLIVFDVDEDTGSK 124

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGK L+
Sbjct: 125  DIKDIKEQGVYMGDMPLMTTNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKFLF 184

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDII+ RIDRRRK+PVTS LMALGMD+ +ILSTFY K+ Y +
Sbjct: 185  AARVIPYRGSWLDIEFDAKDIIYARIDRRRKIPVTSLLMALGMDASDILSTFYNKVTYER 244

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P S  D   G K+ S L+D D+GE V E+GKKLT    K+L EKG+K + ++ 
Sbjct: 245  DGDGWRIPYSV-DRFKGMKLVSDLIDADSGEVVAEAGKKLTVRAAKALAEKGLKAVKVSE 303

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN +TGEIY+EAGD IDEK+L  +F      I IL +D +N  AYIRN
Sbjct: 304  DDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKTLRVLFDVNADQIDILDIDHMNIGAYIRN 363

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFFD ++YDLS VGRVKMN+R+
Sbjct: 364  TLKVDKNESRQDALFDIYRVMRPGEPPTMDTAEAMFHSLFFDPERYDLSAVGRVKMNLRM 423

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 424  DLDCPDTVRVLRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLL 483

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 484  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 543

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 544  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 603

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ 
Sbjct: 604  PYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDH 663

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA
Sbjct: 664  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVA 723

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAA+ A+R+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 724  RDSGAAVAARRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 782

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + +IIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 783  LVHVGDRVEKGNIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 842

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITP
Sbjct: 843  SIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITP 902

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 903  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGAFGTVVEVRVFNRHGVEKDERAMAIE 962

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ AV GPKGF K+  L + ++  YPRSQ
Sbjct: 963  REEIERLAKDRDDEQSILDRNVYARLTDMLVGKVAVEGPKGFSKNKKLDTTIMGHYPRSQ 1022

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQF V+DEK+Q  +E+L+ QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1023 WWQFTVEDEKLQNEIEALRNQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1082

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1083 KRKIQPGDKMAGRHGNKGVVSRILPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1142

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+  GDI PLR  +E ++    H E +  YD++S+ ++A Q 
Sbjct: 1143 LGWACAGMGKKIGDLVDLYQETGDILPLRQRIENLMPDDDHNEPVRQYDNESLYKLALQM 1202

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYMLKL+
Sbjct: 1203 RKGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYMLKLH 1262

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1263 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1322

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++L L+++L+++R 
Sbjct: 1323 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLALNVELDDARE 1370


>gi|319404381|emb|CBI77984.1| DNA-directed RNA polymerase, beta chain [Bartonella rochalimae ATCC
            BAA-1498]
          Length = 1382

 Score = 1742 bits (4512), Expect = 0.0,   Method: Composition-based stats.
 Identities = 933/1372 (68%), Positives = 1129/1372 (82%), Gaps = 6/1372 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQ
Sbjct: 1    MAQTLAMMSQFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPEGGRLDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFDPPKFDV++C  RDLTYA PLK+ LRLIVFDVDE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDPPKFDVEECHQRDLTYAAPLKVILRLIVFDVDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTDNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            K L+A R+IP +G W+DIEFD+KDI++VRIDRRRK+PVTS LMALGMD+ +ILSTFY K+
Sbjct: 181  KFLFAARVIPYRGSWLDIEFDAKDIVYVRIDRRRKIPVTSLLMALGMDASDILSTFYNKV 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y +  + W  P S  D   G K+ S LVD D+GE V E+GKKLT    K L+EKG+K +
Sbjct: 241  SYERTKNGWRTPYSV-DRFRGMKLVSDLVDADSGEVVAEAGKKLTVRAAKLLEEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             ++ D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +       I IL +D +N  A
Sbjct: 300  EVSEDDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKTLKILSDVGADQINILDIDHMNVGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T + AE+MF+ LFFD ++YDLS VGRVKM
Sbjct: 360  YIRNTLKVDKNESRQDALFDIYRVMRPGEPPTINTAEAMFHSLFFDPERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRILRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLLRMERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 600  FIESPYRKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME
Sbjct: 660  PRDHIDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA  SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  AIVACDSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD + + DIIADG STDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRIEKGDIIADGSSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV+PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVHPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +++ERE+IE LA+D+DDEQ ILDR++Y+RL +IL G+ A+ GPKGF K   L S ++ +Y
Sbjct: 959  MAIEREEIERLAKDRDDEQSILDRSVYARLADILTGKVAIEGPKGFSKGKTLDSTVMEQY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PR QWWQFAV+DEK+Q  +E+L  QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRYQWWQFAVEDEKLQNEIEALHKQYDESKKALQRRFMDKVEKVQRGDEMPPGVMKIVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  LI  Y+  GDI PLR  +E +I      E +  YD++S++++
Sbjct: 1139 LETHLGWACAGMGKKIGDLIKLYQETGDILPLRQRIENLIPDDDRNEPVRHYDNESLIKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q K GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYM
Sbjct: 1199 ALQMKQGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +KSDDV GRT+VYE++V G+DTFE G PESFNVLVKEM++LGL+++L+++R 
Sbjct: 1319 VKSDDVAGRTKVYEAVVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDARE 1370


>gi|319408383|emb|CBI82038.1| DNA-directed RNA polymerase, beta chain [Bartonella schoenbuchensis
            R1]
          Length = 1382

 Score = 1741 bits (4509), Expect = 0.0,   Method: Composition-based stats.
 Identities = 931/1372 (67%), Positives = 1127/1372 (82%), Gaps = 6/1372 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+  +   RP+EGLQ
Sbjct: 1    MAQTLAMMSQFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEESEGGRPDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFD+DE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDLPKFDVEECRQRDLTYAAPLKVILRLIVFDIDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG++  SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTSNGTFVINGTERVIVSQMHRSPGVFFDHDKGKSHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            KLL+A R+IP +G W+DIEFD+KDII+ RIDRRRK+PVTS LMALGMD+ +ILSTFY KI
Sbjct: 181  KLLFAARVIPYRGSWLDIEFDAKDIIYARIDRRRKIPVTSLLMALGMDASDILSTFYNKI 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y +  + W  P S  D   G K+ S L+D D+GE V E+GKKLT    K L EKG+K +
Sbjct: 241  TYERVENGWRVPYSI-DRFKGMKLVSDLIDADSGEVVAEAGKKLTVRTAKLLAEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             ++ D L G Y+AEDIVN +TGEIY+EAGD ID+K+L+ +F      I +L +D +N  A
Sbjct: 300  RVSEDDLLGSYLAEDIVNYQTGEIYLEAGDEIDDKALKILFDINADQIDVLDIDHMNVGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKM
Sbjct: 360  YIRNTLKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFLSLFFDPERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDI+ ++K+LV+LR+G G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRTLRQEDILGVVKMLVELRDGHGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 600  FIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME
Sbjct: 660  PRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            S+VA+ SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  SIVARDSGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD V + DIIADGPST+LGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRVEKGDIIADGPSTNLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVQPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +++ERE+IE LA+D+DDEQ ILDRN+Y+RL ++L  + A+ GPKGF K   L S ++  Y
Sbjct: 959  MAIEREEIERLAKDRDDEQSILDRNVYARLADMLKDKVAIEGPKGFSKGKKLDSAIMDSY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PRSQWWQFA+ DEK+Q  +E+L+ QY+ SK  L+  F +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRSQWWQFAIDDEKIQNEIEALRKQYDESKETLQRCFMDKVEKVQRGDEMPPGVMKMVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  L+  Y+  GDI PLR  +E +I      E +  Y+++S+ ++
Sbjct: 1139 LETHLGWACAGMGKKIGDLVELYQGTGDILPLRQCIENLIPDNDRNEPVRQYNNESLFKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q K GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYM
Sbjct: 1199 ALQMKDGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+++R 
Sbjct: 1319 VKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDARG 1370


>gi|36333367|gb|AAP75741.1| RNA polymerase beta subunit [Bosea eneae]
          Length = 1372

 Score = 1741 bits (4509), Expect = 0.0,   Method: Composition-based stats.
 Identities = 896/1374 (65%), Positives = 1105/1374 (80%), Gaps = 5/1374 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                  G  RVRKFFGK  E+ ++P+LIEVQKASYD FLM+      R +EGLQ+ FKSV
Sbjct: 1    MVTSLQGRRRVRKFFGKLKEVAEMPNLIEVQKASYDQFLMVEEPKGGRGDEGLQSVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FSGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+
Sbjct: 61   FPIGDFSGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGEMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEIL+ FY  + Y +  
Sbjct: 181  RIIPYRGSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILARFYNHLSYVRDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P  A   M G K +  ++D DTGE VIE+GKKL +   + L EKG+KFL  T + 
Sbjct: 241  DGWRVPYDAE-RMKGFKATVDMIDADTGEVVIEAGKKLVARTARQLAEKGLKFLRATDED 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+AED+VN +TGE++ EAGD IDEKSL+ +  +   ++P+L +D +    YIRNTL
Sbjct: 300  LYGQYIAEDLVNPQTGEVFAEAGDEIDEKSLKALLDAGFDELPVLDIDHITVGPYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R++AL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNMRL+L
Sbjct: 360  KVDKNSRREEALFDIYRVMRPGEPPTLETAENMFQSLFFDAERYDLSAVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D VR +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLLRM
Sbjct: 420  DAEDTVRILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHTTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ DGK T++++YLSAMEE    +AQAN+++D++G  T++L+ CR AGE I+VP +K+D
Sbjct: 600  RRIRDGKQTDEIIYLSAMEEAKYNVAQANAAVDKEGRLTDDLIVCRRAGEVIVVPVDKVD 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA+ 
Sbjct: 660  FMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGVVARD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQRPLV
Sbjct: 720  SGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+VR+ DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SE +V  DVFTSI
Sbjct: 779  KVGDQVRKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSEXIVXXDVFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKG
Sbjct: 839  HIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKITPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE
Sbjct: 899  ESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIERE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW
Sbjct: 959  EIERLAKDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWW 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             FA  D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1019 LFATSDDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1079 KIQPGDKMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGK+I   I+ Y+   D   LR+  + V       E I+  DD  ++ + +  + 
Sbjct: 1139 WAAAGLGKQIGKAIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDAELIEMGQNLRR 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+
Sbjct: 1196 GVPIATPVFNGAKESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             GRT+VYESIV G D FE G PESFNVLVKEM++LGL+++L N++ K      E
Sbjct: 1316 AGRTKVYESIVRGEDNFEAGIPESFNVLVKEMRSLGLNVELVNTKPKPGEVPAE 1369


>gi|83312239|ref|YP_422503.1| DNA-directed RNA polymerase subunit beta [Magnetospirillum magneticum
            AMB-1]
 gi|109904152|sp|Q2W2I1|RPOB_MAGSA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|82947080|dbj|BAE51944.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Magnetospirillum magneticum AMB-1]
          Length = 1391

 Score = 1740 bits (4507), Expect = 0.0,   Method: Composition-based stats.
 Identities = 857/1392 (61%), Positives = 1077/1392 (77%), Gaps = 29/1392 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  RVRK FG+ P +  +P+LIEVQK+SYDHFL M+ AP++R N GLQ  FKSV
Sbjct: 1    MAKSYTGRKRVRKSFGRIPTVAPMPNLIEVQKSSYDHFLQMDTAPEQRGNVGLQEVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS    LEFV YE + PK+DV++C  R +T+A PLK+TLRL+V+D+DE TG++SI
Sbjct: 61   FPIKDFSERGTLEFVRYELEQPKYDVEECQQRGMTFAAPLKVTLRLVVWDIDEDTGSRSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A 
Sbjct: 121  RDIKEQDVYMGDMPLMTSNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--------------------- 221
            R+IP +G W+D EFD+KD+++VRIDRRRK+PVT+ L AL                     
Sbjct: 181  RVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPVTTLLYALDGMNTAALRAQRAAEGRGLEQ 240

Query: 222  ----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
                GM SEEILS FY K+VY++    W  P  A  L  G K+ S L+D  +GE+V ++G
Sbjct: 241  SEIKGMTSEEILSYFYGKVVYTRGPKGWKTPFDAERL-KGVKLVSDLIDAKSGEKVADAG 299

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             K+T  L K L+E G+  + +  + + G YVAEDI+N +TGEI+ EAGD +    + E+ 
Sbjct: 300  SKMTPRLGKKLREAGLTDIVVFPEDMIGQYVAEDIINEQTGEIFTEAGDELTANLVAELE 359

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
             + I ++P+L +D +N   Y+RNTL  DKN  R++AL+DIYRVMRPG+  T   AE++F 
Sbjct: 360  KAGISELPVLAIDHINVGPYMRNTLAIDKNSSREEALIDIYRVMRPGEPPTLETAEALFT 419

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLN-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
             LFFDS++YDLS VGRVKMN RLN  +  D VR +RKEDI+ +IK+LV+L++GKG IDDI
Sbjct: 420  GLFFDSERYDLSAVGRVKMNSRLNTPEVADTVRVLRKEDILGVIKVLVELKDGKGEIDDI 479

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            D+LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+SSVDIDSVMP DLINAKP  +AV EF
Sbjct: 480  DHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVDIDSVMPHDLINAKPAAAAVREF 539

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 540  FGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 599

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++ARVN YGFIE PYRKV DG+VT+DVVYLSAMEE    +AQANS LD 
Sbjct: 600  GPNIGLINSLATYARVNQYGFIEAPYRKVFDGRVTSDVVYLSAMEEGRYTVAQANSILDA 659

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            DG FTE+LV CR AG+ ++VP  +I+ ID SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 660  DGRFTEDLVSCRRAGDFVMVPPNEINMIDVSPKQLVSVAAALIPFLENDDANRALMGSNM 719

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++AEAP VGTGME  VA+ SGAAI AKR G+V+QVDA R+VIR+ E     + 
Sbjct: 720  QRQAVPLIRAEAPLVGTGMEQAVARDSGAAITAKRTGVVDQVDATRVVIRATEETQASA- 778

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            SGVDIY L+KFQRSNQNTC+ QRPLVKVGD +++ DIIADGPST LG+LALGRN+LVAFM
Sbjct: 779  SGVDIYNLLKFQRSNQNTCITQRPLVKVGDLIQKGDIIADGPSTQLGELALGRNVLVAFM 838

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+V +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE LKN+
Sbjct: 839  PWNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALKNL 898

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ +GAEV PGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVS
Sbjct: 899  DEAGIVYIGAEVKPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVS 958

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+V+VR+F+R G++K+ER++++ER +IE LA+D+DDE+ IL+R+ ++RL  ++ G+  V
Sbjct: 959  GTIVEVRVFSRRGVEKDERALAIERAEIERLAKDRDDERHILERSFFARLKALIIGKKVV 1018

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            SGPKG K  TVL+   + E   S W   A+ D+ V  + E+LK  ++     L++RF+NK
Sbjct: 1019 SGPKGIKAGTVLADANMDELHPSTWRNIAIDDDAVMADAEALKRAFDQQVDKLQERFENK 1078

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG++SRI+P EDMP+L+DG 
Sbjct: 1079 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRIVPLEDMPYLEDGQ 1138

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK-ANGDISPLRSFLEKV 1175
             VDIVLNPLGVPSRMNVGQI ETHLGWAC GLG++I  +++ YK     I  L+S L+ V
Sbjct: 1139 QVDIVLNPLGVPSRMNVGQILETHLGWACAGLGQQIGGMLDKYKRNAATIIDLKSKLKDV 1198

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   + ++I+   D+ +  +A     GVP++TPVFDGA E  I +ML  A    SGQ  
Sbjct: 1199 YGDAIYEDEIAGLADNEITELAHNLTPGVPIATPVFDGARESDIVAMLTKAGRSSSGQVT 1258

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPFDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1259 LVDGRTGEPFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1318

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKE++
Sbjct: 1319 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDTFEAGIPESFNVLVKELR 1378

Query: 1356 ALGLSIDLENSR 1367
            +LGL+++L    
Sbjct: 1379 SLGLNVELTQRN 1390


>gi|163868089|ref|YP_001609293.1| DNA-directed RNA polymerase subunit beta [Bartonella tribocorum CIP
            105476]
 gi|189043847|sp|A9ISG1|RPOB_BART1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|161017740|emb|CAK01298.1| DNA-directed RNA polymerase, beta chain [Bartonella tribocorum CIP
            105476]
          Length = 1383

 Score = 1740 bits (4506), Expect = 0.0,   Method: Composition-based stats.
 Identities = 937/1367 (68%), Positives = 1131/1367 (82%), Gaps = 2/1367 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKS
Sbjct: 6    AMMSQFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPKGGRPDEGLQAVFKS 65

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFD+DE TG+K 
Sbjct: 66   VFPISDFSGTAMLEFVGYEFDLPKFDVEECRQRDLTYAAPLKVILRLIVFDIDEDTGSKD 125

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            IKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+A
Sbjct: 126  IKDIKEQGVYMGDMPLMTTNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFA 185

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+DIEFD+KDII+ RIDRRRK+PVTS LMALGMD  +ILSTFY K+ Y + 
Sbjct: 186  ARVIPYRGSWLDIEFDAKDIIYARIDRRRKIPVTSLLMALGMDGSDILSTFYDKVTYERD 245

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            G+ W  P S  D   G K+ S L+D D+GE V E+GKKLT    KSL EKG+K + ++ D
Sbjct: 246  GEGWRVPYSV-DRFKGMKLISDLIDADSGEVVAEAGKKLTVRTAKSLAEKGLKAVKVSED 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G Y+AEDIVN ETGEIY+EAGD IDEK L+ +       I IL +D +N  AYIRNT
Sbjct: 305  DLLGCYLAEDIVNYETGEIYLEAGDEIDEKVLKILLDVRADQINILDIDHMNIGAYIRNT 364

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFFD ++YDLS VGRVKMN+R++
Sbjct: 365  LKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMD 424

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLR
Sbjct: 425  LDCPDTVRVLRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLR 484

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 485  MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 544

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 545  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 604

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 605  YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHV 664

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+
Sbjct: 665  DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVAR 724

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPL
Sbjct: 725  DSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPL 783

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD V + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTS
Sbjct: 784  VHVGDRVEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTS 843

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITPK
Sbjct: 844  IHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPK 903

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ER
Sbjct: 904  GESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERAMAIER 963

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ AV GPKGF +S  L S ++  YPRSQW
Sbjct: 964  EEIERLAKDRDDEQSILDRNVYARLTDMLTGKVAVEGPKGFSESKKLDSTVMGRYPRSQW 1023

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            WQFAV+DEK+Q  +E+L+ QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+K
Sbjct: 1024 WQFAVEDEKLQNEIEALRKQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKVFVAVK 1083

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1084 RKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHL 1143

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC G+GKKI  L+  Y+  GDI PLR  +E ++   +H E +  YD++S+ ++A Q K
Sbjct: 1144 GWACAGMGKKIGDLLELYQETGDILPLRQRIENLMPDDNHNEPVRQYDNESLYKLALQMK 1203

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYMLKL+H
Sbjct: 1204 KGVSIATPVFDGAHESDINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYMLKLHH 1263

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1264 LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1323

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            V GRT+VYE+IV G+DTFE G PESFNVLVKEM++L L+++L+++R 
Sbjct: 1324 VAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLALNVELDDARE 1370


>gi|36333361|gb|AAP75738.1| RNA polymerase beta subunit [Bosea thiooxidans]
          Length = 1373

 Score = 1739 bits (4505), Expect = 0.0,   Method: Composition-based stats.
 Identities = 886/1365 (64%), Positives = 1097/1365 (80%), Gaps = 5/1365 (0%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            G  RVRKFFGK  E+  +P+LIEVQKASYD FLM++     RP+EGLQ+ FKSVFPI  F
Sbjct: 7    GRRRVRKFFGKLKEVAQMPNLIEVQKASYDQFLMVDEPKGGRPDEGLQSVFKSVFPIGDF 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            SGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+KDIKEQ
Sbjct: 67   SGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSVKDIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +
Sbjct: 127  DVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARIIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEIL+ FY  I Y++    W  P
Sbjct: 187  GSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILNRFYNHINYTKDAKGWRVP 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              A   M G K +  ++D DTGE V+E+GKKL +   + L EKG+KFL    + L   Y+
Sbjct: 247  YDAE-RMKGFKATEDMIDADTGEVVVEAGKKLVARTARQLAEKGLKFLRAQDEDLYTQYI 305

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AED+VN  TGE+Y EAG+ I EK L+++      +IP+L +D +    YIRNTL  DKN 
Sbjct: 306  AEDLVNPATGEVYAEAGEEITEKLLKQLTDDGFDEIPVLDIDHITVGPYIRNTLNVDKNS 365

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             R++AL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKMNMRL+LD  D V
Sbjct: 366  RREEALFDIYRVMRPGEPPTLETAENMFQSLFFDPERYDLSAVGRVKMNMRLDLDAEDTV 425

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLLRMER+IKE
Sbjct: 426  RILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLLRMERAIKE 485

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 486  RMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 545

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++ DG
Sbjct: 546  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIRDG 605

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            KVT++V+YLSAMEE    +AQAN+++D +G  T++L+ CR AGE I+ P +K+DF D SP
Sbjct: 606  KVTDEVIYLSAMEEAKYNVAQANAAVDGEGRLTDDLIVCRRAGEVIVTPVDKVDFQDVSP 665

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA+ SGAAI 
Sbjct: 666  KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVARDSGAAIA 725

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+R GIV+QVDA RIVIR+ +   DP+  GVDIYRL KFQRSNQ+TC+ QRPLV+VGD V
Sbjct: 726  ARRGGIVDQVDATRIVIRASDEM-DPTKPGVDIYRLQKFQRSNQSTCITQRPLVRVGDVV 784

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ DI+ADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SE++VSEDVFTSIHIEEFE
Sbjct: 785  KKGDIVADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSEKIVSEDVFTSIHIEEFE 844

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            VMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKGESPMTP
Sbjct: 845  VMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKITPKGESPMTP 904

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE+IE LA
Sbjct: 905  EEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIEREEIERLA 964

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW FA  +
Sbjct: 965  KDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWWLFATAE 1024

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            + +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR IQ GD
Sbjct: 1025 DSLMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKRKIQPGD 1084

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GL
Sbjct: 1085 KMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGL 1144

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G++I   ++ YK   D   L++  + V       E I+  D++ ++ + +  + GVPV+T
Sbjct: 1145 GRQISQALDAYKKTNDFKALKASFDAVYEDN---EIIASMDENELVEMGQNLRRGVPVAT 1201

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            PVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++
Sbjct: 1202 PVFNGAKEADIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIH 1261

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+V
Sbjct: 1262 ARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKV 1321

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            YESIV G D FE G PESFNVLVKEM++LGL+++L N++ K    
Sbjct: 1322 YESIVRGEDNFEAGIPESFNVLVKEMRSLGLNVELINNKVKPGEL 1366


>gi|319407383|emb|CBI81034.1| DNA-directed RNA polymerase, beta chain [Bartonella sp. 1-1C]
          Length = 1382

 Score = 1739 bits (4505), Expect = 0.0,   Method: Composition-based stats.
 Identities = 933/1372 (68%), Positives = 1128/1372 (82%), Gaps = 6/1372 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQ
Sbjct: 1    MAQTLAMMSQFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPEGGRLDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFDPPKFDV++C  RDLTYA PLK+ LRLIVFDVDE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDPPKFDVEECHQRDLTYAAPLKVILRLIVFDVDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTDNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            K L+A R+IP +G W+DIEFD+KDI++VRIDRRRK+PVTS LMALGMD+ +ILSTFY K+
Sbjct: 181  KFLFAARVIPYRGSWLDIEFDAKDIVYVRIDRRRKIPVTSLLMALGMDASDILSTFYNKV 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y +  + W  P S  D   G K+ S LVD D+GE V E+GKKLT    K L+EKG+K +
Sbjct: 241  SYERTKNGWRIPYSV-DRFRGMKLVSDLVDADSGEVVAEAGKKLTVRAAKLLEEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             I+ D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +       I IL +D +N  A
Sbjct: 300  EISEDDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKTLKILSDVGADQINILDIDHMNVGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T + AE+MF+ LFFD ++YDLS VGRVKM
Sbjct: 360  YIRNTLKVDKNESRQDALFDIYRVMRPGEPPTINTAEAMFHSLFFDPERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRILRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLLRMERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 600  FIESPYRKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME
Sbjct: 660  PRDHIDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA  SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  AIVACDSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD + + DIIADG STDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRIEKGDIIADGSSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV+PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVHPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +++ERE+IE LA+D+DDEQ ILDR++Y+RL +IL G+  + GPKGF K   L S ++ +Y
Sbjct: 959  MAIEREEIERLAKDRDDEQSILDRSVYARLADILTGKVTIEGPKGFPKGKTLDSTVMEKY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PR QWWQFAV+DEK+Q  +E+L  QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRYQWWQFAVEDEKLQNEIEALHKQYDESKKALQRRFMDKVEKVQRGDEMPPGVMKIVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  LI  Y+  GDI PLR  +E +I      E +  YD++S++++
Sbjct: 1139 LETHLGWACAGMGKKIGDLIKLYQETGDILPLRQRIENLIPDDDRNEPVRHYDNESLIKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q K GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYM
Sbjct: 1199 ALQMKQGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +KSDDV GRT+VYE++V G+DTFE G PESFNVLVKEM++LGL+++L+++R 
Sbjct: 1319 VKSDDVAGRTKVYEAVVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDARE 1370


>gi|49474307|ref|YP_032349.1| DNA-directed RNA polymerase subunit beta [Bartonella quintana str.
            Toulouse]
 gi|51338825|sp|Q9KJM5|RPOB_BARQU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|49239811|emb|CAF26202.1| DNA-directed RNA polymerase beta chain [Bartonella quintana str.
            Toulouse]
          Length = 1383

 Score = 1737 bits (4498), Expect = 0.0,   Method: Composition-based stats.
 Identities = 932/1368 (68%), Positives = 1131/1368 (82%), Gaps = 2/1368 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 5    LAMTSQFNGRKRVRKFFGKIPEVTEMPNLIEVQKASYDQFLMIEEPKGGRPDEGLQAVFK 64

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFDVDE TG+K
Sbjct: 65   SVFPISDFSGTAMLEFVGYEFDLPKFDVEECRQRDLTYAAPLKVILRLIVFDVDEDTGSK 124

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGK L+
Sbjct: 125  DIKDIKEQGVYMGDMPLMTTNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKFLF 184

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDII+ RIDRRRK+P+TS LMALGMD+ +ILSTFY K+ Y +
Sbjct: 185  AARVIPYRGSWLDIEFDAKDIIYARIDRRRKIPITSLLMALGMDASDILSTFYNKVTYER 244

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P S      G K+ S LVD D+GE V E+GKKLT    K+L EKG+K + IT 
Sbjct: 245  DGDGWRIPYSV-GRFKGVKLISDLVDADSGEVVAEAGKKLTVRAAKALAEKGLKAVKITE 303

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +F      I IL +D +N  AYIRN
Sbjct: 304  DDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKALKILFDVSADQINILDIDHMNIGAYIRN 363

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ ++DAL DIYRVMRPG+  T   A +MF+ LFFD ++YDLS VGRVKMN+R+
Sbjct: 364  TLKVDKNESQQDALFDIYRVMRPGEPPTMDTAAAMFHSLFFDPERYDLSAVGRVKMNLRM 423

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 424  DLDCPDTVRILRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLL 483

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 484  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 543

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 544  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 603

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FT+E V CR AGE ++ PR+ 
Sbjct: 604  PYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTDEFVVCRHAGEVLMAPRDH 663

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA
Sbjct: 664  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVA 723

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 724  RDSGAAVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 782

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + +IIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 783  LVHVGDRVEKGNIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 842

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITP
Sbjct: 843  SIHIEEFEVAARDTKLGPEEITRDIPNVAEESLRNLDEAGIIYIGAEVQPGDILVGKITP 902

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 903  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGAFGTVVEVRVFNRHGVEKDERAMAIE 962

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ AV GPKGF K   L + ++  YPRSQ
Sbjct: 963  REEIERLAKDRDDEQSILDRNVYARLTDMLTGKIAVEGPKGFSKGKKLDNTIMGHYPRSQ 1022

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQF V+DEK+Q  +E+L+ QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1023 WWQFTVEDEKLQSEIEALRRQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1082

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1083 KRKIQPGDKMAGRHGNKGVVSRILPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1142

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+  GDI PLR  +E ++    H E +  YD++S+ ++A Q 
Sbjct: 1143 LGWACAGMGKKIGDLVDLYQETGDIFPLRQRIENLMPDNDHNEPVRQYDNESLYKLALQM 1202

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  ADLD SGQ +LYDG TGEPFDRPVTVGYIYMLKL+
Sbjct: 1203 RKGVSIATPVFDGAHEADINMMLEDADLDSSGQVVLYDGRTGEPFDRPVTVGYIYMLKLH 1262

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1263 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1322

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++L L+++L+++R 
Sbjct: 1323 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLALNVELDDARE 1370


>gi|8895200|gb|AAF80850.1|AF165994_1 RNA polymerase beta subunit [Bartonella quintana]
          Length = 1383

 Score = 1736 bits (4497), Expect = 0.0,   Method: Composition-based stats.
 Identities = 932/1368 (68%), Positives = 1132/1368 (82%), Gaps = 2/1368 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 5    LAMTSQFNGRKRVRKFFGKIPEVTEMPNLIEVQKASYDQFLMIEEPKGGRPDEGLQAVFK 64

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFDVDE TG+K
Sbjct: 65   SVFPISDFSGTAMLEFVGYEFDLPKFDVEECRQRDLTYAAPLKVILRLIVFDVDEDTGSK 124

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGK L+
Sbjct: 125  DIKDIKEQGVYMGDMPLMTTNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKFLF 184

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP++G W+DIEFD+KDII+ RIDRRRK+P+TS LMALGMD+ +ILSTFY K+ Y +
Sbjct: 185  AARVIPNRGSWLDIEFDAKDIIYARIDRRRKIPITSLLMALGMDASDILSTFYNKVTYER 244

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             GD W  P S      G K+ S LVD D+GE V E+GKKLT    K+L EKG+K + IT 
Sbjct: 245  DGDGWRIPYSV-GRFKGVKLISDLVDADSGEVVAEAGKKLTVRAAKALAEKGLKAVKITE 303

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +F      I IL +D +N  AYIRN
Sbjct: 304  DDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKALKILFDVSADQINILDIDHMNIGAYIRN 363

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ ++DAL DIYRVMRPG+  T   A +MF+ LFFD ++YDLS VGRVKMN+R+
Sbjct: 364  TLKVDKNESQQDALFDIYRVMRPGEPPTMDTAAAMFHSLFFDPERYDLSAVGRVKMNLRM 423

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 424  DLDCPDTVRILRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLL 483

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 484  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 543

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 544  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 603

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FT+E V CR AGE ++ PR+ 
Sbjct: 604  PYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTDEFVVCRHAGEVLMAPRDH 663

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA
Sbjct: 664  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVA 723

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRP
Sbjct: 724  RDSGAAVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRP 782

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV VGD V + +IIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFT
Sbjct: 783  LVHVGDRVEKGNIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFT 842

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITP
Sbjct: 843  SIHIEEFEVAARDTKLGPEEITRDIPNVAEESLRNLDEAGIIYIGAEVQPGDILVGKITP 902

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++E
Sbjct: 903  KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGAFGTVVEVRVFNRHGVEKDERAMAIE 962

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y+RL ++L G+ AV GPKGF K   L + ++  YPRSQ
Sbjct: 963  REEIERLAKDRDDEQSILDRNVYARLTDMLTGKIAVEGPKGFSKGKKLDNTIMGHYPRSQ 1022

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQF V+DEK+Q  +E+L+ QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1023 WWQFTVEDEKLQSEIEALRRQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKVFVAV 1082

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1083 KRKIQPGDKMAGRHGNKGVVSRILPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1142

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+GKKI  L++ Y+  GDI PLR  +E ++    H E +  YD++S+ ++A Q 
Sbjct: 1143 LGWACAGMGKKIGDLVDLYQETGDIFPLRQRIENLMPDNDHNEPVRQYDNESLYKLALQM 1202

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GV ++TPVFDGA E  IN ML  ADLD SGQ +LYDG TGEPFDRPVTVGYIYMLKL+
Sbjct: 1203 RKGVSIATPVFDGAHEADINMMLEDADLDSSGQVVLYDGRTGEPFDRPVTVGYIYMLKLH 1262

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1263 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1322

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++L L+++L+++R 
Sbjct: 1323 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLALNVELDDARE 1370


>gi|319405856|emb|CBI79488.1| DNA-directed RNA polymerase, beta chain [Bartonella sp. AR 15-3]
          Length = 1382

 Score = 1736 bits (4496), Expect = 0.0,   Method: Composition-based stats.
 Identities = 932/1372 (67%), Positives = 1127/1372 (82%), Gaps = 6/1372 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQ
Sbjct: 1    MAQTLAMMSQFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPEGGRLDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFDPPKFDV++C  RDLTYA PLK+ LRLIVFDVDE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDPPKFDVEECHQRDLTYAAPLKVILRLIVFDVDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTHNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            K L+A R+IP +G W+DIEFD+KDI++VRIDRRRK+PVTS LMALGMD+ +ILSTFY KI
Sbjct: 181  KFLFAARVIPYRGSWLDIEFDAKDIVYVRIDRRRKIPVTSLLMALGMDASDILSTFYNKI 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y +  + W    S  D   G K+ S LVD D+GE V E+GKKLT    K L+EKG+K +
Sbjct: 241  SYERTKNGWRISYSV-DRFKGMKLVSDLVDADSGEVVAEAGKKLTVRAAKLLEEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             I+ D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +       I IL +D +N  A
Sbjct: 300  EISEDDLLGAYLAEDIVNYQTGEIYLEAGDEIDEKTLKILSDVGADQINILDIDHMNIGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T + AE+MF+ LFFD ++YDLS VGRVKM
Sbjct: 360  YIRNTLKIDKNESRQDALFDIYRVMRPGEPPTINTAEAMFHSLFFDPERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRVLRQEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLLRMERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 600  FIESPYRKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDTEGRFTEEFVVCRHAGEVLMA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME
Sbjct: 660  PRDHIDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA  SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  AIVACDSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD + + DIIADG STDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRIEKGDIIADGSSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV+PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVHPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +++ERE+IE LA+D+DDEQ ILDR++Y+RL +IL G+  + GPKGF K   L S ++ +Y
Sbjct: 959  MAIEREEIERLAKDRDDEQSILDRSVYARLADILTGKVVIEGPKGFPKGKTLDSTVMEQY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PR QWWQFAV+DEK+Q  +E+L  QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRYQWWQFAVEDEKLQSEIEALHKQYDESKKALQRRFMDKVEKVQRGDEMPPGVMKIVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  LI  Y+  GDISPLR  +E +I      E +  YD++S+ ++
Sbjct: 1139 LETHLGWACAGMGKKIGDLIELYQKTGDISPLRQRIENIIPDDDRNEPVRHYDNESIFKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q ++GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGE FDRPVTVGYIYM
Sbjct: 1199 ALQMRNGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEAFDRPVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +KSDDV GRT+VYE++V G+DTFE G PESFNVLVKEM++LGL+++L+++R 
Sbjct: 1319 VKSDDVAGRTKVYEAVVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDARE 1370


>gi|144900874|emb|CAM77738.1| DNA-directed RNA polymerase beta chain [Magnetospirillum
            gryphiswaldense MSR-1]
          Length = 1393

 Score = 1736 bits (4496), Expect = 0.0,   Method: Composition-based stats.
 Identities = 851/1394 (61%), Positives = 1069/1394 (76%), Gaps = 31/1394 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  RVRK FG+ P +  +P+LIEVQK+SYDHFL M   P++R N GLQ  FKSV
Sbjct: 1    MAKSYTGRKRVRKSFGRIPTVAPMPNLIEVQKSSYDHFLQMETLPEKRTNVGLQEVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS    LEFV YE + PK+DV++C  R +T+A PLK+TLRL+V+D+DE TGA+SI
Sbjct: 61   FPIKDFSERGTLEFVKYELEQPKYDVEECQQRGMTFAAPLKVTLRLVVWDIDEDTGARSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A 
Sbjct: 121  RDIKEQDVYMGDMPLMTANGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--------------------- 221
            R+IP +G W+D EFD+KD+++VRIDRRRK+PVT+ L AL                     
Sbjct: 181  RVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPVTTLLYALDNNATQDLRASRKADSRPVDL 240

Query: 222  ----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
                GM SE+IL+ FY   VY++    W     A + M G K+   L+D  TGE+V E+G
Sbjct: 241  TELKGMTSEDILNYFYETTVYTRGPKGWKTAF-APERMKGIKLVYDLIDAKTGEKVAEAG 299

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             K+T  L K L+E+GV+ + +  + L G Y AED++N +TGEIYIEAG  +    L ++ 
Sbjct: 300  AKMTPRLGKKLREQGVEDILVLPEDLVGQYAAEDLINEKTGEIYIEAGHELTAAVLADLE 359

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
               + ++P L +D +N   YIRNTL  DKN  R++AL+DIYRVMRPG+  T   AE++F 
Sbjct: 360  KLGVTELPCLAIDHINVGPYIRNTLSVDKNSSREEALIDIYRVMRPGEPPTLETAEALFQ 419

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLN---LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             LFFD ++YDLS VGRVKMN RLN    D PD VR +R++DI+A+IKILV+L++GKG ID
Sbjct: 420  GLFFDEERYDLSAVGRVKMNSRLNFTEKDVPDTVRVLRRDDILAVIKILVELKDGKGEID 479

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID+LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+SSVDIDSVMP DLINAKP  +AV 
Sbjct: 480  DIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVDIDSVMPHDLINAKPAAAAVR 539

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET
Sbjct: 540  EFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 599

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL ++ARVN YGFIE PYRKV DGKVT++V Y+SA EE    IAQANS+L
Sbjct: 600  PEGPNIGLINSLATYARVNQYGFIEAPYRKVIDGKVTDEVQYMSANEEGRYTIAQANSTL 659

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            D +G F  +LV CR AGE ++VP  +I  ID SPKQ+VS+AA+LIPFLENDD+NR LMG 
Sbjct: 660  DAEGRFVHDLVSCRQAGEFVMVPPGEITMIDVSPKQLVSVAAALIPFLENDDANRALMGS 719

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL++AEAP VGTGME  VA+ SGAAI AKR GIV+QVDA R+VIR+ E     
Sbjct: 720  NMQRQAVPLIRAEAPLVGTGMEQAVARDSGAAITAKRTGIVDQVDATRVVIRATEDMA-A 778

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            + SGVDIY L+KFQRSNQNTC+ Q+PLVKVGD +R+ DIIADGPST LG+LALGRN+LVA
Sbjct: 779  TESGVDIYNLLKFQRSNQNTCITQKPLVKVGDIIRKGDIIADGPSTQLGELALGRNVLVA 838

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            FMPW+GYNFEDS+LISER+V +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE LK
Sbjct: 839  FMPWNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALK 898

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+DE GI+ +GAEV PGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G
Sbjct: 899  NLDEAGIVYIGAEVKPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPG 958

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V+GT+V+VR+F+R G++K+ER++++ER +IE LA+D+DDE+ IL+R+  +RL ++L GQ 
Sbjct: 959  VAGTIVEVRVFSRRGVEKDERALAIERSEIERLAKDRDDERGILERSFMARLRQLLIGQK 1018

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             VSGPKG K +  L+ ++++E   S W   AV+D+ V  +VE LK  ++ +   L+DRF+
Sbjct: 1019 VVSGPKGVKANAALTEEMLAELHLSAWRNIAVEDDAVMSDVEQLKRAFDMAVERLQDRFE 1078

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            NK+EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG++SRI+P EDMP+L+D
Sbjct: 1079 NKVEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRIMPLEDMPYLED 1138

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK-ANGDISPLRSFLE 1173
            G  VDIVLNPLGVPSRMNVGQI ETHLGWA  GLG++I  ++  Y+     +  LR  L+
Sbjct: 1139 GQQVDIVLNPLGVPSRMNVGQILETHLGWASAGLGQQIGRVLEGYRHNTATVEDLRGTLK 1198

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   ++++I+D  DD VL +    + G+P +TPVFDGA E  I  ML  A    SGQ
Sbjct: 1199 NFYGDDIYSDEIADLKDDEVLELGNNLRPGIPFATPVFDGARESDICDMLDKAGRHRSGQ 1258

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L+DG TG+PFDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 1259 VTLFDGRTGDPFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQR 1318

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D FE G PESFNVLVKE
Sbjct: 1319 FGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNVLVKE 1378

Query: 1354 MQALGLSIDLENSR 1367
            +++LGL+++L    
Sbjct: 1379 LRSLGLNVELTQRD 1392


>gi|197104684|ref|YP_002130061.1| DNA-directed RNA polymerase, beta subunit [Phenylobacterium zucineum
            HLK1]
 gi|226699426|sp|B4R8K5|RPOB_PHEZH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|196478104|gb|ACG77632.1| DNA-directed RNA polymerase, beta subunit [Phenylobacterium zucineum
            HLK1]
          Length = 1356

 Score = 1735 bits (4493), Expect = 0.0,   Method: Composition-based stats.
 Identities = 854/1364 (62%), Positives = 1071/1364 (78%), Gaps = 8/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG+ PE + +P+LIEVQ++SY+ FL   +   ER +EG++A FKSV
Sbjct: 1    MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQREVRAGERRDEGIEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ DE TGA+S+
Sbjct: 61   FPIKDFNERAVLEYVSYEFEEPKYDVEECVQRDMTYAAPLKVKLRLIVFETDEETGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT+ GTF++ G QR++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTEKGTFIVNGTQRVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDRRRK+P T+FLMALGMD EEILSTFY  + Y ++G
Sbjct: 181  RVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLMALGMDGEEILSTFYETVPYEKKG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P        G K    L+D DTGE++  +G+K+++   K   + G+K L +  + 
Sbjct: 241  DGWATPYKPE-RWRGVKPEFPLIDADTGEEIAPAGQKISARNAKKFADNGLKTLLLAPEA 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A+D+VN ETGEIY EAGD +D   L  +       + +L +D V   AYIRNTL
Sbjct: 300  LTGRYLAKDLVNFETGEIYAEAGDELDPTLLAALEEQGFTTLDVLDIDEVTVGAYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFFDS++YDLS+VGRVKMNMRL L
Sbjct: 360  RVDKNTAREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDSERYDLSSVGRVKMNMRLEL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D PDDVR IRKED+IA++  LV LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 420  DCPDDVRVIRKEDVIAVLLTLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + A VN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHAVVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ DGK T++VVY+SAMEE    IAQAN  L E+G   E+LV  R  GE  L+P+  +D
Sbjct: 600  RRIRDGKTTDEVVYMSAMEEAKHVIAQANIKL-ENGEIVEDLVPGRINGEPSLLPKADVD 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLENDD+NR LMG NMQ+QAVPL++++AP VGTGMES+VA  
Sbjct: 659  LMDVSPKQVVSVAASLIPFLENDDANRALMGSNMQKQAVPLIQSDAPLVGTGMESIVAVD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+R G+VEQ+D  RIV+R+ E   DPS  GVDIYRL KFQRSN +TC+NQRPLV
Sbjct: 719  SGAVVVARRTGVVEQIDGTRIVVRATEE-TDPSKPGVDIYRLQKFQRSNTSTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD++   D+IADGPST+LG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DVFTSI
Sbjct: 778  RVGDKINAGDVIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 838  HIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGT+V+VR+FNRHG+DK+ER++++ER 
Sbjct: 898  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTIVEVRVFNRHGVDKDERALAIERA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+ L +D+DDE  IL+RN+  RL ++L G+ AVSGPKG  +   ++++ + E     WW
Sbjct: 958  EIDRLGKDRDDEFAILNRNMQGRLRQLLVGKTAVSGPKGLGRGE-ITAEKLEEIAPGLWW 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A+ DEK    +E+L+ Q++ ++  L+ RF++K++K+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1017 QIALDDEKAMGELEALRKQFDDARKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+ILP EDMP+L+DGT VDIVLNPLGVPSRMNVGQIFETHLG
Sbjct: 1077 KLQPGDKMAGRHGNKGVISKILPIEDMPYLEDGTSVDIVLNPLGVPSRMNVGQIFETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGK+++ L+ D++  G    L   L  V G            ++ ++ +A     
Sbjct: 1137 WAAAGLGKQVQRLLEDWQHGGQKQALIEHLRDVYGPDEELPD----TEEELVELARNLSK 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P +TPVFDGA  + I ++L  A LD SGQS LYDG +GE F RPVTVGYIYMLKL+H+
Sbjct: 1193 GIPFATPVFDGAHIDDIENLLEKAGLDRSGQSYLYDGQSGERFKRPVTVGYIYMLKLHHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT+VYESIV G+DTFE G PESFNVLVKEM++LGL+++LENS
Sbjct: 1313 AGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS 1356


>gi|209964030|ref|YP_002296945.1| DNA-directed RNA polymerase subunit beta [Rhodospirillum centenum SW]
 gi|226699437|sp|B6IRP6|RPOB_RHOCS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|209957496|gb|ACI98132.1| DNA-directed RNA polymerase, beta subunit [Rhodospirillum centenum
            SW]
          Length = 1397

 Score = 1733 bits (4489), Expect = 0.0,   Method: Composition-based stats.
 Identities = 834/1394 (59%), Positives = 1063/1394 (76%), Gaps = 35/1394 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG+ PE+  +P+LIEVQ++SYDHFL M++ P++R N GLQ  F+SV
Sbjct: 1    MAKSFTGRKRIRKSFGRIPEVTRMPNLIEVQRSSYDHFLQMDVPPEKRANVGLQEVFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS  A+L+FV YE + PK+DV++C  R +T+A PLK+TLRL VFDVDE TG +SI
Sbjct: 61   FPIKDFSERAVLDFVRYELEQPKYDVEECQQRGMTFAAPLKVTLRLTVFDVDEDTGLRSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A 
Sbjct: 121  RDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--------------------- 221
            R+IP +G W+D EFD+KDI++VRIDRRRK+P T+ L AL                     
Sbjct: 181  RVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTLLYALDGADSAELRAERRALGKDLLP 240

Query: 222  ----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
                GM  EEIL  FY  I Y +  D W     A   M G K+ + LVD  TGE +    
Sbjct: 241  YEAQGMAKEEILGYFYETITYQRAADGWKTGFDAE-RMKGQKLLTDLVDARTGEVLASRD 299

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             KLT  L++ L+++G++ + +  + + G Y+A DI++ +TGE+  EAGD +   +LE + 
Sbjct: 300  TKLTPRLIRKLQDQGLQEIKVAIEDIIGRYLAIDIIDEKTGEVIYEAGDELSATALERLE 359

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
               + ++P+L VD +N  AYIRNT+  D+N  R+DAL+DIYRVMRPG+  T   AE++F 
Sbjct: 360  KMGVEELPVLNVDHLNIGAYIRNTMAADRNASREDALIDIYRVMRPGEPPTLESAEALFA 419

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             LFFD ++YDLS VGRVKMN RL  +T D +R +RKEDI+ I+KILV+L++G+G IDDID
Sbjct: 420  GLFFDQERYDLSAVGRVKMNARLGFETDDQMRVLRKEDILKILKILVELKDGRGEIDDID 479

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            +LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+SSV+ID+VMP DLINAKP  +AV EFF
Sbjct: 480  HLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFF 539

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG
Sbjct: 540  GSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEG 599

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL ++ARVN YGFIE+PYRKV DG+VT++VVYLSAMEE    +A+AN+ LD  
Sbjct: 600  PNIGLINSLATYARVNQYGFIESPYRKVIDGRVTDEVVYLSAMEEGRYTVAEANAPLDAG 659

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              F + LV CR  GE +LV  + ID ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQ
Sbjct: 660  NRFADPLVSCRKGGEYLLVRPDMIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQ 719

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVPL+KA++P VGTGME+ VA+ SG  IV +RAGIV+QVDA RIVIR+ E   DP+  
Sbjct: 720  RQAVPLIKADSPLVGTGMEATVARDSGVTIVTRRAGIVDQVDATRIVIRATEDT-DPAAP 778

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+KFQRSNQNTC+NQ+PLVKVGD V++ DIIADGPSTDLG+LALGRN+LVAFMP
Sbjct: 779  GVDIYNLLKFQRSNQNTCINQKPLVKVGDRVQKGDIIADGPSTDLGELALGRNVLVAFMP 838

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYNFEDS+LISER+V +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE LKN+D
Sbjct: 839  WNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALKNLD 898

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV PGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+G
Sbjct: 899  EAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAG 958

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TVV+VR+F+R G+DK+ER++++ER +IE LA+D+DDE+ IL+R+ Y+RL E+L GQ +VS
Sbjct: 959  TVVEVRVFSRRGVDKDERALAIERAEIEKLAKDRDDEKAILERSFYTRLKELLLGQTSVS 1018

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            GPKG K    ++ + ++   R QW   +V++++V   +E     ++ S   L++RF+NK+
Sbjct: 1019 GPKGMKGGETITDETLAGLTRGQWRHISVENDQVMEIIEQTGKVFDDSVQRLQERFENKV 1078

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG++SRI P EDMP+L+DG  
Sbjct: 1079 EKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRITPIEDMPYLEDGRN 1138

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK--------ANGDISPLR 1169
            VDIVLNPLGVPSRMNVGQI ETHLGWA  G+G++I  +++  +               L+
Sbjct: 1139 VDIVLNPLGVPSRMNVGQILETHLGWAAAGIGRQIGEMLDRMRAATVEAADKARTAEDLK 1198

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L  + G   +   I+   +  ++ +A   + G+P +TPVFDGA E+ I  ML  A LD
Sbjct: 1199 ERLRSIYGEAVYESDIAPMSEAQLMELAGNLRRGIPFATPVFDGAREDDICRMLEAAGLD 1258

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
             SGQS L DG TGEPFDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  
Sbjct: 1259 RSGQSTLIDGRTGEPFDRRVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1318

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D FE G PESFNV
Sbjct: 1319 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNV 1378

Query: 1350 LVKEMQALGLSIDL 1363
            LVKE+++LGL+++L
Sbjct: 1379 LVKELRSLGLNVEL 1392


>gi|319899056|ref|YP_004159149.1| DNA-directed RNA polymerase, beta chain [Bartonella clarridgeiae 73]
 gi|319403020|emb|CBI76575.1| DNA-directed RNA polymerase, beta chain [Bartonella clarridgeiae 73]
          Length = 1382

 Score = 1732 bits (4486), Expect = 0.0,   Method: Composition-based stats.
 Identities = 928/1370 (67%), Positives = 1124/1370 (82%), Gaps = 6/1370 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      R +EGLQ
Sbjct: 1    MAQTLAMMSQFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIEEPEGGRLDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFDVDE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDSPKFDVEECRQRDLTYAAPLKVILRLIVFDVDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTHNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            K L+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD+ +ILSTFY K+
Sbjct: 181  KFLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDASDILSTFYNKV 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y    + W  P S  D   G K+ S LVD D+GE V E+GKKLT    + L+EKG+K +
Sbjct: 241  TYECAKNGWRIPYSV-DRFKGMKLISDLVDADSGEVVAEAGKKLTVRTARLLEEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             I+ D L G Y+AEDIVN +TGEIY+EAGD IDEK+L+ +       I IL +D +N  A
Sbjct: 300  EISEDDLLGSYLAEDIVNYQTGEIYLEAGDEIDEKALKILSDVGADQINILDIDHMNVGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T + AE+MF+ LFFD ++YDLS VGRVKM
Sbjct: 360  YIRNTLKMDKNESRQDALFDIYRVMRPGEPPTINTAEAMFHSLFFDPERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDIIA++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRILRQEDIIAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLLRMERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DG+VT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 600  FIESPYRKIVDGRVTKEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME
Sbjct: 660  PRDHIDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA  SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  AIVACDSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD + + DIIADG STDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRIEKGDIIADGSSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV+PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVHPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +++ERE+IE LA+D+DDEQ ILDR++Y+RL +IL G+ A+ GPKGF K   L S ++ +Y
Sbjct: 959  MAIEREEIERLAKDRDDEQSILDRSVYARLADILTGKIAIEGPKGFSKGKTLDSTIMEQY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PR QWWQF ++DEK+Q  +E+L  QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRYQWWQFVIEDEKIQSEIEALHKQYDESKKALQCRFMDKVEKVQRGDEMPPGVMKIVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  LI  Y+ +GDI PLR  +E +I      E +  YD++S+ ++
Sbjct: 1139 LETHLGWACAGMGKKIGDLIELYQESGDILPLRQRIENLIPDDERNEPVRHYDNESIFKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q K GV ++TPVFDGA E  IN ML  A LD SGQ  LYDG TGEPFDRPVTVGYIYM
Sbjct: 1199 ALQMKKGVSIATPVFDGAHEADINMMLEDAGLDSSGQVTLYDGRTGEPFDRPVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRT+VYE++V G+DTFE G PESFNVLVKEM++LGL+++L+++
Sbjct: 1319 VKSDDVAGRTKVYEAVVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDDA 1368


>gi|36333373|gb|AAP75744.1| RNA polymerase beta subunit [Bosea sp. 7F]
          Length = 1373

 Score = 1731 bits (4482), Expect = 0.0,   Method: Composition-based stats.
 Identities = 880/1365 (64%), Positives = 1100/1365 (80%), Gaps = 5/1365 (0%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            G  RVRKFFGK  E+ ++P+LIEVQKASYD FLM+      R +EGLQ+ FKSVFPI  F
Sbjct: 7    GRRRVRKFFGKLKEVAEMPNLIEVQKASYDQFLMVEEPKGGRGDEGLQSVFKSVFPIGDF 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            +GA++LEFV Y F+ PK+DVD+C  R LT++ PLK+TLRLIVFD+D  T AKS+KDIKEQ
Sbjct: 67   AGASLLEFVKYTFEAPKYDVDECRQRGLTFSAPLKVTLRLIVFDIDPDTQAKSVKDIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +
Sbjct: 127  DVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFASRIIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEIL+ FY +++Y++  D W  P
Sbjct: 187  GSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILNRFYDRVLYTRDKDGWRVP 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              A   M G K +  L++ DTGE V+E+GKKL +   + L EKG+KFL  T + L   Y+
Sbjct: 247  YDAE-RMKGFKANEDLINADTGEVVLEAGKKLVARTARQLAEKGLKFLRATDEDLYTQYI 305

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AED+VN  TGE++ EAG+ I+EK L+ +      +IP+L +D +N   YIRNTL  DKN 
Sbjct: 306  AEDLVNPATGEVFAEAGEEINEKLLKLLVDEGFDEIPVLDIDHINVGPYIRNTLNVDKNS 365

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             R++AL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKMNMRL+LD  D V
Sbjct: 366  RREEALFDIYRVMRPGEPPTLETAENMFQSLFFDPERYDLSAVGRVKMNMRLDLDAEDTV 425

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLGLLRMER+IKE
Sbjct: 426  RVLRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLGLLRMERAIKE 485

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 486  RMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 545

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++ DG
Sbjct: 546  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIRDG 605

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            K T++++YLSAMEE    +AQAN+++D +G  T++L+ CR AGE I+ P +K+DF D SP
Sbjct: 606  KQTDEIIYLSAMEEAKYNVAQANAAVDAEGRLTDDLIVCRRAGEVIVTPVDKVDFQDVSP 665

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+VVA+ SGAAI 
Sbjct: 666  KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAVVARDSGAAIA 725

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+RAG+V+QVDA RIVIR+ +   DP+  GVDIYRL KFQRSNQ+TC+ QRPLV+ GD +
Sbjct: 726  ARRAGVVDQVDATRIVIRATDE-KDPTKPGVDIYRLQKFQRSNQSTCITQRPLVRAGDVI 784

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ DI+ADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SE++VSEDVFTSIHIEEFE
Sbjct: 785  KKGDIVADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSEKIVSEDVFTSIHIEEFE 844

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            VMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKITPKGESPMTP
Sbjct: 845  VMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKITPKGESPMTP 904

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE+IE LA
Sbjct: 905  EEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIEREEIERLA 964

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D+DDEQ ILDRN ++RL EIL G+  V+GPKGFKK TV+S +++SE+PRSQWW FA  D
Sbjct: 965  KDRDDEQAILDRNTFARLAEILTGKTGVAGPKGFKKDTVISREVMSEFPRSQWWLFATAD 1024

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            + +   +E+++ QY+ SK  LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ GD
Sbjct: 1025 DALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDEMPPGVMKMVKVFVAVKRKIQPGD 1084

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GL
Sbjct: 1085 KMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGL 1144

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK+I   ++ Y+ + D + L++  + + G       +    +  ++ + +  + GVP++T
Sbjct: 1145 GKQISQALDAYRKSSDFTALKNSFDAIYGDND---IVGSMSETELVEMGQNLRRGVPIAT 1201

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            PVF+GA E  I ++L  A L++SGQ  LYDG TGEPFDR VTVGYIYMLKL+H+V DK++
Sbjct: 1202 PVFNGAKEADIENLLEQAGLNKSGQVTLYDGRTGEPFDRKVTVGYIYMLKLHHLVDDKIH 1261

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+V
Sbjct: 1262 ARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKV 1321

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            YESIV G D FE G PESFNVLVKEM++LGL+++L +++ K    
Sbjct: 1322 YESIVRGEDNFEAGIPESFNVLVKEMRSLGLNVELVSNKPKPGEL 1366


>gi|300022534|ref|YP_003755145.1| DNA-directed RNA polymerase subunit beta [Hyphomicrobium
            denitrificans ATCC 51888]
 gi|299524355|gb|ADJ22824.1| DNA-directed RNA polymerase, beta subunit [Hyphomicrobium
            denitrificans ATCC 51888]
          Length = 1383

 Score = 1730 bits (4480), Expect = 0.0,   Method: Composition-based stats.
 Identities = 870/1386 (62%), Positives = 1093/1386 (78%), Gaps = 9/1386 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-GLQAAF 59
            MA+ +      R+RK FG   E+ ++P+LIEVQKASYD FLM+   P  R ++ GLQ+ F
Sbjct: 1    MAQTL--TSRKRLRKQFGSIGEVAEMPNLIEVQKASYDDFLMVKEPPGGRSDDFGLQSVF 58

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            K VFPI+ F+G + LEFVSYEF+PPKFD D+C+ RD+TYA PLK+ LRLIVFD++E TG+
Sbjct: 59   KGVFPISDFAGKSTLEFVSYEFEPPKFDTDECMQRDMTYAAPLKVKLRLIVFDINEETGS 118

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            KSIKD+KEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGKLL
Sbjct: 119  KSIKDVKEQDVYMGDMPLMTLNGTFIINGTERVIVSQMHRSPGVFFDHDRGKTHSSGKLL 178

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A RIIP +G W+D EFD+KDI++VRIDRRRK+PVT+ L ALG+D E+IL+ FY  I   
Sbjct: 179  FAARIIPYRGSWLDFEFDAKDIVYVRIDRRRKLPVTTMLYALGLDDEQILAHFYKHIPIK 238

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            +    W  P        G    S + D  TGE +   G+K+T+   + L E GVK + I+
Sbjct: 239  ESKRGWKMPYIPEK-FRGITPQSDIADAKTGEVIARQGEKITARRARELAESGVKEILIS 297

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            ++ L G ++AEDIV+ ETG+I+ EAGD +D   L E+   ++++  IL +D VN  A+IR
Sbjct: 298  AEDLAGRFIAEDIVDLETGKIFAEAGDELDANLLAELKEQKVKEFHILDIDYVNVGAFIR 357

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN ++++AL+DIYRVMRPG+  T   A ++F+ LFFD +++DLS VGRVKMNMR
Sbjct: 358  NTLNIDKNANQQEALMDIYRVMRPGEPPTIEAATALFHGLFFDPERFDLSAVGRVKMNMR 417

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L LD PD +R +R+EDI+A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYR+GL
Sbjct: 418  LELDAPDTMRVLRREDILAVVKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRVGL 477

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 478  LRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 537

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE
Sbjct: 538  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIE 597

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYRKV +G+VTN+VVYLSAMEE   ++AQAN+ +D  G  TE+LV  R  G+  LVP +
Sbjct: 598  SPYRKVINGRVTNEVVYLSAMEEMRHHVAQANAEIDAKGKMTEDLVTIRHNGDVTLVPTD 657

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            K+D+ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KAEAP VGTGME  V
Sbjct: 658  KVDYIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIKAEAPLVGTGMEERV 717

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SGAAI A+R GIV+QVDA RIVIR+ E   DPS  GVDIYRL KFQRSNQNTC+NQR
Sbjct: 718  AHDSGAAIAARRTGIVDQVDATRIVIRATEEQ-DPSKPGVDIYRLRKFQRSNQNTCINQR 776

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PL+ VGD V   DIIADGPST+LG+LALG+N+LVAFMPW GYNFEDS+L++ER+VSEDVF
Sbjct: 777  PLINVGDHVHAGDIIADGPSTELGELALGKNVLVAFMPWMGYNFEDSILMNERVVSEDVF 836

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKIT
Sbjct: 837  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKIT 896

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+V+VR+FNRHG++K+ER++++
Sbjct: 897  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFNRHGVEKDERAMAI 956

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDE  ILDRN+Y+RL + L G+    GPKG +K T + + ++ + PRS
Sbjct: 957  EREEIERLAKDRDDELQILDRNVYARLKDALMGKEVAKGPKGARKGTTIDTAILDDIPRS 1016

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWW+  + +EK Q  VE+++ QYE +K  L  RF +K++K+Q GD++PPGV+++VKVFVA
Sbjct: 1017 QWWEIGLANEKAQAEVEAIQKQYEDAKKGLGLRFADKVDKLQRGDELPPGVMKMVKVFVA 1076

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VS I+P EDMPFL+DGTPVD+VLNPLGVPSRMNVGQI ET
Sbjct: 1077 VKRKIQPGDKMAGRHGNKGVVSMIVPSEDMPFLEDGTPVDVVLNPLGVPSRMNVGQILET 1136

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            H+GWAC GLG+ I   ++ +  +G    LR  + KV G            DD ++ +AE 
Sbjct: 1137 HMGWACRGLGRLIDDALHQFHESGQAKALRDQMAKVYGDEIKP----TMKDDELVGIAEN 1192

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             ++GVP++TPVFDGA E+ I  ML++A  D SGQ  L+DG +GEPFDR VTVGY Y+LKL
Sbjct: 1193 LRNGVPIATPVFDGAREKDIVEMLQLAGFDTSGQVTLFDGRSGEPFDRKVTVGYKYVLKL 1252

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1253 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1312

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV GRT+VYE+IV G+D FE G PESFNVLVKEM+ALGL+++L NS  +     E  P+
Sbjct: 1313 DDVAGRTKVYEAIVRGDDAFEAGVPESFNVLVKEMRALGLNVELVNSEAQPPEVEEAEPE 1372

Query: 1380 FNKCEL 1385
              + +L
Sbjct: 1373 APQAQL 1378


>gi|167644760|ref|YP_001682423.1| DNA-directed RNA polymerase subunit beta [Caulobacter sp. K31]
 gi|189043850|sp|B0SUP7|RPOB_CAUSK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|167347190|gb|ABZ69925.1| DNA-directed RNA polymerase, beta subunit [Caulobacter sp. K31]
          Length = 1360

 Score = 1728 bits (4476), Expect = 0.0,   Method: Composition-based stats.
 Identities = 850/1368 (62%), Positives = 1073/1368 (78%), Gaps = 12/1368 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG+ PE + +P+LIEVQ++SY+ FL   + P  R +EG++A FKSV
Sbjct: 1    MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQREVRPGVRKDEGIEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+T+A PLK+ LRLIVF+ +E TGA+S+
Sbjct: 61   FPIKDFNERAVLEYVSYEFEEPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            R+IP +G W+D EFD+KD+++VRIDRRRK+P T+FL ALGMD EEIL+TFY  + + +R 
Sbjct: 181  RVIPYRGSWLDFEFDAKDVVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRT 240

Query: 242  ---GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                + W  P        G K   +L+D D+GE+V  +G K+T+   K L + G+K L +
Sbjct: 241  AAGAEGWATPYKPE-RWRGVKPEFALIDADSGEEVAAAGTKITARQAKKLADNGLKTLLL 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              + L G Y+A D VN ETGEIY EAGD +D  S+E +       I +L +D V   AY+
Sbjct: 300  APEALTGRYLARDAVNFETGEIYAEAGDELDVTSIEALAAQGFSTIDVLDIDHVTVGAYM 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNM
Sbjct: 360  RNTLRVDKNAVREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDAERYDLSAVGRVKMNM 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL LD  D++R +RKED++A++K+LV LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+G
Sbjct: 420  RLELDASDEMRVLRKEDVLAVLKLLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMP DLINAKP  ++V EFF SSQLSQ  +  N LS ITH 
Sbjct: 480  LLRMERAIKERMSSVDIDTVMPHDLINAKPAAASVREFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYR+V DGK   +VVY+SAMEE    IAQ+N  +  +G   ++LV  R  GE  L+ +
Sbjct: 600  ESPYRRVADGKPLEEVVYMSAMEESKHVIAQSNIKVL-NGEIVDDLVPGRINGEPTLLQK 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++D +D SP+QVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+V
Sbjct: 659  EQVDLMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGA ++AKR G+VEQ+D  RIV+R+ E   D + SGVDIYRL KFQRSNQ+TC+NQ
Sbjct: 719  VARDSGAVVIAKRTGVVEQIDGTRIVVRATEE-TDAARSGVDIYRLSKFQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD++   DIIADGPST+LG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DV
Sbjct: 778  RPLVKVGDKISAGDIIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKV 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ER +I+ L +D+DDE  IL+RNI  RL E+L G  A+SGPKG  +   ++++ ++E   
Sbjct: 958  IERAEIDRLGKDRDDEFAILNRNISGRLRELLIGNVALSGPKGLSRGQ-ITAEGLAEVQP 1016

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
              WWQ A++DEK    +ESL+  ++ ++  L+ RF++K++K+Q GD++PPGV+++VKVFV
Sbjct: 1017 GLWWQIALEDEKAMGELESLRRLFDENRKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFV 1076

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++SRILP EDMPFL DGT VD+VLNPLGVPSRMNVGQIFE
Sbjct: 1077 AVKRKLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLGVPSRMNVGQIFE 1136

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I +L+ D++A G    L   L ++ G      +      + ++ +A 
Sbjct: 1137 THLGWACAGLGKQITTLLEDWQAGGQKQALIDRLTEIYGPDEELPETE----EELVELAR 1192

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA    I   LRMA LD SGQSILYDG TGE F RPVTVGYIYMLK
Sbjct: 1193 NLGKGVPIATPVFDGARIGDIEDHLRMAGLDPSGQSILYDGQTGEQFKRPVTVGYIYMLK 1252

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1253 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1312

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            SDDV GRT+VYESIV G+DTFE G PESFNVLVKEM++LGL+++LENS
Sbjct: 1313 SDDVAGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS 1360


>gi|114319612|ref|YP_741295.1| DNA-directed RNA polymerase subunit beta [Alkalilimnicola ehrlichii
            MLHE-1]
 gi|122312461|sp|Q0ABI2|RPOB_ALHEH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114226006|gb|ABI55805.1| DNA-directed RNA polymerase subunit beta [Alkalilimnicola ehrlichii
            MLHE-1]
          Length = 1355

 Score = 1728 bits (4476), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1364 (52%), Positives = 986/1364 (72%), Gaps = 9/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P I+++P L+  Q  SY  FL    A + R + GL  AF+SV
Sbjct: 1    MAYSFTEKKRIRKDFGKLPNILEVPYLLATQIDSYRQFLQEERAAESREDVGLHGAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT+ SG A LE+VSY    P FDV +C  R LTYA PL++ +RL+++D D     +S+
Sbjct: 61   FPITSHSGTAALEYVSYRIGDPGFDVKECQSRGLTYAAPLRMLVRLVIYDKDG----QSV 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG+LPLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLL++ 
Sbjct: 117  KDIKEQEVYMGELPLMTRNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD I+VRIDRRRK+P T  L ALG D+++IL  F+ K  +  R 
Sbjct: 177  RVIPYRGSWLDFEFDPKDNIYVRIDRRRKLPATILLRALGFDTQQILDLFFDKNAFHFRD 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G   +  +     G+ ++E+G+++T+  ++ L + GV  L + ++ 
Sbjct: 237  DGSVVLDLVPERLRGETAAFDIK--ANGQVLVEAGRRVTARHIRELGKAGVDTLEVPAEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  VA D+V+  TGEI  EA   +  + ++ I  + ++ +  L+V+ ++   Y+  TL
Sbjct: 295  LEGKIVAHDVVDTGTGEIICEANTELTAELVQAIQDAGVKQLDTLFVNDLDRGPYMSQTL 354

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  + + +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N+R+  
Sbjct: 355  AIDPTRTQLEALVEIYRMMRPGEPPTKEAAENLFQNLFFSPDRYDLSPVGRMKFNLRVGR 414

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DI+A+++ L+++RNG G +DDID+LGNRRVR VGEM +N +R+GL+R+
Sbjct: 415  DEVTGPGVLDNDDILAVLRELINIRNGDGQVDDIDHLGNRRVRCVGEMAENVFRVGLVRV 474

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 475  ERAVRERLSLAESEGLMPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 534

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+ETPY
Sbjct: 535  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNRYGFLETPY 594

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT+ V YLSA+EE    IAQAN+ + EDG   +EL+  R   E  +   +K+ 
Sbjct: 595  RRVENGVVTDKVDYLSAIEEARYVIAQANARVGEDGRLMDELISIRHGNEFGMATPDKVQ 654

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQ+VS+AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 655  YMDVSPKQIVSVAASLVPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVARD 714

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G+VEQVDA RIV+R  + + +    GVDIY L+K+ RSNQNTC+NQ+PLV
Sbjct: 715  SGVIVTAERGGVVEQVDAGRIVVRVNDDETEAGEPGVDIYNLVKYLRSNQNTCMNQKPLV 774

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V R D +ADGPSTD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V ED +T+I
Sbjct: 775  RPGDVVARGDALADGPSTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVKEDRYTTI 834

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLG EEIT DIPNVSE  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 835  HIEELTCVARDTKLGTEEITADIPNVSESALNRLDEAGIVHIGAEVKAGDILVGKVTPKG 894

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G+ G V+DV++F R G++K+ R++++E+ 
Sbjct: 895  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGMDGKVIDVQVFTRDGVEKDSRALAIEQA 954

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++  + +D  D++ I + + +SRL   L GQ A  GP G  +   +++D ++   R +W+
Sbjct: 955  ELAAIRKDLRDQERIFEDDAFSRLERALVGQVAEGGPSGLARGAEVTADYLANLDRKRWF 1014

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE+  R +E+++ Q E  +  LE  F+ K  KI  GDD+ PGV+++VKV++A++R
Sbjct: 1015 EIRMRDEEANRQLEAVRAQLEAQRDSLERHFEEKKGKITAGDDLAPGVVKMVKVYLAVRR 1074

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMPF +DG PVD+VL+PLGVPSRMNVGQ+ ETHLG
Sbjct: 1075 RLQPGDKMAGRHGNKGVISMIVPEEDMPFTEDGEPVDVVLSPLGVPSRMNVGQVLETHLG 1134

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGK+I  ++  +     +  LR+FL++V         +   DD+ +  +A   + 
Sbjct: 1135 WAARGLGKRIGEMLEQH---TKMQELRAFLDQVYNASGQKVDLDSLDDEEIKGLAFNLRE 1191

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I +ML +A L ESGQ+ LYDG TGE FDRPVT+GY+YMLKLNH+
Sbjct: 1192 GVPMATPVFDGAQEPEIKNMLELAGLPESGQATLYDGRTGEAFDRPVTIGYMYMLKLNHL 1251

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DKV+ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1252 VDDKVHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1311

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVLVKE+++LG++I+LE  
Sbjct: 1312 AGRTKMYKNIVDGDHRMEAGMPESFNVLVKEIRSLGINIELEQD 1355


>gi|121602831|ref|YP_988881.1| DNA-directed RNA polymerase subunit beta [Bartonella bacilliformis
            KC583]
 gi|158513078|sp|A1USC8|RPOB_BARBK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120615008|gb|ABM45609.1| DNA-directed RNA polymerase, beta subunit [Bartonella bacilliformis
            KC583]
          Length = 1383

 Score = 1728 bits (4476), Expect = 0.0,   Method: Composition-based stats.
 Identities = 932/1373 (67%), Positives = 1128/1373 (82%), Gaps = 6/1373 (0%)

Query: 1    MAKGVV----FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            MA+ +     FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQ
Sbjct: 1    MAQTLAMMSQFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMIKEPKGGRPDEGLQ 60

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            A FKSVFPI+ FSG AMLEFV YEFD PKFDV++C  RDLTYA PLK+ LRLIVFD+DE 
Sbjct: 61   AVFKSVFPISDFSGTAMLEFVRYEFDAPKFDVEECRQRDLTYAAPLKVILRLIVFDIDED 120

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
            TG+K IKDIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG++  SG
Sbjct: 121  TGSKDIKDIKEQGVYMGDMPLMTSNGTFIINGTERVIVSQMHRSPGVFFDHDKGKSHSSG 180

Query: 177  KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            K+L+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTSFLMALGMD+ +ILSTFY K+
Sbjct: 181  KVLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSFLMALGMDASDILSTFYNKV 240

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             Y +    W  P S  D   G K+ S LVD ++GE V E+GKKLT+   K L EKG+K +
Sbjct: 241  TYERVESGWRIPYSV-DRFKGVKLVSDLVDAESGEVVAEAGKKLTARTAKLLVEKGLKAI 299

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
             ++ D L G Y+A+DIVN ETGEIY+EAGD IDEK L+ +F      I IL +D ++  A
Sbjct: 300  RVSEDELLGSYLADDIVNYETGEIYLEAGDEIDEKVLKVLFDVGANQINILDIDHMSVGA 359

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKM
Sbjct: 360  YIRNTLKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFHSLFFDSERYDLSAVGRVKM 419

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N+R+ LD PD VR +R+EDII ++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR
Sbjct: 420  NLRMGLDCPDTVRVLRQEDIIGVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  VGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYRK+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++V
Sbjct: 600  FIESPYRKITDGKVTTEVVYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMV 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PR+ ID +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGME
Sbjct: 660  PRDHIDLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLIRSEAPFVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA+ SGAAI AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+
Sbjct: 720  AIVARDSGAAISAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRPLV VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++
Sbjct: 779  NQRPLVHVGDRIEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVAD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARD KLGPEEITRDIPNV+EE L+N+DE GI+ +GAEV PGDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDMKLGPEEITRDIPNVAEEALRNLDEAGIVYIGAEVQPGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER+
Sbjct: 899  KITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTFGTVVEVRVFNRHGVEKDERA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            + +ERE+IE LA+D+DDEQ ILDRN+Y+RL  +L  ++A+ GPKGF+K   + S +++ Y
Sbjct: 959  MEIEREEIERLAKDRDDEQSILDRNVYARLAGMLKDKSAIRGPKGFEKGQKIDSTVLNNY 1018

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            PRSQWWQFAV DEKVQ  +E+L  QY+ SK  L+ RF +K+EK+Q GD+MPPGV+++VKV
Sbjct: 1019 PRSQWWQFAVDDEKVQNKIEALCNQYDESKEALQRRFMDKVEKVQRGDEMPPGVMKMVKV 1078

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            FVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI
Sbjct: 1079 FVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQI 1138

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWAC G+GKKI  L++ Y+  GDI PLR  +E +I      E +  YDD+S++++
Sbjct: 1139 LETHLGWACAGMGKKIGDLVDFYQETGDILPLRQRIENLIPDNDRNEPVRQYDDESLVKL 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A Q + GV ++TPVFDGA E  IN+ML  A LD SGQ  LYDG TGEPFDR VTVGYIYM
Sbjct: 1199 AHQMRKGVSIATPVFDGAHEADINAMLEDAGLDSSGQVTLYDGRTGEPFDRQVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            +KSDDV GRT+VYE+IV G+DTFE   PESFNVL+KEM++LGL++ L ++R  
Sbjct: 1319 VKSDDVAGRTKVYEAIVRGDDTFEASIPESFNVLIKEMRSLGLNVKLGDAREF 1371


>gi|220935499|ref|YP_002514398.1| DNA-directed RNA polymerase, beta subunit [Thioalkalivibrio sp.
            HL-EbGR7]
 gi|254765315|sp|B8GV65|RPOB_THISH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219996809|gb|ACL73411.1| DNA-directed RNA polymerase, beta subunit [Thioalkalivibrio sp.
            HL-EbGR7]
          Length = 1358

 Score = 1728 bits (4475), Expect = 0.0,   Method: Composition-based stats.
 Identities = 742/1364 (54%), Positives = 999/1364 (73%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+I+D+P L+  Q  SY  FL  + + D R + GL AAFK+V
Sbjct: 1    MAYSYTEKKRIRKDFGKRPQILDVPYLLTTQLDSYRQFLQADRSEDNRQDVGLHAAFKTV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG   LE+VSY    P FDV +C  R +TYA PL++ LRL+++D D   G++ +
Sbjct: 61   FPIVSYSGTVELEYVSYRLGKPVFDVKECQLRGMTYAAPLRVLLRLVIYDKDAPAGSRVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG+LPLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLL+  
Sbjct: 121  KDIKEQEVYMGELPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALGM++EEIL+TF+     S   
Sbjct: 181  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPATVLLRALGMETEEILATFFETNTVSITK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L    L  G   +         + ++ESG+++T+  ++ L+  G+K L + ++ 
Sbjct: 241  DGFDMELIPERL-RGEVAAFDFKVK--NKVLVESGRRITARHVRELEAAGIKSLEVPAEY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A  +++ ++GE+   A D I ++ L+++  + I+    LY + +++  YI  TL
Sbjct: 298  LVGKVLAHAVIDEDSGELVANANDEITDELLKKLRAAGIKSFKTLYTNDLDHGPYISTTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  + + +A ++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 358  NIDTCRSQLEAQVEIYRMMRPGEPPTKEAAENLFNNLFFTEERYDLSAVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + K+DI+A++K L+D+RNG G +DDID+LGNRRVRSVGEM +N +R+GL+R+
Sbjct: 418  EEITGPGVLDKDDILAVLKTLIDIRNGNGQVDDIDHLGNRRVRSVGEMAENVFRVGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQ+LINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 478  ERAVKERLSVAESEGLMPQELINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNDYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKVTN++VYLSA+EE    IAQAN+SLD  G+  +ELV CR A E  +   +KI+
Sbjct: 598  RKVENGKVTNEIVYLSAIEEGQYVIAQANASLDAKGNLVDELVSCRHANEFTMSTPDKIE 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQ+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+AE   VGTG+E  VA  
Sbjct: 658  FMDISPKQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPCLRAETAVVGTGIERTVAID 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG++IVA+R G+V+ VDA RIV+R  + + +    GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 718  SGSSIVARRGGVVDSVDAARIVVRVNDDETEAGEPGVDIYNLTKYTRSNQNTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD + R D++ADG STDLG++ALG+NM+VAFMPW+GYNFEDS+LISER+V ED FTSI
Sbjct: 778  NVGDVLARGDVLADGSSTDLGEMALGQNMMVAFMPWNGYNFEDSILISERVVQEDRFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLGPEEI+ DIPNVSE  L  +DE GI+ VGAEV P DILVGK+TPKG
Sbjct: 838  HIEELTCVARDTKLGPEEISADIPNVSESLLSKLDESGIVYVGAEVKPNDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DVR+F R G+DK++R++ +E  
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMEGTVIDVRVFTRDGVDKDKRALQIEEA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +  + +D  D+  I + +IY R+ ++L G+ A  GP   K  T ++   ++E PR +W+
Sbjct: 958  ALAAVRKDLKDQLRIYEDDIYDRVEKLLVGKLAAGGPNKLKDGTKVTKTYLTEVPREKWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ E+V   +E +    +      E RFK + EK+  GDD+ PGVL++VKV++A+KR
Sbjct: 1018 EVRMRTEEVNEQLEKMAASLKEQHEAFETRFKEQKEKLTQGDDLAPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS I+P EDMP+L+DGTPVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1078 RMQPGDKMAGRHGNKGVVSMIVPVEDMPYLEDGTPVDIVLNPLGVPSRMNVGQVLETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI  ++   +A   I  LR FL+K+    +    +SD+ D+ +L++    K 
Sbjct: 1138 WAAKGLGQKIGRMV---EAKAKIDELRKFLDKIYNHSAKKVDLSDFSDEEILKLCANLKK 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA+EE I +ML++ADL ESGQ+ L+DG TGE FDRPVTVGY++MLKLNH+
Sbjct: 1195 GVPMATPVFDGAEEEEIKAMLKLADLPESGQTTLFDGRTGESFDRPVTVGYMHMLKLNHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GR ++Y++IV G+   E   PESFNVL+KE+++L ++I+LE  
Sbjct: 1315 QGRNKMYKNIVDGDHRMEANIPESFNVLMKEIRSLAINIELEQD 1358


>gi|83594027|ref|YP_427779.1| DNA-directed RNA polymerase subunit beta [Rhodospirillum rubrum ATCC
            11170]
 gi|109914389|sp|Q2RQV3|RPOB_RHORT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|83576941|gb|ABC23492.1| DNA-directed RNA polymerase, beta subunit [Rhodospirillum rubrum ATCC
            11170]
          Length = 1393

 Score = 1726 bits (4471), Expect = 0.0,   Method: Composition-based stats.
 Identities = 849/1390 (61%), Positives = 1065/1390 (76%), Gaps = 31/1390 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK FG+ P +  +P+LIEVQK+SYD FL + +  D+R + GLQ  FKSV
Sbjct: 1    MTKSLTSRKRIRKDFGRIPTVAPMPNLIEVQKSSYDQFLQIGVPVDKRTDSGLQEVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FSG   LEFV+YE + PK+D D+C  R +T+A PLK+TLRL+V+DVDE TGA+SI
Sbjct: 61   FPIRDFSGKGELEFVAYELEEPKYDTDECQQRGMTFAAPLKVTLRLLVWDVDEETGARSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A 
Sbjct: 121  RDIKEQDVYMGDMPLMTSNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--------------------- 221
            R+IP +G W+D EFD+KD+++VRIDRRRK+PVT+ L AL                     
Sbjct: 181  RVIPYRGSWLDFEFDAKDMVYVRIDRRRKLPVTTLLYALEGAAATALREARTAEGRSVDP 240

Query: 222  ----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
                GM SEEIL  FY K+ Y +    W       D + G K+   LVD  TGE  IE+G
Sbjct: 241  SEIAGMTSEEILDFFYQKLSYKRDDKGWKVDFKP-DHLRGVKLMFDLVDAATGEVKIEAG 299

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             K+T    + L E G+  + + ++ L G Y AED++N  +GEIY EAG+ + E  L ++ 
Sbjct: 300  TKVTPRAARKLAEDGMTEMRVFTEELVGRYAAEDMINEASGEIYAEAGEELTEAMLADME 359

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
             +   ++ +L++D VN   Y+RNTL  DKN  R++AL+DIYRVMRPG+  T   A+++F 
Sbjct: 360  KAGFTELRVLHIDHVNVGPYVRNTLAMDKNTTREEALIDIYRVMRPGEPPTLETADALFK 419

Query: 398  FLFFDSDKYDLSTVGRVKMNMRL---NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             LFFDS++YDLS VGRVKMN RL     + PD +R +RKED++ II+ LV+L++GKG ID
Sbjct: 420  GLFFDSERYDLSAVGRVKMNARLGFTMQEAPDTMRVLRKEDVLHIIRQLVELKDGKGEID 479

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID+LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+SSVDID+VMP DLINAKP  +AV 
Sbjct: 480  DIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVDIDTVMPHDLINAKPAAAAVR 539

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET
Sbjct: 540  EFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 599

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL +FARVN YGFIE+PYRKV +G VT++V Y+SAMEE    IAQAN++L
Sbjct: 600  PEGPNIGLINSLATFARVNQYGFIESPYRKVVEGTVTDEVTYMSAMEEGKYVIAQANAAL 659

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             EDG F ++L+ CR A +  +V  + ID+ID SPKQ+VS+AA+LIPFLENDD+NR LMG 
Sbjct: 660  TEDGHFADDLISCRKASDFEMVQPQDIDYIDVSPKQLVSVAAALIPFLENDDANRALMGS 719

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL+KAEAP+VGTGME+ VA+ SGA I AKRAG+V+QVDA RIVIR+ E  L  
Sbjct: 720  NMQRQAVPLVKAEAPYVGTGMEAAVARDSGATIAAKRAGVVQQVDATRIVIRATED-LKI 778

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            + SGVDIYRL KFQRSNQ+TC+NQRPLVKVGD V R +I+ADGP T++G+LALGRN+LVA
Sbjct: 779  AESGVDIYRLQKFQRSNQSTCINQRPLVKVGDLVGRGEILADGPLTEMGELALGRNVLVA 838

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            FMPW+GYNFEDS+LISER+VS+DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE LK
Sbjct: 839  FMPWNGYNFEDSILISERIVSDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALK 898

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+DE GI+ +GAEV  GDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G
Sbjct: 899  NLDEAGIVYIGAEVQAGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRIPPG 958

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V+GTVV+VR+FNR G++K+ER++++ER++IE LA+D+DDE+ IL+ +   RL E+L GQ 
Sbjct: 959  VTGTVVEVRVFNRRGVEKDERALAIERQEIESLAKDRDDERAILEGSFARRLKELLIGQK 1018

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             V GP+G     V+S DL+S Y  +QW Q AV++++    +E LK  YE S + +++RF+
Sbjct: 1019 VVGGPRGMATGGVISEDLLSGYTAAQWRQIAVENDETATEIEGLKKAYEESIAKIQERFE 1078

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            NK+EK+Q GD++PPGVL++VKVFVA+KR +Q GDKMAGRHGNKG++S+I P EDMP+L+D
Sbjct: 1079 NKVEKLQRGDELPPGVLKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKINPIEDMPYLED 1138

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN-GDISPLRSFLE 1173
            GT VDIVLNPLGVPSRMNVGQI ETHLGWAC GLG +I +L+   K     I+ LR  L+
Sbjct: 1139 GTYVDIVLNPLGVPSRMNVGQILETHLGWACRGLGAQIGALLEQVKRGLIPINDLREKLD 1198

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V G     E ++   DD +  +A   +SGVP++TPVFDGA E  I  MLR A LD SGQ
Sbjct: 1199 DVYGPRHAKEDLAPMGDDQIKELAFNLRSGVPIATPVFDGARESDIVDMLRKAGLDSSGQ 1258

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L DG TGEPFDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 1259 VTLSDGRTGEPFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQR 1318

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKE
Sbjct: 1319 FGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVKGDDTFEAGIPESFNVLVKE 1378

Query: 1354 MQALGLSIDL 1363
            M++LGL ++L
Sbjct: 1379 MRSLGLDVEL 1388


>gi|329890196|ref|ZP_08268539.1| DNA-directed RNA polymerase, beta subunit [Brevundimonas diminuta
            ATCC 11568]
 gi|328845497|gb|EGF95061.1| DNA-directed RNA polymerase, beta subunit [Brevundimonas diminuta
            ATCC 11568]
          Length = 1371

 Score = 1726 bits (4471), Expect = 0.0,   Method: Composition-based stats.
 Identities = 848/1367 (62%), Positives = 1075/1367 (78%), Gaps = 9/1367 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    F G  R+R  FG+ PE + +P+LIEVQ+ASY+ FL     P  R +EG++A FK
Sbjct: 13   IAAATSFTGKKRIRYSFGRIPEAVQMPNLIEVQRASYEQFLQRESRPGLRNDEGIEAVFK 72

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ +E TGA+
Sbjct: 73   SVFPIKDFNERAVLEYVSYEFEDPKYDVEECIQRDMTYAAPLKVKLRLIVFETEEETGAR 132

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 133  SVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 192

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+D EFD+KDI++VRIDRRRK+P ++FL ALGMD EEIL TFY  + Y +
Sbjct: 193  AARVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPASTFLYALGMDGEEILKTFYETVPYEK 252

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RG+ W  P        G K    LVD DTGE V  +G+K+++   K L + G+K L + +
Sbjct: 253  RGEGWVTPYKPE-RWRGVKPEFDLVDADTGEVVAPAGQKISARAAKKLADGGLKSLSLAA 311

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L   Y+A D VN +TGEIY EAGD +D  ++E +  +    I +L +D V   AY+RN
Sbjct: 312  DALLTKYLAADAVNYQTGEIYAEAGDELDAAAIELLEANGFTTIDVLDIDHVTVGAYMRN 371

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL D+YRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 372  TLRVDKNTGREDALFDVYRVMRPGEPPTPEAAEAMFNSLFFDAERYDLSAVGRVKMNMRL 431

Query: 421  N-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
               +  D++R ++K+D++ +++ILV L++G+G IDDIDNLGNRRVRSVGE+L+NQYR+GL
Sbjct: 432  ETPEVSDEIRVLQKDDVLKVLQILVGLKDGRGEIDDIDNLGNRRVRSVGELLENQYRVGL 491

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 492  LRMERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 551

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE
Sbjct: 552  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIE 611

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYR+V +GK T++VVY+SAMEE    IAQAN  L +DG   EELV  R  G+  L+ +E
Sbjct: 612  SPYRRVVEGKATDEVVYISAMEEAKHVIAQANIDL-KDGEIVEELVPGRINGDSQLLTKE 670

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +D +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VV
Sbjct: 671  TVDMMDVSPKQVVSVAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVV 730

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SGA ++A+R G+VEQ+D  RIV+R+  GD+D   SGVDIYRL KFQRSNQ+TC+NQR
Sbjct: 731  AVDSGAVVIARRDGVVEQIDGTRIVVRAT-GDVDAGRSGVDIYRLSKFQRSNQSTCINQR 789

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+V+VGDEV+  D+IADGPSTDLG+LALGRN+LVA+MPW+GYNFEDS+LISER+V +D+F
Sbjct: 790  PIVRVGDEVKAGDVIADGPSTDLGELALGRNVLVAYMPWNGYNFEDSILISERIVRDDIF 849

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIH+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+T
Sbjct: 850  TSIHLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVT 909

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHGIDK+ER++++
Sbjct: 910  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGIDKDERAVAI 969

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ER +IE L +D+DDE  IL+RN+Y R+  +L G+ AVSGPKG  +  V + + ++E  + 
Sbjct: 970  ERAEIERLGKDRDDELKILERNVYGRVKPLLLGKTAVSGPKGMGRGEV-TEEKLAEVSKG 1028

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
             WWQ A+ DEK    +E++K Q+E ++  L+ RF++K+EK+Q GD+MPPGV+++VKVFVA
Sbjct: 1029 LWWQVALDDEKAMGELEAMKKQFEDARKALDRRFEDKVEKLQRGDEMPPGVMKMVKVFVA 1088

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG++S+ILP EDMP L DGT VDIVLNPLGVPSRMN+GQIFET
Sbjct: 1089 VKRKLQPGDKMAGRHGNKGVISKILPIEDMPHLDDGTHVDIVLNPLGVPSRMNIGQIFET 1148

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA  GLGK+IK L+  +   G    L S L ++ G  +   +     D+ ++ +A+ 
Sbjct: 1149 HLGWAAAGLGKQIKGLLEQWMDGGMRDALVSRLTQIYGADTPLPQ----SDEELIELAQN 1204

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               GVP +TPVFDGA    I  +L  ADLD SGQSIL+DG TGE F RPVTVGY+YMLKL
Sbjct: 1205 LSKGVPFATPVFDGARISDIEDLLESADLDRSGQSILFDGQTGEQFKRPVTVGYVYMLKL 1264

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1265 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1324

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT+VYE+IV G+D+FE G PESFNVLVKEM++LGL+++LENS
Sbjct: 1325 DDVAGRTKVYEAIVRGDDSFEAGIPESFNVLVKEMRSLGLNVELENS 1371


>gi|83858573|ref|ZP_00952095.1| DNA-directed RNA polymerase beta subunit [Oceanicaulis alexandrii
            HTCC2633]
 gi|83853396|gb|EAP91248.1| DNA-directed RNA polymerase beta subunit [Oceanicaulis alexandrii
            HTCC2633]
          Length = 1359

 Score = 1726 bits (4469), Expect = 0.0,   Method: Composition-based stats.
 Identities = 858/1365 (62%), Positives = 1079/1365 (79%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G+ F G  R+RK FG+ P  +++P+LIEVQK SY+ FLM + A  +RP+EGLQA FKSV
Sbjct: 1    MGLSFTGKKRIRKSFGRIPGAVEMPNLIEVQKHSYEQFLMKDTAIADRPDEGLQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+  FS  A+LEFVSYEF+PPK+DV++C+ RD+TYA PLK+ +RLIVFDVDE TG+KS+
Sbjct: 61   FPVKDFSERALLEFVSYEFEPPKYDVEECVQRDMTYAAPLKVKMRLIVFDVDEETGSKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDRGKTHASGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+HVRIDRRRK+P T+ L ALG+D EEILSTFY ++ Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDILHVRIDRRRKLPATTLLYALGLDKEEILSTFYGRVTYEAGK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D W  P    +   G K    L+D  +GE V  +GKK+++     + E G++ L ++S+ 
Sbjct: 241  DGWTMPFV-KERWRGIKPQRDLIDAKSGEVVAAAGKKISARAANKMAEDGLEKLLVSSEE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G + AED+VN ETGEI+ EAGD + E+ +  I  + +  + +L +D ++   ++R TL
Sbjct: 300  LMGKFAAEDLVNAETGEIFAEAGDELTEEVINAINEAGVDSLDVLDIDGLSIGGHMRTTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+ AL+DIYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVKMNMRL+L
Sbjct: 360  AADKNDTREQALIDIYRVMRPGEPPTPETAEALFAGLFFDPERYDLSPVGRVKMNMRLDL 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            + PDDVR +R+EDII ++++L+DLR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLLRM
Sbjct: 420  ECPDDVRVLRQEDIIEVLRVLLDLRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+ SVDI++VMP DL+NAKP  +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 480  ERAIKERMGSVDIETVMPHDLVNAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRMS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++ARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG--EEILVPREK 660
            RKV +GK+T+ V YLSAM+E    IAQAN+ +DE+G    E V CR     +  LVPRE 
Sbjct: 600  RKVENGKLTDQVDYLSAMQESRYSIAQANAGVDENGMLANEFVNCRVGPGRDATLVPRED 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+KAEAP VGTGME+VVA
Sbjct: 660  VDYIDVSPKQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKAEAPLVGTGMEAVVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAA+ A+R G+VEQVDA RIV+R+  G++  + SGVDIYRL KFQRSNQ+T +NQRP
Sbjct: 720  RDSGAAVAARRDGVVEQVDAQRIVVRAT-GEIGAAESGVDIYRLSKFQRSNQSTAINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V+VGD VR  DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+LISER+V +DVFT
Sbjct: 779  IVRVGDNVRAGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILISERIVRDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            S+H+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV  GDILVGK+TP
Sbjct: 839  SVHLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVEAGDILVGKVTP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G +GT+V+VR+FNRHG+DK+ER+I++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGTTGTIVEVRVFNRHGVDKDERAIAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE L  D+DDE  IL+R+IY RL EIL G++AVSGPKGFKK  V +++ + E P SQ
Sbjct: 959  REEIERLGEDRDDELAILERDIYGRLREILIGKSAVSGPKGFKKGEV-TAEALEEVPASQ 1017

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW+  ++DE     VE+LK QY+ SK+ L+ RF++K+EK+Q GD+MPPGV+++VKVFVA+
Sbjct: 1018 WWKIGLEDEAAMAGVEALKKQYDESKARLDRRFEDKVEKLQRGDEMPPGVMKMVKVFVAV 1077

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG++S+I P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1078 KRKLQPGDKMAGRHGNKGVISKINPIEDMPFLEDGTSVDIVLNPLGVPSRMNVGQILETH 1137

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLG++I      YK NGD   L   L K  G      +     ++    +    
Sbjct: 1138 LGWACKGLGRQIGEAYEAYKRNGDQGDLNKMLIKAYGDDQELPE----TEEERAELGRNL 1193

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
             +GVP++TPVFDGA E+ I   L+ A  D+SGQS+LYDG TG+ F RPVTVG  Y+LKL+
Sbjct: 1194 ANGVPIATPVFDGAREDDIVDHLQRAGFDKSGQSVLYDGRTGDQFKRPVTVGIKYLLKLH 1253

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KSD
Sbjct: 1254 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKSD 1313

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT+VYE+IV G++ FE G PESFNVLVKEM++LGL+++L N
Sbjct: 1314 DVAGRTKVYEAIVRGDNAFEAGIPESFNVLVKEMRSLGLNVELVN 1358


>gi|312115365|ref|YP_004012961.1| DNA-directed RNA polymerase subunit beta [Rhodomicrobium vannielii
            ATCC 17100]
 gi|311220494|gb|ADP71862.1| DNA-directed RNA polymerase, beta subunit [Rhodomicrobium vannielii
            ATCC 17100]
          Length = 1388

 Score = 1725 bits (4468), Expect = 0.0,   Method: Composition-based stats.
 Identities = 871/1373 (63%), Positives = 1082/1373 (78%), Gaps = 6/1373 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG   +  ++P+LIEVQK SYD FLM+      R N GLQA F S+
Sbjct: 1    MAQTFIGRKRIRKRFGNIADAAEMPNLIEVQKQSYDQFLMVQDPVGGRANTGLQAVFASI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS  A LEFV Y+F+PPK+DVD+C  R +T+A PLK+ LRLI FDV+E TG++S+
Sbjct: 61   FPIKDFSDKAQLEFVRYDFEPPKYDVDECQQRSMTFAAPLKVKLRLITFDVNEETGSRSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ +YMGD+P MT +GTFVI G +R++VSQ+HRSPG+ F HD G++  SGKLL+A 
Sbjct: 121  RDIKEQDVYMGDIPFMTSNGTFVINGTERVIVSQMHRSPGVFFHHDGGKSHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++ RIDR+RK+P T+ L ALGM++EEIL TFY +I +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVYARIDRKRKLPATTLLYALGMNNEEILETFYNRISFEATK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W         M G K +  + D DTGE VIE+GKKL + L++ L E  VKF+ +  + 
Sbjct: 241  QGWRTAFVPE-RMRGLKATQDIYDADTGEVVIEAGKKLNARLVRQLAE-RVKFIAVPDEA 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+AEDIVN  TG IY EAGD +D K L+++    + ++P+L +D VN  ++IRNTL
Sbjct: 299  LFGRYLAEDIVNMTTGVIYAEAGDELDTKMLDKLRDVGVEELPVLDIDHVNTGSFIRNTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN+++++AL DIYRVMRPG+  T   A ++F  LFFD ++YDLS+VGRVKMN+RL++
Sbjct: 359  HLDKNQNQQEALFDIYRVMRPGEPPTEDAARALFKSLFFDEERYDLSSVGRVKMNIRLDI 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               D++R + K+DII++I+ LVDLR+G+G +DDIDNLGNRRVRSVGE+++NQYRLGLLRM
Sbjct: 419  KQSDEMRILTKDDIISVIRTLVDLRDGRGEVDDIDNLGNRRVRSVGELMENQYRLGLLRM 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+I+ER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 479  ERAIRERMSSVDIDTVMPQDLINAKPASAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT++V+YLSAMEE   +IAQAN  L++D SF E+L+ CR  G+  LV +EK D
Sbjct: 599  RKVVDGKVTDEVIYLSAMEEARCHIAQANVKLNDDNSFAEDLIICRHQGDVSLVAKEKAD 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            FID SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAP VGTGMESVVA+ 
Sbjct: 659  FIDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPLVGTGMESVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI AKR+G+++QVDA RIVIR+ +   DPS SGVDIY L KFQRSNQNTC+NQRPLV
Sbjct: 719  SGAAIGAKRSGVIDQVDATRIVIRATDEM-DPSKSGVDIYNLRKFQRSNQNTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V + DIIADGPST+LGDLALG+N+L+AFMPW GYNFEDS+L+SER+VS DVFTSI
Sbjct: 778  RVGDRVEQGDIIADGPSTELGDLALGKNVLLAFMPWQGYNFEDSILLSERIVSTDVFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITPKG
Sbjct: 838  HIEEFEVSARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHG++K+ER++++ERE
Sbjct: 898  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGVEKDERAMAIERE 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE LA+D+DDE  ILDRN+Y RL +IL G+    GPKG +K T  + +L+SE PRSQWW
Sbjct: 958  EIERLAKDRDDELHILDRNVYGRLRDILIGKEVARGPKGLRKGTEANEELLSEVPRSQWW 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              A++DE+    +E+++ QY+ +K  LE RF +KI+K++ GD++PPGV+++VKVFVA+KR
Sbjct: 1018 DIALKDEQAMSGIEAIRRQYDEAKKRLEQRFVDKIDKLKRGDELPPGVMKMVKVFVAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1078 KIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG  I   +  Y+    I  LR  +E           + ++ DD ++ +AE    
Sbjct: 1138 WASRGLGNMINKGLAVYREQHRIDELRQAVEISYKGD---PSVPNFTDDQLVELAENLGK 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVPV+TPVFDGA E  IN+ML  A LD SGQ  LYDG +GEPFDR VTVGY Y+LKL+H+
Sbjct: 1195 GVPVATPVFDGAREADINAMLTAAGLDTSGQVTLYDGRSGEPFDRKVTVGYKYLLKLHHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             GRT+VYE+IV G+DTFE G PESFNVLVKEM+ALG++++L+ +R  N    E
Sbjct: 1315 AGRTKVYEAIVRGDDTFEAGVPESFNVLVKEMRALGMNVELKQTRGANEPAPE 1367


>gi|118591193|ref|ZP_01548592.1| DNA-directed RNA polymerase subunit beta [Stappia aggregata IAM
            12614]
 gi|118436269|gb|EAV42911.1| DNA-directed RNA polymerase subunit beta [Stappia aggregata IAM
            12614]
          Length = 1379

 Score = 1724 bits (4465), Expect = 0.0,   Method: Composition-based stats.
 Identities = 909/1378 (65%), Positives = 1129/1378 (81%), Gaps = 4/1378 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMN-IAPDERPNEGLQAAFKS 61
                FNG  +VRK+FG   ++  +P+LIEVQKASYD FL ++ +    R NEGL+A F+S
Sbjct: 1    MTQTFNGRKKVRKYFGSIRDVAAMPNLIEVQKASYDQFLQVDEMPGGGRKNEGLEAVFQS 60

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI+ F+G ++LEFVSYEF+ PK+DVD+C  RD+T+A PLK+TLRLIVFDVDE TGAKS
Sbjct: 61   VFPISDFAGTSLLEFVSYEFEAPKYDVDECRQRDMTFAAPLKVTLRLIVFDVDEDTGAKS 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A
Sbjct: 121  VKDIKEQDVYMGDMPFMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFA 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALG+D EEIL+TFY +I Y+++
Sbjct: 181  ARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGLDGEEILNTFYKRIDYTRQ 240

Query: 242  GDF-WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             D  W  P   A L  G K S  L+D D+GE VIE G+K+T   +K L+EKGV  L +T 
Sbjct: 241  KDGSWRMPFDGARL-KGTKASYDLIDADSGEVVIEGGRKITQRTIKQLEEKGVTALKVTD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIV+ ++GEIY EAGD I  K LEE+      D+ +L +D VN   YIRN
Sbjct: 300  EDLHGQYLAEDIVDMKSGEIYAEAGDEISGKLLEELVDRGYHDLTMLDIDHVNTGPYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKMNMRL
Sbjct: 360  TLSVDKNESREDALFDIYRVMRPGEPPTIDTAEAMFQSLFFDEERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +++  D VR +RK+DI+ +I++L++LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DVECADTVRTLRKDDILEVIRVLLELRDGKGEIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 480  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG VTN+VVYLSAMEE   Y+AQ+N+  D++G FTEEL+ CR AGE ++VP +K
Sbjct: 600  PYRKVKDGTVTNEVVYLSAMEEAKHYVAQSNAVYDDEGRFTEELITCRHAGENMMVPSDK 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI A+RAGIV+QVDA RIVIR+ E  LDP  SGVDIYRL KFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGARRAGIVDQVDATRIVIRATED-LDPGKSGVDIYRLQKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L+SER+VS+DVFT
Sbjct: 779  LVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIH+EEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAE+NPGDILVGKITP
Sbjct: 839  SIHLEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAELNPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL E+L  + A++GPKGFKK TVL+ D+++++PRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLAEMLMDKTAIAGPKGFKKDTVLTGDVLNDFPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFA +DEK    +E+L+ QY+ S+  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1019 WWQFATEDEKFMSEIEALRGQYDDSRKRLEQRFIDKVEKLQRGDELPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I PCEDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKLQPGDKMAGRHGNKGVVSKINPCEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC G+G +I  + ++Y+ +G+I  LR  + ++ G     + + +YDD+ ++R+AEQ 
Sbjct: 1139 LGWACRGMGNRIGEMYDEYRKSGEIEQLRGKIVEIYGDNMKGDNVKEYDDEGIVRLAEQL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  +   L +A  D SGQS+LYDG TGE FDR VTVGYIYMLKL+
Sbjct: 1199 KKGVSIATPVFDGAREPDVVEALNIAGYDPSGQSVLYDGRTGEEFDRKVTVGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+ +      + E   
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELQRTDVPVIGEEETAD 1376


>gi|260432421|ref|ZP_05786392.1| DNA-directed RNA polymerase, beta subunit [Silicibacter
            lacuscaerulensis ITI-1157]
 gi|260416249|gb|EEX09508.1| DNA-directed RNA polymerase, beta subunit [Silicibacter
            lacuscaerulensis ITI-1157]
          Length = 1382

 Score = 1724 bits (4464), Expect = 0.0,   Method: Composition-based stats.
 Identities = 845/1379 (61%), Positives = 1074/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A      EG+Q  F+SV
Sbjct: 5    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDADQPTDGEGIQGVFQSV 64

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV YE + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 65   FPIKDFNETSVLEFVKYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 124

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 125  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 184

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y    
Sbjct: 185  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYDTVSYKLDK 244

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  L+D  TGE + E+GKK+T   +K L ++G V  L +  D
Sbjct: 245  KKGWITPFFPERVRGTRPTYDLIDAKTGEVIAEAGKKVTPRAVKQLIDEGKVTELLVPFD 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N ETG IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 305  HIVGKFVAKDIINEETGAIYVEAGDELTLEYDKDGELIGGTVKELIDAGITDIPVLDIDN 364

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   YIRNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 365  INVGPYIRNTMAQDKNMNRETALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 424

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD PD  R + +EDI+A IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 425  GRVKMNMRLALDKPDTQRTLDREDIVACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 484

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 485  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 544

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 545  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 604

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V DG+VT++V Y+SA EE    +AQAN++LDE+G F  +LV  R AG
Sbjct: 605  VNKYGFIETPYRVVKDGQVTDEVHYMSATEEMRHTVAQANATLDENGKFINDLVSTRQAG 664

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 665  DYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 724

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAI AKRAGI++QVDA RIVIR+ E  L+   +GVDIYRL KFQRSN
Sbjct: 725  GTGIEEKVAIDSGAAIQAKRAGIIDQVDAQRIVIRATED-LELGDAGVDIYRLRKFQRSN 783

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V++ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 784  QNTCINQRPLVKVGDTVQKGEVIADGPSTDMGELALGKNVIVAFMPWNGYNYEDSILISE 843

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 844  RIARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 903

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 904  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 963

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K  + ++ +
Sbjct: 964  KDERALQIEREEVERLARDRDDELAILDRNIYARLKSMILGKTAVKGPKGVKAGSEITEE 1023

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWWQ A++DEK  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1024 LLDSLTRGQWWQLALEDEKDAQIVEALNEQYEVQKRALDARFEDKVEKVRRGDDLPPGVM 1083

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1084 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1143

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG KI   + +Y+ +GD++P+R  ++   G   + E IS+ D++
Sbjct: 1144 NVGQILETHMGWAARGLGLKIDEALQEYRRSGDLTPVREAMKHAYGEDVYAEGISNMDEN 1203

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  L  A  D SGQSIL+DG TGE F RPVTV
Sbjct: 1204 ELVEAASNVTRGVPIATPVFDGAKEADVNDALVRAGFDTSGQSILFDGRTGEQFARPVTV 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1264 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1324 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1382


>gi|255019480|ref|ZP_05291576.1| DNA-directed RNA polymerase beta subunit [Acidithiobacillus caldus
            ATCC 51756]
 gi|254971075|gb|EET28541.1| DNA-directed RNA polymerase beta subunit [Acidithiobacillus caldus
            ATCC 51756]
          Length = 1362

 Score = 1724 bits (4464), Expect = 0.0,   Method: Composition-based stats.
 Identities = 729/1366 (53%), Positives = 986/1366 (72%), Gaps = 5/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK+  I+ +P L+  Q  SY  FL  ++    R   GLQ  F+S+
Sbjct: 1    MAYSFTEKKRIRKDFGKSQSILQVPYLLATQMDSYRDFLQADVPAAARKEVGLQEVFRSL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ ++SG A L+FVSY  + P FDV +C  R LTY   L++ LRL +++ D+ TGAK I
Sbjct: 61   FPMESYSGNASLDFVSYRLEKPVFDVVECRQRGLTYCAGLRVRLRLALYEKDDSTGAKRI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG+LPLMT  G FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL+  
Sbjct: 121  KDVKEQDVYMGELPLMTDHGAFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD I+ RIDRRRK+P T+ L ALG  +E+IL+ F+    +   G
Sbjct: 181  RIIPYRGSWLDFEFDPKDHIYARIDRRRKLPATTLLRALGYSTEDILAMFFETDTFRIDG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK-FLGITSD 301
                + L    L  G      +V   TGE V+ +GK++T+  ++ L E G +  + +   
Sbjct: 241  KRIFYHLIPQRL-QGETAVFDIVHPKTGEVVVAAGKRVTARHVRQLSELGGEQEVEVPEA 299

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A+D+V+  TGE+ + A + +D + L  ++    R +  LY + ++  AYI  T
Sbjct: 300  FLLGKVLAQDLVDEATGEVIVAANEALDAEILARLYALPARSLRTLYTNELDRGAYISET 359

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D  +D  +A L+IYR+MRPG+  +   A+++F  LFF  D+YDLS VGR+K N R+ 
Sbjct: 360  LRIDTARDAHEAQLEIYRLMRPGEPPSKDAAQNLFQGLFFSPDRYDLSAVGRMKFNRRVG 419

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +       +  EDII ++K+LV LRNG+G IDDID+LGNRRVRSVGE+++NQ+RLGL+R
Sbjct: 420  REEITGPGVLSNEDIIDVLKVLVALRNGQGDIDDIDHLGNRRVRSVGELMENQFRLGLVR 479

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++K+R++  + + + PQDLINAKP+ + V EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 480  VERAVKDRLALAESEGLTPQDLINAKPIAAVVNEFFGSSQLSQFMDQTNPLSEVTHKRRV 539

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+ +AR NAYGF+ETP
Sbjct: 540  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSCYARTNAYGFLETP 599

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V  G+ T++VVYLSA++E N  IAQANS+LD+D    +ELV CR   E +L   +++
Sbjct: 600  YRRVIAGRATDEVVYLSAIDEGNYVIAQANSTLDDDNRLVDELVSCRHRNETVLANPDQV 659

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             F+D SP+Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP ++++AP VGTGME VVA 
Sbjct: 660  QFMDISPRQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTVRSQAPLVGTGMERVVAI 719

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAAI A R G+V+ VD  RIV+R  + +  P   GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 720  DSGAAIKAVRGGVVDSVDGARIVVRVNDEETLPGEPGVDIYNLVKYARSNQNTTLNQRPI 779

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VKVGD V R D++ADGPST++G+LALG+N+LVAFMPW+GYNFEDS+LISER+V+ED +T+
Sbjct: 780  VKVGDVVARGDVLADGPSTEMGELALGQNILVAFMPWNGYNFEDSILISERVVAEDRYTT 839

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF V ARDTKLGPEEITRDIPNV+E  L+++DE GI+ +GAE+ PGDILVGK+TPK
Sbjct: 840  IHIEEFSVFARDTKLGPEEITRDIPNVAEGALRHLDESGIVVIGAELAPGDILVGKVTPK 899

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D S+R+P+G+ GTV+DV++F R GI+K+ R+ ++E 
Sbjct: 900  GETQLTPEEKLLRAIFGEKASDVKDNSMRMPAGMYGTVIDVQVFTRDGIEKDARAKAIEE 959

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            EQ+  + +D  DE  I +++ + R+  +L  + A  GP G      ++   + + PRSQW
Sbjct: 960  EQLRKIRKDVHDEYRIFEQDSFQRIERLLLNKVAEGGPNGLAAGAKITKAYLKDLPRSQW 1019

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   ++ E+    +E ++ Q E  +  L+   + K  K+  GDD+ PGVL++VKV VA+K
Sbjct: 1020 FDIRLRSEESNAALEQIRAQLEQQRERLDAVLEEKRRKLTQGDDLSPGVLKMVKVHVAVK 1079

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP+L DGTPVDIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1080 RQLQPGDKMAGRHGNKGVVSKIVPVEDMPYLADGTPVDIVLNPLGVPSRMNVGQILETHL 1139

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I+ ++   +    +S +R+FL+++       E +   +D+ +L +A   +
Sbjct: 1140 GWAAKGLGRRIEEML---ENQRQVSEIRAFLKEIYNRAGKKEDLDQLNDEDILELARNLR 1196

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA EE I  ML +A L  SGQ  LYDG +GE FDRPVTVGY+YMLKL+H
Sbjct: 1197 GGVPMATPVFDGASEEEIRDMLELAGLPRSGQVTLYDGRSGEAFDRPVTVGYMYMLKLHH 1256

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1257 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1316

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V GR+++YESIV G+   + G PESFNVL+KE+++L + I+LE S 
Sbjct: 1317 VSGRSKMYESIVKGDFRMDAGMPESFNVLLKELRSLAIDIELEQSN 1362


>gi|16124757|ref|NP_419321.1| DNA-directed RNA polymerase subunit beta [Caulobacter crescentus
            CB15]
 gi|221233473|ref|YP_002515909.1| DNA-directed RNA polymerase subunit beta [Caulobacter crescentus
            NA1000]
 gi|41017786|sp|Q9AAU2|RPOB_CAUCR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765280|sp|B8GZW7|RPOB_CAUCN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|13421681|gb|AAK22489.1| DNA-directed RNA polymerase, beta subunit [Caulobacter crescentus
            CB15]
 gi|220962645|gb|ACL94001.1| DNA-directed RNA polymerase beta chain [Caulobacter crescentus
            NA1000]
          Length = 1356

 Score = 1724 bits (4464), Expect = 0.0,   Method: Composition-based stats.
 Identities = 848/1364 (62%), Positives = 1069/1364 (78%), Gaps = 8/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG+ PE + +P+LIEVQ++SY+ FL     P  R +EG++A FKSV
Sbjct: 1    MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQRETRPGLRRDEGVEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+T+A PLK+ LRLIVF+ +E TGA+S+
Sbjct: 61   FPIKDFNERAVLEYVSYEFEEPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDRRRK+P T+FL ALGMD EEIL+TFY  + + +R 
Sbjct: 181  RVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRS 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P        G K    LVD DTGE+V  +G K+T+   K   + G+K L +  + 
Sbjct: 241  GGWATPYKPE-RWRGVKPEFPLVDADTGEEVAPAGTKITARQAKKFADGGLKTLLLAPEA 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A D VN  TGEIY EAGD +D  S++ +       I +L +D V   AY+RNTL
Sbjct: 300  LTGRYLARDAVNMATGEIYAEAGDELDVTSIQALADQGFSTIDVLDIDHVTVGAYMRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS+VGRVKMNMRL  
Sbjct: 360  RVDKNAIREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDAERYDLSSVGRVKMNMRLEQ 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D+VR +RKED++A++K+LV LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 420  DVSDEVRILRKEDVLAVLKVLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGK  ++VVY+SAMEE    IAQ+N  + E G   E+LV  R  GE  L+ +E +D
Sbjct: 600  RRVKDGKPQDEVVYMSAMEESKHVIAQSNIKVAE-GEIVEDLVPGRINGEPTLLQKETVD 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VVA+ 
Sbjct: 659  LMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA ++AKR G+VEQ+D  RIVIR+ E   DP+ SGVDIYR+ KFQRSNQ+TC+NQRPLV
Sbjct: 719  SGAVVIAKRTGVVEQIDGTRIVIRATEE-TDPARSGVDIYRMSKFQRSNQSTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD +   DIIADGPST+LG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DVFTSI
Sbjct: 778  KVGDRIVAGDIIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 838  HIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++ER 
Sbjct: 898  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALAIERA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+ L +D+DDE  IL+RNI  RL E+L G+ A+SGPKG  +   ++++ +++     WW
Sbjct: 958  EIDRLGKDRDDEFAILNRNISGRLKELLIGKVALSGPKGLSRGE-ITAEGLAQVASGLWW 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A++DEK    +ESL+  ++ ++  L+ RF++K++K+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1017 QIALEDEKAMGELESLRRLFDENRKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRILP EDMPFL DGT VD+VLNPLGVPSRMNVGQIFETHLG
Sbjct: 1077 KLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLGVPSRMNVGQIFETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC  LGK+I +L+ D++  G    L   L ++ G            ++ ++ +A     
Sbjct: 1137 WACANLGKQITNLLEDWQQGGQKQALVERLTEIYGPDEELPD----TEEGLVELARNLGK 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA  + I   L MA +++SGQSIL+DGLTGE F RPVTVGYIYMLKL+H+
Sbjct: 1193 GVPIATPVFDGARMDDIEGHLEMAGVNKSGQSILFDGLTGEQFKRPVTVGYIYMLKLHHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT+VYESIV G+DTFE G PESFNVLVKEM++LGL+++LENS
Sbjct: 1313 AGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS 1356


>gi|36333369|gb|AAP75742.1| RNA polymerase beta subunit [Bosea massiliensis]
          Length = 1370

 Score = 1724 bits (4464), Expect = 0.0,   Method: Composition-based stats.
 Identities = 882/1365 (64%), Positives = 1099/1365 (80%), Gaps = 15/1365 (1%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            G  RVRKFFGK  E+  +P+LIEVQKASYD FLM++     R +EGLQ+ FKSVFPI  F
Sbjct: 7    GRRRVRKFFGKLKEVAQMPNLIEVQKASYDQFLMVDEPKGGRGDEGLQSVFKSVFPIGDF 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            SGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+KDIKEQ
Sbjct: 67   SGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSVKDIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +
Sbjct: 127  DVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARIIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEILS FY  I Y++    W  P
Sbjct: 187  GSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILSRFYNTITYTRDAKGWRVP 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              A   M G K +  L+D DTGE V+E+GKKL +   + L EKG+KFL  T + L G Y+
Sbjct: 247  YDAE-RMKGFKATVDLIDADTGEVVVEAGKKLVARTARQLAEKGLKFLRATDEDLVGQYI 305

Query: 309  AEDIVNGETGEIYIEAGDVID----------EKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            AED+V+ +TGE++ EAG+ +           + +L E+ +    +IP+L +D +    YI
Sbjct: 306  AEDLVDFQTGEVHAEAGEELTMSVDAKTGEAKGNLVELINKGYTEIPVLDIDHITVGPYI 365

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R++AL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNM
Sbjct: 366  RNTLAVDKNSRREEALFDIYRVMRPGEPPTLETAENMFQSLFFDAERYDLSAVGRVKMNM 425

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD  D VR +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 426  RLDLDAEDTVRILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLG 485

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH 
Sbjct: 486  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHK 545

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 546  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 605

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYR++ DG+ T++++YLSAMEE    +AQAN+++D+DG  T++L+ CR AGE I+ P 
Sbjct: 606  ESPYRRIRDGRQTDEIIYLSAMEEAKYNVAQANAAVDKDGRLTDDLIVCRRAGEVIVTPV 665

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+V
Sbjct: 666  DKVDFQDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAV 725

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+RAGIV+QVDA RIVIR+ +   DP+  GVDIYRL KFQRSNQ+TC+ Q
Sbjct: 726  VARDSGAAIAARRAGIVDQVDATRIVIRASDEM-DPTKPGVDIYRLQKFQRSNQSTCITQ 784

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLV+VGD +++ DI+ADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SE++VSEDV
Sbjct: 785  RPLVRVGDVIKKGDIVADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSEKIVSEDV 844

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 845  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKI 904

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ +
Sbjct: 905  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQA 964

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN ++RL +IL G+  ++GPKGFKK TV++ + +SE+PR
Sbjct: 965  IEREEIERLAKDRDDEQAILDRNTFARLADILTGKVGLAGPKGFKKDTVITREGMSEFPR 1024

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1025 SQWWLFATADDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1084

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1085 AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1144

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA  GLGK+I + ++ Y+   DI  LR+  + V       E I+  D++ ++ + +
Sbjct: 1145 THLGWAAAGLGKQIGAALDAYRKGHDIKALRASFDAVYEDN---EIIASMDENELVEMGQ 1201

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VTVGYIYMLK
Sbjct: 1202 NLRRGVPIATPVFNGAKEADIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTVGYIYMLK 1261

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1262 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1321

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GRT+VYE+IV G DTFE G PE+FNVLVKEM++LGL+++L
Sbjct: 1322 SDDVAGRTKVYEAIVRGEDTFEAGIPETFNVLVKEMRSLGLNVEL 1366


>gi|307946277|ref|ZP_07661612.1| DNA-directed RNA polymerase, beta subunit [Roseibium sp. TrichSKD4]
 gi|307769941|gb|EFO29167.1| DNA-directed RNA polymerase, beta subunit [Roseibium sp. TrichSKD4]
          Length = 1379

 Score = 1723 bits (4463), Expect = 0.0,   Method: Composition-based stats.
 Identities = 909/1378 (65%), Positives = 1127/1378 (81%), Gaps = 4/1378 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMN-IAPDERPNEGLQAAFKS 61
                FNG  +VRK+FG   ++  +P+LIEVQKASYD FL ++ +    R N+GL+A F+S
Sbjct: 1    MTQTFNGRKKVRKYFGSIRDVAAMPNLIEVQKASYDQFLQVDEMPGGGRINDGLEAVFQS 60

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI+ F+G ++LEFVSYEF+ PK+DVD+C  RD+T+A PLK+TLRLIVFDVDE TGAKS
Sbjct: 61   VFPISDFAGTSILEFVSYEFEAPKYDVDECRQRDMTFAAPLKVTLRLIVFDVDEDTGAKS 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A
Sbjct: 121  VKDIKEQDVYMGDMPFMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFA 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALG+D EEIL+TFY ++ Y+++
Sbjct: 181  ARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGLDGEEILNTFYARVDYTRQ 240

Query: 242  GDF-WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             D  W  P    D + G K S  L+D D+GE V+E G+K+T+  +K L EK V  L +T 
Sbjct: 241  KDGGWRMPFDG-DRLKGTKASYDLIDADSGEVVVEGGRKITARTIKQLAEKNVTALKMTD 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AEDIV+ +TGEIY EAG+ I  K LEE+      D+P+L +D VN   YIRN
Sbjct: 300  EDLHGQYLAEDIVDAQTGEIYAEAGEEITGKLLEELVDRGYHDLPVLDIDHVNVGPYIRN 359

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNMRL
Sbjct: 360  TLSADKNESREDALFDIYRVMRPGEPPTIDTAEAMFQSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++D  D VR +RKEDI+ +I++L+ LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLL
Sbjct: 420  DVDAEDTVRVLRKEDILEVIRVLLQLRDGKGDIDDIDNLGNRRVRSVGELMENQYRVGLL 479

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 480  RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRR 539

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG VTNDVVYLSAMEE   Y+AQ+N+  D DG FTEEL+ CR AGE ++VP ++
Sbjct: 600  PYRKVKDGVVTNDVVYLSAMEEAKHYVAQSNAVYDADGRFTEELITCRHAGENMMVPSDR 659

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA
Sbjct: 660  VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVA 719

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SGAAI AKRAG+V+QVDA RIVIR+ E  LDP  SGVDIYRLMKFQRSNQNTC+NQRP
Sbjct: 720  RDSGAAIGAKRAGVVDQVDATRIVIRATED-LDPGKSGVDIYRLMKFQRSNQNTCINQRP 778

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD+V + DIIADGPSTDLGDLALG+N+LVAFMPW+GYNFEDS+L+SER+VS+DVFT
Sbjct: 779  LVRVGDKVHKGDIIADGPSTDLGDLALGKNVLVAFMPWNGYNFEDSILLSERIVSDDVFT 838

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIH+EEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAE++PGDILVGKITP
Sbjct: 839  SIHLEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAELHPGDILVGKITP 898

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGTVV+VR+FNRHG++K+ER++++E
Sbjct: 899  KGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTVVEVRVFNRHGVEKDERAMAIE 958

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            RE+IE LA+D+DDEQ ILDRN+Y RL E+L G+ AV+GPKGFKK   LS D ++E+PRSQ
Sbjct: 959  REEIERLAKDRDDEQAILDRNVYGRLAEMLLGKTAVAGPKGFKKGGELSGDALNEFPRSQ 1018

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFA  DEK    +E+L+ QY+ S+  LE RF +K+EK+Q GD++PPGV+++VKVFVA+
Sbjct: 1019 WWQFATDDEKFMSEIEALRGQYDDSRKRLEQRFIDKVEKLQRGDELPPGVMKMVKVFVAV 1078

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I PCEDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1079 KRKLQPGDKMAGRHGNKGVVSKINPCEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETH 1138

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +GWAC G+G +I  + ++Y+ +G+I  LR  + ++ G     + + +YDD+ V+R+AEQ 
Sbjct: 1139 MGWACRGMGLRIGEMYDEYRKSGEIEQLRGKIVEIYGDNMKGDNVKEYDDEGVVRLAEQL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GV ++TPVFDGA E  +   L++AD   SGQS+LYDG TGE FDR VTVGYIYMLKL+
Sbjct: 1199 KKGVSIATPVFDGAREPDVVEALKIADYHPSGQSVLYDGRTGEEFDRRVTVGYIYMLKLH 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+ +     +      
Sbjct: 1319 DVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELQRTDQPQISDEPAAD 1376


>gi|84499871|ref|ZP_00998137.1| DNA-directed RNA polymerase beta subunit [Oceanicola batsensis
            HTCC2597]
 gi|84391805|gb|EAQ04073.1| DNA-directed RNA polymerase beta subunit [Oceanicola batsensis
            HTCC2597]
          Length = 1408

 Score = 1721 bits (4457), Expect = 0.0,   Method: Composition-based stats.
 Identities = 846/1379 (61%), Positives = 1079/1379 (78%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQKASYD FL     P+    EG++  F+SV
Sbjct: 31   MAQTFLGQKRLRKYYGKIREVLEMPNLIEVQKASYDLFLKSGDEPEPLDGEGIKGVFQSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVFD+DE TGAKS+
Sbjct: 91   FPIKDFNETAILEFVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDMDEDTGAKSV 150

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 151  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 210

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y  R 
Sbjct: 211  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYETVDYKLRK 270

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD D+GE + E+ KK+T   +K L ++G V+ L +  D
Sbjct: 271  GQGWVTKFFPERVRGTRPTYDLVDADSGEVIAEATKKITPRAVKKLIDEGNVQNLLVPFD 330

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N ETG IY+EAGD +  +          +L+++  + I DIP+L +D+
Sbjct: 331  RIVGKFVAKDIINEETGAIYVEAGDELTLEYDKDGEITGGTLQDLLDAGITDIPVLDIDN 390

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            V+   Y+RNT+  DKN DR  AL+DIYRVMRPG+  T   A S+F+ LFFDS++YDLS V
Sbjct: 391  VSVGPYMRNTMAQDKNMDRNSALMDIYRVMRPGEPPTVEAASSLFDSLFFDSERYDLSAV 450

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI+A IK LV+LR+GKG +DDID+LGNRRVRSVGE++
Sbjct: 451  GRVKMNMRLALDAEDTQRTLRKEDIVACIKALVELRDGKGEVDDIDHLGNRRVRSVGELM 510

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 511  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 570

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 571  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 630

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR+V +G+VT++V Y+SA EE    +AQAN++LDE+G F  +LV  R +G
Sbjct: 631  VNKYGFIETPYRRVENGQVTDEVKYMSATEEMRHTVAQANANLDENGKFVNDLVNTRQSG 690

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 691  EYTLAPNETVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 750

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKR G+++QVDA RIV+R+ E  L+   +GVDIYRL KFQRSN
Sbjct: 751  GTGIEGVVARDSGAAIMAKRGGVIDQVDAQRIVVRATED-LELGDAGVDIYRLRKFQRSN 809

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V + ++IADGPSTDLG+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 810  QNTCINQRPLVKVGDTVEKGEVIADGPSTDLGELALGKNVVVAFMPWNGYNYEDSILISE 869

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 870  RIARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 929

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 930  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 989

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE+I  L RD+DDE  ILDRNIY+RL +++ G+ AV GPKG K ++ ++ D
Sbjct: 990  KDERALQIEREEIARLGRDRDDELAILDRNIYARLRDLIIGKTAVKGPKGVKANSEITED 1049

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S  PRS WWQ A+ +++  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1050 LLSSLPRSHWWQLALAEDQDAQIVEALNEQYEVQKRALDARFEDKVEKVRRGDDLPPGVM 1109

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++SR++P EDMPFL+DGTPVD  LNPLGVPSRM
Sbjct: 1110 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISRVVPQEDMPFLQDGTPVDFCLNPLGVPSRM 1169

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG K+   +++Y+ +GD++P+R  L+ V G   + E  S  D++
Sbjct: 1170 NVGQILETHMGWASRGLGLKVDEALDEYRRSGDMTPVRDALKIVYGDDVYDEGFSPMDEE 1229

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E  +N  L  A  +ESGQSILYDG TGE F RPVTV
Sbjct: 1230 RLLEAAGNVTRGVPIATPVFDGAKEHDVNDALVRAGFNESGQSILYDGRTGEQFARPVTV 1289

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1290 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1349

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1350 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEGEE 1408


>gi|254509921|ref|ZP_05121988.1| DNA-directed RNA polymerase, beta subunit [Rhodobacteraceae bacterium
            KLH11]
 gi|221533632|gb|EEE36620.1| DNA-directed RNA polymerase, beta subunit [Rhodobacteraceae bacterium
            KLH11]
          Length = 1382

 Score = 1720 bits (4455), Expect = 0.0,   Method: Composition-based stats.
 Identities = 837/1379 (60%), Positives = 1068/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A      EG++  F+SV
Sbjct: 5    MAQTFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDAEQPADGEGIKGVFQSV 64

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y+ + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 65   FPIKDFNETSVLEFVKYDLEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 124

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 125  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 184

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y    
Sbjct: 185  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYNTVSYKLDK 244

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  L+D  +GE + E+GKK+T   +K L ++G V  L +  D
Sbjct: 245  KKGWVTPFFPERVRGTRPTYDLIDAKSGEVIAEAGKKVTPRAVKKLIDEGNVTDLLVPFD 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G YVA+DI+N ETG IY+EAGD +  +          + +E+  + I DIP+L +D+
Sbjct: 305  NIVGKYVAKDIINEETGAIYVEAGDELTLEYDKDGDLIGGTAKELIDAGITDIPVLDIDN 364

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 365  VNVGPYMRNTMAQDKNMSRETALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 424

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD PD  R + +EDI+A IK LV+LR+GKG +DDID+LGNRRVRSVGE++
Sbjct: 425  GRVKMNMRLALDKPDTQRTLDREDIVACIKALVELRDGKGDVDDIDHLGNRRVRSVGELM 484

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 485  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 544

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 545  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 604

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V D +VT++V Y+SA EE    +AQAN++LD DG F  +LV  R AG
Sbjct: 605  VNKYGFIETPYRVVKDAEVTDEVHYMSATEEMRHTVAQANATLDADGKFINDLVSTRQAG 664

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 665  DYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 724

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAI AKRAGI++QVDA RIVIR+ E  L+   +GVDIYRL KFQRSN
Sbjct: 725  GTGIEEKVAIDSGAAIQAKRAGIIDQVDAQRIVIRATED-LELGDAGVDIYRLRKFQRSN 783

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPL+KVGD V++ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 784  QNTCINQRPLIKVGDTVQKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 843

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 844  RIARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 903

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 904  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 963

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K  +V++ +
Sbjct: 964  KDERALQIEREEVERLARDRDDELAILDRNIYARLQGLILGKTAVKGPKGVKAGSVITEE 1023

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWWQ A++ E+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1024 LLETLTRGQWWQLALEGEQDAQIVEALNEQYEVQKRALDARFEDKVEKVRRGDDLPPGVM 1083

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1084 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1143

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  I   + +Y+ +GD++P+R  ++   G   + E ++  D+D
Sbjct: 1144 NVGQILETHMGWAARGLGLNIDDALGEYRRSGDLTPVREAMKLAYGENVYEEGVAGMDED 1203

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  L  A   ESGQS+L+DG TGE F RPVTV
Sbjct: 1204 HLIEAAGNVTRGVPIATPVFDGAKEADVNDALVRAGFSESGQSVLFDGRTGEQFARPVTV 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1264 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1324 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1382


>gi|254419061|ref|ZP_05032785.1| DNA-directed RNA polymerase, beta subunit [Brevundimonas sp. BAL3]
 gi|196185238|gb|EDX80214.1| DNA-directed RNA polymerase, beta subunit [Brevundimonas sp. BAL3]
          Length = 1371

 Score = 1719 bits (4453), Expect = 0.0,   Method: Composition-based stats.
 Identities = 845/1367 (61%), Positives = 1075/1367 (78%), Gaps = 10/1367 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    F G  R+RK FG+ PE + +P+LIEVQ+ASY+ FL   + P +R  +G++A FK
Sbjct: 14   IASATSFTGKKRIRKSFGRIPEAVAMPNLIEVQRASYEQFLQREVRPGQRKEQGIEAVFK 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ DE TGA+
Sbjct: 74   SVFPIKDFNERAILEYVSYEFEDPKYDVEECIQRDMTYAAPLKVKLRLIVFETDEETGAR 133

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 134  SVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 193

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+D EFD+KD+++VRIDRRRK+P T+FLM LGMD EEIL TFY  + Y +
Sbjct: 194  AARVIPYRGSWLDFEFDAKDVVYVRIDRRRKLPATTFLMGLGMDGEEILKTFYETVPYEK 253

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RG+ W  P  A     G K    LVD DTGE + ++G+K+++   K L +     L + +
Sbjct: 254  RGEGWVTPYKAE-RWRGVKPEFDLVDADTGEVIAQAGQKISARAAKKLGDT-TTSLSLAA 311

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L   Y+A D VN ETGEI+ EAGD +D  ++E +  +    I +L +D V   AY+RN
Sbjct: 312  DALVTKYLANDAVNFETGEIFAEAGDELDAPTIEVLEQNGFTTIEVLDIDHVTVGAYMRN 371

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL D+YRVMRPG+  T   A++MFN LFFDS++YDLS VGRVKMNMRL
Sbjct: 372  TLRIDKNDTREDALFDVYRVMRPGEPPTPEAADNMFNSLFFDSERYDLSAVGRVKMNMRL 431

Query: 421  N-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
               +  D++R +RK+D++ +++ILV L++G+G IDDIDNLGNRRVRSVGE+L+NQYR+GL
Sbjct: 432  ETPEVSDEIRVLRKDDVLKVLQILVGLKDGRGEIDDIDNLGNRRVRSVGELLENQYRVGL 491

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 492  LRMERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKR 551

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE
Sbjct: 552  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIE 611

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYR+V DG   N+VVY+SAMEE    IAQAN  L ++GS  E+LV  R  GE  L+ R+
Sbjct: 612  SPYRRVKDGVAQNEVVYISAMEESKYTIAQANIEL-KNGSIVEDLVPGRINGESQLLNRD 670

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +D +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VV
Sbjct: 671  AVDMMDVSPKQVVSVAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVV 730

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SGA +VA+R G+VEQ+D  RIV+R+  GD+D + SGVDIYRL KFQRSNQ+TC+NQR
Sbjct: 731  AVDSGAVVVARREGVVEQIDGTRIVVRAT-GDVDAARSGVDIYRLSKFQRSNQSTCINQR 789

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+V+VGD+V+  D+IADGPSTDLG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DVF
Sbjct: 790  PIVRVGDQVKAGDVIADGPSTDLGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVF 849

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIH+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+T
Sbjct: 850  TSIHLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVT 909

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++
Sbjct: 910  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERAMAI 969

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ER +IE L +D+DDE  IL+RN+Y RL  ++ G+NAVSGPKG  +   L+ + ++E  R 
Sbjct: 970  ERAEIERLGKDRDDELKILERNVYGRLKPLILGKNAVSGPKGIGRGE-LTEEKLAEVSRG 1028

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
             WWQ A+ DEK    +E++K Q+E ++  L+ RF++K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1029 LWWQIALDDEKAMGELEAMKRQFEDARKQLDRRFEDKVEKLQRGDELPPGVMKMVKVFVA 1088

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG++S+ILP EDMP L+DGT VD+VLNPLGVPSRMN+GQIFET
Sbjct: 1089 VKRKLQPGDKMAGRHGNKGVISKILPIEDMPHLEDGTHVDVVLNPLGVPSRMNIGQIFET 1148

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA  GLGK+I  L+  ++  G    L   L  + G  +   +    D++ ++ +A+ 
Sbjct: 1149 HLGWAAAGLGKQISGLLEAWQQGGQKQALIDRLTHIYGPETPLPQ----DEEELIELAKN 1204

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               GVP +TPVFDGA    I  +L  A L++S QSILYDG TGE F RPVTVGYIYMLKL
Sbjct: 1205 LSKGVPFATPVFDGAHIGDIERLLEEAGLNKSAQSILYDGQTGEQFKRPVTVGYIYMLKL 1264

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1265 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1324

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT+VYE+IV G+D+FE G PESFNVL+KEM++LGL+++LENS
Sbjct: 1325 DDVAGRTKVYEAIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELENS 1371


>gi|53804616|ref|YP_113541.1| DNA-directed RNA polymerase subunit beta [Methylococcus capsulatus
            str. Bath]
 gi|81682419|sp|Q60A06|RPOB_METCA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|53758377|gb|AAU92668.1| DNA-directed RNA polymerase, beta subunit [Methylococcus capsulatus
            str. Bath]
          Length = 1358

 Score = 1719 bits (4452), Expect = 0.0,   Method: Composition-based stats.
 Identities = 744/1364 (54%), Positives = 985/1364 (72%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK  +++++P L+  Q  SY  FL ++  P  R +EGL AA KSV
Sbjct: 1    MAYSFTEKKRIRKSFGKRQDVLEVPYLLATQVDSYRRFLQLDKQPAARSDEGLHAALKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG  +LE+VSY    P FDV +C  R  TYA PL++ +RL+V+D D   GAK +
Sbjct: 61   FPIKSHSGNIVLEYVSYRLGDPVFDVKECQQRGTTYAAPLRVLVRLVVYDKDAPVGAKVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ IYMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL+  
Sbjct: 121  RDIKEQEIYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P T  L ALG D+E+I++ F+    +    
Sbjct: 181  RIIPYRGSWLDFEFDHKDCVYVRIDRRRKLPATVLLRALGYDNEQIIAEFFDTNRFLLSS 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +   D  + V+E   ++T+  ++ L+++ V  L +  D 
Sbjct: 241  AGIQLELIPERL-RGDIASFDIRLGD--QIVVEKDHRITARHIRMLQKENVNLLDVPKDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++V+  TGE+  +    I E     +  + I +I  LYV+ ++   YI NT+
Sbjct: 298  LYGKILAHNVVDTSTGELIAKVNQEITEDVYARLVAAAIPEIRTLYVNDLDRGPYISNTM 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  + + DAL++IYR+MRPG+  T   A+++F  LFF +++YDLS VGR+K N RL  
Sbjct: 358  RIDLTETQLDALVEIYRMMRPGEPPTKEAAQTLFENLFFSAERYDLSAVGRMKFNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
              P     +  +DIIA++K L+++RNG GT+DDID+LGNRRVRSVGEM++NQ+RLGL+R+
Sbjct: 418  TDPTGPGVLENDDIIAVLKELINIRNGGGTVDDIDHLGNRRVRSVGEMVENQFRLGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D D +MPQ++INAKPV +++ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 478  ERAVKERLSLPDADGLMPQEIINAKPVAASIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+AR RAG E+RDVH THYGR+CP ET EG NIGL++SL  ++R N YGF+ETPY
Sbjct: 538  ALGPGGLARERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLAVYSRTNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG+VT+ + YLSA+EE   YIAQA++S+DE+G   +ELV CR   E  L  RE I+
Sbjct: 598  RKVIDGRVTDQIEYLSAIEEGQYYIAQASASVDENGMLKDELVSCRHKDEFTLASRENIN 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S KQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTGME +VA+ 
Sbjct: 658  YMDVSSKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRTEKPLVGTGMERIVARD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG A+VAKR G VE VDA RIV+R  + + +    GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 718  SGVAVVAKRGGTVEFVDASRIVVRVNDEETEAGVPGVDIYNLTKYTRSNQNTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V RND++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+I
Sbjct: 778  KPGDVVARNDVLADGPSTDMGELALGQNLLVAFMPWNGYNFEDSILISERVVQDDRFTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 838  HIEEKTCVARDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKAGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R G+ K+ER+  +E  
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMDGTVIDVQVFTRDGVKKDERARQIEEA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE + +D +D+  I++++ Y R  +++ G+ A  GP G K+   ++ + +     +QW 
Sbjct: 958  EIERVRKDLNDQLRIIEKDFYQRAEQMVLGKVADMGPGGLKRGATITREYLDSIKPAQWL 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +QDE V   +E++  Q    +  +  R + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1018 EIRLQDEDVNLQIEAIAEQIAQQREEIAKRLEEKRRKITMGDDLAPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++SRI+P EDMP+  DGTPVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1078 RIQPGDKMAGRHGNKGVISRIVPVEDMPYSADGTPVDIVLNPLGVPSRMNVGQVLETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+G KI  ++   +A   I  +RSFL +V       E I+   D  VL +A   + 
Sbjct: 1138 WAAKGVGLKIGRML---EAKAKIEEIRSFLTQVYNVSGRQEDIASLSDAEVLELAGNLQD 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA EE I +MLR+ADL ESGQ+ L+DG TG+ FDRPVTVGY+YMLKLNH+
Sbjct: 1195 GVPMATPVFDGATEEDIKAMLRLADLPESGQATLFDGRTGDVFDRPVTVGYMYMLKLNHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E   PESFNVL+KE+++LG++I+LE  
Sbjct: 1315 NGRTKMYKNIVDGDHRMEAAMPESFNVLIKEIRSLGINIELEQD 1358


>gi|302382706|ref|YP_003818529.1| DNA-directed RNA polymerase subunit beta [Brevundimonas subvibrioides
            ATCC 15264]
 gi|302193334|gb|ADL00906.1| DNA-directed RNA polymerase, beta subunit [Brevundimonas
            subvibrioides ATCC 15264]
          Length = 1371

 Score = 1718 bits (4450), Expect = 0.0,   Method: Composition-based stats.
 Identities = 848/1367 (62%), Positives = 1067/1367 (78%), Gaps = 10/1367 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    F G  R+RK FG+ PE + +P+LIEVQ+ SY+ FL   + P  R  +G++A FK
Sbjct: 14   IASATTFTGKKRIRKSFGRIPEAVQMPNLIEVQRESYEQFLQREVRPGVRKEQGIEAVFK 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ DE TGA+
Sbjct: 74   SVFPIKDFNERAVLEYVSYEFEDPKYDVEECIQRDMTYAAPLKVKLRLIVFEADEETGAR 133

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 134  SVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 193

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+D EFD+KDI+ VRIDRRRK+P ++FLMALGMD EEIL TFY  + Y +
Sbjct: 194  AARVIPYRGSWLDFEFDAKDIVFVRIDRRRKLPASTFLMALGMDGEEILRTFYETVPYEK 253

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGD W  P  A     G K    LVD DTGE V ++G+K+++   K L +   K L + +
Sbjct: 254  RGDGWVTPYKAE-RWRGVKPEFDLVDADTGEIVAQAGQKISARAAKKLGDT-TKSLSLAA 311

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L   Y+A D VN ETGEIY EAGD +D  ++E +       I +L +D V   AY+RN
Sbjct: 312  DALVTRYLAADAVNYETGEIYAEAGDELDAPTIELLEERGFTTIDVLDIDHVTVGAYMRN 371

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DK+  R+DAL DIYRVMRPG+  T   AE+MFN LFFD ++YDLS VGRVKMNMRL
Sbjct: 372  TLRVDKSTGREDALFDIYRVMRPGEPPTPEAAEAMFNSLFFDGERYDLSAVGRVKMNMRL 431

Query: 421  N-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
               +  D++R ++K+D++ +++ILV L++G+G IDDIDNLGNRRVRSVGE+L+NQYR+GL
Sbjct: 432  ETPEVSDEIRVLQKDDVLKVLQILVGLKDGRGEIDDIDNLGNRRVRSVGELLENQYRVGL 491

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSVDID+VMP DLINAKP  ++V EFF SSQLSQ  +  N LS ITH R
Sbjct: 492  LRMERAIKERMSSVDIDTVMPHDLINAKPAAASVREFFGSSQLSQFMDQTNPLSEITHKR 551

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE
Sbjct: 552  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIE 611

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYR+V DGK  ++VVY+SAMEE    IAQAN +L +DG   +ELV  R  G+  L+ R 
Sbjct: 612  SPYRRVKDGKALDEVVYISAMEESKYTIAQANIAL-KDGMIVDELVPGRINGDSQLLIRA 670

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +D +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VV
Sbjct: 671  DVDMMDVSPKQVVSVAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVV 730

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGA +VA+R G+VEQ+D  RIV+R+  GDLD   SGVDIYRL KFQRSNQ+TC+NQR
Sbjct: 731  ARDSGAVVVARRDGVVEQIDGTRIVVRAT-GDLDAGRSGVDIYRLSKFQRSNQSTCINQR 789

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+V+VGDEV+  D+IADGPSTDLG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DVF
Sbjct: 790  PIVRVGDEVKTGDVIADGPSTDLGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVF 849

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIH+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDIL GK+T
Sbjct: 850  TSIHLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILCGKVT 909

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++S+
Sbjct: 910  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERAMSI 969

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ER++IE L +D+DDE  IL+RN Y RL  +L G+NAVSGPKG  +  V +   + E  R 
Sbjct: 970  ERDEIERLGKDRDDELAILERNTYGRLKPLLLGKNAVSGPKGLGRGEV-TDAKLGELSRG 1028

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
             WWQ A+ DEK    +E +K  +E ++  L+ RF++K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1029 LWWQIALDDEKAMGELEQMKKSFEDARKALDRRFEDKVEKLQRGDELPPGVMKMVKVFVA 1088

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG++S+ILP EDMP L+DGT VD+VLNPLGVPSRMN+GQIFET
Sbjct: 1089 VKRKLQPGDKMAGRHGNKGVISKILPIEDMPHLEDGTSVDVVLNPLGVPSRMNIGQIFET 1148

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA  GLGK+I+ L+  ++  G    L   L  + G  +   +    D+  ++ +A+ 
Sbjct: 1149 HLGWASAGLGKQIQGLLEAWQGGGQKQALIDHLTGIYGEDTPLPQ----DEHELVELAQN 1204

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               GVP +TPVFDGA    I  +L  A L+ SGQSI+YDG TGE F RPVTVGYIYMLKL
Sbjct: 1205 LSKGVPFATPVFDGAHISDIEDLLEKAGLERSGQSIVYDGTTGEQFKRPVTVGYIYMLKL 1264

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1265 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1324

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT+VYE+IV G+D+FE G PESFNVL+KEM++LGL+++LENS
Sbjct: 1325 DDVAGRTKVYEAIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELENS 1371


>gi|295688173|ref|YP_003591866.1| DNA-directed RNA polymerase subunit beta [Caulobacter segnis ATCC
            21756]
 gi|295430076|gb|ADG09248.1| DNA-directed RNA polymerase, beta subunit [Caulobacter segnis ATCC
            21756]
          Length = 1356

 Score = 1718 bits (4450), Expect = 0.0,   Method: Composition-based stats.
 Identities = 850/1364 (62%), Positives = 1070/1364 (78%), Gaps = 8/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK FG+ PE + +P+LIEVQ++SY+ FL   + P +R +EG++A FKSV
Sbjct: 1    MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQREVRPGQRRDEGVEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LE+VSYEF+ PK+DV++C+ RD+T+A PLK+ LRLIVF+ +E TGA+S+
Sbjct: 61   FPIKDFNERAVLEYVSYEFEEPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDRRRK+P T+FL ALGMD EEIL+TFY  + + +R 
Sbjct: 181  RVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRA 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P        G K    LVD DTGE+V  +G K+T+   K   + G+K L +  + 
Sbjct: 241  GGWATPYKPE-RWRGVKPEFPLVDADTGEEVAPAGTKITARQAKKFADGGLKTLLLAPEA 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A D VN  TGEIY EAGD +D  +++ +       I +L +D V   AY+RNTL
Sbjct: 300  LTGRYLARDAVNVGTGEIYAEAGDELDVPTIQALADQGFSTIDVLDIDHVTVGAYMRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFFDS++YDLS+VGRVKMNMRL  
Sbjct: 360  RVDKNAIREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDSERYDLSSVGRVKMNMRLEQ 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D+VR +RKED++A++K+LV LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 420  DVSDEVRILRKEDVLAVLKVLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE+PY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGK  ++VVY+SAMEE    IAQ+N  + + G   E+LV  R  GE  L+ +E +D
Sbjct: 600  RRVKDGKPLDEVVYMSAMEESKHVIAQSNIKV-DAGEIVEDLVPGRINGEPTLLQKETVD 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL++++AP VGTGME+VVA+ 
Sbjct: 659  LMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA ++AKR G+VEQ+D  RIVIR+ E   D + SGVDIYR+ KFQRSNQ+TC+NQRPLV
Sbjct: 719  SGAVVIAKRTGVVEQIDGTRIVIRATEE-TDAARSGVDIYRMSKFQRSNQSTCINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD++   DIIADGPST+LG+LALGRN LVAFMPW+GYNFEDS+LISER+V +DVFTSI
Sbjct: 778  KVGDKIVAGDIIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 838  HIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++ER 
Sbjct: 898  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALAIERA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+ L +D+DDE  IL+RNI  RL E+L G  A+SGPKG  +   +++D +S+     WW
Sbjct: 958  EIDRLGKDRDDEFAILNRNISGRLRELLIGNVALSGPKGLSRGE-ITADALSQIQPGLWW 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A++DEK    +ESL+  ++ ++  L+ RF++K++K+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1017 QIALEDEKAMGELESLRRLFDENRKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRILP EDMPFL DGT VD+VLNPLGVPSRMNVGQIFETHLG
Sbjct: 1077 KLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLGVPSRMNVGQIFETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC  LGK+I +L+ D++A G    L   L  + G      +      + ++ +A+    
Sbjct: 1137 WACANLGKQITNLMEDWQAGGQKQALIDRLRDIYGPDEELPETE----EELIELAKNLGK 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA    I   L MA +++SGQSILYDGLTGE F RPVTVGYIYMLKL+H+
Sbjct: 1193 GVPIATPVFDGARMSDIEDHLEMAGVNKSGQSILYDGLTGEQFKRPVTVGYIYMLKLHHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT+VYESIV G+DTFE G PESFNVLVKEM++LGL+++LENS
Sbjct: 1313 AGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS 1356


>gi|254504227|ref|ZP_05116378.1| DNA-directed RNA polymerase, beta subunit [Labrenzia alexandrii
            DFL-11]
 gi|222440298|gb|EEE46977.1| DNA-directed RNA polymerase, beta subunit [Labrenzia alexandrii
            DFL-11]
          Length = 1409

 Score = 1718 bits (4450), Expect = 0.0,   Method: Composition-based stats.
 Identities = 903/1379 (65%), Positives = 1126/1379 (81%), Gaps = 4/1379 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMN-IAPDERPNEGLQAAFK 60
                 FNG  +VRK+FG   ++  +P+LIEVQKASYD FL ++ +    R +EGL+A F+
Sbjct: 30   TMTQTFNGRKKVRKYFGSIRDVAAMPNLIEVQKASYDQFLQVDEMPGGGRKDEGLEAVFQ 89

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ F+G ++LEFVSYEF+ PK+DVD+C  RD+T+A PLK+TLRLIVFDVDE TGAK
Sbjct: 90   SVFPISDFAGTSLLEFVSYEFEAPKYDVDECRQRDMTFAAPLKVTLRLIVFDVDEDTGAK 149

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+P MT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 150  SVKDIKEQDVYMGDMPFMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 209

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALG+D EE+L+TFY ++ Y++
Sbjct: 210  AARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGLDGEEVLNTFYKQVEYTR 269

Query: 241  RGDF-WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            + D  W  P     L  G K S  L+D D+G+ V+E G+K+T+  +K L EKGV  L +T
Sbjct: 270  QKDGSWRMPFDGERL-KGTKASYDLIDADSGDVVVEGGRKITARTIKQLGEKGVTALKVT 328

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             + L G Y+AEDIV+ ++GEIY EAG  I  K LEE+      D+ IL +D VN   YIR
Sbjct: 329  DEDLHGQYLAEDIVDAQSGEIYAEAGGEITGKLLEELVDRGYHDLTILDIDHVNTGPYIR 388

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF  LFFD ++YDLS VGRVKMNMR
Sbjct: 389  NTLNVDKNESREDALFDIYRVMRPGEPPTIDTAEAMFQSLFFDDERYDLSAVGRVKMNMR 448

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L++D  D VR +RKEDI+ +I++L++LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GL
Sbjct: 449  LDVDAEDTVRVLRKEDILEVIRVLLELRDGKGDIDDIDNLGNRRVRSVGELMENQYRVGL 508

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH R
Sbjct: 509  LRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKR 568

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE
Sbjct: 569  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIE 628

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYRKV DG VTN+VVYLSAMEE   Y+AQ+N+  D++G FT EL+ CR AGE ++VP E
Sbjct: 629  SPYRKVKDGTVTNEVVYLSAMEEAKHYVAQSNAEYDDEGRFTTELITCRHAGENMMVPSE 688

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            K+D +D SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPL++AEAPFVGTGMESVV
Sbjct: 689  KVDLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLVRAEAPFVGTGMESVV 748

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+RAG+V+QVDA RIVIR+ E  LDP  SGVDIYRL K+QRSNQNTC+NQR
Sbjct: 749  ARDSGAAIGARRAGVVDQVDATRIVIRATEE-LDPGRSGVDIYRLQKYQRSNQNTCINQR 807

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+L+SER+VS+DVF
Sbjct: 808  PLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILLSERIVSDDVF 867

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIH+EEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAE++PGDILVGKIT
Sbjct: 868  TSIHLEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAELHPGDILVGKIT 927

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGTVV+VR+FNRHG++K+ER++++
Sbjct: 928  PKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTVVEVRVFNRHGVEKDERAMAI 987

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL E+L  + AV+GPKGFKK TVL+ D+++++PRS
Sbjct: 988  EREEIERLAKDRDDEQAILDRNVYGRLAEMLMDKTAVAGPKGFKKDTVLTGDVLNDFPRS 1047

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            QWWQFA +DEK    +E+L+ QY+ S+  LE RF +K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1048 QWWQFASEDEKFMSEIEALRGQYDDSRKRLEQRFIDKVEKLQRGDELPPGVMKMVKVFVA 1107

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VS+I PCEDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1108 VKRKLQPGDKMAGRHGNKGVVSKINPCEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 1167

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            H+GWAC G+G +I  + ++Y+  G+I  LR  + ++ G     + + ++DD+ V+++AEQ
Sbjct: 1168 HMGWACRGMGLRIGEMYDEYRKTGEIEKLRGKVIEIYGDNMKGDAVKEFDDEGVVKLAEQ 1227

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K GV ++TPVFDGA E  +   L++AD D SGQS L+DG TGE FDR VTVGYIYMLKL
Sbjct: 1228 LKKGVSIATPVFDGAREPDVVDALKIADFDTSGQSTLFDGRTGEEFDRKVTVGYIYMLKL 1287

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1288 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1347

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            DDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+ +      + E   
Sbjct: 1348 DDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELQRTDVPAIGEEETAD 1406


>gi|315499974|ref|YP_004088777.1| DNA-directed RNA polymerase, beta subunit [Asticcacaulis excentricus
            CB 48]
 gi|315417986|gb|ADU14626.1| DNA-directed RNA polymerase, beta subunit [Asticcacaulis excentricus
            CB 48]
          Length = 1357

 Score = 1718 bits (4449), Expect = 0.0,   Method: Composition-based stats.
 Identities = 854/1366 (62%), Positives = 1070/1366 (78%), Gaps = 9/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    R+RK FG+ PE I +P+LIEVQ++SY+ FL   +   ER ++GL+A FKSV
Sbjct: 1    MALSFTEKKRIRKSFGRIPEAIRMPNLIEVQRSSYEQFLQRFVRASERVDDGLEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+  F+  A LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ DE TGA+S+
Sbjct: 61   FPVKDFNERATLEYVSYEFEEPKYDVEECIQRDITYAAPLKVKLRLIVFETDEDTGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+  
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFGA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++VRIDRRRK+P T+FL ALGMD EEIL+TFY  + Y +R 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLSALGMDGEEILTTFYDVVPYEKRD 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P    +   G K    L+D D+GE V ++G K+++   K L +  VK L ++ D 
Sbjct: 241  AGWVTPY-KFERWRGVKPEFDLIDADSGEVVAQAGTKISARTAKKLGDT-VKALLLSPDA 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A D VN ETGEIY EAGD +D  +++ +       I +L +D V   AY+RNTL
Sbjct: 299  LNGKYLARDAVNFETGEIYAEAGDELDPAAIKVLEEQGFTTIDVLDIDHVTVGAYLRNTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFF+ ++YDLS VGRVKMNMRL  
Sbjct: 359  RVDKNTSREDALFDIYRVMRPGEPPTIEAAEAMFQGLFFELERYDLSAVGRVKMNMRLEQ 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D  R +RK+DI+ I++IL+ LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 419  DVADSERTLRKDDILKILRILIGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 479  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE+PY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGK  ++VVY+SAMEE    IAQAN  L ++G   E+LV  R  GE  L P   +D
Sbjct: 599  RKVIDGKPQDEVVYMSAMEESKHVIAQANIKLGDEGI-VEDLVPGRVNGEPGLQPAPTVD 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KA+APFVGTGMESVVA+ 
Sbjct: 658  YMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPFVGTGMESVVARD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA I A+R G++EQVDA RIV+R+ +  LDP+  GVDIYRL KFQRSNQNTC+NQRP+V
Sbjct: 718  SGATIAARRTGVIEQVDATRIVVRATDE-LDPTKPGVDIYRLSKFQRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD+V   DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+LISER+V +D+FTSI
Sbjct: 777  NVGDKVSAGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILISERIVRDDIFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+V+VR+FNRHG+DK+ER++++ER 
Sbjct: 897  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFNRHGVDKDERAMAIERA 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE L +D+DDE  IL+RNIY RL E++ GQ AVSGPKG  +   ++ + +SE  +  WW
Sbjct: 957  EIERLGKDRDDELSILERNIYGRLKEVILGQTAVSGPKGLGRGE-ITEEKLSEISKGLWW 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A++DEK+   +E++K Q+E ++  L+ RF++K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1016 QIALEDEKLMGELEAMKRQFEEARKRLDRRFEDKVEKLQRGDELPPGVMKMVKVFVAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+ILP EDMPFL DG  VDIVLNPLGVPSRMNVGQIFETHLG
Sbjct: 1076 KLQPGDKMAGRHGNKGVISKILPVEDMPFLADGEHVDIVLNPLGVPSRMNVGQIFETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC  +GK+I +L+ +++  G    L   L+   G      +     ++ ++++A+    
Sbjct: 1136 WACANIGKQITNLLEEWQNGGQKQALIDHLKGAYGADQELPE----TEEELIQLAKNLAR 1191

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA    I +ML  A LD SGQSILYDGLTGE F RPVTVG IYMLKL+H+
Sbjct: 1192 GVPIATPVFDGAHINDIENMLEFAGLDRSGQSILYDGLTGEQFKRPVTVGIIYMLKLHHL 1251

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1252 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1311

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT+VYE+IV G+D+FE G PESFNVL+KEM++LGL+++LEN + 
Sbjct: 1312 AGRTKVYEAIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELENGQG 1357


>gi|254470475|ref|ZP_05083879.1| DNA-directed RNA polymerase, beta subunit [Pseudovibrio sp. JE062]
 gi|211960786|gb|EEA95982.1| DNA-directed RNA polymerase, beta subunit [Pseudovibrio sp. JE062]
          Length = 1380

 Score = 1717 bits (4448), Expect = 0.0,   Method: Composition-based stats.
 Identities = 902/1374 (65%), Positives = 1119/1374 (81%), Gaps = 3/1374 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                FNG  RVRK+FG   ++  +P+LIEVQKASYD FL ++   D R +EGL+A FKSV
Sbjct: 1    MTQTFNGRKRVRKYFGSIRDVAAMPNLIEVQKASYDQFLQVDKVEDSRVDEGLEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+G ++LEFV YEF+ PK+DV++C  RD+TYA PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPISDFAGNSLLEFVDYEFEAPKYDVEECRQRDMTYAAPLKLTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+P MT +GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYMGDIPFMTDNGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALG+DSE+IL+TFY +I Y + G
Sbjct: 181  RVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGLDSEDILNTFYKRIDYVRSG 240

Query: 243  DF-WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            +  W  P   A L  G K  + +VD  +GE V+E+GKK+T+  ++ L EKGVK L  T +
Sbjct: 241  ENSWSVPFDGARL-KGTKAVNDMVDAASGEVVVEAGKKITARTIRQLTEKGVKSLKGTDE 299

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G Y+AEDIV+  TGEIY EAG+ + EK L E+      D+P+L +D VN   YIRNT
Sbjct: 300  DLYGQYLAEDIVDMGTGEIYAEAGEELTEKLLHELIERGYHDLPVLDIDYVNVGPYIRNT 359

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DKN  R+ AL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNMRL+
Sbjct: 360  LAADKNDSREGALFDIYRVMRPGEPPTLETAEAMFQSLFFDAERYDLSAVGRVKMNMRLD 419

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            L+  D VR +RKEDI+++I +L+DLR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLR
Sbjct: 420  LECEDTVRVLRKEDILSVIGLLLDLRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLR 479

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRL
Sbjct: 480  MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRL 539

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 540  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 599

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT DVVYLSAMEE   Y++QAN+ ++EDGSF  +LV CR AGE ILV  +++
Sbjct: 600  YRRVIDGKVTKDVVYLSAMEESKYYVSQANAEMNEDGSFVNDLVQCRHAGENILVTSDRV 659

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPL++A+APFVGTGME +VA+
Sbjct: 660  DLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLVRAQAPFVGTGMEPIVAR 719

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRLMKFQRSNQ+TC+NQRPL
Sbjct: 720  DSGAAIGARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLMKFQRSNQDTCINQRPL 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD VR+ DIIADGPSTDLGDLALGRN++VAFMPW+GYNFEDS+L+SER+V +DVFTS
Sbjct: 779  VNVGDRVRKGDIIADGPSTDLGDLALGRNVMVAFMPWNGYNFEDSILLSERIVRDDVFTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IH+EEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ VGAEV PGDILVGKITPK
Sbjct: 839  IHLEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYVGAEVKPGDILVGKITPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTSLR+  GV GTVV+VR+FNRHG++K+ER++++ER
Sbjct: 899  GESPMTPEEKLLRAIFGEKASDVRDTSLRLSPGVVGTVVEVRVFNRHGVEKDERAMAIER 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN+Y RL E++ G  AV GPK F+K   +  ++++E+PRSQW
Sbjct: 959  EEIERLAKDRDDEQAILDRNVYGRLAEMIMGHVAVGGPKNFRKGVEIDGNVLNEFPRSQW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            WQFAV+DE++   +E+L+  Y+ S+  LE RF +K+EK+Q GD++PPGV+++VKVFVA+K
Sbjct: 1019 WQFAVEDEQLMSELEALRGSYDESRKRLEQRFIDKVEKLQRGDELPPGVMKMVKVFVAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VS+I PCEDMPFL+DG  VDIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1079 RKIQPGDKMAGRHGNKGVVSKINPCEDMPFLEDGQHVDIVLNPLGVPSRMNVGQILETHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC G+G+KI  L ++Y+ +G+I  LR  + ++ G     E + +YDD+ + ++ EQ +
Sbjct: 1139 GWACAGMGQKIGELYDEYRKSGEIEQLRGKVVEIYGDNLKGEPVKEYDDEGIAKLGEQLR 1198

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GV ++TPVFDGA E  +  ML +A++  SGQS L+DG TGE FDR VTVGYIYMLKL+H
Sbjct: 1199 HGVSIATPVFDGAREPDVVDMLNIAEMKPSGQSTLFDGRTGEQFDRQVTVGYIYMLKLHH 1258

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1259 LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1318

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            V GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L++   ++S   +
Sbjct: 1319 VAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELQDKEPRHSTNDD 1372


>gi|89071237|ref|ZP_01158416.1| DNA-directed RNA polymerase beta subunit [Oceanicola granulosus
            HTCC2516]
 gi|89043223|gb|EAR49453.1| DNA-directed RNA polymerase beta subunit [Oceanicola granulosus
            HTCC2516]
          Length = 1381

 Score = 1717 bits (4447), Expect = 0.0,   Method: Composition-based stats.
 Identities = 830/1370 (60%), Positives = 1066/1370 (77%), Gaps = 12/1370 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL     P+    EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLNSGDQPEPMDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVRYELERPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++ RIDRRRK+PVT+ L ALGMD E I++ +Y  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVYARIDRRRKLPVTTLLYALGMDQEAIMNAYYNTVTYRFEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + +  LVD  TGE + ++G+K+T   +K L ++G V  L +   
Sbjct: 241  NKGWVTKFFPERVRGTRPAFDLVDAATGEVIAKAGEKVTPRQVKKLIDEGEVTELLVPHS 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI+N E G IY+EAGD +  +          +++++  + + DIP+L +D+
Sbjct: 301  HIAGKFVATDIINEENGAIYVEAGDELTIERDKEGEIIGGTVKDLLDAGVTDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAQDKNMNRETALMDIYRVMRPGEPPTVDAASTLFDSLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI++ IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVSCIKALVELRDGKGEIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V D +VT++V Y+SA EE    +AQAN++LD+ G+F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVKDAQVTDEVHYMSATEEMRHTVAQANATLDDAGNFLNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP+V
Sbjct: 661  EYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPYV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAIVA+RAG+++QVDA RIV+R+ E  L+P   GVDIYR+ KFQRSN
Sbjct: 721  GTGIEGKVALDSGAAIVARRAGVIDQVDAARIVVRATED-LEPGDPGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDTVGKGEVIADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V +DVFTSIHI+EFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PG
Sbjct: 840  RIVKDDVFTSIHIDEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVGPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGDFGTIVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E L+RD+DDE  ILDRNIY+RL  +L G+    GP+G K    + ++
Sbjct: 960  KDERALQIEREEVERLSRDRDDELAILDRNIYARLRTLLDGKTVAKGPRGIKAGATIDAE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+   PRS WWQ A+++E   + +E+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLDSLPRSHWWQIALKEEADAQILEALNEQYEAQKRQLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD VLNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPEEDMPFLADGTPVDFVLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG +I   + +Y+ +GD++P+R  +    G   + E +   D+ 
Sbjct: 1140 NVGQILETHMGWAARGLGIQIDEALQEYRRSGDLTPVREAMRLAYGDDVYDEGVESMDEQ 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E  ++  LR A  DESGQS+L+DG TGE F R VTV
Sbjct: 1200 LLLEAAGNVTRGVPIATPVFDGAKEADVDDALRRAGFDESGQSVLFDGRTGEQFSRKVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL++
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNM 1369


>gi|86137185|ref|ZP_01055763.1| DNA-directed RNA polymerase beta subunit [Roseobacter sp. MED193]
 gi|85826509|gb|EAQ46706.1| DNA-directed RNA polymerase beta subunit [Roseobacter sp. MED193]
          Length = 1378

 Score = 1717 bits (4447), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1379 (60%), Positives = 1072/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    +P+    EG++  F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDSPEPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVKYSFEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + YS   
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYNTVNYSLDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      D + G + +  LVD  +GE   E+GKK+T   +K + ++G +  L +  +
Sbjct: 241  SRGWVTPFFPDRVRGTRPTFDLVDAASGEVFAEAGKKVTPRAVKKMIDEGAITNLLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N E G IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 301  NIIGKFVAKDIINEENGAIYVEAGDELTMEYDKGGDIIGGTVKELMDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAADKNMGRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI++ IK LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVSCIKALVDLRDGRGGIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V +G+VT++V Y+SA EE    +AQAN+SLDE+G FT +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVNEGQVTDEVHYMSATEEMRHTVAQANASLDENGKFTNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPSESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKR G+++QVDA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRGGVIDQVDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLV+VG EVR+ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVRVGQEVRKGEVIADGPSTDIGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GT+V+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTIVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  +L G+ AV GPKG +    +  D
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLRSMLLGKTAVKGPKGIRTGAAIDED 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
             +S+  R QWW  A+++E+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 ALSQLSRGQWWMIALEEEQDAKVVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL+DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLQDGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG ++   + +++ +GD++P+R  ++   G   + E ++D  +D
Sbjct: 1140 NVGQILETHMGWAARGLGIQVDDALQEFRRSGDLTPVRDAMKHAYGENVYEEGLADMSED 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E  +N  L  A  D SGQS+LYDG TGE F RPVTV
Sbjct: 1200 DLLEAAGNVTRGVPIATPVFDGAKEADVNDALVRAGFDTSGQSVLYDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEEE 1378


>gi|114570352|ref|YP_757032.1| DNA-directed RNA polymerase subunit beta [Maricaulis maris MCS10]
 gi|122315780|sp|Q0ANP3|RPOB_MARMM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114340814|gb|ABI66094.1| DNA-directed RNA polymerase subunit beta [Maricaulis maris MCS10]
          Length = 1357

 Score = 1716 bits (4445), Expect = 0.0,   Method: Composition-based stats.
 Identities = 858/1364 (62%), Positives = 1075/1364 (78%), Gaps = 9/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G+ F G  R+RK FG+ PE + +P+LIEVQK+SY+HFLM  +   ER + G+QA FKSV
Sbjct: 1    MGLSFTGKKRIRKSFGRIPETVAMPNLIEVQKSSYEHFLMKEVPAAERDDTGMQAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+  F+  A+L+FVSYEF+PPKFDV++C  RD+T+A PLK+ +RLIVFDVDE TGA+S+
Sbjct: 61   FPVKDFAERAVLDFVSYEFEPPKFDVEECQQRDMTFAAPLKVKMRLIVFDVDEETGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT  GTFV+ G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A 
Sbjct: 121  KDIKEQDVYMGDIPLMTDKGTFVVNGTERVIVSQMHRSPGVFFDHDRGKTHASGKYLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++H+R+DRRRK+P T+ L ALG+D EEILSTFY  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDVVHMRLDRRRKLPATTLLYALGLDKEEILSTFYDTVTYKASK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P    +   G K +  LVD  TG+ +  +GKK+++       + G+  L ++ + 
Sbjct: 241  KGWTVPYV-KERWRGVKPARDLVDAKTGDIIAPAGKKISARAANKFADDGLAALLVSDEH 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNT 361
            L G Y+A+D+VN ETGEI+ EAGD + E+ LE +  + ++++ +L +D       YIR T
Sbjct: 300  LLGGYLADDMVNLETGEIFAEAGDEMSEEILETLKDTGVKELNLLDIDPATGVGPYIRAT 359

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DKN  R+ AL+DIYRVMRPG+  T   AE+MF  LFFDS++YDLS VGRVKMNMRL+
Sbjct: 360  LAADKNDSREQALVDIYRVMRPGEPPTPETAEAMFQGLFFDSERYDLSAVGRVKMNMRLD 419

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            LD PDD+R +RKEDI+A++K LV LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLR
Sbjct: 420  LDAPDDMRTLRKEDILAVLKTLVGLRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLR 479

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSVDI++VMP DL+NAKP  +AV EFF SSQLSQ  +  N LS +TH RRL
Sbjct: 480  MERAIKERMSSVDIETVMPHDLVNAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRL 539

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIE+P
Sbjct: 540  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIESP 599

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +GK+T+ V YLSAM+E    IAQAN+ + E G    E V CR AG+  LVPRE +
Sbjct: 600  YRKVENGKLTDQVDYLSAMQESRYSIAQANAHVTESGELDNEFVNCRVAGDVTLVPREDV 659

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            ++ID SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL+KAEAP VGTGMES+VA+
Sbjct: 660  EYIDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKAEAPLVGTGMESIVAR 719

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAAI A+R G++EQVDA RIVIR+ E  LD + SGVDIYRL KFQRSNQ+TC+NQRP+
Sbjct: 720  DSGAAIAARRTGVIEQVDATRIVIRATED-LDAAKSGVDIYRLSKFQRSNQSTCINQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+VGD+V   DIIADGPSTDLG+LALGRN++VAFMPW+GYNFEDS+LISER+V +DVFTS
Sbjct: 779  VRVGDQVHAGDIIADGPSTDLGELALGRNVVVAFMPWNGYNFEDSILISERIVRDDVFTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IH+EEFE+ ARDTKLGPEEITRDIPNV EE L+N+DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 839  IHLEEFEIAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAVGAEVAAGDILVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTSLR+PSG +GTVV+VR+FNRHG+DK+ER+IS+ER
Sbjct: 899  GESPMTPEEKLLRAIFGEKASDVRDTSLRMPSGATGTVVEVRVFNRHGVDKDERAISIER 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE L +D+DDE  IL+RNIY RL ++L G+ AVSGP+GF K   +S D + E PRS W
Sbjct: 959  EEIERLGKDRDDELAILERNIYQRLGDLLLGKTAVSGPRGFAKG-KVSQDALDETPRSGW 1017

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            W+  + DEK    VE+L+ QY+ SK+ L+ RF++K++K+Q GD+MPPGV+++VKVFVA+K
Sbjct: 1018 WRIGLDDEKAMAEVEALQKQYDDSKARLDRRFEDKVDKLQRGDEMPPGVMKMVKVFVAVK 1077

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG++S+I P EDMPFL +G  VDIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1078 RKLQPGDKMAGRHGNKGVISKINPIEDMPFLANGEAVDIVLNPLGVPSRMNVGQILETHL 1137

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC GLGK++    + YK +G  + LRS L++V       E      D  +  +     
Sbjct: 1138 GWACRGLGKQLGEAYDAYKRDGSTATLRSELDRVYEGDELPE-----TDSDIAELGLNLS 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  +   L  A  D SGQS LYDG TGEPF R VTVG  ++LKL+H
Sbjct: 1193 NGVPIATPVFDGAREPDVAHWLTKAGFDPSGQSTLYDGQTGEPFRRKVTVGVKHLLKLHH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+N
Sbjct: 1313 VAGRTKVYEAIVRGDDTFEAGVPESFNVLVKEMRSLGLNVELKN 1356


>gi|126734767|ref|ZP_01750513.1| DNA-directed RNA polymerase beta subunit [Roseobacter sp. CCS2]
 gi|126715322|gb|EBA12187.1| DNA-directed RNA polymerase beta subunit [Roseobacter sp. CCS2]
          Length = 1379

 Score = 1716 bits (4444), Expect = 0.0,   Method: Composition-based stats.
 Identities = 843/1381 (61%), Positives = 1079/1381 (78%), Gaps = 15/1381 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    +      EG++  F+SV
Sbjct: 1    MASTFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDSDTPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVF+VDE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFEVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG D E I++ +Y  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFCRIDRRRKLPVTTLLYALGFDQEGIMNAYYNTVDYKLDK 240

Query: 243  DF--WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
                W         + G + +  LVD  TGE + ++G+K+T   +K L + G V  L + 
Sbjct: 241  KGAAWTTKFFPE-RVRGTRPAHDLVDAKTGEVIAKAGEKVTPRSVKKLIDAGEVTELLVP 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             D + G +V+EDI+N ETG IY+EAGD +  +          +L E+  + ++ IP+L +
Sbjct: 300  YDNIVGKFVSEDIINEETGAIYVEAGDELTVEVDKAGEVTGGTLTELVAAGVKTIPVLDI 359

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+V   AY+RNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS
Sbjct: 360  DNVTVGAYMRNTMAADKNMNRETALMDIYRVMRPGEPPTVDSASALFDTLFFDSERYDLS 419

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+LD  D +R +RKEDI++ IK LV+LR+G+G +DDID+LGNRRVRSVGE
Sbjct: 420  AVGRVKMNMRLDLDAEDTMRTLRKEDIVSCIKALVELRDGRGDVDDIDHLGNRRVRSVGE 479

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 480  LMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 539

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 540  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 599

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV DGKVT++V Y+SA EE    +AQAN++++E+GSF  ELV  R 
Sbjct: 600  ARVNKYGFIETPYRKVTDGKVTDEVSYMSATEEMRHTVAQANANVNEEGSFNNELVSTRK 659

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP
Sbjct: 660  NGDYTLSPRENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAP 719

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E VVA+ SGAAI+AKRAGI++QVDA RIVIR+ E  L+   +GVDIYR+ KFQR
Sbjct: 720  LVGTGIEEVVARDSGAAIMAKRAGIIDQVDAQRIVIRATED-LELGDAGVDIYRMRKFQR 778

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRPLVKVGD+V++  ++ADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LI
Sbjct: 779  SNQNTCINQRPLVKVGDKVQKGQVVADGPSTDIGELALGKNVVVAFMPWNGYNYEDSILI 838

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 839  SERIVRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVG 898

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            P DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GTVV+VR+FNRHG
Sbjct: 899  PADILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGDFGTVVEVRVFNRHG 958

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K+ER++ +ERE++E LARD+DDE VILDRNIY+RL +I+ G+ A  GPKGFK  +V++
Sbjct: 959  VEKDERALQIEREEVERLARDRDDEMVILDRNIYARLWDIIGGKKAAKGPKGFKSGSVVT 1018

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             + +SE  R QWWQ A+ DE   + VE+L  QYE  K  ++ RF++K+EK++ GDD+PPG
Sbjct: 1019 EESVSELTRGQWWQLAMADEDDAKIVEALNEQYEIQKRAMDARFEDKVEKVRRGDDLPPG 1078

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPS
Sbjct: 1079 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPS 1138

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG +I   + +Y+ +GD++P+R  ++ V G   + E I+  D
Sbjct: 1139 RMNVGQILETHMGWAARGLGIQIDEALGEYRRSGDLTPVRDAMKIVYGDNVYDEGIAGMD 1198

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +D ++  A     GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F R V
Sbjct: 1199 EDELVEAAGNVTGGVPIATPVFDGAKEADVNDALTRAGFDTSGQSVLFDGRTGEQFSRKV 1258

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1259 TVGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1318

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1319 TLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEDE 1378

Query: 1370 N 1370
             
Sbjct: 1379 E 1379


>gi|84685445|ref|ZP_01013343.1| DNA-directed RNA polymerase beta subunit [Maritimibacter alkaliphilus
            HTCC2654]
 gi|84666602|gb|EAQ13074.1| DNA-directed RNA polymerase beta subunit [Rhodobacterales bacterium
            HTCC2654]
          Length = 1380

 Score = 1716 bits (4443), Expect = 0.0,   Method: Composition-based stats.
 Identities = 844/1381 (61%), Positives = 1068/1381 (77%), Gaps = 12/1381 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  R+RK++GK  E++++P+LIEVQKASYD FL     P+    EG++  F+SV
Sbjct: 1    MAQSYLGQKRLRKYYGKIREVLEMPNLIEVQKASYDLFLNSGDQPEPADGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+  A LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPISDFNETATLEFVRYELEHPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y+   
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVDYTLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + +  +VD D+GE + E+GKK+T   +K L ++G VK + +  D
Sbjct: 241  NKGWVTKFFPERIRGTRPNMDIVDADSGEILFEAGKKVTPRAVKKLIDEGTVKNILVPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G YVA+DI+N ETG IY+EAGD +  +          S +E+  + I DIP+L +D+
Sbjct: 301  NIVGRYVAKDIINEETGAIYVEAGDELTLEYDKDGDLIGGSAKELIDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   YIRNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYIRNTVAADKNMNRDTALMDIYRVMRPGEPPTVEAASTLFDQLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRLNLD  D  R +R+EDIIA IK LV+LR+G+G +DDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLNLDAEDTQRTLRREDIIACIKALVELRDGRGEVDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V  G+VT++V Y+SA EE    +AQAN+SLDE G F  E+V  R +G
Sbjct: 601  VNKYGFIETPYRVVKGGQVTDEVHYMSATEEMRHTVAQANASLDESGKFVNEMVNTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L P + +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  EYTLAPVDSVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAI A+RAG+++QVDA RIV+R+   DL+P   GVDIYRL KFQRSN
Sbjct: 721  GTGIEGKVAVDSGAAIQARRAGVIDQVDATRIVVRAT-ADLEPGDPGVDIYRLRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNT +NQRPLVKVG +V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTAINQRPLVKVGQDVEKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIAQDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL +++ G+ AV GPKG K  +V+   
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLRDMIEGKTAVKGPKGVKSGSVIDEA 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+ E  R QWWQ A++DE   + VE+L  QYE  K  LE RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLGELSRGQWWQLALEDEADAQMVEALNAQYEAQKRALEHRFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++SR++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  I   + +YK +GD++P+R  ++   G   + E I   D++
Sbjct: 1140 NVGQILETHMGWAARGLGLNIDEALGEYKRSGDLTPVRDAMKHAYGEDVYAEGIEGMDEE 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F R VTV
Sbjct: 1200 RLIEAASNVTRGVPIATPVFDGAKEPEVNDALTRAGFDTSGQSVLFDGRTGEQFARKVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L +S  +  
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDSEGEPD 1379

Query: 1372 A 1372
             
Sbjct: 1380 E 1380


>gi|146278576|ref|YP_001168735.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            ATCC 17025]
 gi|166229300|sp|A4WVL6|RPOB_RHOS5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145556817|gb|ABP71430.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sphaeroides
            ATCC 17025]
          Length = 1377

 Score = 1715 bits (4441), Expect = 0.0,   Method: Composition-based stats.
 Identities = 838/1380 (60%), Positives = 1081/1380 (78%), Gaps = 14/1380 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+  V  G  R+R+++GK  E++++P+LIEVQK+SYD FL     P     EG+Q  F+
Sbjct: 1    MAQSYV--GQKRIRRYYGKIREVLEMPNLIEVQKSSYDLFLKSGEGPKAADGEGIQGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LEFV YE + PK+DVD+C  RD+TYA PLK+TLRLIVFDVDE TGA+
Sbjct: 59   SVFPIKDFNETAVLEFVKYELEKPKYDVDECQQRDMTYAAPLKVTLRLIVFDVDETTGAR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTANGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALGMD E I+  +Y  + +  
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGMDQEGIMDAYYDTVDFKY 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK-GVKFLGIT 299
            + +         + + G + +  LVD  TGE ++++G+K T  ++K   +   +  L + 
Sbjct: 239  QKNRGWVTRFFPERVRGTRPTYDLVDAATGEVILKAGEKATPRMVKKWIDDAQITELLVP 298

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             D + G YVA DI+N ETGEI++EAGD +  +          +L+ +    I DIP+L +
Sbjct: 299  FDHIVGRYVARDIINEETGEIWVEAGDELTMEYDRDGEVKGGTLKLLLDQGITDIPVLDI 358

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+VN   YIRNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS
Sbjct: 359  DNVNVGPYIRNTMAADKNMGRDTALMDIYRVMRPGEPPTVEAAAALFDTLFFDSERYDLS 418

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+L  PD  R + ++DIIA IK L +LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 419  AVGRVKMNMRLDLGKPDTQRTLDRDDIIACIKALTELRDGKGEIDDIDHLGNRRVRSVGE 478

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 479  LMENQYRVGLLRMERAIKERMSSVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 538

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 539  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGQNIGLINSLATF 598

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV +G+VT+DVVY+SA EE    +AQAN++LDE+G F  +L+  R 
Sbjct: 599  ARVNKYGFIETPYRKVIEGQVTDDVVYMSATEEMRHTVAQANATLDEEGRFVSDLISSRK 658

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            AGE +L P + ID ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+++AP
Sbjct: 659  AGEFMLNPPDAIDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQSDAP 718

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            FVGTG+E+VVA+ SGAAI+A+RAG+++QVDA RIV+R+ E  L+P   GVDIYRL KF+R
Sbjct: 719  FVGTGIEAVVARDSGAAIMARRAGVIDQVDATRIVVRATE-MLEPGEPGVDIYRLRKFKR 777

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ++C+NQRPLVKVGD V R +++ADGP TD+G+LALGRN++VAFMPW+GYN+EDS+LI
Sbjct: 778  SNQSSCINQRPLVKVGDVVHRGEVVADGPCTDMGELALGRNVVVAFMPWNGYNYEDSILI 837

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER++ +DV+TSIHIEE+EV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 838  SERILRDDVYTSIHIEEYEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVQ 897

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG
Sbjct: 898  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGAYGTIVEVRVFNRHG 957

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +DK+ER++ +ERE++E LARD+DDE  IL+RNIYSRL  ++ G+ AV GPKG K  + ++
Sbjct: 958  VDKDERALQIEREEVERLARDRDDELAILERNIYSRLKTLIMGKVAVKGPKGIKAGSEIN 1017

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +L+S   R QWWQ A+ +E   + VE+L  Q+E  K  L+ RF++K+EK++ GDD+PPG
Sbjct: 1018 DELLSTLSRGQWWQLALGEEADAKEVEALHEQFEAQKRALDHRFEDKVEKVRRGDDLPPG 1077

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGT VD+VLNPLGVPS
Sbjct: 1078 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPIEDMPFLADGTHVDLVLNPLGVPS 1137

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG +I   + DY+ +GD++P++  +    G  ++    +D D
Sbjct: 1138 RMNVGQILETHMGWAARGLGIQIDEALQDYRRSGDLTPVKEAMRLAYGDETYEGAFADRD 1197

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D+ ++ +A +   GVP++TPVFDGA E  +N  LR A  D+SGQSI++DG TGE F RPV
Sbjct: 1198 DEDLVEMASRVTKGVPIATPVFDGAKEPDVNDALRRAGFDQSGQSIVFDGRTGEQFARPV 1257

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY
Sbjct: 1258 TVGVKYMLKLHHLVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAY 1317

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT++YESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1318 TLQEMLTVKSDDVAGRTKMYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDADEE 1377


>gi|254464810|ref|ZP_05078221.1| DNA-directed RNA polymerase, beta subunit [Rhodobacterales bacterium
            Y4I]
 gi|206685718|gb|EDZ46200.1| DNA-directed RNA polymerase, beta subunit [Rhodobacterales bacterium
            Y4I]
          Length = 1382

 Score = 1713 bits (4437), Expect = 0.0,   Method: Composition-based stats.
 Identities = 841/1379 (60%), Positives = 1073/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A +    EG++  F+SV
Sbjct: 5    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDAAEPLDGEGIKGVFQSV 64

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 65   FPIKDFNETSVLEFVKYSFEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 124

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 125  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 184

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  I +    
Sbjct: 185  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTISFKLEK 244

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE + E+GKK+T   +K + E+G +  L +  D
Sbjct: 245  SRGWVAPFFPERVRGTRPTYDLVDAATGEIICEAGKKVTPRAVKKMIEEGTITELLVPFD 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N + G IY+EAGD +  +          SL+E+  + I DIP+L +D+
Sbjct: 305  HIVGKFVAKDIINEDNGAIYVEAGDELTLEYDKDGDLIGGSLKELLDAGITDIPVLDIDN 364

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN+ R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 365  VNVGPYMRNTMAQDKNRTRESALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 424

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI+A +K LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 425  GRVKMNMRLALDAEDTQRTLRKEDIVACVKALVDLRDGRGDIDDIDHLGNRRVRSVGELM 484

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 485  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 544

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 545  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 604

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V DG+VT++V Y+SA EE    +AQAN+SLDE+G F  +LV  R +G
Sbjct: 605  VNKYGFIETPYRVVKDGQVTDEVHYMSATEEMRHTVAQANASLDENGKFINDLVSTRQSG 664

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 665  DYTLAPNESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 724

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAI AKRAGI++QVDA RIVIR+ E  L+   +GVDIYR+ KFQRSN
Sbjct: 725  GTGIEEKVAIDSGAAIQAKRAGIIDQVDAQRIVIRATED-LELGDAGVDIYRMRKFQRSN 783

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V++ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 784  QNTCINQRPLVKVGDTVQKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 843

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 844  RIARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 903

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 904  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 963

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG +  T ++ D
Sbjct: 964  KDERALQIEREEVERLARDRDDELAILDRNIYARLRGMILGKVAVKGPKGVRAGTEITED 1023

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWW  A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1024 LLDSLSRGQWWMLALEDEQDAQVVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1083

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1084 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1143

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG K+   + +Y+ +GD++P+R  +    G   + E I++ D+D
Sbjct: 1144 NVGQILETHMGWAARGLGIKVDDALQEYRRSGDLTPVREAMHHAYGDDVYDEGIANMDED 1203

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            S++  A     GVP++TPVFDGA E  +N  L+ A  D SGQSIL+DG TGE F RPVTV
Sbjct: 1204 SLIEAAGNVTRGVPIATPVFDGAKEGDVNDALKRAGFDTSGQSILFDGRTGEQFARPVTV 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1264 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1324 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1382


>gi|36333371|gb|AAP75743.1| RNA polymerase beta subunit [Bosea massiliensis]
          Length = 1370

 Score = 1713 bits (4436), Expect = 0.0,   Method: Composition-based stats.
 Identities = 881/1365 (64%), Positives = 1095/1365 (80%), Gaps = 15/1365 (1%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            G  RVRKFFGK  E+  +P+LIEVQKASYD FLM++     R +EGLQ+ FKSVFPI  F
Sbjct: 7    GRRRVRKFFGKLKEVAQMPNLIEVQKASYDQFLMVDEPKGGRGDEGLQSVFKSVFPIGDF 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            SGA++LEFV Y F+PPK+DVD+C  R +T++ PLK+TLRLIVFD+D  T AKS+KDIKEQ
Sbjct: 67   SGASLLEFVKYTFEPPKYDVDECRQRGMTFSAPLKVTLRLIVFDIDPDTQAKSVKDIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +
Sbjct: 127  DVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARIIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+DIEFD+KDI++ RIDR+RK+PVTS L ALGMD EEILS FY  I Y++    W  P
Sbjct: 187  GSWLDIEFDAKDIVYARIDRKRKIPVTSLLFALGMDGEEILSRFYNTITYTRDAKGWRVP 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              A   M G K +  L+D DTGE V+E+GKKL +   + L EKG+KFL  T + L G Y+
Sbjct: 247  YDAE-RMKGFKATVDLIDADTGEVVVEAGKKLVARTARQLAEKGLKFLRATDEDLVGQYI 305

Query: 309  AEDIVNGETGEIYIEAGDVID----------EKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            AED+V+ +TGE++ EAG+ +           + +L E+ +    +IP+L +D +    YI
Sbjct: 306  AEDLVDFQTGEVHAEAGEELTMSVDAKTGEAKGNLVELINKGYTEIPVLDIDHITVGPYI 365

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DKN  R++AL DIYRVMRPG+  T   AE+MF  LFFD+++YDLS VGRVKMNM
Sbjct: 366  RNTLAVDKNSRREEALFDIYRVMRPGEPPTLETAENMFQSLFFDAERYDLSAVGRVKMNM 425

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL+LD  D VR +RKEDI A++K LVDLR+GKG IDDID+LGNRRVRSVGE+++NQYRLG
Sbjct: 426  RLDLDAEDTVRILRKEDIFAVVKALVDLRDGKGEIDDIDHLGNRRVRSVGELMENQYRLG 485

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH 
Sbjct: 486  LLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHK 545

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFI
Sbjct: 546  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFI 605

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYR++ DG+ T++++YLSAMEE    +AQAN+++D+DG  T++L+ CR AGE I+ P 
Sbjct: 606  ESPYRRIRDGRQTDEIIYLSAMEEAKYNVAQANAAVDKDGRLTDDLIVCRRAGEVIVTPV 665

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +K+DF D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++A+APFVGTGME+V
Sbjct: 666  DKVDFQDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRADAPFVGTGMEAV 725

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+RAGIV+QVDA RIVIR+ +   DP+  GVDIYRL KFQRSNQ+TC+ Q
Sbjct: 726  VARDSGAAIAARRAGIVDQVDATRIVIRASDEM-DPTKPGVDIYRLQKFQRSNQSTCITQ 784

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLV+VGD +++ DI+ADGPST+ G+LALGRN+LVAFMPW+GYNFEDS+L+SE++VSEDV
Sbjct: 785  RPLVRVGDVIKKGDIVADGPSTEFGELALGRNVLVAFMPWNGYNFEDSILLSEKIVSEDV 844

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 845  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVAAGDILVGKI 904

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ +
Sbjct: 905  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQA 964

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN ++RL +IL G+  ++GPKGFKK TV++ + +SE+PR
Sbjct: 965  IEREEIERLAKDRDDEQAILDRNTFARLADILTGKVGLAGPKGFKKDTVITREGMSEFPR 1024

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1025 SQWWLFATADDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1084

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1085 AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1144

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA  GLGK+I + ++ Y+   DI  LR+  + V       E I+  D++ ++ + +
Sbjct: 1145 THLGWAAAGLGKQISAALDAYRKGHDIKALRASFDAVYEDN---EIIASMDENELVEMGQ 1201

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VTVGYIYMLK
Sbjct: 1202 NLRRGVPIATPVFNGAKEADIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTVGYIYMLK 1261

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1262 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1321

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GRT+VYESIV G D FE G PES  VLVKEM++LGL++ L
Sbjct: 1322 SDDVAGRTKVYESIVRGEDNFEAGIPESVTVLVKEMRSLGLNVYL 1366


>gi|89095345|ref|ZP_01168262.1| DNA-directed RNA polymerase beta subunit [Oceanospirillum sp. MED92]
 gi|89080387|gb|EAR59642.1| DNA-directed RNA polymerase beta subunit [Oceanospirillum sp. MED92]
          Length = 1366

 Score = 1712 bits (4434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1371 (52%), Positives = 997/1371 (72%), Gaps = 12/1371 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  SY  FL   +   +R + GL AAF SV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPQVMDVPYLLAIQLDSYKKFLQTGVEAADRLDAGLHAAFNSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C  R +TYA PL++ +RL+++D    +  K++
Sbjct: 61   FPIVSYSGNASLEYVGYRLGEPVFDVKECQIRGITYAAPLRVKVRLVIYDR--ESSNKAV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFV+ G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEMPLMTENGTFVVNGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG ++EEIL  F+    ++   
Sbjct: 179  RVIPYRGSWLDFEFDPKDSLFVRIDRRRKLPATILLRALGYEAEEILDIFFDNTSWNLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A D + G  +S  + D + G  ++E+G+++T   ++ + +  ++ L +  + 
Sbjct: 239  DAINMQLIA-DRLRGETLSFEVKDPE-GNVIVEAGRRITPRHIRQMAKANMEQLEVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D+V+  TGE+       I E+ +E++  + I++   LY + ++   +I +TL
Sbjct: 297  VAGKAIAKDVVDPSTGELICGCNAEITEELIEQLRAAGIKEFETLYTNDLDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +++ +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL  
Sbjct: 357  RNDPTRNQLEALVEIYRMMRPGEPPTKESAEALFENLFFTEERYDLSAVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       + K+DI++++K L+D+RNGKGT+DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  DEVTGSGVLDKDDILSVMKTLIDIRNGKGTVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + D++MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVRERLSMAESDNLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR N YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATFARTNDYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D KVT+++ YLSA+EE    IAQA++++D++G   +++V  R   E  ++  EK+ 
Sbjct: 597  RRVVDSKVTDELDYLSAIEENTFVIAQASATMDDEGRLVDDMVTVRHLNETTVMAPEKVQ 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA+ 
Sbjct: 657  YMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIERNVAQD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G++E VDA RIV+R  + ++    +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVVARRGGLIESVDASRIVVRVNDNEVTAGDAGVDIYNLTKYTRSNQNTCINQRSIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+  D++ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+LISER+V ED FT+I
Sbjct: 777  NPGDIVKPGDVMADGPSVDMGELALGQNMRIAFMPWNGYNFEDSILISERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGSEEITSDIPNVGESALAKLDEAGIVHIGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES +TPEEKLLRAIFGEKA DV+DTSLRV +G  G V+DV++F R G+ K+ER++S+E+ 
Sbjct: 897  ESQLTPEEKLLRAIFGEKASDVKDTSLRVKTGTVGKVIDVQVFTRDGVQKDERALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++ + +D ++E  I+++  + RL ++L G  A  G  G KK   +S++ +++  +S W+
Sbjct: 957  ELDAIRKDLNEELRIVEQATFERLEKVLVGLKADGG-AGLKKGEEISAEFLADLNKSDWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               V DE     +E  + Q E  K  L+ RF++K  K+Q GDD+ PGVL++VKV+VA KR
Sbjct: 1016 NIRVSDENAAEQLELAQKQLEDRKESLDKRFEDKKSKLQTGDDLAPGVLKIVKVYVATKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQI ETH+G
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDQNGEPVDIVLNPLGVPSRMNVGQILETHMG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTG------SHTEKISDYDDDSVLR 1195
             A  GLG++I  ++   +   + +  +R FL+K+          S TE +  + DD ++ 
Sbjct: 1136 MAAKGLGRRINEMLEQERERVETVKEVRGFLDKIYNADLGAGMNSRTEDLDSFTDDEIME 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A+    GVP++TP FDGA E  + ++LR+A LD+SGQ+ L+DG TG+ FDRPVTVGY+Y
Sbjct: 1196 LAKNLCGGVPLATPAFDGAKEVELKTLLRLAGLDDSGQTTLFDGRTGDQFDRPVTVGYMY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T+KSDDV GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE+ 
Sbjct: 1316 TVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIELESE 1366


>gi|77462251|ref|YP_351755.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            2.4.1]
 gi|126461113|ref|YP_001042227.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            ATCC 17029]
 gi|126461127|ref|YP_001042241.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            ATCC 17029]
 gi|221638105|ref|YP_002524367.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            KD131]
 gi|88909635|sp|Q3J5T0|RPOB_RHOS4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158513428|sp|A3PGI9|RPOB_RHOS1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765301|sp|B9KL83|RPOB_RHOSK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|77386669|gb|ABA77854.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sphaeroides
            2.4.1]
 gi|126102777|gb|ABN75455.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sphaeroides
            ATCC 17029]
 gi|126102791|gb|ABN75469.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sphaeroides
            ATCC 17029]
 gi|221158886|gb|ACL99865.1| DNA-directed RNA polymerase subunit beta [Rhodobacter sphaeroides
            KD131]
          Length = 1377

 Score = 1712 bits (4434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1380 (60%), Positives = 1079/1380 (78%), Gaps = 14/1380 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+  V  G  R+R+++GK  E++++P+LIEVQK+SYD FL     P     EG+Q  F+
Sbjct: 1    MAQSYV--GQKRIRRYYGKIREVLEMPNLIEVQKSSYDLFLKSGDGPKAADGEGIQGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LEFV YE + PK+DVD+C  RD+TYA PLK+TLRLIVFDVDE TGA+
Sbjct: 59   SVFPIKDFNETAVLEFVKYELEKPKYDVDECQQRDMTYAAPLKVTLRLIVFDVDETTGAR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTANGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALGMD E I+  +Y  + +  
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGMDQEGIMDAYYETVNFKH 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL-KEKGVKFLGIT 299
            + +         + + G + +  LVD  TGE ++++G+K T  ++K    E  +  L + 
Sbjct: 239  QKNRGWVTRFFPERVRGTRPTYDLVDAATGEVILKAGEKATPRMVKKWIDEAQITELLVP 298

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             D + G YVA+DI+N ETGEI++EAGD +  +          +L+ +    I DIP+L +
Sbjct: 299  FDHIVGRYVAQDIINEETGEIWVEAGDELTMEYDRDGEVKGGTLKLLLDQGITDIPVLDI 358

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+VN   YIRNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS
Sbjct: 359  DNVNVGPYIRNTMAADKNMGRDTALMDIYRVMRPGEPPTVEAASNLFDTLFFDSERYDLS 418

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+L  PD  R + ++DIIA IK L +LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 419  AVGRVKMNMRLDLGKPDTQRTLDRDDIIACIKALTELRDGKGEIDDIDHLGNRRVRSVGE 478

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 479  LMENQYRVGLLRMERAIKERMSSVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 538

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 539  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGQNIGLINSLATF 598

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV +G VT+DVVY+SA EE    +AQAN+ LDE+G F  +L+  R 
Sbjct: 599  ARVNKYGFIETPYRKVVEGAVTDDVVYMSATEEMRHTVAQANAQLDEEGRFVSDLISSRK 658

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            AGE +L P + ID ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+++AP
Sbjct: 659  AGEFMLNPPDAIDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQSDAP 718

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            FVGTG+E+VVA+ SGAAI+A+RAG+++QVDA RIV+R+ E  L+P   GVDIYRL KF+R
Sbjct: 719  FVGTGIEAVVARDSGAAIMARRAGVIDQVDATRIVVRATE-MLEPGEPGVDIYRLRKFKR 777

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ++C+NQRPLVKVGD V R +++ADGP TD+G+LALGRN++VAFMPW+GYN+EDS+LI
Sbjct: 778  SNQSSCINQRPLVKVGDVVHRGEVVADGPCTDMGELALGRNVIVAFMPWNGYNYEDSILI 837

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER++ +DV+TSIHIEE+EV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 838  SERILRDDVYTSIHIEEYEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVQ 897

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG
Sbjct: 898  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGAYGTIVEVRVFNRHG 957

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +DK+ER++ +ERE++E LARD+DDE  IL+RNIYSRL  ++ G+ AV GPKG +  + ++
Sbjct: 958  VDKDERALQIEREEVERLARDRDDELAILERNIYSRLRTLIMGKTAVKGPKGIRAGSEIN 1017

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             DL+S   R QWWQ A+ +E   + VE+L  Q+E  K  L+ RF++K+EK++ GDD+PPG
Sbjct: 1018 EDLLSTLSRGQWWQLALGEEADAKEVEALHEQFEAQKRALDHRFEDKVEKVRRGDDLPPG 1077

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGT VD+VLNPLGVPS
Sbjct: 1078 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPIEDMPFLADGTHVDLVLNPLGVPS 1137

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG KI   + DY+ +GD++P++  +    G  ++     D +
Sbjct: 1138 RMNVGQILETHMGWAARGLGIKIDEALQDYRRSGDLTPVKEAMRLAYGDETYEGAFGDRE 1197

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D+ ++ +A +   GVP++TPVFDGA E  +N  LR A  D+SGQSI++DG TGE F RPV
Sbjct: 1198 DEDLVEMAGRVTKGVPIATPVFDGAKEPDVNDALRRAGFDQSGQSIVFDGRTGEQFARPV 1257

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY
Sbjct: 1258 TVGVKYMLKLHHLVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAY 1317

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT++YESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1318 TLQEMLTVKSDDVAGRTKMYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDADEE 1377


>gi|88812764|ref|ZP_01128010.1| DNA-directed RNA polymerase, beta subunit [Nitrococcus mobilis
            Nb-231]
 gi|88790002|gb|EAR21123.1| DNA-directed RNA polymerase, beta subunit [Nitrococcus mobilis
            Nb-231]
          Length = 1354

 Score = 1712 bits (4434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 729/1364 (53%), Positives = 989/1364 (72%), Gaps = 10/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK  +I+D+P L+  Q  SY  FL  +   ++R   GL  AFKSV
Sbjct: 1    MDYSFTEKKRIRKDFGKQSKILDVPYLLATQIESYREFLQFDKRVEDRAEIGLHMAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG+A+LE+VSY    P FDV +C  R  TYA PL++ +RL+++D D  T    +
Sbjct: 61   FPISSYSGSAVLEYVSYRIGEPPFDVKECQLRGQTYAAPLRVRVRLVIYDKDAST----V 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG+LPLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   S KLL++ 
Sbjct: 117  KDIKEQEVYMGELPLMTRNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSKKLLFSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD I VRIDRRRK+P T  L ALG D+E+IL  F+ K  +  R 
Sbjct: 177  RVIPYRGSWLDFEFDPKDAIFVRIDRRRKLPATILLRALGYDNEQILDRFFEKNTFHIRK 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +   D    ++ESG+++T+  ++ L+  G+  L ++ D 
Sbjct: 237  DKAVLELIPERL-RGETASFDIHIDDV--LLVESGQRITARHIRQLERGGLTELDVSDDY 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+V+  +GEI   A   +  + ++ I  + I++I  LYV+ ++  AYI  TL
Sbjct: 294  LTGKILAHDVVDKSSGEILATANTELTGELVQAIRDAGIKNIETLYVNDLDRGAYISTTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    + +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N+R+  
Sbjct: 354  RGDPTTTQLEALVEIYRMMRPGEPPTREAAENLFQHLFFSEDRYDLSPVGRMKFNLRVGR 413

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  EDI+ ++  L+++RNGKG +DDID+LGNRRVR VGEM +N +R+GL+R+
Sbjct: 414  QEVTGSGTLSNEDILDVLHELINIRNGKGQVDDIDHLGNRRVRCVGEMAENVFRVGLVRV 473

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + ++PQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 474  ERAVRERLSLAESEGLIPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 533

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETPY
Sbjct: 534  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNRYGFLETPY 593

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG+VT++V YLSA+EE    IAQAN+ + EDG   ++L+ CR   E  +   E++ 
Sbjct: 594  RKVVDGRVTSEVEYLSAIEEGRFVIAQANARVSEDGRLLDDLISCRFQNEFGMATPERVQ 653

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +PKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA  
Sbjct: 654  YMDVAPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERAVAID 713

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++A+R G VEQVDA RIV+R  + +  P   GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 714  SGVTVIAERGGAVEQVDAARIVVRVNDEEAVPGEPGVDIYNLTKYTRSNQNTCINQRPLV 773

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + G++V R D++ADGPSTD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V ED +T+I
Sbjct: 774  RPGEQVVRGDVLADGPSTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVQEDRYTTI 833

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLG EE+T DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 834  HIEELTCVARDTKLGSEEVTADIPNVGESALSKLDESGIVYIGAEVKAGDILVGKVTPKG 893

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G+ GTV+DV++F R G+ K++R++S+E  
Sbjct: 894  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGMDGTVIDVQVFTRDGVKKDQRALSIEAG 953

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D +D+  I + + ++RL  +L G+    GP G +    +S   ++   R +W+
Sbjct: 954  QLADVRKDLNDQYRIFEDDAFTRLERLLEGKAVAGGPGGLRSGAEVSRAYLAGVERERWF 1013

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE+V + +E+++ Q +  + I + R++ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1014 EIRMRDEEVNQQLEAVQSQLKAQREIFDSRYEEKKAKITAGDDLAPGVLKMVKVYLAVKR 1073

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMP+LKDGTPVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1074 RVQPGDKMAGRHGNKGVISTIVPVEDMPYLKDGTPVDIVLNPLGVPSRMNVGQVLETHLG 1133

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   LG+KI  L++ +    +IS L+ FL+++  +    E +  +     + +A+  +S
Sbjct: 1134 WASKALGRKIADLLDTH---TEISELQGFLQQIYNSSGREEDLDSFSSQQFIELADNLRS 1190

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I +MLR+A L ESG++ILYDG TGE FDRPVT+GY+YMLKLNH+
Sbjct: 1191 GVPMATPVFDGAHENEIKAMLRLAGLPESGKAILYDGRTGEAFDRPVTIGYMYMLKLNHL 1250

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DKV+ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1251 VDDKVHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1310

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE  
Sbjct: 1311 SGRTKMYKNIVDGDHRMEAGMPESFNVLVKEIRSLGIDIELEQD 1354


>gi|149203670|ref|ZP_01880639.1| DNA-directed RNA polymerase subunit beta [Roseovarius sp. TM1035]
 gi|149142787|gb|EDM30829.1| DNA-directed RNA polymerase subunit beta [Roseovarius sp. TM1035]
          Length = 1378

 Score = 1711 bits (4432), Expect = 0.0,   Method: Composition-based stats.
 Identities = 836/1379 (60%), Positives = 1076/1379 (78%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+R+++GK  E++++P+LIEVQK+SYD FL     P  +  EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRRYYGKIREVLEMPNLIEVQKSSYDLFLKSGDQPQPQDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFVSYE + PK+DVD+C+ RD+TYA PLK+ LRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVSYELEKPKYDVDECMQRDMTYAAPLKVKLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+ C
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFTC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L +LG+D E I++ +Y  + Y  + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYSLGLDQEGIMNAYYDTVDYKLKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  L+D +TGE + E+ KK+T   +K L ++G V  L +  +
Sbjct: 241  KKGWVTKFFPERVRGTRPTYDLIDANTGEVIFEASKKITPRAVKQLIDEGNVTELLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI++ ETG IY+EAGD +  +          +L+++  + I DIP+L +D 
Sbjct: 301  HIVGKFVARDIIDEETGAIYVEAGDELTLEYGKDGEISGGTLQDLLDAGITDIPVLDIDG 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N  AYIRNT+  DKN +R+ AL+DIYRVMRPG+  T   + ++F+ LFFD+++YDLS V
Sbjct: 361  INVGAYIRNTMAADKNMNRESALMDIYRVMRPGEPPTEEASAALFDTLFFDAERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRLNLD PD  R + ++DI+A +K LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLNLDKPDTQRTLDRDDIVACVKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV DG+VT++V Y+SA EE    +AQAN++LDE G F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVIDGQVTDEVQYMSATEEMRHTVAQANANLDEGGRFVNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E +L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVP L+AEAP V
Sbjct: 661  EYMLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPTLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAG+++QVDA RIVIR+   DL+    GVDIYR+ KFQRSN
Sbjct: 721  GTGIEGVVARDSGAAIMAKRAGVIDQVDAQRIVIRAT-ADLEIGDPGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QN+C+NQ+PLVKVGD V++ ++IADGP TD+G+LALG+N++ AFMPW+GYN+EDS+LISE
Sbjct: 780  QNSCINQQPLVKVGDTVQKGEVIADGPCTDMGELALGKNVITAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIVRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K ++ ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLRTLIMGKVAVKGPKGVKANSDITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S   + QWWQ A++DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLSTLTKGQWWQLALKDEADAKIVEALHDQYEAQKRTLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG+VS+++P EDMPFL DGTPVDI LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVVSKVIPIEDMPFLADGTPVDICLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA   LG KI   + DY+ +GD++P+R  +    G   + E I   D+ 
Sbjct: 1140 NVGQILETHMGWAARSLGLKIDEALQDYRRSGDLTPVREAMRIAYGDDVYAEGIESMDET 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            +++  A    SGVP++TPVFDGA E  +N  LR A  D SGQS+L+DG TGE F RPVTV
Sbjct: 1200 TLIESAGTVTSGVPIATPVFDGAKEADVNDALRRAGFDTSGQSVLFDGRTGEQFSRPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|56698330|ref|YP_168703.1| DNA-directed RNA polymerase subunit beta [Ruegeria pomeroyi DSS-3]
 gi|81348897|sp|Q5LMQ5|RPOB_SILPO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56680067|gb|AAV96733.1| DNA-directed RNA polymerase, beta subunit [Ruegeria pomeroyi DSS-3]
          Length = 1378

 Score = 1711 bits (4431), Expect = 0.0,   Method: Composition-based stats.
 Identities = 836/1379 (60%), Positives = 1068/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    AP     EG+   F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLNSGDAPQPLDGEGIMGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV YE + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVKYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  ++  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYFKTVSYRLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  L+D  +GE + E+GKK+T   +K L E+G V  L +  D
Sbjct: 241  KRGWVTPFFPERVRGTRPTYDLIDAASGEVIAEAGKKVTPRAVKKLIEEGSVTDLLVPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G + A+DI+N ETG IY+EAGD +  +          +++E+  + + +IP+L +D+
Sbjct: 301  HIVGKFAAKDIINEETGAIYVEAGDELTLEYDKDGDLIGGTVKELIDNGVTNIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   YIRNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  INVGPYIRNTMAQDKNMNRETALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL+LD  D  R +R+EDIIA IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLDLDAADTQRTLRREDIIACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V  G+VT++V Y+SA EE    +AQAN++LDE+G F  ELV  R AG
Sbjct: 601  VNKYGFIETPYRVVKGGQVTDEVHYMSATEEMRHTVAQANATLDENGKFVNELVNTRQAG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPMESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SGAAI AKRAGI++Q+DA RIVIR+ E  L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEKVAIDSGAAIQAKRAGIIDQIDAQRIVIRATED-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG +V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQQVSKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVQPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+D
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVD 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K  + ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLKSLILGKTAVKGPKGIKPGSEITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWW  A++ E+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLTRGQWWMLALEGEQDAQIVEALNEQYELQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  +   + +Y+ +GD++P+R  ++   G   + E IS  D+D
Sbjct: 1140 NVGQILETHMGWAARGLGLNVDEALQEYRRSGDLTPVRDAMKHAYGEDVYAEGISGMDED 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            +++  A     GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F RPVTV
Sbjct: 1200 TLVEAAGNVTRGVPIATPVFDGAKEADVNDALTRAGFDTSGQSVLFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLVKEVRGLGLNMELLDAEVEE 1378


>gi|126737165|ref|ZP_01752900.1| DNA-directed RNA polymerase subunit beta [Roseobacter sp. SK209-2-6]
 gi|126721750|gb|EBA18453.1| DNA-directed RNA polymerase subunit beta [Roseobacter sp. SK209-2-6]
          Length = 1377

 Score = 1711 bits (4431), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1378 (60%), Positives = 1073/1378 (77%), Gaps = 12/1378 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    + +    EG++  F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDSVEPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVKYAFEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++ RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVYARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVNFKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      D + G + +  LVD  TGE   E+GKK+T   +K + ++G +  L +  D
Sbjct: 241  SRGWVTPFFPDRVRGTRPTYDLVDAATGEIFAEAGKKVTPRAVKKMIDEGAITELLVPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVDS 351
             + G YV++DI+N E G IY+EAGD +  +           L+E+  + I +IP+L +D+
Sbjct: 301  HIVGKYVSKDIINEENGAIYVEAGDELTLEHDKDGELIGGSLKELMDAGITEIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A S+F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAADKNMGRETALMDIYRVMRPGEPPTVEAASSLFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI+A IK LV+LR+GKG +DDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVACIKALVELRDGKGDVDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V +G+VT++V Y+SA EE    +AQAN+SLDE+G F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVNEGQVTDEVHYMSATEEMRHTVAQANASLDENGKFKNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPSESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKR GI++QVDA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRGGIIDQVDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG EVR+ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQEVRKGEVIADGPSTDIGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GT+V+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTIVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG +    ++ D
Sbjct: 960  KDERALQIEREEVERLARDRDDELTILDRNIYARLKGMILGKTAVKGPKGVRSGVEITED 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L++   R QWW  A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLASLSRGQWWMLALEDEQDAQVVEALNQQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG ++   + +Y+ +GD++P+R  ++   G   + E ++D  ++
Sbjct: 1140 NVGQILETHMGWAARGLGIQVDDALQEYRRSGDLTPVRDAMQHAYGENVYEEGLADMSEE 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E+ +N+ L  A  D+SGQSIL+DG TGE F RPVTV
Sbjct: 1200 DLLEAAGNVTRGVPIATPVFDGAKEDDVNNALVRAGFDQSGQSILFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEE 1377


>gi|15599466|ref|NP_252960.1| DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa
            PAO1]
 gi|12230977|sp|Q51561|RPOB_PSEAE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|9950488|gb|AAG07658.1|AE004842_7 DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa PAO1]
          Length = 1357

 Score = 1710 bits (4428), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1365 (53%), Positives = 985/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  + D  +G+ ++E G+++T+  +  L++ GV  L +  D 
Sbjct: 239  ETLNLELVPQRL-RGEVASIDIKDG-SGKVIVEQGRRITARHINQLEKAGVSQLEVPFDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ IV+  TGEI  E    +    L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  LIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++F  LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDII ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  GP   KK T ++ D +    R QW+
Sbjct: 957  QLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPA-LKKGTEITDDYLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + +  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357


>gi|152984487|ref|YP_001346216.1| DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa PA7]
 gi|166229297|sp|A6UZI1|RPOB_PSEA7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|150959645|gb|ABR81670.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas aeruginosa
            PA7]
          Length = 1357

 Score = 1710 bits (4428), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1365 (53%), Positives = 985/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  + D  +G+ ++E G+++T+  +  L++ GV  L +  D 
Sbjct: 239  ETLNLELVPQRL-RGEVASIDIKDG-SGKVIVEQGRRITARHINQLEKAGVTQLEVPFDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ IV+  TGEI  E    +    L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  LIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++F  LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDII ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  GP   KK T ++ D +    R QW+
Sbjct: 957  QLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPA-LKKGTEITDDYLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + +  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357


>gi|83949807|ref|ZP_00958540.1| DNA-directed RNA polymerase beta subunit [Roseovarius nubinhibens
            ISM]
 gi|83837706|gb|EAP77002.1| DNA-directed RNA polymerase beta subunit [Roseovarius nubinhibens
            ISM]
          Length = 1378

 Score = 1709 bits (4427), Expect = 0.0,   Method: Composition-based stats.
 Identities = 831/1379 (60%), Positives = 1074/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  R+R++FGK  E++++P+LIEVQK+SYD FL     P     EG++  F+SV
Sbjct: 1    MAQTYLGQKRLRRYFGKIREVLEMPNLIEVQKSSYDLFLNSGDQPQPMDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+  +++EFV YE + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPISDFNETSVIEFVDYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +  + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYDTVEFKLKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + +  LVD +TGE + E+ KK+T   +K L ++G V  L +  +
Sbjct: 241  NKGWVTKFFPERVRGTRPTFDLVDANTGEVIAEASKKVTPRAVKKLIDEGQVTELLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI+N E G IY+EAGD +  +          +L+E+  + I DIP+L +D+
Sbjct: 301  HIVGKFVARDIINEENGAIYVEAGDELTLERDKDGDIIGGTLKELIDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   Y+RNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  INVGPYMRNTMAQDKNMNRESALMDIYRVMRPGEPPTVDAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD PD  R + +EDI+A IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDKPDTQRTLDREDIVACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHATHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR+V DG+VT++V Y+SA EE+   +AQAN+++DE G F  E+V  R AG
Sbjct: 601  VNKYGFIETPYRRVVDGQVTDNVQYMSATEEQRHVVAQANANIDETGRFVNEMVNTRQAG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQA+PLL+AEAP V
Sbjct: 661  EYTLSPIENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQALPLLQAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+ E  L+P   GVDIYRL KFQRSN
Sbjct: 721  GTGIEGVVARDSGAAIMAKRAGIIDQVDAQRIVVRATED-LEPGDPGVDIYRLRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QN+C+NQ+PLVKVGD V + +++ADGP+TD+G+LA+GRN++VAFMPW+GYNFEDS+LISE
Sbjct: 780  QNSCINQKPLVKVGDTVIKGEVVADGPATDMGELAVGRNVVVAFMPWNGYNFEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            RM  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RMARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  IL+RNIY+RL  ++ G+ AV GPKG K ++ ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILERNIYARLKSMILGKVAVKGPKGVKANSDITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    + QWWQ A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLSKGQWWQLALKDEQDAQIVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG+VS+++P EDMPFL DGTPVDI LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVVSKVVPMEDMPFLADGTPVDICLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  G G +I   + DY+ +GD++P+R  ++   G   + E I+  D+ 
Sbjct: 1140 NVGQILETHMGWAARGFGVQIDEALQDYRRSGDLTPVREAMKLAYGEEVYDEGIAGMDEG 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  LR A  D SGQS+L+DG +GE F RPVTV
Sbjct: 1200 QLVEAAGNVTRGVPIATPVFDGAKEADVNDALRRAGFDTSGQSVLFDGRSGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEGDE 1378


>gi|218889402|ref|YP_002438266.1| DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa
            LESB58]
 gi|296387173|ref|ZP_06876672.1| DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa
            PAb1]
 gi|313111424|ref|ZP_07797228.1| DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa 39016]
 gi|226699432|sp|B7V637|RPOB_PSEA8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|218769625|emb|CAW25385.1| DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa
            LESB58]
 gi|310883730|gb|EFQ42324.1| DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa 39016]
          Length = 1357

 Score = 1709 bits (4427), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1365 (53%), Positives = 985/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  + D  +G+ ++E G+++T+  +  L++ GV  L +  D 
Sbjct: 239  ETLNLELVPQRL-RGEVASIDIKDG-SGKVIVEQGRRITARHINQLEKAGVSQLEVPFDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ IV+  TGEI  E    +    L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  LIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++F  LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDII ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  GP   KK T ++ D +    R QW+
Sbjct: 957  QLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPA-LKKGTEITDDYLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + +  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357


>gi|307543818|ref|YP_003896297.1| DNA-directed RNA polymerase subunit beta [Halomonas elongata DSM
            2581]
 gi|307215842|emb|CBV41112.1| DNA-directed RNA polymerase subunit beta [Halomonas elongata DSM
            2581]
          Length = 1359

 Score = 1709 bits (4426), Expect = 0.0,   Method: Composition-based stats.
 Identities = 726/1365 (53%), Positives = 985/1365 (72%), Gaps = 8/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  SY  FL  + +P+ER + GL AAF+SV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPQVMDVPYLLAIQLDSYYDFLQQDRSPEERLDVGLHAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG A LE+VSY F  P FDV +C  R +TY+ PL++ +RLI++D D  +  K+I
Sbjct: 61   FPIESFSGNAALEYVSYRFGTPAFDVKECQLRGVTYSAPLRVKVRLIIYDKD--SSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG++  SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  + ALGM +EEIL  F+    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLPATVLMRALGMSAEEILDEFFETSTFHIEK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L  + L  G   +  + D D G  ++E G+++T   ++ L++ G++ L +  D 
Sbjct: 239  SGFSVDLVPSRL-RGETATFDIKDGD-GNVIVEEGRRITQKHIRQLEKSGLERLEVPMDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D +N  TGE+       I  + LE +  + I  I  LY + ++   +I +TL
Sbjct: 297  LFGKTLAKDQINPNTGELICPCNTAITPELLESLGQAGITTIETLYTNDLDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    + +AL++IYR+MRPG+  T   AE++FN LFF  D+YDLS VGR+K N RL  
Sbjct: 357  KLDTTGSQLEALVEIYRMMRPGEPPTKEAAETLFNNLFFTEDRYDLSGVGRMKFNRRLRR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       + + DI+ ++  L+++RNG G +DDID+LGNRR+R VGEM +NQ+R+GL+R+
Sbjct: 417  DADTGSGVLDQRDILDVLGELINIRNGFGDVDDIDHLGNRRIRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +++  N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLATYSHTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D +VT+DVV+LSA+EE +  IAQA++++DE+G   ++LV  R  GE   +  E++ 
Sbjct: 597  RKVTDAQVTDDVVHLSAIEEGDFVIAQASATVDENGRLVDDLVQVRHRGETTFMRPEQVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA+ 
Sbjct: 657  LMDVSPRQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRAEKPLVGTGMERFVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G+++ VDA RIV+R  E ++    +GVDIY L K+ RSNQNTC NQRP+V
Sbjct: 717  SGVCAVARRGGVIDSVDAKRIVVRVNEDEIIGGEAGVDIYNLTKYLRSNQNTCQNQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPS D+GDLALG+NM +AFMPW+GYNFEDS+L+SER V ED FTSI
Sbjct: 777  HTGDVVARGDILADGPSVDMGDLALGQNMRIAFMPWNGYNFEDSILLSERAVQEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE G++ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVSRDTKLGAEEISSDIPNVGESALSKLDEAGVVYIGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLR P+G+ GTV+DV++F R G++K+ R++S+E++
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRAPTGMKGTVIDVQVFTRDGVEKDSRALSIEQQ 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +   I +   + RL   L GQ    GPK  KK  VLS + + E PR QW+
Sbjct: 957  QLDEVRKDLQETYRIAEDATFERLQRTLSGQVVNGGPK-LKKGDVLSDEYLEELPRQQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +QDE +   +     Q E  +  +++RF++K  K+  GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMQDESLNELLAQADEQLENRRKEMDERFEDKKRKLTQGDDLAPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMPF  +G  +D++LNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RMQPGDKMAGRHGNKGVISAIMPIEDMPFDDNGESIDLILNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG--TGSHTEKISDYDDDSVLRVAEQW 1200
             A  GLG +I+ ++ D +    +  +R FL +V    + +  E++    DD V+ +A+  
Sbjct: 1136 MAARGLGVRIEQMLRDAR-EQQVGEIREFLGQVYNTASSTKVEELDSLSDDEVIALAKNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K+GVP++TPVFDGA E  I  +L +A L ESGQ  LYDG TGE FDRPVTVGY+YMLKLN
Sbjct: 1195 KAGVPMATPVFDGAREHEIKHLLDLAGLPESGQMTLYDGRTGEAFDRPVTVGYMYMLKLN 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1255 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT++Y+SIV G+   + G PESFNVLVKE+++LG+ I+LE+
Sbjct: 1315 DVEGRTKMYKSIVDGDHAMQAGMPESFNVLVKEIRSLGIDIELES 1359


>gi|99080075|ref|YP_612229.1| DNA-directed RNA polymerase subunit beta [Ruegeria sp. TM1040]
 gi|122398437|sp|Q1GK49|RPOB_SILST RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|99036355|gb|ABF62967.1| DNA-directed RNA polymerase beta subunit [Ruegeria sp. TM1040]
          Length = 1379

 Score = 1708 bits (4423), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1380 (60%), Positives = 1071/1380 (77%), Gaps = 13/1380 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    AP     EG++  F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDAPQPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV+Y  + PK+DVD+C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVNYALERPKYDVDECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVNFKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE + E+GKK+T   +K + ++G +  L +  +
Sbjct: 241  SRGWVTPFFPERVRGTRPTYDLVDAATGEIICEAGKKVTPRAVKKMIDEGNITELLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G YVA+DI+N E G IY+EAGD +  +          S++E+  + I DIP+L +D+
Sbjct: 301  HIVGKYVAKDIINEENGAIYVEAGDELTLEYDKDGDIIGGSVKELLDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAQDKNMSRETALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI+A IK LV+LR+GKG +DDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVACIKALVELRDGKGDVDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V DG+VT++V Y+SA EE    +AQAN++LDED  F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVKDGQVTDEVHYMSATEEMRHTVAQANANLDEDNRFVNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPNESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E +VA+ SGAAI+AKRAG+++Q+DA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEIVARDSGAAIMAKRAGVIDQIDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG  V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQTVEKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL ++L G+ AV GPKG + +TV+  D
Sbjct: 960  KDERALQIEREEVERLARDRDDELGILDRNIYARLRDLLLGKTAVKGPKGVRGNTVIDED 1019

Query: 1012 LISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            L+     R QWW  A+++E+  + +E+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1020 LLDNQLTRGQWWMLALEEEQDAQILEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGV 1079

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVF+A+KR +Q GDKMAGRHGNKG++SR++P EDMPFL DGTPVD  LNPLGVPSR
Sbjct: 1080 MKMVKVFIAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLADGTPVDFCLNPLGVPSR 1139

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG KI   + DY+  GD++P+R  + +  G   + E IS  D+
Sbjct: 1140 MNVGQILETHMGWAARGLGLKIDDALQDYRRTGDLTPVRDAMREAYGEDVYEEGISSMDE 1199

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
              ++  A     GVP++TPVFDGA E+ +N  L  A  D+SGQSIL+DG TGE F RPVT
Sbjct: 1200 TQLIEAAGNVTRGVPIATPVFDGAKEDDVNDALVRAGFDQSGQSILFDGRTGEQFARPVT 1259

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1260 VGIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1319

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1379


>gi|116052305|ref|YP_788849.1| DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa
            UCBPP-PA14]
 gi|122261454|sp|Q02T87|RPOB_PSEAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115587526|gb|ABJ13541.1| DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa
            UCBPP-PA14]
          Length = 1357

 Score = 1708 bits (4423), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1365 (53%), Positives = 984/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  + D  +G+ ++E G+++T+  +  L++ GV  L +  D 
Sbjct: 239  ETLNLELVPQRL-RGEVASIDIKDG-SGKVIVEQGRRITARHINQLEKAGVSQLEVPFDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ IV+  TGEI  E    +    L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  LIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++F  LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDII ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMGQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  GP   KK T ++ D +    R QW+
Sbjct: 957  QLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPA-LKKGTEITDDYLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + +  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357


>gi|36333351|gb|AAP75733.1| RNA polymerase beta subunit [Afipia genosp. 3]
          Length = 1374

 Score = 1707 bits (4422), Expect = 0.0,   Method: Composition-based stats.
 Identities = 888/1346 (65%), Positives = 1088/1346 (80%), Gaps = 8/1346 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+   F G  RVRKFFG   E+ ++P+LIEVQKASYD FLM+   P  R +EGLQA F+
Sbjct: 1    MAQQ-TFTGRKRVRKFFGHIREVAEMPNLIEVQKASYDQFLMVAEPPGGREDEGLQAVFR 59

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI+ FS A+MLEFV YEF+PPK+DVD+C  R +TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 60   SVFPISDFSNASMLEFVRYEFEPPKYDVDECRQRGMTYAAPLKVTLRLIVFDIDEETGAR 119

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 120  SVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 179

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D EEILSTFY KI+Y +
Sbjct: 180  AARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEEILSTFYKKILYKR 239

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P  A+    G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ 
Sbjct: 240  TKEGWRVPFDAS-RFRGYSTVNDLIDADTGKVVLEAGKKLTVRNARQLQEKGLKALRLSD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +++P+L +D VN   YIRN
Sbjct: 299  EELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKALNEEGYKELPLLDIDHVNVGPYIRN 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFDS++YDLS VGRVKMNMRL
Sbjct: 359  TLSADKNMTREDALFDIYRVMRPGEPPTLDSAQNMFQSLFFDSERYDLSAVGRVKMNMRL 418

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +LD PD  R +RKEDI+A+I+ LV LR+GKG IDDID+LGNRRVRSVGE+++NQYR+GLL
Sbjct: 419  DLDAPDTHRTLRKEDILAVIQTLVGLRDGKGEIDDIDHLGNRRVRSVGELMENQYRIGLL 478

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+SSVDID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 479  RMERAIKERMSSVDIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 538

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF+ET
Sbjct: 539  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVET 598

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPR 658
            PYRKV DG+VT++VVYLSAMEE    +AQAN SLD  G FT++LV CR     + + +P 
Sbjct: 599  PYRKVKDGRVTDEVVYLSAMEEGRYAVAQANVSLDAKGKFTDDLVVCRAGGTRDVVPLPA 658

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++D++D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME V
Sbjct: 659  DQVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGV 718

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R G+++Q+DA RIVIR+ E  LDP+ SGVDIYRLMK+QRSNQ+TC+NQ
Sbjct: 719  VARDSGAAIAARRTGVIDQIDATRIVIRATED-LDPTKSGVDIYRLMKYQRSNQSTCINQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD+V + DIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+L+SER+V EDV
Sbjct: 778  RPLVKVGDKVAKGDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILLSERIVKEDV 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV  GDILVGKI
Sbjct: 838  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVRAGDILVGKI 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+++
Sbjct: 898  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERALA 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ERE+IE LA+D+DDEQ ILDRN+Y RL ++L G+ AV+GPKGFKK T ++  ++ EYP+
Sbjct: 958  IEREEIERLAKDRDDEQAILDRNVYGRLADLLDGRQAVAGPKGFKKDTKITRAVLEEYPK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            SQWW FA  ++K+   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFV
Sbjct: 1018 SQWWLFAAPNDKLMAEIEAMRKQYDESKKGLEQRFLDKVEKLQRGDELPPGVMKMVKVFV 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   I+ Y    D+ PLR  L K+ G     E I   D+  ++ +  
Sbjct: 1138 THLGWACAGLGKRIGEAIDSYYQREDLKPLRETLRKIYGDD---ETIKSLDEKELVELGR 1194

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML++A  D SGQS +YDG TG+ FDR VTVGYIYMLK
Sbjct: 1195 NLSHGVPIATPVFDGAKEADIEEMLKLAGFDASGQSTVYDGRTGDQFDRRVTVGYIYMLK 1254

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1255 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1314

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTP 1344
            SDDV GRT+VYESIV G DT    +P
Sbjct: 1315 SDDVAGRTKVYESIVRGEDTSRPVSP 1340


>gi|110681145|ref|YP_684152.1| DNA-directed RNA polymerase subunit beta [Roseobacter denitrificans
            OCh 114]
 gi|123361524|sp|Q160X7|RPOB_ROSDO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|109457261|gb|ABG33466.1| DNA-directed RNA polymerase, beta subunit [Roseobacter denitrificans
            OCh 114]
          Length = 1378

 Score = 1707 bits (4422), Expect = 0.0,   Method: Composition-based stats.
 Identities = 840/1379 (60%), Positives = 1062/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLNSGEAEVPTDGEGIAGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LE+V YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEYVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L +LG+D E I+  +Y  I Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYSLGLDQEAIMDAYYDTITYKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         D + G + +  LVD  +GE + E GKK+T   +K L ++G V  L +  +
Sbjct: 241  NKGWVAPFFPDRVRGTRPTYDLVDAASGEVLFERGKKVTPRAVKKLIDEGKVTELLLPYE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N ETG IY+EAGD +  +          + +E+  + I +IP+L +D+
Sbjct: 301  HIAGKFVAKDIINEETGAIYVEAGDELTLEYDKDGTLIGGTAKELVDAGITEIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFD+++YDLS V
Sbjct: 361  VNVGPYMRNTMAQDKNMNRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDAERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +R+EDI+A IK LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRREDIVACIKALVDLRDGRGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV +  VT++V Y+SA EE    +AQAN+ LDEDG F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVENRMVTDEVQYMSATEEMRHTVAQANAQLDEDGRFKNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPSENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRAGIIDQVDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V +  +IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDTVLKGQVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL   + G+ AV GPKG   +  ++ D
Sbjct: 960  KDERALQIEREEVERLARDRDDEMAILDRNIYARLKSTILGKVAVKGPKGVSANAEITED 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+   PR QWWQ A++DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLQMLPRVQWWQLALKDEGDAQVVEALNEQYEIQKRTLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  +   + +Y+ +GD++P+R  L    G   + E I+  D++
Sbjct: 1140 NVGQILETHMGWAARGLGLNVDEALQEYRRSGDLTPVRDALSHAYGENVYDEGIAGMDEE 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            +++  A     GVP++TPVFDGA E  +N  L  A   ESGQSIL+DG TGE F RPVTV
Sbjct: 1200 TLIEAAGNVTRGVPIATPVFDGAKEGDVNDALVRAGFSESGQSILFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|163745526|ref|ZP_02152886.1| DNA-directed RNA polymerase subunit beta [Oceanibulbus indolifex
            HEL-45]
 gi|161382344|gb|EDQ06753.1| DNA-directed RNA polymerase subunit beta [Oceanibulbus indolifex
            HEL-45]
          Length = 1378

 Score = 1707 bits (4421), Expect = 0.0,   Method: Composition-based stats.
 Identities = 838/1379 (60%), Positives = 1071/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLNSGDAETPTDGEGITGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LE+V YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEYVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD ++ RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDNVYARIDRRRKLPVTTLLYALGLDQEAIMDAYYKTVTYKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         D + G + +  LVD DTGE + E+ KK+T   +K L ++G VK L +  D
Sbjct: 241  NKGWVAPFFPDRVRGTRPTYDLVDADTGEILFEATKKVTPRAVKKLLDEGKVKDLLLPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI+N ETG IY+EAGD +  +          + +E+  + I +IP+L +D+
Sbjct: 301  HIVGKFVARDIINEETGAIYVEAGDELTLEYDKDGTLIGGTAKELIDAGITEIPLLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAMDKNMNRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL L+ PD  R + ++DI+A IK LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALEKPDTQRTLDRDDIVACIKALVDLRDGRGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V D  VT++V Y+SA EE    +AQAN++LDE+  F  E+V  R +G
Sbjct: 601  VNKYGFIETPYRVVKDSIVTDEVHYMSATEEMRHTVAQANANLDENMKFVNEMVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPTENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAA +A+RAGI++QVDA RIVIR+ E  L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAYMARRAGIIDQVDASRIVIRATED-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG++V +  +IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGEKVTKGQVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RISQDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL +++ G+ AV GPKG K ++ ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLKDMILGKIAVKGPKGVKANSQITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWWQ A++DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLTRGQWWQLALEDEDDAKIVEALNEQYEIQKRTLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  I   + +YK +GD++P+R  ++   G   + E I+  D+D
Sbjct: 1140 NVGQILETHMGWAARGLGINIDEALQEYKRSGDLTPVREAMQLAYGDDVYEEGITGMDED 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            ++L VA+  + GVP++TPVFDGA E  +N  L+ A  D SGQS+L+DG TGE F RPVTV
Sbjct: 1200 TLLEVADNVRRGVPIATPVFDGAKEADVNDSLKRAGFDTSGQSVLFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|226942770|ref|YP_002797843.1| DNA-directed RNA polymerase subunit beta [Azotobacter vinelandii DJ]
 gi|259494175|sp|C1DKK5|RPOB_AZOVD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226717697|gb|ACO76868.1| DNA-directed RNA polymerase, beta subunit [Azotobacter vinelandii DJ]
          Length = 1358

 Score = 1707 bits (4420), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1366 (52%), Positives = 984/1366 (72%), Gaps = 10/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL   ++ D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGVSKDKLRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   V+    
Sbjct: 179  RIIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASVLLRALGYSTEEVLDIFYDTNVFHVTE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G      + D  +G+ ++E G+++T+  +  L++ G+K L +  + 
Sbjct: 239  QGLSLELVPQRL-RGEIAVFDIKDA-SGKVIVEQGRRITARHINQLEKAGIKELDVPLEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    + +  L +I  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTSAKVIVHPSTGEIIAECNSELTQDLLVKIAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDSTTNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + +EDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  EEIEGAGVLSREDIVDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G+VT+++V+LSA+EE +  IAQA+++LDE+G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGQVTDEIVFLSAIEEADHVIAQASATLDENGRLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R    +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVNNDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDQVARGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVMAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++ER 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIERM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G     G  G KK T +   ++    R QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRAALVGAVCEGG-AGLKKGTEIDDGILDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMADDALNEQLEKAQAYLADRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP+  +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPYDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT--GSHTEKISDYDDDSVLRVAEQW 1200
             A  GLG+KI  ++ + +    ++ LR FL +V     G   E +    D  +L +A   
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRQFLGEVYNEIGGRQKEDLDSLSDSEILDLASNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLN
Sbjct: 1193 RGGVPMATPVFDGARETEIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLN 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 DVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1358


>gi|103486971|ref|YP_616532.1| DNA-directed RNA polymerase subunit beta [Sphingopyxis alaskensis
            RB2256]
 gi|123078349|sp|Q1GT23|RPOB_SPHAL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|98977048|gb|ABF53199.1| DNA-directed RNA polymerase, beta subunit [Sphingopyxis alaskensis
            RB2256]
          Length = 1392

 Score = 1707 bits (4420), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1381 (60%), Positives = 1066/1381 (77%), Gaps = 12/1381 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
            + +      R+RK FG   E +++P+LIEVQ+ SY+ FL  +  P      GL+   +SV
Sbjct: 10   QALEATATKRIRKLFGNIHEAVEMPNLIEVQRESYEQFLRSD--PSIGYVSGLEKTLRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+G A L+FV YE + PK+DV++C  R +TYA P+K+TLRLIVF+VD  T  +S+
Sbjct: 68   FPIRDFAGTAELDFVHYELEAPKYDVEECRQRGITYAAPMKVTLRLIVFEVDSETDTRSV 127

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             DIKEQ +YMGD+PLMT++GTF + G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A 
Sbjct: 128  LDIKEQDVYMGDMPLMTENGTFFVNGTERVIVSQMHRSPGVLFDHDRGKTHSSGKFLFAA 187

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDR+RK+PVTS L ALGM  EEIL+ FY ++V+ +  
Sbjct: 188  RVIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTSLLYALGMTGEEILNHFYDRLVFERAE 247

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + W  P    +   G+K +  +VD  TGE V  +G K++  L     + G+  L I ++ 
Sbjct: 248  NGWKVPFMVEN-WRGSKPAFDVVDAKTGEVVFAAGHKISPRLANKAAKDGLDTLLIPTEE 306

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A D++N  TGEIYIEAGD +  ++LE++  + I  + +L +D  N   +IRNTL
Sbjct: 307  IFGRYSAYDLINESTGEIYIEAGDEVSAENLEKLDAAGIDKLVLLDIDHNNTGPWIRNTL 366

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DK +DR  AL DIYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL L
Sbjct: 367  KADKAEDRDQALSDIYRVMRPGEPPTRETAEALFAGLFFDPERYDLSAVGRVKLNMRLGL 426

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D V  +R EDI+A++K LV+L++GKG IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 427  DAEDTVTTLRSEDILAVVKELVNLKDGKGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 486

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 487  ERAVKERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVS 546

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIETPY
Sbjct: 547  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIETPY 606

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGKVTN+VVYLSAMEE    +AQAN+ L+ DGSF +EL+  R AGE ++ PRE+I 
Sbjct: 607  RRVVDGKVTNEVVYLSAMEESKHTVAQANADLNPDGSFIDELISAREAGEFLMAPREQIT 666

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME  VA+ 
Sbjct: 667  LMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPVVGTGMEETVARD 726

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+R G+++QVDA RIVIR+ +  ++P  SGVDIYRL KFQRSNQNTC+NQRPLV
Sbjct: 727  SGAAIAARRGGVIDQVDATRIVIRATD-MVEPGKSGVDIYRLQKFQRSNQNTCINQRPLV 785

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD VR  DIIADGPST+LG+LALG+N+LVAFMPW+GYN+EDS+LISER+V +DVFTSI
Sbjct: 786  KVGDVVRAGDIIADGPSTELGELALGKNVLVAFMPWNGYNYEDSILISERIVKDDVFTSI 845

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEV ARDT+LGPE+ITRDIPNV EE L+N+DE GI+ +GAEV PGDIL GKITPKG
Sbjct: 846  HIEEFEVTARDTRLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVGPGDILAGKITPKG 905

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGTVV+VR+FNRHGIDK+ER+I++ERE
Sbjct: 906  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTVVEVRVFNRHGIDKDERAIAIERE 965

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE L +D DDE+ IL+R  +S L ++L GQ   + PKG KK  +++ +++    R+ WW
Sbjct: 966  EIERLKQDADDERAILNRATFSSLKDLLVGQATSAVPKGLKKGDIVTEEMLVGLDRADWW 1025

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + AV D+K Q  +E++K QY+ +   +  ++++++EK+Q GD++ PGVL++VKVFVA+KR
Sbjct: 1026 KLAVVDDKAQTALEAIKAQYDDAIKRINAKYEDRVEKLQRGDELAPGVLKMVKVFVAVKR 1085

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRILP EDMPFL+DGTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1086 KLQPGDKMAGRHGNKGVISRILPVEDMPFLEDGTPVDIVLNPLGVPSRMNVGQILETHLG 1145

Query: 1143 WACVGLGKKIKSLINDYKANGD-------ISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            WA  GLG+++   + +++              +R  LE V G   + E I   D + ++ 
Sbjct: 1146 WASRGLGQQVTRALEEWRDANPDATGGEMPEAVREKLEHVYGAE-YVEDIRSRDAEGIIE 1204

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A   K GVP +TPVFDGA E  +++ML +A LDESGQS LYDG TG+ FDR VTVGYIY
Sbjct: 1205 LASNLKVGVPFATPVFDGAKEADVSNMLTLAGLDESGQSDLYDGRTGDKFDRKVTVGYIY 1264

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEML
Sbjct: 1265 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEML 1324

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDV+GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +   ++  +  
Sbjct: 1325 TVKSDDVIGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELSSYAEEDPDEGP 1384

Query: 1376 E 1376
            E
Sbjct: 1385 E 1385


>gi|329850779|ref|ZP_08265624.1| DNA-directed RNA polymerase, beta subunit [Asticcacaulis biprosthecum
            C19]
 gi|328841094|gb|EGF90665.1| DNA-directed RNA polymerase, beta subunit [Asticcacaulis biprosthecum
            C19]
          Length = 1358

 Score = 1706 bits (4419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 850/1366 (62%), Positives = 1060/1366 (77%), Gaps = 8/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    R+RK FG+ PE I +P+LIEVQ++SY+ FL   +   +R  +GL+A F+SV
Sbjct: 1    MPLTFTQKKRIRKSFGRIPEAIQMPNLIEVQRSSYEQFLQRFVRVADRVEDGLEAVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+  F+  A LE+VSYEF+ PK+DV++C+ RD+TYA PLK+ LRLIVF+ DE TGA+S+
Sbjct: 61   FPVKDFNERATLEYVSYEFEEPKYDVEECIQRDITYAAPLKVKLRLIVFETDEDTGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT+ GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+  
Sbjct: 121  KDIKEQDVYMGDIPLMTEKGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFGA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++VRIDRRRK+P TSFL ALGMD EE+L TFY  + Y +R 
Sbjct: 181  RIIPYRGSWLDFEFDAKDILYVRIDRRRKLPATSFLFALGMDGEEVLKTFYEVVPYEKRD 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P    +   G K    L+D ++GE V  +G K+++   K L +  VKFL ++ D 
Sbjct: 241  AGWVTPY-KFERWRGVKPEFDLIDAESGEVVAPAGTKISARNAKKLGDT-VKFLLLSQDA 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A D VN  TGEIY EAGD +D  S++ +  +    + +L +D V    Y+R+TL
Sbjct: 299  LIGRYLAGDAVNFATGEIYAEAGDELDAASVKALEDNGFTTVDVLDIDHVTVGPYMRSTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  R+DAL DIYRVMRPG+  T   AE+MF  LFF+ ++YDLS+VGRVKMNMRL  
Sbjct: 359  RVDKNSSREDALFDIYRVMRPGEPPTIEAAEAMFGSLFFELERYDLSSVGRVKMNMRLEQ 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D  R +R++DI+ I+KILV LR+G+G IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 419  DVADSERVLRRDDILKILKILVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+SSVDID+VMP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 479  ERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YGFIE+PY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG    DVVY+SAMEE    IAQAN  LD D    E+LV  R  GE  L     +D
Sbjct: 599  RKVVDGVAKEDVVYMSAMEESKHVIAQANIVLDSDKRIVEDLVQGRVNGEPGLQQASTVD 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPL+K++APFVGTGME VVA+ 
Sbjct: 659  FMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKSDAPFVGTGMEEVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA + A+R+G+VEQ+D  RIV+R+ E + DP+  GVDIYRL KFQRSNQNTC+NQRP+V
Sbjct: 719  SGATVGARRSGVVEQIDGTRIVVRATEEN-DPTKPGVDIYRLSKFQRSNQNTCINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+V   DIIADGPSTDLGDLALGRN+LVAFMPW+GYNFEDS+LISER+V +D+FTSI
Sbjct: 778  KVGDKVAAGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNFEDSILISERIVRDDIFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H+EEFEVMARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 838  HLEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHG++K+ER+ ++ER 
Sbjct: 898  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGVEKDERAQAIERA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE L +D+DDE  IL+RNIY RL EIL G+NAVSGPKG  +  V + D + E  R  WW
Sbjct: 958  EIERLGKDRDDELHILERNIYGRLKEILIGKNAVSGPKGLGRGEV-TEDKLGEISRGLWW 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q A++DEK+   +E++  Q++ ++  L+ RF++K+EK+Q GD++PPGV+++VKVFVA+KR
Sbjct: 1017 QIALEDEKIMSEIEAMNRQFQDARKRLDRRFEDKVEKLQRGDELPPGVMKMVKVFVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+ILP EDMPFL DG  VDIVLNPLGVPSRMNVGQIFETHLG
Sbjct: 1077 KLQPGDKMAGRHGNKGVISKILPVEDMPFLADGEHVDIVLNPLGVPSRMNVGQIFETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WAC  +GK+I  ++ D++  G    L   L+ V G      +     ++ ++ +A     
Sbjct: 1137 WACANIGKQIGKMLEDWQNGGQKQALIDHLQAVYGKDQELPE----SEEDLIELARNLTR 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA    I  ML MA L+ SGQSIL+DG TGE F RPVTVG IYMLKL+H+
Sbjct: 1193 GVPIATPVFDGAHINDIEDMLEMAGLNRSGQSILFDGQTGEQFKRPVTVGIIYMLKLHHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT+VYE+IV G+D+FE G PESFNVL+KEM++LGL+++LEN + 
Sbjct: 1313 AGRTKVYEAIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELENGQG 1358


>gi|163732880|ref|ZP_02140325.1| DNA-directed RNA polymerase subunit beta [Roseobacter litoralis Och
            149]
 gi|161394240|gb|EDQ18564.1| DNA-directed RNA polymerase subunit beta [Roseobacter litoralis Och
            149]
          Length = 1378

 Score = 1706 bits (4419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 840/1379 (60%), Positives = 1061/1379 (76%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLNSGEADVPTDGEGITGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LE+V YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEYVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L +LG+D E I+  +Y  I Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYSLGLDQEAIMDAYYNTITYKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         D + G + +  LVD  +GE + E GKK+T   +K L ++G V  L +  +
Sbjct: 241  NKGWVAPFFPDRVRGTRPTYDLVDAASGEILFEKGKKVTPRAVKKLIDEGKVTELLLPYE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N ETG IY+EAGD +  +          + +E+  + I +IP+L +D+
Sbjct: 301  HIAGKFVAKDIINEETGAIYVEAGDELTLEYDKDGTLIGGTAKELVEAGITEIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFD+++YDLS V
Sbjct: 361  VNVGPYMRNTMAQDKNMNRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDAERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +R+EDI+A IK LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRREDIVACIKALVDLRDGRGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV +  VT++V Y+SA EE    +AQAN+ LDEDG F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVENRMVTDEVQYMSATEEMRHTVAQANAQLDEDGRFKNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPSENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRAGIIDQVDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V +  +IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDTVLKGQVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL   + G+ AV GPKG   +  ++ D
Sbjct: 960  KDERALQIEREEVERLARDRDDEMAILDRNIYARLKSTIMGKVAVKGPKGVSSNAEITDD 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+   PR QWWQ A++DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLQMLPRGQWWQLALKDEADAQVVEALNEQYEIQKRTLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLGDGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  +   + +Y+ +GD++P+R  L    G   + E I   D+D
Sbjct: 1140 NVGQILETHMGWAARGLGVNVDEALQEYRRSGDLTPVRDALSLAYGQDVYDEGIVGMDED 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            +++  A     GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F RPVTV
Sbjct: 1200 TLIEAAGNVTRGVPIATPVFDGAKEADVNDALTRAGFDTSGQSVLFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|114764154|ref|ZP_01443392.1| DNA-directed RNA polymerase beta subunit [Pelagibaca bermudensis
            HTCC2601]
 gi|114543306|gb|EAU46322.1| DNA-directed RNA polymerase beta subunit [Roseovarius sp. HTCC2601]
          Length = 1378

 Score = 1706 bits (4419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1380 (60%), Positives = 1070/1380 (77%), Gaps = 14/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK+FGK  E++++P+LIEVQK+SY+ FL     P     EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYFGKIREVLEMPNLIEVQKSSYELFLKSGDQPQPTDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFVSYE + PK+DV++C+ RD+TY+ PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVSYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y+ R 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYKTVTYNLRR 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITS 300
            G+ W         + G + +  LVD D+GE + E+ KK+T   +K L ++G V+ L +  
Sbjct: 241  GEGWVTKFFPE-RVRGTRPTYDLVDADSGEIIAEATKKVTPRAVKKLIDEGNVQNLLLPF 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVD 350
            D + G YV++DI+N ETG IY+EAGD +             +L+E+  + I +IP+L +D
Sbjct: 300  DQIVGKYVSKDIINEETGAIYVEAGDELTWTVDKDGDVTGGTLKELVDAGITEIPVLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +V    Y+RNT+  DKN DR  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS 
Sbjct: 360  NVTVGPYMRNTMAQDKNMDRNSALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRL L+ PD  R + ++DI+  IK LV+LR+GKG +DDID+LGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLALEKPDTQRTLDRDDIVKCIKALVELRDGKGEVDDIDHLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FA
Sbjct: 540  PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIETPYR V D +VT++V Y+SA EE    +AQAN+++DE G F  E+V  R +
Sbjct: 600  RVNKYGFIETPYRVVKDKQVTDEVHYMSATEEMRHTVAQANANIDEGGQFINEMVNTRQS 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  L P E +D ID SPKQ+VS+ ASLIPFLENDD+NR LMG NMQRQAVP L++EAP 
Sbjct: 660  GDYTLAPAESVDLIDVSPKQLVSVGASLIPFLENDDANRALMGANMQRQAVPTLRSEAPL 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E  VA  SGAAI A RAGIV+QVDA RIVIR+ E  L+   +GVDIYR+ KFQRS
Sbjct: 720  VGTGIEGKVAIDSGAAIQAHRAGIVDQVDAQRIVIRATED-LELGDAGVDIYRMRKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRPL+KVGD+V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LIS
Sbjct: 779  NQNTCINQRPLIKVGDKVGKGEVIADGPSTDMGELALGKNVIVAFMPWNGYNYEDSILIS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V P
Sbjct: 839  ERIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL +++ G+ AV GPKG K ++ ++S
Sbjct: 959  EKDERALQIEREEVEQLARDRDDELAILDRNIYARLGDLILGKTAVKGPKGVKPNSEITS 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +L+    R QWWQ A+ +E+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1019 ELLETLSRGQWWQLALAEEQDAQIVEALHEQYEAQKRALDARFEDKVEKVRRGDDLPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVFVA+KR +Q GDKMAGRHGNKG++SR++P EDMPFL+DGTPVD  LNPLGVPSR
Sbjct: 1079 MKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLEDGTPVDFCLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG KI   + DY+ +GD++P+R  +    G   + E I+D ++
Sbjct: 1139 MNVGQILETHMGWASRGLGIKIDDALQDYRRSGDLTPVREAMRIAYGDEVYDEGIADMEE 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            D ++  A     GVP++TPVFDGA E  +N  L  A  D SGQS L+DG TGE F R VT
Sbjct: 1199 DLLVEAAGNVTRGVPIATPVFDGAKEADVNDALSRAGFDTSGQSRLFDGRTGEEFARKVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D +E G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVKGEDNYEAGVPESFNVLVKEVRGLGLNMELLDAEGEE 1378


>gi|159042824|ref|YP_001531618.1| DNA-directed RNA polymerase subunit beta [Dinoroseobacter shibae DFL
            12]
 gi|189043854|sp|A8LM40|RPOB_DINSH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157910584|gb|ABV92017.1| DNA-directed RNA polymerase, beta subunit [Dinoroseobacter shibae DFL
            12]
          Length = 1378

 Score = 1706 bits (4417), Expect = 0.0,   Method: Composition-based stats.
 Identities = 848/1382 (61%), Positives = 1080/1382 (78%), Gaps = 16/1382 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+ V+  G  R RK++GK  E++++P+LIEVQK+SYD FL     P     EG+   F+
Sbjct: 1    MAQTVL--GQKRFRKYYGKIREVLEMPNLIEVQKSSYDLFLKSGDQPQPMDGEGIMGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAK
Sbjct: 59   SVFPIKDFNETAVLEFVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS- 239
            ACRIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L +LGMD ++I+  +Y  + Y+ 
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDLVFARIDRRRKLPVTTLLYSLGMDQQDIMDAYYDTVTYTH 238

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGI 298
            ++G+ W         + G + +  +VD  TGE + E+GKK+T   +K L ++G V  + +
Sbjct: 239  RKGEGWVTKFFPE-RIRGTRPTQDVVDAATGEVIAEAGKKVTPRAVKQLIDEGNVSEILV 297

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILY 348
              D + G + A+DI+N E G IY+EAGD +  +          +L+E+  + I +IP+L 
Sbjct: 298  PFDGIIGKFAAKDIINEENGAIYVEAGDELTWEVDKDGAVTGGTLKELLDAGIEEIPVLD 357

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D++   AY+RNTL  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDL
Sbjct: 358  IDNITVGAYMRNTLAADKNMNRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDL 417

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            S VGRVKMNMRL LD  D VR +RKEDI++ IK LVDLR+G+G IDDID+LGNRRVRSVG
Sbjct: 418  SAVGRVKMNMRLALDAEDTVRTLRKEDIVSCIKALVDLRDGRGDIDDIDHLGNRRVRSVG 477

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  + 
Sbjct: 478  ELMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQ 537

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +
Sbjct: 538  TNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLAT 597

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FARVN YGFIETPYR+V DGKVT++V Y+SA EE    +AQAN++LDE GSF  E+V  R
Sbjct: 598  FARVNKYGFIETPYRRVEDGKVTDEVNYMSATEEMRHTVAQANANLDESGSFVNEMVNTR 657

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             +GE  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+A+A
Sbjct: 658  QSGEYTLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQADA 717

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            PFVGTG+E VVA+ SGAAI+A+R G ++QVDA RIVIR+ E  L+P   GVDIYRL KFQ
Sbjct: 718  PFVGTGIEGVVARDSGAAIMARRGGFIDQVDATRIVIRATED-LEPGDPGVDIYRLRKFQ 776

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQRPLVKVGD+V ++D+IADGPSTDLG+LALG+N++VAFMPW+GYN+EDS+L
Sbjct: 777  RSNQNTCINQRPLVKVGDKVGKDDVIADGPSTDLGELALGKNVVVAFMPWNGYNYEDSIL 836

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V
Sbjct: 837  ISERVARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADV 896

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+FNRH
Sbjct: 897  GPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRLPPGDFGTVVEVRVFNRH 956

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K+ER++ +ERE++E LARD+DDE  IL+RNIY+RL +++ G+ AV GPKG K  + +
Sbjct: 957  GVEKDERALQIEREEVESLARDRDDEMAILERNIYARLKDMILGKTAVKGPKGVKPGSEI 1016

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + DL+    R QWWQ A++DE   + VE+L  QYE  K  L  RF++K+EK++ GDD+PP
Sbjct: 1017 TEDLLGTLSRGQWWQLALEDEAEAQMVEALNQQYEAQKRALTARFEDKVEKVRRGDDLPP 1076

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV+++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD VLNPLGVP
Sbjct: 1077 GVMKMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFVLNPLGVP 1136

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMNVGQI ETH+GWA  G+G KI   + +Y+ +GD++P+R  +    G  ++ E IS  
Sbjct: 1137 SRMNVGQILETHMGWAARGMGLKIDEALGEYRRSGDMTPVREAMRLAYGDEAYEEAISGL 1196

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            D D +L  A     GVP++TPVFDGA E  +N  L  A  D SGQS LYDG TGE F R 
Sbjct: 1197 DQDDLLERAGNVTRGVPIATPVFDGAKEADVNDALTRAGFDTSGQSDLYDGRTGEKFARQ 1256

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1257 VTVGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1316

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  
Sbjct: 1317 YTLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEG 1376

Query: 1369 KN 1370
            + 
Sbjct: 1377 EE 1378


>gi|254477218|ref|ZP_05090604.1| DNA-directed RNA polymerase, beta subunit [Ruegeria sp. R11]
 gi|214031461|gb|EEB72296.1| DNA-directed RNA polymerase, beta subunit [Ruegeria sp. R11]
          Length = 1382

 Score = 1706 bits (4417), Expect = 0.0,   Method: Composition-based stats.
 Identities = 838/1379 (60%), Positives = 1072/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 5    MAQSFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDAEQPLDGEGIMGVFQSV 64

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 65   FPIKDFNETSVLEFVKYSFERPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 124

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 125  KDIKEQDVYMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 184

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 185  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVNFKLEK 244

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE   E+GKK+T   +K + ++G +  L +  +
Sbjct: 245  SRGWVTPFFPERVRGTRPTYDLVDAATGEIFAEAGKKVTPRAVKKMIDEGTITELLVPFE 304

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G YVA+DI+N E G IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 305  HIVGKYVAKDIINEENGAIYVEAGDELTLEYDKGGDIIGGTVKELLDAGITDIPVLDIDN 364

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 365  INVGPYMRNTMAQDKNMGRETALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 424

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI++ IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 425  GRVKMNMRLALDAEDTQRTLRKEDIVSCIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 484

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 485  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 544

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 545  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 604

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V +G+VT++V Y+SA EE    +AQAN++LDE+G F  +LV  R +G
Sbjct: 605  VNKYGFIETPYRVVKEGQVTDEVHYMSATEEMRHTVAQANATLDENGKFINDLVSTRQSG 664

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 665  DYTLAPNESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 724

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E +VA+ SGAAI+AKRAGI++Q+DA RIVIR+ E  L+   +GVDIYR+ KFQRSN
Sbjct: 725  GTGIEEIVARDSGAAIMAKRAGIIDQIDAQRIVIRATED-LELGDAGVDIYRMRKFQRSN 783

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG +VR+ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 784  QNTCINQRPLVKVGQQVRKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 843

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 844  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 903

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 904  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 963

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  +L G+ AV GPKG K  +V++ +
Sbjct: 964  KDERALQIEREEVERLARDRDDELGILDRNIYARLRGMLLGKTAVKGPKGIKAGSVITEE 1023

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWW  A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1024 LLDSLSRGQWWMLALEDEQDAQVVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1083

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1084 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1143

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG K+   + +Y+ +GD++P+R  +    G   + E I+D  ++
Sbjct: 1144 NVGQILETHMGWAARGLGIKVDEALQEYRRSGDLTPVREAMHHAYGDDVYDEGIADMSEE 1203

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E+ +N  L  A  D+SGQSIL+DG TGE F RPVTV
Sbjct: 1204 DLLEAAGNVTRGVPIATPVFDGAKEDDVNDALVRAGFDQSGQSILFDGRTGEQFARPVTV 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1264 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1324 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1382


>gi|126724853|ref|ZP_01740696.1| DNA-directed RNA polymerase subunit beta [Rhodobacterales bacterium
            HTCC2150]
 gi|126706017|gb|EBA05107.1| DNA-directed RNA polymerase subunit beta [Rhodobacterales bacterium
            HTCC2150]
          Length = 1378

 Score = 1705 bits (4415), Expect = 0.0,   Method: Composition-based stats.
 Identities = 832/1379 (60%), Positives = 1063/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  R+RK++GK  E++++P+LIEVQK+SYD FL           EG++  F+SV
Sbjct: 1    MATTYLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLKSGDQLQPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C  RD+TY+ PLK+TLRLIVF++DE TGAKS+
Sbjct: 61   FPIKDFNETAILEFVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFEIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYETVTYKLDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + +  +VD  +GE + E+GKK+T   +K L ++G V  + +  D
Sbjct: 241  NKGWVTKFFPERVRGTRPTYDIVDAASGEVIAEAGKKVTPRAVKKLIDEGKVSEVLVPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVDS 351
             + G + A+D++N E G IY+EAGD +  +           L+E+  + +++IPIL +D+
Sbjct: 301  AIIGKFAAKDMINEENGAIYVEAGDELTWELDKAGEVSGGSLKELVDAGVKEIPILDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAVDKNMGRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRLNLD  D +R +R+EDI++ I  LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLNLDAEDTMRTLRREDIVSCIGALVNLRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV  G+VT++V Y+SA EE    +AQAN+SLDE G F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVEKGQVTDEVKYMSATEEMRHTVAQANASLDEKGRFANDLVSTRRSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L  R+ +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+A AP V
Sbjct: 661  EYTLAQRDAVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQATAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+   DL+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRAGIIDQVDATRIVVRAT-ADLEMGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDVVTKGEVIADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+    GPKG K  T++  +
Sbjct: 960  KDERALQIEREEVESLARDRDDEFAILDRNIYARLQGMIFGKEVAKGPKGVKSGTIVDDE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R  WWQ A+ DE   +NVE+L  QYE+ K  LE RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLEMVGRHMWWQLAMADESTAQNVEALNTQYESQKRALEARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++SR++P EDMPFL DGT VD VLNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLADGTSVDFVLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG KI   + +Y+ +GD++P+R  L+   G   + E +++  + 
Sbjct: 1140 NVGQILETHMGWAARGLGLKIDDALGEYRRSGDVTPVRDALKIAYGENVYDEGLANMQEA 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A    +GVP++TPVFDGA E  +N  L  A   ESGQS LYDG TGE F R VTV
Sbjct: 1200 DLLEAAGNVVNGVPIATPVFDGAKEADVNDALARAGFSESGQSDLYDGRTGEKFSRQVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVDE 1378


>gi|126732286|ref|ZP_01748086.1| DNA-directed RNA polymerase subunit beta [Sagittula stellata E-37]
 gi|126707155|gb|EBA06221.1| DNA-directed RNA polymerase subunit beta [Sagittula stellata E-37]
          Length = 1378

 Score = 1705 bits (4415), Expect = 0.0,   Method: Composition-based stats.
 Identities = 842/1380 (61%), Positives = 1073/1380 (77%), Gaps = 14/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+R+++GK  E++++P+LIEVQK+SY+ FL     P     EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRRYYGKIREVLEMPNLIEVQKSSYELFLKSGDQPKPMDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV Y+ + PK+DV++C+ RD+TYA PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVDYDLEKPKYDVEECMQRDMTYAAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS-QR 241
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I   +Y  + +  +R
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAICDAYYNTVNFEYRR 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITS 300
            G+ W         + G + +  LVD DTGE + E+ KK+T   +K L ++G VK L +  
Sbjct: 241  GEGWATKFFPE-RVRGTRPTFDLVDADTGEIIAEATKKVTPRAVKKLIDEGKVKQLLVPF 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVD 350
            + + G YVA+DI+N ETG IY+EAGD +              L+E+  + I +IP+L +D
Sbjct: 300  EHIVGKYVAKDIINEETGAIYVEAGDELTWTVDKDGEVSGGSLKELLDAGITEIPVLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N   YIRNT+  DKN  R+ ALLDIYRVMRPG+  T   A ++F+ LFFDS++YDLS 
Sbjct: 360  NINVGPYIRNTMEQDKNVSRETALLDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRL LD PD  R + ++DI+A IK LVDLR+GKG IDDID+LGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLALDKPDTQRTLDRDDIVACIKALVDLRDGKGDIDDIDHLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FA
Sbjct: 540  PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIETPYR V DG VT++V Y+SA EE    +AQAN+SLDE+G FT E+V  R A
Sbjct: 600  RVNKYGFIETPYRVVTDGVVTDEVHYMSATEEMRHTVAQANASLDENGKFTNEMVNTRQA 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVP L+AEAP 
Sbjct: 660  GDYTLAPSETVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPTLRAEAPL 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E VVA+ SGAA++AKRAGI++QVDA RIVIR+ E  L+   +GVDIYR+ KFQRS
Sbjct: 720  VGTGIEEVVARDSGAAVMAKRAGIIDQVDAQRIVIRATED-LELGDAGVDIYRMRKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQ+PLVKVGD V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LIS
Sbjct: 779  NQNTCINQKPLVKVGDTVTKGEVIADGPSTDMGELALGKNVIVAFMPWNGYNYEDSILIS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V P
Sbjct: 839  ERIAKDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++ +ERE+IE LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG + ++ +  
Sbjct: 959  EKDERALQIEREEIERLARDRDDELAILDRNIYARLKGMILGKTAVKGPKGVRANSEIDE 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +L+S   R QWWQ A+ +E   ++VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1019 ELLSTLTRGQWWQLALGEEDDAKHVEALHEQYEIQKRALDARFEDKVEKVRRGDDLPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVF+A+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL DGTPVD  LNPLGVPSR
Sbjct: 1079 MKMVKVFIAVKRKLQPGDKMAGRHGNKGVVSRVVPQEDMPFLSDGTPVDFCLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA   LG ++   + +Y+ +GD++P+R  L+ V G   + E  +D D+
Sbjct: 1139 MNVGQILETHMGWASRALGIQVDEALQEYRRSGDLTPVRDALKIVYGDEVYQEGFADVDE 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
             +++ +A     GVP++TPVFDGA E  +N  L+ A  D SGQS L+DG TGE F R VT
Sbjct: 1199 TALVEMAGNVTRGVPIATPVFDGAKEADVNDALKRAGFDTSGQSRLFDGRTGEEFSRKVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGMKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|163796927|ref|ZP_02190884.1| 30S ribosomal protein S12 [alpha proteobacterium BAL199]
 gi|159177916|gb|EDP62465.1| 30S ribosomal protein S12 [alpha proteobacterium BAL199]
          Length = 1392

 Score = 1704 bits (4413), Expect = 0.0,   Method: Composition-based stats.
 Identities = 845/1387 (60%), Positives = 1058/1387 (76%), Gaps = 28/1387 (2%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
             F G  RVRK FG+  E+  +P+LIEVQK+SYD FL M + P++R + GLQ  FKSVFPI
Sbjct: 8    SFTGRKRVRKNFGRIAEVAPMPNLIEVQKSSYDAFLQMGVEPEKRTDVGLQEVFKSVFPI 67

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
              FS  AMLEFV YE D PK+DV++C  R LT+A PLK+TLRL+V+DVDE TG+KSI+DI
Sbjct: 68   RDFSERAMLEFVGYELDEPKYDVEECQQRGLTFAAPLKVTLRLVVWDVDEETGSKSIRDI 127

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQ +YMGD+PLMT  GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+I
Sbjct: 128  KEQDVYMGDMPLMTAHGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVI 187

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKV-------------PVTSFL------------MA 220
            P +G W+D EFD+KD ++VRIDRRRK+              +                  
Sbjct: 188  PYRGSWLDFEFDAKDNVYVRIDRRRKLPATTLLLALMSDDSIKYLAECHRTGEEAHRDRV 247

Query: 221  LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
            +GM +EEIL+ FY  + Y++ G  W     A  L  G+K+   LVD DTGE V ++G K+
Sbjct: 248  VGMGAEEILTNFYGTVTYTREGAGWRTSFDAERL-RGSKLVRDLVDADTGEVVAKAGDKI 306

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
            T    + L E G+K + +  + L G YV  D+++  TG ++ +AG+ I  + LE++    
Sbjct: 307  TPRSSRKLIEAGLKDMWVPDEELIGAYVGSDLIDESTGLVHCDAGEEITTELLEKVGGVG 366

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            I  +P+L +D +N  AY+RNTL  DKN  R++AL+DIYRVMRPG+  T   AE++F+ LF
Sbjct: 367  ITLLPVLAIDHLNIGAYMRNTLALDKNATREEALVDIYRVMRPGEPPTLETAEALFHGLF 426

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            FDS++YDLS VGRVKMN RL L+T D +R +RK+DI+AI+K+L++L++GKG IDDID+LG
Sbjct: 427  FDSERYDLSAVGRVKMNARLGLETDDQLRVLRKDDILAILKVLMELKDGKGEIDDIDHLG 486

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+++NQYR+GLLRMER+I+ER+SSV+ID+VMP DLINAKP  +AV EFF SS
Sbjct: 487  NRRVRSVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSS 546

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NI
Sbjct: 547  QLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 606

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL ++ARVN YGFIETPYRKV D KVT++V Y+SAMEE    +AQAN+ +D DG F
Sbjct: 607  GLINSLATYARVNQYGFIETPYRKVTDSKVTDEVRYISAMEEGRYTVAQANAPVDADGKF 666

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             EELV  R  G+  L   E ID ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQA
Sbjct: 667  VEELVPVRKRGDFGLARPEDIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQA 726

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPLL+AEAPFVGTGME  VA+ SG  IVA+R+G+V+QVDA RIVIR+ E  L+ ++S VD
Sbjct: 727  VPLLQAEAPFVGTGMEGTVARDSGVTIVARRSGVVDQVDAQRIVIRANED-LEGASSNVD 785

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IYRL+KFQRSNQNTC+ QRPLVKVGD V R DII DGPSTDLG+LALGRN+LVAFMPW+G
Sbjct: 786  IYRLLKFQRSNQNTCITQRPLVKVGDVVSRGDIIGDGPSTDLGELALGRNVLVAFMPWNG 845

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+LISER+V +DVFTSIHIEEFE+MARDTKLG EEITRDIPNV EE LKN+DE G
Sbjct: 846  YNFEDSILISERIVRDDVFTSIHIEEFEIMARDTKLGQEEITRDIPNVGEEALKNLDEAG 905

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL+VP GV+GT+V
Sbjct: 906  IVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKVPPGVNGTIV 965

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            +VR+F+R G+DK+ERS ++ER +IE LA+D+DDE+ IL+R  + RL E+L G+ A +GPK
Sbjct: 966  EVRVFSRRGVDKDERSQAIERAEIERLAKDRDDERAILERGFFDRLRELLMGKTATAGPK 1025

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            GFK   VL+ ++ ++Y   QW QF   D+K+   +E LK  ++ S   L+ RF NK+EK+
Sbjct: 1026 GFKAG-VLTPEVFAQYTPGQWRQFVSDDDKLMDYLEGLKEHFDRSIDFLKARFDNKVEKL 1084

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG++S+I P EDMP+L DGT VDI
Sbjct: 1085 QRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKINPIEDMPYLDDGTAVDI 1144

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQI ETHLGWA  GLG++I+ ++     N  +  LR  LE V     
Sbjct: 1145 VLNPLGVPSRMNVGQILETHLGWAAAGLGRQIRQMLESMGENPKVPELRVKLENVYSADQ 1204

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
               ++    DD V+ +A     GVP++TPVFDGA E+ I  ML  A L+ SGQ  L+DG 
Sbjct: 1205 FNAEVKPLGDDEVVELARNLTRGVPMATPVFDGAREDDIVDMLGRAGLNSSGQVDLWDGR 1264

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +GE FDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1265 SGEQFDRQVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1324

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D FE G PESFNVLVKE+++LGL+
Sbjct: 1325 ALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNVLVKELRSLGLN 1384

Query: 1361 IDLENSR 1367
            ++L    
Sbjct: 1385 VELNQEE 1391


>gi|146308930|ref|YP_001189395.1| DNA-directed RNA polymerase subunit beta [Pseudomonas mendocina ymp]
 gi|166229298|sp|A4XZ97|RPOB_PSEMY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145577131|gb|ABP86663.1| DNA-directed RNA polymerase subunit beta [Pseudomonas mendocina ymp]
          Length = 1357

 Score = 1704 bits (4412), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL   ++ ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQQGVSKEQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   V+  + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASVLLRALGYSTEEVLDAFYDTNVFHVKN 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D  +G+ ++E G+++T+  +  L + G+K L +  D 
Sbjct: 239  ESLSLELVPQRL-RGEVAVLDIKDA-SGKVIVEQGRRITARHINQLDKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +    L ++  + +     LY + ++   +I +TL
Sbjct: 297  VIGRTTAKAIVHPATGEIIAECNTELTADLLAKMAKANVVRFETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDSTTNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKVT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGKVTDEIVFLSAIEEADHVIAQASATLNDKGELVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDQVARGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEISSDIPNVGEAALNKLDEAGIVYVGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E++
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKQ 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK T ++ + +    R QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGAIAEGG-AGLKKGTAITDEFLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQMLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + ++ D+ +L +A+  K
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLAEIYNEIGGRQENLDEFSDNEILELAKNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++T VFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATAVFDGAKETEIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|330505214|ref|YP_004382083.1| DNA-directed RNA polymerase subunit beta [Pseudomonas mendocina
            NK-01]
 gi|328919500|gb|AEB60331.1| DNA-directed RNA polymerase subunit beta [Pseudomonas mendocina
            NK-01]
          Length = 1357

 Score = 1703 bits (4411), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL   ++ ++  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQQGVSKEQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   VY  + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASVLLRALGYSTEEVLDAFYDTNVYHVKN 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D  +G+ ++E G+++T+  +  L + G+K L +  D 
Sbjct: 239  ESLSLELVPQRL-RGEVAVLDIKDA-SGKVIVEQGRRITARHINQLDKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +    L ++  +++     LY + ++   +I +TL
Sbjct: 297  VIGRTTAKAIVHPATGEIIAECNTELTADLLVKMAKAQVVRFETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDSTTNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G+VT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGQVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDQVSRGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEISSDIPNVGEAALNKLDEAGIVYVGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E++
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKQ 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK T ++ + +    R QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGAIAEGG-AGLKKGTAITDEFLDGLERGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMADDALNEQLEKAQAYISDRRQMLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + ++ D+ +L +A+  K
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLAEIYNEIGGRQENLDEFSDNEILELAKNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++T VFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH
Sbjct: 1193 GGVPMATAVFDGAKETEIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|254487096|ref|ZP_05100301.1| DNA-directed RNA polymerase, beta subunit [Roseobacter sp. GAI101]
 gi|214043965|gb|EEB84603.1| DNA-directed RNA polymerase, beta subunit [Roseobacter sp. GAI101]
          Length = 1378

 Score = 1702 bits (4409), Expect = 0.0,   Method: Composition-based stats.
 Identities = 837/1380 (60%), Positives = 1066/1380 (77%), Gaps = 14/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A      +G+Q  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDAETPTDGDGIQGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LE+V YE + PK+DV++C  RD+TYA PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEYVKYELEKPKYDVEECQQRDMTYAAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + Y+ + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYDTVTYTLKA 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITS 300
            G+ W  P    D + G + +  L+D  TGE + E GKK+T   +K L ++G V  L +  
Sbjct: 241  GEGWVAPFYP-DRVRGTRPTYDLIDAATGEVLFEKGKKVTPRAVKQLVDEGKVSELVLPF 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVD 350
            + + G + A DI+N ETG IY+EAGD +  +          + +E+  + I +IP+L +D
Sbjct: 300  EHIVGKFAARDIINEETGAIYVEAGDEMTLEYDKDGTLIGGTAKELVDAGITEIPLLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N   Y+RNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFD ++YDLS 
Sbjct: 360  NINVGPYMRNTMAMDKNMNRDTALMDIYRVMRPGEPPTVEAASNLFDTLFFDGERYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRL LD  D  R + ++DI++ IK LVDLR+G+G IDDID+LGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLALDKEDTQRTLDRDDIVSCIKALVDLRDGRGDIDDIDHLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FA
Sbjct: 540  PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIETPYRKV +G V++DV Y+SA EE    +AQAN++LDE+  F  +LV  R +
Sbjct: 600  RVNKYGFIETPYRKVSNGVVSDDVQYMSATEEMRHTVAQANANLDENMKFVNDLVSTRKS 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP 
Sbjct: 660  GDYTLSPSENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPL 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E VVA+ SGAA +AKR GI++QVDA RIV+R+ E  L+   +GVDIYR+ KFQRS
Sbjct: 720  VGTGIEEVVARDSGAAYMAKRGGIIDQVDASRIVLRATED-LELGDAGVDIYRMRKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRPLVKVGD V +  +IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LIS
Sbjct: 779  NQNTCINQRPLVKVGDTVVKGQVIADGPSTDMGELALGKNVIVAFMPWNGYNYEDSILIS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V P
Sbjct: 839  ERVSRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K ++ ++ 
Sbjct: 959  EKDERALQIEREEVERLARDRDDELGILDRNIYARLQSMIIGKTAVKGPKGVKSNSEITE 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            DL++   R QWWQ A+ DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1019 DLLATLSRGQWWQLALADEDDAKIVEALNEQYEIQKRTLDARFEDKVEKVRRGDDLPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSR
Sbjct: 1079 MKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG  I   + +YK +GD++P+R  +    G   + E I+  D+
Sbjct: 1139 MNVGQILETHMGWAARGLGINIDEALQEYKRSGDLTPVREAMSHAYGEDVYEEGIAGMDE 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
             ++L VA     GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F RPVT
Sbjct: 1199 ATLLEVAGNVTRGVPIATPVFDGAKEADVNDSLTRAGFDTSGQSVLFDGRTGEQFARPVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|254438477|ref|ZP_05051971.1| DNA-directed RNA polymerase, beta subunit [Octadecabacter antarcticus
            307]
 gi|198253923|gb|EDY78237.1| DNA-directed RNA polymerase, beta subunit [Octadecabacter antarcticus
            307]
          Length = 1380

 Score = 1702 bits (4407), Expect = 0.0,   Method: Composition-based stats.
 Identities = 830/1382 (60%), Positives = 1064/1382 (76%), Gaps = 15/1382 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    +      EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDSDTPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV YE + PK+DV++C  RD+TYA PLK+TLRLIVFD+D+ TG KS+
Sbjct: 61   FPIKDFNETSVLEFVKYELEKPKYDVEECQQRDMTYAAPLKVTLRLIVFDMDDDTGTKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG+D E I++ +Y  + Y+   
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFCRIDRRRKLPVTTLLYALGLDQETIMNAYYDHVDYTFDK 240

Query: 243  D--FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
                W         + G +    LVD  TGE + E+GKK+T   +K+L ++G VK L + 
Sbjct: 241  KANGWKTKFFPE-RVRGTRPVFDLVDAKTGEVIAEAGKKVTPRAVKALIDEGNVKDLLVP 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYV 349
             + + G + A DI+N ETG IY+EAGD +  +           L+E+  + I+ IP+L +
Sbjct: 300  YEQILGKFAANDIINEETGAIYVEAGDELTLEMDKAGDVIGGTLKELVDAGIKTIPVLDI 359

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D++N   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS
Sbjct: 360  DNINVGPYMRNTMAADKNMGRETALMDIYRVMRPGEPPTVDAASNLFDSLFFDSERYDLS 419

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL LD  D +R +RKEDI++ IK LV LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 420  AVGRVKMNMRLALDAEDTIRTLRKEDIVSCIKALVMLRDGKGDIDDIDHLGNRRVRSVGE 479

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 480  LMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 539

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 540  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 599

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYR V DG VT++V Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 600  ARVNKYGFIETPYRVVTDGVVTDEVHYMSATEEMRHTVAQANANLDENMRFVNDLVSTRQ 659

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             GE  L P E ++ ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPLL+AEAP
Sbjct: 660  NGEYTLAPSENVNLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLLQAEAP 719

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+    L+    GVDIYR+ KFQR
Sbjct: 720  LVGTGIEEVVARDSGAAIMAKRAGIIDQVDATRIVVRATSD-LEIGDPGVDIYRMRKFQR 778

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRPLVKVGD V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LI
Sbjct: 779  SNQNTCINQRPLVKVGDTVLKGEVIADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILI 838

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+  +DVFTSIHI+EFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 839  SERITRDDVFTSIHIDEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVE 898

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG
Sbjct: 899  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHG 958

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+    GPKG K   ++ 
Sbjct: 959  VEKDERALQIEREEVERLARDRDDEMTILDRNIYARLRSMIEGKTVAKGPKGIKTGAIID 1018

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ + PRS WWQ A+++E   + VE+L  QYE +K +L+ RF++K+EK++ GDD+PPG
Sbjct: 1019 AAMLDDMPRSHWWQIALKEEGDAQIVEALNEQYEAAKKLLDARFEDKVEKVRRGDDLPPG 1078

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPS
Sbjct: 1079 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPS 1138

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG +I   +  Y+ +GD++P+R  ++   G   + E I+D  
Sbjct: 1139 RMNVGQILETHMGWAARGLGIEIDEALGAYRRSGDLTPVREAMKIAYGDDVYDEGIADMT 1198

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +D ++  A     GVP++TPVFDGA E  +N  L  A  D SGQSIL+DG TGE F R V
Sbjct: 1199 EDELVEAAGNVTHGVPIATPVFDGAKEADVNDSLTRAGFDTSGQSILFDGRTGEQFSRKV 1258

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1259 TVGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1318

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT+VYESIV G D +E G PESFNVLVKE++ LGL+++L ++   
Sbjct: 1319 TLQEMLTVKSDDVAGRTKVYESIVKGEDNYEAGIPESFNVLVKEVRGLGLNMELLDAEED 1378

Query: 1370 NS 1371
            + 
Sbjct: 1379 DE 1380


>gi|119383499|ref|YP_914555.1| DNA-directed RNA polymerase subunit beta [Paracoccus denitrificans
            PD1222]
 gi|158512586|sp|A1B015|RPOB_PARDP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119373266|gb|ABL68859.1| DNA-directed RNA polymerase subunit beta [Paracoccus denitrificans
            PD1222]
          Length = 1382

 Score = 1701 bits (4406), Expect = 0.0,   Method: Composition-based stats.
 Identities = 850/1386 (61%), Positives = 1074/1386 (77%), Gaps = 20/1386 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+  V  G  R+R+++G   E++++P+LIEVQK+SYD FL    A   +  EG+Q  F+
Sbjct: 1    MAQAYV--GQKRIRRYYGNIREVLEMPNLIEVQKSSYDLFLRSGDAEGHQDGEGIQGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A LEFV YE + PK+DV++C  RD+TYA PLK+TLRLIVFDVDE TGAK
Sbjct: 59   SVFPIKDFNETATLEFVKYELEKPKYDVEECQSRDMTYAAPLKVTLRLIVFDVDETTGAK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT++GTF++ G +R+VVSQ+HRSPG+ FDHD+G+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTQNGTFIVNGTERVVVSQMHRSPGVFFDHDRGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALGMD E I+  FY  + Y  
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDLVFARIDRRRKLPVTTLLYALGMDQEGIMDAFYNTVDYKL 238

Query: 241  RGDF------WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            +         W         + G + S  LV+ +TGE + ++G K+T  L+K L EKG  
Sbjct: 239  QRAGKGQAAGWVTKFFPE-RVRGTRPSFDLVNAETGEIITKAGDKVTPRLVKQLAEKGDI 297

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDI 344
             L +  + + G +VA+DI+N +TG IY EAGD I  +           L+ +  + I DI
Sbjct: 298  NLLLPFEKIVGRFVAKDIINEQTGLIYAEAGDEITVEYDRDGEISGGLLKVLLDNGIEDI 357

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            P+L +D VN   YIRNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS+
Sbjct: 358  PVLDIDHVNVGPYIRNTMAADKNMSRDGALMDIYRVMRPGEPPTVEAASALFDSLFFDSE 417

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YDLS VGRVKMNMRL+LD PD  R +RKEDIIA I+ LV+LR+GKG IDDID+LGNRRV
Sbjct: 418  RYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDIIACIRGLVELRDGKGEIDDIDHLGNRRV 477

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            RSVGE+++NQYR+GLLRMER+I+ER+S V+ID+VMPQDLINAKP  +AV EFF SSQLSQ
Sbjct: 478  RSVGELMENQYRIGLLRMERAIRERMSGVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQ 537

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS +T  RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 538  FMDQTNPLSEVTDKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGQNIGLIN 597

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL +FARVN YGFIETPYRKV +GKVT++VVY+SA EE    IAQAN++LDE G F +EL
Sbjct: 598  SLATFARVNKYGFIETPYRKVVEGKVTDEVVYMSATEEMRHTIAQANATLDESGKFVDEL 657

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V  R AG+ +L P E +D ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL
Sbjct: 658  VSTRQAGDFMLNPVEAVDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLL 717

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            +AEAPFVGTGME+ VA+ SGAAI+A+R GI++QVDA RIVIR+ E  L    +GVDIYRL
Sbjct: 718  RAEAPFVGTGMEATVARDSGAAIMARRGGIIDQVDAQRIVIRATED-LGAGDAGVDIYRL 776

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             KF+RSNQ++ +NQRPLVKVGD+V +  ++ADGPSTD G+LA+GRN++VAFMPW+GYN+E
Sbjct: 777  RKFKRSNQSSTINQRPLVKVGDKVVKGQVVADGPSTDQGELAIGRNVVVAFMPWNGYNYE 836

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            DS+LISER+  +DVFTSIHI+E+EV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +
Sbjct: 837  DSILISERIHRDDVFTSIHIDEYEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYI 896

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+
Sbjct: 897  GAEVGPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGAYGTIVEVRV 956

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            FNRHG+DK+ER++ +ERE++E LARD+DDE  IL+RNIY+RL  ++ G+  V GPKG + 
Sbjct: 957  FNRHGVDKDERALQIEREEVERLARDRDDELAILERNIYARLKSLIMGKEVVKGPKGIRA 1016

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              V+  DL+ +  R QWWQ AV DE   + VE+L  Q++  K  L++RF +K+EK++ GD
Sbjct: 1017 GAVVDEDLLGQLSRGQWWQLAVADEDTAKEVEALNQQFDAQKRALDNRFDDKVEKVRQGD 1076

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            D+PPGV+++VKVFVA+KR +Q+GDKMAGRHGNKG+VS+++P EDMPFL DGTPVD+V NP
Sbjct: 1077 DLPPGVMKMVKVFVAVKRKLQAGDKMAGRHGNKGVVSKVVPIEDMPFLSDGTPVDLVFNP 1136

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMNVGQI ETH+GWA  GLG KI   + DY+ NGD++P+R  ++   G   + E 
Sbjct: 1137 LGVPSRMNVGQILETHMGWASRGLGIKIDEALQDYRRNGDMTPVREAMQNGYGDDFYAET 1196

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                +D+++L  A+  + GVP+STPVFDGA E  IN  LR A  D SGQSI++DG TGE 
Sbjct: 1197 FEGMEDETLLEHADAVRGGVPISTPVFDGAKEADINDALRRAGFDTSGQSIVFDGRTGEQ 1256

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F RPVTVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++A
Sbjct: 1257 FARPVTVGMKYVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEA 1316

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L 
Sbjct: 1317 YGAAYTLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELL 1376

Query: 1365 NSRTKN 1370
            ++  + 
Sbjct: 1377 DAEDEE 1382


>gi|163740213|ref|ZP_02147607.1| DNA-directed RNA polymerase subunit beta [Phaeobacter gallaeciensis
            2.10]
 gi|161386071|gb|EDQ10446.1| DNA-directed RNA polymerase subunit beta [Phaeobacter gallaeciensis
            2.10]
          Length = 1378

 Score = 1701 bits (4406), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1379 (60%), Positives = 1065/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDAEQPLDGEGIMGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVKYSFERPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVYMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVNFKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE   E+GKK+T   +K + ++G +  L +  +
Sbjct: 241  SRGWVTPFFPERVRGTRPTYDLVDAATGEIFAEAGKKVTPRAVKKMIDEGNITDLLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N E G IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 301  HIVGKFVAKDIINEENGAIYVEAGDELTLEYDKGGELIGGTVKELIDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  INVGPYMRNTMAQDKNMGRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDII+ IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIISCIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V D KVT++V Y+SA EE    +AQAN++LDEDG F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVNDAKVTDEVHYMSATEEMRHTVAQANATLDEDGKFINDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E +VA+ SGAAI+AKR GI++Q+DA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEIVARDSGAAIMAKRGGIIDQIDAQRIVIRATSD-LEMGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG EVR+ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQEVRKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  +L G+ AV GPKG +  + ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDEMGILDRNIYARLRGMLLGKTAVKGPKGIRAGSEITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWW  A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLDTLSRGQWWMLALEDEQSAQVVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG KI   + DY+ +GD++P+R  +    G   + E I+D  + 
Sbjct: 1140 NVGQILETHMGWAARGLGIKIDDALQDYRRSGDLTPVREAMHHAYGDDVYGEGIADMTET 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  L  A  D SGQSIL+DG TGE F RPVTV
Sbjct: 1200 DLVEAAGNVTRGVPIATPVFDGAKEADVNDSLVRAGFDTSGQSILFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEGEE 1378


>gi|255262039|ref|ZP_05341381.1| DNA-directed RNA polymerase, beta subunit [Thalassiobium sp. R2A62]
 gi|255104374|gb|EET47048.1| DNA-directed RNA polymerase, beta subunit [Thalassiobium sp. R2A62]
          Length = 1378

 Score = 1701 bits (4405), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1379 (60%), Positives = 1071/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LI+VQKASY+ FL           EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIQVQKASYELFLKSGDQLAPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C+ RD+TY+ PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVKYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG+D E I+  +Y  + YS + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVDYSYQK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G +    LVD  TGE + E+GKK+T   +K L ++G V  L +  D
Sbjct: 241  NKGWVTKFFPERVRGTRPIYDLVDAKTGEVIAEAGKKVTPRAVKKLIDEGAVTELLLPYD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N E G IY+EAGD +  +           L+E+  +++  IP+L +D+
Sbjct: 301  QIVGKFVAKDIINEENGAIYVEAGDELTLEMDKDGEVIGGSLKELVDNDVTTIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMANDKNMSRETALMDIYRVMRPGEPPTVDAASTLFDSLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI++ IK LVDLR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVSCIKALVDLRDGRGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV +G VT++V Y+SA EE    +AQAN++LDE+G F  ELV  R +G
Sbjct: 601  VNKYGFIETPYRKVENGVVTDEVQYMSATEEMRHTVAQANANLDENGKFVNELVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            + +L   E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYMLAASESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+    L+    GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRAGIIDQVDAARIVVRATHD-LEVGDPGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V++ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDTVQKGEVIADGPSTDIGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV P 
Sbjct: 840  RITRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVGPA 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGDFGTIVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL + L G+ AV GPKG K +T + +D
Sbjct: 960  KDERALQIEREEVERLARDRDDEMAILDRNIYARLRDQLMGKVAVKGPKGMKANTTVDAD 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+ E PRS WW FA+++E   + VE++  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLEETPRSHWWMFALKEEGDAQIVEAMNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD VLNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFVLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG +I   + +++ +GD++P+R  ++   G   + E I+  D  
Sbjct: 1140 NVGQILETHMGWAARGLGIQIDDALGEFRRSGDLTPVRDAMKIAYGDDVYDEGIAGMDKG 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L  A     GVP++TPVFDGA E  +N  L  A   ESGQS+L+DG TGE F RPVTV
Sbjct: 1200 QLLEAAGNVARGVPIATPVFDGAKEADVNDALVRAGFSESGQSVLFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDTVEDE 1378


>gi|163739425|ref|ZP_02146835.1| DNA-directed RNA polymerase subunit beta [Phaeobacter gallaeciensis
            BS107]
 gi|161387178|gb|EDQ11537.1| DNA-directed RNA polymerase subunit beta [Phaeobacter gallaeciensis
            BS107]
          Length = 1378

 Score = 1701 bits (4405), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1379 (60%), Positives = 1065/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL    A      EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDAEQPLDGEGIMGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y F+ PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVKYSFERPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVYMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVNFKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE   E+GKK+T   +K + ++G +  L +  +
Sbjct: 241  SRGWVTPFFPERVRGTRPTYDLVDAATGEIFAEAGKKVTPRAVKKMIDEGNITDLLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA+DI+N E G IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 301  HIVGKFVAKDIINEENGAIYVEAGDELTLEYDKGGELIGGTVKELIDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N   Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  INVGPYMRNTMAQDKNMGRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDII+ IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIISCIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V D KVT++V Y+SA EE    +AQAN++LDEDG F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVNDAKVTDEVHYMSATEEMRHTVAQANATLDEDGKFINDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E +VA+ SGAAI+AKR GI++Q+DA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEIVARDSGAAIMAKRGGIIDQIDAQRIVIRATSD-LEMGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG EVR+ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQEVRKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  +L G+ AV GPKG +  + ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDEMGILDRNIYARLRGMLLGKTAVKGPKGIRSGSEITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWW  A++DE+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLSRGQWWMLALEDEQSAQVVEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG KI   + DY+ +GD++P+R  +    G   + E I+D  + 
Sbjct: 1140 NVGQILETHMGWAARGLGIKIDDALQDYRRSGDLTPVREAMHHAYGDDVYGEGIADMTET 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  L  A  D SGQSIL+DG TGE F RPVTV
Sbjct: 1200 DLVEAAGNVTRGVPIATPVFDGAKEADVNDSLVRAGFDTSGQSILFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEGEE 1378


>gi|83854989|ref|ZP_00948519.1| DNA-directed RNA polymerase beta subunit [Sulfitobacter sp. NAS-14.1]
 gi|83941511|ref|ZP_00953973.1| DNA-directed RNA polymerase beta subunit [Sulfitobacter sp. EE-36]
 gi|83842832|gb|EAP81999.1| DNA-directed RNA polymerase beta subunit [Sulfitobacter sp. NAS-14.1]
 gi|83847331|gb|EAP85206.1| DNA-directed RNA polymerase beta subunit [Sulfitobacter sp. EE-36]
          Length = 1378

 Score = 1701 bits (4405), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1380 (60%), Positives = 1067/1380 (77%), Gaps = 14/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    A      +G+Q  F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDAETPTDGDGIQGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LE+V YE + PK+DV++C  RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEYVKYELEKPKYDVEECQQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I++ +Y  + Y+ + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMNAYYNTVNYTLKD 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITS 300
            G+ W  P    D + G + S  LVD  TGE + E GKK+T   +K L ++G V  L +  
Sbjct: 241  GEGWVAPFFP-DRVRGTRPSYDLVDAATGEILFEKGKKVTPRAVKQLIDEGKVTELLLPF 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVD 350
              + G + A DI+N ETG IY+EAGD +  +            +E+  + I +IP+L +D
Sbjct: 300  GHIAGKFAARDIINEETGAIYVEAGDELTLEHDKDGTLIGGTAKELIDAGITEIPLLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N   Y+RNT+  DKN +R  AL+DIYRVMRPG+  T   A ++F+ LFFD+D+YDLS 
Sbjct: 360  NINVGPYMRNTMAADKNMNRDTALMDIYRVMRPGEPPTVEAASNLFDTLFFDADRYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRL LD  D  R + ++DI+A IK LVDLR+G+G IDDID+LGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLALDKEDTQRTLDRDDIVACIKALVDLRDGRGDIDDIDHLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FA
Sbjct: 540  PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHATHYGRMCPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIETPYRKV +G V++DV Y+SA EE    +AQAN++LDE+  F  +LV  R +
Sbjct: 600  RVNKYGFIETPYRKVTNGVVSDDVQYMSATEEMRHTVAQANANLDENMKFVNDLVSTRKS 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP 
Sbjct: 660  GDYTLSPSENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAPL 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E VVA+ SGAA +AKR GI++QVDA RIVIR+ E  L+   +GVDIYR+ KFQRS
Sbjct: 720  VGTGIEEVVARDSGAAYMAKRGGIIDQVDASRIVIRATED-LELGDAGVDIYRMRKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRPLVKVG+ V++  +IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LIS
Sbjct: 779  NQNTCINQRPLVKVGETVQKGQVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILIS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V P
Sbjct: 839  ERVSRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K ++ ++ 
Sbjct: 959  EKDERALQIEREEVERLARDRDDELGILDRNIYARLQSMIIGKTAVKGPKGVKANSEITE 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            DL++   R QWWQ A+ DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1019 DLLASLSRGQWWQLALADEDDAKIVEALNEQYEIQKRTLDARFEDKVEKVRRGDDLPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSR
Sbjct: 1079 MKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG  I   + +YK +GD++P+R  +    G   + E IS  D+
Sbjct: 1139 MNVGQILETHMGWAARGLGINIDEALQEYKRSGDLTPVREAMHHAYGDDVYEEGISGMDE 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            +++L  A+    GVP++TPVFDGA E  +N  L  A  D SGQS+L+DG TGE F RPVT
Sbjct: 1199 ETLLDAAKNVARGVPIATPVFDGAKEADVNDSLTRAGFDSSGQSVLFDGRTGEQFARPVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLVKEVRGLGLNMELLDAEEDE 1378


>gi|310817018|ref|YP_003964982.1| DNA-directed RNA polymerase, beta subunit [Ketogulonicigenium vulgare
            Y25]
 gi|308755753|gb|ADO43682.1| DNA-directed RNA polymerase, beta subunit [Ketogulonicigenium vulgare
            Y25]
          Length = 1381

 Score = 1701 bits (4404), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1382 (60%), Positives = 1062/1382 (76%), Gaps = 17/1382 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK +GK  E++++P+LIEVQK+SYD FL    A   +  EG+Q  F+SV
Sbjct: 1    MAQSFLGQKRLRKSYGKIREVLEMPNLIEVQKSSYDLFLKSGDADKPQDGEGIQGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C  RD+TY+  LK+TLRLIVFD+ E TG +S+
Sbjct: 61   FPIKDFNDTAVLEFVKYELEKPKYDVEECQARDMTYSAQLKVTLRLIVFDISEDTGMRSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVYMGDIPLMTQNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALGMD E I+  +Y  + Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFARIDRRRKLPVTTLLYALGMDQEGIMDAYYDTVEYRLEA 240

Query: 242  -GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
                W         + G + +  LVD  +GE ++E+G+K T  ++K   ++G V  L + 
Sbjct: 241  KSKGWITKFFPE-RVRGTRPTYDLVDAASGEVILEAGEKATPRMVKKWIDEGKVTDLLVP 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             + + G +VA+DI+N + G IY+EAGD +  +          SL+E+  +    +P+L +
Sbjct: 300  FEHILGKFVAKDIINEDNGAIYVEAGDELLLERNRDGEITGGSLQELLEAGFTTVPVLDI 359

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+VN  AYIRNT+  DKN  R+ AL+DIYRVMRPG+  T   A  +F  LFFDS++YDLS
Sbjct: 360  DNVNVGAYIRNTMAADKNMGREGALMDIYRVMRPGEPPTVEAASDLFETLFFDSERYDLS 419

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+LD  D VR +R++DII+ IK LV+LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 420  AVGRVKMNMRLDLDVADTVRTLRRDDIISCIKALVELRDGKGEIDDIDHLGNRRVRSVGE 479

Query: 470  MLKNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            +++NQYR+GLLRMER+IKER+S  +  ID+ MPQDLINAKP  +AV EFF SSQLSQ  +
Sbjct: 480  LMENQYRVGLLRMERAIKERMSSGTPAIDTAMPQDLINAKPAAAAVREFFGSSQLSQFMD 539

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 540  QTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLA 599

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            ++ARVN YGFIETPYRKV +GKVT+DV Y+SA EE    IAQAN+ LD++G F +ELV  
Sbjct: 600  TYARVNKYGFIETPYRKVVEGKVTDDVQYMSATEEMRHTIAQANAILDDEGRFVDELVDT 659

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R AG+  L  RE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AE
Sbjct: 660  RQAGDYTLATRETVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAE 719

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            AP +GTG+ESVVA+ SGAAI+A+RAG+V+QVDA R+VIR+ E       +GVDIYRL KF
Sbjct: 720  APLIGTGIESVVARDSGAAIMARRAGVVDQVDAQRVVIRATEDLSL-GDAGVDIYRLRKF 778

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSNQ+TC+NQRPLVKVGD V + ++IADGPST++G+LALG+N++VAFMPW+GYN+EDS+
Sbjct: 779  QRSNQDTCINQRPLVKVGDLVGKGEVIADGPSTEMGELALGKNIVVAFMPWNGYNYEDSI 838

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISER+VSEDV+TSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA 
Sbjct: 839  LISERIVSEDVYTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAH 898

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNR
Sbjct: 899  VGPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGNYGTIVEVRVFNR 958

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
            HG+DK+ER++ +ERE+IE L+RD+DDE  ILDRNIY+RL ++L G+ AV GPKGFK +T 
Sbjct: 959  HGVDKDERALQIEREEIESLSRDRDDELAILDRNIYARLKQVLLGKMAVKGPKGFKANTQ 1018

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            ++ +++ E+ R QWWQ AV+DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+P
Sbjct: 1019 VTEEVLGEFSRGQWWQLAVEDEDDAKIVEALNEQYENQKKQLDARFEDKVEKVRRGDDLP 1078

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV+++VKVFVA+KR +Q GDKMAGRHGNKG++SR++P EDMPFL DGTPVD  LNPLGV
Sbjct: 1079 PGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRVVPAEDMPFLADGTPVDFCLNPLGV 1138

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMNVGQI ETH+GWA   LG +I   +  Y+ +GD++P++  L    G   + E    
Sbjct: 1139 PSRMNVGQILETHMGWASRALGLQIDEALKGYRRSGDLTPVKDALRFAYGDEVYAEGFET 1198

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              +   L  AE    GVP++TPVFDGA E  IN  L  A  D SGQS+L+DG TGE F R
Sbjct: 1199 ASEAVFLERAENATRGVPIATPVFDGAKEADINDALARAGFDTSGQSVLFDGRTGEQFAR 1258

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             VTVG  YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1259 KVTVGVKYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1318

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++ 
Sbjct: 1319 AYTLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAE 1378

Query: 1368 TK 1369
              
Sbjct: 1379 DD 1380


>gi|332185540|ref|ZP_08387288.1| DNA-directed RNA polymerase, beta subunit [Sphingomonas sp. S17]
 gi|332014518|gb|EGI56575.1| DNA-directed RNA polymerase, beta subunit [Sphingomonas sp. S17]
          Length = 1392

 Score = 1701 bits (4404), Expect = 0.0,   Method: Composition-based stats.
 Identities = 831/1376 (60%), Positives = 1065/1376 (77%), Gaps = 12/1376 (0%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                R+RK FG   E++ +P+LIEVQ+ SY+ FL  + +       GL+   +SVFPI  
Sbjct: 19   TAKRRIRKVFGDIHEVVQMPNLIEVQRESYEQFLRSDKSRGHVS--GLEKTLRSVFPIQD 76

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            F+G A L+F  Y  + PKFDV++C  R +TYA P+++TLRL  F+VD  T AKS+ DIKE
Sbjct: 77   FAGTAYLDFDDYVLEDPKFDVEECRQRGITYAAPMRVTLRLTAFEVDPDTEAKSVIDIKE 136

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT++GTF I G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A R+IP 
Sbjct: 137  QDVYMGDMPLMTENGTFFINGTERVIVSQMHRSPGVLFDHDRGKTHASGKYLFAARVIPY 196

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+D EFD+KDI++VRIDR+RK+PVT+ L ALGM+SEEIL+ FY ++ + +    W  
Sbjct: 197  RGSWLDFEFDAKDIVNVRIDRKRKLPVTALLYALGMNSEEILNYFYNRLTFVRGDGGWKI 256

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P  A +   GAK    +VD ++GE V  +G+K++        + G+  L I ++ + G Y
Sbjct: 257  PFQAEN-WRGAKPMFDIVDANSGEVVFPAGQKISPRAANKAAKDGLTQLLIPTEEIFGRY 315

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             A D++N +TGEIY+EAGD I  ++LE +  + +  I +L +D V    +IRNTL  DK 
Sbjct: 316  SAYDLINEQTGEIYVEAGDEISAENLEALDKAGVDTIELLDIDHVATGPWIRNTLKADKA 375

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            ++R+ AL DIYRVMRPG+  T   AE++F  LFFD D+YDLS VGRVK+NMRL+LD PD 
Sbjct: 376  EEREQALSDIYRVMRPGEPPTLETAEALFAGLFFDPDRYDLSAVGRVKLNMRLDLDCPDT 435

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            V  +R EDI+A++K LVDL++GKG IDDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++K
Sbjct: 436  VTTLRTEDILAVVKTLVDLKDGKGEIDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVK 495

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG G
Sbjct: 496  ERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPG 555

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIETPYRKV D
Sbjct: 556  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIETPYRKVID 615

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            G+VT++VVYLSAMEE+   +AQA+++ D D  FTE+LV  R AGE ++   ++I  +D S
Sbjct: 616  GRVTDEVVYLSAMEEQKHTVAQASAATDADNRFTEDLVSARQAGEFLMALPDQITLMDVS 675

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+KAEAPFVGTGME  VA+ SGAAI
Sbjct: 676  PKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKAEAPFVGTGMEETVARDSGAAI 735

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AKRAGIV+QVDA RIV+R+  G++D   SGVDIY LMKFQRSNQ+TC+NQRPLVKVGD 
Sbjct: 736  AAKRAGIVDQVDAARIVVRAT-GEVDAGKSGVDIYTLMKFQRSNQSTCINQRPLVKVGDV 794

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V+  D+IADGPST+ G+LALGRN LVAFMPW+GYN+EDS+LISER+V +DVFTSIHI+EF
Sbjct: 795  VKAGDVIADGPSTEFGELALGRNALVAFMPWNGYNYEDSILISERIVKDDVFTSIHIDEF 854

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ VGAEV PGDILVGKITPKGESPMT
Sbjct: 855  EVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYVGAEVEPGDILVGKITPKGESPMT 914

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHGIDK+ER++++ERE+IE L
Sbjct: 915  PEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGIDKDERAMAIEREEIERL 974

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D DDE+ IL+R  +SRL E+L  Q A + PKG KK  V+ ++++    R +WW+FAV 
Sbjct: 975  KKDADDERTILNRATWSRLREMLLDQTATAAPKGVKKGIVIDAEVLESVDRHEWWKFAVA 1034

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D+  Q ++E++K QY+ +   + D+F ++ +K++ GD++PPGVL++VKVFVA+KR +Q G
Sbjct: 1035 DDARQSDLEAVKAQYDEAAKRITDKFHDRRDKLERGDELPPGVLKMVKVFVAVKRKLQPG 1094

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP EDMPFL DGTPVD+VLNPLGVPSRMNVGQIFETHLGWA   
Sbjct: 1095 DKMAGRHGNKGVISRILPQEDMPFLADGTPVDLVLNPLGVPSRMNVGQIFETHLGWAARN 1154

Query: 1148 LGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG ++ + + D++     +        +++ L ++ G   + E I   DD+ V  + +  
Sbjct: 1155 LGMQVAAQLEDWREANPDAKPGAVPEAVKARLVEIYGD-HYAEDIQARDDEEVAELVQNI 1213

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP+ TPVFDGA E  ++ ML +A L  SGQS L+DG TG+ FDR VTVG IYMLKL+
Sbjct: 1214 RTGVPMGTPVFDGARESDVSEMLELAGLHTSGQSDLFDGRTGDQFDRKVTVGIIYMLKLH 1273

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KSD
Sbjct: 1274 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKSD 1333

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL++DL++        + E
Sbjct: 1334 DVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVDLKSMEEAQDDGLAE 1389


>gi|192360775|ref|YP_001981201.1| DNA-directed RNA polymerase subunit beta [Cellvibrio japonicus
            Ueda107]
 gi|226699384|sp|B3PK30|RPOB_CELJU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|190686940|gb|ACE84618.1| DNA-directed RNA polymerase, beta subunit [Cellvibrio japonicus
            Ueda107]
          Length = 1361

 Score = 1700 bits (4403), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1365 (52%), Positives = 980/1365 (71%), Gaps = 4/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY  F   +++ ++R + GL AAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMDVPYLLAIQLDSYRKFTQADLSANKREDVGLHAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY      FDV++C+ R +TYAVPL++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVSYSLGKAAFDVNECILRGVTYAVPLRVKVRLIIYDR--ESANKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++VRIDRRRK+P T  L AL   S+E+LS F+    ++   
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYVRIDRRRKLPATILLRALNYSSQEMLSMFFETSSFTLGK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D           + G   +  + D D G  ++E G+++T+  ++ L++ GV  + + S+ 
Sbjct: 239  DGQFSYEVVPSRLRGDVATFDIKD-DKGNIIVEEGRRITARHIRQLEKAGVDQMEVPSEY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+DIV+  TGE+  E    I    L +I  + +  +  LY + ++   +I  TL
Sbjct: 298  LLGRSLAKDIVDTRTGELLFECNTEITSDVLSKIVAAGVEKVETLYTNELDCGPFISETL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  + + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL  
Sbjct: 358  RIDPTRTQLEALVEIYRMMRPGEPPTKESAEALFQNLFFSQERYDLSAVGRMKFNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +T      +  +DI+ ++K L+ +RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 418  ETETGEGTLSNDDIVDVMKTLISIRNGKGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+ 
Sbjct: 478  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVF 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNNYGFLESPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKVT+ + YLSA+ E    IAQA++SLD++G  TEELV  R   E  L     + 
Sbjct: 598  RKVIEGKVTDQIEYLSAINESEYVIAQASASLDDNGRLTEELVSVRHQNEFTLKAPTDVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA  
Sbjct: 658  YMDVSARQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSQKPLVGTGMERNVAAD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIV++  + +++   +GVDIY L+K+ RSNQNTC+NQRP+V
Sbjct: 718  SGVCVVAKRGGVIDSVDAGRIVVKVHDAEVEAGDAGVDIYNLIKYTRSNQNTCINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +GD V R DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 778  SMGDIVSRGDILADGPSVDMGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 838  HIQELTCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVGGGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG  GTV+DV++F R G++K++RS+ +E+ 
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGTKGTVIDVQVFTRDGLEKDQRSLEIEKA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ   SG KG KK   L+ D++    + QW+
Sbjct: 958  QLDEVRKDLNEEFRIVETATFERLRAALVGQIVASG-KGVKKGEALTHDILDGLEKDQWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   ++  + Q    + IL++RF++K  K+  GDD+ PGVL++VKV++A+KR
Sbjct: 1017 KLRMNEDALNEQIDRAEEQLAERRKILDERFEDKKRKLSTGDDLAPGVLKIVKVYLAIKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G  VDIVLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1077 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGETVDIVLNPLGVPSRMNVGQVLEMHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG KI  LI + KA  DI      +    G  +  E +  + D  V+ +A+    
Sbjct: 1137 MAAKGLGVKINKLIQEQKAVADIRSFLEEIYNSTGDVAAKEDLVSFSDREVIDLAKNLVD 1196

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I ++LR+A L ++GQ+ L+DG TG+ F R VTVGY+YMLKLNH+
Sbjct: 1197 GVPMATPVFDGAKEHEIKALLRLASLSDTGQTTLFDGRTGDQFSRSVTVGYMYMLKLNHL 1256

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1257 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1316

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV G+   E G PESFNVLVKE+++LG++I+LE   
Sbjct: 1317 AGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGINIELEQED 1361


>gi|198282630|ref|YP_002218951.1| DNA-directed RNA polymerase subunit beta [Acidithiobacillus
            ferrooxidans ATCC 53993]
 gi|218666714|ref|YP_002424823.1| DNA-directed RNA polymerase, beta subunit [Acidithiobacillus
            ferrooxidans ATCC 23270]
 gi|226699362|sp|B7J460|RPOB_ACIF2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699363|sp|B5ELX2|RPOB_ACIF5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|198247151|gb|ACH82744.1| DNA-directed RNA polymerase, beta subunit [Acidithiobacillus
            ferrooxidans ATCC 53993]
 gi|218518927|gb|ACK79513.1| DNA-directed RNA polymerase, beta subunit [Acidithiobacillus
            ferrooxidans ATCC 23270]
          Length = 1362

 Score = 1700 bits (4403), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1366 (53%), Positives = 991/1366 (72%), Gaps = 5/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK+  I+ +P L+  Q  SY  FL  ++ P  R   GL+A F+SV
Sbjct: 1    MAYSFTEKKRIRKDFGKSQSILAVPYLLATQMDSYREFLQESVPPAARKETGLEAVFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ ++SG AML++VSY  + P FDV +C  R LTY   L++ LRL V + D+ TGAK +
Sbjct: 61   FPMESYSGNAMLDYVSYRLEKPVFDVVECRQRGLTYCAGLRVRLRLAVMEKDDTTGAKRV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG+LPLMT+ G+FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL+  
Sbjct: 121  KDVKEQDVYMGELPLMTEHGSFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T+ L ALG  +++IL  F+    +    
Sbjct: 181  RIIPYRGSWLDFEFDPKDHVYARIDRRRKLPATTLLRALGYSTQDILEMFFDMETFRLID 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE-KGVKFLGITSD 301
                + L    L  G   +  +V  +TG+ ++++GK++T    K+L E +G+  + +   
Sbjct: 241  GDLRYVLIPQRL-QGEVAAFDIVSPETGDVLVQAGKRITVRQTKALSEVQGLHEIPVPDS 299

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA DIV+ ETGE+ ++A + +  + L+ +       +  LY++ ++   YI  T
Sbjct: 300  FLLGKVVARDIVHPETGEVVVQANEPVSGELLDALRKMPSLTLHTLYLNELDRGPYISET 359

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D ++D  DA ++IYR+MRPG+  T   A+++F  LFF  D+YDLS VGR+K N R+ 
Sbjct: 360  LRIDTSRDAHDAQMEIYRLMRPGEPPTKDAAQNLFQGLFFSPDRYDLSAVGRMKFNRRVG 419

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +   DIIA++K+LV LRNG G IDDID+LGNRRVRSVGE+++NQ+RLGL+R
Sbjct: 420  RDEITGPGVLNDADIIAVLKVLVALRNGVGEIDDIDHLGNRRVRSVGELMENQFRLGLVR 479

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++K+R++  + + + PQDLINAKP+ + V EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 480  VERAVKDRLALAESEGLTPQDLINAKPIAAVVNEFFGSSQLSQFMDQTNPLSEVTHKRRV 539

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+ +AR N+YGF+ETP
Sbjct: 540  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSCYARTNSYGFLETP 599

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V D + T++V YLSA+EE N  IAQANS++DE G  T+ELV CR   E  L   +++
Sbjct: 600  YRRVVDRRTTDEVEYLSAIEEGNYMIAQANSTVDEHGVLTDELVSCRFKNEFTLANPDQV 659

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             F+D SP+Q+VS+AAS+IPFLE+DD+NR LMG NMQRQAVP ++++AP VGTGME VVA 
Sbjct: 660  QFMDISPRQIVSVAASMIPFLEHDDANRALMGSNMQRQAVPTVRSDAPMVGTGMERVVAI 719

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGAA+VA+R G+V+ VD  RIVIR  + +  P   GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 720  DSGAAVVARRGGVVDIVDGARIVIRVSDEETLPEEPGVDIYNLVKYARSNQNTTLNQRPV 779

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VKVGD V R D++ADGPST++G+LALG+N+LVAFMPW+GYNFEDS+LISER+V+ED +T+
Sbjct: 780  VKVGDVVSRGDVLADGPSTEMGELALGQNILVAFMPWNGYNFEDSILISERVVAEDRYTT 839

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF V ARDTKLGPEEITRDIPNV+E  L+++DE GI+ +GAE+ PGDILVGK+TPK
Sbjct: 840  IHIEEFSVFARDTKLGPEEITRDIPNVAEGALRHLDESGIVVIGAELAPGDILVGKVTPK 899

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D S+R+P+G+ GTV+DV++F R GI+K+ R+ S+E 
Sbjct: 900  GETQLTPEEKLLRAIFGEKASDVKDNSMRMPAGMYGTVIDVQVFTRDGIEKDARAKSIEE 959

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             ++  + +D +D+  I++ + Y R+   L G+ A  GP G      ++   + + PR++W
Sbjct: 960  HELARIRKDLNDQYRIVEEDSYQRIERQLIGKVAEGGPNGLAAGNKVTKAYLKDLPRAKW 1019

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            ++  ++ E+   ++E ++ Q E  +  L+   + K  K+  GDD+ PGVL++VKV VA+K
Sbjct: 1020 FEIRLRTEESNESLEQIRAQLEEQRQRLDAVLEEKRRKLTQGDDLSPGVLKMVKVHVAIK 1079

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP+L DGT VDIVLNPLGVPSRMNVGQI ETHL
Sbjct: 1080 RHLQPGDKMAGRHGNKGVVSKIVPVEDMPYLADGTAVDIVLNPLGVPSRMNVGQILETHL 1139

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLGKKI ++++   +   ++ +R+FL ++       E +    D  +  ++   +
Sbjct: 1140 GWAAKGLGKKIGAMLD---SEVAMAEMRAFLAEIYNRSGKKEDLDSLTDQEIRELSANLR 1196

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA EE I  ML +A L  SGQ  LYDG +G+ FDRPVTVGY+YMLKL+H
Sbjct: 1197 GGVPMATPVFDGASEEEIGDMLELAGLPRSGQVTLYDGRSGDAFDRPVTVGYLYMLKLHH 1256

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1257 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1316

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V GR+++YESIV G+   + G PESFNVL+KE+++LG+ I+LE S+
Sbjct: 1317 VSGRSKMYESIVKGDFRMDAGMPESFNVLLKELRSLGIDIELEQSK 1362


>gi|149913534|ref|ZP_01902067.1| DNA-directed RNA polymerase subunit beta [Roseobacter sp. AzwK-3b]
 gi|149812654|gb|EDM72483.1| DNA-directed RNA polymerase subunit beta [Roseobacter sp. AzwK-3b]
          Length = 1379

 Score = 1700 bits (4403), Expect = 0.0,   Method: Composition-based stats.
 Identities = 840/1370 (61%), Positives = 1069/1370 (78%), Gaps = 12/1370 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK+FGK  E++D+P+LIEVQK+SYD FL     P     EG++  F+SV
Sbjct: 1    MAQTFLGQKRLRKYFGKIREVLDMPNLIEVQKSSYDLFLKSGDQPKPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV Y+ + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVGYDLERPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD ++ RIDRRRK+PVT+ L ALGMD E I+  +Y  + Y  + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDHVYARIDRRRKLPVTTLLYALGMDQEGIMDAYYDTVDYKLKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + +  LVD  TGE + E+ KK+T   +K L + G V  L +  +
Sbjct: 241  NKGWVSKFFPERVRGTRPTFDLVDAKTGEVIAEASKKITPRAVKKLIDDGNVSELLMPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI+N ETG IY+EAGD +  +          S++E+  + I DIP+L +D+
Sbjct: 301  QIAGKFVARDIINEETGAIYVEAGDELTIERDKDGDIIGGSVKELLDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N  AYIRNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFD+++YDLS V
Sbjct: 361  INVGAYIRNTVAMDKNMNRETALMDIYRVMRPGEPPTEEAASALFDTLFFDAERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD PD  R + +EDI+A IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDKPDTQRTLDREDIVACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV  G+VT+DVVY+SA EE    +AQAN+ LD+ G F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVNSGQVTDDVVYMSATEEMRHTVAQANAKLDDAGRFVNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E +L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVP L++EAP +
Sbjct: 661  EYMLAPNESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPTLRSEAPLI 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGA+I+AKRAGI++QVDA RIV+R+ E  L+    GVDIYR+ KFQRSN
Sbjct: 721  GTGIEGVVARDSGASIMAKRAGIIDQVDAARIVVRATED-LEIGDPGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD V++ ++IADGPSTD+G+LALG+N++ AFMPW+GYNFEDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDLVQKGEVIADGPSTDMGELALGKNVVTAFMPWNGYNFEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K ++ ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELGILDRNIYARLKSLILGKVAVKGPKGVKSNSEITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    + QWWQ A++DEK  + VE+L  QYE  K  LE RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLTKGQWWQLALKDEKDAQIVEALNEQYEAQKRTLEARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPIEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG KI   + +Y+ +GD++P+R  ++   G   + E I D D+ 
Sbjct: 1140 NVGQILETHMGWAARGLGIKIDEALQEYRRSGDLTPVREAMKIAYGDDVYDEGIVDMDET 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++  A     GVP++TPVFDGA E  +N  LR A  DESGQS+L+DG TGE F RPVTV
Sbjct: 1200 HLVEAAGNVTKGVPIATPVFDGAKEADVNDALRRAGFDESGQSVLFDGRTGEQFSRPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y++KL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GVKYLMKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            QEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL++
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNM 1369


>gi|311693264|gb|ADP96137.1| DNA-directed RNA polymerase subunit beta [marine bacterium HP15]
          Length = 1361

 Score = 1700 bits (4402), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1367 (52%), Positives = 981/1367 (71%), Gaps = 7/1367 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M     +    R+RK F K P ++D+P L+ +Q  S+  FL M  AP++R   GL AAFK
Sbjct: 1    MQMTYSYTEKKRIRKDFSKLPSVMDVPYLLSIQLDSFRDFLQMEAAPEDRRETGLHAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI ++SG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D    +  K
Sbjct: 61   SVFPIVSYSGNAALEYVSYRIGEPVFDVKECQLRGVTYAAPLRVKVRLIIYDK--ESSNK 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            +IKDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY
Sbjct: 119  AIKDIKEQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLY 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  SE++L  F+    +S 
Sbjct: 179  SARVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPASILLRALGYTSEQMLEMFFETSKFSL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +     L  + L  G   +  + D D G  ++E G+++T+  +K L++ G+  L + +
Sbjct: 239  GAEVCKLELVPSRL-RGDIATFDIKDND-GNVIVEEGRRITARHIKQLEKAGINELEVPT 296

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  +A+D+++  +GE+ +E    + E+ + +I  + ++DI  LY + ++   ++ +
Sbjct: 297  EYLYGRVLAKDMIDQASGEVLVECNSELTEELVTKILDAGVKDIETLYTNDLDCGPFMSD 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D  +   +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K+N RL
Sbjct: 357  TLRIDPTRTPLEALVEIYRMMRPGEPPTKESAENLFNNLFFSEERYDLSAVGRMKLNRRL 416

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              +       +  EDII ++K L+D+RNG+G +DDIDNLGNRRVR VGEM +NQ+R+GL+
Sbjct: 417  RREESTGEGTLTHEDIIDVLKTLIDIRNGQGNVDDIDNLGNRRVRCVGEMAENQFRVGLV 476

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 477  RVERAVRERLSLAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 536

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N+YGF+E+
Sbjct: 537  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARSNSYGFLES 596

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
            PYRKV +G VT++VVYLSA+EE N  IAQA++++DE      +ELV  R   E  + P E
Sbjct: 597  PYRKVENGVVTDEVVYLSAIEESNYVIAQASAAMDEKTKRLTDELVTVRHQNEFTVTPPE 656

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             ++F+D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  V
Sbjct: 657  SVNFMDVSPRQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKAQVPLVGTGVERTV 716

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SG  + A+R G++E VDA RIV+R    + +   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 717  AQDSGVCVSARRGGVIESVDASRIVVRVNNEETEAGDAGVDIYNLTKYTRSNQNTCINQR 776

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             +V+ GD + R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+LISE++V ED  
Sbjct: 777  SIVRQGDIIARGDVLADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILISEKVVQEDRL 836

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+T
Sbjct: 837  TTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVGPGDILVGKVT 896

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+DTS RVP+G  GTV+DV++F R GI+K++R+ S+
Sbjct: 897  PKGETQLTPEEKLLRAIFGEKASDVKDTSSRVPTGTRGTVIDVQVFTRDGIEKDQRAQSI 956

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E+EQ++   +D  DE  I++   + RL   L GQ  +SGP G KK   L    ++E PRS
Sbjct: 957  EKEQLDQYRKDLKDEYRIVEGATFERLNSALKGQEVISGP-GLKKGATLEESYLAELPRS 1015

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
             W++  ++DE +   +E  +   E  K   E RF +K  K+Q GDD+ PGVL++VKV++A
Sbjct: 1016 DWFKLRMKDESLNELLEKSEQGLEDRKKEHEARFDDKKGKLQQGDDLAPGVLKIVKVYLA 1075

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG++S ++P EDMP+ + G  VD+VLNPLGVPSRMNVGQ+ ET
Sbjct: 1076 IKRRIQPGDKMAGRHGNKGVISSVMPIEDMPYDEHGNTVDVVLNPLGVPSRMNVGQVLET 1135

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLG A  GLG++I  ++++ +   ++  L   +            +    D  +L +   
Sbjct: 1136 HLGAAAKGLGERISQMLDEQRKVAELRKLLDEIYN-HSDEVFKVDLDSLSDKEILEMCHN 1194

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GVP++TPVFDGA E  +  ML +A L  +GQ++LYDG TG+ FDRPVTVGY+Y+LKL
Sbjct: 1195 LRGGVPMATPVFDGAKEAEVKRMLELAGLSTTGQTMLYDGRTGDMFDRPVTVGYMYILKL 1254

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH++ DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1255 NHLIDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1314

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1315 DDVNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESE 1361


>gi|70732889|ref|YP_262657.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            Pf-5]
 gi|88909630|sp|Q4K526|RPOB_PSEF5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|68347188|gb|AAY94794.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas fluorescens
            Pf-5]
          Length = 1357

 Score = 1700 bits (4402), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEEVLDAFYTTNVFHVKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ESLSLELVPQRL-RGEIAVLDIQD-DKGKVIVEQGRRITARHINQLEKAGIKELDVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E + 
Sbjct: 597  RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK   ++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGHKAEGG-AGLKKGQEITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR+FL+++    G   E +  + D  +L +A   +
Sbjct: 1136 LAAKGLGEKINRMVEEQR---KVAELRTFLDEIYNQIGGRNEDLDSFSDQEILDLANNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKESEIKAMLKLADLPESGQMQLTDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|260577192|ref|ZP_05845168.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sp. SW2]
 gi|259020572|gb|EEW23892.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter sp. SW2]
          Length = 1377

 Score = 1699 bits (4400), Expect = 0.0,   Method: Composition-based stats.
 Identities = 834/1380 (60%), Positives = 1075/1380 (77%), Gaps = 14/1380 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+  V  G  R+R++FGK  E++++P+LIEVQK+SYD FL     P     +G+Q  F+
Sbjct: 1    MAQSYV--GQKRIRRYFGKIREVLEMPNLIEVQKSSYDLFLKSGDGPKPTDGDGIQGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  ++LEFV YE + PK+DVD+C  RD+TYA PLK+TLRLIVFD+DE TGA+
Sbjct: 59   SVFPIKDFNETSVLEFVKYELEKPKYDVDECQSRDMTYAAPLKVTLRLIVFDIDEDTGAR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT++GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTQNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L A+GMD E I+  +Y  + +  
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLFAMGMDQEGIMDAYYETVAFKH 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
              +           M G + +  LVD  TGE ++++G+K+T  +  S  + G +  L + 
Sbjct: 239  EKNKGWVSRFFPKRMSGTRPAFDLVDAATGEVILKAGEKVTPKMANSWMKDGKITDLLLP 298

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             D + G YVA+DI+N  TGEI++EAGD +  +          SL+ +  + I DIP+L +
Sbjct: 299  FDQILGRYVAKDIINETTGEIWVEAGDELTMEYDRDGAVKGGSLKVLLDNGITDIPVLDI 358

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+V    Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A  +F+ LFFDS++YDLS
Sbjct: 359  DNVTVGPYLRNTMHADKNLGRDTALMDIYRVMRPGEPPTVEAASQLFDTLFFDSERYDLS 418

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+L  PD  R + + DIIA IK L +LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 419  AVGRVKMNMRLDLKAPDTQRTLDRADIIACIKALTELRDGKGEIDDIDHLGNRRVRSVGE 478

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 479  LMENQYRVGLLRMERAIKERMSSVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 538

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 539  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGQNIGLINSLATF 598

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV DGKVT++VVY+SA EE    +AQAN++ D +G FT++L+  R 
Sbjct: 599  ARVNKYGFIETPYRKVIDGKVTDEVVYMSATEEMRHTVAQANAAQDAEGRFTDDLISSRK 658

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            +GE +L P + ID ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+++AP
Sbjct: 659  SGEFMLNPPDAIDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQSDAP 718

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            FVGTG+E+VVA+ SGAAI+A+RAG+++QVDA RIV+R+ E  LDP+  GVDIYRL KF+R
Sbjct: 719  FVGTGIEAVVARDSGAAIMARRAGVIDQVDATRIVVRATE-MLDPAEPGVDIYRLRKFKR 777

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ++C+NQRPLVKVGD V R +++ADGP TD+G+LALGRN++VAFMPW+GYN+EDS+LI
Sbjct: 778  SNQSSCINQRPLVKVGDVVTRGEVVADGPCTDMGELALGRNIVVAFMPWNGYNYEDSILI 837

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER++ +DVFTSIHIEE+EV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 838  SERILRDDVFTSIHIEEYEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVQ 897

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG
Sbjct: 898  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGAFGTIVEVRVFNRHG 957

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +DK+ER++ +ERE++E L+RD+DDE  IL+RNIYSRL  ++ G+ AV GPKG K  + ++
Sbjct: 958  VDKDERALQIEREEVERLSRDRDDELAILERNIYSRLKTLIMGKVAVKGPKGVKAGSEIN 1017

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +L+S   R Q+WQ A+ +E   + VE+L  Q+E  K  L++RF +K+EK++ GDD+PPG
Sbjct: 1018 DELLSTLSRGQYWQLALGEEADAKEVEALHDQFEAQKRALDNRFDDKVEKVRRGDDLPPG 1077

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPS
Sbjct: 1078 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPS 1137

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG KI   + +Y+ +GD++P+R  +    G  ++    +D +
Sbjct: 1138 RMNVGQILETHMGWAARGLGIKIDDALKEYRRSGDLTPVREAVRHAYGDETYEAAFADRN 1197

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +  ++ +A     GVP+S+PVFDGA E  +N  LR A  D SGQS ++DG TGE F RPV
Sbjct: 1198 EADLVELAGNVTRGVPISSPVFDGAKEADVNDALRRAGFDTSGQSEVFDGRTGEKFARPV 1257

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY
Sbjct: 1258 TVGVKYMLKLHHLVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAY 1317

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1318 TLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEEE 1377


>gi|84515197|ref|ZP_01002560.1| DNA-directed RNA polymerase beta subunit [Loktanella vestfoldensis
            SKA53]
 gi|84511356|gb|EAQ07810.1| DNA-directed RNA polymerase beta subunit [Loktanella vestfoldensis
            SKA53]
          Length = 1379

 Score = 1699 bits (4399), Expect = 0.0,   Method: Composition-based stats.
 Identities = 837/1381 (60%), Positives = 1077/1381 (77%), Gaps = 15/1381 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    +      EG++  F+SV
Sbjct: 1    MASSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDSATPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PK+DV++C+ RD+TYA PLK+TLRLIVF+VDE TG+KS+
Sbjct: 61   FPIKDFNETAVLEFVKYELEKPKYDVEECMQRDMTYAAPLKVTLRLIVFEVDEDTGSKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-- 240
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG+D E I++ +Y  + Y+   
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFCRIDRRRKLPVTTLLYALGLDQEGIMNAYYNTVDYTLDP 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
            + + W         + G + +  LVD DTGE + ++G+K+T   +K + ++G VK L + 
Sbjct: 241  KTNAWTTKFFPE-RVRGTRPTYDLVDADTGEIIAKAGEKVTPRSVKKMIDEGKVKNLLVP 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYV 349
             + + G YVA DI+N +TG I++EAGD +  +           L ++  + I  IP+L +
Sbjct: 300  YEHIVGKYVARDIINEQTGAIHVEAGDELTLEIDKTGAVTGGTLRDLIDAGITSIPVLDI 359

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D+++   YIR+T+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFD ++YDLS
Sbjct: 360  DNISVGGYIRSTMAADKNMNRETALMDIYRVMRPGEPPTVDSASALFDTLFFDGERYDLS 419

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+LD  D +R +R+EDI++ IK L +LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 420  AVGRVKMNMRLDLDADDTIRTLRREDIVSCIKALTELRDGKGDIDDIDHLGNRRVRSVGE 479

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 480  LMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 539

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 540  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 599

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV DGKVT+DV Y+SA EE    +AQAN+S++ DGSF  +LV  R 
Sbjct: 600  ARVNKYGFIETPYRKVVDGKVTDDVQYMSATEEMRHTVAQANASMNPDGSFKNDLVSTRV 659

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP
Sbjct: 660  NGDYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQAEAP 719

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E VVA+ SGAAI+AKRAG+++QVDA RIVIR+    L+   +GVDIYR+ KFQR
Sbjct: 720  LVGTGIEEVVARDSGAAIMAKRAGVIDQVDAQRIVIRATSD-LELGDAGVDIYRMRKFQR 778

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRPLVKVGD V++  +IADGPSTDLG+LALG+N++VAFMPW+GYN+EDS+LI
Sbjct: 779  SNQNTCINQRPLVKVGDLVQKGQVIADGPSTDLGELALGKNVVVAFMPWNGYNYEDSILI 838

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 839  SERIVRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVG 898

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            P DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GTVV+VR+FNRHG
Sbjct: 899  PADILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGDFGTVVEVRVFNRHG 958

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K+ER++ +ERE++E L+RD+DDE+ ILDRNIY+RL +I+ G+ A  GPKGFK   V++
Sbjct: 959  VEKDERALQIEREEVERLSRDRDDERAILDRNIYARLWDIIGGKTAAKGPKGFKAGAVVT 1018

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             + +S+  R QWWQ A++DE   + VE+L  QYE  K  ++ RF++K+EK++ GDD+PPG
Sbjct: 1019 EESVSDLSRGQWWQLAMEDEDDAKIVEALNQQYEIQKRAMDARFEDKVEKVRRGDDLPPG 1078

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPS
Sbjct: 1079 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPS 1138

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG +I   + +Y+ +GD++P+R  ++   G   + E I   D
Sbjct: 1139 RMNVGQILETHMGWAARGLGIQIDEALGEYRRSGDLTPVREAMKIAYGDDVYEEGIVGMD 1198

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +  ++  A     GVP++TPVFDGA E  +N  LR A  D SGQSIL+DG TGE F R V
Sbjct: 1199 EADLVEAAGHVTRGVPIATPVFDGAKEADVNDALRRAGFDTSGQSILFDGRTGEQFSRKV 1258

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1259 TVGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1318

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  +
Sbjct: 1319 TLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEDE 1378

Query: 1370 N 1370
             
Sbjct: 1379 E 1379


>gi|114327212|ref|YP_744369.1| DNA-directed RNA polymerase subunit beta [Granulibacter bethesdensis
            CGDNIH1]
 gi|122327807|sp|Q0BUQ6|RPOB_GRABC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114315386|gb|ABI61446.1| DNA-directed RNA polymerase beta chain [Granulibacter bethesdensis
            CGDNIH1]
          Length = 1391

 Score = 1699 bits (4399), Expect = 0.0,   Method: Composition-based stats.
 Identities = 828/1383 (59%), Positives = 1057/1383 (76%), Gaps = 28/1383 (2%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
             F G  R+RK F +  +++ +P+LI+VQ+ASY+ FL MN+ PD R   GLQ  F+SVFPI
Sbjct: 11   SFTGRKRIRKSFARIGDVVPMPNLIDVQRASYEAFLQMNVHPDNRTPTGLQEVFRSVFPI 70

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
              F+G   LEFV+YE + PK+DV++C+ R +T+A PLK+ LRLIV+DVDE TG++SI+DI
Sbjct: 71   DDFAGRGRLEFVNYELEEPKYDVEECIQRGMTFAAPLKVILRLIVWDVDEDTGSRSIRDI 130

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+I
Sbjct: 131  KEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVI 190

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------------------GM 223
            P +G W+D EFDSKD+++VRIDRRRK+PVT+ L AL                      GM
Sbjct: 191  PYRGSWLDFEFDSKDLVYVRIDRRRKLPVTTLLYALEGQRTEAAIASGTDPQDLPEIHGM 250

Query: 224  DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +EEILS FY ++V++     W  P        G  ++ +L+D DTG  V E+G KLT+ 
Sbjct: 251  TAEEILSYFYTQVVFTSTPKGWARPFDPE-AFRGITLAEALIDADTGTVVAEAGTKLTAR 309

Query: 284  LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
              + + E+  K + +    L G Y+AED+VN +TGEIY EAG+ + E  L  +    +  
Sbjct: 310  SARKIAEQA-KTVLVGRADLLGRYMAEDLVNDQTGEIYAEAGEELTEARLAALETLGVTS 368

Query: 344  IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +P L VD      +IRNTL  DKN  R DAL+DIYRVMRPG+  T   AE++F  LFFD 
Sbjct: 369  LPTLAVDQ-TTGPWIRNTLAIDKNSTRDDALIDIYRVMRPGEPPTPETAEALFRGLFFDM 427

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            D+YDLS+VGRVKMNMRL +D PD VR +RKEDI+  +KIL DL++G+G IDDIDNLGNRR
Sbjct: 428  DRYDLSSVGRVKMNMRLGVDAPDTVRTLRKEDILRTVKILCDLKDGRGAIDDIDNLGNRR 487

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            VRSVGE+++NQYRLGLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EFF SSQLS
Sbjct: 488  VRSVGELMENQYRLGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREFFGSSQLS 547

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 548  QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 607

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            +SL ++A+VN YGFIETPYR V DGKV++   YLSAMEE+   +AQA++  D  G  TEE
Sbjct: 608  NSLATYAKVNKYGFIETPYRMVEDGKVSDQWRYLSAMEEDRLVVAQADAPRDSTGKLTEE 667

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            L+  R  G+  LV  E +  +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL
Sbjct: 668  LISVRRQGDFRLVKPEDVTSMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 727

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++A+AP VGTGME+ VA+ SGA IVA+RAG+V+Q+D  RIV+R+     D +T GVDIYR
Sbjct: 728  IRADAPLVGTGMEAAVARDSGATIVARRAGVVDQIDGARIVVRASGE--DGATQGVDIYR 785

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L KF RSNQ+TC+NQRPLVKVGD V   DIIADGPST+LG+LALGRN+L AFMPW+GYNF
Sbjct: 786  LRKFMRSNQSTCINQRPLVKVGDHVISGDIIADGPSTELGELALGRNVLCAFMPWNGYNF 845

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+DE GI+ 
Sbjct: 846  EDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNLDEAGIVY 905

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +GAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +GT+VDVR
Sbjct: 906  IGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTTGTIVDVR 965

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R   +RL E L G  A  G KG K
Sbjct: 966  VFSRRGVDKDERAMAIERAEIERLAKDRDDERGIQERAFLNRLREKLMGHPASGGFKGIK 1025

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
              T+++ ++++E+PR  W   +VQD+ V  ++E LK +++ + + ++ RF+ K+EK+Q G
Sbjct: 1026 AGTIITDEVLAEHPRGAWRNISVQDDAVVADIELLKREFDAAVAKIQARFEGKVEKLQRG 1085

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGTPVD+VLN
Sbjct: 1086 DELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGTPVDLVLN 1145

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKVIGTGSHT 1182
            PLGVPSRMNVGQI ETHLGWAC  LG++I  L+ DY +       L S L ++ G   + 
Sbjct: 1146 PLGVPSRMNVGQILETHLGWACANLGRQIGELVEDYRRNGQQRDELLSRLREIYGENVYN 1205

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
            + I+D ++D ++ +AE  + GVP++TPVFDGA    I +ML  A LD SGQ +L DG TG
Sbjct: 1206 DVIADMNNDQLIELAENLRKGVPIATPVFDGARPSDIENMLSRAGLDTSGQVVLTDGRTG 1265

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF+R VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1266 EPFERKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1325

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D+FE G PESFNVL+KE+++LGL++D
Sbjct: 1326 EAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRDQDSFEAGIPESFNVLMKELKSLGLNVD 1385

Query: 1363 LEN 1365
            LEN
Sbjct: 1386 LEN 1388


>gi|149376693|ref|ZP_01894452.1| DNA-directed RNA polymerase subunit beta [Marinobacter algicola
            DG893]
 gi|149359066|gb|EDM47531.1| DNA-directed RNA polymerase subunit beta [Marinobacter algicola
            DG893]
          Length = 1358

 Score = 1699 bits (4399), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1366 (52%), Positives = 989/1366 (72%), Gaps = 10/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P ++D+P L+ +Q  S+  FL    AP+ R   GL AAFKSV
Sbjct: 1    MTYSYTEKKRIRKDFSKLPSVMDVPYLLSIQLDSFRDFLQSEAAPENRRETGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVSYRIGEPVFDVKECQLRGVTYAAPLRVKVRLIIYDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L ALG +SE++L  F+    +S   
Sbjct: 179  RVIPYRGSWLDFEFDAKDSVFVRIDRRRKLPASILLRALGYNSEQMLEMFFDTSKFSIGP 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L  + L  G   +  + D   G  ++E G+++T+  +K L++ G+  L + ++ 
Sbjct: 239  EVCKLELVPSRL-RGDIATFDIKDKK-GSVIVEEGRRITARHIKQLEKAGLTELEVPTEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +++D+V+ ++GE+ +E    + E+ + +I  + + +I  LY + ++   ++ +TL
Sbjct: 297  LHGRVLSKDMVDTKSGEVLVECNTELTEEVVTKILDAGVTEIETLYTNDLDCGPFMSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS+VGR+K+N RL  
Sbjct: 357  RIDPTRTPLEALVEIYRMMRPGEPPTKESAENLFNNLFFSEERYDLSSVGRMKLNRRLRR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DII ++K L+D+RNG+G +DDIDNLGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  EESTGEGTLTHDDIIDVLKTLIDIRNGQGNVDDIDNLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVRERLSLAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N+YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARSNSYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G+VT++VVYLSA+EE N  IAQA++++DE+   ++ELV  R   E  + P E ++
Sbjct: 597  RKVVEGEVTDEVVYLSAIEESNYIIAQASAAMDENKRLSDELVTVRHQNEFTVTPPENVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+E  VA+ 
Sbjct: 657  FMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSQVPLVGTGVERTVAQD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G++E VDA RIV+R  + + +   +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVTARRGGVIESVDAARIVVRVNDDETEAGDAGVDIYNLTKYTRSNQNTCINQRSIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GDE+ R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+LISE++V ED  T+I
Sbjct: 777  NQGDEIARGDVLADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILISEKVVQEDRLTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RVP+G  GTV+DV++F R GI+K+ R+ S+E+E
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSSRVPTGTRGTVIDVQVFTRDGIEKDTRAQSIEKE 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  DE  I++   + RL   L GQ  +SGP G KK   L    ++E PR  W+
Sbjct: 957  QLDEYRKDLKDEYRIVEGATFERLTNALKGQEVISGP-GLKKGAKLDESYLAELPRDDWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE +   +E  +   E  K   E RF +K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMKDEALNELLEKSEQGLEDRKKEHEARFDDKKGKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S ++P EDMP+ + G  VDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISAVMPIEDMPYDEYGNTVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH--TEKISDYDDDSVLRVAEQW 1200
             A  GLG++I  ++++ +    I+ LR+ L+++           +    D  +L +A   
Sbjct: 1136 AAAKGLGERISQMLDEQR---KIAELRNLLDEIYNHSDEVTKVDLDSLSDKEILALANNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP++TPVFDGA E  +  ML +A L  +GQ++LYDG TG+ FDRPVTVGY+Y+LKLN
Sbjct: 1193 RTGVPMATPVFDGAKEAEVKRMLELAGLSTTGQTVLYDGRTGDEFDRPVTVGYMYILKLN 1252

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H++ DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1253 HLIDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1312

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1313 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESD 1358


>gi|120553645|ref|YP_957996.1| DNA-directed RNA polymerase subunit beta [Marinobacter aquaeolei VT8]
 gi|158513041|sp|A1TYJ0|RPOB_MARAV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120323494|gb|ABM17809.1| DNA-directed RNA polymerase subunit beta [Marinobacter aquaeolei VT8]
          Length = 1358

 Score = 1698 bits (4398), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 978/1364 (71%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P ++++P L+ +Q  S+  +L M  AP++R   GL AAFKSV
Sbjct: 1    MTYSYTEKKRIRKDFSKLPSVMEVPYLLSIQLDSFRDYLQMETAPEDRRETGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVSYRIGEPVFDVKECQLRGVTYAAPLRVKVRLIIYDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFV+ G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEMPLMTENGTFVVNGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L  LG  SE++L  F+    +S   
Sbjct: 179  RVIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASILLRGLGYTSEQMLEMFFETSKFSLGA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L  + L  G   +  + D D G  ++E G+++T+  +K L++ G+  L + ++ 
Sbjct: 239  EVCKLELVPSRL-RGDIATFDIKDND-GNVIVEEGRRITARHIKQLEKAGITELEVPTEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D+++  TGE+ +E    + E+ + +I  + ++DI  LY + ++   ++ +TL
Sbjct: 297  LYGRVLAKDMIDQSTGEVLVECNTELTEEVVTKILDAGVKDIETLYTNDLDCGPFMSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K+N RL  
Sbjct: 357  RIDPTRTPLEALVEIYRMMRPGEPPTKESAENLFNNLFFSEERYDLSAVGRMKLNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DII ++K L+ +RNG+G +DDIDNLGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  EESTGEGTLTHDDIIDVLKTLIAIRNGQGQVDDIDNLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVRERLSLAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N+YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARSNSYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++VVYLSA+EE N  IAQA+++ DE    T+ELV  R   E  + P E ++
Sbjct: 597  RKVVDGVVTDEVVYLSAIEESNYVIAQASAATDEGKRLTDELVTVRHQNEFTVAPPEAVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LK++ P VGTG+E  VA+ 
Sbjct: 657  FMDVSPRQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKSQVPLVGTGVERTVAQD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G++E VDA RIV+R    + +   +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVTARRGGVIESVDAARIVVRVNNEETEAGDAGVDIYNLTKYTRSNQNTCINQRSIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD + R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+LISE++V ED  T+I
Sbjct: 777  RQGDVIARGDVLADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILISEKVVQEDRLTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVGPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RVP+G  GTV+DV++F R GI+K+ R++S+E+E
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSQRVPTGTRGTVIDVQVFTRDGIEKDARALSIEKE 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  DE  I++   + RLM  L GQ  +SGP G KK   L    ++E PR+ W+
Sbjct: 957  QLDKYRKDLKDEYRIVEGATFERLMAALKGQEVISGP-GLKKGAKLEEAYLAELPRADWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE +   +E  +   E  K   E RF +K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMKDEALNELLEKSEQGLEDRKKEHEARFDDKKGKLQQGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S ++P EDMP+ + G  VDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISAVMPIEDMPYDEFGNTVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG++I  ++++ +   ++  L   +            +    D  +  +    + 
Sbjct: 1136 AAAKGLGERISRMLDEQRKVAELRKLLDEIYN-HSDEVFKVDLDSLTDKEIFELCNNLRG 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  +  ML +A LD +GQ+ LYDG TG+ FDRPVTVGY+Y+LKLNH+
Sbjct: 1195 GVPMATPVFDGAKEAEVKRMLELAGLDTTGQTKLYDGRTGDAFDRPVTVGYMYILKLNHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            + DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 IDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1315 NGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESE 1358


>gi|294675848|ref|YP_003576463.1| DNA-directed RNA polymerase subunit beta [Rhodobacter capsulatus SB
            1003]
 gi|294474668|gb|ADE84056.1| DNA-directed RNA polymerase, beta subunit [Rhodobacter capsulatus SB
            1003]
          Length = 1379

 Score = 1698 bits (4397), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1382 (60%), Positives = 1069/1382 (77%), Gaps = 16/1382 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+  V  G  R+R+++GK  E++++P+LIEVQKASYD FL    A      EG+Q  F+
Sbjct: 1    MAQAYV--GQKRIRRYYGKIREVLEMPNLIEVQKASYDLFLRSGDADRPLDGEGIQGVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LEFV YE + PK+DVD+C+ RDLTY+ PLK+TLRLIVFDVDE TGA+
Sbjct: 59   SVFPIKDFNDNAILEFVKYELEKPKYDVDECMSRDLTYSAPLKVTLRLIVFDVDETTGAR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGKLL+
Sbjct: 119  SVKDIKEQDVYMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDRGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +  
Sbjct: 179  ACRIIPYRGSWLDFEFDAKDLVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVTFRA 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL-KEKGVKFLGIT 299
             G          + + G + +  L+D  +GE ++++G+K+T  ++K    E  V  L + 
Sbjct: 239  EGKRGWVSKFFPERVRGTRPTYDLIDAASGEVILKAGEKVTPRMVKKWLDEAKVTELLLP 298

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYV 349
             D + G Y A+DI+N  TG IYIEAGD +  +          S++ +  + I +IP L +
Sbjct: 299  FDHILGRYCAKDIINERTGYIYIEAGDELTAEYDRDGQLVGGSVKTLLDNGITEIPCLDI 358

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D++N   YIRNT+  DKN  R  AL+DIYRVMRPG+  T   A SMF+ LFFDS++YDLS
Sbjct: 359  DNINVGPYIRNTMAADKNMGRDGALMDIYRVMRPGEPPTVEAASSMFDTLFFDSERYDLS 418

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL+LD PD  R +R+ DIIA IK LV+LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 419  AVGRVKMNMRLDLDAPDTQRTLRRADIIACIKGLVELRDGKGEIDDIDHLGNRRVRSVGE 478

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLS   +  
Sbjct: 479  LMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSLFMDQT 538

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 539  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGQNIGLINSLATF 598

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYRKV DG+VT++VVY+SA EE    IAQAN++LDE+G F  +LV  R 
Sbjct: 599  ARVNKYGFIETPYRKVHDGQVTDEVVYMSATEEMRHTIAQANATLDENGKFVNDLVSTRQ 658

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            AGE +L P E +D ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+ EAP
Sbjct: 659  AGEFMLNPVEAVDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRNEAP 718

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            FVGTGME+ VA+ SGAAI+A+R GIV+QVDA RIVIR+ E       +GVDIYRL KF+R
Sbjct: 719  FVGTGMEATVARDSGAAIMARRGGIVDQVDASRIVIRANEDIGM-GDAGVDIYRLRKFKR 777

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ++ +NQRP+VKVGD V +  ++ADGPSTD G+LALGRN++VAFMPW+GYN+EDS+LI
Sbjct: 778  SNQSSTINQRPIVKVGDIVAKGQVVADGPSTDQGELALGRNVVVAFMPWNGYNYEDSILI 837

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+  +DVFTSIHIEE+EV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 838  SERIHRDDVFTSIHIEEYEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVG 897

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GT+V+VR+FNRHG
Sbjct: 898  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGAYGTIVEVRVFNRHG 957

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG--FKKSTV 1007
            +DK+ER++ +ERE+IE LARD+DDE  IL+RNIY+RL  ++ G+  V GPK    K  + 
Sbjct: 958  VDKDERALQIEREEIERLARDRDDEMAILERNIYARLKTLILGKVTVKGPKNTSIKAGSE 1017

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            ++ +L++   R QWWQ A+++E   + VE+L  Q++  K  LE RF +K+EK++ GDD+P
Sbjct: 1018 ITEELLASLSRGQWWQLALENEADAKEVEALNDQFDAQKRALEHRFDDKVEKVRQGDDLP 1077

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV+++VKVFVA+KR +Q+GDKMAGRHGNKG+VS+++P EDMPFL DGTPVD+VLNPLGV
Sbjct: 1078 PGVMKMVKVFVAVKRKLQAGDKMAGRHGNKGVVSKVVPIEDMPFLADGTPVDLVLNPLGV 1137

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMNVGQI ETH+GWA  GLG +I   +  Y+  GD++P+R  +    G  ++ +  ++
Sbjct: 1138 PSRMNVGQILETHMGWASRGLGIRIDEALKAYRRTGDLTPVREEMRHGYGDETYEDVFAE 1197

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
             +++  +  AE  + GVP++TPVFDGA E  +N  L  A  ++SGQSI++DG TG+ F R
Sbjct: 1198 MENERFIECAEHVRGGVPIATPVFDGAKEADVNDALIRAGFNKSGQSIVFDGRTGDQFAR 1257

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVG  Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA
Sbjct: 1258 PVTVGVKYFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGA 1317

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L +S 
Sbjct: 1318 AYTLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDSE 1377

Query: 1368 TK 1369
             +
Sbjct: 1378 EE 1379


>gi|260425426|ref|ZP_05779406.1| DNA-directed RNA polymerase, beta subunit [Citreicella sp. SE45]
 gi|260423366|gb|EEX16616.1| DNA-directed RNA polymerase, beta subunit [Citreicella sp. SE45]
          Length = 1378

 Score = 1698 bits (4397), Expect = 0.0,   Method: Composition-based stats.
 Identities = 831/1380 (60%), Positives = 1068/1380 (77%), Gaps = 14/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SY+ FL     P     EG+   F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYELFLKSGDQPQPSDGEGIMGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV+YE + PK+DV++C+ RD+TY+ PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETAVLEFVNYELEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + YS R 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEAIMDAYYNTVSYSLRR 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITS 300
            G+ W         + G + +  LVD DTGE + E+ KK+T   +K L ++G VK L +  
Sbjct: 241  GEGWVTKFFPE-RVRGTRPTYDLVDADTGEIIAEATKKVTPRAVKKLIDEGKVKQLLLPF 299

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVD 350
            + + G +VA+DI+N +TG IY+EAGD +              L+E+  + I +IP+L +D
Sbjct: 300  EQIVGKFVAKDIINEDTGAIYVEAGDELTWTVDKDGDVTGGSLKELIDAGITEIPVLDID 359

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++   AY+RNT+  DKN DR  AL+DIYRVMRPG+  T   A S+F+ LFFDS++YDLS 
Sbjct: 360  NITVGAYMRNTVAQDKNMDRNSALMDIYRVMRPGEPPTVEAASSLFDTLFFDSERYDLSA 419

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            VGRVKMNMRLNL+ PD  R + ++DI+  IK LV+LR+GKG +DDID+LGNRRVRSVGE+
Sbjct: 420  VGRVKMNMRLNLEKPDTQRTLDRDDIVKCIKALVELRDGKGEVDDIDHLGNRRVRSVGEL 479

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            ++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N
Sbjct: 480  MENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTN 539

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FA
Sbjct: 540  PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFA 599

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN YGFIETPYR V + +VT++V Y+SA EE    +AQAN+SLD+DG F  E+V  R +
Sbjct: 600  RVNKYGFIETPYRVVRESQVTDEVHYMSATEEMRHTVAQANASLDDDGKFVNEMVNTRQS 659

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            G+  L PRE +D ID SPKQ+VS+ ASLIPFLENDD+NR LMG NMQRQAVP L++EAP 
Sbjct: 660  GDYTLAPRESVDLIDVSPKQLVSVGASLIPFLENDDANRALMGANMQRQAVPTLRSEAPL 719

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E  VA  SGAAI A RAGIV+QVDA RIVIR+ E  L+   +GVDIYR+ KFQRS
Sbjct: 720  VGTGIEGKVAIDSGAAIQAHRAGIVDQVDAQRIVIRATED-LELGDAGVDIYRMRKFQRS 778

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQ+PLVKVG  V + +++ADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LIS
Sbjct: 779  NQNTCINQKPLVKVGQLVEKGEVVADGPSTDMGELALGKNVIVAFMPWNGYNYEDSILIS 838

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+  +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V P
Sbjct: 839  ERIARDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEP 898

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG+
Sbjct: 899  GDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGV 958

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL +++ G+ AV GPKG + ++ +  
Sbjct: 959  EKDERALQIEREEVERLARDRDDELAILDRNIYARLKDLILGKTAVKGPKGVRPNSEIDE 1018

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +L++   R QWWQ A+ +E+  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1019 ELLNSLSRGQWWQLALAEEQDAQIVEALHEQYEAQKRTLDARFEDKVEKVRRGDDLPPGV 1078

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVFVA+KR +Q GDKMAGRHGNKG++SR++P EDMPFL+DGTPVD  LNPLGVPSR
Sbjct: 1079 MKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLEDGTPVDFCLNPLGVPSR 1138

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG KI   + DY+ +GD++P+R  +    G   + E I+  D+
Sbjct: 1139 MNVGQILETHMGWASRGLGIKIDEALQDYRRSGDLTPVREAMRIAYGDDVYEEGIAGMDE 1198

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + ++  A     GVP++TPVFDGA E  +N  L  A  D SGQS L+DG +GE F R VT
Sbjct: 1199 EHLVEAAGNVTRGVPIATPVFDGAKEADVNDALTRAGFDTSGQSRLFDGRSGEEFARRVT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1259 VGMKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D +E G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1319 LQEMLTVKSDDVAGRTKVYESIVKGEDNYEAGVPESFNVLVKEVRGLGLNMELLDAEDEE 1378


>gi|259416869|ref|ZP_05740789.1| DNA-directed RNA polymerase, beta subunit [Silicibacter sp.
            TrichCH4B]
 gi|259348308|gb|EEW60085.1| DNA-directed RNA polymerase, beta subunit [Silicibacter sp.
            TrichCH4B]
          Length = 1379

 Score = 1697 bits (4396), Expect = 0.0,   Method: Composition-based stats.
 Identities = 837/1380 (60%), Positives = 1069/1380 (77%), Gaps = 13/1380 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++D+P+LIEVQK+SYD FL     P     EG++  F+SV
Sbjct: 1    MAQTFLGQKRLRKYYGKIREVLDMPNLIEVQKSSYDLFLRSGDEPQPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV+Y  + PK+DVD+C+ RD+TY+ PLK+TLRLIVFDVDE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVNYALERPKYDVDECMQRDMTYSAPLKVTLRLIVFDVDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGLDQEGIMDAYYNTVDFKLEK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE + E+GKK+T   +K + ++G +  L +  +
Sbjct: 241  SRGWVTPFFPERVRGTRPTYDLVDAATGEIICEAGKKVTPRAVKKMIDEGTITELLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G YVA+DI+N E G IY+EAGD +  +          +++E+  + I DIP+L +D+
Sbjct: 301  HIVGKYVAKDIINEENGAIYVEAGDELTLEYDKDGDIIGGTVKELLDAGITDIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTMAADKNMGRDTALMDIYRVMRPGEPPTVEAASALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL LD  D  R +RKEDI+A IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLALDAEDTQRTLRKEDIVACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V +G+VT++V Y+SA EE    +AQAN++LDED  F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVKEGQVTDEVHYMSATEEMRHTVAQANANLDEDNRFVNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLAPNESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E +VA+ SGAAI+AKRAG+++Q+DA RIVIR+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEIVARDSGAAIMAKRAGVIDQIDAQRIVIRATSD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVG  V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGQTVEKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIARDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL ++L G+ AV GPKG + +TV+  D
Sbjct: 960  KDERALQIEREEVERLARDRDDELGILDRNIYARLRDLLLGKTAVKGPKGVRGNTVIDED 1019

Query: 1012 LISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            L+     R QWW  A+++E+  + +E+L  QYE  K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1020 LLDNQLTRGQWWMLALEEEQDAQILEALNEQYEAQKRALDARFEDKVEKVRRGDDLPPGV 1079

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVF+A+KR +Q GDKMAGRHGNKG++SR++P EDMPFL DGTPVD  LNPLGVPSR
Sbjct: 1080 MKMVKVFIAVKRKLQPGDKMAGRHGNKGVISRVVPMEDMPFLADGTPVDFCLNPLGVPSR 1139

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  GLG KI   + DY+  GD++P+R  + +  G   + E IS  D+
Sbjct: 1140 MNVGQILETHMGWAARGLGLKIDDALQDYRRTGDLTPVRDAMREAYGENVYEEGISSMDE 1199

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
              ++  A     GVP++TPVFDGA E+ +N  L  A  D+SGQSIL+DG TGE F RPVT
Sbjct: 1200 TQLIEAAGNVTRGVPIATPVFDGAKEDDVNDALVRAGFDQSGQSILFDGRTGEQFARPVT 1259

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1260 VGIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1319

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEVEE 1379


>gi|254461493|ref|ZP_05074909.1| DNA-directed RNA polymerase, beta subunit [Rhodobacterales bacterium
            HTCC2083]
 gi|206678082|gb|EDZ42569.1| DNA-directed RNA polymerase, beta subunit [Rhodobacteraceae bacterium
            HTCC2083]
          Length = 1378

 Score = 1697 bits (4396), Expect = 0.0,   Method: Composition-based stats.
 Identities = 837/1379 (60%), Positives = 1070/1379 (77%), Gaps = 12/1379 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL     P     EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLNSGDEPIPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV+YE + PK+DV++C  RD+TYA PLK+TLRLIVF++DE TGAKS+
Sbjct: 61   FPIKDFNETSILEFVNYELEKPKYDVEECQQRDMTYAAPLKVTLRLIVFEIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L +LG+D E I+  +Y  + +  + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYSLGLDQEGIMDAYYDTVEFKLKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  LVD  TGE + E+ KK+T   +K L + G V  L I  D
Sbjct: 241  GKGWVTKFFPERVRGTRPTYDLVDAKTGEVIAEANKKVTPRAVKKLIDAGDVTDLLIPYD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYVDS 351
             + G ++A+DI+N ETG IY EAGD +  +           L+E+  + I D+PIL +D+
Sbjct: 301  AIVGKFIAKDIINEETGAIYAEAGDELTLEMDKDGDVIGGSLKELIDAGITDLPILDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN  AY+RNT+  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGAYMRNTMAADKNMNRETALMDIYRVMRPGEPPTVEAASNLFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL+LD  D  R +RKEDI++ IK LV LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLDLDAEDTQRTLRKEDIVSCIKALVHLRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR V +G V+++V Y+SA EE    +AQAN++LDE+  F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRVVNNGVVSDEVHYMSATEEMRHTVAQANANLDENMKFVNDLVSTRKSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+AEAP V
Sbjct: 661  DYTLSPNENVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+    L+   +GVDIYR+ KFQRSN
Sbjct: 721  GTGIEEVVARDSGAAIMAKRAGIIDQVDAQRIVVRATHD-LELGDAGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNT +NQRPLVKVGD V++ ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTTINQRPLVKVGDTVQKGEVIADGPSTDMGELALGKNVVVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RVSRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE VILDRNIY+RL  ++ G+ AV GPKG K +  ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELVILDRNIYARLKGMIMGKVAVKGPKGVKPNAEITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+    R QWWQ A++DEK  + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLETLTRGQWWQLALKDEKDAQIVEALNEQYEVQKRTLDSRFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGVPSRM
Sbjct: 1080 KMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA  GLG  I   + DY+ +GD++P++  +    G   + E +   DDD
Sbjct: 1140 NVGQILETHMGWAARGLGLNIDDALGDYRRSGDLTPVKEAMRLAYGDDVYAEGLEGLDDD 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            ++L  A    +GVP++TPVFDGA E  +N  L+ A   ESGQS+L+DG TGE F RPVTV
Sbjct: 1200 ALLETAGNVTNGVPIATPVFDGAKEHDVNDSLKRAGFSESGQSVLFDGRTGEQFARPVTV 1259

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1260 GIKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1319

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            QEMLT+KSDDV GRT+VYESIV G D +E G PESFNVLVKE++ LGL+++L ++  + 
Sbjct: 1320 QEMLTVKSDDVAGRTKVYESIVKGEDNYEAGVPESFNVLVKEVRGLGLNMELLDAEEEE 1378


>gi|88704391|ref|ZP_01102105.1| RNA polymerase, beta-subunit [Congregibacter litoralis KT71]
 gi|88701442|gb|EAQ98547.1| RNA polymerase, beta-subunit [Congregibacter litoralis KT71]
          Length = 1357

 Score = 1697 bits (4395), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1365 (52%), Positives = 978/1365 (71%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P ++D+P L+ +Q  SY  F    ++ +ER + GL AAFKSV
Sbjct: 1    MPYSYTEKKRIRKDFGTMPTVMDVPYLLAIQLDSYRKFTQQGVSLEERLDYGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C  R +TY+  L++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVDYRLGTPVFDVSECQLRGVTYSCSLRVKVRLIIYDK--ESSNKTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD++  RIDRRRK+P T  L ALG +SEEILS FY   V++   
Sbjct: 179  RIIPYRGSWLDFEFDPKDMVFARIDRRRKLPATILLRALGYESEEILSMFYDFNVFTVDA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G   +  ++     + ++E G+++T+  ++ L++ G   L +  + 
Sbjct: 239  DGGYNMELIPERLRGDVAAFDIMIGK--KVIVEQGRRITARHIRELEKAGATELPVPPEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ ++GE+  E    ++E+ L ++  ++I  I  LY + ++   +I +TL
Sbjct: 297  LHGRALAKNIVDEKSGEVLFECNTEVNEEVLSQLAEAKITAIETLYTNELDCGPFISHTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N RL  
Sbjct: 357  RQDSTRNELEALVEIYRMMRPGEPPTKESAENLFQNLFFSPDRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + +EDI+ +++ LV +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  EEIVGEGTLSREDIVDVLQTLVGIRNGKGMVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNEYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+ E    IAQA++ LD    F ++L+  R   E  ++  E+ID
Sbjct: 597  RKVIDGVVTDEIEYLSAINEAEHVIAQASAELDSKNRFVDDLIAVRHLNEFTVMDPERID 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA  
Sbjct: 657  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERFVAAD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV+R  + ++    + VDIY L K+ RSNQNTC+NQRP+V
Sbjct: 717  SGVCVVAKRPGFIDSVDASRIVVRVDDSEVGAGEAPVDIYNLTKYTRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  SRGDTVARGDILADGPSIDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEI+ DIPNV E  L N+DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEISGDIPNVGEGALSNLDESGIVYIGAEVDAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ R+  +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDARAKHIEKT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  I +   +S L  ++ G   VSG  G  K T L+++++    R QW+
Sbjct: 957  QLDEYRKDLKEEFRIYEEATFSWLGNLISGAKTVSG-GGLSKGTKLTAEVLEGLDREQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + + ++   + S + Q E     LE+RF++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLKLDNPELNEALASAQNQLEEQNKHLEERFEDKKNKLQSGDDLAPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGEPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI  ++ + +   DI   R FLE +   G      I    D+ V+ +A+  +
Sbjct: 1136 MAARGLGDKINEMLEEQRKTADI---RKFLESIYNNGAGRAADIKGLKDNEVMDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TP FDGA EE+I ++L +A LD SGQ  LYDG +G+ FDRPVTVGY+YMLKLNH
Sbjct: 1193 AGVPMATPAFDGAAEESIKALLELAGLDRSGQVTLYDGRSGDAFDRPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1313 VAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESE 1357


>gi|92112547|ref|YP_572475.1| DNA-directed RNA polymerase subunit beta [Chromohalobacter salexigens
            DSM 3043]
 gi|122420789|sp|Q1R0I2|RPOB_CHRSD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91795637|gb|ABE57776.1| DNA-directed RNA polymerase subunit beta [Chromohalobacter salexigens
            DSM 3043]
          Length = 1358

 Score = 1696 bits (4393), Expect = 0.0,   Method: Composition-based stats.
 Identities = 729/1363 (53%), Positives = 988/1363 (72%), Gaps = 7/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  SY  FL  + A +ER + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPQVMDVPYLLAIQLDSYFDFLQQDRAIEERLDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG A LE+VSY F  P FDV +C  R +TY+ PL++ +RLI++D D  T  K+I
Sbjct: 61   FPIESFSGNAALEYVSYRFGTPAFDVKECQLRGVTYSAPLRVKVRLIIYDKDSST--KAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFV+ G +R++VSQLHRSPG+ FDHDKG++  SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVVNGTERVIVSQLHRSPGVFFDHDKGKSHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P T  L ALGM +EEIL TF+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDNVYVRIDRRRKLPATVLLRALGMSAEEILETFFDTSTFHIEK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L  + L  G   +  + D + G  ++E G+++T   ++ +++ G++ L +  + 
Sbjct: 239  SGFSVELVPSRL-RGETATFDIKDGE-GNLIVEEGRRITQKHIRQMEKAGLERLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D V+  TGE+  E    I  + LE+I  + I  +  LY + ++   ++ +TL
Sbjct: 297  LFGKTLAKDQVDPNTGELVCECNTEITPELLEKIGQAGITTLETLYTNDLDTGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    + +AL++IYR+MRPG+  T   AE++F+ LFF  D+YDLS VGR+K N RL  
Sbjct: 357  KIDTTHSQLEALVEIYRMMRPGEPPTKEAAETLFHNLFFTEDRYDLSGVGRMKFNRRLRR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI+ +++ L+++RNG G +DDID+LGNRR+R VGEM +NQ+R+GL+R+
Sbjct: 417  EGDTGSGVLDNQDILDVMRELINIRNGFGEVDDIDHLGNRRIRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +++  N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETLEGPNIGLINSLATYSHTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D +VT++VV+LSA+EE +  IAQA++++DE    T++LV  R  GE   +  +K+ 
Sbjct: 597  RKVVDRQVTDEVVHLSAIEEGDFIIAQASATVDESNKLTDDLVQVRHKGETTFMAPDKVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP LKAE P VGTGME  VA+ 
Sbjct: 657  LMDVSPRQVVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLKAEKPLVGTGMERFVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G+++ VDA RIV+R  E ++    +GVDIY L K+ RSNQNTC+NQRP+V
Sbjct: 717  SGVCAVARRGGVIDSVDAKRIVVRINEDEIIGGEAGVDIYNLTKYVRSNQNTCMNQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V R DI+ADGPS D+GDLALG+NM +AFMPW+GYNFEDS+LISER+V ED FTSI
Sbjct: 777  RPGDVVARGDILADGPSVDMGDLALGQNMRMAFMPWNGYNFEDSILISERVVEEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +D+ GI+ +GAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVSRDTKLGAEEISSDIPNVGEAALGKLDDAGIVYIGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLR P+G+ GTV+DV++F R G++K+ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRAPTGMKGTVIDVQVFTRDGVEKDSRALSIEQS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +   I +   + RL   L GQ    GPK  KK   L    + E PRSQW+
Sbjct: 957  QLDEVRKDLQETYRIAEEATFERLKRALIGQPVNGGPK-LKKGDTLDEAYLDELPRSQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +QDE +   +     Q E  +  +++RF++K  K+  GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLRMQDESLNELLAQADEQLENRRKEMDERFEDKKRKLTQGDDLAPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQSGDKMAGRHGNKG++S I+P EDMPF  +G PVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQSGDKMAGRHGNKGVISSIMPIEDMPFDDNGEPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI  ++ D +    ++ +R FL +V  T  +  E I    DD ++ +A+  +
Sbjct: 1136 MAANGLGVKIDRMLRDAR-QQQVAEIRDFLGQVYNTAETRQEDIDSLSDDEIITLAKNLR 1194

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            SGVPV+TPVFDGA E  I  +L +ADL +SGQ  LYDG TG+ FDR VTVGY+YMLKLNH
Sbjct: 1195 SGVPVATPVFDGAKEHEIKHLLTLADLPDSGQMTLYDGRTGDAFDRQVTVGYMYMLKLNH 1254

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1255 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1314

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            V GRT++Y++IV G+ + + G PESFNVLVKE+++LG+ I+LE
Sbjct: 1315 VEGRTKMYKNIVDGDHSMQAGMPESFNVLVKEIRSLGIDIELE 1357


>gi|254516898|ref|ZP_05128956.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            NOR5-3]
 gi|219674403|gb|EED30771.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            NOR5-3]
          Length = 1357

 Score = 1696 bits (4391), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 979/1365 (71%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P ++D+P L+ +Q  SY  F    ++ +ER + GL AAFKSV
Sbjct: 1    MPYSYTEKKRIRKDFGTMPTVMDVPYLLAIQLDSYRKFTQQGVSLEERLDYGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C  R +TY+  L++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVDYRLGTPVFDVSECQLRGVTYSCSLRVKVRLIIYDK--ESSNKTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD++  RIDRRRK+P T  L ALG +SEEILS FY   V++   
Sbjct: 179  RIIPYRGSWLDFEFDPKDMVFARIDRRRKLPATILLRALGYESEEILSMFYDFNVFTVDA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G   +  ++     + ++E G+++T+  ++ L++ G K L +  + 
Sbjct: 239  DGGFNMELIPERLRGDVAAFDIMVGK--KVIVEQGRRITARHIRELEKAGAKELPVPPEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ ++GE+  E    + E+ L ++  ++I  I  LY + ++   +I +TL
Sbjct: 297  LHGRALAKNIVDEKSGEVLFECNTEVSEEVLTQLADAKITTIETLYTNELDCGPFISHTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IYR+MRPG+  T   AE++F  LFF SD+YDLS VGR+K N RL  
Sbjct: 357  RQDSTRNELEALVEIYRMMRPGEPPTKESAENLFQNLFFSSDRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + +EDI+ +++ LV +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  EEIVGEGTLSREDIVDVLQTLVGIRNGKGMVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNEYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+D+ YLSA+ E    IAQA++ LD    F +EL+  R   E  ++  +++D
Sbjct: 597  RKVVDGVVTDDIEYLSAINEAEHVIAQASAELDSKNRFVDELIAVRHLNEFTVMDPDRVD 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA  
Sbjct: 657  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERFVAAD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIV+R  + ++ P  + VDIY L K+ RSNQNTC+NQRP+V
Sbjct: 717  SGVCVVAKRPGVIDSVDASRIVVRVDDSEVGPGEAPVDIYNLTKYTRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  GRGDSVARGDILADGPSIDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEI+ DIPNV E  L N+DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEISADIPNVGEGALSNLDESGIVYIGAEVDAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ R+  +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDARAKHIEKT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  I +   YS L  ++ G   VSG  G  K T L+  +++E  R QW+
Sbjct: 957  QLDEYRKDLKEEFRIYEEATYSWLGNLIKGAKTVSG-GGLSKGTQLTDAVLAELDREQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + + ++   + S + Q E     LE+RF++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLKLDNAELNDALASAQNQLEEQNKHLEERFEDKKNKLQSGDDLAPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGEPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI  ++ + +   DI   R FLE +   G      I   +D  VL +A+   
Sbjct: 1136 MAARGLGNKINEMLEEQRKTADI---RKFLESIYNNGAGRGADIKGLNDGEVLELAKNLT 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TP FDGA EE+I  +L +A ++ESGQ  LYDG TG+ FDR VTVGY+YMLKLNH
Sbjct: 1193 AGVPMATPAFDGAAEESIKELLELAGMNESGQVRLYDGRTGDAFDRDVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1313 VAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESE 1357


>gi|254454470|ref|ZP_05067907.1| DNA-directed RNA polymerase, beta subunit [Octadecabacter antarcticus
            238]
 gi|198268876|gb|EDY93146.1| DNA-directed RNA polymerase, beta subunit [Octadecabacter antarcticus
            238]
          Length = 1379

 Score = 1695 bits (4390), Expect = 0.0,   Method: Composition-based stats.
 Identities = 829/1381 (60%), Positives = 1062/1381 (76%), Gaps = 15/1381 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F G  R+RK++GK  E++++P+LIEVQK+SYD FL    +      EG++  F+SV
Sbjct: 1    MAQSFLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLRSGDSETPLDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFV YE + PK+DV++C  RD+TYA PLK+TLRLIVFD+D+ TG+KS+
Sbjct: 61   FPIKDFNETSVLEFVKYELEKPKYDVEECQQRDMTYAAPLKVTLRLIVFDMDDDTGSKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-- 240
            RIIP +G W+D EFD+KD++  RIDRRRK+PVT+ L ALG+D E I++ +Y  + Y+   
Sbjct: 181  RIIPYRGSWLDFEFDAKDLVFCRIDRRRKLPVTTLLYALGLDQEMIMNAYYDHVDYTFDA 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT 299
              + W           G +    LVD  TGE V E+GKK+T   +K+L ++G VK L + 
Sbjct: 241  EANSWKTKFFPE-RARGTRPLFDLVDAKTGEVVAEAGKKITPRAVKALIDEGNVKDLLVP 299

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS----------LEEIFHSEIRDIPILYV 349
             D + G + A DI+N ETG IY+EAGD +  +           L+E+  + I+ IP+L +
Sbjct: 300  YDQILGKFAANDIINEETGAIYVEAGDELTLEMDKAGDVIGGTLKELVDAGIKTIPVLDI 359

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D++N   Y+RNT+  DKN  R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS
Sbjct: 360  DNINVGPYMRNTMAADKNMGRETALMDIYRVMRPGEPPTVDAASNLFDSLFFDSERYDLS 419

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGRVKMNMRL LD  D +R +RKEDI++ IK LV LR+GKG IDDID+LGNRRVRSVGE
Sbjct: 420  AVGRVKMNMRLALDAEDTIRTLRKEDIVSCIKALVMLRDGKGDIDDIDHLGNRRVRSVGE 479

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  
Sbjct: 480  LMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQT 539

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 540  NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 599

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            ARVN YGFIETPYR V DG VT++V Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 600  ARVNKYGFIETPYRVVTDGVVTDEVHYMSATEEMRHTVAQANANLDENMRFVNDLVSTRQ 659

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             GE  L P E ++ ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPLL+AEAP
Sbjct: 660  NGEYTLAPSENVNLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLLQAEAP 719

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E VVA+ SGAAI+AKRAGI++QVDA RIV+R+    L+    GVDIYR+ KFQR
Sbjct: 720  LVGTGIEEVVARDSGAAILAKRAGIIDQVDATRIVVRATSD-LEIGDPGVDIYRMRKFQR 778

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRPLVKVGD V + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LI
Sbjct: 779  SNQNTCINQRPLVKVGDTVLKAEVIADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILI 838

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+  +DVFTSIHI+EFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV 
Sbjct: 839  SERITRDDVFTSIHIDEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVE 898

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG
Sbjct: 899  PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDFGTVVEVRVFNRHG 958

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+    GP+G K    + 
Sbjct: 959  VEKDERALQIEREEVERLARDRDDEMTILDRNIYARLRSMIEGKTVAKGPRGIKTGANID 1018

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ + PRS WWQ A+++E   + VE+L  QYE +K +L+ RF++K+EK++ GDD+PPG
Sbjct: 1019 AAMLDDMPRSHWWQIALKEEDDAQIVEALNEQYEAAKKLLDARFEDKVEKVRRGDDLPPG 1078

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKVFVA+KR +Q GDKMAGRHGNKG++S+++P EDMPFL+DGTPVD  LNPLGVPS
Sbjct: 1079 VMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLEDGTPVDFCLNPLGVPS 1138

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQI ETH+GWA  GLG +I   +  Y+ +GD++P+R  ++   G   + + I D  
Sbjct: 1139 RMNVGQILETHMGWAARGLGIEIDEALGAYRRSGDLTPVREAMKIAYGDNVYEDGIKDMT 1198

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +  ++  A     GVP++TPVFDGA E  +N  L  A  D SGQSIL+DG TGE F R V
Sbjct: 1199 EAELVEAAGNVIHGVPIATPVFDGAKEADVNDSLTRAGFDTSGQSILFDGRTGEQFSRKV 1258

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1259 TVGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1318

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQEMLT+KSDDV GRT+VYESIV G D +E G PESFNVLVKE++ LGL+++L ++   
Sbjct: 1319 TLQEMLTVKSDDVAGRTKVYESIVKGEDNYEAGVPESFNVLVKEVRGLGLNMELLDAEED 1378

Query: 1370 N 1370
             
Sbjct: 1379 E 1379


>gi|83648859|ref|YP_437294.1| DNA-directed RNA polymerase subunit beta [Hahella chejuensis KCTC
            2396]
 gi|109903916|sp|Q2S905|RPOB_HAHCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|83636902|gb|ABC32869.1| DNA-directed RNA polymerase, beta subunit [Hahella chejuensis KCTC
            2396]
          Length = 1357

 Score = 1695 bits (4390), Expect = 0.0,   Method: Composition-based stats.
 Identities = 738/1363 (54%), Positives = 992/1363 (72%), Gaps = 9/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY  FL  ++A ++R   GL AAFKSV
Sbjct: 1    MTYSYTEKKRIRKDFGKLPAVMDVPYLLSIQLDSYHDFLQQDVAIEDRQEVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D +  T  K+I
Sbjct: 61   FPIVSFSGNAALEYVSYRLGQPVFDVAECQLRGVTYAAPLRVKVRLIIYDKESST--KAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEVPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  ++E+L  F+   ++   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPATILLRALGYAADEMLEMFFENSLFEVEG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L  + L  G      + D D G  ++E G+++T+  ++ +++ G+K L + S  
Sbjct: 239  GEYFLDLVPSRL-RGDIAIFEIKD-DEGNLIVEEGRRVTARHIRQMEKAGLKRLRVPSSY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A +I +  TGE+ +E    I + ++E+I  + I+ I  LY + ++   ++ +TL
Sbjct: 297  LLGKVTATNIADPSTGEVIVECNTEITDDAIEKIEKAGIKRIETLYTNDLDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  + + +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N RL  
Sbjct: 357  RIDATRSQLEALVEIYRMMRPGEPPTKESAENLFNNLFFSEERYDLSAVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  + +  +   DII +++ L+D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  EETEGLGVLSHSDIIDVLRTLIDIRNGKGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNTYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+D+ YLSA+EE +  IAQA++++DE+G   +ELV  R   E  ++P EK+ 
Sbjct: 597  RKVVDGLVTDDIEYLSAIEESDYVIAQASAAVDENGRLIDELVTVRHKNEFTVMPPEKVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKAE P VGTGME  VA+ 
Sbjct: 657  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKAEKPLVGTGMERYVAQD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+V  VDA RIV+R  + + +   +GVDIY L K+QRSNQNTC+NQR LV
Sbjct: 717  SGVCVVARRGGVVVSVDAARIVVRVSDDETEAGDAGVDIYNLTKYQRSNQNTCINQRSLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GDEV R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  MEGDEVARGDVLADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEE+T DIPNV E  L  +D+ GII +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEVTADIPNVGESALAKLDDSGIIYIGAEVEPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV +G+ GTV+DV++F R G++K++R+  +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVSTGMRGTVIDVQVFTRDGVEKDQRAKEIEQT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D +DE  I++   + RL   L GQ+ + GP G KK   L+    + + + +W+
Sbjct: 957  ELNKFRKDLNDEYKIVEGATFERLRSALLGQSVIGGP-GLKKGDTLTEVHFNAFEKEEWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE++   +E  + Q +  +  +EDR+++K  K+Q GDD+ PGVL++VKV+VA+KR
Sbjct: 1016 KLNMADEQLNELLEKAEGQLQERRKSIEDRYEDKKRKLQSGDDLAPGVLKIVKVYVAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+ + G PVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISAIKPVEDMPYDEQGNPVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI  ++ + K   +I   R FL ++    G   E +    D  VL +A   K
Sbjct: 1136 AAAKGLGDKINRMLAEQKQAAEI---RKFLHEIYNGIGGRNEDLDSLSDSEVLVLAANLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E+ I  MLR+AD+D+SGQ  LYDG TGE F+R VTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEKEIKEMLRLADMDDSGQVWLYDGRTGERFERQVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELE 1355


>gi|296533981|ref|ZP_06896498.1| DNA-directed RNA polymerase subunit beta [Roseomonas cervicalis ATCC
            49957]
 gi|296265694|gb|EFH11802.1| DNA-directed RNA polymerase subunit beta [Roseomonas cervicalis ATCC
            49957]
          Length = 1393

 Score = 1695 bits (4389), Expect = 0.0,   Method: Composition-based stats.
 Identities = 835/1391 (60%), Positives = 1053/1391 (75%), Gaps = 30/1391 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PE+  +P+LI+VQ+ASY+ FL M + PD R N GLQ  FKS
Sbjct: 3    AITKSFTGRKRIRKSFGRLPEVAPMPNLIDVQRASYEAFLQMGVDPDARTNTGLQEVFKS 62

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFV YE + PK+DV++C+ R LT+A PLK+ LRLIV+DVDE TG++S
Sbjct: 63   VFPIDDFAGRGRLEFVQYELEEPKYDVEECIQRGLTFAAPLKVRLRLIVWDVDEDTGSRS 122

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123  VRDIKEQDVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFA 182

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFD+KDI +VR+DR+RK+P T+ L AL                    
Sbjct: 183  ARVIPYRGSWLDFEFDAKDICYVRVDRKRKLPATTLLYALESARTEALRAERGAALEPGE 242

Query: 222  --GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
              GMD+EEIL+TFY ++V+S+    W  P    D   G K+  +LVD  TGE V E   K
Sbjct: 243  VRGMDAEEILNTFYGQVVFSRGPKGWSRPFEP-DAFRGVKLIENLVDAATGEVVAERDTK 301

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            LT  L + + E G K + +    L G YVAED+V+  TGEI+ EAGD + E  L  I  +
Sbjct: 302  LTPRLARKIAEAGTKEVLVGRADLLGRYVAEDLVDLTTGEIWAEAGDELTEPKLAAIEQA 361

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             I  +P L +D      ++RNTL  DKN  R +AL+DIYRVMRPG+  T   AE++F  L
Sbjct: 362  GIDALPTLAIDQ-TVGPWLRNTLAVDKNGSRDEALMDIYRVMRPGEPPTPETAEALFRGL 420

Query: 400  FFDSDKYDLSTVGRVKMNMRLNL---DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            FFD+++YDLSTVGRVKMNMRL     + PD +R +RK+DIIA ++ L++L++GKG IDDI
Sbjct: 421  FFDAERYDLSTVGRVKMNMRLGFTLDEVPDHIRVLRKQDIIATVRTLLELKDGKGQIDDI 480

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 481  DNLGNRRVRSVGELMENQYRVGLLRMERAIKERMGSVDIDTVMPHDLINAKPAAAAVREF 540

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 541  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 600

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD- 635
            G NIGL++SL +FA+VN YGFIETPYR V DGK+  +  YLSAMEEE   +AQA++ ++ 
Sbjct: 601  GPNIGLINSLATFAKVNKYGFIETPYRLVKDGKIVGEPRYLSAMEEEKLVVAQADAEVNA 660

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            E G F  +LV  R  G+  LV  E++  ID SPKQ+VS+AA+LIPFLENDD+NR LMG N
Sbjct: 661  ESGEFLSDLVSVRQGGDFRLVKPEEVTAIDVSPKQLVSVAAALIPFLENDDANRALMGSN 720

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            M RQAVPL++++AP VGTGMES VA+ SGA IVA+R G+V+ +D  RIV+R+   + D +
Sbjct: 721  MMRQAVPLVRSDAPLVGTGMESAVARDSGATIVARRGGVVDSIDGARIVVRAT-NEEDGT 779

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            T GVDIYRL KFQRSNQ+TC+NQRPLVKVGD+V   DIIADGPST+LG+LALGRN+LVAF
Sbjct: 780  TRGVDIYRLRKFQRSNQSTCINQRPLVKVGDQVAPGDIIADGPSTELGELALGRNVLVAF 839

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N
Sbjct: 840  MPWNGYNFEDSILISERIAKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRN 899

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +DE GI+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G 
Sbjct: 900  LDEAGIVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGT 959

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            +GTVVDVR+FNR G+DK+ER+++++R +IE LA+D+DDE+ I +R+ +SRL E L  Q A
Sbjct: 960  TGTVVDVRVFNRRGVDKDERAMAIDRAEIERLAKDRDDEKAIQERSFHSRLREKLLNQKA 1019

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G KG K  T+++ +++ ++ R+ W Q  VQD+ V   +E+LK +++ +   L+ RF++
Sbjct: 1020 SGGFKGVKAGTLINDEVLDQFARATWRQIGVQDDAVMVEIEALKREFDAAVEKLQKRFES 1079

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+EK+Q GD++PPGV+++VKVF+A+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DG
Sbjct: 1080 KVEKLQRGDELPPGVMKMVKVFIAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDG 1139

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP-LRSFLEK 1174
            T VD+VLNPLGVPSRMNVGQI ETHLGWAC  +GK I  L+ DY+  G     L   L  
Sbjct: 1140 TSVDLVLNPLGVPSRMNVGQILETHLGWACANIGKSIGELVEDYRRAGAAREALLEKLRD 1199

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            V G   +   I D  +D ++ + E  + GVP++TPVFDGA    I  ML  A LD SGQS
Sbjct: 1200 VYGDEIYGRDIEDMSEDQLIELGENLRKGVPIATPVFDGARMSDIERMLDKAGLDTSGQS 1259

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG TGE F+R VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1260 RLIDGRTGEYFERKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRF 1319

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D+FE G PESFNVLVKE+
Sbjct: 1320 GEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRDQDSFEAGIPESFNVLVKEL 1379

Query: 1355 QALGLSIDLEN 1365
            ++LGL++DLEN
Sbjct: 1380 KSLGLNVDLEN 1390


>gi|330812082|ref|YP_004356544.1| DNA-directed RNA polymerase, beta chain [Pseudomonas brassicacearum
            subsp. brassicacearum NFM421]
 gi|327380190|gb|AEA71540.1| DNA-directed RNA polymerase, beta chain [Pseudomonas brassicacearum
            subsp. brassicacearum NFM421]
          Length = 1357

 Score = 1694 bits (4387), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEEVLDAFYTTNVFHVQG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDIQD-DKGKVIVEQGRRITARHINQLEKAGIKELQVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKVIVHPATGEILAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTGNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + K+DI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLNKDDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK   ++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGHKAEGG-AGLKKGQEITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  +I + +    ++ LR FL ++    G   E++  + D  +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMIEEQR---KVADLRKFLHEIYNEIGGRNEELDTFSDQEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKESEIKAMLKLADLPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|304391373|ref|ZP_07373315.1| DNA-directed RNA polymerase, beta subunit [Ahrensia sp. R2A130]
 gi|303295602|gb|EFL89960.1| DNA-directed RNA polymerase, beta subunit [Ahrensia sp. R2A130]
          Length = 1405

 Score = 1694 bits (4387), Expect = 0.0,   Method: Composition-based stats.
 Identities = 888/1404 (63%), Positives = 1103/1404 (78%), Gaps = 27/1404 (1%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            ++  VFNG  RVRK +G   E+ ++P+LIEVQ +SYD FLM+      R +EGLQA F S
Sbjct: 5    SQTKVFNGRRRVRKVYGNITEVAEMPNLIEVQMSSYDAFLMVAEPEGGRGDEGLQAVFNS 64

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  FSG+A L+FV Y+F+PPK+D ++C  RD+TY+ PLK+TLRLIVFD+DE TGAKS
Sbjct: 65   VFPIRDFSGSAQLDFVRYDFEPPKYDTEECRQRDMTYSAPLKVTLRLIVFDIDEDTGAKS 124

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A
Sbjct: 125  VKDIKEQEVYMGDMPLMTGNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFA 184

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+DIEFD+KDI++ RIDRRRK+P TS LMALG+  E+IL  FY  +  +  
Sbjct: 185  SRVIPYRGSWLDIEFDAKDIVYARIDRRRKLPATSVLMALGLTGEDILEHFYNNVKVTFE 244

Query: 242  GDF--WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            GD   W  PL    L  G      ++D  TG+ V E+GKK+T+ + + L EK V+ + + 
Sbjct: 245  GDKKGWTMPLDVERL-KGTTPIEDIIDAKTGKSVHEAGKKVTARVARDLAEK-VERIRVA 302

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE-------------------IFHSE 340
               + G YVAEDIVN ETGEI++EAGD +  +  E+                   +    
Sbjct: 303  PSEINGRYVAEDIVNMETGEIFLEAGDELVWELDEKTGEPVANNGKAGTQPTLVDMMELG 362

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
              +  +L +D VN  AY+R+TL  DKN  R++AL DIYRVMRPG+  T   AE+MF  LF
Sbjct: 363  YTEFDVLDIDHVNIGAYMRSTLAADKNSSRQEALFDIYRVMRPGEPPTLESAEAMFESLF 422

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            FD ++YDLS VGRVKMNMRL+LD  D VR +RKEDI++++K LV+LR+G+G IDDIDNLG
Sbjct: 423  FDRERYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDILSVMKTLVELRDGRGDIDDIDNLG 482

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SS
Sbjct: 483  NRRVRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSS 542

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NI
Sbjct: 543  QLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 602

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL +FAR+N YGFIE+PYRKV DGKVT +VVYLSAMEE    +AQAN+ L  DG+F
Sbjct: 603  GLINSLATFARINKYGFIESPYRKVEDGKVTAEVVYLSAMEEAKYTVAQANAPLGADGTF 662

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              + V  R  G+   +P  +I  +D SPKQ+VS+AA+LIPFLENDD+NR LMG NM RQA
Sbjct: 663  ENDTVIARRKGDVQRLPVGEITLMDVSPKQLVSVAAALIPFLENDDANRALMGANMMRQA 722

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPL++AEAPFVGTGMES+VA+ SGAAI AKR G+V+QVDA RIV+R+ E  LDP  SGVD
Sbjct: 723  VPLVRAEAPFVGTGMESIVARDSGAAIGAKRGGVVDQVDATRIVVRATED-LDPGKSGVD 781

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IYRL KFQRSNQ+TC+NQRPLV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+G
Sbjct: 782  IYRLQKFQRSNQSTCINQRPLVRVGDILNKGDIIADGPSTDLGDLALGRNVLVAFMPWNG 841

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V +DVFTSIH+EEFEVMARDTKLGPEEITRDIPNVSEE L+N+DE G
Sbjct: 842  YNFEDSILLSERIVRDDVFTSIHLEEFEVMARDTKLGPEEITRDIPNVSEEALRNLDEAG 901

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I  +GAEV PGDIL GKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+  G  GTVV
Sbjct: 902  ITYIGAEVGPGDILCGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRMSPGAFGTVV 961

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            +VR+FNRHGI+K+ER++++ERE+IE LA+D+DDEQ ILDRN+YSRL+ +L G++ ++GPK
Sbjct: 962  EVRVFNRHGIEKDERAMAIEREEIETLAKDRDDEQAILDRNVYSRLVGMLDGKSGIAGPK 1021

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G+KK T LS + +  YP+SQWW FA+ DEK Q  +E+L+ QY+ SK +L+DRF +K+EK+
Sbjct: 1022 GYKKGTALSEEEMDNYPKSQWWMFAIDDEKAQGQIEALRGQYDESKKLLQDRFMDKVEKL 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL++G   DI
Sbjct: 1082 QRGDELPPGVMKMVKVFVAIKRKLQPGDKMAGRHGNKGVVSRIMPIEDMPFLENGVHADI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQI ETHLGWAC G+G+K+  L+ +Y+  G    LR+ +E++     
Sbjct: 1142 VLNPLGVPSRMNVGQILETHLGWACAGMGEKVGHLLEEYQKTGKQEALRAEIEQIYPEND 1201

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
              E + DYDD+SV+R+A+Q KSGV ++TPVFDGA E  I  ML  A LD SGQS LYDG 
Sbjct: 1202 RNEPVRDYDDESVVRIADQLKSGVRIATPVFDGAHEPDIVDMLEQAGLDGSGQSTLYDGR 1261

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FDRPVT+GYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1262 TGEAFDRPVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1321

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQEMLT+KSDDV GRT+VYESIV G+DTFE+G PESFNVLVKEM++LGLS
Sbjct: 1322 ALEAYGAAYTLQEMLTVKSDDVAGRTKVYESIVRGDDTFESGIPESFNVLVKEMRSLGLS 1381

Query: 1361 IDLENSRTKNSAKMEEIPDFNKCE 1384
            ++LENS+       EE  D+   E
Sbjct: 1382 VELENSK---LEIEEEDEDYVMPE 1402


>gi|114771278|ref|ZP_01448698.1| DNA-directed RNA polymerase beta subunit [alpha proteobacterium
            HTCC2255]
 gi|114548203|gb|EAU51090.1| DNA-directed RNA polymerase beta subunit [alpha proteobacterium
            HTCC2255]
          Length = 1378

 Score = 1694 bits (4387), Expect = 0.0,   Method: Composition-based stats.
 Identities = 839/1382 (60%), Positives = 1066/1382 (77%), Gaps = 17/1382 (1%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA+     G+ R+RK++GK  E++DIP+LI+VQK+SYD FL           EG+ A F+
Sbjct: 1    MAQTHS--GIKRIRKYYGKIREVLDIPNLIQVQKSSYDLFLNSGDQSQPLDGEGINAVFQ 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI  F+  A+LE+V Y+ + PK+DV++C+ RD+TY+ PLK+TLRLIVFDVDE TGA+
Sbjct: 59   SVFPIKDFNETAVLEYVKYDLEKPKYDVEECMQRDMTYSAPLKVTLRLIVFDVDEDTGAR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+KDIKEQ ++MGDLPLMT +GTFV+ G +R+VVSQ+HRSPG+ FDHD+G+   SGKLL+
Sbjct: 119  SVKDIKEQDVFMGDLPLMTPNGTFVVNGTERVVVSQMHRSPGVFFDHDRGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            A RIIP +G W+D EFD+KD+++ RIDRRRK+PVT+ L ALG+D E + S +Y  + Y  
Sbjct: 179  ASRIIPYRGSWLDFEFDAKDVVYARIDRRRKLPVTTLLYALGLDQEGVCSAYYDTVDYKF 238

Query: 241  RGDF--WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLG 297
                  W         + G K +  ++D  TG+ + E+G K+T   +K L E+G V  + 
Sbjct: 239  EKKKNAWVTKFFPQ-RVRGTKPTEDIIDAKTGKVIAEAGTKVTPRTVKKLIEEGKVTEIR 297

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPIL 347
            +  D + G YV++DI+N ETG IY+EAGD +  +          +L E+  + + +IP L
Sbjct: 298  VAFDTIVGRYVSQDIINEETGAIYVEAGDELTLEYDKEGVVNGGTLHELLEAGVTNIPTL 357

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +D++N   YIRNT+  DKN  R  AL+DIYRVMRPG+  T   A ++F+ LFFDS++YD
Sbjct: 358  DIDNINVGPYIRNTMSIDKNMGRDTALMDIYRVMRPGEPPTVDAASALFDTLFFDSERYD 417

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            LS VGRVKMNMRL LD  D  R +RKEDII ++K LV+LR+GKG IDDID+LGNRRVRSV
Sbjct: 418  LSAVGRVKMNMRLQLDAEDTQRTLRKEDIIGVVKALVELRDGKGDIDDIDHLGNRRVRSV 477

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            GE+++NQYR+GLLRMER+IKER+SSV+ID++MPQDLINAKP  +AV EFF SSQLSQ  +
Sbjct: 478  GELMENQYRVGLLRMERAIKERMSSVEIDNIMPQDLINAKPAAAAVREFFGSSQLSQFMD 537

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 538  QTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLA 597

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            SFARVN YGFIETPYR+V DGKVT++V Y+SA EE    +AQAN+ LD+ G F  +LV  
Sbjct: 598  SFARVNKYGFIETPYRRVDDGKVTDEVQYMSATEEMRYTVAQANAKLDDGGKFANDLVST 657

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R AGE +L   E ID+ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLLKA+
Sbjct: 658  RQAGEYMLNTPENIDYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLKAD 717

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            AP+VGTG+E VVA+ SGAAI A R GI++QVDA RIV+R  +  +D    GVDIYRL KF
Sbjct: 718  APYVGTGIEEVVARDSGAAITAARGGIIDQVDATRIVVRVTD-AMDAGDPGVDIYRLRKF 776

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSNQNTC+NQRPLVKVGD V   +++ADGPSTD+G+LALG+N+LVAFMPW+GYN+EDS+
Sbjct: 777  QRSNQNTCINQRPLVKVGDRVSMGEVVADGPSTDIGELALGKNVLVAFMPWNGYNYEDSI 836

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISER+V +DVFTS+HIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAE
Sbjct: 837  LISERIVKDDVFTSVHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAE 896

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V P DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G  GTVV+VR+FNR
Sbjct: 897  VGPSDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGDYGTVVEVRVFNR 956

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
            HGI+K+ER++ +ERE++E LARD+DDE  ILDRN Y+RL  ++ G+ A+ GPKG K  ++
Sbjct: 957  HGIEKDERALQIEREEVERLARDRDDEVGILDRNTYARLKSMIAGKKAIKGPKGVKSGSL 1016

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +  DL+    + QWWQ A++DE    N+ESL  QY+  K  L+ RF++K+EK++ GDD+P
Sbjct: 1017 IDDDLLESLSKGQWWQLALEDEADVANMESLNKQYDLQKGALDARFEDKVEKVRRGDDLP 1076

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV+++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD  LNPLGV
Sbjct: 1077 PGVMKMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPQEDMPFLADGTPVDFCLNPLGV 1136

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMNVGQI ETH+GWA   LGK I   + +Y+ +GD+SP++  ++   G   + E + D
Sbjct: 1137 PSRMNVGQILETHMGWAARNLGKSIDLSLQEYRRSGDMSPVQDAMKIAYGDELYDEVLKD 1196

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
               D+ L  A     GVP++TPVFDGA E  +N ML  A LD SGQSIL+DG TGE F+R
Sbjct: 1197 MPKDNFLEAAGNVTKGVPIATPVFDGAKEADVNDMLTRAGLDTSGQSILFDGRTGEQFNR 1256

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1257 PVTVGMKYILKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1316

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVL+KE+++LGL+I L ++ 
Sbjct: 1317 AYTLQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGIPESFNVLIKEIRSLGLNIQLLDAE 1376

Query: 1368 TK 1369
            ++
Sbjct: 1377 SE 1378


>gi|229592910|ref|YP_002875029.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            SBW25]
 gi|259494189|sp|C3K2Y3|RPOB_PSEFS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|229364776|emb|CAY52777.1| DNA-directed RNA polymerase beta chain [Pseudomonas fluorescens
            SBW25]
          Length = 1357

 Score = 1694 bits (4387), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+S + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFSLKD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A+ L  G      + D   G+ ++E+G+++T+  +  +++ G+K L +  D 
Sbjct: 239  ETLSLELIASRL-RGEIAVLDIQDEK-GKVIVEAGRRITARHINQIEKAGIKSLDVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKVIVHPATGEILAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  RKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK   ++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGHKAEGG-AGLKKGQDITDEILDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  +I + +    ++ LR FL ++    G   E++  + D  +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMIEEQR---KVADLRKFLHEIYNEIGGRKEELDTFSDQEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKESEIKAMLKLADLPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|312963374|ref|ZP_07777857.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            WH6]
 gi|311282454|gb|EFQ61052.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            WH6]
          Length = 1357

 Score = 1694 bits (4386), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+S + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFSLKD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A+ L  G      + D + G+ ++E+G+++T+  +  +++ G+K L +  D 
Sbjct: 239  ETLKLELIASRL-RGEIAVLDIQD-ENGKVIVEAGRRITARHINQIEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEILAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK   ++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGHKAEGG-AGLKKGQDITDEILDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  +I + +    ++ LR FL ++    G   E++  + D  +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMIEEQR---KVADLRKFLHEIYNEIGGRNEELDTFSDQEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKESEIKAMLKLADLPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|77461307|ref|YP_350814.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            Pf0-1]
 gi|88909632|sp|Q3K5Y1|RPOB_PSEPF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|77385310|gb|ABA76823.1| DNA-directed RNA polymerase subunit beta [Pseudomonas fluorescens
            Pf0-1]
          Length = 1357

 Score = 1694 bits (4386), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1365 (52%), Positives = 985/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L  FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEEVLDAFYTTNVFHVKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  EGLSLELVPQRL-RGEVAVLDIQD-DKGKVIVEQGRRITARHINQLEKAGIKELDVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L +I  + +  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTELSTEILAKIAKAGVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK   ++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGHKAEGG-AGLKKGQDITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR+FL+++    G   E +  + D  +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMVEEQR---KVAELRTFLDEIYNQIGGRNEDLDSFSDQEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAKESEIKAMLKLADLPESGQMQLTDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|329114222|ref|ZP_08242984.1| DNA-directed RNA polymerase subunit beta [Acetobacter pomorum DM001]
 gi|326696298|gb|EGE47977.1| DNA-directed RNA polymerase subunit beta [Acetobacter pomorum DM001]
          Length = 1397

 Score = 1693 bits (4384), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1390 (59%), Positives = 1061/1390 (76%), Gaps = 31/1390 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL  N++PD R   GLQ  F+S
Sbjct: 10   AITKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYETFLQANVSPDARTPTGLQEVFRS 69

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFVSYEF+ PK+DV++C+ R LTYA PLK+ LRLIV+DVDE TG++S
Sbjct: 70   VFPINDFAGRGRLEFVSYEFEEPKYDVEECIQRGLTYAAPLKVILRLIVWDVDEDTGSRS 129

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I+DIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 130  IRDIKEQPVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFA 189

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFD+KD+++VRIDR+RK+PVT+ L AL                    
Sbjct: 190  ARVIPYRGSWLDFEFDAKDLLYVRIDRKRKLPVTTLLYALEGAASEAARKAKAAEGGDVD 249

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD+ EILS FY  + + +    W  P  A D   G K+ + LVD +TGE V E+
Sbjct: 250  SMEIKGMDANEILSYFYNAVTFIKTAKGWARPFDA-DSFRGLKLLAPLVDAETGEVVAEA 308

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + EK  + + +    L G Y+A DIVN +TGEIY EAG+ I E  L  +
Sbjct: 309  ETKLTARMVRKIAEK-TREVLVGEIDLLGRYIAHDIVNMQTGEIYGEAGEEITEARLAAL 367

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
              + I ++P+L +D+ N   +IR+TL  DKN  R +AL+DIYRVMRPG+  T   AE+M 
Sbjct: 368  EEAGITELPLLAIDAAN-GPWIRDTLTVDKNSTRDEALIDIYRVMRPGEPPTAETAEAML 426

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            N LFFD D+YDLS VGRVKMNMRL++D PD VR +RKEDI+  IK L DL++G+G IDDI
Sbjct: 427  NGLFFDPDRYDLSAVGRVKMNMRLDMDVPDTVRVLRKEDILRTIKTLCDLKDGRGQIDDI 486

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 487  DNLGNRRVRSVGELMENQYRIGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 546

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 547  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 606

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++A+VN YGFIETPYR V DG + +   YLSAMEEE   +AQA++ +++
Sbjct: 607  GPNIGLINSLATYAKVNKYGFIETPYRLVKDGVLQDGWKYLSAMEEEKLVVAQADAKVND 666

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G+ T +L+  R  G+  LVP  ++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 667  QGALTSDLISVRRNGDFRLVPPTEVTACDVSPKQLVSVAAALIPFLENDDANRALMGSNM 726

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++++AP VGTGME+ VA+ SGA IVAKR GIV+Q+D  RIV+R+   +   ST
Sbjct: 727  QRQAVPLVRSDAPLVGTGMEAAVARDSGATIVAKREGIVDQIDGARIVVRAT--NAAGST 784

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLV VGD VR  DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 785  QGVDIYRLRKYSRSNQSTCINQRPLVHVGDNVRAGDIIADGPSTELGELALGRNVLVAFM 844

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 845  PWNGYNFEDSILISERIAKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 904

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDIL+GK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G S
Sbjct: 905  DEAGIVYVGAEVNPGDILIGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGTS 964

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ YSRL E L GQ A 
Sbjct: 965  GTIVDVRVFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYSRLREKLLGQVAG 1024

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++  ++ E+PR+ W Q  V  + V   +E+L+ +++ + + ++ RF++K
Sbjct: 1025 AGFKGIRSGTEITDAVLDEHPRATWRQIVVASDSVMAELETLRREFDAAIARIQARFESK 1084

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGT
Sbjct: 1085 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGT 1144

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKV 1175
             VD+VLNPLGVPSRMNVGQI ETHLGWAC  +G+ I  ++++Y +       L   L+ V
Sbjct: 1145 AVDLVLNPLGVPSRMNVGQILETHLGWACAKIGRGIGDMVDEYQRNGEKRQELLDRLKDV 1204

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   ++E I++  +D ++ +A   + GVP++TPVFDGA    I +ML  A +++SGQS 
Sbjct: 1205 YGDKVYSEDIANMSNDELIELANNLRKGVPIATPVFDGASIPDIEAMLEKAGVNKSGQSQ 1264

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1265 LIDGRTGEPFERKTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1324

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYESIV   D FE G PESFNVL+KE++
Sbjct: 1325 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYESIVREQDDFEAGIPESFNVLIKELK 1384

Query: 1356 ALGLSIDLEN 1365
            +LGL+++LE 
Sbjct: 1385 SLGLNVELEQ 1394


>gi|26987188|ref|NP_742613.1| DNA-directed RNA polymerase subunit beta [Pseudomonas putida KT2440]
 gi|148545732|ref|YP_001265834.1| DNA-directed RNA polymerase subunit beta [Pseudomonas putida F1]
 gi|41017719|sp|Q88QP2|RPOB_PSEPK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229299|sp|A5VXP0|RPOB_PSEP1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|24981825|gb|AAN66077.1|AE016237_1 DNA-directed RNA polymerase, beta subunit [Pseudomonas putida KT2440]
 gi|148509790|gb|ABQ76650.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas putida F1]
 gi|313496812|gb|ADR58178.1| RpoB [Pseudomonas putida BIRD-1]
          Length = 1357

 Score = 1693 bits (4384), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 990/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL    + D   + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGASKDHFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  L++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRL-RGEVAVMDIHD-ETGKVIVEQGRRITARHINQLEKAGVKQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTEMTTELLIKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V+R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVQRGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +     + LR FL +V    G   E + ++ D+ +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMLEEQR---KAAELRVFLTEVYNEIGGRQENLDEFTDEEILALANNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|292492414|ref|YP_003527853.1| DNA-directed RNA polymerase subunit beta [Nitrosococcus halophilus
            Nc4]
 gi|291581009|gb|ADE15466.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus halophilus
            Nc4]
          Length = 1361

 Score = 1693 bits (4384), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1364 (52%), Positives = 992/1364 (72%), Gaps = 3/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK FGK   I+  P L+  Q  S+ +FL M+  P++R ++GL AAF+SV
Sbjct: 1    MPYSLTEKKRIRKDFGKLYSILKTPFLLATQIDSFRNFLQMDAPPNKREDKGLHAAFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++  A L++VSY    P FDV +C  R LTYA PL++ LRL+++D +     + +
Sbjct: 61   FPIKSYTEYAELQYVSYHLGTPSFDVKECQVRGLTYAAPLRVKLRLVIYDKEAPASEQVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG++PLMT  G FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 121  KDVKEQEVYMGEIPLMTPKGNFVINGTERVIVSQLHRSPGVIFEHDKGKTHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+  T  L ALG  +EEIL  F+  I    +G
Sbjct: 181  RIIPYRGSWLDFEFDPKDCVYARIDRRRKLLATILLRALGYSTEEILMMFFETITVHHQG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G  +   +++ D GE ++E+ +++T+  +K +++ G++ L    + 
Sbjct: 241  SAYLLDLLPQRL-RGESLPFDIINPD-GEVIVEAERRVTARHIKQMEKAGMETLSAPKEF 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+V+ +TGE+   A D I  + +E I  ++I+   ++Y + ++   +I +TL
Sbjct: 299  LIGKTLARDLVDTDTGEVLARANDEITAELMEAIEGADIQAFDLIYTNDLDRGPFISDTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D      +A ++IYRVMRPG+  T   A+++F  LFF+ ++YDLS VGR+K N RL  
Sbjct: 359  RLDLTTTPLEAQMEIYRVMRPGEPPTKEAAQNLFQNLFFNPERYDLSPVGRMKFNRRLGK 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +    +  + KEDI+ +IK L+D+RNG G++DD+D+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 419  EDITGLGVLSKEDIVDVIKTLIDIRNGYGSVDDVDHLGNRRVRSVGEMAENQFRVGLVRV 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 479  ERAVRERLSLAESEGLMPQELINAKPVSAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNQYGFIETPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV + KVT +V YLSA+EE    IAQAN++ DE+G   + LV CR   E  L+P EK+ 
Sbjct: 599  RKVVESKVTGEVEYLSAIEEGQYVIAQANATADEEGRLVDMLVSCRHKNEFTLLPPEKVQ 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +ID SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E VVA+ 
Sbjct: 659  YIDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAETPLVGTGIEKVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R GIV+ VDA R+V+R  + +      GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 719  SGVMVVARRGGIVDSVDAARVVVRVNDEETAADEPGVDIYNLTKYARSNQNTCINQRPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K G+ V   D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V E+ FTSI
Sbjct: 779  KPGEVVVAGDVLADGPSTDMGELALGQNLLVAFMPWNGYNFEDSILISERVVEEERFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE    ARDTKLGPEEI+ DIPNVSE  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 839  HIEELSCFARDTKLGPEEISSDIPNVSEAALSKLDEAGIVYIGAEVKPGDILVGKVTPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R G++K+ R++ +E  
Sbjct: 899  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMHGTVIDVQVFTRDGVEKDSRALQIEEM 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++  + +D  DE  I++ +IY RL ++L G+ A  GP G    + ++ + +++  + +W+
Sbjct: 959  ELAKIKKDLRDEFRIVEADIYQRLEKVLVGKIAEGGPAGLGAGSKITKNYLADLSKDRWF 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ E+  + +E    Q +  ++ ++++F+ +  K+  G D+PPGV ++VKV++A+KR
Sbjct: 1019 EIRLRSEEADKQLEWAAGQLKEQRAAMDEKFQQQRAKLTSGHDLPPGVQKMVKVYLAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMP+++DGTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1079 RVQPGDKMAGRHGNKGVISTIVPLEDMPYMEDGTPVDIVLNPLGVPSRMNIGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI +L+ D  +   +  LR+FLE+V  T    E++S   +  VL +A   ++
Sbjct: 1139 WAAKGLGRKIGALL-DSSSEQQVVELRAFLEQVYNTSGKKEELSSLSNGEVLELANNLRN 1197

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I +ML +ADL  +GQ+ LYDG TGE F RPVTVGY++MLKLNH+
Sbjct: 1198 GVPMATPVFDGASEKEIKAMLELADLPTNGQTALYDGRTGEAFARPVTVGYMHMLKLNHL 1257

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            + DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +++YGAAY LQEMLT+KSDDV
Sbjct: 1258 IDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALESYGAAYTLQEMLTVKSDDV 1317

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL KE++ALG+ I+LE  
Sbjct: 1318 NGRTKMYKNIVDGDYRMEAGMPESFNVLTKEIRALGIDIELEQD 1361


>gi|258542021|ref|YP_003187454.1| DNA-directed RNA polymerase subunit beta [Acetobacter pasteurianus
            IFO 3283-01]
 gi|256633099|dbj|BAH99074.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-01]
 gi|256636156|dbj|BAI02125.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-03]
 gi|256639211|dbj|BAI05173.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-07]
 gi|256642265|dbj|BAI08220.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-22]
 gi|256645320|dbj|BAI11268.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-26]
 gi|256648375|dbj|BAI14316.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-32]
 gi|256651428|dbj|BAI17362.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-01-42C]
 gi|256654419|dbj|BAI20346.1| DNA-directed RNA polymerase beta subunit [Acetobacter pasteurianus
            IFO 3283-12]
          Length = 1397

 Score = 1692 bits (4383), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1390 (59%), Positives = 1061/1390 (76%), Gaps = 31/1390 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL  N++PD R   GLQ  F+S
Sbjct: 10   AITKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYETFLQANVSPDARTPTGLQEVFRS 69

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFVSYEF+ PK+DV++C+ R LTYA PLK+ LRLIV+DVDE TG++S
Sbjct: 70   VFPINDFAGRGRLEFVSYEFEEPKYDVEECIQRGLTYAAPLKVILRLIVWDVDEDTGSRS 129

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I+DIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 130  IRDIKEQPVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFA 189

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFD+KD+++VRIDR+RK+PVT+ L AL                    
Sbjct: 190  ARVIPYRGSWLDFEFDAKDLLYVRIDRKRKLPVTTLLYALEGAASEAARKAKAAEGGDVD 249

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD+ EIL+ FY  + + +    W  P  A D   G K+ + LVD +TGE V E+
Sbjct: 250  SMEIKGMDANEILAYFYNAVTFVKTPKGWARPFDA-DSFRGLKLLAPLVDAETGEVVAEA 308

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + EK  + + +    L G Y+A DIVN +TGEIY EAG+ I E  L  +
Sbjct: 309  ETKLTARMVRKIAEK-TREVLVGEIDLLGRYIAHDIVNMQTGEIYGEAGEEITEARLAAL 367

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
              + I ++P+L +D+ N   +IR+TL  DKN  R +AL+DIYRVMRPG+  T   AE+M 
Sbjct: 368  EEAGITELPLLAIDAAN-GPWIRDTLTVDKNSTRDEALIDIYRVMRPGEPPTAETAEAML 426

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            N LFFD D+YDLS VGRVKMNMRL++D PD VR +RKEDI+  IK L DL++G+G IDDI
Sbjct: 427  NGLFFDPDRYDLSAVGRVKMNMRLDMDVPDTVRVLRKEDILRTIKTLCDLKDGRGQIDDI 486

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 487  DNLGNRRVRSVGELMENQYRIGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 546

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 547  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 606

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++A+VN YGFIETPYR V DG + +   YLSAMEEE   +AQA++ +++
Sbjct: 607  GPNIGLINSLATYAKVNKYGFIETPYRLVKDGVLQDGWKYLSAMEEEKLVVAQADAKVND 666

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G+ T +L+  R  G+  LVP  ++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 667  QGALTSDLISVRRNGDFRLVPPTEVTACDVSPKQLVSVAAALIPFLENDDANRALMGSNM 726

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++++AP VGTGME+ VA+ SGA IVAKR GIV+Q+D  RIV+R+   +   ST
Sbjct: 727  QRQAVPLVRSDAPLVGTGMEAAVARDSGATIVAKRDGIVDQIDGARIVVRAT--NATGST 784

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLV VGD VR  DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 785  QGVDIYRLRKYSRSNQSTCINQRPLVHVGDNVRAGDIIADGPSTELGELALGRNVLVAFM 844

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 845  PWNGYNFEDSILISERIAKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 904

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDIL+GK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P G S
Sbjct: 905  DEAGIVYVGAEVNPGDILIGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGTS 964

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ YSRL E L GQ A 
Sbjct: 965  GTIVDVRVFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYSRLREKLLGQVAG 1024

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++  ++ E+PR+ W Q  V  + V   +E+L+ +++ + + ++ RF++K
Sbjct: 1025 AGFKGIRSGTEITDAVLDEHPRATWRQIVVASDSVMAELETLRREFDAAIARIQARFESK 1084

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGT
Sbjct: 1085 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGT 1144

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKV 1175
             VD+VLNPLGVPSRMNVGQI ETHLGWAC  +G+ I  ++++Y +       L   L+ V
Sbjct: 1145 AVDLVLNPLGVPSRMNVGQILETHLGWACAKIGRGIGDMVDEYQRNGEKRQELLDRLKDV 1204

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   ++E I++  +D ++ +A   + GVP++TPVFDGA    I +ML  A +D+SGQS 
Sbjct: 1205 YGDKVYSEDIANMSNDELVELANNLRKGVPIATPVFDGASIPDIEAMLEKAGVDKSGQSQ 1264

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1265 LIDGRTGEPFERKTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1324

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYESIV   D FE G PESFNVL+KE++
Sbjct: 1325 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYESIVREQDDFEAGIPESFNVLIKELK 1384

Query: 1356 ALGLSIDLEN 1365
            +LGL+++LE 
Sbjct: 1385 SLGLNVELEQ 1394


>gi|161898397|ref|YP_508510.2| DNA-directed RNA polymerase subunit beta [Jannaschia sp. CCS1]
 gi|158564122|sp|Q28UX7|RPOB_JANSC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1385

 Score = 1692 bits (4383), Expect = 0.0,   Method: Composition-based stats.
 Identities = 844/1386 (60%), Positives = 1082/1386 (78%), Gaps = 13/1386 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  R+RKF+GK  E++++P+LIEVQK+SYD FL      +    EG++  F+SV
Sbjct: 1    MPQTYAGQKRIRKFYGKIREVLEMPNLIEVQKSSYDLFLKSGDQLEPMDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  A+LEFV YE + PKFDV++C  RDLTYA PLK+TLRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETAILEFVKYELETPKFDVEECQQRDLTYAAPLKVTLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+AC
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+D E I+  +Y  + +    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFSRIDRRRKLPVTTLLYALGLDQEGIMDAYYDTVTFKMVK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
            +         + + G + ++ LVD  TGE + E+GKK+T   +K   ++G ++ L +  D
Sbjct: 241  NKGWSTKFFPERVRGTRPTTDLVDAKTGEVIAEAGKKVTPRAVKKWIDEGSIENLLVPFD 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G + A+DI+N ETG IY+EAGD +  +          +L+E+  + I +IP+L +D+
Sbjct: 301  GIVGRFAAKDIINEETGAIYVEAGDELTWELDKAGEVSGGTLKELIDAGITEIPVLDIDN 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            VN   Y+RNTL  DKN +R+ AL+DIYRVMRPG+  T   A ++F+ LFFDS++YDLS V
Sbjct: 361  VNVGPYMRNTLAVDKNLNRESALMDIYRVMRPGEPPTVEAASNLFDQLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRL+LD  D +R +RKEDII+ IK LV+LR+G+G IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLDLDAEDTMRTLRKEDIISCIKALVELRDGRGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATYAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYR+V D  V++DVVY+SA EE    +AQAN++LD+DG F  ++V  R +G
Sbjct: 601  VNKYGFIETPYRRVNDAVVSDDVVYMSATEEMRHTVAQANANLDDDGKFVNDMVNTRMSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  L PRE ID ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+A+APFV
Sbjct: 661  EYTLNPREAIDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLQADAPFV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+ESVVAK SGAAI+AKR G+++QVDA RIVIR+ E  L+   +GVDIYRL KFQRSN
Sbjct: 721  GTGIESVVAKDSGAAIMAKRGGVIDQVDAQRIVIRATED-LELGDAGVDIYRLRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLVKVGD++ + ++IADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISE
Sbjct: 780  QNTCINQRPLVKVGDKIGKGEVIADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+  +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PG
Sbjct: 840  RISRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GT+V+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTIVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE VIL+RNIY+RL  ++ G+ AV GPKG K +TV+  D
Sbjct: 960  KDERALQIEREEVERLARDRDDELVILERNIYARLRGMIMGKTAVKGPKGVKPNTVIDED 1019

Query: 1012 LISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            L+     R QWWQ A++DEK   ++E+L  Q++T K  L+ RF++K+EK++ GDD+PPGV
Sbjct: 1020 LLDGQLSRGQWWQLALEDEKDAAHIEALNQQFDTQKRALDHRFEDKVEKVRRGDDLPPGV 1079

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKVF+A+KR +Q GDKMAGRHGNKG++S+++P EDMPFL DGTPVD VLNPLGVPSR
Sbjct: 1080 MKMVKVFIAVKRKLQPGDKMAGRHGNKGVISKVVPMEDMPFLADGTPVDFVLNPLGVPSR 1139

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETH+GWA  G+G +I   +++Y+ +GD++P+R  L+   G   + +  +D D+
Sbjct: 1140 MNVGQILETHMGWAARGMGLQIDEALDEYRRSGDMTPVRDALKIAYGDDVYDDAFADRDE 1199

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            +S+L  A     GVP++TPVFDGA E  +N  L  A    SGQS L+DG TGE F R VT
Sbjct: 1200 ESLLEAAGNVTKGVPIATPVFDGAKEADVNDALIRAGFSTSGQSKLFDGRTGEQFAREVT 1259

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1260 VGVKYLLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1319

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+VYESIV G D FE G PESFNVLVKE++ LGL+++L ++    
Sbjct: 1320 LQEMLTVKSDDVAGRTKVYESIVKGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEDDE 1379

Query: 1371 SAKMEE 1376
                 E
Sbjct: 1380 GGIAAE 1385


>gi|170723913|ref|YP_001751601.1| DNA-directed RNA polymerase subunit beta [Pseudomonas putida W619]
 gi|226699433|sp|B1JDX1|RPOB_PSEPW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|169761916|gb|ACA75232.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas putida W619]
          Length = 1357

 Score = 1692 bits (4383), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL    + D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGASKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  L++ GV  L +  + 
Sbjct: 239  EKLSLELVPQRL-RGEVAVMDIHD-ETGKVIVEQGRRITARHVNQLEKAGVNQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L +I  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEIIAECNTELTTELLIKIAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVARGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  +I + +     + LR FL ++    G   E + ++ D+ +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMIEEQR---KAAELRGFLTEIYNEIGGRQENLEEFTDEEILALAHNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|162149180|ref|YP_001603641.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter
            diazotrophicus PAl 5]
 gi|161787757|emb|CAP57353.1| DNA-directed RNA polymerase beta chain [Gluconacetobacter
            diazotrophicus PAl 5]
          Length = 1390

 Score = 1692 bits (4381), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1393 (59%), Positives = 1058/1393 (75%), Gaps = 31/1393 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL MN++PD R   GLQ  F+S
Sbjct: 3    AMTKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYEAFLQMNVSPDSRTQTGLQEVFRS 62

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFV+YE + PK+DV++C+ R LT+A PLK+ LRLIV+DVDE TG++S
Sbjct: 63   VFPINDFAGRGRLEFVNYELEEPKYDVEECIQRGLTFAAPLKVVLRLIVWDVDEDTGSRS 122

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I+DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123  IRDIKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFA 182

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 183  ARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGASSAAARAAKVAEGGDVD 242

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD++EIL  FY ++V+++    W  P  A     G K+   LVD  +GE V E+
Sbjct: 243  ALEIRGMDADEILGYFYNQVVFTKGPKGWARPFDAE-SFRGLKLLEPLVDAQSGEVVAEA 301

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + E   K + +    L G YVA D+VN ETGEIY EAG+ + E  LE +
Sbjct: 302  DAKLTARMVRKIAET-TKEVLVGPAGLIGRYVAHDLVNMETGEIYAEAGEELTEARLEAL 360

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
              + +  +P L VD+ N   +IRNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF
Sbjct: 361  EEAGVDQLPTLAVDASN-GPWIRNTLTVDKNTSREDALTDIYRVMRPGEPPTPETAEAMF 419

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            + LFFD+D+YDLS VGRVKMNMRL LD PD +R +RKEDI+  +KI+ +L++G+G IDDI
Sbjct: 420  SGLFFDADRYDLSAVGRVKMNMRLGLDAPDTIRVLRKEDILRTVKIMCELKDGRGAIDDI 479

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 480  DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 539

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 540  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 599

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++A+VN YGFIETPYR V +G + +   YLSAMEEE   +AQA++  D 
Sbjct: 600  GPNIGLINSLATYAKVNKYGFIETPYRLVREGVLQDGWKYLSAMEEEKLIVAQADAKQDS 659

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G  T+ELV  R  G+  LV  E++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 660  HGKLTDELVSVRRGGDFRLVKPEEVTACDVSPKQLVSVAAALIPFLENDDANRALMGSNM 719

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++++AP VGTGME+ VA  SGA IVAKR GI++Q+D  RIV+R+ +     +T
Sbjct: 720  QRQAVPLVRSDAPLVGTGMEAAVAHDSGATIVAKRGGIIDQIDGARIVVRATDEAG--AT 777

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLV+VGD VR  DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 778  QGVDIYRLRKYMRSNQSTCINQRPLVRVGDRVRGGDIIADGPSTELGELALGRNVLVAFM 837

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 838  PWNGYNFEDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 897

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +
Sbjct: 898  DEAGIVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTT 957

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ Y+RL E L GQ + 
Sbjct: 958  GTIVDVRVFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYNRLRERLVGQVSG 1017

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++ ++++E+PR  W    V  + V   +E L+ +++ + + ++ RF++K
Sbjct: 1018 TGFKGLRSGTEITEEVLAEHPRGAWRNITVASDPVMVELEVLRREFDAAVARIQARFESK 1077

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGT
Sbjct: 1078 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGT 1137

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKV 1175
            PVD+VLNPLGVPSRMNVGQI ETHLGWAC  +G+ I  L++DY +       L   L+ V
Sbjct: 1138 PVDLVLNPLGVPSRMNVGQILETHLGWACANIGRGIGELVDDYQRTGEKKQELLGRLKTV 1197

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   + + I D  +D ++ +A   + GVP++TPVFDGA    I +ML  A +++SGQS 
Sbjct: 1198 YGDQVYDDAIVDLPNDQLVELANNLRKGVPIATPVFDGASIPDIEAMLESAGVNKSGQSQ 1257

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1258 LIDGRTGEPFERRTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1317

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE++
Sbjct: 1318 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELK 1377

Query: 1356 ALGLSIDLENSRT 1368
            +LGL++DLE S  
Sbjct: 1378 SLGLNVDLEQSND 1390


>gi|167031493|ref|YP_001666724.1| DNA-directed RNA polymerase subunit beta [Pseudomonas putida GB-1]
 gi|189043863|sp|B0KK60|RPOB_PSEPG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166857981|gb|ABY96388.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas putida GB-1]
          Length = 1357

 Score = 1692 bits (4381), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1365 (52%), Positives = 991/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL    + D   + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGASKDHFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  L++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRL-RGEVAVMDIHD-ETGKVIVEQGRRITARHINQLEKAGVKQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTEMTTELLIKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNEKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVITDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +     + LR FL +V    G   E + ++ D+ +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMLEEQR---KAAELRVFLTEVYNEIGGRQENLDEFTDEEILALANNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|237797425|ref|ZP_04585886.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            oryzae str. 1_6]
 gi|331020275|gb|EGI00332.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            oryzae str. 1_6]
          Length = 1357

 Score = 1692 bits (4381), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQETLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|330869438|gb|EGH04147.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            aesculi str. 0893_23]
          Length = 1357

 Score = 1691 bits (4380), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQVQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|90020571|ref|YP_526398.1| DNA-directed RNA polymerase subunit beta [Saccharophagus degradans
            2-40]
 gi|123396502|sp|Q21M93|RPOB_SACD2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|89950171|gb|ABD80186.1| DNA-directed RNA polymerase, beta subunit [Saccharophagus degradans
            2-40]
          Length = 1361

 Score = 1691 bits (4380), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1365 (52%), Positives = 985/1365 (72%), Gaps = 4/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++++P L+ +Q  SY  F   +   D+R + GL AAFKS+
Sbjct: 1    MAYSYTEKKRIRKDFGKLPDVMEVPYLLAIQLDSYRKFTQADTPFDQRKDMGLHAAFKSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C+ R  TYAVPL++ +RLI++D D  + +K+I
Sbjct: 61   FPIVSYSGNAALEYVSYALGKPVFDVKECVLRGATYAVPLRVKVRLIIYDKD--SSSKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFV+ G +R++VSQLHRSPG+ F+HDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFVVNGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++ VRIDRRRK+P +  L ALG  +E++L  FY    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDLVFVRIDRRRKLPASILLRALGYTTEQMLDMFYETSKFGLTE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
               C        + G   +  + D D G  ++E G+++T+  ++ L++ GV  L +  + 
Sbjct: 239  TGECVLELVPSRLRGDVTTFEIKDKD-GNLIVEDGRRITARHIRQLEKAGVTELSVPHEY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+DI+N E+GE+  E    I ++ L E+  S +++   LY + ++   +I +TL
Sbjct: 298  MVGRALAKDIINAESGEVLFECNTEITDEVLAELVKSGVKEFETLYTNELDCGPFISDTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +D  + + +AL++IYR+MRPG+  T   AE++F  LFF S++YDLS VGR+K N RL  
Sbjct: 358  RSDPARTQLEALVEIYRMMRPGEPPTKESAETLFQNLFFSSERYDLSAVGRMKFNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+      +  EDI+ ++K L+D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 418  DSEVGSGTLSNEDIVDVLKTLIDIRNGKGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 478  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N+YGF+E+P+
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNSYGFLESPH 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+++ YLSA+ E    IAQA+++ +E+G  TEELV  R   E  L    ++ 
Sbjct: 598  RKVVDGKVTDEIEYLSAINEAKFVIAQASAAQNENGELTEELVSVRFQNEFTLKGPSEVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VA  
Sbjct: 658  YMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKAQKPLVGTGMERNVAAD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G++E+VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 718  SGVCVVAKRGGVIERVDAARIVVRVADDEVEAGEAGVDIYNLTKYTRSNQNTCINQRSIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + G++V R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 778  RTGEKVSRGDILADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 838  HIQELTCIARDTKLGSEEITADIPNVGEGALSKLDESGIVYVGAEVASGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS V GTV+DV++F R G++K++RS  +E+ 
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSVKGTVIDVQVFTRDGLEKDQRSRDIEKA 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I+    + RL   L G  A++G KG  K   ++ +++ E     W+
Sbjct: 958  QLDQIRKDLNEEYRIVQGATFERLRAALVGNTAMTG-KGVVKGQPVTDEMLDELSHDDWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   +++ +V     +  L+DRF++K  K++ GDD+ PGVL++VKV++A+KR
Sbjct: 1017 KIRMNDDVLNEQIDAAEVALAERRKELDDRFEDKKGKLETGDDLAPGVLKIVKVYLAIKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G P+DIVLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1077 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGNPIDIVLNPLGVPSRMNVGQVLEMHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG+KI  ++   KA  +I      +   IG     E++  + DD ++ +A   + 
Sbjct: 1137 LAAKSLGEKIDEMLKQQKAVAEIRQFLDQIYNQIGESYKAEELDTFSDDEIIELANNLRD 1196

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++T  FDGA E+ I  +L +  + +SGQ  L+DG TG+PF RP TVGY+YMLKLNH+
Sbjct: 1197 GVPMATRAFDGAKEKEIKQLLTLGGMPDSGQMTLFDGRTGDPFQRPTTVGYMYMLKLNHL 1256

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1257 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1316

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV G+   E G PESFNVLVKE+++LG++I+LE   
Sbjct: 1317 AGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGINIELEQDN 1361


>gi|325271158|ref|ZP_08137714.1| DNA-directed RNA polymerase subunit beta [Pseudomonas sp. TJI-51]
 gi|324103710|gb|EGC01001.1| DNA-directed RNA polymerase subunit beta [Pseudomonas sp. TJI-51]
          Length = 1357

 Score = 1691 bits (4380), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 990/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL    + D   + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGASKDNFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  +++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRL-RGEVAVMDIHD-ETGKVIVEQGRRITARHINQIEKAGVKQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTEMTTELLIKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV+S +++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVISDEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +     + LR FL +V    G   E + ++ D  +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMLEEQR---KAAELRVFLTEVYNEIGGRQENLDEFSDAEILALAHNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|209545076|ref|YP_002277305.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter
            diazotrophicus PAl 5]
 gi|209532753|gb|ACI52690.1| DNA-directed RNA polymerase, beta subunit [Gluconacetobacter
            diazotrophicus PAl 5]
          Length = 1390

 Score = 1691 bits (4379), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1393 (59%), Positives = 1058/1393 (75%), Gaps = 31/1393 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL MN++PD R   GLQ  F+S
Sbjct: 3    AMTKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYEAFLQMNVSPDSRTQTGLQEVFRS 62

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFV+YE + PK+DV++C+ R LT+A PLK+ LRLIV+DVDE TG++S
Sbjct: 63   VFPINDFAGRGRLEFVNYELEEPKYDVEECIQRGLTFAAPLKVVLRLIVWDVDEDTGSRS 122

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I+DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123  IRDIKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFA 182

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 183  ARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGASSAAARAAKVAEGGDVD 242

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD++EIL  FY ++V+++    W  P  A     G K+   LVD  +GE V E+
Sbjct: 243  ALEIRGMDADEILGYFYNQVVFTKGPKGWARPFDAE-SFRGLKLLEPLVDAQSGEVVAEA 301

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + E   K + +    L G YVA D+VN ETGEIY EAG+ + E  LE +
Sbjct: 302  DAKLTARMVRKIAET-TKEVLVGPAGLIGRYVAHDLVNMETGEIYAEAGEELTEVRLEAL 360

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
              + +  +P L VD+ N   +IRNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF
Sbjct: 361  EEAGVDQLPTLAVDASN-GPWIRNTLTVDKNTSREDALTDIYRVMRPGEPPTPETAEAMF 419

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            + LFFD+D+YDLS VGRVKMNMRL LD PD +R +RKEDI+  +KI+ +L++G+G IDDI
Sbjct: 420  SGLFFDADRYDLSAVGRVKMNMRLGLDAPDTIRVLRKEDILRTVKIMCELKDGRGAIDDI 479

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 480  DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 539

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 540  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 599

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++A+VN YGFIETPYR V +G + +   YLSAMEEE   +AQA++  D 
Sbjct: 600  GPNIGLINSLATYAKVNKYGFIETPYRLVREGVLQDGWKYLSAMEEEKLIVAQADAKQDS 659

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G  T+ELV  R  G+  LV  E++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 660  HGKLTDELVSVRRGGDFRLVKPEEVTACDVSPKQLVSVAAALIPFLENDDANRALMGSNM 719

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++++AP VGTGME+ VA  SGA IVAKR GI++Q+D  RIV+R+ +     +T
Sbjct: 720  QRQAVPLVRSDAPLVGTGMEAAVAHDSGATIVAKRGGIIDQIDGARIVVRATDEAG--AT 777

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLV+VGD VR  DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 778  QGVDIYRLRKYMRSNQSTCINQRPLVRVGDRVRGGDIIADGPSTELGELALGRNVLVAFM 837

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 838  PWNGYNFEDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 897

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +
Sbjct: 898  DEAGIVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTT 957

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ Y+RL E L GQ + 
Sbjct: 958  GTIVDVRVFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYNRLRERLVGQVSG 1017

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++ ++++E+PR  W    V  + V   +E L+ +++ + + ++ RF++K
Sbjct: 1018 TGFKGLRSGTEITEEVLAEHPRGAWRNITVASDPVMVELEVLRREFDAAVARIQARFESK 1077

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGT
Sbjct: 1078 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGT 1137

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKV 1175
            PVD+VLNPLGVPSRMNVGQI ETHLGWAC  +G+ I  L++DY +       L   L+ V
Sbjct: 1138 PVDLVLNPLGVPSRMNVGQILETHLGWACANIGRGIGELVDDYQRTGEKKQELLGRLKTV 1197

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   + + I D  +D ++ +A   + GVP++TPVFDGA    I +ML  A +++SGQS 
Sbjct: 1198 YGDQVYDDAIVDLPNDQLVELANNLRKGVPIATPVFDGASIPDIEAMLESAGVNKSGQSQ 1257

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1258 LIDGRTGEPFERRTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1317

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE++
Sbjct: 1318 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELK 1377

Query: 1356 ALGLSIDLENSRT 1368
            +LGL++DLE S  
Sbjct: 1378 SLGLNVDLEQSND 1390


>gi|301381714|ref|ZP_07230132.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tomato Max13]
 gi|302061086|ref|ZP_07252627.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tomato K40]
 gi|302130773|ref|ZP_07256763.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tomato NCPPB 1108]
          Length = 1357

 Score = 1691 bits (4379), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLNLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVIELRKFLNEIYNEIGGRQEALEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|294085951|ref|YP_003552711.1| DNA-directed RNA polymerase subunit beta/140 kD subunit [Candidatus
            Puniceispirillum marinum IMCC1322]
 gi|292665526|gb|ADE40627.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Candidatus
            Puniceispirillum marinum IMCC1322]
          Length = 1392

 Score = 1691 bits (4379), Expect = 0.0,   Method: Composition-based stats.
 Identities = 829/1393 (59%), Positives = 1065/1393 (76%), Gaps = 28/1393 (2%)

Query: 1    MAKGVV-FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA  V   +   RVR+ FG+  EI  +P+LI+VQ++SYD FL M++   +R + GLQ  F
Sbjct: 1    MASHVSTLDSRKRVRRTFGQLEEITPMPNLIDVQRSSYDTFLQMDVPVPDRIDHGLQETF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            KSVFPI  F+G ++LEFVSY+ + PK+DV++C  R LT+A PLK+TLRL+V++ DE TGA
Sbjct: 61   KSVFPIGDFAGRSILEFVSYDLEKPKYDVEECQQRGLTFASPLKVTLRLVVWEEDEDTGA 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            +SI+DIKEQ +YMGDLPLMT +GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGKLL
Sbjct: 121  RSIRDIKEQDVYMGDLPLMTSNGTFIVNGTERVIVSQMHRSPGVFFDHDRGKTHASGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------------ 221
            +A R+IP +G W+D EFD+KDI++VRIDR+RK+P T+F+MAL                  
Sbjct: 181  FAARVIPYRGSWLDFEFDAKDILNVRIDRKRKLPSTTFMMALPDADSLAYMDACAESGED 240

Query: 222  -------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
                   GM  EEIL  FY  + Y + GD W + L+   L  G+++   LVD DT + V 
Sbjct: 241  VDPTRIVGMSREEILGYFYNAVDYKRDGDGWRYALNPEAL-KGSQLIRDLVDADTKKVVA 299

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            ++G K+T   LK L E GVK + +    + G ++AEDI+N  TGE+Y EAG+ I E+ + 
Sbjct: 300  KAGTKMTPRALKKLVEDGVKDVLVPDTDVLGRFIAEDIINMSTGEVYAEAGEEITEELMA 359

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                +   DI IL++D+VN   ++RNTL  D+N  R++AL+DIYRVMRPG+  T   + +
Sbjct: 360  RFVENGNDDISILFIDNVNYGPHLRNTLAADRNTCREEALVDIYRVMRPGEPPTLESSHA 419

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            +F  LFF S++YDLS+VGRVKMN RL LDT D VR +RK+D++AI+K+L  L++G+G ID
Sbjct: 420  LFQSLFFTSERYDLSSVGRVKMNSRLELDTDDSVRILRKQDVMAILKVLTGLKDGRGDID 479

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID+LGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ +V+ID+VMP DLINAKP  +AV 
Sbjct: 480  DIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMGAVEIDTVMPADLINAKPAAAAVR 539

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGRICP ET
Sbjct: 540  EFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 599

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL ++A++N YGFIETPYRKV +GKVT++V Y+SAMEE    IAQAN+ L
Sbjct: 600  PEGPNIGLINSLATYAQINRYGFIETPYRKVVEGKVTDEVRYISAMEEGRYTIAQANAEL 659

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            D  G F  EL+  R AGE  L     I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG 
Sbjct: 660  DAKGVFVGELIPVRRAGEIGLARPTDIELMDVSPKQLVSVAAALIPFLENDDANRALMGS 719

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL+KAEAP VGTGME+ VA+ SG  IVAKRAG+++QVDA RIV+R+ E   + 
Sbjct: 720  NMQRQAVPLVKAEAPIVGTGMEARVARDSGVTIVAKRAGVIDQVDATRIVVRASEETAED 779

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              S VDIY L+KFQRSNQNT VNQRPLVKVGD VRR DIIADGPST+ G+LALGRN+LVA
Sbjct: 780  -VSPVDIYSLLKFQRSNQNTTVNQRPLVKVGDTVRRGDIIADGPSTEDGELALGRNVLVA 838

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            FMPW+GYNFEDS+LISER+V +DVFTSIHIEE+EVMARDTKLG EEITRDIPNV EE LK
Sbjct: 839  FMPWNGYNFEDSILISERIVRDDVFTSIHIEEYEVMARDTKLGQEEITRDIPNVGEEALK 898

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+DE GI+ VGAEV P DILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G
Sbjct: 899  NLDEAGIVYVGAEVGPSDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPG 958

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             SGTVV+VR+F+R G++K+ER+++++R +I+ L +D+DDE+ IL+R  Y R+ E+  GQ 
Sbjct: 959  GSGTVVEVRVFSRRGVEKDERALAIDRAEIDRLGKDRDDERSILERGFYGRMTELFAGQT 1018

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              SGPKG K  T +   L+ E P+SQW Q AV+D+ VQ+ +E+    +E++ + L+ RF 
Sbjct: 1019 VASGPKGVKAGTKIDDALLDELPKSQWQQIAVKDDNVQKLIEAQIANFESAVAALQARFN 1078

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K++K+Q GD++ PGV+++VKVFVA+KR +Q GDKMAGRHGNKG++SRI+P EDMP+L+D
Sbjct: 1079 DKVDKLQGGDELLPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRIVPAEDMPYLED 1138

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDIVLNPLGVPSRMNVGQI ETHLGWA  GLGK++ +     +AN D S LR  L  
Sbjct: 1139 GTPVDIVLNPLGVPSRMNVGQILETHLGWAARGLGKQVGAAAEAARANADTSKLRDTLSG 1198

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            +     +  +++  DDD ++  AE    GVP+ TPVFDGA E  + ++L+ A L E+GQ 
Sbjct: 1199 MYSAEQYENELAVMDDDQIIEQAEILGRGVPMGTPVFDGAREADVLALLKKAGLSETGQE 1258

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG TGE FDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1259 WLTDGRTGEVFDRAVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRF 1318

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D FE+G PESFNVLVKE+
Sbjct: 1319 GEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDDFESGIPESFNVLVKEL 1378

Query: 1355 QALGLSIDLENSR 1367
            ++LGL++DL  + 
Sbjct: 1379 RSLGLNVDLHEAE 1391


>gi|330879462|gb|EGH13611.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            morsprunorum str. M302280PT]
 gi|330966918|gb|EGH67178.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            actinidiae str. M302091]
          Length = 1357

 Score = 1691 bits (4378), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1365 (52%), Positives = 989/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLNLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVIELRKFLNEIYNEIGGRQETLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|320322329|gb|EFW78423.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            glycinea str. B076]
          Length = 1357

 Score = 1691 bits (4378), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALLGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|302189270|ref|ZP_07265943.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            syringae 642]
 gi|330891938|gb|EGH24599.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            mori str. 301020]
 gi|330899743|gb|EGH31162.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            japonica str. M301072PT]
 gi|330988289|gb|EGH86392.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            lachrymans str. M301315]
          Length = 1357

 Score = 1690 bits (4377), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|254785056|ref|YP_003072484.1| DNA-directed RNA polymerase subunit beta [Teredinibacter turnerae
            T7901]
 gi|259494194|sp|C5BQ39|RPOB_TERTT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|237687017|gb|ACR14281.1| DNA-directed RNA polymerase, beta subunit [Teredinibacter turnerae
            T7901]
          Length = 1360

 Score = 1690 bits (4377), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1364 (52%), Positives = 982/1364 (71%), Gaps = 5/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++++P L+ +Q  SY  F   +   DER + GLQAAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPNVMEVPYLLAIQLDSYRKFTQADRPADERLDIGLQAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C+ R  TYAVPL++ +RLI++D    + +K+I
Sbjct: 61   FPIVSYSGNAALEYVSYALGKPVFDVSECVLRGATYAVPLRVKVRLIIYDR--ESSSKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ F+HDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L ALG  +EE+L  F+         
Sbjct: 179  RVIPYRGSWLDFEFDPKDLVYVRIDRRRKLPATILLRALGYSAEEMLDMFFETSRVFLAE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L  + L  G   +  + D D G  ++E G+++T+  ++ L++  V  L + ++ 
Sbjct: 239  DNIKLELVPSRL-RGEVTTFEIKDAD-GNVIVEDGRRITARHIRQLEKSNVTELQVPAEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A ++++  TGE+  E    I E+ LE +  + + +  ILY + ++   ++ +TL
Sbjct: 297  VLGKALANNVIDTNTGEVLFECNSEITEEVLEGLRSANVSEFQILYTNDLDCGPFLSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD  +   +AL++IYR+MRPG+  T   AE +F  LFF +++YDLS VGR+K N RL  
Sbjct: 357  RTDPTRTELEALVEIYRMMRPGEPPTKESAEGLFQNLFFSNERYDLSAVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       + +EDI+ +++ L+ +RNG+GT+DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  DEETGEGTLSREDIVDVLRTLISIRNGQGTVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P+
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNNYGFLESPH 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+++ YLSA+ E    IAQA+++ D +G  T++LV  R   E  L     + 
Sbjct: 597  RKVVDGKVTDEIEYLSAINESQYVIAQASAATDGEGRLTDDLVSVRYQNEFTLKAAADVQ 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VA+ 
Sbjct: 657  YMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKADKPVVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G +E VDA RIV+R  + +     +GVDIY L+K+ RSNQNTC+NQRP+V
Sbjct: 717  SGVCVVAKRGGKIESVDAGRIVVRVADEETPAGDAGVDIYNLIKYTRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD + R DI+ADGPS DLG+LALG+NM +AFM W+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  GPGDSISRGDILADGPSVDLGELALGQNMRIAFMTWNGYNFEDSILVSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEITADIPNVGEGALAKLDESGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS V GTV+DV++F R G++K++RS+ +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSVKGTVIDVQVFTRDGLEKDQRSLDIEKA 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   ++RL   L G  A SG KG KK   ++ ++++   R  W+
Sbjct: 957  QLDQVRKDLNEEYRIVEGATFARLRSSLVGNLASSG-KGVKKGEAVTDEMLNAIDRDDWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+ +   ++  + Q    +  L++RF++K  K+  GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KVRMADDALNEQLDLAEQQLVERRKELDERFEDKKRKLATGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G P+DIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGEPIDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG+KI +++   +   ++      +   IG G   E +  + D+ +L +A   + 
Sbjct: 1136 LASKGLGRKIDNMVKQQREIAELRKFLGEIYNEIGQGYKIEDLDSFSDEEILELARNLRG 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++T  FDGA E  I ++L++ADL ESGQ  L+DG TG+ F RPVTVGY+YMLKLNH+
Sbjct: 1196 GVPMATRAFDGAAESEIKALLKLADLPESGQMSLFDGRTGDAFMRPVTVGYMYMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVLVKE+++LG++I+LE  
Sbjct: 1316 NGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGINIELEQD 1359


>gi|146281163|ref|YP_001171316.1| DNA-directed RNA polymerase subunit beta [Pseudomonas stutzeri A1501]
 gi|158514168|sp|A4VHM3|RPOB_PSEU5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145569368|gb|ABP78474.1| DNA-directed RNA polymerase beta chain [Pseudomonas stutzeri A1501]
          Length = 1356

 Score = 1690 bits (4376), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1365 (53%), Positives = 983/1365 (72%), Gaps = 10/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P ++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPHVMDVPYLLAIQLDSYREFLQAGATKDQFRDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   V+  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNVFHVKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  + D D+G+ ++E G+++T+  +  L + G+K L +  D 
Sbjct: 239  ETLALELVPQRL-RGEIATFDIKD-DSGKVIVEQGRRITARHINQLDKSGIKELEMPMDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+ IV+  TGEI  E    +    + +I  +++     LY + ++   +I +TL
Sbjct: 297  VLGRTVAKAIVHPATGEIIAECNTELTVDVMAKIVKAQVVRFETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDSTTNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFAAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSREDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E + 
Sbjct: 597  RVVKDGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPEDVT 655

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ 
Sbjct: 656  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARD 715

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 716  SGVCVVARRGGVIDSVDASRIVVRVRDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 775

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 776  RKGDVVARGDIMADGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRFTTI 835

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 836  HIQELTCVSRDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGPGDILVGKVTPKG 895

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 896  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFIRDGVERDSRALAIEKM 955

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G  A  G  G KK  V++ +++      QW+
Sbjct: 956  QLDEIRKDLNEEFRIVEGATFERLRSALVGATAEGG-AGLKKGVVITDEILDGLEHGQWF 1014

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1015 KLRMAEDALNEQLEKAQAYLSDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1074

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1075 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1134

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D  VL +A   +
Sbjct: 1135 LAAKGLGEKINLMLEEQRK---VAELRKFLHEIYNEIGGRQENLDDLSDQEVLDLANNLR 1191

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+R  TVGY+YMLKLNH
Sbjct: 1192 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMQLFDGRTGNAFERTTTVGYMYMLKLNH 1251

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1252 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1311

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1312 VNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIDLETE 1356


>gi|329897163|ref|ZP_08271904.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium
            IMCC3088]
 gi|328921380|gb|EGG28773.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium
            IMCC3088]
          Length = 1357

 Score = 1689 bits (4375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 732/1365 (53%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P ++DIP L+ +Q  SY  F    +  D+R + GL AAF+SV
Sbjct: 1    MAYSYTEKKRIRKEFGSLPNVMDIPYLLAIQLDSYKKFTQQGVPVDQRGDYGLHAAFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y+   P FDV +C  R +TYA  L++ +RLI++D D  + +K+I
Sbjct: 61   FPIASYSGNAALEYVDYQLGVPAFDVAECQLRGVTYACALRVKVRLIIYDKD--SSSKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQDVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  SEEIL  F+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDQVFVRIDRRRKLPATVLLRALGYSSEEILDMFFDVNEFRVNN 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                      + + G   S  +      + ++E G+++T+  ++ L++  V  L I  + 
Sbjct: 239  ATTLTMALIPERLRGDVASFDIKIGK--KVIVEQGRRITARHIRELEKGEVSELEIPVEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++ V+ +TGE+ +E    +   +++ +  +    I  LY + ++   ++ +TL
Sbjct: 297  LYGRALAKNFVDEKTGEVLVECNTELSADTVKIMLDAGATKIETLYTNDLDCGPFLSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLSTVGR+K N RL  
Sbjct: 357  RQDATRNELEALVEIYRMMRPGEPPTKESAENLFQNLFFSPDRYDLSTVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + ++DI+ ++K+LV +RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  EDVIGSGVLDRDDIVDVLKMLVSIRNGKGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG+VT+D+ YLSA+ E    IAQA++++DE+G FT++LV  R   E  ++P E+ID
Sbjct: 597  RRVVDGQVTDDIEYLSAINEAEHVIAQASATVDENGRFTDDLVAVRHMNEFTVMPPERID 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQVVSIAA+LIPFLE+DD+NR LMG NMQRQAVP L ++ P VGTGME  VA+ 
Sbjct: 657  YMDVSPKQVVSIAAALIPFLEHDDANRALMGSNMQRQAVPTLVSDKPLVGTGMERYVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKRAG+V+ VDA RIV+R+   + D + + VDIY L+K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVVAKRAGVVDSVDASRIVVRASAEEADGNEAPVDIYNLVKYTRSNQNTCINQRAIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPS D+GDLALG+NM +AFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 777  SKGDVVERGDILADGPSVDMGDLALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEISADIPNVGESALSKLDESGIVYIGAEVEPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ R+  +E  
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDSRAREIENH 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +Y+RL   L G+  +SG  G  K TVLS ++++E  R QW+
Sbjct: 957  QLNEFRKDLKEEYRIYEEAVYARLASQLVGKKTLSG-AGLSKGTVLSDEVLAELDREQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D  V   + S + Q E     LE+RF++K  K+Q GDD+ PGVL+VVKV++A+KR
Sbjct: 1016 KIKTDDADVNALIASAEKQLEEENRQLEERFEDKKRKLQTGDDLAPGVLKVVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+  +G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDANGEPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI ++I + +   +++ LR FL K+   G   +E +    DD +  +A+  +
Sbjct: 1136 MAARGLGEKINTMIEEQR---EVAELREFLHKIYNNGAGRSEDLDSLTDDEIRTLAQNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I ++L +AD+ ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAAESEIKALLALADMPESGQFTLFDGRTGDQFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LEN 
Sbjct: 1313 VAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELEND 1357


>gi|304321431|ref|YP_003855074.1| DNA-directed RNA polymerase subunit beta [Parvularcula bermudensis
            HTCC2503]
 gi|303300333|gb|ADM09932.1| DNA-directed RNA polymerase, beta subunit [Parvularcula bermudensis
            HTCC2503]
          Length = 1361

 Score = 1689 bits (4375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 838/1367 (61%), Positives = 1055/1367 (77%), Gaps = 11/1367 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG+  + +++P+LI+VQ+ SY+ FL   +   +R  +GL+A FKSV
Sbjct: 1    MAQSFVEKKRIRKHFGRIGDAVEMPNLIQVQRESYEAFLQRFVPAMDRRRDGLEAVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+ F+  A L++VSYEF+ PKFDVD+C+ RD+TY+ PLK+ L+L VF+VDE T AKS+
Sbjct: 61   FPISDFTDTARLQYVSYEFEEPKFDVDECMQRDMTYSAPLKVKLQLAVFEVDEDTEAKSL 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG+LPLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQEVYMGELPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDII+VRIDRRRK+P T+ L  LG D E+IL  FY  + +    
Sbjct: 181  RIIPYRGSWLDFEFDPKDIINVRIDRRRKLPATTLLYGLGYDQEDILDLFYHSVTHDAVE 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +        L  G K    LVD  TGE  +E+GKK+T+  +K L+E GVK   ++ + 
Sbjct: 241  GGFSTTFDPEKL-KGTKSERDLVDAATGEVAVEAGKKITARTIKQLEEGGVKRFLLSPEQ 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y+A+D+VN ETGEIY EAGD IDE  L E+    I     L +D +N   YIRNTL
Sbjct: 300  MVGRYIAKDLVNRETGEIYAEAGDEIDEDVLAELAERGIDSFETLDIDHINTGGYIRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-N 421
              DKN++R  AL+DIYRVMRPG+  T   AE++F+ LFFD ++YDLS VGRVKMNMRL  
Sbjct: 360  AADKNRNRDMALIDIYRVMRPGEPPTLETAEALFSGLFFDEERYDLSAVGRVKMNMRLGF 419

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D  D+ R +R+EDII ++++L  LR+GKG IDDIDNLGNRRVRSVGE+++NQYR+GLLR
Sbjct: 420  EDVSDEQRTLRREDIIEVLRVLAGLRDGKGEIDDIDNLGNRRVRSVGELMENQYRIGLLR 479

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            MER+IKER+SSV+ID++MP DLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 480  MERAIKERMSSVEIDNIMPNDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRM 539

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + A+VN YGFIE+P
Sbjct: 540  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHAKVNKYGFIESP 599

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPRE 659
            YRKV +G  T++VVYLSA+EE    IAQAN+ +DEDG    E V CR     + +LVPRE
Sbjct: 600  YRKVENGVPTDEVVYLSAVEESRYNIAQANAEIDEDGRLANEFVNCRAGALRDAMLVPRE 659

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++D+ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP+VGTGME VV
Sbjct: 660  EVDYIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLQAEAPYVGTGMEKVV 719

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R+G VEQVDA RIVIR+ E   D +  GVDIY L KFQRSNQNTC+ QR
Sbjct: 720  ARDSGAAIAARRSGFVEQVDAQRIVIRATEE-TDTTKPGVDIYNLRKFQRSNQNTCITQR 778

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLVK+GD V   DI+ADGPSTDLG+LALG+N+LVAFMPW+GYNFEDS+LISER+V +DVF
Sbjct: 779  PLVKIGDIVEAGDIVADGPSTDLGELALGKNVLVAFMPWNGYNFEDSILISERIVRDDVF 838

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIH+EEFE+ ARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +GAEV+PGDILVGKIT
Sbjct: 839  TSIHLEEFEIAARDTKLGPEEITRDIPNVSEEALRNLDEAGIVSIGAEVHPGDILVGKIT 898

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTSL++P GV+GTVV+VR+FNRHG++K+ER+I++
Sbjct: 899  PKGESPMTPEEKLLRAIFGEKAADVRDTSLKLPPGVAGTVVEVRVFNRHGVEKDERAIAI 958

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+I+ LA+D+DDE  IL+RNI+ RL ++L G  AVS PKGF K TV + + + E  R+
Sbjct: 959  EREEIDRLAKDRDDELAILERNIFGRLEDMLVGAEAVSMPKGFDKGTV-TKEQLKEMGRT 1017

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
             WW+  + +E     +E L+ QY+ S++ LE RF++K+EK+Q GD++PPGV+++VKVFVA
Sbjct: 1018 LWWKIGLANEAAMGEIEGLRKQYDESRARLEARFEDKVEKLQRGDELPPGVMKMVKVFVA 1077

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG++S+I P EDMPFL+DGTPVDIVLNPLGVPSRMNVGQI ET
Sbjct: 1078 VKRKLQPGDKMAGRHGNKGVISKIAPMEDMPFLEDGTPVDIVLNPLGVPSRMNVGQILET 1137

Query: 1140 HLGWACVGLGKKI-KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            HLG+AC GLG++I  +L    +           L+ V G           D+  +  +  
Sbjct: 1138 HLGFACRGLGRQIGDALEYWERDESKKDEYIQELKTVYGDDQELPT----DEYELKELGR 1193

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML+ A  +ESGQ  LYDG TG+ F RPVTVGY Y+LK
Sbjct: 1194 NLVRGVPIATPVFDGAREAEIIEMLQKAGFNESGQVELYDGRTGDKFARPVTVGYKYLLK 1253

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1254 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1313

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            SDDV GRT+VYE+IV G+D+FE G PESFNVLVKEM++LGL+++L+N
Sbjct: 1314 SDDVAGRTKVYEAIVRGDDSFEAGIPESFNVLVKEMRSLGLNVELQN 1360


>gi|288942079|ref|YP_003444319.1| DNA-directed RNA polymerase subunit beta [Allochromatium vinosum DSM
            180]
 gi|288897451|gb|ADC63287.1| DNA-directed RNA polymerase, beta subunit [Allochromatium vinosum DSM
            180]
          Length = 1393

 Score = 1689 bits (4375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 737/1399 (52%), Positives = 991/1399 (70%), Gaps = 41/1399 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P I+D+P L+  Q  SY  FL  +++  +R + GL AAFKSV
Sbjct: 1    MAYSFTEKKRIRKDFGKRPSILDVPFLLATQIDSYREFLQADVSVKDRRDLGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A+LE+V Y    P FD  +C  R  T+A PL++ LRL+++D +   G+K +
Sbjct: 61   FPIESYSGNAVLEYVKYRLGDPVFDERECHLRGATFAAPLRVLLRLVIYDKEAPAGSKVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG+LPLMT+ GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGKLL++ 
Sbjct: 121  KDVREQEVYMGELPLMTETGTFIINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG   E+IL  F+    +  +G
Sbjct: 181  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLPATVLLRALGYGVEDILGRFFETDTFRLQG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G  V   +   D  E ++ESG+++T+  ++ L++ GV  L + +D 
Sbjct: 241  QTVTLDLVPERL-RGETVGFDVKIGD--EVLVESGRRVTARHIRELQKAGVDRLEVPADF 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A   V+ +TGE++ EA D I  + LE +F   I  +  L+V+ ++   YI  TL
Sbjct: 298  LLGRILAHAQVDSDTGEVFAEANDPITPELLETLFRKGIETLETLFVNDLDQGPYISETL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +  DA ++IYR+MRPG+  T   A+++F+ LFF SD+YDLS VGR+K N RL  
Sbjct: 358  RIDPTTNDLDAQIEIYRMMRPGEPPTKEAAQNLFHNLFFTSDRYDLSAVGRMKFNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIA-----------------------IIKILVDLRNGKGTIDDIDNL 459
                    I      A                        +K+LV+LRNG+G +DDID+L
Sbjct: 418  ADETGPGVIYDGRYFAGRTDDFSKKLFDQYGEGASDILDSLKVLVELRNGRGMVDDIDHL 477

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            GNRR+R VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQ+LINAKPV +A+ EFF S
Sbjct: 478  GNRRIRCVGEMAENQFRVGLVRVERAVKERLSLAESEGLMPQELINAKPVSAAIKEFFGS 537

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            SQLSQ  +  N LS +TH RR+SALG GG+AR RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 538  SQLSQFMDQNNPLSEVTHKRRVSALGPGGLARERAGFEVRDVHPTHYGRVCPIETPEGPN 597

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            IGL++SL  +AR N+YGF+ETPYRKV DG+VT+ + YLSA+EE N  IAQAN++LD DG 
Sbjct: 598  IGLINSLAVYARTNSYGFLETPYRKVEDGRVTDRIDYLSAIEEGNFVIAQANATLDADGR 657

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              + LV CR A E  +   E++ ++D SP+Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 658  LADALVSCRHANEFAMRAPEEVQYMDVSPRQIVSVAASLIPFLEHDDANRALMGSNMQRQ 717

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD--LDPSTS 757
            AVP L+AE P VGTGME VVA+ SG  +VA+R G++E VDA RIV+R  + +    P   
Sbjct: 718  AVPTLRAEKPLVGTGMERVVARDSGVYVVARRGGVIESVDAARIVVRVNDDEAAKTPDVP 777

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L K+ RSNQNTC+NQRPLVK+GD + R D++ADGPSTD+G+LALG+N+ VAFMP
Sbjct: 778  GVDIYNLTKYTRSNQNTCINQRPLVKLGDAIARGDVLADGPSTDMGELALGQNLRVAFMP 837

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYNFEDS+LISER+V ED FT+IHIEE   +ARDTKLGPEEIT DIPNV E  L  +D
Sbjct: 838  WNGYNFEDSILISERVVQEDRFTTIHIEELSCLARDTKLGPEEITGDIPNVGESALSKLD 897

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G++G
Sbjct: 898  ESGIVYVGAEVRDGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRLPTGMNG 957

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TVVDV++F R G+DK++R+I +E  ++E + +D  D+Q I++ + + R+ ++L G+ A  
Sbjct: 958  TVVDVQVFTRDGVDKDKRAIEIEEMELERVRKDFADQQRIMENDTFQRVEKLLVGRVADG 1017

Query: 998  GPKGFKKSTVLSSDLISEY----PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
            GP GF+  + ++ D +        R  W++  V+DE V   +E++  Q +  +    +R+
Sbjct: 1018 GPGGFRPGSEITKDYLDSLKSKGSRDGWFEIRVRDEDVATQLEAVAAQVKQQREEFRERY 1077

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + K  K+  GDD+ PGVL++VKV+VA+KR IQ GDKMAGRHGNKG++S+++P EDMPF  
Sbjct: 1078 EVKKRKVASGDDLAPGVLKMVKVYVAVKRRIQPGDKMAGRHGNKGVISKVVPVEDMPFSA 1137

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DG PVDIVLNPLGVPSRMNVGQ+ ETHLGWA  GLG+KI  ++   +    I  LR FLE
Sbjct: 1138 DGVPVDIVLNPLGVPSRMNVGQVLETHLGWAAQGLGEKIGRML---QRQTAIGELRDFLE 1194

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD---- 1229
            +V  T    E ++ + DD +L +A     GVP++TPVFDGA EE I +ML++AD D    
Sbjct: 1195 QVYNTSGKQEDLASFSDDEILELARNLTRGVPLATPVFDGATEEEIKAMLKLADRDNTEQ 1254

Query: 1230 --ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
               SGQ+IL+DG +G+ F+RPVTVGY+YM+KLNH+V DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1255 GVPSGQTILFDGRSGDQFERPVTVGYMYMIKLNHLVDDKMHARSTGPYSLVTQQPLGGKA 1314

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G PESF
Sbjct: 1315 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESF 1374

Query: 1348 NVLVKEMQALGLSIDLENS 1366
            NVLVKE+++L ++++L+  
Sbjct: 1375 NVLVKEIRSLAINVELQQD 1393


>gi|331012405|gb|EGH92461.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tabaci ATCC 11528]
          Length = 1357

 Score = 1689 bits (4374), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 987/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMGQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|330953204|gb|EGH53464.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae Cit 7]
          Length = 1357

 Score = 1689 bits (4374), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1365 (52%), Positives = 987/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS IT  RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITCKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLSDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|94497753|ref|ZP_01304320.1| DNA-directed RNA polymerase, beta subunit [Sphingomonas sp. SKA58]
 gi|94422802|gb|EAT07836.1| DNA-directed RNA polymerase, beta subunit [Sphingomonas sp. SKA58]
          Length = 1423

 Score = 1689 bits (4374), Expect = 0.0,   Method: Composition-based stats.
 Identities = 836/1376 (60%), Positives = 1069/1376 (77%), Gaps = 13/1376 (0%)

Query: 5    VVFNG-LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +   G   R+RK FG   E++ +P+LIEVQ+ SY+ FL  +  P      GL+   +SVF
Sbjct: 45   ISNTGAKKRIRKVFGDIHEVVQMPNLIEVQRESYEQFLRSD--PKIGYVSGLEKTLRSVF 102

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI  F+G A ++FV YE + PK+DV++C  R +TYA P+++TLRLIVF+VD+ T  +S+ 
Sbjct: 103  PIRDFAGTAEMDFVHYELEDPKYDVEECRQRGITYAAPMRVTLRLIVFEVDQDTETRSVL 162

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A R
Sbjct: 163  DIKEQDVYMGDMPLMTGNGTFIVNGTERVIVSQMHRSPGVLFDHDRGKTHSSGKYLFAAR 222

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            +IP +G W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+++EEIL+ FY K+V+ +   
Sbjct: 223  VIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTALLYALGLNAEEILAQFYNKVVFLRGEG 282

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             W  P  A     G K +  +VD  +GE V  +G+K++       ++ G++ L I +D +
Sbjct: 283  GWQIPYVAE-AWRGMKPAFDIVDAKSGEVVFAAGQKISPRAANKAEKDGLETLLIPTDEV 341

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G Y A D++N  TGEIYIEAGD +  ++LE++  + I  + +L +D V+   +IRNTL 
Sbjct: 342  YGRYSAYDLINESTGEIYIEAGDEVSPENLEKLDKAGIDRLELLDIDHVSTGPWIRNTLK 401

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             DK +DR  AL DIYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVKMNMRL+LD
Sbjct: 402  ADKAEDRDQALSDIYRVMRPGEPPTKETAEALFAGLFFDPERYDLSAVGRVKMNMRLDLD 461

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
              D V  +R EDI+A++K LV+L++GKG IDDIDNLGNRRVRSVGE+L+NQYR+GLLRME
Sbjct: 462  AEDTVTTLRTEDILAVVKELVNLKDGKGEIDDIDNLGNRRVRSVGELLENQYRVGLLRME 521

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SA
Sbjct: 522  RAVKERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSA 581

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+RVN YGFIETPYR
Sbjct: 582  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKYGFIETPYR 641

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV DGKV+ DVVYLSAMEE    IAQAN+ L EDG F E+L+  R AGE ++ PR+ I  
Sbjct: 642  KVVDGKVSGDVVYLSAMEEAKHTIAQANAELTEDGGFAEDLISAREAGEFLMAPRDHITL 701

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME  VA+ S
Sbjct: 702  MDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGTVARDS 761

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            GAAI AKRAGIV+QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQ+TC+NQRPLV 
Sbjct: 762  GAAITAKRAGIVDQVDATRIVIRAT-GDVEPGQSGVDIYTLQKFQRSNQDTCINQRPLVN 820

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD +   D+IADGPST+ G+LALGRN LVAFMPW+GYN+EDS+LISER+V +DVFTSIH
Sbjct: 821  VGDLIDAGDVIADGPSTEFGELALGRNTLVAFMPWNGYNYEDSILISERIVKDDVFTSIH 880

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEEFEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGKITPKGE
Sbjct: 881  IEEFEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVEPGDILVGKITPKGE 940

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            SPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGIDK+ER++++ERE+
Sbjct: 941  SPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIDKDERAMAIEREE 1000

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            I+ LA+D++DE+ IL+R  ++RL E+L GQ A + PKG KK  V+   L+ E  R +WW+
Sbjct: 1001 IDRLAKDREDERGILNRATFNRLQEMLLGQTASAAPKGVKKGVVIDEALLGEVERHEWWK 1060

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            FAV+D++ Q  +E++K QY+ +  ++ ++F+++++K+Q GD++PPGVL++VKVFVA+KR 
Sbjct: 1061 FAVEDDQRQAGIEAVKAQYDEAVKLIVEKFEDRVDKLQRGDELPPGVLKMVKVFVAVKRK 1120

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q GDKMAGRHGNKG++SRILP EDMPFL+DGT VDIVLNPLGVPSRMNVGQIFETHLGW
Sbjct: 1121 LQPGDKMAGRHGNKGVISRILPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQIFETHLGW 1180

Query: 1144 ACVGLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            A  GLG++IK  + D++     +        ++  L    G   + ++I   D   ++ +
Sbjct: 1181 AARGLGEQIKHALEDWREANPNAEAGAMPDAVKQRLLDAYG-EQYVDQIERRDAGQIIDL 1239

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            AE    GVP++TPVFDGA E  ++ ML +A LD SGQS LYDG TG+ FDR VTVG IYM
Sbjct: 1240 AEHLGRGVPMATPVFDGAREADVSRMLEIAGLDSSGQSDLYDGRTGDKFDRKVTVGIIYM 1299

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT
Sbjct: 1300 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLT 1359

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            +KSDDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L         
Sbjct: 1360 VKSDDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELAAMDEVEDD 1415


>gi|28867847|ref|NP_790466.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tomato str. DC3000]
 gi|41017716|sp|Q889X8|RPOB_PSESM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|28851083|gb|AAO54161.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas syringae pv.
            tomato str. DC3000]
          Length = 1357

 Score = 1689 bits (4373), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLNLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS IT  RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITCKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVIELRKFLNEIYNEIGGRQEALEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|104779748|ref|YP_606246.1| DNA-directed RNA polymerase subunit beta [Pseudomonas entomophila
            L48]
 gi|158564149|sp|Q1IFX3|RPOB_PSEE4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|95108735|emb|CAK13429.1| RNA polymerase, beta subunit [Pseudomonas entomophila L48]
          Length = 1357

 Score = 1689 bits (4373), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL    + D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGASKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHLSG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D  +G+ ++E G+++T+  +  L++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRL-RGEVAVMDIHDG-SGKVIVEQGRRITARHINQLEKAGVKELDVPLEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +    L +I  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTELTTDLLVKIAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS VGR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMGQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNEKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDVVARGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ D+++     QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRAALNGQVVDGG-AGLKKGTVITDDVLNGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  +I + +     + LR+FL ++    G   E + ++ D+ ++ +A   K
Sbjct: 1136 LAAKGLGEKIDRMIEEQR---KAAELRTFLTEIYNEIGGRQENLEEFTDEEIMALANNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMQLFDGRTGNKFERSVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|260752782|ref|YP_003225675.1| DNA-directed RNA polymerase subunit beta [Zymomonas mobilis subsp.
            mobilis NCIMB 11163]
 gi|258552145|gb|ACV75091.1| DNA-directed RNA polymerase, beta subunit [Zymomonas mobilis subsp.
            mobilis NCIMB 11163]
          Length = 1390

 Score = 1688 bits (4371), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1373 (60%), Positives = 1063/1373 (77%), Gaps = 15/1373 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FG   E++D+P+LIEVQ+ SY++FL     P++    GL+   +SVFPI  F 
Sbjct: 14   KKRIRKMFGNIHEVVDMPNLIEVQRDSYENFLRSR--PEDGYVSGLEKTLRSVFPIRDFG 71

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G A L+FV YE + PKFDVD+C  R +TYA P+++TLRLIVF+VD  T  +S+ DIKEQ 
Sbjct: 72   GVAELDFVQYELEEPKFDVDECRQRGITYAAPMRVTLRLIVFEVDPDTETRSVLDIKEQD 131

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMT++GTF I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G
Sbjct: 132  VYMGDMPLMTRNGTFFINGTERVIVSQMHRSPGVLFDHDKGKTHSSGKFLFAARVIPYRG 191

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+++E+IL  FY  I + +    W  P 
Sbjct: 192  SWLDFEFDAKDIVNVRIDRKRKLPVTTLLYALGLNAEQILHHFYNTITFVRGDGGWKVPY 251

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A     G K    +++ DTGE V  +G+K++          G++ L I ++ + G Y A
Sbjct: 252  VAE-SWRGRKPFFDIINGDTGEVVFPAGQKISPRAANKAGRDGLETLLIPTEEIYGHYAA 310

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             D+++  TG I+IEAGD +  ++LE + ++ +  + +L +D V+   +IRNTL  DK +D
Sbjct: 311  YDVIDESTGRIWIEAGDEVTPENLELLDNAGVATLELLDIDHVSTGPWIRNTLKADKAED 370

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            R  AL +IYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+LD PD V 
Sbjct: 371  RDHALAEIYRVMRPGEPPTKETAEALFYGLFFDPERYDLSAVGRVKLNMRLDLDCPDTVT 430

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +R EDI+A++K LVDL++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++KER
Sbjct: 431  TLRAEDILAVVKTLVDLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVKER 490

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+
Sbjct: 491  MSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPGGL 550

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+R+N YGFIETPYRKV D K
Sbjct: 551  TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRINKYGFIETPYRKVVDHK 610

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            VTN+V+YLSAMEE    +AQAN+ LD +G F EELV  R AGE ++ PRE+I  +D SPK
Sbjct: 611  VTNEVIYLSAMEESRYTVAQANAELDAEGHFVEELVSAREAGEFLMAPREQITLMDVSPK 670

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME  VA+ SGAAI A
Sbjct: 671  QLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEETVARDSGAAISA 730

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            +RAGIV+QVDA RIVIR+  G+++    GVDIYRLMKFQRSNQ+TC+NQRPLV VGD V 
Sbjct: 731  RRAGIVDQVDASRIVIRTT-GEIEAGKPGVDIYRLMKFQRSNQSTCINQRPLVSVGDYVN 789

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              D++ADGPST+LG+LALGRN+LVAFMPW+GYN+EDS+LISER+V +DVFTSIHI+EFEV
Sbjct: 790  AGDVLADGPSTELGELALGRNVLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIDEFEV 849

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            MARDTKLGPE+ITRDIPNV E+ L+N+DE GI+ +GAEV PGDILVGKITPKGESPMTPE
Sbjct: 850  MARDTKLGPEDITRDIPNVGEDALRNLDEAGIVYIGAEVQPGDILVGKITPKGESPMTPE 909

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++ERE+IE L +
Sbjct: 910  EKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERAMAIEREEIERLTK 969

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGP-KGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            D++DE+ IL+R  Y++L E L GQ   + P K   K   +  + ++     +W++FAV+D
Sbjct: 970  DREDERAILNRATYAQLQEKLLGQTVAAAPYKHIVKGARIDIETLASVEPHKWFKFAVED 1029

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            +  Q  +E++K QY+++   +  RF++++EK Q GD++PPGVL++VKVFVA+KR +Q GD
Sbjct: 1030 DARQAELEAIKNQYDSADEAIRKRFEDRVEKAQRGDELPPGVLKMVKVFVAVKRKLQPGD 1089

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++SRILP EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFETHLGWA  GL
Sbjct: 1090 KMAGRHGNKGVISRILPAEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFETHLGWAARGL 1149

Query: 1149 GKKIKSLINDYKANG---------DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            G K+++ + +++                +R  + +V G   + E I   +D  ++ +A  
Sbjct: 1150 GAKVRTALEEWREANADRYEWDFSPPEVVRERMIEVYGEK-YAEDIKSREDREIVEMAGL 1208

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             ++GVP++TPVFDGA  E I+ ML +A LD+SGQ  LYDG TGE FDR VTVGYIYMLKL
Sbjct: 1209 LRNGVPMATPVFDGAKPEDISEMLNLAGLDDSGQVELYDGRTGEQFDRKVTVGYIYMLKL 1268

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1269 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1328

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM +LGL+++L+ S+ K+  
Sbjct: 1329 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMHSLGLNVELKTSKAKDED 1381


>gi|330976633|gb|EGH76677.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            aptata str. DSM 50252]
          Length = 1357

 Score = 1688 bits (4371), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMNQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR+N YGF+++PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARINQYGFLKSPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|114799111|ref|YP_761536.1| DNA-directed RNA polymerase subunit beta [Hyphomonas neptunium ATCC
            15444]
 gi|122942154|sp|Q0BYA7|RPOB_HYPNA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114739285|gb|ABI77410.1| DNA-directed RNA polymerase, beta subunit [Hyphomonas neptunium ATCC
            15444]
          Length = 1378

 Score = 1687 bits (4370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 840/1372 (61%), Positives = 1061/1372 (77%), Gaps = 13/1372 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    R+RK FG+ PE I++P+LIEVQ+ SY+ FL MN   ++R ++GL   FKSV
Sbjct: 1    MALSFTEKKRIRKNFGRIPEAIEMPNLIEVQRESYEAFLQMNTPREQRTDDGLGGVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT FS  A LE+VSYEF+ PKFDV++C+ RDLT+  PLK+ L+L+VFDVDE TGA+S+
Sbjct: 61   FPITDFSERATLEYVSYEFEQPKFDVEECVQRDLTFQAPLKVRLQLVVFDVDEDTGARSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ  Y+GD+PLMT  GTFVI G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KEVKEQECYLGDIPLMTDKGTFVINGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++++RIDR+RK+P T+ L ALG D+E+IL  FY + +Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDVLNIRIDRKRKLPATTMLYALGYDTEQILDQFYTRSIYRLDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W     A D   G K    L+D  TG+ V E+GKK+T+   K + E G   + +TS+ 
Sbjct: 241  KGWITSFRA-DAWKGVKPEFELIDAKTGKSVAEAGKKITALKAKRMAEAGTDEILVTSEA 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G ++A D+VN ETGEI+ EAGD ++E  + E+    I  I +L +D+     ++RNTL
Sbjct: 300  LIGKFLARDVVNLETGEIFGEAGDALEEPIIAEMREYGIDSIEVLDIDAGGRGPWLRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-- 420
              DKN+ R +AL DIYRVMRPG+  T   A+++F  LFFD ++YDLS VGRVKMNMRL  
Sbjct: 360  KADKNETRFEALSDIYRVMRPGEPPTQEAADALFGQLFFDPERYDLSAVGRVKMNMRLSV 419

Query: 421  ----NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     D++R +R EDII ++K+++DL++GKG +DDIDNLGNRRVRSVGE+++N YR
Sbjct: 420  AVREYESAADNMRTLRNEDIIGVMKVILDLKDGKGEVDDIDNLGNRRVRSVGELMENNYR 479

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GL+RMER+IKER+ +VDID+VMP DLINAKPVV+AV EFF SSQLSQ  +  N LS IT
Sbjct: 480  IGLVRMERAIKERMGAVDIDTVMPHDLINAKPVVAAVREFFGSSQLSQFMDQTNPLSEIT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + ARVN YG
Sbjct: 540  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE+PYR+V D K+T +VVYLSAMEE    IAQAN+++++ G    E V  R AGE  ++
Sbjct: 600  FIESPYRRVKDAKLTEEVVYLSAMEESIYSIAQANATVNDKGELVNEFVNARVAGEATMI 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             +E++ ++D SPKQVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K+EAPFVGTGME
Sbjct: 660  AKEEVQYMDVSPKQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKSEAPFVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            +VVA+ S AAIVA+RAG+VEQVDA+RIV+R+ E  L+ S SGVDIYRL KF+RSNQN+C+
Sbjct: 720  AVVARDSRAAIVARRAGVVEQVDAMRIVVRATED-LEGSKSGVDIYRLAKFRRSNQNSCI 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRP+ KVGD V +NDIIADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+LISER+V +
Sbjct: 779  NQRPIAKVGDVVSKNDIIADGPSTDLGELALGRNVLVAFMPWNGYNFEDSILISERIVRD 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ VGAEV  GDILVG
Sbjct: 839  DVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAVGAEVKAGDILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP G +GTVVDVRIFNRHGIDK++R+
Sbjct: 899  KVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGDAGTVVDVRIFNRHGIDKDQRA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            + +EREQIE L  DK+DEQ IL+RN YSRL +IL G++A +GPKGFK    ++   + E 
Sbjct: 959  LQIEREQIEKLQEDKEDEQSILERNTYSRLRDILIGKDAATGPKGFKAG-KIAEAALEEL 1017

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             + QWW+  ++ EK Q  +++L+ Q++ S   LE RF +K+EK+Q GDD+PPGV++VVKV
Sbjct: 1018 TQRQWWEIELKSEKAQAELQALREQFDASIRELEARFNDKVEKVQRGDDLPPGVMKVVKV 1077

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            F+A+KR +Q GDKMAGRHGNKG++S+I P EDMPFL+DGTPVDIVLNPLGVPSRMNVGQI
Sbjct: 1078 FLAVKRKLQPGDKMAGRHGNKGVISKINPLEDMPFLEDGTPVDIVLNPLGVPSRMNVGQI 1137

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETH GWAC GLG  I   + ++    D++ L++ L    G      +     D  ++ +
Sbjct: 1138 LETHTGWACRGLGNIIDKALEEFHQKHDVAALKASLTHAYGDKQEMPE----TDAEIIEL 1193

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A   + GVP++TPVFDGA EE IN +L  A LD SGQ  L+DG TG  F RPVTVGY Y+
Sbjct: 1194 AGNLRGGVPIATPVFDGAREEDINDLLTRAGLDTSGQVRLFDGRTGVAFTRPVTVGYKYL 1253

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1254 LKLHHLVDEKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1313

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +KSDD  GR +VYESIV G+D+FE G PESFNVL+KEM++LGL+++L   R 
Sbjct: 1314 VKSDDTAGRAKVYESIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELLEDRG 1365


>gi|213969207|ref|ZP_03397345.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas syringae pv.
            tomato T1]
 gi|213925885|gb|EEB59442.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas syringae pv.
            tomato T1]
          Length = 1357

 Score = 1687 bits (4370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLNLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFVGQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVIELRKFLNEIYNEIGGRQEALEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|254449101|ref|ZP_05062553.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            HTCC5015]
 gi|198261293|gb|EDY85586.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            HTCC5015]
          Length = 1355

 Score = 1687 bits (4370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 726/1364 (53%), Positives = 980/1364 (71%), Gaps = 9/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    RVRK FGK P I+++P L+  Q  SY  FL ++ A D+R   GL AAF SV
Sbjct: 1    MAYSFTDKKRVRKDFGKRPTILEVPFLLATQIESYREFLQLDKASDKRDPMGLHAAFSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG   LE+VSY    P+FDV +C  R  TYA PL++ +RL++ D D     + I
Sbjct: 61   FPIVSYSGHVSLEYVSYRLGEPEFDVRECKVRGSTYASPLRVNVRLVIRDKD---NQEKI 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FDHDKG++  SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEMPLMTDTGTFVINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L +LG D+ +IL  F+ K       
Sbjct: 178  RVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATILLRSLGYDNVQILDMFFEKNNLHVGK 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +      + V+E+G+++T   ++ L++ GV  L +  + 
Sbjct: 238  ENCELELVPERL-RGEIASFDIKSGK--KVVVETGRRITMRHIRELEKDGVNKLEVPDEW 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+V+  TGE+ I A   + E+ L +I  ++I+D  +LY + +++  YI +TL
Sbjct: 295  LLGKRLAHDVVDSATGELLIPANGELTEERLTQIRDAKIKDFQVLYTNDLDHGPYISHTL 354

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +    +A ++IYR+MRPG+  T   A+++F  LFF  D+YDLS VGR+K N RL  
Sbjct: 355  DIDPSTTELEAQVEIYRMMRPGEPPTKDAAQALFKNLFFSEDRYDLSAVGRMKFNRRLGR 414

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  ED++ ++  ++++RNG G +DDID+LGNRRVR VGEM +N +R+GL+R+
Sbjct: 415  EEVTGAGTLSDEDVLDVMHEIINIRNGNGQVDDIDHLGNRRVRCVGEMAENAFRVGLVRV 474

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S V+ + ++PQD+INAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 475  ERAVKERLSLVESEGLVPQDIINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 534

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 535  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYARTNEYGFIETPY 594

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG  T++V YLSA+EE    IAQAN+ +DE G F  +L+ CR   E  +   +K+ 
Sbjct: 595  RKVVDGVATSEVEYLSAIEENRFVIAQANAPMDEKGRFNNDLISCRHMNEFTMSTPDKVQ 654

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AAS+IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 655  YMDVSPRQIVSVAASIIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERTVAVD 714

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAA+ A+R G V+ VDA R+VIR  + +     +GVDIY L K+ RSNQNTCVNQRPLV
Sbjct: 715  SGAAVKAERGGFVDSVDAARVVIRVNDDETIAGETGVDIYNLTKYTRSNQNTCVNQRPLV 774

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD + R DI+ADGPSTDLG+LALG+NMLVAFMPWHGYNFEDS+L+SER+V ED FT+I
Sbjct: 775  RPGDVIARGDILADGPSTDLGELALGQNMLVAFMPWHGYNFEDSILVSERVVKEDRFTTI 834

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   + RDTKLG EEIT DIPNVSE+ L  +DE GI+ VGAEV P DILVGK+TPKG
Sbjct: 835  HIEELTCVCRDTKLGAEEITADIPNVSEQLLSKLDESGIVYVGAEVKPNDILVGKVTPKG 894

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLR+ SGV GTV+DVR+F R G++K+ER+ S+ER 
Sbjct: 895  ETQLTPEEKLLRAIFGEKASDVKDTSLRIGSGVHGTVIDVRVFTRDGVEKDERAKSIERI 954

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++E + +D +D+  I++ ++++R+  +L GQ    GP+G KK   L+++ +SE    +W+
Sbjct: 955  ELEQVRQDLNDQLRIVEGDMFARVERLLVGQTVDGGPRGIKKGDKLTAEQLSEVEHDKWF 1014

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE+  +++E +K   E  +   + RF++K  K+  GD++ PGV ++VKV+VA+KR
Sbjct: 1015 EIRLRDEEASKSLEGMKATLEGFREETDRRFEHKKSKVTAGDELQPGVQKMVKVYVAVKR 1074

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SR++P EDMP+ +DG PVD+VLNPLGVPSRMN+GQI ETHLG
Sbjct: 1075 RLQPGDKMAGRHGNKGVISRVVPVEDMPYGEDGRPVDVVLNPLGVPSRMNIGQILETHLG 1134

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I+ ++   K   D   LR F +K+         +  ++DD +  +AE  K 
Sbjct: 1135 WAARGLGHRIEEMLEQQKKAKD---LRDFFDKIYNHRDKKLDLKQFNDDEIFALAENLKG 1191

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA+E  +  ML++A L ESGQ+ L DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1192 GVPMATPVFDGAEEPEVRQMLKLAGLPESGQTRLIDGRTGEYFERPVTVGYMYMLKLNHL 1251

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1252 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1311

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GR ++Y++IV G    E G PESFNVL+KE+++LGL+I+LEN 
Sbjct: 1312 NGRNKLYKNIVDGEHRMEPGMPESFNVLLKEIRSLGLNIELEND 1355


>gi|331018153|gb|EGH98209.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            lachrymans str. M302278PT]
          Length = 1357

 Score = 1687 bits (4370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLNLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D SLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDASLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVIELRKFLNEIYNEIGGRQEALEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVGDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|71737237|ref|YP_276713.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            phaseolicola 1448A]
 gi|88909628|sp|Q48D29|RPOB_PSE14 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71557790|gb|AAZ37001.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas syringae pv.
            phaseolicola 1448A]
          Length = 1357

 Score = 1687 bits (4369), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1365 (52%), Positives = 987/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS IT  RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITLKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|330962532|gb|EGH62792.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            maculicola str. ES4326]
          Length = 1357

 Score = 1687 bits (4368), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 988/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILGKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLS++ +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSRIMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    +  LR FL ++    G   E + D  D  +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVVELRKFLNEIYNEIGGRQESLEDLSDKEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|298489103|ref|ZP_07007125.1| DNA-directed RNA polymerase beta subunit [Pseudomonas savastanoi pv.
            savastanoi NCPPB 3335]
 gi|298156415|gb|EFH97513.1| DNA-directed RNA polymerase beta subunit [Pseudomonas savastanoi pv.
            savastanoi NCPPB 3335]
          Length = 1357

 Score = 1687 bits (4368), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1365 (52%), Positives = 987/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG   E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTIEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|160872553|ref|ZP_02062685.1| DNA-directed RNA polymerase, beta subunit [Rickettsiella grylli]
 gi|159121352|gb|EDP46690.1| DNA-directed RNA polymerase, beta subunit [Rickettsiella grylli]
          Length = 1377

 Score = 1686 bits (4367), Expect = 0.0,   Method: Composition-based stats.
 Identities = 728/1365 (53%), Positives = 992/1365 (72%), Gaps = 3/1365 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I++ P L+  Q  SY  FL ++ +PD   ++GL AAFKS+F
Sbjct: 15   SYSFTEKKRIRKNFGKQATIMEAPYLLATQIESYHRFLQLDTSPDALEDKGLNAAFKSIF 74

Query: 64   PITAF-SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+++ SG A LE+++Y    P FDV +C  R LTY  PL++ +RL+++D +   G+  I
Sbjct: 75   PISSYASGEATLEYINYRIGQPSFDVKECQARGLTYGAPLRVKMRLVIYDKEAVPGSTKI 134

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K IKEQ +YMG+LPLMT  G+FVI G  R+VVSQLHRSPG+ F+HDKG+   SGKLLYA 
Sbjct: 135  KYIKEQEVYMGELPLMTDTGSFVINGTDRVVVSQLHRSPGVFFEHDKGKTHSSGKLLYAA 194

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  T  L ALG  SEEIL+ F+   V+  +G
Sbjct: 195  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLAATILLRALGYTSEEILALFFNNNVFYLKG 254

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  + +   G+ ++E G+++    ++ +++  +K L +  D 
Sbjct: 255  ENAVLDLVPERL-RGEIASFDIKNAA-GKVIVEQGRRIAVRQIREIEKAKIKQLELPIDY 312

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ +VN ETGEI ++A   +    ++++  + +  I  LY + +++ AYI  TL
Sbjct: 313  LIGKTLAKPVVNTETGEILVDANAELTADIIKKLIEARVEKIETLYTNDLDSGAYISTTL 372

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + ++++AL++IYR+MRPG+  T   AE++F  LFF SD+YDLS+VGR+K N RL  
Sbjct: 373  RIDPSHNQQEALVEIYRMMRPGEPPTKEAAEALFKNLFFVSDRYDLSSVGRMKFNRRLGR 432

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + K+DI+ +++ L+++RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 433  EEITGSGTLTKDDIVGVLRELIEIRNGKGDVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 492

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++++R+S  + +++MPQDLINAKP+ +A+ EFF SSQLSQ  + VN LS ITH RR+S
Sbjct: 493  ERAVRDRLSVAESENLMPQDLINAKPISAAIKEFFGSSQLSQFMDQVNPLSEITHKRRVS 552

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETPY
Sbjct: 553  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNDYGFLETPY 612

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKVT  + YLSA+EE    IAQAN+ LD  G   ++L+ CR   E +L   +K++
Sbjct: 613  RKVENGKVTQTIQYLSAIEEGKYVIAQANTRLDSHGKLIDDLIPCRHRNESMLTTADKVN 672

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTGME  VA  
Sbjct: 673  YMDISPAQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRTEKPLVGTGMERKVAVD 732

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR GI++ VDA RIV+R  + +    T+GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 733  SGVVMVAKRGGIIDSVDAGRIVVRVDDEEALAGTAGVDIYNLTKYTRSNQNTCINQRPLV 792

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD+++++D++ADGPSTDLG+LALGRN+LVAFMPW+GYNFEDS+LISER+VSED FT+I
Sbjct: 793  KKGDKIKKDDVLADGPSTDLGELALGRNLLVAFMPWNGYNFEDSILISERIVSEDCFTTI 852

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLG EE++ DIPNV E  L  +D+ GI+ +GA V  GDILVGK+TPKG
Sbjct: 853  HIEELTCIARDTKLGSEEVSSDIPNVGESALSKLDKSGIVHLGAWVEAGDILVGKVTPKG 912

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R G++K++R++S+E  
Sbjct: 913  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMRGTVIDVQVFTRDGLEKDKRALSIEEM 972

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             ++ + +D  DE  IL+ + Y RL  +L G  A SGP   K  + ++   +    + QW+
Sbjct: 973  ALDKIKKDLYDEFRILENDCYQRLEVLLVGATASSGPNKLKSGSKITLTYLQSLTKDQWF 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              +++DE V + +E++  Q   ++  L+++F+NK +K+  GDD+ PG+L++VKV++A+KR
Sbjct: 1033 SISLRDETVNQQLEAVAKQLADARLALDEKFENKRKKLTQGDDLAPGILKIVKVYLAIKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+++DGTPVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1093 CIQPGDKMAGRHGNKGVISTIIPVEDMPYMEDGTPVDIVLNPLGVPSRMNVGQVLETHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG KI  +++  K+  +I    S +       +    +    D S+L +AE  + 
Sbjct: 1153 WAAKGLGNKIAKMLDAQKSIKEIKHFLSAIYNDNKETAQKVNLDKLSDASILELAENLRQ 1212

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDG  E  I  MLR+AD  ESGQ++LYDG TGE F+RPVT+GY+YMLKLNH+
Sbjct: 1213 GVPMATPVFDGVTEAEIKRMLRLADFPESGQTVLYDGRTGERFERPVTLGYMYMLKLNHL 1272

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1273 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1332

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV G+   E G PESFNVLVKE+++L ++ +LE   
Sbjct: 1333 SGRTKMYKNIVDGDHQMEAGMPESFNVLVKEIRSLAINAELETKD 1377


>gi|320331987|gb|EFW87923.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            glycinea str. race 4]
          Length = 1357

 Score = 1686 bits (4367), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++G+FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGSFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS I H RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMGQNNPLSEIIHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALLGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|241761250|ref|ZP_04759338.1| DNA-directed RNA polymerase, beta subunit [Zymomonas mobilis subsp.
            mobilis ATCC 10988]
 gi|241374157|gb|EER63654.1| DNA-directed RNA polymerase, beta subunit [Zymomonas mobilis subsp.
            mobilis ATCC 10988]
          Length = 1401

 Score = 1686 bits (4365), Expect = 0.0,   Method: Composition-based stats.
 Identities = 825/1373 (60%), Positives = 1063/1373 (77%), Gaps = 15/1373 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FG   E++D+P+LIEVQ+ SY++FL     P++    GL+   +SVFPI  F 
Sbjct: 25   KKRIRKMFGNIHEVVDMPNLIEVQRDSYENFLRSR--PEDGYVSGLEKTLRSVFPIRDFG 82

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G A L+FV YE + PKFDVD+C  R +TYA P+++TLRLIVF+VD  T  +S+ DIKEQ 
Sbjct: 83   GVAELDFVQYELEEPKFDVDECRQRGITYAAPMRVTLRLIVFEVDPDTETRSVLDIKEQD 142

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMT++GTF I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G
Sbjct: 143  VYMGDMPLMTRNGTFFINGTERVIVSQMHRSPGVLFDHDKGKTHSSGKFLFAARVIPYRG 202

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+++E+IL  FY  I + +    W  P 
Sbjct: 203  SWLDFEFDAKDIVNVRIDRKRKLPVTTLLYALGLNAEQILHHFYNTITFVRGDGGWKVPY 262

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A     G K    +++ DTGE V  +G+K++          G++ L I ++ + G Y A
Sbjct: 263  VAE-SWRGRKPFFDIINGDTGEVVFPAGQKISPRAANKAGRDGLETLLIPTEEIYGHYAA 321

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             D+++  TG I+IEAGD +  ++LE + ++ +  + +L +D V+   +IRNTL  DK +D
Sbjct: 322  YDVIDESTGRIWIEAGDEVTPENLELLDNAGVATLELLDIDHVSTGPWIRNTLKADKAED 381

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            R  AL +IYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+LD PD V 
Sbjct: 382  RDHALAEIYRVMRPGEPPTKETAEALFYGLFFDPERYDLSAVGRVKLNMRLDLDCPDTVT 441

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +R EDI+A++K LVDL++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++KER
Sbjct: 442  TLRAEDILAVVKTLVDLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVKER 501

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+
Sbjct: 502  MSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPGGL 561

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+R+N YGFIETPYRKV D K
Sbjct: 562  TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRINKYGFIETPYRKVVDHK 621

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            VTN+V+YLSAMEE    +AQAN+ LD +G F EELV  R AGE ++ PRE+I  +D SPK
Sbjct: 622  VTNEVIYLSAMEESRYTVAQANAELDAEGHFVEELVSAREAGEFLMAPREQITLMDVSPK 681

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME  VA+ SGAAI A
Sbjct: 682  QLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEETVARDSGAAISA 741

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            +RAGIV+QVDA RIVIR+  G+++    GVDIYRLMKFQRSNQ+TC+NQRPLV VGD V 
Sbjct: 742  RRAGIVDQVDASRIVIRTT-GEIEAGKPGVDIYRLMKFQRSNQSTCINQRPLVSVGDYVN 800

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              D++ADGPST+LG+LALGRN+LVAFMPW+GYN+EDS+LISER+V +DVFTSIHI+EFEV
Sbjct: 801  AGDVLADGPSTELGELALGRNVLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIDEFEV 860

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            MARDTKLGPE+ITRDIPNV E+ L+N+DE GI+ +GAEV PGDILVGKITPKGESPMTPE
Sbjct: 861  MARDTKLGPEDITRDIPNVGEDALRNLDEAGIVYIGAEVQPGDILVGKITPKGESPMTPE 920

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++ERE+IE L +
Sbjct: 921  EKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERAMAIEREEIERLTK 980

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGP-KGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            D++DE+ IL+R  Y++L E L GQ   + P K   K   +  + ++     +W++FAV+D
Sbjct: 981  DREDERAILNRATYAQLQEKLLGQTVAAAPYKHIVKGARIDIETLASVEPHKWFKFAVED 1040

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            +  Q  +E++K QY+++   +  RF++++EK Q GD++PPGVL++VKVFVA+KR +Q GD
Sbjct: 1041 DARQAELEAIKNQYDSADEAIRKRFEDRVEKAQRGDELPPGVLKMVKVFVAVKRKLQPGD 1100

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++SRILP EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFETHLGWA  GL
Sbjct: 1101 KMAGRHGNKGVISRILPAEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFETHLGWAARGL 1160

Query: 1149 GKKIKSLINDYKANG---------DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            G K+++ + +++                +R  + +V G   + E I   +D  ++ +A  
Sbjct: 1161 GAKVRTALEEWREANVDRYEWDFSPPEVVRERMIEVYGEK-YAEDIKSREDREIVEMAGL 1219

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             ++GVP++TPVFDGA  E I+ ML +A LD+SGQ  LYDG TGE FDR VTVGYIYMLKL
Sbjct: 1220 LRNGVPMATPVFDGAKPEDISEMLNLAGLDDSGQVELYDGRTGEQFDRKVTVGYIYMLKL 1279

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1280 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1339

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM +LGL+++L+ S+ K+  
Sbjct: 1340 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMHSLGLNVELKTSKAKDED 1392


>gi|77165794|ref|YP_344319.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus oceani ATCC
            19707]
 gi|254433213|ref|ZP_05046721.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus oceani
            AFC27]
 gi|88909147|sp|Q3J8Q7|RPOB_NITOC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|76884108|gb|ABA58789.1| DNA-directed RNA polymerase subunit beta [Nitrosococcus oceani ATCC
            19707]
 gi|207089546|gb|EDZ66817.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus oceani
            AFC27]
          Length = 1359

 Score = 1685 bits (4364), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1364 (52%), Positives = 986/1364 (72%), Gaps = 5/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK F K   I+  P L+ +Q  S+  FL M++ P +R ++GL AAFKSV
Sbjct: 1    MPYSLTEKKRIRKDFSKLHSILKTPFLLTIQIGSFLDFLQMDVPPGKRKDKGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++  A L++ SY    P F+V +C  R LTYA PL++ LRL+++D +     + +
Sbjct: 61   FPIKSYTEYAELQYSSYHLGVPSFEVKECQVRGLTYAAPLRVKLRLVIYDKESPASEQVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG++PLMT  G FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 121  KDVKEQEVYMGEIPLMTPKGNFVINGTERVIVSQLHRSPGVIFEHDKGKTHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+  T  L ALG  +EEIL  F+  I   ++G
Sbjct: 181  RIIPYRGSWLDFEFDPKDCVYARIDRRRKLLATILLRALGYSTEEILIMFFETISVKRQG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G  +   +   D GE ++E+G+++T+  +K +++ G+K L    + 
Sbjct: 241  SSYLLDLVPQRL-RGESLPFDIASPD-GEVIVEAGRRVTARHIKQMEKAGMKTLPAPKEF 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++  TGE+  +A D I  + +  +  + I+   ++Y + ++  ++I ++L
Sbjct: 299  LIGKTLARDLIDAGTGEVLAKANDEITAELMTALEDANIQAFDLIYTNDLDRGSFISDSL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D      +A ++IYRVMRPG+  T   A+++F  LFF+ ++YDLS VGR+K N RL  
Sbjct: 359  RLDPTTTPLEAQMEIYRVMRPGEPPTKEAAQNLFQNLFFNPERYDLSPVGRMKFNRRLGK 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ +IK LVD+RNG G++DD+D+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 419  EDITGPSILSKEDIVDVIKTLVDIRNGYGSVDDVDHLGNRRVRSVGEMAENQFRVGLVRV 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQ+LINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 479  ERAVRERLSLAESEGLMPQELINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGFIETPY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARINQYGFIETPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKV  +V YLSA+EE    IAQAN++ DE+G   + LV CR   E  L+P EK+ 
Sbjct: 599  RKVVDGKVAGEVDYLSAIEEGQYVIAQANAAADEEGRLIDMLVSCRHKNEFTLLPPEKVQ 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +ID SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME VVA+ 
Sbjct: 659  YIDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAETPLVGTGMEQVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R GIV+ VDA R+V+R  + +      GVDIY L+K+ RSNQNTC+NQ PLV
Sbjct: 719  SGVMVVARRGGIVDSVDAARVVVRVNDEETASDEPGVDIYNLIKYARSNQNTCINQSPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V   D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED FTSI
Sbjct: 779  KPGDTVAIGDVLADGPSTDMGELALGQNLLVAFMPWNGYNFEDSILISERVVEEDRFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE    ARDTKLGPEEI+ DIPNVSE  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 839  HIEELTCFARDTKLGPEEISSDIPNVSEAALSKLDEAGIVYIGAEVKPGDILVGKVTPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV SG+ GTV+DV++F R G++K+ R++ +E  
Sbjct: 899  ETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGMQGTVIDVQVFTRDGVEKDTRALEIEEM 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++  + +D  DE  I++ +IY RL ++L G+    GP   K  T ++ + +++ PR +W+
Sbjct: 959  ELAKIKKDLRDEFRIVETDIYQRLEKVLVGKTVEGGPAELKAGTQITQNYLADLPRERWF 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ E+  R +ES+  Q +  +  ++++F+ +  K+  G D+PPGV ++VKV++A+KR
Sbjct: 1019 EIRLRSEEAGRQLESVAGQLKEQRVAMDEKFQQQRAKLTSGHDLPPGVQKMVKVYLAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMP+++DGTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1079 RVQPGDKMAGRHGNKGVISTIVPIEDMPYMEDGTPVDIVLNPLGVPSRMNIGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI +L+   ++    S LR FL+++       E ++   D+ VL +A   K 
Sbjct: 1139 WAAKGLGRKIGALL---ESGEQASELRVFLDRIYNASGKKEDLNSLSDEEVLELANNLKD 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I +ML +ADL  +GQ+ LYDG +GE F RPVTVGY++MLKLNH+
Sbjct: 1196 GVPMATPVFDGASEQEIKTMLELADLPTNGQTNLYDGRSGEAFARPVTVGYMHMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +++YGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALESYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL KE++ALG+ I+LE  
Sbjct: 1316 NGRTKMYKNIVDGDYRMEAGMPESFNVLTKEIRALGIDIELEQD 1359


>gi|56551627|ref|YP_162466.1| DNA-directed RNA polymerase subunit beta [Zymomonas mobilis subsp.
            mobilis ZM4]
 gi|81355250|sp|Q5NPK5|RPOB_ZYMMO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56543201|gb|AAV89355.1| DNA-directed RNA polymerase, beta subunit [Zymomonas mobilis subsp.
            mobilis ZM4]
          Length = 1401

 Score = 1685 bits (4364), Expect = 0.0,   Method: Composition-based stats.
 Identities = 824/1373 (60%), Positives = 1062/1373 (77%), Gaps = 15/1373 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FG   E++D+P+LIEVQ+ SY++FL     P++    GL+   +SVFPI  F 
Sbjct: 25   KKRIRKMFGNIHEVVDMPNLIEVQRDSYENFLRSR--PEDGYVSGLEKTLRSVFPIRDFG 82

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G A L+FV YE + PKFDVD+C  R +TYA P+++TLRLIVF+VD  T  +S+ DIKEQ 
Sbjct: 83   GVAELDFVQYELEEPKFDVDECRQRGITYAAPMRVTLRLIVFEVDPDTETRSVLDIKEQD 142

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMT++GTF I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G
Sbjct: 143  VYMGDMPLMTRNGTFFINGTERVIVSQMHRSPGVLFDHDKGKTHSSGKFLFAARVIPYRG 202

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+++E+IL  FY  I + +    W  P 
Sbjct: 203  SWLDFEFDAKDIVNVRIDRKRKLPVTTLLYALGLNAEQILHHFYNTITFVRGDGGWKVPY 262

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A     G K    +++ DTGE V  +G+K++          G++ L I ++ + G Y A
Sbjct: 263  VAE-SWRGRKPFFDIINGDTGEVVFPAGQKISPRAANKAGRDGLETLLIPTEEIYGHYAA 321

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             D+++  TG I+IEAGD +  ++LE + ++ +  + +L +D V+   +IRNTL  DK +D
Sbjct: 322  YDVIDESTGRIWIEAGDEVTPENLELLDNAGVATLELLDIDHVSTGPWIRNTLKADKAED 381

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            R  AL +IYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+LD PD V 
Sbjct: 382  RDHALAEIYRVMRPGEPPTKETAEALFYGLFFDPERYDLSAVGRVKLNMRLDLDCPDTVT 441

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +R EDI+A++K LVDL++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++KER
Sbjct: 442  TLRAEDILAVVKTLVDLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVKER 501

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+
Sbjct: 502  MSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPGGL 561

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+R+N YGFIETPYRKV D K
Sbjct: 562  TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRINKYGFIETPYRKVVDHK 621

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            VTN+V+YLSAMEE    +AQAN+ LD +G F EELV  R AGE ++ PRE+I  +D SPK
Sbjct: 622  VTNEVIYLSAMEESRYTVAQANAELDAEGHFVEELVSAREAGEFLMAPREQITLMDVSPK 681

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q+VS+AASLIPFLENDD+NR LMG NMQRQAV L++AEAPFVGTGME  VA+ SGAAI A
Sbjct: 682  QLVSVAASLIPFLENDDANRALMGSNMQRQAVSLVRAEAPFVGTGMEETVARDSGAAISA 741

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            +RAGIV+QVDA RIVIR+  G+++    GVDIYRLMKFQRSNQ+TC+NQRPLV VGD V 
Sbjct: 742  RRAGIVDQVDASRIVIRTT-GEIEAGKPGVDIYRLMKFQRSNQSTCINQRPLVSVGDYVN 800

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              D++ADGPST+LG+LALGRN+LVAFMPW+GYN+EDS+LISER+V +DVFTSIHI+EFEV
Sbjct: 801  AGDVLADGPSTELGELALGRNVLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIDEFEV 860

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            MARDTKLGPE+ITRDIPNV E+ L+N+DE GI+ +GAEV PGDILVGKITPKGESPMTPE
Sbjct: 861  MARDTKLGPEDITRDIPNVGEDALRNLDEAGIVYIGAEVQPGDILVGKITPKGESPMTPE 920

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHG+DK+ER++++ERE+IE L +
Sbjct: 921  EKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERAMAIEREEIERLTK 980

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGP-KGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            D++DE+ IL+R  Y++L E L GQ   + P K   K   +  + ++     +W++FAV+D
Sbjct: 981  DREDERAILNRATYAQLQEKLLGQTVAAAPYKHIVKGARIDIETLASVEPHKWFKFAVED 1040

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            +  Q  +E++K QY+++   +  RF++++EK Q GD++PPGVL++VKVFVA+KR +Q GD
Sbjct: 1041 DARQAELEAIKNQYDSADEAIRKRFEDRVEKAQRGDELPPGVLKMVKVFVAVKRKLQPGD 1100

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++SRILP EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFETHLGWA  GL
Sbjct: 1101 KMAGRHGNKGVISRILPAEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFETHLGWAARGL 1160

Query: 1149 GKKIKSLINDYKANG---------DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            G K+++ + +++                +R  + +V G   + E I   +D  ++ +A  
Sbjct: 1161 GAKVRTALEEWREANADRYEWDFSPPEVVRERMIEVYGEK-YAEDIKSREDREIVEMAGL 1219

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             ++GVP++TPVFDGA  E I+ ML +A LD+SGQ  LYDG TGE FDR VTVGYIYMLKL
Sbjct: 1220 LRNGVPMATPVFDGAKPEDISEMLNLAGLDDSGQVELYDGRTGEQFDRKVTVGYIYMLKL 1279

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1280 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1339

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM +LGL+++L+ S+ K+  
Sbjct: 1340 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMHSLGLNVELKTSKAKDED 1392


>gi|74316416|ref|YP_314156.1| DNA-directed RNA polymerase subunit beta [Thiobacillus denitrificans
            ATCC 25259]
 gi|88909645|sp|Q3SLQ6|RPOB_THIDA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|74055911|gb|AAZ96351.1| DNA-directed RNA polymerase, beta subunit [Thiobacillus denitrificans
            ATCC 25259]
          Length = 1359

 Score = 1685 bits (4363), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1363 (52%), Positives = 953/1363 (69%), Gaps = 5/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F      + +P L+  Q  SY  FL    + DER NEGLQAAF S+
Sbjct: 1    MAYTFTEKKRLRKSFASRTNTLPVPFLLATQLESYRAFLQEGRSRDERLNEGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + S  A LE+VSY+   P FD+ +C  R LTY  PL+  +RL++ D        +I
Sbjct: 61   FPIESHSKNARLEYVSYQLGEPVFDIKECQQRGLTYCAPLRAKVRLVIMDK--EASKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI+  R+DRRRK+PVT  L ALG   E IL  F+ K  +    
Sbjct: 179  RVIPYRGSWLDFEFDAKDILFFRVDRRRKMPVTILLKALGYTPESILDAFFNKDTFYINT 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L    L  G      +   D  + ++   K++T+  ++ L   GVK   +  + 
Sbjct: 239  LGIQFELVPERL-RGEIARFDICGKDD-KVIVAKDKRITAKHIRELDAAGVKKWAVPGEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A D+V+ +TGE+   A D I E+ L+++  + I     LY + +++ A+I  TL
Sbjct: 297  VVGRVLAHDVVDKDTGELVARANDEITEELLKKLAAAGIDKFQTLYTNDLDHGAFISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D   A + IYR+MRPG+  T     ++F  LFF  ++YDLS VGR+K N R+  
Sbjct: 357  RTDDTTDEYAAKVAIYRMMRPGEPPTEDAVNALFVNLFFSDERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  EDI+A+IKILV+LRNG+G IDDID+LGNRRVRSVGE+ +NQ+R GL+R+
Sbjct: 417  DELTGTGTLSTEDIVAVIKILVELRNGRGEIDDIDHLGNRRVRSVGELAENQFRAGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + D++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVRERLSQAESDNLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARTNWYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+++ YLSA+EE    IAQAN+ LD  G F ++LV CR   E  L   ++I+
Sbjct: 597  RKVVDNKVTDEIEYLSAIEESKYVIAQANAELDAKGKFKDDLVSCRFKNEFTLSAPDRIE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E PFVGTG+E   A  
Sbjct: 657  YMDVAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPFVGTGIERTAAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++A R G V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRPLV
Sbjct: 717  SGTVVIAHRGGRVDYVDAGRIVIRVHDEEARAGEVGVDIYSLIKYTRSNQNTNINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LI+E++V+ED +TSI
Sbjct: 777  KVGDVIARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILINEKVVAEDRYTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GII +GAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELSVVARDTKLGPEEITRDISNLAERQLARLDESGIIAIGAEVEAGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSL+VPSG+SG V+DV++F R GI++++R+ S+   
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLKVPSGMSGVVIDVQVFTREGIERDKRAQSIIDT 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  D   I++ + ++RL ++L  +    GPK   K + +S + +    R  W+
Sbjct: 957  QLAEYKKDLTDRMRIVEDDTFARLEKLLHLKVVNGGPKKLAKGSKISKEYLDSLNRHDWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++  R VESLK      +   +  F+ K +K+  GD++PPGV ++VKV++A+KR
Sbjct: 1017 DIRLADDEASRQVESLKDSLTQKRVEFDAMFEEKKQKLTAGDELPPGVQKMVKVYLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMPF+ DG PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSKIVPVEDMPFMADGRPVDIVLNPLGVPSRMNIGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI  ++   +    +  LR F ++V       E I ++ DD +L + +  + 
Sbjct: 1137 WASKGLGEKIGQMM-AAQTKSVVKELRHFFKEVYNQSGKAEDIDNFTDDEILELGQNLQK 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP ++PVFDGA EE I  ML +A L E GQ  LYDG TGE FDR VTVGY ++LKL+H+
Sbjct: 1196 GVPFASPVFDGATEEEIRRMLALAGLPEGGQVTLYDGRTGEAFDRQVTVGYKHVLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYE+IV G+   E G PESFNVLVKE+++LG+ IDLE 
Sbjct: 1316 NGRTKVYENIVKGDHKIEAGMPESFNVLVKEIRSLGIDIDLER 1358


>gi|119478600|ref|ZP_01618522.1| DNA-directed RNA polymerase, beta subunit [marine gamma
            proteobacterium HTCC2143]
 gi|119448435|gb|EAW29685.1| DNA-directed RNA polymerase, beta subunit [marine gamma
            proteobacterium HTCC2143]
          Length = 1358

 Score = 1684 bits (4362), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1365 (52%), Positives = 987/1365 (72%), Gaps = 8/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK   ++D+P L+ +Q  SY  F   + A   R + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKMSSVMDVPYLLAIQLDSYKKFTQDDTAVGNRADIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G+A LE+V Y    P FDV +C  R +TYAVPL++ +RLI++D    + AK+I
Sbjct: 61   FPIVSYAGSAALEYVDYVLGAPAFDVTECQSRGVTYAVPLRVKVRLIIYDK--ESAAKTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L +LG  SEEIL  FY    ++   
Sbjct: 179  RVIPYRGSWLDFEFDPKDMVYVRIDRRRKLPATILLRSLGYSSEEILGMFYESDNFAVNK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G   +  +V    G  ++ESG+++T+  ++ ++++ +K L +  + 
Sbjct: 239  DGSFNLELIPERLRGEVATFDIVS-KGGTVIVESGRRITARNIRQIEKEKLKTLAVPEEY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A DIV+ +TGEI  E    + E+ L ++  + ++ I  LY + ++   +I +TL
Sbjct: 298  ILGRALANDIVDEKTGEILAECNTELTEELLVQLSEAGVKSIATLYTNELDCGPFISDTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D ++++ +AL++IYR+MRPG+  T   AE++F  LFF S++YDLSTVGR+K N RL  
Sbjct: 358  RIDPSRNQLEALVEIYRMMRPGEPPTKESAENLFQNLFFSSERYDLSTVGRMKFNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI+ ++K LV +RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 418  EEVLGDGVLSNDDIVDVLKTLVGIRNGKGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQD+INAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLSMAESEGLMPQDMINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV  G  T D+ YLSA+ E    +AQA+++LD+ G   +ELV  R   E  +   E ++
Sbjct: 598  RKVVKGVATEDIEYLSAINEAEYVVAQASATLDKKGKLIDELVAVRHQNEFTVKAPEDVE 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP LKAE P VGTG+E  VA  
Sbjct: 658  YMDVSPKQVVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLKAEKPLVGTGIERFVASD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G+++ VD+ RIV+R  + +++   S VDIY L K+ RSNQNTC+NQRP+V
Sbjct: 718  SGVCEVARRGGVIDSVDSARIVVRVTDTEVEVGQSPVDIYNLTKYTRSNQNTCINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD +RR DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 778  KEGDAIRRGDILADGPSIDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG E++T DIPNV E  L  +D+ GI+ +GAEV  GDILVGK+TPKG
Sbjct: 838  HIQELTCIARDTKLGSEDVTSDIPNVGEGALGKLDDSGIVYIGAEVAAGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS V GTV+DV++F R G++K++R++ +E+ 
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSVKGTVIDVQVFTRDGLEKDQRALEIEKS 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D ++E  I++   ++ L   L GQ  VSG  G KK T++ ++++    + QW+
Sbjct: 958  QLDEYRKDLNEEFRIVEGATFALLSGSLDGQKVVSG-AGVKKGTIVDNEMLEALEKDQWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D+ +   +E+ + Q    ++ +E RF++K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1017 KLRFSDDAINSQLETAETQLTDHRTAIEARFEDKKRKLQSGDDLAPGVLKIVKVYLAIKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ + G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1077 RIQPGDKMAGRHGNKGVISVIMPVEDMPYNEQGEPVDIVLNPLGVPSRMNVGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI +++ + +    I+ LR FLE +    G   E +  + D  ++ +A   +
Sbjct: 1137 LAAKGLGEKIDTMLQEQR---KIAELRKFLESIYNGDGGRKEDLKSFTDQEIIEMAGNLR 1193

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++T VFDGA E  + ++L +ADL +SGQ  LYDG +GE FDR  TVGY+YMLKLNH
Sbjct: 1194 GGVPMATQVFDGASEAEVKNLLTLADLPDSGQMQLYDGRSGEAFDRETTVGYMYMLKLNH 1253

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1254 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1313

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG++++L+  
Sbjct: 1314 VAGRTKMYKNIVDGDQRMEPGMPESFNVLLKEIRSLGINMELDTE 1358


>gi|307823434|ref|ZP_07653663.1| DNA-directed RNA polymerase, beta subunit [Methylobacter
            tundripaludum SV96]
 gi|307735419|gb|EFO06267.1| DNA-directed RNA polymerase, beta subunit [Methylobacter
            tundripaludum SV96]
          Length = 1364

 Score = 1684 bits (4361), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1366 (52%), Positives = 972/1366 (71%), Gaps = 4/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+R  FGK  E++D+P L+  Q  SY  FL   +  ++R + GL AAF SV
Sbjct: 1    MSYSFTEKKRIRNNFGKGTEVLDVPYLLATQINSYAGFLQSGVTAEKREDSGLHAAFSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A+LE+V Y    P FDV +C  R  TYA PL++ +RL+++D +    AK +
Sbjct: 61   FPIESHSGYAVLEYVKYRLGEPVFDVRECQQRGATYAAPLRVLVRLVIYDKEASANAKVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG+LPLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLL+  
Sbjct: 121  KDIREQEVYMGELPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L  LG D+EE+L  F+    ++   
Sbjct: 181  RVIPYRGSWLDFEFDHKDCVFVRIDRRRKIPATILLRGLGYDNEEMLKIFFEMNKFTVDA 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F +     M G   +  +     GE ++E G+++T+  ++ + + G+  + +  D 
Sbjct: 241  QKCIFHIVPE-RMRGEIAAFDI-KSKKGEVLVEEGRRITAKHIREMIKSGLTEVEVPKDY 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +  ++++  TGE+     D +    ++    S I D+  L+V+ ++   Y+ N +
Sbjct: 299  LVGKILGHNLIDRSTGELVANVNDELTVAIIDRCIESGITDLNTLFVNDLDKGPYMSNAM 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +  +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N RL  
Sbjct: 359  RLDTTTNSLEALVEIYRMMRPGEPPTKDSAENLFQNLFFTDERYDLSTVGRMKFNRRLGR 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + K+DII ++K L+D+RNG G +DDID+LGNRRVRSVGEM++NQ+R+GL+R+
Sbjct: 419  QETTGSGTLTKDDIIDVLKELIDIRNGNGNVDDIDHLGNRRVRSVGEMIENQFRVGLVRV 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER++  D + +MPQ++INAKPV +AV EFF SSQLSQ  +  N LS++TH RR+S
Sbjct: 479  ERAVKERLTLADSEGLMPQEIINAKPVSAAVKEFFGSSQLSQFMDQNNPLSQVTHKRRVS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+AR RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 539  ALGPGGLARERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNNYGFLETPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ V YLSA+EE    IAQA+ ++D  G   E LV CR   E  L   + + 
Sbjct: 599  RKVIDGKVTDHVDYLSAIEEGEFVIAQASVAVDASGKLVEGLVSCRHKDEFTLAMSDTVQ 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S KQ+VS+AAS+IPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VAK 
Sbjct: 659  YMDVSSKQIVSVAASIIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERTVAKD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA R G +E VDA RIV+R  + + +  T GVDIY L+K+ RSNQNTC+NQ+PLV
Sbjct: 719  SGVTVVAARGGKIEAVDAARIVVRVNDTETETGTPGVDIYNLIKYTRSNQNTCINQKPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V   DI+ADGPSTD+G+LALG+NMLVAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 779  KPGDIVNAGDIMADGPSTDIGELALGQNMLVAFMPWNGYNFEDSILVSERVVKEDRFTTI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTK  PEEIT DIPNVSEE L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 839  HIEEKTCVARDTKHSPEEITADIPNVSEEALSKLDESGIVYVGAEVKGGDILVGKVTPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP  + GTV+DV++F R G+ K++R++ +E+E
Sbjct: 899  ETQLTPEEKLLRAIFGEKAADVKDTSLRVPGSIEGTVIDVQVFTRDGVKKDKRALDIEQE 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+   +D DD+  IL+ +I++R+  +L G+ A SGP   K  T ++   ++    S+W 
Sbjct: 959  EIKRYRKDLDDQLKILEEDIFARVARLLVGKVAQSGPGQLKAGTEITQAYLNGLKHSEWL 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE +   +E++  Q E  +   +++F+ K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1019 KIRMKDEDINLQLETVVTQVEQQRKDFDEKFEVKRKKITMGDDLAPGVLKMVKVYLAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+  DG PVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1079 RIQPGDKMAGRHGNKGVISMIRPIEDMPYTADGNPVDIVLNPLGVPSRMNVGQVLETHLG 1138

Query: 1143 WACVGLGKKIKSLINDY--KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            WA  GLG KI  ++          ++ +R +L+K+  +  H E +  + D  +L +AE  
Sbjct: 1139 WAAKGLGIKIGKMLEAKYDAEKAKVTAIREYLDKIYNSSGHKEDLDSFTDQEILEMAENL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA EE I +ML++ADL E GQ  LYDGLTGEPF+R VTVGY+YMLKLN
Sbjct: 1199 VGGVPMATPVFDGASEEEIRTMLKLADLPEHGQVTLYDGLTGEPFEREVTVGYMYMLKLN 1258

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1259 HLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1318

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRTR+Y++IV G+   E G PESFNVL+KE+++L ++I+L+  
Sbjct: 1319 DVTGRTRMYKNIVDGDHKMEAGMPESFNVLIKEIRSLAVNIELQRD 1364


>gi|121997656|ref|YP_001002443.1| DNA-directed RNA polymerase subunit beta [Halorhodospira halophila
            SL1]
 gi|158514012|sp|A1WVC9|RPOB_HALHL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|121589061|gb|ABM61641.1| DNA-directed RNA polymerase subunit beta [Halorhodospira halophila
            SL1]
          Length = 1381

 Score = 1684 bits (4361), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1390 (51%), Positives = 977/1390 (70%), Gaps = 34/1390 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-GLQAAFKS 61
                F    R+RK FGK P I+D+P L+  Q  SY  FL   ++ D R  E GL+ AF+S
Sbjct: 1    MAYSFTEKKRIRKDFGKLPNILDVPYLLATQVDSYRQFLQDEVSEDARDTEVGLEGAFRS 60

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI + SG A L++VSY    P F+V +C  R LTYA PL++ +RL ++D +       
Sbjct: 61   VFPIQSHSGNAELQYVSYRIGDPPFEVKECQSRGLTYAAPLRMLVRLALYDKEGG----G 116

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMG++PLMT  GTFV+ G +R++V+QLHRSPG+ FDHDKG++  SGKLL++
Sbjct: 117  VKDIKEQEVYMGEMPLMTSTGTFVVNGTERVIVNQLHRSPGVFFDHDKGKSHSSGKLLFS 176

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+D EFD KD I+VRIDRRRK+P T  L ALG   EEIL  F+    +   
Sbjct: 177  ARVIPYRGSWLDFEFDPKDTIYVRIDRRRKLPATILLRALGYTPEEILYAFFDTDRFHLG 236

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                       + + G   S  +V    GE ++E+G+++T+  +K L++ GV+ L +  D
Sbjct: 237  SGNKVVLDLVPERLRGETASFDIV--AGGETIVEAGRRVTARHVKQLQKSGVEQLEVPED 294

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A D+++  TGEI  EA   +  +  + +F + IR+I  L+V+ ++   Y+  T
Sbjct: 295  YLTGKIIAHDVIDPATGEILAEANTTLTPEITQSLFDAGIREIETLFVNDLDRGPYMSTT 354

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D  + + +AL++IYR+MRPG+  T   AE++F+ LFF SD+YDLS VGR+K N+R+ 
Sbjct: 355  LAADATRSQMEALVEIYRMMRPGEPPTKDAAENLFHTLFFTSDRYDLSPVGRMKFNLRVG 414

Query: 422  LDTPDDVRHIRKEDIIA------------------------IIKILVDLRNGKGTIDDID 457
             D       +      A                        +++ L+D+RNG G +DDID
Sbjct: 415  RDEVRGPGILYDGKYFAGLGNADKEADDLIEQYGESSDILDVLRELIDIRNGNGQVDDID 474

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            +LGNRRVRSVGEM +N +R+GL+R+ER++KER+S  + + +MPQ+LINAKPV +A+ EFF
Sbjct: 475  HLGNRRVRSVGEMAENVFRVGLVRVERAVKERLSLAESEGLMPQELINAKPVAAAIKEFF 534

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG
Sbjct: 535  GSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEG 594

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL  +AR N YGF+ET YRKV DG+VT+ V YLSA+EE    IAQAN+ +DE 
Sbjct: 595  PNIGLINSLAVYARANRYGFLETAYRKVVDGQVTDQVEYLSAIEESRYVIAQANARVDES 654

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G   ++L+ CR   E  +   +++ ++D SP+Q+VS+AASL+PFLE+DD+NR LMG NMQ
Sbjct: 655  GYLADDLISCRHQNEFTMATADRVQYMDVSPRQIVSVAASLVPFLEHDDANRALMGANMQ 714

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+A+ P VGTGME  VA+ SG  + A+R G+VEQVD+ RIV+R  + +  P   
Sbjct: 715  RQAVPTLRADKPLVGTGMERTVARDSGVIVTAERGGVVEQVDSGRIVVRVDDEETTPGEP 774

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L K+ RSNQNTC +Q+PLV VGD V R D +ADGPSTD+G+LALG+NMLVAFMP
Sbjct: 775  GVDIYSLTKYTRSNQNTCFSQKPLVHVGDRVARGDALADGPSTDMGELALGQNMLVAFMP 834

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYNFEDS+LISE++V ED +TS+HIEE   +ARDTKLG EEIT DIPNVSE  L  +D
Sbjct: 835  WNGYNFEDSILISEKLVKEDRYTSVHIEELTCVARDTKLGSEEITSDIPNVSESALSRLD 894

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G+ G
Sbjct: 895  ESGIVYIGAEVKAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGMDG 954

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R G++K+ER+ ++ERE+I  + +D DDE  I + + Y+RL ++L G+ A  
Sbjct: 955  TVIDVQVFTRDGVEKDERARAIEREEIARVRKDLDDEARIFEDDAYARLEKLLVGKVAEG 1014

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            GPKG      ++   + + PR +W++  ++DE V + +E+++ Q ET +   E RF+ K 
Sbjct: 1015 GPKGLGSGAEVTEAYLQDLPRERWFEIRMRDEAVNQQLEAVRHQLETQRDRFERRFQEKK 1074

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            EKI  GDD+ PGVL+ VKV +A+KR +Q GDK AGRHGNKG++S I+P EDMP++ DGTP
Sbjct: 1075 EKITAGDDLSPGVLKTVKVHLAVKRRLQPGDKFAGRHGNKGVISMIVPEEDMPYMDDGTP 1134

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            V++VL+PLGVPSRMNVGQ+ ETHLGWA  GLG +I  ++   +   D   LR +L ++  
Sbjct: 1135 VEVVLSPLGVPSRMNVGQVLETHLGWAARGLGHQIGQML---EQQADAEALRGYLSEIYD 1191

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                 E++    ++ +  +    K GVP +TPVFDGA+E  I   L++A L ESGQ+ LY
Sbjct: 1192 ASGRKEELETLSEEELQELCHNLKGGVPAATPVFDGANEGEIKRWLKLAGLPESGQTTLY 1251

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            DG TG+ FDRP+TVGY+YMLKLNH+V DKV+AR+TG YSLVTQQPLGGK+  GGQR GEM
Sbjct: 1252 DGRTGDAFDRPITVGYMYMLKLNHLVDDKVHARATGPYSLVTQQPLGGKAQFGGQRFGEM 1311

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++L
Sbjct: 1312 EVWALEAYGAAYTLQEMLTVKSDDVSGRTKMYKNIVDGDHRMEAGMPESFNVLVKEIRSL 1371

Query: 1358 GLSIDLENSR 1367
            G++I+LE   
Sbjct: 1372 GINIELERDD 1381


>gi|254483549|ref|ZP_05096775.1| DNA-directed RNA polymerase, beta subunit [marine gamma
            proteobacterium HTCC2148]
 gi|214036206|gb|EEB76887.1| DNA-directed RNA polymerase, beta subunit [marine gamma
            proteobacterium HTCC2148]
          Length = 1357

 Score = 1684 bits (4361), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++D+P L+ +Q  SY  F    +A DER   GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGMLPKVMDVPYLLAIQLDSYRKFTQQGVALDERGAYGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV++C  R +TY+  L++ +RLI++D    +  K+I
Sbjct: 61   FPIVSYSGNAALEYVDYALGTPVFDVNECQLRGVTYSCALRVKVRLIIYDK--ESSNKTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L ALG  +EEIL  F+    +   G
Sbjct: 179  RVIPYRGSWLDFEFDPKDMVYVRIDRRRKLPATILLRALGYQAEEILEMFFDVNTFHTAG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +         + + G   +  +      + V+E G+++T+  ++ L++  V  L I +D 
Sbjct: 239  EGNFTMTLIPERLRGDVAAFDIKVGK--KVVVEEGRRITARHIRELEKAKVTELEIPADY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+ +TGE+ +E    + E+ L  +  + ++++  LY + ++   +I +TL
Sbjct: 297  LYGRALAKNLVDEKTGEVLVECNTELSEEVLAVLEEAGVKEVQTLYTNELDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IYR+MRPG+  T   AE++F  LFF +D+YDLS VGR+K N RL  
Sbjct: 357  RQDTTRNELEALVEIYRMMRPGEPPTKESAENLFQNLFFSADRYDLSAVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ ++K L+++RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  EEVTGSGVLDKEDIVEVLKTLINIRNGKGIVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNDYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKVT+D+ +LSA+ E    IAQA+S LD++  FTEEL+  R   E  +   E ++
Sbjct: 597  RKVVNGKVTDDIEFLSAINEAENVIAQASSPLDKNKKFTEELIAVRYLNEFTVKAPEDVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L ++ P VGTGME  VA  
Sbjct: 657  YMDVSPKQVVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLSSDKPLVGTGMERYVASD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA R G+++ VDA RIV+R  + D+    + VDIY L K+ RSNQNTC+NQRP+V
Sbjct: 717  SGVCVVANRPGVIDSVDASRIVVRVNDKDVGVDEAPVDIYNLTKYTRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V R DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  KQGDAVSRGDILADGPSIDMGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEISSDIPNVGESALSKLDESGIVYIGAEVDAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K++R+  +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDQRAQQIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  I +   ++RL  ++  ++ VSG  G  K T L+  ++SE  R  W+
Sbjct: 957  QLDDYRKDLKEEYRIFEEATFARLSNLIKNKSVVSG-AGLTKGTKLTDKVLSELERELWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++++   + S + Q E   ++LE+RF+ K  K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLKLSEKELNEALASAQRQLEEQNTLLEERFEIKKGKLQSGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDENGEPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI  +I + K    ++ +R FLE +   G    E +    D  V+ +AE  +
Sbjct: 1136 MAAKGLGDKINVMIEEQK---KVAEVRKFLEAIYNNGAGRVEDLKSLSDKEVMDLAENLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I  +L +ADL ESGQ  LYDG +GE FDRPVTVGY+YMLKLNH
Sbjct: 1193 GGVPMATPVFDGAAESQIKDLLELADLPESGQFTLYDGRSGESFDRPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1313 VAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESE 1357


>gi|66047782|ref|YP_237623.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            syringae B728a]
 gi|75500409|sp|Q4ZMN7|RPOB_PSEU2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|63258489|gb|AAY39585.1| DNA-directed RNA polymerase, beta subunit [Pseudomonas syringae pv.
            syringae B728a]
          Length = 1357

 Score = 1684 bits (4360), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1365 (52%), Positives = 986/1365 (72%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL      D+  + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D D G+ ++E G+++T+  +  L++ G+K L +  D 
Sbjct: 239  ENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + ++   ++ +TL
Sbjct: 297  VLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N R+  
Sbjct: 357  KIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMGQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 597  RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 957  QLDEIRKDLNEEFRIVEGATFERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 1136 LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 1193 NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AY AAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYCAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1357


>gi|307295393|ref|ZP_07575232.1| DNA-directed RNA polymerase, beta subunit [Sphingobium
            chlorophenolicum L-1]
 gi|306878896|gb|EFN10115.1| DNA-directed RNA polymerase, beta subunit [Sphingobium
            chlorophenolicum L-1]
          Length = 1388

 Score = 1683 bits (4358), Expect = 0.0,   Method: Composition-based stats.
 Identities = 822/1377 (59%), Positives = 1065/1377 (77%), Gaps = 13/1377 (0%)

Query: 4    GVVFNG-LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G   R+RK FG   E++ +P+LIEVQ+ SY+ FL  +  P      GL+   +SV
Sbjct: 8    TISNTGAKKRIRKVFGDIHEVVQMPNLIEVQRESYEQFLRSD--PKIGYVSGLEKTLRSV 65

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+G A ++FV YE + PK+DV++C  R +TYA P+++TLRLIVF+VD+ T  +S+
Sbjct: 66   FPIRDFAGTAEMDFVHYELEEPKYDVEECRQRGITYAAPMRVTLRLIVFEVDQDTETRSV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             DIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A 
Sbjct: 126  LDIKEQDVYMGDMPLMTGNGTFIVNGTERVIVSQMHRSPGVLFDHDRGKTHSSGKYLFAA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+  E++L  FY K+ + +  
Sbjct: 186  RVIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTALLYALGLTPEDMLGYFYNKVTFVRGE 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P  A     G K +  +VD  +GE V  +G K++       ++ G++ L I ++ 
Sbjct: 246  GGWQIPYLAE-AWRGQKPAFDIVDAKSGEVVFAAGHKISPRAANKAEKDGLETLLIPTEE 304

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A D++N  TGEIYIEAGD +  ++LE++  + I  + +L +D V    +IRNTL
Sbjct: 305  VYGRYSAYDLINETTGEIYIEAGDEVSPENLEKLDKAGIDRLELLDIDHVTTGPWIRNTL 364

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DK ++R  AL DIYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+L
Sbjct: 365  KADKAEERDQALADIYRVMRPGEPPTKETAEALFGGLFFDPERYDLSAVGRVKLNMRLDL 424

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D V  +R EDI+A++K LV+L++GKG IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 425  DAEDTVTTLRTEDILAVVKELVNLKDGKGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 484

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 485  ERAVKERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVS 544

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+RVN YGFIETPY
Sbjct: 545  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKYGFIETPY 604

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVTN+VVYLSAMEE    IAQAN+ L+ DG+  E+L+  R AGE ++ P++ I 
Sbjct: 605  RKVIDGKVTNEVVYLSAMEEAKHTIAQANAELNADGTLAEDLISAREAGEFLMAPKDHIT 664

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME  VA+ 
Sbjct: 665  LMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGTVARD 724

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+RAGI++QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQ+TC+NQRPLV
Sbjct: 725  SGAAIAARRAGIIDQVDATRIVIRAT-GDIEPGQSGVDIYTLQKFQRSNQDTCINQRPLV 783

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD +   D+IADGPST+ G+LALGRN LVAFMPW+GYN+EDS+LISER+V +DVFTSI
Sbjct: 784  KVGDLIEAGDVIADGPSTEFGELALGRNTLVAFMPWNGYNYEDSILISERIVKDDVFTSI 843

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGKITPKG
Sbjct: 844  HIEEFEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVEPGDILVGKITPKG 903

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGIDK+ER++++ERE
Sbjct: 904  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIDKDERAMAIERE 963

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+ LA+D++DE+ IL+R  ++RL E+L GQ A + PKG KK   +   L++E  R +WW
Sbjct: 964  EIDRLAKDREDERAILNRATFNRLQEMLLGQVAAAAPKGIKKGVEIDEALLAEVERHEWW 1023

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +FAV D+  Q  +E++K QY+ +  ++ ++F+++++K+Q GD++PPGVL++VKVFVA+KR
Sbjct: 1024 KFAVADDSRQAGIEAVKAQYDEAVKLIVEKFEDRVDKLQRGDELPPGVLKMVKVFVAVKR 1083

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRILP EDMPFL+DGT VDIVLNPLGVPSRMNVGQIFETHLG
Sbjct: 1084 KLQPGDKMAGRHGNKGVISRILPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQIFETHLG 1143

Query: 1143 WACVGLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            WA  GLG+++K  + D++     +        +++ L +  G   + ++I     + ++ 
Sbjct: 1144 WAARGLGQQLKHALEDWREANPNAQGGEMPDAVKTRLLETYG-PQYADQIEGRSAEQIVD 1202

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +AE    GVP++TPVFDGA E  +++ML +A L  SGQS L+DG TG+ FDR VTVG IY
Sbjct: 1203 LAEHLARGVPMATPVFDGAREADVSAMLELAGLHSSGQSDLFDGRTGDRFDRKVTVGIIY 1262

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEML
Sbjct: 1263 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEML 1322

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            T+KSDDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L         
Sbjct: 1323 TVKSDDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELAAMDEVEED 1379


>gi|294011000|ref|YP_003544460.1| DNA-directed RNA polymerase subunit beta [Sphingobium japonicum
            UT26S]
 gi|292674330|dbj|BAI95848.1| DNA-directed RNA polymerase subunit beta [Sphingobium japonicum
            UT26S]
          Length = 1387

 Score = 1682 bits (4356), Expect = 0.0,   Method: Composition-based stats.
 Identities = 823/1377 (59%), Positives = 1067/1377 (77%), Gaps = 13/1377 (0%)

Query: 4    GVVFNG-LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G   R+RK FG   E++ +P+LIEVQ+ SY+ FL  +  P      GL+   +SV
Sbjct: 8    TISNTGAKKRIRKVFGDIHEVVQMPNLIEVQRESYEQFLRSD--PSIGYVSGLEKTLRSV 65

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+G A ++FV YE + PK+DV++C  R +TYA P+++TLRLIVF+VD  T  +S+
Sbjct: 66   FPIRDFAGTAEMDFVHYELEDPKYDVEECRQRGITYAAPMRVTLRLIVFEVDADTETRSV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             DIKEQ +YMGD+PLMT++GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A 
Sbjct: 126  LDIKEQDVYMGDMPLMTQNGTFIVNGTERVIVSQMHRSPGVLFDHDRGKTHSSGKYLFAA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+  E++L  FY K+ + +  
Sbjct: 186  RVIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTALLYALGLTPEDMLGYFYNKVTFLRGE 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W  P +A     G K +  +VD  +GE V  +G K++       ++ G++ L I ++ 
Sbjct: 246  GGWQIPYTAE-AWRGQKPAFDIVDAKSGEVVFAAGHKISPRAANKAEKDGLETLLIPTEE 304

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A D++N  TGEIYIEAGD +  ++LE++  + I  + +L +D V    +IRNTL
Sbjct: 305  VYGRYSAYDLINEATGEIYIEAGDEVSPENLEKLDKAGIDRLELLDIDHVTTGPWIRNTL 364

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DK ++R  AL DIYRVMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+L
Sbjct: 365  KADKAEERDQALADIYRVMRPGEPPTKETAEALFAGLFFDPERYDLSAVGRVKLNMRLDL 424

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  D V  +R EDI+A++K LV+L++GKG IDDIDNLGNRRVRSVGE+L+NQYR+GLLRM
Sbjct: 425  DAEDTVTTLRTEDILAVVKELVNLKDGKGEIDDIDNLGNRRVRSVGELLENQYRVGLLRM 484

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  E  N LS +TH RR+S
Sbjct: 485  ERAVKERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMEQTNPLSEVTHKRRVS 544

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +F+RVN YGFIETPY
Sbjct: 545  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFSRVNKYGFIETPY 604

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVTN+VVYLSAMEE    IAQAN+ L+ DG+  E+L+  R AGE ++ P++ I 
Sbjct: 605  RKVIDGKVTNEVVYLSAMEEAKHTIAQANAELNADGTLAEDLISAREAGEFLMAPKDHIT 664

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME  VA+ 
Sbjct: 665  LMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEGTVARD 724

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGAAI A+RAGI++QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQ+TC+NQRPLV
Sbjct: 725  SGAAIAARRAGIIDQVDATRIVIRAT-GDIEPGQSGVDIYTLQKFQRSNQDTCINQRPLV 783

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD +   D+IADGPST+ G+LALGRN LVAFMPW+GYN+EDS+LISER+V +DVFTSI
Sbjct: 784  KVGDLIEAGDVIADGPSTEFGELALGRNTLVAFMPWNGYNYEDSILISERIVKDDVFTSI 843

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGKITPKG
Sbjct: 844  HIEEFEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVEPGDILVGKITPKG 903

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGIDK+ER++++ERE
Sbjct: 904  ESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIDKDERAMAIERE 963

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I+ LA+D++DE+ IL+R  ++RL E+L GQ A + PKG KK   +   L++E  R +WW
Sbjct: 964  EIDRLAKDREDERAILNRATFNRLQEMLIGQTAAAAPKGIKKGVEIDEALLAEVERHEWW 1023

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +FAV D+  Q  +E++K QY+ +  ++ ++F+++++K+Q GD++PPGVL++VKVFVA+KR
Sbjct: 1024 KFAVADDARQAGIEAVKAQYDEAVKLIVEKFEDRVDKLQRGDELPPGVLKMVKVFVAVKR 1083

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRILP EDMPFL+DGT VDIVLNPLGVPSRMNVGQIFETHLG
Sbjct: 1084 KLQPGDKMAGRHGNKGVISRILPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQIFETHLG 1143

Query: 1143 WACVGLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            WA  GLG+++K  + +++     +        +++ L +  G   + ++I     + ++ 
Sbjct: 1144 WAARGLGQQLKHALEEWREANPNAQGGEMPDAVKTRLLETYG-PQYADQIEGRTPEQIVD 1202

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +AE    GVP++TPVFDGA E  +++ML +A L  SGQS LYDG TG+ FDR VTVG IY
Sbjct: 1203 LAEHLSRGVPMATPVFDGAREADVSAMLELAGLHSSGQSDLYDGRTGDKFDRKVTVGIIY 1262

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEML
Sbjct: 1263 MLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEML 1322

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            T+KSDDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +       
Sbjct: 1323 TVKSDDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELASMDEIEDD 1379


>gi|330993838|ref|ZP_08317770.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter sp.
            SXCC-1]
 gi|329759106|gb|EGG75618.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter sp.
            SXCC-1]
          Length = 1390

 Score = 1682 bits (4355), Expect = 0.0,   Method: Composition-based stats.
 Identities = 822/1391 (59%), Positives = 1055/1391 (75%), Gaps = 31/1391 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG  PE+  +P+LI+VQ+ASY+ FL MN+APD R   GLQ  F+S
Sbjct: 3    AITKSFTGRKRIRKSFGHIPEVAPMPNLIDVQRASYETFLQMNVAPDSRTPTGLQEVFRS 62

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   LEFVSYE + PK+DV++C+ R LT+A PLK+ LRLIV+DVDE TG++S
Sbjct: 63   VFPINDFAGRGRLEFVSYELEEPKYDVEECIQRGLTFAAPLKVILRLIVWDVDEDTGSRS 122

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I+DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123  IRDIKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFA 182

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 183  ARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGAASEAARAAKAAEGGDVE 242

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD +EIL  FY K+ +++    W     A     G K+   L+D  TGE+V  +
Sbjct: 243  SMEIRGMDPDEILGYFYGKVEFTKTEKGWARRFDAE-AFRGQKLLEPLIDAQTGEEVAPA 301

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + E   K + +    L G ++A+D+VN  TGEIY EAG+ + E+ LEE+
Sbjct: 302  DAKLTARMVRKIAET-TKEVLVGPAGLIGRFIAQDMVNEHTGEIYAEAGEELTEQKLEEL 360

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                +  +  L +D+ N   +IRNTL  DKN  R++AL DIYRVMRPG+  T   AE+MF
Sbjct: 361  EGEGLTTLTTLAIDAAN-GPWIRNTLAVDKNAAREEALTDIYRVMRPGEPPTPETAEAMF 419

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            + LFFD D+YDLS VGRVKMNMRL +D PD VR +RKEDI+  +KI+ +L++G+G IDDI
Sbjct: 420  SGLFFDPDRYDLSAVGRVKMNMRLGVDVPDTVRVLRKEDILRTVKIMCELKDGRGAIDDI 479

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 480  DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 539

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET E
Sbjct: 540  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 599

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL ++A+VN YGFIETPYR V DG + +   YLSAMEEE   +AQA++  D 
Sbjct: 600  GPNIGLINSLATYAKVNKYGFIETPYRMVHDGVLQDGWKYLSAMEEEKLVVAQADAKQDA 659

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G  T++LV  R  G+   VP   +   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 660  QGHLTDDLVSVRRGGDFRQVPPTDVTACDVSPKQLVSVAAALIPFLENDDANRALMGSNM 719

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL++++AP VGTGME+ VA  SGAAIVA+R G+V+Q+D  RIV+R+ +     +T
Sbjct: 720  QRQAVPLVRSDAPLVGTGMEAAVAHDSGAAIVARRDGVVDQIDGARIVVRATD--AGGAT 777

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLV+VGDEVR  +IIADGPST+LG+LALGRN+LVAFM
Sbjct: 778  QGVDIYRLRKYMRSNQSTCINQRPLVRVGDEVRAGEIIADGPSTELGELALGRNVLVAFM 837

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 838  PWNGYNFEDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 897

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDIL+GK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +
Sbjct: 898  DEAGIVYVGAEVNPGDILIGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTT 957

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ Y+RL E L GQ A 
Sbjct: 958  GTIVDVRVFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYNRLREHLIGQTAG 1017

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++ +++SE+PR  W    V  ++V   +E+L+ +++ + S ++ RF NK
Sbjct: 1018 AGFKGIRSGTEITDEVLSEHPRGAWRNITVASDEVMAELETLRREFDAAVSKIQARFDNK 1077

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGT
Sbjct: 1078 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGT 1137

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI-SPLRSFLEKV 1175
             VDIVLNPLGVPSRMNVGQI ETHLGWAC  +G+++  L ++Y+ +G+    L   L+ V
Sbjct: 1138 SVDIVLNPLGVPSRMNVGQILETHLGWACANIGRQVAQLADEYQRHGEKRQELLDELKSV 1197

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G   + E+I D  D  +L +    + GVP++TPVFDGA    I +ML  A +D+SGQS 
Sbjct: 1198 YGDKVYEEQIGDMTDAQLLELCGNLRKGVPIATPVFDGASIPDIEAMLTKAGVDKSGQSQ 1257

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1258 LIDGRTGEPFERKTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1317

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE++
Sbjct: 1318 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELK 1377

Query: 1356 ALGLSIDLENS 1366
            +LGL++DLE S
Sbjct: 1378 SLGLNVDLEQS 1388


>gi|254294447|ref|YP_003060470.1| DNA-directed RNA polymerase subunit beta [Hirschia baltica ATCC
            49814]
 gi|254042978|gb|ACT59773.1| DNA-directed RNA polymerase, beta subunit [Hirschia baltica ATCC
            49814]
          Length = 1366

 Score = 1682 bits (4355), Expect = 0.0,   Method: Composition-based stats.
 Identities = 834/1372 (60%), Positives = 1056/1372 (76%), Gaps = 11/1372 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    R+RK FG  PE I +P+LIE+Q++SY+HFL M+++  ER  EGL A F+SV
Sbjct: 1    MALSFTAKKRIRKSFGNIPESIQMPNLIEIQRSSYEHFLQMHVSSSEREGEGLDAVFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS  A LE+VSYEF+PPKFD  +C+ RDL YA PLK+ LRLIVF+ DE TGA+SI
Sbjct: 61   FPIKDFSDRATLEYVSYEFEPPKFDTQECMQRDLNYAAPLKVKLRLIVFETDEETGARSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +Y+GD+PLMT+ GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A 
Sbjct: 121  KDIKEQDVYLGDIPLMTEKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+HVRIDR+RK+P T+ L ALG D E IL TFY K+ Y    
Sbjct: 181  RIIPYRGSWLDFEFDAKDIMHVRIDRKRKLPATALLQALGYDHERILDTFYSKVGYRIDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W    S  D     +V   +++   G+ V   GKK++    K   E GV+ + + S  
Sbjct: 241  AGWITSFSP-DRWKSVRVEFDILNAADGKVVFNGGKKISPIKAKRAGEAGVEEVLVPSTF 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV-NNNAYIRNT 361
            L G +V EDIVN ETGEI++EAGD + E+S+ E+  + +  I +L  DS      ++RNT
Sbjct: 300  LEGKFVGEDIVNMETGEIFVEAGDELTEESIAELRDAGVDMITVLDTDSEAARGPWLRNT 359

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  DK  +R +AL DIYRVMRPG+  T   +E++FN LFFDS++YDLS VGRVKMNMRL 
Sbjct: 360  LKVDKASNRTEALSDIYRVMRPGEPPTLEASEALFNQLFFDSERYDLSAVGRVKMNMRLG 419

Query: 422  ---LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                + PD  R +R++DI+ ++  ++DL++GKG +DDIDNLGNRRVRS GE+L+N YR+G
Sbjct: 420  FTLEEAPDTERTLREDDILGVMSTVLDLKDGKGEVDDIDNLGNRRVRSCGELLENAYRVG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+RMER+IKER+SSVDID+VMP DL+NAKPV ++V +FF SSQLSQ  +  N LS ITH 
Sbjct: 480  LVRMERAIKERMSSVDIDTVMPHDLVNAKPVHASVRDFFGSSQLSQFMDQTNPLSEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL + AR+N YGFI
Sbjct: 540  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARINKYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYR+V DG   + V YLSAMEE    IAQAN+++ EDG  T E V  R AGE  LV R
Sbjct: 600  ESPYRQVKDGIPQDQVDYLSAMEEYRFKIAQANAAIGEDGKLTNEFVNARVAGEATLVSR 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++D++D SPKQVVS+AA++IPFLENDD+NR LMG NMQRQAVPL+K +AP VGTGME +
Sbjct: 660  DEVDYMDVSPKQVVSVAAAMIPFLENDDANRALMGSNMQRQAVPLVKTDAPLVGTGMERI 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ S AAIVAKR+G+VEQVDA RIV+R+++G LD + SGVDIYRL KFQRSNQN+C+NQ
Sbjct: 720  VARDSRAAIVAKRSGVVEQVDATRIVVRALDG-LDATRSGVDIYRLSKFQRSNQNSCINQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RP+VKVGDE+   DIIADGPSTDLGDLALGRN+LVAFMPW GYNFEDS+LISER+V +DV
Sbjct: 779  RPIVKVGDEIVAGDIIADGPSTDLGDLALGRNVLVAFMPWSGYNFEDSILISERIVRDDV 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFE+ +RDTKLGPEEITRDIPNV EE L+N+DE GII VGAEV  GDILVGK+
Sbjct: 839  FTSIHIEEFEIASRDTKLGPEEITRDIPNVGEEALRNLDEAGIIAVGAEVTAGDILVGKV 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP G +GT+V+VR+FNRHG+DK++R++ 
Sbjct: 899  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGDTGTIVEVRVFNRHGVDKDQRALQ 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +EREQIE L +DKDDE  I++R+ Y RL  +L GQ A++GPKGF K   +S+D +SE   
Sbjct: 959  IEREQIEALQKDKDDELAIIERDSYDRLRSLLLGQKAIAGPKGFSKGE-ISTDSLSEVYE 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            +  W+ AV+DE +Q  ++++K   ++S+S++E RF++K++K+Q GDD+PPGV+++VKVF+
Sbjct: 1018 TDMWKIAVEDEGIQTQIDNIKSALDSSRSLIEARFEDKVDKVQRGDDLPPGVMKIVKVFI 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++SRI P EDMP L+DGTPVDIVLNPLGVPSRMNVGQI E
Sbjct: 1078 AVKRKLQPGDKMAGRHGNKGVISRINPLEDMPHLEDGTPVDIVLNPLGVPSRMNVGQILE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLG+ I   + +Y  + DI  L+  L    G      +     ++ ++ +A 
Sbjct: 1138 THLGWACSGLGRMIDDSLKEYHRDHDIVKLKDQLAHCYGDNQELPE----KEEELVELAG 1193

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K G+P++TPVFDGA  E I+ ML  A  D SGQS +YDG TGE F R VTVGY Y+LK
Sbjct: 1194 NLKKGIPIATPVFDGASSEQIDEMLTRAGFDTSGQSTVYDGRTGERFARKVTVGYKYLLK 1253

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1254 LHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1313

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            SDD  GR +VYESIV G+D+FE G PESFNVL+KEM++LGL+++L  +    
Sbjct: 1314 SDDTAGRAKVYESIVRGDDSFEAGIPESFNVLIKEMRSLGLNVELLEAEDPE 1365


>gi|148361060|ref|YP_001252267.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila str.
            Corby]
 gi|41017593|sp|O86094|RPOB_LEGPN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229295|sp|A5IHS1|RPOB_LEGPC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|3549149|gb|AAC69338.1| RNA polymerase B-subunit [Legionella pneumophila]
 gi|148282833|gb|ABQ56921.1| DNA-directed RNA polymerase beta subunit [Legionella pneumophila str.
            Corby]
          Length = 1368

 Score = 1681 bits (4352), Expect = 0.0,   Method: Composition-based stats.
 Identities = 726/1364 (53%), Positives = 996/1364 (73%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  +I+ IP+L+E+Q  SY  FL  +    E+ N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQTDIMPIPNLLEIQLKSYRDFLQTDTKLSEQLNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL+V D D     K IK
Sbjct: 69   PIESFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKDASDDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFV+ G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVVNGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PVT  L ALG ++E+ILS F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVTILLRALGYEAEDILSEFFETTRCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDIHVPETGELIVEQGRRITARHIKQMEKSQMQDLVVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE   +A D I E+ L+ + +  I  I ++Y + +++ +YI +TL 
Sbjct: 308  IGKTLAKNIIDTSTGEFLAQANDEITEELLDAMANHGILQIDMIYTNDLDHGSYISDTLK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+ + 
Sbjct: 368  IDPTGSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGIK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            + +    + KEDI+++IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  SDEGPGTLTKEDILSVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT++V YLSA+EE ++YIAQ+N  LD  G+   +LV CR   E  L   +KI++
Sbjct: 608  KVVNGRVTDEVEYLSAIEEVDQYIAQSNVELDAQGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+V 
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVS 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVHDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEV  GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGTEEITADIPNVGESALSNLDESGVVYIGAEVKAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  +L  + A  GP   K  + ++ D + +  R +W+ 
Sbjct: 968  LARVRKDLIDERRIREEDIYHRVSHLLLDKVATGGPGSLKPGSKITQDYLDKVEREKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ V + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRIEDDAVSQQLEQLSKQLELLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG+KI  ++++ +    I   +++LEK+    G     +   +DD ++ +A+  ++
Sbjct: 1148 AAKGLGRKIAQMLDERQTPEAI---KAYLEKIYNHDGVQRVNLKCLNDDELMTLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I SML++ADL   G+++L DG TG  FD PVTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGATEQEIKSMLQLADLPADGKTVLIDGRTGNKFDNPVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|148260945|ref|YP_001235072.1| DNA-directed RNA polymerase subunit beta [Acidiphilium cryptum JF-5]
 gi|326404343|ref|YP_004284425.1| DNA-directed RNA polymerase subunit beta [Acidiphilium multivorum
            AIU301]
 gi|166229283|sp|A5FZX1|RPOB_ACICJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146402626|gb|ABQ31153.1| DNA-directed RNA polymerase subunit beta [Acidiphilium cryptum JF-5]
 gi|325051205|dbj|BAJ81543.1| DNA-directed RNA polymerase subunit beta [Acidiphilium multivorum
            AIU301]
          Length = 1400

 Score = 1680 bits (4351), Expect = 0.0,   Method: Composition-based stats.
 Identities = 821/1390 (59%), Positives = 1049/1390 (75%), Gaps = 34/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V F    R+RK FG+ PE   +P+LI+VQ+ASYD FL M+++PD R N GLQ  FKSVF
Sbjct: 10   KVSFTNRKRIRKSFGRIPETTPMPNLIDVQRASYDAFLQMHVSPDSRTNSGLQEVFKSVF 69

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI  F+G   LEFV YE + PK+DV++C+ R +TYA PLK+ LRLIV+DVDE TGA+SI+
Sbjct: 70   PIDDFAGRGRLEFVYYELEEPKYDVEECIQRGMTYAAPLKVVLRLIVWDVDEDTGARSIR 129

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R
Sbjct: 130  DIKEQPVYMGDMPLMTDNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAAR 189

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL---------------------- 221
            +IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL                      
Sbjct: 190  VIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGRATEALRAAREAKGESLEIG 249

Query: 222  ---GMDSEEILSTFYPKIVYSQR----GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
               GMD+EEIL+ FY K+ +++     G+         +   GAK+   LVD +TGE V 
Sbjct: 250  EIRGMDAEEILTYFYGKVPFTRTRTRDGETAWARPFEPETFRGAKLVEDLVDAETGEVVA 309

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            ++  KLT+ + + +  K    + ++   L G YVAED+ +  TGEI+ +AG+ I E  L+
Sbjct: 310  KADDKLTARVARQIAVKTRT-VLVSRADLIGRYVAEDLFDPNTGEIFADAGEEISEAKLK 368

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                + + +IP L +D      +IRNTL  DKN  R+DAL+DIYRV+RPG+  T   AE+
Sbjct: 369  TFEDAGLDEIPTLAIDQA-KGPWIRNTLAADKNASREDALIDIYRVIRPGEPPTSETAEA 427

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            +F  LFFD+++YDLS VGRVKMNMRL L+  D VR +RKEDI+  I+I+ +L++G+G +D
Sbjct: 428  LFRGLFFDAERYDLSAVGRVKMNMRLGLECEDTVRVLRKEDILRTIQIMCELKDGRGQVD 487

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DIDNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID VMP DLINAKP  +AV 
Sbjct: 488  DIDNLGNRRVRSVGELMENQYRIGLLRMERAIRERMGSVDIDGVMPHDLINAKPAAAAVR 547

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET
Sbjct: 548  EFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 607

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL +FA+VN YGFIETPYR V DGKV ++  YLSAMEEE   +AQA++  
Sbjct: 608  PEGPNIGLINSLATFAKVNKYGFIETPYRLVKDGKVLDEYKYLSAMEEERLTVAQADAPK 667

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              DG+ TE+LV  R  G+  LV  +++  ID SP+Q+VS+AA+LIPFLENDD+NR LMG 
Sbjct: 668  LADGTLTEDLVSVRRNGDFRLVKPDEVTAIDVSPRQLVSVAAALIPFLENDDANRALMGS 727

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL+K++AP VGTGME+ VA+ SGA IVA+RAG+++Q+D  RIV+R+     D 
Sbjct: 728  NMQRQAVPLIKSDAPLVGTGMEAPVARDSGATIVARRAGVIDQIDGARIVVRATGE--DG 785

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            +T GVDIYRL KF RSNQ+TC+NQRPLV+VGD V   DIIADGPST+LG+LALGRN+L A
Sbjct: 786  TTQGVDIYRLRKFMRSNQSTCINQRPLVRVGDRVGAGDIIADGPSTELGELALGRNVLCA 845

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            FMPW+GYNFEDS+LISER+  ED+FTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+
Sbjct: 846  FMPWNGYNFEDSILISERVAREDMFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALR 905

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+DE GI+ +GAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G
Sbjct: 906  NLDEAGIVYIGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPG 965

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V+GTVVDVR+FNR G+DK+ER++++ER +IE LA+D+DDE+ I +R   +RL E L GQ 
Sbjct: 966  VNGTVVDVRVFNRRGVDKDERALAIERAEIERLAKDRDDERAIQERAFLNRLREKLLGQV 1025

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            A SG KG +  T ++++L++E PR  W    VQD++V   +E+LK +++ S   L+ RF+
Sbjct: 1026 AGSGYKGVRSGTEITTELLAEIPRGAWRNLTVQDDRVMAEIETLKREFDASVHKLQQRFE 1085

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+EK+Q GD+MPPGV+++VKVF+A+KR +Q GDKMAGRHGNKG+VS+++P EDMPFL+D
Sbjct: 1086 SKVEKLQRGDEMPPGVMKMVKVFIAVKRKLQPGDKMAGRHGNKGVVSKVVPIEDMPFLED 1145

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLE 1173
            GTPVD+VLNPLGVPSRMNVGQI ETHLGWAC  LG++I   +  Y +   +   L + L+
Sbjct: 1146 GTPVDVVLNPLGVPSRMNVGQILETHLGWACANLGRQIGEAVEAYQRDVAERERLHAMLK 1205

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V G   + E+I+   D  +  +    + GVP++TPVFDGA    I  ML  A LD SGQ
Sbjct: 1206 SVYGEEIYNEQIASMSDAELRELCGNIRKGVPIATPVFDGARITDIEDMLAKAGLDVSGQ 1265

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              + DG TGE F+R VTVGY+YMLKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 1266 MTVCDGRTGEQFERKVTVGYMYMLKLGHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQR 1325

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL KE
Sbjct: 1326 FGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDNFEAGVPESFNVLTKE 1385

Query: 1354 MQALGLSIDL 1363
            +++LGL++DL
Sbjct: 1386 LKSLGLNVDL 1395


>gi|300114743|ref|YP_003761318.1| DNA-directed RNA polymerase subunit beta [Nitrosococcus watsonii
            C-113]
 gi|300114755|ref|YP_003761330.1| DNA-directed RNA polymerase subunit beta [Nitrosococcus watsonii
            C-113]
 gi|299540680|gb|ADJ28997.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus watsonii
            C-113]
 gi|299540692|gb|ADJ29009.1| DNA-directed RNA polymerase, beta subunit [Nitrosococcus watsonii
            C-113]
          Length = 1359

 Score = 1680 bits (4351), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1364 (52%), Positives = 987/1364 (72%), Gaps = 5/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK FGK   I+  P L+ +Q  S+  FL M++ P +R ++GL AAFKSV
Sbjct: 1    MPYSLTEKKRIRKDFGKLHSILKTPFLLTIQIGSFLDFLQMDVPPGKRKDKGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++  A L++ SY    P F+V +C  R LTYA PL++ LRL+++D +     + +
Sbjct: 61   FPIKSYTEYAELQYSSYHLGVPSFEVKECQVRGLTYAAPLRVKLRLVIYDKESPASEQVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG++PLMT  G FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 121  KDVKEQEVYMGEIPLMTPKGNFVINGTERVIVSQLHRSPGVIFEHDKGKTHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD I+ RIDRRRK+  T  L ALG  +EEIL  F+  I   ++G
Sbjct: 181  RIIPYRGSWLDFEFDPKDCIYARIDRRRKLLATILLRALGYSTEEILIMFFETISVKRQG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G  +   +   D GE ++E+G+++T+  +K +++ G+K L +  + 
Sbjct: 241  SSYLLDLVPQRL-RGESLPFDIASPD-GEVIVEAGRRVTARHIKQMEKAGMKTLSVPKEF 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +  D+++  TGE+  +A D I  + L  I +++I+   ++Y + ++  ++I ++L
Sbjct: 299  LIGKILTRDLIDTGTGEVLAKANDEITAELLAVIENTDIQAFDLIYTNDLDRGSFISDSL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D      +A ++IYRVMRPG+  T   A+++F  LFF+ ++YDLS VGR+K N RL  
Sbjct: 359  RLDPTTTPLEAQMEIYRVMRPGEPPTKEAAQNLFQNLFFNPERYDLSPVGRMKFNRRLGK 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ +IK LVD+RNG G++DD+D+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 419  EDITGPSILSKEDIVDVIKTLVDIRNGYGSVDDVDHLGNRRVRSVGEMAENQFRVGLVRV 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 479  ERAVRERLSLAESEGLMPQELINAKPVSAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGFIETPY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARINQYGFIETPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG+VT +V YLSA+EE    IAQAN++ DE+G   + LV CR   E  L+P EK+ 
Sbjct: 599  RKVVDGRVTAEVDYLSAIEEGQYVIAQANAAADEEGRLIDMLVSCRHKNEFTLLPPEKVQ 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +ID SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA+ 
Sbjct: 659  YIDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAETPLVGTGMEQFVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA+R GIV+ VDA R+V+R  + +      GVDIY L+K+ RSNQNTC+NQ PLV
Sbjct: 719  SGVMVVARRGGIVDSVDAARVVVRVNDEETASDEPGVDIYNLIKYARSNQNTCINQSPLV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V   D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED FTSI
Sbjct: 779  KPGDTVAIGDVLADGPSTDMGELALGQNLLVAFMPWNGYNFEDSILISERVVEEDRFTSI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE    ARDTKLGPEEI+ DIPNVSE  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 839  HIEELTCFARDTKLGPEEISSDIPNVSEAALSKLDEAGIVYIGAEVKPGDILVGKVTPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV SG+ GTV+DV++F R G++K+ R++ +E  
Sbjct: 899  ETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGMQGTVIDVQVFTRDGVEKDARALEIEEM 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++  + +D  DE  I++ +IY RL ++L G+    GP   K  T ++   +++ PR +W+
Sbjct: 959  ELAKIKKDLRDEFRIVETDIYQRLEKVLVGKTVEGGPAELKAGTQITQSYLADLPRERWF 1018

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ E+  + +ES+  Q +  +  ++++F+ +  K+  G D+PPGV ++VKV++A+KR
Sbjct: 1019 EIRLRSEEAGKQLESVAGQLKEQRIAMDEKFQQQRAKLTSGHDLPPGVQKMVKVYLAVKR 1078

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S I+P EDMP+++DGTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1079 RVQPGDKMAGRHGNKGVISTIVPIEDMPYMEDGTPVDIVLNPLGVPSRMNIGQILETHLG 1138

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI +L++   +   +S LR FL+++       E ++   D  VL +A     
Sbjct: 1139 WAAKGLGRKIGALLD---SGQQVSELRVFLDRIYNASGKREDLNSLSDKEVLELANNLSD 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I +ML +ADL  +GQ+ LYDG +G+ F RP+TVGY++MLKLNH+
Sbjct: 1196 GVPMATPVFDGASEQEIKAMLELADLPINGQTNLYDGRSGKAFARPITVGYMHMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +++YGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALESYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL KE++ALG+ I+LE  
Sbjct: 1316 SGRTKMYKNIVDGDYRMEAGMPESFNVLTKEIRALGIDIELEQD 1359


>gi|52840567|ref|YP_094366.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila
            subsp. pneumophila str. Philadelphia 1]
 gi|81378217|sp|Q5ZYQ0|RPOB_LEGPH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|52627678|gb|AAU26419.1| DNA-directed RNA polymerase beta subunit [Legionella pneumophila
            subsp. pneumophila str. Philadelphia 1]
          Length = 1368

 Score = 1680 bits (4351), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1364 (53%), Positives = 996/1364 (73%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  +I+ IP+L+E+Q  SY  FL  +    E+ N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQTDIMPIPNLLEIQLKSYRDFLQTDTKLSEQLNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL+V D D     K IK
Sbjct: 69   PIESFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKDASDDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFV+ G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVVNGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PVT  L ALG ++E+ILS F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVTILLRALGYEAEDILSEFFETTHCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDIHVPETGELIVEQGRRITARHIKQMEKSQMQDLVVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE   +A D I E+ L+ + +  I  I ++Y + +++ +YI +TL 
Sbjct: 308  IGKTLAKNIIDTSTGEFLAQANDEITEELLDAMANHGILQIDMIYTNDLDHGSYISDTLK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+ + 
Sbjct: 368  IDPTGSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGIK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            + +    + KEDI+++IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  SDEGPGTLTKEDILSVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT++V YLSA+EE ++YIAQ+N  LD  G+   +LV CR   E  L   +KI++
Sbjct: 608  KVVNGRVTDEVEYLSAIEEVDQYIAQSNVELDAQGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+V 
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVS 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVHDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEV  GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGTEEITADIPNVGESALSNLDESGVVYIGAEVKAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  +L  + A  GP   K  + ++ D + +  R +W+ 
Sbjct: 968  LARVRKDLIDERRIREEDIYHRVSHLLLDKVATGGPGSLKPGSKITQDYLDKVEREKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ + + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRIEDDAISQQLEQLSKQLELLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG+KI  ++++ +    I   +++LEK+    G     +   +DD ++ +A+  ++
Sbjct: 1148 AAKGLGRKIAQMLDEKQTPEAI---KAYLEKIYNHDGVQRVNLKCLNDDELMTLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I SML++ADL   G+++L DG TG  FD PVTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGATEQEIKSMLQLADLPADGKTVLIDGRTGNKFDNPVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|54293314|ref|YP_125729.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila str.
            Lens]
 gi|81369318|sp|Q5WZL9|RPOB_LEGPL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|53753146|emb|CAH14593.1| RNA polymerase B-subunit [Legionella pneumophila str. Lens]
 gi|307609131|emb|CBW98577.1| RNA polymerase B-subunit [Legionella pneumophila 130b]
          Length = 1368

 Score = 1680 bits (4351), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1364 (53%), Positives = 995/1364 (72%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  +I+ IP+L+E+Q  SY  FL  +    E+ N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQTDIMPIPNLLEIQLKSYRDFLQTDTKLSEQLNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL+V D D     K IK
Sbjct: 69   PIESFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKDASDDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFV+ G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVVNGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PVT  L ALG ++E+IL+ F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVTILLRALGYEAEDILNEFFETTCCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDIHVPETGELIVEQGRRITARHIKQMEKSQMQDLVVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE   +A D I E+ L+ +    I  I ++Y + +++ +YI +TL 
Sbjct: 308  IGKTLAKNIIDTSTGEFLAQANDEITEELLDAMASHGILQIDMIYTNDLDHGSYISDTLK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+ + 
Sbjct: 368  IDPTGSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGIK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            + +    + KEDI+++IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  SDEGPGTLTKEDILSVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT++V YLSA+EE ++YIAQ+N  LD  G+   +LV CR   E  L   +KI++
Sbjct: 608  KVVNGRVTDEVEYLSAIEEVDQYIAQSNVELDAQGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+V 
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVS 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVHDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEV  GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGTEEITADIPNVGESALSNLDESGVVYIGAEVKAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  +L  + A  GP   K  + ++ D + +  R +W+ 
Sbjct: 968  LARVRKDLIDERRIREEDIYHRVSHLLLDKVATGGPGSLKPGSKITQDYLDKVEREKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ + + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRIEDDAISQQLEQLSKQLELLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG+KI  ++++ +    I   +++LEK+    G     +   +DD ++ +A+  ++
Sbjct: 1148 AAKGLGRKIAQMLDEKQTPEAI---KAYLEKIYNHDGVQRVNLKCLNDDELMTLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I SML++ADL   G+++L DG TG  FD PVTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGATEQEIKSMLQLADLPADGKTVLIDGRTGNKFDNPVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|296105871|ref|YP_003617571.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila
            2300/99 Alcoy]
 gi|295647772|gb|ADG23619.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila
            2300/99 Alcoy]
          Length = 1368

 Score = 1680 bits (4351), Expect = 0.0,   Method: Composition-based stats.
 Identities = 726/1364 (53%), Positives = 996/1364 (73%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  +I+ IP+L+E+Q  SY  FL  +    E+ N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQTDIMPIPNLLEIQLKSYRDFLQTDTKLSEQLNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL+V D D     K IK
Sbjct: 69   PIESFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKDASDDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFV+ G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVVNGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PVT  L ALG ++E+ILS F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVTILLRALGYEAEDILSEFFETTRCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDIHVPETGELIVEQGRRITARHIKQMEKSQMQDLVVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE   +A D I E+ L+ + +  I  I ++Y + +++ +YI +TL 
Sbjct: 308  TGKTLAKNIIDTSTGEFLAQANDEITEELLDAMANHGILQIDMIYTNDLDHGSYISDTLK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+ + 
Sbjct: 368  IDPTGSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGIK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            + +    + KEDI+++IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  SDEGPGTLTKEDILSVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT++V YLSA+EE ++YIAQ+N  LD  G+   +LV CR   E  L   +KI++
Sbjct: 608  KVVNGRVTDEVEYLSAIEEVDQYIAQSNVELDAQGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+V 
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVS 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVHDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEV  GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGTEEITADIPNVGESALSNLDESGVVYIGAEVKAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  +L  + A  GP   K  + ++ D + +  R +W+ 
Sbjct: 968  LARVRKDLIDERRIREEDIYHRVSHLLLDKVATGGPGSLKPGSKITQDYLDKVEREKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ V + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRIEDDAVSQQLEQLSKQLELLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG+KI  ++++ +    I   +++LEK+    G     +   +DD ++ +A+  ++
Sbjct: 1148 AAKGLGRKIAQMLDERQTPEAI---KAYLEKIYNHDGVQRVNLKCLNDDELMTLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I SML++ADL   G+++L DG TG  FD PVTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGATEQEIKSMLQLADLPADGKTVLIDGRTGNKFDNPVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|254283154|ref|ZP_04958122.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            NOR51-B]
 gi|219679357|gb|EED35706.1| DNA-directed RNA polymerase, beta subunit [gamma proteobacterium
            NOR51-B]
          Length = 1365

 Score = 1680 bits (4350), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1366 (52%), Positives = 971/1366 (71%), Gaps = 5/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG   +++DIP L+ +Q  SY  F    +  D+R + GL AAF+SV
Sbjct: 1    MAYSYTEKKRIRKDFGSLEKVMDIPYLLAIQLDSYRKFTQDGVPVDQRGDYGLHAAFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG A LE+V Y    P FDV++C  R  TYA PL++ +RL+++D    T +KSI
Sbjct: 61   FPISSYSGNAALEYVDYSLGKPVFDVEECQLRGTTYACPLRVKVRLMIYDK--ETSSKSI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++ RIDRRRK+P T  L ALG  SEE+L  F+    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDMVYARIDRRRKLPATVLLRALGYQSEEMLEMFFETTSFQLGD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +         + + G   +  ++  D  + ++E G+++T+  ++ L + GV++L +  + 
Sbjct: 239  EHSATMKLVPERLRGDMAAFDIMADD--KVLVERGRRITARHIRELADAGVEYLAVPDEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +++ +V+  TGE+ +E    I ++ L+ +   EI D+  +Y + ++   +I +TL
Sbjct: 297  LLGRRLSKGVVDTSTGEVLVECNTEITQELLDLLREKEISDVDTIYTNEIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +  +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N RL  
Sbjct: 357  AQDSTTNELEALVEIYRMMRPGEPPTKESAENLFQNLFFSPDRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            ++ + +  + KEDI+ ++K LVD+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  ESSEGIGTLDKEDIVDVLKTLVDIRNGKGIVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT D+ YLSA+ E    IAQA+++LDE+  F +EL+  R   E  + P  ++D
Sbjct: 597  RRVVDGVVTEDIEYLSAINEAGHVIAQASATLDENDRFVDELINVRHGNEFTVKPATEVD 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVSIAA+LIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  
Sbjct: 657  FMDVSPKQVVSIAAALIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERYVAAD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G+++ VDA RIV+R     +    S VDIY L K++RSNQNTC+NQRP+V
Sbjct: 717  SGVCEVARRGGVIDSVDASRIVVRVDADKVGSDESPVDIYNLTKYKRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V R DI+ADGPS DLG+LALG+NM + FMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  KPGDVVARGDILADGPSVDLGELALGQNMRIGFMPWNGYNFEDSILVSERVVEEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EE+T DIPNV E  L  +DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEVTSDIPNVGEGALSKLDESGIVYIGAEVDAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ R+  +E  
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSYKGTVIDVQVFTRDGLEKDPRAKQIEAA 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +   ++RL  +L GQ  VSG  G  K T L+  ++++  R  W+
Sbjct: 957  QLGDYRKDLKEEYRIYEEATFARLTGLLKGQKTVSG-GGLPKGTELTDAVLADLDRELWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D  +   + S +   E   ++LE+RF+ K +K+Q GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KIKTDDAALNDQLASAQRLLEEQNTLLEERFEIKKDKLQSGDDLAPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ + G P+DIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDERGEPIDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG KI  ++        +      +            I    D  +L +AE  + 
Sbjct: 1136 MAARGLGVKINDMLEQQAKLSQLRDFLKEIYSHATDSRRDADIDSLSDQELLDLAENLRD 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++T VFDGA E+++ ++LRMAD+ +SGQ  LYDG TG+ FDRPVTVGY+YMLKLNH+
Sbjct: 1196 GVPMATAVFDGAHEDSVKALLRMADIPDSGQLKLYDGRTGDVFDRPVTVGYMYMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE+   
Sbjct: 1316 AGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLESESD 1361


>gi|289209336|ref|YP_003461402.1| DNA-directed RNA polymerase subunit beta [Thioalkalivibrio sp.
            K90mix]
 gi|288944967|gb|ADC72666.1| DNA-directed RNA polymerase, beta subunit [Thioalkalivibrio sp.
            K90mix]
          Length = 1359

 Score = 1680 bits (4350), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1365 (52%), Positives = 986/1365 (72%), Gaps = 7/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + +    R+RK FGK P+I+D+P L+E Q  SY  FL     P+ R   GL AAF+SV
Sbjct: 1    MALSYTEKKRIRKDFGKRPQILDVPYLLETQLTSYRDFLQAEKGPEARHALGLHAAFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG   LE+VSY    P FDV +C  R +TYA PL++ LRL++ D +   G+  +
Sbjct: 61   FPIVSYSGHVQLEYVSYRLGEPLFDVKECQIRGVTYAAPLRVLLRLVIHDKEAPAGSTVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS-GKLLYA 181
            K++KEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD D+G+   S  KLLY 
Sbjct: 121  KEVKEQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDRGKTQGSAQKLLYN 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD+KD ++VRIDRRRK+P +  L ALGMD+EEILSTF+     +  
Sbjct: 181  ARIIPYRGSWLDFEFDAKDGVYVRIDRRRKLPASILLRALGMDTEEILSTFFEFNQITLD 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
             D     L    L  G      + D      ++E+G+++T   ++ +++ G+  L +  +
Sbjct: 241  EDGGELDLIPERL-RGETAVVDITDGKN--VIVEAGRRITPRHIREIEKAGINRLRVPDE 297

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A+ +V+  TGE+   A D + ++ L+++    ++ +  +Y +  ++  ++ +T
Sbjct: 298  YLLGRVLAKGVVDESTGELMAAANDPLTQELLDKLRAEGVKSVETIYTNDYDHGPFMSDT 357

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D  K + +A ++IYRVMRPG+  T   AE++F+ LFF  D+YDLS VGR+K N R+ 
Sbjct: 358  LRLDPTKTQLEAQVEIYRVMRPGEPPTKDAAENLFSNLFFSEDRYDLSAVGRMKFNRRVG 417

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             DT +    +  EDI+ ++K+L+DLRNG G  DDID+LGNRR+RSVGEM +NQ+RLGL+R
Sbjct: 418  RDTDEGPGVLSPEDILDVLKVLIDLRNGNGRTDDIDHLGNRRIRSVGEMAENQFRLGLVR 477

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER++  + + +MPQ+LINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 478  VERAVKERLTVAESEGLMPQELINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 537

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETP
Sbjct: 538  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNRYGFLETP 597

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++VYLSA+EE    IAQAN+++DE G  T++LV CR   E  +   +KI
Sbjct: 598  YRKVEDGKVTDEIVYLSAIEESQYVIAQANAAMDEQGRLTDDLVSCRFQEEFTISSPDKI 657

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SPKQ+VS+AA+L+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 658  QYMDISPKQIVSVAAALLPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGIERTVAI 717

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG+AIVAKR G V+ VDA R+V+R  + +      GVDIY L K+ RSNQNT +NQRPL
Sbjct: 718  DSGSAIVAKRGGTVDSVDAARVVVRVNDDETVAGEPGVDIYNLTKYSRSNQNTSINQRPL 777

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGDE+ R D++ADG STDLG+LALG+NM+VAFMPW+GYNFEDS+LISER+V ED +T+
Sbjct: 778  VAVGDEIARGDVLADGSSTDLGELALGQNMMVAFMPWNGYNFEDSILISERVVQEDRYTT 837

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE   +ARDTKLG EEIT DIPNVSE  L  +DE G++ VGAEVNPGDILVGK+TPK
Sbjct: 838  IHIEELNCVARDTKLGQEEITADIPNVSESLLAKLDESGVVYVGAEVNPGDILVGKVTPK 897

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DVR+F R G++K+ R+ S+E 
Sbjct: 898  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGIEGTVIDVRVFTRDGVEKDARAKSIEE 957

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            + +  + +D  D+  I + +IY+R+ ++L  + A  GP+G    + ++   +    R QW
Sbjct: 958  DDLAAVKKDLKDQLRIYEDDIYARVEKLLVNKAAAGGPEGLGDGSKVTKKYLQGLSRDQW 1017

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            ++  ++D+ V   +E L  Q +    + + +F+++  K+  GDD+PPGV ++VKV+VA+K
Sbjct: 1018 FEVRLKDDAVNSQLEDLGRQLQEQHELFDKKFEHQKAKVAAGDDLPPGVQKMVKVYVAVK 1077

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG++S I+P EDMPFL+DGTPVD+VLNPLGVPSRMNVGQ+ E HL
Sbjct: 1078 RRLQPGDKMAGRHGNKGVISMIVPEEDMPFLEDGTPVDVVLNPLGVPSRMNVGQVLEVHL 1137

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG KI  ++   +A  +I+ LR FL+K+         +    D  ++ +    +
Sbjct: 1138 GWAAKGLGDKINRML---EAQAEIAKLREFLDKIYNHRDKKVDLDSMSDAEIIALCRNLR 1194

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA+E  I  MLR+ADL E+GQ+ L+DG TG+ FDRPVTVGY++MLKLNH
Sbjct: 1195 GGVPMATPVFDGAEEAEIKEMLRLADLPETGQAELFDGRTGDSFDRPVTVGYMHMLKLNH 1254

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K+DD
Sbjct: 1255 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKADD 1314

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GR ++Y++IV G    E   PESFNVL+KE++ALG++I+LE  
Sbjct: 1315 VQGRNKMYKNIVDGEHHMEANVPESFNVLMKEIKALGINIELEQD 1359


>gi|170785434|gb|ACB37713.1| RNA polymerase B' subunit [Candidatus Liberibacter asiaticus]
          Length = 1386

 Score = 1679 bits (4349), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1385/1386 (99%), Positives = 1385/1386 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIK LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKGLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD
Sbjct: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF
Sbjct: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380

Query: 1381 NKCELK 1386
            NKCELK
Sbjct: 1381 NKCELK 1386


>gi|254780143|ref|YP_003064556.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
            asiaticus str. psy62]
 gi|254039820|gb|ACT56616.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
            asiaticus str. psy62]
          Length = 1386

 Score = 1679 bits (4349), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1386/1386 (100%), Positives = 1386/1386 (100%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD
Sbjct: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF
Sbjct: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380

Query: 1381 NKCELK 1386
            NKCELK
Sbjct: 1381 NKCELK 1386


>gi|126666820|ref|ZP_01737797.1| DNA-directed RNA polymerase subunit beta [Marinobacter sp. ELB17]
 gi|126628865|gb|EAZ99485.1| DNA-directed RNA polymerase subunit beta [Marinobacter sp. ELB17]
          Length = 1358

 Score = 1679 bits (4348), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1364 (51%), Positives = 971/1364 (71%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P ++D+P L+ +Q  S+  FL    A ++R   GL AAFKSV
Sbjct: 1    MSYSYTEKKRIRKDFSKLPSVMDVPYLLSIQLDSFRDFLQSESAAEDRRETGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPIASYSGNAALEYVSYRIGEPVFDVKECQLRGVTYAAPLRVKVRLIIYDR--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L +LG  SE++L+ F+    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDAVFVRIDRRRKLPATILLRSLGYTSEQMLAMFFETSKFHIGA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L  + L  G   +  + D D G  + E G+++T+  +K L++  +  L + ++ 
Sbjct: 239  ETCKLELVPSRL-RGDIATFDIKDKD-GNVIAEEGRRITARHIKQLEKANISELEVPTEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D+++ +TGE+ +E    +  + +  I  + + DI  LY + ++   ++ +TL
Sbjct: 297  LYGRVLAKDMIDTKTGEMLVECNSELTAELITTILDAGVTDIETLYTNDLDCGPFMSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D ++   +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K+N RL  
Sbjct: 357  RNDPSRTPLEALVEIYRMMRPGEPPTKESAENLFNNLFFSEERYDLSAVGRMKLNRRLRR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +   DII +++ L+D+RNG+G +DDIDNLGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  DESTGESILTHADIIDVLRTLIDIRNGQGQVDDIDNLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVRERLSLAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR N+YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATFARANSYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++VYLSA+EE N  IAQA++ +D+     EELV  R   E  ++P E ++
Sbjct: 597  RKVADGLVTDELVYLSAIEESNYVIAQASAEMDDGNRLVEELVTVRHQNETTVMPPEAVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E +VA+ 
Sbjct: 657  FMDVSPRQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLRAQVPLVGTGVERIVAQD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G +E VDA RIV+R    + +   +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVTARRGGEIESVDAARIVVRVNNEETEAGDAGVDIYNLTKYTRSNQNTCINQRSIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD + R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+LISE++V ED  T+I
Sbjct: 777  RQGDVIARGDILADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILISEKVVQEDRLTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVSAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RVP+G  GT++DV++F R GI+K++R+  +E++
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSSRVPTGTRGTIIDVQVFTRDGIEKDQRAQVIEKQ 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  DE  I++   Y RL+  L GQ  +S P G KK + L +D +   PR +W+
Sbjct: 957  QLDKYRKDLKDEYRIVEGATYERLLNALEGQEVISSP-GLKKGSKLEADYLLNLPRPEWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ + +   +E  +   E  K   E RF +K  K+Q GDD+ PGV ++VKV++A+KR
Sbjct: 1016 KLRMKGDDLNELLEKSEQGLEERKKDHEARFDDKKGKLQQGDDLAPGVQKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S + P EDMP+ + G  VDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 SIQPGDKMAGRHGNKGVISAVKPIEDMPYDEFGNTVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG++I  ++++ +   ++  L   +            +   +D  +L +    + 
Sbjct: 1136 AAAKGLGERISRMLDEQRKVAELRKLLDEIYN-HSAEVTQVDLDSLNDREILDLCNNLRG 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  +  ML +A L  +GQ+ L+DG TG+ FDRP+TVGY+Y+LKLNH+
Sbjct: 1195 GVPMATPVFDGAQEAEVKHMLELAGLSTTGQTRLFDGRTGDAFDRPITVGYMYILKLNHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            + DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1255 IDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRTR+Y++IV G+   E G PESFNVLVKE+++LG+ I+LE+ 
Sbjct: 1315 NGRTRMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELESD 1358


>gi|304310009|ref|YP_003809607.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium HdN1]
 gi|301795742|emb|CBL43941.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium HdN1]
          Length = 1356

 Score = 1678 bits (4345), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1365 (52%), Positives = 971/1365 (71%), Gaps = 10/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG+  + +D+P L+ +Q  SY  FL ++     R ++GLQAAFKSV
Sbjct: 1    MAYSFTEKKRIRKAFGQINDAMDVPYLLAIQLDSYRKFLQLDKLAAGRGDDGLQAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A LEFV Y    P FDV +C  R  TY+ PL++ LRLI++D D  +  K+I
Sbjct: 61   FPITSYSGSAALEFVEYVLGEPAFDVKECQLRGATYSAPLRVKLRLIIYDKDSPS--KAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++VRIDRRRK+P T  L ALG +SE+IL  F+         
Sbjct: 179  RIIPYRGSWLDFEFDPKDLVYVRIDRRRKLPATVLLRALGYESEQILELFFDTNKVLVES 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      +   DT   V+ESG+++T+  ++ L++  ++ L +  + 
Sbjct: 239  GEFKLELIPERL-RGETALFDIKAGDT--VVVESGRRITARHIRQLEKAELRSLLVPKEY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ +++  TGE+       + ++ L+++    +     LY + ++   ++ +TL
Sbjct: 296  LVGKVLAKGVIDRSTGEVIAPCNAEVTDELLDKLVGLSVTSFETLYTNELDRGPFLSDTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+     +AL++IYR+MRPG+  T   AE +F  LFF +++YDLS VGR+K N RL  
Sbjct: 356  RTDQTTSALEALVEIYRMMRPGEPPTKDAAEGLFKNLFFSAERYDLSAVGRMKFNRRLGR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + +EDI+A++K LV +RNG+G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 416  KETTGEGTLSREDIVAVLKTLVAIRNGQGVVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLSLAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR N YGF+E+PY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAAFARANDYGFLESPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G+ T++VV+LSA+EE    +AQA++ LDE+G+  E+LV  R   E  +   E ++
Sbjct: 596  RKVTNGRATDEVVFLSAIEESEYMVAQASAELDEEGNLVEDLVPVRHKNEFTVTTTENVE 655

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA+ 
Sbjct: 656  YMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMEGTVARD 715

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G++++VDA RIV+R  E ++    +GVDIY L KF RSNQNTC+NQ+PLV
Sbjct: 716  SGVCVVAKRGGLIDRVDASRIVVRVNEDEITDGEAGVDIYSLTKFTRSNQNTCINQKPLV 775

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V RNDI+ADGPS D+G+LALG+NM VAFMPW+GYNFEDS+++SER+V ED FT+I
Sbjct: 776  HVGDRVARNDILADGPSVDIGELALGQNMRVAFMPWNGYNFEDSIMLSERVVQEDRFTTI 835

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNVSE  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 836  HIQELTCVARDTKLGPEEITADIPNVSESALAKLDEAGVVHIGAEVAAGDILVGKVTPKG 895

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG SGTV+DV++F R G++K++R++ +E  
Sbjct: 896  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGTSGTVIDVQVFTRDGVEKDQRALQIENA 955

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE   +D +DE  I+      RL + L  +    G  GFK+   L+ +L+     S  +
Sbjct: 956  EIEKYRKDLNDEFRIIQIATVQRLKKALLDRRVNGG-AGFKRGDSLTQELLEGLDNSALF 1014

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE    ++E  K   +  +S  E +  NK  KI  GDD+  GVL++VKV++A+KR
Sbjct: 1015 ELRLADEDAAESLEKAKAYLDEVRSEQERKLANKKRKITTGDDLAHGVLKIVKVYLAIKR 1074

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS I+P EDMP  ++G  VD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1075 RVQPGDKMAGRHGNKGVVSVIMPIEDMPHDENGVAVDVVLNPLGVPSRMNVGQILETHLG 1134

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG++I  ++ + +   +I  +R FL++V          +    DD V  +A   +
Sbjct: 1135 LAARGLGERINRMLEEQR---EIFEIREFLDRVYNGDKQTRVNLKSLTDDEVRTLATNLR 1191

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++T VFDGA E+ I  MLR+A   ESGQ  L+DG TGE F+  VTVGY+YMLKLNH
Sbjct: 1192 AGVPMATLVFDGAKEQEIKEMLRLAGQPESGQMDLFDGRTGEKFNCKVTVGYMYMLKLNH 1251

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLTIKSDD
Sbjct: 1252 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTIKSDD 1311

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRTRVY++IV G+   E G PESFNVLVKE+++LG+ I+LE  
Sbjct: 1312 VNGRTRVYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELEQD 1356


>gi|254490640|ref|ZP_05103825.1| DNA-directed RNA polymerase, beta subunit [Methylophaga thiooxidans
            DMS010]
 gi|224464096|gb|EEF80360.1| DNA-directed RNA polymerase, beta subunit [Methylophaga thiooxydans
            DMS010]
          Length = 1358

 Score = 1677 bits (4344), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1364 (52%), Positives = 973/1364 (71%), Gaps = 6/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P ++++P+L+  Q  SY  FL + +A DER  +GL AAF+SV
Sbjct: 1    MAYTFTEKKRIRKDFGKRPSVLNVPNLLATQVNSYQDFLQLGVAADERGAKGLHAAFESV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A L++VSY    P FDV +C  R +TYA PL++ +RL+++D D     K +
Sbjct: 61   FPIKSHTGMAELQYVSYRLGTPSFDVKECQLRGVTYAAPLRVKMRLVIYDKDAPAKQKVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT+ G FVI G +R++VSQLHRSPG+ FD D+G+   SGK+LY  
Sbjct: 121  KDIKEQEVYMGEIPLMTEKGNFVINGTERVIVSQLHRSPGVFFDSDRGKTHSSGKILYNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG  ++E+L  F+    + ++G
Sbjct: 181  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPATILLRALGYSNQEMLEIFFSNDSFVKKG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L    L  G  V   +VD D GE ++E+ +++T   ++ +++ G+  L + ++ 
Sbjct: 241  DNFEMALEPQRL-RGQSVPFDIVDPD-GEVIVEAERQITGRHIRRMEKAGMNSLTVPTNF 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D+++ ETGE+   A D I +  LE     +I +I  +Y + +++  ++ +TL
Sbjct: 299  LVGKVLAKDMIDPETGELLAAANDEITDDLLEAFARFDINEIDTIYSNDLDDGPFMSDTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+ +   +A ++IYR+MRPG+  T   AE++F  LFF  D+YDLS+VGR+K N RL  
Sbjct: 359  RLDETRSALEAKIEIYRMMRPGEPPTEDAAENLFTSLFFTMDRYDLSSVGRMKFNRRLGR 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + KEDI+A+++ L+ +RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 419  EELEGEGTLAKEDILAVLRELIAIRNGNGIVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQ LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 479  ERAVRERLSIAESEGLMPQQLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGFIETPY
Sbjct: 539  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFIETPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGK T D+VYLSA++E    IAQA   L++D S  E +V CR   E  L+P E++ 
Sbjct: 599  RKVIDGKATTDIVYLSAIDEGEYKIAQATIELNDDNSIAENMVHCRYRNESSLMPSEQVQ 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E VVAK 
Sbjct: 659  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIERVVAKD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G V+ VDA RIVIR  + + +   SGVDIY L+K+ RSNQ+TC+NQRP+V
Sbjct: 719  SGVMVTAKRGGTVDSVDASRIVIRVNDDEAEAGESGVDIYNLIKYARSNQSTCINQRPIV 778

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD +   D++ADGPSTD G+LALG+N+LVAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 779  KPGDVIASGDVLADGPSTDKGELALGQNILVAFMPWNGYNFEDSILVSERVVEEDRFTTI 838

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EE+T DIPNVSE  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 839  HIQELNCLARDTKLGTEEVTSDIPNVSESALSKLDESGIVYVGAEVKPGDILVGKVTPKG 898

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+ER+  +E+ 
Sbjct: 899  ETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTYGTVIDVQVFTRDGVEKDERTQEIEKA 958

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++E +  D  D+  I+  +++ RL   L G+ A +GP   KK T L+   +     ++W+
Sbjct: 959  ELEKVWADLKDQNRIMTEDVFERLERNLVGKVAEAGP-DLKKGTKLTKAYLQGLEHAKWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ E +   +E      +  +  +E+ F  K EK+  G D+ PGV R+VKVF+A+KR
Sbjct: 1018 DIRMESEDLNTLLEQANTHLKQYRQEMEEAFGIKKEKLTSGHDLAPGVQRMVKVFLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+  DG PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1078 RIQPGDKMAGRHGNKGVISNIVPVEDMPYTADGRPVDIVLNPLGVPSRMNIGQILEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG KI+ ++   K    ++ LR FL KV  T    E +    DD ++ +A+  + 
Sbjct: 1138 WAAKGLGYKIEEMLQQQKG---MAELREFLGKVYNTSGTKEDLDSLTDDEIIELAKNLQG 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I  ML +A L  SGQ+ + DG TGE F RPVT+GY++MLKLNH+
Sbjct: 1195 GVPMATPVFDGAQENEIKDMLELAGLPRSGQAQMIDGRTGEFFHRPVTIGYMHMLKLNHL 1254

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KSDDV
Sbjct: 1255 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKSDDV 1314

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESF VL +E+++LG+ +DL + 
Sbjct: 1315 NGRTKIYKNIVDGDYRMDAGMPESFKVLTREIRSLGIDVDLVDE 1358


>gi|326793551|ref|YP_004311371.1| DNA-directed RNA polymerase subunit beta [Marinomonas mediterranea
            MMB-1]
 gi|326544315|gb|ADZ89535.1| DNA-directed RNA polymerase subunit beta [Marinomonas mediterranea
            MMB-1]
          Length = 1366

 Score = 1677 bits (4343), Expect = 0.0,   Method: Composition-based stats.
 Identities = 728/1371 (53%), Positives = 988/1371 (72%), Gaps = 12/1371 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY  FL       ER   GL  AFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPPVLDVPYLLAIQLESYRKFLQEGKDLAEREELGLHGAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ +FSG A LE+V Y    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPMVSFSGNAALEYVDYRLGKPVFDVKECQLRGVTYAAPLRVRVRLIIYDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL++ 
Sbjct: 119  KDIREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLHSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+PV+  L ALG  +EEIL TF+  + +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDCVFVRIDRRRKLPVSILLRALGYKTEEILDTFFDTVRFYLSK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L A+ L  G      +VD   GE ++E G+++T+  ++++ + G++ L I  + 
Sbjct: 239  DGFEMDLVASRL-RGETALFDIVDG-NGEIIVEEGRRITAKHIRAMDKAGLERLSIPLEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+++V+  TGE+  EA   +    LE +  S I++I +LY + +++  +I +TL
Sbjct: 297  ILGKVSAKNLVHPATGELIAEANTELSVDLLEALVGSGIKEIDVLYTNDLDHGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS+VGR+K N RL  
Sbjct: 357  RIDPTNNQLEALVEIYRMMRPGEPPTKESAEGLFQGLFFAEERYDLSSVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  EDIIA++K L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  DEDKGPGILDNEDIIAVLKTLLDIRNGNGMVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + D +MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAEADGLMPQDLLNAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSTYARTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGK+T++ VY+SA++E    IAQA+ ++DE+G   +ELV  R   E  L+ +EK++
Sbjct: 597  RKVVDGKMTDETVYVSAIDEAKYVIAQASVNVDEEGRLVDELVQVRHMHETTLLAKEKVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VAK 
Sbjct: 657  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKADKPVVGTGMERNVAKD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVA+R G++E VDA RIV+R    +     +GVDIY L K+ RSNQNTC+NQR LV
Sbjct: 717  SGVCIVARRGGVIESVDASRIVVRVNSEETLAGEAGVDIYNLTKYVRSNQNTCINQRTLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G++V   DI+ADGPS D+GDLALG+NM +AFMPW+G+NFEDS+L+SER+V ED FTSI
Sbjct: 777  MKGEKVASGDIMADGPSVDMGDLALGQNMRIAFMPWNGFNFEDSILVSERVVEEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +D  G++ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEGALSKLDSSGVVYIGAEVEPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RV +G  GTV+DV++F R GI+K+ER+ S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSQRVKTGTRGTVIDVQVFTRDGIEKDERAKSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I+++  + RL E L GQ A  GP G  ++ +++ D ++     +W+
Sbjct: 957  QLDQVRKDLNEEFRIVEKATFERLAEALVGQQAEGGP-GLARNAIITEDYLANLDHPEWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  V  E     +E  +      +  L+ +F++K  K+Q GDD+ PGVL++VKV+VA+KR
Sbjct: 1016 KIRVASEDASEQLEKAQAALIERRKELDAKFEDKKRKLQTGDDLAPGVLKIVKVYVAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISKIMPVEDMPYDENGDPVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIG------TGSHTEKISDYDDDSVLR 1195
             A  GLG+KI  +I   +   + +  LRSFL +V          +  E +  + DD +L 
Sbjct: 1136 AAAKGLGRKINEMIQIEREKAETVQELRSFLGEVYNGHEDGLRSARVEDLDSFTDDEILT 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A   K GVP+++  FDGA E  I  MLR+A L+ESGQ  L++G TG+ F+RPVTVGY+Y
Sbjct: 1196 LASNLKGGVPMASGAFDGAKEAEIKRMLRLAGLNESGQIKLFNGRTGDAFERPVTVGYMY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LEN 
Sbjct: 1316 TVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELENE 1366


>gi|149185503|ref|ZP_01863819.1| DNA-directed RNA polymerase 140 kDa subunit [Erythrobacter sp. SD-21]
 gi|148830723|gb|EDL49158.1| DNA-directed RNA polymerase 140 kDa subunit [Erythrobacter sp. SD-21]
          Length = 1393

 Score = 1677 bits (4343), Expect = 0.0,   Method: Composition-based stats.
 Identities = 811/1376 (58%), Positives = 1053/1376 (76%), Gaps = 16/1376 (1%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                R+RK FG   E++D+P+LIEVQ+ SY+ FL  + A       GL+   +SVFP+  
Sbjct: 15   TAKRRIRKIFGDIHEVVDMPNLIEVQRESYEQFLRSDKATGHVS--GLEKTLRSVFPLRD 72

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            F+G A L+FV YE + PK+D+ +C  R +TYA P+K+TLRLIVF+VD+ T  +S+ DIKE
Sbjct: 73   FAGTAELDFVHYELEAPKYDIVECHQRGITYAAPMKVTLRLIVFEVDQETETRSVLDIKE 132

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGKLL+A RIIP 
Sbjct: 133  QDVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVLFDHDRGKTHSSGKLLFAARIIPY 192

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+D EFD+KD+++VRIDR+RK+PVT+ L +LG+D+E+ILS FY K+ + +  D W  
Sbjct: 193  RGSWLDFEFDAKDVVNVRIDRKRKLPVTALLYSLGLDAEDILSHFYDKVTWKRAKDGWEL 252

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P  A +     K +  LVD  TGE+V  +G+K++        + G++ L + ++ + G Y
Sbjct: 253  PFVAEN-WRNQKPAFPLVDAKTGEEVFPAGQKISPRAANKAAKDGLETLLLPTEEIFGRY 311

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             +ED+++  TG IYIEAGD +  ++LE +  + +  + +L +D VN   +IRNT+  DK 
Sbjct: 312  ASEDLIDESTGRIYIEAGDEVSAENLEVLDAAGVDSLELLDIDHVNTGPWIRNTMKVDKA 371

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            ++R + L  IY+VMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL LD  D 
Sbjct: 372  ENRDEGLEAIYKVMRPGEPPTKETAEALFEGLFFDGERYDLSAVGRVKLNMRLELDAEDT 431

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            V  +RKEDI+A++K LVDL++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++K
Sbjct: 432  VTTLRKEDILAVVKELVDLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVK 491

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG G
Sbjct: 492  ERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPG 551

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIETPYRKV D
Sbjct: 552  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIETPYRKVKD 611

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             KVT++V+YLSAMEE+   +AQA++ LDE+G F EELV  R  G+ ++ PRE I  +D S
Sbjct: 612  NKVTDEVIYLSAMEEQKHTVAQASADLDENGGFVEELVSARQNGDNLMAPRETITLMDVS 671

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+ ASLIPFLENDD+NR LMG NMQRQAVPL++AEAP+VGTGME  VA+ SGAAI
Sbjct: 672  PKQLVSVGASLIPFLENDDANRALMGANMQRQAVPLVQAEAPWVGTGMEETVARDSGAAI 731

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AKR G+V+QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQ+TC+NQRPLVKVG+ 
Sbjct: 732  TAKRGGVVDQVDATRIVIRA-IGDVEPGQSGVDIYTLQKFQRSNQDTCINQRPLVKVGET 790

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V   D+IADGPSTDLG+LALGRN LVAFMPW+GYN+EDS+LISER+V +DVFTSIHIEEF
Sbjct: 791  VEPGDVIADGPSTDLGELALGRNTLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIEEF 850

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDIL GKITPKGESPMT
Sbjct: 851  EVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILAGKITPKGESPMT 910

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGI+ ++R+ +++ E+IE L
Sbjct: 911  PEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIEIDDRTRAIQNEEIERL 970

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D  DE+ IL+R  Y+RL ++L GQ A + PKG KK + ++ +++    + +W++FAV 
Sbjct: 971  RKDAADERAILNRATYNRLRDMLVGQTASAAPKGVKKGSEITEEVLEGVDKHEWFKFAVA 1030

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D+  Q+ +E++K QY+ S  +++D+F+++ EK++ GD++ PGVL++VKVFVA+KR +Q G
Sbjct: 1031 DDNRQQQIEAVKSQYDESVKVIDDKFEDRKEKLERGDELAPGVLKMVKVFVAVKRKLQPG 1090

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP EDMPFL DGTPVDIVLNPLGVPSRMNVGQIFETHLG A   
Sbjct: 1091 DKMAGRHGNKGVISRILPVEDMPFLADGTPVDIVLNPLGVPSRMNVGQIFETHLGMAARN 1150

Query: 1148 LGKKIKSLINDYKANGDI-----------SPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            LG +I   + D+K                  +   L  V G   + E +     + ++ +
Sbjct: 1151 LGMQIGEQLEDWKKANPNASEDYAKAKPPEAVIERLNDVYGDR-YAEDLKARSTEEIVEL 1209

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A   + GVP+ TPVFDGA E  +   L  A LD  GQS+L+DG TGE FDR VTVG IYM
Sbjct: 1210 ASNLRFGVPMGTPVFDGAREGDVTVELERAGLDADGQSVLFDGRTGEAFDRKVTVGIIYM 1269

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LT
Sbjct: 1270 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEILT 1329

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            +KSDDV+GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L++       
Sbjct: 1330 VKSDDVIGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELKSLADDEDD 1385


>gi|119502915|ref|ZP_01625000.1| DNA-directed RNA polymerase subunit beta [marine gamma
            proteobacterium HTCC2080]
 gi|119461261|gb|EAW42351.1| DNA-directed RNA polymerase subunit beta [marine gamma
            proteobacterium HTCC2080]
          Length = 1363

 Score = 1676 bits (4341), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1366 (52%), Positives = 967/1366 (70%), Gaps = 5/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG   +++DIP L+ +Q  SY  F    +  D R   GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGSLAKVMDIPYLLAIQLDSYRKFTQDGVEDDARGEHGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y+   P FDVD+C+ R  TYA  L++ +RLI++D    + +KSI
Sbjct: 61   FPIASYSGNAALEYVGYKLGKPVFDVDECVLRGTTYACALRVKVRLIIYDK--ESSSKSI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 119  KDIKEQDVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD +  RIDRRRK+P T  L ALG DSEEIL+ FY    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDQVFARIDRRRKLPATVLLRALGYDSEEILAMFYETTSFQLGE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +           + G   +  +   D  + ++E G+++T+  ++ L + G+ FL    + 
Sbjct: 239  ENSNTMTLVPKRLQGEMAAFDIAIDD--KLIVERGRRITARHIRQLDDAGIDFLAAPDEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+  TGE+ +E    I E+ L  +   EI  I  LY + ++   +I +TL
Sbjct: 297  LLGRRLAKNVVDTSTGEVLVECNVEITEELLAILREKEIDTIETLYTNEIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +++  +AL++IYR+MRPG+  T   AE++F  LFF +D+YDLS VGR+K N RL  
Sbjct: 357  AGDASRNALEALVEIYRMMRPGEPPTKESAENLFQNLFFSADRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+ + +  + +EDI+ ++K LV +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  DSSEGIGTLDREDIVDVLKALVGIRNGKGVVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLEAPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G VT+D+ YLSA+ E    IAQA++ +DE   F ++L+  R   E  + P  ++D
Sbjct: 597  RKVVNGVVTDDIEYLSAINEAEHVIAQASAQMDEKNRFVDDLINVRHMNEFTIKPAAEVD 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D S KQVVSIAA+LIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTGME  VA  
Sbjct: 657  FMDVSAKQVVSIAAALIPFLEHDDANRALMGSNMQRQAVPTLVADKPLVGTGMERYVAGD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+RAG ++ VDA RIV+R    ++    S VDIY L K++RSNQNTC+NQRP+V
Sbjct: 717  SGVCKVARRAGTIDSVDASRIVVRVDADNVAKGESPVDIYNLTKYKRSNQNTCINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + R DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 777  KVGDRIDRGDILADGPSVDMGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGSEEITADIPNVGEGALGKLDESGIVYIGAEVDAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ R+  +E  
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSYKGTVIDVQVFTRDGLEKDPRAKQIENA 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +   Y+RL  +L GQ  +SG  G  K T L+  ++++  R QW+
Sbjct: 957  QLADYRKDLREELRIYEEATYARLAALLKGQTTLSG-GGLAKGTKLTDAVLADLEREQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D ++   + +     E     LE+R+++K +K+  GDD+ PGVL++VKV++A+KR
Sbjct: 1016 KLKLGDAELNDQLTAAHELLEEQNRQLEERYESKKDKLSSGDDLQPGVLKIVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ + G P+DIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDERGEPIDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG KI +++      G +      +            I   +D  +L +A+  + 
Sbjct: 1136 MAAHGLGLKINTMLEQQAKIGQLRDFLKKIYAHASDKRRDADIDSLNDTELLELADNLRK 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA EE + ++LR+AD+ +SGQ  LYDG +G+ F RPVTVGY+YMLKLNH+
Sbjct: 1196 GVPMATPVFDGAAEEEVKALLRLADIPDSGQLTLYDGRSGDTFMRPVTVGYMYMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE+   
Sbjct: 1316 AGRTKMYKNIVDGDHKMEPGMPESFNVLIKEIRSLGIDIDLESESE 1361


>gi|90417542|ref|ZP_01225463.1| DNA-directed RNA polymerase beta subunit [marine gamma
            proteobacterium HTCC2207]
 gi|90330634|gb|EAS45924.1| DNA-directed RNA polymerase beta subunit [marine gamma
            proteobacterium HTCC2207]
          Length = 1380

 Score = 1676 bits (4340), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1388 (51%), Positives = 978/1388 (70%), Gaps = 32/1388 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P ++D+P L+ +Q  SY +F    +A  +R N GL AA  S+
Sbjct: 1    MAYSFTEKKRIRKNFGKLPNVMDLPYLLAIQLDSYKNFTQTGVAVGDRQNTGLHAALNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  +SG A LE+V Y    P FDV++C  R +T++VPL++ +RL+++D    +  K+I
Sbjct: 61   FPIVGYSGHAALEYVDYVLGKPAFDVEECKLRGVTFSVPLRVRVRLVIYDK--ESTNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +Y+G++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGKLLY  
Sbjct: 119  KDIREQEVYLGEIPLMTDNGTFIINGTERVIVSQLHRSPGVIFDHDKGKTHSSGKLLYTA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KDI++VRIDRRRK+P T  L ALG +SEEIL  F+   ++ Q+ 
Sbjct: 179  RVIPYRGSWLDFEFDPKDILYVRIDRRRKLPATILLRALGYNSEEILGMFFDTSIFHQKK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L    L  G      + D   G  V+E G+++T+  ++ L++  V  L + ++ 
Sbjct: 239  DGYTLELDPERL-RGEITVFDIKDKK-GAVVVEKGRRVTARHIRDLEKGKVTSLEVPAEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A DI + +TGE+ +E    I E+ LE++  + ++DI  LY + ++   +I +TL
Sbjct: 297  LLGRATANDIADPKTGELLLECNTEITEEILEQLAEAGVKDIETLYTNDLDCGPFIADTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D ++ + +AL++IYR+MRPG+  T   AE++F  LFF+ ++YDLS+VGR+K N RL+ 
Sbjct: 357  RIDPSRTQLEALVEIYRMMRPGEPPTKESAENLFYNLFFNLERYDLSSVGRMKFNRRLDR 416

Query: 423  DTPDDVRHIRKEDIIAIIKI----------------------LVDLRNGKGTIDDIDNLG 460
                    +  E   ++ K                       L+++RNGKG +DDID+LG
Sbjct: 417  VEEAGCGVLYDERYFSMQKTDEAHELFEEFGEGSDIADVMQTLINIRNGKGGVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRR+RSVGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL+NAKPV +A+ EFF SS
Sbjct: 477  NRRIRSVGEMAENQFRVGLVRVERAVKERLSMAESEELMPQDLVNAKPVAAAMKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL ++AR N+YGFIETPYRKV + KVT+ + YLSA+ E    IAQA++ L+  G F
Sbjct: 597  GLINSLATYARTNSYGFIETPYRKVVNNKVTDQIEYLSAINESQYVIAQASAKLNAKGEF 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             E++V  R   E  +     ID++D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  VEDVVNVRHQNEFTVKLPGDIDYMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L AEAP VGTG+E  VA  SG   VAKR G++E VDA RIV+R  + + +   +GVD
Sbjct: 717  VPTLLAEAPLVGTGIERPVASDSGVCKVAKRGGVIESVDAGRIVVRVSDAETESGDAGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L K+ RSNQNTC+NQRP+V  GD V R D++ADGPS DLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLTKYTRSNQNTCINQRPIVNQGDVVARGDVLADGPSVDLGELALGQNMRIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +NFEDS+LISER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE G
Sbjct: 837  FNFEDSILISERVVKEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGEVALARLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ + GTV+
Sbjct: 897  VVHIGAEVAAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTSIKGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            +V++F R G+DK++RS+ +ER +++   +D +DE  I++     RL   L G   V   +
Sbjct: 957  NVQVFTRDGLDKDQRSLDIERAELDQYRKDLNDEYRIVENATLGRLFTALVGGKVVKA-E 1015

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G KK   L++D ++EY    W+   + +  +   + + + Q    +  L++RF+ K  K+
Sbjct: 1016 GLKKGAELTADAVAEYSSDDWFAIRMDNADLNDQIAAAQTQLGERRVDLDERFEEKRRKL 1075

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            Q GDD+ PGVL+ VKV++A+KR IQ GDKMAGRHGNKG++S I P EDMP+ ++G PVDI
Sbjct: 1076 QSGDDLAPGVLKTVKVYLAVKRRIQPGDKMAGRHGNKGVISVIKPIEDMPYDENGEPVDI 1135

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GT 1178
            VLNPLGVPSRMNVGQ+ ETH+G A  GLG KI ++I   KA    + +R FL+++   G 
Sbjct: 1136 VLNPLGVPSRMNVGQVLETHMGMAAKGLGVKIDAMI---KAQSKAAEIRKFLQEIYDVGE 1192

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
              +   + +  D  VL +A   + GVP++TPVFDGA+E  +  +L +ADL ESGQ+ LYD
Sbjct: 1193 TVYGTDLKELSDKEVLELAGNLRKGVPIATPVFDGANEVELKKLLELADLHESGQTTLYD 1252

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G +G+ FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEME
Sbjct: 1253 GRSGDKFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEME 1312

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++LG
Sbjct: 1313 VWALEAYGAAYTLQEMLTVKSDDVAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEVRSLG 1372

Query: 1359 LSIDLENS 1366
            ++++LEN 
Sbjct: 1373 INMELENE 1380


>gi|107103782|ref|ZP_01367700.1| hypothetical protein PaerPA_01004853 [Pseudomonas aeruginosa PACS2]
          Length = 1336

 Score = 1676 bits (4339), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1344 (53%), Positives = 975/1344 (72%), Gaps = 9/1344 (0%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D+P L+ +Q  SY  FL      ++  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1    MDVPYLLAIQLDSYREFLQAGATKEQFRDIGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61   PAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            F+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119  FIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G+     L    L  G   S  
Sbjct: 179  VRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKGETLNLELVPQRL-RGEVASID 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            + D  +G+ ++E G+++T+  +  L++ GV  L +  D L G  +A+ IV+  TGEI  E
Sbjct: 238  IKDG-SGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPATGEIIAE 296

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                +    L ++  +++  I  LY + ++   +I +TL  D   ++ +AL++IYR+MRP
Sbjct: 297  CNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRP 356

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++F  LFF +++YDLS VGR+K N R+     +    + KEDII ++K L
Sbjct: 357  GEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTL 416

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417  VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 477  INAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHP 536

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE 
Sbjct: 537  THYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEA 596

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            +  IAQA+++L+E G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE
Sbjct: 597  DHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA R+
Sbjct: 657  HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRV 716

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V R DI+ADGPSTD+G
Sbjct: 717  VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMG 776

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 777  ELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 836

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 837  DIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 896

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ Q++ + +D ++E  I++   +
Sbjct: 897  VKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKMQLDQIRKDLNEEFRIVEGATF 956

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             RL   L G  A  GP   KK T ++ D +    R QW++  + D+ +   +E  +    
Sbjct: 957  ERLRAALVGAKAEGGPA-LKKGTEITDDYLDGLERGQWFKLRMADDALNEQLEKAQAYIS 1015

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K  K+Q GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG+VS I
Sbjct: 1016 DRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVI 1075

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 1076 MPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQR--- 1132

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++ LR FL ++    G   E + +  D+ +L +A+  + GVP++TPVFDGA E  I +M
Sbjct: 1133 KVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLRGGVPMATPVFDGAKEREIKAM 1192

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++ADL ESGQ  L+DG TG  F+RP TVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 1193 LKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 1252

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 1253 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAG 1312

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
             PESFNVL+KE+++LG+ I+LE  
Sbjct: 1313 MPESFNVLIKEIRSLGIDIELETE 1336


>gi|152998278|ref|YP_001343113.1| DNA-directed RNA polymerase subunit beta [Marinomonas sp. MWYL1]
 gi|189043859|sp|A6W399|RPOB_MARMS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|150839202|gb|ABR73178.1| DNA-directed RNA polymerase, beta subunit [Marinomonas sp. MWYL1]
          Length = 1366

 Score = 1676 bits (4339), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1371 (52%), Positives = 984/1371 (71%), Gaps = 12/1371 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY +FL    +  ER   GL  AFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPPVLDVPYLLAIQLESYRNFLQEGKSLAERGELGLHGAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ +FSG A LE+V Y    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPMVSFSGNAALEYVDYRLGKPVFDVKECQLRGVTYAAPLRVRVRLIIYDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL++ 
Sbjct: 119  KDIREQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLHSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  +E+IL TF+    +  + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPATILLRALGYGTEQILDTFFDSTRFYLKR 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L A + + G     ++ D   GE ++E G+++T+  ++ +++ G++ L +  + 
Sbjct: 239  DGFEMDLVA-NRLRGETALFNIADA-NGELIVEEGRRITAKHIRVMEKSGLERLSVPLEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+++V+  TGE+  EA   +    LE +  S I ++  LY + ++N  +I +TL
Sbjct: 297  MLGKVTAKNLVHPATGELIAEANTELSVDLLEALVSSGITEVDTLYTNDLDNGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N RL  
Sbjct: 357  RIDPTSNQLEALVEIYRMMRPGEPPTKESAEGLFQGLFFSEDRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI+A++K L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  EEDTGAGVLDNDDIVAVLKTLLDIRNGNGMVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + D +MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSMAEADGLMPQDLLNAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSTYARTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RK+ DGK T++ VY+SA++E    IAQA++++D +G   +ELV  R   E  L+P+EK++
Sbjct: 597  RKIVDGKQTDETVYVSAIDEAKYVIAQASANVDAEGRLVDELVQVRHMHETTLIPKEKVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VAK 
Sbjct: 657  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKADKPVVGTGMEKNVAKD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVA R G++E VDA RIV+R    +     +GVDIY L K+ RSNQNTC+NQR LV
Sbjct: 717  SGVCIVANRGGVIESVDASRIVVRVNSEETIAGEAGVDIYNLTKYVRSNQNTCINQRTLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ +   DI+ADGPS D+G+LALG+NM +AFMPW+G+NFEDS+L+SER+V ED FTSI
Sbjct: 777  MKGERIASGDIMADGPSVDMGELALGQNMRIAFMPWNGFNFEDSILVSERVVEEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +D+ GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEGALSKLDQSGIVYIGAEVEPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RV +G  GTV+DV++F R GI+K++R+  +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSQRVKTGTRGTVIDVQVFTRDGIEKDDRAKFIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I+++  + RL E L GQ A  GP G  ++ +++ + ++     +W+
Sbjct: 957  QLDQVRKDLNEEFRIVEKATFERLAEALIGQQAEGGP-GLARNAIITEEYLANLDHPEWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  V +E     +E  +      +  L+ +F++K  K+Q GDD+ PGVL++VKV+VA+KR
Sbjct: 1016 KIRVANEDASEQLEKAQAALIERRKELDAKFEDKKRKLQTGDDLAPGVLKIVKVYVAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISKIMPVEDMPYDENGDPVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTGS------HTEKISDYDDDSVLR 1195
             A  GLG+KI  ++   +   + ++ LRSFL ++            TE +  + D+ +L 
Sbjct: 1136 AASKGLGRKINEMLVVEREKAEAVAELRSFLGEIYNGYEGDLRCARTEDLDSFTDEEILT 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A     GVP+++  FDGA E  I  MLR+A ++ESGQ  L++G TG+ F+RPVTVGY+Y
Sbjct: 1196 LASNLTGGVPMASGAFDGAKESEIKRMLRLAGINESGQVKLFNGRTGDAFERPVTVGYMY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LEN 
Sbjct: 1316 TVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELENE 1366


>gi|54296358|ref|YP_122727.1| DNA-directed RNA polymerase subunit beta [Legionella pneumophila str.
            Paris]
 gi|81371224|sp|Q5X866|RPOB_LEGPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|53750143|emb|CAH11535.1| RNA polymerase B-subunit [Legionella pneumophila str. Paris]
          Length = 1368

 Score = 1675 bits (4338), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1364 (53%), Positives = 995/1364 (72%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  +I+ IP+L+E+Q  SY  FL  +    E+ N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQTDIMPIPNLLEIQLKSYRDFLQTDTKLSEQLNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL+V D D     K IK
Sbjct: 69   PIESFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKDASDDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFV+ G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVVNGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PV+  L ALG ++E+ILS F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYEAEDILSEFFETTRCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDIHVPETGELIVEQGRRITARHIKQMEKSQMQDLVVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE   +A D I E+ L+ + +  I  I ++Y + +++ +YI +TL 
Sbjct: 308  IGKTLAKNIIDTSTGEFLAQANDEITEELLDAMANHGILQIDMIYTNDLDHGSYISDTLK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+ + 
Sbjct: 368  IDPTGSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGIK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            + +    + KEDI+++IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  SDEGPGTLTKEDILSVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT++V YLSA+EE ++YIAQ+N  LD  G+   +LV CR   E  L   +KI++
Sbjct: 608  KVVNGRVTDEVEYLSAIEEVDQYIAQSNVELDAQGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+V 
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVS 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVHDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEV  GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGTEEITADIPNVGESALSNLDESGVVYIGAEVKAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  +L  + A  GP   K  + ++ D + +  R +W+ 
Sbjct: 968  LARVRKDLIDERRIREEDIYHRVSHLLLDKVATGGPGSLKPGSKITQDYLDKVEREKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ V + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRIEDDAVSQQLEQLSKQLELLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG+KI  ++++ +    I   +++LEK+    G     +   +DD ++ +A+  ++
Sbjct: 1148 AAKGLGRKIAQMLDERQTPEAI---KAYLEKIYNHDGVQRVNLKCLNDDELMTLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E+ I SML++ADL   G+++L DG TG  FD  VTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGATEQEIKSMLQLADLPADGKTVLIDGRTGNKFDNTVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|117924148|ref|YP_864765.1| DNA-directed RNA polymerase subunit beta [Magnetococcus sp. MC-1]
 gi|158512330|sp|A0L5W6|RPOB_MAGSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|117607904|gb|ABK43359.1| DNA-directed RNA polymerase subunit beta [Magnetococcus sp. MC-1]
          Length = 1360

 Score = 1674 bits (4334), Expect = 0.0,   Method: Composition-based stats.
 Identities = 742/1365 (54%), Positives = 1017/1365 (74%), Gaps = 5/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    R+RK FG+   IIDIP+LI VQK S+  FL      ++  + GL   F SV
Sbjct: 1    MALTFTEKKRLRKNFGRISSIIDIPNLISVQKESFVRFLQTGTEFEKMKDTGLHGVFLSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G   LE+VSY    PK+DVD+CL R +T++ PLK+  RL+++D +E TG K++
Sbjct: 61   FPIHDYAGTVSLEYVSYALGEPKYDVDECLQRGMTFSAPLKVAFRLVIWDENEETGTKTV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++IKEQ +Y+G++PLMT  GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGKLL++ 
Sbjct: 121  REIKEQDVYLGEIPLMTNTGTFIINGTERVIVSQMHRSPGVFFDHDRGKTHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  RIDRRRK+PVT+ L A+GM SE+IL  FY    + + G
Sbjct: 181  RVIPYRGSWLDFEFDPKDLLFARIDRRRKLPVTTLLRAMGMSSEQILERFYEIETFRKEG 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              W   +    LM G +++ ++V  ++GE+++++ K++T+  +K  +E G+ +L ++ + 
Sbjct: 241  VVWQKRMVPERLM-GNRLNYAIVHPESGEEIVKAKKRVTARHIKKFEELGMDWLPVSQEE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G +VA ++ +   GE+ IEAG  I E+ ++ +    I++I +L++D ++  AY+RNTL
Sbjct: 300  LIGSFVARNMSDVM-GEVVIEAGAEITEEMVQYLEDGGIKEIDVLFIDGMSVGAYLRNTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DKN  + +AL+DIYR+MRPG+  T   A+++FN LFF+SD+YDLSTVGR+KMN RL+L
Sbjct: 359  ALDKNSGQDEALIDIYRMMRPGEPPTVDAAKALFNNLFFNSDRYDLSTVGRLKMNSRLSL 418

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +T   +R ++ +DI+ ++ IL+ L++G G +DDID+LGNRRVRSVGE+L+NQ R+GL+RM
Sbjct: 419  NTELHIRTLQHDDILGVVDILLKLKDGHGKVDDIDHLGNRRVRSVGELLENQVRIGLVRM 478

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+I+ER+SS + D ++P D++N+KP  + + EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 479  ERAIRERMSSAEADQLVPHDVMNSKPFSAVIREFFGSSQLSQFMDQTNPLSEITHKRRLS 538

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++AR+N +GFIE+PY
Sbjct: 539  ALGPGGMTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARINEFGFIESPY 598

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G   + V +LSA++EEN  IAQAN+ L ++ S  + L+ CR   E ++   ++++
Sbjct: 599  RQVKEGTPIDQVDFLSAIDEENYIIAQANAKLGDEASEEDALIQCRHKLEFMVATPDRVN 658

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            + D SPKQ VS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +AP VGTG+ESVVA+ 
Sbjct: 659  YQDVSPKQTVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPLVGTGIESVVARD 718

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  I A+R G+V++VDA RIV+++ E     +  GVDIY L KF RSNQNTC+NQ PLV
Sbjct: 719  SGVTITARRTGVVDEVDAARIVVKADEEPG-STEPGVDIYNLTKFSRSNQNTCINQVPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K G+ V   DIIADGPST +G+LALGRN+LVAFMPW+GYNFEDS+LISER+V+EDVFTSI
Sbjct: 778  KNGERVTAGDIIADGPSTQIGELALGRNVLVAFMPWNGYNFEDSILISERLVAEDVFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+EFEVMARDTKLG EEITRD+PNV E+ L+N+DE GII VGAEV PGDILVGK+TPKG
Sbjct: 838  HIDEFEVMARDTKLGAEEITRDMPNVGEDALRNLDESGIIYVGAEVKPGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVVDVR+F+R G++K++R+  ++++
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVDVRVFSRRGLEKDDRAKLIDQD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +I LL +D   E+ I++R+   R+  ++ G+   S P G +    +S   + + P S   
Sbjct: 958  EIALLRKDMAAERRIIERDADERIRNLMNGKPVRSAP-GLQPGDHISQSWLDKSPSSHLR 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D+ + + +E ++   E +   L+ RF++K+EK++ GDD+PPGVL++VKV++A+KR
Sbjct: 1017 DVVLDDDAITQQIEGIRHHVEKAADRLKKRFESKVEKLERGDDLPPGVLKMVKVYIAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+I P EDMP++ +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1077 KLQPGDKMAGRHGNKGVISKINPLEDMPYMANGTPVDIVLNPLGVPSRMNVGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+G KI+  +  ++       LR   E++      + +I+   DD ++ +A+  + 
Sbjct: 1137 WAARGMGFKIEEALKQHRKGV-ADVLRRQFEEIYDNTRESAEIAALSDDQLVDMAKNLQY 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TPVFDGA E  I+S L  A L  SGQ  L DG TGEPFDR VTVGYIYMLKL+H+
Sbjct: 1196 GVPTATPVFDGAIESDISSWLNKAGLPTSGQIQLIDGRTGEPFDRHVTVGYIYMLKLHHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++YESIV G+DTFE G PESFNVLVKE+QAL L + L+   
Sbjct: 1316 AGRTKIYESIVKGDDTFEAGVPESFNVLVKELQALALDVTLQRDD 1360


>gi|87122756|ref|ZP_01078630.1| DNA-directed RNA polymerase beta subunit [Marinomonas sp. MED121]
 gi|86161984|gb|EAQ63275.1| DNA-directed RNA polymerase beta subunit [Marinomonas sp. MED121]
          Length = 1366

 Score = 1674 bits (4334), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1369 (52%), Positives = 991/1369 (72%), Gaps = 12/1369 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY +FL       ER + GL  AFKSV
Sbjct: 1    MAYSYTERKRIRKDFGKLPPVLDVPYLLAIQLESYRNFLQEGKPLAERGDLGLHGAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ +FSG A LE+V Y    P FDV +C  R +TYA PL++ +RLI++D    +  K+I
Sbjct: 61   FPMVSFSGNAALEYVDYRLGKPVFDVKECQLRGVTYAAPLRVRVRLIIYDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGKLL++ 
Sbjct: 119  KDIREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLHSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+PVT  L ALG ++E+IL TF+    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDCVFVRIDRRRKLPVTILLRALGYNTEQILETFFETTKFYLGR 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L A + + G     ++ D + G+ ++E G+++T+  ++++ + GV+ L +  + 
Sbjct: 239  DGFEMELIA-NRLRGETAMFNITDTE-GKVIVEEGRRVTAKHIRAMDKAGVERLSVPLEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A ++V+  TG +  EA   +  + LE +  + I++I  LY + +++  +I +TL
Sbjct: 297  MLGKVTATNLVDSATGALISEANTELTVELLEALVAAGIKEIETLYTNDLDHGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +  +AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N RL  
Sbjct: 357  RIDPTNNPLEALVEIYRMMRPGEPPTKESAEGLFQGLFFTEDRYDLSGVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DI+A++K L+D+RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  DEDTGAGILDNDDIVAVLKTLLDIRNGNGMVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + D +MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSMAEADGLMPQDLLNAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSTYARTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGK+T++ VY+SA++E    IAQA+  +DE+G  T+ELV  R   E  L+ +EK++
Sbjct: 597  RKVVDGKMTDETVYVSAIDEAKYVIAQASVKVDEEGRLTDELVQVRHMHETTLIQKEKVN 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VAK 
Sbjct: 657  LMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKADKPVVGTGMERNVAKD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVA+R G++E VDA RIV+R    +     +GVDIY L K+ RSNQNTC+NQR LV
Sbjct: 717  SGVCIVARRGGVIEAVDASRIVVRVNSEETLAGEAGVDIYNLTKYVRSNQNTCINQRTLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V   DI+ADGPS D+G+LALG+NM +AFMPW+G+NFEDS+L+SER+V ED FTSI
Sbjct: 777  MKGENVASGDIMADGPSVDMGELALGQNMRIAFMPWNGFNFEDSILVSERVVEEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +D+ GI+ +GAEV PGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEITADIPNVGEGALSKLDQSGIVYIGAEVEPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RV +G  GTV+DV++F R GIDK+ER+ S+E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSQRVKTGTRGTVIDVQVFTRDGIDKDERAKSIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I+++  + RL E L GQ    GP G  K++++S+D +     S+W+
Sbjct: 957  QLDQVRKDLNEEFRIVEQATFERLAEALVGQTVEGGP-GLAKNSIISADYLEALEHSEWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  V DE     +E  +      +  L+ +F++K  K+Q GDD+ PGVL++VKV+VA+KR
Sbjct: 1016 KIRVVDETASEQLEKAQAALVERRKDLDAKFEDKKRKLQSGDDLAPGVLKIVKVYVAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I+P EDMP+ ++G PVDIVLNPLGVPSRMNVGQ+ ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISKIMPVEDMPYDENGDPVDIVLNPLGVPSRMNVGQVLETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTGS------HTEKISDYDDDSVLR 1195
             A  GLG+KI  ++   +   + ++ LR+FL++V            +E++  + DD ++ 
Sbjct: 1136 AASKGLGRKINEMLEVEREKAEHVAELRTFLDEVYNGHEGGVQCARSEELDSFSDDEIME 1195

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A   K G+P+++  FDGA E  I  MLR+A ++ESGQ  L++G TGE F+RPVTVGY+Y
Sbjct: 1196 LAANLKGGIPMASGAFDGAKESEIKRMLRLAGINESGQIKLFNGRTGESFERPVTVGYMY 1255

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEML
Sbjct: 1256 MLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1315

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            T+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LE
Sbjct: 1316 TVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELE 1364


>gi|161505364|ref|YP_001572476.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866711|gb|ABX23334.1| hypothetical protein SARI_03509 [Salmonella enterica subsp. arizonae
            serovar 62:z4,z23:--]
 gi|322717103|gb|EFZ08674.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Choleraesuis str. A50]
          Length = 1380

 Score = 1674 bits (4334), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 39   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 94

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 95   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 152

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 153  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 212

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 213  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 272

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 273  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 329

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 330  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 389

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 390  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 449

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 450  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 509

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 510  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 569

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 570  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 629

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 630  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 689

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 690  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 749

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 750  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 809

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 810  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 869

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 870  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 929

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 930  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 989

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 990  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 1036

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1037 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1096

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1097 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1156

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1157 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1216

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1217 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1276

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1277 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1336

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1337 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1380


>gi|326386255|ref|ZP_08207879.1| DNA-directed RNA polymerase subunit beta [Novosphingobium
            nitrogenifigens DSM 19370]
 gi|326209480|gb|EGD60273.1| DNA-directed RNA polymerase subunit beta [Novosphingobium
            nitrogenifigens DSM 19370]
          Length = 1391

 Score = 1673 bits (4332), Expect = 0.0,   Method: Composition-based stats.
 Identities = 811/1383 (58%), Positives = 1058/1383 (76%), Gaps = 17/1383 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FG   E++ +P+LIEVQ+ SY+ FL  +  P      GL+   +SVFPI  F+
Sbjct: 16   KKRIRKIFGDIHEVVQMPNLIEVQRESYEQFLRSD--PATGYVSGLEKTLRSVFPIQDFA 73

Query: 70   GAAMLEFV---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            G A L+      Y  + PK+DV++C  R +TYA P+K+TL+L  F+VD  T  KS+ DIK
Sbjct: 74   GTASLDIKEKDGYVLEAPKYDVNECRQRGITYAAPMKVTLKLATFEVDAETETKSLIDIK 133

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            EQ +YMGD+PLMT +GTF I G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A R+IP
Sbjct: 134  EQDVYMGDIPLMTDNGTFFINGTERVIVSQMHRSPGVLFDHDRGKTHSSGKYLFAARVIP 193

Query: 187  DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
             +G W+D EFD+KDI++VRIDR+RK+PVTS L ALG++ E+IL  FY K+ + +    W 
Sbjct: 194  YRGSWLDFEFDAKDIVNVRIDRKRKLPVTSLLYALGLNGEQILDHFYSKVTWVRADGGWR 253

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             P    D   G K +  +VD  +GE +  +G+K++        + G+++L I ++ + G 
Sbjct: 254  VPFV-LDQWRGVKPTFDIVDAKSGEVIFPAGQKISPRSANKAAKDGLEYLLIPTEEIFGR 312

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            + A D+++  TG I+IEAGD +  ++L+ +    +  + +L +D V    +IRNT+  DK
Sbjct: 313  FSALDLIDETTGRIWIEAGDEVTPENLDVLDQVGVDRLELLDIDHVTTGPWIRNTMKADK 372

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             +DR  AL DIYRVMRPG+  T   AE++F+ LFFD+D+YDLS VGRVK+NMRL LD  D
Sbjct: 373  AEDRDHALADIYRVMRPGEPPTRETAEALFDGLFFDNDRYDLSAVGRVKLNMRLGLDCAD 432

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             +  +R +DI+A++K LV+L++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++
Sbjct: 433  TITTLRTDDILAVVKELVNLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAV 492

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 493  KERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGP 552

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIETPYRKV 
Sbjct: 553  GGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIETPYRKVI 612

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DGKVT DVVYLSAMEE+   +AQA+++++EDGSF EEL+  R  GE ++ PR+ +  +D 
Sbjct: 613  DGKVTRDVVYLSAMEEQKHTVAQASAAVNEDGSFVEELISARQNGEFVMAPRDTVTLMDV 672

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+KA+APFVGTGME  VA+ SGAA
Sbjct: 673  SPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKADAPFVGTGMEETVARDSGAA 732

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            I A R GIV+QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQNTC+NQRPLVKVGD
Sbjct: 733  IAALRGGIVDQVDATRIVIRAA-GDIEPGQSGVDIYTLQKFQRSNQNTCINQRPLVKVGD 791

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V + DI+ADGPSTDLG+LALGRN+LVAFMPW+GYN+EDS+LISER+V +DVFTSIHIEE
Sbjct: 792  MVEKGDILADGPSTDLGELALGRNVLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIEE 851

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            FEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDILVGKITPKGESPM
Sbjct: 852  FEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILVGKITPKGESPM 911

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+V+VR+FNRHGI+ ++R+ +++ E+IE 
Sbjct: 912  TPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFNRHGIEIDDRTRAIQAEEIER 971

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            LA+D++DE+ IL+R  ++RL ++L GQ A + PKG KK   +   ++ +  R +WW+FAV
Sbjct: 972  LAKDREDERAILNRATFNRLRDMLIGQVAAAAPKGIKKGVEIDEQVLGDVERHEWWKFAV 1031

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D+  Q  +E++K QY+ +   ++++F+++  K++ GD++ PGVL++VKVFVA+KR +Q 
Sbjct: 1032 ADDARQAQLEAVKQQYDATVKAIQEKFEDRKAKLEAGDELAPGVLKMVKVFVAVKRKLQP 1091

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL DGT VDIVLNPLGVPSRMNVGQIFETHLGWA  
Sbjct: 1092 GDKMAGRHGNKGVISRILPIEDMPFLDDGTHVDIVLNPLGVPSRMNVGQIFETHLGWAAR 1151

Query: 1147 GLGKKIKSLINDYK-------ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            GLG++IK  + D++       A    + L   L+ + G  ++   I     + ++ +AE 
Sbjct: 1152 GLGQQIKHALEDWRIANPDPQAAQPPAALIEKLKDIYG-ENYYADIESRTTNEIIELAEN 1210

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K+GVP+ TPVFDGA E  +++ML  A    SGQ+ L+DG TGE FDR VTVG IYMLKL
Sbjct: 1211 LKAGVPMGTPVFDGAREPDVSAMLAKAGYHTSGQTTLFDGRTGEAFDRKVTVGIIYMLKL 1270

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1271 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1330

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +         +++P+
Sbjct: 1331 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELSSHDEGEED--DDLPE 1388

Query: 1380 FNK 1382
              +
Sbjct: 1389 AAE 1391


>gi|82701892|ref|YP_411458.1| DNA-directed RNA polymerase subunit beta [Nitrosospira multiformis
            ATCC 25196]
 gi|109904478|sp|Q2YB05|RPOB_NITMU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|82409957|gb|ABB74066.1| DNA-directed RNA polymerase subunit beta [Nitrosospira multiformis
            ATCC 25196]
          Length = 1357

 Score = 1672 bits (4330), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1363 (52%), Positives = 956/1363 (70%), Gaps = 7/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++ IP L+  Q  SY  FL  N+ PD+R  EGLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRASVLPIPFLLATQIESYAAFLQANLEPDQRAPEGLQAAFLSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + S  A L+FV+Y    P FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHSRNARLDFVNYVLGAPPFDVKECQQRGLTYASPLRAKVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  REVKEQEVYMGEIPLMTNTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+P+T  L A+G   E+IL  F+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRVDRRRKMPITVLLKAIGYTPEQILENFFSFDSFHISR 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L    L  G      ++   +G+ +++  K++T   ++ +++ G+  L +  D 
Sbjct: 239  KSILFELLPERL-RGDTARFDILS-KSGKVIVQKDKRITVKHVREMQQAGIDRLEVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +  ++V+ ETGEI   A D I E  L ++  + + +I  +Y + ++  AYI  TL
Sbjct: 297  LLGRVLGHNVVDKETGEILALANDEITETLLGKLRDANVEEIRTIYTNDLDQGAYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D   A + IYR+MRPG+  T    +++F  LF+  ++YDLS VGR+K N R+  
Sbjct: 357  KIDETADEMAAQVAIYRMMRPGEPPTEEAVKALFIGLFYAPERYDLSVVGRMKFNRRVGK 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               D    +  EDIIA+I+ILV+LRNG+G IDDID+LGNRRVRSVGE+ +NQ+R GL+R+
Sbjct: 417  TELDGPTTLSNEDIIAVIRILVELRNGRGEIDDIDHLGNRRVRSVGELAENQFRSGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + +++MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSQAESENLMPHDLINAKPVSAAVREFFGSSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A+ N YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQTNEYGFMETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ +LSA+EE    IAQAN+ LD DG FT ++V CR   E  L   ++I+
Sbjct: 597  RKVTDGLVTDEIHFLSAIEEGQYVIAQANAELDGDGRFTNDIVSCRHKNEFTLATPDRIE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E VVA  
Sbjct: 657  YMDVAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRAEKPLVGTGIERVVAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG A+ A R G+V+ VDA RIV+R  + +      GVDIY L K+ RSNQNT +NQRPLV
Sbjct: 717  SGTAVKAVRGGVVDYVDASRIVVRVHDIETRAGEVGVDIYNLTKYTRSNQNTNINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + R D++ADG STD G+LALG+NMLVAFMPW GYNFEDS+LISER+V+ D FTSI
Sbjct: 777  KVGDVIARGDVVADGASTDKGELALGQNMLVAFMPWTGYNFEDSILISERIVANDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V++RDTKLG EEIT DI N+SE  L  +D  GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELSVVSRDTKLGTEEITGDISNLSEAQLGRLDASGIVHIGAEVEAGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI++++R+  +  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGISGTVIDVQVFTREGIERDKRAQQIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++   +D  D+  I++ + + R+  +L G+ A  GPK   K   L+ + +       W+
Sbjct: 957  ELKRYKKDLADQMRIVEADAFVRIERLLIGKIATGGPKKLAKGATLTKEYLESIDPHHWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE     +E ++      +   +  F+ K +K+  GD++PPGV ++VKV+VA+KR
Sbjct: 1017 DIRLADEGASVQLEQIEEGLAQKRKAFDAAFEEKKKKLTQGDELPPGVQKMVKVYVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+I+P EDMP++ DGTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVISKIVPVEDMPYMADGTPVDVVLNPLGVPSRMNVGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG+KI  ++   +A  +I  LR+FL+K+  T    E I+   D  +  +A+  + 
Sbjct: 1137 WAAKGLGQKIGDML---RAGKEIVELRAFLDKIYNTSGKPEDIASLTDGEIADLAQNLQD 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TPVFDGA E+ I  ML +A L  SGQ  L+DG TGE FDRPVTVGY+++LKL+H+
Sbjct: 1194 GVPFATPVFDGATEQEIKDMLELAGLPRSGQVTLHDGRTGEAFDRPVTVGYMHVLKLHHL 1253

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG+AY LQEMLT+KSDDV
Sbjct: 1254 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGSAYTLQEMLTVKSDDV 1313

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYESIV G+   + G PESFNVLVKE+++L + IDLE 
Sbjct: 1314 NGRTKVYESIVKGDHKIDAGMPESFNVLVKEIRSLAMDIDLER 1356


>gi|16767407|ref|NP_463022.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhimurium str. LT2]
 gi|19855075|sp|P06173|RPOB_SALTY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|6960339|gb|AAF33499.1| Salmonella typhimurium DNA-directed RNA polymerase, beta-subunit
            (RPOB) (SW:P06173) contains similarity to Pfam domain
            PF00562 (RNA_pol_B), Score=1088, E=0, N=1 [Salmonella
            enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|16422711|gb|AAL22981.1| RNA polymerase, beta subunit [Salmonella enterica subsp. enterica
            serovar Typhimurium str. LT2]
 gi|226358457|gb|ACO51091.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Typhimurium]
 gi|226358459|gb|ACO51092.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Typhimurium]
 gi|226358461|gb|ACO51093.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Typhimurium]
 gi|226358463|gb|ACO51094.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Typhimurium]
 gi|261249257|emb|CBG27119.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Typhimurium str. D23580]
 gi|267996451|gb|ACY91336.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhimurium str. 14028S]
 gi|301160649|emb|CBW20180.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Typhimurium str. SL1344]
 gi|312915258|dbj|BAJ39232.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhimurium str. T000240]
 gi|321223353|gb|EFX48420.1| DNA-directed RNA polymerase beta subunit [Salmonella enterica subsp.
            enterica serovar Typhimurium str. TN061786]
 gi|323132488|gb|ADX19918.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhimurium str. 4/74]
          Length = 1342

 Score = 1672 bits (4330), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSSGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|29143788|ref|NP_807130.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. Ty2]
 gi|56415980|ref|YP_153055.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Paratyphi A str. ATCC 9150]
 gi|161617291|ref|YP_001591256.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Paratyphi B str. SPB7]
 gi|168264592|ref|ZP_02686565.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Hadar str. RI_05P066]
 gi|168467915|ref|ZP_02701752.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Newport str. SL317]
 gi|194444496|ref|YP_002043405.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Newport str. SL254]
 gi|194450538|ref|YP_002048140.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Heidelberg str. SL476]
 gi|194470339|ref|ZP_03076323.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Kentucky str. CVM29188]
 gi|194737028|ref|YP_002117056.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Schwarzengrund str. CVM19633]
 gi|197251068|ref|YP_002149064.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Agona str. SL483]
 gi|197264694|ref|ZP_03164768.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Saintpaul str. SARA23]
 gi|197364907|ref|YP_002144544.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Paratyphi A str. AKU_12601]
 gi|198242604|ref|YP_002218070.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Dublin str. CT_02021853]
 gi|200387162|ref|ZP_03213774.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Virchow str. SL491]
 gi|204931265|ref|ZP_03222025.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Javiana str. GA_MM04042433]
 gi|207859331|ref|YP_002245982.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Enteritidis str. P125109]
 gi|213650888|ref|ZP_03380941.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. J185]
 gi|224585695|ref|YP_002639494.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Paratyphi C strain RKS4594]
 gi|238913732|ref|ZP_04657569.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Tennessee str. CDC07-0191]
 gi|289826713|ref|ZP_06545678.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E98-3139]
 gi|81361175|sp|Q5PK93|RPOB_SALPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|182676589|sp|A9MHF1|RPOB_SALAR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189043866|sp|A9N0J4|RPOB_SALPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699439|sp|B5F0W7|RPOB_SALA4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699440|sp|B5FQJ9|RPOB_SALDC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699441|sp|B5QYD8|RPOB_SALEP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699443|sp|B4TCS4|RPOB_SALHS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699444|sp|B4T0Y9|RPOB_SALNS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699445|sp|B5BJQ3|RPOB_SALPK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699446|sp|B4TQJ5|RPOB_SALSV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765302|sp|C0Q2R7|RPOB_SALPC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|29139423|gb|AAO70990.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Typhi str. Ty2]
 gi|56130237|gb|AAV79743.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Paratyphi A str. ATCC 9150]
 gi|161366655|gb|ABX70423.1| hypothetical protein SPAB_05142 [Salmonella enterica subsp. enterica
            serovar Paratyphi B str. SPB7]
 gi|194403159|gb|ACF63381.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Newport str. SL254]
 gi|194408842|gb|ACF69061.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Heidelberg str. SL476]
 gi|194456703|gb|EDX45542.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Kentucky str. CVM29188]
 gi|194712530|gb|ACF91751.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Schwarzengrund str. CVM19633]
 gi|195629014|gb|EDX48406.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Newport str. SL317]
 gi|197096384|emb|CAR61989.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Paratyphi A str. AKU_12601]
 gi|197214771|gb|ACH52168.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Agona str. SL483]
 gi|197242949|gb|EDY25569.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Saintpaul str. SARA23]
 gi|197937120|gb|ACH74453.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Dublin str. CT_02021853]
 gi|199604260|gb|EDZ02805.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Virchow str. SL491]
 gi|204319880|gb|EDZ05087.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Javiana str. GA_MM04042433]
 gi|205346980|gb|EDZ33611.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Hadar str. RI_05P066]
 gi|206711134|emb|CAR35508.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Enteritidis str. P125109]
 gi|224470223|gb|ACN48053.1| DNA-directed RNA polymerase beta subunit [Salmonella enterica subsp.
            enterica serovar Paratyphi C strain RKS4594]
 gi|226358423|gb|ACO51074.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Enteritidis]
 gi|226358425|gb|ACO51075.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Enteritidis]
 gi|226358427|gb|ACO51076.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Enteritidis]
 gi|226358429|gb|ACO51077.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Enteritidis]
 gi|226358431|gb|ACO51078.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Enteritidis]
 gi|320088584|emb|CBY98343.1| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp.
            enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|322616263|gb|EFY13173.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 315996572]
 gi|322617294|gb|EFY14196.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 495297-1]
 gi|322625934|gb|EFY22749.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 495297-3]
 gi|322626668|gb|EFY23470.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 495297-4]
 gi|322631503|gb|EFY28260.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 515920-1]
 gi|322635216|gb|EFY31934.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 515920-2]
 gi|322642617|gb|EFY39211.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 531954]
 gi|322646790|gb|EFY43294.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650789|gb|EFY47182.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. OH_2009072675]
 gi|322655912|gb|EFY52213.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657311|gb|EFY53590.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 19N]
 gi|322665573|gb|EFY61758.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 81038-01]
 gi|322669756|gb|EFY65901.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. MD_MDA09249507]
 gi|322670965|gb|EFY67097.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 414877]
 gi|322679211|gb|EFY75264.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 366867]
 gi|322679369|gb|EFY75416.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 413180]
 gi|322688136|gb|EFY84100.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 446600]
 gi|323193404|gb|EFZ78614.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 609458-1]
 gi|323200676|gb|EFZ85749.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 556150-1]
 gi|323202165|gb|EFZ87221.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 609460]
 gi|323209276|gb|EFZ94211.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 507440-20]
 gi|323211601|gb|EFZ96438.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 556152]
 gi|323218061|gb|EGA02774.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. MB101509-0077]
 gi|323221350|gb|EGA05772.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. MB102109-0047]
 gi|323225723|gb|EGA09944.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. MB110209-0055]
 gi|323230989|gb|EGA15106.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. MB111609-0052]
 gi|323235771|gb|EGA19853.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 2009083312]
 gi|323240085|gb|EGA24131.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 2009085258]
 gi|323242582|gb|EGA26604.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. 315731156]
 gi|323249710|gb|EGA33617.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2009159199]
 gi|323252593|gb|EGA36434.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2010008282]
 gi|323256913|gb|EGA40625.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2010008283]
 gi|323262065|gb|EGA45629.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2010008284]
 gi|323263930|gb|EGA47444.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2010008285]
 gi|323268457|gb|EGA51927.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Montevideo str. IA_2010008287]
 gi|326625863|gb|EGE32208.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Dublin str. 3246]
          Length = 1342

 Score = 1672 bits (4329), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|283836723|ref|ZP_06356464.1| DNA-directed RNA polymerase, beta subunit [Citrobacter youngae ATCC
            29220]
 gi|291067270|gb|EFE05379.1| DNA-directed RNA polymerase, beta subunit [Citrobacter youngae ATCC
            29220]
          Length = 1342

 Score = 1672 bits (4329), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1364 (52%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGSDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|296100615|ref|YP_003610761.1| DNA-directed RNA polymerase subunit beta [Enterobacter cloacae subsp.
            cloacae ATCC 13047]
 gi|295055074|gb|ADF59812.1| DNA-directed RNA polymerase subunit beta [Enterobacter cloacae subsp.
            cloacae ATCC 13047]
          Length = 1342

 Score = 1672 bits (4329), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  +  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYVDESTGELICPANMELSLDLLAKLSQAGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGTDVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGGLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|237727879|ref|ZP_04558360.1| DNA-directed RNA polymerase subunit beta [Citrobacter sp. 30_2]
 gi|226910436|gb|EEH96354.1| DNA-directed RNA polymerase subunit beta [Citrobacter sp. 30_2]
          Length = 1342

 Score = 1672 bits (4329), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGSDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|295095127|emb|CBK84217.1| DNA-directed RNA polymerase subunit beta [Enterobacter cloacae subsp.
            cloacae NCTC 9394]
          Length = 1342

 Score = 1671 bits (4328), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYVDESTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGTDVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGGLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|205354444|ref|YP_002228245.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Gallinarum str. 287/91]
 gi|226699442|sp|B5RFK1|RPOB_SALG2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|205274225|emb|CAR39244.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Gallinarum str. 287/91]
 gi|226358433|gb|ACO51079.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358435|gb|ACO51080.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358437|gb|ACO51081.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358439|gb|ACO51082.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358441|gb|ACO51083.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358443|gb|ACO51084.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|226358445|gb|ACO51085.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Gallinarum]
 gi|326629577|gb|EGE35920.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Gallinarum str. 9]
          Length = 1342

 Score = 1671 bits (4328), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQC----GLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITKGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|62182607|ref|YP_219024.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Choleraesuis str. SC-B67]
 gi|62130240|gb|AAX67943.1| RNA polymerase, beta subunit [Salmonella enterica subsp. enterica
            serovar Choleraesuis str. SC-B67]
          Length = 1380

 Score = 1671 bits (4328), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 39   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 94

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 95   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 152

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 153  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 212

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 213  RIIPYRGSWLDFEFDLKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 272

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 273  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 329

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 330  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 389

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 390  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 449

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 450  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 509

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 510  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 569

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 570  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 629

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 630  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 689

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 690  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 749

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 750  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 809

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 810  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 869

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 870  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 929

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 930  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 989

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 990  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 1036

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1037 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1096

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1097 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1156

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1157 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1216

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1217 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1276

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1277 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1336

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1337 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1380


>gi|226358447|gb|ACO51086.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Pullorum]
 gi|226358449|gb|ACO51087.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Pullorum]
 gi|226358451|gb|ACO51088.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Pullorum]
 gi|226358453|gb|ACO51089.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Pullorum]
 gi|226358455|gb|ACO51090.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
            serovar Pullorum]
          Length = 1342

 Score = 1671 bits (4328), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDYIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|87198050|ref|YP_495307.1| DNA-directed RNA polymerase subunit beta [Novosphingobium
            aromaticivorans DSM 12444]
 gi|109904495|sp|Q2GCD7|RPOB_NOVAD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|87133731|gb|ABD24473.1| DNA-directed RNA polymerase subunit beta [Novosphingobium
            aromaticivorans DSM 12444]
          Length = 1392

 Score = 1671 bits (4328), Expect = 0.0,   Method: Composition-based stats.
 Identities = 810/1364 (59%), Positives = 1056/1364 (77%), Gaps = 15/1364 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FG   E++ +P+LIEVQ+ SY+ FL  +  P      GL+   +SVFPI  F+
Sbjct: 17   KKRIRKIFGDIHEVVQMPNLIEVQRESYEQFLRSD--PATGYVSGLEKTLRSVFPIQDFA 74

Query: 70   GAAMLEFV---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            G A L+      Y  + PK+DV++C  R +TYA P+K+TL+L  F+VD  T  KS+ DIK
Sbjct: 75   GTASLDIKEKDGYVLESPKYDVNECRQRGITYAAPMKVTLKLATFEVDAETETKSLIDIK 134

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            EQ +YMGD+PLMT++GTF I G +R++VSQ+HRSPG+ FDHD+G+   SGK L+A R+IP
Sbjct: 135  EQDVYMGDIPLMTENGTFFINGTERVIVSQMHRSPGVLFDHDRGKTHSSGKYLFAARVIP 194

Query: 187  DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
             +G W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+  E+IL  FY  + +++    W 
Sbjct: 195  YRGSWLDFEFDAKDIVNVRIDRKRKLPVTALLHALGLGDEDILHHFYDTVTWARAEGGWK 254

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             P    +   G+K +  +VD  +GE +  +G+K++        + G++ L I ++ + G 
Sbjct: 255  VPFV-LEQWRGSKPAFDIVDAKSGEVIFPAGQKISPRAANKAAKDGLEALLIPTEEIFGR 313

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            Y A D+++  TG I+IEAGD +  ++L+ +  + I ++ +L +D ++   +IRNTL  DK
Sbjct: 314  YAARDLIDESTGRIWIEAGDEVSPENLDLLDKAGIDNLDLLDIDHISTGPWIRNTLKADK 373

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
              DR  AL DIYRVMRPG+  T   AE++F+ LFFD D+YDLS VGRVK+NMRL LD PD
Sbjct: 374  APDRDHALADIYRVMRPGEPPTRETAEALFDGLFFDGDRYDLSAVGRVKLNMRLGLDCPD 433

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             V  +R +DI+A++K LV+L++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++
Sbjct: 434  TVTTLRTDDILAVVKELVNLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAV 493

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 494  KERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGP 553

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIETPYRKV 
Sbjct: 554  GGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIETPYRKVV 613

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DGKVT DV+YLSAMEE+   +AQA++ L  DGSF EELV  R  GE ++ PR+ +  +D 
Sbjct: 614  DGKVTKDVIYLSAMEEQKHTVAQASAELTADGSFVEELVSARQNGEFVMAPRDTVTLMDV 673

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+KA+APFVGTGME  VA+ SGAA
Sbjct: 674  SPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKADAPFVGTGMEETVARDSGAA 733

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            I A R+G+V+QVDA RIVIR+  GD++P  SGVDIYRL KF+RSNQ+TC+NQRPLVKVGD
Sbjct: 734  ISALRSGVVDQVDATRIVIRA-SGDIEPGQSGVDIYRLQKFERSNQSTCINQRPLVKVGD 792

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             + + DIIADGPST+ G+LALGRN+LVAFMPW+GYN+EDS+LISER+V EDVFTSIHIEE
Sbjct: 793  LIEKGDIIADGPSTEFGELALGRNVLVAFMPWNGYNYEDSILISERIVKEDVFTSIHIEE 852

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            FEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDILVGKITPKGESPM
Sbjct: 853  FEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILVGKITPKGESPM 912

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLLRAIFGEKA DVRDTSLR+P GV+GT+VDVR+FNRHGI+ ++R+ +++ E+IE 
Sbjct: 913  TPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGIEIDDRTRAIQNEEIER 972

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            LA+D++DE+ IL+R  ++RL ++L GQ A + PKG KK   +   ++++  R +WW+FAV
Sbjct: 973  LAKDREDERAILNRATFNRLKDMLLGQVAAAAPKGIKKGVEIDEQVLADVERHEWWKFAV 1032

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D+  Q+ +E++K QY+T+   ++++F+++ EK++ GD++ PGVL++VKVFVA+KR +Q 
Sbjct: 1033 ADDARQQQLEAVKAQYDTAVKAIQEKFEDRKEKLERGDELAPGVLKMVKVFVAVKRKLQP 1092

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKGI+SRILP EDMPFL+DGTPVD VLNPLGVPSRMNVGQIFETHLGWA  
Sbjct: 1093 GDKMAGRHGNKGIISRILPQEDMPFLEDGTPVDFVLNPLGVPSRMNVGQIFETHLGWAAR 1152

Query: 1147 GLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            GLGK+I   ++ ++              +R  L+++ G     E I   +D+ ++  A+ 
Sbjct: 1153 GLGKRIGEALDAWREANPNPEAGQPPEAVRELLKEIYGDNYAAE-IDARNDEQIIDFAQS 1211

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GVP+ +PVFDGA E+ +  MLR+A LDESGQ  L+DG TG+ FDR VTVG  Y+LKL
Sbjct: 1212 VRLGVPMGSPVFDGAVEKDVTDMLRLAGLDESGQVTLFDGRTGDAFDRKVTVGMKYVLKL 1271

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1272 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1331

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L
Sbjct: 1332 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1375


>gi|47919|emb|CAA28302.1| unnamed protein product [Salmonella enterica subsp. enterica serovar
            Typhimurium]
          Length = 1342

 Score = 1671 bits (4327), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R  AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRELAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSSGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|170770127|ref|ZP_02904580.1| DNA-directed RNA polymerase, beta subunit [Escherichia albertii
            TW07627]
 gi|170121009|gb|EDS89940.1| DNA-directed RNA polymerase, beta subunit [Escherichia albertii
            TW07627]
          Length = 1342

 Score = 1671 bits (4327), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|315300752|gb|EFU59977.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 16-3]
          Length = 1353

 Score = 1671 bits (4327), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 246  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 303  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLYDGRTGEQFERPVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|331660546|ref|ZP_08361479.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA206]
 gi|331052329|gb|EGI24367.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA206]
          Length = 1342

 Score = 1670 bits (4326), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|270160336|ref|ZP_06188989.1| DNA-directed RNA polymerase beta subunit [Legionella longbeachae
            D-4968]
 gi|289163823|ref|YP_003453961.1| RNA polymerase B-subunit [Legionella longbeachae NSW150]
 gi|269987148|gb|EEZ93406.1| DNA-directed RNA polymerase beta subunit [Legionella longbeachae
            D-4968]
 gi|288856996|emb|CBJ10810.1| RNA polymerase B-subunit [Legionella longbeachae NSW150]
          Length = 1368

 Score = 1670 bits (4326), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1364 (53%), Positives = 993/1364 (72%), Gaps = 5/1364 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
                    R RK FGK  + + IP+L+E+Q  SY  FL  +   +E  N GL AAF SVF
Sbjct: 9    QYSHAEKKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANEHFNTGLHAAFSSVF 68

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI +FSG A LE+V Y+   P FDV +C  R LTY+ PL++ +RL++ D D     K IK
Sbjct: 69   PIDSFSGNARLEYVGYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVILDKDASEDPKPIK 128

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            DI+EQ ++MG++PLMT  GTFVI G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+ R
Sbjct: 129  DIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYSAR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++VRIDRRRK+PV+  L ALG ++E+IL  F+       +  
Sbjct: 189  IIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILGEFFEMTSCHLKNG 248

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
             +   L    L  G   S  ++   TGE ++E G+++T+  +K +++  +K L +  D L
Sbjct: 249  EYHIDLIPQRL-RGEIASFDILVPGTGELIVEQGRRITARHIKQMEKAQMKDLIVPRDYL 307

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A++I++  TGE+  +A D + E  L+ +  S I +  ++Y + +++ +YI +T+ 
Sbjct: 308  IGKTLAKNIIDTLTGELVAQANDEVTEDLLDAMITSGIHEFDMIYTNDLDHGSYISDTVK 367

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D    + +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N R+   
Sbjct: 368  IDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVGRK 427

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
              D    + KEDI+A+IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R+E
Sbjct: 428  NDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVE 487

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER+S V+ +++MPQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+SA
Sbjct: 488  RAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSA 547

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP R
Sbjct: 548  LGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCR 607

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+VT+++ YLSA+EE ++YIAQ++ +LDEDG+   +LV CR   E  L   +KI++
Sbjct: 608  KVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCRHQNEFSLTTPDKINY 667

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME +VA  S
Sbjct: 668  MDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDS 727

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G ++VAKR G+++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+VK
Sbjct: 728  GVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVK 787

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V +D FT+IH
Sbjct: 788  TGDMIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIH 847

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLG EEIT DIPNV E  L ++DE G++ +GAEVN GDILVGK+TPKGE
Sbjct: 848  IEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEVNAGDILVGKVTPKGE 907

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K+ R+ S+E E 
Sbjct: 908  TQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSIEEEH 967

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  + +D  DE+ I + +IY R+  I+  + A  GP   +  + ++ + +    R +W+ 
Sbjct: 968  LARVRKDLVDERRIREEDIYHRVSNIILDKVATGGPGNLRPGSKVTQEYLQSITRDKWFD 1027

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++++   + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 1028 IRLENDTTSQQLEQLSKQLEMLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRR 1087

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHLG 
Sbjct: 1088 IQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGL 1147

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWKS 1202
            A  GLG KI  +++  +   +I   R+FL K+    G     +   +D+ + R+A+  ++
Sbjct: 1148 AAKGLGNKISQMLDLKQNATEI---RTFLNKIYNHDGIQRVNLDCLNDEELYRLADNLRA 1204

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  I SML++ADL   G+++LYDG TG  FD PVTVGY+YMLKLNH+
Sbjct: 1205 GVPMATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHL 1264

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1324

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+LE+ 
Sbjct: 1325 GGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368


>gi|262043780|ref|ZP_06016882.1| DNA-directed RNA polymerase subunit beta [Klebsiella pneumoniae
            subsp. rhinoscleromatis ATCC 13884]
 gi|330005030|ref|ZP_08305085.1| DNA-directed RNA polymerase, beta subunit [Klebsiella sp. MS 92-3]
 gi|259038867|gb|EEW40036.1| DNA-directed RNA polymerase subunit beta [Klebsiella pneumoniae
            subsp. rhinoscleromatis ATCC 13884]
 gi|328536449|gb|EGF62799.1| DNA-directed RNA polymerase, beta subunit [Klebsiella sp. MS 92-3]
          Length = 1353

 Score = 1670 bits (4326), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 246  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 303  IAGKVAAKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|85375719|ref|YP_459781.1| DNA-directed RNA polymerase subunit beta [Erythrobacter litoralis
            HTCC2594]
 gi|122543126|sp|Q2N5Q7|RPOB_ERYLH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|84788802|gb|ABC64984.1| DNA-directed RNA polymerase 140 kDa subunit [Erythrobacter litoralis
            HTCC2594]
          Length = 1396

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 817/1373 (59%), Positives = 1060/1373 (77%), Gaps = 16/1373 (1%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             R+RK FG   E++ +P+LIEVQ+ SY+ FL  N   D     GL+   +SVFPI  F+G
Sbjct: 20   RRIRKIFGDIHEVVKMPNLIEVQRESYEQFLRSNKEIDYVS--GLEKTLRSVFPIRDFAG 77

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             A L+FV YE +PPK+D  +C  R +TYA P+K+TLRLIVF+VD+ T  +S+ DIKEQ +
Sbjct: 78   TAELDFVHYELEPPKYDTTECRQRGITYAAPMKVTLRLIVFEVDQETETRSVLDIKEQDV 137

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGKLL+A R+IP +G 
Sbjct: 138  YMGDMPLMTGNGTFIINGTERVIVSQMHRSPGVLFDHDRGKTHSSGKLLFAARVIPYRGS 197

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS----QRGDFWC 246
            W+D EFD+KDI++VRIDR+RK+PVT+ L ALG+DSEEIL  FY  + +     ++G+ W 
Sbjct: 198  WLDFEFDAKDIVNVRIDRKRKLPVTALLYALGLDSEEILHFFYNTVTWKRAGGKKGEGWK 257

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             P        G K + +LVD  TGE+V  + +K++       ++ G+K L + ++ +   
Sbjct: 258  IPFEPE-AWRGQKPTFALVDAKTGEEVFPANQKISPRAANKAQKDGLKDLLLPTEEVFAR 316

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            Y A+D+++ +TG IYIEAGD +    LE +  + I ++ +L +D +N   +IRNTL  DK
Sbjct: 317  YAAKDMIDEKTGRIYIEAGDEVGPDHLEALDAAGIDELELLDIDEINTGPWIRNTLKVDK 376

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             ++R + L  IY+VMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL+LD  D
Sbjct: 377  AENRDEGLEAIYKVMRPGEPPTKETAEALFEGLFFDGERYDLSAVGRVKLNMRLDLDAED 436

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             V  +RKEDI+A++K LV L++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++
Sbjct: 437  TVTTLRKEDILAVVKELVGLKDGKGDVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAV 496

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 497  KERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGP 556

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL++FARVN YGFIETPYR V 
Sbjct: 557  GGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTFARVNKYGFIETPYRVVK 616

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DGKVT++V+YLSAMEE+   +AQA++ L EDG+F EEL+  R  G+ ++ P E +  +D 
Sbjct: 617  DGKVTSEVIYLSAMEEQKHTVAQASAELTEDGTFVEELISARQNGDNLMAPSETVTLMDV 676

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+KAEAP+VGTGME  VA+ SGAA
Sbjct: 677  SPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKAEAPWVGTGMEETVARDSGAA 736

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            I A R GIV+QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQNTC+NQRPLVKVG+
Sbjct: 737  ITATRGGIVDQVDATRIVIRA-IGDVEPGQSGVDIYTLQKFQRSNQNTCINQRPLVKVGE 795

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V   D+IADGPSTDLG+LALG+N LVAFMPW+GYN+EDS+LISER+V +DVFTSIHIEE
Sbjct: 796  TVEAGDVIADGPSTDLGELALGKNTLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIEE 855

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            FEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDIL GKITPKGESPM
Sbjct: 856  FEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILCGKITPKGESPM 915

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGI+ ++R+ ++++E+IE 
Sbjct: 916  TPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIEVDDRTRAIQQEEIER 975

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            L +D  DE+ IL+R  Y+RL ++L GQ A + PKG KK   +   L+    R +W++FAV
Sbjct: 976  LRKDSQDERTILNRATYNRLRDMLLGQTASAAPKGVKKGVKIDEALLEGIDRHEWFKFAV 1035

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D+  Q+ +E++K QY+ +   ++D+F+++ EK++ GD++ PGVL++VKVFVA+KR +Q 
Sbjct: 1036 ADDNRQQQIEAVKSQYDEAAKGIDDKFEDRKEKLERGDELAPGVLKMVKVFVAVKRKLQP 1095

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL+DGTPVDIVLNPLGVPSRMNVGQIFETHLG+A  
Sbjct: 1096 GDKMAGRHGNKGVISRILPVEDMPFLEDGTPVDIVLNPLGVPSRMNVGQIFETHLGFAAR 1155

Query: 1147 GLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            GLG+++K+ + D++A             ++  L++V G   + + I+   +  ++ +A  
Sbjct: 1156 GLGQQVKNALEDWRAANPDPEAGKPPEAVKETLQRVYGDR-YEDDIAGRSNAEIIELASN 1214

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +GVP+ TPVFDGA E  + + L  A +D SGQS+LYDG TGE FDR VTVG IYMLKL
Sbjct: 1215 LTAGVPMGTPVFDGAREGDVTTQLEAAGIDSSGQSVLYDGRTGEAFDRKVTVGIIYMLKL 1274

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KS
Sbjct: 1275 HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKS 1334

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            DDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L +    +  
Sbjct: 1335 DDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELSSLTDGDED 1387


>gi|218551029|ref|YP_002384820.1| DNA-directed RNA polymerase subunit beta [Escherichia fergusonii ATCC
            35469]
 gi|226699406|sp|B7LUL5|RPOB_ESCF3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|218358570|emb|CAQ91218.1| RNA polymerase, beta subunit [Escherichia fergusonii ATCC 35469]
 gi|323963795|gb|EGB59294.1| DNA-directed RNA polymerase [Escherichia coli M863]
 gi|323974187|gb|EGB69319.1| DNA-directed RNA polymerase [Escherichia coli TW10509]
 gi|324110899|gb|EGC04891.1| DNA-directed RNA polymerase [Escherichia fergusonii B253]
 gi|325499281|gb|EGC97140.1| DNA-directed RNA polymerase subunit beta [Escherichia fergusonii
            ECD227]
 gi|327250457|gb|EGE62167.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli STEC_7v]
          Length = 1342

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVIDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|237654003|ref|YP_002890317.1| DNA-directed RNA polymerase subunit beta [Thauera sp. MZ1T]
 gi|237625250|gb|ACR01940.1| DNA-directed RNA polymerase, beta subunit [Thauera sp. MZ1T]
          Length = 1377

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1384 (51%), Positives = 963/1384 (69%), Gaps = 27/1384 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K   ++D P L+  Q  S+  FL  +  PD R N+GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFAKRAAVLDAPFLLATQIESFAEFLQADTPPDVRRNQGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ SG A LE+V Y    P FDV +C  R LT+A PL+  +RL++ D +      +I
Sbjct: 61   FPISSHSGNARLEYVQYMLGEPAFDVKECQQRGLTFASPLRARVRLVIMDREAPKE--TI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+PVT  L A+GM  EEIL+TF+    +  +G
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRVDRRRKMPVTILLRAIGMTPEEILATFHDTDTFHLQG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L    L  G      +   D G+ ++   K++TS  ++ + + GVK + +  D 
Sbjct: 239  EGAQFELVPERL-RGEVARFDITTPD-GKIIVAREKRITSKHIREIDQAGVKTMAVPDDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++V+  TGE+   A D I E  L+++  + +  +  LY++ ++   YI  TL
Sbjct: 297  LLGRVIATNVVDPATGELLARANDEITEDLLDKLRLAGVTGLSTLYINDLDRGGYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E +F  LF+  ++YDLS+VGR+K N R   
Sbjct: 357  RIDETADQWAAKVAIYRMMRPGEPPTEDAVEGLFQGLFYAEERYDLSSVGRMKFNRRAYP 416

Query: 423  DT--------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +                      D    +  +DI+A++ +LV+LRNG+G IDDID+LGNR
Sbjct: 417  EKIDDKAPGWLKRFYQRVGAQGEDGPGVLVNDDILAVVGVLVELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVRSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKP+ +A+ EFF SSQL
Sbjct: 477  RVRSVGELAENQFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPISAAIKEFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHRRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +AR N +GF+ETPYRKV DGKVT+ + +LSA+EE    IAQAN+ +DE G    
Sbjct: 597  INSLAVYARTNRHGFLETPYRKVNDGKVTDQIDFLSAIEEGQYVIAQANAEIDEAGMLAG 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV CR  GE +L   + + ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLVSCRHKGEFLLATSDMVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ E P VGTG+E  VA  SG A+ A R GIV+ VDA R+VIR  + +  P   GVDIY
Sbjct: 717  CLRPEKPLVGTGIERRVAVDSGTAVQATRGGIVDYVDANRVVIRVNDDETLPGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             ++K+ RSNQNT +NQRP+VKVGD + R D++ADG STDLG+LALG+NMLV FMPW+GYN
Sbjct: 777  NMIKYTRSNQNTNINQRPVVKVGDLIARGDVVADGASTDLGELALGQNMLVGFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+LISER+V++D FTSIHIEE  V+ARDTKLGPEEITRDI ++ E  L  +DE GI+
Sbjct: 837  FEDSILISERVVADDRFTSIHIEELTVVARDTKLGPEEITRDIASLGEAQLSRLDESGIV 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV
Sbjct: 897  YIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GI++++R+ S+  EQ+     D  D+  I++R+ ++R+  ++ GQ A  GPK  
Sbjct: 957  QVFTREGIERDKRAQSIIDEQLRSFKTDLADQMRIVERDAFARIRRMIVGQLANGGPKKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K   L+   +       W+   + DE +   +E+++   E ++   E  F+ K +K+  
Sbjct: 1017 AKGAALTDPYLDSLEHYHWFDIRLADETLAVQLEAVREGLENTRKDFEQAFEIKKKKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP+++DGTP+DIVL
Sbjct: 1077 GDELPPGVQKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMEDGTPLDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI ETHLGWA  GLG+KI  ++   +A      LR FLE++     H 
Sbjct: 1137 NPLGVPSRMNIGQILETHLGWAAKGLGQKIDKML---QAQASALELRGFLEQIYNGSGHP 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
            E I++  D  V  +A   K GVP +TPVFDGA EE I  ML +A L   GQ  LYDG TG
Sbjct: 1194 EDIANLGDSDVRELAGNLKKGVPFATPVFDGAKEEEIQQMLELAGLPTGGQVTLYDGRTG 1253

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E F+R VTVGY ++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1254 EAFERKVTVGYKHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1313

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYE+IV G    ++G PESFNVLVKE+++L + ID
Sbjct: 1314 EAYGAAYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDSGMPESFNVLVKEIRSLAIDID 1373

Query: 1363 LENS 1366
            L+  
Sbjct: 1374 LDRE 1377


>gi|82778838|ref|YP_405187.1| DNA-directed RNA polymerase subunit beta [Shigella dysenteriae Sd197]
 gi|309783938|ref|ZP_07678583.1| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae 1617]
 gi|88909638|sp|Q32AF9|RPOB_SHIDS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|81242986|gb|ABB63696.1| RNA polymerase, beta subunit [Shigella dysenteriae Sd197]
 gi|308928309|gb|EFP73771.1| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae 1617]
          Length = 1342

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 973/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +  + L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLELLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|297717810|gb|ADI50048.1| DNA-directed RNA polymerase beta subunit [Candidatus Odyssella
            thessalonicensis L13]
          Length = 1388

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 811/1386 (58%), Positives = 1047/1386 (75%), Gaps = 28/1386 (2%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
             F G+ R RK FG+  +   +P+LIE+QK+SY+ FL  +IA ++R   GL   FKS FPI
Sbjct: 4    SFTGMKRFRKNFGRISDEAKMPNLIELQKSSYEKFLQQSIAYNKREEIGLHEVFKSTFPI 63

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            T FSG A LE+  Y+FD PK+D D+C  R LTYA PLK+TLRL+V+D+DE TGAKSIKDI
Sbjct: 64   TDFSGKAHLEYFKYDFDKPKYDEDECRQRGLTYAAPLKLTLRLVVWDIDEDTGAKSIKDI 123

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQ +YMGD+PLMT +GTF+I G++R++VSQ+HRSPG+ FDHDKG++  SGK L+A R++
Sbjct: 124  KEQEVYMGDMPLMTDNGTFIINGVERVIVSQMHRSPGVFFDHDKGKSHSSGKYLFAARVV 183

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------------------ 221
            P +G W+D EFD KD++HVRIDRRRK+P+T+FLMAL                        
Sbjct: 184  PYRGSWLDFEFDPKDLVHVRIDRRRKLPITAFLMALDSAATMQKRAEAEAKGQPLPAAMV 243

Query: 222  -GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             GM  EEIL+TFY  I YS+    W       +   G K++S L+D  TG  V  +G K+
Sbjct: 244  TGMSREEILATFYETITYSKHKKGWKTAYLPEN-WRGVKLTSDLIDASTGTVVASAGTKI 302

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI-FHS 339
            T  + K     G+  + + S+ L GLY+A++ +N ETGEIY EAG+ +  K +  +  + 
Sbjct: 303  TPRMAKKFAADGLSEILVYSENLEGLYLAKEYINEETGEIYAEAGEELTLKIISVLEQNL 362

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             +++IP+L++D+VN   Y+RN+L+ DK  +R++AL +IYRVMRPG+  T   AE++F  L
Sbjct: 363  NLKEIPVLHIDNVNVGPYLRNSLIADKINNREEALFEIYRVMRPGEPPTLEGAEALFTGL 422

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD++KYDLS VGRVKMN RL++D  D VR +RKEDI+ I+K L++L++G+G IDDIDNL
Sbjct: 423  FFDAEKYDLSAVGRVKMNARLDIDCSDSVRILRKEDILLILKALLELKDGRGEIDDIDNL 482

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            GNRRVR+VGE+L+NQYR+GL RMER+IKER+SSV+ID+VMP DLINAKP  + V EFF S
Sbjct: 483  GNRRVRAVGELLENQYRVGLSRMERAIKERMSSVEIDTVMPHDLINAKPAAAVVREFFGS 542

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 543  SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRDRAGFEVRDVHPTHYGRICPIETPEGQN 602

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            IGL++SL ++ARVN YGFIE+PYRKV +GKVTN++VYL+AMEE    IAQAN +LD+DG 
Sbjct: 603  IGLINSLATYARVNQYGFIESPYRKVKEGKVTNEIVYLTAMEETRHIIAQANITLDKDGR 662

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +ELV CR  GE ++ PRE I  +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQ
Sbjct: 663  IADELVTCRKNGEFVIQPREDITLVDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQ 722

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVPLL+ EAP VGTGME+ VAK SG+ ++AKRAG+V+ VD  RIVIR +E      + GV
Sbjct: 723  AVPLLRCEAPLVGTGMEATVAKDSGSCVLAKRAGVVDSVDGRRIVIRVLERTEGDDSVGV 782

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            DIY L KFQRSN +TC+NQ+PLVK GD +++ D+IADGP+T+LG+LALGRN+LV FM W 
Sbjct: 783  DIYNLQKFQRSNMSTCINQKPLVKKGDIIKKGDVIADGPATELGELALGRNVLVGFMSWQ 842

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFEDS+++SER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+DE 
Sbjct: 843  GYNFEDSIILSERIAQDDVFTSIHIEEFEVMARDTKLGNEEITRDIPNVGEEALRNLDEA 902

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GII +GAEV  GDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSLRVP G++GT+
Sbjct: 903  GIIYIGAEVKAGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVPPGIAGTI 962

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            VDVR+F+R G+DK+ER++++ER++IE LA+D+D E+ IL+RN Y  L E+L G   VS P
Sbjct: 963  VDVRVFSRRGVDKDERALTIERQEIERLAKDRDAEKAILERNFYKNLEEMLLGHTLVSAP 1022

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
            KG K    ++   ++E P+ QW Q  V ++ V   VE++K   +   + L+D F+ K+EK
Sbjct: 1023 KGIKTGEKITEAFLAELPKHQWKQLLVDNDDVMSRVEAMKRHLDDGFTKLQDWFEGKVEK 1082

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            ++ GD++ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP L+DGT +D
Sbjct: 1083 LRAGDELSPGVLKMVKVFIAVKRKIQPGDKMAGRHGNKGVVSRIVPLEDMPHLEDGTILD 1142

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI-KSLINDYKANGDISPLRSFLEKVIGT 1178
            I+LNPLG+PSRMNVGQI ETH+G A  GL K+I  +++   ++N  +  L++ L+KV   
Sbjct: 1143 IILNPLGLPSRMNVGQILETHMGAAAAGLSKQINDAVLRIQQSNAQLGELKAELKKVYNK 1202

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                + I +  D+ V+ +A   + GVP++TPVFDGA E+ I   L  + +  +GQ  L D
Sbjct: 1203 TEDAKDIDNMPDEQVMELARNLRRGVPIATPVFDGASEQDIADALIASGIPTTGQQYLVD 1262

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TGE  DRP TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEME
Sbjct: 1263 GRTGERLDRPTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEME 1322

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+D  E G PESFNVLVKE+++LG
Sbjct: 1323 VWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNMEAGIPESFNVLVKELRSLG 1382

Query: 1359 LSIDLE 1364
            L++  E
Sbjct: 1383 LNMSFE 1388


>gi|152972845|ref|YP_001337991.1| DNA-directed RNA polymerase subunit beta [Klebsiella pneumoniae
            subsp. pneumoniae MGH 78578]
 gi|238892457|ref|YP_002917191.1| DNA-directed RNA polymerase subunit beta [Klebsiella pneumoniae
            NTUH-K2044]
 gi|150957694|gb|ABR79724.1| DNA-directed RNA polymerase beta subunit [Klebsiella pneumoniae
            subsp. pneumoniae MGH 78578]
 gi|238544773|dbj|BAH61124.1| DNA-directed RNA polymerase beta subunit [Klebsiella pneumoniae
            subsp. pneumoniae NTUH-K2044]
          Length = 1353

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 246  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 303  IAGKVAAKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|119899713|ref|YP_934926.1| DNA-directed RNA polymerase subunit beta [Azoarcus sp. BH72]
 gi|158512919|sp|A1KB34|RPOB_AZOSB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119672126|emb|CAL96040.1| DNA-directed RNA polymerase [Azoarcus sp. BH72]
          Length = 1377

 Score = 1670 bits (4325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1384 (51%), Positives = 972/1384 (70%), Gaps = 27/1384 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K   ++D P L+  Q  S+  FL     P+ R N+GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFAKRAAVLDAPFLLATQIESFASFLQAETPPESRYNQGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ SG A LEFV Y    P FDV +C  R LT+A PL+  +RL++ D +      +I
Sbjct: 61   FPISSHSGNARLEFVQYMLGEPAFDVKECQQRGLTFASPLRARVRLVIMDREAPKE--TI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+PVT  L A+GM  EEIL TF+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRVDRRRKMPVTILLRAIGMTPEEILETFHDFDAFHLSA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L   D + G      +VD  TG+ ++   K++T+  ++ L + G+K +G+  D 
Sbjct: 239  EGAQFELVP-DRLRGEVARFDIVDP-TGKVIVARDKRITAKHIRELDQAGIKMIGVPDDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A ++V+ ETGE+   A + I E  L ++  + +RD+  LYV+ ++  AYI +TL
Sbjct: 297  VLGRIIARNVVDPETGELLARANEEITEDLLGKLRDAGVRDLVTLYVNDLDRGAYISSTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  ++YDLSTVGR+K N R   
Sbjct: 357  RIDETADQWAARVAIYRMMRPGEPPTEEAVEALFQGLFYAPERYDLSTVGRMKFNRRAYP 416

Query: 423  DT--------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +                      +    +  EDI+A+I +LV+LRNG+G IDDID+LGNR
Sbjct: 417  EKIDDKAPGWLKRFYDKVGPHGEEGEGVLANEDILAVIGVLVELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVRSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKP+ +A+ EFF SSQL
Sbjct: 477  RVRSVGELAENQFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPISAAIKEFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +AR N +GF+ETPYRKV DGKVT+ + +LSA+EE    IAQAN+ +  DG+   
Sbjct: 597  INSLAVYARTNRHGFLETPYRKVTDGKVTDQIDFLSAIEEGQYVIAQANAEIGGDGALEG 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV CR  GE +L   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLVSCRHKGEFMLATADQVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ E P VGTG+E  VA  SG A+ A R G+V+ VDA R+V+R  + +      GVDIY
Sbjct: 717  CLRPEKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAQRVVVRVNDNEALAGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             ++K+ RSNQNT +NQRP+V+VGD + + D+IADG STDLG+LALG+NMLVAFMPW+GYN
Sbjct: 777  NMIKYTRSNQNTNINQRPVVRVGDLIAKGDVIADGASTDLGELALGQNMLVAFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+LISER+V++D FTSIH+EE  V+ARDTKLGPEEITRDI ++ E  L  +DE GI+
Sbjct: 837  FEDSILISERVVADDRFTSIHVEELTVVARDTKLGPEEITRDIASLGEAQLSRLDESGIV 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV
Sbjct: 897  YIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GI++++R+ S+  +Q+     D  D+  I++R+ ++R+  ++ GQ A  GPK  
Sbjct: 957  QVFTREGIERDKRAQSIIDDQLRSFKTDLADQMRIVERDAFARIQRMIVGQKANGGPKKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K   ++++ +       W+   + DE++   +E+++   E ++   E  F+ K +K+  
Sbjct: 1017 AKGAAITAEYLETLEFYHWFDIRMADEELAIQLEAVREGLEKTRKDFEQAFEIKKKKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PP V ++VKV++A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP+++DGTPVDIVL
Sbjct: 1077 GDELPPDVQKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMEDGTPVDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI ETHLGWA  GLG+KI  L+   +AN     +R  LE++       
Sbjct: 1137 NPLGVPSRMNIGQILETHLGWAAKGLGQKIDRLL---RANAAAGEVRGLLEEIYNGSGKP 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
            E  S++ D  V+ +A   K GVP +TPVFDGA EE I  ML +A L   GQ  L+DG TG
Sbjct: 1194 EDFSEFTDGDVIELATNLKKGVPFATPVFDGAKEEEIAKMLELAGLPVGGQVTLFDGRTG 1253

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E F+R VTVGY ++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1254 EAFERKVTVGYKHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1313

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYE+IV G    ++G PESFNVLVKE+++L + ID
Sbjct: 1314 EAYGAAYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDSGMPESFNVLVKEIRSLAIDID 1373

Query: 1363 LENS 1366
            L+  
Sbjct: 1374 LDRE 1377


>gi|283787340|ref|YP_003367205.1| DNA-directed RNA polymerase, beta-subunit [Citrobacter rodentium
            ICC168]
 gi|282950794|emb|CBG90470.1| DNA-directed RNA polymerase, beta-subunit [Citrobacter rodentium
            ICC168]
          Length = 1342

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+  TGE+   A   +    L ++  +  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVASKDYVDESTGELICPANMELSLDLLAKLSQAGHKRIETLFTNDLDHGPYISETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNFVIAQANSNLDDDGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIHAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|182676584|sp|A6TGP0|RPOB_KLEP7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|110644322|ref|YP_672052.1| DNA-directed RNA polymerase subunit beta [Escherichia coli 536]
 gi|123343346|sp|Q0TA78|RPOB_ECOL5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110345914|gb|ABG72151.1| DNA-directed RNA polymerase beta chain [Escherichia coli 536]
          Length = 1342

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLSPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|26250758|ref|NP_756798.1| DNA-directed RNA polymerase subunit beta [Escherichia coli CFT073]
 gi|91212806|ref|YP_542792.1| DNA-directed RNA polymerase subunit beta [Escherichia coli UTI89]
 gi|117626250|ref|YP_859573.1| DNA-directed RNA polymerase subunit beta [Escherichia coli APEC O1]
 gi|227885483|ref|ZP_04003288.1| DNA-directed RNA polymerase subunit beta [Escherichia coli 83972]
 gi|237702755|ref|ZP_04533236.1| RNA polymerase beta subunit [Escherichia sp. 3_2_53FAA]
 gi|254039244|ref|ZP_04873293.1| RNA polymerase beta subunit [Escherichia sp. 1_1_43]
 gi|293413423|ref|ZP_06656083.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|300819798|ref|ZP_07099985.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 107-1]
 gi|300824634|ref|ZP_07104742.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 119-7]
 gi|300897599|ref|ZP_07116008.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 198-1]
 gi|300907539|ref|ZP_07125178.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 84-1]
 gi|300919403|ref|ZP_07135908.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 115-1]
 gi|300925854|ref|ZP_07141698.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 182-1]
 gi|300928805|ref|ZP_07144313.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 187-1]
 gi|300938788|ref|ZP_07153501.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 21-1]
 gi|300947408|ref|ZP_07161600.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 116-1]
 gi|300954783|ref|ZP_07167213.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 175-1]
 gi|300979612|ref|ZP_07174628.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 45-1]
 gi|300985544|ref|ZP_07177478.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 200-1]
 gi|301019410|ref|ZP_07183585.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 69-1]
 gi|301047721|ref|ZP_07194780.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 185-1]
 gi|301302201|ref|ZP_07208333.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 124-1]
 gi|301326082|ref|ZP_07219480.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 78-1]
 gi|301645759|ref|ZP_07245679.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 146-1]
 gi|309797690|ref|ZP_07692076.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 145-7]
 gi|331644721|ref|ZP_08345839.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H736]
 gi|331649840|ref|ZP_08350918.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli M605]
 gi|331655684|ref|ZP_08356674.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli M718]
 gi|331675473|ref|ZP_08376222.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA280]
 gi|331680107|ref|ZP_08380768.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H591]
 gi|26111189|gb|AAN83372.1|AE016770_172 DNA-directed RNA polymerase beta chain [Escherichia coli CFT073]
 gi|91074380|gb|ABE09261.1| RNA polymerase beta subunit [Escherichia coli UTI89]
 gi|115515374|gb|ABJ03449.1| DNA-directed RNA polymerase beta chain protein RpoB [Escherichia coli
            APEC O1]
 gi|226838479|gb|EEH70509.1| RNA polymerase beta subunit [Escherichia sp. 1_1_43]
 gi|226903068|gb|EEH89327.1| RNA polymerase beta subunit [Escherichia sp. 3_2_53FAA]
 gi|227837557|gb|EEJ48023.1| DNA-directed RNA polymerase subunit beta [Escherichia coli 83972]
 gi|291468018|gb|EFF10517.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|300300386|gb|EFJ56771.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 185-1]
 gi|300306524|gb|EFJ61044.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 200-1]
 gi|300318282|gb|EFJ68066.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 175-1]
 gi|300358675|gb|EFJ74545.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 198-1]
 gi|300399264|gb|EFJ82802.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 69-1]
 gi|300400729|gb|EFJ84267.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 84-1]
 gi|300409465|gb|EFJ93003.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 45-1]
 gi|300413520|gb|EFJ96830.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 115-1]
 gi|300418069|gb|EFK01380.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 182-1]
 gi|300452987|gb|EFK16607.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 116-1]
 gi|300456298|gb|EFK19791.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 21-1]
 gi|300463186|gb|EFK26679.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 187-1]
 gi|300522883|gb|EFK43952.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 119-7]
 gi|300527619|gb|EFK48681.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 107-1]
 gi|300842364|gb|EFK70124.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 124-1]
 gi|300847175|gb|EFK74935.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 78-1]
 gi|301075970|gb|EFK90776.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 146-1]
 gi|308118702|gb|EFO55964.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 145-7]
 gi|315253059|gb|EFU33027.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 85-1]
 gi|315288332|gb|EFU47731.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 110-3]
 gi|315294356|gb|EFU53707.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 153-1]
 gi|324009493|gb|EGB78712.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 57-2]
 gi|324015273|gb|EGB84492.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 60-1]
 gi|324017338|gb|EGB86557.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 117-3]
 gi|331036021|gb|EGI08258.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H736]
 gi|331041306|gb|EGI13458.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli M605]
 gi|331046609|gb|EGI18696.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli M718]
 gi|331067351|gb|EGI38757.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA280]
 gi|331072262|gb|EGI43596.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H591]
 gi|332105287|gb|EGJ08633.1| RNA polymerase beta subunit [Shigella sp. D9]
          Length = 1353

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 246  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 303  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|15834164|ref|NP_312937.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            str. Sakai]
 gi|16131817|ref|NP_418414.1| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr.
            MG1655]
 gi|30064730|ref|NP_838901.1| DNA-directed RNA polymerase subunit beta [Shigella flexneri 2a str.
            2457T]
 gi|56480500|ref|NP_709782.2| DNA-directed RNA polymerase subunit beta [Shigella flexneri 2a str.
            301]
 gi|74314481|ref|YP_312900.1| DNA-directed RNA polymerase subunit beta [Shigella sonnei Ss046]
 gi|82546329|ref|YP_410276.1| DNA-directed RNA polymerase subunit beta [Shigella boydii Sb227]
 gi|89110052|ref|AP_003832.1| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr.
            W3110]
 gi|157155952|ref|YP_001465480.1| DNA-directed RNA polymerase subunit beta [Escherichia coli E24377A]
 gi|157163455|ref|YP_001460773.1| DNA-directed RNA polymerase subunit beta [Escherichia coli HS]
 gi|168758620|ref|ZP_02783627.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4401]
 gi|168764565|ref|ZP_02789572.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4501]
 gi|168771457|ref|ZP_02796464.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4486]
 gi|168777402|ref|ZP_02802409.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4196]
 gi|168780370|ref|ZP_02805377.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4076]
 gi|168790345|ref|ZP_02815352.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC869]
 gi|168798381|ref|ZP_02823388.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC508]
 gi|170022010|ref|YP_001726964.1| DNA-directed RNA polymerase subunit beta [Escherichia coli ATCC 8739]
 gi|170083447|ref|YP_001732767.1| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr.
            DH10B]
 gi|170680149|ref|YP_001746371.1| DNA-directed RNA polymerase subunit beta [Escherichia coli SMS-3-5]
 gi|187731358|ref|YP_001882672.1| DNA-directed RNA polymerase subunit beta [Shigella boydii CDC
            3083-94]
 gi|188495017|ref|ZP_03002287.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 53638]
 gi|191168659|ref|ZP_03030440.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli B7A]
 gi|191174299|ref|ZP_03035807.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli F11]
 gi|193066419|ref|ZP_03047466.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E22]
 gi|193067811|ref|ZP_03048777.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E110019]
 gi|194429975|ref|ZP_03062484.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli B171]
 gi|194434765|ref|ZP_03067016.1| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae 1012]
 gi|194439780|ref|ZP_03071847.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 101-1]
 gi|195939612|ref|ZP_03084994.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            str. EC4024]
 gi|208808239|ref|ZP_03250576.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4206]
 gi|208814392|ref|ZP_03255721.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4045]
 gi|208820515|ref|ZP_03260835.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4042]
 gi|209395910|ref|YP_002273503.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4115]
 gi|209921465|ref|YP_002295549.1| DNA-directed RNA polymerase subunit beta [Escherichia coli SE11]
 gi|215489319|ref|YP_002331750.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O127:H6
            str. E2348/69]
 gi|217325660|ref|ZP_03441744.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. TW14588]
 gi|218556541|ref|YP_002389455.1| DNA-directed RNA polymerase subunit beta [Escherichia coli IAI1]
 gi|218561053|ref|YP_002393966.1| DNA-directed RNA polymerase subunit beta [Escherichia coli S88]
 gi|218697694|ref|YP_002405361.1| DNA-directed RNA polymerase subunit beta [Escherichia coli 55989]
 gi|218702617|ref|YP_002410246.1| DNA-directed RNA polymerase subunit beta [Escherichia coli IAI39]
 gi|218707605|ref|YP_002415124.1| DNA-directed RNA polymerase subunit beta [Escherichia coli UMN026]
 gi|238903043|ref|YP_002928839.1| RNA polymerase, beta subunit [Escherichia coli BW2952]
 gi|253775384|ref|YP_003038215.1| DNA-directed RNA polymerase subunit beta [Escherichia coli
            'BL21-Gold(DE3)pLysS AG']
 gi|254163928|ref|YP_003047036.1| DNA-directed RNA polymerase subunit beta [Escherichia coli B str.
            REL606]
 gi|254795985|ref|YP_003080822.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            str. TW14359]
 gi|256021693|ref|ZP_05435558.1| DNA-directed RNA polymerase subunit beta [Shigella sp. D9]
 gi|256026302|ref|ZP_05440167.1| DNA-directed RNA polymerase subunit beta [Escherichia sp. 4_1_40B]
 gi|260846787|ref|YP_003224565.1| RNA polymerase, beta subunit [Escherichia coli O103:H2 str. 12009]
 gi|260858096|ref|YP_003231987.1| RNA polymerase, beta subunit [Escherichia coli O26:H11 str. 11368]
 gi|260870698|ref|YP_003237100.1| RNA polymerase, beta subunit [Escherichia coli O111:H- str. 11128]
 gi|261227302|ref|ZP_05941583.1| RNA polymerase, beta subunit [Escherichia coli O157:H7 str. FRIK2000]
 gi|261257049|ref|ZP_05949582.1| RNA polymerase, beta subunit [Escherichia coli O157:H7 str. FRIK966]
 gi|291285401|ref|YP_003502219.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O55:H7
            str. CB9615]
 gi|293407603|ref|ZP_06651521.1| DNA-directed RNA polymerase beta subunit [Escherichia coli FVEC1412]
 gi|293417490|ref|ZP_06660113.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|293474293|ref|ZP_06664702.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|298383351|ref|ZP_06992943.1| DNA-directed RNA polymerase subunit beta [Escherichia coli FVEC1302]
 gi|301023356|ref|ZP_07187146.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 196-1]
 gi|306812002|ref|ZP_07446210.1| DNA-directed RNA polymerase subunit beta [Escherichia coli NC101]
 gi|307140678|ref|ZP_07500034.1| DNA-directed RNA polymerase subunit beta [Escherichia coli H736]
 gi|307315040|ref|ZP_07594626.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli W]
 gi|312965360|ref|ZP_07779593.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 2362-75]
 gi|312974227|ref|ZP_07788397.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 1827-70]
 gi|331665641|ref|ZP_08366537.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA143]
 gi|331670839|ref|ZP_08371674.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA271]
 gi|331685728|ref|ZP_08386310.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H299]
 gi|67472412|sp|P0A8V2|RPOB_ECOLI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|67472413|sp|P0A8V3|RPOB_ECOL6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|67472414|sp|P0A8V4|RPOB_ECO57 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|67472415|sp|P0A8V5|RPOB_SHIFL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88909637|sp|Q31U10|RPOB_SHIBS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88909639|sp|Q3YUZ7|RPOB_SHISS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158512696|sp|A1AIF9|RPOB_ECOK1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158564244|sp|Q1R5V3|RPOB_ECOUT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166991523|sp|A7ZUK1|RPOB_ECO24 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166991524|sp|A8A786|RPOB_ECOHS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189043855|sp|B1IUR0|RPOB_ECOLC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699397|sp|B7MIX3|RPOB_ECO45 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699398|sp|B5Z083|RPOB_ECO5E RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699399|sp|B7NRR5|RPOB_ECO7I RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699400|sp|B7M734|RPOB_ECO8A RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699401|sp|B1XBY9|RPOB_ECODH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699402|sp|B7NFS7|RPOB_ECOLU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699403|sp|B6I5J7|RPOB_ECOSE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699404|sp|B1LNT9|RPOB_ECOSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699449|sp|B2TWH3|RPOB_SHIB3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765288|sp|B7UPE2|RPOB_ECO27 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765289|sp|B7LA80|RPOB_ECO55 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|259494181|sp|C5A0S7|RPOB_ECOBW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|266618717|pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-
            Dependent Transcription Initiation Complex
 gi|1666534|gb|AAB18647.1| RNA polymerase beta subunit [Escherichia coli]
 gi|1790419|gb|AAC76961.1| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr.
            MG1655]
 gi|13364386|dbj|BAB38333.1| RNA polymerase beta subunit [Escherichia coli O157:H7 str. Sakai]
 gi|22774032|gb|AAN07182.1| RNA polymerase beta subunit [Cloning vector pIA423]
 gi|30042990|gb|AAP18712.1| RNA polymerase, beta subunit [Shigella flexneri 2a str. 2457T]
 gi|56384051|gb|AAN45489.2| RNA polymerase, beta subunit [Shigella flexneri 2a str. 301]
 gi|73857958|gb|AAZ90665.1| RNA polymerase, beta subunit [Shigella sonnei Ss046]
 gi|81247740|gb|ABB68448.1| RNA polymerase beta subunit [Shigella boydii Sb227]
 gi|85676083|dbj|BAE77333.1| RNA polymerase, beta subunit [Escherichia coli str. K12 substr.
            W3110]
 gi|157069135|gb|ABV08390.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli HS]
 gi|157077982|gb|ABV17690.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E24377A]
 gi|169756938|gb|ACA79637.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli ATCC
            8739]
 gi|169891282|gb|ACB04989.1| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr.
            DH10B]
 gi|170517867|gb|ACB16045.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli SMS-3-5]
 gi|187428350|gb|ACD07624.1| DNA-directed RNA polymerase, beta subunit [Shigella boydii CDC
            3083-94]
 gi|187767357|gb|EDU31201.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4196]
 gi|188490216|gb|EDU65319.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 53638]
 gi|189001730|gb|EDU70716.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4076]
 gi|189354590|gb|EDU73009.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4401]
 gi|189359774|gb|EDU78193.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4486]
 gi|189365467|gb|EDU83883.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4501]
 gi|189370171|gb|EDU88587.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC869]
 gi|189379158|gb|EDU97574.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC508]
 gi|190901299|gb|EDV61067.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli B7A]
 gi|190905431|gb|EDV65062.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli F11]
 gi|192925943|gb|EDV80590.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E22]
 gi|192958786|gb|EDV89223.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E110019]
 gi|194412004|gb|EDX28317.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli B171]
 gi|194416989|gb|EDX33107.1| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae 1012]
 gi|194421277|gb|EDX37297.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 101-1]
 gi|208728040|gb|EDZ77641.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4206]
 gi|208735669|gb|EDZ84356.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4045]
 gi|208740638|gb|EDZ88320.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4042]
 gi|209157310|gb|ACI34743.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. EC4115]
 gi|209751808|gb|ACI74211.1| RNA polymerase beta prime subunit [Escherichia coli]
 gi|209751810|gb|ACI74212.1| RNA polymerase beta prime subunit [Escherichia coli]
 gi|209751812|gb|ACI74213.1| RNA polymerase beta prime subunit [Escherichia coli]
 gi|209751814|gb|ACI74214.1| RNA polymerase beta prime subunit [Escherichia coli]
 gi|209751816|gb|ACI74215.1| RNA polymerase beta prime subunit [Escherichia coli]
 gi|209914724|dbj|BAG79798.1| RNA polymerase beta subunit [Escherichia coli SE11]
 gi|215267391|emb|CAS11842.1| RNA polymerase, beta subunit [Escherichia coli O127:H6 str. E2348/69]
 gi|217321881|gb|EEC30305.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7
            str. TW14588]
 gi|218354426|emb|CAV01228.1| RNA polymerase, beta subunit [Escherichia coli 55989]
 gi|218363310|emb|CAR00960.1| RNA polymerase, beta subunit [Escherichia coli IAI1]
 gi|218367822|emb|CAR05617.1| RNA polymerase, beta subunit [Escherichia coli S88]
 gi|218372603|emb|CAR20478.1| RNA polymerase, beta subunit [Escherichia coli IAI39]
 gi|218434702|emb|CAR15634.1| RNA polymerase, beta subunit [Escherichia coli UMN026]
 gi|238863495|gb|ACR65493.1| RNA polymerase, beta subunit [Escherichia coli BW2952]
 gi|242379517|emb|CAQ34333.1| RNA polymerase, beta subunit, subunit of RNA polymerase, core enzyme,
            RNA polymerase sigma 70, RNA polymerase sigma 54, RNA
            polymerase sigma 32, RNA polymerase sigma 38, RNA
            polymerase sigma 28, RNA polymerase sigma 19 and RNA
            polymerase sigma 24 [Escherichia coli BL21(DE3)]
 gi|253326428|gb|ACT31030.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli
            'BL21-Gold(DE3)pLysS AG']
 gi|253975829|gb|ACT41500.1| DNA-directed RNA polymerase subunit beta [Escherichia coli B str.
            REL606]
 gi|253979985|gb|ACT45655.1| DNA-directed RNA polymerase subunit beta [Escherichia coli BL21(DE3)]
 gi|254595385|gb|ACT74746.1| RNA polymerase, beta subunit [Escherichia coli O157:H7 str. TW14359]
 gi|257756745|dbj|BAI28247.1| RNA polymerase, beta subunit [Escherichia coli O26:H11 str. 11368]
 gi|257761934|dbj|BAI33431.1| RNA polymerase, beta subunit [Escherichia coli O103:H2 str. 12009]
 gi|257767054|dbj|BAI38549.1| RNA polymerase, beta subunit [Escherichia coli O111:H- str. 11128]
 gi|260451186|gb|ACX41608.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli DH1]
 gi|281181051|dbj|BAI57381.1| RNA polymerase beta subunit [Escherichia coli SE15]
 gi|281603373|gb|ADA76357.1| DNA-directed RNA polymerase subunit beta [Shigella flexneri 2002017]
 gi|284924079|emb|CBG37178.1| DNA-directed RNA polymerase, beta-subunit [Escherichia coli 042]
 gi|290765274|gb|ADD59235.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O55:H7
            str. CB9615]
 gi|291321323|gb|EFE60764.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|291425371|gb|EFE98411.1| DNA-directed RNA polymerase beta subunit [Escherichia coli FVEC1412]
 gi|291430817|gb|EFF03814.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|294492658|gb|ADE91414.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli IHE3034]
 gi|298276230|gb|EFI17751.1| DNA-directed RNA polymerase subunit beta [Escherichia coli FVEC1302]
 gi|299880876|gb|EFI89087.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli MS 196-1]
 gi|305854607|gb|EFM55043.1| DNA-directed RNA polymerase subunit beta [Escherichia coli NC101]
 gi|306905545|gb|EFN36078.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli W]
 gi|307556130|gb|ADN48905.1| DNA-directed RNA polymerase beta chain [Escherichia coli ABU 83972]
 gi|307628396|gb|ADN72700.1| DNA-directed RNA polymerase subunit beta [Escherichia coli UM146]
 gi|309704402|emb|CBJ03751.1| DNA-directed RNA polymerase, beta-subunit [Escherichia coli ETEC
            H10407]
 gi|310331394|gb|EFP98659.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 1827-70]
 gi|312290034|gb|EFR17921.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 2362-75]
 gi|312948561|gb|ADR29388.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O83:H1
            str. NRG 857C]
 gi|313648637|gb|EFS13077.1| DNA-directed RNA polymerase, beta subunit [Shigella flexneri 2a str.
            2457T]
 gi|315063312|gb|ADT77639.1| RNA polymerase, beta subunit [Escherichia coli W]
 gi|315138543|dbj|BAJ45702.1| DNA-directed RNA polymerase subunit beta [Escherichia coli DH1]
 gi|315617350|gb|EFU97956.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 3431]
 gi|320179552|gb|EFW54503.1| DNA-directed RNA polymerase beta subunit [Shigella boydii ATCC 9905]
 gi|320185975|gb|EFW60723.1| DNA-directed RNA polymerase beta subunit [Shigella flexneri CDC
            796-83]
 gi|320190917|gb|EFW65567.1| DNA-directed RNA polymerase beta subunit [Escherichia coli O157:H7
            str. EC1212]
 gi|320197118|gb|EFW71736.1| DNA-directed RNA polymerase beta subunit [Escherichia coli WV_060327]
 gi|320200174|gb|EFW74763.1| DNA-directed RNA polymerase beta subunit [Escherichia coli EC4100B]
 gi|320639077|gb|EFX08717.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            str. G5101]
 gi|320644471|gb|EFX13534.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H-
            str. 493-89]
 gi|320649790|gb|EFX18311.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H-
            str. H 2687]
 gi|320655123|gb|EFX23079.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O55:H7
            str. 3256-97 TW 07815]
 gi|320660767|gb|EFX28221.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O55:H7
            str. USDA 5905]
 gi|320665885|gb|EFX32916.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            str. LSU-61]
 gi|323161291|gb|EFZ47201.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli E128010]
 gi|323167457|gb|EFZ53165.1| DNA-directed RNA polymerase, beta subunit [Shigella sonnei 53G]
 gi|323177540|gb|EFZ63125.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 1180]
 gi|323190156|gb|EFZ75434.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli RN587/1]
 gi|323380624|gb|ADX52892.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli KO11]
 gi|323933971|gb|EGB30445.1| DNA-directed RNA polymerase [Escherichia coli E1520]
 gi|323938896|gb|EGB35116.1| DNA-directed RNA polymerase [Escherichia coli E482]
 gi|323943596|gb|EGB39705.1| DNA-directed RNA polymerase [Escherichia coli H120]
 gi|323948841|gb|EGB44738.1| DNA-directed RNA polymerase [Escherichia coli H252]
 gi|323953800|gb|EGB49607.1| DNA-directed RNA polymerase [Escherichia coli H263]
 gi|323958913|gb|EGB54588.1| DNA-directed RNA polymerase [Escherichia coli H489]
 gi|323969060|gb|EGB64368.1| DNA-directed RNA polymerase [Escherichia coli TA007]
 gi|324115418|gb|EGC09363.1| DNA-directed RNA polymerase [Escherichia coli E1167]
 gi|326347163|gb|EGD70893.1| DNA-directed RNA polymerase beta subunit [Escherichia coli O157:H7
            str. 1125]
 gi|326347586|gb|EGD71308.1| DNA-directed RNA polymerase beta subunit [Escherichia coli O157:H7
            str. 1044]
 gi|330908304|gb|EGH36823.1| DNA-directed RNA polymerase beta subunit [Escherichia coli AA86]
 gi|331057159|gb|EGI29151.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA143]
 gi|331061927|gb|EGI33851.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli TA271]
 gi|331077038|gb|EGI48254.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli H299]
 gi|332083875|gb|EGI89088.1| DNA-directed RNA polymerase, beta subunit [Shigella boydii 5216-82]
 gi|332091111|gb|EGI96201.1| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae
            155-74]
 gi|332092313|gb|EGI97388.1| DNA-directed RNA polymerase, beta subunit [Shigella boydii 3594-74]
          Length = 1342

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|88909636|sp|Q57H69|RPOB_SALCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1670 bits (4324), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDLKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|297180339|gb|ADI16556.1| DNA-directed RNA polymerase, beta subunit/140 kd subunit [uncultured
            gamma proteobacterium HF0010_01E20]
          Length = 1350

 Score = 1669 bits (4323), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1358 (52%), Positives = 972/1358 (71%), Gaps = 9/1358 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK  E +++P L+ +Q  SY  FL +    ++R   GL AAFKSV
Sbjct: 1    MAYSFTERKRIRKDFGKLAEKMELPYLLAIQTDSYSKFLQVGTDAEDRAESGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG+A LE+V Y+   P FDV +C+ R +TYA PL++ +RLI++D    + +K +
Sbjct: 61   FPIVSYSGSAELEYVDYKLGEPIFDVKECVSRSITYAAPLRVKVRLIIYDK--ESSSKKV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +YMG++PLMT++GTFVI G +R+VVSQLHRSPG+ FDHDKG+   SGKLLY  
Sbjct: 119  KDVKEQEVYMGEIPLMTENGTFVINGTERVVVSQLHRSPGVFFDHDKGKTHSSGKLLYNA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  SEEIL TF+     S +G
Sbjct: 179  RVIPYRGSWLDFEFDPKDAVFVRIDRRRKLPASIILRALGFSSEEILETFFETNTISIKG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G   S  +V    G+ ++E+G+++T+  ++ +++ G+K L +  D 
Sbjct: 239  EDVAVSLIAERL-RGEVASFDIVGP-NGKTIVEAGRRITARHVRVIEDSGMKQLAVPKDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     A+DIV+  TGE+ I    VI E+ L+ +   +++    +Y + ++   +I +T+
Sbjct: 297  LLEQVTAKDIVDESTGEVAIPCNSVISEEVLDRLLELKVKSFETIYTNDLDCGPFISDTM 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R ++L++IYR+MRPG+  T   AE++F  LFF +D+YDLS+VGR+K N RL  
Sbjct: 357  RIDPSSNRMESLVEIYRMMRPGEPPTKESAENLFGNLFFSNDRYDLSSVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + +EDI+ ++K L+D+RNGKGT+DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  EETEGEGTLSREDIVDVLKTLIDIRNGKGTVDDIDHLGNRRIRSVGEMAENQFRVGLIRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQD+INAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVKERLSLAESEGLMPQDMINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
             +V +G VT +V +LSA++E    IAQA++ +D  G F +ELV  R   E        ID
Sbjct: 597  HRVVNGVVTKEVEFLSAIDEAQYVIAQASAPVDTKGKFIDELVDVRHQNEFTRTAPANID 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  
Sbjct: 657  FMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVALD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++AKR G+V+ VDA R+VIR  + +++   +GVDIY L KF RSNQNTC+NQRPLV
Sbjct: 717  SGVCVIAKRGGVVDSVDASRVVIRVADSEVESGDAGVDIYTLTKFTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD +   DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 777  KPGDVISARDILADGPSIDMGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCIARDTKLGPEEITSDIPNVGEGALSKLDESGIVYIGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTS RVPS V GTV+DV++F R G++K+ER+  +ER 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSQRVPSSVKGTVIDVQVFTRDGVEKDERAKDIERA 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D DDE  I++   + RL   L G    + P G  K   +  + ++      W+
Sbjct: 957  QLAQIRKDLDDEMRIIEVATFERLQRALVGNKVATAP-GLAKDKAIYEEYLAGLATDDWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+++   +E  +      +  L+  +++K  KI+ GDD+ PGVL++VKV++A+KR
Sbjct: 1016 RIRMKDDQLNEQLERAEAHLLERREGLDAVYQDKRSKIETGDDLAPGVLKIVKVYLAIKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMPF ++G PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPFDENGDPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
            WA  G+G+KI  ++   K     + +R FL++V    G   E +   +D  +L +A    
Sbjct: 1136 WAAHGIGQKIDLML---KQQQKAAEIRKFLDEVYNHVGGAPENLKSLNDGQILEMARNLT 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+P +T  FDGA E  I  ML +A+L  SGQ+ LYDG TG+ FDRP+T+GY+YMLKLNH
Sbjct: 1193 GGLPFATRAFDGASEAEIKKMLELAELPGSGQTTLYDGRTGDAFDRPITLGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            V GRT++Y++IV G+   E G PESFNVLVKE+++LG+
Sbjct: 1313 VNGRTKMYKNIVDGDFKMEPGMPESFNVLVKEIRSLGI 1350


>gi|288937721|ref|YP_003441780.1| DNA-directed RNA polymerase subunit beta [Klebsiella variicola At-22]
 gi|290513229|ref|ZP_06552590.1| DNA-directed RNA polymerase, beta subunit [Klebsiella sp. 1_1_55]
 gi|288892430|gb|ADC60748.1| DNA-directed RNA polymerase, beta subunit [Klebsiella variicola
            At-22]
 gi|289774326|gb|EFD82333.1| DNA-directed RNA polymerase, beta subunit [Klebsiella sp. 1_1_55]
          Length = 1342

 Score = 1669 bits (4322), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVASKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|206579488|ref|YP_002241076.1| DNA-directed RNA polymerase, beta subunit [Klebsiella pneumoniae 342]
 gi|226699413|sp|B5XYF5|RPOB_KLEP3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|206568546|gb|ACI10322.1| DNA-directed RNA polymerase, beta subunit [Klebsiella pneumoniae 342]
          Length = 1342

 Score = 1669 bits (4322), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVASKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVAGGV-------------EADKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|16762300|ref|NP_457917.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. CT18]
 gi|41018098|sp|Q8Z320|RPOB_SALTI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|25288392|pir||AE0933 DNA-directed RNA polymerase, beta-chain [imported] - Salmonella
            enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504604|emb|CAD09487.1| DNA-directed RNA polymerase, beta-subunit [Salmonella enterica subsp.
            enterica serovar Typhi]
          Length = 1342

 Score = 1669 bits (4321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+ LRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSFLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|302877794|ref|YP_003846358.1| DNA-directed RNA polymerase, beta subunit [Gallionella
            capsiferriformans ES-2]
 gi|302580583|gb|ADL54594.1| DNA-directed RNA polymerase, beta subunit [Gallionella
            capsiferriformans ES-2]
          Length = 1359

 Score = 1669 bits (4321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1365 (51%), Positives = 966/1365 (70%), Gaps = 7/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK    + +P L+  Q  ++  FL    AP++R NEGLQAAF  +
Sbjct: 1    MSYSFTEKKRIRKSFGKRIGALPVPFLLSTQLEAFAAFLQEATAPEKRKNEGLQAAFNGI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + S  A L+FVSY    P FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHSKNARLDFVSYMLGTPAFDVKECQQRGLTYASPLRARVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEMPLMTNTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD ++ RIDRRRK+PVT  L +LG  +E++L  FY    +    
Sbjct: 179  RIIPYRGSWLDFEFDAKDYVYFRIDRRRKMPVTILLRSLGYTNEDMLGMFYEFDTFQLGK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                     A+ + G      ++D  +G+ ++ + K++T   ++ ++E G+  L +  D 
Sbjct: 239  KGGIQFEVVAERLRGEIARFDILD-KSGKTIVATDKRITVRHIRQMQEAGIDKLAVADDF 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++++ E+GEI   A DV+ E+ L ++  + +  +  LY + ++  AYI  TL
Sbjct: 298  LLGRVIANNVIDKESGEIIANANDVMTEELLRKLQDANVTKLNTLYTNDLDQGAYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E +FN LFF  ++YDLS VGR+K N R+  
Sbjct: 358  RTDETTDKWTARVAIYRMMRPGEPPTEESVEGLFNGLFFSEERYDLSVVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDI+A++KILV+LRNG+G IDDID+LGNRRVR+VGE+ +NQ+R+GL R+
Sbjct: 418  EELTGSPILSNEDIVAVVKILVELRNGRGEIDDIDHLGNRRVRAVGELAENQFRVGLARV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLINAKP+ +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINAKPISAAIKEFFGSSQLSQFMDQTNPLSEVTHKRRIS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARTNEYGFIETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G V+NDV YLSA+EE    IAQAN+ LD+ G FT+++V  R   E +L   + I+
Sbjct: 598  RKVTNGCVSNDVDYLSAIEESTYTIAQANAELDKKGRFTDDIVSARRHNEFVLAAPDTIN 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP QVVS+AA LIPFLE+DD+NR LMG NM RQAVP L+AE P VGTG+E  VA  
Sbjct: 658  YMDVSPSQVVSVAACLIPFLEHDDANRALMGANMSRQAVPCLRAEKPLVGTGIERTVALD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG A+ A R G ++ VDA RIV+R  + +      GVDIY L+K+ RSNQNT +NQRPLV
Sbjct: 718  SGTAVQAIRGGRIDYVDAARIVVRVNDEETTAGEVGVDIYNLIKYTRSNQNTNINQRPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + R D++ADG STD+G+LALG+N+LVAFMPW+GYN+EDS+LISER++++D FTSI
Sbjct: 778  KVGDVIARGDVVADGASTDMGELALGQNVLVAFMPWNGYNYEDSILISERIIAQDRFTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDIPN+SE  L  +D+CGI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELTVVARDTKLGTEEITRDIPNLSEVQLGRLDDCGIVHIGAEVAVGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV +G SGTV+DV++F R G+ +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVSAGSSGTVIDVQVFTREGLQRDKRAQQIVDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D  D+  I++ + ++RL ++L  + A  GPK   K ++L++D +S     QW+
Sbjct: 958  ELNRYKKDLADQMRIVESDAFTRLEKLLLDKVANGGPKKLAKGSLLTADYLSGVEHHQWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++V   +E +K      +   +  F+ K +K+  GD++  GV ++VKV+VA+KR
Sbjct: 1018 DIRLADDEVAAQMEQVKDGLAQKRLEFDAAFELKKKKMTQGDELQAGVQKMVKVYVAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRI+P EDMP++ DGTPVD+VLNPLGVPSRMN+GQI ETHLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVISRIVPVEDMPYMADGTPVDVVLNPLGVPSRMNIGQILETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI-GTGSHTEKISDYDDDSVLRVAEQWK 1201
            WA  GLGKKI  ++   + N  I+ LR FL+K+       +     + DD ++ +    +
Sbjct: 1138 WAANGLGKKIDQML---QTNAKITELRGFLDKIYNNNNGQSVDFKSFTDDEIIELCRNLR 1194

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP +TPVFDGA EE I  ML +ADL  SGQ+ L+DG TGE FDRPVTVGY ++LKL+H
Sbjct: 1195 KGVPFATPVFDGASEEEIKYMLALADLPLSGQTTLHDGRTGEAFDRPVTVGYKHVLKLHH 1254

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1255 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1314

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT+VYE+IV G+   + G PESFNV++KE+++L + +DLE +
Sbjct: 1315 VAGRTKVYENIVKGDHKIDAGMPESFNVVIKEIRSLAIDMDLERN 1359


>gi|320172752|gb|EFW47986.1| DNA-directed RNA polymerase beta subunit [Shigella dysenteriae CDC
            74-1112]
          Length = 1342

 Score = 1669 bits (4321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI++   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQKLACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|218692268|ref|YP_002400480.1| DNA-directed RNA polymerase subunit beta [Escherichia coli ED1a]
 gi|254765290|sp|B7MRB3|RPOB_ECO81 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|218429832|emb|CAR10801.2| RNA polymerase, beta subunit [Escherichia coli ED1a]
          Length = 1342

 Score = 1669 bits (4321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 973/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + ++ + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVSVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|58038861|ref|YP_190825.1| DNA-directed RNA polymerase subunit beta [Gluconobacter oxydans 621H]
 gi|58001275|gb|AAW60169.1| DNA-directed RNA polymerase beta chain [Gluconobacter oxydans 621H]
          Length = 1447

 Score = 1669 bits (4321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 806/1391 (57%), Positives = 1053/1391 (75%), Gaps = 31/1391 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL MN++PD R + GLQ  F+S
Sbjct: 60   AITKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYEAFLQMNVSPDSRQDAGLQEVFRS 119

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   L+F+SYEF+ PK+DV++C+ R LTYA PLK+ LRL  +D+DE TG++S
Sbjct: 120  VFPINDFAGRGRLDFMSYEFEDPKYDVEECIQRGLTYAAPLKVILRLTTWDIDEDTGSRS 179

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I D+KEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 180  IHDMKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFA 239

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 240  ARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYLAQREQKIAEGGDVE 299

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD +EILS FY  + +++ G  W  P    D   G K+ S LVD DTGE V E+
Sbjct: 300  GLDIRGMDQDEILSYFYEAVPFTRLGGEWARPFDP-DAFRGLKLLSPLVDADTGEVVAEA 358

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + EK  + + +    + G ++A D+VN  TGEIY EAG+ + E  L  +
Sbjct: 359  DAKLTARMVRKIAEK-TRVVQVGRLDILGRFLAYDLVNENTGEIYGEAGEELTEDRLAAL 417

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                I ++P+L VD  ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T   AE+MF
Sbjct: 418  EEMGITELPLLSVDG-SHGPWIRNTLAADKNSCRDEALIDIYRIMRPGEPPTKETAEAMF 476

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            + LFFD  +YDLS VGRVKMNMRL++D PD +R +RKEDI+  IKI+ +L++G+G IDDI
Sbjct: 477  HGLFFDQGRYDLSAVGRVKMNMRLDVDAPDTLRVLRKEDILRTIKIMCELKDGRGQIDDI 536

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 537  DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 596

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET+ 
Sbjct: 597  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETAG 656

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              NIGL++SL+++A+VN YGFIETPYR V +G + +   YLSAMEEE   +AQA++  D+
Sbjct: 657  RPNIGLINSLSTYAKVNKYGFIETPYRLVEEGVLQDGWKYLSAMEEEKLVVAQADAKQDD 716

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G  T+ELV  R +G+  +VP +++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 717  QGRLTDELVSVRRSGDFRVVPPDQVTACDVSPKQLVSVAAALIPFLENDDANRALMGANM 776

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL+KA+AP VGTGME+ VA  SGA IVAKR G+++Q+D  RIV+R+ +     +T
Sbjct: 777  QRQAVPLVKADAPLVGTGMEAAVAHDSGATIVAKRRGVIDQIDGARIVVRATDEAG--AT 834

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLVKVGD V   DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 835  QGVDIYRLRKYMRSNQSTCINQRPLVKVGDTVHAGDIIADGPSTELGELALGRNVLVAFM 894

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 895  PWNGYNFEDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 954

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +
Sbjct: 955  DEAGIVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTT 1014

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE L +D+DDE+ I +R+ Y+RL E L GQ A 
Sbjct: 1015 GTIVDVRVFSRRGVDKDERAMAIERAEIERLTKDRDDERGIQERSFYNRLRERLIGQTAG 1074

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++ +++ E+ R+ W    V  ++V   +E L+ +++ +   ++ RF +K
Sbjct: 1075 AGFKGIRSGTPITEEVLDEHHRATWASITVTSDEVMAELEKLRGEFKEATRRIDARFDSK 1134

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL++G 
Sbjct: 1135 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLENGQ 1194

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS-PLRSFLEKV 1175
             VDIVLNPLGVPSRMN+GQI ETHLGWAC  +G  I  ++++Y+  G+    L   L +V
Sbjct: 1195 AVDIVLNPLGVPSRMNIGQILETHLGWACANIGASIGDMVDEYQRTGERKQELLDRLHEV 1254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G     E ++   ++ ++ +A   + G+P++TPVFDGA    I  ML  A +++SGQS 
Sbjct: 1255 YGDVIFNEDVATLPNEQLIELANNLRKGLPIATPVFDGASIPDIEEMLEKAGVNKSGQSQ 1314

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1315 LIDGRTGEPFERQTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1374

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE++
Sbjct: 1375 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELK 1434

Query: 1356 ALGLSIDLENS 1366
            +LGL+++LE S
Sbjct: 1435 SLGLNVELEQS 1445


>gi|297518012|ref|ZP_06936398.1| DNA-directed RNA polymerase subunit beta [Escherichia coli OP50]
          Length = 1342

 Score = 1668 bits (4320), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 973/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA +
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVN 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|15804577|ref|NP_290618.1| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7
            EDL933]
 gi|25288387|pir||C86090 RNA polymerase, beta subunit [imported] - Escherichia coli  (strain
            O157:H7, substrain EDL933)
 gi|12518912|gb|AAG59183.1|AE005630_3 RNA polymerase, beta subunit [Escherichia coli O157:H7 str. EDL933]
          Length = 1342

 Score = 1668 bits (4320), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q +   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QXKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|311281463|ref|YP_003943694.1| DNA-directed RNA polymerase, beta subunit [Enterobacter cloacae SCF1]
 gi|308750658|gb|ADO50410.1| DNA-directed RNA polymerase, beta subunit [Enterobacter cloacae SCF1]
          Length = 1342

 Score = 1668 bits (4320), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELLPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  T+
Sbjct: 292  IAGKVAAKDYVDESTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDDGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGLVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|307776497|pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
 gi|42818|emb|CAA23625.1| rpoB [Escherichia coli]
 gi|42821|emb|CAA23627.1| unnamed protein product [Escherichia coli]
 gi|223475|prf||0808236A polymerase beta,RNA
          Length = 1342

 Score = 1668 bits (4320), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|94500503|ref|ZP_01307034.1| DNA-directed RNA polymerase, beta subunit [Oceanobacter sp. RED65]
 gi|94427293|gb|EAT12272.1| DNA-directed RNA polymerase, beta subunit [Oceanobacter sp. RED65]
          Length = 1359

 Score = 1668 bits (4319), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1367 (52%), Positives = 990/1367 (72%), Gaps = 11/1367 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D+P L+ +Q  SY  FL  +   D R + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLPRVMDVPYLLAIQLDSYRSFLQADKGVDARGDIGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG+A LE+VSY    P FD  +C+ R +TYA PL++ +RLI++D D  +  K+I
Sbjct: 61   FPIVSYSGSAALEYVSYRLGVPVFDEKECMLRGVTYAAPLRVKVRLIIYDKD--SSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGKLLY  
Sbjct: 119  KDIKEQEVYMGEMPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKLLYNA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L ALG +S+++L  F+        G
Sbjct: 179  RVIPYRGSWLDFEFDPKDLVYVRIDRRRKLPATILLRALGFESQQMLEMFFDNDKLEIVG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  L D   G+ ++E G+++T+  ++ ++++G+  L + SD 
Sbjct: 239  DTVRLELIPERL-RGETASFDLKDPK-GKVIVEEGRRITARHIRQMEKEGMTSLEVPSDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+DIV+  TGE+  E    I  + LE++  + I++I  +Y + ++  ++I +TL
Sbjct: 297  IFGKVIAKDIVDPSTGELVAECNSEITVELLEKLTSAGIKEIETIYSNELDCGSFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D ++ + +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS+VGR+K N RL  
Sbjct: 357  RIDPSRTQLEALVEIYRMMRPGEPPTKESAEGLFENLFFTDERYDLSSVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    +  +DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 417  EEVEGEGTLSNDDIIDVLKELIGIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  ERAVRERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSTYARTNDYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+D+ Y+SA++E    IAQA++ +DEDG  T +L+  R   E  + P E + 
Sbjct: 597  RKVVDGKVTDDINYISAIDEAKYTIAQASAPVDEDGRLTGDLISVRHKNEFTVTPPENVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QV+S+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG+ES VA+ 
Sbjct: 657  LMDVSPQQVISVAASLIPFLEHDDANRALMGSNMQRQAVPTLVADKPLVGTGIESNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV+R  + ++    +GVDIY L K+ RSNQNTC+NQ+PLV
Sbjct: 717  SGVCVVAKRGGKIDSVDASRIVVRVNDDEVQAGEAGVDIYNLTKYTRSNQNTCINQKPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SE++  ED  T+I
Sbjct: 777  RQGDSVVRGDIMADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILLSEKVAQEDRLTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE G++ +GAEVNPGDILVGK+TPKG
Sbjct: 837  HIQELTCVARDTKLGPEEISADIPNVGESALSKLDESGVVYIGAEVNPGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV +G +GTV+DV++F R G++K++R++ +E+ 
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVKTGTTGTVIDVQVFTRDGVEKDQRALDIEKS 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY-PRSQW 1021
            Q++ + +D ++E  I++   + RL   L G    + P G KK  VLS++         Q 
Sbjct: 957  QLDKVRKDLNEEFRIVEEATFERLKRSLDGVKVAAAP-GLKKGDVLSAEYFDGLESSDQL 1015

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            ++   QDE+    +E  +      + +L+++F++K +K+Q GDD+ PGVL++VKV++A+K
Sbjct: 1016 FKIRPQDEEAAELLERAEEALTDRRKLLDEKFEDKKKKLQTGDDLAPGVLKIVKVYLAIK 1075

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S I+P EDMP+ + G PVD+VLNPLGVPSRMNVGQI ETHL
Sbjct: 1076 RKIQPGDKMAGRHGNKGVISAIMPIEDMPYDEKGVPVDLVLNPLGVPSRMNVGQILETHL 1135

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG--TGSHTEKISDYDDDSVLRVAEQ 1199
            G A  GLG+KI  +I   +    I+ +R FL ++         E +  + D+ ++ +A  
Sbjct: 1136 GMAAKGLGEKINEMI---RQQKAIAEIRDFLGQIYNHSDEVKQEALDTFSDEEIMELAGN 1192

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               GVP++TP FDGA E  + S+LR+AD+ +SGQ  L+DG TG+ FDRPVTVGY+YMLKL
Sbjct: 1193 LVGGVPMATPAFDGAQESEVKSLLRLADVPDSGQVTLFDGRTGDQFDRPVTVGYMYMLKL 1252

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1253 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1312

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LEN 
Sbjct: 1313 DDVAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELEND 1359


>gi|296282035|ref|ZP_06860033.1| DNA-directed RNA polymerase subunit beta [Citromicrobium
            bathyomarinum JL354]
          Length = 1397

 Score = 1667 bits (4318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 822/1381 (59%), Positives = 1060/1381 (76%), Gaps = 14/1381 (1%)

Query: 1    MAKGVVFNG--LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            M +G    G    R+RK FG   E++ +P+LIEVQ+ SY+ FL  +   D     GL+  
Sbjct: 14   MKRGTAKTGTAKRRIRKIFGDIHEVVQMPNLIEVQRESYEQFLRSDKEIDYVS--GLEKT 71

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
             +SVFPI  F+G A L+FV YE +PPK+D  +C  R +TYA P+++TLRLIVF+VD+ T 
Sbjct: 72   LRSVFPIRDFAGTAELDFVDYELEPPKYDTTECRQRGITYAAPMRVTLRLIVFEVDQDTE 131

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            A+S+ DIKEQ +YMGD+PLMT++GTF++ G +R++VSQ+HRSPG+ FDHD+G+   SGKL
Sbjct: 132  ARSVLDIKEQEVYMGDMPLMTENGTFIVNGTERVIVSQMHRSPGVLFDHDRGKTHSSGKL 191

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L+A R+IP +G W+D EFD+KDI++VRIDR+RK+PVTS L  LG+DSEEIL  FY  +V+
Sbjct: 192  LFAARVIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTSLLYGLGLDSEEILHHFYDTVVW 251

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
             +  D W  P  A     GAK +  LVD  TGE+V  + +K++       ++ G++ L +
Sbjct: 252  QRAKDGWTIPFVAE-QWRGAKPTFPLVDAKTGEEVFPANQKISPRAANKAEKDGLETLLL 310

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             S+ +   Y A D+++  TG IYIEAGD +  + LE +  + +  + +L +D VN   +I
Sbjct: 311  PSEEIFSRYAARDMIDESTGRIYIEAGDEVTPEHLEVLDAAGVDQVELLDIDEVNTGPWI 370

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  DK ++R + L  IY+VMRPG+  T   AE++F  LFFDS++YDLS VGRVK+NM
Sbjct: 371  RNTLKADKAENRDEGLEAIYKVMRPGEPPTKETAEALFEGLFFDSERYDLSAVGRVKLNM 430

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RL LD  D V  +RKEDI+A++K LV L++GKG +DDIDNLGNRRVRSVGE+L+NQYR+G
Sbjct: 431  RLELDAEDTVTTLRKEDILAVVKELVGLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVG 490

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LLRMER++KER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH 
Sbjct: 491  LLRMERAVKERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHK 550

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL SF+RVN YGFI
Sbjct: 551  RRVSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLASFSRVNKYGFI 610

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV DGKVT+DVVYLSAMEE+   +AQA++ LDE+GSF EELV  R +G+ ++ PR
Sbjct: 611  ETPYRKVVDGKVTSDVVYLSAMEEQKHTVAQASAELDENGSFVEELVSARQSGDNLMAPR 670

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E I  +D SPKQ+VS+ ASLIPFLENDD+NR LMG NMQRQAVPL+KAEAP+VGTGME  
Sbjct: 671  ETITLMDVSPKQLVSVGASLIPFLENDDANRALMGANMQRQAVPLVKAEAPWVGTGMEET 730

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA+ SGAAI A+R GIV+QVDA RIVIR+  GD++P  SGVDIY L KFQRSNQ+TC+NQ
Sbjct: 731  VARDSGAAITARRGGIVDQVDATRIVIRA-IGDVEPGQSGVDIYTLQKFQRSNQDTCINQ 789

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVG+ V + D+IADGPSTDLG+LALG+N LVAFMPW+GYN+EDS+LISER+V +DV
Sbjct: 790  RPLVKVGETVEQGDVIADGPSTDLGELALGKNSLVAFMPWNGYNYEDSILISERIVKDDV 849

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDIL GKI
Sbjct: 850  FTSIHIEEFEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILCGKI 909

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GV+GTVV+VR+FNRHGI+ ++R+ +
Sbjct: 910  TPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTVVEVRVFNRHGIEIDDRTRA 969

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            ++ E+IE L +D  DE+ IL+R  Y+RL ++L GQ A + PKG KK T L+ ++I    R
Sbjct: 970  IQNEEIERLRKDSADERAILNRATYNRLKDMLVGQTASAAPKGIKKGTELTDEVIESVDR 1029

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
             +W++FAV+D+  Q  +E++K QY+ +  +++ +F+++ EK++ GD++ PGVL++VKVFV
Sbjct: 1030 HEWFKFAVEDDDRQAQLEAIKGQYDDAVKVIDAKFEDRKEKLERGDELAPGVLKMVKVFV 1089

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++SRILP EDMPFL DGTPVDIVLNPLGVPSRMNVGQIFE
Sbjct: 1090 AVKRKLQPGDKMAGRHGNKGVISRILPEEDMPFLADGTPVDIVLNPLGVPSRMNVGQIFE 1149

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISP-------LRSFLEKVIGTGSHTEKISDYDDD 1191
            THLG A    G +IK  + D++A    +        ++  L+++ G   + + I     +
Sbjct: 1150 THLGMAARSFGHQIKDALEDWRAKNPDAEPGEPPAVIKDKLKEIYG-EDYHDSIDSRSGE 1208

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +  +A     GVP+ TPVFDGA E  + + L  + LD  GQSIL+DG TG+ F R VTV
Sbjct: 1209 EIAELAGNLTRGVPMGTPVFDGARESDVTTQLTKSGLDADGQSILFDGRTGDAFHRKVTV 1268

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L
Sbjct: 1269 GIIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTL 1328

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDVVGR +VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L++   ++ 
Sbjct: 1329 QEMLTVKSDDVVGRQKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGLNVELKSIADEDD 1388

Query: 1372 A 1372
             
Sbjct: 1389 E 1389


>gi|242241127|ref|YP_002989308.1| DNA-directed RNA polymerase subunit beta [Dickeya dadantii Ech703]
 gi|242133184|gb|ACS87486.1| DNA-directed RNA polymerase, beta subunit [Dickeya dadantii Ech703]
          Length = 1342

 Score = 1667 bits (4318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG+A L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGSAELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ KIVY    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYSTEDILGLFFDKIVYEINN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D V+  TGE+   A   +    L  +  +  + I  L+ + +++  Y+  T+
Sbjct: 292  IAGKVLAKDYVDTSTGEVIAMANMELSLDLLARLSQAGHKRIETLFTNDLDHGPYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DAIEGSGILSKEDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F +ELV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFIDELVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EAEKLGKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+A+  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGSGVRQKVDLNTFSDEEVLRLADNLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|288549953|ref|ZP_05968754.2| DNA-directed RNA polymerase, beta subunit [Enterobacter cancerogenus
            ATCC 35316]
 gi|288316949|gb|EFC55887.1| DNA-directed RNA polymerase, beta subunit [Enterobacter cancerogenus
            ATCC 35316]
          Length = 1353

 Score = 1667 bits (4318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQYTTEQILDLFFEKVIFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 246  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDDIKLIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  T+
Sbjct: 303  IAGKVSAKDYVDESTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYISETI 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTTDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                 + ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIYAVLVAGG-------------IEAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 QIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + DD VLR+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQEEVAKLREFIQRAYDLGTDVRQKVDLNTFSDDEVLRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLQLGGLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|301069211|dbj|BAJ11985.1| mutated RNA polymerase beta subunit [Escherichia coli]
          Length = 1342

 Score = 1667 bits (4318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   S K+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSDKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|157147219|ref|YP_001454538.1| DNA-directed RNA polymerase subunit beta [Citrobacter koseri ATCC
            BAA-895]
 gi|157084424|gb|ABV14102.1| hypothetical protein CKO_03002 [Citrobacter koseri ATCC BAA-895]
          Length = 1353

 Score = 1667 bits (4318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQYTTEQILDLFFEKVIFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 246  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 303  IAGKVASKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RIDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 603  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 723  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 783  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLSEELQILEAGLFSRIHAVLVSGGV-------------EAEKLDKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1190 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERSVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|182676599|sp|A8AKT9|RPOB_CITK8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1667 bits (4317), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVASKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RIDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIHAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERSVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|56477587|ref|YP_159176.1| DNA-directed RNA polymerase subunit beta [Aromatoleum aromaticum
            EbN1]
 gi|81357338|sp|Q5P339|RPOB_AZOSE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56313630|emb|CAI08275.1| DNA-directed RNA polymerase, beta chain [Aromatoleum aromaticum EbN1]
          Length = 1377

 Score = 1667 bits (4317), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1383 (51%), Positives = 962/1383 (69%), Gaps = 27/1383 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K   ++++P L+  Q  S+  FL  +  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFAKRAAVLNVPFLLATQIESFASFLQADTPPPSRLNHGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ SG A LEFV Y    P FDV +C  R LT+A PL+  +RL++ D D      ++
Sbjct: 61   FPISSHSGNARLEFVQYMLGEPAFDVKECQQRGLTFASPLRARVRLVILDRDAPKE--TV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+P T  L A+GM  EEIL+TF+    +  RG
Sbjct: 179  RIIPYRGSWLDFEFDPKDALYFRVDRRRKMPATILLRAIGMGPEEILATFHDFDAFHLRG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L   D + G      + D   G  ++   K++T+  ++ L + GVK + +  + 
Sbjct: 239  NEAAFELVP-DRLRGDVAKFDITDGA-GNVIVARDKRITAKHIRELDQAGVKMISVPDEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A +IV+ ETGEI   A D I E  L+++  + ++D+  LYV+ ++  AYI  TL
Sbjct: 297  LLGRIIARNIVDAETGEIVARANDEITEDLLDKLRDAGVKDLETLYVNDLDRGAYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  ++YDLS+VGR+K N R   
Sbjct: 357  RIDETADQWAARVAIYRMMRPGEPPTEDAVEALFQGLFYSEERYDLSSVGRMKFNRRAYP 416

Query: 423  DT--------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +                      +    +  EDI+A+I +LV+LRNG+G IDDID+LGNR
Sbjct: 417  EKIEDKAPSWLKRFYETVGPRGEEGPATLSNEDILAVIGVLVELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVRSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKP+ +A+ EFF SSQL
Sbjct: 477  RVRSVGELAENQFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPISAAIKEFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +A+ N +GF+ETPYRKV D KVT+ + +LSA+EE    IAQAN+ +D DG    
Sbjct: 597  INSLAVYAQTNRHGFLETPYRKVVDSKVTDQIDFLSAIEEGQYVIAQANAEIDADGMLEG 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV CR  GE  L   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLVSCRHKGEFALSTADQVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ E P VGTG+E  VA  SG A+ A R GIV+ VDA RIV+R  + +      GVDIY
Sbjct: 717  CLRPEKPLVGTGIERTVAVDSGTAVQAMRGGIVDYVDANRIVVRVNDDETLAGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             ++K+ RSNQNT +NQRP+VKVGD + + D+IADG STDLG+LALG+NMLVAFMPW+GYN
Sbjct: 777  NMIKYTRSNQNTNINQRPVVKVGDHIGKGDVIADGASTDLGELALGQNMLVAFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+LISER+V+ED FTSIHIEE  V+ARDTKLGPEEITRDI ++ E  L  +DE GI+
Sbjct: 837  FEDSILISERVVAEDRFTSIHIEELTVVARDTKLGPEEITRDIASLGEAQLSRLDESGIV 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV+ GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV SG++GTV+DV
Sbjct: 897  YIGAEVDAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGMNGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GI++++R+ S+  + +     D  D+  I++R+ ++R+  ++ GQ A  GPK  
Sbjct: 957  QVFTREGIERDKRAQSIIDDMLRSFKTDLADQMRIVERDAFARIRRLIVGQKANGGPKKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K T ++ + +       W+   + DE++   +E+++   E ++   +  F+ K +K+  
Sbjct: 1017 LKGTAITGEYLDSLEFYHWFDIRMADEELAAQLEAIREGLEKTRKDFDQAFEIKKKKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR +Q GDKMAGRHGNKG+VSRI+P EDMP + DGTPVDIVL
Sbjct: 1077 GDELPPGVQKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSRIVPIEDMPHMADGTPVDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI ETHLGWA   LG KI +++   +AN   + +R  LE +       
Sbjct: 1137 NPLGVPSRMNIGQILETHLGWASKALGNKIGTML---RANAAAAEVRELLEHIYNDNGRP 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
            E +    DD V+ +A     GVP +TPVFDGA EE I +M  +A L   GQ  LYDG TG
Sbjct: 1194 EDMGSLKDDEVIELASNLSKGVPFATPVFDGAKEEEIEAMFELAGLQPGGQVTLYDGRTG 1253

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            + FDR VTVGY ++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1254 DAFDRQVTVGYKHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1313

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYESIV G    + G PESFNVLVKE+++L + ID
Sbjct: 1314 EAYGAAYTLQEMLTVKSDDVTGRTKVYESIVKGEHKIDAGMPESFNVLVKEIRSLAIDID 1373

Query: 1363 LEN 1365
            L+ 
Sbjct: 1374 LDT 1376


>gi|251791443|ref|YP_003006164.1| DNA-directed RNA polymerase subunit beta [Dickeya zeae Ech1591]
 gi|247540064|gb|ACT08685.1| DNA-directed RNA polymerase, beta subunit [Dickeya zeae Ech1591]
          Length = 1342

 Score = 1667 bits (4316), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPISSYSGNSELQYVSYRLGEPVFDVQECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+VY    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYSTEEILDLFFDKVVYEIHN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D V+  TGE+   A   +    L ++  +  + I  L+ + +++  Y+  T+
Sbjct: 292  IAGKVLAKDYVDESTGEVIAMANMELSLDLLAKLSQAGHKRIDTLFTNDLDHGPYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F +ELV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFIDELVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++  ++    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQHQEVAKLREFIQRAYDLGNDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKENEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|256821655|ref|YP_003145618.1| DNA-directed RNA polymerase subunit beta [Kangiella koreensis DSM
            16069]
 gi|256795194|gb|ACV25850.1| DNA-directed RNA polymerase, beta subunit [Kangiella koreensis DSM
            16069]
          Length = 1355

 Score = 1666 bits (4315), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1366 (52%), Positives = 980/1366 (71%), Gaps = 12/1366 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG+   I+D+P L+ +QK SY  FL     P    + GL +AFKS+
Sbjct: 1    MAYSYTEKKRIRKDFGRRSNILDVPYLLAIQKDSYREFLE----PRGDEDSGLDSAFKSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            F I ++SG A LE+V Y    P F+V +C  R +TYA PL++ +RL+++D D  T  K +
Sbjct: 57   FAIESYSGNAALEYVGYSLGEPVFNVKECQIRGITYAAPLRVKIRLVIYDKDSKT--KKV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ ++MG+LPLMT++GTFVI G +R++VSQLHRSPG+ FD D+G+   SGKLLY  
Sbjct: 115  KDIREQEVFMGELPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDRGKTHSSGKLLYQA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P +  L +LG +++++L  F+ +  +    
Sbjct: 175  RVIPYRGSWLDFEFDPKDMLYVRIDRRRKLPASIILRSLGYNTQDMLDMFFERNNFYITK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                        + G   +  +     G+ V+E G+++T   +  L++ GVK L + ++ 
Sbjct: 235  KGEVQLELIPSRLRGETATFEIK--AKGKVVVEEGRRITPRHIAQLEKAGVKKLDVPTEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A DI++ E+GEI  EA   I E+ LE++  S + ++P LY + +++  Y+ +TL
Sbjct: 293  IYGRALATDIIDKESGEIIAEANAEITEEILEKMIESGVTEVPTLYTNDLDHGPYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +A ++IYR+MRPG+  T   AE++F  LFF+ ++YDLS VGR+K N R+  
Sbjct: 353  RIDSTRTPLEAKVEIYRMMRPGEPPTQDAAEALFENLFFNLERYDLSRVGRMKFNRRVGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    +  +DII +IK L+++RNG GT+DDID+LGNRR+R VGEM +NQ+R+GL+R+
Sbjct: 413  DEIEGEGTLSNQDIIDVIKTLIEIRNGSGTVDDIDHLGNRRIRCVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + +++MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 473  ERAVKERLSQAESENLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLACYARTNQYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGK T DV YLSA++E    IAQAN++LD++G+F+++LV  R  GE +L   +++ 
Sbjct: 593  RRVADGKPTADVDYLSAIDEGKFVIAQANANLDKNGTFSDDLVPSRFQGEFMLATPDQVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AAS+IPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  
Sbjct: 653  YMDVSPQQIVSVAASMIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERTVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+V+QVDA R+VIR  E ++  + SGVDIY   K+ RSNQNTC+NQRP+V
Sbjct: 713  SGVVVAAKRGGVVDQVDASRVVIRVNEDEVGDNDSGVDIYNFTKYTRSNQNTCINQRPIV 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+LISE +V ED FTSI
Sbjct: 773  KQGDIVARGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILISENVVQEDRFTSI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKG
Sbjct: 833  HIQELTCISRDTKLGPEEITADIPNVGESALSKLDESGIVYIGAEVKPGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV +   GTV+DV++F R G++K+ R+  +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDTSLRVGTSTHGTVIDVQVFTRDGVEKDARAKEIENA 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D +DE  IL  +IY R   ++ G     GP  FKK + ++ D + E   SQ+ 
Sbjct: 953  EVASAKKDLNDEFRILADSIYQRARNLVMGCVGEKGPNKFKKGSKITVDYLDELEPSQYL 1012

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++ E+ Q+ +ESL       +   + +F+ +  KI  GDD+ PGV ++VKV++A+KR
Sbjct: 1013 EIQLRVEEKQQALESLANYLAEQRKEYDKKFEVQKLKITQGDDLAPGVQKIVKVYLAVKR 1072

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1073 RIQPGDKMAGRHGNKGVISTIVPIEDMPYDENGEPVDIVLNPLGVPSRMNIGQILETHLG 1132

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRVAEQWK 1201
            WA  G+G KI  L++  KA      +R+FL KV          +S+  DD V+ +A   +
Sbjct: 1133 WAAKGVGTKIGELLDTGKAP---KTVRTFLNKVYNHRDDKTVDLSEMTDDEVMTMAGNLR 1189

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP+ TPVFDGA EE I++M  +A+L +SGQ+ LYDG TG+ F+RPVTVGY+YMLKLNH
Sbjct: 1190 FGVPMGTPVFDGATEEDIHAMFDLAELPKSGQTWLYDGRTGDRFERPVTVGYMYMLKLNH 1249

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1250 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1309

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V GRTR+Y++IV G+   E G PESFNVL KE+++L ++I+LE+  
Sbjct: 1310 VNGRTRMYKNIVDGDHRMEPGMPESFNVLTKEIRSLAINIELEHED 1355


>gi|182676596|sp|A7MQQ9|RPOB_ENTS8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1666 bits (4315), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIKHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVAAKDYVDASTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTTDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR GIV+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGIVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + + V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLNEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLIAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + DD VLR+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKRQEEVAKLREFIQKAYDLGQDVRQKVDLNTFSDDEVLRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPLATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|396326|gb|AAC43085.1| DNA-directed RNA polymerase, beta-subunit [Escherichia coli str. K-12
            substr. MG1655]
          Length = 1342

 Score = 1666 bits (4315), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++V Y    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVXYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMXQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|223297|prf||0705170A polymerase beta,RNA
          Length = 1342

 Score = 1666 bits (4314), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE+ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEEEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|156935814|ref|YP_001439730.1| DNA-directed RNA polymerase subunit beta [Cronobacter sakazakii ATCC
            BAA-894]
 gi|156534068|gb|ABU78894.1| hypothetical protein ESA_03690 [Cronobacter sakazakii ATCC BAA-894]
          Length = 1356

 Score = 1666 bits (4314), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 15   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 70

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 71   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 128

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 129  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 188

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 189  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDYTTEQILDLFFEKVVFEIRD 248

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 249  NKLQMELIPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIKHIEVPVEY 305

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 306  IAGKVAAKDYVDASTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 365

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 366  RVDPTTDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 425

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 426  DEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 485

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 486  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 545

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 546  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 605

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D
Sbjct: 606  RKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVD 665

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 666  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 725

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR GIV+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 726  SGVTAVAKRGGIVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 785

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + + V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 786  SLNEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 845

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 846  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 905

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 906  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 965

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 966  QLKQAKKDLSEELQILEAGLFSRIRAVLIAGGV-------------EAEKLDKLPRDRWL 1012

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1013 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1072

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1073 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1132

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + DD VLR+AE  + 
Sbjct: 1133 MAAKGIGDKINAMLKRQEEVAKLREFIQKAYDLGQDVRQKVDLNTFSDDEVLRLAENLRK 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1193 GMPLATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1313 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1356


>gi|88909139|sp|Q5FTX7|RPOB_GLUOX RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1390

 Score = 1666 bits (4314), Expect = 0.0,   Method: Composition-based stats.
 Identities = 806/1391 (57%), Positives = 1053/1391 (75%), Gaps = 31/1391 (2%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL MN++PD R + GLQ  F+S
Sbjct: 3    AITKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYEAFLQMNVSPDSRQDAGLQEVFRS 62

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI  F+G   L+F+SYEF+ PK+DV++C+ R LTYA PLK+ LRL  +D+DE TG++S
Sbjct: 63   VFPINDFAGRGRLDFMSYEFEDPKYDVEECIQRGLTYAAPLKVILRLTTWDIDEDTGSRS 122

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            I D+KEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123  IHDMKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFA 182

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
             R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 183  ARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYLAQREQKIAEGGDVE 242

Query: 222  -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                 GMD +EILS FY  + +++ G  W  P    D   G K+ S LVD DTGE V E+
Sbjct: 243  GLDIRGMDQDEILSYFYEAVPFTRLGGEWARPFDP-DAFRGLKLLSPLVDADTGEVVAEA 301

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
              KLT+ +++ + EK  + + +    + G ++A D+VN  TGEIY EAG+ + E  L  +
Sbjct: 302  DAKLTARMVRKIAEK-TRVVQVGRLDILGRFLAYDLVNENTGEIYGEAGEELTEDRLAAL 360

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                I ++P+L VD  ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T   AE+MF
Sbjct: 361  EEMGITELPLLSVDG-SHGPWIRNTLAADKNSCRDEALIDIYRIMRPGEPPTKETAEAMF 419

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            + LFFD  +YDLS VGRVKMNMRL++D PD +R +RKEDI+  IKI+ +L++G+G IDDI
Sbjct: 420  HGLFFDQGRYDLSAVGRVKMNMRLDVDAPDTLRVLRKEDILRTIKIMCELKDGRGQIDDI 479

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 480  DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 539

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET+ 
Sbjct: 540  FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETAG 599

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              NIGL++SL+++A+VN YGFIETPYR V +G + +   YLSAMEEE   +AQA++  D+
Sbjct: 600  RPNIGLINSLSTYAKVNKYGFIETPYRLVEEGVLQDGWKYLSAMEEEKLVVAQADAKQDD 659

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G  T+ELV  R +G+  +VP +++   D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 660  QGRLTDELVSVRRSGDFRVVPPDQVTACDVSPKQLVSVAAALIPFLENDDANRALMGANM 719

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVPL+KA+AP VGTGME+ VA  SGA IVAKR G+++Q+D  RIV+R+ +     +T
Sbjct: 720  QRQAVPLVKADAPLVGTGMEAAVAHDSGATIVAKRRGVIDQIDGARIVVRATDEAG--AT 777

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIYRL K+ RSNQ+TC+NQRPLVKVGD V   DIIADGPST+LG+LALGRN+LVAFM
Sbjct: 778  QGVDIYRLRKYMRSNQSTCINQRPLVKVGDTVHAGDIIADGPSTELGELALGRNVLVAFM 837

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYNFEDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+
Sbjct: 838  PWNGYNFEDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNL 897

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GI+ VGAEVNPGDILVGK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G +
Sbjct: 898  DEAGIVYVGAEVNPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTT 957

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GT+VDVR+F+R G+DK+ER++++ER +IE L +D+DDE+ I +R+ Y+RL E L GQ A 
Sbjct: 958  GTIVDVRVFSRRGVDKDERAMAIERAEIERLTKDRDDERGIQERSFYNRLRERLIGQTAG 1017

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G KG +  T ++ +++ E+ R+ W    V  ++V   +E L+ +++ +   ++ RF +K
Sbjct: 1018 AGFKGIRSGTPITEEVLDEHHRATWASITVTSDEVMAELEKLRGEFKEATRRIDARFDSK 1077

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +EK+Q GD++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL++G 
Sbjct: 1078 VEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLENGQ 1137

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS-PLRSFLEKV 1175
             VDIVLNPLGVPSRMN+GQI ETHLGWAC  +G  I  ++++Y+  G+    L   L +V
Sbjct: 1138 AVDIVLNPLGVPSRMNIGQILETHLGWACANIGASIGDMVDEYQRTGERKQELLDRLHEV 1197

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
             G     E ++   ++ ++ +A   + G+P++TPVFDGA    I  ML  A +++SGQS 
Sbjct: 1198 YGDVIFNEDVATLPNEQLIELANNLRKGLPIATPVFDGASIPDIEEMLEKAGVNKSGQSQ 1257

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGEPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1258 LIDGRTGEPFERQTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFG 1317

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE++
Sbjct: 1318 EMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELK 1377

Query: 1356 ALGLSIDLENS 1366
            +LGL+++LE S
Sbjct: 1378 SLGLNVELEQS 1388


>gi|222035698|emb|CAP78443.1| DNA-directed RNA polymerase beta chain [Escherichia coli LF82]
          Length = 1342

 Score = 1665 bits (4313), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK   GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKEQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|85709549|ref|ZP_01040614.1| DNA-directed RNA polymerase beta subunit [Erythrobacter sp. NAP1]
 gi|85688259|gb|EAQ28263.1| DNA-directed RNA polymerase beta subunit [Erythrobacter sp. NAP1]
          Length = 1400

 Score = 1665 bits (4312), Expect = 0.0,   Method: Composition-based stats.
 Identities = 810/1379 (58%), Positives = 1049/1379 (76%), Gaps = 16/1379 (1%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                R+RK FG   E++ +P+LIEVQ+ SY+ FL  +         GL+   +SVFPI  
Sbjct: 21   TAKKRIRKIFGDIHEVVQMPNLIEVQRESYEQFLRSDKETGYVS--GLEKTLRSVFPIRD 78

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            F+G A L+FV YE + PK+D  +C  R +TYA P+K+TLRLIVF+VD+ T  +S+ DIKE
Sbjct: 79   FAGTAELDFVHYELEEPKYDTTECRQRGITYAAPMKVTLRLIVFEVDQETETRSVLDIKE 138

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +YMGD+PLMT++GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGKLL+A R+IP 
Sbjct: 139  QDVYMGDMPLMTENGTFIINGTERVIVSQMHRSPGVLFDHDRGKTHSSGKLLFAARVIPY 198

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+D E+D+KDI++VRIDR+RK+PVT+ L ALG+DSE IL  FY  + + +  D W  
Sbjct: 199  RGSWLDFEYDAKDIVNVRIDRKRKLPVTALLYALGLDSEAILHHFYDTVTWERAKDGWKI 258

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            P  A +   G K +  LVD  TGE++  + +K++        + G+  L + ++ +   Y
Sbjct: 259  PFVAEN-WRGQKPTFPLVDASTGEEIFAANQKISPRAANKAAKDGLTELLLPTEEVVSRY 317

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             A D+++  TG IYIEAGD I  + +E   ++ I  + +L +D +N   +IRNTL  DK 
Sbjct: 318  AANDMIDETTGRIYIEAGDEITLEHVETFDNAGIDSLELLDIDEINTGPWIRNTLKVDKA 377

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            ++R + L  IY+VMRPG+  T   AE++F  LFFD ++YDLS VGRVK+NMRL LD  D 
Sbjct: 378  ENRDEGLEAIYKVMRPGEPPTKETAEALFEGLFFDGERYDLSAVGRVKLNMRLGLDAEDT 437

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            V  +RKEDI+A++K LV L++GKG +DDIDNLGNRRVRSVGE+L+NQYR+GLLRMER++K
Sbjct: 438  VTTLRKEDILAVVKELVGLKDGKGEVDDIDNLGNRRVRSVGELLENQYRVGLLRMERAVK 497

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+SSVD+ +VMP DLINAKP V+AV EFF SSQLSQ  +  N LS +TH RR+SALG G
Sbjct: 498  ERMSSVDVSTVMPNDLINAKPAVAAVREFFGSSQLSQFMDQTNPLSEVTHKRRVSALGPG 557

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL SF+RVN YGFIETPYRKV D
Sbjct: 558  GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLASFSRVNKYGFIETPYRKVED 617

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             KVT DV+YLSAMEE+   +AQA++ L++DGSF E+L+  R +G+ ++ P ++I  +D S
Sbjct: 618  NKVTGDVIYLSAMEEQKHTVAQASAELNDDGSFVEDLISARQSGDNLMAPNDQITLMDVS 677

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+KAEAP+VGTGME  VA+ SGAAI
Sbjct: 678  PKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVKAEAPWVGTGMEETVARDSGAAI 737

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AKR GIV+QVDA RIVIR+ +GD++P  SGVDIY L KFQRSNQNTC+NQRPLVKVG+ 
Sbjct: 738  AAKRGGIVDQVDATRIVIRA-QGDVEPGQSGVDIYTLQKFQRSNQNTCINQRPLVKVGEV 796

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +   DIIADGPSTDLG+LALG+N LVAFMPW+GYN+EDS+LISER+V +DVFTSIHIEEF
Sbjct: 797  IEPGDIIADGPSTDLGELALGKNSLVAFMPWNGYNYEDSILISERIVKDDVFTSIHIEEF 856

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +GAEV+PGDILVGKITPKGESPMT
Sbjct: 857  EVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIGAEVHPGDILVGKITPKGESPMT 916

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DVRDTSLR+P GV+GT+V+VR+FNRHGI+ ++R+ +++ E+IE L
Sbjct: 917  PEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFNRHGIEIDDRTRAIQNEEIERL 976

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D  DE+ IL+R  Y+RL ++L GQ A + PKG KK   +S  ++ +  R +W++FAV 
Sbjct: 977  RKDAADERNILNRATYNRLRDMLLGQTASAAPKGVKKGIEISEQVLQDVERHEWFKFAVA 1036

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D+  Q  +E++K QY+ S ++++ +F+++ EK++ GD++ PGVL++VKVFVA+KR +Q G
Sbjct: 1037 DDGRQAQLEAIKSQYDDSAAMIDAKFEDRKEKLERGDELAPGVLKMVKVFVAVKRKLQPG 1096

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP EDMPFL+DGTPVD+VLNPLGVPSRMNVGQIFETHLG+A  G
Sbjct: 1097 DKMAGRHGNKGVISRILPIEDMPFLEDGTPVDLVLNPLGVPSRMNVGQIFETHLGFAARG 1156

Query: 1148 LGKKIKSLI-----------NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            LG  I   +            DY +      +   L+ V G   + E +       ++ +
Sbjct: 1157 LGMDIADKLEEWHAANPNAKEDYASAKPPEAVVERLKDVYG-EQYFEDLESRSTAGIVEL 1215

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+   +GVP+ TPVFDGA E  +   L  A +D SGQS L+DG TGE FDR VTVG IYM
Sbjct: 1216 AQNLSAGVPMGTPVFDGAREADVTDYLVKAGVDGSGQSTLFDGRTGEAFDRKVTVGIIYM 1275

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT
Sbjct: 1276 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLT 1335

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            +KSDDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LG++++L++       + E
Sbjct: 1336 VKSDDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLGMNVELKSLSDGEEDEDE 1394


>gi|146309864|ref|YP_001174938.1| DNA-directed RNA polymerase subunit beta [Enterobacter sp. 638]
 gi|166991525|sp|A4W5A7|RPOB_ENT38 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145316740|gb|ABP58887.1| DNA-directed RNA polymerase subunit beta [Enterobacter sp. 638]
          Length = 1342

 Score = 1665 bits (4312), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVVYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235  NKLQMELLPERL-RGETASFDIEF--DGKVYVEKGRRITARHIRQLEKDDIKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVAAKDYVDASTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DAIEGSGILSKEDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L   +++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIYAVLVSGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQQEEVAKLREFIQRAYDLGTDVRQKVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|110807837|ref|YP_691357.1| DNA-directed RNA polymerase subunit beta [Shigella flexneri 5 str.
            8401]
 gi|123342223|sp|Q0SY13|RPOB_SHIF8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110617385|gb|ABF06052.1| RNA polymerase, beta subunit [Shigella flexneri 5 str. 8401]
          Length = 1342

 Score = 1665 bits (4311), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VK ++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKGYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|260596086|ref|YP_003208657.1| DNA-directed RNA polymerase subunit beta [Cronobacter turicensis
            z3032]
 gi|260215263|emb|CBA27171.1| DNA-directed RNA polymerase subunit beta [Cronobacter turicensis
            z3032]
          Length = 1356

 Score = 1665 bits (4311), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 15   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 70

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 71   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 128

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 129  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 188

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 189  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDYTTEQILDLFFEKVVFEIRD 248

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 249  NKLQMELIPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIKLIEVPVEY 305

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  T+
Sbjct: 306  IAGKVAAKDYVDASTGELICPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYMSETV 365

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 366  RVDPTTDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 425

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 426  DEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 485

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 486  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 545

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 546  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 605

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D
Sbjct: 606  RKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVD 665

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 666  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 725

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 726  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 785

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + + V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 786  SLNEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 845

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 846  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 905

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 906  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 965

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 966  QLKQAKKDLSEELQILEAGLFSRIRAVLIAGGV-------------EAEKLDKLPRDRWL 1012

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1013 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1072

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1073 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1132

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  + 
Sbjct: 1133 MAAKGIGDKINAMLKRQEEVAKLREFIQKAYDLGQDVRQKVDLNTFSDEEVLRLAENLRK 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1193 GMPLATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1313 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1356


>gi|254427266|ref|ZP_05040973.1| DNA-directed RNA polymerase, beta subunit [Alcanivorax sp. DG881]
 gi|196193435|gb|EDX88394.1| DNA-directed RNA polymerase, beta subunit [Alcanivorax sp. DG881]
          Length = 1380

 Score = 1665 bits (4311), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1387 (51%), Positives = 972/1387 (70%), Gaps = 30/1387 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P+++++P L+ +Q  SY  FL  + + +ER  EGL+AAF+SV
Sbjct: 1    MAYSFTEKKRIRKDFGKLPKVMEVPYLLAIQLDSYRKFLQQDKSAEERLEEGLEAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+  YEF  P FDV +C+ R  TYA PL++ +RL+++D +       I
Sbjct: 61   FPIASYSGNAALEYAGYEFGKPVFDVKECIIRGTTYAAPLRVRIRLVIYDRESSGA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 118  KDIREQQVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG  S+E+L  F+     +   
Sbjct: 178  RVIPYRGSWLDFEFDPKDQVFVRIDRRRKLPATILLRALGYTSDEVLEMFFDTNEIAVED 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G   +  ++    GE V+E G+++T+  ++ L++  +++L I ++ 
Sbjct: 238  GIYRMKLVPERL-RGETATFDIL--ADGEVVVERGRRITARHIRQLEKANIEYLEIPAEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A+ I++ +TGEI +E    +  ++LE++    I D   LY + ++N  ++ +TL
Sbjct: 295  LQGKYLAKSIIDQDTGEILVECNTELTAETLEKLEQGGIADFETLYTNDLDNGPFMADTL 354

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL  
Sbjct: 355  RADPTRTPLEALVEIYRMMRPGEPPTKEAAENLFKNLFFTDERYDLSGVGRMKFNRRLGR 414

Query: 423  DTPDDVRHI-----------------------RKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +       +                          DII +++ LVD+RNG G +DDID+L
Sbjct: 415  EDETGPGILYDGRYFSARSDEEGKQYFEQMGGETSDIIEVLRTLVDIRNGNGVVDDIDHL 474

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            GNRRVRSVGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLIN+KPV +AV EFF S
Sbjct: 475  GNRRVRSVGEMAENQFRVGLVRVERAVKERLSLAESEGLMPQDLINSKPVAAAVKEFFGS 534

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 535  SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 594

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            IGL++SL ++AR N YGF+E+PY KV DGKV+ ++ YLSA+EE    IAQ ++ + EDG 
Sbjct: 595  IGLINSLATYARANEYGFLESPYLKVIDGKVSEEIEYLSAIEEAECVIAQVDAKMTEDGG 654

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            F E+ V  R   E  ++ R+ I  +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 655  FEEDFVTVRHRYEFTVMERDTITHMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQ 714

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVP L+A+ P VGTG E  VA+ SG  +VA R GIV++VDA RI+++  + ++    +GV
Sbjct: 715  AVPTLRADKPLVGTGFERHVARDSGVCVVATRGGIVDKVDASRIIVKVNDSEVSEGEAGV 774

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            DIY L K+ RSNQNTC+NQRPLVKVGD V   DI+ADGPS D+G+LALG+NM VAFMPW+
Sbjct: 775  DIYNLTKYTRSNQNTCINQRPLVKVGDRVAARDIMADGPSVDMGELALGQNMRVAFMPWN 834

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFEDS+LISE++V +D FTSIHI+E   +ARDTKLGPEEIT DIPNV E  L  +DE 
Sbjct: 835  GYNFEDSILISEKVVKDDRFTSIHIQELTCIARDTKLGPEEITADIPNVGEAALSKLDES 894

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTS RV SGV GT+
Sbjct: 895  GIVYIGAEVEAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSQRVSSGVKGTI 954

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            +DV++F R G++K+ER+  +E+  +E   +D  DE  IL+++I  RL  ++ G+    G 
Sbjct: 955  IDVQVFTRDGVEKDERARQIEQAALEQFRKDLKDEYRILEQDILERLRTVMVGKKVNGG- 1013

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             GFK+   L+ D++      +W++    D+ V   +E  +   E  K   ++R+K+K  K
Sbjct: 1014 AGFKRGAELTGDVLDGLDAEKWFELRPADDDVAEQLERAQQYLEQHKKEQDERYKDKQAK 1073

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            I  GDD+  GVL+VVKV++A+KR IQ GDKMAGRHGNKG++S I+P EDMP  ++G PVD
Sbjct: 1074 ISGGDDLAHGVLKVVKVYLAIKRRIQPGDKMAGRHGNKGVISVIMPEEDMPHDENGVPVD 1133

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +VLNPLGVPSRMNVGQI ETHLGWA  GLG++I  ++ + K   DI      +    G G
Sbjct: 1134 VVLNPLGVPSRMNVGQILETHLGWAAKGLGERIGEMLAEQKKIADIRVFLDKIYNQAGAG 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
               E +  + DD ++ +A+    GVP++T VFDGA E  I  +L +A  D SGQ  L+DG
Sbjct: 1194 GTPEDLDSFSDDEIIDLAKNLVGGVPMATAVFDGAKEFEIKELLELAGHDRSGQVQLWDG 1253

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TGE FDR VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1254 RTGEAFDRKVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1313

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAAY LQEMLT+KSDDV GRTRVY++IV G+   + G PESFNVL+KE+++LG+
Sbjct: 1314 WALEAYGAAYTLQEMLTVKSDDVNGRTRVYKNIVDGDHRMDPGMPESFNVLLKEIRSLGI 1373

Query: 1360 SIDLENS 1366
            +I+LEN 
Sbjct: 1374 NIELEND 1380


>gi|271498792|ref|YP_003331817.1| DNA-directed RNA polymerase subunit beta [Dickeya dadantii Ech586]
 gi|270342347|gb|ACZ75112.1| DNA-directed RNA polymerase, beta subunit [Dickeya dadantii Ech586]
          Length = 1342

 Score = 1665 bits (4311), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG++ L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPISSYSGSSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+VY    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYSTEEILDLFFDKVVYEIHN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D V+  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  TL
Sbjct: 292  IAGKVLAKDYVDESTGEVIAMANMELSLDLLAKLSQSGHKRIDTLFTNDLDHGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F +ELV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFIDELVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGNDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKENEIKELLKLGDLPTSGQITLFDGRTGEQFERSVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|38049094|gb|AAR10354.1| RNA polymerase B subunit [Candidatus Legionella jeonii]
          Length = 1368

 Score = 1664 bits (4309), Expect = 0.0,   Method: Composition-based stats.
 Identities = 725/1366 (53%), Positives = 986/1366 (72%), Gaps = 6/1366 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
                      R RK FG+  + + IP+L+E+Q  SY  FL  +   +E+ N GL AAF S
Sbjct: 8    THQYSHAEKKRFRKSFGRQADKMAIPNLLEIQLKSYRDFLQTDSKFNEQQNTGLHAAFSS 67

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            VFPI +FSG A LE+VSY+   P FDV +C  R LTY+ PL++ +RL+V D +     K 
Sbjct: 68   VFPIESFSGNARLEYVSYKLGEPAFDVRECKLRGLTYSAPLRVKIRLVVLDKEAAGEPKP 127

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            IKDI+EQ ++MG++PLMT  GTFVI G +R+VVSQLHRSPG+ F+HDKG+   SGKLLY+
Sbjct: 128  IKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHSSGKLLYS 187

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD + VRIDRRRK+PV+  L +LG + E+IL+ F+       R
Sbjct: 188  ARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPVSILLRSLGYEIEDILAEFFESTTCQLR 247

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
               +   +     + G   S  +   +TGE ++E G+++T+  +K +++  ++ L +  D
Sbjct: 248  NGEFINLI--PSRLRGEMASFDIAIPETGELIVEQGRRITARHIKQMEKSNMQDLVVPRD 305

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A+  VN ETGEI   A D ++ + L+++  + I     +Y + +++ +YI +T
Sbjct: 306  YLIGKILAKHAVNTETGEILAHANDEVNAELLDQLAQNGILSFETIYTNDLDHGSYISDT 365

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D    + +AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N R+ 
Sbjct: 366  LKIDPTASQLEALVEIYRMMRPGEPPTKEAAEGLFKNLFFAEDRYDLSAVGRMKFNRRVG 425

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     ++KEDI+A+IK L+D+RNG G +DDID+LGNRRVRSVGEM +NQ+R+GL+R
Sbjct: 426  RKEDTGPGTLKKEDILAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMAENQFRVGLVR 485

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S V+ +++MPQDLINAKPV +AV EFF SSQLSQ  + VN LS +TH RR+
Sbjct: 486  VERAVKERLSLVESENLMPQDLINAKPVSAAVKEFFGSSQLSQFMDQVNPLSGVTHKRRV 545

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGFIETP
Sbjct: 546  SALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNNYGFIETP 605

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             RKV DG+VT+++ YLSA+EE ++YIAQ++ ++D DG    +LV CR   E  L   +KI
Sbjct: 606  CRKVIDGRVTDEIEYLSAIEEVDQYIAQSSVAVDADGKILADLVPCRHQNEFSLTTPDKI 665

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            +++D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA 
Sbjct: 666  NYMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERTVAS 725

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG ++VAKR GI++ VDA RIV+R  + +     +GVDIY L K+ RSNQ+TC+NQRP+
Sbjct: 726  DSGVSVVAKRGGIIDLVDASRIVVRVNDDETTAGETGVDIYNLTKYFRSNQDTCINQRPI 785

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD ++R D++ADGP TD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED FT+
Sbjct: 786  VSTGDRIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQEDRFTT 845

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE   +ARDTKLG EEIT DIPNV E  L N+DE G++ +GAEVN GDILVGK+TPK
Sbjct: 846  IHIEELTCIARDTKLGTEEITSDIPNVGESALANLDESGVVYIGAEVNAGDILVGKVTPK 905

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+DV++F R G++K++R+ S+E 
Sbjct: 906  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDQRAKSIEE 965

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E +  + +D  DE+ I + +IY R+  +L  ++A  GP   K  T ++   + +  R +W
Sbjct: 966  EHLARVRKDLIDERRIREEDIYHRVHTLLLNKSATGGPASIKPGTQITEAYLEKIDRDKW 1025

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   V D+ + + +E L  Q E     +E RF +  +KI  GDD+ PGVL++VKV++A+K
Sbjct: 1026 FDIRVDDDVISQQLEQLSKQLELLGKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVK 1085

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIVLNPLGVPSRMN+GQ+ ETHL
Sbjct: 1086 RRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHL 1145

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLG++I +L++       IS +R +L K+    G    ++   DD  +L +A+  
Sbjct: 1146 GLAAKGLGQRIANLLDRKSP---ISEVRDYLNKIYNHDGMERVRLDSLDDSELLLLADNL 1202

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP++TPVFDGA E  I +ML +A L   G++ L DG TG  FD PVTVGY+YMLKLN
Sbjct: 1203 RAGVPMATPVFDGASEAEIKAMLELAGLRSDGKTTLIDGRTGNQFDNPVTVGYMYMLKLN 1262

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1263 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1322

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   + G PESFNVL+KE++ALG+ I+L++ 
Sbjct: 1323 DVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELDHD 1368


>gi|300714847|ref|YP_003739650.1| DNA-directed RNA polymerase beta chain [Erwinia billingiae Eb661]
 gi|299060683|emb|CAX57790.1| DNA-directed RNA polymerase beta chain [Erwinia billingiae Eb661]
          Length = 1342

 Score = 1664 bits (4309), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ KIVY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKIVYEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGDTASFDIES--NGTIYVEKGRRITARHIRQLEKDGIEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+ + A   +    L ++  S  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVAKDYVDESTGELIVAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII +++ L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMRKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVREGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRISYLLVAGGV-------------EAEKLEKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVSKLREFIQRAYDLGSDLRQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|307128979|ref|YP_003880995.1| RNA polymerase, subunit beta [Dickeya dadantii 3937]
 gi|306526508|gb|ADM96438.1| RNA polymerase, beta subunit [Dickeya dadantii 3937]
          Length = 1342

 Score = 1664 bits (4308), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPISSYSGNSELQYVSYRLGEPVFDVQECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+VY    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALSYSTEEILDLFFDKVVYEIHN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D V+  TGE+   A   +    L ++  +  + +  L+ + +++  Y+  TL
Sbjct: 292  IAGKVLAKDYVDESTGEVIAMANMELSLDLLAKLSQAGHKRLDTLFTNDLDHGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKADIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F EELV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFIEELVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHYVLVAGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGNDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKENEIKELLKLGDLPTSGQIRLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|323174504|gb|EFZ60129.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli LT-68]
          Length = 1372

 Score = 1664 bits (4308), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1364 (52%), Positives = 974/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G++     R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 31   YGLLLYREKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 86

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 87   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 144

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 145  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 204

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 205  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 264

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 265  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 321

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 322  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 381

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 382  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 441

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 442  EEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 501

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 502  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 561

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 562  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 621

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 622  RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD 681

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 682  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 741

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 742  SGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 801

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 802  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 861

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 862  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 921

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 922  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 981

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 982  QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWL 1028

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1029 ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1088

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1089 RIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1148

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  + 
Sbjct: 1149 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRK 1208

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1209 GMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHL 1268

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1269 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1328

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1329 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1372


>gi|282599827|ref|ZP_05972033.2| DNA-directed RNA polymerase, beta subunit [Providencia rustigianii
            DSM 4541]
 gi|282567662|gb|EFB73197.1| DNA-directed RNA polymerase, beta subunit [Providencia rustigianii
            DSM 4541]
          Length = 1350

 Score = 1664 bits (4308), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 9    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PNGQNGLEAAFRSV 64

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRLIV++ +   G  ++
Sbjct: 65   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLIVYEREAPEG--TV 122

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 123  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 182

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+  ++EEIL+ F+ K V+  R 
Sbjct: 183  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYNTEEILNLFFDKTVFQIRD 242

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ V  + +  + 
Sbjct: 243  NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKEEVNSIEVPVEY 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGE+   A   +    L  +  S  + I  L+ + +++ AYI  T+
Sbjct: 300  IAGKVVARDYIDESTGELICAANMELSLDMLARLSQSGHKTIETLFTNDLDHGAYISETV 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  LN 
Sbjct: 360  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLNR 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + KEDII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 420  EEIEGSGILSKEDIIEVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 480  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 599

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ L +DG F EEL+ CR  GE  L  RE+++
Sbjct: 600  RLVRDGIVTDEIHYLSAIEEGNFIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVE 659

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 660  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 719

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 720  SGVTAVARRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 779

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 780  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 839

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 840  HIQELSCVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 899

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLR+P+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 900  ETQLTPEEKLLRAIFGEKASDVKDSSLRIPNGVSGTVIDVQVFTRDGVEKDKRALEIEET 959

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  ++SR+  +L                 + ++ + + PR +W 
Sbjct: 960  QLRDAKKDLTEELRIFESALFSRIRSVLISGG-------------IEAEKLDKLPRDRWL 1006

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + ++ DE+ Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1007 ELSLADEEKQNQLEQLAEQYDELKSDFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1066

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1067 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPVDIVLNPLGVPSRMNIGQILETHLG 1126

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + D+ V+R+AE  K 
Sbjct: 1127 MAAKGIGEKINAMLKQQQEVAKLREFIQKAYDLGDDPRQKVDLSTFSDEEVMRLAENLKK 1186

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++A L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1187 GMPIATPVFDGAKEKEIKELLKLAGLPTSGQITLFDGRTGEKFERQVTVGYMYMLKLNHL 1246

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1247 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1306

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1307 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1350


>gi|110833239|ref|YP_692098.1| DNA-directed RNA polymerase subunit beta [Alcanivorax borkumensis
            SK2]
 gi|123050736|sp|Q0VSM2|RPOB_ALCBS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110646350|emb|CAL15826.1| DNA-directed RNA polymerase, beta subunit [Alcanivorax borkumensis
            SK2]
          Length = 1380

 Score = 1664 bits (4308), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1387 (51%), Positives = 971/1387 (70%), Gaps = 30/1387 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P+++++P L+ +Q  SY  FL  + + +ER  EGL+AAF+SV
Sbjct: 1    MAYSFTEKKRIRKDFGKLPKVMEVPYLLAIQLDSYRKFLQQDKSAEERLEEGLEAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+  YEF  P FDV +C+ R  TYA PL++ +RL+++D +       I
Sbjct: 61   FPIASYSGNAALEYAGYEFGKPVFDVKECIIRGTTYAAPLRVRIRLVIYDRESSGA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 118  KDIREQQVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG  S+E+L  F+     +   
Sbjct: 178  RVIPYRGSWLDFEFDPKDQVFVRIDRRRKLPATILLRALGYTSDEVLEMFFDTNEIAVED 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G   +  ++    GE V+E G+++T+  ++ L++  +++L I ++ 
Sbjct: 238  GIYRMKLVPERL-RGETATFDIL--ADGEVVVERGRRITARHIRQLEKANIEYLDIPAEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A+ I++ +TGEI +E    +  ++LE++    I D   LY + ++N  ++ +TL
Sbjct: 295  LQGKYLAKSIIDQDTGEILVECNTELTAETLEKLEQGGITDFETLYTNDLDNGPFMADTL 354

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N RL  
Sbjct: 355  RADPTRTPLEALVEIYRMMRPGEPPTKEAAENLFKNLFFTDERYDLSTVGRMKFNRRLGR 414

Query: 423  DTPDDVRHIRKEDIIA-----------------------IIKILVDLRNGKGTIDDIDNL 459
            +       +      +                       +++ LVD+RNG G +DDID+L
Sbjct: 415  EDETGPGILYDGRYFSARSDEEGKQYFEQMGGETSDIIDVLRTLVDIRNGNGVVDDIDHL 474

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            GNRRVRSVGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLIN+KPV +AV EFF S
Sbjct: 475  GNRRVRSVGEMAENQFRVGLVRVERAVKERLSLAESEGLMPQDLINSKPVAAAVKEFFGS 534

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 535  SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 594

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            IGL++SL ++AR N YGF+E+PY KV DGKV+ ++ YLSA+EE    IAQ ++ + E+G 
Sbjct: 595  IGLINSLATYARANEYGFLESPYLKVIDGKVSEEIEYLSAIEEAECVIAQVDAKMTEEGG 654

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            F E+ V  R   E  ++ R+ I  +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 655  FEEDFVTVRHRYEFTVMERDTITHMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQ 714

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVP L+A+ P VGTG E  VA+ SG  +VA R GIV++VDA RI+++  + ++    +GV
Sbjct: 715  AVPTLRADKPLVGTGFERHVARDSGVCVVATRGGIVDKVDASRIIVKVNDDEVSEGEAGV 774

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            DIY L K+ RSNQNTC+NQRPLVKVGD V   DI+ADGPS D+G+LALG+NM VAFMPW+
Sbjct: 775  DIYNLTKYTRSNQNTCINQRPLVKVGDRVAARDIMADGPSVDMGELALGQNMRVAFMPWN 834

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFEDS+LISE++V +D FTSIHI+E   +ARDTKLGPEEIT DIPNV E  L  +DE 
Sbjct: 835  GYNFEDSILISEKVVKDDRFTSIHIQELTCIARDTKLGPEEITADIPNVGEAALSKLDES 894

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTS RV SGV GT+
Sbjct: 895  GIVYIGAEVEAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSQRVSSGVKGTI 954

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            +DV++F R G++K+ER+  +E+  +E   +D  DE  IL+ +I  RL  ++ G+    G 
Sbjct: 955  IDVQVFTRDGVEKDERARQIEQAALEQFRKDLKDEYRILELDILERLRAVMVGKKVNGG- 1013

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             GFK+ T ++ +++      +W++    D+ V   +E  +   E  K   ++R+K+K  K
Sbjct: 1014 AGFKRGTEMTGEILDGLDAEKWFELRPADDDVAEQLERAQQYLEQHKKEQDERYKDKQAK 1073

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            I  GDD+  GVL+VVKV++A+KR IQ GDKMAGRHGNKG++S I+P EDMP  ++G PVD
Sbjct: 1074 ISGGDDLAHGVLKVVKVYLAIKRRIQPGDKMAGRHGNKGVISVIMPEEDMPHDENGVPVD 1133

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +VLNPLGVPSRMNVGQI ETHLGWA  GLG++I  ++ + K   DI      +    G G
Sbjct: 1134 VVLNPLGVPSRMNVGQILETHLGWAAKGLGERIGEMLAEQKKIADIRVFLDKIYNQAGAG 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
               E +  + DD ++ +A+    GVP++T VFDGA E  I  +L +A  D SGQ  L+DG
Sbjct: 1194 GTPEDLDSFSDDEIIELAKNLVGGVPMATAVFDGAKEFEIKELLELAGHDRSGQVQLWDG 1253

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TGE FDR VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1254 RTGEAFDRKVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1313

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAAY LQEMLT+KSDDV GRTRVY++IV G+   + G PESFNVL+KE+++LG+
Sbjct: 1314 WALEAYGAAYTLQEMLTVKSDDVNGRTRVYKNIVDGDHRMDPGMPESFNVLLKEIRSLGI 1373

Query: 1360 SIDLENS 1366
            +I+LEN 
Sbjct: 1374 NIELEND 1380


>gi|88799211|ref|ZP_01114790.1| DNA-directed RNA polymerase, beta subunit [Reinekea sp. MED297]
 gi|88777970|gb|EAR09166.1| DNA-directed RNA polymerase, beta subunit [Reinekea sp. MED297]
          Length = 1360

 Score = 1663 bits (4307), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1365 (52%), Positives = 974/1365 (71%), Gaps = 5/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK   ++D+P L+ +Q  SY  FL  +    +R + GL AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFGKLEPVMDVPYLLAIQLDSYRSFLQADADAADRQDSGLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+VSY    P FDV +C  R +TYA PL++ +RLI++D D  +  K+I
Sbjct: 61   FPIVSYSGNAALEYVSYNLGKPAFDVKECQLRGVTYAAPLRVKVRLIIYDKDSPS--KAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF++ G +R+VVSQLHRSPG+ +DHDKG+   SGKLL++ 
Sbjct: 119  KDIKEQEVYMGEIPLMTDNGTFIVNGTERVVVSQLHRSPGVFYDHDKGKTHSSGKLLHSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +   G
Sbjct: 179  RVIPYRGSWLDFEFDPKDQVFVRIDRRRKLPATILLRALEYTNQEILDMFFERVSFKVNG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L A D + G   +  + D + G  ++E G+++T+  +K  +  G+  + +    
Sbjct: 239  AEIEMDLVA-DRLKGETAAFEIRDGE-GNVLLEEGRRITARHIKQFESAGLTSVVVPDTY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A D+VN  TGEI  +  D I    LE+I  + I     LY + ++   ++ +TL
Sbjct: 297  VLGKSLATDLVNASTGEILAQCNDEITVDLLEQIKENGIAAFETLYTNDLDCGPFVSDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D      +AL++IYR+MRPG+  T   AE++F  LFF SD+YDLS+VGR+K N RL  
Sbjct: 357  RNDPTSTPLEALVEIYRMMRPGEPPTKEAAETLFQNLFFTSDRYDLSSVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+ +    + +EDI+ +++ L+D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 417  DSDEGEGILSREDIVDVLRTLIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  + + +MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS IT+ RR+S
Sbjct: 477  ERAVRERLSMAESEGLMPQDLVNAKPVAAAIKEFFGSSQLSQFMDQNNPLSGITNKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+++L+++AR N+YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINTLSTYARTNSYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +GKVT+D+VYLSA++E    IAQAN  + +DG   +E V  R   E  L P +K+D
Sbjct: 597  RRVENGKVTDDIVYLSAIDEAKHTIAQANVPVSDDGMIEDEFVQVRHQNEFTLAPIDKVD 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LK++ P VGTG+E  VA  
Sbjct: 657  MMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLKSDKPLVGTGIERNVAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA R G+VE VDA RIV++    ++    +GVDIY L K+ RSNQNTC+NQR +V
Sbjct: 717  SGVCVVADRGGVVEYVDASRIVVKVAHDEIGDDDAGVDIYNLTKYTRSNQNTCINQRTIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD + R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+L+SE++V ED FTSI
Sbjct: 777  RQGDMIARGDVLADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILVSEKVVQEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK 
Sbjct: 837  HIQELTCIARDTKLGPEEITADIPNVGESALSKLDESGIVYIGAEVGAGDILVGKVTPKS 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV  G+ GTV+DV+ F R G+++++RS  +ER+
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVKGGMRGTVIDVQTFTRDGVERDQRSKDIERQ 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +E   +D + E  I++  ++ RL   L GQ    GP   KK   L++D ++  PRS W+
Sbjct: 957  ALEEFRKDLNAEYRIVEDTVFERLHNALVGQKVAGGP-DLKKGDELTADYLNGLPRSDWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +QDE +   +E+ + Q +  K   ++RF +K  K+Q GDD+ PGVL+VVKV++A+KR
Sbjct: 1016 KLRLQDETLAAQLEAAEAQLKERKQDQDERFDDKKRKLQSGDDLQPGVLKVVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+ + G PVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVISVIMPVEDMPYDEKGNPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  GLG +I  ++ + ++  ++      +    G    +E ++++ D  +  +A   K 
Sbjct: 1136 AAAKGLGDRINEMVEEQRSAAELRDFMDQVYNQSGDSKRSEALAEFSDAEIQELASNLKK 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  +  +LR+A +D+SGQ  L+DG TG+ F+   TVGY+YMLKLNH+
Sbjct: 1196 GVPIATPVFDGAKETEVKELLRLAGMDDSGQIQLWDGRTGDAFENKTTVGYMYMLKLNHL 1255

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1256 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1315

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV G+   E G PESFNVLVKE+++LG+ I+LEN  
Sbjct: 1316 NGRTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGIDIELENEE 1360


>gi|197286614|ref|YP_002152486.1| DNA-directed RNA polymerase subunit beta [Proteus mirabilis HI4320]
 gi|227355193|ref|ZP_03839602.1| DNA-directed RNA polymerase, beta-subunit [Proteus mirabilis ATCC
            29906]
 gi|226699431|sp|B4EYU9|RPOB_PROMH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|194684101|emb|CAR45495.1| DNA-directed RNA polymerase, beta-subunit [Proteus mirabilis HI4320]
 gi|227164702|gb|EEI49556.1| DNA-directed RNA polymerase, beta-subunit [Proteus mirabilis ATCC
            29906]
          Length = 1342

 Score = 1663 bits (4307), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1364 (51%), Positives = 961/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PDGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +E+IL+ F+ K  +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMNYSTEDILNLFFEKTTFEISN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ ++ + +  + 
Sbjct: 235  NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKEQIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGE+   A   I    L  +  +  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVARDYIDEATGELICAANMEISLDVLARLSQAGHKTIETLFTNDLDHGAYISETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + +EDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEVEGSGILSQEDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +  VT+++ YLSA+EE N  IAQANS LD+DG F EELV CR  GE  L  R+++ 
Sbjct: 592  RVVENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDGHFVEELVTCRHKGESSLFSRDQVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDETYAGEAGIDIYSLTKYTRSNQNTCINQTPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN+EDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNYEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEES 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  +E  I +  +++R+  +L                 + +D + + PR +W 
Sbjct: 952  QLREVKKDLTEELRIFEAGLFARIRGVLIAGG-------------IEADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K+    + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKAEFAKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVD+VLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGNPVDLVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +  + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGMAPRQKVDLDTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P +TPVFDGA+E  I  ML++ADL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPTATPVFDGAEEMEIKEMLKLADLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|22124399|ref|NP_667822.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis KIM 10]
 gi|45442864|ref|NP_994403.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis biovar
            Microtus str. 91001]
 gi|51594638|ref|YP_068829.1| DNA-directed RNA polymerase subunit beta [Yersinia pseudotuberculosis
            IP 32953]
 gi|108809610|ref|YP_653526.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis Antiqua]
 gi|108810385|ref|YP_646152.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis Nepal516]
 gi|145600988|ref|YP_001165064.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis Pestoides
            F]
 gi|153950044|ref|YP_001402811.1| DNA-directed RNA polymerase subunit beta [Yersinia pseudotuberculosis
            IP 31758]
 gi|153997219|ref|ZP_02022326.1| DNA-directed RNA polymerase beta chain [Yersinia pestis CA88-4125]
 gi|165928322|ref|ZP_02224154.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. F1991016]
 gi|165938253|ref|ZP_02226812.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. IP275]
 gi|166012038|ref|ZP_02232936.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. E1979001]
 gi|166214411|ref|ZP_02240446.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. B42003004]
 gi|167402417|ref|ZP_02307877.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. UG05-0454]
 gi|167422935|ref|ZP_02314688.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. MG05-1020]
 gi|167426825|ref|ZP_02318578.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Mediaevalis str. K1973002]
 gi|170022598|ref|YP_001719103.1| DNA-directed RNA polymerase subunit beta [Yersinia pseudotuberculosis
            YPIII]
 gi|186893640|ref|YP_001870752.1| DNA-directed RNA polymerase subunit beta [Yersinia pseudotuberculosis
            PB1/+]
 gi|218930752|ref|YP_002348627.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis CO92]
 gi|229837493|ref|ZP_04457655.1| RNA polymerase, beta subunit [Yersinia pestis Pestoides A]
 gi|229839429|ref|ZP_04459588.1| RNA polymerase, beta subunit [Yersinia pestis biovar Orientalis str.
            PEXU2]
 gi|229899991|ref|ZP_04515131.1| RNA polymerase, beta subunit [Yersinia pestis biovar Orientalis str.
            India 195]
 gi|229900560|ref|ZP_04515686.1| RNA polymerase, beta subunit [Yersinia pestis Nepal516]
 gi|270488916|ref|ZP_06205990.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis KIM D27]
 gi|294505415|ref|YP_003569477.1| DNA-directed RNA polymerase beta subunit [Yersinia pestis Z176003]
 gi|41018099|sp|Q8ZAP5|RPOB_YERPE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|81640666|sp|Q66FQ2|RPOB_YERPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|122382592|sp|Q1C1U1|RPOB_YERPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|122385351|sp|Q1CN78|RPOB_YERPN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158514113|sp|A4TS29|RPOB_YERPP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166991529|sp|A7FNI3|RPOB_YERP3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699464|sp|B2K113|RPOB_YERPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699466|sp|B1JJJ9|RPOB_YERPY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21957181|gb|AAM84073.1|AE013649_3 RNA polymerase, beta subunit [Yersinia pestis KIM 10]
 gi|45437730|gb|AAS63280.1| DNA-directed RNA polymerase beta chain [Yersinia pestis biovar
            Microtus str. 91001]
 gi|51587920|emb|CAH19523.1| DNA-directed RNA polymerase beta chain [Yersinia pseudotuberculosis
            IP 32953]
 gi|108774033|gb|ABG16552.1| DNA-directed RNA polymerase beta chain [Yersinia pestis Nepal516]
 gi|108781523|gb|ABG15581.1| DNA-directed RNA polymerase beta chain [Yersinia pestis Antiqua]
 gi|115349363|emb|CAL22334.1| DNA-directed RNA polymerase beta chain [Yersinia pestis CO92]
 gi|145212684|gb|ABP42091.1| DNA-directed RNA polymerase beta chain [Yersinia pestis Pestoides F]
 gi|149289327|gb|EDM39406.1| DNA-directed RNA polymerase beta chain [Yersinia pestis CA88-4125]
 gi|152961539|gb|ABS49000.1| DNA-directed RNA polymerase, beta subunit [Yersinia
            pseudotuberculosis IP 31758]
 gi|165913914|gb|EDR32532.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. IP275]
 gi|165919661|gb|EDR36994.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. F1991016]
 gi|165989033|gb|EDR41334.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. E1979001]
 gi|166204415|gb|EDR48895.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. B42003004]
 gi|166957146|gb|EDR55167.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Orientalis str. MG05-1020]
 gi|167048197|gb|EDR59605.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Antiqua str. UG05-0454]
 gi|167054207|gb|EDR64032.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis biovar
            Mediaevalis str. K1973002]
 gi|169749132|gb|ACA66650.1| DNA-directed RNA polymerase, beta subunit [Yersinia
            pseudotuberculosis YPIII]
 gi|186696666|gb|ACC87295.1| DNA-directed RNA polymerase, beta subunit [Yersinia
            pseudotuberculosis PB1/+]
 gi|229682380|gb|EEO78470.1| RNA polymerase, beta subunit [Yersinia pestis Nepal516]
 gi|229686976|gb|EEO79052.1| RNA polymerase, beta subunit [Yersinia pestis biovar Orientalis str.
            India 195]
 gi|229695795|gb|EEO85842.1| RNA polymerase, beta subunit [Yersinia pestis biovar Orientalis str.
            PEXU2]
 gi|229704181|gb|EEO91192.1| RNA polymerase, beta subunit [Yersinia pestis Pestoides A]
 gi|262363481|gb|ACY60202.1| DNA-directed RNA polymerase beta subunit [Yersinia pestis D106004]
 gi|262367409|gb|ACY63966.1| DNA-directed RNA polymerase beta subunit [Yersinia pestis D182038]
 gi|270337420|gb|EFA48197.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis KIM D27]
 gi|294355874|gb|ADE66215.1| DNA-directed RNA polymerase beta subunit [Yersinia pestis Z176003]
          Length = 1342

 Score = 1663 bits (4307), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYVDASTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  RE++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFLEDLVTCRSKGESSLFSREQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMHPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + ++ +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEAEKLSKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|315064608|gb|ADT78388.1| RpoB [Yersinia entomophaga]
          Length = 1342

 Score = 1663 bits (4307), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTEQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ GV  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGVDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQAGHKRIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEDVAKLREFIQKAYDLGDNVCQKVDLNTFTDDEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKETEIKELLKLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|30249986|ref|NP_842056.1| DNA-directed RNA polymerase subunit beta [Nitrosomonas europaea ATCC
            19718]
 gi|41017697|sp|Q82T75|RPOB_NITEU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|30139093|emb|CAD85957.1| RNA polymerases beta subunit [Nitrosomonas europaea ATCC 19718]
          Length = 1357

 Score = 1663 bits (4306), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1363 (52%), Positives = 956/1363 (70%), Gaps = 7/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   I+  P L+  Q  SY  FL   IAP +R N+GLQAAF SV
Sbjct: 1    MSYSFAEKKRIRKSFAKRASILPFPFLLATQIQSYTDFLQAEIAPGKRKNQGLQAAFNSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + S  A L+F+SY    P FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHSNNARLDFISYMLGSPVFDVKECQQRGLTYAAPLRARVRLTILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FV+ G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTDTGSFVVNGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT+ L A+G    +IL+ F+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYVYFRIDRRRKMPVTTLLKAMGYSPAQILADFFEFDHFILVD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L    L  G      +V  D G+  ++  K++T+  ++ L++  +  + +  + 
Sbjct: 239  NKIFFNLIPERL-RGELAGFDIVSED-GKVFVQKDKRITAKHVRDLQQANLTKIPVPEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+V+ ETGEI   A   I E  L  I  ++  +I  L+V+ +N   YI  TL
Sbjct: 297  LLGKILAADLVDKETGEIIALANSEISETLLGRIRQTQSSEISTLFVNDLNYGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T     ++FN LF+  ++YDLS VGR+K N R+  
Sbjct: 357  RIDETTDQMSAQVAIYRMMRPGEPPTEEAVLALFNGLFYSPERYDLSVVGRMKFNRRVGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DII +IKILV+LRNG+G IDDID+LGNRRVRSVGE+ +NQ+R GL R+
Sbjct: 417  EELTGSTTLSNDDIIDVIKILVELRNGRGEIDDIDHLGNRRVRSVGELAENQFRAGLARV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            E+++KER+S  + +++MP D INAKPV SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 477  EKAVKERLSQAESENLMPHDFINAKPVSSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARTNEYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G+VT +VVYLSA+EE    IAQAN++ D++G FT+E+V CR   E  L  R++I+
Sbjct: 597  RMVRNGRVTEEVVYLSAIEESQYVIAQANANFDQNGVFTDEVVSCRHKNEFTLASRDQIE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E VVA  
Sbjct: 657  YVDIAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRAEKPLVGTGIERVVAVH 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG A+   R G+V+ VDA RIVIR  + +      GVDIY L K+ RSNQNT +NQRP+V
Sbjct: 717  SGTAVRTIRGGVVDYVDASRIVIRVHDAEARAGEVGVDIYNLTKYTRSNQNTNINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            ++GD + R+D+IADG STDLG+LALG+NML+AFMPW+G NFEDS+LISER+VS+D FTSI
Sbjct: 777  RMGDVLSRDDVIADGASTDLGELALGQNMLIAFMPWNGLNFEDSILISERVVSDDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   ++RDTKLG EEIT DIPN+SE     +DE GI+ +GAEV  GD+LVGK+TPK 
Sbjct: 837  HIEELAAVSRDTKLGTEEITADIPNLSERQRARLDESGIVYIGAEVEAGDVLVGKVTPKS 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSL VP+G+SGTV+DV+IF R G+D+++RS  +  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLHVPAGISGTVIDVQIFTREGVDRDKRSKQIIAD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D  D+  I++ + + R   +L G+ A  GPK   K++ ++ D +    +  W+
Sbjct: 957  ELGRFKKDLADQMRIVEADAFQRAERLLTGKVAAGGPKKLAKNSTITRDYLENVEKHHWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE     +E +K      + + +  F+ K  K+  GD++PPGV ++VKV++A+KR
Sbjct: 1017 DIRLVDENTSLQLEQIKDSLVQKRKLFDLAFEEKHRKLSQGDELPPGVQKMVKVYIAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +QSGDKMAGRHGNKG++S+I+P EDMP++ DGTPVD+VLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1077 RLQSGDKMAGRHGNKGVISKIVPIEDMPYMADGTPVDVVLNPLGVPSRMNIGQVLEVHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   LGK++  ++   +   DI   R FL K+       E ++  +DD VL +A    S
Sbjct: 1137 WAAKELGKRVNEMLASQRNVSDI---RDFLNKIYNNSGKQEDLTSLEDDEVLALARNLSS 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TPVFDGA E  I  ML++A L ESGQ+ LYDG TGE FDRPVTVGY+++LKL+H+
Sbjct: 1194 GVPFATPVFDGAHESEIKQMLKLAGLPESGQTTLYDGRTGEAFDRPVTVGYMHVLKLHHL 1253

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1254 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1313

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYESIV G+   + G PESFNVLVKE+++LGL IDLE 
Sbjct: 1314 NGRTKVYESIVKGDHKIDAGMPESFNVLVKEIRSLGLDIDLEE 1356


>gi|259906929|ref|YP_002647285.1| DNA-directed RNA polymerase subunit beta [Erwinia pyrifoliae Ep1/96]
 gi|224962551|emb|CAX54006.1| similar to bifunctional DNA-directed RNA polymerase subunit
            beta-beta\' [Erwinia pyrifoliae Ep1/96]
 gi|283476722|emb|CAY72551.1| DNA-directed RNA polymerase beta chain [Erwinia pyrifoliae DSM 12163]
          Length = 1342

 Score = 1663 bits (4306), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+VY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVYQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIES--NGTVYVEKGRRITARHIRQLEKDAVAHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ I A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVAKDYIDESTGELLIAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                 + ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRINYLLVSGG-------------IEAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEDVSRLREFIQRAYDLGTDVRQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|292486727|ref|YP_003529597.1| DNA-directed RNA polymerase subunit beta [Erwinia amylovora CFBP1430]
 gi|292897960|ref|YP_003537329.1| DNA-directed RNA polymerase subunit beta [Erwinia amylovora ATCC
            49946]
 gi|291197808|emb|CBJ44903.1| DNA-directed RNA polymerase beta-subunit [Erwinia amylovora ATCC
            49946]
 gi|291552144|emb|CBA19181.1| DNA-directed RNA polymerase beta chain [Erwinia amylovora CFBP1430]
 gi|312170793|emb|CBX79054.1| DNA-directed RNA polymerase beta chain [Erwinia amylovora ATCC
            BAA-2158]
          Length = 1342

 Score = 1663 bits (4306), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 965/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+VY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVYQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIES--NGTVYVEKGRRITARHIRQLEKDAVAHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ I A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVAKDYIDESTGELLIAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRINYLLVSGGV-------------EAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLSDEDKQNQLEQLAEQYDELKHEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVSKLREFIQRAYDLGTDVRQKVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|304399303|ref|ZP_07381168.1| DNA-directed RNA polymerase, beta subunit [Pantoea sp. aB]
 gi|304353159|gb|EFM17541.1| DNA-directed RNA polymerase, beta subunit [Pantoea sp. aB]
          Length = 1342

 Score = 1662 bits (4305), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V++ +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVVYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQFTTPQILDIFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G   +E  +++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETATFDIE--ANGTVYVEKARRITARHIRQLEKDGIQHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ I A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELIIAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVIDGLVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMHAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIQNVLISGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEAKQNQLEQLAEQYDELKHEFEKKLEGKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQRAYDLGSDLRQKVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|290477016|ref|YP_003469928.1| RNA polymerase subunit beta [Xenorhabdus bovienii SS-2004]
 gi|289176361|emb|CBJ83166.1| RNA polymerase, beta subunit [Xenorhabdus bovienii SS-2004]
          Length = 1342

 Score = 1662 bits (4305), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1364 (51%), Positives = 963/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L A+   +E+IL+ F+ K ++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRAMNYSTEDILNLFFNKTIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMTLVPERL-RGETASFDIE--ANGKLYVEKGRRITARHIRQLEKDQVDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGEI   A   +    L  +  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDQNTGEILCAANMELSLDLLARLSQSGHKTIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L+ 
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLDR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  TEIEGSGILSKEDITDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ LDE+G F E+LV CR   E  L  R+++ 
Sbjct: 592  RLVRDGVVTDEIHYLSAIEEGNYVIAQANTVLDEEGHFVEDLVTCRHYDESSLFNRDQVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGVIQYVDASRIVIKVNEDEMYAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGELVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV+GT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVAGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                   ++ +S+ PR +W 
Sbjct: 952  QLRQAKKDLTEELRIFEAGLFARIHSVLVAGGV-------------EAEKLSKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K+  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKTEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGDDTRQKVDLNTFTDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++A L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKETEIKELLQLAGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|325982732|ref|YP_004295134.1| DNA-directed RNA polymerase, beta subunit [Nitrosomonas sp. AL212]
 gi|325532251|gb|ADZ26972.1| DNA-directed RNA polymerase, beta subunit [Nitrosomonas sp. AL212]
          Length = 1357

 Score = 1662 bits (4305), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1363 (52%), Positives = 967/1363 (70%), Gaps = 7/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++ IP L+  Q  SY  FL  NIAP +R  +GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRASVLSIPFLLATQIESYAAFLQENIAPSKRRTQGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +  A L+F+SYE   P FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHTKNARLDFISYELGSPVFDVKECQQRGLTYASPLRARVRLTIMDK--EISKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT+ G+FVI G +R+VVSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTETGSFVINGTERVVVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT+ L A+G  SE+IL  F+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDCLYFRIDRRRKMPVTTLLKAIGCTSEQILKEFFIFDCFHFSD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L   D + G   S  +      + +++  K++T+  ++ ++E  +  L +  D 
Sbjct: 239  KGIRFELVP-DRLRGEVASFDIF-AKGKKIIVQKDKRITAKHIREMQEAKIDQLEVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGEI   A D I E+++ +     ++ I  LYV+ +N+ AYI  TL
Sbjct: 297  LLGRILAQNIVDPDTGEIIALANDEISEETIAKFRIGNVKKINTLYVNDLNHGAYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D  +A + IYR+MRPG+  T    +++F  LF+  ++YDLS VGR+K N R+  
Sbjct: 357  KIDETTDEMNAQIAIYRMMRPGEPPTEDAVKALFAGLFYSPERYDLSVVGRMKFNRRVGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  EDIIA+IKILV+LRNG+G IDDID+LGNRRVRSVGE+ +NQ+R GL+R+
Sbjct: 417  TELTGSPTLSNEDIIAVIKILVELRNGRGEIDDIDHLGNRRVRSVGELAENQFRSGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + +++MP DLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLSQAESENLMPHDLINAKPVSAAAREFFGSSQLSQFMDQTNPLSEITHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARTNEYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
             +V + +VT+++ YLSA+EE N  IAQAN+ LD +     E+V CR   E  L   ++I+
Sbjct: 597  SRVKNSQVTDEIDYLSAIEEGNFMIAQANAELDHNHRLISEIVSCRYKNEFALSSPDRIE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E VVA  
Sbjct: 657  YVDVAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRAEKPLVGTGIERVVAMH 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR GIV+ VDA RIV+R  + +      GVDIY L+K+ RSNQNT +NQRPLV
Sbjct: 717  SGTTVRAKRGGIVDYVDAGRIVVRVHDIETHMGEVGVDIYNLIKYTRSNQNTNINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + ++D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED FTSI
Sbjct: 777  KVGDNISKDDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERIVAEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V++RDTKLG EEIT DIPN+SE  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELSVVSRDTKLGTEEITADIPNLSEYQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI++++R+ ++  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGISGTVIDVQVFTREGIERDKRAQNIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++   +D  D+  I++ + +SRL  +L G+ A  GP    K   ++++ +  +    W+
Sbjct: 957  ELDRYKKDLADQMRIVEEDAFSRLERLLIGKVATGGPNKLAKGKEITAEYLQSFDPHYWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE     +E ++      +   +  F+ K +K+  GD++ PGV ++VK+++A+KR
Sbjct: 1017 DIRLMDEDASIQLEQVRESMVQKRKAFDVAFEEKKKKLTQGDELAPGVQKMVKIYIAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++S+I+P EDMP++ DGTPVD+VL+PLGVPSRMNVGQI E HLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVISKIVPLEDMPYMADGTPVDVVLHPLGVPSRMNVGQILEVHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGKKI  ++   KA  +I+ +R F++K+       E IS   D  +L +AE   +
Sbjct: 1137 WAAKGLGKKIDGML---KAQRNINEIRDFIDKIYNESGKKENISSLSDKEILSLAENLIA 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TPVFDGA E+ I  ML +A L  SGQ  LYDG TGE FDR VTVGY+++LKL+H+
Sbjct: 1194 GVPFATPVFDGATEKEIKDMLELAGLPRSGQITLYDGRTGEAFDRSVTVGYMHVLKLHHL 1253

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1254 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1313

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYESIV G+   + G PESFNVLVKE+++LG+ IDLE 
Sbjct: 1314 TGRTKVYESIVKGDHKIDAGMPESFNVLVKEIRSLGMDIDLEQ 1356


>gi|238790616|ref|ZP_04634381.1| DNA-directed RNA polymerase subunit beta [Yersinia frederiksenii ATCC
            33641]
 gi|238721285|gb|EEQ12960.1| DNA-directed RNA polymerase subunit beta [Yersinia frederiksenii ATCC
            33641]
          Length = 1342

 Score = 1662 bits (4304), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYVDENTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +  +      +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDSVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|310766074|gb|ADP11024.1| DNA-directed RNA polymerase beta-subunit [Erwinia sp. Ejp617]
          Length = 1342

 Score = 1662 bits (4304), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 965/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+VY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVYQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIES--NGTVYVEKGRRITARHIRQLEKDAVAHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ I A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVAKDYIDESTGELLIAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRINYLLVSGGV-------------EAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLSDEDKQNQLEQLAEQYDELKHEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEDVSRLREFIQRAYDLGTDVRQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|308188908|ref|YP_003933039.1| DNA-directed RNA polymerase beta chain [Pantoea vagans C9-1]
 gi|308059418|gb|ADO11590.1| DNA-directed RNA polymerase beta chain [Pantoea vagans C9-1]
          Length = 1342

 Score = 1662 bits (4304), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQFTTPQILDIFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G   +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETATFDIE--ANGTVYVEKGRRITARHIRQLEKDGIQHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ + A   +    L ++  S  + I  L+ + +++  Y+  TL
Sbjct: 292  IAGKVVAKDYIDESTGELIVAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVIDGLVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMHAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIQNVLISGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEAKQNQLEQLAEQYDELKHEFEKKLEGKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQRAYDLGTDLRQRVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|188025530|ref|ZP_02958950.2| hypothetical protein PROSTU_00731 [Providencia stuartii ATCC 25827]
 gi|188023206|gb|EDU61246.1| hypothetical protein PROSTU_00731 [Providencia stuartii ATCC 25827]
          Length = 1357

 Score = 1662 bits (4304), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 16   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PDGQNGLEAAFRSV 71

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRLIV++ +   G  ++
Sbjct: 72   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLIVYEREAPEG--TV 129

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 130  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 189

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +E+IL+ F+ K V+  R 
Sbjct: 190  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYSTEDILNLFFDKTVFQIRD 249

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ V  + +  + 
Sbjct: 250  NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRLLEKEEVNSIEVPVEY 306

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGE+   A   +    L  +  +  + I  L+ + +++ AYI  TL
Sbjct: 307  IAGKVVARDYIDESTGELICAANMELSLDMLARLSQAGHKTIETLFTNDLDHGAYISETL 366

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ LFF  D+YDLS VGR+K N  L  
Sbjct: 367  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFDNLFFSEDRYDLSAVGRMKFNRSLGR 426

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + +EDII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 427  DEIEGSGILSEEDIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 486

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 487  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 546

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 547  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 606

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ L EDGSF EEL+ CR  GE  L  R++++
Sbjct: 607  RLVRDGIVTDEIHYLSAIEEGNFIIAQANTVLAEDGSFVEELITCRNRGESSLFSRDQVE 666

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 667  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 726

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 727  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 786

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 787  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 846

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 847  HIQELSCVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 906

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 907  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEET 966

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  I++R+  +L                 + ++ + + PR +W 
Sbjct: 967  QLRDAKKDLTEELRIFEAGIFARIRSVLISGG-------------IEAEKLDKLPRDRWL 1013

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + ++ DE+ Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1014 ELSLADEEKQNQLEQLAEQYDELKSEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1073

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1074 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPVDIVLNPLGVPSRMNIGQILETHLG 1133

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1134 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGDDPRQKVDLNTFSDEEVLRLAENLKK 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1194 GMPIATPVFDGAKEIEIKELLKLGGLPTSGQITLFDGRTGEKFERQVTVGYMYMLKLNHL 1253

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1254 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1313

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1314 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1357


>gi|88862608|gb|ABD53485.1| DNA-directed RNA polymerase subunit beta [Jannaschia sp. CCS1]
          Length = 1362

 Score = 1662 bits (4304), Expect = 0.0,   Method: Composition-based stats.
 Identities = 836/1363 (61%), Positives = 1068/1363 (78%), Gaps = 13/1363 (0%)

Query: 26   IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
            +P+LIEVQK+SYD FL      +    EG++  F+SVFPI  F+  A+LEFV YE + PK
Sbjct: 1    MPNLIEVQKSSYDLFLKSGDQLEPMDGEGIKGVFQSVFPIKDFNETAILEFVKYELETPK 60

Query: 86   FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
            FDV++C  RDLTYA PLK+TLRLIVFD+DE TGAKS+KDIKEQ ++MGD+PLMT +GTFV
Sbjct: 61   FDVEECQQRDLTYAAPLKVTLRLIVFDIDEDTGAKSVKDIKEQDVFMGDMPLMTPNGTFV 120

Query: 146  IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
            + G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+ACRIIP +G W+D EFD+KDI+  R
Sbjct: 121  VNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFACRIIPYRGSWLDFEFDAKDIVFSR 180

Query: 206  IDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
            IDRRRK+PVT+ L ALG+D E I+  +Y  + +    +         + + G + ++ LV
Sbjct: 181  IDRRRKLPVTTLLYALGLDQEGIMDAYYDTVTFKMVKNKGWSTKFFPERVRGTRPTTDLV 240

Query: 266  DIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            D  TGE + E+GKK+T   +K   ++G ++ L +  D + G + A+DI+N ETG IY+EA
Sbjct: 241  DAKTGEVIAEAGKKVTPRAVKKWIDEGSIENLLVPFDGIVGRFAAKDIINEETGAIYVEA 300

Query: 325  GDVIDEK----------SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            GD +  +          +L+E+  + I +IP+L +D+VN   Y+RNTL  DKN +R+ AL
Sbjct: 301  GDELTWELDKAGEVSGGTLKELIDAGITEIPVLDIDNVNVGPYMRNTLAVDKNLNRESAL 360

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            +DIYRVMRPG+  T   A ++F+ LFFDS++YDLS VGRVKMNMRL+LD  D +R +RKE
Sbjct: 361  MDIYRVMRPGEPPTVEAASNLFDQLFFDSERYDLSAVGRVKMNMRLDLDAEDTMRTLRKE 420

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DII+ IK LV+LR+G+G IDDID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+
Sbjct: 421  DIISCIKALVELRDGRGDIDDIDHLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSVE 480

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RA
Sbjct: 481  IDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERA 540

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVHPTHYGR+CP ET EG NIGL++SL ++ARVN YGFIETPYR+V D  V++DV
Sbjct: 541  GFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATYARVNKYGFIETPYRRVNDAVVSDDV 600

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            VY+SA EE    +AQAN++LD+DG F  ++V  R +GE  L PRE ID ID SPKQ+VS+
Sbjct: 601  VYMSATEEMRHTVAQANANLDDDGKFVNDMVNTRMSGEYTLNPREAIDLIDVSPKQLVSV 660

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AASLIPFLENDD+NR LMG NMQRQAVPLL+A+APFVGTG+ESVVAK SGAAI+AKR G+
Sbjct: 661  AASLIPFLENDDANRALMGSNMQRQAVPLLQADAPFVGTGIESVVAKDSGAAIMAKRGGV 720

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            ++QVDA RIVIR+ E  L+   +GVDIYRL KFQRSNQNTC+NQRPLVKVGD++ + ++I
Sbjct: 721  IDQVDAQRIVIRATED-LELGDAGVDIYRLRKFQRSNQNTCINQRPLVKVGDKIGKGEVI 779

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGPSTD+G+LALG+N++VAFMPW+GYN+EDS+LISER+  +DVFTSIHIEEFEV ARDT
Sbjct: 780  ADGPSTDIGELALGKNVIVAFMPWNGYNYEDSILISERISRDDVFTSIHIEEFEVAARDT 839

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE L+N+DE GI+ +GAEV PGDILVGKITPKGESPMTPEEKLLR
Sbjct: 840  KLGPEEITRDIPNVGEEALRNLDEAGIVYIGAEVEPGDILVGKITPKGESPMTPEEKLLR 899

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFGEKA DVRDTSLRV  G  GT+V+VR+FNRHG++K+ER++ +ERE++E LARD+DDE
Sbjct: 900  AIFGEKASDVRDTSLRVKPGDYGTIVEVRVFNRHGVEKDERALQIEREEVERLARDRDDE 959

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE-YPRSQWWQFAVQDEKVQR 1033
             VIL+RNIY+RL  ++ G+ AV GPKG K +TV+  DL+     R QWWQ A++DEK   
Sbjct: 960  LVILERNIYARLRGMIMGKTAVKGPKGVKPNTVIDEDLLDGQLSRGQWWQLALEDEKDAA 1019

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            ++E+L  Q++T K  L+ RF++K+EK++ GDD+PPGV+++VKVF+A+KR +Q GDKMAGR
Sbjct: 1020 HIEALNQQFDTQKRALDHRFEDKVEKVRRGDDLPPGVMKMVKVFIAVKRKLQPGDKMAGR 1079

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+++P EDMPFL DGTPVD VLNPLGVPSRMNVGQI ETH+GWA  G+G +I 
Sbjct: 1080 HGNKGVISKVVPMEDMPFLADGTPVDFVLNPLGVPSRMNVGQILETHMGWAARGMGLQID 1139

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
              +++Y+ +GD++P+R  L+   G   + +  +D D++S+L  A     GVP++TPVFDG
Sbjct: 1140 EALDEYRRSGDMTPVRDALKIAYGDDVYDDAFADRDEESLLEAAGNVTKGVPIATPVFDG 1199

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A E  +N  L  A    SGQS L+DG TGE F R VTVG  Y+LKL+H+V DK++ARSTG
Sbjct: 1200 AKEADVNDALIRAGFSTSGQSKLFDGRTGEQFAREVTVGVKYLLKLHHLVDDKIHARSTG 1259

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYESIV
Sbjct: 1260 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYESIV 1319

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             G D FE G PESFNVLVKE++ LGL+++L ++         E
Sbjct: 1320 KGEDNFEAGVPESFNVLVKEVRGLGLNMELLDAEDDEGGIAAE 1362


>gi|320013657|gb|ADV97228.1| RNA polymerase, beta subunit [Yersinia pestis biovar Medievalis str.
            Harbin 35]
          Length = 1342

 Score = 1662 bits (4303), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYVDASTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  RE++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFLEDLVTCRSKGESSLFSREQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMHPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R  ++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDDVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + ++ +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEAEKLSKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|238794959|ref|ZP_04638556.1| DNA-directed RNA polymerase subunit beta [Yersinia intermedia ATCC
            29909]
 gi|238725717|gb|EEQ17274.1| DNA-directed RNA polymerase subunit beta [Yersinia intermedia ATCC
            29909]
          Length = 1342

 Score = 1662 bits (4303), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALSFTTAQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDTNTGELICAANMELSLDLLAKLSQSGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|297181147|gb|ADI17344.1| hypothetical protein [uncultured Oceanospirillales bacterium
            HF0070_21F08]
          Length = 1380

 Score = 1662 bits (4303), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1387 (51%), Positives = 976/1387 (70%), Gaps = 30/1387 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P+++++P L+ +Q  SY  FL  + + DER  EGL+AAF+SV
Sbjct: 1    MAYSFTEKKRIRKDFGKLPKVMEVPYLLAIQLDSYRKFLQHDKSADERFEEGLEAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI+++SG A LE+  YEF  P FDV +C+ R  TYA PL++ +RL+++D +      +I
Sbjct: 61   FPISSYSGNAALEYAGYEFGKPVFDVKECIIRGTTYAAPLRVRIRLVIYDKE---SNGAI 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ 
Sbjct: 118  KDIREQQVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L ALG  S+EIL  F+         
Sbjct: 178  RVIPYRGSWLDFEFDPKDMVYVRIDRRRKLPATILLRALGYTSDEILDIFFETNEILVED 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G   +  ++  D  E V+E G+++T+  ++ L++  +++L I ++ 
Sbjct: 238  GVYRMRLVPERL-RGETATFDILAGD--EVVVERGRRVTARHIRQLEKANIEYLEIPAEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G Y+A+ I++ ETGE+ +E    +   +LE++    I+    LY + ++N  ++ +TL
Sbjct: 295  LQGRYLAKSIIDEETGEVLLECNTELGADALEKLEKGGIKRFETLYTNDLDNGPFMSDTL 354

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +   +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL  
Sbjct: 355  RADPTRSPLEALVEIYRMMRPGEPPTKEAAENLFRNLFFTDERYDLSGVGRMKFNRRLGR 414

Query: 423  DTPDDVRHIRKEDIIA-----------------------IIKILVDLRNGKGTIDDIDNL 459
            +       +      +                       ++K LVD+RNG G  DDID+L
Sbjct: 415  EDVTGPGIVYDGRYFSNRTDDEGKQYFEQIGGETSDIIDVLKTLVDIRNGNGVTDDIDHL 474

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            GNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF S
Sbjct: 475  GNRRIRSVGEMAENQFRVGLVRVERAVKERLSLAESEGLMPQDLINAKPVAAAVKEFFGS 534

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 535  SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 594

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            IGL++SL S+AR N YGF+E+PYRKV DGKVT+++ YLSA+EE    IAQ ++ + +DG 
Sbjct: 595  IGLINSLASYARTNEYGFLESPYRKVVDGKVTDEIEYLSAIEEAECVIAQVDAKMTDDGG 654

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            F E+ V  R   E  ++ R+ I  +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 655  FVEDFVTVRHRYEFTVMERDTITHMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQ 714

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVP L+AE P VGTGME  VA+ SG  +VA+R G+V +VDA RI+++  + ++    +GV
Sbjct: 715  AVPTLRAEKPLVGTGMERHVARDSGVCVVAQRGGVVNKVDASRIIVKVNDDEVVEGEAGV 774

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            DIY L K+ RSNQNTC+NQRPLVKVGD V   DI+ADGPS D+G+LALG+NM VAFMPW+
Sbjct: 775  DIYNLTKYTRSNQNTCINQRPLVKVGDRVSARDIMADGPSVDMGELALGQNMRVAFMPWN 834

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFEDS+LISER+V ED FTSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE 
Sbjct: 835  GYNFEDSILISERVVKEDRFTSIHIQELTAIARDTKLGAEEITADIPNVGEAALGKLDES 894

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV SGV GTV
Sbjct: 895  GIVYIGAEVEAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGVKGTV 954

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            +DV++F R G++K+ER+  +E++ ++   +D  DE  IL+R+   RL  ++ G+    G 
Sbjct: 955  IDVQVFTRDGVEKDERAKQIEQDALDKFRKDLKDEYRILERDSLDRLRTVMVGKKVNGG- 1013

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             G K+ T L+  ++ +   +QW++    D+ V   +E      E  K   ++R+K+K  K
Sbjct: 1014 AGLKRGTELTDAILDDLDAAQWFELRPADDDVAEQLERTHQYLEQHKKEQDERYKDKQSK 1073

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            I  GDD+  GVL+VVKV++A+KR IQ GDKMAGRHGNKG++S I+P EDMP+ + G PVD
Sbjct: 1074 ISGGDDLSHGVLKVVKVYLAIKRRIQPGDKMAGRHGNKGVISVIMPEEDMPYDEHGVPVD 1133

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +VLNPLGVPSRMNVGQI ETHLGWA  GLG++I  +++  K   ++      +    G G
Sbjct: 1134 VVLNPLGVPSRMNVGQILETHLGWAAKGLGERIGEMLDQEKKATEVRDFLDQIYNKTGAG 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
               E+   + +  ++ +AE  ++GVP++T VFDGA E  I ++L +A  D SGQ  L+DG
Sbjct: 1194 GTDEEWGSFSEADIMELAENLRAGVPMATAVFDGAKEFEIKALLELAGYDRSGQIQLWDG 1253

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             +GE FDR VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1254 RSGEQFDRKVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1313

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV G+   + G PESFNVL+KE+++LG+
Sbjct: 1314 WALEAYGAAYTLQEMLTVKSDDVNGRTRIYKNIVDGDHRMDPGMPESFNVLLKEIRSLGI 1373

Query: 1360 SIDLENS 1366
            +I+LEN 
Sbjct: 1374 NIELEND 1380


>gi|161523421|ref|YP_001578433.1| DNA-directed RNA polymerase subunit beta [Burkholderia multivorans
            ATCC 17616]
 gi|189351806|ref|YP_001947434.1| DNA-directed RNA polymerase subunit beta [Burkholderia multivorans
            ATCC 17616]
 gi|221201557|ref|ZP_03574595.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD2M]
 gi|221207368|ref|ZP_03580378.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD2]
 gi|221213506|ref|ZP_03586481.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD1]
 gi|226699381|sp|A9ADI5|RPOB_BURM1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|160340850|gb|ABX13936.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            ATCC 17616]
 gi|189335828|dbj|BAG44898.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            ATCC 17616]
 gi|221166958|gb|EED99429.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD1]
 gi|221172956|gb|EEE05393.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD2]
 gi|221178373|gb|EEE10782.1| DNA-directed RNA polymerase, beta subunit [Burkholderia multivorans
            CGD2M]
          Length = 1368

 Score = 1662 bits (4303), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1374 (50%), Positives = 965/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSAPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+GETGE+   A D I E  LE++  + I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGETGEVIANANDEITESVLEKLREAGIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++D++G  T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDGKVTDQIDYLSAIEEGRYMIAQANAAIDDEGRLTDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRAFLTKIYNESGRAEDLDSFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA E+ +  ML +A  D+  +            LYDG TGEPF+R VTVG
Sbjct: 1195 GVPFATPVFDGATEDEMAKMLDLAFPDDIAKQLDMNPSKNQVRLYDGRTGEPFERRVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|332159912|ref|YP_004296489.1| DNA-directed RNA polymerase subunit beta [Yersinia enterocolitica
            subsp. palearctica 105.5R(r)]
 gi|318607538|emb|CBY29036.1| DNA-directed RNA polymerase beta subunit [Yersinia enterocolitica
            subsp. palearctica Y11]
 gi|325664142|gb|ADZ40786.1| DNA-directed RNA polymerase subunit beta [Yersinia enterocolitica
            subsp. palearctica 105.5R(r)]
 gi|330863591|emb|CBX73703.1| DNA-directed RNA polymerase subunit beta [Yersinia enterocolitica
            W22703]
          Length = 1342

 Score = 1661 bits (4302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|293394022|ref|ZP_06638326.1| DNA-directed RNA polymerase subunit beta [Serratia odorifera DSM
            4582]
 gi|291423462|gb|EFE96687.1| DNA-directed RNA polymerase subunit beta [Serratia odorifera DSM
            4582]
          Length = 1365

 Score = 1661 bits (4302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 24   MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 79

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 80   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 137

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 138  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 197

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ KI +  R 
Sbjct: 198  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKITFEIRD 257

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  ++ + +  + 
Sbjct: 258  NKLQMELVPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIQSIEVPVEY 314

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  T+
Sbjct: 315  IAGKVVAKDYIDTNTGELICSANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYISETV 374

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 375  RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 434

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 435  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 494

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 495  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 554

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 555  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 614

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 615  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVD 674

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 675  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 734

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 735  SGVTAVAKRGGVIQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 794

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 795  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 854

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 855  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 914

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 915  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 974

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   ++ +++ PR +W 
Sbjct: 975  QLKQAKKDLTEELQILEAGLFARIHAVLVAGGV-------------EAEKLAKLPRDRWL 1021

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1022 ELGLTDEDKQNQLEQLAEQYDELKSDFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1081

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1082 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1141

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1142 MAAKGIGEKINQMLKQQQEVAKLREFIQKAYDLGDDVCQKVDLNTFSDDEVLRLAENLKK 1201

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L M  +  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1202 GMPIATPVFDGAKETEIKQLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1261

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1262 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1321

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1322 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1365


>gi|317494913|ref|ZP_07953323.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316917101|gb|EFV38450.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 1342

 Score = 1661 bits (4302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1364 (51%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTEQILELFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDGITLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQAGYKRIETLFTNDLDHGAYISETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIEVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D +MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDMLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGIVTDEIHYLSAIEEGNYVIAQANSNLDDEGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGVIQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTSI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   ++ +++ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVSGGV-------------EAEKLAKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEAKQNQLEQLAEQYDELKSDFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +      T  +S + DD V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQQQEVAKLREFIQKAYDLGDNTRQTVDLSTFTDDEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L +  +  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPIATPVFDGAKEKEIKELLTLGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|212709026|ref|ZP_03317154.1| hypothetical protein PROVALCAL_00058 [Providencia alcalifaciens DSM
            30120]
 gi|212688315|gb|EEB47843.1| hypothetical protein PROVALCAL_00058 [Providencia alcalifaciens DSM
            30120]
          Length = 1342

 Score = 1661 bits (4302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PDGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRLIV++ +   G  ++
Sbjct: 57   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLIVYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+  ++EEIL+ F+ K V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYNTEEILNLFFEKTVFQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ +  + +  + 
Sbjct: 235  NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKEEINSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGE+   A   +    L  +  S  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVARDYIDESTGELICAANMELSLDMLARLSQSGHKTIETLFTNDLDHGAYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ LFF  D+YDLS VGR+K N  LN 
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFDNLFFSEDRYDLSAVGRMKFNRSLNR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + +EDII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSEEDIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ L +DG F EEL+ CR  GE  L  RE+++
Sbjct: 592  RLVRDGIVTDEIHYLSAIEEGNFIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVARRGGSVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLR+P+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRIPNGVSGTVIDVQVFTRDGVEKDKRALEIEET 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  ++SR+  +L                 + ++ + + PR +W 
Sbjct: 952  QLRDAKKDLTEELRIFESALFSRIRSVLISGG-------------IEAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A+ DE+ Q  +E L  QY+  KS  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELALADEEKQNQLEQLAEQYDELKSEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + D+ V+R+AE  + 
Sbjct: 1119 MAAKGIGEKINAMLKQQQEVAKLREFIQKAYDLGDDPRQKVDLNTFSDEEVMRLAENLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLKLGGLPTSGQITLFDGRTGEKFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|238785550|ref|ZP_04629531.1| DNA-directed RNA polymerase subunit beta [Yersinia bercovieri ATCC
            43970]
 gi|238713535|gb|EEQ05566.1| DNA-directed RNA polymerase subunit beta [Yersinia bercovieri ATCC
            43970]
          Length = 1342

 Score = 1661 bits (4302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTTQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|294634221|ref|ZP_06712766.1| DNA-directed RNA polymerase, beta subunit [Edwardsiella tarda ATCC
            23685]
 gi|291092346|gb|EFE24907.1| DNA-directed RNA polymerase, beta subunit [Edwardsiella tarda ATCC
            23685]
          Length = 1353

 Score = 1661 bits (4301), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 12   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 67

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 68   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 125

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 126  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 185

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 186  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDFTTEQILDLFFDKVIFEIRD 245

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 246  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 302

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  TL
Sbjct: 303  IVGKVAAKDYIDESTGELICAANMELSLDLLAKLSQSGYKRIETLFTNDLDHGPYMSETL 362

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 363  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLMR 422

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 423  DEIEGSGILSKEDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 482

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D +MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 483  ERAVKERLSLGDLDMLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 542

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 543  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 602

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 603  RRVRDGIVTDEIHYLSAIEEGNFVIAQANSNLDDEGRFVEDLVTCRSKGESSLFSRDQVD 662

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 663  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 722

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 723  SGVTSVAKRGGMVQYVDASRIVIKVNEDEMFPGEAGIDIYNLTKYTRSNQNTCISQMPCV 782

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 783  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTSI 842

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 843  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 902

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E  
Sbjct: 903  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEM 962

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   ++ + + PR +W 
Sbjct: 963  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EAEKLEKLPRDRWL 1009

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1010 ELGLADEAKQNQLEQLAEQYDELKAEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1069

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1070 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1129

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1130 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGDNTRQQVDLNTFSDDEVLRLAENLKK 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I  +L +  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1190 GLPVATPVFDGAKEREIKGLLELGGIPTSGQITLYDGRTGERFERQVTVGYMYMLKLNHL 1249

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1250 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1309

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1310 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1353


>gi|188532314|ref|YP_001906111.1| DNA-directed RNA polymerase subunit beta [Erwinia tasmaniensis
            Et1/99]
 gi|226699405|sp|B2VG96|RPOB_ERWT9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|188027356|emb|CAO95201.1| DNA-directed RNA polymerase beta chain [Erwinia tasmaniensis Et1/99]
          Length = 1342

 Score = 1661 bits (4301), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K++Y  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALSYTTEQILDLFFEKVIYQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIES--NGTVYVEKGRRITARHIRQLEKDAVAHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ I A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292  IAGKVVAKDYIDESTGELLIAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                 + ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRINYLLVAGG-------------IEAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLSDEDKQNQLEQLAEQYDELKHEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVSKLREFIQRAYDLGTDVRQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|123440675|ref|YP_001004668.1| DNA-directed RNA polymerase subunit beta [Yersinia enterocolitica
            subsp. enterocolitica 8081]
 gi|158512670|sp|A1JII0|RPOB_YERE8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|122087636|emb|CAL10418.1| DNA-directed RNA polymerase beta chain [Yersinia enterocolitica
            subsp. enterocolitica 8081]
          Length = 1342

 Score = 1661 bits (4301), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + ++++AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHSAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +  +      +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDSVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|238798663|ref|ZP_04642137.1| DNA-directed RNA polymerase subunit beta [Yersinia mollaretii ATCC
            43969]
 gi|238717481|gb|EEQ09323.1| DNA-directed RNA polymerase subunit beta [Yersinia mollaretii ATCC
            43969]
          Length = 1342

 Score = 1660 bits (4300), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTTQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQSGHKHIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|253686611|ref|YP_003015801.1| DNA-directed RNA polymerase, beta subunit [Pectobacterium carotovorum
            subsp. carotovorum PC1]
 gi|259494188|sp|C6DHR5|RPOB_PECCP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|251753189|gb|ACT11265.1| DNA-directed RNA polymerase, beta subunit [Pectobacterium carotovorum
            subsp. carotovorum PC1]
          Length = 1342

 Score = 1660 bits (4300), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1364 (52%), Positives = 973/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  +E+IL  F+ KIVY   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALGYSTEQILDLFFDKIVYEING 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMDLVPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVLSKDYIDESTGELIGAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D  VT+++ YLSA+EE N  IAQAN++LDE+G F +ELV CR  GE  L  R++++
Sbjct: 592  RRVRDNVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVIR  + ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIRVNDDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQHEEVTKLREFIQRAYDLGDDVRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQMGGIPTSGQITLYDGRTGEKFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|238756060|ref|ZP_04617383.1| DNA-directed RNA polymerase subunit beta [Yersinia ruckeri ATCC
            29473]
 gi|238705727|gb|EEP98121.1| DNA-directed RNA polymerase subunit beta [Yersinia ruckeri ATCC
            29473]
          Length = 1342

 Score = 1660 bits (4300), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALSFTTAQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ GV  + +  + 
Sbjct: 235  NKLQMELIPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGVDSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQAGHKRIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|291613229|ref|YP_003523386.1| DNA-directed RNA polymerase subunit beta [Sideroxydans lithotrophicus
            ES-1]
 gi|291583341|gb|ADE10999.1| DNA-directed RNA polymerase, beta subunit [Sideroxydans
            lithotrophicus ES-1]
          Length = 1356

 Score = 1660 bits (4300), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1363 (51%), Positives = 960/1363 (70%), Gaps = 8/1363 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K    + +P L+  Q  SY  FL   +AP++R NEGLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRVGALPVPFLLSTQLESYSDFLQAWVAPEQRKNEGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +  A L+FVSY    P FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHTKFARLDFVSYTLGMPPFDVRECQQRGLTYASPLRARVRLTILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTNTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++ RIDRRRK+PVT  L +LG   E+IL  F+    +    
Sbjct: 179  RVIPYRGSWLDFEFDAKDYVYFRIDRRRKMPVTILLKSLGYTPEQILQMFFQFDTFHFGK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F +    L  G      + +   G+ ++   K++T   ++ ++E G+  L + +D 
Sbjct: 239  KGIQFEVVPERL-RGEIARFDI-EGKGGKLIVAKDKRITVRHIREMQEAGIDKLTVGTDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A +IV+ ++GEI   A D I E  L+++  + I  I  LY + ++   +I  TL
Sbjct: 297  LVGRVLAHNIVDKDSGEIIANANDEITETLLDKLEAAGIAKINTLYTNDLDQGGFISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++FN LFF+ D+YDLS VGR+K N R+  
Sbjct: 357  RTDETTDQWTARVAIYRMMRPGEPPTEDAVEALFNGLFFNEDRYDLSAVGRMKFNRRVGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDI+ +I+ILV+LRNG+G IDDID+LGNRRVR+VGE+ +NQ+R GL R+
Sbjct: 417  EELTGAVTLSNEDIVEVIRILVELRNGRGEIDDIDHLGNRRVRAVGELAENQFRTGLARV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLINAKP+ +AV EFF SSQLSQ  +  N L+ +TH RR+S
Sbjct: 477  ERAVKERLGQAEADNLMPHDLINAKPISAAVKEFFGSSQLSQFMDQTNPLAEVTHKRRIS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARTNEYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V   + T+DV YLSA+EE    IAQAN+ LD+ G FT ++V  R   E +L   +K++
Sbjct: 597  RRVVKSRATDDVDYLSAIEEGKFTIAQANAELDKKGHFTNDIVSARQHNEFVLAEPDKLE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP+L+AE   VGTG+E  VA  
Sbjct: 657  YMDVAPAQVVSVAASLIPFLEHDDANRALMGANMQRQAVPVLRAEKALVGTGIERTVAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG A+ A R G V+ VD+ RIV+R  + +      GVDIY L K+ RSNQNT +NQRPLV
Sbjct: 717  SGTAVQAWRGGRVDYVDSGRIVVRVNDDETTAGEVGVDIYNLTKYTRSNQNTNINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD + R D++ADG STD+G+LALG+NM++AFMPW+GYNFEDS+LISER+V+ED FTSI
Sbjct: 777  RVGDVIARGDVVADGASTDMGELALGQNMMIAFMPWNGYNFEDSILISERVVAEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  VMARDTKLG EEITRDIPN+SE  +  +DECGI+ +GAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGAEVGVGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV +G+SGTV+DV++F R G+ +++R+  +  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGISGTVIDVQVFTREGLQRDKRAQQIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D  D+  I++ ++++RL ++L  + A  GPK   K T L+ + +      QW+
Sbjct: 957  ELSRYKKDLADQMRIVEADLFARLEKLLHNKVANGGPKKLAKGTKLNKEYLHSIEHHQWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               V D++V   +E +K      +   +  F+ K +K+  GD++  GV ++VKV+VA+KR
Sbjct: 1017 DIRVADDEVAAQMEQVKEALAQKRVEFDAAFELKKKKLTQGDELQAGVQKMVKVYVAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRI+P EDMP + DGTPV++VLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSRIVPVEDMPRMADGTPVEVVLNPLGVPSRMNIGQVLEVHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLGKKI  ++   +A   I+ +R FL K+   G   ++I+ + D+ V+ +    K+
Sbjct: 1137 WAAKGLGKKINQML---EAEAKIADVRKFLGKIY-KGDQADEIATFTDEEVVELCRNLKA 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TPVFDGA EE I  +L +ADL  SGQ  LYDG TG+ FDR VTVGY+++LKL+H+
Sbjct: 1193 GVPFATPVFDGASEEEIKDLLELADLPRSGQIQLYDGRTGDAFDRKVTVGYMHVLKLHHL 1252

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1253 VDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1312

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT+VYE+IV G+   + G PESFNVL KE+++LG+ IDLE 
Sbjct: 1313 NGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLGIDIDLER 1355


>gi|238760256|ref|ZP_04621400.1| DNA-directed RNA polymerase subunit beta [Yersinia aldovae ATCC
            35236]
 gi|238701520|gb|EEP94093.1| DNA-directed RNA polymerase subunit beta [Yersinia aldovae ATCC
            35236]
          Length = 1342

 Score = 1660 bits (4299), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALSFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDTNTGELICAANMELSLDLLAKLSQSGHKHIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFLEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|162420540|ref|YP_001607196.1| DNA-directed RNA polymerase subunit beta [Yersinia pestis Angola]
 gi|226699465|sp|A9R0H8|RPOB_YERPG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|162353355|gb|ABX87303.1| DNA-directed RNA polymerase, beta subunit [Yersinia pestis Angola]
          Length = 1342

 Score = 1660 bits (4299), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1364 (52%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGPWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTAQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYVDASTGELICAANMELSLDLLAKLSQAGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  RE++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFLEDLVTCRSKGESSLFSREQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMHPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + ++ +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEAEKLSKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|269137533|ref|YP_003294233.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Edwardsiella tarda EIB202]
 gi|267983193|gb|ACY83022.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Edwardsiella tarda EIB202]
 gi|304557607|gb|ADM40271.1| DNA-directed RNA polymerase beta subunit [Edwardsiella tarda FL6-60]
          Length = 1342

 Score = 1660 bits (4299), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDFTTEQILDLFFDKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  TL
Sbjct: 292  IVGKVAAKDYIDESTGELICAANMELSLDLLAKLSQSGYKRIETLFTNDLDHGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLMR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D +MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDMLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGIVTDEIHYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTSVAKRGGMVQYVDASRIVIKVNEDEMFPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTSI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EAEKLEKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEAKQNQLEQLAEQYDELKAEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGDHTRQQVDLNTFTDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I  +L +  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPVATPVFDGAKEREIKGLLELGGIPTSGQITLYDGRTGERFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|315122745|ref|YP_004063234.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
            solanacearum CLso-ZC1]
 gi|313496147|gb|ADR52746.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
            solanacearum CLso-ZC1]
          Length = 1382

 Score = 1660 bits (4299), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1247/1382 (90%), Positives = 1311/1382 (94%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAK VVFNGLGR RKFFGK PEIIDIPDLIEVQ+ASYD FLMMN +P+ERPNEGLQAAFK
Sbjct: 1    MAKDVVFNGLGRARKFFGKIPEIIDIPDLIEVQRASYDQFLMMNSSPEERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEF SYEFD PKFDVDDCL RDLTYA PLKI LRLIVFD+DEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFESYEFDSPKFDVDDCLRRDLTYAAPLKIILRLIVFDIDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGD+PLMTKDGTFVI G QRIVVSQLHRSPGI FDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDVPLMTKDGTFVINGTQRIVVSQLHRSPGILFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM+SE+ILSTFY KIVY +
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMNSEDILSTFYSKIVYVK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +G++WCFPLS ADL+VG+KVSSSL+D+DTGE+VIESGK+ T+ LLK+LKEKGV FLG+TS
Sbjct: 241  KGEYWCFPLSCADLIVGSKVSSSLIDVDTGERVIESGKRFTANLLKNLKEKGVGFLGVTS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G YVAEDIVN  TGEIY+EAGD IDE +L  I    I DIP+L+VDS+++NAY+RN
Sbjct: 301  DYLYGSYVAEDIVNETTGEIYLEAGDAIDEPTLAAIVSCGIEDIPVLHVDSIDSNAYVRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLV DKNKD KDALLDIYRVMRPGDV T S AESMFNFLFFD DKYDLS VGRVKMNMRL
Sbjct: 361  TLVLDKNKDYKDALLDIYRVMRPGDVPTVSAAESMFNFLFFDPDKYDLSAVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLD PD VRH+RKED+IAIIKILVDLR+GKG IDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDVPDTVRHVRKEDVIAIIKILVDLRDGKGKIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVREFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTN++VYLSA+EEENRYIAQ+N+SL EDGSF EELVFCRCAGEE+LVPRE 
Sbjct: 601  PYRKVCDGKVTNEIVYLSAIEEENRYIAQSNASLKEDGSFAEELVFCRCAGEEVLVPREN 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+F+D SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  INFMDTSPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIR VE DL+PS SGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRVVEEDLNPSASGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG+ICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGVICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KG+SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV+VRIFNRHGIDKNERS+SVE
Sbjct: 901  KGDSPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVEVRIFNRHGIDKNERSLSVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARD+DDEQ ILDRNIYSRL EILC Q A+SGPKGFKKS+VLSSDLIS Y RSQ
Sbjct: 961  REQIELLARDRDDEQAILDRNIYSRLKEILCSQTAISGPKGFKKSSVLSSDLISGYQRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRN+ESL+ QYE SKS+LE RFKNKIEKIQWGDDM PGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNIESLRAQYEHSKSVLESRFKNKIEKIQWGDDMSPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQSGDKMAGRHGNKGIVSRILPCEDMPFL+DGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRSIQSGDKMAGRHGNKGIVSRILPCEDMPFLEDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKS+INDYKANGDI+PLRSFLEK+IGTG H EKISDYDD SVLR+AEQW
Sbjct: 1141 LGWACVGLGKKIKSIINDYKANGDIAPLRSFLEKIIGTGPHAEKISDYDDASVLRLAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVSDKV+ARS GSYSLVTQQPLGGKSNRGGQRLGEMEVWC QAYGAAYVLQEMLTIKSD
Sbjct: 1261 HMVSDKVHARSIGSYSLVTQQPLGGKSNRGGQRLGEMEVWCTQAYGAAYVLQEMLTIKSD 1320

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGRT+VYESIV+G+++FETG PESFNVLVKEMQALGLSIDLENSR K++ KMEEIPD 
Sbjct: 1321 DVVGRTKVYESIVSGDNSFETGIPESFNVLVKEMQALGLSIDLENSRAKSTVKMEEIPDL 1380

Query: 1381 NK 1382
            N+
Sbjct: 1381 NE 1382


>gi|300309447|ref|YP_003773539.1| DNA-directed RNA polymerase subunit beta [Herbaspirillum seropedicae
            SmR1]
 gi|300072232|gb|ADJ61631.1| DNA-directed RNA polymerase subunit beta protein [Herbaspirillum
            seropedicae SmR1]
          Length = 1368

 Score = 1660 bits (4298), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 958/1374 (69%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+  Q  SY +FL    A  ER NEGLQ+AF S+
Sbjct: 1    MHYSFTEKKRIRKSFAKRANVHNVPFLLATQIESYQNFLQPERAASERKNEGLQSAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF+SY    P FDV +C  R LT+A PL+  +RL++ D +  T    +
Sbjct: 61   FPIVSHNGFARLEFLSYVLGAPPFDVKECQQRGLTFASPLRAKVRLVILDKESPT-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  R+DRRRK+PVT  L A+GM SE+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILLKAIGMTSEQILANFFVFDNFNLHA 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       +  L  G      + D  +G+ ++   K++ +  ++ ++  G+K + +  D 
Sbjct: 240  EGADMEFVSERL-RGEVARFDITD-KSGKVMVAKDKRINAKHVRDIEAAGIKHISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ ETGE+   A D + E+ L ++  + I  I  LY + ++   YI  TL
Sbjct: 298  LLGRVLAKNIVDPETGEVVASANDELTEELLAKLREANISAIQTLYTNDLDQGGYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++FN LF+  D+YDLS VGR+K N R+  
Sbjct: 358  RTDDTADQTAARVAIYRMMRPGEPPTEESVEALFNGLFYSEDRYDLSAVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DI+A+IKILV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DELTGTMTLSNDDILAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV   KVTN + YLSA+EE    IAQAN+++D +G  ++ELV  R AGE ILV  E++ 
Sbjct: 598  RKVEGSKVTNQIDYLSAIEEGRYVIAQANATIDGEGKLSDELVSAREAGETILVSPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRVVIRVNDDEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD V ++D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KIGDRVAKHDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD LVGK+TPKG
Sbjct: 838  HIEELSVVARDTKLGAEEITRDISNLAENQLARLDESGIVYIGAEVEAGDTLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T L    + +  +  W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLERLLIGKVANGGPKKLVKGTKLDKAYLDDLDKFHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 D+ +   +E++K      +   +  F+ K +K+  GD++PPGV ++VKV++A+KR
Sbjct: 1018 DIRPADDDIANALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRILP EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG ++  ++   +A   ++ LR FL  +       E++  + D+ ++ + E  K 
Sbjct: 1138 WAAKGLGLRLGEMV---QAQAKVAELRKFLTTIYNESGKQEELDSFTDEEIIELVENLKK 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE    ML +A  D   +            +YDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGAHEEETRRMLDLAYPDPIAKQLGMTPSKNQVTMYDGRTGEAFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE  
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERE 1368


>gi|329296849|ref|ZP_08254185.1| DNA-directed RNA polymerase subunit beta [Plautia stali symbiont]
          Length = 1342

 Score = 1659 bits (4297), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1364 (51%), Positives = 969/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+++  +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVTECQIRGVTYSAPLRVKLRLVIYVREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALDYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGTVYVEKGRRITARHIRQLEKDNIQHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ + A   +    L ++  S  + I  L+ + +++ +YI  TL
Sbjct: 292  IAGKVVAKDYIDLNTGELIVPANMELSLDLLAKLSQSGHKRIETLFTNDLDHGSYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEERYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RA  E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERASFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGKV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGKVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIQAVLISGGV-------------EAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  QLGLTDEEKQNALEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +      T  ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQRAYDLGTDVRQTVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|268592961|ref|ZP_06127182.1| DNA-directed RNA polymerase, beta subunit [Providencia rettgeri DSM
            1131]
 gi|291311432|gb|EFE51885.1| DNA-directed RNA polymerase, beta subunit [Providencia rettgeri DSM
            1131]
          Length = 1342

 Score = 1659 bits (4296), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PDGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRLIV++ +   G  ++
Sbjct: 57   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLIVYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+  ++EEIL+ F+ K V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYNTEEILNLFFEKTVFQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ V  + +  + 
Sbjct: 235  NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKEEVNSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGE+   A   +    L  +  S  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVARDYIDESTGELICAANMELSLDMLARLSQSGHKTIETLFTNDLDHGAYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ LFF  D+YDLS VGR+K N  LN 
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFDNLFFSEDRYDLSAVGRMKFNRSLNR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + +EDII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSEEDIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++
Sbjct: 592  RLVRDGLVTDEIHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVARRGGSVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEET 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                 + ++ + + PR +W 
Sbjct: 952  QLRDAKKDLTEELRIFEAGLFARIRSVLVNGG-------------IEAEKLDKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + ++ DE+ Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELSLADEEKQNQLEQLAEQYDELKSEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQQEEVAKLREFIQKAYDLGDDPRQKVDLNTFTDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLKLGGLPTSGQITLFDGRTGERFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|258543814|ref|ZP_05704048.1| DNA-directed RNA polymerase subunit beta [Cardiobacterium hominis
            ATCC 15826]
 gi|258520943|gb|EEV89802.1| DNA-directed RNA polymerase subunit beta [Cardiobacterium hominis
            ATCC 15826]
          Length = 1357

 Score = 1659 bits (4296), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1364 (51%), Positives = 966/1364 (70%), Gaps = 7/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K+P ++D P L+ +Q  SY  FL   I  D+R + GL  AF S+
Sbjct: 1    MTYTFTEKKRIRKNFSKHPTVLDTPYLLSMQLDSYRDFLQKGIPSDKRADIGLHEAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V YE   P+FDV +C  R +TYA PL++ +RL ++D       K  
Sbjct: 61   FPIESHNGLVELQYVGYELGRPEFDVRECQLRGVTYASPLRVRMRLAIYDKGNHDKRKLK 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            + I+ + ++MG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG    SGKLL++ 
Sbjct: 121  QIIESEPVFMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGVGHSSGKLLFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD+++ RIDRRRK+PVT  L ALG    EIL  F+    +    
Sbjct: 181  RVIPYRGSWLDFEFDAKDLLYCRIDRRRKLPVTVLLHALGYTDAEILGEFFETQTFKISK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +        A    G  V+  ++    GE ++E+GK++TS  ++ L+EK V    +  D 
Sbjct: 241  NKLEMKFQPA-QFKGEAVAFDIM--ADGEVLVEAGKRITSRHVRQLEEKNVTSQVVPMDF 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D+++ E+GE+ ++A  V+ E+ + +     ++    LYV+ ++  AYI +TL
Sbjct: 298  VVGKILAKDLIDKESGELVLQANTVLTEEHIVKFIELGVKTFETLYVNELDRGAYIADTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D++ D+ +A  +IYR+MRPG+  T   A+ +F  LFF+ ++YDLS VGR+K N RL +
Sbjct: 358  RADESTDQDNARAEIYRMMRPGEPPTKDAADGLFENLFFNEERYDLSRVGRMKFNRRLGI 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + +EDI+ ++K L+ +++G GT+DDID+LGNRR+R VGEM  N +R+GL+R+
Sbjct: 418  EEKEGSGVLSREDIVRVLKTLIAIKDGDGTVDDIDHLGNRRIRCVGEMAANAFRIGLVRL 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ERSIKER+S V+ + + P+DLIN KPV +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 478  ERSIKERLSQVESEQLTPKDLINQKPVSAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A+ N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAVYAKTNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT +  YLSA+EE    IAQAN++L+EDG+F ++LV  R   E +L   ++ID
Sbjct: 598  RKVVDGKVTMETEYLSAIEESKYVIAQANAALNEDGTFRDDLVSARYENEFMLARADRID 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME VVA  
Sbjct: 658  YMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERVVASD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G+++ VD+ RIV++  + ++ P   GVDIY L K+ RSNQNTC+NQ+PLV
Sbjct: 718  SGVLVRAERGGVIDLVDSSRIVVKVNDDEVQPGGLGVDIYNLTKYTRSNQNTCINQKPLV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V R D++ADGPSTDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V ED FT+I
Sbjct: 778  KPGDVVARGDVLADGPSTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVQEDRFTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLG EEI+ DIPNV E  L  +D  GI+ +GAEV  GDILVGK+TPKG
Sbjct: 838  HIEELTCVARDTKLGSEEISSDIPNVKESALAKLDGTGIVHIGAEVKAGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E   +PEEKLLRAIFGEKA DV+D+SLRVP+G+ GTVVDVR++ R G++K+ R+  +E  
Sbjct: 898  ERSQSPEEKLLRAIFGEKASDVKDSSLRVPTGMDGTVVDVRVYTRDGVEKDARAKEIEAM 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE +A++  D+  + + +I+ R+  +L GQ     PK  K   ++   L++E    QW+
Sbjct: 958  EIESIAKNIKDQLRVFESDIHERVARLLLGQAVKKAPK-RKSGDLVDQALLNELKPEQWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               +Q+  +   ++ +       +  L+D ++ K  K   GDD+ PGVL++VKV++A+KR
Sbjct: 1017 DLRLQEADINEQLDGMHQLLLDKRRELQDYYEEKKAKFAQGDDLAPGVLKMVKVYLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRI+P EDMP+++DGTPVDI LNPLGVPSRMN+GQ+ ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSRIVPVEDMPYMEDGTPVDICLNPLGVPSRMNIGQVLETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+G +I  +++    N     LR +L +V    S  E +   DD   + + +  ++
Sbjct: 1137 WAARGIGLRIGEMLDQ---NEKPRKLRDYLNEVYNHDSQREALDSLDDGDFVALCQNLRA 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TPVFDGA E  +  ML +A L +SGQ+ LYDG TGEPFDR VTVGY+YMLKLNH+
Sbjct: 1194 GVPMATPVFDGAKEAEVQRMLELAGLPKSGQTRLYDGRTGEPFDRDVTVGYMYMLKLNHL 1253

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGG++  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1254 VDDKMHARSTGPYSLVTQQPLGGRAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1313

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL KE++AL ++IDLE  
Sbjct: 1314 EGRTKMYKNIVDGNLQIDPGMPESFNVLTKEIKALAINIDLEQE 1357


>gi|238918142|ref|YP_002931656.1| DNA-directed RNA polymerase subunit beta [Edwardsiella ictaluri
            93-146]
 gi|259494182|sp|C5BHE3|RPOB_EDWI9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|238867710|gb|ACR67421.1| DNA-directed RNA polymerase, beta subunit, putative [Edwardsiella
            ictaluri 93-146]
          Length = 1342

 Score = 1659 bits (4296), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1364 (51%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALDFTTEQILDLFFDKVIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVTLIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  Y+  TL
Sbjct: 292  IVGKVAAKDYIDESTGELICAANMELSLDLLAKLSQSGYKRIDTLFTNDLDHGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLMR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKNDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D +MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDMLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGIVTDEIHYLSAIEEGNFVIAQANSNLDDEGRFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTSVAKRGGMVQYVDASRIVIKVNEDEMFPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FTSI
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTSI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+ ++L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHDVLVAGGV-------------EAEKLEKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEAKQNQLEQLAEQYDELKAEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGDNTRQQVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I  +L +  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPVATPVFDGAKEREIKGLLELGGIPTSGQITLYDGRTGERFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGSHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|83719958|ref|YP_443580.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            E264]
 gi|167582630|ref|ZP_02375504.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            TXDOH]
 gi|167620744|ref|ZP_02389375.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            Bt4]
 gi|115305560|sp|Q2SU19|RPOB_BURTA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|83653783|gb|ABC37846.1| DNA-directed RNA polymerase, beta subunit [Burkholderia thailandensis
            E264]
          Length = 1368

 Score = 1659 bits (4295), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1375 (50%), Positives = 964/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++ P +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVLPAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  L+++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLDKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++  DGS  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAISNDGSLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSI
Sbjct: 778  KMGDKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---ARQTKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++ ML +A   +             Q  LYDG TGEPF+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSKMLDLA-FPDDIAEQLDMNPSKNQVRLYDGRTGEPFERRVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|300725143|ref|YP_003714471.1| RNA polymerase subunit beta [Xenorhabdus nematophila ATCC 19061]
 gi|297631688|emb|CBJ92401.1| RNA polymerase, beta subunit [Xenorhabdus nematophila ATCC 19061]
          Length = 1342

 Score = 1659 bits (4295), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG++ L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGSSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L A+   +E+IL+ F+ K V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRAMDYTAEDILNLFFNKTVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NKLQMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDQVDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGEI   A   +    L  +  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDQNTGEIICAANMELSLDLLARLSQSGHKSIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L+ 
Sbjct: 352  RIDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLDR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  NEVEGCGILSKEDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ LDE+G F EELV CR   E  L  R+++ 
Sbjct: 592  RLVRDGVVTDEIHYLSAIEEGNYVIAQANTVLDEEGHFVEELVTCRHYDESSLFNRDQVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGVVQYVDASRIVIKVNEDEMYAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGELVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                 + ++ +S+ PR++W 
Sbjct: 952  QLRQAKKDLTEELQIFEAGLFARIYSVLVSGG-------------IEAEKLSKLPRARWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K+  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKAEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGDDTRQKVDLNTFTDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKETEIKELLKLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|270265424|ref|ZP_06193683.1| hypothetical protein SOD_o00070 [Serratia odorifera 4Rx13]
 gi|270040617|gb|EFA13722.1| hypothetical protein SOD_o00070 [Serratia odorifera 4Rx13]
          Length = 1342

 Score = 1658 bits (4294), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALQFTTEQILDLFFAKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKIYIEKGRRITARHIRQLEKDEIQSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDTNTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDDDGRFEEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVIQYVDASRIVIKVNEDEMLAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G+DK++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVDKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   ++ +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVAGGV-------------EAEKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKSDFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++  ++    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINQMLKQHQEVAKLREFIQKAYDLGDNVCQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L M  +  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKQLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|291615768|ref|YP_003518510.1| RpoB [Pantoea ananatis LMG 20103]
 gi|291150798|gb|ADD75382.1| RpoB [Pantoea ananatis LMG 20103]
 gi|327396034|dbj|BAK13456.1| DNA-directed RNA polymerase beta chain RpoB [Pantoea ananatis
            AJ13355]
          Length = 1342

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   + +IL  F+ K+VY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALHYTTAQILDVFFEKVVYEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G   +E G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETATFDIES--NGTVYVEKGRRITARHIRQLEKDGIQHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D ++  TGE+ + A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVSKDYIDENTGELIVAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D
Sbjct: 592  RRVIDGVVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++SR+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFSRIQSVLISGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEAKQNQLEQLAEQYDELKHEFEKKLEGKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQRAYDLGTDVRQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLELGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|227115007|ref|ZP_03828663.1| DNA-directed RNA polymerase subunit beta [Pectobacterium carotovorum
            subsp. brasiliensis PBR1692]
          Length = 1342

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  +E+IL  F+ KIVY   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALGYSTEQILDLFFDKIVYEING 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMDLVPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVLSKDYIDESTGELIGAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH R +S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRHIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D  VT+++ YLSA+EE N  IAQAN++LDE+G F +ELV CR  GE  L  R++++
Sbjct: 592  RRVRDNVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVIR  + ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIRVNDDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQHEEVTKLREFIQRAYDLGDDVRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQMGGIPTSGQITLYDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEEK 1342


>gi|170701420|ref|ZP_02892378.1| DNA-directed RNA polymerase, beta subunit [Burkholderia ambifaria
            IOP40-10]
 gi|170133672|gb|EDT02042.1| DNA-directed RNA polymerase, beta subunit [Burkholderia ambifaria
            IOP40-10]
          Length = 1368

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1374 (50%), Positives = 964/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPGTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R++ 
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVSR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  +R+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEEMRAFLTKIYNDSGRKEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|289623856|ref|ZP_06456810.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            aesculi str. NCPPB3681]
          Length = 1336

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1344 (53%), Positives = 978/1344 (72%), Gaps = 9/1344 (0%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D+P L+ +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1    MDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61   PAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119  FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG+     L    L  G      
Sbjct: 179  VRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRGENLSLELVPQRL-RGEIAVLD 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            ++D D G+ ++E G+++T+  +  L++ G+K L +  D + G   A+ IV+  TGEI  E
Sbjct: 238  ILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDYVLGRTTAKVIVHPATGEIIAE 296

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                ++ + L +I  +++  I  LY + ++   ++ +TL  D   ++ +AL++IYR+MRP
Sbjct: 297  CNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTLKIDSTSNQLEALVEIYRMMRP 356

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++FN LFF  ++YDLS VGR+K N R+     +    + KEDI+A++K L
Sbjct: 357  GEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTL 416

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417  VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 477  INAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHP 536

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+LSA+EE 
Sbjct: 537  THYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVFLSAIEEA 596

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE
Sbjct: 597  DHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RI
Sbjct: 657  HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRI 716

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G
Sbjct: 717  VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMG 776

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 777  ELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 836

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 837  DIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 896

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ Q++ + +D ++E  I++   +
Sbjct: 897  VKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKSQLDEIRKDLNEEFRIVEGATF 956

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             RL   L G+ A  G  G KK   ++++++      QW++  + ++ +   +E  +    
Sbjct: 957  ERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWFKLRMAEDALNEQLEKAQAYIV 1015

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I
Sbjct: 1016 DRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVI 1075

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 1076 MPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQR--- 1132

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++ LR FL ++    G   E + D  D+ +L +A+  ++GVP++TPVFDGA E  I +M
Sbjct: 1133 KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLRNGVPMATPVFDGAKESEIKAM 1192

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 1193 LKLADMPESGQVQLFDGRTGNKFERAVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 1252

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 1253 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPG 1312

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
             PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 MPESFNVLIKEIRSLGIDIDLETE 1336


>gi|261819566|ref|YP_003257672.1| DNA-directed RNA polymerase subunit beta [Pectobacterium wasabiae
            WPP163]
 gi|261603579|gb|ACX86065.1| DNA-directed RNA polymerase, beta subunit [Pectobacterium wasabiae
            WPP163]
          Length = 1342

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  +E+IL  F+ KIVY   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALGYSTEQILDLFFDKIVYEING 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMDLVPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDDIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVLSKDYIDESTGELIGAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSSDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +  VT+++ YLSA+EE N  IAQAN++LDE+G F +ELV CR  GE  L  R++++
Sbjct: 592  RRVRENVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVIR  + ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIRVNDDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++ R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFGRIHAVLVSGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQHEEVTKLREFIQRAYDLGDDVRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQMGGIPTSGQITLYDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEEK 1342


>gi|325529729|gb|EGD06586.1| DNA-directed RNA polymerase subunit beta [Burkholderia sp. TJI49]
          Length = 1368

 Score = 1658 bits (4293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1374 (50%), Positives = 965/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL   +   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQAEVPATQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++  G
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMG 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+GETGE+   A D + E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGETGEVIASANDEVTESVLEKLREADIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDGKVTDQIDYLSAIEEGRYMIAQANAAIDENGMLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAYRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRAFLTKIYNESGRQEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|172059333|ref|YP_001806985.1| DNA-directed RNA polymerase subunit beta [Burkholderia ambifaria
            MC40-6]
 gi|226699378|sp|B1YRC2|RPOB_BURA4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|171991850|gb|ACB62769.1| DNA-directed RNA polymerase, beta subunit [Burkholderia ambifaria
            MC40-6]
          Length = 1368

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1374 (50%), Positives = 963/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPGTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  +R+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEEMRAFLTKIYNDSGRKEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|254697596|ref|ZP_05159424.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 2 str.
            86/8/59]
          Length = 1301

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 892/1300 (68%), Positives = 1078/1300 (82%), Gaps = 2/1300 (0%)

Query: 77   VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
            V YEFDPPKFDVD+C  RDLTY+ PLK+TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+P
Sbjct: 1    VRYEFDPPKFDVDECRQRDLTYSAPLKVTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMP 60

Query: 137  LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
            LMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEF
Sbjct: 61   LMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEF 120

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  P SA     
Sbjct: 121  DSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRIPYSAE-RFK 179

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y+AED+VN  
Sbjct: 180  GMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYA 239

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN+ R++AL D
Sbjct: 240  TGEIYLEAGDEIDEKVLKTLIDTGETEIDVLDIDHVNIGAYIRNTLAVDKNESRQEALFD 299

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  D VR +RKEDI
Sbjct: 300  IYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDI 359

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            +A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SS++ID
Sbjct: 360  LAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSIEID 419

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG 
Sbjct: 420  TVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGF 479

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRKV DGKVTNDVVY
Sbjct: 480  EVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVY 539

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            LSAMEE    +AQAN  LDE G F +E V CR AGE ++ PRE +D +D SPKQ+VS+AA
Sbjct: 540  LSAMEEAKHSVAQANVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVSPKQLVSVAA 599

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME +VA+ SGAAI A+R GIV+
Sbjct: 600  ALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAIAARRGGIVD 659

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV+VGD + + DIIAD
Sbjct: 660  QVDATRIVIRATEE-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIAD 718

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SE++VS+DVFTSIHIEEFEV ARDTKL
Sbjct: 719  GPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKL 778

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            GPEEITRDIPNVSEE LKN+DE GI+ +GAEV+PGDILVGKITPKGESPMTPEEKLLRAI
Sbjct: 779  GPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMTPEEKLLRAI 838

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FGEKA DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE LA+D+DDEQ 
Sbjct: 839  FGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERLAKDRDDEQA 898

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            ILDRN+Y RL +++ G+ A +GPKGFKK T ++ +L++EYPRSQWWQFAV+DEK+Q  +E
Sbjct: 899  ILDRNVYGRLADMIDGKVAAAGPKGFKKGTTITRELMTEYPRSQWWQFAVEDEKLQGELE 958

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
            +L+ QY+ SK +LE RF +K+EK+Q GD+MPPGV+++VKVFVA+KR IQ GDKMAGRHGN
Sbjct: 959  ALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGN 1018

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+VSRILP EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G+GKKI  L+
Sbjct: 1019 KGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMGKKIGELL 1078

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
            + Y+   +I PLR  LE +       E +  YDDD++L +A Q K GV ++TPVFDGA E
Sbjct: 1079 DVYRKTANIEPLRQTLEHIYPDNDRNEPVRSYDDDAILMLANQVKRGVSIATPVFDGAVE 1138

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
              IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++ARS G YS
Sbjct: 1139 ADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYS 1198

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G+
Sbjct: 1199 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGD 1258

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DTFE G PESFNVLVKEM++LGL+++L+++R      + +
Sbjct: 1259 DTFEAGIPESFNVLVKEMRSLGLNVELDDTREAEQPALPD 1298


>gi|121600456|ref|YP_994465.1| DNA-directed RNA polymerase subunit beta [Burkholderia mallei SAVP1]
 gi|167003564|ref|ZP_02269350.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei
            PRL-20]
 gi|166229288|sp|A1V8B2|RPOB_BURMS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|121229266|gb|ABM51784.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei SAVP1]
 gi|243060924|gb|EES43110.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei
            PRL-20]
          Length = 1368

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 965/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++   +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVPTAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  + +  +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPSKS-VV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLEKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ +DG+  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIGDDGALVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAVQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---ARQTKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++ ML +A   +             Q  LYDG TGEPF+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSKMLDLA-FPDDIAEQLDMNPSKNQVRLYDGRTGEPFERRVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|107024311|ref|YP_622638.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia AU
            1054]
 gi|116688364|ref|YP_833987.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia
            HI2424]
 gi|170731674|ref|YP_001763621.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia
            MC0-3]
 gi|123244305|sp|Q1BRU0|RPOB_BURCA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158512275|sp|A0K3L7|RPOB_BURCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699379|sp|B1JU14|RPOB_BURCC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|105894500|gb|ABF77665.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia AU
            1054]
 gi|116646453|gb|ABK07094.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia
            HI2424]
 gi|169814916|gb|ACA89499.1| DNA-directed RNA polymerase, beta subunit [Burkholderia cenocepacia
            MC0-3]
          Length = 1368

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1374 (50%), Positives = 963/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRTFLTKIYNESGRQEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|317046444|ref|YP_004114092.1| DNA-directed RNA polymerase subunit beta [Pantoea sp. At-9b]
 gi|316948061|gb|ADU67536.1| DNA-directed RNA polymerase, beta subunit [Pantoea sp. At-9b]
          Length = 1342

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1364 (51%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIASYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALHYTTEQILDLFFEKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   +E G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGTVYVEKGRRITARHIRQLEKDNIQHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+ + A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 292  IAGKVVAKDYIDQNTGELIVAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKSDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGKV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D
Sbjct: 592  RRVVDGKVSDEIHYLSAIEEGNFVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G ++ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTIQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++ R+  +L                   ++ + + PR +W 
Sbjct: 952  QLKQAKKDLSEELQILEAGLFGRIQAVLISGGV-------------EAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNALEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQRAYDLGTDVRQKVDLNTFSDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKELLQLGGLPSSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|115350314|ref|YP_772153.1| DNA-directed RNA polymerase subunit beta [Burkholderia ambifaria
            AMMD]
 gi|122324274|sp|Q0BJ54|RPOB_BURCM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115280302|gb|ABI85819.1| DNA-directed RNA polymerase subunit beta [Burkholderia ambifaria
            AMMD]
          Length = 1368

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1374 (50%), Positives = 963/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPGTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  +RSFL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEEMRSFLTKIYNDSGRKEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|53720829|ref|YP_109815.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            K96243]
 gi|67640298|ref|ZP_00439110.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei GB8
            horse 4]
 gi|76808643|ref|YP_335150.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            1710b]
 gi|124385809|ref|YP_001027885.1| DNA-directed RNA polymerase subunit beta [Burkholderia mallei NCTC
            10229]
 gi|126439516|ref|YP_001060758.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            668]
 gi|126449748|ref|YP_001082981.1| DNA-directed RNA polymerase subunit beta [Burkholderia mallei NCTC
            10247]
 gi|126454290|ref|YP_001068046.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            1106a]
 gi|134283232|ref|ZP_01769933.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            305]
 gi|167721584|ref|ZP_02404820.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            DM98]
 gi|167740558|ref|ZP_02413332.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            14]
 gi|167826160|ref|ZP_02457631.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            9]
 gi|167847672|ref|ZP_02473180.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            B7210]
 gi|167896244|ref|ZP_02483646.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            7894]
 gi|167904626|ref|ZP_02491831.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            NCTC 13177]
 gi|167912891|ref|ZP_02499982.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            112]
 gi|167920851|ref|ZP_02507942.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            BCC215]
 gi|217424839|ref|ZP_03456336.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            576]
 gi|226198179|ref|ZP_03793750.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            Pakistan 9]
 gi|237814156|ref|YP_002898607.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            MSHR346]
 gi|242315692|ref|ZP_04814708.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1106b]
 gi|254174896|ref|ZP_04881557.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei ATCC
            10399]
 gi|254180333|ref|ZP_04886931.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1655]
 gi|254190294|ref|ZP_04896802.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            Pasteur 52237]
 gi|254198573|ref|ZP_04904994.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            S13]
 gi|254201247|ref|ZP_04907611.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei FMH]
 gi|254206588|ref|ZP_04912939.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei JHU]
 gi|254260861|ref|ZP_04951915.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1710a]
 gi|254300572|ref|ZP_04968017.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            406e]
 gi|254357127|ref|ZP_04973401.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei
            2002721280]
 gi|81378946|sp|Q63Q03|RPOB_BURPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88909125|sp|Q3JMQ3|RPOB_BURP1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115305559|sp|P0C151|RPOB_BURMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158513539|sp|A3P0C5|RPOB_BURP0 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229286|sp|A3MRU5|RPOB_BURM7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229287|sp|A2S7G6|RPOB_BURM9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229289|sp|A3NEI7|RPOB_BURP6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|52211243|emb|CAH37232.1| DNA-directed RNA polymerase beta chain [Burkholderia pseudomallei
            K96243]
 gi|76578096|gb|ABA47571.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1710b]
 gi|124293829|gb|ABN03098.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei NCTC
            10229]
 gi|126219009|gb|ABN82515.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            668]
 gi|126227932|gb|ABN91472.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1106a]
 gi|126242618|gb|ABO05711.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei NCTC
            10247]
 gi|134245427|gb|EBA45520.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            305]
 gi|147747141|gb|EDK54217.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei FMH]
 gi|147752130|gb|EDK59196.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei JHU]
 gi|148026191|gb|EDK84276.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei
            2002721280]
 gi|157810569|gb|EDO87739.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            406e]
 gi|157937970|gb|EDO93640.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            Pasteur 52237]
 gi|160695941|gb|EDP85911.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei ATCC
            10399]
 gi|169655313|gb|EDS88006.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            S13]
 gi|184210872|gb|EDU07915.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1655]
 gi|217392295|gb|EEC32320.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            576]
 gi|225929699|gb|EEH25715.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            Pakistan 9]
 gi|237505206|gb|ACQ97524.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            MSHR346]
 gi|238520992|gb|EEP84447.1| DNA-directed RNA polymerase, beta subunit [Burkholderia mallei GB8
            horse 4]
 gi|242138931|gb|EES25333.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1106b]
 gi|254219550|gb|EET08934.1| DNA-directed RNA polymerase, beta subunit [Burkholderia pseudomallei
            1710a]
          Length = 1368

 Score = 1657 bits (4292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 964/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++   +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVPTAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLEKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ +DG+  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIGDDGALVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAVQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---ARQTKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++ ML +A   +             Q  LYDG TGEPF+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSKMLDLA-FPDDIAEQLDMNPSKNQVRLYDGRTGEPFERRVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|237749509|ref|ZP_04579989.1| DNA-directed RNA polymerase subunit beta [Oxalobacter formigenes
            OXCC13]
 gi|229380871|gb|EEO30962.1| DNA-directed RNA polymerase subunit beta [Oxalobacter formigenes
            OXCC13]
          Length = 1368

 Score = 1657 bits (4290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1374 (51%), Positives = 965/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY+ FL  ++ P +R NEGLQ+AF S+
Sbjct: 1    MHYSFTEKKRIRKSFAKRDNVHQVPFLLATQLESYESFLQADVPPLKRKNEGLQSAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF+SY    P FDV +C  R LT A PL+  +RL++ D +  T    +
Sbjct: 61   FPIVSHNGFARLEFISYTLGDPPFDVKECQQRGLTLAAPLRAKVRLVILDKESPT-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  RIDRRRK+PVT  L A+GM SEEIL  F+    +  R 
Sbjct: 180  RIIPYRGSWLDFEFDPKDILFFRIDRRRKMPVTILLKAIGMSSEEILENFFVFDDFLLRP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +        +  M G      +VD   G+ ++E  K++ +  ++ ++  G+  + +  D 
Sbjct: 240  EGAEMEFVTS-RMRGEIARFDIVD-KEGKVLVEKDKRINARNIREIEAAGITRISVPEDF 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++++ +TGE+  +A D I E+ L  +  + +++I  LY + ++  AYI  TL
Sbjct: 298  LYGRALAKNVIDQDTGEVIAKANDEITEELLTRLREANVKEIQTLYTNDLDQGAYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF++ ++YDLS VGR+K N R+  
Sbjct: 358  RIDETVDQMAARIAIYRMMRPGEPPTEESVEALFNGLFYNEERYDLSAVGRMKFNSRIGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI+++IKILV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  EELTGTMTLSNDDILSVIKILVELRNGRGEIDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRIS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAMYARLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D  VT+++ YLSA+EE    IAQANS++DEDG   +ELV  R AGE ILV  E++ 
Sbjct: 598  RKVVDSHVTDEIDYLSAIEEGKYIIAQANSTIDEDGKLIDELVSSREAGETILVSPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E  FVGTG+E   A  
Sbjct: 658  YMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKAFVGTGVERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ +DA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYIDAGRVVIRVNDDEAAAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V R D+IADG STDLG+LALG+NMLVAF PW+G N+EDS+LISE++V +D +TS+
Sbjct: 778  QVGDRVERGDVIADGASTDLGELALGQNMLVAFTPWNGLNYEDSILISEKVVEDDRYTSV 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TP+G
Sbjct: 838  HIEELSVVARDTKLGPEEITRDISNLAENQLARLDESGIVYIGAEVEAGDVLVGKVTPRG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R G+ +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGLVRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+    GPK   +   ++ + +++  R  W+
Sbjct: 958  ELQRYRIDLNDQMRIVEGDAFQRLSRLLIGKKVNGGPKKLARGAEITQEYLADLERYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE     +E++K   E  +   +  F+ K +K+  GD++ PGV ++VKV++A+KR
Sbjct: 1018 DIRPSDEDTAMALEAIKESIEEKRHQFDIAFEEKRKKLTQGDELQPGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP D+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGTPADVVLNPLGVPSRMNVGQILETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +A   +  LR+FL+ +       E +    ++ VL +A+  K+
Sbjct: 1138 WAAKGLGLRIGEML---QAKQKVEELRTFLKSIYLDSGKPEDLDSLTEEEVLHLADNLKN 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA E  I  ML +A  DE            Q  L+DG TGE F+RPVTVG
Sbjct: 1195 GVPFATPVFDGAKEAEIRRMLDLAYPDEIASKLGMTEAKNQVTLFDGRTGEAFERPVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE  
Sbjct: 1315 EMLTVKSDDVSGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERD 1368


>gi|78064916|ref|YP_367685.1| DNA-directed RNA polymerase subunit beta [Burkholderia sp. 383]
 gi|88909126|sp|Q39KH5|RPOB_BURS3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|77965661|gb|ABB07041.1| DNA-directed RNA polymerase subunit beta [Burkholderia sp. 383]
          Length = 1368

 Score = 1657 bits (4290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1374 (50%), Positives = 963/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVLAAQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSAPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEMPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  DR  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R++ 
Sbjct: 358  RVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVSR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  +R FL K+       E +  + D+ +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEEMRVFLTKIYNDSGRQEDLESFTDEEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|284009044|emb|CBA76000.1| DNA-directed RNA polymerase, beta-subunit [Arsenophonus nasoniae]
          Length = 1342

 Score = 1657 bits (4290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  ++        GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFAKFIEQDLE----GQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +EEIL+ F+ K ++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYGTEEILNLFFEKTIFQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++  +  + +  + 
Sbjct: 235  NKLLMTLIPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDKITSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L  +     + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDESTGELICTANTELSLDMLARLSQGGYKTIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N  L+ 
Sbjct: 352  RTDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEERYDLSAVGRMKFNRSLDR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DAIEGSSILSKQDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ LD+DG F EEL+ CR  GE  L  +E+++
Sbjct: 592  RLVRDGIVTDEIHYLSAIEEGNYIIAQANTVLDDDGRFVEELITCRNKGESSLFSQEQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRSDKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  ALGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                 +  + + + PR +W 
Sbjct: 952  QLRDAKKDLTEELRIFEAGLFARIRAVLTNGG-------------IEGEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + + +DE+ Q  +E L  QY+  K+  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELSFKDEEKQNQLEQLAEQYDELKAEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDESGNPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +      T  +S + D+ VLR+A   K 
Sbjct: 1119 MAAKGIGDKINTMLKQQREVAKLKEFIQKAYDLGDDPRQTVDLSTFSDEEVLRLAHNLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L +A+L  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLTLAELPTSGQITLYDGRTGEKFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|289648949|ref|ZP_06480292.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            aesculi str. 2250]
 gi|289675478|ref|ZP_06496368.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            syringae FF5]
          Length = 1336

 Score = 1657 bits (4290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1344 (53%), Positives = 978/1344 (72%), Gaps = 9/1344 (0%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D+P L+ +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1    MDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61   PAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119  FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG+     L    L  G      
Sbjct: 179  VRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRGENLSLELVPQRL-RGEIAVLD 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            ++D D G+ ++E G+++T+  +  L++ G+K L +  D + G   A+ IV+  TGEI  E
Sbjct: 238  ILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDYVLGRTTAKVIVHPATGEIIAE 296

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                ++ + L +I  +++  I  LY + ++   ++ +TL  D   ++ +AL++IYR+MRP
Sbjct: 297  CNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTLKIDSTSNQLEALVEIYRMMRP 356

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++FN LFF  ++YDLS VGR+K N R+     +    + KEDI+A++K L
Sbjct: 357  GEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTL 416

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417  VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 477  INAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHP 536

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+LSA+EE 
Sbjct: 537  THYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVFLSAIEEA 596

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE
Sbjct: 597  DHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RI
Sbjct: 657  HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRI 716

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G
Sbjct: 717  VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMG 776

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 777  ELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 836

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 837  DIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 896

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ Q++ + +D ++E  I++   +
Sbjct: 897  VKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKSQLDEIRKDLNEEFRIVEGATF 956

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             RL   L G+ A  G  G KK   ++++++      QW++  + ++ +   +E  +    
Sbjct: 957  ERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWFKLRMAEDALNEQLEKAQAYIV 1015

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I
Sbjct: 1016 DRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVI 1075

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 1076 MPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQR--- 1132

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++ LR FL ++    G   E + D  D+ +L +A+  ++GVP++TPVFDGA E  I +M
Sbjct: 1133 KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLRNGVPMATPVFDGAKESEIKAM 1192

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 1193 LKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 1252

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 1253 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPG 1312

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
             PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 MPESFNVLIKEIRSLGIDIDLETE 1336


>gi|157368526|ref|YP_001476515.1| DNA-directed RNA polymerase subunit beta [Serratia proteamaculans
            568]
 gi|166991528|sp|A8G8E7|RPOB_SERP5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157320290|gb|ABV39387.1| DNA-directed RNA polymerase, beta subunit [Serratia proteamaculans
            568]
          Length = 1342

 Score = 1657 bits (4290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+VY  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFAKVVYEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKIYIEKGRRITARHIRQLEKDEIQSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVAKDYIDTNTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYISETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIGIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDDDGRFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G+++ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVARRGGVIQYVDASRIVIKVNEDEMLAGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   ++ +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVAGGV-------------EAEKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEEKQNQLEQLAEQYDELKSDFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++  ++    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINQMLKQHQEVAKLREFIQKAYDLGDDVCQKVDLNTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L M  +  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKESEIKQLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEGE 1342


>gi|227328365|ref|ZP_03832389.1| DNA-directed RNA polymerase subunit beta [Pectobacterium carotovorum
            subsp. carotovorum WPP14]
          Length = 1342

 Score = 1656 bits (4289), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  +E+IL  F+ KIVY   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALGYSTEQILDLFFDKIVYEING 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++ G++ + +  + 
Sbjct: 235  NKLQMDLVPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDGIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVLSKDYIDESTGELIGAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMYQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +  VT+++ YLSA+EE N  IAQAN++LDE+G F +ELV CR  GE  L  R++++
Sbjct: 592  RRVRENVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVIR  + ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIRVNDDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQHEEVTKLREFIQRAYDLGDDVRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQMGGIPTSGQITLYDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|134294435|ref|YP_001118170.1| DNA-directed RNA polymerase subunit beta [Burkholderia vietnamiensis
            G4]
 gi|166229290|sp|A4JAN2|RPOB_BURVG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|134137592|gb|ABO53335.1| DNA-directed RNA polymerase subunit beta [Burkholderia vietnamiensis
            G4]
          Length = 1368

 Score = 1656 bits (4289), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 960/1375 (69%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  DR  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR FL K+       E +  + D+ +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRVFLTKIYNESGRQEDLESFTDEEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE +  ML +A   +             Q  LYDG TGE F+R VT+
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLA-FPDDIAQQLDMNPSKNQVRLYDGRTGEQFERRVTL 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|39997954|ref|NP_953905.1| DNA-directed RNA polymerase subunit beta [Geobacter sulfurreducens
            PCA]
 gi|81701325|sp|Q748Y6|RPOB_GEOSL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|39984899|gb|AAR36255.1| DNA-directed RNA polymerase, beta subunit [Geobacter sulfurreducens
            PCA]
 gi|298506895|gb|ADI85618.1| DNA-directed RNA polymerase, beta subunit [Geobacter sulfurreducens
            KN400]
          Length = 1370

 Score = 1656 bits (4289), Expect = 0.0,   Method: Composition-based stats.
 Identities = 738/1364 (54%), Positives = 1005/1364 (73%), Gaps = 11/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +IIDIP+LI++QK SY  FL ++  P+ R N GL+A FKSVFPI  FS  A
Sbjct: 11   LRKNFAKIKKIIDIPNLIDIQKNSYKRFLQIDTPPEARKNSGLEAVFKSVFPIKDFSDTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+V+Y    PK+DV++C  R +T+A P+K+ +RL+V+DV++ TG +SI+DIKEQ +Y 
Sbjct: 71   SLEYVTYTLGAPKYDVEECHQRGMTFAAPMKVKVRLVVWDVNKDTGVRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI+ VRIDRRRK+P T  L ALG  +E +L+ FY         +         
Sbjct: 191  DFEFDHKDILFVRIDRRRKMPATVLLKALGYSAEALLNYFYKSEEILVAAEGMWKKADPE 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
             L+   K S  +V   TGE ++++ +K T   ++ + E G+  + IT + + G Y + DI
Sbjct: 251  -LLASQKASVDIVAPKTGEVLLKANRKFTKAAIRKMTEHGITQIPITMEEVLGKYASNDI 309

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+  TGE+ +E  D I +  L++I    I +  +L++D+++  + +R+TL+ DK    ++
Sbjct: 310  VDPSTGEVIVECNDEITQARLDDIKAKGITEFKVLFIDNLHVTSSLRDTLIADKIAATEE 369

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A+++F  LFF++++YDLS VGR+K+N +L L+ P D + + 
Sbjct: 370  ALIEIYRRLRPGDPPTLKSAQALFENLFFNAERYDLSAVGRLKLNFKLGLNVPLDCQTLT 429

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            K+D++ +++ L+DL+NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 430  KDDVLEVVRYLIDLKNGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 489

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 490  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 549

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V DGKVT+
Sbjct: 550  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRIVQDGKVTS 609

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            DV + SA+EEE   IAQAN+ +D DG F  E V  R +GE +LV R++++ +D +P Q+V
Sbjct: 610  DVKFFSALEEEGHAIAQANAEMDADGRFVNEYVSARKSGEFLLVHRDELELMDVAPMQLV 669

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLLKA++P VGTGME VVAK SG ++VA+  
Sbjct: 670  SVAASLIPFLENDDANRALMGSNMQRQAVPLLKADSPLVGTGMERVVAKDSGVSVVARHT 729

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            GIVE VDA RIV++  E + D + +GVDIY L+KF RSNQNTC+NQRP+VKVGD V+R D
Sbjct: 730  GIVESVDASRIVVKIDEDEFDETGTGVDIYNLIKFARSNQNTCINQRPVVKVGDHVKRGD 789

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGPSTD+G+LALG+N++VAFMPW GYNFEDS+L+SE++V +D +TSIHIEEFE +AR
Sbjct: 790  VIADGPSTDMGELALGQNVVVAFMPWGGYNFEDSILVSEKLVKDDRYTSIHIEEFECVAR 849

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 850  DTKLGKEEITSDIPNLGEEALKDLDESGIIRIGAEVKPGDILVGKITPKGETQLSPEEKL 909

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +ER + + L +D+ 
Sbjct: 910  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDSRTEMIERMEEDKLRKDEQ 969

Query: 973  DEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++L G++A       SG     K   ++ + +   P  +W + +V
Sbjct: 970  DEIRIIRNSAVGKLKKLLVGKSAAVKVEDKSGRTVIAKGAAITEEALDAIPLDRWDEISV 1029

Query: 1027 QDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              E  V   V ++    +    I+   F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1030 SGEAGVDEKVSAILQTLQQQIDIIRYVFDDKVQKLKRGDDLPPGVIKMVKVYIAIKRKLQ 1089

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+++DG PV+IVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1090 VGDKMAGRHGNKGVVSRILPEEDMPYMEDGRPVEIVLNPLGVPSRMNVGQILETHLGWAA 1149

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G KI+ ++  Y        ++ +L+ V GT      +   D D ++ VA++ + GV 
Sbjct: 1150 KGIGWKIEEMLESYSP---ADHIKGYLKDVYGTTEMDTFLDSLDKDELMNVAKRLQRGVA 1206

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+GA EE I SML  A  DE+ Q  LYDG +GEPF   VTVG +Y+LKL+H+V D
Sbjct: 1207 MASPVFEGASEEQIRSMLDKAGFDETAQVSLYDGKSGEPFKHKVTVGVMYVLKLHHLVDD 1266

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1267 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1326

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+L L ++L      
Sbjct: 1327 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLCLDVELLEGDED 1370


>gi|133418|sp|P19175|RPOB_PSEPU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|45729|emb|CAA33846.1| beta-subunit of RNA polymerase [Pseudomonas putida]
          Length = 1357

 Score = 1656 bits (4288), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1365 (51%), Positives = 974/1365 (71%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL         P   L AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGSIQGSLPRRRLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQ+HRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQMHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  L++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRLA-GEVAVMDIHD-ETGKVIVEQGRRITARHINQLEKAGVKQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTEMTTELLIKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS +GR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSPLGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRCS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +V +R G+++ VDA RIV+R  + +++     VDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVRRRGGVIDSVDASRIVVRVADDEVETGERRVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V+R DI+AD  STD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVQRGDIMADRASTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARD KLGP EIT  IPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDNKLGPREITSGIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             + +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  HTQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTQGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ +++      QW+
Sbjct: 957  QLDEIPQDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVITDEVLDGLDDGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K   +Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRNVQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +     + LR FL +V    G   E + ++ D+ +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMLEEQR---KAAELRVFLTEVYNEIGGRQENLDEFTDEEILALANNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG T   F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTRNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G  ESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMAESFNVLIKEIRSLGIDIDLETE 1357


>gi|322834821|ref|YP_004214848.1| DNA-directed RNA polymerase, subunit beta [Rahnella sp. Y9602]
 gi|321170022|gb|ADW75721.1| DNA-directed RNA polymerase, beta subunit [Rahnella sp. Y9602]
          Length = 1342

 Score = 1656 bits (4288), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1364 (52%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+ Y  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKVTYQIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ADGKVYVEKGRRITARHIRQLEKDEIQRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V++D ++  TGE+ + A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVVSKDYIDTNTGELIVPANMELSLDLLAKLSQSGHKTIETLFTNDLDHGAYMSETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+ +RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIQVMKKLIGIRNGQGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR GIV+ VDA RIVIR  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGIVQYVDASRIVIRVNEEEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+   L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIQSALVAGGV-------------EADKLGKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + ++ DE  Q  +E L  QY+  KS  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELSLTDEDKQNQLEQLAEQYDELKSEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         ++ + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVSKLREFIQRAYDLGDDVRQKVDLTTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L M  +  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKETEIKQLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|83749356|ref|ZP_00946352.1| DNA-directed RNA polymerase beta chain [Ralstonia solanacearum UW551]
 gi|83723981|gb|EAP71163.1| DNA-directed RNA polymerase beta chain [Ralstonia solanacearum UW551]
          Length = 1368

 Score = 1656 bits (4288), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1376 (51%), Positives = 964/1376 (70%), Gaps = 20/1376 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  +++  +R  EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHVSVAQRKTEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSHPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      + D   G+ VIE  K++ +  ++ L   G K + +  D 
Sbjct: 238  DGALMEFVPERL-RGEVARFDISD-KNGKVVIEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + ++DI  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKDIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF++ D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYNEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SEGTGPMVLTDDDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T++V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDEVHYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLSKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPSDEEVAAQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + LR  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAELRKLLGQIYNESGKVEDLDSLTDAEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A   +  +            L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPADIAKEKGLTASKQQVTLFDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|190572937|ref|YP_001970782.1| DNA-directed RNA polymerase subunit beta [Stenotrophomonas
            maltophilia K279a]
 gi|226699451|sp|B2FQ38|RPOB_STRMK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|190010859|emb|CAQ44468.1| putative DNA-directed RNA polymerase, beta-subunit [Stenotrophomonas
            maltophilia K279a]
          Length = 1388

 Score = 1655 bits (4287), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1390 (50%), Positives = 970/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  N+ P +R + GL AA KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQENVDPAKRTDHGLHAALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 67   PIASYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 185  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +   L D D  + ++E+GK++T+  +K L+  G+  L +  D +
Sbjct: 245  EGVQLELVPERLRGETLGFDLADGD--KVIVEAGKRITARHIKQLEASGIAALAVPDDYI 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+  TGE+  +A D I ++ L+    + +  +  L+V+ ++   Y+ NTL 
Sbjct: 303  VGRILSHDVVDASTGELLAQANDEITDEQLQAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLS VGR+K N R+   
Sbjct: 363  IDPTKTQLEALVEIYRMMRPGEPPTKDAAQNLFHNLFFTFERYDLSAVGRMKFNRRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +                             +IK+L ++RNG+G +DDID+LGN
Sbjct: 423  ETTGEAVLYDSKYFGERNDEESKRLVAAHGDSSDILDVIKVLTEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 543  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  +AR N YGF+ETPYRKV DGKV ++V +LSA+EE    IAQAN+  D  G+ T
Sbjct: 603  LINSLAVYARTNQYGFLETPYRKVVDGKVYDEVEFLSAIEENEYVIAQANALTDAKGTLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-PSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G + Q+DA RIV++  E ++   + +GVD
Sbjct: 723  PTLRAQKPLVGTGIERAVARDSGVTVNARRGGEIVQIDAARIVVKVNEEEIVGATDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV+VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYNLVKYTRSNQNTCINQRPLVQVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY RL   + G+    G  
Sbjct: 963  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYMRLRSQIVGKVVNGG-A 1021

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G KK  V++   +    ++ W+   ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1022 GLKKGDVITDAFLDGLKKADWFALRMKDEDASEAIERAQKQIQAHEKEFERRFADKRGKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1082 TAGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMASGETVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI++++   +A   ++ LR FL+ +     
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQAMM---EAQAAVADLRKFLDDIYNHDD 1198

Query: 1181 ----HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                +   +S + D+ +LR+A     GVP++TPVFDGA E  I  ML +ADL  SGQ+ L
Sbjct: 1199 TNVANRVDLSQFSDEELLRLARNLTDGVPMATPVFDGATEAEIKRMLELADLPSSGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGRTGEAFDRHTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLENS 1366
            L ++++LE++
Sbjct: 1379 LAINMELEDN 1388


>gi|50119183|ref|YP_048350.1| DNA-directed RNA polymerase subunit beta [Pectobacterium atrosepticum
            SCRI1043]
 gi|81646553|sp|Q6DAN0|RPOB_ERWCT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|49609709|emb|CAG73142.1| DNA-directed RNA polymerase, beta-subunit [Pectobacterium
            atrosepticum SCRI1043]
          Length = 1342

 Score = 1655 bits (4287), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1364 (51%), Positives = 970/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L ALG  + +IL  F+ KIVY   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALGYSTAQILDLFFDKIVYEING 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  ++ L++  ++ + +  + 
Sbjct: 235  NKLQMDLVPERL-RGETASFDIE--ANGKVYIEKGRRITARHIRQLEKDSIERIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AY+  T+
Sbjct: 292  IAGKVLSKDYIDESTGELIGAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGAYMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSSDRLSALVEIYRMMRPGEPPTREAAETLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +  VT+++ YLSA+EE N  IAQAN++LDE+G F +ELV CR  GE  L  R++++
Sbjct: 592  RRVRENVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVIR  + ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVIRVNDDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  ++ R+  +L                   +D + + PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFGRIHAVLVSGGV-------------EADKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKQHEEVTKLREFIQRAYDLGDDLRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQMGGIPTSGQITLYDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEEK 1342


>gi|238765329|ref|ZP_04626255.1| DNA-directed RNA polymerase subunit beta [Yersinia kristensenii ATCC
            33638]
 gi|238696456|gb|EEP89247.1| DNA-directed RNA polymerase subunit beta [Yersinia kristensenii ATCC
            33638]
          Length = 1342

 Score = 1655 bits (4286), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1364 (52%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTTQILDLFFDKVVFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQSGHKQIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQA S+LDEDG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGVVTDEINYLSAIEEGNFVIAQAKSNLDEDGRFIEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VA MPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVASMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W 
Sbjct: 952  QLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K 
Sbjct: 1119 MAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|167587779|ref|ZP_02380167.1| DNA-directed RNA polymerase subunit beta [Burkholderia ubonensis Bu]
          Length = 1368

 Score = 1655 bits (4285), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1374 (50%), Positives = 965/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVLTAQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEVTESVLEKLREAGIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++DE+G+  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDGKVTDQIDYLSAIEEGRYMIAQANAAIDENGTLIDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRAFLTKIYNESGRQEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|206558633|ref|YP_002229393.1| DNA-directed RNA polymerase subunit beta [Burkholderia cenocepacia
            J2315]
 gi|226699380|sp|B4E5B2|RPOB_BURCJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|198034670|emb|CAR50537.1| DNA-directed RNA polymerase beta chain [Burkholderia cenocepacia
            J2315]
          Length = 1368

 Score = 1655 bits (4285), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1374 (50%), Positives = 964/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  LE++  + I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + I+R+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RVDETTDKTAARIAIHRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++DEDG   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDEDGRLIDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++   ++E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAASLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRTFLTKIYNESGRQEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE +  ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMGKMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|134096328|ref|YP_001101403.1| DNA-directed RNA polymerase subunit beta [Herminiimonas
            arsenicoxydans]
 gi|158513609|sp|A4G9U5|RPOB_HERAR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|133740231|emb|CAL63282.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
            (Transcriptase subunit beta) (RNA polymerase subunit
            beta) [Herminiimonas arsenicoxydans]
          Length = 1368

 Score = 1655 bits (4285), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1374 (50%), Positives = 955/1374 (69%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+  Q  SY  FL  +  P +R NEGLQ+AF S+
Sbjct: 1    MHYSFTEKKRIRKSFAKRANVHNVPFLLATQLESYHDFLQEDKIPSQRKNEGLQSAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF+SY    P F++ +C  R LTYA PL+  +RL++ D +  T    +
Sbjct: 61   FPIVSHNGFARLEFLSYVLGDPPFNIKECQQRGLTYASPLRAKVRLVILDKESPT-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEMKEQEVYMGELPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  R+DRRRK+PVT  L A+GM  E+IL  F+    ++   
Sbjct: 180  RIIPYRGSWLDYEFDPKDILFFRVDRRRKMPVTILLKAIGMTPEQILENFFVFDDFTLHA 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D       A  L  G      + D   G+ ++   K++ S  ++ ++  G+K + +  D 
Sbjct: 240  DGAEMKFVAERL-RGEVARFDITD-KAGKVLVAKDKRINSKHVRDVEAAGIKQISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + +  L  +   +I  I  LY + ++   YI  TL
Sbjct: 298  LLGRILAKNIVDADTGEVIASANDELTDDLLARLREGKISHIQTLYTNDLDQGGYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  A + IYR+MRPG+  T    E++FN LF++ D+YDLS VGR+K N R+  
Sbjct: 358  RMDDTNDQMAAKVAIYRMMRPGEPPTEDSVEALFNGLFYNPDRYDLSAVGRMKFNRRIGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+      +  ED++A+IKILV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DSLTGDMTLSNEDVLAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV   KVT+ + YLSA+EE    IAQAN+++D+ G  ++ELV  R AGE ILV  E++ 
Sbjct: 598  RKVEGSKVTDQIDYLSAIEEGRYIIAQANATIDKAGMLSDELVSAREAGETILVSPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKALVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R GIV+ +DA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGIVDYIDAGRVVIRVNDDEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V ++D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  QVGDRVAKHDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD LVGK+TPKG
Sbjct: 838  HIEELSVVARDTKLGAEEITRDISNLAENQLARLDESGIVYIGAEVTAGDTLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIPRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+    GPK   K T ++++ +++  +  W+
Sbjct: 958  ELQRYRLDLNDQLRIVEGDAFQRLEKMLVGKVVNGGPKKIAKGTKITAEYLADLDKYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 D+     +E++K      +   +  F+ K +K+  GD++PPGV ++VKV++A+KR
Sbjct: 1018 DIRPSDDTSANALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRILP EDMP + DGTP D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++N       I+ LR FL  +      TE +  + D  +L +A   K+
Sbjct: 1138 WAAKGLGLRIGEMLN---TQVQIAELRKFLAAIYNESGKTEDLDSFSDAEILELASNLKN 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGADE     ML +A  D   +            +YDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGADEGETRRMLDLAYPDHIAKQLGMTASKNQVTMYDGRTGEAFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE  
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERD 1368


>gi|257483178|ref|ZP_05637219.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            tabaci ATCC 11528]
          Length = 1336

 Score = 1654 bits (4284), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1344 (52%), Positives = 976/1344 (72%), Gaps = 9/1344 (0%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D+P L+ +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1    MDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61   PAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119  FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG+     L    L  G      
Sbjct: 179  VRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRGENLSLELVPQRL-RGEIAVLD 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            ++D D G+ ++E G+++T+  +  L++ G+K L +  D + G   A+ IV+  TGEI  E
Sbjct: 238  ILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDYVLGRTTAKVIVHPATGEIIAE 296

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                ++ + L +I  +++  I  LY + ++   ++ +TL  D   ++ +AL++IYR+MRP
Sbjct: 297  CNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTLKIDSTSNQLEALVEIYRMMRP 356

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++FN LFF  ++YDLS VGR+K N R+     +    + KEDI+A++K L
Sbjct: 357  GEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTL 416

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417  VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKPV +AV EFF SSQLSQ     N LS ITH RR+SALG G + R RAG E+RDVHP
Sbjct: 477  INAKPVAAAVKEFFGSSQLSQFMGQNNPLSEITHKRRVSALGPGSLTRERAGFEVRDVHP 536

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+LSA+EE 
Sbjct: 537  THYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVFLSAIEEA 596

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE
Sbjct: 597  DHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RI
Sbjct: 657  HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRI 716

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G
Sbjct: 717  VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMG 776

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 777  ELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 836

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 837  DIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 896

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ Q++ + +D ++E  I++   +
Sbjct: 897  VKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKSQLDEIRKDLNEEFRIVEGATF 956

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             RL   L G+ A  G  G KK   ++++++      QW++  + ++ +   +E  +    
Sbjct: 957  ERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWFKLRMAEDALNEQLEKAQAYIV 1015

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I
Sbjct: 1016 DRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVI 1075

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 1076 MPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQR--- 1132

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++ LR FL ++    G   E + D  D+ +L +A+  ++GVP++TPVFDGA E  I +M
Sbjct: 1133 KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLRNGVPMATPVFDGAKESEIKAM 1192

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 1193 LKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 1252

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 1253 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPG 1312

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
             PESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 MPESFNVLIKEIRSLGIDIDLETE 1336


>gi|114331772|ref|YP_747994.1| DNA-directed RNA polymerase subunit beta [Nitrosomonas eutropha C91]
 gi|122313481|sp|Q0AF53|RPOB_NITEC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114308786|gb|ABI60029.1| DNA-directed RNA polymerase subunit beta [Nitrosomonas eutropha C91]
          Length = 1359

 Score = 1654 bits (4283), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1365 (52%), Positives = 962/1365 (70%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   I+  P L+  Q  SY  FL  ++AP +R N+GLQAAF +V
Sbjct: 1    MSYSFAEKKRIRKSFAKRTSILPFPFLLATQIESYADFLQADVAPGKRKNQGLQAAFNAV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + S  A L+F+SY      FDV +C  R LTYA PL+  +RL + D        ++
Sbjct: 61   FPIESHSNNARLDFISYMLGTSVFDVKECQQRGLTYASPLRARVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT+ G+FV+ G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTETGSFVVNGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT+ L A+G  S +IL+ F+    ++  G
Sbjct: 179  RIIPYRGSWLDFEFDPKDYVYFRIDRRRKMPVTTLLKAMGYSSTQILADFFEFDHFTLAG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L    L  G   S  +V  D G+  ++  K++T+  ++ L++  +  + +  + 
Sbjct: 239  NKILFHLIPERL-RGELASFDIVSED-GKVFVQKDKRITAKHVRDLQQANLTKISVPEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR--DIPILYVDSVNNNAYIRN 360
            L G  +AEDIV+ ETGE+   A   I+E  LE I  ++ +  +I  L+V+ +N   YI  
Sbjct: 297  LLGKILAEDIVDKETGEVVATANSEINETLLERIKQTQNKNSEISTLFVNDLNYGPYISQ 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D++ D+  A + IYR+MRPG+  T     ++FN LF+  ++YDLS VGR+K N R+
Sbjct: 357  TLRVDESTDQMSAQVAIYRMMRPGEPPTEDAVLALFNGLFYSPERYDLSVVGRMKFNRRV 416

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              +       +  EDI  +IKILV LRNG+G IDDID+LGNRRVRSVGE+ +NQ+R GL 
Sbjct: 417  GREELTGSTTLSNEDITDVIKILVGLRNGRGEIDDIDHLGNRRVRSVGELAENQFRAGLA 476

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E+++KER+S  + +++MP D INAKPV SA+ EFF SSQLSQ  +  N LS ITH RR
Sbjct: 477  RVEKAVKERLSQAESENLMPHDFINAKPVSSAIREFFGSSQLSQFMDQTNPLSEITHKRR 536

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGFIET
Sbjct: 537  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARTNEYGFIET 596

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR V + +VT +VVYLSA+EE    IAQAN++ D+ G FT+E+V CR   E  L  R++
Sbjct: 597  PYRMVKNSRVTEEVVYLSAIEESQYVIAQANANFDQTGVFTDEVVSCRHKNEFTLASRDQ 656

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E VVA
Sbjct: 657  IEYVDIAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRAEKPLVGTGIERVVA 716

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA RIVIR  + +      GVDIY L K+ RSNQNT +NQRP
Sbjct: 717  VHSGTAVKALRGGVVDYVDAGRIVIRVHDAETRAGEVGVDIYNLTKYIRSNQNTNINQRP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD + R D+IADG STDLG+LALG+NML+AFMPW+G NFEDS+LISER+VS+D FT
Sbjct: 777  IVKIGDILSREDVIADGASTDLGELALGQNMLIAFMPWNGLNFEDSILISERVVSDDRFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE   ++RDTKLG EE+T DIPN+SE     +DE GI+ +GAEV  GD+LVGK+TP
Sbjct: 837  SIHIEELTAVSRDTKLGTEEVTADIPNLSERQRARLDESGIVYIGAEVEAGDVLVGKVTP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ +TPEEKLLRAIFGEKA DV+DTSL VP+G+SGTV+DV+IF R G+D+++RS  + 
Sbjct: 897  KSETQLTPEEKLLRAIFGEKASDVKDTSLHVPAGISGTVIDVQIFTREGVDRDKRSKQII 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +++    +D  D+  I++ + + R   +L G+ A  GPK   K++ ++ + +    +  
Sbjct: 957  ADELGRFKKDLADQMRIVEADAFQRAKRLLAGKVAAGGPKKLAKNSTITQEYLESVEKHH 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+   + DE     +E +K      + + +  F+ K  K+  GD++PPGV ++VKV++A+
Sbjct: 1017 WFDIRLIDENTSLQLEQIKDSLVQKRKLFDLAFEEKQRKLSQGDELPPGVQKMVKVYIAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +QSGDKMAGRHGNKG++S+I+P EDMP++ DGTPVD+VLNPLGVPSRMN+GQ+ E H
Sbjct: 1077 KRRLQSGDKMAGRHGNKGVISKIVPVEDMPYMADGTPVDVVLNPLGVPSRMNIGQVLEVH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLGKKI  ++   +   D S +R FL K+       E +   DD  +L +A+  
Sbjct: 1137 LGWAAKGLGKKINEMLISQR---DASEIRDFLSKIYSDNGKQEDLVSLDDKEILELAKNL 1193

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP +TPVFDGA E  I  ML++ADL ESGQ+ LYDG TGE FDR VTVGY+++LKL+
Sbjct: 1194 SDGVPFATPVFDGAHESEIKHMLKLADLPESGQTTLYDGRTGEAFDRLVTVGYMHVLKLH 1253

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1254 HLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1313

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT+VYESIV G+   + G PESFNVLVKE+++LGL IDLE 
Sbjct: 1314 DVNGRTKVYESIVKGDHKIDAGMPESFNVLVKEIRSLGLDIDLEQ 1358


>gi|300702765|ref|YP_003744366.1| RNA polymerase subunit beta [Ralstonia solanacearum CFBP2957]
 gi|299070427|emb|CBJ41722.1| RNA polymerase, beta subunit [Ralstonia solanacearum CFBP2957]
          Length = 1368

 Score = 1654 bits (4283), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1376 (51%), Positives = 963/1376 (69%), Gaps = 20/1376 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  +++  +R  EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHVSVAQRKTEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSHPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      + D   G+ VIE  K++ +  ++ L   G K + +  D 
Sbjct: 238  DGALMEFVPERL-RGEVARFDISD-KNGKVVIEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SEGIGPMVLTDDDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T++V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDEVHYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLSKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPSDEEVAAQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEIRKLLGQIYNESGKVEDLDSLSDAEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A   +  +            L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPADIAKEKGLTASKQQVTLFDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|254521295|ref|ZP_05133350.1| DNA-directed RNA polymerase, beta subunit [Stenotrophomonas sp.
            SKA14]
 gi|219718886|gb|EED37411.1| DNA-directed RNA polymerase, beta subunit [Stenotrophomonas sp.
            SKA14]
          Length = 1384

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1390 (50%), Positives = 969/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  N+ P +R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQENVDPAKRTDHGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PIASYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +   L D D  + ++E+GK++T+  +K L+  G+  L +  D +
Sbjct: 241  EGVQLELVPERLRGETLGFDLADGD--KVIVEAGKRITARHIKQLEASGIAALAVPDDYI 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+  TGE+  +A D I ++ L+    + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDASTGELLAQANDEITDEQLQSFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLS VGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKDAAQNLFHNLFFTFERYDLSAVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +                             +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  ETTGEAVLYDRKYYGERNDEESKRLVAAHGDSSDILDVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  +AR N YGF+ETPYRKV DGKV ++V +LSA+EE    IAQAN+  + D   T
Sbjct: 599  LINSLAVYARTNQYGFLETPYRKVVDGKVYDEVEFLSAIEENEYVIAQANALTNADSVLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-PSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G + Q+DA RIV++  E ++   + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERAVARDSGVTVNARRGGEIVQIDAARIVVKVNEEEIVGATDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV+VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLVKYTRSNQNTCINQRPLVQVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY RL   + G+    G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYMRLRSQIVGKVVNGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G KK  V+S   +    ++ W+   ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 GLKKGDVISDAFLDGLKKADWFALRMKDEDASEAIERAQKQIQAHEKEFERRFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TAGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMASGETVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI++++   +A   ++ LR FL+ +     
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQAMM---EAQAAVADLRKFLDDIYNHDD 1194

Query: 1181 ----HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                +   +S + D+ +LR+A     GVP++TPVFDGA E  I  ML +ADL  SGQ+ L
Sbjct: 1195 TNVANRVDLSQFSDEELLRLARNLTDGVPMATPVFDGATEAEIKRMLELADLPSSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRHTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLENS 1366
            L ++++LE++
Sbjct: 1375 LAINMELEDN 1384


>gi|253987832|ref|YP_003039188.1| DNA-directed RNA polymerase subunit beta [Photorhabdus asymbiotica
            subsp. asymbiotica ATCC 43949]
 gi|253779282|emb|CAQ82443.1| DNA-directed RNA polymerase beta chain [Photorhabdus asymbiotica]
          Length = 1342

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG++ L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGSSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +EEIL+ F+ K ++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMDYSTEEILNLFFSKTIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NRLQMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVNRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGEI   A   +    L  +  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVARDYIDVNTGEIICAANMELSLDLLARLSQAGHKSIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L+ 
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLSR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEVEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ LD++G F E+L+ CR  GE  L  RE+++
Sbjct: 592  RLVRDGVVTDEIHYLSAIEEGNFVIAQANTVLDDEGHFVEDLITCRNFGESSLFNREQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + + V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLAEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                 + ++ + + PR +W 
Sbjct: 952  QLRQAKKDLTEELQIFEAGLFARIRSVLVSGG-------------IEAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K+  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKAEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGDETRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++ DL  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLKLGDLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|323527610|ref|YP_004229763.1| DNA-directed RNA polymerase subunit beta [Burkholderia sp. CCGE1001]
 gi|323384612|gb|ADX56703.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. CCGE1001]
          Length = 1368

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1375 (51%), Positives = 964/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  +    +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTPSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITETVLEKLREAKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++ EDG+ T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDGKVTDQIDYLSAIEEGRYVIAQANAAVAEDGTLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDEEAVAGDVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDKVSRGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLTGKVANGGPKKLAKGTKIEQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR FL K+       E++  + D+ ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELREFLTKIYNESGRAEELDSFTDEEIVELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++  L +A   +      G      Q  LYDG TGE F+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLA-FPDDIAQNLGMTPSKNQVRLYDGRTGEMFERTVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|307731263|ref|YP_003908487.1| DNA-directed RNA polymerase subunit beta [Burkholderia sp. CCGE1003]
 gi|307585798|gb|ADN59196.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. CCGE1003]
          Length = 1368

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1375 (51%), Positives = 964/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  +    +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTPSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITETVLEKLREAKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++ EDG+ T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDGKVTDQIDYLSAIEEGRYVIAQANAAVAEDGTLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRIVIRVNDEEAVAGDVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDKVSRGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLTGKVANGGPKKLAKGTKIEQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR FL K+       E++  + DD ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELREFLTKIYNESGRAEELDSFTDDEIVELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++  L +A   +      G      Q  LYDG TGE F+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLA-FPDDIAQNLGMTPSKNQVRLYDGRTGEMFERTVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|237747359|ref|ZP_04577839.1| DNA-directed RNA polymerase subunit beta [Oxalobacter formigenes
            HOxBLS]
 gi|229378710|gb|EEO28801.1| DNA-directed RNA polymerase subunit beta [Oxalobacter formigenes
            HOxBLS]
          Length = 1368

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 968/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY+ FL  ++ P +R NEGLQ+AF S+
Sbjct: 1    MHYSFTEKKRIRKSFAKRDNVHQVPFLLATQLESYEKFLQADVPPLKRKNEGLQSAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF+SY    P FDV +C  R LT A PL+  +RL++ D +  T    +
Sbjct: 61   FPIVSHNGFARLEFISYTLGDPPFDVKECQQRGLTLASPLRAKVRLVILDKESPT-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  RIDRRRK+PVT  L A+GM SEEIL  F+    +  R 
Sbjct: 180  RIIPYRGSWLDFEFDPKDILFFRIDRRRKMPVTILLKAIGMSSEEILENFFVFDDFLLRA 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +        +  M G      ++D   G+ ++E  K++ +  ++ ++  G+K + +  D 
Sbjct: 240  EGAEMEFVPS-RMRGEIARFDILD-REGKVLVEKDKRINARNIRDIEAAGIKRISVPEDF 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  +  +  + I +I  LY + ++  AYI  TL
Sbjct: 298  LYGRALAKNIVDPDTGEVVARANDEITEDVMARLREAGIEEIQTLYTNDLDQGAYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF++ ++YDLS VGR+K N R+  
Sbjct: 358  RIDETVDQMAARIAIYRMMRPGEPPTEESVEALFNGLFYNEERYDLSAVGRMKFNSRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DI+++IKILV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DELTGPMTLSNDDILSVIKILVELRNGRGEIDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D  VT+ + YLSA+EE    IAQANS +DE+G+  +ELV  R AGE ILV  E++ 
Sbjct: 598  RKVIDSHVTDQIEYLSAIEEGRYIIAQANSKIDENGALIDELVSAREAGETILVSPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ +   VGTG+E  VA  
Sbjct: 658  YMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPQKALVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ +DA R+V+R  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYIDAGRVVVRVNDEEAKAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD + + D+IADG STDLG+LALG+N+LVAF PW+G N+EDS+LISE++V +D +TSI
Sbjct: 778  KVGDRIAKGDVIADGASTDLGELALGQNLLVAFTPWNGLNYEDSILISEKVVEDDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TP+G
Sbjct: 838  HIEELSVVARDTKLGPEEITRDISNLAENQLARLDESGIVYIGAEVEAGDVLVGKVTPRG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R G+ +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGLVRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+    GPK   +   ++ + +++  R  W+
Sbjct: 958  ELKRYRIDLNDQMRIVEGDAFQRLSKLLIGKKVNGGPKKLARGAEITQEYLADLERYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE    ++E++K   E  +   +  F+ K +K+  GD++ PGV ++VKV++A+KR
Sbjct: 1018 DIRPADEDTAMSLEAIKDSIEEKRHQFDLAFEEKRKKLTQGDELQPGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGTPADIVLNPLGVPSRMNIGQILETHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +A   +  +R+FL+++  +    E + D  +  VL +AE  K 
Sbjct: 1138 WASKGLGLRIGEML---QAKQKVEEIRAFLKQIYLSSGKPEDLDDLSETEVLTLAENLKD 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA+E+ I  ML +A  D+            Q  LYDG TGEPF+RPVTVG
Sbjct: 1195 GVPFATPVFDGAEEDEIRRMLDLAYPDDIARKLGMTEMKNQVTLYDGRTGEPFERPVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y +MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YKHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1315 EMLTVKSDDVAGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|300690145|ref|YP_003751140.1| RNA polymerase, beta subunit [Ralstonia solanacearum PSI07]
 gi|299077205|emb|CBJ49831.1| RNA polymerase, beta subunit [Ralstonia solanacearum PSI07]
          Length = 1368

 Score = 1654 bits (4282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1376 (51%), Positives = 961/1376 (69%), Gaps = 20/1376 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  N    +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQENAPIAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKT 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  DGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SEGTGPMVLTDDDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T+ V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDQVDYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGLVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD++VGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVMVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLLGKVANGGPKKLAKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     D+ V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPADDDVATQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEIRKLLGQIYNESGKVEDLDSLTDAEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A  +E  +            L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPEEIAKEKGLTASKQQVTLFDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|222056712|ref|YP_002539074.1| DNA-directed RNA polymerase, beta subunit [Geobacter sp. FRC-32]
 gi|254765291|sp|B9M6V2|RPOB_GEOSF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|221566001|gb|ACM21973.1| DNA-directed RNA polymerase, beta subunit [Geobacter sp. FRC-32]
          Length = 1370

 Score = 1653 bits (4281), Expect = 0.0,   Method: Composition-based stats.
 Identities = 730/1364 (53%), Positives = 1006/1364 (73%), Gaps = 11/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +IIDIP+LI++QK SY  FL +++  + R   GL+A FKSVFPI  FS  A
Sbjct: 11   LRKNFAKIKKIIDIPNLIDIQKNSYKRFLQLDVPAEARKYSGLEAVFKSVFPIKDFSETA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV++    +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGIPKYDVEECHQRGMTFAAPMKVKVRLVVWDVNKEPSTRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  ++E+L+ FY     +  G+     ++  
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGYSTDELLNFFYKSEEINFAGEKL-TKVADP 249

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+   K +  +VD  TGE ++++ +K T   ++ + E G+KF+ IT + L G   + DI
Sbjct: 250  ELLTNQKAAIDIVDSATGEVLVKANRKFTKAAIRKMAEHGIKFIPITIEELVGKISSHDI 309

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+  TGEI  E  + + +  LEEI    I    +L++D+++  +  R+T++ DK     D
Sbjct: 310  VDPSTGEIVAECNEELTQAKLEEIKSKGINTFKVLFIDNLHVTSSFRDTIIIDKIGSTDD 369

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A S+F  LFF+ ++YDLS VGR+K+N +L L  P D   + 
Sbjct: 370  ALIEIYRRLRPGDPPTLKSALSLFENLFFNPERYDLSAVGRLKLNYKLGLQVPLDCMTLT 429

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +ED++ +++ L+DL+NG+G IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 430  REDVLEVVRYLIDLKNGRGNIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 489

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 490  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 549

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +GKVTN
Sbjct: 550  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRLVQEGKVTN 609

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +D+DG F  + +  R +GE +LV R++++ +D +P Q+V
Sbjct: 610  EVRFFSALEEEGHAIAQANAEVDKDGRFVADYISARKSGEFVLVGRDELELMDVAPMQLV 669

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A++P VGTGME VVA+ SG ++VA+  
Sbjct: 670  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADSPLVGTGMERVVARDSGVSVVARHN 729

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E + D + +GVDIY L+KF RSNQNTC+NQRP+VK+GD V+R D
Sbjct: 730  GVVESVDASRIVVKIDEDEYDETGTGVDIYNLIKFARSNQNTCINQRPVVKIGDHVKRGD 789

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGPSTD+G+LALG+N+LVAFMPW GYNFEDS+LISER+V +D +TSIHIEEFE +AR
Sbjct: 790  VIADGPSTDMGELALGQNVLVAFMPWGGYNFEDSILISERLVKDDRYTSIHIEEFECVAR 849

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDIL+GKITPKGE+ ++PEEKL
Sbjct: 850  DTKLGKEEITADIPNLGEETLKDLDESGIIRIGAEVRPGDILIGKITPKGETQLSPEEKL 909

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +E+ + + L +D+ 
Sbjct: 910  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDARTELIEQAEEKKLRKDEQ 969

Query: 973  DEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +  S+L ++L G+ A        G     K   +S + +S  P  +W + +V
Sbjct: 970  DEIRIIRESAVSKLKKLLVGKTAAVKVEGKDGKILIVKGKAISEEALSSIPIDRWDEISV 1029

Query: 1027 -QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              DE     V  +         I++  F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1030 ADDESTDDKVAQILSTLNQQIDIIKYVFDDKVQKLKRGDDLPPGVIKMVKVYIAIKRKLQ 1089

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+L+DG PV+IVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1090 VGDKMAGRHGNKGVVSRILPEEDMPYLEDGRPVEIVLNPLGVPSRMNVGQILETHLGWAA 1149

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G +I+ ++   + N + + ++++L++V G     + +   DD+ +  VA++ K GVP
Sbjct: 1150 KGIGWQIEEML---EKNSEKTKIKTYLKEVYGNKEMNKFLDTLDDEELSNVAKRLKRGVP 1206

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+G+ EE I  ML  A    + Q  LYDG +G+ F   VTVG +Y+LKL+H+V D
Sbjct: 1207 MASPVFEGSSEEGIREMLGKAGFAHTAQVTLYDGKSGDAFKHKVTVGVMYVLKLHHLVDD 1266

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1267 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1326

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+LGL ++L  +   
Sbjct: 1327 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLGLDVELLENEED 1370


>gi|297182726|gb|ADI18882.1| DNA-directed RNA polymerase, beta subunit/140 kd subunit [uncultured
            Pseudomonadales bacterium HF0010_05E14]
          Length = 1380

 Score = 1653 bits (4280), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1388 (51%), Positives = 971/1388 (69%), Gaps = 32/1388 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK P  +D+P L+ +Q  SY  F  + +  +ER + GL AA KSV
Sbjct: 1    MTYSFTEKKRIRKNFGKLPNTMDLPYLLSIQLDSYQKFTQIGLDDNERTDTGLHAALKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  +SG A LE+V Y+   P F+ ++C  R +T++VPL++ +RLI++D D  + +K++
Sbjct: 61   FPIIGYSGNAALEYVDYKLGSPAFEEEECKLRGVTFSVPLRVRVRLIIYDKD--SASKAV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +Y+G++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGKLLY  
Sbjct: 119  KDIREQEVYLGEIPLMTDNGTFIINGTERVIVSQLHRSPGVIFDHDKGKTHSSGKLLYTA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++VRIDRRRK+P T  L ALG  SEEIL+ F+   V+S + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDLLYVRIDRRRKLPSTILLRALGYSSEEILNMFFDTNVFSVKK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D +   L    L  G   + ++      + V+E G+++T+  ++ L++  +  L +  + 
Sbjct: 239  DQFSLALDPERL-RGEIAAFAIKGKQN-KVVVEKGRRITARHIRQLEKDKISSLQVPREY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  VA DI + +TGE+ +E    I +++L+ +  + +  I  LY + ++   +I +TL
Sbjct: 297  LIGRPVAMDIADEKTGELMLECNTEISDENLDALLKAGVTRIETLYTNDLDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +D  K + +A+++IYR+MRPG+  T   AE++F+ LFF+ ++YDLS VGR+K N RL+ 
Sbjct: 357  RSDATKTQLEAMVEIYRMMRPGEPPTKESAENLFHNLFFNEERYDLSAVGRMKFNRRLDR 416

Query: 423  DTPDDVRHIRKEDI----------------------IAIIKILVDLRNGKGTIDDIDNLG 460
                    +                           I++++ L+ +RNGKG++DDID+LG
Sbjct: 417  HDESGPGILYDHRYLLQNKAEECAELIEQFGDASDIISVMQKLISIRNGKGSVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRR+RSVGEM +NQ+R+GL+R+ER++KER+   + + +MPQDL+NAKPV +A+ EFF SS
Sbjct: 477  NRRIRSVGEMAENQFRVGLVRVERAVKERLGVAESEGLMPQDLVNAKPVAAAMKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL S+AR N YGFIETPYRKV DG+VT+++ YLSA+ E    IAQA++S+DE G+F
Sbjct: 597  GLINSLASYARTNDYGFIETPYRKVIDGRVTSEIEYLSAINESQFVIAQASASIDEKGNF 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             ++LV  R   E        ID++D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  KDDLVAVRHLNEFTSKNPTDIDYMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+AE P VGTG+E  VA  SG   VA R G VE VDA RIV+R    +     +GVD
Sbjct: 717  VPTLRAETPLVGTGIERKVASDSGVCKVALRGGYVESVDAGRIVVRVDHNETQAGEAGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY+L K+ RSNQNTC++Q+P+V+ GD V + D++ADGPS DLG+LALG+NM +AFMPW+G
Sbjct: 777  IYKLTKYTRSNQNTCIDQKPIVRQGDVVSKGDVLADGPSVDLGELALGQNMRIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+LISER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE G
Sbjct: 837  YNFEDSILISERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALGRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV+ GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPS + GTV+
Sbjct: 897  IVHIGAEVSAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSSIKGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R G++K++RSI +E   ++   +D +DE  I++    +RL +++  +  +   K
Sbjct: 957  DVQVFTRDGLEKDQRSIDIESAALDQFKKDLNDEYRIVENATLARLSDLIKNKKVMKA-K 1015

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            GFKK         +E+    W    +++ ++   +  +  Q E  K+ ++ RF+ K EK+
Sbjct: 1016 GFKKGDKFDLKKCAEFSVEDWMAIRMENPEINEQISEMSGQLELQKTAIDSRFEAKREKL 1075

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            Q GDD+ PGVL+ VKV++A+KR IQ GDKMAGRHGNKG++S I P EDMP  + G PVDI
Sbjct: 1076 QSGDDLSPGVLKTVKVYLAVKRRIQPGDKMAGRHGNKGVISVIKPVEDMPHDEHGEPVDI 1135

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQ+ E H+G A  GLG  +  +I     N   S +R F++K+   G 
Sbjct: 1136 VLNPLGVPSRMNVGQVLEVHMGLAAKGLGDAVNQMI---AKNSKASDMRDFMQKIYNIGD 1192

Query: 1181 --HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  ++D  DD VL +A   K GVP++TPVFDGA E  +  ML +A L ESGQ  L+D
Sbjct: 1193 TVFGTDLTDLSDDEVLELANNLKHGVPIATPVFDGAHESELKKMLSLAGLPESGQMTLFD 1252

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+ FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEME
Sbjct: 1253 GRTGDKFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEME 1312

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGA+Y LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNVLVKE+++LG
Sbjct: 1313 VWALEAYGASYTLQEMLTVKSDDVAGRTKMYKNIVDGDHRMEPGMPESFNVLVKEVRSLG 1372

Query: 1359 LSIDLENS 1366
            ++++LEN 
Sbjct: 1373 INMELEND 1380


>gi|91785473|ref|YP_560679.1| DNA-directed RNA polymerase subunit beta [Burkholderia xenovorans
            LB400]
 gi|122970100|sp|Q13TG2|RPOB_BURXL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91689427|gb|ABE32627.1| DNA-directed RNA polymerase subunit beta [Burkholderia xenovorans
            LB400]
          Length = 1368

 Score = 1652 bits (4279), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 964/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  + +  +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTSSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  S+I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITETVLEKLRESKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ EDGS T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGSLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRMVIRVNDDEAVAGDVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDIVSRGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLTGKVANGGPKKLAKGTKIEQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I+ LR FL K+       E++  + DD ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIAELREFLTKIYNESGRAEELDSFTDDEIVELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++  L +A  D+  +            LYDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLAFPDDIAKNLGMTPSKNQVRLYDGRTGEMFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|78221839|ref|YP_383586.1| DNA-directed RNA polymerase subunit beta [Geobacter metallireducens
            GS-15]
 gi|109903820|sp|Q39Y13|RPOB_GEOMG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78193094|gb|ABB30861.1| DNA-directed RNA polymerase subunit beta [Geobacter metallireducens
            GS-15]
          Length = 1370

 Score = 1652 bits (4279), Expect = 0.0,   Method: Composition-based stats.
 Identities = 738/1364 (54%), Positives = 1014/1364 (74%), Gaps = 11/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +R+ F K  +IIDIP+LI++QK SY  FL ++  P+ R N GL+A FKSVFPI  FS  A
Sbjct: 11   LRQNFAKIKKIIDIPNLIDIQKNSYKRFLQIDTPPEARKNSGLEAVFKSVFPIKDFSDTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV++ TG +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGTPKYDVEECHQRGMTFAAPMKVKVRLVVWDVNKDTGVRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  +EE+L+ +Y        G+       A 
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGNSAEELLNFYYRSEEIGLDGERMWKKADAE 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
             L+   K SS +VD  TGE +I++ +K T   ++ + E G+  + I ++ +CG Y + DI
Sbjct: 251  -LLTTQKTSSDIVDSKTGEVIIKANRKFTKAAIRKMTEHGITEIPIKAEEVCGKYASTDI 309

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+  TGE+ +E  + I +  L+EI    I +  +L++D+++  + +R+TL+ DK     D
Sbjct: 310  VDPATGEVLVECNEEISQAKLDEIKARGISEFKVLFIDNLHVTSSLRDTLLVDKINTTDD 369

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A+++F+ LFF++++YDLS VGR+K+N +L L  P D + + 
Sbjct: 370  ALIEIYRRLRPGDPPTLKSAQALFDNLFFNAERYDLSAVGRLKLNYKLGLGVPLDCQVLT 429

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            KEDI+ +++ L+DL+NG+GTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 430  KEDILEVVRYLIDLKNGRGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 489

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 490  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 549

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +GKVT 
Sbjct: 550  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRIVSEGKVTA 609

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +D DG F  + V  R +GE +LV R++++ +D +P Q+V
Sbjct: 610  EVKFFSALEEEGHAIAQANAEMDADGRFVNDYVSARKSGEFLLVHRDELELMDVAPMQLV 669

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLLKA++P VGTGME VVAK SG ++VA+  
Sbjct: 670  SVAASLIPFLENDDANRALMGSNMQRQAVPLLKADSPLVGTGMERVVAKDSGVSVVARHT 729

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E + D + +GVDIY L+KF RSNQNTC+NQRP+VKVGD V+R D
Sbjct: 730  GVVESVDASRIVVKIDEDEYDETGTGVDIYNLIKFARSNQNTCINQRPVVKVGDHVKRGD 789

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGPSTD+G+LALG+N++VAFMPW GYNFEDS+LISE++  +D +TSIHIEEFE +AR
Sbjct: 790  VIADGPSTDMGELALGQNVVVAFMPWGGYNFEDSILISEKLTKDDRYTSIHIEEFECVAR 849

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDI+VGKITPKGE+ ++PEEKL
Sbjct: 850  DTKLGKEEITSDIPNLGEETLKDLDESGIIRIGAEVKPGDIMVGKITPKGETQLSPEEKL 909

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  ++F+R G DK+ R+  +ER + E L +D+ 
Sbjct: 910  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKVFSRKGNDKDSRTEMIERMEEEKLRKDEQ 969

Query: 973  DEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L  +L G+ A       +G     K   ++ + ++  P  +W + +V
Sbjct: 970  DEIRIIRDSAVGKLKRLLVGKTAAVKVEDKNGKTVIAKDAAITEEALTAIPLDRWDEISV 1029

Query: 1027 Q-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               E V+  V ++    +    I++  F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1030 SGGEGVEEKVAAILATLQQQIDIIKYVFDDKVQKLKRGDDLPPGVIKMVKVYIAIKRKLQ 1089

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+++DG PV+IVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1090 VGDKMAGRHGNKGVVSRILPEEDMPYMEDGRPVEIVLNPLGVPSRMNVGQILETHLGWAA 1149

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G KI+ ++  +  +  I   + +L+KV G+      +   +++ ++ VA++ + GVP
Sbjct: 1150 KGIGWKIEEMLEKHSPSATI---KEYLQKVYGSKEMNAFLDSLNEEELINVAKRLQRGVP 1206

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+GA EE I SML  A  DE+ Q  L+DG TGEPF   VTVG +Y+LKL+H+V D
Sbjct: 1207 MASPVFEGASEEQIRSMLDKAGFDETAQVRLFDGKTGEPFKHKVTVGVMYVLKLHHLVDD 1266

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1267 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1326

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+L L ++L      
Sbjct: 1327 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLCLDVELLEGDED 1370


>gi|37524448|ref|NP_927792.1| DNA-directed RNA polymerase subunit beta [Photorhabdus luminescens
            subsp. laumondii TTO1]
 gi|41017640|sp|Q7N9A4|RPOB_PHOLL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|36783872|emb|CAE12734.1| RNA polymerase, beta subunit [Photorhabdus luminescens subsp.
            laumondii TTO1]
          Length = 1342

 Score = 1652 bits (4279), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1364 (51%), Positives = 968/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG++ L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGSSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +EEIL+ F+ K ++  R 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMNYSTEEILNLFFSKTIFEIRD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  NRLQMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDEVNRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA D ++  TGEI   A   +    L  +  S  + I  L+ + +++ AYI  TL
Sbjct: 292  IAGKVVARDYIDVNTGEIICAANMELSLDLLARLSQSGHKSIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L+ 
Sbjct: 352  RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLSR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEVEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ YLSA+EE N  IAQAN+ LD++G F E+L+ CR  GE  L  RE+++
Sbjct: 592  RLVRDGVVTDEIHYLSAIEEGNFVIAQANTVLDDEGHFVEDLITCRNYGESSLFNREQVE 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I +  +++R+  +L                 + ++ + + PR +W 
Sbjct: 952  QLRQAKKDLTEELQIFEAGLFARIRSVLIAGG-------------IEAEKLDKLPRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K+  E +   K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKAEFEKKLDAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +    +         +         +S + D+ V+R+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQQQEVAKLREFIQKAYNLGDETRQKVDLSTFSDEEVMRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++ DL  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLKLGDLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEGE 1342


>gi|186477596|ref|YP_001859066.1| DNA-directed RNA polymerase subunit beta [Burkholderia phymatum
            STM815]
 gi|226699382|sp|B2JIH4|RPOB_BURP8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|184194055|gb|ACC72020.1| DNA-directed RNA polymerase, beta subunit [Burkholderia phymatum
            STM815]
          Length = 1368

 Score = 1652 bits (4279), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1375 (50%), Positives = 969/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL   +   +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQAEVPTAQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLENAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D + E  L+++  ++I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEVTESVLDKLREAKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++ EDG+ T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVTDGKVTDQIDYLSAIEEGRYVIAQANAAVAEDGTLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+ 
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGDVGVDIYNLIKYTRSNQNTNINQRPIA 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDKVARGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLEGKVANGGPKKLAKGTKIERAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  +R+FL K+       E++  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQARIEEVRAFLTKIYNESGRAEELESFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++SML +A   +      G      Q  LYDG TGE F+R VTV
Sbjct: 1195 GVPFATPVFDGATEEEMSSMLDLA-FPDDIAQNLGMTKSKNQVRLYDGRTGEAFERTVTV 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|167564424|ref|ZP_02357340.1| DNA-directed RNA polymerase subunit beta [Burkholderia oklahomensis
            EO147]
 gi|167571570|ref|ZP_02364444.1| DNA-directed RNA polymerase subunit beta [Burkholderia oklahomensis
            C6786]
          Length = 1368

 Score = 1652 bits (4278), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1374 (50%), Positives = 967/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++   +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVLTAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLEKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++D++G   +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVADSKVTDQIDYLSAIEEGRYMIAQANAAIDDNGQLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    +  LR+FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQVKLEELRAFLTKIYNESGRAEDLDSFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++ ML +A          ++ S  Q  LYDG TGE F+R VT+G
Sbjct: 1195 GVPFATPVFDGATEEEMSKMLDLAFPDEIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|91774628|ref|YP_544384.1| DNA-directed RNA polymerase subunit beta [Methylobacillus flagellatus
            KT]
 gi|122400331|sp|Q1H4P4|RPOB_METFK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91708615|gb|ABE48543.1| DNA-directed RNA polymerase subunit beta [Methylobacillus flagellatus
            KT]
          Length = 1390

 Score = 1652 bits (4278), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1397 (50%), Positives = 962/1397 (68%), Gaps = 40/1397 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+ +Q  SY  FL  +   D+R + GLQAAF SV
Sbjct: 1    MSYSFTEKKRLRKSFAKRESVQEVPYLLAMQLESYAAFLQADTPADKRTDTGLQAAFSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L+FVSY      FDV +C  R LTYA PL++ +RL + D        ++
Sbjct: 61   FPIVSHSGNARLDFVSYNLGQEPFDVKECQQRGLTYAAPLRVKVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT++G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGELPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+PVT  L ALG   E+IL TFY    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRVDRRRKMPVTILLKALGFTPEQILETFYDFDTFHIAK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L    L  G      ++D D G+ ++   K++T   ++ +++ G+  + +  + 
Sbjct: 239  KGVQFELVPERL-RGEVAKFDILDKD-GKVIVAKDKRITVKHIRDMEKSGISKITVPEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A  IV+  TGEI   A D + E  L+++  +++  I  LY + +++  YI  TL
Sbjct: 297  LLGRSLAAGIVDKTTGEIIANANDEVTESLLDKLREADVNKINTLYANDLDHGDYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D   A + IYR+MRPG+  T    +++F  LFF+ D+YDLS VGR+K N R   
Sbjct: 357  RIDEIPDEYSARVAIYRMMRPGEPPTEEAVQALFEGLFFNEDRYDLSAVGRMKFNRRAFP 416

Query: 423  DT--------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +                      +    +  +DI+A+I +L++LRNG+G IDDID+LGNR
Sbjct: 417  EKIEERTAAWLRRFYEKVGPQGAEGPGTLSNDDILAVIAVLIELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+RSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKPV SA+ EFF SSQ 
Sbjct: 477  RIRSVGELAENQFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPVSSAIREFFGSSQP 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  ++R N YGF+ETPYR+V D KV++ + YLSA+EE    IAQANS LD+DG F E
Sbjct: 597  INSLALYSRTNQYGFLETPYRRVADNKVSDQIDYLSAIEESQYMIAQANSELDQDGRFKE 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV  R   E  +   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLVSARYHNEFTMAQPDRVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+AE   VGTG+E  VA  SG  + A+R G+V+ VD+ RIV+R  + +      GVDIY
Sbjct: 717  CLRAEKALVGTGIERTVAVDSGTVVTARRGGVVDYVDSSRIVVRVHDEEAAAGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L+K+ RSNQNT +NQRPLV VGD + R D+IADG STD+G+LALG+NMLVAFMPW+GYN
Sbjct: 777  NLIKYTRSNQNTNINQRPLVNVGDVLARGDVIADGASTDMGELALGQNMLVAFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+LISER+V++D +TSIHIEE  V+ARDTKLG EEITRDI N+SE  L  +DE GII
Sbjct: 837  FEDSILISERVVADDRYTSIHIEELSVVARDTKLGAEEITRDISNLSERMLGRLDESGII 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV
Sbjct: 897  YIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GI+++ R+  +  +Q+    +D  D+  I++ + + R+  ++ G+ A  GP+  
Sbjct: 957  QVFTREGIERDARAQQIIDDQLADYKQDLADQMRIVEDDAFGRIRRLIEGKVATGGPQKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK   ++++ +    R  W+   + DE V R +E L+     ++   + +F+ K  K+  
Sbjct: 1017 KKGETVTAEYLDGLARYDWFDIRLSDEDVARQLEQLRDSLSQARIEFDSKFEEKKRKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR IQ GDKMAGRHGNKG+VS+I+P EDMP + DGTP+DIVL
Sbjct: 1077 GDELPPGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVVSKIVPIEDMPHMADGTPMDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SH 1181
            NPLGVPSRMN+GQI E HLGWA  GLG +I +++   +A    + LR FLE+V       
Sbjct: 1137 NPLGVPSRMNIGQILEVHLGWAAKGLGIRIGNML---QAQAKAAELRDFLEQVYNKSNGK 1193

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---------- 1231
            +E I+   DD V+ +A+  +SGVP +TPVFDGA E  I +ML +A  D+           
Sbjct: 1194 SEDIASLSDDEVIDLAKNLRSGVPFATPVFDGATEADIKAMLDLAFPDDDPRTQQLQFAS 1253

Query: 1232 GQS--ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            G++   L+DG TG+ F+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1254 GKTQVTLFDGRTGDAFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1313

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT+VYE+IV G    + G PESFNV
Sbjct: 1314 GGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDAGMPESFNV 1373

Query: 1350 LVKEMQALGLSIDLENS 1366
            LVKE+++L + IDL+ +
Sbjct: 1374 LVKEIRSLAIDIDLDRN 1390


>gi|167838219|ref|ZP_02465078.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            MSMB43]
          Length = 1368

 Score = 1652 bits (4278), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1375 (50%), Positives = 964/1375 (70%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++ P +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVLPAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDK-ESPNKPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPELILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLETAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLEKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  DR  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ EDG+  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVADSKVTDQIDYLSAIEEGRYMIAQANAAIGEDGTLVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAAAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I  LR FL K+       E +  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIEELRVFLTKIYNESGRAEDLESFTDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++ ML +A   +             Q  LYDG TGEPF+R VT+
Sbjct: 1195 GVPFATPVFDGATEEEMSKMLDLA-FPDDIAEQLDMNPSKNQVRLYDGRTGEPFERRVTL 1253

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1254 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1313

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|17547753|ref|NP_521155.1| DNA-directed RNA polymerase subunit beta [Ralstonia solanacearum
            GMI1000]
 gi|41017774|sp|Q8XUZ8|RPOB_RALSO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|17430058|emb|CAD16743.1| probable dna-directed rna polymerase beta chain (rnap betasubunit)
            (transcriptase beta chain) (rna polymerase beta subunit)
            protein [Ralstonia solanacearum GMI1000]
          Length = 1368

 Score = 1652 bits (4278), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1377 (51%), Positives = 961/1377 (69%), Gaps = 22/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  + +  +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHASVAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  DGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SEGTGPMVLTDDDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T+ V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDQVDYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGLVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD++VGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVMVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+    GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVVNGGPKKLAKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     D+ V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPSDDDVATQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEMRKLLGQIYNESGKVEDLDSLSDAEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPV 1249
            K GVP +TPVFDGA E+ I  ML +A   E      G      Q  L+DG TGE F+RPV
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLA-YPEDIAKEKGLTASKQQVTLFDGRTGEAFERPV 1251

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            T+G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y
Sbjct: 1252 TLGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASY 1311

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1312 VLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|296163259|ref|ZP_06846023.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. Ch1-1]
 gi|295886495|gb|EFG66349.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. Ch1-1]
          Length = 1368

 Score = 1652 bits (4277), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 964/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  + +  +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTSSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  S+I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITETVLEKLRESKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ EDGS T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGSLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRMVIRVNDDEAVAGDVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDIVSRGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLDGKVANGGPKKLAKGTKIEQAYLQDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I+ LR FL K+       E++  + DD ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIAELREFLAKIYNESGRAEELDSFTDDEIVELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++  L +A  D+  +            LYDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLAFPDDIAKQLGMTPSKNQVRLYDGRTGEMFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|320540634|ref|ZP_08040284.1| RNA polymerase, beta subunit [Serratia symbiotica str. Tucson]
 gi|320029565|gb|EFW11594.1| RNA polymerase, beta subunit [Serratia symbiotica str. Tucson]
          Length = 1342

 Score = 1652 bits (4277), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1364 (52%), Positives = 972/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK+P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKSPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T+  PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFFAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ KI +  RG
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKITFEIRG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +  + +  + 
Sbjct: 235  NKLQMELVPERL-RGETASFDIE--ANGKIYVEKGRRITARHIRQLEKDEIYSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  L+ + +++ AYI  T+
Sbjct: 292  IAGKVVAQDYIDTNTGELICTANMELSLDLLAKLSQAGHKCIETLFTNDLDHGAYISETI 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPSSDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + K DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKNDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D
Sbjct: 592  RRVRDGMVTDEINYLSAIEEGNFVIAQANSNLDDDGRFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRVDKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTAVAKRGGVIQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQIPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  IL+  +++R+  +L                   ++ +S+ PR +W 
Sbjct: 952  QLKQVKKDLTEELQILEAGLFARIHAVLVAGGV-------------EAEKLSKLPRDRWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +  E+ Q  +E L  QY+  KS  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLTVEEKQNQLEHLAEQYDELKSDFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++   +    +         +         ++ + DD VLR+AE  K+
Sbjct: 1119 MAAKGIGEKINQMLKQQQEVARLREFIQKAYDLGDDVCQKVDLNTFTDDEVLRLAENLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L M  +  SGQ  LYDG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKETEIKQLLEMGGIPTSGQITLYDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342


>gi|187925624|ref|YP_001897266.1| DNA-directed RNA polymerase subunit beta [Burkholderia phytofirmans
            PsJN]
 gi|226699383|sp|B2T759|RPOB_BURPP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|187716818|gb|ACD18042.1| DNA-directed RNA polymerase, beta subunit [Burkholderia phytofirmans
            PsJN]
          Length = 1368

 Score = 1652 bits (4277), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 965/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  + +  +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTSSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  S+I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITETVLEKLRESKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ EDGS T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGSLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA R+VIR  + +     +GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQAFRGGVVDYVDAGRMVIRVNDDEAAAGETGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KVGDIVSRGDVLADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLDGKVANGGPKKLAKGTKIEQAYLQDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I+ LR FL K+       E++  + DD ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIAELREFLTKIYNESGRAEELDSFTDDEIVELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++  L +A  D+  +            LYDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLAFPDDIAKNLGMTPSKNQVRLYDGRTGEMFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|226798|prf||1606216A RNA polymerase beta
          Length = 1357

 Score = 1651 bits (4276), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1365 (51%), Positives = 973/1365 (71%), Gaps = 9/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY  FL         P   L AAFKSV
Sbjct: 1    MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGSIQGSLPRRRLHAAFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61   FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDK--ESSNKAI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQ+HRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQMHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EE+L+TFY   V+   G
Sbjct: 179  RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEVLNTFYTTNVFHISG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      + D +TG+ ++E G+++T+  +  L++ GVK L +  + 
Sbjct: 239  EKLSLELVPQRLA-GEVAVMDIHD-ETGKVIVEQGRRITARHINQLEKAGVKQLDVPMEY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+ IV+  TGEI  E    +  + L ++  +++  I  LY + ++   +I +TL
Sbjct: 297  VLGRTTAKAIVHPATGEILAECNTEMTTELLIKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE++FN LFF +++YDLS +GR+K N R+  
Sbjct: 357  KIDTTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSAERYDLSPLGRMKFNRRIGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+ ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417  TEIEGSGVLSKEDIVEVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR S
Sbjct: 477  ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRCS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 597  RVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVT 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 657  LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +V +R G+++ VDA RIV+R  + +++     VDIY L K+ RSNQNTC+NQRPLV
Sbjct: 717  SGVCVVRRRGGVIDSVDASRIVVRVADDEVETGERRVDIYNLTKYTRSNQNTCINQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD+V+R DI+AD  STD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 777  SKGDKVQRGDIMADRASTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARD KLGP EIT  IPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 837  HIQELTCVARDNKLGPREITSGIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             + +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++++ R++++E+ 
Sbjct: 897  HTQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTQGTVIDVQVFTRDGVERDSRALAIEKM 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L GQ    G  G KK TV++ +++      QW+
Sbjct: 957  QLDEIPQDLNEEFRIVEGATFERLRSALNGQVVDGG-AGLKKGTVITDEVLDGLDDGQWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K   +Q GDD+ PGVL++VKV++A++R
Sbjct: 1016 KLRMAEDALNEQLEKAQQYIVDRRRLLDDKFEDKKRNVQQGDDLAPGVLKIVKVYLAIRR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +     + LR FL +V    G   E + ++ D+ +L +A   K
Sbjct: 1136 LAAKGLGEKIDRMLEEQR---KAAELRVFLTEVYNEIGGRQENLDEFTDEEILALANNLK 1192

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVFDGA E  I +ML++ADL ESGQ +L+DG T   F+RPVTVGY+YMLKLNH
Sbjct: 1193 KGVPMATPVFDGAKEREIKAMLKLADLPESGQMVLFDGRTRNKFERPVTVGYMYMLKLNH 1252

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGG +  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1253 LVDDKMHARSTGSYSLVTQQPLGGLAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1312

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G  ESFNVL+KE+++LG+ IDLE  
Sbjct: 1313 VNGRTKMYKNIVDGDHRMEPGMAESFNVLIKEIRSLGIDIDLETE 1357


>gi|299065400|emb|CBJ36569.1| RNA polymerase, beta subunit [Ralstonia solanacearum CMR15]
          Length = 1368

 Score = 1651 bits (4276), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1377 (51%), Positives = 961/1377 (69%), Gaps = 22/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  + +  +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHASVAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  DGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SEGTGPMVLTDDDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T+ V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDQVDYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGLVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD++VGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVMVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+    GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVVNGGPKKLAKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     D++V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPSDDEVATQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA      +R  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAVEMRKLLGQIYNESGKVEDLDSLSDAEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPV 1249
            K GVP +TPVFDGA E+ I  ML +A   E      G      Q  L+DG TGE F+RPV
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLA-YPEDIAKEKGLTASKQQVTLFDGRTGEAFERPV 1251

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            T+G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y
Sbjct: 1252 TLGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASY 1311

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1312 VLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|309782817|ref|ZP_07677537.1| DNA-directed RNA polymerase, beta subunit [Ralstonia sp. 5_7_47FAA]
 gi|308918241|gb|EFP63918.1| DNA-directed RNA polymerase, beta subunit [Ralstonia sp. 5_7_47FAA]
          Length = 1368

 Score = 1651 bits (4275), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1377 (51%), Positives = 965/1377 (70%), Gaps = 22/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  N    +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQENTPVAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKT 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSATL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTADQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             T      +  EDI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  STGTGPMVLTDEDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV +GK+T+ V YLSA+EE    +AQAN++LD+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENGKLTDQVDYLSAIEEGKYVVAQANATLDKDGNLIDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVVRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLAKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++V   +E++KV  E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPAEDEVALQLEAVKVAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  +L +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEIRKLLGQIYNESGKVEDLDSLSDAEILELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPV 1249
            K GVP +TPVFDGA E+ I  ML +A   E      G      Q  L+DG TGE F+RPV
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLA-YPEDIAKEKGLTASKQQVTLFDGRTGEAFERPV 1251

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            T+G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y
Sbjct: 1252 TLGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASY 1311

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1312 VLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|194364527|ref|YP_002027137.1| DNA-directed RNA polymerase subunit beta [Stenotrophomonas
            maltophilia R551-3]
 gi|254765306|sp|B4SKV6|RPOB_STRM5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|194347331|gb|ACF50454.1| DNA-directed RNA polymerase, beta subunit [Stenotrophomonas
            maltophilia R551-3]
          Length = 1384

 Score = 1650 bits (4274), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1390 (50%), Positives = 970/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  N+ P +R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQENVDPAKRTDHGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PIASYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +   L D D  + ++E+GK++T+  +K L+  G+  L +  D +
Sbjct: 241  EGVQLELVPERLRGETLGFDLADGD--KVIVEAGKRITARHIKQLEASGIAALAVPDDYI 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+  TGE+  +A D I ++ L+    + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDASTGELLAQANDEITDEQLQAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLS VGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKDAAQNLFHNLFFTFERYDLSAVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +                             +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  ETTGEAVLYDRKYYGERNDEESKRLVAAHGDSSDILDVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  +AR N YGF+ETPYRKV DGKV ++V +LSA+EE    IAQAN+  + D   T
Sbjct: 599  LINSLAVYARTNQYGFLETPYRKVVDGKVYDEVEFLSAIEENEYVIAQANALTNADSVLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-PSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G + Q+DA RIV++ VE ++   + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERAVARDSGVTVNARRGGEIVQIDAARIVVKVVEEEIVGATDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV+VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLVKYTRSNQNTCINQRPLVQVGDIIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY RL   + G+    G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYMRLRSQIVGKVVNGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G KK  V+S   +    ++ W+   ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 GLKKGDVISDAFLDGLKKADWFALRMKDEDASEAIERAQKQIQAHEKEFERRFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TAGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMASGETVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI++++   +A   ++ LR FL+ +     
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQAMM---EAQAAVADLRKFLDDIYNHDD 1194

Query: 1181 ----HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                +   +S + D+ +LR+A     GVP++TPVFDGA E  I  ML +ADL  SGQ+ L
Sbjct: 1195 TNVANRVDLSQFSDEELLRLARNLTDGVPMATPVFDGATEAEIKRMLELADLPSSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRHTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLENS 1366
            L ++++LE++
Sbjct: 1375 LAINMELEDN 1384


>gi|188992861|ref|YP_001904871.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            campestris str. B100]
 gi|226699459|sp|B0RU89|RPOB_XANCB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|167734621|emb|CAP52831.1| DNA directed RNA polymerase (beta subunit) [Xanthomonas campestris
            pv. campestris]
          Length = 1387

 Score = 1650 bits (4273), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1389 (50%), Positives = 973/1389 (70%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 67   PISSYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 185  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 245  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 303  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 363  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 423  EVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 543  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 603  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A+R G++EQ+DA RIV++  E      + +GVD
Sbjct: 723  PTLRSQKPLVGTGIERAVARDSGVTVNARRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 963  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1021

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++D+     +E  + Q +  +   E RF +K  KI
Sbjct: 1022 NLKKGDNVTDAYLDGLKKSDWFQLRMKDDDAADAIERAQKQIQAHEKEFEARFADKRGKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1082 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    S
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQTAVSELRKFLDDIYNHDS 1198

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1199 AINAERVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1379 LAINMELEE 1387


>gi|241664549|ref|YP_002982909.1| DNA-directed RNA polymerase subunit beta [Ralstonia pickettii 12D]
 gi|240866576|gb|ACS64237.1| DNA-directed RNA polymerase, beta subunit [Ralstonia pickettii 12D]
          Length = 1368

 Score = 1650 bits (4272), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1377 (51%), Positives = 965/1377 (70%), Gaps = 22/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  N    +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQENTPVAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKT 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSATL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTADQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             T      +  EDI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  STGTGPMVLTDEDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV +GK+T+ V YLSA+EE    +AQAN++LD+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENGKLTDQVDYLSAIEEGKYVVAQANATLDKDGNLIDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVVRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + + +  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLAKGTALTKEYLGDLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++V   +E++KV  E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPAEDEVALQLEAVKVAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  LE++       E +    D  +L +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEIRKLLEQIYNESGKVEDLDSLSDAEILELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPV 1249
            K GVP +TPVFDGA E+ I  ML +A   E      G      Q  L+DG TGE F+RPV
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLA-YPEDIAKEKGLTASKQQVTLFDGRTGEAFERPV 1251

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            T+G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y
Sbjct: 1252 TLGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASY 1311

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1312 VLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|194291035|ref|YP_002006942.1| DNA-directed RNA polymerase subunit beta [Cupriavidus taiwanensis LMG
            19424]
 gi|226699392|sp|B3R7T6|RPOB_CUPTR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|193224870|emb|CAQ70881.1| RNA polymerase, beta subunit [Cupriavidus taiwanensis LMG 19424]
          Length = 1368

 Score = 1650 bits (4272), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1375 (50%), Positives = 956/1375 (69%), Gaps = 20/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  +  P  R  EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIESYTQFLQADTPPARRKTEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +       +
Sbjct: 61   FPISSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPG---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLQS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGAQLEFVPERL-RGEVARFDIAD-KNGRVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++I++ +TGE+   A D + E  LE +  + ++ I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIIDPDTGEVIANANDELTEALLENLREAGVKQIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 356  RVDETADQTAARIAIYRMMRPGEPPTEEAVEALFQRLFYSEESYDLSRVGRMKVNSRLGR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             + +    ++ EDI+  IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PSGEGAMVLQDEDILETIKILVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV D K+T++V YLSA+EE    +AQAN+++D DG+ T+ELV  R     E  +V  ++
Sbjct: 596  RKVVDSKLTDEVDYLSAIEEGKYVVAQANATVDADGNLTDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRPDKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA+RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQAMRGGVVDYVDAMRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDHVARGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SG V+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGIVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + RL  +L  +    GPK   K   ++ + +++  +  
Sbjct: 956  DDELKRYRLDLNDQLRIVEGDAFQRLERLLVDKTVNGGPKKLAKGAKITKEYLADIDKYH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE++   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPADEELAAQLEAVKEAIEQKRHEFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I  ++   KA      LR+ L ++       E +    D  VL +A   
Sbjct: 1136 LGWAARGLGQRIGDML---KAQAKAQELRTLLSQIYNESGKPEDLDSLSDAEVLELANNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A  D    E G      Q  L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPDDVAREKGLTASKQQVTLFDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDL+ 
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLDR 1367


>gi|325916480|ref|ZP_08178749.1| DNA-directed RNA polymerase subunit beta [Xanthomonas vesicatoria
            ATCC 35937]
 gi|325537269|gb|EGD08996.1| DNA-directed RNA polymerase subunit beta [Xanthomonas vesicatoria
            ATCC 35937]
          Length = 1383

 Score = 1650 bits (4272), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1389 (50%), Positives = 969/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P +R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPTKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  EVLGESVLYDKKYFAERNDEESKRLVAEHTDTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAINEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDNVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLDDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|85058112|ref|YP_453814.1| DNA-directed RNA polymerase subunit beta [Sodalis glossinidius str.
            'morsitans']
 gi|109914396|sp|Q2NWR6|RPOB_SODGM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|84778632|dbj|BAE73409.1| RNA polymerase beta subunit [Sodalis glossinidius str. 'morsitans']
          Length = 1342

 Score = 1650 bits (4272), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1364 (51%), Positives = 962/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+  L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVSYLLSIQLDSFQKFIERD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +T++ PL++ LRLI+++ +   G  ++
Sbjct: 57   FPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLIIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL TF+ K+VY    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYSTGQILDTFFDKVVYEIHD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +     G   +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  KKLQMELLPERL-RGETASFDIE--ANGTVYVEKGRRITARHIRQLEKDGVAQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V +D ++  TGEI + A   +    L ++  +  + I  L+ + +++ AYI  TL
Sbjct: 292  IIGKAVVKDYIDENTGEIIVPANMELTLDLLAKLSQAGHKRIETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT+++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D
Sbjct: 592  RRVQDGVVTDEIHYLSAIEEGNFVIAQANTNLGDDGSFVDDLVTCRSKGESSLFSRDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L  + P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLCTDKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI     ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 712  SGVTAVAKRGGTVQYVDASRIVINVNPDEMYPGEAGIDIYNLTKYIRSNQNTCISQTPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDSML+SER+V ED FT+I
Sbjct: 772  SLGEPVERGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSMLVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  I +  +++R+ ++L                 + ++ + +  R +W 
Sbjct: 952  QLKQAKKDLTEELQIFEAGLFARIRDVLISGG-------------IEAEKLDKLTRERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELGLADEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGVPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++  ++    +         +         ++ + D+ VLR+AE  K 
Sbjct: 1119 MAAKGIGDKINAMLKQHEEVAKLREFIQKAYNLGDDVRQKVDLNTFSDEEVLRLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGAKEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGNHMMEPGMPESFNVLLKEIRSLGINIELEED 1342


>gi|295677940|ref|YP_003606464.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. CCGE1002]
 gi|295437783|gb|ADG16953.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. CCGE1002]
          Length = 1368

 Score = 1650 bits (4272), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1374 (50%), Positives = 967/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  + +  +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTSSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++++G+TGE+   A D I E  LE++  ++I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVIDGDTGEVIANANDEITESVLEKLREAKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++ +DG+ T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVADGKVTDQIDYLSAIEEGRYVIAQANAAVADDGTLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLEGKVANGGPKKLAKGTKIERAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I+ LR FL K+       E++  + DD +L +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIAELREFLIKIYNESGRAEELDSFSDDEILELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++  L +A  DE            Q  L+DG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLAFPDEIAQNLGMTPSKNQVRLFDGRTGEMFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|187930381|ref|YP_001900868.1| DNA-directed RNA polymerase subunit beta [Ralstonia pickettii 12J]
 gi|226699434|sp|B2UEN6|RPOB_RALPJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|187727271|gb|ACD28436.1| DNA-directed RNA polymerase, beta subunit [Ralstonia pickettii 12J]
          Length = 1368

 Score = 1649 bits (4270), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1377 (51%), Positives = 965/1377 (70%), Gaps = 22/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL  N    +R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQENAPVAQRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61   FPIVSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKT 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGALMEFVPERL-RGEVARFDISD-KNGKVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D + E  LE++  + +++I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKEIQTLYTNDLDQGPYMSATL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD   D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDDTADQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEDSYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +      +  EDI+  IK+LV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  SSGTGPMVLTDEDILDTIKLLVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEVTHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNDYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV +GK+T+ V YLSA+EE    +AQAN++LD+DG+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENGKLTDQVDYLSAIEEGKYVVAQANATLDKDGNLIDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGVERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDANRVVIRVNDAEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDVVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD++VGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVMVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVVRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 956  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKIANGGPKKLAKGTALTKEYLADLDKWH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++V   +E++KV  E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPAEDEVALQLEAVKVAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  +L +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEIRKLLGQIYNESGKVEDLDSLSDAEILELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPV 1249
            K GVP +TPVFDGA E+ I  ML +A   E      G      Q  L+DG TGE F+RPV
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLA-YPEDIAKEKGLTASKQQVTLFDGRTGEAFERPV 1251

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            T+G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y
Sbjct: 1252 TLGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASY 1311

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1312 VLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLERN 1368


>gi|285017313|ref|YP_003375024.1| DNA-directed RNA polymerase, beta subunit protein [Xanthomonas
            albilineans GPE PC73]
 gi|283472531|emb|CBA15036.1| probable dna-directed rna polymerase, beta subunit protein
            [Xanthomonas albilineans]
          Length = 1383

 Score = 1649 bits (4270), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 967/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  N  P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQENTDPNKRSDHGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGDPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTDNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+LS F+    +     
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLSEFFEINTFHIDPK 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                    A+ + G  +   L D D  + ++E+GK++T+  +K L+  G+  L +  + L
Sbjct: 241  EGVQLELVAERLRGETLDFDLADGD--KVIVEAGKRITARHVKQLEASGIAALAVPDEYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+  TGE+   A D I E+ L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDAATGELLANANDEITEEQLNAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKDAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +                          +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  EVIGESVLYDKKYFGERSDEESKRLVAERADSSDILDVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTTETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DG++T++V YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVVDGQITDEVEYLSAIEENEYVIAQANALHDAKNRLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERAVARDSGVTVNARRGGVIEQIDAGRIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDAIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   L G+ A  GP 
Sbjct: 959  DVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILESAIYARLRSQLIGKVANGGP- 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   +S   +    +S+W+   ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDTISDAYLDGLKKSEWFALRMKDEDASDAIERAQKQIQAHEQEFERRFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS I P EDMP++ +G  VDI
Sbjct: 1078 TAGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSMIQPIEDMPYMANGETVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-- 1178
            VLNPLGVPSRMN+GQ+ E HLGWA  GLG+KI+++++       ++ LR FL ++     
Sbjct: 1138 VLNPLGVPSRMNIGQVLEVHLGWAAKGLGRKIQNMLDAQAN---VADLRKFLTQIYNHDQ 1194

Query: 1179 --GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G     +  + D  +L +++    GVP++TPVFDGA E  I  ML +ADL  SGQ+ L
Sbjct: 1195 KLGEDRVDLDQFSDAELLSLSKNLTDGVPMATPVFDGATEAEIKHMLELADLPISGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++MLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRRTTVGYMHMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE+
Sbjct: 1375 LAINMELED 1383


>gi|253701929|ref|YP_003023118.1| DNA-directed RNA polymerase subunit beta [Geobacter sp. M21]
 gi|259494184|sp|C6E4R4|RPOB_GEOSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|251776779|gb|ACT19360.1| DNA-directed RNA polymerase, beta subunit [Geobacter sp. M21]
          Length = 1371

 Score = 1649 bits (4270), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1364 (52%), Positives = 992/1364 (72%), Gaps = 10/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +IIDIP+LI++QK SY  FL ++   D R N GL+A F+SVFPI  FS  A
Sbjct: 11   LRKNFAKIHKIIDIPNLIDIQKNSYKRFLQLDTPVDARKNSGLEAVFRSVFPIRDFSDTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV +  G +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGAPKYDVEECHQRGMTFAAPMKVKVRLVVWDVAKDPGTRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT +GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTDNGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  ++ +++ FY         +     ++ A
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGYSNDALINYFYKSEDVKVGDNGSMTKIADA 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+   K ++ +VD  TGE ++++ +K T   ++ + E G+K + I+ + + G   + DI
Sbjct: 251  ELLSNQKATADIVDPATGEVILKANRKFTKAAIRKMSEHGIKEIPISEEEVVGKVASHDI 310

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +  TGEI +E  + + +  LEEI    I    +L++D+++  +  R+T++ DK     +
Sbjct: 311  YDPATGEIIVECNEELTQAKLEEIIQKGITTFQVLFIDNLHVTSSFRDTILIDKIGSTDE 370

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A  +F  LFF++++YDLS VGR+K+N +L +D P D   + 
Sbjct: 371  ALIEIYRRLRPGDPPTLKSALVLFENLFFNAERYDLSAVGRLKLNYKLGVDVPLDCMTLT 430

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +EDI+ +++ L++L+NGKG IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 431  REDILEVVRYLIELKNGKGNIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 490

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 491  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 550

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +G+VT+
Sbjct: 551  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVKEGRVTD 610

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +DE G F  + +  R +GE +LV R++++ +D +P Q+V
Sbjct: 611  EVRFFSALEEEGHAIAQANAEIDETGRFAADYISARKSGEFVLVGRDELELMDVAPMQLV 670

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A++P VGTGME VVA+ SG ++VA+  
Sbjct: 671  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADSPLVGTGMERVVARDSGVSLVARHN 730

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E   D + +GVDIY L+KF RSNQNTC+NQRPLVKVGD V   D
Sbjct: 731  GVVESVDASRIVVKIDEDQYDATGTGVDIYNLIKFARSNQNTCINQRPLVKVGDHVTAGD 790

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGPSTD+G+LALG+N+L+AFMPW GYN+EDS+LISER+V +D +TSIHIEEFE +AR
Sbjct: 791  IIADGPSTDMGELALGQNVLIAFMPWGGYNYEDSILISERLVKDDRYTSIHIEEFEAVAR 850

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 851  DTKLGKEEITSDIPNLGEETLKDLDESGIIRIGAEVRPGDILVGKITPKGETQLSPEEKL 910

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +E+ +   L +D+ 
Sbjct: 911  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDARTEIIEKAEEMRLRKDEQ 970

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKG------FKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++L G+ A    +G        K   ++ +++  +   +W + ++
Sbjct: 971  DEIRIIRDSAIGKLKKLLVGKTAAVKIEGTDGKVLIPKGAAITEEMLKSFSMDRWDEISI 1030

Query: 1027 QDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D+  V   V            I++  F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1031 ADDDTVDEKVAQTLSTLNQQIDIIKYVFDDKVQKLRRGDDLPPGVIKMVKVYIAIKRKLQ 1090

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+++DG PV+IVLNPLGVPSRMNVGQI E HLGWA 
Sbjct: 1091 VGDKMAGRHGNKGVVSRILPEEDMPYMEDGRPVEIVLNPLGVPSRMNVGQILEMHLGWAA 1150

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG KI+  ++    + +I   + FL+           +   + + +L VA++ K GVP
Sbjct: 1151 KGLGWKIEEFLDKNAPHDEI---KRFLKGAYNNPDMDRFLDKLEGEELLNVAKRLKRGVP 1207

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +S+PVF+GA EE+I SML  A    +GQ  L+DG +G+ F   VTVG +Y LKL+H+V D
Sbjct: 1208 MSSPVFEGASEESIQSMLSHAGFSTTGQVTLFDGKSGDKFMHQVTVGIMYFLKLHHLVDD 1267

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1268 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1327

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+LGL ++L      
Sbjct: 1328 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLGLDVELLEGDED 1371


>gi|209520982|ref|ZP_03269718.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. H160]
 gi|209498584|gb|EDZ98703.1| DNA-directed RNA polymerase, beta subunit [Burkholderia sp. H160]
          Length = 1368

 Score = 1649 bits (4270), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1374 (50%), Positives = 967/1374 (70%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  + +  +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTSSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMP 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  +++  K++ +  ++ L     KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRINAKHIRDLDNAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++++G+TGE+   A D I E  LE++  ++I+DI  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVIDGDTGEVIANANDEITESVLEKLREAKIKDIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R+  
Sbjct: 358  RIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN+++ +DG+ T+ELV  R AGE ++V  ++I 
Sbjct: 598  RKVADGKVTDQIDYLSAIEEGRYVIAQANAAVGDDGTLTDELVSSREAGETLMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  KMGDKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLEGKVANGGPKKLAKGTKIERAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADEEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++   +    I+ LR FL K+       E++  + DD ++ +A+  + 
Sbjct: 1138 WAAKGLGWRIGEML---QRQAKIAELREFLTKIYNESGRAEELESFSDDEIIELAKNLRE 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGA EE ++  L +A  DE            Q  L+DG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGATEEEMSRALDLAFPDEIAQNLGMTPSKNQVRLFDGRTGEMFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 EMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368


>gi|66769649|ref|YP_244411.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            campestris str. 8004]
 gi|81304396|sp|Q4URD2|RPOB_XANC8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|66574981|gb|AAY50391.1| RNA polymerase beta subunit [Xanthomonas campestris pv. campestris
            str. 8004]
          Length = 1387

 Score = 1648 bits (4268), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1389 (50%), Positives = 973/1389 (70%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 67   PISSYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 185  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 245  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 303  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 363  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNHRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 423  EVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LS+  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 543  LSRFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 603  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A+R G++EQ+DA RIV++  E      + +GVD
Sbjct: 723  PTLRSQKPLVGTGIERAVARDSGVTVNARRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 963  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1021

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++D+     +E  + Q +  +   E RF +K  KI
Sbjct: 1022 NLKKGDNVTDAYLDGLKKSDWFQLRMKDDDAADAIERAQKQIQAHEKEFEARFADKRGKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1082 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    S
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQTAVSELRKFLDDIYNHDS 1198

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1199 AINAERVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1379 LAINMELEE 1387


>gi|262273339|ref|ZP_06051154.1| DNA-directed RNA polymerase beta subunit [Grimontia hollisae CIP
            101886]
 gi|262222712|gb|EEY74022.1| DNA-directed RNA polymerase beta subunit [Grimontia hollisae CIP
            101886]
          Length = 1341

 Score = 1648 bits (4268), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1366 (52%), Positives = 971/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++VRIDRRRK+P +  L AL   +E+IL  F+ K+V+  +G
Sbjct: 175  RIIPYRGSWLDFEFDPKDLLYVRIDRRRKLPASIILRALEYTTEQILDLFFEKVVFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ G+K + +  + 
Sbjct: 235  KSLVMELVP-DRLRGETASFDIE--ADGKVYVEQGRRITARHIRQLEKDGIKQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A D +N ETGEI   A   +  ++L  +  +  + I  L+ + +++  Y+ +TL
Sbjct: 292  IVGKVAARDYINEETGEIIAAANQELSLETLAYLSQAGHKKIETLFTNDLDHGPYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RIDSTTDRLTALVEIYRMMRPGEPPTREAAEQLFESLFFSEDRYDLSAVGRMKFNSSLGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DII +++ L+D+RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEMTGSGVLSHDDIIEVMRKLIDIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAFARTNPYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+++ YLSA+EE    IAQAN+ L+EDGSF +EL+  R  GE  L PR+ + 
Sbjct: 592  RKVVDGKVTDEIDYLSAIEEGQFVIAQANAVLNEDGSFADELITARQKGESGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V+R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MPGEPVQRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCVARDTKLGSEEITADIPNVGEAALSKLDESGVVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S D ++   R    
Sbjct: 952  QLKEAKKDLTEEFSILEGGLVARVRGVLAQAG-------------YSEDKLANMDRQTML 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F  K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SQTLDDEALQTQLEQLAEQYDELKADFDKKFDTKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEHGEPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++  R FL+KV   G       IS   DD V  + E  
Sbjct: 1119 LAAKGIGNKINKMI---KEQQELAKFREFLQKVYDLGDTRQKVDISALTDDEVRTLIENL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E AI  +L++ DL ESGQ  L+DG TGE F+RPVTVGY+YMLKLN
Sbjct: 1176 RDGLPIATPVFDGAPEPAIKELLKLGDLPESGQLTLFDGRTGEKFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|148263134|ref|YP_001229840.1| DNA-directed RNA polymerase subunit beta [Geobacter uraniireducens
            Rf4]
 gi|189043857|sp|A5GAY1|RPOB_GEOUR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146396634|gb|ABQ25267.1| DNA-directed RNA polymerase subunit beta [Geobacter uraniireducens
            Rf4]
          Length = 1370

 Score = 1648 bits (4268), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1364 (52%), Positives = 1003/1364 (73%), Gaps = 11/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +II+IP+LI++QK SY  FL +++  + R   GL+A FKSVFPI  FS  A
Sbjct: 11   LRKNFAKIKKIIEIPNLIDIQKNSYKRFLQLDVPAEARKYSGLEAVFKSVFPIKDFSETA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV++    +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGIPKYDVEECHQRGMTFAAPMKVKVRLVVWDVNKEPSTRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  ++++L+ FY        GD     ++  
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGYSTDKLLNFFYKSEEIFFEGDKL-MKIADP 249

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+   K    +VD +TGE ++++ +K T   ++ + E G+K++ IT + + G   + DI
Sbjct: 250  ELLTNQKAVVDIVDPNTGEVLVKANRKFTKAAIRKMAEHGIKYIPITIEEVLGKVASHDI 309

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+  TGE+  E  + + +  ++EI    I    +L++D+++  + +R+T++ DK     D
Sbjct: 310  VDPATGEVLAECNEELTQVKIDEIKGRGIATFKVLFIDNLHVTSSLRDTILIDKIGSTDD 369

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A ++F  LFF+ ++YDLS VGR+K+N +L L  P D   + 
Sbjct: 370  ALIEIYRRLRPGDPPTLKSALALFENLFFNPERYDLSAVGRLKLNYKLGLQIPLDCMTLT 429

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +ED++ +++ L+DL+NGKG+IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 430  REDVLEVVRYLIDLKNGKGSIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 489

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 490  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 549

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +GKVT 
Sbjct: 550  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRLVKEGKVTT 609

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +D DG F  + +  R +GE +LV R++++ +D +P Q+V
Sbjct: 610  EVRFFSALEEEGHAIAQANAEVDSDGRFVADYISARKSGEFVLVGRDELELMDVAPMQLV 669

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A++P VGTGME VVA+ SG ++VA+  
Sbjct: 670  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADSPLVGTGMERVVARDSGVSVVARHN 729

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E + D + +GVDIY L+KF RSNQNTC+NQRP+VK+GD V+R+D
Sbjct: 730  GVVESVDASRIVVKIDEDEYDETGTGVDIYNLIKFARSNQNTCINQRPVVKIGDHVKRSD 789

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGPSTD+G+LALG+N+LVAFMPW GYNFEDS+LISER+V +D +TSIHIEEFE +AR
Sbjct: 790  VIADGPSTDMGELALGQNVLVAFMPWGGYNFEDSILISERLVKDDRYTSIHIEEFECVAR 849

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDIL+GKITPKGE+ ++PEEKL
Sbjct: 850  DTKLGKEEITADIPNLGEETLKDLDESGIIRIGAEVRPGDILIGKITPKGETQLSPEEKL 909

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +E+ + + L +D+ 
Sbjct: 910  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDARTELIEKAEEQKLRKDEQ 969

Query: 973  DEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++L G+ A        G     K   ++ + +   P  +W + ++
Sbjct: 970  DEIRIIRESAVGKLKKLLVGKTAAVKFEGKDGKVLIVKGKAITEEALLSVPVDRWDEISI 1029

Query: 1027 QDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D+  V   V  +         I++  F +KI+K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1030 ADDDTVDEKVAQILGTLNQQIDIIKYVFDDKIQKLKRGDDLPPGVIKMVKVYIAIKRKLQ 1089

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+L+DG PV+IVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1090 VGDKMAGRHGNKGVVSRILPEEDMPYLEDGRPVEIVLNPLGVPSRMNVGQILETHLGWAA 1149

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G +I+ ++        I   +++L++V G     + +   +++ +  VA++ K GVP
Sbjct: 1150 KGIGWQIEDMLEKNSPQNQI---KTYLKEVYGNKEMNKFLDSLEEEELNNVAKRLKRGVP 1206

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+GA E+ I  ML  A  + +GQ  LYDG +G  F   VTVG +Y+LKL+H+V D
Sbjct: 1207 MASPVFEGASEQGIQEMLGKAGFEYTGQVTLYDGKSGVAFKHKVTVGIMYVLKLHHLVDD 1266

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1267 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1326

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+LGL ++L  +  +
Sbjct: 1327 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLGLDVELLENEEE 1370


>gi|238025924|ref|YP_002910155.1| DNA-directed RNA polymerase subunit beta [Burkholderia glumae BGR1]
 gi|237875118|gb|ACR27451.1| DNA-directed RNA polymerase, beta subunit [Burkholderia glumae BGR1]
          Length = 1369

 Score = 1648 bits (4268), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1375 (51%), Positives = 966/1375 (70%), Gaps = 17/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL   ++  +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQAEVSAAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  L+++  ++I+DI  +Y + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITESVLDKLREAKIKDIQTIYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETADKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS IT  RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITLKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-DGSFTEELVFCRCAGEEILVPREKI 661
            RKV DGKVT+ + YLSA+EE    IAQAN+S+DE  G  T+ELV  R AGE ++V  ++I
Sbjct: 598  RKVTDGKVTDQIDYLSAIEEGRYVIAQANASVDEATGELTDELVSAREAGETMMVTPDRI 657

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A 
Sbjct: 658  QYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAV 717

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A+R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 718  DSGTTVQAERGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPI 777

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 778  VKMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTS 837

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPK
Sbjct: 838  IHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPK 897

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  
Sbjct: 898  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIVRDKRAQQIID 957

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    +S+     W
Sbjct: 958  DELKRYRLDLNDQLRIVEGDAFQRLARMLDGKVANGGPKKLAKGTQIDQAYLSDLDHYHW 1017

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+K
Sbjct: 1018 FDIRLADEEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVK 1077

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HL
Sbjct: 1078 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHL 1137

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG +I  ++   +    I  LR FL K+       E +  + DD +L +A   +
Sbjct: 1138 GWAAKGLGWRIGEML---QRQAKIEELRVFLTKIYNESGRAEDLDSFSDDEILELARNLR 1194

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE ++ ML +A  DE            Q  LYDG TGE F+R VTV
Sbjct: 1195 EGVPFATPVFDGATEEEMSKMLDLAFPDEIAQQLGMTPSKNQVRLYDGRTGEAFERTVTV 1254

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1255 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1314

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1315 QEMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1369


>gi|21241730|ref|NP_641312.1| DNA-directed RNA polymerase subunit beta [Xanthomonas axonopodis pv.
            citri str. 306]
 gi|41018077|sp|Q8PNT0|RPOB_XANAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21107099|gb|AAM35848.1| RNA polymerase beta subunit [Xanthomonas axonopodis pv. citri str.
            306]
          Length = 1383

 Score = 1648 bits (4267), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1389 (50%), Positives = 968/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I+E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEINEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDTVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL  +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLNDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|33599007|ref|NP_886567.1| DNA-directed RNA polymerase subunit beta [Bordetella bronchiseptica
            RB50]
 gi|33575053|emb|CAE30516.1| DNA-directed RNA polymerase beta chain [Bordetella bronchiseptica
            RB50]
          Length = 1378

 Score = 1647 bits (4266), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1375 (50%), Positives = 958/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + A  +R NEGLQAAF S+
Sbjct: 9    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTATSDRVNEGLQAAFSSI 68

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 69   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 126

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 127  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 186

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 187  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 246

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       A     G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 247  EGGMMEFVAE-RWKGEMARFDIAD-RDGKVIVEKDKRINAKHLRDLAAGGIQRVSVPEDF 304

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 305  LYGRVLAKNIVDPDTGEVVAHANDEITESVLNAMRAANVRDIQTLYTNDLDRGPYISQTL 364

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 365  RADETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 424

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 425  GDDSTGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 484

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 485  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 544

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 545  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 604

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE +  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 605  YRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDDEGRFVDDLVACREAGETMLTAPGNV 664

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 665  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 724

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 725  DSGTTVQALRGGVVDHVDADRVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 784

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 785  VARGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 844

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV+  D+LVGK+TPK
Sbjct: 845  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVSADDVLVGKVTPK 904

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 905  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 964

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   L+   +++  R QW
Sbjct: 965  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKAVNGGPRKLAKGATLTKAYLADLDRWQW 1024

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1025 FDIRLADEQHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1084

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1085 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1144

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +       +R +LEKV  T   +  I    D+ VL +A   K
Sbjct: 1145 GWAAKGVGYRIADMLRDERT-AQAKSVRGYLEKVYNTTGSSAHIDSLTDEEVLELANNLK 1203

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE I  ML +A  D             Q+ LYDG TGE F+RPVT+
Sbjct: 1204 KGVPFATPVFDGATEEEIGKMLELAYPDDVAARMRLTASRSQAWLYDGRTGEQFERPVTI 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1264 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1324 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1378


>gi|322418357|ref|YP_004197580.1| DNA-directed RNA polymerase subunit beta [Geobacter sp. M18]
 gi|320124744|gb|ADW12304.1| DNA-directed RNA polymerase, beta subunit [Geobacter sp. M18]
          Length = 1371

 Score = 1647 bits (4266), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1364 (52%), Positives = 993/1364 (72%), Gaps = 10/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +IIDIP+LI++QK SY  FL ++   D R N GL+A F+SVFPI  FS  A
Sbjct: 11   LRKNFAKIHKIIDIPNLIDIQKNSYKRFLQLDTPVDARKNSGLEAVFRSVFPIRDFSDTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV +  G +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGAPKYDVEECHQRGMTFAAPMKVKVRLVVWDVSKDPGTRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT +GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTDNGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  ++ +++ FY        G+     L  A
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGYSNDALINYFYKSEEVKVGGNGAMTKLVDA 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+   K ++ +VD  T E ++++ +K T   L+ + E G+K + I  + + G   + DI
Sbjct: 251  ELLSSQKATADIVDPGTAEVILKANRKFTKAALRKMAEHGIKEIPIAEEEVVGKVASHDI 310

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +  TGEI +E  + I    LEE+    I    +L++D+++  +  R+T++ DK     +
Sbjct: 311  YDPATGEILVECNEEITPAKLEEMIQKGITSFQVLFIDNLHVTSSFRDTILIDKIGSTDE 370

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A  +F  LFF++++YDLS VGR+K+N +L +D P D   + 
Sbjct: 371  ALIEIYRRLRPGDPPTLKSALVLFENLFFNAERYDLSAVGRLKLNYKLGVDVPLDCMTLT 430

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +EDI+ +++ L++L+NGKG IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 431  REDILEVVRYLIELKNGKGNIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 490

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 491  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 550

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +GKVT+
Sbjct: 551  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVKEGKVTD 610

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +DE G F  + +  R +GE +LV R++++ +D +P Q+V
Sbjct: 611  EVRFFSALEEEGHAIAQANAEMDETGRFMADYISARKSGEFVLVGRDELELMDVAPMQLV 670

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A++P VGTGME VVA+ SG + VA+  
Sbjct: 671  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADSPLVGTGMERVVARDSGVSSVARHN 730

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E   D + +GVDIY L+KF RSNQNTC+NQRP+VKVGD V+  D
Sbjct: 731  GVVESVDASRIVVKIDEDQYDATGTGVDIYNLIKFARSNQNTCINQRPVVKVGDHVKAGD 790

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGPSTD+G+LALG+N+LVAFMPW GYN+EDS+LISER+V +D +TSIHIEEFE +AR
Sbjct: 791  IIADGPSTDMGELALGQNVLVAFMPWGGYNYEDSILISERLVKDDRYTSIHIEEFEAVAR 850

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 851  DTKLGKEEITSDIPNLGEETLKDLDESGIIRIGAEVRPGDILVGKITPKGETQLSPEEKL 910

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +E+ + + L +D+ 
Sbjct: 911  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDARTEIIEKAEEQRLRKDEQ 970

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKG------FKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++L G+ A    +G        K   ++ +++  +   +W + ++
Sbjct: 971  DEIRIIRDSAIGKLKKLLVGKTAAVKIEGTDGKVLIPKGAAITEEMLKSFSMDRWDEISI 1030

Query: 1027 QDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D+  V   V            I++  F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1031 ADDDTVDEKVAQTLATLNQQIDIIKYVFDDKVQKLRRGDDLPPGVIKMVKVYIAIKRKLQ 1090

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+++DG PV+IVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1091 VGDKMAGRHGNKGVVSRILPEEDMPYMEDGRPVEIVLNPLGVPSRMNVGQILETHLGWAA 1150

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG KI+  +     + +I   + FL+           I   + + ++ VA++ K GVP
Sbjct: 1151 RGLGWKIEEFLEKNSPHDEI---KRFLKGTYHDPDMHRFIDKLEGEELINVAKRLKRGVP 1207

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+GA EE+I +M++ A  + +GQ  LYDG +G+ F   VTVG +Y+LKL+H+V D
Sbjct: 1208 MASPVFEGASEESIQAMMKQAGFETTGQVTLYDGKSGDKFMHKVTVGIMYVLKLHHLVDD 1267

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1268 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1327

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+LGL ++L      
Sbjct: 1328 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLGLDVELLEGDED 1371


>gi|158518624|sp|Q7WRD9|RPOB_BORBR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1370

 Score = 1647 bits (4265), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1375 (50%), Positives = 958/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + A  +R NEGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTATSDRVNEGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 61   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       A     G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGGMMEFVAE-RWKGEMARFDIAD-RDGKVIVEKDKRINAKHLRDLAAGGIQRVSVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDPDTGEVVAHANDEITESVLNAMRAANVRDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RADETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GDDSTGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE +  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDDEGRFVDDLVACREAGETMLTAPGNV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGVVDHVDADRVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 777  VARGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV+  D+LVGK+TPK
Sbjct: 837  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   L+   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKAVNGGPRKLAKGATLTKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEQHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +       +R +LEKV  T   +  I    D+ VL +A   K
Sbjct: 1137 GWAAKGVGYRIADMLRDERT-AQAKSVRGYLEKVYNTTGSSAHIDSLTDEEVLELANNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE I  ML +A  D             Q+ LYDG TGE F+RPVT+
Sbjct: 1196 KGVPFATPVFDGATEEEIGKMLELAYPDDVAARMRLTASRSQAWLYDGRTGEQFERPVTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|94312265|ref|YP_585475.1| DNA-directed RNA polymerase subunit beta [Cupriavidus metallidurans
            CH34]
 gi|158564201|sp|Q1LI20|RPOB_RALME RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|93356117|gb|ABF10206.1| RNA polymerase, beta subunit [Cupriavidus metallidurans CH34]
          Length = 1368

 Score = 1647 bits (4265), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1375 (50%), Positives = 955/1375 (69%), Gaps = 20/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL     P  R +EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIESYTQFLQAETPPARRKSEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +       +
Sbjct: 61   FPISSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPG---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLQS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      +VD   G  V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGAQLEFVPERL-RGEVARFDIVD-KNGRVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++I++ +TGE+   A D + E  LE +  + ++DI  LY + ++   YI  TL
Sbjct: 296  LLGRVLAKNIIDPDTGEVIANANDELTETLLENLREAGVKDIQTLYTNDLDQGPYISQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL+ 
Sbjct: 356  RADDTADQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYSEESYDLSRVGRMKVNSRLSR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             + +    ++ EDI+  IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PSGEGSMVLQDEDILETIKILVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T+ V YLSA+EE    +AQAN+++D +G+  +ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDQVDYLSAIEEGKYVVAQANATVDAEGNLIDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRPDKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA+R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQATRGGVVDYVDAMRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SG V+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGIVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + RL  +L  +    GPK   K   L+ + +++  +  
Sbjct: 956  DDELKRYRLDLNDQLRIVEGDAFQRLERMLLDKTVNGGPKKLAKGAKLTREYLADLDKYH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPADEEVAAQLEAVKEAIEQKRHEFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I  ++   KA+     LR  L ++       E +    D  VL +A   
Sbjct: 1136 LGWAARGLGQRIGDML---KASAKAQELRPLLAQIYNESGKAEDLDSLSDAEVLELAGNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E  I  ML +A  D    E G      Q  L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEAEIRRMLDLAYPDDIAKERGLTASKQQVTLHDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDL+ 
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLDR 1367


>gi|33591288|ref|NP_878932.1| DNA-directed RNA polymerase subunit beta [Bordetella pertussis Tohama
            I]
 gi|41017676|sp|Q7W0R9|RPOB_BORPE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|33570930|emb|CAE40394.1| DNA-directed RNA polymerase beta chain [Bordetella pertussis Tohama
            I]
          Length = 1370

 Score = 1647 bits (4265), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1375 (50%), Positives = 958/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + A  +R NEGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTATSDRVNEGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 61   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       A     G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGGMMEFVAE-RWKGEMARFDIAD-RDGKVIVEKDKRINAKHLRDLAAGGIQRVSVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDPDTGEVVAHANDEITESVLNAMRAANVRDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RADETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GDDSTGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE +  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDDEGRFVDDLVACREAGETMLTAPGNV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGVVDHVDADRVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 777  VARGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV+  D+LVGK+TPK
Sbjct: 837  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   L+   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKTVNGGPRKLAKGATLTKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEQHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +       +R +LEKV  T   +  I    D+ VL +A   K
Sbjct: 1137 GWAAKGVGYRIADMLRDERT-AQAKSVRGYLEKVYNTTGSSAHIDSLTDEEVLELANNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE I  ML +A  D             Q+ LYDG TGE F+RPVT+
Sbjct: 1196 KGVPFATPVFDGATEEEIGKMLELAYPDDVAARMRLTASRSQAWLYDGRTGEQFERPVTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|182676590|sp|A6T3L3|RPOB_JANMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1368

 Score = 1647 bits (4265), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1374 (50%), Positives = 955/1374 (69%), Gaps = 16/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+  Q  SY  FL  +  P +R NEGLQ+AF S+
Sbjct: 1    MHYSFTEKKRIRKSFAKRANVHNVPFLLATQLESYHGFLQEDKIPSQRKNEGLQSAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF+SY    P F++ +C  R LTYA PL+  +RL++ D +  T    +
Sbjct: 61   FPIVSHNGFARLEFLSYVLGDPPFNIKECQQRGLTYASPLRAKVRLVILDKESPT-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEMKEQEVYMGELPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  R+DRRRK+PVT  L A+GM  E+IL  F+    ++   
Sbjct: 180  RIIPYRGSWLDYEFDPKDILFFRVDRRRKMPVTILLKAIGMTPEQILENFFVFDDFALHA 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D       A  L  G      + D   G+ ++   K++ S  ++ ++  G+K + +  D 
Sbjct: 240  DGAEMAFVAERL-RGEVARFDITD-KAGKVLVAKDKRINSKHVRDVEAAGIKNISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ ETGE+   A D + E  L  +   ++  I  LY + ++   YI  TL
Sbjct: 298  LLGRILAKNIVDKETGEVIANANDELTEDLLARLREGKVTHIQTLYTNDLDQGGYISQTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  A + IYR+MRPG+  T    E++FN LF+++D+YDLS VGR+K N R+  
Sbjct: 358  RMDDTTDQMAAKVAIYRMMRPGEPPTEDSVEALFNGLFYNADRYDLSAVGRMKFNRRIGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +D++A+IKILV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DELTGDMTLSNDDVLAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV   K+T+ + YLSA+EE    IAQAN+++D+ G+ ++ELV  R AGE ILV  E++ 
Sbjct: 598  RKVEGSKITDQIDYLSAIEEGRYIIAQANATIDKSGALSDELVSAREAGETILVSPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E  FVGTG+E  VA  
Sbjct: 658  YMDVAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKAFVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R GIV+ +DA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGIVDYIDAGRVVIRVNDDEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD V ++D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 778  QVGDRVAKHDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD LVGK+TPKG
Sbjct: 838  HIEELSVVARDTKLGAEEITRDISNLAENQLARLDESGIVYIGAEVTAGDTLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIPRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+    GPK   K   ++ + + +  +  W+
Sbjct: 958  ELQRYRLDLNDQLRIVEGDAFQRLEKMLIGKVVNGGPKKIAKGAKITKEYLDDLDKYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 D+     +E++K      +   +  F+ K +K+  GD++PPGV ++VKV++A+KR
Sbjct: 1018 DIRPADDTSANALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRILP EDMP + DGTP D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADVVLNPLGVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++N   A   I+ LR FL  +      TE +  + D  +L +A   K+
Sbjct: 1138 WAAKGLGLRIGEMLN---AQVQIAELRKFLAAIYNESGKTEDLDSFSDAEILELAGNLKN 1194

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVG 1252
            GVP +TPVFDGADE     ML +A  D   +            +YDG TGE F+R VTVG
Sbjct: 1195 GVPFATPVFDGADEGETRRMLDLAYPDHIAKQLGMTASKNQVTMYDGRTGEAFERTVTVG 1254

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1255 YMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1314

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE  
Sbjct: 1315 EMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERD 1368


>gi|325921474|ref|ZP_08183329.1| DNA-directed RNA polymerase subunit beta [Xanthomonas gardneri ATCC
            19865]
 gi|325548021|gb|EGD19020.1| DNA-directed RNA polymerase subunit beta [Xanthomonas gardneri ATCC
            19865]
          Length = 1383

 Score = 1647 bits (4264), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1389 (50%), Positives = 968/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++  ++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEQNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTDNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                ++ D+V+  TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VTRILSHDVVDSSTGELLANANDEITEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      ++K+L ++RNG+G +DDID+LGN
Sbjct: 419  EVLGESVLYDKKYFAERNDEESKRLVAEHTDTSDILEVLKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDNVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    S
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLDDIYNHDS 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|330815232|ref|YP_004358937.1| DNA-directed RNA polymerase, beta subunit [Burkholderia gladioli
            BSR3]
 gi|327367625|gb|AEA58981.1| DNA-directed RNA polymerase, beta subunit [Burkholderia gladioli
            BSR3]
          Length = 1369

 Score = 1646 bits (4263), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1376 (50%), Positives = 963/1376 (69%), Gaps = 19/1376 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL   ++  +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQAEVSAAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PV+  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVSILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDISD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  L+++  ++I++I  +Y + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITESVLDKLRDAKIKEIQTIYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETADKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEIVGPMTLLDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCRCAGEEILVPREKI 661
            RKV D KVT+ + YLSA+EE    IAQAN+S+DE+ G  T+ELV  R AGE ++V  ++I
Sbjct: 598  RKVTDSKVTDQIDYLSAIEEGRYVIAQANASVDENTGELTDELVSAREAGETMMVTPDRI 657

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A 
Sbjct: 658  QYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAV 717

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 718  DSGTTVQAYRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPI 777

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE +V++D +TS
Sbjct: 778  VKMGDKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISENVVADDRYTS 837

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD++VGK+TPK
Sbjct: 838  IHIEELNVVARDTKLGPEEITRDISNLAEIQLGRLDESGIVYIGAEVEAGDVMVGKVTPK 897

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  
Sbjct: 898  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIVRDKRAQQIID 957

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    +S+     W
Sbjct: 958  DELKRYRLDLNDQLRIVEGDAFQRLARMLDGKVANGGPKKLAKGTKIDQAYLSDLDHYHW 1017

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+K
Sbjct: 1018 FDIRLADEEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVK 1077

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HL
Sbjct: 1078 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHL 1137

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  +
Sbjct: 1138 GWAAKGLGWRIGEML---ARQAKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLR 1194

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDES-----G------QSILYDGLTGEPFDRPVT 1250
             GVP +TPVFDGA EE ++ ML +A   +      G      Q  LYDG TGE F+R VT
Sbjct: 1195 EGVPFATPVFDGATEEEMSKMLDLA-FPDDIAQQLGMTPSKNQVRLYDGRTGEAFERTVT 1253

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1254 VGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1313

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 LQEMLTVKSDDVNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1369


>gi|190151057|ref|YP_001969582.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 7 str. AP76]
 gi|307264420|ref|ZP_07546006.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 13 str. N273]
 gi|189916188|gb|ACE62440.1| DNA-directed RNA polymerase beta chain [Actinobacillus
            pleuropneumoniae serovar 7 str. AP76]
 gi|306870236|gb|EFN01994.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 13 str. N273]
          Length = 1361

 Score = 1646 bits (4263), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1369 (51%), Positives = 976/1369 (71%), Gaps = 28/1369 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+
Sbjct: 18   LAMAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFR 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  
Sbjct: 74   SVFPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG-- 131

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY
Sbjct: 132  TVKDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLY 191

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  
Sbjct: 192  NARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEI 251

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            + +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  
Sbjct: 252  QDNKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDGITQIEVPV 308

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  
Sbjct: 309  EYIVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISE 368

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L
Sbjct: 369  TLRVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSL 428

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NL+       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+
Sbjct: 429  NLEEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLV 488

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 489  RVERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 548

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ET
Sbjct: 549  ISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLET 608

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPRE 659
            P+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E
Sbjct: 609  PFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPE 668

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +
Sbjct: 669  DIHYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPI 728

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ 
Sbjct: 729  ALDSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQI 788

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED F
Sbjct: 789  PCVNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRF 848

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+T
Sbjct: 849  TTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVT 908

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +
Sbjct: 909  PKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEI 968

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E  Q++   +D  +E  IL+  +++R+  +L                  S   + +  R 
Sbjct: 969  EEMQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVARE 1015

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +W +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A
Sbjct: 1016 KWLEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLA 1075

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            ++R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ET
Sbjct: 1076 VRRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILET 1135

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVA 1197
            HLG A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ VLR+A
Sbjct: 1136 HLGLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVLRLA 1192

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            E  + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YML
Sbjct: 1193 ENLRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYML 1252

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1253 KLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1312

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            KSDDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1313 KSDDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1361


>gi|78046547|ref|YP_362722.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            vesicatoria str. 85-10]
 gi|88909647|sp|Q3BWZ1|RPOB_XANC5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78034977|emb|CAJ22622.1| DNA directed RNA polymerase (beta subunit) [Xanthomonas campestris
            pv. vesicatoria str. 85-10]
          Length = 1383

 Score = 1646 bits (4262), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 967/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I+E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEINEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+ ALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVFALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDTVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL  +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLNDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|164686033|ref|ZP_01947509.2| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii 'MSU
            Goat Q177']
 gi|165918641|ref|ZP_02218727.1| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii RSA 334]
 gi|164601588|gb|EAX31867.2| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii 'MSU
            Goat Q177']
 gi|165917669|gb|EDR36273.1| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii RSA 334]
          Length = 1375

 Score = 1645 bits (4261), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 11   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 70

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 71   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 131  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 191  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 251  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 309  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 369  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 429  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 489  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 549  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 609  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 669  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 729  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 788

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 789  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 848

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 849  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 908

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R G+ K+ER++
Sbjct: 909  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGVKKDERTL 968

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 969  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1028

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1029 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1088

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1089 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1148

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1149 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1205

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1206 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1265

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1266 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1325

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1326 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1375


>gi|307253400|ref|ZP_07535271.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 6 str. Femo]
 gi|306859079|gb|EFM91121.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 6 str. Femo]
          Length = 1361

 Score = 1645 bits (4261), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1369 (51%), Positives = 976/1369 (71%), Gaps = 28/1369 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+
Sbjct: 18   LAMAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFR 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  
Sbjct: 74   SVFPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG-- 131

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY
Sbjct: 132  TVKDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLY 191

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  
Sbjct: 192  NARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEI 251

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            + +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  
Sbjct: 252  QDNKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDGITQIEVPV 308

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  
Sbjct: 309  EYIVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISE 368

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L
Sbjct: 369  TLRVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSL 428

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NL+       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+
Sbjct: 429  NLEEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLV 488

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 489  RVERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 548

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ET
Sbjct: 549  ISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLET 608

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPRE 659
            P+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E
Sbjct: 609  PFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPE 668

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +
Sbjct: 669  DIHYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPI 728

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ 
Sbjct: 729  ALDSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQI 788

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED F
Sbjct: 789  PCVNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRF 848

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+T
Sbjct: 849  TTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVT 908

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +
Sbjct: 909  PKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEI 968

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E  Q++   +D  +E  IL+  +++R+  +L                  S   + +  R 
Sbjct: 969  EEMQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVARE 1015

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +W +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A
Sbjct: 1016 KWLEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLA 1075

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            ++R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ET
Sbjct: 1076 VRRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILET 1135

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVA 1197
            HLG A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+A
Sbjct: 1136 HLGLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLA 1192

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            E  + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YML
Sbjct: 1193 ENLRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYML 1252

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1253 KLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1312

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            KSDDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1313 KSDDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1361


>gi|166710820|ref|ZP_02242027.1| DNA-directed RNA polymerase subunit beta [Xanthomonas oryzae pv.
            oryzicola BLS256]
          Length = 1383

 Score = 1645 bits (4261), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 967/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P +R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPTKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEISEDQLTAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLAAEHTDTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D      
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLA 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDSVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLDDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|224493270|sp|P0C8S4|RPOB_COXBU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1375

 Score = 1645 bits (4261), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 11   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 70

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 71   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 131  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 191  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 251  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 309  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 369  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 429  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 489  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 549  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 609  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 669  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 729  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 788

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 789  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 848

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 849  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 908

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R GI K+ER++
Sbjct: 909  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGIKKDERTL 968

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 969  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1028

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1029 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1088

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1089 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1148

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1149 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1205

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1206 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1265

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1266 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1325

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1326 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1375


>gi|212218065|ref|YP_002304852.1| DNA-directed RNA polymerase subunit beta [Coxiella burnetii
            CbuK_Q154]
 gi|212012327|gb|ACJ19707.1| DNA-directed RNA polymerase beta chain [Coxiella burnetii CbuK_Q154]
          Length = 1377

 Score = 1645 bits (4260), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 13   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 72

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 73   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 132

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 133  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 192

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 193  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 252

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 253  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 310

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 311  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 370

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 371  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 430

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 431  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 490

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 491  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 550

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 551  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 610

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 611  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 670

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 671  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 730

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 731  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 790

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 791  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 850

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 851  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 910

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R G+ K+ER++
Sbjct: 911  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGVKKDERTL 970

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 971  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1030

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1031 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1090

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1091 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1150

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1151 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1207

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1208 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1267

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1268 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1327

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1328 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1377


>gi|21230357|ref|NP_636274.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            campestris str. ATCC 33913]
 gi|41018075|sp|Q8PC56|RPOB_XANCP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21111911|gb|AAM40198.1| RNA polymerase beta subunit [Xanthomonas campestris pv. campestris
            str. ATCC 33913]
          Length = 1387

 Score = 1645 bits (4260), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1389 (50%), Positives = 972/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 67   PISSYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++ SQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YVKEQEVYLGEIPLMTENGTFIVNGTERVIFSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 185  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 245  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 303  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 363  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 423  EVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 543  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 603  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  EQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A+R G++EQ+DA RIV++  E      + +GVD
Sbjct: 723  PTLRSQKPLVGTGIERAVARDSGVTVNARRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 963  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1021

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++D+     +E  + Q +  +   E RF +K  KI
Sbjct: 1022 NLKKGDNVTDAYLDGLKKSDWFQLRMKDDDAADAIERAQKQIQAHEKEFEARFADKRGKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1082 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    S
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQTAVSELRKFLDDIYNHDS 1198

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1199 AINAERVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1379 LAINMELEE 1387


>gi|161831303|ref|YP_001596175.1| DNA-directed RNA polymerase subunit beta [Coxiella burnetii RSA 331]
 gi|182676561|sp|A9NAL4|RPOB_COXBR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|161763170|gb|ABX78812.1| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii RSA 331]
          Length = 1375

 Score = 1645 bits (4260), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 11   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 70

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 71   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 131  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 191  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 251  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 309  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 369  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 429  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 489  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 549  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++D  G   ++L+ CR  GE  L   
Sbjct: 609  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDGKGRLVDDLISCRYKGEFTLTTP 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 669  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 729  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 788

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 789  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 848

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 849  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 908

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R GI K+ER++
Sbjct: 909  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGIKKDERTL 968

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 969  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1028

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1029 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1088

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1089 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1148

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR+ L+ +          +   +D  ++ +
Sbjct: 1149 ETHLGWAAKGLGKKIGEMI---EKGADAKELRNSLKPIYDLSKTQRFDLEALEDPEIVTL 1205

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1206 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1265

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1266 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1325

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1326 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1375


>gi|215918919|ref|NP_819275.2| DNA-directed RNA polymerase subunit beta [Coxiella burnetii RSA 493]
 gi|206583804|gb|AAO89789.2| DNA-directed RNA polymerase beta chain [Coxiella burnetii RSA 493]
          Length = 1377

 Score = 1645 bits (4259), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 13   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 72

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 73   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 132

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 133  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 192

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 193  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 252

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 253  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 310

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 311  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 370

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 371  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 430

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 431  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 490

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 491  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 550

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 551  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 610

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 611  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 670

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 671  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 730

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 731  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 790

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 791  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 850

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 851  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 910

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R GI K+ER++
Sbjct: 911  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGIKKDERTL 970

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 971  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1030

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1031 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1090

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1091 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1150

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1151 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1207

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1208 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1267

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1268 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1327

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1328 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1377


>gi|224493307|sp|B6J270|RPOB_COXB2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|3660649|gb|AAC61666.1| RNA polymerase beta-subunit [Coxiella burnetii]
          Length = 1375

 Score = 1645 bits (4259), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 11   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 70

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 71   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 131  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 191  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 251  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 309  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 369  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 429  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 489  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 549  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 609  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 669  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 729  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 788

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 789  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 848

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 849  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 908

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R G+ K+ER++
Sbjct: 909  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGVKKDERTL 968

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 969  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1028

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1029 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1088

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1089 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1148

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1149 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVML 1205

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1206 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1265

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1266 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1325

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1326 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1375


>gi|307262218|ref|ZP_07543868.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 12 str. 1096]
 gi|306868092|gb|EFM99918.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 12 str. 1096]
          Length = 1361

 Score = 1645 bits (4259), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1369 (51%), Positives = 976/1369 (71%), Gaps = 28/1369 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+
Sbjct: 18   LAMAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFR 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  
Sbjct: 74   SVFPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG-- 131

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY
Sbjct: 132  TVKDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLY 191

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  
Sbjct: 192  NARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEI 251

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            + +     L    L  G   +  +     G+  +E G+++T+  +++L++  +K + +  
Sbjct: 252  QDNKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDEIKQIEVPV 308

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  
Sbjct: 309  EYIVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISE 368

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L
Sbjct: 369  TLRVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSL 428

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NL+       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+
Sbjct: 429  NLEEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLV 488

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 489  RVERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 548

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ET
Sbjct: 549  ISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLET 608

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPRE 659
            P+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E
Sbjct: 609  PFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPE 668

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +
Sbjct: 669  DIHYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPI 728

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ 
Sbjct: 729  ALDSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQI 788

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED F
Sbjct: 789  PCVNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRF 848

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+T
Sbjct: 849  TTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVT 908

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +
Sbjct: 909  PKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEI 968

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E  Q++   +D  +E  IL+  +++R+  +L                  S   + +  R 
Sbjct: 969  EEMQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVSRE 1015

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +W +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A
Sbjct: 1016 KWLEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLA 1075

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            ++R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ET
Sbjct: 1076 VRRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILET 1135

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVA 1197
            HLG A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+A
Sbjct: 1136 HLGLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLA 1192

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            E  + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YML
Sbjct: 1193 ENLRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYML 1252

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1253 KLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1312

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            KSDDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1313 KSDDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1361


>gi|307246656|ref|ZP_07528726.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 1 str. 4074]
 gi|307248781|ref|ZP_07530794.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 2 str. S1536]
 gi|307251024|ref|ZP_07532949.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 4 str. M62]
 gi|307255641|ref|ZP_07537445.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307260092|ref|ZP_07541803.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 11 str. 56153]
 gi|306852356|gb|EFM84591.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 1 str. 4074]
 gi|306854708|gb|EFM86898.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 2 str. S1536]
 gi|306856964|gb|EFM89095.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 4 str. M62]
 gi|306861318|gb|EFM93308.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306865826|gb|EFM97703.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 11 str. 56153]
          Length = 1361

 Score = 1644 bits (4258), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1369 (51%), Positives = 976/1369 (71%), Gaps = 28/1369 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +A    ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+
Sbjct: 18   LAMAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFR 73

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  
Sbjct: 74   SVFPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG-- 131

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY
Sbjct: 132  TVKDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLY 191

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  
Sbjct: 192  NARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEI 251

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            + +     L    L  G   +  +     G+  +E G+++T+  +++L++  +K + +  
Sbjct: 252  QDNKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDEIKQIEVPV 308

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  
Sbjct: 309  EYIVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISE 368

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L
Sbjct: 369  TLRVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSL 428

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NL+       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+
Sbjct: 429  NLEEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLV 488

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 489  RVERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 548

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ET
Sbjct: 549  ISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLET 608

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPRE 659
            P+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E
Sbjct: 609  PFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPE 668

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +
Sbjct: 669  DIHYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPI 728

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ 
Sbjct: 729  ALDSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQI 788

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED F
Sbjct: 789  PCVNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRF 848

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+T
Sbjct: 849  TTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVT 908

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +
Sbjct: 909  PKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEI 968

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E  Q++   +D  +E  IL+  +++R+  +L                  S   + +  R 
Sbjct: 969  EEMQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVARE 1015

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +W +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A
Sbjct: 1016 KWLEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLA 1075

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            ++R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ET
Sbjct: 1076 VRRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILET 1135

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVA 1197
            HLG A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+A
Sbjct: 1136 HLGLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLA 1192

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            E  + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YML
Sbjct: 1193 ENLRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYML 1252

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+
Sbjct: 1253 KLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1312

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            KSDDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1313 KSDDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1361


>gi|120596982|ref|YP_961556.1| DNA-directed RNA polymerase subunit beta [Shewanella sp. W3-18-1]
 gi|146294848|ref|YP_001185272.1| DNA-directed RNA polymerase subunit beta [Shewanella putrefaciens
            CN-32]
 gi|158512970|sp|A1REA7|RPOB_SHESW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|166229306|sp|A4YBZ0|RPOB_SHEPC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120557075|gb|ABM23002.1| DNA-directed RNA polymerase, beta subunit [Shewanella sp. W3-18-1]
 gi|145566538|gb|ABP77473.1| DNA-directed RNA polymerase, beta subunit [Shewanella putrefaciens
            CN-32]
 gi|319424573|gb|ADV52647.1| DNA-directed RNA polymerase, beta subunit [Shewanella putrefaciens
            200]
          Length = 1343

 Score = 1644 bits (4258), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1364 (51%), Positives = 961/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMALVPERL-RGETASYDIKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+DI  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKDISTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN  +D +G   EE + CR  GE   +    I 
Sbjct: 593  RKVIDGVITDEVEYLSAIEEGRYVIAQANIEVDANGRMVEEQIACRHKGESTFMRASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGYIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  AVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L G                +   I+  PR    
Sbjct: 953  HIAQARKDLSEEFKILEEGVLSRARNLLLGAG-------------FTETQIAAMPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQVIDDEAKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD V+R+A+  K 
Sbjct: 1120 AAAKGIGNKITAMLEEQRELAEVRGYIKQVYELGDEVQQRVDIDSFTDDEVMRLAQNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  LYDG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKQMLELAGLPTSGQLKLYDGRTGNEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1343


>gi|289663455|ref|ZP_06485036.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            vasculorum NCPPB702]
 gi|289667613|ref|ZP_06488688.1| DNA-directed RNA polymerase subunit beta [Xanthomonas campestris pv.
            musacearum NCPPB4381]
          Length = 1383

 Score = 1644 bits (4258), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 969/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLVAEHTDTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDSVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQTAVSELRKFLDDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|33594737|ref|NP_882380.1| DNA-directed RNA polymerase subunit beta [Bordetella parapertussis
            12822]
 gi|33564813|emb|CAE39755.1| DNA-directed RNA polymerase beta chain [Bordetella parapertussis]
          Length = 1378

 Score = 1644 bits (4257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 956/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + A  +R NEGLQAAF S+
Sbjct: 9    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTATSDRVNEGLQAAFSSI 68

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 69   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 126

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 127  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 186

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 187  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 246

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       A     G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 247  EGGMMEFVAE-RWKGEMARFDIAD-RDGKVIVEKDKRINAKHLRDLAAGGIQRVSVPEDF 304

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 305  LYGRVLAKNIVDPDTGEVVAHANDEITESVLNAMRAANVRDIQTLYTNDLDRGPYISQTL 364

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+       E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 365  RADETADQMAARVAIYRMMRPGEPPAEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 424

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 425  GDDSTGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 484

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 485  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 544

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 545  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 604

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE +  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 605  YRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDDEGRFVDDLVACREAGETMLTAPGNV 664

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 665  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 724

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 725  DSGTTVQALRGGVVDHVDADRVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 784

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 785  VARGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 844

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV+  D+LVGK+TPK
Sbjct: 845  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVSADDVLVGKVTPK 904

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV SG++GTV+DV++F R GI +++R+ S+  
Sbjct: 905  GETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGMTGTVIDVQVFTREGIVRDKRAQSIID 964

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   L+   +++  R QW
Sbjct: 965  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKAVNGGPRKLAKGATLTKAYLADLDRWQW 1024

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1025 FDIRLADEQHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1084

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1085 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1144

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +       +R +LEKV  T   +  I    D+ VL +A   K
Sbjct: 1145 GWAAKGVGYRIADMLRDERT-AQAKSVRGYLEKVYNTTGSSAHIDSLTDEEVLELANNLK 1203

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE I  ML +A  D             Q+ LYDG TGE F+RPVT+
Sbjct: 1204 KGVPFATPVFDGATEEEIGKMLELAYPDDVAARMRLTASRSQAWLYDGRTGEQFERPVTI 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1264 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1324 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1378


>gi|212213257|ref|YP_002304193.1| DNA-directed RNA polymerase subunit beta [Coxiella burnetii
            CbuG_Q212]
 gi|212011667|gb|ACJ19048.1| DNA-directed RNA polymerase beta chain [Coxiella burnetii CbuG_Q212]
          Length = 1377

 Score = 1644 bits (4257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 717/1370 (52%), Positives = 985/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 13   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 72

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 73   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 132

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 133  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 192

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 193  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 252

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 253  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 310

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 311  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGPYV 370

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 371  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 430

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 431  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 490

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 491  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 550

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 551  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 610

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 611  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 670

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 671  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 730

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 731  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 790

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 791  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 850

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 851  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 910

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+DVRIF R G+ K+ER++
Sbjct: 911  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIDVRIFTREGVKKDERTL 970

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 971  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1030

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1031 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1090

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1091 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1150

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1151 ETHLGWAAKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVML 1207

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1208 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1267

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1268 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1327

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1328 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1377


>gi|187476527|ref|YP_784551.1| DNA-directed RNA polymerase subunit beta [Bordetella avium 197N]
 gi|115421113|emb|CAJ47597.1| DNA-directed RNA polymerase beta chain [Bordetella avium 197N]
          Length = 1378

 Score = 1644 bits (4257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1375 (50%), Positives = 960/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL    A  +R NEGLQAAF S+
Sbjct: 9    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQAETATADRVNEGLQAAFTSI 68

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 69   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 126

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 127  KEVKEQEVYMGEIPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 186

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 187  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 246

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 247  EGAMMEFVPE-RWKGEMARFDITD-RAGKVIVEKDKRINAKHLRDLANGGIQRISVPEDF 304

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+ +TGE+   A D I E  L+ +  +++ D+  LY + ++   YI  TL
Sbjct: 305  LYGRVLAKNVVDPDTGEVIALANDEITESVLDAMRAAKVLDLQTLYTNDLDRGPYISQTL 364

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 365  RTDETVDQTAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 424

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D  +    +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 425  GDDANGPMTLTDEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 484

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 485  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 544

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 545  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 604

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DG+V++ + YLSA+EE +  IAQAN++LD +G F ++LV CR AGE +L     +
Sbjct: 605  YRKIIDGRVSDQIDYLSAIEESHYVIAQANAALDAEGRFVDDLVACREAGETMLTSPVNV 664

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 665  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAV 724

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 725  DSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 784

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 785  VKRGDRVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 844

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV+  D+LVGK+TPK
Sbjct: 845  VHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDESGIVYIGAEVSADDVLVGKVTPK 904

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 905  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 964

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   ++   +++  R QW
Sbjct: 965  DELRRYRQDLNDQLRIVENDQFDRIEKLLVGKTVNGGPRKLAKGATVTKAYLADLDRWQW 1024

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1025 FDIRLSDEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1084

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGT  DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1085 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTTADIVLNPLGVPSRMNVGQVLEVHL 1144

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I  ++ D +    +  +R++LEKV  T     +IS+  D+ V+ +A   K
Sbjct: 1145 GWAAKGVGQRIADMLQDERT-AQVKNIRAYLEKVYNTTGTGARISELSDEEVIELANNLK 1203

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA E+ I  ML +A                Q+ L+DG TGE F+RPVT+
Sbjct: 1204 RGVPFATPVFDGATEDEITMMLELAYPDDVAKRMQLTPSRAQAWLFDGRTGEKFERPVTI 1263

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1264 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1323

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1324 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1378


>gi|158518634|sp|Q7W2G9|RPOB_BORPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1370

 Score = 1644 bits (4257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 956/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + A  +R NEGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTATSDRVNEGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 61   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +       A     G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGGMMEFVAE-RWKGEMARFDIAD-RDGKVIVEKDKRINAKHLRDLAAGGIQRVSVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDPDTGEVVAHANDEITESVLNAMRAANVRDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+       E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RADETADQMAARVAIYRMMRPGEPPAEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GDDSTGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE +  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDDEGRFVDDLVACREAGETMLTAPGNV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGVVDHVDADRVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 777  VARGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV+  D+LVGK+TPK
Sbjct: 837  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV SG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVSSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   L+   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKAVNGGPRKLAKGATLTKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEQHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +       +R +LEKV  T   +  I    D+ VL +A   K
Sbjct: 1137 GWAAKGVGYRIADMLRDERT-AQAKSVRGYLEKVYNTTGSSAHIDSLTDEEVLELANNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA EE I  ML +A  D             Q+ LYDG TGE F+RPVT+
Sbjct: 1196 KGVPFATPVFDGATEEEIGKMLELAYPDDVAARMRLTASRSQAWLYDGRTGEQFERPVTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|158518562|sp|Q2L2M3|RPOB_BORA1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1370

 Score = 1644 bits (4257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1375 (50%), Positives = 960/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL    A  +R NEGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQAETATADRVNEGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 61   FPIVSHNGMARLEFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGAMMEFVPE-RWKGEMARFDITD-RAGKVIVEKDKRINAKHLRDLANGGIQRISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+ +TGE+   A D I E  L+ +  +++ D+  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNVVDPDTGEVIALANDEITESVLDAMRAAKVLDLQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RTDETVDQTAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  -DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D  +    +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GDDANGPMTLTDEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DG+V++ + YLSA+EE +  IAQAN++LD +G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGRVSDQIDYLSAIEESHYVIAQANAALDAEGRFVDDLVACREAGETMLTSPVNV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 777  VKRGDRVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV+  D+LVGK+TPK
Sbjct: 837  VHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDESGIVYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   ++   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKLLVGKTVNGGPRKLAKGATVTKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLSDEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGT  DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTTADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I  ++ D +    +  +R++LEKV  T     +IS+  D+ V+ +A   K
Sbjct: 1137 GWAAKGVGQRIADMLQDERT-AQVKNIRAYLEKVYNTTGTGARISELSDEEVIELANNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA E+ I  ML +A                Q+ L+DG TGE F+RPVT+
Sbjct: 1196 RGVPFATPVFDGATEDEITMMLELAYPDDVAKRMQLTPSRAQAWLFDGRTGEKFERPVTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|197117316|ref|YP_002137743.1| DNA-directed RNA polymerase subunit beta [Geobacter bemidjiensis Bem]
 gi|226699409|sp|B5EFP3|RPOB_GEOBB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|197086676|gb|ACH37947.1| DNA-directed RNA polymerase, beta subunit [Geobacter bemidjiensis
            Bem]
          Length = 1371

 Score = 1644 bits (4256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1364 (52%), Positives = 989/1364 (72%), Gaps = 10/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K  +IIDIP+LI++QK SY  FL ++   D R N GL+A F+SVFPI  FS  A
Sbjct: 11   LRKNFAKIHKIIDIPNLIDIQKNSYKRFLQLDTPVDARKNSGLEAVFRSVFPIRDFSDTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK+DV++C  R +T+A P+K+ +RL+V+DV +  G +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYSLGAPKYDVEECHQRGMTFAAPMKVKVRLVVWDVAKDPGTRSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT +GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEIPLMTDNGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD KDI++VRIDRRRK+P T  L ALG  ++ +++ FY         +     L+ A
Sbjct: 191  DFEFDHKDILYVRIDRRRKMPATVLLKALGYSNDALINYFYKSEEVKLGDNGAMTKLADA 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+   K ++ +VD  TGE ++++ +K T   L+ + E G+K + I+ + +     + DI
Sbjct: 251  ELLSNQKATADIVDPATGEVILKANRKFTKAALRKMAEHGIKEIPISEEEVVAKVASHDI 310

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +  TGEI +E  + + +  LEEI    I    +L++D+++  +  R+T++ DK     +
Sbjct: 311  YDPATGEIIVECNEELTQAKLEEIIQKGITTFQVLFIDNLHVTSSFRDTILIDKIGSTDE 370

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IYR +RPGD  T   A  +F  LFF++++YDLS VGR+K+N +L +D P D   + 
Sbjct: 371  ALIEIYRRLRPGDPPTLKSALVLFENLFFNAERYDLSAVGRLKLNYKLGVDVPLDCMTLT 430

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +EDI+ +++ L++L+NGKG IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 431  REDILEVVRYLIELKNGKGNIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSL 490

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 491  QEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 550

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +GKVT+
Sbjct: 551  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVSEGKVTD 610

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V + SA+EEE   IAQAN+ +D+DG F  + +  R +GE +LV R++++ +D +P Q+V
Sbjct: 611  EVRFFSALEEEGHAIAQANAEIDKDGRFAADYISARKSGEFVLVGRDELELMDVAPMQLV 670

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A++P VGTGME VVA+ SG + VA+  
Sbjct: 671  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADSPLVGTGMERVVARDSGVSSVARHN 730

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  E   D + +GVDIY L+KF RSNQNTC+NQRP+VKVGD V+  D
Sbjct: 731  GVVESVDASRIVVKIDEDQYDATGTGVDIYNLIKFARSNQNTCINQRPVVKVGDHVKAGD 790

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGPSTD+G+LALG+N+L+AFMPW GYN+EDS+LISER+V +D +TSIHIEEFE +AR
Sbjct: 791  IIADGPSTDMGELALGQNVLIAFMPWGGYNYEDSILISERLVKDDRYTSIHIEEFEAVAR 850

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ EE LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 851  DTKLGKEEITSDIPNLGEETLKDLDESGIIRIGAEVRPGDILVGKITPKGETQLSPEEKL 910

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV GTV+  +IF+R G DK+ R+  +E+ +   L +D+ 
Sbjct: 911  LRAIFGEKAGDVRDTSLRVPPGVEGTVIGAKIFSRKGADKDARTEIIEKAEEMRLRKDEQ 970

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKG------FKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++L G+ A    +G        K   ++ +++  +   +W + ++
Sbjct: 971  DEIRIIRDSAIGKLKKLLVGKAAAVKIEGSDGKVLIPKGAAITEEMLKSFSMDRWDEISI 1030

Query: 1027 QDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D+  +   V            I++  F +K++K++ GDD+PPGV+++VKV++A+KR +Q
Sbjct: 1031 ADDDTIDEKVAQTLSTLNQQIDIIKYVFDDKVQKLRRGDDLPPGVIKMVKVYIAIKRKLQ 1090

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+++DG PV+IVLNPLGVPSRMNVGQI E HLGW  
Sbjct: 1091 VGDKMAGRHGNKGVVSRILPEEDMPYMEDGRPVEIVLNPLGVPSRMNVGQILEMHLGWGA 1150

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG KI+  +     + +I   + FL+           +   + + +L +A + K G+P
Sbjct: 1151 KGLGWKIEEFLEKNAPHDEI---KRFLKGAYDNPEMDRFLDTLEGEELLNLARRLKRGIP 1207

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +S+PVF+GA EE+I SML  A    +GQ  LYDG +G+ F   VTVG +Y LKL+H+V D
Sbjct: 1208 MSSPVFEGASEESIQSMLTHAGFSTTGQVTLYDGKSGDKFMHQVTVGIMYFLKLHHLVDD 1267

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1268 KIHARSIGPYSLVTQQPLGGKARFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDVAGR 1327

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+LGL ++L      
Sbjct: 1328 TRMYEAIVKGKHTLEPGLPESFNVLIKELQSLGLDVELLEGDED 1371


>gi|167817763|ref|ZP_02449443.1| DNA-directed RNA polymerase subunit beta [Burkholderia pseudomallei
            91]
          Length = 1363

 Score = 1644 bits (4256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1375 (50%), Positives = 961/1375 (69%), Gaps = 23/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  S+  FL  ++   +R +EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVPTAQRKSEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120  KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D 
Sbjct: 240  EGAQMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+++V+G+TGE+   A D I E  LE++  ++I++I  LY + ++   YI +TL
Sbjct: 298  LLGRVLAKNVVDGDTGEVIANANDEITEGVLEKLREAKIKEIQTLYTNDLDQGPYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358  RVDETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN+++ +DG+  +ELV  R AGE ++V  ++I 
Sbjct: 598  RKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIGDDGALVDELVSSREAGETMMVTPDRIQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 718  SGTTVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSI
Sbjct: 778  KMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+
Sbjct: 958  ELKRYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1018 DIRLADDEAAVQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP++      D+VLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSKIVPVEDMPYMA-----DVVLNPLGVPSRMNVGQVLEVHLG 1132

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  + 
Sbjct: 1133 WAAKGLGWRIGEML---ARQTKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLRE 1189

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES-----------GQSILYDGLTGEPFDRPVTV 1251
            GVP +TPVFDGA EE ++ ML +A   +             Q  LYDG TGEPF+R VTV
Sbjct: 1190 GVPFATPVFDGATEEEMSKMLDLA-FPDDIAEQLDMNPSKNQVRLYDGRTGEPFERRVTV 1248

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1249 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1308

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1309 QEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1363


>gi|319944812|ref|ZP_08019075.1| DNA-directed RNA polymerase subunit beta [Lautropia mirabilis ATCC
            51599]
 gi|319741926|gb|EFV94350.1| DNA-directed RNA polymerase subunit beta [Lautropia mirabilis ATCC
            51599]
          Length = 1371

 Score = 1644 bits (4256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1378 (50%), Positives = 963/1378 (69%), Gaps = 21/1378 (1%)

Query: 3    KGVVFNGLGRVRKFFG--KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
                F    R+RK FG  +   + ++P L+  Q  SY  FL   +  D+R + GLQAA K
Sbjct: 1    MTYSFTEKKRIRKSFGHRRARAVQEVPYLLATQLESYAEFLQEGVPADQRKDVGLQAALK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            S+FPI++ +  A LEFV Y    P FD+ +C  R L +  PL+  +RL++ D        
Sbjct: 61   SIFPISSHNDMARLEFVGYTLGQPAFDMKECQQRGLNFCAPLRARVRLVIMDR--EASKP 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL+
Sbjct: 119  TVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD+KDI++ RIDRRRK+PVT  L A+GM  E+IL+ F+    ++ 
Sbjct: 179  SARIIPYRGSWLDFEFDAKDILYFRIDRRRKMPVTILLKAIGMTPEQILAHFFVFDTFTL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +     L    L  G      + D   G  ++   K++ +  ++ +++ G+K + +  
Sbjct: 239  ESEGAKMELVPERL-KGETARFDITD-REGNVIVAKDKRINAKHIRDMEKAGLKLISVPD 296

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  VA DIV+ ETGEI + A D + E SL  +  + I +   LY + ++   +I  
Sbjct: 297  EFLLGRAVATDIVDPETGEIVMRANDELTEDSLGRLRAANIHEFRTLYTNDLDAGPFISQ 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D + D+  A + IYR+MRPG+  T    E++FN LF++ D YDLS VGR+K N R+
Sbjct: 357  TLRLDDSADQISARIAIYRMMRPGEPPTEDAVEALFNRLFYNEDTYDLSRVGRMKFNSRV 416

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              + P     +  +DI+A+IK+LVDLRNGKG IDDID+LGNRRVR VGE+ +NQ+R GL+
Sbjct: 417  GREEPTGPMTLEDDDIVAVIKLLVDLRNGKGEIDDIDHLGNRRVRCVGELAENQFRAGLV 476

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+   + ++++P DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR
Sbjct: 477  RVERAVRERLGQAETENLLPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRR 536

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N +GF+ET
Sbjct: 537  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEFGFLET 596

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV + K+T+ + +LSA+EE    IAQAN+ LDE+G  T ELV  R  GE  LV  ++
Sbjct: 597  PYRKVENQKLTDQIDFLSAIEEGRYVIAQANAELDEEGRLTGELVSVRINGETQLVSADR 656

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +++ID +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E   A
Sbjct: 657  VEYIDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPQKPLVGTGIERTCA 716

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  + A R G V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 717  VDSGTVVTALRGGTVDYVDANRVVIRVNDEEATAGEVGVDIYNLVKYTRSNQNTNINQRP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V  GD +   D+IADG STDLG+LALG+NML+AFMPW+GYNFEDS++ISE++VS+D +T
Sbjct: 777  IVSKGDRLAAGDVIADGASTDLGELALGQNMLIAFMPWNGYNFEDSVMISEKVVSDDRYT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N+SE  L  +DE GI+ +GAEV+ GD LVGK+TP
Sbjct: 837  SIHIEELSVLARDTKLGPEEITRDISNLSESQLARLDESGIVYIGAEVSAGDTLVGKVTP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+ 
Sbjct: 897  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMNGTVIDVQVFTREGITRDKRAQSII 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + +SR+   L G+ A  GPK   K TV++ D + +  R  
Sbjct: 957  DDELKRFRLDLNDQLRIVENDAFSRIERFLDGKEANGGPKKLAKGTVVTRDYLKDLDRYH 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W++  + +E+  R +E +K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+
Sbjct: 1017 WFEVRLANEEDARWLEGMKDAIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAV 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VSRI+P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRRLQPGDKMAGRHGNKGVVSRIVPIEDMPYMADGTPCDIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  G+G +I  +++ +     +S LR +L+KV         +S+  DD +L +A   
Sbjct: 1137 LGWAAKGVGLRIGEMLDRH---VKVSELRRYLDKVYNDRGEKANLSELSDDELLAMANNL 1193

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMA-----------DLDES-GQSILYDGLTGEPFDRP 1248
            + GVP +TPVFDGA EE I++ L +A               S  Q IL DG TG+PFDRP
Sbjct: 1194 RDGVPFATPVFDGATEEEIHAALDLAFPSDDPRTEKLGFTPSKTQLILRDGRTGDPFDRP 1253

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1254 VTVGYMHFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAS 1313

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            Y LQEMLT+KSDDV GR +VYE++V G    + G PESFNVLVKE+++LG+ IDLE +
Sbjct: 1314 YTLQEMLTVKSDDVTGRAKVYENMVKGEHAIDAGMPESFNVLVKEIRSLGIDIDLERA 1371


>gi|117621409|ref|YP_858456.1| DNA-directed RNA polymerase subunit beta [Aeromonas hydrophila subsp.
            hydrophila ATCC 7966]
 gi|117562816|gb|ABK39764.1| DNA-directed RNA polymerase, beta subunit [Aeromonas hydrophila
            subsp. hydrophila ATCC 7966]
          Length = 1363

 Score = 1644 bits (4256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 22   MVYSYTEKKRIRKDFGKRDQVLDTPYLLSIQLDSFKQFIEAD----PEGEYGLEAAFRSV 77

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A L++VSY    P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 78   FPITSYSGSAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 135

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 136  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 195

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L AL   SE+IL+TF+  I +  + 
Sbjct: 196  RVIPYRGSWLDFEFDAKDNLFVRIDRRRKLPASIILRALDFSSEQILATFFETIGFEVKD 255

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +V    G  V+E+G+++T+  ++ L++  V  + +  + 
Sbjct: 256  GKLMMDLVPERL-RGETATFDIV--ANGAVVVETGRRVTARHIRQLEKDSVTQIEVPVEY 312

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D  + +TGE+ + A   +  +++  +  +  +   +L+ + +++ AY+  TL
Sbjct: 313  VVGKVAAKDYAHPQTGEMVVTANQALSLEAVANLSQAGFKHFEVLFTNELDHGAYMSETL 372

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE +F  LFF S++YDLSTVGR+K N RL  
Sbjct: 373  RIDSSSSRLEALVEIYRMMRPGEPPTREAAEQLFENLFFSSERYDLSTVGRMKFNRRLAR 432

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +    V  + K+DI+ ++K L+D+RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 433  EDETGVGTLTKDDIVDVMKRLIDIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 492

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 493  ERAVKERLSLGDLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 552

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPY
Sbjct: 553  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPY 612

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I 
Sbjct: 613  RKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQ 672

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 673  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVD 732

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 733  SGVTVVAKRGGMIDYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCV 792

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L++ER+V ED  T+I
Sbjct: 793  MLGEPVMAGDVLADGPSTDLGELALGQNLRVAFMPWNGYNFEDSILVNERVVQEDRLTTI 852

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 853  HIQELACISRDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKG 912

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  
Sbjct: 913  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEM 972

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  I+ R   +L                  S D +++  RS+W+
Sbjct: 973  QLKEAKKDLTEEFKILEDGIFGRSRNLLLAAG-------------YSEDRLNKLDRSKWF 1019

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A++DE  Q  +E +  Q+   K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1020 ELAIEDEAKQIELEQIAEQHVELKAEFDKKFENKRRKIIQGDDLAPGVLKIVKVYLAVKR 1079

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP  + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1080 RIQPGDKMAGRHGNKGVISKICPVEDMPHDEYGRPVDIVLNPLGVPSRMNIGQILEVHLG 1139

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++ + +   ++      +  +    +    +++  DD V  +    + 
Sbjct: 1140 LAAKGIGEKIDRMVKEQRELHEMRDFLQQVYDLGEKDTQQVNVAELSDDDVRTLVGNLRK 1199

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I ++L++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1200 GLPVATPVFDGAKEREIKALLKLADLPESGQIALFDGRTGNAFERKVTVGYMYMLKLNHL 1259

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1260 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1319

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1320 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELDEE 1363


>gi|163859286|ref|YP_001633584.1| DNA-directed RNA polymerase subunit beta [Bordetella petrii DSM
            12804]
 gi|226699375|sp|A9IJ25|RPOB_BORPD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|163263014|emb|CAP45317.1| DNA-directed RNA polymerase beta chain [Bordetella petrii]
          Length = 1370

 Score = 1644 bits (4256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1375 (50%), Positives = 958/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ D+P L+  Q  SY  FL  +  P +R +EGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQDVPFLLATQLQSYLTFLQADTPPSDRASEGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        +I
Sbjct: 61   FPIVSHNGMARLEFVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT  L A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILLKAIGMTPESILAHFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      +     G  ++E  K++ +  L+ +    ++ + +  + 
Sbjct: 239  EGGMIEFVPE-RWKGEMARFDI-TGRDGNVIVEKDKRINAKHLRDMANANIQRVSVPEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDPDTGEVVAHANDEITESVLSALRAANVRDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RTDETADQMAARVAIYRMMRPGEPPTEDAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GEDITGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV++ + YLSA+EE N  IAQAN++LD++G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSDQIDYLSAIEESNYVIAQANAALDDEGRFVDDLVACREAGETMLTAPANV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPVVGTGVERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGVVDHVDAERVVIRVNDDENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 777  VKRGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI+ +GAEV   D+LVGK+TPK
Sbjct: 837  IHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGIVYIGAEVTADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   ++   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKLLIGKTVNGGPRKLAKGATITKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +    +  +R++L+KV  T    E+I    DD V+ +A+  K
Sbjct: 1137 GWAAKGVGHRIADMLRDERT-AQVKNVRAYLDKVYNTTGTGEQIDTLTDDEVMELAQNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA EE I  ML +A  DE            Q+ L+DG TGE F+RPVTV
Sbjct: 1196 NGVPFATPVFDGATEEEIGKMLELAYPDEVAKRMQLTDSRTQAWLFDGRTGEKFERPVTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|327479317|gb|AEA82627.1| DNA-directed RNA polymerase subunit beta [Pseudomonas stutzeri DSM
            4166]
          Length = 1329

 Score = 1643 bits (4255), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1337 (53%), Positives = 968/1337 (72%), Gaps = 10/1337 (0%)

Query: 31   EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
             +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    P FDV +
Sbjct: 2    AIQLDSYREFLQAGATKDQFRDIGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKE 61

Query: 91   CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
            C+ R +T+AVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GTF+I G +
Sbjct: 62   CVLRGVTFAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGTFIINGTE 119

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
            R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + VRIDRRR
Sbjct: 120  RVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDAVFVRIDRRR 179

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
            K+P +  L AL   +EEIL  FY   V+  +G+     L    L  G   +  + D D+G
Sbjct: 180  KLPASVLLRALNYSTEEILDAFYDTNVFHVKGETLALELVPQRL-RGEIATFDIKD-DSG 237

Query: 271  EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            + ++E G+++T+  +  L + G+K L +  D + G  VA+ IV+  TGEI  E    +  
Sbjct: 238  KVIVEQGRRITARHINQLDKSGIKELEMPMDYVLGRTVAKAIVHPATGEIIAECNTELTV 297

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
              + +I  +++     LY + ++   +I +TL  D   ++ +AL++IYR+MRPG+  T  
Sbjct: 298  DVMAKIVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQLEALVEIYRMMRPGEPPTKD 357

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             AE++FN LFF +++YDLS VGR+K N R+     +    + +EDI+A++K LVD+RNGK
Sbjct: 358  AAETLFNNLFFAAERYDLSAVGRMKFNRRIGRTEIEGSGVLSREDIVAVLKTLVDIRNGK 417

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
            G +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV 
Sbjct: 418  GIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVA 477

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 478  AAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVC 537

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P ET EG NIGL++SL ++AR N YGF+E+PYR V DG+VT+++V+LSA+EE +  IAQA
Sbjct: 538  PIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDGEVTDEIVFLSAIEEADHVIAQA 597

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            ++ L +     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR 
Sbjct: 598  SAKL-DGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRA 656

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + 
Sbjct: 657  LMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVRDD 716

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+ADGPSTD+G+LALG+N
Sbjct: 717  EVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVARGDIMADGPSTDMGELALGQN 776

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            M VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTKLGPEEIT DIPNV E
Sbjct: 777  MRVAFMPWNGYNFEDSILLSERVVQEDRFTTIHIQELTCVSRDTKLGPEEITADIPNVGE 836

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              L  +DE GI+ VGAEV PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR
Sbjct: 837  AALNKLDEAGIVYVGAEVGPGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLR 896

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
            VP+G  GTV+DV++F R G++++ R++++E+ Q++ + +D ++E  I++   + RL   L
Sbjct: 897  VPTGTKGTVIDVQVFIRDGVERDSRALAIEKMQLDEIRKDLNEEFRIVEGATFERLRSAL 956

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G  A  G  G KK  V++ +++      QW++  + ++ +   +E  +      + +L+
Sbjct: 957  VGATAEGG-AGLKKGVVITDEILDGLEHGQWFKLRMAEDALNEQLEKAQAYLSDRRQLLD 1015

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
            D+F++K  K+Q GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG+VS I+P EDMP
Sbjct: 1016 DKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMP 1075

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +    ++ LR 
Sbjct: 1076 HDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINLMLEEQRK---VAELRK 1132

Query: 1171 FLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
            FL ++    G   E + D  D  VL +A   + GVP++TPVFDGA E  I +ML++ADL 
Sbjct: 1133 FLHEIYNEIGGRQENLDDLSDQEVLDLANNLRKGVPMATPVFDGAKEREIKAMLKLADLP 1192

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            ESGQ  L+DG TG  F+R  TVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  
Sbjct: 1193 ESGQMQLFDGRTGNAFERTTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1252

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNV
Sbjct: 1253 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNV 1312

Query: 1350 LVKEMQALGLSIDLENS 1366
            L+KE+++LG+ IDLE  
Sbjct: 1313 LIKEIRSLGIDIDLETE 1329


>gi|78099466|gb|ABB20869.1| RNA polymerase subunit B [Acinetobacter towneri]
          Length = 1362

 Score = 1643 bits (4254), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 973/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKSREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG  +E+IL  F+ K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYSNEQILDLFFEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDTD-GKVIVEQGKRINARHVRQMEAAGLEKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  ++  + + ++    ++   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAEDIQLKD-GDVIA-ANTLLSHEIMVKLAEGGVKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R+DAL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTVGREDALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K L+++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLIEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+SS+D+DG+ TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTIIAQADSSVDQDGNLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIANRGGRIEYVDASRVVIRVNEEEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LVK+GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVKMGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++   +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLALVDLLEIQPSDEAIAERLTQIQTFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K   +I+ LR+FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGEQIDKML---KQQREIAELRAFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLAGNLRAGVPLATPVFDGAEEGQIKELLELAELPRSGQTVLYDGRTGEKFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|46143683|ref|ZP_00134648.2| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126209191|ref|YP_001054416.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae L20]
 gi|307257815|ref|ZP_07539572.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 10 str. D13039]
 gi|158513515|sp|A3N325|RPOB_ACTP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|126097983|gb|ABN74811.1| DNA-directed RNA polymerase beta chain [Actinobacillus
            pleuropneumoniae serovar 5b str. L20]
 gi|306863721|gb|EFM95647.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 10 str. D13039]
          Length = 1342

 Score = 1643 bits (4254), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 974/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDGITQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYVDLSTGEVVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LNL
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 592  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 952  MQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+AE 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1342


>gi|126090320|ref|YP_001041763.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS155]
 gi|152998742|ref|YP_001364423.1| DNA-directed RNA polymerase subunit beta [Shewanella baltica OS185]
 gi|304412758|ref|ZP_07394360.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS183]
 gi|307307422|ref|ZP_07587157.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica BA175]
 gi|166229305|sp|A6WHS1|RPOB_SHEB8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|182676572|sp|A3DB95|RPOB_SHEB5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|125999940|gb|ABN64008.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS155]
 gi|151363360|gb|ABS06360.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS185]
 gi|304348838|gb|EFM13254.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS183]
 gi|306910210|gb|EFN40643.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica BA175]
 gi|315265546|gb|ADT92399.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS678]
          Length = 1343

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1364 (51%), Positives = 961/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIMLRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMALVPERL-RGETASYDIKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+++  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN  +D +G   EE + CR  GE   +    I 
Sbjct: 593  RKVIDGVITDEVEYLSAIEEGRYVIAQANIEIDANGRMAEEQIACRHKGESTFMRAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGFVDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L G                +   I+  PR    
Sbjct: 953  HIAQARKDLGEEFKILEEGVLSRARNLLIGAG-------------FTDAQIAALPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 IQVIDDETKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD VLR+A   K 
Sbjct: 1120 AAAKGIGNKITAMLEEQRELAEVRGYIKQVYELGDEVQQRVDIDSFTDDEVLRLATNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKQMLELAGLPTSGQLKLFDGRTGNEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+ +
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQA 1343


>gi|325926960|ref|ZP_08188238.1| DNA-directed RNA polymerase subunit beta [Xanthomonas perforans
            91-118]
 gi|325542672|gb|EGD14136.1| DNA-directed RNA polymerase subunit beta [Xanthomonas perforans
            91-118]
          Length = 1383

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 967/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++ SQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIFSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I+E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEINEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDTVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL  +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLNDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|114045700|ref|YP_736250.1| DNA-directed RNA polymerase subunit beta [Shewanella sp. MR-7]
 gi|123031029|sp|Q0I0B2|RPOB_SHESR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158564100|sp|Q0HNU4|RPOB_SHESM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|113887142|gb|ABI41193.1| DNA-directed RNA polymerase, beta subunit [Shewanella sp. MR-7]
          Length = 1345

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 967/1367 (70%), Gaps = 25/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMTLVPERL-RGETASYDIKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+++  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDPTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T+DV YLSA+EE    IAQAN  +D  G   EE + CR  GE   +    I 
Sbjct: 593  RKVVDGVITDDVEYLSAIEEGRYVIAQANIEVDSQGRMVEEQIACRHKGESTFMRASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R+I +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAIEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L                  +   I+  PR    
Sbjct: 953  HIAQARKDLGEEFKILEEGVLSRARNLLLSAG-------------FTEAQIAALPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQVIDDETKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE---KISDYDDDSVLRVAEQ 1199
             A  G+G KI +++ D +  G ++ +RS++++V   G   +    I  + DD +LR+A  
Sbjct: 1120 AAAKGIGNKIAAMLEDQREKG-LAEVRSYIKQVYELGDEVQQRVDIDSFTDDELLRLANN 1178

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K G+PV+TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+RPVTVGY+YMLKL
Sbjct: 1179 LKGGIPVATPAFDGAKEKEIKQMLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKL 1238

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1239 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1298

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 DDVNGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1345


>gi|308047973|ref|YP_003911539.1| DNA-directed RNA polymerase subunit beta [Ferrimonas balearica DSM
            9799]
 gi|307630163|gb|ADN74465.1| DNA-directed RNA polymerase subunit beta [Ferrimonas balearica DSM
            9799]
          Length = 1341

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1366 (52%), Positives = 975/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK FGK P+++D+P L+ +Q  S+ +FL  +         GL+AAF+SV
Sbjct: 1    MVYSDFEKKRIRKDFGKRPKVLDVPYLLSIQLDSFQNFLEQD----PDGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LRL++ D +       +
Sbjct: 57   FPIKSFSGYSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRLVLMDKEAGGA---V 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGDIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  ++EIL  F+ K+ +S + 
Sbjct: 174  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALGYSTQEILDLFFEKVQFSLKK 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L   D + G      + D + G+ ++E G+++T+  ++ L++  VK L +  + 
Sbjct: 234  DKLVMDLVP-DRLRGETALFDIKD-NNGDLIVEKGRRVTARHIRQLEKGDVKQLEVAVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A+D ++  TGE+ + A   +  + + ++  + I+    LY + +++  YI  TL
Sbjct: 292  LVGKVAAQDYIDDATGEVVVHANQELSLEDVAKLSQAGIKSFETLYTNDLDHGPYISTTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLSTVGR+K N RL  
Sbjct: 352  QVDNTSDRMEALVEIYRMMRPGEPPTREAAEALFENLFFSEDRYDLSTVGRMKFNRRLGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D    V  + KEDI+ +++ ++++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DESTGVGILTKEDIVDVMRKIIEIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDALMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSTFARTNEYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DGKVT +V YLSA+EE N  IAQAN+ LD+DG+ T+ELV  R  GE I    +++D
Sbjct: 592  RRVIDGKVTEEVEYLSAIEEGNFVIAQANAQLDDDGNLTDELVAARQKGESIFASADQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  FMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIVI+  E +L    +G+DIY L K+ RSNQNTC+NQRP+ 
Sbjct: 712  SGVTVVAKRGGVVDYVDASRIVIKVSEDELMAGEAGIDIYNLTKYTRSNQNTCINQRPVC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFM W+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  AVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMTWNGYNFEDSILLSERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAE+ PGDILVGK+TPKG
Sbjct: 832  HIQELSCIARDTKLGPEEITADIPNVGESALSKLDESGIVYVGAEMKPGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVIDVQVFTRDGVEKDKRAVDIENM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  IL+  IY+R   +L G                S   + +  R +W 
Sbjct: 952  QLRDAKKDLTEEFSILENGIYNRARTLLLGAG-------------FSEAQLDKLSRDKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QYE  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQPLDDEGKQTELEQLADQYEELKAEFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP  ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPVEDMPHDENGVPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   +    +  LR F++K    G       ++ + D  VLR+A+  
Sbjct: 1119 MAAKGIGDKINGMLEQQR---KVEELREFMQKAYDLGNTQQKVDLATFSDAEVLRLADNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+PV+TP FDGA E  I  MLR+A+L +SGQ  LYDG TG  F+RPVTVGY+YMLKLN
Sbjct: 1176 KGGLPVATPAFDGAAEAEIKEMLRLAELPDSGQFTLYDGRTGNAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   + G PESFNV++KE+++LG++I+L+  
Sbjct: 1296 DVNGRTQMYKNIVDGNYQMQPGMPESFNVVLKEIRSLGINIELDQE 1341


>gi|73542873|ref|YP_297393.1| DNA-directed RNA polymerase subunit beta [Ralstonia eutropha JMP134]
 gi|88909634|sp|Q46WD4|RPOB_RALEJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|72120286|gb|AAZ62549.1| DNA-directed RNA polymerase, beta subunit [Ralstonia eutropha JMP134]
          Length = 1368

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1375 (50%), Positives = 952/1375 (69%), Gaps = 20/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL        R  EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIESYTQFLQAETPAARRKTEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +       +
Sbjct: 61   FPIASHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPG---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLQS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGAQLEFVPERL-RGEVARFDIAD-KNGRVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++I++ +TGE+   A D + E  LE +  + ++ I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIIDPDTGEVIANANDELTETVLENLREAGVKQIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL+ 
Sbjct: 356  RVDETADQTAARIAIYRMMRPGEPPTEEAVEALFQRLFYSEESYDLSRVGRMKVNSRLSR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             + +    ++ EDI+  IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PSGEGSMVLQDEDILETIKILVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T+ V YLSA+EE    +AQAN+++D +G+ T+ELV  R     E  +V  ++
Sbjct: 596  RKVENSKLTDQVDYLSAIEEGKYVVAQANATVDAEGNLTDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRPDKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA+RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQAMRGGVVDYVDAMRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDIVARGDVVADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SG V+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGIVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + RL  +L  +    GPK   K   L+ + ++E  +  
Sbjct: 956  DDELKRYRLDLNDQLRIVEGDAFQRLERLLIDKTVNGGPKKLAKGAKLTKEYLAEIDKYH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPADEEVAAQLEAVKEAIEQKRHEFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I  ++   KA+     LR  L ++       E +    D  VL +A   
Sbjct: 1136 LGWAARGLGQRIGDML---KASAKAQELRPLLAQIYNESGKAEDLDSLSDAEVLELATNL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A  D+  +            L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPDDIAKEKGLTASKQQVTLHDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDL+ 
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLDR 1367


>gi|217975208|ref|YP_002359959.1| DNA-directed RNA polymerase subunit beta [Shewanella baltica OS223]
 gi|254765303|sp|B8EBL2|RPOB_SHEB2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|217500343|gb|ACK48536.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS223]
          Length = 1343

 Score = 1642 bits (4253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1364 (51%), Positives = 961/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIMLRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMALVPERL-RGETASYDIKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+++  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN  +D +G   EE + CR  GE   +    I 
Sbjct: 593  RKVIDGVITDEVEYLSAIEEGRYVIAQANIEIDANGRMAEEQIACRHKGESTFMRAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGFVDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L G                S   I+  PR    
Sbjct: 953  HIAQARKDLGEEFKILEEGVLSRARNLLIGAG-------------FSDAQIAALPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 IQVIDDETKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD VLR+A   K 
Sbjct: 1120 AAAKGIGNKITAMLEEQRELAEVRGYIKQVYELGDEVQQRVDIDSFTDDEVLRLATNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKQMLELAGLPTSGQLKLFDGRTGNEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+ +
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQA 1343


>gi|78099462|gb|ABB20867.1| RNA polymerase subunit B [Acinetobacter tandoii]
          Length = 1362

 Score = 1642 bits (4252), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1374 (51%), Positives = 968/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L AL   +E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALDYSNEQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDND-GKVIVEQGKRINARHVRQMEASGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     A+DI   + GE+   A  ++  + + ++    ++   IL+ + ++  ++I ++L
Sbjct: 295  LYERITAQDITLRD-GEVI-PANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFIADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +   DI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNSDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAEADNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D D   TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAVDADNHLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEEEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V++GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVVVRMGDKVARGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVAAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G  G K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLSGQESNGG-GGTKRGDKLSEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPSDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K   +I+ LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGEQIDKML---KQQREIAELRVFLDKIYNKVGGQQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +A++  SGQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLAGNLRAGVPLATPVFDGAEESQIKELLELAEIPRSGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|303249970|ref|ZP_07336172.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 6 str. Femo]
 gi|302651033|gb|EFL81187.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 6 str. Femo]
          Length = 1342

 Score = 1642 bits (4252), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 974/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDGITQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LNL
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 592  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 952  MQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+AE 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1342


>gi|24371822|ref|NP_715864.1| DNA-directed RNA polymerase, beta subunit [Shewanella oneidensis
            MR-1]
 gi|41018043|sp|Q8EK74|RPOB_SHEON RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|24345631|gb|AAN53309.1|AE015472_1 DNA-directed RNA polymerase, beta subunit [Shewanella oneidensis
            MR-1]
          Length = 1345

 Score = 1642 bits (4252), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1367 (51%), Positives = 968/1367 (70%), Gaps = 25/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMTLVPERL-RGETASYDIKDAE-GTVLVEAGRRVTARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+++  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDPTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN  +D +G   EE + CR  GE   +    I 
Sbjct: 593  RKVVDGVITDEVEYLSAIEEGRYVIAQANIEVDSEGRMVEEQIACRHKGESTFMRASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R+I +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAIEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L                  S   I+  PR    
Sbjct: 953  HIAQARKDLGEEFKILEEGVLSRARNLLLSAG-------------FSEAQIAALPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQVIDDEAKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE---KISDYDDDSVLRVAEQ 1199
             A  G+G KI +++ D +  G ++ +R+++++V   G   +    I  + DD +LR+A  
Sbjct: 1120 AAAKGIGHKIAAMLEDQREKG-LAEVRNYIKQVYELGDEVQQRVDIDSFTDDELLRLANN 1178

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K G+PV+TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+RPVTVGY+YMLKL
Sbjct: 1179 LKGGIPVATPAFDGAKEKEIKQMLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKL 1238

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1239 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1298

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 DDVNGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1345


>gi|158512718|sp|A0KQA5|RPOB_AERHH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRDQVLDTPYLLSIQLDSFKQFIEAD----PEGEYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A L++VSY    P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPITSYSGSAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L AL   SE+IL+TF+  I +  + 
Sbjct: 175  RVIPYRGSWLDFEFDAKDNLFVRIDRRRKLPASIILRALDFSSEQILATFFETIGFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +V    G  V+E+G+++T+  ++ L++  V  + +  + 
Sbjct: 235  GKLMMDLVPERL-RGETATFDIV--ANGAVVVETGRRVTARHIRQLEKDSVTQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D  + +TGE+ + A   +  +++  +  +  +   +L+ + +++ AY+  TL
Sbjct: 292  VVGKVAAKDYAHPQTGEMVVTANQALSLEAVANLSQAGFKHFEVLFTNELDHGAYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE +F  LFF S++YDLSTVGR+K N RL  
Sbjct: 352  RIDSSSSRLEALVEIYRMMRPGEPPTREAAEQLFENLFFSSERYDLSTVGRMKFNRRLAR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +    V  + K+DI+ ++K L+D+RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDETGVGTLTKDDIVDVMKRLIDIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I 
Sbjct: 592  RKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTVVAKRGGMIDYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L++ER+V ED  T+I
Sbjct: 772  MLGEPVMAGDVLADGPSTDLGELALGQNLRVAFMPWNGYNFEDSILVNERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACISRDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  I+ R   +L                  S D +++  RS+W+
Sbjct: 952  QLKEAKKDLTEEFKILEDGIFGRSRNLLLAAG-------------YSEDRLNKLDRSKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A++DE  Q  +E +  Q+   K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELAIEDEAKQIELEQIAEQHVELKAEFDKKFENKRRKIIQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP  + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKICPVEDMPHDEYGRPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++ + +   ++      +  +    +    +++  DD V  +    + 
Sbjct: 1119 LAAKGIGEKIDRMVKEQRELHEMRDFLQQVYDLGEKDTQQVNVAELSDDDVRTLVGNLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I ++L++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPVATPVFDGAKEREIKALLKLADLPESGQIALFDGRTGNAFERKVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELDEE 1342


>gi|319787932|ref|YP_004147407.1| DNA-directed RNA polymerase subunit beta [Pseudoxanthomonas
            suwonensis 11-1]
 gi|317466444|gb|ADV28176.1| DNA-directed RNA polymerase, beta subunit [Pseudoxanthomonas
            suwonensis 11-1]
          Length = 1396

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1402 (50%), Positives = 965/1402 (68%), Gaps = 47/1402 (3%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  +    +R + GL AA KSVF
Sbjct: 3    TYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYRDFLQADTDSAKRRDTGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R L+Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PIASYSGNAALEYVGYKLGEPVFDERECRNRGLSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT+ GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTEHGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD ++ RIDRRRK+PVT  L ALG ++EE+L  F+    +     
Sbjct: 181  IIPYRGSWLDFEFDPKDALYTRIDRRRKLPVTILLRALGYNNEEMLRAFFEINTFHIDPS 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +   L D +  + ++E+GK++T+  ++ L++ G+  L +  + L
Sbjct: 241  EGVQLELVPERLRGETLGFDLADGE--KVIVEAGKRITARHVRQLEQSGITALAVPDEYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  +A D+V+  TGE+   A D I ++ L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  LGRILAHDVVDAATGELLAAANDEITDEHLAAFRKAGVASVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D ++ + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLS VGR+K N R+   
Sbjct: 359  IDPSRTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSAVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +      +                      ++++L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGPAVLFDHKYFSERNDEDSKALVAAQGETSDILDVLRVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DG++T+ V YLSA+EE    IAQ N++ D++G  T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVVDGRITDQVEYLSAIEENEYVIAQVNAAHDKEGRLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V  R  GE +L P  +I ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EAFVPVRHQGESLLKPPGEIHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD-LDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G V QVDA RIV+++ E +      +GVD
Sbjct: 719  PTLRAQTPLVGTGIERAVARDSGVTVNARRGGEVVQVDAGRIVVKANEEEISGEHDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L K+ RSNQNTC+NQRPLV VGD V R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYTLTKYTRSNQNTCINQRPLVHVGDVVARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEIT DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVQEDRYTTIHIEELTCVARDTKLGPEEITADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I  + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 959  DVQVFTRDGIEKDKRAKQIEENEIRRVKKDFDDQFRILEAAIYARLRGQIVGKVANGGP- 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G KK   ++   +    ++ W+   ++DE+    +E  + Q    +   E RF +K  KI
Sbjct: 1018 GLKKGDAITDAYLDGLKKADWFLLRMKDEEASDAIERAQKQIAAHEKEFERRFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++ DGTPVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMADGTPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
             LNPLGVPSRMN+GQI E HLGWA  GLGK+I+ ++++ +A   +S LR FL+KV     
Sbjct: 1138 CLNPLGVPSRMNIGQILEVHLGWAAKGLGKRIQKMLDEQRA---VSELREFLDKVYNHDS 1194

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES----- 1231
                    +S + D+ +L +A     GVP++TPVFDGA E+ I  ML +A   +      
Sbjct: 1195 SLVGQRVDLSQFSDEELLGMARNLTGGVPMATPVFDGAYEDEIRQMLELAYPTDDPETVR 1254

Query: 1232 -G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             G      Q  L+DG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLG
Sbjct: 1255 LGFNATKTQMQLHDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLG 1314

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV GN     G P
Sbjct: 1315 GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGNHEMVAGMP 1374

Query: 1345 ESFNVLVKEMQALGLSIDLENS 1366
            ESFNVLVKE+++L ++++LE+ 
Sbjct: 1375 ESFNVLVKEIRSLAINMELEDE 1396


>gi|113869444|ref|YP_727933.1| DNA-directed RNA polymerase subunit beta [Ralstonia eutropha H16]
 gi|122946533|sp|Q0K606|RPOB_RALEH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|113528220|emb|CAJ94565.1| DNA-directed RNA polymerase beta subunit [Ralstonia eutropha H16]
          Length = 1368

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 953/1375 (69%), Gaps = 20/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +  +P L+  Q  SY  FL        R  EGLQAAF ++
Sbjct: 1    MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIESYTQFLQAETPTARRKTEGLQAAFNAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +       +
Sbjct: 61   FPISSHNGLARMEFVSYHLSNPPFDVKECQQRGLTFHSALRAKVRLIINDRENPG---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLQA 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G      + D   G  V+E  K++ +  ++ L   G K + +  D 
Sbjct: 238  EGAQLEFVPERL-RGEVARFDIAD-KNGRVVVEKDKRINAKHIRDLDSAGTKLISVPEDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++I++ +TGE+   A D + E  LE +  + ++ I  LY + ++   Y+  TL
Sbjct: 296  LLGRVLAKNIIDPDTGEVIANANDELTETLLENLREAGVKQIQTLYTNDLDQGPYMSQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 356  RVDETADQTAARIAIYRMMRPGEPPTEEAVEALFQRLFYSEESYDLSRVGRMKVNSRLGR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             + +    ++ EDI+  IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PSGEGAMVLQDEDILETIKILVNLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV D K+T+ V YLSA+EE    +AQAN+++D DG+ T+ELV  R     E  +V  ++
Sbjct: 596  RKVVDSKLTDQVDYLSAIEEGKYVVAQANATVDADGNLTDELVSAREGSERETRMVTPDR 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E  VA
Sbjct: 656  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRPDKPLVGTGIERTVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA+RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 716  VDSGTAVQAMRGGVVDYVDAMRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 776  MVKVGDHVARGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 836  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SG V+DV++F R G+ +++R+ S+ 
Sbjct: 896  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGIVIDVQVFTREGVTRDKRAQSII 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + RL  +L  +    GPK   K   ++ + +++  R  
Sbjct: 956  DDELKRYRLDLNDQLRIVEGDAFQRLERLLIDKTVNGGPKKLAKGAKITKEYLADIDRYH 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE++   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 1016 WFDIRPADEELAAQLEAVKEAIEQKRHEFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 1076 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + +R  L ++       E +    D  VL +AE  
Sbjct: 1136 LGWAARGLGERIGNML---KAQAKAAEVRKLLTQIYNESGKVEDLDSLSDSEVLELAENL 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A  +E  +            L+DG TGE F+RPVT
Sbjct: 1193 KKGVPFATPVFDGAHEDEIRRMLDLAYPEEIAKEKGLTASKQQVTLFDGRTGEAFERPVT 1252

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1253 LGVMHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1312

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++LG+ IDL+ 
Sbjct: 1313 LQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRSLGIDIDLDR 1367


>gi|117918650|ref|YP_867842.1| DNA-directed RNA polymerase subunit beta [Shewanella sp. ANA-3]
 gi|158512308|sp|A0KRL7|RPOB_SHESA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|117610982|gb|ABK46436.1| DNA-directed RNA polymerase, beta subunit [Shewanella sp. ANA-3]
          Length = 1345

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1367 (51%), Positives = 968/1367 (70%), Gaps = 25/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  ++E+G+++T+  ++ L++     L +  + 
Sbjct: 235  DTLVMTLVPERL-RGETASYDIKDAE-GTVLVEAGRRVTARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I+++  LY++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDPDTGEVLVSANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDPTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PDDEGSGVLSKEDIVAVMKNIIHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T+DV YLSA+EE    IAQAN  +D +G   EE + CR  GE   +    I 
Sbjct: 593  RKVVDGVITDDVEYLSAIEEGRYVIAQANIEVDSEGRMVEEQIACRHKGESTFMRASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R+I +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAIEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L                  +   I+  PR    
Sbjct: 953  HIAQARKDLGEEFKILEEGVLSRARNLLLSAG-------------FTEAQIAALPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQVIDDETKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE---KISDYDDDSVLRVAEQ 1199
             A  G+G KI +++ D +  G ++ +R+++++V   G   +    I  + DD +LR+A  
Sbjct: 1120 AAAKGIGNKIAAMLEDQREKG-LAEVRNYIKQVYELGDEVQQRVDIDSFTDDELLRLANN 1178

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K G+PV+TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+RPVTVGY+YMLKL
Sbjct: 1179 LKGGIPVATPAFDGAKEKEIKQMLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKL 1238

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1239 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1298

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 DDVNGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1345


>gi|85712785|ref|ZP_01043829.1| DNA-directed RNA polymerase beta subunit [Idiomarina baltica OS145]
 gi|85693425|gb|EAQ31379.1| DNA-directed RNA polymerase beta subunit [Idiomarina baltica OS145]
          Length = 1342

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 981/1365 (71%), Gaps = 26/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S+  F+ ++       N GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLEVPYLLSMQLDSFKKFIEVD----PEANNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV++C  R +TY+ PL++ LRL++FD +   G  ++
Sbjct: 57   FPIASYSGNAELQYVSYHLGEPAFDVEECQIRGITYSAPLRVKLRLVLFDKEAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL  F+    +    
Sbjct: 175  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLPASIILRALEYTTEEILEMFFETTYFEILK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G      + D   GE V+E G+++T+  ++ L++  +K L +  + 
Sbjct: 235  TKVKMQLVPERL-RGETAKFDIKDS-NGEIVVEKGRRVTARHIRQLEKSEMKELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D V+ ETGE+  +A D +  + +  +  + ++ I  L+V+ +++  Y+  TL
Sbjct: 293  MVGKVLAKDYVSKETGEVVAKANDELTLELIANLSEAGVKKIETLFVNDLDHGPYMSETL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F+ LFF  ++YDLSTVGR+K N RL  
Sbjct: 353  RVDSTTNRLEALVEIYRMMRPGEPPTREAAEALFDNLFFSEERYDLSTVGRMKFNRRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDII ++K L+++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  EDLSGKNTLTNEDIIDVMKKLIEIRNGLDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+ MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVKERLSLGDLDNTMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNEYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ +G VT++V YLSA+EE N  IAQAN +L++ G   ++LV CR   E  L+ RE++ 
Sbjct: 593  RRIENGVVTDEVEYLSAIEEGNYVIAQANVALNDQGELVDDLVPCRHKNEFTLMNREQVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D +P+Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 653  FMDVAPQQIVSIAASMIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIERTIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G+V+ VDA RIV++  E ++ P  +G+DIY L K++RSNQNTC+NQ+P V
Sbjct: 713  SGVTIVAKRGGVVDYVDAARIVVKVNEEEMVPGEAGIDIYNLTKYKRSNQNTCINQKPTV 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            ++G+ V R D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L+SER+  ED  T+I
Sbjct: 773  RLGEPVMRGDVLADGPSTDLGELALGQNLRVAFMPWNGYNFEDSILLSERVAQEDRLTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE G++ VGAEV  GDILVGK+TPKG
Sbjct: 833  HIQELNCVARDTKLGAEEITSDIPNVGESALGKLDEAGVVYVGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV+GTV+DV++F R G++K++R++++E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVNGTVIDVQVFTRDGVEKDKRAVAIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  +E  IL+  IY R   +L                      ++   RS W 
Sbjct: 953  QLAKVKKDLTEEFKILEDGIYGRARSLLLNNG-------------FDEAKLASMDRSNWL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E +  QY+ ++   + +F+ K  KI  GDD+ PGVL++VKV++A++R
Sbjct: 1000 TQGLADESAQEQLEQIAEQYQQTREDFDQKFEMKRRKITQGDDLAPGVLKIVKVYLAVRR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDK+AGRHGNKG++S I+P EDMP  ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 RIQPGDKLAGRHGNKGVISTIIPNEDMPHDEEGNPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   KA   ++ LR F+++V   G G     ++++ DD VLR+A   
Sbjct: 1120 MAARGIGTKIDKML---KAQRAMAELRDFIQQVYDLGEGRQKVDLAEFSDDEVLRLAGNL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+P +TP FDGA EE I ++L++AD+ ESGQ  L DG TGE F+R VTVGY+YMLKLN
Sbjct: 1177 RAGLPTATPAFDGAIEEEIKALLKLADIPESGQIPLIDGRTGERFERDVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT++Y++IV  N   E G PESFNVL+KE+++LG++I+LE 
Sbjct: 1297 DVNGRTKMYKNIVDNNLQMEAGMPESFNVLLKEIRSLGINIELEE 1341


>gi|239993452|ref|ZP_04713976.1| DNA-directed RNA polymerase subunit beta [Alteromonas macleodii ATCC
            27126]
          Length = 1342

 Score = 1641 bits (4250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1366 (52%), Positives = 981/1366 (71%), Gaps = 26/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P++++IP L+ +Q  S+  F+ ++         GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLEIPYLLSIQLDSFKKFIEIDADAQ----YGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG++ L++VSY    P FDV +C  R +T++ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIKSYSGSSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVLFDKDAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL M SEEIL TF+ K+      
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALEMTSEEILDTFFDKVSVRIDK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     +   D + G   +  ++D + G  V+E+G+++++   ++L++ G+  L + +D 
Sbjct: 235  DKLMMEVVP-DRLRGETAAFDIIDGE-GNVVVETGRRISARHTRALEKAGLTELEVPADY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A   VN +TGE+ + A D +  ++L  +  + I++   LY++ +++ +YI +TL
Sbjct: 293  LIGRVYAATYVNEDTGEVIVSANDELTLENLAALSQAGIKEFETLYINELDHGSYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F+ LFF  ++YDLS+VGR+K N RL  
Sbjct: 353  RIDSSTNRLEALVEIYRMMRPGEPPTKDAAETLFDNLFFSDERYDLSSVGRMKFNRRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII+++K L+ +R+GK  +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  EELIGAGTLDKEDIISVMKQLIMIRDGKDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N +GF+ETP+
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGLNIGLINSLASFARTNDFGFLETPF 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ DG VT+++ YLSA+EE    IAQAN +L E G   ++L+ CR  GE  L+P+E I 
Sbjct: 593  RRIVDGVVTDEIDYLSAIEEGQFAIAQANIALTEAGELVDDLIPCRHRGETTLMPKEDIK 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A  
Sbjct: 653  YMDVSPQQIVSIAASIIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERTIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 713  SGVTVVAKRGGVVDYVDASRIVIKVDEDEMLPGEAGIDIYNLTKYTRSNQNTCINQKPTC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD +   D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPIVAGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGPEEISSDIPNVGESALSKLDESGVVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V GTV+DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVHGTVIDVQVFTRDGVEKDKRALEIEDM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  DE  IL   I++R    L                      +   PR +W+
Sbjct: 953  QLRQVKKDLTDEFEILADGIFARAQTALLRAGV-------------DQAKLDSLPREKWF 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A+  E  Q  ++ +  Q+   K   + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 EIALNSEDAQLELDQIADQHAEIKLDFDKKFEGKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+  +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 HIQPGDKMAGRHGNKGVISTIQPVEDMPYDANGTPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  GLG KI  +I   K   +++ LR FL+KV   G       I  + D  V R+AE  
Sbjct: 1120 MAAHGLGVKIDRMI---KEQRELAELRDFLKKVYELGENHQEVDIDSFTDHEVRRLAENL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVPV+TPVFDGA E  I  ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLN
Sbjct: 1177 RKGVPVATPVFDGARESEIKEMLKLADIPESGQIALFDGRTGREFERPVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1297 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEK 1342


>gi|237809522|ref|YP_002893962.1| DNA-directed RNA polymerase subunit beta [Tolumonas auensis DSM 9187]
 gi|259494195|sp|C4LBV2|RPOB_TOLAT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|237501783|gb|ACQ94376.1| DNA-directed RNA polymerase, beta subunit [Tolumonas auensis DSM
            9187]
          Length = 1342

 Score = 1641 bits (4249), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1361 (51%), Positives = 962/1361 (70%), Gaps = 22/1361 (1%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
             +    R+RK FGK  ++++ P L+ +Q  S+  FL  +         GL+AAF+SVFPI
Sbjct: 4    SYTEKKRIRKDFGKRDQVLETPYLLSIQLDSFKQFLDADPEGA----YGLEAAFRSVFPI 59

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            T++SG A L++VSY    P FDV +C  R +TY+ PL++ LRL++FD +   G  ++K+I
Sbjct: 60   TSYSGTAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVLFDKEAAAG--TVKEI 117

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  R+I
Sbjct: 118  KEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNARVI 177

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
            P +G W+D EFD+KD + VRIDRRRK+P T  L AL   +EEIL+TF+  I +  +    
Sbjct: 178  PYRGSWLDFEFDAKDNLFVRIDRRRKLPATIILRALEFTTEEILTTFFETIKFEIKDGKV 237

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
               L    L  G   +  +V    G+ V+E G+++T+  ++ L++ G+  + +  + + G
Sbjct: 238  LMELVPERL-RGETATFDIV--AGGDVVVEKGRRITARHIRQLEKAGISQIEVPVEYVVG 294

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
               A D VN +TGE+ I A   +  +++  +  +  +   +L+ + +++ +YI  TL  D
Sbjct: 295  KISARDYVNPQTGEVMINANTALSLEAIANLSQAGFKQFEVLFTNELDHGSYISETLRID 354

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             + +R +AL++IYR+MRPG+  T   AE +F  LFF +D+YDLSTVGR+K N RL     
Sbjct: 355  SSTNRLEALVEIYRMMRPGEPPTKDAAEQLFENLFFSADRYDLSTVGRMKFNSRLARPDH 414

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                 + ++DI+ ++K L+ +RNGK  +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER+
Sbjct: 415  IGSGILSQDDIVDVMKQLIAIRNGKDDVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERA 474

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            +KER+S  D+D++ PQDLINAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 475  VKERLSLGDLDAIQPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 534

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  ++R N YGF+ETPYRKV
Sbjct: 535  PGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAVYSRTNEYGFLETPYRKV 594

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             DG +T++V YLSA+EE N  IAQAN+++D D    +EL+ CR  GE   +  E+I ++D
Sbjct: 595  IDGVITDEVDYLSAIEEGNFVIAQANANVDADARLKDELIPCRHKGESTFMNAEQIQYMD 654

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 655  VSPQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVDSGV 714

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             +VAKR G ++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V VG
Sbjct: 715  TVVAKRGGTIDYVDASRIVVKVNEDELLPGEAGIDIYNLTKYTRSNQNTCINQRPCVSVG 774

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            + V   D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED  T+IHI+
Sbjct: 775  EPVMLGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRLTTIHIQ 834

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ 
Sbjct: 835  ELSCIARDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKGETQ 894

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTV+DV++F R G++K++R+  VE  Q+ 
Sbjct: 895  LTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVIDVQVFTRDGVEKDKRAKEVEDMQLR 954

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               +D  +E  IL+  I+ R   +L                    D +S+  R +W + +
Sbjct: 955  DAKKDLTEEFKILEDGIFGRARSLLIANG-------------FGEDRLSKLDRKRWLEQS 1001

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            + DE  Q  +E +  Q+   K   + +F+ K +KI  GDD+ PGVL++VKV++A+KR IQ
Sbjct: 1002 LDDEGKQVELEQIAEQHIALKEEFDRKFEAKRQKIIQGDDLAPGVLKIVKVYLAVKRRIQ 1061

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG++S+I P EDMP+  +G PVDIVLNPLGVPSRMN+GQI E HLG A 
Sbjct: 1062 PGDKMAGRHGNKGVISKICPVEDMPYDDEGNPVDIVLNPLGVPSRMNIGQILEVHLGLAA 1121

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G+KI  ++ + +   ++      +  + G+      I+   DD V  + +  + G+P
Sbjct: 1122 KGIGEKIDRMVKEQRELAELREFLQRVYDLGGSDQQQIDIATLSDDDVRTLVQNLRKGLP 1181

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            V+TPVFDGA E  I  +L++AD  ESGQ  L+DG TG PF+R VTVGY+YMLKLNH+V D
Sbjct: 1182 VATPVFDGAKESEIKELLKLADKPESGQITLFDGRTGMPFERVVTVGYMYMLKLNHLVDD 1241

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GR
Sbjct: 1242 KMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGR 1301

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1302 TKMYKNIVDGDHRMEPGIPESFNVLLKEIRSLGINIELEEE 1342


>gi|330831427|ref|YP_004394379.1| DNA-directed RNA polymerase subunit beta [Aeromonas veronii B565]
 gi|328806563|gb|AEB51762.1| DNA-directed RNA polymerase subunit beta [Aeromonas veronii B565]
          Length = 1342

 Score = 1641 bits (4249), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRDQVLDTPYLLSIQLDSFKQFIEAD----PEGEYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A L++VSY    P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPITSYSGSAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L AL   SE+IL+TF+  I +  + 
Sbjct: 175  RVIPYRGSWLDFEFDAKDNLFVRIDRRRKLPASIILRALDFTSEQILATFFETIGFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +V    G  V+E+G+++T+  ++ L++  V  + +  + 
Sbjct: 235  GKLMMDLVPERL-RGETATFDIV--ANGAVVVETGRRVTARHIRQLEKDAVTQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D  + +TGE+ + A   +  +++  +  +  +   +L+ + +++ AY+  TL
Sbjct: 292  VVGKVAAKDYAHPQTGEMVVTANQALSLEAIANLSQAGFKHFEVLFTNELDHGAYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE +F  LFF +++YDLSTVGR+K N RL  
Sbjct: 352  RVDSSSNRLEALVEIYRMMRPGEPPTREAAEQLFENLFFSAERYDLSTVGRMKFNRRLGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + K+DI+ ++K L+D+RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDETGAGVLTKDDIVDVMKRLIDIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I 
Sbjct: 592  RKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTVVAKRGGVIDYVDASRIVLKVNEDELMPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L++ER+V ED  T+I
Sbjct: 772  MLGEPVMAGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVNERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACISRDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  I+ R   +L                  S D +++  RS+W+
Sbjct: 952  QLKEAKKDLTEEFKILEDGIFGRSRNLLLAAG-------------YSEDRLNKLDRSKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A++DE  Q  +E +  Q+   K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELAIEDEGKQTELEQIAEQHVELKAEFDKKFENKRRKIIQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP  + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKICPVEDMPHDEFGRPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  ++ + +   ++      +  +    +    I++  DD V  +    + 
Sbjct: 1119 LAAKGIGEKIDRMVKEQRELHEMRNFLQQVYDLGEKDTQQVNIAELSDDDVRTLVGNLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I ++L++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPVATPVFDGAKEREIKALLKLADLPESGQIDLFDGRTGNRFERKVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELDEE 1342


>gi|269103665|ref|ZP_06156362.1| DNA-directed RNA polymerase beta subunit [Photobacterium damselae
            subsp. damselae CIP 102761]
 gi|268163563|gb|EEZ42059.1| DNA-directed RNA polymerase beta subunit [Photobacterium damselae
            subsp. damselae CIP 102761]
          Length = 1341

 Score = 1641 bits (4249), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1366 (51%), Positives = 964/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDAPYLLSIQLDSFQKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +++IL  F+ K+ +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPASIILRALGYTTDQILDMFFEKVKFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G   +E G+++T+  ++ L + GV  + +  + 
Sbjct: 235  KSLVMELVP-DRLRGETASFDIE--ANGTVYVEKGRRITARHIRQLAKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+   A   +  +SL  +  +  + I +L+ + +++  Y+ +TL
Sbjct: 292  IVGKVAAKDYVNEATGELIAAANQELSLESLALLSQAGHKSIEVLFTNDLDHGPYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N  L  
Sbjct: 352  RIDSTTDRLSALVEIYRMMRPGEPPTREAAEQLFESLFFSEERYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DETTGPGTLDNQDIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVFARCNPYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKV+ ++ YLSA+EE    IAQAN++L+EDGSF +EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDGKVSEEIEYLSAIEEGQYVIAQANAALNEDGSFADELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE++D+NR LMG NMQRQAVP ++A+ P VGTG+E  +   
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHNDANRALMGANMQRQAVPTIRADKPLVGTGIERQIGVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  + +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGQVQFVDASRIVIKVNDDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP  V+GTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPGSVTGTVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S D I+   R + +
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRTLLLASG-------------YSEDKIASMDREKLF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  AQTLDDEALQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQTVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++  +R FL++V   G       I+   D+ VL +A+  
Sbjct: 1119 LAAKGIGDKINEMM---KQQQELHKIREFLQRVYDLGDTRQKVDIALLSDEEVLTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL  SGQ  L+DG TG PF+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPIATPVFDGAPEASIKELLQLGDLPSSGQLQLFDGRTGNPFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|182676560|sp|A9KD39|RPOB_COXBN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1375

 Score = 1640 bits (4248), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1370 (52%), Positives = 984/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 11   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 70

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 71   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 131  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 191  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 251  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 309  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGLYV 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 369  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 429  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 489  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 549  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 609  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 669  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 729  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 788

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 789  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 848

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 849  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 908

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+ VRIF R G+ K+ER++
Sbjct: 909  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIGVRIFTREGVKKDERTL 968

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 969  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1028

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1029 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1088

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1089 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1148

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1149 ETHLGWATKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1205

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1206 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1265

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1266 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1325

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1326 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1375


>gi|149925884|ref|ZP_01914147.1| DNA-directed RNA polymerase, beta subunit [Limnobacter sp. MED105]
 gi|149825172|gb|EDM84383.1| DNA-directed RNA polymerase, beta subunit [Limnobacter sp. MED105]
          Length = 1369

 Score = 1640 bits (4248), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1376 (50%), Positives = 971/1376 (70%), Gaps = 19/1376 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK F K P ++D+P L+  Q  SY  FL + +  ++R  +GLQAAF+SV
Sbjct: 1    MSYSATEKKRIRKSFAKRPPVLDVPYLLTTQLDSYTDFLQLGLPVEKRAEQGLQAAFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FDV +C  R LT+  PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVQYALGEPAFDVKECQQRGLTFCSPLRARVRLVLLDR--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT++G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGELPLMTQNGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+GM++E+ILSTF+    +  + 
Sbjct: 179  RIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGMNNEQILSTFFEFDQFEIKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L  + L  G      +VD  +G+ +++  K++ +  ++ ++  G+K + +  D 
Sbjct: 239  EGASMDLVTSRL-KGEVAKFDIVD-KSGKVLVQKDKRINAKHIRDIEAAGLKKISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+  TGE+   A D I E+ + +I  + ++ +  ++ + +++ AYI  TL
Sbjct: 297  LIGRTLAKNIVDASTGEVVASANDEITEEIMGKIRDAGVKVVETIFTNELDHGAYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E +FN LF+  D YDLS VGR+K N R+  
Sbjct: 357  RTDETADQTAARVAIYRMMRPGEPPTEEAVEMLFNRLFYSEDSYDLSRVGRMKFNRRVGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    ++ +DI+A+IKILVDLRNG G IDDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 417  PEVEGAMVLQDDDILAVIKILVDLRNGNGEIDDIDHLGNRRVRCVGELAENQFRAGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLGQAEAENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S+  FAR+N YGF+ETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSMAMFARLNEYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV  G V++++VYLSA+EE    IAQAN+ +DE      +LV CR AGE  L+    ++
Sbjct: 597  RKVEGGVVSDEIVYLSAIEEGRFVIAQANAEIDEKKRLVGDLVSCRVAGEFELMDPSGVE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E PF GTG+E  VA  
Sbjct: 657  LMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPFAGTGIERTVAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVA   G+V+ VDA RIVIR  + +++  + GVDIY L K+ RSNQNT +NQRP+V
Sbjct: 717  SGTVIVADHGGVVDYVDANRIVIRVNDNEVESGSVGVDIYNLTKYTRSNQNTNINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD + + D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +TSI
Sbjct: 777  NKGDIIAKGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N+SE  L  +DE GI+ +GAEV  GD++VGK+TPKG
Sbjct: 837  HIEELSVVARDTKLGSEEITRDISNLSEAQLSRLDESGIVYIGAEVQAGDVMVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + +SR+   L G+ A  GP    K T ++++ + E     W+
Sbjct: 957  ELKRYRLDLNDQMRIVEADAFSRIERFLVGKVANGGPAKLAKGTKITTEYLKEVDHHHWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + +E+    +E+LK   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR
Sbjct: 1017 DIRLAEEEAAGQLETLKKSIEDKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P ED+P + DG PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSKIVPVEDLPHMADGRPVDIVLNPLGVPSRMNVGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+G +I  ++   +    ++ LR +L KV      T  +    D  ++ + +    
Sbjct: 1137 WAAKGIGDRINEML---REQNAVARLREYLHKVYNGTGTTVDLDSLTDIEIINMGKNLTK 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDES------G------QSILYDGLTGEPFDRPVT 1250
            G+P +TPVFDGA+EE I  MLR+A  DE       G      Q  LYDG TG+ FDR VT
Sbjct: 1194 GMPFATPVFDGANEEDILEMLRLAYPDEDPRMQALGFNESKTQVTLYDGRTGDAFDRKVT 1253

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY ++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1254 VGYKHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1313

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYE++V G+ T + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 1314 LQEMLTVKSDDVNGRTKVYENLVKGDHTIDAGMPESFNVLVKEIRSLGIDIDLDRN 1369


>gi|303253142|ref|ZP_07339291.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 2 str. 4226]
 gi|302647824|gb|EFL78031.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 2 str. 4226]
          Length = 1342

 Score = 1640 bits (4248), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 974/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++  +K + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDEIKQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LNL
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 592  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 952  MQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+AE 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1342


>gi|224713636|gb|ACN62088.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
          Length = 1362

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 982/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYDRITAEDITLLD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|58583214|ref|YP_202230.1| DNA-directed RNA polymerase subunit beta [Xanthomonas oryzae pv.
            oryzae KACC10331]
 gi|84625051|ref|YP_452423.1| DNA-directed RNA polymerase subunit beta [Xanthomonas oryzae pv.
            oryzae MAFF 311018]
 gi|188575481|ref|YP_001912410.1| DNA-directed RNA polymerase subunit beta [Xanthomonas oryzae pv.
            oryzae PXO99A]
 gi|75434343|sp|Q5GWS6|RPOB_XANOR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|109914409|sp|Q2NZX8|RPOB_XANOM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699460|sp|B2SQQ1|RPOB_XANOP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|58427808|gb|AAW76845.1| RNA polymerase beta subunit [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84368991|dbj|BAE70149.1| RNA polymerase beta subunit [Xanthomonas oryzae pv. oryzae MAFF
            311018]
 gi|188519933|gb|ACD57878.1| DNA-directed RNA polymerase, beta subunit [Xanthomonas oryzae pv.
            oryzae PXO99A]
          Length = 1383

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1389 (50%), Positives = 966/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++   +R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVESTKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEISEDQLTAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  DVLGESVLYDKKYFAERNDEESKRLVAEHTDTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G  
Sbjct: 959  DVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-A 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI
Sbjct: 1018 NLKKGDSVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL+ +    +
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLDDIYNHDN 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ L
Sbjct: 1195 AINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L + ++LE 
Sbjct: 1375 LAIHMELEE 1383


>gi|209364192|ref|YP_001425190.2| DNA-directed RNA polymerase subunit beta [Coxiella burnetii Dugway
            5J108-111]
 gi|207082125|gb|ABS77649.2| DNA-directed RNA polymerase beta chain [Coxiella burnetii Dugway
            5J108-111]
          Length = 1377

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1370 (52%), Positives = 984/1370 (71%), Gaps = 10/1370 (0%)

Query: 2    AKGVVFNGLGRVRKFFGKNP-EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            +  + +    R R   GK   EI+  P L+E Q  SY  FL  +IA ++R + GL AAFK
Sbjct: 13   SATISYPEKRRARVNLGKREVEILKTPYLLETQIESYRKFLQKDIAAEKREDNGLHAAFK 72

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            SVFPIT++SG A+LE+V Y        FDV++C  R LTYA PLK+ +RL+++D +   G
Sbjct: 73   SVFPITSYSGYAVLEYVGYSLGGESTLFDVEECKLRGLTYAAPLKVNMRLVIYDKEAPAG 132

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
             K+IKDIKEQ +YMG++PLMT+ G+ VI G +R+VVSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 133  KKAIKDIKEQEVYMGEIPLMTETGSLVINGTERVVVSQLHRSPGVFFEHDKGKTHSSGKL 192

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ R+IP +G W+D EFD KD + VRIDRRRK+P T  L ALG D+E+IL  FY    +
Sbjct: 193  LYSARVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPATVILRALGYDTEQILDMFYKTNHF 252

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                +     L    L  G      + D   G+ ++E+ +++++  ++ +++  +  L +
Sbjct: 253  HLNQETVTLDLIPQRL-RGELAVVEIKDKK-GKVIVEANRRISARHIRLIEKAEINKLEL 310

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  + + I++ ETGEI   A + I  + L+ +  ++   +  LY++ +    Y+
Sbjct: 311  PDDYLYGKVIGKTIIDKETGEIIAHANEEITAELLKNLRATKTASLDTLYINEIECGLYV 370

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +TL  D   ++ +AL++IYR+MRPG+  T   AES+F  LFF  ++Y LS VGR+K N 
Sbjct: 371  SDTLRLDTTTNQLEALVEIYRIMRPGEPPTKEAAESLFENLFFSPERYSLSAVGRMKFNR 430

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+       +  + KEDI+ ++++LVD+R+GKG +DDID+LGNRR+RSVGEM +NQ+R+G
Sbjct: 431  RVGRKELTGLDVLSKEDIVDVLRVLVDIRDGKGDVDDIDHLGNRRIRSVGEMAENQFRVG 490

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+R+ER++K+R+S  D++++MPQDL+NAKPV +A+ EFF SSQLSQ  +  N LS ITH 
Sbjct: 491  LVRVERAVKDRLSLADVENLMPQDLVNAKPVSAAIKEFFGSSQLSQFMDQNNPLSEITHK 550

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FAR N YGF+
Sbjct: 551  RRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLAVFARANEYGFL 610

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYRKV D  VT++  YLSA+EE + YIAQAN+++DE G   ++L+ CR  GE  L   
Sbjct: 611  ETPYRKVVDRVVTDETEYLSAIEEGDYYIAQANTNVDEKGRLVDDLISCRYKGEFTLTTP 670

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +KI+++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP ++ E P VGTGME  
Sbjct: 671  DKINYMDVSPRQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTIRPETPLVGTGMERT 730

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG  ++AKR+G+++ VDA RIV+R   +   D    GVDIY L KF RSNQNTC+N
Sbjct: 731  VAVDSGVTVIAKRSGVIDSVDASRIVVRVDRKETEDDDDIGVDIYNLTKFTRSNQNTCIN 790

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+VGD+V++ D++ADGPSTD+G+LALG+N+LVAFMPW+GYNFEDS+LISER+V ED
Sbjct: 791  QHPIVEVGDKVQKGDVLADGPSTDIGELALGQNLLVAFMPWNGYNFEDSILISERLVEED 850

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHI+EF  +ARDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK
Sbjct: 851  RFTTIHIQEFTCVARDTKLGPEEITSDIPNVGESALAKLDESGIVHIGAEVNAGDILVGK 910

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G++GTV+ VRIF R G+ K+ER++
Sbjct: 911  VTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVTPGITGTVIGVRIFTREGVKKDERTL 970

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E+ ++  + +D +DE  + +  ++  L ++L G+ A  GP    K T ++   +++ P
Sbjct: 971  EIEKAELSKVEKDLNDELRVREDALFENLEKLLTGRVAAGGPNKLAKGTKITKSYLADLP 1030

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R +W++  +QD+   + +E+    ++  +   + + K+  +K+  G D+ PGV+++VKV+
Sbjct: 1031 RQKWFEIRLQDDAATKRLEASHEHFKELRETRDAKLKDSRQKLTQGGDLAPGVIKIVKVY 1090

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR IQ GDKMAGRHGNKG++S I+P EDMP+L+DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1091 LAVKRRIQPGDKMAGRHGNKGVISTIVPIEDMPYLEDGTPVDIVLNPLGVPSRMNIGQVL 1150

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRV 1196
            ETHLGWA  GLGKKI  +I   +   D   LR  L+ +          +   +D  ++ +
Sbjct: 1151 ETHLGWATKGLGKKIGEMI---EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTL 1207

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A+  + GVP+S+PVFDGA EE I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YM
Sbjct: 1208 AKNLRKGVPISSPVFDGATEEEIKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYM 1267

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT
Sbjct: 1268 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLT 1327

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +KSDDV GRTR+Y++IV G+   + G PESFNVLVKE+++L + I LEN 
Sbjct: 1328 VKSDDVAGRTRMYKNIVDGDHRMDAGMPESFNVLVKEIRSLAIDIGLEND 1377


>gi|332108093|gb|EGJ09317.1| DNA-directed RNA polymerase subunit beta [Rubrivivax benzoatilyticus
            JA2]
          Length = 1373

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1379 (50%), Positives = 976/1379 (70%), Gaps = 19/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     F    R+RK FGK   ++ +P L+ +Q  SY  FL  ++ P +R  EGLQAA
Sbjct: 1    MAQATPYTFTERKRIRKSFGKRESVLKVPYLLTMQSDSYVAFLQKDVPPQQRKPEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F S FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  L++I++D  E   
Sbjct: 61   FLSAFPIVSHNGFVEMKFLEYNIAKPPFDVRECQQRGLTFAAAVRAKLQMIIYDR-ESHP 119

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            AK +K+IKEQ +YMG++PLMT  G+F++ G +R++VSQLHRSPG+ F+HDKG+   SGKL
Sbjct: 120  AKVVKEIKEQEVYMGEVPLMTDYGSFIVNGTERVIVSQLHRSPGVFFEHDKGKTHSSGKL 179

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            L++ RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E+ILS F+    +
Sbjct: 180  LFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPEQILSHFFVFDNF 239

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                           L  G      L D   G  ++E  K++T+  ++ L++ G  F+ +
Sbjct: 240  RLMDSGAQMEFVPERL-KGEIARFDLTD-KNGAVIVEKDKRITARHVRQLEQSGTTFVSV 297

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  +A ++V+ +TGEI  +A D + E  L+++  + I+DI  L+ + +N  AYI
Sbjct: 298  PEDFLVGRVIARNMVDPDTGEIVAKANDEVTESLLKKLRSAGIKDIQCLFTNELNQGAYI 357

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
              TL +D+  D+  A + IYR+MRPG+  T    E++F+ LF+  D YDLS VGR+K N 
Sbjct: 358  SQTLASDETADQLAARVAIYRMMRPGEPPTEDAVEALFHRLFYSEDTYDLSRVGRMKFNA 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            R+  D PD    +  EDI+ ++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR G
Sbjct: 418  RVGRDVPDGKMTLSNEDILDVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRSG 477

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L R+E+++KER+   + +++MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH 
Sbjct: 478  LARIEKAVKERLGQAETEALMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITHK 537

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF+
Sbjct: 538  RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNEYGFL 597

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYR+V DGKVT+ + YLSA+EE    IAQAN++LD +G   +ELV  R  GE +L+  
Sbjct: 598  ETPYRRVVDGKVTDQIDYLSAIEEGKYVIAQANATLDGEGRLIDELVSARENGESVLLSP 657

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++ ++D +P Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E V
Sbjct: 658  ERVQYMDVAPTQIVSVAASLVPFLEHDDANRALMGANMQRQAVPTLRPEKALVGTGVERV 717

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             A  SG  + A+R GIV+ VD  RIVIR  + +      GVDIY L+K+QRSNQNT ++Q
Sbjct: 718  AAVDSGTVVTARRGGIVDYVDTNRIVIRVNDDETVAGEVGVDIYNLIKYQRSNQNTNIHQ 777

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RP+V+ GD V   D++ADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V++D 
Sbjct: 778  RPIVRRGDHVGAGDVVADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVADDR 837

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            +TSIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GI+ +GAEVNPGD+LVGK+
Sbjct: 838  YTSIHIEELVVMARDTKLGSEEITRDIPNLSEQQLARLDESGIVYIGAEVNPGDVLVGKV 897

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  
Sbjct: 898  TPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGTSGTVIDVQVFTREGIQRDKRAQQ 957

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +  ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T ++ + ++   +
Sbjct: 958  IIDDELKRFRLDLNDQLRIVEADAFDRIEKLLAGKVANGGPQKIAKGTTITKEYLATVEK 1017

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
              W+     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++
Sbjct: 1018 YHWFDIRPSEDEVANQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYL 1077

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG+VS+I+  EDMP++ DGTP DIVLNPLGVPSRMNVGQ+ E
Sbjct: 1078 AVKRRLQPGDKMAGRHGNKGVVSKIVAVEDMPYMADGTPCDIVLNPLGVPSRMNVGQVLE 1137

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVA 1197
             HLGWA  G+G +I  ++   +     + LR FL+++   +G  TE + D  DD ++ +A
Sbjct: 1138 VHLGWAGKGIGHRIGDML---QQQARAAELREFLDELYNQSGGKTESLQDLSDDEIVEMA 1194

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFDR 1247
            +  + GVP +TPVFDGA EE I  ML++A  DE            Q+ L+DG TGE F+R
Sbjct: 1195 KNLQHGVPFATPVFDGAHEEEIRGMLKLAYPDELAARKGLTATRTQATLHDGRTGEAFER 1254

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1255 PVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1314

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +Y+LQEMLT+KSDDV GRT+VYE+IV G  + E G PESFNVLVKE+++LG+ I+LE  
Sbjct: 1315 SYILQEMLTVKSDDVNGRTKVYENIVKGEHSIEAGMPESFNVLVKEIRSLGIDIELERD 1373


>gi|317401596|gb|EFV82223.1| DNA-directed RNA polymerase subunit beta [Achromobacter xylosoxidans
            C54]
          Length = 1370

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1375 (50%), Positives = 958/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + AP +R  +GLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTAPSDRVADGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGMARLEFVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KDI+  R+DRRRK+PVT    A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILCKAIGMTPESILANFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D  +G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGAMMEFVPE-RWKGEMARFDIAD-RSGKVIVEKDKRINAKHLRDLAAGGIQRISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  + + DI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDADTGEVIANANDEITESVLGALRAANVHDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RTDETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GEDITGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DG+V++ + YLSA+EE +  IAQAN++LDE+G F ++LV CR AGE +L     +
Sbjct: 597  YRKIVDGRVSDQIDYLSAIEESHYVIAQANAALDEEGKFVDDLVACREAGETMLTAPANV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPVVGTGIERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 777  VKRGDRVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI  +GAEV+  D+LVGK+TPK
Sbjct: 837  VHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGITYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L G+    GP+   K   ++   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVGKTVNGGPRKLAKGATITKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +    +  +R++L+KV  T     +I +  D+ V+ +A+  K
Sbjct: 1137 GWAAKGVGHRIADMLRDERT-AQVKNVRAYLDKVYNTTGTGARIDELTDEEVMEMAQNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA EE I  ML +A                Q+ LYDG TGE F+RPVTV
Sbjct: 1196 NGVPFATPVFDGATEEEITKMLELAYPDDVAKRMALTPSRTQAWLYDGRTGEKFERPVTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|145297378|ref|YP_001140219.1| DNA-directed RNA polymerase subunit beta [Aeromonas salmonicida
            subsp. salmonicida A449]
 gi|142850150|gb|ABO88471.1| DNA-directed RNA polymerase, beta subunit [Aeromonas salmonicida
            subsp. salmonicida A449]
          Length = 1379

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 38   MVYSYTEKKRIRKDFGKRDQVLDTPYLLSIQLDSFKQFIEAD----PEGEYGLEAAFRSV 93

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A L++VSY    P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 94   FPITSYSGSAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 151

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 152  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 211

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L AL   SEEIL+ F+  I +  + 
Sbjct: 212  RVIPYRGSWLDFEFDAKDNLFVRIDRRRKLPASIILRALDFSSEEILANFFETIGFEVKD 271

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +V    G  V+E+G+++T+  ++ L++  V  + +  + 
Sbjct: 272  GKLMMDLVPERL-RGETATFDIV--ANGAVVVETGRRVTARHIRQLEKDAVTQIEVPVEY 328

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A++  + +TGE+ + A   +  +++  +  +  +   +L+ + +++ AY+  TL
Sbjct: 329  VVGKVAAKNYTHPQTGEMVVTANQALSLEAVANLSQAGFKHFEVLFTNELDHGAYMSETL 388

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE +F  LFF S++YDLSTVGR+K N RL+ 
Sbjct: 389  RIDSSSSRLEALVEIYRMMRPGEPPTREAAEQLFENLFFSSERYDLSTVGRMKFNRRLSR 448

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + K+DI+ ++K L+D+RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 449  EDETGAGTLTKDDIVEVMKRLIDIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 508

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 509  ERAVKERLSLGDLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 568

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPY
Sbjct: 569  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPY 628

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I 
Sbjct: 629  RKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQ 688

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 689  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVD 748

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 749  SGVTVVAKRGGMIDYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCV 808

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L++ER+V ED  T+I
Sbjct: 809  MLGEPVMAGDVVADGPSTDLGELALGQNLRVAFMPWNGYNFEDSILVNERVVQEDRLTTI 868

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 869  HIQELACISRDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKG 928

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  
Sbjct: 929  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEM 988

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  I+ R   +L                  S D +++  R++W+
Sbjct: 989  QLKEAKKDLTEEFKILEDGIFGRSRNLLLAAG-------------YSEDRLNKLDRTKWF 1035

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A++DE  Q  +E +  Q+   K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1036 ELAIEDEAKQIELEQIAEQHIELKADFDKKFENKRRKIIQGDDLAPGVLKIVKVYLAVKR 1095

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP  + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1096 RIQPGDKMAGRHGNKGVISKICPVEDMPHDEYGRPVDIVLNPLGVPSRMNIGQILEVHLG 1155

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  +I + +A  ++      +  +    +    I++  DD V  +    + 
Sbjct: 1156 LAAKGIGEKIDRMIKEQRALHEMRDFLQQVYDLGEKDTKQVDIAELSDDDVRTLVGNLRK 1215

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I ++L++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1216 GLPVATPVFDGAKEHEIKALLKLADLPESGQISLFDGRTGNVFERKVTVGYMYMLKLNHL 1275

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1276 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1335

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1336 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELDEE 1379


>gi|251793498|ref|YP_003008227.1| DNA-directed RNA polymerase subunit beta [Aggregatibacter aphrophilus
            NJ8700]
 gi|247534894|gb|ACS98140.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
            aphrophilus NJ8700]
          Length = 1342

 Score = 1640 bits (4247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1367 (51%), Positives = 971/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++IP L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNIPYLLTIQIDSFEKFIQRD----PDGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSTNGNTELQYVSYQLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +E+IL  F+ KI +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEQILDLFFDKISFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--AKGKVYVERGRRITARHIKALEKDKVTQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   +  + L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  IVGKVAAKDYVDLATGELVCPANMELSLELLAKLAQAGYTQIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F+ LFF SD+YDLS VGR+K N  L +
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTKEAAEALFDNLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDI++++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEATGNGTLSNEDIVSVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANSSLDED  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSSLDEDFRFTDAFVTCRGEHGESGLYKPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPIERGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++ R+  +L                   +  + +  R++W
Sbjct: 952  MQLKQAKKDLSEEFEILEAGLFMRIRNLLLSGG-------------FDAKSLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + +E+ Q  +E L  Q+E  +   E + + +  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLDNEEKQHQLEQLAEQHEELRKEFERKLEVQRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    I+ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSIAKLREYMQKAYDLGGGSQKVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E+ I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPIATPVFDGAHEKEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV+GN   + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|296137521|ref|YP_003644763.1| DNA-directed RNA polymerase, beta subunit [Thiomonas intermedia K12]
 gi|295797643|gb|ADG32433.1| DNA-directed RNA polymerase, beta subunit [Thiomonas intermedia K12]
          Length = 1367

 Score = 1640 bits (4246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 962/1374 (70%), Gaps = 17/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG    ++D+P L+  Q  SY+ FL  ++   +R +EGL+AAF+++
Sbjct: 1    MSYSFTEKKRIRKSFGSRQSVLDVPYLLATQINSYEAFLQKDLPLPQRKDEGLEAAFRAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +    +E+  Y    P FDV +C  R LT+A  L+  +RLIV D        ++
Sbjct: 61   FPIVSHNQYVRMEYNGYTLARPVFDVRECQQRGLTFASALRAKVRLIVMDR--EAAKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++ R+DRRRK+PVT  L ALG++ E+IL+ F+         
Sbjct: 179  RIIPYRGSWLDFEFDAKDILYFRVDRRRKMPVTILLKALGLNPEQILAHFFAFDHMQLMD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         D   G      L+D   G+ V+   K++ +  L+ L++ G + L +  D 
Sbjct: 239  DGALLEFVP-DHFKGEVARFDLID-QNGKVVVAKDKRINTRHLRELEQGGTQRLSVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++V+ +TGEI   A + + E  L++I  + I+ I  LY++ ++  A+I  TL
Sbjct: 297  LLGKVLARNLVSQDTGEIVARANEELTEALLKKIREAGIQQIQTLYINDLDQGAFISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LFFD+D YDLS VGR+K N RL  
Sbjct: 357  RIDEVADQLGAKVAIYRMMRPGEPPTEDAVEALFNRLFFDADAYDLSRVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    +  EDI+A+IK+LV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 417  EEIEGEMVLSHEDIMAVIKLLVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLSRI 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP D IN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLGQAETENLMPHDFINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR+N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARLNEYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D KVT+ + YLSA+EE    IAQAN+ +DE G   +ELV  R AGE I+V  E++ 
Sbjct: 597  RRVIDRKVTDQIDYLSAIEEGKYVIAQANAGMDEHGMLNDELVSAREAGESIMVSPERVQ 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E P VGTG+E V A  
Sbjct: 657  YMDVSPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKPLVGTGVERVTAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VD+ RIV+R  + +      GVDIY L+K+QRSNQNT ++QRPLV
Sbjct: 717  SGTVVTALRGGVVDYVDSARIVVRVNDDETQAGEVGVDIYNLIKYQRSNQNTNIHQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD++ + D++ADG STDLG+LALG+NMLVAFMPW+GYN+EDS+L+SER+V+ED FTSI
Sbjct: 777  KRGDKLAKGDVVADGASTDLGELALGQNMLVAFMPWNGYNYEDSILLSERVVAEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V ARDTKLG EEITRDIPN+SE  L  +DE GII VGAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELNVPARDTKLGSEEITRDIPNLSEHQLARLDESGIIYVGAEVEAGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMYGTVIDVQVFTREGIPRDKRAQQIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+ A  GP    K   +++D + E  R  W+
Sbjct: 957  ELKRYRLDLNDQMRIVEADTFDRLGKLLTGKTANGGPNKLAKGATITADYLGETDRYNWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE + + +E LK   E  +   +  F+ K  K+  GD++P GVL++VKV++A+KR
Sbjct: 1017 DIRPADEALAQQMEQLKDSLEKRRHAFDLMFEEKRRKLTQGDELPTGVLKMVKVYLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP + DGT VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSKIVPVEDMPHMPDGTTVDIVLNPLGVPSRMNIGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA +G+GK++  ++   +++   + LR FL  +       E +    D  VL +A   K+
Sbjct: 1137 WASIGIGKRVNDML---QSHAKAAELRKFLGTLYNFSGKQEALDQLSDAEVLELASNLKA 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            G+P+++PVFDGA E  I  ML +A  D+            Q +L DG TGE F+RPVTVG
Sbjct: 1194 GLPIASPVFDGASEAEIGQMLDLAYPDDIAEKLQLTAAKKQVMLTDGRTGEVFERPVTVG 1253

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1254 IMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1313

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDD  GRT++YESIV G+   E G PESFNVL+KE+++LGL I+LE +
Sbjct: 1314 EMLTVKSDDTQGRTKMYESIVKGDHIIEAGMPESFNVLIKEIRSLGLDIELERN 1367


>gi|294838498|ref|ZP_06783181.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. 6013113]
 gi|294859142|ref|ZP_06796911.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. 6013150]
          Length = 1362

 Score = 1640 bits (4246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 983/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            +       +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 DLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|169797453|ref|YP_001715246.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            AYE]
 gi|184156623|ref|YP_001844962.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            ACICU]
 gi|213155733|ref|YP_002317778.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            AB0057]
 gi|215484890|ref|YP_002327129.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            AB307-0294]
 gi|239500978|ref|ZP_04660288.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            AB900]
 gi|260556345|ref|ZP_05828564.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            ATCC 19606]
 gi|294840894|ref|ZP_06785577.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. 6014059]
 gi|301346448|ref|ZP_07227189.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            AB056]
 gi|301512026|ref|ZP_07237263.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            AB058]
 gi|301597220|ref|ZP_07242228.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            AB059]
 gi|226699357|sp|B7H1J8|RPOB_ACIB3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699358|sp|B7I360|RPOB_ACIB5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699359|sp|B2I1Z1|RPOB_ACIBC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699361|sp|B0VDI0|RPOB_ACIBY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78099422|gb|ABB20847.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|169150380|emb|CAM88277.1| DNA-directed RNA polymerase beta chain (Transcriptase beta chain)
            (RNA polymerase beta subunit) [Acinetobacter baumannii
            AYE]
 gi|183208217|gb|ACC55615.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Acinetobacter baumannii ACICU]
 gi|213054893|gb|ACJ39795.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            AB0057]
 gi|213986220|gb|ACJ56519.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            AB307-0294]
 gi|260410400|gb|EEX03699.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter baumannii
            ATCC 19606]
          Length = 1362

 Score = 1640 bits (4246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 982/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|15839222|ref|NP_299910.1| DNA-directed RNA polymerase subunit beta [Xylella fastidiosa 9a5c]
 gi|17369366|sp|Q9PA86|RPOB_XYLFA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|9107862|gb|AAF85430.1|AE004070_2 RNA polymerase beta subunit [Xylella fastidiosa 9a5c]
          Length = 1388

 Score = 1640 bits (4246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1390 (50%), Positives = 968/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK+  I+ +P L+ +Q  SY  FL  ++   +R + GL AA KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKHRSILKVPFLLAIQVDSYRAFLQGDVESSQRKDIGLHAALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K++K
Sbjct: 67   PIVSYSGNAALEYVGYKLGEPMFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAVK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             IKEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YIKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +    D
Sbjct: 185  IIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +  + L
Sbjct: 245  KGVQLELVPERLRGEILSFNLTD--GGGVIVEAGKRITARHVKQLEASGISALAVPDEYL 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+ NTL 
Sbjct: 303  IGRILSHDVIDATTGELLASANSEVNEDRIVAFRKAGIDSVGTLWVNDLDRGAYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N R+   
Sbjct: 363  IDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNRRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   +                      +IK L ++RNG+G +DDID+LGN
Sbjct: 423  EVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET EG NIG
Sbjct: 543  LSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D++G  T
Sbjct: 603  LINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDDNGQLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  ESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G+++QVDA RIV++  E   +  + +GVD
Sbjct: 723  PTLRAQKPLVGTGIERTVARDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGATDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD V   D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYGLIKYTRSNQNTCINQRPLVNVGDIVTSGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+   SG  
Sbjct: 963  DVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVVNSGVD 1022

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +K  KI
Sbjct: 1023 -IKKGEVITGAYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSDKRSKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMPF++DGTPVDI
Sbjct: 1082 TQGDDLAPGVLKMVKVFLAVKRCIQPGDKMAGRHGNKGVVSNVVPVEDMPFMEDGTPVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
            VLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++     
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEIYNHDK 1198

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + DD +L +A+    GVP+++PVFDGA E+ I  ML +A+L   GQ+ L
Sbjct: 1199 SVVGERVDLSQFSDDELLNMAKNLTDGVPMASPVFDGASEQEIKRMLDLAELPTGGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPFDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGHTGEPFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+     G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGDHQMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLENS 1366
            L ++I+LE++
Sbjct: 1379 LAINIELEDN 1388


>gi|121596184|ref|YP_988080.1| DNA-directed RNA polymerase subunit beta [Acidovorax sp. JS42]
 gi|158513932|sp|A1WCM9|RPOB_ACISJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120608264|gb|ABM44004.1| DNA-directed RNA polymerase subunit beta [Acidovorax sp. JS42]
          Length = 1374

 Score = 1639 bits (4245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1379 (50%), Positives = 968/1379 (70%), Gaps = 18/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FG    ++ +P L+++Q+ +Y  FL  + AP +R NEGLQAA
Sbjct: 1    MAQTSTYSYTERKRIRKSFGSRDSVLKVPYLLQMQRDAYTAFLQADTAPQKRSNEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F S FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T 
Sbjct: 61   FNSAFPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTS 120

Query: 119  -AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    
Sbjct: 181  LLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +               L  G      + D   G+ ++   K++T+   + L++ G   + 
Sbjct: 241  FRLMDSGAQLEFVPERL-RGEVARFDITD-KAGKVIVAKDKRVTARHTRELEQSGTTHIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  VA +IV+G+TGEI  +A + + E  L+++  + ++D+ ++Y + ++  AY
Sbjct: 299  VPEDFLIGRVVARNIVDGDTGEILAKANEELTEALLKKLRAAGVQDLQVIYTNELDQGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N
Sbjct: 359  ISQTLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             ++  D       +  +DI+A++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  AKIGRDEATGPMVLSNDDILAVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRT 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH
Sbjct: 479  GLARIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR+V DGKVT ++ YLSA+EE    IAQAN++LD +G  T +LV  R  GE  LV 
Sbjct: 599  IETPYRRVVDGKVTMEIDYLSAIEEGKYIIAQANATLDAEGRLTGDLVSAREKGESTLVS 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E 
Sbjct: 659  ADRVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + A R G+V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VAAVDSGTVVTANRGGVVDYVDATRIVVRVNDDEAVAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+VK GD++ + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED
Sbjct: 779  QRPIVKKGDKLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAED 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T +    ++   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLTGRVANGGPQKLAKGTKIDKAYLASVE 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     +E+V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KFHWFDIRPAEEEVATQLESIKNALEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGWA  G+G++I  ++   +     + LR FLE++  +    E +S   DD +L +A
Sbjct: 1139 EVHLGWAGKGMGQRIGDML---QREAKTAELRKFLEEIYNSRGRKEDLSQLSDDEILAMA 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDR 1247
             +  SGVP ++PVFDGA EE I  ML++A  D             Q+ LYDG TGE F+R
Sbjct: 1196 RELTSGVPFASPVFDGASEEEIKDMLKLAYPDDLAQAKGLTETRTQAYLYDGRTGERFER 1255

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P TVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1256 PTTVGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1315

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AYVLQEMLT+KSDDV GRT+VYE+IV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 AYVLQEMLTVKSDDVQGRTKVYENIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|127511085|ref|YP_001092282.1| DNA-directed RNA polymerase, beta subunit [Shewanella loihica PV-4]
 gi|158513462|sp|A3Q975|RPOB_SHELP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|126636380|gb|ABO22023.1| DNA-directed RNA polymerase, beta subunit [Shewanella loihica PV-4]
          Length = 1343

 Score = 1639 bits (4245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1364 (51%), Positives = 962/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  +  L AL   +++IL  F+ ++ Y  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLAASIILRALDYSTQDILDLFFERVQYKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A D + G   S  + D + G  ++E G+++T+  ++ L++     L +  + 
Sbjct: 235  DSLVMALVA-DRLRGETASYDIKDAE-GNIIVEKGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++ +TGE+ + A   I  + L ++  + I+DI  LYV+ +++ AYI +TL
Sbjct: 293  ISGKIAAQDYIDPDTGEVLVSANAEISLEDLAKLSMAGIKDIDTLYVNELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL +
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLGI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI+A+++ ++++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDDEGTGILTKEDIVAVMQKIIEIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T+ V YLSA+EE    IAQAN  +D DG   EE + CR  GE   +    + 
Sbjct: 593  RKVVDGVITDQVDYLSAIEEGRYVIAQANIEVDADGRMVEEQIACRHKGESTFMRAADVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGYVDYVDASRIVVKVNEDELTPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  ++ R   +L G                +   +   PR Q  
Sbjct: 953  HIAQAKKDLTEEFKILEEGVFGRARNLLIGAG-------------FAEAELDALPRPQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQTIEDETKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPIEDMPYDENGNPVDIVLNPLGVPSRMNIGQVLEVHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I +++ + +   ++      + ++         I  + D+ VLR+A+  K 
Sbjct: 1120 AAAKGIGDRITAMLEEQRELAELRGYIKKVYELGEDVQQQVDIDSFTDEEVLRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P +TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+RPVTVGY+YMLKLNH+
Sbjct: 1180 GIPTATPAFDGAKEKEIKDMLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1343


>gi|169634594|ref|YP_001708330.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            SDF]
 gi|226699360|sp|B0VLZ6|RPOB_ACIBS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|169153386|emb|CAP02513.1| DNA-directed RNA polymerase beta chain (Transcriptase beta chain)
            (RNA polymerase beta subunit) [Acinetobacter baumannii]
          Length = 1362

 Score = 1639 bits (4245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 982/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKLPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|294341866|emb|CAZ90295.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase beta subunit)
            [Thiomonas sp. 3As]
          Length = 1367

 Score = 1639 bits (4244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1374 (51%), Positives = 961/1374 (69%), Gaps = 17/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG    ++D+P L+  Q  SY+ FL  ++   +R +EGL+AAF+++
Sbjct: 1    MSYSFTEKKRIRKSFGSRQSVLDVPYLLATQINSYEAFLQKDLPLPQRKDEGLEAAFRAI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +    +E+  Y    P FDV +C  R LT+A  L+  +RLIV D        ++
Sbjct: 61   FPIVSHNQYVRMEYNGYTLARPVFDVRECQQRGLTFASALRAKVRLIVMDR--EAAKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI++ R+DRRRK+PVT  L ALG++ E+IL+ F+         
Sbjct: 179  RIIPYRGSWLDFEFDAKDILYFRVDRRRKMPVTILLKALGLNPEQILAHFFAFDHMQLMD 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         D   G      L+D   G+ V+   K++ +  L+ L++ G + L +  D 
Sbjct: 239  DGALLEFVP-DHFKGEVARFDLID-QNGKVVVAKDKRINTRHLRELEQGGTQRLSVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++V+ +TGEI   A + + E  L++I  + I+ I  LY++ ++  A+I  TL
Sbjct: 297  LLGKVLARNLVSQDTGEIVARANEELTEALLKKIREAGIQQIQTLYINDLDQGAFISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LFFD+D YDLS VGR+K N RL  
Sbjct: 357  RIDEVADQLGAKVAIYRMMRPGEPPTEDAVEALFNRLFFDADAYDLSRVGRMKFNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    +  EDI+A+IK+LV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 417  EEIEGEMVLSHEDIMAVIKLLVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLSRI 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP D IN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKERLGQAETENLMPHDFINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR+N YGFIETPY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARLNEYGFIETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D KVT+ + YLSA+EE    IAQAN+ +DE G   +ELV  R AGE I+V  E++ 
Sbjct: 597  RRVIDRKVTDQIDYLSAIEEGKYVIAQANAGMDEHGMLNDELVSAREAGESIMVSPERVQ 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E P VGTG+E V A  
Sbjct: 657  YMDVSPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKPLVGTGVERVTAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A R G+V+ VD+ RIV+R  + +      GVDIY L+K+QRSNQNT ++QRPLV
Sbjct: 717  SGTVVTALRGGVVDYVDSARIVVRVNDDETQAGEVGVDIYNLIKYQRSNQNTNIHQRPLV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD + + D++ADG STDLG+LALG+NMLVAFMPW+GYN+EDS+L+SER+V+ED FTSI
Sbjct: 777  KRGDILAKGDVVADGASTDLGELALGQNMLVAFMPWNGYNYEDSILLSERVVAEDRFTSI 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V ARDTKLG EEITRDIPN+SE  L  +DE GII VGAEV  GD+LVGK+TPKG
Sbjct: 837  HIEELNVPARDTKLGSEEITRDIPNLSEHQLARLDESGIIYVGAEVEAGDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  +
Sbjct: 897  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMYGTVIDVQVFTREGIPRDKRAQQIIDD 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+ A  GP    K   +++D + E  R  W+
Sbjct: 957  ELKRYRLDLNDQMRIVEADTFDRLGKLLTGKTANGGPNKLAKGATITADYLGETDRYNWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE + + +E LK   E  +   +  F+ K  K+  GD++P GVL++VKV++A+KR
Sbjct: 1017 DIRPADEALAQQMEQLKDSLEKRRHAFDLMFEEKRRKLTQGDELPTGVLKMVKVYLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I+P EDMP + DGT VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSKIVPVEDMPHMPDGTTVDIVLNPLGVPSRMNIGQILETHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA +G+GK++  ++   +++   + LR FL  +       E +    D  VL +A   K+
Sbjct: 1137 WASIGIGKRVNDML---QSHAKAAELRKFLGTLYNFSGKQEALDQLSDAEVLELASNLKA 1193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVG 1252
            G+P+++PVFDGA E  I  ML +A  D+            Q +L DG TGE F+RPVTVG
Sbjct: 1194 GLPIASPVFDGASEAEIGQMLDLAYPDDIAEKLQLTAAKKQVMLTDGRTGEVFERPVTVG 1253

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1254 IMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1313

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDD  GRT++YESIV G+   E G PESFNVL+KE+++LGL I+LE +
Sbjct: 1314 EMLTVKSDDTQGRTKMYESIVKGDHIIEAGMPESFNVLIKEIRSLGLDIELERN 1367


>gi|152977728|ref|YP_001343357.1| DNA-directed RNA polymerase subunit beta [Actinobacillus succinogenes
            130Z]
 gi|171472908|sp|A6VKC5|RPOB_ACTSZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|150839451|gb|ABR73422.1| DNA-directed RNA polymerase, beta subunit [Actinobacillus
            succinogenes 130Z]
          Length = 1342

 Score = 1639 bits (4244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1367 (52%), Positives = 973/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +    R+RK FGK  +++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYTEKKRIRKDFGKRSQVLNVPYLLTIQLDSFDKFIQRD----PDGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSY+   P FDV +C  R  T+A PL++ LRL+ +D D   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYKLGEPVFDVRECQIRGTTFAAPLRVKLRLVSYDKDAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQDVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L AL   +EEIL  F+ K+V+  +G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALNYTTEEILDLFFDKVVFEIQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   +  +     G+  +E G+++T+  +K+L++ GVK + + ++ 
Sbjct: 235  DKLLMELVPERL-RGETATFDIE--AEGKVYVERGRRITARHIKALEKDGVKKVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ E+GE+   A   I  + L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  IIGKVAAKDYVDLESGEVICAANTEISLELLAKLAQAGYTAIEALFTNDLDFGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF  ++YDLS VGR+K N  L +
Sbjct: 352  RVDPSCDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSQERYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+      + KEDI++++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DSETGSGVLSKEDIVSVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVTPQDLINAKPISAAVREFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQAN++LD+D  FT+  V  R   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYIIAQANANLDDDFRFTDTFVTARGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGEPVGRGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++SR+  +L                 +S   +    R++W
Sbjct: 952  MQLKQAKKDLVEELEILEAGLFSRVRNLLVDGG-------------ISEKELDTMERAKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  +  E  Q  +E L  QYE  +   E + + K  KI  GDD+ PGV +VVKV++A+K
Sbjct: 999  LEQTLSSESKQSRLEQLAEQYEELRKDFEHKLEVKRSKIIQGDDLAPGVQKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGRPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G++I  ++   K   DI  LR +++K    G GS    ++ + D+ VLR+AE 
Sbjct: 1119 GLAAKGIGEQINIML---KQKQDIEKLRGYIQKAYDLGGGSQVVDLNTFTDEEVLRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGADE  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGMPLATPVFDGADESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E GTPESFNV++KE+++LGL+IDL+ +
Sbjct: 1296 DDVNGRTKMYKNIVGGTHYMEPGTPESFNVIMKEIRSLGLNIDLDEA 1342


>gi|78099438|gb|ABB20855.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
          Length = 1362

 Score = 1639 bits (4244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1374 (51%), Positives = 974/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AE+I   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAENITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   L  +++S
Sbjct: 953  RALAIEKAQLDAYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLVEEVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D  V
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +A +  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|258620703|ref|ZP_05715738.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM573]
 gi|258586901|gb|EEW11615.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM573]
          Length = 1375

 Score = 1639 bits (4244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1366 (52%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 209  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 268

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+GSF +ELV  R  GE  L PRE +D
Sbjct: 626  RRVVNGIVTDEVDYLSAIEEGQFVIAQANAKLTEEGSFADELVTARQKGESGLHPREHVD 685

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 926  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 985

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 986  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1033 EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1093 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       I+   D+ V  +A+  
Sbjct: 1153 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDIAALSDEEVRTLAQNL 1209

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1210 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1269

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1270 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1329

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1330 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1375


>gi|261209791|ref|ZP_05924094.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. RC341]
 gi|260841147|gb|EEX67664.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. RC341]
          Length = 1341

 Score = 1639 bits (4244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  D+   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDADEQGTLDQVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +S   R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLSSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS   D+ V  +A+  
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISALSDEDVRTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|258624488|ref|ZP_05719434.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM603]
 gi|258583237|gb|EEW08040.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM603]
          Length = 1375

 Score = 1639 bits (4243), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1366 (52%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 209  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 268

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+GSF +ELV  R  GE  L PRE +D
Sbjct: 626  RRVVNGIVTDEVDYLSAIEEGQFVIAQANAKLTEEGSFADELVTARQKGESGLHPREHVD 685

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 926  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 985

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 986  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1033 EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1093 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       I+   D+ V  +A+  
Sbjct: 1153 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDIAALSDEEVRTLAQNL 1209

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1210 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1269

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1270 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1329

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1330 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1375


>gi|260550476|ref|ZP_05824686.1| RNA polymerase subunit B [Acinetobacter sp. RUH2624]
 gi|260406391|gb|EEW99873.1| RNA polymerase subunit B [Acinetobacter sp. RUH2624]
          Length = 1362

 Score = 1638 bits (4242), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1374 (52%), Positives = 978/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|229527011|ref|ZP_04416407.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae 12129(1)]
 gi|229335534|gb|EEO01015.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae 12129(1)]
          Length = 1341

 Score = 1638 bits (4242), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L P E +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPCEHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +S   R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLSSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|262401579|ref|ZP_06078146.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. RC586]
 gi|262352294|gb|EEZ01423.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. RC586]
          Length = 1341

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  D+   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDADEQGTLDQVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS   D+ V  +A+  
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISALSDEDVRTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|165977163|ref|YP_001652756.1| DNA-directed RNA polymerase subunit beta [Actinobacillus
            pleuropneumoniae serovar 3 str. JL03]
 gi|226699364|sp|B0BSF5|RPOB_ACTPJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|165877264|gb|ABY70312.1| RNA polymerase beta subunit [Actinobacillus pleuropneumoniae serovar
            3 str. JL03]
          Length = 1342

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1367 (51%), Positives = 975/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIQRDSD----GQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSMFFDKVNFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++  +K + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--ANGKVYVERGRRITARHIRTLEKDEIKQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYVDLSTGELVCPANMEISMEMLAKLSQAGYKEIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LNL
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEGVGSGILSNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 592  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR GIV++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGIVQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 952  MQLKEAKKDLTEELEILEAGLFTRVRNLLIEGGV-------------SEAELDKVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+AE 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFTDEEVMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L + DL  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGDLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDEE 1342


>gi|52424267|ref|YP_087404.1| DNA-directed RNA polymerase subunit beta [Mannheimia
            succiniciproducens MBEL55E]
 gi|81387641|sp|Q65W41|RPOB_MANSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|52306319|gb|AAU36819.1| RpoB protein [Mannheimia succiniciproducens MBEL55E]
          Length = 1342

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1367 (52%), Positives = 976/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +    R+RK FGK P+++++P L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFEKFIQRD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSY+   P FDV +C  R  T+A PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSNNGSTELQYVSYKLGEPVFDVRECQIRGTTFAAPLRVNLRLVSYDRDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQDVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL  F+ KI +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYSTEEILDLFFEKIQFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  +++L++  V  + + ++ 
Sbjct: 235  NKLLMALVPERL-RGETASFDIE--ANGKVYVERGRRITARHIRTLEKDNVTKIDVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++ E+GE+   A   I    L ++  +  + I  L+ + ++   YI  TL
Sbjct: 292  IVGKVSAKDYIDLESGELVCPANMEISLDILAKLAQAGYKSIETLFTNDLDFGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F+ LFF +++YDLS VGR+K N  L L
Sbjct: 352  RVDPSSDRLSALVEIYRMMRPGEPPTKEAAEALFDNLFFSAERYDLSAVGRMKFNRSLGL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + KEDI+ ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  AEGVGNGVLSKEDIVGVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+V PQDLINAKPV +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVTPQDLINAKPVSAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNNYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA+EE N  IAQAN+SLDED  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVDGQVTEEIEYLSAIEEGNYVIAQANASLDEDFRFTDAFVTCRGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP+QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  QYMDVSPQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR GI++ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGIIQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGEPIGRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGETALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++SR+  +L                   +  +    R++W
Sbjct: 952  MQLKEAKKDIAEELEILEAGLFSRVRNLLIDGGV-------------DAKELDRLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  QYE  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLNDEAKQNQLEQLAEQYEELRKDFEHKLEVKRGKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G++I  ++   K   +I  LR +++K    G GS    ++ + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGEQINRML---KEKQEIEKLRGYIQKAYDLGGGSQKVDLNTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA+E+ I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGMPLATPVFDGAEEKEIKDLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV+G    + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVSGTHQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|15640355|ref|NP_229982.1| DNA-directed RNA polymerase subunit beta [Vibrio cholerae O1 biovar
            El Tor str. N16961]
 gi|121591007|ref|ZP_01678325.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 2740-80]
 gi|153216324|ref|ZP_01950402.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 1587]
 gi|153819682|ref|ZP_01972349.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae NCTC 8457]
 gi|153823145|ref|ZP_01975812.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae B33]
 gi|153827137|ref|ZP_01979804.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MZO-2]
 gi|227080540|ref|YP_002809091.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae M66-2]
 gi|254227011|ref|ZP_04920572.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae V51]
 gi|254292044|ref|ZP_04962821.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae AM-19226]
 gi|254851637|ref|ZP_05240987.1| DNA-directed RNA polymerase [Vibrio cholerae MO10]
 gi|9654742|gb|AAF93501.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae O1 biovar
            El Tor str. N16961]
 gi|121547148|gb|EAX57278.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 2740-80]
 gi|124114319|gb|EAY33139.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 1587]
 gi|125620473|gb|EAZ48846.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae V51]
 gi|126509770|gb|EAZ72364.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae NCTC 8457]
 gi|126519332|gb|EAZ76555.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae B33]
 gi|149738965|gb|EDM53281.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MZO-2]
 gi|150422030|gb|EDN14000.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae AM-19226]
 gi|227008428|gb|ACP04640.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae M66-2]
 gi|254847342|gb|EET25756.1| DNA-directed RNA polymerase [Vibrio cholerae MO10]
          Length = 1375

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 209  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 268

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 626  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 685

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 926  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 985

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 986  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1033 EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1093 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1153 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1209

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1210 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1269

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1270 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1329

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1330 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1375


>gi|261866784|ref|YP_003254706.1| DNA-directed RNA polymerase subunit beta [Aggregatibacter
            actinomycetemcomitans D11S-1]
 gi|261412116|gb|ACX81487.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
            actinomycetemcomitans D11S-1]
          Length = 1342

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 973/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++IP L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNIPYLLTIQIDSFEKFIKRD----PDGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSTNGNTELQYVSYQLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +E+IL  F+ KI +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEQILDLFFYKITFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIETK--GKVYVERGRRITARHIKALEKDKVTQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ ETGE+   A   +  + L ++  +    +  L+ + ++   YI  TL
Sbjct: 292  IIGKVAAKDYVDLETGELICPANMELSLELLAKLAQAGYTTLETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F+ LFF SD+YDLS VGR+K N  L +
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTKEAAEALFDNLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDI++++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EETTGGGTLSNEDIVSVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+++V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LD+D  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFRFTDAFVTCRGEHGESGLYKPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V++GD V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VELGDPVERGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++ R+  +L                   +  + +  R++W
Sbjct: 952  MQLKQAKKDLSEEFEILEAGLFMRVRNLLLSGG-------------FDAKSLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + +E+ Q  +E L  Q+E  +   E + + +  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLDNEEKQHQLEQLAEQHEELRKEFERKLEIQRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    I+ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSIAKLREYMQKAYDLGGGSQKVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+PV+TPVFDGA E+ I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPVATPVFDGAHEKEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV+GN   + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|81251487|gb|ABB70065.1| RpoB [Acinetobacter ursingii DSM 16037]
          Length = 1362

 Score = 1638 bits (4241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1374 (52%), Positives = 972/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVILRALGYNNEQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDND-GKVIVEQGKRINARHVRQMEASGLSKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   +     I A  ++  + + ++    ++   ILY + +++  +I +TL
Sbjct: 295  LYERITAEDITLKDGD--IIPANTLLSHEVMVKLAEGGVKQFNILYTNDIDHGPFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S +D +G+  EE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSGVDAEGNLVEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G++E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEATVARDSGVCVIAKRGGVIEFVDASRVVIRVHENEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ++  G    K+   L+ DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERIVRLLKGQDSNGGGTT-KRGDKLTEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPSDEGIAERLSQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   +    I+ LR FL+K+    G   E ++   DD V
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMLQQQRT---IAELRIFLDKIYNKVGGEQEDLNSLTDDEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   + GVP++TPVFDGA+E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 LVLAGNLRKGVPLATPVFDGAEESQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|27364616|ref|NP_760144.1| DNA-directed RNA polymerase subunit beta [Vibrio vulnificus CMCP6]
 gi|37681343|ref|NP_935952.1| DNA-directed RNA polymerase subunit beta [Vibrio vulnificus YJ016]
 gi|320155010|ref|YP_004187389.1| DNA-directed RNA polymerase subunit beta [Vibrio vulnificus MO6-24/O]
 gi|41017905|sp|Q7MGR8|RPOB_VIBVY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|41018024|sp|Q8DD20|RPOB_VIBVU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|27360735|gb|AAO09671.1| DNA-directed RNA polymerase, beta subunit [Vibrio vulnificus CMCP6]
 gi|37200094|dbj|BAC95923.1| DNA-directed RNA polymerase, beta subunit [Vibrio vulnificus YJ016]
 gi|319930322|gb|ADV85186.1| DNA-directed RNA polymerase beta subunit [Vibrio vulnificus MO6-24/O]
          Length = 1342

 Score = 1637 bits (4240), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1367 (52%), Positives = 975/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P T  L ALG  +EEIL TF+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPSTIILRALGKSTEEILDTFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   +  +     G   +E G+++T+  ++ L+++GV  + +  + 
Sbjct: 235  QTLMMELVP-DRLRGETATFDIE--ANGTVYVEKGRRVTARHIRQLEKEGVDQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L ++  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSSKDYINEATGEIIVAANQEISLEALAKLSQAGHKQLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSSVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DDAEEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKAE P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKAEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR GI++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTSVAKRGGIIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVLRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTTDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQYDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   D+ V  +    
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGETRQKVDIASLSDEEVRTLIGNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++  L ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEASIKELLKLGGLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ +
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDEQ 1342


>gi|262172574|ref|ZP_06040252.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus MB-451]
 gi|261893650|gb|EEY39636.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus MB-451]
          Length = 1341

 Score = 1637 bits (4240), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+GSF +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGIVTDEVDYLSAIEEGQFVIAQANAKLTEEGSFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       I+   D+ V  +A+  
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDIAALSDEEVRTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|262163610|ref|ZP_06031353.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM223]
 gi|262027977|gb|EEY46639.1| DNA-directed RNA polymerase beta subunit [Vibrio mimicus VM223]
          Length = 1341

 Score = 1637 bits (4240), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1366 (52%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+GSF +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGIVTDEVDYLSAIEEGQFVIAQANAKLTEEGSFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENDELQTQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       I+   D+ V  +A+  
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDIAALSDEEVRTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|113461701|ref|YP_719770.1| DNA-directed RNA polymerase subunit beta [Haemophilus somnus 129PT]
 gi|123031469|sp|Q0I5B7|RPOB_HAES1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|112823744|gb|ABI25833.1| DNA-directed RNA polymerase subunit beta [Haemophilus somnus 129PT]
          Length = 1342

 Score = 1637 bits (4240), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1367 (52%), Positives = 970/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+S+
Sbjct: 1    MVYSYTEKKRIRKSFGKRPQVLNVPYLLTIQLDSFDKFIQRD----PDGQQGLEAAFRSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA  L++ LRL+ +D D  +G  +I
Sbjct: 57   FPIVSNNGNTELQYVSYQLGEPVFDVRECQIRGTTYAASLRVKLRLVSYDKDAASG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTSNGTFVINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L AL   +EEIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILDLFFDKVSFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  +K+L++  +  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETASFDIE--ANGKVYIERGRRITARHIKALEKDKITQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGEI   A   I  + LE++  +  ++I  L+ + ++   YI  TL
Sbjct: 292  IVGKVSAKDYVDLTTGEIICPANMEISLELLEKLSQAGYKNIETLFTNDLDFGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF S++YDLS VGR+K N  L +
Sbjct: 352  RVDPSYDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSSERYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ +++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDTTGSGTLSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D++SV PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLESVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LD +  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDGELRFTDAFVTCRGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V++G+ + R +I+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VQLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  +   +    R+QW
Sbjct: 952  MQLKQAKKDLVEELEILEAGLFARVRNLLLSGG-------------FNDKQLENLDRTQW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  QYE  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLVDEDKQNQLEQLAEQYEELRKDFEHKLEIKRSKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K   D+  LR +++K    G GS    +S + D+ VLR+A+ 
Sbjct: 1119 GLAAKGIGDQINAMI---KQKQDVEKLRGYIQKAYDLGDGSQKVDLSTFTDEEVLRLAKN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E+ I ++L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGMPLATPVFDGAHEKEIKALLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVGGTHQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|262166945|ref|ZP_06034665.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae RC27]
 gi|262024650|gb|EEY43331.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae RC27]
          Length = 1341

 Score = 1637 bits (4239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1366 (52%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +S   R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLSSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|71275247|ref|ZP_00651534.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Dixon]
 gi|170731246|ref|YP_001776679.1| DNA-directed RNA polymerase subunit beta [Xylella fastidiosa M12]
 gi|226699463|sp|B0U5X7|RPOB_XYLFM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71164056|gb|EAO13771.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Dixon]
 gi|167966039|gb|ACA13049.1| DNA-directed RNA polymerase [Xylella fastidiosa M12]
          Length = 1384

 Score = 1637 bits (4239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1390 (50%), Positives = 966/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK+  I+ +P L+ +Q  SY  FL  ++   +R + GL  A KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKHRSILKVPFLLAIQVDSYRAFLQGDVESSQRKDIGLHGALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K++K
Sbjct: 63   PIVSYSGNAALEYVGYKLGEPMFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAVK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             IKEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YIKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +    D
Sbjct: 181  IIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +  D L
Sbjct: 241  KGVQLELVPERLRGEILSFNLTD--GGGVIVEAGKRITARHVKQLEASGISALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+ NTL 
Sbjct: 299  IGRILSHDVIDATTGELLASANSEVNEDRIVAFRKAGIESVGTLWVNDLDRGAYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N R+   
Sbjct: 359  IDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   +                      +IK L ++RNG+G +DDID+LGN
Sbjct: 419  EVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D++G  T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDDNGQLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  ESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA  SG  + A+R G+++QVDA RIV++  E   +  + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERTVALDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGATDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD +   D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYGLIKYTRSNQNTCINQRPLVNVGDIIASGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+   SG  
Sbjct: 959  DVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVVNSGVD 1018

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +K  KI
Sbjct: 1019 -IKKGEVITGPYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSDKRSKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG++S I+P EDMPF++DGTPVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRCIQCGDKMAGRHGNKGVISNIVPVEDMPFMEDGTPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
            VLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++     
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEIYNHDK 1194

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + DD +L +A+    GVP+++PVFDGA E+ I  ML +A+L   GQ+ L
Sbjct: 1195 SLVGERVDLSQFSDDELLNMAKNLTDGVPMASPVFDGASEQEIKRMLDLAELPTGGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPFDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGHTGEPFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+     G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGDHQMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLENS 1366
            L ++I+LE++
Sbjct: 1375 LAINIELEDN 1384


>gi|261491916|ref|ZP_05988493.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            serotype A2 str. BOVINE]
 gi|261312383|gb|EEY13509.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            serotype A2 str. BOVINE]
          Length = 1341

 Score = 1637 bits (4239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1366 (51%), Positives = 966/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSFEKFIEKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ +D +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFEKIKFEIAD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  +++L++  V  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETASFDI--AANGKVYVEMGRRITARHIRALEKDNVAQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  +GE+   A   I  + L  +  +    I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAQDYVDLSSGEVICPANMEISMEMLANLSQAGYNQIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +++YDLS VGR+K N  L +
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSAERYDLSAVGRMKFNRSLEI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGSGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V CR  GE  L   E++ 
Sbjct: 592  RKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFTDTYVTCRQQGESGLFKPEEVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A  
Sbjct: 652  YMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIALD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG AIVAKR G V+ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P V
Sbjct: 712  SGVAIVAKRGGTVQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQVPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+I
Sbjct: 772  NLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  IL+  +++R+  +L          G K+S       +    R +W 
Sbjct: 952  QLCEAKKDLAEELEILEAGLFTRVRNLLI-------EGGVKESA------LDGVAREKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+KR
Sbjct: 999  EQTLEDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G +I  +I   K   +++ LR +++K    G GS    +S + D+ V+R+A+  
Sbjct: 1119 LAARGIGDQIDKMI---KQQQEVAKLREYMQKAYDLGHGSQVVDLSTFSDEEVMRLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1296 DVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1341


>gi|158514189|sp|A4SHU9|RPOB_AERS4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1342

 Score = 1637 bits (4239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRDQVLDTPYLLSIQLDSFKQFIEAD----PEGEYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT++SG+A L++VSY    P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPITSYSGSAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD + VRIDRRRK+P +  L AL   SEEIL+ F+  I +  + 
Sbjct: 175  RVIPYRGSWLDFEFDAKDNLFVRIDRRRKLPASIILRALDFSSEEILANFFETIGFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +V    G  V+E+G+++T+  ++ L++  V  + +  + 
Sbjct: 235  GKLMMDLVPERL-RGETATFDIV--ANGAVVVETGRRVTARHIRQLEKDAVTQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A++  + +TGE+ + A   +  +++  +  +  +   +L+ + +++ AY+  TL
Sbjct: 292  VVGKVAAKNYTHPQTGEMVVTANQALSLEAVANLSQAGFKHFEVLFTNELDHGAYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE +F  LFF S++YDLSTVGR+K N RL+ 
Sbjct: 352  RIDSSSSRLEALVEIYRMMRPGEPPTREAAEQLFENLFFSSERYDLSTVGRMKFNRRLSR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + K+DI+ ++K L+D+RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDETGAGTLTKDDIVEVMKRLIDIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I 
Sbjct: 592  RKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSPQQIVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTVVAKRGGMIDYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L++ER+V ED  T+I
Sbjct: 772  MLGEPVMAGDVVADGPSTDLGELALGQNLRVAFMPWNGYNFEDSILVNERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACISRDTKLGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  I+ R   +L                  S D +++  R++W+
Sbjct: 952  QLKEAKKDLTEEFKILEDGIFGRSRNLLLAAG-------------YSEDRLNKLDRTKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            + A++DE  Q  +E +  Q+   K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELAIEDEAKQIELEQIAEQHIELKADFDKKFENKRRKIIQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP  + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKICPVEDMPHDEYGRPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI  +I + +A  ++      +  +    +    I++  DD V  +    + 
Sbjct: 1119 LAAKGIGEKIDRMIKEQRALHEMRDFLQQVYDLGEKDTKQVDIAELSDDDVRTLVGNLRK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+PV+TPVFDGA E  I ++L++ADL ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1179 GLPVATPVFDGAKEHEIKALLKLADLPESGQISLFDGRTGNVFERKVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELDEE 1342


>gi|330432333|gb|AEC17392.1| DNA-directed RNA polymerase subunit beta [Gallibacterium anatis
            UMN179]
          Length = 1345

 Score = 1637 bits (4239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1370 (51%), Positives = 968/1370 (70%), Gaps = 28/1370 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++IP L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNIPYLLTIQIDSFEKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y+   P FDV +C  R  TYA PL++ LRL+ +D D   G  ++
Sbjct: 57   FPIVSNNGNTELQYVDYKLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQDVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKILYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KIV+  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFEKIVFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L   D + G   +  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  NQLLMTLVP-DRLRGETATFDIE--ANGKVYVERGRRITARHIRQLEKDGVTQVVVPPEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TG+I   A   +  + L  +  +    I  L+ + ++   YI  TL
Sbjct: 292  IVGKVAAKDYVDLTTGDIICPANAELSLELLANLSQAGYNTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF SD+YDLS VGR+K N  L++
Sbjct: 352  RVDPSYDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSSDRYDLSAVGRMKFNRSLDI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDII ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGTGILSKEDIILVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+DSV PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDSVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V  R   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTFVTARGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +Q+VS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+E  VA 
Sbjct: 652  QYMDISTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRSDKPLVGTGIEKAVAV 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  +VAKR G ++ +DA RIV++  E +  P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVTVVAKRGGYIQYIDASRIVVKVNEDETIPGEAGIDIYNLTKYTRSNQNTCINQVPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ + R +++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VSLGEPIGRGEVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCIARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+  +GTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSTTGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D   E  IL+  +++R+  +L                  S+D + +  R +W
Sbjct: 952  MQLKQAKKDLTAELDILEAGLFTRVRNLLLANG-------------FSADKLEQMDRMKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + ++ DE+ Q  +E L  Q +  +   + + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQSLADEEKQAQLEQLSEQLDELRKEFDHKLEVKRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G+A  G+G +I  +I   K   +++ LR +++K    G       +S + D+ V+R+A+ 
Sbjct: 1119 GFAAKGIGDQINRMI---KEKQEVAKLREYIQKAYDLGDACQKVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA+E+ I  +L +A L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAEEKEIKGLLELAGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            DDV GRT++Y++IV G    +   PESFNVL+KE+++L ++IDL++ + +
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMDPSMPESFNVLLKEIRSLAINIDLDDEQAE 1345


>gi|261496280|ref|ZP_05992685.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            serotype A2 str. OVINE]
 gi|261308111|gb|EEY09409.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            serotype A2 str. OVINE]
          Length = 1341

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1366 (51%), Positives = 966/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSFEKFIEKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ +D +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFEKIKFEIAD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  +++L++  V  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETASFDI--AANGKVYVEMGRRITARHIRALEKDNVTQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  +GE+   A   I  + L  +  +    I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAQDYVDLSSGEVICPANMEISMEMLANLSQAGYNQIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +++YDLS VGR+K N  L +
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSAERYDLSAVGRMKFNRSLEI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGSGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V CR  GE  L   E++ 
Sbjct: 592  RKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFTDTYVTCRQQGESGLFKPEEVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A  
Sbjct: 652  YMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIALD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG AIVAKR G V+ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P V
Sbjct: 712  SGVAIVAKRGGTVQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQVPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+I
Sbjct: 772  NLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  IL+  +++R+  +L          G K+S       +    R +W 
Sbjct: 952  QLCEAKKDLAEELEILEAGLFTRVRNLLI-------EGGVKESA------LDGVAREKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+KR
Sbjct: 999  EQTLEDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G +I  +I   K   +++ LR +++K    G GS    +S + D+ V+R+A+  
Sbjct: 1119 LAARGIGDQIDKMI---KQQQEVAKLREYMQKAYDLGHGSQVVDLSTFSDEEVMRLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1296 DVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1341


>gi|253995711|ref|YP_003047775.1| DNA-directed RNA polymerase subunit beta [Methylotenera mobilis JLW8]
 gi|253982390|gb|ACT47248.1| DNA-directed RNA polymerase, beta subunit [Methylotenera mobilis
            JLW8]
          Length = 1390

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1397 (49%), Positives = 951/1397 (68%), Gaps = 40/1397 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + +IP L+ +Q  SY  FL  N+  D+R   GLQ+ F SV
Sbjct: 1    MSYSFTEKKRLRKSFAKRESVQEIPYLLAMQLESYAAFLQTNVPADQRTETGLQSTFSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L++VSY+     FDV +C  R LTYA PL++ +RL + D        ++
Sbjct: 61   FPIVSHSGNARLDYVSYQLGAEPFDVKECQQRGLTYAAPLRVRVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT++G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGELPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT  L ALG   E+I+STFY    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRIDRRRKMPVTILLKALGYTPEQIISTFYDFDTFHISK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F +    L  G      ++    G  ++   K++T   ++ +++ GV  + +  D 
Sbjct: 239  SGVEFTVVPERL-RGEVAKFDIL-AKDGSVIVAKDKRITVKHIRDMEKAGVSEIAVPQDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A  IV+ ETGE+   A D + E  L ++  + IR +  LY + +++  YI  TL
Sbjct: 297  ILGRALANTIVDQETGEVVANANDEVTESLLGKLVDANIRTVSTLYSNDLDHGDYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LFF  ++YDLS VGR+K N R   
Sbjct: 357  RIDEIPDQYSARVAIYRMMRPGEPPTEESVEALFQGLFFSEERYDLSRVGRMKFNRRAFP 416

Query: 423  DT--------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +                      +    +  EDI+A+I +L++LRNG+G IDDID+LGNR
Sbjct: 417  EKAEERQSNWIRRFYEAVGVQGDEGANTLSNEDILAVIGVLLELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+RSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKPV SA+ EFF SSQL
Sbjct: 477  RIRSVGELAENQFRTGLVRVERAVKERLSQAESDNLMPHDLINAKPVSSAIREFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +AR N YGF+ETPYR+V   KV++ + YLSA+EE    IAQAN+ LD    F +
Sbjct: 597  INSLALYARTNEYGFLETPYRRVDANKVSDTIDYLSAIEESQYMIAQANTDLDTKNLFVD 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +L+  R   E  +   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLISSRHHNEFTMTQPDRVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+AE   VGTG+E  VA  SG  + A+R G+V+ VD+ RIVIR  + +      GVDIY
Sbjct: 717  CLRAEKAVVGTGIERTVAVDSGTVVTARRGGLVDYVDSARIVIRVNDEEAKAGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L K+ RSNQNT +NQRPLVKVGD++ R D+IADG STD+G+LALG+NMLV FMPW+GYN
Sbjct: 777  NLTKYTRSNQNTNINQRPLVKVGDKLARGDVIADGASTDMGELALGQNMLVGFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +EDS+LISER+V++D +TSIHIEE  V+ARDTKLG EEIT+DI N+SE  L  +DE GII
Sbjct: 837  YEDSILISERVVADDRYTSIHIEELSVVARDTKLGAEEITQDISNLSERMLARLDEVGII 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV
Sbjct: 897  HIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GID++ R+  +  +Q+    +D  D+  I++ + + R+  ++ G+ A  GP   
Sbjct: 957  QVFTREGIDRDARAQQIIDDQLAHYKQDLADQMRIVEDDAFGRIRRLIEGKVATGGPNKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK   L+++ +    R  W+   + DE+  R +E LK     ++   ++RF+ K  K+  
Sbjct: 1017 KKGEALTAEYLESVGRYDWFDIRLSDEEAARQLEQLKDSLSQARIEFDNRFEEKKRKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP + DGTP+DIVL
Sbjct: 1077 GDELPPGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVISKICPVEDMPHMADGTPLDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SH 1181
            NPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +    ++ +R FLEK+       
Sbjct: 1137 NPLGVPSRMNIGQILEVHLGWAAKGLGLRIEEML---REESKVAEIRKFLEKIYNDSTGK 1193

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------- 1232
             E I  + D  +L +A+  K GVP +TPVFDGA E  I +ML +A  D+           
Sbjct: 1194 HEDIKSFTDAEILDLAQNLKRGVPFATPVFDGAAESDIKAMLDLAFPDDDARTKQLQFHA 1253

Query: 1233 ---QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
               Q  L+DG TG+ F+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1254 GKTQVTLFDGRTGDKFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1313

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT+VYE+IV G    + G PESFNV
Sbjct: 1314 GGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDAGMPESFNV 1373

Query: 1350 LVKEMQALGLSIDLENS 1366
            LVKE+++L + IDL+ +
Sbjct: 1374 LVKEIRSLAIDIDLDRN 1390


>gi|303256441|ref|ZP_07342455.1| DNA-directed RNA polymerase, beta subunit [Burkholderiales bacterium
            1_1_47]
 gi|331000382|ref|ZP_08324062.1| DNA-directed RNA polymerase, beta subunit [Parasutterella
            excrementihominis YIT 11859]
 gi|302859932|gb|EFL83009.1| DNA-directed RNA polymerase, beta subunit [Burkholderiales bacterium
            1_1_47]
 gi|329572088|gb|EGG53757.1| DNA-directed RNA polymerase, beta subunit [Parasutterella
            excrementihominis YIT 11859]
          Length = 1377

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 688/1377 (49%), Positives = 962/1377 (69%), Gaps = 15/1377 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P ++++P L+E Q  SY  FL  ++   ER +EGLQ AFKS+
Sbjct: 1    MSYSFTEKKRIRKSFAKRPSVLEVPSLLETQLHSYHEFLQADVPAAERRDEGLQGAFKSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF  Y  D P FDV +C  R L Y   L+  +RL++FD D+   + ++
Sbjct: 61   FPIVSHNGLARLEFQEYILDDPVFDVSECQLRGLNYCSRLRAKVRLVIFDRDQPKQS-TV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+I+E  +YMG++PLMTK G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEIRESEVYMGEIPLMTKKGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+H RIDRRRK+P T  L ALGM  E IL  FY    Y+   
Sbjct: 180  RIIPYRGSWLDFEFDAKDILHFRIDRRRKMPGTIMLKALGMTPESILKQFYEFDHYTLTQ 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     +  + L  G   +  + D + G+ ++   K++ +  ++ +++ G+  L +  D 
Sbjct: 240  DGATLEIIPSRL-RGEIAAFDIKDPE-GKVIVAKDKRINARHVREIEKLGITELPVPLDN 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++ + ++GE+   A D I  + LE+I    I     LY++ +N   YI +TL
Sbjct: 298  LIGKVIATNLYDEDSGEVVANANDEITPELLEKIREHGIDSFDTLYINELNRGPYISDTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F  LFFD + YDLS VGR+K+N R N 
Sbjct: 358  RLDETPDQLSARIAIYRMMRPGEPPTEEAVETLFRRLFFDPETYDLSRVGRMKINSRFNR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             T      +  EDII  +K +V LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418  GTETGPMTLEPEDIIDTMKAIVQLRNGEGQVDDIDHLGNRRVRCVGELTENQFRSGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+   + D++MP DLIN+KP+ +A+ +FF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478  ERAVRERLGQAESDNLMPHDLINSKPISAAIRDFFGSSQLSQFMDQTNPLSEITHKRRIS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNDYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VTN++ YLSA++E N  IAQAN+S+D+ G+ ++ELV CR  GE +L+  E++ 
Sbjct: 598  RKVIDGHVTNEIAYLSAIDEGNYIIAQANASIDDKGNLSDELVSCRDKGEFVLMRPERVQ 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ VP L+ E P VGTG+E  VA  
Sbjct: 658  YMDVAPAQIVSVAASLIPFLEHDDANRALMGSNMQRQGVPCLRPEKPVVGTGIERTVAVD 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G+V+ VDA RIV+R  + +  P   GVDIY L KF RSNQ T +NQRP+V
Sbjct: 718  SGTTVQAERGGVVDYVDANRIVVRVNDEENVPGRVGVDIYNLQKFTRSNQGTNINQRPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              GD + + D+IADG STDLG+LALG+NM+VAFMPW+GYN+EDS+++SE++V++D ++SI
Sbjct: 778  NPGDHIAKGDVIADGASTDLGELALGQNMIVAFMPWNGYNYEDSVMVSEKVVADDRYSSI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V ARDTKLG EEITRDI N+SE  +  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 838  HIEELSVQARDTKLGSEEITRDISNLSENQINRLDESGIVYIGAEVKAGDVLVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI++++R+ S+  +
Sbjct: 898  ETTLTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIERDKRAQSIIDD 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    + +D+  I++R+ + RL   L G  A  GP G  K   ++ + +      +W+
Sbjct: 958  ELKRYRTNLNDQLRIVERDAFERLARQLIGNVAQGGPDGLGKGKKVTKEYLDGLNVHKWF 1017

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE++Q+ +E +++  E  +   ++ +  K +K+  GD++P GV ++VKV++A+KR
Sbjct: 1018 DIRMADEELQKQIEEVRISLEAKRKEFDEAWNEKRKKLTQGDELPTGVQKMVKVYLAVKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRI   EDMPF+ DG PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1078 RLQPGDKMAGRHGNKGVVSRITRVEDMPFMADGRPVDIVLNPLGVPSRMNIGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQWK 1201
            WA  GLG +I  ++  ++ +  ++ +R FL  +   +    E      DD ++ +A+  K
Sbjct: 1138 WAAFGLGWRIAEML-KHERSKQVAEIREFLNTIYNKSSGKKEDFDSLTDDEIIDLAKHLK 1196

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA E  I  ML +A  +E+ +          + L+DG TG+ FDRPVTV
Sbjct: 1197 KGVPFATPVFDGASESDIREMLNLAFPEETAKKLHLTPSKTQAQLFDGRTGDAFDRPVTV 1256

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G ++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1257 GVMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1316

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            QEMLT+KSDDV GRT++YE+IV G+   + G PESFNVLVKE+++LG+ IDL+  + 
Sbjct: 1317 QEMLTVKSDDVTGRTKLYENIVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRDKE 1373


>gi|145635405|ref|ZP_01791107.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
            PittAA]
 gi|145267411|gb|EDK07413.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
            PittAA]
          Length = 1343

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFHSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|78099460|gb|ABB20866.1| RNA polymerase subunit B [Acinetobacter schindleri]
          Length = 1362

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1374 (51%), Positives = 969/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADKD-GKIIVEQGKRINARHVRQMEASGLEKLAVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  V+  + + +I    ++   +L+ + ++  ++I +TL
Sbjct: 295  LYERITAEDIQLKD-GDVIA-ANTVLSHEIMVKIAEGGVKQFNLLFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNDDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAIDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++AKR G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAKRGGRIEYVDASRVVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNMGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLDIQPVDEAIAERLTQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI  ++ + +    +  LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGDKIDKMLQEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   + GVP++TPVFDGA+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRKGVPLATPVFDGAEESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|254361140|ref|ZP_04977284.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            PHL213]
 gi|153092631|gb|EDN73680.1| DNA-directed RNA polymerase subunit beta [Mannheimia haemolytica
            PHL213]
          Length = 1341

 Score = 1637 bits (4238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1366 (51%), Positives = 966/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSFEKFIEKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ +D +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFEKIKFEIAD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++T+  +++L++  V  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETASFDI--AANGKVYVEMGRRITARHIRALEKDNVTQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  +GE+   A   I  + L  +  +    I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAQDYVDLSSGEVICPANMEISMEMLANLSQAGYNQIEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +++YDLS VGR+K N  L +
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSAERYDLSAVGRMKFNRSLEI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGSGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V CR  GE  L   E++ 
Sbjct: 592  RKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFTDTYVTCRQQGESGLFKPEEVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A  
Sbjct: 652  YMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIALD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG AIVAKR G V+ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P V
Sbjct: 712  SGVAIVAKRGGTVQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQVPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+I
Sbjct: 772  NLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R+  +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRAKEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  IL+  +++R+  +L          G K+S       +    R +W 
Sbjct: 952  QLCEAKKDLAEELEILEAGLFTRVRNLLI-------EGGVKESA------LDGVAREKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+KR
Sbjct: 999  EQTLEDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G +I  +I   K   +++ LR +++K    G GS    +S + D+ V+R+A+  
Sbjct: 1119 LAAHGIGDQIDKMI---KQQQEVAKLREYMQKAYDLGHGSQVVDLSTFSDEEVMRLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1296 DVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1341


>gi|170718704|ref|YP_001783895.1| DNA-directed RNA polymerase subunit beta [Haemophilus somnus 2336]
 gi|189043858|sp|B0URZ6|RPOB_HAES2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|168826833|gb|ACA32204.1| DNA-directed RNA polymerase, beta subunit [Haemophilus somnus 2336]
          Length = 1342

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1367 (52%), Positives = 971/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+S+
Sbjct: 1    MVYSYTEKKRIRKSFGKRPQVLNVPYLLTIQLDSFDKFIQRD----PDGQQGLEAAFRSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA  L++ LRL+ +D D  +G  +I
Sbjct: 57   FPIVSNNGNTELQYVSYQLGEPVFDVRECQIRGTTYAASLRVKLRLVSYDKDAASG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTSNGTFVINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L AL   +EEIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILDLFFDKVSFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  IE G+++T+  +K+L++  +  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETASFDIE--ANGKVYIERGRRITARHIKALEKDKITQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGEI   A   I  + LE++  +  ++I  L+ + ++   YI  TL
Sbjct: 292  IVGKVSAKDYVDLTTGEIICPANMEISLELLEKLSQAGYKNIETLFTNDLDFGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF S++YDLS VGR+K N  L +
Sbjct: 352  RVDPSYDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSSERYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ +++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDTTGSGTLSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D++SV PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLESVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LD +  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDNELRFTDAFVTCRGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V++G+ + R +I+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VQLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  +   +    R+QW
Sbjct: 952  MQLKQAKKDLVEELEILEAGLFARVRNLLLSGG-------------FNDKQLENLDRTQW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  QYE  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLVDEDKQNQLEQLAEQYEELRKDFEHKLEIKRSKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K   D+  LR +++K    G GS    +S + D+ VLR+A+ 
Sbjct: 1119 GLAAKGIGDQINAMI---KQKQDVEKLRGYIQKAYDLGDGSQKVDLSTFTDEEVLRLAKN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E+ I ++L +  L  SGQ IL+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGMPLATPVFDGAHEKEIKALLELGGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVGGTHQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|262375148|ref|ZP_06068382.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter lwoffii
            SH145]
 gi|262310161|gb|EEY91290.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter lwoffii
            SH145]
          Length = 1362

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1374 (51%), Positives = 974/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG  +E IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYSNENILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      ++D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDILDKD-GKAIVEQGKRINARHVRQMEASGLEKLAVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED +  + G++   A  V+  + + +I    ++   IL+ + ++  +++ ++L
Sbjct: 295  LYERITAED-IPLKDGDVIA-ANTVLSHEIMVKIAEGGVKQFNILFTNDIDRGSFVADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSNREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAMDKDGNLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A+R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAQRGGRIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEFKIFEEAARERVIRLLNGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPVDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG +I  ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDQIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L+++   ++GVP++TPVFDGA+E  I  +L++A L  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LKLSGNLRAGVPLATPVFDGAEEGQIKELLQLAGLSSTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|71899985|ref|ZP_00682131.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Ann-1]
 gi|71730272|gb|EAO32357.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Ann-1]
          Length = 1384

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1390 (50%), Positives = 967/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK+  I+ +P L+ +Q  SY  FL  ++   +R + GL  A KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKHRSILKVPFLLAIQVDSYRAFLQGDVESSQRKDIGLHGALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K++K
Sbjct: 63   PIVSYSGNAALEYVGYKLGEPMFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAVK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             IKEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YIKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +    D
Sbjct: 181  IIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +  + L
Sbjct: 241  EGVQLELVPERLRGEILSFNLTD--GGGVIVEAGKRITARHVKQLEASGISALAVPDEYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+ NTL 
Sbjct: 299  IGRILSHDVIDATTGELLASANSEVNEDRIVAFRKAGIESVGTLWVNDLDRGAYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N R+   
Sbjct: 359  IDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   +                      +IK L ++RNG+G +DDID+LGN
Sbjct: 419  EVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D++G  T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDDNGQLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  ESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G+++QVDA RIV++  E   +  + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERTVARDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGATDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD V   D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYGLIKYTRSNQNTCINQRPLVNVGDIVASGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+   SG  
Sbjct: 959  DVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVVNSGVD 1018

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +K  KI
Sbjct: 1019 -IKKGEVITDPYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSDKRSKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG++S ++P EDMPF++DGTPVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRCIQCGDKMAGRHGNKGVISNVVPVEDMPFMEDGTPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
            VLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++     
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEIYNHDK 1194

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + DD +L +A+    GVP+++PVFDGA E+ I  ML +A+L   GQ+ L
Sbjct: 1195 SLVGERVDLSQFSDDELLNMAKNLTDGVPMASPVFDGASEQEIKRMLDLAELPTGGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPFDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGHTGEPFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+     G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGDHQMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLENS 1366
            L ++I+LE++
Sbjct: 1375 LAINIELEDN 1384


>gi|229506877|ref|ZP_04396385.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae BX 330286]
 gi|229508682|ref|ZP_04398176.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae B33]
 gi|229512395|ref|ZP_04401870.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae TMA 21]
 gi|229516064|ref|ZP_04405515.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae RC9]
 gi|229519866|ref|ZP_04409299.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae TM
            11079-80]
 gi|229606391|ref|YP_002877039.1| DNA-directed RNA polymerase subunit beta [Vibrio cholerae MJ-1236]
 gi|255747129|ref|ZP_05421072.1| DNA-directed RNA polymerase beta subunit [Vibrio cholera CIRS 101]
 gi|262149005|ref|ZP_06028150.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae INDRE 91/1]
 gi|41019520|sp|Q9KV30|RPOB_VIBCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|229343107|gb|EEO08092.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae TM
            11079-80]
 gi|229346967|gb|EEO11934.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae RC9]
 gi|229350610|gb|EEO15555.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae TMA 21]
 gi|229354317|gb|EEO19246.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae B33]
 gi|229355982|gb|EEO20901.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae BX 330286]
 gi|229369046|gb|ACQ59469.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae MJ-1236]
 gi|255735178|gb|EET90580.1| DNA-directed RNA polymerase beta subunit [Vibrio cholera CIRS 101]
 gi|262031195|gb|EEY49814.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae INDRE 91/1]
          Length = 1341

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|222112411|ref|YP_002554675.1| DNA-directed RNA polymerase subunit beta [Acidovorax ebreus TPSY]
 gi|254765287|sp|B9MH47|RPOB_ACIET RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|221731855|gb|ACM34675.1| DNA-directed RNA polymerase, beta subunit [Acidovorax ebreus TPSY]
          Length = 1374

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1379 (50%), Positives = 968/1379 (70%), Gaps = 18/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FG    ++ +P L+++Q+ +Y  FL  + AP +R  EGLQAA
Sbjct: 1    MAQTSTYSYTERKRIRKSFGSRDSVLKVPYLLQMQRDAYTAFLQADTAPQKRSIEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F S FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T 
Sbjct: 61   FNSAFPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTS 120

Query: 119  -AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    
Sbjct: 181  LLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +               L  G      + D   G+ ++   K++T+   + L++ G   + 
Sbjct: 241  FRLMDSGAQLEFVPERL-RGEVARFDITD-KAGKVIVAKDKRVTARHTRELEQSGTTHIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  VA +IV+G+TGEI  +A + + E  L+++  + ++D+ ++Y + ++  AY
Sbjct: 299  VPEDFLIGRVVARNIVDGDTGEILAKANEELTEALLKKLRAAGVQDLQVIYTNELDQGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N
Sbjct: 359  ISQTLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             ++  D       +  +DI+A++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  AKIGRDEATGPMVLSNDDILAVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRT 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH
Sbjct: 479  GLARIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR+V DGKVT ++ YLSA+EE    IAQAN++LD +G  T +LV  R  GE  LV 
Sbjct: 599  IETPYRRVVDGKVTMEIDYLSAIEEGKYIIAQANATLDAEGRLTGDLVSAREKGESTLVS 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E 
Sbjct: 659  ADRVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + A R G+V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VAAVDSGTVVTANRGGVVDYVDATRIVVRVNDDEAVAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+VK GD++ + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED
Sbjct: 779  QRPIVKKGDKLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAED 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T +    ++   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLTGRVANGGPQKLAKGTKIDKAYLASVE 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     +E+V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KFHWFDIRPAEEEVATQLESIKNALEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGWA  G+G++I  ++   +     + LR FLE++  +    E++S   DD +L +A
Sbjct: 1139 EVHLGWAGKGMGQRIGDML---QREAKTAELRKFLEEIYNSRGRKEELSQLSDDEILAMA 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDR 1247
             +  SGVP ++PVFDGA EE I  ML++A  D             Q+ LYDG TGE F+R
Sbjct: 1196 RELTSGVPFASPVFDGASEEEIKDMLKLAYPDDLAQAKGLTETRTQAYLYDGRTGERFER 1255

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P TVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1256 PTTVGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1315

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AYVLQEMLT+KSDDV GRT+VYE+IV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 AYVLQEMLTVKSDDVQGRTKVYENIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|153802862|ref|ZP_01957448.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MZO-3]
 gi|124121617|gb|EAY40360.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MZO-3]
          Length = 1375

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 976/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 209  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 268

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 626  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 685

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++  E+ 
Sbjct: 926  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEXEQM 985

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 986  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1033 EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1093 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1153 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1209

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1210 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1269

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1270 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1329

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1330 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1375


>gi|315635146|ref|ZP_07890424.1| DNA-directed RNA polymerase subunit beta [Aggregatibacter segnis ATCC
            33393]
 gi|315476108|gb|EFU66862.1| DNA-directed RNA polymerase subunit beta [Aggregatibacter segnis ATCC
            33393]
          Length = 1342

 Score = 1636 bits (4237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1367 (51%), Positives = 973/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++IP L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNIPYLLTIQLDSFEKFIQRD----PDGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY    P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSTNGNTELQYVSYRLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +E+IL  F+ K+V+  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPSTIILRALGYTTEQILDLFFDKVVFEIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  +K + + ++ 
Sbjct: 235  NKLLMNLMPERL-RGETAAFDIE--ANGKVYVERGRRITARHIKALEKDNIKQVDVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN +TGE+   A   +  + L ++  +    +  L+ + ++   YI  TL
Sbjct: 292  IVGKVAAKDYVNLDTGELVCAANMELSLEVLAKLAQAGYTTVETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE++F  LFF SD+YDLS VGR+K N  L +
Sbjct: 352  RVDPSSDRLSALVEIYRMMRPGEPPTKEAAEALFENLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +  EDI++++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EETTGSGTLSNEDIVSVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+++V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LD++  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDEFRFTDAFVTCRGEHGESGLYKPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V++G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VELGEPVERGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++ R+  +L                   +  + +  R++W
Sbjct: 952  MQLKQAKKDLSEEFEILEAGLFMRVRNLLLSGG-------------FDAKSLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + +E+ Q  +E L  Q+E  +   E + + +  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLDNEEKQHQLEQLAEQHEELRKEFERKLEVQRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    I+ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGDQINAMI---KQQQSIAKLREYMQKAYDLGGGSQKVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E+ I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPIATPVFDGAHEKEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV+GN   + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 1342


>gi|264676494|ref|YP_003276400.1| DNA-directed RNA polymerase subunit beta [Comamonas testosteroni
            CNB-2]
 gi|299531359|ref|ZP_07044769.1| DNA-directed RNA polymerase subunit beta [Comamonas testosteroni S44]
 gi|262207006|gb|ACY31104.1| DNA-directed RNA polymerase, beta subunit [Comamonas testosteroni
            CNB-2]
 gi|298720766|gb|EFI61713.1| DNA-directed RNA polymerase subunit beta [Comamonas testosteroni S44]
          Length = 1370

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1375 (50%), Positives = 970/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++++P L+++QK +Y  FL  ++AP +R  +GLQAAF S 
Sbjct: 1    MAYSYTERKRIRKSFGSRDSVLEVPYLLQMQKDAYTAFLQADVAPKKRTIDGLQAAFNSA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKS 121
            FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTAQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD+++ R+DRRRK+PV+  L A+GM  E IL+TF+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDLLYFRVDRRRKMPVSILLKAIGMTPETILATFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A D + G      + D  +G+ V+   K++T+   + L++ G KF+ +  D
Sbjct: 241  DSGAQMEFVA-DRLKGEVARFDITD-KSGKVVVAKDKRITARHTRELEQSGTKFVSVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A++IV+ +TGEI  +A + + E  L+++  + ++D+  +Y + ++  AYI  T
Sbjct: 299  FLLGRVLAKNIVDPDTGEIIAKANEELTEALLKKLRSAGVQDVQCIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L TD+  D   A + IYR+MRPG+  T    +++F  LF+++D YDLS VGR+K N ++ 
Sbjct: 359  LRTDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNADTYDLSRVGRMKFNAKIG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +       +  EDI+A++KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  REGATGPMVLSNEDILAVVKILVDLRNGRGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT D+ YLSA+EE    IAQAN+ LD +G+   ELV  R AGE  LV  E++
Sbjct: 599  YRRVVDGKVTMDIDYLSAIEEGKYVIAQANADLDAEGNLVGELVSAREAGESTLVSAERV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + AKR GIV+ VDA RIVIR  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTAKRGGIVDYVDATRIVIRVNDDEAVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD++ + D++ADG STDLG++A+G+NML+AFMPW+GYN+EDS++I+ER+V++D +TS
Sbjct: 779  VSRGDKLAKGDVLADGASTDLGEIAIGQNMLIAFMPWNGYNYEDSVMINERIVADDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD+LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDVLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K   +    +    +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLTGRVANGGPQKLSKGAKIDKAYLDGVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     ++ V   +ES+K   E  +   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDDVAAQLESIKNSIEQQRHTFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I P EDMPFL DGT  DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKITPVEDMPFLADGTTADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++   +     + +R+FLE++       E++S  DD  V+ +A++  
Sbjct: 1139 GWAGKGLGQRIGDML---QKEARAAEVRAFLEEIYNRSGRKEELSQLDDGEVMSMAKELT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA E  I  ML++A  D             Q+ LYDG TGE F+RP TV
Sbjct: 1196 TGVPFATPVFDGASEAEIKDMLKLAYPDDIAAAKGLTETRTQAYLYDGRTGERFERPTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDVVGRT+VYESIV G  + E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVVGRTKVYESIVKGEHSIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|148825209|ref|YP_001289962.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittEE]
 gi|166229294|sp|A5U9X8|RPOB_HAEIE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|148715369|gb|ABQ97579.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittEE]
 gi|309972334|gb|ADO95535.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase beta chain
            [Haemophilus influenzae R2846]
          Length = 1343

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 968/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEISG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINTMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|78099442|gb|ABB20857.1| RNA polymerase subunit B [Acinetobacter genomosp. 9]
          Length = 1362

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1374 (51%), Positives = 973/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG  +E IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYSNENILDMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      ++D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDILDKD-GKAIVEQGKRINARHVRQMEASGLEKLAVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  V+  + + +I    ++   IL+ + ++  +++ ++L
Sbjct: 295  LYERITAEDIQLKD-GDVIA-ANTVLSHEIMVKIAEGGVKQFNILFTNDIDRGSFVADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSNREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAMDKDGNLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A+R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAQRGGRIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEFKIFEEAARERVIRLLNGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPVDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG +I  ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDQIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L+++   ++GVP++TPVFDGA+E  I  +L++A L  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LKLSGNLRAGVPLATPVFDGAEEGQIKELLQLAGLSSTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|223041809|ref|ZP_03611999.1| DNA-directed RNA polymerase subunit beta [Actinobacillus minor 202]
 gi|198246534|gb|ACH82225.1| DNA-directed RNA polymerase subunit beta [Actinobacillus minor 202]
          Length = 1343

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1367 (51%), Positives = 968/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTLQLDSYEKFIQQD----PEGLQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEIL+ F+  + ++   
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILAMFFETVKFTVSS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G      +     G+  +E G+++T+   + L + GV  + +  + 
Sbjct: 235  DNKLQMELVPERLRGETALFDIES--EGKVYVEKGRRITAKHTRDLVKAGVTKIDVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  +GEI   A   I  + L  +  +  ++I +L+ + ++   YI  TL
Sbjct: 293  IVGKVAAKDYVDLSSGEIICPANMEISLEMLANLSQAGYKEIEVLFTNDLDYGPYISETL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F+ +FF +D+YDLS VGR+K N  LN+
Sbjct: 353  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEGLFDNMFFSADRYDLSAVGRMKFNRSLNI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               + +  +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PEGEGLGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDED  FT+  V CR   GE  L   E+I
Sbjct: 593  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDEDFRFTDTYVTCRGEHGESGLYKPEEI 652

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 653  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 712

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 713  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 773  VKLGEPVGRGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 833  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 893  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 953  MQLREAKKDLTEELEILEAGLFTRVRNLLVEGGV-------------SEAELDKVAREKW 999

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  ++DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 1000 LEQTLEDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVK 1059

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1060 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1119

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+A+ 
Sbjct: 1120 GLAARGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFSDEEVMRLAQN 1176

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1177 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1236

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1237 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1296

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1297 DDVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1343


>gi|332172379|gb|AEE21633.1| DNA-directed RNA polymerase, beta subunit [Glaciecola agarilytica
            4H-3-7+YE-5]
          Length = 1342

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1365 (52%), Positives = 976/1365 (71%), Gaps = 26/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P++++IP L+ +Q  S+  F+ +++        GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLEIPYLLSIQLDSFKKFIDLDVD----GQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +T++ PL++ LRL++FD +   G  ++
Sbjct: 57   FPIKSYSGNAELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVLFDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P T  L AL + +EEIL  F+ K      G
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPATIMLRALEIPTEEILGMFFEKNQVRIDG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +       D + G      ++D D G  ++E+G+++++   ++L++ G+  L + ++ 
Sbjct: 235  NRF-MSDIVPDRLRGETAQFDILDSD-GNVLVEAGRRISARHTRALEKAGIVELEVPAEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A D V+ ETGE+ + A D++  +++  +  +       LY++ +++ AYI +TL
Sbjct: 293  LVGRVFACDYVDQETGELVVAANDILTLENVLALKEAGYTTFETLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS+VGR+K N RL  
Sbjct: 353  RIDSSTNRLEALVEIYRMMRPGEPPTKDAAETLFQNLFFSDDRYDLSSVGRMKFNRRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +T      + K+DI+ ++K L+ +R+GK  +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  ETSIGAGTLDKDDIVDVMKQLITIRDGKDDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N +GF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLASFARTNDFGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RK+ DG VT+++ YLSA+EE    IAQAN +LDE+G   ++L+ CR  GE  L    +I 
Sbjct: 593  RKIVDGVVTDEIDYLSAIEEGQFSIAQANVALDENGRLADDLIPCRHRGETTLKESSEIT 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVP L A+ P VGTGME  VA  
Sbjct: 653  YMDVSPQQIVSIAASIIPFLEHDDANRALMGANMQRQAVPTLIADKPLVGTGMEKTVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVTVVAKRGGRVDYVDASRIVIKVNEEETVAGEAGIDIYNLTKYTRSNQNTCINQRPTC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ +   D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  NVGEPIVAGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILISERVAMEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCVARDTKLGPEEISSDIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V GTV+DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVRGTVIDVQVFTRDGVEKDKRALEIEGM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  DE  IL   I++R   +L                 +    +    R +W+
Sbjct: 953  QLRQVKKDLSDEFNILADGIFARAKNLLVKSG-------------IEESRLESAQREKWF 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D+  Q  ++ +  Q+   K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 DLTLADDDAQTELDQIAEQFVEIKADFDKKFEIKRRKITQGDDLQPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+  +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 QIQPGDKMAGRHGNKGVISTIKPVEDMPYDVNGTPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG--SHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K + +++ LR FL++V G G       +  + DD + R+A+  
Sbjct: 1120 MAAHGIGVKIDRML---KEHEEMAKLRGFLKEVYGAGTTDQEVDLDSFSDDEITRLADNL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDGA E  I  ML +ADL ESGQ  L+DG TG  F+RPVTVGY+YMLKLN
Sbjct: 1177 RKGVPMATPVFDGATEAEIKHMLTLADLPESGQIALFDGRTGREFERPVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE 
Sbjct: 1297 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEE 1341


>gi|182682618|ref|YP_001830778.1| DNA-directed RNA polymerase subunit beta [Xylella fastidiosa M23]
 gi|226699462|sp|B2IA68|RPOB_XYLF2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|182632728|gb|ACB93504.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa M23]
          Length = 1384

 Score = 1636 bits (4236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1390 (50%), Positives = 967/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK+  I+ +P L+ +Q  SY  FL  ++   +R + GL  A KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKHRSILKVPFLLAIQVDSYRAFLQGDVESSQRKDIGLHGALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K++K
Sbjct: 63   PIVSYSGNAALEYVGYKLGEPMFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAVK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             IKEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YIKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +    D
Sbjct: 181  IIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +  + L
Sbjct: 241  EGVQLELVPERLRGEILSFNLTD--GGSVIVEAGKRITARHVKQLEASGISALAVPDEYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+ NTL 
Sbjct: 299  IGRILSHDVIDATTGELLASANSEVNEDRIIAFRKAGIESVGTLWVNDLDRGAYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N R+   
Sbjct: 359  IDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   +                      +IK L ++RNG+G +DDID+LGN
Sbjct: 419  EVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D++G  T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDDNGQLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  ESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G+++QVDA RIV++  E   +  + +GVD
Sbjct: 719  PTLRAQKPLVGTGIERTVARDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGATDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD V   D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYGLIKYTRSNQNTCINQRPLVNVGDIVASGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+   SG  
Sbjct: 959  DVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVVNSGVD 1018

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +K  KI
Sbjct: 1019 -IKKGEVITDPYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSDKRSKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG++S ++P EDMPF++DGTPVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRCIQCGDKMAGRHGNKGVISNVVPVEDMPFMEDGTPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
            VLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++     
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEIYNHDK 1194

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + DD +L +A+    GVP+++PVFDGA E+ I  ML +A+L   GQ+ L
Sbjct: 1195 SLVGERVDLSQFSDDELLNMAKNLTDGVPMASPVFDGASEQEIKRMLDLAELPAGGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPFDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGHTGEPFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+     G PESFNVLVKE+++
Sbjct: 1315 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGDHQMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLENS 1366
            L ++I+LE++
Sbjct: 1375 LAINIELEDN 1384


>gi|322513233|ref|ZP_08066359.1| DNA-directed RNA polymerase subunit beta [Actinobacillus ureae ATCC
            25976]
 gi|322121009|gb|EFX92850.1| DNA-directed RNA polymerase subunit beta [Actinobacillus ureae ATCC
            25976]
          Length = 1342

 Score = 1635 bits (4235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 972/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSFEKFIERD----PDGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEILS F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILSIFFEKVTFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  + 
Sbjct: 235  NKLLMTLVPERL-RGETAAFDIE--ADGKVYVERGRRITARHIRTLEKDGITQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++  TGE+   A   I  + L ++  +  ++I +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYIDLSTGELVCPANMEISMEMLAKLSQAGYKEIDVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LNL
Sbjct: 352  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNL 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII I++ L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  AEGVGSGILSNDDIIGIMQKLLEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 592  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDEEFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGTIQYVDASRIVVKVNEDETILGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 952  MQLKEAKKDLTEELEILEAGLFTRVRNLLVEGGV-------------SEAELDKVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEEKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I  +I   K   +++ LR +++K    G GS    +S + D+ V+R+AE 
Sbjct: 1119 GLAAKGIGDQINKMI---KQQQEVAKLREYIQKAYDLGHGSQVVDLSTFTDEEVMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHEAEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDED 1342


>gi|15603602|ref|NP_246676.1| DNA-directed RNA polymerase subunit beta [Pasteurella multocida
            subsp. multocida str. Pm70]
 gi|41017792|sp|Q9CK91|RPOB_PASMU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|12722152|gb|AAK03821.1| RpoB [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 1342

 Score = 1635 bits (4235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1367 (51%), Positives = 970/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSNNGNTELQYVSYQLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L AL   +E+IL  F+ K+V+    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEQILDIFFDKVVFEISN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++  +  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETATFDIE--ANGKVYVERGRRITARHIRALEKDQITQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ E+GEI   A   I  + L ++  +  + I  L+ + ++   YI  TL
Sbjct: 292  IVGKVAAKDYVDLESGEIVCPANMEISLEMLAKLAQAGYKTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF SD+YDLS VGR+K N  L +
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEETGSGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   GE  L   ++I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAFVTCRGEHGESGLYRPDEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAV 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  ++AKR G+V+ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVTVIAKRGGMVQYVDASRIVVKVNEDETIPGEAGIDIYNLVKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ + R +++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VSLGEPIGRGEVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                   +  + +  R++W
Sbjct: 952  MQLKQAKKDLVEELEILEAGLFTRVRSLLIAGG-------------FDAKNLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + ++ DE  Q  +E L  QYE  +   E + + +  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQSLSDEAQQNQLEQLAEQYEELRKEFERKLEVQRGKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G KI ++I   K   D++ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGDKINAMI---KQQQDVAKLREYMQKAYDLGHGSQKVDLSTFSDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVGGTHQMDPGTPESFNVIMKEIRSLGINIDLDED 1342


>gi|240949956|ref|ZP_04754273.1| DNA-directed RNA polymerase subunit beta [Actinobacillus minor NM305]
 gi|240295578|gb|EER46302.1| DNA-directed RNA polymerase subunit beta [Actinobacillus minor NM305]
          Length = 1343

 Score = 1635 bits (4235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 967/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTLQLDSYEKFIQQD----PEGLQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEIL+ F+  + ++   
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILAMFFETVKFTVSS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G      +     G+  +E G+++T+   + L + GV  + +  + 
Sbjct: 235  DNKLQMELVPERLRGETALFDIES--EGKVYVEKGRRITAKHTRDLVKAGVTKIDVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  +GEI   A   I  + L  +  +  ++I +L+ + ++   YI  TL
Sbjct: 293  IVGKVAAKDYVDLSSGEIICPANMEISLEMLANLSQAGYKEIEVLFTNDLDYGPYISETL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F+ +FF +D+YDLS VGR+K N  LN+
Sbjct: 353  RVDPTYDRLSALVEIYRMMRPGEPPTKEAAEGLFDNMFFSADRYDLSAVGRMKFNRSLNI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               + +  +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  PEGEGLGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  FT+  V CR   GE  L   E I
Sbjct: 593  RKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYKPEDI 652

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 653  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 712

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G ++ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 713  DSGVAVVAKRGGTIQYVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 773  VKLGEPVGRGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 833  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 893  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L                  S   + +  R +W
Sbjct: 953  MQLREAKKDLTEELEILEAGLFTRVRNLLVEGGV-------------SEAELDKVAREKW 999

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  ++DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 1000 LEQTLEDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVK 1059

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1060 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1119

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K    ++ LR +++K    G GS +  +S + D+ V+R+A+ 
Sbjct: 1120 GLAARGIGDQINAMI---KQQQSVAKLREYIQKAYDLGHGSQSVDLSTFSDEEVMRLAQN 1176

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1177 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1236

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1237 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1296

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1297 DDVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1343


>gi|262370133|ref|ZP_06063460.1| RNA polymerase subunit B [Acinetobacter johnsonii SH046]
 gi|262315172|gb|EEY96212.1| RNA polymerase subunit B [Acinetobacter johnsonii SH046]
          Length = 1362

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1374 (51%), Positives = 972/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L ALG ++ +IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVVLRALGYNNAQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      +VD D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIVDND-GKTIVEQGKRINARHVRQMEAAGLEKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED +  + G++   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAED-IPLKDGDVIA-ANTLLSHEIMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S +D+DG+ TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVLDGRVTDEVEYLSAIEEVGTVIAQADSGVDKDGNLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAGRGGRIEFVDASRVVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LVK+GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVKLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS+D++S
Sbjct: 953  RAQAIEKAQLDSYRKDLKEEYKIFEEAARERIVRLLTGQESNGGGTT-KRGDKLSADVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   KA   +  LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGEEIDKML---KAQRTVLELRGFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +A++  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRAGVPLATPVFDGAEESQIKDLLELANISRTGQTVLYDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|145637446|ref|ZP_01793105.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittHH]
 gi|145269392|gb|EDK09336.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittHH]
          Length = 1343

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 968/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  LEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINTMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|229844327|ref|ZP_04464467.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            6P18H1]
 gi|229812576|gb|EEP48265.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            6P18H1]
          Length = 1343

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFHSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|260913280|ref|ZP_05919762.1| DNA-directed RNA polymerase subunit beta [Pasteurella dagmatis ATCC
            43325]
 gi|260632867|gb|EEX51036.1| DNA-directed RNA polymerase subunit beta [Pasteurella dagmatis ATCC
            43325]
          Length = 1342

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 969/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++VSY+   P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57   FPIVSNNGNTELQYVSYQLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L AL   +E+IL  F+ K+V+    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEQILDIFFDKVVFEISN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETATFDIE--ANGKVYVERGRRITARHIKALEKDNVTQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ E+GEI   A   I  + L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  IVGKVAAKDYVDLESGEIVCPANMEISLEMLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYR+MRPG+  T   AE +F+ LFF SD+YDLS VGR+K N  L +
Sbjct: 352  RVDPSNDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +  EDII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEETGSGILSNEDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   GE  L   ++I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAFVTCRGEHGESGLYRPDEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAV 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  ++AKR G+V+ VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVTVIAKRGGVVQYVDASRIVVKVNEDETVPGEAGIDIYNLVKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ + R +++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VSLGEPIGRGEVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                   +  + +  R++W
Sbjct: 952  MQLKQAKKDLVEELEILEAGLFTRVRSLLIAGG-------------FEAKNLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + ++ DE  Q  +E L  QYE  +   E + + +  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQSLSDEAQQNQLEQLAEQYEELRKEFERKLEIQRGKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RHIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G KI ++I   K   +++ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAAKGIGDKINAMI---KQQQEVAKLREYMQKAYDLGHGSQKVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    + GTPESFNV++KE+++LG++IDL+  
Sbjct: 1296 DDVNGRTKMYKNIVGGTHQMDPGTPESFNVIMKEIRSLGINIDLDED 1342


>gi|28199867|ref|NP_780181.1| DNA-directed RNA polymerase subunit beta [Xylella fastidiosa
            Temecula1]
 gi|32129997|sp|Q87A32|RPOB_XYLFT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|28057988|gb|AAO29830.1| RNA polymerase beta subunit [Xylella fastidiosa Temecula1]
          Length = 1388

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1390 (50%), Positives = 967/1390 (69%), Gaps = 35/1390 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK+  I+ +P L+ +Q  SY  FL  ++   +R + GL  A KSVF
Sbjct: 7    SYSFTEKKRIRKDFGKHRSILKVPFLLAIQVDSYRAFLQGDVESSQRKDIGLHGALKSVF 66

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI ++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K++K
Sbjct: 67   PIVSYSGNAALEYVGYKLGEPMFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAVK 124

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             IKEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 125  YIKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 184

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +    D
Sbjct: 185  IIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTFHINPD 244

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +  + L
Sbjct: 245  EGVQLELVPERLRGEILSFNLTD--GGSVIVEAGKRITARHVKQLEASGISALAVPDEYL 302

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+ NTL 
Sbjct: 303  IGRILSHDVIDATTGELLASANSEVNEDRIIAFRKAGIESVGTLWVNDLDRGAYLSNTLR 362

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N R+   
Sbjct: 363  IDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNRRVGRK 422

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   +                      +IK L ++RNG+G +DDID+LGN
Sbjct: 423  EVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDIDHLGN 482

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 483  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 542

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET EG NIG
Sbjct: 543  LSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPEGPNIG 602

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D++G  T
Sbjct: 603  LINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDDNGQLT 662

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 663  ESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 722

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+A+ P VGTG+E  VA+ SG  + A+R G+++QVDA RIV++  E   +  + +GVD
Sbjct: 723  PTLRAQKPLVGTGIERTVARDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGATDAGVD 782

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD V   D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 783  IYGLIKYTRSNQNTCINQRPLVNVGDIVASGDVLADGPSTDIGELALGQNMLIAFMPWNG 842

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  +DE G
Sbjct: 843  YNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNRLDESG 902

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 903  VVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 962

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+   SG  
Sbjct: 963  DVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVVNSGVD 1022

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +K  KI
Sbjct: 1023 -IKKGEVITDPYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSDKRSKI 1081

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG++S ++P EDMPF++DGTPVDI
Sbjct: 1082 TQGDDLAPGVLKMVKVFLAVKRCIQCGDKMAGRHGNKGVISNVVPVEDMPFMEDGTPVDI 1141

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG- 1179
            VLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++     
Sbjct: 1142 VLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEIYNHDK 1198

Query: 1180 ---SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + DD +L +A+    GVP+++PVFDGA E+ I  ML +A+L   GQ+ L
Sbjct: 1199 SLVGERVDLSQFSDDELLNMAKNLTDGVPMASPVFDGASEQEIKRMLDLAELPAGGQTQL 1258

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPFDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1259 YDGHTGEPFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1318

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+     G PESFNVLVKE+++
Sbjct: 1319 MEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGDHQMVAGMPESFNVLVKEIRS 1378

Query: 1357 LGLSIDLENS 1366
            L ++I+LE++
Sbjct: 1379 LAINIELEDN 1388


>gi|145633533|ref|ZP_01789262.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            3655]
 gi|144985902|gb|EDJ92510.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            3655]
          Length = 1343

 Score = 1635 bits (4234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLS VGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSAVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGTGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|78099454|gb|ABB20863.1| RNA polymerase subunit B [Acinetobacter lwoffii]
          Length = 1362

 Score = 1635 bits (4233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1374 (51%), Positives = 971/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG  +E IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYSNENILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      ++D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDILDKD-GKAIVEQGKRINARHVRQMEASGLEKLAVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  V+  + + +I    ++   +L+ + ++  +++ ++L
Sbjct: 295  LYERITAEDIALKD-GDVIA-ANTVLSHEVMVKIAEGGVKQFNVLFTNDIDRGSFVADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTTREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT D+ YLSA+EE    IAQA+S++D DG+  EE+V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTMDIEYLSAIEEVGTVIAQADSAVDADGNLLEEVVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A+R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAQRGGRIEFVDASRVVIRVNEEEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEFKIFEEAARERVIRLLNGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPVDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG +I  ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDQIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L+++   ++GVP++TPVFDGA+E  I  +L++A L  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LKLSGNLRAGVPLATPVFDGAEEGQIKELLQLAGLSSTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|145630307|ref|ZP_01786088.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            R3021]
 gi|144984042|gb|EDJ91479.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            R3021]
          Length = 1343

 Score = 1635 bits (4233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 968/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDKISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRNYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|229846598|ref|ZP_04466706.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            7P49H1]
 gi|229810691|gb|EEP46409.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            7P49H1]
          Length = 1343

 Score = 1635 bits (4233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 968/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEISG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINTMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHTDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|16272459|ref|NP_438673.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae Rd
            KW20]
 gi|145638570|ref|ZP_01794179.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittII]
 gi|260580962|ref|ZP_05848785.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            RdAW]
 gi|1173148|sp|P43738|RPOB_HAEIN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|1573496|gb|AAC22173.1| DNA-directed RNA polymerase, beta chain (rpoB) [Haemophilus
            influenzae Rd KW20]
 gi|145272165|gb|EDK12073.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittII]
 gi|260092321|gb|EEW76261.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            RdAW]
 gi|309750074|gb|ADO80058.1| DNA-directed RNA polymerase beta chain [Haemophilus influenzae R2866]
          Length = 1343

 Score = 1635 bits (4233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKLDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|120613164|ref|YP_972842.1| DNA-directed RNA polymerase subunit beta [Acidovorax citrulli
            AAC00-1]
 gi|158513036|sp|A1TVT0|RPOB_ACIAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120591628|gb|ABM35068.1| DNA-directed RNA polymerase subunit beta [Acidovorax citrulli
            AAC00-1]
          Length = 1374

 Score = 1635 bits (4233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1376 (50%), Positives = 968/1376 (70%), Gaps = 16/1376 (1%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
                 +    R+RK FG    ++ +P L+++QK +Y  FL  ++AP +R NEGLQAAF +
Sbjct: 4    TSTYSYTERKRIRKSFGSRDSVLKVPYLLQMQKDAYTAFLQADMAPQKRTNEGLQAAFNA 63

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AK 120
             FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K
Sbjct: 64   AFPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSK 123

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL+
Sbjct: 124  VVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLF 183

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +  
Sbjct: 184  SARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRL 243

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                      A D + G      + D  +G+ V+   K++T+   + L++ G   + +  
Sbjct: 244  MDSGAQMEFVA-DRLKGEVARFDITD-KSGKVVVAKDKRITARHTRELEQSGTTHISVPE 301

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G  VA +IV+G+TGEI  +A + + E  L+++  + ++D+ ++Y + ++  AYI  
Sbjct: 302  DFLIGRVVARNIVDGDTGEIVAKANEELTEALLKKLRSAGVQDLQVIYTNELDQGAYISQ 361

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++
Sbjct: 362  TLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKI 421

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              D       +  +DI+A++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR GL 
Sbjct: 422  GRDESTGPMVLSNDDILAVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRTGLA 481

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR
Sbjct: 482  RIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRR 541

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIET
Sbjct: 542  VSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIET 601

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR+V DGKVT+ + YLSA+EE    IAQAN++LD +G  T +LV  R  GE  L+  E+
Sbjct: 602  PYRRVVDGKVTDQIDYLSAIEEGKYVIAQANAALDAEGRLTGDLVSAREKGESTLLSAER 661

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A
Sbjct: 662  VQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAA 721

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP
Sbjct: 722  VDSGTVVTANRGGIVDYVDATRIVVRVNDDEAVAGEVGVDIYNLIKYQRSNQNTNIHQRP 781

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK GD + + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 782  IVKKGDVLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAEDRYT 841

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TP
Sbjct: 842  SIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTP 901

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  + 
Sbjct: 902  KGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTVIDVQVFTREGIQRDKRAQQII 961

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T +    ++   +  
Sbjct: 962  DDELKRFRLDLNDQLRIVEADAFDRIEKLLNGRVANGGPQKLAKGTKIDKAYLASVEKFH 1021

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+
Sbjct: 1022 WFDIRPAEDEVATQLESIKNALEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAV 1081

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ E H
Sbjct: 1082 KRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVLEVH 1141

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  G+G++I  ++   +     + +R FLE+V  +    E +S   DD V+ +A   
Sbjct: 1142 LGWAGKGIGQRIGDML---RDQAKAAEMRKFLEEVYNSRGRKEDLSVLSDDEVMAMAANL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEPFDRPVT 1250
             +GVP +TPVFDGA E  I  ML++A  D      G      Q+ LYDG TGE F+RP T
Sbjct: 1199 TNGVPYATPVFDGASEAEIKDMLKLAYPDDIKERKGLTESRTQAYLYDGRTGERFERPTT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1259 IGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1319 LQEMLTVKSDDVQGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|241765528|ref|ZP_04763490.1| DNA-directed RNA polymerase, beta subunit [Acidovorax delafieldii
            2AN]
 gi|241364685|gb|EER59710.1| DNA-directed RNA polymerase, beta subunit [Acidovorax delafieldii
            2AN]
          Length = 1370

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1375 (50%), Positives = 969/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++++P L+++QK +Y  FL  + AP +R  EGLQAAF + 
Sbjct: 1    MAYSYTERKRIRKSFGTRDSVLEVPYLLQMQKDAYTAFLQADKAPQKRTIEGLQAAFDAA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFIEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     +  L  G      + D  +G+ V+   K++T+   + L++ G   + +  D
Sbjct: 241  DSGAQMEFVSERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTTHISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA +IV+ +TGEI  +A D + E  L+++  + ++D+  +Y + ++  AY+  T
Sbjct: 299  FLIGRVVARNIVDADTGEIIAKANDELTEALLKKLRSAGVQDVQCIYTNELDQGAYMSQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++ 
Sbjct: 359  LRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RDESTGPMVLSNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVTN++ YLSA+EE    IAQAN+ LD+DG  T +LV  R  GE IL   +++
Sbjct: 599  YRRVVDGKVTNEIDYLSAIEEGKYVIAQANAVLDKDGRLTGDLVSAREKGESILCGADRV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPLVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGIVDYVDATRIVVRVNDEEAVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD++ + D++ADG STD G++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED +TS
Sbjct: 779  VKKGDKLVKGDVVADGASTDFGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTVIDVQVFTREGIQRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T +    ++   +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLNGRVANGGPQKLAKGTKIDKAYLASVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDEVATQLESIKNALEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I +++   +     S +R+FLE+V  +    E +S   DD ++ +AE   
Sbjct: 1139 GWAGKGIGQRIGNML---QEQAKASEMRTFLEEVYNSRGRKEDLSQLSDDDLMAMAENLT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA E+ I +ML++A             E  Q+ L+DG TG+ F+RP T+
Sbjct: 1196 NGVPYATPVFDGASEDEIKAMLKLAYPDELAERKGLTPERTQAYLFDGRTGDRFERPTTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDVVGRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|262392947|ref|YP_003284801.1| DNA-directed RNA polymerase subunit beta [Vibrio sp. Ex25]
 gi|262336541|gb|ACY50336.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. Ex25]
          Length = 1342

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1367 (51%), Positives = 972/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDTTDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA EE+I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEESIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|311109625|ref|YP_003982478.1| DNA-directed RNA polymerase subunit beta [Achromobacter xylosoxidans
            A8]
 gi|310764314|gb|ADP19763.1| DNA-directed RNA polymerase, beta subunit [Achromobacter xylosoxidans
            A8]
          Length = 1370

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1375 (50%), Positives = 959/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + AP +R  +GLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTAPSDRVADGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGMARLEFVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT    A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILCKAIGMTPESILANFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGAMMEFVPE-RWKGEMARFDISD-RDGKVIVEKDKRINAKHLRDLAAGGIQRISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  S + DI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDPDTGEVIANANDEITESVLGALRASNVYDIQALYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RTDETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GEDITGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV+  + YLSA+EE +  IAQAN++LDE+G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSEQIDYLSAIEESHYVIAQANAALDEEGRFVDDLVACREAGETMLTAPANV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPVVGTGIERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 777  VKRGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI  +GAEV+  D+LVGK+TPK
Sbjct: 837  VHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGITYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L  +    GP+   K   ++   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVNKTVNGGPRKLAKGATITKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D +    +  +R++L+KV  T     +I +  D+ V+ +A+  K
Sbjct: 1137 GWAAKGVGHRIADMLRDERT-AQVKNIRAYLDKVYNTTGTGARIDELTDEEVMEMAQNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA EE I +ML +A  DE            Q+ LYDG TGE F+RPVTV
Sbjct: 1196 NGVPFATPVFDGATEEEITTMLELAYPDEVAKRMALTPSRTQAWLYDGRTGEQFERPVTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|158513683|sp|A3M1G3|RPOB_ACIBT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|193076143|gb|ABO10757.2| RNA polymerase subunit B [Acinetobacter baumannii ATCC 17978]
          Length = 1357

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1369 (52%), Positives = 979/1369 (71%), Gaps = 21/1369 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVIDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++ID
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINID 1357


>gi|77918308|ref|YP_356123.1| DNA-directed RNA polymerase subunit beta [Pelobacter carbinolicus DSM
            2380]
 gi|88909624|sp|Q3A6Q4|RPOB_PELCD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|77544391|gb|ABA87953.1| DNA-directed RNA polymerase subunit beta [Pelobacter carbinolicus DSM
            2380]
          Length = 1368

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1363 (53%), Positives = 994/1363 (72%), Gaps = 12/1363 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F     II+IP+LI++QK SY  FL   + P  R N GL+A F+SVFPI  FS   
Sbjct: 11   LRKHFSTIKGIIEIPNLIDIQKNSYKRFLQAGLPPSARKNIGLEAVFRSVFPIRDFSETC 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L++VSY    PK+DV +C  R +T+A P+K+ +RL+ +DVD+ +G ++I+DIKEQ +Y 
Sbjct: 71   SLDYVSYSLGTPKYDVGECHQRGMTFAAPVKVCVRLVSWDVDKESGVQAIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKILYNARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D +FD KD+++VRIDRRRK+P T  L ALG  +EE+L+ +Y     +  GD +   ++  
Sbjct: 191  DFDFDHKDLLYVRIDRRRKLPATVLLKALGYSAEELLNYYYQVETVTVDGDSFKKKVN-L 249

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            DL+ G + S+ ++  D GE ++++ +K T   ++ L +  V+++ ++ + + G   + DI
Sbjct: 250  DLLAGQRASTDVLGND-GEIIVKANRKFTKAAIRKLADSNVEYIPVSEEEIVGKVASTDI 308

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+  TGE+ +E  + I E  LEE+    I +  IL++D ++   Y+R TL+ D+    +D
Sbjct: 309  VDVSTGEVIVECNEEISESKLEELRTRGIVEFNILFIDHLHVGPYLRETLLLDRMATPED 368

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A ++IYR +RPGD  T   A ++F  LFF+ ++YDLS VGR+K+N +L L +P+D   + 
Sbjct: 369  ARIEIYRRLRPGDPPTIKSANALFESLFFNPERYDLSVVGRIKLNYKLGLQSPEDQTTLT 428

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            K+DI+ +++ L+ LR+G+GTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 429  KDDILEVVRYLIGLRDGRGTIDDIDHLGNRRVRAVGELLENQYRVGLVRMERAIKERMSL 488

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++DS+MP DLIN+KPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R 
Sbjct: 489  QEVDSLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRE 548

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V  GKVTN
Sbjct: 549  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRIVEQGKVTN 608

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            ++ Y SA+EE    IAQAN+ LD+DG F  ELV  R  GE +L+ RE+I  +D SPKQ+V
Sbjct: 609  EIRYFSALEEGGHAIAQANAPLDDDGRFLNELVNARQNGEFVLIQREEIGLMDVSPKQLV 668

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLL+A+AP VGTGME +VA  SGAA+VA+  
Sbjct: 669  SVAASLIPFLENDDANRALMGSNMQRQAVPLLRADAPLVGTGMERIVAHDSGAAVVARHN 728

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV++  EG++D   +GVDIY L+KF RSNQNTC+NQ+P+VKVGD V    
Sbjct: 729  GVVESVDASRIVVKIDEGEVDEDGTGVDIYNLIKFARSNQNTCLNQKPIVKVGDRVASGG 788

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGPST+ G+LALG+N+LVAFMPW GYNFEDS+LISE++V ED +TSIHIEE E +AR
Sbjct: 789  IIADGPSTEWGELALGQNVLVAFMPWEGYNFEDSILISEKLVKEDRYTSIHIEELECVAR 848

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ E+ LK++DE GI+ +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 849  DTKLGKEEITNDIPNLGEDALKDLDESGIVRIGAEVKPGDILVGKITPKGETQLSPEEKL 908

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLR+P GV G V+  R+F+R G DK+ R+  +E+ +IE L +D+ 
Sbjct: 909  LRAIFGEKAGDVRDTSLRLPPGVEGVVIGARVFSRKGSDKDSRTEYIEKTEIEKLLKDQH 968

Query: 973  DEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  + + +L  +L GQ + S      G +   +   ++S++++E P ++W + ++
Sbjct: 969  DEIRIIRESTHGKLESLLVGQTSASALFDAAGKELLGQGEKITSEVLAEVPFARWREISL 1028

Query: 1027 QDEKVQ-RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D       + ++       + +++  F +KIEKI+ GDD+PPGV+++VKV++A+KR + 
Sbjct: 1029 LDASENEEKLSAIMTSLAQREELIKAVFADKIEKIKRGDDLPPGVIKMVKVYIAIKRKLS 1088

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG++SR+LP EDMP++ DGTPV+IVLNPLGVPSRMNVGQI ETHLG A 
Sbjct: 1089 VGDKMAGRHGNKGVLSRVLPEEDMPYMADGTPVEIVLNPLGVPSRMNVGQILETHLGLAA 1148

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG +I+  ++ Y        +R+ + +        E +    DD V+++A Q   GVP
Sbjct: 1149 RGLGVQIQEHLDRYYTP---EAMRTKIGECYEDDRVAEFVDALPDDEVMQLARQLSRGVP 1205

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++PVF+G  EE + + +  A    SGQ  LY+G TGE F   VTVG +YMLKL+H+V D
Sbjct: 1206 MASPVFEGVTEEQMKNQMERAGFASSGQMTLYNGKTGEAFKEKVTVGIMYMLKLHHLVDD 1265

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA+ LQE LT+KSDDV GR
Sbjct: 1266 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAHALQEFLTVKSDDVTGR 1325

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            TR+YE+IV G  T E G PESFNVL+KE+Q+L L ++L   + 
Sbjct: 1326 TRMYEAIVKGKHTLEAGLPESFNVLIKELQSLCLDVELLEEQE 1368


>gi|326319225|ref|YP_004236897.1| DNA-directed RNA polymerase subunit beta [Acidovorax avenae subsp.
            avenae ATCC 19860]
 gi|323376061|gb|ADX48330.1| DNA-directed RNA polymerase, beta subunit [Acidovorax avenae subsp.
            avenae ATCC 19860]
          Length = 1374

 Score = 1634 bits (4232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1376 (50%), Positives = 968/1376 (70%), Gaps = 16/1376 (1%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
                 +    R+RK FG    ++ +P L+++QK +Y  FL  ++AP +R NEGLQAAF +
Sbjct: 4    TSTYSYTERKRIRKSFGSRDSVLKVPYLLQMQKDAYTAFLQADMAPQKRTNEGLQAAFNA 63

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AK 120
             FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K
Sbjct: 64   AFPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSK 123

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL+
Sbjct: 124  VVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLF 183

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +  
Sbjct: 184  SARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRL 243

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                      A D + G      + D  +G+ V+   K++T+   + L++ G   + +  
Sbjct: 244  MDSGAQMEFVA-DRLKGEVARFDITD-KSGKVVVAKDKRITARHTRELEQSGTTHISVPE 301

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G  VA +IV+G+TGEI  +A + + E  L+++  + ++D+ ++Y + ++  AYI  
Sbjct: 302  DFLIGRVVARNIVDGDTGEIVAKANEELTEALLKKLRSAGVQDLQVIYTNELDQGAYISQ 361

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++
Sbjct: 362  TLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKI 421

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              D       +  +DI+A++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR GL 
Sbjct: 422  GRDESTGPMVLSNDDILAVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRTGLA 481

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR
Sbjct: 482  RIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRR 541

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIET
Sbjct: 542  VSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIET 601

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR+V DGKVT+ + YLSA+EE    IAQAN++LD +G  T +LV  R  GE  L+  E+
Sbjct: 602  PYRRVVDGKVTDQIDYLSAIEEGKYVIAQANATLDAEGRLTGDLVSAREKGESTLLSAER 661

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A
Sbjct: 662  VQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAA 721

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP
Sbjct: 722  VDSGTVVTANRGGIVDYVDATRIVVRVNDAEAVAGEVGVDIYNLIKYQRSNQNTNIHQRP 781

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK GD + + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 782  IVKKGDVLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAEDRYT 841

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TP
Sbjct: 842  SIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTP 901

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  + 
Sbjct: 902  KGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTVIDVQVFTREGIQRDKRAQQII 961

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T +    ++   +  
Sbjct: 962  DDELKRFRLDLNDQLRIVEADAFDRIEKLLNGRVANGGPQKLAKGTKIDKAYLASVEKFH 1021

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+
Sbjct: 1022 WFDIRPAEDEVATQLESIKNALEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAV 1081

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ E H
Sbjct: 1082 KRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVLEVH 1141

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  G+G++I  ++   +     + +R FLE+V  +    E +S   DD V+ +A   
Sbjct: 1142 LGWAGKGIGQRIGDML---RDQAKAAEMRKFLEEVYNSRGRKEDLSMLSDDEVMAMAGNL 1198

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEPFDRPVT 1250
             +GVP +TPVFDGA E  I  ML++A  D      G      Q+ LYDG TGE F+RP T
Sbjct: 1199 TNGVPYATPVFDGASEAEIKDMLKLAYPDDIKERKGLTDSRTQAYLYDGRTGEQFERPTT 1258

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YV
Sbjct: 1259 IGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYV 1318

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1319 LQEMLTVKSDDVQGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|37912997|gb|AAR05326.1| DNA-directed RNA polymerase beta subunit [uncultured marine alpha
            proteobacterium HOT2C01]
          Length = 1367

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 795/1365 (58%), Positives = 1036/1365 (75%), Gaps = 4/1365 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  + F    RVRK FGK  E+   P+LIE+QK SY+ FL+    P ERP++GLQ  FK
Sbjct: 1    MANTLSFTERKRVRKNFGKLKEVSKFPNLIEIQKKSYEDFLLEEENPSERPDKGLQKVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFP+  FSG+A +E++ Y+F  PKFDVD+C  RD TYA PL + LRLIVFD+DE T ++
Sbjct: 61   SVFPLEDFSGSARIEYIEYDFQSPKFDVDECRQRDKTYAAPLNVKLRLIVFDIDEETESR 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ IY+ DLPLMT+ GTF+  G +R+VVSQ+HRSPG+ FDHD G+   SGKLL+
Sbjct: 121  TVKDIKEQEIYLCDLPLMTQKGTFITNGTERVVVSQMHRSPGVFFDHDNGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              R+IP +G W+DIEFD KDIIH RIDR++K+P+T+FLMA+G+  +EILS FY    YS 
Sbjct: 181  GARVIPYRGSWLDIEFDHKDIIHCRIDRKKKIPITTFLMAMGIKRDEILSLFYNTETYSL 240

Query: 241  --RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
              +   W    +  ++  G K+  SLV+   G+  ++ G K+   L K L   G+K L +
Sbjct: 241  NTKDGKWKVGFNPKNIKTG-KLQKSLVNAADGKVAVKQGTKINPALAKKLFNDGLKNLLL 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G ++A+DI+N +TGEIY E+ D I  +++E++   +I  IP+L +D +N  ++I
Sbjct: 300  EDDELIGKFIADDIINEKTGEIYFESSDEIVPETIEKMKELKISKIPVLEIDGINIGSFI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            R+TL  DKN   ++A+++IY+V+RPG+      A  +FN LFF S+KYDLS VGRVKMN 
Sbjct: 360  RDTLRVDKNFSPEEAVVEIYKVLRPGEPPNLETAFEVFNSLFFKSEKYDLSDVGRVKMNY 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RLNL+  D V  +R ED+I +IK ++DLR GKG +DDID+LGNRRVRSVGE+++NQ+R+G
Sbjct: 420  RLNLECSDTVTVLRSEDVIEVIKTVMDLRTGKGEVDDIDHLGNRRVRSVGELVENQFRMG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+RMERSIKER++S+++D+  PQD+INAKP+V+++ EFF +SQLSQ  +  N L+ ITH 
Sbjct: 480  LIRMERSIKERMNSLEVDAATPQDIINAKPLVASLKEFFGTSQLSQFMDQTNPLAEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG++R RAG E+RDVHPTHYGRICP ET EG NIGL++SL S ARVN YGFI
Sbjct: 540  RRLSALGPGGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLASHARVNQYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV  GKV+N+V YL AMEE +  IAQANS LD+ GSF  +LV CR  G+ ++   
Sbjct: 600  ESPYRKVIKGKVSNEVEYLPAMEEADYTIAQANSELDDRGSFVTKLVSCRRNGDFVMTVP 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E+ID++D SPKQVVS AASLIPFLENDD+NR LMG NM RQAVPL++AE+P VGTG+E V
Sbjct: 660  EEIDYMDVSPKQVVSCAASLIPFLENDDANRALMGSNMMRQAVPLIQAESPLVGTGVEKV 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SG  IVA R GIV+++D  RIV+R  E     + SGVDIY L KFQRSNQ+TC+NQ
Sbjct: 720  VAVDSGVTIVANRDGIVDKIDGKRIVVRVTEKIK-TTESGVDIYTLQKFQRSNQSTCINQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD+V + DIIADGPST  G+L LGRN++VAFMPW GYNFEDS+LISE++V ED 
Sbjct: 779  RPLVKVGDQVSKGDIIADGPSTHFGELGLGRNVVVAFMPWRGYNFEDSILISEKIVQEDK 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVM+RDTKLG EEITRDIPN  +E L+N+DE GI+ VGA+VNPGDILVGK+
Sbjct: 839  FTSIHIEEFEVMSRDTKLGSEEITRDIPNAGDEVLRNLDEAGIVYVGADVNPGDILVGKV 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESP+TPEEKLLRAIFGEKA DV+DTSLR+P G SG VVDV++FNR+GI+K++R++S
Sbjct: 899  TPKGESPVTPEEKLLRAIFGEKATDVKDTSLRLPPGSSGIVVDVKVFNRYGIEKDDRALS 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ER++IE LA+D++ E  IL+RNI  RL+ ++ G++    P   ++        + +   
Sbjct: 959  IERDEIEKLAKDREAELGILNRNIKERLVSLISGKSINESPGDIERQNNYDKATLLDVKL 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W+  +Q    Q  +++LK QY+ ++S ++ RF NK++K+Q GD++ PGV+++VKVFV
Sbjct: 1019 DSLWKMKLQSSSDQNEIDNLKKQYDIARSAIQTRFDNKVDKVQRGDELLPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++S+I P EDMP+L+DG  VDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AVKRKLQPGDKMAGRHGNKGVISKIAPVEDMPYLEDGRTVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G+ I   ++ YK + D S +   LEKV G   +  +IS    +    +A 
Sbjct: 1139 THLGWACAGIGEIINKSLSQYKVSNDHSIIGQSLEKVYGKDQYKNEISSLSKEEQKELAM 1198

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               SGVP+ TPVFDGA E  I+ ML  A  D+SGQ+ L+DGLTGE F+R VTVGYIYMLK
Sbjct: 1199 NISSGVPIKTPVFDGASEAEISEMLGEAGFDKSGQTQLWDGLTGEKFERKVTVGYIYMLK 1258

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+K
Sbjct: 1259 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVK 1318

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GRT+VYE+I+ G D F++GTPESFNVL+KE+++LGL+I+L
Sbjct: 1319 SDDVAGRTKVYETIIRGEDVFQSGTPESFNVLIKEIRSLGLNIEL 1363


>gi|68249112|ref|YP_248224.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            86-028NP]
 gi|81336482|sp|Q4QN33|RPOB_HAEI8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|68057311|gb|AAX87564.1| DNA-directed RNA polymerase beta chain [Haemophilus influenzae
            86-028NP]
          Length = 1343

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|260582781|ref|ZP_05850568.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            NT127]
 gi|260094231|gb|EEW78132.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            NT127]
          Length = 1343

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1365 (51%), Positives = 966/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLS VGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSAVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|182676594|sp|A5UH20|RPOB_HAEIG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1343

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKISALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|221069398|ref|ZP_03545503.1| DNA-directed RNA polymerase, beta subunit [Comamonas testosteroni
            KF-1]
 gi|220714421|gb|EED69789.1| DNA-directed RNA polymerase, beta subunit [Comamonas testosteroni
            KF-1]
          Length = 1370

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1375 (50%), Positives = 969/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++++P L+++QK +Y  FL  ++AP +R  +GLQAAF S 
Sbjct: 1    MAYSYTERKRIRKSFGSRDSVLEVPYLLQMQKDAYTAFLQADVAPKKRTIDGLQAAFNSA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKS 121
            FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTAQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD+++ R+DRRRK+PV+  L A+GM  E IL+TF+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDLLYFRVDRRRKMPVSILLKAIGMTPETILATFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A D + G      + D  +G+ V+   K++T+   + L++ G KF+ +  D
Sbjct: 241  DSGAQMEFVA-DRLKGEVARFDITD-KSGKVVVAKDKRITARHTRELEQSGTKFVSVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  +A++IV+ +TGEI  +A + + E  L+++  + ++D+  +Y + ++  AYI  T
Sbjct: 299  FLLGRVLAKNIVDPDTGEIIAKANEELTEALLKKLRSAGVQDVQCIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L TD+  D   A + IYR+MRPG+  T    +++F  LF+++D YDLS VGR+K N ++ 
Sbjct: 359  LRTDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNADTYDLSRVGRMKFNAKIG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +       +  EDI+A++KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  REGATGPMVLSNEDILAVVKILVDLRNGRGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT D+ YLSA+EE    IAQAN+ LD  G+   ELV  R AGE  LV  E++
Sbjct: 599  YRRVVDGKVTMDIDYLSAIEEGKYVIAQANADLDAAGNLVGELVSAREAGESTLVSAERV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + AKR GIV+ VDA RIVIR  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTAKRGGIVDYVDATRIVIRVNDDEAVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD++ + D++ADG STDLG++A+G+NML+AFMPW+GYN+EDS++I+ER+V++D +TS
Sbjct: 779  VSRGDKLAKGDVLADGASTDLGEIAIGQNMLIAFMPWNGYNYEDSVMINERIVADDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD+LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDVLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K   +    +    +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLTGRVANGGPQKLSKGAKIDKAYLDGVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     ++ V   +ES+K   E  +   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDDVAAQLESIKNSIEQQRHTFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I P EDMPFL DG+  DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKITPVEDMPFLADGSTADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++   +     + +R+FLE++       E++S  DD  V+ +A++  
Sbjct: 1139 GWAGKGLGQRIGDML---QKEARAAEVRAFLEEIYNRSGRKEELSQLDDGEVMSMAKELT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA E  I  ML++A  D             Q+ LYDG TGE F+RP TV
Sbjct: 1196 TGVPFATPVFDGASEAEIKDMLKLAYPDDIAAAKGLTETRTQAYLYDGRTGERFERPTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDVVGRT+VYESIV G  + E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVVGRTKVYESIVKGEHSIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|304414674|ref|ZP_07395727.1| DNA-directed RNA polymerase subunit beta [Candidatus Regiella
            insecticola LSR1]
 gi|304283175|gb|EFL91584.1| DNA-directed RNA polymerase subunit beta [Candidatus Regiella
            insecticola LSR1]
          Length = 1342

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1364 (51%), Positives = 958/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +        +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----REGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL    E+IL  F+ K+ +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIMLRALSYTPEQILDLFFEKVGFEICD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G+  +E G+++ +  ++ L++  +  + +  + 
Sbjct: 235  NKLQMALIPERL-RGETASFDIK--ANGKIYVEKGQRIAARHVRQLEKDNINSIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D V+  TGE+       +    L ++  S  + +  L+ + +++ AYI  TL
Sbjct: 292  IVGKVVAKDYVDTSTGEVICAVNTELSLDLLAKLSKSGYKCVETLFTNDLDHGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLSTVGR+K N  L+ 
Sbjct: 352  RVDPTNDRLGALVEIYRMMRPGEPPTRDAAENLFENLFFSEDRYDLSTVGRMKFNRSLSR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DQIEGSGILSKEDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D++++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLETLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPVETPEGPNIGLINSLSVYARTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V  G VTN++ YL A+EE N  IAQANS+LDE   F ++L+ CR   E  L  RE++D
Sbjct: 592  RCVQGGVVTNEIRYLYAIEEGNYVIAQANSNLDEKNCFIDDLITCRNKDESSLFSREQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  
Sbjct: 652  YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRAEKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VA+R G ++ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712  SGVTSVARRGGKIQYVDASRIVIKVNEKEMKSDEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + D + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLNDSIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELACVSRDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVTSGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G+DK++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVDKDKRALDIEKM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+E   +D  +E  IL+  + +R+  +L                 + S+ + + P  +W 
Sbjct: 952  QLEQAKQDLKEELKILEAGLLARIRAVLIAGG-------------IESEKLDKLPSERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE+ Q  +E L  Q +  KS  E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  GLCLSDEEKQCQLEQLAEQCDELKSEFEKKLEGKRRKIIQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDEYGTPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G+KI +++  ++    +         +         ++ + DD VL +AE  K 
Sbjct: 1119 MAAKGIGEKINAMLRKHEKVAKLREFIQKAYDLGDHVCQKVDLNTFSDDEVLNLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+++PVFDGA E  I  +L++A L  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPITSPVFDGAKETEIKELLKLAGLPASGQITLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAGYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1299 NGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1342


>gi|147674155|ref|YP_001218596.1| DNA-directed RNA polymerase subunit beta [Vibrio cholerae O395]
 gi|146316038|gb|ABQ20577.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae O395]
 gi|227012184|gb|ACP08394.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae O395]
          Length = 1375

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L  LG  S EIL  F+ K+ +  + 
Sbjct: 209  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRVLGKTSAEILDIFFEKVNFEVKD 268

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 626  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 685

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 926  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 985

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +S   R +W 
Sbjct: 986  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLSSIERKKWL 1032

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1033 EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1092

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1093 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1152

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1153 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1209

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1210 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1269

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1270 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1329

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1330 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1375


>gi|119713232|gb|ABL97298.1| DNA-directed RNA polymerase beta subunit [uncultured marine bacterium
            HF10_12C08]
          Length = 1367

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 796/1365 (58%), Positives = 1035/1365 (75%), Gaps = 4/1365 (0%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M   + F    RVRK FGK  E+   P+LIE+QK SY+ FL+ +    ERP++GLQ  FK
Sbjct: 1    MVNTLSFTERKRVRKNFGKLKEVSKFPNLIEIQKKSYEDFLLEHANSSERPDKGLQRVFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFP+  FSG+A +E++ Y F  PKFDVD+C  RD TYA PL + LRLIVFD+DE T ++
Sbjct: 61   SVFPLEDFSGSARIEYIDYNFQSPKFDVDECRQRDKTYAAPLNVKLRLIVFDIDEETESR 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++KDIKEQ IY+ DLPLMT+ GTF+  G +R+VVSQ+HRSPG+ FDHD G+   SGKLL+
Sbjct: 121  TVKDIKEQEIYLCDLPLMTQKGTFITNGTERVVVSQMHRSPGVFFDHDNGKTHSSGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS- 239
              R+IP +G W+DIEFD KDIIH RIDR++K+P+T+FLMA+G+  +EILS FY    YS 
Sbjct: 181  GARVIPYRGSWLDIEFDHKDIIHCRIDRKKKIPITTFLMAMGIKRDEILSLFYGTETYSL 240

Query: 240  -QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
              + D W    +  ++  G K+  SLV+   G+  ++ G K+   + K L   G+K L +
Sbjct: 241  SIKDDKWKVGFNPKNIKTG-KLQKSLVNAANGKVAVKQGTKINPAIAKKLFNDGLKNLLL 299

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G ++AEDI+N +TGEIY E+ D I  +++E+I   +I  IP+L +D +N  ++I
Sbjct: 300  EDDELIGKFIAEDIINEKTGEIYFESSDEITSETIEKIKELKISKIPVLEIDGINIGSFI 359

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            R+TL  DKN   ++A+++IY+V+RPG+      A  +FN LFF S+KYDLS VGRVKMN 
Sbjct: 360  RDTLRVDKNLSPEEAVVEIYKVLRPGEPPNLETAFEVFNSLFFKSEKYDLSDVGRVKMNY 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            RLN++  D V  +R ED+I +IK ++DLR GKG +DDID+LGNRRVRSVGE+++NQ+R+G
Sbjct: 420  RLNIECSDTVTVLRSEDVIEVIKTVMDLRTGKGEVDDIDHLGNRRVRSVGELVENQFRMG 479

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L+RMERSIKER++S+++D+  PQD+INAKP+V+++ EFF +SQLSQ  +  N L+ ITH 
Sbjct: 480  LIRMERSIKERMNSLEVDAATPQDIINAKPLVASLKEFFGTSQLSQFMDQTNPLAEITHK 539

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG++R RAG E+RDVHPTHYGRICP ET EG NIGL++SL S ARVN YGFI
Sbjct: 540  RRLSALGPGGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLASHARVNQYGFI 599

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV  GKV+N+V YL AMEE +  IAQANS LD+ GSF  +LV CR  G+ ++   
Sbjct: 600  ESPYRKVIKGKVSNEVEYLPAMEEADFTIAQANSELDDKGSFITKLVSCRRNGDFVMTVP 659

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E+ID++D SPKQVVS AASLIPFLENDD+NR LMG NM RQAVPL++AE+P VGTG+E V
Sbjct: 660  EEIDYMDVSPKQVVSCAASLIPFLENDDANRALMGSNMMRQAVPLIQAESPLVGTGVEKV 719

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SG  IVA R GIV+++D  RIV+R  E     + SGVDIY L KFQRSNQ+TC+NQ
Sbjct: 720  VAVDSGVTIVANRDGIVDKIDGKRIVVRVTEKIK-TTESGVDIYTLQKFQRSNQSTCINQ 778

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLVKVGD+V + DIIADGPST  G+L LGRN++VAFMPW GYNFEDS+LISE++V ED 
Sbjct: 779  RPLVKVGDKVSKGDIIADGPSTHFGELGLGRNVVVAFMPWRGYNFEDSILISEKIVQEDK 838

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFEVM+RDTKLG EEITRDIPN  +E L+N+DE GI+ VGA+VNPGDILVGK+
Sbjct: 839  FTSIHIEEFEVMSRDTKLGSEEITRDIPNAGDELLRNLDEAGIVYVGADVNPGDILVGKV 898

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGESP+TPEEKLLRAIFGEKA DV+DTSLR+P G SG VVDV++FNR+GI+K++R++S
Sbjct: 899  TPKGESPVTPEEKLLRAIFGEKATDVKDTSLRLPPGSSGIVVDVKVFNRYGIEKDDRALS 958

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +ER++IE LA D++ E  IL+RNI  RL+ ++  +N     +  +  +      +S+   
Sbjct: 959  IERDEIEKLANDREAELGILNRNIKERLILLINDKNISDTSEDIESMSKYDKATLSDIKL 1018

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W+  +++   Q  VE+LK QY+ ++S ++ RF NK++K+Q GD++ PGV+++VKVFV
Sbjct: 1019 DSLWKMRLENSNDQNEVENLKKQYDIARSAIQSRFDNKVDKVQRGDELLPGVMKMVKVFV 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++S+I P EDMP+L+DG  VDIVLNPLGVPSRMNVGQI E
Sbjct: 1079 AVKRKLQPGDKMAGRHGNKGVISKIAPVEDMPYLEDGRTVDIVLNPLGVPSRMNVGQILE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G+ I   +  YK++ D S +   LEKV G   +  +IS    D    +A 
Sbjct: 1139 THLGWACAGIGEIINKSLAQYKSSNDHSVIGQSLEKVYGKDQYKNEISSLSKDEQKELAM 1198

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               SGVP+ TPVFDGA E  I+ ML  A  D+SGQ+ L+DGLTGE F+R VTVGYIYMLK
Sbjct: 1199 NIASGVPIKTPVFDGASEAEISEMLGEAGFDKSGQTQLWDGLTGEKFERKVTVGYIYMLK 1258

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+K
Sbjct: 1259 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVK 1318

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GRT+VYE+I+ G D F++GTPESFNVL+KE+++LGL+I+L
Sbjct: 1319 SDDVAGRTKVYETIIRGEDVFQSGTPESFNVLIKEIRSLGLNIEL 1363


>gi|28899696|ref|NP_799301.1| DNA-directed RNA polymerase subunit beta [Vibrio parahaemolyticus
            RIMD 2210633]
 gi|153838924|ref|ZP_01991591.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ3810]
 gi|260364010|ref|ZP_05776744.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            K5030]
 gi|260878164|ref|ZP_05890519.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AN-5034]
 gi|260897873|ref|ZP_05906369.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            Peru-466]
 gi|41017994|sp|Q87KQ4|RPOB_VIBPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|28807948|dbj|BAC61185.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            RIMD 2210633]
 gi|149747632|gb|EDM58556.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ3810]
 gi|308085539|gb|EFO35234.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            Peru-466]
 gi|308090227|gb|EFO39922.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AN-5034]
 gi|308115549|gb|EFO53089.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            K5030]
          Length = 1342

 Score = 1634 bits (4231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1367 (51%), Positives = 971/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDATDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEASIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|319897971|ref|YP_004136168.1| RNA polymerase, beta subunit [Haemophilus influenzae F3031]
 gi|317433477|emb|CBY81860.1| RNA polymerase, beta subunit [Haemophilus influenzae F3031]
          Length = 1343

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1365 (51%), Positives = 966/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRSDKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  +    R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRHLLISSGA-------------DATQLDNLDRAKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|301169230|emb|CBW28827.1| RNA polymerase, beta subunit [Haemophilus influenzae 10810]
          Length = 1343

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1365 (51%), Positives = 967/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYVQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   E GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMEPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|328471083|gb|EGF41989.1| DNA-directed RNA polymerase subunit beta [Vibrio parahaemolyticus
            10329]
          Length = 1342

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 971/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDATDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEASIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|293602648|ref|ZP_06685090.1| DNA-directed RNA polymerase subunit beta [Achromobacter piechaudii
            ATCC 43553]
 gi|292818958|gb|EFF77997.1| DNA-directed RNA polymerase subunit beta [Achromobacter piechaudii
            ATCC 43553]
          Length = 1370

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1375 (50%), Positives = 957/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ ++P L+  Q  SY  FL  + AP +R  +GLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQNVPFLLATQLQSYLTFLQADTAPSDRVADGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGMARLEFVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVT    A+GM  E IL+ F+    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDVLFFRVDRRRKMPVTILCKAIGMTPESILANFFDFDNFELKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D   G+ ++E  K++ +  L+ L   G++ + +  D 
Sbjct: 239  EGAMMEFVPE-RWKGEMARFDISD-RDGKVIVEKDKRINAKHLRDLAAGGIQRISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A++IV+ +TGE+   A D I E  L  +  S + DI  LY + ++   YI  TL
Sbjct: 297  LYGRVLAKNIVDEDTGEVIANANDEITESVLGALRASNVYDIQTLYTNDLDRGPYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS VGR+K+N RL  
Sbjct: 357  RTDETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYSEETYDLSRVGRMKVNSRLGR 416

Query: 423  DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GEDITGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DG+V+  + YLSA+EE +  IAQAN++LDE G+F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGRVSEQIDYLSAIEESHYVIAQANAALDEQGAFVDDLVACREAGETMLTSPANV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPVVGTGIERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD+V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 777  VKRGDKVAKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEE  V+ARDTKLGPEEITRDI N++E  L  +D+ GI  +GAEV+  D+LVGK+TPK
Sbjct: 837  VHIEELTVVARDTKLGPEEITRDISNLAETQLNRLDDSGITYIGAEVSADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIVRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ ++L  +    GP+   K   ++   +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVENDQFDRIEKMLVNKTVNGGPRKLAKGATITKAYLADLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE     +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLADEPHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  L+ D +    +  +R++L+KV  T     +I +  D+ V+ +A+  K
Sbjct: 1137 GWAAKGVGHRIADLLRDERT-AQVKNIRAYLDKVYNTTGSGARIDELTDEEVMEMAQNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA EE I +ML +A                Q+ L+DG TGE F+RPVTV
Sbjct: 1196 NGVPFATPVFDGATEEEITTMLELAYPDDVAERMALTPSRTQAWLFDGRTGEKFERPVTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE +
Sbjct: 1316 QEMLTVKSDDITGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLALDMDLERN 1370


>gi|269965860|ref|ZP_06179954.1| DNA-directed RNA polymerase beta subunit [Vibrio alginolyticus 40B]
 gi|269829524|gb|EEZ83764.1| DNA-directed RNA polymerase beta subunit [Vibrio alginolyticus 40B]
          Length = 1342

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1367 (51%), Positives = 972/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDTTDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA EE+I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEESIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|299771831|ref|YP_003733857.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. DR1]
 gi|284158679|gb|ADB80052.1| RNA polymerase beta subunit [Acinetobacter sp. DR1]
 gi|298701919|gb|ADI92484.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. DR1]
          Length = 1362

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1374 (51%), Positives = 975/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMEAPYLLSIQVDSYRTFLQGGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDIADND-GKIIVEQGKRINARHVRQMEASGLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI     G++   A  ++  + + ++    ++   IL+ + ++  +++ ++L
Sbjct: 295  LYERITAEDIT-LRNGDVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   L  D++S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLVEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLSQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D  V
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|229526890|ref|ZP_04416293.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae bv.
            albensis VL426]
 gi|229336059|gb|EEO01078.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae bv.
            albensis VL426]
          Length = 1341

 Score = 1634 bits (4230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVLFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|226939179|ref|YP_002794250.1| DNA-directed RNA polymerase subunit beta [Laribacter hongkongensis
            HLHK9]
 gi|226714103|gb|ACO73241.1| RpoB [Laribacter hongkongensis HLHK9]
          Length = 1389

 Score = 1633 bits (4229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1395 (50%), Positives = 970/1395 (69%), Gaps = 39/1395 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL + +  D R N GL+AAF+S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRETVLDVPFLLATQIDSYADFLQLGVPFDRRENAGLEAAFRSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A L+FV Y    P FDV +C  R +T+A PL+  +RL + D    +    +
Sbjct: 61   FPILSNNGYARLDFVHYVLGDPPFDVPECQLRGITFAAPLRARIRLTILDR--ESSKPVV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT++G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENDVYMGEIPLMTQNGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT+ L ALG   E ILS FY    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTTLLKALGYSEERILSEFYDTDSFRLTR 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     +    L  G    S +V  D G  + +  K++T+  ++ ++  G+  + + +D 
Sbjct: 239  DGVYMAVVPERL-RGEVAKSDIVAPD-GRVLAQKDKRITAKTIRDIQAAGITEIEVPADT 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A  +++ ETGEI   A + I E++L +   +EI  + +L+V+ +++ AYI  T+
Sbjct: 297  LLGKVLARTVIHPETGEIIARANNEITEETLAKFAIAEIETVDVLFVNELDHGAYIAQTM 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +D   D+  A + IYR+MRPG+  T    E++F  LFF+ + YDLS VGR+K N R   
Sbjct: 357  RSDDVNDQLSARVAIYRMMRPGEPPTEDAVEALFQRLFFNEESYDLSRVGRMKFNRRAYA 416

Query: 423  DTPD-------------------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
               D                       +  +DI+A+I +LV++RNG+G +DDID+LGNRR
Sbjct: 417  HLDDKAPGWIKRFYERVGERGETGPGTLDYDDIVAVIMLLVEMRNGRGEVDDIDHLGNRR 476

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            VRSVGE+ +NQ+R GL+R+ER++KER++  + D++MP DLINAKPV +A+ EFF SSQLS
Sbjct: 477  VRSVGELAENQFRAGLVRVERAVKERLNQAESDNLMPHDLINAKPVSAAIKEFFGSSQLS 536

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 537  QFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 596

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            +SL  +AR N YGF+ETPYR+V D KVT+ + YLSA+EE    IAQAN++L+ DG+  +E
Sbjct: 597  NSLAIYARTNDYGFLETPYRRVVDSKVTDQIDYLSAIEEGRYVIAQANATLNADGTLVDE 656

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 657  LVTCREKGETILATPDRVQYMDVATSQVVSVAASLIPFLEHDDANRALMGANMQRQAVPC 716

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            L+AE PFVGTG+E  VA  SG AI A+R G+V+ VDA R+VIR  + +      GVDIY 
Sbjct: 717  LRAEKPFVGTGIERAVAVDSGTAIAAQRGGVVDYVDATRVVIRVNDDEAVAGEVGVDIYN 776

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+K+ RSNQNT +NQRP+VKVGD V R D+IADG STDLG+LALG+NM +AFMPW+GYN+
Sbjct: 777  LVKYTRSNQNTNINQRPIVKVGDVVARGDVIADGASTDLGELALGQNMTIAFMPWNGYNY 836

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+LISER+V++D +TSIHIEE  V+ARDTKLGPEEITRDIPN+SE     +D+ GI+ 
Sbjct: 837  EDSVLISERVVADDRYTSIHIEELSVVARDTKLGPEEITRDIPNLSERMQGRLDDAGIVY 896

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G+ GTV+DV+
Sbjct: 897  IGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGMQGTVIDVQ 956

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R GI++++R+ S+   +++    D +D+  I + + +SR+  ++ G+ A  GPK   
Sbjct: 957  VFTREGIERDKRAQSIIDAELKRYRLDLNDQVRIFENDAFSRIERLIIGKVANGGPKRLP 1016

Query: 1004 KSTVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            K T +  + ++    +  W+   + DE + R +E +K      +   +++F++K  K+  
Sbjct: 1017 KGTAIDLEYLNSLLSKHDWFDIRMADEDIARQLELMKESLAQKRVEFDEKFEDKKRKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR +Q GDKMAGRHGNKG+VS+ILP EDMP++ DGTPVDIVL
Sbjct: 1077 GDELPPGVQKMVKVYIAVKRRLQPGDKMAGRHGNKGVVSKILPVEDMPYMADGTPVDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI E HLGWA  G+G++   ++   KA   ++ LR+++EKV  +    
Sbjct: 1137 NPLGVPSRMNIGQILEVHLGWAGKGIGQQFDKML---KAEAAVADLRAYIEKVYNSAGKQ 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G---- 1232
            E I+   DD +  +AE  + G+P STPVFDGA EE I  ML +A  DE       G    
Sbjct: 1194 EDIAGLSDDEIRMLAENLRRGMPFSTPVFDGAKEEEIRKMLDLAYPDEDPRTPQLGFNGS 1253

Query: 1233 --QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
              Q  L+DG +GE FDR VTVG ++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  G
Sbjct: 1254 KTQMTLFDGRSGEAFDRKVTVGVMHFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 1313

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESFNVL
Sbjct: 1314 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESFNVL 1373

Query: 1351 VKEMQALGLSIDLEN 1365
            VKE+++LGL IDLE 
Sbjct: 1374 VKEIRSLGLDIDLER 1388


>gi|78099450|gb|ABB20861.1| RNA polymerase subunit B [Acinetobacter johnsonii]
          Length = 1362

 Score = 1633 bits (4229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1374 (51%), Positives = 971/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLAIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L ALG ++ +IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVVLRALGYNNAKILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      +VD D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIVDND-GKTIVEQGKRINARHVRQMEAAGLEKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED +  + G++   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAED-IPLKDGDVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S +D+DG+ TEE V  R  G+ +
Sbjct: 593  FGFLETPYRKVLDGRVTDEVEYLSAIEEVGTVIAQADSGVDKDGNLTEEFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAGRGGRIEFVDASRVVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LVK+GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVKLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDSYRKDLKEEYKIFEEAARERIVRLLTGQESNGGGTT-KRGDKLSVDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   KA   +  LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGEEIDKML---KAQRTVLELRGFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +A++  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRAGVPLATPVFDGAEESQIKDLLELANISRTGQTVLYDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|253998007|ref|YP_003050070.1| DNA-directed RNA polymerase subunit beta [Methylovorus sp. SIP3-4]
 gi|313200075|ref|YP_004038733.1| DNA-directed RNA polymerase subunit beta [Methylovorus sp. MP688]
 gi|253984686|gb|ACT49543.1| DNA-directed RNA polymerase, beta subunit [Methylovorus sp. SIP3-4]
 gi|312439391|gb|ADQ83497.1| DNA-directed RNA polymerase, beta subunit [Methylovorus sp. MP688]
          Length = 1390

 Score = 1633 bits (4229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1397 (50%), Positives = 961/1397 (68%), Gaps = 40/1397 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+ +Q  SY  FL  N+  D+R N GLQA F SV
Sbjct: 1    MSYSFTEKKRIRKSFAKRESVQEVPYLLAMQLESYAAFLQANVPVDKRENAGLQATFNSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L++VSY      FDV +C  R LTYA PL++ +RL + D        ++
Sbjct: 61   FPIVSHSGNARLDYVSYTLGQEPFDVKECQQRGLTYAAPLRVKVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT++G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGELPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ R+DRRRK+PVT  L ALG   E+IL TFY    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRVDRRRKMPVTILLKALGFTPEQILETFYDLDTFHISA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L    L  G      ++D  +G  ++   K++T   ++ +++ G+  + +  + 
Sbjct: 239  KGVQFELLPERL-RGEVAKFDIIDG-SGNVIVAKDKRITVKHIRDMEKAGISKINVPEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  ++  I++ ETGE+   A D I E  LE++  +++  I  LY + +++  YI  TL
Sbjct: 297  VLGRALSSGIIDKETGEVVANANDEITESLLEKLREAKVGKINTLYANDLDHGDYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++F+ LFF+ ++YDLSTVGR+K N R   
Sbjct: 357  RIDEIPDQYSARVAIYRMMRPGEPPTEDAVEALFDGLFFNEERYDLSTVGRMKFNRRAFP 416

Query: 423  DTPDDVR--------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +  ++                       +  EDI+A+I +LV+LRNG+G IDDID+LGNR
Sbjct: 417  EKIEERTAAWLRRFYEKSGARGAEGAPVLSNEDILAVIAVLVELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+RSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKPV SA+ EFF SSQL
Sbjct: 477  RIRSVGELAENQFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPVSSAIREFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  ++R N YGF+ETPYR+V   KV++ + +LSA+EE    IAQANS LD++G F E
Sbjct: 597  INSLALYSRTNQYGFLETPYRRVDGNKVSDKIDFLSAIEESQYMIAQANSELDKNGQFKE 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            EL+  R   E  +   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  ELISARYHNEFTMAQPDRVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+AE   VGTG+E  VA  SG  + A+R GIV+ VD+ RIV+R  + +      GVDIY
Sbjct: 717  CLRAEKAIVGTGIERTVAVDSGTTVQARRGGIVDYVDSGRIVVRVHDAEAAAGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L+K+ RSNQNT +NQRPLVK+GD + R D+IADG STD+G+LALG+NMLVAFMPW+GYN
Sbjct: 777  NLIKYTRSNQNTNINQRPLVKIGDVLARGDVIADGASTDMGELALGQNMLVAFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+LISER+V++D +TSIHIEE  V+ARDTKLG EEITRDI N+SE  L  +DE GII
Sbjct: 837  FEDSILISERVVADDRYTSIHIEELSVVARDTKLGAEEITRDISNLSERMLGRLDESGII 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV
Sbjct: 897  YIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R GID++ R+  +  +Q+    +D  D+  I++ + + R+  ++ G+ A  GP   
Sbjct: 957  QVFTREGIDRDTRAQQIIDDQLGHYKQDLADQMRIVEDDAFGRIRRLIEGKVATGGPNKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK   L+++ +    R  W+   + DE+  R +E LK     ++   + +F+ K  K+  
Sbjct: 1017 KKGETLTAEYLESIGRYDWFDIRLSDEEAARQLEQLKDSLAQARVEFDSKFEEKKRKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGV ++VKV++A+KR IQ GDKMAGRHGNKG+VS+I+P EDMP + DGTP+DIVL
Sbjct: 1077 GDELPPGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVVSKIVPVEDMPHMADGTPMDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SH 1181
            NPLGVPSRMN+GQI E HLGWA  GLG +I +++   +A    + +R F++++       
Sbjct: 1137 NPLGVPSRMNIGQILEVHLGWAAKGLGMRIGAML---QAETKANEIRKFIDQIYNNSNGK 1193

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---------- 1231
             E I    D+ V  +A   + GVP +TPVFDGA E+ I  ML +A  D+           
Sbjct: 1194 KEDIKSLTDEEVFELARNLERGVPFATPVFDGATEQDIRDMLDLAFPDDDARTQQLQFAA 1253

Query: 1232 GQSI--LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            G++   L DG +GEPF+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1254 GKTQVKLIDGRSGEPFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1313

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT+VYE+IV G    + G PESFNV
Sbjct: 1314 GGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVSGRTKVYENIVKGEHKIDAGMPESFNV 1373

Query: 1350 LVKEMQALGLSIDLENS 1366
            LVKE+++L + IDL+ +
Sbjct: 1374 LVKEIRSLAIDIDLDRN 1390


>gi|15676060|ref|NP_273190.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis
            MC58]
 gi|7225349|gb|AAF40591.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            MC58]
          Length = 1394

 Score = 1633 bits (4228), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1400 (49%), Positives = 959/1400 (68%), Gaps = 42/1400 (3%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M     F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF 
Sbjct: 1    MCMNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFN 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            S+FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        
Sbjct: 61   SIFPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKP 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL+
Sbjct: 119  TVKEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +  
Sbjct: 179  SARIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +     L A D + G      ++D   G  ++  GK++T+  ++ +   G+  L +  
Sbjct: 239  SSNGVQTDLVA-DRLKGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEP 296

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI N
Sbjct: 297  ESLLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISN 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R 
Sbjct: 357  TLRTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRT 416

Query: 421  NLDTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                  + +                       +  EDI+A I  LV+LRNG G +DDID+
Sbjct: 417  YEQKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDH 476

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            LGNRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF 
Sbjct: 477  LGNRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFG 536

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 537  SSQLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 596

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG
Sbjct: 597  NIGLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDG 656

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +   +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQR
Sbjct: 657  NLIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQR 716

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      G
Sbjct: 717  QAVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVG 776

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            VDIY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STD G+LALG+NM +AFMPW
Sbjct: 777  VDIYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDFGELALGQNMTIAFMPW 836

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            +GYN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE
Sbjct: 837  NGYNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDE 896

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GI+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGT
Sbjct: 897  SGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGT 956

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            V+DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  G
Sbjct: 957  VIDVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGG 1016

Query: 999  PKGFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            P    K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K 
Sbjct: 1017 PMKLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKK 1076

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG P
Sbjct: 1077 KKLTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRP 1136

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++  
Sbjct: 1137 VDIVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYN 1193

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA----------- 1226
                 E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A           
Sbjct: 1194 GSGKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKL 1253

Query: 1227 DLDES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGG
Sbjct: 1254 GFNDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGG 1313

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PE
Sbjct: 1314 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPE 1373

Query: 1346 SFNVLVKEMQALGLSIDLEN 1365
            SFNVLVKE+++LGL IDLE 
Sbjct: 1374 SFNVLVKEIRSLGLDIDLER 1393


>gi|255320109|ref|ZP_05361301.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter
            radioresistens SK82]
 gi|262379966|ref|ZP_06073121.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter
            radioresistens SH164]
 gi|255302827|gb|EET82052.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter
            radioresistens SK82]
 gi|262298160|gb|EEY86074.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter
            radioresistens SH164]
          Length = 1362

 Score = 1633 bits (4228), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1374 (52%), Positives = 977/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMEAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  + ALG ++E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVMRALGYNNEQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRINARHVRQMEASGLTKLPVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED ++ ++G++   A  ++  + + +I    ++   ILY + ++  +++ +TL
Sbjct: 295  LYERITAED-ISLKSGDVIA-ANTLLSHEIMVKIAEGGVKQFNILYTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKTNE 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S+LD+DG  TEELV  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSALDKDGYLTEELVSVRYQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E+I  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMAPERITHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAKRGGTIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L  Q +  G    K+   LS +L+S
Sbjct: 953  RALAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKDQVSNGG-GNTKRGEKLSEELLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELIDLLEIQPSDEAIAERLTQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTHGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS+ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSQILPVEDMPHDANGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K    I+ LR FL+K+    G   E++    DD +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKML---KQQRAIAELRDFLDKIYNKVGGEQEQLDTLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L++A     GVP++TPVFDGA+E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 LKLAGNLSKGVPLATPVFDGAEEGQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|197335552|ref|YP_002157204.1| DNA-directed RNA polymerase, beta subunit [Vibrio fischeri MJ11]
 gi|226699458|sp|B5FC88|RPOB_VIBFM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|197317042|gb|ACH66489.1| DNA-directed RNA polymerase, beta subunit [Vibrio fischeri MJ11]
          Length = 1342

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 966/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFTKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + LE+VSY    P+FDV +C  R +TY+ PL++ LRL+V+D D      ++
Sbjct: 57   FPIQSYNGNSKLEYVSYNLREPEFDVKECQIRGVTYSAPLRVKLRLVVYDKDAPAN--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+V+  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNKTTEEILDLFFDKVVFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E+G+++T+  ++ L +  +  + +  D 
Sbjct: 235  QTLMMELLPERL-RGETATFDIE--ANGKVYVEAGRRITARHIRQLTKDDITHIEVPVDY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN +TGEI I A      + L  +  +  + I +L+ + +++ AYI +TL
Sbjct: 292  IVGKVASHDYVNEDTGEIIIAANQEFSLEDLANLSQAGYKKIEVLFTNDLDHGAYISDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRLSALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + + DII +++ L+D+RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DNDEGAGVLDETDIIEVMRKLIDIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAFAQCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG+VT+ V YLSA+EE    IAQAN+ L E+G+F +EL+  R  GE  L PRE I 
Sbjct: 592  RRVVDGQVTDQVDYLSAIEEGTFVIAQANAVLTEEGTFADELIIARQKGESGLHPREHIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVVQSVDASRIVIKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLVAAGV-------------SEVKLDAMDRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EITLDDEAQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R+FL+KV   G   +   I+   DD V  + +  
Sbjct: 1119 LAAKGVGDKINQML---KEQQELHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPIFDGAPEASIKELLKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|260774679|ref|ZP_05883584.1| DNA-directed RNA polymerase beta subunit [Vibrio coralliilyticus ATCC
            BAA-450]
 gi|260609398|gb|EEX35547.1| DNA-directed RNA polymerase beta subunit [Vibrio coralliilyticus ATCC
            BAA-450]
          Length = 1342

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1367 (51%), Positives = 973/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++ +TL
Sbjct: 292  IVGKVSSKDYINEATGEIIVAANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DI+ ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIVEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E G+F EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLSEQGTFAEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLDGG-------------YTEAKLDAIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+  Q  +E L  QY+  ++  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDAQQTQLEQLAEQYDELRADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       ++   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFRDFLQKVYDLGDTRQKVDVASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E++I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEQSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|172087773|ref|YP_205797.2| RNA polymerase, beta subunit [Vibrio fischeri ES114]
 gi|171902360|gb|AAW86909.2| RNA polymerase, beta subunit [Vibrio fischeri ES114]
          Length = 1342

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 966/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFTKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + LE+VSY    P+FDV +C  R +TY+ PL++ LRL+V+D D      ++
Sbjct: 57   FPIQSYNGNSKLEYVSYNLREPEFDVKECQIRGVTYSAPLRVKLRLVVYDKDAPAN--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+V+  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNKTTEEILDLFFDKVVFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E+G+++T+  ++ L +  +  + +  D 
Sbjct: 235  QTLMMELIPERL-RGETATFDIE--ANGKVYVEAGRRITARHIRQLTKDDITHIEVPVDY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN +TGEI I A      + L  +  +  + I +L+ + +++ AYI +TL
Sbjct: 292  IVGKVASHDYVNEDTGEIIIAANQEFSLEDLANLSQAGYKKIEVLFTNDLDHGAYISDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRLSALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + + DII +++ L+D+RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DNDEGAGVLDETDIIEVMRKLIDIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA+ N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAFAQCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG+VT+ V YLSA+EE    IAQAN+ L E+G+F +EL+  R  GE  L PRE I 
Sbjct: 592  RRVVDGQVTDQVDYLSAIEEGTFVIAQANAVLTEEGTFADELIIARQKGESGLHPREHIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVVQSVDASRIVIKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLVAAGV-------------SEVKLDAMDRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EITLDDEAQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R+FL+KV   G   +   I+   DD V  + +  
Sbjct: 1119 LAAKGVGDKINQML---KEQQELHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPIFDGAPEASIKELLKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|182676587|sp|A5F3P5|RPOB_VIBC3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1341

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1366 (52%), Positives = 977/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L  LG  S EIL  F+ K+ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRVLGKTSAEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 592  RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +S   R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLSSIERKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|262197199|ref|YP_003268408.1| DNA-directed RNA polymerase subunit beta [Haliangium ochraceum DSM
            14365]
 gi|262080546|gb|ACY16515.1| DNA-directed RNA polymerase, beta subunit [Haliangium ochraceum DSM
            14365]
          Length = 1403

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 727/1364 (53%), Positives = 984/1364 (72%), Gaps = 12/1364 (0%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F K  ++IDIP+LI++QK SYD FL ++I  +ER + GLQ  FKSVFPI  FS  
Sbjct: 10   RVRKSFAKLKKVIDIPNLIDIQKRSYDKFLQIDIPAEEREDVGLQGVFKSVFPIKDFSET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +T+A P+K+ +RL+V+DV+E TG +SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYNLERPKYDVDECRARGMTFAAPVKVVIRLVVWDVNEETGVQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT  GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGKLLY+ R+IP +G W
Sbjct: 130  FGEIPLMTDSGTFIINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLYSARVIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KDI++VRIDRRRK+  T  L ALG  +E++L+ FY   V    G         
Sbjct: 190  LDFEFDHKDILYVRIDRRRKLYATVLLRALGYSTEDLLNYFYDTEVIHIEGPQKFSRTIN 249

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             DL++G + +  +   D+ E ++   +K T   ++ L++  ++ L I  + L G   A D
Sbjct: 250  YDLLLGQRATRDIRHPDSREILVRKNRKFTRAAIRKLRDSDIEKLTIDLEELVGKVSARD 309

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            I++  TGE+ ++  + + E+ LEE+    +    +L++D++N   Y+R TL+ DK +  +
Sbjct: 310  IIDESTGEVLLQCNEELSEEKLEELRTRGVERFDVLFIDNLNVGPYLRTTLLADKLQGPE 369

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+++IYR +RPGD  T   A+++F  LFF+ ++YDLS VGR+K+N +  LD   D   +
Sbjct: 370  EAIMEIYRRLRPGDPPTIDTAQNLFQNLFFNPERYDLSQVGRLKLNYKFRLDESLDNPVL 429

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             + DI+  ++ L++LRNG+G IDDID+LGNRRVR+VGE+++NQYR+GL+RMER+IKER+S
Sbjct: 430  TRRDILETVRYLIELRNGRGIIDDIDHLGNRRVRAVGELMENQYRIGLVRMERAIKERMS 489

Query: 492  S-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
               +I+++MP DLINAKPV + V E+F SSQLSQ  +  N LS +TH RRLSALG GG+ 
Sbjct: 490  MSQEIETLMPHDLINAKPVSAVVKEYFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLT 549

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++ARVN YGFIETPYR+V DGKV
Sbjct: 550  RERAGFEVRDVHPTHYGRICPIETPEGPNIGLIASLSTYARVNQYGFIETPYRRVNDGKV 609

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            T +V + SA++EE + IAQAN++ D  G+F+E+ V CR AG+  +V  E +  +D SP Q
Sbjct: 610  TEEVQFYSALQEEGQVIAQANAAHDPSGAFSEDFVSCRRAGDVSMVRPEDVTLMDVSPNQ 669

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS+AASLIPFLE+DD+NR LMG NMQRQAVPL++  AP VGTG+E++VA+ SG  +VAK
Sbjct: 670  LVSVAASLIPFLEHDDANRALMGSNMQRQAVPLVRTAAPLVGTGIENIVARDSGVTVVAK 729

Query: 731  RAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            R G+VE VD  RIVI+       D   +  DIY L+KFQRSNQNTC NQ+P+V+ GD VR
Sbjct: 730  RDGVVESVDGARIVIKPFETDGEDSLGAKPDIYNLVKFQRSNQNTCSNQKPIVRRGDTVR 789

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              D+IADGP+T+ G+LALG+N +VAFMPW GYNFEDS+L++ER+V  D FTS+HIEEFE 
Sbjct: 790  VGDVIADGPATECGELALGQNTVVAFMPWGGYNFEDSILVNERLVKNDTFTSVHIEEFEC 849

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            +ARDTKLG EEITRDIPNV EE LK++D+ GI+ +GAEV  GDILVGKITPKGE+ ++PE
Sbjct: 850  VARDTKLGKEEITRDIPNVGEEALKDLDDSGIVRIGAEVKAGDILVGKITPKGETQLSPE 909

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DVRDTSLRVP GVSG V++ R+F R G +K++R+  +E  + E L  
Sbjct: 910  EKLLRAIFGEKAGDVRDTSLRVPPGVSGVVINARVFARKGTEKDDRAKDIEDAEKEKLLL 969

Query: 970  DKDDEQVILDRNIYSRLMEILCGQ------NAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +K  E  I+  + Y ++ ++L G+          G     K   + +  + + P   W +
Sbjct: 970  NKQTEIKIISDSYYGKMRKLLVGKTTAARLVDDKGKVLLPKGQKIDAAALDQVPARYWHE 1029

Query: 1024 FAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D KV+ ++E L  Q E    ++E+++  KI K+  GD++PPGV+++VKV++A+KR
Sbjct: 1030 VQAEGDTKVEESLEKLAAQREEDVRLIEEQYDEKIGKLTKGDELPPGVIKLVKVYLAIKR 1089

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+VSR+LP EDMP+L DGTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1090 KLSVGDKMAGRHGNKGVVSRLLPEEDMPYLSDGTPVDIVLNPLGVPSRMNVGQILETHLG 1149

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   +G++I   +   + +     LR  L+KV  T    E +   D++ + R A + + 
Sbjct: 1150 WAAREIGRQIDMYM---ETSWSADVLREKLKKVFNTAQAHEFLDRLDNEDIGRFATKLRK 1206

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+  +TPVFDGA E+ I + L MA +  SGQS L DG +GEPFD PVTVG +YMLKL+H+
Sbjct: 1207 GIHFATPVFDGAAEDEIKAALNMAGMRPSGQSQLCDGKSGEPFDNPVTVGVMYMLKLHHL 1266

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV
Sbjct: 1267 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDV 1326

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +GRTR+YESIV G    E G PESFNVL+KE+Q+L L ++L   
Sbjct: 1327 LGRTRMYESIVKGEHVLEAGLPESFNVLLKELQSLCLDVELIED 1370


>gi|239813607|ref|YP_002942517.1| DNA-directed RNA polymerase subunit beta [Variovorax paradoxus S110]
 gi|239800184|gb|ACS17251.1| DNA-directed RNA polymerase, beta subunit [Variovorax paradoxus S110]
          Length = 1374

 Score = 1632 bits (4227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1379 (50%), Positives = 964/1379 (69%), Gaps = 18/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FG    +++IP L+++QK +Y  FL   I P +R  EGLQAA
Sbjct: 1    MAQSSAYSYTERKRIRKSFGNRDSVVEIPYLLQMQKDAYTAFLQAGIPPKQRTVEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F + FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T 
Sbjct: 61   FDAAFPIVSHNGFVEMKFLEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTS 120

Query: 119  -AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G++ E IL+ F+    
Sbjct: 181  LLFSARVIPYRGSWLDFEFDPKDMLYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +               L  G      + D  +G+ V+   K++T+   + L++ G   + 
Sbjct: 241  FRLMDSGAQMEFVPERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTTHIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  +A +IV+ ++GEI  +A D + E  L+++  + ++DI ++Y + ++  AY
Sbjct: 299  VPEDFLVGRVIARNIVDADSGEILAKANDELTEALLKKLRTAGVQDIQVIYTNELDQGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N
Sbjct: 359  ISQTLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             ++  D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  AKVGRDESTGPMVLTNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRT 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH
Sbjct: 479  GLARIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR+V D KVTN++ YLSA+EE    IAQAN+ LD++G  T +LV  R AGE ILV 
Sbjct: 599  IETPYRRVVDSKVTNEIDYLSAIEEGKYVIAQANAVLDKEGKLTGDLVSAREAGESILVG 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E+I ++D SP Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E P VGTG+E 
Sbjct: 659  AERIQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKPMVGTGIER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VSAVDSGTVVTATRGGIVDYVDATRIVVRVNDAEAAAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+VK GD++ + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V+ED
Sbjct: 779  QRPIVKRGDKIAKGDVVADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVAED 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN++E+ L  +DE GII VGAEV PGD LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGAEEITRDIPNLAEQQLNRLDESGIIYVGAEVQPGDTLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGITRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP    K T L    +S   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLTGKVANGGPNKLAKGTKLDKAYLSSVE 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     D++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KFHWFDIRPADDEVATQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP + DGTP DI LNPLGVPSRMNVGQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPHMADGTPCDICLNPLGVPSRMNVGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGWA  G+G +I  L+   +    ++ LR F+E++       E +S   D  VL +A
Sbjct: 1139 EVHLGWAGKGIGHRIGDLL---QQEAKVAELRKFMEQLYNGSGRPEDLSQLSDSDVLAMA 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDR 1247
               +SG   +TPVFDGA EE I  ML++A  D             Q+ LYDG TG+ F+R
Sbjct: 1196 ANLQSGATFATPVFDGASEEEIRGMLKLAYPDDIAKLKGLTETRTQAYLYDGRTGDQFER 1255

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1256 PVTVGYMHFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1315

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AYVLQEMLT+KSDDV GRT+VYESIV G  + E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 AYVLQEMLTVKSDDVQGRTKVYESIVKGEHSIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|149189253|ref|ZP_01867540.1| DNA-directed RNA polymerase subunit beta [Vibrio shilonii AK1]
 gi|148837007|gb|EDL53957.1| DNA-directed RNA polymerase subunit beta [Vibrio shilonii AK1]
          Length = 1341

 Score = 1632 bits (4226), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1366 (51%), Positives = 978/1366 (71%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDRDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  SEEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +     G+  +E+G+++T+  ++ L++ GV+F+ +  + 
Sbjct: 235  QTLLMELVPERL-RGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  + ++ + +L+ + +++  ++ +TL
Sbjct: 292  IVGKVASKDYINEATGEIIVGANQEISLEALANLSQAGVKKLEVLFTNDLDHGPFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + ++DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDGLEQGTLDEQDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL+  R  GE  L PR+ ++
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADELITARQKGESGLHPRDHVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGTVQSVDASRIVIKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLQGG-------------YSDAKLDTIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  QY+  ++  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQSQLEQLAEQYDELRADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G   +   I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGGTRQNVDIASLSDDEVRTLVKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E++I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEKSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|78099458|gb|ABB20865.1| RNA polymerase subunit B [Acinetobacter radioresistens]
          Length = 1362

 Score = 1632 bits (4225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1374 (52%), Positives = 976/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMEAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  + ALG ++E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVMRALGYNNEQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRINARHVRQMEASGLTKLPVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED ++ ++G++   A  ++  + + +I    ++   ILY + ++  +++ +TL
Sbjct: 295  LYERITAED-ISLKSGDVIA-ANTLLSHEIMVKIAEGGVKQFNILYTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKTNE 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S+LD+DG  TEELV  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSALDKDGYLTEELVSVRYQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E+I  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMAPERITHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAKRGGTIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L  Q +  G    K+   LS +L+S
Sbjct: 953  RALAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKDQVSNGG-GNTKRGEKLSEELLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELIDLLEIQPSDEAIAERLTQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTHGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS+ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSQILPVEDMPHDANGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K    I  LR FL+K+    G   E++    DD +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKML---KQQRAIVELRDFLDKIYNKVGGEQEQLDTLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L++A     GVP++TPVFDGA+E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 LKLAGNLSKGVPLATPVFDGAEEGQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|56459456|ref|YP_154737.1| DNA-directed RNA polymerase beta subunit [Idiomarina loihiensis L2TR]
 gi|81362632|sp|Q5QWA5|RPOB_IDILO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56178466|gb|AAV81188.1| DNA-directed RNA polymerase beta subunit [Idiomarina loihiensis L2TR]
          Length = 1342

 Score = 1632 bits (4225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1366 (51%), Positives = 983/1366 (71%), Gaps = 26/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  S+  F+ ++       N GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLEVPYLLSMQLDSFKKFIEVD----PEANNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV++C  R +TY+ PL++ LRL++FD +   G  ++
Sbjct: 57   FPIASYSGTAELQYVSYHMGEPAFDVEECQIRGITYSAPLRVKLRLVLFDKEAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL  F+    +    
Sbjct: 175  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLPASIILRALEYSTEEILDMFFDTTYFEILK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G      +   + GE ++E G+++T+  ++ L++  +K + + ++ 
Sbjct: 235  TKVKMQLVPERL-RGETAKFDIKGAE-GEVLVEKGRRITARHIRQLEQLDIKEMEVPAEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+D  N +TGE+   A DV+  + + E+  + I+ I  L+V+ +++  Y+  TL
Sbjct: 293  MVGKVLAKDYANKKTGEVVGHANDVLTLELIAELSEAGIKKIETLFVNDLDHGPYMSETL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F+ LFF  ++YDLSTVGR+K N RL  
Sbjct: 353  RVDSSNNRLEALVEIYRMMRPGEPPTREAAETLFDNLFFSEERYDLSTVGRMKFNRRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + +EDI+ ++K L+++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  EDLSGDNTLSREDIVEVMKKLIEIRNGLDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+ MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVKERLSLGDLDNTMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++F+R N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFSRTNEYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R++ +G VT+DV YLSA+EE N  IAQAN  L++ G  TE+LV CR   E  L+ +E++ 
Sbjct: 593  RRIENGSVTDDVDYLSAIEEGNYVIAQANVGLNDKGELTEDLVPCRHKNEFTLMSKEQVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P+Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 653  YMDVAPQQIVSIAASMIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIERTIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIV++  E ++ P  +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 713  SGVTVVAKRGGVVDYVDASRIVVKVNEEEMVPGEAGIDIYNLTKYTRSNQNTCINQKPTV 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+LISER+  ED  T+I
Sbjct: 773  NPGEPVTRGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILISERVAQEDRMTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE G++ VGAEVN GDILVGK+TPKG
Sbjct: 833  HIQELNCVARDTKLGAEEITSDIPNVGESALGKLDESGVVYVGAEVNGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV+GTV+DV++F R G++K++R++++E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVNGTVIDVQVFTRDGVEKDKRAVAIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  +E  IL+  IY+R   +L                      ++   RS W 
Sbjct: 953  QLAKVKKDLTEEFKILEEGIYNRARNLLLSNG-------------FDEAKLASVDRSSWL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + +E  Q  +E +  QY+  +   + +F+ K  KI  GDD+ PGVL++VKV++A++R
Sbjct: 1000 TQDLGNEDAQAQLEQIAEQYQQIRDDFDTKFETKRRKITQGDDLAPGVLKIVKVYLAVRR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDK+AGRHGNKG++S I+P EDMP   +G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 SIQPGDKLAGRHGNKGVISTIIPVEDMPHDDEGNPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI+ ++   K    IS LR FL++V   G       I+++ DD V+R+A   
Sbjct: 1120 MAARGIGSKIEKML---KQQRAISELRDFLQQVYDLGESRQKVDITEFTDDEVMRLAGNL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K+G+P +TPVFDGA EE I ++L++ADL ESGQ  L+DG TG+ F+R VTVGY+YMLKLN
Sbjct: 1177 KAGLPTATPVFDGAVEEEIKALLKLADLPESGQIRLFDGRTGDKFERDVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV  N   E G PESFNVL+KE+++LG++I+LE +
Sbjct: 1297 DVNGRTKMYKNIVDNNLQMEAGMPESFNVLLKEIRSLGINIELEQN 1342


>gi|224713634|gb|ACN62087.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
          Length = 1362

 Score = 1632 bits (4225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1374 (51%), Positives = 978/1374 (71%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D + G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+  T EE LLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQSTREENLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS DL+S
Sbjct: 953  RALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK +ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKKHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|78099452|gb|ABB20862.1| RNA polymerase subunit B [Acinetobacter junii]
          Length = 1362

 Score = 1632 bits (4225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1374 (51%), Positives = 975/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKAIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   ++G++   A  V+  + + ++    ++   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAEDIT-LKSGDVI-PANTVLSHEIMVKLAEGGVKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAVDKDGNLTEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAGRGGVIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGEKLSEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K    I+ LRSFL+K+    G   E++    D+ +
Sbjct: 1132 QILETHLGMAAKGLGEQIDKML---KQQRTIAELRSFLDKIYNKVGGEQEQLDTLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
             ++A   ++GVP++TPVFDGA+E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 FKLAGNLRAGVPLATPVFDGAEESQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|262373982|ref|ZP_06067259.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter junii SH205]
 gi|78099446|gb|ABB20859.1| RNA polymerase subunit B [Acinetobacter junii]
 gi|262310993|gb|EEY92080.1| DNA-directed RNA polymerase, beta subunit [Acinetobacter junii SH205]
          Length = 1362

 Score = 1632 bits (4225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1374 (51%), Positives = 975/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKAIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  V+  + + ++    ++   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAEDIT-LKNGDVI-PANTVLSHEIMVKLAEGGVKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAVDKDGNLTEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAGRGGVIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGEKLSEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K    I+ LRSFL+K+    G   E++    D+ +
Sbjct: 1132 QILETHLGMAAKGLGEQIDKML---KQQRTIAELRSFLDKIYNKVGGEQEQLDTLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L+++   ++GVP++TPVFDGA+E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 LKLSGNLRAGVPLATPVFDGAEESQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|78099426|gb|ABB20849.1| RNA polymerase subunit B [Acinetobacter bouvetii]
          Length = 1362

 Score = 1631 bits (4224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1374 (51%), Positives = 967/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D+P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPKVMDVPYLLAIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLILKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L ALG ++ +IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVVLRALGYNNSQILDLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G++ L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADKD-GKVIVEQGKRINARHVRQMEAAGLEKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    +AED+     G   I A  V+  + + ++    ++   IL+ + ++  ++I ++L
Sbjct: 295  LYERIIAEDV--ALRGGDVIAANTVLSHEIMVKLAEGGVKQFNILFTNDIDRGSFIADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSSREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDI  +++ L+++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDITDVLQTLIEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S +D+DG+  EE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSGVDKDGNLQEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLIADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++A R G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIANRGGRIEFVDASRVVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LVK+GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVKLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRV S V GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVSSSVKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS +++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEEVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                +   +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELADLLEIQPTDEGIAERLTQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI  ++ + +    +  LR FL+K+    G   E +    DD +
Sbjct: 1132 QILETHLGMAAKGLGDKIDKMMKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|153835070|ref|ZP_01987737.1| DNA-directed RNA polymerase, beta subunit [Vibrio harveyi HY01]
 gi|156972585|ref|YP_001443492.1| DNA-directed RNA polymerase subunit beta [Vibrio harveyi ATCC
            BAA-1116]
 gi|166229309|sp|A7MXF1|RPOB_VIBHB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|148868466|gb|EDL67572.1| DNA-directed RNA polymerase, beta subunit [Vibrio harveyi HY01]
 gi|156524179|gb|ABU69265.1| hypothetical protein VIBHAR_00225 [Vibrio harveyi ATCC BAA-1116]
          Length = 1342

 Score = 1631 bits (4224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 971/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  SEEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + +  L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKSLETLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDELDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN++L E+G F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGGFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVRAVLIDGG-------------YSEAKLDTTDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGETRQKVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I ++L++ADL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEASIKALLKLADLPESGQLKLFDGRTGDQFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|319639542|ref|ZP_07994289.1| DNA-directed RNA polymerase subunit beta [Neisseria mucosa C102]
 gi|317399113|gb|EFV79787.1| DNA-directed RNA polymerase subunit beta [Neisseria mucosa C102]
          Length = 1409

 Score = 1631 bits (4224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1398 (49%), Positives = 959/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 18   MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 77

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 78   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 135

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 136  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 195

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 196  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 255

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A+ L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 256  NGVQTDLVASRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 313

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L ++  + +++I  LY++ ++   YI +TL
Sbjct: 314  LLGKALATDLIDPETGEVLASANDEITEELLAKLDINGVKEITTLYINELDQGGYISSTL 373

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 374  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 433

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+  I  LV+LRNG G +DDID+LG
Sbjct: 434  QKLSEAQQNSWYGRLLNETLAGAAEKGGYVLSVEDIVVSIATLVELRNGHGEVDDIDHLG 493

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 494  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 553

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 554  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 613

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V +GKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 614  GLINSLSVYARTNDYGFLETPYRRVINGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 673

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 674  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 733

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 734  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 793

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D+IADG STDLG+LALG+NM +AFMPW+G
Sbjct: 794  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLIADGASTDLGELALGQNMTIAFMPWNG 853

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 854  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 913

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 914  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 973

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 974  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1033

Query: 1001 GFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++    +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1034 KLAKGSEITTEYLASLSSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1093

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1094 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1153

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+  + 
Sbjct: 1154 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNSS 1210

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1211 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1270

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1271 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1330

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1331 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1390

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1391 NVLVKEIRSLGLDIDLER 1408


>gi|330430114|gb|AEC21448.1| DNA-directed RNA polymerase subunit beta [Pusillimonas sp. T7-7]
          Length = 1370

 Score = 1631 bits (4224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1375 (50%), Positives = 954/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K  ++ D+P L+  Q  S+  FL  +  P +R +EGLQAAF S+
Sbjct: 1    MPYSYTEKKRIRKSFAKREDVQDVPYLLATQLQSFKTFLQADTTPSKRKDEGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +  A LEFVSY    P FDV +C  R LTYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNQMARLEFVSYVLGEPVFDVKECQLRGLTYASPLRAKVRLVLMDR--EVSKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT +G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTNNGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KDI+  R+DRRRK+PV+  L A+GM  E IL+ F     +   G
Sbjct: 179  RVIPYRGSWLDFEFDPKDILFFRVDRRRKMPVSILLKAIGMMPEAILAYFSDFDNFEILG 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +             G      + D  +G  ++E  K++ +  L+ L    V+ + +  D 
Sbjct: 239  EGGMLEFVPE-RWKGEVAHFDISD-RSGTVIVEKDKRINAKHLRDLANAKVERISVPEDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+ +VN ETGE+   A D I+E  L EI  + IR+I  LY++ ++   YI  TL
Sbjct: 297  VLGRILAKGLVNPETGEVIANANDEINETILAEIRVANIREIQTLYINDLDRGGYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF+  D YDLS VGR+K+N RL  
Sbjct: 357  RTDETADQMAARVAIYRMMRPGEPPTEDAVEALFQRLFYSEDAYDLSRVGRMKVNSRLGR 416

Query: 423  DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  +DI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R
Sbjct: 417  GDDITGPMTLTDDDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGELAENQFRAGLVR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+   + +++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 477  VERAVKERLGQAETENLMPHDLINSKPISAAIKEFFGSSQLSQFMDQTNPLSEITHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR+N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARLNEYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRK+ DGKV+  + YLSA+EE N  IAQAN+ LDE G F ++LV CR AGE +L     +
Sbjct: 597  YRKIIDGKVSEQIDYLSAIEESNYVIAQANAELDETGKFVDDLVACRQAGETMLTAPSNV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  HYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGVERTVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R GIV+ VDA R+VIR  + +      GVDIY L K+ RSNQNT +NQRP+
Sbjct: 717  DSGTTVQAIRGGIVDHVDAERVVIRVNDDENVAGEVGVDIYNLTKYTRSNQNTNINQRPI 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TS
Sbjct: 777  VKRGDQVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKIVADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLG EEITRDI N++E  L  +D+ GI+ +GAEV   D+LVGK+TPK
Sbjct: 837  IHIEELTVVARDTKLGAEEITRDISNLAETQLNRLDDSGIVYIGAEVRADDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI++++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMIGTVIDVQVFTREGIERDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +++    +D +D+  I++ + + R+ + L G+    GP+   K   L    +++  R QW
Sbjct: 957  DELRRYRQDLNDQLRIVEDDTFDRIGKFLVGKTVNGGPRKLAKGATLDKAYLTDLDRWQW 1016

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   + DE+    +E  K   E  +   +  F+ K +K+  GD++PPGVL+++KV++A+K
Sbjct: 1017 FDIRLSDEEHAVVLEQAKESLEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMIKVYLAVK 1076

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VSRI P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1077 RRLQPGDKMAGRHGNKGVVSRITPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHL 1136

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G +I  ++ D K    +  +R++LEKV  +   +  I +  DD ++ +A   K
Sbjct: 1137 GWAAKGVGYRIADMLQDEKNV-QVKNVRAYLEKVYNSAGASAHIDELTDDEIIEMARNLK 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
            +GVP++TPVFDGA EE I+ ML +A  D             Q+ L DG TGE F+RPVT+
Sbjct: 1196 NGVPLATPVFDGATEEEISKMLELAYPDDIAQRLNLTETRAQAWLIDGRTGEQFERPVTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDD+ GRT+VYE+IV G+   + G PESFNVLVKE+++L L +DLE  
Sbjct: 1316 QEMLTVKSDDISGRTKVYENIVKGDHVIDAGMPESFNVLVKEIRSLSLDMDLERK 1370


>gi|313667426|ref|YP_004047710.1| DNA-directed RNA polymerase beta chain [Neisseria lactamica ST-640]
 gi|313004888|emb|CBN86314.1| DNA-directed RNA polymerase beta chain [Neisseria lactamica 020-06]
          Length = 1392

 Score = 1631 bits (4224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDIANAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|262280712|ref|ZP_06058495.1| RNA polymerase subunit B [Acinetobacter calcoaceticus RUH2202]
 gi|78099428|gb|ABB20850.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|262257612|gb|EEY76347.1| RNA polymerase subunit B [Acinetobacter calcoaceticus RUH2202]
          Length = 1362

 Score = 1631 bits (4223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1374 (51%), Positives = 974/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMEAPYLLSIQVDSYRTFLQGGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG ++E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDIADND-GKIIVEQGKRINARHVRQMEASGLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI     G++   A  ++  + + ++    ++   IL+ + ++  +++ ++L
Sbjct: 295  LYERITAEDIT-LRNGDVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D+DG+ TE+ V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAIDKDGNLTEDFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   L   ++S
Sbjct: 953  RAMAIEKAQLDAYRKDLKEEYKIFEEAARERVIRLLNGQESNGG-GSTKRGDKLVDGMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLSQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E +    D  V
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|260770580|ref|ZP_05879512.1| DNA-directed RNA polymerase beta subunit [Vibrio furnissii CIP
            102972]
 gi|260614410|gb|EEX39597.1| DNA-directed RNA polymerase beta subunit [Vibrio furnissii CIP
            102972]
 gi|315178364|gb|ADT85278.1| DNA-directed RNA polymerase subunit beta [Vibrio furnissii NCTC
            11218]
          Length = 1342

 Score = 1631 bits (4223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1367 (52%), Positives = 977/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ KI +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKINFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 235  QTLMMELVPERL-RGETASFDIE--ADGKLYVEKGRRVTARHIRQLEKDGVTFIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  +SL  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVSSKDYINEATGEIIVAANQEISLESLANLSQAGYKKLEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               ++   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  ADAEEQGTLDETDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE ++
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKAE PFVGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKAEKPFVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLARVRSLLITGG-------------YSEAKLDAIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++++++Q  +E +  QY+  ++  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQTLENDELQTQLEQMAEQYDELRAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G   +   I+   DD V  +A+  
Sbjct: 1119 LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGETRQQVDIAALSDDEVRTLAQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +SG+P++TPVFDGA+E +I ++L++ DL ESGQ  L+DG TG+ F+R VTVGY+YMLKLN
Sbjct: 1176 RSGLPIATPVFDGANEASIKALLKLGDLPESGQLTLFDGRTGDAFERSVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|332040077|gb|EGI76462.1| DNA-directed RNA polymerase subunit beta [Hylemonella gracilis ATCC
            19624]
          Length = 1370

 Score = 1631 bits (4223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1375 (50%), Positives = 970/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG    +++IP L+++QK +Y  FL  +++  +R  EGLQAAF+S 
Sbjct: 1    MAYTFTERKRIRKSFGSRDSVLEIPYLLQMQKDAYTSFLQADLSSTKRRPEGLQAAFESA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKS 121
            FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T   K 
Sbjct: 61   FPIVSHNGFVEMKFLEYNLAKPAFDVRECQTRGLTFASAVRARVQLIIYDRESSTPQNKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +  +
Sbjct: 181  ARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPETILANFFVNDNFRLQ 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     +  L  G      + D  +G+ ++   K++T+   + L++ G   + +  D
Sbjct: 241  DSGAQMEFVSERL-RGEVARFDITD-KSGKVIVAKDKRITARHTRELEQSGTTHISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA +IV+ +TGEI  +A + + E  L+++  + ++++  +Y + ++  AYI  T
Sbjct: 299  FLIGRVVARNIVDPDTGEIIAKANEELTEALLKKLRSANVQELQCIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N +L 
Sbjct: 359  LRIDETTDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKLG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
               P     +  EDI+A++KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  NSDPAGPMVLTNEDILAVVKILVDLRNGRGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT  + YLSA+EE    IAQAN++LD+DG  T+ELV  R  GE IL   ++I
Sbjct: 599  YRRVEDGKVTTKIDYLSAIEEGKYVIAQANATLDKDGKLTDELVSAREKGESILCGADRI 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPLVGTGIERVAAI 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA RIVIR  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGVVDSVDATRIVIRVNDNEAVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD++ + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V++D +TS
Sbjct: 779  VKKGDKLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVADDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD+LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVVPGDVLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP    K + +    ++   +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLNGKTANGGPSKLAKGSKIDKAYLASIEKHHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     D++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPADDEVASQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTPVDIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKITPVEDMPYMADGTPVDIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++    A  +I   R FLE+V  +    E+++   DD +  +A++  
Sbjct: 1139 GWAGKGLGQRIGDMLQREAATTEI---RGFLEQVYNSAGRKEELAKLKDDELRLMAQELT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTV 1251
            SGVP ++PVFDGA EE I  ML++A          L+E+  Q+ LYDG TG+ F+R  TV
Sbjct: 1196 SGVPFASPVFDGATEEEIRGMLKLAYPDDVAKAKGLNETRTQAQLYDGRTGDAFERTTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE+IV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVQGRTKVYENIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|78099440|gb|ABB20856.1| RNA polymerase subunit B [Acinetobacter genomosp. 6]
          Length = 1362

 Score = 1631 bits (4223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 969/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   + +IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNAQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      + D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLIP-DRLRGEMAQFDIADND-GKVIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED +  + GE+   A  ++  + + ++    ++   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAED-IPLKDGEVIA-ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   A+++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAADNLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAEADNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKTNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D++G+ TEE+V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAIDKEGTLTEEMVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNMGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L G+ +  G    K+   L+ D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGKESNGGGTT-KRGDKLAEDMLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSIEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   +    ++ LR FL+K+    G   E +    D+ V
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMLQQQRT---VAELRLFLDKIYNKVGGEQEDLDSLTDEEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L++A   ++GVP++TPVFDGA+E  I  +L +A+L  SGQ  L+DG TGE FDRPVTVGY
Sbjct: 1189 LKLAGNLRAGVPLATPVFDGAEESQIKELLELAELPRSGQQTLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|315125341|ref|YP_004067344.1| DNA-directed RNA polymerase subunit beta [Pseudoalteromonas sp.
            SM9913]
 gi|315013854|gb|ADT67192.1| DNA-directed RNA polymerase subunit beta [Pseudoalteromonas sp.
            SM9913]
          Length = 1341

 Score = 1630 bits (4222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1364 (51%), Positives = 963/1364 (70%), Gaps = 23/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+  Q  S+  FL     PD   + GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLDIPFLLSTQLESFKKFL----VPDADGDHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V D +      ++
Sbjct: 57   FPIKSYSGNSELQYVSYRIGEPVFDVKECQIRGVTYSAPLRVKLRLVVMDKEAPG---TV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FD+D+G+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDNDRGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++VRIDRRRK+P +  L AL   SEEIL  F+    +    
Sbjct: 174  RVIPYRGSWLDFEFDAKDNLYVRIDRRRKLPASIILRALEYTSEEILDIFFDTTAFEIAD 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L  + L  G   +  +   + GE ++ESG+++T+  +KS+++KG+  L +  + 
Sbjct: 234  GKVLMELVPSRL-RGETAAFDI-KSEDGEVLVESGRRVTARHIKSIEKKGINQLEVPHEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A++ V+  TGEI   A D +  + + E+  +    I  LY++ V++ AY+ NTL
Sbjct: 292  IIGRVLAKNYVDESTGEIIATANDELTLEMMAELVKAGHTTIDTLYINEVDSGAYMSNTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N R+  
Sbjct: 352  NIDSSSNRLEALVEIYRMMRPGEPPTKDAAEALFENLFFSEERYDLSTVGRMKFNSRVGY 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+      + KEDI+A++K+L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DSDTGPGTLSKEDIVAVMKVLIAIRNGVGDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLSTYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQANS+L E   F +EL+ CR  GE   + R    
Sbjct: 592  RKVVDGVVTDEVDYLSAIEEGQFVIAQANSNLTETNEFVDELIPCRHKGESTFMGRMDQQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +AK 
Sbjct: 652  YMDVSPQQVISVAAALIPFLEHDDANRALMGSNMQRQAVPTLKADKPLVGTGIELTLAKD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G V   DA RIV+   E +  P  +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 712  SGVTIVAKRGGEVMYADASRIVVNVHEEERIPGEAGIDIYNLTKYTRSNQNTCINQKPTC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMPWNGYNFEDSILLSERVVEEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCIARDTKLGSEEITADIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R++ VE  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRALEVEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D ++E  IL+  +  R  ++L                    D ++     +  
Sbjct: 952  QLREAKKDFNEEFRILEAGVLDRARKLLVAAG-------------FDEDNLASLNAEKLL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ +E  Q  +E L  QY+  K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  TQSLAEEDKQAELEQLAAQYDELKAEYDKKFENKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+   G  VDIVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPVEDMPYDDKGRTVDIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G++++ ++ + +   ++        ++ G       I+ + DD + R+AE  K 
Sbjct: 1119 LAARGIGERLEEMMKEQRELHELRAFIKQAYEI-GESRQVVDIASFSDDEIRRLAENLKG 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E  I  ML +     SGQ  LYDG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1178 GLPIATPAFDGAKESEIKDMLELGGYPRSGQVTLYDGRTGDQFERQVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE +
Sbjct: 1298 NGRTKMYKNIVDGNHKMEPGMPESFNVLLKEIRSLGINIELEEN 1341


>gi|109896926|ref|YP_660181.1| DNA-directed RNA polymerase, beta subunit [Pseudoalteromonas
            atlantica T6c]
 gi|122972315|sp|Q15YB1|RPOB_PSEA6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|109699207|gb|ABG39127.1| DNA-directed RNA polymerase subunit beta [Pseudoalteromonas atlantica
            T6c]
          Length = 1342

 Score = 1630 bits (4222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 713/1365 (52%), Positives = 978/1365 (71%), Gaps = 26/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P++++IP L+ +Q  S+  F+ +++        GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLEIPYLLSIQLDSFKKFIDLDVD----GQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R +T++ PL++ LRL++FD +   G  ++
Sbjct: 57   FPIKSYSGNAELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVLFDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P T  L AL + +EEIL  F+ K      G
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPATIMLRALEIPTEEILGMFFEKNQVRIDG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +       D + G      ++D D G  ++E+G+++++   ++L++ G+  L + ++ 
Sbjct: 235  NRF-MSDIVPDRLRGETAQFDILDSD-GNVLVEAGRRISARHTRALEKAGIVELEVPAEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A D V+ ETGE+ + A D++  +++  +  +       LY++ +++ AYI +TL
Sbjct: 293  LVGRVFACDYVDQETGELVVAANDLLTLENVLALKEAGYTTFETLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS+VGR+K N RL  
Sbjct: 353  RIDSSTNRLEALVEIYRMMRPGEPPTKDAAETLFTNLFFSEDRYDLSSVGRMKFNRRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +T      + K+DI+ ++K L+ +R+GK  +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  ETSIGAGTLDKDDIVDVMKQLITIRDGKDDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +T  RR+S
Sbjct: 473  ERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTDKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N +GF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLASFARTNDFGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RK+ DG VT+++ YLSA+EE    IAQAN  LDE G   ++L+ CR  GE  L    +I 
Sbjct: 593  RKIVDGVVTDEIDYLSAIEEGQFSIAQANVVLDETGRLADDLIPCRHRGETTLKESSEIT 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVP L A+ P VGTGME  VA  
Sbjct: 653  YMDVSPQQIVSIAASIIPFLEHDDANRALMGANMQRQAVPTLIADKPLVGTGMEKTVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVTVVAKRGGRVDYVDASRIVIKVNEEETVAGEAGIDIYNLTKYTRSNQNTCINQRPTC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ +   D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  NVGEPIVAGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILISERVAMEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCVARDTKLGPEEISSDIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V GTV+DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVRGTVIDVQVFTRDGVEKDKRALEIEGM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  DE  IL   I++R   +L            K    +    +    R +W+
Sbjct: 953  QLRQVKKDLSDEFNILADGIFARAKNLL-----------IKSG--IEESRLESAQREKWF 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  ++ +  Q+   K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 DLTLTDEDAQTELDQIAEQFVEIKADFDKKFEIKRRKITQGDDLQPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+  +GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 QIQPGDKMAGRHGNKGVISTIKPVEDMPYDVNGTPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K + +++ LRSFL++V G G+  +   + ++ DD + R+A+  
Sbjct: 1120 MAAHGIGVKIDRML---KEHEEMAKLRSFLKEVYGAGTTHQEVDLDNFSDDEITRLADNL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDGA E  I  ML +ADL ESGQ  L+DG TG  F+RPVTVGY+YMLKLN
Sbjct: 1177 RKGVPMATPVFDGATEAEIKHMLTLADLPESGQIALFDGRTGREFERPVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE 
Sbjct: 1297 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEE 1341


>gi|302347128|gb|ADL27732.1| RNA polymerase beta subunit [Vibrio vulnificus]
          Length = 1336

 Score = 1630 bits (4222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1361 (52%), Positives = 975/1361 (71%), Gaps = 27/1361 (1%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
            +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SVFPI 
Sbjct: 1    YTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSVFPIQ 56

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++KDIK
Sbjct: 57   SYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TVKDIK 114

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  RIIP
Sbjct: 115  EQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIP 174

Query: 187  DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
             +G W+D EFD KD ++VRIDRRRK+P T  L ALG  +EEIL TF+ K+ +  +     
Sbjct: 175  YRGSWLDFEFDPKDNLYVRIDRRRKLPSTIILRALGKSTEEILDTFFEKVNFEVKDQTLM 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              L   D + G   +  +     G   +E G+++T+  ++ L+++GV  + +  + + G 
Sbjct: 235  MELVP-DRLRGETATFDIE--ANGTVYVEKGRRVTARHIRQLEKEGVDQIEVPVEYIVGK 291

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
              ++D +N  TGEI + A   I  ++L ++  +  + + +L+ + +++  ++  TL  D 
Sbjct: 292  VSSKDYINEATGEIIVAANQEISLEALAKLSQAGHKQLEVLFTNDLDHGPFMSETLRIDS 351

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            + DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  D  +
Sbjct: 352  SVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGRDDAE 411

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++
Sbjct: 412  EQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAV 471

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 472  KERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGP 531

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V 
Sbjct: 532  GGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVV 591

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE +D++D 
Sbjct: 592  DGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHVDYMDV 651

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKAE P VGTG+E  VA  SG  
Sbjct: 652  ATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKAEKPLVGTGIERNVAVDSGVT 711

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
             VAKR GI++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V  G+
Sbjct: 712  SVAKRGGIIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGE 771

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IHI+E
Sbjct: 772  PVLRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQE 831

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
               +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +
Sbjct: 832  LTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQL 891

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ Q++ 
Sbjct: 892  TPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKE 951

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  +E  IL+  + +R+  +L                  S   +    R +W +  +
Sbjct: 952  AKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTTDRKKWLELTL 998

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +D+ +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ 
Sbjct: 999  EDDALQTQLEQLAEQYDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKRRIQP 1058

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG A  
Sbjct: 1059 GDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAK 1118

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
            G+G KI  ++   K   +++  R FL+KV   G       I+   D+ V  +    + G+
Sbjct: 1119 GIGDKINQMV---KEQQELAKFREFLQKVYDLGETRQKVDIASLSDEEVRTLIGNLRGGL 1175

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P++TPVFDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V 
Sbjct: 1176 PIATPVFDGASEASIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLNHLVD 1235

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV G
Sbjct: 1236 DKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG 1295

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            RT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+
Sbjct: 1296 RTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELED 1336


>gi|78099444|gb|ABB20858.1| RNA polymerase subunit B [Acinetobacter gerneri]
          Length = 1362

 Score = 1630 bits (4222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1374 (52%), Positives = 973/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK PE+++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPEVMEAPYLLAIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  T+A P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTFAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T+ L AL   +E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATAILRALDYTNEQILEMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDAD-GKVIVEQGKRINARHVRQMEASGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+  +A  V+    + ++    I+   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAEDITLKD-GEVI-QANTVLGHDIMVKLAEGGIKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RTDTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDIIDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT DV YLSA+EE    IAQA+SS+D D + TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTEDVEYLSAIEEVGTVIAQADSSVDGDNNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G++E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAKRGGMIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVSLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R GI+K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGIEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS +L+S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEELLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPSDEGIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDINGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++ + +    I+ LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMLKEQRT---IAELRVFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   + GVP++TPVFDGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRKGVPLATPVFDGAEEGQIKELLELAELPRSGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTRVY++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRVYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|121634009|ref|YP_974254.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis
            FAM18]
 gi|120865715|emb|CAM09442.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis FAM18]
          Length = 1394

 Score = 1630 bits (4222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1400 (49%), Positives = 958/1400 (68%), Gaps = 42/1400 (3%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M     F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF 
Sbjct: 1    MYMSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFN 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            S+FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        
Sbjct: 61   SIFPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKP 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL+
Sbjct: 119  TVKEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +  
Sbjct: 179  SARIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  
Sbjct: 239  SSNGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEP 296

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI N
Sbjct: 297  ESLLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISN 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R 
Sbjct: 357  TLRTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRT 416

Query: 421  NLDTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                  + +                       +  EDI+A I  LV+LRNG G +DDID+
Sbjct: 417  YEQKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDH 476

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            LGNRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF 
Sbjct: 477  LGNRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFG 536

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 537  SSQLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 596

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG
Sbjct: 597  NIGLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDG 656

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +   +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQR
Sbjct: 657  NLIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQR 716

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      G
Sbjct: 717  QAVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVG 776

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            VDIY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW
Sbjct: 777  VDIYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPW 836

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            +GYN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE
Sbjct: 837  NGYNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDE 896

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GI+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGT
Sbjct: 897  SGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGT 956

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            V+DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  G
Sbjct: 957  VIDVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGG 1016

Query: 999  PKGFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            P    K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K 
Sbjct: 1017 PMKLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKK 1076

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG P
Sbjct: 1077 KKLTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRP 1136

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++  
Sbjct: 1137 VDIVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYN 1193

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                 E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       
Sbjct: 1194 GSGKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKL 1253

Query: 1232 G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            G      Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGG
Sbjct: 1254 GFNDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGG 1313

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PE
Sbjct: 1314 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPE 1373

Query: 1346 SFNVLVKEMQALGLSIDLEN 1365
            SFNVLVKE+++LGL IDLE 
Sbjct: 1374 SFNVLVKEIRSLGLDIDLER 1393


>gi|323492154|ref|ZP_08097315.1| DNA-directed RNA polymerase subunit beta [Vibrio brasiliensis LMG
            20546]
 gi|323313605|gb|EGA66708.1| DNA-directed RNA polymerase subunit beta [Vibrio brasiliensis LMG
            20546]
          Length = 1342

 Score = 1630 bits (4221), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1367 (51%), Positives = 971/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + +  L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVGANQEISLEALANLSQAGHKALQTLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E+G+F EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEEGTFAEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YTEAKLDAIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+  Q  +E L  QY+  ++  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDAQQTQLEQLAEQYDELRADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  +    
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFRDFLQKVYDLGETRQKVDIASLSDDEVRTLISNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA+E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGANESSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|260222516|emb|CBA32157.1| DNA-directed RNA polymerase subunit beta [Curvibacter putative
            symbiont of Hydra magnipapillata]
          Length = 1370

 Score = 1630 bits (4221), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1375 (50%), Positives = 971/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    +++IP L+++QK +Y  FL  ++ P +R NEGLQAAF++ 
Sbjct: 1    MAYTYTERKRIRKNFGSRDSVLEIPYLLQMQKDAYTAFLQADVGPKKRTNEGLQAAFEAA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++++ Y    P FDV +C  R LTYA  ++  ++LI++D +  TG  K 
Sbjct: 61   FPIVSHNGFVEMKYLEYNLAKPAFDVRECQTRGLTYASAVRAKVQLIIYDRESSTGQNKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTGKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+++E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDLLYFRVDRRRKMPVTILLKAIGLNNESILANFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A  L  G      + D  +G+ V+   K++T+   + L++ G   + +  D
Sbjct: 241  DSGAQMEFVAERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTSHISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA ++V+G+TGEI  +A + + E  L+++  + I+D+  +Y + ++  AYI  T
Sbjct: 299  FLIGRVVARNVVDGDTGEIVAKANEELTEALLKKLRTAGIQDLACIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L TD+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++ 
Sbjct: 359  LRTDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKMG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+A++KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RSESTGPMVLTNEDILAVVKILVDLRNGRGDVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ     N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMNQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V D KVTN++ YLSA+EE    IAQAN++LD++G+ T +LV  R  GE ILV  +++
Sbjct: 599  YRRVVDSKVTNEIDYLSAIEEGKYVIAQANAALDKEGTLTGDLVSAREKGESILVSADRV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R GIV+ VDA R+VIR  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGIVDYVDATRVVIRVNDAEAQAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD++ + D+IADG STDLG++A+G+NMLVAFMPW+GYNFEDS+LISER+V+ED +TS
Sbjct: 779  VKKGDKLSKGDVIADGASTDLGEIAIGQNMLVAFMPWNGYNFEDSILISERVVAEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVLPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI ++ R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTVIDVQVFTREGIQRDRRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K T L    ++   +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLTGKVANGGPQKLAKGTKLDKAYLTSVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     DE+V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPADEEVASQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYIAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I P EDMP+L DGTPVDIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKITPVEDMPYLADGTPVDIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++    A+ +I   R FLE+V  +    E ++   D  V  +A++  
Sbjct: 1139 GWAGKGLGQRIGDMLQREAASTEI---RGFLEQVYNSTGRKEDLAQLSDAEVQEMAKELT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
            SGVP ++PVFDGA E+ I  ML++A  D             Q+ LYDG +G+ F+R  TV
Sbjct: 1196 SGVPFASPVFDGATEKEIGDMLQLAYPDDVAKAKGLTATRTQAQLYDGRSGDAFERTTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYE+IV G  + E G PESFNVLVKE+++LG+ I+L+ S
Sbjct: 1316 QEMLTVKSDDVQGRTKVYENIVKGEHSIEAGMPESFNVLVKEIRSLGIDIELDRS 1370


>gi|261381386|ref|ZP_05985959.1| DNA-directed RNA polymerase, beta subunit [Neisseria subflava NJ9703]
 gi|284795633|gb|EFC50980.1| DNA-directed RNA polymerase, beta subunit [Neisseria subflava NJ9703]
          Length = 1392

 Score = 1630 bits (4221), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1398 (49%), Positives = 955/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLNVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L ++    +++I  LY++ ++   YI +TL
Sbjct: 297  LIGKALAADLIDPETGEVLASANDEITEELLAKLDIHGVKEITTLYINELDQGGYISSTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETLAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++    +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLASLSSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|77359193|ref|YP_338768.1| DNA-directed RNA polymerase subunit beta [Pseudoalteromonas
            haloplanktis TAC125]
 gi|88909631|sp|Q3ILP9|RPOB_PSEHT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|76874104|emb|CAI85325.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase beta subunit)
            [Pseudoalteromonas haloplanktis TAC125]
          Length = 1341

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1364 (51%), Positives = 962/1364 (70%), Gaps = 23/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+  Q  S+  FL     PD   + GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLDIPFLLSTQLKSFKKFL----VPDADGDHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V D +      ++
Sbjct: 57   FPIKSYSGNSELQYVSYRIGEPVFDVKECQIRGVTYSAPLRVKLRLVVMDKEAPG---TV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FD+D+G+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDNDRGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++VRIDRRRK+P +  L AL   SE+IL  F+    +    
Sbjct: 174  RVIPYRGSWLDFEFDAKDNLYVRIDRRRKLPASIILRALEYSSEDILGIFFDNTTFEVTD 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L  + L  G   +  +   + GE  +ESG+++T+  +K++++KG+K L +  + 
Sbjct: 234  GKVLMELVPSRL-RGETAAFDI-KSEDGEVFVESGRRVTARHIKNIEKKGIKQLEVPHEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A++ V+  TGE+   A D +  + + E+  +    I  LY++ V++ AY+ NTL
Sbjct: 292  IIGRVLAKNYVDESTGEVVANANDELTLELMAELVKAGHTKIDTLYINEVDSGAYMSNTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N R+  
Sbjct: 352  NIDSSSSRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSTVGRMKFNSRVGY 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            DT      + KEDI++++K+L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DTDTGPGTLSKEDIVSVMKVLIAIRNGVGDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLSTYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQANS+L E   F +EL+ CR  GE   + R    
Sbjct: 592  RKVVDGVVTDEVDYLSAIEEGQFVIAQANSNLTETNEFVDELIPCRHKGESTFMGRMDQQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +AK 
Sbjct: 652  YMDVSPQQVISVAAALIPFLEHDDANRALMGSNMQRQAVPTLKADKPLVGTGIELTLAKD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G V   DA RIV+   E +  P  +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 712  SGVTIVAKRGGEVMYCDASRIVVNVHEEERVPGEAGIDIYNLTKYTRSNQNTCINQKPTC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMPWNGYNFEDSILLSERVVEEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCIARDTKLGSEEITADIPNVGESALGKLDESGVVYIGAEVKSGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R++ VE  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRALEVEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D ++E  IL+  +  R  ++L                    D ++     +  
Sbjct: 952  QLRDAKKDFNEEFRILEAGVLDRARKLLIAAG-------------FDEDKLALLNAEKLL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ +E  Q  +E L  QY+  K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  TQSLAEEDKQAELEQLAAQYDELKAEYDKKFENKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+   G  VDIVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 CIQPGDKMAGRHGNKGVISTIVPVEDMPYDDKGRTVDIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G++I+ ++ + +   ++        ++ G       I  + DD + R+AE  K 
Sbjct: 1119 LAARGIGERIEEMMKEQRELHELRAFIKQAYEI-GESRQVVDIDSFTDDEIRRLAENLKG 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E  I  ML +A    SGQ  LYDG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1178 GLPIATPAFDGAKENEIKDMLELAGYPRSGQVTLYDGRTGDQFERQVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE +
Sbjct: 1298 NGRTKMYKNIVDGNHKMEPGMPESFNVLLKEIRSLGINIELEEN 1341


>gi|297537524|ref|YP_003673293.1| DNA-directed RNA polymerase subunit beta [Methylotenera sp. 301]
 gi|297256871|gb|ADI28716.1| DNA-directed RNA polymerase, beta subunit [Methylotenera sp. 301]
          Length = 1390

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1397 (49%), Positives = 961/1397 (68%), Gaps = 40/1397 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + +IP L+ +Q  SY  FL   I  D+R  +GLQ+ F SV
Sbjct: 1    MSYSFTEKKRLRKSFAKRESVQEIPYLLAMQLESYKAFLQAEIPADKRTEDGLQSTFASV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L++VSY+     FDV +C  R LTYA PL++ +RL + D        ++
Sbjct: 61   FPIISHSGNARLDYVSYQLGAEPFDVKECQQRGLTYAAPLRVKVRLTIMDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG+LPLMT++G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGELPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT  L ALG   E+I++TF+    +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRIDRRRKMPVTILLKALGYTPEQIIATFFDFDTFHVSA 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                F L   D + G      +V    GE ++   K++T   ++ +++ GV  + +  D 
Sbjct: 239  KGVEFTLVP-DRLRGEVAKFDIV-AKDGEVLVAKDKRITVKHIRDMEKAGVSKIAVPQDF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  + ++IV+ ETGEI   A D I E  LE++  +++ +I  LY + +++  YI  TL
Sbjct: 297  ILGRAIGKNIVDKETGEIVANANDEITESLLEKLIDAKVGEINTLYSNDLDHGDYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E++FN LFF+ D+YDLS VGR+K N R   
Sbjct: 357  RIDEIPDQYSARVAIYRMMRPGEPPTEDSVEALFNGLFFNEDRYDLSRVGRMKFNRRAFP 416

Query: 423  DTPDDVR--------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            +  +D +                     +  +DI+A+I +L++LRNG+G IDDID+LGNR
Sbjct: 417  EKAEDRQSNWMRKFYETVGPRGAEGAYILSNDDILAVIGVLLELRNGRGEIDDIDHLGNR 476

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+RSVGE+ +NQ+R GL+R+ER++KER+S  + D++MP DLINAKPV SA+ EFF SSQL
Sbjct: 477  RIRSVGELAENQFRTGLVRVERAVKERLSQAESDNLMPHDLINAKPVSSAIREFFGSSQL 536

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 537  SQFMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHSTHYGRMCPIETPEGPNIGL 596

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +AR N YGF+ETPYR+V   KV++ + YLSA+EE    IAQAN+ LD    F E
Sbjct: 597  INSLALYARTNEYGFLETPYRRVEGNKVSDTIDYLSAIEESQYMIAQANTDLDAKNMFVE 656

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV  R   E  +   +++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 657  DLVSSRHHNEFTMTQPDRVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVP 716

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+AE   VGTG+E  VA  SG  + A+R G+V+ VD+ RIV+R  + +      GVDIY
Sbjct: 717  CLRAEKAVVGTGIERTVAVDSGTTVQARRGGLVDYVDSGRIVVRVNDDEAKDGEVGVDIY 776

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L K+ RSNQNT +NQRPLV+VGD++ R D+IADG STD+G+LALG+NMLV FMPW+GYN
Sbjct: 777  NLTKYTRSNQNTNINQRPLVRVGDKLARGDVIADGASTDMGELALGQNMLVGFMPWNGYN 836

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +EDS+LISER+V++D +TSIHIEE  V+ARDTKLG EEIT+DI N+SE  L  +DE GII
Sbjct: 837  YEDSILISERVVADDRYTSIHIEELTVVARDTKLGAEEITQDISNLSERMLGRLDEVGII 896

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GA+V  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV
Sbjct: 897  YIGADVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDV 956

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R G++++ R+  +  +Q+    +D  D+  I++ + + R+  ++ G+ A  GP   
Sbjct: 957  QVFTREGLERDSRAQQIIDDQLTHYKQDLADQMRIVEDDAFGRIRRLIEGKTATGGPNKL 1016

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK  VL+++ ++   R  W+   + DE+  R +E LK     ++   + +F+ K  K+  
Sbjct: 1017 KKGDVLTAEYLASVGRYDWFDIRLTDEETARQLEQLKDSLAQARVNFDSKFEEKKRKLTQ 1076

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++P GV ++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP + DGTP+DIVL
Sbjct: 1077 GDELPAGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVISKICPIEDMPHMADGTPMDIVL 1136

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG-SH 1181
            NPLGVPSRMN+GQI E HLGWA  GLG +I  ++   +    ++ +R FLE++       
Sbjct: 1137 NPLGVPSRMNIGQILEVHLGWAAKGLGLRIDEML---REEAKVADIRKFLEQIYNDSTGK 1193

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----------ES 1231
             E I+ + D  VL +A    +GVP +TPVFDGA E  I +ML +A  D           +
Sbjct: 1194 KEDINSFTDTEVLELARNLTNGVPFATPVFDGAAESDIKAMLDLAYPDDAARTKQLKFHA 1253

Query: 1232 GQS--ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            G++   L+DG TG+ F+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1254 GKTQVTLFDGRTGDAFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1313

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT+VYE+IV G    + G PESFNV
Sbjct: 1314 GGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDAGMPESFNV 1373

Query: 1350 LVKEMQALGLSIDLENS 1366
            LVKE+++L + IDL+ +
Sbjct: 1374 LVKEIRSLAIDIDLDRN 1390


>gi|9911111|sp|Q59622|RPOB_NEIMB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|316985974|gb|EFV64913.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            H44/76]
 gi|325141146|gb|EGC63646.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            CU385]
 gi|325199345|gb|ADY94800.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            H44/76]
          Length = 1392

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1398 (49%), Positives = 958/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A D + G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVA-DRLKGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STD G+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDFGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|325203251|gb|ADY98704.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M01-240355]
          Length = 1392

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 960/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A D + G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVA-DRLKGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|329122393|ref|ZP_08250980.1| DNA-directed RNA polymerase subunit beta [Haemophilus aegyptius ATCC
            11116]
 gi|327473675|gb|EGF19094.1| DNA-directed RNA polymerase subunit beta [Haemophilus aegyptius ATCC
            11116]
          Length = 1343

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 705/1365 (51%), Positives = 966/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E +FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEVLFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITVDIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  + +  R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G +I +++   +    +         ++G GS    +S + D+ VLR+A   +
Sbjct: 1119 GLAAKGIGDQINAMLKQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLR 1178

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH
Sbjct: 1179 KGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1238

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1239 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1298

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1299 VNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1343


>gi|225076433|ref|ZP_03719632.1| hypothetical protein NEIFLAOT_01479 [Neisseria flavescens
            NRL30031/H210]
 gi|224952233|gb|EEG33442.1| hypothetical protein NEIFLAOT_01479 [Neisseria flavescens
            NRL30031/H210]
          Length = 1409

 Score = 1630 bits (4220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1398 (49%), Positives = 955/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 18   MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 77

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 78   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 135

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 136  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 195

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 196  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 255

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 256  NGVQTDLIAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 313

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L ++    +++I  LY++ ++   YI +TL
Sbjct: 314  LIGKALAADLIDPETGEVLASANDEITEELLAKLDIHGVKEITTLYINELDQGGYISSTL 373

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 374  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 433

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 434  QKLSEAQQNSWYGRLLNETLAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 493

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 494  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 553

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 554  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 613

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 614  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 673

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 674  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 733

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 734  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 793

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 794  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 853

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 854  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 913

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 914  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 973

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 974  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1033

Query: 1001 GFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++    +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1034 KLAKGSEITTEYLASLSSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1093

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1094 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1153

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1154 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1210

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ V+ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1211 GKKEDLDSLTDEEVIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1270

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1271 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1330

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1331 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1390

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1391 NVLVKEIRSLGLDIDLER 1408


>gi|163803770|ref|ZP_02197626.1| DNA-directed RNA polymerase subunit beta [Vibrio sp. AND4]
 gi|159172428|gb|EDP57298.1| DNA-directed RNA polymerase subunit beta [Vibrio sp. AND4]
          Length = 1342

 Score = 1629 bits (4219), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 971/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+VFD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVVFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  SEEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E G+++T+  ++ L++  V  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVEQGRRVTARHIRQLEKDSVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D VN  TGEI + A   I  ++L  +  +  + +  L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYVNEATGEIIVNANQEISLEALANLSQAGHKSLETLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RVDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFAEERYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDELDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA+EE    IAQAN++L E+G F +EL+  R  GE  L PRE   
Sbjct: 592  RRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGGFADELITARQKGESGLHPREHAQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YSEAKLDTTDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G   +   I+   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGETRQQVDIASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I ++L++ADL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGAPEASIKALLKLADLPESGQLKLFDGRTGDEFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|71278694|ref|YP_271413.1| DNA-directed RNA polymerase subunit beta [Colwellia psychrerythraea
            34H]
 gi|88909130|sp|Q47UV9|RPOB_COLP3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71144434|gb|AAZ24907.1| DNA-directed RNA polymerase, beta subunit [Colwellia psychrerythraea
            34H]
          Length = 1342

 Score = 1629 bits (4219), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1366 (51%), Positives = 980/1366 (71%), Gaps = 26/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK+ ++++ P L+ +Q  S+  F+  +         GL+AAF+S+
Sbjct: 1    MAYSYFEKKRIRKDFGKSVQVMEYPFLLSIQLDSFRKFIDTD----PTGETGLEAAFRSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI A+SG++ L++VSY    P FDV +C  R +TY+ PL++ LRL+V+D +   G  ++
Sbjct: 57   FPIKAYSGSSELQYVSYRLGEPLFDVKECQIRGVTYSAPLRVKLRLVVYDKEAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL+ FY    Y+ +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALEYSTEEILAMFYDTTDYTIKG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G      +  I  GE ++ESG+++T+  +++L +  ++ L + +D 
Sbjct: 235  DKLIMDLIPERL-RGETAIFDI-SIKKGEVLVESGRRITARHIRALSKAKLEKLEVPADY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +++  ++  TGE+  EA  +I  + L E+  +  + +  LY++  +  +Y+ +TL
Sbjct: 293  IVGRVLSKAYIDKSTGEVIAEANAIITLELLAELSQAGHKVLSTLYMNEFDVGSYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + ++ +AL+++YR+MRPG+  T   AE +F+ LFF S++YDLSTVGR+K N R+  
Sbjct: 353  RVDSSTNKLEALVEVYRMMRPGEPPTKDAAEGLFSNLFFASERYDLSTVGRMKFNRRVGN 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + KEDII+++K L+ +R+GKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  ADDVGTGILSKEDIISVMKTLIGIRDGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N +GF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSCYARTNDFGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+++ YLSA+EE N  IAQAN+  ++     ++LV CR   E IL    ++ 
Sbjct: 593  RKVIDGLVTDEIDYLSAIEEGNFVIAQANAERNDSNKLVQDLVNCRHRNEFILKASAEVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME VVA  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGSNMQRQAVPTLRVDKPLVGTGMEKVVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V  VDA RIV++  E ++    +G+DIY L K+ RSNQNTC+NQRP+ 
Sbjct: 713  SGVTAVAKRGGVVSYVDASRIVVKVNENEMHAGEAGIDIYNLTKYTRSNQNTCINQRPVC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            ++G+ V R D++ADGPSTD+G+LALG+NM +AFMPW+GYNFEDSML+SER+  ED FT+I
Sbjct: 773  RMGEPVVRGDVLADGPSTDMGELALGQNMRIAFMPWNGYNFEDSMLLSERVAIEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEVN GDILVGK+TPKG
Sbjct: 833  HIQELTCIARDTKLGSEEITADIPNVGESALSKLDEAGVVYIGAEVNGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV+IF R G++K+ R++ +E+ 
Sbjct: 893  ETQLTPEEKLLRAIFGEKAADVKDSSLRVPNSVKGTIIDVQIFTRDGVEKDARAVEIEQM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  DE  IL+  IY+R  ++L                 L+   ++   R +W 
Sbjct: 953  QLKEVKKDLGDELSILEDGIYARTKKLLLSAG-------------LNESDLTSMSRDKWL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E +  Q++  K   + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 TQNLADEGQQAELEQIAEQFDNIKEDFDKKFEVKRRKITQGDDLQPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S ++P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 HIQPGDKMAGRHGNKGVISNVVPVEDMPYDQFGVPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             AC G+G+KI  ++   +A  +I  LR+F+++V   G   +   ++ + DD VLR+A   
Sbjct: 1120 MACRGIGEKINRML---EAQQEIHKLRNFIQEVYNVGESRQVVDVASFSDDEVLRLAGNL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+P++TP FDGA E+ I  +  +AD+ +SGQ +L DG TG  F+RPVTVGY+YMLKLN
Sbjct: 1177 RAGLPIATPAFDGAAEKEIKELFVLADMPQSGQFVLTDGRTGREFERPVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y+++V G+   E G PESFNVL+KE+++LG++I+L+  
Sbjct: 1297 DVNGRTKMYKNLVDGDHRMEPGIPESFNVLLKEIRSLGINIELDKD 1342


>gi|330444941|ref|ZP_08308595.1| DNA-directed RNA polymerase, beta subunit [Photobacterium leiognathi
            subsp. mandapamensis svers.1.1.]
 gi|328493059|dbj|GAA03092.1| DNA-directed RNA polymerase, beta subunit [Photobacterium leiognathi
            subsp. mandapamensis svers.1.1.]
          Length = 1341

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1366 (51%), Positives = 961/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P++++ P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLEAPYLLSIQLDSFQKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +++IL  F+ KI +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPASIILRALNYTTDQILDMFFEKIHFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G   +E G+++T+  ++ L + GV  + +  + 
Sbjct: 235  KSLVMELVP-DRLRGETASFDIE--ANGTVYVEKGRRITARHIRQLGKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D ++  TGE+ + A   +  ++L  +  +  + I +L+ + +++  Y+ +TL
Sbjct: 292  IVGKIASRDYIDENTGELIVAANQELSLEALALLSQAGHKSIDVLFTNDLDHGPYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RIDNTTDRLSALVEIYRMMRPGEPPTREAAEQLFESLFFSEDRYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +   DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DETTGPGTLDHADIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVFARCNPYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKV+ ++ YLSA+EE    IAQAN++L+EDGSF +EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDGKVSEEIEYLSAIEEGLYVIAQANAALNEDGSFADELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP ++A+ P VGTG+E  +   
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTIRADKPLVGTGIERQIGVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  + +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGTVQSVDASRIVIKVNDDELIPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP  V+GT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPGSVTGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S D I+   R   +
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLLSAG-------------YSEDKIASMNRDALF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F++K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  AVTLDDEALQNQLEQLAEQYDELKAEFDKKFESKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQTVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL+KV   G       ++   DD V  + +  
Sbjct: 1119 LAAKGIGDKLNDML---KEQQELHKFRNFLQKVYDLGDTRQKVDVAALTDDEVRTLVQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPIATPVFDGAPEPSIKELLKLGDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|226951786|ref|ZP_03822250.1| RNA polymerase subunit B [Acinetobacter sp. ATCC 27244]
 gi|294649034|ref|ZP_06726480.1| DNA-directed RNA polymerase subunit beta [Acinetobacter haemolyticus
            ATCC 19194]
 gi|78099448|gb|ABB20860.1| RNA polymerase subunit B [Acinetobacter haemolyticus]
 gi|226837326|gb|EEH69709.1| RNA polymerase subunit B [Acinetobacter sp. ATCC 27244]
 gi|292825065|gb|EFF83822.1| DNA-directed RNA polymerase subunit beta [Acinetobacter haemolyticus
            ATCC 19194]
          Length = 1362

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1374 (51%), Positives = 970/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYTNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKAIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   +   I   A  V+  + + +I    ++   IL+ + ++   ++ +TL
Sbjct: 295  LYERITAEDITLKDGDVI--PANTVLSHEVMVKIAEGGVKQFNILFTNDIDRGPFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG+ TEE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGNLTEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPADEAIAERLTQIQVFLKEKSIEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP    G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDIHGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   +    I+ LR+FL+K+    G   E +    D+ V
Sbjct: 1132 QILETHLGMAAKGLGEQIDKMLQQQRT---IAELRAFLDKIYNKVGGEQEDLDSLTDEEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L++A   ++GVP++TPVFDGA+E  I  +L +A+L  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LKLAGNLRAGVPLATPVFDGAEESQIKELLELAELPRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|254671128|emb|CBA08144.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            alpha153]
          Length = 1392

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   S +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDISGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|309379169|emb|CBX22300.1| DNA-directed RNA polymerase, beta subunit [Neisseria lactamica
            Y92-1009]
          Length = 1392

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L I  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDIANAGLTRLDIEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLTGLPSKHDWFDIRLTDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|260902138|ref|ZP_05910533.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ4037]
 gi|308110161|gb|EFO47701.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ4037]
          Length = 1343

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1368 (51%), Positives = 971/1368 (70%), Gaps = 28/1368 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHD-KGRASLSGKLLYA 181
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD D KG+   SGK+LY 
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDDKGKTHSSGKVLYN 174

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 175  ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 234

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                   L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 235  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 291

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 292  YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 351

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 352  LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 411

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 412  REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 471

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 472  VERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 531

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 532  SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 591

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 592  YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA 
Sbjct: 652  QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAV 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP 
Sbjct: 712  DSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+
Sbjct: 772  VMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQ 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  + +R+  +L                  S   +    R +W
Sbjct: 952  MQLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDATDRKKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+K
Sbjct: 999  LELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HL
Sbjct: 1059 RRIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + + 
Sbjct: 1119 GLAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E +I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKL
Sbjct: 1176 LRGGLPIATPVFDGAPEASIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DDV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DDVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1343


>gi|325135137|gb|EGC57763.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M13399]
          Length = 1392

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|261254078|ref|ZP_05946651.1| DNA-directed RNA polymerase beta subunit [Vibrio orientalis CIP
            102891]
 gi|260937469|gb|EEX93458.1| DNA-directed RNA polymerase beta subunit [Vibrio orientalis CIP
            102891]
          Length = 1342

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1367 (51%), Positives = 970/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + +  L+ + +++  ++  T+
Sbjct: 292  IVGKVASQDYINEATGEIIVGANQEISLEALANLSQAGHKALQTLFTNDLDHGPFMSETV 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E+G+F EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGIVTDEVDYLSAIQEGQYVIAQANTVLTEEGTFAEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   V+KR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVSKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YTEAKLDSIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDAQQSQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       I+   D  V  +    
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFRDFLQKVYDLGETRQKVDIASLSDGEVRTLINNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA+E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGANESSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|254509112|ref|ZP_05121213.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            16]
 gi|219547950|gb|EED24974.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            16]
          Length = 1342

 Score = 1629 bits (4218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1367 (51%), Positives = 972/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKVYVETGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVGANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DI+ ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDETDIVEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E+G+F EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEEGTFAEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YTEAKLDAIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDAQQSQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       ++   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFRDFLQKVYDLGETRQKVDVASLSDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E++I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEQSIKELLKLGDLPESGQLKLFDGRTGDEFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|78099434|gb|ABB20853.1| RNA polymerase subunit B [Acinetobacter genomosp. 16BJ]
          Length = 1362

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1374 (51%), Positives = 971/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVVLRALNYSNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKAIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AED +  + G++   A  V+  + L ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAED-IPLKNGDVIA-ANTVLSHEILVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+DG  TEE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKDGHLTEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIADRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   L+ D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLAEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG K++ ++ + +    +  LR FL+K+    G   E++    D  +
Sbjct: 1132 QILETHLGMAAKGLGDKLEKMLKEQRT---VLELRDFLDKIYNKVGGEQEELDSLTDAEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|325131073|gb|EGC53796.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            OX99.30304]
          Length = 1392

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1398 (50%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|167855652|ref|ZP_02478410.1| DNA-directed RNA polymerase beta chain [Haemophilus parasuis 29755]
 gi|167853224|gb|EDS24480.1| DNA-directed RNA polymerase beta chain [Haemophilus parasuis 29755]
          Length = 1342

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1367 (51%), Positives = 960/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK  +++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRSQVLNVPYLLTIQLDSFDKFIQRD----PEGLQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSSNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHASGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEIL+ F+    +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILNMFFETATFHIED 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +ESG+++T+  +++L++  +  + + ++ 
Sbjct: 235  NRLLMTLVPERL-RGETAAFDIE--ANGKIYVESGRRITARHIRALEKDNITQIQVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A D V+  TGEI   A   I  ++L  +  +   +I +L+ + ++   YI  TL
Sbjct: 292  IVGRVTARDYVDLSTGEIVCPANSEIGLETLAALAQAGYNEIEVLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L++
Sbjct: 352  RIDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSTDRYDLSAVGRMKFNRSLDI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGTGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGSGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A++AKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVIAKRGGTIQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VKLGEPVGRGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ + PEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R+  +E 
Sbjct: 892  GETQLIPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRAKDIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L                      +    R +W
Sbjct: 952  IQLREAKKDLTEELEILEAGLFTRVRNLLLEGGVA-------------QATLDNLAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I  +I   K   +I+ LR +++K    G G+ +  +S + D+ V+R+A+ 
Sbjct: 1119 GLAARGIGDQIDKMI---KQQQEIAKLREYIQKAYDLGHGAQSVDLSTFSDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQLGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1296 DDVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1342


>gi|319761186|ref|YP_004125123.1| DNA-directed RNA polymerase, beta subunit [Alicycliphilus
            denitrificans BC]
 gi|330823046|ref|YP_004386349.1| DNA-directed RNA polymerase subunit beta [Alicycliphilus
            denitrificans K601]
 gi|317115747|gb|ADU98235.1| DNA-directed RNA polymerase, beta subunit [Alicycliphilus
            denitrificans BC]
 gi|329308418|gb|AEB82833.1| DNA-directed RNA polymerase, beta subunit [Alicycliphilus
            denitrificans K601]
          Length = 1374

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1379 (50%), Positives = 962/1379 (69%), Gaps = 18/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FG    ++ +P L+++Q+ +Y  FL     P +R +EGLQAA
Sbjct: 1    MAQTSTYSYTERKRIRKSFGSRDSVLKVPYLLQMQRDAYTAFLQAETPPQKRTSEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT- 117
            F + FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T 
Sbjct: 61   FNAAFPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTA 120

Query: 118  GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    
Sbjct: 181  LLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +               L  G      + D  +G+ V+   K++T+   + L++ G   + 
Sbjct: 241  FRLMDSGAQMEFVPERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTTHIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  VA +IV+ +TGEI  +A + + E  L+++  + ++++  +Y + ++  AY
Sbjct: 299  VPEDFLLGRVVARNIVDPDTGEILAKANEELTEALLKKLRSAGVQELQAIYTNELDQGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N
Sbjct: 359  ISQTLRIDETADEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             ++          +  +DI++++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  AKVGRSEATGPMVLDNDDILSVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRT 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH
Sbjct: 479  GLARIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR+V DGKVT+++ YLSA+EE    IAQAN++LDE+G  T +LV  R  GE  LV 
Sbjct: 599  IETPYRRVVDGKVTSEIDYLSAIEEGKYIIAQANAALDEEGRLTGDLVSAREQGESTLVS 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E 
Sbjct: 659  AERVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + A+R G+V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VAAVDSGTVVTARRGGVVDYVDATRIVVRVHDAEAVAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+VK GD + + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+V+ED
Sbjct: 779  QRPIVKKGDVLAKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVAED 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTVIDVQVFTREGIQRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP    K   +  + ++   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLVGKKANGGPHKLAKGATIDKEYLAGVE 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     DE V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KFHWFDIRPADEAVAAQLESMKNAMEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I P EDMP + DGTPVDIVLNPLGVPSRMN+GQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKITPVEDMPHMADGTPVDIVLNPLGVPSRMNIGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGWA  GLG++I  ++   +   +++ +R FL +V  +    E +S   DD V+ +A
Sbjct: 1139 EVHLGWAGKGLGQRIGDML---RDQANVAEMRKFLGEVYNSRGRKEDLSQLSDDEVMSMA 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEPFDR 1247
                 GVP ++PVFDGA E  I  ML++A  D      G      Q+ L DG TGE F+R
Sbjct: 1196 ANLTGGVPYASPVFDGASEAEIKDMLKLAYPDDIKERKGLTDTRTQAWLIDGRTGERFER 1255

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1256 PTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1315

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AYVLQEMLT+KSDDV GRT+VYE+IV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 AYVLQEMLTVKSDDVQGRTKVYENIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|78099456|gb|ABB20864.1| RNA polymerase subunit B [Acinetobacter parvus]
          Length = 1362

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1374 (51%), Positives = 974/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKAIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   ++G++   A  V+    + +I  + ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDIT-LKSGDVI-PANTVLSHDIMVKIAENGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG+ TEE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAVDKDGNLTEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS++++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSAEVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPNDEAIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E++    D  +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|158513168|sp|A1KRG6|RPOB_NEIMF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|325143224|gb|EGC65563.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            961-5945]
 gi|325197420|gb|ADY92876.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            G2136]
          Length = 1392

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|145588235|ref|YP_001154832.1| DNA-directed RNA polymerase, beta subunit [Polynucleobacter
            necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|189043862|sp|A4SUV4|RPOB_POLSQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145046641|gb|ABP33268.1| DNA-directed RNA polymerase subunit beta [Polynucleobacter
            necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 1366

 Score = 1629 bits (4217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1374 (51%), Positives = 959/1374 (69%), Gaps = 18/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    RVRK F K      +P LI  Q  SY  FL  +     R  EGLQAAF S 
Sbjct: 1    MNYSFTERKRVRKSFAKRVNNHQVPYLIATQLESYAKFLQADKPAMSRLTEGLQAAFTSA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +E+VSY+   P FDV +C  R  TY   L+  +RLI++D +  T    +
Sbjct: 61   FPIVSNNGYARMEYVSYQLSQPPFDVKECQQRGYTYHSALRAKVRLIIYDREAPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KE  +YMG++PLMT++G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKESEVYMGEIPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+++E+IL+ F+    +S   
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNNEQILANFFNFDHFSLTA 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G   +  ++D   G  VI+  K++ +  ++ L+    K + +  D 
Sbjct: 238  NGGSMEFVPERL-RGQLANFDVLD-KNGVVVIQKDKRINAKHIRELEAAKTKTIAVPDDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  VA +IV+ ++GEI   A D I E+ L  +  + I+ +  +Y + +++ AYI  TL
Sbjct: 296  LVGRVVARNIVDPDSGEILAYANDEITEELLATLRDAGIKQLETIYTNDLDSGAYISQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR+MRPG+  T    E++F  LF++ D YDLS VGR+K+N RLN 
Sbjct: 356  RTDETADQMAARIAIYRMMRPGEPPTEDAVEALFQRLFYNEDTYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDI+  IK LVDLRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PEMEGPMVLSNEDILDTIKSLVDLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR+N +GF+ETPY
Sbjct: 536  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARLNEHGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV + KV+++VVYLSA+EE    IAQAN+++D+ G   +ELV  R AGE I+V  E+ID
Sbjct: 596  RKVSNSKVSDEVVYLSAIEEAKYVIAQANATIDKSGKLADELVSARQAGETIMVSPERID 655

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            FID +P Q+VS AASL+PFLE+DD+NR LMG NM RQAVP L+ + P VGTG+E +VA  
Sbjct: 656  FIDVAPSQIVSAAASLVPFLEHDDANRALMGANMSRQAVPCLRPDKPLVGTGLERIVAVD 715

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  I+A R GIV+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 716  SGTVILATRGGIVDYVDANRIVIRVNDDETAAGEVGVDIYNLIKYTRSNQNTNINQRPIV 775

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V R D++ADG STDLG+LALG+NM VAFMPW+GYNFEDS+LISE++V+ED +TSI
Sbjct: 776  QAGDRVVRGDVVADGASTDLGELALGQNMTVAFMPWNGYNFEDSILISEKVVAEDRYTSI 835

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 836  HIEELSVVARDTKLGSEEITRDISNLAESQLSRLDESGIVYIGAEVEAGDVLVGKVTPKG 895

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI+++ R+ ++ +E
Sbjct: 896  ETTLTPEEKLLRAIFGEKASDVKDTSLRVPSGMIGTVIDVQVFTREGIERDARAQAIIQE 955

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++    D +D+  I++ + + RL ++L G+ A  GP+   K T +  + ++   +  W+
Sbjct: 956  ELQRYRLDLNDQLRIVEGDAFMRLEKLLIGKVANGGPQKLAKGTKIDKEYLASLDKYHWF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE+V   VE++K   E  +   ++ F+ K  K+  GDD+  GV ++VKV++A+KR
Sbjct: 1016 DVRPADEEVATQVEAIKSSIEAKRKQFDEAFEEKRTKLTQGDDLQAGVTKMVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I P EDMPF+ DG PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RLQPGDKMAGRHGNKGVVSKIAPAEDMPFMADGRPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+GK+I  ++   +     + LR FL+++       E I ++ D+ +  +AE  + 
Sbjct: 1136 WAAQGIGKRIDEMV---RQQVKQAELRKFLKQLYNETGRIEDIDNFTDEQITVLAENLRQ 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTVG 1252
            G+P +TPVFDGA E  I  ML +A                Q IL DG TG+ F+RPVTVG
Sbjct: 1193 GLPFATPVFDGATEAEIGRMLELAYPEEVATSLKMTPSRQQMILCDGRTGDQFERPVTVG 1252

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1253 VMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1312

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE+IV G  T + G PESFNVLVKE+++LG+ ID+E +
Sbjct: 1313 EMLTVKSDDVAGRTKVYENIVKGEHTIDAGMPESFNVLVKEIRSLGIDIDMERN 1366


>gi|325133045|gb|EGC55717.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M6190]
 gi|325139024|gb|EGC61570.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            ES14902]
 gi|325145329|gb|EGC67606.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M01-240013]
 gi|325205224|gb|ADZ00677.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M04-240196]
          Length = 1392

 Score = 1628 bits (4216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|88909646|sp|Q5E238|RPOB_VIBF1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1341

 Score = 1628 bits (4216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 964/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFTKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + LE+VSY    P+FDV +C  R +TY+ PL++ LRL+V+D D      ++
Sbjct: 57   FPIQSYNGNSKLEYVSYNLREPEFDVKECQIRGVTYSAPLRVKLRLVVYDKDAPAN--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+      
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNKTTEEILDLFFDKVFEV--K 232

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D         + + G   +  +     G+  +E+G+++T+  ++ L +  +  + +  D 
Sbjct: 233  DQTLMMELIPERLRGETATFDIE--ANGKVYVEAGRRITARHIRQLTKDDITHIEVPVDY 290

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN +TGEI I A      + L  +  +  + I +L+ + +++ AYI +TL
Sbjct: 291  IVGKVASHDYVNEDTGEIIIAANQEFSLEDLANLSQAGYKKIEVLFTNDLDHGAYISDTL 350

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 351  RADSTVDRLSALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 410

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + + DII +++ L+D+RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 411  DNDEGAGVLDETDIIEVMRKLIDIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 470

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 471  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 530

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA+ N YGF+ETPY
Sbjct: 531  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAFAQCNEYGFLETPY 590

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG+VT+ V YLSA+EE    IAQAN+ L E+G+F +EL+  R  GE  L PRE I 
Sbjct: 591  RRVVDGQVTDQVDYLSAIEEGTFVIAQANAVLTEEGTFADELIIARQKGESGLHPREHIQ 650

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 651  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 710

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 711  SGVTAVAKRGGVVQSVDASRIVIKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 770

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 771  LPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 830

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 831  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 890

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 891  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 950

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 951  QLKEAKKDITEEFQILEGGLLARVRTLLVAAGV-------------SEVKLDAMDRKQWL 997

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 998  EITLDDEAQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1057

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1058 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMG 1117

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R+FL+KV   G   +   I+   DD V  + +  
Sbjct: 1118 LAAKGVGDKINQML---KEQQELHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLIKNL 1174

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1175 RGGLPIATPIFDGAPEASIKELLKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLN 1234

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1235 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1294

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1295 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDEE 1341


>gi|254672709|emb|CBA06638.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            alpha275]
          Length = 1392

 Score = 1628 bits (4216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   S +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDISGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|241760439|ref|ZP_04758533.1| DNA-directed RNA polymerase, beta subunit [Neisseria flavescens
            SK114]
 gi|241319108|gb|EER55601.1| DNA-directed RNA polymerase, beta subunit [Neisseria flavescens
            SK114]
          Length = 1409

 Score = 1628 bits (4216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 18   MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 77

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 78   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 135

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 136  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 195

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 196  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 255

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 256  NGVQTDLIAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPEN 313

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L ++    +++I  LY++ ++   YI +TL
Sbjct: 314  LIGKALAVDLIDPETGEVLASANDEITEELLAKLDIHGVKEITTLYINELDQGGYISSTL 373

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 374  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 433

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 434  QKLSEAQQNSWYGRLLNETLAGVAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 493

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 494  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 553

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 554  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 613

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 614  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 673

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 674  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 733

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 734  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 793

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 794  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 853

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 854  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 913

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 914  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 973

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 974  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1033

Query: 1001 GFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++    +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1034 KLAKGSEITTEYLASLSSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1093

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1094 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1153

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+  + 
Sbjct: 1154 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNSS 1210

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1211 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1270

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1271 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1330

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1331 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1390

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1391 NVLVKEIRSLGLDIDLER 1408


>gi|218767181|ref|YP_002341693.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis
            Z2491]
 gi|9910857|sp|P57009|RPOB_NEIMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|121051189|emb|CAM07460.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis Z2491]
 gi|319411386|emb|CBY91797.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit;
            transcriptase beta chain; RNA polymerase beta subunit)
            [Neisseria meningitidis WUE 2594]
          Length = 1392

 Score = 1628 bits (4215), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1398 (49%), Positives = 958/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|124268635|ref|YP_001022639.1| DNA-directed RNA polymerase subunit beta [Methylibium petroleiphilum
            PM1]
 gi|158512810|sp|A2SLG5|RPOB_METPP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|124261410|gb|ABM96404.1| DNA-directed RNA polymerase [Methylibium petroleiphilum PM1]
          Length = 1375

 Score = 1628 bits (4215), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1380 (50%), Positives = 976/1380 (70%), Gaps = 19/1380 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FGK   ++ +P L+ +QK SY  FL  ++ P +R  EGLQAA
Sbjct: 1    MAQATPYSYTERKRIRKSFGKRENVLGVPYLLTMQKDSYVAFLQKDVPPQKRKPEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F S FPI + +G   ++++ +    P FD  +C  R LTYA  ++  L++I++D +  T 
Sbjct: 61   FLSAFPIVSHNGFVEMKYIEFNMAKPAFDTRECQQRGLTYAAAVRAKLQMIIYDRETSTS 120

Query: 119  -AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K+IKEQ +YMG++PLMT  G+F++ G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEIKEQEVYMGEVPLMTDYGSFIVNGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E+IL+ F+    
Sbjct: 181  LLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPEQILANFFVFDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +            A D + G      L D   G  ++E  K++T+   ++L+  G  F+ 
Sbjct: 241  FRLMDSGAQMEFVA-DRLRGEIARFDLTD-KAGAVIVEKDKRITARHTRALEASGTSFIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  +A+++V+ +TGEI  +A D + +  L+++  + I+DI  LY + ++  AY
Sbjct: 299  VPEDFLVGRVLAKNMVDADTGEIIAKANDELTDSLLKKLRTAGIKDIQCLYTNELDMGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL +D+  D   A + IYR+MRPG+  T    +++FN LF+  D YDLS VGR+K N
Sbjct: 359  ISQTLASDETADELAARVAIYRMMRPGEPPTEDAVQALFNRLFYSEDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             R+  DT +    +  +DI+ ++KILV+LRNG+G +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  ARVGRDTAEGRMVLANDDILDVVKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQYRS 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + +++MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH
Sbjct: 479  GLARIEKAVKERLGQAETEALMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A++N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAQLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +ETPYR+V D KVT+ + YLSA+EE    IAQAN+ LD+DG   +ELV  R +GE +L  
Sbjct: 599  LETPYRRVIDSKVTDQIDYLSAIEEGKYVIAQANAGLDKDGKLIDELVSARESGESVLTS 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E+I ++D +P Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E  FVGTG+E 
Sbjct: 659  PERIQYMDVAPTQIVSVAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKAFVGTGVER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + AKR G+V+ +D  RIVIR  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VSAVDSGTVVTAKRGGVVDYIDTNRIVIRVNDAETVAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+V+ GD+V   D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V++D
Sbjct: 779  QRPIVQRGDQVGAGDVIADGASTDIGELALGQNMLVAFMPWNGYNFEDSILISERVVADD 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GI+ +GAEVNPGD+LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGSEEITRDIPNLSEQQLGRLDESGIVYIGAEVNPGDVLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G +GTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGTNGTVIDVQVFTREGIQRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP    K T +    ++   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLAGKTANGGPNKLAKGTPIDKAYLASVD 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     D+ +   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KYHWFDIRPADDDIANQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMNVGQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPCDIVLNPLGVPSRMNVGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRV 1196
            E HLGWA  G+G++I  L+   +    I+ +R FL+++   +G  +E ++   D  +  +
Sbjct: 1139 EVHLGWAAKGIGQRIGDLL---QQEAKIADVRKFLDELYNKSGGKSEGLNGLSDAEITEM 1195

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFD 1246
            A     GVP +TPVFDGA EE I +M+ +A  DE            Q+ L+DG TG+ F+
Sbjct: 1196 ATNLAQGVPFATPVFDGATEEEIRAMMHLAYPDEIAAAKGLNATRTQATLHDGRTGDAFE 1255

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1256 RPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1315

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNVLVKE+++LG+ I+LE +
Sbjct: 1316 ASYVLQEMLTVKSDDVNGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGIDIELERN 1375


>gi|269214076|ref|ZP_06158337.1| DNA-directed RNA polymerase, beta subunit [Neisseria cinerea ATCC
            14685]
 gi|269144581|gb|EEZ70999.1| DNA-directed RNA polymerase, beta subunit [Neisseria cinerea ATCC
            14685]
          Length = 1425

 Score = 1628 bits (4215), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 34   MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 93

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 94   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 151

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 152  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 211

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 212  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 271

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A+ L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 272  NGVQTDLIASRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 329

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L ++    +++I  LY++ ++   YI +TL
Sbjct: 330  LIGKALAADLIDPETGEVLASANDEITEELLAKLDIHGVKEITTLYINELDQGGYISSTL 389

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 390  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 449

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 450  QKLSEAQQNSWYGRLLNETLAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 509

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 510  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 569

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 570  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 629

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 630  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 689

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 690  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 749

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 750  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 809

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 810  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 869

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 870  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 929

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 930  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 989

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 990  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1049

Query: 1001 GFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++    +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1050 KLAKGSEITTEYLASLSSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1109

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1110 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1169

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1170 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1226

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1227 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1286

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1287 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1346

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+YE+IV G    + G PESF
Sbjct: 1347 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTRMYENIVKGEHKIDAGMPESF 1406

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1407 NVLVKEIRSLGLDIDLER 1424


>gi|332037824|gb|EGI74274.1| DNA-directed RNA polymerase beta subunit [Pseudoalteromonas
            haloplanktis ANT/505]
          Length = 1341

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1364 (51%), Positives = 963/1364 (70%), Gaps = 23/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+  Q  S+  FL     PD   + GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLDIPFLLSTQLESFKKFL----VPDADGDHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V D +      ++
Sbjct: 57   FPIKSYSGNSELQYVSYRIGEPVFDVKECQIRGVTYSAPLRVKLRLVVMDKEAPG---TV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FD+D+G+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDNDRGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++VRIDRRRK+P +  L AL   SEEIL  F+    +    
Sbjct: 174  RVIPYRGSWLDFEFDAKDNLYVRIDRRRKLPASIILRALEYSSEEILDMFFDNTTFEVTN 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L  + L  G   +  +   + GE  +ESG+++T+  +KS+++KG+K L +  + 
Sbjct: 234  GKVLMELVPSRL-RGETAAFDI-KSEDGEVFVESGRRVTARHIKSIEKKGIKQLEVPHEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA++ V+  TGE+   A D +  + + E+  +    I  LY++ V++ AY+ NTL
Sbjct: 292  IIGRIVAKNYVDESTGEVIANANDELTLELMAELVKAGHTKIDTLYINEVDSGAYMSNTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +  R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N R+  
Sbjct: 352  NIDSSSSRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSTVGRMKFNSRVGY 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            DT      + KEDI++++K+L+ +RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DTDTGPGTLSKEDIVSVMKVLIAIRNGQGDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLSTYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQANS+L E   F +EL+ CR  GE   + R    
Sbjct: 592  RKVVDGVVTDEVDYLSAIEEGQFVIAQANSNLTETNEFVDELIPCRHKGESTFMGRMDQQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +AK 
Sbjct: 652  YMDVSPQQVISVAAALIPFLEHDDANRALMGSNMQRQAVPTLKADKPLVGTGIELTLAKD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G V   DA RIV+   E +  P  +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 712  SGVTIVAKRGGEVMYADASRIVVNVHEEERIPGEAGIDIYNLTKYTRSNQNTCINQKPTC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMPWNGYNFEDSILLSERVVEEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLGPEEIT DIPNV E  L  +DE G++ + AEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCVARDTKLGPEEITADIPNVGESALGKLDESGVVYISAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R++ VE  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRALEVEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D ++E  IL+  +  R  ++L                    D ++     +  
Sbjct: 952  QLREAKKDFNEEFRILEAGVLDRARKLLIAAG-------------FDEDKLASLNAEKVL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ +E  Q  +E L  QY+  K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  TQSLAEEDKQAELEQLAAQYDELKAEYDKKFENKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+   G  VDIVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPVEDMPYDDKGRTVDIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G++I+ ++ + +   ++        ++ G       I+ + DD + R+AE  K 
Sbjct: 1119 LAARGIGERIEEMMKEQRELHELREFIKQAYEI-GESRQVVDIASFTDDEIRRLAENLKG 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E  I  ML +     SGQ  LYDG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1178 GLPIATPAFDGAKESEIKDMLELGGYPRSGQVTLYDGRTGDQFERQVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE +
Sbjct: 1298 NGRTKMYKNIVDGNHKMEPGMPESFNVLLKEIRSLGINIELEEN 1341


>gi|304388932|ref|ZP_07370979.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis ATCC
            13091]
 gi|304337066|gb|EFM03253.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis ATCC
            13091]
          Length = 1392

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 955/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|90413408|ref|ZP_01221401.1| DNA-directed RNA polymerase beta subunit [Photobacterium profundum
            3TCK]
 gi|90325650|gb|EAS42119.1| DNA-directed RNA polymerase beta subunit [Photobacterium profundum
            3TCK]
          Length = 1341

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1366 (50%), Positives = 960/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPRVLDAPYLLSIQLDSFQKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+  +  L AL   +E+IL  F+ K+ +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLAASVILRALDYTTEQILDMFFDKVSFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +     G+  +E G+++T+  ++ L + GV  + +  + 
Sbjct: 235  KSLVMELVPERL-RGETASFDIE--ANGKVYVEQGRRITARHIRQLGKDGVDQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN ETGE+   A   +  ++L  +  +  + I +L+ + ++   Y+  TL
Sbjct: 292  IVGKISSRDYVNEETGELIAAANQELSLETLALLSQAGHKSIEVLFTNDLDYGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +FN LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDSTTDRLSALVEIYRMMRPGEPPTREAAEQLFNSLFFSEDRYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +   DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EETTGSGILDHSDIIEVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N+YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVYARCNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+ + YLSA+EE    IAQAN++L+ DGSF++EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDGKVTDQIDYLSAIEEGQYVIAQANAALETDGSFSDELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERSVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+N+ +AFMPW+GYNFEDS+L+SER+V +D  T+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNIRIAFMPWNGYNFEDSILVSERVVQQDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S + I+   R + +
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLLSIG-------------YSEEKIASMDRERLF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ALTLDDESLQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  V+IVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKICPVEDMPYDEKGQTVEIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL+KV   G    T  I+   D  V  + +  
Sbjct: 1119 LAAKGIGDKLNEML---KQQQELHKFRNFLQKVYDLGDTRQTVDIAALSDAQVHTLIQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL ESGQ  ++DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RDGLPIATPVFDGAPEASIKELLKLGDLPESGQLKMFDGRTGDMFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|319775564|ref|YP_004138052.1| RNA polymerase subunit beta [Haemophilus influenzae F3047]
 gi|317450155|emb|CBY86369.1| RNA polymerase, beta subunit [Haemophilus influenzae F3047]
          Length = 1342

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1367 (51%), Positives = 971/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKENEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  +K+L++  +  + + S+ 
Sbjct: 235  DKLLMTLVPERL-RGETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D V+ E+GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL
Sbjct: 292  ILGKVASKDYVDLESGEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL +IYR+MRPG+  T   +E +FN LFF +++YDLSTVGR+K N  L  
Sbjct: 352  RVDPTYDKTSALYEIYRMMRPGEPPTPESSEVLFNNLFFSAERYDLSTVGRMKFNRSLAF 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDIIA+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGAGILSNEDIIAVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLS ++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I
Sbjct: 592  RKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L    A              +  +    R++W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFARVRHLLISSGA-------------DAAQLDNLDRAKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I +++   K   ++  LR +++K    G GS    +S + D+ VLR+AE 
Sbjct: 1119 GLAAKGIGDQINAML---KQKQEVEKLRGYIQKAYDLGNGSQKVDLSTFTDEEVLRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+PV+TPVFDGADE  I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPVATPVFDGADEAEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV+GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1296 DDVNGRTKMYKNIVSGNQHMDPGTPESFNVIMKEIRSLGLNIELDEE 1342


>gi|261391669|emb|CAX49117.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit;
            transcriptase beta chain; RNA polymerase beta subunit)
            [Neisseria meningitidis 8013]
          Length = 1392

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|78099464|gb|ABB20868.1| RNA polymerase subunit B [Acinetobacter tjernbergiae]
          Length = 1362

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1374 (51%), Positives = 969/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L ALG  + +IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVILRALGYANAQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      + D D G+ ++E GK++    ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDIADND-GKVIVEQGKRINVRHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   +   I   A  ++  + + ++    ++   IL+ + ++  ++I ++L
Sbjct: 295  LYERITAEDITLKDGDVI--PANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFIADSL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S +D+DG+ TEE+   R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSGVDKDGNLTEEMASVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIADRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS+D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLTGQESNGG-GSTKRGDKLSADVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPTDEAIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E++    D  V
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEV 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|325127126|gb|EGC50080.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            N1568]
          Length = 1392

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|33152866|ref|NP_874219.1| DNA-directed RNA polymerase subunit beta [Haemophilus ducreyi
            35000HP]
 gi|41017666|sp|Q7VKL7|RPOB_HAEDU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|33149091|gb|AAP96608.1| RNA polymerase beta subunit [Haemophilus ducreyi 35000HP]
          Length = 1342

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1367 (51%), Positives = 972/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++++P L+ +Q  SY+ F+  ++       +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIHRDLD----GQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVAFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEIL+ F+ K+++  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILTMFFEKVLFEIQD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +++L++ G+  + +  + 
Sbjct: 235  NKLLMILVPERL-RGETAAFDIE--ANGKIYVERGRRITARHIRTLEKDGITQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+  TGE+   A   I    L ++  +  +++ +L+ + +++  YI  TL
Sbjct: 292  IVGKVAAKDYVDLSTGELVCPANTEISMDMLAKLSQAGYKELEVLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  LN+
Sbjct: 352  RVDSTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAVGRMKFNRSLNI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI  ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGTGILTNDDITGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGITPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
             KV +G+VT ++ YLSA+EE N  +AQANS+LDE   FT+  V CR   GE  L   E I
Sbjct: 592  HKVVNGQVTEEIEYLSAIEEGNYVVAQANSNLDEHFRFTDTYVTCRGEHGESGLYKPEDI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG AIVAKR GI+++VDA RIV++  E +  P  +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAIVAKRGGIIQRVDASRIVVKVNEDETIPGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VNLGEPVARGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R  ++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDSVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L               + +S   ++   R +W
Sbjct: 952  MQLREAKKDLTEELEILEAGLFTRVRNLLI-------------ESGVSEVNLNNVAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E      E + + K  KI  GDD+ PGVL+VVKV++A++
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELCKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVR 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGEPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K   +++ LR +++K    G GS    +S + D+ V+R+A+ 
Sbjct: 1119 GLAARGIGDQINAMI---KQQQEVTKLREYIQKAYDLGHGSQVVDLSTFTDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  L+DG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHEAEIKGLLELGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNVL+KE++ALG+ ++L+  
Sbjct: 1296 DDVNGRTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDED 1342


>gi|261854943|ref|YP_003262226.1| DNA-directed RNA polymerase subunit beta [Halothiobacillus
            neapolitanus c2]
 gi|261835412|gb|ACX95179.1| DNA-directed RNA polymerase, beta subunit [Halothiobacillus
            neapolitanus c2]
          Length = 1388

 Score = 1627 bits (4214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1392 (49%), Positives = 952/1392 (68%), Gaps = 30/1392 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG   +I+ +P L+  Q  SY  FL   +    R N GL AA  SV
Sbjct: 1    MSYSFTEKKRIRKEFGHRADILPVPYLLATQVESYKSFLQSGVPAKGRTNAGLHAALSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A + +V Y F  P FDV +C  R L+Y  PL++ +RL+++D D   G+K +
Sbjct: 61   FPIRSHSGNAEIAYVDYYFGEPAFDVRECQIRGLSYGAPLRVKMRLVIYDRDAPAGSKVV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +Y+G++PLMT+ GTFVI G +R++VSQLHRSPG+ FDHDKG+ S S K+L++ 
Sbjct: 121  KDIREQDVYLGEIPLMTESGTFVINGTERVIVSQLHRSPGVFFDHDKGKTSSSKKILFSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ RIDRRRK+P +  L ALG  ++ +L  F+    +    
Sbjct: 181  RIIPYRGSWLDFEFDQKDILYARIDRRRKIPASIILRALGYTNQNMLDIFFDHDEFHIDK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D        AD + G   +  +     GE +I++GK++T+  ++ L    V  L +  D 
Sbjct: 241  DGGLALTLVADRLKGTDAAFDIDI--NGENLIKTGKRITARHVRELVAAKVTSLPVPVDF 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A D+++  TGE+  +  + +  + + ++  + I     LY + V+   ++  TL
Sbjct: 299  VVGRVLASDVIDTSTGEVLAQGNEELTTELVAKLAKAGITQFKTLYFNDVDRGPFMSLTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D +    +A+++IY++MRPG+  T   AE++F+ LFF  D+YDLS VGR+K N R+  
Sbjct: 359  RADPSTTPLEAMVEIYKMMRPGEPPTKDSAEALFHGLFFTEDRYDLSEVGRMKFNRRIER 418

Query: 423  DTPDDVRHIRKEDIIAI-------------------------IKILVDLRNGKGTIDDID 457
            +       +                                 +K L+D+RNG G  DDID
Sbjct: 419  EGDVGPGVLYDGKYFTTRAAQGDEAAKQLLKEQGGVSDILDVMKELIDIRNGNGKTDDID 478

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            +LGNRR+RSVGEM +N +R+GL+R+ER++KER++  + + + PQDLINAKPV +A+ EFF
Sbjct: 479  HLGNRRIRSVGEMTENVFRIGLVRVERAVKERLTQAESEGLTPQDLINAKPVAAAIKEFF 538

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG
Sbjct: 539  GSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEG 598

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL ++AR N YGF+ETPYR V DG V+ +V +LSA EEE   IAQAN+ LD++
Sbjct: 599  PNIGLINSLATYARTNGYGFLETPYRTVKDGVVSKEVDWLSAYEEEKFTIAQANAPLDDN 658

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G     L+  R AGE +L   E+I ++D SPKQ+VSIAAS+IPFLE+DD+NR LMG NMQ
Sbjct: 659  GVLQGNLISVRRAGEFMLASPEEIQYMDVSPKQIVSIAASIIPFLEHDDANRALMGSNMQ 718

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+A+ P VGTGME VVA  SG+ +VA+R G+V++VDA R+V+R    +      
Sbjct: 719  RQAVPTLRADKPLVGTGMERVVATDSGSCVVARRGGVVDRVDAARVVVRVNAEEASQGDV 778

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L K+ RSNQNTC+NQ PLVK GD + + D++ADGPS D+G+LALG+N+L AFMP
Sbjct: 779  GVDIYNLTKYTRSNQNTCINQTPLVKAGDVIAKGDVLADGPSVDMGELALGQNILCAFMP 838

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYNFEDS+L+SER+V ED  T+IH+EE   +ARDTKLG EEIT DIPNV+E  L  +D
Sbjct: 839  WNGYNFEDSILLSERVVREDRLTTIHVEELNCIARDTKLGAEEITADIPNVAESLLNKLD 898

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
              G++ VGAEV PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP G+ G
Sbjct: 899  AAGVVHVGAEVRPGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPPGMEG 958

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DVR+F R GI+K+ R+ ++E   +E + +D  D   I++ +I +R+  +L  Q AV 
Sbjct: 959  TVIDVRVFTRDGIEKDSRARAIEEADLEAVRKDLKDRMRIIEGDILARVKSVLVNQVAVG 1018

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            GP G K  + +++  + +   S+W +  V+ E+  + +E    Q   ++  ++ RF++K 
Sbjct: 1019 GP-GVKAGSKITAAQLEKIEPSKWLEIRVEGEEAAQAMEEYIAQLAQAQVDIDKRFEDKK 1077

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +KIQ GDD+ PGVL++VKV+VA+KR IQ GDK+AGRHGNKG+VS I+P EDMP++++G P
Sbjct: 1078 KKIQQGDDLAPGVLKMVKVYVAVKRRIQPGDKLAGRHGNKGVVSMIVPEEDMPYMENGQP 1137

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI LNPLGVPSRMN+GQI ETHLG+A  GLG KI+ ++   +A   I  LR+FL+KV  
Sbjct: 1138 VDICLNPLGVPSRMNIGQILETHLGFAARGLGVKIEEMLKLERAKALI-ELRAFLDKVYN 1196

Query: 1178 -TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +    DD ++ +A   K GVP++TPVFDGA E+ I  ML +A L  SGQ  L
Sbjct: 1197 YKSDKPVDLDALSDDELIELARNLKKGVPMATPVFDGAVEDEIKYMLELAGLPTSGQVQL 1256

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG +GEPF+R  TVGY+YMLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1257 YDGRSGEPFERTTTVGYMYMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1316

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G+   + G PESFNVL+KE+++
Sbjct: 1317 MEVWALEAYGAAYTLQEMLTVKSDDVNGRNKMYKNIVDGDLKMDAGMPESFNVLLKEIRS 1376

Query: 1357 LGLSIDLENSRT 1368
            L ++++LE  + 
Sbjct: 1377 LAINVELEQGKE 1388


>gi|91791532|ref|YP_561183.1| DNA-directed RNA polymerase, beta subunit [Shewanella denitrificans
            OS217]
 gi|123166591|sp|Q12SW6|RPOB_SHEDO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91713534|gb|ABE53460.1| DNA-directed RNA polymerase, beta subunit [Shewanella denitrificans
            OS217]
          Length = 1343

 Score = 1627 bits (4213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 960/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR+++FD +   G  ++
Sbjct: 57   FPIKSFSGYSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +++IL  F+ +I +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIMLRALEYSTQDILDLFFERIQFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L   D + G   S  +   D G  ++E+G+++T+  +K L++     L +  D 
Sbjct: 235  DSLVMALVP-DRLRGETASYDIKAAD-GSVLVEAGRRITARHIKQLEQSNTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A + I  + L ++  + I++I  L+++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDEDTGEVLVSANNEISLEDLAKLSIAGIKEIDTLFINDLDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL +
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLEI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + K+DI+ ++K ++++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  AEDEGNGVLSKDDIVCVMKKIIEIRNGYDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G +T++V YLSA+EE    IAQAN  +D  G   EE + CR  GE   +    I 
Sbjct: 593  RKVVEGVITDEVEYLSAIEEGRYVIAQANIEVDSTGRMVEEQIACRHKGESTFMRAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGVVDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  FVGEPVVRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRALEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +    +D  +E  IL+  + SR   +L                  S   ++E PR    
Sbjct: 953  HVAQARKDLGEEFKILEEGVLSRARNLLLSAG-------------YSEAKLAELPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 IQVIDDEAKQTELEQLAEQHEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPVEDMPYDEEGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD V+R+A   K 
Sbjct: 1120 AAAKGIGNKITAMLEEQREIAELRGYIKQVYELGDDVLQRVDIDSFSDDEVVRLATHLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L ESGQ  L DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKQMLALAGLPESGQLTLCDGRTGNEFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1343


>gi|319791335|ref|YP_004152975.1| DNA-directed RNA polymerase, beta subunit [Variovorax paradoxus EPS]
 gi|315593798|gb|ADU34864.1| DNA-directed RNA polymerase, beta subunit [Variovorax paradoxus EPS]
          Length = 1374

 Score = 1627 bits (4213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1379 (50%), Positives = 969/1379 (70%), Gaps = 18/1379 (1%)

Query: 1    MAKG--VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
            MA+     +    R+RK FG    +++IP L+++QK +Y  FL   IAP +R  EGLQAA
Sbjct: 1    MAQSSAYSYTERKRIRKSFGNRDSVVEIPYLLQMQKDAYTAFLQAGIAPKQRTVEGLQAA 60

Query: 59   FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
            F + FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T 
Sbjct: 61   FDAAFPIVSHNGFVEMKFLEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTS 120

Query: 119  -AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +K +K++KEQ +YMG++PLMT+ G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGK
Sbjct: 121  QSKVVKEVKEQEVYMGEVPLMTEKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGK 180

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G++ E IL+ F+    
Sbjct: 181  LLFSARVIPYRGSWLDFEFDPKDMLYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDN 240

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +            +  L  G      + D  +G+ V+   K++T+   + L++ G   + 
Sbjct: 241  FRLMDSGAQMEFVSERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTTHIS 298

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  D L G  +A +IV+ ++GEI  +A D + E  L+++  + ++DI ++Y + ++  AY
Sbjct: 299  VPEDFLVGRVIARNIVDADSGEILAKANDELTEALLKKLRTAGVQDIQVIYTNELDQGAY 358

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I  TL  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N
Sbjct: 359  ISQTLRIDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFN 418

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             ++  D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR 
Sbjct: 419  AKVGRDESTGPMVLTNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRT 478

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL R+E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH
Sbjct: 479  GLARIEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGF
Sbjct: 539  KRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR+V D KVTN++ YLSA+EE    IAQAN++LD+DG  T +LV  R AGE ILV 
Sbjct: 599  IETPYRRVVDSKVTNEIDYLSAIEEGKYVIAQANAALDKDGVLTGDLVSAREAGESILVG 658

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E+I ++D SP Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E P VGTG+E 
Sbjct: 659  AERIQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKPMVGTGIER 718

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V A  SG  + A R GIV+ VDA R+V+R  + +      GVDIY L+K+QRSNQNT ++
Sbjct: 719  VSAVDSGTVVTASRGGIVDYVDATRVVVRVNDAEAAAGEVGVDIYNLIKYQRSNQNTNIH 778

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRP+VK GD++ + D+IADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V+ED
Sbjct: 779  QRPIVKRGDKIAKGDVIADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVAED 838

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +TSIHIEE  VMARDTKLG EEITRDIPN++E+ L  +DE GII VGAEV PGD LVGK
Sbjct: 839  RYTSIHIEELVVMARDTKLGAEEITRDIPNLAEQQLNRLDESGIIYVGAEVQPGDTLVGK 898

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+ 
Sbjct: 899  VTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGITRDKRAQ 958

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  ++++    D +D+  I++ + + R+ ++L G+ A  GP    K T L    +S   
Sbjct: 959  QIIDDELKRFRLDLNDQLRIVEADAFDRIEKLLTGKVANGGPNKLAKGTKLDKAYLSSVE 1018

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +  W+     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV+
Sbjct: 1019 KFHWFDIRPAEDEVATQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVY 1078

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP + DGTP DI LNPLGVPSRMNVGQ+ 
Sbjct: 1079 LAVKRRLQPGDKMAGRHGNKGVVSKIVPVEDMPHMADGTPCDICLNPLGVPSRMNVGQVL 1138

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGWA  G+G++I  ++   +    ++ +R F+E++       E +S   D  VL +A
Sbjct: 1139 EVHLGWAGKGIGQRIGDML---QQEAKVAEVRKFMEQLYNGSGRPEDLSQLSDTDVLAMA 1195

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDR 1247
               +SG   +TPVFDGA EE I  ML++A            D   Q+ LYDG +G+ F+R
Sbjct: 1196 ANLQSGATFATPVFDGASEEEIRGMLKLAYPDDIAKLKGLTDTRTQAYLYDGRSGDQFER 1255

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1256 PVTVGYMHFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1315

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AYVLQEMLT+KSDDV GRT+VYESIV G  + E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 AYVLQEMLTVKSDDVQGRTKVYESIVKGEHSIEAGMPESFNVLVKEIRSLGLDIELERS 1374


>gi|290082953|gb|ADD22985.1| RNA polymerase subunit B [Acinetobacter sp. BM-8]
          Length = 1362

 Score = 1627 bits (4212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1374 (51%), Positives = 975/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVILRALNFSNEQILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADSD-GKAIVEQGKRINARHVRQMEASGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    +AED+V  + GE    A  V++ + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERIIAEDVVLRD-GETIA-ANTVLNHEIMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR++AL++IY+VMRPG+  T   A+++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADLTRDREEALVEIYKVMRPGEPPTKEAADNLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DI+ ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGNDQKSREVECILSNDDIVDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+   + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLGQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANH 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA++++D D +FTEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADATVDADNNFTEEFVSVRHQGESV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G++E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGMIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R GI+K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGIEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L  Q +  G    K+   L+ DL+S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKDQQSNGG-GNTKRGDKLTEDLLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 HLALVDLLEIQPNDEAIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   K    I+ LR FL+K+    G   E++    DD +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMV---KQQRTIAELREFLDKIYNKVGGEQEQLDTLTDDEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            +++A   ++GVP++TPVFDGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 MKLAGNLRAGVPLATPVFDGAEEGQIKELLELAELPRSGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|119468175|ref|ZP_01611301.1| DNA-directed RNA polymerase beta chain [Alteromonadales bacterium
            TW-7]
 gi|119448168|gb|EAW29432.1| DNA-directed RNA polymerase beta chain [Alteromonadales bacterium
            TW-7]
          Length = 1341

 Score = 1627 bits (4212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1364 (51%), Positives = 965/1364 (70%), Gaps = 23/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+  Q  S+  FL     PD   + GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLDIPFLLSTQLESFKKFL----VPDADGDHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+V D +      ++
Sbjct: 57   FPIKSYSGNSELQYVSYRIGEPVFDVKECQIRGVTYSAPLRVKLRLVVMDKEAPG---TV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FD+D+G+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDNDRGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++VRIDRRRK+P +  L AL   SEEIL  F+    +    
Sbjct: 174  RVIPYRGSWLDFEFDAKDNLYVRIDRRRKLPASIILRALEYSSEEILDIFFDTTAFEVAD 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L  + L  G   +  +   D GE ++ESG+++T+  +KS+++KG+  L +  + 
Sbjct: 234  GKVLMELVPSRL-RGETAAFDIKGED-GEVLVESGRRVTARHIKSIEKKGITQLEVPHEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  ++++ V+  TGE+   A D +  + + E+  +    I  LY++ V++ AY+ NTL
Sbjct: 292  IIGRIISKNYVDESTGEVIANANDELTLELMAELVKAGHTTIDTLYINEVDSGAYMSNTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N R+  
Sbjct: 352  NIDSSSNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSTVGRMKFNSRVGY 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D+      + KEDI++++K+L+ +RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DSDTGPGTLSKEDIVSVMKVLIAIRNGQGDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLSTYARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQANS+L E   F +EL+ CR  GE   + R    
Sbjct: 592  RKVVDGVVTDEVDYLSAIEEGQFVIAQANSNLTETNEFVDELIPCRHKGESTFMGRMDQQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +AK 
Sbjct: 652  YMDVSPQQVISVAAALIPFLEHDDANRALMGSNMQRQAVPTLKADKPLVGTGIELTLAKD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G V   DA RIV+   E +  P  +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 712  SGVTIVAKRGGEVMYADASRIVVNVHEEERIPGEAGIDIYNLTKYTRSNQNTCINQKPTC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMPWNGYNFEDSILLSERVVEEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLGPEEIT DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCVARDTKLGPEEITADIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R++ VE  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRALEVEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D ++E  IL+  +  R  ++L                    + +      +  
Sbjct: 952  QLREAKKDFNEEFRILEAGVLERARKLLVAAG-------------FDENNLVSLNAEKLL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ +E  Q  +E L  QY+  K+  + +F+NK  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  TQSLAEEDKQAELEQLAAQYDELKAEYDKKFENKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+   G  VDIVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPVEDMPYDDKGRTVDIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G++++ ++ + +   ++        ++ G       I+ + DD + R+AE  K 
Sbjct: 1119 LAARGIGERLEEMMKEQRELHELREFIKQAYEI-GESRQVVDIASFSDDEIRRLAENLKG 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +     SGQ  LYDG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1178 GLPIATPAFDGAKEDEIKDMLELGGYPRSGQVTLYDGRTGDQFERQVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE +
Sbjct: 1298 NGRTKMYKNIVDGNHKMEPGMPESFNVLLKEIRSLGINIELEEN 1341


>gi|325137190|gb|EGC59785.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M0579]
          Length = 1392

 Score = 1627 bits (4212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTKEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|89075377|ref|ZP_01161799.1| DNA-directed RNA polymerase beta subunit [Photobacterium sp. SKA34]
 gi|89048926|gb|EAR54495.1| DNA-directed RNA polymerase beta subunit [Photobacterium sp. SKA34]
          Length = 1341

 Score = 1627 bits (4212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1366 (51%), Positives = 959/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDAPYLLSIQLDSFQKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +E+IL  F+ KI +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPASIILRALNYTTEQILDMFFDKINFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S ++     G   +E G+++T+  ++ L + G+  + +  + 
Sbjct: 235  KSLVMELVP-DRLRGETASFNIE--ANGTVYVEQGRRITARHIRQLGKDGIDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D +N ETGE+ + A   +  ++L  +  +  + I +L+ + +++  Y+ +TL
Sbjct: 292  IVGKIASRDYINEETGELIVAANQELSLEALALLSQAGHKSIEVLFTNDLDHGPYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RIDNTTDRLSALVEIYRMMRPGEPPTREAAEQLFESLFFSEDRYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       +   DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DETTGPGILDHADIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVFARCNPYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+D+ YLSA+EE    IAQAN++L+EDGSF +EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDGKVTDDIEYLSAIEEGLYVIAQANAALNEDGSFADELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP ++A+ P VGTG+E  +   
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTIRADKPLVGTGIERQIGVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  + +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGTVQSVDASRIVIKVNDDELIPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP  V+GT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPGSVTGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                    D I+   R   +
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLLSAG-------------YGEDKIASMNRDALF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A++R
Sbjct: 999  AVTLDDEALQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVRR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQTVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG--TGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL++V           I    D  V  + +  
Sbjct: 1119 LAAKGIGDKLNDML---KEQQELHKFRNFLQRVYNLGDTRQKVDIEALTDQEVRTLVQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPIATPVFDGAPESSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|323498403|ref|ZP_08103400.1| DNA-directed RNA polymerase subunit beta [Vibrio sinaloensis DSM
            21326]
 gi|323316545|gb|EGA69559.1| DNA-directed RNA polymerase subunit beta [Vibrio sinaloensis DSM
            21326]
          Length = 1342

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1367 (51%), Positives = 973/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ KI +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKINFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  +SL  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINEATGEIIVGANQEISLESLANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDELDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E+G+F+EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEEGTFSEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YTEAKLDTIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLEDDAQQSQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +++  R FL+KV   G       ++   DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELAKFRDFLQKVYDLGDTRQKVDVASLTDDEVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E++I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEQSIKELLKLGDLPESGQLKLFDGRTGDEFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|50083579|ref|YP_045089.1| DNA-directed RNA polymerase subunit beta [Acinetobacter sp. ADP1]
 gi|81393894|sp|Q6FF90|RPOB_ACIAD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|49529555|emb|CAG67267.1| DNA-directed RNA polymerase beta chain (Transcriptase beta chain)
            (RNA polymerase beta subunit) [Acinetobacter sp. ADP1]
          Length = 1362

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1374 (51%), Positives = 974/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  SY  FL    +P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPSVMDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYGLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  +  L ALG ++ +IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLASVILRALGYNNAQILDLFYEKVPVYLDF 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRINARHVRQMEASGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + G++   A  ++  + + ++    ++   ILY + +++ +++ +TL
Sbjct: 295  LYERITAEDITLRD-GDVIA-ANTLLSHEIMVKLAEGGVKQFNILYTNDIDHGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R+DAL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTMGREDALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+V++DV YLSA+EE    IAQA+S++D DG   EE+V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVSDDVEYLSAIEEVGTVIAQADSAVDADGHLMEEMVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G++E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAKRGGMIEFVDASRVVIRVNEEEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDD 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RALAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLNGQESNGGGTT-KRGDKLSDDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLDIQPTDEGIAERLSQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++   +    I+ LR FL+K+    G   E++    D+ +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMLQQQRT---IAELRIFLDKIYNKVGGEQEELDTLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +A   + GVP++TPVFDGA+E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY
Sbjct: 1189 LVLAGNLRKGVPLATPVFDGAEEGQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|18496615|gb|AAL74153.1|AF426390_1 RNA polymerase beta subunit [Xanthomonas campestris pv. campestris]
          Length = 1383

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1389 (50%), Positives = 966/1389 (69%), Gaps = 35/1389 (2%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3    SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63   PISSYSGNAALEYVGYKLGEPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             +KEQ +Y+G++PLMT++GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121  YVKEQEVYLGEIPLMTENGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG ++EE+L+ F+    +    D
Sbjct: 181  IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPD 240

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                     + + G  ++  L D D  + ++E+GK++T+  +K L+   V  L +  D L
Sbjct: 241  EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAAVAALAVPDDYL 298

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G  ++ D+V+G TGE+   A D I E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299  VGRILSHDVVDGSTGELLANANDEISEDQLAAFRKAGVDAVATLWVNDLDRGPYLSNTLR 358

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359  IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424  TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                   +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419  EVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479  RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539  LSQFMDQNNPLSEVTHKRRSSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599  LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E+ V CR  GE +L    ++ F+D SP Q VS+ A+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659  EQFVPCRFQGESLLNAPAEVHFMDVSPMQTVSVPAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
            P L+++ P VGTG+E  VA+ SG  + A+R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719  PTLRSQKPLVGTGIERAVARDSGVTVNARRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779  IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839  YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+
Sbjct: 899  VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVI 958

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  GP 
Sbjct: 959  DVQVFTRDGIEKDKRARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGP- 1017

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK   ++   +    +S W+Q  ++D+     +E  + Q +  +   E  F +K  KI
Sbjct: 1018 NLKKGDNVTDAYLDGLKKSDWFQLRMKDDDAADAIERAQKQIQAHEKEFEAPFADKRGKI 1077

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GDD+ PGVL++VKVF+A+KR +Q GD MAGRHGNKG+VS ++P EDMP++  G PVDI
Sbjct: 1078 TQGDDLAPGVLKMVKVFLAVKRRVQPGDNMAGRHGNKGVVSNVVPVEDMPYMATGEPVDI 1137

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S +R FL+ +    S
Sbjct: 1138 VLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQTAVSDVRKFLDDIYNHDS 1194

Query: 1181 HTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                    +S + D+ +L + +    GVP++TPVFDGA E  I  ML +A+L +SGQ+ L
Sbjct: 1195 AINAERVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELAELPQSGQTQL 1254

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GE
Sbjct: 1255 YDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1314

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++ YGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++
Sbjct: 1315 MEVWALERYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRS 1374

Query: 1357 LGLSIDLEN 1365
            L ++++LE 
Sbjct: 1375 LAINMELEE 1383


>gi|325203034|gb|ADY98488.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            M01-240149]
          Length = 1392

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++  +D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAEDDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|90581313|ref|ZP_01237110.1| DNA-directed RNA polymerase beta subunit [Vibrio angustum S14]
 gi|90437552|gb|EAS62746.1| DNA-directed RNA polymerase beta subunit [Vibrio angustum S14]
          Length = 1341

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1366 (51%), Positives = 958/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++D P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDAPYLLSIQLDSFQKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +E+IL  F+ KI +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDSVFVRIDRRRKLPASIILRALNYTTEQILDMFFEKIHFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G   +E G+++T+  ++ L + GV  + +  + 
Sbjct: 235  KSLVMELVP-DRLRGETASFDIE--ANGTVYVEQGRRITARHIRQLGKDGVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D +N +TGE+ + A   +  ++L  +  +  + I +L+ + +++  Y+ +TL
Sbjct: 292  IVGKIASRDYINEDTGELIVAANQELSLEALALLSQAGHKSIEVLFTNDLDHGPYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RIDNTTDRLSALVEIYRMMRPGEPPTREAAEQLFESLFFSEDRYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +   DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EETTGPGILDHADIIDVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVFARCNPYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGKVT+D+ YLSA+EE    IAQAN++L+EDGSF +EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDGKVTDDIEYLSAIEEGLYVIAQANAALNEDGSFADELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP ++A+ P VGTG+E  +   
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTIRADKPLVGTGIERQIGVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  + +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGTVQSVDASRIVIKVNDDELIPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP  V+GT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPGSVTGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                    D I+   R   +
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLLSAG-------------YGEDKIASMNRDALF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A++R
Sbjct: 999  AVTLDDEALQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVRR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  VDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQTVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG--TGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL++V           I    D  V  + +  
Sbjct: 1119 LAAKGIGDKLNDML---KEQQELHKFRNFLQRVYNLGDTRQKVDIEALTDQEVRTLVQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RKGLPIATPVFDGAPESSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1341


>gi|78099436|gb|ABB20854.1| RNA polymerase subunit B [Acinetobacter genomosp. 13]
          Length = 1362

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1374 (51%), Positives = 972/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P +++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPHVMEAPYLLSIQVDSYRTFLQGGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  TYA P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNEQILNLFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L   D + G      ++D D G+ ++E GK++ +  ++ ++   +  L +  + 
Sbjct: 237  GSYQIDLVP-DRLRGEMAQFDILDND-GKTIVEQGKRINARHVRQMEAANLAKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   ++G++   A  V+  + + ++    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDIT-LKSGDVI-PANTVLSHEIMVKLAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSHDDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKAND 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+DG  TEE+V  R  G+ +
Sbjct: 593  FGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAVDKDGMLTEEMVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  E++  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG
Sbjct: 653  RMSPERVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPNDEAIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G   E++    D  +
Sbjct: 1132 QILETHLGMAAKGLGDKIEKMLKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY
Sbjct: 1189 LALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|194099908|ref|YP_002003045.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            NCCP11945]
 gi|239997913|ref|ZP_04717837.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            35/02]
 gi|240015108|ref|ZP_04722021.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            DGI18]
 gi|240081700|ref|ZP_04726243.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae FA19]
 gi|240113976|ref|ZP_04728466.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae MS11]
 gi|240116712|ref|ZP_04730774.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID18]
 gi|240118934|ref|ZP_04732996.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae PID1]
 gi|240124472|ref|ZP_04737428.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID332]
 gi|240124660|ref|ZP_04737546.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-92-679]
 gi|240129146|ref|ZP_04741807.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-93-1035]
 gi|254494732|ref|ZP_05107903.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae 1291]
 gi|260439529|ref|ZP_05793345.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae DGI2]
 gi|268593764|ref|ZP_06127931.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            35/02]
 gi|268597797|ref|ZP_06131964.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae FA19]
 gi|268600040|ref|ZP_06134207.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae MS11]
 gi|268602382|ref|ZP_06136549.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID18]
 gi|268604644|ref|ZP_06138811.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae PID1]
 gi|268683102|ref|ZP_06149964.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID332]
 gi|268683235|ref|ZP_06150097.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-92-679]
 gi|268687529|ref|ZP_06154391.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-93-1035]
 gi|291042765|ref|ZP_06568506.1| DNA-directed RNA polymerase beta subunit [Neisseria gonorrhoeae DGI2]
 gi|226699425|sp|B4RQW2|RPOB_NEIG2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|193935198|gb|ACF31022.1| DNA-directed RNA polymerase beta subunit [Neisseria gonorrhoeae
            NCCP11945]
 gi|226513772|gb|EEH63117.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae 1291]
 gi|268547153|gb|EEZ42571.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            35/02]
 gi|268551585|gb|EEZ46604.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae FA19]
 gi|268584171|gb|EEZ48847.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae MS11]
 gi|268586513|gb|EEZ51189.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID18]
 gi|268588775|gb|EEZ53451.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae PID1]
 gi|268623386|gb|EEZ55786.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            PID332]
 gi|268623519|gb|EEZ55919.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-92-679]
 gi|268627813|gb|EEZ60213.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            SK-93-1035]
 gi|291013199|gb|EFE05165.1| DNA-directed RNA polymerase beta subunit [Neisseria gonorrhoeae DGI2]
 gi|317165365|gb|ADV08906.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            TCDC-NG08107]
          Length = 1392

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVYYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEQES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKERRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|308388349|gb|ADO30669.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            alpha710]
 gi|325207167|gb|ADZ02619.1| DNA-directed RNA polymerase, beta subunit [Neisseria meningitidis
            NZ-05/33]
          Length = 1392

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTKEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL ++    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGE---LREFLNRLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|59802172|ref|YP_208884.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae FA
            1090]
 gi|293398215|ref|ZP_06642420.1| DNA-directed RNA polymerase, beta subunit [Neisseria gonorrhoeae F62]
 gi|75355443|sp|Q5F5R5|RPOB_NEIG1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|59719067|gb|AAW90472.1| putative DNA-directed RNA polymerase beta chain [Neisseria
            gonorrhoeae FA 1090]
 gi|291611478|gb|EFF40548.1| DNA-directed RNA polymerase, beta subunit [Neisseria gonorrhoeae F62]
          Length = 1392

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVYYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEQES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLTKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKERRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|114561329|ref|YP_748842.1| DNA-directed RNA polymerase, beta subunit [Shewanella frigidimarina
            NCIMB 400]
 gi|122301120|sp|Q089R1|RPOB_SHEFN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|114332622|gb|ABI70004.1| DNA-directed RNA polymerase, beta subunit [Shewanella frigidimarina
            NCIMB 400]
          Length = 1343

 Score = 1626 bits (4211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 957/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVLDIPYLLSIQLDSFKKF----TDHDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR+++FD +   G  ++
Sbjct: 57   FPIKSFSGYSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+P+MT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPMMTNNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +++IL  F+ +I +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQDILDLFFERIEFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L   D + G      + D + G  ++E+G+++T+  +K L++     L +  D 
Sbjct: 235  DSLVMALVP-DRLRGETAGYDIKDAE-GALLVEAGRRITARHIKQLEKTNTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+D ++ +TGE+ + A   I  + L ++  + I++I  L+++ +++ AYI +TL
Sbjct: 293  IVGKYAAQDYIDEDTGEVLVTANSEITLEDLAKLSLAGIKNIDTLFINDLDHGAYIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N RL +
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEGLFQNLFFSEERYDLSKVGRMKFNRRLEI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI++++K ++++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  AEDEGNGVLSKEDIVSVMKKIIEIRNGYDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG +T+DV YLSA+EE    IAQAN  +D DG   EE + CR  GE   +    + 
Sbjct: 593  RKVVDGVITDDVEYLSAIEEGRYVIAQANIEVDADGRMAEEQIACRHKGESTFMRAADVQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+V+ VDA RIV++  E +L    +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGVVDYVDASRIVVKVNEDELHAGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGEPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRALEIEDM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +    +D  +E  IL+  +  R   +L                  S   ++E PR    
Sbjct: 953  HVRQARKDLGEEFKILEEGVLGRARNLLLSVG-------------YSEAKLAEIPRKDVL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  +  F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 IQVIDDETKQTELEQLAEQHEELKADFDKTFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPVEDMPYDEEGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD V+R+A   K 
Sbjct: 1120 AAAKGIGNKITAMLEEQREIAELRGYIKQVYELGDDVLQRVDIDSFTDDEVVRLATNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L ESGQ  L DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKQMLALAGLPESGQLTLCDGRTGNEFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1343


>gi|218511584|gb|ACK77784.1| RNA polymerase subunit B [Acinetobacter sp. HY-7]
          Length = 1362

 Score = 1626 bits (4210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1374 (52%), Positives = 972/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK PE+++ P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPEVMEAPYLLAIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  T+A P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTFAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++VRIDRRRK+  T+ L AL   +E+IL  FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATAILRALDYTNEQILEMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDITDAD-GKVIVEQGKRINARHVRQMEASGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+  +A  V+    + ++    I+   IL+ + ++  ++I +TL
Sbjct: 295  LYERITAEDITLKD-GEVI-QANTVLGHDIMVKLAEGGIKQFNILFTNDIDRGSFIADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF S++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  EDII ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNEDIIDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKCNN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT DV YLSA+EE    IAQA+SS+D D + TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTEDVEYLSAIEEVGTVIAQADSSVDGDNNLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA+ SG  ++AKR G++E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVARDSGVCVIAKRGGMIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVSLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV++F R GI+K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGIEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS +L+S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEELLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEIQPSDEGIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDINGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG++I  ++ + +    I+ LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGLAAKGLGEQIDKMLKEQRT---IAELRVFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   + GVP++TPVFDGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRKGVPLATPVFDGAEEGQIKELLELAELPRSGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWPLEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTRVY++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRVYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|219871716|ref|YP_002476091.1| DNA-directed RNA polymerase subunit beta [Haemophilus parasuis
            SH0165]
 gi|254765292|sp|B8F741|RPOB_HAEPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219691920|gb|ACL33143.1| DNA-directed RNA polymerase subunit beta [Haemophilus parasuis
            SH0165]
          Length = 1342

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1367 (50%), Positives = 959/1367 (70%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK  +++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKSFGKRSQVLNVPYLLTIQLDSFDKFIQRD----PEGLQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +GA  L++VSYE   P FDV +C  R  TYA PL++ LRL+ FD +   G  ++
Sbjct: 57   FPIVSSNGATELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKLRLVTFDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ++YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHASGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +EEIL+ F+    +    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEEILNMFFETATFHIED 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +ESG+++T+  +++L++  +  + + ++ 
Sbjct: 235  NRLLMTLVPERL-RGETAAFDIE--ANGKIYVESGRRITARHIRALEKDNITQIQVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A D V+  TGEI   A   I  ++L  +  +   +I +L+ + ++   YI  TL
Sbjct: 292  IVGRVTARDYVDLSTGEIVCPANSEIGLETLAALAQAGYNEIEVLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F+ +FF +D+YDLS VGR+K N  L++
Sbjct: 352  RIDPTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSTDRYDLSAVGRMKFNRSLDI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGVGTGILSNDDIIGVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDGVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP+
Sbjct: 532  ALGSGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   GE  L   E+I
Sbjct: 592  RKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENFRFTDTYVTCRGEHGESGLYRPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A++AKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVIAKRGGTIQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+G+ V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V ED FT+
Sbjct: 772  VKLGEPVGRGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQEDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ + PEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R+  +E 
Sbjct: 892  GETQLIPEEKLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRAKDIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q+    +D  +E  IL+  +++R+  +L                      +    R +W
Sbjct: 952  IQLREAKKDLTEELEILEAGLFTRVRNLLLEGGVA-------------QATLDNLAREKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  Q+E  +   E + + K  KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTLDDEAKQNQLEQLAEQHEELRKEFERKLEIKRNKIIQGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I  +I   K   +I+ LR +++K    G G+ +  +S + D+ V+R+A+ 
Sbjct: 1119 GLAARGIGDQIDKMI---KQQQEIAKLREYIQKAYDLGHGAQSVDLSTFSDEEVMRLAQN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+P++TPVFDGA E  I  +L +  L  SGQ  LYDG TGE F+R VTVGY+YMLKL
Sbjct: 1176 LRKGLPLATPVFDGAHESEIKGLLELGGLPTSGQITLYDGRTGEKFERLVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQLGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV G    E G PESFNV+ KE++AL + ++L+ +
Sbjct: 1296 DDVNGRTKMYKNIVDGTHYMEPGIPESFNVITKEIRALAIDMELDEA 1342


>gi|212634821|ref|YP_002311346.1| DNA-directed RNA polymerase subunit beta [Shewanella piezotolerans
            WP3]
 gi|226699447|sp|B8CNC5|RPOB_SHEPW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|212556305|gb|ACJ28759.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase beta subunit)
            [Shewanella piezotolerans WP3]
          Length = 1343

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 953/1364 (69%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK  +++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRQKVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGITYSAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLAASIILRALDYSTQDILDLFFDRVNFKIKQ 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A D + G   S  + D + G  ++E G+++T+  ++ L++     L +  + 
Sbjct: 235  DSLVMDLVA-DRLRGETASYDIKDAE-GTVLVEKGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I+++  LY++ ++N AYI +TL
Sbjct: 293  IAGKISGQDYIDPDTGEVLVSANAEIGLEDLAKLSLAGIKEVSTLYINELDNGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFNNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDDEGTGILSKEDIVAVMKNIIAIRNGLDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNNYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQA   LDE+    +EL+ CR  G+   +    I 
Sbjct: 593  RKVIDGVVTDEVDYLSAIEEGRYVIAQAIVELDENNRMMDELIACRHKGDSTFMGAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGYVDYVDASRIVVKVDEAELTPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G+DK++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVDKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  +  R   +L G                    +   PRSQ  
Sbjct: 953  HIAQAKKDLTEEFQILEDGVLGRARNLLLGAG-------------FDEAQLDAIPRSQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 MQTIDDEAKQTELEQLAEQAEELKADFDKKFEVKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPVEDMPYDEKGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I  ++ + +   ++      + ++         I  + DD VLR+A+  K 
Sbjct: 1120 AAAKGIGNRITEMLEEQRELAELRGYIKEVYELGDEVQQRVDIDSFTDDEVLRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TP FDGA E+ I  ML +A L  SGQ  L DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GVPTATPAFDGAKEKEIKQMLALAGLPTSGQLTLCDGRTGNEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQK 1343


>gi|254805823|ref|YP_003084044.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            alpha14]
 gi|254669365|emb|CBA08472.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            alpha14]
          Length = 1392

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYALQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|301155467|emb|CBW14933.1| RNA polymerase, beta subunit [Haemophilus parainfluenzae T3T1]
          Length = 1342

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 974/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +    R+RK FGK  +++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYTEKKRIRKDFGKRSQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKESEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG   EEIL+ F+ K+ +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTVEEILNLFFDKVTFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETATFDIE--ANGKVYVERGRRITARHIKALEKDNVTQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ E+GEI   A   I  + L ++  +  + I  L+ + ++   YI  TL
Sbjct: 292  IAGKVAAKDYVDLESGEIICPANGEISLEVLAKLSQAGYKVIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL +IYR+MRPG+  T   +E++FN LFF +++YDLS VGR+K N  L +
Sbjct: 352  RVDPTYDRVSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  +DII ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGTGILSNDDIIRVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E+I
Sbjct: 592  RKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR GIV+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGIVQYVDASRIVIKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  DE  IL+  +++R+  +L                 + +  + +  R++W
Sbjct: 952  MQLKQAKKDLSDELEILEAGLFARVRNLLIAGG-------------IDAAQLDKMDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTISDEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RHIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K   D+  LR +++K    G G+    +S + DD ++R+AE 
Sbjct: 1119 GLAAKGIGDQINTMI---KQKQDVEKLRGYMQKAYDLGHGAQKVDLSTFSDDEIMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+PV+TPVFDGADE+ I  ML++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPVATPVFDGADEQEIKEMLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1296 DDVNGRTKMYKNIVGGNQQMDPGTPESFNVIMKEIRSLGLNIELDEE 1342


>gi|209696266|ref|YP_002264196.1| DNA-directed RNA polymerase subunit beta [Aliivibrio salmonicida
            LFI1238]
 gi|226699365|sp|B6ENR3|RPOB_ALISL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|208010219|emb|CAQ80550.1| DNA-directed RNA polymerase, beta-subunit [Aliivibrio salmonicida
            LFI1238]
          Length = 1342

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1367 (52%), Positives = 969/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFTKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + LE+VSY    P+FDV +C  R +TY+ PL++ LRL+V+D D   G  ++
Sbjct: 57   FPIQSYNGNSKLEYVSYNLREPEFDVKECQIRGVTYSAPLRVKLRLVVYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   +EEIL  F+ K+V+  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALRKTTEEILDLFFDKVVFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   +  +     G+  +E+G+++T+  ++ L +  V  + +  D 
Sbjct: 235  QTLMMELLPERL-RGETATFDIES--NGKVYVEAGRRITARHIRQLTKDEVNNIEVPVDY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN +TGEI I A      + L  +  +  + I +L+ + +++ AYI +TL
Sbjct: 292  IVGKVASHDYVNEDTGEIIIAANQEFSLEDLANLSQAGHKKIEVLFTNDLDHGAYISDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL+++YR+MRPG+  T   AES+F  LFF  D+YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRLSALVEVYRMMRPGEPPTKEAAESLFESLFFSEDRYDLSTVGRMKFNSSIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + + DII +++ L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DNGEGAGILDETDIIEVMRKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAYARCNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V D  VT DV YLSA+EE    IAQAN+ L E+G+F +EL+  R  GE  L PRE I 
Sbjct: 592  RRVVDNIVTEDVDYLSAIEEGTFVIAQANAVLTEEGTFADELIIARQKGESGLHPREHIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERCVAID 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMVQSVDASRIVIKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L     ++G    K         +    R QW 
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLT----LAGTSEVK---------LDAMDRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EITLDDESQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL+KV   G   +   I+   DD V  + +  
Sbjct: 1119 LAAKGVGDKLNQML---KEQQELHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLVKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPIFDGAPESSIKELLKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|34499648|ref|NP_903863.1| DNA-directed RNA polymerase subunit beta [Chromobacterium violaceum
            ATCC 12472]
 gi|41017646|sp|Q7NQE6|RPOB_CHRVO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|34105498|gb|AAQ61853.1| DNA-directed RNA polymerase, beta subunit [Chromobacterium violaceum
            ATCC 12472]
          Length = 1390

 Score = 1625 bits (4209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1397 (49%), Positives = 961/1397 (68%), Gaps = 42/1397 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +    DER + GLQAAFKS+
Sbjct: 1    MSYSFTEKKRIRKSFAKRASVLDVPFLLATQIDSYTEFLQLGTPLDERKDVGLQAAFKSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A L+F  Y    P FDV +C  R +T+A PL+  +RL +FD    +    +
Sbjct: 61   FPIVSHNGYARLDFAHYVLGEPPFDVQECQLRGITFAAPLRARIRLTIFDK--ESSKPVV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT +G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTANGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +EEILS FY    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYTNEEILSEFYSFDTFYLTK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  +    L  G      +V  D G+ ++   K++T+  ++ ++   +  + + +D 
Sbjct: 239  SGVFMRVVPERL-KGEVAKFDIVAAD-GKLIVAKDKRITAKHIRDIQTAELDRIEVPADA 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++VN  TGE+   A + + E+ L ++  +E+  + +L+ + ++  AYI  TL
Sbjct: 297  LLGKMLAHNVVNQNTGEVIARANEEVTEEILAKLALAEVEQVEVLFTNDLDQGAYISQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD  +D+  A + IYR+MRPG+  T    E++F  LFF  + YDLS VGR+K + R   
Sbjct: 357  RTDDIQDQTQARVAIYRMMRPGEPPTEDAVEALFQRLFFSDETYDLSRVGRMKFSSRTYQ 416

Query: 423  DTPDD---------------------VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               DD                        +  EDI+++I IL +LRNG+G +DDID+LGN
Sbjct: 417  YKFDDKTPEWFKTLIGEKFASRRDVMEGTLATEDIVSVIAILTELRNGRGEVDDIDHLGN 476

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGE+ +NQ+R GL+R+ER++KER++  + D++MP DLINAKPV +A+ EFF SSQ
Sbjct: 477  RRVRSVGELAENQFRAGLVRVERAVKERLNQAESDNLMPHDLINAKPVSAAIKEFFGSSQ 536

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIG
Sbjct: 537  LSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 596

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL+ +AR N +GF+ETPYRKV DGKVTN++ YLSA+EE    IAQAN+ LD +G+  
Sbjct: 597  LINSLSVYARTNEFGFLETPYRKVVDGKVTNEIDYLSAIEEGRYVIAQANAELDGEGALI 656

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +ELV CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 657  DELVTCREKGETILATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAV 716

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            P L+ E  FVGTG+E  VA  SG  +VA+R G+V+ VDA R+V+R  + +      GVDI
Sbjct: 717  PCLRPEKAFVGTGIERSVAVDSGTTVVARRGGVVDYVDAGRVVVRVNDEEATAGEVGVDI 776

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y L KF RSNQNT +NQRP+VKVGD + R D++ADG STDLG+LALG+NM +AFMPW+GY
Sbjct: 777  YNLTKFTRSNQNTNINQRPVVKVGDHIARGDVVADGASTDLGELALGQNMTIAFMPWNGY 836

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N+EDS+LISE++V+ED +TSIHIEE  V+ARDTKLGPEEITRDIPN+SE     +DE GI
Sbjct: 837  NYEDSILISEKLVAEDRYTSIHIEELSVVARDTKLGPEEITRDIPNLSERMAGRLDESGI 896

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+D
Sbjct: 897  VYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTVGTVID 956

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            V++F R GI++++R+ S+   +++    D +D+  I D + +SR+  ++ G+ A  GPK 
Sbjct: 957  VQVFTREGIERDKRAQSIIDAELKRYRLDLNDQLRIFDNDAFSRIERLIVGKAANGGPKR 1016

Query: 1002 FKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K TV+  + ++  P +  W+   + DE + + +E +K      +   + +F++K  K+
Sbjct: 1017 LAKGTVIDQEYLAGLPTKHDWFDIRMADEDIAKQLELIKESLAQKREEFDLKFEDKKRKL 1076

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++PPGV ++VKV++A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDI
Sbjct: 1077 TQGDELPPGVQKMVKVYLAVKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMGDGRPVDI 1136

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++         + +R++LE++     
Sbjct: 1137 VLNPLGVPSRMNIGQILEVHLGWAAKGIGERINRMV----REQSAAEIRAYLERIYNETG 1192

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DLD 1229
              E+I+   D  V+++A+    G+  +TPVFDGA E  I  ML +A             +
Sbjct: 1193 KPEEIAALSDAEVMQLAQNLSKGMTFATPVFDGAKEAEIKHMLDLAYPDGDELTEKMGFN 1252

Query: 1230 ES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
            ES  Q  L+DG +GE FDR VTVG ++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1253 ESKTQMTLFDGRSGEAFDRKVTVGVMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQ 1312

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G    + G PESFN
Sbjct: 1313 FGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDAGMPESFN 1372

Query: 1349 VLVKEMQALGLSIDLEN 1365
            VLVKE+++LGL +DLE 
Sbjct: 1373 VLVKEIRSLGLDMDLER 1389


>gi|54310498|ref|YP_131518.1| DNA-directed RNA polymerase subunit beta [Photobacterium profundum
            SS9]
 gi|81398906|sp|Q6LLW2|RPOB_PHOPR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|46914941|emb|CAG21716.1| putative DNA-directed RNA polymerase, beta subunit [Photobacterium
            profundum SS9]
          Length = 1341

 Score = 1625 bits (4208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1366 (50%), Positives = 959/1366 (70%), Gaps = 27/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P ++D P L+ +Q  S+  F+  +       + GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPRVLDAPYLLSIQLDSFKKFIEQD----PEGHYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL+++D D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVMYDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+  +  L AL   +E+IL  F+ K+ +  +G
Sbjct: 175  RVIPYRGSWLDFEFDPKDNVFVRIDRRRKLAASVILRALDYTTEQILDMFFDKVSFEVQG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G   S  +     G+  +E G+++T+  ++ L + GV  + +  + 
Sbjct: 235  KSLVMELVPERL-RGETASFDIE--ANGKVYVEQGRRITARHIRQLGKDGVDQIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   + D VN ETGE+   A   ++ + L  +  +  + I +L+ + ++   Y+  TL
Sbjct: 292  IVGKISSRDYVNEETGELIAAANQELNLEILALLSQAGHKSIEVLFTNDLDYGPYMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE +FN LFF  D+YDLS VGR+K N  L  
Sbjct: 352  RVDSTTDRLSALVEIYRMMRPGEPPTREAAEQLFNSLFFSEDRYDLSAVGRMKFNSSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       +   DII ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EETTGSGILDHSDIIEVMKKLIEIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N+YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSVYARCNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT+ + YLSA+EE    IAQAN++L+ DGSF++EL+  R  G+  L PR+ + 
Sbjct: 592  RKVVDSKVTDQIDYLSAIEEGQYVIAQANAALETDGSFSDELITARQKGDSGLHPRDHVQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  
Sbjct: 652  YMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERSVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+N+ +AFMPW+GYNFEDS+L+SER+V +D  T+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNIRIAFMPWNGYNFEDSILVSERVVQQDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S + I+   R + +
Sbjct: 952  QLKEAKKDITEEFQILEGGLLARVRTLLLSIG-------------YSEEKIASMDRERLF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ALTLDDESLQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G  V+IVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKICPVEDMPYDEKGQTVEIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS--DYDDDSVLRVAEQW 1200
             A  G+G K+  ++   K   ++   R+FL+KV   G   + +      DD V  + +  
Sbjct: 1119 LAAKGIGDKLNEML---KQQQELHKFRNFLQKVYDLGDTRQDVDIAALSDDQVHTLVQNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E +I  +L++ DL ESGQ  ++DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RDGLPIATPVFDGAPESSIKELLKLGDLPESGQLKMFDGRTGDMFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1296 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDK 1341


>gi|157960007|ref|YP_001500041.1| DNA-directed RNA polymerase subunit beta [Shewanella pealeana ATCC
            700345]
 gi|189043867|sp|A8GYW9|RPOB_SHEPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157845007|gb|ABV85506.1| DNA-directed RNA polymerase, beta subunit [Shewanella pealeana ATCC
            700345]
          Length = 1343

 Score = 1625 bits (4208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1364 (51%), Positives = 957/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P ++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPRVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLAASIILRALDYSTQDILDLFFDRVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A D + G   S  + D + G  ++E G+++T+  ++ L++     L +  + 
Sbjct: 235  DSLVMDLVA-DRLRGETASYDIKDAE-GTVLVEKGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I++I  LY++ ++N AYI +TL
Sbjct: 293  IAGKISGQDYIDPDTGEVLVSANADISLEDLAKLSMAGIKEISTLYINELDNGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFNNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDDEGTGILSKEDIVAVMKNIIAIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNNYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT++V YLSA+EE    IAQA   LDE+G   +EL+ CR  G+   +    I 
Sbjct: 593  RKVIDGVVTDEVDYLSAIEEGRYVIAQAIVQLDENGRMMDELIACRHKGDSTFMGAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGYVDYVDASRIVVKVNEAELTPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD + R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPIVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  +  R   +L G                    ++  PRSQ  
Sbjct: 953  HIAQAKKDLTEEFQILEDGVIGRARNLLIGAG-------------FDEAQLAAIPRSQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q E  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQTIDDEVKQTELEQLAEQAEELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPVEDMPYDEKGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I  ++ + +   ++      + ++         I  + DD +LR+A+  K 
Sbjct: 1120 AAAKGIGNRITEMLEEQRELAELRGYIKQVYELGDEVIQKVDIDSFTDDEILRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP++TP FDGA E+ I  ML +A L +SGQ  L DG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GVPIATPAFDGAKEKEIKQMLELAGLPQSGQLTLIDGRTGNEFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDTK 1343


>gi|325576515|ref|ZP_08147268.1| DNA-directed RNA polymerase subunit beta [Haemophilus parainfluenzae
            ATCC 33392]
 gi|325161205|gb|EGC73319.1| DNA-directed RNA polymerase subunit beta [Haemophilus parainfluenzae
            ATCC 33392]
          Length = 1342

 Score = 1625 bits (4207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1367 (51%), Positives = 973/1367 (71%), Gaps = 28/1367 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +    R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1    MGYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57   FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKESEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG   EEIL+ F+ K+ +   G
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTVEEILNLFFDKVTFEIAG 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235  NKLLMTLVPERL-RGETATFDIE--ANGKVYVERGRRITARHIKALEKDNVTQVEVPTEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D V+ E+GEI   A   I  + L ++  +  + I  L+ + ++   YI  TL
Sbjct: 292  IAGKVAAKDYVDLESGEIICPANGEISLEVLAKLSQAGYKIIETLFTNDLDYGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL +IYR+MRPG+  T   +E++FN LFF +++YDLS VGR+K N  L +
Sbjct: 352  RVDPTYDRVSALYEIYRMMRPGEPPTPESSEALFNNLFFSAERYDLSAVGRMKFNRSLGI 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  +DII ++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGEGTGILSNDDIIRVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++ PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
            RKV  G+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E+I
Sbjct: 592  RKVVYGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEEI 651

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A 
Sbjct: 652  HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIAL 711

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG A+VAKR G V+ VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712  DSGVAVVAKRGGTVQYVDASRIVIKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +GD + R +++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772  VNLGDPINRGEVLADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPK
Sbjct: 832  IHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPK 891

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E 
Sbjct: 892  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEE 951

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  DE  IL+  +++R+  +L                 + +  + +  R++W
Sbjct: 952  MQLKQAKKDLSDELEILEAGLFARVRNVLIAGG-------------IDAAQLDKMDRTKW 998

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+K
Sbjct: 999  LEQTISDEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVK 1058

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHL
Sbjct: 1059 RHIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHL 1118

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQ 1199
            G A  G+G +I ++I   K   D+  LR +++K    G G+    +S + DD ++R+AE 
Sbjct: 1119 GLAAKGIGDQINAMI---KQKQDVEKLRGYMQKAYDLGHGAQKVDLSTFSDDEIMRLAEN 1175

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + G+PV+TPVFDGADE+ I  ML++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKL
Sbjct: 1176 LRKGLPVATPVFDGADEQEIKEMLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            NH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++Y++IV GN   + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1296 DDVNGRTKMYKNIVGGNQQMDPGTPESFNVIMKEIRSLGLNIELDEE 1342


>gi|240017557|ref|ZP_04724097.1| DNA-directed RNA polymerase subunit beta [Neisseria gonorrhoeae
            FA6140]
          Length = 1392

 Score = 1625 bits (4207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 957/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVYYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEQES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGSGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G+   LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKERRKAGE---LREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E       G 
Sbjct: 1194 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEKLGF 1253

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|160895959|ref|YP_001561541.1| DNA-directed RNA polymerase subunit beta [Delftia acidovorans SPH-1]
 gi|226699393|sp|A9BR98|RPOB_DELAS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|160361543|gb|ABX33156.1| DNA-directed RNA polymerase, beta subunit [Delftia acidovorans SPH-1]
          Length = 1370

 Score = 1624 bits (4205), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1375 (50%), Positives = 968/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++++P L+++QK +Y  FL  ++AP +R  EGLQAAF S 
Sbjct: 1    MAYSYTERKRIRKSFGSRDSVLEVPYLLQMQKDAYTAFLQSDVAPKKRTIEGLQAAFNSA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++FV Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFVEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT+ G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTEKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD++  R+DRRRK+PV+  L A+G+  E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDLLFFRVDRRRKMPVSILLKAIGLTPESILANFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     +  L  G      + D  +G+ V+   K++T+   + L++ G KF+ +  D
Sbjct: 241  DSGAQMEFVSERL-RGEVARFDITD-KSGKVVVAKDKRVTARHTRELEQSGTKFISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA++IV+ +TGEI  +A + + E  L+++  + I+D+  +Y + ++  AYI  T
Sbjct: 299  FLIGRVVAKNIVDPDTGEIIAKANEELTESLLKKLRSAGIQDLQCIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L TD+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++ 
Sbjct: 359  LRTDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKVG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+A++KILVDLRNGKG +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RDGATGPMVLSNEDILAVVKILVDLRNGKGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT ++ YLSA+EE    IAQAN+ LD +G    +LV  R  G+  LV  E++
Sbjct: 599  YRRVADGKVTMEIDYLSAIEEGKYIIAQANAELDAEGRLIGDLVSAREKGDSTLVSAERV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGIVDYVDATRIVVRVNDAEAVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD++ + D++ADG STDLG++A+G+NML+AFMPW+GYNFEDS+LI+ER+V+ED +TS
Sbjct: 779  VKRGDKLAKGDVVADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILINERVVAEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD+LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDVLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIQRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K   +    +    +  W
Sbjct: 959  DELKRYRLDLNDQLRIVEADAFDRIEKLLNGRVANGGPQKLAKGAKIDKAYLDGVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDEVATQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG+  DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGSTADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++   +     + +R+F+E++  +    E ++  DD  ++ +A+   
Sbjct: 1139 GWAGKGLGQRIGDML---QQEARAAEIRTFMEEIYNSRGRKEDLTQLDDKEIVSMAQALT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA E+ I  ML +A          L ES  Q+ LYDG TG+ F+RP T+
Sbjct: 1196 TGVPFATPVFDGASEQEIQDMLHLAYPEELAQRKGLTESRTQAYLYDGRTGDRFERPTTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDVVGRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|158564304|sp|Q21SF7|RPOB_RHOFD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1370

 Score = 1624 bits (4205), Expect = 0.0,   Method: Composition-based stats.
 Identities = 687/1375 (49%), Positives = 959/1375 (69%), Gaps = 18/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    +++IP L+++QK +Y  FL  ++ P +R  EGLQAAF++ 
Sbjct: 1    MAYSYTERKRIRKNFGSRDSVLEIPYLLQMQKDAYTAFLQADVHPKKRTAEGLQAAFEAA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++++ Y    P FDV +C  R LT+A  ++  ++L ++D +  T   K 
Sbjct: 61   FPIISHNGFVEMKYLEYNLAKPAFDVRECQTRGLTFASAVRAKVQLFIYDRESSTSQNKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            IK++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  IKEVKEQEVYMGEVPLMTTKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD ++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDFLYFRVDRRRKMPVTILLKAIGLNHESILANFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A  L  G      + D  +G+ ++   K++T+   + L++ G   + +  D
Sbjct: 241  DSGAQMEFVAERL-RGEVARFDITD-KSGKVIVAKEKRVTARHTRELEQSGTTHISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA +IV+ +TGEI  +A + + E  ++++  + ++D+P +Y + ++  AYI  T
Sbjct: 299  FLLGRVVARNIVDTDTGEILAKANEELTEALIKKLRLAGVQDLPCIYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L +D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++ 
Sbjct: 359  LRSDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKMG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+A++KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RPESTGPMVLTNEDILAVVKILVDLRNGRGDVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNDYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG  T E++  R AGE I    E++
Sbjct: 599  YRRVVDGKVTMEIDYLSAIEEGKFVIAQANAVLDKDGKLTGEMISAREAGETIFAGPERV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPILRPEKPMVGTGIERVAAI 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGMVDYVDATRVVIRVNDDEAQAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD + + D+IADG STDLG+LALG+NML+ FM W+GYNFEDS+LISER+V++D +TS
Sbjct: 779  VKKGDMLAKGDVIADGASTDLGELALGQNMLIGFMTWNGYNFEDSILISERVVADDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGCEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI ++ R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGTVIDVQVFTREGIVRDRRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  +++ + + R+ ++L G+ A  GP+   K T +    ++   +  W
Sbjct: 959  DELKRFRLDLNDQLRLVEADSFDRIEKLLVGKVANGGPQKLAKGTTIDKAYLTSVEKHHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     ++ V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDDVAAQLESIKNSMEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMPF+ DGTP DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RHLQPGDKMAGRHGNKGVVSKIVPVEDMPFMADGTPCDIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I  ++   +A   ++ LR FL+++       E ++   DD VL +A    
Sbjct: 1139 GWAAKGIGQRIGDML---QAEAKVAELRKFLDELYNGTGRKEDLAQLSDDEVLEMAGNLT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESG-----------QSILYDGLTGEPFDRPVT 1250
            SGVP +TPVFDGA E  I +ML++A   E             Q+ LYDG TG+PF+RP T
Sbjct: 1196 SGVPFATPVFDGASEADIGAMLKLA-YPEDAIRQKGLTPARTQAYLYDGRTGDPFERPTT 1254

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1255 IGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1314

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GRT+VYESIV G  + E G PESFNVLVKE+++LG+ I+LE 
Sbjct: 1315 LQEMLTVKSDDVQGRTKVYESIVKGEHSIEAGMPESFNVLVKEIRSLGIDIELER 1369


>gi|261364718|ref|ZP_05977601.1| DNA-directed RNA polymerase, beta subunit [Neisseria mucosa ATCC
            25996]
 gi|288567014|gb|EFC88574.1| DNA-directed RNA polymerase, beta subunit [Neisseria mucosa ATCC
            25996]
          Length = 1392

 Score = 1624 bits (4204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1398 (49%), Positives = 955/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVVGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDISNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +     ++ +  LY++ ++   YI NTL
Sbjct: 297  LLGKALAADLIDPETGEVLAVANDEITEELLAKFDIHGVKQLTTLYINELDQGGYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETVDQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQHSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D+IADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLIADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + +S++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEISTEYLAGLPSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|255067807|ref|ZP_05319662.1| DNA-directed RNA polymerase, beta subunit [Neisseria sicca ATCC
            29256]
 gi|255047898|gb|EET43362.1| DNA-directed RNA polymerase, beta subunit [Neisseria sicca ATCC
            29256]
          Length = 1392

 Score = 1624 bits (4204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1398 (49%), Positives = 955/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVVGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDISNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +     ++ +  LY++ ++   YI NTL
Sbjct: 297  LIGKALAADLIDPETGEVLAVANDEITEELLAKFDIHGVKQLTTLYINELDQGGYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETVDQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQHSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D+IADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLIADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEITTEYLAGLPSKHDWFDIRLSDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|148981195|ref|ZP_01816321.1| DNA-directed RNA polymerase subunit beta [Vibrionales bacterium
            SWAT-3]
 gi|145960951|gb|EDK26277.1| DNA-directed RNA polymerase subunit beta [Vibrionales bacterium
            SWAT-3]
          Length = 1342

 Score = 1623 bits (4203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1367 (51%), Positives = 974/1367 (71%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDRDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALGKSTEEILDLFFDKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKVYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++ +TL
Sbjct: 292  IVGKVASKDYINEATGEIIVGANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEEEERGTLDESDIIEVMKKLIGIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E+G+F +EL+  R  GE  L PR+ +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQFVIAQANTVLTEEGTFADELITARQKGESGLHPRDHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGMIQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTIGRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R FL+KV   G       I++  DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELHKFREFLQKVYDLGDTRQKVDIAELSDDQVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEALIKELLKLGDLPESGQLKLFDGRTGDSFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|298370599|ref|ZP_06981914.1| DNA-directed RNA polymerase, beta subunit [Neisseria sp. oral taxon
            014 str. F0314]
 gi|298281209|gb|EFI22699.1| DNA-directed RNA polymerase, beta subunit [Neisseria sp. oral taxon
            014 str. F0314]
          Length = 1392

 Score = 1623 bits (4203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 697/1398 (49%), Positives = 956/1398 (68%), Gaps = 42/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDQRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSE 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVVGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDISNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +     ++ +  LY++ ++   YI NTL
Sbjct: 297  LIGKALAADLIDPETGEVLAVANDEITEELLAKFDIHGVKQLTTLYINELDQGGYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D++ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETADQQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                +V+                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEVQQQSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD+DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDKDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D+IADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLIADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++   +D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRQDLGDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + +S++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +K
Sbjct: 1017 KLAKGSEISTEYLAGLPSKHDWFDIRLSDEDLAKQLELIKLSLQQKREEADELYEIKKKK 1076

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1077 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1136

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++   K     S LR FL K+    
Sbjct: 1137 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGS 1193

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DL 1228
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A             
Sbjct: 1194 GKKEDLDALTDEEIIELAFNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGF 1253

Query: 1229 DES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1254 NDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1313

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESF
Sbjct: 1314 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDAGMPESF 1373

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1374 NVLVKEIRSLGLDIDLER 1391


>gi|91790275|ref|YP_551227.1| DNA-directed RNA polymerase subunit beta [Polaromonas sp. JS666]
 gi|123059302|sp|Q123G3|RPOB_POLSJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91699500|gb|ABE46329.1| DNA-directed RNA polymerase subunit beta [Polaromonas sp. JS666]
          Length = 1370

 Score = 1623 bits (4202), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1375 (50%), Positives = 966/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++ +P L+++QK +Y  FL  + AP +R  EGLQAAF++ 
Sbjct: 1    MAYSYTERKRIRKSFGNRESVLTVPYLLQMQKDAYTAFLQADRAPQKRTVEGLQAAFENA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFIEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLNPESILANFFVFDHFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A   M G      + D  +G+ V+   K++T    + L++ G   + +  D
Sbjct: 241  DSGAQMEFVAE-RMRGEVARFDITD-KSGKVVVAKDKRITVRHTRELEQSGTTTISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA++IV+ ETGEI  +A D + E  L+++  + ++D+ +LY + ++  AYI  T
Sbjct: 299  FLVGRVVAKNIVDAETGEIIAKANDELTELLLKKLRLAGVQDLQVLYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N R+ 
Sbjct: 359  LRADETADEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSKVGRMKFNARVG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RDDSTGPMVMTNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V D K+T+ + YLSA+EE    IAQAN+ LD+ G+ T +LV  R  GE +LV  E+I
Sbjct: 599  YRRVVDSKITDQIDYLSAIEEGKYVIAQANALLDDSGTLTGDLVSARENGESVLVGAERI 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E  FVGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKAFVGTGIERVSAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTANRGGVVDYVDATRIVVRVNDAEALAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+GD++ + D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +TS
Sbjct: 779  VKIGDKLAKGDVIADGASTDIGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGSEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVSQGSQGTVIDVQVFTREGIVRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GPK   K T +    +++  +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLNGKVANGGPKKLAKGTKIDKAYLADVEKYHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     D++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPADDEVASQLESIKNAMEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPCDIVLNPLGVPSRMNVGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++   +A   ++ LR F++ +       E +++  D  VL +A    
Sbjct: 1139 GWAAKGLGQRIGDML---QAEAKVAELRKFMDTLYNKSGRVEDLANLSDTDVLEMARNLT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA EE I +ML++A  D             Q+ LYDG TG+ F+R  TV
Sbjct: 1196 TGVPFATPVFDGASEEDIMTMLKLAYPDDIAKAKGLTATRTQAQLYDGRTGDQFERTTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y L
Sbjct: 1256 GYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYESIV G      G PESFNVLVKE+++LG+ I+LE S
Sbjct: 1316 QEMLTVKSDDVQGRTKVYESIVKGEHAITAGMPESFNVLVKEIRSLGIDIELERS 1370


>gi|119773347|ref|YP_926087.1| DNA-directed RNA polymerase subunit beta [Shewanella amazonensis
            SB2B]
 gi|158513005|sp|A1S211|RPOB_SHEAM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119765847|gb|ABL98417.1| DNA-directed RNA polymerase [Shewanella amazonensis SB2B]
          Length = 1342

 Score = 1623 bits (4202), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1366 (51%), Positives = 968/1366 (70%), Gaps = 26/1366 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR+++FD +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLFDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +++IL  F+ ++ ++ + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALDFSTQDILDIFFERVDFTIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D + G  V+E G+++T+  ++ L++     L +  + 
Sbjct: 235  DSLVMKLLPERL-RGETASYDIKDAE-GNIVVEKGRRITARHIRQLEKTNTTELEVPVEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A+D ++ +TGE+ + A + I  + L ++  + I+DI  LY++ +++ AYI +TL
Sbjct: 293  IVGKIAAQDYIDPDTGEVLVTANNEIRLEDLAQLSLAGIKDISTLYINELDHGAYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL +
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLEI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    +  +DI+A++K ++++RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  ADDVGTGVLSNDDIVAVMKKIIEIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLATFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+DV YLSA+EE    IAQAN  LD +G   EE V CR  GE   +    I 
Sbjct: 593  RKVVDGVVTDDVEYLSAIEEGRYVIAQANIELDGEGRILEEQVACRHKGESTFMRASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERALAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +VGD + R D++ADGPSTDLGDLALG+NM VAFMPW+GYNFEDS+LISER+V +D FT+I
Sbjct: 773  QVGDPIVRGDVLADGPSTDLGDLALGQNMRVAFMPWNGYNFEDSILISERVVQDDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R+I +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRAIEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  + SR   +L                  +   +   PR +  
Sbjct: 953  HIAQARKDLSEEFKILEEGVLSRARNLLLAGG-------------YTQAQLDAIPRKELL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q+E  K+  + +F++K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 TQVIDDETKQTELEQLAEQHEELKADFDKKFEHKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKICPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G +I++++ + +   +++ LR ++++    G       I  + D+ V+R+A+  
Sbjct: 1120 AAAKGIGNRIQAMLEEQR---EVAELRGYIKQAYDLGETQQKVDIESFTDEEVIRLAKHL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+P +TP FDGA E+ I  ML +A L  SGQ  L+DG TG  F+R VTVGY+YMLKLN
Sbjct: 1177 KDGLPTATPAFDGAKEKEIKQMLELAGLPTSGQLRLFDGRTGNAFEREVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1297 DVNGRTQMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQE 1342


>gi|224827271|ref|ZP_03700365.1| DNA-directed RNA polymerase, beta subunit [Lutiella nitroferrum 2002]
 gi|224600560|gb|EEG06749.1| DNA-directed RNA polymerase, beta subunit [Lutiella nitroferrum 2002]
          Length = 1391

 Score = 1622 bits (4201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1397 (50%), Positives = 959/1397 (68%), Gaps = 41/1397 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL + +  D+R   GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRDSVLDVPFLLATQIDSYTEFLQLGVPIDQRKEAGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A L+F  Y    P FDV +C  R +TYA PL+  +RL + D    +    +
Sbjct: 61   FPIVSHNGYARLDFAHYILGEPPFDVQECQLRGITYASPLRARIRLTILDK--ESSKPVV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT +G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTTNGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++ RIDRRRK+PVT  L ALG + E+ILS FY    +    
Sbjct: 179  RVIPYRGSWLDFEFDPKDHLYFRIDRRRKMPVTILLKALGYNEEQILSEFYNTDTFYLGN 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D        AD + G      +V  D G+ ++   K++T+  ++ +    +  + + SD 
Sbjct: 239  DGVHMK-VVADRLKGEVAKFDIVAPD-GKLIVAKDKRITAKHIRDIVAANLDRIEVPSDA 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A  +VN ++GE+   A + I E+ L ++  +EI  + +L+ + ++  +YI  TL
Sbjct: 297  LLGKMLARAVVNTDSGEVIARANEEISEEILAKLALAEIPQVDVLFTNDLDQGSYIAQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR  A + IYR+MRPG+  T    E +F  LFF  D YDLS VGR+K N R   
Sbjct: 357  RVDDIQDRLQARVAIYRMMRPGEPPTEDAVEQLFQRLFFSPDTYDLSRVGRMKFNTRTYQ 416

Query: 423  DTPDDVR---------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               DD                        +  EDI+++I IL +L+NG+G +DDID+LGN
Sbjct: 417  YKFDDKTPEWFKTLIGEKFAERRDVADATLTTEDIVSVIAILCELKNGRGEVDDIDHLGN 476

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGE+ +NQ+R GL+R+ER++KER++  + D++MP DLINAKPV +A+ EFF SSQ
Sbjct: 477  RRVRSVGELAENQFRAGLVRVERAVKERLNQAESDNLMPHDLINAKPVSAAIKEFFGSSQ 536

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIG
Sbjct: 537  LSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 596

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++SL+ +AR N +GF+ETPYRKV +GKVT ++ YLSA+EE    IAQAN+ LD DG+  
Sbjct: 597  LINSLSVYARTNEFGFLETPYRKVIEGKVTMEIDYLSAIEEGRYVIAQANAELDSDGTLI 656

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +ELV CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 657  DELVTCREKGETILATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAV 716

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            P L+ E PFVGTG+E  VA  SG  +VA+R G+V+ VDA RIV+R  + +      GVDI
Sbjct: 717  PCLRPEKPFVGTGIERSVAVDSGTTVVARRGGVVDYVDANRIVVRVNDEEALAGEVGVDI 776

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y L KF RSNQNT +NQRP+VK+GD++ R D++ADG STDLG+LALG+NM +AFMPW+GY
Sbjct: 777  YNLTKFTRSNQNTNINQRPVVKMGDKIARGDVVADGASTDLGELALGQNMTIAFMPWNGY 836

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFEDS+LISE++V+ED +TSIHIEE  V+ARDTKLGPEEITRDIPN+SE     +D+ GI
Sbjct: 837  NFEDSILISEKVVAEDRYTSIHIEELSVVARDTKLGPEEITRDIPNLSERMAGRLDDSGI 896

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G++GTV+D
Sbjct: 897  VYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGMTGTVID 956

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            V++F R GI++++R+ S+   +++    D +D+  I D + +SR+  ++ G+ A  GPK 
Sbjct: 957  VQVFTREGIERDKRAQSIIDAELKRYRLDLNDQLRIFDNDAFSRIERLIMGKVANGGPKR 1016

Query: 1002 FKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K T +  + +   P +  W+   + DE + + +E +K      +   + +F++K  K+
Sbjct: 1017 LAKGTAIDREYLDGLPSKHDWFDIRMADEDIAKQLELIKESLAQKREEFDLKFEDKKRKL 1076

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++PPGV ++VKV++A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDI
Sbjct: 1077 TQGDELPPGVQKMVKVYLAVKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMGDGRPVDI 1136

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLGWA  G+G+++  ++   +A  DI   R +LE+V     
Sbjct: 1137 VLNPLGVPSRMNIGQILEVHLGWAGKGIGEQVNRMLQSQRAVADI---RGYLERVYNQTG 1193

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS------ 1234
              E+I+   D+ +L +A     G+P +TPVFDGA E  I  ML +A  DE  Q+      
Sbjct: 1194 KPEEIAAMSDEEILDLASNLAKGMPFATPVFDGAKEAEIKMMLDLAYPDEDPQTDLLDFN 1253

Query: 1235 ------ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
                   L+DG +GE FDR VTVG ++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1254 ESKTQMTLFDGRSGEAFDRKVTVGVMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQ 1313

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+IV G    + G PESFN
Sbjct: 1314 FGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKVYENIVKGEHKIDAGMPESFN 1373

Query: 1349 VLVKEMQALGLSIDLEN 1365
            VLVKE+++LGL IDLE 
Sbjct: 1374 VLVKEIRSLGLDIDLER 1390


>gi|312882834|ref|ZP_07742567.1| DNA-directed RNA polymerase subunit beta [Vibrio caribbenthicus ATCC
            BAA-2122]
 gi|309369526|gb|EFP97045.1| DNA-directed RNA polymerase subunit beta [Vibrio caribbenthicus ATCC
            BAA-2122]
          Length = 1342

 Score = 1622 bits (4201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1367 (51%), Positives = 970/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EE+L  F+ KI +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEVLDIFFEKINFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++  V  + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDSVDHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292  IVGKVASKDYINESTGEIIVAANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352  RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +   +   + ++DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EDAQEQGTLDEQDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N +GF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNDFGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT++V YLSA++E    IAQAN+ L E G+F+EEL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTDEVDYLSAIQEGQYVIAQANTILTEQGTFSEELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   V+KR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVSKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EE+T DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGAEEVTADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S + +    R +W 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLIDGG-------------YSEERVDAIDRKKWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D+  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELTLDDDAQQTQLEQLAEQYDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+   G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDDKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   +I+  R FL++V   G       +S   D  V+ +    
Sbjct: 1119 LAAKGIGDKINQMV---KEQQEIAKFRDFLQRVYDLGDTRQKVDVSSLSDAEVVTLVNNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E++I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASEKSIKELLKLGDLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|209395131|gb|ACI45386.1| RNA polymerase subunit B [Verminephrobacter sp. At4]
          Length = 1370

 Score = 1622 bits (4201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 688/1375 (50%), Positives = 953/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG    ++++P L+++QK +Y  FL  + AP +R  EGLQAAF + 
Sbjct: 1    MAYSYTERKRIRKSFGTRDSVLEVPYLLQMQKDAYTAFLQADTAPLKRSVEGLQAAFDAA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   + F  Y    P FDV +C  R LTYA  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMRFTEYNLAKPAFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDLLYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A  L  G      + D  +G+ ++   K++T   ++ L++ G   + +  D
Sbjct: 241  DSGAQMEFVAERL-RGEVARFDITD-KSGKVIVAKDKRVTVRHIRELEQSGTTHVSVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA  IV+ +TGEI  +A D + E  L+++  + + D+  +Y + ++   YI  T
Sbjct: 299  FLVGRIVARGIVDADTGEILAKANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L TD  +D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N ++ 
Sbjct: 359  LRTDDTQDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RAESTGAMVLSNEDILAVVKILVDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V   KV+ND+ YLSA+EE    IAQAN+ LD+DG  T ELV  R  GE IL   +++
Sbjct: 599  YRRVVGAKVSNDIDYLSAIEEGKYVIAQANAVLDKDGHLTGELVSAREKGESILCAADRV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPLVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R GIV+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGIVDYVDATRIVVRVNDAEAAAGEVGVDIYSLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD + + D+IADG STDLG++A+G+NML+AFMPW+GYN+EDS+LISER+V++D +TS
Sbjct: 779  VKKGDRLVKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNYEDSILISERVVAQDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  G V+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSQGIVIDVQVFTREGIPRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP    K   +    ++   +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFDRIEKLLTGRVANGGPHKLAKGAQIDRAYLATVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     +++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAEDEVAAQLESIKNALEQTRHGFDLGFEEKRKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I  L+   +    +S LRSFLE+V  +    E ++   D  +L +A   +
Sbjct: 1139 GWAGKGIGQRIGDLL---QQQAKVSELRSFLEEVYNSRGRKEDLTQLSDADLLSMAANLQ 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFDRPVTV 1251
             GVP +TPVFDGA E  I  ML +A  DE            Q+ LYDG +G+ F+RP T+
Sbjct: 1196 QGVPYATPVFDGASEAEIKDMLALAYPDEIARRKGLTPSRTQAYLYDGRSGDRFERPTTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE +
Sbjct: 1316 QEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERA 1370


>gi|218710879|ref|YP_002418500.1| DNA-directed RNA polymerase subunit beta [Vibrio splendidus LGP32]
 gi|218323898|emb|CAV20259.1| DNA-directed RNA polymerase beta chain [Vibrio splendidus LGP32]
          Length = 1374

 Score = 1622 bits (4200), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1367 (51%), Positives = 970/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 33   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 88

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 89   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDRDAPAG--TV 146

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 147  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 206

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 207  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALGKSTEEILDLFFDKVNFEVKD 266

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 267  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 323

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +     A+D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++ +TL
Sbjct: 324  IVEKIAAKDYINEATGEIIVGANQEISLEALANLSQAGHKTLEVLFTNDLDHGPFMSDTL 383

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLSTVGR+K N  +  
Sbjct: 384  RADSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEDRYDLSTVGRMKFNSSIER 443

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 444  EEEEERGTLDESDIIEVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 503

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 504  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 563

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 564  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNDYGFLETPY 623

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT +V YLSA++E    IAQAN+ L E+G+F +EL+  R  GE  L PR+ +D
Sbjct: 624  RRVVDGVVTEEVDYLSAIQEGQFVIAQANTILTEEGTFADELITARQKGESGLHPRDHVD 683

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 684  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERNIAVD 743

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 744  SGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 803

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 804  LPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 863

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 864  HIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 923

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 924  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 983

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 984  QLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTIGRKQWL 1030

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1031 EQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1090

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1091 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1150

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R FL+KV   G       I++  DD V  + +  
Sbjct: 1151 LAAKGIGDKINQMV---KEQQELHKFREFLQKVYDLGDTRQKVDIAELSDDQVRTLIKNL 1207

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1208 RGGLPIATPVFDGASESLIKELLKLGDLPESGQLKLFDGRTGDSFERPVTVGYMYMLKLN 1267

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1268 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1327

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1328 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1374


>gi|115378469|ref|ZP_01465628.1| DNA-directed RNA polymerase, beta subunit [Stigmatella aurantiaca
            DW4/3-1]
 gi|310822260|ref|YP_003954618.1| bifunctional DNA-directed RNA polymerase subunit beta-beta'
            [Stigmatella aurantiaca DW4/3-1]
 gi|115364531|gb|EAU63607.1| DNA-directed RNA polymerase, beta subunit [Stigmatella aurantiaca
            DW4/3-1]
 gi|309395332|gb|ADO72791.1| Bifunctional DNA-directed RNA polymerase subunit beta-beta'
            [Stigmatella aurantiaca DW4/3-1]
          Length = 1408

 Score = 1622 bits (4199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 736/1376 (53%), Positives = 1000/1376 (72%), Gaps = 26/1376 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F K  +IIDIP+LI +QK SY+ FL  +IAP++R + GLQ  FKSVFPI  F+  
Sbjct: 10   RVRKTFAKIAKIIDIPNLINIQKQSYEKFLQADIAPEKREDLGLQGVFKSVFPIRDFNET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +TY+ P+K+ +RL+V+D DE TGA+SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYHLEKPKYDVDECHQRGMTYSAPIKVVVRLVVWDKDEETGAQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT++GTF+I G +R+VVSQLHRSPG  FDHDKG++  SGKLLY  RIIP +G W
Sbjct: 130  FGEIPLMTQNGTFIINGTERVVVSQLHRSPGAFFDHDKGKSHSSGKLLYNARIIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--------------DSEEILSTFYPKIV 237
            +D EFD KD+++VRIDRRRK+P T  + ALG                +EEIL+ +Y    
Sbjct: 190  IDFEFDHKDLLYVRIDRRRKLPATVLIRALGAVQDTAKKNPLTFSGSTEEILNYYYATET 249

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
                 +         +L+ G + +  +    TG+ +++  +K T   +K L+   +K L 
Sbjct: 250  IYLTSNVDFEKSVELELLPGQRATRDI-KTKTGDLIVKKNRKFTRAAIKKLEAAKMKTLP 308

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            I +D L     A D+V+  TGE+ +E  + + ++ ++E+   +I++  +L++D++N   Y
Sbjct: 309  IDADELFTKVSAYDVVDENTGEVILECNEEVSQEKVDELLKRDIKEFKVLFIDNLNVGPY 368

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +R TL+ DK +  + A+++IYR +RPGD  T   A ++F+ LFF+ ++YDLS VGR+K+N
Sbjct: 369  LRETLMMDKIETPEQAIMEIYRRLRPGDPPTPETATNLFSNLFFNPERYDLSKVGRLKLN 428

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             + +L+ P D + + K DI+ +I+ LVDL+NGKGTIDDID+LGNRRVR+VGE+L+NQYR+
Sbjct: 429  FKFSLEEPLDGQILTKRDILEVIRYLVDLKNGKGTIDDIDHLGNRRVRAVGELLENQYRI 488

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+RMER+IKER+S  +I+++MP DLINAKPV + + EFF SSQLSQ  +  N LS +TH
Sbjct: 489  GLVRMERAIKERMSLQEIETLMPHDLINAKPVTAVIKEFFGSSQLSQFMDQTNPLSEVTH 548

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++ARVN +GF
Sbjct: 549  KRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIASLSTYARVNEFGF 608

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +ETPYRKV  G VT DV + SA+EEE   I QAN+  D+ G F   LV  R  GE +   
Sbjct: 609  VETPYRKVEAGSVTADVAFYSALEEEKHTIGQANAETDKKGKFVNALVSSRRGGEFVQAK 668

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E +D +D SP Q+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+  AP VGTG+E+
Sbjct: 669  AEDVDLMDVSPNQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRTAAPLVGTGIEA 728

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            +VA+ SG   VA+R G+VE VDA RIV+++  +  L   +S VDIY L+K+QRSNQNTC+
Sbjct: 729  IVARDSGVTCVARRDGVVESVDASRIVVKADSQAALSDVSSEVDIYNLLKYQRSNQNTCL 788

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ+P+V+ GD VR+ D+IADGP+T+ G+LALG+N++VAFMPW GYNFEDS+LISER++ +
Sbjct: 789  NQKPIVRKGDRVRKGDVIADGPATETGELALGQNVVVAFMPWQGYNFEDSILISERILRD 848

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFE +ARDTKLG EEITRDIPNV EE LK++DE GII +GAEV PGD+LVG
Sbjct: 849  DVFTSIHIEEFECIARDTKLGKEEITRDIPNVGEEALKDLDESGIIRIGAEVKPGDVLVG 908

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGE+ ++PEEKLLRAIFGEKA DVRD+SLRVP GV GTV++ ++F+R G++K+ER+
Sbjct: 909  KITPKGETQLSPEEKLLRAIFGEKAGDVRDSSLRVPPGVQGTVINAKVFSRKGVEKDERA 968

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVLSS 1010
              +E  +   L +D++DE  +L  + +SRL  +L G+ A        G    KK  +L+ 
Sbjct: 969  KQIESAEEAKLLKDQNDEIKVLQDSAFSRLRNLLRGKEAQGKLVDDKGKILLKKGDILND 1028

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +L++  P   W + +V D  +   +  +    E +K  ++  F  KI +I+ GD++PPGV
Sbjct: 1029 ELLATVPYKYWAEISVGDP-LDGRIRDILKSLEDTKEAVKLAFGEKIARIKKGDELPPGV 1087

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKV+VA+KR +  GDKMAGRHGNKG+VSRI P EDMP+L DG PVDIVLNPLGVPSR
Sbjct: 1088 IKMVKVYVAIKRKLAVGDKMAGRHGNKGVVSRIHPEEDMPYLDDGRPVDIVLNPLGVPSR 1147

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQI ETHLGWA  G+G++++  I +  +      L+  L+ V    +  + +    D
Sbjct: 1148 MNIGQILETHLGWAAKGVGEQLQRYIEENYSG---EQLKKQLKTVYDDKAFGDFVDALPD 1204

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            D V  + ++ K G+ V+TPVFDGA E  I+S+   A L  +GQ +L+DG TGEPFD+ VT
Sbjct: 1205 DEVKILCQRLKKGIHVATPVFDGAREPEIHSLFDEARLPRTGQMVLFDGRTGEPFDQNVT 1264

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY 
Sbjct: 1265 VGVMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYT 1324

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQE LT+KSDDVVGRTR+YE+IV G++  E+G PESFNVL+KE+Q+L L ++L  S
Sbjct: 1325 LQEFLTVKSDDVVGRTRMYEAIVKGDNVLESGLPESFNVLLKELQSLALDVELLES 1380


>gi|78099430|gb|ABB20851.1| RNA polymerase subunit B [Acinetobacter berezinae]
          Length = 1362

 Score = 1622 bits (4199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1374 (51%), Positives = 964/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++  P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMHAPYLLAIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  T+A P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTFAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVILRALNYSNEQILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      + D D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDI   + GE+   A  ++  + L +I    ++   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDITLRD-GEVIA-ANTILSHEVLVKIAEGGVKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF +++YDLS VGR+K N RL  
Sbjct: 353  RADTTTGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSTERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNDDIIDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER++  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLNQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S +D+DG  TEE V  R  GE +
Sbjct: 593  FGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSGVDKDGHLTEEFVSVRHQGEFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++AKR G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAKRGGRIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVSLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV+ GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVSAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRV S V GTV+DV++F R GI+K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVSSSVKGTVIDVQVFTRDGIEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   L+ D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEFKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLTEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 NLELVDLLEVQPADEGIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI  ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIDKMMKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   + GVP++TPVFDGA+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRKGVPLATPVFDGAEEGQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|257454924|ref|ZP_05620172.1| DNA-directed RNA polymerase, beta subunit [Enhydrobacter aerosaccus
            SK60]
 gi|257447634|gb|EEV22629.1| DNA-directed RNA polymerase, beta subunit [Enhydrobacter aerosaccus
            SK60]
          Length = 1372

 Score = 1621 bits (4198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1380 (51%), Positives = 972/1380 (70%), Gaps = 19/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P ++D+P L+ +Q  SY+ FL  N  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFAKLPTVMDVPYLLAIQVDSYEQFLQENKKPKGRENIGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPI + +G A L+FV Y    P+FDV +C+ R  TYA PL++ +RL++ D D        
Sbjct: 61   FPIESHTGNAELQFVEYYLGTPEFDVRECILRGSTYAAPLRVKIRLVIKDKDVKDKDAKA 120

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDI+EQS+YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG++  SGK+LY
Sbjct: 121  AIKDIREQSVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD+KD++  RIDRRRK+  T  L A+GM++++IL  FY K    +
Sbjct: 181  NARIIPYRGSWLDFEFDAKDLVFARIDRRRKLLATVILHAIGMNTQQILDAFYEKTHVYK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + +   L   D + G      +V  D GE ++E GK++ +  ++ +++ G+  L +  
Sbjct: 241  GDEQFEIDLV-TDRLRGEMAQFEIVSPD-GEVIVEQGKRINARAIRKIEQAGMTKLPVPD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    +A+DIV  +  E+   A  ++D ++L +I +++I++  IL+ + +++ +YI +
Sbjct: 299  EYLYERILAQDIVVDD--EVIARANQLLDHETLVKISNNDIKEFDILFTNDIDHGSYIAD 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D    R++AL++IY+VMRPG+  T   AE +F  +FF++D+YDLS VGR+K N RL
Sbjct: 357  TLRADTAMSREEALIEIYKVMRPGEPPTLDTAEKLFESMFFNADRYDLSNVGRMKFNRRL 416

Query: 421  NL--------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
                      D   +   +  EDII ++K+L+++R+G+G +DDID+LGNRRVRSVGEM +
Sbjct: 417  GRAYEPTNDPDVQRERSVLTNEDIIDVLKMLIEIRDGRGVVDDIDHLGNRRVRSVGEMTE 476

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            NQ+R+GL+R+ER++KER+SS + D++ PQDLIN+KPV +A+ EFF SSQLSQ  +  N L
Sbjct: 477  NQFRVGLVRVERAVKERLSSAETDNLSPQDLINSKPVAAAIKEFFGSSQLSQFMDQNNPL 536

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +A+ 
Sbjct: 537  SEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLAVYAKT 596

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            N +GF+ETPYRKV DGKVT+++ YLSA+EE    IAQA+S +D+ G  TE+ V  R  GE
Sbjct: 597  NEFGFLETPYRKVVDGKVTDEIEYLSAIEEVGTVIAQADSPIDQSGQLTEDYVSVRNYGE 656

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  EK+  +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VG
Sbjct: 657  FVRMAPEKVTHMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVG 716

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TGME  VA+ SG  + AKR G++  VDA R+V++  E ++    +G+DIY L+K+ RSNQ
Sbjct: 717  TGMERHVARDSGVCVTAKRGGVIMDVDASRVVVKVNEDEMQAGEAGIDIYNLIKYTRSNQ 776

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC+NQR +V  GD + R DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER
Sbjct: 777  NTCINQRIIVNQGDVIARGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILLSER 836

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L N+DE GI+ +GAEV  GD
Sbjct: 837  VVKEDRFTTIHIQELTCVARDTKLGTEEITADIPNVGEAALANLDEAGIVYIGAEVQGGD 896

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K
Sbjct: 897  ILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDTSLRVPSSTKGTVIDVQVFTRDGVEK 956

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            + R+ ++E+ Q++   +D  +E  I +     R++ +L GQ    G  G K  TVLS D 
Sbjct: 957  DSRAQAIEKAQLDSYRKDLKEELRIFENAARGRIISLLDGQTVSGG-AGLKSGTVLSEDS 1015

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + +             E     +  +       +  ++++F  K  K+  GDD+  GV +
Sbjct: 1016 MQDMSLETLLDIQPTQEDTAERLSQIGDFLTDKQKEIDEKFTEKKRKLTAGDDLTHGVQK 1075

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVPSRMN
Sbjct: 1076 IVKVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPIEDMPYDENGNPVDIVLNPLGVPSRMN 1135

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDD 1191
            VGQI ETHLG A  GLG KI  +I   K    ++ LR FL+K+    G     +    DD
Sbjct: 1136 VGQILETHLGGAARGLGIKIDEMI---KQQAAVAELRDFLDKIYNQIGGEQVDLGSISDD 1192

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++ +++  ++GVP+ T VFDGA E+ I S+L +A +  SGQ +L+DG TG+ FDRPVTV
Sbjct: 1193 EIIAMSKNLRAGVPMGTAVFDGAKEQQIKSLLELAGMPTSGQQVLFDGRTGQQFDRPVTV 1252

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1253 GYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1312

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRTR+Y++IV G      G PESFNVL KE+++LG++I+L++     +
Sbjct: 1313 QEMLTVKSDDVEGRTRMYKNIVDGEQNMSAGMPESFNVLTKEIKSLGINIELKDHSKSKN 1372


>gi|116748984|ref|YP_845671.1| DNA-directed RNA polymerase subunit beta [Syntrophobacter
            fumaroxidans MPOB]
 gi|158512347|sp|A0LII4|RPOB_SYNFM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|116698048|gb|ABK17236.1| DNA-directed RNA polymerase, beta subunit [Syntrophobacter
            fumaroxidans MPOB]
          Length = 1370

 Score = 1621 bits (4197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 752/1365 (55%), Positives = 995/1365 (72%), Gaps = 10/1365 (0%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK FGK  +IIDIP+LI++QK SY+ FL  ++  + R   GLQ  FKSVFPI  FSG 
Sbjct: 10   RVRKNFGKIHKIIDIPNLIQMQKESYELFLQRDVPSEARSERGLQEVFKSVFPIEDFSGT 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            A LEFV Y F   K++V++CL R +TY  P+KI +RL+V+DVD+  G +SI+DIKEQ IY
Sbjct: 70   ASLEFVQYSFGEVKYEVEECLARGMTYEAPVKIVVRLVVYDVDKEAGTRSIRDIKEQEIY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G LPLMT +GTF+I G +R++VSQLHRSPGI FDHD+G+   SGK+LY+ RIIP +G W
Sbjct: 130  FGTLPLMTDNGTFIINGTERVIVSQLHRSPGIFFDHDRGKTHSSGKILYSARIIPLRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D+EFD KDI+++RIDRRRK PVT  L ALG  +EE+L+ FYP      + +        
Sbjct: 190  LDLEFDPKDILYIRIDRRRKFPVTVLLKALGYATEELLNYFYPSEKIFLKSEAQSEKELN 249

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             D+++G++    ++   TGE +I+  +KL    L+ L+E G+  L + S  L G  +A+D
Sbjct: 250  PDILMGSRAPEDILHPQTGEVLIKKNRKLGKQALRRLQEVGINRLPMKSTELIGQVLAQD 309

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +++  TGEI  E  D ID   L+E     + +I +L+++  + +   RNTL+ DK   ++
Sbjct: 310  VIDYGTGEIVAECNDSIDADMLKEFVERGVGEIELLHLEGQDVSPSFRNTLLMDKVNTQE 369

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            DAL++IYR +RP +  T  VA   FN LFF+ D YDLS VGR+K+N++L L+ P D R +
Sbjct: 370  DALIEIYRRLRPSNPPTLEVATEFFNNLFFNPDHYDLSEVGRLKLNLQLGLEVPLDYRTL 429

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            RK+DI+  ++ L+ L++ +G +DDIDNLGNRRVR+VGE+L+NQYR+GL+RMER+IKER++
Sbjct: 430  RKDDILMAVRQLIRLKDSQGPVDDIDNLGNRRVRAVGELLENQYRIGLVRMERAIKERMT 489

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +++++MP DLINAKPV + V EFF +SQLSQ  +  N LS ITH RRLSALG GG+ R
Sbjct: 490  LQEVEALMPHDLINAKPVSAVVKEFFGTSQLSQFMDQTNPLSEITHKRRLSALGPGGLTR 549

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGRICP ET EG NIGL+ SL+++ARVN YGFIETPYRKV      
Sbjct: 550  ERAGFEVRDVHPTHYGRICPIETPEGPNIGLIVSLSTYARVNPYGFIETPYRKVDGSSAR 609

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             DV YL+AM+E+   IAQAN+ LDE G F  +LV  R AGE ++VP  +I ++D SP Q+
Sbjct: 610  KDVSYLTAMDEKEYPIAQANAPLDEKGRFLLDLVSARVAGEPVMVPPNEIRYMDVSPNQL 669

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS++ASLIPFLE+DD+NR LMG NMQRQAVPL++  AP VGTG+E +VAK SG AIVA+R
Sbjct: 670  VSVSASLIPFLEHDDANRALMGSNMQRQAVPLIQTRAPLVGTGIERIVAKDSGVAIVARR 729

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G+VE VDA RIVIR++E + +   SGVDIY+L+KFQRSNQNTC+NQ+PLV+ GD V + 
Sbjct: 730  TGVVEYVDATRIVIRAIEDNGEMG-SGVDIYKLIKFQRSNQNTCINQKPLVQHGDLVTKG 788

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             IIADGPSTD G+LALGRN++VAFM W GYNFEDS+L+SER+  EDVFTSIHIEEFEV+A
Sbjct: 789  QIIADGPSTDHGELALGRNVMVAFMSWGGYNFEDSILVSERIGKEDVFTSIHIEEFEVVA 848

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG E+ITRDIPNV EE LKN+DE GII VGA + P DILVGK+TPKGES +TPEEK
Sbjct: 849  RDTKLGKEDITRDIPNVGEEALKNLDESGIIRVGAYIKPNDILVGKVTPKGESQLTPEEK 908

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DV+DTSLRVP GV G ++D ++F+R G++K+ER+ ++E ++I  L +D+
Sbjct: 909  LLRAIFGEKASDVKDTSLRVPPGVEGIIIDAKVFSRKGVEKDERTKTIEDQEISRLMKDQ 968

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKG-----FKKSTVLSSDLISEYPRSQWWQFAV 1026
             DE  I+ ++   RL ++L  Q + S  K       KK  V + +++   P   W Q  V
Sbjct: 969  RDELEIIFKSTVKRLAKLLENQVSDSAIKDGKKVYIKKGEVFTEEILLNLPSGHWDQLTV 1028

Query: 1027 -QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             +D  V   +E++   Y     +++  F+ KI K++ GD++PPGV+++VKV+VA+KR +Q
Sbjct: 1029 AKDPTVSMEIENILANYREQVQLVKSLFEEKIGKLKRGDELPPGVIKMVKVYVAVKRKLQ 1088

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRILP EDMP+  DGTPVDIVLNPLGVPSRMNVGQ+ ETH+GWA 
Sbjct: 1089 VGDKMAGRHGNKGVVSRILPAEDMPYFPDGTPVDIVLNPLGVPSRMNVGQVLETHIGWAA 1148

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             G+G ++  ++ + +   +   +   L+++           D  +  +  +   +K G+ 
Sbjct: 1149 KGIGMQLAQMLEECR---ERETMNEKLQRIYNKLEFGTYFKDASERELRGLIPDFKEGIH 1205

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            V++PVFDGA+E  I + L  A + E+GQS+LYDG TG PFD+PVTVG +YMLKL+H+V D
Sbjct: 1206 VASPVFDGAEEAEIRAFLSEAGVSETGQSVLYDGRTGMPFDQPVTVGVMYMLKLHHLVDD 1265

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV GR
Sbjct: 1266 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWTMEAYGAAYALQEFLTVKSDDVAGR 1325

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            TR+YE IV G++T E G PESFNVLVKE+QAL L + L      N
Sbjct: 1326 TRMYEKIVKGDNTLEAGLPESFNVLVKELQALALDVRLLEEEEGN 1370


>gi|121609223|ref|YP_997030.1| DNA-directed RNA polymerase subunit beta [Verminephrobacter eiseniae
            EF01-2]
 gi|158514001|sp|A1WK55|RPOB_VEREI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|121553863|gb|ABM58012.1| DNA-directed RNA polymerase, beta subunit [Verminephrobacter eiseniae
            EF01-2]
          Length = 1370

 Score = 1620 bits (4196), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1375 (50%), Positives = 956/1375 (69%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG    ++++P L+++QK +Y  FL  +  P +R  EGLQAAF + 
Sbjct: 1    MAYSFTERKRIRKSFGTRDSVLEVPYLLQMQKDAYTAFLQADKEPRKRTIEGLQAAFDAA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFIEYNLARPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                        L  G      + D  +G+ ++   K++T+   + L++ G   + +  D
Sbjct: 241  DSGAQMEFVPERL-RGEVARFDITD-KSGKLIVAKDKRVTARHTRDLEQSGSTHISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA  IV+ ++GEI  +A D + E  L+++  + +R++  +Y + ++  AYI +T
Sbjct: 299  FLVGRVVARTIVDADSGEILAKANDELTEALLKKLRSAAVRELQCIYTNELDQGAYISHT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L +D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N R+ 
Sbjct: 359  LRSDETVDEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARIG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RDESTGPMVLSNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V  G VTND+ YLSA+EE    IAQAN+ LD++G  T +LV  R  GE IL   +++
Sbjct: 599  YRRVVGGMVTNDIDYLSAIEEGKYVIAQANAVLDKEGRLTGDLVSAREKGESILCAADRV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  RYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPLVGTGIERVAAI 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGSVDYVDATRIVVRVNDDETVAGEVGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD + + D+IADG STDLG++A+G+NML+AFMPW+GYNFEDS+LISER+VSED +TS
Sbjct: 779  VKKGDRLVKGDVIADGASTDLGEIAIGQNMLIAFMPWNGYNFEDSILISERVVSEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G  GTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVEQGSQGTVIDVQVFTREGIARDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GP    K   +    +S   +  W
Sbjct: 959  DELKRFRLDLNDQLRIVEADAFERIEKLLLGRVANGGPHKLLKGAKIDKPYLSSVEKFHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +      ++V   +E +K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPAQDEVAAQLELIKDALEQTRHSFDLAFEEKKKKLTQGDELPAGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP++ DGTP DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPYMADGTPADIVLNPLGVPSRMNIGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  G+G++I  ++   +     + LR FL+KV      TE ++   D+ ++ +A   +
Sbjct: 1139 GWASKGIGQRIGDML---QQQAKAAELRKFLDKVYNARGRTEDLAQLCDEELVAMAAHLR 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDE----------SGQSILYDGLTGEPFDRPVTV 1251
             G+P +TPVFDGA EE I  ML++A  DE            Q+ LYDG TGE F+RP T+
Sbjct: 1196 HGMPYATPVFDGASEEEIKDMLKIAYPDEIAQRKGLTATRTQAFLYDGRTGERFERPTTI 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDV GRT+VYESIV G    E G PESFNVLVKE+++LGL I+LE S
Sbjct: 1316 QEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNVLVKEIRSLGLDIELERS 1370


>gi|84393084|ref|ZP_00991850.1| DNA-directed RNA polymerase beta subunit [Vibrio splendidus 12B01]
 gi|84376336|gb|EAP93218.1| DNA-directed RNA polymerase beta subunit [Vibrio splendidus 12B01]
          Length = 1342

 Score = 1620 bits (4196), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1367 (51%), Positives = 970/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDRDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALGKSTEEILDLFFDKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIES--NGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +     A+D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++ +TL
Sbjct: 292  IVEKIAAKDYINEATGEIIVGANQEISLEALANLSQAGHKTLEVLFTNDLDHGPFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEDRYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEEEERGTLDESDIIEVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT +V YLSA++E    IAQAN+ L E+G+F +EL+  R  GE  L PRE +D
Sbjct: 592  RRVVDGVVTEEVDYLSAIQEGQFVIAQANTILTEEGTFADELITARQKGESGLHPREHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTIGRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R FL+KV   G       I++  DD V  + +  
Sbjct: 1119 LAAKGIGDKINQML---KEQQELHKFREFLQKVYDLGDTRQKVDIAELSDDQVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASESLIKDLLKLGDLPESGQLKLFDGRTGDSFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|163752494|ref|ZP_02159682.1| DNA-directed RNA polymerase, beta subunit [Shewanella benthica KT99]
 gi|161327613|gb|EDP98809.1| DNA-directed RNA polymerase, beta subunit [Shewanella benthica KT99]
          Length = 1343

 Score = 1620 bits (4195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1364 (51%), Positives = 961/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVMDIPYLLSIQLDSFKKF----TDQDPTGELGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TYA PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGYSELQYVSYKLGEPVFDVKECQIRGITYAAPLRVKLRMVLYDREAAAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+P MT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPQMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPASIMLRALDYSTQDILDLFFERVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A  L  G   S  + D D G  ++E+G+++T+  ++ L++     L +  D 
Sbjct: 235  DSLVMDLVAERL-RGETASYDIKDAD-GSILVENGRRITARHIRQLEKSKTTELEVPIDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I++I  L+++ + N AY+ +TL
Sbjct: 293  IVGKIAGQDYIDPDTGEVLVSANAEITLEDLAKLSMAGIKEISTLFINDLANGAYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N RLN+
Sbjct: 353  RIDPTTNRLEALVEIYRMMRPGEPPTKDAAEGLFQNLFFSEERYDLSKVGRMKFNRRLNI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  GEDEGSGILSKEDIVAVMKNIITIRNGGDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+ + YLSA+EE    IAQAN  +D++G   EE V CR  G+   +    I 
Sbjct: 593  RKVEDGVVTDQIDYLSAIEEGRYVIAQANIDIDKNGRLLEEQVACRHKGDSTFMSASDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E ++A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERIIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +V+KR G+V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVSKRGGVVDYVDASRIVVKVDESELCPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPVVRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV+ GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVSGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  +Y R   +L                      +   PRSQ  
Sbjct: 953  HIAQAKKDLTEEFKILEEGVYGRARNLLLNAG-------------FEQAQLDAIPRSQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 IQTIDDEAKQIELEQLAEQHDELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS+I P EDMP+ ++G P+DIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1060 MIQPGDKMAGRHGNKGVVSKINPVEDMPYDENGNPIDIVLNPLGVPSRMNIGQILEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I +++ + +   +I      + ++         I  + DD +LR+A+  K+
Sbjct: 1120 AAAKGIGDQITAMLEEQRQLAEIRAYIKEVYELGDDVLQRVDIDSFTDDEILRLAKNLKA 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  LYDG TG+ FDR VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKEMLTLAKLPTSGQRTLYDGRTGDKFDRQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNYQMQPGMPESFNVLLKEIRSLGINIELDQD 1343


>gi|86147869|ref|ZP_01066174.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. MED222]
 gi|85834296|gb|EAQ52449.1| DNA-directed RNA polymerase beta subunit [Vibrio sp. MED222]
          Length = 1342

 Score = 1620 bits (4195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 706/1367 (51%), Positives = 970/1367 (70%), Gaps = 27/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57   FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDRDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALGKSTEEILDLFFDKVNFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L   D + G   S  +     G+  +E+G+++T+  ++ L++ GV+ + +  + 
Sbjct: 235  QTLLMELVP-DRLRGETASFDIE--ANGKTYVETGRRVTARHIRQLEKDGVEHIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +     A+D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++ +TL
Sbjct: 292  IVEKIAAKDYINEATGEIIVGANQEISLEALANLSQAGHKTLEVLFTNDLDHGPFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLSTVGR+K N  +  
Sbjct: 352  RADSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEDRYDLSTVGRMKFNSSIER 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  ++   + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEEEERGTLDESDIIEVMKKLIGIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNDYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT +V YLSA++E    IAQAN+ L E+G+F +EL+  R  GE  L PR+ +D
Sbjct: 592  RRVVDGVVTEEVDYLSAIQEGQFVIAQANTILTEEGTFADELITARQKGESGLHPRDHVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 652  YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERNIAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  LPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  S   +    R QW 
Sbjct: 952  QLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTIGRKQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  ++   K   ++   R FL+KV   G       I++  DD V  + +  
Sbjct: 1119 LAAKGIGDKINQMV---KEQQELHKFREFLQKVYDLGDTRQKVDIAELSDDQVRTLIKNL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TPVFDGA E  I  +L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPVFDGASESLIKELLKLGDLPESGQLKLFDGRTGDSFERPVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1296 DVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1342


>gi|170729016|ref|YP_001763042.1| DNA-directed RNA polymerase subunit beta [Shewanella woodyi ATCC
            51908]
 gi|226699448|sp|B1KMZ0|RPOB_SHEWM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|169814363|gb|ACA88947.1| DNA-directed RNA polymerase, beta subunit [Shewanella woodyi ATCC
            51908]
          Length = 1343

 Score = 1620 bits (4194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1364 (50%), Positives = 959/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLAASIILRALDYSTQDILDLFFDRVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A  L  G   S  + D++ G  ++E G+++T+  ++ L++     L +  D 
Sbjct: 235  DSLVMDLVAERL-RGETASYDIKDVE-GTIIVEKGRRITARHIRQLEKSNTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   +  + L ++  + I++I  LY++ ++N AY+ +TL
Sbjct: 293  IVGKISGQDYIDPDTGEVLVSANAEMTLEDLAKLSLAGIKEISTLYINELDNGAYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL +
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLGI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDDEGTGILSKEDIVAVMKNIITIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+ V YLSA+EE    IAQA   LDE+G   +EL+ CR  G+   +    I 
Sbjct: 593  RKVIDGVVTDQVDYLSAIEEGRYVIAQAIVDLDENGRMMDELIACRHKGDSTFMGAADIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGYIDYVDASRIVVKVNESELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +GD V   D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  AMGDPVVTGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +    +D  +E  IL+  +Y R   +L                  +   +   PRSQ  
Sbjct: 953  HVRQAKKDLTEEFQILEEGVYGRARNLLLSAG-------------FNEAQLDAIPRSQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ DE  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 SQSIDDEGKQTELEQLAEQHDELKADFDKKFEVKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G P+DIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPIDIVLNPLGVPSRMNIGQVLEVHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++ + +   ++      + ++         I  + DD V+R+A+  K 
Sbjct: 1120 AAAKGIGDKIAAMLEEQRELAELRGYIKEVYELGEEVQQRVDIDSFTDDEVVRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P +TP FDGA E+ I  ML +A L  +GQ  L+DG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPTATPAFDGAKEKEIKEMLALAGLPTTGQRKLFDGRTGDEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT +Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTNMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQD 1343


>gi|146329600|ref|YP_001210158.1| DNA-directed RNA polymerase, beta subunit [Dichelobacter nodosus
            VCS1703A]
 gi|158513302|sp|A5EX70|RPOB_DICNV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146233070|gb|ABQ14048.1| DNA-directed RNA polymerase, beta subunit [Dichelobacter nodosus
            VCS1703A]
          Length = 1361

 Score = 1619 bits (4193), Expect = 0.0,   Method: Composition-based stats.
 Identities = 690/1366 (50%), Positives = 950/1366 (69%), Gaps = 10/1366 (0%)

Query: 4    GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
               F    R+RK F K P +++ P L+ +Q  SY+ FL  ++    R  +GLQ AF+S+F
Sbjct: 3    TYSFTEKKRIRKNFSKRPTVLETPYLLSMQIDSYNDFLQQHVPMQSRAKKGLQEAFESIF 62

Query: 64   PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            PI + +    L+FV YEF  P+FDV +C  R +TYA PL++ +RL ++D +  T  K  +
Sbjct: 63   PIKSHNEMVELQFVGYEFGKPEFDVRECQLRGVTYAAPLRVRMRLAIYDKN-STKKKLKQ 121

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             ++ +S+YMGD+PLMT DGTFVI G +R++VSQLHRSPG+ F  D G+   SGK LY  R
Sbjct: 122  VVESESVYMGDIPLMTDDGTFVINGTERVIVSQLHRSPGVFFGDDDGQGHSSGKKLYNAR 181

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            IIP +G W+D+EFD KD+I+ RIDRRRK+ +T  L ALG+ ++E+L  F+ K  +     
Sbjct: 182  IIPYRGSWLDLEFDVKDLIYCRIDRRRKLLITILLRALGLSNQEMLDIFFSKQTFKLNKT 241

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                 +   +   G      ++    GE ++  G+K++S  ++ L EK VK   +  D +
Sbjct: 242  GKIELVFEPEQFAGELAQFDII--ADGEVIVPMGRKISSRFVRQLIEKKVKKQTVPVDFV 299

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G ++A D+V+ ETGE+ + A   + E+ L       +++   L ++   +  Y+ +TL 
Sbjct: 300  VGKFLATDLVDKETGELILAANSELTEELLTRFVELGVKEFQTLLINENGHGGYLADTLR 359

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D+     +A  +IYR+MRPG+  T   A+S+F  LFFD  +YDLS VGR+K N  L  +
Sbjct: 360  LDETTTELEARAEIYRMMRPGEPPTKEAADSLFEGLFFDEARYDLSRVGRMKFNRSLGRE 419

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
              +    + KEDII ++K L+ +++G G+ DDID+LGNRR+RSVGEM +N +R+GL+R+E
Sbjct: 420  ESEGSGILSKEDIIGVVKKLIAIKDGFGSTDDIDHLGNRRIRSVGEMAENAFRIGLVRLE 479

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R++KER++  + + + P+DLIN KPV +AV EFF SSQLSQ  +  N LS +TH RR+SA
Sbjct: 480  RTVKERLAQAESEGLTPKDLINVKPVGAAVKEFFSSSQLSQFMDQNNPLSEVTHKRRISA 539

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETPYR
Sbjct: 540  LGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAVYARTNEYGFLETPYR 599

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV DGKVT+++ YLSA++E    IAQAN+ LDE G+F + L+  R   E  L+P  ++ +
Sbjct: 600  KVIDGKVTDEIEYLSAIDESKYVIAQANAHLDEHGAFMDGLISTRFENEFTLMPSSRVQY 659

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SP+Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME VVA  S
Sbjct: 660  MDVSPRQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERVVAMDS 719

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G  + A R G+++ VD+ RIV++  + ++     GVDIY L K+ RSNQNTC+NQ+PLV 
Sbjct: 720  GVLVKAARGGVIDSVDSSRIVVKVNDDEVQAGGLGVDIYNLTKYTRSNQNTCINQKPLVS 779

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD V R D++ADGPSTD+G+LALG+N+LVAFMPW+GYN+EDS+LISER+  ED FT+IH
Sbjct: 780  PGDIVARGDVLADGPSTDMGELALGQNVLVAFMPWNGYNYEDSILISERVSQEDRFTTIH 839

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE   +ARDTKLGPEEI+ DIPNV E  L  +D  GI+ VGAEV  GDILVGK+TPKGE
Sbjct: 840  IEELTCIARDTKLGPEEISSDIPNVKESALAKLDTTGIVYVGAEVKFGDILVGKVTPKGE 899

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
               +PEEKLLRAIFGEKA DV+D+SLRVP+G+ GTVVDVR++ R GI+K+ER+ ++E+ +
Sbjct: 900  RSQSPEEKLLRAIFGEKASDVKDSSLRVPTGMDGTVVDVRVYTRDGIEKDERAKAIEKME 959

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            I+ +A+D  D+  I   +I+ R   +L GQ     PK  K    +   L+ E    QW+ 
Sbjct: 960  IDSIAKDIKDQLRIFSADIHDRAARLLLGQAIKKAPK-RKSGDTVDQALLDETTPEQWFD 1018

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            F +QDE +   ++++K   E     L+D ++ K  K   GDD+ PGVL++VKV++A+KR 
Sbjct: 1019 FRMQDEAINEKLDAMKQLLEDKHKELQDYYEEKKAKFSQGDDLAPGVLKMVKVYLAVKRR 1078

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q GDKMAGRHGNKG+VS ++P EDMP+++DGTPVDIVLNPLGVPSRMN+GQ+ E HLGW
Sbjct: 1079 LQPGDKMAGRHGNKGVVSLVVPVEDMPYMEDGTPVDIVLNPLGVPSRMNIGQVLELHLGW 1138

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS--HTEKISDYDDDSVLRVAEQWK 1201
            A  GLGK++  ++++      I  LR +L+ V         E +    D+   ++    +
Sbjct: 1139 AAAGLGKRLAQMMDEGAP---IKELRRYLDAVYNHNPACKKEDLDALSDEDFWQLCRNLR 1195

Query: 1202 SGVPVSTPVFDGADE-EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
             G+P++TPVFDGA+E E +  ML +A+L  +GQ+ LYDG TGE FDR V+VGY+YMLKL+
Sbjct: 1196 QGIPMATPVFDGAEEVEDLQKMLELAELPATGQTHLYDGRTGERFDREVSVGYMYMLKLH 1255

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YSLVTQQPLGG++  GGQR GEMEVW +QAYGA+Y LQEMLT+KSD
Sbjct: 1256 HLVDDKMHARSTGPYSLVTQQPLGGRAQFGGQRFGEMEVWALQAYGASYTLQEMLTVKSD 1315

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL KE++ALG+ I L   
Sbjct: 1316 DVDGRTKMYKNIVDGNLKIEPGLPESFNVLTKEIRALGIDIGLTQD 1361


>gi|121606528|ref|YP_983857.1| DNA-directed RNA polymerase subunit beta [Polaromonas
            naphthalenivorans CJ2]
 gi|158513872|sp|A1VTF8|RPOB_POLNA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120595497|gb|ABM38936.1| DNA-directed RNA polymerase subunit beta [Polaromonas
            naphthalenivorans CJ2]
          Length = 1370

 Score = 1618 bits (4191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1375 (50%), Positives = 964/1375 (70%), Gaps = 16/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FG    ++ +P L+++QK +Y  FL  + AP +R  EGLQAAF++ 
Sbjct: 1    MAYSFTERKRIRKSFGNRESVLTVPYLLQMQKDAYIAFLQADRAPQKRMVEGLQAAFQNA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI + +G   ++F+ Y    P FDV +C  R LT+A  ++  ++LI++D +  T  +K 
Sbjct: 61   FPIVSHNGFVEMKFIEYNLAKPAFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKV 120

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121  VKEVKEQEVYMGEVPLMTDKGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G++ E IL+ F+    +   
Sbjct: 181  ARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLNHESILANFFVFDNFRLM 240

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                     A   M G      L D   G+ V+   K++T    + L++ G   + +  D
Sbjct: 241  DSGAQMEFVAE-RMRGEVARFDLTD-KAGKVVVAKDKRITVRHTRELEQSGTTSISVPED 298

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  VA++I++ +TGEI  +A D + E  L+++  + I+++ +LY + ++  AYI  T
Sbjct: 299  FLIGRVVAKNIIDTDTGEIIAKANDELTELLLKKLRTAGIQNLQVLYTNELDQGAYISQT 358

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D+  D   A + IYR+MRPG+  T    +++F  LF++ D YDLS VGR+K N R+ 
Sbjct: 359  LRADETADEFAARVAIYRMMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARVG 418

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  EDI+A++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419  RDESTGPMVMTNEDILAVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 478

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+++KER+   + + +MP DLIN+KP+ +A+ EFF +SQLSQ  +  N L+ ITH RR+
Sbjct: 479  IEKAVKERLGQAEQEPLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLAEITHKRRV 538

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETP
Sbjct: 539  SALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETP 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V D KVT ++ YLSA+EE    IAQAN++LD +G  T +LV  R  GE ILV  E++
Sbjct: 599  YRRVADSKVTMEIDYLSAIEEGKYVIAQANAALDNEGRLTGDLVSAREKGESILVSAERV 658

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A 
Sbjct: 659  QYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQAVPVLRPEKPLVGTGIERVAAV 718

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  + A R G+V+ VDA RIV+R  + +      GVDIY L+K+QRSNQNT ++QRP+
Sbjct: 719  DSGTVVTATRGGVVDYVDATRIVVRVNDAEALAGEIGVDIYNLIKYQRSNQNTNIHQRPI 778

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK+GD++ + D++ADG STDLG++A+G+NML+ FMPW+GYNFEDS+LISER+V+ED +TS
Sbjct: 779  VKMGDKLAKGDVVADGASTDLGEIAIGQNMLIGFMPWNGYNFEDSILISERVVAEDRYTS 838

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  VMARDTKLG EEITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPK
Sbjct: 839  IHIEELVVMARDTKLGSEEITRDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPK 898

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  +  
Sbjct: 899  GETTLTPEEKLLRAIFGEKASDVKDTSLRVSQGSSGTVIDVQVFTREGITRDKRAQQIID 958

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++++    D +D+  I++ + + R+ ++L G+ A  GPK   K T L    +++  +  W
Sbjct: 959  DELKRYRLDLNDQLRIVEADAFDRIEKLLIGKIANGGPKKLAKGTKLDKAYLTDVEKYHW 1018

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +     D++V   +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+K
Sbjct: 1019 FDIRPADDEVASQLESIKNSMEQTRHSFDLSFEEKRKKLTQGDELPSGVLKMVKVYLAVK 1078

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDKMAGRHGNKG+VS+I+P EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HL
Sbjct: 1079 RRLQPGDKMAGRHGNKGVVSKIVPVEDMPHMADGTPCDIVLNPLGVPSRMNVGQVLEVHL 1138

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLG++I  ++   +A   ++ LR F++ +      TE ++   D+ V+ +A+   
Sbjct: 1139 GWAAKGLGQRIGDML---QAESKVAELRQFMDTLYNKSGRTEDLASLSDEQVVEMAQNLT 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTV 1251
            +GVP +TPVFDGA E  I +ML++A                Q+ LYDG TG+ F+R  TV
Sbjct: 1196 TGVPFATPVFDGASEADIMTMLQLAYPDAVAKAKGLTPTRTQAQLYDGRTGDAFERTTTV 1255

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAYVL
Sbjct: 1256 GYMHFLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYVL 1315

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            QEMLT+KSDDVVGRT+VYESIV G      G PESFNVLVKE+++LG+ ++LE S
Sbjct: 1316 QEMLTVKSDDVVGRTKVYESIVKGEHAITAGMPESFNVLVKEIRSLGIDMELERS 1370


>gi|221135383|ref|ZP_03561686.1| DNA-directed RNA polymerase, beta subunit [Glaciecola sp. HTCC2999]
          Length = 1343

 Score = 1618 bits (4191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1367 (51%), Positives = 971/1367 (71%), Gaps = 26/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P++++IP L+ +Q  S+  F+ +N       + GL+AAF SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLEIPYLLSIQLDSFKKFIDVN----GGNDAGLEAAFGSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD +   G  ++
Sbjct: 57   FPIKSYSGNSELQYVSYRLGEPMFDVRECQIRSVTYSAPLRVKLRLVLFDKEAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL  F+ K+      
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPASIILRALEYSTEEILEMFFEKVKIRFEE 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     +   D + G      ++D   G  ++E G+++++   +SL++  +  L +  + 
Sbjct: 235  EKTFMEIVP-DHLRGETAQFDILD-KEGNVLVEHGRRISARHTRSLEKAKITELEVPPEY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+ +I++  TGE+   A D +    +E++  + I     LY++ +++ +YI +TL
Sbjct: 293  IIGRVVSNNIIDENTGEVVANANDELTVDLVEKLKEAGINSFDTLYINEIDHGSYISDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR +AL++IYR+MRPG+  T   AE++F+ LFF  ++YDLSTVGR+K N RL  
Sbjct: 353  RVDSTNDRLEALVEIYRMMRPGEPPTKDAAETLFDNLFFSEERYDLSTVGRMKFNKRLGR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       + KEDI+A+++ L+ +R+GK  +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DEITGPGILSKEDIVAVMQQLITIRDGKDDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVKERLSLGDLDNIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+SFAR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSSFARTNDYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+V DG VT ++ +LSA+EE    IAQAN  +D      +EL+ CR  GE  L+ +  I 
Sbjct: 593  RRVVDGVVTEEIDFLSAIEEGQFAIAQANVEIDAAQQLVDELIPCRYRGETTLMQKSDIK 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+AAS+IPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTGME  VA  
Sbjct: 653  YMDVSSQQIVSVAASIIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGMERTVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIV++  E ++    +G+DIY L K+ RSNQNTC+NQ+P  
Sbjct: 713  SGVTVVAKRGGVVDYVDASRIVVKVNEAEMTAGEAGIDIYNLTKYTRSNQNTCINQKPTC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD +   D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  NVGDPIVTGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAEEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLGPEEI+ DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCVARDTKLGPEEISADIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V GTV+DV++F R G++K+ R+  +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVRGTVIDVQVFTRDGVEKDARAKEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+  + +D  DE  IL+  I++R   +L                  S D +++  R  W+
Sbjct: 953  QLREVKKDLSDELAILEDGIFARARNLLINNGV-------------SEDKLNDSARESWF 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              A++D+    + E +  Q+   ++  + + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 DIAIKDDDAAADFEQIIEQHAEVRATFDKKLEVKRQKIIQGDDLQPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 HIQPGDKMAGRHGNKGVISTIQPVEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQW 1200
             A  GLG KI  +I   K   +++ LRSFL +V   G+  +   I  + D  + R+AE  
Sbjct: 1120 MAAHGLGVKIDRMI---KEQEEVTKLRSFLNEVYNLGTSRQEVDIDSFTDHEIRRLAENL 1176

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVPV+TPVFDGA E  I  ML++AD+ ESGQ  L+DG TG  F+RPVTVGY+YMLKLN
Sbjct: 1177 RKGVPVATPVFDGATEAEIKEMLKLADIPESGQITLFDGRTGRAFERPVTVGYMYMLKLN 1236

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE + 
Sbjct: 1297 DVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEENE 1343


>gi|330879362|gb|EGH13511.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            glycinea str. race 4]
          Length = 1308

 Score = 1618 bits (4191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1316 (53%), Positives = 963/1316 (73%), Gaps = 9/1316 (0%)

Query: 52   NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
            + GL AAFKSVFPI ++SG A LE+V Y    P FDV +C+ R +TYAVPL++ +RLI+F
Sbjct: 1    DVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTYAVPLRVKVRLIIF 60

Query: 112  DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
            D    +  K+IKDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHD+G+
Sbjct: 61   DK--ESSNKAIKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDRGK 118

Query: 172  ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
               SGKLLY+ RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +E++L  
Sbjct: 119  THSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYTTEQVLDA 178

Query: 232  FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
            FY   V+  RG+     L    L  G      ++D D G+ ++E G+++T+  +  L++ 
Sbjct: 179  FYTTNVFHVRGENLSLELVPQRL-RGEIAVLDILD-DKGKVIVEQGRRITARHINQLEKA 236

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            G+K L +  D + G   A+ IV+  TGEI  E    ++ + L +I  +++  I  LY + 
Sbjct: 237  GIKELEVPLDYVLGRTTAKVIVHPATGEIIAECNTELNTEILAKIAKAQVVRIETLYTND 296

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   ++ +TL  D   ++ +AL++IYR+MRPG+  T   AE++FN LFF  ++YDLS V
Sbjct: 297  IDCGPFVSDTLKIDSTSNQLEALVEIYRMMRPGEPPTKDAAETLFNNLFFSPERYDLSAV 356

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR+K N R+     +    + KEDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM 
Sbjct: 357  GRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMA 416

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ     N 
Sbjct: 417  ENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMGQNNP 476

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR
Sbjct: 477  LSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYAR 536

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
             N YGF+E+PYR V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   
Sbjct: 537  TNQYGFLESPYRVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLN 596

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E  +     +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P V
Sbjct: 597  EFTVKAPADVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLV 656

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSN
Sbjct: 657  GTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSN 716

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SE
Sbjct: 717  QNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSE 776

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  G
Sbjct: 777  RVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVGAG 836

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  GTV+DV++F R G++
Sbjct: 837  DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVE 896

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            ++ R++S+E+ Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++
Sbjct: 897  RDARALSIEKSQLDEIRKDLNEEFRIVEGATFERLRSALLGRVAEGG-AGLKKGQEITNE 955

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            ++      QW++  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL
Sbjct: 956  VLDGLEHGQWFKLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVL 1015

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A++R IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRM
Sbjct: 1016 KIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRM 1075

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDD 1190
            NVGQI ETHLG A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D
Sbjct: 1076 NVGQILETHLGLAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTD 1132

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + +L +A+  ++GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VT
Sbjct: 1133 NEILDLAKNLRNGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVT 1192

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1193 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1252

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 1253 LQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 1308


>gi|157377456|ref|YP_001476056.1| DNA-directed RNA polymerase, beta subunit [Shewanella sediminis
            HAW-EB3]
 gi|189043868|sp|A8G1F5|RPOB_SHESH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157319830|gb|ABV38928.1| DNA-directed RNA polymerase, beta subunit [Shewanella sediminis
            HAW-EB3]
          Length = 1343

 Score = 1618 bits (4190), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1364 (50%), Positives = 958/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+P+MT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPMMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+  +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLAASIILRALDYSTQDILDLFFDRVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A  L  G   S  + D + G  ++E G+++T+  ++ L++     L +  D 
Sbjct: 235  DSLVMDLVAERL-RGETASYDIKDSE-GSILVEKGRRITARHIRQLEKTNTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I++I  LY++ ++N AY+ +TL
Sbjct: 293  ISGKISGQDYIDPDTGEVLVSANAEISLEDLAKLSLAGIKEISTLYINELDNGAYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDDEGTGILSKEDIVAVMKNIITIRNGNDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+ V YLSA+EE    IAQA   LD DG   +EL+ CR  G+   +    I 
Sbjct: 593  RKVIDGVVTDQVDYLSAIEEGRYVIAQAIVDLDADGRMMDELIACRHKGDSTFMGAGDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERTLAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + AKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVAAKRGGYVDYVDASRIVVKVNESELTPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +GD V R D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SMGDPVVRGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAMEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +    +D  +E  IL+  +Y R   +L                  + D ++  PRSQ  
Sbjct: 953  HVGQAKKDLSEEFQILEEGVYGRARNLLLNAG-------------FTEDQLATIPRSQLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQTIDDEAKQTELEQLAEQHDELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G P+DIVLNPLGVPSRMN+GQ+ E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPIDIVLNPLGVPSRMNIGQVLEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I +++ + +   ++      + ++         I  + DD VLR+A+  K 
Sbjct: 1120 AAAKGIGDRITAMLEEQRELAELRGYIKEVYELGEEVQQRVDIDSFTDDEVLRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GVP +TP FDGA E+ I  ML +A L  SGQ  L+DG TG+ F+R VTVGY+YMLKLNH+
Sbjct: 1180 GVPTATPAFDGAKEKEIKEMLALAGLPTSGQRRLFDGRTGDEFERQVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT +Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTHMYKNIVDGNHQMQPGMPESFNVLLKEIRSLGINIELDQD 1343


>gi|329118714|ref|ZP_08247414.1| DNA-directed RNA polymerase subunit beta [Neisseria bacilliformis
            ATCC BAA-1200]
 gi|327465149|gb|EGF11434.1| DNA-directed RNA polymerase subunit beta [Neisseria bacilliformis
            ATCC BAA-1200]
          Length = 1398

 Score = 1618 bits (4189), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1400 (49%), Positives = 959/1400 (68%), Gaps = 40/1400 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL    A D+R +EGLQAAF S+
Sbjct: 1    MTYSFTEKKRIRKSFAKRENVLEVPFLLATQLDSYAKFLQQEKAYDKREDEGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D +       +
Sbjct: 61   FPIVSHNGYARLEFVHYVLGEPLFDIPECQLRGITYAAPLRARIRLVILDKESSKQD-VV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEVRENEVYMGEIPLMTPSGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL TFY K  +    
Sbjct: 180  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYTNEQILDTFYDKETFYLLK 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L A  L  G      +VD   G  ++ +GK++ +  ++ +++ G+K L + +D 
Sbjct: 240  DGVRTDLVAGRL-KGETAKLDIVD-KNGNVLVAAGKRINAKHIRDIEKAGLKHLPVEADA 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+V  +TGE+   A D I E+ L +   + +++I  LY++ ++   YI  TL
Sbjct: 298  LVGKVLARDVVAEDTGEVLALANDEITEELLAQFDINGVKEIHTLYINDLDQGGYISATL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   +  A + IYR+MRPG+  T    E +FN LFF+ D YDLS VGR+K N R   
Sbjct: 358  RTDETNGQHAARIAIYRMMRPGEPPTDEAVELLFNRLFFNEDSYDLSRVGRMKFNTRTYE 417

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 418  QKLSEEQKNSWYGRLLNETFAGAAEKGGFVLNVEDIVASIATLVELRNGHGEVDDIDHLG 477

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 478  NRRVRSVGELAENQFRSGLSRVERAVKERLNQAESENLMPTDLINAKPVSAAIKEFFGSS 537

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 538  QLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 597

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V +GKVT+++ YLSA+EE    IAQAN++LD  G  
Sbjct: 598  GLINSLSVYARTNEYGFLETPYRRVVNGKVTDEIEYLSAIEEGRFVIAQANAALDSKGRL 657

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            T++LV CR  GE I+   +++ ++D +  Q VS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 658  TDDLVTCREKGETIMATVDRVQYMDVATGQAVSVAASLIPFLEHDDANRALMGANMQRQA 717

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+AE P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 718  VPCLRAEKPMVGTGIERDVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEAVAGEVGVD 777

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 778  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 837

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 838  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQSRLDESG 897

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 898  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 957

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 958  DVQVFTREGIQRDKRAQSIIDAELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1017

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P +  W+   V DE + + +E +K   +  +   E  F+ K +K
Sbjct: 1018 KLAKGSEITAEYLASLPSKHDWFDVRVADENIAKQMELIKSSLQDKREEAESLFEIKKKK 1077

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1078 MTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1137

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL--EKVIG 1177
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++++ +   +I      +    + G
Sbjct: 1138 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIGRMLDEKRKVREIRKFLDTMYNGNLGG 1197

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
               H E +S   D  +L +A+  ++G   ++PVFDGA E  I + L +A   +       
Sbjct: 1198 PDRHKEDLSQLSDAEILTLAQNLRNGATFASPVFDGAHESEIKAFLELAYPSDDPEVQKL 1257

Query: 1232 G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            G      Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGG
Sbjct: 1258 GFNDTKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGG 1317

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT++YE+IV G    + G PE
Sbjct: 1318 KAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPE 1377

Query: 1346 SFNVLVKEMQALGLSIDLEN 1365
            SFNVLVKE+++LGL IDLE 
Sbjct: 1378 SFNVLVKEIRSLGLDIDLER 1397


>gi|171462871|ref|YP_001796984.1| DNA-directed RNA polymerase, beta subunit [Polynucleobacter
            necessarius subsp. necessarius STIR1]
 gi|226699428|sp|B1XSP3|RPOB_POLNS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|171192409|gb|ACB43370.1| DNA-directed RNA polymerase, beta subunit [Polynucleobacter
            necessarius subsp. necessarius STIR1]
          Length = 1366

 Score = 1617 bits (4188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 957/1374 (69%), Gaps = 18/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    RVRK F K      +P LI  Q  SY  FL  +     R  EGLQAAF S 
Sbjct: 1    MNYSFTERKRVRKSFAKRVNNHQVPYLIATQLESYAKFLQADKPAMSRLTEGLQAAFTSA 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A +E+VSY+   P FDV +C  R  TY   L+  +RLI++D +  T    +
Sbjct: 61   FPIVSNNGYARMEYVSYQLSQPPFDVKECQQRGYTYHSALRAKVRLIIYDREAPT---KV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KE  +YMG++PLMT++G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118  KEVKESEVYMGEIPLMTENGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI++ RIDRRRK+PVT  L A+G+++E+IL+ F+    +S   
Sbjct: 178  RIIPYRGSWLDFEFDPKDILYFRIDRRRKMPVTILLKAIGLNNEQILANFFNFDHFSLTA 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +          L  G   S  ++D + G  VI+  K++ +  ++ L+    K + +  D 
Sbjct: 238  NGGSMEFVPERL-RGQLASFDVLD-ENGVVVIQKDKRINTKHIRELEAAKTKTIAVPDDY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  VA +IV+ ++GEI   A D I E+ L  +  + I+ +  +Y + +++ AYI  TL
Sbjct: 296  LIGRVVARNIVDPDSGEILAYANDEITEELLATLRDAGIKQLETIYTNDLDSGAYISQTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  D+  A + IYR++RPG+       E +F  LF+  D YDLS VGR+K+N RLN 
Sbjct: 356  RTDETADQMAARIAIYRMLRPGEPPIEDAVEVLFQRLFYSEDTYDLSRVGRMKVNSRLNR 415

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  EDI+  IK LVDLRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL R+
Sbjct: 416  PEMEGPMVLSSEDILDTIKSLVDLRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLSRV 475

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+   + +++MP DL N+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 476  ERAVKERLGQAETENLMPHDLTNSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRIS 535

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR+N +GF+ETPY
Sbjct: 536  ALGPGGLMRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARLNEHGFLETPY 595

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV + KV+++VVYLSA+EE    IAQAN+++D+ G   +ELV  R AGE ++V  E+ID
Sbjct: 596  RKVSNSKVSDEVVYLSAIEEAKYVIAQANATIDKSGKLADELVSARQAGETMMVSPERID 655

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            FID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E +VA  
Sbjct: 656  FIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRPDKPLVGTGLERIVAVD 715

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++A R GIV+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V
Sbjct: 716  SGTVVLAARGGIVDYVDANRVVIRVNDDETTAGEVGVDIYNLIKYTRSNQNTNINQRPIV 775

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD V R D++ADG STDLG+LALG+NM VAFMPW+GYNFEDS+LISE++V++D +TSI
Sbjct: 776  KVGDRVARGDVVADGASTDLGELALGQNMTVAFMPWNGYNFEDSILISEKVVADDRYTSI 835

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+ARDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 836  HIEELSVVARDTKLGSEEITRDISNLAESQLSRLDESGIVYIGAEVEAGDVLVGKVTPKG 895

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GT++DV++F R GI+++ R+ S+ +E
Sbjct: 896  ETTLTPEEKLLRAIFGEKASDVKDTSLRVPSGMIGTIIDVQVFTREGIERDARAQSIIQE 955

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++      +D+  I++ + + RL ++L G+ A  GPK   K T +  + +++  +   +
Sbjct: 956  ELQRYRLGLNDQLRIVEGDAFMRLEKLLIGKVANGGPKKLAKGTKIDKEYLADLDKYHRF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 D++V   VE++K   E  +   ++ F+ K  K+  GDD+ PGV ++VKV++A+KR
Sbjct: 1016 DVRPADDEVASQVEAIKSSIEAKRKQFDEAFEEKRTKLTQGDDLQPGVTKMVKVYLAVKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS+I P EDMPF+ DG PVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 RLQPGDKMAGRHGNKGVVSKIAPAEDMPFMADGRPVDIVLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+GK++  ++   +     + LR FL+++       E I ++ D+ +  +AE  + 
Sbjct: 1136 WAAQGIGKRVDEMV---RQQAKQAELREFLKQLYNETGRIEDIDNFTDEQITVLAENLRQ 1192

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTVG 1252
            G+P +TPVFDGA E  I  ML +A                Q IL DG TG+ F+RP TVG
Sbjct: 1193 GLPFATPVFDGATEAEIGRMLELAYPEEVATSLKMTPSRQQMILCDGRTGDQFERPATVG 1252

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQ
Sbjct: 1253 VMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQ 1312

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            EMLT+KSDDV GRT+VYE+IV G  T + G PESFNVLVKE+++LG+ ID+E +
Sbjct: 1313 EMLTVKSDDVAGRTKVYENIVKGEHTIDAGMPESFNVLVKEIRSLGIEIDMERN 1366


>gi|78099424|gb|ABB20848.1| RNA polymerase subunit B [Acinetobacter baylyi]
 gi|78099432|gb|ABB20852.1| RNA polymerase subunit B [Acinetobacter guillouiae]
          Length = 1362

 Score = 1617 bits (4186), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1374 (51%), Positives = 965/1374 (70%), Gaps = 21/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++  P L+ +Q  SY  FL     P  R + GLQAAF+SV
Sbjct: 1    MAYSYTEKKRIRKNFGKLPQVMHAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A LEFV Y    P+FDV +C+ R  T+A P+++ +RLI+ D +     KSI
Sbjct: 61   FPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTFAAPMRVKIRLIIKDRE----TKSI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 117  KDVREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD++ VRIDRRRK+  T  L AL   +E+IL+ FY K+      
Sbjct: 177  RIIPYRGSWLDFEFDAKDLVFVRIDRRRKLLATVVLRALSYSNEQILNMFYEKVPVYLDM 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L    L  G      +VD D G+ ++E GK++ +  ++ ++  G+  L +  + 
Sbjct: 237  GSYQIDLVPERL-RGEMAQFDIVDND-GKAIVEQGKRINARHVRQMEAAGLTKLPVPDEY 294

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L     AEDIV  + GE+   A  V+  + L  I    I+   IL+ + ++  +++ +TL
Sbjct: 295  LYERITAEDIVLKD-GEVI-TANTVLSHEILVRIAEGGIKQFNILFTNDIDRGSFVADTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE++FN LFF +++YDLS VGR+K N RL  
Sbjct: 353  RADTTSGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSTERYDLSPVGRMKFNRRLGR 412

Query: 423  DTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                       +    +  +DII ++K LV++RNGKG +DDID+LGNRRVRSVGEM +NQ
Sbjct: 413  PYEVGTDQKSREVEGILSNDDIIDVLKTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQ 472

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER++  + D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS 
Sbjct: 473  FRVGLVRVERAVKERLNQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSE 532

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 533  ITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANN 592

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYR+V DG+VT+DV YLSA+EE    IAQA+S+LD+DG  TE+ V  R  G+ +
Sbjct: 593  FGFLETPYRRVVDGRVTDDVEYLSAIEEVGTVIAQADSALDKDGHLTEDFVSVRHQGDFV 652

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG
Sbjct: 653  RMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTG 712

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME+ VA  SG  ++AKR G +E VDA R+VIR  E ++    +GVDIY L+K+ RSNQNT
Sbjct: 713  MEANVAHDSGVCVIAKRGGRIEFVDASRVVIRVNEDEMIAGEAGVDIYNLIKYTRSNQNT 772

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM W+GYN+EDS+L+SER++
Sbjct: 773  CINQKVLVSMGDKVGRGDVLADGPSTDGGELALGQNMRVAFMTWNGYNYEDSILLSERVL 832

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 833  QEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVAAGDIL 892

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRV S V GTV+DV++F R GI+K+E
Sbjct: 893  VGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVSSSVKGTVIDVQVFTRDGIEKDE 952

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  G    K+   LS D++S
Sbjct: 953  RAQAIEKAQLDAYRKDLKEEFKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLS 1011

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    +    DE +   +  ++V  +     ++++F  K  K+  GD++  GVL+VV
Sbjct: 1012 GLELVDLLEVQPTDEGIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVV 1071

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVG
Sbjct: 1072 KVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVG 1131

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            QI ETHLG A  GLG KI  ++ + +    +  LR FL+K+    G   E +    D+ +
Sbjct: 1132 QILETHLGMAAKGLGDKIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEI 1188

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L ++   + GVP++TPVFDGA+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY
Sbjct: 1189 LVLSGNLRKGVPLATPVFDGAEESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGY 1248

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1249 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1308

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 MLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362


>gi|238897913|ref|YP_002923592.1| RNA polymerase, beta subunit [Candidatus Hamiltonella defensa 5AT
            (Acyrthosiphon pisum)]
 gi|259494185|sp|C4K4F1|RPOB_HAMD5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|229465670|gb|ACQ67444.1| RNA polymerase, beta subunit [Candidatus Hamiltonella defensa 5AT
            (Acyrthosiphon pisum)]
          Length = 1341

 Score = 1616 bits (4185), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1363 (50%), Positives = 964/1363 (70%), Gaps = 22/1363 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +     +  +GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKNFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PKGQQGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++S  + L++V+Y    P FDV +C  R  TY+ PL++ LRL+V++ +   G  ++
Sbjct: 57   FPIQSYSAHSELQYVNYRLGEPVFDVKECQIRGATYSAPLRVKLRLVVYEKEAPEG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT++GTFV+ G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTENGTFVVNGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D+EFD KD + VRIDRRRK+P T  L AL   + +IL+ F+ K+ +    
Sbjct: 175  RVIPYRGSWLDLEFDPKDNLFVRIDRRRKLPATIILRALDYSTTDILNLFFEKVRFEICN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  +     G+  +E G+++T+  ++ L +  ++ + +  + 
Sbjct: 235  DKLEMNLVPERL-RGETASFDIQI--NGKIYVEKGRRVTARHIRQLDKDQIQRIEVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA+D ++  TGE+   A   +    L ++  +  + I  ++ + +++  YI  TL
Sbjct: 292  IIGKVVAQDYIDENTGELICSANTELSFDLLAKLSQAGHQQIETIFTNDLDHGDYISQTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+K N  L  
Sbjct: 352  KVDPTTDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEERYDLSAVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D  +    + KEDII ++K L+ +RNGKG IDDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  DEIEGSGILSKEDIIEVMKKLIGIRNGKGEIDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYG++CP ET EG NIGL++SL+ +A  N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGKVCPIETPEGPNIGLINSLSVYACTNEYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VTN++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  +E++D
Sbjct: 592  RSVHEGAVTNEIHYLSAIEEGNFVIAQANSNLDDNGYFIEDLVTCRNKGESSLFRKEQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P +
Sbjct: 712  SGVTCVAKRGGSVQYVDASRIVIKVNENEMHPGEAGIDIYNLNKYTRSNQNTCINQIPCI 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R +++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER++ ED FT+I
Sbjct: 772  NLGELVERGNVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVMQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             I+E   ++RDTKLG EE+T DIPNV E  L  +DE GI+ +GAEVN GDILVGK+TPKG
Sbjct: 832  QIQELACISRDTKLGSEEVTADIPNVGEAALSKLDESGIVYIGAEVNGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ ++PEEKLLRAIFGEKA DV+D+SLRVP+GVS TV+DV+IF R G++K++R++ +E  
Sbjct: 892  ETQLSPEEKLLRAIFGEKASDVKDSSLRVPNGVSATVIDVQIFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++ + +D  +E  IL+  ++ R+  +L                 ++S+ +S  P  +W 
Sbjct: 952  ELKQVKKDLSEELKILEAALFGRIKAVLISGG-------------ITSEKLSRLPCERWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + +E+ Q  +E L  QY+  K+  + + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  ELPLSEEQKQEQLEQLAEQYDEMKAEFDKKMEVKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVL+PLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDEEGNPVDIVLSPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +    +         +      T  +S + D  +L +AE  K 
Sbjct: 1119 MAAKGIGNKINEMLKKNERVSKLRKFIQKAYDLGDGVCQTVDLSTFSDKEILSLAENLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+ ++TPVFDGA E+ I  +L++ADL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMTIATPVFDGAKEKEIKQLLKLADLPTSGQINLFDGRTGEQFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK+++RSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1239 VDDKMHSRSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE 
Sbjct: 1299 NGRTKMYKNIVDGDHRMEAGIPESFNVLLKEIRSLGINIELEE 1341


>gi|95930693|ref|ZP_01313426.1| DNA-directed RNA polymerase, beta subunit [Desulfuromonas acetoxidans
            DSM 684]
 gi|95133173|gb|EAT14839.1| DNA-directed RNA polymerase, beta subunit [Desulfuromonas acetoxidans
            DSM 684]
          Length = 1369

 Score = 1615 bits (4181), Expect = 0.0,   Method: Composition-based stats.
 Identities = 720/1364 (52%), Positives = 992/1364 (72%), Gaps = 12/1364 (0%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F +   II+IP+LI++QK SY  FL  ++    R N GL+A F+SVFPI  FS   
Sbjct: 11   LRKHFSEIQRIIEIPNLIDIQKNSYKRFLQADLPASARQNIGLEAVFRSVFPIRDFSETC 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY  + PK+DV++C  R +T+A P+K+ +RL+ +DVD+ TG +SI+DIKEQ +Y 
Sbjct: 71   SLEYVSYVLEVPKYDVEECHQRGMTFAAPVKVRVRLVSWDVDKDTGVQSIRDIKEQEVYF 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT++GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGKLLY  R+IP +G W+
Sbjct: 131  GEIPLMTENGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKLLYNARVIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D +FD KDI++VRIDRRRK+P T  L ALG  +EE+L  +Y         + +   ++  
Sbjct: 191  DFDFDHKDILYVRIDRRRKLPATVLLQALGYSAEELLKYYYDTETLQINAEGYTKTVN-L 249

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            DL+ G +    +V    G+ ++++ +K T   ++ + E G++ + I    + G  VA D+
Sbjct: 250  DLLAGQRTVLDVV-APNGDVLVKANRKFTKAAIRKISESGLETIAIDESEVLGKVVATDV 308

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+ ETGE+ IE    + E  ++ +    I  + +L++D++    Y+R+TL+ D   + +D
Sbjct: 309  VDTETGEVLIECNQELTETGIQLLREKGITSVDVLFIDNLYVGPYLRDTLLQDTVNNPED 368

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A+++IYR +RPGD  T   A ++F  LFF+S++YDLS VGR+K+N +L ++TP + R + 
Sbjct: 369  AMIEIYRRLRPGDPPTVRSATALFEGLFFNSERYDLSVVGRLKLNYKLGVETPLEHRTLT 428

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            KEDI+ +++ L+DLRNGKG +DDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S 
Sbjct: 429  KEDILEVVRYLIDLRNGKGHVDDIDHLGNRRVRAVGELLENQYRVGLVRMERAIKERMSL 488

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++DS+MP DLIN+KPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R 
Sbjct: 489  QEVDSLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRE 548

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V DG+VT+
Sbjct: 549  RAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRLVQDGRVTS 608

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            ++ Y SA+EEE   IAQAN+ LD+DG F  E++  R +GE +++ RE I  +D SPKQ+V
Sbjct: 609  EIKYFSALEEEGHAIAQANAELDDDGCFVNEVINARQSGEFMMLRREDIQLMDVSPKQLV 668

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AA+LIPFLENDD+NR LMG NMQRQAVPLL+A+AP VGTGME +VA  SGAA+VA+  
Sbjct: 669  SVAAALIPFLENDDANRALMGSNMQRQAVPLLRADAPLVGTGMERIVAHDSGAAVVARHD 728

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA RIV+R  EG  D + +GVDIY L+KF RSNQNTC+NQ+P+V+VGD V R  
Sbjct: 729  GVVESVDASRIVVRIDEGQDDETGTGVDIYNLIKFIRSNQNTCLNQKPIVEVGDHVERGA 788

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGPST  G+L LG+N+LVAFMPW GYNFEDS+LISE++V ED +TSIHIEEFE +AR
Sbjct: 789  IIADGPSTQWGELGLGQNVLVAFMPWEGYNFEDSILISEKLVKEDRYTSIHIEEFECVAR 848

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLG EEIT DIPN+ ++ LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKL
Sbjct: 849  DTKLGKEEITDDIPNLGDDALKDLDESGIIRIGAEVKPGDILVGKITPKGETQLSPEEKL 908

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DVRDTSLRVP GV G V+  R+F+R G DK+ R+  +E+ +I+ L +D++
Sbjct: 909  LRAIFGEKAGDVRDTSLRVPPGVEGVVIGARVFSRKGSDKDSRTEKIEQHEIDKLLKDQN 968

Query: 973  DEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            DE  I+  +   +L ++LCG    +      G    KK++VL +D +     +++ + ++
Sbjct: 969  DEIRIIRESARHKLTDLLCGNKLAASVTDDDGKVLLKKNSVLEADQLEALSVARFQEISL 1028

Query: 1027 QD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             D E ++  V  L       + +++  F +KI+KI+ GDD+PPGV+++VK+++A+KR + 
Sbjct: 1029 VDGEAIEDRVAELMRGLADREELIKRVFSDKIDKIKRGDDLPPGVIKMVKIYIAIKRKLS 1088

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG++SRILP EDMP+ +DGTPV+IVLNPLGVPSRMNVGQI E HLG A 
Sbjct: 1089 VGDKMAGRHGNKGVLSRILPVEDMPYSEDGTPVEIVLNPLGVPSRMNVGQILEIHLGLAA 1148

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG +I+ +++    + +   LR  ++ V         + D  +  V ++A++   G+P
Sbjct: 1149 RGLGNQIQEVLDRQHTHNE---LREKIKDVYDDQELNPFLDDLSEMDVNKLAKRLAPGIP 1205

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            ++TPVF+G  E  I   +  +    SGQ  LY+G TGE F   VTVG +YMLKL+H+V D
Sbjct: 1206 MATPVFEGVSESMIKEQITRSGFSPSGQMTLYNGKTGEAFKEKVTVGIMYMLKLHHLVDD 1265

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE LT+KSDDV GR
Sbjct: 1266 KIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGASHALQEFLTVKSDDVAGR 1325

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            TR+YE+IV G  T E G PESFNVL+KE+Q+L L ++L     K
Sbjct: 1326 TRMYEAIVKGRHTLEAGLPESFNVLIKELQSLCLDVELLEDEEK 1369


>gi|90407965|ref|ZP_01216138.1| DNA-directed RNA polymerase, beta subunit [Psychromonas sp. CNPT3]
 gi|90310903|gb|EAS39015.1| DNA-directed RNA polymerase, beta subunit [Psychromonas sp. CNPT3]
          Length = 1344

 Score = 1613 bits (4177), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1367 (51%), Positives = 985/1367 (72%), Gaps = 25/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +     +RK FGK P++++ P L+ +Q  S+  F+ +++        GL+AAF+S+
Sbjct: 1    MGYSYTEKKLIRKDFGKRPQVMEKPYLLSIQLDSFKRFIEVDLT----GEVGLEAAFRSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+  +++ LRL+++D D   G  +I
Sbjct: 57   FPIASYSGTSELQYVSYRLGEPVFDVKECQIRGVTYSASVRVKLRLVIYDRDAPAG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIREQEVYMGEMPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   +++IL  F+    +    
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIMLRALEYSTQDILDMFFDTTKFEI-K 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D        AD + G ++S  +V    G+  +E+GK++T+  ++ L++  +K L + ++ 
Sbjct: 234  DGAISMALIADRLRGEQLSFDIVSA--GKVYVEAGKRVTARHIRQLQKDKIKHLEVPAEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   A+D ++ ETGEI I A D++  +SL E+  S I+   ++Y + ++  +++ +TL
Sbjct: 292  LEGKVSAKDYISSETGEIIINANDILTLESLAELAQSGIKAFEVIYTNELDCGSFMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + +R +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N R+  
Sbjct: 352  RVDSSTNRLEALVEIYRMMRPGEPPTKDAAEGLFQNLFFAEERYDLSKVGRMKFNRRVGN 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + KEDI++++K L+D+RNG G +DDID+LGNRR+R VGEM +NQ+R+GL+R+
Sbjct: 412  EGDEGKGILSKEDILSVMKTLIDIRNGNGVVDDIDHLGNRRIRCVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D+ MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVKERLSLGDLDATMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR N+YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLATFARTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DGK ++ V YLSA+EE +  IAQA++ +DE+G   EE + CR  GE   +  ++ID
Sbjct: 592  RKVVDGKPSDKVEYLSAIEEGSFVIAQASARIDENGFLNEESIPCRHEGETTFMAPDQID 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++SIAASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A  
Sbjct: 652  YMDVSPQQIISIAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERRIAID 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++AKR+G+V+ VDA RIVI+  + +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 712  SGVTVIAKRSGLVDYVDASRIVIKVDDSELLPGEAGIDIYNLTKYTRSNQNTCINQRPTC 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K G+ + + D++ADGPSTD+G+LALG+NM +AFMPW+G+NFEDS+LISER+  ED FT+I
Sbjct: 772  KPGEPIVKGDVLADGPSTDMGELALGQNMKIAFMPWNGFNFEDSILISERVAQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+EF  +AR+TKLG EEI+ DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 832  HIQEFSCVARETKLGCEEISADIPNVGEAALSKLDESGIVYVGAEVKPGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRV +    TV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVANSTYATVIDVQVFTRDGVEKDKRALEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D +++  IL+  I+ + ++IL                      + + PR+QW 
Sbjct: 952  QLKSAKKDLNEKFKILENAIFEKALKILVSAGQ-------------DEQRLKQMPRAQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  V D+  Q  ++ +  QY+  K+  E  F  K  KI  GDD+ PGV ++VKV++A++R
Sbjct: 999  EIIVDDQTQQSYLDQIIAQYDDIKADYEKEFDIKRRKITQGDDLAPGVQKIVKVYLAVRR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VS I+P EDMP  + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 RLQPGDKMAGRHGNKGVVSNIVPVEDMPHDEFGVPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT--EKISDYDDDSVLRVAEQW 1200
             AC G+G+K++ +I + +   +++ +R F++K+   G       IS++DD++V+R+A+  
Sbjct: 1119 LACKGVGEKLERMIKNQR-EVEMAKVREFIQKLYSFGEAPCHVDISEFDDEAVMRLAKNL 1177

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G+PV+TP FDGA E  I  +L++ADL ESGQ IL DG TG PF+RPVTVGY+YMLKLN
Sbjct: 1178 YRGLPVATPAFDGAYESEIRELLKLADLPESGQLILTDGRTGIPFERPVTVGYMYMLKLN 1237

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QA+GAAY LQEMLT+KSD
Sbjct: 1238 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAFGAAYTLQEMLTVKSD 1297

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   E G PESFNVL+KE+++L ++I+L+   
Sbjct: 1298 DVNGRTKMYKNIVDGDHRMEPGIPESFNVLLKEIRSLSINIELDEEN 1344


>gi|171060537|ref|YP_001792886.1| DNA-directed RNA polymerase subunit beta [Leptothrix cholodnii SP-6]
 gi|170777982|gb|ACB36121.1| DNA-directed RNA polymerase, beta subunit [Leptothrix cholodnii SP-6]
          Length = 1375

 Score = 1612 bits (4173), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1377 (50%), Positives = 969/1377 (70%), Gaps = 17/1377 (1%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A    +    R+RK FGK   ++++P L+ +QK SY  FL  ++ P +R  EGLQAAF S
Sbjct: 4    ASPYSYTERKRIRKSFGKRASVLNVPYLLTMQKDSYVAFLQKDVPPKQRKPEGLQAAFIS 63

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AK 120
             FPI + +G   ++F+ +    P FDV +C  R LT+A  ++  L++IV+D +  T  +K
Sbjct: 64   AFPIVSHNGFVEMKFIEFNIAKPPFDVRECQQRGLTFAAAVRAKLQMIVYDREASTSQSK 123

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K+IKEQ +YMG++PLMT  G+F++ G +R++VSQLHRSPG+ F+HDKG+   SGKLL+
Sbjct: 124  VVKEIKEQEVYMGEVPLMTDYGSFIVNGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLF 183

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI+  R+DRRRK+PVT  L A+G++ E+IL+ F+    +  
Sbjct: 184  SARIIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILLKAIGLNPEQILAHFFKFDNFRL 243

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                      A   + G      + D   G  V+E  K++T+  ++SL   G +++ +  
Sbjct: 244  MDTGAQMEFVAE-RIKGEVARFDITD-KNGNVVVEKDKRITAKHIRSLDASGTQYISVPE 301

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            D L G  VA ++V+ +TGEI  +A D + E  L+++  + I+D+  LY + +N  A+I  
Sbjct: 302  DFLVGRVVARNMVDADTGEIVAKANDELTELLLKKLRSAGIKDLQCLYTNELNQGAFISQ 361

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL +D+  D+  A + IYR+MRPG+  T    E++F+ LF+++D YDLS VGR+K N R+
Sbjct: 362  TLASDETADQLAARVAIYRMMRPGEPPTEDAVEALFHRLFYNADTYDLSRVGRMKFNARV 421

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              +  +    +  +DI+ ++KILVDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL 
Sbjct: 422  GREASEGAMTLANDDILDVVKILVDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRSGLA 481

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E+++KER+   + +S+MP DLIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH RR
Sbjct: 482  RIEKAVKERLGQAETESLMPHDLINSKPISAALKEFFGASQLSQFMDQTNPLSEITHKRR 541

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR+N YGF+ET
Sbjct: 542  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARLNDYGFLET 601

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR+V DG  T  + YLSA+EE    IAQAN+SLD D   T+ELV  R  G+ +L   E+
Sbjct: 602  PYRRVKDGIATTQIDYLSAIEEGKYVIAQANASLDADSRLTDELVSAREKGDSVLTQPER 661

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I ++D +P Q+VS+AASL+PFLE+DD+NR LMG NMQRQAVP+L+ E   VGTG+E V A
Sbjct: 662  IQYMDVAPTQIVSVAASLVPFLEHDDANRALMGANMQRQAVPVLRPEKALVGTGVERVAA 721

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  + A+R GIV+ +D  RIVIR  + +      GVDIY L+K+ RSNQNT ++QRP
Sbjct: 722  VDSGTVVTARRGGIVDYIDTNRIVIRVNDAETVAGEVGVDIYNLIKYHRSNQNTNIHQRP 781

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V  G  V   D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 782  IVSRGHLVGAGDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 841

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  VMARDTKLGPE+ITRDIPN+SE  L  +DE GI+ VGAEVNPGD+LVGK+TP
Sbjct: 842  SIHIEELVVMARDTKLGPEDITRDIPNLSEAQLSRLDESGIVYVGAEVNPGDVLVGKVTP 901

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRV  G SGTV+DV++F R GI +++R+  + 
Sbjct: 902  KGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGTSGTVIDVQVFTREGITRDKRAQQII 961

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++++    D +D+  I++ + + R+ ++L G+ A  GP+   K TV+    +++  +  
Sbjct: 962  DDELKRFRLDLNDQLRIVEADAFDRIEKLLTGKIANGGPRKIAKGTVIDKAYLTDVEKYH 1021

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     +++    +ES+K   E ++   +  F+ K +K+  GD++P GVL++VKV++A+
Sbjct: 1022 WFDIRPAEDEAANQLESIKNSLEQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAV 1081

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQ+ E H
Sbjct: 1082 KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQVLEVH 1141

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQ 1199
            LGWA  G+G++I  ++   +    ++ LR F +++   +G  +E + D  D+ V+ +A  
Sbjct: 1142 LGWAGKGIGQRIGDML---QGEARVAELRKFFDELYNQSGGKSESLDDLSDEDVIEMAGN 1198

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPV 1249
              +GVP +TPVFDGA EE I  ML++A                Q+ L DG TGE F+RPV
Sbjct: 1199 LSNGVPFATPVFDGAKEEEIRGMLKLAYPDDIAARKGLTPTRTQAWLCDGRTGEQFERPV 1258

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1259 TVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1318

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            VLQEMLT+KSDDV GRT+VYESIV G  + + G PESFNVLVKE+++LG+ I+LE +
Sbjct: 1319 VLQEMLTVKSDDVNGRTKVYESIVKGEHSIDAGMPESFNVLVKEIRSLGIDIELERN 1375


>gi|225024705|ref|ZP_03713897.1| hypothetical protein EIKCOROL_01591 [Eikenella corrodens ATCC 23834]
 gi|224942531|gb|EEG23740.1| hypothetical protein EIKCOROL_01591 [Eikenella corrodens ATCC 23834]
          Length = 1393

 Score = 1612 bits (4173), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1398 (49%), Positives = 962/1398 (68%), Gaps = 41/1398 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK F K   ++++P L+  Q  SY  FL    A D+R +EGLQAAF S+
Sbjct: 1    MSYSVTEKKRIRKSFAKRDSVLEVPYLLATQLESYRKFLQQETAFDKRLDEGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEF  Y    P FD+ +C  R +TYA PL+  +RL++ D +       +
Sbjct: 61   FPIVSHNGYARLEFTHYILGEPLFDIAECQLRGITYAAPLRARIRLVILDKESSKPN-VV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 120  KEVRENEVYMGEIPLMTPYGSFIINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D+EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL TFY K  +    
Sbjct: 180  RIIPYRGSWLDLEFDPKDLLYFRIDRRRKMPVTILLKALGYSAEQILDTFYDKETFYLSK 239

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L  + L  G  V + + D D G+ ++ +GK++T+  L+ +++ G+K L + ++ 
Sbjct: 240  DGVETELVLSRL-KGETVKTDICDAD-GKVLVAAGKRVTAKGLRDIEKAGLKRLRVDAEA 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+D++  +TGEI   A   I E+ L ++    + +I  LY++ +    YI +TL
Sbjct: 298  LIGKMLAKDVIVPDTGEILASANSEITEELLAQLEIHGVNEIQTLYINELGYGGYISSTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A + IYR+MRPG+  T    E +F+ LFF+   YDLS VGR+K N R   
Sbjct: 358  QVDETADQMAARIAIYRMMRPGEPPTEEAVEMLFDRLFFNEASYDLSRVGRMKFNTRTYE 417

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 418  QKLSEDQQQSWYGRLLNETLAGAAEKGGFILSTEDIVASIATLVELRNGHGEVDDIDHLG 477

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + D++MP DLINAKPV +A+ EFF SS
Sbjct: 478  NRRVRSVGELTENQFRSGLARVERAVKERLNQAEADNLMPTDLINAKPVSAAIKEFFGSS 537

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 538  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 597

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT+++ YLSA+EE    IAQAN+ +D+ G  
Sbjct: 598  GLINSLSVYARTNDYGFLETPYRRVVDGKVTDEIDYLSAIEEGRYVIAQANAEVDKKGYL 657

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +L+ CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 658  KGDLITCREKGETIMASADRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 717

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+AE P VGTG+E  VA  S  AIVA+R G+VE VDA RIV+R  + +      GVD
Sbjct: 718  VPCLRAEKPLVGTGIERSVAVDSATAIVARRGGVVEYVDANRIVVRVHDEETVAGEVGVD 777

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D+IADG STDLG+LALG+NM +AFMPW+G
Sbjct: 778  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLIADGASTDLGELALGQNMTIAFMPWNG 837

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ + D +TSIHIEE  V+ARDTKLG EEITRDIPN+SE     +DE G
Sbjct: 838  YNYEDSILISEKVAAADRYTSIHIEELNVVARDTKLGAEEITRDIPNLSERMQNRLDESG 897

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 898  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 957

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 958  DVQVFTREGIQRDKRAQSIIDAELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1017

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K   ++ + ++  P +  W+   + DE+  + +E +K+  +  +   +++++ K +K
Sbjct: 1018 KLGKGKEITVEYLASLPTKHDWFDIRLSDEERAKQLELIKLSLQQKREEADEQYEIKKKK 1077

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++PPGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG  VD
Sbjct: 1078 MTQGDELPPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRTVD 1137

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I+ ++ + +    +  +R+FLEK+    
Sbjct: 1138 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGQRIEKMLAEQR---KMKEIRAFLEKLYNGS 1194

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G- 1232
               E +    D+ +L +AE  K G   ++PVFDGA E+ I  ML +A   +       G 
Sbjct: 1195 GKKEDLKSLSDEEILTLAENLKGGATFASPVFDGAKEQEIYDMLELAYPSDDPEVQKLGF 1254

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1255 NDTKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1314

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    E G PESF
Sbjct: 1315 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIEAGMPESF 1374

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL ID+E 
Sbjct: 1375 NVLVKEIRSLGLDIDMER 1392


>gi|86158017|ref|YP_464802.1| DNA-directed RNA polymerase subunit beta [Anaeromyxobacter
            dehalogenans 2CP-C]
 gi|115305555|sp|Q2II86|RPOB_ANADE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|85774528|gb|ABC81365.1| DNA-directed RNA polymerase subunit beta [Anaeromyxobacter
            dehalogenans 2CP-C]
          Length = 1422

 Score = 1611 bits (4172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1401 (51%), Positives = 1003/1401 (71%), Gaps = 30/1401 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R+ FGK  +I +IP+LI +QK SYD FL  ++ P++R + GLQ  FKSVFPI  F+  
Sbjct: 10   RIRRNFGKINKIAEIPNLIAIQKFSYDKFLQADVPPEKRDDTGLQGVFKSVFPIKDFNET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +TY+ P+K+ +RL+V+D DE TGA+SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYHLEKPKYDVDECHQRGMTYSAPIKVVVRLVVWDKDEETGAQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT++GTF+I G +R+VVSQLHRSPG  FDHDKG++  SGKLLY  RIIP +G W
Sbjct: 130  FGEIPLMTENGTFIINGTERVVVSQLHRSPGAFFDHDKGKSHSSGKLLYNARIIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--------------DSEEILSTFYPKIV 237
            +D EFD KDI++VRIDRRRK+P T  L ALG                +EEIL  +Y    
Sbjct: 190  IDFEFDHKDILYVRIDRRRKLPATVLLRALGATPDTAKKDPVEFHGSAEEILKYYYDTET 249

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
                G          DL+ G + +  + D  + E +++  +K T   +K L    +K L 
Sbjct: 250  IRVEGKGKFEKDLVPDLLKGQRATRDIRDPKSSEVIVKKNRKYTESAIKKLVAAKMKSLP 309

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  + +     AED+V+  TGE+ +E  + + E  +EE+    I +  +L++D++N    
Sbjct: 310  VEPEEVYTKISAEDVVDETTGEVLLEVNEEVTEAKVEELRKRNINEFKVLFIDNLNILPA 369

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +R+TL+ DK    ++A+++IYR +RPGD  T   A ++F  LFF++++YDLS VGR+K+N
Sbjct: 370  LRDTLMQDKISTPEEAIMEIYRRLRPGDPPTPETATNLFVNLFFNAERYDLSKVGRLKLN 429

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT--IDDIDNLGNRRVRSVGEMLKNQY 475
             +  ++ P +   + K DI+ +++ L+DL+NGK    +DDID+LGNRRVR+VGE+L+NQY
Sbjct: 430  YKFGIEEPLENTVLTKRDILEVVRFLIDLKNGKPNKDVDDIDHLGNRRVRAVGELLENQY 489

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+RMER+IKER+S  +I+++MP DLINAKPV + + EFF SSQLSQ  +  N LS +
Sbjct: 490  RIGLVRMERAIKERMSLQEIETLMPHDLINAKPVTAVIKEFFGSSQLSQFMDQTNPLSEV 549

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            TH RRLSALG GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL+++ARVN Y
Sbjct: 550  THKRRLSALGPGGLTRERAGFEVRDVHSTHYGRICPIETPEGPNIGLIASLSTYARVNEY 609

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPYRKV  G+VT++V + SA+EEE   IAQAN+ +D+ G+FTE  V+CR  GE I 
Sbjct: 610  GFVETPYRKVEKGRVTDEVTFYSALEEEKHIIAQANAPVDKKGNFTEAKVWCRKEGEYIY 669

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            V  +++D +D SP Q+VS+AASL+PFLENDD+NR LMG NMQRQAVPLL+ +AP VGTG+
Sbjct: 670  VRPDEVDLMDVSPNQLVSVAASLVPFLENDDANRALMGSNMQRQAVPLLRTQAPLVGTGI 729

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNT 774
            E++VA+ SG   VAKR G+V+ VDA RIV+++          + VDIY L+K+QRSNQNT
Sbjct: 730  EAIVARDSGVTTVAKRDGVVQSVDASRIVVKADVPTSATDVANEVDIYNLIKYQRSNQNT 789

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+P+VK G+ VR+ D+IADGP+T++G+LALG+N++VAFMPW GYNFEDS+L+SER++
Sbjct: 790  CINQKPIVKPGERVRKGDVIADGPATEMGELALGQNVVVAFMPWQGYNFEDSILLSERLI 849

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             EDVFTS+HIEEFE +ARDTKLG EEITRDIPNV EE LK++DE GII +GAEV PGDIL
Sbjct: 850  KEDVFTSVHIEEFECVARDTKLGKEEITRDIPNVGEEALKDLDESGIIRIGAEVKPGDIL 909

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGKITPKGE+ ++PEEKLLRAIFGEKA DVRD+SLRVP GVSGTV++ ++F+R G++K+E
Sbjct: 910  VGKITPKGETQLSPEEKLLRAIFGEKAGDVRDSSLRVPPGVSGTVINAKVFSRKGVEKDE 969

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV------SGPKGFKKSTVL 1008
            R+ ++E  +   L +D++DE  I+  + + ++  +L G+          G +  KK  VL
Sbjct: 970  RAKAIEEMEEAKLLKDQNDEIRIIQDSAFQKIRRLLLGKEVTARLVDDKGEQLLKKGDVL 1029

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               L+   P+  W + AV  + VQ     +   +E  K +++  F  KI +++ GD++PP
Sbjct: 1030 DDALLDTVPQRYWGEIAVAGD-VQDLARKIIDNFEEQKELVKLLFGEKIGRLKKGDELPP 1088

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV+++VKV+VA+KR +  GDKMAGRHGNKG+VSR+LP ED+P+L+DGTPVDIVLNPLGVP
Sbjct: 1089 GVIKMVKVYVAIKRKLAVGDKMAGRHGNKGVVSRVLPEEDLPYLEDGTPVDIVLNPLGVP 1148

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMNVGQI ETHLGWA   +G +++ +I        +             G  +++++  
Sbjct: 1149 SRMNVGQILETHLGWAARNVGLRLQEMIEKEYGPEQLRKKLRAAFAGTEGGPASDRLAAL 1208

Query: 1189 DDD----SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
             DD     + ++A++ + G+ V+TPVFDGA E+ + +++       + QSIL+DG TGEP
Sbjct: 1209 IDDVPEKELPKLAQKLRRGMHVATPVFDGAREDEMKALMEEG--SATLQSILFDGRTGEP 1266

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD+ VTVG +YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++A
Sbjct: 1267 FDQDVTVGVMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEA 1326

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE LT+KSDDVVGRTR+YE+IV G +T E+G PESFNVL+KE+Q+L L ++L 
Sbjct: 1327 YGAAYSLQEFLTVKSDDVVGRTRMYEAIVKGENTLESGLPESFNVLIKELQSLALDVELL 1386

Query: 1365 NSRTKNSAKMEEIPDFNKCEL 1385
             +    +A+     D     L
Sbjct: 1387 ETPEAQAAREAAERDLGGGPL 1407


>gi|113968537|ref|YP_732330.1| DNA-directed RNA polymerase subunit beta [Shewanella sp. MR-4]
 gi|113883221|gb|ABI37273.1| DNA-directed RNA polymerase, beta subunit [Shewanella sp. MR-4]
          Length = 1325

 Score = 1611 bits (4171), Expect = 0.0,   Method: Composition-based stats.
 Identities = 700/1346 (52%), Positives = 955/1346 (70%), Gaps = 25/1346 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +DIP L+ +Q  S+  F       D     GL+AAF+SVFPI +FSG + L++VSY+   
Sbjct: 2    LDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSVFPIKSFSGNSELQYVSYKLGE 57

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C  R +TY+ PL++ LR++++D +   G  ++KDIKEQ +YMGD+PLMT +GT
Sbjct: 58   PVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TVKDIKEQEVYMGDIPLMTDNGT 115

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  RIIP +G W+D EFD KD + 
Sbjct: 116  FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDALF 175

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + D     L    L  G   S  
Sbjct: 176  VRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKKDTLVMTLVPERL-RGETASYD 234

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            + D + G  ++E+G+++T+  ++ L++     L +  + + G Y A+D ++ +TGE+ + 
Sbjct: 235  IKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEYIVGKYAAQDYIDPDTGEVLVS 293

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A   I  + L ++  + I+++  LY++ +++ AYI +TL  D   +R +AL++IYR+MRP
Sbjct: 294  ANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTLRIDPTTNRLEALVEIYRMMRP 353

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++F  LFF  ++YDLS VGR+K N RL++   +    + KEDI+A++K +
Sbjct: 354  GEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSIPDDEGSGVLSKEDIVAVMKNI 413

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            + +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER+++ER+S  D++ +MPQDL
Sbjct: 414  IHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVRERLSLGDLNELMPQDL 473

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 474  INAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHP 533

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPYRKV DG +T+DV YLSA+EE 
Sbjct: 534  THYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPYRKVVDGVITDDVEYLSAIEEG 593

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
               IAQAN  +D  G   EE + CR  GE   +    I ++D SP+Q++S+AASLIPFLE
Sbjct: 594  RYVIAQANIEVDSQGRMVEEQIACRHKGESTFMRASDIQYMDVSPQQIISVAASLIPFLE 653

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  SG  + AKR G+++ VDA RI
Sbjct: 654  HDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVDSGVVVAAKRGGVIDYVDASRI 713

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   VG+ V R D++ADGPSTDLG
Sbjct: 714  VVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSVGEPVVRGDVLADGPSTDLG 773

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            DLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+IHI+E   +ARDTKLG EEIT 
Sbjct: 774  DLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTIHIQELSCIARDTKLGSEEITA 833

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 834  DIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 893

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+D+SLRVP+ V GT++DV++F R G++K++R+I +E   I    +D  +E  IL+  + 
Sbjct: 894  VKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAIEIEEMHIAQARKDLGEEFKILEEGVL 953

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
            SR   +L                  +   I+  PR       + DE  Q  +E L  Q+E
Sbjct: 954  SRARNLLLSAG-------------FTEAQIAALPRKDVLVQVIDDETKQTELEQLAEQHE 1000

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I
Sbjct: 1001 ELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKRTIQPGDKMAGRHGNKGVISKI 1060

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
             P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E HLG A  G+G KI +++ D +  G
Sbjct: 1061 NPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHLGAAAKGIGNKIAAMLEDQREKG 1120

Query: 1164 DISPLRSFLEKVIGTGSHTE---KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
             ++ +RS++++V   G   +    I  + DD +LR+A   K G+PV+TP FDGA E+ I 
Sbjct: 1121 -LAEVRSYIKQVYELGDEVQQRVDIDSFTDDELLRLANNLKGGIPVATPAFDGAKEKEIK 1179

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             ML +A L  SGQ  L+DG TG  F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQ
Sbjct: 1180 QMLELAGLPTSGQLKLFDGRTGNEFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQ 1239

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   +
Sbjct: 1240 QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTQMYKNIVDGNHQMQ 1299

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENS 1366
             G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 PGMPESFNVLLKEIRSLGINIELDQE 1325


>gi|254468259|ref|ZP_05081665.1| DNA-directed RNA polymerase, beta subunit [beta proteobacterium KB13]
 gi|207087069|gb|EDZ64352.1| DNA-directed RNA polymerase, beta subunit [beta proteobacterium KB13]
          Length = 1389

 Score = 1610 bits (4168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1398 (50%), Positives = 963/1398 (68%), Gaps = 43/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + ++P L+ +Q  SY  +L M+I  DER ++GLQ  F SV
Sbjct: 1    MSYSFTEKKRLRKNFAKRQTVAEVPYLLSMQLESYKDYLQMDIPADERKDQGLQNTFNSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ SG A L+FVSY      FDV +C  R LT+ VPL++ +RL + D D      ++
Sbjct: 61   FPISSHSGNAKLDFVSYSLGKVVFDVKECQLRGLTFGVPLRVKVRLSIMDKDAS--EPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT +G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEMPLMTNNGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD ++ RIDRRRK+PVT+ L ALG+ SEEILSTFY    +S   
Sbjct: 179  RIIPYRGSWLDFEFDPKDYLYFRIDRRRKMPVTTLLKALGLSSEEILSTFYDFDQFSFVK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +   F L    L  G      + D   GE ++   K++T   ++ +++  +K + ++ + 
Sbjct: 239  NKLNFTLYPERL-RGEIAKFDIADKK-GELIVAKDKRITVKHIREIEKANIKKIEVSEEF 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  +A+ I++ +TGE+  EA   I E+ L +I    I +I  LY + ++   +I +TL
Sbjct: 297  IIGRKLAKGIIDADTGEVIAEANAEITEELLAQIKELSINEIETLYYNDLDQGDFISHTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR--- 419
             TD+  D   A + IYR+MRPG+  T    +++F  +FF  D+YDLS VGR+K N R   
Sbjct: 357  STDEIPDEYSARVAIYRMMRPGEPPTEDSVKALFEGMFFSEDRYDLSNVGRMKFNRRAYP 416

Query: 420  ----------------LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
                            +     +    +  +DI+A++ ILV+LRNG+G IDDID+LGNRR
Sbjct: 417  KSFEKSAGWMQRFYQRVGEQNDEGAGILSIDDILAVVGILVELRNGRGEIDDIDHLGNRR 476

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            +RSVGE+++NQ+R GL+R+ER++KER+   + D++MP DLIN+KP+ SA+ EFF SSQLS
Sbjct: 477  IRSVGELVENQFRTGLVRVERAVKERLGQAEADNLMPHDLINSKPISSAIREFFGSSQLS 536

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 537  QFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGLI 596

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            +SL  FA+ N YGF+ETPYR+V +GKVT ++ YLSA+EE    IAQANS LDE  +F EE
Sbjct: 597  NSLALFAKTNKYGFLETPYRRVENGKVTAEIDYLSAIEESQFTIAQANSELDEKSNFKEE 656

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV  R   E +L    +I+++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 657  LVSSRFKNEFVLSNNNEINYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPC 716

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            L+AE   VGTG+E  VA  SG  + A+R G+V+ VD+ RIV++  + +      GVDIY 
Sbjct: 717  LRAEKAVVGTGIERTVAMDSGTTVQAERGGVVDYVDSRRIVVKVNDKETSAEDVGVDIYN 776

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L K+ RSNQNT +NQ+PLVK+GD + R DIIADG STD+G+LALG+NMLV FMPW+GYNF
Sbjct: 777  LTKYTRSNQNTNINQKPLVKIGDTIARGDIIADGASTDVGELALGQNMLVGFMPWNGYNF 836

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+LISE++V++D +TS+HIEE  V++RDTKLGPEEITRDI N+SE  L  +DE GII 
Sbjct: 837  EDSILISEKVVADDRYTSVHIEELSVVSRDTKLGPEEITRDISNLSERMLGRLDESGIIY 896

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            VGAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV+
Sbjct: 897  VGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQ 956

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R GID++ER+  + +EQ+    +D +D+  I++ + ++R+ ++L G+    GPKG K
Sbjct: 957  VFTREGIDRDERAEQIIQEQLSHFEQDLNDQLRIVEDDTFARIEKLLVGKTVSGGPKGIK 1016

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K   ++ D + E  R  W+   + D+K  +++ESLK     +K   + R++ K +K+  G
Sbjct: 1017 KGDKVTKDQLKEIGRYDWFDIRLADDKDSKSLESLKENLNKAKKDFDLRYEEKKQKLTQG 1076

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++ PGV ++VKV++A+KR IQ GDKMAGRHGNKG++S+I+P EDMP + DGT +DIVLN
Sbjct: 1077 DELQPGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVISKIVPVEDMPHMADGTTLDIVLN 1136

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHT 1182
            PLGVPSRMN+GQI E HLGWA  GLG +I  ++   K    ++ +R  LEK+        
Sbjct: 1137 PLGVPSRMNIGQILEVHLGWAAKGLGNRIDEML---KEERKVAEVRDLLEKIYNESSGKQ 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS-------- 1234
            E I    D  V+ +A   K GVP +T VFDGA E  I  ML +A     G          
Sbjct: 1194 EDIKSLKDGEVIEMAHNLKQGVPFATSVFDGAAESDIQYMLDLAY--PDGHELTKKLNFS 1251

Query: 1235 ------ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
                   L+DG TGE F+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1252 AKKTQLQLFDGRTGEAFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQ 1311

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT+VYE+IV G    + G PESFN
Sbjct: 1312 FGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVSGRTKVYENIVKGEHKIDAGMPESFN 1371

Query: 1349 VLVKEMQALGLSIDLENS 1366
            VL KE+++L + IDL+  
Sbjct: 1372 VLTKEIRSLAIDIDLDRD 1389


>gi|119947049|ref|YP_944729.1| DNA-directed RNA polymerase, beta subunit [Psychromonas ingrahamii
            37]
 gi|158513125|sp|A1T065|RPOB_PSYIN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119865653|gb|ABM05130.1| DNA-directed RNA polymerase, beta subunit [Psychromonas ingrahamii
            37]
          Length = 1346

 Score = 1609 bits (4167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1369 (50%), Positives = 979/1369 (71%), Gaps = 27/1369 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G  +    R+RK FGK P++++ P L+ +Q  S+  F+ +++        GL+AAF S+
Sbjct: 1    MGYSYTEKKRIRKDFGKRPQVMEKPYLLSIQLDSFKRFIEVDLT----GEVGLEAAFNSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+  L++ LRL+++D D   G  ++
Sbjct: 57   FPIASYSGTSELQYVSYRLGEPVFDVKECQIRGVTYSASLRVKLRLVIYDRDAPAG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDI+EQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIREQEVYMGEMPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL+ FY    +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIMLRALEYSTQEILAIFYDTTKFDIKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L A D + G      +     G+  +E GK++T+  +K L++  +  L +  + 
Sbjct: 235  GVISMSLIA-DRLRGEMALFDI--AANGKIYVEQGKRITARHIKQLEKDNINTLDVPVEY 291

Query: 303  LCGLYV--AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            +    +  A+D ++ ETGEI + A D++  + L E+  S I    I+Y + ++  ++I +
Sbjct: 292  IAEKDLVVAKDYISKETGEIIVSANDILTLEILAELTQSGITSFDIIYTNELDCGSFISD 351

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D + +R +AL++IYR+MRPG+  T   AE +F+ LFF  ++Y+LS VGR+K N R+
Sbjct: 352  TLRVDSSSNRLEALVEIYRMMRPGEPPTKDAAEGLFHNLFFAEERYELSKVGRMKFNRRV 411

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             +D  +    + K+DI++++K L+ +RNG G +DDID+LGNRR+R VGEM +NQ+R+GL+
Sbjct: 412  GIDGDEGAGILSKDDILSVMKTLIAIRNGDGIVDDIDHLGNRRIRCVGEMAENQFRVGLV 471

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER+++ER+S  D+D+ MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 472  RVERAVRERLSLGDLDATMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 531

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F+R N+YGF+ET
Sbjct: 532  ISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLATFSRTNSYGFLET 591

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +GK T+ V YLSA+EE +  IAQA++S+DE+G   EEL+ CR  GE   +    
Sbjct: 592  PYRKVENGKPTDQVEYLSAIEEGSFVIAQASASIDENGLLDEELIPCRHKGESTFLSPAD 651

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ID++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +A
Sbjct: 652  IDYMDVSPQQIISVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIERRLA 711

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  I+AKR+G+++ VDA RIV++  + +L P  +G+DIY L K+ RSNQNTC+NQ+P
Sbjct: 712  IDSGVTIIAKRSGVIDYVDASRIVVKVDDNELLPGEAGIDIYNLTKYTRSNQNTCINQKP 771

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
              + G+ + R D++ADGPSTD+GDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT
Sbjct: 772  TCEPGEPIVRGDVLADGPSTDMGDLALGQNMKIAFMPWNGYNFEDSILISERVSQEDRFT 831

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +IHI+EF  +AR+TKLG EEI+ DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TP
Sbjct: 832  TIHIQEFSCVARETKLGSEEISADIPNVGEAALSKLDESGIVYVGAEVKPGDILVGKVTP 891

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+D+SLRV +    TV+DV++F R G++K++R++ +E
Sbjct: 892  KGETQLTPEEKLLRAIFGEKASDVKDSSLRVAASTYATVIDVQVFTRDGVEKDKRALEIE 951

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
              Q++   +D  ++  IL+  IY + + IL G                    + + PR+Q
Sbjct: 952  EMQLKAAKKDLTEKFKILENAIYEKALAILVGAGQ-------------DEARLLQMPRAQ 998

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W +  + DE  Q  ++ +  QY+  K+  +  F  K  KI  GDD+ PGV ++VKV++A+
Sbjct: 999  WLEVQIDDETKQSYLDQIITQYDEVKADYDKEFDIKRRKITQGDDLAPGVQKIVKVYLAV 1058

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            +R +Q GDKMAGRHGNKG++S I+P EDMP  + G PVDIVLNPLGVPSRMN+GQ+ ETH
Sbjct: 1059 RRRLQPGDKMAGRHGNKGVISNIVPVEDMPHDEFGVPVDIVLNPLGVPSRMNIGQVLETH 1118

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAE 1198
            LG A  G+G+K++ +I  Y+ + +I+ +R F++K+   G       ++D+DD++V+R+A+
Sbjct: 1119 LGLAAKGVGEKLERMI-KYQRDIEITKVREFVQKLYSFGDAPCHVDLNDFDDEAVMRLAK 1177

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                G+PV+TP FDGA+E  I  +LRMADL ESGQ  L DG TG  F+RPVTVGY+YMLK
Sbjct: 1178 NLYKGLPVATPAFDGANEGEIRELLRMADLPESGQLQLTDGRTGIQFERPVTVGYMYMLK 1237

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            LNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 1238 LNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1297

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            SDDV GRT++Y++IV G+   E G PESFNVL+KE+++L ++I+L+ S 
Sbjct: 1298 SDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLSINIELDESN 1346


>gi|296112484|ref|YP_003626422.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis RH4]
 gi|295920178|gb|ADG60529.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis RH4]
 gi|326567994|gb|EGE18086.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis BC7]
 gi|326577818|gb|EGE27686.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis O35E]
          Length = 1363

 Score = 1609 bits (4167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 971/1374 (70%), Gaps = 20/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY+ FL  +  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFSKLPDVMDVPYLLAIQVDSYEQFLQEHKKPKARANIGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A PL++ +RLI+ D +  T    I
Sbjct: 61   FPIESHSGNAQLQFVEYYLGEPEFDERECIMRGSTFAAPLRVKIRLIIKDKENKTA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 118  KDVREQSVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++ RIDRRRK+  T  L A+GMD+ +IL  F+ K+   +  
Sbjct: 178  RIIPYRGSWLDFEFDAKDLVYARIDRRRKLLATIILRAIGMDTAQILDQFFEKVEVFKGD 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +   L A D + G      ++  D G  ++E G+++ +  +K +   G+  L +  + 
Sbjct: 238  ESFEIELVA-DRLKGEMAQFDIIGPD-GNVIVEQGQRINALRVKRILNSGMTKLAVPDEY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    + EDIV G+  E+ + A  +ID + L ++    ++   IL+ + +++ AYI +TL
Sbjct: 296  LYERIIGEDIVVGD--EVLVRANTLIDHEILVKLAEKNVQSFKILFTNDIDHGAYIADTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE +F  +FF  ++YDLS VGR+K N RL  
Sbjct: 354  RADTIVTREEALIEIYKVMRPGEPPTLDTAEKLFESMFFSQERYDLSNVGRMKFNRRLGR 413

Query: 423  DTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +  D        +   +  +DI+ ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ
Sbjct: 414  EFIDTDDMDVQREQGVLSNQDIVDVLKELIEIRNGRGEVDDIDHLGNRRIRSVGEMTENQ 473

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL R+ER++KER+++ D D++ PQDLIN+KPV +++ EFF SSQLSQ  +  N LS 
Sbjct: 474  FRIGLARVERAVKERLTTADSDNLSPQDLINSKPVAASIKEFFGSSQLSQFMDQNNPLSE 533

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FA+ N 
Sbjct: 534  ITHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLATFAKTNN 593

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYR+V DG+VT+++ Y+SA+EE    IAQA+S +++ G  TEE+V  R  GE +
Sbjct: 594  FGFLETPYRRVVDGRVTDEIEYVSAIEEVGMVIAQADSPMNDKGELTEEMVSVRHDGEFV 653

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  +K+  +D SP+QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG
Sbjct: 654  RMSADKVTHMDVSPRQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTG 713

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME  VA+ SG  +VAKR G++E+VDA RI++R  E ++    +G+DIY L+K+ RSNQNT
Sbjct: 714  MERHVARDSGVCVVAKRGGVIEEVDASRIIVRVNEDEMTAGEAGIDIYNLIKYTRSNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQR +V  GDE+ R DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V
Sbjct: 774  CINQRVIVNEGDEIERGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILLSERVV 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L N+DE GI+ +GAEV+ GDIL
Sbjct: 834  QEDRFTTIHIQELTCVARDTKLGPEEITGDIPNVGEAALANLDEAGIVYIGAEVDAGDIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ 
Sbjct: 894  VGKVTPKGESQLTPEEKLLRAIFGEKAADVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDS 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ S+E+  ++   +D  +E VI +     R++ +L G+    G  GFK  T+LS+  I 
Sbjct: 954  RAKSIEKAMLDDYRKDLKEELVIFEAAAKGRILSLLDGKKVSGG-AGFKAGTILSTKDIE 1012

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
              P          +E+V   +  +       +  ++++F  K  K+  GDD+  GV ++V
Sbjct: 1013 NLPLESLLDIQPAEEEVSERLGQIAEFLSDKQKDIDNKFTEKKRKLTQGDDLAHGVQKIV 1072

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVPSRMN+G
Sbjct: 1073 KVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNPVDIVLNPLGVPSRMNIG 1132

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            Q+ ETHLG A  GLG KI +++   ++   +S LR FL+K+    G     +    D+ +
Sbjct: 1133 QVLETHLGMAAKGLGDKINAML---RSQVAVSELREFLDKIYNQVGGEQVDLDSLSDEDL 1189

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L + +  K GVP+ T VFDGA E  I  +L +ADL  +GQ  LYDG TG+ FDRPVTVGY
Sbjct: 1190 LALCQNLKDGVPMGTAVFDGAKETQIKELLSLADLSTTGQQTLYDGRTGKKFDRPVTVGY 1249

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA Y LQE
Sbjct: 1250 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGATYTLQE 1309

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV G      G PESFNVL KE+++LG++IDL+  +
Sbjct: 1310 MLTVKSDDVEGRTRMYKNIVDGEQYMNPGMPESFNVLTKEIRSLGINIDLKEKK 1363


>gi|160873319|ref|YP_001552635.1| DNA-directed RNA polymerase subunit beta [Shewanella baltica OS195]
 gi|160858841|gb|ABX47375.1| DNA-directed RNA polymerase, beta subunit [Shewanella baltica OS195]
          Length = 1322

 Score = 1609 bits (4167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1343 (51%), Positives = 949/1343 (70%), Gaps = 21/1343 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +DIP L+ +Q  S+  F       D     GL+AAF+SVFPI +FSG + L++VSY+   
Sbjct: 1    MDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSVFPIKSFSGNSELQYVSYKLGE 56

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FDV +C  R +TY+ PL++ LR++++D +   G  ++KDIKEQ +YMGD+PLMT +GT
Sbjct: 57   PVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TVKDIKEQEVYMGDIPLMTDNGT 114

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  RIIP +G W+D EFD KD + 
Sbjct: 115  FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDALF 174

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + D     L    L  G   S  
Sbjct: 175  VRIDRRRKLPATIMLRALEYSTQEILDLFFERVEFKIKKDTLVMALVPERL-RGETASYD 233

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            + D + G  ++E+G+++T+  ++ L++     L +  + + G Y A+D ++ +TGE+ + 
Sbjct: 234  IKDAE-GSVLVEAGRRITARHIRQLEKTNTTELEVPVEYIVGKYAAQDYIDPDTGEVLVS 292

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A   I  + L ++  + I+++  LY++ +++ AYI +TL  D   +R +AL++IYR+MRP
Sbjct: 293  ANSEISLEDLAKLSLAGIKELSTLYINELDHGAYISDTLRIDSTTNRLEALVEIYRMMRP 352

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            G+  T   AE++F  LFF  ++YDLS VGR+K N RL++   +    + KEDI+A++K +
Sbjct: 353  GEPPTKDAAEALFQNLFFSEERYDLSKVGRMKFNRRLSIPDDEGSGVLSKEDIVAVMKNI 412

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            + +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER+++ER+S  D++ +MPQDL
Sbjct: 413  IHIRNGFDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVRERLSLGDLNELMPQDL 472

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 473  INAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHP 532

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            THYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPYRKV DG +T++V YLSA+EE 
Sbjct: 533  THYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPYRKVIDGVITDEVEYLSAIEEG 592

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
               IAQAN  +D +G   EE + CR  GE   +    I ++D SP+Q++S+AASLIPFLE
Sbjct: 593  RYVIAQANIEIDANGRMAEEQIACRHKGESTFMRAADIQYMDVSPQQIISVAASLIPFLE 652

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +DD+NR LMG NMQRQAVP L++E P VGTG+E  +A  SG  +VAKR G V+ VDA RI
Sbjct: 653  HDDANRALMGANMQRQAVPTLRSEKPLVGTGIERTLAVDSGVVVVAKRGGFVDYVDASRI 712

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   VG+ V R D++ADGPSTDLG
Sbjct: 713  VVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSVGEPVVRGDVLADGPSTDLG 772

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            DLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+IHI+E   +ARDTKLG EEIT 
Sbjct: 773  DLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTIHIQELSCIARDTKLGSEEITA 832

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 833  DIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 892

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+D+SLRVP+ V GT++DV++F R G++K++R++ +E   I    +D  +E  IL+  + 
Sbjct: 893  VKDSSLRVPNSVKGTIIDVQVFIRDGVEKDKRAVEIEEMHIAQARKDLGEEFKILEEGVL 952

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
            SR   +L G                +   I+  PR       + DE  Q  +E L  Q+E
Sbjct: 953  SRARNLLIGAG-------------FTDAQIAALPRKDVLIQVIDDETKQTELEQLAEQHE 999

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I
Sbjct: 1000 ELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKRTIQPGDKMAGRHGNKGVISKI 1059

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
             P EDMP+ + G PVDIVLNPLGVPSRMN+GQ+ E H+G A  G+G KI +++ + +   
Sbjct: 1060 CPIEDMPYDEQGNPVDIVLNPLGVPSRMNIGQVLEVHMGAAAKGIGNKITAMLEEQRELA 1119

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            ++      + ++         I  + DD VLR+A   K G+P++TP FDGA E+ I  ML
Sbjct: 1120 EVRGYIKQVYELGDEVQQRVDIDSFTDDEVLRLATNLKGGIPIATPAFDGAKEKEIKQML 1179

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
             +A L  SGQ  L+DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPL
Sbjct: 1180 ELAGLPTSGQLKLFDGRTGNEFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1239

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   + G 
Sbjct: 1240 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTQMYKNIVDGNHQMQPGM 1299

Query: 1344 PESFNVLVKEMQALGLSIDLENS 1366
            PESFNVL+KE+++LG++I+L+ +
Sbjct: 1300 PESFNVLLKEIRSLGINIELDQA 1322


>gi|326564349|gb|EGE14578.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis
            46P47B1]
 gi|326566148|gb|EGE16304.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis
            103P14B1]
 gi|326570704|gb|EGE20738.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis BC1]
 gi|326571259|gb|EGE21282.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis BC8]
 gi|326573059|gb|EGE23032.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis CO72]
 gi|326577243|gb|EGE27136.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis
            101P30B1]
          Length = 1363

 Score = 1609 bits (4166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1374 (51%), Positives = 971/1374 (70%), Gaps = 20/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY+ FL  +  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFSKLPDVMDVPYLLAIQVDSYEQFLQEHKKPKARANIGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A PL++ +RLI+ D +  T    I
Sbjct: 61   FPIESHSGNAQLQFVEYYLGEPEFDERECIMRGSTFAAPLRVKIRLIIKDKENKTA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 118  KDVREQSVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++ RIDRRRK+  T  L A+GMD+ +IL  F+ K+   +  
Sbjct: 178  RIIPYRGSWLDFEFDAKDLVYARIDRRRKLLATIILRAIGMDTAQILDQFFEKVEVFKGD 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +   L A D + G      +V  D G  ++E G+++ +  +K +   G+  L +  + 
Sbjct: 238  ESFEIELVA-DRLKGEMAQFDIVGPD-GNVIVEQGQRINALRVKRILNSGMTKLAVPDEY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    + EDIV G+  E+ + A  +ID + L ++    ++   IL+ + +++ AYI +TL
Sbjct: 296  LYERIIGEDIVVGD--EVLVRANTLIDHEILVKLAEKNVQSFKILFTNDIDHGAYIADTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE +F  +FF  ++YDLS VGR+K N RL  
Sbjct: 354  RADTIVTREEALIEIYKVMRPGEPPTLETAEKLFESMFFSQERYDLSNVGRMKFNRRLGR 413

Query: 423  DTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +  D        +   +  +DI+ ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ
Sbjct: 414  EFIDTDDMDVQREQGVLSNQDIVDVLKELIEIRNGRGEVDDIDHLGNRRIRSVGEMTENQ 473

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL R+ER++KER+++ D D++ PQDLIN+KPV +++ EFF SSQLSQ  +  N LS 
Sbjct: 474  FRIGLARVERAVKERLTTADSDNLSPQDLINSKPVAASIKEFFGSSQLSQFMDQNNPLSE 533

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FA+ N 
Sbjct: 534  ITHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLATFAKTNN 593

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYR+V DG+VT+++ Y+SA+EE    IAQA+S +++ G  TEE+V  R  GE +
Sbjct: 594  FGFLETPYRRVVDGRVTDEIEYVSAIEEVGMVIAQADSPMNDKGELTEEMVSVRHDGEFV 653

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  +K+  +D SP+QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG
Sbjct: 654  RMSADKVTHMDVSPRQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTG 713

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME  VA+ SG  +VAKR G++E+VDA RI++R  E ++    +G+DIY L+K+ RSNQNT
Sbjct: 714  MERHVARDSGVCVVAKRGGVIEEVDASRIIVRVNEDEMTAGEAGIDIYNLIKYTRSNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQR +V  GDE+ R DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V
Sbjct: 774  CINQRVIVNEGDEIERGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILLSERVV 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L N+DE GI+ +GAEV+ GDIL
Sbjct: 834  QEDRFTTIHIQELTCVARDTKLGPEEITGDIPNVGEAALANLDEAGIVYIGAEVDAGDIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ 
Sbjct: 894  VGKVTPKGESQLTPEEKLLRAIFGEKAADVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDS 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ S+E+  ++   +D  +E VI +     R++ +L G+    G  GFK  T+LS+  I 
Sbjct: 954  RAKSIEKAMLDDYRKDLKEELVIFEAAAKGRILSLLDGKKVSGG-AGFKAGTILSTKDIE 1012

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
              P          +E+V   +  +       +  ++++F  K  K+  GDD+  GV ++V
Sbjct: 1013 NLPLESLLDIQPAEEEVSERLGQIAEFLSDKQKDIDNKFTEKKRKLTQGDDLAHGVQKIV 1072

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVPSRMN+G
Sbjct: 1073 KVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNPVDIVLNPLGVPSRMNIG 1132

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            Q+ ETHLG A  GLG KI +++   ++   +S LR FL+K+    G     +    D+ +
Sbjct: 1133 QVLETHLGMAAKGLGDKINAML---RSQVAVSELREFLDKIYNQVGGEQVDLDSLSDEDL 1189

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L + +  K GVP+ T VFDGA E  I  +L +ADL  +GQ  LYDG TG+ FDRPVTVGY
Sbjct: 1190 LALCQNLKDGVPMGTAVFDGAKETQIKELLSLADLSTTGQQTLYDGRTGKKFDRPVTVGY 1249

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA Y LQE
Sbjct: 1250 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGATYTLQE 1309

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV G      G PESFNVL KE+++LG++IDL+  +
Sbjct: 1310 MLTVKSDDVEGRTRMYKNIVDGEQYMNPGMPESFNVLTKEIRSLGINIDLKEKK 1363


>gi|108761304|ref|YP_631280.1| DNA-directed RNA polymerase subunit beta [Myxococcus xanthus DK 1622]
 gi|122389067|sp|Q1D7U3|RPOB_MYXXD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|108465184|gb|ABF90369.1| DNA-directed RNA polymerase, beta subunit [Myxococcus xanthus DK
            1622]
          Length = 1408

 Score = 1609 bits (4166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 733/1376 (53%), Positives = 989/1376 (71%), Gaps = 26/1376 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F K  +IIDIP+LI +QK SY+ FL  +IA D+R + GLQ  FKSVFPI  F+  
Sbjct: 10   RVRKTFAKIAKIIDIPNLINIQKQSYEKFLQADIAADKREDLGLQGVFKSVFPIRDFNET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +TY+ P+K+ +RL+V+D DE TGA+SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYHLERPKYDVDECHQRGMTYSAPIKVVVRLVVWDKDEETGAQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT++GTF+I G +R+VVSQLHRSPG  FDHDKG++  SGKLLY  RIIP +G W
Sbjct: 130  FGEIPLMTQNGTFIINGTERVVVSQLHRSPGAFFDHDKGKSHSSGKLLYNARIIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--------------DSEEILSTFYPKIV 237
            +D EFD KD+++VRIDRRRK+P T  + ALG                +EEIL+ +Y    
Sbjct: 190  IDFEFDHKDLLYVRIDRRRKLPATVLIRALGAVPDTAKKNPLEFKGSTEEILNYYYATET 249

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
                           +L+ G + +  +    TGE +++  +K T   +K L+   +K L 
Sbjct: 250  IYLHSAEEFEKSVELELLPGQRATRDI-KAKTGELIVKKNRKFTRAAIKKLEAAKMKTLP 308

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            I +D L     A D+V    G + +E  + + ++ ++E+    I++  +L++D++N   Y
Sbjct: 309  IDADELFTKVSAYDVVEETNGVVLLECNEEVTQEKVDELLKHGIKEFKVLFIDNLNVGPY 368

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +R TL+ DK +  + ++++IYR +RPGD  T   A ++F  LFF+ ++YDLS VGR+K+N
Sbjct: 369  LRETLMLDKLETPEQSIMEIYRRLRPGDPPTPETAINLFTNLFFNPERYDLSKVGRLKLN 428

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  L+ P D + + K DI+ +I+ L+DL+NGKGTIDDID+LGNRRVR+VGE+L+NQYR+
Sbjct: 429  FKFGLEEPLDGQILTKRDILEVIRYLIDLKNGKGTIDDIDHLGNRRVRAVGELLENQYRI 488

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+RMER+IKER+S  +I+++MP DLINAKPV + + EFF SSQLSQ  +  N LS +TH
Sbjct: 489  GLVRMERAIKERMSLQEIETLMPHDLINAKPVTAVIKEFFGSSQLSQFMDQTNPLSEVTH 548

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++ARVN +GF
Sbjct: 549  KRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIASLSTYARVNEFGF 608

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +ETPYRKV  G VTNDV + SA+EEE   IAQAN+  D+ G F   LV  R  GE +   
Sbjct: 609  VETPYRKVEAGVVTNDVAFYSALEEEKHTIAQANAETDKKGKFANALVSSRRGGEFVQAR 668

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             E +D +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL+  AP VGTG+ES
Sbjct: 669  AEDVDLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLRTAAPLVGTGIES 728

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            +VA+ SG   VA+R GIVE VDA RIV+++     L   TS VDIY L+K+QRSNQNTC+
Sbjct: 729  IVARDSGVTCVARRDGIVESVDAGRIVVKADVPASLSDVTSEVDIYNLLKYQRSNQNTCL 788

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ+P++  GD V + D+IADGP+T+ G+LALG+N++VAFMPW GYNFEDS+LISER++ +
Sbjct: 789  NQKPIISKGDRVMKGDVIADGPATETGELALGQNVVVAFMPWQGYNFEDSILISERILKD 848

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEEFE +ARDTKLG EEITRDIPNV EE LK++DE GII +GAEV PGD+LVG
Sbjct: 849  DVFTSIHIEEFECIARDTKLGKEEITRDIPNVGEEALKDLDESGIIRIGAEVKPGDVLVG 908

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGE+ ++PEEKLLRAIFGEKA DVRD+SLRVP GV GTV++ ++F+R G++K+ER+
Sbjct: 909  KITPKGETQLSPEEKLLRAIFGEKAGDVRDSSLRVPPGVVGTVINAKVFSRKGVEKDERA 968

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC------GQNAVSGPKGFKKSTVLSS 1010
              +E  +   L +D++DE  +L  + + R+  ++             G    KK  +L  
Sbjct: 969  KQIESMEEAKLLKDQNDEIKVLQDSAFGRIRGLVRTKEVQGKLVDDKGKILLKKGDILDD 1028

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +L+S  P   W + +V D  +   +  +    E +K  ++  F  KI +I+ GD++PPGV
Sbjct: 1029 ELLSTVPYKYWGEISVGDP-LDSRLRDILRNLEETKEAVKLAFGEKIARIKKGDELPPGV 1087

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKV+VA+KR +  GDKMAGRHGNKG+VSRILP EDMP+L+DG PVDIVLNPLGVPSR
Sbjct: 1088 IKMVKVYVAIKRKLAVGDKMAGRHGNKGVVSRILPEEDMPYLEDGRPVDIVLNPLGVPSR 1147

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQI ETHLGWA  G G+ ++  +   +AN     ++  L+ +    +  E +   DD
Sbjct: 1148 MNIGQILETHLGWAAKGTGEALQRYV---EANWSSDAIKERLKVIYSDPAFGEFLDKLDD 1204

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + + ++  + K G+ V+TPVFDGA E  I+++L    L  SGQ +L+DG TGEPFD+ VT
Sbjct: 1205 EEIKQLCLRSKRGIHVATPVFDGAQETEIHALLDEGQLPRSGQMVLFDGRTGEPFDQNVT 1264

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY 
Sbjct: 1265 VGVMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYT 1324

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LQE LT+KSDDVVGRTR+YE+IV G++  E+G PESFNVL+KE+Q+L L ++L  S
Sbjct: 1325 LQEFLTVKSDDVVGRTRMYEAIVKGDNVLESGLPESFNVLLKELQSLALDVELLES 1380


>gi|197122676|ref|YP_002134627.1| DNA-directed RNA polymerase subunit beta [Anaeromyxobacter sp. K]
 gi|220917459|ref|YP_002492763.1| DNA-directed RNA polymerase, beta subunit [Anaeromyxobacter
            dehalogenans 2CP-1]
 gi|226699366|sp|B4UDT2|RPOB_ANASK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765267|sp|B8JB70|RPOB_ANAD2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|196172525|gb|ACG73498.1| DNA-directed RNA polymerase, beta subunit [Anaeromyxobacter sp. K]
 gi|219955313|gb|ACL65697.1| DNA-directed RNA polymerase, beta subunit [Anaeromyxobacter
            dehalogenans 2CP-1]
          Length = 1422

 Score = 1609 bits (4166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 722/1401 (51%), Positives = 1001/1401 (71%), Gaps = 30/1401 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R+ FGK  +I +IP+LI +QK SYD FL  ++ P++R + GLQ  FKSVFPI  F+  
Sbjct: 10   RIRRNFGKINKIAEIPNLIAIQKFSYDKFLQADVPPEKRDDTGLQGVFKSVFPIKDFNET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +TY+ P+K+ +RL+V+D DE TGA+SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYHLEKPKYDVDECHQRGMTYSAPIKVVVRLVVWDKDEETGAQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT++GTF+I G +R+VVSQLHRSPG  FDHDKG++  SGKLLY  RIIP +G W
Sbjct: 130  FGEIPLMTENGTFIINGTERVVVSQLHRSPGAFFDHDKGKSHSSGKLLYNARIIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--------------DSEEILSTFYPKIV 237
            +D EFD KDI++VRIDRRRK+P T  L ALG                +EEIL  +Y    
Sbjct: 190  IDFEFDHKDILYVRIDRRRKLPATVLLRALGATPDTAKKDPVEFHGSAEEILKYYYDTET 249

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
                G          DL+ G + +  + D  + E +++  +K T   +K L    +K L 
Sbjct: 250  IRIEGKGKYEKDLVPDLLKGQRATRDIRDPKSNEVIVKKNRKYTESAIKKLVAAKMKSLP 309

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            +  + +     AED+V+  TGE+ +E  + + E  +EE+    I +  +L++D++N    
Sbjct: 310  VEPEEVYTKISAEDVVDETTGEVLLEVNEEVTEAKVEELRKRNINEFKVLFIDNLNILPA 369

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +R+TL+ DK    ++A+++IYR +RPGD  T   A ++F  LFF++++YDLS VGR+K+N
Sbjct: 370  LRDTLMQDKISTPEEAIMEIYRRLRPGDPPTPETATNLFVNLFFNAERYDLSKVGRLKLN 429

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT--IDDIDNLGNRRVRSVGEMLKNQY 475
             +  ++ P +   + K DI+ +++ L+DL+NGK    +DDID+LGNRRVR+VGE+L+NQY
Sbjct: 430  YKFGIEEPLENTVLTKRDILEVVRFLIDLKNGKPNKDVDDIDHLGNRRVRAVGELLENQY 489

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+RMER+IKER+S  +I+++MP DLINAKPV + + EFF SSQLSQ  +  N LS +
Sbjct: 490  RIGLVRMERAIKERMSLQEIETLMPHDLINAKPVTAVIKEFFGSSQLSQFMDQTNPLSEV 549

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            TH RRLSALG GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL+++ARVN Y
Sbjct: 550  THKRRLSALGPGGLTRERAGFEVRDVHSTHYGRICPIETPEGPNIGLIASLSTYARVNEY 609

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPYRKV  G+VT++V + SA+EEE   IAQAN+ +D+ G+FTE  V+CR  GE I 
Sbjct: 610  GFVETPYRKVEKGRVTDEVTFYSALEEEKHIIAQANAPVDKKGNFTEAKVWCRKEGEYIY 669

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            V  +++D +D SP Q+VS+AASL+PFLENDD+NR LMG NMQRQAVPLL+ +AP VGTG+
Sbjct: 670  VRPDEVDLMDVSPNQLVSVAASLVPFLENDDANRALMGSNMQRQAVPLLRTQAPLVGTGI 729

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNT 774
            E++VA+ SG   VAKR G+V+ VDA RIV+++          + VDIY L+K+QRSNQNT
Sbjct: 730  EAIVARDSGVTTVAKRDGVVQSVDASRIVVKADVPTSATDVANEVDIYNLIKYQRSNQNT 789

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+P+VK G+ V++ D+IADGP+T++G+LALG+N++VAFMPW GYNFEDS+L+SER++
Sbjct: 790  CINQKPIVKPGERVKKGDVIADGPATEMGELALGQNVVVAFMPWQGYNFEDSILLSERLI 849

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             EDVFTS+HIEEFE +ARDTKLG EEITRDIPNV EE LK++DE GII +GAEV PGDIL
Sbjct: 850  KEDVFTSVHIEEFECVARDTKLGKEEITRDIPNVGEEALKDLDESGIIRIGAEVKPGDIL 909

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGKITPKGE+ ++PEEKLLRAIFGEKA DVRD+SLRVP GVSGTV++ ++F+R G++K+E
Sbjct: 910  VGKITPKGETQLSPEEKLLRAIFGEKAGDVRDSSLRVPPGVSGTVINAKVFSRKGVEKDE 969

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV------SGPKGFKKSTVL 1008
            R+ ++E  +   L +D++DE  I+  + + ++  +L G+          G +  KK  VL
Sbjct: 970  RAKAIEEMEEAKLLKDQNDEIKIIQDSAFQKIRRLLLGKEVTARLVDDKGEQLLKKGDVL 1029

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               L+   P+  W + AV  + VQ     +   +E  K +++  F  KI +++ GD++PP
Sbjct: 1030 DDALLDTVPQRYWGEIAVAGD-VQDLARKIIENFEEQKELVKLLFGEKIGRLKKGDELPP 1088

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV+++VKV+VA+KR +  GDKMAGRHGNKG+VSR+LP ED+P+L+DGTPVDIVLNPLGVP
Sbjct: 1089 GVIKMVKVYVAIKRKLAVGDKMAGRHGNKGVVSRVLPEEDLPYLEDGTPVDIVLNPLGVP 1148

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMNVGQI ETHLGWA   +G +++ +I        +             G   E+++  
Sbjct: 1149 SRMNVGQILETHLGWAARNVGLRLQEMIEKEWGADPLRKKLKAAFAGTEGGPVGERLAAL 1208

Query: 1189 DDD----SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
             +D     + ++ ++ + G+ V+TPVFDGA E+ + +++       + QSIL+DG TGEP
Sbjct: 1209 IEDVPEKELPKLVQKLRRGMHVATPVFDGAREDEMKALMEEG--SATLQSILFDGRTGEP 1266

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD+ VTVG +YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++A
Sbjct: 1267 FDQDVTVGVMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEA 1326

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE LT+KSDDVVGRTR+YE+IV G +T E+G PESFNVL+KE+Q+L L ++L 
Sbjct: 1327 YGAAYSLQEFLTVKSDDVVGRTRMYEAIVKGENTLESGLPESFNVLIKELQSLALDVELL 1386

Query: 1365 NSRTKNSAKMEEIPDFNKCEL 1385
             +    +A+     D     L
Sbjct: 1387 ETPEAQAAREAAERDLGGGPL 1407


>gi|326566158|gb|EGE16313.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis
            12P80B1]
          Length = 1363

 Score = 1608 bits (4165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 970/1374 (70%), Gaps = 20/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY+ FL  +  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFSKLPDVMDVPYLLAIQVDSYEQFLQEHKKPKARANIGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A PL++ +RLI+ D +  T    I
Sbjct: 61   FPIESHSGNAQLQFVEYYLGEPEFDERECIMRGSTFAAPLRVKIRLIIKDKENKTA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 118  KDVREQSVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++ RIDRRRK+  T  L A+GMD+ +IL  F+ K+   +  
Sbjct: 178  RIIPYRGSWLDFEFDAKDLVYARIDRRRKLLATIILRAIGMDTAQILDQFFEKVEVFKGD 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +   L A D + G      +V  D G  ++E G+++ +  +K +   G+  L +  + 
Sbjct: 238  ESFEIELVA-DRLKGEMAQFDIVGPD-GNVIVEQGQRINALRVKRILNSGMTKLAVPDEY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    + EDIV G+  E+ + A  +ID + L ++    ++   IL+ + +++ AYI +TL
Sbjct: 296  LYERIIGEDIVVGD--EVLVRANTLIDHEILVKLAEKNVQSFKILFTNDIDHGAYIADTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE +F  +FF  ++YDLS VGR+K N RL  
Sbjct: 354  RADTIVTREEALIEIYKVMRPGEPPTLETAEKLFESMFFSQERYDLSNVGRMKFNRRLGR 413

Query: 423  DTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +  D        +   +  +DI+ ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ
Sbjct: 414  EFIDTDDMDVQREQGVLSNQDIVDVLKELIEIRNGRGEVDDIDHLGNRRIRSVGEMTENQ 473

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL R+ER++KER+++ D D++ PQDLIN+KPV +++ EFF SSQLSQ  +  N LS 
Sbjct: 474  FRIGLARVERAVKERLTTADSDNLSPQDLINSKPVAASIKEFFGSSQLSQFMDQNNPLSE 533

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FA+ N 
Sbjct: 534  ITHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLATFAKTNN 593

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYR+V DG+VT+++ Y+SA+EE    IAQA+S +++ G  TEE+V  R  GE +
Sbjct: 594  FGFLETPYRRVVDGRVTDEIEYVSAIEEVGMVIAQADSPMNDKGELTEEMVSVRHDGEFV 653

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  +K+  +D SP+QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG
Sbjct: 654  RMSADKVTHMDVSPRQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTG 713

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME  VA+ SG  +VAKR G++E+VDA RI++R  E ++    +G+DIY L+K+ RSNQNT
Sbjct: 714  MERHVARDSGVCVVAKRGGVIEEVDASRIIVRVNEDEMTAGEAGIDIYNLIKYTRSNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQR +V  GDE+ R DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V
Sbjct: 774  CINQRVIVNEGDEIERGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILLSERVV 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L N+DE GI+ +GAEV+ GDIL
Sbjct: 834  QEDRFTTIHIQELTCVARDTKLGPEEITGDIPNVGEAALANLDEAGIVYIGAEVDAGDIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ 
Sbjct: 894  VGKVTPKGESQLTPEEKLLRAIFGEKAADVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDS 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ S+E+  ++   +D  +E VI +     R++ +L G+    G  GFK   +LS+  I 
Sbjct: 954  RAKSIEKAMLDDYRKDLKEELVIFEAAAKGRILSLLDGKKVSGG-AGFKAGAILSTKDIE 1012

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
              P          +E+V   +  +       +  ++++F  K  K+  GDD+  GV ++V
Sbjct: 1013 NLPLESLLDIQPAEEEVSERLGQIAEFLSDKQKDIDNKFTEKKRKLTQGDDLAHGVQKIV 1072

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVPSRMN+G
Sbjct: 1073 KVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNPVDIVLNPLGVPSRMNIG 1132

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            Q+ ETHLG A  GLG KI +++   ++   +S LR FL+K+    G     +    D+ +
Sbjct: 1133 QVLETHLGMAAKGLGDKINAML---RSQVAVSELREFLDKIYNQVGGEQVDLDSLSDEDL 1189

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L + +  K GVP+ T VFDGA E  I  +L +ADL  +GQ  LYDG TG+ FDRPVTVGY
Sbjct: 1190 LALCQNLKDGVPMGTAVFDGAKETQIKELLSLADLSTTGQQTLYDGRTGKKFDRPVTVGY 1249

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA Y LQE
Sbjct: 1250 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGATYTLQE 1309

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV G      G PESFNVL KE+++LG++IDL+  +
Sbjct: 1310 MLTVKSDDVEGRTRMYKNIVDGEQYMNPGMPESFNVLTKEIRSLGINIDLKEKK 1363


>gi|326561524|gb|EGE11867.1| DNA-directed RNA polymerase subunit beta [Moraxella catarrhalis 7169]
          Length = 1363

 Score = 1608 bits (4165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1374 (51%), Positives = 971/1374 (70%), Gaps = 20/1374 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K P+++D+P L+ +Q  SY+ FL  +  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFSKLPDVMDVPYLLAIQVDSYEQFLQEHKKPKARANIGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A PL++ +RLI+ D +  T    I
Sbjct: 61   FPIESHSGNAQLQFVEYYLGEPEFDERECIMRGSTFAAPLRVKIRLIIKDKENKTA---I 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD++EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY  
Sbjct: 118  KDVREQSVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLYNA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD+++ RIDRRRK+  T  L A+GMD+ +IL  F+ K+   +  
Sbjct: 178  RIIPYRGSWLDFEFDAKDLVYARIDRRRKLLATIILRAIGMDTAQILDQFFEKVEVFKGD 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +   L A D + G      +V  D G  ++E G+++ +  +K +   G+  L +  + 
Sbjct: 238  ESFEIELVA-DRLKGEMAQFDIVGPD-GNVIVEQGQRINALRVKRILNSGMTKLAVPDEY 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    + EDIV G+  E+ + A  +ID + L ++    ++   IL+ + +++ AYI +TL
Sbjct: 296  LYERIIGEDIVVGD--EVLVRANTLIDHEILVKLAEKNVQSFKILFTNDIDHGAYIADTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R++AL++IY+VMRPG+  T   AE +F  +FF  ++YDLS VGR+K N RL  
Sbjct: 354  RADTIVTREEALIEIYKVMRPGEPPTLDTAEKLFESMFFSQERYDLSNVGRMKFNRRLGR 413

Query: 423  DTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +  D        +   +  +DI+ ++K L+++RNG+G +DDID+LGNRR+RSVGEM +NQ
Sbjct: 414  EFIDTDDMDVQREQGVLSNQDIVDVLKELIEIRNGRGEVDDIDHLGNRRIRSVGEMTENQ 473

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL R+ER++KER+++ D D++ PQDLIN+KPV +++ EFF SSQLSQ  +  N LS 
Sbjct: 474  FRIGLARVERAVKERLTTADSDNLSPQDLINSKPVAASIKEFFGSSQLSQFMDQNNPLSE 533

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +FA+ N 
Sbjct: 534  ITHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLATFAKTNN 593

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GF+ETPYR+V DG+VT+++ Y+SA+EE    IAQA+S +++ G  TEE+V  R  GE +
Sbjct: 594  FGFLETPYRRVVDGRVTDEIEYVSAIEEVGMVIAQADSPMNDKGELTEEMVSVRHDGEFV 653

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +  +K+  +D SP+QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTG
Sbjct: 654  RMSADKVTHMDVSPRQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTG 713

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME  VA+ SG  +VAKR G++E+VDA RI++R  E ++    +G+DIY L+K+ RSNQNT
Sbjct: 714  MERHVARDSGVCVVAKRGGVIEEVDASRIIVRVNEDEMTAGEAGIDIYNLIKYTRSNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQR +V  GDE+ R DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V
Sbjct: 774  CINQRVIVNEGDEIERGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILLSERVV 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L N+DE GI+ +GAEV+ GDIL
Sbjct: 834  QEDRFTTIHIQELTCVARDTKLGPEEITGDIPNVGEAALANLDEAGIVYIGAEVDAGDIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPS   GTV+DV++F R G++K+ 
Sbjct: 894  VGKVTPKGESQLTPEEKLLRAIFGEKAADVKDTSLRVPSSTKGTVIDVQVFTRDGLEKDS 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ S+E+  ++   +D  +E VI +     R++ +L G+    G  GFK  T+LS+  I 
Sbjct: 954  RAKSIEKAMLDDYRKDLKEELVIFEAAAKGRILSLLDGKKVSGG-AGFKAGTILSTKDIE 1012

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
              P          +E+V   +  +       +  ++++F  K  K+  GDD+  GV ++V
Sbjct: 1013 NLPLESLLDIQPAEEEVSERLGQIAEFLSDKQKDIDNKFTEKKRKLTQGDDLAHGVQKIV 1072

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVPSRMN+G
Sbjct: 1073 KVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNPVDIVLNPLGVPSRMNIG 1132

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSV 1193
            Q+ ETHLG A  GLG KI +++   ++   +S LR FL+K+    G     +    ++ +
Sbjct: 1133 QVLETHLGMAAKGLGDKINAML---RSQVAVSELREFLDKIYNQVGGEQVDLDSLSNEDL 1189

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L + +  K GVP+ T VFDGA E  I  +L +ADL  +GQ  LYDG TG+ FDRPVTVGY
Sbjct: 1190 LALCQNLKDGVPMGTAVFDGAKETQIKELLSLADLSTTGQQTLYDGRTGKKFDRPVTVGY 1249

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA Y LQE
Sbjct: 1250 MYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGATYTLQE 1309

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            MLT+KSDDV GRTR+Y++IV G      G PESFNVL KE+++LG++IDL+  +
Sbjct: 1310 MLTVKSDDVEGRTRMYKNIVDGEQYMNPGMPESFNVLTKEIRSLGINIDLKEKK 1363


>gi|148556370|ref|YP_001263952.1| DNA-directed RNA polymerase subunit beta [Sphingomonas wittichii RW1]
 gi|182676573|sp|A5VBZ8|RPOB_SPHWW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|148501560|gb|ABQ69814.1| DNA-directed RNA polymerase, beta subunit [Sphingomonas wittichii
            RW1]
          Length = 1455

 Score = 1608 bits (4163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 828/1454 (56%), Positives = 1057/1454 (72%), Gaps = 90/1454 (6%)

Query: 1    MA-KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
            MA + V      R+RK FG   E++ +P+LIEVQ+ SY+ FL     P +    GL+   
Sbjct: 1    MATQAVPATAKKRIRKVFGNIHEVVQMPNLIEVQRESYEQFLRSR--PADGYVSGLEKTL 58

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +SVFPI  F+G A L+FV YE + PK+D D+C  R +TYA P+++TLRLIVF+VD  T  
Sbjct: 59   RSVFPIRDFAGTAELDFVQYELEDPKYDTDECRQRGMTYAAPMRVTLRLIVFEVDPDTET 118

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            +S+ DIKEQ +YMGD+PLMT++GTF+I G +R++VSQ+HRSPG+ FDHD+G+   SGK L
Sbjct: 119  RSVLDIKEQDVYMGDMPLMTENGTFLINGTERVIVSQMHRSPGVLFDHDRGKTHASGKYL 178

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            +A R+IP +G W+D EFD+KDI++VRIDR+RK+PVTS L ALG   + ++     K  + 
Sbjct: 179  FAARVIPYRGSWLDFEFDAKDIVNVRIDRKRKLPVTSLLRALG---DAVIEVNPDKGKFE 235

Query: 240  QRG-------------DFWCFPLSAADLMVGAKVSSSLVDIDTGEQV---------IESG 277
                                  L   +   GA +   L+    GE++           SG
Sbjct: 236  AGDIVAISGVNRACRVKAVAGRLVTVEDPTGAIIPGGLIQTAEGEKIGHVARIRLQGMSG 295

Query: 278  KKLTSGLLKSLK----EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI----------- 322
            + + +   ++ +    E G K   +  +   G   A D+VN +TGE+             
Sbjct: 296  EDILNYFYRTQRFVRGENGWKVPFVAENW-RGQKPAFDVVNADTGEVVFPAGTKISPRAA 354

Query: 323  -------------------------------------EAGDVIDEKSLEEIFHSEIRDIP 345
                                                 EAGD +  ++LE +  +    + 
Sbjct: 355  NKAGKDGLETLLIPTDQIFGRYSAYDLIDESTGRIYIEAGDEVTPENLEALDKAGFDHVD 414

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
            +L +D V+   +IRNTL  DK +DR  AL +IYRVMRPG+  T   AE++F  LFFDS++
Sbjct: 415  LLDIDHVSTGPWIRNTLKADKVEDRDHALSEIYRVMRPGEPPTKETAEALFAGLFFDSER 474

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            YDLS VGRVK+NMRL LD  D V  +R EDI+A++K LVDL++GKG IDDIDNLGNRRVR
Sbjct: 475  YDLSAVGRVKLNMRLELDAEDTVTTLRSEDILAVVKTLVDLKDGKGEIDDIDNLGNRRVR 534

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            SVGE+L+NQYR+GLLRMER++KER+SSVD+ + MP DLINAKP V+AV EFF SSQLSQ 
Sbjct: 535  SVGELLENQYRVGLLRMERAVKERMSSVDVSTAMPNDLINAKPAVAAVREFFGSSQLSQF 594

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++S
Sbjct: 595  MDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINS 654

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L SF+RVN YGFIETPYRK+ DGKVTN+VVYLSAMEE    IAQAN+ LD +G F E+L+
Sbjct: 655  LASFSRVNKYGFIETPYRKIVDGKVTNEVVYLSAMEEAKHTIAQANAELDSEGRFVEDLI 714

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R AGE ++ PR+ +  +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 715  SAREAGEFLMAPRDHVTLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLVR 774

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            AEAPFVGTGME  VA+ SGAAI AKR+GIV+QVDA RIV+R+  G +D   SGVDIY LM
Sbjct: 775  AEAPFVGTGMEETVARDSGAAIAAKRSGIVDQVDATRIVVRAT-GAVDAGKSGVDIYTLM 833

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            KFQRSNQ+TC+NQRPLVKVGD V   DIIADGPST+ G+LALGRN+LVAFMPW+GYN+ED
Sbjct: 834  KFQRSNQSTCINQRPLVKVGDVVNAGDIIADGPSTEFGELALGRNVLVAFMPWNGYNYED 893

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            S+LISER+V +DVFTSIHI+EFEVMARDTKLGPE+ITRDIPNV EE L+N+DE GI+ +G
Sbjct: 894  SILISERIVKDDVFTSIHIDEFEVMARDTKLGPEDITRDIPNVGEEALRNLDEAGIVYIG 953

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            AEV PGDIL GKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLR+P GVSGTVVDVR+F
Sbjct: 954  AEVEPGDILCGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVSGTVVDVRVF 1013

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            NRHGIDK+ER++++ERE+I+ L +D++DE+ IL+R  Y+RL E+L GQ A + PKG KK 
Sbjct: 1014 NRHGIDKDERAMAIEREEIDRLTKDREDERAILNRANYARLKEMLLGQIATAAPKGIKKG 1073

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            + ++ +L++E  + +WW+FAVQD+  Q ++E++K QY+ +  ++  +F++++EK+Q GD+
Sbjct: 1074 SEINEELLAEVEKREWWKFAVQDDARQADLEAVKAQYDDAVGLIVKKFEDRVEKLQRGDE 1133

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGVL++VKVFVA+KR +Q GDKMAGRHGNKG++SRILP EDMPFL+DGTPVDIVLNPL
Sbjct: 1134 LPPGVLKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPL 1193

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIN-------DYKANGDISPLRSFLEKVIGT 1178
            GVPSRMNVGQIFETHLGWA  GLGK++ S +        D +A    + +   L++V G 
Sbjct: 1194 GVPSRMNVGQIFETHLGWAARGLGKQVTSALEAWREANPDAQAATPPAAVVDRLKEVYG- 1252

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
              +   I     D ++ +A   K+GVP++TPVFDGA E  +  MLR A LDESGQ  L+D
Sbjct: 1253 KEYHADIEGRSTDQIVEMAGLLKNGVPMATPVFDGAREADVAEMLRRAGLDESGQVELFD 1312

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+ FDR VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEME
Sbjct: 1313 GRTGDQFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEME 1372

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW +QAYGAAY LQEMLT+KSDDVVGRT+VYE+IV G+DTFE G PESFNVLVKEM++LG
Sbjct: 1373 VWALQAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGDDTFEAGIPESFNVLVKEMRSLG 1432

Query: 1359 LSIDLENSRTKNSA 1372
            L+++L +   ++  
Sbjct: 1433 LNVELSSIEDQSDD 1446


>gi|148653833|ref|YP_001280926.1| DNA-directed RNA polymerase subunit beta [Psychrobacter sp. PRwf-1]
 gi|172048569|sp|A5WH35|RPOB_PSYWF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|148572917|gb|ABQ94976.1| DNA-directed RNA polymerase, beta subunit [Psychrobacter sp. PRwf-1]
          Length = 1372

 Score = 1608 bits (4163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1380 (52%), Positives = 968/1380 (70%), Gaps = 23/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F + P ++DIP L+ +Q  SY+ FL  N  P  R N GLQAAF S+
Sbjct: 1    MAYSYTEKKRIRKSFAELPHVMDIPYLLAIQVDSYEQFLQENKKPKARENTGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPI + S  A L+FV Y    P+FD  +C+ R  T+A PL++ +RL++ D D        
Sbjct: 61   FPIESNSNNAELQFVEYYLGAPEFDERECISRGSTFAAPLRVKIRLVIKDKDSKDKNSKA 120

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDI+EQ++YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY
Sbjct: 121  AIKDIREQNVYMGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD+KD++  RIDRRRK+  T  L ALGMD+ EIL TF+ K+   +
Sbjct: 181  NARIIPYRGSWLDFEFDAKDLVFARIDRRRKLLGTIILRALGMDTNEILDTFFEKVSVYK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + +   L A D + G      +V  D GE ++E GK++ +  ++ +++ G+K L +  
Sbjct: 241  GEEQFEIDLVA-DRLRGEMAQFDIVSPD-GEVLVEQGKRINARRIRQIEQSGMKKLAVPD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE----IRDIPILYVDSVNNNA 356
            + L    +AEDIV     E+  +A  +ID + L ++   E    I++  IL+ + +++  
Sbjct: 299  EYLYERILAEDIV--VNDEVIAKANTLIDHELLVKLSAFEASESIKEFKILFTNDIDHGT 356

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YI +TL  D    R++AL++IY+VMRPG+  T   AE +F  +FF++D+YDLS VGR+K 
Sbjct: 357  YIADTLRADSTGSREEALIEIYKVMRPGEPPTIDTAEKLFESMFFNADRYDLSNVGRMKF 416

Query: 417  NMRLNL--------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            N RL          D   +   + K+DII ++K L+++RNG G +DDID+LGNRR+RSVG
Sbjct: 417  NRRLGRTFENTDDPDIKREQSVLTKDDIIDVLKELINIRNGIGEVDDIDHLGNRRIRSVG 476

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            EM +NQ+R+GL+R+ER++KER+SS + D++ PQDLIN+KPV +AV EFF SSQLSQ  + 
Sbjct: 477  EMAENQFRVGLVRVERAVKERLSSAESDNLSPQDLINSKPVAAAVKEFFGSSQLSQFMDQ 536

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +
Sbjct: 537  NNPLSEITHKRRISALGPGGLTRERAGFEVRDVHNTHYGRVCPIETPEGPNIGLINSLAT 596

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FA+ N +GF+ETPYRKV DGKVT+D+ YLSA+EE    IAQA+S LDE+G   EE+V  R
Sbjct: 597  FAKTNEFGFLETPYRKVVDGKVTDDIEYLSAIEEVGTVIAQADSELDENGVLAEEMVMVR 656

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              GE + +P +K+  +D SP QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ 
Sbjct: 657  SGGESVRMPSDKVTHMDVSPSQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADK 716

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTGME  VA+ SG  ++A+R G++E VDA RIV+R  E ++    +G+DIY L+K+ 
Sbjct: 717  PLVGTGMERHVARDSGVCVIARRGGVIEDVDASRIVVRVNEDEMQAGEAGIDIYNLIKYT 776

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQR +V  GDE+   DI+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L
Sbjct: 777  RSNQNTCINQRIIVNQGDEIAGGDILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSIL 836

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV
Sbjct: 837  LSERVVKEDRFTTIHIQELTCVARDTKLGTEEITADIPNVGEAALSALDESGIVYIGAEV 896

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            + GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+   GTV+DV++F R 
Sbjct: 897  DAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDTSLRVPTSTKGTVIDVQVFTRD 956

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K+ R+ S+E+ Q++   +D  +E  I +    SR+  +L GQ    G  G K  TVL
Sbjct: 957  GVEKDARAKSIEKSQLDNYRKDLKEELRIFEEAARSRISHLLDGQAISGG-AGLKSGTVL 1015

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +   + E            +E++   +  ++      +  ++ +F  K  K+  GDD+  
Sbjct: 1016 AESELLEMSLETLLDIQPVEEEIAERLTQIQEFLVDKQKDIDTKFAEKKRKLTAGDDLAH 1075

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++VKV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G PVDIVLNPLGVP
Sbjct: 1076 GVQKIVKVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNPVDIVLNPLGVP 1135

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISD 1187
            SRMN+GQ+ ETHLG A  GLG KI  +I   KA   ++ LR FL+K+    G     +  
Sbjct: 1136 SRMNIGQVLETHLGMAAKGLGDKINGMI---KAQAAVTELREFLDKIYNKVGGEQVDLDS 1192

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              DD +  +A+  + GVP+ T VFDGA E  I+ +L +A    SGQ  LYDG TG+ FDR
Sbjct: 1193 LSDDDIRALAQNLRDGVPMGTAVFDGAREVQIDELLELAGYPSSGQQTLYDGRTGQKFDR 1252

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1253 PVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1312

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             Y LQEMLT+KSDDV GRTR+Y++IV G    + G PESFNVL KE+++LG++I+L+ S 
Sbjct: 1313 TYTLQEMLTVKSDDVEGRTRMYKNIVDGEQYMDPGMPESFNVLTKEIKSLGINIELKESN 1372


>gi|41018148|sp|Q9KW14|RPOB_SHEVI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|9049401|dbj|BAA99392.1| RNA polymerase beta subunit [Shewanella violacea]
          Length = 1343

 Score = 1607 bits (4160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1364 (50%), Positives = 954/1364 (69%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TYA PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGITYAAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTNNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPASIMLRALDYSTQDILDLFFDRVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D D G  ++E G+++T+  ++ L++     L +  D 
Sbjct: 235  DSLVMDLVPERL-RGETASYDIKDSD-GSILVEKGRRVTARHIRQLEKSKTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I++I  LY++ ++N AY+ +TL
Sbjct: 293  IEGKIAGQDYIDPDTGEVLVSANAEITLEDLAKLSMAGIKEISTLYINDLDNGAYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEGLFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  GEDEGSGILSKEDIVAVMKNIITIRNGGDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+ + YLSA+EE    IAQAN  +D++G   EE V CR  G+   +    I 
Sbjct: 593  RKVEDGVVTDQIDYLSAIEEGRYVIAQANIDIDKNGRLLEEQVACRHKGDSTFMRGTDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E ++A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERIIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGSIDYVDASRIVVKVNESELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V   D++ADGPSTDLGDLA G+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPVVVGDVLADGPSTDLGDLAFGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  +Y R   +L                      +   PRS   
Sbjct: 953  HIAQAKKDLTEEFKILEEGVYGRARNLLLNAG-------------FEQAQLDAIPRSHLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQTIDDEAKQTELEQLAEQHDELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G P+DIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPIDIVLNPLGVPSRMNIGQILEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I +++ + +   +I      + ++         I  + DD VLR+A+  K 
Sbjct: 1120 AAAKGIGDQITAMLEEQRQLAEIRGYIKEVYELGDEVLQRVDIDSFTDDEVLRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  LYDG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKEMLALAKLPTSGQRTLYDGRTGNEFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNYQMQPGMPESFNVLLKEIRSLGINIELDQD 1343


>gi|294142940|ref|YP_003558918.1| DNA-directed RNA polymerase subunit beta [Shewanella violacea DSS12]
 gi|293329409|dbj|BAJ04140.1| DNA-directed RNA polymerase, beta subunit [Shewanella violacea DSS12]
          Length = 1343

 Score = 1607 bits (4160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 955/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     G +AAF+SV
Sbjct: 1    MVYSYSEKKRIRKDFGKRPKVLDIPYLLSIQLDSFKKF----TDQDPTGERGFEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +FSG + L++VSY+   P FDV +C  R +TYA PL++ LR++++D +   G  ++
Sbjct: 57   FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGITYAAPLRVKLRMVLYDREAAPG--TV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGDIPLMTNNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P +  L AL   +++IL  F+ ++ +  + 
Sbjct: 175  RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPASIMLRALDYSTQDILDLFFDRVNFKIKK 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G   S  + D D G  ++E G+++T+  ++ L++     L +  D 
Sbjct: 235  DSLVMDLVPERL-RGETASYDIKDSD-GSILVEKGRRVTARHIRQLEKSKTTELEVPVDY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G    +D ++ +TGE+ + A   I  + L ++  + I++I  LY++ ++N AY+ +TL
Sbjct: 293  IEGKIAGQDYIDPDTGEVLVSANAEITLEDLAKLSMAGIKEISTLYINDLDNGAYMSDTL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE +F  LFF  ++YDLS VGR+K N RL++
Sbjct: 353  RIDSTTNRLEALVEIYRMMRPGEPPTKDAAEGLFQNLFFSEERYDLSKVGRMKFNRRLSI 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + KEDI+A++K ++ +RNG   +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  GEDEGSGILSKEDIVAVMKNIITIRNGGDEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 473  ERAVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL SFAR N+YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRLCPTETPEGPNIGLINSLASFARTNSYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+ + YLSA+EE    IAQAN  +D++G   EE V CR  G+   +    I 
Sbjct: 593  RKVEDGVVTDQIDYLSAIEEGRYVIAQANIDIDKNGRLLEEQVACRHKGDSTFMRGTDIQ 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E ++A  
Sbjct: 653  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERIIAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G ++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP  
Sbjct: 713  SGVVVVAKRGGSIDYVDASRIVVKVNESELRPGEAGIDIYNLTKYTRSNQNTCINQRPCC 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V   D++ADGPSTDLGDLALG+NM +AFMPW+GYNFEDS+LISER+  ED FT+I
Sbjct: 773  SVGDPVVVGDVLADGPSTDLGDLALGQNMRIAFMPWNGYNFEDSILISERVAQEDRFTTI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 833  HIQELSCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GT++DV++F R G++K++R++ +E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEM 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             I    +D  +E  IL+  +Y R   +L                      +   PRS   
Sbjct: 953  HIAQAKKDLTEEFKILEEGVYGRARNLLLNAG-------------FEQAQLDAIPRSHLL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + DE  Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 1000 VQTIDDEAKQTELEQLAEQHDELKADFDKKFEIKRRKITQGDDLAPGVLKIVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G P+DIVLNPLGVPSRMN+GQI E H+G
Sbjct: 1060 TIQPGDKMAGRHGNKGVISKINPVEDMPYDENGNPIDIVLNPLGVPSRMNIGQILEVHMG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I +++ + +   +I      + ++         I  + DD VLR+A+  K 
Sbjct: 1120 AAAKGIGDQITAMLEEQRQLAEIRGYIKEVYELGDEVLQRVDIDSFTDDEVLRLAKNLKG 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E+ I  ML +A L  SGQ  LYDG TG  F+R VTVGY+YMLKLNH+
Sbjct: 1180 GIPIATPAFDGAKEKEIKEMLALAKLPTSGQRTLYDGRTGNEFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   + G PESFNVL+KE+++LG++I+L+  
Sbjct: 1300 NGRTQMYKNIVDGNYQMQPGMPESFNVLLKEIRSLGINIELDQD 1343


>gi|149911142|ref|ZP_01899768.1| DNA-directed RNA polymerase beta subunit [Moritella sp. PE36]
 gi|149805819|gb|EDM65809.1| DNA-directed RNA polymerase beta subunit [Moritella sp. PE36]
          Length = 1345

 Score = 1606 bits (4159), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1368 (51%), Positives = 960/1368 (70%), Gaps = 23/1368 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK FGK+  ++  P ++ +Q +S+  FL M+         GL+AAF+SV
Sbjct: 1    MVYSNTEKKRIRKDFGKSAPVVAKPQMLAIQTSSFKKFLEMD----HTGEHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY      F+V +C  R +TY+ PL++ LRL+++D D   G  +I
Sbjct: 57   FPIKSYSGTSELQYVSYRLGESVFEVKECQTRGITYSAPLRVKLRLVLYDRDAPAG--TI 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTHTGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD + VRIDRRRK+P +  L AL   +EEIL+ F+    +  + 
Sbjct: 175  RVIPYRGSWLDFEFDPKDCLFVRIDRRRKLPSSIILRALEFTTEEILAIFFDTTRFEVKD 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G      +V    GE  +E+G+++T+  +K  ++ G+  + +  + 
Sbjct: 235  GKILMELLPERL-RGETAVFDIV--ANGEVYVENGRRITARHIKKFEKAGITEIEVPLEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G   ++D +N ETGE+ + A   +  +S+ E+  + I+ I +LY + ++  +Y+ +TL
Sbjct: 292  LAGKVASKDYINEETGEVIVAANAELTLESVAELSQAGIKVIDVLYTNDLDVGSYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ +AL++IYR+MRPG+  T   AE +FN LFF  ++YDLSTVGR+K N R+  
Sbjct: 352  RVDSTTNKLEALVEIYRMMRPGEPPTREAAEGLFNNLFFAEERYDLSTVGRMKFNRRIGR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDI+ ++K L+++RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  EEDTGSGILNKEDIVEVMKTLINIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D+VMPQDLINAKP+ +A+ EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAVMPQDLINAKPISAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YGF+ETP+
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAVFARTNDYGFLETPF 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKVTNDV YLSA+EE    +AQAN+++D +G   +E + CR  GE   +  + I 
Sbjct: 592  RKVINGKVTNDVQYLSAIEEGLYAVAQANATIDTNGMLQDEFIPCRHKGETTFMSADNIQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTG+E  VA  
Sbjct: 652  YMDVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLNADKPLVGTGIERAVAID 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VA R G ++  DA RI+++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTVVALRGGSIDYADASRIIVKVNEEELVPGEAGIDIYTLTKYTRSNQNTCINQRPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V + D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  LTGEAVVKGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 832  HIQELSSIARDTKLGSEEITADIPNVGESALSKLDESGIVYVGAEVKPGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V GTV+DV++F R G+DK++R+  +E+ 
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVYGTVIDVQVFTRDGVDKDKRAQDIEQM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D  +E  I + +++ R+  +L                  + + ++   R QW 
Sbjct: 952  QLREAKKDLTEELSIFEESLFGRVKNLLLAAG-------------KTEEQLTAISRGQWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + DE+ Q  +ESL  Q++  ++  + +F  K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  EMVLVDEEQQTQLESLAKQHDELRADFDSKFDIKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP  K G PVDIVLNPLGVPSRMN+GQ+ E HLG
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPIEDMPHDKFGEPVDIVLNPLGVPSRMNIGQVLEVHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI ++I + +    I         + G       +S Y D+ V  +A   + 
Sbjct: 1119 LAARGIGTKIDNMIKEQQDLAKIREFMQKAYDI-GDSHQKVDLSTYSDEEVRVLAHNLRK 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TP FDGA E  I  MLR+ADL ESGQ  LYDG TG+ F+RPVTVGY+YMLKLNH+
Sbjct: 1178 GLPMATPAFDGAAEAEIKEMLRLADLPESGQLELYDGRTGDLFERPVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
             GRT++Y+SIV G+   + G PESFNVL+KE+++LG++I+L+ ++ K 
Sbjct: 1298 NGRTKMYKSIVDGDHRMDPGMPESFNVLLKEIRSLGINIELDENKGKK 1345


>gi|322506510|gb|ADX01964.1| rpoB [Acinetobacter baumannii 1656-2]
 gi|323516389|gb|ADX90770.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            TCDC-AB0715]
          Length = 1341

 Score = 1605 bits (4156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 709/1353 (52%), Positives = 971/1353 (71%), Gaps = 21/1353 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D P L+ +Q  SY  FL    +P  R + GLQAAF+SVFPI ++SG A LEFV Y    
Sbjct: 1    MDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGK 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P+FDV +C+ R  TYA P+++ +RLI+ D +     KSIKD++EQ +YMG++PLMT++GT
Sbjct: 61   PEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSIKDVREQEVYMGEIPLMTENGT 116

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ RIIP +G W+D EFD+KD+++
Sbjct: 117  FVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSARIIPYRGSWLDFEFDAKDLVY 176

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+  T  L ALG ++E+IL+ FY K+        +   L    L  G      
Sbjct: 177  VRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDMGSYQIDLVPERL-RGEMAQFD 235

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            + D + G+ ++E GK++ +  ++ ++  G+  L +  + L     AEDI   + GE+   
Sbjct: 236  ITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEYLYERITAEDITLRD-GEVIA- 292

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  ++  + + ++    ++   IL+ + ++  +++ +TL  D  +DR++AL++IY+VMRP
Sbjct: 293  ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTLRADLTRDREEALVEIYKVMRP 352

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------DDVRHIRKED 435
            G+  T   AE++FN LFF S++YDLS VGR+K N RL             +    +  ED
Sbjct: 353  GEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGRPYEVGTDQKSREVEGILSHED 412

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            II +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+ER++KER+S  + 
Sbjct: 413  IIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAET 472

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 473  DNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 532

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N +GF+ETPYRKV DG+VT+DV 
Sbjct: 533  FEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDDVE 592

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE + +P EK+  +D S +QVVS+A
Sbjct: 593  YLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVA 652

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME+ VA+ SG  ++A R G++
Sbjct: 653  ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCVIANRGGVI 712

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNTC+NQ  +V +GD+V R DI+A
Sbjct: 713  EYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNTCINQNVIVNLGDKVARGDILA 772

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            DGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++ ED  TSIHI+E   +ARDTK
Sbjct: 773  DGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTK 832

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            LG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRA
Sbjct: 833  LGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRA 892

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            IFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++R++++E+ Q++   +D  +E 
Sbjct: 893  IFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDDRALAIEKAQLDSYRKDLKEEY 952

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 953  KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPADEAIAERL 1011

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 1012 TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 1071

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 1072 NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 1131

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D+ +L +A   ++GVP++TPVFDGA
Sbjct: 1132 LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPLATPVFDGA 1188

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGS
Sbjct: 1189 EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGS 1248

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV 
Sbjct: 1249 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVD 1308

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 1309 GNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1341


>gi|238020179|ref|ZP_04600605.1| hypothetical protein GCWU000324_00054 [Kingella oralis ATCC 51147]
 gi|237868573|gb|EEP69577.1| hypothetical protein GCWU000324_00054 [Kingella oralis ATCC 51147]
          Length = 1398

 Score = 1605 bits (4155), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1403 (49%), Positives = 957/1403 (68%), Gaps = 44/1403 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL  + AP +R +EGLQAAF S+
Sbjct: 1    MSYTFTEKKRIRKSFAKRETVLDVPYLLTTQLESYSKFLQQDCAPQKRKDEGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD--EFTGAK 120
            FPI + +G A L+F  Y    P+FD+ +C  R +TYA PL+  ++L +F+ +       +
Sbjct: 61   FPIVSNNGYAELQFDQYVLGEPEFDIAECQLRGITYAAPLRAKIKLAIFNKEGSNKVEER 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K+I+   +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL+
Sbjct: 121  ELKEIRANDVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHASGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL+ F+    Y  
Sbjct: 181  SARIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLRALGYNNEQILAMFFDLETYYL 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             G      L    L  G      + D + G  ++ +GK++ +  ++ ++  G+  L I +
Sbjct: 241  SGTGVQTALVPERL-RGETAKFDIADNE-GNVLVAAGKRINARNIRDIQAAGLTRLNIDA 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  +A D++  +TGE+   A   I E+ L +     I++I  L+V      AYI  
Sbjct: 299  ESLIGKIIARDVIVPDTGEVLATANAEITEELLAQFDIQGIKEIQTLFVSETEAGAYISA 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL TD+  D++ A + IYR+MRPG+  T    E++FN LFF  + YDLS VGR+K N R 
Sbjct: 359  TLNTDETADQQAAKIAIYRMMRPGEPPTEEAVEALFNRLFFQEESYDLSRVGRMKFNTRT 418

Query: 421  NL------------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                                      +    +  +  EDI+  I  LV+LRNG G +DDI
Sbjct: 419  YEQKLLPVQENNWYGRLLNQTFAGVGEKEAKLHILSVEDIVVTIATLVELRNGHGEVDDI 478

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            D+LGNRRVRSVGE+++NQ+R GL R+ER++KER++  + + +MP DLINAKPV +A+ EF
Sbjct: 479  DHLGNRRVRSVGELVENQFRSGLARVERAVKERLNQAESEGLMPTDLINAKPVSAAIKEF 538

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET E
Sbjct: 539  FGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 598

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL+ +AR N YGF+ETPYR+V DGKVTN++ YLSA+EE    IAQAN+ LD+
Sbjct: 599  GPNIGLINSLSVYARTNEYGFLETPYRRVVDGKVTNEIDYLSAIEEGRYVIAQANTDLDK 658

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             G    +L+ CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NM
Sbjct: 659  HGKLLGDLITCREKGETILATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANM 718

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            QRQAVP L+AE P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +     
Sbjct: 719  QRQAVPCLRAEKPLVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAKE 778

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             GVDIY L+KF RSNQ+T +NQRP V  GD ++R D+IADG STDLG+LALG+NM +AFM
Sbjct: 779  GGVDIYNLVKFTRSNQSTNINQRPAVSAGDVLQRGDLIADGASTDLGELALGQNMTIAFM 838

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            PW+GYN+EDS+LISER+ ++D +TSIHIEE  V+ARDTKLG EEITRDIPN+SE+    +
Sbjct: 839  PWNGYNYEDSILISERVAADDRYTSIHIEELNVVARDTKLGAEEITRDIPNLSEKMQNRL 898

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            DE GII +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+S
Sbjct: 899  DESGIIYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMS 958

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
            GTV+DV++F R GI +++R+ ++   +++   +D +D+  I D + + R+  ++ GQ A 
Sbjct: 959  GTVIDVQVFTREGIQRDKRAQAIIDAELKRYRQDLNDQIRIFDNDTFDRIQRMIVGQKAN 1018

Query: 997  SGPKGFKKSTVLSSDLISEY-PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             GP    K  V++ + +     R  W+   V DE++ + +E +K+  +  +S  E  F+ 
Sbjct: 1019 GGPNKLGKGKVITQEYLDGLTSRHDWFDIRVADEEIAKQLELMKLSLQEKRSEAEALFEV 1078

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K +K+  GD++P GV + VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG
Sbjct: 1079 KKKKMTQGDELPAGVQKTVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADG 1138

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
              VDIVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ +++    +  +R+FL K+
Sbjct: 1139 RTVDIVLNPLGVPSRMNIGQILEVHLGWAAKGIGQRIDKMLQEHR---KVKEIRAFLNKL 1195

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA--------- 1226
                   E +    D+ +L +A+  + G   ++PVFDGA E+ I  ML +A         
Sbjct: 1196 YNGSGKHEDLDSLSDEDILVLADNLRRGATFASPVFDGAKEKEIYEMLNLAYPSDDPEVQ 1255

Query: 1227 --DLDES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                ++S  Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPL
Sbjct: 1256 KLGFNDSKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPL 1315

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G 
Sbjct: 1316 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDAGM 1375

Query: 1344 PESFNVLVKEMQALGLSIDLENS 1366
            PESFNV+VKE+++LGL IDLEN+
Sbjct: 1376 PESFNVIVKEIRSLGLDIDLENN 1398


>gi|153005082|ref|YP_001379407.1| DNA-directed RNA polymerase subunit beta [Anaeromyxobacter sp.
            Fw109-5]
 gi|166229284|sp|A7HCH7|RPOB_ANADF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|152028655|gb|ABS26423.1| DNA-directed RNA polymerase, beta subunit [Anaeromyxobacter sp.
            Fw109-5]
          Length = 1416

 Score = 1604 bits (4154), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1394 (51%), Positives = 1003/1394 (71%), Gaps = 27/1394 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R+ FGK  +I +IP+LI +QK+SYD FL  ++ P++R + GLQ  FKSVFPI  F+  
Sbjct: 10   RIRRNFGKINKIAEIPNLIAIQKSSYDKFLQADVPPEKREDTGLQGVFKSVFPIKDFNET 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  + PK+DVD+C  R +TY+ P+K+ +RL+V+D DE TGA+SI+D+KEQ +Y
Sbjct: 70   SSLEFVSYHLEKPKYDVDECHQRGMTYSAPIKVVVRLVVWDKDEETGAQSIRDVKEQEVY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT++GTF+I G +R+VVSQLHRSPG  FDHDKG++  SGKLL+  RIIP +G W
Sbjct: 130  FGEIPLMTENGTFIINGTERVVVSQLHRSPGAFFDHDKGKSHSSGKLLFNARIIPYRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALG--------------MDSEEILSTFYPKIV 237
            +D EFD KDI++VRIDRRRK+P T  L ALG                +EEIL  +Y    
Sbjct: 190  IDFEFDHKDILYVRIDRRRKLPATVLLRALGGVPDTAKKTPIEFHGSAEEILKYYYDTET 249

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
                G          DL+ G + +  + D  T E V++  +K T   +K L    +K L 
Sbjct: 250  IRIEGKGKFEKDLNPDLLKGQRATRDIRDPKTNEIVVKKNRKFTESAIKKLVAAKMKSLP 309

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            I  + +     AED+V+ +TGE+ +E  + + E+ LEE+    I +  +L++D++N    
Sbjct: 310  IEPEEVYTKISAEDVVDEQTGEVLLEVNEEVSEEKLEELRKRGIGEFKVLFIDNLNVLPS 369

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +R+TL+ DK    ++A+++IYR +RPGD  T   A ++F  LFF++++YDLS VGR+K+N
Sbjct: 370  LRDTLMQDKISTPEEAIMEIYRRLRPGDPPTPETATNLFVNLFFNAERYDLSKVGRLKLN 429

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQY 475
             +  ++ P D   + K DI+ +++ L+DL+NG     +DDID+LGNRRVR+VGE+L+NQY
Sbjct: 430  YKFGIEEPLDNTVVTKRDILEVVRFLIDLKNGTPNKDVDDIDHLGNRRVRAVGELLENQY 489

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+RMER+IKER+S  +I+++MP DLINAKPV + + EFF SSQLSQ  +  N LS +
Sbjct: 490  RIGLVRMERAIKERMSLQEIETLMPHDLINAKPVTAVIKEFFGSSQLSQFMDQTNPLSEV 549

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            TH RRLSALG GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL+++ARVN Y
Sbjct: 550  THKRRLSALGPGGLTRERAGFEVRDVHSTHYGRICPIETPEGPNIGLIASLSTYARVNEY 609

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPYRKV  G+VT++V + SA+EEE   IAQAN+ +D+ G FT  +V CR  GE I 
Sbjct: 610  GFVETPYRKVEKGRVTDEVSFYSALEEEKHIIAQANAPVDKKGVFTGNIVSCRKEGEYIN 669

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
               +++D +D SP Q+VS+AASL+PFLENDD+NR LMG NMQRQAVPLL+  AP VGTG+
Sbjct: 670  ARPDEVDLMDVSPNQLVSVAASLVPFLENDDANRALMGSNMQRQAVPLLRTRAPLVGTGI 729

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNT 774
            E +VA+ SG  +VAKR G+++ VDA RIV+++          + VDIY L+K+QRSNQNT
Sbjct: 730  EGIVARDSGVCVVAKRDGVIQSVDAARIVVKADVPTSATDVANEVDIYNLIKYQRSNQNT 789

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQ+P+VK G+ V++ D+IADGP+T++G+LALG+N++VAFMPW GYNFEDS+L+SER +
Sbjct: 790  CINQKPIVKPGERVKKGDVIADGPATEMGELALGQNVVVAFMPWQGYNFEDSILLSERFL 849

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS+HIEEFE +ARDTKLG EEITRDIPNV EE LK++DE GII +GAEV PGDIL
Sbjct: 850  KDDVFTSVHIEEFECVARDTKLGKEEITRDIPNVGEEALKDLDESGIIRIGAEVKPGDIL 909

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGKITPKGE+ ++PEEKLLRAIFGEKA DVRD+SLRVP GVSGTV++ ++F+R G++K+E
Sbjct: 910  VGKITPKGETQLSPEEKLLRAIFGEKAGDVRDSSLRVPPGVSGTVINAKVFSRKGVEKDE 969

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVL 1008
            R+ ++E  +   L +D++DE  I+  + + ++  +L G+          G +  K+  VL
Sbjct: 970  RAKAIEEMEEAKLLKDQNDEIRIIQDSAFQKIRRLLLGKEVSGRLVDDKGNQLLKRGDVL 1029

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               L+   P+  W + AV+ + VQ  V  +   +E  K +++  F  KI +++ GD++PP
Sbjct: 1030 DDALLDTVPQRYWGEIAVEGD-VQDLVRKIVENFEEQKELVKLLFGEKIGRLKKGDELPP 1088

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV+++VKV+VA+KR +  GDKMAGRHGNKG+VSR+LP ED+P+L+DG PVDIVLNPLGVP
Sbjct: 1089 GVIKMVKVYVAIKRKLAVGDKMAGRHGNKGVVSRVLPEEDLPYLEDGRPVDIVLNPLGVP 1148

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLIN-DYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            SRMNVGQI ETHLGWA   +G +++ +I  ++  +     L+   E V G+    + I +
Sbjct: 1149 SRMNVGQILETHLGWAAKNVGWRLQEMIEKNFGPDQLRKKLKKAFEGVEGSDRLGQLIDE 1208

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                 + ++A + K G+ V+TPVFDGA E+ + ++L       + QSIL+DG TGEPFD+
Sbjct: 1209 LPAQELPKLATKLKEGMHVATPVFDGAHEDEMKALLGEG--SATMQSILFDGRTGEPFDQ 1266

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             VTVG +YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA
Sbjct: 1267 DVTVGVMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGA 1326

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE LT+KSDDVVGRTR+YE+IV G +T E+G PESFNVL+KE+Q+L L ++L  + 
Sbjct: 1327 AYSLQEFLTVKSDDVVGRTRMYEAIVKGENTLESGLPESFNVLIKELQSLALDVELLETP 1386

Query: 1368 TKNSAKMEEIPDFN 1381
               +A+ +   +  
Sbjct: 1387 EAKAAREQAEGELG 1400


>gi|88861460|ref|ZP_01136087.1| DNA-directed RNA polymerase beta chain [Pseudoalteromonas tunicata
            D2]
 gi|88816542|gb|EAR26370.1| DNA-directed RNA polymerase beta chain [Pseudoalteromonas tunicata
            D2]
          Length = 1341

 Score = 1604 bits (4153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1365 (51%), Positives = 964/1365 (70%), Gaps = 27/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                ++   R+RK FGK P+++DIP L+  Q  S+  FL    +PD   N GL+AAF+SV
Sbjct: 1    MAYSYSEKKRIRKDFGKRPQVLDIPFLLSTQLESFKKFL----SPDAEGNHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++ D +      ++
Sbjct: 57   FPIKSYSGNSELQYVSYRIGEPVFDVKECQIRGVTYSAPLRVKLRLVLMDKEAPG---TV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT  GTFVI G +R++VSQLHRSPG+ FD+D+G+   SGK+LY  
Sbjct: 114  KDIKEQEVYMGEIPLMTDTGTFVINGTERVIVSQLHRSPGVFFDNDRGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD+KD ++VRIDRRRK+P +  L AL   +EEIL  F+    +    
Sbjct: 174  RVIPYRGSWLDFEFDAKDNLYVRIDRRRKLPASIILRALDFSNEEILKIFFETTAFEIAN 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L  + L  G      + D D GE V+E G+++T+  +K L+++ V  L +  + 
Sbjct: 234  GKVMMELVPSRL-RGEVAQFEIKDND-GEVVVEKGRRITARHIKQLEKEQVNSLEVPHEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA + ++ ++GEI  EA   +  + + E+  +    I  LY++ V++ AY+ +TL
Sbjct: 292  IIGRVVARNYISEDSGEIIAEANAELTLELMAELVKAGFNRIDTLYINDVDSGAYMSDTL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N R++ 
Sbjct: 352  RIDSTTNRLEALVEIYRMMRPGEPPTRDAAEALFQNLFFSEERYDLSTVGRMKFNSRVDN 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + KEDI+A++K+L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  PEGTGDGTLSKEDIVAVMKVLIDIRNGKGDVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472  ERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N +GF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPNIGLINSLSCYARTNEFGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG VT+DV YLSA+EE    IAQAN++L+E+  F E+L+ CR  GE   + +  + 
Sbjct: 592  RKVVDGVVTDDVDYLSAIEEGRFVIAQANANLNENNEFLEDLIPCRFKGESTFMGKTDMQ 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  +AK 
Sbjct: 652  YMDVSPQQVISVAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIEMTLAKD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  IVAKR G V   DA RIV+   E +     +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTIVAKRGGQVTYADASRIVVNVNENERIAGEAGIDIYNLTKYTRSNQNTCINQKPTV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VG+ V R D++ADGPSTDLGDLALG+N+ VAFMPW+GYNFEDS+L+SER+V ED  T+I
Sbjct: 772  MVGEPVTRGDVLADGPSTDLGDLALGQNLRVAFMPWNGYNFEDSILLSERVVQEDRLTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E + +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELQCIARDTKLGSEEITADIPNVGESALGKLDESGVVYIGAEVKGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ V+GTV+DV++F R G++K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVTGTVIDVQVFTRDGVEKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q+    +D ++E  IL+  + +R  ++L G                  + +      +  
Sbjct: 952  QLREAKKDFNEEFRILEAGVVARARQLLVGAG-------------FDEEKLLGLSSEKVL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              ++ DE+ Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  TQSLADEEKQAELEQLAAQYDELKAEYDKKFEVKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S I+P EDMP+   G  VDIVLNPLGVPSRMN+GQI ETH+G
Sbjct: 1059 RIQPGDKMAGRHGNKGVISTIVPVEDMPYDDKGRTVDIVLNPLGVPSRMNIGQILETHMG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G++I+ +I   K    +  LR F++K    G       IS + DD V R+A   
Sbjct: 1119 LAARGIGERIEEMI---KEQRALHELREFIQKAYSLGDCRQKVDISTFTDDEVRRLAHHL 1175

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+P++TP FDGA E  I  ML +     SGQ  LYDG TG+ F+R VTVGY+YMLKLN
Sbjct: 1176 RGGLPIATPAFDGAKESEIKEMLELGGYPTSGQVTLYDGRTGDKFERQVTVGYMYMLKLN 1235

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 1236 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1295

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE 
Sbjct: 1296 DVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEE 1340


>gi|78484633|ref|YP_390558.1| DNA-directed RNA polymerase, beta subunit [Thiomicrospira crunogena
            XCL-2]
 gi|109914407|sp|Q31IY9|RPOB_THICR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78362919|gb|ABB40884.1| DNA-directed RNA polymerase, beta subunit [Thiomicrospira crunogena
            XCL-2]
          Length = 1352

 Score = 1603 bits (4152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1365 (51%), Positives = 966/1365 (70%), Gaps = 14/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     R+RK F     I+++P L+ +QK S+  FL  +  P ER   GL +AF SV
Sbjct: 1    MTYSLTEKKRIRKDFATRSSILEVPYLLSLQKESFKEFLQKDKKPLERDPIGLHSAFSSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI   +G A LE+VSY    P+FDV +C  R +TY+ PL++ +RL++FD D   G + +
Sbjct: 61   FPIHGVAGTADLEYVSYTMGQPEFDVKECKQRGVTYSSPLRVKMRLVLFDKDAPAGKRPV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KD+KEQ +Y+GD+PLMT++GTFVI G +R++V+QLHRSPG+ FD DKG++  SGK+L+  
Sbjct: 121  KDVKEQEVYLGDVPLMTENGTFVINGTERVIVTQLHRSPGVIFDSDKGKSHSSGKVLFNA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD  D + VRIDRRRK+PV+    A+G  SEEIL TF+     S + 
Sbjct: 181  RIIPYRGSWLDFEFDHNDCVFVRIDRRRKLPVSIIFRAMGYSSEEILDTFFDHTHISYKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L  +  + G   +  + D D  + +I++GKK+T+  +K L+E  V  + +  + 
Sbjct: 241  GAFVMQLVPS-QLKGQTAAFDIADGD--KVIIKAGKKITARNIKQLQEAKVDSVVVPEEY 297

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  ++  I N ETGE+   + +VI    +E +   +     IL++D + N +YI +TL
Sbjct: 298  LLGKVLSSGITNEETGELVARSNEVIASDLIETMKSIKDLSFRILFIDDLENGSYISDTL 357

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    + +A ++IYR+MRPG+  T   +E++FN LFFD  +YDLS+VGR+K+N RL  
Sbjct: 358  NLDTTTSQLEAQIEIYRMMRPGEPPTKESSEALFNSLFFDEARYDLSSVGRMKLNRRLGR 417

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    +  +D++ ++K L+++RNG  TIDDID LGNRR+R+VGEM +N +R+GL+R+
Sbjct: 418  KDNEGSLVLENQDVVDVVKELLNIRNGLSTIDDIDTLGNRRIRAVGEMAENAFRVGLVRV 477

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER++  + D ++PQDLINAKPV +A+ EFF SSQLSQ  + VN LS +TH RR+S
Sbjct: 478  ERAVKERLNQAETDGLLPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSEVTHKRRVS 537

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+++L  +A+ N YGF+ETPY
Sbjct: 538  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINTLAIYAKTNKYGFLETPY 597

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV DG+VT +V Y+SA++E    IAQA++++D D    +ELV  R   E IL   + ID
Sbjct: 598  RKVIDGQVTEEVEYVSAIDEAQFVIAQASAAMDSDNKLLDELVTARHKNETILASSQDID 657

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  
Sbjct: 658  YMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGIEKTVAID 717

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  ++A R G +   D+ RIV+R+ + ++    +GVDIY L+K+QRSNQNTC+NQ+P+V
Sbjct: 718  SGVTVIALRGGEIVSSDSARIVVRANQEEIAEGETGVDIYNLIKYQRSNQNTCINQKPIV 777

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V R D++ADGPSTDLG+LA+G+NM +AFMPW+GYNFEDS+L+SER+V ED +T+I
Sbjct: 778  KAGDVVSRGDVLADGPSTDLGELAIGQNMRIAFMPWNGYNFEDSILVSERVVQEDRYTTI 837

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE   +ARDTKLGPEE+T DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKG
Sbjct: 838  HIEELTCLARDTKLGPEEVTSDIPNVGEAALSRLDESGIVYVGAEVKQGDILVGKVTPKG 897

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRV  GV GTV+DV++F R G+ K+ R+++++ +
Sbjct: 898  ETQLTPEEKLLRAIFGEKASDVKDTSLRVSKGVEGTVIDVQVFTREGVKKDARALAIQED 957

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++ + +D D++  IL+ +   R+  +L GQ  V         T +++D ++    S+W+
Sbjct: 958  ELQKVRKDIDEQYKILEEDTIDRIQPMLIGQKLVD-------GTEITADFLASQDSSKWF 1010

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               V D+ +  ++ESL+ Q    K  L   F+ K +K+  GDD+ PGV ++VKV+VA+KR
Sbjct: 1011 GLNVADDALSSHLESLEKQLVAKKEELNGVFEEKKKKLTQGDDLQPGVSKMVKVYVAVKR 1070

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++SRI P EDMP+ + G PVDI LNPLGVPSRMNVGQI ETHLG
Sbjct: 1071 RIQPGDKMAGRHGNKGVISRICPVEDMPYDETGRPVDICLNPLGVPSRMNVGQILETHLG 1130

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG KI +++   +   DI  L+SFL K+               D  ++ +A   +
Sbjct: 1131 LAAEGLGAKINAML---EQQADIKELKSFLHKIYNETQGQKVDFDSLTDAEIIELAGNLR 1187

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP+++PVFDGA E+ I ++LR+ADL ESGQ  LYDG++GE FDRPVTVGY+Y LKLNH
Sbjct: 1188 KGVPMASPVFDGASEDEIKALLRLADLPESGQMKLYDGISGEEFDRPVTVGYMYYLKLNH 1247

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD
Sbjct: 1248 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEMLTVKSDD 1307

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            + GRTR+Y++IV GN+  E G PESF+VL KE++ALG+ I+LE  
Sbjct: 1308 LNGRTRMYKNIVDGNEYMEPGIPESFSVLRKEIRALGIDIELEQE 1352


>gi|219681976|ref|YP_002468360.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. Tuc7
            (Acyrthosiphon pisum)]
 gi|254765278|sp|B8D6V0|RPOB_BUCAT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219621709|gb|ACL29865.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. Tuc7
            (Acyrthosiphon pisum)]
 gi|311085782|gb|ADP65864.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str.
            LL01 (Acyrthosiphon pisum)]
          Length = 1342

 Score = 1603 bits (4150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+     PD     GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFKKFIQ----PDLSGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+ PL++ LRL++++ D      ++
Sbjct: 57   FPIRGYNGNSELQYVSYRLGETIFDVKECQIRGATYSAPLRVKLRLVIYERDI--LEATV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PV+  L AL  ++EEIL+ F+ K ++    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVSIILRALNYNTEEILNIFFEKNIFKIEN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S ++     G   +E G+++T+  ++ LK   +K + +  + 
Sbjct: 235  NKIVLELVPERL-RGETASFNIK--KNGIIYVEKGRRITAKHIQELKNNKIKSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ V+ +TGE  I +   +  + LE++  S    I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYVDKKTGETIISSNTELSLEILEKLKKSGFYSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLSTVGR+K N  L  
Sbjct: 352  RIDSSNDRMSALIEIYRVMRPGEPPTKEATENLFENLFFSEDRYDLSTVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII +IK ++D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 412  EETKGSSTLNKEDIIDVIKKIIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSIGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N+YGF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKVC+G V+ ++ YLSA+EE N  IAQAN+++D+ G FT++LV CR  GE  L  R +++
Sbjct: 592  RKVCNGLVSEEIHYLSAIEEGNYIIAQANTNIDKTGFFTDDLVTCRHKGESSLFNRNQVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP LK + P +GTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLKTDKPLIGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR+G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTAVAKRSGVVQYVDASRIVIKVDEKEMYSREAGIDIYNLTKYTRSNQNTCINQQPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+++++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEKIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGAEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  I + ++++ + +     +             + +  +   P  +W+
Sbjct: 952  QLKKIKQDLTEEFKIFESSLFTHIKKTFISLD-------------IETKQLDTLPFEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ +  ++ +E L  Q+   K     + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SVDIKQKDKKKEIEKLAKQHHELKEEFNKKIEIKRQKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +   ++         +         +  + ++ +LR+A+  K+
Sbjct: 1119 MAAKGIGDKINHMLKTQEKISNLRKFIQKAFDLGDNLRQKVNLDTFSNEEILRLAKNLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ A L  SGQ IL+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GIPISTPVFDGAQENEIKQMLKFAGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELESE 1342


>gi|219681420|ref|YP_002467805.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. 5A
            (Acyrthosiphon pisum)]
 gi|257471095|ref|ZP_05635094.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str.
            LSR1 (Acyrthosiphon pisum)]
 gi|254765277|sp|B8D8J6|RPOB_BUCA5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219624263|gb|ACL30418.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. 5A
            (Acyrthosiphon pisum)]
          Length = 1342

 Score = 1602 bits (4149), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1364 (50%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+     PD     GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFKKFIQ----PDLSGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+ PL++ LRL++++ D      ++
Sbjct: 57   FPIRGYNGNSELQYVSYRLGETIFDVKECQIRGATYSAPLRVKLRLVIYERDI--LEATV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PV+  L AL  ++EEIL+ F+ K ++    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVSIILRALNYNTEEILNIFFEKNIFKIEN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S ++     G   +E G+++T+  ++ LK   +K + +  + 
Sbjct: 235  NKIVLELVPERL-RGETASFNIK--KNGIIYVEKGRRITAKHIQELKNNKIKSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ V+ +TGE  I +   +  + LE++       I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYVDKKTGETIISSNTELSLEILEKLKKLGFYSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLSTVGR+K N  L  
Sbjct: 352  RIDSSNDRMSALIEIYRVMRPGEPPTKEATENLFENLFFSEDRYDLSTVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII +IK ++D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 412  EETKGSSTLNKEDIIDVIKKIIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSIGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N+YGF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKVC+G V+ ++ YLSA+EE N  IAQAN+++D+ G FT++LV CR  GE  L  R +++
Sbjct: 592  RKVCNGLVSEEIHYLSAIEEGNYIIAQANTNIDKTGFFTDDLVTCRHKGESSLFNRNQVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP LK + P +GTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLKTDKPLIGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR+G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTAVAKRSGVVQYVDASRIVIKVDEKEMYSREAGIDIYNLTKYTRSNQNTCINQQPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+++++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEKIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGAEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  I + ++++ + +     +             + +  +   P  +W+
Sbjct: 952  QLKKIKQDLTEEFKIFESSLFTHIKKTFISLD-------------IETKQLDTLPFEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ +  ++ +E L  Q+   K     + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SVDIKQKDKKKEIEKLAKQHHELKEEFNKKIEIKRQKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +   ++         +         +  + ++ +LR+A+  K+
Sbjct: 1119 MAAKGIGDKINHMLKTQEKISNLRKFIQKAFDLGDNLRQKVNLDTFSNEEILRLAKNLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ A L  SGQ IL+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GIPISTPVFDGAQENEIKQMLKFAGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELESE 1342


>gi|311086935|gb|ADP67015.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str.
            JF99 (Acyrthosiphon pisum)]
          Length = 1342

 Score = 1602 bits (4147), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 967/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+     PD     GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFKKFIQ----PDLSGQNGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+ PL++ LRL++++ D      ++
Sbjct: 57   FPIRGYNGNSELQYVSYRLGETIFDVKECQIRGATYSAPLRVKLRLVIYERDI--LEATV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PV+  L AL  ++EEIL+ F+ K ++    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVSIILRALNYNTEEILNIFFEKNIFKIEN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S ++     G   +E G+++T+  ++ LK   +K + +  + 
Sbjct: 235  NKIVLELVPERL-RGETASFNIK--KNGIIYVEKGRRITAKHIQELKNNKIKSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ V+ +TGE  I +   +  + LE++  S    I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYVDKKTGETIISSNTELSLEILEKLKKSGFYSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLSTVGR+K N  L  
Sbjct: 352  RIDSSNDRMSALIEIYRVMRPGEPPTKEATENLFENLFFSEDRYDLSTVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII +IK ++D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 412  EETKGSSTLNKEDIIDVIKKIIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSIGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N+YGF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKVC+G V+ ++ YLSA+EE N  IAQAN+++D+ G FT++LV CR  GE  L  R +++
Sbjct: 592  RKVCNGLVSEEIHYLSAIEEGNYIIAQANTNIDKTGFFTDDLVTCRHKGESSLFNRNQVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP LK + P +GTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLKTDKPLIGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR+G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTAVAKRSGVVQYVDASRIVIKVDEKEMYSREAGIDIYNLTKYTRSNQNTCINQQPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+++++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEKIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGAEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  I + ++++ + +     +             + +  +   P  +W+
Sbjct: 952  QLKKIKQDLTEEFKIFESSLFTHIKKTFISLD-------------IETKQLDTLPFEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ +  ++ +E L  Q+   K     + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SVDIKQKDKKKEIEKLAKQHHELKEEFNKKIEIKRQKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +   ++         +         +  + ++ +LR+A+  K+
Sbjct: 1119 MAAKGIGDKINHMLKTQEKISNLRKFIQKAFDLGDNLRQKVNLDTFSNEEILRLAKNLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ A L  SGQ IL+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GIPISTPVFDGAQENEIKQMLKFAGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELESE 1342


>gi|260762027|ref|ZP_05874370.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 2 str.
            86/8/59]
 gi|260672459|gb|EEX59280.1| DNA-directed RNA polymerase subunit beta [Brucella abortus bv. 2 str.
            86/8/59]
          Length = 1274

 Score = 1600 bits (4142), Expect = 0.0,   Method: Composition-based stats.
 Identities = 871/1272 (68%), Positives = 1054/1272 (82%), Gaps = 2/1272 (0%)

Query: 105  TLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
            TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ 
Sbjct: 2    TLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVF 61

Query: 165  FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
            FDHDKG+   SGKLL+A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD
Sbjct: 62   FDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMD 121

Query: 225  SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
             EEILSTFY  + Y++ GD W  P SA     G K+ S LVD DTGE V+E+GKKLT+  
Sbjct: 122  GEEILSTFYKTVTYTRDGDNWRIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARA 180

Query: 285  LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
             K L EKG+K +  T D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I
Sbjct: 181  AKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEI 240

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             +L +D VN  AYIRNTL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS+
Sbjct: 241  DVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSE 300

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YDLS VGRVKMNMRL+LD  D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRV
Sbjct: 301  RYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRV 360

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            RSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ
Sbjct: 361  RSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQ 420

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++
Sbjct: 421  FMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIN 480

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL +FARVN YGFIE+PYRKV DGKVTNDVVYLSAMEE    +AQAN  LDE G F +E 
Sbjct: 481  SLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQANVELDEQGGFVDEF 540

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V CR AGE ++ PRE +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+
Sbjct: 541  VICRHAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLV 600

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            +AEAPFVGTGME +VA+ SGAAI A+R GIV+QVDA RIVIR+ E  LDPS SGVDIYRL
Sbjct: 601  RAEAPFVGTGMEPIVARDSGAAIAARRGGIVDQVDATRIVIRATEE-LDPSKSGVDIYRL 659

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             KFQRSNQ+TC+NQRPLV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+E
Sbjct: 660  QKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYE 719

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            DS+L+SE++VS+DVFTSIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +
Sbjct: 720  DSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYI 779

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            GAEV+PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GTVV+VR+
Sbjct: 780  GAEVHPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRV 839

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            FNRHG++K+ER++++ERE+IE LA+D+DDEQ ILDRN+Y RL +++ G+ A +GPKGFKK
Sbjct: 840  FNRHGVEKDERAMAIEREEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAAGPKGFKK 899

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             T ++ +L++EYPRSQWWQFAV+DEK+Q  +E+L+ QY+ SK +LE RF +K+EK+Q GD
Sbjct: 900  GTTITRELMTEYPRSQWWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGD 959

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            +MPPGV+++VKVFVA+KR IQ GDKMAGRHGNKG+VSRILP EDMPFL+DGT  DIVLNP
Sbjct: 960  EMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNP 1019

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMNVGQI ETHLGWAC G+GKKI  L++ Y+   +I PLR  LE +       E 
Sbjct: 1020 LGVPSRMNVGQILETHLGWACAGMGKKIGELLDVYRKTANIEPLRQTLEHIYPDNDRNEP 1079

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            +  YDDD++L +A Q K GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEP
Sbjct: 1080 VRSYDDDAILMLANQVKRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEP 1139

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FDR VT+GYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1140 FDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1199

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQEMLT+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKEM++LGL+++L+
Sbjct: 1200 YGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELD 1259

Query: 1365 NSRTKNSAKMEE 1376
            ++R      + +
Sbjct: 1260 DTREAEQPALPD 1271


>gi|126640375|ref|YP_001083359.1| DNA-directed RNA polymerase subunit beta [Acinetobacter baumannii
            ATCC 17978]
          Length = 1336

 Score = 1600 bits (4142), Expect = 0.0,   Method: Composition-based stats.
 Identities = 708/1348 (52%), Positives = 968/1348 (71%), Gaps = 21/1348 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D P L+ +Q  SY  FL    +P  R + GLQAAF+SVFPI ++SG A LEFV Y    
Sbjct: 1    MDAPYLLSIQVDSYRTFLQDGKSPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGK 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P+FDV +C+ R  TYA P+++ +RLI+ D +     KSIKD++EQ +YMG++PLMT++GT
Sbjct: 61   PEFDVRECILRGSTYAAPMRVKIRLIIKDRE----TKSIKDVREQEVYMGEIPLMTENGT 116

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ RIIP +G W+D EFD+KD+++
Sbjct: 117  FVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSARIIPYRGSWLDFEFDAKDLVY 176

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            VRIDRRRK+  T  L ALG ++E+IL+ FY K+        +   L    L  G      
Sbjct: 177  VRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDMGSYQIDLVPERL-RGEMAQFD 235

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            + D + G+ ++E GK++ +  ++ ++  G+  L +  + L     AEDI   + GE+   
Sbjct: 236  ITDNE-GKVIVEQGKRINARHVRQMEAAGLTKLSVPDEYLYERITAEDITLRD-GEVIA- 292

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  ++  + + ++    ++   IL+ + ++  +++ +TL  D  +DR++AL++IY+VMRP
Sbjct: 293  ANTLLSHEVMVKLAEGGVKQFNILFTNDIDRGSFVADTLRADLTRDREEALVEIYKVMRP 352

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------DDVRHIRKED 435
            G+  T   AE++FN LFF S++YDLS VGR+K N RL             +    +  ED
Sbjct: 353  GEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLGRPYEVGTDQKSREVEGILSHED 412

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            II +++ LV++RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+ER++KER+S  + 
Sbjct: 413  IIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAET 472

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            D++ PQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 473  DNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 532

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             E+RDVH THYGR+CP ET EG NIGL++SL+ +A+ N +GF+ETPYRKV DG+VT+DV 
Sbjct: 533  FEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVIDGRVTDDVE 592

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            YLSA+EE    IAQA+S++D+DG+ TEE V  R  GE + +P EK+  +D S +QVVS+A
Sbjct: 593  YLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVA 652

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME+ VA+ SG  ++A R G++
Sbjct: 653  ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCVIANRGGVI 712

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA RIVIR  E ++    +GVDIY L+K+ RSNQNTC+NQ  +V +GD+V R DI+A
Sbjct: 713  EYVDASRIVIRVNEDEMVAGEAGVDIYNLIKYTRSNQNTCINQNVIVNLGDKVARGDILA 772

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            DGPSTD+G+LALG+NM VAFM W+GYN+EDS+L+SER++ ED  TSIHI+E   +ARDTK
Sbjct: 773  DGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTK 832

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            LG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRA
Sbjct: 833  LGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRA 892

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            IFGEKA DV+D+SLRVPSG  GTV+DV++F R G++K++R++++E+ Q++   +D  +E 
Sbjct: 893  IFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDDRALAIEKAQLDSYRKDLKEEY 952

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 953  KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPADEAIAERL 1011

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 1012 TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 1071

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 1072 NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 1131

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D+ +L +A   ++GVP++TPVFDGA
Sbjct: 1132 LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPLATPVFDGA 1188

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGS
Sbjct: 1189 EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGS 1248

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV 
Sbjct: 1249 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVD 1308

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSID 1362
            GN   + G PESFNVL KE+++LG++ID
Sbjct: 1309 GNHYMDPGMPESFNVLTKEIRSLGINID 1336


>gi|94676492|ref|YP_588937.1| DNA-directed RNA polymerase, beta subunit [Baumannia cicadellinicola
            str. Hc (Homalodisca coagulata)]
 gi|158564233|sp|Q1LSX7|RPOB_BAUCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|94219642|gb|ABF13801.1| DNA-directed RNA polymerase, beta subunit [Baumannia cicadellinicola
            str. Hc (Homalodisca coagulata)]
          Length = 1340

 Score = 1599 bits (4140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 947/1364 (69%), Gaps = 24/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK  +++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MLYSYTEKKRIRKDFGKRSQVLDVPYLLSIQLESFQKFIERD----NEGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L++VSY    P FDV +C  R LT++ PL++ LRLI+ D    T     
Sbjct: 57   FPIQSYSGNAELQYVSYHLGEPVFDVKECQTRGLTFSAPLRVILRLIIRDATTETP---- 112

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
              IKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+L+  
Sbjct: 113  --IKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKIHSSGKVLFNA 170

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL + + +IL TF+ K+++    
Sbjct: 171  RIIPYRGSWLDFEFDQKDHLFVRIDRRRKLPATIILRALQLSTNQILDTFFEKVIFHLND 230

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  ++    G   +  G+++T+  +  LK   +  + +  + 
Sbjct: 231  EHIQMELVPERL-RGETASFDII--ANGTIYVNKGRRITARHIHQLKIDSIDRINVPREY 287

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D ++  TGEI + A   I  + L+++  +  + I  L+ + +++ AYI  TL
Sbjct: 288  LVGKIIAIDYIHDNTGEIIVPANIEITLEILDKLGKANFKRIETLFTNDLDHGAYISETL 347

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  +DR  AL++IYR+MRPG+  T   AE++F  +FF  D+YDLS VGR+K N  L  
Sbjct: 348  RIDSTRDRLSALVEIYRMMRPGEPPTREAAENLFENIFFSEDRYDLSAVGRMKFNRALLR 407

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +  +    + K DII ++K L+D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 408  EEIEGSGLLSKSDIIEVMKKLIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 467

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D++S+MPQD+INAKP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 468  ERAVKERLSLSDLESLMPQDIINAKPISAAIKEFFGSSQLSQFMDQNNPLSEITHKRRIS 527

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 528  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAKTNEYGFLETPY 587

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +  VT ++ YLSA+EE N  IAQAN++LD+ G+F EELV CR  GE     REK+ 
Sbjct: 588  RLVHNSVVTEEIHYLSAIEEGNFIIAQANTNLDDKGNFVEELVTCRHKGESGFFSREKVH 647

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME +VA  
Sbjct: 648  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRTDKPLVGTGMERIVAVD 707

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR GIV+ VDA RIVI     ++    +G+DIY + K+ RSNQNTC++Q+P V
Sbjct: 708  SGVTVVAKRGGIVQYVDASRIVINVHSDEMYSGEAGIDIYHMTKYIRSNQNTCISQKPCV 767

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V R +++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDSML+SER+V +D FT+I
Sbjct: 768  TLGELVERGNVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSMLVSERVVQKDCFTTI 827

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   M+RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 828  HIQELACMSRDTKLGPEEITSDIPNVGEAALCKLDESGIVYIGAEVTSGDILVGKVTPKG 887

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G SGTV+DV+IF R G+ K++R++ +E  
Sbjct: 888  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGYSGTVIDVQIFTRDGVKKDKRTLEIEEM 947

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E+ I +  +++R+  +L             K             R  W 
Sbjct: 948  QLQQAKKDLTEERRIFEAALFTRIRHVLGSDITNIDIVKILK-----------LKREDWS 996

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            QF ++D      +E L  QY     +  ++ + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 997  QFNIKDNNKYCQLEQLAEQYYELNKVFANKLEEKRRKITQGDDLSPGVLKIVKVYIAVKR 1056

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1057 QIQPGDKMAGRHGNKGVISKINPIEDMPYDEKGIPVDIVLNPLGVPSRMNIGQILETHLG 1116

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++  +K    +         +         ++ + D  +L +AE  K 
Sbjct: 1117 MAAKGIGDKINKMLKQHKNAEQLRQFIQKAYDIGDQVRQKVNLNLFSDQEILLLAENLKH 1176

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  ML++A+L  SGQ  L+DG TGEPF+R VTVGY+YMLKLNH+
Sbjct: 1177 GMPMATPVFDGAKEKEIKQMLQLAELPVSGQITLFDGRTGEPFERQVTVGYMYMLKLNHL 1236

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1237 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1296

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV  N T E   PESFNVL+KE+++LG++I+LE +
Sbjct: 1297 NGRTKMYKNIVDCNHTMEPAMPESFNVLLKEIRSLGINIELEKN 1340


>gi|15616663|ref|NP_239875.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str.
            APS (Acyrthosiphon pisum)]
 gi|11134500|sp|P57146|RPOB_BUCAI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|25288384|pir||A84934 DNA-directed RNA polymerase (EC 2.7.7.6) beta chain [imported] -
            Buchnera sp. (strain APS)
 gi|10038726|dbj|BAB12761.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. APS
            (Acyrthosiphon pisum)]
          Length = 1342

 Score = 1599 bits (4140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1364 (50%), Positives = 964/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+     PD     GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFKKFIQ----PDLSGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+  L++ LRL++++ D      ++
Sbjct: 57   FPIRGYNGNSELQYVSYRLGETIFDVKECQIRGATYSAALRVKLRLVIYERDI--LEATV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PV+  L AL  ++EEIL+ F+ K ++    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVSIILRALNYNTEEILNIFFEKNIFKIEN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S ++     G   +E G+++T+  ++ LK   +K + +  + 
Sbjct: 235  NKIVLELVPERL-RGETASFNIK--KNGIIYVEKGRRITAKHIQELKNNKIKSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ V+ +TGE  I +   +  + LE++       I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYVDKKTGETIISSNTELSLEILEKLKKLGFYSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLSTVGR+K N  L  
Sbjct: 352  RIDSSNDRMSALIEIYRVMRPGEPPTKEATENLFENLFFSEDRYDLSTVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII +IK ++D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 412  EETKGSSTLNKEDIIDVIKKIIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSIGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N++GF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSHGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKVC+G V+ ++ YLSA+EE N  IAQAN+++D+ G FT++LV CR  GE  L  R +++
Sbjct: 592  RKVCNGLVSEEIHYLSAIEEGNYIIAQANTNIDKTGFFTDDLVTCRHKGESSLFNRNQVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPF E+DD+NR LMG NMQRQAVP LK + P +GTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFPEHDDANRALMGANMQRQAVPTLKTDKPLIGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR+G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTAVAKRSGVVQYVDASRIVIKVDEKEMYSREAGIDIYNLTKYTRSNQNTCINQQPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+++++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEKIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGAEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  I + ++++ + +     +             + +  +   P  +W+
Sbjct: 952  QLKKIKQDLTEEFKIFESSLFTHIKKTFISLD-------------IETKQLDTLPFEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ +  ++ +E L  Q+   K     + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SVDIKQKDKKKEIEKLAKQHHELKEEFNKKIEIKRQKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +   ++         +         +  + ++ +LR+A+  K+
Sbjct: 1119 MAAKGIGDKINHMLKTQEKISNLRKFIQKAFDLGDNLRQKVNLDTFSNEEILRLAKNLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ A L  SGQ IL+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GIPISTPVFDGAQENEIKQMLKFAGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELESE 1342


>gi|311086357|gb|ADP66438.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str.
            TLW03 (Acyrthosiphon pisum)]
          Length = 1342

 Score = 1598 bits (4139), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1364 (50%), Positives = 966/1364 (70%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+     PD     GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFKKFIQ----PDLSGQHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+ PL++ LRL++++ D      ++
Sbjct: 57   FPIRGYNGNSELQYVSYRLGETIFDVKECQIRGATYSAPLRVKLRLVIYERDI--LEATV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PV+  L AL  ++EEIL+ F+ K ++    
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVSIILRALNYNTEEILNIFFEKNIFKIEN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S ++     G   +E G+++T+  ++ LK   +K + +  + 
Sbjct: 235  NKIVLELVPERL-RGETASFNIK--KNGIIYVEKGRRITAKHIQELKNNKIKSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ V+ +TGE  I +   +  + LE++  S    I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYVDKKTGETIISSNTELSLEILEKLKKSGFYSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLSTVGR+K N  L  
Sbjct: 352  RIDSSNDRMSALIEIYRVMRPGEPPTKEATENLFENLFFSEDRYDLSTVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            +       + KEDII +IK ++D+RNGKG +DDID+LGNRRVRSVGEM +NQ+R+GL+R+
Sbjct: 412  EETKGSSTLNKEDIIDVIKKIIDIRNGKGEVDDIDHLGNRRVRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSIGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N+YGF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKVC+G V+ ++ YLSA+EE N  IAQAN+++D+ G FT++LV CR  GE  L  R +++
Sbjct: 592  RKVCNGLVSEEIHYLSAIEEGNYIIAQANTNIDKTGFFTDDLVTCRHKGESSLFNRNQVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP LK + P +GTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLKTDKPLIGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR+G+V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTAVAKRSGVVQYVDASRIVIKVDEKEMYSREAGIDIYNLTKYTRSNQNTCINQQPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+++++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772  NLGEKIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLG EEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGAEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIEDM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D  +E  I + ++++ + +     +             + +  +   P  +W+
Sbjct: 952  QLKKIKQDLTEEFKIFESSLFTHIKKTFISLD-------------IETKQLDTLPFEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++ +  ++ +E L  Q+   K     + + K +KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  SVDIKQKDKKKEIEKLAKQHHELKEEFNKKIEIKRQKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++   +   ++         +         +  + ++ +LR+A+  K+
Sbjct: 1119 MAAKGIGDKINHMLKTQEKISNLRKFIQKAFDLGDNLRQKVNLDTFSNEEILRLAKNLKN 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ A L  SGQ IL+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GIPISTPVFDGAQENEIKQMLKFAGLPTSGQIILFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLV QQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVAQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELESE 1342


>gi|319942164|ref|ZP_08016481.1| hypothetical protein HMPREF9464_01700 [Sutterella wadsworthensis
            3_1_45B]
 gi|319804299|gb|EFW01188.1| hypothetical protein HMPREF9464_01700 [Sutterella wadsworthensis
            3_1_45B]
          Length = 1387

 Score = 1598 bits (4138), Expect = 0.0,   Method: Composition-based stats.
 Identities = 688/1394 (49%), Positives = 953/1394 (68%), Gaps = 37/1394 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-GLQAAFKS 61
                F    R+RK F   P ++++P L+++Q  SY+ FL +N+ P  R N  GLQAAF S
Sbjct: 1    MSYSFTEKKRIRKSFASRPSVLEVPSLLDIQLRSYEDFLQVNVKPAARSNNLGLQAAFTS 60

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            +FPIT+ +G A L F  YE   P+FDV +C  R LTY+  L+  +RL ++D +      +
Sbjct: 61   IFPITSHNGFARLRFAGYELAEPEFDVAECQLRGLTYSSRLRAKIRLEIYDREAAQPE-T 119

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            IK+I+E  +YMG++PLMT+ G+F++ G +R++VSQLHRSPGI F+HDKG+   SGKLL++
Sbjct: 120  IKEIRENDVYMGEVPLMTEKGSFIVNGTERVIVSQLHRSPGIFFEHDKGKTHSSGKLLFS 179

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             R+IP +G W+D EFD+KDI++ R+DRRRK+P T  L A+G   E+IL+ F+    ++  
Sbjct: 180  ARVIPYRGSWLDFEFDAKDILYFRVDRRRKMPGTILLKAIGYSVEDILARFFAFDSFTLL 239

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  P+    L     +S  +VD + G+ ++   K++T+  L+ L +  V  + +  D
Sbjct: 240  KSGAKLPVVPERL-KAQTMSFDIVDAE-GKVIVPHDKRITAKHLRDLNKANVTTITVPDD 297

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  + + I++ ETGE+   A D I E  L  +  + +R    L+ + +++ AYI NT
Sbjct: 298  YLLGRVLGKTIIDQETGEVIANANDEITETVLAAMRAARVRKFDALFTNELDHGAYISNT 357

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D   D+  A + IYR+MRPG+  T    ES+F+ LFFD D YDLS VGR+K+N R  
Sbjct: 358  LRLDDTPDQFSARVAIYRMMRPGEPPTEEAVESLFDRLFFDPDAYDLSRVGRMKVNARFG 417

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID-----------------DIDNLGNRRV 464
              + +  R + KEDI+  + +LV LRNG+  +D                 DID+LGNRRV
Sbjct: 418  RPSAEGERTLTKEDIVDTMAMLVALRNGQDNVDLVNEKGEVRTCVVNGVDDIDHLGNRRV 477

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            R VGE+ +NQ+R GL+R+ER++KER++  + D + PQDLIN+KP+ +A+ EFF SSQLSQ
Sbjct: 478  RCVGELAENQFRAGLVRVERAVKERLNQAESDGLTPQDLINSKPISAAIREFFGSSQLSQ 537

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 538  FMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGLIN 597

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL  +AR+N YGF+ETPYRKV DG  T ++ YLSA+EE    IAQAN+ +D++G  T+EL
Sbjct: 598  SLALYARLNEYGFLETPYRKVVDGVATKEIHYLSAIEEGKYIIAQANAEMDDNGRLTQEL 657

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V  R  GE IL   E+I ++D +P Q+VS AA+LIPFLE+DD+NR LMG NMQRQ VP L
Sbjct: 658  VSARDNGETILASPERIQYMDVAPAQIVSCAAALIPFLEHDDANRALMGANMQRQGVPCL 717

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            + E P VGTG+E  VA  S  A+ A+R G+V+ VDA R+VIR  + +     +GVDIY L
Sbjct: 718  RPEKPVVGTGIERTVAVDSKTAVQARRGGVVDYVDANRVVIRVNDDESVAGETGVDIYNL 777

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             KF RSNQ+T +NQRP+V  GD V   D++ADG STD G+LALG+NML+AFMPW+GYN+E
Sbjct: 778  QKFTRSNQSTNINQRPIVVKGDHVAVGDVLADGASTDTGELALGQNMLIAFMPWNGYNYE 837

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            DS+LISER+V++D +TSIHIEE  V++RDTKLGPEEITRDI N+SE  L  +D+ GI+ +
Sbjct: 838  DSVLISERVVADDRYTSIHIEELSVVSRDTKLGPEEITRDISNLSESQLARLDDSGIVFI 897

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            GAEV  GD+LVGK+TPKGE+ +TPEEKLLR IFGEKA DV+DTSLRVPSG++GTV+DV++
Sbjct: 898  GAEVKAGDVLVGKVTPKGETQLTPEEKLLRVIFGEKASDVKDTSLRVPSGMTGTVIDVQV 957

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK--GF 1002
            F R G+ +++R+ S+  + ++   RD DD+  I++R+ + RL   L G   VS  K  G 
Sbjct: 958  FTRDGVKRDKRAESIIADALKRYRRDLDDQLRIVERDSFDRLRRQLAGHKVVSTMKFDGL 1017

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                VL+ + ++       +   +++E  Q  ++  K   E ++     +++ K +K+  
Sbjct: 1018 PADGVLTPEFLASVQGYDLFGLRMEEEVAQHFIDLTKQAIEHTREDNARKYEIKNDKLTR 1077

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++PPGVL++VKV++A +R +Q GDKMAGRHGNKG+VS+I P EDMP++ DG P DIVL
Sbjct: 1078 GDELPPGVLKMVKVYIAERRRLQPGDKMAGRHGNKGVVSKICPVEDMPYMADGRPADIVL 1137

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  GLG +I+ ++           +R+FL ++       
Sbjct: 1138 NPLGVPSRMNIGQVLEVHLGWAAKGLGWRIEKML----KTETARQIRAFLNEIYNRTGKH 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG---------- 1232
            E +    D+ ++R+A   ++GVP +TPVFDGA+EE I  ML +A  D+            
Sbjct: 1194 EDLDSLSDEELMRMARNLQNGVPFATPVFDGANEEQIRMMLDLAFPDDEAQRLQLTSSKT 1253

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RPVTVGY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1254 QATLYDGRTGDAFERPVTVGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 1313

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT++YE+IV G    E G PESFNVLVK
Sbjct: 1314 RFGEMEVWALEAYGAAYVLQEMLTVKSDDVNGRTKMYENIVKGEHKIEAGMPESFNVLVK 1373

Query: 1353 EMQALGLSIDLENS 1366
            E+++LG+ IDL  +
Sbjct: 1374 EIRSLGIDIDLVKN 1387


>gi|118594007|ref|ZP_01551354.1| DNA-directed RNA polymerase beta subunit [Methylophilales bacterium
            HTCC2181]
 gi|118439785|gb|EAV46412.1| DNA-directed RNA polymerase beta subunit [Methylophilales bacterium
            HTCC2181]
          Length = 1389

 Score = 1595 bits (4131), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1396 (50%), Positives = 971/1396 (69%), Gaps = 39/1396 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   +++IP L+ +Q  SY  FL   +  ++R   GL++ F ++
Sbjct: 1    MSYSFTEKKRIRKSFAKRETVLEIPYLLAMQLESYKAFLQREVKVEDREIAGLESTFNTL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI++ SG A L++VSY      FDV +C  R LTYAVPL++ +RL + D        +I
Sbjct: 61   FPISSHSGNAKLDYVSYNLGKEVFDVKECQQRGLTYAVPLRVKVRLTIMDK--EASQPTI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT++G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVKEQEVYMGEIPLMTQNGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++ RIDRRRK+PVT+ L ALG+ SEEILSTFY    +  + 
Sbjct: 179  RVIPYRGSWLDFEFDPKDYLYFRIDRRRKMPVTTLLKALGLSSEEILSTFYDLDTFEIKS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + + F +       G      + D   G  +I   K++T   ++ +++ G+K + + SD 
Sbjct: 239  NAFQFHIIPE-RFRGEIAKFDIKDKK-GNVIIAKDKRITVKHIREIEKAGIKTISVDSDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +++ I++ ++GE+  E    I E+ +E++   ++ +   LY + +++  ++  TL
Sbjct: 297  LVGRKISKAIIDKDSGEVIAETNAEITEELIEKLLELKVPEFNTLYSNDLDHGDFLSQTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +D   D+  A + IYR+MRPG+  T      +F  LFF++D+YDLS VGR+K N R   
Sbjct: 357  ASDDVPDQYSAKVAIYRMMRPGEPPTEDSVNGLFEGLFFNADRYDLSNVGRMKFNRRAFP 416

Query: 423  DT-------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             T                         +  +DI+A++ +L++LRNG+G IDDID+LGNRR
Sbjct: 417  KTYDQYAEWMKRFHDGVGDKDETGESILSHQDILAVVGLLIELRNGRGEIDDIDHLGNRR 476

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            +RSVGE+++NQ+R GL+R+ER++KER+   + D++MP DLIN+KP+ SA+ EFF SSQLS
Sbjct: 477  IRSVGELVENQFRTGLVRVERAVKERLGQAEADNLMPHDLINSKPISSAIREFFGSSQLS 536

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 537  QFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHSTHYGRVCPIETPEGPNIGLI 596

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            +SL  FAR N YGF+ETPYR+V  GKVT D+ YLSA+EE +  IAQANS L  +G F EE
Sbjct: 597  NSLAMFARTNKYGFLETPYRRVEGGKVTADIEYLSAIEESDYTIAQANSELGTNGKFKEE 656

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV  R   E  +   + +DF+D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 657  LVSSRYKNEFTMAGNDSVDFMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPC 716

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            L+AE   VGTG+E  VA  SG  + AKR GIV+ VD+ RIV++  E +      GVDIY 
Sbjct: 717  LRAEKALVGTGIERTVAMDSGTTVQAKRGGIVDYVDSNRIVVKVNEKETAQDGIGVDIYN 776

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L K+ RSNQNT +NQ+PLV++GD++ R  +IADG STDLG+LALG+NMLV FMPW+GYNF
Sbjct: 777  LTKYTRSNQNTNINQKPLVRMGDKIDRGAVIADGASTDLGELALGQNMLVGFMPWNGYNF 836

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+LISER+VS+D +TSIHIEE  V+ARDTKLGPEEIT+DI N+SE  +  +D  GII 
Sbjct: 837  EDSILISERVVSDDRYTSIHIEELSVVARDTKLGPEEITQDISNLSERMIGRLDNAGIIF 896

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGT++DV+
Sbjct: 897  IGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTIIDVQ 956

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R GID+++R+  +  +Q+    +D  D+  I++ +I+ R+ +IL  + AV GPKG K
Sbjct: 957  VFTREGIDRDDRAEQIIGDQLIAFKKDVADQLRIVESDIFGRIEKILLNKIAVGGPKGIK 1016

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K   LS + ++E  + +W+   V D+K  + +E++K  +  +K   ++RF+ K  K+  G
Sbjct: 1017 KGDKLSKEKLAELGKYEWFDIRVSDDKDSKQLEAMKESFNFAKKEFDNRFEEKKRKLTQG 1076

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++PPGV ++VKV++A+KR IQ GDKMAGRHGNKG++S+I+P EDMP++ DG  +DIVLN
Sbjct: 1077 DELPPGVQKMVKVYLAVKRRIQPGDKMAGRHGNKGVISKIVPVEDMPYMADGKTLDIVLN 1136

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHT 1182
            PLGVPSRMN+GQI E HLGWA  GLG +I  ++   ++N +I+ +R FL+K+   +    
Sbjct: 1137 PLGVPSRMNIGQILEVHLGWAAKGLGDRIDEMM---RSNTNIAEVRKFLDKIYNTSSGKG 1193

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES----------- 1231
            E I    D+ V  +AE   +GVP +TPVFDG  E  I  ML +A  DES           
Sbjct: 1194 EDIQSLKDNEVKELAENLSNGVPFATPVFDGGAESDIQQMLDLAYPDESDHTKILNFAAN 1253

Query: 1232 -GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
              Q  L+DG TGE F+RPVTVGY+++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  G
Sbjct: 1254 KTQVRLFDGRTGESFERPVTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 1313

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGA+Y LQEMLT+KSDDV+GRT+VYE+IV G    + G PESFNVL
Sbjct: 1314 GQRFGEMEVWALEAYGASYTLQEMLTVKSDDVMGRTKVYENIVKGEHKIDAGMPESFNVL 1373

Query: 1351 VKEMQALGLSIDLENS 1366
             KE+++L + IDL+ +
Sbjct: 1374 TKEIRSLAIDIDLDRN 1389


>gi|71066442|ref|YP_265169.1| DNA-directed RNA polymerase subunit beta [Psychrobacter arcticus
            273-4]
 gi|88909633|sp|Q4FQH3|RPOB_PSYA2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71039427|gb|AAZ19735.1| RNA polymerase beta-subunit [Psychrobacter arcticus 273-4]
          Length = 1372

 Score = 1594 bits (4127), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1379 (50%), Positives = 964/1379 (69%), Gaps = 23/1379 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F + P ++DIP L+ +Q  SY+ FL  +  P  R N GLQAA+ S+
Sbjct: 1    MAYSYTEKKRIRKSFAELPTVMDIPYLLSIQVDSYEQFLQEHKKPKARENTGLQAAYSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A P+++ +RLI+ D D        
Sbjct: 61   FPIESHSGNAELQFVEYYLGTPEFDERECILRGSTFAAPMRVKIRLIIKDKDSKDKDSKA 120

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDI+EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY
Sbjct: 121  AIKDIREQSVYMGEMPLMTANGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD+KD++  RIDRRRK+  +  L ALG+ + EIL  F+ K+   +
Sbjct: 181  NARIIPYRGSWLDFEFDAKDLVFARIDRRRKLLASIILRALGLSTSEILDLFFDKVKVYK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + +   L A D + G      +V  + G+ V+E GK++ +  ++ L+E G+  + I  
Sbjct: 241  GEEQFEIDLVA-DRLRGEMAQFDIVTPE-GDVVVEQGKRINARRIRQLEEAGMTKISIPD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE----IRDIPILYVDSVNNNA 356
            + L    +AEDI+     E+   A  +ID + L ++   E    I++  IL+ + ++  +
Sbjct: 299  EYLYERILAEDII--VNDEVIARANTLIDHELLVKLSAFEASESIKEFSILFTNDIDQGS 356

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YI +TL  D    R++AL++IY+VMRPG+  T   AE +F+ +FF++D+YDLS VGR+K 
Sbjct: 357  YIADTLRADSTSSREEALIEIYKVMRPGEPPTVETAEKLFDSMFFNADRYDLSNVGRMKF 416

Query: 417  NMRLNLDTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            N RL LD  D        +   +   DI+ ++K L+++RNG+G +DDID+LGNRR+RSVG
Sbjct: 417  NRRLGLDFVDTDDADIQRERSVLTNADIVNVLKELIEIRNGRGEVDDIDHLGNRRIRSVG 476

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            EM +NQ+R+GL+R+ER++KER+SS + D++ PQDLIN+KPV +AV EFF SSQLSQ  + 
Sbjct: 477  EMAENQFRVGLVRVERAVKERLSSAESDNLSPQDLINSKPVAAAVKEFFGSSQLSQFMDQ 536

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +
Sbjct: 537  NNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHDTHYGRVCPIETPEGPNIGLINSLAT 596

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FA+ N++GF+ETPYR+V DGKVT+ + YLSA+EE    IAQA+S +  DG+ ++E+V  R
Sbjct: 597  FAKTNSFGFLETPYRRVVDGKVTDVIEYLSAIEEVGTVIAQADSPVTADGALSDEMVSVR 656

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              GE + +P EK+  +D SP QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+A+ 
Sbjct: 657  SYGEFVRMPPEKVTHMDVSPSQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRADK 716

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTGME  VA+ SG  ++AKR G++E VDA RIV+R  E ++    +G+DIY L+K+ 
Sbjct: 717  PLVGTGMERHVARDSGVCVIAKRGGVIEDVDASRIVVRVNEAEMIAGEAGIDIYNLVKYT 776

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQR +V  GDE+   DI+ADGPSTDLG+LALG+N+ +AFMPW+GYNFEDS+L
Sbjct: 777  RSNQNTCINQRIIVNQGDEIAFGDILADGPSTDLGELALGQNIRIAFMPWNGYNFEDSIL 836

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SE++V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L ++DE GI+ +GAEV
Sbjct: 837  LSEKVVKEDRFTTIHIQELTCVARDTKLGTEEITADIPNVGEAALSSLDEAGIVYIGAEV 896

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            + GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+   GTV+DV++F R 
Sbjct: 897  DAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDTSLRVPTSSKGTVIDVQVFTRD 956

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K+ R+ ++E+ Q++   +D  +E  I +     R+  +L GQ    G  G K  T++
Sbjct: 957  GVEKDARARAIEKSQLDSYRKDLKEELRIFEEAARGRIGNLLDGQKVSGGS-GLKAGTIM 1015

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +   + +            +E++   +  +       +  ++ +F  K  K+  GDD+  
Sbjct: 1016 ALADMKDMSLETLLDIQPVEEEISERLTQIAEYLVDKQKDIDVKFAEKKRKLTAGDDLQH 1075

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++VKV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ + G  VDIVLNPLGVP
Sbjct: 1076 GVQKIVKVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDEHGNTVDIVLNPLGVP 1135

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISD 1187
            SRMN+GQ+ ETHLG A  GLG+KI  ++   K+   I  LR FL+K+    G     +  
Sbjct: 1136 SRMNIGQVLETHLGMAAKGLGEKIDGML---KSQAAIKDLREFLDKIYNQVGGEQVDLDS 1192

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              DD ++ +A+  ++GVP+ T VFDGA E  +  +L +A +D  GQ  LYDG TG+ FDR
Sbjct: 1193 LTDDDIMALADNLRAGVPMGTAVFDGAKESQVKDLLELAGMDRDGQQTLYDGRTGQKFDR 1252

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1253 KVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1312

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             Y LQEMLT+KSDDV GRTR+Y++IV G    + G PESFNVL KE+++LG++I+L+ +
Sbjct: 1313 TYTLQEMLTVKSDDVEGRTRMYKNIVDGEQYMDPGMPESFNVLTKEIKSLGINIELKQT 1371


>gi|21672328|ref|NP_660395.1| DNA-directed RNA polymerase subunit beta [Buchnera aphidicola str. Sg
            (Schizaphis graminum)]
 gi|730609|sp|P41184|RPOB_BUCAP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|296969|emb|CAA77970.1| beta subunit of RNA polymerase [Buchnera aphidicola]
 gi|21622929|gb|AAM67606.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. Sg
            (Schizaphis graminum)]
 gi|739393|prf||2003233A RNA polymerase:SUBUNIT=beta
          Length = 1342

 Score = 1594 bits (4127), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1364 (51%), Positives = 971/1364 (71%), Gaps = 22/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+ ++         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKFIKID----PEGLHGLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  ++G + L++VSY      FDV +C  R  TY+ PL++ LRL++++ D      ++
Sbjct: 57   FPICGYNGNSELQYVSYRLGDAIFDVKECQIRGATYSAPLRVRLRLVIYERD--VLEPTV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KDIKEQEVYMGEIPLMTNNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PVT  L AL  ++EEIL+ F+ K +++   
Sbjct: 175  RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPVTIILRALNYNTEEILNLFFEKNIFNINN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L +  L  G   S  +     G+  ++ G+++T+  ++ LK+  +  + +  + 
Sbjct: 235  NKIQLELVSERL-RGETASFDIK--KNGKIYVKKGRRITAKHIQELKKDKINSITVPVEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V+++ ++ +TGE  I A   +  + L ++ +S    I  L+ + +++  YI  TL
Sbjct: 292  ILGRIVSKNYLDPKTGETIILANTELSLEILTKLKNSSFFSIETLFTNDLDHGPYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D + DR  AL++IYRVMRPG+  T    E++F  LFF  D+YDLS+VGR+K N  L  
Sbjct: 352  RIDSSHDRISALMEIYRVMRPGEPLTKEATENLFENLFFSEDRYDLSSVGRMKFNRSLLR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               + V  + KEDII +IK L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  KKIEGVSTLNKEDIIDVIKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +A+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSVGDLDTLMPQDMINAKPISAAIKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N+YGF+ETPY
Sbjct: 532  ALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNSYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +  VT+++ YLSA+EE N  IAQAN+++D++  F ++LV CR  GE  L    ++D
Sbjct: 592  RKVHNRLVTDEIHYLSAIEEGNYVIAQANTNIDKNNYFIDDLVTCRHKGESSLFNCNQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP LK + P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLKTDKPLVGTGMERAVAVD 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR GI++ +DA RI+I+  E +     +G+DIY L K+ RSNQNTC+NQ+P V
Sbjct: 712  SGVTVVAKRGGIIQYIDASRIIIKVNEEETYTGEAGIDIYNLTKYTRSNQNTCINQKPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K+ +++ +ND++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SE++V ED FT+I
Sbjct: 772  KLREKINKNDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSEKVVQEDRFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEI+ DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELSCISRDTKLGPEEISSDIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV+IF R G+ K++R++ +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQIFTRDGVKKDKRALEIENM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  I + +++SR+ + L   N             +  D +++ P  +W+
Sbjct: 952  QLKKAKKDLTEEFKIFELSLFSRIKKTLVSFN-------------IKEDFLNKLPYEKWF 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +QD   ++ +E L  Q+   K   E + + K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 999  KIDIQDRNKKKEIEKLLQQHNQLKKEFEKKIEVKRRKITQGDDLAPGVLKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPVEDMPYDENGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI +++   +   ++         +         + D+ ++ +L +A+  K 
Sbjct: 1119 MAAKGIGNKINNMLKKQEKISNLKKFIQKAFDLGENLRQKVNLDDFSNEEILDLAKNLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E  I  ML+ ++L  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+
Sbjct: 1179 GMPISTPVFDGAQENEIKQMLKFSNLPTSGQISLFDGRTGEKFERPVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LEN 
Sbjct: 1299 NGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELENE 1342


>gi|67459538|ref|YP_247162.1| DNA-directed RNA polymerase subunit beta [Rickettsia felis URRWXCal2]
 gi|75536057|sp|Q4UKD4|RPOB_RICFE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|67005071|gb|AAY61997.1| DNA-directed RNA polymerase beta chain [Rickettsia felis URRWXCal2]
          Length = 1373

 Score = 1593 bits (4126), Expect = 0.0,   Method: Composition-based stats.
 Identities = 765/1358 (56%), Positives = 1027/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITSDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AE++F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAENLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V D 
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDR 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V  +++DFID +
Sbjct: 615  HVTDEVVYLSAIEEGKYKIGQANSKVDKDGKLQGEFINCRVEGGNFVMVEPQEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E  +D  +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLEQKID-GSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  V+GPK  K    ++S+++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLIGQVIVNGPKQVKAGQTITSEMLKGLSKGQFWQLTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +KV Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKVHYDEKKDALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLLELYGENI--NYILERSEEEIISFCNKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|37912944|gb|AAR05276.1| DNA-directed RNA polymerase beta subunit [uncultured marine gamma
            proteobacterium EB000-45B06]
 gi|40063171|gb|AAR38008.1| DNA-directed RNA polymerase, beta subunit [uncultured marine
            bacterium 562]
          Length = 1353

 Score = 1593 bits (4126), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1367 (52%), Positives = 982/1367 (71%), Gaps = 16/1367 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG   +++D+P+LIE Q  SY  FL  ++APD R  +GL+  F+S+
Sbjct: 1    MSYSYTEKKRIRKNFGTFTKVMDLPNLIETQTKSYSEFLQADVAPDARKKQGLEDVFQSL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A LE+VSYE     +DV +CL + L+Y+ PL+I ++L+++D D  T  K +
Sbjct: 61   FPIKSVSGNAALEYVSYELGKNTYDVQECLVQGLSYSAPLRIKVKLVLYDRD--TNFKEV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  ++MG++PLMT D +FV+ G +R+VV+QLHRSPG+ +DHDKG+   SGK+LY+ 
Sbjct: 119  KDIKEGEVFMGEVPLMTSDASFVVNGTERVVVAQLHRSPGVFYDHDKGKTHSSGKVLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  RIDRRRK+P T  L AL M +EEILS FY + V+S   
Sbjct: 179  RIIPYRGSWLDFEFDPKDILFSRIDRRRKIPATIMLRALDMGTEEILSEFYDEDVFSLEK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G  +   +      +  +E+GK++T+  +K L    V  + +  + 
Sbjct: 239  DSVKLALIPERL-RGETLPVDIKVK--SKVYVEAGKRITARHIKELSNANVSEITLAEEF 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +++DI N ETGE+   A   ID + LE +  + + DI  L+++ ++   YI NTL
Sbjct: 296  LIGKVLSKDIFNKETGEVLYSANTEIDNEVLEALKENNVSDITCLFINELDKGPYISNTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++FN LFF+ ++YDLS VGR+K N RL L
Sbjct: 356  RADPTSNRLEALVEIYRMMRPGEPPTKDSAETLFNNLFFNEERYDLSEVGRMKFNRRLKL 415

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D   ++   + KEDII ++K +V++R+G   +DDID+LGNRRVRSVGEM  NQ+R+GL+R
Sbjct: 416  DSKKENDNILDKEDIIEVMKGIVNIRDGHDIVDDIDHLGNRRVRSVGEMTANQFRVGLIR 475

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER+++ER+S  + D + PQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 476  VERAVRERLSMAEADELGPQDLINAKPVTAAIKEFFGSSQLSQFMDQNNPLSEITHKRRV 535

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S  S++R N YGFIETP
Sbjct: 536  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSFASYSRTNQYGFIETP 595

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +G VT+++ YLSA++E    IAQAN +LD++  F ++LV  R A E  L+  +++
Sbjct: 596  YRKVINGTVTDEITYLSAIDEAEHVIAQANVTLDKNNKFVDDLVAVRHASEFELMSSDRV 655

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SP+QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP+L+AE P VGTG+ESVVA+
Sbjct: 656  DLMDVSPQQVVSIAASLIPFLEHDDANRALMGSNMQRQAVPVLRAEKPLVGTGLESVVAR 715

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  IVAK +G+VE VDA RIV+R  +     S S  D+Y L+K+ RSNQNTC+NQRP+
Sbjct: 716  DSGVCIVAKNSGVVENVDASRIVVRVTDK---KSKSASDVYNLVKYTRSNQNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+VGD V+  D++ADGPS D G+LALG+N+ +AFMPW+GYNFEDS+LISE++  ED FTS
Sbjct: 773  VRVGDVVKSGDVLADGPSVDNGELALGQNIRIAFMPWNGYNFEDSILISEKVAREDRFTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +D+CGI+ VGAEV PGDILVGKITPK
Sbjct: 833  IHIQEIVCVARDTKLGSEEITADIPNVGEGSLNKLDDCGIVYVGAEVEPGDILVGKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ ++PEEKLLRAIFGEKA DV+DTS R  S   GTV++V +F R G++K+ER+ ++E+
Sbjct: 893  GETQLSPEEKLLRAIFGEKASDVKDTSQR--SSAKGTVINVEVFTRDGVEKDERTQAIEQ 950

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            + ++   +D DDE  ++++   +RL ++L G+ A+ G  G KK   LS + + E   +  
Sbjct: 951  DHLDKSKKDADDEAFVVEQATKTRLCDLLKGKKAIKG-NGIKKGETLSLERLEELDLNDL 1009

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +      + +   +E  +  Y++    ++ RF+ K  KI  G D+ PGV+++VKV++A+K
Sbjct: 1010 FSIRTDTDTINDVIEDTEKSYKSYAKDIKARFEEKKAKIIRGHDLAPGVIKIVKVYLAIK 1069

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S I+P EDMP+ KDG PVDIVLNPLGVPSRMNVGQI ETH+
Sbjct: 1070 RRIQPGDKMAGRHGNKGVISEIMPVEDMPYDKDGQPVDIVLNPLGVPSRMNVGQILETHM 1129

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQW 1200
            G A  G+G+KI  ++   K N   + L+++L+K+     ++ E I+ +++  ++ +A   
Sbjct: 1130 GCAAKGIGQKIDLML---KENAKPAELKTYLDKLYNTNAANKEDINSFNNTEIMELAHNL 1186

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+P++TPVFDGA E  +  +L++ADL ESGQ  LYDG TG  FDRPVTVGY+Y++KLN
Sbjct: 1187 KDGLPIATPVFDGAKESEVKDLLKLADLPESGQFTLYDGRTGSKFDRPVTVGYMYIIKLN 1246

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSD
Sbjct: 1247 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSD 1306

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            DV GRT++Y++IV G+   +   PESFNVL KE+++LG++++L++  
Sbjct: 1307 DVSGRTKMYKNIVDGSYEMDANIPESFNVLSKEIKSLGINLELDSEN 1353


>gi|162448680|ref|YP_001611047.1| DNA-directed RNA polymerase [Sorangium cellulosum 'So ce 56']
 gi|189043869|sp|A9GRB1|RPOB_SORC5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|161159262|emb|CAN90567.1| DNA-directed RNA polymerase [Sorangium cellulosum 'So ce 56']
          Length = 1378

 Score = 1593 bits (4125), Expect = 0.0,   Method: Composition-based stats.
 Identities = 718/1365 (52%), Positives = 986/1365 (72%), Gaps = 25/1365 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK  G+   IID+P+LI++QK+SYD FL M++ P+ER   GLQA F+SVFPI  F+G 
Sbjct: 10   RVRKNLGRVRRIIDVPNLIDIQKSSYDKFLQMSVPPNEREEVGLQAVFRSVFPIKDFNGT 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + L FVSY  +PPK+DVD+C  R +TY+ P+K+T +L+++D     G + ++DIKEQ +Y
Sbjct: 70   SELVFVSYNLEPPKYDVDECRQRGMTYSAPIKVTNQLMIYDT-RDGGERIVRDIKEQEVY 128

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G+LPLMT+ GTF+I G +R+VVSQLHRSPG+ FDHDKG+   SGKLLY+ R+IP +G W
Sbjct: 129  FGELPLMTETGTFIINGTERVVVSQLHRSPGVFFDHDKGKTHSSGKLLYSARVIPYRGSW 188

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KDII+VRIDRRRK+  T  L ALG  ++++L+ FY                  
Sbjct: 189  LDFEFDPKDIIYVRIDRRRKMHATVLLRALGYSTQDLLNYFYSTETVYLEKGGKYAKSIE 248

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             DL+ G + +  +      + +++   K T   ++ +KE  ++ L +  + L G   A D
Sbjct: 249  YDLLAGQRTTRDIKI--GNDVIVKKNTKFTRAAIRKMKEAKLERLSLEPEELVGKVAAHD 306

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            IV+ ETGE+ +E  + + E  LE +  + I    IL++D +N  +Y+R+TL+TDK K  +
Sbjct: 307  IVDPETGEVVVEVNEELTEAKLERLRDANIEQFRILFIDGLNVGSYLRDTLLTDKVKTME 366

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR-- 429
            D++L+IYR +RPGD  T   A+++F+ LFF++++YDLS VGR+K+N +   D P+D R  
Sbjct: 367  DSILEIYRRLRPGDPPTLETAKTLFHNLFFNAERYDLSKVGRLKLNYKFYRDVPEDERPG 426

Query: 430  ----HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                 +  +DI+  ++ L++L+NG+G++DDID+LGNRRVR+VGE+++NQYR+GL+RMER+
Sbjct: 427  LDLTVLTPQDILETVRHLIELKNGRGSVDDIDHLGNRRVRAVGELMENQYRIGLVRMERA 486

Query: 486  IKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            IKER+S   +ID++MP DLINAKPV + V E+F SSQLSQ  +  N LS +TH RRLSAL
Sbjct: 487  IKERMSMSQEIDTLMPHDLINAKPVSAVVKEYFGSSQLSQFMDQTNPLSEVTHKRRLSAL 546

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL++FARVN +GF+ETPYRK
Sbjct: 547  GPGGLTRERAGFEVRDVHATHYGRICPIETPEGPNIGLIASLSTFARVNEFGFVETPYRK 606

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V +G+VT DV++LSA+EEE +YIAQA  +LDE G F E LV  R  GE  +V  E ++ +
Sbjct: 607  VENGRVTEDVIWLSALEEEGKYIAQATVNLDEGGRFKESLVSARYNGEFKIVTPEMVELM 666

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+VS+AA+L+PFLE+DD+NR LMG NMQRQAVPL+++ AP VGTGME  +A+ SG
Sbjct: 667  DVAPNQMVSVAAALVPFLEHDDANRALMGANMQRQAVPLVQSHAPLVGTGMEERLARDSG 726

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              ++A+R G+VE VDA RIV+R+     +      DIY LMKFQRSNQ+TC  Q+P+V+ 
Sbjct: 727  VCVIARRPGVVESVDATRIVVRAEGEGAEV----PDIYHLMKFQRSNQSTCYTQKPVVRT 782

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G+ V++ D++ADGPSTD+G+LALG+N+LVAFMPW GYNFEDS+L+SER+  +DVFTSIHI
Sbjct: 783  GEVVKKGDVLADGPSTDMGELALGQNVLVAFMPWQGYNFEDSILVSERIAKDDVFTSIHI 842

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE +ARDTKLG EEITRDIPNV EE LK++D+ GI+ +GAEV PGDILVGKITPKGE+
Sbjct: 843  EEFECVARDTKLGKEEITRDIPNVGEEALKDLDDSGIVRIGAEVRPGDILVGKITPKGET 902

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             ++PEEKLLRAIFGEKA DVRD+SL+VP GV G V++ R+F+R G +K++R+  +E ++ 
Sbjct: 903  QLSPEEKLLRAIFGEKAGDVRDSSLKVPPGVGGIVINARVFSRKGTEKDDRARDIEDQER 962

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVLSSDLISEYPR 1018
              + R +D+E  IL  + + R+ E+L G+ A        G   F+K  ++    ++E PR
Sbjct: 963  ARIERTRDEEIKILRDSFFRRIRELLLGKEATGKLVDDKGKVLFQKGAIIDEPSLAEIPR 1022

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
              W +  V D      V+ +    E      E+ F++KI+++  GD++PPGV+++VKV++
Sbjct: 1023 KYWGEIPVDD---AERVQQILRDLEELVRTREEHFRDKIDRLSKGDELPPGVIKMVKVYI 1079

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR +Q GDKMAGRHGNKG++SRILP EDMP+L+DG PVD+VLNPLGVPSRMNVGQI E
Sbjct: 1080 AIKRKLQVGDKMAGRHGNKGVISRILPEEDMPYLQDGRPVDLVLNPLGVPSRMNVGQILE 1139

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
             HLGW    LG +++ +I   +A+ +I      +    G  +      + DD  V R  +
Sbjct: 1140 IHLGWGAFELGNQLQRMIEQQRASAEIKEHLKAI--YAGDETMNGFFDNLDDGDVKRFVK 1197

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GV + +PVFDGA E  I   L +A L  SGQ+IL+DG TG+ FD+ VTVG +YMLK
Sbjct: 1198 TVDEGVFMGSPVFDGAHESDIKGALDLAGLPTSGQAILFDGRTGDAFDQNVTVGIMYMLK 1257

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+K
Sbjct: 1258 LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVK 1317

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV+GRTR+YE+IV G+ T E G PESFNVL+KE+Q+L L+++L
Sbjct: 1318 SDDVMGRTRMYEAIVKGDYTLEAGLPESFNVLIKELQSLCLNVEL 1362


>gi|93007001|ref|YP_581438.1| DNA-directed RNA polymerase subunit beta [Psychrobacter
            cryohalolentis K5]
 gi|122414836|sp|Q1Q8P9|RPOB_PSYCK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|92394679|gb|ABE75954.1| DNA-directed RNA polymerase, beta subunit [Psychrobacter
            cryohalolentis K5]
          Length = 1372

 Score = 1593 bits (4124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1380 (50%), Positives = 963/1380 (69%), Gaps = 23/1380 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F + P ++DIP L+ +Q  SY+ FL  +  P  R N GLQAA+ S+
Sbjct: 1    MAYSYTEKKRIRKSFAELPTVMDIPYLLSIQVDSYEQFLQEHKKPKARENTGLQAAYSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPI + SG A L+FV Y    P+FD  +C+ R  T+A P+++ +RLI+ D D        
Sbjct: 61   FPIESHSGNAELQFVEYYLGTPEFDERECILRGSTFAAPMRVKIRLIIKDKDSKDKDSKA 120

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IKDI+EQS+YMG++PLMT +GTF+I G +R++VSQLHRSPG+ FDHDKG++  SGK+LY
Sbjct: 121  AIKDIREQSVYMGEMPLMTANGTFIINGTERVIVSQLHRSPGVFFDHDKGKSHSSGKVLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD+KD++  RIDRRRK+  +  L ALG+ + EIL  F+ K+   +
Sbjct: 181  NARIIPYRGSWLDFEFDAKDLVFARIDRRRKLLASIILRALGLSTSEILDLFFDKVRVYK 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + +   L A D + G      +V    G+ V+E GK++ +  ++ L+E G+  + I  
Sbjct: 241  GEEQFEIDLVA-DRLRGEMAQFDIVTPA-GDVVVEQGKRINARRIRQLEEAGMTKISIPD 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE----IRDIPILYVDSVNNNA 356
            + L    +AEDI+     E+   A  +ID + L ++   E    I++  IL+ + ++  +
Sbjct: 299  EYLYERILAEDII--VNDEVIARANTLIDHELLVKLSAFEASESIKEFSILFTNDIDQGS 356

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            YI +TL  D    R++AL++IY+VMRPG+  T   AE +F+ +FF++D+YDLS VGR+K 
Sbjct: 357  YIADTLRADSTSSREEALIEIYKVMRPGEPPTVETAEKLFDSMFFNADRYDLSNVGRMKF 416

Query: 417  NMRLNLDTPD--------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            N RL LD  D        +   +   DI+ ++K L+++RNG+G +DDID+LGNRR+RSVG
Sbjct: 417  NRRLGLDFVDTDDADIQRERSVLTNADIVNVLKELIEIRNGRGEVDDIDHLGNRRIRSVG 476

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            EM +NQ+R+GL+R+ER++KER+SS + D++ PQDLIN+KPV +AV EFF SSQLSQ  + 
Sbjct: 477  EMAENQFRVGLVRVERAVKERLSSAESDNLSPQDLINSKPVAAAVKEFFGSSQLSQFMDQ 536

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +
Sbjct: 537  NNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHDTHYGRVCPIETPEGPNIGLINSLAT 596

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FA+ N++GF+ETPYR+V DGKVT+ + YLSA+EE    IAQA+S +  DG+ ++E+V  R
Sbjct: 597  FAKTNSFGFLETPYRRVVDGKVTDVIEYLSAIEEVGTVIAQADSPVTADGALSDEMVSVR 656

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              GE + +P EK+  +D SP QVVS+AA LIPFLE+DD+NR LMG NMQRQAVP L+A+ 
Sbjct: 657  SYGEFVRMPPEKVTHMDVSPSQVVSVAAGLIPFLEHDDANRALMGSNMQRQAVPTLRADK 716

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTGME  VA+ SG  ++AKR G++E VDA R+V+R  E ++    +G+DIY L+K+ 
Sbjct: 717  PLVGTGMERHVARDSGVCVIAKRGGVIEDVDASRVVVRVNEDEMIAGEAGIDIYNLVKYT 776

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQR +V  GD +   DI+ADGPSTDLG+LALG+N+ +AFMPW+GYNFEDS+L
Sbjct: 777  RSNQNTCINQRIIVNQGDAIAVGDILADGPSTDLGELALGQNIRIAFMPWNGYNFEDSIL 836

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SE++V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L ++DE GI+ +GAEV
Sbjct: 837  LSEKVVKEDRFTTIHIQELTCVARDTKLGTEEITADIPNVGEAALSSLDEAGIVYIGAEV 896

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            + GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+   GTV+DV++F R 
Sbjct: 897  DAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDTSLRVPTSSKGTVIDVQVFTRD 956

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K+ R+ ++E+ Q++   +D  +E  I +     R+  +L GQ    G  G K  TV+
Sbjct: 957  GVEKDARARAIEKSQLDSYRKDLKEELRIFEEAARGRIGNLLDGQKVSGGS-GLKAGTVM 1015

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +   + +            +E++   +  +       +  ++ +F  K  K+  GDD+  
Sbjct: 1016 ALADMKDMSLETLLDIQPVEEEISERLTQIAEYLVDKQKDIDVKFAEKKRKLTAGDDLQH 1075

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++VKV++A+KR IQ GDKMAGRHGNKG+VSRI+P EDMP+ ++G  VDIVLNPLGVP
Sbjct: 1076 GVQKIVKVYLAVKRRIQPGDKMAGRHGNKGVVSRIMPVEDMPYDENGNTVDIVLNPLGVP 1135

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISD 1187
            SRMN+GQ+ ETHLG A  GLG+KI  ++   K+   I  LR FL+K+    G     +  
Sbjct: 1136 SRMNIGQVLETHLGMAAKGLGEKIDGML---KSQAAIKDLRDFLDKIYNQVGGEQVDLDS 1192

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              DD ++ +A+  ++GVP+ T VFDGA E  +  +L +A +D  GQ  LYDG TG+ FDR
Sbjct: 1193 LSDDDIMALADNLRAGVPMGTAVFDGARESQVKDLLELAGMDRDGQQTLYDGRTGQKFDR 1252

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1253 KVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1312

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             Y LQEMLT+KSDDV GRTR+Y++IV G    + G PESFNVL KE+++LG++I+L+ S 
Sbjct: 1313 TYTLQEMLTVKSDDVEGRTRMYKNIVDGEQYMDPGMPESFNVLTKEIKSLGINIELKQSN 1372


>gi|161870923|ref|YP_001600103.1| DNA-directed RNA polymerase subunit beta [Neisseria meningitidis
            053442]
 gi|161596476|gb|ABX74136.1| DNA-directed RNA polymerase beta chain [Neisseria meningitidis
            053442]
          Length = 1371

 Score = 1593 bits (4124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1377 (50%), Positives = 950/1377 (68%), Gaps = 42/1377 (3%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +++P L+  Q  SY  FL +  A D+R ++GLQAAF S+FPI + +G A LEFV Y    
Sbjct: 1    MEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSIFPIVSHNGYARLEFVHYTLGE 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P FD+ +C  R +TYA PL+  +RL++ D        ++K+++E  +YMG++PLMT  G+
Sbjct: 61   PLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTVKEVRENEVYMGEIPLMTPSGS 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 119  FVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
             RIDRRRK+PVT  L ALG ++E+IL  FY K  +    +     L A  L  G      
Sbjct: 179  FRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSSNGVQTDLVAGRL-KGETAKVD 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            ++D   G  ++  GK++T+  ++ +   G+  L +  + L G  +A D+++ ETGE+   
Sbjct: 238  ILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPESLLGKALAADLIDSETGEVLAS 296

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A D I E+ L +   + +++I  LY++ ++  AYI NTL TD+   R+ A + IYR+MRP
Sbjct: 297  ANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTLRTDETAGRQAARVAIYRMMRP 356

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR-------------- 429
            G+  T    E +FN LFF  D YDLS VGR+K N R       + +              
Sbjct: 357  GEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYEQKLSEAQQNSWYGRLLNETFA 416

Query: 430  --------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+R GL R
Sbjct: 417  GAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQFRSGLAR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 477  VERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEVTHKRRV 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP
Sbjct: 537  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+   +++
Sbjct: 597  YRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIMATPDRV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA 
Sbjct: 657  QYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGIERSVAV 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             S  AIVA+R G+VE VDA R+VIR  + +      GVDIY L+KF RSNQ+T +NQRP 
Sbjct: 717  DSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVDIYNLVKFTRSNQSTNINQRPA 776

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+GYN+EDS+LISE++ ++D +TS
Sbjct: 777  VKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNGYNYEDSILISEKVAADDRYTS 836

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE GI+ +GAEV  GD+LVGK+TPK
Sbjct: 837  IHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESGIVYIGAEVEAGDVLVGKVTPK 896

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+DV++F R GI +++R+ S+  
Sbjct: 897  GETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVIDVQVFTREGIQRDKRAQSIID 956

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP-RSQ 1020
             +++    D +D+  I D + + R+  ++ GQ A  GP    K + ++++ ++  P R  
Sbjct: 957  SELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPMKLAKGSEITTEYLAGLPSRHD 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+   + DE + + +E +KV  +  +   ++ ++ K +K+  GD++ PGV ++VKVF+A+
Sbjct: 1017 WFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKKLTQGDELQPGVQKMVKVFIAI 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDIVLNPLGVPSRMN+GQI E H
Sbjct: 1077 KRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVPSRMNIGQILEVH 1136

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  G+G++I  ++ + +  G+   LR FL K+       E +    D+ ++ +A   
Sbjct: 1137 LGWAAKGIGERIDRMLKEQRKAGE---LREFLNKLYNGSGKKEDLDALTDEEIIELASNL 1193

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMA-----------DLDES-GQSILYDGLTGEPFDRP 1248
            + G   ++PVFDGA E  I  ML +A             ++S  Q  LYDG +GE FDR 
Sbjct: 1194 RKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGFNDSKTQITLYDGRSGEAFDRK 1253

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1254 VTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1313

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            Y LQEMLT+KSDDV GRT++YE+IV G    + G PESFNVLVKE+++LGL IDLE 
Sbjct: 1314 YTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESFNVLVKEIRSLGLDIDLER 1370


>gi|89902356|ref|YP_524827.1| DNA-directed RNA polymerase subunit beta [Rhodoferax ferrireducens
            T118]
 gi|89347093|gb|ABD71296.1| DNA-directed RNA polymerase, beta subunit [Rhodoferax ferrireducens
            T118]
          Length = 1350

 Score = 1593 bits (4124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 682/1354 (50%), Positives = 951/1354 (70%), Gaps = 18/1354 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            ++IP L+++QK +Y  FL  ++ P +R  EGLQAAF++ FPI + +G   ++++ Y    
Sbjct: 2    LEIPYLLQMQKDAYTAFLQADVHPKKRTAEGLQAAFEAAFPIISHNGFVEMKYLEYNLAK 61

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDG 142
            P FDV +C  R LT+A  ++  ++L ++D +  T   K IK++KEQ +YMG++PLMT  G
Sbjct: 62   PAFDVRECQTRGLTFASAVRAKVQLFIYDRESSTSQNKVIKEVKEQEVYMGEVPLMTTKG 121

Query: 143  TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
            +F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD +
Sbjct: 122  SFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKDFL 181

Query: 203  HVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            + R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G     
Sbjct: 182  YFRVDRRRKMPVTILLKAIGLNHESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARF 240

Query: 263  SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA +IV+ +TGEI  
Sbjct: 241  DITD-KSGKVIVAKEKRVTARHTRELEQSGTTHISVPEDFLLGRVVARNIVDTDTGEILA 299

Query: 323  EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
            +A + + E  ++++  + ++D+P +Y + ++  AYI  TL +D+  D   A + IYR+MR
Sbjct: 300  KANEELTEALIKKLRLAGVQDLPCIYTNELDQGAYISQTLRSDETVDEFAARVAIYRMMR 359

Query: 383  PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            PG+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A++KI
Sbjct: 360  PGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKMGRPESTGPMVLTNEDILAVVKI 419

Query: 443  LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
            LVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP D
Sbjct: 420  LVDLRNGRGDVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHD 479

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            LIN+KP+ +A+ EFF +SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH
Sbjct: 480  LINSKPISAALKEFFGASQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVH 539

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             THYGR+CP ET EG NIGL++SL  +AR+N YGFIETPYR+V DGKVT ++ YLSA+EE
Sbjct: 540  VTHYGRVCPIETPEGPNIGLINSLALYARLNDYGFIETPYRRVVDGKVTMEIDYLSAIEE 599

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                IAQAN+ LD+DG  T E++  R AGE I    E++ ++D SP Q+VS+AASL+PFL
Sbjct: 600  GKFVIAQANAVLDKDGKLTGEMISAREAGETIFAGPERVQYMDVSPAQIVSVAASLVPFL 659

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            E+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A  SG  + A R G+V+ VDA R
Sbjct: 660  EHDDANRALMGANMSRQAVPILRPEKPMVGTGIERVAAIDSGTVVTATRGGMVDYVDATR 719

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            +VIR  + +      GVDIY L+K+QRSNQNT ++QRP+VK GD + + D+IADG STDL
Sbjct: 720  VVIRVNDDEAQAGEVGVDIYNLIKYQRSNQNTNIHQRPIVKKGDMLAKGDVIADGASTDL 779

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G+LALG+NML+ FM W+GYNFEDS+LISER+V++D +TSIHIEE  VMARDTKLG EEIT
Sbjct: 780  GELALGQNMLIGFMTWNGYNFEDSILISERVVADDRYTSIHIEELVVMARDTKLGCEEIT 839

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            RDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPKGE+ +TPEEKLLRAIFGEKA 
Sbjct: 840  RDIPNLSEQQLNRLDESGIIYVGAEVQPGDTLVGKVTPKGETTLTPEEKLLRAIFGEKAS 899

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            DV+DTSLRV  G  GTV+DV++F R GI ++ R+  +  ++++    D +D+  +++ + 
Sbjct: 900  DVKDTSLRVDQGSQGTVIDVQVFTREGIVRDRRAQQIIDDELKRFRLDLNDQLRLVEADS 959

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            + R+ ++L G+ A  GP+   K T +    ++   +  W+     ++ V   +ES+K   
Sbjct: 960  FDRIEKLLVGKVANGGPQKLAKGTTIDKAYLTSVEKHHWFDIRPAEDDVAAQLESIKNSM 1019

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            E ++   +  F+ K +K+  GD++P GVL++VKV++A+KR +Q GDKMAGRHGNKG+VS+
Sbjct: 1020 EQTRHSFDLAFEEKRKKLTQGDELPAGVLKMVKVYLAVKRHLQPGDKMAGRHGNKGVVSK 1079

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+P EDMPF+ DGTP DIVLNPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +A 
Sbjct: 1080 IVPVEDMPFMADGTPCDIVLNPLGVPSRMNIGQVLEVHLGWAAKGIGQRIGDML---QAE 1136

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              ++ LR FL+++       E ++   DD VL +A    SGVP +TPVFDGA E  I +M
Sbjct: 1137 AKVAELRKFLDELYNGTGRKEDLAQLSDDEVLEMAGNLTSGVPFATPVFDGASEADIGAM 1196

Query: 1223 LRMADLDESG-----------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            L++A   E             Q+ LYDG TG+PF+RP T+GY++ LKL+H+V DK++ARS
Sbjct: 1197 LKLA-YPEDAIRQKGLTPARTQAYLYDGRTGDPFERPTTIGYMHYLKLHHLVDDKMHARS 1255

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYES
Sbjct: 1256 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVQGRTKVYES 1315

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            IV G  + E G PESFNVLVKE+++LG+ I+LE 
Sbjct: 1316 IVKGEHSIEAGMPESFNVLVKEIRSLGIDIELER 1349


>gi|157828055|ref|YP_001494297.1| DNA-directed RNA polymerase subunit beta [Rickettsia rickettsii str.
            'Sheila Smith']
 gi|165932752|ref|YP_001649541.1| DNA-directed RNA polymerase subunit beta [Rickettsia rickettsii str.
            Iowa]
 gi|166229304|sp|A8GQW4|RPOB_RICRS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189043865|sp|B0BWA9|RPOB_RICRO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157800536|gb|ABV75789.1| DNA-directed RNA polymerase subunit beta [Rickettsia rickettsii str.
            'Sheila Smith']
 gi|165907839|gb|ABY72135.1| DNA-directed RNA polymerase beta chain [Rickettsia rickettsii str.
            Iowa]
          Length = 1373

 Score = 1592 bits (4123), Expect = 0.0,   Method: Composition-based stats.
 Identities = 760/1358 (55%), Positives = 1024/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NVANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIIAFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|14916699|sp|Q9RH43|RPOB_RICMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|6652714|gb|AAF22431.1| RNA polymerase beta subunit [Rickettsia massiliae]
          Length = 1373

 Score = 1592 bits (4122), Expect = 0.0,   Method: Composition-based stats.
 Identities = 762/1358 (56%), Positives = 1025/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+ +T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYITTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPTSDEVLAKIGEMITADMLNVINALKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD D+YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDVDRYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFNTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKVNKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|157964206|ref|YP_001499030.1| DNA-directed RNA polymerase subunit beta [Rickettsia massiliae MTU5]
 gi|166991527|sp|A8F0P7|RPOB_RICM5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157843982|gb|ABV84483.1| DNA-directed RNA polymerase beta chain [Rickettsia massiliae MTU5]
          Length = 1373

 Score = 1592 bits (4121), Expect = 0.0,   Method: Composition-based stats.
 Identities = 761/1358 (56%), Positives = 1025/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+ +T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYITTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPTSDEVLAKIGEMITADMLNVINALKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD ++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDVERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFNTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKVNKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|6652723|gb|AAF22437.1|AF076436_1 RNA polymerase beta subunit [Rickettsia sp. Bar29]
          Length = 1373

 Score = 1592 bits (4121), Expect = 0.0,   Method: Composition-based stats.
 Identities = 759/1358 (55%), Positives = 1026/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+ +T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYITTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            D + AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DHEAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFNTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V +G
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKNG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKVNKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDKKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERSEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V++K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVNNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|319778778|ref|YP_004129691.1| DNA-directed RNA polymerase beta subunit [Taylorella equigenitalis
            MCE9]
 gi|317108802|gb|ADU91548.1| DNA-directed RNA polymerase beta subunit [Taylorella equigenitalis
            MCE9]
          Length = 1370

 Score = 1591 bits (4120), Expect = 0.0,   Method: Composition-based stats.
 Identities = 692/1375 (50%), Positives = 957/1375 (69%), Gaps = 15/1375 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   + D+P L+E Q  SY  FL  ++ P +R + GLQAAF S+
Sbjct: 1    MPYSFTEKKRIRKNFAKRQVVQDVPYLLETQIQSYRSFLQKDLTPSKRADIGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G+A LEFVSY    P+FDV +C  R LTY   L   +RL + D        ++
Sbjct: 61   FPIESNNGSARLEFVSYVLKEPQFDVKECQLRGLTYYSGLYAKVRLEILDR--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KE+ +YMGDLPLMT +G+F+I G +R++VSQLHRSPG+ F+HDKG+   S KLL++ 
Sbjct: 119  KEVKEEEVYMGDLPLMTDNGSFIINGTERVIVSQLHRSPGVFFEHDKGKNHSSNKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD ++ RIDRRRK+PVT  L A+GM S+EIL TF+    Y    
Sbjct: 179  RVIPYRGSWLDFEFDHKDYLYFRIDRRRKMPVTILLKAIGMSSDEILGTFFEFSKYDLND 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D          L  G      +VD   G  +++  K++ S  ++ +    +  L +  D 
Sbjct: 239  DGAVLHFVPERL-KGEVARFDIVDKK-GNVIVQKDKRINSKNIRDIAAAKLTKLPVPDDY 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A+ I++ ETGE+ ++A   I E  L ++  S I++I  LY + +++ AYI  TL
Sbjct: 297  LVGQTIAKTIIDEETGEVLVQANTEITESVLAQLRKSSIKEIETLYTNELDHGAYISATL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D+  D+  A   IY++MRPG++      ES+FN +F++SD YDLSTVGR+K+N RL  
Sbjct: 357  AIDETLDQTAARKSIYKMMRPGELPADDAVESLFNRMFYNSDTYDLSTVGRMKVNRRLGR 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            ++      +  EDI+  IK LVDLRNG+G IDDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 417  NSDKGPTTLTNEDILDTIKTLVDLRNGRGEIDDIDHLGNRRVRCVGELAENQFRSGLVRV 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KE +   + ++++P DLIN+KP+ SA+ EFF S+QLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAVKEHLGHAESENLLPNDLINSKPISSAIKEFFSSNQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALGQGG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +AR N YGF+ETPY
Sbjct: 537  ALGQGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYARQNEYGFLETPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKV + + YLSA+EE    IAQAN++LDE G+F ++L+ CR AGE +L+  EK++
Sbjct: 597  RKVENGKVVDQIDYLSAIEESKYVIAQANANLDEHGNFIDDLIACRQAGETMLMSPEKVE 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +ID +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTG+E  VA  
Sbjct: 657  YIDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPQKPLVGTGIERTVAVD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+R G V+ VD+ RIVIR  + +    + GVDIY L K+ RSNQNT +NQRP+V
Sbjct: 717  SGTTVQARRGGEVDYVDSERIVIRVNDDESVSGSVGVDIYNLNKYTRSNQNTNINQRPIV 776

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V+R D+IADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISE++++ D +TS+
Sbjct: 777  KKGDVVQRGDVIADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVIANDRYTSV 836

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE  V+AR+T+LG EEITRDIPN++ E L  +DE GI+ +GAEV   D+LVGK+TPKG
Sbjct: 837  HIEELSVVARETQLGDEEITRDIPNLAAEQLNRLDESGIVHIGAEVRARDVLVGKVTPKG 896

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+  +PE KLLR IF +KA+DV+DTSLRVPSG+ GTV+DV++     +++++R+ S+  E
Sbjct: 897  ETQQSPETKLLREIFQDKALDVKDTSLRVPSGMVGTVIDVQVLTGKRVERDKRAQSIIEE 956

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++    +D D +  I+++++++RL ++L G+    GP    K + ++ + +   P   W+
Sbjct: 957  ELRRYRQDLDSQLRIVEKDMFNRLRKVLVGKKVNGGPISLSKGSSITEEYLKNLPTWDWF 1016

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 DE V   +E  K   E  +   + +F+ K +K+  GD++PPGV ++VKVF+A+KR
Sbjct: 1017 DIRPVDEDVAIVLEQAKDSIEKKRHEFDIKFEEKQKKLTQGDELPPGVRKMVKVFLAVKR 1076

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG+VSRILP EDMP + DGTP DIVLNPLGVPSRMNVGQ+ E HLG
Sbjct: 1077 RLQPGDKMAGRHGNKGVVSRILPVEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHLG 1136

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA  G+G++I  ++ D +     S +R +LEKV      TE + ++ D+ ++ +A   K 
Sbjct: 1137 WAAKGIGQRIADMLADERKI-QASEIRKYLEKVYNRTGKTEDLKEFTDEQIIEMAHNLKD 1195

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTVG 1252
            G+P +TPVFDGA EE IN ML +A            D   Q+ L DG TGEPF+RPVT+G
Sbjct: 1196 GIPFATPVFDGATEEEINDMLELAYPDDIKEKLHLTDSRTQAYLIDGRTGEPFERPVTIG 1255

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQ
Sbjct: 1256 YMHYLKLHHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQ 1315

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            EMLT KSDD+ GR  V  +I+ G+   + G PESFNV+VKE+++LGL ++LE  +
Sbjct: 1316 EMLTEKSDDMEGRNNVNRNIIQGDHVIDAGMPESFNVIVKEIRSLGLDMELEGKQ 1370


>gi|325267351|ref|ZP_08134012.1| DNA-directed RNA polymerase subunit beta [Kingella denitrificans ATCC
            33394]
 gi|324981146|gb|EGC16797.1| DNA-directed RNA polymerase subunit beta [Kingella denitrificans ATCC
            33394]
          Length = 1400

 Score = 1591 bits (4120), Expect = 0.0,   Method: Composition-based stats.
 Identities = 699/1405 (49%), Positives = 964/1405 (68%), Gaps = 46/1405 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   I+++P L+  Q  SYD FL  + A D+R +EGLQAAF S+
Sbjct: 1    MNYTFTEKKRIRKSFAKRETILEVPYLLTTQLESYDKFLQQDRAADKRVDEGLQAAFGSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD--EFTGAK 120
            FPI + +G A L+F  Y    P+FD+ +C  R +TYA PL+  ++L++F+ +       +
Sbjct: 61   FPIVSNNGYAELQFEQYILGEPEFDIPECQLRGITYAAPLRAKIKLVIFNKEGSSKVEDR 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K+I+E ++YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL+
Sbjct: 121  EVKEIRENTVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHASGKLLF 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG    E+L+ FY    Y  
Sbjct: 181  SARIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLRALGYSDSEMLNMFYDCETYYL 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              D     L   D + G      +VD D G  ++ +GK++   +++ +++ G+  L I +
Sbjct: 241  GKDGVQTDLVV-DRLRGETAKFDIVDND-GNVLVSAGKQINGKVIREIQKAGLTRLTIDA 298

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G  +A DI+  +TGE+   A   I E+ L E+   E+++I  L+++  +   Y+  
Sbjct: 299  EILLGKTLANDIIVPDTGEVLAAANSEITEELLAELDIQEVKEIKTLFINDTDAGNYLSA 358

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL TD+ +D++ A + IYR+MRPG+  T    E++FN +FF  + YDLS VGR+K N R 
Sbjct: 359  TLRTDETRDKQAARIAIYRMMRPGEPPTDEAVEALFNRMFFQEESYDLSRVGRMKFNTRT 418

Query: 421  NL------------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                                      +    +  +  EDI+  I  LV+LRNG G +DDI
Sbjct: 419  YEQKLLPAQENNWYGRLLNETFAGVGEKEAKLHILSVEDIVMTIATLVELRNGHGEVDDI 478

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            D+LGNRRVRSVGE+++NQ+R GL R+ER++KER++  + + +MP DLINAKPV +A+ EF
Sbjct: 479  DHLGNRRVRSVGELVENQFRAGLARVERAVKERLNQAESEGLMPTDLINAKPVSAAIKEF 538

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET E
Sbjct: 539  FGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 598

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL+ +AR N YGF+ETPYR+V DGKVTN++ YLSA+EE    IAQANS +DE
Sbjct: 599  GPNIGLINSLSVYARTNDYGFLETPYRRVVDGKVTNEIDYLSAIEEGRYVIAQANSEIDE 658

Query: 637  D-GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   +EL+ CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG N
Sbjct: 659  KTGKLKDELITCREKGETILATADRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGAN 718

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVP L+AE P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +   +
Sbjct: 719  MQRQAVPCLRAEKPLVGTGIERAVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAA 778

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              GVDIY L+KF RSNQ+T +NQRP V  GD ++R D+IADG STDLG+LALG+NM +AF
Sbjct: 779  EGGVDIYNLVKFTRSNQSTNINQRPAVNKGDVLQRGDLIADGASTDLGELALGQNMTIAF 838

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW+GYN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE+    
Sbjct: 839  MPWNGYNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSEKMQNR 898

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +DE GII +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+
Sbjct: 899  LDESGIIYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGM 958

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            SGTV+DV++F R GI +++R+ S+   ++    +D +D+  I D + + R+  +L GQ A
Sbjct: 959  SGTVIDVQVFTREGIQRDKRAQSIIDAELRRYRQDLNDQVRIFDNDAFDRIERMLVGQKA 1018

Query: 996  VSGPKGFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              GP    K   ++++ +   P R  W+   V DE + + +E +K+  +  +   E  F+
Sbjct: 1019 NGGPMKLGKGKAITAEYLHGLPSRHDWFDIRVADEDIAKQLELIKLSLQQKREEAEAAFE 1078

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K +K+  GD++PPGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ D
Sbjct: 1079 VKKKKMTQGDELPPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMAD 1138

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G  VDIVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +    +  +R FL +
Sbjct: 1139 GRTVDIVLNPLGVPSRMNIGQILEVHLGWAAKGIGQRIDKMLAEQR---KVKEIRKFLNE 1195

Query: 1175 VIGTG-SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-- 1231
            +     +H E +    DD +L +A+  + G   ++PVFDGA E+ I  ML +A       
Sbjct: 1196 LYNKNAAHKEDLDSLSDDEILLLADNLRKGATFASPVFDGAKEKEIYDMLELAYPSNDPD 1255

Query: 1232 ----G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                G      Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQ
Sbjct: 1256 VQKLGFNDTKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQ 1315

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + 
Sbjct: 1316 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDA 1375

Query: 1342 GTPESFNVLVKEMQALGLSIDLENS 1366
            G PESFNV+VKE+++LGL IDLE +
Sbjct: 1376 GMPESFNVIVKEIRSLGLDIDLEQN 1400


>gi|71892326|ref|YP_278060.1| DNA-directed RNA polymerase subunit beta [Candidatus Blochmannia
            pennsylvanicus str. BPEN]
 gi|88909123|sp|Q492B9|RPOB_BLOPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71796432|gb|AAZ41183.1| DNA-directed RNA polymerase, beta-subunit [Candidatus Blochmannia
            pennsylvanicus str. BPEN]
          Length = 1341

 Score = 1590 bits (4118), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1363 (50%), Positives = 951/1363 (69%), Gaps = 22/1363 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1    MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQIDSFQKFIKQDPEEPC----GLEAAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G A L+++ Y+   P FDV +C  R  T++ PL++ L LI+++         I
Sbjct: 57   FPIKSYNGNAELQYIKYQLGEPTFDVKECQTRGATFSAPLRVRLCLIIYER--EGLNNII 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+ KEQ +YMG++PLMT +GTF+I GI+R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KNTKEQEVYMGEIPLMTNNGTFIINGIERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PVT  L AL   +++IL+ F+ K++Y  + 
Sbjct: 175  RIIPYRGSWLDFEFDLKDNLFVRIDRRRKLPVTVILRALNYTTDQILNIFFNKVIYEIQN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L    L  G   S  +     G   ++ G+++ +  ++ LK+  +  + +  D 
Sbjct: 235  NTLYMHLIPERL-RGETASFDI--AVNGVIYVKKGRRIAAKHIRQLKKDKISKIEVPMDY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  V +D  +  T    + A   I    L  +  S    I  L+ + ++   YI  TL
Sbjct: 292  IIGKVVIKDYFDKNTNIPIVTANTEISSDILHNLIRSGYESIETLFSNDLDYGNYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   ++ DAL++IYRVMRPG+  T   AE +F  LFF  ++YDLS+VGR+K N  L  
Sbjct: 352  RIDATTNKFDALVEIYRVMRPGEPPTKEAAEYLFENLFFSEERYDLSSVGRMKFNRSLQR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +D+  ++K+DI+ +IK L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412  VQIEDLGTLKKDDIVDVIKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472  ERAVKERLSLGDLDVLTPQDLINAKPISAAVREFFTSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARANKYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G V+ND+ YLSA+EE +  IAQAN++L+  G F ++LV CR  GE  L  ++++D
Sbjct: 592  RKVQNGVVSNDIHYLSAIEEGDFVIAQANTNLNSIGEFIDDLVTCRNKGESGLFKKDQVD 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP+L +E P VGTGME  VA  
Sbjct: 652  YMDVSTQQIVSVAASLIPFLEHDDANRALMGANMQRQAVPVLCSEKPLVGTGMERAVAID 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+++ VDA RIVI   + +     SG+DIY+L K+ RSNQNTC+NQRP V
Sbjct: 712  SGVTVVAKRGGVIKYVDASRIVIHVNKNETHTEESGIDIYQLTKYIRSNQNTCINQRPCV 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +G+ V   D+IADGPSTDLG+LALG+NM +AFMPW+GYNFEDSML+SER+V ED FTSI
Sbjct: 772  SLGELVEHGDVIADGPSTDLGELALGQNMRIAFMPWNGYNFEDSMLVSERVVQEDKFTSI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GII +GAEV  GDILVGK+TPKG
Sbjct: 832  HIQELTCVSRDTKLGPEEITADIPNVGETALSKLDESGIIYIGAEVIGGDILVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTV+DV+IF R GI+K++RS+ +E E
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVCGTVIDVQIFTRDGINKDKRSLIIESE 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +++ + +D  +E  I +  ++ R+ ++L              ++ +    + E  R+ W 
Sbjct: 952  KLKQVKKDLSEELQIFESALFDRVCDVLM-------------TSGIDKKKLFETSRNAWL 998

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D + Q  +  L  QY   K + E + + +  KI  GD++ PG+L++VKV++A+KR
Sbjct: 999  DLVLSDPEKQYQLSQLTKQYFDLKRMFEKKLEIQHRKITQGDELAPGILKIVKVYLAVKR 1058

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1059 QIQPGDKMAGRHGNKGVISKINPIEDMPYDQHGIPVDIVLNPLGVPSRMNIGQILETHLG 1118

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G KI  ++  +K    +         +         ++ + D  +L++A+  K 
Sbjct: 1119 MAAKGIGDKINFMLQQHKEANQLRRFMQQAYNLGEGSRQHINLNSFSDIEILKLAKNLKK 1178

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+++ L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1179 GMPIATPVFDGATEKEIKDLLKLSGLPSSGQITLFDGCTGEAFERQVTVGYMYMLKLNHL 1238

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1239 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1298

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT++Y++IV GN   E G PESFNVL+KE+++L ++I+LE+
Sbjct: 1299 NGRTKMYKNIVDGNHMMEPGMPESFNVLLKEIRSLAINIELED 1341


>gi|15604016|ref|NP_220531.1| DNA-directed RNA polymerase subunit beta [Rickettsia prowazekii str.
            Madrid E]
 gi|6094124|sp|O52271|RPOB_RICPR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|2746230|gb|AAC38354.1| RNA polymerase beta subunit [Rickettsia prowazekii]
 gi|3860707|emb|CAA14608.1| DNA-DIRECTED RNA POLYMERASE BETA CHAIN (rpoB) [Rickettsia prowazekii]
 gi|292571735|gb|ADE29650.1| DNA-directed RNA polymerase beta chain [Rickettsia prowazekii Rp22]
          Length = 1374

 Score = 1590 bits (4118), Expect = 0.0,   Method: Composition-based stats.
 Identities = 767/1363 (56%), Positives = 1029/1363 (75%), Gaps = 9/1363 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DVD+C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVDECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D EFD+KDII+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDFEFDAKDIIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKFVKNKGWSVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L +     G+  + +T + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAQKYFGVGLNNILVTHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L+ I   +I+++ +L ++   + +YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITSDMLKVINDLKIKNVNVLVINPQ-SGSYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I++ILV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRILVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V +G
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKNG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V  +++DFID +
Sbjct: 615  YVTDEVVYLSAIEEGKYKIGQANSKVDQDGKLQGEFINCRVEGGNFVMVEPDEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K EAPFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTEAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVE+VD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVERVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VRIF+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRIFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L G   ++GPK       ++++++    + Q WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGHVIINGPKQITAGQTITTEMLKGLSKGQLWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K+ Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKIHYDEKKYALDKRFTTKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK N  DI  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAKKISTLVKEYKDNHIDIEEIKKFLLELYGKDI--NYILEGSEEEIISFCNKVSKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML +A  D SGQ  L DG TGE FDR VTVG+ Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLELAGQDLSGQVKLIDGRTGEYFDRLVTVGHKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE + +K
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLEVTPSK 1374


>gi|149922217|ref|ZP_01910655.1| DNA-directed RNA polymerase subunit beta [Plesiocystis pacifica
            SIR-1]
 gi|149816957|gb|EDM76442.1| DNA-directed RNA polymerase subunit beta [Plesiocystis pacifica
            SIR-1]
          Length = 1384

 Score = 1588 bits (4113), Expect = 0.0,   Method: Composition-based stats.
 Identities = 729/1368 (53%), Positives = 983/1368 (71%), Gaps = 15/1368 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK FGK  +II++P+LI++QK SYD  L  ++  DER   GLQA F SVFPI  F   
Sbjct: 9    RVRKNFGKLKKIIEVPNLIDIQKRSYDKLLQADVPADEREMVGLQAVFSSVFPIKDFGET 68

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            + LEFVSY  D PK+DVD+C  R +T+A P+K+ +RL+V+DVD+ TG +SI+D+KEQ +Y
Sbjct: 69   SSLEFVSYSLDRPKYDVDECRARGMTFAAPIKVVVRLVVWDVDDETGTQSIRDVKEQEVY 128

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G++PLMT+ GTF+I G +R+VVSQLHRSPG+ F+HD+G+   SGK L++ R+IP +G W
Sbjct: 129  FGEIPLMTQHGTFIINGTERVVVSQLHRSPGVFFNHDRGKTHSSGKKLFSARVIPYRGSW 188

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KD ++VRIDRRRK+  +  L ALG  ++E+L  +Y K     R D        
Sbjct: 189  LDFEFDHKDFVYVRIDRRRKLHASVILRALGYSTQELLDYYYDKETIHLR-DGKISREVD 247

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             DL+ G + +  + D ++G+ +++ GKKL   L+K ++  G+  + +  + L G   AED
Sbjct: 248  YDLIAGQRSTQEIRDPESGQVLVKKGKKLNKVLIKRMRNAGISEIPLEPEELIGKVAAED 307

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            + + +TGE+ +   D + E  L  I  + I    IL++D  N  +++R+TL+ DK    +
Sbjct: 308  VFDEDTGEVLLNCNDEVTEDVLANIVEAGIDSFRILFIDDFNVGSFLRDTLIADKLTSSE 367

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            DA+++IYR +RPGD  T   A ++F  LFF SD+YDLSTVGR+K+N +  +D P + + +
Sbjct: 368  DAIMEIYRRLRPGDPPTIDTARNLFESLFFRSDRYDLSTVGRLKLNHKFGIDEPLETKVL 427

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K DI+  ++ LV+LRNG+G IDDID+LGNRRVR+VGE+++NQYR+GL+RMER+IKER+S
Sbjct: 428  TKRDILETVRYLVELRNGRGKIDDIDHLGNRRVRAVGELMENQYRIGLVRMERAIKERMS 487

Query: 492  S-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
               ++D++MP DLINAKPV + V E+F SSQLSQ  +  N LS +TH RRLSALG GG+ 
Sbjct: 488  MSQEMDALMPADLINAKPVSAVVKEYFASSQLSQFMDQTNPLSEVTHKRRLSALGPGGLT 547

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGRICP ET EG NIGL++SL+++AR+N +GFIETPYR V  GK 
Sbjct: 548  RERAGFEVRDVHATHYGRICPIETPEGPNIGLIASLSTYARINEFGFIETPYRTVEGGKA 607

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            T++V Y SA++E+  YIAQANS +D  G F  E V CR   E  +V   ++  +D SP Q
Sbjct: 608  TSEVAYYSALQEQGHYIAQANSQMDAAGKFIGETVQCRHNEEFEMVSPAEVTLMDVSPNQ 667

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ +AP VGTG+E+ VA+ SG+ +VA 
Sbjct: 668  LVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRTDAPLVGTGIETNVARDSGSTVVAH 727

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPS----TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            R GIVEQVD  RIV++ V G  +       +  DIY L+KF+RSNQNT +NQ+P+V VGD
Sbjct: 728  RDGIVEQVDGGRIVVKPVSGRGEEDRSILGAKPDIYNLVKFRRSNQNTALNQKPIVNVGD 787

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V+  D+IADG +T+ G+LALG+N+LVAFMPW GYNFEDS+L+SER++ EDV+T+IHIEE
Sbjct: 788  RVKSGDVIADGAATERGELALGQNLLVAFMPWQGYNFEDSILVSERLIREDVYTTIHIEE 847

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            FE +ARDTKLG EEITRDIPNV EE LKN+D+ GI+ +GAEV+ GDILVGKITPKGE+ +
Sbjct: 848  FECVARDTKLGKEEITRDIPNVGEEALKNLDDAGIVRIGAEVHAGDILVGKITPKGETQL 907

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            +PEEKLLRAIFGEKA DVRDTSLR+P GVSG ++D R+F R G+DK+ R+  +E  + E 
Sbjct: 908  SPEEKLLRAIFGEKAGDVRDTSLRLPPGVSGIIIDARVFARKGVDKDVRAQQIEDAERER 967

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQ------NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            L++D  D   I+    ++R+ EIL G+          G      +  L++ L+   PR  
Sbjct: 968  LSQDHHDNVAIVSAGYHNRIKEILLGKTTAAKLVDDQGAMLVDANVQLTAALVDAAPRKY 1027

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W QF++   +    +E+L  + E     +E  ++ K+ K+  GD++PPGV+++VKV+VA+
Sbjct: 1028 WSQFSLTTAEDTELIEALGRRLEKDLDEIETIYREKLAKLTKGDELPPGVIKMVKVYVAI 1087

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG++SRILP ED+P+L+DGTPVDIVLNPLGVPSRMNVGQI E H
Sbjct: 1088 KRKLQVGDKMAGRHGNKGVISRILPTEDLPYLEDGTPVDIVLNPLGVPSRMNVGQILEVH 1147

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LG +I + +   + N     LR+ L+K+  T      I    DD V+R A++ 
Sbjct: 1148 LGWAARELGNQINAYM---ETNYSAEVLRAQLKKIYETEEAMRFIEQLPDDDVIRFADKV 1204

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + G+ V+TPVFDGA E  +   L+ A L +SGQ+IL+DG TGE F+  VTVG +YMLKL+
Sbjct: 1205 RRGIHVATPVFDGAHESEVKGFLQKAGLPDSGQAILFDGRTGEAFEEDVTVGIMYMLKLH 1264

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE+LT+KSD
Sbjct: 1265 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYALQELLTVKSD 1324

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DVVGR R+YESIV G  T + G PESFNVL+KE+QAL L ++L N   
Sbjct: 1325 DVVGRMRMYESIVKGQPTMQPGVPESFNVLLKELQALCLDVELINVED 1372


>gi|15892104|ref|NP_359818.1| DNA-directed RNA polymerase subunit beta [Rickettsia conorii str.
            Malish 7]
 gi|14916698|sp|Q9RH41|RPOB_RICCN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|6652717|gb|AAF22433.1|AF076434_1 RNA polymerase beta subunit [Rickettsia conorii]
 gi|15619229|gb|AAL02719.1| DNA-directed RNA polymerase beta chain [Rickettsia conorii str.
            Malish 7]
          Length = 1373

 Score = 1588 bits (4112), Expect = 0.0,   Method: Composition-based stats.
 Identities = 760/1358 (55%), Positives = 1024/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYTTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYSGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQIIVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|229586379|ref|YP_002844880.1| DNA-directed RNA polymerase subunit beta [Rickettsia africae ESF-5]
 gi|259494191|sp|C3PMH7|RPOB_RICAE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|228021429|gb|ACP53137.1| DNA-directed RNA polymerase beta chain [Rickettsia africae ESF-5]
          Length = 1373

 Score = 1588 bits (4111), Expect = 0.0,   Method: Composition-based stats.
 Identities = 759/1358 (55%), Positives = 1023/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYTTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +    E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPANDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E +VAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGIVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQIIVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|262277088|ref|ZP_06054881.1| DNA-directed RNA polymerase, beta subunit [alpha proteobacterium
            HIMB114]
 gi|262224191|gb|EEY74650.1| DNA-directed RNA polymerase, beta subunit [alpha proteobacterium
            HIMB114]
          Length = 1358

 Score = 1587 bits (4110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 764/1362 (56%), Positives = 1010/1362 (74%), Gaps = 6/1362 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F    ++RK FGK   I++IPDLIEVQK SYD FL  N    E    GL+  FK V
Sbjct: 1    MELSFTDKKKIRKSFGKLENIVNIPDLIEVQKKSYDSFLHFN----EDNKSGLEKVFKEV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+G A +E+VSY F+  K+DV++C  R LTY+ PLK TLRL+ +DV+E    K I
Sbjct: 57   FPIEDFAGLATIEYVSYRFEKEKYDVEECKQRGLTYSAPLKATLRLVAYDVNEEEQTKQI 116

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KEQ +YMGDLPLMT  GTFV+ GI+R+VV+Q+HRSPGI  DHDKG+   SGKLL+ C
Sbjct: 117  LSAKEQEVYMGDLPLMTPRGTFVVNGIERVVVNQMHRSPGIFLDHDKGKGHSSGKLLFNC 176

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D E+D KDI++ RIDR++K+P T+ LMALG   +E+L+ F+ KI +    
Sbjct: 177  RVIPYRGSWLDFEYDIKDILYFRIDRKKKIPSTTLLMALGYPRDELLNLFHEKIKFDFVD 236

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                            K+   LV+ D  ++V++ G K+   +   L+++G+K +  + + 
Sbjct: 237  KDKLKTKFIPQRYKNYKLKHDLVNADDKKKVLKEGTKVNIPIAMKLQKEGLKNIFASLEE 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y A+DI N +TGE+Y E+GD + E+SLE++    I+   +  +D +N  +Y+RNTL
Sbjct: 297  VHGRYFADDIFNEKTGEVYFESGDEVTEESLEKLKALNIKSFYLSEIDGLNIGSYLRNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            + DKN    +A++DIYR++RPG+  T   + ++FN LFF++ +YDLS VGRVK+N RL+L
Sbjct: 357  IVDKNNTADEAVMDIYRILRPGEPPTLETSRNLFNNLFFNNTRYDLSDVGRVKLNSRLDL 416

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D    +  +RKEDI+ I + ++ L++GK  +DDID+LGNRRVRSVGE+++NQ+R+GL+RM
Sbjct: 417  DCDPKITVLRKEDILKIAETMLRLKDGKEEVDDIDHLGNRRVRSVGELVENQFRIGLVRM 476

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKE++SSV+ID+VMPQDLIN+KP+ +++ EF+ +SQLSQ  +  N LS ITH RR+S
Sbjct: 477  ERAIKEKMSSVEIDTVMPQDLINSKPIAASLKEFYGTSQLSQFMDQTNPLSEITHKRRVS 536

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +++RVN YGFIE+PY
Sbjct: 537  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYSRVNKYGFIESPY 596

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKVT ++ YLSAMEE    +AQANS L+ +G+F +ELV CR      L   E ID
Sbjct: 597  RSVKNGKVTKEIHYLSAMEEGRYTVAQANSVLNTNGTFKDELVSCRRNLGFELAKPENID 656

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            F+D SPKQVVS+A++LIPFLENDD+NR LMG NM RQAVPL+K E+P VGTG+E  VA  
Sbjct: 657  FMDVSPKQVVSVASALIPFLENDDANRALMGSNMMRQAVPLIKNESPLVGTGIEKDVALD 716

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA I+AKR G+VE++D  RIV+++     D + SGVDIY L+KFQRSNQNTC+NQRPLV
Sbjct: 717  SGATIIAKRDGVVEKIDGKRIVVKATSD-KDLTKSGVDIYNLLKFQRSNQNTCINQRPLV 775

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD +++ D+IADGPST LG+LALG+N+ VAFMPW GYNFEDS+LISER VS+DVFTSI
Sbjct: 776  KVGDVIKKGDVIADGPSTQLGELALGKNVTVAFMPWLGYNFEDSILISERCVSDDVFTSI 835

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEE+EVMARDTKLGPEEITRDIPN SEE L+N+DE GI+ VGAEV PGDILVGK+TPKG
Sbjct: 836  HIEEYEVMARDTKLGPEEITRDIPNTSEEALRNLDESGIVYVGAEVKPGDILVGKLTPKG 895

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ++ ++ EEKLLR+IFGEKA DVRDTSL++PSG  GTVV+VR+FNRHGI+K+ER++S+E+ 
Sbjct: 896  DTKVSSEEKLLRSIFGEKATDVRDTSLKMPSGTGGTVVEVRVFNRHGIEKDERALSIEKS 955

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +IE +  DK  E+ IL+ NI  R  +IL   +     + F K + LS D +     S  +
Sbjct: 956  EIEAVMSDKQAEESILELNIKIRAQQILSKTSLTEDYRAFSKGSKLSDDEVRTLSLSDIF 1015

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + D K   ++ +LK QY  +K  ++ RF++K++KI+ GD++ PGV+++VKVFVAMKR
Sbjct: 1016 KLKLDDAKSNEDLFALKEQYNKAKKDIQSRFEDKVDKIERGDELLPGVMKMVKVFVAMKR 1075

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +Q GDKMAGRHGNKG++SRI+P EDMP++ +G PVD+ LNPLGVPSRMNVGQI ETHLG
Sbjct: 1076 KLQPGDKMAGRHGNKGVISRIVPVEDMPYMANGKPVDVCLNPLGVPSRMNVGQILETHLG 1135

Query: 1143 WACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            WAC  LG+K+  L N+YKA        +  L K+       ++I    +D    +     
Sbjct: 1136 WACSELGEKVNKLYNEYKAKQKTFEQAKDALGKIYNNSEIDKEIKKLKEDETKDLLHNLS 1195

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            SGVP++TPVFDGA  E +  ML+ ADL ESGQ+ L+DG TGE FDR VTVG IYMLKL H
Sbjct: 1196 SGVPIATPVFDGASVEDVTGMLKFADLPESGQTTLFDGRTGEKFDREVTVGIIYMLKLYH 1255

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD
Sbjct: 1256 MVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDD 1315

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            V GRT+VYE+IV G+D FE+G PESFNVLVKE+++L L+++L
Sbjct: 1316 VAGRTKVYETIVKGDDDFESGIPESFNVLVKEIRSLALNLEL 1357


>gi|294789168|ref|ZP_06754407.1| DNA-directed RNA polymerase, beta subunit [Simonsiella muelleri ATCC
            29453]
 gi|294482909|gb|EFG30597.1| DNA-directed RNA polymerase, beta subunit [Simonsiella muelleri ATCC
            29453]
          Length = 1391

 Score = 1587 bits (4109), Expect = 0.0,   Method: Composition-based stats.
 Identities = 702/1402 (50%), Positives = 956/1402 (68%), Gaps = 47/1402 (3%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDER-PNEGLQAAF 59
            M     F    R+RK F K   ++D+P L+  Q  SY+ FL    A D+R  +EGLQAAF
Sbjct: 1    MTMSYTFTEKKRIRKSFAKRETVLDVPYLLTTQLESYEKFLQQGRAYDQRLNDEGLQAAF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             S+FPI + +G A L+FV Y    P FD+ +C  R +TYA PL+  +RL ++D +    +
Sbjct: 61   TSIFPILSNNGYAELDFVHYVLGEPLFDIPECQLRGITYAAPLRARIRLKIYDKETPVES 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
            K+IK+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL
Sbjct: 121  KTIKEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHASGKLL 180

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            ++ RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG   E++L  FY K  Y 
Sbjct: 181  FSARIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLRALGYSDEQMLDMFYDKETYY 240

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
               +     L A  L  G      +VD D G+ ++       +  ++ ++  G+K L + 
Sbjct: 241  LGKNGVQTDLIAERL-RGEIAKFDIVD-DNGKVLV------NAKNVRDIQAAGLKRLTVE 292

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             D L G  +A D++  ETGE+  +A   I E+ L ++  + I++I  L+V+  +   YI 
Sbjct: 293  PDALIGKTLARDVIVAETGEVMAKANSEITEELLAQLDINNIKEIQTLFVNETSAGNYIS 352

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             TL TD+  D+  A + IYR+MRPG+  T    E++F  +FF  + YDLS VGR+K N R
Sbjct: 353  ATLRTDETADQTAARVAIYRMMRPGEPPTEDAVEALFKRMFFQEETYDLSRVGRMKFNTR 412

Query: 420  LNLDTPDDVR---------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                     +                      +  EDI+  I  LV+LRN  G +DDID+
Sbjct: 413  TYEQKLLPEQIGNWYERLLNDMSEKTDKISFILSNEDIVMTIATLVELRNSHGEVDDIDH 472

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            LGNRRVRSVGE+++NQ+R GL R+ER++KER++  + + +MP DLINAKPV +A+ EFF 
Sbjct: 473  LGNRRVRSVGELVENQFRSGLARVERAVKERLNQAESEGLMPTDLINAKPVSAAIKEFFG 532

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 533  SSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 592

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL++SL+ +AR N YGF+ETPYR+V DGKVTN++ YLSA+EE    IAQANS LD  G
Sbjct: 593  NIGLINSLSVYARTNEYGFLETPYRRVIDGKVTNEIDYLSAIEEGRYVIAQANSELDSSG 652

Query: 639  S-FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               T++L+ CR  GE IL   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 653  CLKTDQLITCREKGETILATADRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQ 712

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+AE P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      
Sbjct: 713  RQAVPCLRAEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDEEATAEHG 772

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+KF RSNQ+T +NQRP V  GD +++ D+IADG STDLG+LALG+NM +AFMP
Sbjct: 773  GVDIYNLVKFTRSNQSTNINQRPAVNAGDVLQKGDLIADGASTDLGELALGQNMTIAFMP 832

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYN+EDS+LISER+ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE+    +D
Sbjct: 833  WNGYNYEDSILISERVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSEKMQNRLD 892

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SG
Sbjct: 893  ESGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSG 952

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R GI +++R+ S+   +++   +D +D+  I D + + R+  ++ GQ A  
Sbjct: 953  TVIDVQVFTREGIQRDKRAQSIIEVELKRYRQDLNDQIRIFDNDAFDRIERMIVGQKANG 1012

Query: 998  GPKGFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            GP    K   ++S+ + E P R  W+   V DE + + +E +K+  +  +   E+ ++ K
Sbjct: 1013 GPNKLAKGKEITSEYLRELPSRHDWFDVRVADEDIAKQMELIKLSLQQKRQEAEELYEVK 1072

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              K+  GD++PPGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG 
Sbjct: 1073 KRKMTQGDELPPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGR 1132

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
             VDIVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +    +S LR FL K+ 
Sbjct: 1133 TVDIVLNPLGVPSRMNIGQILEVHLGWAAKGIGQRIDKMLAEQR---KVSELRDFLNKLY 1189

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES----- 1231
                  E +    DD ++ +AE  + G   ++PVFDGA E+ I  ML +A   E      
Sbjct: 1190 NGSGKKEDLDSLSDDEIITLAENLRRGATFASPVFDGAKEQEIYEMLNLAYPSEDPDIQK 1249

Query: 1232 -G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             G      Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLG
Sbjct: 1250 LGFNDTKTQITLYDGRSGEAFDRRVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLG 1309

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G P
Sbjct: 1310 GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVTGRTKMYENIVKGEHKIDAGMP 1369

Query: 1345 ESFNVLVKEMQALGLSIDLENS 1366
            ESFNV+VKE+++LGL IDLE +
Sbjct: 1370 ESFNVIVKEIRSLGLDIDLEQN 1391


>gi|34580865|ref|ZP_00142345.1| DNA-directed RNA polymerase beta chain [Rickettsia sibirica 246]
 gi|28262250|gb|EAA25754.1| DNA-directed RNA polymerase beta chain [Rickettsia sibirica 246]
          Length = 1373

 Score = 1587 bits (4108), Expect = 0.0,   Method: Composition-based stats.
 Identities = 761/1358 (56%), Positives = 1023/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYTTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G+VI    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEVITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALYDIFRVLRPGEPANIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTVDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWSGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQIIVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|239947111|ref|ZP_04698864.1| DNA-directed RNA polymerase, beta subunit [Rickettsia endosymbiont of
            Ixodes scapularis]
 gi|239921387|gb|EER21411.1| DNA-directed RNA polymerase, beta subunit [Rickettsia endosymbiont of
            Ixodes scapularis]
          Length = 1371

 Score = 1586 bits (4106), Expect = 0.0,   Method: Composition-based stats.
 Identities = 759/1358 (55%), Positives = 1023/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TGA+ IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGAREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFDSKD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDSKDVIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITVDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++Y+LS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYNLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V +G
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKNG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  HVTDEVVYLSAIEEGKYKIGQANSKVDKDGKLQGEFINCRVEGGNFVMVEPHEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA D++D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDIKDSSLYVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++S+++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKAGQTITSEMLKSLSKGQFWQLTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ R   K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKDALDKRLATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL++GT +DIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLENGTVIDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI  L+ +YK     I  ++ FL ++ G       + +  ++ ++    +   GV  
Sbjct: 1154 LAKKISELVKEYKNKHIGIEQIKKFLLELYGENI--NYVLERSEEEIISFCNKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|157803327|ref|YP_001491876.1| DNA-directed RNA polymerase subunit beta [Rickettsia canadensis str.
            McKiel]
 gi|166229303|sp|A8EXK8|RPOB_RICCK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157784590|gb|ABV73091.1| DNA-directed RNA polymerase subunit beta [Rickettsia canadensis str.
            McKiel]
          Length = 1373

 Score = 1585 bits (4104), Expect = 0.0,   Method: Composition-based stats.
 Identities = 761/1358 (56%), Positives = 1023/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKIHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KDII+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDIIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVQNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L +    +G+  + +  + L G Y+
Sbjct: 257  FMPGHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAQKYFREGLNNVLVARETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + EI  + G++I    L  I   +I+++ +L V+   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPVSDEILAKIGEMITADMLNVINDLKIKNVNVLVVNPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AE +F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DRETALCDIFRVLRPGEPANIEAAEGLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D++MP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTLMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
            +VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  RVTDEVVYLSAIEEGKYKIGQANSKVDKDGVLQGEFINCRVEGGNFVMVEPHEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++       +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTL-AQKADGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V ED+FTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDIFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L ++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALSHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VRIF+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRIFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIVEHFVFSWLEKLLVGQVIINGPKQVKAGQTITTEVLKGLSKGQFWQLTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  +   +E +K  Y+  K  L  RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANIMNEIEQIKTHYDEKKEALNKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +Y+     I  ++ FL K+ G       + +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVQEYQNKKIAIEQIKKFLIKLYGENI--NSVLERSEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++AD D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLADQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|297170814|gb|ADI21834.1| hypothetical protein [uncultured gamma proteobacterium HF0130_25M15]
          Length = 1370

 Score = 1585 bits (4104), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1378 (51%), Positives = 984/1378 (71%), Gaps = 15/1378 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK    +D+PDL+ +Q  SY+ FL  ++ P++R N GLQA F ++
Sbjct: 1    MSFSFTEKKRIRKDFGKQKPALDVPDLLTLQVNSYEGFLQKDVDPEKRENVGLQATFNNL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KS 121
            FPI +FS  A LEFVSY  + P+F+  +C  R L+YA PL++  +LI +D +      K 
Sbjct: 61   FPIESFSKNARLEFVSYRLEEPEFNERECQLRGLSYAAPLRVKTKLITYDKNTDKETVKE 120

Query: 122  IKDIKEQ----SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
            +KDIK+      +Y G++PLMT+ GTF+I G  R++VSQLHRSPG+ FDHDKG    SGK
Sbjct: 121  VKDIKQTGDTTDVYFGEIPLMTEHGTFIINGTDRVIVSQLHRSPGVFFDHDKG-VQTSGK 179

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD+KD I  RIDRRRK+P T  L AL    +EI+  F+ K  
Sbjct: 180  LLFSARVIPYRGSWLDFEFDAKDNIFARIDRRRKIPATILLHALDFTDQEIIDIFFEKDS 239

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            Y          ++  D + G      +      + V+  GK++ +  +K +KE   K+L 
Sbjct: 240  YRLSKKGVEVEIN-TDHLKGTIAEFDIKFGR--KLVVSKGKRINALHIKKIKETRKKYLQ 296

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            I    L G  ++++IV+ +TGEI  ++ D +  + +E      + +I  +Y++ V+   Y
Sbjct: 297  IDESDLLGKILSQEIVDKKTGEIIAKSNDEVTTELIELFKEHGVNNIQTIYINDVDQGPY 356

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I N+L  D + D++ AL++IYR+MRPG+  T   A+++F  LFF+ ++YDLS VGR+K N
Sbjct: 357  ISNSLSIDPSSDKESALIEIYRMMRPGEPPTKEAADNLFTNLFFNDERYDLSEVGRMKFN 416

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             R+ +D       + KEDII ++K L+++RNG  T+DDID+LGNRR+R+VGEM +N +R+
Sbjct: 417  RRVGIDKDVGSSVLSKEDIINVLKTLINIRNGSDTVDDIDHLGNRRIRTVGEMAENAFRV 476

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+R+ER+++ER+S V+ + +MP+DLIN+KPV +A+ EFF SSQLSQ  +  N LS I H
Sbjct: 477  GLIRVERAVRERLSLVEQEELMPRDLINSKPVSAAIKEFFGSSQLSQFMDQNNPLSEIAH 536

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +ARVN YGF
Sbjct: 537  KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMAIYARVNEYGF 596

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +ETPYR+V +GK TN + YLSA++E N  IAQAN+ LD   +  +EL+  R   E  L+P
Sbjct: 597  LETPYRQVSNGKATNKIKYLSAIDEGNFVIAQANTMLDSKNNLVDELISARYQNEFTLMP 656

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             + I+++D SPKQ+VSIAASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTGME 
Sbjct: 657  PDSIEYMDVSPKQIVSIAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTGMER 716

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             VA  SG  I+AKR G V+ VDA R+VI   + +     SGVDIY L K+ RSNQNTC+N
Sbjct: 717  KVATDSGVTIIAKRGGTVDSVDASRVVIAVNDDEAITGESGVDIYNLTKYTRSNQNTCIN 776

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRPLVKVGD +++ D+IADG ST LG+LA+G+N+LVAFMPW+G+NFEDS+LISER+V ED
Sbjct: 777  QRPLVKVGDSIQKGDVIADGASTSLGELAIGQNLLVAFMPWNGFNFEDSILISERVVQED 836

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHIEE + +ARDTKLG EE+T DIPNV +  L+ +DE GI  +GAEV  GDILVGK
Sbjct: 837  RFTTIHIEELQCIARDTKLGSEEVTSDIPNVGDTALRKLDESGIAYIGAEVVAGDILVGK 896

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ITPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DVR+F+R G++K++RS 
Sbjct: 897  ITPKGESQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMDGTVIDVRVFSREGVEKDDRSN 956

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E  +IE + +D  D+  I++ +I++RL ++L  +NA  G K  K    +   L+    
Sbjct: 957  EIEAAEIESVRKDLKDQLRIVEADIFNRLEKLLLNKNAKVGRKKLK----IDKALLESMK 1012

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
              +W++  +Q++K+   +E+    ++  +   + + +   +KI+  D++PPGVL++VKVF
Sbjct: 1013 PQKWFEIKLQNQKLNDELETYYKAHKELEKEFKQKLEAARKKIEAYDELPPGVLKMVKVF 1072

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDK+AGRHGNKG++SRI+P EDMP+++DGTP+DIVLNPLGVPSRMNVGQI 
Sbjct: 1073 LAVKRRVQPGDKVAGRHGNKGVISRIVPVEDMPYMEDGTPIDIVLNPLGVPSRMNVGQIL 1132

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI--SDYDDDSVLR 1195
            ETHLGWA  GLG K+K+++ + +    +  LR+FL+KV  T   +EKI  +   D+ ++ 
Sbjct: 1133 ETHLGWAAKGLGSKVKTMLKEKEGASRVKALRTFLDKVYNTNKLSEKIPLNKLKDEEIVE 1192

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            ++E  K GVP+ TPVFDGA E  I  +L++ADL ESGQ+ L DG TGE FDRP+TVGY+Y
Sbjct: 1193 LSENLKDGVPMGTPVFDGARENEIKELLKLADLPESGQTRLIDGRTGEFFDRPITVGYMY 1252

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ L+E+L
Sbjct: 1253 ILKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLRELL 1312

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            T+KSDDV GRTR+Y+ IV G +  +TG PESFNVL+KE+++LGL++DL     + + K
Sbjct: 1313 TVKSDDVQGRTRMYKQIVDGTNEVDTGIPESFNVLMKEIRSLGLNMDLVEDPKQANEK 1370


>gi|302344363|ref|YP_003808892.1| DNA-directed RNA polymerase, subunit beta [Desulfarculus baarsii DSM
            2075]
 gi|301640976|gb|ADK86298.1| DNA-directed RNA polymerase, beta subunit [Desulfarculus baarsii DSM
            2075]
          Length = 1386

 Score = 1585 bits (4103), Expect = 0.0,   Method: Composition-based stats.
 Identities = 726/1381 (52%), Positives = 977/1381 (70%), Gaps = 17/1381 (1%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              RVRK FGK  +IIDIP+LI++QK SY+ FL  ++A   R + GL A F+SVFPI  FS
Sbjct: 8    RTRVRKNFGKIAKIIDIPNLIDMQKQSYERFLQKDVAHAARRDVGLHAVFRSVFPIRDFS 67

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G + LE+VSY+F   K+D ++CL R +T+  PLK+T+RL+V+D+D+ T  +SI+DIKEQ 
Sbjct: 68   GTSSLEYVSYDFGEVKYDEEECLARGMTFEAPLKLTVRLVVYDIDKETDVQSIRDIKEQE 127

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            IY G LPLMT  GTF++ G +R+VVSQLHRSPGI FDHD+GR   SGKLLY+ RIIP +G
Sbjct: 128  IYFGTLPLMTDRGTFIVNGTERVVVSQLHRSPGIFFDHDRGRTHSSGKLLYSARIIPLRG 187

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D+EFD KDI++VRIDRRRK PVT  L ALG  ++++L   Y K V+   G+     +
Sbjct: 188  SWIDLEFDPKDILYVRIDRRRKFPVTLLLKALGYSAQDLLDMMYVKDVFFIDGEQVKRKI 247

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                +M+G + +  + D +  + +++ GKK+T   +K L+E G+  + +  + L G + A
Sbjct: 248  QPE-IMMGREATMEIQDPEGEKPLVKLGKKITRRAIKRLEELGLDRIPVREEDLLGRFAA 306

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             D V+  TGE+       I  + L ++  + I ++P L++D    ++  R+TL  DK +D
Sbjct: 307  VDFVDAGTGELICSLNQPITHEILLKLRAAGIDEVPTLFIDGQTRSSSFRDTLELDKVED 366

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
              +A++DIYR +RP +  T  VA + FN LFF  + YDLS VGR+K+N+RL LD  +++R
Sbjct: 367  PDEAIIDIYRKLRPSNPPTLEVARTFFNNLFFSPEHYDLSAVGRLKVNLRLGLDVAEELR 426

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +R+EDI+  ++ L+DL++ +G  DDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER
Sbjct: 427  TLRREDIMEAVRQLIDLKDAEGPADDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKER 486

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +S  +I+++MP DLIN+KPV + V EFF +SQLSQ  +  N LS +TH RRLSALG GG+
Sbjct: 487  MSLQEIEALMPHDLINSKPVSAVVKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGL 546

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVH THYGRICP ET EG NIGL+ SL+++ARVN YGFIETPYR   DG+
Sbjct: 547  TRERAGFEVRDVHNTHYGRICPIETPEGPNIGLIVSLSTYARVNDYGFIETPYRTAGDGR 606

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            V  +  +LSA+EE +  IAQAN+ LD++G F  +LV  R  GE +L+  +++ ++D SP 
Sbjct: 607  VHAETRFLSALEEADHPIAQANALLDDEGRFVNDLVSVRKEGEFMLLGPQEVHYMDVSPN 666

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q+VS+AASL+PFLENDD+NR LMG NMQRQAVP+L+  AP VGTG+E VVA+ SG  +VA
Sbjct: 667  QLVSVAASLVPFLENDDANRALMGSNMQRQAVPVLRTMAPLVGTGIEEVVARDSGVCVVA 726

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               G++  VDA RIV+R  +     + S V IY+L+KFQRSNQNTC++Q+P+V  G  V 
Sbjct: 727  AADGVINDVDASRIVVRYDKPLTAQAHSQVKIYKLIKFQRSNQNTCISQKPIVVRGQRVV 786

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
            +  I+ADG + D GDLALG+N +VAFM W GYN+EDS+LISER+V +D+FTS+HIEEFE 
Sbjct: 787  KGQILADGAAVDHGDLALGQNAMVAFMSWGGYNYEDSILISERIVKDDIFTSVHIEEFET 846

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            +ARDTKLG EEITRDIPNV EE L N+DE GI+ +GAE+  GDILVGKITPKGE+ ++PE
Sbjct: 847  VARDTKLGKEEITRDIPNVGEEALANLDESGIVRIGAEIKAGDILVGKITPKGETQLSPE 906

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DV+DTSLRVP GV G V+D ++F+R GI+K+ER+ ++E E++  L +
Sbjct: 907  EKLLRAIFGEKAGDVKDTSLRVPPGVEGIVIDAKVFSRKGIEKDERAQAIEDEEVSSLLK 966

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKG------FKKSTVLSSDLISEYPRSQWWQ 1023
            D+ DE  I+ RN    +   L G+      K        +    L++  +      Q   
Sbjct: 967  DESDEVRIIHRNAMDDIEAFLKGRVLAKPLKNDMGRVLIEAKKELTAADLKGVTLQQLRH 1026

Query: 1024 FAVQ--DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              +   DE VQ + E +   Y     ++   F+NKI K++ GD++PPGV+++VKV+VAMK
Sbjct: 1027 LELAGVDEDVQSDFERIVDGYAEQIEMIRQAFENKIGKLRRGDELPPGVIKMVKVYVAMK 1086

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +  GDKMAGRHGNKG+VSRILP EDMP   DGTPVDIVLNPLGVPSRMNVGQ+ ETHL
Sbjct: 1087 RKLAVGDKMAGRHGNKGVVSRILPVEDMPHFADGTPVDIVLNPLGVPSRMNVGQVLETHL 1146

Query: 1142 GWACVGLGKKIKSLI-------NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            GWAC GLG+++  L           +    ++ L+ +L ++       + IS   D+ ++
Sbjct: 1147 GWACAGLGRRVGQLAEAVAAAREQMEKEARLAALKDYLTQIYSPEELAK-ISQSGDEGLV 1205

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            R A   + G+P++TPVFDGA E  I  +L +A L  +GQS+L DG TGEPFDR VTVG +
Sbjct: 1206 RNALWLEDGLPIATPVFDGASEAEIRRLLELAGLPTTGQSVLIDGRTGEPFDRTVTVGAM 1265

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE 
Sbjct: 1266 YMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYSLQEF 1325

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDDV GRTR+YE IV G +  E G PESFNVLVKE+QAL L ++L     +    +
Sbjct: 1326 LTVKSDDVAGRTRMYEKIVKGENHLEAGLPESFNVLVKELQALCLDVELVEQNRETPYVL 1385

Query: 1375 E 1375
            E
Sbjct: 1386 E 1386


>gi|145628895|ref|ZP_01784695.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
            22.1-21]
 gi|144979365|gb|EDJ89051.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
            22.1-21]
          Length = 1312

 Score = 1584 bits (4101), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1333 (52%), Positives = 946/1333 (70%), Gaps = 23/1333 (1%)

Query: 35   ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
             S+D F+  +        +GL+AAF+SVFPI + +G   L++V Y  + P+FDV +C  R
Sbjct: 2    DSFDKFIQKD----PEGQQGLEAAFRSVFPIVSNNGYTELQYVDYRLEEPEFDVRECQIR 57

Query: 95   DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
              TYA  L++ LRL+ +D    + ++++KDIKE  +YMG++PLMT +GTFVI G +R++V
Sbjct: 58   GSTYAAGLRVKLRLVSYDK--ESSSRAVKDIKENEVYMGEIPLMTDNGTFVINGTERVIV 115

Query: 155  SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
            SQLHRSPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD KD +  RIDRRRK+P 
Sbjct: 116  SQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFARIDRRRKLPA 175

Query: 215  TSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
            T  L ALG  +EEIL+ F+ KI +   GD     L    L  G   S  +     G+  +
Sbjct: 176  TIILRALGYTTEEILNLFFDKITFEIAGDKLLMTLVPERL-RGETASFDIE--ANGKVYV 232

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            E G+++T+  +K+L++  +  + + S+ + G   ++D V+ E+GEI   A   I  ++L 
Sbjct: 233  ERGRRITARHIKALEKDNISQVVVPSEYILGKVASKDYVDLESGEIICPANGEISLETLA 292

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
            ++  +    I  L+ + ++   YI  TL  D   D+  AL +IYR+MRPG+  T   +E+
Sbjct: 293  KLAQAGYTTIETLFTNDLDYGPYISETLRVDPTYDKTSALYEIYRMMRPGEPPTPESSEA 352

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            +FN LFF +++YDLSTVGR+K N  L     +    +  EDIIA+++ L+D+RNG+G +D
Sbjct: 353  LFNNLFFSAERYDLSTVGRMKFNRSLAFPEGEGAGILSNEDIIAVMRKLIDIRNGRGEVD 412

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++ PQDLIN KP+ +AV 
Sbjct: 413  DIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLDAITPQDLINPKPISAAVK 472

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET
Sbjct: 473  EFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIET 532

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLS ++E N  IAQANS+L
Sbjct: 533  PEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSVIDEANYIIAQANSNL 592

Query: 635  DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            DE+  FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 593  DENNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 652

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             NMQRQAVP L+A+ P VGTGME  +A  SG A+VAKR G V+ VDA RIVI+  E +  
Sbjct: 653  ANMQRQAVPTLRADKPLVGTGMEKPIALDSGVAVVAKRGGTVQYVDASRIVIKVNEDETI 712

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               +G+DIY L+K+ RSNQNTC+NQ P V +GD + R +++ADGPSTDLG+LALG+N+ V
Sbjct: 713  AGEAGIDIYNLIKYTRSNQNTCINQIPCVNLGDPINRGEVLADGPSTDLGELALGQNIRV 772

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            AFMPW+GYNFEDSML+SER+V +D FT+IHI+E   +ARDTKLG EEIT DIPNV E  L
Sbjct: 773  AFMPWNGYNFEDSMLVSERVVQQDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESAL 832

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+
Sbjct: 833  SKLDESGIVYVGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPN 892

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
            G SGTV+DV++F R G++K++R++ +E  Q+    +D  +E  IL+  +++R+  +L   
Sbjct: 893  GTSGTVIDVQVFTRDGVEKDKRALEIEEMQLREAKKDLTEELEILEAGLFARVRNLLISS 952

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             A              +  + +  R++W +  + DE+ Q  +E L  QYE  +   E + 
Sbjct: 953  GA-------------DAAQLDKLDRTKWLEQTIADEEKQNQLEQLAEQYEELRKEFEHKL 999

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + K +KI  GDD+ PGVL+VVKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ +
Sbjct: 1000 EVKRKKIIKGDDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDE 1059

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G PV+IVLNPLGVPSRMN+GQI ETHLG A  G+G +I +++   +    +        
Sbjct: 1060 NGQPVEIVLNPLGVPSRMNIGQILETHLGLAAKGIGDQINAMLKQKQEVEKLRSYIQKAY 1119

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             ++G GS    +S + D+ VLR+A   + G+PV+TPVFDGADE  I  +L++  L  SGQ
Sbjct: 1120 DLLGNGSQKVDLSTFTDEEVLRLAGNLRKGLPVATPVFDGADEAEIKELLKLGGLPTSGQ 1179

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR
Sbjct: 1180 ITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR 1239

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV+GN   E GTPESFNV++KE
Sbjct: 1240 FGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQHMEPGTPESFNVIMKE 1299

Query: 1354 MQALGLSIDLENS 1366
            +++LGL+I+L+  
Sbjct: 1300 IRSLGLNIELDEE 1312


>gi|148827706|ref|YP_001292459.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittGG]
 gi|148718948|gb|ABR00076.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            PittGG]
          Length = 1312

 Score = 1583 bits (4099), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1333 (52%), Positives = 946/1333 (70%), Gaps = 23/1333 (1%)

Query: 35   ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
             S+D F+  +        +GL+AAF+SVFPI + +G   L++V Y  + P+FDV +C  R
Sbjct: 2    DSFDKFIQKD----PEGQQGLEAAFRSVFPIVSNNGYTELQYVDYRLEEPEFDVRECQIR 57

Query: 95   DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
              TYA  L++ LRL+ +D    + ++++KDIKE  +YMG++PLMT +GTFVI G +R++V
Sbjct: 58   GSTYAAGLRVKLRLVSYDK--ESSSRAVKDIKENEVYMGEIPLMTDNGTFVINGTERVIV 115

Query: 155  SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
            SQLHRSPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD KD +  RIDRRRK+P 
Sbjct: 116  SQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFARIDRRRKLPA 175

Query: 215  TSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
            T  L ALG  +EEIL+ F+ KI +   GD     L    L  G   S  +     G+  +
Sbjct: 176  TIILRALGYTTEEILNLFFDKITFEIAGDKLLMTLVPERL-RGETASFDIE--ANGKVYV 232

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            E G+++T+  +K+L++  +  + + S+ + G   ++D V+ E+GEI   A   I  ++L 
Sbjct: 233  ERGRRITARHIKALEKDNISQVVVPSEYILGKVASKDYVDLESGEIICPANGEISLETLA 292

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
            ++  +    I  L+ + ++   YI  TL  D   D+  AL +IYR+MRPG+  T   +E+
Sbjct: 293  KLAQAGYTTIETLFTNDLDYGPYISETLRVDPTYDKISALYEIYRMMRPGEPPTPESSEA 352

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            +FN LFF +++YDLSTVGR+K N  L     +    +  EDIIA+++ L+D+RNG+G +D
Sbjct: 353  LFNNLFFSAERYDLSTVGRMKFNRSLAFPEGEGAGILSNEDIIAVMRKLIDIRNGRGEVD 412

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++ PQDLIN KP+ +AV 
Sbjct: 413  DIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLDAITPQDLINPKPISAAVK 472

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET
Sbjct: 473  EFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIET 532

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLS ++E N  IAQANS+L
Sbjct: 533  PEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSVIDEANYIIAQANSNL 592

Query: 635  DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            DE+  FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 593  DENNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 652

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             NMQRQAVP L+A+ P VGTGME  +A  SG A+VAKR G V+ VDA RIVI+  E +  
Sbjct: 653  ANMQRQAVPTLRADKPLVGTGMEKPIALDSGVAVVAKRGGTVQYVDASRIVIKVNEDETI 712

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               +G+DIY L+K+ RSNQNTC+NQ P V +GD + R +++ADGPSTDLG+LALG+N+ V
Sbjct: 713  AGEAGIDIYNLIKYTRSNQNTCINQIPCVNLGDPINRGEVLADGPSTDLGELALGQNIRV 772

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            AFMPW+GYNFEDSML+SER+V +D FT+IHI+E   +ARDTKLG EEIT DIPNV E  L
Sbjct: 773  AFMPWNGYNFEDSMLVSERVVQQDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESAL 832

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+
Sbjct: 833  SKLDESGIVYVGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPN 892

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
            G SGTV+DV++F R G++K++R++ +E  Q+    +D  +E  IL+  +++R+  +L   
Sbjct: 893  GTSGTVIDVQVFTRDGVEKDKRALEIEEMQLREAKKDLTEELEILEAGLFARVRNLLISS 952

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             A              +  + +  R++W +  + DE+ Q  +E L  QYE  +   E + 
Sbjct: 953  GA-------------DAAQLDKVDRTKWLEQTIADEEKQNQLEQLAEQYEELRKEFEHKL 999

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + K +KI  GDD+ PGVL+VVKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ +
Sbjct: 1000 EVKRKKIIKGDDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDE 1059

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G PV+IVLNPLGVPSRMN+GQI ETHLG A  G+G +I +++   +    +        
Sbjct: 1060 NGQPVEIVLNPLGVPSRMNIGQILETHLGLAAKGIGDQINAMLKQKQEVEKLRSYIQKAY 1119

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             ++G GS    +S + D+ VLR+A   + G+PV+TPVFDGADE  I  +L++  L  SGQ
Sbjct: 1120 DLLGNGSQKVDLSTFTDEEVLRLAGNLRKGLPVATPVFDGADEAEIKELLKLGGLPTSGQ 1179

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR
Sbjct: 1180 ITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR 1239

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV+GN   E GTPESFNV++KE
Sbjct: 1240 FGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQHMEPGTPESFNVIMKE 1299

Query: 1354 MQALGLSIDLENS 1366
            +++LGL+I+L+  
Sbjct: 1300 IRSLGLNIELDEE 1312


>gi|238752789|ref|ZP_04614257.1| DNA-directed RNA polymerase subunit beta [Yersinia rohdei ATCC 43380]
 gi|238708987|gb|EEQ01237.1| DNA-directed RNA polymerase subunit beta [Yersinia rohdei ATCC 43380]
          Length = 1287

 Score = 1583 bits (4099), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1305 (53%), Positives = 938/1305 (71%), Gaps = 18/1305 (1%)

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            +FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  +
Sbjct: 1    MFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--T 58

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY 
Sbjct: 59   VKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYN 118

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   + +IL  F+ K+V+  R
Sbjct: 119  ARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNFTTTQILDLFFEKVVFEIR 178

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
             +     L    L  G   S  +     G+  +E  +++T+  ++ L++ G+  + +  +
Sbjct: 179  DNKLQMELVPERL-RGETASFDIE--ANGKVYVEKARRITARHIRQLEKDGIDRIEVPVE 235

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++ AYI  T
Sbjct: 236  YIAGKVVAKDYIDENTGELICAANMELSLDLLAKLSQSGHKQIETLFTNDLDHGAYISET 295

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L 
Sbjct: 296  LRVDPTSDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLL 355

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D  +    + KEDI  ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 356  RDEIEGSGILSKEDITEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 415

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 416  VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 476  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R+++
Sbjct: 536  YRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 596  DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 656  DSGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPC 715

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+
Sbjct: 716  VNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTT 775

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 776  IHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 835

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E 
Sbjct: 836  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEE 895

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  +++R+  +L                 + +D +S+ PR +W
Sbjct: 896  MQLKQAKKDLTEELQILEAGLFARIHAVLVSGG-------------IEADKLSKLPRDRW 942

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE  Q  +E L  QY+  KS  E +   K  KI  GDD+ PGVL++VKV++A+K
Sbjct: 943  LELGLTDEDKQNQLEQLAEQYDEMKSEFEKKMDAKRRKITQGDDLAPGVLKIVKVYLAVK 1002

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1003 RQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHL 1062

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G+KI +++   +    +         +         +S + DD VLR+AE  K
Sbjct: 1063 GMAAKGIGEKINAMLKKQEEVAKLREFIQKAYDLGDNVCQKVDLSTFTDDEVLRLAENLK 1122

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+P++TPVFDGA E+ I  +L++  L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH
Sbjct: 1123 KGMPIATPVFDGATEKEIKELLQLGGLPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNH 1182

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 1183 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1242

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE  
Sbjct: 1243 VNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEEE 1287


>gi|6652720|gb|AAF22435.1| RNA polymerase beta subunit [Rickettsia conorii]
          Length = 1373

 Score = 1583 bits (4098), Expect = 0.0,   Method: Composition-based stats.
 Identities = 759/1358 (55%), Positives = 1022/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA P K+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPPKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYTTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYSGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVEDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQVKVGQTITTEMLKGLSKGQFWQIIVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIISFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|51473339|ref|YP_067096.1| DNA-directed RNA polymerase subunit beta [Rickettsia typhi str.
            Wilmington]
 gi|55584169|sp|P77941|RPOB_RICTY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|51459651|gb|AAU03614.1| RNA nucleotidyltransferase (DNA-directed) [Rickettsia typhi str.
            Wilmington]
          Length = 1374

 Score = 1582 bits (4097), Expect = 0.0,   Method: Composition-based stats.
 Identities = 770/1363 (56%), Positives = 1031/1363 (75%), Gaps = 9/1363 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             RVRK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRVRKNFGHINLVADIPNLIEIQKNSYERNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DVD+C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVDECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS-QRGDFWCFP 248
             W+D EFD+KD+I+ RIDR+RK+  T+ L A+GM++EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDFEFDAKDVIYFRIDRKRKLYATTLLRAIGMNTEEIMKFYYNSVTYKCIKNKGWSVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L +     G+  + +T + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAQKYFSIGLNNILVTHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ + E+ EI  + G++I    L+ I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPESDEILAKIGEMITADMLQVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  +++
Sbjct: 375  DRETALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEI 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I++ILV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+R+E+S+ E
Sbjct: 435  TVLTIDDIKNIVRILVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRIEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  YVTDEVVYLSAIEEGKYKIGQANSKVDQDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K EAPFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTEAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVE+VD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVERVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VRIF+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRIFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L G   +SGPK       ++++++    + Q WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGHVIISGPKQITAGQTITTEMLKGLSKGQLWQLIVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K+ Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKIHYDEKKHALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK N  DI  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAKKISTLVKEYKDNNIDIEQIKKFLLELYGKDI--NYILEGSEEGIISFCNKVSKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++AD D SGQ  L DG TGE FDR VTVG+ Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLADQDLSGQVKLIDGRTGEYFDRLVTVGHKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE + +K
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLEVTASK 1374


>gi|157825320|ref|YP_001493040.1| DNA-directed RNA polymerase subunit beta [Rickettsia akari str.
            Hartford]
 gi|166229301|sp|A8GMA7|RPOB_RICAH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157799278|gb|ABV74532.1| DNA-directed RNA polymerase subunit beta [Rickettsia akari str.
            Hartford]
          Length = 1373

 Score = 1582 bits (4096), Expect = 0.0,   Method: Composition-based stats.
 Identities = 758/1358 (55%), Positives = 1022/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+++ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVLYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKKKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L +    +G+  + +  + L G Y+
Sbjct: 257  FIPKHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAQKYCAEGINNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEIITSDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFDS++YDLS VGR+KMN RL L   ++V
Sbjct: 375  DREAALCDIFRVLRPGEPTNIEAAESLFYNLFFDSERYDLSEVGRIKMNSRLGLSISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYRKV DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRKVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
            +V ++V+YLSA+EE    I QANS +D DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  RVIDEVIYLSAIEEGKYKIGQANSKVDRDGKLQGEFINCRVEGGNFVMVEPHEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E  +D  +  V IY L+KFQ+SN NTC+NQ+PLV+VG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLEQKID-GSPSVYIYNLLKFQKSNHNTCINQKPLVQVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V ED+FTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDIFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++G K  K    ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSLLEKLLVGQVIINGLKQVKAGQTITTEMLKGLSKGQFWQLTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K+ Y+  K  L  RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKIHYDEKKDALNKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVVSRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L +KI +L+ +YK     I  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAQKISTLVKEYKNKNIGIEKIKKFLLELYGENI--NYILERSEEEIISFCNKVGKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|238650685|ref|YP_002916538.1| DNA-directed RNA polymerase subunit beta [Rickettsia peacockii str.
            Rustic]
 gi|259494192|sp|C4K1N9|RPOB_RICPU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|238624783|gb|ACR47489.1| DNA-directed RNA polymerase subunit beta [Rickettsia peacockii str.
            Rustic]
          Length = 1373

 Score = 1581 bits (4093), Expect = 0.0,   Method: Composition-based stats.
 Identities = 756/1358 (55%), Positives = 1020/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD  K+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTTKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYTTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNILLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITADMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+      AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPVNIEAAESLFYNLFFDTERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +V+ V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVAVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +++DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  CVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR +E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRILE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII +GAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYIGAEVQAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGV+GTVV+VR+F+R G++K++R+I++E++QIE  
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVNGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKF 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  ++GPK       ++++++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVIINGPKQATVGQTITTEMLKGLSKGQFWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K  Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKTHYDEKKEALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++   ++   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLIELYGENI--NSILERPEEEIIAFCKKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|6652726|gb|AAF22439.1|AF076437_1 RNA polymerase beta subunit [Rickettsia prowazekii]
          Length = 1374

 Score = 1581 bits (4093), Expect = 0.0,   Method: Composition-based stats.
 Identities = 764/1363 (56%), Positives = 1024/1363 (75%), Gaps = 9/1363 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRLRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP  G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYIG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D EFD+KDII+ RIDRRRK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDFEFDAKDIIYFRIDRRRKLYATTLLRAIGMSTEEIIKFYYNSVTYKFVKNKGWSVE 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LV  DTG  ++ +G+K+T  L +      +  + +T +   G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVYADTGNVLLNAGQKITPRLAQKYFGVSLNNILVTHETFIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L+ I   +I+++ +L ++   + +YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITSDMLKVINDLKIKNVNVLVINPQ-SGSYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I++ILV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRILVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V +G
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKNG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V  +++DFID +
Sbjct: 615  YVTDEVVYLSAIEEGKYKIGQANSKVDQDGKLQGEFINCRVEGGNFVMVEPDEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K EAPFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTEAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVE+VD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVERVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VRIF+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRIFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L G   ++GPK       ++++++    + Q WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGHVIINGPKQITAGQTITTEMLKGLSKGQLWQITVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +K+ Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKIHYDEKKYALDKRFTTKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK N  DI  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAKKISTLVKEYKDNHIDIEEIKKFLLELYGKDI--NYILEGSEEEIISFCNKVSKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML +A  D SGQ  L DG TGE FDR VTVG+ Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLELAGQDLSGQVKLIDGRTGEYFDRLVTVGHKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            + Y+SIV G + FE+G PESFNV++KE ++L L++ LE + +K
Sbjct: 1332 KTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLEVTPSK 1374


>gi|167626046|ref|YP_001676340.1| DNA-directed RNA polymerase subunit beta [Shewanella halifaxensis
            HAW-EB4]
 gi|167356068|gb|ABZ78681.1| DNA-directed RNA polymerase, beta subunit [Shewanella halifaxensis
            HAW-EB4]
          Length = 1316

 Score = 1580 bits (4092), Expect = 0.0,   Method: Composition-based stats.
 Identities = 686/1336 (51%), Positives = 941/1336 (70%), Gaps = 21/1336 (1%)

Query: 31   EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
             +Q  S+  F       D     G +AAF+SVFPI +FSG + L++VSY+   P FDV +
Sbjct: 2    SIQLDSFKKF----TDQDPTGERGFEAAFRSVFPIKSFSGNSELQYVSYKLGEPVFDVKE 57

Query: 91   CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
            C  R +TY+ PL++ LR++++D +   G  ++KDIKEQ +YMGD+PLMT +GTFVI G +
Sbjct: 58   CQIRGVTYSAPLRVKLRMVLYDREAAPG--TVKDIKEQEVYMGDIPLMTDNGTFVINGTE 115

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
            R++VSQLHRSPG+ FDHD+G+   SGK+LY  RIIP +G W+D EFD KD + VRIDRRR
Sbjct: 116  RVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDALFVRIDRRR 175

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
            K+  +  L AL   +++IL  F+ ++ +  + D     L A D + G   S  + D + G
Sbjct: 176  KLAASIILRALDYSTQDILDLFFDRVNFKIKKDSLVMDLVA-DRLRGETASYDIKDAE-G 233

Query: 271  EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
              ++E G+++T+  ++ L++     L +  + + G    +D ++ +TGE+ + A   I  
Sbjct: 234  TVLVEKGRRITARHIRQLEKSNTTELEVPVEYISGKISGQDYIDPDTGEVLVSANAEISL 293

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            + L ++  + I++I  LY++ ++N AYI +TL  D   +R +AL++IYR+MRPG+  T  
Sbjct: 294  EDLAKLSMAGIKEISTLYINELDNGAYISDTLRIDSTTNRLEALVEIYRMMRPGEPPTKD 353

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             AE++FN LFF  ++YDLS VGR+K N RL++D  +    + KEDI+A++K ++ +RNG 
Sbjct: 354  AAEALFNNLFFSEERYDLSKVGRMKFNRRLSIDDDEGTGILSKEDIVAVMKNIIAIRNGF 413

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
              +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER+++ER+S  D++ +MPQDLINAKP+ 
Sbjct: 414  DEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVRERLSLGDLNELMPQDLINAKPIS 473

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 474  AAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLC 533

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P ET EG NIGL++SL++FAR N YGF+ETPYRKV DG VT++V YLSA+EE    IAQA
Sbjct: 534  PIETPEGPNIGLINSLSTFARTNNYGFLETPYRKVIDGVVTDEVDYLSAIEEGRYVIAQA 593

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
               LDE+G   +EL+ CR  G+   +    I ++D SP+Q++S+AASLIPFLE+DD+NR 
Sbjct: 594  IVQLDENGRMMDELIACRHKGDSTFMGAADIQYMDVSPQQIISVAASLIPFLEHDDANRA 653

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            LMG NMQRQAVP LKA+ P VGTG+E  +A  SG  + AKR G V+ VDA RIV++  E 
Sbjct: 654  LMGANMQRQAVPTLKADKPLVGTGIERTLAVDSGVVVAAKRGGYVDYVDASRIVVKVNEA 713

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            +L P  +G+DIY L K+ RSNQNTC+NQRP   VGD + R D++ADGPSTDLGDLALG+N
Sbjct: 714  ELTPGEAGIDIYNLTKYTRSNQNTCINQRPCCSVGDPIVRGDVLADGPSTDLGDLALGQN 773

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            M +AFMPW+GYNFEDS+LISER+  ED FT+IHI+E   +ARDTKLG EEIT DIPNV E
Sbjct: 774  MRIAFMPWNGYNFEDSILISERVAQEDRFTTIHIQELSCIARDTKLGSEEITADIPNVGE 833

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLR
Sbjct: 834  SALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLR 893

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
            VP+ V GT++DV++F R G++K++R++ +E   I    +D  +E  IL+  +  R   +L
Sbjct: 894  VPNSVKGTIIDVQVFTRDGVEKDKRAVEIEEMHIAQAKKDLTEEFKILEDGVLGRARNLL 953

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
                          +T      ++  PRSQ     + DE  Q  +E L  Q E  K+  +
Sbjct: 954  L-------------ATGFDEAQLNAIPRSQLLVQTIDDEAKQTELEQLAEQAEELKADFD 1000

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
             +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP
Sbjct: 1001 KKFEIKRRKITQGDDLAPGVLKIVKVYLAVKRTIQPGDKMAGRHGNKGVISKICPVEDMP 1060

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            + + G PVDIVLNPLGVPSRMN+GQ+ E H+G A  G+G +I  ++ + +   ++     
Sbjct: 1061 YDEKGNPVDIVLNPLGVPSRMNIGQVLEVHMGAAAKGIGNRITEMLEEQRELAELRGYIK 1120

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
             + ++         I  + DD +LR+A+  K GVP++TP FDGA E+ I  ML +A L +
Sbjct: 1121 QVYELGDEVIQKVDIDSFTDDEILRLAKNLKGGVPIATPAFDGAKEKEIKQMLELAGLPQ 1180

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
            SGQ  L DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  G
Sbjct: 1181 SGQLTLIDGRTGNEFERKVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFG 1240

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   + G PESFNVL
Sbjct: 1241 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTQMYKNIVDGNYQMQPGMPESFNVL 1300

Query: 1351 VKEMQALGLSIDLENS 1366
            +KE+++LG++I+L+  
Sbjct: 1301 LKEIRSLGINIELDTK 1316


>gi|157826668|ref|YP_001495732.1| DNA-directed RNA polymerase subunit beta [Rickettsia bellii OSU
            85-389]
 gi|166229302|sp|A8GV24|RPOB_RICB8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157801972|gb|ABV78695.1| DNA-directed RNA polymerase subunit beta [Rickettsia bellii OSU
            85-389]
          Length = 1372

 Score = 1578 bits (4085), Expect = 0.0,   Method: Composition-based stats.
 Identities = 767/1358 (56%), Positives = 1023/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             RVRK FG    + DIP+LIE+QK SY+  FL ++    ER N+GLQ+   S+FPI+  S
Sbjct: 17   KRVRKNFGHINLVADIPNLIEIQKNSYEKNFLQLDTKDSERKNKGLQSILNSIFPISDPS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+Y   LK+TLRL ++D+DE TG++ IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECTQRSLSYDSALKVTLRLSIWDIDEDTGSREIKGIKEQQ 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMG++PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   S KLLY+ R+IP +G
Sbjct: 137  VYMGNIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSRKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KDII+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDIIYFRIDRKRKLYATTLLKAIGMSTEEIIKFYYDSVNYKVVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               + +    +++S L+D DTG  ++++G+K+T  L K    +G+  + ++ + L G Y+
Sbjct: 257  FMPSHI-TAHRLTSDLIDADTGNVLLKAGQKITPRLAKKYAGEGLNNILVSHEALIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ + E+ EI  + G++I  + L  I   +I++I +L ++   +  YIRNTL +DKN+
Sbjct: 316  SEDLKDPESDEILAKIGEMITVELLSVISDLKIKNISVLVINPQ-SGPYIRNTLFSDKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD ++YDLS VGR+KMN RL L+  D+ 
Sbjct: 375  DRESALFDIFRVLRPGEPANIEAAESLFYNLFFDPERYDLSEVGRIKMNSRLELNISDET 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++ KG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTTDDIKNILRVLVELKDRKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVVE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ DID+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDIDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYRKV DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRKVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  HVTDEVVYLSAIEEGKYKIGQANSKVDKDGILQGEFINCRVEGGNFVMVEPHEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR+  G    S   VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALNDGIVEQVDSNRIVIRA-IGQKTESAPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTS+HIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSVHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ +++GPK  K    ++S+++    + Q WQF V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVSINGPKTVKTGQTITSEILKGLSKGQLWQFTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E LK  Y+  K  L  RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQLKGHYDGKKEALNKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQ+ ETHLGWA V 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQVLETHLGWASVN 1153

Query: 1148 LGKKIKSLINDYK-ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI  L+ ++K  +  I  ++ FL ++ G       I +  D+ ++    +   GV  
Sbjct: 1154 LAKKIAGLVEEHKTKHASIEKIKKFLIELYGENI--NHILEKSDEEIISFCNEAAKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  E +  MLR+A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVEDVKDMLRLAGQDLSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            ++Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KIYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|85858138|ref|YP_460340.1| DNA-directed RNA polymerase subunit beta [Syntrophus aciditrophicus
            SB]
 gi|109914401|sp|Q2LQ87|RPOB_SYNAS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|85721229|gb|ABC76172.1| DNA-directed RNA polymerase beta chain [Syntrophus aciditrophicus SB]
          Length = 1363

 Score = 1576 bits (4080), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1364 (53%), Positives = 993/1364 (72%), Gaps = 15/1364 (1%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            RK FG+  EI+++P+LI++Q  SY+ FL  ++AP+ R N GLQ AFKSVFPI+ FSG   
Sbjct: 5    RKNFGRIEEILEVPNLIDIQTRSYETFLQEDVAPENRKNFGLQGAFKSVFPISDFSGKCS 64

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFVSY+    ++DV++C+ + +TYA PLKI +RL+VFD D  +  K+I+DIKEQ IY G
Sbjct: 65   LEFVSYKIGAVRYDVNECIQKGMTYAAPLKIVVRLVVFDTDRLSDQKNIRDIKEQEIYFG 124

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            ++PLMT+ GTF++ G +R++VSQLHRSPGI FDHDKG+   SGKL+Y+ RIIP +G W+D
Sbjct: 125  EIPLMTEKGTFIVNGTERVIVSQLHRSPGIFFDHDKGKTLTSGKLIYSARIIPIRGSWLD 184

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            +EFDSKD+++VRIDRRRK+PVT  L A+G  +E++L+ FY        G+ +       +
Sbjct: 185  LEFDSKDLLYVRIDRRRKMPVTILLKAMGYSTEDLLNYFYDVEHIFCEGENFYAA--VDE 242

Query: 254  LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
             +VG K+   + DI+TGE + + G+++   +LK ++E+ V+ + +  + L G  +A DI+
Sbjct: 243  SLVGHKLYDDIRDINTGEILFKKGRRINKVILKRIREQRVERIKMDVEELPGRILATDIL 302

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
            + ETGE+     + +    ++ +    IR++ ++ +    +N  IR+TL+ D+ +   DA
Sbjct: 303  DPETGEVLFHCNEALSAAGIDVVREKGIRELSVINLGEDLSNVSIRDTLLIDRMETPGDA 362

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            +++IYR +RP +  T   A+  FN LFF+++ YDLSTVGR KMN +L LD   DV  +RK
Sbjct: 363  IIEIYRRLRPSNPPTPDTAQKFFNSLFFENESYDLSTVGRAKMNYKLRLDVSTDVTVLRK 422

Query: 434  EDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            EDI+A +K L+DL+NG  + ++DDID+LGNRRVRSVGE+++NQYR+GL+RMER+IKE++S
Sbjct: 423  EDIMAAVKYLIDLKNGVPECSVDDIDHLGNRRVRSVGELIENQYRIGLVRMERAIKEKMS 482

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              DI+++MP DL+N KPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R
Sbjct: 483  LQDIETMMPHDLVNVKPVSAVVSEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTR 542

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGRICP ET EG NIGL+ SL+++ARVN +GFIETPYR V +G+V 
Sbjct: 543  ERAGFEVRDVHPTHYGRICPVETPEGPNIGLIVSLSTYARVNEFGFIETPYRIVKEGRVL 602

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             +V +L+A+EEEN+ IA A+  ++ DGSF  +L+  R  G+ + V   +++ +D SP Q+
Sbjct: 603  PEVKFLTAIEEENQVIAPADQPVNHDGSFKGDLISARKGGDFVNVVPSEVNMVDVSPNQL 662

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+AA+LIPFLE+DD+NR LMG NMQRQAVPL++ E P VGTGME +VA+ SGA +VAKR
Sbjct: 663  VSVAATLIPFLEHDDANRALMGSNMQRQAVPLMRPEIPLVGTGMERIVARDSGAVVVAKR 722

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +GIVE VDA RIVI+    +     +GVDIY L+K+QRSNQ+TC NQ+ +V  G  VR+ 
Sbjct: 723  SGIVESVDASRIVIKCESAEKTDRDTGVDIYTLIKYQRSNQDTCFNQKAIVNKGQRVRKG 782

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            DIIADGP+TD G+LALG N++VAFM W GYN+EDS+L+SER+V ED++TSIHIEEFE MA
Sbjct: 783  DIIADGPATDNGELALGHNVMVAFMSWGGYNYEDSILVSERIVKEDIYTSIHIEEFETMA 842

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG E+ITRDIPNV EE L+N+D+ GI+ +G  V  GDILVGKITPKGE+ ++ EEK
Sbjct: 843  RDTKLGKEDITRDIPNVGEEALRNLDDSGIVRMGVSVKSGDILVGKITPKGETQLSSEEK 902

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DVRDTSLRVP GV GTV+D ++F R G +K+ RS  +E E I +L +D+
Sbjct: 903  LLRAIFGEKASDVRDTSLRVPPGVEGTVIDAKVFTRKGAEKDHRSQYIEDEAIAMLQKDR 962

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLISEYPRSQWWQF 1024
            +DE  I+   +   +  +L G+ + +            KK  +++ +++SE P   W + 
Sbjct: 963  EDEIRIITEAVKKEVGTLLQGKQSGAKIVDPKRKKIYLKKGDIITPEILSEIPLHLWKEI 1022

Query: 1025 AV-QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
             V  DE+ +R V  +         ++E  F  K EK++  D++PPGV+++VKV++A+KR 
Sbjct: 1023 TVADDEETERAVGQMMANLYDKIEVVEAYFNEKTEKLKASDELPPGVIKMVKVYIAIKRK 1082

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q+GDKMAGRHGNKG++SRILP EDMP+ KDG PVDIVLNPLGVPSRMNVGQI ETHLGW
Sbjct: 1083 LQAGDKMAGRHGNKGVLSRILPEEDMPYFKDGRPVDIVLNPLGVPSRMNVGQILETHLGW 1142

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A  GLG+K+  +++ Y+       LR  L+ +  +    + +    ++   +   + + G
Sbjct: 1143 AAKGLGEKLNDMLDSYQKGNQ---LRDELKGIYQSREFEKFVDGATEEETYQFVRKLRRG 1199

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            + VS+PVFDGA E  I +ML++A+L  +GQ+ILYDG TGEPFD+ +TVG IYMLKL+H+V
Sbjct: 1200 IAVSSPVFDGATESDIRNMLKLANLPSTGQAILYDGRTGEPFDQEITVGMIYMLKLHHLV 1259

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             +K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV 
Sbjct: 1260 DNKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYSLQEFLTVKSDDVA 1319

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            GRTR+YE+IV G +T E G PESFNVLVKE+Q+L L ++L    
Sbjct: 1320 GRTRIYEAIVKGENTSEPGLPESFNVLVKELQSLCLDVELIEEE 1363


>gi|91205968|ref|YP_538323.1| DNA-directed RNA polymerase subunit beta [Rickettsia bellii RML369-C]
 gi|122425304|sp|Q1RHD0|RPOB_RICBR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|91069512|gb|ABE05234.1| DNA-directed RNA polymerase beta chain [Rickettsia bellii RML369-C]
          Length = 1372

 Score = 1575 bits (4079), Expect = 0.0,   Method: Composition-based stats.
 Identities = 766/1358 (56%), Positives = 1021/1358 (75%), Gaps = 9/1358 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             RVRK FG    + DIP+LIE+QK SY+  FL ++    ER N+GLQ+   S+FPI+  S
Sbjct: 17   KRVRKNFGHINLVADIPNLIEIQKNSYEKNFLQLDTKDSERKNKGLQSILNSIFPISDPS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+Y   LK+TLRL ++D+DE TG++ IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECTQRSLSYDSALKVTLRLSIWDIDEDTGSREIKGIKEQQ 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMG++PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   S KLLY+ R+IP +G
Sbjct: 137  VYMGNIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSRKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KDII+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDIIYFRIDRKRKLYATTLLKAIGMSTEEIIKFYYDSVNYKVVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               + +    +++S L+D DTG  ++++G+K+T  L K    +G+  + ++   L G Y+
Sbjct: 257  FMPSHI-TAHRLTSDLIDADTGNVLLKAGQKITPRLAKKYAGEGLNNILVSHKALIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ + E+ EI  + G++I  + L  I   +I++I +L ++   +  YIRNTL +DKN+
Sbjct: 316  SEDLKDPESDEILAKIGEMITVELLSVISDLKIKNISVLVINPQ-SGPYIRNTLFSDKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD ++YDLS VGR+KMN RL L+  D+ 
Sbjct: 375  DRESALFDIFRVLRPGEPANIEAAESLFYNLFFDPERYDLSEVGRIKMNSRLELNISDET 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++ KG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTTDDIKNILRVLVELKDRKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVVE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ DID+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDIDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYRKV DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRKVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  HVTDEVVYLSAIEEGKYKIGQANSKVDKDGILQGEFINCRVEGGNFVMVEPHEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR+       S   VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALNDGIVEQVDSNRIVIRA-IAQKTESAPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTS+HIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSVHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ +++GPK  K    ++S+++    + Q WQF V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLVGQVSINGPKTVKTGQTITSEILKGLSKGQLWQFTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E LK  Y+  K  L  RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQLKGHYDGKKEALNKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQ+ ETHLGWA V 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQVLETHLGWASVN 1153

Query: 1148 LGKKIKSLINDYK-ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI  L+ ++K  +  I  ++ FL ++ G       I +  D+ ++    +   GV  
Sbjct: 1154 LAKKIAGLVEEHKTKHASIEKIKKFLIELYGENI--NHILEKSDEEIISFCNEAAKGVYF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  E +  MLR+A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVEDVKDMLRLAGQDLSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            +++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR 
Sbjct: 1272 IHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRI 1331

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            ++Y+SIV G + FE+G PESFNV++KE ++L L++ LE
Sbjct: 1332 KIYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKLE 1369


>gi|42524381|ref|NP_969761.1| DNA-directed RNA polymerase beta chain [Bdellovibrio bacteriovorus
            HD100]
 gi|39576590|emb|CAE80754.1| DNA-directed RNA polymerase beta chain [Bdellovibrio bacteriovorus
            HD100]
          Length = 1422

 Score = 1574 bits (4076), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1384 (52%), Positives = 978/1384 (70%), Gaps = 21/1384 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F KN ++IDIP+LIE+QK+SY+ F+  ++ PD R + GL   FKSVFPIT F+  
Sbjct: 32   RVRKSFAKNKQVIDIPNLIELQKSSYEAFIQKDMDPDRRGDAGLNGVFKSVFPITDFNNT 91

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            A LEFVSY  +P K+DVD+C  R +T+A P+K+TLRLIVFDVDE T A+SI+D+KEQ +Y
Sbjct: 92   ASLEFVSYTLEPAKYDVDECRQRGMTFAAPIKVTLRLIVFDVDEETEARSIRDVKEQEVY 151

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G++PLMT +G+F+I G +R+VVSQLHRSPG+ FDHD G+ + SGKL+Y+ R+IP +G W
Sbjct: 152  LGEIPLMTANGSFIINGTERVVVSQLHRSPGVFFDHDGGKNNASGKLIYSARVIPYRGSW 211

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KD+IHVRIDRRRK PVT  L ALG +SE++L  FY       +G      L  
Sbjct: 212  LDAEFDQKDLIHVRIDRRRKFPVTILLKALGYNSEQLLEYFYDLDEVYVKGGKLFRKLDI 271

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
               M G +  + +VD  TGE ++++G+++T  ++K +K+  +  L +  + L G  +A+ 
Sbjct: 272  E-RMSGQRALTDIVDPKTGEALVKAGRRITRAIVKKIKDLDITELDVLPEDLEGKVLAKP 330

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +++  TGEI  +A   ++   ++    + I    +++ D +    Y+RNTL+ DK  +++
Sbjct: 331  LIDESTGEIIADANAELNAAIIKRSIEAGIESFFMIFFDGLTVGPYLRNTLLVDKVSNKE 390

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL---NLDTPDDV 428
            ++L++IY+ +RPG+  T   A + F  LFFD + YDLS VGR+K+N R      + P   
Sbjct: 391  ESLVEIYKRLRPGEPPTLEAATTFFGRLFFDPETYDLSEVGRIKINHRFGISMDECPPSH 450

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +  +DI++ IK L+DL+NG+G IDDID+LGNRRVRSVGE+L+NQYR+GL+RMER+I+E
Sbjct: 451  RTLTHKDILSTIKTLIDLKNGRGVIDDIDHLGNRRVRSVGELLENQYRIGLVRMERAIRE 510

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S  D++++MP DL+NAKPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 511  RMSLQDVETMMPHDLVNAKPVNAVVKEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 570

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL ++AR+N YGFIETPYRKV  G
Sbjct: 571  LTRDRAGFEVRDVHPTHYGRICPIETPEGPNIGLIASLATYARINNYGFIETPYRKVEAG 630

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            +V+ D+ YLSA+EE   +IA A      + +        R  GE  +V ++K+  +D SP
Sbjct: 631  QVSKDINYLSALEEAGHHIAPAARDEAGNKAIQTATTITRRDGEYEIVDKDKVALMDVSP 690

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+VSIAASLIPFLE+DD+NR LMG NMQRQAVPLL++ AP VGTG+E +VA+ SG +IV
Sbjct: 691  SQLVSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRSRAPLVGTGVERLVARDSGTSIV 750

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+  GIVE+VDA RIVIR          + VDIY L K+QR+NQNTC NQ+P+V VGD++
Sbjct: 751  AQNDGIVEEVDASRIVIRRF-AKGGELGANVDIYNLTKYQRTNQNTCFNQKPIVTVGDKI 809

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             + DIIADGPST+LG+LALG+N+LVAF PW GYNFEDS+LISER++ +DV+TSIHIEEFE
Sbjct: 810  SKGDIIADGPSTELGELALGQNILVAFTPWQGYNFEDSILISERLLKDDVYTSIHIEEFE 869

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +ARDTKLG EEITRDI NV EE LK++D  GII +GAEV PG ILVGK+TPKGE+ ++P
Sbjct: 870  CVARDTKLGKEEITRDIANVGEEALKDLDSSGIIRIGAEVRPGFILVGKVTPKGETQLSP 929

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DVRDTSLR PSGV GTV+D ++++R G D++ER   +  E+   L 
Sbjct: 930  EEKLLRAIFGEKAGDVRDTSLRAPSGVYGTVIDAQVYSREGADRDERLSLIIEEKKRKLE 989

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQ-------NAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +D   EQ ++  N  S+L +IL G+       N     K   K   ++   +   P    
Sbjct: 990  KDLAVEQNVIKNNAISKLRDILVGKITTGVLLNEDGSQKLLNKGQEITEADLETVPFELL 1049

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                ++ + ++  V  +          ++  F  KI++++ GD++PPGV+++VKV+VA+K
Sbjct: 1050 NYIPLEQD-LEFQVNKIIDNARNQLDAVKLVFNEKIDRLRKGDELPPGVIKMVKVYVAIK 1108

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDK AGRHGNKG+VS++LP EDMP+L DGTPVD+VLNPLGVPSRMN+GQI E HL
Sbjct: 1109 RKMQVGDKFAGRHGNKGVVSKVLPAEDMPYLADGTPVDMVLNPLGVPSRMNIGQILEVHL 1168

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA   LGK++ + +  + A       R+ ++ +      + K+   DD S+  + ++ K
Sbjct: 1169 GWAAHNLGKQLGAHLEKWNAENA----RTEMKDIFSDSDISAKLDKADDASLKSMVQRMK 1224

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+ V TPVFDGA E  +  +L  A +  SG+S+L+DG TGEPF  PVTVG +YMLKL+H
Sbjct: 1225 HGIHVGTPVFDGARESDVKGLLAKAQVPSSGKSVLFDGRTGEPFTNPVTVGIMYMLKLHH 1284

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARS G YSLV+QQPLGGK+  GGQRLGEMEVW I+AYGAAY LQE LT+KSDD
Sbjct: 1285 LVEEKIHARSIGPYSLVSQQPLGGKAQFGGQRLGEMEVWAIEAYGAAYSLQEFLTVKSDD 1344

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            V GRTR+YESIV G +  E G PESFNVLVKE+Q+L L+++L  S        ++  DF 
Sbjct: 1345 VAGRTRMYESIVKGENILEPGLPESFNVLVKELQSLALNVELMESD----ILRDQDEDFG 1400

Query: 1382 KCEL 1385
              E+
Sbjct: 1401 DEEV 1404


>gi|88909122|sp|Q6MJ09|RPOB_BDEBA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1412

 Score = 1574 bits (4075), Expect = 0.0,   Method: Composition-based stats.
 Identities = 723/1384 (52%), Positives = 978/1384 (70%), Gaps = 21/1384 (1%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F KN ++IDIP+LIE+QK+SY+ F+  ++ PD R + GL   FKSVFPIT F+  
Sbjct: 22   RVRKSFAKNKQVIDIPNLIELQKSSYEAFIQKDMDPDRRGDAGLNGVFKSVFPITDFNNT 81

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            A LEFVSY  +P K+DVD+C  R +T+A P+K+TLRLIVFDVDE T A+SI+D+KEQ +Y
Sbjct: 82   ASLEFVSYTLEPAKYDVDECRQRGMTFAAPIKVTLRLIVFDVDEETEARSIRDVKEQEVY 141

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G++PLMT +G+F+I G +R+VVSQLHRSPG+ FDHD G+ + SGKL+Y+ R+IP +G W
Sbjct: 142  LGEIPLMTANGSFIINGTERVVVSQLHRSPGVFFDHDGGKNNASGKLIYSARVIPYRGSW 201

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KD+IHVRIDRRRK PVT  L ALG +SE++L  FY       +G      L  
Sbjct: 202  LDAEFDQKDLIHVRIDRRRKFPVTILLKALGYNSEQLLEYFYDLDEVYVKGGKLFRKLDI 261

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
               M G +  + +VD  TGE ++++G+++T  ++K +K+  +  L +  + L G  +A+ 
Sbjct: 262  E-RMSGQRALTDIVDPKTGEALVKAGRRITRAIVKKIKDLDITELDVLPEDLEGKVLAKP 320

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +++  TGEI  +A   ++   ++    + I    +++ D +    Y+RNTL+ DK  +++
Sbjct: 321  LIDESTGEIIADANAELNAAIIKRSIEAGIESFFMIFFDGLTVGPYLRNTLLVDKVSNKE 380

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL---NLDTPDDV 428
            ++L++IY+ +RPG+  T   A + F  LFFD + YDLS VGR+K+N R      + P   
Sbjct: 381  ESLVEIYKRLRPGEPPTLEAATTFFGRLFFDPETYDLSEVGRIKINHRFGISMDECPPSH 440

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +  +DI++ IK L+DL+NG+G IDDID+LGNRRVRSVGE+L+NQYR+GL+RMER+I+E
Sbjct: 441  RTLTHKDILSTIKTLIDLKNGRGVIDDIDHLGNRRVRSVGELLENQYRIGLVRMERAIRE 500

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S  D++++MP DL+NAKPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 501  RMSLQDVETMMPHDLVNAKPVNAVVKEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 560

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL ++AR+N YGFIETPYRKV  G
Sbjct: 561  LTRDRAGFEVRDVHPTHYGRICPIETPEGPNIGLIASLATYARINNYGFIETPYRKVEAG 620

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            +V+ D+ YLSA+EE   +IA A      + +        R  GE  +V ++K+  +D SP
Sbjct: 621  QVSKDINYLSALEEAGHHIAPAARDEAGNKAIQTATTITRRDGEYEIVDKDKVALMDVSP 680

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+VSIAASLIPFLE+DD+NR LMG NMQRQAVPLL++ AP VGTG+E +VA+ SG +IV
Sbjct: 681  SQLVSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRSRAPLVGTGVERLVARDSGTSIV 740

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+  GIVE+VDA RIVIR          + VDIY L K+QR+NQNTC NQ+P+V VGD++
Sbjct: 741  AQNDGIVEEVDASRIVIRRF-AKGGELGANVDIYNLTKYQRTNQNTCFNQKPIVTVGDKI 799

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             + DIIADGPST+LG+LALG+N+LVAF PW GYNFEDS+LISER++ +DV+TSIHIEEFE
Sbjct: 800  SKGDIIADGPSTELGELALGQNILVAFTPWQGYNFEDSILISERLLKDDVYTSIHIEEFE 859

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +ARDTKLG EEITRDI NV EE LK++D  GII +GAEV PG ILVGK+TPKGE+ ++P
Sbjct: 860  CVARDTKLGKEEITRDIANVGEEALKDLDSSGIIRIGAEVRPGFILVGKVTPKGETQLSP 919

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DVRDTSLR PSGV GTV+D ++++R G D++ER   +  E+   L 
Sbjct: 920  EEKLLRAIFGEKAGDVRDTSLRAPSGVYGTVIDAQVYSREGADRDERLSLIIEEKKRKLE 979

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQ-------NAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +D   EQ ++  N  S+L +IL G+       N     K   K   ++   +   P    
Sbjct: 980  KDLAVEQNVIKNNAISKLRDILVGKITTGVLLNEDGSQKLLNKGQEITEADLETVPFELL 1039

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                ++ + ++  V  +          ++  F  KI++++ GD++PPGV+++VKV+VA+K
Sbjct: 1040 NYIPLEQD-LEFQVNKIIDNARNQLDAVKLVFNEKIDRLRKGDELPPGVIKMVKVYVAIK 1098

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +Q GDK AGRHGNKG+VS++LP EDMP+L DGTPVD+VLNPLGVPSRMN+GQI E HL
Sbjct: 1099 RKMQVGDKFAGRHGNKGVVSKVLPAEDMPYLADGTPVDMVLNPLGVPSRMNIGQILEVHL 1158

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA   LGK++ + +  + A       R+ ++ +      + K+   DD S+  + ++ K
Sbjct: 1159 GWAAHNLGKQLGAHLEKWNAENA----RTEMKDIFSDSDISAKLDKADDASLKSMVQRMK 1214

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+ V TPVFDGA E  +  +L  A +  SG+S+L+DG TGEPF  PVTVG +YMLKL+H
Sbjct: 1215 HGIHVGTPVFDGARESDVKGLLAKAQVPSSGKSVLFDGRTGEPFTNPVTVGIMYMLKLHH 1274

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARS G YSLV+QQPLGGK+  GGQRLGEMEVW I+AYGAAY LQE LT+KSDD
Sbjct: 1275 LVEEKIHARSIGPYSLVSQQPLGGKAQFGGQRLGEMEVWAIEAYGAAYSLQEFLTVKSDD 1334

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            V GRTR+YESIV G +  E G PESFNVLVKE+Q+L L+++L  S        ++  DF 
Sbjct: 1335 VAGRTRMYESIVKGENILEPGLPESFNVLVKELQSLALNVELMESD----ILRDQDEDFG 1390

Query: 1382 KCEL 1385
              E+
Sbjct: 1391 DEEV 1394


>gi|328953165|ref|YP_004370499.1| DNA-directed RNA polymerase subunit beta [Desulfobacca acetoxidans
            DSM 11109]
 gi|328453489|gb|AEB09318.1| DNA-directed RNA polymerase subunit beta [Desulfobacca acetoxidans
            DSM 11109]
          Length = 1386

 Score = 1573 bits (4074), Expect = 0.0,   Method: Composition-based stats.
 Identities = 735/1388 (52%), Positives = 989/1388 (71%), Gaps = 20/1388 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               VF+     RK FGK   IIDI +LIE+QK SY+ FL  +  P++R   GLQ  FKSV
Sbjct: 1    MAEVFSPQKLYRKNFGKIERIIDISNLIEMQKESYNRFLQKDTPPEQRGEFGLQGVFKSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPIT +SGAA LEFV+Y F  PK+D ++CL R +T+  P+K+T+RL+V+DV+  T  +SI
Sbjct: 61   FPITDYSGAASLEFVNYSFAEPKYDEEECLQRGMTFEAPMKLTVRLVVYDVESETKMQSI 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DIKEQ IY G +PLMT +GTF++ G +R++VSQLHRSPG+  DHD+GR   SGKLLY+ 
Sbjct: 121  RDIKEQEIYFGTMPLMTDNGTFIVNGTERVIVSQLHRSPGLFIDHDRGRTHSSGKLLYSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KDI++ RIDRRRK PVT  L ALG  +EE+L+ FY         
Sbjct: 181  RLIPMRGSWIDFEFDPKDILYARIDRRRKFPVTVLLKALGYSTEELLNFFYKTEKVFLDS 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +      +   L+   KVS  +VD  TGE +++  KK+T  L++ L++ GV+ L +    
Sbjct: 241  EGIEKKFNPEFLLQ-RKVSMDIVDPSTGELLVKKNKKITPELIRKLQKAGVERLSLMPGE 299

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G  VA DI++ E GE+ I   + + E+ L+ +    IR+I +LY++ +N +  +RNTL
Sbjct: 300  IIGRVVAHDILDTENGEVLINCNEPVTEEKLDRLRQRRIREIDVLYIEGINVSPCLRNTL 359

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              DK    ++A+ +IYR +RPG+  T  VA + F+ LFF  + YDLS VGR+K+N++L  
Sbjct: 360  AVDKTGSTREAIFEIYRKLRPGNPPTLEVAANFFDNLFFRPEYYDLSPVGRLKLNLKLKR 419

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            + P     + KEDI+  ++ L+  +  +G IDDID+LGNRRVR+VGE+L+NQYR+GL+RM
Sbjct: 420  EAPVTQSTLDKEDILFAVRELITQKELEGPIDDIDHLGNRRVRAVGELLENQYRIGLVRM 479

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+IKER+S  +ID++MP DLINAKPV   V EFF +SQLSQ  +  N LS ITH RRLS
Sbjct: 480  ERAIKERMSLQEIDALMPHDLINAKPVSGVVKEFFGTSQLSQFMDQTNPLSEITHKRRLS 539

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+ SL+++ARVN +GFIETPY
Sbjct: 540  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIVSLSTYARVNEFGFIETPY 599

Query: 603  RKVCDG--------KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            R V            V+  + +LSA++E +  IAQAN+ LD+D  F  +L+  R AGE I
Sbjct: 600  RVVEKKEENGVWSVHVSRQIKFLSALDEGDNVIAQANAPLDQDSRFINDLISARQAGESI 659

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +V  E++D++D SP Q+VS+AASLIPFLENDD+NR LMG NMQRQAVPLL    P +GTG
Sbjct: 660  MVRPEEVDYMDVSPSQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLLTCTPPLIGTG 719

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E+VVA+ SG  +VAKR+GIVE VD  RIV+R+  GD   S S VDIY+L KFQR+NQNT
Sbjct: 720  LENVVARDSGVTLVAKRSGIVEVVDGTRIVVRAYNGDEGDSQSIVDIYKLTKFQRTNQNT 779

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C NQRP+VK GD V +  IIADGP+T  G+LALG+N++VAFMPW GYNFEDS+L+SER+ 
Sbjct: 780  CFNQRPIVKPGDRVEKGQIIADGPATAFGELALGKNVMVAFMPWGGYNFEDSILVSERIA 839

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             EDVFTS+HIEEFEV+ARDTKLG EEITRDIPNVSEE L N+DE GII +GAE+ PGDIL
Sbjct: 840  KEDVFTSVHIEEFEVVARDTKLGKEEITRDIPNVSEEALANLDESGIIRIGAEIKPGDIL 899

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ ++PEEKLLRAIFGEKA DVRDTSLRVP G+ G ++D RIF+R G++K+E
Sbjct: 900  VGKVTPKGETQLSPEEKLLRAIFGEKAGDVRDTSLRVPPGIEGIIIDARIFSRKGVEKDE 959

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF-------KKSTV 1007
            RS ++E E I  L +D+ DE  I+ +++  RL E+L  Q     P          +K  +
Sbjct: 960  RSRAIEAEAIAKLQKDQGDEISIITQSVSHRLKELLVNQTVFDIPDDITSASYILEKGVI 1019

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            ++ D++++ P   W   +  + +++ +V+ L   Y+     + ++F+ KI +++  D++P
Sbjct: 1020 ITPDMVTKLPLHHWRNVSFDNPELEGSVDRLLESYQVQIQQVNNQFEEKINRLRKVDELP 1079

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV+++VKVF+AMKR +  GDKMAGRHGNKG+VSRILP EDMP+  DGTPVDIVLNPLGV
Sbjct: 1080 PGVIKMVKVFIAMKRKLAVGDKMAGRHGNKGVVSRILPEEDMPYFADGTPVDIVLNPLGV 1139

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMNVGQ+ ETHLGWA   LG++I+ LI+++    D+  +++ +  +         +  
Sbjct: 1140 PSRMNVGQVLETHLGWASRLLGQQIRRLIDEFY---DLDAVKNRIRALYNNPQVDAWLES 1196

Query: 1188 YDDDSVLRVAEQW-KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
               + + +  E++ K G+ +++PVFDGA E  I + L  A + E G++ L+DG TGEPFD
Sbjct: 1197 ATLEDIRQFWEKFHKEGMFMASPVFDGALESEIRACLTQAGVSEVGKAKLFDGRTGEPFD 1256

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            R VTVG +YM+KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYG
Sbjct: 1257 RSVTVGTMYMMKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYG 1316

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE LT+KSDDV GRTR+YE IV G    E G PESFNVL++E+Q+L L+++L   
Sbjct: 1317 AAYSLQEFLTVKSDDVAGRTRMYEKIVKGQYDLEAGLPESFNVLIRELQSLALNVELLED 1376

Query: 1367 RTKNSAKM 1374
            +    A+ 
Sbjct: 1377 KESEVAEN 1384


>gi|33520000|ref|NP_878832.1| DNA-directed RNA polymerase subunit beta [Candidatus Blochmannia
            floridanus]
 gi|41017672|sp|Q7VRP7|RPOB_BLOFL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|33504346|emb|CAD83239.1| DNA-directed RNA polymerase, beta-subunit [Candidatus Blochmannia
            floridanus]
          Length = 1342

 Score = 1572 bits (4070), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1363 (51%), Positives = 957/1363 (70%), Gaps = 21/1363 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL++AF+SV
Sbjct: 1    MVFSYTEKKRIRKDFGKRPQVLDIPYLLSIQLGSFQKFVKKD----PEGQNGLESAFRSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G A L ++ Y+   P FDV +C  R +T+A PL++ L L++++ D      +I
Sbjct: 57   FPIKSYNGNAELRYLDYKLGEPVFDVKECQIRGMTFAAPLRVQLCLVIYERDGSAYN-TI 115

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K  ++Q +YMG++PLMT +GTF+I GI+R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 116  KRTQQQEVYMGEIPLMTDNGTFIINGIERVVVSQLHRSPGVFFDSDKGKTHSSGKILYTA 175

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD + VRIDRRRK+PVT  L AL   +++IL+TF+  +VY  + 
Sbjct: 176  RIIPYRGSWLDFEFDLKDNLFVRIDRRRKLPVTVLLRALDYTNDQILNTFFNTVVYEFKD 235

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G  VS  +   D     +E G+++TS  +  LK   +  + +  + 
Sbjct: 236  DLLFMNLVPERL-RGETVSFDIKANDI--IYVERGRRITSKHINKLKADNIIKVEVPLNY 292

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  + +D ++ + GE+ + A   I    L  +  S    I  L+ + ++   YI  TL
Sbjct: 293  LMGKVIIKDYLDIKNGELIVAANTEISMDILHNLVKSGFNIIETLFSNDLDYGNYISETL 352

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D    R DAL++IYRVMRPG+  T   AE +F  LFF  ++YDLS VGR+K N  L  
Sbjct: 353  RIDSTVTRFDALVEIYRVMRPGEPPTKEAAEYLFESLFFLEERYDLSDVGRMKFNRSLQR 412

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            D       + K DII +IK L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 413  DDISGSGVLTKNDIIDVIKKLIDIRNGKGDVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 472

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 473  ERAVKERLSLGDLDVLTPQDLINAKPISAAVREFFNSSQLSQFMDQNNPLSEITHKRRIS 532

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 533  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNKYGFLETPY 592

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R+VCDGKV+ND+ YLSA+EE +  IAQAN++L++DG F ++L+ CR  GE  L  +++ID
Sbjct: 593  RRVCDGKVSNDIHYLSAIEEGDFIIAQANTNLNKDGQFIDDLITCRNKGESGLFRKDQID 652

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP++++E P VGTGME  VA  
Sbjct: 653  YMDVSTQQIVSVAASLIPFLEHDDANRALMGANMQRQAVPVIRSEKPLVGTGMERSVAVD 712

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  +VAKR G+V+ VDA RIVI     ++    +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 713  SGVTVVAKRGGMVKYVDASRIVIHVNVNEISVEEAGIDIYNLKKYVRSNQNTCINQRPCV 772

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            ++G+ +++ D+IADGPSTDLG+LALG+NM +AFMPW+GYNFEDSML+SER+V ED FTSI
Sbjct: 773  ELGELIKKGDVIADGPSTDLGELALGQNMRIAFMPWNGYNFEDSMLVSERVVQEDRFTSI 832

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPN+ E  L  +DE G++ +GAEV  GDILVGKITPKG
Sbjct: 833  HIQELSCISRDTKLGPEEITSDIPNIGETALSKLDEVGVVYIGAEVVGGDILVGKITPKG 892

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G+ GTV+DV+IF R GI K++R++++E  
Sbjct: 893  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGICGTVIDVQIFTRDGIKKDKRALNIELT 952

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ++  + +D  +E  I +  ++ R+  +L          G KK      + + +  R  W 
Sbjct: 953  KLNQIKKDLGEELKIFESALFDRVYALLISS-------GVKK------ESLLDMNRCAWL 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               ++D   Q  +  L  QY   K I E++   + +KI  GD++ PG+L+VVKV++A+KR
Sbjct: 1000 NLKLKDITKQNQLLQLSHQYLDLKRIFEEKISIQYQKITQGDELAPGILKVVKVYLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 QIQPGDKMAGRHGNKGVISKINPVEDMPYDEYGVPVDIVLNPLGVPSRMNIGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I  ++  ++    +        K+         ++ + D  VLR+A+  KS
Sbjct: 1120 MAAKGIGDQINLMLQQHQEINKLRKFIQKAYKLGVGVRQNIDLNTFSDLEVLRLAKNLKS 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E+ I  +L+++ L  SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1180 GMPIATPVFDGATEQEIKELLQLSGLPTSGQITLFDGCTGEVFERKVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             GRT++Y++I+ GN   E G PESFNVL+KE+++L ++I+L++
Sbjct: 1300 NGRTKMYKNIIDGNHMMEPGMPESFNVLLKEIRSLAINIELDD 1342


>gi|1325955|emb|CAA91164.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 1389

 Score = 1569 bits (4063), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1398 (48%), Positives = 931/1398 (66%), Gaps = 45/1398 (3%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P LI  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLEVPFLIATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+ L  F  +       
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQNLGYFLRQRNVLFVF 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                                 ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  KRCSNRFG-RRPSESETAKVDILD-KEGNVLVAKGKRITAKNIRDITLAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++         
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGVISPIPC 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            V  K   R+ A + IYR+MRP +  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  VRMKTAGRQAARVAIYRMMRP-EPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 415

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 416  QKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 475

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 476  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 535

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 536  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 595

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN  LD DG+ 
Sbjct: 596  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANGDLDSDGNL 655

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 656  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRPLMGANMQRQA 715

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
               L+ E P VGTG+E  VA  S  AIVA+R  +VE VDA R+VIR  + +      GVD
Sbjct: 716  SACLRPEKPMVGTGIERSVAVDSATAIVARR-AVVEYVDANRVVIRVHDDEATAGEVGVD 774

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+ 
Sbjct: 775  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNV 834

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
             N+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 835  NNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 894

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 895  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 954

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 955  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1014

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +K
Sbjct: 1015 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKKK 1074

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1075 LTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 1134

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++ + +  G++    + L +     
Sbjct: 1135 IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIDRMLKEQRKAGELREFLNRLSR----S 1190

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
               E +    D+ ++ +A   + G   ++PVFDGA E  I  ML +A   E         
Sbjct: 1191 GKKEDLDSLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDAEVEKLGF 1250

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 Q  LYDG +GE FDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+
Sbjct: 1251 NDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKA 1310

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PES 
Sbjct: 1311 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESL 1370

Query: 1348 NVLVKEMQALGLSIDLEN 1365
            NVLVKE+++LGL IDLE 
Sbjct: 1371 NVLVKEIRSLGLDIDLER 1388


>gi|27904547|ref|NP_777673.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. Bp
            (Baizongia pistaciae)]
 gi|31340404|sp|Q89B20|RPOB_BUCBP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|27903944|gb|AAO26778.1| DNA-directed RNA polymerase beta chain [Buchnera aphidicola str. Bp
            (Baizongia pistaciae)]
          Length = 1343

 Score = 1568 bits (4060), Expect = 0.0,   Method: Composition-based stats.
 Identities = 687/1362 (50%), Positives = 973/1362 (71%), Gaps = 22/1362 (1%)

Query: 5    VVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP 64
                   R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL++AF+S+FP
Sbjct: 4    YSSTEKKRIRKDFGKRPKVLDIPYLLSIQLNSFQKFIKHD----PNGIHGLESAFRSIFP 59

Query: 65   ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            I +++G + L++++Y+   P F+V +C  R +TY+ PL++ LRL++++    T   ++KD
Sbjct: 60   IRSYNGNSELQYINYKLGQPIFNVKECQTRGMTYSSPLRVKLRLVIYEK--ETLDITVKD 117

Query: 125  IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
            IKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  RI
Sbjct: 118  IKEQEVYMGEIPLMTTNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNARI 177

Query: 185  IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
            IP +G W+D EFD KD +  RIDRRRK+P++  L AL  ++E+IL TF+ K ++    + 
Sbjct: 178  IPYRGSWLDFEFDPKDNLFFRIDRRRKLPISIILKALNYNTEQILDTFFKKNIFKFTENS 237

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                L     + G   S  +      +  I+ G+++T+  +  LKEK +  + + ++ L 
Sbjct: 238  ILMKLVP-HRLRGETASFDICI--DNKTYIKKGQRITARHINILKEKKIHTIKVPTEYLI 294

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
            G   A++  N +T EI + A   ++   ++E+ ++E  +I  ++ + +++  YI  TL  
Sbjct: 295  GKISAKNYFNKKTNEIIVSANTELNINIIKELKNNEYTNIETIFTNDLDHGPYISETLNI 354

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D   D+  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS+VGR+K N  L    
Sbjct: 355  DPTHDKLSALVEIYRMMRPGEPPTREAAENLFENLFFSEERYDLSSVGRMKFNRSLQKQN 414

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              +   + + DII++IK L+D+RNG G IDDID+LGNRRVRSVGEM +NQ+R+GL+R+ER
Sbjct: 415  ITERGVLNQSDIISVIKKLIDIRNGHGEIDDIDHLGNRRVRSVGEMAENQFRIGLIRVER 474

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++K+R+S  D+D +MPQD+INAKP+ +A+ EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 475  AVKDRLSLGDLDMLMPQDMINAKPISAAIKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 534

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N+YGF+ETPYRK
Sbjct: 535  GLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNSYGFLETPYRK 594

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            + +GKVTN++ YLSA+EE N  IAQAN++LDE G+F E+L+ CR  GE  L  + +I+++
Sbjct: 595  IHNGKVTNEIKYLSAIEEGNFIIAQANTNLDETGAFVEDLITCRYKGESSLFNKNQINYM 654

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME  VA  SG
Sbjct: 655  DVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGMERAVAVDSG 714

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              I+AKR GIV+ VDA RI+I+  + +++   +G+DIY L K+ RSNQNTC+NQ P + +
Sbjct: 715  VTIIAKRGGIVQYVDASRIIIKVKKNEINSEEAGIDIYNLKKYTRSNQNTCINQIPCISL 774

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G+ V + +++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+LISE++V ED FT+IHI
Sbjct: 775  GENVEKGNVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILISEKVVQEDRFTTIHI 834

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E   ++RDTKLG EEIT DIPNV E  L  +DE GI+ +GAEVN GDILVGK+TPKGE+
Sbjct: 835  QELACISRDTKLGSEEITSDIPNVGEAALSKLDESGIVYIGAEVNGGDILVGKVTPKGET 894

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTV+DV+IF R G+ K++R++ +E  Q+
Sbjct: 895  QLTPEEKLLRAIFGEKASDVKDSSLRVPNGVLGTVIDVQIFTRDGVKKDKRALEIEEMQL 954

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            +   +D  +EQ + +  +++++   L                 ++ D +++ P+S+ ++ 
Sbjct: 955  KQAKKDLTEEQKVFELGLFTQIKSTLINSG-------------MNIDQLNKIPKSELFKV 1001

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             V +   Q+ +  L ++YE  K     + +    KI  GDD+ PGVL++VKV++A+KR I
Sbjct: 1002 KVTNNLYQKKIHKLFLKYEELKKCFNKKLETTRNKITQGDDLAPGVLKIVKVYLAVKRHI 1061

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG++S+I P EDMP+ ++G PVD+VLNPLGVPSRMN+GQI ETHLG A
Sbjct: 1062 QPGDKMAGRHGNKGVISKINPIEDMPYDQNGLPVDVVLNPLGVPSRMNIGQILETHLGLA 1121

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
              GLG  I +++   K+  +I         +         ++++ DD +L +A+ +K+G+
Sbjct: 1122 SKGLGNIIDTMLKQQKSILNIRKFIQKAFNLGNNTRQKTNLNNFSDDEILSLAKNFKNGI 1181

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P+STPVFDGA E  I ++L++ADL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+V 
Sbjct: 1182 PISTPVFDGAQESEIKALLKLADLPSSGQITLFDGRTGEKFERPVTVGYMYMLKLNHLVD 1241

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV G
Sbjct: 1242 DKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG 1301

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            RT++Y++IV GN   E G PESFNVL+KE+++L ++I+LEN 
Sbjct: 1302 RTKMYKNIVDGNYKMEPGMPESFNVLLKEIRSLAINIELENE 1343


>gi|297172929|gb|ADI23890.1| hypothetical protein [uncultured gamma proteobacterium HF4000_48J03]
          Length = 1371

 Score = 1564 bits (4049), Expect = 0.0,   Method: Composition-based stats.
 Identities = 701/1373 (51%), Positives = 973/1373 (70%), Gaps = 18/1373 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK    +D+P+L+ +Q  SY+ FL  +I P++R N GL+AAF ++
Sbjct: 1    MTYSFTEKKRIRKDFGKQKSALDVPNLLLIQLDSYNVFLQKDINPEKRENTGLEAAFNTL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KS 121
            FPI +FS  A LEFVSY  + P F V +C  R L+YA PL++  +L  ++ +      K 
Sbjct: 61   FPIESFSKNAKLEFVSYRLEEPMFSVRECQLRGLSYAAPLRVKTKLTTYNKETGKHTVKE 120

Query: 122  IKDIK----EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
            +K+IK       +Y G++PLMT+ GTFVI G  R++VSQLHRSPG+ FDHDKG    SGK
Sbjct: 121  VKNIKVSGDTTDVYFGEIPLMTEHGTFVINGTDRVIVSQLHRSPGVFFDHDKGA-QSSGK 179

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD+KD I  RIDRRRK+PVT  L AL +  EEIL TF+ K  
Sbjct: 180  LLFSARVIPYRGSWLDFEFDAKDAIFARIDRRRKIPVTVILHALDLSDEEILDTFFEKDK 239

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK--F 295
            YS         ++  D + G      +      + ++  G  +  G LK LK  GVK  +
Sbjct: 240  YSISKKDIKLKINP-DHLKGTVSDFDIKVGR--KLIVSKGNIVNVGHLKQLKNSGVKGAY 296

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            L + ++ L    +++D+++ ETGE+   A +++    +E +  ++I++I  +Y++ +++ 
Sbjct: 297  LTVPAEHLEDKIMSQDVIDQETGELLASANEILTADKIELLIANDIKEIETIYINDLDHG 356

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            +YI N+L  D +  + +AL++IYR+MRPG+  T   +E++F  LFF+ ++YDLS VGR+K
Sbjct: 357  SYISNSLRIDPSSSKLEALIEIYRMMRPGEPPTKDSSENLFQNLFFNPERYDLSDVGRMK 416

Query: 416  MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             N R+   +      + KEDII ++K L+++RN K T+DDID+LGNRR+R+VGEM +N +
Sbjct: 417  FNRRIGKKSDSGSSILSKEDIIDVLKTLINIRNSKDTVDDIDHLGNRRIRTVGEMTENAF 476

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+R+ER++K+R+S V+ + +MP+DLIN+KPV +A+ EFF SSQLSQ  +  N LS I
Sbjct: 477  RVGLIRVERAVKDRLSLVETEELMPRDLINSKPVSAAIKEFFGSSQLSQFMDQNNPLSEI 536

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
             H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A+VN +
Sbjct: 537  AHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAKVNKF 596

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPY+KV  GKVT  + YLSA++E    IAQAN+ +D       EL+  R   E  L
Sbjct: 597  GFLETPYQKVVKGKVTKKIEYLSAIDESQYVIAQANTPIDAQNRLQGELISSRYNNEFSL 656

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            +P +KID++D SPKQ+VSIAASLIPFLE+DD+NR LMG NMQRQAVP L AE P VGTGM
Sbjct: 657  MPVDKIDYMDVSPKQIVSIAASLIPFLEHDDANRALMGSNMQRQAVPTLLAETPLVGTGM 716

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +VA  SG  I+AKR G+V+ VDA RIVI   + +     SGVDIY L K+ RSNQNTC
Sbjct: 717  ERIVATDSGVTIIAKRGGVVDSVDASRIVIAVDDEETQSGESGVDIYSLTKYTRSNQNTC 776

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +NQRPLVKV D++   D+IADG ST LG+LA+G+N+LVAFMPW+G+NFEDS+LISE+++ 
Sbjct: 777  INQRPLVKVRDKISIGDVIADGASTSLGELAIGQNLLVAFMPWNGFNFEDSILISEKVLK 836

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++ FT+IHIEE + +ARDTKLG EEIT DIPNV +  L+ +DE GI  +GAEV  GDILV
Sbjct: 837  DERFTTIHIEELQCIARDTKLGSEEITADIPNVGDAALRKLDESGIAYIGAEVVAGDILV 896

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPKGE+ ++PEEKLLRAIFGEKA DV+DTSLRVPSG+ G V+DVR+F+R G++K++R
Sbjct: 897  GKITPKGETQLSPEEKLLRAIFGEKASDVKDTSLRVPSGMDGAVIDVRVFSREGVEKDDR 956

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            + ++E   ++ + +D +D+Q I++ +IY+R+ ++L  + A  G    KK+  +S D + +
Sbjct: 957  ANTIEASDVDAVKKDLNDQQRIVEDDIYNRIEKLLLNKMAKVG----KKTKKISKDDLEK 1012

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R QW+   ++D+K    +ES   + +  +   + + +    KI+  D++ PGVL++VK
Sbjct: 1013 LNRDQWFGIKLKDKKKNSELESYYQRLQLLEEEFQGKLQAAKNKIEAADELAPGVLKMVK 1072

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            VF+A+KR IQ GDK+AGRHGNKG++SRI+P EDMP+++DGT VDIVLNPLGVPSRMNVGQ
Sbjct: 1073 VFLAVKRRIQPGDKIAGRHGNKGVISRIVPVEDMPYMEDGTTVDIVLNPLGVPSRMNVGQ 1132

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG--SHTEKISDYDDDSV 1193
            + ETHLGWA   LG KI+SL+ D      +  ++ FL K+  +G       +S + D+ +
Sbjct: 1133 VLETHLGWAAKELGVKIQSLLKD-NTGNQVKKIKDFLSKIYNSGAQGSKVNLSKFSDNEI 1191

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            + +A   K+GVP++TPVFDGA E  I  +L +A L  +GQ+ L DG TGE F RPVT+GY
Sbjct: 1192 IELAHNLKAGVPMATPVFDGAHESEIKDLLELAGLPTTGQTELTDGRTGEIFARPVTIGY 1251

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ L+E
Sbjct: 1252 MYMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLRE 1311

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +LT KSDDV GRTR+Y+ IV G    ETG PESFNVL+KE+++LGL+IDL  +
Sbjct: 1312 LLTYKSDDVQGRTRMYKQIVDGTHEVETGMPESFNVLMKEIRSLGLNIDLIET 1364


>gi|297183424|gb|ADI19557.1| hypothetical protein [uncultured gamma proteobacterium HF0770_27E13]
          Length = 1371

 Score = 1563 bits (4047), Expect = 0.0,   Method: Composition-based stats.
 Identities = 710/1373 (51%), Positives = 979/1373 (71%), Gaps = 18/1373 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK    +D+P+L+ +Q  SY+ FL  +I P++R N GL+AAF ++
Sbjct: 1    MTYSFTEKKRIRKDFGKQKSALDVPNLLSIQLDSYNVFLQKDINPEKRKNTGLEAAFNTL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KS 121
            FPI +FS  A LEFVSY  + P F V +   R L+YA PL++  +LI ++ +      K 
Sbjct: 61   FPIESFSKNARLEFVSYRLEEPVFSVRESQLRGLSYAAPLRVKTKLITYNKETNKETVKE 120

Query: 122  IKDIKEQ----SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
            +K+IKE      +Y G++PLMT+ GTFVI G  R++VSQLHRSPG+ FDHDKG    SGK
Sbjct: 121  VKNIKESGDTTDVYFGEIPLMTEHGTFVINGTDRVIVSQLHRSPGVFFDHDKG-VQSSGK 179

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD+KD I  RIDRRRK+ VT  L AL    +EIL TF+ K  
Sbjct: 180  LLFSARVIPYRGSWLDFEFDAKDAIFARIDRRRKISVTIILHALDFSDKEILDTFFEKDK 239

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK--F 295
            YS         ++  D + G      +      + ++  G  +    LK LK+ G K  +
Sbjct: 240  YSISKKEIKLKINP-DHLKGTVSDFDIKVGR--KLIVGKGNMVNVRHLKQLKDSGKKGAY 296

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            L + ++ L    ++ D+++ ETGE+ + A +++    +E +   +I++I  +Y++ +++ 
Sbjct: 297  LTVPAEHLEDKIMSHDVIDQETGELLVSANEILTADKIELLIAKDIKEIETIYINDLDHG 356

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            +YI N+L  D +  + +AL++IYR+MRPG+  T   +E++FN LFF+ ++YDLS VGR+K
Sbjct: 357  SYISNSLRIDPSSSKLEALIEIYRMMRPGEPPTKDSSENLFNNLFFNPERYDLSEVGRMK 416

Query: 416  MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             N R+  ++      + KEDII ++K L+++RNGK T+DDID+LGNRR+R+VGEM +N +
Sbjct: 417  FNRRIGKNSDSGSSILSKEDIIDVLKTLINIRNGKDTVDDIDHLGNRRIRTVGEMTENAF 476

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+R+ER++K+R+S V+ + +MP+DLIN+KPV +A+ EFF SSQLSQ  +  N LS I
Sbjct: 477  RVGLVRVERAVKDRLSLVETEELMPRDLINSKPVSAAIKEFFGSSQLSQFMDQNNPLSEI 536

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
             H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A+VN +
Sbjct: 537  AHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAKVNKF 596

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPY+KV  GKVT  + YLSA++E    IAQAN+++D      EEL+  R   E  L
Sbjct: 597  GFLETPYQKVVKGKVTKKIEYLSAIDESQYVIAQANTTIDAKNHLQEELISSRYNNEFSL 656

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            +P +KID+ID SPKQ+VSIAASLIPFLE+DD+NR LMG NMQRQAVP L AE P VGTGM
Sbjct: 657  MPVDKIDYIDVSPKQIVSIAASLIPFLEHDDANRALMGSNMQRQAVPTLLAETPLVGTGM 716

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E VVA  SG  I+AKR G+V+ VDA RIVI   + +     SGVDIY L K+ RSNQNTC
Sbjct: 717  ERVVATDSGVTIIAKRGGVVDSVDASRIVIAVDDEETQSGESGVDIYSLTKYTRSNQNTC 776

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +NQRPLVKV D++   D+IADG ST LG+LA+G+N+LVAFMPW+G+NFEDS+LISE++V 
Sbjct: 777  INQRPLVKVRDKISVGDVIADGASTSLGELAIGQNLLVAFMPWNGFNFEDSILISEKVVK 836

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ED FT+IHIEE + +ARDTKLG EEIT DIPNV +  L+ +DE GI  +GAEV  GDILV
Sbjct: 837  EDRFTTIHIEELQCIARDTKLGSEEITADIPNVGDAALRKLDESGIAYIGAEVVGGDILV 896

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPKGE+ ++PEEKLLRAIFGEKA DV+DTSLRVPSG+ G V+DVRIF+R G++K++R
Sbjct: 897  GKITPKGETQLSPEEKLLRAIFGEKASDVKDTSLRVPSGMDGAVIDVRIFSREGVEKDDR 956

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            + ++E   ++ + +D +D+Q I++ +IY+R+ ++L  + A  G    +K+  +S D + +
Sbjct: 957  ANTIEASDVDAVKKDLNDQQRIVEDDIYNRIEKLLLNKMAKVG----RKTKKISKDDLEK 1012

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R +W+   ++D+K    +ES   + +  +   + + K    KI+  D++ PGVL++VK
Sbjct: 1013 LNRDKWFGIKLKDKKKNSELESYYQRLQLLQEEFQGKLKAAKNKIEAADELSPGVLKMVK 1072

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            VF+A+KR IQ GDK+AGRHGNKG++SRI+P EDMP+++DGTPVDIVLNPLGVPSRMNVGQ
Sbjct: 1073 VFLAVKRRIQPGDKIAGRHGNKGVISRIVPVEDMPYMQDGTPVDIVLNPLGVPSRMNVGQ 1132

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG--SHTEKISDYDDDSV 1193
            + ETHLGWA   LG KI+SL+ D      I  ++ FL K+  +G       +S + +D +
Sbjct: 1133 VLETHLGWAAKELGAKIQSLLKD-NTGKKIKKIKDFLSKIYNSGAPGSKVNLSKFSEDEI 1191

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            + +A   K GVP++TPVFDGA E  I ++L +A+L  +GQ+ L DG TG PFDRPVTVGY
Sbjct: 1192 IELAHNLKDGVPMATPVFDGAHESEIKNLLELAELPVTGQTELIDGRTGAPFDRPVTVGY 1251

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ L+E
Sbjct: 1252 MYMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLRE 1311

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +LT KSDDV GRTR+Y+ IV G +  ETG PESFNVL+KE+++LGL+IDL + 
Sbjct: 1312 LLTFKSDDVQGRTRMYKQIVDGTNEVETGMPESFNVLMKEIRSLGLNIDLIDD 1364


>gi|319760673|ref|YP_004124611.1| DNA-directed RNA polymerase, beta subunit [Candidatus Blochmannia
            vafer str. BVAF]
 gi|318039387|gb|ADV33937.1| DNA-directed RNA polymerase, beta subunit [Candidatus Blochmannia
            vafer str. BVAF]
          Length = 1345

 Score = 1562 bits (4045), Expect = 0.0,   Method: Composition-based stats.
 Identities = 689/1364 (50%), Positives = 951/1364 (69%), Gaps = 20/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    RVRK FGK P+++DIP L+ +Q  S++ F+  ++        GL AAFKSV
Sbjct: 1    MVYSYTEKKRVRKDFGKRPKVLDIPYLLSIQLDSFEKFINKDLN----GQYGLDAAFKSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
            FPI +++G + L+++ Y    P FDV +C  R +T++  L++ L L+V++ D        
Sbjct: 57   FPIKSYNGNSELQYIDYTLGEPVFDVKECQARGVTFSASLRVQLCLVVYEKDGSGSCNVI 116

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             K I+EQ +YMG++PLMT +GTF+I GI+R+VVSQLHRSPG+ FD DKG+   SGK+LY 
Sbjct: 117  AKKIQEQEVYMGEIPLMTNNGTFIINGIERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYT 176

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD + VRIDRRRK+PVT  L AL   +++IL+ F+  +VY   
Sbjct: 177  ARIIPYRGSWLDFEFDLKDNLFVRIDRRRKLPVTVLLKALSYTNDQILNIFFDVVVYEVV 236

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            G+ W   L   D + G      +   DT    ++ G+++T+  +  LK   +  + I  +
Sbjct: 237  GNRWYMHLIP-DRLRGETALFEVRVNDT--VYVDKGRRITTQHINKLKFDNISKIEIPVE 293

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             L G  + +D +N  TG + + A   I  + L  +  S    I +L+ + ++   YI  T
Sbjct: 294  YLLGKVLIKDYINSSTGALIVSANTEISYEILNNLIKSGFNFIEVLFSNDLDCGNYISET 353

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D    R DAL++IYRVMRPG+  T   AE +F+ LFF  ++YDLS VGR+K N  L 
Sbjct: 354  LRIDTTITRFDALVEIYRVMRPGEPPTKDAAEYLFSSLFFSEERYDLSNVGRMKFNRSLQ 413

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             ++ + +  + K+DI+ +IK L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 414  RNSIEGLGVLTKKDIVDVIKKLIDIRNGKGDVDDIDHLGNRRIRSVGEMAENQFRIGLVR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S  D+  + PQDLINAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 474  VERAVKERLSLGDVHMLSPQDLINAKPISAAVREFFNSSQLSQFMDQNNPLSEITHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETP
Sbjct: 534  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARANEYGFLETP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +G V N++ YLSA+EE +  IAQAN++L+  G F ++ + CR  GE  L  +++I
Sbjct: 594  YRKVNNGVVGNNIHYLSAIEEGDFIIAQANTNLNFQGQFIDDFIICRNKGESGLFRKDQI 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D++D S +Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVPL+++E P VGTGME  VA 
Sbjct: 654  DYMDVSTQQIVSVAASLIPFLEHDDANRALMGANMQRQAVPLIRSEKPLVGTGMERAVAV 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  +VA R G+V+ VD+ RI+I    G+L+   SG+DIY L K+ RSNQNTC+NQRP 
Sbjct: 714  DSGVTVVANRGGVVKYVDSSRIIIHVNLGELNSEESGIDIYSLTKYIRSNQNTCINQRPC 773

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V   D+IADGPSTDLG+L+LG+NM +AFMPW+GYNFEDSML+SER+V ED FTS
Sbjct: 774  VSLGERVSIGDVIADGPSTDLGELSLGQNMRIAFMPWNGYNFEDSMLVSERVVQEDRFTS 833

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   ++RDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  G+ILVGKITPK
Sbjct: 834  IHIQELICISRDTKLGSEEITADIPNVGETALSKLDESGIVYIGAEVIGGEILVGKITPK 893

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GV GTV+DV+IF R G++K++R++ +E 
Sbjct: 894  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVCGTVIDVQIFTRDGVNKDKRALQIES 953

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             ++  + +D ++E  I +  ++ R+ E+L                 +  + + +  R  W
Sbjct: 954  MKLNQVKKDLEEEFKIFESALFDRVYELLLNSG------------EVEEERLLKMERRFW 1001

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + D   +  +  L  QY   KS+ E + + + +K+  GD++ PG+L+VVKV++A+K
Sbjct: 1002 LKLELNDLVNRNQLFQLYNQYLDLKSLFEKKIEAQYQKVTQGDELAPGILKVVKVYLAVK 1061

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1062 RHIQPGDKMAGRHGNKGVISKINPVEDMPYDEYGVPVDIVLNPLGVPSRMNIGQILETHL 1121

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A  G+G KI  L+  +K    +         +         + ++ D  +L +A+  K
Sbjct: 1122 GMAAKGIGDKINYLLQQHKEVYRLREFIQKAYDLGKGLRQNVNLDNFSDVEILELAKNLK 1181

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+P++TPVFDGA E+ I  +L+++ L ESGQ  L+DG TGE F+R VTVGY+YMLKLNH
Sbjct: 1182 KGMPIATPVFDGATEQEIKDLLKLSGLPESGQITLFDGCTGEVFERQVTVGYMYMLKLNH 1241

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDD
Sbjct: 1242 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDD 1301

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V GRT++Y++I+ GN + E G PESFNVL+KE+++L ++I+LE 
Sbjct: 1302 VNGRTKMYKNIIDGNHSMEPGMPESFNVLLKEIRSLAINIELEE 1345


>gi|218779768|ref|YP_002431086.1| DNA-directed RNA polymerase, beta subunit [Desulfatibacillum
            alkenivorans AK-01]
 gi|226699394|sp|B8FEU1|RPOB_DESAA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|218761152|gb|ACL03618.1| DNA-directed RNA polymerase, beta subunit [Desulfatibacillum
            alkenivorans AK-01]
          Length = 1364

 Score = 1562 bits (4045), Expect = 0.0,   Method: Composition-based stats.
 Identities = 724/1360 (53%), Positives = 977/1360 (71%), Gaps = 12/1360 (0%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+RK FGK  +I+DIP+LIE+Q+ SY  FL M++ P++R   GLQA F SVFPI  FSG 
Sbjct: 10   RLRKSFGKIAKIVDIPNLIEMQRISYQRFLQMDVPPEKRETIGLQAVFHSVFPIRDFSGT 69

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            A LEFVSY F   K+ V+DC+ R +TY VP++IT+RL+VFDVD+  G ++I+DIKEQ IY
Sbjct: 70   ASLEFVSYRFGEIKYSVEDCVHRGMTYEVPIRITVRLVVFDVDKEKGIQNIRDIKEQEIY 129

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
             G +PLMT+ GTFVI G +R+VVSQLHRS G+ FDHDKG++  SGK++Y  RIIP +G W
Sbjct: 130  FGTIPLMTEQGTFVINGTERVVVSQLHRSSGVFFDHDKGKSHASGKVIYTARIIPVRGSW 189

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D+E D KD++++RIDRRRK P T    A G  +E++L+ FY     +           A
Sbjct: 190  IDMEIDPKDVLYIRIDRRRKFPATLLFKAFGYSTEDLLNYFYQTEKLTLTPKTLFKEFDA 249

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              L  G + S ++   D+ E +++ G+  T   +K++ + G++ + I  + L    +A  
Sbjct: 250  KTL-RGQRASITVKMPDSDEVIVKKGRLFTQRAVKTMAQAGIEKVAILQEDLEDKVLARR 308

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +++ +TGE+   A   IDE +LE +  + ++   ILY         +R  L+ DK + R+
Sbjct: 309  VLDPKTGEVLYPANHEIDEATLEAMRDAGVQKFEILYSAPGTGGDSVRKALLLDKVESRE 368

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL++IYR +RP + ST  VA+   + LFF    YDLS VGR+K+NMRL LDTP +V+ +
Sbjct: 369  EALVEIYRRLRPSNPSTVEVAKDFIDQLFFRPSHYDLSAVGRMKLNMRLGLDTPVEVKTL 428

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            R+EDI+   K LVDL++ +G +DDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S
Sbjct: 429  RREDILLTAKTLVDLKDSQGAVDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMS 488

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +ID++MP DLIN KPV + V EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R
Sbjct: 489  LQEIDALMPNDLINPKPVSAVVKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTR 548

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHP+HYGRICP ET EG NIGL+ SL+++ARVN +GF+ETPYR V +G+ T
Sbjct: 549  ERAGFEVRDVHPSHYGRICPIETPEGPNIGLIVSLSTYARVNEFGFVETPYRVVTEGQAT 608

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             ++ YLSAMEE++  IAQAN+ LDE+G F    V  R  GE  +V +E +  +D SP Q+
Sbjct: 609  KEIKYLSAMEEKDLPIAQANAPLDEEGFFINPTVSSRVEGELTIVKKEDVKLMDISPNQL 668

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+++S+IPFLENDD+NR LMG NMQRQAVPLL  EAP +GTG+E VVA+ SG  +VAKR
Sbjct: 669  VSVSSSMIPFLENDDANRALMGSNMQRQAVPLLATEAPLIGTGLERVVARDSGVTLVAKR 728

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G V  VDA RIV++  +   D     V IY L KF RSNQNTC NQRP+VK+G EV+  
Sbjct: 729  DGKVVAVDASRIVLQHEDERKDRMDKQVTIYNLSKFTRSNQNTCFNQRPIVKLGQEVKAG 788

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            DIIADGP+T+ G+LALGRN+ VAF+PW GYNFEDS+L+SER+V + VFTS+HIEEFEV++
Sbjct: 789  DIIADGPATENGELALGRNVTVAFLPWGGYNFEDSILVSERLVRDGVFTSVHIEEFEVVS 848

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG EEITRDIPNV EE LKN+D+ GI+ +GAEV PGDILVGKITPKGE+ ++PEEK
Sbjct: 849  RDTKLGKEEITRDIPNVGEEALKNLDDSGIVRLGAEVRPGDILVGKITPKGETQLSPEEK 908

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DV+DTSLRVP GV G VVD ++F R G++K++R+  +E E+I  L +D+
Sbjct: 909  LLRAIFGEKAGDVKDTSLRVPPGVEGVVVDAKVFARRGVEKDDRTRLIEDEEIAALEKDR 968

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRSQWWQFAV 1026
            DDE  I++  + S+L+ I+ GQ A +  K  K     K   ++++++ + P +      +
Sbjct: 969  DDELKIMEDTVRSKLITIVLGQEATAPVKKGKAVLIPKGQPITAEMLEDCPLAPLEALVL 1028

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +DE     V  L   Y   +  ++  F+ ++ + Q GDD+PPGV+++VK++VAMKR +  
Sbjct: 1029 KDEDHSERVHELLEIYREQRESVQMSFEEQVNRYQKGDDLPPGVIKMVKIYVAMKRRLSV 1088

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP ED+P+ ++GTPVD+VLNPLGVPSRMNVGQI E HLG A  
Sbjct: 1089 GDKMAGRHGNKGVVSCILPQEDLPYFENGTPVDMVLNPLGVPSRMNVGQILEIHLGRAAK 1148

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG +I++L+ + K    +  LR  ++++  +    ++++   +  +L VA Q+K GV +
Sbjct: 1149 SLGDQIEALLEEQK----LDGLRQKMQEIFSSD--ADEVAGLTEQELLEVAGQYKRGVHM 1202

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA E+ I  +L  A +  SGQ++LYDG TGE F   +TVG +YMLKL+H+V DK
Sbjct: 1203 ATPVFDGAKEDEITDLLSSAGVSPSGQAVLYDGRTGERFKGEITVGTMYMLKLHHLVDDK 1262

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDD+VGRT
Sbjct: 1263 IHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDMVGRT 1322

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            R+YE IV G +  E G PESFNVLVKE+Q+LGL + L   
Sbjct: 1323 RMYEKIVKGQNVLEPGMPESFNVLVKELQSLGLEMSLIEE 1362


>gi|269469118|gb|EEZ80666.1| DNA-directed RNA polymerase, beta subunit [uncultured SUP05 cluster
            bacterium]
          Length = 1360

 Score = 1562 bits (4045), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1365 (49%), Positives = 948/1365 (69%), Gaps = 8/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+R  FG    I+  PDL+ +Q  S++ F+        + + GL   F+SV
Sbjct: 1    MAYSFTEKKRIRNNFGSRESILTEPDLLAIQIDSFNGFIQAG--EKNKKDVGLHGVFQSV 58

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPITA +G A +E+V YE   PKF+V +C  R +T+A  L++ L L++FD +  T  K  
Sbjct: 59   FPITAVNGYAEIEYVDYELQEPKFNVKECKLRGVTFASTLRVKLNLVLFDKNGSTLKKKR 118

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K I E+ +Y+G LPLMT+ GTFVI G +R+VVSQLHRSPG+ F+HDKG+   SGK+L+
Sbjct: 119  RVKQIIEEDVYLGQLPLMTETGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHSSGKILF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD  + ++ RIDRRRK+PVT+ L A+G++  EIL TF+ K+    
Sbjct: 179  SSRVIPYRGSWLDFEFDHHEHLYARIDRRRKLPVTTLLRAMGLNGSEILDTFFGKVNVKL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +       LSA  L  G      ++       V+E G+++T+   K L++  VK +    
Sbjct: 239  KAKSCDVGLSAEKL-RGVIAEFDIISGKD--VVVEKGRRITAKHTKILEKSKVKSINAPL 295

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    ++ED+++ ETGEI   A  VI E+ LE +  ++++ I ILY++     AYI +
Sbjct: 296  EYLLDKVISEDLIDKETGEILFAANTVISEEVLEALGTNKVKKIEILYINESEGGAYISD 355

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D+ +   +A + IY VMRPG+ +T      +FN LFF +D+YDLS VGR+K+N RL
Sbjct: 356  TLRLDETQTELEARMSIYHVMRPGEPATEDAVNLLFNNLFFKNDRYDLSKVGRMKLNRRL 415

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             + +      +  +DII+++K+L++++NG  ++DD+D L NRRVR++GEM++NQ+R+GL+
Sbjct: 416  GIKSETGEHVLTNDDIISVLKLLINIKNGNDSVDDVDTLANRRVRAIGEMIENQFRIGLV 475

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E++++E ++  + D + PQDLIN+KPV +AV EFF SSQLSQ  + VN LS +TH RR
Sbjct: 476  RVEKAVREGLNLAETDELTPQDLINSKPVSAAVREFFGSSQLSQFMDQVNPLSGVTHKRR 535

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHP+HYGR+CP ET EG NIGL+++L  +A+ N YGF+ET
Sbjct: 536  ISALGPGGLTRERAGFEVRDVHPSHYGRLCPIETPEGPNIGLINTLAVYAKTNNYGFLET 595

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PY+ V DGKVT++++Y+SA++E    IAQAN+++   G   + L+ CR   E +LV  E 
Sbjct: 596  PYQVVKDGKVTDEIIYVSAIDELEHTIAQANAAVSSKGQLMDNLIPCRRKNEFVLVNSED 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +  ID   KQ+ S+AASLIPFLE+DD+NR LMG NMQRQAVP+L+AE P VGTG+E VVA
Sbjct: 656  VTLIDIDSKQISSVAASLIPFLEHDDANRALMGSNMQRQAVPVLRAEKPLVGTGIERVVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              S   + AK  G+VE VDA RIVIR           GVDIY L K+ RSNQNTC+NQ+P
Sbjct: 716  TDSRVCVTAKHGGVVEAVDASRIVIRVDSKQAKAGELGVDIYNLTKYSRSNQNTCINQKP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV  GD+V   D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+LISER+V ED +T
Sbjct: 776  LVNTGDKVAIGDVLADGPSTDLGELALGQNMKIAFMPWNGYNFEDSILISERVVQEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +IHIEE    +RDTKLGPEEIT DIPNVSE  L  +DE G++ VGA V  GDILVGK+TP
Sbjct: 836  TIHIEELTAYSRDTKLGPEEITADIPNVSESALAKLDEVGVVYVGARVKGGDILVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ ++PEEKLLRAIFGEKA +V+D+SLR+ +  SG V+DV++F R  ++K+ R++S++
Sbjct: 896  KSETVLSPEEKLLRAIFGEKANNVKDSSLRIGASKSGVVIDVQVFTRDRVEKDSRALSID 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +++  + +D DDE  I+D +IY R+   L G     G    K    L++  +     S 
Sbjct: 956  EDRLAKIRKDIDDEFGIIDGDIYRRVRLKLSGNTVTKGVSNIKAGDKLNAKTMKPLDNSD 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              +  V+D  V + V +L  Q +  +   +  F+ +  KI+ G ++PPGV+++VKV+VA 
Sbjct: 1016 IAKLKVEDAAVNKEVAALVKQAKAKQVEFDKFFEEERAKIEEGAELPPGVMKMVKVYVAT 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            ++ +Q GDKMAGRHGNKG++SR+ P EDMP+L+DG+ VD+VLNPLGVPSRMNVGQ+ E H
Sbjct: 1076 RKTLQVGDKMAGRHGNKGVISRVSPIEDMPYLEDGSTVDVVLNPLGVPSRMNVGQVLEVH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG+A  GLG KI  ++ D +    +  +R+FL+KV  +    E  + + D+ ++ +A   
Sbjct: 1136 LGYAAKGLGHKIAVML-DEQKKTMVKEIRAFLDKVYNSYGKKEDFNSFSDEEIIELARNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDG  E+ I S+L++ADL ESGQ  LYDG TGE FDR VTVGY++MLKLN
Sbjct: 1195 RGGVPMATPVFDGIKEDDIKSLLKLADLPESGQEQLYDGRTGEAFDRLVTVGYMHMLKLN 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YSLVTQQPL GK+  GGQR GEMEVW ++AYGAA+ L+EMLT+KSD
Sbjct: 1255 HLVDDKMHARSTGPYSLVTQQPLSGKAQFGGQRFGEMEVWALEAYGAAHTLREMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GR ++Y+SIV G +  E+  PESFNVLVKE+++LG+ ++LE 
Sbjct: 1315 DVAGRAKMYKSIVDGVNLTESVMPESFNVLVKEIRSLGIDVELEQ 1359


>gi|45644665|gb|AAS73053.1| predicted DNA-directed RNA polymerase beta subunit [uncultured marine
            gamma proteobacterium EBAC20E09]
          Length = 1332

 Score = 1561 bits (4042), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1346 (52%), Positives = 968/1346 (71%), Gaps = 16/1346 (1%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +D+P+LIE Q  SY  FL  ++APD+R  +GL+  F+++FPI + SG A LE+VSYE   
Sbjct: 1    MDLPNLIETQTKSYAEFLQADVAPDKRKKQGLEEVFQTLFPIKSVSGNAALEYVSYELGK 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
              +DV +CL + L+Y+ PL+I ++L++FD D  +  K +KDIKE  ++MG++PLMT+D +
Sbjct: 61   NTYDVQECLIQGLSYSAPLRIKVKLVLFDRD--SNFKEVKDIKEGEVFMGEVPLMTEDAS 118

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            F+I G +R+VVSQLHRSPG+ +DHDKG+   SGK+LY+ RIIP +G W+D EFD KDI+ 
Sbjct: 119  FIINGTERVVVSQLHRSPGVFYDHDKGKTHSSGKVLYSARIIPYRGSWLDFEFDPKDILF 178

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
             RIDRRRK+P T  L AL M +EEILS FY + +++   D     L    L  G  +   
Sbjct: 179  SRIDRRRKIPATIMLRALDMGTEEILSEFYEEELFTLDKDTVKVELVPERL-RGETLPVD 237

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +      +  +E+GK++T+  +K L       + ++ + L G  +++DI N ETGE+   
Sbjct: 238  IKVK--SKVYVEAGKRITARHIKELTNSKASQISLSDEFLLGKVLSKDIFNTETGEVLFS 295

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A   IDE+ LE+I  + +++I  LY++ ++   YI NTL  D   +R +AL++IYR+MRP
Sbjct: 296  ANTEIDEQVLEDIKSNNLKEIKCLYINELDKGPYISNTLRADPTTNRLEALVEIYRMMRP 355

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKI 442
            G+  T   AE++F  LFF+ ++YDLS VGR+K N RL LD   ++   + K+DII ++K 
Sbjct: 356  GEPPTKDSAETLFTNLFFNDERYDLSEVGRMKFNRRLRLDENKENPHILDKKDIIEVMKG 415

Query: 443  LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
            +V++R+G   +DDID+LGNRRVRSVGEM  NQ+R+GL+R+ER+++ER+S+ + D + PQD
Sbjct: 416  IVNIRDGHDIVDDIDHLGNRRVRSVGEMTANQFRVGLIRVERAVRERLSNAEADELGPQD 475

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            LINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH
Sbjct: 476  LINAKPVTAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVH 535

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            PTHYGR+CP ET EG NIGL++S  S++R N YGFIETPYRKV +GKVT++++YLSA++E
Sbjct: 536  PTHYGRVCPIETPEGPNIGLINSFASYSRTNQYGFIETPYRKVTNGKVTDEIIYLSAIDE 595

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                IAQAN  LD++  F ++LV  R A E  L+  ++ID +D SP+QVVSIAASLIPFL
Sbjct: 596  AEHVIAQANVMLDKNNRFIDDLVAVRHANEFELMSPDRIDLMDVSPQQVVSIAASLIPFL 655

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            E+DD+NR LMG NMQRQAVP+L++E P VGTG+E+VVA+ SG  IVA+ +G+VE VDA R
Sbjct: 656  EHDDANRALMGSNMQRQAVPVLRSEKPLVGTGLETVVARDSGVCIVARNSGVVESVDASR 715

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            IV+R  +     S +  D+Y L+K+ RSNQNTC+NQRP+VKVGD V+  DI+ADGPS D 
Sbjct: 716  IVVRVTDK---KSKTASDVYNLIKYTRSNQNTCINQRPIVKVGDTVKAGDILADGPSVDN 772

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G+LALG+N+ +AFMPW+GYNFEDS+LISE++  ED FTSIHI+E   +ARDTKLG EEIT
Sbjct: 773  GELALGQNIRIAFMPWNGYNFEDSILISEKVAREDRFTSIHIQEIVCIARDTKLGSEEIT 832

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             DIPNV E  L  +DECGI+ VGAEV PGDILVGKITPKGE+ ++PEEKLLRAIFGEKA 
Sbjct: 833  ADIPNVGEGSLNKLDECGIVYVGAEVEPGDILVGKITPKGETQLSPEEKLLRAIFGEKAS 892

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            DV+DTS R  S   GTV+ V +F R G++K+ER++++E++ ++   +D DDE  +++R  
Sbjct: 893  DVKDTSQR--SSSKGTVIGVEVFTRDGMEKDERTLAIEQDHLDQSKKDADDEAAVVERAT 950

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              RL E+L     V G  G KK  +L+S+ +     S  +   +  E     +E  +  Y
Sbjct: 951  KRRLSELLKSNKVVKG-NGVKKGEILTSEKLDSLKISDIFSIRIAKEATNNIIEETETSY 1009

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +     ++ RF+ K  KI  G D+ PGV+++VKV++A+KR IQ GDKMAGRHGNKG++S 
Sbjct: 1010 KQFIKDIKSRFEEKKSKIIRGHDLAPGVIKIVKVYLAIKRRIQPGDKMAGRHGNKGVISE 1069

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+P EDMP+ + G P+DIVLNPLGVPSRMNVGQI ETH+G A  G+G KI  ++   K N
Sbjct: 1070 IMPVEDMPYDESGNPIDIVLNPLGVPSRMNVGQILETHMGSAAKGIGDKIDLML---KEN 1126

Query: 1163 GDISPLRSFLEKVIGTGS-HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               + L+ +L+K+    + + E I  +++  +  +A   + G+P++TPVFDGA E  I  
Sbjct: 1127 AKPAELKDYLDKLYNKNAANKEDIQSFNNTEINELANNLRKGLPIATPVFDGAKESEIKE 1186

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L++ADL ESGQ  L+DG TG  FD PVTVGY+YM+KLNH+V DK++ARSTGSYSLVTQQ
Sbjct: 1187 LLKLADLPESGQITLFDGRTGNKFDSPVTVGYMYMIKLNHLVDDKMHARSTGSYSLVTQQ 1246

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT++Y++IV G    + 
Sbjct: 1247 PLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVSGRTKMYKNIVDGTYEMDA 1306

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSR 1367
              PESFNVL KE+++LG++I+L+  +
Sbjct: 1307 NVPESFNVLSKEIKSLGINIELDEEK 1332


>gi|218886550|ref|YP_002435871.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio vulgaris str.
            'Miyazaki F']
 gi|226699396|sp|B8DLM7|RPOB_DESVM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|218757504|gb|ACL08403.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio vulgaris
            str. 'Miyazaki F']
          Length = 1372

 Score = 1556 bits (4028), Expect = 0.0,   Method: Composition-based stats.
 Identities = 686/1367 (50%), Positives = 938/1367 (68%), Gaps = 14/1367 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK P  + IP L+ +Q  SY  FL   +A + + +EGL+  F+SVFPI  F+  A L
Sbjct: 6    KKFGKIPVSLGIPHLLNLQVDSYVKFLQEGLA-ERKTDEGLEGVFRSVFPIEDFNRTASL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSY+   PKFD  +C+ + LTY  P++I +RL+V+DVD+ +G ++I+DIKEQ IY G 
Sbjct: 65   EYVSYDIGEPKFDQAECISKGLTYEAPIRIKVRLVVYDVDDDSGNRTIRDIKEQDIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKTHSSRKVLYSCRVIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T    A+GM   +IL  FY K  Y    D   F     D+
Sbjct: 185  DFDHKDILYVRIDRRRKMPATILFKAMGMTKTDILDYFYKKEFYRISADGRVFWEVQKDM 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                   + +   D G   +++GK +T    + + E G++ + + +D L GL++A+D+VN
Sbjct: 245  FRKDSAFADIAGPD-GTVFVKAGKPITKRAWRQICEAGLETIEVAADTLDGLFLADDVVN 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D +     E +  + I  +PIL+   ++ ++ +R+TLV DK  D++ A 
Sbjct: 304  PATGEVLAEAADEVTPGVQERLREAGIDRLPILHTKGIDTSSSLRDTLVLDKTADKEAAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +AES F+ LF  +D YDLS VGR K+N RL LD   ++R +  E
Sbjct: 364  VEIYRRLRPSSPPTPEIAESFFDNLFRSADYYDLSPVGRYKLNQRLGLDQSLELRVLTDE 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  I++L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILTAIRVLLHLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N+LS +TH RRLSALG GG+ R RA
Sbjct: 484  VSTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN YGFIETPY  + D K+T +V
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDYGFIETPYHVIRDTKMTGEV 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            VYL A  E    IAQAN+  D +G   +E V  R  G+ ++ PRE++  +D SP Q+VSI
Sbjct: 604  VYLDASREHGEVIAQANAPFDAEGKLADEYVTTRVKGDVLMSPREEVTLMDVSPSQMVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTGME  VA+ SGA I+A+  GI
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLQCEKPLVGTGMEGPVAQDSGACIIAEGPGI 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RI++    G L P   GV  Y L KF +SNQN+C  Q+P    G  V + DI+
Sbjct: 724  VRYADADRIIVSYENG-LYPERGGVRAYDLQKFHKSNQNSCFGQKPTCHPGQIVAKGDIL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP  + G+LALG+N++VAFMPW GYNFEDS+LISER V ED FTS+HIEEFEV+ARDT
Sbjct: 783  ADGPGIEDGELALGKNLVVAFMPWCGYNFEDSILISERTVKEDTFTSVHIEEFEVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ L+N+D  GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 843  KLGPEEITRDIPNVGEDMLRNLDGSGIIRIGANVKPDDILVGKITPKGETQLTPEEKLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV++V++FNR   +K+ER+  +E  ++  L R + D 
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTVIEVKVFNRRSGEKDERARLIEEYELGRLDRKEQDH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               L      +LM ++ G+   +   G KK  V+       +++++++ P  +      +
Sbjct: 963  IRGLGDATRVKLMAVVEGKQIATTLAGKKKGEVIAEAGASVTAEMLADVPLKKLSGL-FK 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            + +V   V++L   Y+     + + +++K  K+  GDD+PPGV+++VKV++A+KR +  G
Sbjct: 1022 NREVNEAVDALLESYDQQVQFISNIYESKRGKVTEGDDLPPGVIKMVKVYIAVKRKLSVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGWA   
Sbjct: 1082 DKMAGRHGNKGVVSCILPAEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWAAKE 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +G+++  ++   + N  +  LR+ +++   + +    +   DD+       +   G+   
Sbjct: 1142 MGRQLAEML---ERNDPLKALRNEVKRAFDSPAIDSLVDSMDDEDFRASVAKLGRGIVTK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I S L  A++DE G+++LYDG TGE F   VT G +YMLKL+H+V +K+
Sbjct: 1199 TPVFDGAAEEEIWSWLVRANIDEDGKTVLYDGRTGERFHNRVTTGVMYMLKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            +YE IV G++  E G PESFNVLVKE+ +LGL + L     K   K 
Sbjct: 1319 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVTLHQEEGKKRPKR 1365


>gi|303247797|ref|ZP_07334066.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio
            fructosovorans JJ]
 gi|302490881|gb|EFL50780.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio
            fructosovorans JJ]
          Length = 1368

 Score = 1553 bits (4022), Expect = 0.0,   Method: Composition-based stats.
 Identities = 684/1362 (50%), Positives = 927/1362 (68%), Gaps = 14/1362 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK  + + IP L+ +Q  SY+ FL  +I P  R + GL+  F+SVFPI  F+  A L
Sbjct: 6    KNFGKIVKTLTIPHLLNLQIDSYELFLQKDIPPTSREDAGLEGVFRSVFPIEDFNRTASL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSYE   PK+DV +C+ + LTY  PL+I +RL+V+DVDE T  ++I+DIKEQ IY G 
Sbjct: 66   EYVSYEIGEPKYDVPECIVKGLTYEAPLRIKVRLVVYDVDEETENRTIRDIKEQVIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +PLMT+ GTF+I G +R++V+QL RSPGI F+HD G++  S K+LY+CR+IP +G W+D 
Sbjct: 126  VPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKSHTSRKVLYSCRVIPMRGSWLDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            ++D KDI++VRIDRRRK+P T    A+GM   +IL  FY    +   G    F     + 
Sbjct: 186  DYDHKDILYVRIDRRRKMPATILFKAMGMSRVDILRYFYEIEHFFLEG-SRVFRPVLPEF 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                K  + + D D G+ ++   K +T    + + E G++ + I    L G ++AEDI +
Sbjct: 245  YRKEKAYAEVRDTD-GKVIVGVDKPITKRSWRLMLEAGIEKIEIDPTTLTGQFLAEDIAD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D +    +E++  + I D+P+L+   ++ ++ IR+TLV DK  D   A 
Sbjct: 304  PATGEVLAEAADELTPDLVEKLKDAGIADLPVLHTRGIDTSSSIRDTLVLDKTTDTISAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A + F  LF + D YDLS VGR K+N RL +D P D R +  +
Sbjct: 364  VEIYRRLRPSSPPTPEIAANFFENLFRNPDYYDLSPVGRYKLNARLKIDQPLDFRTLAND 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  +K L  L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILKAVKHLTFLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N+LS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT+ ++VN +GFIETPYR V +G+VT++V
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTHSKVNDFGFIETPYRVVREGRVTDEV 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            VYL A  E +  IA AN+ LD +G F   +V  R  G+ I+ P E+I  +D SP Q+VS+
Sbjct: 604  VYLDATREIDEVIAGANAELDAEGHFIHPVVGARIRGDLIMTPPEQITLMDISPSQIVSV 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTGME  VAK SGA ++A+  G 
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRCEQPLVGTGMEGPVAKDSGACLLAEGPGY 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA R+V+   +GD+  ++ G   Y L+K  +SNQNTC  Q P V+VG  V + D++
Sbjct: 724  VHYADAERVVVCY-DGDVGAASGGAKTYELLKHHKSNQNTCFGQVPRVRVGQHVEKGDVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP    G+LALG+N+LVAFMPW GYN+EDS+LISE+ V +D FTS+HIEEFEV+ARDT
Sbjct: 783  ADGPGIRDGELALGKNLLVAFMPWCGYNYEDSILISEKAVKDDTFTSVHIEEFEVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE L ++DECGII +GA V P DI+VGKITPKGE+ +TPEEKLLR
Sbjct: 843  KLGPEEITRDIPNVGEEMLNDLDECGIIRIGARVAPDDIMVGKITPKGETQLTPEEKLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DVR+FNR   +K++R+  +E  ++  +   +   
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTVIDVRVFNRRSGEKDDRTRQIEDFELARIDVKEGQH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAVQ 1027
               +  N+  RL  I+ G+      KG KK+ V       L+ +L+ + P  +       
Sbjct: 963  IDAIADNLRRRLWPIVSGKAVFQTIKGPKKNEVLLEANHPLTQELLDQLPVKKLSGI-FA 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             ++    V  L   Y+     ++  +  K EK+  GDD+PPGV+++VKV+VA+KR +  G
Sbjct: 1022 SKETNEAVAELLDDYDRHIHFVKGVYDQKREKVTEGDDLPPGVIKMVKVYVAVKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  +G PVDIVLNPLGVPSRMN+GQI ETHLGWA + 
Sbjct: 1082 DKMAGRHGNKGVVSCILPEEDMPFFANGRPVDIVLNPLGVPSRMNIGQIMETHLGWAGME 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  L+    +   +  LR+  + V         I    D+ +    +  K G+   
Sbjct: 1142 LGRQLSELV---ASGKPMETLRAEAKAVFSEPETVAMIDGMSDEELRVALKSLKKGIVAK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E+ +   L+ A L E+G+  LYDG TGE F RPVTVG +YMLKL+H+V +K+
Sbjct: 1199 TPVFDGATEDEMWGWLKQAGLPENGKVTLYDGRTGEAFHRPVTVGCMYMLKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVGGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            +YE IV G++  E G PESFNVLVKE+ +LGL +DL     K
Sbjct: 1319 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVDLIQDEKK 1360


>gi|220904901|ref|YP_002480213.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio
            desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|254765285|sp|B8J1A8|RPOB_DESDA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219869200|gb|ACL49535.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio
            desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 1378

 Score = 1553 bits (4022), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1378 (50%), Positives = 938/1378 (68%), Gaps = 18/1378 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA-PDERPNEGLQAAFKSVFPITAFSGAAM 73
            K FGK    + IP L+ +Q  SY+ FL   +   + RP+EGL+  F +VFPI  F+  A 
Sbjct: 6    KQFGKIKISLPIPHLLNLQIDSYEKFLQEGVPEAERRPDEGLEGVFHTVFPIEDFNKTAS 65

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFVSYE   PK+D  +C+ + LTY  P++I +RL+V+D DE +G ++I+DIKEQ IY G
Sbjct: 66   LEFVSYEIGEPKYDQAECISKGLTYEAPMRIKVRLVVYDADEASGNRTIRDIKEQDIYFG 125

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D
Sbjct: 126  TLPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDGGKTHTSRKVLYSCRVIPMRGSWLD 185

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
             +FD KDI++VRIDRRRK+P T    A+GM  E+IL  FY +  Y        F     +
Sbjct: 186  FDFDHKDILYVRIDRRRKMPATILFKAMGMSKEQILDYFYTQETYRLEERNTIFWEVRKE 245

Query: 254  LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
            L       + +VD + G  ++++GK +T    + + E G++ + +  D L G+++A D+ 
Sbjct: 246  LYRKDNAYADIVDSE-GNVIVKAGKPITKRSWRLICEAGIEAIEMRPDTLDGMFLAGDVA 304

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
            + +TGE+  EA D I    L+ +  + I  + +L+    + ++ IR+TL+ D+  D+  A
Sbjct: 305  DPKTGELLAEAADEITPGLLDRMRDAGINRVSVLHTKGNDTSSSIRDTLMLDRIPDQLKA 364

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
              +IYR +RP    T  +A S F+ LF + D YDLS VGR K+N RL+LD P D+R +  
Sbjct: 365  QEEIYRRLRPSSPPTAEIAASFFDNLFRNPDYYDLSPVGRYKLNQRLSLDEPSDLRTLTD 424

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             DI+  IK+LV L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  
Sbjct: 425  NDILTAIKVLVHLKDSHGPADDIDHLGNRRVRLVGELVENQYRIGLVRMERAIKERMSLQ 484

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            +I ++MP DLIN KPV + + EFF +SQLSQ  +  NSLS +TH RRLSALG GG+ R R
Sbjct: 485  EISTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNSLSEVTHKRRLSALGPGGLTRER 544

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            AG E+RDVH +HYGRICP ET EG NIGL+ SLT+FA+VN YGFIETPY  V +G+VT++
Sbjct: 545  AGFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTFAKVNDYGFIETPYHVVREGRVTDE 604

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            V++L A  E ++ +AQAN+ LDE G+  +E V  R  GE  +  R+++  +D SP Q+VS
Sbjct: 605  VLHLDASREGDQVVAQANALLDEQGNLVDEFVTVRVKGEVEMRHRDEVTLMDISPSQMVS 664

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I+A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA IVA   G
Sbjct: 665  ISAALIPFLEHDDANRALMGSNMQRQAVPLLRSEKPLVGTGMEVDVARDSGACIVAPADG 724

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +E VDA RIV+   EGD+     GV  Y L+K+ +SNQN+C  Q+P    G  V++  I
Sbjct: 725  KIEYVDADRIVVAY-EGDVYKKQGGVRAYDLLKYHKSNQNSCFGQKPSCHPGQIVKKGQI 783

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADGP  D G+LALG+N++VAFMPW GYN+EDS+LISER V EDVFTSIHIEEFEV+ARD
Sbjct: 784  LADGPGIDDGELALGKNLVVAFMPWCGYNYEDSILISERTVKEDVFTSIHIEEFEVVARD 843

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            TKLGPEEITRDIPNVSE+ L+N+DE GII +GA V P DILVGKITPKGE+ +TPEEKLL
Sbjct: 844  TKLGPEEITRDIPNVSEDMLRNLDESGIIRIGAAVKPDDILVGKITPKGETQLTPEEKLL 903

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            RAIFGEKA DV++TSL+VP GV GT++DV++FNR   +K++R++++E     +L + + D
Sbjct: 904  RAIFGEKARDVKNTSLKVPPGVEGTIIDVKVFNRRSGEKDDRTLAIEGHDTAVLDQKEAD 963

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAV 1026
                L     + L+  + G+   +   G KK  V       L+ ++++  P  +      
Sbjct: 964  HMRALTDRTRALLIPHVVGKQVAASLPGKKKGEVLVEAGAALTEEMLASLPVKKLSGL-F 1022

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            + ++V   V  +   Y+     L   + +K EK+  GDD+PPGV+++VKV +A+KR +  
Sbjct: 1023 KSKEVNDAVAEILKPYDQQVDYLHAIYDSKREKVTEGDDLPPGVIKMVKVHIAIKRKLSV 1082

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGW   
Sbjct: 1083 GDKMAGRHGNKGVVSCILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWGAK 1142

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG+++  L++   +   +  LR  ++ +  +      + + DD+       + ++G+  
Sbjct: 1143 ELGRQLAELLD---SGAAMQVLRDEVKSIFSSDDINALVDEMDDEEFKASVSKLRNGIVT 1199

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFDGA EE I S +  A L   G++ LYDG TGE F   VT G +YMLKL+H+V +K
Sbjct: 1200 KTPVFDGATEEEIWSWMERAGLANDGKTTLYDGRTGEAFKNRVTTGVMYMLKLHHLVDEK 1259

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR 
Sbjct: 1260 IHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGRV 1319

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK----MEEIPDF 1380
            ++YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K    M E  D 
Sbjct: 1320 KMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKKPKRTGYMREREDE 1377


>gi|71905954|ref|YP_283541.1| DNA-directed RNA polymerase subunit beta [Dechloromonas aromatica
            RCB]
 gi|88909132|sp|Q47JB0|RPOB_DECAR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71845575|gb|AAZ45071.1| DNA-directed RNA polymerase subunit beta [Dechloromonas aromatica
            RCB]
          Length = 1427

 Score = 1551 bits (4015), Expect = 0.0,   Method: Composition-based stats.
 Identities = 691/1432 (48%), Positives = 940/1432 (65%), Gaps = 75/1432 (5%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  S+  FL   +AP++R NEGLQAAF S+
Sbjct: 1    MTYSFTEKKRIRKSFAKRASVLDVPYLLATQLQSFKDFLQDEVAPEKRKNEGLQAAFTSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A LEFVSY    P FDV +C  R LT+A  L+  +RL++ D +      ++
Sbjct: 61   FPIVSHSGNARLEFVSYMLGEPAFDVTECQQRGLTFASSLRARVRLVIMDREAPD---TV 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT +G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTTNGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD +  R+DRRRK+PVT+ L A+GM SEEIL  F+    +    
Sbjct: 178  RVIPYRGSWLDFEFDPKDTLFFRVDRRRKMPVTTLLKAIGMSSEEILDQFFDFDTFLLSK 237

Query: 243  DFWCFPLSAA----------------------------------------------DLMV 256
            D   F L                                                 D ++
Sbjct: 238  DKVEFTLVPERLRGEVARFDFVGPDGVLIVPKDKRITAKHIRDIGAAAIKQIVVPEDFLI 297

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVN 314
            G  V+ ++VD  TGE V  +  ++T  LL  L+E  +  +    T++   G +++  +  
Sbjct: 298  GRVVAKNIVDKATGEVVANANDEITETLLAKLREAEITTVETLYTNELDRGAFISNTLRA 357

Query: 315  GETG-----EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             ET       + I       E   EE        +         +             +D
Sbjct: 358  DETATRQAARVAIYRMMRPGEPPTEEAVEILFNGLFYSDERYDLSGVGRMKFNRRLARQD 417

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--- 426
              +  L +  +    + +  ++AE+    L    D   L   G   M     L   +   
Sbjct: 418  VIEYKLMVKGLASKAEAALKNLAEASGFALSAIQDLVSLMPFGARAMVENSTLSEVEALA 477

Query: 427  -------------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                         +   +   DI+ +IKILV+LRNG+G IDDID+LGNRRVRSVGE+ +N
Sbjct: 478  AKLKPLGANVEVREQLTLSPRDIVEVIKILVELRNGRGEIDDIDHLGNRRVRSVGELAEN 537

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
            Q+R GL+R+ER++KER+S  + D++MP DLINAKP+ +A+ EFF SSQLSQ  +  N LS
Sbjct: 538  QFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPISAAIKEFFGSSQLSQFMDQTNPLS 597

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FA+VN
Sbjct: 598  EITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFAQVN 657

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            +YGFIET YRKV +G+VT+D+ YLSA+EE N  +AQAN+SLD +G  +++LV CR  GE 
Sbjct: 658  SYGFIETAYRKVNNGQVTSDIEYLSAIEEGNYVVAQANASLDANGRLSDDLVTCREKGET 717

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            IL    ++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGT
Sbjct: 718  ILAEPGRVQYMDVAPGQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGT 777

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+E  VA  SG A+VA R G+V+ VDA R+V+R  + +      GVDIY L+K+ RSNQN
Sbjct: 778  GIERTVAVDSGTAVVALRGGMVDYVDAARVVVRVNDDETIAGEVGVDIYNLVKYTRSNQN 837

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            T +NQRP+V+VGD + + D++ADG STD G+LALG+NML+AFMPW+GYNFEDS+LISER+
Sbjct: 838  TNINQRPMVRVGDHIAKGDVVADGASTDKGELALGQNMLIAFMPWNGYNFEDSILISERV 897

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V+ED +TSIHIEE  V+ARDTKLGPEEITRDI ++ E  L  +D+ GI+ +GAEV  GD+
Sbjct: 898  VAEDRYTSIHIEELTVVARDTKLGPEEITRDIASLGEAQLSRLDDSGIVYIGAEVEAGDV 957

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI+++
Sbjct: 958  LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGIAGTVIDVQVFTREGIERD 1017

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +R+ ++  E +     D  D+  I++R+ ++R+  ++ G+ A  GPK   K TV+    +
Sbjct: 1018 KRAQAIIDEHLRHYKLDLADQMRIVERDAFARVERLITGKKANGGPKKLAKGTVIDKVYL 1077

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                   W+   + D++  + +E +K   E ++   +  F+ K +K+  GD++PPGV ++
Sbjct: 1078 DSMDPHHWFDIRLADDEAAQQLEQVKDGLEQARKDFDIAFEGKRKKLTQGDELPPGVQKM 1137

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA+KR +Q GDKMAGRHGNKG+VSRILP EDMP ++DG+PVDIVLNPLGVPSRMNV
Sbjct: 1138 VKVYVAVKRRLQPGDKMAGRHGNKGVVSRILPVEDMPHMEDGSPVDIVLNPLGVPSRMNV 1197

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI E HLG A  GLG KI +++   +A      +R FL+++  +   +E + + +D  V
Sbjct: 1198 GQILEVHLGLAAKGLGHKIGAML---RAQSSAKEVRGFLDQIYNSSGKSENLDELNDVEV 1254

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L +AE  K GVP +TPVFDGA EE I +ML MA +  SGQ  L+DG TGE F+R VTVGY
Sbjct: 1255 LEMAENLKGGVPFATPVFDGAKEEEIKAMLAMAGMPSSGQMTLFDGRTGEAFERKVTVGY 1314

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            ++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQE
Sbjct: 1315 MHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQE 1374

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            MLT+KSDDV GRT+VYE+IV G    E G PESFNVLVKE+++L + IDLE 
Sbjct: 1375 MLTVKSDDVNGRTKVYENIVKGEHRIEAGMPESFNVLVKEIRSLAIDIDLER 1426


>gi|78358037|ref|YP_389486.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio desulfuricans
            subsp. desulfuricans str. G20]
 gi|88909135|sp|Q30X05|RPOB_DESDG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78220442|gb|ABB39791.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio desulfuricans
            subsp. desulfuricans str. G20]
          Length = 1375

 Score = 1551 bits (4015), Expect = 0.0,   Method: Composition-based stats.
 Identities = 681/1363 (49%), Positives = 933/1363 (68%), Gaps = 15/1363 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK    + IP L+ +Q  SY  FL    A    P+EGL+  F+SVFPI  F+  A L
Sbjct: 6    KKFGKIEVTLPIPHLLNLQVDSYKKFLQEGAAALA-PDEGLEGVFRSVFPIEDFNRTASL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSYE   PK+D  +C+ + LTY  P++I +RL+V+DVDE +  ++I+DIKEQ IY G 
Sbjct: 65   EYVSYEIGEPKYDQAECISKGLTYEAPIRIKVRLVVYDVDEDSENRTIRDIKEQDIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDAGKTHSSRKVLYSCRVIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            ++D KDI++VRIDRRRK+P T    A+GM   +IL  FY K  Y+   D         DL
Sbjct: 185  DYDHKDILYVRIDRRRKMPATILFKAMGMSRSDILEYFYKKEYYTLEDDGRLMWELDKDL 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                   + + D + G+ + ++GK  T    + + E G+  + +  D + G+++AEDIV+
Sbjct: 245  YRKDVAYADVADGE-GKVIAKAGKPYTKRSWRLMLEAGIPAVEVAPDYIAGMFLAEDIVD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D I    ++ +    I+ +P+L+    + ++ IR+TL+ DK  D++ A 
Sbjct: 304  EATGEVLAEAADEITLDLIDRLRECSIKRVPVLHTKGSDTSSSIRDTLLLDKTADQEQAR 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A + F  LF + D YDLS VGR K+N RL L T  + R +  E
Sbjct: 364  VEIYRRLRPSSPPTPEIASTFFENLFRNPDYYDLSPVGRYKLNQRLGLTTTQE-RVLTDE 422

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  I++L  L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 423  DILTAIRVLNHLKDTHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 482

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N+LS +TH RRLSALG GG+ R RA
Sbjct: 483  VSTLMPHDLINPKPVQAVLKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLTRERA 542

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN +GFIETPYR V DG+VT++V
Sbjct: 543  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDFGFIETPYRVVRDGQVTDEV 602

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YL A  E    +AQAN+ LD D  F +E V  R  G+ I+ PRE++  +D SP Q+VSI
Sbjct: 603  KYLDASSEHGEVVAQANARLDGDHRFVDEFVTTRVRGDVIMSPREEVTLMDISPSQMVSI 662

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL++  P VGTGME+ VA+ SGA I+A+  G+
Sbjct: 663  SAALIPFLEHDDANRALMGSNMQRQAVPLLRSTKPIVGTGMEADVARDSGACIIAEADGV 722

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RIV+   EGDL P T GV  Y L K+ +SNQ++C  Q+PLV  G  +R+ D++
Sbjct: 723  VRYADADRIVVSY-EGDLYPRTGGVRSYDLQKYHKSNQSSCFGQKPLVSRGQVIRKGDVL 781

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP  + G+LALG+N++VAFMPW GYNFEDS+LISER V EDVFTS+HIEEFEV+ARDT
Sbjct: 782  ADGPGIEDGELALGKNLVVAFMPWCGYNFEDSILISERCVKEDVFTSVHIEEFEVVARDT 841

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ L+N+D  GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 842  KLGPEEITRDIPNVGEDMLRNLDGSGIIRIGANVKPDDILVGKITPKGETQLTPEEKLLR 901

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFGEKA DV++TSL+VP G+ GTV+DV++FNR   +K+ER+ ++E  ++  L + + D 
Sbjct: 902  AIFGEKARDVKNTSLKVPPGIEGTVIDVKLFNRRSGEKDERTRNIEDYELARLDQKEKDH 961

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               L      +L  ++ G+    G  G KK  V+       +++++   P  +      +
Sbjct: 962  IRALTETTREKLAPVVVGKQLAYGLAGQKKGEVIAEAGQTLTAEMLEGLPVKKLSGL-FK 1020

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             +     V+     Y+     +   +++K EK+  GDD+PPGV+++ KV +A+KR +  G
Sbjct: 1021 SKDTNEAVQQALESYDRQIEFINAMYESKREKVTEGDDLPPGVIKMAKVHIAVKRKLNVG 1080

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGWA   
Sbjct: 1081 DKMAGRHGNKGVVSCILPQEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWAAKE 1140

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +G+K+  ++   +   D++ +R  ++ V  + + + ++ + DD++ +R   + + G+   
Sbjct: 1141 MGRKLALML---EHGQDLASVREQVKTVFASDAISSEVDNMDDETFVRSVRRLRDGIVTK 1197

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I S +  A L   G++ LYDG TG  F   VT G +Y+LKL+H+V +K+
Sbjct: 1198 TPVFDGATEEQIWSWMEQAGLANDGKTELYDGRTGVRFHNRVTTGVMYILKLHHLVDEKI 1257

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR +
Sbjct: 1258 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGRVK 1317

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            +YE +V G++  E G PESFNVLVKE+ +LGL + L     K 
Sbjct: 1318 MYEKVVKGDNFLEAGLPESFNVLVKELMSLGLDVTLHQEEGKK 1360


>gi|254455987|ref|ZP_05069416.1| DNA-directed RNA polymerase, beta subunit [Candidatus Pelagibacter
            sp. HTCC7211]
 gi|207082989|gb|EDZ60415.1| DNA-directed RNA polymerase, beta subunit [Candidatus Pelagibacter
            sp. HTCC7211]
          Length = 1361

 Score = 1549 bits (4010), Expect = 0.0,   Method: Composition-based stats.
 Identities = 733/1364 (53%), Positives = 985/1364 (72%), Gaps = 7/1364 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F     +RK FGK  E + IP+LIEVQK SY          +    +G    FKS+
Sbjct: 1    MQLSFTEKKNIRKSFGKLKESLSIPNLIEVQKNSYKEL--TEFYSEAELTKGFDRVFKSI 58

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI   +  A LE+VSY  D PKFDV++C+ R LTY+  LK TLRL+V+++D+    K I
Sbjct: 59   FPIEDLNDKATLEYVSYRLDKPKFDVEECITRGLTYSSALKCTLRLVVYEIDQDNNTKDI 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KEQ +YMG++P+MT  GTF+  G+QR+VV+Q+HRSPG+ FDHDKG+   SGKLL+ C
Sbjct: 119  LSAKEQEVYMGEVPMMTNSGTFITNGVQRVVVNQMHRSPGVFFDHDKGKTHASGKLLFNC 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-- 240
            R+IP++G W+D E+D KD ++ +IDR++K+  ++ L+ALG    EI   FY   +Y+   
Sbjct: 179  RVIPNRGSWLDFEYDVKDFLYFKIDRKKKIFASTLLLALGYSKAEIADEFYANELYTFDP 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            + + W    +  +       S  ++D  TGE VI+ G K+     K L   G+K + ++ 
Sbjct: 239  KTEKWKTKFNPENY-KAKNFSEEVIDAKTGEVVIKLGDKINFLNAKKLANDGLKDILVSR 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L G ++  D+   E  E   + G  +++  +++I  + I  + I   +S+N   Y+  
Sbjct: 298  ESLFGKFLHRDVKVSEEEEGVFKIGTELNDTIIQQISDANIHSLQISVTNSINKGPYLLT 357

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            T++ DKN  + +A+ +IY+++RPG+  T  +A  +FN LFF SD+YDLS VGRVKMN RL
Sbjct: 358  TILNDKNNSKDEAITEIYKMLRPGEPPTIEIATQIFNNLFFSSDRYDLSDVGRVKMNSRL 417

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            N D  D +  +R +DIIAI+  ++DLR+GK  +DDID+LGNRRVRSVGE+++NQ R+G+ 
Sbjct: 418  NQDCSDKITILRNDDIIAIVHKMLDLRDGKDDVDDIDHLGNRRVRSVGELVENQARIGVY 477

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKE+++++D++S MPQDLINAKP+  ++ +FF SSQLSQ  +  N LS ITH RR
Sbjct: 478  RMERAIKEKMTTLDVESAMPQDLINAKPLTVSLKDFFASSQLSQFMDQTNPLSEITHKRR 537

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++A++N YGFIE+
Sbjct: 538  VSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYAKINKYGFIES 597

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PY+KV DG V ++VVYLSAMEE    IAQAN+ LD++G   EELV CR     +L   + 
Sbjct: 598  PYKKVKDGVVQDNVVYLSAMEETKFTIAQANTKLDKNGKIVEELVSCRQNLNFLLAKPDT 657

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ID+ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPLLK E+P VGTG+ES VA
Sbjct: 658  IDYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLLKPESPLVGTGIESDVA 717

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  IV+KR GIV+++D  RIVI++ E   D S SGVDIY L KF+RSNQNTC+NQ+P
Sbjct: 718  LDSGVTIVSKRDGIVDKIDGKRIVIKATEET-DFSKSGVDIYNLQKFKRSNQNTCINQKP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+VGD+V+  DIIADGPST LG+LALG+N+ VAFMPW GYNFEDS+LISER V++DVFT
Sbjct: 777  LVRVGDKVKTGDIIADGPSTKLGELALGKNVTVAFMPWQGYNFEDSILISERCVTDDVFT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            S+HI E+E+MARDTKLG E+ITRDIPNV+EE LKN+DE GI+ +GAEVN GDILVGK+TP
Sbjct: 837  SVHIVEYEIMARDTKLGEEDITRDIPNVNEEALKNLDESGIVYIGAEVNAGDILVGKVTP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KG+S   PEEKLLR+IFGEKA+DV DTSLR+  G SGTVVDVR+FNRHGI+K+ERSI++E
Sbjct: 897  KGDSASGPEEKLLRSIFGEKAIDVTDTSLRMSRGSSGTVVDVRVFNRHGIEKDERSITIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            R +IE + +DK  E+ IL+R+I  R  + L G + +   K   + T L  + I +   + 
Sbjct: 957  RAEIEQVQQDKIVEEEILERSIKQRASQFLSGSSLIKKVKDLSEGTKLDFETIDKLSVND 1016

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             ++  V +   +  +  LK QY  +K  + +RF++K+ KI+ GDD+ P V+++VKVFVA+
Sbjct: 1017 VFKITVGNVNDEATLAQLKDQYNKAKQDITERFEDKVLKIRSGDDLLPSVMKMVKVFVAI 1076

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKM+GRHGNKG+VS+I+P EDMP+ +DG PVDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1077 KRRLRPGDKMSGRHGNKGVVSKIVPVEDMPYREDGRPVDIVLNPLGVPSRMNVGQILETH 1136

Query: 1141 LGWACVGLGKKIKSLIND-YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            LGWAC   G+++K L+N+  K       +  FL+ V G     EK+          + E 
Sbjct: 1137 LGWACKEFGEEVKKLVNENNKKIEKTEKISKFLKSVYGEEIFNEKVEKLSKPEFKDLCEN 1196

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             ++G+ +STPVFDGA E+ +  ML +A+L  SGQ+ L+DG TGE FDRPVTVG IYMLKL
Sbjct: 1197 LQNGIAISTPVFDGAKEKNVTDMLELANLPGSGQTYLWDGRTGEKFDRPVTVGIIYMLKL 1256

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KS
Sbjct: 1257 HHLVEDKIHARSTGPYSLVTQQPLGGKAQLGGQRFGEMEVWALEAYGASYTLQEILTVKS 1316

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            DDV GR +VYE+IV G + FE+G PESFNVLVKE+++L L+++L
Sbjct: 1317 DDVAGRVKVYETIVKGEENFESGIPESFNVLVKEIKSLALNVEL 1360


>gi|158520719|ref|YP_001528589.1| DNA-directed RNA polymerase, beta subunit [Desulfococcus oleovorans
            Hxd3]
 gi|226699395|sp|A8ZV51|RPOB_DESOH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158509545|gb|ABW66512.1| DNA-directed RNA polymerase, beta subunit [Desulfococcus oleovorans
            Hxd3]
          Length = 1368

 Score = 1548 bits (4008), Expect = 0.0,   Method: Composition-based stats.
 Identities = 707/1365 (51%), Positives = 945/1365 (69%), Gaps = 10/1365 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             R+RK FGK  +I++IPDLI +QK SY  FL   + P++R   GLQA F+SVFPI  F+ 
Sbjct: 9    RRIRKQFGKLDKIVEIPDLIGMQKESYGRFLQQGVPPEKREKIGLQAIFQSVFPIKDFTK 68

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            +A LEFVSY F   K  V +C+ R +TY +P++I +RL+V+D+DE +G  SI+DIKEQ I
Sbjct: 69   SASLEFVSYSFGGVKHSVAECIQRGMTYEIPVRIRVRLVVYDMDETSGTSSIRDIKEQEI 128

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y G +PLMT +GTF+I G +R+VVSQLHRS GI FDHD+G+   SGK++Y+ RIIP +G 
Sbjct: 129  YFGAIPLMTDNGTFIINGTERVVVSQLHRSSGIFFDHDQGKTHSSGKVVYSSRIIPVRGS 188

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+DIE D KDI+H+RIDRRRK P T    ALG   ++IL  FY K     R     F   
Sbjct: 189  WIDIEIDPKDIVHMRIDRRRKFPGTILFKALGYTVKDILDYFYTKERVFVRKKK-VFKAF 247

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            + D + G + +  +   +TG+ +++ G+     +LK++K  G+  + I  + + G  +A 
Sbjct: 248  SEDSLRGQRATVRIKHPETGDLIVDKGRIFNKTVLKNMKSAGIDMVPIRPEDVVGAVLAA 307

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             + +  TGE+  +AGD I E+  E I    I ++ IL++D   +   I  TL+ DK   +
Sbjct: 308  PLADSSTGEMLADAGDFISEEVFERIGELGIEELQILFIDGAGSTDSIVKTLLLDKVNTK 367

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            ++AL+DIYR +RPG+ +T  VA+   + LFF  D YDLS VGR+K+N RL  + P  +R 
Sbjct: 368  EEALIDIYRRIRPGNPATPEVAQDFIDHLFFKPDYYDLSAVGRLKLNHRLGANAPVSLRT 427

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +R+ED++  +K L+ L+N +G +DDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+
Sbjct: 428  LRREDLLLAVKTLIHLKNTQGPVDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERM 487

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            S  ++D++MP DLIN KPV + V EFF +SQLSQ  +  N LS  TH RRLSALG GG+ 
Sbjct: 488  SLQEVDALMPHDLINPKPVSAVVREFFGTSQLSQFMDQTNPLSETTHKRRLSALGPGGLT 547

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVHP+HYGRICP ET EG NIGL+ SL+++ARVN YGFIETPYR V D KV
Sbjct: 548  RERAGFEVRDVHPSHYGRICPIETPEGPNIGLIVSLSTYARVNGYGFIETPYRVVKDTKV 607

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            + ++  L A EE    IAQAN+ + +DG +   +V  R AGE  ++    ++ +D SP Q
Sbjct: 608  SKEIKMLPAFEEGEHPIAQANAPIGKDGRYVNPVVIARVAGEFSMIKASDVELMDVSPNQ 667

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS++ASLIPFLENDD+NR LMG NMQRQ+VPL +  AP VGTG+E VVA+ SG A+VA+
Sbjct: 668  LVSVSASLIPFLENDDANRALMGSNMQRQSVPLARTSAPLVGTGVEKVVARDSGVAVVAR 727

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            R G V  VD+ RIV+R    D DP    V +Y L KF RSNQNTC N RP+VK G  V  
Sbjct: 728  RPGEVVYVDSGRIVVRHDTDDKDPEAKPVTVYNLSKFIRSNQNTCFNHRPIVKKGQRVAP 787

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
             D++ADGP+T+ G+LALG+N+ VAFMPW GYNFEDS+L+ E +V + VFTSIHIEEFEV+
Sbjct: 788  GDVLADGPATEKGELALGKNVTVAFMPWGGYNFEDSILVGETLVRDGVFTSIHIEEFEVV 847

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            ARDTKLG EEIT DIPNV EE L ++DE GI+ +GAEV PGD+LVGKITPKGE+ ++PEE
Sbjct: 848  ARDTKLGKEEITCDIPNVGEESLVDLDESGIVRLGAEVKPGDVLVGKITPKGETQLSPEE 907

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
            KLLRAIFGEK  +V+DTSLRVP GVSGTV+D ++F R G++K+ R+  +E E+I +L ++
Sbjct: 908  KLLRAIFGEKGGNVKDTSLRVPPGVSGTVIDAKVFTRRGVEKDTRTRMIEEEEIRVLEKN 967

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRSQWWQFA 1025
            +DDE  +++     RL  +L GQ   +  K  K     K   +++ L  E P SQ+ + A
Sbjct: 968  RDDEIAVIEEVTRERLKALLTGQKCDTPVKKGKKTILAKGDKITAALFDEVPTSQFEKLA 1027

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            V  + V      +   Y T      + F+ +I +   G+++PPGV+++VKV+VAMKR + 
Sbjct: 1028 VTSDSVTEQAHRVFEWYRTQVDACREEFEARISRYGAGEELPPGVIKMVKVYVAMKRVLS 1087

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
            +GDKMAGRHGNKG+VSRILP ED+P+ +DGT VD+VLNPLGVPSRMNVGQI E HLG A 
Sbjct: 1088 TGDKMAGRHGNKGVVSRILPQEDLPYFEDGTTVDMVLNPLGVPSRMNVGQILEIHLGRAA 1147

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG +I +++           L+  L  V        +I       +   A ++K GV 
Sbjct: 1148 RVLGDQISTML----EEKKYKDLKKKLSAVFNKEIPAAEIEAMSSARLCEFASEYKDGVH 1203

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            + TPVFDGA E  I ++L+    DE+GQ+ILYDG TG+PFD  +TVG +YMLKL+H+V D
Sbjct: 1204 METPVFDGAKEAEIKALLKEGGADETGQAILYDGRTGQPFDERITVGTMYMLKLHHLVDD 1263

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDD+ GR
Sbjct: 1264 KLHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYALQEFLTVKSDDIAGR 1323

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            TR+YE IV G +  + G PESF VL KEM+ALGL + L   + K 
Sbjct: 1324 TRMYEKIVKGQNVLDPGIPESFKVLTKEMKALGLDVTLIEQQDKE 1368


>gi|320352910|ref|YP_004194249.1| DNA-directed RNA polymerase subunit beta [Desulfobulbus propionicus
            DSM 2032]
 gi|320121412|gb|ADW16958.1| DNA-directed RNA polymerase subunit beta [Desulfobulbus propionicus
            DSM 2032]
          Length = 1357

 Score = 1548 bits (4007), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1361 (51%), Positives = 960/1361 (70%), Gaps = 13/1361 (0%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F K  +II+ P LI +Q+ SY+HFL  +IAP+ R + GLQ+ F+S+FPIT F+G 
Sbjct: 3    RVRKSFAKTSQIIEPPHLIAMQRESYEHFLQRDIAPELRKDHGLQSIFQSIFPITDFNGL 62

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              LEFV Y F  PK+ V +C+ R +TY  PLKIT+RLI FDVDE TG +S++DIKEQ ++
Sbjct: 63   CSLEFVRYSFGEPKYTVAECIERGMTYEAPLKITVRLITFDVDEATGVQSVRDIKEQEVF 122

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G LPLMT+DG FV+ G +R++V+QL RSPG+ + HD G++  SGK LY+ RIIP +G W
Sbjct: 123  LGALPLMTQDGVFVVNGTERVIVNQLQRSPGLFYTHDHGKSHASGKRLYSARIIPVRGSW 182

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KDI++VRIDRRRK+PV+  L ALG   E++L+ FY   V +  G+ +    +A
Sbjct: 183  LDFEFDIKDILYVRIDRRRKLPVSVLLKALGYGDEQLLNEFYHSDVITCEGEKYSIAFNA 242

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                   ++++ ++    G  + + GKK+T  L K ++  GV  + I  + L G Y A D
Sbjct: 243  I-TFANQRLNTDIIHPGDGTIIAKKGKKVTKTLAKKIESLGVASISIDVEELYGRYFARD 301

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            IVN +TGE+ ++  D +   +LE +  + I    +L++D VN +   R TL+ DK KD  
Sbjct: 302  IVNEQTGEVVVKCNDTVTPATLEALAVAGINSFSLLFIDGVNFSESFRKTLLLDKIKDTD 361

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL++IYR +RP    T  VA++ F+ LFF+   YDLS VGR K+N +L +DTP +VR +
Sbjct: 362  EALIEIYRRLRPSSPPTLEVAKAFFDNLFFNPATYDLSEVGRYKINTKLGVDTPIEVRTL 421

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +EDII  +K LV +++     DDID+LGNRRVR+VGE+ +NQ+R+GL+RMER+IKER++
Sbjct: 422  TQEDIIKSVKYLVRIKDELKDGDDIDHLGNRRVRTVGELCENQFRMGLVRMERAIKERMT 481

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +I+++MP DL+N KPV SA+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R
Sbjct: 482  LQEIETLMPHDLVNPKPVTSAIKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLSR 541

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGRICP ET EG NIGL+ SL ++A VN YGFIETPYR V D  V+
Sbjct: 542  ERAGFEVRDVHPTHYGRICPVETPEGPNIGLIVSLATYAMVNPYGFIETPYRYVQDRIVS 601

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            N+  YLSA++EE+  IA A   LD D    ++ +  R   E  +V  + I  +D +P Q+
Sbjct: 602  NEYKYLSALQEEDHVIAPAKIPLDGD-RIADDYLIARQESEVAMVAADDITMMDIAPNQM 660

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP VGTG+E  VA+ SGA ++A  
Sbjct: 661  VSVAASLIPFLENDDANRALMGSNMQRQAVPLLKTSAPLVGTGVEKYVARDSGACLLAGG 720

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G+VE+ DA RIV+R  +  +D   +G+ +Y L K+++SNQNTC NQ+ LV  G  V + 
Sbjct: 721  DGVVEEADANRIVVRYDQPGVDGFDTGIGVYHLSKYKKSNQNTCFNQKALVLPGQRVVKG 780

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             ++ADGPST++G+LALG+N+ +AFMPW GYNFEDS+LI+ER++ ED FTS+HIE FE MA
Sbjct: 781  TVLADGPSTEVGELALGKNVTIAFMPWRGYNFEDSILINERLLKEDTFTSVHIEIFETMA 840

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG EEITRDIPNV EEGL+N+D+ GI+ +GAEV  GD+LVGK+TPKGES ++PEEK
Sbjct: 841  RDTKLGKEEITRDIPNVGEEGLRNLDDSGIVRIGAEVRAGDMLVGKVTPKGESMLSPEEK 900

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DV+D+SLRVP G+ G V+D ++F+R G+DK+ER++ +E  +IE L RD 
Sbjct: 901  LLRAIFGEKAGDVKDSSLRVPPGIEGVVIDAKVFSRKGVDKDERTLMIEEMEIERLNRDM 960

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKG------FKKSTVLSSDLISEYPRSQWWQFA 1025
            + E   L   + + L  +L G+ A S  K        K    L++ ++S+   ++     
Sbjct: 961  EAELRSLKNGVRNSLAVLLEGRTAKSDIKDKKGKIILKLGKQLTAKVVSQISFAELHDLD 1020

Query: 1026 VQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
              +  K +  ++++  +Y T  S++  R++  +E+++ GDD+PPGV+++VK++VA KR +
Sbjct: 1021 FSERAKYEDEIDAIFKRYNTQASVVRGRYQGIVERMEKGDDLPPGVVKMVKIYVATKRKL 1080

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSR+LP EDMPF  DGT VDIVLNPLGVPSRMNVGQ+ E HLG+A
Sbjct: 1081 AVGDKMAGRHGNKGVVSRLLPEEDMPFFADGTTVDIVLNPLGVPSRMNVGQVLECHLGFA 1140

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG+++ ++        + + L+  L ++     +        D+ +L +  ++  G+
Sbjct: 1141 AKRLGEQLSAVA----KQKEAARLKQRLAQIYSQEEYARLTEGLSDEELLDMMCKYGHGI 1196

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             V+TPVFDGA E  I   L  A +DE GQS LYDGLTGEPFD  VTVG +YMLKL+H+V 
Sbjct: 1197 HVATPVFDGASENEIRQALVEAGVDEVGQSTLYDGLTGEPFDNQVTVGVMYMLKLHHLVD 1256

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            +K++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY L+E LT+KSDDV G
Sbjct: 1257 NKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYTLKEFLTVKSDDVEG 1316

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            RT +YE IV GN+  ETG PESF+VLVKE++ L L I+L  
Sbjct: 1317 RTTMYEKIVKGNNFLETGLPESFHVLVKELKGLCLDIELLE 1357


>gi|323700800|ref|ZP_08112712.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio sp. ND132]
 gi|323460732|gb|EGB16597.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio
            desulfuricans ND132]
          Length = 1379

 Score = 1548 bits (4007), Expect = 0.0,   Method: Composition-based stats.
 Identities = 689/1363 (50%), Positives = 937/1363 (68%), Gaps = 15/1363 (1%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK FGK    + IP L+E+Q  SY+ FL  +  P  R + GL+  F+SVFPI  F+  A
Sbjct: 4    LRKKFGKIVNTLPIPHLLELQVDSYNRFLQADTPPASRGDFGLEGVFRSVFPIEDFNKTA 63

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L+FVSYE   PK+DVD+C+ + LTY  P++IT+RL+VFDVDE T  ++I+DIKEQ IY 
Sbjct: 64   SLDFVSYEIGEPKYDVDECISKGLTYETPIRITVRLVVFDVDEETDNRTIRDIKEQDIYF 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G LPLMT+ GT+VI G +R++V+QL RSPGI F+HD G++  S K+LY+ RIIP +G W+
Sbjct: 124  GTLPLMTEKGTYVINGTERVIVNQLQRSPGIIFEHDSGKSHSSRKVLYSSRIIPMRGSWL 183

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D +FD KDI++VRIDRRRK+PVT  L A+G+   +IL  FY    Y+         + A 
Sbjct: 184  DFDFDHKDILYVRIDRRRKMPVTILLKAMGLSRADILDYFYEIESYTLLKTKVMRTVVAE 243

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                 A  +   VD   G+ +++ G  +T G  K L +  VK + +  D L G ++A D+
Sbjct: 244  QYRKEAAYADVDVD---GKSILKKGVDITRGAWKKLIKAEVKAIEVDPDSLIGQFLARDM 300

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+ + GE+  EA + +    L+++  ++I+D+ +L+   +  ++ +R+TL+ DK  D + 
Sbjct: 301  VD-KNGEVIAEAAEELTADLLDKLRDAKIKDLDVLHTRGMEVSSSLRDTLLLDKTTDMES 359

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A ++IYR +RP    T  +A S F  LF  SD YDLS+VGR K+N RLN D    +R + 
Sbjct: 360  AQIEIYRRLRPSSPPTPEIAASFFENLFRSSDYYDLSSVGRYKLNSRLNQDVDLSIRTLT 419

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             EDI+  +K L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S 
Sbjct: 420  NEDILLAVKELMRLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSL 479

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++ ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 480  QEVATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 539

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN YGFIETPYRKV D K+T+
Sbjct: 540  RAGFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDYGFIETPYRKVVDKKITD 599

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
             V Y+ A +E    +AQAN+ LD++G FT + V  R AGE  L   E +  +D SP Q V
Sbjct: 600  VVTYMDASKEAKEVVAQANAPLDKNGVFTNQRVNARWAGEVQLTAAEDVTCMDISPSQTV 659

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            SI+A+LIPFLE+DD+NR LMG NM RQAVPLLKAE P VGT ME  VA+ SGA ++AK  
Sbjct: 660  SISAALIPFLEHDDANRALMGSNMMRQAVPLLKAEEPLVGTDMEGPVARDSGACVLAKED 719

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++  VDA RI+I    G   P T G   Y L K+ +SNQN+C  Q P V+VG  VR+ D
Sbjct: 720  GVIHYVDAERIIINYDNGLF-PETGGAKHYELQKWHKSNQNSCFGQTPRVQVGQRVRKGD 778

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            ++ADGP  D G+LALG+N+LVAFMPW G+N+EDS+LISERMV EDV+TSIHIEEFE++AR
Sbjct: 779  VLADGPGIDHGELALGKNLLVAFMPWCGFNYEDSVLISERMVKEDVYTSIHIEEFELVAR 838

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLGPEE+TRDI NVSEE L+N+DECGII +GA + P DI+VGKITPKGE+ +TPEEKL
Sbjct: 839  DTKLGPEEVTRDISNVSEEMLRNLDECGIIRIGARIKPDDIMVGKITPKGETQLTPEEKL 898

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFG+KA DV++TSL+VP G++GT+VDV++FNR   +K++R+ ++E  ++      + 
Sbjct: 899  LRAIFGDKARDVKNTSLKVPPGIAGTIVDVKVFNRRSGEKDDRTKAIEDAELAAFDVKEQ 958

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKK------STVLSSDLISEYPRSQWWQFAV 1026
                 L   I  ++  ++ G        G KK        V+  + + E P  +     +
Sbjct: 959  KHVAALTDAIREKVWAVVEGAKLKKDLAGPKKATLGKTGEVIDRESVDEVPVKKL--IGL 1016

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D +V   ++ +   YE   + +++ +  K EK+  GDD+PPGV+++VKV+VA+KR +  
Sbjct: 1017 FDREVNDQLKLIVADYEQQIAFIKNIYDVKREKVTEGDDLPPGVIKMVKVYVAVKRKLSV 1076

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMPF +DGT +DIVLNPLGVPSRMN+GQI ETHLG A  
Sbjct: 1077 GDKMAGRHGNKGVVSCILPEEDMPFFEDGTSMDIVLNPLGVPSRMNIGQIMETHLGMAGR 1136

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG++++ ++   ++   +  +R  ++ ++ T    E I    D+  +   ++ K+G+  
Sbjct: 1137 KLGQQVQQML--EESGNSLKAIREEVKSILDTQDMNELIDTMSDEEFVDAVKKLKNGIVA 1194

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFDGA+E+ I   L  A L   G+ ILYDG TGEPF   VTVG +Y LKL+H+V +K
Sbjct: 1195 KTPVFDGAEEDGIWGWLEKAGLASDGKFILYDGRTGEPFHNRVTVGIMYYLKLHHLVDEK 1254

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR 
Sbjct: 1255 IHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVQGRV 1314

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            ++YE IV G++  E G PESFNVLVKE+ +LGL + L     K
Sbjct: 1315 KMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVTLHYEDRK 1357


>gi|283851496|ref|ZP_06368776.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio sp. FW1012B]
 gi|283573030|gb|EFC21010.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio sp. FW1012B]
          Length = 1368

 Score = 1548 bits (4007), Expect = 0.0,   Method: Composition-based stats.
 Identities = 685/1362 (50%), Positives = 929/1362 (68%), Gaps = 14/1362 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK  + + IP L+ +Q  SY+ FL  ++ P  R + GL+  F+SVFPI  F+  A L
Sbjct: 6    KNFGKIVKTLTIPHLLNLQIDSYELFLQKDVPPTSREDAGLEGVFRSVFPIEDFNRTASL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSYE   PK+DV +C+ + LTY  PL+I +RL+V+DVDE T  ++I+DIKEQ IY G 
Sbjct: 66   EYVSYEIGEPKYDVPECIGKGLTYEAPLRIKVRLVVYDVDEETENRTIRDIKEQVIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +PLMT+ GTF+I G +R++V+QL RSPGI F+HD G++  S K+LY+CR+IP +G W+D 
Sbjct: 126  VPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKSHTSRKVLYSCRVIPMRGSWLDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            ++D KDI++VRIDRRRK+P T    A+GM   +IL  FY    ++  G    F     D 
Sbjct: 186  DYDHKDILYVRIDRRRKMPATILFKAMGMSRVDILRYFYEIEHFTVEG-PRVFRQVHPDF 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                K    + D + G+ ++   K +T    + + E G++ + +    L GL++AED+++
Sbjct: 245  YRKEKAYGEVRDAE-GKTIVAVDKPITKRAWRLMLEAGIEKIEVDPATLTGLFLAEDVLD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D +    +E++  + + D P+L+   V+ ++ IR+T+  DK  D   A 
Sbjct: 304  VATGEVLAEAADELTPDVVEKLKDAGVADFPVLHTRGVDTSSSIRDTMALDKTIDTITAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A + F  LF +SD YDLS VGR K+N RL +D P D R +  +
Sbjct: 364  VEIYRRLRPSSPPTPEIAANFFENLFRNSDYYDLSPVGRYKLNARLKIDQPLDFRTLAND 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  +K L  L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILKAVKHLTFLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT+ ++VN +GFIETPYR V D +VT++V
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTHSKVNDFGFIETPYRVVRDSQVTDEV 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            VYL A  E +  IA AN+ LD +  F   +V  R  G+ I+ PRE++  +D SP Q+VS+
Sbjct: 604  VYLDATREIDEVIAGANAELDAEARFIHPMVGSRIRGDLIMTPREQVTLMDISPSQIVSV 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTGME  VAK SG+ ++A+  G+
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRCEQPLVGTGMEGPVAKDSGSCLLAEAPGV 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA R VI   +G + P T G   Y L+K  +SNQNTC  Q P V+VG  V + D++
Sbjct: 724  VHYADAER-VIVCYDGTVSPDTGGAKTYELLKHHKSNQNTCFGQVPRVRVGQRVVKGDVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP    G+LALG+N+LVAFMPW GYN+EDS+LI+E+ V +D FTS+HIEEFEV+ARDT
Sbjct: 783  ADGPGIRDGELALGKNLLVAFMPWCGYNYEDSILIAEKAVKDDTFTSVHIEEFEVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE L ++DECGII +GA+V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 843  KLGPEEITRDIPNVGEEMLNDLDECGIIRIGAKVVPDDILVGKITPKGETQLTPEEKLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DVR+FNR   +K+ER+ S+E  ++  L   +   
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTVIDVRVFNRRSGEKDERTRSIEDYELSRLDIKEGQH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAVQ 1027
               +  N+  R+  ++ G+      KG KK+ V       ++ +L+   P  +       
Sbjct: 963  IDAIAANMRRRIWPLVAGKTVFQTIKGSKKNEVLLEANHPITQELLETLPIKKLSGI-FS 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             ++    V  L  +Y+     ++  +  K EK+  GDD+PPGV+++VKV+VA+KR +  G
Sbjct: 1022 SKEANEAVAELLDEYDRHIHFVKGVYDQKREKVTEGDDLPPGVIKMVKVYVAVKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DGTPVDIVLNPLGVPSRMN+GQI ETHLGWA + 
Sbjct: 1082 DKMAGRHGNKGVVSCILPEEDMPFFADGTPVDIVLNPLGVPSRMNIGQIMETHLGWAGME 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LGK++ +LI   K    +  +R+  + V         I    DD + +  +  K G+   
Sbjct: 1142 LGKQLAALIESGKP---MEGVRAEAKSVFSAADTVAMIDGMTDDELRKALKGLKKGIVAK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E+ +   L+ A L E G+  LYDG TGE F RPVTVG +Y+LKL+H+V +K+
Sbjct: 1199 TPVFDGATEDEMWGWLKQAGLPEDGKVTLYDGRTGEAFHRPVTVGCMYILKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVGGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            +YE IV G++  E G PESFNVLVKE+ +LGL +DL     K
Sbjct: 1319 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVDLIQDEKK 1360


>gi|239907752|ref|YP_002954493.1| DNA-directed RNA polymerase beta subunit [Desulfovibrio magneticus
            RS-1]
 gi|259494180|sp|C4XIN9|RPOB_DESMR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|239797618|dbj|BAH76607.1| DNA-directed RNA polymerase beta subunit [Desulfovibrio magneticus
            RS-1]
          Length = 1369

 Score = 1545 bits (4001), Expect = 0.0,   Method: Composition-based stats.
 Identities = 679/1362 (49%), Positives = 924/1362 (67%), Gaps = 13/1362 (0%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK  + + IP L+ +Q  SY+ FL  +I P  R + GL+  F+SVFPI  F+  A L
Sbjct: 6    KNFGKIVKTLTIPHLLNLQIDSYELFLQKDIPPTSREDAGLEGVFRSVFPIEDFNRTASL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSYE   PK+DV +C+ + LT+  PL+I +RL+V+DVDE T  ++I+DIKEQ IY G 
Sbjct: 66   EYVSYEIGEPKYDVPECIAKGLTFEAPLRIKVRLVVYDVDEETENRTIRDIKEQIIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +PLMT+ GTF+I G +R++V+QL RSPGI F+HD G++  S K+LY+CRIIP +G W+D 
Sbjct: 126  VPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKSHTSRKVLYSCRIIPMRGSWLDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            ++D KDI++VRIDRRRK+P T    A+GM   +IL  FY    ++       F     D 
Sbjct: 186  DYDHKDILYVRIDRRRKMPATILFKAMGMSRADILRYFYEVEHFTFEP-HHVFRQVLPDF 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                K  S + D + G+ ++   K +T    + + E G++ + +    L GL++AED+ +
Sbjct: 245  YRKEKAYSEIRDSE-GKVIVAVDKPITKRAWRLMLEAGIEKVEVDPATLLGLFLAEDLAD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EAGD ++   +E++  + I ++ +L+   V+ ++ IR+TL  DK  D   A 
Sbjct: 304  PATGEVMAEAGDELNADLIEKLKDAGIVELSLLHTRGVDTSSSIRDTLALDKTIDTITAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A + F  LF + D YDLS VGR K+N RL +D P D R +  +
Sbjct: 364  VEIYRRLRPSSPPTPEIAANFFENLFRNPDYYDLSPVGRYKINARLKVDQPLDFRTLAND 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  +K L  L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILKAVKHLTFLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT+ ++VN +GFIETPY+ V DG++T + 
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTHSKVNDFGFIETPYKVVKDGQLTGET 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            +YL A  E +  IA AN+ LDE+ +F   +V  R  G+++++PRE++  +D SP Q+VS+
Sbjct: 604  IYLDATREIDEVIAGANAPLDENKAFINSMVGARIRGDQVVIPREQVTLMDISPSQIVSV 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTGME  VAK SG+ I+A+  G 
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRCEQPLVGTGMEGAVAKDSGSCILAEGEGF 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RI++   +  +   T     Y L+K  +SNQNTC  Q P V VG  V + D++
Sbjct: 724  VHYADAERIIVCYDDPAVGTDTGSAKTYELLKHHKSNQNTCFGQVPRVLVGQRVVKGDVL 783

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP    G+LALG+N+LVAFMPW GYN+EDS+LISE  V +D FTS+HIEEFEV+ARDT
Sbjct: 784  ADGPGIRDGELALGKNLLVAFMPWCGYNYEDSILISENAVKDDTFTSVHIEEFEVVARDT 843

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE LK++D+CGII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 844  KLGPEEITRDIPNVGEEMLKDLDDCGIIRIGARVAPDDILVGKITPKGETQLTPEEKLLR 903

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DVR+FNR   +K++R+  +E  ++  L   +   
Sbjct: 904  AIFGDKARDVKNTSLKVPPGIEGTVIDVRVFNRRSGEKDDRTRQIEDFELARLDTKEGQH 963

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               +  N+  RL  ++ G+      KG KK  VL       + +++   P  +       
Sbjct: 964  AAAIAANVRRRLWPVVSGKTVFQTIKGVKKGEVLLEANHPMTQEVLEALPVKKLSGLFTS 1023

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             E     V  +  +Y+     ++  +  K EK   GDD+PPGV+++VKV+VA+KR +  G
Sbjct: 1024 KE-TNEAVAEVLDEYDRHIQFIKGLYDQKREKTTEGDDLPPGVIKMVKVYVAVKRKLNVG 1082

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF   G PVDIVLNPLGVPSRMN+GQI ETHLGWA + 
Sbjct: 1083 DKMAGRHGNKGVVSCILPIEDMPFFSHGRPVDIVLNPLGVPSRMNIGQILETHLGWAGME 1142

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  +++  KA   +  +R   + V  T   T  I    DD +       K+G+   
Sbjct: 1143 LGRQLAEMVDSGKA---MEGVRDRAKAVFDTEETTALIDGMSDDDLRDALRALKNGIVAK 1199

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E+ + S L++A L E G+  LYDG TGE F RPVTVG +Y+LKL+H+V +K+
Sbjct: 1200 TPVFDGATEDELWSWLKLAGLPEDGKVTLYDGRTGEAFHRPVTVGCMYILKLHHLVDEKI 1259

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1260 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVGGRVK 1319

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            +YE IV G++  E G PESFNVLVKE+ +LGL +DL     K
Sbjct: 1320 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVDLIQDEKK 1361


>gi|94266150|ref|ZP_01289862.1| DNA-directed RNA polymerase, beta subunit [delta proteobacterium
            MLMS-1]
 gi|93453265|gb|EAT03714.1| DNA-directed RNA polymerase, beta subunit [delta proteobacterium
            MLMS-1]
          Length = 1372

 Score = 1543 bits (3996), Expect = 0.0,   Method: Composition-based stats.
 Identities = 703/1363 (51%), Positives = 969/1363 (71%), Gaps = 12/1363 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             R+RK F K   I++ P LIE+Q  SY+ FL ++  P++R +EGLQ  FKSVFPI  F+ 
Sbjct: 5    RRLRKNFAKTKAIVEKPHLIEMQSRSYEQFLQLHTPPEQRLDEGLQGIFKSVFPIKDFNE 64

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            A  LE+V+Y F  PK+ V++C  R +TY VP+++T+RL+ +D D  +GAKSI+DIKEQ++
Sbjct: 65   ACSLEYVNYTFGEPKYTVEECAQRGMTYEVPVRMTVRLVTYDTDPDSGAKSIRDIKEQAV 124

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+G +PLMTK G FV+ G +R++VSQL RSPG+ + HD G+    GKLLY+ RIIP +G 
Sbjct: 125  YLGSIPLMTKAGVFVVNGTERVIVSQLQRSPGLFYSHDGGKTHAGGKLLYSARIIPVRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+D+EFD+KDI++VRIDRRRK PV++ L ALG  SEE+L  FY         + +     
Sbjct: 185  WIDLEFDAKDILYVRIDRRRKFPVSTLLKALGYSSEELLRYFYQTEQIKISRNKFKKKFD 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             A  MVG ++   L++   GE +   G+K+   L K + E G+  L I +  L G     
Sbjct: 245  PA-TMVGQRLPHDLINPADGEVLARKGRKVGKALAKKISEAGIASLDIEAADLVGKVTVA 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             I N ETGE+ I A   + E  LEEI  ++++   IL +D +  +     TL  D+ + R
Sbjct: 304  PIANPETGEVMIPANTELTESMLEEILAAKVKAFEILVIDGITVSDSFSKTLQLDRVESR 363

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            +DAL++IYR +RP    T  VAES FN LFF+ + YDLS VGR K+N RL ++T   +  
Sbjct: 364  EDALIEIYRRLRPSSPPTMEVAESFFNNLFFNPELYDLSVVGRFKINARLGIETDTSIHT 423

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +  EDI+  ++ L  L++ +G IDDID+LGNRRVR+VGE+++NQYR+GL+RMER+IKER+
Sbjct: 424  LTVEDIMLAVRKLAQLKDAQGGIDDIDHLGNRRVRTVGELVENQYRMGLVRMERAIKERM 483

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            S  +++++MP DLIN KP+ +AV EFF +SQLSQ  +  N LS +TH RRLSALG GG++
Sbjct: 484  SLQEVETLMPHDLINPKPITAAVKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLS 543

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVHPTHYGRICP ET EG NIGL+ SL S+ARVN YGFIETPYR+V + ++
Sbjct: 544  RERAGFEVRDVHPTHYGRICPVETPEGPNIGLIVSLASYARVNQYGFIETPYRQVKNRQL 603

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            T+++ Y++A++EE R IA A + +D  G  T E +  R  GE ++   ++I  +D SP Q
Sbjct: 604  TDEINYMTALDEEGRVIAPARTEVDAQGKLTPETLIARLDGEVMISTADEITDMDVSPNQ 663

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS+AASL+PFLENDD+NR LMG NMQRQ VPLL++E+P VGTG+ES VA+ SG  ++A 
Sbjct: 664  LVSVAASLVPFLENDDANRALMGSNMQRQGVPLLRSESPLVGTGLESAVARDSGVCLLAG 723

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              G++E+VDA RIV+R  E   D  T+G+ IYRL K+++SNQNTC  QRPLV  G  V++
Sbjct: 724  GDGVIEEVDANRIVVRYDEPGTDGFTTGIGIYRLEKYKKSNQNTCFTQRPLVDPGVRVKK 783

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
             +I+ADGP+ + G+LAL +N+ VAFMPW GYN+EDS+L++ER++ +D +TS+HIE FE +
Sbjct: 784  GEILADGPACEQGELALAKNVTVAFMPWRGYNYEDSILVNERLLKQDTYTSLHIEVFETV 843

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            ARDTKLG EE+TRDIPNVSE+ L+N+DE GII  GAE+  GDILVGKITPKGE+ ++PEE
Sbjct: 844  ARDTKLGKEEVTRDIPNVSEDALRNLDESGIIRSGAEIKSGDILVGKITPKGETQLSPEE 903

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
            KLLRAIFGEKA DV+DTSLRVP GV G VVD ++F+R G++K+ER++++E  +I+ L RD
Sbjct: 904  KLLRAIFGEKAGDVKDTSLRVPPGVEGVVVDAKVFSRKGVEKDERTLAIEEAEIKALERD 963

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK------KSTVLSSDLISEYPRSQWWQF 1024
             +DE  +L  ++ + + E+L G+ A S  K  K      K   L+ +++++   S+  + 
Sbjct: 964  LEDELQLLAGSVRNGVAELLVGKVAKSVVKNRKGEEILAKGKKLNREVLNKLSPSEIKKL 1023

Query: 1025 AVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                 E ++  V+ L  ++E+    +  R++ +I ++Q GDD+PPGV+R+VKV+VA+KR 
Sbjct: 1024 DYAGRESLEGEVKLLFDRHESQIKAVRSRYEARISRLQKGDDLPPGVIRMVKVYVAIKRK 1083

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +  GDKMAGRHGNKG+VSRILP EDMP+  DGT VD+VLNPLGVPSRMNVGQ+ E HLG 
Sbjct: 1084 LAVGDKMAGRHGNKGVVSRILPEEDMPYFADGTSVDVVLNPLGVPSRMNVGQLLEIHLGL 1143

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LGK+++ +        D++ ++  L  V     + + + D  DD +L +A +  +G
Sbjct: 1144 AAKELGKQVQQMA----EARDLAAVKKKLAAVYSPQEYEQLVGDLSDDELLELASRMGNG 1199

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            + ++TPVFDGA E+ I  +L  A LDE GQ  LYDGL+GE FD  VTVG +Y+LKL+H+V
Sbjct: 1200 LHMATPVFDGAREDEIRQLLVEAGLDEIGQIELYDGLSGEKFDNKVTVGSMYVLKLHHLV 1259

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y LQE LT+KSDDV 
Sbjct: 1260 DDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGASYTLQEFLTVKSDDVG 1319

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            GRTR+YE IV GN+  E G PESF+VLVKE+Q L L ++L + 
Sbjct: 1320 GRTRMYERIVKGNNFLEAGLPESFHVLVKELQGLCLDMELLDE 1362


>gi|303327284|ref|ZP_07357726.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio sp.
            3_1_syn3]
 gi|302863272|gb|EFL86204.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio sp.
            3_1_syn3]
          Length = 1379

 Score = 1543 bits (3994), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1368 (50%), Positives = 930/1368 (67%), Gaps = 14/1368 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA-PDERPNEGLQAAFKSVFPITAFSGAAM 73
            K FGK    + IP L+ +Q  SY  FL   +   D RP+EGL+  F +VFPI  F+  A 
Sbjct: 6    KQFGKIKISLPIPHLLNLQIDSYQKFLQEGVPEADRRPDEGLEGVFHTVFPIEDFNKTAS 65

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFVSYE   PK+D  +C+ + LTY  P++I +RL+V+D DE +G ++I+DIKEQ IY G
Sbjct: 66   LEFVSYEVQEPKYDQAECISKGLTYEAPMRIKVRLVVYDADEASGNRTIRDIKEQDIYFG 125

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D
Sbjct: 126  TLPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDGGKTHTSRKVLYSCRVIPMRGSWLD 185

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
             +FD KDI++VRIDRRRK+P T    A+GM  E+IL  FY +  Y        F     D
Sbjct: 186  FDFDHKDILYVRIDRRRKMPATILFKAMGMSKEQILDYFYSREQYLLEDGGRLFWEVRKD 245

Query: 254  LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
            L       + +   D G  ++++GK +T    + + E G+  + +  D L G+++AED V
Sbjct: 246  LYRKDNAYADITAPD-GNVLVKAGKPITKRSWRLICEAGIPAIEVRPDLLDGMFLAEDAV 304

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
              ++GE+  EA D I    LE +  + I+ + +L+    + ++ IR+TLV D+  D++ A
Sbjct: 305  APQSGEVLAEAADEITPGLLERMREAGIKRLSVLHTKGTDTSSSIRDTLVLDRIPDQQKA 364

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
              +IYR +RP    T  +A S F+ LF + D YDLS VGR K+N RL +D P D+R +  
Sbjct: 365  QEEIYRRLRPSSPPTAEIAASFFDNLFRNPDYYDLSPVGRYKLNQRLGIDAPADLRTLND 424

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            EDI+  IK+LV L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  
Sbjct: 425  EDILTAIKVLVQLKDSHGPADDIDHLGNRRVRLVGELVENQYRIGLVRMERAIKERMSLQ 484

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            +I ++MP DLIN KPV + + EFF +SQLSQ  +  NSLS +TH RRLSALG GG+ R R
Sbjct: 485  EISTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNSLSEVTHKRRLSALGPGGLTRER 544

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            AG E+RDVH +HYGRICP ET EG NIGL+ SLT+FA+VN YGFIETPYR V +G+VT++
Sbjct: 545  AGFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTFAKVNDYGFIETPYRVVREGRVTDE 604

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            VV+L A  E ++ +AQA++ LD +G   EE V  R  GE  +  R+++  +D SP Q+VS
Sbjct: 605  VVHLDASREGDQVVAQADARLDGEGHLLEEFVTVRVKGEVEMRHRDEVTLMDISPSQMVS 664

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I+A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA IVA   G
Sbjct: 665  ISAALIPFLEHDDANRALMGSNMQRQAVPLLRSEKPLVGTGMEVDVARDSGACIVAPADG 724

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             V+  DA RIV+   EGD+     GV  Y L+KF +SNQN+C  Q+P    G  V++  I
Sbjct: 725  KVQYADADRIVVAY-EGDIYKDQGGVRAYDLLKFHKSNQNSCFGQKPTCYPGQIVKKGQI 783

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADGP  D G LALG+N++VAFMPW GYN+EDS+LISER V EDVFTSIHIEEFEV+ARD
Sbjct: 784  LADGPGIDEGQLALGKNLVVAFMPWCGYNYEDSILISERTVKEDVFTSIHIEEFEVVARD 843

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            TKLGPEEITRDIPNVSE+ L+N+DE GII +GA V P DILVGKITPKGE+ +TPEEKLL
Sbjct: 844  TKLGPEEITRDIPNVSEDMLRNLDESGIIRIGAAVKPDDILVGKITPKGETQLTPEEKLL 903

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            RAIFGEKA DV++TSL+VP GV GT++DV++FNR   +K+ER++++E     +L + + D
Sbjct: 904  RAIFGEKARDVKNTSLKVPPGVEGTIIDVKVFNRRSGEKDERTLAIEAHDTSVLDQKEAD 963

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAV 1026
                L       L   + G+   +   G KK  V       L+ + +++ P  +      
Sbjct: 964  HMRALTERTRDLLAPHVLGKQIAASLPGKKKGEVLAEAGAALTEEQLAQLPVKKLAGL-F 1022

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            + ++V   V  L   Y+     L+  +  K EK+  GDD+PPGV+++VKV +A+KR +  
Sbjct: 1023 KSKEVNDEVAELLRAYDHEVDYLKAIYDAKREKVTEGDDLPPGVIKMVKVHIAIKRKLSV 1082

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGW   
Sbjct: 1083 GDKMAGRHGNKGVVSCILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWGAK 1142

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG+++  L++   +   +  LR  ++ V G+      +   DD+  +   ++ ++G+  
Sbjct: 1143 ELGRQLAELVD---SGAAMQVLRKEVKDVFGSEEVRALVDGMDDEEFVASVKKLRNGIVT 1199

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFD A EE I   +  A L+  G++ LYDG TG PF   VT G +Y+LKL+H+V +K
Sbjct: 1200 KTPVFDSATEEDIWGWMDKAGLENDGKTTLYDGRTGVPFRNRVTTGVMYILKLHHLVDEK 1259

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR 
Sbjct: 1260 IHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGRV 1319

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            ++YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K 
Sbjct: 1320 KMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKKPKR 1367


>gi|317485872|ref|ZP_07944734.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
 gi|316922887|gb|EFV44111.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
          Length = 1387

 Score = 1541 bits (3990), Expect = 0.0,   Method: Composition-based stats.
 Identities = 686/1367 (50%), Positives = 933/1367 (68%), Gaps = 13/1367 (0%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK    ++IP L+ +Q  SY  F+      +  P+EGL+  F+SVFPI  F+  A L
Sbjct: 6    KQFGKIKVEVEIPHLLNLQVDSYRKFMQEGRT-ERLPDEGLEGVFRSVFPIEDFNRTASL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            EFVSYE   PK+D  +C+ + LTY  P++I +RL+V+DVD+ T A++++DIKEQ IY G 
Sbjct: 65   EFVSYEVGEPKYDQAECISKGLTYESPVRIKVRLVVYDVDDETEARTVRDIKEQDIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDGGKTHTSRKVLYSCRVIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T  L A+GM   EIL  FY K +Y    D         +L
Sbjct: 185  DFDHKDILYVRIDRRRKMPATILLKAMGMSKTEILDCFYKKEIYELEDDGRVSWHFNPEL 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                   + +VD   G  ++++GK +T    + ++  GV+ + +  +   GL++AED+V+
Sbjct: 245  HRKEAAFADIVD-KEGNVLVKAGKPITKRAWRQMEAAGVEKIEVAPETPLGLFLAEDLVD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGEI  EA D I     +    + I  I  L+    + ++ IR+TLV DK    + A 
Sbjct: 304  NATGEILAEAADEITAGLFDACREAGITTISALHTRGTDTSSSIRDTLVQDKTPTMEKAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             +IYR +RP    T  +A S F+ LF + D YDLS VGR K+N RLN     D+R +  +
Sbjct: 364  EEIYRRLRPSSPPTPEIAASFFDNLFRNGDYYDLSPVGRYKLNQRLNKTDHADLRTLADD 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  IK+LV L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILDAIKVLVQLKDSHGPADDIDHLGNRRVRLVGELVENQYRIGLVRMERAIKERMSIQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  NSLS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNSLSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN YGFIETPYR + DG +T++ 
Sbjct: 544  GFEVRDVHVSHYGRICPIETPEGPNIGLIVSLTTYAKVNDYGFIETPYRVIRDGYMTDEF 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            V+L A  E    IAQAN+++D D    ++ V  R   + ++  RE+I  +D SP Q+VSI
Sbjct: 604  VHLDASRETGHVIAQANAAVDADRRLVDDYVTARVGDDVLMAAREEITLMDISPSQMVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA I+A+ +G+
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRSERPLVGTGMEVDVARDSGACILAESSGV 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RI++   +  L P+  GV  Y L+KF +SNQN+C  Q P    G  V++ D++
Sbjct: 724  VHYADANRIIVAYDDPALYPNMGGVRAYDLLKFHKSNQNSCFGQVPSCVPGQIVKKGDVL 783

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP+   G LALG+NML+AFMPW GYN+EDS+LISER+V ED++TS+HIEEFEV+ARDT
Sbjct: 784  ADGPAIHDGGLALGKNMLIAFMPWCGYNYEDSVLISERVVKEDIYTSVHIEEFEVVARDT 843

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE L+N+DE GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 844  KLGPEEITRDIPNVGEEMLRNLDESGIIRIGAPVKPEDILVGKITPKGETQLTPEEKLLR 903

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP GV GTV+DV++FNR   +K+ER+ ++E  +I  L   + D 
Sbjct: 904  AIFGDKARDVKNTSLKVPPGVEGTVIDVKVFNRRSGEKDERTRNIEDYEISRLDAKEQDH 963

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               + R +  RL+ I+ G+   +   G KK  VL       + +L+   P  +      Q
Sbjct: 964  IRAITRRMRERLLPIVDGKQIATTLLGDKKGEVLAEAGAAMTEELLMALPVKKLADL-FQ 1022

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             ++V  NV  L VQY+     ++  + +K EK+  GDD+PPGV+++VKV +A+KR +  G
Sbjct: 1023 SKEVNENVGELLVQYDHQIEYIKSIYDSKREKVTEGDDLPPGVIKMVKVHIAIKRKLSVG 1082

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI E HLGWA   
Sbjct: 1083 DKMAGRHGNKGVVSRILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMEVHLGWAARE 1142

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  +++       +  +R  ++ +  +     ++   DD+   +   + ++G+   
Sbjct: 1143 LGRQLAEMVD---KGTALQSVRDEVKDIFASPEIAAEVDGMDDEEFRKSVLKLRNGIITY 1199

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA+E  I + L  A LD+ G+S+LYDG TGE  +  VT G +Y LKL+H+V +K+
Sbjct: 1200 TPVFDGAEESEIWNWLSRAGLDDDGKSVLYDGRTGEKLENRVTTGVMYYLKLHHLVDEKI 1259

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1260 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVTGRVK 1319

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            +YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K 
Sbjct: 1320 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKRPKR 1366


>gi|46581332|ref|YP_012140.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio vulgaris str.
            Hildenborough]
 gi|81404163|sp|Q727C7|RPOB_DESVH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|46450754|gb|AAS97400.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio vulgaris
            str. Hildenborough]
 gi|311234992|gb|ADP87846.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio vulgaris
            RCH1]
          Length = 1372

 Score = 1541 bits (3989), Expect = 0.0,   Method: Composition-based stats.
 Identities = 676/1367 (49%), Positives = 936/1367 (68%), Gaps = 14/1367 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK    + IP L+ +Q  SY  FL    A + R +EGL+  F+SVFPI  F+  A L
Sbjct: 6    KKFGKIDVSLPIPHLLNLQVDSYVKFLQEG-ATERRHDEGLEGVFRSVFPIEDFNRTASL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            EFVSYE   PK+D  +C+ + LTY  P++I +RL+V+DVDE +G ++I+DIKEQ IY G 
Sbjct: 65   EFVSYEVGEPKYDQPECISKGLTYEAPIRIKVRLVVYDVDEDSGNRTIRDIKEQEIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CRIIP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKTHSSRKVLYSCRIIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T    A+GM   +IL  FY K  Y              D+
Sbjct: 185  DFDHKDILYVRIDRRRKMPATILFKAMGMSKTDILDYFYKKEFYRLDPMGRLMWEVQKDM 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                     + D   G  ++++GK +T    + + E G++ + +  D + G+++AEDIVN
Sbjct: 245  YRKDSAFVDIEDGKGG-TIVKAGKPITKRAWRLISEAGLETIEVAPDTIEGMFLAEDIVN 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D I    +E +  + I  +P+L+   +  ++ +R+TLV DK  D + A 
Sbjct: 304  PATGEVLAEAADEITASLVENLREAGISRLPVLHTKGLETSSSLRDTLVLDKTPDMEAAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A S F+ LF  +D YDLS VGR K+N RL +D   D+R +  +
Sbjct: 364  VEIYRRLRPSSPPTPEIAASFFDNLFRSADYYDLSPVGRYKLNQRLGIDQSVDLRTLTDD 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  I++L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILRAIRVLLHLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N+LS +TH RRLSALG GG+ R RA
Sbjct: 484  VSTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN +GFIETPYR + +G +T+++
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDFGFIETPYRIIREGALTDEI 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             +L A  E+   +AQAN+++D DG   +E V  R  G+ ++  R+++  +D SP Q+VSI
Sbjct: 604  KFLDASREQGEVVAQANAAVDADGKLADEYVTARVRGDVLMSHRDEVTLMDISPSQMVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA I+A+  GI
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRSEKPIVGTGMEGDVARDSGACILAEGPGI 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RI++    G L P   GV  Y L K+ +SNQN+C  QRP    G  V++ D++
Sbjct: 724  VRYADATRIIVSYENG-LYPDRGGVRAYDLQKYHKSNQNSCFGQRPTCHPGQIVKKGDVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP  + G+LALG+N++VAFMPW GYNFEDS+LISER+V EDVFTSIHIEEFEV+ARDT
Sbjct: 783  ADGPGIEDGELALGKNLVVAFMPWCGYNFEDSILISERVVKEDVFTSIHIEEFEVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ L+N+D  GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 843  KLGPEEITRDIPNVGEDMLRNLDGSGIIRIGASVKPDDILVGKITPKGETQLTPEEKLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GT++DV++FNR   +K+ER+ ++E  +   + + + D 
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTIIDVKVFNRRSGEKDERTRNIEDYETARIDKKEQDH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               L   +  RL + L G+       G +K  VL       + +L+   P  +      +
Sbjct: 963  VRALGDALRDRLADTLVGKQIAVTLPGKRKGEVLAEAGAPMTRELLDALPVKRLAGL-FK 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
              +V   V++    Y+   + L+  + +K EK+  GDD+PPGV+++VKV +A+KR +  G
Sbjct: 1022 SREVDEMVDTALEDYDRQVAFLKGIYDSKREKVTEGDDLPPGVIKMVKVHIAVKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGW    
Sbjct: 1082 DKMAGRHGNKGVVSCILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWGAKE 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  +++   +   ++ LR  ++ V  + +  + + + DD++  +   + ++G+   
Sbjct: 1142 LGRQLAEMLD---SGAAMATLRHEVKDVFRSATIAKLVDEMDDETFRKAVSKLRTGIVTK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I S +  A +D  G+++LYDG TG+ F   VT G +Y+LKL+H+V +K+
Sbjct: 1199 TPVFDGASEEDIWSWIERAGMDGDGKTVLYDGRTGDKFYNRVTTGVMYILKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVTGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            +YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K 
Sbjct: 1319 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKRPKR 1365


>gi|258406192|ref|YP_003198934.1| DNA-directed RNA polymerase subunit beta [Desulfohalobium retbaense
            DSM 5692]
 gi|257798419|gb|ACV69356.1| DNA-directed RNA polymerase, beta subunit [Desulfohalobium retbaense
            DSM 5692]
          Length = 1363

 Score = 1540 bits (3987), Expect = 0.0,   Method: Composition-based stats.
 Identities = 678/1361 (49%), Positives = 946/1361 (69%), Gaps = 14/1361 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K+FGK P+ ++IP L+ +Q  SY  FL  ++    R ++GL+  F+SVFPI  F+  A L
Sbjct: 6    KYFGKIPQALEIPHLLSLQCDSYLDFLQADVPAASRADKGLEGVFRSVFPIEDFNKTATL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            EFV+YE   PK+D+ +C+ + LTY   ++I +RL+V+DVDE +  ++I+DIKEQ IY G 
Sbjct: 66   EFVNYELGEPKYDIKECISKGLTYEATVRIKVRLVVYDVDEESSHRTIRDIKEQDIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +PLMT+ GTFVI G +R++V+QL RSPG+ F+HD G++  S K+LY+ RIIP +G W+D 
Sbjct: 126  IPLMTEKGTFVINGTERVIVNQLQRSPGLIFEHDYGKSHSSRKVLYSSRIIPMRGSWIDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI+HVRIDRRRK+P T  L A+G+  EEIL+ FY    Y   G+   F     D 
Sbjct: 186  DFDHKDILHVRIDRRRKMPATILLKAMGLSREEILNYFYDVEHYYVIGNR-VFREVQKDY 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
               +     + D + G+ ++ +GK ++  + + + + G++ + +    L   + A ++++
Sbjct: 245  YRRSNAYVDITDAE-GKVLVAAGKAISKPMWRRIVKAGIERIEVDPMELAQQFAASELIH 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             ETGE+  E GD I  ++++ +  +    +P L+   +  +  IR+TL  DK +D + A 
Sbjct: 304  PETGEVLAEPGDQIAPETIDLLGETAETAVPTLFTSGLEVSTSIRDTLELDKTEDEESAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IY+ +RP    T  VA++ F+ LF + + YDLS VGR K+N RL +D P D + +  E
Sbjct: 364  IEIYKRLRPSSPPTSEVAKTFFDNLFRNKEYYDLSPVGRYKLNARLGIDLPLDHQTLSNE 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  IK L  L++  G  DDID+LG RRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILRTIKHLTALKDAHGQPDDIDHLGKRRVRPVGELVENQYRIGLVRMERAIKERMSLRE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RA
Sbjct: 484  VATLMPHDLINPKPVTAVIKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLSRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVHP+HYGRICP ET EG NIGL+ SLT++ RVN YGFIETPYR V  G+VT++V
Sbjct: 544  GFEVRDVHPSHYGRICPIETPEGPNIGLIVSLTTYGRVNPYGFIETPYRVVDKGQVTSEV 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YL A  EE   IAQAN+ +D+ G F ++ V  R  GE  +V R+++  +D SP Q+VS+
Sbjct: 604  KYLDADAEEGEIIAQANAPMDDQGRFVKDQVAARVEGEFAVVDRDEVTLMDISPNQIVSV 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +++LIPFLE+DD+NR LMG NMQRQA PLL+ E P VGTG+E VVA++SGA I+A+  G 
Sbjct: 664  SSALIPFLEHDDANRALMGSNMQRQATPLLRTELPLVGTGLEGVVARNSGACILAEGRGQ 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA R+V+R  +G   P + GV  Y + KF +SNQ++   QRP+V  G+ V +  ++
Sbjct: 724  VTYADADRVVVRYEDGTA-PQSGGVACYTMQKFHKSNQSSSFGQRPVVHTGELVEKGSVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGPS + G+LALG+N+LVAFMPW GYNFEDS+LISER V EDV+TS+HIEEF+V+ARDT
Sbjct: 783  ADGPSIEHGELALGKNLLVAFMPWCGYNFEDSILISERCVKEDVYTSMHIEEFDVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ L+N+DE G+I +GA+V P DILVGKITPKGE+ +TPEE+LLR
Sbjct: 843  KLGPEEITRDIPNVGEDMLRNLDESGMIRIGAKVRPDDILVGKITPKGETQLTPEERLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DV++FNR   +K+ER+  +E +++ +L R++   
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTVIDVKVFNRRSGEKDERTKEIEDQELAVLDRNEQQH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAVQ 1027
               L +N+  ++ EI+ G        G KK  V       LS + ++  P  +     V 
Sbjct: 963  IEGLSQNVRHKVWEIIQGHRVDQSIMGQKKGEVLVEANKTLSEEDLARLPIKKLRGVFVH 1022

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             E     +E L  +Y+ +   ++  +  K EK+  GDD+PPGV+++VKV +A+KR +  G
Sbjct: 1023 KE-TNEALEELLDEYDRNIQFIKSIYDQKREKVTEGDDLPPGVIKMVKVHIAIKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DGTP+DIVLNPLGVPSRMN+GQI ETHLGWA   
Sbjct: 1082 DKMAGRHGNKGVVSCILPEEDMPFFNDGTPMDIVLNPLGVPSRMNIGQIMETHLGWAAKE 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  ++ D     DI  LR  +++V  + S T  +   DD+ ++   ++   G+   
Sbjct: 1142 LGQQLAKMVED---KADIQALRQEVKEVFHSDSVTTLVDTLDDEELVESVKRLDKGIATK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I   L  A L   G+++LYDG TG+PF   VTVGY+YMLKL+H+V +K+
Sbjct: 1199 TPVFDGAQEEEIWEWLERAGLPSDGKAVLYDGRTGDPFYSRVTVGYMYMLKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA++LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAHLLQEFLTVKSDDVQGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +YE IV G++  E+G PESFNVLVKE++ALGL + L +   
Sbjct: 1319 MYEKIVKGDNFLESGMPESFNVLVKELKALGLDVTLLHDEG 1359


>gi|120601489|ref|YP_965889.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio vulgaris DP4]
 gi|158513865|sp|A1VAJ6|RPOB_DESVV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|120561718|gb|ABM27462.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio vulgaris DP4]
          Length = 1372

 Score = 1540 bits (3987), Expect = 0.0,   Method: Composition-based stats.
 Identities = 677/1367 (49%), Positives = 936/1367 (68%), Gaps = 14/1367 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK    + IP L+ +Q  SY  FL    A + R +EGL+  F+SVFPI  F+  A L
Sbjct: 6    KKFGKIDVSLPIPHLLNLQVDSYVKFLQEG-ATERRHDEGLEGVFRSVFPIEDFNRTASL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            EFVSYE   PK+D  +C+ + LTY  P++I +RL+V+DVDE +G ++I+DIKEQ IY G 
Sbjct: 65   EFVSYEVGEPKYDQPECISKGLTYEAPIRIKVRLVVYDVDEDSGNRTIRDIKEQEIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CRIIP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKTHSSRKVLYSCRIIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T    A+GM   +IL  FY K  Y              D+
Sbjct: 185  DFDHKDILYVRIDRRRKMPATILFKAMGMSKTDILDYFYKKEFYRLDPMGRLMWEVQKDM 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                     + D   G  ++++GK +T    + + E G++ + +  D + G+++AEDIVN
Sbjct: 245  YRKDSAFVDIEDGKGG-TIVKAGKPITKRAWRLISEAGLETIEVAPDTIEGMFLAEDIVN 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+  EA D I    +E +  + I  +P+L+   +  ++ +R+TLV DK  D + A 
Sbjct: 304  PATGEVLAEAADEITASLVENLREAGISRLPVLHTKGLETSSSLRDTLVLDKTPDMEAAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR +RP    T  +A S F+ LF  +D YDLS VGR K+N RL +D   D+R +  +
Sbjct: 364  VEIYRRLRPSSPPTPEIAASFFDNLFRSADYYDLSPVGRYKLNQRLGIDQSVDLRTLTDD 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  I++L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILRAIRVLLHLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N+LS +TH RRLSALG GG+ R RA
Sbjct: 484  VSTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN +GFIETPYR + +G +T+D+
Sbjct: 544  GFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDFGFIETPYRIIREGALTDDI 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             +L A  E+   +AQAN+++D DG   +E V  R  G+ ++  R+++  +D SP Q+VSI
Sbjct: 604  KFLDASREQGEVVAQANAAVDADGKLADEYVTARVRGDVLMSHRDEVTLMDISPSQMVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA I+A+  GI
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRSEKPIVGTGMEGDVARDSGACILAEGPGI 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V   DA RI++    G L P   GV  Y L K+ +SNQN+C  QRP    G  V++ D++
Sbjct: 724  VRYADATRIIVSYENG-LYPDRGGVRAYDLQKYHKSNQNSCFGQRPTCHPGQIVKKGDVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP  + G+LALG+N++VAFMPW GYNFEDS+LISER+V EDVFTSIHIEEFEV+ARDT
Sbjct: 783  ADGPGIEDGELALGKNLVVAFMPWCGYNFEDSILISERVVKEDVFTSIHIEEFEVVARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ L+N+D  GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 843  KLGPEEITRDIPNVGEDMLRNLDGSGIIRIGASVKPDDILVGKITPKGETQLTPEEKLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GT++DV++FNR   +K+ER+ ++E  +   + + + D 
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTIIDVKVFNRRSGEKDERTRNIEDYETARIDKKEQDH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-------SSDLISEYPRSQWWQFAVQ 1027
               L   +  RL + L G+       G +K  VL       + +L+   P  +      +
Sbjct: 963  VRALGDALRDRLADTLVGKQIAVTLPGKRKGEVLAEAGAPMTRELLDALPVKRLAGL-FK 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
              +V   V++    Y+   + L+  + +K EK+  GDD+PPGV+++VKV +A+KR +  G
Sbjct: 1022 SREVDEMVDTALEDYDRQVAFLKGIYDSKREKVTEGDDLPPGVIKMVKVHIAVKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGW    
Sbjct: 1082 DKMAGRHGNKGVVSCILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWGAKE 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  +++   +   ++ LR  ++ V  + +  + + + DD++  +   + ++G+   
Sbjct: 1142 LGRQLAEMLD---SGAAMATLRHEVKDVFRSATIAKLVDEMDDETFRKAVSKLRTGIVTK 1198

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I S +  A +D  G+++LYDG TG+ F   VT G +Y+LKL+H+V +K+
Sbjct: 1199 TPVFDGASEEDIWSWIERAGMDGDGKTVLYDGRTGDKFYNRVTTGVMYILKLHHLVDEKI 1258

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1259 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVTGRVK 1318

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            +YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K 
Sbjct: 1319 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKRPKR 1365


>gi|91763154|ref|ZP_01265118.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique HTCC1002]
 gi|91717567|gb|EAS84218.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique HTCC1002]
          Length = 1363

 Score = 1538 bits (3982), Expect = 0.0,   Method: Composition-based stats.
 Identities = 733/1365 (53%), Positives = 982/1365 (71%), Gaps = 7/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F     VRK FGK  E + IP+LIEVQK SY   L    +     ++G    FKS+
Sbjct: 1    MQLSFTQKKNVRKSFGKLSETLSIPNLIEVQKNSYKQ-LTDFDSEAGDLSKGFDRVFKSI 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI   +  A LE+VSY  + PKFD ++C+ R L++   LK TLRL+V+++D+    K I
Sbjct: 60   FPIEDLNDKATLEYVSYRLEKPKFDTEECIQRGLSFTSALKCTLRLVVYEIDQENNTKDI 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KEQ +YMG++P+MT  GTF+  G+QR+VV+Q+HRSPG+ FDHDKG++  SGKLL+ C
Sbjct: 120  LSAKEQEVYMGEVPMMTDSGTFITNGVQRVVVNQMHRSPGVFFDHDKGKSHASGKLLFNC 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP++G W+D+E+D KD ++ +IDR++K+  ++ LMALG+   EI   FY K  YS   
Sbjct: 180  RVIPNRGSWLDLEYDVKDFLYFKIDRKKKIFASTLLMALGLTKSEIADEFYDKDTYSFDA 239

Query: 243  D--FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W    +  +       S  + D  TG  VI+ G K+     K L   G+K + ++ 
Sbjct: 240  KTGKWKTKFNPENY-KAKNFSEEVTDAKTGNVVIKLGDKINFLTAKKLASDGLKDILVSQ 298

Query: 301  DCLCGLYVAEDI-VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + L G Y+  ++ V+ +  E     G  +++  +++I  + I  I I   +S+N   Y+ 
Sbjct: 299  ESLIGKYLHNEVKVSDDEEEGTFGIGTELNDTIIKQILEANITSIEISITNSINKGPYLL 358

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             T++ DKN  + DA+ +IY+V+RPG+  T  +A  +FN LFF SD+YDLS VGRVKMN R
Sbjct: 359  TTILNDKNNSKNDAITEIYKVLRPGEPPTVEIATQIFNNLFFSSDRYDLSDVGRVKMNSR 418

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            LNL+  D +  +R +DIIAI+  ++DLR+GK  +DDID+LGNRRVRSVGE+++NQ R+G+
Sbjct: 419  LNLECSDKITILRNDDIIAIVHKMLDLRDGKDEVDDIDHLGNRRVRSVGELVENQARIGV 478

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             RMER+IKE+++++DI+S MPQDLINAKP+  ++ +FF SSQLSQ  +  N LS ITH R
Sbjct: 479  YRMERAIKEKMTTLDIESAMPQDLINAKPLTVSLKDFFVSSQLSQFMDQTNPLSEITHKR 538

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            R+SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++A++N YGFIE
Sbjct: 539  RVSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYAKINKYGFIE 598

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PY+KV +G V + V YLSAMEE    IAQAN+ +D+ G   EELV CR     +L    
Sbjct: 599  SPYKKVLNGVVQDKVEYLSAMEETKYTIAQANAKIDKSGKILEELVPCRENLNFVLSNPS 658

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            KID+ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPLLK E+P VGTG+ES V
Sbjct: 659  KIDYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLLKPESPLVGTGIESDV 718

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG  IVA R G V+++D  RIVI++ E   D + SGVDIY L KF+RSNQNTC+NQ+
Sbjct: 719  ALDSGVTIVASRDGTVDKIDGKRIVIKATEET-DFTKSGVDIYNLQKFKRSNQNTCINQK 777

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLV+VGD+V+  DIIADGPST LG+LALG+N+ VAFMPW GYNFEDS+LISER V++DVF
Sbjct: 778  PLVRVGDKVKSGDIIADGPSTKLGELALGKNVTVAFMPWQGYNFEDSILISERCVTDDVF 837

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HI E+EVMARDTKLG EEITRDIPNV+EE LKN+DE GI+ +GAEV  GDILVGK+T
Sbjct: 838  TSVHIVEYEVMARDTKLGEEEITRDIPNVNEEALKNLDESGIVYIGAEVKAGDILVGKVT 897

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKG+S   PEEKLLR+IFGEKA+DV DTSL++  G SGTVVDVR+FNRHGI+K+ERSI++
Sbjct: 898  PKGDSASGPEEKLLRSIFGEKAIDVTDTSLKMSRGSSGTVVDVRVFNRHGIEKDERSITI 957

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ER +I+ + +DK  E+ IL+R+I  R  +IL G +     K   + T L  + I++   +
Sbjct: 958  ERAEIDTVQQDKIVEEEILERSIKQRANQILSGASLTKKIKDLDEGTKLDLETINKININ 1017

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
              ++  V +   + ++  LK QY  +K  +++RF++K+ KI+ GDD+ P V+++VKVFVA
Sbjct: 1018 DVFKITVGNVNDEASIAQLKDQYNQAKQDIQERFEDKVLKIRSGDDLLPSVMKMVKVFVA 1077

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR ++ GDKM+GRHGNKG+VS+I+P EDMP+ +DG PVDIVLNPLGVPSRMNVGQI ET
Sbjct: 1078 IKRRLRPGDKMSGRHGNKGVVSKIVPVEDMPYREDGRPVDIVLNPLGVPSRMNVGQILET 1137

Query: 1140 HLGWACVGLGKKIKSLINDYKAN-GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            HLGWAC   G+++K L+N+          + SFL+ V G       I   +      + E
Sbjct: 1138 HLGWACKEFGEEVKRLVNENNKKFEKTEKISSFLKSVYGKEVFDGGIDKLNKTEFSDLCE 1197

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+ +STPVFDGA E+ ++ ML +A L  SGQ+ L+DG TGE FDRPVTVG IYMLK
Sbjct: 1198 NIQNGIAISTPVFDGAKEKDVSEMLELAKLPTSGQTNLWDGRTGEMFDRPVTVGIIYMLK 1257

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+K
Sbjct: 1258 LHHLVEDKIHARSTGPYSLVTQQPLGGKAQLGGQRFGEMEVWALEAYGASYTLQEILTVK 1317

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GR +VYE+IV G + FE+G PESFNVLVKE+++L L+I+L
Sbjct: 1318 SDDVAGRVKVYETIVKGEENFESGIPESFNVLVKEIKSLALNIEL 1362


>gi|71083810|ref|YP_266530.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique HTCC1062]
 gi|88909625|sp|Q4FLL2|RPOB_PELUB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71062923|gb|AAZ21926.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique HTCC1062]
          Length = 1363

 Score = 1538 bits (3982), Expect = 0.0,   Method: Composition-based stats.
 Identities = 733/1365 (53%), Positives = 983/1365 (72%), Gaps = 7/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              + F     VRK FGK  E + IP+LIEVQK SY   L    +     ++G    FKS+
Sbjct: 1    MQLSFTQKKNVRKSFGKLAETLSIPNLIEVQKNSYKQ-LTDFDSEAGDLSKGFDRVFKSI 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI   +  A LE+VSY  + PKFD ++C+ R L++   LK TLRL+V+++D+    K I
Sbjct: 60   FPIEDLNDKATLEYVSYRLEKPKFDTEECIQRGLSFTSALKCTLRLVVYEIDQENNTKDI 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KEQ +YMG++P+MT  GTF+  G+QR+VV+Q+HRSPG+ FDHDKG++  SGKLL+ C
Sbjct: 120  LSAKEQEVYMGEVPMMTDSGTFITNGVQRVVVNQMHRSPGVFFDHDKGKSHASGKLLFNC 179

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP++G W+D+E+D KD ++ +IDR++K+  ++ LMALG+   EI   FY K  YS   
Sbjct: 180  RVIPNRGSWLDLEYDVKDFLYFKIDRKKKIFASTLLMALGLTKSEIADEFYDKDTYSFDA 239

Query: 243  D--FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W    +  +       S  + D  TG  VI+ G K+     K L   G+K + ++ 
Sbjct: 240  KTGKWKTKFNPENY-KAKNFSEEVTDAKTGNVVIKLGDKINFLTAKKLASDGLKDILVSQ 298

Query: 301  DCLCGLYVAEDI-VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + L G Y+  ++ V+ +  E     G  +++  +++I  + I  I I   +S+N   Y+ 
Sbjct: 299  ESLIGKYLHNEVKVSDDEEEGTFGIGTELNDTIIKQILEANISSIEISITNSINKGPYLL 358

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             T++ DKN  + DA+ +IY+V+RPG+  T  +A  +FN LFF SD+YDLS VGRVKMN R
Sbjct: 359  TTILNDKNNSKNDAITEIYKVLRPGEPPTVEIATQIFNNLFFSSDRYDLSDVGRVKMNSR 418

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            LNL+  D +  +R +DIIAI+  ++DLR+GK  +DDID+LGNRRVRSVGE+++NQ R+G+
Sbjct: 419  LNLECSDKITILRNDDIIAIVHKMLDLRDGKDEVDDIDHLGNRRVRSVGELVENQARIGV 478

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             RMER+IKE+++++DI+S MPQDLINAKP+  ++ +FF SSQLSQ  +  N LS ITH R
Sbjct: 479  YRMERAIKEKMTTLDIESAMPQDLINAKPLTVSLKDFFVSSQLSQFMDQTNPLSEITHKR 538

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            R+SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL+++A++N YGFIE
Sbjct: 539  RVSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYAKINKYGFIE 598

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PY+KV +G V + V YLSAMEE    IAQAN+ +D+ G   EELV CR     +L    
Sbjct: 599  SPYKKVLNGIVQDKVEYLSAMEETKYTIAQANAKIDKSGKILEELVPCRENLNFVLSNPS 658

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            KID+ID SPKQ+VS+AASLIPFLENDD+NR LMG NM RQAVPLLK E+P VGTG+ES V
Sbjct: 659  KIDYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMMRQAVPLLKPESPLVGTGIESDV 718

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG  IVA R G V+++D  RIVI++ E   D + SGVDIY L KF+RSNQNTC+NQ+
Sbjct: 719  ALDSGVTIVASRDGTVDKIDGKRIVIKATEET-DFTKSGVDIYNLQKFKRSNQNTCINQK 777

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLV+VGD+V+  DIIADGPST LG+LALG+N+ VAFMPW GYNFEDS+LISER V++DVF
Sbjct: 778  PLVRVGDKVKSGDIIADGPSTKLGELALGKNVTVAFMPWQGYNFEDSILISERCVTDDVF 837

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HI E+EVMARDTKLG EEITRDIPNV+EE LKN+DE GI+ +GAEV  GDILVGK+T
Sbjct: 838  TSVHIVEYEVMARDTKLGEEEITRDIPNVNEEALKNLDESGIVYIGAEVKAGDILVGKVT 897

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKG+S   PEEKLLR+IFGEKA+DV DTSL++  G SGTVVDVR+FNRHGI+K+ERSI++
Sbjct: 898  PKGDSASGPEEKLLRSIFGEKAIDVTDTSLKMSRGSSGTVVDVRVFNRHGIEKDERSITI 957

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ER +I+ + +DK  E+ IL+R+I  R  +IL G +     K   + T L  ++I++   +
Sbjct: 958  ERAEIDTVQQDKIVEEEILERSIKQRANQILSGASLTKKIKDLDEGTKLDLEIINKININ 1017

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
              ++  V +   + ++  LK QY  +K  +++RF++K+ KI+ GDD+ P V+++VKVFVA
Sbjct: 1018 DVFKITVGNVNDEASIAQLKDQYNQAKQDIQERFEDKVLKIRSGDDLLPSVMKMVKVFVA 1077

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR ++ GDKM+GRHGNKG+VS+I+P EDMP+ +DG PVDIVLNPLGVPSRMNVGQI ET
Sbjct: 1078 IKRRLRPGDKMSGRHGNKGVVSKIVPVEDMPYREDGRPVDIVLNPLGVPSRMNVGQILET 1137

Query: 1140 HLGWACVGLGKKIKSLINDYKAN-GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            HLGWAC   G+++K L+N+          + SFL+ V G       I   +      + E
Sbjct: 1138 HLGWACKEFGEEVKRLVNENNKKFEKTEKISSFLKSVYGKEVFDGGIEKLNKTEFSDLCE 1197

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+ +STPVFDGA E+ ++ ML +A L  SGQ+ L+DG TGE FDRPVTVG IYMLK
Sbjct: 1198 NLQNGIAISTPVFDGAKEKDVSEMLELAKLPTSGQTNLWDGRTGEMFDRPVTVGIIYMLK 1257

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+K
Sbjct: 1258 LHHLVEDKIHARSTGPYSLVTQQPLGGKAQLGGQRFGEMEVWALEAYGASYTLQEILTVK 1317

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV GR +VYE+IV G + FE+G PESFNVLVKE+++L L+I+L
Sbjct: 1318 SDDVAGRVKVYETIVKGEENFESGIPESFNVLVKEIKSLALNIEL 1362


>gi|297569429|ref|YP_003690773.1| DNA-directed RNA polymerase, beta subunit [Desulfurivibrio
            alkaliphilus AHT2]
 gi|296925344|gb|ADH86154.1| DNA-directed RNA polymerase, beta subunit [Desulfurivibrio
            alkaliphilus AHT2]
          Length = 1373

 Score = 1538 bits (3982), Expect = 0.0,   Method: Composition-based stats.
 Identities = 715/1373 (52%), Positives = 967/1373 (70%), Gaps = 12/1373 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             R+RK F K   I++ P LIE+Q  SY+ FL M   PD+R +EGLQ  FKSVFPI  F  
Sbjct: 5    RRIRKNFAKTRAIVEKPHLIEMQSRSYEKFLQMETPPDQRLDEGLQGIFKSVFPIKDFKD 64

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            A  LEFV+Y F  PK+ V++C+ R LT+ VP+K+T+RL+ +D D  +GA+SI+DIKEQS+
Sbjct: 65   ACSLEFVNYTFGEPKYTVEECIQRGLTFEVPVKMTVRLVTYDTDPDSGAQSIRDIKEQSV 124

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+G +PLMTK G FVI G +R++VSQL RSPG+ + HD G+    GKLLY+ RIIP +G 
Sbjct: 125  YLGSIPLMTKAGVFVINGTERVIVSQLQRSPGLFYTHDGGKTHAGGKLLYSARIIPVRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+D+EFD+KDI++VRIDRRRK PVT+ L  LG  SE++L  FY     S           
Sbjct: 185  WVDLEFDAKDILYVRIDRRRKFPVTTLLKTLGYGSEDLLRYFYQIESVSIEEGKLKKGFD 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                MVG ++   L+    GE +   G+K+   L + + + G+  L I +  L G   A 
Sbjct: 245  PE-TMVGQRLPHDLISPADGEVLARKGRKVGKALARKIADAGITGLEIEAADLVGKVTAS 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +VN ETGEI I     + E  LEEI  + +++  IL +D +  +   R TL  D+ + R
Sbjct: 304  PVVNPETGEIMIPVNTELSETMLEEISAAGVKNFDILLIDGIKVSDSFRKTLALDRVESR 363

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            +DAL++IYR +RP    T  VAES FN LFF  + YDLS VGR K+N RL +DT  ++R 
Sbjct: 364  EDALIEIYRRLRPSSPPTLEVAESFFNNLFFSPELYDLSVVGRFKLNARLGIDTDINIRT 423

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +  EDI+  +  LV L++ +G IDDID+LGNRRVR+VGE+++NQYR+GL+RMER+IKER+
Sbjct: 424  LTVEDIMLAVLHLVRLKDSQGPIDDIDHLGNRRVRTVGELVENQYRMGLVRMERAIKERM 483

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            S  +++S+MP DLIN KP+ +A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++
Sbjct: 484  SLQEVESLMPHDLINPKPITAAIKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLS 543

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVHPTHYGRICP ET EG NIGL+ SL S+ARVN YGFIETPYRKV + KV
Sbjct: 544  RERAGFEVRDVHPTHYGRICPVETPEGPNIGLIVSLASYARVNEYGFIETPYRKVENRKV 603

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            +N + Y++A++EE++ IA A S  D  G   +  +  R AGE ++   +++ ++D SP Q
Sbjct: 604  SNQIEYMTALDEEDQVIAPARSETDGKGKLVDGPLIARQAGEVMISIADEVTYMDVSPNQ 663

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS+ ASL+PFLENDD+NR LMG NMQRQ VPLL++EAP VGTG+ES VA+ SG  ++A 
Sbjct: 664  LVSVGASLVPFLENDDANRALMGSNMQRQGVPLLRSEAPLVGTGLESAVAQDSGVCLLAG 723

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              G+VE+VDA RIV+R  E   D  T+G+ IYRL K+++SNQNTC  QRPLV+ G  V++
Sbjct: 724  GDGVVEEVDANRIVVRYDEPGTDGFTTGIGIYRLEKYKKSNQNTCFTQRPLVEPGVRVKK 783

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
             DI+ADGP+ D G+LAL +N+ VAFMPW GYN+EDS+L++ER++  D +TS HIE FE +
Sbjct: 784  GDILADGPACDHGELALAKNVTVAFMPWRGYNYEDSILVNERLLKNDTYTSFHIEVFETV 843

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            ARDTKLG EE+TRDIPNVSEE L+N+DE GI+ VGAE+  GDILVGKITPKGE+ ++PEE
Sbjct: 844  ARDTKLGKEEVTRDIPNVSEEALRNLDESGIVRVGAEIKAGDILVGKITPKGETQLSPEE 903

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
            KLLRAIFGEKA DV+DTSLRVP GV G VVD ++F+R G++K+ERS+++E  +I+ L RD
Sbjct: 904  KLLRAIFGEKAGDVKDTSLRVPPGVEGVVVDAKVFSRKGVEKDERSLAIEEAEIKALERD 963

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK------KSTVLSSDLISEYPRSQWWQF 1024
             +DE  +L R++ + L ++L G+   +  K  K      K   ++ +++ +   S+  + 
Sbjct: 964  LEDELNLLARSVRNGLADLLVGKKVKNAVKNRKGEELLAKDKKITREVLEKLSPSEIKKL 1023

Query: 1025 AVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                 + ++  +  L  ++++   ++  R++ +I ++Q GDD+PPGV+R+VKV++A+KR 
Sbjct: 1024 DYAGRDSLEGEINLLFDRHDSQVKMVRSRYEARIARLQKGDDLPPGVIRMVKVYLAIKRK 1083

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +  GDKMAGRHGNKG+VSRILP EDMP+  DGT VDIVLNPLGVPSRMNVGQ+ E HLG 
Sbjct: 1084 LAVGDKMAGRHGNKGVVSRILPEEDMPYFADGTAVDIVLNPLGVPSRMNVGQLLEIHLGL 1143

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG++++ L        D++ ++  L  V     + + ++D  DD +L +A +   G
Sbjct: 1144 AAKKLGEQVQRLA----QTRDLAAVKKKLAAVYSKEEYEQLLADLTDDDLLELASRMGKG 1199

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            + ++TPVFDGA EE I  +L  A LDE GQ  LYDGLTGE FD  VTVG +YMLKL+H+V
Sbjct: 1200 LHMATPVFDGAQEEEIRRLLVEAGLDEIGQLDLYDGLTGEKFDNQVTVGSMYMLKLHHLV 1259

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV 
Sbjct: 1260 DDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYTLQEFLTVKSDDVG 1319

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            GRT++YE IV GN+  E G PESF+VLVKE+Q L L ++L +         +E
Sbjct: 1320 GRTKMYERIVKGNNFLEAGLPESFHVLVKELQGLCLDMELLDELPPVRENEKE 1372


>gi|308272985|emb|CBX29589.1| DNA-directed RNA polymerase subunit beta [uncultured Desulfobacterium
            sp.]
          Length = 1366

 Score = 1538 bits (3981), Expect = 0.0,   Method: Composition-based stats.
 Identities = 714/1365 (52%), Positives = 961/1365 (70%), Gaps = 11/1365 (0%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+RK FGK   I++IPDLI +Q  SY  FL M++ P++R + GLQA FKSVFPI  ++
Sbjct: 8    KKRLRKNFGKIQRIVEIPDLIGMQLESYKRFLQMDVVPEKREDIGLQAVFKSVFPIKDYT 67

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G+A LE+VSY F   K  V +C+ R +TY +P++IT+RL+V+DVD+ TG  SI+DIKEQ 
Sbjct: 68   GSASLEYVSYRFGEIKHGVAECIHRGMTYEIPVRITVRLVVYDVDKETGISSIRDIKEQE 127

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            IY G +PLMT  GTF++ G +R+VV QLHRS G+ FDHDKG+   SGK++Y+ RIIP +G
Sbjct: 128  IYFGTVPLMTNKGTFIVNGTERVVVGQLHRSSGVFFDHDKGKTHSSGKIIYSSRIIPVRG 187

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D+E D KDI+++RIDRRRK P+T F  A G   E++LS FY       RG      L
Sbjct: 188  SWIDLEIDPKDIVYIRIDRRRKFPITIFFKAFGYTPEDLLSYFYKSEKIIIRGKSLYKEL 247

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
               DL    K +  + D DTGE V + G+  T  L+K L    +  + I  + +     +
Sbjct: 248  R-EDLCKDQKFTRDIKDPDTGEIVAKKGRPYTPKLIKKLISSKIDAIPINIEDIFERAFS 306

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
              I   ET  I ++A ++++E S+ ++  + I +  IL+ D  +++  IR TL  DK   
Sbjct: 307  YTIYEPETNNILVKANEIVNEDSISKLKDAGINEFGILFFDGASSSDSIRKTLSVDKVAS 366

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            +++AL++IYR +RPG+  T  VA++  + LFF +  YDLS+VGRVK+N RL +++  D++
Sbjct: 367  KEEALVEIYRRLRPGNPVTPEVAQNFIDNLFFKTAYYDLSSVGRVKINQRLGIESSPDLK 426

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +R+EDI+   K L+DLR+ +G +DDID+LGNRR+R+VGE+L+NQYR+GL+RMER+IKER
Sbjct: 427  ILRREDILLTAKTLIDLRDTQGIVDDIDHLGNRRIRAVGELLENQYRIGLVRMERAIKER 486

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +S  ++D++MP DLIN KPV + V EFF +SQLSQ  +  N LS  TH RRLSALG GG+
Sbjct: 487  MSLQEVDTLMPHDLINPKPVSAIVKEFFGTSQLSQFMDQTNPLSETTHKRRLSALGPGGL 546

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVHP+HYGRICP ET EG NIGL+ SL+++ARVN YGFIETPYR V DG 
Sbjct: 547  TRERAGFEVRDVHPSHYGRICPIETPEGPNIGLIVSLSTYARVNDYGFIETPYRVVNDGT 606

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            VTN+V +L A EE++  IAQAN+ +DE G +T  +V  R AGE + V +E I  +D SP 
Sbjct: 607  VTNEVKFLDAFEEKDLPIAQANAPIDEKGRYTNPIVTSRMAGEFMTVQKEDIALMDVSPN 666

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q+VS++ASLIPFLENDD+NR LMG NMQRQAVPL+ +EAP VGTG+E VVAK SG  IVA
Sbjct: 667  QLVSVSASLIPFLENDDANRALMGSNMQRQAVPLIVSEAPLVGTGIEGVVAKDSGVTIVA 726

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            +R GIVE VDA RI I S +         V IY L K+ RSNQNTC N RP+V  G  V+
Sbjct: 727  ERDGIVESVDAYRI-ILSHDPSDKRYDKHVTIYNLSKYMRSNQNTCFNHRPIVVKGQRVQ 785

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              +IIADGP+T+ G+L+LG+N+ VAFMPW G+NFEDS+L++ER+V + V+TS+HIEEFE+
Sbjct: 786  AGEIIADGPATEKGELSLGKNVTVAFMPWGGFNFEDSILVNERLVRDGVYTSVHIEEFEI 845

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            +ARDTKLG E+ITRDIPNV +E LK++DE GII +GAEV PGDILVGKITPK E+ ++PE
Sbjct: 846  VARDTKLGKEDITRDIPNVGDEALKDLDESGIIRLGAEVEPGDILVGKITPKDETQLSPE 905

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKLLRAIFGEKA DV+DTSLRVP GV GTV+D ++F+R GI+K+ER+  +E  +I++L R
Sbjct: 906  EKLLRAIFGEKAGDVKDTSLRVPPGVEGTVIDAKVFSRRGIEKDERTCFIEETEIKVLER 965

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRSQWWQF 1024
            ++DDE  +++      +++ L GQ   +  K  K     K   + ++++S+ P +Q    
Sbjct: 966  NRDDELAVIEEIARGPVIQALDGQICNTPIKKGKKVLIAKGDKIDAEILSDIPLAQLEGV 1025

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             ++D  V   +  L  QY T ++   D F+  I + + GDD+PPGV+++VKV++AMKR +
Sbjct: 1026 VLKDAGVTEQLHDLLEQYRTQRTACHDNFEKHISRYEKGDDLPPGVIKMVKVYIAMKRKL 1085

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRILP EDMP+ +DGTPVD+VLNPLGVPSRMN GQI E HLG A
Sbjct: 1086 SVGDKMAGRHGNKGVVSRILPQEDMPYFEDGTPVDMVLNPLGVPSRMNAGQILEIHLGRA 1145

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG ++  LI       +I  LR  + K+       + IS  DD  +      +K+GV
Sbjct: 1146 AKSLGDQLNRLI----EENNIVSLRDKMNKIFNDKDSNKIISQMDDQELCDYVGNYKNGV 1201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             ++TPVFDGA E  I ++L  A    +GQ+ L+DG TGE F   +TVG +YMLKL+H+V 
Sbjct: 1202 HMATPVFDGAKETEIKALLEEAGQYTTGQATLFDGRTGENFKGKITVGTMYMLKLHHLVD 1261

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA+ LQE LT+KSDD+ G
Sbjct: 1262 DKLHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAHALQEFLTVKSDDMAG 1321

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            RTR+YE IV G +  E G PESF V+ +E+Q+LGL I+L     +
Sbjct: 1322 RTRMYEKIVKGQNMLEPGIPESFKVMTRELQSLGLDINLLEEHKE 1366


>gi|32491271|ref|NP_871525.1| hypothetical protein WGLp522 [Wigglesworthia glossinidia endosymbiont
            of Glossina brevipalpis]
 gi|41018021|sp|Q8D233|RPOB_WIGBR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|25166478|dbj|BAC24668.1| rpoB [Wigglesworthia glossinidia endosymbiont of Glossina
            brevipalpis]
          Length = 1342

 Score = 1535 bits (3974), Expect = 0.0,   Method: Composition-based stats.
 Identities = 681/1365 (49%), Positives = 941/1365 (68%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAFKS+
Sbjct: 1    MVYSYTERKRIRKDFGKRPQVLDIPYLLAIQINSFKKFIEKD----PEGLYGLEAAFKSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI ++SG A L+++SY      F+V +C  R  T++ PL++ L+LI++  +       +
Sbjct: 57   FPIKSYSGNAELKYISYRLGCSVFNVKECQTRGTTFSAPLRVILQLIIYCDE---SKHVV 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+IKEQ +YMG++PLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 114  KNIKEQEVYMGEIPLMTDNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KD + +RIDRRRK+PVT  L AL     EIL+ F+ K+ +  R 
Sbjct: 174  RIIPYRGSWLDFEFDAKDHLFIRIDRRRKLPVTVLLKALNFSDGEILNIFFEKVNFFIRK 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G      +   + G   I+ G+++T+  +++L+   +  + +  + 
Sbjct: 234  KNLLMELIPKRL-RGETALFDIC--ENGITYIKKGRRITAKHIRNLENDKISQITVPFEY 290

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G   A++  + +T +  I A   +    +  +F S  + I  L+ + +++ +YI  TL
Sbjct: 291  IIGKVSAKNYFDKKTEKPIITANTELTVDLMLNLFKSGYKSIETLFTNDLDHGSYISETL 350

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   D+  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS+VGR+K N  L++
Sbjct: 351  RIDSTTDKTSALIEIYRMMRPGEPPTKEAAENLFYNLFFSEDRYDLSSVGRMKFNKSLSI 410

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            ++ +    + K DII + K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 411  NSSEGSSLLDKFDIIEVTKKLIDIRNGKGDVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 470

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 471  ERAVKERLSLGDLDTIMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 530

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 531  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNEYGFLETPY 590

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VTN++ YLSA+EE    IAQAN++LD++G F  E V CR  GE  L  R +++
Sbjct: 591  RCVLNGIVTNNIHYLSAIEEGKFIIAQANTNLDKNGYFINEFVTCRNKGESSLFNRNQVN 650

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L  E P +GTGME  VA  
Sbjct: 651  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLMTEKPLIGTGMERAVAVD 710

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   VAKR GIV+ +D+ +I+I+  + ++     G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 711  SGVTAVAKRGGIVQFLDSSKIIIKVNQEEIIKEKIGIDIYHLTKYVRSNQNTCINQTPCV 770

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + D V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDSML+SE++V ED FT+I
Sbjct: 771  CLNDVVERGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSMLVSEKVVHEDRFTTI 830

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   M+RDTKLG EEIT DIPNVSE  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 831  HIQELACMSRDTKLGSEEITSDIPNVSETSLLKLDESGIVYIGAEVKGGDILVGKVTPKG 890

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV IF R G+ K++R++ +E  
Sbjct: 891  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVEIFTRDGVKKDKRALEIEYM 950

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            QI+   +D  +E  I   ++  ++   L             K   +  D +SE  +    
Sbjct: 951  QIKEAKKDIYEELEIFKSSLKIQIEYFL-------------KENNIEYDSLSELLKGNIK 997

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                ++  +    E L  ++   K   E + + KI+KI  GDD+ PGVL++VKV++A+KR
Sbjct: 998  NLIFKNNNLNNIFEELINKFLRLKEEFEKKLEIKIKKITQGDDLAPGVLKIVKVYLAVKR 1057

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVD+VLNPLGVPSRMN+GQI ETHLG
Sbjct: 1058 QIQPGDKMAGRHGNKGVISKINPIEDMPYDENGVPVDMVLNPLGVPSRMNIGQILETHLG 1117

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G  I +++ + K    I         +        ++  + D  ++++A   + 
Sbjct: 1118 LAAKGIGNIIDNMLKNNKKIYKIKKFIQNAYNLGIGIRQKVELDHFSDKEIIKLANNLRK 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  I  +L+ +   ESGQ  L+DG TGE FDRPVTVGY+YMLKLNH+
Sbjct: 1178 GMPIATPVFDGAQEIEIKELLKFSGNPESGQITLFDGQTGEKFDRPVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYSLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV G+   E G PESFNVL+KE+++LG++I+LE + 
Sbjct: 1298 NGRTKMYKNIVDGSHLMEPGMPESFNVLLKEIRSLGINIELEENN 1342


>gi|118602788|ref|YP_904003.1| DNA-directed RNA polymerase subunit beta [Candidatus Ruthia magnifica
            str. Cm (Calyptogena magnifica)]
 gi|158512581|sp|A1AX75|RPOB_RUTMC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|118567727|gb|ABL02532.1| DNA-directed RNA polymerase subunit beta [Candidatus Ruthia magnifica
            str. Cm (Calyptogena magnifica)]
          Length = 1360

 Score = 1533 bits (3970), Expect = 0.0,   Method: Composition-based stats.
 Identities = 677/1365 (49%), Positives = 956/1365 (70%), Gaps = 8/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+R  FG    I+  PDL+ +Q  S++ F+  +     + + GL A F+SV
Sbjct: 1    MAYSFTEKKRIRNNFGSRESILTEPDLLAIQIDSFNSFIQKD--SKTKQDIGLHAVFQSV 58

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT--GAK 120
            FPITA +G A +E+V YE   PKF+V++C  R +T+A  L++ L L++FD +  T    +
Sbjct: 59   FPITAVNGYAQIEYVDYELQEPKFNVEECKLRGVTFASTLRVKLSLVLFDKNGSTLKKKR 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             IK I E+ IY+G LPLMT+ GTFVI G +R+VVSQLHRSPG+ F+HDKG+   SGK+L+
Sbjct: 119  KIKQIIEEDIYLGQLPLMTETGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHSSGKILF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D E+D  + ++VRIDRRRK+PVT+ L A+G+ SE IL TF+ K     
Sbjct: 179  SSRIIPYRGSWLDFEYDHHEHLYVRIDRRRKLPVTTLLRAMGLSSEGILETFFEKTTIKL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +       +    L         +V     + ++E G+++T+  +K LK+ G+K + +  
Sbjct: 239  KAKSCDLNMVPIRLQR-TIAEFDIV--ANQDVIVEKGRRITAKHVKLLKKVGIKSINVPL 295

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    ++ DI + +TGEI I A  +I E+ LE +  ++I+ I ILY+++    AYI +
Sbjct: 296  EYLLDKVISADIFDKDTGEILISANTIILEEVLELLNINKIKKIEILYINASETGAYISD 355

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D+ +   +A + IY VMRPG+ +T      +FN LFF +D+YDLS VGR+K+N RL
Sbjct: 356  TLRLDETQTEIEARMSIYHVMRPGEPATEDAVNLLFNNLFFKNDRYDLSKVGRMKLNRRL 415

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             + +      +  +DII++IK+L+++++G  ++DD+D L NRRVR++GEM++NQ+R+GL+
Sbjct: 416  GIGSETGEHVLTNDDIISVIKLLINIKDGNDSVDDVDTLANRRVRAIGEMIENQFRVGLV 475

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E+ ++E ++  + D + PQDLIN+KPV +AV EFF SSQLSQ  + VN LS +TH RR
Sbjct: 476  RVEKVVREGLNLAETDELTPQDLINSKPVSAAVREFFGSSQLSQFMDQVNPLSGVTHKRR 535

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHP+HYGR+CP ET EG NIGL+++L  +A+ N+YGF+ET
Sbjct: 536  ISALGPGGLTRERAGFEVRDVHPSHYGRLCPIETPEGPNIGLINTLAVYAKTNSYGFLET 595

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PY+ V +GKVT +VVY+SA++E    IAQ N+ +++ G    +L+ CR   E +LV   K
Sbjct: 596  PYQVVKNGKVTKEVVYVSAIDEITHTIAQVNAIVNDKGKLMSDLISCRHKNEFVLVNSSK 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +  ID   KQ+ S+AASLIPFLE+DD+NR LMG NMQRQAVP+LKAE P VGTG+E VVA
Sbjct: 656  VTLIDIDSKQIASVAASLIPFLEHDDANRALMGSNMQRQAVPVLKAEKPLVGTGIERVVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              S   + AK +G+VE VDA RIVIR        S  GVDIY L K+ RSNQNTC+NQ+P
Sbjct: 716  TDSRVCVTAKHSGVVEAVDASRIVIRVDSKKTKASELGVDIYNLTKYSRSNQNTCINQKP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD++   D++ADGPSTD+G+LALG+NM +AFMPW+GYNFEDS+LISE+++ ED +T
Sbjct: 776  LVKTGDKISAADVLADGPSTDMGELALGQNMKIAFMPWNGYNFEDSILISEKVIQEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +IHIEE    +RDTKLGPEEIT DIPNVSE  L  +DE G++ VGA V  GDILVGK+TP
Sbjct: 836  TIHIEELTAYSRDTKLGPEEITADIPNVSELALAKLDEVGVVYVGARVKGGDILVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ ++PEEKLLRAIFGEKA +V+D+SLRV +  SG V+DV+IF R  ++K++R++S++
Sbjct: 896  KSETVLSPEEKLLRAIFGEKANNVKDSSLRVGASKSGVVIDVQIFTRDRVEKDDRALSID 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E++E + +D DDE  I+D +I+ R+   L G          K    LS+ L+ +     
Sbjct: 956  AERLERIKKDIDDEFGIIDGDIFRRVRLKLSGNMLSKVAGDIKAGEKLSAKLMKKLDNKD 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              +  V+D  V + V +L  Q +  +   +  F+ +  KI  G ++PPGV+++VKV+VA 
Sbjct: 1016 ISKLKVEDAAVNKEVAALIKQAKAKQIEFKKFFEEEKAKINEGAELPPGVMKMVKVYVAT 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             + +Q GDKMAGRHGNKG++SR+ P EDMP+L DG+ +D+VLNPLGVPSRMNVGQ+ E H
Sbjct: 1076 SKTLQVGDKMAGRHGNKGVISRVSPVEDMPYLVDGSTIDVVLNPLGVPSRMNVGQVLEVH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG+A  GLG KI +++ D K    +  +R FL++V  +    E ++ + D+ ++ +A   
Sbjct: 1136 LGYAAKGLGYKITAML-DEKRTDMVKQIRDFLDEVYNSYGKQENLASFSDEEIIELASNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDG  E+ I S+L++ADL ESGQ  LYDG TGEPFDR VTVGY++MLKLN
Sbjct: 1195 REGVPMATPVFDGIKEKDIKSLLKLADLPESGQEQLYDGRTGEPFDRHVTVGYMHMLKLN 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V+DK++ARSTG YSLVTQQPL GK+  GGQR GEMEVW ++AYGAA+ L+EMLT+KSD
Sbjct: 1255 HLVNDKMHARSTGPYSLVTQQPLSGKAQFGGQRFGEMEVWALEAYGAAHTLREMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GR ++Y+SIV G +  E+  PESFNVLVKE+++LG+ ++LE 
Sbjct: 1315 DVGGRAKMYKSIVDGKNLTESIMPESFNVLVKEIRSLGIDVELEQ 1359


>gi|295698608|ref|YP_003603263.1| DNA-directed RNA polymerase, beta subunit [Candidatus Riesia
            pediculicola USDA]
 gi|291157153|gb|ADD79598.1| DNA-directed RNA polymerase, beta subunit [Candidatus Riesia
            pediculicola USDA]
          Length = 1342

 Score = 1533 bits (3968), Expect = 0.0,   Method: Composition-based stats.
 Identities = 679/1365 (49%), Positives = 958/1365 (70%), Gaps = 23/1365 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             G+ +    R+RK F K P+++ +P L+ +Q  S+  F+            G+++A  SV
Sbjct: 1    MGLDYKNKRRIRKNFSKRPQVLSVPYLLSIQVDSFSQFINGCRD----KKSGIESALHSV 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G A L +++Y  + P FDV +C  R  TY+  LK+ LRL+V+D +    +K I
Sbjct: 57   FPIRSYNGCAELRYINYRLEDPIFDVKECRTRSTTYSSSLKVKLRLVVYDKE---SSKKI 113

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            + IK+Q +YMG++P+MT++GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 114  QKIKDQEVYMGEIPIMTENGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKILYNA 173

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD I VRIDRRRK+P T  L A+G + EE+L+ F+ K  + +  
Sbjct: 174  RIIPYRGSWLDFEFDIKDHIFVRIDRRRKLPATVILRAMGYNEEEMLNLFFKKTTFKRYQ 233

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            + +   L    L  G   S  ++    G++ +  G ++T+  +++L++  ++ + + S+ 
Sbjct: 234  NKFFMKLIPKRL-RGETASFDII--KDGKKYVHKGNRITTLHIENLEKDNIQEIEVPSEY 290

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  + +D  N   G++   A   I ++ LE++  +    I  L+ + ++  +YI NTL
Sbjct: 291  LIGKIIDKDYFNQSDGKLICSANTKISKEILEDLKTTNHETIQTLFTNDLDRGSYISNTL 350

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  KD+ DAL++IYR+MRPG+  T   AE +F  LFF  D+YDLS+VGR+K N+ LN 
Sbjct: 351  RIDSTKDQFDALIEIYRMMRPGEPPTKESAEHLFKNLFFSEDRYDLSSVGRMKFNLSLNK 410

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + ++DII +I+ L+D+R+GKG +DDID+LGNRR+RS+GEM +NQ+RLGL+R+
Sbjct: 411  SRDQGNNVLDQQDIIDVIRKLIDIRDGKGEVDDIDHLGNRRIRSIGEMAENQFRLGLIRV 470

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER++KER+S  D++S+ PQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 471  ERAVKERLSLGDLESLSPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 530

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 531  ALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLSVYARTNQYGFLETPY 590

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G V+ND+ YLSA+EE N  IAQAN+ L+EDGSF  +LV CR  GE  L  +++++
Sbjct: 591  RVVRNGIVSNDIHYLSAIEEGNHIIAQANTILNEDGSFYTDLVTCRNKGESNLFNKKQVE 650

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTGME VVA  
Sbjct: 651  YMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGMERVVAID 710

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  I+AKR+G V+ VD+ +IVI++   DL  +  G+DIY L+K+ RSNQNTC+NQ P V
Sbjct: 711  SGVTIIAKRSGKVQYVDSSKIVIKTDHHDLLSNDFGIDIYDLIKYSRSNQNTCINQVPCV 770

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +GD+V+  +I+ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+LISER+V +D FT+I
Sbjct: 771  SLGDKVKSGEILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILISERIVQKDRFTTI 830

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   ++RDTKLGPEEIT DIPNV    L  +DE GI+ +GAEV  G+ILVGK+TPKG
Sbjct: 831  HIQELSCISRDTKLGPEEITADIPNVGVSALSKLDESGIVYIGAEVIGGEILVGKVTPKG 890

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G  GTV+DV+IF R G+ K++R++ +E+ 
Sbjct: 891  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTCGTVIDVQIFTRDGVKKDKRTLEIEKI 950

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            + + + +D  +E  IL+  ++  + + L                 +    I      + +
Sbjct: 951  RTKEMEKDLHEELEILESCLFCEVRDFLIRNG-------------MEKSEIDSLEGRKLF 997

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q  +++++ ++ +   + +Y   +   +++   K  +I  GDD+ PGVL++VKV +A+KR
Sbjct: 998  QIDLKNDQAKKTLNQFQRRYYELQKTFKEKLNKKSHQITQGDDLSPGVLKIVKVHLAVKR 1057

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1058 QIQPGDKMAGRHGNKGVISKINPIEDMPYDQEGNPVDIVLNPLGVPSRMNIGQILETHLG 1117

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G +I  +I   +    +         +         + ++ D  VL +A   K+
Sbjct: 1118 MAAKGVGNQIDRMIRRKEKIEKLRKFIQKAYDIGIGTYQRVNLDEFSDKEVLELANNLKN 1177

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P+STPVFDGA E+ I  ML +A L  SGQ +L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1178 GLPMSTPVFDGAKEDEIKKMLNLAGLPTSGQIVLFDGCTGEKFERLVTVGYMYMLKLNHL 1237

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLT+KSDDV
Sbjct: 1238 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTVKSDDV 1297

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             GRT++Y++IV+G    E G P+SFNVL+KE+++LG++I+LE  R
Sbjct: 1298 NGRTKMYKNIVSGEHKMEPGMPDSFNVLLKEIRSLGINIELERKR 1342


>gi|148244878|ref|YP_001219572.1| DNA-directed RNA polymerase subunit beta [Candidatus Vesicomyosocius
            okutanii HA]
 gi|158514265|sp|A5CW25|RPOB_VESOH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146326705|dbj|BAF61848.1| DNA-directed RNA polymerase beta subunit [Candidatus Vesicomyosocius
            okutanii HA]
          Length = 1360

 Score = 1531 bits (3965), Expect = 0.0,   Method: Composition-based stats.
 Identities = 675/1365 (49%), Positives = 950/1365 (69%), Gaps = 8/1365 (0%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+R  FG    I+  PDL+ +Q  S++ F+  +    +  + GL    +SV
Sbjct: 1    MAYSFTEKKRIRNNFGSRESILTEPDLLAIQIDSFNSFIQADNKIKQ--DIGLHNVLQSV 58

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS- 121
            FPITA +G A +E+V Y+   PKF+V++C  R +T+A  L++ L L++FD +  T  K  
Sbjct: 59   FPITAVNGYAQIEYVDYQLKEPKFNVEECKLRGVTFASTLRVKLNLVLFDKNGSTLKKKR 118

Query: 122  -IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +K I E+ +Y+G LPLMT+ GTFVI G +R+VVSQLHRSPG+ F+HDKG+   SGK+L+
Sbjct: 119  KVKQIIEEDVYLGQLPLMTETGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHSSGKILF 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D E+D  + ++VRIDRRRK+PVT+ L A+G+ SE+IL TF+ K     
Sbjct: 179  SSRIIPYRGSWLDFEYDHHEHLYVRIDRRRKLPVTTLLRAMGLSSEDILETFFEKTPVKL 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +       +    L         +V       V+E G+++T+  +K L + G+K +    
Sbjct: 239  KAKSCDLSMLPIHLQR-TIAEFDIVVNQH--VVVEKGRRITAKHVKLLGKAGIKSINAPL 295

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    +  DI+N +TGEI I A  +  E+ LE +  ++++ I ILY++S    AYI +
Sbjct: 296  EYLLDKVICADIINKDTGEILISANTITSEEVLELLNTNKVKKIEILYINSSETGAYISD 355

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D+ +   +A + IY VMRPG+ +T      +FN LFF +D+YDLS VGR+K+N RL
Sbjct: 356  TLRLDETQTEIEARMSIYHVMRPGEPATEDAVNLLFNNLFFKNDRYDLSKVGRMKLNRRL 415

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             +        +  +DII +IK+L+++++G  ++DDID L NRRVR++GEM++NQ+R+GL+
Sbjct: 416  GISRETGEHVLTNDDIIRVIKLLINIKDGNDSVDDIDTLANRRVRAIGEMIENQFRIGLV 475

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+E++++E ++  + D + PQDLIN+KPV +AV EFF SSQLSQ  + VN LS +TH RR
Sbjct: 476  RVEKAVREGLNLAETDELTPQDLINSKPVSAAVREFFGSSQLSQFMDQVNPLSGVTHKRR 535

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVHP+HYGR+CP ET EG NIGL+++L  +A+ N+YGF+ET
Sbjct: 536  ISALGPGGLTRERAGFEVRDVHPSHYGRLCPIETPEGPNIGLINTLAVYAKTNSYGFLET 595

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PY+ V +GKVT +V+Y+SA++E    IAQAN+ +D+ G   ++L+ CR   E +LV   +
Sbjct: 596  PYQIVKNGKVTKEVIYVSAIDEITHTIAQANALVDDRGKLMDDLISCRHKNEFVLVDSSE 655

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +  ID   KQ+ S+AASLIPFLE+DD+NR LMG NMQRQAVP+LKAE P VGTG+E VVA
Sbjct: 656  VTLIDIDSKQISSVAASLIPFLEHDDANRALMGSNMQRQAVPVLKAEKPLVGTGIERVVA 715

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            K S   + AK  G+VE VDA RIVIR        +  GVDIY L K+ RSNQNTC+NQ+P
Sbjct: 716  KDSRVCVTAKHGGVVEAVDASRIVIRVDSKKTKANELGVDIYNLTKYSRSNQNTCINQKP 775

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LV+ GD++   D++ADGPSTD+G+LALG+NM +AFMPW+GYNFEDS+LISE++V ED +T
Sbjct: 776  LVRTGDKITFGDVLADGPSTDMGELALGQNMKIAFMPWNGYNFEDSILISEKVVQEDRYT 835

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +IHIEE    +RDTKLGPEEIT DIPNVSE  L  +DE G++ VGA V  GDILVGK+TP
Sbjct: 836  TIHIEELTAYSRDTKLGPEEITSDIPNVSESALSKLDEVGVVYVGARVKGGDILVGKVTP 895

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ ++PEEKLLRAIFGEKA +V+D+SLR+ +  SG V+DV++F R  ++K+ R++S++
Sbjct: 896  KSETVLSPEEKLLRAIFGEKANNVKDSSLRIGASKSGVVIDVQVFTRDRVEKDIRALSID 955

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E++E + +D DDE  I+D +I+ R+   L G          +    LS  L+ ++    
Sbjct: 956  AERLERIKKDIDDEFSIIDGDIFRRIRLKLLGNVLSKAIGDIRIGERLSIKLMKKFDNKD 1015

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              +F V++  V + V  L  Q +  K   E  FK +  KI  G ++PPGV+++VKV+VA 
Sbjct: 1016 IAKFKVENATVNKEVAVLVKQAKAKKVEFEKFFKKEKAKINEGAELPPGVMKMVKVYVAT 1075

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            ++ +Q GDKMAGRHGNKG++SR+ P EDMP+L DG+ +DIVLNPLGVPSRMNVGQ+ E H
Sbjct: 1076 RKTLQVGDKMAGRHGNKGVISRVSPVEDMPYLADGSTIDIVLNPLGVPSRMNVGQVLEVH 1135

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG+A  GLG KI +++ D +    +  +R FL+KV       E ++ + ++ ++ +A   
Sbjct: 1136 LGYAAKGLGYKIAAIL-DERRPDMVKQIRVFLDKVYNLHGKKEDLTLFSNEEIIELANNL 1194

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++TPVFDG  E+ I S+LR+ADL ESGQ  LYDG TGEPFDR VTVGY++MLKLN
Sbjct: 1195 REGVPMATPVFDGIREQDIKSLLRLADLPESGQEQLYDGRTGEPFDRHVTVGYMHMLKLN 1254

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YSLVTQQPL GK+  GGQR GEMEVW ++AYGAA+ L+EMLT+KSD
Sbjct: 1255 HLVDDKMHARSTGPYSLVTQQPLSGKAQFGGQRFGEMEVWALEAYGAAHTLREMLTVKSD 1314

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV GR ++Y+SIV G +  E+  PESFNVLVKE+++LG+ ++LE 
Sbjct: 1315 DVAGRAKMYKSIVDGKNLTESVMPESFNVLVKEIRSLGIDVELEQ 1359


>gi|242278652|ref|YP_002990781.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio salexigens
            DSM 2638]
 gi|259494178|sp|C6C179|RPOB_DESAD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|242121546|gb|ACS79242.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio salexigens
            DSM 2638]
          Length = 1366

 Score = 1531 bits (3963), Expect = 0.0,   Method: Composition-based stats.
 Identities = 670/1370 (48%), Positives = 940/1370 (68%), Gaps = 14/1370 (1%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK FGK    + IP L+E+Q  S+  FL   +AP  R + GL+  F+SVFPI  F+  A
Sbjct: 4    LRKIFGKIKVTLPIPHLLELQVDSFKKFLQEGVAPASRADVGLEGVFRSVFPIEDFNKTA 63

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY+   PK+D+D+C+ + LTY  P++I +RL+VFDVDE T +++I+DIKEQ IY 
Sbjct: 64   SLEYVSYDIGEPKYDMDECISKGLTYEAPIRIKVRLVVFDVDEETESRTIRDIKEQDIYF 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +PLM++ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CRIIP +G W+
Sbjct: 124  GTVPLMSEQGTFIINGTERVIVNQLQRSPGIIFEHDSGKTHTSRKVLYSCRIIPMRGSWL 183

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D +FD KDI++VRIDRRRK+P T  L A+G+  ++IL  +Y    Y              
Sbjct: 184  DFDFDHKDILYVRIDRRRKMPATVLLKAMGLSKQDILDYYYDVEEYQIDRHIVRRK-VVE 242

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +          L  ++ G+ ++   K++T    K L   GV+++ +    L G +   DI
Sbjct: 243  NQYRKENAWVDLC-LEDGKVIVARDKQITKFGWKKLVRGGVEYIEVDPKSLVGQFAFNDI 301

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             + +TGE+  EA D I E+  E I    ++D+ +L+    + ++ +R++++ DK  D + 
Sbjct: 302  TDPDTGEVIAEAADEITEEIFERIQEVGLKDVKVLHTQGADVSSALRDSMMLDKTTDVES 361

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A ++IYR +RP    T  +A + F  LF  SD YDLS+VGR K+N RLN++TP ++R + 
Sbjct: 362  AQIEIYRRLRPSSPPTAEIAANFFENLFRSSDYYDLSSVGRYKLNARLNIETPLELRTLT 421

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             EDI+  +K+L  L++  G  DDIDNLGNRRVR VGE+++NQYR+GL+RMER+IKER+S 
Sbjct: 422  NEDILTAVKVLCKLKDSHGPADDIDNLGNRRVRPVGELVENQYRIGLVRMERAIKERMSL 481

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++ ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 482  QEVATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 541

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++++VN +GFIE+PYR + D  +T+
Sbjct: 542  RAGFEVRDVHVSHYGRICPIETPEGPNIGLIVSLTTYSKVNDFGFIESPYRTIKDSTMTD 601

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +++Y  A  E    +AQAN+ +DE GSFT  LV CR  G+  + PRE    +D SP Q V
Sbjct: 602  EILYYDATREVGHVVAQANAPIDEKGSFTNPLVTCRLNGDVSMHPREDATLMDISPSQTV 661

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S++A+LIPFLE+DD+NR LMG NMQRQAVPLLK   P VGTGME+ VA+ SG+ ++A+  
Sbjct: 662  SVSAALIPFLEHDDANRALMGSNMQRQAVPLLKTSQPLVGTGMEANVAQDSGSCVLAEND 721

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+++ VDA R+V+R  +G   P T GV  Y L K+ +SNQN+C  QRP + +G  V++ D
Sbjct: 722  GVIDYVDAERLVVRYDDGVY-PDTGGVKHYELQKWHKSNQNSCYGQRPRLPIGTPVKKGD 780

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            ++ADGP    G+LALG+N+LVAFMPW GYNFEDS+LISER+V EDVFTS+HIEEFE++AR
Sbjct: 781  VLADGPGIKDGELALGKNLLVAFMPWCGYNFEDSILISERVVKEDVFTSVHIEEFELVAR 840

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLGPEE+TRDIPNVSEE L+N+DECGII +GA + P DILVGKITPKGE+ +TPEEKL
Sbjct: 841  DTKLGPEEVTRDIPNVSEEMLRNLDECGIIRLGARIAPDDILVGKITPKGETQLTPEEKL 900

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFG+KA DV++TSL+VP G+ GTVVDV++FNR   +K++R+ ++E  ++      + 
Sbjct: 901  LRAIFGDKARDVKNTSLKVPPGIEGTVVDVKVFNRRSGEKDDRTRNIEDFELAKHDMKES 960

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST-------VLSSDLISEYPRSQWWQFA 1025
                 L      ++ +++  +       G KK         +++ ++++E P  +     
Sbjct: 961  KHIESLTNKTRVKIADVVANKQIAQTLMGRKKGEVLAEAGHIITDEILAEVPLKKLGGL- 1019

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              D++    V+ L  +Y+    I++  +  K EK+  GDD+PPGV+++VKV++A+KR + 
Sbjct: 1020 FADKETNEAVKQLLAEYDKQIRIIKGIYDVKREKVTEGDDLPPGVIKMVKVYIAVKRKLS 1079

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VS ILP +DMPF  +GTP+DIVLNPLGVPSRMN+GQI ETHLGWA 
Sbjct: 1080 VGDKMAGRHGNKGVVSNILPEQDMPFFDNGTPMDIVLNPLGVPSRMNIGQIMETHLGWAA 1139

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
            + LG+K  ++++  +A G I   R  ++    +    E I   DD+       + + G+ 
Sbjct: 1140 LALGQKFAAMLDTGEALGVI---RQEIKDTFESEDVYELIDSLDDEEFRLAVNKAREGIV 1196

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              TPVFDGA EE I  ++    + + G+  LYDG TG+PF   VTVG +Y+LKL+H+V +
Sbjct: 1197 TKTPVFDGATEEEIWDLVGKTGIGDDGKVTLYDGRTGDPFHNRVTVGVMYILKLHHLVDE 1256

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR
Sbjct: 1257 KIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGR 1316

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             ++YE IV G++  E G PESFNVLVKE+ +LGL ++L     + +A  +
Sbjct: 1317 VKMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVNLLQDEVEETADKK 1366


>gi|317153964|ref|YP_004122012.1| DNA-directed RNA polymerase subunit beta [Desulfovibrio aespoeensis
            Aspo-2]
 gi|316944215|gb|ADU63266.1| DNA-directed RNA polymerase, beta subunit [Desulfovibrio aespoeensis
            Aspo-2]
          Length = 1367

 Score = 1531 bits (3963), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1372 (49%), Positives = 924/1372 (67%), Gaps = 17/1372 (1%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK FG     + IP L+E+Q  SY  FL +   P  R + GL++ F+SVFPI  F+  A
Sbjct: 4    LRKKFGNIVNTLPIPHLLELQVDSYKRFLQLGTPPASRGDFGLESVFRSVFPIEDFNKTA 63

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L+FV YE   PK+DVD+C+ + LTY  P++IT+RL+VFDVDE T  ++I+DIKEQ IY 
Sbjct: 64   SLDFVKYEIGEPKYDVDECISKGLTYETPIRITVRLVVFDVDEETDNRTIRDIKEQDIYF 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G LPLMT  GT+VI G +R++V+QL RSPGI F+HD G++  S K+LY+ RIIP +G W+
Sbjct: 124  GTLPLMTDKGTYVINGTERVIVNQLQRSPGIIFEHDSGKSHSSRKVLYSSRIIPMRGSWL 183

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D +FD KDI++VRIDRRRK+P T  L A+G+   +IL  +Y    Y+            A
Sbjct: 184  DFDFDHKDILYVRIDRRRKMPATILLKAMGLSRSDILEYYYDIESYTLLKSK-VQRSVVA 242

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +        + + D D  + ++  G  +T G  K +   GVK + I  D L GL++A DI
Sbjct: 243  EQFRKEIAFADIKDGD--QILVAKGTPVTRGAWKKIVRAGVKSVEIDPDTLVGLFLAADI 300

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+ + GE+  EA D + +  +  I  + I+++ +L+   ++ ++ +R+TL+ DK  D + 
Sbjct: 301  VD-KNGEVIAEAADELTQDMITRIREAGIKELNVLHTRGLDVSSSLRDTLLLDKTTDLET 359

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A ++IYR +RP    T  +A + F  LF  +D YDLS+VGR K+N RLN +   ++R + 
Sbjct: 360  AQIEIYRRLRPSSPPTPEIAANFFENLFRSADYYDLSSVGRYKLNSRLNQEVDLNIRTLT 419

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             EDI+  +K L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S 
Sbjct: 420  NEDILLAVKELLRLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSL 479

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++ ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 480  QEVATLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRE 539

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN YGFIETPYR V + +VT+
Sbjct: 540  RAGFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTYAKVNDYGFIETPYRMVRNKQVTS 599

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V Y+ A +E    +AQAN+ LDE G+F    V  R +G+  L   E++  +D SP Q V
Sbjct: 600  EVHYMDASKEAKEVVAQANAPLDETGTFVNPRVNARISGDVQLTLAEEVTCMDISPSQTV 659

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            SI+A+LIPFLE+DD+NR LMG NM RQAVPLL+AE P VGT ME  VA+ SGA ++A+  
Sbjct: 660  SISAALIPFLEHDDANRALMGSNMMRQAVPLLQAEQPLVGTDMEGPVARDSGACVLAEED 719

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+V  VDA R+++    G    ++ G   Y   K+ +SNQN+C  QRP V+VG  +++ D
Sbjct: 720  GVVHFVDAERVIVNYDNGIYG-NSGGAKHYEFQKWHKSNQNSCFGQRPRVQVGQVIKKGD 778

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            ++ADGP  + G+LALG+N+LVAFMPW G+NFEDS+LISERMV EDVFTSIHIEEFE++AR
Sbjct: 779  VLADGPGIEDGELALGKNLLVAFMPWCGFNFEDSILISERMVKEDVFTSIHIEEFELVAR 838

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLGPEE+TRDI NVSEE L+N+DECGII +GA + P DI+VGKITPKGE+ +TPEEKL
Sbjct: 839  DTKLGPEEVTRDISNVSEEMLRNLDECGIIRIGARIKPDDIMVGKITPKGETQLTPEEKL 898

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFG+KA DV++TSL+VP G+SGT+VDV++FNR   DK+ER+ ++E  ++      + 
Sbjct: 899  LRAIFGDKARDVKNTSLKVPPGISGTIVDVKVFNRRSGDKDERTKAIEDAELAAFDAKEM 958

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKK------STVLSSDLISEYPRSQWWQFAV 1026
                 L      ++   + G+       G KK        V+  + I   P  +      
Sbjct: 959  KHIASLTDATREKIWAAVKGETYKKDLAGNKKALLGKIGDVVDREAIDSVPVKKLLGIFD 1018

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +D      ++ +   Y+     +++ +  K EK+  GDD+PPGV+++VKV+VA+KR +  
Sbjct: 1019 KDP--NEQIKMIMADYDQHIHFIKNLYDVKREKVTEGDDLPPGVIKMVKVYVAVKRKLSV 1076

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMPF +DGTP+DIVLNPLGVPSRMN+GQI ETHLG A  
Sbjct: 1077 GDKMAGRHGNKGVVSSILPEEDMPFFEDGTPMDIVLNPLGVPSRMNIGQIMETHLGMAGR 1136

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG+++ ++            +R  ++           I    D+ ++   ++ + G+  
Sbjct: 1137 KLGEQLNAM----YEENAFKDMRKDVKGFFEDKDMDILIDSLSDEQLVEAIKKVRKGIVA 1192

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFDGA+EE I   L  A L + G+ ILYDG TGEPF   VTVG +Y+LKL+H+V +K
Sbjct: 1193 KTPVFDGANEEEIWGWLEKAGLADDGKFILYDGRTGEPFHSRVTVGVMYILKLHHLVDEK 1252

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR 
Sbjct: 1253 IHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVQGRV 1312

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            ++YE IV G++  E G PESFNVLVKE+ +LGL + L     K  +   + P
Sbjct: 1313 KMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVTLHYEDRKRQSTAPQRP 1364


>gi|189184701|ref|YP_001938486.1| DNA-directed RNA polymerase subunit beta [Orientia tsutsugamushi str.
            Ikeda]
 gi|189181472|dbj|BAG41252.1| DNA-directed RNA polymerase beta chain [Orientia tsutsugamushi str.
            Ikeda]
          Length = 1374

 Score = 1528 bits (3956), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1357 (52%), Positives = 989/1357 (72%), Gaps = 6/1357 (0%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAF 68
              R+RK FGK   +  IP+LIEVQK SY+  FL + +  D R N+GLQ    S+FPI   
Sbjct: 7    KKRIRKNFGKINLVSSIPNLIEVQKNSYNKEFLQLGVPVDCRENKGLQGVLNSIFPIHDL 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             G+A+LEFV Y+FD PK+DV++C+ R L+Y   LKITL LIV D  + + +K IK IKEQ
Sbjct: 67   DGSAILEFVRYDFDEPKYDVEECIQRGLSYTAALKITLSLIVLDDSDKSDSKEIKGIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++Y GD+PLMT +GTF+I G +R+VVSQ+HRSPG+ FDHD G+   +GKL+Y+ R+IP +
Sbjct: 127  AVYFGDIPLMTANGTFIINGTERVVVSQMHRSPGVFFDHDDGKTHSTGKLIYSARVIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+D EFD+KD+++ RIDR+RK+ VT+ LMALGM S +IL+ +Y    Y +  + W   
Sbjct: 187  GSWLDFEFDAKDLLYFRIDRKRKLYVTTLLMALGMSSHDILNFYYESAAYKKSENGWIVD 246

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 L+    ++  L+D  TG+ ++ +G+K+T  + K L +KGVK + + +D L G  +
Sbjct: 247  FLPE-LVSTKHLAYDLIDAQTGKVLLNAGQKITVRIAKMLADKGVKQILVKNDSLVGKLL 305

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AED+VN +TGE+ +  G+ I    L  +   +I  + +L V       Y+RNTL  DKNK
Sbjct: 306  AEDLVNNQTGEVLLGVGEEITNDILTIVNDLQITTVRVLAV-GGQCGPYVRNTLFLDKNK 364

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            D+K +L++I+RV++PG+++T + +  + + L FD+++YDLS VGR+K+N RLNLD     
Sbjct: 365  DQKSSLVEIFRVLKPGEMATTAASRGLLDSLLFDNNRYDLSEVGRIKINSRLNLDVDLKN 424

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              I  EDI  IIK+LVD+++GK  +DDID+LGNRRVRSVGE+++NQ+R GL+R+ + I E
Sbjct: 425  TCITVEDIKKIIKLLVDIKDGKALVDDIDHLGNRRVRSVGELVENQFRTGLVRIAKFIVE 484

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            RI SV+ID+V+P DL+NAK + S + EFF +SQLSQ  +  N+LS+ITH RRLSALG GG
Sbjct: 485  RIGSVEIDAVVPNDLVNAKLLTSVIKEFFGTSQLSQFMDQTNALSQITHIRRLSALGPGG 544

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RA +E+RDVHPTHYGRICP ET EG NIGL++SL  FA++N YGFIE+PYR+V + 
Sbjct: 545  LNRDRAALEVRDVHPTHYGRICPIETPEGQNIGLINSLAIFAKINRYGFIESPYRRVINR 604

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            +VT++VVYLSA+EE    IAQA++SL  +    + LV CR  G  ++VP +++DFID +P
Sbjct: 605  RVTDEVVYLSALEEGRYKIAQADTSLCTNDCLIDGLVSCRYDGNFVMVPAQEVDFIDLTP 664

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             QVVS+AAS+IPFLENDD+NR LMG NMQRQAVPLLK++AP VGTG+ESVVA  SG  + 
Sbjct: 665  MQVVSVAASMIPFLENDDANRALMGANMQRQAVPLLKSQAPLVGTGIESVVAHDSGTVVA 724

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A   GIVEQVD+ RIV++      D    GVDIY L KFQRSN NTC+NQ+ LV VGD V
Sbjct: 725  ALHDGIVEQVDSTRIVVK-TSVKKDAGAPGVDIYNLKKFQRSNYNTCINQKVLVNVGDIV 783

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ D+IADG +T+ G++ALGRN+LVAF+ W+GY FEDS+L+SER+V ED++TSIHIEE E
Sbjct: 784  KKGDVIADGVATNKGEIALGRNVLVAFIAWNGYTFEDSILVSERIVKEDIYTSIHIEELE 843

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            ++ARDT+LGPEEITRDIPNV++E L+++DE GI+ +GA+V  GDILVGK+TPK ESP+TP
Sbjct: 844  LVARDTRLGPEEITRDIPNVNDESLRHLDEVGIVNIGAKVRTGDILVGKVTPKSESPVTP 903

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA +V+D+SL VP G++GTV+DVR+F+R GIDK+ER++++E+++I  L 
Sbjct: 904  EEKLLRAIFGEKASEVKDSSLYVPPGITGTVIDVRVFSRRGIDKDERTLAIEKQKIRKLV 963

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D +DE  ++      R+ E+L GQ A            L   ++++    Q  +    +
Sbjct: 964  KDYEDELAVIQHFTIVRVKELLVGQVAACSLDSIIIGDKLDEAMLNKLTNEQLLKLKADN 1023

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +   +  +K  YET+++ L  +  +KIEKIQ GDD+P G LRVVKVF+A+K  +Q GD
Sbjct: 1024 SSIMAEISEIKCHYETTRAQLTSQLNSKIEKIQCGDDLPQGALRVVKVFIAIKHRLQPGD 1083

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VS+++P EDMPFL+DGT VDIVLNPLG+P+RMNVGQI ETHLGWA V L
Sbjct: 1084 KMAGRHGNKGVVSKVVPEEDMPFLEDGTVVDIVLNPLGLPARMNVGQILETHLGWAGVNL 1143

Query: 1149 GKKIKSLINDYKANGD--ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            G+KI  +++DY    +     +R F++K+    S  + I   +D  ++ + ++ + G+  
Sbjct: 1144 GRKIGKMVDDYYFGNNQCTDEIRKFVKKIYANNSIADTIDQVNDQQLIEICQELRQGIYF 1203

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            STPVFDGA    I  ML +AD+D+SGQ  L DG TGE FDR  TVGY Y+LKL+H+V +K
Sbjct: 1204 STPVFDGAKIADIKQMLELADVDKSGQVRLIDGRTGEYFDRRCTVGYQYLLKLHHLVDEK 1263

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSLVTQQPLGGKS+ GGQR GEME W ++AYGAAY LQE+LT KSD V GR 
Sbjct: 1264 IHARSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALEAYGAAYTLQELLTTKSDSVEGRI 1323

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            ++Y++I+ GN+ F +G PES NV++KE+++L L+I L
Sbjct: 1324 KMYQAIIRGNNNFVSGVPESLNVMIKELRSLCLNIQL 1360


>gi|212702083|ref|ZP_03310211.1| hypothetical protein DESPIG_00090 [Desulfovibrio piger ATCC 29098]
 gi|212674488|gb|EEB34971.1| hypothetical protein DESPIG_00090 [Desulfovibrio piger ATCC 29098]
          Length = 1378

 Score = 1528 bits (3956), Expect = 0.0,   Method: Composition-based stats.
 Identities = 689/1378 (50%), Positives = 925/1378 (67%), Gaps = 14/1378 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDER-PNEGLQAAFKSVFPITAFSGAAM 73
            K FGK    + IP L+ +Q  SY  FL   +A  +R   EGL+  F +VFPI  F+  A 
Sbjct: 6    KQFGKINVTLPIPHLLNLQIDSYSKFLQEGVAEADRNKEEGLEGVFHTVFPIEDFNKTAS 65

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFVSYE   PK+D  +C+ + LTY  P+ I +RL+V+D DE TG ++I+DIKEQ IY G
Sbjct: 66   LEFVSYEIREPKYDQAECISKGLTYEAPVHIKVRLVVYDTDEATGNRTIRDIKEQGIYFG 125

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CR+IP +G W+D
Sbjct: 126  TLPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDGGKTHTSRKVLYSCRVIPMRGSWLD 185

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
             +FD KDI++VRIDRRRK+P T    A+GM   +IL  FY +  Y  +            
Sbjct: 186  FDFDHKDILYVRIDRRRKMPATILFKAMGMSKMDILEYFYTREHYLLKPHNTLMWEVEKS 245

Query: 254  LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
            L       S +   D G  +I++GK +T    + + E G+K + +  D L G+++AED++
Sbjct: 246  LYRKDNAYSDIATED-GTVLIKAGKPITKRGWRQVCEAGIKAIEVRPDTLDGMFLAEDVI 304

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
               +GE+  EA D I    LE +  + I  I +L+    + ++ IR+TL+ D+  D++ A
Sbjct: 305  APGSGEVLAEAADEITPGLLERMREAGIERIAVLHTKGTDTSSSIRDTLMQDRIPDQEKA 364

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
              +IYR +RP    T  +A S F+ LF   D YDLS VGR K+N RL L   +D R +  
Sbjct: 365  QEEIYRRLRPSSPPTAEIAASFFDNLFRSPDYYDLSPVGRYKLNQRLGLPDTEDSRTLTD 424

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             DI+  IK+LV L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  
Sbjct: 425  NDILTAIKVLVQLKDSHGPADDIDHLGNRRVRLVGELVENQYRIGLVRMERAIKERMSIQ 484

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            +I ++MP DLIN KPV + + EFF +SQLSQ  +  NSLS +TH RRLSALG GG+ R R
Sbjct: 485  EISTLMPHDLINPKPVAAVLKEFFGTSQLSQFMDQTNSLSEVTHKRRLSALGPGGLTRER 544

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            AG E+RDVH +HYGRICP ET EG NIGL+ SLT+FA+VN +GFIETPYR V +G++T++
Sbjct: 545  AGFEVRDVHTSHYGRICPIETPEGPNIGLIVSLTTFAKVNDFGFIETPYRVVRNGRMTDE 604

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            +V+L A  E ++ +AQAN+ +D DG+F +E V  R  GE  +  R+++  +D SP Q+VS
Sbjct: 605  IVHLDASREGDQVVAQANARVDADGNFLDEFVTVRVKGEVEMRSRDEVTLMDISPSQMVS 664

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I+A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA+ SGA IVA+  G
Sbjct: 665  ISAALIPFLEHDDANRALMGSNMQRQAVPLLRSEKPLVGTGMEIDVARDSGACIVAQADG 724

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             VE  DA RIV+   EGDL     GV  Y L+KF +SNQN+C  Q+P    G   ++ +I
Sbjct: 725  KVEYADADRIVVSY-EGDLYKKQGGVRAYDLLKFHKSNQNSCFGQKPTCYPGQVFKKGEI 783

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADGP  D G LALG+N++VAFMPW GYN+EDS+LISER V ED+FTSIHIEEFEV+ARD
Sbjct: 784  LADGPGIDEGQLALGKNLVVAFMPWCGYNYEDSILISERTVKEDIFTSIHIEEFEVVARD 843

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            TKLGPEEITRDIPNVSE+ L+N+D+ GII +GA V P DILVGKITPKGE+ +TPEEKLL
Sbjct: 844  TKLGPEEITRDIPNVSEDMLRNLDDSGIIRIGAAVKPDDILVGKITPKGETQLTPEEKLL 903

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            RAIFGEKA DV++TSL+VP GV GTV+DV++FNR   +K++R++++E     +L + + D
Sbjct: 904  RAIFGEKARDVKNTSLKVPPGVEGTVIDVKVFNRRSGEKDDRTLAIEAHDTAVLDQKESD 963

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAV 1026
                L       L   + G+       G KK  V       L+ + +   P  +      
Sbjct: 964  HMRALGNRTREVLAPHVLGKLTAVSVPGNKKGEVLVEAGAALTREQLDAIPVKKLQGL-F 1022

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            + ++V   V      Y+     L   + +K EK+  GDD+PPGV+++VKV +A+KR +  
Sbjct: 1023 ESKEVNDIVADQLKDYDHQVDYLHAIYDSKREKVTEGDDLPPGVIKMVKVHIAIKRKLSV 1082

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMPF  DG PVDIVLNPLGVPSRMN+GQI ETHLGW   
Sbjct: 1083 GDKMAGRHGNKGVVSCILPEEDMPFFADGRPVDIVLNPLGVPSRMNIGQIMETHLGWGAK 1142

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG+++  L++   +   +  +R  ++ V  + + +E +   DD+  +   ++ ++G+  
Sbjct: 1143 ELGRQLAELLD---SGAALQVVRDEVKDVFDSPAISELVDKMDDEEFIASVKKLRNGIVT 1199

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFDGA EE I   +  A  D  G++ILYDG TG PF   VT G +Y+LKL+H+V +K
Sbjct: 1200 KTPVFDGATEEEIWGWMEKAGKDSDGKTILYDGRTGVPFKNRVTTGVMYILKLHHLVDEK 1259

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR 
Sbjct: 1260 IHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVTGRV 1319

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            ++YE IV G++  E G PESFNVLVKE+ +LGL + L     K   K        + E
Sbjct: 1320 KMYEKIVKGDNFLEAGLPESFNVLVKELMSLGLDVTLHQEDGKKKPKRIGFVRDQEPE 1377


>gi|94987347|ref|YP_595280.1| DNA-directed RNA polymerase subunit beta [Lawsonia intracellularis
            PHE/MN1-00]
 gi|158564217|sp|Q1MPW8|RPOB_LAWIP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|94731596|emb|CAJ54959.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Lawsonia
            intracellularis PHE/MN1-00]
          Length = 1373

 Score = 1528 bits (3956), Expect = 0.0,   Method: Composition-based stats.
 Identities = 665/1372 (48%), Positives = 928/1372 (67%), Gaps = 13/1372 (0%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK    + IP L+ +Q  SY  FL   +  +  P EGL++ F+SVFPI  F+  + L
Sbjct: 6    KQFGKIKVEVPIPHLLNLQVDSYKKFLQEGLL-EPLPEEGLESVFRSVFPIEDFNRTSSL 64

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            EFV+Y+   PK+D  +C+ + LTY  P++I +RLI++DVD  T ++++ DIKEQ IY G 
Sbjct: 65   EFVNYKIGEPKYDQAECIAKGLTYEAPIRIKVRLIIYDVDSDTESRTVHDIKEQDIYFGT 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CRIIP +G W+D 
Sbjct: 125  LPLMTEKGTFIINGTERVIVNQLQRSPGIIFEHDSGKTHASRKVLYSCRIIPMRGSWLDF 184

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T  L A+GM  ++IL+ FY K  Y    D          L
Sbjct: 185  DFDHKDILYVRIDRRRKMPATILLKAMGMGKQDILNFFYKKETYILDNDGRIKWKFDPSL 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                   + ++D D    ++ +GK +T  + + ++  G++   +    + G ++AEDI++
Sbjct: 245  FRKDIAYTDILDNDN-NLLVAAGKTITKRVWRQMEASGLEAFEVDPSTVIGQFLAEDIID 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGEI  E+ + I E  ++    + I    +L+    + ++ IR+TLV DK    + A 
Sbjct: 304  TSTGEILAESAEEITEGLIQTFRDAGITTFTVLHTRGNDTSSSIRDTLVQDKIPTTEKAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             +IYR +RP    T  +A S F+ LF ++  YDLS VGR K+N RL+      +R +   
Sbjct: 364  EEIYRRLRPSSPPTPEIAASFFDNLFRNNSYYDLSPVGRYKLNQRLDNYENATLRTLSDN 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+  IK+L  L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DILEAIKLLTHLKDSHGPADDIDHLGNRRVRLVGELVENQYRIGLVRMERAIKERMSIQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  NSLS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLINPKPVAALLKEFFGTSQLSQFMDQTNSLSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT++A+VN YGFIETPYR V +G VT+++
Sbjct: 544  GFEVRDVHVSHYGRICPIETPEGPNIGLIVSLTTYAKVNDYGFIETPYRVVRNGYVTDEI 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            ++L A  E +  IAQAN+S+D +G   ++ V  R  G+ ++  RE++  +D SP Q+VSI
Sbjct: 604  IHLDASCEFSEVIAQANASIDSEGRLIDDYVTTRARGDVLMSAREEVTLMDISPSQMVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +A+LIPFLE+DD+NR LMG NMQRQAVPLL++E P VGTGME  VA  SG+ I+A+  GI
Sbjct: 664  SAALIPFLEHDDANRALMGSNMQRQAVPLLRSERPLVGTGMEVDVAHDSGSCILAEGDGI 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +   DA RI++   + +L P   GV  Y L+K+ +SNQN C  QRP    G  V++ +++
Sbjct: 724  IRYADANRIIVSYDDPNLYPEFGGVRAYDLLKYHKSNQNFCFGQRPSCIPGQIVKKGEVL 783

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP+   G LALG+N++VAFMPW GYNFEDS+LISER+V ED +TS+HIEEFE++ARDT
Sbjct: 784  ADGPAIRDGGLALGKNLVVAFMPWCGYNFEDSILISERVVKEDTYTSVHIEEFEIVARDT 843

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV EE L N+DE GII +GA V P DILVGKITPKGE+ +TPEEKLLR
Sbjct: 844  KLGPEEITRDIPNVGEEMLSNLDENGIIRIGAAVKPEDILVGKITPKGETQLTPEEKLLR 903

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DV++FNR   +K++R+  +E  +I L+   + + 
Sbjct: 904  AIFGDKARDVKNTSLKVPPGIEGTVIDVKVFNRRSGEKDDRTRLIEDYEISLMDSKEQNY 963

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAVQ 1027
               + + +  +++ ++ G+   +   G  K  V       ++ +L+   P  +    A +
Sbjct: 964  IKSITQRMKEKILPLINGKQLGTTILGKGKGEVLAEENSAITPELLDSLPLKKLEG-AFK 1022

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             +++   +  +  QYE   + ++  + +K  K+  GDD+PPGV+R+VKV +A+KR +  G
Sbjct: 1023 SKELNETITEMLSQYEKQINYIKTIYDSKRGKVTEGDDLPPGVIRMVKVHIAVKRKLAVG 1082

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DG+PVDIVLNPLGVPSRMN+GQI ETHLGWA   
Sbjct: 1083 DKMAGRHGNKGVVSCILPEEDMPFFADGSPVDIVLNPLGVPSRMNIGQIMETHLGWAAKE 1142

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++ +++   +    I  LR  ++ V  +   + +I   DDD+     ++ K G+   
Sbjct: 1143 LGQQLNNMV---EQGVAIQSLREQVKSVFESPEISAEIDAMDDDTFRTSVQKLKKGIITM 1199

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA E  +   L  A L   G++ILYDG TGE F   VT G +Y+LKL+H+V +K+
Sbjct: 1200 TPVFDGAGESEVWDWLAKAGLPSDGKAILYDGRTGEAFKNRVTTGVMYILKLHHLVDEKI 1259

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y+LQE LT+KSDDV GR +
Sbjct: 1260 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASYLLQEFLTVKSDDVSGRVK 1319

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +YE IV G++  E G PESFNVLVKE+ +LGL++ L     K   K   + D
Sbjct: 1320 MYEKIVKGDNFLEAGLPESFNVLVKELMSLGLNVTLHQEEGKKKPKRTGLID 1371


>gi|257095047|ref|YP_003168688.1| DNA-directed RNA polymerase subunit beta [Candidatus Accumulibacter
            phosphatis clade IIA str. UW-1]
 gi|257047571|gb|ACV36759.1| DNA-directed RNA polymerase, beta subunit [Candidatus Accumulibacter
            phosphatis clade IIA str. UW-1]
          Length = 1427

 Score = 1524 bits (3945), Expect = 0.0,   Method: Composition-based stats.
 Identities = 685/1432 (47%), Positives = 937/1432 (65%), Gaps = 75/1432 (5%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK F K   ++D+P L+  Q  S+  FL  N+   +R N+GLQAAF S+
Sbjct: 1    MTYSYTEKKRIRKSFAKRASVLDVPFLLATQLESFTAFLQANVPVAQRRNQGLQAAFSSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A LEFVSY    P FDV +C  R LT+A  L+  +RL++ D +      +I
Sbjct: 61   FPIVSHSGNARLEFVSYALSDPAFDVTECQQRGLTFASALRAKVRLVILDRETPD---TI 117

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ 
Sbjct: 118  KEVKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KD++  R+DRRRK+PVTS L A+G+  + IL  F+    +   G
Sbjct: 178  RVIPYRGSWLDFEFDPKDLLFFRVDRRRKMPVTSLLKAIGLTPQRILREFFEFDTFHVGG 237

Query: 243  DFWCFPLSAA----------------------------------------------DLMV 256
                F L                                                 D ++
Sbjct: 238  KIIEFALVPERLRGEVARFDFNDPSGKLIIAKDKRITAKHIRELDAAGIKQVAVPDDFLI 297

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVN 314
            G  V+  +VD +TGE +  + +++T GLL  L E GV  L     +D   G ++++ +  
Sbjct: 298  GRVVAEEIVDQNTGEILANANEEITEGLLAKLVEAGVATLQTLYINDLDRGGFISQTLRT 357

Query: 315  GET---------GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR------ 359
             ET             +  G+   E+++E +F+          + +V    + R      
Sbjct: 358  DETATRQAARIAIYRMMRPGEPPTEEAVEILFNGLFYSDDRYDLSAVGRMKFNRRVGRKA 417

Query: 360  ----NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  ++      R+  +  +  V+         V   +       ++         + 
Sbjct: 418  VVEHKVMLKHVPSKREGLVKLVNEVVSDSVPVVDQVMAELSYGPRAVAENLTQEAAVTLF 477

Query: 416  MNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
              ++    T +  +   +   DI+ +IK+LV+LRNG+G IDDID+LGNRRVRSVGE+ +N
Sbjct: 478  EQLKAMGATGEVREQLTLSPRDIVEVIKLLVELRNGRGEIDDIDHLGNRRVRSVGELAEN 537

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
            Q+R GL+R+ER++KER+S  + D++MP DLINAKP+ +AV EFF SSQLSQ  +  N LS
Sbjct: 538  QFRAGLVRVERAVKERLSQAESDNLMPHDLINAKPISAAVREFFGSSQLSQFMDQTNPLS 597

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N
Sbjct: 598  EITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALFARTN 657

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
             YGF+ETPYRKV DG+V++ + YLSA+EE    IAQANS L E G   ++LV CR  GE 
Sbjct: 658  EYGFLETPYRKVADGRVSDQIEYLSAIEEGAYIIAQANSDLGEGGVLMDQLVTCREKGET 717

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            IL    ++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGT
Sbjct: 718  ILAEPARVQYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGT 777

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+E  VA  SG A+ AKR G V+ VDA R+V+R  + +  P   GVDIY L+K+ RSNQN
Sbjct: 778  GIERTVAVDSGTAVQAKRGGKVDYVDASRVVVRVNDDETGPGEVGVDIYNLVKYTRSNQN 837

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            T +NQRPLV+VGD + R D++ADG STD G+LALG+NMLVAFMPW+GYNFEDS+LISER+
Sbjct: 838  TNINQRPLVRVGDLIARGDVVADGASTDKGELALGQNMLVAFMPWNGYNFEDSILISERV 897

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V++D FTSIHIEE  V+ARDTKLGPEEITRDI ++ E  L  +DE GI+ +GAEV  GD+
Sbjct: 898  VAQDRFTSIHIEELTVVARDTKLGPEEITRDIASLGESQLSRLDESGIVYIGAEVEAGDV 957

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRV SG++GTV+DV++F R GI+++
Sbjct: 958  LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVQSGIAGTVIDVQVFTREGIERD 1017

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +R+ S+  + +     D  D+  I++R+ ++R+  ++ G+ A  GPK   K T++  + +
Sbjct: 1018 KRAQSIIDDHLRSYKLDLADQLRIVERDAFARVERLIVGKPANGGPKRLAKGTLVVQEYL 1077

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                   W+   + DE+V   +ESL+   E ++   +  F+ K +K+  GD++PPGV ++
Sbjct: 1078 DGIEPHHWFDIRMADEEVAHQLESLREGLEQTRKGFDIAFEEKRKKLTQGDELPPGVQKM 1137

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA+KR +Q+GDKMAGRHGNKG+VSRI+P EDMP++ DG PVDIVLNPLGVPSRMNV
Sbjct: 1138 VKVYVAVKRRLQAGDKMAGRHGNKGVVSRIVPVEDMPYMADGRPVDIVLNPLGVPSRMNV 1197

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI E HLG A  GLG KI  ++       + + +R FLE++      +E +   +D  +
Sbjct: 1198 GQILEVHLGLAAKGLGIKIGEML---SRQANANEVRGFLEQIYNGTGKSEDLDQLNDVEI 1254

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
              +A   ++GVP +TPVFDGA E  I SML +A + ESGQ  LYDG TGE F+R VTVGY
Sbjct: 1255 NEMAGNLEAGVPFATPVFDGAKESEIKSMLALAGMPESGQMTLYDGRTGEQFERQVTVGY 1314

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +++LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQE
Sbjct: 1315 MHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQE 1374

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            MLT+KSDDV GRT+VYE+IV G+   + G PESFNVLVKE+++L + IDLE 
Sbjct: 1375 MLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLVKEIRSLAIDIDLER 1426


>gi|148284106|ref|YP_001248196.1| DNA-directed RNA polymerase subunit beta [Orientia tsutsugamushi str.
            Boryong]
 gi|158514258|sp|A5CC93|RPOB_ORITB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146739545|emb|CAM79274.1| DNA-directed RNA polymerase beta chain [Orientia tsutsugamushi str.
            Boryong]
          Length = 1377

 Score = 1519 bits (3933), Expect = 0.0,   Method: Composition-based stats.
 Identities = 719/1360 (52%), Positives = 987/1360 (72%), Gaps = 9/1360 (0%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAF 68
              R+RK FGK   +  IP+LIEVQK SY+  FL + +  D R N+GLQ    S+FPI   
Sbjct: 7    KKRIRKNFGKINLVSSIPNLIEVQKNSYNKEFLQLGVPVDCRENKGLQGVLNSIFPIHDL 66

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             G+A+LEFV Y+FD PK+DV++C+ R L+Y   LKITL LIV D  + +  K IK IKEQ
Sbjct: 67   DGSAILEFVRYDFDEPKYDVEECIQRGLSYTAALKITLSLIVLDDSDKSDPKEIKGIKEQ 126

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++Y GD+PLMT +GTFVI G +R+VVSQ+HRSPG+ FDHD G+   +GKL+Y+ R+IP +
Sbjct: 127  AVYFGDIPLMTANGTFVINGTERVVVSQMHRSPGVFFDHDDGKTHSTGKLIYSARVIPYR 186

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD---FW 245
            G W+D EFD+KD+++ RIDR+RK+ VT+ LMALGM S +IL+ +Y    Y +       W
Sbjct: 187  GSWLDFEFDAKDLLYFRIDRKRKLYVTTLLMALGMSSHDILNFYYESATYKKYKKSENGW 246

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                    L+    ++  L+D  TG+ ++ +G+K+T  + K L +KGVK + + +D L G
Sbjct: 247  IVDFLPE-LVSTKHLAYDLIDAQTGKVLLNAGQKITFRIAKMLADKGVKQILVKNDSLVG 305

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              +AED+VN +TGE+ +  G+ I    L  +   +I  + +L V       Y+RNTL  D
Sbjct: 306  KLLAEDLVNNQTGEVLLGVGEEITNDILTIVNDLQITTVKVLAV-GGQCGPYVRNTLFLD 364

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            KNKD+K +L++I+RV++PG+++T + +  + + L FD+++YDLS VGR+K+N RLNLD  
Sbjct: 365  KNKDQKSSLVEIFRVLKPGEMATTAASRGLLDSLLFDNNRYDLSEVGRIKINSRLNLDID 424

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                 I  EDI  IIK+LVD+++GK  +DDID+LGNRRVRSVGE+++NQ+R GL+R+ + 
Sbjct: 425  LKNTCITVEDIKKIIKLLVDIKDGKALVDDIDHLGNRRVRSVGELVENQFRTGLVRIAKF 484

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I ERI SV+ID+V+P DL+NAK + S + EFF +SQLSQ  +  N+LS+ITH RRLSALG
Sbjct: 485  IVERIGSVEIDAVVPNDLVNAKLLTSVIKEFFGTSQLSQFMDQTNALSQITHIRRLSALG 544

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RA +E+RDVHPTHYGRICP ET EG NIGL++SL  FA++N YGFIE+PYR+V
Sbjct: 545  PGGLNRDRAALEVRDVHPTHYGRICPIETPEGQNIGLINSLAIFAKINRYGFIESPYRRV 604

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             + +VT++VVYLSA+EE    IAQA++SL  +    + LV CR  G  ++V  +++DFID
Sbjct: 605  INRRVTDEVVYLSALEEGRYKIAQADTSLCTNDCLIDGLVSCRYDGNFVMVLAQEVDFID 664

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             +P QVVS+AAS+IPFLENDD+NR LMG NMQRQAVPLLK++AP VGTG+ESVVA  SG 
Sbjct: 665  LTPMQVVSVAASMIPFLENDDANRALMGANMQRQAVPLLKSQAPLVGTGIESVVAHDSGT 724

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + A   GIVEQVD+ RIV++      D    GVDIY L KFQRSN NTC+NQ+ LV VG
Sbjct: 725  VVAALHDGIVEQVDSTRIVVK-TSVKKDAGAPGVDIYNLKKFQRSNYNTCINQKVLVNVG 783

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V++ D+IADG +T+ G++ALGRN+LVAF+ W+GY FEDS+L+SER+V ED++TSIHIE
Sbjct: 784  DIVKKGDVIADGVATNKGEIALGRNVLVAFIAWNGYTFEDSILVSERIVKEDIYTSIHIE 843

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E E++ARDT+LGPEEITRDIPNV++E L+++DE GI+ +GA+V  GDILVGK+TPK ESP
Sbjct: 844  ELELVARDTRLGPEEITRDIPNVNDESLRHLDEVGIVNIGAKVRTGDILVGKVTPKSESP 903

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLLRAIFGEKA +V+D+SL VP G++GTV+DVR+F+R GIDK+ER++++E+++I 
Sbjct: 904  VTPEEKLLRAIFGEKASEVKDSSLYVPPGITGTVIDVRVFSRRGIDKDERTLAIEKQKIR 963

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             L +D +DE  ++      R+ E+L GQ A            L   ++++    Q  +  
Sbjct: 964  KLVKDYEDELAVIQHFTIVRVKELLVGQVAACSLDSIIIGDKLDEAMLNKLTNEQLLKLK 1023

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              +  +   +  +K  YET+++ L  +  +KIEKIQ GDD+P G LRVVKVF+A+K  +Q
Sbjct: 1024 ADNSSIMDEISEIKCHYETTRAQLTSQLNSKIEKIQCGDDLPQGALRVVKVFIAIKHRLQ 1083

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VS+++P EDMPFL+DGT VDIVLNPLG+P+RMNVGQI ETHLGWA 
Sbjct: 1084 PGDKMAGRHGNKGVVSKVVPEEDMPFLEDGTVVDIVLNPLGLPARMNVGQILETHLGWAG 1143

Query: 1146 VGLGKKIKSLINDYKANGD--ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            V LG+KI  +++DY +  +     +R F++K+    S  + I   +D  ++ + ++ + G
Sbjct: 1144 VNLGRKIGKMVDDYYSGNNQCTDEIRKFVKKIYANNSIADTIDQVNDQQLIEICQELRQG 1203

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +  STPVFDGA    I  ML +AD+D+SGQ  L DG TGE FDR  TVGY Y+LKL+H+V
Sbjct: 1204 IYFSTPVFDGAKIADIKQMLELADVDKSGQVRLIDGRTGEYFDRRCTVGYQYLLKLHHLV 1263

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             +K++ARS G YSLVTQQPLGGKS+ GGQR GEME W ++AYGAAY LQE+LT KSD V 
Sbjct: 1264 DEKIHARSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALEAYGAAYTLQELLTTKSDSVE 1323

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            GR ++Y++I+ GN+ F +G PES NV++KE+++L L+I L
Sbjct: 1324 GRIKMYQAIIRGNNNFVSGVPESLNVMIKELRSLCLNIQL 1363


>gi|256830545|ref|YP_003159273.1| DNA-directed RNA polymerase, beta subunit [Desulfomicrobium baculatum
            DSM 4028]
 gi|256579721|gb|ACU90857.1| DNA-directed RNA polymerase, beta subunit [Desulfomicrobium baculatum
            DSM 4028]
          Length = 1363

 Score = 1517 bits (3928), Expect = 0.0,   Method: Composition-based stats.
 Identities = 672/1362 (49%), Positives = 934/1362 (68%), Gaps = 16/1362 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FG+  + IDIP L+ +Q  SY+ FL  ++ P  R + GL+  F+SVFPI  F+  A L
Sbjct: 6    KKFGRIKDSIDIPHLLSLQLDSYNKFLQTDVPPSMRTDIGLEGVFRSVFPIHDFNKTATL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSY+   PK+DVD+C+ + LT+  PL+I +RL V+DVDE +G+++I DIKEQ IY G 
Sbjct: 66   EYVSYDIGKPKYDVDECIAKGLTFEAPLRIKVRLAVYDVDEASGSRTIHDIKEQDIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +PL+T+ GTF+I G +R++V+QL RSPGI F+HD G+   S K+LY+CRIIP +G W+D 
Sbjct: 126  IPLITQKGTFLINGTERVIVNQLQRSPGIIFEHDSGKTHSSRKILYSCRIIPMRGSWLDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +FD KDI++VRIDRRRK+P T  L A+GM SE+IL  +Y K  +   G      +   + 
Sbjct: 186  DFDHKDILYVRIDRRRKMPATILLKAMGMTSEDILDYYYAKETFRLEGTSVLRRVEEYNF 245

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                 ++ S V    G  ++ +GK LT G+ K + + G+++  +  D L   Y A+DIV+
Sbjct: 246  RKE--LAHSDVVAPDGTVIVAAGKALTKGMWKRMIKAGIEYYEVRPDTLETEYAAKDIVD 303

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+ + AGD     ++E+   + I ++  ++      +A +R+TL  DK +D + A 
Sbjct: 304  PGTGEVILRAGDPFTAGAVEKCLAAGITEMGAIFSTGAEASACLRDTLAMDKCEDLESAQ 363

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            +DIY+ +RP    T  ++ S F+ LF ++D YDLS VGR K+N RLNL  P D R +  +
Sbjct: 364  IDIYKRLRPSSPPTAEISASFFDNLFRNADYYDLSPVGRYKLNSRLNLSLPIDHRTLSND 423

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI   +K L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER+IKER+S  +
Sbjct: 424  DIFRSVKKLIQLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAIKERMSLQE 483

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DL+N KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RA
Sbjct: 484  VATLMPHDLVNPKPVTAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERA 543

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVH +HYGRICP ET EG NIGL+ SLT+   VN YGFIETPYR V D  VT+++
Sbjct: 544  GFEVRDVHLSHYGRICPIETPEGPNIGLIVSLTTHGLVNDYGFIETPYRVVKDAIVTDEI 603

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             Y+ A  E    IAQAN+   +D  F    V  R  GE  +VPRE++  +D SP Q+VSI
Sbjct: 604  QYMEASTESGHIIAQANALFGDDRQFINAQVEARVEGEFAIVPREEVTLMDISPGQIVSI 663

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +++LIPFLE+DD+NR LMG NMQRQ+VPLL  E P +GTG+E  VA+ SG+ ++A+  G 
Sbjct: 664  SSALIPFLEHDDANRALMGSNMQRQSVPLLVTEEPLIGTGIEGKVAQDSGSCLLAEGDGE 723

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +  VDA R+++   +  L P   GV  Y + K+ +SNQN+C  Q+P VK+GD+V++  ++
Sbjct: 724  IMYVDADRVIVAYSDD-LYPEAGGVRFYEVQKYHKSNQNSCFGQKPRVKIGDKVKKGAVL 782

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGP+   G+LALG+N+LVAFMPW GYN+EDS+LISER+V EDV+TSIHIEEF+V ARDT
Sbjct: 783  ADGPAIHNGELALGKNLLVAFMPWCGYNYEDSILISERVVKEDVYTSIHIEEFDVFARDT 842

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEE+TRDIPNV EE L+N+DE GII +GA V P DILVGKITPKGE+ +TPEE+LLR
Sbjct: 843  KLGPEEVTRDIPNVGEEMLRNLDESGIIRIGARVKPDDILVGKITPKGETQLTPEERLLR 902

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+DV++FNR   DK+ER+  +E  ++E +   +   
Sbjct: 903  AIFGDKARDVKNTSLKVPPGIEGTVIDVKVFNRRSGDKDERTHLIENYELERIDVRERQH 962

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV-------LSSDLISEYPRSQWWQFAVQ 1027
               L      ++ ++  G++      G +K  V       +  D+ +E P  +    A  
Sbjct: 963  AAALTETTRRKIWDVCKGKSVAKTIMGKRKGEVLLEANQPIKEDVFAEIPLKKLVG-AFA 1021

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             + V   V+     ++     ++D +++K  K+  GDD+PPGV+++ KV+VA+KR +  G
Sbjct: 1022 AKDVNEAVKVQLDYFDLQLKFVKDVYESKRGKVTEGDDLPPGVIKMAKVYVAVKRKLNVG 1081

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DGT +D+VLNPLGVPSRMN+GQI ETHLGWA   
Sbjct: 1082 DKMAGRHGNKGVVSNILPEEDMPFFADGTSMDVVLNPLGVPSRMNIGQIMETHLGWAAKS 1141

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG++I +++++      ++ +RS ++ +  +   +  +    DD V+  A     G+ + 
Sbjct: 1142 LGQQIAAMVDEG-----VAKVRSEIKDIFDSPETSALLDTMTDDEVIEAARDLNRGIIMK 1196

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGADE  I ++L+ A L E G+++L+DG TG PF   VTVGY+Y LKL+H+V +K+
Sbjct: 1197 TPVFDGADESEIWALLKRAGLPEDGKALLFDGRTGVPFHNRVTVGYMYYLKLHHLVDEKI 1256

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY+LQE LT+KSDDV GR +
Sbjct: 1257 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYLLQEFLTVKSDDVNGRVK 1316

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            +YE IV G++  E+G PESFNVLVKEM ALGL + L     K
Sbjct: 1317 MYEKIVKGSNFLESGMPESFNVLVKEMMALGLEVTLLEDDKK 1358


>gi|224370697|ref|YP_002604861.1| RpoB [Desulfobacterium autotrophicum HRM2]
 gi|259494179|sp|C0Q9X9|RPOB_DESAH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|223693414|gb|ACN16697.1| RpoB [Desulfobacterium autotrophicum HRM2]
          Length = 1401

 Score = 1517 bits (3928), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1405 (51%), Positives = 957/1405 (68%), Gaps = 41/1405 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M   ++ +   R+RK FG    ++DIPDLI +Q+ S++ FL  N+ P+ER + G+   FK
Sbjct: 1    MTGSLLAS--KRIRKEFGSKSRVVDIPDLIGMQRTSFERFLQRNVPPEEREDIGIHLVFK 58

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SV PI  F+G + LE+VSY F   K  + +C+ R +TY +P+ IT+RL+V+DVD+  G  
Sbjct: 59   SVLPIKDFTGTSSLEYVSYSFGETKHSMKECISRGMTYEIPVNITVRLVVYDVDKDAGVT 118

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SI+DIKEQ IY G +PLMTK GTF+I G +R VVSQLHRS G+ FDHDKG++  SGK++Y
Sbjct: 119  SIRDIKEQEIYFGTIPLMTKRGTFIINGTERAVVSQLHRSSGVFFDHDKGKSHSSGKIIY 178

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D+E D KDI+++RIDRRRK PVT    A G  +E+ILS FY K    +
Sbjct: 179  TARIIPVRGSWIDMEIDPKDIVNIRIDRRRKFPVTILFKAFGYTNEDILSFFYKKEQIVK 238

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +        +  +L    + S  ++D +TGE V++ G+  T   LK L+  G+K + I+ 
Sbjct: 239  KDGILFKEFNPDNLKRN-RASFDILDPETGEAVVKKGRLFTLRALKQLQVAGLKSIPISE 297

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + G   A  +V+ ET EI  +AG +ID + LE+I  + I +  ILYVD+ ++++ +R 
Sbjct: 298  EDIIGRGFATSVVHPETEEILAKAGSLIDPEVLEKIADAGITEFSILYVDTYSSDS-MRK 356

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DK   R +AL++IYR +RPG+ +T  VA+   + LFF    YDLS VGR+KMN RL
Sbjct: 357  TLAVDKVTSRAEALIEIYRRLRPGNPATPEVAQDFIDHLFFKPAYYDLSNVGRLKMNHRL 416

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             + T  DVR +R+EDI+     LV+L++ +G +DDID+LGNRRVR+VGE+L+NQYR+GL+
Sbjct: 417  GMSTGIDVRTLRREDILLTAATLVELKDTQGAVDDIDHLGNRRVRAVGELLENQYRIGLV 476

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMER+IKER+S  ++D++MP DL+N KPV + V EFF +SQLSQ  +  N LS  TH RR
Sbjct: 477  RMERAIKERMSMQEVDAMMPHDLVNPKPVSAVVREFFGTSQLSQFMDQTNPLSETTHKRR 536

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL+ SL ++ARVN +GFIET
Sbjct: 537  LSALGPGGLTRERAGFEVRDVHPSHYGRICPIETPEGPNIGLIVSLCTYARVNDFGFIET 596

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYR   DG V+  + +LSA EE+   IAQAN+ LD+ G    +LV  R  GE  +V +  
Sbjct: 597  PYRIAKDGVVSKQITHLSAFEEKEHPIAQANAVLDDQGHLMNDLVTSRVGGEFEMVAKND 656

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I+F+D SP Q+VS++ASLIPFLENDD+NR LMG NMQRQAVPL+++EAP VGTG+E VVA
Sbjct: 657  IEFMDVSPNQLVSVSASLIPFLENDDANRALMGSNMQRQAVPLIRSEAPLVGTGIEGVVA 716

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + SG AIVA+  GIV  VDA RIV+++ E         V IY   KF RSNQNTC N RP
Sbjct: 717  RDSGVAIVAEHDGIVVDVDAKRIVVKNTENGKGSDDRTVTIYTASKFVRSNQNTCFNHRP 776

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK GD VR+ ++IADGPST++G+LALG+N+ VAFMPW GYN+EDS+L+SER+V E V+T
Sbjct: 777  IVKKGDAVRKGEVIADGPSTEMGELALGKNVTVAFMPWGGYNYEDSILVSERLVKEGVYT 836

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            S+H+EEFEV+ARDTKLG EEITRDIPN  EE LK++D+ GII +GAEV PGDILVGKITP
Sbjct: 837  SVHVEEFEVVARDTKLGKEEITRDIPNAGEEALKDLDDSGIIRLGAEVKPGDILVGKITP 896

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ ++PEEKLLRAIFGEKA DV+DTSLRVP GV G V   ++F+R G+ K++R+  +E
Sbjct: 897  KGETQLSPEEKLLRAIFGEKAGDVKDTSLRVPPGVEGVVTAAKVFSRRGLPKDDRTRLIE 956

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE 1015
              +IE L +D+DDE  I+   I  RL +IL GQ   +             T+++  L   
Sbjct: 957  DLEIEKLEKDRDDEVRIITETIQERLEDILAGQALQAVVKKGKKVVVPAGTLVTRGLFEG 1016

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
               +      V+D  +      +  + ET      + F N+  + + GDD+PPGVL+++K
Sbjct: 1017 ISLTDLMGLTVEDSSLTEMAHVILEKAETQIKKARENFNNQASRYEKGDDLPPGVLKLIK 1076

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + VAMKR +  GDKMAGRHGNKG+VSRILP  D+P+ +DG  VD+VLNPLGVPSRMNVGQ
Sbjct: 1077 INVAMKRVLSVGDKMAGRHGNKGVVSRILPVADLPYFEDGRTVDMVLNPLGVPSRMNVGQ 1136

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL----------------------- 1172
            I E HLG A  GLG++I  LI + K +   + ++                          
Sbjct: 1137 ILEIHLGCAARGLGRQIDDLIYEKKTDELRARIKRIFTTPLIKTGERANKDKTHYDFSSH 1196

Query: 1173 ---------EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                               + I   DD   L  A  +K+GV ++TPVFDGA E  I S++
Sbjct: 1197 YTVEKSMAKRTNEEEIQFVDTIDHMDDTEFLEFASMYKNGVHMATPVFDGAAESEIKSLI 1256

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
              A LD SGQS LYDG TGEPFD+P+TVG +YMLKL+H+V DK++ARS G YSLVTQQPL
Sbjct: 1257 SYAGLDPSGQSTLYDGRTGEPFDKPITVGIMYMLKLHHLVDDKIHARSIGPYSLVTQQPL 1316

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQRLGEMEVW ++AYGAA+ LQE +T+KSDD+ GRTR+YE IV G +  E G 
Sbjct: 1317 GGKAQFGGQRLGEMEVWAMEAYGAAHALQEFITVKSDDMTGRTRMYEKIVKGQNVLEPGM 1376

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
            PESF VL KE+Q+LGL I+L   + 
Sbjct: 1377 PESFRVLTKELQSLGLDINLLEGKK 1401


>gi|258591309|emb|CBE67608.1| RNA polymerase, beta subunit [NC10 bacterium 'Dutch sediment']
          Length = 1338

 Score = 1503 bits (3892), Expect = 0.0,   Method: Composition-based stats.
 Identities = 653/1382 (47%), Positives = 918/1382 (66%), Gaps = 82/1382 (5%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F K  E+I IP+LIE+Q+ S+D FL M + P  R   GLQ AF S+FPI  +  +A
Sbjct: 11   ERWNFSKIKEVISIPNLIEIQRRSFDQFLQMKVPPHAREEIGLQGAFASIFPIYNYDQSA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L+FV YEF  PK+  ++ L + +TY+VPLK+TLRL+V+D    + A SI+DIKEQ +Y+
Sbjct: 71   SLDFVKYEFGAPKYRAEESLEKGMTYSVPLKVTLRLMVWDKPVGSEAGSIRDIKEQEVYL 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT  GTF+I G +R+VVSQLHRSPG+ FDHD G+   SGK+LY+ R+IP +G W+
Sbjct: 131  GEMPLMTPQGTFIINGTERVVVSQLHRSPGVFFDHDSGKTHPSGKILYSARLIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            + EFD+ D+++VR+DRRR+   +  L A+G   +EEIL+ FY + +              
Sbjct: 191  EFEFDANDVLYVRVDRRRRFLASILLRAIGYGSNEEILNLFYERDMLRIEKGKEILIHVG 250

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +      + S  + D  T + ++ + K++T    K L+   +  + +  + L G   A D
Sbjct: 251  SRGATSFRASKDIPDPQTKQLILGTAKRITKTAQKRLQALKITEISLYKEDLIGRIAAAD 310

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            IVN  +GE+ +E    I  ++LE +  S      +L          IR +++ D  +  K
Sbjct: 311  IVNTASGEVILECAQEITAEALERMLSSGTASFAVLASLDGRETFEIRESIIRDSTRSEK 370

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            DAL ++YR MRPGD       ++    +FF+  +YDLS VGR+K+N +L LD P +V  +
Sbjct: 371  DALTEMYRRMRPGDPPNEEATKAFLESIFFNPKRYDLSKVGRLKINRKLGLDVPLEVHAL 430

Query: 432  RK---------------EDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQ 474
                             +D++  I+ L+ L++G+   ++DDID+LGNRRVRS GE+L+ Q
Sbjct: 431  MCRRYRPSGMETRIGQIDDVVEAIRYLLRLKHGEAGTSVDDIDHLGNRRVRSAGELLEEQ 490

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL RMER+++ER+S+ +++++MP DL+NAKPV +A+ EFF SSQLSQ  +  N L+ 
Sbjct: 491  FRIGLARMERAVRERMSTQELETLMPHDLVNAKPVTAALKEFFGSSQLSQFMDQTNPLAE 550

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG GG++R RAG E+RDVHPTHYGR+CP ET EG N+GL++SL+++ARVN 
Sbjct: 551  LTHKRRLSALGPGGLSRERAGFEVRDVHPTHYGRMCPIETPEGPNVGLIASLSTYARVND 610

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            +GFIETPYRKV DG VT+++ YL+A EEE   IAQAN+ LD  G FT + +  R  G  +
Sbjct: 611  FGFIETPYRKVRDGVVTDEIEYLTADEEEKYTIAQANAELDGRGRFTSDRISARTGGNFV 670

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             VP   ++++D +PKQ+V ++ SL+PFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG
Sbjct: 671  TVPPMNVEYMDVAPKQLVGVSTSLVPFLEHDDANRALMGANMQRQAVPLLRPEAPVVGTG 730

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS--TSGVDIYRLMKFQRSNQ 772
            ME   A+ SG  + A+R GIVE V A RI++R+ +G  +     +GVDIY L+KF+RSNQ
Sbjct: 731  MEYPAARDSGTVVTARRGGIVESVTADRIIVRASDGKGEEGEDDTGVDIYSLVKFRRSNQ 790

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC+ Q+P+V  G+ + R  +IADGP+T  G+LALG+N++VAFMPW GYNFED++LISER
Sbjct: 791  NTCLTQKPIVSKGERITRGQVIADGPATQNGELALGQNVMVAFMPWGGYNFEDAILISER 850

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V +D +TSIHIEEFE+ AR+TKLG EEITRD PNV E+ LK++DE GI+ +GAEV PGD
Sbjct: 851  LVKDDRYTSIHIEEFEIEARETKLGKEEITRDTPNVGEDALKDLDESGIVRIGAEVKPGD 910

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ILVGK+TPKGE+ +TPEE+LLRAIFGEKA DVRD SL VP G+ GTVVDV++F+R G++K
Sbjct: 911  ILVGKVTPKGETVLTPEERLLRAIFGEKAEDVRDASLYVPPGICGTVVDVKVFSRKGVEK 970

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK-------GFKKS 1005
            +ER+ S+E E++  L +D +DE  I+  +   +L  +L G +     +          K 
Sbjct: 971  DERAKSIEDEEVSRLRKDFEDEISIIAADRDRKLRSLLDGIDVSREIRSRITRKIVVSKG 1030

Query: 1006 TVLSSDLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              L+ +++ +    Q    A + DE++ +    +    +    +L+   + +I +   GD
Sbjct: 1031 KTLTGEMLDKLSHEQLVDLAGRLDEELGQKASRIGDAADNQVHVLQTLLEERISRATRGD 1090

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            ++ PGV ++VKV+VAMKR +  GDKMAGRHGNKG+++++LP EDMP+L DGTPV++VLNP
Sbjct: 1091 ELAPGVFKMVKVYVAMKRKLSVGDKMAGRHGNKGVIAKVLPEEDMPYLPDGTPVEVVLNP 1150

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMNVGQI ETHLGWA   LG ++ S + D     +I       +           
Sbjct: 1151 LGVPSRMNVGQILETHLGWAAGALGLRVASPVFDGAKEQEIKVWLKRAKL---------- 1200

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                    PV                    SG+++LYDG TG+P
Sbjct: 1201 ------------------------PV--------------------SGKTVLYDGRTGKP 1216

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F + VTVGYIY++KL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1217 FHQEVTVGYIYLMKLAHLVDDKIHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 1276

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ LQE+LT+KSDDVVGRT++YESIV G+ T + G PESFNVLVKE+Q+L L ++L+
Sbjct: 1277 YGAAHTLQEILTVKSDDVVGRTKMYESIVRGDCTLDPGLPESFNVLVKELQSLALDVELK 1336

Query: 1365 NS 1366
              
Sbjct: 1337 KE 1338


>gi|51244969|ref|YP_064853.1| DNA-directed RNA polymerase, beta-subunit [Desulfotalea psychrophila
            LSv54]
 gi|81642549|sp|Q6AP78|RPOB_DESPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|50876006|emb|CAG35846.1| probable DNA-directed RNA polymerase, beta-subunit [Desulfotalea
            psychrophila LSv54]
          Length = 1360

 Score = 1499 bits (3880), Expect = 0.0,   Method: Composition-based stats.
 Identities = 682/1363 (50%), Positives = 937/1363 (68%), Gaps = 13/1363 (0%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            RVRK F     +++ P LI +Q+ SY+ FL ++ AP+ER + GLQA  K++FPI  F+G 
Sbjct: 3    RVRKNFATADNVLEPPHLISMQRISYEEFLQIDRAPEEREDVGLQAILKNIFPINDFNGL 62

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              LEF+ Y+F  PK+ V +C  R ++Y +PLKI +RLI FDVDE TG ++I+D+KEQ ++
Sbjct: 63   CSLEFLKYKFGEPKYTVQECQQRGMSYEIPLKIVVRLITFDVDEETGVQTIRDMKEQEVF 122

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G LPLMT DG FV+ G +R++VSQL RSPG+ + HD G++  SGKLLY+ RIIP +G W
Sbjct: 123  LGSLPLMTADGVFVVNGTERVIVSQLQRSPGLFYSHDNGKSHSSGKLLYSARIIPVRGSW 182

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D+EFD KD++HVRIDRRRK PVT+ L ALG  SEE+L  FYP          +     A
Sbjct: 183  IDLEFDIKDVLHVRIDRRRKFPVTTLLKALGYSSEELLREFYPLENVKLSDGKYWVRFVA 242

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                 G ++   LV+   GE + + G+K++  L +   E G++F+  +S+ + G  +A  
Sbjct: 243  EHTA-GQRLEFDLVNPQDGEILAKKGRKISKALCRKAVEAGIEFIEASSETILGKVLASA 301

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            I      E        I E  LE +  + I +   L++D VN +A   +TL  DK     
Sbjct: 302  ITLAGAEEPLYPCNTEITETVLENLAENGINEFETLFMDGVNYSASFSHTLRLDKVITTA 361

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +ALL+IYR +RP    T  +A + F  LFF+ D YDLS VGR K+N +L L T  + R +
Sbjct: 362  EALLEIYRRLRPSSPPTLEIATTFFENLFFNPDLYDLSEVGRYKINAKLGLKTDIEHRAL 421

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             ++DII  ++ LV L++ +G IDDID+LGNRRVR+VGE+++NQYR+GL+RMER+IKER++
Sbjct: 422  TRDDIIYGVRYLVRLKDNQGGIDDIDHLGNRRVRTVGELVENQYRMGLVRMERAIKERMT 481

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D++++MP DLIN KP+ +A+ EFF +SQLSQ  +  N+LS +TH RRLSALG GG++R
Sbjct: 482  LQDVETLMPHDLINPKPISAAIKEFFGTSQLSQFMDQTNALSEVTHKRRLSALGPGGLSR 541

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGRICP ET EG NIGL+ SL ++ARVN YGFIETPYRKV +  + 
Sbjct: 542  ERAGFEVRDVHPTHYGRICPIETPEGPNIGLIVSLATYARVNPYGFIETPYRKVENRVIL 601

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE-LVFCRCAGEEILVPREKIDFIDASPKQ 670
            +D+ YLSA+EE+ + IA A  +L+ D     E  +  R  G+ I +  + + ++D +P Q
Sbjct: 602  DDIRYLSALEEQKQIIAPALVALEADHQSISEGNLIAREEGDVITIGSDNVTYMDVAPNQ 661

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            ++S+AASL+PFLENDD+NR LMG NMQRQAVPLL   AP VGTGME  VA+ SGA +++ 
Sbjct: 662  MISVAASLVPFLENDDANRALMGSNMQRQAVPLLVTAAPLVGTGMERYVARDSGACLLSA 721

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              G+VE+VD+ R+V+R  +  +D   +GV +YRL K+++SNQNTC  Q P +  G +V +
Sbjct: 722  GDGVVEEVDSNRVVVRYDKPGVDGYDTGVAVYRLTKYKKSNQNTCFTQTPTILPGLKVEK 781

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
              ++ADGP  + G+LALG+N+ VAFMPW G+N+EDS+LI+ER++ ED +TSIHI+ FE M
Sbjct: 782  GTLLADGPGCEAGELALGKNLTVAFMPWRGFNYEDSILINERLLKEDAYTSIHIDVFETM 841

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            ARDTKLG EEITRDIPNVSE+ L+N+D+ GI+ VGAE+ PGD LVGK+TPKGE+ ++PEE
Sbjct: 842  ARDTKLGKEEITRDIPNVSEDTLRNLDDSGIVRVGAEIKPGDTLVGKVTPKGETVLSPEE 901

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
            KLLRAIFGEKA DV+D+SLRVP GV+G V+D ++F+R G+DK+ERS+ +E  +IE L  D
Sbjct: 902  KLLRAIFGEKAQDVKDSSLRVPPGVTGVVIDAKVFSRKGVDKDERSLMIEDLEIERLEGD 961

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-SSDLISEYPRSQWWQFAVQD- 1028
            K DE   L   +   L E++ G  A+      K   ++ S D I            ++D 
Sbjct: 962  KRDELRSLKNGVCRELGELIAGNTALGDILDSKGELLISSGDKIEVVHAIAIGFHRLKDI 1021

Query: 1029 -----EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                       +++   +Y+    ++  R+   IE+ + GDD+PPGV+++VKV+VA KR 
Sbjct: 1022 DFSGMADCTDRMDAAYERYQKQAEVIAQRYDGIIERQKKGDDLPPGVVKMVKVYVATKRK 1081

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +  GDKMAGRHGNKG+VSRILP EDMP+  +G  VDIVLNPLGVPSRMNVGQI E HLG+
Sbjct: 1082 LSVGDKMAGRHGNKGVVSRILPEEDMPYFANGDTVDIVLNPLGVPSRMNVGQILEVHLGF 1141

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG +++ L   Y     +  +++ L +V     +   I    D  V+  A + + G
Sbjct: 1142 AAKNLGAQLEKLAEQYA----VEEIKAKLSRVYSDSEYHAIIDGKTDAEVIDWAYRHRKG 1197

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            + ++TPVFDGA+E  I  +L  + +D+ GQS LYDGLTGEPF   VTVG +YMLKL+H+V
Sbjct: 1198 LHMATPVFDGAEEAEIRKLLIESGVDKGGQSQLYDGLTGEPFANLVTVGVMYMLKLHHLV 1257

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             +K++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY L+E LT+KSDDV 
Sbjct: 1258 DNKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYTLKEFLTVKSDDVE 1317

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            GRT +YE IV GN+   TG PESF+VLVKE+Q L L+++L   
Sbjct: 1318 GRTTMYERIVKGNNFLTTGLPESFHVLVKELQGLCLNMELIEE 1360


>gi|118498136|ref|YP_899186.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. novicida U112]
 gi|158512428|sp|A0Q867|RPOB_FRATN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|118424042|gb|ABK90432.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Francisella
            novicida U112]
          Length = 1358

 Score = 1498 bits (3879), Expect = 0.0,   Method: Composition-based stats.
 Identities = 675/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTAD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSETKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|194323363|ref|ZP_03057147.1| DNA-directed RNA polymerase, beta subunit [Francisella tularensis
            subsp. novicida FTE]
 gi|208779451|ref|ZP_03246796.1| DNA-directed RNA polymerase, beta subunit [Francisella novicida FTG]
 gi|194322727|gb|EDX20207.1| DNA-directed RNA polymerase, beta subunit [Francisella tularensis
            subsp. novicida FTE]
 gi|208744412|gb|EDZ90711.1| DNA-directed RNA polymerase, beta subunit [Francisella novicida FTG]
          Length = 1361

 Score = 1498 bits (3879), Expect = 0.0,   Method: Composition-based stats.
 Identities = 675/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 4    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTAD-AAKGRLHSGLEIVLKQS 62

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 63   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 122

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 123  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 178  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSETKTITFNS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 238  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 297  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 357  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 416

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 417  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 477  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 537  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 597  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDLIQCRSGGEAIFTESSRV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 657  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 717  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 775

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 776  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 835

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 836  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 895

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 896  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 955

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 956  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1014

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1015 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1074

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1075 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1134

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1135 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1191

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1192 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1251

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1252 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1311

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1312 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1361


>gi|254373487|ref|ZP_04988975.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            novicida GA99-3549]
 gi|151571213|gb|EDN36867.1| DNA-directed RNA polymerase beta chain [Francisella novicida
            GA99-3549]
          Length = 1358

 Score = 1498 bits (3879), Expect = 0.0,   Method: Composition-based stats.
 Identities = 676/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTAD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSETKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + +S  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLSTLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|56707314|ref|YP_169210.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. tularensis SCHU S4]
 gi|110669784|ref|YP_666341.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. tularensis FSC198]
 gi|134301353|ref|YP_001121321.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. tularensis WY96-3418]
 gi|224456379|ref|ZP_03664852.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. tularensis MA00-2987]
 gi|254369992|ref|ZP_04985999.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            tularensis FSC033]
 gi|254374947|ref|ZP_04990428.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|254874151|ref|ZP_05246861.1| DNA-directed RNA polymerase beta subunit [Francisella tularensis
            subsp. tularensis MA00-2987]
 gi|81598038|sp|Q5NID2|RPOB_FRATT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|123169674|sp|Q14JT5|RPOB_FRAT1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158513846|sp|A4IW99|RPOB_FRATW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56603806|emb|CAG44777.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            tularensis SCHU S4]
 gi|110320117|emb|CAL08160.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            tularensis FSC198]
 gi|134049130|gb|ABO46201.1| DNA-directed RNA polymerase, beta subunit [Francisella tularensis
            subsp. tularensis WY96-3418]
 gi|151568237|gb|EDN33891.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            tularensis FSC033]
 gi|151572666|gb|EDN38320.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|254840150|gb|EET18586.1| DNA-directed RNA polymerase beta subunit [Francisella tularensis
            subsp. tularensis MA00-2987]
 gi|282158440|gb|ADA77831.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. tularensis NE061598]
          Length = 1358

 Score = 1498 bits (3878), Expect = 0.0,   Method: Composition-based stats.
 Identities = 675/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTAD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|332184682|gb|AEE26936.1| DNA-directed RNA polymerase beta subunit [Francisella cf. novicida
            3523]
          Length = 1358

 Score = 1497 bits (3875), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYRKFLTAD-AAKGRLHSGLELVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      + +  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGEVLKFDIVDAQD-NVIAKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DI+N  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIINEATGEVIAYANDDVTENLLEACVEIGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQDVIGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGK+I+  +   +    ++ LR  LE+V  + G     +   +D+ +L + E  
Sbjct: 1132 GLASYGLGKRIEKAL---EKTRKVAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCENL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KHGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|254369863|ref|ZP_04985873.1| DNA-directed RNA polymerase [Francisella tularensis subsp. holarctica
            FSC022]
 gi|157122822|gb|EDO66951.1| DNA-directed RNA polymerase [Francisella tularensis subsp. holarctica
            FSC022]
          Length = 1358

 Score = 1496 bits (3873), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL ++ A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTVD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ I+   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEIIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+++ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDIIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+  G V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNVGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|115315373|ref|YP_764096.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica OSU18]
 gi|122324640|sp|Q0BKC5|RPOB_FRATO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|115130272|gb|ABI83459.1| DNA-directed RNA polymerase [Francisella tularensis subsp. holarctica
            OSU18]
          Length = 1358

 Score = 1496 bits (3872), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL ++ A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTVD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+++ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDIIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+  G V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNVGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVVDSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPLSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|167627269|ref|YP_001677769.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia
            subsp. philomiragia ATCC 25017]
 gi|189043856|sp|B0TX10|RPOB_FRAP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|167597270|gb|ABZ87268.1| DNA-directed RNA polymerase, beta subunit [Francisella philomiragia
            subsp. philomiragia ATCC 25017]
          Length = 1358

 Score = 1495 bits (3871), Expect = 0.0,   Method: Composition-based stats.
 Identities = 672/1370 (49%), Positives = 935/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  +     R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYRKFLNAD-DAKGRLHSGLELVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ +     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKEALPSEKVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   EEIL+ F      S   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEEILNRFSDSKTISFNN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   ++D      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALKLDDLSSMKGEVLKFDIIDEKD-NTIVKKNKKLTSRDIKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE    + + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTENLLEACVEAGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  K+  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTKNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DNVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +GKVTN++ YLSA++E++  IAQA++ LD++  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVNGKVTNEIEYLSAIDEDHYVIAQASTKLDKNNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG + +VD+ RIV++        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEIAEVDSNRIVVKVDTEKSKTSKL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD++   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKIEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEE+T DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEVTADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S +   + G       KG KK  VL+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIETDVIGAKIQKA-KGLKKGAVLTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK+++ V++ +  YE +K  ++ RF+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEQKVQNAREYYEEAKIAVDARFEAKKKSIMQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + E  
Sbjct: 1132 GLASYGLGKKIEQTL---EKTRKAAELRKTLEEVYNSVGDKKVDLKALNDEEILNLCENL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DITGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|290954467|ref|ZP_06559088.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica URFT1]
 gi|295312072|ref|ZP_06802885.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica URFT1]
 gi|182676593|sp|A7NEC0|RPOB_FRATF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1358

 Score = 1495 bits (3871), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1370 (49%), Positives = 933/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL ++ A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTVD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+++ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDIIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+  G V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNVGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV+ V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVVDSSLRMPSGTSGTVISVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPLSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|156503214|ref|YP_001429279.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica FTNF002-00]
 gi|156253817|gb|ABU62323.1| DNA-directed RNA polymerase, beta subunit [Francisella tularensis
            subsp. holarctica FTNF002-00]
          Length = 1361

 Score = 1495 bits (3871), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1370 (49%), Positives = 933/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL ++ A   R + GL+   K  
Sbjct: 4    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTVD-AAKGRLHSGLEIVLKQS 62

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 63   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 122

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 123  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 177

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 178  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 237

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 238  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 297  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGMLELEVIDFITTERGRYISDTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 357  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 416

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 417  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 476

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 477  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 536

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 537  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 596

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+++ CR  GE I     ++
Sbjct: 597  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDIIQCRSGGEAIFTESSRV 656

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 657  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 716

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+  G V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 717  DSGNCIIARNVGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 775

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 776  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 835

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 836  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 895

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV+ V++F      K++R++ +E+
Sbjct: 896  AEQQLTPEERLLRAIFNEKASNVVDSSLRMPSGTSGTVISVQVFENDKGGKSKRALKIEK 955

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 956  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPLSKW 1014

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1015 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1074

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1075 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1134

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1135 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1191

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1192 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1251

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1252 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1311

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1312 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1361


>gi|187931083|ref|YP_001891067.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. mediasiatica FSC147]
 gi|226699408|sp|B2SFD6|RPOB_FRATM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|187711992|gb|ACD30289.1| DNA-directed RNA polymerase, beta subunit [Francisella tularensis
            subsp. mediasiatica FSC147]
          Length = 1358

 Score = 1495 bits (3871), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1370 (49%), Positives = 934/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  + A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTAD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITSNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L +   M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDSLSNMKGELLKFDIVDAQD-YVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLESCVEVGLLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNYFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG + D G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFAADFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE++  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEIYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|298531092|ref|ZP_07018493.1| DNA-directed RNA polymerase, beta subunit [Desulfonatronospira
            thiodismutans ASO3-1]
 gi|298509115|gb|EFI33020.1| DNA-directed RNA polymerase, beta subunit [Desulfonatronospira
            thiodismutans ASO3-1]
          Length = 1363

 Score = 1495 bits (3870), Expect = 0.0,   Method: Composition-based stats.
 Identities = 679/1349 (50%), Positives = 940/1349 (69%), Gaps = 15/1349 (1%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FG+    +D+P L+++Q  SY +FL     P  R ++GL+A F+SVFPI  F+ +A L
Sbjct: 6    KNFGQIEYGLDVPHLLKLQLDSYMNFLQEEADPMNRQDQGLEAVFRSVFPIEDFNKSATL 65

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSYE + PK+DV +CL + LTY  P++I +RLIV+DVD+ +G ++++DIKEQ IY G 
Sbjct: 66   EYVSYEINQPKYDVAECLSKGLTYEAPIRIKVRLIVYDVDDESGNRTVRDIKEQDIYFGT 125

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LPLMT+ GTF+I G +RI+V+QL RSPGI F+HD G+   S K+LY+ RIIP +G W+D 
Sbjct: 126  LPLMTEKGTFIINGTERIIVNQLQRSPGIIFEHDSGKTHTSRKVLYSSRIIPMRGSWLDF 185

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            EFD KDI++VRIDRRRK+ VT  L ALGM  E+IL+ FY +       D   +    +  
Sbjct: 186  EFDPKDILYVRIDRRRKMYVTILLKALGMSEEDILNYFYDREQLKF-KDQKVYRKVRSSH 244

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                     ++D + G  ++ +G+ +T  + + + +   + + I    L   +VA D+V+
Sbjct: 245  FRKEIAYKDILDSE-GNVLVRAGRPVTKRVWRQMAKAK-EHMEIDPGILPKQFVAHDLVH 302

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             ETGE+  E GD +++  +++IF S I D+ ILY    + ++ +R+TL  DK +D+ +A 
Sbjct: 303  PETGEVLAEVGDALEQDVVDKIFASGIEDVEILYTGGQDVSSSLRDTLKLDKTQDQLEAQ 362

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IY+ +RP    T  +A S F+ LF +SD YDLS VGR K+N RL L+ P D R +  E
Sbjct: 363  VEIYKRLRPSSPPTPEIASSFFDNLFRNSDYYDLSPVGRYKLNARLGLNLPTDYRTLSNE 422

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DI+ ++K L+ L++  G  DDID+LGNRRVR VGE+++NQYR+GL+RMER++KER+S  +
Sbjct: 423  DILRVVKHLIKLKDSHGPADDIDHLGNRRVRPVGELVENQYRIGLVRMERAVKERMSLQE 482

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++MP DLIN KPV + + EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RA
Sbjct: 483  VATLMPHDLINPKPVTAVLKEFFGTSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERA 542

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVHP+HYGRICP ET EG NIGL+ SLT+ A+VN +GFIETPYR V DG VTN+V
Sbjct: 543  GFEVRDVHPSHYGRICPIETPEGPNIGLIVSLTTHAQVNDFGFIETPYRIVKDGMVTNEV 602

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YL A +E +  IAQAN+ +DE+G FT EL+  R  GE  L+PR+++  +D SP Q+VSI
Sbjct: 603  KYLDASKEADEVIAQANAPVDEEGRFTSELITSRIHGELNLMPRDEVTLMDVSPTQIVSI 662

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            +++LIPFLE+DD+NR LMG NMQRQAVPLLK E P VGTGME +VA+ SG+  +A+  GI
Sbjct: 663  SSALIPFLEHDDANRALMGSNMQRQAVPLLKPERPLVGTGMEGLVARDSGSCEIARADGI 722

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V  VDA ++++   E   D S+     Y L K+ +SNQN+C  QRP V      +  D++
Sbjct: 723  VRYVDANKVIVSYDE-PPDKSSQDTVCYDLQKYHKSNQNSCFGQRPRVLPDQRFKAGDVL 781

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGPS   G+LALG+N+ VAFMPW GYNFEDS+LISERMV +DVF+S+HIEEFEV+ARDT
Sbjct: 782  ADGPSIVDGELALGKNLSVAFMPWCGYNFEDSILISERMVKDDVFSSVHIEEFEVIARDT 841

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEITRDIPNV E+ LK +D+ GII +GA++   DILVGKITPKGE+ +TPEE+LLR
Sbjct: 842  KLGPEEITRDIPNVGEDMLKYLDDSGIIMIGAKIQQDDILVGKITPKGETQLTPEERLLR 901

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV++TSL+VP G+ GTV+D+++FNR   +K+ER+  +E  +++ LA+ ++  
Sbjct: 902  AIFGDKARDVKNTSLKVPPGIEGTVIDIKVFNRRSGEKDERTRIIEDRELDRLAQSEEKH 961

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ------- 1027
               L      R+ E++ G+       G KK  VL ++  S   R    +  ++       
Sbjct: 962  VQGLTAQTRDRIWEVVSGKRLAQTIMGRKKGQVL-AEANSTLQREDLDRIPLKKLAGSFA 1020

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             ++V   +E L   YE     +++ +  K +K+  GDD+PPGV ++VKV+VA+KR +  G
Sbjct: 1021 SKEVNEAIEHLIKLYEEQLKFIQNVYSQKRDKVVEGDDLPPGVTKMVKVYVAVKRKLNVG 1080

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMPF  DGTP+DIVL+PLGVPSRMN+GQI ETHLGWA   
Sbjct: 1081 DKMAGRHGNKGVVSCILPEEDMPFFDDGTPIDIVLSPLGVPSRMNIGQIMETHLGWAARE 1140

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG+++  ++   +   D+  LR  ++ +  +   +   ++ DD+S +R   + + G+   
Sbjct: 1141 LGRQLGRML---EQGVDVGVLRKEVDDIFNSPEISRLAAEMDDESFVRAVRELEPGILTK 1197

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I   L+ A L + G+++LYDG TG+ F   +TVG +YMLKL+H+V +K+
Sbjct: 1198 TPVFDGAKEEEIWPWLKKAGLSDDGKAVLYDGRTGDAFHNRITVGNMYMLKLHHLVDEKI 1257

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW I+AYGA+Y+LQE LT+KSDDV GR  
Sbjct: 1258 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWAIEAYGASYLLQEFLTVKSDDVAGRVN 1317

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            +YE IV GN+  E+  PESFNVL+KE+ A
Sbjct: 1318 MYEKIVKGNNFLESAMPESFNVLIKELMA 1346


>gi|241667825|ref|ZP_04755403.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia
            subsp. philomiragia ATCC 25015]
 gi|254876368|ref|ZP_05249078.1| DNA-directed RNA polymerase beta subunit [Francisella philomiragia
            subsp. philomiragia ATCC 25015]
 gi|254842389|gb|EET20803.1| DNA-directed RNA polymerase beta subunit [Francisella philomiragia
            subsp. philomiragia ATCC 25015]
          Length = 1358

 Score = 1494 bits (3869), Expect = 0.0,   Method: Composition-based stats.
 Identities = 672/1370 (49%), Positives = 935/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL  +     R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYRKFLNAD-DAKGRLHSGLELVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ +     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKEALPSEKVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG+ F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGVFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   EEIL+ F      S   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEEILNRFSDSKTISFNN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   ++D      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALKLDDLSSMKGEVLKFDIIDEKD-NTIVKKNKKLTSRDIKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  LE    + + ++ ++   +     YI +TL
Sbjct: 294  VGTLRVAKDIVNEATGEVIAYANDDVTENLLEACVEAGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  K+  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTKNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DNVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +GKVTN++ YLSA++E++  IAQA++ LD++  F E+L+ CR  GE I     ++
Sbjct: 594  YRKVVNGKVTNEIEYLSAIDEDHYVIAQASTKLDKNNHFVEDLIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+ AG + +VD+ RIV++        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNAGEIAEVDSNRIVVKVDTEKSKTSKL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD++   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKIEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEE+T DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEVTADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVADSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S +   + G       KG KK  VL+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIETDVIGAKIQKA-KGLKKGAVLTKEFLATLPFSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK+++ V++ +  YE +K  ++ RF+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEQKVQNAREYYEEAKIAVDARFEAKKKSIMQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + E  
Sbjct: 1132 GLASYGLGKKIEQTL---EKTRKAAELRKTLEEVYNSVGDKKVDLKALNDEEILNLCENL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DITGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|89257013|ref|YP_514375.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica LVS]
 gi|167009393|ref|ZP_02274324.1| DNA-directed RNA polymerase subunit beta [Francisella tularensis
            subsp. holarctica FSC200]
 gi|122500258|sp|Q2A1M7|RPOB_FRATH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|89144844|emb|CAJ80183.1| DNA-directed RNA polymerase beta chain [Francisella tularensis subsp.
            holarctica LVS]
          Length = 1358

 Score = 1493 bits (3866), Expect = 0.0,   Method: Composition-based stats.
 Identities = 672/1370 (49%), Positives = 933/1370 (68%), Gaps = 14/1370 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG  P I+D+P L+ +Q  SY  FL ++ A   R + GL+   K  
Sbjct: 1    MSYSYAEKKRIRKEFGVLPHILDVPYLLSIQTESYKKFLTVD-AAKGRLHSGLEIVLKQS 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FP+ + +G   L +V Y+   P FD  +C  R  TY  PL + LRL+V++ D     K +
Sbjct: 60   FPVESKNGQYELHYVDYQIGEPTFDETECQVRGATYDAPLNVKLRLVVYNKDALPNEKIV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +DI+E+ +YMGD+PLMT +GTF+I G +R+VVSQLHRSPG  F  D           ++ 
Sbjct: 120  EDIREEYVYMGDIPLMTTNGTFIINGTERVVVSQLHRSPGAFFSKDDSEEGA-----FSA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFDSK II  RIDR+RK   T  L ALG   E+IL  F      +   
Sbjct: 175  RIIPYRGSWLDFEFDSKGIIWARIDRKRKFCATVILKALGYTQEQILENFSESKTITFNS 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L     M G  +   +VD      +++  KKLTS  +K +K+ GV  + I  D 
Sbjct: 235  KGFALRLDNLSNMKGELLKFDIVDAQD-NVIVKKNKKLTSRDVKKIKDAGVDSVAIDFDL 293

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +  L VA+DIVN  TGE+   A D + E  L+      + ++ ++   +     YI +TL
Sbjct: 294  VSTLRVAKDIVNEATGEVIAYANDDVTESLLKSCVEVGMLELEVIDFITTERGRYISDTL 353

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  ++  +AL++IY+V+RPGD    +  +++F  LFF   +Y LS +GR+K+N RL  
Sbjct: 354  KYDLTRNTDEALVEIYKVLRPGDPPAAASVKALFEGLFFIESRYSLSDIGRMKLNARLGS 413

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D    D+  +   DI+ +I+ L+++R+GKG +DDID+LGNRRVRSVGEM++NQ+R+GL R
Sbjct: 414  DKVSKDIYTLENSDIVGVIEELINIRDGKGKVDDIDHLGNRRVRSVGEMVENQFRIGLYR 473

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I+E +S V  D +MP+D++N+KP+ +A+ EFF S  LSQ  +  N LS +TH RR+
Sbjct: 474  VEKGIRESMSLVHKDKLMPKDIVNSKPITAAIKEFFTSGALSQFMDQDNPLSEVTHKRRI 533

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E P
Sbjct: 534  SALGPGGLSRDRAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLASYARVNDYGFLEAP 593

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV DGKVT+++ YLSA++E+N  IAQA++ LDE+  F E+++ CR  GE I     ++
Sbjct: 594  YRKVVDGKVTDEIEYLSAIDEDNYVIAQASTKLDENNHFVEDIIQCRSGGEAIFTESSRV 653

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             ++D S KQ+VS AA+LIPFLE+DD+NRVLMG NMQRQAVP LK+E P VGTGME +VA+
Sbjct: 654  QYMDVSAKQMVSAAAALIPFLEHDDANRVLMGANMQRQAVPTLKSEKPLVGTGMEKIVAR 713

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  I+A+  G V +VD+ RIVI+        S   VDIY L KF+RSN+NTC+NQRP+
Sbjct: 714  DSGNCIIARNVGEVAEVDSNRIVIKVDTEKSQTSNL-VDIYSLTKFKRSNKNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V VGD+V   DI+ADG +TD G+L+LG N++VAFMPW+GYNFEDS+L+SER+V +D +TS
Sbjct: 773  VNVGDKVEAGDILADGFATDFGELSLGHNLMVAFMPWNGYNFEDSILLSERIVKDDKYTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF  +ARDTKLGPEEIT DIPNVSE  L  +DE GI+ +GA V  GDILV KITPK
Sbjct: 833  IHIEEFTCVARDTKLGPEEITADIPNVSESSLAKLDESGIVHIGANVEAGDILVAKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E  +TPEE+LLRAIF EKA +V D+SLR+PSG SGTV++V++F      K++R++ +E+
Sbjct: 893  AEQQLTPEERLLRAIFNEKASNVVDSSLRMPSGTSGTVINVQVFENDKGGKSKRALKIEK 952

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E I+   +D D+E  +++  + S + + + G       KG KK  +L+ + ++  P S+W
Sbjct: 953  ELIDKARKDFDEEFAVIESVVKSSIEQEVVGAKIQKA-KGLKKGAILTKEFLATLPLSKW 1011

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + + +DEK++  V++ +  YE +K  ++ +F+ K + I   +++ PGVL+ VKVFVA+K
Sbjct: 1012 LEISFEDEKLEEKVQNAREYYEEAKIAIDAKFEAKKKSITQSNELSPGVLKTVKVFVAIK 1071

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            + IQ GDKMAGRHGNKG+VSR+LP EDMP+++DGTPVD+ LNPLG+PSRMN+GQI E HL
Sbjct: 1072 KRIQPGDKMAGRHGNKGVVSRVLPVEDMPYMEDGTPVDVCLNPLGIPSRMNIGQILEAHL 1131

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQW 1200
            G A  GLGKKI+  +   +     + LR  LE+V  + G     +   +D+ +L + +  
Sbjct: 1132 GLASYGLGKKIEKTL---EKTRKAAELRKTLEEVYNSVGDKKVNLEALNDEEILTLCDNL 1188

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K GVP++TPVFDGA EE I S+L++     +GQ  L+DG TG+PFDR VTVGY+YMLKL+
Sbjct: 1189 KGGVPIATPVFDGAKEEDIKSLLKIGGFATNGQMKLFDGRTGKPFDRHVTVGYMYMLKLD 1248

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +QAYGAAY L+EMLT+KSD
Sbjct: 1249 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAAYTLREMLTVKSD 1308

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            D+ GR+++Y++IV G  T     PESFNVL  E++ALG+ +D + S  + 
Sbjct: 1309 DIAGRSKMYKNIVDGKLTMNVDVPESFNVLRNEVRALGIDMDFDYSSEEE 1358


>gi|301059228|ref|ZP_07200165.1| DNA-directed RNA polymerase, beta subunit [delta proteobacterium
            NaphS2]
 gi|300446663|gb|EFK10491.1| DNA-directed RNA polymerase, beta subunit [delta proteobacterium
            NaphS2]
          Length = 1434

 Score = 1491 bits (3860), Expect = 0.0,   Method: Composition-based stats.
 Identities = 711/1431 (49%), Positives = 967/1431 (67%), Gaps = 79/1431 (5%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R RK FGK  ++I+ P+LI +QK SY+ +L  ++ P+ER + GLQAA+  VFPI  F+
Sbjct: 8    RRRARKSFGKISKVIETPNLIAMQKRSYERYLQQDVPPEEREDVGLQAAYAGVFPIHDFA 67

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G + LEFV Y F+  K+  +DCL + +TY   L++T+RL+VFD D  +  KSI+DIKEQ 
Sbjct: 68   GTSSLEFVKYAFEGAKYSEEDCLSKGMTYEASLRLTVRLVVFDTDTVSETKSIRDIKEQE 127

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            IY G LP+MT  GTF+I G +R VVSQLHRSPG  FDHDKG+   SGKLLY+ RIIP +G
Sbjct: 128  IYFGTLPIMTDRGTFIINGTERAVVSQLHRSPGAFFDHDKGKTHASGKLLYSARIIPLRG 187

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG------- 242
             W+D EFD KD ++VRIDRRRK PVT  L ALG  + ++L  FY   +            
Sbjct: 188  SWLDFEFDPKDFLYVRIDRRRKFPVTILLKALGYTANDLLHYFYDTEMVEIGETGAWREA 247

Query: 243  -------DFWCFPLSAADLMVGAK------------------------------------ 259
                   D     +   D  V AK                                    
Sbjct: 248  IPELLAQDRVEKDIVGEDEAVIAKKGVKFTKRLLRNLGTNEAATARIPMVKRLPFDVEKD 307

Query: 260  ----VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL----------GITSDCLCG 305
                ++  + D +TG+ ++ +G  LT  +   L EKG+  +           +  + + G
Sbjct: 308  AELQLTEEITDSETGDMIVAAGSILTEEIYALLDEKGISRITCVDRKRIRIPVEPESIEG 367

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              V +DI++ ETGEI +E+ + +  + ++ +    I  +  L +D    +  IR TLV D
Sbjct: 368  RVVCDDIIDPETGEILLESNNHLTMEKIKALLERGIVHLECLVLDGHGISRSIRETLVGD 427

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-NLDT 424
            +    ++A LDIYR MRP    T  VAE+ F+ LFF+ D YDLS VGR+K+N RL   D 
Sbjct: 428  RINTPEEARLDIYRKMRPSSPPTPEVAETFFHNLFFNLDTYDLSRVGRLKLNYRLGMEDV 487

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              + R +RKEDI   ++ L+ L++ +  +DDIDNLGNRRVR+VGE+L+NQYR+GL+RMER
Sbjct: 488  SLEERTLRKEDIFGTVQELIRLKSAEAMVDDIDNLGNRRVRAVGELLENQYRVGLVRMER 547

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            +IKER+S  +++++MP DLIN+KPV + V EFF +SQLSQ  +  N LS +TH RRLSAL
Sbjct: 548  AIKERMSLQEVETLMPHDLINSKPVSAVVKEFFGTSQLSQFMDQTNPLSEVTHKRRLSAL 607

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+ SL+++A+VN +GFIETPYR+
Sbjct: 608  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIVSLSTYAQVNEFGFIETPYRR 667

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V + K T  + YLSA++E++  IAQAN+ LDE+G+F  +    R  GE   VP   + ++
Sbjct: 668  VNEKKATGSLEYLSALDEKDFPIAQANAPLDEEGNFIRDEAAVRIEGEAYKVPVGDVKYM 727

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D SP Q+VSI+ASLIPFLE+DD+NR LMG NMQRQAVPLL+A+AP VGTG+E VVA+ SG
Sbjct: 728  DVSPDQLVSISASLIPFLEHDDANRALMGSNMQRQAVPLLRAKAPLVGTGVEKVVARDSG 787

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +++A+R GI+E VDA RIVIR  + D +   S V+I +L KF+RSNQN+C NQ+P+VK 
Sbjct: 788  ISVIARRDGIIEHVDASRIVIRFTDTDEND-DSEVEICKLTKFRRSNQNSCYNQKPIVKK 846

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G+ V++  IIADGP+ + G+LALGRN++VAFM W GYNFEDS+LISER+V +DV+TSIHI
Sbjct: 847  GEFVKKGQIIADGPAMEQGELALGRNVMVAFMSWGGYNFEDSILISERVVKDDVYTSIHI 906

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +EFE+++RDTKLG EEITRDIPNV E+ L+N+D+ GI+ +GAE+ PGDILVGKITPKGE+
Sbjct: 907  DEFEILSRDTKLGKEEITRDIPNVGEDALRNLDDSGIVKIGAEIGPGDILVGKITPKGET 966

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             ++PEEKLLRAIFG+KA DV+D+S+RVP GV GTV+D ++F+R G++K+ R++++E E+ 
Sbjct: 967  QLSPEEKLLRAIFGDKAGDVKDSSMRVPPGVYGTVIDAKVFSRGGVEKDARALAIEAEET 1026

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-------GPKGFKKSTVLSSDLISEYP 1017
              L +D  DE  +++R+   +L+ I  G+   S       G    KK+  L+ + I+  P
Sbjct: 1027 RRLRKDLQDEVEVVERSAREKLLGIFEGKALKSNLRDKKSGAILLKKTEHLTREDIASIP 1086

Query: 1018 RSQ--WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                 W    V  +++    E++  +       L    +NKIE    GD++ PGV+++VK
Sbjct: 1087 IEAIAWADVKVPMDEI-EKAETIVSKCTAKVERLTTICENKIENFDLGDELAPGVVKMVK 1145

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V+VA+KR +  GDKMAGRHGNKG++SRILP EDMP+  DGTPVDIVLNPLGVPSRMNVGQ
Sbjct: 1146 VYVAVKRKLSVGDKMAGRHGNKGVLSRILPVEDMPYFADGTPVDIVLNPLGVPSRMNVGQ 1205

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ETHLGWA  G+G K++ L   +    ++  L+   +K      +    ++ +DD +L+
Sbjct: 1206 VLETHLGWASHGMGMKVREL---FGKINNVQRLKDKFKKWFSKDEYEAFFANLEDDELLK 1262

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             +     GVP++TPVFDGA E+ I S L  A L  +GQ+ LYDG TGEPFD+ VTVG +Y
Sbjct: 1263 ESSLMLDGVPLATPVFDGASEDEIKSFLEEAGLSATGQATLYDGRTGEPFDQDVTVGIMY 1322

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            ++KL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE L
Sbjct: 1323 IMKLHHLVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWAMEAYGAAYTLQEFL 1382

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T+KSDDV GRTR+YE IV GN+  E G PESF VL+KE+Q+LGL ++L   
Sbjct: 1383 TVKSDDVAGRTRMYERIVKGNNALEPGLPESFKVLMKELQSLGLEMELFED 1433


>gi|57238903|ref|YP_180039.1| DNA-directed RNA polymerase subunit beta [Ehrlichia ruminantium str.
            Welgevonden]
 gi|58578835|ref|YP_197047.1| DNA-directed RNA polymerase subunit beta [Ehrlichia ruminantium str.
            Welgevonden]
 gi|81353036|sp|Q5HC05|RPOB_EHRRW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|57160982|emb|CAH57888.1| DNA-directed RNA polymerase beta chain [Ehrlichia ruminantium str.
            Welgevonden]
 gi|58417461|emb|CAI26665.1| DNA-directed RNA polymerase beta chain [Ehrlichia ruminantium str.
            Welgevonden]
          Length = 1380

 Score = 1483 bits (3839), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1376 (51%), Positives = 963/1376 (69%), Gaps = 28/1376 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ ++       + G++  F+S+FPI    G A
Sbjct: 19   RLSYAKSIDIKDSLTDLIKIQRDSYNAFIGIDQDV----DSGIKNIFQSMFPIQDLLGRA 74

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +L+FVSY    P++D  +C+ R +TY+VP++I LR IV+ V            DE T  K
Sbjct: 75   VLQFVSYSIGEPQYDEYECIKRGITYSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 134

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I G++R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 135  SIKYIKEQEVSIGDLPTMTSYGTFIINGVERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 194

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + EIL TFY KI Y +
Sbjct: 195  LARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNSEILDTFYDKIRYER 254

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P    D   G ++S  LVDID G  ++++  ++T  L K L   G+K   +  
Sbjct: 255  CENGWVVPFVV-DRFRGVRLSYDLVDID-GNVLVKANTRITLRLAKKLASDGLKKYLVPF 312

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + GL++A D+V+  +  + + AG+ I  + + ++   +I +I IL +D +    YI N
Sbjct: 313  AEIQGLFIANDLVDPASNVMIMCAGESITSEHINKLKLFDINEIFILNIDFLTVGPYILN 372

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L
Sbjct: 373  TLFLDKNISYEDALFEIYKVLRSGESPSLDTMKAFFDGLFFEKERYDLSTVGRIKLNDHL 432

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  +DV  + K+DII +IK LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 433  GLDISEDVTVLTKDDIIHVIKKLVLLRDGEGFVDDIDHLGNRRVRSVGEFIENQFRIGIL 492

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 493  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 552

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+
Sbjct: 553  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIES 612

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 613  PYRKVDNGVVTDKVEYLLAMQESNYYIADASATLDENNRFVDDMLYCRHDGNFVMVKREQ 672

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP VGTGMES+VA
Sbjct: 673  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLVGTGMESIVA 732

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR+GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQ+P
Sbjct: 733  AGSGTVVLAKRSGIVHRVDGLYIVIRAFDKEKNEY-LGVDIYNLRKFQRSNHNTCINQKP 791

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD VR ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 792  LVKPGDYVRENDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 851

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R IP+V+E+ L ++D+ GI+ VGAEV+ GDILVGK+TP
Sbjct: 852  SIHIEEFECVVRDTALGPEKIMRSIPDVNEDSLSHLDDVGIVNVGAEVSAGDILVGKVTP 911

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 912  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPIDVEGTVVDVHVFVRRGVEENDRSLLIK 971

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    Y  L  +L   N     +  +       D +   P+  
Sbjct: 972  QNEINGFIKERDYEIDVVSEYFYDELKRVLVNTNTEYNNQNIE-------DYLKSIPQKS 1024

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE V   +  LK ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1025 WWDIKLSDESVLSQISDLKEKFDSMIENAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1084

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP+L+DGTPVDI+LN LGVPSRMNVGQI ETH
Sbjct: 1085 KHNLQPGDKMAGRHGNKGVISRIVPVEDMPYLEDGTPVDIILNSLGVPSRMNVGQILETH 1144

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI +++ D      I+ LR+FL++V         I    DD +L  AE+ 
Sbjct: 1145 LGWASVNLGKKIGNIL-DNIDELTIAHLRNFLDQVYDGQDLKYSIRSMSDDDLLAFAERL 1203

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+++L++ADLD SGQ  LYDG  GE FDR VTVGYIYMLKL+
Sbjct: 1204 RDGVPMAAPVFEGPKDNQISNLLKLADLDVSGQVDLYDGRIGEKFDRKVTVGYIYMLKLH 1263

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1264 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1323

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L + L+  +     +   
Sbjct: 1324 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVALKQDKDFLHDRKIN 1379


>gi|58616892|ref|YP_196091.1| DNA-directed RNA polymerase subunit beta [Ehrlichia ruminantium str.
            Gardel]
 gi|75356604|sp|Q5FFD9|RPOB_EHRRG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|58416504|emb|CAI27617.1| DNA-directed RNA polymerase beta chain [Ehrlichia ruminantium str.
            Gardel]
          Length = 1380

 Score = 1483 bits (3838), Expect = 0.0,   Method: Composition-based stats.
 Identities = 704/1376 (51%), Positives = 963/1376 (69%), Gaps = 28/1376 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ ++       + G++  F+S+FPI    G A
Sbjct: 19   RLSYAKSIDIKDSLTDLIKIQRDSYNAFIGIDQDV----DSGIKNIFQSMFPIQDLLGRA 74

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +L+FVSY    P++D  +C+ R +TY+VP++I LR IV+ V            DE T  K
Sbjct: 75   VLQFVSYSIGEPQYDEYECIKRGITYSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 134

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I G++R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 135  SIKYIKEQEVSIGDLPTMTSYGTFIINGVERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 194

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + EIL TFY KI Y +
Sbjct: 195  LARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNSEILDTFYDKIRYER 254

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              + W  P    D   G ++S  LVDID G  ++++  ++T  L K L   G+K   +  
Sbjct: 255  CENGWVVPFVV-DRFRGVRLSYDLVDID-GNVLVKANTRITLRLAKKLASDGLKKYLVPF 312

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + GL++A D+V+  +  + + AG+ I  + + ++   +I +I IL +D +    YI N
Sbjct: 313  AEIQGLFIANDLVDPASNVMIMCAGESITSEHINKLKLFDINEIFILNIDFLTVGPYILN 372

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L
Sbjct: 373  TLFLDKNISYEDALFEIYKVLRSGESPSLDTMKAFFDGLFFEKERYDLSTVGRIKLNDHL 432

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  +DV  + K+DII +IK LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 433  GLDISEDVTVLTKDDIIHVIKKLVLLRDGEGFVDDIDHLGNRRVRSVGEFIENQFRIGIL 492

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 493  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 552

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+
Sbjct: 553  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIES 612

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 613  PYRKVDNGIVTDKVEYLLAMQESNYYIADASATLDENNRFVDDMLYCRHDGNFVMVKREQ 672

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP VGTGMES+VA
Sbjct: 673  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLVGTGMESIVA 732

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR+GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQ+P
Sbjct: 733  AGSGTVVLAKRSGIVHRVDGLYIVIRAFDKEKNEY-LGVDIYNLRKFQRSNHNTCINQKP 791

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD VR ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 792  LVKPGDYVRENDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 851

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R IP+V+E+ L ++D+ GI+ VGAEV+ GDILVGK+TP
Sbjct: 852  SIHIEEFECVVRDTALGPEKIMRSIPDVNEDSLSHLDDVGIVNVGAEVSAGDILVGKVTP 911

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 912  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPIDVEGTVVDVHVFVRRGVEENDRSLLIK 971

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    Y  L  +L   N     +  +       D +   P+  
Sbjct: 972  QNEINGFIKERDYEIDVVSEYFYDELKRVLVNTNTEYNNQNIE-------DYLKSIPQKS 1024

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE V   +  LK ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1025 WWDIKLSDESVLSQISDLKEKFDSMIENAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1084

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP+L+DGTPVDI+LN LGVPSRMNVGQI ETH
Sbjct: 1085 KHNLQPGDKMAGRHGNKGVISRIVPVEDMPYLEDGTPVDIILNSLGVPSRMNVGQILETH 1144

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI +++ D      I+ LR+FL++V         I    DD +L  AE+ 
Sbjct: 1145 LGWASVNLGKKIGNIL-DNIDELTIAHLRNFLDQVYDGQDLKYSIRSMSDDDLLAFAERL 1203

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+++L++ADLD SGQ  LYDG  GE FDR VTVGYIYMLKL+
Sbjct: 1204 RDGVPMAAPVFEGPKDNQISNLLKLADLDVSGQVDLYDGRIGEKFDRKVTVGYIYMLKLH 1263

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1264 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1323

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L + L+  +     +   
Sbjct: 1324 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVALKQDKDFLHDRKIN 1379


>gi|88658392|ref|YP_507740.1| DNA-directed RNA polymerase subunit beta [Ehrlichia chaffeensis str.
            Arkansas]
 gi|97537056|sp|Q8KWX2|RPOB_EHRCR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88599849|gb|ABD45318.1| DNA-directed RNA polymerase, beta subunit [Ehrlichia chaffeensis str.
            Arkansas]
          Length = 1380

 Score = 1482 bits (3837), Expect = 0.0,   Method: Composition-based stats.
 Identities = 695/1376 (50%), Positives = 966/1376 (70%), Gaps = 28/1376 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ ++    +    G++  F+S+FPI    G A
Sbjct: 20   RLSYAKSIDIKDSLTDLIKIQRDSYNAFIGID----QNTESGIKNIFQSMFPIQDLLGRA 75

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVSY    P++D  +C+ R +T++VP++I LR IV+ V            DE T  K
Sbjct: 76   VLEFVSYSIGEPQYDEYECIKRGITFSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 135

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 136  SIKYIKEQEVSIGDLPTMTSHGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 195

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + +IL TFY KI Y +
Sbjct: 196  SARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNNDILDTFYDKIRYVK 255

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P  A D   G ++S  L+D D G  ++++  ++T  + + L   G+    +  
Sbjct: 256  SEKGWVVPFVA-DRFRGVRLSHDLMDSD-GNVLVKANTRITLRMARKLANDGLTKYLVPF 313

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + GL++A D+++     + I AG+ I  + + ++    I +I +L +D +    YI N
Sbjct: 314  NEIQGLFIANDLLDSTGNALIISAGENITSEHINKLELFNIEEIFVLNIDFLTVGPYILN 373

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L
Sbjct: 374  TLFLDKNVSYEDALFEIYKVLRSGESPSLDTIKAFFDGLFFEKERYDLSTVGRIKLNDHL 433

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L+  +D+  + K+DII +IK LV LR+G+G++DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 434  GLNVSEDITVLTKDDIIHVIKKLVLLRDGEGSVDDIDHLGNRRVRSVGEFIENQFRIGIL 493

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 494  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 553

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+
Sbjct: 554  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIES 613

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV  G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 614  PYRKVDKGVVTDKVEYLLAMQESNYYIADASATLDENNQFVDDMLYCRHDGNFVMVKREE 673

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP +GTGMES+VA
Sbjct: 674  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLIGTGMESIVA 733

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQRP
Sbjct: 734  AGSGTVVLAKRGGIVHRVDGLYIVIRAFDQEKNEY-LGVDIYNLRKFQRSNHNTCINQRP 792

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 793  LVKPGDYVKANDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 852

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+++E+ L ++D+ GI+ VGAEV+ GDILVGK+TP
Sbjct: 853  SIHIEEFECVVRDTTLGPEKIMRSVPDINEDSLSHLDDVGIVNVGAEVSAGDILVGKVTP 912

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 913  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPLDVEGTVVDVHVFVRRGVEENDRSLLIK 972

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    Y  L  +L          G + +     D ++  P+ +
Sbjct: 973  QNEINGFIKERDYEIDVVSEYFYDELKRVLVSS-------GVQYNNQNIDDYLASIPKKE 1025

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE +   V+ LK ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1026 WWDINLSDEAMLLQVKDLKEKFDSMIQNAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1085

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP+L+DGTPVDI+LN LGVPSRMNVGQI ETH
Sbjct: 1086 KHNLQPGDKMAGRHGNKGVISRIVPVEDMPYLEDGTPVDIILNSLGVPSRMNVGQILETH 1145

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  ++ D      +S LR+FL +V       + I    D+ +L  AE+ 
Sbjct: 1146 LGWASVNLGKKIGHIL-DNLDELTVSHLRNFLYQVYDGQDLKDNIQSMSDEDLLVFAERL 1204

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+++LR+ADLD SGQ  LYDG  GE FDR VTVGYIYMLKL+
Sbjct: 1205 RDGVPMAAPVFEGPKDSQISNLLRLADLDVSGQVDLYDGRIGEKFDRKVTVGYIYMLKLH 1264

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1265 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1324

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L + L+  +   S ++++
Sbjct: 1325 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVALKQDKDFLSNEVKD 1380


>gi|73666802|ref|YP_302818.1| DNA-directed RNA polymerase subunit beta [Ehrlichia canis str. Jake]
 gi|88909136|sp|Q3YST5|RPOB_EHRCJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|72393943|gb|AAZ68220.1| DNA-directed RNA polymerase subunit beta [Ehrlichia canis str. Jake]
          Length = 1380

 Score = 1482 bits (3836), Expect = 0.0,   Method: Composition-based stats.
 Identities = 689/1376 (50%), Positives = 959/1376 (69%), Gaps = 28/1376 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ +     +    G++  F+S+FPI    G A
Sbjct: 20   RLSYAKSIDIKDSLTDLIKIQRDSYNAFIGVG----QNTESGIKNIFESMFPIEDLLGRA 75

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVSY    P++D  +C+ R +T++VP++I LR IV+ V            DE T  K
Sbjct: 76   VLEFVSYSIGEPQYDEYECIKRGITFSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 135

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 136  SIKYIKEQEVSIGDLPTMTPHGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 195

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + +IL+TFY KI Y +
Sbjct: 196  SARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNNDILNTFYDKIRYVK 255

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  LVD+  G  ++++  ++T  + K L   G+    +  
Sbjct: 256  CEKGWIVPFVV-DRFRGVRLSHDLVDV-NGNVLVKANTRITLRMAKKLANDGLTEYLVPF 313

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + GL++A D+ +     + I AG+ I  + + ++   +I++I +L +D +    YI N
Sbjct: 314  AEIQGLFIANDLFDPSGNALIISAGENITSEHINKLELFDIKEIFVLNIDFLTVGPYILN 373

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L
Sbjct: 374  TLFLDKNVTYEDALFEIYKVLRSGESPSLDTIKAFFDGLFFEKERYDLSTVGRIKLNDHL 433

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L+  +D+  + K+DII +IK LV LR+G+G++DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 434  GLNVSEDITVLTKDDIIHVIKKLVLLRDGEGSVDDIDHLGNRRVRSVGEFIENQFRIGIL 493

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 494  RLERMIMDYMSSVNFDNAMPCDFVNPKILATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 553

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+
Sbjct: 554  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIES 613

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV  G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 614  PYRKVDKGVVTDKVEYLLAMQESNYYIADASATLDENNQFVDDMLYCRHDGNFVMVKREE 673

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP +GTGMES+VA
Sbjct: 674  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLIGTGMESIVA 733

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR GIV +VD + IVIR+ + + +    GVD+Y L KFQRSN NTC+NQRP
Sbjct: 734  AGSGTVVLAKRGGIVHRVDGLYIVIRAFDQEKNEY-LGVDVYNLRKFQRSNHNTCINQRP 792

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 793  LVKPGDYVKANDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 852

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+++E+ L ++D+ GI+ +GAEV+ GDILVGK+TP
Sbjct: 853  SIHIEEFECVVRDTTLGPEKIMRSVPDINEDSLSHLDDVGIVNIGAEVSAGDILVGKVTP 912

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 913  RPPISLPPETKLLVTIFGEKVFDCVDSSLYLPLDVEGTVVDVHVFVRRGVEENDRSLLIK 972

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    Y  L  +L         +          D +   P+  
Sbjct: 973  QNEINGFIKERDYEIDVVSEYFYDELKRVLVNSGVQCNNQNVN-------DYLESTPKKD 1025

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE V   + +L+ ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1026 WWNVNLSDETVLLQINNLREKFDSMIQNAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1085

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKM+GRHGNKG++SRI+P EDMP+L+DGTPVDI+LN LGVPSRMNVGQI ETH
Sbjct: 1086 KHNLQPGDKMSGRHGNKGVISRIVPVEDMPYLEDGTPVDIILNSLGVPSRMNVGQILETH 1145

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             GWA V LGKKI  ++ D      IS LR+FL++V         I    D+ +L  AE+ 
Sbjct: 1146 FGWASVNLGKKIGHIL-DNIDELTISHLRNFLDQVYDGQDLKYNIQSMSDEDLLAFAERL 1204

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+++L++ADLD SGQ  LYDG  GE FDR VTVGYIYMLKL+
Sbjct: 1205 RGGVPMAAPVFEGPKDSQISNLLKLADLDVSGQVDLYDGRIGEKFDRKVTVGYIYMLKLH 1264

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1265 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1324

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L + L+  +   S+++  
Sbjct: 1325 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVALKQDKDFLSSEVNN 1380


>gi|302036657|ref|YP_003796979.1| DNA-directed RNA polymerase subunit beta [Candidatus Nitrospira
            defluvii]
 gi|300604721|emb|CBK41053.1| DNA-directed RNA polymerase, beta subunit [Candidatus Nitrospira
            defluvii]
          Length = 1319

 Score = 1481 bits (3834), Expect = 0.0,   Method: Composition-based stats.
 Identities = 694/1364 (50%), Positives = 939/1364 (68%), Gaps = 63/1364 (4%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             RK F +    IDIPDLIE+QK SY+ FL M + PD R ++GLQAA  SVFPIT ++  A
Sbjct: 11   ERKDFSRIRTSIDIPDLIEIQKRSYEEFLQMEVEPDRRKDQGLQAALASVFPITDYNNTA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LEF +Y    PK+D  +CL + +T+AVPLK+ +RLIVFD ++    K + D++EQ +Y+
Sbjct: 71   ALEFSNYSLGTPKYDERECLEQGMTFAVPLKLRVRLIVFDKEDKGPKKKVLDVREQEVYV 130

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G+LPLMT+ GTF+I G +R+VVSQLHRSPG  F HDKGR   SGK+LY+ RIIP +G W+
Sbjct: 131  GELPLMTERGTFLINGTERVVVSQLHRSPGASFTHDKGRTHASGKVLYSARIIPYRGSWL 190

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD++DI++VRIDRRRK+P T  L A G  ++++L  +YP              L   
Sbjct: 191  DFEFDARDILYVRIDRRRKMPATILLKAFGYSTDDLLRMYYPVEEIRVSKGKLYRKLDPE 250

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
             +  G K S+ +++    + ++  G KLT  L+  LK  G+K + +T   L G  V  ++
Sbjct: 251  -IHHGLKCSTEVMEKGGKDPLVREGAKLTKVLIAKLKAAGIKEIPVTPAELVGRAVLTEL 309

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+    +   E    + E+ LE+I  S+I +  ++Y+D+ N    I +TL  ++   +++
Sbjct: 310  VDSGKKQSLAEKNQRLTEEILEKILDSDIEEFKVIYLDTTNATLVILDTLDMERTGSKEE 369

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A+++IYR +RPG+  +   A ++F+ LF    +YDLS VGR+K+N +L LD   + R + 
Sbjct: 370  AMVEIYRRLRPGETPSVETARALFDNLFLSPKRYDLSPVGRLKLNKKLGLDFALEQRTLT 429

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             +DI+ +++ LV+L+ G+G IDDID+LGNRRVRSVGE+L+NQ+RLGL+RMERSIKER++ 
Sbjct: 430  AQDIVEVVRYLVNLKIGRGEIDDIDHLGNRRVRSVGELLENQFRLGLVRMERSIKERMNL 489

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            +D+++V+P DLINAKPVV+AV EFF SSQLSQ  +  N L+ ITH RRLSALG GG+ R 
Sbjct: 490  LDMETVLPHDLINAKPVVAAVKEFFSSSQLSQFMDQTNPLAEITHKRRLSALGPGGLTRE 549

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHP+HY RICP ET EG NIGL++SL ++AR+N +GFIE PYRKV  G+V++
Sbjct: 550  RAGFEVRDVHPSHYSRICPIETPEGPNIGLITSLATYARINEFGFIEAPYRKVVKGRVSD 609

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            ++ YLSA+E +   IAQANS +D  G    E V  R AG+ I    +KI+++D SPKQVV
Sbjct: 610  ELEYLSAIEGDKYIIAQANSKVDTSGRLVSETVSARSAGDFITATPDKIEYMDVSPKQVV 669

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+A +L+PFLE+DD+NR LMG NMQRQAVPLLKAE+P VGTGME+VVA+ SG  + AKR 
Sbjct: 670  SVATALVPFLEHDDANRALMGSNMQRQAVPLLKAESPLVGTGMEAVVARDSGYVVQAKRE 729

Query: 733  GIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+VE VDA RIV+R+  +     + SG+D+Y ++KFQRSNQNTC+ Q P+V++G+ V+R 
Sbjct: 730  GVVESVDATRIVVRADAKEGRKRNDSGLDVYEMIKFQRSNQNTCITQTPVVRIGEPVKRG 789

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             ++ADGP+ D G+LALG+N+LVAFMPW GYNFED++L+SE++V ED FTSIHIEEFEV A
Sbjct: 790  QVLADGPAIDHGELALGKNVLVAFMPWGGYNFEDAILLSEKLVREDAFTSIHIEEFEVEA 849

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG E+ITRDIPNV EE L+++DE GII +GAEV PGDILVGK+TPKGE+ +TPEEK
Sbjct: 850  RDTKLGKEDITRDIPNVGEEALRDLDESGIIRIGAEVKPGDILVGKVTPKGETQLTPEEK 909

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DV+DTSL VP GV G VVDV+IF+R G+DK+ERS S+E E    L RD 
Sbjct: 910  LLRAIFGEKAGDVKDTSLTVPPGVEGIVVDVKIFSRKGLDKDERSKSIESEDHMKLQRDH 969

Query: 972  DDEQVILDRNIYSRLMEILCGQNA-------VSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
             +E  I++     ++ ++L G+          +G    KK   L+++++   P       
Sbjct: 970  QEELRIIEDEKTKKVRKLLLGKVVGRDLMDPETGGVILKKKGKLTAEILKRLPDDMVRHI 1029

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             + D   Q+ +E ++ + +    IL+  +  K+ +++ GD++PPGV+++VKV++AMKR I
Sbjct: 1030 ILSDPDEQKELEDVERRAKEQIEILQTLYDEKVGRLRRGDELPPGVIKLVKVYIAMKRKI 1089

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG+VSR+LP EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA
Sbjct: 1090 QVGDKMAGRHGNKGVVSRVLPEEDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWA 1149

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG K+ S + D  +  +I  L    +                               
Sbjct: 1150 ARALGIKVASPVFDGASEKEIKELLKKAKLSPSGQ------------------------- 1184

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               T + DG   E+                          F  PVTVGY+Y+LKL+H+V 
Sbjct: 1185 ---TMLMDGRTGES--------------------------FSSPVTVGYMYVLKLHHLVD 1215

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW +QAYGAA +LQE LT+KSDDV G
Sbjct: 1216 DKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALQAYGAASILQEFLTVKSDDVPG 1275

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R+R+YE+IV G    E G PESFNVLVKE+Q+LGL ++L  S+ 
Sbjct: 1276 RSRMYEAIVKGEPFLEPGLPESFNVLVKELQSLGLDVELVKSKD 1319


>gi|317052110|ref|YP_004113226.1| DNA-directed RNA polymerase subunit beta [Desulfurispirillum indicum
            S5]
 gi|316947194|gb|ADU66670.1| DNA-directed RNA polymerase, beta subunit [Desulfurispirillum indicum
            S5]
          Length = 1347

 Score = 1481 bits (3833), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1384 (48%), Positives = 930/1384 (67%), Gaps = 64/1384 (4%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R R  F + P I+DIPDL  +QK SY  FL M     +R + GL+A F+SVFPI  ++  
Sbjct: 14   RKRHNFSRIPNILDIPDLNAIQKESYVKFLQMGKDFQQRSDMGLEAVFRSVFPIQDYNET 73

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT--GAKSIKDIKEQS 129
            A LE++SY    PK++V++C  R  T+A P++I +RL++F+ +     G + +KD+KEQ 
Sbjct: 74   AQLEYISYSLGEPKYNVNECQDRGATFAAPVRIKVRLVLFEREGSAAPGERPVKDVKEQE 133

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G+LPLMT  GTF+I GI+R++VSQLHRSPG+ F+ D G+   + K++Y+ RIIP +G
Sbjct: 134  VYLGELPLMTDKGTFIINGIERVIVSQLHRSPGVFFEDDGGKGGANAKVIYSARIIPYRG 193

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             WMD EFD+KDI++VRID++RK P T  L ALG    +ILS FY         D     L
Sbjct: 194  SWMDFEFDAKDILYVRIDKKRKFPATVVLKALGYSERDILSHFYTNETIRVSEDGSVEKL 253

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC--GLY 307
            +    +   K+   ++  ++GE ++++G K+T G ++ L    V+ + +    +     Y
Sbjct: 254  TDLANLYNQKLMQDILHPESGEVLVKAGHKITRGNIRKLTNANVQSIRLDRMEVVRDTSY 313

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-K 366
             AEDI +  +GE+       + +   + +    +R+  IL++D++ ++  IR+TL  D K
Sbjct: 314  FAEDIYDPSSGELLASINQPVTDDIYDLLLERGVREFAILFIDNIKSDTSIRDTLAADSK 373

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                ++AL++I+R MRPG+  T   A  +F+ LFF + +YDLS VGR+K+N RL L+ P 
Sbjct: 374  VTSAEEALIEIFRKMRPGEPPTVEAATQLFDNLFFVAKRYDLSRVGRLKINRRLGLEVPM 433

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            DV  + +EDI+ ++K L D++NGKG++DDID+L NRR+RSVGE+L+NQ+R+GL+RMER++
Sbjct: 434  DVTTLTREDILQVVKTLSDIKNGKGSVDDIDHLSNRRIRSVGELLENQFRIGLVRMERTV 493

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER+S  D+  + PQ+L+N+KP+V+++ EFF SSQLSQ  +  N L+ ITH RRLSALG 
Sbjct: 494  KERMSIQDLSELSPQELLNSKPIVASIKEFFGSSQLSQFMDQTNPLAEITHKRRLSALGP 553

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVH THYGRICP ET EG NIGL++SL +  R+N YGFIETPYRKV 
Sbjct: 554  GGLTRERAGFEVRDVHTTHYGRICPIETPEGPNIGLITSLATHGRINEYGFIETPYRKVE 613

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
              KVT  + YLSA++E  + IAQAN  LD+   F  ELV  R  GE ++   E I ++D 
Sbjct: 614  KKKVTTQIDYLSAIDEYGQIIAQANEPLDKGNCFVNELVSARDEGEFVMTEAENITYMDV 673

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+VS+AA LIPFLENDD+NR LMG NMQRQAVPLL+ ++P VGTG+E  VA  SGAA
Sbjct: 674  APVQMVSVAAGLIPFLENDDANRALMGSNMQRQAVPLLRTQSPLVGTGLERKVAVDSGAA 733

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            I A R G +  V+A +I++   E ++ P    VDIY L+KF+RSNQNTC+NQ P+V  GD
Sbjct: 734  ITATRGGTIVSVEADKIIVHVNESEIAPGEGRVDIYNLIKFRRSNQNTCINQTPIVFPGD 793

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            +V+  D+IADGP+T+ GDLALG+N++VAFMPW GYNFEDS+LISER+V EDV+TSIHIEE
Sbjct: 794  QVKAGDVIADGPATESGDLALGKNVVVAFMPWMGYNFEDSILISERVVLEDVYTSIHIEE 853

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            F+V ARDTKLGPE+ITRDIPNV E+ LK+ID+ GII +GAEV  GDI+VGK+TPKGE+  
Sbjct: 854  FDVEARDTKLGPEDITRDIPNVGEDALKDIDDSGIIRIGAEVKAGDIMVGKVTPKGETQP 913

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLLRAIFGEKA + RD SL VP G+ GT+VDV++F R G +K++R   +E E+I+ 
Sbjct: 914  TPEEKLLRAIFGEKAGEFRDASLTVPPGIEGTIVDVKVFTRRGTEKDDRVKDIEEEEIKK 973

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQW 1021
            L  D  DE  ++ +   +++  +L G+         G    ++   ++ +++ +   ++ 
Sbjct: 974  LEVDYQDECTLIRKERLNKIRRLLVGKKLADDLVLRGKILGREGEAITMEMVEKLTLNEL 1033

Query: 1022 WQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             +  V+D E   R  ES++   E       + +  K  ++  GDD+PPGV ++VKV+VA+
Sbjct: 1034 LETPVEDSEGFIRKAESIREIMEEQLEKTHEMYTEKKSRVNMGDDLPPGVFKMVKVYVAV 1093

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKG+VSRILP ED+P+L DGTPVDIVLNPLGVPSRMNVGQI ETH
Sbjct: 1094 KRKLKVGDKMAGRHGNKGVVSRILPQEDLPYLPDGTPVDIVLNPLGVPSRMNVGQILETH 1153

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LG  + + + D    GDI  L                                
Sbjct: 1154 LGWAAKALGMHVATNVFDGANEGDIKELLRK----------------------------- 1184

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                      +DG               +++GQ+ LYDG TGE FD+PVTVG IYMLKL+
Sbjct: 1185 ---------AYDG---------------NDTGQTDLYDGRTGEKFDQPVTVGVIYMLKLH 1220

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V  K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQE+LT+KSD
Sbjct: 1221 HLVDTKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHCLQELLTVKSD 1280

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GRT++YE+IV G +T   G PESFNVLVKE+Q+L L ++L ++      +  E  + 
Sbjct: 1281 DVNGRTKMYEAIVKGENTLTPGLPESFNVLVKELQSLCLDVELISTDEAVEVEAGESSEV 1340

Query: 1381 NKCE 1384
               E
Sbjct: 1341 LTEE 1344


>gi|301168466|emb|CBW28056.1| DNA-directed RNA polymerase beta chain [Bacteriovorax marinus SJ]
          Length = 1348

 Score = 1479 bits (3829), Expect = 0.0,   Method: Composition-based stats.
 Identities = 664/1349 (49%), Positives = 923/1349 (68%), Gaps = 16/1349 (1%)

Query: 32   VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDC 91
            +Q  S++ FL  ++ P +R   GLQ  F SVFPI  F+    LEFVSY  + PK+ V +C
Sbjct: 3    LQLKSFEEFLQKDVPPAQRKMVGLQQVFHSVFPIHDFNKTVSLEFVSYTLEEPKYSVKEC 62

Query: 92   LWRDLTYAVPLKITLRLIVFDVDEFT---GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
              R L+Y  PLK+ +RL+ ++V+        +++  IKEQ +Y+G++PLM + G+FV  G
Sbjct: 63   RQRGLSYEAPLKVVVRLVFYEVNVDKDGNEQRTVSSIKEQEVYLGNIPLMAETGSFVYNG 122

Query: 149  IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
             +R++VSQLHRSPGI F+HD G+   SGKLLY+ RIIP +G W+D EFD K+++  RIDR
Sbjct: 123  TERVIVSQLHRSPGIIFEHDSGKKHSSGKLLYSARIIPHRGSWLDFEFDHKNVLFARIDR 182

Query: 209  RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
            +RK+  T  L A+G  + ++L  FY     +   D          LM+G +  + ++D  
Sbjct: 183  KRKLHATVVLKAMGYSTTDLLEMFYEMETLNINKDATFTRELDFSLMIGTRALNDILDPS 242

Query: 269  TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
            +G+ +++ GKK T   +K L E G+  +    + + G   AEDI +  TGE+   A + +
Sbjct: 243  SGKALVKKGKKFTKASVKKLNEAGITEISAELEEVIGKVAAEDIFDENTGEVLCLANEAL 302

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             E  ++E+  + I  + ++Y+D +N    +RNTL+ DK   R  AL+ I+  +RPG+  T
Sbjct: 303  SEAKIQELIAAGITKVKVIYIDMINFGDQVRNTLLLDKTDTRDTALIKIFERLRPGEPPT 362

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
               AE +F+ LFF+ +KYDLS VGR+K+N +  L+ P +   + KEDII   K LV+L N
Sbjct: 363  VEAAEQLFDNLFFNEEKYDLSKVGRMKINYKFGLNVPVENTVLTKEDIIMTAKYLVELNN 422

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            GKG +DDID+LGNRRVR+VGE+L+NQ+R+GL+RMER++KER++  +I+++MP DL+N KP
Sbjct: 423  GKGKVDDIDHLGNRRVRAVGELLENQFRVGLVRMERAVKERMAIQEIETMMPYDLVNQKP 482

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            V ++V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH THYGR
Sbjct: 483  VSASVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHSTHYGR 542

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +CP ET EG NIGL++SL ++ARV+ YGFIETPY+ V +        Y +A EEE + IA
Sbjct: 543  MCPVETPEGPNIGLITSLATYARVSEYGFIETPYQTVNEDLSLGAAKYFTAFEEEGKVIA 602

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            Q +++   DG    E V  R AGE  LVP ++++ +D SP+Q++SIA SLIPFLE+DD+N
Sbjct: 603  QIDNNHIVDGKVDGEHVPSRAAGEFTLVPNDQVELMDVSPQQMISIATSLIPFLEHDDAN 662

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            R LMG NM RQAVP+++ +AP VGTG+ES VA+ SGA + AK +G V  VD+ RIVI+  
Sbjct: 663  RALMGSNMMRQAVPVVRTDAPIVGTGIESTVARDSGAILFAKHSGRVIFVDSNRIVIQRD 722

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V +  +IADGP T LGDLALG
Sbjct: 723  K--FDEGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDVVSKGMVIADGPGTHLGDLALG 780

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +EV ARDTKLG EEITRDIPNV
Sbjct: 781  QNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESYEVEARDTKLGKEEITRDIPNV 840

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            SEE LK++DE GII VGA + PGDILVGKITPKGE+ ++PEEKLL+AIFG+KA DV+DTS
Sbjct: 841  SEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLSPEEKLLKAIFGDKAGDVKDTS 900

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            LR PS V GTV+D +++ R G++   RS  +  ++  L+ RD+  E   +  +   ++ E
Sbjct: 901  LRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLIRRDERIEIKAIQTSSILKIAE 960

Query: 989  ILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L G              +   K   L+ ++++  P        ++   ++  +      
Sbjct: 961  MLKGAKTTDRLVSEDGSSELLPKGAELTGEVLASIPFELIGYLPLE-PALEERLSEYFAD 1019

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                 + +  +  ++I K   GD++PPGV++ V ++VA+KR +Q GDKMAGRHGNKG++S
Sbjct: 1020 VRNRINRVRQKANDEIAKHHRGDELPPGVIKKVTIYVAIKRKLQPGDKMAGRHGNKGVIS 1079

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             +LP EDMPFL DGTPV+IVLNPLGVPSRMN+GQ+ E HLGWA  GLG+K+K+LI D   
Sbjct: 1080 NVLPQEDMPFLADGTPVEIVLNPLGVPSRMNIGQLLELHLGWAGRGLGEKMKALIED--- 1136

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              +++ ++ ++ K+  T      +    D  V  VA+Q  +GV  ST  FDGA EE I  
Sbjct: 1137 QVEMAEIKDYIYKIYETEEVKNWLKKASDKEVRAVADQLATGVRFSTSAFDGAKEEKIRQ 1196

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML + DL+E+G++ L+DG+TG+ F   VTVG +YMLKL+H+V +K++ARSTG YSLVTQQ
Sbjct: 1197 MLALGDLEENGKTTLFDGITGDAFAEDVTVGAMYMLKLHHLVDEKLHARSTGPYSLVTQQ 1256

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDDV+GRTR+YESIV G    E 
Sbjct: 1257 PLGGKAQFGGQRLGEMEVWALEAYGAAYTLQEFLTVKSDDVIGRTRMYESIVKGEQVLEP 1316

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            G PESFNVL++E+QAL L + L+ +  + 
Sbjct: 1317 GLPESFNVLIRELQALCLDVKLDETTEEE 1345


>gi|88606872|ref|YP_505583.1| DNA-directed RNA polymerase subunit beta [Anaplasma phagocytophilum
            HZ]
 gi|115305556|sp|Q2GJ68|RPOB_ANAPZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88597935|gb|ABD43405.1| DNA-directed RNA polymerase, beta subunit [Anaplasma phagocytophilum
            HZ]
          Length = 1383

 Score = 1477 bits (3824), Expect = 0.0,   Method: Composition-based stats.
 Identities = 681/1376 (49%), Positives = 959/1376 (69%), Gaps = 27/1376 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+S+FPI    G A
Sbjct: 21   RLSYARSIDIRDSLSDLIRIQRDSYDAFIGIDEGSSG----GIQSIFQSMFPIRDPLGRA 76

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVS     P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 77   VLEFVSCNIGEPQYDEYECIKRGITFSVPMRITLRFVVWKVQEVSFKEVKYVVDEGTLER 136

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 137  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 196

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDII+ RID++RK+PVT  L ALGM + +IL TFY K++Y +
Sbjct: 197  SARIIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVTYLLKALGMSNNDILDTFYDKVLYVR 256

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  +I++  ++T  + K L   G++   +  
Sbjct: 257  SDKGWKVPFVV-DRFKGVRLSYDLMDVD-GNVLIKANTRITLRIAKKLYADGLREYLVPF 314

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + GL+VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 315  AGISGLFVATDLVDPASGAVIVSAGEAIAAEHIVKLELFDISEIAFLNIDFLTVGPYVLN 374

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D++  ++DAL +IYRV+R G+       +S F  LFF+ D+YDLS VGR+K+N  L
Sbjct: 375  TLFLDRHITQEDALFEIYRVLRSGESPNLEAVKSFFKGLFFEPDRYDLSVVGRIKLNSHL 434

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  +++  + K+DI+ +IK LV L +G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 435  RLDIDENLTVLTKDDIVHVIKKLVLLPDGEGVVDDIDHLGNRRVRSVGEFIENQFRVGIL 494

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ +P D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 495  RLERMIMDYMSSVNFDNAVPCDFVNPKILATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 554

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 555  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 614

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG VT+ V YL A +E + YIA A ++LDE+  F +++++CR  G  ++V RE 
Sbjct: 615  PYRKVIDGVVTDSVEYLLATQESDYYIADAGAALDENNRFVDDMLYCRHGGNFVMVKRED 674

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +++ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKAEAP VGTGMESVVA
Sbjct: 675  VNYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKAEAPLVGTGMESVVA 734

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR G+V +VD   IVIR+ + + D    GVDIY+L KFQRSN NTC+NQRP
Sbjct: 735  AGSGAVVLAKRDGVVHRVDGSYIVIRAFDKNKDEY-LGVDIYKLRKFQRSNHNTCINQRP 793

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD VR ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 794  IVKIGDYVRTNDVIADGAAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 853

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+ G +LVGK+TP
Sbjct: 854  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSAGSVLVGKVTP 913

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 914  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 973

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + ++    +++D E  ++    Y  L ++LC  +                 L++      
Sbjct: 974  QSEVNSFRKERDYEIDVVSEYFYDELKKLLCSADLPLN------GHADVESLLAAKSLEA 1027

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W+  + + K+   V  +K +++   +    +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1028 LWEIGLSNPKISAKVADMKGKFDELITEAHSKFDQKIDKLNYGYDLPQGVLTIVKVFVAV 1087

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1088 KHNLQPGDKMAGRHGNKGVISRIVPVEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1147

Query: 1141 LGWACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            LGWA V LG ++  +++  +  G  +  +RSFL +V       E ++   D+++L+ A +
Sbjct: 1148 LGWAAVNLGHRVGRMLDSGEEEGPVVESIRSFLSEVYEGQKLKEDVASMSDEALLKFANR 1207

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GVP++ PVF+G  +  I+ +L +AD+D SGQ  LYDG +G+ FDR VTVGYIYMLKL
Sbjct: 1208 LRRGVPMAAPVFEGPKDAQISRLLELADVDPSGQVDLYDGRSGQKFDRKVTVGYIYMLKL 1267

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KS
Sbjct: 1268 HHLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKS 1327

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            DD+VGR R+YESI+ G+  FE G PESFNV+VKE+++L L + L+  +   S+K+E
Sbjct: 1328 DDIVGRVRIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVVLKQDKEFTSSKVE 1383


>gi|116514968|ref|YP_802597.1| RNA polymerase, b subunit [Buchnera aphidicola str. Cc (Cinara
            cedri)]
 gi|122285636|sp|Q058E5|RPOB_BUCCC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|116256822|gb|ABJ90504.1| RNA polymerase, b subunit [Buchnera aphidicola str. Cc (Cinara
            cedri)]
          Length = 1343

 Score = 1471 bits (3809), Expect = 0.0,   Method: Composition-based stats.
 Identities = 676/1364 (49%), Positives = 962/1364 (70%), Gaps = 21/1364 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+R+ FGK P+I+DIP L+ +Q  S+  F+     P +   +GL++AF+S+
Sbjct: 1    MIYSYTEKKRIRENFGKQPKILDIPYLLSIQIDSFKKFIE----PKKNNYQGLESAFQSI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI +++G A L++VSY      FD+ +   R  TY+VPL++ L+LI+++ D  +   ++
Sbjct: 57   FPIRSYNGCAELQYVSYTLGKKLFDMYESKTRGTTYSVPLRVKLQLIIYEKD--SKNTNV 114

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K IKEQ +YMG+LPLMT +GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115  KHIKEQEVYMGELPLMTHNGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKILYNA 174

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D+EFD KD + +RIDRRRK+P T  L AL   +E+IL  F+   ++  + 
Sbjct: 175  RIIPYRGSWLDVEFDPKDHLFIRIDRRRKIPATVLLHALNFSTEKILKIFFKHDIFYIKN 234

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L    L  G  +   ++     ++ I+ G+++T+  +K LK+K +K + I  + 
Sbjct: 235  KNIYMYLIPKRL-KGEIIPFEII--KNKKRYIKKGERITTEHIKKLKKKKIKTIQIPEEY 291

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  ++++  + +T EI I++   + +    +I +   +   +L+ ++++N AYI  TL
Sbjct: 292  LYGKTISKNYYHPKTKEILIKSNTTLTQDEFNKIKNFNNKKFYVLFTNNIDNGAYISETL 351

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D  KDR  AL++IY++MRPG+  T   AE++FN LFF  ++YDLS VGR+K N  L  
Sbjct: 352  KIDTTKDRLTALIEIYKIMRPGEPPTKEAAENLFNNLFFSQERYDLSPVGRMKFNKSLKR 411

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                    + KEDII +IK L++++NGKG IDDID+L NRRVRSVGEM++NQ+R+GL+R+
Sbjct: 412  KEKKGSGILNKEDIIDVIKKLINIKNGKGEIDDIDHLSNRRVRSVGEMVENQFRIGLVRV 471

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER+++ER+S  D+D++MPQD+INAKP+ SA+ EFF SSQLSQ  +  N L+ ITH RR+S
Sbjct: 472  ERAVRERLSLSDLDTLMPQDIINAKPISSAIKEFFGSSQLSQFMDQNNPLAEITHKRRIS 531

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532  ALGIGGLTRERAGFEVRDVHPTHYGRVCPVETPEGPNIGLINSLSIYARTNQYGFLETPY 591

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +G VT  + YLSA+EE N  IAQAN+ +++ G F ++ V CR  GE  L   +K++
Sbjct: 592  RKVKNGTVTTKIKYLSAIEEGNYIIAQANTKINKFGKFYKKFVTCRYNGEFGLFKNKKVN 651

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP +K+E P VGTGME  VA  
Sbjct: 652  YMDISTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTIKSEKPLVGTGMERSVAID 711

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  I+AKR+G +E VDA RIV+R  +  +    SG+DIY L K+ RSNQNTC+NQ P +
Sbjct: 712  SGVTIIAKRSGKIEYVDASRIVVRIKDEKIRTYESGIDIYNLTKYSRSNQNTCINQIPCI 771

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             + D +++ D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+LISE++  ED FT+I
Sbjct: 772  NLNDSIKKGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILISEKVEREDKFTTI 831

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   + RDTKLG EEIT DIPN+ E  L  +D  GII +GA+V+ GD+LVGK+TPKG
Sbjct: 832  HIQELSCICRDTKLGIEEITSDIPNIGESALSKLDTSGIIYIGADVSSGDVLVGKVTPKG 891

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+G +GTV+DV+IF R G+ K++R+I +E  
Sbjct: 892  ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGTNGTVIDVQIFTRDGVKKDKRTIEIEEM 951

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             ++   +D  +E  I + NI +R+ +IL             K   + ++ ++EY    + 
Sbjct: 952  LLKKAKKDLTEELKIFELNIINRINKILL--------TLKTKINCIVANSLNEY----FK 999

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +     +K+++ + +LK+QY+  +   + + K K +KI  GD++ PG+L++VK+F+A+KR
Sbjct: 1000 KKIKYPKKIKKKIHTLKIQYKQLQKKFKKKIKEKTKKIIQGDELAPGILKIVKIFLAVKR 1059

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS+I P EDMP+  +G P+DIVLNPLGVPSRMN+GQI ETHLG
Sbjct: 1060 KIQPGDKMAGRHGNKGVVSKINPVEDMPYDNNGEPIDIVLNPLGVPSRMNLGQILETHLG 1119

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A  G+G  I  ++   K    I      +  +    +    + ++ D  +L++A+  + 
Sbjct: 1120 LAAKGIGNIINRMLKTNKKIYKIRKFLQKVYNLGENINQKINLDNFSDIEILQLAKNLRI 1179

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDG +E+ I  +L+M++   SGQ  L+DG TGE F+R VTVGY+YMLKLNH+
Sbjct: 1180 GLPIATPVFDGVNEKEIKKLLKMSNFSTSGQITLFDGRTGEKFERNVTVGYMYMLKLNHL 1239

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTGSYSL+TQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLT+KSDDV
Sbjct: 1240 VDDKMHARSTGSYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTVKSDDV 1299

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GRT++Y++IV+G    E G PESFNVLVKE+++LG++I+L N+
Sbjct: 1300 TGRTKMYKNIVSGKHNMEPGMPESFNVLVKEIRSLGINIELNNN 1343


>gi|254994766|ref|ZP_05276956.1| DNA-directed RNA polymerase subunit beta [Anaplasma marginale str.
            Mississippi]
          Length = 1382

 Score = 1469 bits (3804), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1375 (49%), Positives = 953/1375 (69%), Gaps = 27/1375 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A
Sbjct: 22   RLSYAKSIDIRDSLTDLIRIQRDSYDAFIGIDRDGSS----GIQSIFEAMFPIRDLLGRA 77

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFV Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 78   VLEFVGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEDTSER 137

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 138  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 197

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL  FY K++Y++
Sbjct: 198  SARVIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDAFYDKVIYTR 257

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P +  D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +  
Sbjct: 258  CDKGWRVPFTV-DRFKGVRLSYDLMDVD-GSVLVKANTRITLRIAKKLYADGLREYMVPF 315

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + G++VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 316  SGITGMFVAADLVDPSSGAVIVSAGETITSEHIVKLELFDISEIAFLNIDFLTVGPYVLN 375

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  ++DAL +IYRV+R G+       +S F  LFF+S++YDLS VGR+K+N  L
Sbjct: 376  TLFLDKNMTQEDALFEIYRVLRSGESPNLDAVKSFFKGLFFESERYDLSVVGRIKLNSHL 435

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  ++   + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 436  GLDVDENTTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGIL 495

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 496  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 555

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 556  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 615

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +  VT+ V YL AM+E + YIA A +++DE+  F +++++CR  G  ++V  E 
Sbjct: 616  PYRKVENRVVTDKVEYLLAMQEGDYYIADAGAAIDENNRFVDDMLYCRHGGNFVMVKSED 675

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGME VVA
Sbjct: 676  VDYVDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMEFVVA 735

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR GIV +VD   IVIR+ + + D    GVDIYRL KFQRSN NTC+NQRP
Sbjct: 736  AGSGAVVLAKRDGIVHRVDGSYIVIRAFDANKDEC-LGVDIYRLRKFQRSNHNTCINQRP 794

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 795  VVKLGDYVKANDVIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 854

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+   ILVGK+TP
Sbjct: 855  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSASSILVGKVTP 914

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 915  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 974

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    +  L ++L             K         +E     
Sbjct: 975  QSEISSFVKERDYEIDVVSEYFHDELRKLLRNAGVKV------KGYSDLDSFFAEASDDT 1028

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W   + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+
Sbjct: 1029 LWSTGLADAKVAAKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAV 1088

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1089 KHNLQPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1148

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  +++       I+ LR FL+K+         I+    +++L  A + 
Sbjct: 1149 LGWAAVNLGKKIGRILDKGGP-SMIADLRDFLDKIYDGQKLKSDIASMSSEALLVFANRL 1207

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+
Sbjct: 1208 RKGVPMAAPVFEGPKDAQISKLLELAEVDPSGQVYLYDGRLGKKFDRKITVGYIYMLKLH 1267

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1268 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1327

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L++ L+  +   S ++E
Sbjct: 1328 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLNVVLKQDKEFTSGEVE 1382


>gi|255002887|ref|ZP_05277851.1| DNA-directed RNA polymerase subunit beta [Anaplasma marginale str.
            Puerto Rico]
 gi|255004018|ref|ZP_05278819.1| DNA-directed RNA polymerase subunit beta [Anaplasma marginale str.
            Virginia]
 gi|229462746|sp|Q8KWX4|RPOB_ANAMF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1382

 Score = 1469 bits (3804), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1375 (49%), Positives = 952/1375 (69%), Gaps = 27/1375 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A
Sbjct: 22   RLSYAKSIDIRDSLTDLIRIQRDSYDAFIGIDRDGSS----GIQSIFEAMFPIRDLLGRA 77

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFV Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 78   VLEFVGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEDTSER 137

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 138  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 197

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL  FY K++Y++
Sbjct: 198  SARVIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDAFYDKVIYTR 257

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +  
Sbjct: 258  CDKGWRVPFIV-DRFKGVRLSYDLMDVD-GSVLVKANTRITLRIAKKLYADGLREYMVPF 315

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + G++VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 316  SGITGMFVAADLVDPSSGAVIVSAGETITSEHIVKLELFDISEIAFLNIDFLTVGPYVLN 375

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  ++DAL +IYRV+R G+       +S F  LFF+S++YDLS VGR+K+N  L
Sbjct: 376  TLFLDKNMTQEDALFEIYRVLRSGESPNLDAVKSFFKGLFFESERYDLSVVGRIKLNSHL 435

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  ++   + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 436  GLDVDENTTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGIL 495

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 496  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 555

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 556  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 615

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +  VT+ V YL AM+E + YIA A +++DE+  F +++++CR  G  ++V  E 
Sbjct: 616  PYRKVENRVVTDKVEYLLAMQEGDYYIADAGAAIDENNRFVDDMLYCRHGGNFVMVKSED 675

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGME VVA
Sbjct: 676  VDYVDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMEFVVA 735

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR GIV +VD   IVIR+ + + D    GVDIYRL KFQRSN NTC+NQRP
Sbjct: 736  AGSGAVVLAKRDGIVHRVDGSYIVIRAFDANKDEC-LGVDIYRLRKFQRSNHNTCINQRP 794

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 795  VVKLGDYVKANDVIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 854

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+   ILVGK+TP
Sbjct: 855  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSASSILVGKVTP 914

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 915  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 974

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    +  L ++L             K         +E     
Sbjct: 975  QSEISSFVKERDYEIDVVSEYFHDELRKLLRNAGVKV------KGYSDLDSFFAEASDDT 1028

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W   + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+
Sbjct: 1029 LWSTGLADAKVAAKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAV 1088

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1089 KHNLQPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1148

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  +++       I+ LR FL+K+         I+    +++L  A + 
Sbjct: 1149 LGWAAVNLGKKIGRILDKGGP-SMIADLRDFLDKIYDGQKLKSDIASMSSEALLVFANRL 1207

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+
Sbjct: 1208 RKGVPMAAPVFEGPKDAQISKLLELAEVDPSGQVYLYDGRLGKKFDRKITVGYIYMLKLH 1267

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1268 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1327

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L++ L+  +   S ++E
Sbjct: 1328 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLNVVLKQDKEFTSGEVE 1382


>gi|114778903|ref|ZP_01453700.1| DNA-directed RNA polymerase beta subunit [Mariprofundus ferrooxydans
            PV-1]
 gi|114550872|gb|EAU53438.1| DNA-directed RNA polymerase beta subunit [Mariprofundus ferrooxydans
            PV-1]
          Length = 1339

 Score = 1469 bits (3803), Expect = 0.0,   Method: Composition-based stats.
 Identities = 696/1349 (51%), Positives = 963/1349 (71%), Gaps = 16/1349 (1%)

Query: 30   IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVD 89
            +++Q  SY  F+      +   +  L   F++VFP+  ++G A L F   E+ PP++D D
Sbjct: 2    LQLQTESYHEFVGYG---EAVNDSRLSTVFQTVFPVRDYAGNAELSFEGLEYSPPRYDQD 58

Query: 90   DCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
            +C  RDLT+A+P+K+ LRL +++ +    AK  +K++++QS+YMG++P MT+ G+F+I G
Sbjct: 59   ECRRRDLTFALPVKVKLRLKIYEPEVERRAKRKVKEVRDQSVYMGEIPYMTEYGSFIING 118

Query: 149  IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
             +R +VSQ+HRSPG+ FDHDKG+   SGK L+  R+IP +G W+D EFDSKD +H RID 
Sbjct: 119  TERAIVSQMHRSPGVFFDHDKGKTHSSGKFLFKARVIPYRGSWLDFEFDSKDKVHFRIDL 178

Query: 209  RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
            RRK+P    L ALG+ +++IL  FY +  Y            A  L+    V++  +D  
Sbjct: 179  RRKMPAGVLLKALGLSTQDILDRFYQRRTYRFTKSGVQVKFDADKLLGTRAVTAVKLDNK 238

Query: 269  TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
            T   ++  GKK T+  ++ L E  VK++ +  + + G   AE I+  + GEI I+    +
Sbjct: 239  T---IVAEGKKFTALAIRRLTEADVKWIDVPIESMVGEVAAEPIM-IDGGEILIDHNQEL 294

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             E S+  +  + I+ +  L +DS     ++ +TL  D  + R++A ++IYR+MRPG+  T
Sbjct: 295  TEDSISALQGAGIKQLECLLIDSSVRGPWLADTLRLDMVQSREEARVEIYRMMRPGEPPT 354

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL---NLDTPDDVRHIRKEDIIAIIKILVD 445
               A+++F  LF+D+ +YDLS VGR+K+N RL   ++D P D   +R EDI+  +  L+ 
Sbjct: 355  VETAKALFESLFYDASRYDLSRVGRMKLNSRLGISDVDVPLDHGTLRNEDILIALDTLLS 414

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            LR+G G +DDID+LGNRR+RSVGE+L+NQ R+GL+RMER+I+ER++S D+  +MP D++N
Sbjct: 415  LRDGIGEVDDIDHLGNRRLRSVGELLENQIRIGLVRMERAIRERLTSGDLTEMMPSDVVN 474

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            AKP++++V EFF SSQLSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHPTH
Sbjct: 475  AKPLIASVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHPTH 534

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            YGR+CP ET EG NIGL++SL ++A+VN +GFIE+PYRKV DGK T+ V YLSA++E + 
Sbjct: 535  YGRLCPIETPEGPNIGLINSLATYAKVNDFGFIESPYRKVIDGKATDIVDYLSAIDESDP 594

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             IAQAN+ LD++G F  +LV CR  GE I+  R+KI+++D SP QVVS+ A LIPFLE+D
Sbjct: 595  IIAQANAVLDDEGRFAADLVQCRQGGEFIMAARDKINYMDVSPSQVVSVCAGLIPFLEHD 654

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+NR LMG NMQRQAVPLL++E P VGTGME+ +A+ SG + VA+R G +E+VD  RIV+
Sbjct: 655  DANRALMGSNMQRQAVPLLRSEKPLVGTGMEAPLARDSGVSQVARRGGFIERVDGERIVV 714

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            R  E +      GVDIYRL K++RSNQNTC NQRPLVK+GD+V + DIIADGPSTD+G+L
Sbjct: 715  RVGEDEQVEGEPGVDIYRLFKYRRSNQNTCFNQRPLVKMGDKVVKGDIIADGPSTDMGEL 774

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ALGRN+LVA MPW GYNFED+++ISE++V EDV+TSIHIEEFE ++RDTKLG EEITRDI
Sbjct: 775  ALGRNVLVALMPWRGYNFEDAIVISEKLVREDVYTSIHIEEFECVSRDTKLGSEEITRDI 834

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            PNV E+ L+++D+CGI  VGAEV  GDILVGKITPKGES ++PEEKLLRAIFGEKA DVR
Sbjct: 835  PNVGEDALRHLDDCGIAYVGAEVKQGDILVGKITPKGESQLSPEEKLLRAIFGEKASDVR 894

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            DTS+RV  G  G VVDV+IF R G +K+ER+ ++E   IE L  DK++E+ IL+ N  SR
Sbjct: 895  DTSMRVKPGEEGVVVDVQIFTRRGDEKDERAKAIEESGIEQLYADKEEERRILEGNAASR 954

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
            L  ++ GQ A +  KG  +   +++  +           +V D+ V   +  +    +  
Sbjct: 955  LCSLVVGQKAAT-FKGLNRGVTITAADVESMSLRDLSGVSVDDDAVNEKIAEILESMDKE 1013

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
            +S LE RF+ K+ K++ G ++ PGV++VVKVFVA+KR +Q GDKMAGRHGNKG++S I+P
Sbjct: 1014 RSRLESRFEQKVAKVREGSELKPGVIKVVKVFVAVKRKLQPGDKMAGRHGNKGVISIIVP 1073

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  DGTPV+I LNPLGVPSRMN+GQIFE H+GWA   LGK+I+      +A    
Sbjct: 1074 EEDMPYTADGTPVEICLNPLGVPSRMNIGQIFEIHMGWAGSELGKRIEE---KMRAKVGN 1130

Query: 1166 SPLRSFLEKVIGTGSHT-EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
              +RSFL  +         +I + +D  ++ ++   K GVP++TPVFDGA+E  I  ML+
Sbjct: 1131 EEMRSFLLDIYAEDKTACRQIGEMNDAELVELSTNLKGGVPIATPVFDGANEAHIRRMLK 1190

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
            +A L E+GQ+ILYDG TGE FDRPVT+G +Y+LKL+H+V +K++ARSTG YSLVTQQPLG
Sbjct: 1191 LAGLPETGQTILYDGRTGEAFDRPVTIGQMYILKLHHLVDEKIHARSTGPYSLVTQQPLG 1250

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAA+VLQEMLT+KSDDV GRT++YESIV G+ +F+ G P
Sbjct: 1251 GKAQFGGQRFGEMEVWALEAYGAAHVLQEMLTVKSDDVQGRTKMYESIVRGDMSFDAGIP 1310

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            ESFNV+ KE+ ALG+ + +    T+N  +
Sbjct: 1311 ESFNVMTKELNALGIDLAMVKRPTENEGE 1339


>gi|56416546|ref|YP_153620.1| DNA-directed RNA polymerase subunit beta [Anaplasma marginale str.
            St. Maries]
 gi|81359248|sp|Q5PBG4|RPOB_ANAMM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|56387778|gb|AAV86365.1| RNA polymerase beta subunit [Anaplasma marginale str. St. Maries]
          Length = 1382

 Score = 1469 bits (3803), Expect = 0.0,   Method: Composition-based stats.
 Identities = 673/1375 (48%), Positives = 952/1375 (69%), Gaps = 27/1375 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A
Sbjct: 22   RLSYAKSIDIRDSLTDLIRIQRDSYDAFIGIDRDGSS----GIQSIFEAMFPIRDLLGRA 77

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFV Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 78   VLEFVGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEDTSER 137

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 138  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 197

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL  FY K++Y++
Sbjct: 198  SARVIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDAFYDKVIYTR 257

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +  
Sbjct: 258  CDKGWRVPFIV-DRFKGVRLSYDLMDVD-GSVLVKANTRITLRIAKKLYADGLREYMVPF 315

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + G++VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 316  SGITGMFVAADLVDPSSGAVIVSAGETITSEHIVKLELFDISEIAFLNIDFLTVGPYVLN 375

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  ++DAL +IYRV+R G+       +S F  LFF+S++YDLS VGR+K+N  L
Sbjct: 376  TLFLDKNMTQEDALFEIYRVLRSGESPNLDAVKSFFKGLFFESERYDLSVVGRIKLNSHL 435

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  ++   + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 436  GLDVDENTTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGIL 495

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 496  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 555

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 556  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 615

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +  VT+ V YL AM+E + YIA A +++DE+  F +++++CR  G  ++V  E 
Sbjct: 616  PYRKVENRVVTDKVEYLLAMQEGDYYIADAGAAIDENNRFVDDMLYCRHGGNFVMVKSED 675

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGME VVA
Sbjct: 676  VDYVDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMEFVVA 735

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR GIV +VD   IVIR+ + + D    GVDIYRL KFQRSN NTC+NQRP
Sbjct: 736  AGSGAVVLAKRDGIVHRVDGSYIVIRAFDANKDEC-LGVDIYRLRKFQRSNHNTCINQRP 794

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 795  VVKLGDYVKANDVIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 854

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+   ILVGK+TP
Sbjct: 855  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSASSILVGKVTP 914

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 915  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 974

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    +  L ++L             K         +E     
Sbjct: 975  QSEISSFVKERDYEIDVVSEYFHDELRKLLRNAGVKV------KGYSDLDSFFAEASDDT 1028

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W   + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+
Sbjct: 1029 LWSTGLADAKVAAKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAV 1088

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1089 KHNLQPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1148

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  +++       I+ LR FL+K+         I+    +++L  A + 
Sbjct: 1149 LGWAAVNLGKKIGRILDKGGP-SMIADLRDFLDKIYDGQKLKSDIASMSSEALLVFANRL 1207

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+
Sbjct: 1208 RKGVPMAAPVFEGPKDAQISKLLELAEVDPSGQVYLYDGRLGKKFDRKITVGYIYMLKLH 1267

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1268 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1327

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            D+VGR ++YESI+ G+  FE G PESFNV++KE+++L L++ L+  +   S ++E
Sbjct: 1328 DIVGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVVLKQDKEFTSGEVE 1382


>gi|222474914|ref|YP_002563329.1| RNA polymerase beta subunit (rpoB) [Anaplasma marginale str. Florida]
 gi|222419050|gb|ACM49073.1| RNA polymerase beta subunit (rpoB) [Anaplasma marginale str. Florida]
          Length = 1386

 Score = 1469 bits (3802), Expect = 0.0,   Method: Composition-based stats.
 Identities = 674/1375 (49%), Positives = 952/1375 (69%), Gaps = 27/1375 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A
Sbjct: 26   RLSYAKSIDIRDSLTDLIRIQRDSYDAFIGIDRDGSS----GIQSIFEAMFPIRDLLGRA 81

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFV Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 82   VLEFVGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEDTSER 141

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 142  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 201

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL  FY K++Y++
Sbjct: 202  SARVIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDAFYDKVIYTR 261

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +  
Sbjct: 262  CDKGWRVPFIV-DRFKGVRLSYDLMDVD-GSVLVKANTRITLRIAKKLYADGLREYMVPF 319

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + G++VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 320  SGITGMFVAADLVDPSSGAVIVSAGETITSEHIVKLELFDISEIAFLNIDFLTVGPYVLN 379

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  ++DAL +IYRV+R G+       +S F  LFF+S++YDLS VGR+K+N  L
Sbjct: 380  TLFLDKNMTQEDALFEIYRVLRSGESPNLDAVKSFFKGLFFESERYDLSVVGRIKLNSHL 439

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  ++   + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 440  GLDVDENTTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGIL 499

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 500  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 559

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 560  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 619

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +  VT+ V YL AM+E + YIA A +++DE+  F +++++CR  G  ++V  E 
Sbjct: 620  PYRKVENRVVTDKVEYLLAMQEGDYYIADAGAAIDENNRFVDDMLYCRHGGNFVMVKSED 679

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGME VVA
Sbjct: 680  VDYVDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMEFVVA 739

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR GIV +VD   IVIR+ + + D    GVDIYRL KFQRSN NTC+NQRP
Sbjct: 740  AGSGAVVLAKRDGIVHRVDGSYIVIRAFDANKDEC-LGVDIYRLRKFQRSNHNTCINQRP 798

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 799  VVKLGDYVKANDVIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 858

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+   ILVGK+TP
Sbjct: 859  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSASSILVGKVTP 918

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 919  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 978

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    +  L ++L             K         +E     
Sbjct: 979  QSEISSFVKERDYEIDVVSEYFHDELRKLLRNAGVKV------KGYSDLDSFFAEASDDT 1032

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W   + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+
Sbjct: 1033 LWSTGLADAKVAAKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAV 1092

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1093 KHNLQPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1152

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  +++       I+ LR FL+K+         I+    +++L  A + 
Sbjct: 1153 LGWAAVNLGKKIGRILDKGGP-SMIADLRDFLDKIYDGQKLKSDIASMSSEALLVFANRL 1211

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+
Sbjct: 1212 RKGVPMAAPVFEGPKDAQISKLLELAEVDPSGQVYLYDGRLGKKFDRKITVGYIYMLKLH 1271

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1272 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1331

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L++ L+  +   S ++E
Sbjct: 1332 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLNVVLKQDKEFTSGEVE 1386


>gi|206890934|ref|YP_002249156.1| DNA-directed RNA polymerase, beta subunit [Thermodesulfovibrio
            yellowstonii DSM 11347]
 gi|206742872|gb|ACI21929.1| DNA-directed RNA polymerase, beta subunit [Thermodesulfovibrio
            yellowstonii DSM 11347]
          Length = 1312

 Score = 1468 bits (3800), Expect = 0.0,   Method: Composition-based stats.
 Identities = 693/1363 (50%), Positives = 950/1363 (69%), Gaps = 66/1363 (4%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R R  FGK P ++++P L+E Q+ S+D FL  +I P+ER +EGLQ+A  SVFPI+ ++G 
Sbjct: 6    RERINFGKVPPLVEVPYLLEFQRKSFDKFLQKDIPPEERADEGLQSALNSVFPISDYNGT 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              +EF+SY    PK    +C+ + LTY+VP+K+ +RL ++D DE  G K +K+ +EQ ++
Sbjct: 66   TTIEFISYSVGEPKLTPYECMVKGLTYSVPIKMKVRLNIWDKDEE-GRKFLKESREQEVF 124

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +GDLP+MT+ G+F+I G++R++VSQLHRSPG++F  D+ ++ +SG+ LY+ RIIP +G W
Sbjct: 125  LGDLPMMTETGSFIINGVERVIVSQLHRSPGVYFAPDRSKSRISGRFLYSARIIPVRGSW 184

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFDSKD+++VRID+R+K+P T  L ALG  +E++L  FYP        D   +    
Sbjct: 185  LDFEFDSKDLLYVRIDKRKKLPATIVLKALGYTNEDLLRIFYPIEEIRI-KDETTYTRVV 243

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +D++ G +    +   D  + +++ G K+T   LK +KE G++ + I+   + G     D
Sbjct: 244  SDILTGVRTKVDICSADGKDIIVKEGSKITRYSLKKMKELGIQEIPISKSEIIGRITLSD 303

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            IV+ ETGE+ +++   I E+S   I  + I+ + +L++D++N    +R TL+TDK +++K
Sbjct: 304  IVDPETGEVIVDSNKEITEESFHRIISARIQKLELLFIDNINYLPSLRETLLTDKVENKK 363

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             AL +IY+ +RPG+ +T   AE +F  LFFD  +YDLS+VGR+K+N +L LD P DVR +
Sbjct: 364  HALREIYKKLRPGEPATEEAAEELFYGLFFDPKRYDLSSVGRLKLNQKLGLDIPLDVRVL 423

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              +DII I+K L++LR GKG +DDID+LGNRRVR VGE+L+NQ+R+GL+RMER+I+E+++
Sbjct: 424  TDKDIIEIVKYLLNLRTGKGEVDDIDHLGNRRVRGVGELLENQFRIGLVRMERAIREKMT 483

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D+++ MP D+IN KPV++AV EFF +SQLSQ  +  N LS ITH RRLSALG GG+ R
Sbjct: 484  ITDVETAMPHDVINTKPVMAAVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGGLTR 543

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGRICP ET EG NIGL++SL ++AR+N +GFIE+PYRKV +GKVT
Sbjct: 544  ERAGFEVRDVHPTHYGRICPIETPEGPNIGLITSLATYARINDFGFIESPYRKVVNGKVT 603

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            NDV +LSA+E EN  IA+A + +DE+G+   E V  R  G+  +V RE+++++D SPKQ+
Sbjct: 604  NDVHFLSALESENYVIAEATTPVDEEGNIIGETVSARVKGDFKMVSREEVEYMDVSPKQI 663

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS++ASLIPFLENDD+NR LMG NMQRQAVPL+  EAP VGTGME   A+ SG  +VAKR
Sbjct: 664  VSLSASLIPFLENDDANRALMGSNMQRQAVPLIHTEAPIVGTGMELYAARDSGWLVVAKR 723

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            AGIVE VD+ RIVIR  E        GVDIY L+KF +SNQ TC+ Q+P+VKVG  V R 
Sbjct: 724  AGIVENVDSRRIVIRVTEE-----GGGVDIYNLVKFHKSNQGTCMTQKPIVKVGQTVERG 778

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             I+ADGP  D G+LALGRN+LVAFMPW GYNFED++L+SER+V EDV+TSIHI+EFE+  
Sbjct: 779  TILADGPCMDNGELALGRNVLVAFMPWGGYNFEDAILVSERLVKEDVYTSIHIDEFEIEC 838

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLGPEEITR+IPNV+EE LKN+DE GII +GA+V  GDILVGK+TPKGE  +TPEEK
Sbjct: 839  RDTKLGPEEITREIPNVNEELLKNLDEDGIIRIGAKVKAGDILVGKVTPKGERVLTPEEK 898

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LL AIFGEKA DV+++ L VP G+ G V+DV+I  R G +K+ R+ ++E E+I+ + RD+
Sbjct: 899  LLYAIFGEKAEDVKESCLYVPPGIEGVVIDVKILTRKGKEKSRRANAIEEEEIKRIERDR 958

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRSQWWQFAV 1026
            +DE  IL     SR+ +IL G+  +   K  +     K   L+  +++    +Q  +  V
Sbjct: 959  EDEIRILKETKASRIRKILKGKIILEDVKKGEKIICPKGKALTEKVVNLLDVNQLLKLKV 1018

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +D  V+  V  +  + E +   +  ++  KIE+I+ GD++PPGV ++VKV++AMKR IQ 
Sbjct: 1019 EDPDVKAEVSRVNKEVEQNIKQIYAKYNEKIERIKKGDELPPGVNQIVKVYIAMKRKIQV 1078

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VS ILP EDMP+L+DGTPVDIVLNPLGVPSRMNVGQI ETHLG A  
Sbjct: 1079 GDKMAGRHGNKGVVSMILPEEDMPYLEDGTPVDIVLNPLGVPSRMNVGQILETHLGLAAK 1138

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  + S + +     +I  +   +                                  
Sbjct: 1139 ALGLYVASPVFEGAKEDEIKEMFRKVGYPTTGQVTL------------------------ 1174

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                     G+       TGEPF+RPVTVGY+YMLKL+H+V+DK
Sbjct: 1175 -----------------------YDGK-------TGEPFERPVTVGYMYMLKLHHLVADK 1204

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAAY LQE LT+KSDD+ GRT
Sbjct: 1205 IHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAAYTLQEFLTVKSDDITGRT 1264

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            R+YE+IV G+   E G PESFNVL+KE+Q+L L +DL   + K
Sbjct: 1265 RMYEAIVKGHPVLEPGVPESFNVLIKELQSLCLDVDLLEKKKK 1307


>gi|269959039|ref|YP_003328828.1| DNA-directed RNA polymerase subunit beta [Anaplasma centrale str.
            Israel]
 gi|269848870|gb|ACZ49514.1| DNA-directed RNA polymerase subunit beta [Anaplasma centrale str.
            Israel]
          Length = 1382

 Score = 1466 bits (3796), Expect = 0.0,   Method: Composition-based stats.
 Identities = 675/1375 (49%), Positives = 954/1375 (69%), Gaps = 27/1375 (1%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A
Sbjct: 22   RLSYAKSIDIRDSLTDLIRIQRDSYDAFIGIDRGGSS----GIQSIFQAMFPIRDLLGRA 77

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFV Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 78   VLEFVGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEGTSER 137

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 138  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 197

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + R+IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL +FY K++Y +
Sbjct: 198  SARVIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDSFYDKVLYVR 257

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +  
Sbjct: 258  CDKGWRVPFIV-DRFKGVRLSYDLMDVD-GNVLVKANTRITLRIAKKLHADGLREYLVPF 315

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + G++VA D+V+  +G + I AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 316  SGIAGMFVATDLVDPGSGAVIIHAGETITPEHIVKLELFDISEIAFLNIDFLTVGPYVLN 375

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN  ++DAL +IYRV+R G+        S F  LFF+S++YDLS VGR+K+N  L
Sbjct: 376  TLFLDKNMTQEDALFEIYRVLRSGESPNLDAVRSFFKGLFFESERYDLSVVGRIKLNSHL 435

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  +++  + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 436  GLDVDENLTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGIL 495

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 496  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 555

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 556  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 615

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV +  VT+ V YL AM+E + YIA A +++D++  F +++++CR  G  ++V  E 
Sbjct: 616  PYRKVENRVVTDKVEYLLAMQEGDYYIADAGAAIDKNNRFVDDMLYCRHGGNFVMVKSED 675

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D++D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGMESVVA
Sbjct: 676  VDYVDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMESVVA 735

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SGA ++AKR GIV +VD   IVIR+ +   D    GVDIYRL KFQRSN NTC+NQRP
Sbjct: 736  AGSGAVVLAKRDGIVHRVDGSYIVIRAFDSSKDEC-LGVDIYRLRKFQRSNHNTCINQRP 794

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V++GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFT
Sbjct: 795  VVRLGDYVKANDVIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFT 854

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+   ILVGK+TP
Sbjct: 855  SIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSASSILVGKVTP 914

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ ++
Sbjct: 915  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIK 974

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    +  L ++L             K         +E     
Sbjct: 975  QSEISSFVKERDYEIDVVSEYFHDELKKLLRNAGVKV------KGHSDLDSFFAEASDDA 1028

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W   + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+
Sbjct: 1029 LWNTGLADVKVADKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAV 1088

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETH
Sbjct: 1089 KHNLQPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETH 1148

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA V LGKKI  ++ D      I+ LR FL+K+       + ++   D+++L  A + 
Sbjct: 1149 LGWAAVNLGKKIGRIL-DGGGPSMIADLRDFLDKIYDGQKLKDDVASMSDEALLVFANRL 1207

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + GVP++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+
Sbjct: 1208 RKGVPMAAPVFEGPKDAQISKLLELAEVDPSGQVDLYDGRLGKKFDRKITVGYIYMLKLH 1267

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSD
Sbjct: 1268 HLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1327

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            D+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L++ L+  +   S ++E
Sbjct: 1328 DIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLNVVLKQDKEFTSGEVE 1382


>gi|85706810|ref|ZP_01037901.1| DNA-directed RNA polymerase beta subunit [Roseovarius sp. 217]
 gi|85668603|gb|EAQ23473.1| DNA-directed RNA polymerase beta subunit [Roseovarius sp. 217]
          Length = 1322

 Score = 1466 bits (3794), Expect = 0.0,   Method: Composition-based stats.
 Identities = 760/1280 (59%), Positives = 990/1280 (77%), Gaps = 13/1280 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                + G  R+RK++GK  E++++P+LIEVQK+SYD FL     P  +  EG++  F+SV
Sbjct: 1    MAQSYLGQKRLRKYYGKIREVLEMPNLIEVQKSSYDLFLKSGDQPQPQDGEGIKGVFQSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  F+  ++LEFVSYE + PK+DV++C+ RD+TYA PLK+ LRLIVFD+DE TGAKS+
Sbjct: 61   FPIKDFNETSVLEFVSYELEKPKYDVEECMQRDMTYAAPLKVKLRLIVFDIDEDTGAKSV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+ C
Sbjct: 121  KDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFTC 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L +LG+D E I++ +Y  + +  + 
Sbjct: 181  RIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYSLGLDQEGIMNAYYDTVDFKLKK 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGITSD 301
                      + + G + +  L+D  TGE + E+ KK+T   +K L ++G V  L +  +
Sbjct: 241  KKGWVTKFFPERVRGTRPTYDLIDAKTGEVIFEASKKITPRAVKQLIDEGTVSELLVPFE 300

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEK----------SLEEIFHSEIRDIPILYVDS 351
             + G +VA DI++ ETG IY+EAGD +  +          +L+++  + I DIP+L +D 
Sbjct: 301  HIVGKFVARDIIDEETGAIYVEAGDELTLEYDKAGEISGGTLQDLLDAGITDIPVLDIDG 360

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +N  AYIRNT+  DKN +R+ AL+DIYRVMRPG+  T   + ++F+ LFFDS++YDLS V
Sbjct: 361  INVGAYIRNTMAADKNMNRESALMDIYRVMRPGEPPTEEASAALFDTLFFDSERYDLSAV 420

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GRVKMNMRLNL+ PD  R + ++DI+A IK LV+LR+GKG IDDID+LGNRRVRSVGE++
Sbjct: 421  GRVKMNMRLNLNKPDTQRTLDRDDIVACIKALVELRDGKGDIDDIDHLGNRRVRSVGELM 480

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N 
Sbjct: 481  ENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNP 540

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +FAR
Sbjct: 541  LSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATFAR 600

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN YGFIETPYRKV DG+VT++V Y+SA EE    +AQAN++LDE G F  +LV  R +G
Sbjct: 601  VNKYGFIETPYRKVIDGQVTDEVQYMSATEEMRHTVAQANANLDEGGRFVNDLVSTRQSG 660

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E +L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVP L+AEAP V
Sbjct: 661  EYMLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPTLRAEAPLV 720

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E VVA+ SGAAI+AKRAG+++QVDA RIV+R+ E  L     GVDIYR+ KFQRSN
Sbjct: 721  GTGIEGVVARDSGAAIMAKRAGVIDQVDAQRIVVRATED-LQIGDPGVDIYRMRKFQRSN 779

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QN+C+NQ+PLVKVGD V + ++IADGP TD+G+LALG+N++ AFMPW+GYN+EDS+LISE
Sbjct: 780  QNSCINQQPLVKVGDTVLKGEVIADGPCTDMGELALGKNVITAFMPWNGYNYEDSILISE 839

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V +DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV EE L+N+DE GI+ +GA+V PG
Sbjct: 840  RIVRDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVGEEALRNLDEAGIVYIGADVEPG 899

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPKGESPMTPEEKLLRAIFGEKA DVRDTSLRV  G  GTVV+VR+FNRHG++
Sbjct: 900  DILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSLRVKPGDYGTVVEVRVFNRHGVE 959

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K+ER++ +ERE++E LARD+DDE  ILDRNIY+RL  ++ G+ AV GPKG K ++ ++ +
Sbjct: 960  KDERALQIEREEVERLARDRDDELAILDRNIYARLRTLILGKMAVKGPKGVKANSDITEE 1019

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S   + QWWQ A++DE   + VE+L  QYE  K  L+ RF++K+EK++ GDD+PPGV+
Sbjct: 1020 LLSTLTKGQWWQLALKDEADAKIVEALHDQYEAQKRTLDARFEDKVEKVRRGDDLPPGVM 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A+KR +Q GDKMAGRHGNKG+VS+++P EDMPFL DGTPVDI LNPLGVPSRM
Sbjct: 1080 KMVKVFIAVKRKLQPGDKMAGRHGNKGVVSKVIPIEDMPFLADGTPVDICLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETH+GWA   LG KI   + +Y+ +GD++P+R  +    G   + E I   D+ 
Sbjct: 1140 NVGQILETHMGWAARSLGLKIDEALQEYRRSGDLTPVREAMRIAYGDDVYAEGIEGMDET 1199

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
            +++  A    +GVP++TPVFDGA E  +N  LR A  D SGQS+L+DG +GE F RPVTV
Sbjct: 1200 TLVESASTVTNGVPIATPVFDGAKEADVNDALRRAGFDTSGQSVLFDGRSGEQFSRPVTV 1259

Query: 1252 GYIYMLKLNHMVSDK-VYAR 1270
            G  Y+LKL+H+V D+  +AR
Sbjct: 1260 GIKYLLKLHHLVDDRSTHAR 1279


>gi|152980439|ref|YP_001355110.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Janthinobacterium sp. Marseille]
 gi|151280516|gb|ABR88926.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Janthinobacterium sp. Marseille]
          Length = 1240

 Score = 1465 bits (3792), Expect = 0.0,   Method: Composition-based stats.
 Identities = 648/1245 (52%), Positives = 879/1245 (70%), Gaps = 15/1245 (1%)

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            MG+LPLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ RIIP +G W
Sbjct: 1    MGELPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARIIPYRGSW 60

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KDI+  R+DRRRK+PVT  L A+GM  E+IL  F+    ++   D       A
Sbjct: 61   LDYEFDPKDILFFRVDRRRKMPVTILLKAIGMTPEQILENFFVFDDFALHADGAEMAFVA 120

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              L  G      + D   G+ ++   K++ S  ++ ++  G+K + +  D L G  +A++
Sbjct: 121  ERL-RGEVARFDITD-KAGKVLVAKDKRINSKHVRDVEAAGIKNISVPEDYLLGRILAKN 178

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            IV+ ETGE+   A D + E  L  +   ++  I  LY + ++   YI  TL  D   D+ 
Sbjct: 179  IVDKETGEVIANANDELTEDLLARLREGKVTHIQTLYTNDLDQGGYISQTLRMDDTTDQM 238

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             A + IYR+MRPG+  T    E++FN LF+++D+YDLS VGR+K N R+  D       +
Sbjct: 239  AAKVAIYRMMRPGEPPTEDSVEALFNGLFYNADRYDLSAVGRMKFNRRIGRDELTGDMTL 298

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              +D++A+IKILV+LRNG+G +DDID+LGNRRVR VGE+ +NQ+R GL+R+ER++KER+ 
Sbjct: 299  SNDDVLAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLG 358

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              + D++MP DLIN+KP+ +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 359  QAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTR 418

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR+N YGF+ETPYRKV   K+T
Sbjct: 419  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPYRKVEGSKIT 478

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            + + YLSA+EE    IAQAN+++D+ G+ ++ELV  R AGE ILV  E++ ++D +P QV
Sbjct: 479  DQIDYLSAIEEGRYIIAQANATIDKSGALSDELVSAREAGETILVSPERVQYMDVAPGQV 538

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E  FVGTG+E  VA  SG  + A R
Sbjct: 539  VSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKAFVGTGIERTVAVDSGTTVQALR 598

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             GIV+ +DA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+V+VGD V ++
Sbjct: 599  GGIVDYIDAGRVVIRVNDDEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIVQVGDRVAKH 658

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D+IADG STDLG+LALG+NMLVAFMPW+GYNFEDS+LISE++V++D +TSIHIEE  V+A
Sbjct: 659  DVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELSVVA 718

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDTKLG EEITRDI N++E  L  +DE GI+ +GAEV  GD LVGK+TPKGE+ +TPEEK
Sbjct: 719  RDTKLGAEEITRDISNLAENQLARLDESGIVYIGAEVTAGDTLVGKVTPKGETQLTPEEK 778

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA DV+DTSLRVPSG+ GTV+DV++F R GI +++R+  +  ++++    D 
Sbjct: 779  LLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIPRDKRAQQIIDDELQRYRLDL 838

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            +D+  I++ + + RL ++L G+    GPK   K   ++ + + +  +  W+     D+  
Sbjct: 839  NDQLRIVEGDAFQRLEKMLIGKVVNGGPKKIAKGAKITKEYLDDLDKYHWFDIRPADDTS 898

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +E++K      +   +  F+ K +K+  GD++PPGV ++VKV++A+KR +Q GDKMA
Sbjct: 899  ANALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKRRLQPGDKMA 958

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRILP EDMP + DGTP D+VLNPLGVPSRMNVGQ+ E HLGWA  GLG +
Sbjct: 959  GRHGNKGVVSRILPIEDMPHMADGTPADVVLNPLGVPSRMNVGQVLEVHLGWAAKGLGLR 1018

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I  ++N   A   I+ LR FL  +      TE +  + D  +L +A   K+GVP +TPVF
Sbjct: 1019 IGEMLN---AQVQIAELRKFLAAIYNESGKTEDLDSFSDAEILELAGNLKNGVPFATPVF 1075

Query: 1212 DGADEEAINSMLRMADLDESGQ----------SILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            DGADE     ML +A  D   +            +YDG TGE F+R VTVGY++ LKL+H
Sbjct: 1076 DGADEGETRRMLDLAYPDHIAKQLGMTASKNQVTMYDGRTGEAFERTVTVGYMHYLKLHH 1135

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQEMLT+KSDD
Sbjct: 1136 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDD 1195

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDLE  
Sbjct: 1196 VNGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLERD 1240


>gi|330720212|gb|EGG98590.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium
            IMCC2047]
          Length = 1252

 Score = 1461 bits (3782), Expect = 0.0,   Method: Composition-based stats.
 Identities = 657/1258 (52%), Positives = 895/1258 (71%), Gaps = 29/1258 (2%)

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            MG++PLMT +GTFV+ G +R+VVSQLHRSPG+ FDHDKG+   SGKLLY+ R+IP +G W
Sbjct: 1    MGEMPLMTDNGTFVVNGTERVVVSQLHRSPGVFFDHDKGKTHSSGKLLYSARVIPYRGSW 60

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +D EFD KD + VRIDRRRK+P T  L ALG  +E+IL+ F+    +   G  +   L A
Sbjct: 61   LDFEFDPKDSLFVRIDRRRKLPATVLLRALGYTAEQILAEFFENSAFQFDGSAYKLELVA 120

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             + + G   +  + D   G+ V+E G+++T+  ++ +++     L +  + L G  +A+D
Sbjct: 121  -NRLRGETATFDIKDS-NGKVVVEEGRRITARHIREMEKTKTTQLEVPREYLFGKVIAKD 178

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            ++N ETGEI  E    I E  L ++  + +++I  LY + ++  ++I +TL  D + ++ 
Sbjct: 179  MINPETGEIICECNAEITEDILTQLEEAGVKEIQTLYTNDLDCGSFISDTLRADTSTNQL 238

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL++IYR+MRPG+  T   AE++F  LFF  ++YDLS VGR+KMN R++ +       +
Sbjct: 239  EALVEIYRMMRPGEPPTKESAENLFYNLFFADERYDLSAVGRMKMNRRIDREETKGAGIL 298

Query: 432  ----------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                                   + DI+ ++K L+ +RNG G +DDID+LGNRR+RSVGE
Sbjct: 299  YDGCYFGMRNEETAKKLVEKYGDQSDIVDVMKTLIAIRNGFGVVDDIDHLGNRRIRSVGE 358

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            M +NQ+R+GL+R+ER+++ER+S  + D +MPQDLINAKPV +A+ EFF SSQLSQ  +  
Sbjct: 359  MAENQFRVGLVRVERAVRERLSMAESDGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQN 418

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 419  NPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATF 478

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR N YGF+E+PYRKV DGKVT+++ ++SA++E    IAQA++S+D++G  T+ELV  R 
Sbjct: 479  ARTNNYGFLESPYRKVVDGKVTDEIQFVSAIDESAFVIAQASASVDKNGKLTDELVQVRH 538

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E  + P E +  +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P
Sbjct: 539  ENEFTVKPPETVSLMDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLQAQTP 598

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTGME  VA+ SG  IVAKR G+++ VDA ++V+R+ E +     +GVDIY L K+ R
Sbjct: 599  LVGTGMERFVARDSGVCIVAKRGGVIDSVDAGKVVVRANEDESVSGEAGVDIYNLTKYIR 658

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRPLV  GD V R DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+LI
Sbjct: 659  SNQNTCINQRPLVSEGDVVARGDILADGPSVDIGELALGQNMRIAFMPWNGYNFEDSILI 718

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+  ED FT+IHI+E   +ARDTKLG E+I+ DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 719  SERVAQEDRFTTIHIQELTCVARDTKLGSEDISSDIPNVGESALSKLDESGIVYIGAEVG 778

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR  +G+SGTV+DV++F R G
Sbjct: 779  PGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRCKTGMSGTVIDVQVFTRDG 838

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K++R++ +E   +    +D D+E  I++   + RL +I+     V G  G  K   L+
Sbjct: 839  VEKDKRAMDIENSMLADYRQDLDEEYRIVEAATFERLKQIIV-GQEVVGGVGLNKGDKLT 897

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
               + E       +  + D+   + VE+ +      ++ L+++++ K  K+Q GDD+ PG
Sbjct: 898  QAYLDEATSEDLLKLRLSDDAAAQEVENAETVLADVRAELDEKYEIKRGKLQTGDDLAPG 957

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            VL++VKV++A KR IQ GDKMAGRHGNKG++S I P EDMP   +GTPVDIVLNPLGVPS
Sbjct: 958  VLKIVKVYLATKRRIQPGDKMAGRHGNKGVISAIKPVEDMPHDANGTPVDIVLNPLGVPS 1017

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDY 1188
            RMNVGQ+ ETHLG A  GLG KI  ++   K+   +S +R FL+K+    G   E + ++
Sbjct: 1018 RMNVGQVLETHLGLAAKGLGDKINGML---KSQAKVSEIRGFLDKIYNKIGGRNEDLKEF 1074

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             DD ++ +A   K GVP++TP FDGA E  I +ML +ADL  SGQ  L+DG TG+ FDRP
Sbjct: 1075 SDDEIIELASNLKKGVPMATPAFDGAHETEIKAMLELADLPSSGQMTLFDGRTGDAFDRP 1134

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1135 VTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1194

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            Y LQEMLT+KSDDV GRTR+Y++IV G+   E G PESFNVL KE+++LG+ I+LEN 
Sbjct: 1195 YTLQEMLTVKSDDVNGRTRMYKNIVDGDHRMEPGMPESFNVLTKEIRSLGIDIELENE 1252


>gi|145640490|ref|ZP_01796074.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            R3021]
 gi|145275076|gb|EDK14938.1| DNA-directed RNA polymerase subunit beta [Haemophilus influenzae
            22.4-21]
          Length = 1214

 Score = 1453 bits (3761), Expect = 0.0,   Method: Composition-based stats.
 Identities = 654/1230 (53%), Positives = 881/1230 (71%), Gaps = 17/1230 (1%)

Query: 138  MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
            MT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD
Sbjct: 1    MTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFD 60

Query: 198  SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
             KD +  RIDRRRK+P T  L ALG  +EEIL+ F+ KI +   GD     L    L  G
Sbjct: 61   PKDNLFARIDRRRKLPATIILRALGYTTEEILNLFFDKITFEIAGDKLLMTLVPERL-RG 119

Query: 258  AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
               S  +     G+  +E G+++T+  +K+L++  +  + + S+ + G   ++D V+ E+
Sbjct: 120  ETASFDIE--ANGKVYVERGRRITARHIKALEKDNISQVVVPSEYILGKVASKDYVDLES 177

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            GEI   A   I  ++L ++  +    I  L+ + ++   YI  TL  D   D+  AL +I
Sbjct: 178  GEIICPANGEISLETLAKLAQAGYTTIETLFTNDLDYGPYISETLRVDPTYDKTSALYEI 237

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            YR+MRPG+  T   +E++FN LFF +++YDLSTVGR+K N  L     +    +  EDII
Sbjct: 238  YRMMRPGEPPTPESSEALFNNLFFSAERYDLSTVGRMKFNRSLAFPEGEGAGILSNEDII 297

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            A+++ L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+
Sbjct: 298  AVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLDA 357

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + PQDLIN KP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E
Sbjct: 358  ITPQDLINPKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFE 417

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            +RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YL
Sbjct: 418  VRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYL 477

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAA 676
            SA++E N  IAQANS+LDE+  FT+  V  R   GE  L   E I ++D S +QVVS+AA
Sbjct: 478  SAIDEANYIIAQANSNLDENNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAA 537

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  +A  SG A+VAKR G V+
Sbjct: 538  ALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPIALDSGVAVVAKRGGTVQ 597

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VDA RIVI+  E +     +G+DIY L+K+ RSNQNTC+NQ P V +GD + R +++AD
Sbjct: 598  YVDASRIVIKVNEDETIAGEAGIDIYNLIKYTRSNQNTCINQIPCVNLGDPINRGEVLAD 657

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+IHI+E   +ARDTKL
Sbjct: 658  GPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTTIHIQELSCVARDTKL 717

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G EEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAI
Sbjct: 718  GSEEITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPKGETQLTPEEKLLRAI 777

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FGEKA DV+D+SLRVP+G SGTV+DV++F R G++K++R++ +E  Q+    +D  +E  
Sbjct: 778  FGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDGVEKDKRALEIEEMQLREAKKDLTEELE 837

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            IL+  +++R+  +L    A              +  + +  R++W +  + DE+ Q  +E
Sbjct: 838  ILEAGLFARVRNLLISSGA-------------DAAQLDKVERTKWLEQTIADEEKQNQLE 884

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L  QYE  +   E + + K +KI  GDD+ PGVL+VVKV++A+KR IQ GDKMAGRHGN
Sbjct: 885  QLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGN 944

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHLG A  G+G +I +++
Sbjct: 945  KGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHLGLAAKGIGDQINAML 1004

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
               +    +         ++G GS    +S + D+ VLR+A   + G+PV+TPVFDGADE
Sbjct: 1005 KQKQEVEKLRSYIQKAYDLLGNGSQKVDLSTFTDEEVLRLAGNLRKGLPVATPVFDGADE 1064

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
              I  +L++  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYS
Sbjct: 1065 AEIKELLKLGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYS 1124

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV+GN
Sbjct: 1125 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGN 1184

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
               + GTPESFNV++KE+++LGL+I+L+  
Sbjct: 1185 QHMDPGTPESFNVIMKEIRSLGLNIELDEE 1214


>gi|291280155|ref|YP_003496990.1| DNA-directed RNA polymerase subunit beta [Deferribacter desulfuricans
            SSM1]
 gi|290754857|dbj|BAI81234.1| DNA-directed RNA polymerase, beta subunit [Deferribacter
            desulfuricans SSM1]
          Length = 1315

 Score = 1445 bits (3740), Expect = 0.0,   Method: Composition-based stats.
 Identities = 678/1365 (49%), Positives = 933/1365 (68%), Gaps = 65/1365 (4%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F K  +++DIPDL+EVQK SY  FL MN+ PD+R  +GL+A F+ +FPIT F+ ++
Sbjct: 9    ERFNFSKIRKVLDIPDLLEVQKNSYKEFLQMNVDPDKREVKGLEAVFREIFPITDFNESS 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE+VSY  + PK+   + L R+ TYA PLK+ +RL+ +D DE TG K +   KE  +Y+
Sbjct: 69   VLEYVSYTLEKPKYTPREALDRNTTYAAPLKVRVRLVNYDTDESTGEKIVVSAKESDVYL 128

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
             D+PLMT+  TFVI G++R++V+QLHRSPGI F+      S+  K LY+ RIIP +G W+
Sbjct: 129  CDIPLMTERATFVINGVERVIVNQLHRSPGIFFEDATADKSVVEKHLYSARIIPYRGSWI 188

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD+KD++HVRID++RK+ VT+ L ALG   ++ILS FY         D         
Sbjct: 189  DFEFDNKDVMHVRIDKKRKILVTTLLKALGYTEKDILSEFYEVETVHFADDGMFIDFDP- 247

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            D ++G + S  + D + GE ++++  K+T    + L   GVK++ +T D +   + AED+
Sbjct: 248  DKILGRRFSLDIKD-EYGETIVKANHKITKAARRRLVNAGVKYIPVTIDDIAETFFAEDV 306

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V  E GE+  E    ID++ ++ I    I++I IL++D  N ++ IR+ L  DK  +R++
Sbjct: 307  V-TEDGEVIAEVNQKIDQEVIDRILSEGIKEIKILFIDKNNYDSVIRDILEIDKTSNREE 365

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL++IY+ MRPG+ ++   AE+ F  LFF+  +YDLS VGR+K+N RL L+ P +   + 
Sbjct: 366  ALIEIYKKMRPGEPASLETAEAFFENLFFNPKRYDLSKVGRLKINKRLGLNVPLEHTILT 425

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            KEDI+  +K L  +R G  T+DDID+LG+RRVR+VGE L+N  R+GL RME++++ER+S 
Sbjct: 426  KEDILESVKTLDKIRRGLDTVDDIDHLGHRRVRAVGEQLENFIRIGLTRMEKTVRERMSI 485

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             D++ + PQDL+NAKP+ + + EFF S QLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 486  SDVEDMTPQDLLNAKPLSATIKEFFGSYQLSQFMDQTNPLSEVTHKRRLSALGPGGLNRE 545

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGRICP ET EG NIGL++SLT++ARVN +GFIETPYRKV DGKVT+
Sbjct: 546  RAGFEVRDVHTSHYGRICPIETPEGPNIGLITSLTTYARVNEFGFIETPYRKVVDGKVTD 605

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +VVYLSA+EEE  YIAQAN+ L+EDG+F  + V  R  GE + VP   I F+D  P Q+V
Sbjct: 606  EVVYLSAIEEEEYYIAQANAPLNEDGTFVRDYVAARYKGESVTVPPSYIQFMDVDPMQIV 665

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S++++LIPFLE+DD+NR LMG NMQRQAVPL++ +AP VGTG+E  VA  SGA IVAK  
Sbjct: 666  SVSSALIPFLEHDDANRALMGSNMQRQAVPLVRTDAPIVGTGLERKVAVDSGAVIVAKNG 725

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA +IVIR  +        G+D Y L+K++RSNQ+TC+N +P+V+ G +V +  
Sbjct: 726  GVVEYVDARKIVIRYEKSGH---EFGIDTYDLIKYRRSNQDTCINYKPIVQKGQKVEKGQ 782

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGP+TD GDLALGRN++VAFMPW GYN+EDS+LI+E++V ED FTSIH+E FEV AR
Sbjct: 783  VIADGPATDRGDLALGRNVVVAFMPWMGYNYEDSILINEKLVKEDAFTSIHVEIFEVEAR 842

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLGPEEITRDIPNVS+E LK++D+ GII +GA V  GDILVGK+TPKGES  TPEEKL
Sbjct: 843  DTKLGPEEITRDIPNVSDEALKDLDDSGIIRIGAYVKEGDILVGKVTPKGESQATPEEKL 902

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DV+D SLRVP G+ GTV+DV++  R G++K+ER+  +E  + E + +D +
Sbjct: 903  LRAIFGEKAGDVKDASLRVPPGIRGTVIDVQVLTRRGVEKDERTEHIEAAEYEQIKKDYE 962

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKG----FKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +E  I+++    +++++L G+  +          K+ TVL+ +L+++   +      +++
Sbjct: 963  NEVAIIEQGRKKKIIKLLTGRKLIEDFIDDNITIKEGTVLTEELLNDLDYATLSTLPIEN 1022

Query: 1029 E-KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            + +    +  + + Y       E++FK++ +KI+ GD++P GVL+ V+V+VA+KR +  G
Sbjct: 1023 KAEFDEKLSQINLIYFDRVKRAEEKFKDRKKKIEKGDELPAGVLKQVRVYVAIKRKLMVG 1082

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQI ETHLG A   
Sbjct: 1083 DKMAGRHGNKGVISRILPEEDMPYLPDGTPVDIVLNPLGVPSRMNVGQILETHLGIAAKA 1142

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG  + + + D     DI  +                                       
Sbjct: 1143 LGLYVATPVFDGAKESDIKEMLKKAGLQEDGQ---------------------------- 1174

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            T ++DG                           TGEPFD+ VTVG +YMLKL+H+V  K+
Sbjct: 1175 TVLYDG--------------------------RTGEPFDQEVTVGVMYMLKLHHLVETKI 1208

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++ YGAAY+LQEMLT+KSDDV GRT+
Sbjct: 1209 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEGYGAAYLLQEMLTVKSDDVEGRTK 1268

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            VYE+IV GN +F+TG PESFNVL+KE+Q L L ++L         
Sbjct: 1269 VYEAIVNGNYSFKTGLPESFNVLIKELQGLALDVELIKKEDLKEE 1313


>gi|294664237|ref|ZP_06729612.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans subsp.
            aurantifolii str. ICPB 10535]
 gi|292605996|gb|EFF49272.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans subsp.
            aurantifolii str. ICPB 10535]
          Length = 1249

 Score = 1444 bits (3739), Expect = 0.0,   Method: Composition-based stats.
 Identities = 650/1255 (51%), Positives = 879/1255 (70%), Gaps = 33/1255 (2%)

Query: 138  MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
            MT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD
Sbjct: 1    MTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFD 60

Query: 198  SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
             KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D         + + G
Sbjct: 61   PKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPDEGVQLELVPERLRG 120

Query: 258  AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
              ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L G  ++ D+V+G T
Sbjct: 121  ETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYLVGRILSHDVVDGST 178

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            GE+   A D I+E  L     + +  +  L+V+ ++   Y+ NTL  D  K + +AL++I
Sbjct: 179  GELLANANDEINEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLRIDPTKTQLEALVEI 238

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            YR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+          +  +   
Sbjct: 239  YRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRKDVLGESVLYDKKYF 298

Query: 438  A----------------------IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
            A                      +IK+L ++RNG+G +DDID+LGNRRVRSVGEM +N +
Sbjct: 299  AERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGNRRVRSVGEMAENVF 358

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +
Sbjct: 359  RVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEV 418

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIGL++SL  FAR N Y
Sbjct: 419  THKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQY 478

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     TE+ V CR  GE +L
Sbjct: 479  GFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLL 538

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
             P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+
Sbjct: 539  KPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGI 598

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNT 774
            E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVDIY L+K+ RSNQNT
Sbjct: 599  ERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVDIYNLIKYTRSNQNT 658

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+GYNFEDS+L+SER+V
Sbjct: 659  CINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNGYNFEDSILLSERVV 718

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G++ +GAEV  GDI+
Sbjct: 719  EEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESGVVYIGAEVRAGDIM 778

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+ GTV+DV++F R GI+K++
Sbjct: 779  VGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVIDVQVFTRDGIEKDK 838

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+ A  G    KK   ++   + 
Sbjct: 839  RARQIEESEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGG-ANLKKGDTVTDAYLD 897

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               +S W+Q  ++DE     +E  + Q +  +   E RF +K  KI  GDD+ PGVL++V
Sbjct: 898  GLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKITQGDDLAPGVLKMV 957

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++  G  VDIVLNPLGVPSRMN+G
Sbjct: 958  KVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDIVLNPLGVPSRMNIG 1017

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE----KISDYDD 1190
            QI E HLGWA  GLG+KI+ ++   +A   +S LR FL  +    +        +S + D
Sbjct: 1018 QILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLNDIYNHDNAINAQRVDLSQFSD 1074

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + +L + +    GVP++TPVFDGA E  I  ML +ADL +SGQ+ LYDG TGE FDR  T
Sbjct: 1075 EELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQLYDGRTGEAFDRKTT 1134

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1135 VGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1194

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LQEMLT+KSDDV GR ++Y++IV G      G PESFNVLVKE+++L ++++LE 
Sbjct: 1195 LQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRSLAINMELEE 1249


>gi|41017787|sp|Q9AIU3|RPOB_ANAPH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|13183060|gb|AAK15035.1| RNA polymerase beta subunit [Anaplasma phagocytophilum]
          Length = 1394

 Score = 1440 bits (3728), Expect = 0.0,   Method: Composition-based stats.
 Identities = 669/1384 (48%), Positives = 948/1384 (68%), Gaps = 38/1384 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ +I D + DLI +Q+ SYD F+ ++         G+Q+ F+S+FPI    G A
Sbjct: 27   RLSYARSIDIRDSLSDLIRIQRDSYDAFIGIDEGSSG----GIQSIFQSMFPIRDPLGRA 82

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVS     P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +
Sbjct: 83   VLEFVSCNIGEPQYDEYECIKRGITFSVPMRITLRFVVWKVQEVSFKEVKYVVDEGTLER 142

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            S+K +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 143  SVKYMKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 202

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDII+ RID++RK+PVT  L ALGM + +IL TFY K++Y +
Sbjct: 203  SARIIPYRGSWLDFEFDIKDIIYFRIDKKRKLPVTYLLKALGMSNNDILDTFYDKVLYVR 262

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P    D   G ++S  L+D+D G  +I++  ++T  + K L   G++   +  
Sbjct: 263  SDKGWKVPFVV-DRFKGVRLSYDLMDVD-GNVLIKANTRITLRIAKKLYADGLREYLVPF 320

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              + GL+VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ N
Sbjct: 321  AGISGLFVATDLVDPASGAVIVSAGEAIAAEHIVKLELFDISEIAFLNIDFLTVGPYVLN 380

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  D++  ++DAL +IYRV+R G+       +S F  LFF+ D+YDLS VGR+K+N  L
Sbjct: 381  TLFLDRHITQEDALFEIYRVLRSGESPNLEAVKSFFKGLFFEPDRYDLSVVGRIKLNSHL 440

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             LD  +++  + K+DI+ +IK LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 441  RLDIDENLTVLTKDDIVHVIKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRVGIL 500

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ +P D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 501  RLERMIMDYMSSVNFDNAVPCDFVNPKILATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 560

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+
Sbjct: 561  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIES 620

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV DG VT+ V YL A +E + YIA A ++LDE+  F +++++CR  G  ++V RE 
Sbjct: 621  PYRKVIDGVVTDSVEYLLATQESDYYIADAGAALDENNRFVDDMLYCRHGGNFVMVKRED 680

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +++ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKAEAP VGTGMESVVA
Sbjct: 681  VNYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKAEAPLVGTGMESVVA 740

Query: 721  KSSGAAIVAKRAGIVEQVDAI-RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
              SGA ++AKR G++ +VD +   VIR+ + + D     V IY   K QRSN NTC+NQR
Sbjct: 741  AGSGAVVLAKRDGVLHRVDRVLYPVIRAFDKNKDS--ILVLIYTTEKVQRSNHNTCINQR 798

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+VK+GD VR ND+IADG + D G+LALG+N+LVAFM W G NFEDS++IS  +V  DVF
Sbjct: 799  PIVKIGDYVRTNDVIADGAAIDRGELALGKNVLVAFMSWQGCNFEDSIVISSDVVKRDVF 858

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFE + RDT LGPE+I R +P+V+EE L ++D+ GI+ +GAEV+ G +LVGK+T
Sbjct: 859  TSIHIEEFECVVRDTPLGPEKIMRSVPDVNEESLSHLDDVGIVNIGAEVSAGSVLVGKVT 918

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            P+    + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ +
Sbjct: 919  PRPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLI 978

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ++ ++    +++D E  ++    Y  L ++LC  +                 L++     
Sbjct: 979  KQSEVNSFRKERDYEIDVVSEYFYDELKKLLCSADLPLN------GHADVESLLAAKSLE 1032

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
              W+  + + K+   V  +K +++   +    +F  KI+K+ +G D+P GVL +VKVFVA
Sbjct: 1033 ALWEIGLSNPKISAKVADMKGKFDELITEAHSKFDQKIDKLNYGYDLPQGVLTIVKVFVA 1092

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +K  +Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ET
Sbjct: 1093 VKHNLQPGDKMAGRHGNKGVISRIVPVEDMPHLEDGTPVDIILNSLGVPSRMNIGQILET 1152

Query: 1140 HLGWACVGLGKKIKSLINDYKANGD-ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            HLGWA V LG ++  +++  +  G  +  +RSFL +V       E ++   D+++L+ A 
Sbjct: 1153 HLGWAAVNLGHRVGRMLDSGEEEGPVVERIRSFLSEVYEGQKLKEDVASMSDEALLKFAN 1212

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            + + GVP++ PVF+G  +  I+ +L +AD+D SGQ  LYDG +G+ FDR VTVGYIYMLK
Sbjct: 1213 RLRRGVPMAAPVFEGPKDAQISRLLELADVDPSGQVDLYDGRSGQKFDRKVTVGYIYMLK 1272

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+K
Sbjct: 1273 LHHLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVK 1332

Query: 1319 SDDVV-GR------TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            SDD   GR      +  Y   + G+  FE G PESFNV+VKE+++L L + L++ +   S
Sbjct: 1333 SDDTSPGRRPRVPYSESY--YIKGDSNFECGIPESFNVMVKELRSLCLDVVLKHDKEFTS 1390

Query: 1372 AKME 1375
            + +E
Sbjct: 1391 SNVE 1394


>gi|330814205|ref|YP_004358444.1| DNA-directed RNA polymerase beta subunit [Candidatus Pelagibacter sp.
            IMCC9063]
 gi|327487300|gb|AEA81705.1| DNA-directed RNA polymerase beta subunit [Candidatus Pelagibacter sp.
            IMCC9063]
          Length = 1259

 Score = 1434 bits (3713), Expect = 0.0,   Method: Composition-based stats.
 Identities = 716/1259 (56%), Positives = 951/1259 (75%), Gaps = 2/1259 (0%)

Query: 106  LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
            +RL+ +D++E    K I   KEQ +YM D+PLMT+ GTFV+ G  R+VV+Q+HRSPG+  
Sbjct: 1    MRLVAYDINEEAQTKQILSAKEQEVYMSDVPLMTEKGTFVVNGTDRVVVNQMHRSPGLFL 60

Query: 166  DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
            DHDKG+   SGKLL+ CR+IP +G W+D+E+D KDI++ RIDR+RK+PVT+ LMALG   
Sbjct: 61   DHDKGKGHSSGKLLFNCRVIPYRGSWLDLEYDIKDILYFRIDRKRKIPVTTLLMALGHAK 120

Query: 226  EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +E+L+ F+  I +    +  C     A     +K+   L++ DT ++V++ G K+   L 
Sbjct: 121  DELLNLFHKSIRFDFTNENTCKTKFIASGYKNSKIRFDLINADTNKKVVKEGTKIPLPLA 180

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
               +++G+K + I  + L G Y + DI+N +TGE+Y E+GD I  ++LE++ H  I+   
Sbjct: 181  MKFEKEGLKNILINFEELHGRYFSSDIINEKTGEVYFESGDEITVETLEKLNHLNIKTFY 240

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
            +  +D +N  +Y+RNTLV DKN +  +A +DIYRV+RPG+  T   + ++FN LFF++ +
Sbjct: 241  LADIDGMNIGSYLRNTLVVDKNNNSDEACMDIYRVLRPGEPPTPETSRNLFNNLFFNNTR 300

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            YDLS VGRVK+N +L+LD       + KEDI+ I++ ++ L++GK   DDID+LGNRRVR
Sbjct: 301  YDLSDVGRVKLNSKLDLDVDVKNTVLTKEDILRIVEKMLRLKDGKEDTDDIDHLGNRRVR 360

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            SVGE+++NQ+R+GL+RMER+IKE++SSV+ID+VMPQDLIN+KP+ +++ EFF +SQLSQ 
Sbjct: 361  SVGELVENQFRVGLVRMERAIKEKMSSVEIDTVMPQDLINSKPIAASLKEFFGTSQLSQF 420

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RR+SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++S
Sbjct: 421  MDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINS 480

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L ++++VN YGFIE+PYR V + KVT ++ +LSAMEE    IAQANSSL +D SF +ELV
Sbjct: 481  LATYSKVNRYGFIESPYRVVKNSKVTKEIHHLSAMEEGKFTIAQANSSLKDDSSFKDELV 540

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             CR +    L   + ID++D SPKQVVS+AA+LIPFLENDD+NR LMG NM RQAVPL+K
Sbjct: 541  SCRKSLGFELAKPDNIDYMDVSPKQVVSVAAALIPFLENDDANRALMGSNMMRQAVPLIK 600

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             E+P VGTGME  VA  SGA IVAKR G+VE++D  RIV+++     D + S VDIY L 
Sbjct: 601  NESPLVGTGMEKDVALDSGATIVAKREGVVEKIDGKRIVVKATSE-KDLTISSVDIYNLQ 659

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            KFQRSNQNTC NQRPLVKVGD V++ D+IADGPST  G+LALG+N++VAFMPW GYNFED
Sbjct: 660  KFQRSNQNTCTNQRPLVKVGDVVKQGDVIADGPSTQFGELALGKNVMVAFMPWLGYNFED 719

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            S+LISER VSEDVFTSIHIEE++VMARDTKLGPEEITRDIPN SEE L+N+DE GI+ VG
Sbjct: 720  SILISERCVSEDVFTSIHIEEYDVMARDTKLGPEEITRDIPNTSEEALRNLDESGIVYVG 779

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            AEV PGDILVGK+TPKG++ +T EEKLLRAIFGEKA+DVRDTSL++PSG  GTVV+VR+F
Sbjct: 780  AEVKPGDILVGKLTPKGDTKVTSEEKLLRAIFGEKAIDVRDTSLKMPSGTGGTVVEVRVF 839

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            NRHGI+K+ER++S+E+ +IE +  DK  E+ IL+ NI SR +EIL G +     K   K 
Sbjct: 840  NRHGIEKDERALSIEKAEIESVLEDKYAEEAILELNIKSRAIEILEGSSLGDDYKKITKG 899

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T L+ +++SE    +  + +   EK   ++  LK QY  +K  +E RF +KI+KI+ GD+
Sbjct: 900  TKLTKEILSELTLGETLKLSTDSEKSLSDLAILKEQYSKAKKDIELRFDDKIDKIERGDE 959

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            + PGV+++VKVFVAMKR +Q GDKMAGRHGNKG++SRI+P EDMP++ +G  VDIVLNPL
Sbjct: 960  LLPGVMKMVKVFVAMKRKLQPGDKMAGRHGNKGVISRIVPVEDMPYMANGKQVDIVLNPL 1019

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKVIGTGSHTEK 1184
            GVPSRMNVGQI ETHLGWAC  LG+KIK ++++Y K   + +  +  L  +       ++
Sbjct: 1020 GVPSRMNVGQILETHLGWACSELGEKIKKILDEYQKTTKNAAHTKDALSSIYNDKEIEKE 1079

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            I ++ ++ +  V +   SGVP++TPVFDGA  E +  ML+ + L ESGQ+ LYDG TGE 
Sbjct: 1080 IQNFTNNELKDVLQNLSSGVPIATPVFDGASVEDVTDMLKFSGLPESGQTTLYDGRTGEK 1139

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FDR VTVG IYMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1140 FDREVTVGIIYMLKLYHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1199

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            YGAAY LQE+LT+KSDDV GRT+VYE+IV G+D FE+G PESFNVLVKE+++L L+++L
Sbjct: 1200 YGAAYTLQEILTVKSDDVAGRTKVYETIVKGDDDFESGIPESFNVLVKEIRSLALNLEL 1258


>gi|195973818|gb|ACG63474.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia]
          Length = 1306

 Score = 1432 bits (3707), Expect = 0.0,   Method: Composition-based stats.
 Identities = 654/1318 (49%), Positives = 905/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDSKTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLVSTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEAGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESGIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|195973814|gb|ACG63472.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia]
          Length = 1306

 Score = 1432 bits (3706), Expect = 0.0,   Method: Composition-based stats.
 Identities = 654/1318 (49%), Positives = 906/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDSKTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLVSTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEAGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESGIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +    ++ LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKVAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|195973812|gb|ACG63471.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia]
          Length = 1306

 Score = 1431 bits (3705), Expect = 0.0,   Method: Composition-based stats.
 Identities = 654/1318 (49%), Positives = 905/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDSKTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVGSVAIDFDLVSTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEAGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESGIVHIGANVESGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|195973810|gb|ACG63470.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia
            subsp. philomiragia ATCC 25015]
          Length = 1306

 Score = 1431 bits (3705), Expect = 0.0,   Method: Composition-based stats.
 Identities = 653/1318 (49%), Positives = 904/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDSKTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLVGTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +T   D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEAGMLELEVIDFITTERGRYISDTRKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESGIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|195973816|gb|ACG63473.1| DNA-directed RNA polymerase subunit beta [Francisella philomiragia]
          Length = 1306

 Score = 1431 bits (3705), Expect = 0.0,   Method: Composition-based stats.
 Identities = 654/1318 (49%), Positives = 904/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDSKTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D    L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLFSTLRVAKDIVNEATGEVIAYANDHVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACAEAGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LGKLDESGIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|313673488|ref|YP_004051599.1| DNA-directed RNA polymerase subunit beta [Calditerrivibrio
            nitroreducens DSM 19672]
 gi|312940244|gb|ADR19436.1| DNA-directed RNA polymerase subunit beta [Calditerrivibrio
            nitroreducens DSM 19672]
          Length = 1316

 Score = 1429 bits (3700), Expect = 0.0,   Method: Composition-based stats.
 Identities = 658/1367 (48%), Positives = 937/1367 (68%), Gaps = 65/1367 (4%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F K  +++++PDL+EVQK SY  FL +++  D+R N+GL+  F+ +FPIT F+  A
Sbjct: 9    QRVSFSKIKKVLEMPDLVEVQKKSYLDFLQLDVPADKRENKGLEQVFREIFPITDFNETA 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY  + PK+D  + + R  +YA PLK+ +RL+ ++  E    K +   KE  +Y+
Sbjct: 69   ILEYISYTIEKPKYDAKESIIRKTSYAAPLKVKVRLVCYENSEDGSEKVVASAKESDVYL 128

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
             D+PLMT   TF+I G++R++VSQLHRSPGI F+      S+  K L+  RIIP +G W+
Sbjct: 129  CDIPLMTDRATFIINGVERVIVSQLHRSPGIFFEDLTAGKSVVEKHLFGSRIIPYRGSWI 188

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            D EFD+K+ I+VRID++RK+  T  L ALG+  ++IL+T+Y   V   +G  +       
Sbjct: 189  DFEFDTKNFIYVRIDKKRKILATVLLKALGLSEQDILNTYYKTEVVRFKGLNFERYFEPE 248

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +L+ G + S  + D  TGE + ++G K++ G+++ L + G+K +    + +   + AEDI
Sbjct: 249  NLI-GRRNSLDIKDEQTGEVIYKAGHKISKGIIRKLTKAGIKKMNCQYEDISETFFAEDI 307

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V  + GE+ ++A   I  + LE++  ++I +  +L +DS  ++  IR+ L  DK +  ++
Sbjct: 308  VTKD-GELLVKANTKISAEILEKLRENDIEEFKVLLIDSKGSDTAIRDMLEADKIESTEE 366

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            ALL+IY+ MRPG+ +T   A++ F+ LFF+  KYDLS VGR+K+N RL LD P ++  + 
Sbjct: 367  ALLEIYKKMRPGEPATVETAKTYFDNLFFNDKKYDLSRVGRLKINKRLKLDKPLELTTLT 426

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            KEDI+  I++L ++R G+  +DDID+LG+RRV++VGE L+N  R+G++RME+++KER+S 
Sbjct: 427  KEDIVETIRVLNNIRLGEDDVDDIDHLGHRRVKAVGEQLQNHIRIGMVRMEKTVKERMSI 486

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             D   + PQDL+NAKP+ S++ EFF S QLSQ  +  N LS ITH RRLSALG GG+ R 
Sbjct: 487  QDTKDLGPQDLLNAKPLSSSIKEFFGSYQLSQFMDQTNPLSEITHKRRLSALGPGGLNRD 546

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGR+CP ET EG NIGL++SLT++ARVN YGFIETPYRKV +G+VT+
Sbjct: 547  RAGFEVRDVHTSHYGRLCPIETPEGPNIGLITSLTTYARVNDYGFIETPYRKVENGRVTD 606

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +VVY+SA+EEE+ +IAQAN+ LD +G+F  E V  R  GE + V +++I F+D +P Q++
Sbjct: 607  EVVYMSAIEEEDYFIAQANAKLDSEGNFLNEYVIARKKGEIVTVHKDEIQFMDVAPNQII 666

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S++ +LIPFLE+DD+NR LMG NMQRQ VPL++ +AP VGTG+E  VA  SGA +VAKR+
Sbjct: 667  SVSTALIPFLEHDDANRALMGSNMQRQGVPLIRTDAPIVGTGLERKVAIDSGAVLVAKRS 726

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+V+ VDA  I+I   +GD      G+D+Y L K++R+NQ+TC+N  PLV+ G +V + D
Sbjct: 727  GVVQYVDAKTIIIGYTDGD----DFGIDVYELDKYRRTNQDTCINYVPLVQKGQKVEKGD 782

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IIADGP+TD GDLALGRN++VAFMPW GYN+EDS+L+S+++V ED +TSIHIEEFE+ AR
Sbjct: 783  IIADGPATDRGDLALGRNVVVAFMPWMGYNYEDSILVSQKLVKEDAYTSIHIEEFEIEAR 842

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DTKLGPEEITRDIPNVSEE LK++DE GII +GA+V  GDILVGK+TPKGES  TPEEKL
Sbjct: 843  DTKLGPEEITRDIPNVSEEALKDLDESGIIRIGAKVKEGDILVGKVTPKGESQTTPEEKL 902

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            LRAIFGEKA DV+D SLRVPSG+SG V+DV +  R G++K++R++ +E+ +++ + R+  
Sbjct: 903  LRAIFGEKAGDVKDASLRVPSGISGVVIDVVVMTRRGVEKDDRTVKIEKAELQEIQRNYK 962

Query: 973  DEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
             E + LD    S + +IL  +          + FKK + +  +++ +   ++     V+ 
Sbjct: 963  IEMLTLDETRKSAIAKILENRKLSKAVTLKGESFKKGSSVPFEILKDLDYTELSGLPVEK 1022

Query: 1029 EKVQRNVESLKVQ-YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             +            Y     ++E++FK+K  KI+ GD++P GVL+ V+V++A+KR +  G
Sbjct: 1023 REEIEPEIEKINNKYYAQLKLIEEKFKDKKSKIEKGDELPAGVLKSVRVYLAVKRKLMVG 1082

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP +DMP+L +G PV+IVLNPLGVPSRMNVGQ+ ETHLGWA   
Sbjct: 1083 DKMAGRHGNKGVISRILPEQDMPYLPNGVPVEIVLNPLGVPSRMNVGQVLETHLGWAAKA 1142

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG  I + + D     DI  L                                       
Sbjct: 1143 LGLHIATPVFDGAKESDIKELLKKA----------------------------------- 1167

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                 G +E+              GQ++LYDG TGE F++ VTVG +Y++KL+H+V  K+
Sbjct: 1168 -----GFNED--------------GQTVLYDGRTGERFEQEVTVGVMYVMKLHHLVETKM 1208

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +LQEMLT+KSDDV GRTR
Sbjct: 1209 HARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNILQEMLTVKSDDVEGRTR 1268

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VYESIV GN +F+   PESF+VL+KEMQ L L ++L      N+ + 
Sbjct: 1269 VYESIVNGNFSFKPSMPESFHVLIKEMQGLCLDVELVKKEDINNDEN 1315


>gi|253993140|gb|ACT52811.1| DNA-directed RNA polymerase beta chain [Rickettsia sp. SGL01]
          Length = 1299

 Score = 1429 bits (3699), Expect = 0.0,   Method: Composition-based stats.
 Identities = 721/1287 (56%), Positives = 968/1287 (75%), Gaps = 7/1287 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY   FL +NI   ER N+GLQ+   S+FPI+   
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYKKNFLQLNIKDSERKNKGLQSILNSIFPISDSF 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+D+EFD+KD+I+ RIDR+RK+ VT+ L A+GM +EEI+  +Y  + Y    +  C   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYVTTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGCAVK 256

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +   +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y++
Sbjct: 257  FIPQHITAHRLTSDLVDADTGNVLLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYLS 316

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+D
Sbjct: 317  EDLRDPASDEVLAKIGEMITSDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQD 375

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            R+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  ++V 
Sbjct: 376  REAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEVT 435

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ ER
Sbjct: 436  GLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIER 495

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG+
Sbjct: 496  MSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGGL 555

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG 
Sbjct: 556  SRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDGH 615

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASP 668
            VT++VVY SA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +P
Sbjct: 616  VTDEVVYFSAIEEGKYKIGQANSKVDKDGKLQGEFINCRVEGGNFVMVEPHEVDFIDVTP 675

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA+++
Sbjct: 676  MQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASVL 735

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A   GIVEQVD+ RIVIR++E  +D  +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  V
Sbjct: 736  ALHDGIVEQVDSNRIVIRTLEQKID-GSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHYV 794

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEFE
Sbjct: 795  KKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEFE 854

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V+ARDT+LGPEE+TRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+TP
Sbjct: 855  VIARDTRLGPEEVTRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPITP 914

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE LA
Sbjct: 915  EEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKLA 974

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D+DDE  I++  ++S L ++L GQ  V+GPK  K    ++S+++    + Q+WQ  V+D
Sbjct: 975  KDRDDELEIIEHFVFSWLEKLLIGQVIVNGPKQVKAGQTITSEMLKGLSKGQFWQLTVED 1034

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              V   +E +KV Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q GD
Sbjct: 1035 ANVMNEIEQIKVHYDEKKDALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPGD 1094

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + L
Sbjct: 1095 KMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASINL 1154

Query: 1149 GKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++    +   GV  +
Sbjct: 1155 AKKISTLVKEYKNKHIGIEQIKKFLLELYGENI--NYILERSEEEIISFCSKVSKGVHFA 1212

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA  + +  ML+ AD D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K+
Sbjct: 1213 TPVFDGAKVQDVKDMLKFADQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNKI 1272

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++RS G YSLVTQQPLGGKS+ GGQR 
Sbjct: 1273 HSRSIGPYSLVTQQPLGGKSHFGGQRF 1299


>gi|21666266|gb|AAM73633.1|AF389472_1 RNA polymerase beta subunit [Anaplasma marginale]
          Length = 1381

 Score = 1429 bits (3698), Expect = 0.0,   Method: Composition-based stats.
 Identities = 652/1371 (47%), Positives = 924/1371 (67%), Gaps = 31/1371 (2%)

Query: 17   FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
            + K+     + DLI +Q+ SYD F+ ++         G+Q+ F+++FPI    G A+LEF
Sbjct: 30   YAKSYNSRFLTDLIRIQRDSYDAFIGIDRDGSS----GIQSIFEAMFPIRDLLGKAVLEF 85

Query: 77   VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAKSIKD 124
            V Y    P++D  +C+ R +T++VP++ITLR +V+ V            DE T  +S+K 
Sbjct: 86   VGYNIGEPQYDEYECIKRGITFSVPIRITLRFVVWKVQEVSFKEVKYVVDEDTSERSVKY 145

Query: 125  IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
            +KEQ + +GDLP+MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y+ R+
Sbjct: 146  MKEQEVSIGDLPMMTSYGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIYSARV 205

Query: 185  IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
            IP +G W+D EFD KDII+ RID++RK+PV+  L ALGM + +IL  FY K++Y++    
Sbjct: 206  IPYRGSWLDFEFDIKDIIYFRIDKKRKLPVSYLLKALGMSNNDILDAFYDKVIYTRCDKG 265

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
            W  P    D   G ++S  L+D+D G  ++++  ++T  + K L   G++   +    + 
Sbjct: 266  WRVPFIV-DRFKGVRLSYDLMDVD-GSVLVKANTRITLRIAKKLYADGLREYMVPFSGIT 323

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
            G++VA D+V+  +G + + AG+ I  + + ++   +I +I  L +D +    Y+ NTL  
Sbjct: 324  GMFVAADLVDPSSGAVIVSAGETITSEHIVKLELFDISEIAFLNIDFLTVGPYVLNTLFL 383

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            DKN  ++DAL +IYRV+R G+       +S F  LFF+S++YDLS VGR+K+N  L LD 
Sbjct: 384  DKNMTQEDALFEIYRVLRSGESPNLDAVKSFFKGLFFESERYDLSVVGRIKLNSHLGLDV 443

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             ++   + KEDI+ ++K LV LR+G+G +DDID+LGNRRVRSVGE ++NQ+R+G+LR+ER
Sbjct: 444  DENTTVLTKEDIVQVVKKLVLLRDGEGVVDDIDHLGNRRVRSVGEFIENQFRIGILRLER 503

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RRLSAL
Sbjct: 504  MIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRRLSAL 563

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N YGFIE+PYRK
Sbjct: 564  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYAKINKYGFIESPYRK 623

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V +  VT+ V YL AM+E + YIA A +++DE+  F +++++CR  G  ++V  E +D++
Sbjct: 624  VENRVVTDKVEYLLAMQEGDYYIADAGAAIDENNRFVDDMLYCRHGGNFVMVKSEDVDYV 683

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLK+EAP VGTGME VVA  SG
Sbjct: 684  DVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKSEAPLVGTGMEFVVAAGSG 743

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            A ++AKR GIV +VD   IVIR+ + + D    GVDIYRL KFQRSN NTC+NQRP+VK+
Sbjct: 744  AVVLAKRDGIVHRVDGSYIVIRAFDANKDEC-LGVDIYRLRKFQRSNHNTCINQRPVVKL 802

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V  DVFTSIHI
Sbjct: 803  GDYVKANDLIADGSAIDRGELALGKNVLVAFMSWQGYNFEDSIVISSDVVKRDVFTSIHI 862

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE + RDT    E+    +   S   L ++D   +      V+ G         +   
Sbjct: 863  EEFECVVRDTLRSREDNAVCLMYESLSHLDDVDRDIVPRYLQVVSGGQGY-----ARPPV 917

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             + PE KLL  IFGEK  D  D+SL +P  V GTV+DV +F R G+++N+RS+ +++ +I
Sbjct: 918  SLPPETKLLVTIFGEKVFDCVDSSLYLPPDVEGTVIDVHVFVRRGVEENDRSLLIKQSEI 977

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                +++D E  ++    +  L ++L             K         +E      W  
Sbjct: 978  SSFVKERDYEIDVVSEYFHDELRKLLRNAGVKV------KGYSDLDSFFAEASDDTLWST 1031

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             + D KV   V+ ++ ++++       +F+ K++K+ +G D+P GVL +VKVFVA+K  +
Sbjct: 1032 GLADAKVAAKVKDMRERFDSIVGEAHRKFEQKVDKLNYGYDLPQGVLTIVKVFVAVKHNL 1091

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG++SRI+P EDMP L+DGTPVDI+LN LGVPSRMN+GQI ETHLGWA
Sbjct: 1092 QPGDKMAGRHGNKGVISRIVPAEDMPHLEDGTPVDIILNSLGVPSRMNIGQILETHLGWA 1151

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
             V LGKKI  +++       I+ LR FL+K+         I+    +++L  A + + GV
Sbjct: 1152 AVNLGKKIGRILDKGGP-SMIADLRDFLDKIYDGQKLKSDIASMSSEALLVFANRLRKGV 1210

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P++ PVF+G  +  I+ +L +A++D SGQ  LYDG  G+ FDR +TVGYIYMLKL+H+V 
Sbjct: 1211 PMAAPVFEGPKDAQISKLLELAEVDPSGQVYLYDGRLGKKFDRKITVGYIYMLKLHHLVD 1270

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+VG
Sbjct: 1271 DKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIVG 1330

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            R ++YESI+ G+  FE G PESFNV+VKE+++L L++ L+  +   S ++E
Sbjct: 1331 RVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLNVVLKQDKEFTSGEVE 1381


>gi|140063973|gb|ABO82472.1| RNA polymerase B' subunit [Candidatus Liberibacter asiaticus]
          Length = 1258

 Score = 1427 bits (3693), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1257/1258 (99%), Positives = 1257/1258 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIK LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKGLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258


>gi|195973822|gb|ACG63476.1| DNA-directed RNA polymerase subunit beta [Francisella noatunensis]
 gi|198417153|gb|ACH87847.1| RpoB [Francisella noatunensis subsp. noatunensis]
          Length = 1306

 Score = 1424 bits (3685), Expect = 0.0,   Method: Composition-based stats.
 Identities = 650/1318 (49%), Positives = 904/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL++++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVIYNKEILPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F  +   S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSDRRTISFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NII 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDSGVDSVAIDFDLVSTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E    + + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEAGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAEASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTG+E +VA+ SG  I+A+  G + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGIEKIVARDSGNCIIARNVGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE  I+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESSIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|237753296|ref|ZP_04583776.1| bifunctional DNA-directed RNA polymerase [Helicobacter winghamensis
            ATCC BAA-430]
 gi|229375563|gb|EEO25654.1| bifunctional DNA-directed RNA polymerase [Helicobacter winghamensis
            ATCC BAA-430]
          Length = 1974

 Score = 1423 bits (3684), Expect = 0.0,   Method: Composition-based stats.
 Identities = 620/1395 (44%), Positives = 908/1395 (65%), Gaps = 36/1395 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I +P+L+++Q+ SYD+FLM      +    GL+  FKS+FPI      
Sbjct: 10   RLRVDFTKIPQNIAVPNLLQLQRNSYDNFLMT----SDTNESGLEKVFKSIFPIHDAQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+   EF  P++ V + + R LTY++PLKI +RL++++ DE TG K  +KDIKEQSI
Sbjct: 66   ISLEYAGCEFGKPRYTVREAMERGLTYSIPLKIKIRLVLWERDEKTGEKLGVKDIKEQSI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++   S S KL+Y  +IIPD+G 
Sbjct: 126  FVREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEES-TSTSNKLVYTGQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD + VR+++RRKVPVT    ALG   ++IL  FYP +    +   +  P +
Sbjct: 185  WLYFEYDAKDTLFVRVNKRRKVPVTILFRALGYSRQDILKMFYPLVNIKYKNGKYLIPFN 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +   +V   L D   G  ++ +GK+LT+   K+L+E+ +  +   ++ L   Y+AE
Sbjct: 245  PEEFI--GRVEFDLKDAK-GNLILAAGKRLTAKKAKALEEEKLNMIEYPTEILMNRYLAE 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
             I++  +GE+  +A  ++DE  L+++    + D  I    ++  +A I N  + D     
Sbjct: 302  PIIDKASGEVLFDALTLMDESKLKKLTELGVNDFVIANDLALGVDASIINAFIADAESLK 361

Query: 366  -------KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                    + +   A++ IY+VMRPG+  T   A+     LFFD D+YDL+ VGR+KMN 
Sbjct: 362  LLKQTEKIDNENDLAMIRIYKVMRPGEPVTKEAAKQFVQQLFFDPDRYDLTRVGRMKMNH 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L++  PD V  +  EDII  ++ L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 422  KLDIGVPDYVTVLTHEDIIKTVRYLMRVKNGQGRIDDRDHLGNRRIRAIGELLANELHTG 481

Query: 479  LLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I+++++++    + +MP DL+N+K +   + EFF   QLSQ  +  N LS +T
Sbjct: 482  LVKMQKAIRDKLTTISAGLEELMPHDLVNSKMITGTILEFFTGGQLSQFMDQTNPLSEVT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 542  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTYAKVNELG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PYRKV DG+VT+++VYL+A +EE   IA A++ L  + +  EE++  R  GE IL+
Sbjct: 602  FIEAPYRKVVDGRVTDEIVYLTATQEEGAVIAPASTILTSNQTIKEEMIEVRKDGEIILM 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +K+D ID SP+ +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 662  ESKKVDLIDLSPRMIVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLKPDAPVVGTGIE 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +V++ S  A  A R GIVE+VDA  I +   +     + + +D Y L K  R+NQNT  
Sbjct: 722  KIVSRDSWEATKATRGGIVEKVDAKNIYVLGEDE----NGAFIDHYSLQKNLRTNQNTSF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q P+VK G++V    +IADGP+ D G+LALG+N+ VAFMPW+GYNFED++++SE+++  
Sbjct: 778  SQCPIVKAGEQVEAGQVIADGPNMDQGELALGKNIRVAFMPWNGYNFEDAIVVSEKLIRN 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G  V  G ILVG
Sbjct: 838  DAFTSIHIYEKEIEARELKHGVEEITRDIPNIREEELAHLDESGIVKIGTYVTGGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K +PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+IF + G DK++R+
Sbjct: 898  KASPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKIFTKKGYDKDKRA 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
            I+   E+   L  +  D+ ++LDR    R+  IL  +  VS    G K +KK +V+    
Sbjct: 958  IAAYEEEKSRLDLEHHDKLLMLDREESLRIGSILAKEKLVSVAKIGDKEYKKGSVIPKAD 1017

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R           +++Q + ++LK  +   K  L    + K+  I+  D +P GV+
Sbjct: 1018 LENVNRFAMGTLIKSYPKEIQSSYDALKANFLEQKKNLSQEHEEKLSIIEKDDILPSGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK++VA KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG PV+IVLNPLGVPSRM
Sbjct: 1078 KLVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYTKDGRPVEIVLNPLGVPSRM 1137

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE---KISDY 1188
            N+GQI E HLG     LG++I + I + + +  +  LRS + ++            +   
Sbjct: 1138 NIGQILEVHLGLVGKNLGEQI-ANIFEQEKDKWVGALRSKMLEIAENSGMKSAKGFLEKL 1196

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            DD+S+L  A  W +GV  +TPVF+G + +    +  +A +D  G++ LYDG TGE     
Sbjct: 1197 DDESLLNFARDWSNGVKFATPVFEGVNAQEFEKLFALAKIDTDGKTELYDGRTGEKMMER 1256

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1257 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1316

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR + Y++I  G    E+  PE+F VL KE+Q+L L + +     
Sbjct: 1317 HTLKEMLTIKSDDVEGRVKAYKAITRGEAVKESEIPETFYVLTKELQSLALDVSVFAKNK 1376

Query: 1369 KNSAKMEEIPDFNKC 1383
            +   +   I + N+ 
Sbjct: 1377 EGVDEAITIREENRP 1391


>gi|195973824|gb|ACG63477.1| DNA-directed RNA polymerase subunit beta [Francisella noatunensis]
          Length = 1306

 Score = 1421 bits (3677), Expect = 0.0,   Method: Composition-based stats.
 Identities = 650/1318 (49%), Positives = 902/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  +     R + GL+   K  FP+ + +G   L +V Y+   P FD  +C  
Sbjct: 1    TESYRKFLNAD-DAKGRLHSGLELVLKQSFPVESKNGQYELHYVDYQIGEPTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +     K ++DI+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEILPSEKVVEDIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D           ++ RIIP +G W+D EFDSK I+  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDDSEEGA-----FSARIIPYRGSWLDFEFDSKGIMWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F            +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNRFSNSRTIGFNNKGFALKLDDLSSMKGEVLKFDIIDEKD-NII 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLVSTLRVAKDIVNEATGEVIAYANDDVTENLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E      + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  EACVEVGMLELEVIDFITTERGRYISDTLKYDLTKNTYEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDNVSKDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYRKV +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRKVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTG+E +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGIEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  KTSKL-VDIYSLTKFKRSNKNTCINQRPIVNVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE  I+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SLR+P
Sbjct: 833  LAKLDESSIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLRMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVIG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + +DEK+++ V++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEDEKLEQKVQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSIMQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPVEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKKI+  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKIEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKIDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFATN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|291286305|ref|YP_003503121.1| DNA-directed RNA polymerase, beta subunit [Denitrovibrio acetiphilus
            DSM 12809]
 gi|290883465|gb|ADD67165.1| DNA-directed RNA polymerase, beta subunit [Denitrovibrio acetiphilus
            DSM 12809]
          Length = 1331

 Score = 1419 bits (3673), Expect = 0.0,   Method: Composition-based stats.
 Identities = 650/1374 (47%), Positives = 925/1374 (67%), Gaps = 65/1374 (4%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                  R+ F +  ++IDIPDLIEVQ+ SY  FL     P+ R  +GL+  F+ +FPIT 
Sbjct: 4    TSKPTERRNFSRIQKVIDIPDLIEVQRDSYVDFLQAEYTPETRVVKGLEEVFREIFPITD 63

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            F+  A+LE++SY  +  K+   + + R  T+A PLKI +RL+ +DV+E TG K +   KE
Sbjct: 64   FNETAVLEYISYSIEKYKYTPGEAIDRSTTFAAPLKIKVRLVTYDVNEETGEKMVVSAKE 123

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
              +Y+ D+P+MT  GTFVI G++R++V+QLHRSPGI F+       +  K L++ RIIP 
Sbjct: 124  SEVYLCDIPMMTDRGTFVINGVERVIVNQLHRSPGIFFEDLTASKGVMEKHLFSARIIPY 183

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            +G W+D +FDSK+I++VRID++RK+PVT  L ALG   ++IL T+Y K   +       F
Sbjct: 184  RGSWIDFDFDSKNIMYVRIDKKRKIPVTVLLKALGYTEKDILDTYYTKEKITFDERDRIF 243

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                 D+++G + S  ++D   G  V+++  K+T    K + +  ++ + +  + +   +
Sbjct: 244  KEFNEDIILGLRNSLDILD-KEGNVVVKANHKITKAARKRMVKAEIEKIPVAFEDIEHTF 302

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             AED+V  + GE+ IE+   I E+  +++  + IR+  +L++D + +++ +R+ L  DK 
Sbjct: 303  FAEDVVTPD-GEVLIESNTAISEEMFDKLKENNIREFQVLFIDRLTSDSIMRDILAVDKV 361

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            K +++AL+DIY+ +RPG+ +T   A+++F+ LFF+  +YDLS VGR+K+N RL LD   D
Sbjct: 362  KTQEEALIDIYKKLRPGEPATEETAKTLFDNLFFNPKRYDLSKVGRLKINKRLGLDVDLD 421

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
               +  EDI+  +++L ++R G   +DDID+LG+RRVR+ GE L+N  R+GL RME+++K
Sbjct: 422  TTTLTAEDIVETVRVLENIRKGLDKVDDIDHLGHRRVRAAGEQLQNHIRIGLSRMEKTVK 481

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+S  D++ + PQDL+NAKP+ +++ EFF S QLSQ  +  N LS ITH RRLSALG G
Sbjct: 482  ERMSIQDVEDLTPQDLLNAKPLSASIKEFFGSYQLSQFMDQTNPLSEITHKRRLSALGPG 541

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH +HYGRICP ET EG NIGL++SLT+FA+VN +GFIETPYRKV D
Sbjct: 542  GLNRDRAGFEVRDVHTSHYGRICPIETPEGPNIGLITSLTTFAKVNEFGFIETPYRKVHD 601

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              V+NDVVY+SA+EEE+ Y+AQAN+ L+ DG+F  + V  R  G+ +L  +E I ++D S
Sbjct: 602  CVVSNDVVYMSAIEEEDYYVAQANAPLNPDGTFIRDFVAARYQGDSLLTGKENIQYMDIS 661

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS++A+LIPFLE+DD+NR LMG NMQRQAVPL++ ++P VGTGME  VA  SGA I
Sbjct: 662  PKQIVSVSAALIPFLEHDDANRALMGSNMQRQAVPLVRTDSPIVGTGMEGKVAVDSGAVI 721

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AKR G++E +D+ +I +R  +GD      G+D+Y L+K++RSNQ+TC+N +P+VK G++
Sbjct: 722  TAKRPGVIEYIDSAKIAVRYKDGD----DFGLDVYDLVKYRRSNQDTCINYKPIVKPGEK 777

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  ++A GP+TD G+LALG+NM++AFMPW GYN+EDS+LISE +V ED +TSIHIEEF
Sbjct: 778  VEQGAMLAGGPATDNGELALGQNMVLAFMPWMGYNYEDSILISENVVKEDRYTSIHIEEF 837

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+ ARDTKLGPEEIT DIPNVS+E LK++DE GII +GA V P DILVGK+TPKGE+  T
Sbjct: 838  EIEARDTKLGPEEITADIPNVSDEALKDLDESGIIRIGARVKPRDILVGKVTPKGETQAT 897

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D SLRVP  ++GTVVDV++  R GI+K+ R+  +E+ + E +
Sbjct: 898  PEEKLLRAIFGEKAGDVKDASLRVPPSITGTVVDVQVMTRRGIEKDSRTEIIEKAEYESI 957

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             +D + E   L+++   ++   L G+   S          K T L+++L+ ++  +   Q
Sbjct: 958  QKDYERELKALEKSRNDQISSFLVGKKLKSDYSNNEIRIAKDTELTAELVKDFLYTDLIQ 1017

Query: 1024 FAVQDEKVQR-NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              + ++     +++S+  QY       E+ F++K +K++ GD++P GVL+ VKV+VA+KR
Sbjct: 1018 IEINEQSAFEAHIQSVNGQYFVKVQAAEEYFRDKKKKVEKGDELPAGVLKSVKVYVAIKR 1077

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+VSRILP EDMP+L DGTPVD+V+NPL VPSRMNVGQ+ E HLG
Sbjct: 1078 KLSVGDKMAGRHGNKGVVSRILPAEDMPYLPDGTPVDVVMNPLAVPSRMNVGQVLEVHLG 1137

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   LG K+ + + D     DI  +                                  
Sbjct: 1138 WAGRKLGMKVATEVFDGARESDIKKMLVEAGFQE-------------------------- 1171

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                     DG                  G++       GE F++ VTVG +Y+LKL+H+
Sbjct: 1172 ---------DGQTVL------------YDGRT-------GERFEQEVTVGVMYILKLHHL 1203

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V  K++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA VLQEMLT+KSDDV
Sbjct: 1204 VDTKLHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANVLQEMLTVKSDDV 1263

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             GRT VYE+IV GN +F    PESFNVL+KE+Q L L +DL +       +M E
Sbjct: 1264 EGRTTVYEAIVNGNFSFTPSMPESFNVLIKELQGLALDMDLLSMDEDGVLQMPE 1317


>gi|195973820|gb|ACG63475.1| DNA-directed RNA polymerase subunit beta [Francisella noatunensis
            subsp. orientalis]
 gi|225624847|gb|ACN96558.1| RpoB [Francisella noatunensis subsp. orientalis]
          Length = 1306

 Score = 1418 bits (3670), Expect = 0.0,   Method: Composition-based stats.
 Identities = 650/1318 (49%), Positives = 904/1318 (68%), Gaps = 14/1318 (1%)

Query: 34   KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
              SY  FL  N     R   GL+   K  FP+ + +G   L +V Y+     FD  +C  
Sbjct: 1    TESYKKFLNAN-DAKGRLYSGLELVLKQSFPVESKNGQYELHYVDYQVGESTFDETECQV 59

Query: 94   RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
            R  TY  PL + LRL+V++ +   G K +++I+E+ +YMGD+PLMT +GTF+I G +R+V
Sbjct: 60   RGATYDAPLNVKLRLVVYNKEALPGEKVVENIREEYVYMGDIPLMTTNGTFIINGTERVV 119

Query: 154  VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
            VSQLHRSPG+ F  D      S +  ++ RIIP +G W+D EFDSK II  RIDR+RK  
Sbjct: 120  VSQLHRSPGVFFSKDD-----SEEGTFSARIIPYRGSWLDFEFDSKGIIWARIDRKRKFC 174

Query: 214  VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
             T  L ALG   EEIL+ F      S     +   L     M G  +   ++D      +
Sbjct: 175  ATVILKALGYTQEEILNKFSDSKTISFNNKGFALKLDDLSNMKGEVLKFDIIDEKD-NTI 233

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            ++  KKLTS  +K +K+ GV  + I  D +  L VA+DIVN  TGE+   A D + E  L
Sbjct: 234  VKKNKKLTSRDIKKIKDAGVDSVAIDFDLVSTLRVAKDIVNEVTGEVIAYANDDVTESLL 293

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E      + ++ ++   +     YI +TL  D  K+  +AL++IY+V+RPGD    +  +
Sbjct: 294  ESCVEVGMLELEVIDFITTERGRYISDTLKYDLTKNTDEALVEIYKVLRPGDPPAAASVK 353

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-TPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++F  LFF   +Y LS +GR+K+N RL  D    D+  +   DI+ +I+ L+++R+GKG 
Sbjct: 354  ALFEGLFFIESRYSLSDIGRMKLNARLGSDKVSGDIYTLENSDIVGVIEELINIRDGKGK 413

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DDID+LGNRRVRSVGEM++NQ+R+GL R+E+ I+E +S V  D +MP+D++N+KP+ +A
Sbjct: 414  VDDIDHLGNRRVRSVGEMVENQFRIGLYRVEKGIRESMSLVHKDKLMPKDIVNSKPITAA 473

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            + EFF S  LSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH THYGR+CP 
Sbjct: 474  IKEFFTSGALSQFMDQDNPLSEVTHKRRISALGPGGLSRDRAGFEVRDVHATHYGRLCPI 533

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL++SL S+ARVN YGF+E PYR+V +GKVTN++ YLSA++E++  IAQA++
Sbjct: 534  ETPEGPNIGLINSLASYARVNDYGFLEAPYRRVVNGKVTNEIEYLSAIDEDHYVIAQAST 593

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LD++  F E+L+ CR  GE I     ++ ++D S KQ+VS AA+LIPFLE+DD+NRVLM
Sbjct: 594  KLDKNNHFVEDLIQCRSGGEAIFTESSRVQYMDVSAKQMVSAAAALIPFLEHDDANRVLM 653

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVP LK+E P VGTGME +VA+ SG  I+A+ AG + +VD+ RIV++      
Sbjct: 654  GANMQRQAVPTLKSEKPLVGTGMEKIVARDSGNCIIARNAGEIAEVDSNRIVVKVDTEKS 713

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S   VDIY L KF+RSN+NTC+NQRP+V VGD++   DI+ADG +TD G+L+LG N++
Sbjct: 714  QTSKL-VDIYSLTKFKRSNKNTCINQRPIVDVGDKIEAGDILADGFATDFGELSLGHNLM 772

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW+GYNFEDS+L+SER+V +D +TSIHIEEF  +ARDTKLGPEE+T DIPNVSE  
Sbjct: 773  VAFMPWNGYNFEDSILLSERIVKDDKYTSIHIEEFTCVARDTKLGPEEVTADIPNVSESS 832

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L  +DE GI+ +GA V  GDILV KITPK E  +TPEE+LLRAIF EKA +V D+SL++P
Sbjct: 833  LAKLDESGIVHIGANVEAGDILVAKITPKAEQQLTPEERLLRAIFNEKASNVADSSLKMP 892

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            SG SGTV++V++F      K++R++ +E+E I+   +D D+E  +++  + S +   + G
Sbjct: 893  SGTSGTVINVQVFENDKGGKSKRALKIEKELIDKARKDFDEEFAVIESVVKSSIETDVVG 952

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                   KG KK  VL+ + ++  P S+W + + + EK+++ +++ +  YE +K  ++ R
Sbjct: 953  AKIQKA-KGLKKGAVLTKEFLATLPFSKWLEISFEAEKLEQKIQNAREYYEEAKIAVDAR 1011

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F+ K + I   +++ PGVL+ VKVFVA+K+ IQ GDKMAGRHGNKG+VSR+LP EDMP++
Sbjct: 1012 FEAKKKSITQSNELSPGVLKTVKVFVAIKKRIQPGDKMAGRHGNKGVVSRVLPIEDMPYM 1071

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+ LNPLG+PSRMN+GQI E HLG A  GLGKK++  +   +     + LR  L
Sbjct: 1072 EDGTPVDVCLNPLGIPSRMNIGQILEAHLGLASYGLGKKVEQTL---EKTRKAAELRKTL 1128

Query: 1173 EKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            E+V  + G     +   +D+ +L + E  K GVP++TPVFDGA EE I S+L++     +
Sbjct: 1129 EEVYNSVGDKKVDLKALNDEEILNLCENLKGGVPIATPVFDGAKEEDIKSLLKIGGFVTN 1188

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ  L+DG TG+PFDR VTVGY+YMLKL+H+V DK++ARSTGSYSLVTQQPLGGK+  GG
Sbjct: 1189 GQMKLFDGRTGKPFDRHVTVGYMYMLKLDHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1248

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            QR GEMEVW +QAYGAAY L+EMLT+KSDD+ GR+++Y++IV G  T     PESFNV
Sbjct: 1249 QRFGEMEVWALQAYGAAYTLREMLTVKSDDITGRSKMYKNIVDGKLTMNVDVPESFNV 1306


>gi|225874479|ref|YP_002755938.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium capsulatum
            ATCC 51196]
 gi|225794200|gb|ACO34290.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium capsulatum
            ATCC 51196]
          Length = 1496

 Score = 1416 bits (3665), Expect = 0.0,   Method: Composition-based stats.
 Identities = 661/1354 (48%), Positives = 909/1354 (67%), Gaps = 73/1354 (5%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D  +C  R +T++ PLK+T+RL ++D D  TGAK+I+DIKEQ ++ GD+PLMT++GTF
Sbjct: 143  KYDQAECEERGMTFSAPLKVTVRLTIYDKDPETGAKTIRDIKEQEVFFGDIPLMTQNGTF 202

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            ++ G +R++VSQLHRSPG+ F+    R    GK      IIP +G W++ E+D K+ ++V
Sbjct: 203  IVNGTERVIVSQLHRSPGVFFETANNRTYFLGK------IIPYRGSWVEFEYDQKNTLYV 256

Query: 205  RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFW---CFPLSAADLMVGAKV 260
            RIDR+RK   T FL ALG+   EEIL TFY       +                ++GAK 
Sbjct: 257  RIDRKRKFLGTIFLRALGLKSDEEILKTFYTVDRIQVKDGKLYWTVAEAGTPTHLLGAKP 316

Query: 261  SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
            + ++V    G++++ SG+K+T+ +LK+++E  ++ + I +  L G   A D+++ ETGE+
Sbjct: 317  AHAVVH--NGQEIVHSGRKITASVLKAIREAKLEQIEIDTTDLDGAMTAADVIDTETGEV 374

Query: 321  YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             +EA   +    L +I  + I  + + + +  +    I NTL  D  +  ++AL++IYR 
Sbjct: 375  LLEANHELTPDKLHKIVEAGIPTVEVFFPERDDVGNIITNTLRRDSVRKPEEALIEIYRK 434

Query: 381  MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL---DTPDDVRHIRKEDII 437
            +RPGD  T   A ++F  +FFD  KYD S VGR+K N++L     +TP D R +   D  
Sbjct: 435  LRPGDPPTLDTATALFEGMFFDPRKYDFSRVGRLKFNIKLYENAEETPLDHRTLTAGDFY 494

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DID 496
            + I+ L+ LR   G +DDID+LGNRRVR+VGE+++NQ+R+GL+RMER+IKE++S   ++ 
Sbjct: 495  STIRYLLKLRKNIGVVDDIDHLGNRRVRAVGELMENQFRIGLVRMERAIKEKMSVYQEMS 554

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            + MP DLINAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG 
Sbjct: 555  TAMPHDLINAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGF 614

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV- 615
            E+RDVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYR+V DG+V + V  
Sbjct: 615  EVRDVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRRVRDGQVLDFVAV 674

Query: 616  -----------------------------------------YLSAMEEENRYIAQANSSL 634
                                                     YLSA EE+   IAQAN  L
Sbjct: 675  TNAGESGLRVGDYLEKAEALKLNDKLRAEKKRIIEFEPFSFYLSAWEEDRHTIAQANVKL 734

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DE+    E+LV  R  G  +LV RE++D++D SPKQ+VS+AASL+PFLE+DD+NR LMG 
Sbjct: 735  DENKHIVEDLVNARRQGNFVLVNREEVDYVDVSPKQLVSVAASLVPFLEHDDANRALMGA 794

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD- 753
            NMQRQ+VPLL +EAP VGTGME V A+ SGA I+A+R G+V+ VD+ RI++R        
Sbjct: 795  NMQRQSVPLLVSEAPLVGTGMEGVTARDSGAVILARRNGVVDSVDSERIIVRVEGEHHPT 854

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G DIY+L+KF+RSNQNTC+NQ+P+V+ GD V +  +IADGP T+ G+L LGRN+
Sbjct: 855  QLSREVGSDIYQLIKFKRSNQNTCINQKPIVRKGDRVLKGQVIADGPCTEQGELGLGRNV 914

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++LISE++V ED +TS+HIEEFE+ ARDTKLGPEEITRDIPNVSE 
Sbjct: 915  LVAFMPWRGYNFEDAILISEKLVKEDYYTSVHIEEFEIEARDTKLGPEEITRDIPNVSEH 974

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+++DE GII +GA+V   DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRD SL  
Sbjct: 975  ALRDLDESGIIRIGAKVKHNDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVRDASLTC 1034

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P G+ GTVVDVRIF+R G +K+ER+  +E EQ+  L ++ +DE  IL      RL  IL 
Sbjct: 1035 PPGIEGTVVDVRIFSRKGQEKDERAKQIEAEQVAKLEKNLEDEIRILTDERLKRLEAILG 1094

Query: 992  GQNA-------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQY 1042
            G+          +  +   K  VL  D I         +     +D +V   ++ ++   
Sbjct: 1095 GKVVLADLHDERTNKRLLVKDAVLDRDAIERISTRNLKRIRYADKDPRVNEQIDEIEEMT 1154

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +L      +I K+Q GD++ PGV+++VK+++AMKR +  GDKMAGRHGNKG+++R
Sbjct: 1155 SRQIDVLRKITNERIAKLQKGDELSPGVIKMVKIYIAMKRKLSVGDKMAGRHGNKGVIAR 1214

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LG ++ +++   K +
Sbjct: 1215 ILPEEDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAHDLGVQVAAIV---KQH 1271

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             D + +R  +++     +   ++ + +D+ +LRV      G+   T VFDGA EE I ++
Sbjct: 1272 QDANVIREVIKERFKGTAVINQLIELEDEQLLRVGAGMARGIWFGTAVFDGAKEEEIKAL 1331

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L  A L  SG++ L+DG+TGE F++PVTVG+IYMLKL+H+V DK++ARS G YSL+TQQP
Sbjct: 1332 LESAGLPTSGKTKLFDGMTGEAFEQPVTVGFIYMLKLSHLVDDKIHARSIGPYSLITQQP 1391

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GRT++YE+IV G    E G
Sbjct: 1392 LGGKAQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVYGRTKIYEAIVKGEAAIEPG 1451

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             PESFNVL++E+Q+L L ++L         + E+
Sbjct: 1452 VPESFNVLIRELQSLCLDVELIKQAPGAGPEAED 1485



 Score =  106 bits (265), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 35/71 (49%), Positives = 43/71 (60%)

Query: 12 RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
          R R  F K P  I IP+LIEVQ+ SY+ FL M+  P ER + GLQ+ F SVFPI  F   
Sbjct: 9  RSRLDFSKIPTSIKIPNLIEVQRRSYERFLQMDKLPTEREDNGLQSVFTSVFPIADFRNI 68

Query: 72 AMLEFVSYEFD 82
          + L+FV Y   
Sbjct: 69 SQLDFVDYSIG 79


>gi|34556892|ref|NP_906707.1| DNA-directed RNA polymerase subunit beta/beta' [Wolinella
            succinogenes DSM 1740]
 gi|41017624|sp|Q7MA56|RPOBC_WOLSU RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase subunit
            beta'; AltName: Full=Transcriptase subunit beta'
 gi|34482607|emb|CAE09607.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT RPOB [Wolinella
            succinogenes]
          Length = 2883

 Score = 1415 bits (3663), Expect = 0.0,   Method: Composition-based stats.
 Identities = 627/1403 (44%), Positives = 913/1403 (65%), Gaps = 42/1403 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I IP+L+++Q+ SYD FLM    P E    G++  F+S+FPI      
Sbjct: 10   RLRVDFTKIPQNIAIPNLLQLQRNSYDSFLM----PIENGESGIEKVFRSIFPIHDAQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+   E+  P++ V + + R LTY+VPLK+ +RL++++ DE TG K  +KDIKEQSI
Sbjct: 66   ITLEYAGCEYGKPRYTVREAMERGLTYSVPLKVKIRLVLWEKDEKTGEKLGVKDIKEQSI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+G 
Sbjct: 126  FVREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEESAT-SSNKLIYTGQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD ++VRI++RRKVPVT    ALG   ++++ TFYP +        +  P +
Sbjct: 185  WLYFEYDAKDTLYVRINKRRKVPVTILFRALGYSKQDVIKTFYPLMKVKAEAGKYLMPFN 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +   ++   + D  +G  +I +GK+LT    K+LKE+G++++    + L   ++AE
Sbjct: 245  PEEFI--GRIEFDIRDT-SGNLIIGAGKRLTQKRAKTLKEQGLEWVEYPVEILLDRHLAE 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             IV+ E+GE+ ++    +DE  L++I    I++  I    +   +A I ++ V D     
Sbjct: 302  PIVDKESGEVILDTLVQLDEGKLKKIHELGIKEFTIANDLAQGVDASIIHSFVADNESLK 361

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      D   A + IY+VMRPG+  T   A+S    LFFD ++YDL+ VGR+KMN 
Sbjct: 362  LLKQTEKIDDDNDLAAIRIYKVMRPGEPVTKDAAKSFVQQLFFDPERYDLTRVGRMKMNH 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L+++ PD V  +  EDII  +K L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 422  KLDIEVPDYVTVLTHEDIICTVKYLIRVKNGQGHIDDRDHLGNRRIRAIGELLANELHTG 481

Query: 479  LLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I+++++++  ++D +MP DL+N+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 482  LVKMQKAIRDKLTTMSGNLDELMPHDLVNSKMITSTILEFFTGGQLSQFMDQTNPLSEVT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++++VN  G
Sbjct: 542  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTYSKVNDLG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV +GKVT++VVYL+A +EE   IA A++ L+ DG+  E+L+  R  GE +L 
Sbjct: 602  FIEAPYKKVIEGKVTDEVVYLTATQEEGLVIAPASTVLETDGAIKEDLIETRIDGEIVLS 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             + K+D ID SP  VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL  +AP VGTGME
Sbjct: 662  EKSKVDLIDLSPGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLNPDAPVVGTGME 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              VA+ S  AI A R GIVE+VDA  I I   +     + + +D Y L K  R+NQNTC 
Sbjct: 722  KTVARDSWEAIKATRGGIVEKVDAKNIYILGEDE----NGAYIDHYSLQKNLRTNQNTCF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q P+V  G+ +    +IADGP+ D G+LALG+N+ VAFMPW+GYNFED++++SE+++ E
Sbjct: 778  SQAPIVHEGETIEAGQVIADGPNMDKGELALGKNIRVAFMPWNGYNFEDAIVVSEKLIRE 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI E E+ AR+ K G EEITRDIPNV EE L ++DE GI+ +G  VN G ILVG
Sbjct: 838  DTFTSIHIYEKEIEARELKHGVEEITRDIPNVREEELAHLDESGIVKIGTFVNAGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+IF + G DK++R+
Sbjct: 898  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKIFTKKGYDKDQRA 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
            I+   E+   L  +  D+ ++LDR    RL  +L  +   S      K +KK  ++    
Sbjct: 958  IAAYEEEKARLDLEHHDKLMMLDREEMLRLTSMLSKEPLASDVVVNEKSYKKGELIEKGD 1017

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +++  R           + +Q   + LK  +   K  L +  + K+  ++  D +P GV+
Sbjct: 1018 LAKINRFAMNALVKSFPKSIQEAYDQLKSNFLEQKKNLSEEHEEKLSVLEKDDILPSGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK++VA KR ++ GDKMAGRHGNKGIVS I+   DMP+ KDG PV+IVLNPLGVPSRM
Sbjct: 1078 KLVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVREIDMPYTKDGEPVEIVLNPLGVPSRM 1137

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT---EKISDY 1188
            N+GQI E HLG     LG +I  +  + +    +  LR+ + ++      T   E +S  
Sbjct: 1138 NIGQILEVHLGLVGKKLGAQINEM-FENQTKDWMGALRAKIIEIAQVSKMTGVDEFVSSL 1196

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+++L  A  W+ GV  +TPVF+G +EE    +  +A +D  G++ LYDG TG      
Sbjct: 1197 SDEALLSYARDWRRGVKFATPVFEGVNEEEFTKLFELARIDTDGKTELYDGKTGAKMKER 1256

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1257 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1316

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLT+KSDDV GR + Y++I  G    E+  PE+F VL KE+Q+L L + +     
Sbjct: 1317 HTLKEMLTVKSDDVEGRVKAYKAITRGEPVKESEIPETFYVLTKELQSLALDVTVYGETE 1376

Query: 1369 KN------SAKMEEIPDFNKCEL 1385
            ++        + +   DFN  +L
Sbjct: 1377 EDSFVPMPIKEDDRPSDFNAFQL 1399



 Score = 40.1 bits (92), Expect = 2.7,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 43/87 (49%)

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            ++  L+D+    +++        G+  +    G + +    + + G  VAED+++  T E
Sbjct: 2158 LTRKLIDVSQNVKIVMEDCGTHEGVEITDIAIGSELIEPLEERIFGRVVAEDVIDPITNE 2217

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            I +  G +IDE+  ++I  + ++ + I
Sbjct: 2218 ILVSEGSLIDEEMAKKIKEAGVKAVII 2244


>gi|94971702|ref|YP_593750.1| DNA-directed RNA polymerase subunit beta [Candidatus Koribacter
            versatilis Ellin345]
 gi|158564152|sp|Q1IHH4|RPOB_ACIBL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|94553752|gb|ABF43676.1| DNA-directed RNA polymerase subunit beta [Candidatus Koribacter
            versatilis Ellin345]
          Length = 1489

 Score = 1415 bits (3662), Expect = 0.0,   Method: Composition-based stats.
 Identities = 666/1348 (49%), Positives = 909/1348 (67%), Gaps = 73/1348 (5%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+DV +C  R +TY+ PLK+T+RL +FD D  T  ++I+DIKEQ ++ GD+PLMT++GTF
Sbjct: 143  KYDVAECEERGMTYSAPLKVTMRLTIFDKDPETNNRTIRDIKEQEVFFGDVPLMTQNGTF 202

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            +I G +R++VSQLHRSPG+ F+    R    GK      IIP +G W++ E+D K+I++V
Sbjct: 203  IINGTERVIVSQLHRSPGVFFETANNRTYFLGK------IIPYRGSWVEFEYDQKNILYV 256

Query: 205  RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSA----ADLMVGAK 259
            RIDR+RK   T FL ALG+   E+IL TFY     + +     + L         +VG K
Sbjct: 257  RIDRKRKFLGTIFLRALGLRTDEDILRTFYTVDRIAVKDKKLYWTLEPGIERPTNLVGLK 316

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            +S ++     GE+V  SG+K+T+ +LK +++  +  L I    L G YVA D+++  TGE
Sbjct: 317  LSHAI-KAKNGEEVAHSGRKVTASVLKEIQKHKISELEIELGDLEGAYVASDVIDTNTGE 375

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + +EA   +    L ++  + I ++ + + +  +    I  TL  D  K  ++AL++IYR
Sbjct: 376  VLLEANQELTADKLSKMIDAGIGEVNVFFPERDDVGTVISATLRRDSVKTPQEALIEIYR 435

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDI 436
             +RPGD  T   A ++F+ +FFD+ KYD S VGR+K N++L         D R +  +D 
Sbjct: 436  KLRPGDPPTLDTATALFHGMFFDARKYDFSRVGRLKFNIKLFDRQDPTGLDKRTLDPDDF 495

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DI 495
               I+ L+ LR   G +DDID+LGNRRVR+VGE+L+NQ+R+GL+RMER+IKE++S   ++
Sbjct: 496  YHTIRYLLKLRRNLGAVDDIDHLGNRRVRAVGELLENQFRIGLVRMERAIKEKMSVYQEM 555

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
             + MP DL+NAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG
Sbjct: 556  STAMPHDLVNAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAG 615

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             E+RDVHPTHYGRICP ET EG NIGL+SSL+ +AR+N YGFIE+PYR+V  G+V + V 
Sbjct: 616  FEVRDVHPTHYGRICPIETPEGPNIGLISSLSCYARINDYGFIESPYRRVKGGRVIDYVQ 675

Query: 616  ------------------------------------------YLSAMEEENRYIAQANSS 633
                                                      YLSA EE+   IAQAN+ 
Sbjct: 676  VTHAGDSDYRVGDKMEKSEAQKANEELRGRKKRGIELEPYSFYLSAWEEDKWTIAQANAE 735

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            LDE G  T ELV  R AG  +L+ R+ ID+ID SPKQ+VS+AASL+PFLE+DD+NR LMG
Sbjct: 736  LDEKGKITSELVNARKAGNFVLISRDDIDYIDVSPKQLVSVAASLVPFLEHDDANRALMG 795

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EG 750
             NMQRQ+VPLL+AEAP VGTGME V A+ SGA ++A+R+GI++ VD+ R+++R       
Sbjct: 796  ANMQRQSVPLLRAEAPIVGTGMEGVTARDSGAVVLARRSGIIDSVDSERVIVRVEGEHHP 855

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                   G DIY+L KF+RSNQNTC+NQ+P+VK GD V++  +IADGP TD G+L LGRN
Sbjct: 856  MQLSREVGSDIYQLTKFKRSNQNTCINQKPIVKQGDHVKKGQVIADGPCTDHGELGLGRN 915

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +LV+FMPW GYNFED++L+SE++V ED +TS+HIEEFE+ ARDTKLGPEEITRDIPNVSE
Sbjct: 916  VLVSFMPWRGYNFEDAILVSEKLVKEDYYTSVHIEEFEIEARDTKLGPEEITRDIPNVSE 975

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              L+++DE G+I +GA V  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRD SL 
Sbjct: 976  SALRDLDESGVIRIGAPVKAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVRDASLT 1035

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
             P G+ G VVDV+IF+R G +K+ER+  +E  QI  L ++  DE  IL      RL  +L
Sbjct: 1036 CPPGIEGVVVDVKIFSRKGQEKDERAKQIEGTQIAKLEKNLADEIRILTDERLKRLEGLL 1095

Query: 991  CGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQ 1041
              +          +  +   K  VL  + I         +     +D +V   ++ ++  
Sbjct: 1096 GAKVVQADLHDERTNKRLLTKDAVLDRETIERISTRNLKRIKYADKDPRVNEQIDEIEEM 1155

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                  +L    + KIEK+Q GD++PPGV+++VKV++AMKR +  GDKMAGRHGNKG+++
Sbjct: 1156 TSRQIDVLRKIVREKIEKLQKGDELPPGVIKLVKVYIAMKRKLSVGDKMAGRHGNKGVIA 1215

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RILP EDMP+L+DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LGKKI         
Sbjct: 1216 RILPEEDMPYLEDGTPVEIVLNPLGVPSRMNVGQILETHLGWAGHELGKKI---AEFMVE 1272

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            N +   +R  L+++    +  + +++ DD+ +L+VA+  + GV   + VFDG+ E  I S
Sbjct: 1273 NSEAGQVRKHLKQLFKDTAFVDHVTELDDEMLLKVAKGMQDGVFFGSAVFDGSTEAEIKS 1332

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L  A L  SG++ LYDG+TG+ F++PVTVGYIYMLKL+H+V DK++ARS G YSL+TQQ
Sbjct: 1333 LLDQAGLPTSGKTFLYDGMTGDRFEQPVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQ 1392

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GRT++YE+IV G    E 
Sbjct: 1393 PLGGKAQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVYGRTKIYEAIVKGEAAIEP 1452

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTK 1369
            G PESFNVL++E+Q+L L ++L  ++ K
Sbjct: 1453 GVPESFNVLIRELQSLCLDVELIKTKEK 1480



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 40/77 (51%), Positives = 47/77 (61%), Gaps = 3/77 (3%)

Query: 9  GLG---RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
                R R+ F K P  I IP+LIEVQK SYD FL M++ P ER + GLQA F+SVFPI
Sbjct: 3  EKKIAFRNRQDFSKIPATIQIPNLIEVQKRSYDRFLQMDLLPSERDDAGLQAVFQSVFPI 62

Query: 66 TAFSGAAMLEFVSYEFD 82
          T F   + LEFV Y   
Sbjct: 63 TDFRNVSQLEFVDYAIG 79


>gi|12082654|gb|AAG48562.1|AF236795_1 RNA polymerase beta subunit [Rickettsia felis]
          Length = 1289

 Score = 1409 bits (3646), Expect = 0.0,   Method: Composition-based stats.
 Identities = 712/1278 (55%), Positives = 962/1278 (75%), Gaps = 9/1278 (0%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+RK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRIRKNFGHINLVADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DV++C  R L+YA PLK+TLRL ++D+DE TG++ IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGSREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLVDADTGNVLLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ +  + E+  + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPASDEVLAKIGEMITSDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AE++F  LFFD+++YDLS VGR+KMN RL L+  ++V
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAENLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEV 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I+++LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ E
Sbjct: 435  TVLTIDDIKNIVRVLVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V D 
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDR 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V  +++DFID +
Sbjct: 615  HVTDEVVYLSAIEEGKYKIGQANSKVDKDGKLQGEFINCRVEGGNFVMVEPQEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVEQVD+ RIVIR++E  +D  +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVEQVDSNRIVIRTLEQKID-GSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV+ARDT+LGPEEITRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+T
Sbjct: 854  EVIARDTRLGPEEITRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPIT 913

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFGEKA DV+D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE L
Sbjct: 914  PEEKLLRAIFGEKAFDVKDSSLHVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKL 973

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            A+D+DDE  I++  ++S L ++L GQ  V+GPK  K    ++S+++    + Q+WQ  V+
Sbjct: 974  AKDRDDELEIIEHFVFSWLEKLLIGQVIVNGPKQVKAGQTITSEMLKGLSKGQFWQLTVE 1033

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V   +E +KV Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q G
Sbjct: 1034 DANVMNEIEQIKVHYDEKKDALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPG 1093

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + 
Sbjct: 1094 DKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASIN 1153

Query: 1148 LGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            L KKI +L+ +YK     I  ++ FL ++ G       I +  ++ ++    +   GV  
Sbjct: 1154 LAKKISTLVKEYKNKHIGIEQIKKFLLELYGENI--NYILERSEEEIISFCNKVSKGVHF 1211

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VTVG  Y+LKL+H+V +K
Sbjct: 1212 ATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVTVGQKYLLKLHHLVDNK 1271

Query: 1267 VYARSTGSYSLVTQQPLG 1284
            +++RS G YSLVT QPLG
Sbjct: 1272 IHSRSIGPYSLVTLQPLG 1289


>gi|242309992|ref|ZP_04809147.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter pullorum MIT 98-5489]
 gi|239523289|gb|EEQ63155.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter pullorum MIT 98-5489]
          Length = 2883

 Score = 1408 bits (3645), Expect = 0.0,   Method: Composition-based stats.
 Identities = 619/1414 (43%), Positives = 907/1414 (64%), Gaps = 42/1414 (2%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M   +      R+R  F K P+ I +P+L+++Q++SY+ FL       +    G++  FK
Sbjct: 1    MIMPISLKSGNRLRVDFTKIPQNIAVPNLLQLQRSSYEAFL----KSQDNNESGIEKVFK 56

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            S+FPI        LE+   E+  P++ V + + R LTY++PLKI +RL++++ DE TG K
Sbjct: 57   SIFPIHDTQNRISLEYAGCEYGKPRYTVREAMERGLTYSIPLKIKIRLVLWERDEKTGEK 116

Query: 121  -SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
              +KDIKEQ+I++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     S KL+
Sbjct: 117  LGVKDIKEQNIFVREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEESST-ASNKLV 175

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            Y  +IIPD+G W+  E+D+KD + VR+++RRK+PVT    ALG   ++IL  FYP +   
Sbjct: 176  YTGQIIPDRGSWLYFEYDAKDTLFVRVNKRRKIPVTILFRALGYSKQDILKMFYPLLTIK 235

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
             +   +  P    + +   +V   + D   G+ ++ +GK+LT+   K+LKE+ +  +   
Sbjct: 236  HKSGKYFIPFDPEEFI--GRVDFDIRDTK-GKLILAAGKRLTAKKAKALKEEKLNMIEYP 292

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             D L   Y+AE I++ E+GEI  +A  ++D+  L+++    I +  I    +   ++ + 
Sbjct: 293  IDILANRYLAEPIIDKESGEILFDALTLMDDSKLKKLAELGINEFVIANDLASGVDSSVI 352

Query: 360  NTLVTD------------KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
            N  + D             + +   A + IY+VMRPG+  T   A+     LFFD ++YD
Sbjct: 353  NAFIADAESLKLLKQTEKIDNENDLATIRIYKVMRPGEPVTKEAAKQFVQQLFFDPERYD 412

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            L+ VGR+KMN +L++  PD V  +  EDII  ++ L+ ++NG+G IDD D+LGNRR+R++
Sbjct: 413  LTRVGRMKMNHKLDISVPDYVTVLTHEDIIKTVRYLIHVKNGQGRIDDRDHLGNRRIRAI 472

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            GE+L N+  LGL++M+++I++++S++    + +MP DLIN+K +   + EFF   QLSQ 
Sbjct: 473  GELLANELHLGLVKMQKAIRDKLSTISSGLEELMPHDLINSKMITGTILEFFTGGQLSQF 532

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++
Sbjct: 533  MDQTNPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINT 592

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L+++A+VN  GFIE PYRKV D KVT+++VYL+A +EE   IA A++ L  D    E+++
Sbjct: 593  LSTYAKVNELGFIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPASTVLTNDNVIKEDII 652

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R  GE IL+   K++ ID SP+ VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL 
Sbjct: 653  EVRKDGEIILMESSKVELIDLSPRMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLC 712

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             +AP VGTG+E +V++ S  ++ A R G+VE+VDA  I I   +     + + +D Y L 
Sbjct: 713  PDAPVVGTGIEKIVSRDSWESVKATRGGVVEKVDAKNIYILGEDE----NGAFIDHYSLQ 768

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            K  R+NQNT  +Q+P+VK GD V+  D+IADGP+ D G+LALG+N+ VAFMPW+GYNFED
Sbjct: 769  KNLRTNQNTSFSQKPIVKAGDVVQAGDVIADGPNMDKGELALGKNIRVAFMPWNGYNFED 828

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            ++++SE+++  D FTSIHI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G
Sbjct: 829  AIVVSEKLICNDAFTSIHIYEKEIEARELKHGVEEITRDIPNIREEELAHLDESGIVKIG 888

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
              V  G ILVGK +PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+IF
Sbjct: 889  TYVTGGMILVGKASPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKIF 948

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKG 1001
             + G DK++R+I    E+   L  +  D+ ++LDR    R+  IL  +   S    G K 
Sbjct: 949  TKKGYDKDKRAIVAYEEEKARLDLEHHDKLLMLDREESLRIGSILSKEKLASNVKIGDKE 1008

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAV-QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            +KK +V+  + +    R           +++Q   ++LK  +   K  L    + K+  I
Sbjct: 1009 YKKGSVIPKEDLENVNRFVMGTIIKGYSKEIQSKYDALKANFLEQKKNLSQEHEEKLSII 1068

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            +  D +P GV+++VK++VA KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG PV+I
Sbjct: 1069 EKDDILPSGVVKLVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYTKDGRPVEI 1128

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQI E HLG     LG++I SL+ + +    I  LR  ++++  T  
Sbjct: 1129 VLNPLGVPSRMNIGQILEVHLGLVGKNLGEQI-SLVFEEEKGKWIGKLRDKMQEIAETSG 1187

Query: 1181 HTE---KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
              E    ++   D+ +L  A  W  GV  +TPVF+G + +    +  +A +D  G++ LY
Sbjct: 1188 MKEIKTFLNSLSDEDLLTYARDWSKGVKFATPVFEGVNAKEFEKLFALAKIDSDGKTELY 1247

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            DG TGE     V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEM
Sbjct: 1248 DGRTGEKMMERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEM 1307

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++AYGAA+ L+EMLTIKSDDV GR + Y++I  G    E+  PE+F VL KE+Q+L
Sbjct: 1308 EVWALEAYGAAHTLKEMLTIKSDDVEGRVKAYKAITRGESVKESEIPETFYVLTKELQSL 1367

Query: 1358 GLSIDLENSRT---KNSAKMEEI---PDFNKCEL 1385
             L +++             ++E     DFN  +L
Sbjct: 1368 ALDVNVFAKNKEGVNEPILIKEDNRPSDFNAFQL 1401



 Score = 38.5 bits (88), Expect = 7.4,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 42/87 (48%)

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            ++  L+D+    +++        G+  +    G + +    + + G  +AE+I++  T E
Sbjct: 2162 LTRKLIDVSQNVKIVMDDCGTNEGVEITDITIGSELIESLDERIFGRVIAENIIDPITNE 2221

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            + I  G +IDE+   ++  + ++ + I
Sbjct: 2222 VLISEGVLIDEEKARKVKEAGVKSVII 2248


>gi|5813831|gb|AAD52032.1|AF083622_1 RNA polymerase beta subunit [Rickettsia typhi str. Wilmington]
          Length = 1376

 Score = 1408 bits (3645), Expect = 0.0,   Method: Composition-based stats.
 Identities = 685/1376 (49%), Positives = 937/1376 (68%), Gaps = 39/1376 (2%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             RVRK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17   RRVRKNFGHINLVADIPNLIEIQKNSYERNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              A LEFV YEFD PK+DVD+C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77   NIANLEFVKYEFDTPKYDVDECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137  VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS-QRGDFWCFP 248
             W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM++EEI+  +Y  + Y   +   W   
Sbjct: 197  SWLDLEFDAKDVIYFRIDRKRKLYATTLLRAIGMNTEEIMKFYYNSVTYKCIKNKGWSVK 256

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                 +    +++S L+D DTG  ++++G+K+T  L +     G+  + +T + L G Y+
Sbjct: 257  FIPQHI-TAHRLTSDLIDADTGNVLLKAGQKITPRLAQKYFSIGLNNILVTHETLIGKYL 315

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +ED+ + E+ EI  + G++I    L+ I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316  SEDLRDPESDEILAKIGEMITADMLQVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  +++
Sbjct: 375  DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEI 434

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +  +DI  I++ILV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+R+E+S+ E
Sbjct: 435  TVLTIDDIKNIVRILVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRIEKSVIE 494

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495  RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555  LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
             VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615  YVTDEVVYLSAIEEGKYKIGQANSKVDQDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K EAPFVGTG+E VVAK SGA++
Sbjct: 675  PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTEAPFVGTGVEGVVAKDSGASV 734

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +A   GIVE+VD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735  LALHDGIVERVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794  VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI-------------------ICVGAEV 888
            EV+ARDT+LG E+    I N   +  K   + GI                       +  
Sbjct: 854  EVIARDTRLGGEDFDTRILNHLIDVFKK--DSGIDLSKDPLALQRLKEAAEKAKKELSST 911

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            +  DI +  IT     P     K  RA   +   D+ + ++         + D       
Sbjct: 912  SATDINLPYITADSTGPKHLNIKFTRAELEKLVDDLIEKTIEP---CRPALKDAGFKPTD 968

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              +            + L   +   +   +  +  ++L  ++         +      + 
Sbjct: 969  IQEVVLVGGMTRMPTVLLSCFENSLDVNHIQVSFLTKLFHLVQPSYGGVFFQEMNGYLLF 1028

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
                +S   ++  W        V   +E +K+ Y+  K  L+ RF  K+EK+Q GDD+P 
Sbjct: 1029 DVSPLSPVFKTPGW------SNVMNEIEQIKIHYDEKKHALDKRFATKVEKLQSGDDLPQ 1082

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G L+VVKVF+A K  +Q GDKMAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+P
Sbjct: 1083 GALKVVKVFIATKHKLQPGDKMAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLP 1142

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISD 1187
            SRMN+GQI ETHLGWA + L KKI +L+ +YK N  DI  ++ FL ++ G       I +
Sbjct: 1143 SRMNIGQILETHLGWASINLAKKISTLVKEYKDNNIDIEQIKKFLLELYGKDI--NYILE 1200

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              ++ ++    +   GV  +TPVFDGA  + +  ML++AD D SGQ  L DG TGE FDR
Sbjct: 1201 GSEEGIISFCNKVSKGVYFATPVFDGAKVQDVKDMLKLADQDLSGQVKLIDGRTGEYFDR 1260

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             VTVG+ Y+LKL H+V +K+++RS G YSLVTQQPLG KS+ GGQR GEME W +QAYGA
Sbjct: 1261 LVTVGHKYLLKLPHLVDNKIHSRSIGPYSLVTQQPLGSKSHFGGQRFGEMECWALQAYGA 1320

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AY LQEMLT+KSDDV GR + Y+SIV G + FE+G PESFNV++KE ++L L++ L
Sbjct: 1321 AYTLQEMLTVKSDDVNGRIKTYDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKL 1376


>gi|299137934|ref|ZP_07031114.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium sp.
            MP5ACTX8]
 gi|298599864|gb|EFI56022.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium sp.
            MP5ACTX8]
          Length = 1498

 Score = 1408 bits (3645), Expect = 0.0,   Method: Composition-based stats.
 Identities = 662/1362 (48%), Positives = 908/1362 (66%), Gaps = 72/1362 (5%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D  +C  R +TY+ PLK+T+RL ++D D  TG KS++D+KEQ ++ GD+PLM+ +GTF
Sbjct: 147  KYDQAECEERGMTYSAPLKVTIRLKIYDKDPETGVKSLRDMKEQEVFFGDIPLMSANGTF 206

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            ++ G +R++VSQLHRSPG+ F+    R    GK      IIP +G W++ E+D K+ ++V
Sbjct: 207  IVNGTERVIVSQLHRSPGVFFETANNRTYFLGK------IIPYRGSWVEFEYDQKNTLYV 260

Query: 205  RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADL---MVGAKV 260
            RIDR+RK   T FL ALG+   EEIL TFY     + +     + + A +    +VG + 
Sbjct: 261  RIDRKRKFLGTIFLRALGLRTDEEILKTFYTVDTINVKDGKLSWTVGAEEKPSHLVGTRS 320

Query: 261  SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
            +++L   D G++++ SGKK+ +  LK L+  GV  + + +    G  +A D+++  TGE+
Sbjct: 321  TAALNGAD-GKELVASGKKIGASALKHLRAGGVTSVEVETSEFDGAMIAADVIDMGTGEL 379

Query: 321  YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
              EA   +    L +I  S +    + + +  +    I NTL  D  +  ++AL++IYR 
Sbjct: 380  LYEANAELTADKLHKILQSGVATFEVFFPERDDVGNIISNTLRRDSVRKPEEALIEIYRK 439

Query: 381  MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDII 437
            +RPGD  T   A ++F  +FFD  KYD S VGR+K N++L  D      D R +  ED  
Sbjct: 440  LRPGDPPTLDTATALFEGMFFDPRKYDFSRVGRLKFNIKLYEDQDPSGLDKRTLTPEDFY 499

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DID 496
              I+ L+ LR   G +DDID+LGNRRVR+VGE+++NQ+R+GL+RMER+IKE++S   ++ 
Sbjct: 500  GTIRYLLKLRKNIGVVDDIDHLGNRRVRAVGELMENQFRIGLVRMERAIKEKMSVYQEMS 559

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            + MP DLINAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG 
Sbjct: 560  TAMPHDLINAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGF 619

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV- 615
            E+RDVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYR+V DG+V + V  
Sbjct: 620  EVRDVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRRVKDGRVLDYVAV 679

Query: 616  -----------------------------------------YLSAMEEENRYIAQANSSL 634
                                                     YLSA EE+   IAQAN  L
Sbjct: 680  TNAGESGLRQGDFLEISESIKQNKELKKNGKRTMDLEPFSFYLSAWEEDRHTIAQANIEL 739

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            D + +  E+LV  R  G  +LVP+ ++D++D SPKQ+VS+AASL+PFLE+DD+NR LMG 
Sbjct: 740  DAELNIVEDLVNARKQGNFVLVPKAEVDYVDVSPKQLVSVAASLVPFLEHDDANRALMGA 799

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD- 753
            NMQRQ+VPLL AEAPFVGTGME V A+ SGA I+AKR GI++ VD+ RI++R        
Sbjct: 800  NMQRQSVPLLVAEAPFVGTGMEGVTARDSGAVILAKRNGIIDSVDSERIIVRVEGEHHPT 859

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G DIY+L KF+RSNQNTC+NQ+P+V+ GD V +  +IADGP T+ G+L LGRN+
Sbjct: 860  QLSREVGSDIYQLTKFKRSNQNTCINQKPIVRKGDRVLKGQVIADGPCTEQGELGLGRNV 919

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++LISE++V ED +TSIHIEEFE+ ARDTKLGPEEITRDIPNVSE 
Sbjct: 920  LVAFMPWRGYNFEDAILISEKLVREDYYTSIHIEEFEIEARDTKLGPEEITRDIPNVSEH 979

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+++DE GII +GA++   DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRD SL  
Sbjct: 980  ALRDLDESGIIRIGAKIGHNDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVRDASLTC 1039

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P G+ GTVVDVRIF+R G +K++R++ +E+E +E L R+  DE  IL      RL  IL 
Sbjct: 1040 PPGIEGTVVDVRIFSRKGQEKDQRALQIEQEMVEKLERNLADEIRILTDERLKRLEGILG 1099

Query: 992  G-------QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQY 1042
                     +  +  K   K  +L+ D+I         +     +D +V   ++ ++   
Sbjct: 1100 SKEVLADLHDERTNKKLLSKGDILTRDIIELISTRNLKRIRYADKDPRVNEQIDEIEEMT 1159

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +L      KI K+Q GD++ PGV+++VKV++AMKR +  GDKMAGRHGNKG+++R
Sbjct: 1160 SRQIDVLRKITNEKIGKMQKGDELSPGVIKMVKVYIAMKRKLSVGDKMAGRHGNKGVIAR 1219

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LG K+ +L   ++  
Sbjct: 1220 ILPEEDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAHELGAKVAALAAQHQ-- 1277

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             +   +R   ++     +   ++   DD+  +RVA   K G+   T VFDGA E  I ++
Sbjct: 1278 -EAGEVREIFKEAFKNTAALNQLLTLDDEQTMRVAAGMKRGIWFGTAVFDGARETEIKAL 1336

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L  A L  SG+S+++DG+TG+ F++PVTVGYIYMLKL+H+V DK++ARS G YSL+TQQP
Sbjct: 1337 LAAAGLPSSGKSMMFDGMTGDQFEQPVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQP 1396

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GRT++YE+IV G    E G
Sbjct: 1397 LGGKAQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVYGRTKIYEAIVKGEAAIEPG 1456

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
             PESFNVL++E+Q+L L ++L    + + +++  +P+    +
Sbjct: 1457 VPESFNVLIRELQSLCLDVELVKKTSTDESEVIALPELAVAD 1498



 Score =  112 bits (281), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 39/89 (43%), Positives = 48/89 (53%), Gaps = 8/89 (8%)

Query: 12 RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
          R R  F K P  I IP+LIEVQ+ SY+ FL M+  P ER + GLQ+ F SVFPIT F   
Sbjct: 13 RSRLDFSKIPTSIQIPNLIEVQRRSYERFLQMDKLPQEREDNGLQSVFTSVFPITDFRNV 72

Query: 72 AMLEFVSYEFDPPKFDVDDCL---WRDLT 97
          + LEFV Y          +C     + L 
Sbjct: 73 SELEFVDYSIGN-----WECKCGYLKGLN 96


>gi|224418578|ref|ZP_03656584.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter
            canadensis MIT 98-5491]
          Length = 2881

 Score = 1408 bits (3644), Expect = 0.0,   Method: Composition-based stats.
 Identities = 612/1403 (43%), Positives = 905/1403 (64%), Gaps = 42/1403 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I +P+L+++Q++SY+ FL       E    G++  FKS+FPI      
Sbjct: 10   RLRVDFTKIPQNIAVPNLLQLQRSSYEAFLQ----SKENNESGIEKVFKSIFPIHDTQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+   E+  P++ V + + R LTY++PLKI +RL++++ DE TG K  IKDIKEQ+I
Sbjct: 66   ISLEYAGCEYGKPRYTVREAMERGLTYSIPLKIKIRLVLWERDEKTGEKLGIKDIKEQNI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+G 
Sbjct: 126  FVREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-TSNKLVYTGQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD + VR+++RRK+PVT    ALG   ++IL  FYP +    +   +     
Sbjct: 185  WLYFEYDAKDTLFVRVNKRRKIPVTILFRALGYSKQDILKMFYPSLSVKAKSGKYFIAFD 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +   +V   + D   G+ ++ +GK+LT+   K+LKE+ +  +    + L   Y+AE
Sbjct: 245  PEEFI--GRVDFDIKDSK-GKLILAAGKRLTAKKAKALKEEKINMIEYPVETLVNRYLAE 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
             I++ E+GE+  +   ++D+  L+++    I +  I    +   ++ I N  + D     
Sbjct: 302  PIIDKESGEVIFDTLTLMDDSKLKKLAEMGINEFVIANDLANGVDSSIINAFIADAESLK 361

Query: 366  -------KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                    + +   A + IY+VMRPG+  T   A+     LFFD ++YDL+ VGR+KMN 
Sbjct: 362  LLKQTEKIDNENDLATIRIYKVMRPGEPVTKEAAKQFVQQLFFDPERYDLTRVGRMKMNH 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L++  PD V  +  EDII  ++ L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 422  KLDISVPDYVTILTHEDIIKTVRYLIHVKNGQGRIDDRDHLGNRRIRAIGELLANELHTG 481

Query: 479  LLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++    + +MP DL+N+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 482  LVKMQKAIRDKLSTISSGLEELMPHDLVNSKMITSTILEFFTGGQLSQFMDQTNPLSEVT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 542  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTYAKVNDLG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PYRKV D KVT+++VYL+A +EE   IA A++ L  D    E+++  R  GE IL+
Sbjct: 602  FIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPASTILTNDNMIKEDIIEVRKDGEIILM 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               K++ ID SP+ VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL  +AP VGTG+E
Sbjct: 662  ESSKVELIDLSPRMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLCPDAPVVGTGIE 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +V++ S  ++ A R GIVE+VDA  I I   +     + + +D Y L K  R+NQNT  
Sbjct: 722  KIVSRDSWESLKATRGGIVEKVDAKNIYILGEDE----NGAFIDHYSLQKNLRTNQNTSF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q+P+VK GD +   D+IADGP+ D G+LALG+N+ VAFMPW+GYNFED++++SE+++  
Sbjct: 778  SQKPIVKAGDVIESGDVIADGPNMDQGELALGKNIRVAFMPWNGYNFEDAIVVSEKLIRN 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G  V  G ILVG
Sbjct: 838  DAFTSIHIYEKEIEARELKHGVEEITRDIPNIREEELAHLDESGIVKIGTYVTGGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K +PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTV+DV+IF + G DK+ R+
Sbjct: 898  KASPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVIDVKIFTKKGYDKDRRA 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN----AVSGPKGFKKSTVLSSDL 1012
            +    E+   L  +  D+ ++LDR    R+  IL  +        G K +KK +V+  + 
Sbjct: 958  VIAYEEEKARLDLEHHDKLLMLDREESLRIGSILAKEKLIANVKVGDKEYKKGSVIPKEE 1017

Query: 1013 ISEYPRSQWWQFAV-QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R           +++Q   + LK  +   K  L +  + K+  I+  D +P GV+
Sbjct: 1018 LENVNRFVMGTIIKGYSKEIQSQYDLLKANFLEQKKSLSEEHEEKLSIIEKDDILPSGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK++VA KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG PV+IVLNPLGVPSRM
Sbjct: 1078 KLVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYTKDGRPVEIVLNPLGVPSRM 1137

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI---GTGSHTEKISDY 1188
            N+GQI E HLG     LG++I + + + + +  IS LR  ++++    G     E ++  
Sbjct: 1138 NIGQILEVHLGLVGKKLGEQI-AFVFEQEKSQWISQLREKMQEIAEVSGMKETKEFLASL 1196

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            +D+++L  A  W  GV  +TPVF+G + +    +  +A +D  G++ LYDG TGE     
Sbjct: 1197 NDEALLAYARDWSKGVKFATPVFEGVNAQEFEKLFNLAKIDTDGKTELYDGRTGEKMMER 1256

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1257 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1316

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR + Y++I  G    E+  PE+F VL KE+Q+L L +++     
Sbjct: 1317 HTLKEMLTIKSDDVEGRVKAYKAITRGEAVKESEIPETFYVLTKELQSLALDVNVFADNQ 1376

Query: 1369 K---NSAKMEEI---PDFNKCEL 1385
            +       ++E     DFN  +L
Sbjct: 1377 EGMSEPIVIKEDNRPSDFNAFQL 1399



 Score = 38.9 bits (89), Expect = 5.8,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 42/87 (48%)

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            ++  L+D+    +++        G+  +    G + +    + + G  +AE+I++  T E
Sbjct: 2160 LTRKLIDVSQNVKIVMDDCGTNEGVEITDITVGSELIESLDERIFGRVIAENIIDPITNE 2219

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            + I  G +IDE+   ++  + ++ + I
Sbjct: 2220 VLISEGTLIDEEKARKVKEAGVKSVII 2246


>gi|253826871|ref|ZP_04869756.1| DNA-directed RNA polymerase beta subunit rpoB [Helicobacter
            canadensis MIT 98-5491]
 gi|313142106|ref|ZP_07804299.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter canadensis MIT 98-5491]
 gi|253510277|gb|EES88936.1| DNA-directed RNA polymerase beta subunit rpoB [Helicobacter
            canadensis MIT 98-5491]
 gi|313131137|gb|EFR48754.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter canadensis MIT 98-5491]
          Length = 2883

 Score = 1407 bits (3643), Expect = 0.0,   Method: Composition-based stats.
 Identities = 612/1403 (43%), Positives = 905/1403 (64%), Gaps = 42/1403 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I +P+L+++Q++SY+ FL       E    G++  FKS+FPI      
Sbjct: 12   RLRVDFTKIPQNIAVPNLLQLQRSSYEAFLQ----SKENNESGIEKVFKSIFPIHDTQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+   E+  P++ V + + R LTY++PLKI +RL++++ DE TG K  IKDIKEQ+I
Sbjct: 68   ISLEYAGCEYGKPRYTVREAMERGLTYSIPLKIKIRLVLWERDEKTGEKLGIKDIKEQNI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+G 
Sbjct: 128  FVREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-TSNKLVYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD + VR+++RRK+PVT    ALG   ++IL  FYP +    +   +     
Sbjct: 187  WLYFEYDAKDTLFVRVNKRRKIPVTILFRALGYSKQDILKMFYPSLSVKAKSGKYFIAFD 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +   +V   + D   G+ ++ +GK+LT+   K+LKE+ +  +    + L   Y+AE
Sbjct: 247  PEEFI--GRVDFDIKDSK-GKLILAAGKRLTAKKAKALKEEKINMIEYPVETLVNRYLAE 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
             I++ E+GE+  +   ++D+  L+++    I +  I    +   ++ I N  + D     
Sbjct: 304  PIIDKESGEVIFDTLTLMDDSKLKKLAEMGINEFVIANDLANGVDSSIINAFIADAESLK 363

Query: 366  -------KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                    + +   A + IY+VMRPG+  T   A+     LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEKIDNENDLATIRIYKVMRPGEPVTKEAAKQFVQQLFFDPERYDLTRVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L++  PD V  +  EDII  ++ L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLDISVPDYVTILTHEDIIKTVRYLIHVKNGQGRIDDRDHLGNRRIRAIGELLANELHTG 483

Query: 479  LLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++    + +MP DL+N+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 484  LVKMQKAIRDKLSTISSGLEELMPHDLVNSKMITSTILEFFTGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTYAKVNDLG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PYRKV D KVT+++VYL+A +EE   IA A++ L  D    E+++  R  GE IL+
Sbjct: 604  FIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPASTILTNDNMIKEDIIEVRKDGEIILM 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               K++ ID SP+ VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL  +AP VGTG+E
Sbjct: 664  ESSKVELIDLSPRMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLCPDAPVVGTGIE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +V++ S  ++ A R GIVE+VDA  I I   +     + + +D Y L K  R+NQNT  
Sbjct: 724  KIVSRDSWESLKATRGGIVEKVDAKNIYILGEDE----NGAFIDHYSLQKNLRTNQNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q+P+VK GD +   D+IADGP+ D G+LALG+N+ VAFMPW+GYNFED++++SE+++  
Sbjct: 780  SQKPIVKAGDVIESGDVIADGPNMDQGELALGKNIRVAFMPWNGYNFEDAIVVSEKLIRN 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G  V  G ILVG
Sbjct: 840  DAFTSIHIYEKEIEARELKHGVEEITRDIPNIREEELAHLDESGIVKIGTYVTGGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K +PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTV+DV+IF + G DK+ R+
Sbjct: 900  KASPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVIDVKIFTKKGYDKDRRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN----AVSGPKGFKKSTVLSSDL 1012
            +    E+   L  +  D+ ++LDR    R+  IL  +        G K +KK +V+  + 
Sbjct: 960  VIAYEEEKARLDLEHHDKLLMLDREESLRIGSILAKEKLIANVKVGDKEYKKGSVIPKEE 1019

Query: 1013 ISEYPRSQWWQFAV-QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R           +++Q   + LK  +   K  L +  + K+  I+  D +P GV+
Sbjct: 1020 LENVNRFVMGTIIKGYSKEIQSQYDLLKANFLEQKKSLSEEHEEKLSIIEKDDILPSGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK++VA KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG PV+IVLNPLGVPSRM
Sbjct: 1080 KLVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYTKDGRPVEIVLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI---GTGSHTEKISDY 1188
            N+GQI E HLG     LG++I + + + + +  IS LR  ++++    G     E ++  
Sbjct: 1140 NIGQILEVHLGLVGKKLGEQI-AFVFEQEKSQWISQLREKMQEIAEVSGMKETKEFLASL 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            +D+++L  A  W  GV  +TPVF+G + +    +  +A +D  G++ LYDG TGE     
Sbjct: 1199 NDEALLAYARDWSKGVKFATPVFEGVNAQEFEKLFNLAKIDTDGKTELYDGRTGEKMMER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1259 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR + Y++I  G    E+  PE+F VL KE+Q+L L +++     
Sbjct: 1319 HTLKEMLTIKSDDVEGRVKAYKAITRGEAVKESEIPETFYVLTKELQSLALDVNVFADNQ 1378

Query: 1369 K---NSAKMEEI---PDFNKCEL 1385
            +       ++E     DFN  +L
Sbjct: 1379 EGMSEPIVIKEDNRPSDFNAFQL 1401



 Score = 38.9 bits (89), Expect = 5.8,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 42/87 (48%)

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            ++  L+D+    +++        G+  +    G + +    + + G  +AE+I++  T E
Sbjct: 2162 LTRKLIDVSQNVKIVMDDCGTNEGVEITDITVGSELIESLDERIFGRVIAENIIDPITNE 2221

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            + I  G +IDE+   ++  + ++ + I
Sbjct: 2222 VLISEGTLIDEEKARKVKEAGVKSVII 2248


>gi|322434564|ref|YP_004216776.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium sp.
            MP5ACTX9]
 gi|321162291|gb|ADW67996.1| DNA-directed RNA polymerase, beta subunit [Acidobacterium sp.
            MP5ACTX9]
          Length = 1493

 Score = 1397 bits (3615), Expect = 0.0,   Method: Composition-based stats.
 Identities = 655/1342 (48%), Positives = 891/1342 (66%), Gaps = 72/1342 (5%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D  +C  R +TY+ PLK+T+RL ++D D  TG KS++D+KEQ ++ GD+PLM+++GTF
Sbjct: 146  KYDQAECEERGMTYSAPLKVTIRLKIYDKDPETGVKSLRDMKEQEVFFGDIPLMSQNGTF 205

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            ++ G +R++VSQLHRSPG+ F+    R    GK      IIP +G W++ E+D K+ ++V
Sbjct: 206  IVNGTERVIVSQLHRSPGVFFETANNRTYFLGK------IIPYRGSWVEFEYDQKNTLYV 259

Query: 205  RIDRRRKVPVTSFLMALGM-DSEEILSTFY--PKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            RIDR+RK   T FL ALG+   EEIL TFY    I  ++    W         ++G + +
Sbjct: 260  RIDRKRKFLGTIFLRALGLRTDEEILKTFYTVDTINVAEGKLTWKVSAEGVTNLLGTRPT 319

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            +++ +    E++  +G+K+++ +LK+L+   ++ + + +    G   A D+V+  TGE+ 
Sbjct: 320  AAIKN--GAEEIGVAGRKISASVLKALRAAKIETVEVETSEFDGAMTASDVVDLSTGELL 377

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
             EA   +    L +I  S +    + + +  +    I NTL  D  +  ++AL++IYR +
Sbjct: 378  YEANQELTADKLHKILQSGVSSFELFFPERDDVGNIITNTLRRDSVRKPEEALIEIYRKL 437

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDIIA 438
            RPGD  T   A ++F  +FFD  KYD S VGR+K N++L  D      D R +  ED   
Sbjct: 438  RPGDPPTLDTATALFEGMFFDPRKYDFSRVGRLKFNIKLYEDQSPAGLDKRTLTPEDFYG 497

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDS 497
             I+ L+ LR   G +DDID+LGNRRVR+VGE+++NQ+R+GL+RMER+IKE++S   ++ +
Sbjct: 498  TIRYLLKLRKNIGVVDDIDHLGNRRVRAVGELMENQFRIGLVRMERAIKEKMSVYQEMST 557

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             MP DLINAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG E
Sbjct: 558  AMPHDLINAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGFE 617

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN----- 612
            +RDVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYR+V DG+  +     
Sbjct: 618  VRDVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRRVKDGRALDFVAVT 677

Query: 613  -------------DVV------------------------YLSAMEEENRYIAQANSSLD 635
                         ++                         YLSA EE+   IAQAN  LD
Sbjct: 678  NAGESGLRQGDYLEIEESKAKNEELRAAGKRTMDLEPFSFYLSAWEEDRHTIAQANIQLD 737

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            E  +  +++V  R  G  +LV + ++D++D SPKQ+VS+AASL+PFLE+DD+NR LMG N
Sbjct: 738  EQLNIVQDIVDARRQGNFVLVNKAEVDYVDVSPKQLVSVAASLVPFLEHDDANRALMGAN 797

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-- 753
            MQRQ+VPLL AEAPFVGTGME V A+ SGA I+AKR GI++ VD+ RI++R         
Sbjct: 798  MQRQSVPLLVAEAPFVGTGMEGVTARDSGAVILAKRNGIIDSVDSERIIVRVEGEHHPTQ 857

Query: 754  -PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G DIY+L KF+RSNQNTC+NQ+P+V+ GD V +  +IADGP T+ G+L LGRN+L
Sbjct: 858  LSREVGSDIYQLTKFKRSNQNTCINQKPIVRQGDRVLKGQVIADGPCTEQGELGLGRNVL 917

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW GYNFED++LISE++V ED +TSIHIEEFE+ ARDTKLGPEEITRDIPNVSE  
Sbjct: 918  VAFMPWRGYNFEDAILISEKLVREDYYTSIHIEEFEIEARDTKLGPEEITRDIPNVSEHA 977

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L+++DE GII +GA++   DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRD SL  P
Sbjct: 978  LRDLDESGIIRIGAKIGHNDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVRDASLTCP 1037

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
             G+ GTVVDVRIF+R G +K+ER+  +E+E IE L R+  DE  IL      RL  IL  
Sbjct: 1038 PGIEGTVVDVRIFSRKGQEKDERAKQIEQEMIEKLERNLADEIRILTDERLKRLEAILGK 1097

Query: 993  -------QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQYE 1043
                    +  +  K   K  +L  D+I         +     +D +V   ++ ++    
Sbjct: 1098 KEVLADLHDERTNKKLLNKGELLDRDMIELISTRNLKRIRYADKDPRVNEQIDEIEEMTS 1157

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                +L      KI K+Q GD++ PGV+++VK+++AMKR +  GDKMAGRHGNKG+V+RI
Sbjct: 1158 RQIDVLRKITNEKISKMQKGDELSPGVIKMVKIYIAMKRRLSVGDKMAGRHGNKGVVARI 1217

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LG +I  L        
Sbjct: 1218 LPEEDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAHTLGAQIAELA---SKME 1274

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
              + +R   +      +   ++ D DD+  +RVA   K G+   T VFDGA E  I ++L
Sbjct: 1275 SANEVRELFKARFEGTAALNQLLDLDDEQTMRVAAGMKRGIWFGTAVFDGARETEIKALL 1334

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            + A L  SG++ LYDG+ G+PF++P TVGYIYMLKL+H+V DK++ARS G YSL+TQQPL
Sbjct: 1335 KSAGLPSSGKTQLYDGMLGDPFEQPATVGYIYMLKLSHLVDDKIHARSIGPYSLITQQPL 1394

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GRT++YE+IV G    E G 
Sbjct: 1395 GGKAQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVFGRTKIYEAIVKGEAAIEPGV 1454

Query: 1344 PESFNVLVKEMQALGLSIDLEN 1365
            PESFNVL++E+Q+L L ++L  
Sbjct: 1455 PESFNVLIRELQSLCLDVELIK 1476



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 39/100 (39%), Positives = 49/100 (49%), Gaps = 10/100 (10%)

Query: 3  KGVVFNGLG--RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
                 +   R R  F K P  I IP+LIEVQ+ SY+ FL M+  P ER + GLQ+ F 
Sbjct: 1  MSDQSTEMRAIRSRLDFSKIPTAIQIPNLIEVQRRSYERFLQMDKLPQEREDNGLQSVFT 60

Query: 61 SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCL---WRDLT 97
          SVFPIT F   + LEFV Y          +C     + L 
Sbjct: 61 SVFPITDFRNVSELEFVDYSIGN-----WECKCGYLKGLN 95


>gi|283362188|dbj|BAI65970.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362198|dbj|BAI65979.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362208|dbj|BAI65988.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362228|dbj|BAI66006.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
          Length = 1243

 Score = 1394 bits (3607), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1242/1243 (99%), Positives = 1242/1243 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243


>gi|152990017|ref|YP_001355739.1| DNA-directed RNA polymerase subunit beta [Nitratiruptor sp. SB155-2]
 gi|182676569|sp|A6Q1M3|RPOB_NITSB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|151421878|dbj|BAF69382.1| DNA-directed RNA polymerase, beta subunit [Nitratiruptor sp. SB155-2]
          Length = 1386

 Score = 1392 bits (3604), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1384 (44%), Positives = 903/1384 (65%), Gaps = 34/1384 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ +D+P+L+++QK+SY++FLM +     R N G++  F+SVFPI      
Sbjct: 10   RLRVDFSKIPQELDVPNLLQLQKSSYENFLMAD--SKSRENSGIEKVFRSVFPIHDPHNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+   E   PK+ V +C+ R +TY+V LK+ +RLI+++ DE +G K+ +KD+KEQSI
Sbjct: 68   ISLEYAGSEIIKPKYTVRECMERGITYSVSLKMNIRLILWERDEKSGEKTGVKDVKEQSI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ D+P MT   +F+I G++R+VV+QLHRSPG+ F  ++     SG +++  +IIPD+G 
Sbjct: 128  YVRDIPYMTDRTSFIINGVERVVVNQLHRSPGVIFKEEEAST-SSGTMIHTAQIIPDRGA 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KDI++VRI++RRK+P T    ALG    +IL  FYP      + + +     
Sbjct: 187  WLYFEYDPKDILYVRINKRRKIPSTILFRALGYSKLDILKLFYPITKIIIKENKFFIEFR 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D +   +V   + D + G  ++E+GK+LT    + L E+GVK++    D L   ++A 
Sbjct: 247  PEDFI--GRVEFDVRD-ENGNLIVEAGKRLTKKKAQKLIEEGVKYIEFPLDVLMDRHLAS 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  +    +DE  L++I    I +  I+   +   +  I N+ + D+    
Sbjct: 304  PIIDQESGEVLYDTLTQLDEHKLKKILELGIDEFEIVNDIASGKDRAIINSFIADQESLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A++    LFFD ++YD++ VGR+KMN 
Sbjct: 364  LLKQTEGIEDENDLAAIRIYKVMRPGEPVTKETAKAFIQQLFFDPERYDITRVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L LD P+ V  +  EDII  ++ L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLGLDVPEYVTVLTSEDIIKTVQYLIKVKNGQGHIDDRDHLGNRRIRAIGELLANELHSG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++   +D +MP DLIN+K + + + EFF + QLSQ  +  N LS IT
Sbjct: 484  LVKMQKAIRDKMSTISGSLDELMPHDLINSKMITNTILEFFATGQLSQFMDQTNPLSEIT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTYAKVNELG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE  Y+ V DGK+T+++VYL+A +EE + IA AN+ + +      + V  R  GE ILV
Sbjct: 604  FIEAAYKVVKDGKITDEIVYLTAAQEEGKIIAPANTEIIDGNEIKGDYVEARKDGEIILV 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             + K++ ID +P+ VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTGME
Sbjct: 664  EKNKVELIDLTPRMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPIVGTGME 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VVA+ +  +I A+R+G+VE++D+  I I   +     + + +D YRL K  R+NQNTC 
Sbjct: 724  KVVARDAWESIRARRSGVVEKIDSENIYILGEDE----NGAYIDHYRLQKNLRTNQNTCF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q+P+VK G  V    +I DGP+ D  +LALG+NMLVAFMPW+GYNFED++++SER++ +
Sbjct: 780  TQKPIVKKGQFVEAGQVITDGPNMDHAELALGKNMLVAFMPWNGYNFEDAIVVSERILRD 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEITRDIPNV EE ++++DE GI+ +G  V PG ILVG
Sbjct: 840  DEFTSVHIYEKEIEARELKHGVEEITRDIPNVKEEEIEHLDESGIVKIGTYVKPGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   +PEE+LLRAIFGEKA  V + SL  P  + G VVDV+IF + G DK+ R+
Sbjct: 900  KVSPKGEVRPSPEERLLRAIFGEKAGHVVNKSLYCPQSMEGVVVDVKIFTKKGYDKDPRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG----PKGFKKSTVLSSDL 1012
            I    E+ E L+++  D+ +++DR    +++ +L  +          K FK    +S + 
Sbjct: 960  IKAYEEEKERLSKEHHDKLLMIDREEMLKIISLLSKEPLEKDAKIKDKEFKAGEKISKEE 1019

Query: 1013 ISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +S+  R            +VQ+   ++K  ++  K  L +  + K+  ++  D +P GV+
Sbjct: 1020 LSQINRFALNALVKSYAPEVQKKYNAIKTHFQNEKRKLTEEHEEKLAILEKEDILPSGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVF+A KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG  VDIVLNPLGVPSRM
Sbjct: 1080 KLVKVFIATKRKLKVGDKMAGRHGNKGIVSVIVPEIDMPYTKDGRIVDIVLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E HLG     LG++I+ +  + K    +  LR  + ++       +  E I   
Sbjct: 1140 NIGQILEVHLGLIGKKLGEQIQEI-FEAKRADFVKELRQKMIEIADVAKLMNAKETIEKM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ ++  A  W  GV  +TPVF+G   E    +  +A +D  G++ LYDG TGE F   
Sbjct: 1199 SDEELIEYARDWSKGVKFATPVFEGVTAEEFEKLYELAKMDLDGKTELYDGRTGEKFKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++A+GAA
Sbjct: 1259 VTVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAHGAA 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y++I  G    + G PE+  VL KE+Q+LG+ +++ +   
Sbjct: 1319 HTLKEMLTIKSDDVEGRVAAYKAITKGEPIPQPGIPETLFVLTKELQSLGIDVEILDEVK 1378

Query: 1369 KNSA 1372
             +  
Sbjct: 1379 DDEE 1382


>gi|21666269|gb|AAM73635.1|AF389473_1 RNA polymerase beta subunit [Ehrlichia chaffeensis]
          Length = 1378

 Score = 1392 bits (3604), Expect = 0.0,   Method: Composition-based stats.
 Identities = 681/1380 (49%), Positives = 945/1380 (68%), Gaps = 38/1380 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ ++    +    G++  F+S+FPI    G A
Sbjct: 20   RISYAKSIDIKDSLTDLIKIQRDSYNAFIGID----QNTESGIKNIFQSMFPIQDLLGRA 75

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVSY    P++D  +C+ R +T++VP++I LR IV+ V            DE T  K
Sbjct: 76   VLEFVSYSIGEPQYDEYECIKRGITFSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 135

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 136  SIKYIKEQEVSIGDLPTMTSHGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 195

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + +IL TFY KI Y +
Sbjct: 196  SARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNNDILDTFYDKIRYVK 255

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P  A D   G ++S  L+D D G  ++++  ++T  + + L   G+    +  
Sbjct: 256  SEKGWVVPFVA-DRFRGVRLSHDLMDSD-GNVLVKANTRITLRMARKLANDGLTKYLVPF 313

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + GL VA D  +     + I AG+ I  + + ++    I ++       +    YI N
Sbjct: 314  NEIQGL-VANDFPDSTGNALIISAGENITSEHINKLELFNIGNLWFKDGPGI-VGPYILN 371

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    +S+F+   F+  KYDLSTVGR+K+N  L
Sbjct: 372  TLFLDKNVSYEDALFEIYKVLRSGESPSL-TYKSLFDGFIFEKGKYDLSTVGRIKLNDHL 430

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L+  +D+  + K+DII +IK LV LR+G+G++DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 431  GLNVSEDITVLTKDDIIHVIKKLVLLRDGEGSVDDIDHLGNRRVRSVGEFIENQFRIGIL 490

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 491  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 550

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSAL  GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+
Sbjct: 551  LSALSPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIES 610

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV  G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 611  PYRKVDKGVVTDKVEYLLAMQESNYYIADASATLDENNQFVDDMLYCRHDGNFVMVKREE 670

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP +GTGMES+VA
Sbjct: 671  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLIGTGMESIVA 730

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQRP
Sbjct: 731  AGSGTVVLAKRGGIVHRVDGLYIVIRAFDQEKNEY-LGVDIYNLRKFQRSNHNTCINQRP 789

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 790  LVKPGDYVKANDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 849

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+++E+ L ++D+ GI+ VGAEV+ GDILVGK+TP
Sbjct: 850  SIHIEEFECVVRDTTLGPEKIMRSVPDINEDSLSHLDDVGIVNVGAEVSAGDILVGKVTP 909

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 910  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPLDVEGTVVDVHVFVRRGVEENDRSLLIK 969

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +       +++D E  ++    Y  L  +L          G + +T    D ++  P+ +
Sbjct: 970  QMN-HGFIKERDYEIDVVSEYFYDELKRVLVSS-------GVQYNTQNIDDYLASIPKKE 1021

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE +   V+ LK ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1022 WWDINLSDEAMLLQVKDLKEKFDSMIQNAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1081

Query: 1081 KRPIQ---SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV-PSRMNVGQI 1136
            K  +Q      K  GRH  +G++SRI+P EDMP+L+DGTP DI+LN  GV   RMNVGQI
Sbjct: 1082 KHNLQAQEI--KWLGRHVIQGVISRIVPVEDMPYLEDGTPCDIILNSFGVYLLRMNVGQI 1139

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             ETHLGWA V LGKKI  ++ D      +S LR+FL +V       + I    D+ +L  
Sbjct: 1140 LETHLGWASVNLGKKIGHIL-DNLDELTVSHLRNFLYQVYDGQDLKDNIQSMSDEDLLVF 1198

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            AE+ + GVP++ PVF+G  +  I+++LR+ADLD SGQ  LYDG  GE FDR VTVGYIYM
Sbjct: 1199 AERLRDGVPMAAPVFEGPKDSQISNLLRLADLDVSGQVDLYDGRIGEKFDRKVTVGYIYM 1258

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL+H+V DK++ARS G Y LVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT
Sbjct: 1259 LKLHHLVDDKIHARSVGPYGLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLT 1318

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            +KSDD+VGR ++YESI+ G+  FE G PESFNV+VKE+++L L + L+  +   S ++++
Sbjct: 1319 VKSDDIVGRVKIYESIIKGDSNFECGIPESFNVMVKELRSLCLDVALKQDKDFLSNEVKD 1378


>gi|283362148|dbj|BAI65934.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362158|dbj|BAI65943.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362168|dbj|BAI65952.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
          Length = 1243

 Score = 1392 bits (3604), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1241/1243 (99%), Positives = 1241/1243 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVYEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243


>gi|283362178|dbj|BAI65961.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
          Length = 1243

 Score = 1392 bits (3603), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1240/1243 (99%), Positives = 1240/1243 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVYEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS LDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSFLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243


>gi|320105627|ref|YP_004181217.1| DNA-directed RNA polymerase subunit beta [Terriglobus saanensis
            SP1PR4]
 gi|319924148|gb|ADV81223.1| DNA-directed RNA polymerase, beta subunit [Terriglobus saanensis
            SP1PR4]
          Length = 1490

 Score = 1392 bits (3602), Expect = 0.0,   Method: Composition-based stats.
 Identities = 662/1342 (49%), Positives = 886/1342 (66%), Gaps = 72/1342 (5%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D  +C  R +TY+ PLK+T+RL ++D D  TG K+++D+KEQ ++ GD+PLM+++GTF
Sbjct: 143  KYDQGECEERGMTYSAPLKVTIRLKIYDKDPETGVKTLRDMKEQEVFFGDIPLMSQNGTF 202

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            ++ G +R++VSQLHRSPG+ F+    R+   GK      IIP +G W++ E+D K+ ++V
Sbjct: 203  IVNGTERVIVSQLHRSPGVFFETANNRSYFLGK------IIPYRGSWVEFEYDQKNTLYV 256

Query: 205  RIDRRRKVPVTSFLMALGM-DSEEILSTFY--PKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            RIDR+RK   T FL ALG+   EEIL TFY    I    +  FW      A  ++G K  
Sbjct: 257  RIDRKRKFLGTIFLRALGLRTDEEILKTFYTVDNINVRDQKLFWSVKPEGATNLLGVKPG 316

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             S+     G++V  + +K+++  L  L+   V  + + +    G   A D+V+  TGE+ 
Sbjct: 317  ESV--SVNGDEVAPTARKISASTLHKLRGGSVNEVSVENTEFDGAIFAADVVDLTTGELL 374

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
             EA        L +I  S   +  I + D  +    I NTL  D  +  ++AL++IYR +
Sbjct: 375  YEANQEATTDKLHKITQSGCTNFEIFFPDRDDVGNIITNTLKRDSVRKPEEALIEIYRKL 434

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDIIA 438
            RPGD  T   A ++F  +FFD  KYD S VGR+K N++L         D R +  ED   
Sbjct: 435  RPGDPPTLDTATALFEGMFFDPRKYDFSRVGRLKFNIKLYESQDATNLDKRTLTPEDFYG 494

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDS 497
             I+ L+ LR   G +DDID+LGNRRVR+VGE+++NQ+R+GL+RMER+IKE++S   ++ +
Sbjct: 495  TIRYLLKLRKNIGLVDDIDHLGNRRVRAVGELMENQFRIGLVRMERAIKEKMSVYQEMST 554

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             MP DLINAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG E
Sbjct: 555  AMPHDLINAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGFE 614

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV-- 615
            +RDVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYR+V   +V + V   
Sbjct: 615  VRDVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRRVKGSQVIDYVAVT 674

Query: 616  ----------------------------------------YLSAMEEENRYIAQANSSLD 635
                                                    YLSA EE+   IAQAN  LD
Sbjct: 675  NAGESGLRQGDPLEVAEAIKLKKQLKKDGKRVLETEPFSFYLSAWEEDRHTIAQANVELD 734

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             + +  ++LV  R  G  ILVP+ ++D++D SPKQ+VS+AASL+PFLE+DD+NR LMG N
Sbjct: 735  AEANIKDDLVIARRQGNFILVPKGEVDYVDVSPKQLVSVAASLVPFLEHDDANRALMGAN 794

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-- 753
            MQRQ+VPLL AEAPFVGTGME V A+ SGA I+A+R GIV+ VD+ RI++R         
Sbjct: 795  MQRQSVPLLVAEAPFVGTGMEGVTARDSGAVILARRNGIVDSVDSERIIVRVEGEHHPTQ 854

Query: 754  -PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G DIY+L KF+RSNQNTC+NQ+P+V+ GD V + ++IADGP T+ G+L LGRN+L
Sbjct: 855  LSREVGSDIYQLTKFKRSNQNTCINQKPIVRKGDRVLKGEVIADGPCTEQGELGLGRNVL 914

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW GYNFED++LISE++V ED +TSIHIEEFE+ ARDTKLGPEEITRDIPNVSE  
Sbjct: 915  VAFMPWRGYNFEDAILISEKLVREDYYTSIHIEEFEIEARDTKLGPEEITRDIPNVSEHA 974

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L+++DE GII +GA+++  DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRD SL  P
Sbjct: 975  LRDLDESGIIRIGAKISHNDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVRDASLTCP 1034

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
             G+ GTVVDVRIF+R G +K+ER+ ++E EQIE L R+  DE  IL      RL  IL  
Sbjct: 1035 PGIEGTVVDVRIFSRKGQEKDERAKAIETEQIEKLERNLADEIRILTDERLKRLEGILGA 1094

Query: 993  QNAV-------SGPKGFKKSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQYE 1043
            +          +  K   K  +L  D I         +     +D +V   ++ ++    
Sbjct: 1095 KEVQADLHDERTNKKLLSKGDLLDRDTIELISTRNLKRIRYADKDPRVNEQIDEIEEMTS 1154

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                +L     +KI K+Q GD++ PGV+++VKV++AMKR +  GDKMAGRHGNKG+++RI
Sbjct: 1155 RQIDVLRKITNDKIGKLQKGDELSPGVIKMVKVYIAMKRKLSVGDKMAGRHGNKGVIARI 1214

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LGKK+  L    +   
Sbjct: 1215 LPEEDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAFELGKKVAELAAQSQKAN 1274

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            +I   R    +     +   ++ + DD   +RVA   K G+   T VFDGA E  I ++L
Sbjct: 1275 EI---REIFSEAFKNTAALNQLLELDDTQTIRVAAGMKRGIWFGTAVFDGASEHEIKALL 1331

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
              A L  SG++ L+DG+TG+ F++P TVGYIYMLKL+H+V DK++ARS G YSL+TQQPL
Sbjct: 1332 LAAGLPSSGKTELFDGMTGDVFEQPATVGYIYMLKLSHLVDDKIHARSIGPYSLITQQPL 1391

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GRT++YE+IV G    E G 
Sbjct: 1392 GGKAQFGGQRFGEMEVWALEAYGAAYILQELLTSKSDDVFGRTKIYEAIVKGEAAIEPGV 1451

Query: 1344 PESFNVLVKEMQALGLSIDLEN 1365
            PESFNVL++E+Q+L L ++L  
Sbjct: 1452 PESFNVLIRELQSLCLDVELVK 1473



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 39/89 (43%), Positives = 48/89 (53%), Gaps = 8/89 (8%)

Query: 12 RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
          R R  F K P  I IP+LIEVQ+ SY+ FL M+  P ER + GLQ+ F SVFPIT F   
Sbjct: 9  RSRLDFSKIPTAIQIPNLIEVQRRSYERFLQMDKLPQEREDNGLQSVFTSVFPITDFRNV 68

Query: 72 AMLEFVSYEFDPPKFDVDDCL---WRDLT 97
          + LEFV Y          +C     + L 
Sbjct: 69 SELEFVDYSIGN-----WECKCGYLKGLN 92


>gi|283362218|dbj|BAI65997.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
 gi|283362238|dbj|BAI66015.1| partial DNA-directed RNA polymerase subunit beta [Candidatus
            Liberibacter asiaticus]
          Length = 1243

 Score = 1392 bits (3602), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1243/1243 (100%), Positives = 1243/1243 (100%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW
Sbjct: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE
Sbjct: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243


>gi|313683392|ref|YP_004061130.1| DNA-directed RNA polymerase subunit beta [Sulfuricurvum kujiense DSM
            16994]
 gi|313156252|gb|ADR34930.1| DNA-directed RNA polymerase subunit beta [Sulfuricurvum kujiense DSM
            16994]
          Length = 1381

 Score = 1378 bits (3567), Expect = 0.0,   Method: Composition-based stats.
 Identities = 607/1383 (43%), Positives = 890/1383 (64%), Gaps = 34/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I++P+L+++Q++SY+ FLM++    +R   G++  F+SVFPI      
Sbjct: 10   RLRVDFAKTPQQIEVPNLLQLQQSSYESFLMLD--QKDRTKSGIERVFQSVFPIHDSQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE++  E   PK+ V +C+ R LTY+V L++  RL+++D DE T  K+ +KDIKEQ+I
Sbjct: 68   LSLEYLGSEVGRPKYTVRECMERGLTYSVSLRMKTRLMIWDRDENTKEKTGVKDIKEQTI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT   +FVI G++R+VV+QLHRSPG+ F  ++   + S K+++  +IIPD+G 
Sbjct: 128  FIRDIPLMTDRTSFVINGVERVVVNQLHRSPGVIFKEEESTTAGS-KMIFTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KDI+++RI++RRKVPVT    ALG   ++IL  FYP        + +     
Sbjct: 187  WLYFEYDPKDILYMRINKRRKVPVTIMFRALGYSKQDILKMFYPLQKIRVEENKYLMDFD 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                    ++   L+D + G+ ++ +GK+L++   + L  +GVK +    + L   ++AE
Sbjct: 247  PEQFA--GRLGYDLIDSE-GKLLVAAGKRLSTKKAEKLISEGVKAIQYPIETLIERHLAE 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ ETGE+  +    +DE  L+++  + +++  I    +   ++ I N  + D +   
Sbjct: 304  PIIDAETGEVMFDTMTQLDETKLKKMVEAGVKEFVIANDLAEGYDSAIINAFIADADSLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+   N LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLRQTEIIEDENDLAAIRIYKVMRPGEPVTKEAAKVFVNQLFFDPERYDLTRVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII  +K +V ++NG+G IDD D+LGNRR+RS+GE+L N+   G
Sbjct: 424  KLGLNIPEYVTVLTNEDIINTVKYVVKVKNGQGHIDDRDHLGNRRIRSIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++IK+++S++   +  +MP DLIN+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 484  LVKMQKAIKDKLSTMSGPTTELMPHDLINSKMITSTIMEFFSGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++++VN +G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATYSKVNEHG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY  V DG VT++VVYL+A +EE + IA A+S +D+ G+F ++LV  R  GE  LV
Sbjct: 604  FIEAPYNVVKDGVVTDEVVYLTATQEEGKVIAAASSRIDDKGNFLDDLVETRQDGEYPLV 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +  +  D +P  VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E
Sbjct: 664  SPKDCELRDLTPHMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPMVGTGVE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +VA+ S   + A+R+GIVE+VD+  I I   + D     + +D Y L K  R+NQNT  
Sbjct: 724  KLVARDSWECVKAERSGIVEKVDSKHIYIMGEDED----GTFIDYYPLQKNLRTNQNTTF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q+P+VK G  V +  IIADGP+ D G+LALG N LVAFMPW+GYNFED++++SERM+ E
Sbjct: 780  LQKPIVKQGQMVTKGQIIADGPNMDKGELALGINALVAFMPWNGYNFEDAIVMSERMIRE 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E  AR+ K G EEITRDIPNV ++ L ++D+ GI+ +G  V  G ILVG
Sbjct: 840  DAFTSVHIYEKEAEARELKHGVEEITRDIPNVRDDELAHLDDSGIVKIGTYVKGGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL     + G VVDV++F + G DK+ R+
Sbjct: 900  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCTPSMEGVVVDVKVFTKKGYDKDPRT 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG----FKKSTVLSSDL 1012
            + +E+++ + L R+  D  +++D+    R++ +L     +S        +K    +  D 
Sbjct: 960  LELEKQERDELEREHYDRLLMIDKEEMLRIISLLTKHPLLSDVSINGNEYKAGENVKGDD 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + E  R           + +Q      K  ++  K    D  + K+  ++  D +P GV+
Sbjct: 1020 LKEVNRFAMNNVVKAFSDDIQEKYNQTKNHFQKEKKKFRDEHEEKLSILEKDDILPNGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP++ +G  VD+ LNPLGVPSRM
Sbjct: 1080 KFVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPQVDMPYMANGRSVDVCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL---EKVIGTGSHTEKISDY 1188
            N+GQI E HLG     LG +I+ +  + K    IS LR  +     V G  +  + + + 
Sbjct: 1140 NIGQILEMHLGMVGKELGFQIQDI-FEAKQKEFISELREKMITFADVAGLMNAAKLLGEM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            DD ++L  A+ W  GV  +TP+F+G  E     +  +A LD  G+  LYDG TG+     
Sbjct: 1199 DDQTLLGYAQDWSKGVKFATPIFEGVTEAEFAKLFELAKLDTDGKMELYDGKTGDKMKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1259 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAS 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLTIKSDDV GR R Y++I  G     +G PE+  VL KE+Q+L L I++ +   
Sbjct: 1319 AVLKEMLTIKSDDVDGRVRAYKAITKGESVPASGIPETLFVLTKELQSLALDIEIFDEVD 1378

Query: 1369 KNS 1371
             N 
Sbjct: 1379 DNE 1381


>gi|222823479|ref|YP_002575053.1| DNA-directed RNA polymerase, beta chain [Campylobacter lari RM2100]
 gi|254765279|sp|B9KFG7|RPOB_CAMLR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|222538701|gb|ACM63802.1| DNA-directed RNA polymerase, beta chain [Campylobacter lari RM2100]
          Length = 1377

 Score = 1376 bits (3561), Expect = 0.0,   Method: Composition-based stats.
 Identities = 616/1383 (44%), Positives = 886/1383 (64%), Gaps = 37/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F   P+ IDIP+L+++QK S+D+FL ++    +    G++  FKS+FPI      
Sbjct: 9    RLRIDFSNVPQQIDIPNLLQLQKKSFDYFLNID---AKNSESGIEKVFKSIFPIHDPQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  IKDIKEQ I
Sbjct: 66   LSLEYVSSEVGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKIGIKDIKEQEI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 126  YIREIPLMTDRISFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVP+T    ALG   ++I+  FYP      + D +    +
Sbjct: 185  WLYFEYDAKDVLYVRINKRRKVPITILFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D +   +V   L D + G  + ++GK++T    + L + G+K++    + L   Y+A 
Sbjct: 245  PNDFL--DRVEYDLKD-EKGNIIHQAGKRMTKKKAEQLVKDGIKWVEYPVEILTNRYLAN 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I+N ETGE+  ++  ++DE  L +I     +   I    +   +A I N+ + D     
Sbjct: 302  PIINKETGEVLFDSLTLLDESKLAKIKEQ--KTFDIANDLANGVDAAIINSFIQDNETLK 359

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 360  LLKQTENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L LDTP+ V  +  EDI+   K L+ ++NG+G IDD D+LGNRR+RS+GE+L N+  +G
Sbjct: 420  KLGLDTPEYVTVLTNEDIVKTAKYLIKVKNGRGHIDDRDHLGNRRIRSIGELLANELHVG 479

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + DID VMP DLIN K +   + EFF   QLSQ  +  N LS +T
Sbjct: 480  LAKMQKAIRDKFTALNTDIDKVMPYDLINPKTITVTIMEFFTGGQLSQFMDQTNPLSEVT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 540  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNDLG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PY+KV +GKV+N++VYL+A +EE   IA A++ +DE GS  EE V  R  GE IL 
Sbjct: 600  FVEAPYKKVENGKVSNEIVYLTATQEEGLVIAAASTKIDEKGSIVEEFVEARQDGETILA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL A+AP VGTGME
Sbjct: 660  RREEVHLIDLCSGMIVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTAQAPIVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  AI AKRAGIVE+VD   I I   +     +   +D Y++ K  R+NQNT  
Sbjct: 720  KIIARDAWEAIKAKRAGIVEKVDNKNIFILGEDE----NGPFIDHYKMEKNLRTNQNTTF 775

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK G+ V+   IIADGPS D G+LA+G+N L+AFMPWHGYN+ED+++ISE+++ E
Sbjct: 776  TQHPIVKKGEFVQVGQIIADGPSMDQGELAIGKNALIAFMPWHGYNYEDAIVISEKILRE 835

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E EV AR+ K G EEIT+DIPNV E+ L ++DE GI  +G  + PG ILVG
Sbjct: 836  DTFTSVHIYEKEVEARELKDGVEEITKDIPNVKEDDLAHLDESGIAKIGTHIKPGMILVG 895

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K+ R+
Sbjct: 896  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASMEGVVVDVKIFTKKGYEKDARA 955

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK----GFKKSTVLSSDL 1012
            I    E+   L ++  D  +++DR    R+  +L      S  +     +KK   +    
Sbjct: 956  IKAYDEEKLNLEKEHHDRLLMMDREETLRVCSLLSKSALNSDEEINGQKYKKGAKVDIKE 1015

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           + VQ+  E LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1016 LEKINRFALNSLVKAYSKDVQKEYEDLKNHFQNEKKKLKSEHDEKLEILEKDDILPSGVV 1075

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L DG P+DI LNPLGVPSRM
Sbjct: 1076 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYLPDGRPIDIALNPLGVPSRM 1135

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS---HTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    I  LR+ + ++          + +   
Sbjct: 1136 NIGQILESHLGIVGMRLGDQIQEI-FDKKQKDFIKQLRTKILEICSVSRLTLEKKFVESL 1194

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            +D+ ++  A  W  GV  +TPVF+G   E  + +  MA +   G+S LYDG TGE     
Sbjct: 1195 NDEQLISYARDWARGVKFATPVFEGVTVEEFSKLFEMAKIAMDGKSELYDGRTGEKMAER 1254

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1255 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1314

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1315 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1374

Query: 1369 KNS 1371
             N 
Sbjct: 1375 NNE 1377


>gi|86151640|ref|ZP_01069854.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 260.94]
 gi|315124021|ref|YP_004066025.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni ICDCCJ07001]
 gi|85841269|gb|EAQ58517.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 260.94]
 gi|315017743|gb|ADT65836.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni ICDCCJ07001]
          Length = 1375

 Score = 1376 bits (3561), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITATIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|224372232|ref|YP_002606604.1| DNA-directed RNA polymerase subunit beta [Nautilia profundicola AmH]
 gi|223589582|gb|ACM93318.1| DNA-directed RNA polymerase, beta subunit [Nautilia profundicola AmH]
          Length = 1379

 Score = 1376 bits (3561), Expect = 0.0,   Method: Composition-based stats.
 Identities = 595/1385 (42%), Positives = 895/1385 (64%), Gaps = 38/1385 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+I+DIP+L+ +Q+ S+  F+ +          G+   FKS+FPIT     
Sbjct: 10   RLRLDFSKIPQILDIPNLLHLQQNSFQDFINLKEP----EKSGIHKVFKSMFPITDAQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+   EF  PK+ V +C+ + LTY++P++I +RLIV + DE TG K  IKDIKEQ++
Sbjct: 66   ITLEYAGIEFKKPKYTVRECMEKGLTYSIPIRIKIRLIVHERDEKTGEKIGIKDIKEQTL 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ D+PLMT+  +F+I G++R++V+QLHRSPG+ F  ++ +   S KLLY+ +IIPD+G 
Sbjct: 126  YIRDIPLMTERTSFIINGVERVIVNQLHRSPGVIFKQEEAQN--SNKLLYSAQIIPDRGS 183

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KD+++VR+++RRKVPVT  L A+    E+IL  FYP +    + + +     
Sbjct: 184  WVYFEYDVKDVLYVRVNKRRKVPVTILLRAMDYSKEDILRMFYPIVDIKIQDNKFLMSTK 243

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A   +   K+   L D D G  ++ +GK+L+   LK ++E+ ++++    + L   ++AE
Sbjct: 244  A---LQSGKLDYDLKDPD-GNIILAAGKRLSDRKLKKIQEE-LEYVEYPIEVLLDRHLAE 298

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN--- 367
             I +  TGE+  +   V++E  L++I  S+I D  I+   +   +  I      D     
Sbjct: 299  PIYDPVTGEVLFDTLTVLNEVKLKKIIESQIEDFKIVNDLAEGVDDSILRAFHQDIETLK 358

Query: 368  ---------KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+ +T   A+ +F  LFFD ++YDL+ VGR+KMN 
Sbjct: 359  ILRQVEGIENENDLARIRIYKVMRPGEPATPQTAKELFEKLFFDPERYDLTKVGRMKMNH 418

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ PDDV  +  +DII  I+ L+ ++NG G IDD D+LGNRR+RS+GE+L N+ + G
Sbjct: 419  KLGLNVPDDVTVLTYQDIIKTIQYLIGVKNGVGQIDDRDHLGNRRIRSIGELLANRLQDG 478

Query: 479  LLRMERSIKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            L +M+++I++++++  +++ ++P DL+N K V + + +FF + QLSQ  +  N LS + H
Sbjct: 479  LAKMQKTIRDKMTTVTNVNDLLPMDLVNTKLVTTTILDFFATGQLSQFMDQTNPLSEVAH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG+GGV R RAG E+RDVHP+HYGRICP ET EG NIGLV++L+++A+VN +GF
Sbjct: 539  KRRLSALGEGGVTRERAGFEIRDVHPSHYGRICPIETPEGQNIGLVNTLSTYAKVNEFGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCRCAGEEILV 656
            IE PYR V DG+VT++VVYL+A +EE + IA A+  +DE+ G   ++L+  R  GE ILV
Sbjct: 599  IEAPYRVVKDGRVTDEVVYLTATQEEEKTIAPASVKIDEETGEILDDLIEARKDGEIILV 658

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             ++++D  D +PK +V + ASLIPFLE+DD+NR LMG NMQRQ VPLL++EAP VGTGME
Sbjct: 659  DKKEVDLYDLNPKMIVGVGASLIPFLEHDDANRALMGSNMQRQGVPLLRSEAPMVGTGME 718

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              VA+ +   + AKR G V +VDA  I I   +     + + +D Y L K+ R+NQNTC 
Sbjct: 719  KYVARDAWQIVKAKRGGKVIKVDAKNIYILGEDE----NGAYIDHYGLEKYLRTNQNTCF 774

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +QRP+VK GD V+  D+IADGP+ D G+L +G+N++VAFMPW+GYNFED++++SER++ +
Sbjct: 775  DQRPIVKEGDVVKAGDVIADGPNMDNGELGVGKNVMVAFMPWNGYNFEDAIVLSERIIKD 834

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DV+TS+HI E     R+ K G EEIT DIP V  E L ++DE GII +G  V PG ILVG
Sbjct: 835  DVYTSVHIYEEVCEVRELKHGLEEITADIPGVKPEYLTHLDESGIIKIGTYVKPGMILVG 894

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KI+PKG+   TPEE+LL++IFG+K+  V ++SL  P+ + G V+DV+++ + G + +ER+
Sbjct: 895  KISPKGDVKPTPEERLLKSIFGDKSGHVVNSSLYAPASMEGVVIDVKVYTKKGYELDERA 954

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP----KGFKKSTVLSSDL 1012
             +   E+   +     ++  I+D+     L  +L  +  +       K +K    L  + 
Sbjct: 955  KAAYDEEKAKIEEIYKNQLSIIDKEEVLALANLLSSKPLIKDVELNGKTYKAGEKLPKEE 1014

Query: 1013 ISEYPRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    +          D+   +  E++K +Y   K  +   +  K+E ++  D +P GV 
Sbjct: 1015 LVNINKFLLLSLVEYFDDATVQEFENIKAKYLNEKDNIRKEYDEKLEVLERDDILPNGVA 1074

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR I+ GDKMAGRHGNKGIVS I+P EDMP+++DG  VD+VLNPLGVPSRM
Sbjct: 1075 KMVKVYIANKRKIKVGDKMAGRHGNKGIVSIIVPQEDMPYMEDGRTVDVVLNPLGVPSRM 1134

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKAN---GDISPLRSFLEKVIGTGSHTEKISDY 1188
            N+GQI E HLG     LG++I+ ++ + + +      + ++  +E       + + +   
Sbjct: 1135 NIGQILEVHLGLVGKNLGRQIEEILKEKQNDMMDKLRNKMKEIVEVAHFGEHYKDFLDSL 1194

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             ++ +L+ A+ W  GV  +TPVF+G +EE    +  +A + E G++ LYDG TGEP    
Sbjct: 1195 TNEELLKYAQDWAKGVKFATPVFEGVNEEEFKKLFELAGIPEDGKTQLYDGRTGEPIKER 1254

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V DKV+ARS G YSL+TQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1255 VNVGYMYMLKLHHLVDDKVHARSIGPYSLITQQPVGGKALFGGQRFGEMEVWALEAYGAA 1314

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y L+EMLT KSDDV GR + Y ++  G +    G  E+F VL KE++ALGL ++      
Sbjct: 1315 YNLKEMLTTKSDDVEGRNKAYRALTRGENVPIEGLSETFFVLSKELRALGLDLEFYKKEE 1374

Query: 1369 KNSAK 1373
             N   
Sbjct: 1375 DNEEI 1379


>gi|121613040|ref|YP_001000185.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni 81-176]
 gi|158513882|sp|A1VYJ4|RPOB_CAMJJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|121504217|gb|EAQ73187.2| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 81-176]
          Length = 1378

 Score = 1375 bits (3559), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 12   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 186  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 246  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 303  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 360

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 361  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 420

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 421  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 480

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 481  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 540

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 541  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 600

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 601  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 660

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 661  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 720

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 721  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 776

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 777  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 836

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 837  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 896

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 897  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 956

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 957  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1016

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1017 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1076

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1077 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1136

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D +    +  LR+ + ++       S  E I   
Sbjct: 1137 NIGQILESHLGLIGLRLGDQIQEI-FDRRQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1195

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1196 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1255

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1256 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1315

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1316 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1375

Query: 1369 KNS 1371
             N 
Sbjct: 1376 DNE 1378


>gi|167005143|ref|ZP_02270901.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni 81-176]
          Length = 1375

 Score = 1375 bits (3558), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D +    +  LR+ + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FDRRQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|157414771|ref|YP_001482027.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni 81116]
 gi|182676555|sp|A8FKR3|RPOB_CAMJ8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157385735|gb|ABV52050.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 81116]
 gi|307747410|gb|ADN90680.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni M1]
 gi|315931081|gb|EFV10055.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 327]
          Length = 1375

 Score = 1375 bits (3558), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|205355351|ref|ZP_03222122.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni CG8421]
 gi|205346585|gb|EDZ33217.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni CG8421]
          Length = 1378

 Score = 1374 bits (3557), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 12   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 186  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 246  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 303  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 360

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 361  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 420

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 421  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 480

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 481  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 540

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 541  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 600

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 601  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 660

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 661  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 720

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 721  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 776

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 777  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 836

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 837  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 896

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 897  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 956

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 957  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1016

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1017 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1076

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1077 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1136

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1137 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLANEKEFIKSL 1195

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1196 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1255

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1256 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1315

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1316 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1375

Query: 1369 KNS 1371
             N 
Sbjct: 1376 DNE 1378


>gi|57237532|ref|YP_178546.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni
            RM1221]
 gi|148925857|ref|ZP_01809544.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni CG8486]
 gi|81353964|sp|Q5HVY9|RPOB_CAMJR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|57166336|gb|AAW35115.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            RM1221]
 gi|145844843|gb|EDK21947.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni CG8486]
          Length = 1378

 Score = 1374 bits (3557), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 12   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 186  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 246  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 303  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 360

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 361  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 420

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 421  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 480

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 481  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 540

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 541  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 600

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 601  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 660

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 661  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 720

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 721  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 776

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 777  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 836

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 837  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 896

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 897  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 956

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 957  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1016

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1017 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1076

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1077 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1136

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1137 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLANEKEFIKSL 1195

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1196 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1255

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1256 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1315

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1316 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1375

Query: 1369 KNS 1371
             N 
Sbjct: 1376 DNE 1378


>gi|218562133|ref|YP_002343912.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni NCTC 11168]
 gi|9297126|sp|Q46124|RPOB_CAMJE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|112359839|emb|CAL34626.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni NCTC 11168]
          Length = 1378

 Score = 1374 bits (3557), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 12   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 186  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 246  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 303  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 360

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 361  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 420

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 421  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 480

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 481  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 540

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 541  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 600

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 601  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 660

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 661  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 720

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 721  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 776

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 777  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 836

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 837  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 896

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 897  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 956

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 957  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1016

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1017 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1076

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1077 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1136

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1137 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKILEICSIPRLANEKEFIKSL 1195

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1196 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1255

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1256 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1315

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1316 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1375

Query: 1369 KNS 1371
             N 
Sbjct: 1376 DNE 1378


>gi|315057898|gb|ADT72227.1| DNA-directed RNA polymerase beta subunit [Campylobacter jejuni subsp.
            jejuni S3]
          Length = 1375

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1134 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLANEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|86149044|ref|ZP_01067276.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni CF93-6]
 gi|85840402|gb|EAQ57659.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni CF93-6]
 gi|315928193|gb|EFV07510.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni DFVF1099]
          Length = 1375

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1134 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKILEICSIPRLANEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|284925745|gb|ADC28097.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni IA3902]
          Length = 1378

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 12   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 186  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 246  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 303  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 360

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 361  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 420

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 421  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 480

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 481  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 540

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 541  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 600

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 601  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 660

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 661  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 720

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 721  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 776

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 777  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 836

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 837  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 896

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 897  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 956

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 957  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1016

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1017 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1076

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1077 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1136

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1137 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKILEICSIPRLANEKEFIKSL 1195

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1196 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1255

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1256 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1315

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +    G PE+F VL  E+++L L +++ +   
Sbjct: 1316 HTLREMLTIKSDDVEGRFSAYKALTKGENVPAIGIPETFFVLTNELKSLALDVEIFDKDE 1375

Query: 1369 KNS 1371
             N 
Sbjct: 1376 DNE 1378


>gi|283955900|ref|ZP_06373390.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 1336]
 gi|283792560|gb|EFC31339.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 1336]
          Length = 1375

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKTGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FDRKQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|86153591|ref|ZP_01071794.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni HB93-13]
 gi|85842552|gb|EAQ59764.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni HB93-13]
          Length = 1375

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1383 (44%), Positives = 882/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+   L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCAFLSKAPLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D +    +  LR+ + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FDRRQKDFLKELRAKMLEICSIPRLASEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|57242438|ref|ZP_00370376.1| DNA-directed RNA polymerase, beta subunit [Campylobacter upsaliensis
            RM3195]
 gi|57016723|gb|EAL53506.1| DNA-directed RNA polymerase, beta subunit [Campylobacter upsaliensis
            RM3195]
          Length = 1377

 Score = 1374 bits (3556), Expect = 0.0,   Method: Composition-based stats.
 Identities = 609/1383 (44%), Positives = 886/1383 (64%), Gaps = 37/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R R  F    + I+IP+L+++QKAS+D+FL +    D +   G++  FKS+FPI      
Sbjct: 9    RFRVDFSNISKQIEIPNLLQLQKASFDYFLNL---SDTKSESGIEKVFKSIFPIHDPQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  IKDIKEQ I
Sbjct: 66   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGIKDIKEQEI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 126  FIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVP+T    ALG   ++I+  FYP      + D +    +
Sbjct: 185  WLYFEYDAKDVLYVRINKRRKVPITMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D +   +V   + D + G+ V  +GK+LT   ++ L + G+K++    + L   Y+A 
Sbjct: 245  PNDFV--DRVEYDIKD-EKGKIVHPAGKRLTKKKIEQLIKDGLKWVEYPLEVLINRYLAS 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             IV+ ++GE+  ++  +IDE  L +I     +   I    +   +A I N+ + D     
Sbjct: 302  PIVDKQSGEVLFDSLTLIDEGKLAKIKEQ--KSFNIANDLANGVDAAIINSFIQDNETLK 359

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 360  LLKQSENLEDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L LD P+    +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 420  KLALDVPEYTTVLTNEDIIKTAKYLIKVKNGKGYIDDRDHLGNRRIRSIGELLANELHLG 479

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ S  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 480  LTKMQKAIRDKFSSLNADLDKVMPYDLINPKMITTTILEFFTGGQLSQFMDQTNPLSEVT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 540  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKV++++VYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 600  FVEAPYRKVENGKVSDEIVYLTATQEEGLFIAPASTKIDAKGNIIEEFVEARQDGETILA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL + AP VGTGME
Sbjct: 660  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTSSAPIVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  AI A+R G++E+VD   I I   +         +D Y L K  R+NQNT  
Sbjct: 720  RIIARDAWEAIKARRGGMIEKVDNKSIFILGEDEK----GPFIDHYSLEKNLRTNQNTNY 775

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 776  VQHPIVKKGDVVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 835

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV E+ + ++DE GI  +G  + PG ILVG
Sbjct: 836  DTFTSVHIYEKEIEARELKDGVEEITKDIPNVKEDDVAHLDESGIAKIGTHIKPGMILVG 895

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 896  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRT 955

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEIL----CGQNAVSGPKGFKKSTVLSSDL 1012
            +    ++  +L ++  D  +++DR    R+  +L           G K +KK   +S + 
Sbjct: 956  LKSYDKEKIVLEKEYHDRLLMMDREEMLRVYALLAKAPLNSEQKVGSKTYKKGQKVSKED 1015

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           ++VQ+  E LK  ++  K   +     K+E ++  D +P GV+
Sbjct: 1016 LEKVNRFILTSLIKAYSKEVQKQYEDLKNHFQNEKKKFKAEHDEKLEILEKDDILPSGVV 1075

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1076 KLVKIYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1135

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG++I+ L  D K    I  LR  + ++       +    +   
Sbjct: 1136 NIGQILESHLGLVGLKLGEQIQEL-FDKKQKDFIKSLRKKMLEICSIPRLANEKAFVESL 1194

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E    + +MA +D  G++ LYDG TGE     
Sbjct: 1195 SDEELLNYARDWSKGVKFATPVFEGVNIEEFAELFKMAKVDMDGKTELYDGRTGEKIAER 1254

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1255 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1314

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1315 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1374

Query: 1369 KNS 1371
            KN 
Sbjct: 1375 KNE 1377


>gi|315639008|ref|ZP_07894178.1| DNA-directed RNA polymerase subunit beta [Campylobacter upsaliensis
            JV21]
 gi|315480920|gb|EFU71554.1| DNA-directed RNA polymerase subunit beta [Campylobacter upsaliensis
            JV21]
          Length = 1377

 Score = 1374 bits (3555), Expect = 0.0,   Method: Composition-based stats.
 Identities = 608/1383 (43%), Positives = 886/1383 (64%), Gaps = 37/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R R  F    + I+IP+L+++QKAS+D+FL +    D +   G++  FKS+FPI      
Sbjct: 9    RFRVDFSNISKQIEIPNLLQLQKASFDYFLNL---SDTKSESGIEKVFKSIFPIHDPQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  IKDIKEQ I
Sbjct: 66   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGIKDIKEQEI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 126  FIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 184

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVP+T    ALG   ++I+  FYP      + D +    +
Sbjct: 185  WLYFEYDAKDVLYVRINKRRKVPITMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 244

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D +   +V   + D + G+ V  +GK+LT   ++ L + G+K++    + L   Y+A 
Sbjct: 245  PNDFV--DRVEYDIKD-EKGKIVHPAGKRLTKKKIEQLIKDGLKWVEYPLEVLINRYLAS 301

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             IV+ ++GE+  ++  +IDE  L +I     +   I    +   +A I N+ + D     
Sbjct: 302  PIVDKQSGEVLFDSLTLIDEGKLAKIKEQ--KSFNIANDLANGVDAAIINSFIQDNETLK 359

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 360  LLKQSENLEDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L LD P+    +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 420  KLALDVPEYTTVLTNEDIIKTAKYLIKVKNGKGYIDDRDHLGNRRIRSIGELLANELHLG 479

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ S  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 480  LTKMQKAIRDKFSSLNADLDKVMPYDLINPKMITTTILEFFTGGQLSQFMDQTNPLSEVT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 540  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKV+++VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 600  FVEAPYRKVENGKVSDEVVYLTATQEEGLFIAPASTKIDAKGNIIEEFVEARQDGETILA 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL + AP VGTGME
Sbjct: 660  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTSSAPIVGTGME 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ A+R G++E+VD   I I   +         +D Y L K  R+NQNT  
Sbjct: 720  RIIARDAWEAVKARRGGVIEKVDNKSIFILGEDEK----GPFIDHYSLEKNLRTNQNTNY 775

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 776  VQHPIVKKGDVVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 835

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV E+ + ++DE GI  +G  + PG ILVG
Sbjct: 836  DTFTSVHIYEKEIEARELKDGVEEITKDIPNVKEDDVAHLDESGIAKIGTHIKPGMILVG 895

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 896  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 955

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEIL----CGQNAVSGPKGFKKSTVLSSDL 1012
            +    ++  +L ++  D  +++DR    R+  +L           G K +KK   +S + 
Sbjct: 956  LKSYDKEKIVLEKEYHDRLLMMDREEMLRVYALLAKAPLNSEQKVGSKTYKKGQKVSKED 1015

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           ++VQ+  E LK  ++  K   +     K+E ++  D +P GV+
Sbjct: 1016 LEKVNRFILTSLIKAYSKEVQKQYEDLKNHFQNEKKKFKAEHDEKLEILEKDDILPSGVV 1075

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1076 KLVKIYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1135

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG++I+ L  D K    I  LR  + ++       +    +   
Sbjct: 1136 NIGQILESHLGLVGLKLGEQIQEL-FDKKQKDFIKSLRKKMLEICSIPRLANEKAFVESL 1194

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E    + +MA +D  G++ LYDG TGE     
Sbjct: 1195 SDEELLNYARDWSKGVKFATPVFEGVNIEEFAELFKMAKVDMDGKTELYDGRTGEKIAER 1254

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1255 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1314

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1315 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1374

Query: 1369 KNS 1371
            +N 
Sbjct: 1375 ENE 1377


>gi|254797031|ref|YP_003081868.1| DNA-directed RNA polymerase, beta subunit [Neorickettsia risticii
            str. Illinois]
 gi|254590263|gb|ACT69625.1| DNA-directed RNA polymerase, beta subunit [Neorickettsia risticii
            str. Illinois]
          Length = 1358

 Score = 1373 bits (3553), Expect = 0.0,   Method: Composition-based stats.
 Identities = 646/1369 (47%), Positives = 916/1369 (66%), Gaps = 36/1369 (2%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
             D PDL++VQK SY  F+    A        +   F SVFP+    G A LEFVS     
Sbjct: 14   FDFPDLVKVQKDSYASFVGGGDAVSS-----INDIFASVFPVNDGYGRASLEFVSCRMGE 68

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF-------TGAKSIKDIKEQSIYMGDLP 136
            PK D   C+ R +TY+ PL+  LRL+VF  +         +   ++KD++EQ IYMGD+P
Sbjct: 69   PKHDEYGCVERGITYSAPLRAILRLVVFGDETSGEGGEGVSTEPAVKDVREQEIYMGDIP 128

Query: 137  LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
            +M+K+GTF+I G++R+VVSQ+HR+PG+ FD+DK R+ +SGKL Y  RIIP +G W+D EF
Sbjct: 129  IMSKNGTFIINGVERVVVSQMHRAPGVFFDNDKARS-ISGKLNYIARIIPYRGSWLDFEF 187

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D+KD+++ RID++RK+PVT  L ALG+ +++I + F          D         +   
Sbjct: 188  DAKDVLYFRIDKKRKLPVTLLLRALGLSNKDIFAQFCEVSECRLTKDGKWTVCFVPERFK 247

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            G ++   L++ +TGE V+  G +++  L ++L  KG+++  +  + +  +Y+A+D+V+ +
Sbjct: 248  GVRLQYDLINAETGELVLAKGNRISIVLARNLYAKGLRYCYMDLEVMKDMYLADDLVSAK 307

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             GE+ +  G  + ++ + ++   ++  I ++ +       YI +T++       ++A+L 
Sbjct: 308  -GEVLLPHGTRLTKEHVAKLEFLDVDSIKLVEL----KGNYIFSTVLQYDC-SYEEAMLS 361

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IYRV+RPG++ +   AE +F  LFF  ++YDL  VGR+++N + NL   + +  + KEDI
Sbjct: 362  IYRVIRPGEIPSIESAEKLFESLFFSPERYDLLNVGRIRLNAKFNLSHDESLTVLTKEDI 421

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
               ++ L  L+   G +DDID+LGNRRVRSVGE + NQ+R+GL+RM + I E +++ D D
Sbjct: 422  FCTVRELALLQREVGDVDDIDHLGNRRVRSVGEFMDNQFRIGLVRMAKVIVENMATADFD 481

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +VMP ++IN+K + + + EFF SS LSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 482  TVMPCEMINSKILGAVIREFFMSSALSQFMDQTNPLSEITHKRRISALGPGGLNRGRAGF 541

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            E+RDVH THYGRIC  ET EG  IGL++SL  +A++N YGFIETPYR V DG+VT++V Y
Sbjct: 542  EVRDVHTTHYGRICATETPEGATIGLINSLAIYAKINKYGFIETPYRYVRDGRVTDEVTY 601

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            LSA++E    I QA+  +DE+G   ++LV+CR   E + +PR ++ F D S KQ+VS+AA
Sbjct: 602  LSAIDEIKANICQASVRVDEEGYILDDLVYCRRNYENVFIPRSEVQFADVSAKQIVSVAA 661

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            SLIPFLENDD+NR LMG NMQRQAVPL+  EAP VGTGME  VA+ SGA IVAKRAGIV+
Sbjct: 662  SLIPFLENDDANRALMGSNMQRQAVPLIVPEAPLVGTGMEGYVARGSGAVIVAKRAGIVQ 721

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA  IV+ S           +D Y L KF++SN NTC++QR +V  G  V++ DI+AD
Sbjct: 722  YIDARNIVVASES----KDDFWIDSYTLCKFRKSNHNTCIHQRCVVYQGQRVKKGDILAD 777

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GP+   G+LALGRN++VAF+ W GYNFEDS++IS  +V +D+FTS+H+E FE + RDT+L
Sbjct: 778  GPAIQQGELALGRNLVVAFLSWRGYNFEDSVVISSNVVRDDLFTSVHLEGFECVVRDTRL 837

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            GPEEITRD+  V+EE L  +DE GI CVGA V  GD+LVGK+TPK  SP+TPEEKLLRAI
Sbjct: 838  GPEEITRDVSGVAEEFLHCLDEFGIACVGANVEAGDVLVGKVTPKSSSPVTPEEKLLRAI 897

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FGEKA+DV+D+SL +P GVSG VVDV++  R GI+K  R++ +E++ I+     +D E  
Sbjct: 898  FGEKAIDVKDSSLYLPPGVSGCVVDVKVLQRRGIEKVGRALLIEKQAIDAEKARRDHELA 957

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +L   IYS L E+L G+ A++      K  +++ + + +  R  WW+ +V +     +++
Sbjct: 958  VLTNYIYSLLKEMLVGKVALNTLAPISKGDLITGEALEKIDRESWWKLSVDE---ISSIK 1014

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L+ ++      +   ++   EKI+  DD+  GVL VVKVFVA+K  +Q GDKM+GRHGN
Sbjct: 1015 LLRQRFVDRFDEINKTYEENFEKIRGDDDLAQGVLMVVKVFVAVKHTLQPGDKMSGRHGN 1074

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++SRI+P EDMP+L DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LGKKI  L+
Sbjct: 1075 KGVISRIVPAEDMPYLADGTPVDIILNPLGVPSRMNVGQILETHLGWAAYNLGKKISKLL 1134

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
            ++   +   S +    +          ++    D  ++  +   + GVPV+  VF+G   
Sbjct: 1135 DEGNYSEVKSLILEIYK---NDRKMMARLKRMTDTEIVEYSRSLRRGVPVAASVFEGPKT 1191

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            + I  +L +A  D SGQ +LYDG+TGE FDR VTVG  YMLKL+H+V+DK++ARS GSYS
Sbjct: 1192 DEIERLLVLAGKDPSGQEVLYDGVTGEKFDRKVTVGCKYMLKLHHLVNDKIHARSIGSYS 1251

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            L+TQQPLGGKS+ GGQR GEME W +QAYGA + LQEMLTIKSDDVVGR  VY+SIV G+
Sbjct: 1252 LITQQPLGGKSHFGGQRFGEMECWALQAYGATFALQEMLTIKSDDVVGRVNVYDSIVRGD 1311

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            + F  G PESFNV++ E++AL L+++         + +E   DF+   L
Sbjct: 1312 NDFYYGVPESFNVMMNELRALCLNVEF-------CSDLERKEDFSDLPL 1353


>gi|305433033|ref|ZP_07402189.1| DNA-directed RNA polymerase subunit beta [Campylobacter coli JV20]
 gi|304443734|gb|EFM36391.1| DNA-directed RNA polymerase subunit beta [Campylobacter coli JV20]
          Length = 1375

 Score = 1372 bits (3551), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1385 (44%), Positives = 884/1385 (63%), Gaps = 39/1385 (2%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F    + I+IP+L+++QKAS+D+FL +          G++  FKS+FPI    
Sbjct: 7    RNRLRVDFSNISKQIEIPNLLQLQKASFDYFLNLE-----NGESGIEKVFKSIFPIHDPQ 61

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQ 128
                LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  IKDIKEQ
Sbjct: 62   NRLSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGIKDIKEQ 121

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             IY+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++    ++ KL+Y  +IIPD+
Sbjct: 122  EIYIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVVN-KLVYTAQIIPDR 180

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +   
Sbjct: 181  GSWLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTE 240

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             + +D M   ++   + D + G  + ++GK+LT    + L + G+K++    + L   Y+
Sbjct: 241  FNPSDFM--DRIEYDIKD-EKGNIIHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYL 297

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A  I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D   
Sbjct: 298  ANPIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFEIANDLANGVDAAIINSFAQDNET 355

Query: 369  ------------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                        +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KM
Sbjct: 356  LKLLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKM 415

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  
Sbjct: 416  NHKLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELH 475

Query: 477  LGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            LGL +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS 
Sbjct: 476  LGLAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSE 535

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN 
Sbjct: 536  VTHKRRLSALGEGGLVKERAGFEVRDVHSTHYGRICPVETPEGQNIGLINTLSTYAKVNE 595

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE I
Sbjct: 596  LGFVEAPYRKVANGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETI 655

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTG
Sbjct: 656  LARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTG 715

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ME ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT
Sbjct: 716  MEQIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNT 771

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
               Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++
Sbjct: 772  NYIQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERII 831

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG IL
Sbjct: 832  REDTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMIL 891

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++
Sbjct: 892  VGKVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDD 951

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSS 1010
            R+I    ++   L ++  D  +++DR    R+  +L       +   G K +KK      
Sbjct: 952  RAIKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQTADI 1011

Query: 1011 DLISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P G
Sbjct: 1012 SELEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSG 1071

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V+++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPS
Sbjct: 1072 VIKLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPS 1131

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKIS 1186
            RMN+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I 
Sbjct: 1132 RMNIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFVKELRAKMLEICSIPRLVNEKEFIK 1190

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
            +  D+ +L  A  W  GV  +TPVF+G + E    +  +A +D  G++ LYDG TGE   
Sbjct: 1191 NLSDEELLNYARDWSKGVKFATPVFEGVNIEEFAKLFEIAKIDMDGKTELYDGRTGEKIA 1250

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYG
Sbjct: 1251 ERVHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYG 1310

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AA+ L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ + 
Sbjct: 1311 AAHTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDK 1370

Query: 1367 RTKNS 1371
               N 
Sbjct: 1371 DEDNE 1375


>gi|283954231|ref|ZP_06371755.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni 414]
 gi|283794249|gb|EFC32994.1| DNA-directed RNA polymerase beta chain [Campylobacter jejuni subsp.
            jejuni 414]
          Length = 1375

 Score = 1371 bits (3549), Expect = 0.0,   Method: Composition-based stats.
 Identities = 609/1383 (44%), Positives = 883/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRK PVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKTPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTILEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVENGKVTNEVVYLTATQEEGLFIAPASTKIDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +       S +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GSFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADG S D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDVVKAGQIIADGSSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK     +  
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMIDREEMLRVCSLLSKAPLNSDQKIGDKNYKKGQTADTSE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  ++LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDNLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG---TGSHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  + K    I  LR  + ++       S  E I   
Sbjct: 1134 NIGQILESHLGLIGLRLGDQIQEI-FNRKQKDFIKELRIKMLEICSIPRLSSEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  +TPVF+G + E  + +  MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFATPVFEGVNIEEFSKLFEMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSL+TQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLITQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|88597126|ref|ZP_01100362.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 84-25]
 gi|88190815|gb|EAQ94788.1| DNA-directed RNA polymerase, beta subunit [Campylobacter jejuni
            subsp. jejuni 84-25]
          Length = 1375

 Score = 1371 bits (3549), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1383 (44%), Positives = 884/1383 (63%), Gaps = 39/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9    RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124  YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183  WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243  PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300  PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358  LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418  KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478  LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598  FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658  RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718  QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ E
Sbjct: 774  IQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIRE 833

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT+DIPNV EE + +++E GI  +G  + PG ILVG
Sbjct: 834  DTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLEESGIAKIGTHIKPGMILVG 893

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+
Sbjct: 894  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRA 953

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDL 1012
            I    ++   L ++  D  +++DR    R+  +L       +   G K +KK        
Sbjct: 954  IKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISE 1013

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+
Sbjct: 1014 LEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVI 1073

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRM
Sbjct: 1074 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRM 1133

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I   
Sbjct: 1134 NIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKILEICSIPRLANEKEFIKSL 1192

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     
Sbjct: 1193 SDEELLNYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAER 1252

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1253 VHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1312

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1313 HTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDE 1372

Query: 1369 KNS 1371
             N 
Sbjct: 1373 DNE 1375


>gi|88608380|ref|YP_506556.1| DNA-directed RNA polymerase, beta subunit [Neorickettsia sennetsu
            str. Miyayama]
 gi|109904440|sp|Q2GD90|RPOB_NEOSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|88600549|gb|ABD46017.1| DNA-directed RNA polymerase, beta subunit [Neorickettsia sennetsu
            str. Miyayama]
          Length = 1358

 Score = 1371 bits (3548), Expect = 0.0,   Method: Composition-based stats.
 Identities = 641/1356 (47%), Positives = 906/1356 (66%), Gaps = 29/1356 (2%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
             D PDL++VQK SY  F+          +      F SVFP+    G A LEFVS     
Sbjct: 14   FDFPDLVKVQKDSYASFVGGGDTVFSISD-----IFASVFPVNDGYGRASLEFVSCRMGE 68

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-------IKDIKEQSIYMGDLP 136
            PK D   C+ R +TY+ PL+  LRL+VF  +              +KD++EQ IYMGD+P
Sbjct: 69   PKHDEYGCVERGITYSAPLRAILRLVVFGDETSGEGSEGVSTEPAVKDVREQEIYMGDIP 128

Query: 137  LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
            +M+K+GTF+I G++R+VVSQ+HR+PG+ FD+DK R+ +SGKL Y  RIIP +G W+D EF
Sbjct: 129  IMSKNGTFIINGVERVVVSQMHRAPGVFFDNDKARS-ISGKLNYIARIIPYRGSWLDFEF 187

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D+KD+++ RID++RK+PVT  L ALG+ +++I + F          D         +   
Sbjct: 188  DAKDVLYFRIDKKRKLPVTFLLRALGLSNKDIFAQFCEVSECRLTKDGKWTVCFVPEKFK 247

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            G ++   L++ +TGE V+  G +++  L ++L  KG+++  +  + +  +Y+A+D+V+ +
Sbjct: 248  GVRLQYDLINAETGELVLAKGNRISIVLARNLYAKGLRYCYMDLEVMKDMYLADDLVSTK 307

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             GE+ +  G  + ++ + ++   ++  I ++ +      +      V   +   ++A+L 
Sbjct: 308  -GEVLLPHGTKLTKEHVAKLEFLDVDSIKLVELKGNYVFS-----TVLQYDCSYEEAMLS 361

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IYRV+RPG++ +   AE +F  LFF  ++YDL  VGR+++N + NL   + +  + KEDI
Sbjct: 362  IYRVVRPGEIPSVESAEKLFESLFFSPERYDLLNVGRIRLNAKFNLSHDESLTVLTKEDI 421

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
               +K L  L+   G +DDID+LGNRRVRSVGE + NQ+R+GL+RM + I E +++ D D
Sbjct: 422  FCTVKELALLQREVGDVDDIDHLGNRRVRSVGEFMDNQFRIGLVRMAKVIVENMATADFD 481

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +VMP ++IN+K + + + EFF SS LSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 482  TVMPCEMINSKILGAVIREFFMSSALSQFMDQTNPLSEITHKRRISALGPGGLNRGRAGF 541

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            E+RDVH THYGRIC  ET EG  IGL++SL  +A++N YGFIETPYR V DG+VT++V Y
Sbjct: 542  EVRDVHTTHYGRICATETPEGATIGLINSLAIYAKINKYGFIETPYRYVRDGRVTDEVTY 601

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            LSA++E    I QA+  +DE+G   ++LV+CR   E + +PR ++ F D S KQ+VS+AA
Sbjct: 602  LSAIDEIKANICQASVRVDEEGYIVDDLVYCRRNYENVFIPRSEVQFADVSAKQIVSVAA 661

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            SLIPFLENDD+NR LMG NMQRQAVPL+  EAP VGTGME  VA+ SGA IVAKRAG+V+
Sbjct: 662  SLIPFLENDDANRALMGSNMQRQAVPLIMPEAPLVGTGMEGYVARGSGAVIVAKRAGVVQ 721

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA  IV+ S           +D Y L KF++SN NTC++QR +V  G  V++ DI+AD
Sbjct: 722  YIDARNIVVASES----KDDFWIDSYTLCKFRKSNHNTCIHQRCVVHQGQRVKKGDILAD 777

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GP+   G+LALGRN++VAF+ W GYNFEDS++IS  +V +D+FTS+H+E FE + RDT+L
Sbjct: 778  GPAIQKGELALGRNLVVAFLSWRGYNFEDSVVISSNVVRDDLFTSVHLEGFECVVRDTRL 837

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            GPEEITRD+  V+EE L  +DE GI CVGA V  GD+LVGK+TPK  SP+TPEEKLLRAI
Sbjct: 838  GPEEITRDVSGVAEEFLHCLDEFGIACVGANVEAGDVLVGKVTPKSSSPVTPEEKLLRAI 897

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FGEKA+DV+D+SL +P GVSG VVDV++  R GI+K  R++ +E++ I+     +D E  
Sbjct: 898  FGEKAIDVKDSSLYLPPGVSGCVVDVKVLQRRGIEKVGRALLIEKQAIDAEKTRRDHELA 957

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +L   IYS L E+L G+ A+S      K  +++ + + +  R  WW+ +V       +++
Sbjct: 958  VLTNYIYSLLKEMLVGKVALSTLAPISKGDLITEEALEKIDRENWWKISVDG---ISSIK 1014

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L+ ++      +   ++   EKI+  DD+  GVL VVKVFVA+K  +Q GDKM+GRHGN
Sbjct: 1015 LLRQRFVDRFDEINKTYEENFEKIRGDDDLAQGVLMVVKVFVAVKHTLQPGDKMSGRHGN 1074

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++SRI+P EDMP+L DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LGKKI  L+
Sbjct: 1075 KGVISRIVPAEDMPYLADGTPVDIILNPLGVPSRMNVGQILETHLGWAAYNLGKKISKLL 1134

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
            ++   +   S +    +          ++++  D  ++  +   + GVPV+  VF+G   
Sbjct: 1135 DEGNYSEVKSLVLEIYK---NDRKMMARLNEMTDAEIVEYSRSLRGGVPVAASVFEGPKT 1191

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            + I  +L +A  D SGQ +LYDG+TGE FDR VTVG  YMLKL+H+V+DK++ARS GSYS
Sbjct: 1192 DEIERLLVLAGKDPSGQEVLYDGVTGEKFDRKVTVGCKYMLKLHHLVNDKIHARSIGSYS 1251

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            L+TQQPLGGKS+ GGQR GEME W +QAYGA + LQEMLTIKSDDVVGR  VY+SIV G+
Sbjct: 1252 LITQQPLGGKSHFGGQRFGEMECWALQAYGATFALQEMLTIKSDDVVGRVNVYDSIVRGD 1311

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            + F  G PESFNV++ E++AL L+++  +   K   
Sbjct: 1312 NDFYYGVPESFNVMMNELRALCLNVEFCSDLEKKKD 1347


>gi|32265860|ref|NP_859892.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter
            hepaticus ATCC 51449]
 gi|41017664|sp|Q7VJ82|RPOBC_HELHP RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|32261909|gb|AAP76958.1| DNA-dependent RNA polymerase beta subunit [Helicobacter hepaticus
            ATCC 51449]
          Length = 2894

 Score = 1370 bits (3547), Expect = 0.0,   Method: Composition-based stats.
 Identities = 614/1413 (43%), Positives = 899/1413 (63%), Gaps = 48/1413 (3%)

Query: 7    FNG-LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
            F     R+R  F KNP+ ID+P+L+ +Q+ SYD FL ++         G++  FKSVFPI
Sbjct: 4    FTKLKNRLRADFTKNPQSIDVPNLLLLQRNSYDDFLCVDSD----KESGIERVFKSVFPI 59

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKD 124
                    LE+VS +F  PK+  ++ + R +TYAV L+I +RL++++ DE TG +  IKD
Sbjct: 60   QDSQNRITLEYVSCKFGKPKYTTNEAMVRGVTYAVSLQIKIRLVLWEKDEKTGERLGIKD 119

Query: 125  IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
             KEQ+I++ D+PLMT   +F+I G++R+VV+QLHRSPG+ F  ++  ++ S KL+Y  +I
Sbjct: 120  AKEQNIFVRDIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEES-SASSNKLIYTGQI 178

Query: 185  IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
            IPD+G W+  E+DSKD+++ RI++RRKVPVT  L A+G   ++IL  FYP      +   
Sbjct: 179  IPDRGSWLYFEYDSKDVLYARINKRRKVPVTIILRAMGYSKQDILKIFYPLQRVKYKKGK 238

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
            +  P     +  G +    + D   G  ++ SGK+L++  +K LKE  +  +    + L 
Sbjct: 239  YLIPFDVDSI--GNRAEFDIKDAK-GNLLVSSGKRLSTKKIKELKEAKIDLIEYPLENLT 295

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
              ++AE I+N + GE+  +    +DE  L+++   +I +  I    +   +  I N+ + 
Sbjct: 296  NKFLAEPIINAQ-GEVLFDTLTQLDESKLKKLLELKINEFVIANASAAGVDNSIINSFMA 354

Query: 365  DKNK------------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            D               + + A + IY+VMRPG+  T  VA+S    LFFD ++YDL+ VG
Sbjct: 355  DAESLKMLRQSEKIDDENELAAIRIYKVMRPGEPVTKEVAKSFVRQLFFDPERYDLTRVG 414

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            R+KMN +L ++ PD V  +  EDII  I+ L+ ++NG G IDD D+LGNRR+RS+GE+L 
Sbjct: 415  RMKMNHKLQINVPDYVTVLTHEDIIRTIQYLLKVKNGLGKIDDRDHLGNRRIRSIGELLA 474

Query: 473  NQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            N+   GL++M+++I+++++S+    D++MP DLIN K + S + EFF   QLSQ  +  N
Sbjct: 475  NELHTGLVKMQKAIRDKLTSLSGAFDTIMPHDLINGKMITSTIMEFFTGGQLSQFMDQTN 534

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L+++ 
Sbjct: 535  PLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTYT 594

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN  GFIE PYRKV +G V+ ++VYL+A +EE   IA A++++D++G   E+L+  R  
Sbjct: 595  RVNDLGFIEAPYRKVENGIVSQEIVYLTAAQEEGIVIAPASTAVDKNGHIIEDLIETRKD 654

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            GE IL  + ++  ID SP+ +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLK +AP 
Sbjct: 655  GEIILSEKSRVQLIDLSPRMLVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLKPDAPV 714

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E ++A+ S  A  A R+G+VE+VDA  I I   +     + + +D Y L K  R+
Sbjct: 715  VGTGIEQIIARDSWEATKATRSGVVERVDAKNIYILGEDD----NGAYIDHYHLGKNLRT 770

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC +Q+P+V+ GD V +  IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++S
Sbjct: 771  NQNTCFSQQPIVRQGDRVEQGQIIADGPSMDNGELALGKNIRVAFMPWNGYNFEDAIVVS 830

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER++ ED FTSIHI E E+ AR+ K G EEIT DIP   E    ++DE GI+ +G  V+ 
Sbjct: 831  ERLIKEDAFTSIHIYEKEIEARELKHGLEEITADIPGTKEAETAHLDESGIVRIGTYVSA 890

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            G ILVGK++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+IF + G 
Sbjct: 891  GMILVGKVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKIFTKKGY 950

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKST 1006
            +K+ R+IS   E+  +L  +  D   ++ +    R+  +L  +  +S      K FKK  
Sbjct: 951  EKDARAISAYEEEKRVLDIEHHDRLTMIQQEETLRISLMLSKEKLLSEVKVADKVFKKGA 1010

Query: 1007 VLSSDLISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             +  + +S               +++Q   E +K  +   K  L +  + K+  ++  D 
Sbjct: 1011 QIPKEELSVLNPFILSTLIKHYPKEIQTRYEQIKTNFLEQKKTLGEEHEEKLSILEKDDI 1070

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +P GV+++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPL
Sbjct: 1071 LPSGVVKLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPMVDMPYTADGEPVDIVLNPL 1130

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI-----GTGS 1180
            GVPSRMN+GQI E HLG     LG++I+ ++   ++   +  LRS + ++         S
Sbjct: 1131 GVPSRMNIGQILEVHLGLVGKRLGQQIQEIL-SSQSKQWLDTLRSKMIEIAQVVNSDDKS 1189

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
              E + + D++++L  A  W +GV  + PVF+G ++E  + +  +  +D  G++ LYDG 
Sbjct: 1190 MIEFLKNLDNEALLAYARDWSNGVKFAIPVFEGIEQEKFDKLFSLVKVDMDGKTELYDGK 1249

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE     V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW
Sbjct: 1250 TGEKMRERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVW 1309

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ L+EMLTIKSDD  GR   Y++I  G    E+  PE+F VL KE+Q+L L 
Sbjct: 1310 ALEAYGAAHTLKEMLTIKSDDTEGRRGAYKAITKGEHVGESEIPETFYVLTKELQSLALD 1369

Query: 1361 IDLENSRTKN--------SAKMEEIPDFNKCEL 1385
            +++                 + E   DF+  +L
Sbjct: 1370 VNIYGDEQDENGMPVPIAIKEDERPKDFSSFQL 1402


>gi|255322044|ref|ZP_05363192.1| DNA-directed RNA polymerase, beta subunit [Campylobacter showae
            RM3277]
 gi|255300857|gb|EET80126.1| DNA-directed RNA polymerase, beta subunit [Campylobacter showae
            RM3277]
          Length = 1378

 Score = 1370 bits (3546), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1382 (43%), Positives = 885/1382 (64%), Gaps = 35/1382 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + ID+P+L+++QK S+D FL ++     +   G++  FKS+FPI      
Sbjct: 10   RLRVDFSNVAKEIDVPNLLQLQKKSFDQFLNVD---KNQGESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+VS E   PK+ + +C+ R LTY+V LK+ +RLIV + DE TG K  IKDIKEQ I
Sbjct: 67   LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLIVHERDEKTGEKIGIKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++    ++ KL+Y  +IIPD+G 
Sbjct: 127  FVREIPLMTDRISFIINGVERVVVNQLHRSPGVIFKEEESPTVVN-KLIYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP    + + + +  P +
Sbjct: 186  WLYFEYDTKDVLYVRINKRRKVPVTILFRALGYKKQDIIKLFYPIQTLTIKDNKFLTPFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D     +V   + D + G  + E+GK+LT      +   GVKF+   ++ L   ++A 
Sbjct: 246  PDDY--QGRVEYDIKD-EEGNVLHEAGKRLTKKKADKIIADGVKFVEYPTEILVNRFLAH 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             +++  +GE+  +    +DE  L +I  ++   I I    +   +  I N+ + D     
Sbjct: 303  PVIDKNSGEVLYDTLAQLDENKLVKIL-ADQESIEIANDLAAGVDDAIINSFIADNETLK 361

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A +  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 362  LLRQTENVDDENDLAAIRIYKVMRPGEPVVKDAARAFVNDLFFNPERYDLTGVGRMKMNH 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  EDII   K L+ ++NG+G IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 422  KLALEVPEYVTVLTNEDIIKTAKYLIKVKNGQGHIDDRDHLGNRRIRSIGELLANELHLG 481

Query: 479  LLRMERSIKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             ++M+++I+++ ++  + + +MP DL+N K + + + EFF   QLSQ  +  N LS +TH
Sbjct: 482  FVKMQKAIRDKFTTLGNTEEIMPYDLVNPKMITTTIMEFFTGGQLSQFMDQTNPLSEVTH 541

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  GF
Sbjct: 542  KRRLSALGEGGLVKDRAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTYAKVNNLGF 601

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +E PY+KV DGKVT+++VYL+A +EEN  IA A+++LDE G   E+L+  R  GE IL  
Sbjct: 602  VEAPYKKVVDGKVTDEIVYLTATQEENLVIAPASTALDESGYIVEDLIEARQDGEMILAK 661

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            RE +  ID     +  +AASLIPFLE+DD+NR LMG NMQRQAVPLL++ AP VGTGMES
Sbjct: 662  REDVKLIDLCSGMIAGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSSAPIVGTGMES 721

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             VA+ +  AI A+RAG+VE+VD   I I   +     +   +D Y + K  R+NQNT  +
Sbjct: 722  TVARDAWEAIKARRAGVVEKVDNKNIFILGEDE----AGPYIDHYSMEKNLRTNQNTTFS 777

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+VK G+ V    IIADGPS + G+LA+G+N L+AFMPW+GYN+ED+++ISE+M+ ED
Sbjct: 778  QHPIVKKGESVAAGQIIADGPSMERGELAIGKNALIAFMPWNGYNYEDAIVISEKMIRED 837

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FTS+HI E E+ AR+ K G EEIT+DIPN+ EE L ++D+ GII +G +V PG ILVGK
Sbjct: 838  AFTSVHIYEKEIEARELKDGVEEITKDIPNIKEEDLLHLDDSGIIKIGTQVKPGMILVGK 897

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K+ RS 
Sbjct: 898  VSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASMEGVVVDVKIFTKKGHEKDNRSN 957

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDLI 1013
             V  E+     ++  D  ++LDR    ++  +LC     S    G K +KK   +  +  
Sbjct: 958  KVYEEEKAAFEKEHHDRLLMLDREEMLKVGALLCKTPLSSAQTIGKKTYKKGEKIDKEEF 1017

Query: 1014 SEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                R           + VQ++ + +K  ++  K  L++    K+E ++  D +P GV++
Sbjct: 1018 ENINRFTLSAIVKGFSKDVQKSYDDIKNHFQNEKKKLKEEHDAKMEILEKDDILPSGVVK 1077

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L  G PVDIVLNPLGVPSRMN
Sbjct: 1078 LVKVYIATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYLPSGQPVDIVLNPLGVPSRMN 1137

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDYD 1189
            +GQI E+HLG     LG++I  +    K    I  LR+ + ++          + +    
Sbjct: 1138 IGQILESHLGLVGYRLGEQINQI-FQEKKGEWIKELRAKMIEIASASKFMDAKKTLGKMS 1196

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D+ +L  A  W +GV  +TP+F+G   + +  +  +A +D  G++ LYDG TG      V
Sbjct: 1197 DEQLLDYARDWANGVKFATPIFEGVRVDELMKLFELAKIDMDGKTELYDGRTGSKIKERV 1256

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA+
Sbjct: 1257 NVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAAH 1316

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             L+EMLT+KSDDV GR   Y+++  G +  ETG PE+F VL  E+++L L +++ +    
Sbjct: 1317 TLREMLTVKSDDVEGRLSAYKALTRGENVPETGIPETFFVLTNELKSLALDVEIYDEDEN 1376

Query: 1370 NS 1371
            N 
Sbjct: 1377 NE 1378


>gi|149195228|ref|ZP_01872318.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT RPOB [Caminibacter
            mediatlanticus TB-2]
 gi|149134661|gb|EDM23147.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT RPOB [Caminibacter
            mediatlanticus TB-2]
          Length = 1379

 Score = 1369 bits (3544), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1385 (43%), Positives = 894/1385 (64%), Gaps = 38/1385 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+I+DIP+L+ +Q+ S+  F+ +          G+   FKS+FPIT     
Sbjct: 10   RLRLDFSKIPQILDIPNLLHLQQNSFKDFINIEEP----EKSGIHKVFKSMFPITDAQNR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+V  EF  PK+ V +C+ + LTY++P+KI +RLIV + DE TG K  IKDIKEQ++
Sbjct: 66   ITLEYVGIEFKKPKYTVRECMEKGLTYSIPIKIKVRLIVHERDEKTGEKIGIKDIKEQTL 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT+  +F+I G++R++V+QLHRSPG+ F  ++ +   S KLLY+ +IIPD+G 
Sbjct: 126  FIRDIPLMTERTSFIINGVERVIVNQLHRSPGVIFKQEEAQN--SNKLLYSAQIIPDRGS 183

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KD+++VR+++RRKVPVT  L A+    E+IL  FYP +    +   +  P +
Sbjct: 184  WVYFEYDVKDVLYVRVNKRRKVPVTILLRAMDYSKEDILKLFYPILDIIVKNGKFLMPST 243

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              +     K+   L D D G  +I +GK++T   LK ++EK  +F+    + L   ++AE
Sbjct: 244  QLE---AGKLDYDLKDED-GNIIIPAGKRITRRKLKEIQEKY-EFVEYPLELLFDRHLAE 298

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN--- 367
             I +  TGE+  +   +++E  L++I  S+I +  I+   +   +  I      D     
Sbjct: 299  PIYDPLTGEVLFDTLTILNEVKLKKIVESQINEFKIVNDLADGVDDGILRAFHQDIETLK 358

Query: 368  ---------KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+ +T   A+ +F+ LFFD ++YDL+ VGR+KMN 
Sbjct: 359  ILKQTEGIENENDLARIRIYKVMRPGEPATPQTAKELFDKLFFDPERYDLTKVGRMKMNH 418

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ PDDV  +  +DII  I+ L+ +RNG G IDD D+LGNRR+RS+GE+L N+ + G
Sbjct: 419  KLGLNVPDDVTVLTYQDIIKTIQYLIGVRNGIGQIDDRDHLGNRRIRSIGELLANKLQDG 478

Query: 479  LLRMERSIKERIS-SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            L +M+++IK++++   +++ ++P DL+N K V + + +FF + QLSQ  +  N LS + H
Sbjct: 479  LAKMQKTIKDKMTTITNVNELLPMDLVNTKLVTTTILDFFATGQLSQFMDQTNPLSEVAH 538

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG+GGV R RAG E+RDVHP+HYGRICP ET EG NIGLV++L+++A+VN +GF
Sbjct: 539  KRRLSALGEGGVTRERAGFEIRDVHPSHYGRICPIETPEGQNIGLVNTLSTYAKVNEFGF 598

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCRCAGEEILV 656
            IE PYR V DG+VT+++VYL+A +EE + IA A+  +DE  G   ++L+  R  GE +LV
Sbjct: 599  IEAPYRVVKDGRVTDEIVYLTATQEEEKVIAPASVKIDEQTGEIIDDLIEARKDGEIVLV 658

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             ++++D  D +PK +V + ASLIPFLE+DD+NR LMG NMQRQ VPLL++EAP VGTG+E
Sbjct: 659  DKKEVDLYDLNPKMIVGVGASLIPFLEHDDANRALMGSNMQRQGVPLLRSEAPIVGTGIE 718

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              VA+ +   + AKR G V +VDA  I I   +     + + +D Y L K+ R+NQNTC 
Sbjct: 719  KYVARDAWQIVKAKRDGKVIKVDAKNIYILGEDE----NGAYIDHYGLEKYLRTNQNTCF 774

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +QRP+VKVGD V+  D+IADGP+ D G++ALG+N+LVAFMPW+GYNFED++++SER++ +
Sbjct: 775  DQRPIVKVGDVVKAGDVIADGPNMDNGEIALGKNVLVAFMPWNGYNFEDAIVLSERIIRD 834

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DV+TS+HI E     R+ K G EE+T DIP V  E L ++DE GI+ VG  V PG ILVG
Sbjct: 835  DVYTSVHIYEEVCEVRELKHGLEELTADIPGVKPEYLSHLDESGIVKVGTYVKPGMILVG 894

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KI+PKG+   TPEE+LL++IFG+K+  V ++SL  P+ + G V+DV+++ + G + +ER+
Sbjct: 895  KISPKGDVKPTPEERLLKSIFGDKSGHVVNSSLYAPASMEGVVIDVKVYTKKGYELDERA 954

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
                 E+ + +     ++  I+D      L  +L  +  +       K FK+   +  + 
Sbjct: 955  KKAYEEEKQKIEDVYKNKLAIIDEEEMIALTTLLSSKPLIKEVALNSKIFKEGEKIPKEE 1014

Query: 1013 ISEYPRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    +          DE+ +R  E +K +Y+  K  +   +  KIE ++  D +P GV 
Sbjct: 1015 LQNINKFLLLSLVEYYDEETKREFEEIKSKYQKEKENIRKEYDEKIEVLERDDILPNGVA 1074

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR I+ GDKMAGRHGNKGIVS I+P EDMP+++DG  VD+VLNPLGVPSRM
Sbjct: 1075 KMVKVYIANKRKIKVGDKMAGRHGNKGIVSIIVPEEDMPYMEDGRTVDVVLNPLGVPSRM 1134

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKA---NGDISPLRSFLEKVIGTGSHTEKISDY 1188
            N+GQI E HLG     LG++I+ ++ + +    N   + ++  ++         + +   
Sbjct: 1135 NIGQILEVHLGLVGKKLGEQIEEILKEKQDDMMNKLRAKMKEIVKVAHFGEHFEKFLDSL 1194

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             ++ +L+ A  W  GV  STPVF+G  EE    +  MA + E G+  LYDG TGEP    
Sbjct: 1195 TNEELLKYARDWAKGVKFSTPVFEGVTEEEFKKLFEMAGIPEDGKMQLYDGRTGEPIKER 1254

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YM+KL+H+V DKV+ARS G YSL+TQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1255 VNVGYMYMMKLHHLVDDKVHARSIGPYSLITQQPVGGKALFGGQRFGEMEVWALEAYGAA 1314

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y L+EMLT KSDDV GR + Y ++  G +    G  E+F VL KE++ALGL ++      
Sbjct: 1315 YNLKEMLTTKSDDVEGRNKAYRALTRGENVPIEGLSETFFVLSKELRALGLDLEFYKKEE 1374

Query: 1369 KNSAK 1373
             N   
Sbjct: 1375 DNEEI 1379


>gi|291276552|ref|YP_003516324.1| putative DNA-directed RNA polymerase subunit beta' [Helicobacter
            mustelae 12198]
 gi|290963746|emb|CBG39581.1| putative DNA-directed RNA polymerase beta' chain [Helicobacter
            mustelae 12198]
          Length = 2883

 Score = 1369 bits (3542), Expect = 0.0,   Method: Composition-based stats.
 Identities = 621/1407 (44%), Positives = 891/1407 (63%), Gaps = 45/1407 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F ++ + ++IP+L+ +Q+ SY+ FL       +    G++  F+SVFPI    
Sbjct: 8    KNRLRLDFTQSSQNLEIPNLLLLQRDSYNSFLE----SKDGKESGVEKVFRSVFPIQDAQ 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LE+   EF  PK+ V + + R +TY++PLKI +RL++ D DE T   SIKDIKEQ+
Sbjct: 64   NRLILEYDGCEFGKPKYTVREAMERGITYSIPLKIKIRLLLLDKDEKTEKISIKDIKEQN 123

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            I++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+G
Sbjct: 124  IFIREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEESST-TSNKLVYTGQIIPDRG 182

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
             W+  E+D+KD + VRI++RRKVP+T  L A+G   +EIL  FYP +    + +      
Sbjct: 183  SWLYFEYDAKDTLFVRINKRRKVPITILLRAMGYTKQEILKIFYPLLKVKIKKEKHFIEF 242

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
               +     +V   + ++D GE V+E+GK+LT    + L EKG+ ++   +  L   Y+A
Sbjct: 243  KPENF--EGRVEYDIKNMD-GEVVVEAGKRLTKKKAQELSEKGLGWIEYPA--LIDRYLA 297

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD---- 365
            E I++ +TGE+  +    IDE  L++I    I++  I    ++ +++ I  +   D    
Sbjct: 298  EPIIDPKTGEVLFDILTQIDEGKLKKIMEHRIKEFVIADDLAIGHDSGILKSFHVDADPL 357

Query: 366  --------KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                       +   A + IY+VMRPG+  T  VA+     LFFD ++YDL+ VGR+KMN
Sbjct: 358  RMLKQSEKHENENDLAAIRIYKVMRPGEPVTKEVAKQFVKQLFFDPERYDLTRVGRMKMN 417

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +L L+ PD V  + +EDII  IK L+ ++NG+G IDD D+LGNRR+R++GE+L N+   
Sbjct: 418  HKLGLEIPDYVTVLTQEDIIKSIKYLIKVKNGQGRIDDRDHLGNRRIRAIGELLANELHA 477

Query: 478  GLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            GL++M+++IK+++++ +I  +++MP DLIN+K + SA+ EFF   QLSQ  +  N LS +
Sbjct: 478  GLVKMQKAIKDKLTTPNINLETLMPLDLINSKMITSAILEFFTGGQLSQFMDQTNPLSEV 537

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN  
Sbjct: 538  THKRRLSALGEGGLVKERVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNEL 597

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GFIE PYRKV  G VT +VVYL+A +E+   IA A++ LD + +  E+L+  R  GE  L
Sbjct: 598  GFIEAPYRKVVQGHVTQEVVYLTATQEDGHIIAPASTKLDANDNIVEDLIDARVGGEITL 657

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              + KI  ID SP+ +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL  +AP VGTG+
Sbjct: 658  SEKNKITLIDLSPRMLVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLIPDAPIVGTGI 717

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E ++A+ +  AI A R G+VE+VDA  I I   +     + + +D Y L K  R+NQNT 
Sbjct: 718  EKIIARDAWEAIKASRPGVVEKVDAKNIYILGEDE----AGAYIDSYPLQKNLRTNQNTS 773

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              QRP+VKVGD+V  + IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SE ++ 
Sbjct: 774  FAQRPIVKVGDKVETHQIIADGPSMDTGELALGKNVRVAFMPWNGYNFEDAIVVSEHLIK 833

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ED FTS+HI E E+ AR+ K G EEITRDIPNV E+ + ++D+ GI+ +G  V+ G ILV
Sbjct: 834  EDYFTSVHIYEKEIEARELKHGIEEITRDIPNVREDDIAHLDDSGIVKIGTYVSSGMILV 893

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GK++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+I  + G +K+ER
Sbjct: 894  GKVSPKGEVKSTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKILTKKGYEKDER 953

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEIL----CGQNAVSGPKGFKKSTVLSSD 1011
            + S   ++  +L  +  D   +LD+    R+  +L     G +A    K +KK  ++   
Sbjct: 954  TRSAYEKEKAVLDIEHHDRLTMLDKEERLRINTMLAKEVLGSDADISGKVYKKGEMVPQA 1013

Query: 1012 LISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             I+   R           + VQ+    +K  +   K  L +  + K+  ++  D +P GV
Sbjct: 1014 EIAGISRFALNTLIKSYSKNVQQKYNQIKSNFLEQKKTLGEEHEEKLSILEKDDILPSGV 1073

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            ++ VK++VA KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPSR
Sbjct: 1074 VKRVKIYVATKRKLKVGDKMAGRHGNKGIVSNIVPAVDMPYTADGEPVDIVLNPLGVPSR 1133

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK----VIGTGSHTEKIS 1186
            MN+GQI E HLG      G++I  ++   K     S     LE             + ++
Sbjct: 1134 MNIGQILEVHLGLVGKRFGEQILEVLEQQKKGFLKSLRAKMLEISDVINPNDSVMKDLLT 1193

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
              DD+ +L  A  W  GV  + PVF+G  +E  + +  MA +   G++ LYDG TGE   
Sbjct: 1194 HADDEELLGYARDWSKGVKFAIPVFEGITQEKFHKLFEMAKIQMDGKTDLYDGKTGEKIR 1253

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYG
Sbjct: 1254 ERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYG 1313

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY L+EMLT+KSDDV GR   Y++I  G    E+  PE+F VL KE+Q+LGL +++   
Sbjct: 1314 AAYTLKEMLTVKSDDVKGRENAYKAITKGEAVGESEIPETFYVLTKELQSLGLDVNIFGD 1373

Query: 1367 RTKNS--------AKMEEIPDFNKCEL 1385
                +         + +   DFN  +L
Sbjct: 1374 DVDENGQPKPIVVEEEKRPKDFNTFQL 1400



 Score = 39.3 bits (90), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 27/55 (49%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  VAEDI++  T E+   AG +I+E     I    I+ + I
Sbjct: 2191 GSELIESLEERIFGRVVAEDIIDPITNEVLYSAGILINEDMARHIVEVGIKSVII 2245


>gi|41017780|sp|Q93MK8|RPOB_EHRRI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|15081476|gb|AAK83925.1|AF401089_1 RNA polymerase beta-subunit [Neorickettsia risticii]
          Length = 1363

 Score = 1367 bits (3539), Expect = 0.0,   Method: Composition-based stats.
 Identities = 646/1374 (47%), Positives = 916/1374 (66%), Gaps = 41/1374 (2%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
             D PDL++VQK SY  F+    A        +   F SVFP+    G A LEFVS     
Sbjct: 14   FDFPDLVKVQKDSYASFVGGGDAVSS-----INDIFASVFPVNDGYGRASLEFVSCRMGE 68

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF-------TGAKSIKDIKEQSIYMGDLP 136
            PK D   C+ R +TY+ PL+  LRL+VF  +         +   ++KD++EQ IYMGD+P
Sbjct: 69   PKHDEYGCVERGITYSAPLRAILRLVVFGDETSGEGGEGVSTEPAVKDVREQEIYMGDIP 128

Query: 137  LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
            +M+K+GTF+I G++R+VVSQ+HR+PG+ FD+DK R+ +SGKL Y  RIIP +G W+D EF
Sbjct: 129  IMSKNGTFIINGVERVVVSQMHRAPGVFFDNDKARS-ISGKLNYIARIIPYRGSWLDFEF 187

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D+KD+++ RID++RK+PVT  L ALG+ +++I + F          D         +   
Sbjct: 188  DAKDVLYFRIDKKRKLPVTLLLRALGLSNKDIFAQFCEVSECRLTKDGKWTVCFVPERFK 247

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            G ++   L++ +TGE V+  G +++  L ++L  KG+++  +  + +  +Y+A+D+V+ +
Sbjct: 248  GVRLQYDLINAETGELVLAKGNRISIVLARNLYAKGLRYCYMDLEVMKDMYLADDLVSAK 307

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             GE+ +  G  + ++ + ++   ++  I ++ +       YI +T++       ++A+L 
Sbjct: 308  -GEVLLPHGTRLTKEHVAKLEFLDVDSIKLVEL----KGNYIFSTVLQYDC-SYEEAMLS 361

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IYRV+RPG++ +   AE +F  LFF  ++YDL  VGR+++N + NL   + +  + KEDI
Sbjct: 362  IYRVIRPGEIPSIESAEKLFESLFFSPERYDLLNVGRIRLNAKFNLSHDESLTVLTKEDI 421

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGN-----RRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
               ++ L  L+   G +DDID+LGN     RRVRSVGE + NQ+R+GL+RM + I E ++
Sbjct: 422  FCTVRELALLQREVGDVDDIDHLGNSALGLRRVRSVGEFMDNQFRIGLVRMAKVIVENMA 481

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            + D D+VMP ++IN+K + + + EFF SS LSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 482  TADFDTVMPCEMINSKILGAVIREFFMSSALSQFMDQTNPLSEITHKRRISALGPGGLNR 541

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVH THYGRIC  ET EG  IGL++SL  +A++N YGFIETPYR V DG+VT
Sbjct: 542  GRAGFEVRDVHTTHYGRICATETPEGATIGLINSLAIYAKINKYGFIETPYRYVRDGRVT 601

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            ++V YLSA++E    I QA+  +DE+G   ++LV+CR   E + +PR ++ F D S KQ+
Sbjct: 602  DEVTYLSAIDEIKANICQASVRVDEEGYILDDLVYCRRNYENVFIPRSEVQFADVSAKQI 661

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+AASLIPFLENDD+NR LMG NMQRQAVPL+  EAP VGTGME  VA+ SGA IVAKR
Sbjct: 662  VSVAASLIPFLENDDANRALMGSNMQRQAVPLIVPEAPLVGTGMEGYVARGSGAVIVAKR 721

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            AGIV+ +DA  IV+ S           +D Y L KF++SN NTC++QR +V  G  V++ 
Sbjct: 722  AGIVQYIDARNIVVASES----KDDFWIDSYTLCKFRKSNHNTCIHQRCVVYQGQRVKKG 777

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            DI+ADGP+   G+LALGRN++VAF+ W GYNFEDS++IS  +V +D+FTS+H+E FE + 
Sbjct: 778  DILADGPAIQQGELALGRNLVVAFLSWRGYNFEDSVVISSNVVRDDLFTSVHLEGFECVV 837

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            RDT+LGPEEITRD+  V+EE L  +DE GI CVGA V  GD+LVGK+TPK  SP+TPEEK
Sbjct: 838  RDTRLGPEEITRDVSGVAEEFLHCLDEFGIACVGANVEAGDVLVGKVTPKSSSPVTPEEK 897

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            LLRAIFGEKA+DV+D+SL +P GVSG VVDV++  R GI+K  R++ +E++ I+     +
Sbjct: 898  LLRAIFGEKAIDVKDSSLYLPPGVSGCVVDVKVLQRRGIEKVGRALLIEKQAIDAEKARR 957

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            D E  +L   IYS L E+L G+ A++      K  +++ + + +  R  WW+ +V +   
Sbjct: 958  DHELAVLTNYIYSLLKEMLVGKVALNTLAPISKGDLITGEALEKIDRESWWKLSVDE--- 1014

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
              +++ L+ ++      +   ++   EKI+  DD+  GVL VVKVFVA+K  +Q GDKM+
Sbjct: 1015 ISSIKLLRQRFVDRFDEINKTYEENFEKIRGDDDLAQGVLMVVKVFVAVKHTLQPGDKMS 1074

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRI+P EDMP+L DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LGKK
Sbjct: 1075 GRHGNKGVISRIVPAEDMPYLADGTPVDIILNPLGVPSRMNVGQILETHLGWAAYNLGKK 1134

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I  L+++   +   S +    +          ++    D  ++  +   + GVPV+  VF
Sbjct: 1135 ISKLLDEGNYSEVKSLILEIYK---NDRKMMARLKRMTDTEIVEYSRSLRRGVPVAASVF 1191

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            +G   + I  +L +A  D SGQ +LYDG+TGE FDR VTVG  YMLKL+H+V+DK++ARS
Sbjct: 1192 EGPKTDEIERLLVLAGKDPSGQEVLYDGVTGEKFDRKVTVGCKYMLKLHHLVNDKIHARS 1251

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             GSYSL+TQQPLGGKS+ GGQR GEME W +QAYGA + LQEMLTIKSDDVVGR  VY+S
Sbjct: 1252 IGSYSLITQQPLGGKSHFGGQRFGEMECWALQAYGATFALQEMLTIKSDDVVGRVNVYDS 1311

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            IV G++ F  G PESFNV++ E++AL L+++         + +E   DF+   L
Sbjct: 1312 IVRGDNDFYYGVPESFNVMMNELRALCLNVEF-------CSDLERKEDFSDLPL 1358


>gi|254458778|ref|ZP_05072202.1| DNA-directed RNA polymerase, beta subunit [Campylobacterales
            bacterium GD 1]
 gi|207084544|gb|EDZ61832.1| DNA-directed RNA polymerase, beta subunit [Campylobacterales
            bacterium GD 1]
          Length = 1381

 Score = 1365 bits (3533), Expect = 0.0,   Method: Composition-based stats.
 Identities = 606/1383 (43%), Positives = 896/1383 (64%), Gaps = 34/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I++P+L+++Q++SYD+FLM++    +R   G+++ F+SVFPI      
Sbjct: 10   RLRVDFSKTPQQIEVPNLLQLQQSSYDNFLMLD--AKDRSASGIESVFQSVFPIHDTQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              +E++  E   PK+ V +C+ R LTYAV L++  RL+++D DE T  K  +KDIKEQSI
Sbjct: 68   LTVEYIGSEVANPKYTVRECMERGLTYAVSLRMKTRLVLWDRDENTKEKLGVKDIKEQSI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   +   KL+Y  +IIPD+G 
Sbjct: 128  FVRDIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEES-TTAGNKLIYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KDI+++RI++RRKVPVT    ALG   ++IL  FYP    S   + +    +
Sbjct: 187  WLYFEYDPKDILYMRINKRRKVPVTIMFRALGYSKQDILKLFYPIQTISIEDNKFTMDFN 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             +D    A+++  L+DI  G+  + +GK+L+    + L + G+K +    + L   Y+AE
Sbjct: 247  PSDFA--ARLTYDLIDI-NGKIHVPAGKRLSVKKAQKLIDDGLKSVEYPLETLIDRYLAE 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ ETGEI  +    IDE  L+++    + +  +    +   +  I N    D +   
Sbjct: 304  PIIDPETGEILFDTMTHIDETKLKKMTEIGVSEFKVANDLAEGVDRSIINAFNADSDSLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+   N LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEDIEDENDLAAIRIYKVMRPGEPVTKEAAKVFVNQLFFDPERYDLTKVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ V  +  ED+I  +K ++ ++NG+G IDD D+LGNRR+RS+GE+L N+   G
Sbjct: 424  KLGLNIPEYVTVLTHEDVINSVKYVIKVKNGQGHIDDRDHLGNRRIRSIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++      +MP DLIN+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 484  LIKMQKAIRDKLSTMSGPMAELMPHDLINSKMITSTIMEFFSGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L ++++VN +G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHQTHYGRICPIETPEGQNIGLINTLATYSKVNEHG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+ + DGKVTN++VYL+A +EE   IA A++ LD++G F + LV  R  GE +L 
Sbjct: 604  FIEAPYKVMKDGKVTNEIVYLTATQEEGVKIAAASNKLDDNGQFIDTLVTTRIDGEILLR 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            P  +  + D S   VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL+  +P VGTG+E
Sbjct: 664  PPVECQYADLSSHMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPLSPMVGTGVE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +VA+ S   I AKR+G+VE+VD   I +   +         +D Y L K  R+NQNT  
Sbjct: 724  KLVARDSWECIKAKRSGVVEKVDGKHIYVMGDDD----GEIYIDYYPLQKNLRTNQNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q+P+V VGD V+   +IADGP+ D G+LALG N +VAFMPW+GYNFED+++ISER++ +
Sbjct: 780  SQKPIVNVGDLVKTGQVIADGPNMDQGELALGVNAMVAFMPWNGYNFEDAIVISERLIRK 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEITRDIPNV ++ L ++DE GI+ +G +VN G ILVG
Sbjct: 840  DAFTSVHIYEKELEARELKHGVEEITRDIPNVRDDELVHLDESGIVKIGTQVNGGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + G VVDV+IF + G DK+ R+
Sbjct: 900  KVSPKGEVKPTPEERLLRAIFGEKAGHVINKSLYCPPSMEGVVVDVKIFTKKGYDKDPRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG----FKKSTVLSSDL 1012
            + +E+E+ + L R+  D  +++D+    R+ ++L  +  V+  K     +K   +++   
Sbjct: 960  LELEKEERDYLEREHYDRLLMIDKEEMLRITKLLTKEALVNDIKIGDTAYKAGDIINGAD 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + E  R           E++Q      K  ++  K +  D  + K+  ++  D +  GV+
Sbjct: 1020 LVEVNRFAMNAIVKSFSEEIQDEYNKTKNYFQKEKRLFRDEHEEKLNILEKDDILANGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+++DG  VD+ LNPLGVPSRM
Sbjct: 1080 KYVKVYIATKRQLKVGDKMAGRHGNKGIVSIIVPEVDMPYMEDGRSVDVCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT---EKISDY 1188
            N+GQI E HLG A   LG +I     + K    I  LRS +  +          E I   
Sbjct: 1140 NIGQILEMHLGMAGRELGNQILEQ-FETKQKDFIDNLRSKMIAIADVAKMMNAVEVIGAM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+  L  A  W +G+  +TP+F+G + E  + + ++A +D  G+++LY+G+TGE     
Sbjct: 1199 SDEKFLHYARDWSNGIRFATPIFEGVNAEEFDKLFKLAKMDADGKTVLYNGMTGEKIKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+Y+LKL+H+V +K++ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1259 VNVGYMYILKLHHLVDEKIHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAS 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLTIKSDDV GR R Y++I  G     +G PE+  VL KE+QAL L +++ +   
Sbjct: 1319 AVLKEMLTIKSDDVDGRVRAYKAITKGELIPASGIPETLFVLTKELQALALDVEIFDEVK 1378

Query: 1369 KNS 1371
             + 
Sbjct: 1379 DDE 1381


>gi|224436425|ref|ZP_03657442.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter cinaedi
            CCUG 18818]
 gi|313142939|ref|ZP_07805132.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter cinaedi CCUG 18818]
 gi|313127970|gb|EFR45587.1| bifunctional DNA-directed RNA polymerase subunit beta-beta
            [Helicobacter cinaedi CCUG 18818]
          Length = 2891

 Score = 1365 bits (3533), Expect = 0.0,   Method: Composition-based stats.
 Identities = 609/1413 (43%), Positives = 896/1413 (63%), Gaps = 48/1413 (3%)

Query: 7    FNG-LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
            F     R+R  F KNP+ ID+P+L+ +Q+ SYD FL ++         G++  FKSVFPI
Sbjct: 4    FTKLKNRLRADFTKNPQSIDVPNLLLLQRNSYDDFLCIDGD----KESGIERVFKSVFPI 59

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKD 124
                    LE+   +F  PK+  ++ + R +TYA+ L+I +RL++++ DE TG +  +KD
Sbjct: 60   QDNQNRITLEYAGCKFGKPKYTTNEAMVRGVTYAISLQIKIRLVLWEKDEKTGERLGVKD 119

Query: 125  IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
            +KEQ+I++ D+PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +I
Sbjct: 120  VKEQNIFVRDIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEESNT-SSNKLIYTGQI 178

Query: 185  IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
            IPD+G W+  E+D+KD+++ RI++RRKVPVT  L A+G   ++IL  FYP      +   
Sbjct: 179  IPDRGSWLYFEYDAKDVLYARINKRRKVPVTIILRAMGYSKQDILKIFYPLQKVKYQKGK 238

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
            +  P     +  G +    + D   G  ++ SGK+L++  +K LKE  +  +    + L 
Sbjct: 239  YLIPFDIDSI--GTRAEFDIKDSK-GNLLVASGKRLSAKKIKELKEAKIGLIEYPLESLS 295

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
              ++AE +VN E GE+  +    +DE  L+++   ++ +  I    +   +  I N+ + 
Sbjct: 296  NKFLAEPVVNAE-GEVLFDTLTQLDELKLKKLHELKVNEFVIANDSAAGVDNSIINSFIA 354

Query: 365  DKNK------------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            D               +   A + IY+VMRPG+  T  VA+S    LFFDS++YDL+ VG
Sbjct: 355  DAESLKMLRQSEKIDDENDLAAIRIYKVMRPGEPVTKEVAKSFVRQLFFDSERYDLTRVG 414

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            R+KMN +L ++ PD V  +  EDI+  I+ L+ ++NG G IDD D+LGNRR+RS+GE+L 
Sbjct: 415  RMKMNHKLQINVPDYVTVLTHEDILKTIQYLLKVKNGLGKIDDRDHLGNRRIRSIGELLA 474

Query: 473  NQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            N+   GL++M+++I+++++S+    D++MP DL+N K + S + EFF   QLSQ  +  N
Sbjct: 475  NELHSGLVKMQKAIRDKLTSLSGVFDTIMPHDLVNGKMITSTIMEFFTGGQLSQFMDQTN 534

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L+++ 
Sbjct: 535  PLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTYT 594

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            RVN  GFIE PY+KV +G VT+++VYL+A +EE   IA A++++D+DG   E+L+  R  
Sbjct: 595  RVNDLGFIEAPYKKVENGIVTDEIVYLTAAQEEGLVIAPASTAVDKDGRIIEDLIETRKD 654

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            GE +L  + ++  ID SP+ +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLK +AP 
Sbjct: 655  GEILLGEKSRVQLIDLSPRMLVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLKPDAPI 714

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E V+A+ S  A  AKR G+VE+VD+  I I   +     + + +D Y L K  R+
Sbjct: 715  VGTGIEQVIARDSWEATKAKRGGVVEKVDSKNIYILGEDD----NGAYIDHYYLGKNLRT 770

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC +Q+P+V+ GD V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++S
Sbjct: 771  NQNTCFSQQPIVRQGDSVEEGQIIADGPSMDSGELALGKNIRVAFMPWNGYNFEDAIVVS 830

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            E+++ ED FTSIHI E E+ AR+ K G EEIT DIP   E    ++DE GI+ +G  V+ 
Sbjct: 831  EKLIEEDAFTSIHIYEKEIEARELKHGLEEITADIPGTKETETAHLDESGIVRIGTYVSG 890

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            G ILVGK++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + GTVVDV+IF + G 
Sbjct: 891  GMILVGKVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSLEGTVVDVKIFTKKGY 950

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKST 1006
            +K+ R+IS   E+ ++L  +  D   ++ +    R+  +L  +  +S      K FKK T
Sbjct: 951  EKDARAISAYEEEKKVLDIEHHDRLTMIQQEEILRISLMLSKEKLISEAKIADKTFKKGT 1010

Query: 1007 VLSSDLISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             +  + +S               ++VQ   E +K  +   K  L +  + K+  ++  D 
Sbjct: 1011 QIPKEELSVLNPFALSTLIKSYSKEVQSRYEQIKTNFLEQKKTLGEEHEEKLSILEKDDI 1070

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +P GV+++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPL
Sbjct: 1071 LPSGVVKLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPMVDMPYTADGEPVDIVLNPL 1130

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI-----GTGS 1180
            GVPSRMN+GQI E HLG     LG++++ ++N       +  LRS + ++         +
Sbjct: 1131 GVPSRMNIGQILEVHLGLVGKNLGRQLEEVLNSQSKQW-VEILRSKMIEIHKLVNPEDKA 1189

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
              + +   DD+ ++  A  W  GV  + PVF+G  +E  + +  +A +D  G++ LYDG 
Sbjct: 1190 MLDFLQKLDDERLIGYARDWSRGVKFAIPVFEGIKQEQFDKLFALAKIDTDGKTELYDGK 1249

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE     V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW
Sbjct: 1250 TGEKMRERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVW 1309

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ L+EMLTIKSDD  GR   Y++I  G    E+  PE+F VL KE+Q+L L 
Sbjct: 1310 ALEAYGAAHTLKEMLTIKSDDTEGRRGAYKAITKGERVGESEIPETFYVLTKELQSLALD 1369

Query: 1361 IDLENSRTKNSAK-----MEEIP---DFNKCEL 1385
            +++       +       ++E     DF+  +L
Sbjct: 1370 VNIYGEEVDENGMPVPITIKEDDRPKDFSSFQL 1402


>gi|78776554|ref|YP_392869.1| DNA-directed RNA polymerase subunit beta [Sulfurimonas denitrificans
            DSM 1251]
 gi|109914408|sp|Q30TP7|RPOB_SULDN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78497094|gb|ABB43634.1| DNA-directed RNA polymerase, beta subunit [Sulfurimonas denitrificans
            DSM 1251]
          Length = 1381

 Score = 1359 bits (3518), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1383 (43%), Positives = 901/1383 (65%), Gaps = 34/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I++P+L+++Q++SY+ FLM+     +R   G++  F+SVFPI      
Sbjct: 10   RLRVDFSKTPQQIEVPNLLQLQQSSYNKFLMLE--EKDRSQSGVETVFQSVFPIHDTQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              +E++  E   PK+ V +C+ R LTYAV L++  RLI++D DE T  K  +KDIKEQSI
Sbjct: 68   LTVEYIDSEVGKPKYTVRECMERGLTYAVSLRMKTRLILWDRDENTKEKLGVKDIKEQSI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   +   KL+Y  +IIPD+G 
Sbjct: 128  FVRDIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEES-TTSGNKLIYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KDI+++RI++RRKVPVT    ALG   ++IL  FYP    +   + +    +
Sbjct: 187  WLYFEYDPKDILYMRINKRRKVPVTIMFRALGYSKQDILKLFYPIQHINIVDNKFLMSFN 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D    ++++  LVD   G+ ++ SGK+L++   ++  ++G+  +    + L   Y+A+
Sbjct: 247  PNDY--SSRLTYDLVD-KNGKILLASGKRLSAKKAQNFIDEGLSEVEYPLEVLLDRYLAK 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
             IV+ ETGEI  +A   IDE  L+++    +++  I    +   +  I N    D     
Sbjct: 304  PIVDPETGEILFDAMTRIDETKLKKLSEIGVKNFSIANDLAEGVDGSIINAFNADADSLK 363

Query: 366  ---KNKDRKDAL----LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
               + +D +D      + IY+VMRPG+  T   A+   N LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEDIEDENHLSAIRIYKVMRPGEPVTKEAAKVFVNQLFFDPERYDLTKVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+ P+ +  +  EDII  +K ++ ++NG+G IDD D+LGNRR+RS+GE+L N+   G
Sbjct: 424  KLGLNIPEYITVLTHEDIIESVKYVIKVKNGQGHIDDRDHLGNRRIRSIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++   ++ +MP DLIN+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 484  LIKMQKAIRDKLSTMSGPMNELMPHDLINSKMITSTIMEFFSGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++++VN +G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATYSKVNEHG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+ + +GKVT+++VYL+A +EE + IA A++ LD+DG F +++V  R  GE +  
Sbjct: 604  FIEAPYKVMKEGKVTDEIVYLTATQEEGKKIAAASNKLDKDGQFIDKMVVTRVDGEILHR 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            P  + ++ D S   VV +AASLIPFLE+DD+NR LMG NMQRQAVPL+K EAP VGTG+E
Sbjct: 664  PVTECNYADLSSHMVVGVAASLIPFLEHDDANRALMGANMQRQAVPLIKHEAPIVGTGVE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +VA+ S   + A+R+GIVE+VD   I +   +         +D Y L K  R+NQNT  
Sbjct: 724  KLVARDSWECVKARRSGIVEKVDGKHIYVMGDDD----GEIYIDYYPLQKNLRTNQNTAF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q+P+V +G  V    +IADGP+ D G+LALG N +VAFMPW+GYNFED+++ISER++ +
Sbjct: 780  GQKPIVNIGQRVEIGQVIADGPNMDQGELALGVNAMVAFMPWNGYNFEDAIVISERLIRK 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E EV AR+ K G EEITRDIPNV ++ L ++DE GII +G  V  G ILVG
Sbjct: 840  DAFTSVHIYEKEVEARELKHGVEEITRDIPNVRDDELSHLDESGIIKIGTNVTGGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + G VVDV+IF + G DK+ R+
Sbjct: 900  KVSPKGEVKPTPEERLLRAIFGEKAGHVINKSLYCPPSMEGVVVDVKIFTKKGYDKDART 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK----GFKKSTVLSSDL 1012
            + +E+E+ + L R+  D  +++D+    R+ ++L  +  ++  K     +K   +++ + 
Sbjct: 960  LELEKEERDYLEREHYDRLLMIDKEEMLRVTKLLTKEPLINDIKIGNTSYKAGDIINGED 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + E  R           E++Q      K  ++  K +  D  + K+  ++  D +P GV+
Sbjct: 1020 LVEVNRFAMNAIIKSFSEEIQSEYNKTKNYFQKEKRLFRDEHEEKLNILEKDDILPNGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+++DG  VD+ LNPLGVPSRM
Sbjct: 1080 KHVKIYIATKRQLKVGDKMAGRHGNKGIVSTIVPEVDMPYMEDGRGVDVCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH---TEKISDY 1188
            N+GQI E HLG A   LG +I +   + K    I  LR+ + ++          + + D 
Sbjct: 1140 NIGQILEMHLGMAGRELGHQI-TKEFESKQKDFIKNLRAKMIEIADVAQMMNAAKTLGDM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L  A  W  GV  ++P+F+G +      +  +A +D  G+++LY+GLTGE     
Sbjct: 1199 SDELLLHHARDWSRGVKFASPIFEGVNAVEFEKLFALAKMDTDGKTVLYNGLTGEKIKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+Y+LKL+H+V +K++ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1259 VNVGYMYILKLHHLVDEKIHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAS 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLTIKSDDV GR R Y++I  G    E+G PE+  VL KE+Q+L L +++ +   
Sbjct: 1319 AVLKEMLTIKSDDVDGRVRAYKAITKGELVPESGIPETLFVLTKELQSLALDVEIFDEVE 1378

Query: 1369 KNS 1371
             N 
Sbjct: 1379 DNE 1381


>gi|296274141|ref|YP_003656772.1| DNA-directed RNA polymerase subunit beta [Arcobacter nitrofigilis DSM
            7299]
 gi|296098315|gb|ADG94265.1| DNA-directed RNA polymerase, beta subunit [Arcobacter nitrofigilis
            DSM 7299]
          Length = 1381

 Score = 1356 bits (3509), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1383 (43%), Positives = 887/1383 (64%), Gaps = 34/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F KNP+ I+IP+L+++Q+ SYD+FLM  +  + R + G++  FKS+FPI    G 
Sbjct: 10   RLRVDFAKNPQHIEIPNLLQLQQNSYDNFLM--VGKESRTDAGIEKVFKSIFPIHDAQGR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              L+++  E   PK+DV + + R LTY++PLKI +RL ++D++E TG K  +KD+KEQS+
Sbjct: 68   ITLDYIESEVGKPKYDVRESMVRGLTYSIPLKIKIRLTLWDLNEKTGEKIGVKDMKEQSL 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F++ G++R+VV+QLHRSPG+ F  ++       KL+Y  +IIPD+G 
Sbjct: 128  FVREIPLMTDRTSFIVNGVERVVVNQLHRSPGVIFKEEESNT-AGNKLIYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVPVT    ALG   E+I+  FYP +    + + +    S
Sbjct: 187  WLYFEYDAKDVLYVRINKRRKVPVTILFRALGYSKEDIIKMFYPILNIKIKNNKFLTEFS 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D     +V   + D D G  VI +GK+LT+   K+L + G+K +    + L     A 
Sbjct: 247  PEDF--TGRVEFDIKD-DKGNLVIAAGKRLTARKAKALVDGGLKLVEYPVELLMDRSTAG 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I + E+GE+  ++   +DE  L+++         I    +   +  I N    D     
Sbjct: 304  TIFDPESGEVLFDSLTHLDELKLKKLLDLGFESFDIANDLAEGVDDSIINAFAADAESLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+     LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLRQTEQLEDENDLAAIRIYKVMRPGEPVTKEAAKDFVKKLFFDPERYDLTKVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L ++ P+ V  +  ED+I  ++ LV +++G G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLGVNVPEYVTTLTYEDVIKTVQYLVKVKSGHGHIDDRDHLGNRRIRAIGELLANEMHSG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I+++++++   ++ +MP DL+N+K + S + EFF S QLSQ  +  N LS +T
Sbjct: 484  LIKMQKAIRDKMTTLSGTLEDIMPHDLVNSKMITSTITEFFTSGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L++FA+VN  G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTFAKVNELG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV DG V+N+++Y++A +EE   IA  ++ +D++G   E L+  R  GE ++V
Sbjct: 604  FIEAPYKKVNDGIVSNEIIYVTATQEEGLLIAPGSTKVDDNGKIVEPLIEARQDGEILIV 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             R K++ ID S + V+ +AASLIPFLE+DD+NR LMG NM RQAVPLL+  AP VGTG+E
Sbjct: 664  ERGKVNLIDISSQMVMGVAASLIPFLEHDDANRALMGSNMMRQAVPLLRPNAPIVGTGLE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              VA+ +  AI A R GIVE+ DA  I +R  +     + + +D Y + K  R+N NT  
Sbjct: 724  KTVARDAWEAIKADRTGIVEKADAKNIYVRGEDE----NGAFIDHYSVNKNVRTNNNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             QR  VK GD V +  +IADGPS D G+LA+G N  VAFMPW+GYN+ED++++S+R++ E
Sbjct: 780  GQRIAVKEGDIVEKGQVIADGPSMDKGELAVGVNACVAFMPWNGYNYEDAIVLSQRLIKE 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI E +V  R+ K G EEITRD+P V +E + ++DE GI+ VG  + PG I+VG
Sbjct: 840  DAFTSIHIYEKDVECRELKHGNEEITRDLPGVKDESITHLDESGIVKVGTFIKPGMIMVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKGE   TPEE+LLRAIFGEKA  V + SL  P+ + GTVVDV++F + G +K+ R+
Sbjct: 900  KVTPKGEIKPTPEERLLRAIFGEKAGHVINKSLYCPTSMEGTVVDVKVFTKKGYEKDSRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK----GFKKSTVLSSDL 1012
            ++    +   L     D+ ++LDR    ++ ++L               +KK  V+  D+
Sbjct: 960  VAEIESEKAELDLKHHDKLLMLDREEILKINDLLSKALLAKDVDLDDVVYKKGQVIPLDV 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +S   R    +     D+ V++    +K  +   KS L    + K+E ++  D +  GV+
Sbjct: 1020 LSSVNRFAMKKVVSSYDKDVEKKYNDIKEYFINQKSRLRTDHEEKLEVLEHDDILQSGVI 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV+VA KR I+ GDKMAGRHGNKGIVS I+P  DMP+L+DG+ VD++LNPLGVPSRM
Sbjct: 1080 KQVKVYVATKRKIKVGDKMAGRHGNKGIVSNIVPQVDMPYLEDGSTVDVILNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH---TEKISDY 1188
            N+GQI E HLG     LG +I+ +  D K    +S LR+ + ++          E ++  
Sbjct: 1140 NIGQILEVHLGLVGKRLGTQIQDI-FDAKKTEFVSELRAKMTEIADVAKLMNGKEFLAKL 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             DD ++  A+ W  GV  +T VFDG  E+    +  +A +D  G++ L DG TG+     
Sbjct: 1199 SDDELVDYAQDWTKGVRFATQVFDGVKEDEFLKLFELAKIDLDGKTNLIDGKTGDKMKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA 
Sbjct: 1259 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAT 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLT KSDDV GRTR Y +I  G +  ++G PE+F VL KE++ALGL +++ +   
Sbjct: 1319 AVLKEMLTTKSDDVEGRTRAYRAISNGENVPDSGVPETFFVLTKELKALGLDVEIFDEVE 1378

Query: 1369 KNS 1371
             N 
Sbjct: 1379 NNE 1381


>gi|157738103|ref|YP_001490787.1| DNA-directed RNA polymerase subunit beta [Arcobacter butzleri RM4018]
 gi|315636455|ref|ZP_07891697.1| DNA-directed RNA polymerase subunit beta [Arcobacter butzleri JV22]
 gi|182676551|sp|A8EVZ4|RPOB_ARCB4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157699957|gb|ABV68117.1| DNA-directed RNA polymerase, beta chain [Arcobacter butzleri RM4018]
 gi|315479236|gb|EFU69927.1| DNA-directed RNA polymerase subunit beta [Arcobacter butzleri JV22]
          Length = 1382

 Score = 1355 bits (3508), Expect = 0.0,   Method: Composition-based stats.
 Identities = 599/1384 (43%), Positives = 889/1384 (64%), Gaps = 34/1384 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F KNP+ I+IP+L+++Q+ SYD FLM+    ++R   G++  FKS+FPI      
Sbjct: 10   RLRVDFAKNPQKIEIPNLLQLQQTSYDTFLMIG--QEDRTTAGIEKVFKSIFPIHDVQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              L+++  E   PK+DV + + R LTY++PLKI +RL ++D+DE TG K  +KD+KEQS+
Sbjct: 68   LTLDYLGSEVGKPKYDVRESMVRGLTYSIPLKINIRLTLWDLDEKTGEKIGVKDMKEQSL 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F++ G++R+VV+QLHRSPG+ F  ++       KL+Y  +IIPD+G 
Sbjct: 128  FIREIPLMTDRTSFIVNGVERVVVNQLHRSPGVIFKEEESNT-ADNKLIYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+DSKD+++VRI++RRKVPVT    ALG   E+I+  FYP +    + + +    +
Sbjct: 187  WLYFEYDSKDVLYVRINKRRKVPVTILFRALGYSKEDIIKLFYPIVNIKIKNNKFLTEFN 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D M   ++   + D D G  VI +GK+LT+   K+L E G+K +    + L     A 
Sbjct: 247  PDDFM--GRIEFDVKD-DKGNLVIGAGKRLTARKAKALIEGGLKLIEYPLELLMDRSTAN 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I + E+GE+  +A   +DE  L+++         I    +V  +A I N    D     
Sbjct: 304  TIYDPESGEVLFDALTNLDELKLKKLLDLGFESFDIANDLAVGIDASIINAFKADAESLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+     LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEQIDDENDLAAIRIYKVMRPGEPVTKEAAKDFVKKLFFDPERYDLTKVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L ++ P+ V  +  ED+I  ++ LV +++G G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLGVNVPEYVTTLTYEDVIKTVQYLVKVKSGHGHIDDRDHLGNRRIRAIGELLANELHAG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I+++++++   ++ +MP DL+N+K + S + EFF S QLSQ  +  N LS +T
Sbjct: 484  LIKMQKAIRDKMTTLSGTLEDLMPHDLVNSKMITSTITEFFTSGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F++VN  G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTFSKVNDLG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R  GE +L+
Sbjct: 604  FIEAPYKKVVDGVVTNEISYYTATQEEGLVIAPGSTKVDENGKIIEPLIEVRKNGEILLM 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             R  +D ID S + V+ +AASLIPFLE+DD+NR LMG NM RQAVPLL+  AP VGTG+E
Sbjct: 664  ERNSVDLIDISSQMVMGVAASLIPFLEHDDANRALMGSNMMRQAVPLLRPSAPVVGTGLE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +VA+ +  AI A RAG+VE+ DA  I IR  +     + + +D Y + K  R+N NT  
Sbjct: 724  KIVARDAWEAIKANRAGLVEKADAKNIYIRGEDE----NGAFIDHYTVNKNVRTNNNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             QR  VK GD V++  +IADGPS D G+LA+G N +VAFMPW+GYN+ED++++SER++ E
Sbjct: 780  GQRIAVKEGDFVQKGQVIADGPSMDKGELAVGINAMVAFMPWNGYNYEDAIILSERLIEE 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+  R+ K G EEITRD+P V EE + ++D  GI+ VG  V PG ILVG
Sbjct: 840  DAFTSVHIYEKEIECRELKHGNEEITRDLPGVKEESISHLDNSGIVKVGTYVTPGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKGE   TPEE+LLRAIFGEKA  V + SL  P+ + GTVVDV++F + G +K++R+
Sbjct: 900  KVTPKGEIKPTPEERLLRAIFGEKAGHVINKSLVCPTSMEGTVVDVKVFTKKGYEKDDRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK----GFKKSTVLSSDL 1012
            ++    +   L     D+ ++LDR    ++ ++L         +     +KK   +  D+
Sbjct: 960  VAEIESEKAELDLKHHDKLLMLDREEILKINDLLLKATLTKDVELDDVVYKKGETIPVDV 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            ++   R    +      +++++    +K  +   K+ L +  + K++ ++  D +  GV+
Sbjct: 1020 LNNVNRFAMKKVVSSYSKEIEKAYNDIKEYFIKQKAHLREEHEEKLQILEHDDILSSGVI 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV++A KR I+ GDKMAGRHGNKGIVS I+P  DMP+L+DGT VD++LNPLGVPSRM
Sbjct: 1080 KQVKVYIATKRKIKVGDKMAGRHGNKGIVSNIVPKVDMPYLEDGTTVDVILNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH---TEKISDY 1188
            N+GQI E HLG A   LG +I+ +  + K    I+ LR+ + ++            +   
Sbjct: 1140 NIGQILEVHLGLAGKKLGNQIQDI-FEAKRADFIAELRAKMTEIASVAKLMNGKAFMDSL 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            +D+ +++ A+ W  GV  +T +FDG   E    +  +A +D  G+ +L+DG TGE     
Sbjct: 1199 NDEELVQYAQDWAKGVRFATQIFDGVKAEEFAKLFELAKIDSDGKCVLFDGKTGEKMKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA 
Sbjct: 1259 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAT 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLT KSDDV GRT+ Y +I  G +   +G PE+F VL KE++AL L +++     
Sbjct: 1319 NVLKEMLTTKSDDVEGRTKAYRAIANGENVPNSGVPETFFVLTKELKALALDVEIFGEVE 1378

Query: 1369 KNSA 1372
             N  
Sbjct: 1379 NNEQ 1382


>gi|118475419|ref|YP_892468.1| DNA-directed RNA polymerase subunit beta [Campylobacter fetus subsp.
            fetus 82-40]
 gi|158512509|sp|A0RQI5|RPOB_CAMFF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|118414645|gb|ABK83065.1| DNA-directed RNA polymerase, beta subunit [Campylobacter fetus subsp.
            fetus 82-40]
          Length = 1379

 Score = 1355 bits (3508), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1383 (43%), Positives = 884/1383 (63%), Gaps = 36/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F    + ID+P+L+++QK S+DHFL ++   + +   G++  FKS+FPI      
Sbjct: 10   RLRVDFSNVAKEIDVPNLLQLQKKSFDHFLNLD---NSQTESGIEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+VS E   P++ V +C+ R LTY V LKI +RLIV D DE T  K  +KDIKEQ I
Sbjct: 67   LTLEYVSSEISKPRYTVRECMERGLTYCVNLKIKIRLIVHDRDEKTSEKVGVKDIKEQEI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++    ++ KL+Y  +IIPD+G 
Sbjct: 127  FVREIPLMTDRISFIINGVERVVVNQLHRSPGVIFKEEESPTVVN-KLIYTAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD+++VRI++RRKVP+T    ALG   ++I+  FYP    + + + +    +
Sbjct: 186  WLYFEYDTKDVLYVRINKRRKVPITILFRALGYKKQDIVKLFYPIQTLNIKNNKFLTMFN 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D     +V   + D D G  + ++GK+LT      L E G+KF+    + L   Y+A 
Sbjct: 246  PDDF--SGRVDYDIKDED-GNILHQAGKRLTKKKADKLIEDGLKFVEYPIEVLVNRYLAS 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             +++ E+GE+  +    +DE  L +I  +E   I I    +   +  I N+ + D     
Sbjct: 303  PVIDKESGEVIYDTLTQLDENKLAKIV-AEQNSIEIANDLASGVDDAIINSFLQDYETLK 361

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A +  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 362  LLKQTEGLEDENDLAAIRIYKVMRPGEPVVKEAARTFVNDLFFNPERYDLTKVGRMKMNH 421

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L  P+ V  +  EDII   K L+ ++NG+G IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 422  KLGLSVPEYVTVLTNEDIIKTAKYLIKVKNGQGYIDDRDHLGNRRIRSIGELLANELHLG 481

Query: 479  LLRMERSIKERISS--VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
             ++M+++I+++ +S   ++D +MP DL+N K + + + EFF   QLSQ  +  N LS +T
Sbjct: 482  FVKMQKAIRDKFTSLSNNVDELMPYDLVNPKMITTTIMEFFTGGQLSQFMDQTNPLSEVT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 542  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTYAKVNDLG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E+PYR+V DGKVTN++VYL+A +EE   IA A++ LD +    E+L+  R  GE +L 
Sbjct: 602  FVESPYRRVIDGKVTNEIVYLTATQEEGHIIAPASTVLDANDIIKEDLIEVRRDGEMLLA 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE +  ID     V+ +AASLIPFLE+DD+NR LMG NMQRQAVPLL++ AP VGTGME
Sbjct: 662  KREDVTLIDLCSGMVMGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSTAPIVGTGME 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA+ +  AI AKR G++E+VD   I I   +     +   +D Y + K  R+NQNT  
Sbjct: 722  AIVARDAWEAIKAKRGGVIEKVDNRNIFILGEDE----NGPYIDQYTMEKNLRTNQNTTF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +Q P+VK GD V+   IIADG S + G+LA+G+N L+AFMPW+GYN+ED++++SERM+  
Sbjct: 778  SQHPIVKKGDMVKSGQIIADGSSMEKGELAIGKNALIAFMPWNGYNYEDAIVMSERMIRA 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G  + PG ILVG
Sbjct: 838  DAFTSVHIYEKEIEARELKDGVEEITRDIPNMKEEDLMHLDESGIVKIGTHIKPGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G V+DV+IF + G +K+ RS
Sbjct: 898  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYAGASLEGVVIDVKIFTKKGYEKDARS 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
                 ++  +L ++  D  ++LDR    R+  +L      S    G   +KK   +    
Sbjct: 958  FKAYEDEKNILEKEHHDRLLMLDREEMLRVTALLSKNPLESELEIGKNSYKKGDKIKRSD 1017

Query: 1013 ISEYPRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R     +     +++Q+  E +K  ++  K  L+D    K+E ++  D +P GV+
Sbjct: 1018 LDNVNRFTLNTYVKCFSKEIQKTYEDMKAYFQNEKKKLKDEHDAKLEILEKDDILPSGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDIVLNPLGVPSRM
Sbjct: 1078 KLVKVYLATKRKLKVGDKMAGRHGNKGIVSNIVPDVDMPYLPNGRTVDIVLNPLGVPSRM 1137

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG   + LG++I+ +  + K    I  LR+ + ++            +S  
Sbjct: 1138 NIGQILESHLGLVGMKLGEQIEEI-FENKKAEWIKELRAKMTEIADVSRLMDAKAILSKI 1196

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            DDD ++  A  W SGV  +TP+F+G   +    +  MA +D  G++ LYDG TG      
Sbjct: 1197 DDDKLIDYARDWASGVRFATPIFEGVKADEFKKLFEMAKIDMDGKTELYDGRTGSKMAER 1256

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1257 VNVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALSGGQRFGEMEVWALEAYGAA 1316

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLT+KSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +   
Sbjct: 1317 HTLREMLTVKSDDVEGRLAAYKALTRGENVPSTGIPETFFVLTNELKSLALDVEIYDEEE 1376

Query: 1369 KNS 1371
             N 
Sbjct: 1377 NNE 1379


>gi|319957693|ref|YP_004168956.1| DNA-directed RNA polymerase subunit beta [Nitratifractor salsuginis
            DSM 16511]
 gi|319420097|gb|ADV47207.1| DNA-directed RNA polymerase subunit beta [Nitratifractor salsuginis
            DSM 16511]
          Length = 1385

 Score = 1354 bits (3505), Expect = 0.0,   Method: Composition-based stats.
 Identities = 599/1372 (43%), Positives = 883/1372 (64%), Gaps = 32/1372 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P  I+IP L+++Q+ SY++FLMM+    +R N  ++  F+S FPI      
Sbjct: 10   RLRVDFSKTPRQIEIPHLLQLQQNSYENFLMMD--AKDRSNSIIEKVFRSSFPIHDQQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              L +   E   PK+ + +C+ R LTY+V LK+ + L +++ DE TG +   K+IKEQ+I
Sbjct: 68   ITLSYKGSEIIKPKYTIRECMERGLTYSVSLKLKIALTIWNRDERTGERLDPKEIKEQAI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+ D+PLMT   +F++ G++R++V+QLHRSPG+ F   +     + KL+Y+ +IIPD+G 
Sbjct: 128  YVRDIPLMTDRTSFIVNGVERVIVNQLHRSPGVIFKEAEAATVAN-KLIYSAQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KDI++ RI++RRK+PVT    AL    E+I+  FYP      R   +     
Sbjct: 187  WLYFEYDAKDILYARINKRRKIPVTILFRALDYTKEDIIKLFYPTKEIHIRDGRFIVRFD 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             AD +   +    + D+D G  ++  GK+LT    + L ++G++++    + L   ++AE
Sbjct: 247  PADFV--GRAEYDIRDVD-GNVIVNMGKRLTKKKAQKLADEGLEWVEYPVEILMDRHLAE 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN--- 367
             I++ E+GE+  +    +DE  + +I    I    I    +   ++ I  + + D+    
Sbjct: 304  PIIDQESGEVIYDVITQLDENKIRKIVEMGIESFKIADDLAEGTDSSIIRSFIADQESLK 363

Query: 368  --KDRKDAL-------LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
              K  ++         + IY+VMRPG+  T   A++    LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEEIDDENLLSAIRIYKVMRPGEPVTPEAAKAFLRQLFFDPERYDLTKVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L  D P+ V  +  EDII  +K L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLGQDVPEYVTVLTSEDIINTVKYLIKVKNGEGQIDDRDHLGNRRIRAIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++IK+++++V   +D +MP DL+N+K + + + EFF   QLSQ  +  N LS +T
Sbjct: 484  LMKMQKAIKDKMTTVSGSLDDLMPHDLVNSKMITNTILEFFSGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++A+VN  G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATYAKVNDLG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+ V D KVT+++VY++A +EEN+ IA A++ +DE+G   E+L+  R  G   L 
Sbjct: 604  FIEAPYKVVKDRKVTDEIVYITATQEENKVIAPASTKVDENGYIVEDLIETRLNGNIGLN 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              EK++ ID +P  V    A+LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTGME
Sbjct: 664  EAEKVNLIDVAPLMVSGATAALIPFLEHDDANRALMGSNMQRQAVPLLKPEAPMVGTGME 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++VA+ +  AI AKR G+VE+VDA  I ++  +     +   +D Y L K  R+NQNT  
Sbjct: 724  AIVARDAWEAIKAKRTGVVEKVDARNIYVKGEDE----NGLFIDHYVLEKNMRTNQNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+V VG EV++  +IADGP+ D G+LA+G+N+LVAFMPW+GYN+ED++++SE+++ E
Sbjct: 780  GQVPIVHVGQEVKKGQVIADGPNMDQGELAIGKNILVAFMPWNGYNYEDAIILSEKLIRE 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEITRDIPN+ EE L ++DE GI+ +G  V PG ILVG
Sbjct: 840  DTFTSVHIYEKEIEARELKHGTEEITRDIPNIREEDLMHLDESGIVKIGTHVKPGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFG+KA  V + SL  P+ + G VVD++IF + G +K+ R+
Sbjct: 900  KVSPKGEIKPTPEERLLRAIFGDKAGHVVNKSLYCPASMEGVVVDIKIFTKKGYEKDARA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEIL----CGQNAVSGPKGFKKSTVLSSDL 1012
            I    E+   L RD  D+ +++DR    ++   L      Q+   G K +K    +  + 
Sbjct: 960  IRAYEEERARLDRDHHDKLLMIDREEILQITSFLAKQPLAQDVTVGEKTYKAGEKIPEEE 1019

Query: 1013 ISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            I+   R           E+VQ+  E++K  +   K  L+   + K++ ++  D +P GV 
Sbjct: 1020 IASINRFALRNVVASYPEEVQKEYEAMKNSFLKQKKRLKTEHEEKLQILEKDDILPSGVT 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR I+ GDKMAGRHGNKGIVS I+P  DMP+++DGTPVD++LNPLGVPSRM
Sbjct: 1080 KLVKVYIATKRKIKVGDKMAGRHGNKGIVSNIVPEIDMPYMEDGTPVDLILNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKAN--GDISPLRSFLEKVIGTGSHTEKISDYD 1189
            N+GQI E HLG     LG +I+ +    +A+   ++      +           ++    
Sbjct: 1140 NIGQILEVHLGLIGKKLGAQIQEIYESKRADFVKELRAKMKEIADTAKLMKAKNELETMS 1199

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D+ +L  A  W  GV  + P F+  +EE    +  +A +D  G+++LYDG TGE     V
Sbjct: 1200 DEELLEYARDWAKGVKFAAPAFESPNEEEFAKLFELAKIDSDGKTVLYDGKTGERMLERV 1259

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA+
Sbjct: 1260 NVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAAH 1319

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
             L+EMLTIKSDDV GR R Y +I  G    E+G PE+  VL KE+QALGL +
Sbjct: 1320 TLKEMLTIKSDDVEGRARAYRAITRGESVPESGIPETMFVLTKELQALGLDV 1371


>gi|257460967|ref|ZP_05626067.1| DNA-directed RNA polymerase, beta subunit [Campylobacter gracilis
            RM3268]
 gi|257441630|gb|EEV16773.1| DNA-directed RNA polymerase, beta subunit [Campylobacter gracilis
            RM3268]
          Length = 1397

 Score = 1353 bits (3503), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1382 (43%), Positives = 883/1382 (63%), Gaps = 36/1382 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I+IP+L+++QK S+DHFL ++   +     G++  FK++FPI      
Sbjct: 29   RLRVDFSKVPKDIEIPNLLQLQKKSFDHFLNLD---NSGGESGIEKVFKAIFPIHDAQNR 85

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              +E+VS E   PK+ + +C+ R LTY+V LK+ LRL+V + DE TG K  +K+IKEQ I
Sbjct: 86   LSIEYVSSEISKPKYSIRECMERGLTYSVNLKMKLRLLVHERDEKTGKKIGVKEIKEQDI 145

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT   +F+I G++R+VV+QLHRSPG+ F  ++    L+ KL+Y  +IIPD+G 
Sbjct: 146  FIRDIPLMTDRISFIINGVERVVVNQLHRSPGVIFKEEESPTVLN-KLIYTAQIIPDRGS 204

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KD+++VRI++RRKVP+T    ALG   ++I+  FYP      +   +     
Sbjct: 205  WLYFEYDVKDVLYVRINKRRKVPITILFRALGYKKQDIIKLFYPIKTIYIKKGKFLTDFD 264

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              +     ++   ++  + GE + ++ K+LT    + L E G+K +   ++ L   Y+A+
Sbjct: 265  PKEYA--GRLDYDIIS-EKGEVLHQASKRLTVKKAEKLAEDGLKLIEYPAEILAERYLAD 321

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             IV+  +GE+  ++   +DE  L +I ++E +   I    +   +  I N+ + D +   
Sbjct: 322  AIVDKNSGEVLFDSLTALDEGKLAKIANTE-KKFTIANDLASGVDTSIINSFIQDADALK 380

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+      A+S  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 381  LLQQSEGIDDENDLAAIRIYKVMRPGEPVVKEAAKSFVNDLFFNPERYDLTKVGRMKMNH 440

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L ++ P+ V  +  EDII   K L+ ++NG G IDD DNLGNRR+RS+GE+L N+  LG
Sbjct: 441  KLGIEAPEYVTVLSSEDIIKTAKYLIRVKNGDGFIDDRDNLGNRRIRSIGELLANEMHLG 500

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
             ++++++IK++ +  S ++D +MP D +N K + + + EFF   QLSQ  +  N LS +T
Sbjct: 501  FIKVQKAIKDKFTGISGNLDELMPYDFVNPKIITTTLMEFFTGGQLSQFMDQTNPLSEVT 560

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++A+VN  G
Sbjct: 561  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATYAKVNDLG 620

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PY+KV +GKVT+++VYL+A +EE   IA A++ LDE+G+  EEL+  R  GE I+ 
Sbjct: 621  FVEAPYKKVVNGKVTDEIVYLTATQEEGLVIAPASAKLDEEGNIVEELLEVRKDGENIMA 680

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             RE I  ID     V  +AASLIPFLE+DD+NR LMG NMQRQAVPLL + AP VGTGME
Sbjct: 681  KREDISLIDLCSGMVAGVAASLIPFLEHDDANRALMGSNMQRQAVPLLHSTAPIVGTGME 740

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            +++A+ S  AI A R G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 741  AIIARDSWEAIKANRDGVVEKVDNKNIFILGEDEK----GPFIDHYSMEKNLRTNQNTTF 796

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +QRP+V+ GD ++   IIADGPS D G+LA+G+N L+AFMPWHGYN+ED++++SE+M+  
Sbjct: 797  SQRPIVRKGDVIKAGQIIADGPSMDGGELAIGKNALIAFMPWHGYNYEDAVVMSEKMIRA 856

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D +TS+H+ E E+ AR+ K G EEITRDIPN+ EE L ++D+ GI+ +G  V PG ILVG
Sbjct: 857  DEYTSVHVYEKEIEARELKDGVEEITRDIPNIKEEELTHLDDSGIVKIGTHVKPGMILVG 916

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKGE   TPEE+LLRAIFGEKA  V + SL   + + G V+DV+IF + G +K+ R+
Sbjct: 917  KVTPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASMEGVVIDVKIFTKKGYEKDPRT 976

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
                 ++   L R+  D  ++LDR    +++ +L      S      K +KK   +  + 
Sbjct: 977  NKAYEDEKTELEREHHDRLLMLDREEMLKVVALLSKSALQSDQSLNKKDYKKGDKVKKEE 1036

Query: 1013 ISEYPRSQWWQFAVQDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R     F     K VQ+  E LK  ++  K  L++    KIE ++  D +P GV+
Sbjct: 1037 LESSNRFTLNSFVKAYSKAVQKEYEELKNHFQNEKRKLKEEHDEKIEILEKDDILPSGVV 1096

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L  G  VDIVLNPLGVPSRM
Sbjct: 1097 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSNIVPEVDMPYLPSGQRVDIVLNPLGVPSRM 1156

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E+HLG     LG++I  ++ + K    I  LR+ + ++ G        + +   
Sbjct: 1157 NIGQIMESHLGLVGWRLGEQIAKIL-EEKTGEWIKTLRAKMIEIAGVSKLMQAKKTLEKI 1215

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L+ A  W  GV  S P+F+G   E    +  MA +D+ G++ LYDG TGE     
Sbjct: 1216 SDEDLLKYARDWAKGVRFSAPIFEGIVPEDFKKLFEMAGIDQDGKTELYDGRTGEKIKER 1275

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VG +Y LKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1276 VNVGCMYYLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1335

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++  +  
Sbjct: 1336 YTLREMLTIKSDDVDGRLAAYKALTKGENVPSTGIPETFFVLTNELKSLALDVEIYENGE 1395

Query: 1369 KN 1370
              
Sbjct: 1396 NK 1397


>gi|77921157|gb|ABB05344.1| RpoB [Micavibrio sp. EPB]
          Length = 1193

 Score = 1353 bits (3501), Expect = 0.0,   Method: Composition-based stats.
 Identities = 698/1195 (58%), Positives = 899/1195 (75%), Gaps = 34/1195 (2%)

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            D+PLMTK+GTF++ G +R++VSQ+HRSPG+ FDHD G+   SGK L+A R+IP +G W+D
Sbjct: 1    DMPLMTKNGTFIVNGTERVIVSQMHRSPGVFFDHDGGKTHASGKYLFAARVIPYRGSWLD 60

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------------GMDSEEI 228
             EFD+KD+++VRIDRRRK+PVT+ L AL                         GM +EEI
Sbjct: 61   FEFDAKDLMYVRIDRRRKLPVTTLLRALDSSMTADYRAKCEENDQPVDPLMVQGMSNEEI 120

Query: 229  LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
            L TFY  + YS+    W      A  M G K+   L+D  TG+ V+++G K+T+ ++K L
Sbjct: 121  LRTFYGVVTYSKEKKGWKTAFDGA-RMRGVKLDHDLIDAKTGKSVLDAGTKITARVIKQL 179

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            +EKG+K + +    L G Y+AEDI + +TG++  EAG  I E+ L+    S + DIP+L 
Sbjct: 180  EEKGLKDMLVEDAQLIGQYLAEDIFDAKTGQVIFEAGHEITEEELKAFDKSGVTDIPVLA 239

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D VN   Y+RNTL+ DK   R++AL+DIYRVMRPG+  T   A+++F+ LFFD+++YDL
Sbjct: 240  IDHVNVGPYVRNTLLADKCDTREEALIDIYRVMRPGEPPTVESAQALFDSLFFDAERYDL 299

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            S VGRVKMN+RLNLD  D VR +RK+DI+AI+K L  L++G G IDDIDNLGNRRVRSVG
Sbjct: 300  SAVGRVKMNLRLNLDAEDTVRVLRKDDILAILKYLHGLKDGAGEIDDIDNLGNRRVRSVG 359

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E+++NQ R+GLLRMER+I+ER+SSVDID+ MP DLIN KPV  +V EFF SSQLSQ  + 
Sbjct: 360  ELMENQVRVGLLRMERAIRERMSSVDIDNYMPHDLINPKPVAVSVREFFGSSQLSQFMDQ 419

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +
Sbjct: 420  TNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLAT 479

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FARVN YGFIE+PYR+V DGKVT++VVY+SAMEE    IAQA++ L +DG F ++LV CR
Sbjct: 480  FARVNQYGFIESPYRRVVDGKVTDEVVYMSAMEEAKYTIAQASTPLSKDGKFLDDLVSCR 539

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             AGE ++   + I+ ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+++A
Sbjct: 540  QAGENLMATPDTINMIDVSPKQIVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRSDA 599

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTGME+ VA+ SGAA+ A+R+GIV QVDA R+VIR+ E         VDIY+L KFQ
Sbjct: 600  PLVGTGMEAAVARDSGAAVTARRSGIVVQVDATRVVIRATEMTRAD-EPTVDIYKLSKFQ 658

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQ+TC+ Q+PLVKVGD+++  DIIADGPST  G+LALGRN+LVAFMPW+GYNFEDS+L
Sbjct: 659  RSNQSTCITQKPLVKVGDQIKAGDIIADGPSTQFGELALGRNVLVAFMPWNGYNFEDSIL 718

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SER+V+ED+FTSIHIEEFEVMARDTKLG EEITRDIPNV EE LK++DE GI+ +GAEV
Sbjct: 719  LSERIVAEDIFTSIHIEEFEVMARDTKLGTEEITRDIPNVGEEALKHLDEAGIVHIGAEV 778

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              GDILVGK+TPKGESPMTPEEKLLRAIFGEKA DV+DTSLRVP GV+GT+V+VR+FNR 
Sbjct: 779  QAGDILVGKVTPKGESPMTPEEKLLRAIFGEKAADVKDTSLRVPPGVTGTIVEVRVFNRR 838

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK--GFKKST 1006
            G+DK+ R++S+ER +IE LA+D+DDE+ IL+   Y+RL E+L GQ   + PK     K +
Sbjct: 839  GVDKDARALSIERAEIEQLAKDRDDERSILEGGFYARLAEMLVGQTLAAAPKQLDLAKGS 898

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +    +    R  W Q  V++E     +E++   ++ +   L+ RF++K+EK+Q GD++
Sbjct: 899  KIKQSDLDSISRGLWRQIGVENETRMEEIEAMSKTFDDAVDDLKARFESKVEKLQRGDEL 958

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV+++VKVF+A+KR +Q GDKMAGRHGNKG+VSRI+P EDMP+ +DG PVDIVLNPLG
Sbjct: 959  PPGVMKMVKVFIAVKRKMQPGDKMAGRHGNKGVVSRIVPAEDMPYTEDGQPVDIVLNPLG 1018

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA-----NGDISPLRSFLEKVIGTGSH 1181
            VPSRMNVGQI ETHLGWA   LGK+I  LI+ +       +GD+  L+  L+ V G   +
Sbjct: 1019 VPSRMNVGQILETHLGWASANLGKQIGQLIDSFADRKAPSDGDVKKLKEHLKGVYGDKEY 1078

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
             EK++   D  ++ +A   + GVP++TPVFDGA E  I+++L  A L+ SGQ  L DG T
Sbjct: 1079 EEKVTKLSDQHLVEMANNLRGGVPMATPVFDGAVEADIDTLLAKAGLNTSGQVRLIDGRT 1138

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            GE F R VTVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1139 GEYFHRNVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1193


>gi|261838520|gb|ACX98286.1| DNA-dependent RNA polymerase beta-beta prime subunit [Helicobacter
            pylori 51]
          Length = 2890

 Score = 1351 bits (3497), Expect = 0.0,   Method: Composition-based stats.
 Identities = 606/1409 (43%), Positives = 892/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ +KDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGVKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +S 
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQISK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|41017781|sp|Q93MK9|RPOB_EHRSE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|15081474|gb|AAK83924.1|AF401088_1 RNA polymerase beta-subunit [Neorickettsia sennetsu]
          Length = 1357

 Score = 1351 bits (3496), Expect = 0.0,   Method: Composition-based stats.
 Identities = 638/1357 (47%), Positives = 902/1357 (66%), Gaps = 32/1357 (2%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
             D PDL++VQK SY  F+          +      F SVFP+    G A LEFVS     
Sbjct: 14   FDFPDLVKVQKDSYASFVGGGDTGFSISD-----IFASVFPVNDGYGRASLEFVSCRMGE 68

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-------IKDIKEQSIYMGDLP 136
            PK D   C+ R +TY+ PL+  LRL+VF  +              +KD++EQ IYMGD+P
Sbjct: 69   PKHDEYGCVERGITYSAPLRAILRLVVFGDETSGEGSEGVSTEPAVKDVREQEIYMGDIP 128

Query: 137  LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
            +M+K+GTF+I G++R+VVSQ+HR+PG+ FD+DK R+ +SGKL Y  RIIP +G W+D EF
Sbjct: 129  IMSKNGTFIINGVERVVVSQMHRAPGVFFDNDKARS-ISGKLNYIARIIPYRGSWLDFEF 187

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D+KD+++ RID++RK+PVT  L ALG+ +++I + F          D         +   
Sbjct: 188  DAKDVLYFRIDKKRKLPVTFLLRALGLSNKDIFAQFCEVSECRLTKDGKWTVCFVPEKFK 247

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            G ++   L++ +TGE V+  G +++  L ++L  KG+++  +  + +  +Y+A+D+V+ +
Sbjct: 248  GVRLQYDLINAETGELVLAKGNRISIVLARNLYAKGLRYCYMDLEVMKDMYLADDLVSTK 307

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             GE+ +  G  + ++ + ++   ++  I ++ +      +      V   +   ++A+L 
Sbjct: 308  -GEVLLPHGTKLTKEHVAKLEFLDVDSIKLVELKGNYVFS-----TVLQYDCSYEEAMLS 361

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IYRV+RPG++ +   AE +F  LFF  ++YDL  VGR+++N + NL   + +  + KEDI
Sbjct: 362  IYRVVRPGEIPSVESAEKLFESLFFSPERYDLLNVGRIRLNAKFNLSHDESLTVLTKEDI 421

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
               +K L  L+   G +DDID+LGNRRVRSVGE + NQ+R+GL+RM + I E +++ D D
Sbjct: 422  FCTVKELALLQREVGDVDDIDHLGNRRVRSVGEFMDNQFRIGLVRMAKVIVENMATADFD 481

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +VMP ++IN+K + + + EFF SS LSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 482  TVMPCEMINSKILGAVIREFFMSSALSQFMDQTNPLSEITHKRRISALGPGGLNRGRAGF 541

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            E+RDVH THYGRIC  ET EG  IGL++SL  +A++N YGFIETPYR V DG+VT++V Y
Sbjct: 542  EVRDVHTTHYGRICATETPEGATIGLINSLAIYAKINKYGFIETPYRYVRDGRVTDEVTY 601

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            LSA++E    I QA+  +DE+G   ++LV+CR   E + +PR ++ F D S KQ+VS+AA
Sbjct: 602  LSAIDEIKANICQASVRVDEEGYIVDDLVYCRRNYENVFIPRSEVQFADVSAKQIVSVAA 661

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            SLIPFLENDD+NR LMG NMQRQAVPL+  EAP VGTGME  VA+ SGA IVAKRAG+V+
Sbjct: 662  SLIPFLENDDANRALMGSNMQRQAVPLIMPEAPLVGTGMEGYVARGSGAVIVAKRAGVVQ 721

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA  IV+ S           +D Y L KF++SN NTC++QR +V  G  V++ DI+AD
Sbjct: 722  YIDARNIVVASES----KDDFWIDSYTLCKFRKSNHNTCIHQRCVVHQGQRVKKGDILAD 777

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GP+   G+LALGRN++VAF+ W GYNFEDS++IS  +V +D+FTS+H+E FE + RDT+L
Sbjct: 778  GPAIQKGELALGRNLVVAFLSWRGYNFEDSVVISSNVVRDDLFTSVHLEGFECVVRDTRL 837

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            GPEEITRD+  V+EE L  +DE GI CVGA V  GD+LVGK+TPK  SP+TPEEKLLRAI
Sbjct: 838  GPEEITRDVSGVAEEFLHCLDEFGIACVGANVEAGDVLVGKVTPKSSSPVTPEEKLLRAI 897

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FGEKA+DV+D+SL +P GVSG VVDV++  R GI+K  R++ +E++ I+     +D E  
Sbjct: 898  FGEKAIDVKDSSLYLPPGVSGCVVDVKVLQRRGIEKVGRALLIEKQAIDAEKTRRDHELA 957

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +L   IYS L E+L G+ A+S      K  +++ + + +  R  WW+ +V       +++
Sbjct: 958  VLTNYIYSLLKEMLVGKVALSTLAPISKGDLITEEALEKIDRENWWKISVDG---ISSIK 1014

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L+ ++      +   ++   EKI+  DD+  GVL VVKVFVA+K  +Q GDKM+GRHGN
Sbjct: 1015 LLRQRFVDRFDEINKTYEENFEKIRGDDDLAQGVLMVVKVFVAVKHTLQPGDKMSGRHGN 1074

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++SRI+P ED P+L DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LGKKI  L+
Sbjct: 1075 KGVISRIVPAEDTPYLADGTPVDIILNPLGVPSRMNVGQILETHLGWAAYNLGKKISKLL 1134

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
            ++   +   S +    +          ++++  D  ++  +   + GVPV+  VF+G   
Sbjct: 1135 DEGNYSEVKSLVLEIYK---NDRKMMARLNEMTDAEIVEYSRSLRGGVPVAASVFEGPKT 1191

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            + I  +L +A  D SGQ +LYDG+TGE FDR VTVG  YMLKL+H+V+DK++ARS G  S
Sbjct: 1192 DEIERLLVLAGKDPSGQEVLYDGVTGEKFDRKVTVGCKYMLKLHHLVNDKIHARSIG--S 1249

Query: 1277 LV-TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
             V TQQPLGGKS+ GGQR GEME W +QAYGA + LQEMLTIKSDDVVGR  VY+SIV G
Sbjct: 1250 TVDTQQPLGGKSHFGGQRFGEMECWALQAYGATFALQEMLTIKSDDVVGRVNVYDSIVRG 1309

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            ++ F  G PESFNV++ E++AL L+++  +   K   
Sbjct: 1310 DNDFYYGVPESFNVMMNELRALCLNVEFCSDLEKKKD 1346


>gi|307720239|ref|YP_003891379.1| DNA-directed RNA polymerase subunit beta [Sulfurimonas autotrophica
            DSM 16294]
 gi|306978332|gb|ADN08367.1| DNA-directed RNA polymerase subunit beta [Sulfurimonas autotrophica
            DSM 16294]
          Length = 1381

 Score = 1351 bits (3496), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1383 (43%), Positives = 898/1383 (64%), Gaps = 34/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ I++P+L+++Q++SYD FLM  +    R   G++  F+SVFPI      
Sbjct: 10   RLRVDFSKTPQEIEVPNLLQLQQSSYDTFLM--LHAKNRSQSGIEKVFQSVFPIHDAQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              +E++  E   PK+ V +C+ R LTYAV L++  RLI+++ DE T  K  + DIKEQSI
Sbjct: 68   LTVEYIESEVTNPKYTVRECMERGLTYAVSLRMKTRLILWERDENTKEKLGVADIKEQSI 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++       KL+Y  +IIPD+G 
Sbjct: 128  FVRDIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-AGNKLIYTGQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D KDI+++RI++RRKVPVT    ALG   ++IL  FYP        + +    +
Sbjct: 187  WLYFEYDPKDILYMRINKRRKVPVTIMFRALGYSKQDILKLFYPIQTIKIHDNMFSIDFN 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              D    +++S  L+D+   + ++ SGK+L+S   + L + GVK +    + L   Y+AE
Sbjct: 247  PKDYA--SRISYDLIDM-NDKVLVSSGKRLSSKKAQKLLDDGVKEVQYPLEILLERYLAE 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ ETGE+  +    IDE  L+++    + +  I    +   ++ I N    D +   
Sbjct: 304  SIIDPETGEVLFDTMTHIDETKLKKMAEIGVTEFKIANDIAEGVDSSIINAFNADADSLK 363

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+   N LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEEIEDENDLAAIRIYKVMRPGEPVTKEAAKIFVNQLFFDPERYDLTQVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L ++ P+ V  +  EDII  +K ++ ++NG+G +DD D+LGNRR+RS+GE+L N+   G
Sbjct: 424  KLGMNIPEYVTVLTHEDIIESVKYVIKVKNGQGHLDDRDHLGNRRIRSIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I++++S++   ++ +MP DLIN+K + S + EFF   QLSQ  +  N LS +T
Sbjct: 484  LVKMQKAIRDKLSTMSGPMNELMPHDLINSKMITSTIMEFFSGGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L  +A+VN +G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLAMYAKVNEHG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+ + DGKVT+++VYL+A +EE + IA A++ LDE+G F E+L+  R  GE +L 
Sbjct: 604  FIEAPYKVMKDGKVTHEIVYLTATQEEGKMIAAASNKLDENGQFIEDLIAVRQDGEILLR 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              ++ ++ D S + V+ +AASLIPFLE+DD+NR LMG NMQRQAVPLL+A AP VGTG+E
Sbjct: 664  DPKECEYADLSSQMVIGVAASLIPFLEHDDANRALMGSNMQRQAVPLLRANAPMVGTGIE 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +VA+ +   + AKRAG +E+VD   I +   E         +D Y L K  R+NQNT  
Sbjct: 724  KLVARDAWECVKAKRAGKIEKVDGKHIYVMGEED----GEIFIDYYPLQKNLRTNQNTSF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q+P+VK+G+ V +  IIADGP+ D G+LALG N +VAFMPW+GYNFED+++ISER++ +
Sbjct: 780  TQKPIVKIGEMVEKGQIIADGPNMDQGELALGVNAMVAFMPWNGYNFEDAIVISERLIRQ 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E EV AR+ K G EEITRDIPNV ++ L ++DE GI+ +G  V+ G ILVG
Sbjct: 840  DAFTSVHIYEKEVEARELKHGVEEITRDIPNVRDDELAHLDESGIVKIGTTVSGGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL  P  + G VVD+++F + G DK+ R+
Sbjct: 900  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYCPPSMEGVVVDIKVFTKKGYDKDPRA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG----FKKSTVLSSDL 1012
            + +E+E+ + L R+  D  +++D+    R+ ++L  +   S  K     +K    ++ D 
Sbjct: 960  LELEKEERDYLEREHYDRLIMIDKEEMLRVTKLLTREPLQSDIKIGDTEYKAGDTINGDD 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + E  R           +++Q      K  ++  K I  D  + K+  ++  D +P GV+
Sbjct: 1020 LKEVNRFAMNAIVKSFSQEIQDEYNKTKNHFQKQKRIFRDEHEEKLTILEKDDILPNGVV 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+++DG  VD+ LNPLGVPSRM
Sbjct: 1080 KYVKIYIATKRHLKVGDKMAGRHGNKGIVSNIVPEVDMPYMEDGRSVDVCLNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH---TEKISDY 1188
            N+GQI E HLG A   LG +I+    + K    I  LR+ + ++         ++ I + 
Sbjct: 1140 NIGQILEMHLGMAGRELGNQIQEQ-FEAKQKDFIDDLRAKMIEIADVAGMMHASKVIGEM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            DD++ L+ A  W  GV  +TP+F+G D +    +  +A +D  G+ +LYDG TGE     
Sbjct: 1199 DDETFLKYARDWSKGVKFATPIFEGTDAKEFEKLYELAKMDSDGKRVLYDGKTGEKMKER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+Y+LKL+H+V +K++ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1259 VNVGYMYILKLHHLVDEKIHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAS 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             VL+EMLTIKSDDV GR R Y+++  G    E+G PE+  VL KE+QAL L +++ +   
Sbjct: 1319 AVLKEMLTIKSDDVDGRVRAYKALTKGELVPESGIPETLFVLTKELQALALDVEIMDEVE 1378

Query: 1369 KNS 1371
             + 
Sbjct: 1379 DDE 1381


>gi|317182449|dbj|BAJ60233.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            F57]
          Length = 2890

 Score = 1350 bits (3495), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1409 (43%), Positives = 895/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMTK  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTKRTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FTSLD--ANQRMEFDLKDSQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE I
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEII 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I   +       + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGED----KEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDV 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K    +  LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFVKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGTPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317011400|gb|ADU85147.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            SouthAfrica7]
          Length = 2890

 Score = 1350 bits (3495), Expect = 0.0,   Method: Composition-based stats.
 Identities = 609/1409 (43%), Positives = 893/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-SSNKLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPIDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE ++ GE  E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPVMVGE--EVLLDMLAQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFTADYES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  IK L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTIKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV ++ +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVMSETIYLTAIQEDSHVIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++DA  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDAKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S+  E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSMYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ   E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNQYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K    +  LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFVKALRAKMLEIANAINEKDPLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKLAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSAK-----MEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDEMDEDGMPKPIVIKEDDRPKDFSAFQL 1401


>gi|315587086|gb|ADU41467.1| DNA-directed RNA polymerase [Helicobacter pylori 35A]
          Length = 2890

 Score = 1350 bits (3493), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1409 (42%), Positives = 892/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELY 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGEPIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   ++   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSTYEKEKAKLDMEHFDRLTMLNREELLRVSLLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E +K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEIIKNNFLEQKKVLGEEHEEKLSILERDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKRVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401


>gi|307637872|gb|ADN80322.1| DNA-directed RNA polymerase beta subunit [Helicobacter pylori 908]
 gi|325996469|gb|ADZ51874.1| DNA-directed RNA polymerase beta subunit [Helicobacter pylori 2018]
 gi|325998058|gb|ADZ50266.1| DNA-directed RNA polymerase beta subunit [Helicobacter pylori 2017]
          Length = 2890

 Score = 1350 bits (3493), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1399 (43%), Positives = 884/1399 (63%), Gaps = 44/1399 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-SSNKLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K  KE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKEFKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIHSFSADHES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +++R    R+  +L      +      K +KK   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMINREELLRVSSLLSQAILEEPFSHKGKDYKKGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 ----NSRTKNSAKMEEIPD 1379
                +        M +  D
Sbjct: 1373 GDDVDEDGAPKPIMIKEDD 1391



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|108563562|ref|YP_627878.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            HPAG1]
 gi|123373708|sp|Q1CS68|RPOBC_HELPH RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|107837335|gb|ABF85204.1| DNA-directed RNA polymerase, beta subunit [Helicobacter pylori HPAG1]
          Length = 2890

 Score = 1350 bits (3493), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1409 (42%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLSLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDSQ-GKIILLAGKKLTSKKIKELKENHLEWVEYPMDILINRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFLADYES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LRLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGAVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I  ++ D K       LR  + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRVKMLEIANAINEKDPLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +IV G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIVKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|268678994|ref|YP_003303425.1| DNA-directed RNA polymerase subunit beta [Sulfurospirillum deleyianum
            DSM 6946]
 gi|268617025|gb|ACZ11390.1| DNA-directed RNA polymerase, beta subunit [Sulfurospirillum
            deleyianum DSM 6946]
          Length = 1385

 Score = 1349 bits (3492), Expect = 0.0,   Method: Composition-based stats.
 Identities = 599/1383 (43%), Positives = 886/1383 (64%), Gaps = 35/1383 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P+ ID+P+L+++Q+ SY+ FL +    + +   G++  FKS+FPI      
Sbjct: 10   RLRVDFSKVPKKIDVPNLLQLQQKSYEQFLNVE---NLKDESGVEKVFKSIFPIHDPQNR 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE+   E   P++ V +C+ R LTY+V +K+ +RLI++D DE TG K+ +KDIKEQ+I
Sbjct: 67   ITLEYAGSEIGKPRYTVRECMERGLTYSVSIKMNIRLILWDKDEKTGEKTGVKDIKEQAI 126

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +FVI G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 127  FIREIPLMTDRTSFVINGVERVVVNQLHRSPGVIFKEEESPTVAN-KLIYNAQIIPDRGS 185

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD + VRI++RRKVP+T    ALG   ++IL  FYP +    R + +    S
Sbjct: 186  WLYFEYDAKDTLFVRINKRRKVPITILFRALGYSKQDILKLFYPVLNIMIRENKFLIEFS 245

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A + +   +V   L D + G  ++ +GK+L     +   E GVKF+    + L   +++ 
Sbjct: 246  ADNFL--GRVDFDLKD-EHGNLLLAAGKRLARKKAEKFIEDGVKFIEYPVEILVNRFLSS 302

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
             I++ E+GE+  +    +DE  L +I   +   I I    +   +  I N+ + D     
Sbjct: 303  PIIDQESGEVLYDTLAQLDEGKLAKIIEQKCETIEIANDLASGVDDAIINSFIADTETLK 362

Query: 369  ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      +   A + IY+VMRPG+  T   A+     LFF+S++YDL+ VGR+KMN 
Sbjct: 363  LLRQTENVEDENDLAAIRIYKVMRPGEPVTKEAAKLFVKDLFFNSERYDLTKVGRMKMNH 422

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L  P+ V  +  EDII   K L+ ++NG+G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 423  KLGLSVPEYVTIMTSEDIIKTAKYLIKVKNGQGHIDDRDHLGNRRIRAIGELLANELHSG 482

Query: 479  LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++I+++ +  S  ++ +MP DLIN+K + S + EFF S QLSQ  +  N LS IT
Sbjct: 483  LIKMQKAIRDKFTALSGSVEELMPHDLINSKMITSTIAEFFSSGQLSQFMDQTNPLSEIT 542

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+ +A+VN  G
Sbjct: 543  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSMYAKVNDLG 602

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+E PYRKV +  +T++++Y++A +EE   IA A++ ++E+    E+L+  R  GE +++
Sbjct: 603  FVEAPYRKVENATITDEIIYITATQEEGLVIAPASTKINENNEIVEDLIEVRVDGETVMI 662

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             +EK+D ID S   +  +AASLIPFLE+DD+NR LMG NMQRQAVPL+K++AP VGTG+E
Sbjct: 663  EKEKVDLIDLSSMMIAGVAASLIPFLEHDDANRALMGSNMQRQAVPLVKSDAPIVGTGVE 722

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A+ S  AI A+RAGIVE+VD   I I   + D     + +D Y L K  R+NQNT  
Sbjct: 723  KIAARDSWEAIKARRAGIVEKVDNKNIYILGEDED----GAFIDHYALQKNLRTNQNTTF 778

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q+ +V+ GD V +  +IADGPS D G+LA+G+N +VAFMPW+GYN+ED+++ISERM+ E
Sbjct: 779  TQKVIVRRGDFVEKGGVIADGPSMDQGELAIGKNAMVAFMPWNGYNYEDAIIISERMIRE 838

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E EV AR+ K G EEIT+DIPNV EE L ++D+ GI+ VG  + PG ILVG
Sbjct: 839  DAFTSVHIYEKEVEARELKDGVEEITKDIPNVKEEELAHLDDSGIVKVGTYITPGMILVG 898

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL     + G +VDV+IF + G DK+ R+
Sbjct: 899  KVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYASPSLEGIIVDVKIFTKKGYDKDPRA 958

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV----SGPKGFKKSTVLSSDL 1012
            +    ++ E+L R+  D+ ++LDR    R+  +L             + +KK   + ++ 
Sbjct: 959  VQAYEQEKEILDREHHDKLLMLDREEMLRINALLLKNPLQEDQEINKQSYKKGQFIKAED 1018

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +    R          D+ VQ   + LK  ++  K  L++    K+  ++  D +P GV+
Sbjct: 1019 LQNVNRFSINSIVKAFDDGVQDAYKDLKAYFQNEKKKLKEEHDEKLNILEKDDILPSGVV 1078

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV++A KR ++ GDKMAGRHGNKGIVS I+   DMP+LK+G  VDIVLNPLGVPSRM
Sbjct: 1079 KLVKVYIATKRKLKVGDKMAGRHGNKGIVSNIVREVDMPYLKNGEIVDIVLNPLGVPSRM 1138

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E HLG     LG +I+ +    K    I  LR  +  +            +   
Sbjct: 1139 NIGQILEVHLGLIGKRLGDQIEDI-FKEKQGDWIKSLREKMISIADVAKLMDSRNFMDTL 1197

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            +D+ +L  A  W  GV  ++P+F+G + E    +  MA +D  G++ LYDG+TG+     
Sbjct: 1198 NDEQLLGYARDWSKGVRFASPIFEGVNTEEFAKLFEMAKIDMDGKTDLYDGMTGQKMHEK 1257

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1258 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1317

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLT+KSDDV GR   Y+++  G +  +TG PE+F VL  E+++L L +++ +   
Sbjct: 1318 HTLREMLTVKSDDVEGRILAYKALTRGENVPQTGIPETFYVLTNELKSLALDVEIYDEVE 1377

Query: 1369 KNS 1371
            ++ 
Sbjct: 1378 EDD 1380


>gi|237751206|ref|ZP_04581686.1| bifunctional DNA-directed RNA polymerase [Helicobacter bilis ATCC
            43879]
 gi|229372572|gb|EEO22963.1| bifunctional DNA-directed RNA polymerase [Helicobacter bilis ATCC
            43879]
          Length = 2883

 Score = 1349 bits (3492), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1397 (42%), Positives = 875/1397 (62%), Gaps = 35/1397 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K+ E +D+P+L+ +QK SYD FL      ++    G++   KS+FPI   +G 
Sbjct: 10   RLRVDFSKSQEELDVPNLLMLQKDSYDSFL----YSNDSRESGIERVLKSIFPIQDSAGR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              LE+   EF   K+ + + + R LTY++PLKI +RL+++D D+      +KDIKEQ+IY
Sbjct: 66   VTLEYAGCEFGKQKYTIAETMVRGLTYSIPLKIKIRLVLWDKDDKGEQVGVKDIKEQTIY 125

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            + ++PLMT   +F+I G++R+VV+QLHRSPG+ F  D+   S + KL+Y  +IIP+ G W
Sbjct: 126  VREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEDESNTSAN-KLIYTGQIIPNMGAW 184

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +  E+D+KDI++VRI++RRK+PVT    ALG   ++I+   YP +  S + D +  P + 
Sbjct: 185  LYFEYDAKDIMYVRINKRRKMPVTILFRALGYSKQQIIQMLYPVLDVSVKKDKFYIPFNP 244

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD--CLCGLYVA 309
             D+     +   L++   G+ V+ +GK+     ++ L E+ + +  +      L   Y+A
Sbjct: 245  NDI--EGSLEYDLINEK-GQVVLPAGKRFNKKRIRDLNEQNISYDKVEFSTTNLLNTYLA 301

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK- 368
            E +++ ++GE+ ++    ++E +++++  ++I    I++  +   +  I N+ + D    
Sbjct: 302  EPVIDSKSGEVILDTLSPLNEANIKKLNDNKITKFKIIHDTAPGYDNSIINSFLADMESL 361

Query: 369  -----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                       +   A + IY+VMRP +  T  VA      LFFD  +YDL+ VGR+KMN
Sbjct: 362  KNIRQTEKIDDECDLAAIRIYKVMRPAEPVTREVAHKFIEQLFFDPSRYDLTGVGRMKMN 421

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +LNL  PD V  +  EDII  +K L+ +RNGKG IDD D+LGNRR+R++GE+L N+   
Sbjct: 422  HKLNLKVPDYVSVLTYEDIIETVKYLMQVRNGKGRIDDRDHLGNRRIRAIGELLANELHS 481

Query: 478  GLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            GL++M++SIK++++     ++VMP DLI++K + S + EFF S QLSQ  +  N LS IT
Sbjct: 482  GLVKMQKSIKDKLTQQTSFENVMPHDLISSKMITSTIMEFFASGQLSQFMDQTNPLSEIT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F +VN  G
Sbjct: 542  HKRRLSALGEGGLVKERVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTKVNDLG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV DGK TN+VVYL+A +E+ + IA A++ LD      E L+  RC GE  L 
Sbjct: 602  FIEAPYKKVVDGKTTNEVVYLTATQEDGKVIAPASTKLDSTNKIVEGLIETRCGGEISLR 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              E ++ ID S + +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 662  KTEDVELIDLSARMLVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLKPDAPIVGTGIE 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            SV+A+ S AAI AK+ G+VE+VD   I I         + + +D Y + K  R+NQNT  
Sbjct: 722  SVIARDSWAAIKAKQGGVVEKVDGKNIYILGENE----NGAYIDSYSMQKNMRTNQNTSF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             QRP+VKVGD+++   IIADG S D G+LALG+N+ VAFMPW+GYNFED++++SE ++ +
Sbjct: 778  TQRPIVKVGDKIKAGQIIADGASMDSGELALGKNIRVAFMPWYGYNFEDAIVVSENIIKD 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT DIPNV E+ + ++DE GI+ +G  V  G ILVG
Sbjct: 838  DAFTSVHIYEKEIEARELKHGIEEITADIPNVREDSIAHLDESGIVKIGTYVTGGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKG+   TPEE+LLRAIFGEKA  V + SL  P  + G VVDV+IF + G +K+ R+
Sbjct: 898  KVTPKGDVKPTPEERLLRAIFGEKAGHVVNKSLYCPQSMEGYVVDVKIFTKKGYEKDARA 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ----NAVSGPKGFKKSTVLSSDL 1012
                 ++   L  +  +   +L++    R+  +L  +     A    K FKK   +    
Sbjct: 958  RQAYEDEKSDLDIEHHERLTMLNKEEMLRISYVLSKEPLSAEAKINDKVFKKGECIPKKE 1017

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              +  R           +++Q   E +K  +   K +L    + K+  ++  D +P GV+
Sbjct: 1018 FDDINRFALNTLIKSYSKEIQNQYEQIKNNFLEQKRVLGVEHEEKLAILEKDDILPNGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG P+DI+LNPLGVPSRM
Sbjct: 1078 KLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPAVDMPYTKDGEPIDIILNPLGVPSRM 1137

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS---PLRSFLEKVIGTGSHTEKISDY 1188
            N+GQI E HLG      G++I+  +   +          +    + V    S  + +   
Sbjct: 1138 NIGQILEVHLGLIGKRFGEQIEDELKKSQYEFSTELKAKMIEIAKAVNEDDSVIKILESA 1197

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
              D +L  A  W +GV  + PVF+G  +E  N +  MA +D  G++ LYDG TGE     
Sbjct: 1198 SKDDLLAYARDWSNGVKFAIPVFEGISQEKFNKLFEMARIDMDGKTELYDGKTGEKIKER 1257

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1258 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAA 1317

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            + L+EMLTIKSDDV GR   YE+I  G    ++  PE+F VL KE+Q+L L +++     
Sbjct: 1318 HTLKEMLTIKSDDVNGRREAYEAITKGYPIGDSAIPETFYVLTKELQSLALDVNVYGENQ 1377

Query: 1369 KNSAKMEEIPDFNKCEL 1385
                 + E       + 
Sbjct: 1378 DEPLVISEKEKDRPKDF 1394


>gi|109948061|ref|YP_665289.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter
            acinonychis str. Sheeba]
 gi|123066105|sp|Q17VN6|RPOBC_HELAH RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|109715282|emb|CAK00290.1| DNA-directed RNA polymerase beta chain [Helicobacter acinonychis str.
            Sheeba]
          Length = 2890

 Score = 1349 bits (3492), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1409 (42%), Positives = 891/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDAQ 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D   G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKAKYTVREAMERGITYSIPLKIKVRLILWEKDAKNGEKTGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTEHTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKDI++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDILYARINKRRKVPVTILFRAMDYQKQDIIKIFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLT   +K LKE  ++++    D L   Y+
Sbjct: 243  FASLD--ANQRMEFDLKDAQ-GKTILLAGKKLTPRKIKELKENHLEWVEYPMDILLNRYL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      EI ++    +D+  L++I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MAGKEILLDMLTQLDKNKLDKIHDLGVQEFVIINDLALGHDASIIHSFLADYES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + IY+VMRPG+  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LRLLKQTEKIDDENALAAIRIYKVMRPGEPITTEVAKQFVKQLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVMGETIYLTAIQEDSHVIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            ++I+   R        +  ++VQ   E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EVIASINRFTLASLVKKYSKEVQNQYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ + +    +  LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASML-ENQTRDFVKELRTKMLEIANAINEKDLLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSRGVKLAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSAK-----MEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDEMDEDGMPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.7 bits (91), Expect = 3.5,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 31/55 (56%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+S +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEESAKKVVEAGIKSITI 2247


>gi|325104981|ref|YP_004274635.1| DNA-directed RNA polymerase subunit beta [Pedobacter saltans DSM
            12145]
 gi|324973829|gb|ADY52813.1| DNA-directed RNA polymerase subunit beta [Pedobacter saltans DSM
            12145]
          Length = 1266

 Score = 1348 bits (3490), Expect = 0.0,   Method: Composition-based stats.
 Identities = 593/1368 (43%), Positives = 822/1368 (60%), Gaps = 118/1368 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F ++  +ID PD ++VQ  S+  F  +    D R  EGL   F   FPI+   
Sbjct: 4    KNNQRINFAQSKHVIDYPDFLDVQIQSFKEFFQLETTSDNRHTEGLFQVFAENFPISDSR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++D+ +C+ R LTY+VPLK  LRL   D +       +     Q 
Sbjct: 64   NIFVLEFLDYFIDPPRYDIQECIERGLTYSVPLKAKLRLSCNDEEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTFVI G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPKGTFVINGAERVIVSQLHRSPGVFFGVSR---HTNGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D  ++++  IDR++K PVT+ L A+G D++ +IL  F                
Sbjct: 176  SWIEFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDADKDILEIFDLADEVKVSKSGLKK- 234

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                        G+KL + +LK   E  V               
Sbjct: 235  --------------------------YVGRKLAARVLKKWVEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKN 367
              ++V+ +  EI +E   ++++  ++ I  + ++ + +   DS + +   I NTL  D +
Sbjct: 258  -GEVVSIDRNEIILERETILEDDHIDMIVDAGVKTLILSKEDSNSGDYTIIYNTLQKDTS 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +YDL  VGR ++N +L LDTP++
Sbjct: 317  NSAKEAVEHIYRQLRNAEPPDEETARGIIDRLFFSDKRYDLGDVGRYRINRKLQLDTPEE 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KEDIIAI+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  TKVLTKEDIIAIVKYLIKLINSKEEVDDIDHLSNRRVRTVGEQLYAQFGVGLSRMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC- 606
            G++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GFIETPYRKV  
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKINNLGFIETPYRKVVE 556

Query: 607  -DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                V   V+YLSA +E+ + IAQAN+  D+ G+F +E V  R  G+  ++  EK+D++D
Sbjct: 557  GKVSVNEPVIYLSAEDEDAKTIAQANAQYDDKGNFIDEKVKARYEGDFPVIEPEKLDYMD 616

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA  S  
Sbjct: 617  VSPNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVASDSRT 676

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A+  GIVE VDA +I I+     + +L         Y L+KF+++NQ+TC+N +P+V
Sbjct: 677  LINAEGNGIVEYVDANQITIKYDRNEDDELVSFDGESKTYNLIKFKKTNQSTCINLKPIV 736

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + G+ V +  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISER+VS+D+FTS+
Sbjct: 737  RKGERVVKGQVLCEGYATENGELALGRNLKVAFMPWQGYNFEDAIVISERVVSQDIFTSV 796

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIEEFE+  RDTK G EE+T DIPNVSEE  K++DE GII VGAEV  GDIL+GKITPKG
Sbjct: 797  HIEEFELEVRDTKRGEEELTPDIPNVSEEATKDLDENGIIRVGAEVKEGDILIGKITPKG 856

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  +PEEKLLRAIFG+KA DV+D SL+ P  ++G V+D ++F+R      + S + E+ 
Sbjct: 857  ESDPSPEEKLLRAIFGDKAGDVKDASLKTPPSINGVVIDTKLFSRA----KKTSKAEEKS 912

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYP 1017
            Q++ L    +     L   +  +L  I+ G+ +      +K     K    +  L+ E  
Sbjct: 913  QLDKLEAKHEKAVRELRETLVDKLFNIVNGKTSQGVYNVYKELLIAKGVKFTQKLLMELD 972

Query: 1018 RSQWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             +         DE     +++L   Y    +     ++     I  GD++P G++++ KV
Sbjct: 973  YNHINPTKWTTDEDKNELIKALLHNYGIKVNEELGAYRRDKFAISVGDELPSGIVQMAKV 1032

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1033 YVAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLADGTPVDIVLNPLGVPSRMNLGQI 1092

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG K  + I D  +  ++                               
Sbjct: 1093 YETILGWAGKELGLKFATPIFDGASQEEV------------------------------- 1121

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                               E+ I      A + ESG++ L+DGLTGE FD+P TVG IYM
Sbjct: 1122 -------------------EDYIK----KAGIPESGRTYLHDGLTGERFDQPTTVGIIYM 1158

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA +LQE+LT
Sbjct: 1159 LKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAANILQEILT 1218

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +KSDDVVGR + YE+IV G +    G PESFNVLV E++ LGL I L+
Sbjct: 1219 VKSDDVVGRAKTYEAIVKGENLPTPGVPESFNVLVHELRGLGLDITLD 1266


>gi|308184945|ref|YP_003929078.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            SJM180]
 gi|308060865|gb|ADO02761.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            SJM180]
          Length = 2890

 Score = 1348 bits (3490), Expect = 0.0,   Method: Composition-based stats.
 Identities = 608/1409 (43%), Positives = 893/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFMIINDLALGHDASIIHSFLADYES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E+N  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDNHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ + K       LR+ + ++  T +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASML-EGKTKDFAKELRAKMLEIANTINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D  +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDGELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317177942|dbj|BAJ55731.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            F16]
          Length = 2890

 Score = 1348 bits (3490), Expect = 0.0,   Method: Composition-based stats.
 Identities = 607/1409 (43%), Positives = 893/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++ S L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMESDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEVLAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA----VSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L  +          K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDIEHFDRLTMLNREELLRVSSLLSQEILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K    +  LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFVKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.5 bits (88), Expect = 8.3,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 29/55 (52%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED ++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDAIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|210135356|ref|YP_002301795.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            P12]
 gi|210133324|gb|ACJ08315.1| DNA-directed RNA polymerase beta subunit [Helicobacter pylori P12]
          Length = 2874

 Score = 1348 bits (3490), Expect = 0.0,   Method: Composition-based stats.
 Identities = 606/1409 (43%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++DA  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDAKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGAEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTRDFAKELRAKMLEIANAINEKDPLTTHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|308063978|gb|ADO05865.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            Sat464]
          Length = 2890

 Score = 1348 bits (3489), Expect = 0.0,   Method: Composition-based stats.
 Identities = 608/1409 (43%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRNDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317014586|gb|ADU82022.1| bifunctional DNA-directed RNA polymerase subunit beta/beta'
            [Helicobacter pylori Gambia94/24]
          Length = 2890

 Score = 1348 bits (3489), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1399 (43%), Positives = 883/1399 (63%), Gaps = 44/1399 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++     S KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST-SSNKLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIHSFSADHES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W   V ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKSVKIAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 ----NSRTKNSAKMEEIPD 1379
                +        M +  D
Sbjct: 1373 GDDVDEDGAPKPIMIKEDD 1391



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|188527984|ref|YP_001910671.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            Shi470]
 gi|212288452|sp|B2UUV9|RPOBC_HELPS RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|188144224|gb|ACD48641.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            Shi470]
          Length = 2890

 Score = 1348 bits (3488), Expect = 0.0,   Method: Composition-based stats.
 Identities = 608/1409 (43%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRNDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINGKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317180925|dbj|BAJ58711.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            F32]
          Length = 2890

 Score = 1347 bits (3486), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1409 (42%), Positives = 891/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDDH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +S 
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQISK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I +++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIANMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL +E+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTRELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|217034097|ref|ZP_03439518.1| hypothetical protein HP9810_893g44 [Helicobacter pylori 98-10]
 gi|216943492|gb|EEC22946.1| hypothetical protein HP9810_893g44 [Helicobacter pylori 98-10]
          Length = 2890

 Score = 1347 bits (3485), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1409 (42%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDSQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADFES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I             +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEVYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADG S D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGSSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +++ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYERDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R     F  +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASFVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317178505|dbj|BAJ56293.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            F30]
          Length = 2890

 Score = 1346 bits (3484), Expect = 0.0,   Method: Composition-based stats.
 Identities = 608/1409 (43%), Positives = 893/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+V  EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYVGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKGEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKVKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGTPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|308183302|ref|YP_003927429.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            PeCan4]
 gi|308065487|gb|ADO07379.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            PeCan4]
          Length = 2890

 Score = 1346 bits (3483), Expect = 0.0,   Method: Composition-based stats.
 Identities = 607/1408 (43%), Positives = 884/1408 (62%), Gaps = 46/1408 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE I      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPI--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE  
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIA 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK----I 1185
            RMN+GQI E HLG      GK+I S++ D   +         LE               +
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDFAKELHAKMLEIANAINEKDPLTIHVL 1193

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                ++ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE  
Sbjct: 1194 ESCSNEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKM 1253

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++AY
Sbjct: 1254 RERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAY 1313

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL-- 1363
            GAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++  
Sbjct: 1314 GAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFG 1373

Query: 1364 ----ENSRTKNSAKMEEIP--DFNKCEL 1385
                E+   K     E+    DF+  +L
Sbjct: 1374 DDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|15645812|ref|NP_207989.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            26695]
 gi|41017590|sp|O25806|RPOBC_HELPY RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase subunit
            beta'; AltName: Full=Transcriptase subunit beta'
 gi|2314357|gb|AAD08242.1| DNA-directed RNA polymerase, beta subunit (rpoB) [Helicobacter pylori
            26695]
          Length = 2890

 Score = 1346 bits (3483), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1409 (42%), Positives = 888/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGES----KEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SE + 
Sbjct: 774  SFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSECIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I  ++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|308062478|gb|ADO04366.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            Cuz20]
          Length = 2890

 Score = 1345 bits (3482), Expect = 0.0,   Method: Composition-based stats.
 Identities = 606/1409 (43%), Positives = 889/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SE + 
Sbjct: 774  SFNQIPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSECIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R     +  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLHVSSLLSQAILEEPFSHNGKDYKEGDRIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINKKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317012978|gb|ADU83586.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            Lithuania75]
          Length = 2890

 Score = 1345 bits (3482), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1409 (42%), Positives = 888/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDSQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K   +NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLHTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I  ++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|297380379|gb|ADI35266.1| DNA-directed RNA polymerase, beta subunit [Helicobacter pylori v225d]
          Length = 2890

 Score = 1345 bits (3481), Expect = 0.0,   Method: Composition-based stats.
 Identities = 607/1409 (43%), Positives = 888/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SY  FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYVSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I  +   D   
Sbjct: 300  AEPV--MVGKEVVLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRNDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I +           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYLLGE----GKEEAYIDTYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  K VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLAGLVKKYPKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL- 1363
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1364 -----ENSRTKNSAKMEEIP--DFNKCEL 1385
                 E+   K     E+    DF+  +L
Sbjct: 1373 GDDVDEDGSPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|254779745|ref|YP_003057851.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            B38]
 gi|254001657|emb|CAX29831.1| Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'[DNA-directed RNA polymerase subunit beta
            (Transcriptase subunit beta) (RNA polymerase subunit
            beta); DNA-directed RNA polymerase subunit beta'
            (Transcriptase subunit beta') (RNA polymerase subunit
            beta')] [Helicobacter pylori B38]
          Length = 2890

 Score = 1345 bits (3480), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1409 (42%), Positives = 892/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL++  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIHTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILINRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFLADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|261839919|gb|ACX99684.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            52]
          Length = 2890

 Score = 1344 bits (3478), Expect = 0.0,   Method: Composition-based stats.
 Identities = 603/1409 (42%), Positives = 888/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIHSFLADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGTFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +        +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGNDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I  ++ D K       LR  + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRVKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 38.9 bits (89), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|317009875|gb|ADU80455.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            India7]
          Length = 2890

 Score = 1342 bits (3474), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1409 (42%), Positives = 890/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVRETMERGITYSIPLKIRVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFLADSES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRISSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I  ++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                 D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LESCSDEELLDYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|217032208|ref|ZP_03437706.1| hypothetical protein HPB128_2g10 [Helicobacter pylori B128]
 gi|216946079|gb|EEC24690.1| hypothetical protein HPB128_2g10 [Helicobacter pylori B128]
          Length = 2890

 Score = 1340 bits (3469), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1409 (42%), Positives = 891/1409 (63%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       E    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKEGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++ LKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSISLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+   +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLICTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I +  +++  I+   ++ ++A I ++ + D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNKLEKIHNLGVQEFVIINDLALGHDASIIHSFLADYES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VK+GD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKMGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I +++ + K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIANML-ENKTKDFAKELRAKMLEIANAINEKDPLTIHA 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGVPKPIVIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|322379399|ref|ZP_08053769.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter suis
            HS1]
 gi|321148108|gb|EFX42638.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter suis
            HS1]
          Length = 2900

 Score = 1340 bits (3468), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1419 (43%), Positives = 895/1419 (63%), Gaps = 51/1419 (3%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
                 R+R  F + P+ + +P+L+ +QK SY+ FL       +    G++  FKSVFPI 
Sbjct: 2    KTLKNRLRADFTRVPQELQVPNLLFLQKESYEAFL----YAKDGKESGIERVFKSVFPIH 57

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDI 125
                   LE+  YE+  PK+ V + + R +TY+V LKI +RLI+++ D  TG K   KDI
Sbjct: 58   DSQNRITLEYGGYEYGEPKYTVREAMERGITYSVYLKIKIRLILWEKDPKTGEKLGPKDI 117

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQSI++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  +K   + + KL+YA +II
Sbjct: 118  KEQSIFIREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEKS-TTSTNKLIYAGQII 176

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP--KIVYSQRGD 243
            PD+G W+  E+D KDI+HVRI++RRKV  T    A+G   ++I+  FYP  K+ +     
Sbjct: 177  PDRGSWLYFEYDVKDILHVRINKRRKVSATILFRAIGYSKQDIIKIFYPLLKVRHRVIKG 236

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
               + +    ++V +++   L D   G  ++ + KK+T+   K ++E GV+++   +  L
Sbjct: 237  ESKYYIPFESIIVDSRLDFDLKDEK-GRVLLAASKKVTARKAKEIRESGVEWVEYPTKIL 295

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
               Y+AE I++     + ++A  ++++  L++I  + I    I    ++ ++A I  +  
Sbjct: 296  LNRYLAEPIMDTNQS-VLLDALTLLEQPKLDKIREAGIDAFVIANDLALGHDASIIRSFT 354

Query: 364  TDKNKDRKD-----------------ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
            +D    R +                 A + IY+VMRPGD  T  VA++    LFFD ++Y
Sbjct: 355  SDAESLRNESLKLLKQSEKIEDESALAAIRIYKVMRPGDPVTTEVAKTYVQQLFFDPERY 414

Query: 407  DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            DL+ VGR+KMN +L+L  P+ V  +  EDII  +K L+ ++NG+G IDD D+LGNRR+R+
Sbjct: 415  DLTMVGRMKMNHKLHLKVPNYVTVLTHEDIIETVKYLIKIKNGQGRIDDRDHLGNRRIRA 474

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            VGE+L N+   GL++M+++IK+++++++   DS+MP DL+N+K + S + EFF S QLSQ
Sbjct: 475  VGELLSNELHEGLMKMQKTIKDKLTTMNNALDSLMPHDLVNSKMITSTILEFFMSGQLSQ 534

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL++
Sbjct: 535  FMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLIN 594

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +L++F RVN  GFIE PY+KV +G V   + YL+A++EE   IA A++ +D  G   E+L
Sbjct: 595  TLSTFTRVNDLGFIEAPYKKVVEGHVGEQIEYLTAIQEEGHVIAPASTVVDSKGYIQEDL 654

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V  R  GE +L  + K+  +D S + +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL
Sbjct: 655  VETRVGGEIVLNEKHKVTLMDLSSRILVGVAASLIPFLEHDDANRALMGTNMQRQAVPLL 714

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            ++EAP VGTG+ESV+A+ S  +I A+R G+V++VDA  I I   +         +  Y L
Sbjct: 715  RSEAPIVGTGIESVIARDSWGSIKAERKGVVDEVDAGNIYIVEKDPQK---GPHITSYLL 771

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             K  R+NQNTC NQ P+VKVGD V    IIADGPS D G+LALG+N+ VAFMPW+GYNFE
Sbjct: 772  QKNLRTNQNTCFNQVPIVKVGDVVEEGQIIADGPSMDKGELALGKNVRVAFMPWNGYNFE 831

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            D++++SE+++ EDVFTS+HI E E+ AR+ K G EE T DIP+V EE + ++D  GI+ +
Sbjct: 832  DAIVVSEKIIKEDVFTSVHIYEKEIEARELKHGIEEFTADIPDVKEEEVAHLDSGGIVKI 891

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V PG ILVGK++PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+ V+I
Sbjct: 892  GTYVAPGMILVGKVSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIGVKI 951

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ----NAVSGPK 1000
            F + G +++ R+ +   E+  +L    D    ++D+    ++ +I   +     AV    
Sbjct: 952  FTKKGYERDTRATNAYEEEKWVLDDRHDKHFKMIDKEELLQISDIFSQEPLEEEAVFNEI 1011

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             + K + +  ++I    R      A +  ++VQ   E +K+     K +L    + K+  
Sbjct: 1012 TYPKGSKIPREVIEGSNRFGLISLAKKYSKEVQDRFEQIKINILEQKKLLGQGHEKKLSI 1071

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            ++  D +P GV+++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVD
Sbjct: 1072 LEKDDILPNGVIKLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPIADMPYTADGEPVD 1131

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--- 1176
            IVLNPLGVPSRMN+GQI E HLG     LGK+IK+L+ D +    I+ LRS + ++    
Sbjct: 1132 IVLNPLGVPSRMNIGQILEVHLGLVGKELGKQIKALL-DSQTKDFIAKLRSKMLEIARVV 1190

Query: 1177 --GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                 +  + +    D  +L  A  W SGV  + PVF+G  EE    + ++A +D  G++
Sbjct: 1191 NVDNQTLAQILESCSDTDLLSYARDWSSGVKFAIPVFEGISEEQFMELFKLAKIDLDGKT 1250

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             LYDG TGE     V VGY+YMLKL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR 
Sbjct: 1251 ELYDGRTGEKMKERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRF 1310

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ L+EMLT+KSDD+ GR   Y +I  G    E+  PE+F VL KE+
Sbjct: 1311 GEMEVWALEAYGAAHTLKEMLTVKSDDIKGRENAYRAIARGEHVGESEIPETFYVLTKEL 1370

Query: 1355 QALGLSIDLENSRTKN------SAKMEEIP--DFNKCEL 1385
            Q+L L +++ N               E+    DFN  +L
Sbjct: 1371 QSLALDVNIFNEEVDEFGMPKPIVIKEDDRPKDFNSFQL 1409



 Score = 41.2 bits (95), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 27/55 (49%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + EDI++  T EI   A  +I E+  + I  + I+ + I
Sbjct: 2201 GSELIEPLEERIFGRVIVEDILDPLTNEILFSADTLITEEKAKRIIEAGIKSVII 2255


>gi|223038986|ref|ZP_03609278.1| DNA-directed RNA polymerase, beta subunit [Campylobacter rectus
            RM3267]
 gi|222879959|gb|EEF15048.1| DNA-directed RNA polymerase, beta subunit [Campylobacter rectus
            RM3267]
          Length = 1352

 Score = 1340 bits (3468), Expect = 0.0,   Method: Composition-based stats.
 Identities = 599/1364 (43%), Positives = 873/1364 (64%), Gaps = 35/1364 (2%)

Query: 30   IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVD 89
            +++QK S+D FL ++     +   G++  FKS+FPI        LE+VS E   PK+ + 
Sbjct: 2    LQLQKKSFDQFLNVD---KNQSESGIEKVFKSIFPIHDPQNRLSLEYVSSEIGKPKYTIR 58

Query: 90   DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSIYMGDLPLMTKDGTFVIKG 148
            +C+ R LTY+V LK+ +RLIV + DE TG K  IKDIKEQ I++ ++PLMT   +F+I G
Sbjct: 59   ECMERGLTYSVNLKMKIRLIVHERDEKTGEKIGIKDIKEQEIFVREIPLMTDRISFIING 118

Query: 149  IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            ++R+VV+QLHRSPG+ F  ++    ++ KL+Y  +IIPD+G W+  E+D+KD++ VRI++
Sbjct: 119  VERVVVNQLHRSPGVIFKEEESPTVVN-KLIYTAQIIPDRGSWLYFEYDTKDVLCVRINK 177

Query: 209  RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
            RRKVPVT    ALG   ++I+  FYP    + + + +  P +  D     +V   + D +
Sbjct: 178  RRKVPVTILFRALGYKKQDIIKLFYPIQTLTIKNNKFLTPFNPDDY--QGRVEYDIKD-E 234

Query: 269  TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             G  + E+GK+LT      +   G+KF+   ++ L   ++A  +++  +GE+  +    +
Sbjct: 235  EGNVLHEAGKRLTKKKADKIIADGIKFVEYPTEILVNRFLAHPVIDKNSGEVLYDTLAQL 294

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK------------DRKDALLD 376
            DE  L +I  ++   I I    +   +  I N+ + D               +   A + 
Sbjct: 295  DENKLVKIL-ADQESIEIANDLAAGVDDAIINSFIADNETLKLLRQTENVDDENDLAAIR 353

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IY+VMRPG+      A +  N LFF+ ++YDL+ VGR+KMN +L L+ P+ V  +  EDI
Sbjct: 354  IYKVMRPGEPVVKDAARAFVNDLFFNPERYDLTGVGRMKMNHKLALEVPEYVTVLTNEDI 413

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-VDI 495
            I   K L+ ++NG+G IDD D+LGNRR+RS+GE+L N+  LG ++M+++I+++ ++  + 
Sbjct: 414  IKTAKYLIKVKNGQGHIDDRDHLGNRRIRSIGELLANELHLGFVKMQKAIRDKFTTLSNT 473

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            + +MP DL+N K + + + EFF   QLSQ  +  N LS +TH RRLSALG+GG+ + RAG
Sbjct: 474  EEIMPYDLVNPKMITTTIMEFFTGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRAG 533

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             E+RDVHPTHYGRICP ET EG NIGL+++L+++A+VN  GF+E PY+KV DGKVT+++V
Sbjct: 534  FEVRDVHPTHYGRICPVETPEGQNIGLINTLSTYAKVNNLGFVEAPYKKVIDGKVTDEIV 593

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            YL+A +EEN  IA A++ LDE G   E+L+  R  GE IL  RE +  ID     +  +A
Sbjct: 594  YLTATQEENLVIAPASTVLDESGYIVEDLIEARQDGEMILAKREDVKLIDLCSGMIAGVA 653

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ASLIPFLE+DD+NR LMG NMQRQAVPLL++ AP VGTGMES VA+ +  AI A+RAGIV
Sbjct: 654  ASLIPFLEHDDANRALMGSNMQRQAVPLLRSSAPIVGTGMESTVARDAWEAIKARRAGIV 713

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E+VD   I I   +     +   +D Y + K  R+NQNT  +Q P+VK G+ V    IIA
Sbjct: 714  EKVDNKNIFILGEDE----AGPYIDHYSMEKNLRTNQNTTFSQCPIVKKGESVVAGQIIA 769

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            DGPS + G+LA+G+N L+AFMPW+GYN+ED+++ISE+M+ ED FTS+HI E E+ AR+ K
Sbjct: 770  DGPSMERGELAIGKNALIAFMPWNGYNYEDAIVISEKMIREDAFTSVHIYEKEIEARELK 829

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G EEIT+DIPN+ EE L ++D+ GII +G +V PG ILVGK++PKGE   TPEE+LLRA
Sbjct: 830  DGVEEITKDIPNIKEEDLLHLDDSGIIKIGTQVKPGMILVGKVSPKGEVKPTPEERLLRA 889

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            IFGEKA  V + SL   + + G VVDV+IF + G +K+ RS  V  E+     ++  D  
Sbjct: 890  IFGEKAGHVVNKSLYATASMEGVVVDVKIFTKKGHEKDSRSNKVYEEEKAAFEKEHHDRL 949

Query: 976  VILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDLISEYPRSQWWQFAVQ-DEK 1030
            ++LDR    ++  +LC     S    G K +KK   +  +      R           + 
Sbjct: 950  LMLDREEMLKVGALLCKTPLSSAQTIGKKTYKKGEKIDKEEFENINRFTLSAIVKGFSKD 1009

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            VQR+ + +K  ++  K  L++    K+E ++  D +P GV+++VKV++A KR ++ GDKM
Sbjct: 1010 VQRSYDDIKNHFQNEKKKLKEEHDAKMEILEKDDILPSGVVKLVKVYIATKRKLKVGDKM 1069

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGIVS I+P  DMP+L  G PVDIVLNPLGVPSRMN+GQI E+HLG     LG+
Sbjct: 1070 AGRHGNKGIVSNIVPEVDMPYLPSGQPVDIVLNPLGVPSRMNIGQILESHLGLVGYRLGE 1129

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSH---TEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +I  +    K +  I  LR  + ++          + +    D+ +L  A+ W +GV  +
Sbjct: 1130 QINQI-FQEKKSEWIKELRVKMIEIASVSKFMSAKKTLGKMSDEQLLEYAKDWANGVKFA 1188

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TP+F+G   + +  +  MA +D  G++ LYDG TG      V VG +YMLKL+H+V +KV
Sbjct: 1189 TPIFEGVKVDELMKLFEMAKVDMDGKTELYDGRTGSKIKERVNVGCMYMLKLHHLVDEKV 1248

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA+ L+EMLT+KSDDV GR  
Sbjct: 1249 HARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAAHTLREMLTVKSDDVEGRLS 1308

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
             Y+++  G +  ETG PE+F VL  E+++L L +++ +    N 
Sbjct: 1309 AYKALTRGENVPETGIPETFFVLTNELKSLALDVEIYDEDENNE 1352


>gi|152991727|ref|YP_001357448.1| DNA-directed RNA polymerase subunit beta [Sulfurovum sp. NBC37-1]
 gi|182676575|sp|A6Q6I2|RPOB_SULNB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|151423588|dbj|BAF71091.1| DNA-directed RNA polymerase, beta subunit [Sulfurovum sp. NBC37-1]
          Length = 1385

 Score = 1338 bits (3464), Expect = 0.0,   Method: Composition-based stats.
 Identities = 594/1387 (42%), Positives = 894/1387 (64%), Gaps = 34/1387 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K P  I+IP+L+++Q+ SY++FLM+     +R +  L+  F+S FPI      
Sbjct: 10   RLRVDFSKTPREIEIPNLLQLQQKSYENFLMLG--ERDRKHSTLERVFRSAFPIHDQQNR 67

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              L + + E   PK+ V +C+ R LTY+V LK+ + L +++ DE TG K   K+IKEQ++
Sbjct: 68   LTLTYKNSEIIKPKYTVRECMERGLTYSVSLKMNIALTIWNRDEKTGEKLDPKEIKEQAV 127

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ D+PLMT+  +FV+ G++R++V+QLHRSPG+ F  ++   +   KLLY+ +IIPD+G 
Sbjct: 128  FVRDIPLMTERTSFVVNGVERVIVNQLHRSPGVIFKEEES-TTAGHKLLYSAQIIPDRGS 186

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KDI++ RI++RRK+PVT    AL    E+I+  FYP    S + + +     
Sbjct: 187  WLYFEYDAKDILYARINKRRKIPVTILFRALDYTKEDIVKLFYPTKEISIKDNRFLVKFD 246

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             +D     +    + D+D G  ++ +GK+LT    + L E G++++    + L   ++A 
Sbjct: 247  PSDF--SGRAEYDVKDMD-GNVIVNAGKRLTKKKAQQLIENGLEWIEYPLEMLMERHLAT 303

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN--- 367
             +++ E+GE+  +    +DE  L+++    I  I I+   +   +  I N  + D     
Sbjct: 304  AVIDQESGEVLYDVVAPLDETKLKKMIEQGIESIEIINDLAEGTDKSIINAFIADNESLR 363

Query: 368  --KDRKDAL-------LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
              K  ++         + IY+VMRPG+  T   A+S    LFFD ++YDL+ VGR+KMN 
Sbjct: 364  LLKQTEEIDDENVLSAIRIYKVMRPGEPVTPEAAKSFLRQLFFDPERYDLTEVGRMKMNH 423

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L LD P     +  ED+I  +K L+ ++NG G IDD D+LGNRR+R++GE+L N+   G
Sbjct: 424  KLGLDIPQYATVLTAEDLINTVKYLIKVKNGHGHIDDRDHLGNRRIRAIGELLGNELHNG 483

Query: 479  LLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++IK++++++   +D +MP DL+N+K + + + EFF S QLSQ  +  N LS +T
Sbjct: 484  LVKMQKAIKDKMTTISGTLDELMPHDLVNSKMITNTILEFFSSGQLSQFMDQTNPLSEVT 543

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++++VN +G
Sbjct: 544  HKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATYSKVNEHG 603

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+ V D +VT+++VY++A +EE++ IA A++ +DE+G   E+L+  R  G   L 
Sbjct: 604  FIEAPYKVVKDAQVTDEIVYITATQEEDKCIAPASTKVDENGKIVEDLIETRLNGNIELN 663

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +++D ID SP  +   AA+LIPFLE+DD+NR LMG NMQRQAVPLLK +AP VGTGME
Sbjct: 664  EAKRVDLIDISPLMISGSAAALIPFLEHDDANRALMGSNMQRQAVPLLKTDAPVVGTGME 723

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++V++ +  A+ AKRAG VE+VDA  I I   +     +   +D Y L K  R+NQNT  
Sbjct: 724  AIVSRDAWEAVKAKRAGKVEKVDAKNIYIMGEDE----TGVFIDHYPLEKNMRTNQNTTF 779

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P+VK+GD +    +IADG + D G+LA+G+N++VAFMPW+GYN+ED++++SE+++ E
Sbjct: 780  TQTPIVKLGDVIEVGQVIADGANMDQGELAIGKNIMVAFMPWYGYNYEDAIIVSEKIIRE 839

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+H  E EV AR+ K G EEITRDIPN+ E+ L ++DE GI+ +G  V PG ILVG
Sbjct: 840  DTFTSVHTYEKEVEARELKHGTEEITRDIPNIREDELLHLDESGIVQLGTYVKPGMILVG 899

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFGEKA  V + SL  P+ + G VVD+++F + G +K+ R+
Sbjct: 900  KVSPKGEIKPTPEERLLRAIFGEKAGHVVNKSLYCPASMEGVVVDIKVFTKKGYEKDARA 959

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
            I    E+  +L  D  D+ +++DR    R+   L GQ        G K +K  + +  + 
Sbjct: 960  IQAYEEEKAILDSDHHDQLLMIDREEILRIAHYLSGQELAKDVTIGDKEYKAGSKIDEET 1019

Query: 1013 ISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            I    R           + VQ   E+LK  +   K  L++  + K+  ++  D +P GV 
Sbjct: 1020 IKGVNRFALRGVVQSYSDDVQNEYEALKNYFLKQKKRLKNEHEEKLSILEKDDILPSGVT 1079

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+++DG PV+I+LNPLGVPSRM
Sbjct: 1080 KLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPEIDMPYMEDGRPVEIILNPLGVPSRM 1139

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDY 1188
            N+GQI E HLG   + LG++I+ +  D K    I  LR+ + ++       +  E +S  
Sbjct: 1140 NIGQILEVHLGLVGMRLGEQIQEM-FDNKTADFIKELRAKMIEIADVAKLMNAKEVLSQM 1198

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ +L     W  GV  + PVF+G ++   + +  +A ++  G+  LYDG TGE     
Sbjct: 1199 SDEELLAYGRDWSRGVKFAAPVFEGTNQTEFDKLFELAKIESDGKMTLYDGKTGEKMIER 1258

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGA+
Sbjct: 1259 VNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAS 1318

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            ++L+EMLTIKSDDV GR R Y ++  G     +G PE+  VL KE+QALGL  +L  S+ 
Sbjct: 1319 HILKEMLTIKSDDVEGRARAYRALTKGESVPASGVPETMFVLTKELQALGLDAELYESKK 1378

Query: 1369 KNSAKME 1375
            +  ++ E
Sbjct: 1379 EVESEDE 1385


>gi|315452940|ref|YP_004073210.1| bifunctional DNA-directed RNA polymerase beta' chain [Helicobacter
            felis ATCC 49179]
 gi|315131992|emb|CBY82620.1| bifunctional DNA-directed RNA polymerase beta' chain [Helicobacter
            felis ATCC 49179]
          Length = 2886

 Score = 1338 bits (3463), Expect = 0.0,   Method: Composition-based stats.
 Identities = 606/1406 (43%), Positives = 885/1406 (62%), Gaps = 46/1406 (3%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K  + +++P+L+ +QK SY+ FL     P      G++  FKSVFPI      
Sbjct: 9    RLRADFTKMAQELEVPNLLLLQKNSYEAFL----HPKGGRESGIERVFKSVFPIHDTQNR 64

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
              LE+   E+   K+ V + + R +TY+VPLKI +RLI+++ D  T  +   KDIKEQSI
Sbjct: 65   ITLEYDGCEYGKSKYTVREAMERGITYSVPLKIKIRLILWEKDPKTEERLGPKDIKEQSI 124

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  +K   S + KL+Y  +IIPD+G 
Sbjct: 125  FIREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEKSTTSAN-KLIYTGQIIPDRGS 183

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W+  E+D+KD +HVRI++RRKV  T    ALG   ++I+  FYP +     G+ +  P  
Sbjct: 184  WLYFEYDAKDTLHVRINKRRKVSATILFRALGYSKQDIIRIFYPLLKVRCVGEKYYIPF- 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             AD+ +       L D D G  ++ + KKL++   + L+   ++++   SD L   Y+AE
Sbjct: 243  -ADINLDQHFDFDLKD-DKGNVLVVANKKLSNKKARDLRASKIEWVEYPSDVLRNRYLAE 300

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
             ++N + GE+ +++  +++   LE+I  + I +  I    ++ ++  +  + + D     
Sbjct: 301  PVLNAQ-GEVLLDSLTLLETSKLEKIQEAGISEFVIANDLALGHDVALIQSFLGDADALR 359

Query: 366  ----KNKDRKD---ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                  K   +   A + IY+VMRPGD  T  VA++    LFFD ++YDL+ VGR+KMN 
Sbjct: 360  LLRQSEKIEDESALAAIRIYKVMRPGDPVTPDVAKAYVQQLFFDPERYDLTMVGRMKMNH 419

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L +  PD V  +  EDIIA +K L+ ++NG+G IDD D+LGNRR+R+VGE+L N+   G
Sbjct: 420  KLQVKVPDYVTVLTHEDIIATMKYLIKIKNGQGQIDDRDHLGNRRIRAVGELLANELHEG 479

Query: 479  LLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            L++M+++IK+++S+++   +S+MP DL+N+K + S + EFF S QLSQ  +  N LS +T
Sbjct: 480  LMKMQKTIKDKLSTMNNALESLMPHDLVNSKTITSTILEFFMSGQLSQFMDQTNLLSEVT 539

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR+SALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN  G
Sbjct: 540  HKRRISALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLG 599

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV +GKV+ +VVYL+A++EE + IA A++ +D  G   ++ +  R +GE ++ 
Sbjct: 600  FIEAPYKKVINGKVSEEVVYLTAIQEEGQVIAPASTRIDAQGYIQDDFLETRVSGEIVMR 659

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             ++K+  +D S + +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLKAE P VGTG+E
Sbjct: 660  EKDKVTLMDLSSRMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLKAETPIVGTGIE 719

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            S++A+ S  ++ A R+GIVE+VD+  I I           + +D Y L K  R+NQNTC 
Sbjct: 720  SIIARDSWGSVKATRSGIVEKVDSKNIYILGEGE-----QTYIDAYLLQKNLRTNQNTCF 774

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ P+VKVGD V+   IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SE++  +
Sbjct: 775  NQTPIVKVGDRVQAGQIIADGPSMDSGELALGKNIRVAFMPWNGYNFEDAIVVSEKITKD 834

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTS+HI E EV AR+ K G EE T DIP+V EE + ++D  GI+ +G  VN G ILVG
Sbjct: 835  DVFTSVHIYEKEVEARELKHGIEEFTADIPDVKEEEVAHLDSGGIVKIGTYVNAGMILVG 894

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++PKGE   TPEE+LLRAIFG+KA  V + SL  P  + G V+ V I  + G +K+ R+
Sbjct: 895  KVSPKGEMKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGVVIGVHILTKKGYEKDARA 954

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS----GPKGFKKSTVLSSDL 1012
            +S   E+   L  +  D   +L+R    ++  +   +            + K + +  D+
Sbjct: 955  VSAYEEEKATLDIEHFDRLTMLNREELLQISALFSKEPLEESTTLNDITYPKGSKIPKDV 1014

Query: 1013 ISEYPRSQWWQFAVQDEK-VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + E  R      A +  K VQ   E +K  +   K IL    + K+  ++  D +P GV+
Sbjct: 1015 VMEINRFGLASLAKKYRKAVQDQFEHIKTNFLEQKKILGQEHEEKLSILEKDDILPNGVI 1074

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPSRM
Sbjct: 1075 KKVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPIADMPYTADGEPVDIVLNPLGVPSRM 1134

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY--- 1188
            N+GQI E HLG     LG +I +L+  +  +         LE         + ++     
Sbjct: 1135 NIGQILEVHLGLVGKQLGGQIDALLKSHTQDMLAKLRAKMLEIAHVVNIQNDSLAKMLEN 1194

Query: 1189 -DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              D+++L  A  W SGV  + PVF+G  EE    +  +A +D  G+  LYDG TGE    
Sbjct: 1195 CPDETLLAYARDWSSGVKFAIPVFEGISEEQFKRLFELAQIDPDGKVELYDGRTGEKMKE 1254

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V VGY+YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW +++YGA
Sbjct: 1255 RVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALESYGA 1314

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            A+ L+EMLTIKSDD+ GR   Y+++  G    E+  PE+F VL KE+Q+LGL + +    
Sbjct: 1315 AHTLKEMLTIKSDDIKGRENAYKAVARGEHVGESEIPETFYVLTKELQSLGLEVSIFGDE 1374

Query: 1368 TKN--------SAKMEEIPDFNKCEL 1385
                         + E   DF+  +L
Sbjct: 1375 VDEFGAPKPIAIKEDERPKDFSSFQL 1400



 Score = 39.3 bits (90), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 29/55 (52%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + EDI++  T EI +    +IDE+  ++I  + I+ + I
Sbjct: 2192 GSELIEPLEERIFGRVLVEDIIDPLTNEILLNTDTLIDEEKAKKIVEAGIKSVTI 2246


>gi|15612186|ref|NP_223838.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            J99]
 gi|41017814|sp|Q9ZK23|RPOBC_HELPJ RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase subunit
            beta'; AltName: Full=Transcriptase subunit beta'
 gi|4155718|gb|AAD06699.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT [Helicobacter pylori J99]
          Length = 2890

 Score = 1337 bits (3459), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1409 (42%), Positives = 887/1409 (62%), Gaps = 48/1409 (3%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
              R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8    KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
                LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64   NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQ 123

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            SI++ ++PLMT+  +F+I G++R+VV+QL+RSPG+ F  ++     S KL+Y  +IIPD+
Sbjct: 124  SIFIREIPLMTERTSFIINGVERVVVNQLYRSPGVIFKEEESST-SSNKLIYTGQIIPDR 182

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183  GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243  FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHL 299

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++   D   
Sbjct: 300  AEPV--MVGKEVLLDMLTQLDKNRLEKIHDLGVQEFVIINDLALGHDASIIHSFSADHES 357

Query: 369  ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                      D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358  LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418  NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477  LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478  SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RRLSALG+GG+ + R G E RDVHPT+YG+  P ET EG NIGL+++L++F RVN 
Sbjct: 538  VTHKRRLSALGEGGLVKDRVGFEARDVHPTYYGQFGPIETPEGQNIGLINTLSTFTRVND 597

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598  LGFIEAPYKKVVDGKVAGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658  LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718  IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774  SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG  V+ G IL
Sbjct: 834  KDDVFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMIL 893

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK +PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+DV++F + G +K+ 
Sbjct: 894  VGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDA 953

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSS 1010
            R +S   E+   L  +  D   +L+R    R+  +L      +      K +K+   +  
Sbjct: 954  RVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPK 1013

Query: 1011 DLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + I+   R        +  ++VQ + E  K  +   K +L +  + K+  ++  D +P G
Sbjct: 1014 EEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNG 1073

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPS
Sbjct: 1074 VIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI---- 1185
            RMN+GQI E HLG      GK+I S++ D K       LR+ + ++    +  + +    
Sbjct: 1134 RMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAINEKDPLTIHV 1192

Query: 1186 -SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG TGE 
Sbjct: 1193 LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
                V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++A
Sbjct: 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEA 1312

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++ 
Sbjct: 1313 YGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIF 1372

Query: 1365 NSRTKNSA-----KMEEIP---DFNKCEL 1385
                          ++E     DF+  +L
Sbjct: 1373 GDDVDEDGAPRPIMIKEDDRPKDFSSFQL 1401



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2193 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247


>gi|260063557|ref|YP_003196637.1| DNA-directed RNA polymerase subunit beta [Robiginitalea biformata
            HTCC2501]
 gi|88783001|gb|EAR14175.1| DNA-directed RNA polymerase beta subunit [Robiginitalea biformata
            HTCC2501]
          Length = 1269

 Score = 1336 bits (3458), Expect = 0.0,   Method: Composition-based stats.
 Identities = 588/1369 (42%), Positives = 817/1369 (59%), Gaps = 116/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F     I + PD +++Q  S+  F  +    D+R NEGL   F   FPIT   
Sbjct: 4    KQTERISFASAKNIPEYPDFLDIQIQSFQDFFQLETKSDQRANEGLYNTFMENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFIDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLSEEVKVSKTGLKKV 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L                           G+KL + +L +  E  V               
Sbjct: 236  L---------------------------GRKLAARVLNTWHEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKN 367
              ++V+ E  EI ++   V++++ +++I  ++++ I +   ++  ++ A I NTL  D  
Sbjct: 258  -GEVVSIERNEIVLDRDTVLEKEHIDQIIETDVKTILLHKENNAQSDYAIIHNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIGMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  KQVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSAQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ FA+VN+ GF+ETPYRKV +
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVFAKVNSMGFLETPYRKVEE 556

Query: 608  GKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            GKV T +  +LSA EEE + IAQAN  L +DG+   E V  R   +  +V  ++I++ D 
Sbjct: 557  GKVDTANYTFLSAEEEEGKKIAQANIPLKKDGAIDAEKVIARLEADYPVVDPKEINYTDV 616

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK E+P VGTG+E  VA  S   
Sbjct: 617  APNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPESPIVGTGLERQVATDSRVL 676

Query: 727  IVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G+VE VD+ RI I+     E  L         Y L+KF+++NQ T +N +P+V+
Sbjct: 677  INAEGDGVVESVDSKRITIKYGRTDEERLVSFDEDSKTYELVKFRKTNQGTSINLKPIVR 736

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             G++V++  ++ +G +T+ G+LALG+N+ VAFMPW GYNFED+++ISE++V ED+FTSIH
Sbjct: 737  KGEKVKKGQVLCEGYATESGELALGQNLKVAFMPWKGYNFEDAIVISEKVVREDIFTSIH 796

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGE
Sbjct: 797  IDEYALEVRDTKLGAEELTNDIPNVSEEATKDLDEYGMIRIGAEVKPGDILIGKITPKGE 856

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  TPEEKLLRAIFG+KA DV+D SL+ P  ++G V+D ++F+R    K++R  S ++E 
Sbjct: 857  SDPTPEEKLLRAIFGDKAGDVKDASLKAPPSLNGVVIDKKLFSR--SIKDKRKRSEDKEA 914

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            I  L  + + +   L   +  +L +++ G+ +       G +   K    +  +++    
Sbjct: 915  IAKLELEYETKFEQLKDVLVEKLFQLVNGKTSQGVMNDLGEEVLPKGKKYTLKMLNAVDD 974

Query: 1019 SQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                       D K    V  L   Y+   + L+   +     I  GD++P G++++ KV
Sbjct: 975  FAHLVGGSWTTDSKTNDLVADLLHNYKIKLNDLQGNLRRDKFTISVGDELPAGIMKLAKV 1034

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1035 YIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQI 1094

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LGKK  + I D     +I+ L    E                       
Sbjct: 1095 YETVLGWAGQKLGKKFATPIFDGATLDEINELTDKGEI---------------------- 1132

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                        P F                    G + LYDG TGE F +P TVG IYM
Sbjct: 1133 ------------PRF--------------------GHTYLYDGGTGERFHQPATVGVIYM 1160

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT
Sbjct: 1161 LKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILT 1220

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1221 VKSDDVIGRAKTYESIVKGESMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|116624533|ref|YP_826689.1| DNA-directed RNA polymerase subunit beta [Candidatus Solibacter
            usitatus Ellin6076]
 gi|116227695|gb|ABJ86404.1| DNA-directed RNA polymerase, beta subunit [Candidatus Solibacter
            usitatus Ellin6076]
          Length = 1392

 Score = 1336 bits (3457), Expect = 0.0,   Method: Composition-based stats.
 Identities = 639/1343 (47%), Positives = 871/1343 (64%), Gaps = 121/1343 (9%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D+ +C  R +TYA PLK+T+RL V+  D  T  KS++DIKEQ ++ G++PLMT +GTF
Sbjct: 104  KYDMQECQERGMTYAAPLKVTIRLTVYSKDPETQKKSVRDIKEQEVFFGEIPLMTDNGTF 163

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            +I G +R++VSQLHRSPG+ F+    +    GK      IIP +G W++ E+D+K+I++V
Sbjct: 164  IINGTERVIVSQLHRSPGVFFERVPAQGYFLGK------IIPYRGSWVEFEYDNKNILYV 217

Query: 205  RIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            RIDR+RK   + FL ALG+ ++E IL  FY       R        +  + + G K+S +
Sbjct: 218  RIDRKRKFYGSVFLRALGLKTDEQILRAFYRVSKMEIRDKK--IYWNVDEGLTGLKLSHA 275

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +    +G+ V+  GKK+T+ L K L++  ++ + +  + L G +V  D+V+  TGE+ I+
Sbjct: 276  ITT-KSGDTVVGQGKKITASLFKELQKAKIEKVEVAPNDLEGAHVVADVVDMTTGEVMID 334

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A   +    + ++  + I +  I + +  +    I  T+  D  K + +AL++IYR +RP
Sbjct: 335  ANSELTTTVMSKLIEAGITEFEIFFPERDDVGTVIAATIRKDAVKTQNEALIEIYRKLRP 394

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDIIAII 440
            GD  T   A  +F  +FFD  KYD S VGR+K N++L   +     D R +  +D  + I
Sbjct: 395  GDPPTLDTATQLFQGMFFDPRKYDFSRVGRMKFNIKLYDRSDATALDKRTLDSDDFKSTI 454

Query: 441  KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVM 499
            + L+ LR G G +DDID+LGNRRVR+VGE+L+NQ+R+GL+RMER+IKE++S   ++ + M
Sbjct: 455  RYLLKLRKGIGAVDDIDHLGNRRVRAVGELLENQFRIGLVRMERAIKEKMSVYQEMSTAM 514

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            P DL+NAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG E+R
Sbjct: 515  PHDLVNAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVR 574

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV----- 614
            DVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYRKV  G V ++V     
Sbjct: 575  DVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRKVIKGAVVDEVKVLNP 634

Query: 615  ------------------------------------VYLSAMEEENRYIAQANSSLDEDG 638
                                                 YLSA EE+   IAQAN  LDE G
Sbjct: 635  GDTDYKVGDIVRRGDMDEANRKLGGKKQAAEFEAHCEYLSAWEEDKWTIAQANVELDEKG 694

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                +L   R AG  +L P+E+I++ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQR
Sbjct: 695  RIVPDLSNARQAGNFVLKPKEEIEYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQR 754

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPS 755
            QAVPLL+A+AP+VGTGME V A+ SGA ++ KRAG+V+ VD+ RI++R            
Sbjct: 755  QAVPLLRADAPYVGTGMEMVTARDSGAVVLNKRAGVVDSVDSERIIVRVEGAAHEGQLSR 814

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              G DIY+L KF+RSNQNTC+NQ+P+V+VG  V +  ++ADGP TDLG+LALGRN+LVAF
Sbjct: 815  EVGADIYQLTKFKRSNQNTCINQKPIVRVGQRVPKGAVLADGPCTDLGELALGRNVLVAF 874

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++L+SE++V ED +TSIHIEEFE+ ARDTKLGPEEITRDIPN+++  L+N
Sbjct: 875  MPWRGYNFEDAILVSEKLVKEDYYTSIHIEEFEIEARDTKLGPEEITRDIPNIADSFLRN 934

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +DE GII +GA V PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D SL  P G+
Sbjct: 935  LDESGIIRIGATVKPGDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVKDASLYCPPGI 994

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
             GT+VD +IF+R G +K+ERS ++E  QI+ L R+  DE  IL      RL  +L G+  
Sbjct: 995  EGTIVDCKIFSRKGQEKDERSKAIEESQIQRLQRNLQDEIRILTDERAKRLGTLLDGKKL 1054

Query: 996  VSGPKGFK-------KSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQYETSK 1046
            ++     K       K T L+ +LI +       +  +  +D ++   ++ ++       
Sbjct: 1055 LADLHDEKTNKRLLSKDTELTRELIEKMKSRDLKRMRLANKDPRLNEQIDEIEEMTSRQI 1114

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            ++LE     KI K++ GD++PPGV+++VKV++AMKR +  GDKMAGRHGNKG+++RILP 
Sbjct: 1115 AVLEKITDEKIAKLRKGDELPPGVIKLVKVYIAMKRKLSVGDKMAGRHGNKGVIARILPE 1174

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LG +  + + D     +I 
Sbjct: 1175 EDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAKALGVQFATPVFDGATEREIK 1234

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
               +                                     T +FD              
Sbjct: 1235 KNLTAAGLPTSGK----------------------------TALFD-------------- 1252

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                        G+TG  F++PVTVGYIYMLKL+H+V DK++ARS G YSL+TQQPLGGK
Sbjct: 1253 ------------GMTGTQFEQPVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQPLGGK 1300

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GR ++YE+IV G    E G PES
Sbjct: 1301 AQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVYGRAKIYEAIVKGEAAIEPGVPES 1360

Query: 1347 FNVLVKEMQALGLSIDLENSRTK 1369
            FNVL++E+Q+L L ++L     +
Sbjct: 1361 FNVLIRELQSLCLDVELMKKPRE 1383



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 26/40 (65%)

Query: 43 MNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
          M++ P+ER + GLQ  F SVFPI+ F G + LEFV Y   
Sbjct: 1  MDLLPNEREDIGLQTVFNSVFPISDFRGVSDLEFVDYSIG 40


>gi|322379978|ref|ZP_08054251.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter suis
            HS5]
 gi|321147595|gb|EFX42222.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter suis
            HS5]
          Length = 1868

 Score = 1335 bits (3456), Expect = 0.0,   Method: Composition-based stats.
 Identities = 611/1419 (43%), Positives = 895/1419 (63%), Gaps = 51/1419 (3%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
                 R+R  F + P+ + +P+L+ +QK SY+ FL       +    G++  FKSVFPI 
Sbjct: 2    KTLKNRLRADFTRVPQELQVPNLLFLQKESYEAFL----YAKDGKESGIERVFKSVFPIH 57

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDI 125
                   LE+  YE+  PK+ V + + R +TY+V LKI +RLI+++ D  TG K   KDI
Sbjct: 58   DSQNRITLEYGGYEYGEPKYTVREAMERGITYSVYLKIKIRLILWEKDPKTGEKLGPKDI 117

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            KEQSI++ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  +K   + + KL+YA +II
Sbjct: 118  KEQSIFIREIPLMTDRTSFIINGVERVVVNQLHRSPGVIFKEEKS-TTSTNKLIYAGQII 176

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP--KIVYSQRGD 243
            PD+G W+  E+D KDI+HVRI++RRKV  T    A+G   ++I+  FYP  K+ +     
Sbjct: 177  PDRGSWLYFEYDVKDILHVRINKRRKVSATILFRAIGYSKQDIIKIFYPLLKVRHRVIKG 236

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
               + +    ++V +++   L D   G  ++ + KK+T+   K ++E GV+++   +  L
Sbjct: 237  ESKYYIPFESIIVDSRLDFDLKDEK-GRVLLAASKKVTARKAKEIRESGVEWVEYPTKIL 295

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
               Y+AE I++     + ++A  ++++  L++I  + I    I    ++ ++A I  +  
Sbjct: 296  LNRYLAEPIMDTNQS-VLLDALTLLEQPKLDKIREAGIDAFVIANDLALGHDASIIRSFT 354

Query: 364  TDKNKDRKD-----------------ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
            +D    R +                 A + IY+VMRPGD  T  VA++    LFFD ++Y
Sbjct: 355  SDAESLRNESLKLLKQSEKIEDESALAAIRIYKVMRPGDPVTTEVAKTYVQQLFFDPERY 414

Query: 407  DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            DL+ VGR+KMN +L+L  P+ V  +  EDII  +K L+ ++NG+G IDD D+LGNRR+R+
Sbjct: 415  DLTMVGRMKMNHKLHLKVPNYVTVLTHEDIIETVKYLIKIKNGQGRIDDRDHLGNRRIRA 474

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
            VGE+L N+   GL++M+++IK+++++++   DS+MP DL+N+K + S + EFF S QLSQ
Sbjct: 475  VGELLSNELHEGLMKMQKTIKDKLTTMNNALDSLMPHDLVNSKMITSTILEFFMSGQLSQ 534

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
              +  N LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL++
Sbjct: 535  FMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLIN 594

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +L++F RVN  GFIE PY+KV +G V   + YL+A++EE   IA A++ +D  G   E+L
Sbjct: 595  TLSTFTRVNDLGFIEAPYKKVVEGHVGEQIEYLTAIQEEGHVIAPASTVVDSKGYIQEDL 654

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V  R  GE +L  + K+  +D S + +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL
Sbjct: 655  VETRVGGEIVLNEKHKVTLMDLSSRILVGVAASLIPFLEHDDANRALMGTNMQRQAVPLL 714

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            ++EAP VGTG+ESV+A+ S  +I A+R G+V++VDA  I I   +         +  Y L
Sbjct: 715  RSEAPIVGTGIESVIARDSWGSIKAERKGVVDEVDAGNIYIVEKDPQK---GPHITSYLL 771

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             K  R+NQNTC NQ P+VKVGD V    IIADGPS D G+LALG+N+ VAFMPW+GYNFE
Sbjct: 772  QKNLRTNQNTCFNQVPIVKVGDVVEEGQIIADGPSMDKGELALGKNVRVAFMPWNGYNFE 831

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            D++++SE+++ EDVFTS+HI E E+ AR+ K G EE T DIP+V EE + ++D  GI+ +
Sbjct: 832  DAIVVSEKIIKEDVFTSVHIYEKEIEARELKHGIEEFTADIPDVKEEEVAHLDSGGIVKI 891

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V PG ILVGK++PKGE   TPEE+LLRAIFG+KA  V + SL  P  + GTV+ V+I
Sbjct: 892  GTYVAPGMILVGKVSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIGVKI 951

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ----NAVSGPK 1000
            F + G +++ R+ +   E+  +L    D    ++D+    ++ +I   +     AV    
Sbjct: 952  FTKKGYERDTRATNAYEEEKWVLDDRHDKHFKMIDKEELLQISDIFSQEPLEEEAVFNEI 1011

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQ-DEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             + K + +  ++I    R      A +  ++VQ   E +K+     K +L    + K+  
Sbjct: 1012 TYPKGSKIPREVIEGSNRFGLISLAKKYSKEVQDRFEQIKINILEQKKLLGQGHEKKLSI 1071

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            ++  D +P GV+++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVD
Sbjct: 1072 LEKDDILPNGVIKLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPIADMPYTADGEPVD 1131

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--- 1176
            IVLNPLGVPSRMN+GQI E HLG     LGK+IK+L+ D +    I+ LRS + ++    
Sbjct: 1132 IVLNPLGVPSRMNIGQILEVHLGLVGKELGKQIKALL-DSQTKDFIAKLRSKMLEIARVV 1190

Query: 1177 --GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                 +  + +    D  +L  A  W SGV  + PVF+G  EE    + ++A +D  G++
Sbjct: 1191 NVDNQTLAQILESCSDTDLLSYARDWSSGVKFAIPVFEGISEEQFMELFKLAKIDLDGKT 1250

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             LYDG TGE     V VGY+YMLKL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR 
Sbjct: 1251 ELYDGRTGEKMKERVNVGYMYMLKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRF 1310

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ L+EMLT+KSDD+ GR   Y +I  G    E+  PE+F VL KE+
Sbjct: 1311 GEMEVWALEAYGAAHTLKEMLTVKSDDIKGRENAYRAIARGEHVGESEIPETFYVLTKEL 1370

Query: 1355 QALGLSIDLENSRTKN------SAKMEEIP--DFNKCEL 1385
            Q+L L +++ N               E+    DFN  +L
Sbjct: 1371 QSLALDVNIFNEEVDEFGMPKPIVIKEDDRPKDFNSFQL 1409


>gi|268316668|ref|YP_003290387.1| DNA-directed RNA polymerase, beta subunit [Rhodothermus marinus DSM
            4252]
 gi|262334202|gb|ACY47999.1| DNA-directed RNA polymerase, beta subunit [Rhodothermus marinus DSM
            4252]
          Length = 1279

 Score = 1335 bits (3456), Expect = 0.0,   Method: Composition-based stats.
 Identities = 616/1368 (45%), Positives = 839/1368 (61%), Gaps = 118/1368 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F +   ++D PDL+E+Q  ++  F+  ++ P+ER ++GLQA FK  FPIT      +
Sbjct: 13   RISFARTKTVLDYPDLLEIQLQAFKEFVQDDVPPEEREDKGLQAVFKEHFPITDSRERYI 72

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  D PK  +++CL + LTY+VPLK  LRL + + ++   A    +     +Y+G
Sbjct: 73   LEFLYYALDTPKHTIEECLAQGLTYSVPLKAKLRLSILEDEDEEEAGEAIEQ---EVYLG 129

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +LP MT+ GTF+I G +R++VSQLHRSPG+ F         +G  LY+ R+IP +G W++
Sbjct: 130  NLPYMTERGTFIINGAERVIVSQLHRSPGVFFSQS---VHPNGTELYSARVIPLRGSWLE 186

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAA 252
               D   I+   IDRR+K+PVT+ L ALG  S+E I+  F                    
Sbjct: 187  FSTDVAGILWAYIDRRKKIPVTTLLRALGYSSDEDIIQLFELAEEADISTKKAFKNYIGR 246

Query: 253  DLMVGAKVSS--SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             L     +     +VD DTGE + E  ++                               
Sbjct: 247  KLASSITLERIIEIVDEDTGEVLEEKRER------------------------------- 275

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI----PILYVDSVNNNAYIRNTLVTDK 366
                    E+ + A   + E   + +  + I  +         +   + + + NTL  D 
Sbjct: 276  --------EVLLPAEHELQEGDYDRLKEAGITKLYLLKEDEDEEEALDKSLLLNTLRKDP 327

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                 +AL  IY  +R  +      A ++ + LFF+  +YDL  VGR ++N RL  +TP 
Sbjct: 328  THSEAEALEYIYFQLRGTETPDLETARALLDRLFFNEKRYDLGAVGRYRLNKRLRQNTPM 387

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            DV  + KEDI+AI++ LV L+NG+ T+DDID+LGNRRVR+V E L  Q+ +GL RM R+I
Sbjct: 388  DVLTLTKEDIVAIVRELVLLQNGRSTVDDIDHLGNRRVRTVAEQLAAQFSVGLARMARTI 447

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            KER++  D +S  PQDL+NA+ + S +  FF ++QLSQ  +  N L+ +TH RR+SALG 
Sbjct: 448  KERMNLRDAESFTPQDLVNARTIASVINTFFGTNQLSQFMDQTNPLAELTHKRRVSALGP 507

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+ SLT  AR+N +GFIETPYR V 
Sbjct: 508  GGLTRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLICSLTVHARINEFGFIETPYRVVR 567

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            +GKVTN++VYL+A EE+N  IAQAN+ +DE+G+F  E V CR  G+  L+  E+I ++D 
Sbjct: 568  NGKVTNEIVYLTAEEEDNAVIAQANAPIDEEGNFLNEFVKCRYRGDFPLMRPEQIQYMDV 627

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+VS +ASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTGME+ VA+ S A 
Sbjct: 628  APNQIVSPSASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGMEARVARDSRAL 687

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLD---PSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            +VA+  G+VE VDA RIVIR  +   D        V  YRL+KF+R+NQ+TC+N RP+VK
Sbjct: 688  LVAEGPGVVEYVDAERIVIRYDQDPEDAEVSFEEPVKEYRLIKFRRTNQDTCINMRPIVK 747

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VG  V +  ++ DG +T+ G+LALG+N+LVAFMPW GYNFED+++ISER+V+EDVFTS+H
Sbjct: 748  VGQRVEKGTVLCDGFATEKGELALGKNVLVAFMPWRGYNFEDAIVISERLVAEDVFTSVH 807

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEEFE   RDTK G EE+TR+IPNVSEE  K++DE GII VGAEV  GDILVGK+TPKGE
Sbjct: 808  IEEFECQVRDTKRGQEELTREIPNVSEEATKDLDERGIIRVGAEVKAGDILVGKVTPKGE 867

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            +  TPEEKLLRAIFG+KA DV+D SL+ P G+ G V+D ++F+R  +  +  S   E+++
Sbjct: 868  TEPTPEEKLLRAIFGDKAGDVKDASLKAPPGMKGVVIDTKLFSRRKL--DPASKKREQQR 925

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            +  +      +   LDR  + +   ++ GQ +       G     +    + +   +   
Sbjct: 926  LAEIDEQLQRDLAELDRRFWEKFFNLVEGQVSAGVETREGDIVLPEGMPFTREAFEKISP 985

Query: 1019 SQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             +        QDE V R V+ L   YE     +    K    +IQ GD++PPG++++ KV
Sbjct: 986  LRLNPMFPFTQDETVNRKVQKLLRNYEQVHRRITGEAKRLKHQIQMGDELPPGIVQLAKV 1045

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A KR IQ GDKMAGRHGNKG+V++I+P EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1046 YIARKRKIQVGDKMAGRHGNKGVVAKIVPVEDMPFLEDGTPVDIVLNPLGVPSRMNLGQI 1105

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG+K  S + D     DI  L                            
Sbjct: 1106 YETLLGWAGKVLGRKFASPVFDGATLDDIKALLR-------------------------- 1139

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                ++G+P           E     L        G++       GEP D   TVGYIYM
Sbjct: 1140 ----EAGLP-----------EDGRVQL------YDGRT-------GEPLDEKTTVGYIYM 1171

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KLNH+V DK++ARS G YSL+TQQPLGGK+  GGQRLGEMEVW + AYGAA+ LQEMLT
Sbjct: 1172 MKLNHLVEDKIHARSIGPYSLITQQPLGGKAQFGGQRLGEMEVWALYAYGAAHTLQEMLT 1231

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             KSDDV GR++ YE+IV G +  E G PESFNVLV+E+Q LGL + L+
Sbjct: 1232 YKSDDVQGRSKAYEAIVKGENLPEPGIPESFNVLVRELQGLGLEVRLD 1279


>gi|158563891|sp|Q01VB1|RPOB_SOLUE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1432

 Score = 1334 bits (3452), Expect = 0.0,   Method: Composition-based stats.
 Identities = 639/1343 (47%), Positives = 871/1343 (64%), Gaps = 121/1343 (9%)

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            K+D+ +C  R +TYA PLK+T+RL V+  D  T  KS++DIKEQ ++ G++PLMT +GTF
Sbjct: 144  KYDMQECQERGMTYAAPLKVTIRLTVYSKDPETQKKSVRDIKEQEVFFGEIPLMTDNGTF 203

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            +I G +R++VSQLHRSPG+ F+    +    GK      IIP +G W++ E+D+K+I++V
Sbjct: 204  IINGTERVIVSQLHRSPGVFFERVPAQGYFLGK------IIPYRGSWVEFEYDNKNILYV 257

Query: 205  RIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            RIDR+RK   + FL ALG+ ++E IL  FY       R        +  + + G K+S +
Sbjct: 258  RIDRKRKFYGSVFLRALGLKTDEQILRAFYRVSKMEIRDKK--IYWNVDEGLTGLKLSHA 315

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +    +G+ V+  GKK+T+ L K L++  ++ + +  + L G +V  D+V+  TGE+ I+
Sbjct: 316  ITT-KSGDTVVGQGKKITASLFKELQKAKIEKVEVAPNDLEGAHVVADVVDMTTGEVMID 374

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A   +    + ++  + I +  I + +  +    I  T+  D  K + +AL++IYR +RP
Sbjct: 375  ANSELTTTVMSKLIEAGITEFEIFFPERDDVGTVIAATIRKDAVKTQNEALIEIYRKLRP 434

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDIIAII 440
            GD  T   A  +F  +FFD  KYD S VGR+K N++L   +     D R +  +D  + I
Sbjct: 435  GDPPTLDTATQLFQGMFFDPRKYDFSRVGRMKFNIKLYDRSDATALDKRTLDSDDFKSTI 494

Query: 441  KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVM 499
            + L+ LR G G +DDID+LGNRRVR+VGE+L+NQ+R+GL+RMER+IKE++S   ++ + M
Sbjct: 495  RYLLKLRKGIGAVDDIDHLGNRRVRAVGELLENQFRIGLVRMERAIKEKMSVYQEMSTAM 554

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            P DL+NAKPV++A+ EFF SSQLSQ  +  N LS ITH RRLSALG GG++R RAG E+R
Sbjct: 555  PHDLVNAKPVMAAIREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVR 614

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV----- 614
            DVHPTHYGRICP ET EG NIGL+SSL+ FAR+N YGFIE+PYRKV  G V ++V     
Sbjct: 615  DVHPTHYGRICPIETPEGPNIGLISSLSCFARINEYGFIESPYRKVIKGAVVDEVKVLNP 674

Query: 615  ------------------------------------VYLSAMEEENRYIAQANSSLDEDG 638
                                                 YLSA EE+   IAQAN  LDE G
Sbjct: 675  GDTDYKVGDIVRRGDMDEANRKLGGKKQAAEFEAHCEYLSAWEEDKWTIAQANVELDEKG 734

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                +L   R AG  +L P+E+I++ID SPKQ+VS+AASLIPFLENDD+NR LMG NMQR
Sbjct: 735  RIVPDLSNARQAGNFVLKPKEEIEYIDVSPKQLVSVAASLIPFLENDDANRALMGSNMQR 794

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPS 755
            QAVPLL+A+AP+VGTGME V A+ SGA ++ KRAG+V+ VD+ RI++R            
Sbjct: 795  QAVPLLRADAPYVGTGMEMVTARDSGAVVLNKRAGVVDSVDSERIIVRVEGAAHEGQLSR 854

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              G DIY+L KF+RSNQNTC+NQ+P+V+VG  V +  ++ADGP TDLG+LALGRN+LVAF
Sbjct: 855  EVGADIYQLTKFKRSNQNTCINQKPIVRVGQRVPKGAVLADGPCTDLGELALGRNVLVAF 914

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++L+SE++V ED +TSIHIEEFE+ ARDTKLGPEEITRDIPN+++  L+N
Sbjct: 915  MPWRGYNFEDAILVSEKLVKEDYYTSIHIEEFEIEARDTKLGPEEITRDIPNIADSFLRN 974

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +DE GII +GA V PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D SL  P G+
Sbjct: 975  LDESGIIRIGATVKPGDILVGKVTPKGETQLTPEEKLLRAIFGEKAGDVKDASLYCPPGI 1034

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
             GT+VD +IF+R G +K+ERS ++E  QI+ L R+  DE  IL      RL  +L G+  
Sbjct: 1035 EGTIVDCKIFSRKGQEKDERSKAIEESQIQRLQRNLQDEIRILTDERAKRLGTLLDGKKL 1094

Query: 996  VSGPKGFK-------KSTVLSSDLISEYPRSQWWQFAV--QDEKVQRNVESLKVQYETSK 1046
            ++     K       K T L+ +LI +       +  +  +D ++   ++ ++       
Sbjct: 1095 LADLHDEKTNKRLLSKDTELTRELIEKMKSRDLKRMRLANKDPRLNEQIDEIEEMTSRQI 1154

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            ++LE     KI K++ GD++PPGV+++VKV++AMKR +  GDKMAGRHGNKG+++RILP 
Sbjct: 1155 AVLEKITDEKIAKLRKGDELPPGVIKLVKVYIAMKRKLSVGDKMAGRHGNKGVIARILPE 1214

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP+L DGTPV+IVLNPLGVPSRMNVGQI ETHLGWA   LG +  + + D     +I 
Sbjct: 1215 EDMPYLPDGTPVEIVLNPLGVPSRMNVGQILETHLGWAAKALGVQFATPVFDGATEREIK 1274

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
               +                                     T +FD              
Sbjct: 1275 KNLTAAGLPTSGK----------------------------TALFD-------------- 1292

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                        G+TG  F++PVTVGYIYMLKL+H+V DK++ARS G YSL+TQQPLGGK
Sbjct: 1293 ------------GMTGTQFEQPVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQPLGGK 1340

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY+LQE+LT KSDDV GR ++YE+IV G    E G PES
Sbjct: 1341 AQFGGQRFGEMEVWALEAYGAAYILQELLTAKSDDVYGRAKIYEAIVKGEAAIEPGVPES 1400

Query: 1347 FNVLVKEMQALGLSIDLENSRTK 1369
            FNVL++E+Q+L L ++L     +
Sbjct: 1401 FNVLIRELQSLCLDVELMKKPRE 1423



 Score =  110 bits (276), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 36/70 (51%), Positives = 44/70 (62%)

Query: 13 VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           R  F K    I IP+LIEVQK SY+ FL M++ P+ER + GLQ  F SVFPI+ F G +
Sbjct: 11 ERVDFSKIKTSIPIPNLIEVQKKSYERFLQMDLLPNEREDIGLQTVFNSVFPISDFRGVS 70

Query: 73 MLEFVSYEFD 82
           LEFV Y   
Sbjct: 71 DLEFVDYSIG 80


>gi|325285440|ref|YP_004261230.1| DNA-directed RNA polymerase subunit beta [Cellulophaga lytica DSM
            7489]
 gi|324320894|gb|ADY28359.1| DNA-directed RNA polymerase subunit beta [Cellulophaga lytica DSM
            7489]
          Length = 1269

 Score = 1334 bits (3452), Expect = 0.0,   Method: Composition-based stats.
 Identities = 586/1369 (42%), Positives = 812/1369 (59%), Gaps = 116/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F     I D PD +++Q  S+  F  +    DER +EGL   F   FPIT   
Sbjct: 4    KQTQRINFASAKNIPDYPDFLDIQIKSFQDFFQLETKSDERGDEGLYNTFLENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFIDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINGVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLSEEIKVSNAGLKKV 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L                           G+KL + +L +  E  V               
Sbjct: 236  L---------------------------GRKLAARVLNTWHEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKN 367
              ++V+ E  EI ++   V++++ + EI  ++++ I +   ++  ++ A I NTL  D  
Sbjct: 258  -GEVVSIERNEIVLDRDTVLEKEHIAEIMEADVKTILLHKENNAQSDYAIIHNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLQLDIGMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  KQVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VN  GF+ETPYRKV +
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNPMGFLETPYRKVTN 556

Query: 608  GKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            G V T +  YLSA EEE   I+QAN  L EDG    + V  R  G+  +V   +I++ D 
Sbjct: 557  GVVDTEEYAYLSAEEEEGMKISQANIPLKEDGEIDVDKVIAREEGDFPVVDPAEINYTDV 616

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ E+P VGTG+E  VA  S   
Sbjct: 617  APNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGLERQVASDSRVL 676

Query: 727  IVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G+VE VD+ ++ I+     E  L         Y L+KF+++NQ T +N +P+V+
Sbjct: 677  INAEGDGVVEYVDSQKVTIKYDRTEEERLVSFEEDSKTYNLVKFRKTNQGTSINLKPIVE 736

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD+V++  ++ +G +T LG+LALGRNM VAFMPW GYNFED+++ISE++V ED+FTSIH
Sbjct: 737  KGDKVKKGQVLCEGYATQLGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSIH 796

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGE
Sbjct: 797  IDEYSLEVRDTKLGAEELTHDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGE 856

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  TPEEKLLRAIFG+KA DV+D SL+    + G V+  ++F+R    K++R+   +++ 
Sbjct: 857  SDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIGKKLFSR--SIKDKRTRVEDKDA 914

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            I  L  + + +   L   +  +L  ++ G+ +       G +   K    S  +++    
Sbjct: 915  INKLELEYEVKFQQLKDILVEKLFTLVNGKTSQGVLNDLGEEVLPKGKKYSMKMLNSVDD 974

Query: 1019 SQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                       D+ +   V  L   Y+   + L+   +     I  GD++PPG++++ KV
Sbjct: 975  FAHLVGGSWTVDKDLNAMVADLIHNYKIKLNDLQGNLRRDKFTISVGDELPPGIMKLAKV 1034

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1035 YVAKKRKLKVGDKMAGRHGNKGIVARIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQI 1094

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA + LGKK  + I D      I+                              
Sbjct: 1095 YETVLGWAGLKLGKKYATPIFDGATLEQINGYTD-------------------------- 1128

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                ++G+P                          G + LYDG TG+ FD+P TVG IYM
Sbjct: 1129 ----EAGIP------------------------RFGHTYLYDGGTGKRFDQPATVGVIYM 1160

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT
Sbjct: 1161 LKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILT 1220

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1221 VKSDDVIGRAKTYESIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|255530761|ref|YP_003091133.1| DNA-directed RNA polymerase subunit beta [Pedobacter heparinus DSM
            2366]
 gi|255343745|gb|ACU03071.1| DNA-directed RNA polymerase, beta subunit [Pedobacter heparinus DSM
            2366]
          Length = 1267

 Score = 1333 bits (3449), Expect = 0.0,   Method: Composition-based stats.
 Identities = 591/1369 (43%), Positives = 822/1369 (60%), Gaps = 119/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F ++  IID PD ++VQ  S+  F  +    D R  EGL   F   FPIT   
Sbjct: 4    KVDQRVNFARSKHIIDYPDFLDVQLQSFREFFQIETTSDNRHTEGLFKVFAENFPITDSR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++D+ +C+ R LTY+VPLK  L+L   D +       I     Q 
Sbjct: 64   NIFVLEFLDYFIDPPRYDIPECIDRGLTYSVPLKAKLKLSCNDAEHEDFETII-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTFVI G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPKGTFVINGAERVIVSQLHRSPGVFFGQSR---HTNGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D  ++++  IDR++K PVT+ L A+G DS+ +IL  F                
Sbjct: 176  SWIEFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDSDKDILELFDLADEVKVSKSGLKKY 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            +                           G+KL + +L+   E  V               
Sbjct: 236  I---------------------------GRKLAARVLRKWVEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDK 366
              ++V+ +  E+ ++   V+++  ++ I  + ++ I +   D  +   Y  I NTL  D 
Sbjct: 258  -GEVVSIDRNEVILDRDTVLEDDHIDMIIDAGVKTIILSKDDGASQADYTIIYNTLQKDT 316

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +   K+A+ +IYR +R  +      A  +   LFF   +YDL  VGR ++N +L +DTPD
Sbjct: 317  SNSEKEAVENIYRALRNAEPPDEETARGIIERLFFSDKRYDLGDVGRYRINRKLKMDTPD 376

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             V+ + K DIIAI+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I
Sbjct: 377  HVKVLTKADIIAIVKYLIKLINSKEEVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTI 436

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RRLSALG 
Sbjct: 437  RERMNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGP 496

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GFIETPY+KV 
Sbjct: 497  GGLSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKINNLGFIETPYKKVE 556

Query: 607  DGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G V+    V+YLSA +E+ + IAQAN++ D+ G+FT   V  R  G+  ++  EK+D +
Sbjct: 557  NGIVSVDEPVIYLSAEDEDGKTIAQANAAYDDKGNFTTSRVKARYEGDFPVIEPEKLDLM 616

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA+ S 
Sbjct: 617  DVAPNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVARDSR 676

Query: 725  AAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
              I A+  G+VE VDA  I I+        L         Y+L+KF+++NQNTC+N +P+
Sbjct: 677  TLINAEGDGVVEYVDANEITIKYVRNDSDRLVSFEGDSKTYKLIKFKKTNQNTCINLKPI 736

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G +V +  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISER+V ED+FTS
Sbjct: 737  VKKGQKVVKGQVLCEGYATENGELALGRNLKVAFMPWQGYNFEDAIVISERIVREDIFTS 796

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEEFE+  RDTK G EE+T DIPNVSEE  K++DE GII +GAEV  GDIL+GKITPK
Sbjct: 797  LHIEEFELEVRDTKRGEEELTPDIPNVSEEATKDLDENGIIRIGAEVKEGDILIGKITPK 856

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GES  +PEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F+R      + + + E+
Sbjct: 857  GESDPSPEEKLLRAIFGDKAGDVKDASLKTPPSIRGVVIDTKLFSRA----KKTTKAEEK 912

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEY 1016
              IE L +  D   + L   +  +L +I+ G+ +      +K     K    +   +S+ 
Sbjct: 913  SAIEKLDKKYDLAVLNLKNELVDKLFQIVNGKTSQGVYNVYKELLFPKGAKFTQKSLSDL 972

Query: 1017 PRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              +    +    D+     ++ L   Y    +     +K     I  GD++P G++++ K
Sbjct: 973  EYAHINPYKWTTDDDKNEQIKMLLHNYGIRVNEELGAYKRDKFAISVGDELPSGIVQMAK 1032

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V+VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1033 VYVAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNLGQ 1092

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET L WA   LG K  + I D   + ++    +                         
Sbjct: 1093 IYETVLAWAGKELGVKFATPIFDGAKHDEVEDWIA------------------------- 1127

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 K+GVP                         SG++ L++GLTGE FD+P TVG IY
Sbjct: 1128 -----KAGVPA------------------------SGRTYLHNGLTGEKFDQPTTVGIIY 1158

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA +LQE+L
Sbjct: 1159 MLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAANILQEIL 1218

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            T+KSDDV+GR + YE+IV G +    G PESFNVLV E++ LGL I L+
Sbjct: 1219 TVKSDDVIGRAKTYEAIVKGENLPTPGVPESFNVLVHELRGLGLDITLD 1267


>gi|327404146|ref|YP_004344984.1| DNA-directed RNA polymerase subunit beta [Fluviicola taffensis DSM
            16823]
 gi|327319654|gb|AEA44146.1| DNA-directed RNA polymerase subunit beta [Fluviicola taffensis DSM
            16823]
          Length = 1270

 Score = 1332 bits (3447), Expect = 0.0,   Method: Composition-based stats.
 Identities = 575/1365 (42%), Positives = 818/1365 (59%), Gaps = 116/1365 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F  +      PD +++Q  S+  F  +   P+ R +EGL   F   FPIT      
Sbjct: 9    TRINFASSKNQFAYPDFLDIQLKSFQEFFQLETTPENRESEGLFKVFAENFPITDTRNQF 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D +       +     Q +Y+
Sbjct: 69   VLEFLDYFIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPEHEDFETIV-----QDVYL 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  G+FVI G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G W+
Sbjct: 124  GTIPYMTPKGSFVINGAERVIVSQLHRSPGVFFGQSR---HANGTKLYSARVIPFKGSWI 180

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D   +++  IDR++K+PVT+   A+G +++ +IL  F                   
Sbjct: 181  EFATDINSVMYAYIDRKKKLPVTTLFRAIGYETDKDILEIFG------------------ 222

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                      +  V  +        G++L + +LKS  E              G     +
Sbjct: 223  ---------LADEVKANKANLKKCVGRRLAARVLKSWIED------------FGDEDTGE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDR 370
            +V+ E  E+ ++   V++E  ++ +  + ++ +     D+ + +   I NTL  D +   
Sbjct: 262  VVSIERNEVILDRETVLEEHHVDLVIDAGVKTVIFHKEDANSADYTIIYNTLQKDTSNSE 321

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+  IYR +R  +   +  A+ +F  LFF   +YDL  VGR +MN +LN+D  ++ R 
Sbjct: 322  KEAVEHIYRQLRNAEPPDYETAKGVFEKLFFSDARYDLGEVGRYRMNKKLNIDNSEESRV 381

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K DI++IIK L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER+
Sbjct: 382  LTKNDILSIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIRERM 441

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++QLSQ  +  N LS +TH RRLSALG GG++
Sbjct: 442  NVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLSEVTHKRRLSALGPGGLS 501

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+C  ET EG NIGL+SSL  FA+VN  GFIETPYR V +GKV
Sbjct: 502  RERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVFAKVNKLGFIETPYRSVSNGKV 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
              T++ +YLSA EE+ + IAQAN+ +DE G+F   +V  R  G+  +V  + +  +D   
Sbjct: 562  DTTSEPIYLSAEEEDEKMIAQANAIVDEKGNFLSNVVKARFEGDFPVVQPKDLHLMDVGA 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+ SIAAS IPFLE+DD+NR LMG NMQRQAVPLLK ++P VGTG+E +VA+ S   I 
Sbjct: 622  NQIASIAASSIPFLEHDDANRALMGSNMQRQAVPLLKPQSPVVGTGIEQLVARDSRVLIN 681

Query: 729  AKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G VE VDA  IVIR     +  L    S V  Y L KFQ++NQ+T +N +P+V+ G
Sbjct: 682  AEGPGTVEYVDANEIVIRYDWSADDKLVSFDSEVIRYSLTKFQKTNQSTTINLKPIVRKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D +    ++ +G +T  G+LALG+N+ VAFMPW GYNFED+++ISER+V +D+FTSIHI+
Sbjct: 742  DRIDFGQVLCEGYATQGGELALGQNLKVAFMPWKGYNFEDAIVISERVVRDDIFTSIHID 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  RDTK G EE+T DIPNVSEE  K++DE G+I +GAE+  GDIL+GKITPKGE+ 
Sbjct: 802  EYSLDVRDTKRGMEELTSDIPNVSEEATKDLDENGLIRIGAEIKEGDILIGKITPKGETD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D SL+    + G V+  ++F+R    K+ +S + ++  +E
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDASLKAGPSLRGVVIQKKLFSRA--IKDRKSKAQDKPVLE 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +L  + D +   L   +  +LM IL      G       +  KK T  +   +     + 
Sbjct: 920  VLDTEYDRDYADLKEKLADKLMTILGETKSAGVFNNFKEEIIKKGTKFTHKNLLVIDYTI 979

Query: 1021 WW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    +  +   +  L   +    + L   +K K   I  GD++P G++++ KV+VA
Sbjct: 980  VNPTSWTAEAHINALISRLLHNFTIKANDLLGIYKRKKFHISVGDELPAGIVKMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR ++ GDKMAGRHGNKGIV+ I+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET
Sbjct: 1040 QKRKLKVGDKMAGRHGNKGIVANIVRAEDMPFLEDGTPVDIVLNPLGVPSRMNLGQIYET 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LGWA   LG K  + I D     +I+                                 
Sbjct: 1100 VLGWAGQKLGVKFATPIFDGAKPEEINEWTD----------------------------- 1130

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K+GVP                         SG++ LYDG TG+ F +P TVG IYMLKL
Sbjct: 1131 -KAGVP------------------------RSGKTYLYDGGTGDRFHQPATVGIIYMLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA +LQE+LT+KS
Sbjct: 1166 SHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAANILQEILTVKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DDV+GR + YE+IV G++  E G PESFNVL+ E++ LGL++ ++
Sbjct: 1226 DDVMGRAKAYEAIVKGDNIPEPGIPESFNVLLHELRGLGLNVSMD 1270


>gi|149278890|ref|ZP_01885025.1| DNA-directed RNA polymerase subunit beta [Pedobacter sp. BAL39]
 gi|149230509|gb|EDM35893.1| DNA-directed RNA polymerase subunit beta [Pedobacter sp. BAL39]
          Length = 1267

 Score = 1332 bits (3446), Expect = 0.0,   Method: Composition-based stats.
 Identities = 589/1369 (43%), Positives = 820/1369 (59%), Gaps = 119/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F ++  IID PD ++VQ  S+  F  +    D R  EGL   F   FPIT   
Sbjct: 4    KVDQRVNFARSKHIIDYPDFLDVQLQSFREFFQIETTSDNRHTEGLFKVFAENFPITDSR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++D+ +C+ R LTY+VPLK  L+L   D +       I     Q 
Sbjct: 64   NIFVLEFLDYFIDPPRYDIPECIDRGLTYSVPLKAKLKLSCNDAEHEDFETII-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTFVI G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPKGTFVINGAERVIVSQLHRSPGVFFGQSR---HTNGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D  ++++  IDR++K PVT+ L A+G DS+ +IL  F                
Sbjct: 176  SWIEFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDSDKDILELFDLADEVKVSKSGLKKY 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            +                           G+KL + +L+   E  V               
Sbjct: 236  I---------------------------GRKLAARVLRKWVEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDK 366
              ++V+ +  E+ ++   V+++  ++ I  + ++ I +   D  +   Y  I NTL  D 
Sbjct: 258  -GEVVSIDRNEVILDRDTVLEDDHIDMIIDAGVKTIILSKDDGASQADYTIIYNTLQKDT 316

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +   K+A+ +IYR +R  +      A  +   LFF   +YDL  VGR ++N +L +DTPD
Sbjct: 317  SNSEKEAVENIYRALRNAEPPDEETARGIIERLFFSDKRYDLGDVGRYRINRKLKMDTPD 376

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             V+ + K DIIAI+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I
Sbjct: 377  HVKVLTKADIIAIVKYLIKLINSKEEVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTI 436

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RRLSALG 
Sbjct: 437  RERMNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGP 496

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GFIETPY+KV 
Sbjct: 497  GGLSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKINNLGFIETPYKKVK 556

Query: 607  DGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            DG V    +V+YLSA +E+ + IAQAN++ D+ G+FT   V  R  G+  ++  EK+D +
Sbjct: 557  DGIVQVDEEVIYLSAEDEDGKTIAQANAAYDDQGNFTTSRVKARYEGDFPVIEPEKLDLM 616

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA+ S 
Sbjct: 617  DVAPNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVARDSR 676

Query: 725  AAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
              I A+  G VE VDA  I I+        L         Y+L+KF+++NQNTC+N +P+
Sbjct: 677  TLINAEGDGTVEYVDANEITIKYVRNDGDRLVSFEGDSKTYKLIKFKKTNQNTCINLKPI 736

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G +V +  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++I+ER+V ED+FTS
Sbjct: 737  VKKGQKVVKGQVLCEGYATENGELALGRNLKVAFMPWQGYNFEDAIVINERIVREDIFTS 796

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +HIEEFE+  RDTK G EE+T DIPNVSEE  K++DE GII VGAEV  GDIL+GKITPK
Sbjct: 797  LHIEEFELEVRDTKRGEEELTPDIPNVSEEATKDLDENGIIRVGAEVKEGDILIGKITPK 856

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GES  +PEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F+R      + + + E+
Sbjct: 857  GESDPSPEEKLLRAIFGDKAGDVKDASLKTPPSIKGVVIDTKLFSRA----KKTTKAEEK 912

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEY 1016
              I+ L +  +     L   +  +L +I+ G+ +      +K     K    +   +++ 
Sbjct: 913  AAIDKLDKKYEIATTNLKNELVDKLFQIVNGKTSQGIFNVYKELLFPKGAKFTQKSLADL 972

Query: 1017 PRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              +    +    D+     ++ L   Y    +     +K     I  GD++P G++++ K
Sbjct: 973  EYAHINPYKWTTDDDKNEQIKMLLHNYGIRVNEELGAYKRDKFAISVGDELPSGIVQMAK 1032

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V+VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1033 VYVAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNLGQ 1092

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET L WA   LG K  + I D   + ++    +                         
Sbjct: 1093 IYETVLAWAGKELGVKFATPIFDGAKHDEVEEWIA------------------------- 1127

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 K+GVP                         SG++ L++GLTGE FD+P TVG IY
Sbjct: 1128 -----KAGVPA------------------------SGRTYLHNGLTGEKFDQPTTVGIIY 1158

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA +LQE+L
Sbjct: 1159 MLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAANILQEIL 1218

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            T+KSDDV+GR + YE+IV G +    G PESFNVLV E++ LGL I L+
Sbjct: 1219 TVKSDDVIGRAKTYEAIVKGENLPTPGVPESFNVLVHELRGLGLDITLD 1267


>gi|332169095|gb|AEE18350.1| DNA-directed RNA polymerase, beta subunit [Krokinobacter diaphorus
            4H-3-7-5]
          Length = 1273

 Score = 1330 bits (3443), Expect = 0.0,   Method: Composition-based stats.
 Identities = 591/1368 (43%), Positives = 811/1368 (59%), Gaps = 117/1368 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F       D PD +++Q  S+  F  +    DER +EGL   F   FPIT      
Sbjct: 9    ERISFSSVKNRPDYPDFLDIQVKSFQDFFQLETKSDERGDEGLYNTFLENFPITDTRNNF 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y+
Sbjct: 69   VLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDEEHEDFETIV-----QDVYL 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W+
Sbjct: 124  GTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSWI 180

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D   +++  IDR++K+PVT+   A+G + + +IL  F                L  
Sbjct: 181  EFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKYL-- 238

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +L +  E  V                 +
Sbjct: 239  -------------------------GRKLAARVLNTWHEDFVDEDT------------GE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDR 370
            +V+ E  EI ++   V++++ +EEI  +  + + +   D+   + A I NTL  D     
Sbjct: 262  VVSIERNEIVLDRDTVLEKEHVEEILEAGAKTVLLHKEDNQQADYAIIHNTLQKDPTNSE 321

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D + 
Sbjct: 322  KEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIEMDKQV 381

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K DII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER+
Sbjct: 382  LTKLDIITIIKYLIELINAKAEIDDIDHLSNRRVRTVGEQLSAQFGVGLARMARTIRERM 441

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 442  NVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLS 501

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV +GK+
Sbjct: 502  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVYAKVNNMGFIETPYRKVENGKI 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               ++ +YLSA EEE   IAQAN+ +D+ G+ TEE V  R  G+  +V  + + + D SP
Sbjct: 562  DLKSEPLYLSAEEEEGMLIAQANNPMDDSGAITEEKVIARMEGDFPVVDPDTVHYADVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPL+ A+AP VGTG+E  VA  S   I 
Sbjct: 622  NQIASISASLIPFLEHDDANRALMGSNMMRQAVPLIMADAPIVGTGLERQVATDSRVLIN 681

Query: 729  AKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+ AG VE VDA  I I+     +  L         Y L+KF+++NQ T +N +P+VKVG
Sbjct: 682  AEGAGTVEYVDANMITIKYDRTEDERLVSFDEDSKSYNLIKFRKTNQGTNINLKPIVKVG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V +  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V +D+FTSIHI+
Sbjct: 742  DRVEKGQVLCQGYATEKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHID 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES 
Sbjct: 802  EYSLDVRDTKLGNEELTNDIPNVSEEATKDLDEHGMIRIGAEVKPGDILIGKITPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             TPEEKLLRAIFG+KA DV+D SL+    + G V++ ++F R   DK +R+   E   I 
Sbjct: 862  PTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVINKKLFARAIKDKRKRAKDKED--IA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQ 1020
            +L  + DD+   L   +  +L +++ G+ A       G +   K    +  +++      
Sbjct: 920  VLENEYDDKFDDLQAVVIEKLFKLVNGKTAQGVMNDLGEEVLPKGKKFTLKMLNSVEDYT 979

Query: 1021 WWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+K    +  L   Y+  ++ L+   + +   I  GD++P G++++ KV++
Sbjct: 980  HLTQGTWTTDDKTNTLIADLLHNYKIKENDLQGNLRREKFTISVGDELPAGIIKLAKVYI 1039

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+E
Sbjct: 1040 AKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYE 1099

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA   LG+   + I D      I+ L                              
Sbjct: 1100 TVLGWAGQKLGRTYATPIFDGATLDQINALTD---------------------------- 1131

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+P                          G + LYDG TG+ FD+P TVG IYMLK
Sbjct: 1132 --EAGIP------------------------RFGHTYLYDGGTGDRFDQPATVGVIYMLK 1165

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+K
Sbjct: 1166 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILTVK 1225

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            SDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LEN 
Sbjct: 1226 SDDVIGRAKTYESIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLENK 1273


>gi|163755836|ref|ZP_02162954.1| DNA-directed RNA polymerase subunit beta [Kordia algicida OT-1]
 gi|161324357|gb|EDP95688.1| DNA-directed RNA polymerase subunit beta [Kordia algicida OT-1]
          Length = 1269

 Score = 1328 bits (3438), Expect = 0.0,   Method: Composition-based stats.
 Identities = 588/1372 (42%), Positives = 807/1372 (58%), Gaps = 117/1372 (8%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
            F      R  F       D PD +++Q  S+  F  +    +ER  EGL   F+  FPIT
Sbjct: 2    FTNQ-TERLNFASAKHTPDYPDFLDIQIKSFQDFFQLETKSEERGEEGLYNTFQENFPIT 60

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  +LEF+ Y  DPP++++ +C+ R LTY+VPLK  L+L   D +       +    
Sbjct: 61   DTRNQFVLEFLDYFVDPPRYNIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV---- 116

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
             Q +Y+G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP
Sbjct: 117  -QDVYLGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIP 172

Query: 187  DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
             +G W++   D   +++  IDR++K+PVT+   A+G +S+ +IL  F             
Sbjct: 173  FKGSWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFESDKDILEIFDLAEEVKVSKSGL 232

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
               L                           G+KL + +L +  E  V            
Sbjct: 233  KKVL---------------------------GRKLAARVLNTWHEDFVDEDT-------- 257

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV-DSVNNNAYIRNTLVT 364
                 ++V+ E  EI ++   +++++ +EEI  + ++ I +    +   + A I NTL  
Sbjct: 258  ----GEVVSIERNEIVLDRDTILEKEHIEEIVEAGVKTILLHKEENQAGDYAIIHNTLQK 313

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D     K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L L+ 
Sbjct: 314  DPTNSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGGVGRYRMNKKLGLNI 373

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              D + + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R
Sbjct: 374  DMDKQVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLAQQFGVGLARMAR 433

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            +I+ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSAL
Sbjct: 434  TIRERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSAL 493

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN+ GF+ETPYRK
Sbjct: 494  GPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVFAKVNSMGFLETPYRK 553

Query: 605  VCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +GKV      YLSA EEE   IAQAN  L EDG+   E V  R  G+  +V   +I +
Sbjct: 554  VENGKVDIEKFAYLSAEEEEGMKIAQANIPLKEDGTINVEKVIAREEGDFPVVNPSEIQY 613

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ ++P VGTG+E  VA  S
Sbjct: 614  TDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPQSPIVGTGLERQVASDS 673

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               + A+  G+VE VDA +I I+     +  L         Y L+KF+++NQ+T +N +P
Sbjct: 674  RVLVNAEGDGLVEYVDANKITIKYDRTDDERLVSFDGDSKTYNLIKFRKTNQSTSINLKP 733

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V+ GD V++  ++ +G +T  G+LALGRNM VAFMPW GYNFED+++ISE++V ED+FT
Sbjct: 734  IVRRGDRVKKGQVLCEGYATQKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFT 793

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITP
Sbjct: 794  SIHIDEYSMDVRDTKLGAEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITP 853

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGES  TPEEKLLRAIFG+KA DV+D SL+    + G V++ ++F+R   DK +R+   E
Sbjct: 854  KGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVINKKLFSRAIKDKRKRAKDKE 913

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE 1015
              +I  L  +   +   L   +  +L  I+ G+ +       G +   K    +  +++ 
Sbjct: 914  --EIATLELEYATKFEELRGVLIEKLFTIVNGKTSQGVQNDLGEEVLPKGKKFTLKMLNA 971

Query: 1016 YPRSQWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                          D+   R V  L   Y+   + L+   +     I  GD++P G+L++
Sbjct: 972  VEDYAHLTGGTWTTDDDTNRAVADLVHNYKIKLNDLQGALRRDKFTISVGDELPAGILKL 1031

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             KV++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+
Sbjct: 1032 AKVYIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNI 1091

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI+ET LGWA   L KK  + I D  +   I+ +                         
Sbjct: 1092 GQIYETVLGWAGEKLDKKYATPIFDGASLDQINEITD----------------------- 1128

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   ++GVP                          G + LYDG TGE FD+P TVG 
Sbjct: 1129 -------EAGVP------------------------RFGHTYLYDGGTGERFDQPATVGI 1157

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E
Sbjct: 1158 IYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLRE 1217

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +LT+KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1218 ILTVKSDDVIGRAKTYESIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|163787871|ref|ZP_02182318.1| DNA-directed RNA polymerase subunit beta [Flavobacteriales bacterium
            ALC-1]
 gi|159877759|gb|EDP71816.1| DNA-directed RNA polymerase subunit beta [Flavobacteriales bacterium
            ALC-1]
          Length = 1270

 Score = 1328 bits (3436), Expect = 0.0,   Method: Composition-based stats.
 Identities = 591/1371 (43%), Positives = 814/1371 (59%), Gaps = 119/1371 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F       D PD +++Q  S+  F  +    +ER NEGL   F   FPIT   
Sbjct: 4    KKAERINFSSIVNRTDYPDFLDIQIKSFQDFFQLETKSEERGNEGLYNTFMENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ +++C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFIDPPRYSIEECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFSQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIF---------------- 219

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                       ++  +    +G + +  G+KL + +L +  E  V               
Sbjct: 220  ----------DLAEEVKVSKSGLKKV-IGRKLAARVLNTWHEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDK 366
              ++V+ E  EI ++   +ID+ ++EEI  +E++ I +L+ +S     Y  I NTL  D 
Sbjct: 258  -GEVVSIERNEIVLDRDTIIDKDNIEEILEAEVKTI-LLHKESAQQGDYAIIHNTLQKDP 315

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                K+A+  IYR +R  +      A  + + LFF   +Y L  VGR +MN +L LD   
Sbjct: 316  TNSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYSLGEVGRYRMNKKLLLDIGM 375

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            D + + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L +Q+ +GL RM R+I
Sbjct: 376  DKQVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSSQFGVGLARMARTI 435

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG 
Sbjct: 436  RERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGP 495

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ FA+VN+ GFIETPYRKV 
Sbjct: 496  GGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVFAKVNSMGFIETPYRKVD 555

Query: 607  DGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G V   N   YLSA EEE+  IAQA   +DE G    E +  R  G+  ++    +++ 
Sbjct: 556  NGVVDIKNAPTYLSAEEEEDMLIAQATIEVDEKGKILPEKIISRQEGDFPVIEPSNVNYT 615

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  S 
Sbjct: 616  DVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLERQVASDSR 675

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
              I A+ AG VE VDA +I IR     E  +    S    Y L+KF+++NQ T +N +P+
Sbjct: 676  VLINAEGAGTVEYVDAEKITIRYERTKEEGMVSFDSDTKTYPLVKFRKTNQGTSINLKPI 735

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ GD+V R  ++ +G +T  G+LALGRNM VAFMPW GYNFED+++ISE++V EDVFTS
Sbjct: 736  VEKGDKVERGQVLCEGYATQNGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDVFTS 795

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAE+ PGDIL+GKITPK
Sbjct: 796  IHIDEYSLDVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEIKPGDILIGKITPK 855

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R    K++R  + ++
Sbjct: 856  GESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFARA--VKDKRKRAQDK 913

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEY 1016
            E IE L    D+    L   +  +L  I+ G+ A       G +   K    +  +++  
Sbjct: 914  EDIEKLEDAYDNRFDDLKNTLVEKLFTIVNGKTAQGIYNDLGEEIIPKGKKYTLKMLNAV 973

Query: 1017 PRSQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         D+     V  L   Y+  ++ L+   + +   I  GD++P G++++ 
Sbjct: 974  DDYTHLTSGRWTTDDHTNELVADLIHNYKIKENDLQGSLRREKFTISVGDELPAGIIKLA 1033

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+G
Sbjct: 1034 KVYIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIG 1093

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            QI+ET LGWA   LG+   + I D      I+                            
Sbjct: 1094 QIYETVLGWAGQDLGRTYATPIFDGATLDQINGFTD------------------------ 1129

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                  ++G+P                          G + LYDG TG+ FD+P TVG I
Sbjct: 1130 ------EAGIP------------------------RFGHTYLYDGGTGDRFDQPATVGVI 1159

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YM+KL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+
Sbjct: 1160 YMIKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREI 1219

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            LT+KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1220 LTVKSDDVIGRAKTYEAIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|150025248|ref|YP_001296074.1| DNA-directed RNA polymerase subunit beta [Flavobacterium
            psychrophilum JIP02/86]
 gi|158513724|sp|A6GYU0|RPOB_FLAPJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|149771789|emb|CAL43263.1| DNA-directed RNA polymerase beta subunit RpoB [Flavobacterium
            psychrophilum JIP02/86]
          Length = 1270

 Score = 1327 bits (3435), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1368 (42%), Positives = 811/1368 (59%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F     I   PD ++VQ  S+  F  +    DER NEGL   F   FPIT     
Sbjct: 6    TERLNFASTKNIPAYPDFLDVQVKSFQDFFQLETKSDERGNEGLYNTFMENFPITDTRNN 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFIDYFVDPPRYTIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G  S+ +IL  F                + 
Sbjct: 178  IEFATDINSVMYAYIDRKKKLPVTTLFRAIGFQSDKDILEIFDLAEEIKVSKSGLKKYI- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +L +  E  V                 
Sbjct: 237  --------------------------GRKLAARVLNTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   ++D+ ++EEI  S ++ I +   D+ V + + I NTL  D    
Sbjct: 259  EVVSIERNEIILDRDTILDKDNVEEIVESNVKSILLHKEDNNVVDYSIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR ++N +L LDTP + +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRINKKLGLDTPMEKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIVKYLIELINAKADIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV +G 
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVYAKVNGMGFIETPYRKVTNGV 558

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V  T+   YLSA EEE   IAQAN  +DE+G  T + V  R  G+  ++    + + D +
Sbjct: 559  VDLTSVPKYLSAEEEEGMLIAQANIQMDENGKITADNVIARQEGDFPVIDPTAVHYTDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPL++ EAP VGTG+E  VA  S   I
Sbjct: 619  PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLIRPEAPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+ AG+VE VDA  I I+             S    Y+L+KF+++NQ T +N +P+V+ 
Sbjct: 679  NAEGAGVVEYVDADMITIKYDRTDAERAVSFESDEKTYKLIKFRKTNQGTSINLKPIVRK 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD+V +  ++ +G +T  G+LALGRN+ VAFMPW GYNFED+++ISE++V +D+FTSIH+
Sbjct: 739  GDKVIKGQVLCEGYATQNGELALGRNLKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHV 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +++ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DDYSLEVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R    K++R  + +++ +
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVLDKKLFARA--VKDKRKRTQDKDAL 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + + + V L   +  +L  I+ G+ +       G +   K    +  ++      
Sbjct: 917  SDLEMEFEVKFVELKDKLVDKLFTIVNGKTSQGVMNDLGEEVLPKGKKYTQKMLYAVEDF 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                    V D++  + V  L   Y+   + L+   + +   I  GD++P G+L++ KV+
Sbjct: 977  AHLTRGQWVADDETNKMVNDLIHNYKIKLNDLQGALRREKFTITVGDELPAGILKLAKVY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVARIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LG+K  + I D  +   I+ +                             
Sbjct: 1097 ETVLGWAGQNLGRKYATPIFDGASLDQINAITD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++GVP                          G + LYDG TGE F +  TVG IYML
Sbjct: 1130 ---EAGVP------------------------RFGHTHLYDGGTGERFHQAATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVIGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|325954353|ref|YP_004238013.1| DNA-directed RNA polymerase subunit beta [Weeksella virosa DSM 16922]
 gi|323436971|gb|ADX67435.1| DNA-directed RNA polymerase subunit beta [Weeksella virosa DSM 16922]
          Length = 1278

 Score = 1327 bits (3435), Expect = 0.0,   Method: Composition-based stats.
 Identities = 586/1381 (42%), Positives = 816/1381 (59%), Gaps = 119/1381 (8%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA       +   R  F     +   PD +++Q  S++ F  +   PD+R NEGL   F 
Sbjct: 1    MATTTNNPAVKNERLSFASTKAVAQFPDFLDIQIKSFEDFFQLETRPDQRNNEGLFKTFA 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              FPIT      +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D +      
Sbjct: 61   ENFPITDTRNQFVLEFLDYFVDPPRYSIDECIERGLTYSVPLKARLKLYCTDEEHEDFET 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +     Q +Y+G +P MT  G+F+I G +R++VSQLHRSPG+ F         +G  LY
Sbjct: 121  VV-----QDVYLGTIPYMTPSGSFIINGAERVIVSQLHRSPGVFFGQSF---HANGTKLY 172

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
            + RIIP +G W++   D   +++  IDR++K+P+T+ L A+G + + +IL  F       
Sbjct: 173  SSRIIPFKGSWIEFATDINSVMYAYIDRKKKLPLTTLLRAIGYERDKDILEIFDLAEEVK 232

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
                     L                           G+KL + +L +  E  V      
Sbjct: 233  VTKANLKKIL---------------------------GRKLAARVLNTWHEDFVDEDT-- 263

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYI 358
                       ++V+ E  EI ++   +I++  +++I  S ++ I +   D+ + +   I
Sbjct: 264  ----------GEVVSIERNEIILDRETIIEKDHIDQIVDSGVKTILLHKEDNNSADYGII 313

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D     K+A+  IYR +R  +      A  + + LFF   +Y L  VGR ++N 
Sbjct: 314  HNTLQKDPTNTEKEAVEYIYRQLRNAEPPDEETARGIIDKLFFSDQRYSLGEVGRYRLNK 373

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L+  +D+  + K+DII+IIK L++L N K  +DDID+L NRRVR+VGE +  Q+ +G
Sbjct: 374  KLGLNISEDIEVLTKDDIISIIKYLIELINSKAEVDDIDHLSNRRVRTVGEQMAAQFGVG 433

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L RM R+I+ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N LS ITH 
Sbjct: 434  LARMARTIRERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLSEITHK 493

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN  GFI
Sbjct: 494  RRLSALGPGGLSRERAGFEVRDVHHTHYGRLCPIETPEGPNIGLISSLCVFAKVNNLGFI 553

Query: 599  ETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            ETPYR+V  GKV    D +YLSA EEE + I QAN  + EDG+   E V  R  G+  +V
Sbjct: 554  ETPYREVEKGKVNLEKDPIYLSAEEEEGKIITQANIEMGEDGTIQTERVVAREDGDFPVV 613

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               ++D +D +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK +AP VGTG+E
Sbjct: 614  EPHEVDLMDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQAPIVGTGLE 673

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQN 773
              VAK S   + A+R G V  VDA +I+I        +L    S    Y L KF+++NQ 
Sbjct: 674  KQVAKDSRILVNAEREGTVTYVDANKIIIAYDRTENEELVSFDSNEKTYSLTKFRKTNQG 733

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            T +  +P+VKVGD V +  ++ +G +T+ G+LA+GRNM+VAFMPW GYNFED+++ISE+ 
Sbjct: 734  TTICLKPIVKVGDRVDKGQVLCEGYATEGGELAIGRNMVVAFMPWQGYNFEDAIVISEKA 793

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V ED FTSIHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDI
Sbjct: 794  VREDWFTSIHIDEYSLDVRDTKLGMEELTADIPNVSEEATKDLDENGMIRIGAEVKPGDI 853

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L+GKITPKGES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R    K+
Sbjct: 854  LIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSR--SIKD 911

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVL 1008
            +R  S ++  IE +  + + +   L   +  +L  +L G+ +         +  KK    
Sbjct: 912  KRKRSQDKAIIESIENEFEVKFNELRNVLLEKLYILLNGKTSQGVYNDLKEEVIKKGVKY 971

Query: 1009 SSDLISE----YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +  ++         +        DE     V+ L   Y+   + L+     +   I  GD
Sbjct: 972  TQKMLQNVEDYLNLNGSETVWTTDEDKNELVKELLHNYKIKHNDLQGALNRERFTIAVGD 1031

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            ++P G++++ K+++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGT VDIVLNP
Sbjct: 1032 ELPAGIVKLAKIYIAKKRKLRVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTAVDIVLNP 1091

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMN+GQI+ET LGWA + LGKK  + I D     DI  +                
Sbjct: 1092 LGVPSRMNIGQIYETVLGWAGMKLGKKFATPIFDGAEIEDIDNITD-------------- 1137

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                            ++G+P                        + G + LYDG TGE 
Sbjct: 1138 ----------------EAGIP------------------------KHGTTYLYDGNTGER 1157

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F +  TVG IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1158 FAQKATVGVIYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 1217

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +GAA +L+E+LT+KSDDVVGR + YE+IV G    E G PESFNVL+ E+Q LGL I+LE
Sbjct: 1218 FGAANILREILTVKSDDVVGRAKTYEAIVKGEPMPEPGIPESFNVLLHELQGLGLDINLE 1277

Query: 1365 N 1365
            +
Sbjct: 1278 D 1278


>gi|326334994|ref|ZP_08201194.1| DNA-directed RNA polymerase subunit beta [Capnocytophaga sp. oral
            taxon 338 str. F0234]
 gi|325692799|gb|EGD34738.1| DNA-directed RNA polymerase subunit beta [Capnocytophaga sp. oral
            taxon 338 str. F0234]
          Length = 1269

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1365 (42%), Positives = 816/1365 (59%), Gaps = 116/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F     + D PD +++Q  S+  F  M    DER NEGL + FK  FPIT      +
Sbjct: 8    RINFASTKHVPDYPDFLDIQVKSFQDFFQMETKSDERRNEGLYSTFKENFPITDTRNQFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ V++C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 68   LEFLDYFVDPPRYSVEECIERGLTYSVPLKARLKLFCTDPEHEDFETIV-----QDVYLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  GTF+I G +R++VSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 123  TIPYMTGSGTFIINGAERVIVSQLHRSPGVFFGQS---YHANGTKLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+   A+G + + +IL  F                L   
Sbjct: 180  FTTDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKYL--- 236

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +L +  E  V                 ++
Sbjct: 237  ------------------------GRRLAARVLNTWHEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRK 371
            V+ E  EI ++   V++++ ++EI ++ ++ I +   D    +   I NTL  D     K
Sbjct: 261  VSIERNEIILDRDTVLEKEHIDEIINANVKTILLHKEDERAIDYNIIHNTLQKDPTNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD P + + +
Sbjct: 321  EAVEHIYRQLRNAEPPDEETARDIIDKLFFSDQRYNLGDVGRYRMNKKLGLDIPMEKQVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 381  TKEDIITIVKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAAQFGVGLSRMARTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF +SQLSQ  +  N L+ ITH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPLDLINAKTLSSVINSFFGTSQLSQFMDQTNPLAEITHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN+ GFIETPYRKV +GK+ 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVYAKVNSMGFIETPYRKVENGKIK 560

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
             +++VY+SA EEE   I QAN  +D+ G+  EE +  +  G+  +VPRE++++ID +P Q
Sbjct: 561  LDELVYMSAEEEEGLKIPQANIQVDDQGNILEERLVVKEDGDFPIVPREEVNYIDVAPNQ 620

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  S   + A+
Sbjct: 621  IASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLEQRVATDSRVLMNAE 680

Query: 731  RAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            R G VE VDA +IVI+     +  L    S +  Y L+KF+R+NQ TC+N +P+V+ GD 
Sbjct: 681  REGTVEYVDAKKIVIKYDRTEDEILVSFDSELTTYDLIKFRRTNQGTCINLKPIVRKGDR 740

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++  ++ +G +T  G+LALGRNM VAFMPW GYNFED+++ISER++ ED+FTSIHI+E+
Sbjct: 741  VKKGQVLCEGYATQNGELALGRNMKVAFMPWKGYNFEDAIVISERVIREDIFTSIHIDEY 800

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSE+  K++DE GI+ +GA + PGDIL+GK+TPKGES  T
Sbjct: 801  TLDVRDTKLGVEELTNDIPNVSEDATKDLDENGIVRIGANIKPGDILIGKVTPKGESDPT 860

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+    + G V+  ++F+R    K +RS   E+++I  L
Sbjct: 861  PEEKLLRAIFGDKAGDVKDASLKASPSLEGVVIGKKLFSRAVKTKQKRSK--EKDEIAAL 918

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQ-- 1020
                + +   L   +  +L  ++ G+ +       G +   K    +   + E       
Sbjct: 919  DAAFNAKAGELRDRLLEKLFSLVNGKTSQGVFNDLGEEIIPKGRKHTQKGLREIEDYTHL 978

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+   + +  L   Y+   + L+   +     +  GD++P G++++ K+++A 
Sbjct: 979  LSGGWTTDDHTNQLINDLIHNYKIKLNDLQGMLRRDKFTLSVGDELPAGIMKLAKIYIAK 1038

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1039 KRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLADGTPVDIVLNPLGVPSRMNIGQIYETV 1098

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LG K  + I D  +   I+                                  
Sbjct: 1099 LGWAGQKLGLKFATPIFDGASLEQITEYTEKAG--------------------------- 1131

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                    P F                    G + LYDG TGE FD+  TVG IYM+KL 
Sbjct: 1132 -------VPAF--------------------GHTYLYDGGTGERFDQKATVGVIYMIKLG 1164

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+KSD
Sbjct: 1165 HMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTVKSD 1224

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV+GR R YE+IV G+   E G PESFNVL+ E++ LGL I LE 
Sbjct: 1225 DVIGRARTYEAIVHGDTMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|218264355|ref|ZP_03478212.1| hypothetical protein PRABACTJOHN_03903 [Parabacteroides johnsonii DSM
            18315]
 gi|218222053|gb|EEC94703.1| hypothetical protein PRABACTJOHN_03903 [Parabacteroides johnsonii DSM
            18315]
          Length = 1270

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1366 (42%), Positives = 805/1366 (58%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F         PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASIKNQFPYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPRYTIDECIARGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT+ GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTERGTFVINGAERVVVSQLHRSPGVFFGQS---THANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFESDKDILEIFNLAEEVKVSKANLKKLI-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWVEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  ++ I+   V+D  ++E I  S  ++I +   D  +++ A I NTL  D +   
Sbjct: 261  VVSIERNDVIIDRESVLDSDNIEAILESGTQNILLHREDQNLSDYAIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  + +  + A  +   LFF   +YDL  VGR ++N +LNL T DD++ 
Sbjct: 321  KEAVLYIYRQLRNAEPADEASAREVIQNLFFSEKRYDLGEVGRYRINKKLNLTTSDDIKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+++ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKAIVDDIDHLSNRRVRTVGEQLYNQFGIGLARMSRTVRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S V  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DGKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFISTPYRKVVDGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + Y +A EEE   IAQ N+ LD DG F  + V  R   +  +VP  +ID +D +
Sbjct: 561  DFSEEGLQYYTAEEEEELTIAQGNAPLDNDGKFVRDRVKARFEADFPVVPPTEIDLMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ +AP VGTG+E+ VA+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTDAPIVGTGIEAQVARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +A+R G V  VDA  I I+     + +       V  Y + K++++NQ+T V+ RP+   
Sbjct: 681  MAEREGEVVFVDATCIKIKYDRSEDEEFVSFEDAVKTYNIPKWRKTNQSTTVDLRPICHR 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V+  DI+ +G ST  G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED FTS+H+
Sbjct: 741  GQRVKAGDILTEGYSTQNGELALGRNVKVAYMPWKGYNYEDAIVLNERMVREDFFTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDERGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V++  +F++    K  +S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIETALFSKA--VKKRKSRLTDKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + + +   L   +  +L      ++  G       +   K    S   + E   +
Sbjct: 919  PKLDEEYEMKMADLKNLLVDKLLVLTNGKVSQGVKDYMNTEIIAKGVKFSRKALEELDYN 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      ++ + + Y      L+   + K   +  GD++P G++++ KV++
Sbjct: 979  SIQVSKWTADADKNELIKQVILNYLKKYKELDAELRRKKFDLTIGDELPTGIVQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL+DGTPVDI LNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLEDGTPVDICLNPLGVPSRMNLGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LGWA   +G K  + I D     D++                                
Sbjct: 1099 AVLGWAGRTMGVKFATPIFDGATLDDMNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G+S LYDG TGE FD+P TVG  Y LK
Sbjct: 1131 --KAGLP------------------------RYGKSYLYDGGTGERFDQPATVGVTYFLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G+   + G PES NVL+ E++ LGLS  L+
Sbjct: 1225 SDDVVGRSKAYEAIVKGDPMPQPGIPESLNVLLHELRGLGLSFTLD 1270


>gi|313204192|ref|YP_004042849.1| DNA-directed RNA polymerase subunit beta [Paludibacter
            propionicigenes WB4]
 gi|312443508|gb|ADQ79864.1| DNA-directed RNA polymerase subunit beta [Paludibacter
            propionicigenes WB4]
          Length = 1270

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 589/1368 (43%), Positives = 813/1368 (59%), Gaps = 117/1368 (8%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  F      ++ PD +EVQ  S+  F  M+ AP++R +EGL   F   FPI     
Sbjct: 6    KAQRINFASIKNQLEYPDFLEVQLKSFQDFFQMDTAPEKRKSEGLYKVFSENFPIADTRN 65

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +
Sbjct: 66   NFILEFLDYYVDPPRYSIDECVERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDV 120

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+G +P MT  GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RIIP +G 
Sbjct: 121  YLGPIPYMTAKGTFVINGAERVIVSQLHRSPGVFFGQS---THANGTKLYSARIIPFRGS 177

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            W++   D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                +
Sbjct: 178  WIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFESDKDILEIFNLAEEIKVSKTSLKKAI 237

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                       G+KL + +LK+  E  V                
Sbjct: 238  ---------------------------GQKLAARVLKTWVEDFVDEDT------------ 258

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNK 368
             ++V  E  E+ I+   +++   ++EI  +    I +   D + N+ A I NTL  D + 
Sbjct: 259  GEVVTIERNEVIIDRETILENSHIDEIIEAGTPTILLHKADANQNDYAIIYNTLQKDPSN 318

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              K+A+L IYR +R    +  S A  + N LFF   +YDL  VGR ++N +LNL T  D 
Sbjct: 319  SEKEAVLYIYRQLRNAVPADDSTAREVINNLFFPEKRYDLGNVGRFRINRKLNLTTSMDT 378

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+E
Sbjct: 379  KVLTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLYNQFGVGLSRMARTIRE 438

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG
Sbjct: 439  RMNVRDNEVFTPIDLINAKSISSVINSFFGTNALSQFMDQQNPLAEITHKRRMSALGPGG 498

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFIETPYRKV D 
Sbjct: 499  LSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCIYAKINELGFIETPYRKVTDS 558

Query: 609  KV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             V      + Y +A EEEN  IAQ N+ L++DG F    V  R   +  +V  ++++ +D
Sbjct: 559  VVDISEAGIEYFTAEEEENLIIAQGNAPLNDDGGFIRTKVKSRLGADFPVVAPDEVNLMD 618

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SIAA+LIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E+ + + S  
Sbjct: 619  VSPSQIASIAAALIPFLEHDDANRALMGSNMMRQAVPLLRCEAPIVGTGIEAQLIRDSRT 678

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             + A+  G VE VDA  I IR     + +     S V  Y+L KFQ++NQNT ++ RP+V
Sbjct: 679  QVAAEGEGEVEFVDATCIKIRYDRTEDEEFVSFESAVKEYKLPKFQKTNQNTTIDLRPIV 738

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K G+ V    I+ +G +T  G+LA+G+N+ VAFMPW GYNFED+++I+ER+V ED+FTSI
Sbjct: 739  KKGERVTNGQIMTEGYATQNGELAIGKNLKVAFMPWKGYNFEDAIVINERVVREDIFTSI 798

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H+ E  +  R+TK G EE T DIPNVSEE  K++DE GII +GA + PGDI++GKITPKG
Sbjct: 799  HVVEQLLDVRETKRGIEEFTSDIPNVSEEATKDLDENGIIRIGARIEPGDIIIGKITPKG 858

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  +PEEKLLRAIFG+KA DV+D SL+    +SG V+  R+F++    KN +S   ++ 
Sbjct: 859  ESDPSPEEKLLRAIFGDKAGDVKDASLKATPSLSGVVIGKRLFSKA--QKNRKSKLADKA 916

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  L  + +++  IL   +  +L+ +L      G     G     +++  + + + E  
Sbjct: 917  VLPKLDEEFENQAAILRDTLVEKLIVLLGDKTSAGVKDFLGADVISRNSKFTIERLREID 976

Query: 1018 RSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             +         D      V+ L + Y      L+ + K +   I  GD++P G++++ KV
Sbjct: 977  YTAVQLSKWTTDSHKNELVKQLIMNYLRKYKELDAQIKRQKFNITIGDELPNGIVQIAKV 1036

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A KR I+ GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1037 YIAKKRKIRVGDKMAGRHGNKGIVSRIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNLGQI 1096

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FET LGWA   LG +  + I D  +  D++                              
Sbjct: 1097 FETVLGWAGKELGLRFATPIFDGASLDDLN------------------------------ 1126

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A   K+GVP                          G++ LYDG TGE FD+  TVG IYM
Sbjct: 1127 AWTDKAGVP------------------------NYGKTYLYDGGTGERFDQTATVGVIYM 1162

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LT
Sbjct: 1163 LKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILT 1222

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +KSDDV+GR R YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1223 VKSDDVMGRARTYEAIVKGDPMPTPGIPESLNVLLHELRGLGLSISLD 1270


>gi|154491721|ref|ZP_02031347.1| hypothetical protein PARMER_01332 [Parabacteroides merdae ATCC 43184]
 gi|154087962|gb|EDN87007.1| hypothetical protein PARMER_01332 [Parabacteroides merdae ATCC 43184]
          Length = 1270

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1366 (42%), Positives = 806/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F         PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASIKNQFPYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPRYTIDECIARGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT+ GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTERGTFVINGAERVVVSQLHRSPGVFFGQS---THANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFESDKDILEIFNLAEEVKVSKANLKKLI-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWVEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  ++ I+   V+D  ++E I  S  ++I +   D  +++ A I NTL  D +   
Sbjct: 261  VVSIERNDVIIDRESVLDSDNIEAILESGTQNILLHREDQNLSDYAIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  + +  + A  +   LFF   +YDL  VGR ++N +LNL T DD++ 
Sbjct: 321  KEAVLYIYRQLRNAEPADEASAREVIQNLFFSEKRYDLGEVGRYRINKKLNLTTSDDIKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+++ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKAIVDDIDHLSNRRVRTVGEQLYNQFGIGLARMSRTVRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S V  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DGKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFISTPYRKVVDGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + Y +A EEE   IAQ N+ LD++G F  + V  R   +  +VP  +ID +D +
Sbjct: 561  DFSEEGLQYYTAEEEEELTIAQGNAPLDDNGKFVRDRVKARFEADFPVVPPTEIDLMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ +AP VGTG+E+ VA+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTDAPIVGTGIEAQVARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +A+R G V  VDA  I I+     + +       V  Y + K++++NQ+T V+ RP+   
Sbjct: 681  MAEREGEVVFVDATCIKIKYDRSEDEEFVSFEDAVKTYNIPKWRKTNQSTTVDLRPICHR 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V+  DI+ +G ST  G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED FTS+H+
Sbjct: 741  GQRVKAGDILTEGYSTQNGELALGRNVKVAYMPWKGYNYEDAIVLNERMVREDFFTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDERGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V++  +F++    K  +S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIETALFSKA--IKKRKSRLTDKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + + +   L   +  +L      ++  G       +   K    S   + E   +
Sbjct: 919  PKLDEEYEMKMADLKNLLVDKLLVLTNGKVSQGVKDYMNTEIIAKGVKFSRKALEELDYN 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      ++ + + Y      L+   + K   +  GD++P G++++ KV++
Sbjct: 979  SIQVSKWTADADKNELIKQVILNYLKKYKELDAELRRKKFDLTIGDELPTGIVQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL+DGTPVDI LNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLEDGTPVDICLNPLGVPSRMNLGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LGWA   +G K  + I D     D++                                
Sbjct: 1099 AVLGWAGRTMGVKFATPIFDGATLDDMNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G+S LYDG TGE FD+P TVG  Y LK
Sbjct: 1131 --KAGLP------------------------RYGKSYLYDGGTGERFDQPATVGVTYFLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G+   + G PES NVL+ E++ LGLS  L+
Sbjct: 1225 SDDVVGRSKAYEAIVKGDPMPQPGIPESLNVLLHELRGLGLSFTLD 1270


>gi|86131817|ref|ZP_01050414.1| DNA-directed RNA polymerase beta chain [Dokdonia donghaensis MED134]
 gi|85817639|gb|EAQ38813.1| DNA-directed RNA polymerase beta chain [Dokdonia donghaensis MED134]
          Length = 1273

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 587/1368 (42%), Positives = 805/1368 (58%), Gaps = 117/1368 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F       D PD +++Q  S+  F  +    DER +EGL   F   FPIT      
Sbjct: 9    ERISFSSVKNRPDYPDFLDIQVKSFQDFFQLETKSDERGDEGLYNTFLENFPITDTRNNF 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y+
Sbjct: 69   VLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDEEHEDFETIV-----QDVYL 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W+
Sbjct: 124  GTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSWI 180

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D   +++  IDR++K+PVT+   A+G + + +IL  F                L  
Sbjct: 181  EFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKYL-- 238

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +L +  E  V                 +
Sbjct: 239  -------------------------GRKLAARVLNTWHEDFVDEDT------------GE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDR 370
            +V+ E  EI ++   V++++ +EEI  +  + + +   D+   + A I NTL  D     
Sbjct: 262  VVSIERNEIVLDRDTVLEKEHVEEILEAGAKTVLLHKEDNQQADYAIIHNTLQKDPTNSE 321

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D + 
Sbjct: 322  KEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIEMDKQV 381

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K DII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER+
Sbjct: 382  LTKLDIITIIKYLIELINAKAEIDDIDHLSNRRVRTVGEQLSAQFGVGLARMARTIRERM 441

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 442  NVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLS 501

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DG 608
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV     
Sbjct: 502  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVYAKVNNMGFIETPYRKVEGGKI 561

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
             + ++  YLSA EEE   IAQAN+ ++++G+ TEE V  R  G+  +V  + + + D SP
Sbjct: 562  DLKSEPQYLSAEEEEGMLIAQANNPMNDEGTITEEKVIARMEGDFPVVDPDTVHYADVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPL+ A+AP VGTG+E  VA  S   I 
Sbjct: 622  NQIASISASLIPFLEHDDANRALMGSNMMRQAVPLIMADAPIVGTGLERQVATDSRVLIN 681

Query: 729  AKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+ AG VE VDA  I I+     +  L         Y L+KF+++NQ T +N +P+VKVG
Sbjct: 682  AEGAGTVEYVDANMITIKYDRTDDERLVSFDEDSKSYNLIKFRKTNQGTNINLKPIVKVG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V R  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V +D+FTSIHI+
Sbjct: 742  DRVERGQVLCQGYATEKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHID 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES 
Sbjct: 802  EYSLDVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             TPEEKLLRAIFG+KA DV+D SL+    + G V++ ++F R   DK +R+   E   I 
Sbjct: 862  PTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVINKKLFARAIKDKRKRAKDKED--IA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQ 1020
            +L    D +   L   +  +L +++ G+ A       G +   K    +  +++      
Sbjct: 920  VLEDKYDVKFDDLQAVLIEKLFKLVNGKTAQGVMNDLGEEVLPKGKKFTLKMLNSVEDYT 979

Query: 1021 WWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+K    +  L   Y+  ++ L+   + +   I  GD++P G++++ KV++
Sbjct: 980  HLTQGTWTTDDKTNTLIADLLHNYKIKENDLQGNLRREKFTISVGDELPAGIIKLAKVYI 1039

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+E
Sbjct: 1040 AKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYE 1099

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA   LG+   + I D      I+ L                              
Sbjct: 1100 TVLGWAGQKLGRTYATPIFDGATLDQINALTD---------------------------- 1131

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+P                          G + LYDG TG+ FD+P TVG IYMLK
Sbjct: 1132 --EAGIP------------------------RFGHTYLYDGGTGDRFDQPATVGVIYMLK 1165

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+K
Sbjct: 1166 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILTVK 1225

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            SDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE  
Sbjct: 1226 SDDVIGRAKTYESIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLEEK 1273


>gi|86140281|ref|ZP_01058840.1| DNA-directed RNA polymerase beta subunit [Leeuwenhoekiella blandensis
            MED217]
 gi|85832223|gb|EAQ50672.1| DNA-directed RNA polymerase beta subunit [Leeuwenhoekiella blandensis
            MED217]
          Length = 1270

 Score = 1327 bits (3434), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1370 (42%), Positives = 803/1370 (58%), Gaps = 117/1370 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F       + PD +++Q  S+  F  +    +ER NEGL   F   FPIT   
Sbjct: 4    KQAERLNFSSVKNRPEYPDFLDIQIKSFQDFFQLETKSEERGNEGLYNTFLENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NNFVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDEEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKY 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L                           G+KL + +L +  E  V               
Sbjct: 236  L---------------------------GRKLAARVLNTWHEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKN 367
              ++V+ E  EI ++   V++++ +EEI  +  + I +   D  + + A I NTL  D  
Sbjct: 258  -GEVVSIERNEIVLDRDTVLEKEHVEEILDAGAKTILLHKEDNQLADYAIIHNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIGMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + K+DII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  KQVLTKQDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSTQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYR V D
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVYAKVNNMGFIETPYRTVTD 556

Query: 608  GKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            GK+  +    YLSA EEE   IAQAN+ +D+ G   EE V  R  G+  +V    + + D
Sbjct: 557  GKIDLETKPKYLSAEEEEGMLIAQANNPMDDSGKIEEERVIARMEGDFPVVEPNTVHYAD 616

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+A++P VGTG+E  VA  S  
Sbjct: 617  VSPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRADSPIVGTGLERQVASDSRV 676

Query: 726  AIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A+  G VE VDA  I I+     E  +         Y+L+KF+++NQ+T +N +P+V
Sbjct: 677  LINAEGDGEVEYVDANEITIKYDRTDEERMVSFDGDSKTYQLIKFRKTNQSTSINLKPIV 736

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V++  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V +D+FTSI
Sbjct: 737  RRGDRVKKGQVLCQGYATEAGELALGRNMKVAFMPWKGYNFEDAIVISEKVVRDDIFTSI 796

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H++E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKG
Sbjct: 797  HVDEYSLDVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKG 856

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R   DK +R+   E  
Sbjct: 857  ESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFARAIKDKRKRAKDKED- 915

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYP 1017
             I  L  + D +   L   +  +L +++ G+ A       G +   K    +  +++   
Sbjct: 916  -IAALEAEYDQKFDDLKAVLVDKLFQLVNGKTAQGVKNDLGEEVLPKGKKFTLKMLNAVE 974

Query: 1018 RSQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        D+     +  L   Y   ++ L+   + +   I  GD++P G++++ K
Sbjct: 975  DYTHLNQGTWTTDDATNVLIADLLHNYRIKENDLQGNLRREKFTISVGDELPSGIIKLAK 1034

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V+VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1035 VYVAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQ 1094

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET LGWA   LG+K  + I D      I+ L                           
Sbjct: 1095 IYETVLGWAGQKLGRKYATPIFDGATLDQINELTD------------------------- 1129

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 ++G+P                          G + LYDG TG+ FD+P TVG IY
Sbjct: 1130 -----QAGIP------------------------RFGHTYLYDGGTGDRFDQPATVGVIY 1160

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+L
Sbjct: 1161 MLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREIL 1220

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            T+KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1221 TVKSDDVIGRAKTYESIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|89890192|ref|ZP_01201703.1| RNA polymerase beta subunit rpoB [Flavobacteria bacterium BBFL7]
 gi|89518465|gb|EAS21121.1| RNA  polymerase beta subunit rpoB [Flavobacteria bacterium BBFL7]
          Length = 1271

 Score = 1326 bits (3432), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1368 (42%), Positives = 800/1368 (58%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F       D PDL+++Q  S+  F  +    D+R  EGL   F   FPIT     
Sbjct: 7    TERINFSTVTTKADYPDLLDIQIKSFQDFFQLETKSDKREVEGLYNTFMENFPITDTRNQ 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 67   FVLEFLDYFVDPPRYSIQECIERGLTYSVPLKSRLKLYCTDPEHEDFETIV-----QDVY 121

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 122  LGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 178

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G + + +IL  F                L 
Sbjct: 179  IEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILGIFDLAEEVKASKTGLKKYL- 237

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +L++  E  V                 
Sbjct: 238  --------------------------GRKLAARVLRTWHEDFVDEDT------------G 259

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   V+D++ ++EI  S+ + I +   D+ + + A I NTL  D    
Sbjct: 260  EVVSIERNEIVLDRDTVLDKEHIDEIMESQAKTILLHKEDNQSADYAIIHNTLQKDPTNS 319

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D +
Sbjct: 320  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIAMDKQ 379

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 380  VLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRER 439

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 440  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 499

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN+ GFIETPYR V DG 
Sbjct: 500  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFAKVNSMGFIETPYRSVKDGV 559

Query: 610  VT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V    +  YLSA EEE  +IAQAN  L+  G   ++ V  R  G+  +V   ++ + D +
Sbjct: 560  VNLEEEPTYLSAEEEEGMHIAQANLPLNGKGKIDQDKVIARMEGDFPVVDPTEVVYADVA 619

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ +AP VGTG+E  VA  S   I
Sbjct: 620  PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRVDAPIVGTGLERQVATDSRVLI 679

Query: 728  VAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G V  VDA RI I+                  Y L+KF+++NQ T +  +P+VK 
Sbjct: 680  NAEGDGEVTYVDAQRISIKYDRTDREIAISFEPEETTYNLIKFRKTNQGTSITLKPIVKK 739

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V R  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V ED+FTSIH+
Sbjct: 740  GDRVNRGQVLCQGYATEAGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSIHV 799

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  RDTKLG EE+T DIPNVSEE   ++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 800  DEYSLDVRDTKLGNEELTPDIPNVSEEATADLDEQGMIRIGAEVKPGDILIGKITPKGES 859

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R    K++R  + ++E I
Sbjct: 860  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSRA--VKDKRKRAQDKEDI 917

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L +    +   L   +  +L EI+ G+ +       G +   K    +  ++      
Sbjct: 918  AKLEQAYQSKFDNLQERLIEKLFEIVSGKTSQGVFNDLGEEVLPKGKKYTLKMLHSVDDY 977

Query: 1020 QWW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       +     +  L   Y+  ++ L+   + +   I  GD++P G++++ KV+
Sbjct: 978  THLVSGTWTTSKDTNEMIADLLHNYKIKENDLQGSLRREKFTISVGDELPAGIIKLAKVY 1037

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1038 IAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1097

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LGK   + I D      I+                              A
Sbjct: 1098 ETVLGWAGQKLGKTFATPIFDGATLDQIN------------------------------A 1127

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++G+P                          G + LYDG TG+ FD+P TVG IYML
Sbjct: 1128 YTDEAGIP------------------------RFGHTYLYDGGTGDRFDQPATVGVIYML 1163

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1164 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1223

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL + LE+
Sbjct: 1224 KSDDVIGRAKTYEAIVKGEPMPEPGLPESFNVLMHELKGLGLDLRLED 1271


>gi|45439264|gb|AAS64308.1| putative RNA polymerase beta subunit [Flavobacterium psychrophilum]
          Length = 1270

 Score = 1326 bits (3431), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1368 (42%), Positives = 810/1368 (59%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F     I   PD ++VQ  S+  F  +    DER NEGL   F   FPIT     
Sbjct: 6    TERLNFASTKNIPAYPDFLDVQVKSFQDFFQLETKSDERGNEGLYNTFMENFPITDTRNN 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFIDYFVDPPRYTIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G  S+ +IL  F                + 
Sbjct: 178  IEFATDINSVMYAYIDRKKKLPVTTLFRAIGFQSDKDILEIFDLAEEIKVSKSGLKKYI- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +L +  E  V                 
Sbjct: 237  --------------------------GRKLAARVLNTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   ++D+ ++EEI  S ++ I +   D+ V + + I NTL  D    
Sbjct: 259  EVVSIERNEIILDRDTILDKDNVEEIVESNVKSILLHKEDNNVVDYSIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
              +A+  IYR +R  +      A  + + LFF   +Y+L  VGR ++N +L LDTP + +
Sbjct: 319  EIEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRINKKLGLDTPMEKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIVKYLIELINAKADIDDIDHLSNRRVRTVGEQLSQQFGVGLARMVRTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV +G 
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVYAKVNGMGFIETPYRKVTNGV 558

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V  T+   YLSA EEE   IAQAN  +DE+G  T + V  R  G+  ++    + + D +
Sbjct: 559  VDLTSVPKYLSAEEEEGMLIAQANIQMDENGKITADNVIARQEGDFPVIDPTAVHYTDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPL++ EAP VGTG+E  VA  S   I
Sbjct: 619  PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLIRPEAPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+ AG+VE VDA  I I+             S    Y+L+KF+++NQ T +N +P+V+ 
Sbjct: 679  NAEGAGVVEYVDADMITIKYDRTDAERAVSFESDEKTYKLIKFRKTNQGTSINLKPIVRK 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD+V +  ++ +G +T  G+LALGRN+ VAFMPW GYNFED+++ISE++V +D+FTSIH+
Sbjct: 739  GDKVIKGQVLCEGYATQNGELALGRNLKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHV 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +++ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DDYSLEVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R    K++R  + +++ +
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVLDKKLFARA--VKDKRKRTQDKDAL 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + + + V L   +  +L  I+ G+ +       G +   K    +  ++      
Sbjct: 917  SDLEMEFEVKFVELKDKLVDKLFTIVNGKTSQGVMNDLGEEVLPKGKKYTQKMLYAVEDF 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                    V D++  + V  L   Y+   + L+   + +   I  GD++P G+L++ KV+
Sbjct: 977  AHLTRGQWVADDETNKMVNDLIHNYKIKLNDLQGALRREKFTITVGDELPAGILKLAKVY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVARIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LG+K  + I D  +   I+ +                             
Sbjct: 1097 ETVLGWAGQNLGRKYATPIFDGASLDQINAITD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++GVP                          G + LYDG TGE F +  TVG IYML
Sbjct: 1130 ---EAGVP------------------------RFGHTHLYDGGTGERFHQAATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVIGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|256420754|ref|YP_003121407.1| DNA-directed RNA polymerase, beta subunit [Chitinophaga pinensis DSM
            2588]
 gi|256035662|gb|ACU59206.1| DNA-directed RNA polymerase, beta subunit [Chitinophaga pinensis DSM
            2588]
          Length = 1269

 Score = 1325 bits (3430), Expect = 0.0,   Method: Composition-based stats.
 Identities = 588/1363 (43%), Positives = 813/1363 (59%), Gaps = 114/1363 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  FGK  ++ + PDL+ +Q  S+  F  +   PD+R NEGL   FK  FPIT      
Sbjct: 10   ERVNFGKIKQVTETPDLLAIQIQSFKDFFQLETTPDKRNNEGLFKVFKENFPITDTRNIF 69

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LEF+ Y  DPP++ +++C+ R LTY+VPLK  LRL   D +       +     Q +++
Sbjct: 70   NLEFLDYFVDPPRYTIEECIERGLTYSVPLKAKLRLSCNDEEHVDFQTIV-----QDVFL 124

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  +Y+ R+IP +G WM
Sbjct: 125  GNIPYMTPRGTFVINGAERVVVSQLHRSPGVFFGQS---IHPNGTKIYSARVIPFKGAWM 181

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K PVT+ L A+G +++ +IL  F                   
Sbjct: 182  EFATDINNVMYAYIDRKKKFPVTTLLRAIGYETDKDILQLFGMADEVKADKKSLEK---- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                    +GKKL + +L+S  E  V                 +
Sbjct: 238  -----------------------YAGKKLGARVLRSWVEDFVDEDT------------GE 262

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +V+ E  EI +E   ++DE ++E I    ++ + +   +   + + I NTL  D +    
Sbjct: 263  VVSIERNEIMLERDSILDEANIETIVDMGVKSVFVQKEEVSGDFSIIYNTLNKDTSNSEL 322

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D      A  + + LFF   +YDL  VGR K+N +L L TP +++ +
Sbjct: 323  EAVQHIYRQLRGADAPDDETARGIIDKLFFSDKRYDLGDVGRYKINRKLGLPTPLNMKVL 382

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDIIAIIK LV L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 383  TKEDIIAIIKYLVQLTNSKAEIDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIRERMN 442

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINA+ + S +  FF +SQLSQ  +  N LS ITH RR+SALG GG++R
Sbjct: 443  VRDNEVFTPVDLINARTLSSVINSFFGTSQLSQFLDQTNPLSEITHKRRISALGPGGLSR 502

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH +HYGR+C  ET EG NIGL+S+L   A+VN  GFIETPYRKV +GKV 
Sbjct: 503  ERAGFEVRDVHYSHYGRLCTIETPEGPNIGLISTLCVHAKVNDMGFIETPYRKVNEGKVD 562

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
             ++V +LSA EE++  IAQAN+ LDE+G F  + V  R  G+  ++ RE+++++D +P Q
Sbjct: 563  MDNVRFLSAEEEDSVKIAQANAPLDEEGHFVNDKVKSRETGDFPILDREEVEYMDVAPNQ 622

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +V ++ASLIPFLE+DD+NR LMG NMQRQAVPL+  + P VGTG+E   A+ S   I ++
Sbjct: 623  IVGLSASLIPFLEHDDANRALMGSNMQRQAVPLINPQVPIVGTGLEGKAARDSRLQITSE 682

Query: 731  RAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              G+VE VDA  I +R        L      + IY+L KF ++NQ+TC+N RP VK G +
Sbjct: 683  GKGVVEFVDANEIHVRYERDEMQKLVSFEDDLKIYQLTKFVKTNQSTCINLRPAVKKGQQ 742

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +   D + +G +T  G+LALGRNM VAFMPW GYNFED+++ISER+  ED+FTSIHI+E+
Sbjct: 743  LVFGDFLTEGYATRGGELALGRNMKVAFMPWKGYNFEDAIVISERVGREDLFTSIHIDEY 802

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  RDTKLG EE+T DIPNVSEE  K++D+ GII VGA +  GDIL+GKITP+GES  +
Sbjct: 803  ELEVRDTKLGEEELTPDIPNVSEEATKDLDQNGIIRVGAHIKEGDILIGKITPRGESDPS 862

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA D +D SL+ P    G V+D ++F+R    K++ S + E+  +E L
Sbjct: 863  PEEKLLRAIFGDKASDAKDASLKAPPSTEGVVIDKKLFSRA--KKDKNSKTREKAALEKL 920

Query: 968  ARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +     +  L   +  +L+ +L      G     G     K +  SS  ++        
Sbjct: 921  EKVHQKNEEDLLEVLMGKLLTLLKDKTSQGITNTYGEVLISKGSKFSSKNLANIDFQNVN 980

Query: 1023 QF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                  DE     + +L   Y    +    R+K +   I  GD++P GVL++ KV++A K
Sbjct: 981  PLGWTTDEVTNDQINTLLHNYNIKYNEELGRYKREKFNISIGDELPAGVLKLAKVYLASK 1040

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R ++ GDKMAGRHGNKGIV++I+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET L
Sbjct: 1041 RKLKVGDKMAGRHGNKGIVAKIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNLGQIYETVL 1100

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA + LG +  + I D     +I+                                   
Sbjct: 1101 GWAGLKLGVRFATPIFDGATTEEIAEYIDEAGL--------------------------- 1133

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                   P F                    G + LYDG TGE F +  TVG IYMLKL+H
Sbjct: 1134 -------PSF--------------------GHTYLYDGETGERFHQKATVGVIYMLKLSH 1166

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+ +LQE+LTIKSDD
Sbjct: 1167 MVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASNILQELLTIKSDD 1226

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +VGR + YESIV G++  + G PESFNVL+ E++ LGL +  +
Sbjct: 1227 IVGRAKAYESIVKGDNIPKAGVPESFNVLIHELRGLGLDLKFD 1269


>gi|160888406|ref|ZP_02069409.1| hypothetical protein BACUNI_00819 [Bacteroides uniformis ATCC 8492]
 gi|270294759|ref|ZP_06200960.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. D20]
 gi|317477758|ref|ZP_07936951.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
 gi|156862083|gb|EDO55514.1| hypothetical protein BACUNI_00819 [Bacteroides uniformis ATCC 8492]
 gi|270274006|gb|EFA19867.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. D20]
 gi|316906103|gb|EFV27864.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
          Length = 1270

 Score = 1325 bits (3430), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1366 (42%), Positives = 817/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFNLAEDVKVNKTNLKK---- 235

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 236  -----------------------MVGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINRKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVAEGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L++DG+F  + V  R   +  +VP  +++ +D S
Sbjct: 561  DLSDEGLVYLTAEEEEAKIIAQGNAPLNDDGTFVRDKVKSRQDADYPVVPPSEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I I   R+ E +       +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGDGVVEFVDATTIRILYDRTEEEEFVSFEPALKEYNIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V    I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVTAGQILTEGYSTEDGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIGKRLFSR--VVKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L + + ++L+++       G     G     K    S+   S+   +
Sbjct: 919  PKIDDEFDAKIGDLKKVLINKLLKLTENYTSEGVKDYMGADIISKGARFSASDFSDLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AVQLSNWTKDEHTNGLIRALVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D  +  D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGASLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLYDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPAPGIPESLNVLLHELRGLGLSINLE 1270


>gi|319953899|ref|YP_004165166.1| DNA-directed RNA polymerase subunit beta [Cellulophaga algicola DSM
            14237]
 gi|319422559|gb|ADV49668.1| DNA-directed RNA polymerase subunit beta [Cellulophaga algicola DSM
            14237]
          Length = 1269

 Score = 1324 bits (3427), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1367 (42%), Positives = 816/1367 (59%), Gaps = 116/1367 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F     I + PD +++Q  S+  F  +    DER +EGL   F+  FPIT     
Sbjct: 6    TERINFASAKNIPNYPDFLDIQVKSFQDFFQLETKSDERGDEGLYNTFQENFPITDTRNQ 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LT++VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFLDYFIDPPRYSIQECIERGLTHSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G +S+ +IL  F                L 
Sbjct: 178  IEFATDINGVMYAYIDRKKKLPVTTLFRAIGFESDKDILEIFDLSEEVKVSVAGLKKVL- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +L +  E  V                 
Sbjct: 237  --------------------------GRKLAARVLNTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   +++++ +E+I  ++++ + +    +  ++   I NTL  D    
Sbjct: 259  EVVSIERNEIVLDRDTILEKEHIEQIVDADVKTVLLHKESAAQSDYGIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIGMDKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  F++VN+ GF+ETPYRKV +GK
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFSKVNSMGFLETPYRKVENGK 558

Query: 610  V-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V   +  YLSA EEE   IAQAN  +DE+G+ T E V  R  G+  +V   +I + D +P
Sbjct: 559  VDIQNFGYLSAEEEEGMKIAQANIPMDEEGNITAEKVIAREEGDFPVVDPSEIQYTDVAP 618

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK +AP VGTG+E  VA  S   I 
Sbjct: 619  NQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQAPIVGTGLERQVASDSRVLIN 678

Query: 729  AKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+++ VD++ I I+     E  L         Y L+KF+++NQ T +N +P+V+ G
Sbjct: 679  AEGDGVIQYVDSLMITIKYDRTEEERLVSFEDDSKTYELVKFRKTNQGTSINLKPIVRKG 738

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D+VR+  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISE++V ED+FTSIH++
Sbjct: 739  DKVRKGQVLCEGYATENGELALGRNLKVAFMPWKGYNFEDAIVISEKVVREDIFTSIHVD 798

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES 
Sbjct: 799  EYSLEVRDTKLGAEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGESD 858

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R    K++R  S ++E I 
Sbjct: 859  PTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSR--SVKDKRKRSEDKEAIS 916

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQ 1020
             L  + + +   L   +  +L  ++ G+ +       G +   K    +  +++      
Sbjct: 917  NLELEYEVKFQQLKDVLIEKLFNLVNGKTSQGVLNDLGEEVLPKGKKYTMKMLNAVDDFA 976

Query: 1021 WW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     V  L   Y+   + L+   +     I  GD++P G++++ KV+V
Sbjct: 977  HLVGGLWTTDKDNNNLVTDLLHNYKIKLNDLQGNLRRDKFTISVGDELPAGIMKLAKVYV 1036

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+E
Sbjct: 1037 AKKRKLKVGDKMAGRHGNKGIVSRIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYE 1096

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA + LGKK  + I D  +   I+                              A 
Sbjct: 1097 TVLGWAGLKLGKKYATPIFDGASLDQIN------------------------------AY 1126

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+P                          G + LYDG TG+ FD+P TVG IYMLK
Sbjct: 1127 TDEAGIP------------------------RFGHTYLYDGGTGQRFDQPATVGVIYMLK 1162

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+K
Sbjct: 1163 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILTVK 1222

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            SDDVVGR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 SDDVVGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|319900917|ref|YP_004160645.1| DNA-directed RNA polymerase subunit beta [Bacteroides helcogenes P
            36-108]
 gi|319415948|gb|ADV43059.1| DNA-directed RNA polymerase subunit beta [Bacteroides helcogenes P
            36-108]
          Length = 1270

 Score = 1323 bits (3424), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1366 (42%), Positives = 823/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRRNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + I  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKI-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIESEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDEGLVYLTAEEEEAKIIAQGNAPLNDDGTFIRDKVKARQDADYPVVTPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPVVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ E +       +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGDGVIDFVDATTIRILYDRTEEEEFVSFEPALKEYNIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V    I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TSIH+
Sbjct: 741  GQRVTAGQILTEGYSTEDGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSIHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIGKRLFSR--VIKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L + + ++L+++       G     G     K    S+   S+   +
Sbjct: 919  PKIDDEFDGKIAELKKILVNKLLKLTENYTSEGVKDYMGADVISKGAKFSASDFSDLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSNWTKDEHTNGLIRALVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D  +  D++                                
Sbjct: 1099 AVLGRAGKKLGVKFATPIFDGASLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLYDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSINLE 1270


>gi|228472584|ref|ZP_04057344.1| DNA-directed RNA polymerase, beta subunit [Capnocytophaga gingivalis
            ATCC 33624]
 gi|228275997|gb|EEK14753.1| DNA-directed RNA polymerase, beta subunit [Capnocytophaga gingivalis
            ATCC 33624]
          Length = 1269

 Score = 1323 bits (3423), Expect = 0.0,   Method: Composition-based stats.
 Identities = 576/1365 (42%), Positives = 811/1365 (59%), Gaps = 116/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F     + D PD +++Q  S+  F  M    D R  EGL + FK  FPIT      +
Sbjct: 8    RINFASTKHVPDYPDFLDIQVKSFQDFFQMETKSDARSGEGLYSTFKENFPITDTRNQFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ V++C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 68   LEFLDYFIDPPRYSVEECIERGLTYSVPLKARLKLFCTDPEHEDFETIV-----QDVYLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  GTF+I G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 123  TIPYMTGSGTFIINGAERVVVSQLHRSPGVFFGQS---YHANGTKLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+   A+G + + +IL  F                L   
Sbjct: 180  FTTDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKYL--- 236

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +L +  E  V                 ++
Sbjct: 237  ------------------------GRRLAARVLNTWHEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDRK 371
            V+ E  EI ++   +++++ +++I  S  + I +   D  + +   I NTL  D     K
Sbjct: 261  VSIERNEIILDRDTILEKEHIDQIVESNAKTILLHKEDERSVDYNIIHNTLQKDPTNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD P + + +
Sbjct: 321  EAVEHIYRQLRNAEPPDEETARDIIDKLFFSDQRYNLGDVGRYRMNKKLGLDIPMEKQVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 381  TKEDIITIVKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAAQFGVGLARMARTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF +SQLSQ  +  N L+ ITH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPLDLINAKTLSSVINSFFGTSQLSQFMDQTNPLAEITHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV +GK+ 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVYAKVNNMGFIETPYRKVENGKIK 560

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
             ++++Y+SA EEE   I QAN  +D+ G+  +E +  +  G+  ++ RE++D+ID +P Q
Sbjct: 561  LDELIYMSAEEEEGLKIPQANIQVDDQGNILDERLVVKEDGDFPVISREEVDYIDVAPNQ 620

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  V   S   I A+
Sbjct: 621  IASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLEKRVVTDSRVLINAE 680

Query: 731  RAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            R G V  VDA +IVI+     +  L    S +  Y L+KF+R+NQ TC+N +P+V+ GD 
Sbjct: 681  REGTVTYVDADKIVIKYDRTEDEILVSFDSELTTYDLIKFRRTNQGTCINLKPIVRKGDR 740

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISER++ ED+FTSIHI+E+
Sbjct: 741  VHKGQVLCQGYATEQGELALGRNMKVAFMPWKGYNFEDAIVISERVIREDIFTSIHIDEY 800

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSE+  K++DE GI+ +GA + PGDIL+GK+TPKGES  T
Sbjct: 801  TLDVRDTKLGVEELTNDIPNVSEDATKDLDENGIVRIGANIKPGDILIGKVTPKGESDPT 860

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+    + G V+  ++F+R    K +R+   E++++  L
Sbjct: 861  PEEKLLRAIFGDKAGDVKDASLKASPSLEGVVIGKKLFSRAVKTKQKRAK--EKDEMAAL 918

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQ-- 1020
                + +   L   +  +L  ++ G+ +       G +   K    +   + E       
Sbjct: 919  DAAFNAKAEALKDVLLEKLFSLVNGKTSQGVFNDLGEEMIPKGRKHTQRGLKEIEDYTHL 978

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE     +  L   Y+   + L+   +     +  GD++P G++++ K+++A 
Sbjct: 979  LSGGWTTDEHTNELINDLIHNYKIKLNDLQGMLRRDKFTLTVGDELPAGIMKLAKIYIAK 1038

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1039 KRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETV 1098

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LGKK  + I D  +   I+   +                              
Sbjct: 1099 LGWAGQKLGKKFATPIFDGASLEQITEYTNEAG--------------------------- 1131

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                    P F                    G + LYDG TGE FD+  TVG IYM+KL 
Sbjct: 1132 -------VPAF--------------------GHTYLYDGGTGERFDQKATVGVIYMIKLG 1164

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+KSD
Sbjct: 1165 HMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTVKSD 1224

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV+GR R YE+IV G+   E G PESFNVL+ E++ LGL I LE+
Sbjct: 1225 DVIGRARTYEAIVHGDTMPEPGLPESFNVLMHELKGLGLDIRLED 1269


>gi|255011635|ref|ZP_05283761.1| DNA-directed RNA polymerase subunit beta [Bacteroides fragilis
            3_1_12]
 gi|313149470|ref|ZP_07811663.1| RNA polymerase subunit beta [Bacteroides fragilis 3_1_12]
 gi|313138237|gb|EFR55597.1| RNA polymerase subunit beta [Bacteroides fragilis 3_1_12]
          Length = 1270

 Score = 1323 bits (3423), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1366 (42%), Positives = 822/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKV-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++EI  S +++I I   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVIEPEHIDEIIDSGVQNILIHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLMTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVDNGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N +VYL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   +++ +D +
Sbjct: 561  DLSENGLVYLTAEEEEAKIIAQGNAPLNDDGTFIRNKVKSRQDADYPVVEPSEVELMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  AAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICNK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GDRVTKGQILTEGYSTENGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIQPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMALTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSDWTNDDHANGMIRDLILNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGERFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GA+++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGASHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|170696796|ref|ZP_02887904.1| DNA-directed RNA polymerase, beta subunit [Burkholderia graminis
            C4D1M]
 gi|170138297|gb|EDT06517.1| DNA-directed RNA polymerase, beta subunit [Burkholderia graminis
            C4D1M]
          Length = 1279

 Score = 1323 bits (3423), Expect = 0.0,   Method: Composition-based stats.
 Identities = 621/1295 (47%), Positives = 858/1295 (66%), Gaps = 60/1295 (4%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K P +  +P L+  Q  S+  FL  +    +R  EGLQAAF SV
Sbjct: 1    MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADTPSTQRKPEGLQAAFTSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFVSY   PP F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61   FPIVSHNGFARLEFVSYMLSPPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGI----------------------QRIVVSQLHRS 160
            K++K               GT    G                        R   SQLHRS
Sbjct: 120  KEVK---------------GT----GSVHGRNSAHDADGFVRHQRYGACDR---SQLHRS 157

Query: 161  PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
            PG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A
Sbjct: 158  PGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKA 217

Query: 221  LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
            +G+  E+IL+ F+    ++   +          L  G      + D   G  +++  K++
Sbjct: 218  IGLTPEQILANFFVFDNFTLMPEGAQMEFVPERL-RGEVARFDITD-RDGNVIVQKDKRI 275

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
             +  ++ L     KF+ +  D L G  +A+++V+G+TGE+   A D I E  LE++  S+
Sbjct: 276  NAKHIRDLDNAKTKFISVPEDYLLGRVLAKNVVDGDTGEVIANANDEITETVLEKLRESK 335

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            I+DI  LY + ++   YI +TL  D+  D+  A + IYR+MRPG+  T    E++FN LF
Sbjct: 336  IKDIQTLYTNDLDQGPYISSTLRIDETADKMAARIAIYRMMRPGEPPTEEAVEALFNRLF 395

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            +  D YDLS VGR+K N R+  D       ++ +DI+A IKILV+LRNGKG +DDID+LG
Sbjct: 396  YSEDAYDLSKVGRMKFNRRVGRDEIIGPMTLQDDDILATIKILVELRNGKGEVDDIDHLG 455

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVR VGE+ +NQ+R GL+R+ER++KER+   + +++MP DLIN+KP+ SA+ EFF SS
Sbjct: 456  NRRVRCVGELAENQFRAGLVRVERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSS 515

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 516  QLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 575

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++ EDGS 
Sbjct: 576  GLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGSL 635

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 636  TDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQA 695

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E   VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +      GVD
Sbjct: 696  VPCLRPEKAVVGTGIERTVAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDEEAVAGDVGVD 755

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+K+ RSNQNT +NQRP+VKVGD+V R D++ADG STDLG+LALG+NMLVAFMPW+G
Sbjct: 756  IYNLIKYTRSNQNTNINQRPIVKVGDKVSRGDVLADGASTDLGELALGQNMLVAFMPWNG 815

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFEDS+LISE++V++D +TSIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE G
Sbjct: 816  YNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESG 875

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+
Sbjct: 876  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVI 935

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+  +  ++++    D +D+  I++ + + RL  +L G+ A  GPK
Sbjct: 936  DVQVFTREGIQRDKRAQQIIDDELKRYRLDLNDQLRIVEGDAFQRLARMLTGKVANGGPK 995

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T +    + +     W+   + DE+    +E++K   E  +   +  F+ K +K+
Sbjct: 996  KLAKGTKIEQAYLEDLDHYHWFDIRLADEEAAAQLEAIKDSIEQKRHQFDLAFEEKRKKL 1055

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++PPGVL++VKV++A+KR +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+
Sbjct: 1056 TQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADV 1115

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQ+ E HLGWA  GLG +I  ++   +    I+ LR FL K+     
Sbjct: 1116 VLNPLGVPSRMNVGQVLEVHLGWAAKGLGWRIGEML---QRQAKIAELREFLTKIYNESG 1172

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ------- 1233
              E++  + D+ ++ +A+  + GVP +TPVFDGA EE ++  L +A  D+  +       
Sbjct: 1173 RAEELDSFTDEEIVELAKNLREGVPFATPVFDGATEEEMSRALDLAFPDDIAKNLGMTPS 1232

Query: 1234 ---SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                 LYDG TGE F+R VTVGY++ LKL+H+V D
Sbjct: 1233 KNQVRLYDGRTGEMFERSVTVGYMHYLKLHHLVDD 1267


>gi|329962259|ref|ZP_08300265.1| DNA-directed RNA polymerase, beta subunit [Bacteroides fluxus YIT
            12057]
 gi|328530367|gb|EGF57244.1| DNA-directed RNA polymerase, beta subunit [Bacteroides fluxus YIT
            12057]
          Length = 1270

 Score = 1322 bits (3422), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1366 (42%), Positives = 822/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRRNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + I  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKI-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINRKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVANGKV 560

Query: 611  T---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSGEGLVYLTAEEEEAKIIAQGNAPLNDDGTFVRDKVKARQDADYPVVTPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPVVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I I      E +     S +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGDGVVEFVDATTIRILYDRTEEEEFVSFESALKEYSIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V    I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVTAGQILTEGYSTEDGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIGKRLFSR--VIKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L + + ++L+++       G     G     K    S+   S+   +
Sbjct: 919  PKIDDEFDAKVGELKKVLVNKLLKLTENYTSEGVKDYMGADVISKGAKFSASDFSDLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSNWTKDEHTNGLIRALVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D  +  D++                                
Sbjct: 1099 AVLGRAGKKLGVKFATPIFDGASLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLYDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPAPGIPESLNVLLHELRGLGLSINLE 1270


>gi|91215208|ref|ZP_01252180.1| DNA-directed RNA polymerase beta subunit [Psychroflexus torquis ATCC
            700755]
 gi|91186813|gb|EAS73184.1| DNA-directed RNA polymerase beta subunit [Psychroflexus torquis ATCC
            700755]
          Length = 1270

 Score = 1322 bits (3422), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1369 (42%), Positives = 814/1369 (59%), Gaps = 117/1369 (8%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  F       D PD +++Q  S+  F  +   P+ER NEGL   FK  FPIT    
Sbjct: 5    HNERISFSSVQNKPDYPDFLDIQVKSFQDFFQLETKPEERSNEGLYNTFKENFPITDTRN 64

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +
Sbjct: 65   QFVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDV 119

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G 
Sbjct: 120  YLGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGS 176

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                L
Sbjct: 177  WIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKYL 236

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                       G+KL + +L +  E  V                
Sbjct: 237  ---------------------------GRKLAARVLNTWYEDFVDEDT------------ 257

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNK 368
             ++V+ E  EI ++   V+++  +EEI  +  + I +   +++  + A I NTL  D   
Sbjct: 258  GEVVSIERNEIVLDRDTVLEKDHIEEILETGSKTILLHKEENLTGDYAIIYNTLQKDPTN 317

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L L+   D 
Sbjct: 318  SEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLNISMDS 377

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + + K DII IIK L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+E
Sbjct: 378  KVLTKLDIITIIKYLIELVNSKAEVDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRE 437

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ +T+ RRLSALG GG
Sbjct: 438  RMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAELTNKRRLSALGPGG 497

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVH THYGR+CP ET EG NIGL+SS++ + +VN+ GFIETPYRKV +G
Sbjct: 498  LSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSMSVYGKVNSMGFIETPYRKVENG 557

Query: 609  KV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            K+   +D +YLSA EEEN+ IAQAN  + EDG+ T E V  R  G+  +V  + +D+ID 
Sbjct: 558  KIDFKSDPLYLSAEEEENKLIAQANIPISEDGAITSERVIARMEGDFPVVDPKDVDYIDV 617

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQA+PLL+ +AP VGTG+E  VA+ S   
Sbjct: 618  APNQISSISASLIPFLEHDDANRALMGSNMMRQALPLLRVDAPIVGTGLERRVAQDSRVL 677

Query: 727  IVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G V+ VDA +I+I         L         Y L+KF+++NQ + +N +P+V+
Sbjct: 678  INAEGEGRVQYVDARKIIIDYDRTENERLVSFDEDHKTYNLIKFRKTNQGSTINLKPIVR 737

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD V +  ++ +G +TD G+LALGRNM VAFMPW GYNFED+++ISER+V +D+ TS+H
Sbjct: 738  VGDRVTKGQVLCEGYATDNGELALGRNMKVAFMPWKGYNFEDAIVISERVVKDDILTSVH 797

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAE+ PGDIL+GKITPKGE
Sbjct: 798  IDEYSLEVRDTKLGNEELTSDIPNVSEEATKDLDEHGMIRIGAEIKPGDILIGKITPKGE 857

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  TPEEKLLRAIFG+KA DV+D SL+    ++G V+D ++F R    K++R  + ++++
Sbjct: 858  SDPTPEEKLLRAIFGDKAGDVKDASLKASPSLNGVVIDKKLFTRA--VKDKRKRAQDKQE 915

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            I+ L  +   +   L   +  +L  I+ G+ A       G     K    +  +++    
Sbjct: 916  IDALEGNFQIKFEDLRNRLIDKLFGIVGGKTAQGVQNDLGEDTLPKGKKYTLKMLNSVED 975

Query: 1019 SQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                       D+     V  L   Y+  ++ L+   + +   I  GD++P G+L++ K+
Sbjct: 976  FSHLTKGTWTTDKGTNALVADLLHNYKIKQNDLQGNLRREKFTITVGDELPSGILKLAKI 1035

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA KR ++ GDKMAGRHGNKGIV++I+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1036 YVAKKRKLKVGDKMAGRHGNKGIVAKIVREEDMPFLDDGTPVDIVLNPLGVPSRMNIGQI 1095

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LGKK  + I D      I+ L                            
Sbjct: 1096 YETVLGWAGQKLGKKFATPIFDGATLDQINELTD-------------------------- 1129

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                ++G+P                          G + L+DG TGE FD+P TVG IYM
Sbjct: 1130 ----EAGIP------------------------RFGHTYLFDGGTGERFDQPATVGVIYM 1161

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT
Sbjct: 1162 LKLGHMIEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILT 1221

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +KSDDVVGR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1222 VKSDDVVGRAKTYEAIVKGEPMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|237717392|ref|ZP_04547873.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D1]
 gi|262406157|ref|ZP_06082707.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_22]
 gi|293372126|ref|ZP_06618517.1| DNA-directed RNA polymerase, beta subunit [Bacteroides ovatus SD CMC
            3f]
 gi|294644052|ref|ZP_06721829.1| DNA-directed RNA polymerase, beta subunit [Bacteroides ovatus SD CC
            2a]
 gi|298483057|ref|ZP_07001238.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. D22]
 gi|229443375|gb|EEO49166.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D1]
 gi|262357032|gb|EEZ06122.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_22]
 gi|292632918|gb|EFF51505.1| DNA-directed RNA polymerase, beta subunit [Bacteroides ovatus SD CMC
            3f]
 gi|292640576|gb|EFF58817.1| DNA-directed RNA polymerase, beta subunit [Bacteroides ovatus SD CC
            2a]
 gi|295085435|emb|CBK66958.1| DNA-directed RNA polymerase subunit beta [Bacteroides xylanisolvens
            XB1A]
 gi|298270801|gb|EFI12381.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. D22]
          Length = 1270

 Score = 1322 bits (3420), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1366 (42%), Positives = 823/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------DLAEDVKVNKTNLKKV-LGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E+ ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEEHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N ++YL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D +
Sbjct: 561  DLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVLNRVKSRQDADFPVVEPSEVDLMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+ +   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKTLGVKFATPIFDGATMEDLDQWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGEQFDQAATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|149372365|ref|ZP_01891553.1| DNA-directed RNA polymerase subunit beta [unidentified eubacterium
            SCB49]
 gi|149354755|gb|EDM43318.1| DNA-directed RNA polymerase subunit beta [unidentified eubacterium
            SCB49]
          Length = 1270

 Score = 1321 bits (3419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 590/1368 (43%), Positives = 803/1368 (58%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F       D PD +++Q  S+  F  +    DER  EGL   F   FPIT     
Sbjct: 6    TERLNFSSVQNKPDYPDFLDIQIKSFQDFFQLETKSDERGQEGLYKTFLENFPITDTRNQ 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFLDYFVDPPRYAIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G + + +IL  F                L 
Sbjct: 178  IEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKASKTGLKKYL- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +LK+  E  V                 
Sbjct: 237  --------------------------GRKLAARVLKTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   V+++  +EEI  S  + I +   D  +++ A I NTL  D    
Sbjct: 259  EVVSIERNEIILDRDTVLEKDHIEEIIDSGSKTILLHKEDNHMSDYAIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + N LFF   +Y+L  VGR +MN +L LD   D +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIINKLFFSDQRYNLGEVGRYRMNKKLQLDIAMDKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L +Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSSQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VN  GFIETPYRKV D  
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNNLGFIETPYRKVTDAT 558

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            +   N+ +YLSA EEE + IAQAN  L E G      V  R  G+  ++   ++++ D +
Sbjct: 559  IDFKNEPIYLSAEEEEGQLIAQANIPLTESGKIDSAKVIARMEGDFPVIDPTEVNYADVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL A++P VGTG+E  VA  S   I
Sbjct: 619  PNQISSISASLIPFLEHDDANRALMGSNMMRQAVPLLIADSPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VD+  I I+     E  +    S    Y+L+KF+++NQ T +N +P+V  
Sbjct: 679  NAEGDGVVQYVDSREITIKYDRTEEARMVSFESDEKTYKLVKFRKTNQGTSINLKPIVNK 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V++  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISER+V ED+FTSIHI
Sbjct: 739  GDRVKKGQVLCQGYATEKGELALGRNMKVAFMPWKGYNFEDAIVISERVVREDIFTSIHI 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DEYSLEVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V++ ++F R   DK +R+   E  +I
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVINKKLFARALKDKRKRAKDKEDIEI 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L    D +   L   +  +L  I+ G+ A       G   F K    +  +++     
Sbjct: 919  --LEAKFDAKFEALQDTLIEKLFTIVSGKTAQGVSNDLGEVVFPKGKKFTLKMLNSVDDY 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      D+     V  L   Y+  ++ L+   +     I  GD++P G+L++ K++
Sbjct: 977  THLTGGTWTTDDATNLLVADLMHNYKIKENDLQGNLRRDKFTISVGDELPSGILKLAKIY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 VAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LG+K  + I D      I+ L                             
Sbjct: 1097 ETVLGWAGQKLGRKYATPIFDGATIDQINELTD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++G+P                          G + LYDG TG+ FD+P TVG IYML
Sbjct: 1130 ---EAGIP------------------------RYGHTYLYDGGTGQRFDQPATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVIGRAKTYESIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|124005812|ref|ZP_01690650.1| DNA-directed RNA polymerase, beta subunit [Microscilla marina ATCC
            23134]
 gi|123988495|gb|EAY28136.1| DNA-directed RNA polymerase, beta subunit [Microscilla marina ATCC
            23134]
          Length = 1289

 Score = 1321 bits (3419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 590/1381 (42%), Positives = 817/1381 (59%), Gaps = 130/1381 (9%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F    +++  PD ++VQ  S+  F  +    + R  EGL   F   FPI+      
Sbjct: 8    ERHSFATVEKVVKYPDFLDVQIQSFQDFFQLETPAEFRQQEGLYKVFSENFPISDSRENF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPPK+ VD+C+ R LTY+VPLK  LRL   D D         +  EQ +++
Sbjct: 68   LLEFIDYSIDPPKYSVDECIDRGLTYSVPLKAKLRLSCSDEDNEDF-----ETIEQEVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++P MT  G+F+I G +R++VSQLHRSPG+ F   K     +G  LY+ RIIP +G W+
Sbjct: 123  GNIPYMTTKGSFIINGAERVIVSQLHRSPGVFFAQSK---HTNGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K PVT+ L  +G  S+ +IL  F                   
Sbjct: 180  EFTTDVNNVMYAYIDRKKKFPVTTLLRVIGFGSDKQILDLFNLSEEIEAEDKVLRDKAI- 238

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 239  -------------------------GRKLAARILKTWTEDFVDEDT------------GE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  EI +E   +++ + ++ I  S ++ I +   D +V + + I NTL  D +   
Sbjct: 262  VVSIERNEILLERDSILEAEDIDTIVDSGVKSIIVHRDDVNVTDYSIIYNTLQKDNSNSE 321

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+AL  IYR +R  +      A  +   LFF   +YDL  VGR ++N +L L    D R 
Sbjct: 322  KEALEQIYRQLRNTEAPDEQTAREIIQSLFFSDKRYDLGEVGRYRINKKLELAIDSDTRV 381

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + +EDI++I+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+IKER+
Sbjct: 382  LTREDIVSIVKRLIKLINAKAVVDDIDHLSNRRVRTVGEQLYTQFGVGLARMARTIKERM 441

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 442  NVRDNEDFKPVDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRMSALGPGGLS 501

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A+VN+ GFIETPYRKV +GKV
Sbjct: 502  RERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKVNSMGFIETPYRKVAEGKV 561

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            TND+ YL+A EE+  +IAQAN  + E G F  + V  R  G+  +V    + ++D +P Q
Sbjct: 562  TNDISYLTAEEEDTHHIAQANVPISESGEFLRDKVKARLEGDFPVVDPAVLSYMDVAPNQ 621

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +VS+AASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG+E  VA  S A +VA+
Sbjct: 622  IVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPQAPIVGTGLEEQVAVDSRALVVAE 681

Query: 731  RAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              G+++ VDA +I++R     E  L      +  Y L+KF+R+NQ+TCVN  P+V  G +
Sbjct: 682  YDGVIDYVDAKKIIVRYDFNEEQQLTSFQDDIVSYNLIKFRRTNQDTCVNLSPIVYKGQK 741

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++   + +G +T+ G+LALG NM VAFMPW GYNFED+++ISER+V +DVFTSIHIEE 
Sbjct: 742  VKKGQALCEGYATNDGELALGANMKVAFMPWQGYNFEDAIVISERVVRDDVFTSIHIEEK 801

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  RDTK G EE+T +IPNVSE+ +K +DE GI+ VG ++  GDIL+GKITPKGES  T
Sbjct: 802  ELEVRDTKRGQEELTAEIPNVSEDAIKYLDENGIVMVGTKIREGDILIGKITPKGESDPT 861

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQIE 965
            PEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F+R   DK+ R+ + E  +  I 
Sbjct: 862  PEEKLLRAIFGDKAGDVKDASLKAPPSLRGVVIDTKLFSRPKKDKDLRAKAKEEVKSLIT 921

Query: 966  LLARDKDDEQVILDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLISE--------- 1015
               +D    Q I+   + + L  +   G     G     K    +   I E         
Sbjct: 922  QYRKDLQAIQEIVVEKLVTLLEGKTSKGIKHKFGNIVMSKGVKFNQTNIHENLFPKENVY 981

Query: 1016 -------------YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                         +        A +DEK  R +  L   Y   ++ +  +FK +   ++ 
Sbjct: 982  RDESTYNVPEEANFVADLILDNATEDEKTNRLLVGLVKNYNKKRNEISGKFKRERFALEV 1041

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++P G++++ KV++A KR ++ GDKMAGRHGNKG+V++I+  EDMPFL+DGTPVDIVL
Sbjct: 1042 GDELPAGIVKLAKVYIAKKRKLKVGDKMAGRHGNKGVVAKIVRAEDMPFLEDGTPVDIVL 1101

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI+ET LGWA + LGKK  + I D      ++                
Sbjct: 1102 NPLGVPSRMNLGQIYETVLGWAGLKLGKKYATPIFDGATEDQVTTELD------------ 1149

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                              K+G+P                        E G++ LYDGLTG
Sbjct: 1150 ------------------KAGLP------------------------EFGRTYLYDGLTG 1167

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD+P TVG IYMLKL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW +
Sbjct: 1168 ERFDQPTTVGIIYMLKLGHLVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAL 1227

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +A+GAA VLQE+LT+KSDDV+GR + YESIV G +      PESFNVLV E++ L L I 
Sbjct: 1228 EAFGAANVLQEILTVKSDDVIGRAKAYESIVKGENIPNPNIPESFNVLVHELRGLALEIT 1287

Query: 1363 L 1363
            L
Sbjct: 1288 L 1288


>gi|120436715|ref|YP_862401.1| DNA-directed RNA polymerase subunit beta [Gramella forsetii KT0803]
 gi|158512449|sp|A0M3Y9|RPOB_GRAFK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|117578865|emb|CAL67334.1| DNA-directed RNA polymerase subunit beta [Gramella forsetii KT0803]
          Length = 1270

 Score = 1321 bits (3419), Expect = 0.0,   Method: Composition-based stats.
 Identities = 579/1370 (42%), Positives = 802/1370 (58%), Gaps = 117/1370 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F         PD +++Q  S+  F  +    +ER NEGL   F   FPIT   
Sbjct: 4    KQTERLSFSSVKNKPAYPDFLDLQIKSFQDFFQLETKSEERGNEGLYNTFLENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKY 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L                           G+KL + +L +  E  V               
Sbjct: 236  L---------------------------GRKLAARVLNTWYEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKN 367
              ++V+ E  EI ++    +++  +EEI  +  + I +   D+   + A I NTL  D  
Sbjct: 258  -GEVVSIERNEIVLDRDTELEKDHIEEILETGSKTILLHKEDNQTGDYAIIHNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYSLGEVGRYRMNKKLGLDVEMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + K DII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  KQVLTKLDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VN  GFIETPYR V D
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNGMGFIETPYRSVTD 556

Query: 608  --GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                 + + +YLSA EEE + IAQAN  L +DG+   + V  R  G+  +V  ++I + D
Sbjct: 557  GKINTSEEPIYLSAEEEEGKKIAQANIPLKDDGTIDTDRVIARMEGDFPVVDPKEIHYTD 616

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ ++P VGTG+E  VA  S  
Sbjct: 617  VAPNQISSISASLIPFLEHDDANRALMGSNMMRQAVPLLRTDSPIVGTGLERQVATDSRV 676

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A+  G VE VDA +IVI+     E  +         Y L+KF+++NQ +C+N +P++
Sbjct: 677  LINAEGEGEVEYVDANKIVIKYDRTEEERMVSFDDDSKSYNLIKFRKTNQGSCINLKPII 736

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V +  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V +D+FTSI
Sbjct: 737  SVGDRVTKGQVLCQGYATEAGELALGRNMKVAFMPWKGYNFEDAIVISEKVVRDDIFTSI 796

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I VGAEV PGDIL+GKITPKG
Sbjct: 797  HIDEYSLEVRDTKLGNEELTNDIPNVSEEATKDLDEHGMIRVGAEVKPGDILIGKITPKG 856

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  TPEEKLLRAIFG+KA DV+D SL+    +SG V++ ++F R    K++R  + ++E
Sbjct: 857  ESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLSGVVINKKLFARA--IKDKRKRAQDKE 914

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYP 1017
             +  L +  D +   L  ++  +L  I+ G+ A       G +   K    +  +++   
Sbjct: 915  DVAALEKKYDAKFANLKADLVEKLFTIIGGKTAQGVQNDLGEEVMPKGKKYTLKMLNAVD 974

Query: 1018 RS--QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        D+ +   V  L   Y+  ++ L+   + +   +  GD++P G+L++ K
Sbjct: 975  DYTHLTTGTWTTDDHLNELVADLLHNYKIKENDLQGNLRREKFTVSVGDELPSGILKLAK 1034

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1035 VYIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQ 1094

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET LGWA    GKK  + I D     +I+ L                           
Sbjct: 1095 IYETVLGWAGQKNGKKYATPIFDGATIEEINDLTD------------------------- 1129

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 K+G+P                          G + LYDG TG  FD+  TVG IY
Sbjct: 1130 -----KAGIP------------------------RYGHTYLYDGGTGMRFDQRATVGVIY 1160

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+L
Sbjct: 1161 MLKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREIL 1220

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            T+KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1221 TVKSDDVIGRAKTYEAIVKGEPMPEPGLPESFNVLMHELKGLGLDIKLEE 1270


>gi|146299703|ref|YP_001194294.1| DNA-directed RNA polymerase subunit beta [Flavobacterium johnsoniae
            UW101]
 gi|182676564|sp|A5FIJ3|RPOB_FLAJ1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146154121|gb|ABQ04975.1| DNA-directed RNA polymerase, beta subunit [Flavobacterium johnsoniae
            UW101]
          Length = 1270

 Score = 1321 bits (3418), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1368 (42%), Positives = 804/1368 (58%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F     I D PD ++VQ  S+  F  +    DER NEGL   F   FPIT     
Sbjct: 6    TERLNFASTKNIPDYPDFLDVQVKSFKDFFQLETKSDERGNEGLYNTFMENFPITDTRNN 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFLDYFVDPPRYTIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G + +VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFVINGAECVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G + + +IL  F                + 
Sbjct: 178  IEFSTDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEIKVSKTGIKKYI- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G++L + +L +  E  V                 
Sbjct: 237  --------------------------GRRLAARVLNTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   +ID+ ++EEI  S ++ I +   D+   + A I NTL  D    
Sbjct: 259  EVVSIERNEIILDRDTIIDKDNVEEIIDSNVKSILLHKEDNNQADYAIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L+LD P D +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLDLDIPMDKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV DG 
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVYAKVNGMGFIETPYRKVTDGV 558

Query: 610  VTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V  +   +YLSA EEE + IAQAN  +D  G  T   V  R  G+  +V    + + D +
Sbjct: 559  VDLESAPIYLSAEEEEGKMIAQANIEMDASGKITASNVIAREEGDFPVVEPSSVHYTDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPL++ EAP VGTG+E  VA  S   I
Sbjct: 619  PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLIRPEAPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G VE VDA  I I+     +  +    +    Y L+KF+++NQ T +N +P+V+ 
Sbjct: 679  NAEGHGTVEYVDANIITIKYDRTEDERMVSFDADEKTYNLIKFRKTNQGTSINLKPIVRR 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V    ++++G +T  G+LALGRN+ VAFMPW GYNFED+++ISE++V +D+FTSIH+
Sbjct: 739  GDRVVPGQVLSEGYATQNGELALGRNLKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHV 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +++ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DDYSLEVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R    K++R  + +++ +
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVLDKKLFARA--VKDKRKRTQDKDAL 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + + + V L   +  +L  I+ G+ +       G +   K    +  ++      
Sbjct: 917  GALEMEFETKFVELKDRLVEKLFLIVNGKTSQGVMNDLGEEVLPKGKKYTQKMLYAVEDF 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                    V D+   + V  L   Y+   + L+   + +   I  GD++P G+L++ K++
Sbjct: 977  AHLSKGQWVADDATNKMVNDLIHNYKIKLNDLQGALRREKFTITVGDELPSGILKLAKIY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVARIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA + LG+K  + I D  +  +I+ L                             
Sbjct: 1097 ETVLGWAGMNLGRKFATPIFDGASLDEINALTDEAN------------------------ 1132

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                       P F                    G + LYDG TGE F +  TVG IYML
Sbjct: 1133 ----------VPRF--------------------GHTYLYDGGTGERFAQKATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL + LE 
Sbjct: 1223 KSDDVIGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDLRLEE 1270


>gi|126663352|ref|ZP_01734350.1| DNA-directed RNA polymerase subunit beta [Flavobacteria bacterium
            BAL38]
 gi|126625010|gb|EAZ95700.1| DNA-directed RNA polymerase subunit beta [Flavobacteria bacterium
            BAL38]
          Length = 1270

 Score = 1321 bits (3418), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1368 (42%), Positives = 806/1368 (58%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F     I   PD +++Q  S+  F  +    DER NEGL   F   FPIT     
Sbjct: 6    TERLNFASTKNIPQYPDFLDIQVKSFKDFFQLETKSDERGNEGLYNTFMENFPITDTRNQ 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ +++C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFLDYFIDPPRYTIEECIDRGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W
Sbjct: 121  LGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARIIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D  ++++  IDR++K+PVT+   A+G + + +IL  F                  
Sbjct: 178  IEFATDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEIKVSKTGIKK--- 234

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                     +G++L + +L +  E  V                 
Sbjct: 235  ------------------------YAGRRLAARVLNTWHEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++   ++D+ ++EEI  ++++ I +   D+   +   I NTL  D    
Sbjct: 259  EVVSIERNEIILDRDTILDKDNIEEIIEADVKTILLHKEDNNAADYTIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +LNLD P + +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLNLDIPMEKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSAQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV +G 
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVYAKVNGMGFIETPYRKVTEGV 558

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V   +  VYLSA EEE + IAQAN  +D +G  T + V  R  G+  +V   +I + D +
Sbjct: 559  VDLQSTPVYLSAEEEEGKMIAQANIEMDANGKITADKVIAREEGDFPVVDPTEIHYTDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  S   I
Sbjct: 619  PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G VE VDA  I I+     E  +    S    Y+L+K++++NQ+TC+N +P+V+ 
Sbjct: 679  NAEGNGTVEYVDANMITIKYDRTEEERMVSFDSDDKTYQLIKYRKTNQSTCINLKPIVRK 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V +  ++ +G +T  G+LA+GRN+ VAFMPW GYNFED+++ISE++V +D+FTS+HI
Sbjct: 739  GDRVAKGQVLCEGYATQNGELAIGRNLKVAFMPWKGYNFEDAIVISEKVVRDDIFTSLHI 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +++ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DDYTLEVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F +   DK +RS   E   +
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVLDKKLFAKAVKDKRKRSKDKED--V 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
            + L  + + +   L   +  +L  I+ G+ +       G +   K    +  ++      
Sbjct: 917  DKLETEFEVKYTDLKDKLIEKLFVIIDGKTSQGVMNDLGEEVLPKGKKFTKKMLQGVEDF 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      DE     V  L   Y+   + L+   + +   I  GD++P G+L++ KV+
Sbjct: 977  AHLTKGQWTTDEHTNAMVNDLIHNYKIKLNDLQGWLRREKFTITVGDELPSGILKLAKVY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV++I+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVAKIVRHEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   L KK  + I D      I+                               
Sbjct: 1097 ETVLGWAGQKLNKKFATPIFDGATLDQINEFTD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++G+P                          G + LYDG TGE F +  TVG IYML
Sbjct: 1130 ---EAGIP------------------------RFGHTYLYDGGTGERFHQRATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVIGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|160883073|ref|ZP_02064076.1| hypothetical protein BACOVA_01036 [Bacteroides ovatus ATCC 8483]
 gi|156111545|gb|EDO13290.1| hypothetical protein BACOVA_01036 [Bacteroides ovatus ATCC 8483]
          Length = 1270

 Score = 1320 bits (3416), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1366 (42%), Positives = 817/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFNLAEDVKVNKTNLKKVL-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E  ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEVHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N ++YL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D S
Sbjct: 561  DLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVRNKVKSRQDADFPVVEPTEVDLMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDR 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+ +   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKTLGVKFATPIFDGATMEDLDQWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGEQFDQAATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|53715477|ref|YP_101469.1| DNA-directed RNA polymerase subunit beta [Bacteroides fragilis YCH46]
 gi|60683450|ref|YP_213594.1| DNA-directed RNA polymerase subunit beta [Bacteroides fragilis NCTC
            9343]
 gi|253566658|ref|ZP_04844111.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 3_2_5]
 gi|265767536|ref|ZP_06095202.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_16]
 gi|81313502|sp|Q5L897|RPOB_BACFN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|81381122|sp|Q64NJ7|RPOB_BACFR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|52218342|dbj|BAD50935.1| DNA-directed RNA polymerase beta chain [Bacteroides fragilis YCH46]
 gi|60494884|emb|CAH09691.1| putative DNA-directed RNA polymerase beta chain [Bacteroides fragilis
            NCTC 9343]
 gi|251944830|gb|EES85305.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 3_2_5]
 gi|263252841|gb|EEZ24353.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_16]
          Length = 1270

 Score = 1320 bits (3416), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1366 (42%), Positives = 821/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKV-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++EI  S +++I I   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVIEPEHIDEIIDSGVQNILIHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVDNGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N +VYL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   +++ +D +
Sbjct: 561  DLSENGLVYLTAEEEEAKIIAQGNAPLNDDGTFIRNKVKSRQDADYPVVEPSEVELMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP    
Sbjct: 681  AAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPTCNK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GDRVTKGQILTEGYSTENGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIQPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMVLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSDWTNDDHANGMIRDLILNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGERFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GA+++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGASHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|325299612|ref|YP_004259529.1| DNA-directed RNA polymerase subunit beta [Bacteroides salanitronis
            DSM 18170]
 gi|324319165|gb|ADY37056.1| DNA-directed RNA polymerase subunit beta [Bacteroides salanitronis
            DSM 18170]
          Length = 1270

 Score = 1320 bits (3416), Expect = 0.0,   Method: Composition-based stats.
 Identities = 576/1366 (42%), Positives = 806/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD +EVQ  S+  FL +N  P++R N+GL   F   FPI       
Sbjct: 8    QRINFASIKNPMKYPDFLEVQLKSFQDFLQLNTPPEKRKNDGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP + +D+CL R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPHYTIDECLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---IHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIFNLAEDVKVNKANLKKII-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   + + ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHIDLILESGVQNILVHNEEANASDYSIIFNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNLDTP DV+ 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINKKLNLDTPMDVKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K+DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKQDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV D  V
Sbjct: 501  RDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFIVTPYRKVKDATV 560

Query: 611  T---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YLSA EEE++ IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSPEGIEYLSAEEEEDKIIAQGNAPLNDDGTFIRDRVKARRDADYPVVTPDQVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTEAPIVGTGIEKQLCEDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G++E VDA  I +      E +       +  YR+ KF+++NQ+  ++ RP+   
Sbjct: 681  AAEGDGVIEFVDATTIRVLYDRTQEEEFVSFEPALKEYRIPKFRKTNQSMTIDLRPICNK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ERMV ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTANGELALGKNLLVAYMPWKGYNYEDAIVLNERMVREDILTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R  + K     + +++ +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLYSR--VIKTRSEKNADKQIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   +  +L      ++  G     G +   K        +     +
Sbjct: 919  PKLNEEFEEKAAALKEILVEKLLVLTEDKVSQGVKDYLGTEVIAKGAKFIKHDLESLDYT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      +  L + Y      L+   K K   +  GD++P G++++ KV++
Sbjct: 979  VIQLSKWTSDAHKNEMIRDLVMNYLKKYKELDAELKRKKFALTIGDELPSGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKELGVKFATPIFDGATLDDLDKWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ LYDG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLYDGGTGEQFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ L LSI LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLCLSITLE 1270


>gi|237718750|ref|ZP_04549231.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 2_2_4]
 gi|260175409|ref|ZP_05761821.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D2]
 gi|299144630|ref|ZP_07037698.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_23]
 gi|315923639|ref|ZP_07919879.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D2]
 gi|229451882|gb|EEO57673.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 2_2_4]
 gi|298515121|gb|EFI39002.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_23]
 gi|313697514|gb|EFS34349.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D2]
          Length = 1270

 Score = 1320 bits (3415), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1366 (42%), Positives = 817/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFNLAEDVKVNKTNLKKVL-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E  ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEVHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N ++YL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D S
Sbjct: 561  DLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVRNKVKSRQDADFPVVEPTEVDLMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDR 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+ +   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLSDGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKTLGVKFATPIFDGATMEDLDQWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGEQFDQAATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|301164934|emb|CBW24495.1| putative DNA-directed RNA polymerase beta chain [Bacteroides fragilis
            638R]
          Length = 1270

 Score = 1320 bits (3415), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1366 (42%), Positives = 820/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKV-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++EI  S +++I I   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVIEPEHIDEIIDSGVQNILIHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+ ALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMFALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVDNGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N +VYL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   +++ +D +
Sbjct: 561  DLSENGLVYLTAEEEEAKIIAQGNAPLNDDGTFIRNKVKSRQDADYPVVEPSEVELMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP    
Sbjct: 681  AAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPTCNK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GDRVTKGQILTEGYSTENGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIQPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMALTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSDWTNDDHANGMIRDLILNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGERFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GA+++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGASHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|150008874|ref|YP_001303617.1| DNA-directed RNA polymerase subunit beta [Parabacteroides distasonis
            ATCC 8503]
 gi|255014702|ref|ZP_05286828.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 2_1_7]
 gi|256841132|ref|ZP_05546639.1| DNA-directed RNA polymerase, beta subunit [Parabacteroides sp. D13]
 gi|262383747|ref|ZP_06076883.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_33B]
 gi|298375897|ref|ZP_06985853.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_19]
 gi|301311919|ref|ZP_07217841.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 20_3]
 gi|158513751|sp|A6LE81|RPOB_PARD8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|149937298|gb|ABR43995.1| DNA-directed RNA polymerase, beta chain [Parabacteroides distasonis
            ATCC 8503]
 gi|256736975|gb|EEU50302.1| DNA-directed RNA polymerase, beta subunit [Parabacteroides sp. D13]
 gi|262294645|gb|EEY82577.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 2_1_33B]
 gi|298266934|gb|EFI08591.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_19]
 gi|300830021|gb|EFK60669.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 20_3]
          Length = 1270

 Score = 1319 bits (3414), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1366 (42%), Positives = 803/1366 (58%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F         PD +EVQ  S+  FL ++  P++R  EGL   F   FPI       
Sbjct: 8    QRVNFASIKNQFPYPDFLEVQLKSFQDFLQLDTPPEKRKKEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPRYCIDECIARGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDRGTFVINGAERVVVSQLHRSPGVFFGQS---THANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFESDRDILEIFNLAEEVKVTKANLKKFI-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWVEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  ++ I+   V+D  ++E I  S  ++I +   D  +++ A I NTL  D +   
Sbjct: 261  VVSIERNDVIIDRESVLDSDNIEAILDSGTQNILLHREDQNLSDYAIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  + +  + A  +   LFF   +YDL  VGR ++N +L L T  DV+ 
Sbjct: 321  KEAVLYIYRQLRNAEPADEASAREVITNLFFSEKRYDLGEVGRYRINKKLGLTTSADVKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+++ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKAIVDDIDHLSNRRVRTVGEQLYNQFGIGLARMSRTVRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S V  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DGKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFISTPYRKVADGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + Y +A EEE   IAQ N+ LD++G F  + V  R   +  +VP  +ID +D +
Sbjct: 561  DFSEEGLQYYTAEEEEELTIAQGNAPLDDNGKFIRDKVKARFEADFPVVPPSEIDLMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ +AP VGTG+E+ VA+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTDAPIVGTGIEAQVARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +A+R G V  VDA  I I+     + +       V  Y + K++++NQ+T V+ +P    
Sbjct: 681  MAEREGEVVFVDATCIKIKYDRTEDEEFVSFEDAVKTYNIPKWRKTNQSTTVDLKPTCHR 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V+  DI+ +G ST  G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED FTS+H+
Sbjct: 741  GQRVKAGDILTEGYSTQKGELALGRNVKVAYMPWKGYNYEDAIVLNERMVREDFFTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDERGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V++  +F++    K  +S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIETALFSKA--VKKRKSRLTDKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   +  +L      ++  G       +   K    +   + E   +
Sbjct: 919  PKLDEEYEEKMASLKTLLVDKLLVLTNGKVSQGVKDYMNTEIIAKGAKFTRKSLEELDYN 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D +    ++ + + Y      L+   + K   +  GD++P G++++ KV++
Sbjct: 979  SIQVSKWTADAQKNELIKQVILNYLKKYKELDAELRRKKFDLTIGDELPTGIVQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL+DGTPVDI LNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLEDGTPVDICLNPLGVPSRMNLGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LGWA   L  K  + I D     D++                                
Sbjct: 1099 AVLGWAGRELDVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G+S LYDG TGE FD+P TVG  Y LK
Sbjct: 1131 --KAGIP------------------------RYGKSYLYDGGTGERFDQPATVGVTYFLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G+   + G PES NVL+ E++ LGLS  L+
Sbjct: 1225 SDDVVGRSKAYEAIVKGDPMPQPGIPESLNVLLHELRGLGLSFTLD 1270


>gi|198277436|ref|ZP_03209967.1| hypothetical protein BACPLE_03655 [Bacteroides plebeius DSM 17135]
 gi|198269934|gb|EDY94204.1| hypothetical protein BACPLE_03655 [Bacteroides plebeius DSM 17135]
          Length = 1270

 Score = 1319 bits (3414), Expect = 0.0,   Method: Composition-based stats.
 Identities = 579/1371 (42%), Positives = 810/1371 (59%), Gaps = 117/1371 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            +     R  F      +  PD +EVQ  S+  FL ++  P++R N+GL   F   FPI  
Sbjct: 3    SETQNQRINFASIKNPMQYPDFLEVQLKSFQDFLQLDTPPEKRKNDGLYKVFAENFPIAD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPP + +DDCL R LTY+VPLK  L+L   D D       I     
Sbjct: 63   TRNNFVLEFLDYYIDPPHYTIDDCLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVYLGPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---IHANGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIFNLAEDVKVNKTNLK 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              +                           G+KL + +LK+  E  V             
Sbjct: 235  KII---------------------------GRKLAARVLKTWTEDFVDEDT--------- 258

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTD 365
                ++V+ E  E+ I+   VI+ + ++ I  S +++I +   + + ++ + I NTL  D
Sbjct: 259  ---GEVVSIERNEVVIDRETVIEPEHIDLIIESGVQNILVHNEEANASDYSIIFNTLQKD 315

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             +   K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNLDTP
Sbjct: 316  PSNSEKEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLDTP 375

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             DVR + K+DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+
Sbjct: 376  MDVRVLTKQDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRT 435

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG
Sbjct: 436  IRERMNVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALG 495

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV
Sbjct: 496  PGGLSRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINELGFIVTPYRKV 555

Query: 606  CDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
             DG V      + YLSA EEE++ IAQ N+ L++DG+F  E V  R   +  +V  ++++
Sbjct: 556  KDGVVDLSNEGIEYLSAEEEEDKIIAQGNAPLNDDGTFIREKVKARRDADYPVVTPDQVE 615

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D +P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  + + 
Sbjct: 616  LMDVAPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKTEAPIVGTGIEKQLCED 675

Query: 723  SGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            S   I A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQ+  ++ R
Sbjct: 676  SRTQIAAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQSMTIDLR 735

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+   G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ 
Sbjct: 736  PICNKGQRVKKGDILTEGYSTANGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDIL 795

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+H++E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDIL+GKIT
Sbjct: 796  TSVHVDEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDILIGKIT 855

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R  + K     + 
Sbjct: 856  PKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLYSR--VIKTRSEKNA 913

Query: 960  EREQIELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            ++  +  L  + +++   L   +  +L      ++  G     G +   K    +   + 
Sbjct: 914  DKAILPKLNEEFEEKAAALKAILIDKLLVLTADKVSQGVKDYLGTEVIAKGAKFTKYDLE 973

Query: 1015 EYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                +         D      +  L V Y      L+   K K   +  GD++P G++++
Sbjct: 974  SLDYTVIQLSKWTADAHKNDMIRDLIVNYLKKYKELDAELKRKKFALTIGDELPSGIIQM 1033

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+
Sbjct: 1034 AKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNI 1093

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQIFE  LG A   LG K  + I D     D+                            
Sbjct: 1094 GQIFEAVLGRAGKELGVKFATPIFDGATLDDLDEWTD----------------------- 1130

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   K+G+P                           ++ LYDG TG+ FD+P TVG 
Sbjct: 1131 -------KAGLP------------------------RYCKTYLYDGGTGDQFDQPATVGV 1159

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GAA+VLQE
Sbjct: 1160 TYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGAAHVLQE 1219

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +LTIKSDDVVGR++ YE+IV G      G PES NVL+ E++ L LSI LE
Sbjct: 1220 ILTIKSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLCLSITLE 1270


>gi|312892225|ref|ZP_07751722.1| DNA-directed RNA polymerase subunit beta [Mucilaginibacter paludis
            DSM 18603]
 gi|311295355|gb|EFQ72527.1| DNA-directed RNA polymerase subunit beta [Mucilaginibacter paludis
            DSM 18603]
          Length = 1267

 Score = 1319 bits (3414), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1366 (42%), Positives = 822/1366 (60%), Gaps = 119/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F  + ++++ PD ++VQ  S+  F  +    D R  EGL   F   FPI+      
Sbjct: 7    QRVNFATSRKVLEYPDFLDVQLQSFQEFFQLQTTSDNRHKEGLFKVFAENFPISDSRNIF 66

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++D+ +C+ R LT++VPLK  LRL   D +       +     Q +Y+
Sbjct: 67   VLEFLDYFIDPPRYDIQECIERGLTHSVPLKAKLRLSCNDEEHEDFETIV-----QDVYL 121

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G W+
Sbjct: 122  GTIPYMTPKGTFVINGAERVIVSQLHRSPGVFFGQSR---HTNGTKLYSARVIPFKGSWI 178

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K PVT+ L A+G DS+ +IL  F                +  
Sbjct: 179  EFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDSDKDILELFELADEVKVSKSGLKKFI-- 236

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK   E  V                 +
Sbjct: 237  -------------------------GRKLAARVLKKWVEDFVDEDT------------GE 259

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ +  EI +E   V+++  ++ I  + ++ I +   D+  +  Y  I NTL  D +  
Sbjct: 260  VVSIDRNEIILERETVLEDDHIDMIIDAGVKTIILNKEDAATSGDYTIIYNTLQKDTSNS 319

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +YDL  VGR ++N +L L+TP++V+
Sbjct: 320  EKEAVEHIYRQLRNAEPPDEETARGIIDRLFFSDKRYDLGDVGRYRINRKLKLNTPNEVK 379

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + K+DIIAI+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 380  VLTKDDIIAIVKYLIKLINSKAEVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIRER 439

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 440  MNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 499

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GFIETPY++V DGK
Sbjct: 500  SRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCIHAKINNLGFIETPYKRVSDGK 559

Query: 610  VTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V  D  VVYLSA +E+ + I QAN+  D++G+F+   V  R  G+  ++   ++D++D +
Sbjct: 560  VMMDEPVVYLSAEDEDGKTIGQANAIYDDNGNFSTPRVKARFEGDFPIIEPARLDYMDIA 619

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VAK S   I
Sbjct: 620  PNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVAKDSRTLI 679

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I I+     E  L         YRL+KF+++NQ+T +N +P+VK 
Sbjct: 680  NAEGDGVVEYVDANEIRIKYDRNEEDRLVSFEGDSKSYRLIKFKKTNQSTTINLKPIVKK 739

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  ++ +G +T  G+LALGRN+ VAFMPW G+NFED+++ISER+VS+D+FTS+H+
Sbjct: 740  GQRVEKGQVLCEGYATQDGELALGRNLKVAFMPWQGFNFEDAIVISERVVSQDIFTSLHV 799

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE+  RDTK G EE+T DIPNVSEE  K++DE GII VGAEV  GDIL+GKITPKGES
Sbjct: 800  EEFELEVRDTKRGEEELTPDIPNVSEEATKDLDENGIIRVGAEVKEGDILIGKITPKGES 859

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+ P  ++G V+D ++F+R      + S + E+  I
Sbjct: 860  DPSPEEKLLRAIFGDKAGDVKDASLKTPPSIAGVVIDTKLFSRA----KKTSKAEEKAAI 915

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRS 1019
            + L    +     L   +  +L EI+ G+ +      +K     K    +  ++ E   +
Sbjct: 916  DKLDTKHEKAIKDLKNTLVDKLFEIVNGKTSQGVYNVYKELLVAKGVKFTQKILLELEYA 975

Query: 1020 QWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     ++ L   Y    +     ++     I  GD++P G++++ KV++
Sbjct: 976  NINPTKWTTDDDKNDLIKLLLHNYNIKVNEELGAYRRDKFAISVGDELPSGIVQMAKVYI 1035

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+E
Sbjct: 1036 AKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNLGQIYE 1095

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA   LG K  + I D  ++ ++    +                            
Sbjct: 1096 TVLGWAGKELGVKFATPIFDGASHDEVEEWVA---------------------------- 1127

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                         SG++ LY+GLTG+ FD+  TVG IYMLK
Sbjct: 1128 --KAGIPA------------------------SGRTYLYNGLTGDRFDQQTTVGIIYMLK 1161

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA +LQE+LT+K
Sbjct: 1162 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAANILQEILTVK 1221

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR + YE+IV G +      PESFNVLV E++ LGL I LE
Sbjct: 1222 SDDVVGRAKTYEAIVKGENLPTPSVPESFNVLVHELRGLGLDITLE 1267


>gi|255692641|ref|ZP_05416316.1| DNA-directed RNA polymerase, beta subunit [Bacteroides finegoldii DSM
            17565]
 gi|260621617|gb|EEX44488.1| DNA-directed RNA polymerase, beta subunit [Bacteroides finegoldii DSM
            17565]
          Length = 1270

 Score = 1319 bits (3414), Expect = 0.0,   Method: Composition-based stats.
 Identities = 587/1367 (42%), Positives = 820/1367 (59%), Gaps = 119/1367 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFNLAEDVKVNKTNLKKVL-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ E  E+ I+   V++E+ ++EI  S +++I +L+ D  N + Y  I NTL  D +  
Sbjct: 261  VVSIERNEVIIDRETVLEEEHIDEILESGVQNI-LLHKDEPNQSDYSIIYNTLQKDPSNS 319

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  +VR
Sbjct: 320  EKEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMEVR 379

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER
Sbjct: 380  VLTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRER 439

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG+
Sbjct: 440  MNVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGL 499

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GK
Sbjct: 500  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINDLGFIETPYRKVENGK 559

Query: 610  V---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            V    N +VYL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   +++ +D 
Sbjct: 560  VDLSENGLVYLTAEEEEEKIIAQGNAPLNDDGTFVRNKVKSRQDADFPVVEPSEVNLMDV 619

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SP+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   
Sbjct: 620  SPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQ 679

Query: 727  IVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+  
Sbjct: 680  ITAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICD 739

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H
Sbjct: 740  KGQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVH 799

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            +EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGE
Sbjct: 800  VEEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGE 859

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  
Sbjct: 860  SDPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKAL 917

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            +  +  + + +   L R +  +LM +  G+ +       G +   K    S+        
Sbjct: 918  LPKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGAKFSASDFDSLDF 977

Query: 1019 SQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +         DE     +  L + +      L+   K K   I  GD++P G++++ KV+
Sbjct: 978  TSIQLSNWTSDEHANGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVY 1037

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIF
Sbjct: 1038 IAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIF 1097

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  LG A   LG K  + I D     D++                               
Sbjct: 1098 EAVLGRAGKTLGVKFATPIFDGATMEDLNEWTD--------------------------- 1130

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               K+G+P                           ++ L DG TGE FD+P TVG  YML
Sbjct: 1131 ---KAGLP------------------------RYCKTYLCDGGTGEQFDQPATVGVTYML 1163

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTI
Sbjct: 1164 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTI 1223

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1224 KSDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|189465411|ref|ZP_03014196.1| hypothetical protein BACINT_01764 [Bacteroides intestinalis DSM
            17393]
 gi|189437685|gb|EDV06670.1| hypothetical protein BACINT_01764 [Bacteroides intestinalis DSM
            17393]
          Length = 1270

 Score = 1319 bits (3413), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1366 (42%), Positives = 823/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRINFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDIKVNKTNLKRV-LGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINVLGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDAGLAYLTAEEEEAKIIAQGNAPLNDDGTFIRDKVKARQDADYPVVTPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ K++R+NQN  ++ RP+ ++
Sbjct: 681  TAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKWRRTNQNMTIDLRPICEI 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TSIH+
Sbjct: 741  GQRVTKGQILTEGYSTENGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDILTSIHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIQPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D R+F+R  + K+  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKRLFSR--VIKSRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L   +  +L+++       G     G     K    S     +   +
Sbjct: 919  PKIDDEFDAKVADLRGVLIRKLLKLTENYVSEGVKDYMGADIISKGAKFSPSDFGDLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+++   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTNDDRINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGEPFD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTKLYDGGTGEPFDQHATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|224023600|ref|ZP_03641966.1| hypothetical protein BACCOPRO_00307 [Bacteroides coprophilus DSM
            18228]
 gi|224016822|gb|EEF74834.1| hypothetical protein BACCOPRO_00307 [Bacteroides coprophilus DSM
            18228]
          Length = 1270

 Score = 1318 bits (3412), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1366 (42%), Positives = 812/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD +EVQ  S+  FL ++  P++R N+GL   F   FPI       
Sbjct: 8    QRINFASIKNPMQYPDFLEVQLKSFQDFLQLDTPPEKRKNDGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP + +DDCL R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPHYSIDDCLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---IHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIFNLAEDIKVNK--------- 230

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                               ++++  G+KL + +LK+  E  V                 +
Sbjct: 231  ----------------ANLKKIV--GRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   +I+ + ++ I  S +++I +   + + ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETIIEPEHIDLIIESGVQNILVHNEEANTSDYSIIFNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +L+LDT  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINKKLSLDTSMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKHDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DG V
Sbjct: 501  RDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFIVTPYRKVKDGVV 560

Query: 611  T---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YLSA EEE++ IAQ N+ L++DG+F  E V  R   +  +V  ++++ +D S
Sbjct: 561  DLSPEGIEYLSAEEEEDKIIAQGNAPLNDDGTFIREKVKARRDADYPVVTPDQVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKTEAPIVGTGIERQLCEDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQ+  ++ RP+ + 
Sbjct: 681  AAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQSMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTANGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDILTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R  + K     + ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLYSR--VIKTRSEKNADKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   + ++L      ++  G     G +   K    +   +     +
Sbjct: 919  PKLNEEFEEKAAALKEVMVNKLLVLTNDKVSQGVKDYLGTEVIAKGAKFTKRDLESLDYT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      +  L V Y      L+   K K   +  GD++P G++++ KV++
Sbjct: 979  IIQLSKWTADAHKNDMIRDLIVNYLKKYKELDAELKRKKFALTIGDELPSGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKELGVKFATPIFDGATLEDLDKWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ LYDG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLYDGGTGEQFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ L LSI LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLCLSITLE 1270


>gi|224537809|ref|ZP_03678348.1| hypothetical protein BACCELL_02696 [Bacteroides cellulosilyticus DSM
            14838]
 gi|224520629|gb|EEF89734.1| hypothetical protein BACCELL_02696 [Bacteroides cellulosilyticus DSM
            14838]
          Length = 1270

 Score = 1318 bits (3411), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1366 (42%), Positives = 823/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRINFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDIKVNKTNLKRV-LGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGNVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINVLGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDEGLAYLTAEEEEAKIIAQGNAPLNDDGTFIRDKVKARQDADYPVVTPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G++E VDA  I I   R+ + +       +  YR+ K++R+NQN  ++ RP+ ++
Sbjct: 681  TAEGDGVIEFVDATVIRILYDRTEDEEFVSFEPALKEYRIPKWRRTNQNMTIDLRPICEI 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TSIH+
Sbjct: 741  GQRVTKGQILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDILTSIHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIQPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D R+F+R  + K+  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKRLFSR--VIKSRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L   +  +L+++       G     G     K    S     +   +
Sbjct: 919  PKIDDEFDAKVADLRGVLIRKLLKLTENHVSEGVKDYMGADIISKGAKFSPSDFGDLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+++   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTNDDRINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGEPFD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTKLYDGGTGEPFDQHATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|313677113|ref|YP_004055109.1| DNA-directed RNA polymerase subunit beta [Marivirga tractuosa DSM
            4126]
 gi|312943811|gb|ADR23001.1| DNA-directed RNA polymerase subunit beta [Marivirga tractuosa DSM
            4126]
          Length = 1290

 Score = 1318 bits (3410), Expect = 0.0,   Method: Composition-based stats.
 Identities = 588/1386 (42%), Positives = 849/1386 (61%), Gaps = 137/1386 (9%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F     +ID PD ++VQ  S+  F  +    ++R  EG+   F+  FPI+      
Sbjct: 8    ERINFSSIKTVIDYPDFLDVQLQSFQDFFQLETPAEKRAEEGIFKVFQENFPISDSRENF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEFV Y  DPPK+D+D C+ R LTY+VPLK  LRLI  D D         +  EQ +++
Sbjct: 68   VLEFVDYLVDPPKYDIDGCIDRGLTYSVPLKAKLRLICNDEDNEDF-----ETIEQEVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++P MT+ G+F+I G +R++VSQLHRSPG+ F   K     +G  LY+ RIIP +G W+
Sbjct: 123  GNIPYMTEKGSFIINGAERVIVSQLHRSPGVFFAQSK---HTNGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K PVT+ L A+G  S+ +IL  F                 + 
Sbjct: 180  EFATDVNNVMYAYIDRKKKFPVTTLLRAIGYGSDKDILDLF-----------------NL 222

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
            ++ + G K +         + +   G+KL + +LK+  E  V                 +
Sbjct: 223  SEEVDGTKAAL-------KKVI---GRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ +  E+ +E   VI+E+ ++ I  + ++ I +   D ++ + + + NTL  D +   
Sbjct: 261  VVSIDRNEVLLERDSVIEEEDIDLIIDAGVKSIILHRTDVNITDYSIVYNTLQKDNSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+  IYR +R  +    + A  +   LFF   +YDL  VGR ++N +L LD   + + 
Sbjct: 321  KEAVEQIYRQLRNTEAPDEATAREIIQNLFFSEKRYDLGEVGRYRINKKLGLDIDAETKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K DII I+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER+
Sbjct: 381  LTKVDIIHIVKYLIGLINSKAIVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINA+ + S +  FF ++QLSQ  +  N LS +TH RR+SALG GG++
Sbjct: 441  NVRDNEDFKPVDLINARTLSSVINSFFGTNQLSQFMDQTNPLSEVTHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DG 608
            R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A+VN  GFIETPYRKV     
Sbjct: 501  RERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKVNGMGFIETPYRKVEGGKV 560

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
             ++ +V+YL+A EE++  IAQAN+ +D+ G +  + V  R  G+  ++  +++ ++D +P
Sbjct: 561  DMSGNVLYLTAEEEDDHNIAQANAPIDDSGKYLNDRVKARFEGDFPVLEPKELSYMDIAP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+VS+AAS+IPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA+ S + IV
Sbjct: 621  NQIVSVAASMIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVARDSRSMIV 680

Query: 729  AKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A++ G+V  VDA +IV++     E +L        +Y L+KF+R+NQNT +N RPLV  G
Sbjct: 681  AEKDGVVVFVDATKIVVKYDMNEEEELVSFEDDERVYDLIKFRRTNQNTTINLRPLVYKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D+V++  I+ DG +T+ G+LA+GRNM VAFMPW GYNFED+++ISER+V ED+FTSIHIE
Sbjct: 741  DKVKKGQILCDGYATEKGELAIGRNMKVAFMPWQGYNFEDAIVISERVVREDIFTSIHIE 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            EFE+  RDTK G EE+T +IPNVSEE +KN+DE GII  G E+  GDIL+GKITPKGE+ 
Sbjct: 801  EFELEVRDTKRGEEELTSEIPNVSEEAVKNLDENGIIRTGTEIKEGDILIGKITPKGETD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             TPEEKLLRAIFG+KA DV+D S++    + G V+D ++F RH  DK+ R+ +  ++++E
Sbjct: 861  PTPEEKLLRAIFGDKAGDVKDASMKASPSLRGVVIDTKLFARHKKDKDGRADA--KKEVE 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE----- 1015
            +LA++   + + L      +L  +L G+         G +   K    + + I +     
Sbjct: 919  VLAKEYSRQLLKLRNLKIEKLATLLEGKTCQGIKHKFGDEIMSKGVKFTQNNIEKNLFPE 978

Query: 1016 -----------------YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                                         DE   + +  L   Y   ++ +  +FK +  
Sbjct: 979  KNIYRDESNYNVPEEVNLISDLILDNWTNDENTNKLIVDLVRNYNKRRNEIAGKFKRERF 1038

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
             I+ GD++P G++++ KV+VA KR ++ GDKMAGRHGNKG+V++I+  EDMPFL+DGTPV
Sbjct: 1039 TIEVGDELPAGIVQLAKVYVAKKRKLKVGDKMAGRHGNKGVVAKIVRDEDMPFLEDGTPV 1098

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIVLNPLGVPSRMN+GQI+ET LGWA + LG+K  + I D  ++ ++S            
Sbjct: 1099 DIVLNPLGVPSRMNIGQIYETVLGWAGLKLGRKYATPIFDGASSDEVS------------ 1146

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                              AE  ++G+P                        E G++ LYD
Sbjct: 1147 ------------------AELAEAGLP------------------------EFGRTHLYD 1164

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            GLTG+ FD+ VTVG IYMLKL H++ DK++ARS G YSL+TQQPLGGK+  GGQR GEME
Sbjct: 1165 GLTGDIFDQKVTVGVIYMLKLGHLIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEME 1224

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++A+GA++VLQE+LTIKSDDV+GR + YE+IV G +  +   PESFNVLV E++ L 
Sbjct: 1225 VWALEAFGASHVLQEILTIKSDDVIGRAKAYEAIVKGENMGKPNIPESFNVLVHELRGLA 1284

Query: 1359 LSIDLE 1364
            L I L+
Sbjct: 1285 LEITLD 1290


>gi|167764379|ref|ZP_02436504.1| hypothetical protein BACSTE_02763 [Bacteroides stercoris ATCC 43183]
 gi|167697784|gb|EDS14363.1| hypothetical protein BACSTE_02763 [Bacteroides stercoris ATCC 43183]
          Length = 1270

 Score = 1317 bits (3408), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1366 (42%), Positives = 822/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + I  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKI-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   +I+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETIIEPEHIDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINRKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINQLGFIETPYRKVANGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L+EDG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDEGLVYLTAEEEEEKIIAQGNAPLNEDGTFVRDKVKSRQDADYPVVAPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I      E +     S +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGEGVVDFVDATTIRILYDRTEEEEFVSFESALKEYTIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVTKGQILTEGYSTEQGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIGKRLFSR--VIKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L++ + ++L+++       G     G +   K     +   S+   +
Sbjct: 919  PKIDDEFDSKVADLEKILVNKLLKLTENHTSEGVKDYMGAEVISKGAKFYASDFSDIDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L   +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSNWTKDEHTNELIRALVTNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLYDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPAPGIPESLNVLLHELRGLGLSINLE 1270


>gi|298206596|ref|YP_003714775.1| DNA-directed RNA polymerase beta subunit [Croceibacter atlanticus
            HTCC2559]
 gi|83849226|gb|EAP87094.1| DNA-directed RNA polymerase beta subunit [Croceibacter atlanticus
            HTCC2559]
          Length = 1270

 Score = 1317 bits (3407), Expect = 0.0,   Method: Composition-based stats.
 Identities = 588/1368 (42%), Positives = 806/1368 (58%), Gaps = 117/1368 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F       D PD +++Q  S+  F  +    DER  EGL   F   FPIT     
Sbjct: 6    TERLNFSNVKNRPDYPDFLDIQIQSFQDFFQLETKSDEREAEGLYKTFMENFPITDTRNQ 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y
Sbjct: 66   FVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVY 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W
Sbjct: 121  LGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D   +++  IDR++K+PVT+   A+G + + +IL  F                L 
Sbjct: 178  IEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVTKSGLKKVL- 236

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+KL + +L +  E  V                 
Sbjct: 237  --------------------------GRKLAARVLNTWYEDFVDEDT------------G 258

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKD 369
            ++V+ E  EI ++    ++++ +EEI  +  + I +   D+   + A I NTL  D    
Sbjct: 259  EVVSIERNEIVLDRDTELEKEHIEEILETGTKTILLHKEDNSTGDYAIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDIAMDKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VNA GFIETPYRKV DGK
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNALGFIETPYRKVDDGK 558

Query: 610  VT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            +      +YLSA EEE   IAQAN  LD+ G+   E V  R  G+  +   + +++ID +
Sbjct: 559  INLDESPIYLSAEEEEGMKIAQANIPLDDKGNIEAERVIARLEGDFPVEDPKNVNYIDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ ++P VGTG+E  VA  S   I
Sbjct: 619  PNQISSISASLIPFLEHDDANRALMGSNMMRQAVPLLRVDSPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+ AG VE VDA  + I+     E       S    Y L+KF+++NQ T +N +P+VKV
Sbjct: 679  NAEGAGTVEYVDANMVTIKYDRSEEERQVSFDSDSKSYNLIKFRKTNQGTSINLKPIVKV 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V R  ++  G +T+ G+LALGRNM VAFMPW GYNFED+++ISE++V ED+FTSIH+
Sbjct: 739  GDRVERGQVLCQGYATEAGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSIHV 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DEYSLDVRDTKLGNEELTNDIPNVSEEATKDLDEYGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    ++G V+D ++F R    K++R  + ++E I
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLNGVVIDKKLFERA--IKDKRKRAQDKEDI 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + D +   L   +  +L  ++ G+ A       G     K    +  +++     
Sbjct: 917  ARLEVEYDAKFDDLKAVLVEKLFNLIGGKTAQGVKNDLGEDILPKGKKYTLKMLNSVEDY 976

Query: 1020 QWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      D+++   V  L   Y+  ++ L+   + +   I  GD++P G++++ K++
Sbjct: 977  THLTQGTWTTDDELNSMVADLIHNYKIKENDLQGNLRREKFTISVGDELPAGIIKLAKIY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVARIVREEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LG+K  + I D      I+ L                             
Sbjct: 1097 ETVLGWAGQKLGRKFATPIFDGATLDQINELTD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++G+P                          G + LYDG TG+ FD+P TVG IYML
Sbjct: 1130 ---EAGIP------------------------RFGHTHLYDGGTGDRFDQPATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDV+GR + YESIV G    E G  ESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVIGRAKTYESIVKGEPMPEPGLRESFNVLMHELKGLGLDIRLEE 1270


>gi|329956690|ref|ZP_08297263.1| DNA-directed RNA polymerase, beta subunit [Bacteroides clarus YIT
            12056]
 gi|328524062|gb|EGF51138.1| DNA-directed RNA polymerase, beta subunit [Bacteroides clarus YIT
            12056]
          Length = 1270

 Score = 1317 bits (3407), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1366 (42%), Positives = 825/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + I  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKI-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   +I+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETIIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINRKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVANGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDEGLVYLTAEEEEEKIIAQGNAPLNDDGTFVRDRVKSRQDADYPVVAPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +     S +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGEGVVDFVDATTIRILYDRTEDEEFVSFESALKEYTIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVTKGQILTEGYSTEQGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIGKRLFSR--VIKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L + + ++L+++       G     G +   K    S+   S+   +
Sbjct: 919  PKIDDEFDGKVADLKKILVNKLLKLTENYTSEGVKDYMGAEVISKGAKFSASDFSDMDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSNWTKDEHTNGLIRALVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ L+DG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLFDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPAPGIPESLNVLLHELRGLGLSINLE 1270


>gi|330997385|ref|ZP_08321236.1| DNA-directed RNA polymerase, beta subunit [Paraprevotella xylaniphila
            YIT 11841]
 gi|329570759|gb|EGG52475.1| DNA-directed RNA polymerase, beta subunit [Paraprevotella xylaniphila
            YIT 11841]
          Length = 1271

 Score = 1316 bits (3406), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1368 (42%), Positives = 811/1368 (59%), Gaps = 120/1368 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD ++VQ  S+  FL ++  P++R N+GL   F   FPI       
Sbjct: 8    QRVNFATVKSPMPYPDFLDVQLKSFKDFLQLDTPPEKRKNDGLYKVFSENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +++CL R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIEECLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT +GTF+I G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDNGTFIINGAERVVVSQLHRSPGVFFGSS---IHANGTQLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G + + +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFEDDKDILEIFNLAEEVKATKTNLKKYI-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     GKKL + +LKS  E  V                 +
Sbjct: 238  -------------------------GKKLAARVLKSWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ E  E+ ++   ++DE ++  I  S ++ + +L+ + +N + Y  I NTL  D +  
Sbjct: 261  VVSIERNEVILDREAILDEDNICIILDSGVQSV-LLHKEEINTSDYSIIFNTLQKDPSNS 319

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR
Sbjct: 320  EKEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINRKLNLSTDMDVR 379

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER
Sbjct: 380  VLTKEDIIEIIKYLIELINSKALVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRER 439

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG+
Sbjct: 440  MNVRDNEVFTPTDLINAKTISSVINSFFGTNALSQFMDQTNPLAEVTHKRRLSALGPGGL 499

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFIETPYRKV DG 
Sbjct: 500  SRERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKINDLGFIETPYRKVQDGV 559

Query: 610  V----TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            V       + YL+A EEE + I Q N+ L++DG+F  + V CR   +  +VP   ++ +D
Sbjct: 560  VDLSLETGIEYLTAEEEEGKIIGQGNAPLNDDGTFIRKKVKCRQDDDYPVVPPSDVNLMD 619

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             +P+Q+ SIAASLIPFLE+DD++R LMG NM RQAVPLL++E+P VGTG+E  V + S  
Sbjct: 620  VAPQQIASIAASLIPFLEHDDAHRALMGSNMMRQAVPLLRSESPIVGTGIEKQVCEDSRT 679

Query: 726  AIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+ 
Sbjct: 680  MITAEGDGVIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPIC 739

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G  V+  DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TSI
Sbjct: 740  DKGQRVKAGDILTEGYSTQQGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDILTSI 799

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H+EEF +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDI++GKITPKG
Sbjct: 800  HVEEFSLEVRETKRGVEELTADIPNVSEEATKDLDENGIVRVGARIQPGDIMIGKITPKG 859

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  +PEEKLLRAIFG+KA DV+D SL+    ++G V+D ++F+R    K   + + ++ 
Sbjct: 860  ESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLNGVVIDKKLFSRA--IKTRAAKAADKL 917

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  +  + + +   L   +  +L+E+       G     G          ++  +    
Sbjct: 918  ILPKIDEEFNSKVEDLKAILIDKLLELTKDKVSQGVKDYMGSDVIASGRKFAASALEGLD 977

Query: 1018 RSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             +         DE +   +  L + +     +L+   K K   I  GD++P G++++ KV
Sbjct: 978  FTTIQLSGWTDDEHLNGLISQLIINFLKKYKLLDAELKRKKFAITIGDELPSGIIQMAKV 1037

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A KR I  GDKMAGRHGNKGIVS+I+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1038 YIAKKRKIGVGDKMAGRHGNKGIVSKIVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQI 1097

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FET LG A   LG K  + I D     D+                               
Sbjct: 1098 FETVLGAAGKELGVKFATPIFDGATLDDLCEWTD-------------------------- 1131

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                K+G+P                            + LYDG TGE FD+  TVG  YM
Sbjct: 1132 ----KAGLP------------------------RYCSTQLYDGETGEKFDQLATVGIAYM 1163

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LT
Sbjct: 1164 LKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILT 1223

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            IKSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI LE
Sbjct: 1224 IKSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSITLE 1271


>gi|189460677|ref|ZP_03009462.1| hypothetical protein BACCOP_01324 [Bacteroides coprocola DSM 17136]
 gi|189432636|gb|EDV01621.1| hypothetical protein BACCOP_01324 [Bacteroides coprocola DSM 17136]
          Length = 1270

 Score = 1315 bits (3404), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1366 (42%), Positives = 808/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD +EVQ  S+  FL ++  P++R N+GL   F   FPI       
Sbjct: 8    QRINFASIKNPMKYPDFLEVQLKSFQDFLQLDTPPEKRKNDGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP + +DDCL R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPHYTIDDCLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---IHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                +  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIFNLAEDVKVNKANLKKII-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+ + ++ I  S I++I +   + + ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETVIEPEHIDLILESGIQNILVHNEEANSSDYSIIFNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNLDT  DV+ 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINKKLNLDTDMDVKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K+DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKQDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DG V
Sbjct: 501  RDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFIVTPYRKVKDGVV 560

Query: 611  T---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YLSA EEE++ IAQ N+ L++DG+F  E V  R   +  +V  ++++ +D +
Sbjct: 561  DLSPEGIEYLSAEEEEDKIIAQGNAPLNDDGTFIREKVKARRDADYPVVTPDQVELMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKTEAPIVGTGIEKQLCEDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+++ VDA  I I   R+ + +       +  YR+ KF+++NQ+  ++ RP+   
Sbjct: 681  TAEGDGVIDFVDATTIRILYDRTDDEEFVSFEPALKEYRIPKFRKTNQSMTIDLRPICTK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTANGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDILTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R  + K     + ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLYSR--VIKTRSEKNADKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   +  +L      ++  G     G +   K    +   +     +
Sbjct: 919  PKLNEEFEEKAAALKEILVEKLLVLTNDKVSQGVKDYLGTEVIAKGAKFTKRDLESLDYT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      +  L + Y      L+   K K   +  GD++P G++++ KV++
Sbjct: 979  IIQLSKWTSDAHKNDMIRDLIMNYLKKYKELDAELKRKKFALTIGDELPSGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKELGVKFATPIFDGATLDDLDKWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ LYDG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLYDGGTGEQFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GAA+VLQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGAAHVLQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ L LSI LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLCLSITLE 1270


>gi|218131345|ref|ZP_03460149.1| hypothetical protein BACEGG_02956 [Bacteroides eggerthii DSM 20697]
 gi|317476372|ref|ZP_07935621.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
 gi|217986277|gb|EEC52614.1| hypothetical protein BACEGG_02956 [Bacteroides eggerthii DSM 20697]
 gi|316907398|gb|EFV29103.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
          Length = 1270

 Score = 1315 bits (3402), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1366 (42%), Positives = 823/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFKDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +D+C+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDECIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + I  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKI-VGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   +I+ + ++ I  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVVIDRETIIEPEHVDIILESGVQNILVHKEEPNQSDYSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINQLGFIETPYRKVANGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  +VYL+A EEE + IAQ N+ L++DG+F  + V  R   +  +V  ++++ +D S
Sbjct: 561  DLSDEGLVYLTAEEEEEKIIAQGNAPLNDDGTFVRDRVKSRQDADYPVVAPDEVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLLK+EAP VGTG+E  +A+ S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLKSEAPIVGTGIERQLARDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I      E +     S +  Y + K++R+NQN  ++ RP+ + 
Sbjct: 681  TAEGEGVVDFVDATTIRILYDRTEEEEFVSFESALKEYTIPKWRRTNQNMTIDLRPICEK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  I+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVTKGQILTEGYSTEQGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G ++  R+F+R  + K   S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVIIGKRLFSR--VIKTRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              +  + D +   L + + ++L+++       G     G +   K    S+   S+   +
Sbjct: 919  PKIDDEFDGKVADLKKILVNKLLKLTERYTSEGVKDYMGAEVISKGAKFSASDFSDMDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +DE     + +L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  AIQLSNWTKDEHTNGLIRALVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D++                                
Sbjct: 1099 AVLGRAGKNLGVKFATPIFDGATLDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                          G++ LYDG TGE F++  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYGKTTLYDGGTGEAFEQQATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPAPGIPESLNVLLHELRGLGLSINLE 1270


>gi|305664386|ref|YP_003860673.1| DNA-directed RNA polymerase subunit beta [Maribacter sp. HTCC2170]
 gi|88708403|gb|EAR00639.1| DNA-directed RNA polymerase beta subunit [Maribacter sp. HTCC2170]
          Length = 1269

 Score = 1314 bits (3401), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1372 (42%), Positives = 814/1372 (59%), Gaps = 117/1372 (8%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
            F      R  F       + PD +++Q  S+  F  +    D+R  EGL   F   FPIT
Sbjct: 2    FTNQ-TERINFASAKNTPEYPDFLDIQIKSFQDFFQLETKSDQRGTEGLYNTFMENFPIT 60

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +    
Sbjct: 61   DTRNQFVLEFLDYFIDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV---- 116

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
             Q +Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP
Sbjct: 117  -QDVYLGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIP 172

Query: 187  DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
             +G W++   D   +++  IDR++K+PVT+   A+G +S+ +IL  F             
Sbjct: 173  FKGSWIEFATDINGVMYAYIDRKKKLPVTTLFRAIGFESDKDILEIFDLSEEVKVSKAGL 232

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
               L                           G+KL + +L +  E  V            
Sbjct: 233  KKVL---------------------------GRKLAARVLNTWHEDFVDEDT-------- 257

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVT 364
                 ++V+ E  EI ++   V+++  +EEI  ++++ I +   ++  ++ A I NTL  
Sbjct: 258  ----GEVVSIERNEIILDRDTVLEKDHIEEILGTDVKTILLHKENNAQSDYAIIHNTLQK 313

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D     K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD 
Sbjct: 314  DPTNSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGEVGRYRMNKKLQLDI 373

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              D + + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L +Q+ +GL RM R
Sbjct: 374  GMDKQVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSSQFGVGLARMAR 433

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            +I+ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSAL
Sbjct: 434  TIRERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSAL 493

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN  GF+ETPYRK
Sbjct: 494  GPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFAKVNPMGFLETPYRK 553

Query: 605  VCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V   KV T + +YLSA EEE   IAQAN  L ++G+   E V  R  G+  +V  +++++
Sbjct: 554  VDGAKVDTKEYMYLSAEEEEGMKIAQANIPLKDNGAIDSEKVIAREEGDFPVVDPKEVNY 613

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK ++P VGTG+E  VA  S
Sbjct: 614  TDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQSPIVGTGLERQVASDS 673

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               I A+  G +E VD+ +I I+        L         Y L+KF+++NQ T +N +P
Sbjct: 674  RVLINAEGDGTIEYVDSQKITIKYKRTDAERLISFDEDEKTYNLVKFRKTNQGTSINLKP 733

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK GD+V++  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISE++V ED+FT
Sbjct: 734  IVKKGDKVKKGQVLCEGYATEKGELALGRNLTVAFMPWKGYNFEDAIVISEKVVREDIFT 793

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIH++E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITP
Sbjct: 794  SIHVDEYALEVRDTKLGAEELTHDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITP 853

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R    K++R  S +
Sbjct: 854  KGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSR--SIKDKRKRSED 911

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE 1015
            +E I  L  + + +   L   +  +L  ++ G+ +       G +   K    +  +++ 
Sbjct: 912  KEAISTLELEYEVKFQQLKDVLVEKLFTLINGKTSQGVLNDLGEEVLPKGKKYTMKMLNS 971

Query: 1016 YPRSQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                          D+ V  +V  L   Y+   + L+   +     I  GD++P G++++
Sbjct: 972  VDDFAHLVAGTWTTDKDVNHSVADLLHNYKIKLNDLQGNLRRDKFTISVGDELPAGIMKL 1031

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             KV+VA KR ++ GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+
Sbjct: 1032 AKVYVAKKRKLKVGDKMAGRHGNKGIVSRIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNI 1091

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI+ET LGWA + LG+K  + I D     +I+                           
Sbjct: 1092 GQIYETVLGWAGLKLGRKYATPIFDGATLDEIN--------------------------- 1124

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
               A   ++G+P                          G + LYDG TG+ FD+  TVG 
Sbjct: 1125 ---AYTDEAGIP------------------------RFGHTHLYDGGTGKRFDQAATVGV 1157

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E
Sbjct: 1158 IYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLRE 1217

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +LT+KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1218 ILTVKSDDVIGRAKTYESIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|110639542|ref|YP_679751.1| DNA-directed RNA polymerase subunit beta [Cytophaga hutchinsonii ATCC
            33406]
 gi|123058539|sp|Q11QA5|RPOB_CYTH3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110282223|gb|ABG60409.1| DNA-directed RNA polymerase subunit beta [Cytophaga hutchinsonii ATCC
            33406]
          Length = 1291

 Score = 1314 bits (3400), Expect = 0.0,   Method: Composition-based stats.
 Identities = 589/1387 (42%), Positives = 825/1387 (59%), Gaps = 139/1387 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K    ++ PD +++Q  S+  F  ++   + R  EGL   F   FPI+      
Sbjct: 9    LRKSFAKTRSTVEYPDFLDIQVRSFKDFFQIDTPAENRFKEGLYKVFAENFPISDSRDNF 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +L+F+ Y  D PK++VD+C+ R LTYAVPLK  LRL   D D            EQ +++
Sbjct: 69   ILDFIDYNIDTPKYNVDECIDRGLTYAVPLKAKLRLTCNDKDNEDF-----QTIEQEVFL 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++P MT+ G+FVI G +R++VSQLHRSPG+ F   K     +G  LY+ R+IP +G W+
Sbjct: 124  GNIPYMTERGSFVINGAERVIVSQLHRSPGVFFAQSK---HTNGTKLYSARVIPFKGSWI 180

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  +++   IDR++K PVT+ L A+G  S+ +IL  F                +  
Sbjct: 181  EFATDVNNVMFAYIDRKKKFPVTTLLRAIGYGSDKDILDLFGLSEEVEATKANIKKAI-- 238

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +L++  E  V                 +
Sbjct: 239  -------------------------GRKLAARVLRTWTEDFVDEDT------------GE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ +  E+ +E   +I E+ +  I  S  + I IL+ + VN   Y  I NTL  D +  
Sbjct: 262  VVSIDRNEVLLERDSIIKEEDINIIVESGSKSI-ILHREDVNIADYTIIYNTLQKDNSNS 320

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  D      A  + + LFF   +YDL  VGR ++N +L      +V+
Sbjct: 321  EKEAVEQIYRQLRNTDAPDEQTARDIIHNLFFSDKRYDLGEVGRYRINKKLGSGMGSEVK 380

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII I+K L+ L N +  +DDID+L NRRVR++GE L +Q+ +GL RM R+IKER
Sbjct: 381  VLTKEDIINIVKYLIGLINSRAVVDDIDHLSNRRVRTMGEQLYSQFSVGLARMARTIKER 440

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RR+SALG GG+
Sbjct: 441  MNVRDNEDFKPVDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRMSALGPGGL 500

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-- 607
            +R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A+VN+ GFIETPYRKV D  
Sbjct: 501  SRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKVNSMGFIETPYRKVIDGI 560

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              V N  V+L+A EE+  +IAQAN+  D++G+F  + +  R  G+  ++  +K+D ID +
Sbjct: 561  VDVKNQPVFLTAEEEDGAHIAQANAMYDDNGNFISDRIKARYEGDFPVIAPDKVDLIDIA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
              Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA  S   +
Sbjct: 621  TNQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLERRVAMDSRTLL 680

Query: 728  VAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +A+  G+VE VDA  I +R     E  L    S +  Y L+KF+R+NQ+TC+N +P+++ 
Sbjct: 681  IAEADGVVEFVDANEIKMRYDLTDEDRLVSFDSDIITYSLIKFRRTNQDTCINLKPVIQH 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G+ V++  ++ +G +TD G+LALGRN++VAFMPW GYNFED+++ISE++V +D+FTSIHI
Sbjct: 741  GERVKKGQVLCEGYATDKGELALGRNLMVAFMPWQGYNFEDAIVISEKVVRDDIFTSIHI 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE+  RDTK G EE+T +IPNVSEE +KN+DE GII  GAE+  GDIL+GKITPKGES
Sbjct: 801  EEFELEVRDTKRGEEELTSEIPNVSEEAVKNLDENGIIRTGAEIKEGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D S++ P  + G V+D ++F+R   DK+ R  S  ++Q+
Sbjct: 861  DPTPEEKLLRAIFGDKAGDVKDASMKAPPSLRGVVIDTKLFSRPKKDKDLRIKS--KKQV 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLIS----- 1014
            E +      + + L   +  +L  +L GQ +       G +   K    S   I      
Sbjct: 919  ETIKGKYSKDLLALREQMIEKLAALLDGQTSQGVKHKFGDEVISKGVKFSRKNIEANVFP 978

Query: 1015 -----------------EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                                          D+K+  NV  L   Y T ++    +FK + 
Sbjct: 979  DKNPYRDESNYNVQEEANLLGDLIIDNWTSDKKINENVLRLVKNYLTKRNETAGKFKRER 1038

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
              ++ GD++P G++++ KV++A KR ++ GDKMAGRHGNKG+V+RI+  EDMPFL+DGTP
Sbjct: 1039 FTLEVGDELPAGIVQLAKVYIAKKRKLKVGDKMAGRHGNKGVVARIVRDEDMPFLEDGTP 1098

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQI+ET LG A   LG+K  + I D  +  ++            
Sbjct: 1099 VDIVLNPLGVPSRMNIGQIYETLLGLAGKKLGRKYATPIFDGASEEEV------------ 1146

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                     IN + R A L   G++ L 
Sbjct: 1147 -----------------------------------------INEL-RDAGLPTIGRTKLV 1164

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            DGL+G PFD+PVTVG IYM+KL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEM
Sbjct: 1165 DGLSGNPFDQPVTVGVIYMMKLGHLVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEM 1224

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++A+GAA +LQE+LT+KSDDVVGR + YE IV G +      PESFNVLV E++ L
Sbjct: 1225 EVWALEAFGAANILQEILTVKSDDVVGRAKTYECIVKGENLPRPNIPESFNVLVHELRGL 1284

Query: 1358 GLSIDLE 1364
             L I L 
Sbjct: 1285 ALEITLH 1291


>gi|150003395|ref|YP_001298139.1| DNA-directed RNA polymerase subunit beta [Bacteroides vulgatus ATCC
            8482]
 gi|254881315|ref|ZP_05254025.1| RNA polymerase subunit beta [Bacteroides sp. 4_3_47FAA]
 gi|294777815|ref|ZP_06743259.1| DNA-directed RNA polymerase, beta subunit [Bacteroides vulgatus
            PC510]
 gi|319640317|ref|ZP_07995042.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 3_1_40A]
 gi|158513736|sp|A6KYK3|RPOB_BACV8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|149931819|gb|ABR38517.1| DNA-directed RNA polymerase beta chain [Bacteroides vulgatus ATCC
            8482]
 gi|254834108|gb|EET14417.1| RNA polymerase subunit beta [Bacteroides sp. 4_3_47FAA]
 gi|294448269|gb|EFG16825.1| DNA-directed RNA polymerase, beta subunit [Bacteroides vulgatus
            PC510]
 gi|317388092|gb|EFV68946.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 3_1_40A]
          Length = 1270

 Score = 1313 bits (3398), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1366 (42%), Positives = 817/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD +EVQ  S+  FL ++  P++R N+GL   F   FPI       
Sbjct: 8    QRVNFASIKNPMKYPDFLEVQLKSFQDFLQLDTPPEKRKNDGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP + +D+CL R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPHYSIDECLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKV-VGRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+E  ++EI  S +++I +   + + ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVIEEDHIDEIIDSGVQNILVHKEEANSSDYSIIFNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +L L T  DV+ 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINKKLGLTTDMDVKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K+DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKQDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DGKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINELGFISTPYRKVADGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YL+A EEE++ IAQ N+ LD++G F  E V  R   +  +V  ++++ +D S
Sbjct: 561  DISDEGIEYLTAEEEEDKIIAQGNAPLDDEGKFVREKVKARRDADYPVVTPDQVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTEAPIVGTGIEKQLVEDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I I   R+ + +       +  YR+ KF+++NQ+  ++ RP    
Sbjct: 681  AAEGDGVVEYVDATTIRILYDRNEDEEFVSFEPALKEYRIPKFRKTNQSMTIDLRPTCDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTQGGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + K+    + ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSR--VIKSRSEKNADKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   +  +L+ +  G+ +       G +   K    +   +     +
Sbjct: 919  PKLNDEFEEKAAKLKDILIEKLLVLTNGKVSQGVKDYLGTEVIAKGAKFTKRDLESLDYT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      +  L + Y      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  IIQLSKWTADAHKNDMIRDLVMNYLKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D  +  D++                                
Sbjct: 1099 AVLGRAGKELGVKFATPIFDGASMDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGERFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSINLE 1270


>gi|295133028|ref|YP_003583704.1| DNA-directed RNA polymerase subunit beta [Zunongwangia profunda
            SM-A87]
 gi|294981043|gb|ADF51508.1| DNA-directed RNA polymerase subunit beta [Zunongwangia profunda
            SM-A87]
          Length = 1270

 Score = 1313 bits (3398), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1358 (42%), Positives = 798/1358 (58%), Gaps = 117/1358 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F       D PD +++Q  S+  F  +    +ER NEGL   F   FPIT   
Sbjct: 4    KQTERFSFSSVKNRPDYPDFLDIQIKSFQDFFQLETKSEERGNEGLYNTFLENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VYLGTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKTGLKKV 235

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L                           G+KL + +L +  E  V               
Sbjct: 236  L---------------------------GRKLAARVLNTWYEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKN 367
              ++V+ E  EI ++    +D+  +EEI  +  + I +   D+   + A I NTL  D  
Sbjct: 258  -GEVVSIERNEIVLDRDTELDKDHIEEILETGTKTILLHKEDNSTGDYAIIHNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYSLGEVGRYRMNKKLGLDVAMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KEDII I+K L++L N K  IDDID+L NRRVR+VGE L  Q+ +GL RM R+I+
Sbjct: 377  KQVLTKEDIITIVKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VN  GFIETPYR V D
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNGMGFIETPYRTVED 556

Query: 608  --GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                ++ + +YLSA EEE + IAQAN  L +DG+   + V  R  G+  +V  +++ + D
Sbjct: 557  GKINISEEPIYLSAEEEEGKKIAQANIPLGDDGTIDTDKVIARMEGDFPVVDPKEVHYTD 616

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+A++P VGTG+E  VA  S  
Sbjct: 617  VAPNQISSISASLIPFLEHDDANRALMGSNMMRQAVPLLRADSPIVGTGLERQVATDSRV 676

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A+  G VE VDA +I I+     E  +    S    Y L+KF+++NQ T +N +P+V
Sbjct: 677  LINAEGEGEVEYVDAQKITIKYDRTEEERMVSFDSDSKTYDLIKFRKTNQGTSINLKPIV 736

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V +  ++  G +TD G+LALGRNM VAFMPW GYNFED+++ISE++V +D+FTSI
Sbjct: 737  SVGDRVTKGQVLCQGYATDKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVRDDIFTSI 796

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E+ +  RDTKLG EE+T DIPNVSE+  K++DE G+I +GAEV PGDIL+GKITPKG
Sbjct: 797  HIDEYSLEVRDTKLGNEELTNDIPNVSEDATKDLDEHGMIRIGAEVKPGDILIGKITPKG 856

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  TPEEKLLRAIFG+KA DV+D SL+    +SG V++ ++F R    K++R  + ++E
Sbjct: 857  ESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLSGVVINKKLFARA--IKDKRKRAQDKE 914

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYP 1017
             + +L +  + +  +L   +  +L  I+ G+ A       G +   K    +  +++   
Sbjct: 915  DVAVLEKKYEAKFAVLKSQLVDKLFAIVGGKTAQGVQNDLGEEVLPKGKKYTLKMLNSVD 974

Query: 1018 RSQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        D+     V  L   Y+  ++ L+   + +   I  GD++P G+L++ K
Sbjct: 975  DYTHLTQGTWTTDDHTNALVADLLHNYKIKENDLQGNLRREKFTISVGDELPSGILKLAK 1034

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1035 VYIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLDDGTPVDIVLNPLGVPSRMNIGQ 1094

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET LGWA   LGKK  + I D  +   I+ L                           
Sbjct: 1095 IYETVLGWAGQKLGKKYATPIFDGASLDKINELTD------------------------- 1129

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 ++G+P                          G + L+DG TGE FD+  TVG IY
Sbjct: 1130 -----EAGIP------------------------RFGHTYLFDGGTGERFDQRATVGVIY 1160

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+L
Sbjct: 1161 MLKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREIL 1220

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
            T+KSDDV+GR + YESIV G    E G PESFNVL+ E
Sbjct: 1221 TVKSDDVIGRAKTYESIVKGEPMPEPGLPESFNVLMHE 1258


>gi|189502704|ref|YP_001958421.1| DNA-directed RNA polymerase subunit beta [Candidatus Amoebophilus
            asiaticus 5a2]
 gi|189498145|gb|ACE06692.1| hypothetical protein Aasi_1396 [Candidatus Amoebophilus asiaticus
            5a2]
          Length = 1286

 Score = 1313 bits (3397), Expect = 0.0,   Method: Composition-based stats.
 Identities = 576/1389 (41%), Positives = 829/1389 (59%), Gaps = 139/1389 (10%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
            +   R  F     + + PD +E+Q  S++ F  +   P++R +EGL   F+  FPI    
Sbjct: 1    MKSSRISFAATQSVSEYPDFLEIQLKSFNDFFQLGTPPEKRIDEGLHKVFREHFPIEDSR 60

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G  +LEF+ Y  D PK++  +C+ R +TY+VPLK  LRL+  D D+        +  EQ 
Sbjct: 61   GNFVLEFIDYNLDAPKYEPRECVERGVTYSVPLKAKLRLLRNDNDDDEF-----ETIEQE 115

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +++G++P MT  G+F+I G +R+VVSQ+H+SPG+ F   K    +SG  LY+ RIIP +G
Sbjct: 116  VFLGNIPYMTSQGSFIINGAERVVVSQIHKSPGVFFAQSK---HISGAKLYSARIIPFKG 172

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D  +I++  IDR++K P+T+ L A+G  ++ EIL  F                
Sbjct: 173  AWIEFATDVNNIMYAYIDRKKKFPITTLLRAIGYGTDKEILDLFELSEEIKVTKSTLNQH 232

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            +                           G+KL + +L+S  E  +               
Sbjct: 233  I---------------------------GRKLAARVLRSWSEDFIDEDT----------- 254

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDK 366
              +++  +  E+ +E   ++DE ++E I  S    + +LY + +N   Y  I NTL  D 
Sbjct: 255  -GEVITLDRNEVVLERNSILDETAVELILQSGSSSV-VLYREDINIADYEIIYNTLHKDN 312

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                K+A+  IYR +R  +      A      LFF + +Y L  VGR K+N +L ++   
Sbjct: 313  ANSEKEAVEQIYRQLRSSEPPDEQTAREAIQSLFFSTKRYSLGEVGRYKINTKLGINIAM 372

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            DV  + KEDI+ I+K L+ L N K T+DDID+L NRR+R+VGE L  Q+ LGL RM R+I
Sbjct: 373  DVSVLTKEDILHIVKYLLGLINSKATVDDIDHLSNRRLRTVGEQLYTQFELGLSRMARTI 432

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D +   P DL+NA+ + S +  FF ++ LSQ  + VN LS +TH RR+SALG 
Sbjct: 433  RERMNVRDNEEFKPSDLVNARTLSSVINTFFGTNPLSQFMDQVNPLSEVTHKRRISALGP 492

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RD+H THYGR+CP ET EG NIGL+SSL+  AR+N  GFI TPYRKV 
Sbjct: 493  GGLSRDRAGFEIRDIHYTHYGRLCPVETPEGPNIGLISSLSVHARINEMGFIVTPYRKVQ 552

Query: 607  D--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +    V  +  YL+A +E+   IAQANS ++E G F EE V  R AG+  +V  E I ++
Sbjct: 553  NGVVDVEGNTQYLTAEQEDKVKIAQANSQINEKGHFIEEKVKTRYAGDFPIVGPEDITYM 612

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+VSI+ASLIPFLE++D++R LMG NMQRQ+VPL+K EAP +GTG+E  +A    
Sbjct: 613  DIAPNQIVSISASLIPFLEHNDASRALMGSNMQRQSVPLIKPEAPIIGTGIEQHIAHDFR 672

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
              + A++ G++E VDA +I++      +  L         Y L+K + +NQ TC+N RP+
Sbjct: 673  GLVRAEKDGVIEYVDANKIIVNYDLNEDEKLVSFERASITYPLLKMKGTNQGTCINLRPI 732

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD V++  I+ +G +T+ G+LALGRN+ VAFM W GYN+ED+++ISER+V +DVFTS
Sbjct: 733  VAKGDRVKQGQILCEGYATENGELALGRNLKVAFMSWQGYNYEDAIVISERIVRDDVFTS 792

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHIEEF + ARDTKLG EE+T +IPN+SEE L N+D+ GI+ VG  +  GD+L+GKITPK
Sbjct: 793  IHIEEFTMEARDTKLGEEELTAEIPNLSEEALTNLDKNGIVAVGTSIKEGDVLIGKITPK 852

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+  +PEEKLLRAIFG+KA DV+D SL+VP  + G V+  R+F++   DKN R+ S  +
Sbjct: 853  GEADPSPEEKLLRAIFGDKAGDVKDASLKVPPSMQGVVIKTRLFSKPKSDKNSRAKS--K 910

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISE- 1015
            +++ELL +    +   L   +  +L ++L      G     G +   K   L+++LI + 
Sbjct: 911  KELELLKKSHAKQLTNLRAIMIGKLGKLLESEKSQGVYHQFGDELIAKGKPLTAELIEKN 970

Query: 1016 ---------------------YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                                             +++    V++L   Y T +++L   F+
Sbjct: 971  LFPGKNLYRDESYYNIPEETNLIGEVILDNWTDNKRKNELVKTLVANYNTKRNMLIGDFR 1030

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +   ++ GD++P G+L++ KV+VA KR +Q+GDKMAGRHGNKGIV++++  EDMPFL+D
Sbjct: 1031 REKFALEIGDELPTGILKLAKVYVANKRKLQAGDKMAGRHGNKGIVAKVVREEDMPFLED 1090

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDIVL+PLG+PSRMN+GQI+ET LGWA   LG+K  + I D     D+S   +    
Sbjct: 1091 GTPVDIVLSPLGLPSRMNLGQIYETLLGWAGEKLGRKYATPIFDGATIEDVSKELAEANL 1150

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                              P F                    G++
Sbjct: 1151 ----------------------------------PAF--------------------GKA 1156

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             LYDGLTGE FD+ +TVG IYMLKL+H+V DK++ARS G YSL+TQQPLGG+S  GGQR 
Sbjct: 1157 DLYDGLTGEKFDQQITVGVIYMLKLDHLVDDKMHARSIGPYSLITQQPLGGRSQFGGQRF 1216

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++A+GAA++LQEMLTIKSDDVVGR++ YE+IV G    + G PESFNVL+ E+
Sbjct: 1217 GEMEVWALEAFGAAHILQEMLTIKSDDVVGRSKAYEAIVKGTSFPKPGIPESFNVLIHEL 1276

Query: 1355 QALGLSIDL 1363
            + LGL I L
Sbjct: 1277 RGLGLEITL 1285


>gi|29348143|ref|NP_811646.1| DNA-directed RNA polymerase subunit beta [Bacteroides
            thetaiotaomicron VPI-5482]
 gi|253569583|ref|ZP_04846993.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 1_1_6]
 gi|298386174|ref|ZP_06995731.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 1_1_14]
 gi|41017727|sp|Q8A469|RPOB_BACTN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|29340046|gb|AAO77840.1| DNA-directed RNA polymerase beta chain [Bacteroides thetaiotaomicron
            VPI-5482]
 gi|251841602|gb|EES69683.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 1_1_6]
 gi|298261402|gb|EFI04269.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 1_1_14]
          Length = 1270

 Score = 1312 bits (3396), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1366 (42%), Positives = 821/1366 (60%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKRV-LGRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E  ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEVHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N +VYL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D S
Sbjct: 561  DLSDNGLVYLTAEEEEEKIIAQGNAPLNDDGTFVRNKVKSRQDADFPVVEPSEVDLMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     V  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDDHTNGMVRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKTLGVKFATPIFDGATMDDLDQWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGEQFDQAATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|153805950|ref|ZP_01958618.1| hypothetical protein BACCAC_00195 [Bacteroides caccae ATCC 43185]
 gi|149130627|gb|EDM21833.1| hypothetical protein BACCAC_00195 [Bacteroides caccae ATCC 43185]
          Length = 1270

 Score = 1312 bits (3395), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1366 (42%), Positives = 817/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFNLAEDVKVNKTNLKKVL-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E+ ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEEHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N ++YL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D S
Sbjct: 561  DLSDNGLIYLTAEEEEEKIIAQGNAPLNDDGTFVRNKVKSRQDADFPVVEPAEVDLMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDFVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMILTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     DE     +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDEHANGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D     D+                                 
Sbjct: 1099 AVLGRAGKTLGVKFATPIFDGATMEDLDEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+  TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGEQFDQAATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G    + G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLGLSINLE 1270


>gi|255037203|ref|YP_003087824.1| DNA-directed RNA polymerase subunit beta [Dyadobacter fermentans DSM
            18053]
 gi|254949959|gb|ACT94659.1| DNA-directed RNA polymerase, beta subunit [Dyadobacter fermentans DSM
            18053]
          Length = 1288

 Score = 1311 bits (3393), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1387 (41%), Positives = 830/1387 (59%), Gaps = 138/1387 (9%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               RK F +  +IID PDL+ +Q  S+  F  ++ + ++R  EGL   F   FPI     
Sbjct: 7    KTPRKNFSRINQIIDYPDLLGIQVQSFRDFFSLDTSVEDRSGEGLYKVFAENFPIADSRE 66

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              +LEF+ Y  +PPK+ VD+ + R LTYAVPLK  LRLI  D D         +  EQ +
Sbjct: 67   NFVLEFIDYLLEPPKYSVDESIDRGLTYAVPLKAKLRLICNDADHEEF-----ETIEQEV 121

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            ++G++P MT+ G+FVI G +R++VSQLHRSPG+ F   K     +G  LY+ RIIP +G 
Sbjct: 122  FLGNIPYMTERGSFVINGAERVIVSQLHRSPGVFFSMSK---HTNGSKLYSARIIPFKGS 178

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            W++   D  ++++  IDR++K PVT+ L A+G  S+ +IL  F      S          
Sbjct: 179  WIEFSTDVNNVMYAYIDRKKKFPVTTLLRAIGFGSDKDILDLFGLSEEIS---------- 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                       G++L + +L++  E  V                
Sbjct: 229  -----------------ATPANLKKAVGRRLAARVLRTWTEDFVDEDT------------ 259

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNK 368
             ++V+ +  E+ +E    I    ++ I  S  + I +   D  V +   I NTL  D + 
Sbjct: 260  GEVVSIQRNEVLLERDSTISADDIDVILESGQKSIIMHKEDMNVADYNIIYNTLQKDSSN 319

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              K+A+  IYR +R  +      A  +   LFF   +YDL  VGR ++N +L  DT  DV
Sbjct: 320  SDKEAVEQIYRQLRNAEAPDEQTARDVIQSLFFSDKRYDLGDVGRYRINKKLGSDTSLDV 379

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +   DI++I+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+IKE
Sbjct: 380  RVLTTGDIVSIVKYLIGLINAKAVVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIKE 439

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RR+SALG GG
Sbjct: 440  RMNVRDNEDFKPVDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRMSALGPGG 499

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL  FA+VN  GFIETPYR +   
Sbjct: 500  LSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVFAKVNGMGFIETPYRVIDGS 559

Query: 609  -KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             K+T++++Y++A EE+++YIAQAN+S+D++G+FT E +  R  G+  +V   +  ++D +
Sbjct: 560  GKLTDELIYMTAEEEDSKYIAQANASVDKEGNFTVEKIKTRFEGDFPMVDPSQASYMDVA 619

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
              Q+VS+AASLIPFLE+DD+NR LMG NMQRQ VPLL+ +AP VGTG+E  VA  S A +
Sbjct: 620  ANQIVSVAASLIPFLEHDDANRALMGSNMQRQGVPLLRPQAPIVGTGLERRVAMDSRALV 679

Query: 728  VAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            VA+  G +E VD+ +IV++     E  L         Y L+KF+R+NQ+TC+N +P+V  
Sbjct: 680  VAEGDGEIEFVDSKKIVVKYDRTDEDRLVSFIDDSVTYNLVKFRRTNQDTCLNLQPMVLK 739

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G +V++ + +  G  T+ G+LALGRN+LVAFMPW GYNFED+++ISE++V +D+FTSIHI
Sbjct: 740  GQKVKKGEPLCQGYGTEGGELALGRNLLVAFMPWQGYNFEDAIVISEKVVRDDIFTSIHI 799

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE+  RDTK G EE+T +IPNVSEE +KN+DE GI+ VG EV  GDIL+GKITPKGES
Sbjct: 800  EEFELEVRDTKRGEEELTAEIPNVSEETVKNLDENGIVQVGTEVKEGDILIGKITPKGES 859

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D S + P  + G V+D ++F+R    K ER+    ++++
Sbjct: 860  DPTPEEKLLRAIFGDKAGDVKDASKKAPPSMKGVVIDTKLFSRP--TKEERAKH--KDEL 915

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE---- 1015
             LL +    +   L   +  +L+++  G+ +       G +   K    +   ISE    
Sbjct: 916  RLLMKKYSRDLTALRGRVIDKLVQLTDGKTSSGVKHKFGDELISKGMKFNVRNISENLFP 975

Query: 1016 ------------------YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                                          D    R +  +   Y  ++S +  RFK   
Sbjct: 976  ANNPYRDESQYAVPEEVNLIGDVLTDSWSDDADTNRQISLVLKNYLNARSEVMGRFKRDR 1035

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
              ++ GD++P G++++ KV++A KR ++ GDKMAGRHGNKG+V+RI+  EDMPFL+DGTP
Sbjct: 1036 FALEVGDELPAGIVKLAKVYIAKKRKLKVGDKMAGRHGNKGVVARIVRDEDMPFLEDGTP 1095

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            V+IVLNPLGVPSRMN+GQI+ET L WA + LG++  + I D     +++           
Sbjct: 1096 VNIVLNPLGVPSRMNIGQIYETILAWAGLKLGRRYATPIFDGATEAEVA----------- 1144

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                               AE  ++G+P                        + G++ LY
Sbjct: 1145 -------------------AELKEAGLP------------------------DWGRTYLY 1161

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            +GLTGE FD+PVTVG +YM+KL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEM
Sbjct: 1162 NGLTGEQFDQPVTVGLMYMMKLGHLVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEM 1221

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++A+GA+++LQE+LT+KSDDVVGR + YE+IV G +  +   PESFNVLV E++ L
Sbjct: 1222 EVWALEAFGASHILQEILTVKSDDVVGRAKAYEAIVKGENLPKPNIPESFNVLVHELRGL 1281

Query: 1358 GLSIDLE 1364
             L I L+
Sbjct: 1282 ALEITLD 1288


>gi|88802467|ref|ZP_01117994.1| DNA-directed RNA polymerase beta subunit [Polaribacter irgensii 23-P]
 gi|88781325|gb|EAR12503.1| DNA-directed RNA polymerase beta subunit [Polaribacter irgensii 23-P]
          Length = 1269

 Score = 1310 bits (3391), Expect = 0.0,   Method: Composition-based stats.
 Identities = 585/1370 (42%), Positives = 811/1370 (59%), Gaps = 115/1370 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                  R  F  +  I + PD +++Q  S+  F  +    +ER  EGL   F   FPIT 
Sbjct: 3    TKNTTERINFATSQMIKEYPDFLDIQVKSFQDFFQLQTKAEERGEEGLYKTFMDNFPITD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPP++ + +C+ R LT++VPLK  L+L   D +       +     
Sbjct: 63   TRNHFVLEFLDYFVDPPRYSIQECIERGLTHSVPLKARLKLYCTDPEHEDFETIV----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y+G +P MT  G FVI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP 
Sbjct: 118  QDVYLGTIPYMTNSGAFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D   +++  IDR++K+PVT+   A+G + + +IL  F              
Sbjct: 175  KGSWIEFATDINQVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKAGLK 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              L                           G+KL + +LK+  E  V             
Sbjct: 235  KVL---------------------------GRKLAARVLKTWHEDFVDEDT--------- 258

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTD 365
                ++V+ E  EI  +   ++D++ ++EI  +  + + +   D+   + A I NTL  D
Sbjct: 259  ---GEVVSIERNEIIFDRDTILDKEHIDEIIEAGAKTVLLHKEDNDTADYAIIHNTLQKD 315

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L L+ P
Sbjct: 316  PTNSEKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSEQRYNLGEVGRFRMNTKLQLNEP 375

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             D + + K DII IIK L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+
Sbjct: 376  IDQKVLTKLDIITIIKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAGQFGVGLARMART 435

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG
Sbjct: 436  IRERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALG 495

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN  GFIETPYRKV
Sbjct: 496  PGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFAKVNNLGFIETPYRKV 555

Query: 606  CDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             +G V T++ +YLSA EEE   IAQ+N  L  +G+ T + V  R  G+  +V  ++I+++
Sbjct: 556  ENGVVTTDEPIYLSAEEEEGMKIAQSNLQLSNEGNITLDRVIAREEGDFPVVNPDEINYM 615

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ E+P VGTG+E  VAK S 
Sbjct: 616  DVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGLERRVAKDSR 675

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
              I A+ AG+V+ VDA +I I+     E  L    S    Y L+KF+++NQ T +N +P+
Sbjct: 676  ILINAEGAGVVQYVDANKITIKYDRTEEEKLVSFDSDEISYNLIKFRKTNQGTSINLKPI 735

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  GD V    ++ +G +T  G+LALGRNM VAFMPW GYNFED+++ISER+V ED+FTS
Sbjct: 736  VVRGDRVTEGQVLCEGYATQKGELALGRNMKVAFMPWKGYNFEDAIVISERVVREDIFTS 795

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEVNPGDIL+GKITPK
Sbjct: 796  IHIDEYSLDVRDTKLGIEELTNDIPNVSEEATKDLDENGMIRIGAEVNPGDILIGKITPK 855

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F R   DKN+R    ++
Sbjct: 856  GESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFRRAVKDKNKRLQ--DK 913

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEY 1016
            E +  L      +   L   +  +L  ++ G+ +       G +   K    +  +++  
Sbjct: 914  EAVANLESSFVSQFEGLKDELIEKLFTLISGKTSQGVFNDLGEEVLPKGKKYTLKMLNSV 973

Query: 1017 PRS-QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        D+++   V  L   Y+   + L+   + +   I  GD++P G+L++ K
Sbjct: 974  DDYVHLTGSWTTDKELNDLVGELVHNYKIKVNDLQGSLRRQKFTISVGDELPAGILKLAK 1033

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQ
Sbjct: 1034 VYIAKKRKLKVGDKMAGRHGNKGIVARIVRAEDMPFLEDGTPVDIVLNPLGVPSRMNIGQ 1093

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I+ET LGWA   LG K  + I D  +   I+ +                           
Sbjct: 1094 IYETVLGWAGQKLGTKYATPIFDGASLDQINVITD------------------------- 1128

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                  +GVP                          G + LYDG TG+ FD+P TVG IY
Sbjct: 1129 -----SAGVP------------------------RFGHTYLYDGGTGKRFDQPATVGIIY 1159

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            M+KL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+ +L+E+L
Sbjct: 1160 MIKLGHMIEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSILREIL 1219

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            T+KSDDV+GR + YESIV G    E G PESFNVL+ E++ LGL + LE 
Sbjct: 1220 TVKSDDVMGRAKTYESIVKGEAMPEPGLPESFNVLMHELKGLGLDVRLEE 1269


>gi|196233588|ref|ZP_03132429.1| DNA-directed RNA polymerase, beta subunit [Chthoniobacter flavus
            Ellin428]
 gi|196222258|gb|EDY16787.1| DNA-directed RNA polymerase, beta subunit [Chthoniobacter flavus
            Ellin428]
          Length = 1268

 Score = 1310 bits (3390), Expect = 0.0,   Method: Composition-based stats.
 Identities = 626/1375 (45%), Positives = 849/1375 (61%), Gaps = 146/1375 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             RK+FGK  E  + P+LIE+Q  SY  FL  +++  +R   GLQA FK VFPIT++    
Sbjct: 3    ERKYFGKLREGAEPPNLIEIQLDSYVEFLQTDVSLSKRKETGLQAVFKEVFPITSYDEKV 62

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L+F SYE   PK  + + +    T++ PL +T  L           K     KE+ +YM
Sbjct: 63   TLDFASYEIGEPKLSIREAMREGQTFSAPLHVTFLL-----------KEEHGTKEEKVYM 111

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PLMT  GTFVI G +R+VVSQLHRSPGI F+       L+GK+L++ RIIPD+G W+
Sbjct: 112  GEIPLMTPQGTFVINGAERVVVSQLHRSPGICFESSL---HLNGKVLFSFRIIPDRGSWV 168

Query: 193  DIEFDSKDIIHVRID---RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +++FD+ D+++V +D   RRRK   T+FL ALG  S+ EI+  FY         +     
Sbjct: 169  EVQFDTNDLLYVYLDRRKRRRKFLATTFLRALGYGSDEEIIKLFYTI-------EKLKLS 221

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +  +  KV   + D+  GE  +  + + LT   ++ +   GVK + +         
Sbjct: 222  EGLEEEEIATKVL--ISDVRDGEITVARAFEPLTKATIRQILTLGVKDVQV--------- 270

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                 V+ +  +  I+A                                     L  D  
Sbjct: 271  -----VDTKADDTIIKA-------------------------------------LKKDPA 288

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN---LDT 424
             D ++AL DIYR +RPGD  T   A  +   LFFD  KYDL  VGR K+N +L    +D 
Sbjct: 289  HDEEEALKDIYRRLRPGDPPTVPNARGLLKRLFFDPKKYDLGRVGRYKINQKLQDNGVDV 348

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              D R + KED IA +K L  LR G+GT+DDID+LG+RRVR+VGE+L NQ R+GL R ER
Sbjct: 349  KGDERVMTKEDFIAAMKYLTGLRRGEGTLDDIDHLGSRRVRTVGELLANQCRVGLARTER 408

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             +KER++  D  I+ + PQ LIN K + + + +FF  SQLSQ  +  N L+ +TH RRLS
Sbjct: 409  LVKERMTLFDVNIEGMTPQKLINPKALSAVIRDFFGRSQLSQFMDQTNPLAELTHKRRLS 468

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG E+RDVHP+HYGRICP ET EG NIGL+SS+++FA++N +GFIETPY
Sbjct: 469  ALGPGGLSRDRAGFEVRDVHPSHYGRICPIETPEGPNIGLISSMSTFAKINDFGFIETPY 528

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV +GKV   + YL+   EEN  +AQANS +DE G FT E V  R  G+ + V   K+ 
Sbjct: 529  RKVVNGKVLEHIDYLTGDREENYLVAQANSPIDEKGHFTAEKVSVRYRGDFLEVEPSKVH 588

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D SPKQ+VS+AA LIPFLE+DD+NR LMG NMQRQ VPLL +E+P VGTGME  VA+ 
Sbjct: 589  YMDVSPKQLVSVAAGLIPFLEHDDANRALMGSNMQRQGVPLLVSESPLVGTGMEGKVARD 648

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD-------PSTSGVDIYRLMKFQRSNQNTC 775
            S A IV++  G V  V A  I++       +           G+ +Y L KF RSN  TC
Sbjct: 649  SKAVIVSEANGKVASVSADLIIVTKDGEMPEGKKKLKHDPEEGIYLYDLRKFMRSNAGTC 708

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            VNQ+P+VK G  V++ D+IADGP+T+ G+LALGRN+LVAFMPW+GYNFED++ ISE++V 
Sbjct: 709  VNQKPIVKKGQHVKKGDVIADGPNTENGELALGRNVLVAFMPWNGYNFEDAITISEKVVK 768

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ED++TSIHI+EFE+ ARDTKLGPEEITRDIPNVSEE L+N+   G+I VGAEV PGDILV
Sbjct: 769  EDIYTSIHIDEFEIGARDTKLGPEEITRDIPNVSEEALRNLGPDGVIRVGAEVKPGDILV 828

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPK E+ + PEE+LLRAIFGEKA DV+DTSL VPSG  G V+DV++ +R  I + + 
Sbjct: 829  GKITPKSETELAPEERLLRAIFGEKAADVKDTSLTVPSGTYGIVMDVKVSSRKEITRVKL 888

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA-------VSGPKGFKKSTVL 1008
            S +  ++Q +++  D    +  L   +   L  IL G+          +G      +  +
Sbjct: 889  SPTESKKQAKVIEEDYTKRKDELHEQLTEALSNILLGEKIPLDVVNAQTGEIIIPANRKI 948

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +  L+ +     +    +    ++  +  +  Q+E   + LE   +  ++K++ GDD+ P
Sbjct: 949  TKTLLRKLA-GVYDHVDIDPSPIRNKIREIIGQFEHKFAELELEHERSMDKVESGDDVDP 1007

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G+++ VKV++A KR +  GDKMAGRHGNKG+V+RI+P EDMPFL DGTPV+I LNPLGVP
Sbjct: 1008 GIIKQVKVYIASKRKLSVGDKMAGRHGNKGVVARIVPEEDMPFLADGTPVEICLNPLGVP 1067

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMNVGQ+ ETHLG A   LG K+ + + D      I       +KV G           
Sbjct: 1068 SRMNVGQVLETHLGVAAKALGFKVATPVFDGIHESQIFQYLKDAKKVEG----------- 1116

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F    E              +G++ ++DG TG+ F++P
Sbjct: 1117 ----------------------FTWVTE--------------TGKAQVFDGRTGDAFEQP 1140

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VGYIYMLKL H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1141 IVVGYIYMLKLGHLVADKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWALEAYGAA 1200

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            Y LQE+LT+KSDDV GRTR+YESIV G+++ E GTPESFNVL+KEMQ+LGL + +
Sbjct: 1201 YTLQELLTVKSDDVQGRTRIYESIVKGDNSLEAGTPESFNVLIKEMQSLGLDVKV 1255


>gi|188995435|ref|YP_001929687.1| DNA-directed RNA polymerase subunit beta [Porphyromonas gingivalis
            ATCC 33277]
 gi|226699429|sp|B2RL45|RPOB_PORG3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|188595115|dbj|BAG34090.1| DNA-directed RNA polymerase beta subunit [Porphyromonas gingivalis
            ATCC 33277]
          Length = 1269

 Score = 1310 bits (3389), Expect = 0.0,   Method: Composition-based stats.
 Identities = 564/1372 (41%), Positives = 800/1372 (58%), Gaps = 122/1372 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                R+   F      +  PD +EVQ  S+  FL ++  P+ R  EGL   F   FPIT 
Sbjct: 5    TNNKRI--NFASIKNPLFYPDFLEVQLKSFHDFLQLDTPPERRKKEGLYKVFAENFPITD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPPK+ +++CL R LTY+VPLK  L+L   D D    A  I     
Sbjct: 63   TRNNFVLEFLDYYIDPPKYSIEECLSRGLTYSVPLKAKLKLYCTDPDHEDFATVI----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +++G +P MT  GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVFLGPIPYMTSSGTFVINGAERVIVSQLHRSPGVFFGQSL---HTNGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFEADKDILDIFNLAEEVKVTKANLK 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              +                           G+KL + ++ +  +         SD   G 
Sbjct: 235  KCI---------------------------GRKLAARVINTYIDD-------LSDEDTG- 259

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVT 364
                ++V+ E   + ++    + E ++E I +S  + I +L+ +  N + Y  I NTL  
Sbjct: 260  ----EVVSMERITVVVDREVELTEDNIEAILNSNTQTI-LLHRNDSNTSDYSIIFNTLQK 314

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D     K+AL  +YR +R  + +  + A  +   LFF   +YDL  VGR ++N +LNL+ 
Sbjct: 315  DPCNSEKEALYYVYRQLRNAEPADDASAREVITNLFFSDKRYDLGDVGRYRINKKLNLNI 374

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              D++ +  EDII IIK L++L N K ++DDID+L NRRVR+VGE L NQ+ +GL RM R
Sbjct: 375  DPDIKVLTNEDIIEIIKYLIELVNSKASVDDIDHLSNRRVRTVGEQLYNQFGIGLARMAR 434

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++++R++  D +   P DL+NAK + S V  FF ++ LSQ  +  N L+ ITH RRLSAL
Sbjct: 435  TVRDRMNVRDNEVFTPIDLVNAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSAL 494

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+++  GFI TPYR+
Sbjct: 495  GPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKISDLGFITTPYRE 554

Query: 605  VCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V +GKV    N + Y +A EEE + +AQ N+ LDE+G F  E V  R   +  LV  +++
Sbjct: 555  VKNGKVDFSDNGLKYYTAEEEEEKTVAQGNAPLDENGRFVRERVKARYESDFPLVTPDEV 614

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SP Q+ SIAA+LIPFLE+DD+NR LMG NM RQAVPLL+ E+P VGTG+E  + K
Sbjct: 615  DLMDVSPTQIASIAAALIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGIEGKLVK 674

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             S   IVA+R G V  VDA  I IR     + +       +  Y L K++++NQ+T ++ 
Sbjct: 675  DSRTQIVAERGGEVVFVDASCIKIRYDRTADEEFVSFDDAIVTYYLPKYRKTNQSTTIDL 734

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
             P+   GD V    I+ +G ST  G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED 
Sbjct: 735  HPICSKGDRVEAGQILTEGYSTQGGELALGRNVQVAYMPWKGYNYEDAIVLNERMVREDF 794

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTS+H++E+ +  R+TK G EE+T DIPNVSE+  +++DE GI+ +GA + PGDIL+GKI
Sbjct: 795  FTSVHVDEYILEVRETKRGLEELTSDIPNVSEDATRDLDENGIVRIGAHIEPGDILIGKI 854

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F++    K   S +
Sbjct: 855  TPKGESDPTPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIDTKLFSKAAKKK---SRT 911

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLI 1013
              +E +  L       Q  L   +  +L E+  G+           +  K  + L+   +
Sbjct: 912  STKETVSKLDETYAKRQQQLHERLIEKLTELTKGKTCCGVKDYLNVELIKAGSKLTKKDL 971

Query: 1014 SEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                 +         D      ++++ V Y      +E   + +      GD++P G+++
Sbjct: 972  EALDFNVIQLSDWTNDAHTNELIKAVAVNYLKHSKEIEAELRRRKLDETIGDELPAGIVQ 1031

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            + KV++A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL DGTPVDI LNPLGVPSRMN
Sbjct: 1032 MAKVYIAKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLADGTPVDICLNPLGVPSRMN 1091

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQIFE  L WA   +  K  + I D  +  D++                          
Sbjct: 1092 LGQIFEAVLAWAGRKMNVKFATPIFDGASLNDMNEWTD---------------------- 1129

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    K+G+P                          G++ LYDG TGE FD+P TVG
Sbjct: 1130 --------KAGLP------------------------RDGKTYLYDGGTGERFDQPATVG 1157

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+++LQ
Sbjct: 1158 VTYFLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHILQ 1217

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            E+LT+KSDDVVGR++ YE+IV G+     G PES NVL+ E++ LGLS  L+
Sbjct: 1218 EILTVKSDDVVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELKGLGLSFSLD 1269


>gi|34540221|ref|NP_904700.1| DNA-directed RNA polymerase subunit beta [Porphyromonas gingivalis
            W83]
 gi|41017634|sp|Q7MX27|RPOB_PORGI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|34396533|gb|AAQ65599.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas gingivalis
            W83]
          Length = 1269

 Score = 1309 bits (3387), Expect = 0.0,   Method: Composition-based stats.
 Identities = 563/1372 (41%), Positives = 799/1372 (58%), Gaps = 122/1372 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                R+   F      +  PD +EVQ  S+  FL ++  P+ R  EGL   F   FPIT 
Sbjct: 5    TNNKRI--NFASIKNPLFYPDFLEVQLKSFHDFLQLDTPPERRKKEGLYKVFAENFPITD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPPK+ +++CL R LTY+VPLK  L+L   D D    A  I     
Sbjct: 63   TRNNFVLEFLDYYIDPPKYSIEECLSRGLTYSVPLKAKLKLYCTDPDHEDFATVI----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +++G +P MT  GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVFLGPIPYMTSSGTFVINGAERVIVSQLHRSPGVFFGQSL---HTNGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFEADKDILDIFNLAEEVKVTKANLK 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              +                           G+KL + ++ +  +         SD   G 
Sbjct: 235  KCI---------------------------GRKLAARVINTYIDD-------LSDEDTG- 259

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVT 364
                ++V+ E   + ++    + E ++E I +S  + I +L+ +  N + Y  I NTL  
Sbjct: 260  ----EVVSMERITVVVDREVELTEDNIEAILNSNTQTI-LLHRNDSNTSDYSIIFNTLQK 314

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D     K+AL  +YR +R  + +  + A  +   LFF   +YDL  VGR ++N +LNL+ 
Sbjct: 315  DPCNSEKEALYYVYRQLRNAEPADDASAREVITNLFFSDKRYDLGDVGRYRINKKLNLNI 374

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              D++ +  EDII IIK L++L N K ++DDID+L NRRVR+VGE L NQ+ +GL RM R
Sbjct: 375  DPDIKVLTNEDIIEIIKYLIELVNSKASVDDIDHLSNRRVRTVGEQLYNQFGIGLARMAR 434

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++++R++  D +   P DL+NAK + S V  FF ++ LSQ  +  N L+ ITH RRLSAL
Sbjct: 435  TVRDRMNVRDNEVFTPIDLVNAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSAL 494

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+++  GFI TPYR+
Sbjct: 495  GPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKISDLGFITTPYRE 554

Query: 605  VCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V +GKV    N + Y +A EEE + +AQ N+ LDE+G F  E V  R   +  LV  +++
Sbjct: 555  VKNGKVDFSDNGLKYYTAEEEEEKTVAQGNAPLDENGRFVRERVKARYESDFPLVTPDEV 614

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SP Q+ SIAA+LIPFLE+DD+NR LMG NM RQAVPLL+ E+P VGTG+E  + K
Sbjct: 615  DLMDVSPTQIASIAAALIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGIEGKLVK 674

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             S   IVA+R G V  VDA  I IR     + +       +  Y L K++++NQ+T ++ 
Sbjct: 675  DSRTQIVAERGGEVVFVDASCIKIRYDRTADEEFVSFDDAIVTYYLPKYRKTNQSTTIDL 734

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
             P+   GD V    I+ +G ST  G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED 
Sbjct: 735  HPICSKGDRVEAGQILTEGYSTQGGELALGRNVQVAYMPWKGYNYEDAIVLNERMVREDF 794

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTS+H++E+ +  R+TK G EE+T DIPNVSE+  +++DE GI+ +GA + PGDIL+GKI
Sbjct: 795  FTSVHVDEYILEVRETKRGLEELTSDIPNVSEDATRDLDENGIVRIGAHIEPGDILIGKI 854

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGES  TPEEKLLRAIFG+KA DV+D SL+    + G V+D ++F++    K   S +
Sbjct: 855  TPKGESDPTPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIDTKLFSKAAKKK---SRT 911

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLI 1013
              +E +  L       Q  L   +  +L E+  G+           +  K  +  +   +
Sbjct: 912  STKEAVSKLDETYAKRQQQLHERLIDKLTELTKGKTCCGVKDYLNVELIKAGSKFAKKDL 971

Query: 1014 SEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                 +         D      ++++ V Y      +E   + +      GD++P G+++
Sbjct: 972  EALDFNVIQLSDWTNDAHTNELIKAVAVNYLKHSKEIEAELRRRKLDETIGDELPAGIVQ 1031

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            + KV++A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL DGTPVDI LNPLGVPSRMN
Sbjct: 1032 MAKVYIAKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLADGTPVDICLNPLGVPSRMN 1091

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQIFE  L WA   +  K  + I D  +  D++                          
Sbjct: 1092 LGQIFEAVLAWAGRKMNVKFATPIFDGASLNDMNEWTD---------------------- 1129

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    K+G+P                          G++ LYDG TGE FD+P TVG
Sbjct: 1130 --------KAGLP------------------------RDGKTYLYDGGTGERFDQPATVG 1157

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+++LQ
Sbjct: 1158 VTYFLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHILQ 1217

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            E+LT+KSDDVVGR++ YE+IV G+     G PES NVL+ E++ LGLS  L+
Sbjct: 1218 EILTVKSDDVVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELKGLGLSFSLD 1269


>gi|332042972|gb|EGI79170.1| DNA-directed RNA polymerase, beta subunit [Lacinutrix algicola
            5H-3-7-4]
          Length = 1270

 Score = 1308 bits (3386), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1368 (42%), Positives = 810/1368 (59%), Gaps = 119/1368 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F       + PD +++Q  S+  F  +    +ER NEGL   F   FPIT      
Sbjct: 7    ERLNFSSIINRTEYPDFMDIQIKSFQDFFQLETKSEERGNEGLYNTFMENFPITDTRNQF 66

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +++C+ R LTY+VPLK  L+L   D +       +     Q +Y+
Sbjct: 67   VLEFLDYFVDPPRYAIEECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVYL 121

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTF I G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W+
Sbjct: 122  GTIPYMTPSGTFCINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSWI 178

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D   +++  IDR++K+PVT+   A+G + + +IL  F                L  
Sbjct: 179  EFATDINQVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKSGLKKVL-- 236

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +L +  E  V                 +
Sbjct: 237  -------------------------GRKLAARVLNTWYEDFVDEDT------------GE 259

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ E  EI ++    +D+ ++EEI    ++ I +L+ ++     Y  I NTL  D    
Sbjct: 260  VVSIERNEIVLDRDTELDKDNIEEILEIGVKTI-LLHKETAQQGDYAIIHNTLQKDPTNS 318

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +Y L  VGR +MN +L LD   D +
Sbjct: 319  EKEAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYSLGEVGRYRMNKKLQLDIGMDKQ 378

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + KEDII IIK L++L N K  IDDID+L NRRVR+VGE L +Q+ +GL RM R+I+ER
Sbjct: 379  VLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSSQFGVGLARMARTIRER 438

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 439  MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 498

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL+ +A+VN+ GFIETPYRKV DG 
Sbjct: 499  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVYAKVNSMGFIETPYRKVTDGV 558

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            V   +   YLSA EEE + IAQA   +DE+G    + V  R  G+  ++  + I + D +
Sbjct: 559  VDIKSTPTYLSAEEEEEKLIAQATVDVDENGKILHDKVIARMEGDFPVMDPKDIHYTDVA 618

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ +AP VGTG+E  VA  S   I
Sbjct: 619  PNQISSISASLIPFLEHDDANRALMGSNMMRQAVPLLRPQAPIVGTGLERQVASDSRVLI 678

Query: 728  VAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I+I+     +       S V  Y L+KF+++NQ T +N +P+VK 
Sbjct: 679  NAEGNGVVEYVDAKEIIIKYERTEDEAKVSFDSDVKSYPLVKFRKTNQGTSINLKPIVKK 738

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD+V++  ++++G +T  G+LALGRNM VAFMPW GYNFED+++ISE++V ED+FTSIHI
Sbjct: 739  GDKVKKGQVLSEGYATQNGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSIHI 798

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDIL+GKITPKGES
Sbjct: 799  DEYSLDVRDTKLGNEELTNDIPNVSEEATKDLDENGMIRIGAEVKPGDILIGKITPKGES 858

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              TPEEKLLRAIFG+KA DV+D SL+    + G V++ ++F+R    K++R  + ++E I
Sbjct: 859  DPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVVINKKLFSRA--IKDKRKRAQDKEDI 916

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L    + +   L   +  +L  I+ G+ +       G +   K    +  +++     
Sbjct: 917  AQLETVYNIKFDELQSVLVEKLFAIVNGKTSQGIFNDLGEEVLPKGKKFTLKMLNAVDDY 976

Query: 1020 QWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      D+   + V  L   Y+  ++ L+   + +   I  GD++P G++++ KV+
Sbjct: 977  THLTGGTWTTDDHTNKLVADLIHNYKIKENDLQGSLRREKFTISVGDELPAGIIKLAKVY 1036

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+
Sbjct: 1037 IAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIY 1096

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ET LGWA   LG+   + I D  +   I+                               
Sbjct: 1097 ETVLGWAGQDLGRTYATPIFDGASIDQINEFTD--------------------------- 1129

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               ++G+P                          G + LYDG TGE FD+P TVG IYML
Sbjct: 1130 ---EAGIP------------------------RYGHTYLYDGGTGERFDQPATVGVIYML 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+
Sbjct: 1163 KLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            KSDDVVGR + YE+IV G    + G PESFNVL+ E++ LGL I LE 
Sbjct: 1223 KSDDVVGRAKTYEAIVKGEPMPDPGLPESFNVLMHELKGLGLDIRLEE 1270


>gi|325280608|ref|YP_004253150.1| DNA-directed RNA polymerase subunit beta [Odoribacter splanchnicus
            DSM 20712]
 gi|324312417|gb|ADY32970.1| DNA-directed RNA polymerase subunit beta [Odoribacter splanchnicus
            DSM 20712]
          Length = 1270

 Score = 1308 bits (3385), Expect = 0.0,   Method: Composition-based stats.
 Identities = 570/1373 (41%), Positives = 800/1373 (58%), Gaps = 119/1373 (8%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
                  R+   F      +  PD +EVQ  S+  F  +   P+ R NEGL   FK  FPI
Sbjct: 3    SNTSNKRI--SFASTKNQLQYPDFLEVQLKSFKDFFQLGTTPENRKNEGLYTVFKENFPI 60

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            T      +LEF+ Y  DPP++ +D+CL + LTY  PLK  L+L   D +       I   
Sbjct: 61   TDTRNNFVLEFLDYFIDPPRYSIDECLEQGLTYGAPLKAKLKLYCTDPEHEDFDTVI--- 117

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
              + +Y+G++P MT  GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RII
Sbjct: 118  --EDVYLGNVPYMTPKGTFVINGAERVIVSQLHRSPGVFFGQS---VHANGTKLYSARII 172

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDF 244
            P +G W++   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F            
Sbjct: 173  PFKGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFETDKDILQIF------------ 220

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                           ++  +    TG + +  G++L + +LK+  E  V           
Sbjct: 221  --------------DLADEINVSKTGLKKV-VGRRLAARVLKTWVEDFVDEDT------- 258

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLV 363
                  ++V+ E  EI ++   V++ + ++ I  S  + I +      + + A I NTL 
Sbjct: 259  -----GEVVSIERNEIIVDRETVLENEHIDAIVDSGAKTILLHKEKQNLADYAIIYNTLQ 313

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D     K+A++ IYR +R  +    + A  + + LFF   +YDL  VGR K+N +L L 
Sbjct: 314  KDPCNSEKEAVMHIYRQLRSSEPPDEATARDVIDKLFFSDKRYDLGDVGRYKLNKKLGLS 373

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            T   VR + KED+I IIK L+ L N +  +DDID+L NRRVR+VGE L NQ+ +GL RM 
Sbjct: 374  TDPAVRVLTKEDMIEIIKYLIKLLNARTDVDDIDHLSNRRVRTVGEQLYNQFGVGLARMA 433

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            R+I+ER++  D +   P DLIN+K + S +  FF ++ LSQ  +  N L+ ITH RR+SA
Sbjct: 434  RTIRERMNVRDNEVFTPVDLINSKILSSVINSFFGTNALSQFMDQTNPLAEITHKRRMSA 493

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFIETPYR
Sbjct: 494  LGPGGLSRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFIETPYR 553

Query: 604  KVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            KV  G V      V YLSA EEE   IAQAN+ +D++G F  +    R  G+  +   E 
Sbjct: 554  KVEAGVVDLSPEGVKYLSAEEEEGLVIAQANAKIDDEGHFVNKRAKSRKDGDFPVEEIEN 613

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            ++ +D +P Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP++K +AP VGTG+E  + 
Sbjct: 614  VNLMDVAPNQIASIAASLIPFLEHDDANRALMGSNMMRQAVPIIKPQAPIVGTGLEGALV 673

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            + S   IVA+  G+V+ VD  RIVI+     E            Y L K++R+NQ+T + 
Sbjct: 674  RDSRTQIVAEGPGVVDFVDGRRIVIKYDQTEEERFVSFDGDTKEYVLPKYKRTNQSTTMT 733

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
             RP+V+ G  V   +I+ +G S++ G+LALGRN+ VA+MPW GYN+ED+++ISE +V  D
Sbjct: 734  LRPIVRKGQRVEEGEILTEGYSSEGGELALGRNLKVAYMPWKGYNYEDAIVISENIVRND 793

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            VFTS+H++E+ +  R+TK G EE+T DIPNVSE+  K++DE GII +GA V PGDIL+GK
Sbjct: 794  VFTSVHVDEYSLEVRETKRGLEELTADIPNVSEDATKDLDENGIIRIGARVKPGDILIGK 853

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ITPKGES  +PEEKLLRAIFG+KA DV+D SL+    +SG ++D ++F R  +  + +S 
Sbjct: 854  ITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLSGVIIDKKLFQR--MIGDRKSK 911

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDL 1012
            +  +  +  +    + +   L   +  +L E+  G+ +             K    +   
Sbjct: 912  AAGKTILAEIDEQFERKVGDLTDLLIDKLFELTNGKTSQGVKNYLNEDVIPKGVKFTLKT 971

Query: 1013 ISEYPRSQWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +      +        D++    +  L   +      +E + K K      GD++P G++
Sbjct: 972  LQNLNYLEINPNKWTTDKQKNDMIRDLLHNFVIKYKEIEGQMKRKKYNATVGDELPSGII 1031

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ KV+VA KR +Q GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDI LNPLGVPSRM
Sbjct: 1032 KMAKVYVAKKRKLQIGDKMAGRHGNKGIVSRVVRVEDMPFLADGTPVDICLNPLGVPSRM 1091

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQIFE  LGWA   LG K  + I D  +  DI+                         
Sbjct: 1092 NLGQIFEAVLGWAGKELGLKFATPIFDGASLDDIN------------------------- 1126

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                 A   K+GVP                          G + LYDG TGE FD+P TV
Sbjct: 1127 -----AYTDKAGVP------------------------RYGTTYLYDGGTGERFDQPATV 1157

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++L
Sbjct: 1158 GVTYFLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHIL 1217

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            QE+LT+KSDDV+GRT+ YE IV G      G PESFNVL+ E++ LGLS++L 
Sbjct: 1218 QEILTVKSDDVMGRTKTYEHIVKGEPMPTPGLPESFNVLLHELRGLGLSVNLI 1270


>gi|212695312|ref|ZP_03303440.1| hypothetical protein BACDOR_04852 [Bacteroides dorei DSM 17855]
 gi|237711666|ref|ZP_04542147.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 9_1_42FAA]
 gi|237725892|ref|ZP_04556373.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. D4]
 gi|265753086|ref|ZP_06088655.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_33FAA]
 gi|212662222|gb|EEB22796.1| hypothetical protein BACDOR_04852 [Bacteroides dorei DSM 17855]
 gi|229435700|gb|EEO45777.1| DNA-directed RNA polymerase subunit beta [Bacteroides dorei
            5_1_36/D4]
 gi|229454361|gb|EEO60082.1| DNA-directed RNA polymerase subunit beta [Bacteroides sp. 9_1_42FAA]
 gi|263236272|gb|EEZ21767.1| DNA-directed RNA polymerase, beta subunit [Bacteroides sp. 3_1_33FAA]
          Length = 1270

 Score = 1308 bits (3384), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1366 (42%), Positives = 818/1366 (59%), Gaps = 117/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      +  PD +EVQ  S+  FL ++  P++R N+GL   F   FPI       
Sbjct: 8    QRVNFASIKNPMKYPDFLEVQLKSFQDFLQLDTPPEKRKNDGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP + +D+CL R LTY+VPLK  L+L   D D       I     Q +Y+
Sbjct: 68   VLEFLDYYIDPPHYSIDECLERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVYL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTPKGTFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                   
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAVGFENDKDILEIF------------------- 220

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                    ++  +    T  + +  G+KL + +LK+  E  V                 +
Sbjct: 221  -------NLAEDVKVNKTNLKKV-VGRKLAARVLKTWTEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   VI+E+ ++EI  S +++I +   + + ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVIEEEHIDEIIDSGVQNILVHKEEANSSDYSIIFNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +L L T  DV+ 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGEVGRYRINKKLGLTTDMDVKV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + K+DII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKQDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAIGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RRLSALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DGKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINELGFISTPYRKVADGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                  + YL+A EEE++ IAQ N+ LD++G F  E V  R   +  +V  ++++ +D S
Sbjct: 561  DISDEGIEYLTAEEEEDKIIAQGNAPLDDEGKFVREKVKARRDADYPVVTPDQVELMDVS 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRTEAPIVGTGIEKQLVEDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I I   R+ + +       +  YR+ KF+++NQ+  ++ RP    
Sbjct: 681  AAEGDGVVEYVDATTIRILYDRNEDEEFVSFEPALKEYRIPKFRKTNQSMTIDLRPTCDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST  G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTQGGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ VGA + PGDIL+GKITPKGES
Sbjct: 801  DEYILEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRVGARIEPGDILIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + K+    + ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSR--VIKSRSEKNADKAIL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              L  + +++   L   +  +L+ +  G+ +       G +   K    +   +     +
Sbjct: 919  PKLNDEFEEKAAKLKDILIEKLLVLTNGKVSQGVKDYLGTEVIAKGAKFTKRDLESLDYT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D      +  L + Y      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  IIQLSKWTADAHKNDMIRDLVMNYLKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKGIVSR++  EDMPFL DGTPVDIVLNPLGVPSRMN+GQIFE
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLADGTPVDIVLNPLGVPSRMNIGQIFE 1098

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   LG K  + I D  +  D++                                
Sbjct: 1099 AVLGRAGKELGVKFATPIFDGASMDDLNEWTD---------------------------- 1130

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K+G+P                           ++ L DG TGE FD+P TVG  YMLK
Sbjct: 1131 --KAGLP------------------------RYCKTYLCDGGTGERFDQPATVGVTYMLK 1164

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GAA++LQE+LTIK
Sbjct: 1165 LGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGAAHILQEILTIK 1224

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI+LE
Sbjct: 1225 SDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSINLE 1270


>gi|83816372|ref|YP_445876.1| DNA-directed RNA polymerase subunit beta [Salinibacter ruber DSM
            13855]
 gi|83757766|gb|ABC45879.1| DNA-directed RNA polymerase, beta subunit [Salinibacter ruber DSM
            13855]
          Length = 1335

 Score = 1307 bits (3383), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1368 (42%), Positives = 828/1368 (60%), Gaps = 118/1368 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R+ F   PE+ D PD ++VQ  ++  F+  ++ P +R + GLQA F   FPI        
Sbjct: 69   RESFADIPEVWDYPDFLDVQLKTFHDFVQDDVPPADREDVGLQAVFNEHFPIKDNRDRYT 128

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFV+YE D PK  V++C+ + LTY++PLK TLRL   + +    A    +   Q +Y+G
Sbjct: 129  LEFVNYELDAPKHTVEECIAQGLTYSIPLKATLRLTSKEEEGGEEAIEAIE---QEVYLG 185

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LP MT  GTF++ G +R++VSQLHRSPG  F+ +      +G  L++ R+IP +G WM+
Sbjct: 186  TLPFMTDRGTFIVNGAERVIVSQLHRSPGAFFEKE---IHSNGTELFSARVIPFRGSWME 242

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D +D++   +DR++KVPVT+ L ALG  S+ EI+  F          +         
Sbjct: 243  FSTDVRDVLWAYVDRKKKVPVTTLLRALGFSSDEEIVKMFDLADAVDIGDEDEFEEHLGR 302

Query: 253  DLMVGAKVSS--SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +L     +     +VD DTGE V E  ++                               
Sbjct: 303  ELATSVTIEKTIEIVDEDTGEVVDEEMER------------------------------- 331

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN---NNAYIRNTLVTDKN 367
                    E+ + A   ++E   EE+   ++  + ++  D  +   + + +  TL  D +
Sbjct: 332  --------EVLLPAEHELEEGDWEELDEYDVSRLYLVREDVEDEALDKSTLVETLQKDSS 383

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               ++AL  IY  +R  +      A      LFF+ D+YDL  VGR +MN RL++D   D
Sbjct: 384  HTEEEALEVIYEKLRGSEAPDLDSAREALERLFFNEDRYDLGDVGRHRMNARLDVDVDTD 443

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KED++ I++ L+ L+NG+ T DDID+L NRRV+SVGE L +Q+ LGL RM R+IK
Sbjct: 444  EKVLTKEDVVGIVRELIRLQNGESTADDIDHLSNRRVKSVGEQLGSQFSLGLARMARTIK 503

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D D   P+DL+NA+ + S +  FF ++QLSQ  +  N+L+ +TH RR+SALG G
Sbjct: 504  ERMNLRDADKFTPKDLVNARTIESVINTFFGTNQLSQFMDQTNALAEMTHKRRMSALGPG 563

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH THYGR+CP ET EG NIGL+ SL   + +N +GF+ETPYR V D
Sbjct: 564  GLTRERAGFEVRDVHHTHYGRLCPIETPEGPNIGLMLSLCVHSTINDFGFLETPYRVVED 623

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            G+VT+ V YLSA EE+   +AQAN+ + +DG F  + V CR  G+  +V  E++D++D +
Sbjct: 624  GRVTDRVEYLSAEEEDQATVAQANAPIGDDGHFERDEVRCRHQGDFPIVEPEEVDYMDVA 683

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+VS +ASL+PFL ++D+NR LMG NMQRQ VPLL++++P VGTG+E  VAK S + +
Sbjct: 684  PNQIVSPSASLVPFLSHNDANRALMGSNMQRQGVPLLRSDSPIVGTGLEGRVAKDSRSCV 743

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLD---PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            VA+  G+VE VDA R+V+R  E            V  Y L KF+R+NQ TC+NQ+P+V+ 
Sbjct: 744  VAEGEGVVEYVDAERLVVRYDEEQDKTDLTFGEPVQEYELTKFRRTNQGTCMNQKPIVQA 803

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V   +++ DG + + G+LALG+N+L AFMPWHGYN+ED+++ISER+V++DV+TS+HI
Sbjct: 804  GDRVEEGEVLTDGFAMEKGELALGKNVLCAFMPWHGYNYEDAIVISERLVADDVYTSVHI 863

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE   RDTK G EE+TR+IPNVSEE  K++DE GI+ VGAE+ PGDI+VGKITPKGE+
Sbjct: 864  EEFEHEVRDTKRGEEELTREIPNVSEEATKDLDERGIVRVGAEITPGDIIVGKITPKGET 923

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT-VVDVRIFNRHGIDKNERSISVEREQ 963
              TPEEKLLRAIFG+KA DV+D SL+   G+ G  V+D R+F+R   + +  S  +E ++
Sbjct: 924  DPTPEEKLLRAIFGDKAGDVKDASLKAKPGMEGGVVIDTRLFSRR--ELDPASKKMEEKR 981

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +E +  D + +   L+   + +   ++      G     G     +      D   E   
Sbjct: 982  LENIESDHERKLADLNERFWEKFFALVEDATSAGLEDREGEVLLTEGADFEEDAFDEVDP 1041

Query: 1019 SQWWQFA--VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            S     A   +DE++   + +L   Y++ +  +E   K +  +++ GD++P GV+++ KV
Sbjct: 1042 SDLSTRAEFTEDEELNDQISTLLRNYKSRRRDIEGTTKRQKHQVEMGDELPSGVVQMAKV 1101

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA K+ I+ GDKMAGRHGNKG++++I P EDMPFL DGTPVD+VLNPLGVPSRMN+GQI
Sbjct: 1102 YVARKKKIEVGDKMAGRHGNKGVIAKIAPVEDMPFLDDGTPVDLVLNPLGVPSRMNLGQI 1161

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG K  + I D  +  D+                               
Sbjct: 1162 YETLLGWAGDRLGVKYATPIFDGASLEDVGDELE-------------------------- 1195

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                K+G+P                          G+  LYDG TGEPFD   TVG IYM
Sbjct: 1196 ----KAGLP------------------------RDGKVQLYDGRTGEPFDEKTTVGQIYM 1227

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KL H+V DK++ARS G YSL+TQQPLGGK+  GGQRLGEMEVW + AYGA+  LQEMLT
Sbjct: 1228 MKLEHLVEDKMHARSIGPYSLITQQPLGGKAQFGGQRLGEMEVWALYAYGASNTLQEMLT 1287

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             KSDDV GR+  YESIV G +    G PESFNVLV+E+Q LGL + L+
Sbjct: 1288 FKSDDVEGRSEAYESIVKGENLPSPGVPESFNVLVRELQGLGLEVTLD 1335


>gi|294507786|ref|YP_003571844.1| DNA-directed RNA polymerase beta chain [Salinibacter ruber M8]
 gi|294344114|emb|CBH24892.1| DNA-directed RNA polymerase beta chain [Salinibacter ruber M8]
          Length = 1335

 Score = 1307 bits (3382), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1368 (42%), Positives = 828/1368 (60%), Gaps = 118/1368 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R+ F   PE+ D PD ++VQ  ++  F+  ++ P +R + GLQA F   FPI        
Sbjct: 69   RESFADIPEVWDYPDFLDVQLKTFHDFVQDDVPPADREDVGLQAVFNEHFPIKDNRDRYT 128

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFV+YE D PK  V++C+ + LTY++PLK TLRL   + +    A    +   Q +Y+G
Sbjct: 129  LEFVNYELDAPKHTVEECIAQGLTYSIPLKATLRLTSKEEEGGEEAIEAIE---QEVYLG 185

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LP MT  GTF++ G +R++VSQLHRSPG  F+ +      +G  L++ R+IP +G WM+
Sbjct: 186  TLPFMTDRGTFIVNGAERVIVSQLHRSPGAFFEKE---IHSNGTELFSARVIPFRGSWME 242

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D +D++   +DR++KVPVT+ L ALG  S+ EI+  F          +         
Sbjct: 243  FSTDVRDVLWAYVDRKKKVPVTTLLRALGFSSDEEIVKMFDLADAVDIGDEDEFEEHLGR 302

Query: 253  DLMVGAKVSS--SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +L     +     +VD DTGE V E  ++                               
Sbjct: 303  ELATSVTIEKTIEIVDEDTGEVVDEEMER------------------------------- 331

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN---NNAYIRNTLVTDKN 367
                    E+ + A   ++E   EE+   ++  + ++  D  +   + + +  TL  D +
Sbjct: 332  --------EVLLPAEHELEEGDWEELDEYDVSRLYLVREDVEDEALDKSTLVETLQKDSS 383

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               ++AL  IY  +R  +      A      LFF+ D+YDL  VGR +MN RL++D   D
Sbjct: 384  HTEEEALEVIYEKLRGSEAPDLDSAREALERLFFNEDRYDLGDVGRHRMNARLDVDVDTD 443

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KED++ I++ L+ L+NG+ T DDID+L NRRV+SVGE L +Q+ LGL RM R+IK
Sbjct: 444  EKVLTKEDVVGIVRELIRLQNGESTADDIDHLSNRRVKSVGEQLGSQFSLGLARMARTIK 503

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D D   P+DL+NA+ + S +  FF ++QLSQ  +  N+L+ +TH RR+SALG G
Sbjct: 504  ERMNLRDADKFTPKDLVNARTIESVINTFFGTNQLSQFMDQTNALAEMTHKRRMSALGPG 563

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH THYGR+CP ET EG NIGL+ SL   + +N +GF+ETPYR V D
Sbjct: 564  GLTRERAGFEVRDVHHTHYGRLCPIETPEGPNIGLMLSLCVHSTINDFGFLETPYRVVED 623

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            G+VT+ V YLSA EE+   +AQAN+ + +DG F  + V CR  G+  +V  E++D++D +
Sbjct: 624  GRVTDRVEYLSAEEEDQATVAQANAPIGDDGHFERDEVRCRHQGDFPIVEPEEVDYMDVA 683

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+VS +ASL+PFL ++D+NR LMG NMQRQ VPLL++++P VGTG+E  VAK S + +
Sbjct: 684  PNQIVSPSASLVPFLSHNDANRALMGSNMQRQGVPLLRSDSPIVGTGLEGRVAKDSRSCV 743

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLD---PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            VA+  G+VE VDA R+V+R  E            V  Y L KF+R+NQ TC+NQ+P+V+ 
Sbjct: 744  VAEGEGVVEYVDAERLVVRYDEEQDKTDLTFGEPVQEYELTKFRRTNQGTCMNQKPIVQA 803

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V   +++ DG + + G+LALG+N+L AFMPWHGYN+ED+++ISER+V++DV+TS+HI
Sbjct: 804  GDRVEEGEVLTDGFAMEKGELALGKNVLCAFMPWHGYNYEDAIVISERLVADDVYTSVHI 863

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE   RDTK G EE+TR+IPNVSEE  K++DE GI+ VGAE+ PGDI+VGKITPKGE+
Sbjct: 864  EEFEHEVRDTKRGEEELTREIPNVSEEATKDLDERGIVRVGAEITPGDIIVGKITPKGET 923

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT-VVDVRIFNRHGIDKNERSISVEREQ 963
              TPEEKLLRAIFG+KA DV+D SL+   G+ G  V+D R+F+R   + +  S  +E ++
Sbjct: 924  DPTPEEKLLRAIFGDKAGDVKDASLKAKPGMEGGVVIDTRLFSRR--ELDPASKKMEEKR 981

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +E +  D + +   L+   + +   ++      G     G     +      D   E   
Sbjct: 982  LENIESDHERKLADLNERFWEKFFALVEDATSAGLEDREGEVLLTEGADFEEDAFDEVDP 1041

Query: 1019 SQWWQFA--VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            S     A   +DE++   + +L   Y++ +  +E   K +  +++ GD++P GV+++ KV
Sbjct: 1042 SDLSTRAEFTEDEELNDQISTLLRNYKSRRRDIEGTTKRQKHQVEMGDELPSGVVQMAKV 1101

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA K+ I+ GDKMAGRHGNKG++++I P EDMPFL DGTPVD+VLNPLGVPSRMN+GQI
Sbjct: 1102 YVARKKKIEVGDKMAGRHGNKGVIAKIAPVEDMPFLDDGTPVDLVLNPLGVPSRMNLGQI 1161

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG K  + I D  +  D+                               
Sbjct: 1162 YETLLGWAGDRLGVKYATPIFDGASLEDVGDELE-------------------------- 1195

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                K+G+P                          G+  LYDG TGEPFD   TVG IYM
Sbjct: 1196 ----KAGLP------------------------RDGKVQLYDGRTGEPFDEKTTVGQIYM 1227

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KL H+V DK++ARS G YSL+TQQPLGGK+  GGQRLGEMEVW + AYGA+  LQEMLT
Sbjct: 1228 MKLEHLVEDKMHARSIGPYSLITQQPLGGKAQFGGQRLGEMEVWALYAYGASNTLQEMLT 1287

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             KSDDV GR+  YESIV G +    G PESFNVLV+E+Q LGL + L+
Sbjct: 1288 FKSDDVEGRSEAYESIVKGENLPSPGVPESFNVLVRELQGLGLEVTLD 1335


>gi|311748521|ref|ZP_07722306.1| DNA-directed RNA polymerase, beta subunit [Algoriphagus sp. PR1]
 gi|311302795|gb|EAZ81285.2| DNA-directed RNA polymerase, beta subunit [Algoriphagus sp. PR1]
          Length = 1275

 Score = 1306 bits (3379), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1377 (41%), Positives = 829/1377 (60%), Gaps = 138/1377 (10%)

Query: 23   IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
            + D PD +++Q  S+  F  ++   ++R  +GL   F   FPI+       LEF+ Y  D
Sbjct: 2    VKDYPDFLDIQLQSFKDFFQLDTPAEKRRADGLFKVFAENFPISDSRENFTLEFIDYAVD 61

Query: 83   PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PPK+ V +C+ R LTY+VPLK  LRL+  D D         +  EQ +++G+LP MT+ G
Sbjct: 62   PPKYSVGECIDRGLTYSVPLKAKLRLLCHDEDNEDF-----ETIEQEVFLGNLPYMTEKG 116

Query: 143  TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
            +FVI G +R++VSQLHRSPG+ F   K     +G  LY+ RIIP +G W++   D  +++
Sbjct: 117  SFVINGAERVIVSQLHRSPGVFFAQSK---HTNGTKLYSARIIPFKGSWIEFATDINNVM 173

Query: 203  HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            +  IDR++K PVT+ L A+G  S+ +IL  F      S                      
Sbjct: 174  YAYIDRKKKFPVTTLLRAIGYGSDKDILDLFGLSEEVSATKTALKK-------------- 219

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
                          +G+KL + +L++  E  V                 ++V+ +  E+ 
Sbjct: 220  -------------VAGRKLAARVLRTWVEDFVDEDT------------GEVVSIDRNEVL 254

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            +E   V+ E+ +E I  S  + I +   D ++ + + + NTL  D +   K+A+  IYR 
Sbjct: 255  LERDSVLTEEDIEMILDSGSKSIILHREDVNIADFSIVYNTLQKDNSNSEKEAVEVIYRQ 314

Query: 381  MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
            +R  +    + A  + + LFF   +YDL  VGR ++N +L L+   +   + K+DII+I+
Sbjct: 315  LRNTEAPDEATAREVIHSLFFSDKRYDLGEVGRYRINKKLGLEIEAEKIVLTKQDIISIV 374

Query: 441  KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
            K L+ L N K  +DDID+L NRRVR+VGE L +Q+ +GL RM R+I+ER++  D +   P
Sbjct: 375  KYLIGLINSKAVVDDIDHLSNRRVRTVGEQLYSQFGVGLARMARTIRERMNVRDNEDFKP 434

Query: 501  QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
             DLINA+ + S +  FF ++QLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RD
Sbjct: 435  VDLINARTLSSVINSFFGTNQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRD 494

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV---TNDVVYL 617
            VH THYGR+C  ET EG NIGL+SSL   A+VN+ GF+ETPYRKV DGKV     D+V+L
Sbjct: 495  VHYTHYGRLCTIETPEGPNIGLISSLCVHAKVNSMGFLETPYRKVKDGKVAMDKGDIVFL 554

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            +A EE++  IAQAN+ LD  G+F  E V  R  G+  ++   +I+F+D +P Q+VS+AAS
Sbjct: 555  TAEEEDDNNIAQANAPLDPKGNFVNEKVKARFEGDFPVLEPSEINFMDVAPNQIVSVAAS 614

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            LIPFLE+DD+NR LMG NMQRQAVPLLKAE+P VGTG+E+  A  S + I+A+  G+V+ 
Sbjct: 615  LIPFLEHDDANRALMGSNMQRQAVPLLKAESPIVGTGLEAKAAVDSRSLIIAEANGVVDY 674

Query: 738  VDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            VDA +I I+     +  L   T     Y L+KF+R+NQ+T +N  PLV  G +V +  ++
Sbjct: 675  VDAKKITIKYDLTDDELLVNFTDEYKSYDLIKFRRTNQDTTINLTPLVLQGQKVVKGQVL 734

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
             +G ST+ G+LALG+N+ VA+MPW GYNFED+++ISER+V EDVFTSIH+EEF++  RDT
Sbjct: 735  VEGYSTNEGELALGKNLKVAYMPWQGYNFEDAIVISERVVREDVFTSIHVEEFQLEVRDT 794

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            K G EE+T +IPNVSEE +K++DE G+I VGAEV  GDI++GKITPKGE+  TPEEKLLR
Sbjct: 795  KRGEEELTSEIPNVSEEAVKHLDENGVIRVGAEVKEGDIIIGKITPKGETDPTPEEKLLR 854

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFG+KA DV+D SL+    ++G V++ ++F+R   DK+ R+ +  + ++E L      +
Sbjct: 855  AIFGDKAGDVKDASLKASPSLNGVVIETKLFSRPKKDKDVRAKA--KAEVEKLKAKYSKD 912

Query: 975  QVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLIS--------------- 1014
             + +   + ++L+ IL G+ ++      G +   K    +++ I                
Sbjct: 913  LLGIRARMINKLVTILDGKTSLGVKHKFGDEIISKGVKFNANNIENNLFPAKNPYRDESN 972

Query: 1015 -------EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
                                D  +   +  L   Y  S++ +   FK     ++ GD++P
Sbjct: 973  YNVPEEANLISDIILDDWTDDAHINDLIVKLVKNYTNSRNEISGLFKRDRFTLEVGDELP 1032

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
             G++++ KV+VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTP+DIVLNPLGV
Sbjct: 1033 AGIVQLAKVYVAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPMDIVLNPLGV 1092

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQIFET L WA   LGKK  + I D  +  ++                      
Sbjct: 1093 PSRMNIGQIFETVLAWAGQVLGKKYATPIFDGASMEEV---------------------- 1130

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                      A E  +      A +   G++ LYDGL+G  FD+
Sbjct: 1131 --------------------------ATELEL------AGVPAYGRTYLYDGLSGSKFDQ 1158

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVG  YMLKL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA
Sbjct: 1159 PVTVGIAYMLKLGHLVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGA 1218

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            ++VLQE+LT+KSDDV+GR + YE+IV G +  +   PESFNVLV E++ L L I L+
Sbjct: 1219 SHVLQEILTVKSDDVIGRAKAYEAIVKGENLPKPNIPESFNVLVHELRGLALEITLD 1275


>gi|283362138|dbj|BAI65925.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
            asiaticus]
          Length = 1159

 Score = 1305 bits (3377), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1157/1159 (99%), Positives = 1157/1159 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVYEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM
Sbjct: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH
Sbjct: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140

Query: 1141 LGWACVGLGKKIKSLINDY 1159
            LGWACVGLGKKIKSLINDY
Sbjct: 1141 LGWACVGLGKKIKSLINDY 1159


>gi|315224714|ref|ZP_07866537.1| DNA-directed RNA polymerase subunit beta [Capnocytophaga ochracea
            F0287]
 gi|314945342|gb|EFS97368.1| DNA-directed RNA polymerase subunit beta [Capnocytophaga ochracea
            F0287]
          Length = 1269

 Score = 1304 bits (3375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1365 (42%), Positives = 811/1365 (59%), Gaps = 116/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F     + + PD +++Q  S+  F  M    ++R +EGL   FK  FPI+      +
Sbjct: 8    RVNFASVKHVPEYPDFLDIQIKSFQEFFQMETKSEDRVHEGLYHTFKENFPISDTRNQFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 68   LEFLDYFVDPPRYTIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVYLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 123  TIPYMTASGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+   A+G + + +IL  F                +   
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEIKVSKTGLKKYI--- 236

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G +L + +L +  E  V                 ++
Sbjct: 237  ------------------------GHRLAARVLNTWHEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRK 371
            V+ E  EI ++   V+DE +++EI  ++++ I +   D    +   I NTL  D     K
Sbjct: 261  VSIERNEIILDRDTVLDEDNIQEILEADVKTILLHKEDSQATDYTIIHNTLQKDPTNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +      A  + + LFF   +Y+L  VGR ++N +L LDTP + + +
Sbjct: 321  EAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGDVGRYRINKKLGLDTPMEKQVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 381  TKEDIITIVKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAAQFGVGLSRMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP ET EG NIGL+SSL  F++VN  GFIETPY KV +GKV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFSKVNGMGFIETPYHKVTNGKVD 560

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              D+ YL+A +EE   I  AN +LD+  + TEE V  +  G+  ++   ++ +ID +P Q
Sbjct: 561  LKDMTYLTAEDEEGLKIGMANIALDDKANITEEKVVVKEDGDFPVIEPNEVQYIDVAPNQ 620

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  +   + A+
Sbjct: 621  IASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLERRVASDARVLMNAE 680

Query: 731  RAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              G V+ VDA +I+I   R+ E  L    +   +Y L+KFQ++NQ TC+N +P+V+ G+ 
Sbjct: 681  GDGTVDYVDADKIIITYDRTDEQKLVSFDADETVYNLIKFQKTNQGTCINLKPIVEKGER 740

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++  ++ +G +T+ G+LALGRNM VAFMPW GYNFED+++ISER V ED+FTSIHI+E+
Sbjct: 741  VKKGQVLCEGYATENGELALGRNMKVAFMPWKGYNFEDAIVISERAVREDLFTSIHIDEY 800

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSE+  K++DE G+I +GAEV PGDIL+GKITPKGES  T
Sbjct: 801  ALEVRDTKLGAEELTNDIPNVSEDATKDLDEYGMIRIGAEVRPGDILIGKITPKGESDPT 860

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R   DK +RS   E   +  L
Sbjct: 861  PEEKLLRAIFGDKAGDVKDASLKASPSLYGVVIDKKLFSRAVKDKRKRSKDKED--VAQL 918

Query: 968  ARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              D + +   L   +  +L  ++      G     G +   K    +  ++         
Sbjct: 919  EADYNAKFEALRSKLLEKLYSLVAEKTSEGVVNDLGEEIVPKGKKYTKKVLEGIEDYAHL 978

Query: 1023 QF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+ +   ++ L   Y   ++ L+   +     I  GD++P G+L++ K++VA 
Sbjct: 979  TSAGWTDDKHINGLIDDLLHNYRIRENDLQGGLRRDKFTIAVGDELPAGILKLAKIYVAK 1038

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1039 KRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETV 1098

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LGKK  + I D  +   I+ L                                
Sbjct: 1099 LGWAGQKLGKKFATPIFDGASLEQINELTD------------------------------ 1128

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP                          G + LYDG TGE FD+  TVG IYM+KL 
Sbjct: 1129 EAGVP------------------------RFGHTYLYDGGTGERFDQKATVGVIYMIKLG 1164

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+KSD
Sbjct: 1165 HMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTVKSD 1224

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DVVGR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1225 DVVGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|313159478|gb|EFR58841.1| DNA-directed RNA polymerase, beta subunit [Alistipes sp. HGB5]
          Length = 1286

 Score = 1304 bits (3375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 575/1386 (41%), Positives = 814/1386 (58%), Gaps = 131/1386 (9%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                + R  F      +  PDL+EVQ  S+  F  M+   + R NEGL   F+  FPIT 
Sbjct: 3    TAKTQQRISFSTVKNRVPYPDLLEVQLKSFRDFFQMDTTAENRKNEGLYKVFQENFPITD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPP++ +++CL R LTY+VPLK  L+L   D +       +     
Sbjct: 63   TRNNFVLEFIDYYIDPPRYSIEECLERGLTYSVPLKAKLKLYCTDDEHEDFGVVV----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y G +P MT+ GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVYFGTIPYMTERGTFVINGAERVIVSQLHRSPGVFFGQSM---HTNGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+PVT+ L A+G ++++ IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGYEADQQILEIF-------------- 220

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                  DL    KV+ + +    G       +KL + +L +  E  V             
Sbjct: 221  ------DLADEVKVTKANLKKAVG-------RKLAARVLSTWVEDFVDEDT--------- 258

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTD 365
                ++V+ E   + ++   V++E+ +++I  S  + I +        + + I NTL  D
Sbjct: 259  ---GEVVSIERNNVIVDRETVLEEEHVDQILESGAKTILLHKESLSGIDFSIIYNTLQKD 315

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 K+A++ IYR +R  +    + A  +   LFF   +YDL  VGR ++N +L+LDT 
Sbjct: 316  PCNSEKEAVVYIYRQLRASEPPDEATARDVIEKLFFSDKRYDLGDVGRYRINKKLDLDTD 375

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              +R + +EDIIAIIK L+ L N K  +DDID+L NRRVR+VGE L NQ+ +G +RM R+
Sbjct: 376  PAIRTLTREDIIAIIKYLIQLINSKADVDDIDHLSNRRVRTVGEQLSNQFSVGFVRMART 435

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +   P DLINAK + S +  FF +SQLSQ  + +N L+ ITH RRLSALG
Sbjct: 436  IRERMNVRDNEVFTPVDLINAKTLSSVINSFFGTSQLSQFMDQINPLAEITHKRRLSALG 495

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A+++  GFIETPYRKV
Sbjct: 496  PGGLSRDRAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKISPMGFIETPYRKV 555

Query: 606  CD---GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI 661
             +       +D+ Y SA EEE + +AQAN  +D++G F + + +  R   +  +V  E++
Sbjct: 556  ENGQIDMNNDDIRYYSAEEEEGKIVAQANMPIDDEGHFLQPDRIKAREGADFPVVTAEEV 615

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            + +D +P Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPL+  +AP VGTG+E  +  
Sbjct: 616  NLMDVAPNQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLVTTDAPIVGTGIEKDMIS 675

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             S   IVA+  G V   DA +I IR     +  L      V  Y L +++R+NQNT +  
Sbjct: 676  DSRIQIVAEGDGEVTFADATKIQIRYERTEDEILASFEPEVTTYELPRYRRTNQNTSITL 735

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +P+V  GD+V +  I+ +G ST  G+LALGRN+ VAFMPW GYNFED+++ISER+  ED+
Sbjct: 736  KPIVLTGDKVVKGQILTEGYSTQHGELALGRNLKVAFMPWKGYNFEDAIVISERIQREDI 795

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTS+H++E+ +  RDTK G EE+T DIPNVSE+  K++D  GII +GA V+PGDIL+GKI
Sbjct: 796  FTSVHVDEYIMEVRDTKRGVEELTSDIPNVSEDATKDLDANGIIRIGANVHPGDILIGKI 855

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R   +  ++  S
Sbjct: 856  TPKGESDPSPEEKLLRAIFGDKAGDVKDASLKAQPSLHGVVIDTKLYSRANKE-GKKGKS 914

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLI 1013
             E+ QIE L      E   L + + ++L  +L G+         G + +   T  S  ++
Sbjct: 915  AEKVQIEKLDEKFAAEIAELTKRLVAKLWTLLQGKTTTGVTDYFGVELYPAGTKFSQKML 974

Query: 1014 SEYPRSQWWQ--------------FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             E  R    +                  D      +E+    Y       +   K +   
Sbjct: 975  EEIARKTTDEKTGVVMGYLNLGTCKWTGDAHTDALIEATINNYTIEWKKADAAIKREKYN 1034

Query: 1060 IQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            I  GD++P  GV+++ KV++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGT V
Sbjct: 1035 ITNGDELPQTGVIQMAKVYIAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTIV 1094

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI LNPLGVPSRMN+GQI+ET LGWA   LG K  + I D  +   I+   +        
Sbjct: 1095 DICLNPLGVPSRMNLGQIYETVLGWAGRELGLKFATPIFDGASLDQINEYTA-------- 1146

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                  K+G+P                         SG++ LYD
Sbjct: 1147 ----------------------KAGIP------------------------HSGRTYLYD 1160

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TGE FD+P TVG IYMLKL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEME
Sbjct: 1161 GGTGEMFDQPATVGVIYMLKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEME 1220

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++ +GAA +LQE+LTIKSDDV+GR + YE+IV G +  + G PE+ NVL+ E++ L 
Sbjct: 1221 VWALEGFGAANILQEILTIKSDDVMGRAKAYEAIVKGENLPKPGIPEAMNVLLHELRGLA 1280

Query: 1359 LSIDLE 1364
            LS+ LE
Sbjct: 1281 LSVKLE 1286


>gi|256819271|ref|YP_003140550.1| DNA-directed RNA polymerase subunit beta [Capnocytophaga ochracea DSM
            7271]
 gi|256580854|gb|ACU91989.1| DNA-directed RNA polymerase, beta subunit [Capnocytophaga ochracea
            DSM 7271]
          Length = 1269

 Score = 1304 bits (3375), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1365 (42%), Positives = 812/1365 (59%), Gaps = 116/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F     + + PD +++Q  S+  F  M    ++R +EGL   FK  FPI+      +
Sbjct: 8    RVNFASVKHVPEYPDFLDIQIKSFQEFFQMETKSEDRVHEGLYHTFKENFPISDTRNQFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 68   LEFLDYFVDPPRYTIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVYLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 123  TIPYMTASGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+   A+G + + +IL  F                +   
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEIKVSKTGLKKYI--- 236

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +L +  E  V                 ++
Sbjct: 237  ------------------------GRRLAARVLNTWHEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRK 371
            V+ E  EI ++   V+DE +++EI  ++++ I +   D    +   I NTL  D     K
Sbjct: 261  VSIERNEIILDRDTVLDEDNIQEILEADVKTILLHKEDSQATDYTIIHNTLQKDPTNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +      A  + + LFF   +Y+L  VGR ++N +L LDTP + + +
Sbjct: 321  EAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGDVGRYRINKKLGLDTPMEKQVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 381  TKEDIITIVKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAAQFGVGLSRMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP ET EG NIGL+SSL  F++VN  GFIETPY KV +GKV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFSKVNGMGFIETPYHKVTNGKVD 560

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              D+ YL+A +EE   I  AN +LD+  + TEE V  +  G+  ++   ++ +ID +P Q
Sbjct: 561  LKDMTYLTAEDEEGLKIGMANIALDDKANITEEKVVVKEDGDFPVIEPNEVQYIDVAPNQ 620

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  +   + A+
Sbjct: 621  IASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLERRVASDARVLMNAE 680

Query: 731  RAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              G V+ VDA +I+I   R+ E  L    +   +Y L+KFQ++NQ TC+N +P+V+ G+ 
Sbjct: 681  GDGTVDYVDADKIIITYDRTDEQKLVSFDADETVYNLIKFQKTNQGTCINLKPIVEKGER 740

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++  ++ +G +T+ G+LALGRNM VAFMPW GYNFED+++ISER V ED+FTSIHI+E+
Sbjct: 741  VKKGQVLCEGYATENGELALGRNMKVAFMPWKGYNFEDAIVISERAVREDLFTSIHIDEY 800

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSE+  K++DE G+I +GAEV PGDIL+GKITPKGES  T
Sbjct: 801  ALEVRDTKLGAEELTNDIPNVSEDATKDLDEYGMIRIGAEVRPGDILIGKITPKGESDPT 860

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R   DK +RS   E   +  L
Sbjct: 861  PEEKLLRAIFGDKAGDVKDASLKASPSLYGVVIDKKLFSRAVKDKRKRSKDKED--VAQL 918

Query: 968  ARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              + + +   L   +  +L  ++      G     G +   K    +  ++         
Sbjct: 919  EANYNAKFETLRSKLLEKLYSLVAEKTSEGVVNDLGEEIVPKGKKYTKKVLEGIEDYAHL 978

Query: 1023 QF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+ +   ++ L   Y   ++ L+   +     I  GD++P G+L++ K++VA 
Sbjct: 979  TSAGWTDDKHINGLIDDLLHNYRIRENDLQGGLRRDKFTIAVGDELPAGILKLAKIYVAK 1038

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1039 KRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETV 1098

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LGKK  + I D  +   I+ L                                
Sbjct: 1099 LGWAGQKLGKKFATPIFDGASLEQINELTD------------------------------ 1128

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP                          G + LYDG TGE FD+  TVG IYM+KL 
Sbjct: 1129 EAGVP------------------------RFGHTYLYDGGTGERFDQKATVGVIYMIKLG 1164

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+KSD
Sbjct: 1165 HMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTVKSD 1224

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DVVGR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1225 DVVGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|312131295|ref|YP_003998635.1| DNA-directed RNA polymerase subunit beta [Leadbetterella byssophila
            DSM 17132]
 gi|311907841|gb|ADQ18282.1| DNA-directed RNA polymerase subunit beta [Leadbetterella byssophila
            DSM 17132]
          Length = 1285

 Score = 1304 bits (3374), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1394 (41%), Positives = 826/1394 (59%), Gaps = 143/1394 (10%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +   G    RK F      ++ PD +++Q  S+  F  ++   + R  EGL   F   
Sbjct: 1    MKLTETG----RKSFASVQPALEYPDFLDIQLQSFTEFFQIDTPAESRRAEGLYQTFMDN 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI       +LEFV Y  D PK+ VD+C+ R LTY+VPLK  L+L   D D        
Sbjct: 57   FPIADSRENYVLEFVDYTIDQPKYSVDECIDRGLTYSVPLKAKLKLTCNDADNEDF---- 112

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             +  EQ +++G++P MT  G+FVI G +R++VSQLHRSPG+ F   K     +G  LY+ 
Sbjct: 113  -ETIEQEVFLGNIPYMTSRGSFVINGAERVIVSQLHRSPGVFFSMSK---HTNGTKLYSA 168

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            R+IP +G W++   D  ++++  IDR++K PVT+ L ++G  ++ EIL  F      +  
Sbjct: 169  RVIPMKGSWIEFSTDVNNVMYAYIDRKKKFPVTTLLRSIGFGTDKEILDLFGLSEEIAAT 228

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
             D                                 G++L + +LK+  E  V        
Sbjct: 229  RDNLKQ---------------------------VVGRRLAARVLKTWTEDFVDEDT---- 257

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IR 359
                     ++V+ +  E+ +E   VI E  +E I  +E++ + IL+ +  N + Y  I 
Sbjct: 258  --------GEVVSIDRNEVILERDSVITEDDVELILSTELKSV-ILHREDANVSEYNIIY 308

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  D +   K+A+  IYR +R  +    + A  +   LFF   +YDL  VGR ++N +
Sbjct: 309  NTLQKDSSNSEKEAVEQIYRQLRNTEAPDEATAREIIQGLFFSDKRYDLGEVGRYRVNTK 368

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            LNLDTP + R + KEDII+I+K L+ L N K  +DDID+L NRRVR+VGE L  Q+ +GL
Sbjct: 369  LNLDTPLETRVLSKEDIISIVKYLIGLINSKAVVDDIDHLSNRRVRTVGEQLSGQFGVGL 428

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             RM R+IKER++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH R
Sbjct: 429  ARMARTIKERMNVRDNEDFKPVDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKR 488

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL ++A++N+ GFIE
Sbjct: 489  RLSALGPGGLSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCTYAKINSMGFIE 548

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPY K+ DGK+T  + YL+A EE+ + IA A + ++ DGSFT + + CR  G+  +   +
Sbjct: 549  TPYNKIEDGKLTGKIEYLTAEEEDGKNIAMATADVNPDGSFTVDTLKCRYEGDFPMKSPD 608

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +I+++D +P Q+VSIAAS+IPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  +
Sbjct: 609  EIEYMDIAPNQIVSIAASMIPFLEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGKL 668

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            A+ S   +VA+  G+++ VDA +IV+         L    +    Y+L+KF+R+NQ+TC+
Sbjct: 669  ARDSRTLVVAEGDGVIDYVDAEKIVVNYDWTDNQKLVSFDTNFTTYKLIKFRRTNQDTCI 728

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            N RP+V  G  V++  I+ +G +T  G+LALGRN+ VAFMPW GYNFED+++ISER+V E
Sbjct: 729  NLRPIVLKGQRVKKGQILVEGYATQGGELALGRNLQVAFMPWQGYNFEDAIVISERVVRE 788

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D+FTSIHIEEF++  RDTK G EE+T +IPNVSEE +KN+DE GI+ VG  +  GDIL+G
Sbjct: 789  DIFTSIHIEEFDLEVRDTKRGEEELTSEIPNVSEEAVKNLDENGIVRVGTHIKEGDILIG 848

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPKGES  TPEEKLLRAIFG+KA DV+D S + P  + G ++D ++F+R    K ER 
Sbjct: 849  KITPKGESDPTPEEKLLRAIFGDKAGDVKDASKKAPPSLRGVIIDTKLFSRP--SKEERL 906

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSD 1011
                +E+++ L      +   L   +  +++ +L G+ +       G +   K    +  
Sbjct: 907  KH--KEEVKRLMVKHSKDLSALKEVMIDKMVTLLDGKTSNGVKHKFGEELISKGVKFNRS 964

Query: 1012 LI----------------------SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
             I                      +        +    D +    +  L   Y T +S +
Sbjct: 965  NITNNLFPEKNPFVDESTYNVPEEANLLGDIILEGWTNDAETNSLLVQLVKNYLTRRSEI 1024

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
               FK +   ++ GD++P G++++ KV++A KR ++ GDKMAGRHGNKG+V+RI+  EDM
Sbjct: 1025 IGVFKREKFVLEVGDELPAGIVKLAKVYIAKKRKLKVGDKMAGRHGNKGVVARIVRDEDM 1084

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PFL+DGT +DIVLNPLGVPSRMN+GQ++E  LGWA   LG+K  + I D  ++ +++   
Sbjct: 1085 PFLEDGTTMDIVLNPLGVPSRMNIGQLYEVCLGWAGKKLGRKYATPIFDGASSEEVAAEL 1144

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                                 L+     
Sbjct: 1145 KEAG-------------------------------------------------LQEFG-- 1153

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
               ++ LY+GLTGE FD+P TVG +YMLKL H+V DK++ARS G YSL+TQQPLGGK+  
Sbjct: 1154 ---RTYLYNGLTGERFDQPTTVGIMYMLKLGHLVDDKMHARSIGPYSLITQQPLGGKAQF 1210

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++A+GA++VL+E+LT+KSDDV+GR + YE+IV G +  +   PESFNV
Sbjct: 1211 GGQRFGEMEVWALEAFGASHVLREILTLKSDDVLGRAKAYEAIVKGENLPKASIPESFNV 1270

Query: 1350 LVKEMQALGLSIDL 1363
            LV E++ L L I L
Sbjct: 1271 LVHELRGLALEITL 1284


>gi|109914393|sp|Q2S1Q5|RPOB_SALRD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1287

 Score = 1304 bits (3374), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1368 (42%), Positives = 828/1368 (60%), Gaps = 118/1368 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R+ F   PE+ D PD ++VQ  ++  F+  ++ P +R + GLQA F   FPI        
Sbjct: 21   RESFADIPEVWDYPDFLDVQLKTFHDFVQDDVPPADREDVGLQAVFNEHFPIKDNRDRYT 80

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFV+YE D PK  V++C+ + LTY++PLK TLRL   + +    A    +   Q +Y+G
Sbjct: 81   LEFVNYELDAPKHTVEECIAQGLTYSIPLKATLRLTSKEEEGGEEAIEAIE---QEVYLG 137

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             LP MT  GTF++ G +R++VSQLHRSPG  F+ +      +G  L++ R+IP +G WM+
Sbjct: 138  TLPFMTDRGTFIVNGAERVIVSQLHRSPGAFFEKE---IHSNGTELFSARVIPFRGSWME 194

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D +D++   +DR++KVPVT+ L ALG  S+ EI+  F          +         
Sbjct: 195  FSTDVRDVLWAYVDRKKKVPVTTLLRALGFSSDEEIVKMFDLADAVDIGDEDEFEEHLGR 254

Query: 253  DLMVGAKVSS--SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +L     +     +VD DTGE V E  ++                               
Sbjct: 255  ELATSVTIEKTIEIVDEDTGEVVDEEMER------------------------------- 283

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN---NNAYIRNTLVTDKN 367
                    E+ + A   ++E   EE+   ++  + ++  D  +   + + +  TL  D +
Sbjct: 284  --------EVLLPAEHELEEGDWEELDEYDVSRLYLVREDVEDEALDKSTLVETLQKDSS 335

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               ++AL  IY  +R  +      A      LFF+ D+YDL  VGR +MN RL++D   D
Sbjct: 336  HTEEEALEVIYEKLRGSEAPDLDSAREALERLFFNEDRYDLGDVGRHRMNARLDVDVDTD 395

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + KED++ I++ L+ L+NG+ T DDID+L NRRV+SVGE L +Q+ LGL RM R+IK
Sbjct: 396  EKVLTKEDVVGIVRELIRLQNGESTADDIDHLSNRRVKSVGEQLGSQFSLGLARMARTIK 455

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D D   P+DL+NA+ + S +  FF ++QLSQ  +  N+L+ +TH RR+SALG G
Sbjct: 456  ERMNLRDADKFTPKDLVNARTIESVINTFFGTNQLSQFMDQTNALAEMTHKRRMSALGPG 515

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH THYGR+CP ET EG NIGL+ SL   + +N +GF+ETPYR V D
Sbjct: 516  GLTRERAGFEVRDVHHTHYGRLCPIETPEGPNIGLMLSLCVHSTINDFGFLETPYRVVED 575

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            G+VT+ V YLSA EE+   +AQAN+ + +DG F  + V CR  G+  +V  E++D++D +
Sbjct: 576  GRVTDRVEYLSAEEEDQATVAQANAPIGDDGHFERDEVRCRHQGDFPIVEPEEVDYMDVA 635

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+VS +ASL+PFL ++D+NR LMG NMQRQ VPLL++++P VGTG+E  VAK S + +
Sbjct: 636  PNQIVSPSASLVPFLSHNDANRALMGSNMQRQGVPLLRSDSPIVGTGLEGRVAKDSRSCV 695

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLD---PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            VA+  G+VE VDA R+V+R  E            V  Y L KF+R+NQ TC+NQ+P+V+ 
Sbjct: 696  VAEGEGVVEYVDAERLVVRYDEEQDKTDLTFGEPVQEYELTKFRRTNQGTCMNQKPIVQA 755

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V   +++ DG + + G+LALG+N+L AFMPWHGYN+ED+++ISER+V++DV+TS+HI
Sbjct: 756  GDRVEEGEVLTDGFAMEKGELALGKNVLCAFMPWHGYNYEDAIVISERLVADDVYTSVHI 815

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE   RDTK G EE+TR+IPNVSEE  K++DE GI+ VGAE+ PGDI+VGKITPKGE+
Sbjct: 816  EEFEHEVRDTKRGEEELTREIPNVSEEATKDLDERGIVRVGAEITPGDIIVGKITPKGET 875

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT-VVDVRIFNRHGIDKNERSISVEREQ 963
              TPEEKLLRAIFG+KA DV+D SL+   G+ G  V+D R+F+R   + +  S  +E ++
Sbjct: 876  DPTPEEKLLRAIFGDKAGDVKDASLKAKPGMEGGVVIDTRLFSRR--ELDPASKKMEEKR 933

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +E +  D + +   L+   + +   ++      G     G     +      D   E   
Sbjct: 934  LENIESDHERKLADLNERFWEKFFALVEDATSAGLEDREGEVLLTEGADFEEDAFDEVDP 993

Query: 1019 SQWWQFA--VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            S     A   +DE++   + +L   Y++ +  +E   K +  +++ GD++P GV+++ KV
Sbjct: 994  SDLSTRAEFTEDEELNDQISTLLRNYKSRRRDIEGTTKRQKHQVEMGDELPSGVVQMAKV 1053

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA K+ I+ GDKMAGRHGNKG++++I P EDMPFL DGTPVD+VLNPLGVPSRMN+GQI
Sbjct: 1054 YVARKKKIEVGDKMAGRHGNKGVIAKIAPVEDMPFLDDGTPVDLVLNPLGVPSRMNLGQI 1113

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG K  + I D  +  D+                               
Sbjct: 1114 YETLLGWAGDRLGVKYATPIFDGASLEDVGDELE-------------------------- 1147

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                K+G+P                          G+  LYDG TGEPFD   TVG IYM
Sbjct: 1148 ----KAGLP------------------------RDGKVQLYDGRTGEPFDEKTTVGQIYM 1179

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KL H+V DK++ARS G YSL+TQQPLGGK+  GGQRLGEMEVW + AYGA+  LQEMLT
Sbjct: 1180 MKLEHLVEDKMHARSIGPYSLITQQPLGGKAQFGGQRLGEMEVWALYAYGASNTLQEMLT 1239

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             KSDDV GR+  YESIV G +    G PESFNVLV+E+Q LGL + L+
Sbjct: 1240 FKSDDVEGRSEAYESIVKGENLPSPGVPESFNVLVRELQGLGLEVTLD 1287


>gi|288926248|ref|ZP_06420173.1| DNA-directed RNA polymerase, beta subunit [Prevotella buccae D17]
 gi|315606514|ref|ZP_07881529.1| DNA-directed RNA polymerase subunit beta [Prevotella buccae ATCC
            33574]
 gi|288336939|gb|EFC75300.1| DNA-directed RNA polymerase, beta subunit [Prevotella buccae D17]
 gi|315251920|gb|EFU31894.1| DNA-directed RNA polymerase subunit beta [Prevotella buccae ATCC
            33574]
          Length = 1269

 Score = 1303 bits (3373), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1367 (42%), Positives = 810/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVHNPYPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYIDPPRYTIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VV+QLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVAQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLLRAIGYENDKDILQIFDLAEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LKS  E  V                 ++
Sbjct: 234  ---------------------AAIGRKLAARVLKSWNEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    + E ++EEI  S    + I    +  N  + I NTL  D +   K
Sbjct: 261  VSIERNEVIMERETELTEDNIEEILESGTSTVLIHKDEEGANRFSIIFNTLAKDPSNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LDT  DVR +
Sbjct: 321  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDTDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIIEIIKYLIQLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYRKV DGKV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYATINELGFIETPYRKVVDGKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               + VVY++A EEEN  I Q N+ L+EDGSF  ++V CR   +  +VP  ++D +D +P
Sbjct: 561  LDNDHVVYITAEEEENHIIGQGNAPLNEDGSFIRDVVKCRQDADFPVVPPAEVDMMDVAP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   RS + +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRSEDEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICSKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            + V+  DI+ +G +T+ G++ALGRN+LVA++PW GYN+ED+++ISER+V +DV TS+H++
Sbjct: 741  ERVKAGDILTEGYATENGEIALGRNLLVAYIPWKGYNYEDAVVISERIVRDDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    KN  S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKNRESKKQDKIILA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +  G         +G +   K +  ++  +       
Sbjct: 919  KIDEEYEAKNNDLKDILVDKLLTLTEGMVSEGVKDYTGAEIITKGSKFTTAALKNLEYDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                   +D      ++ L + Y      L+   K +   I  GD++P G+L++ KV++A
Sbjct: 979  IQSNDWTKDAHANGLIQKLIMNYIRKYKQLDAEMKRRKFAITIGDELPSGILQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGKKLGVKFATPIFDGAKLADLQEWTD----------------------------- 1129

Query: 1200 WKSGVP--VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPRLCSTHLYDGE--------------------------TGEQFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGDTMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|288929385|ref|ZP_06423230.1| DNA-directed RNA polymerase, beta subunit [Prevotella sp. oral taxon
            317 str. F0108]
 gi|288329487|gb|EFC68073.1| DNA-directed RNA polymerase, beta subunit [Prevotella sp. oral taxon
            317 str. F0108]
          Length = 1270

 Score = 1303 bits (3372), Expect = 0.0,   Method: Composition-based stats.
 Identities = 569/1365 (41%), Positives = 808/1365 (59%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFASVHNPMPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYTIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L   
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYENDRDILQIFDLAEEVKVNKKNMKEAL--- 237

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    GK+L + +LKS  E  V                 ++
Sbjct: 238  ------------------------GKRLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I E+++ EI  S +  + +    D+ N  + I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETEITEENVGEILDSGVSTVLLHKDADAANKFSIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+L IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LDT  D R +
Sbjct: 322  EAVLYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDTDMDTRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYRKV +G V 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYANINELGFIETPYRKVSNGVVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                 +VYL+A EEE+  I Q N+ L+EDG+F  ++V CR   +  +V   ++D +D SP
Sbjct: 562  LNNKHLVYLTAEEEEDHIIGQGNAPLNEDGTFIRDVVKCRQDADFPVVEPAEVDLMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 622  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+++ VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGDGVIDYVDATTIRILYDRTEDEEYVSFEPALKEYRVPKFRRTNQNMTIDLRPICVKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED++++SER+V +DV TS+H++
Sbjct: 742  QRVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAIVLSERLVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G++ +GA + PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVVRIGARIEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    ++  S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRAIKTRD--SKKQDKVILA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+E+       G    +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNEDLKDILVDKLLELTEDKVSQGVKDYTGAEIINKGSKFTAAALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D      ++ L + Y     +L+   K +   I  GD++P G+L++ KV+VA
Sbjct: 980  IQSNDWTDDAHTNDLIQKLIMNYIRKYKLLDAELKRRKFAITIGDELPSGILQMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKIGVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+S                          + R+   
Sbjct: 1100 ILGAAGKKLGVKFATPIFDGAQLEDLSEWTDKA-------------------ELPRLC-- 1138

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TGE FD+P TVG  Y LKL
Sbjct: 1139 -------STYLYDGE--------------------------TGEKFDQPATVGVTYFLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA+++LQE+LTIKS
Sbjct: 1166 GHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHILQEILTIKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI ++
Sbjct: 1226 DDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKMD 1270


>gi|213963169|ref|ZP_03391427.1| DNA-directed RNA polymerase, beta subunit [Capnocytophaga sputigena
            Capno]
 gi|213954253|gb|EEB65577.1| DNA-directed RNA polymerase, beta subunit [Capnocytophaga sputigena
            Capno]
          Length = 1269

 Score = 1303 bits (3371), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1365 (42%), Positives = 811/1365 (59%), Gaps = 116/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F     + + PD +++Q  S+  F  M    ++R +EGL   FK  FPI+      +
Sbjct: 8    RVNFASVKHVPEYPDFLDIQIKSFQEFFQMETKSEDRVHEGLYQTFKENFPISDTRNQFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 68   LEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QDVYLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 123  TVPYMTSSGTFVINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+   A+G + + +IL  F                +   
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEIKVSKTGLKKYI--- 236

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +L +  E  V                 ++
Sbjct: 237  ------------------------GRRLAARVLNTWHEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRK 371
            V+ E  EI ++   V+DE + +EI  ++++ I +   D    +   I NTL  D     K
Sbjct: 261  VSIERNEIILDRDTVLDEDNTQEILEADVKTILLHKEDSQATDYTIIHNTLQKDPTNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +      A  + + LFF   +Y+L  VGR ++N +L LDTP + + +
Sbjct: 321  EAVEHIYRQLRNAEPPDEETARGIIDKLFFSDQRYNLGDVGRYRINKKLGLDTPMEKQVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++
Sbjct: 381  TKEDIITIVKYLIELINSKAEVDDIDHLSNRRVRTVGEQLAAQFGVGLSRMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP ET EG NIGL+SSL  F++VN  GFIETPY KV +GKV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLAVFSKVNGMGFIETPYHKVTNGKVD 560

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              D+ YL+A +EE   I  AN +LD+  +  EE V  +  G+  ++   ++ +ID +P Q
Sbjct: 561  LKDMTYLTAEDEEGLKIGMANIALDDKANIIEEKVVVKEDGDFPVIEPNEVQYIDVAPNQ 620

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  +A  +   + A+
Sbjct: 621  IASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPEAPIVGTGLERRIASDARVLMNAE 680

Query: 731  RAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            R G+V+ VDA +I+I   R+ E  L        +Y L+KFQ++NQ TC+N +P+V+ G+ 
Sbjct: 681  RDGVVDYVDAEKIIITYDRTDEEKLVSFDPDETVYNLIKFQKTNQGTCINLKPIVEKGER 740

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++  ++ +G +T+ G+LALGRNM VAFMPW GYNFED+++ISER V +D+FTSIHI+E+
Sbjct: 741  VKKGQVLCEGYATENGELALGRNMKVAFMPWKGYNFEDAIVISERAVRDDIFTSIHIDEY 800

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSE+  K++DE G+I +GAEV PGDIL+GKITPKGES  T
Sbjct: 801  ALEVRDTKLGAEELTNDIPNVSEDATKDLDENGMIRIGAEVRPGDILIGKITPKGESDPT 860

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R   DK +RS   E   +  L
Sbjct: 861  PEEKLLRAIFGDKAGDVKDASLKASPSLYGVVIDKKLFSRAVKDKRKRSKDKED--VAQL 918

Query: 968  ARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              D + +   L   +  +L  ++      G     G +   K    S  ++         
Sbjct: 919  EADYNAKFEALRTKLLEKLFSLVAEKTSEGVVNDLGEEIVPKGKKYSKKVLEGIEDYAHL 978

Query: 1023 QF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+ +   ++ L   Y   ++ L+   +     I  GD++P G+L++ K++VA 
Sbjct: 979  TSAGWTDDKHINGLIDDLLHNYRIRENDLQGMLRRDKFTIAVGDELPAGILKLAKIYVAK 1038

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1039 KRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETV 1098

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LGKK  + I D  +   I+ L                                
Sbjct: 1099 LGWAGQKLGKKFATPIFDGASLEQINELTD------------------------------ 1128

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++GVP                          G + LYDG TGE FD+  TVG IYM+KL 
Sbjct: 1129 EAGVP------------------------RFGHTYLYDGGTGERFDQKATVGVIYMIKLG 1164

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  L+E+LT+KSD
Sbjct: 1165 HMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLREILTVKSD 1224

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DVVGR + YE+IV G    E G PESFNVL+ E++ LGL I LE 
Sbjct: 1225 DVVGRAKTYEAIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|260909710|ref|ZP_05916404.1| DNA-directed RNA polymerase subunit beta [Prevotella sp. oral taxon
            472 str. F0295]
 gi|260636135|gb|EEX54131.1| DNA-directed RNA polymerase subunit beta [Prevotella sp. oral taxon
            472 str. F0295]
          Length = 1270

 Score = 1303 bits (3371), Expect = 0.0,   Method: Composition-based stats.
 Identities = 570/1365 (41%), Positives = 804/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFASVHNPMPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYTIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L   
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYENDRDILQIFDLAEEVKVNKKNMKEAL--- 237

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    GK+L + +LKS  E  V                 ++
Sbjct: 238  ------------------------GKRLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I E+++ EI  S +  + +    D+ N  + I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETEITEENVGEILDSGVSTVLLHKDADAANKFSIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+L IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LDT  D R +
Sbjct: 322  EAVLYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDTDMDTRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYR V +G V 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYANINELGFIETPYRNVNNGVVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                ++VYL+A EEE+  I Q N+ L+EDG+F  E+V CR   +  +V   ++D +D SP
Sbjct: 562  LDNKNLVYLTAEEEEDHIIGQGNAPLNEDGTFIREVVKCRQDADFPVVAPAEVDLMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 622  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+++ VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGDGVIDYVDATTIRILYDRTEDEEYVSFEPALKEYRVPKFRRTNQNMTIDLRPICVKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED++++SER+V +DV TS+H++
Sbjct: 742  QRVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAIVLSERLVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G++ VGA + PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVVRVGARIEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKKQDKVILA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+E+       G    +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNEDLKDILVDKLLELTEDKVSQGVKDYTGAEIINKGSKFTAATLKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D      ++ L + Y     +L+   K +   I  GD++P G+L++ KV+VA
Sbjct: 980  IQSSDWTDDAHTNDLIQKLIMNYIRKYKLLDAELKRRKFAITIGDELPSGILQMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKIGVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+S                                 
Sbjct: 1100 ILGAAGKNLGVKFATPIFDGAQLEDLSEWTDKAGLPHLC--------------------- 1138

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TGE FD+P TVG  Y LKL
Sbjct: 1139 -------STYLYDGE--------------------------TGEKFDQPATVGVTYFLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA+++LQE+LTIKS
Sbjct: 1166 GHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHILQEILTIKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI ++
Sbjct: 1226 DDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKMD 1270


>gi|254494926|ref|ZP_01052582.2| DNA-directed RNA polymerase beta chain [Polaribacter sp. MED152]
 gi|213690508|gb|EAQ42010.2| DNA-directed RNA polymerase beta chain [Polaribacter sp. MED152]
          Length = 1253

 Score = 1302 bits (3370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 587/1353 (43%), Positives = 807/1353 (59%), Gaps = 115/1353 (8%)

Query: 25   DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
            + PD +++Q  S+  F  +    +ER  EGL   F   FPIT      +LEF+ Y  DPP
Sbjct: 4    EYPDFLDIQVKSFQDFFQLQTKAEERGEEGLYKTFMDNFPITDTRNQFVLEFLDYFVDPP 63

Query: 85   KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            ++ + +C+ R LT++VPLK  L+L   D +       +     Q +Y+G +P MT  GTF
Sbjct: 64   RYSIQECIERGLTHSVPLKARLKLYCTDPEHEDFETIV-----QDVYLGTIPYMTNSGTF 118

Query: 145  VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
            VI G +R+VVSQLHRSPG+ F         +G  LY+ R+IP +G W++   D   +++ 
Sbjct: 119  VINGAERVVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKGSWIEFATDINQVMYA 175

Query: 205  RIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
             IDR++K+PVT+   A+G + + +IL  F                L              
Sbjct: 176  YIDRKKKLPVTTLFRAIGFERDKDILEIFDLAEEVKVSKAGLKKVL-------------- 221

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
                         G+KL + +LK+  E  V                 ++V+ E  EI  +
Sbjct: 222  -------------GRKLAARVLKTWHEDFVDEDT------------GEVVSIERNEIIFD 256

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
               V++++ ++EI  +  + I +  VD  + + A I NTL  D     K+A+  IYR +R
Sbjct: 257  RDTVLEKEHIDEIIEAGAKTILLHKVDNHMADYAIIHNTLQKDPTNSEKEAVEHIYRQLR 316

Query: 383  PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
              +      A  + + LFF   +Y+L  VGR +MN +L L+ P D + + K DII IIK 
Sbjct: 317  NAEPPDEETARGIIDKLFFSEQRYNLGEVGRFRMNTKLQLNEPIDQKVLTKLDIITIIKY 376

Query: 443  LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
            L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER++  D +   P D
Sbjct: 377  LIELINSKAEVDDIDHLSNRRVRTVGEQLAGQFGVGLARMARTIRERMNVRDNEVFTPID 436

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            LINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG++R RAG E+RDVH
Sbjct: 437  LINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVH 496

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAME 621
             THYGR+CP ET EG NIGL+SSL+ FA+VN  GFIETPYRKV +G V   + +YLSA E
Sbjct: 497  YTHYGRLCPIETPEGPNIGLISSLSVFAKVNNLGFIETPYRKVNNGIVEGEEPIYLSAEE 556

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EE + IAQ+N  L EDGS   + V  R  G+  +V  E ID++D +P Q+ SI+ASLIPF
Sbjct: 557  EEGKKIAQSNLELKEDGSIVLDRVIAREEGDFPVVNPEVIDYMDVAPNQIASISASLIPF 616

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LE+DD+NR LMG NM RQAVPLL+ E+P VGTG+E  VAK S   I A+  G V  VDA 
Sbjct: 617  LEHDDANRALMGSNMMRQAVPLLRPESPIVGTGLERRVAKDSRILINAEGEGEVTYVDAN 676

Query: 742  RIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            +I IR     E  L    S    Y L+KF+++NQ T +N +P+V+ GD V+   ++ +G 
Sbjct: 677  KITIRYDKTDEERLVSFDSDEVSYDLIKFRKTNQGTSINLKPIVETGDRVQEGQVLCEGY 736

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +T  G+LALGRNM VAFMPW GYNFED+++ISE++V ED+FTSIHI+E+ +  RDTKLG 
Sbjct: 737  ATQKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSIHIDEYSLDVRDTKLGT 796

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            EE+T DIPNVSEE  K++DE G+I +GAEVNPGDIL+GKITPKGES  TPEEKLLRAIFG
Sbjct: 797  EELTNDIPNVSEEATKDLDENGMIRIGAEVNPGDILIGKITPKGESDPTPEEKLLRAIFG 856

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
            +KA DV+D SL+    + G V+D ++F R   DKN+R    ++E +  L +    +   L
Sbjct: 857  DKAGDVKDASLKASPSLRGVVIDKKLFRRAVKDKNKRIR--DKEAVATLEQSFVSKFEGL 914

Query: 979  DRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS-QWWQFAVQDEKVQ 1032
               +  +L  ++ G+ +       G +   K    +  +++              D  + 
Sbjct: 915  KDELIEKLFTLISGKTSQGVFNDLGEEVLPKGKKYTLKMLNSVDDYVHLTGSWTTDSDLN 974

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              V  L   Y+   + L+   + +   I  GD++P G+L++ KV++A KR ++ GDKMAG
Sbjct: 975  ALVGELVHNYKIKVNDLQGSLRRQKFTISVGDELPAGILKLAKVYIAKKRKLKVGDKMAG 1034

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET LGWA   LG K 
Sbjct: 1035 RHGNKGIVARIVRAEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETVLGWAGEKLGTKY 1094

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + I D  +   I+ +                                ++GVP       
Sbjct: 1095 ATPIFDGASLDQINEITD------------------------------EAGVP------- 1117

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G + LYDG TG+ FD+P TVG IYM+KL HM+ DK++ARS 
Sbjct: 1118 -----------------RFGHTYLYDGGTGKRFDQPATVGIIYMIKLGHMIEDKMHARSI 1160

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+ +L+E+LT+KSDDV+GR + YESI
Sbjct: 1161 GPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSILREILTVKSDDVMGRAKTYESI 1220

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V G    E G PESFNVL+ E++ LGL + LE 
Sbjct: 1221 VKGEAMPEPGLPESFNVLMHELKGLGLDVRLEE 1253


>gi|167753041|ref|ZP_02425168.1| hypothetical protein ALIPUT_01307 [Alistipes putredinis DSM 17216]
 gi|167659355|gb|EDS03485.1| hypothetical protein ALIPUT_01307 [Alistipes putredinis DSM 17216]
          Length = 1287

 Score = 1302 bits (3370), Expect = 0.0,   Method: Composition-based stats.
 Identities = 569/1386 (41%), Positives = 812/1386 (58%), Gaps = 130/1386 (9%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                + R  F      +  PDL+EVQ  S+  F  M+   + R NEGL   F+  FPIT 
Sbjct: 3    TTKTQQRVSFSTVKNRVPYPDLLEVQLKSFRDFFQMDTTAENRKNEGLYKVFQENFPITD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 +LEF+ Y  DPP++ +++CL R LTY+VPLK  L+L   D +       +     
Sbjct: 63   TRNNFVLEFIDYYIDPPRYSIEECLERGLTYSVPLKAKLKLYCTDDEHEDFGVVV----- 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y G +P MT+ GTFVI G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVYFGTIPYMTERGTFVINGAERVIVSQLHRSPGVFFGQSM---HTNGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+PVT+ L A+G ++++ IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFEADQQILEIF-------------- 220

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                  DL    KV+ + +    G       +KL + +L +  E  V             
Sbjct: 221  ------DLADEVKVTKAALKKAVG-------RKLAARVLSTWVEDFVDEDT--------- 258

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTD 365
                ++V+ E   + ++   V+ E+ +++I  S  + I +   +    + + I NTL  D
Sbjct: 259  ---GEVVSIERNNVIVDRETVLQEEHIDQIIESGAKTILLHKENLSGIDFSIIYNTLQKD 315

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 K+A++ IYR +R  +    + A  +   LFF   +YDL  VGR ++N +L+LD  
Sbjct: 316  PCNSEKEAVVYIYRQLRASEPPDEATARDVIEKLFFSDKRYDLGDVGRYRINKKLDLDID 375

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              +R + +EDIIAIIK L+ L N K  +DDID+L NRRVR+VGE L NQ+ +G +RM R+
Sbjct: 376  PAIRTLTREDIIAIIKYLIQLINSKAEVDDIDHLSNRRVRTVGEQLSNQFSVGFVRMART 435

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +   P DLINAK + S +  FF +SQLSQ  + +N L+ ITH RRLSALG
Sbjct: 436  IRERMNVRDNEVFTPVDLINAKTLSSVINSFFGTSQLSQFMDQINPLAEITHKRRLSALG 495

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A+++  GFIETPYR V
Sbjct: 496  PGGLSRDRAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKISDMGFIETPYRTV 555

Query: 606  CDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI 661
             +G+V     D+ Y SA EEE + +AQ+N  +D++G F + + +  R   +  +V  +++
Sbjct: 556  TNGQVDLNNADIKYYSAEEEEGQVVAQSNVPIDDEGHFLQPDRIKAREGADFPVVTAQEV 615

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D +P Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPL+  E+P VGTG+E  +  
Sbjct: 616  TLMDVAPNQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLVTCESPIVGTGIEKDMIS 675

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             S   I+A+  G V   DA +I I+     E  +      +  Y L +++R+NQNT +  
Sbjct: 676  DSRIQIIAEGDGEVVFADATKIQIKYQRTEEEVICSFEPEITTYELPRYRRTNQNTSITL 735

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +P V  GD+V +  I+ +G ST  G+LALGRN+ VAFMPW GYNFED+++ISER+  ED+
Sbjct: 736  KPAVLTGDKVTKGQILTEGYSTQKGELALGRNLKVAFMPWKGYNFEDAIVISERIQREDI 795

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTS+H++E+ +  RDTK G EE+T DIPNVSE+  K++D  GII +GA V+PGDIL+GKI
Sbjct: 796  FTSVHVDEYIMEVRDTKRGVEELTSDIPNVSEDATKDLDANGIIRIGANVHPGDILIGKI 855

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++++R G +      S
Sbjct: 856  TPKGESDPSPEEKLLRAIFGDKAGDVKDASLKAQPSLHGVVIDTKLYSRAGKENKRAGKS 915

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLI 1013
             E+ QIE L      +   L + + ++L  +L G+         G + +   T  +  L+
Sbjct: 916  SEKLQIEKLDEKFAAQVADLTKQLVNKLYTLLQGKTTTGITDYFGVELYPAGTKFTQKLL 975

Query: 1014 SEYPRSQWWQ--------------FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             E  R    +                  D  +   VE     Y       +   K +   
Sbjct: 976  DELSRKVTDEKSGVAMGYLNLGTCKWTGDSHLDALVEKTINNYTIEWKKADAAIKREKYN 1035

Query: 1060 IQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            +  GD++P  GV+++ KV++A KR ++ GDKMAGRHGNKGIV+R++  EDMPFL+DGT V
Sbjct: 1036 LTNGDELPQTGVIQMAKVYIAKKRKLKVGDKMAGRHGNKGIVARVVRDEDMPFLEDGTIV 1095

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI LNPLGVPSRMN+GQI+ET LGWA   LG K  + I D  +   I+   +        
Sbjct: 1096 DICLNPLGVPSRMNLGQIYETVLGWAGKELGLKFATPIFDGASLDQINEYTA-------- 1147

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                  K+G+P                         SG++ LYD
Sbjct: 1148 ----------------------KAGIP------------------------RSGRTYLYD 1161

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TGE FD+P TVG IYMLKL HM+ DK++ARS G YSL+TQQPLGGK+  GGQR GEME
Sbjct: 1162 GGTGEKFDQPATVGVIYMLKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEME 1221

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++ +GAA +LQE+LTIKSDDV+GR + YE+IV G++  + G PE+ NVL+ E++ L 
Sbjct: 1222 VWALEGFGAANILQEILTIKSDDVMGRAKAYEAIVKGDNLPKPGIPEAMNVLLHELRGLA 1281

Query: 1359 LSIDLE 1364
            LS+ LE
Sbjct: 1282 LSVKLE 1287


>gi|304384449|ref|ZP_07366853.1| DNA-directed RNA polymerase subunit beta [Prevotella marshii DSM
            16973]
 gi|304334469|gb|EFM00758.1| DNA-directed RNA polymerase subunit beta [Prevotella marshii DSM
            16973]
          Length = 1270

 Score = 1302 bits (3369), Expect = 0.0,   Method: Composition-based stats.
 Identities = 568/1365 (41%), Positives = 797/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      I  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFASVKNPIPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYSITECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTF+I G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTDNGTFIINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ EIL  F                    
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGFESDKEILKIFDLAEEVKVNKKNMK------ 234

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + ++K   E  V                 ++
Sbjct: 235  ---------------------AAVGRKLAARIMKRWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ IE    I  +++ +I +S    I +    +  N    I NTL  D +   K
Sbjct: 262  VSIERNEVLIERETEITTENVGDILNSGSSTILLHKDAEGANKYTIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+L IYR +R  D +  + A  +   LFF   +YDL  VGR ++N +L LDT    R +
Sbjct: 322  EAVLYIYRQLRNADPADDASAREIIQNLFFSDKRYDLGEVGRYRINKKLGLDTDIATRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKEDIIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLGNQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTLSSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYRKV DG   
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYATINELGFIETPYRKVDDGVTN 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               N +VYL+A EEE+  I Q N+ L++DG+F  E+V CR   +  +V  +++D +D SP
Sbjct: 562  LDNNSIVYLTAEEEEDHIIGQGNAPLNDDGTFIREVVKCRQDADFPVVAPKQVDLMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++ASLIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTGME  V ++S   I 
Sbjct: 622  QQIASVSASLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGMEKQVCENSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++  VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGDGVISYVDATTIRILYDRTEEEEFVSFEPALKEYRVPKFRRTNQNMTIDLRPICVKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED++++SER+V +DV TS+H++
Sbjct: 742  QRVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAIVLSERLVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++DE GII +GA V PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDENGIIRIGARVEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    ++G V+D ++F+R    ++  S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLTGVVIDKKLFSRAIKTRD--SKKQDKVILA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +       G    +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNADLKDILVEKLITLAKRFSSQGVKDYTGAEIITKGSKFTATALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D      ++ L + Y     +L+   K +   I  GD++P G+L++ KV+VA
Sbjct: 980  IQSGKWTSDAHTNEMIQKLIMNYIRKYKLLDAELKRRKFAITIGDELPSGILQMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKIGVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   L  K  + I D     D+S                                 
Sbjct: 1100 ILGAAGRKLNVKFATPIFDGAKLEDLSEWTEKAGLPHLC--------------------- 1138

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TGE FD+P TVG  Y LKL
Sbjct: 1139 -------STHLYDGE--------------------------TGEQFDQPATVGVTYFLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK+++RS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LTIKS
Sbjct: 1166 GHMVEDKMHSRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTIKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DDVVGR++ YE+IV G      G PES NVL+ E++ LGLS+ L+
Sbjct: 1226 DDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSVKLD 1270


>gi|261880895|ref|ZP_06007322.1| DNA-directed RNA polymerase subunit beta [Prevotella bergensis DSM
            17361]
 gi|270332403|gb|EFA43189.1| DNA-directed RNA polymerase subunit beta [Prevotella bergensis DSM
            17361]
          Length = 1269

 Score = 1301 bits (3368), Expect = 0.0,   Method: Composition-based stats.
 Identities = 569/1367 (41%), Positives = 802/1367 (58%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F K       PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFAKVQNPFPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYFIDPPRYSISECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTF+I G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTDNGTFIINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLLRAIGYESDKDILQIFDLAEEVKVNK---------- 229

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                              +Q++  G+KL + +L+S  E  V                 ++
Sbjct: 230  ---------------RNRKQLL--GRKLAARVLRSWNEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V  E  E+ +E    I + + ++I  S    + I    ++ +  A I  TL  D +   K
Sbjct: 261  VTVERNEVILERETEITKDNYDDILESGASTVLIHKDAEAASKYAIIFETLKKDTSNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  +    + A  +F  LFF   +YDL  VGR ++N +L  D   D R +
Sbjct: 321  EAVNYIYRQLRNAEPVDEASAREVFQNLFFSDKRYDLGEVGRYRINKKLGEDISMDTRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII II+ ++ L +    +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKEDIIEIIRYMIKLIHSNAVVDDIDHLSNRRVRTVGEQLSNQFSIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYRKV D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYATINELGFIETPYRKVTDKKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               +DV YL+A EEE   +AQ N+ L+ DG+F  + V CR A +  +V  + +  +D SP
Sbjct: 561  LDNHDVEYLTAEEEEGLMVAQGNAPLNPDGTFIRDFVHCRYAADFPVVDPDDVTLMDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A+LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSAALIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  Y + KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGEGVIEYVDATTIRILYDRTEDEEFVSFEPAIKEYCIPKFRRTNQNMIIDLRPICVKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G E  T DIPNVSEE  K++DE G+I VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEVFTNDIPNVSEEATKDLDENGVIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R   +K   S   ++  ++
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--EKTRESRKQDKILLQ 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +LM +       G    +G +   K +  S  ++       
Sbjct: 919  KIDGEYEAKCDDLKNMLVDKLMTLTENKTSQGVKDFTGAEIITKGSKFSVAVLKNMEYDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE +   ++ L + Y      L      +   I  GD++P GV+++ KV+VA
Sbjct: 979  IQSNDWTDDEHINGMIQKLIMNYIRKAKQLMAEQNRRKFAISIGDELPSGVIKMAKVYVA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+I+  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKIVRAEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LGKK  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGKKFATPIFDGAKLDDLREWTE----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST V+DG                           TGEPFD+  TVG  Y L
Sbjct: 1130 -KAGLPNLCSTTVYDGE--------------------------TGEPFDQKATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ +GA++VLQEMLTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGASHVLQEMLTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G+     G PES NVL+ E++ LGLS+ ++
Sbjct: 1223 KSDDVVGRSKAYEAIVKGDPMPNPGIPESLNVLLHELRGLGLSVKMD 1269


>gi|281425125|ref|ZP_06256038.1| DNA-directed RNA polymerase, beta subunit [Prevotella oris F0302]
 gi|281400717|gb|EFB31548.1| DNA-directed RNA polymerase, beta subunit [Prevotella oris F0302]
          Length = 1269

 Score = 1301 bits (3367), Expect = 0.0,   Method: Composition-based stats.
 Identities = 576/1367 (42%), Positives = 805/1367 (58%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVHNPLPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---IHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G + + +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLLRAMGYEQDKDILQIFDLAEELKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LKS  E  V                 ++
Sbjct: 234  ---------------------AAIGRKLAARVLKSWNEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    + E +++EI  S    I +    ++ N    I NTL  D +   K
Sbjct: 261  VSIERNEVIMERETELTEDNIDEILESGASTILLHKDAEAANKYTIIFNTLSKDPSNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LDT  D R +
Sbjct: 321  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDTDMDTRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+D+I IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDVIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLANQFAIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV + KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCIYAKINDLGFIVTPYRKVNNAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVVYL+A EEE++ I Q N+ L  DG+F  + V CR   +  +V   ++D +D SP
Sbjct: 561  MDNKDVVYLTAEEEEDKIIGQGNAPLSVDGAFQRDTVKCRQDADYPVVTPNQVDLVDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++ASLIPFLE+DD +R LMGCNM RQAVPL+  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSASLIPFLEHDDGHRALMGCNMMRQAVPLIHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTEEDEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA++PW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKAGDILTEGYATENGELALGRNLLVAYIPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G+I VGA V PGDIL+GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVIRVGARVEPGDILIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    ++  S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRAVKTRD--SKKQDKILLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLM-----EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +LM     +I  G    +G +   K +  +   +       
Sbjct: 919  KIDEEYEAKNNDLKDILVDKLMTLTEGKISQGVKDYTGAEIITKGSKFTVPTLKNLEFDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D+     ++ L + Y     +L+   K K   I  GD++P G+L++ KV+VA
Sbjct: 979  IQSNNWTDDDHTNALIQKLIMNYIRKYKLLDAEMKRKKFAISIGDELPSGILQMAKVYVA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGQKLGCKFATPIFDGAKLEDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDD VGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDTVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|258647508|ref|ZP_05734977.1| DNA-directed RNA polymerase, beta subunit [Prevotella tannerae ATCC
            51259]
 gi|260852281|gb|EEX72150.1| DNA-directed RNA polymerase, beta subunit [Prevotella tannerae ATCC
            51259]
          Length = 1252

 Score = 1301 bits (3367), Expect = 0.0,   Method: Composition-based stats.
 Identities = 572/1355 (42%), Positives = 799/1355 (58%), Gaps = 117/1355 (8%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            +  PD ++VQ  S+  FL ++   ++R N+GL   F   FPI       +LEF+ Y  D 
Sbjct: 1    MPYPDFLDVQLKSFKDFLQLDTPAEQRKNDGLYKVFAENFPIADTRNNFVLEFLDYYIDA 60

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            P++ V++CL R LTY+VPLK  L+L   D D       +     Q +++G +P MT++GT
Sbjct: 61   PRYSVEECLERGLTYSVPLKAKLKLYCTDPDHEDFDTVV-----QDVFLGPIPYMTENGT 115

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            FVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++   D  ++++
Sbjct: 116  FVINGAERVVVSQLHRSPGVFFGSS---IHANGTQLYSARIIPFKGSWIEFATDINNVMY 172

Query: 204  VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
              IDR++K+PVT+ L A+G + + +IL  F                +             
Sbjct: 173  AYIDRKKKLPVTTLLRAIGFEKDKDILQIFGLSEEVKVTKANLKKYI------------- 219

Query: 263  SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                          G+KL + +LK+  E  V                 ++V+ E  E+ +
Sbjct: 220  --------------GRKLAARVLKTWVEDFVDEET------------GEVVSIERTEVIL 253

Query: 323  EAGDVIDEKSLEEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            E    I   ++EEI +S  + I + L      + + I NT   D     K+A+  IYR++
Sbjct: 254  ERETEITADNVEEILNSGSKTIEVHLDSSIGIDYSIIFNTFQKDPCNSEKEAVNYIYRLL 313

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            R  D +  + A  + N LFF   +YDL  VGR +MN +L L T  D R + +EDII IIK
Sbjct: 314  RNADPADDASAREVINNLFFSEKRYDLGEVGRYRMNRKLGLSTDGDTRVLTREDIIEIIK 373

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             L++L N K ++DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++  D +   P 
Sbjct: 374  YLIELINSKASVDDIDHLSNRRVRTVGEQLANQFSVGLARMTRTIRERMNVRDNEVFTPT 433

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            DLINAK + S +  FF ++ LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDV
Sbjct: 434  DLINAKTISSVINSFFGTNALSQFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDV 493

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV---TNDVVYLS 618
            H THYGR+CP E+ EG NIGL+SSL  +A++++ GFIETPYRKV + KV     DVVYLS
Sbjct: 494  HYTHYGRLCPIESPEGPNIGLISSLCVYAKIDSLGFIETPYRKVENSKVDLENKDVVYLS 553

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            A EEE++ I Q N+ L+ DG+F    V CR   +  +V  E+++ +D +P+Q+ SIAA L
Sbjct: 554  AEEEEDKIIGQGNAPLNSDGTFILSKVKCRQDADYPVVSPEQVELMDVAPQQIASIAAGL 613

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            IPFLE+DD++R LMG NM RQAVPL+++EAP VGTG+E  V   S   I A+  G+V+ V
Sbjct: 614  IPFLEHDDAHRALMGSNMMRQAVPLIRSEAPIVGTGIERQVCVDSRTMISAEGDGVVDFV 673

Query: 739  DAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            DA  I +   R+ + +       +  YR+ KF+R+NQN   + RP+ + G  V++ DI+ 
Sbjct: 674  DATTIRVLYDRTEDEEFVSFEPALKEYRIPKFRRTNQNMVFDLRPICEKGQRVKKGDILT 733

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            +G +T+ G+LALGRN+LVA+MPW GYN+ED+++++ER+V +D+ TS+H++EF +  R+TK
Sbjct: 734  EGYATESGELALGRNLLVAYMPWKGYNYEDAIVLNERLVRDDILTSVHVDEFSLDVRETK 793

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G EE+T DIPNVSEE  K++DE GII +GA V PGDIL+GKITPKGES  TPEEKLLRA
Sbjct: 794  RGVEELTNDIPNVSEEATKDLDENGIIRIGARVVPGDILIGKITPKGESDPTPEEKLLRA 853

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            IFG+KA DV+D SL+    +SG V+D R++++    K+  S + ++  +  L    D E 
Sbjct: 854  IFGDKAGDVKDASLKANPSLSGVVIDRRLYSKA--QKSRSSKAADKSTLLELDEQFDKET 911

Query: 976  VILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDE 1029
              L   +  +L      +   G     G +   K T  S  L+     +         DE
Sbjct: 912  SALKSAMIDKLLVLTKGKTSLGVKDTIGTEIIAKGTKFSKSLLDSLSYTSLQLNDWTNDE 971

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 + +L + Y    + ++   K +   I  GD++P G+++  KV++A KR I  GDK
Sbjct: 972  HTNLLIRTLVLNYLKKYNKMDAVLKRRKFAITIGDELPSGIIQQAKVYIAKKRKIGVGDK 1031

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+I+  EDMPFL DG PVDIVLNPLGVPSRMN+GQIFE  LG A   LG
Sbjct: 1032 MAGRHGNKGIVSKIVRQEDMPFLADGRPVDIVLNPLGVPSRMNLGQIFEAILGAAGKRLG 1091

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K  + I D     ++                                   K+G+P    
Sbjct: 1092 VKFATPIFDGAKLDELCEWTD------------------------------KAGLP---- 1117

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                      L+DG TGEPFD+  TVG  YMLKL HMV DK++A
Sbjct: 1118 --------------------RYCAEQLFDGGTGEPFDQKATVGVTYMLKLGHMVEDKMHA 1157

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTIKSDDV GR + Y
Sbjct: 1158 RSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTIKSDDVTGRAKAY 1217

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            E++V G      G PES NVL+ E++ LGLSI L+
Sbjct: 1218 EAVVKGETMPTPGIPESLNVLLHELRGLGLSITLD 1252


>gi|317503999|ref|ZP_07962006.1| DNA-directed RNA polymerase subunit beta [Prevotella salivae DSM
            15606]
 gi|315664859|gb|EFV04519.1| DNA-directed RNA polymerase subunit beta [Prevotella salivae DSM
            15606]
          Length = 1269

 Score = 1301 bits (3366), Expect = 0.0,   Method: Composition-based stats.
 Identities = 576/1367 (42%), Positives = 804/1367 (58%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVHNPLPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTANGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G + + +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLLRAMGFEQDKDILQIFDLAEEIKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LKS  E  V                 ++
Sbjct: 234  ---------------------AAVGRKLAARVLKSWNEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    + E ++ EI  S    I +    ++ N    I NTL  D +   K
Sbjct: 261  VSIERNEVIMERETELTEDNIGEILDSGASTILLHKDAEAANKYTIIFNTLSKDPSNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LD   DVR +
Sbjct: 321  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDIDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KED+IAIIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKEDVIAIIKYLIQLVNSNVTVDDIDHLSNRRVRTVGEQLANQFAIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCIYAKINDLGFIVTPYRTVHDHKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVVYL+A EEE + I Q N+ L  DG F +E V CR   +  +V  +++D +D SP
Sbjct: 561  MDNKDVVYLTAEEEEEKIIGQGNAPLSTDGKFLKETVKCRQDADYPVVTPDEVDLVDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++ASLIPFLE+DD +R LMGCNM RQAVPL+  +AP VGTG+E  V + S   + 
Sbjct: 621  QQIASVSASLIPFLEHDDGHRALMGCNMMRQAVPLIHNDAPIVGTGLEKQVCEDSRTMVT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICNKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA++PW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKAGDILTEGYATENGELALGRNLLVAYIPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G+I VGA V PGDIL+GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVIRVGARVEPGDILIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    ++  S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRAIKTRD--SKKQDKVLLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +LM +  G+        +G +   K +  +   +       
Sbjct: 919  KIDEEYEAKNNDLKDILVDKLMTLTEGKTSQGVKDYTGAEIITKGSKFTVPALKNLEFDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D+     ++ L + Y     +L+   K K   I  GD++P G+L++ KV++A
Sbjct: 979  IQSNNWTDDDHTNALIQKLIMNYIRKYKLLDAEMKRKKFAISIGDELPSGILQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGQKLGCKFATPIFDGAKLDDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGVTYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDD VGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDTVGRSKAYEAIVKGDTMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|294674790|ref|YP_003575406.1| DNA-directed RNA polymerase subunit beta [Prevotella ruminicola 23]
 gi|294473818|gb|ADE83207.1| DNA-directed RNA polymerase, beta subunit [Prevotella ruminicola 23]
          Length = 1270

 Score = 1300 bits (3365), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1367 (41%), Positives = 809/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  FG     +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFGSVKNPMPFPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  L+L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKLKLYCTDPDHEDFGTVI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G LLY+ R+IP +G W++
Sbjct: 124  PIPYMTANGTFVINGAERVVVSQLHRSPGVFFGQS---VHANGTLLYSARVIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                +   
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGFEADKDILQIFNLAEEVKVNKKSLKAVI--- 237

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G KL + +LKS  E  V                 ++
Sbjct: 238  ------------------------GCKLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  ++ +E    I E+++ +I  S  + I +       ++ + I NTL  D +   K
Sbjct: 262  VSIERNQMIMERETEITEENMMDILESGAQTILVHKDASVASDYSIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+L IYR +R  D +  + A  +   LFF   +YDL  VGR ++N +L L+T  DVR +
Sbjct: 322  EAVLYIYRQLRNADPADDASAREVIQNLFFSDKRYDLGDVGRYRINKKLGLNTDMDVRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII IIK L+ L N K T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKEDIIEIIKYLIQLVNSKATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD---G 608
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI+TPYRKV +    
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKINELGFIQTPYRKVENGVAD 561

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               N +VYL+A EE    I Q N+ L++DG+F   +V CR   +  +VP   +D +D SP
Sbjct: 562  LSDNGIVYLTAEEEAEHIIGQGNAPLNDDGTFIRSVVKCRQDADFPVVPPTDVDLMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ SIAASLIPFLE+DD++R LMG NM RQAVPLL  EAP VGTG+E  V + S   + 
Sbjct: 622  QQIASIAASLIPFLEHDDAHRALMGSNMMRQAVPLLHNEAPIVGTGIEKQVCEDSRTMVT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+ + G
Sbjct: 682  AEGDGVIEYVDATTIRILYDRTEDEEFVSFEPALKEYRIAKFRRTNQNMTIDLRPICEKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++++ER+V +DV TS+H++
Sbjct: 742  QRVKAGDILTEGYATEDGELALGRNLLVAYMPWKGYNYEDAIVLNERIVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G+I VGA V PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTADIPNVSEEATKDLDDNGVIRVGARVEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG ++D ++F R    K+ +S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVIIDKKMFQRA--IKDRKSKQQDKIVLA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +LME+  G+        +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKVEDLKDILIDKLMELTKGKTSQGVKDYTGAEIITKGSKFTATALRNLEYGD 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     +  L + +     +L+   K K   I  GD++P G+L++ KV+VA
Sbjct: 980  VQISNWTTDEHKNELIAKLIINFMKKYKLLDAEMKRKKFAITIGDELPNGILQMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+I+  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKIGVGDKLAGRHGNKGIVSKIVRQEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D++                                 
Sbjct: 1100 ILGAAGKKLGVKFATPIFDGAKLEDLAEWTD----------------------------- 1130

Query: 1200 WKSGVP--VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1131 -KAGLPRLCSTHLYDGE--------------------------TGERFDQPATVGITYFL 1163

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LTI
Sbjct: 1164 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTI 1223

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDD VGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1224 KSDDTVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSITLD 1270


>gi|313207005|ref|YP_004046182.1| DNA-directed RNA polymerase subunit beta [Riemerella anatipestifer
            DSM 15868]
 gi|312446321|gb|ADQ82676.1| DNA-directed RNA polymerase subunit beta [Riemerella anatipestifer
            DSM 15868]
 gi|315024081|gb|EFT37083.1| DNA-directed RNA polymerase subunit beta [Riemerella anatipestifer
            RA-YM]
 gi|325335561|gb|ADZ11835.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Riemerella
            anatipestifer RA-GD]
          Length = 1275

 Score = 1300 bits (3365), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1379 (42%), Positives = 815/1379 (59%), Gaps = 120/1379 (8%)

Query: 3    KGVVFNGLG---RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
                          R  F      ++ PD +++Q  S+  F  ++  P++R NEGL   F
Sbjct: 1    MSKSKTTQKAQGNQRINFSSAKGRVETPDFLDIQIQSFKEFFQLDTLPEQRVNEGLYKTF 60

Query: 60   KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            +  FPIT      +LEF+ Y  D P++ +D+C+ R LTY+VPLK  L+L   D +     
Sbjct: 61   QENFPITDSRNQFVLEFLDYLVDSPRYSIDECVERGLTYSVPLKARLKLYCTDPEYDDFQ 120

Query: 120  KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
              I     Q +Y+G +P MT  G+F+I G +R+VV+QLHRSPG+ F         +G  L
Sbjct: 121  TVI-----QDVYLGTVPYMTPSGSFIINGAERVVVTQLHRSPGVFFGQT---YHANGTKL 172

Query: 180  YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY 238
            Y  RIIP +G WM+   D   +++  IDR++K+P+T+ L A+G +S+ EIL  F      
Sbjct: 173  YYSRIIPFKGSWMEFTTDINSVMYAYIDRKKKLPLTTLLRAIGYESDKEILQIF------ 226

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                          DL    KVS + +    G       + L + +L +  E  V     
Sbjct: 227  --------------DLAEEVKVSKAALKKVEG-------RTLAARVLNTWFEDFVDEDT- 264

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                        ++V+ E  EI ++   V++++ L+ I  + ++ I +++ ++    + I
Sbjct: 265  -----------GEVVSVERNEIILDRETVLEKEHLDLILEAGVKTI-LIHNENTKEFSII 312

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            +NTL  D     K+A+  IYR +R  D      A  +   LFF   +Y L  VGR ++N 
Sbjct: 313  QNTLQKDPTNSEKEAVEYIYRQLRNADPPDEETARGIIEKLFFSEQRYSLGEVGRYRLNK 372

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +L L   + V  + KEDII+I+K L++L N K  +DDID+L NRR+R+VGE L  Q+ +G
Sbjct: 373  KLGLSVDESVEVLTKEDIISIVKHLIELANSKAEVDDIDHLSNRRIRTVGEQLAGQFGVG 432

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L R+ R+I+ER++  D +   P DL+NAK + S +  FF ++QLSQ  +  N LS ITH 
Sbjct: 433  LSRIARTIRERMNVRDNELFSPTDLVNAKTLTSVINSFFGTNQLSQFMDQTNPLSEITHK 492

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+SSL  +A++N  GFI
Sbjct: 493  RRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLISSLGIYAKINNLGFI 552

Query: 599  ETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            ETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F  E +  R  G+  +V
Sbjct: 553  ETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFETERIIARLDGDYPVV 612

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              E++D ID +P Q+  I+ASLIPFLE+DD+NR LMG NM RQAVPLLK +AP VGTG+E
Sbjct: 613  EPEQVDLIDVAPNQISGISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQAPIVGTGLE 672

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQN 773
              VA+ S   I A+  G+VE VDA RIVI+     + D+    S    Y L KF+++NQ+
Sbjct: 673  KQVARDSRILINAEGTGVVEYVDAERIVIKYDRTEDEDIVSFESATKTYHLTKFRKTNQS 732

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            T +  +P+V+VGD V +  ++ DG +T+ G+LALGRN++VAFMPW GYNFED+++I+E++
Sbjct: 733  TTITLKPIVRVGDTVEKGQVLCDGYATENGELALGRNLVVAFMPWKGYNFEDAIVINEKV 792

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V ED FTSIH++E+ +  RDTKLG EE+T DIPN+SE+  K++DE G+I +GAEV PGDI
Sbjct: 793  VREDWFTSIHVDEYSLEVRDTKLGMEELTADIPNISEDATKDLDENGMIRIGAEVKPGDI 852

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L+GKITPKGES  TPEEKLLRAIFG+KA DV+D SL+  S + G V+D ++F+R+  DK 
Sbjct: 853  LIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKADSSLRGVVIDKKLFSRNIKDKK 912

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVL 1008
            +R+    + +          +   L   +  +L  I+ G+ +       G +   K    
Sbjct: 913  KRTEEKIKLEEIENQ--YKAKFNELRTVLLDKLNTIVNGKTSQGVKNDLGEEIIGKGAKF 970

Query: 1009 SSDLISEYPRSQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            S  L+                D      ++ L   Y+   + L+     +   I  GD++
Sbjct: 971  SMKLLQSVEDYVNVSGSDWTVDADKNELIKQLIHNYKIKYNDLQGVKNREKYAISIGDEL 1030

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            P G++++ KV++A KR +  GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLG
Sbjct: 1031 PSGIIKLAKVYIAKKRKLNVGDKMAGRHGNKGIVSRIVREEDMPFLEDGTPVDIVLNPLG 1090

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQI+ET LGWA   LG K  + I D      I+                    
Sbjct: 1091 VPSRMNIGQIYETVLGWAGKQLGLKFATPIFDGAKLDQITEYTE---------------- 1134

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                          K+G+P+                         G + LYDG TGE F 
Sbjct: 1135 --------------KAGLPI------------------------YGNTYLYDGGTGERFT 1156

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            +P TVG IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+G
Sbjct: 1157 QPATVGVIYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFG 1216

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            A+ +L+E+LT+KSDDV+GR + YE+I  G    E G PESFNVL+ E+Q LGL + LE 
Sbjct: 1217 ASNILREILTVKSDDVIGRAKTYEAIAKGEAMPEPGIPESFNVLLHELQGLGLDVRLEE 1275


>gi|299141110|ref|ZP_07034247.1| DNA-directed RNA polymerase, beta subunit [Prevotella oris C735]
 gi|298577070|gb|EFI48939.1| DNA-directed RNA polymerase, beta subunit [Prevotella oris C735]
          Length = 1269

 Score = 1298 bits (3360), Expect = 0.0,   Method: Composition-based stats.
 Identities = 575/1367 (42%), Positives = 805/1367 (58%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVHNPLPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---IHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G + + +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTLLRAMGYEQDKDILQIFDLAEELKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LKS  E  V                 ++
Sbjct: 234  ---------------------AAIGRKLAARVLKSWNEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    + E +++EI  S    I +    ++ N    I NTL  D +   K
Sbjct: 261  VSIERNEVIMERETELTEDNIDEILESGASTILLHKDAEAANKYTIIFNTLSKDPSNSEK 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF    YDL  VGR ++N +L LDT  D R +
Sbjct: 321  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKCYDLGEVGRYRINKKLGLDTDMDTRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+D+I IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDVIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLANQFAIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +T+ RRLSALG GG++R
Sbjct: 441  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTYKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV + KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCIYAKINDLGFIVTPYRKVNNAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVVYL+A EEE++ I Q N+ L  DG+F  + V CR   +  +V  +++D +D SP
Sbjct: 561  MDNKDVVYLTAEEEEDKIIGQGNAPLSVDGAFQRDTVKCRQDADYPVVTPDQVDLVDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++ASLIPFLE+DD +R LMGCNM RQAVPL+  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSASLIPFLEHDDGHRALMGCNMMRQAVPLIHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTEEDEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA++PW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKAGDILTEGYATENGELALGRNLLVAYIPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G+I VGA V PGDIL+GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVIRVGARVEPGDILIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    ++  S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRAVKTRD--SKKQDKILLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLM-----EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +LM     +I  G    +G +   K +  +   +       
Sbjct: 919  KIDEEYEAKNNDLKDILVDKLMTLTEGKISQGVKDYTGAEIITKGSKFTVPTLKNLEFDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D+     ++ L + Y     +L+   K K   I  GD++P G+L++ KV+VA
Sbjct: 979  IQSNNWTDDDHTNALIQKLIMNYIRKYKLLDAEMKRKKFAISIGDELPSGILQMAKVYVA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGQKLGCKFATPIFDGAKLEDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDD VGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDTVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|282879907|ref|ZP_06288632.1| DNA-directed RNA polymerase, beta subunit [Prevotella timonensis CRIS
            5C-B1]
 gi|281306209|gb|EFA98244.1| DNA-directed RNA polymerase, beta subunit [Prevotella timonensis CRIS
            5C-B1]
          Length = 1270

 Score = 1298 bits (3359), Expect = 0.0,   Method: Composition-based stats.
 Identities = 567/1365 (41%), Positives = 801/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL +   P+ER N+GL   F   FPIT      +
Sbjct: 9    RINFASVHNPVPYPDFLDVQLKSFKDFLQLETPPEERKNDGLYKVFSENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYFIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W++
Sbjct: 124  TIPYMTDNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTTLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                +   
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYESDKDILQIFDLAEEVKVNKKNMNASI--- 237

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +LKS  E  V                 ++
Sbjct: 238  ------------------------GRRLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I E ++ +I  S    I +    +  N  A I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETEITEDNVADIIDSGASTILLHRDSELANKFAIIFNTLSKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +FN LFF   +YDL  VGR ++N +L L+T  D+R +
Sbjct: 322  EAVNYIYRQLRNADPADDASAREVFNNLFFSDKRYDLGEVGRYRINKKLGLETDMDIRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLSNQFSVGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTITSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV + KV 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCIYAKINDLGFIVTPYRKVKNAKVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               + +V+++A EEE+  + Q N+ L  DGSF  + V CR   +  +V  +++  +D SP
Sbjct: 562  MNNDHIVFMTAEEEEDLIVGQGNAPLRPDGSFIRDYVKCRQDADYPVVDPDQVALVDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 622  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+VE VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGNGVVEYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICNKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISER+V +DV TS+H++
Sbjct: 742  QRVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAIVISERVVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++DE G+I VGA V PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGMEEFTSDIPNVSEESTKDLDENGVIRVGARVEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKKHDKVVLA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +       G    +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNNDLKDILVDKLLTLTEDKKSQGVKDYTGAEIITKGSSFTAAALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE   + +++L + Y     +L+   K +   I  GD++P GVL++ KV++A
Sbjct: 980  IQSNDWTVDEHTNKLIQALIMNYIRKYKMLDAELKRRKFAISIGDELPSGVLQMAKVYIA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+I+  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKISVGDKLAGRHGNKGIVSKIVRAEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A + LG K  + I D     D+S                                 
Sbjct: 1100 ILGAAGLKLGVKFATPIFDGAKLEDLSEWTEKAGLPHLC--------------------- 1138

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TGE FD+P TVG  Y LKL
Sbjct: 1139 -------STHLYDGE--------------------------TGEKFDQPATVGITYFLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK+++RS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LT+KS
Sbjct: 1166 GHMVEDKMHSRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTVKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DD VGR++ YE+IV G+     G PES NVL+ E++ LGLS+ L+
Sbjct: 1226 DDTVGRSKAYEAIVKGDGMPAPGIPESLNVLLHELRGLGLSVKLD 1270


>gi|255534439|ref|YP_003094810.1| DNA-directed RNA polymerase subunit beta [Flavobacteriaceae bacterium
            3519-10]
 gi|255340635|gb|ACU06748.1| DNA-directed RNA polymerase beta subunit [Flavobacteriaceae bacterium
            3519-10]
          Length = 1275

 Score = 1298 bits (3358), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1369 (42%), Positives = 820/1369 (59%), Gaps = 117/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             G  R  F      I+ PD +++Q  S+  F  ++  P++R NE L   F+  FPIT   
Sbjct: 11   QGTERINFSAAKGKIETPDFLDIQIQSFKDFFQLDTLPEQRANEALYKTFEENFPITDSR 70

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  D P++ +D+C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 71   NQFVLEFLDYLVDSPRYSIDECVERGLTYSVPLKARLKLYCTDPEHEDFQTVV-----QD 125

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +Y+G +P MT  G+F+I G +R++V+QLHRSPG+ F         +G  LY  RIIP +G
Sbjct: 126  VYLGPVPYMTPSGSFIINGAERVIVTQLHRSPGVFFGQT---YHANGTKLYYSRIIPFKG 182

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             WM+   D  ++++  IDR++K+P+T+ L A+G +S+ +IL  F                
Sbjct: 183  SWMEFTTDINNVMYAYIDRKKKLPLTTLLRAIGFESDKDILQIF---------------- 226

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                DL    KVS + +    G       + L + +L +  E  V               
Sbjct: 227  ----DLAEEVKVSKAALKKVEG-------RTLAARVLNTWFEDFVDEDT----------- 264

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
              ++V+ E  EI ++   V++++ L+ I  + ++ I +++ ++ N  + I+NTL  D   
Sbjct: 265  -GEVVSIERNEIILDRETVLEKEHLDLILDAGVKSI-LIHKENSNEFSIIQNTLQKDPTN 322

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              K+A+  IYR +R  D      A  +   LFF   +Y L  VGR ++N +L L+ P   
Sbjct: 323  SEKEAVEYIYRQLRNADPPDEETARGIIEKLFFSEQRYSLGEVGRYRLNKKLGLNIPAKT 382

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              + KEDII+I++ L++L N K  +DDID+L NRR+++VGE L  Q+ +GL R+ R+I+E
Sbjct: 383  EVLTKEDIISIVRHLIELVNSKAEVDDIDHLSNRRIKTVGEQLSGQFGVGLSRIARTIRE 442

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DL+NAK + S +  FF ++QLSQ  +  N LS ITH RRLSALG GG
Sbjct: 443  RMNVRDNEIFTPIDLVNAKTLTSVINSFFGTNQLSQFMDQTNPLSEITHKRRLSALGPGG 502

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVH THYGRICP ET EG NIGL+SSL  +A++N+ GFIETPYRKV +G
Sbjct: 503  LSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLISSLGLYAKINSLGFIETPYRKVTNG 562

Query: 609  KVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            KV      V+L+A +EE++ IAQAN  + EDG+ + + V  R  G+  +V  +++D ID 
Sbjct: 563  KVDLKTTAVFLNAEDEEDKVIAQANVEMKEDGTISTDRVIARLDGDYPVVEPQQVDLIDV 622

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+  I+ASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  VA+ S   
Sbjct: 623  APNQISGISASLIPFLEHDDANRALMGSNMMRQAVPLLKPEAPIVGTGLEQQVARDSRIL 682

Query: 727  IVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G VE VDA +I I+     + DL    S    Y+L KF+++NQ+T +  RP V+
Sbjct: 683  INAEGNGTVEYVDADKITIKYERTEDDDLVSFESATKTYKLTKFRKTNQSTTITLRPNVR 742

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD+V++  ++ DG +T+ G+LALGRN++VAFMPW GYNFED+++I+E++V ED FTSIH
Sbjct: 743  VGDKVQKGQVLCDGYATENGELALGRNLVVAFMPWKGYNFEDAIVINEKVVREDWFTSIH 802

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            ++E+ +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GA+V PGDI++GKITPKGE
Sbjct: 803  VDEYSLEVRDTKLGMEELTADIPNVSEEATKDLDENGMIRIGADVKPGDIMIGKITPKGE 862

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  TPEEKLLRAIFG+KA DV+D SL+  S + G V++ ++F+R+  DK +R+      +
Sbjct: 863  SDPTPEEKLLRAIFGDKAGDVKDASLKADSSLRGVVINKKLFSRNIKDKKKRTEEK--LK 920

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            +E +      +   L   +  +L  ++ G+ +         +   K    ++ L+     
Sbjct: 921  LEEIENTYKAKFDQLRNTLLEKLGTLVNGKTSQGVNNDLDEEIIGKGVKFTTKLLQSVED 980

Query: 1019 SQWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                       D      ++ L   Y+   + ++     +   I  GD++P G++++ KV
Sbjct: 981  YVNVSGADWTVDADKNELIKQLIHNYKIKFNDIQGVKNREKFAISIGDELPAGIIKLAKV 1040

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            +VA KR +  GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1041 YVAKKRKLNVGDKMAGRHGNKGIVSRIVREEDMPFLEDGTPVDIVLNPLGVPSRMNIGQI 1100

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG K  + I D      I                               
Sbjct: 1101 YETVLGWAGQKLGLKFATPIFDGANIDQI------------------------------- 1129

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                            G  E+        A L E G + LYDG TGE F +P TVG IYM
Sbjct: 1130 ---------------TGYTEQ--------AGLPEFGSTYLYDGGTGERFSQPATVGVIYM 1166

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +L+E+LT
Sbjct: 1167 LKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNILREILT 1226

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +KSDDV+GR + YE+I  G    E G PESFNVL+ E+Q LGL + LE 
Sbjct: 1227 VKSDDVIGRAKTYEAIAKGEAMPEPGIPESFNVLLHELQGLGLDVRLEE 1275


>gi|281422258|ref|ZP_06253257.1| DNA-directed RNA polymerase, beta subunit [Prevotella copri DSM
            18205]
 gi|281403763|gb|EFB34443.1| DNA-directed RNA polymerase, beta subunit [Prevotella copri DSM
            18205]
          Length = 1270

 Score = 1295 bits (3350), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1367 (41%), Positives = 808/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFASVHNPYPYPDFLDVQLKSFKDFLQLDTPPEERKNDGLYKVFSENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTDNGTFVINGAERVVVSQLHRSPGVFFSQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G + + +IL  F                    
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYEQDKDILQIFDLAEEVKVNKKNMK------ 234

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LKS  E  V                 ++
Sbjct: 235  ---------------------AAIGRKLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    +   ++EEI  S  + I +    ++ N    I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETELTADNIEEIVESGAQTILLHKDEEAANKFTIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNLDT  DVR +
Sbjct: 322  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLDTDIDVRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKEDIIEIIKYLIQLINSSATVDDIDHLSNRRVRTVGEQLANQFSIGLARMTRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV D KV 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRKVNDSKVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVVYL+A +EE++ I Q N+ L  DGSF  ++V CR   +  +V  +++D++D SP
Sbjct: 562  MANEDVVYLTAEDEESKIIGQGNAPLTVDGSFIRDVVKCRQDADYPVVGPDQVDYVDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 622  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGEGVIEYVDATTIRILYDRTEDDEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICNKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA++PW GYN+ED+++ISERMV +DV TS+H++
Sbjct: 742  QRVKKGDILTEGYATEKGELALGRNLLVAYIPWKGYNYEDAVVISERMVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GI+ VGA + PGDI++GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGIVRVGARIEPGDIMIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKKQDKIILA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +  G         +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKGNDLKDILVDKLLTLTEGMTSEGVKDYTGAEIITKGSTFTATALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                   +DE     ++ L + Y      L+   K +   I  GD++P G+L++ KV++A
Sbjct: 980  VQSNKWTKDEHTNGLIQRLIMNYIRKYKQLDAELKRRKFAITIGDELPSGILQMAKVYIA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPF+ DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKIQVGDKLAGRHGNKGIVSKVVRLEDMPFMADGRPVDMVLNPLGVPSRMNLGQIFEC 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+S                                 
Sbjct: 1100 ILGAAGKKLGVKFATPIFDGAKLDDLSEWTD----------------------------- 1130

Query: 1200 WKSGVP--VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                            GE FD+P TVG  Y L
Sbjct: 1131 -KAGLPRFCSTYLYDGET--------------------------GEQFDQPATVGMTYFL 1163

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LT+
Sbjct: 1164 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTV 1223

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1224 KSDDVVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELRGLGLSIKLD 1270


>gi|323344620|ref|ZP_08084844.1| DNA-directed RNA polymerase subunit beta [Prevotella oralis ATCC
            33269]
 gi|323093890|gb|EFZ36467.1| DNA-directed RNA polymerase subunit beta [Prevotella oralis ATCC
            33269]
          Length = 1270

 Score = 1293 bits (3346), Expect = 0.0,   Method: Composition-based stats.
 Identities = 571/1367 (41%), Positives = 807/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RVNFASVHNPMPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYTIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VV+QLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTDNGTFVINGAERVVVAQLHRSPGVFFGQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYEADKDILRIFDLAEELKVNKK--------- 231

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +LKS  E  V                 ++
Sbjct: 232  ------------------NVKAAVGRRLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I   +++EI  S    I +    DS    + I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETEITADNVDEILDSGASTILLHKDADSAGKYSIIFNTLAKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L L+T  D+R +
Sbjct: 322  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINRKLGLNTDMDIRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIEIIKYLIQLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFIETPYR V +GKV 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKINELGFIETPYRNVKNGKVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+V+L+A EEE++ I Q N+ L   GSF    V CR   +  +V  +++D +D SP
Sbjct: 562  MDNKDIVFLTAEEEEDKLIGQGNAPLTSSGSFVRNYVKCRQDADYPVVSPDQVDLMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 622  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKKVCEDSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGDGVIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICNKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
             +V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV +DV TS+H++
Sbjct: 742  QKVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ G+I VGA V PGDI++GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGVIRVGARVEPGDIIIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG ++D ++F+R    K   +   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVIIDKKMFSRA--IKTRETKKQDKITLA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +L G+        +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNNDLKDILVDKLLTLLEGKNSQGVKDYTGAEIITKGSKFTAAALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     V+ L + Y     +L+   K +   I  GD++P G+L++ KV+VA
Sbjct: 980  IQSNGWTNDEHKNVLVQKLIMNYIRKYKLLDAELKRRKFAISIGDELPSGILQMAKVYVA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1040 KKRKIQVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K+ + I D     D+                                  
Sbjct: 1100 ILGAAGKKLGVKLATPIFDGAKLEDLQEWTD----------------------------- 1130

Query: 1200 WKSGVP--VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TG  FD+P TVG  Y L
Sbjct: 1131 -KAGLPRLCSTYIYDGE--------------------------TGTRFDQPATVGITYFL 1163

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1164 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1223

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDD VGR++ YESIV G+     G PES NVL+ E++ LGLS+ L+
Sbjct: 1224 KSDDTVGRSKAYESIVKGDAMPTPGIPESLNVLLHELRGLGLSVKLD 1270


>gi|284039326|ref|YP_003389256.1| DNA-directed RNA polymerase subunit beta [Spirosoma linguale DSM 74]
 gi|283818619|gb|ADB40457.1| DNA-directed RNA polymerase, beta subunit [Spirosoma linguale DSM 74]
          Length = 1271

 Score = 1293 bits (3345), Expect = 0.0,   Method: Composition-based stats.
 Identities = 571/1373 (41%), Positives = 807/1373 (58%), Gaps = 139/1373 (10%)

Query: 26   IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
             PD +++Q  S+  F  ++   ++R  EGL   F+  FPI+       LEF+ Y  DPPK
Sbjct: 4    YPDFLDIQVKSFKDFFQLDTPSNQRSEEGLFKVFQENFPISDSRENFKLEFIDYLVDPPK 63

Query: 86   FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
            + VD+ + R LTY+VPLK  LRL   D D         +  EQ +++G++P MT+ G+FV
Sbjct: 64   YSVDESIDRGLTYSVPLKAKLRLTNNDPDNEDF-----ETIEQEVFLGNIPYMTEKGSFV 118

Query: 146  IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
            I G +R++VSQLHRSPG+ F   K     +G  LY+ RIIP +G W++   D  ++++  
Sbjct: 119  INGAERVIVSQLHRSPGVFFSMSK---HTNGTKLYSARIIPFKGSWIEFSTDVNNVMYAY 175

Query: 206  IDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
            IDR++K PVT+ L A+G  S+ +IL  F                                
Sbjct: 176  IDRKKKFPVTTLLRAIGFGSDKDILDLFGLSEE--------------------------- 208

Query: 265  VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            V           G++L + +L++  E  V                 ++V+    E+ +E 
Sbjct: 209  VPATPANLKKAIGRRLAARVLRTWTEDFVDEDT------------GEVVSISRNEVLLER 256

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDS-VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
               I    ++ I  S  + + +   D  + +   I NTL  D +   K+A+  IYR +R 
Sbjct: 257  DSAISADDIDVITESGQKSVILHKEDMNMADYNIIYNTLQKDSSNSEKEAVEQIYRQLRN 316

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
             D      A  +   LFF   +YDL  VGR ++N +L LD   D++ +  EDI++I+K L
Sbjct: 317  ADAPDEQTAREIIQSLFFSDKRYDLGDVGRYRINKKLGLDISSDMKVLTTEDIVSIVKYL 376

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            + L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+IKER++  D +   P DL
Sbjct: 377  IGLINSKAVVDDIDHLSNRRVRTVGEQLYAQFGVGLARMARTIKERMNVRDNEDFKPVDL 436

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            INA+ + S +  FF ++QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+RDVH 
Sbjct: 437  INARTLSSVINSFFGTNQLSQFMDQTNPLAEVTHKRRMSALGPGGLSRERAGFEVRDVHY 496

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAME 621
            THYGR+C  ET EG NIGL+SSL  +A++N+ GFIETPYR + +GKV+ D  V+YL+A E
Sbjct: 497  THYGRLCTIETPEGPNIGLISSLCVYAKINSMGFIETPYRIIENGKVSMDKPVMYLTAEE 556

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+  YIAQAN+ +D+ G+F  + +  R  G+  +     + F+D +P Q+VS+AAS+IPF
Sbjct: 557  EDTHYIAQANAGIDKKGNFQVDRLKARFEGDFPMAEPANVTFMDIAPNQIVSVAASMIPF 616

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LE+DD+NR LMG NMQRQAVPLL+ EAP VGTG+E  VA  S   ++A+  G++E VD+ 
Sbjct: 617  LEHDDANRALMGSNMQRQAVPLLRPEAPIVGTGLEGRVAVDSRTLVIAEADGVIEFVDST 676

Query: 742  RIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            +I+++     +            Y L+KF+R+NQ+TC+N +P V  G  V++ D++ +G 
Sbjct: 677  KIIVKYNLDEDQMAVTFDEDRKTYNLIKFRRTNQDTCINIKPTVLKGQRVKKGDVLCEGY 736

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +T  G+LALGRNM VAFMPW GYNFED+++ISER+V ED+FTSIHIEEFE+  RDTK G 
Sbjct: 737  ATQAGELALGRNMKVAFMPWQGYNFEDAIVISERVVREDIFTSIHIEEFELEVRDTKRGE 796

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            EE+T +IPNVSEE ++N+DE GI+ VG EV  GDIL+GKITPKGES  TPEEKLLRAIFG
Sbjct: 797  EELTSEIPNVSEETVRNLDENGIVRVGTEVKEGDILIGKITPKGESDPTPEEKLLRAIFG 856

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
            +KA DV+D S + P  + G V+D ++F R    K +R     +++++ L +    E    
Sbjct: 857  DKAGDVKDASKKAPPSLKGVVIDTKLFARP--AKEDRGKH--KDEVKALMKKYGRELNDF 912

Query: 979  DRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQWWQF--------- 1024
               +  +L+ +L G+ +       G +   K    S   I+E        +         
Sbjct: 913  RARMIEKLVALLDGKTSAGVKHKFGDEIVSKGVKFSRKNITENLFPDRNAYRDESSYAVP 972

Query: 1025 -------------AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                            DEKV   V  L   Y   +S +  RFK +   ++ GD++P G++
Sbjct: 973  EEANLLSDMNLEGWTDDEKVNMMVVELVKSYNNRRSEITGRFKRERFTLEVGDELPAGIV 1032

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ KV++A KR ++ GDKMAGRHGNKG+V+RI+  EDMPFL+DGT VDIVLNPLGVPSRM
Sbjct: 1033 KLAKVYIAKKRKLKVGDKMAGRHGNKGVVARIVRDEDMPFLEDGTKVDIVLNPLGVPSRM 1092

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQI+ET L WA   L +K  + I D      ++   +                     
Sbjct: 1093 NLGQIYETVLAWAGQKLDRKYATPIFDGATEQQVADELNEAGL----------------- 1135

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                             P F                    G++ LY+GLTG+ FD+PVTV
Sbjct: 1136 -----------------PSF--------------------GRTYLYNGLTGDRFDQPVTV 1158

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IYMLKL H+V DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +L
Sbjct: 1159 GIIYMLKLGHLVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNIL 1218

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            QE+LT+KSDDVVGR + YE+IV G +  +   PESFNVLV E++ L L I LE
Sbjct: 1219 QEILTVKSDDVVGRAKAYEAIVKGENLPKPNIPESFNVLVHELRGLALEITLE 1271


>gi|288801081|ref|ZP_06406537.1| DNA-directed RNA polymerase, beta subunit [Prevotella sp. oral taxon
            299 str. F0039]
 gi|288332015|gb|EFC70497.1| DNA-directed RNA polymerase, beta subunit [Prevotella sp. oral taxon
            299 str. F0039]
          Length = 1269

 Score = 1292 bits (3344), Expect = 0.0,   Method: Composition-based stats.
 Identities = 566/1365 (41%), Positives = 801/1365 (58%), Gaps = 118/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 9    RINFASVHNPMPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYYIDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VV+QLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTHNGTFVINGAERVVVAQLHRSPGVFFGQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                +   
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYETDNDILQIFDLAEEVKVNKKVLKASI--- 237

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL + +LK+  E  V                 ++
Sbjct: 238  ------------------------GRKLAARVLKTWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ ++    I E+++E+I  S    I +    +  N  + I NTL  D +   K
Sbjct: 262  VSIERNEMIMDRETEITEENMEDILDSGCSTILLHKDSEMANKYSLIFNTLAKDPSNTEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L L+   D R +
Sbjct: 322  EAVNYIYRQLRNADPADDASAREVFQNLFFSDKRYDLGEVGRYRINRKLGLEIDMDTRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DIIAII+ L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIAIIRYLIQLINSNATVDDIDHLSNRRVRNVGEQLANQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFI TPYR V D KV 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYANINDLGFIVTPYRTVKDSKVE 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                +VVYL+A EEEN+ I Q N+ L  DGSF    V CR   +  +V  E +D +D SP
Sbjct: 562  MDNKNVVYLTA-EEENKIIGQGNAPLTVDGSFIRTTVKCRQDADYPVVAPEHVDLVDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++ASLIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSASLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKKVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+++ VDA  I I   R+ E D       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 681  AEGDGVIDYVDATTIRILYDRTEEEDFVSFEPALKEYRIPKFRRTNQNMTIDLRPICTKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED++++SER+V +D+ TS+H++
Sbjct: 741  QRVKQGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAIVLSERIVRDDILTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GI+ VGA + PGDIL+GKI+PKGES 
Sbjct: 801  EYSLDVRETKRGVEEFTSDIPNVSEEATKDLDDNGIVRVGARIEPGDILIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   +   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRETKKQDKVLLA 918

Query: 966  LLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             L  + + +   L   +  +L      ++  G    +G +   K +  ++ ++       
Sbjct: 919  SLEEEYEAKNNDLKDILVDKLLVLTEDKVSEGVKDYTGAEIVTKGSKFTTTILKNLEYDG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + Y     +L+   K +   I  GD++P G+L++ KV++A
Sbjct: 979  IQAGGWTSDEHTNGLIKQLIMNYIHKYKLLDAELKRRKFAISIGDELPSGILQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1039 KKRKIGVGDKLAGRHGNKGIVSKVVRMEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+S                                 
Sbjct: 1099 ILGAAGKKLGVKFATPIFDGAKLDDLSEWTEKAGLPHLC--------------------- 1137

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TGE FD+P TVG  Y LKL
Sbjct: 1138 -------STHLYDGE--------------------------TGEQFDQPATVGVTYFLKL 1164

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LT+KS
Sbjct: 1165 GHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTVKS 1224

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DD VGR++ YE+IV G+     G PES NVL+ E++ LGLSI L+
Sbjct: 1225 DDTVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|282878714|ref|ZP_06287482.1| DNA-directed RNA polymerase, beta subunit [Prevotella buccalis ATCC
            35310]
 gi|281299105|gb|EFA91506.1| DNA-directed RNA polymerase, beta subunit [Prevotella buccalis ATCC
            35310]
          Length = 1270

 Score = 1292 bits (3344), Expect = 0.0,   Method: Composition-based stats.
 Identities = 568/1365 (41%), Positives = 802/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      +  PD ++VQ  S+  FL +   P+ER N+GL   F   FPIT      +
Sbjct: 9    RINFASVHNPVPFPDFLDVQLKSFKDFLQLETPPEERKNDGLYKVFAENFPITDTRNNFV 68

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +++CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 69   LEFLDYFIDPPRYSIEECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 123

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 124  TIPYMTDNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTMLYSARIIPFKGSWIE 180

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G  S+ +IL  F                    
Sbjct: 181  FATDINNVMYAYIDRKKKLPVTTLLRAIGYQSDKDILQIFDLAEEVKVNKKNMK------ 234

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G++L + +LKS  E  V                 ++
Sbjct: 235  ---------------------AAVGRRLAARVLKSWNEDFVDEDT------------GEV 261

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I  +++++I  S    + +    +  N  A I NTL  D +   K
Sbjct: 262  VSIERNEVIMERETEITAENVQDILDSGASTLLLHKDSELANKFAIIFNTLSKDPSNSEK 321

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A+ +FN LFF   +YDL  VGR ++N +L LDT  D+R +
Sbjct: 322  EAVTYIYRQLRNADPADDASAKEVFNNLFFSDKRYDLGEVGRYRINKKLGLDTDMDIRVL 381

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 382  TKDDIIEIIKYLIQLVNSNATVDDIDHLSNRRVRTVGEQLSNQFSIGLARMSRTIRERMN 441

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 442  VRDNEVFTPTDLINAKTITSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 501

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV D KV 
Sbjct: 502  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYAKINDMGFIVTPYRKVKDKKVD 561

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               + +V+++A EEE+  + Q N+ L +DGSF  + V CR   +  +V  +++  +D SP
Sbjct: 562  MNNDHIVFMTAEEEEDLPVGQGNAPLRKDGSFIRDYVKCRQDADYPVVDPDEVALMDVSP 621

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A+LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V ++S   I 
Sbjct: 622  QQIASVSAALIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCENSRTMIT 681

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+   G
Sbjct: 682  AEGDGVIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMTIDLRPICVKG 741

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRNMLVA+MPW GYN+ED+++ISER+V +DV TS+H++
Sbjct: 742  QRVKDGDILTEGYATENGELALGRNMLVAYMPWKGYNYEDAVVISERVVRDDVLTSVHVD 801

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++DE GII VGA V PGDIL+GKI+PKGES 
Sbjct: 802  EYSLDVRETKRGMEEFTNDIPNVSEEATKDLDENGIIRVGARVEPGDILIGKISPKGESD 861

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F R    K   +   ++  + 
Sbjct: 862  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFTRA--IKTRETKKHDKLILA 919

Query: 966  LLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  + + +   L   +  +L+ +       G    +G +   K +  ++  +       
Sbjct: 920  KIDEEYEAKNTDLKDILVDKLLTLTESKKSQGVKDYTGAEIITKGSNFTAAALKNLEYDG 979

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     +++L + Y     +L+   K +   I  GD++P GVL++ KV++A
Sbjct: 980  IQSNDWTDDEHTNGLIQTLILNYIRKYKLLDAELKRRKFAISIGDELPTGVLQMAKVYIA 1039

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKGIVS+I+  EDMPFL+DG PVD+VLNPLGVPSRMN+GQIFE 
Sbjct: 1040 KKRKISVGDKLAGRHGNKGIVSKIVRVEDMPFLEDGRPVDLVLNPLGVPSRMNLGQIFEA 1099

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+S                                 
Sbjct: 1100 ILGAAGRKLGVKFATPIFDGAKLDDLSEWTDKAGLPHLC--------------------- 1138

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   ST ++DG                           TG+ FD+P TVG  Y LKL
Sbjct: 1139 -------STHLYDGE--------------------------TGKKFDQPATVGVTYFLKL 1165

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA++VLQE+LTIKS
Sbjct: 1166 GHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHVLQEILTIKS 1225

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DD VGR++ YE+IV G+     G PES NVL+ E++ LGLS+ L+
Sbjct: 1226 DDTVGRSKAYEAIVKGDAMPTPGIPESLNVLLHELRGLGLSVKLD 1270


>gi|171914821|ref|ZP_02930291.1| DNA-directed RNA polymerase subunit beta [Verrucomicrobium spinosum
            DSM 4136]
          Length = 1282

 Score = 1286 bits (3329), Expect = 0.0,   Method: Composition-based stats.
 Identities = 614/1398 (43%), Positives = 845/1398 (60%), Gaps = 148/1398 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  FGK  E ++ P+LIE+Q  SY+ FL  +IAP +R + GLQA F+ VFPI+++    
Sbjct: 3    QRINFGKLKEPVEPPNLIEIQLKSYEEFLQKDIAPSKRKDLGLQAVFREVFPISSYDEKM 62

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L+F  YE   PK +    +    T++ PL +T     +++ +  GA      K++ +YM
Sbjct: 63   TLDFTQYEIGEPKLNPLQAIREAETFSAPLYVT-----YELRDEAGA------KQERVYM 111

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G+LP+MT  GTFVI G +R+VVSQLHRSPGI F+  +    L+G+ LY  RIIPD+G W+
Sbjct: 112  GELPMMTTRGTFVINGAERVVVSQLHRSPGICFETQQ---HLNGRWLYGFRIIPDRGTWL 168

Query: 193  DIEFDSKDIIHVRID---RRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFP 248
            +++FD+ D+++V +D   RRRK   T+ L  +G    E+IL  FYP      +       
Sbjct: 169  EVQFDTNDLLYVYLDRRRRRRKFLATTLLRVIGYPGDEDILKLFYPIEDLKLKE-----T 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            ++  DL           DI  GE ++  + + LT G+++ L + G K +           
Sbjct: 224  MNEEDLAQKVIFR----DILDGELIVARAYEPLTLGIVRQLIQLGHKSI----------- 268

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                                  +  L                        I  +L  D  
Sbjct: 269  ----------------RCVTATQDDL------------------------IIASLRKDPA 288

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
             D  +AL +IYR +RPGD  T   A ++   LFFD  +YDL+ VGR K+N +L +    +
Sbjct: 289  HDEDEALKEIYRRLRPGDPPTIPNARALVKRLFFDPKRYDLTRVGRYKINQKLGIKVDSE 348

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             R +   D+++ ++ L  LR G+G +DDID+LG+RRVR+VGE+L NQ R+GL R ER +K
Sbjct: 349  ERILTAMDVVSSLRYLFKLRAGEGVLDDIDHLGSRRVRAVGELLANQCRVGLARTERLVK 408

Query: 488  ERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            ER++  D  +D + PQ LIN K + + V +FF  SQLSQ  + +N L+ +TH RRLSALG
Sbjct: 409  ERMTLFDVNMDVMTPQKLINPKALSAVVRDFFARSQLSQFMDQINPLAELTHKRRLSALG 468

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL S+AR+N +GFIETP+RKV
Sbjct: 469  PGGLNRDRAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLCSYARINEFGFIETPFRKV 528

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
              G VT+ + YL+A +EEN  +AQAN+ +DE+G F  + V  R  G+ + V  E+   +D
Sbjct: 529  ESGVVTDKIEYLTADQEENHNVAQANNIIDENGKFKSDKVSVRYRGDFLEVAPEQATLMD 588

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQ VPLL+AEAP VGTGMES  A+ S A
Sbjct: 589  VSPKQMVSVAASLIPFLEHDDANRALMGSNMQRQGVPLLEAEAPLVGTGMESKAARDSQA 648

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS--------------GVDIYRLMKFQRSN 771
             IV+   GIV    A  I++           +              G+  Y L KF RSN
Sbjct: 649  VIVSDSGGIVAAATADYIIVTKDGQLPISEKAFAAEPTKITTDPERGIYFYPLRKFMRSN 708

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
              TC+NQRPLV+ G +V++ D++ADGP TD G+LALGRNMLVAFMPW+GYNFED+++IS 
Sbjct: 709  AGTCINQRPLVERGQKVKKGDVLADGPCTDHGELALGRNMLVAFMPWNGYNFEDAIVISR 768

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED++TSIHIE+FEV ARDTKLGPEEITRDIPNV +E L+N+   G++ +GAEV PG
Sbjct: 769  RVVKEDIYTSIHIEDFEVGARDTKLGPEEITRDIPNVGDEALRNLGADGVVRIGAEVKPG 828

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGKITPK E+ + PEE+LLRAIFGEKA DV+DTSLRVPSG +G V+DVR+ +R+G D
Sbjct: 829  DILVGKITPKSETELAPEERLLRAIFGEKAADVKDTSLRVPSGCTGIVMDVRVSSRNGAD 888

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL--- 1008
            K   S S +++QI+ +  +  ++   L   +  +L EIL  +         +   V+   
Sbjct: 889  KERLSPSEQKKQIKQVTEEHKNKVEQLTEQLTEKLSEILLNEKIPLDVVNGETGEVIIGA 948

Query: 1009 ---SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                +  +       +    +    ++  +  +   +E      +   +  +++++ G++
Sbjct: 949  NKKITKTLLRTLAENYRTVEIDQSPIRNKIMDIVAAFEAKFDEADIERERGLDRLEQGEE 1008

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            M  GV++ V+VF+A KR +  GDKMAGRHGNKG+V+ I+P EDMPFL+DGTPVDI LNPL
Sbjct: 1009 MESGVIKQVRVFIASKRKLSVGDKMAGRHGNKGVVATIVPEEDMPFLEDGTPVDICLNPL 1068

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMNVGQ+ ETHLG A   LG  + + + D      I       +            
Sbjct: 1069 GVPSRMNVGQVLETHLGVAAKALGFTVATPVFDGIKEDKILGYLKEAK------------ 1116

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F+               L+  G+S L DG +GEPF
Sbjct: 1117 ---------------------ATPGFEWI------------GLN--GKSKLIDGRSGEPF 1141

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               V VGYIYMLKL H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 1142 ALEVVVGYIYMLKLGHLVADKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWALEAY 1201

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            GAAY LQE+LT+KSDDV GRTR+YESIV G+++ E GTPESFNVL+KEMQ+LGL + + N
Sbjct: 1202 GAAYTLQELLTVKSDDVQGRTRIYESIVKGDNSLEAGTPESFNVLIKEMQSLGLDVKVVN 1261

Query: 1366 SRTKNSAKMEEIPDFNKC 1383
              +     +     +   
Sbjct: 1262 RNSGEEEILGGGGSYATA 1279


>gi|227536131|ref|ZP_03966180.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
            33300]
 gi|300772103|ref|ZP_07081973.1| DNA-directed RNA polymerase subunit beta [Sphingobacterium
            spiritivorum ATCC 33861]
 gi|227244028|gb|EEI94043.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
            33300]
 gi|300760406|gb|EFK57232.1| DNA-directed RNA polymerase subunit beta [Sphingobacterium
            spiritivorum ATCC 33861]
          Length = 1269

 Score = 1285 bits (3325), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1366 (42%), Positives = 801/1366 (58%), Gaps = 119/1366 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F  + ++ID PD ++VQ  S+  F  +    D R  EGL   F   FPI+      
Sbjct: 9    ERVNFATSKKVIDYPDFLDVQLQSFKEFFQLETTSDNRHQEGLFKVFSENFPISDSRNIF 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++D+ +C+ R LTY+VPLK  L+L   D +       +     Q +Y+
Sbjct: 69   VLEFLDYFIDPPRYDIQECIERGLTYSVPLKAKLKLSCNDEEHEDFETIV-----QDVYL 123

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFV+ G +R++VSQLHRSPG+ F   +     +G  LY+ R+IP +G W+
Sbjct: 124  GTIPYMTPKGTFVVNGAERVIVSQLHRSPGVFFGQSR---HTNGTKLYSARVIPFKGSWI 180

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K PVT+ L A+G DS+ +IL  F                   
Sbjct: 181  EFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDSDKDILELFDLADEVKVSKSGLKK---- 236

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G++L + +LK   E  V                 +
Sbjct: 237  -----------------------YVGRRLAARVLKKWVEDFVDEDT------------GE 261

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNKD 369
            +V+ +  EI +E   V++E  ++ I  + ++ + +   D+ NN  Y  I NTL  D +  
Sbjct: 262  VVSIDRNEIILERETVLEEDHIDFIIDAGVKSVILAKDDASNNADYSIIYNTLQKDTSNS 321

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             K+A+  IYR +R  +      A  + + LFF   +YDL  VGR ++N +L LDTP D +
Sbjct: 322  EKEAVEHIYRQLRNAEPPDEETARGIIDRLFFSDKRYDLGDVGRYRINRKLQLDTPADTK 381

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             + +EDIIAI+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+I+ER
Sbjct: 382  VLTREDIIAIVKYLINLINSKAEVDDIDHLSNRRVRTVGEQLYAQFGVGLSRMARTIRER 441

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 442  MNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 501

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--D 607
            +R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GFIETPYRKV    
Sbjct: 502  SRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLAVHAKINNLGFIETPYRKVEAGR 561

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              V   V+YLSA +E+ + IAQAN+  DE G+F +  V  R  G+  ++  EK+D +D S
Sbjct: 562  VVVEEPVIYLSAEDEDEKTIAQANAIYDEKGNFEDPKVKARYEGDFPIIEPEKLDLMDVS 621

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG+E  VA+ S   I
Sbjct: 622  PNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPQAPIVGTGLEGRVARDSRTLI 681

Query: 728  VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+VE VDA  I IR     +  L      +  Y+L+KF+++NQ+TC+N +P+V+ 
Sbjct: 682  NAEGNGVVEYVDAEEIKIRYDRTEDDRLVSFDDDIKTYKLIKFKKTNQSTCINLKPIVRK 741

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V +  ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISER+VS+D+FTS+HI
Sbjct: 742  GQRVEKGQVLCEGYATEDGELALGRNLKVAFMPWQGYNFEDAIVISERVVSQDIFTSLHI 801

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFE+  RDTK G EE+T DIPNVSEE  K++DE GII +GAEV  GDIL+GKITPKGES
Sbjct: 802  EEFELEVRDTKRGEEELTADIPNVSEEATKDLDENGIIRIGAEVGEGDILIGKITPKGES 861

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F+R      + S  VER+ +
Sbjct: 862  DPSPEEKLLRAIFGDKAGDVKDASLKTPPSIKGVVIDTKLFSRA----KKMSKEVERKTL 917

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTVLSSDLISEYPRS 1019
            E L    D    +L   +  +L  I+ G+ +      +K     K    +  ++++    
Sbjct: 918  EKLETTHDRNVKVLKDRLVDKLFTIVNGKTSQGIYNVYKELLVPKGAKFTQKILADLNYD 977

Query: 1020 QWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+     +++    +    +     FK +   I  GD++P G++++ KV+V
Sbjct: 978  NINPTGWTTDDDKNELIKAALHFFNIKLNEELGAFKREKFAISVGDELPSGIVQMAKVYV 1037

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+E
Sbjct: 1038 AKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLGVPSRMNLGQIYE 1097

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA   LG K  + I D     ++    +         ++       D         
Sbjct: 1098 TVLGWAGQKLGVKFATPIFDGAEPSEVEGWIAKAGLPASGRTYLYNGLTGDR-------- 1149

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                        FD      +  ML                                  K
Sbjct: 1150 ------------FDQPTTVGVIYML----------------------------------K 1163

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +LQE+LT+K
Sbjct: 1164 LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNILQEILTVK 1223

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDDVVGR + YE+IV GN+      PESFNVLV E++ LGL I L+
Sbjct: 1224 SDDVVGRAKTYEAIVKGNNLPTPSVPESFNVLVHELRGLGLDITLD 1269


>gi|300776017|ref|ZP_07085876.1| DNA-directed RNA polymerase subunit beta [Chryseobacterium gleum ATCC
            35910]
 gi|300505150|gb|EFK36289.1| DNA-directed RNA polymerase subunit beta [Chryseobacterium gleum ATCC
            35910]
          Length = 1273

 Score = 1283 bits (3321), Expect = 0.0,   Method: Composition-based stats.
 Identities = 571/1365 (41%), Positives = 805/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F      I  PD +++Q  S+  F  ++  P+ R  E L   F+  FPIT      +
Sbjct: 13   RINFSSAKGKIITPDFLDIQIESFREFFQLDTLPEARKTEALYKTFQENFPITDSRNQFV 72

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  D P++ +D+C+ R LTY+VPLK  L+L   D +       +     Q +Y+G
Sbjct: 73   LEFLDYLVDSPRYSIDECVERGLTYSVPLKARLKLYCTDPEHEDFQTVV-----QDVYLG 127

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT  G+F+I G +R++V+QLHRSPG+ F         +G  LY  RIIP +G WM+
Sbjct: 128  PVPYMTPSGSFIINGAERVIVTQLHRSPGVFFGQT---YHANGTKLYYSRIIPFKGSWME 184

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D   +++  IDR++K+P+T+ L A+G +S+ +IL  F                    
Sbjct: 185  FTTDINSVMYAYIDRKKKLPLTTLLRAIGYESDKDILQIF-------------------- 224

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            DL    KVS + +    G       + L + +L +  E  V                 ++
Sbjct: 225  DLAEEVKVSKAALKKVEG-------RTLAARVLNTWFEDFVDEDT------------GEV 265

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            V+ E  EI ++   +++++ L+ I  + ++ I +++ ++ N  + I+NTL  D     K+
Sbjct: 266  VSIERNEIILDRETILEKEHLDLILDAGVKSI-LIHKENSNEFSIIQNTLQKDPTNSEKE 324

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A+  IYR +R  D      A  +   LFF   +Y L  VGR ++N +L L+ P     + 
Sbjct: 325  AVEYIYRQLRNADPPDEETARGIIEKLFFSEQRYSLGEVGRYRLNKKLGLNIPTTTEVLT 384

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            KEDIIAI++ L++L N K  +DDID+L NRR+++VGE L  Q+ +GL R+ R+IKER++ 
Sbjct: 385  KEDIIAIVRHLIELVNSKAEVDDIDHLSNRRIKTVGEQLAGQFGVGLSRIARTIKERMNV 444

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             D +   P DL+NAK + S +  FF ++QLSQ  +  N LS ITH RRLSALG GG++R 
Sbjct: 445  RDNEIFTPLDLVNAKTLTSVINSFFGTNQLSQFMDQTNPLSEITHKRRLSALGPGGLSRE 504

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV-- 610
            RAG E+RDVH THYGRICP ET EG NIGL+SSL  +A++N  GFIETPYRKV  GKV  
Sbjct: 505  RAGFEVRDVHHTHYGRICPIETPEGPNIGLISSLGIYAKINNLGFIETPYRKVESGKVDL 564

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              D +YL+A +EE + IAQAN  L ++G F  + +  R  G+  +V   ++D ID +P Q
Sbjct: 565  NADPIYLNAEDEEAKVIAQANVELSDNGDFETDRIIARLDGDYPVVEPNQVDLIDVAPNQ 624

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +  I+ASLIPFLE+DD+NR LMG NM RQAVPLLK +AP VGTG+E  VA+ S   I A+
Sbjct: 625  ISGISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQAPIVGTGLEQQVARDSRILINAE 684

Query: 731  RAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              G V+ VDA +IVI+     + DL    S    Y L KF+++NQ+T +  RP V+VGD 
Sbjct: 685  GTGTVQYVDADKIVIKYERSEDEDLVQFESATKTYNLTKFRKTNQSTTITLRPNVRVGDV 744

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  ++ DG +T+ G+LALGRN++VAFMPW GYNFED+++I+E++V ED FTSIH++E+
Sbjct: 745  VEKGQVLCDGYATEKGELALGRNLVVAFMPWKGYNFEDAIVINEKVVREDWFTSIHVDEY 804

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE+T DIPNVSEE  K++DE G+I +GAEV PGDI++GKITPKGES  T
Sbjct: 805  SLEVRDTKLGMEELTADIPNVSEEATKDLDENGMIRIGAEVKPGDIMIGKITPKGESDPT 864

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLLRAIFG+KA DV+D SL+  S + G V++ ++F+R+  DK +R+      ++E +
Sbjct: 865  PEEKLLRAIFGDKAGDVKDASLKADSSLRGVVINKKLFSRNIKDKKKRTEEK--LKLEEI 922

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRSQWW 1022
                  +   L   +  +L  ++ G+ +         +   K    +  L++        
Sbjct: 923  ENTYKAKFDELRNTLIEKLNTLVSGKTSQGVHNDLDEEIIGKGVKFTHKLLTSVEDYVNV 982

Query: 1023 --QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D      ++ L   Y+   + ++     +   I  GD++P G++++ KV++A 
Sbjct: 983  SGSDWTVDADKNELIKQLIHNYKIKYNDIQGVKNREKFAISIGDELPAGIMKLAKVYIAK 1042

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +  GDKMAGRHGNKGIVSRI+  EDMPFL+DGTPVDIVLNPLGVPSRMN+GQI+ET 
Sbjct: 1043 KRKLNVGDKMAGRHGNKGIVSRIVREEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETV 1102

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA   LG K  + I D      I+                                  
Sbjct: 1103 LGWAGQKLGMKFATPIFDGATLDQITEYTDKAGL-------------------------- 1136

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                    P F                    G + LYDG TGE F +  TVG IYMLKL 
Sbjct: 1137 --------PKF--------------------GHTYLYDGGTGERFTQAATVGVIYMLKLG 1168

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +L+E+LT+KSD
Sbjct: 1169 HMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNILREILTVKSD 1228

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DV+GR + YE+I  G    E G PESFNVL+ E+Q LGL + LE 
Sbjct: 1229 DVIGRAKTYEAIAKGESMPEPGIPESFNVLLHELQGLGLDVRLEE 1273


>gi|223936435|ref|ZP_03628347.1| DNA-directed RNA polymerase, beta subunit [bacterium Ellin514]
 gi|223894953|gb|EEF61402.1| DNA-directed RNA polymerase, beta subunit [bacterium Ellin514]
          Length = 1282

 Score = 1283 bits (3319), Expect = 0.0,   Method: Composition-based stats.
 Identities = 601/1373 (43%), Positives = 828/1373 (60%), Gaps = 144/1373 (10%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  FGK  EII  P+LIE+Q  SY  FL   +AP +R N GLQA F  VFPI ++ 
Sbjct: 17   RVTERINFGKIKEIIAPPNLIELQTNSYKEFLQAEVAPSKRKNLGLQAVFTEVFPIESYD 76

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            G  +L+F SYE   PK D  +CL   LT+  PL +T  L      +              
Sbjct: 77   GKCVLDFHSYEIGEPKLDWLECLREGLTFGAPLYVTFLLKEEKGTKEEK----------- 125

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            ++MG+LPLMT  GTFVI G +R++VSQLHRSPG+ F+        +GK L++ RIIPD+G
Sbjct: 126  VFMGELPLMTPQGTFVINGAERVIVSQLHRSPGLAFEKS---IHPNGKELFSFRIIPDRG 182

Query: 190  LWMDIEFDSKDIIHVRID---RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
             W + +FD+ D+++V +D   RRRK   T+F  ALG  S+ +IL  FY     S +    
Sbjct: 183  SWYEAQFDTSDLLYVYLDRKKRRRKFLTTTFFRALGYGSDADILKLFYDIEELSVK---- 238

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                   + +    +    +D D G  V  + + L+  ++K + E G+  + +       
Sbjct: 239  --EAEKLEDLQNKVLIEDALDADKGIVVARAFEPLSKAVVKQISEVGINKIKV------- 289

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
                   V+  + E  +                                       +  D
Sbjct: 290  -------VDTTSDEGIV------------------------------------IKCMKKD 306

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
              K+  +AL DIYR +RPGD  T + A ++   LFFD+ +YDL  VGR K+N +L +   
Sbjct: 307  PAKNEDEALKDIYRRLRPGDPPTAANARALIKRLFFDAKRYDLGRVGRYKINQKLGIK-G 365

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             D R + KED++A  K L+ L+ G+GT+DDID+LG+RRVR+VGE+L NQ R+GL R ER 
Sbjct: 366  GDSRILTKEDLVAATKYLLRLKKGEGTLDDIDHLGSRRVRTVGELLANQCRVGLARTERL 425

Query: 486  IKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            +KER++  D  ++S+ PQ LIN K + + + +FF  SQLSQ  + +N L+ +TH RRLSA
Sbjct: 426  VKERMTLFDQGMESMTPQKLINPKALSAVIRDFFGRSQLSQFMDQINPLAELTHKRRLSA 485

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG GG++R RAG E+RDVHP+HYGRICP ET EG NIGL++SL +FAR+N +GF+ETPYR
Sbjct: 486  LGPGGLSRDRAGFEVRDVHPSHYGRICPVETPEGPNIGLIASLATFARINDFGFLETPYR 545

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +G+V+N + YL+A  EE   +AQAN+ +DE G F  E V CR  G+ + V   ++D+
Sbjct: 546  KVENGRVSNHIDYLTADREEAFTVAQANAVIDEKGHFLTERVMCRAKGDFVDVEPARVDY 605

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVPLL  +AP V TG+E  VA+ S
Sbjct: 606  MDVSPKQLVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLITDAPLVATGLEDRVARDS 665

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSV-------EGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             A I A+  G V  V   +++I +        +       +GV +Y++ KF RSN  TC+
Sbjct: 666  RAVIAAEEGGKVASVIGNQVIITADGKLPETKKKIKHSPENGVYVYQIRKFMRSNAATCI 725

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ+ LV  GD V++  +IADGP T  G+LALGRN+L AFMPW+GYNFED++LISER+V +
Sbjct: 726  NQKILVNKGDTVKKGQVIADGPCTQGGELALGRNVLCAFMPWNGYNFEDAILISERIVKD 785

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D+FTSIHI+EFEV ARDTKLGPEEITRDIPN+ +E LKN+   G+I VGAEV PGDILVG
Sbjct: 786  DIFTSIHIDEFEVGARDTKLGPEEITRDIPNLGDEALKNLGPDGVIRVGAEVKPGDILVG 845

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            KITPK E+ + PEE+LLRAIFGEKA DV+DTSL+VPSG  G V+DV++  +   +++ R 
Sbjct: 846  KITPKSETELAPEERLLRAIFGEKAADVKDTSLKVPSGTYGIVMDVKVSAKKEAEQSMRV 905

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL------SS 1010
             + E+ Q + +  +   +   L   +   L  IL G+         +   ++       +
Sbjct: 906  STEEKRQSKEVEEEYKKKMDELREQLTEALSNILLGEKIPLDVVNSETGEIIIPANRKIT 965

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              +     + + +  +    ++  +  +   ++     L+ ++  ++E+ + GD +  G+
Sbjct: 966  KTLLRKLATVYDRIEIDPSPIRNKINEIIGSFKKKFDDLQMQYDEELERAESGDGVDTGI 1025

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            ++ VKV++A KR +  GDKMAGRHGNKG+V++I+  EDMPFL +GTPVDIVLNPLGVPSR
Sbjct: 1026 IKSVKVYIASKRKLSVGDKMAGRHGNKGVVAKIVAEEDMPFLDNGTPVDIVLNPLGVPSR 1085

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQ+ ETHLGWA   LG K  + + D     DI                         
Sbjct: 1086 MNVGQVLETHLGWAAKLLGLKFATPVFDGIKEKDIRGYLKEAGLPEHAK----------- 1134

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             T + DG                           TG+ FD+ + 
Sbjct: 1135 -----------------TKLIDG--------------------------RTGQVFDQEIV 1151

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGYIYM+KL H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1152 VGYIYMMKLGHLVADKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWAMEAYGAAYT 1211

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            LQE+LT+KSDDV GRTR+YESIV G+++ E G PESFNVLVKEMQ+LGL + +
Sbjct: 1212 LQELLTVKSDDVQGRTRIYESIVKGDNSLEAGVPESFNVLVKEMQSLGLDVKV 1264


>gi|225164279|ref|ZP_03726550.1| DNA-directed RNA polymerase, beta subunit [Opitutaceae bacterium
            TAV2]
 gi|224801121|gb|EEG19446.1| DNA-directed RNA polymerase, beta subunit [Opitutaceae bacterium
            TAV2]
          Length = 1267

 Score = 1282 bits (3318), Expect = 0.0,   Method: Composition-based stats.
 Identities = 612/1376 (44%), Positives = 844/1376 (61%), Gaps = 147/1376 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  FGK  E+I  P+LIE+Q  SY  FL   +   +R  +GL+A F+ VFPI ++ G  
Sbjct: 8    ERLNFGKLREVIQPPNLIEIQITSYLDFLQKGVPDKQRKPQGLEAVFREVFPIESYDGRL 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    PK    +C+   +T++VPL + LRL           +    IK++ IYM
Sbjct: 68   NLEYVSYTLGEPKSSEIECIREGITFSVPLYVKLRL-----------REEDFIKDEEIYM 116

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++P++T+ G+F+I G +R+VVSQLHRSPG+ F+ D+     +GK L+A RIIPD+G W+
Sbjct: 117  GEIPMVTERGSFIINGAERVVVSQLHRSPGLCFEKDR---HTNGKELFAFRIIPDRGTWL 173

Query: 193  DIEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +++FD  D+++V +DRRR   K  +T+   ALG     +IL  FY               
Sbjct: 174  EVQFDINDLLYVYLDRRRRRRKFLITTLFRALGYSDNTKILELFYN-------------- 219

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                           + DI   + +                           + +  L  
Sbjct: 220  ---------------VQDIKVSKLL-------------------------EMENVSTLAF 239

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
             ED+++   G +   A + + ++ +      ++  + ++  D+  +   I   L  D  +
Sbjct: 240  VEDVIDAHKGVVLARALEPLTKQIVRSFEKHDVTSLRVI--DTAIDEGAIVRALKKDPTR 297

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            + ++AL +IY+ +RPG+  T + A+++   LFFD  +YDL  VGR K+N +LNLDT  + 
Sbjct: 298  NEEEALKEIYKRLRPGEPPTTANAKALLKRLFFDPKRYDLGAVGRYKINQKLNLDTSLEE 357

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +  EDII   K LV LR G+G +DDID+LG+RRVR+VGE+L N+ R GL R ER ++E
Sbjct: 358  RIVNSEDIILSTKYLVKLRQGQGVVDDIDHLGSRRVRTVGELLANECRKGLARTERLVRE 417

Query: 489  RISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            R++  D   DS+ P  LIN K + + + +FF  SQLSQ  + +N L+ +TH RRLSALG 
Sbjct: 418  RMTMYDQSVDSITPNKLINPKALTTVIRDFFARSQLSQFMDQINPLAEVTHKRRLSALGP 477

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL+++A VN +GFIETPYR V 
Sbjct: 478  GGLNRERAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLSTYAHVNMFGFIETPYRIVK 537

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DG+VT+ + YL+A +EE + IAQAN+ +D+ G F    V  R  GE + V   ++ ++D 
Sbjct: 538  DGRVTDKIEYLTANQEEAKIIAQANAEIDDKGHFVG-KVTVRQDGEFLEVDASEVHYMDV 596

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SPKQV+SIAA +IPFLE+DD+NR LMG NMQRQ VPLL+A++P+VGTG+E  VA+ S   
Sbjct: 597  SPKQVISIAAGMIPFLEHDDANRALMGANMQRQGVPLLQAQSPYVGTGIEERVARDSKIV 656

Query: 727  IVAKRAGIVEQVDAIRIVIRSV--------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             VA+ AG+V  VDA RIV+           +   +   +GV IY L K+ RSN +TC NQ
Sbjct: 657  QVAEEAGLVALVDAKRIVVTPDGQLPKNFDKNPKNDPKNGVRIYELRKYMRSNASTCFNQ 716

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +P+VK G  V+  DIIADGPST+ G++ALGRN+LVAFMPW+GYNFED++LISE+++ ED+
Sbjct: 717  KPIVKKGQPVKIGDIIADGPSTEKGEMALGRNVLVAFMPWNGYNFEDAILISEKVLKEDI 776

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHI EFEV ARDTKLGPEEITRDIPNV EE LKN+D  G+I VGAEV PGDILVGKI
Sbjct: 777  FTSIHIHEFEVTARDTKLGPEEITRDIPNVGEEALKNLDHNGVIRVGAEVKPGDILVGKI 836

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPK E+ + PEEKLLRAIFGEKA DV+DTSL VPSG SG V+DV++ +R      + S S
Sbjct: 837  TPKSETELAPEEKLLRAIFGEKAADVKDTSLIVPSGESGIVMDVKVSSRIDNQAEKLSPS 896

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSD 1011
              R Q + +  +   +   L  ++   L  IL G+          +G      +  ++  
Sbjct: 897  DRRRQTKQIQEEYKTQMDKLRESLTESLSNILLGEKIPLDVVNGANGEIIIPANRKITKT 956

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+ +          +    V+  +  +   +++    LE   + K+  ++ G+D   G +
Sbjct: 957  LLRKLAAVS-KHIEIDPSPVRIKIMEIIGSFQSKFDELETDRERKVSSVESGEDNGNGAI 1015

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV++A K+ ++ GDKMAGRHGNKG+V++I+P EDMPFL DGTP+ I LNPLGVPSRM
Sbjct: 1016 KQVKVYIATKQKLEVGDKMAGRHGNKGVVAKIVPEEDMPFLPDGTPIQICLNPLGVPSRM 1075

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQ+ ETHLGWAC  LG K+ + + D      I                          
Sbjct: 1076 NVGQVLETHLGWACSKLGIKVATPVFDGIPEKKIREYLKDA------------------- 1116

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G+PV                        SG+S LYDG TGE  D+ V V
Sbjct: 1117 -----------GLPV------------------------SGKSPLYDGRTGEKIDQEVVV 1141

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GYIYM+KLNH+VS K++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ L
Sbjct: 1142 GYIYMMKLNHLVSHKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWALEAYGAAHTL 1201

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            QE+LT+KSDDV GRT++YES+V G++T   GTPESFNVL+KE+Q+LGL I L    
Sbjct: 1202 QELLTVKSDDVQGRTKIYESLVKGDNTLIAGTPESFNVLIKEIQSLGLDIKLNKRD 1257


>gi|212550363|ref|YP_002308680.1| DNA-directed RNA polymerase subunit beta [Candidatus Azobacteroides
            pseudotrichonymphae genomovar. CFP2]
 gi|212548601|dbj|BAG83269.1| DNA-directed RNA polymerase beta subunit [Candidatus Azobacteroides
            pseudotrichonymphae genomovar. CFP2]
          Length = 1268

 Score = 1280 bits (3313), Expect = 0.0,   Method: Composition-based stats.
 Identities = 571/1370 (41%), Positives = 808/1370 (58%), Gaps = 117/1370 (8%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
                 R  FG     ++ PD +EVQ  S+  FL ++   ++R NEGL    K  FPIT  
Sbjct: 2    KKNDQRISFGSIKRPVEYPDFLEVQLKSFQDFLQLDTPLEKRKNEGLYKICKENFPITDI 61

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              + +L+F+ Y  D P++   +C+ + LTY+VPLK  L+L   D D       I     Q
Sbjct: 62   RNSFVLDFLDYYIDSPRYSFKECIEKGLTYSVPLKARLKLYCTDSDHEDFDTVI-----Q 116

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +Y+G +P MT+ GTFVI G +R+VVSQLHRS G+ F         +G  LY+ RIIP +
Sbjct: 117  DVYLGTIPYMTEKGTFVINGAERVVVSQLHRSAGVFFGQSL---HSNGTKLYSARIIPTK 173

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
            G W++   D  ++++  IDRR+K+P+T+ L A+G   + +IL  F          D    
Sbjct: 174  GSWIEFATDINNVMYAYIDRRKKLPITTLLRAIGFGRDKDILDIFDIAEEIDVSEDNLKK 233

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
             +                           G+KL + +LK   E  V              
Sbjct: 234  VI---------------------------GRKLAARVLKVWVEDFVDEDT---------- 256

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDK 366
               ++V+ E  E+ I+   ++ E  +++I     + I +   D ++++ A I NTL+ D 
Sbjct: 257  --GEVVSIERNEVVIDREMILQEIYIDKIIECGAKIILLHREDKNLSDYAIIYNTLLKDP 314

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +   +DA++ IYR +R  D +    A      LFF + +YDL  VGR ++N +LNL  P 
Sbjct: 315  SNSEQDAVIYIYRQLRNMDPTDDISARETVQNLFFSNKRYDLGEVGRYRINKKLNLSLPI 374

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            DVR + KED+  IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ + L RM R +
Sbjct: 375  DVRVLTKEDVTEIIKYLIELANSKADVDDIDHLSNRRVRTVGEQLSNQFGVALARMARIV 434

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D +   P DLINAK V S +  FF ++ LSQ  +  N L+ ITH RR+SALG 
Sbjct: 435  RERMNVRDNEVFTPIDLINAKTVSSVINTFFGTNALSQFMDQTNPLAEITHKRRMSALGP 494

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+++  GF+ETPYRKV 
Sbjct: 495  GGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKISNMGFVETPYRKVS 554

Query: 607  DGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            + KV   +  +VYL A EEE + IAQ ++ +++DG+F ++ +  R   +  +V   +++ 
Sbjct: 555  NSKVDNSSGGIVYLVAEEEEGKIIAQGDALVNDDGTFVDDRIKARKDADYPVVTPSEVEL 614

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SP Q+ SIAA+LIPFLE++D+NR LMG NM RQAVPLL +E P VGTG+E  +   S
Sbjct: 615  MDVSPTQIASIAAALIPFLEHNDANRALMGSNMMRQAVPLLNSEVPIVGTGLEGRIISDS 674

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               I+++ AG V  VD+ RI I+     E +     S V  Y + K++++NQNT ++  P
Sbjct: 675  RTQIMSEGAGEVVFVDSTRIDIKYDRTEEEEFVSFESAVKTYAIPKYKKTNQNTSIDLHP 734

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK GD V R  I+ +G +++ G+LALG+N+ VAFMPW GYNFED+++ISER+V ED+FT
Sbjct: 735  IVKKGDRVERGQILTEGYASENGELALGKNLKVAFMPWKGYNFEDAIIISERVVREDIFT 794

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+E+ +  R+TK G EE+T DIPNVSEE  +N+DE GI+ +GA + PGDIL+GK+TP
Sbjct: 795  SIHIDEYILDVRETKRGAEELTSDIPNVSEEATRNLDENGIVRLGARIEPGDILIGKVTP 854

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGES  +PEEKLLRAIFGEKA DV+D SL+    ++G V++  +F+R    K ++S    
Sbjct: 855  KGESDPSPEEKLLRAIFGEKAGDVKDVSLKASPSLNGIVIERNLFSRA--IKRDKSRQDS 912

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILC-----GQNAVSGPKGFKKSTVLSSDLISE 1015
            +  +  L ++ + +   L+  +  +L+ ++      G     G +   K    S   + +
Sbjct: 913  KSNLIQLNKEYEIKVNELESILVKKLLSLVKDEISQGVKDFMGIELISKGAKFSEGDLRK 972

Query: 1016 YPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               +         D +    + +L   Y      L    K K      GD++P GVL++ 
Sbjct: 973  IDYTSVQISKWTADSRKNTMISNLIANYIKKYKQLSAELKRKEFNCAIGDELPSGVLQMA 1032

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV+VA KR +Q GDKMAGRHGNKGIVSRI+  EDMPFL+DGT +DIVLNPLGVPSRMN+G
Sbjct: 1033 KVYVAKKRKLQVGDKMAGRHGNKGIVSRIVRDEDMPFLEDGTIIDIVLNPLGVPSRMNLG 1092

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            QIFET LGW+   LG +  + I D  +  D+                             
Sbjct: 1093 QIFETVLGWSGEKLGVRFATPIFDGASLKDLDKWTD------------------------ 1128

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                  K+G+P                          G++ LYDG TGE FD+P TVG I
Sbjct: 1129 ------KAGLP------------------------RYGKTYLYDGGTGERFDQPATVGVI 1158

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+++LQE+
Sbjct: 1159 YMLKLGHMVDDKMHARSVGPYSLITQQPLGGKAQVGGQRFGEMEVWALEAFGASFILQEI 1218

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            LTIKSDDV+GR   YE+IV GN   + G PES NVL+ EM+ L L+I LE
Sbjct: 1219 LTIKSDDVIGRAMTYEAIVKGNPIPDPGIPESLNVLLYEMRGLALNIILE 1268


>gi|34112959|gb|AAQ62404.1| DNA-directed RNA polymerase beta subunit (RpoB) [uncultured marine
            gamma proteobacterium EBAC31A08]
          Length = 1218

 Score = 1280 bits (3312), Expect = 0.0,   Method: Composition-based stats.
 Identities = 618/1225 (50%), Positives = 863/1225 (70%), Gaps = 16/1225 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                +    R+RK FG   +++D+P+LIE Q  SY  FL  ++APD R  +GL+  F+S+
Sbjct: 1    MSYSYTEKKRIRKNFGTFTKVMDLPNLIETQTKSYSEFLQADVAPDARKKQGLEDVFQSL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + SG A LE+VSYE     +DV +CL + L+Y+ PL+I ++L+++D    T  K +
Sbjct: 61   FPIKSVSGNAALEYVSYELGKNTYDVQECLVQGLSYSAPLRIKVKLVLYDR--ETNFKEV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKE  ++MG++PLMT D +FV+ G +R+VV+QLHRSPG+ +DHDKG+   SGK+LY+ 
Sbjct: 119  KDIKEGEVFMGEVPLMTSDASFVVNGTERVVVAQLHRSPGVFYDHDKGKTHSSGKVLYSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KDI+  RIDRRRK+P T  L AL M +EEILS FY + V+S   
Sbjct: 179  RIIPYRGSWLDFEFDPKDILFSRIDRRRKIPATIMLRALDMGTEEILSEFYDEDVFSLEK 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            D     L    L  G  +   +      +  +E+GK++T+  +K L    V  + +  + 
Sbjct: 239  DSVKLALIPERL-RGETLPVDIKVK--SKVYVEAGKRITARHIKELSNANVSEITLAEEF 295

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +++DI N ETGE+   A   ID + LE +  + + DI  L+++ ++   YI NTL
Sbjct: 296  LIGKVLSKDIFNKETGEVLYSANTEIDNEVLEALKENNVSDITCLFINELDKGPYISNTL 355

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
              D   +R +AL++IYR+MRPG+  T   AE++FN LFF+ ++YDLS VGR+K N RL L
Sbjct: 356  RADPTSNRLEALVEIYRMMRPGEPPTKDSAETLFNNLFFNEERYDLSEVGRMKFNRRLKL 415

Query: 423  D-TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            D   ++   + KEDII ++K +V++R+G   +DDID+LGNRRVRSVGEM  NQ+R+GL+R
Sbjct: 416  DSKKENDNILDKEDIIEVMKGIVNIRDGHDIVDDIDHLGNRRVRSVGEMTANQFRVGLIR 475

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER+++ER+S  + D + PQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 476  VERAVRERLSMAEADELGPQDLINAKPVTAAIKEFFGSSQLSQFMDQNNPLSEITHKRRV 535

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S  S++R N YGFIETP
Sbjct: 536  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSFASYSRTNQYGFIETP 595

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YRKV +G VT++++YLSA++E    IAQAN +LD++  F ++LV  R A E  L+  +++
Sbjct: 596  YRKVINGTVTDEIMYLSAIDEAEHVIAQANVTLDKNNKFVDDLVAVRHASEFELMSSDRV 655

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D +D SP+QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP+L+AE P VGTG+ESVVA+
Sbjct: 656  DLMDVSPQQVVSIAASLIPFLEHDDANRALMGSNMQRQAVPVLRAEKPLVGTGLESVVAR 715

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG  IVAK +G+VE VDA RIV+R  +     S S  D+Y L+K+ RSNQNTC+NQRP+
Sbjct: 716  DSGVCIVAKNSGVVENVDASRIVVRVTDK---KSKSASDVYNLVKYTRSNQNTCINQRPI 772

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+VGD V+  D++ADGPS D G+LALG+N+ +AFMPW+GYNFEDS+LISE++  ED FTS
Sbjct: 773  VRVGDVVKSGDVLADGPSVDNGELALGQNIRIAFMPWNGYNFEDSILISEKVAREDRFTS 832

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   +ARDTKLG EEIT DIPNV E  L  +D+CGI+ VGAEV PGDILVGKITPK
Sbjct: 833  IHIQEIVCVARDTKLGSEEITADIPNVGEGSLNKLDDCGIVYVGAEVEPGDILVGKITPK 892

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ ++PEEKLLRAIFGEKA DV+DTS R  S   GTV++V +F R G++K+ER+ ++E+
Sbjct: 893  GETQLSPEEKLLRAIFGEKASDVKDTSQR--SSAKGTVINVEVFTRDGVEKDERTQAIEQ 950

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            + ++   +D DDE  ++++   +RL ++L G+ A+ G  G KK   LS + + E   +  
Sbjct: 951  DHLDKSKKDADDEAFVVEQATKTRLCDLLKGKKAIKG-NGIKKGETLSLERLEELDLNDL 1009

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +      + +   +E  +  Y++    ++ RF+ K  KI  G D+ PGV+++VKV++A+K
Sbjct: 1010 FSIRTDTDTINDVIEDTEKSYKSYAKDIKARFEEKKAKIIRGHDLAPGVIKIVKVYLAIK 1069

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S I+P EDMP+ KDG PVDIVLNPLGVPSRMNVGQI ETH+
Sbjct: 1070 RRIQPGDKMAGRHGNKGVISEIMPVEDMPYDKDGHPVDIVLNPLGVPSRMNVGQILETHM 1129

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGSHTEKISDYDDDSVLRVAEQW 1200
            G A  G+G+KI  ++   K N   + L+++L+K+     ++ E I+ +++  ++ +A   
Sbjct: 1130 GCAAKGIGQKIDLML---KENAKPAELKTYLDKLYNTNAANKEDINSFNNTEIMELAHNL 1186

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRM 1225
            K G+P++TPVFDGA E  +  +L++
Sbjct: 1187 KDGLPIATPVFDGAKESEVKDLLKL 1211


>gi|326799811|ref|YP_004317630.1| DNA-directed RNA polymerase subunit beta [Sphingobacterium sp. 21]
 gi|326550575|gb|ADZ78960.1| DNA-directed RNA polymerase subunit beta [Sphingobacterium sp. 21]
          Length = 1269

 Score = 1280 bits (3311), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1378 (41%), Positives = 807/1378 (58%), Gaps = 123/1378 (8%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA   + N     R  F  +  +ID PD ++VQ  S+  F  +    D R  EGL   F 
Sbjct: 1    MANKDIRNE----RVNFATSKRVIDYPDFLDVQLQSFKEFFQLETTSDNRHQEGLFKVFS 56

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              FPI+      +LEF+ Y  DPP++D+ +C+ R LTY+VPLK  LRL   D +      
Sbjct: 57   ENFPISDSRNIFVLEFLDYFIDPPRYDIQECIERGLTYSVPLKAKLRLSCNDEEHEDFET 116

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +     Q +Y+G +P MT  GTFVI G +R++VSQLHRSPG+ F   +     +G  LY
Sbjct: 117  IV-----QDVYLGTIPYMTPKGTFVINGAERVIVSQLHRSPGVFFGQSR---HTNGTKLY 168

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
            + R+IP +G W++   D  ++++  IDR++K PVT+ L A+G DS+ +IL  F       
Sbjct: 169  SARVIPFKGSWIEFATDVNNVMYAYIDRKKKFPVTTLLRAIGYDSDKDILELFELADEVK 228

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
                                           ++++  G+KL + +LK   E  V      
Sbjct: 229  VSKSGL-------------------------KKLV--GRKLAARVLKRWVEDFVDEDT-- 259

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY-- 357
                       ++V+ +  EI +E   ++++  ++ I  + ++ I +   DS NN  Y  
Sbjct: 260  ----------GEVVSIDRNEIILERETILEDDHIDMIIDAGVKSIILTKEDSSNNADYSI 309

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I NTL  D +   K+A+  IYR +R  +      A  +   LFF   +YDL  VGR ++N
Sbjct: 310  IYNTLQKDTSNSEKEAVEHIYRQLRNAEPPDEETARGIIERLFFSDKRYDLGDVGRYRIN 369

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +L LDTPD+++ + K+DIIAI+K L++L N K  +DDID+L NRRVR+VGE L  Q+ +
Sbjct: 370  RKLQLDTPDEIKVLTKQDIIAIVKYLINLINSKAEVDDIDHLSNRRVRTVGEQLYAQFGV 429

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL RM R+I+ER++  D +   P DLINA+ + S +  FF ++QLSQ  +  N L+ ITH
Sbjct: 430  GLSRMARTIRERMNIRDNEVFTPTDLINARTLSSVINSFFGTNQLSQFMDQTNPLAEITH 489

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG++R RAG E+RDVH THYGR+C  ET EG NIGL+SSL   A++N  GF
Sbjct: 490  KRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCTIETPEGPNIGLISSLCVHAKINNLGF 549

Query: 598  IETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            IETPYRKV DG+V  +  VVYLSA +E+ + IAQAN+  DE G+FT   V  R  G+  +
Sbjct: 550  IETPYRKVQDGRVVVEEPVVYLSAEDEDGKTIAQANAEYDEKGNFTTPKVKARFEGDFPI 609

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            +  E++D +D +P Q+ SIAASLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG+
Sbjct: 610  IEPERLDLMDIAPNQITSIAASLIPFLEHDDANRALMGSNMQRQAVPLLRPQAPIVGTGL 669

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQ 772
            E  VA  S   I A+  G+VE VDA  I IR     +  L      +  YRL+KF+++NQ
Sbjct: 670  EGRVASDSRTLINAEGNGVVEYVDANEIKIRYDRNEDEKLVSFDDDIKTYRLIKFKKTNQ 729

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +TC+N +P+V+ G  V    ++ +G +T+ G+LALGRN+ VAFMPW GYNFED+++ISER
Sbjct: 730  STCINLKPIVRKGQRVVEGQVLCEGYATENGELALGRNLKVAFMPWQGYNFEDAIVISER 789

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +VS+D+FTS+HIEEFE+  RDTK G EE+T DIPNVSEE  K++DE GII +GAEV  GD
Sbjct: 790  VVSQDIFTSLHIEEFELEVRDTKRGEEELTSDIPNVSEEATKDLDENGIIRIGAEVREGD 849

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F+R     
Sbjct: 850  ILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKTPPSIRGVVIDTKLFSRAKKA- 908

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-----KSTV 1007
                   E+  +E L  + +     L   +  +L  I+ G+ +      +K     K   
Sbjct: 909  ---DKKEEKAALERLDLNHERAVRQLRERLIDKLFAIVNGKTSQGVYNVYKELLIPKGAK 965

Query: 1008 LSSDLISEYPRSQWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +++E   +         D+     V+     Y    +     ++     I  GD++
Sbjct: 966  FTQKMLAELDFANINPSKWTTDDDKNELVKQALHFYNIKLNEELGAYRRDKFAITVGDEL 1025

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            P G++++ KV+VA KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL+DGTPVDIVLNPLG
Sbjct: 1026 PSGIVQMAKVYVAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFLEDGTPVDIVLNPLG 1085

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQI+ET LGWA   LG K  + I D  +  ++    +         ++     
Sbjct: 1086 VPSRMNLGQIYETVLGWAGQKLGVKFATPIFDGASTEEVEEWVAKAGLPASGRTYLYNGL 1145

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
              +                     FD      +  ML+                      
Sbjct: 1146 TGER--------------------FDQPTTVGVIYMLK---------------------- 1163

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
                        L HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+G
Sbjct: 1164 ------------LGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFG 1211

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            A+ +LQE+LT+KSDDV+GR + YE+IV G++      PESFNVLV E++ LGL I LE
Sbjct: 1212 ASNILQEILTVKSDDVIGRAKTYEAIVKGDNLPTPSVPESFNVLVHELRGLGLDITLE 1269


>gi|327399530|ref|YP_004340399.1| DNA-directed RNA polymerase subunit beta [Hippea maritima DSM 10411]
 gi|327182159|gb|AEA34340.1| DNA-directed RNA polymerase subunit beta [Hippea maritima DSM 10411]
          Length = 1344

 Score = 1279 bits (3310), Expect = 0.0,   Method: Composition-based stats.
 Identities = 623/1373 (45%), Positives = 872/1373 (63%), Gaps = 52/1373 (3%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K  ++++IPDL+ +   SY  FL  N     +  + L  A KS+FPI    G 
Sbjct: 10   RMRVNFSKAKKVLEIPDLLRLNINSYQTFLEKN----SKKEKNLDNALKSIFPIDDVHGR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSI 130
              LE V ++  PPKFD D+C  + ++Y   L I +RL  + VDE TG K  ++DIKEQ I
Sbjct: 66   LRLELVDWDITPPKFDPDECKVKGISYTGNLIIKVRLTQWTVDEQTGEKIGVEDIKEQEI 125

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            Y+G++PL+T+ G+F+I G++R++V QLHRSPG+ F        + GK LY  +IIP++G 
Sbjct: 126  YVGEIPLITESGSFIINGVERVIVGQLHRSPGVIFKKTGD---IGGKGLYYAQIIPERGS 182

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            W++ E + ++++  RIDR++K P T  L A+GM   +IL  FY  +            LS
Sbjct: 183  WVEFETEPREVLSTRIDRKKKFPATILLQAMGMSEADILREFYEVVRVKIENGQIFAQLS 242

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + ++G KV   +     GE VI+ G+KLT+ L + LK+ GV+++ I    L   Y AE
Sbjct: 243  --ESIIGFKVDKDVEI--DGEVVIKEGRKLTTRLFRQLKDVGVEYVPIRESELYNKYSAE 298

Query: 311  DIV--NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI---------- 358
             +   + E  ++ +  G  I ++ L  +     ++  +LY    +               
Sbjct: 299  IVEAEDEEGVDVVLGIGTKITKEKLGFL-KKFDKEFNVLYSKFDDYLILNTVIASREVLR 357

Query: 359  -RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
             R   + D       A + I+ ++RPG+ ++   A+  F  LFF+ ++YD+S  GR+++N
Sbjct: 358  KRKVALPDSIAIDDLARVFIHTLLRPGEHTSIEDAKKFFENLFFNPERYDVSQEGRIRLN 417

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
               N++ P+DVR + +ED + +IK +V L N +   DD+D+L NR+V  VG+ L  + R 
Sbjct: 418  ETFNINVPEDVRTLTREDFVGLIKHVVLLENDQVIPDDVDSLSNRKVNLVGDQLYREIRN 477

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GLLRM+R IK+++   D +++MP D+INAKPV  A+ +FF + QLSQ  +  N LS I+H
Sbjct: 478  GLLRMQRLIKDKMVMSDAENIMPYDVINAKPVAVAIKDFFSTGQLSQFLDQTNILSEISH 537

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +A++N +GF
Sbjct: 538  KRRLSALGSGGLTRERAGFEVRDVHPTHYGRICPIETPEGANIGLISSLAVYAKINEFGF 597

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IETPYR V DG+VT++VVYLSA +E+   IAQA++ L+EDG+F  E V  R  GE ++V 
Sbjct: 598  IETPYRIVKDGRVTDEVVYLSASKEKGHIIAQASAPLNEDGTFKNEYVSARKDGEFVVVK 657

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            RE +D +D S  Q+VS+AA LIPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTG+E 
Sbjct: 658  REDVDLMDISTNQIVSVAAGLIPFLEHDDANRALMGSNMQRQAVPLIRPEAPLVGTGLEP 717

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VVAK S  A+VAKR G V ++D    +    E   +     +D+Y L KF RSNQ+TC +
Sbjct: 718  VVAKYSRYAVVAKRDGKVVRIDDKIYISCKTENGYE-----LDVYPLKKFIRSNQDTCFS 772

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
              P+V VGDEV+   IIADGPS D G+LALG+N++VAF+ W GYN+ED + IS R+V ED
Sbjct: 773  HNPIVDVGDEVKTGQIIADGPSMDKGELALGKNLVVAFVSWRGYNYEDGITISRRVVEED 832

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            ++TSIHI+EF +  RDTK G EEIT DIPN S E L+N+D+ GI+ +GA V P D+LVGK
Sbjct: 833  LYTSIHIKEFTLYVRDTKFGMEEITADIPNASSETLRNLDKNGIVRIGAYVKPNDVLVGK 892

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPK E+  +PEEKLLR+IFGEKA +V DTSLRVP   SG VVDVRI +R G   N R  
Sbjct: 893  VTPKAETHYSPEEKLLRSIFGEKATNVADTSLRVPPDTSGIVVDVRIMHRRGAKINPREK 952

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +  +Q E + ++   +  +L +     + + +             +S + + + +    
Sbjct: 953  EIIEQQKEKINKELKHKLELLSKLRLDSIKDAII------------ESDIKTKEELEGLS 1000

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
              +      +D      +++L   Y+  +  ++D     I+ ++   D+PPGV+ VV V+
Sbjct: 1001 EKELVPLLPKDFD----IKALNRHYKEMEKSIKDYHTKLIKGVEKESDLPPGVISVVNVY 1056

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            VA KR +  GDKM+GRHGNKG+VS+ILP +D+PFL+DGTPVDIVLNPLGVPSRMN+GQI 
Sbjct: 1057 VATKRKLSVGDKMSGRHGNKGVVSKILPVQDLPFLEDGTPVDIVLNPLGVPSRMNIGQIM 1116

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            ETHLGW   GLGKKI  L+   + +     L+ FL+K+  +    E I    D+ V + A
Sbjct: 1117 ETHLGWLSKGLGKKIDHLLKAGRKDI----LKDFLKKIYNSEKAGELIESLSDEEVEKYA 1172

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            ++W  GV  + PVF+GA E+ +  +  +       +S +YDG+TGE F  PVTVG +Y+L
Sbjct: 1173 KEWVRGVHFANPVFEGAKEKDLEYLEGLLGFKRL-KSEVYDGITGEKFLEPVTVGVMYVL 1231

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DKV+ARS G YSLVTQQPLGGK+N GGQR GEMEVW ++ YGAAY L EMLT+
Sbjct: 1232 KLHHLVDDKVHARSVGPYSLVTQQPLGGKANFGGQRFGEMEVWALEGYGAAYTLHEMLTV 1291

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            KSDDV GR   YE+IV G      G PESFNVLVKEMQAL L ++L     + 
Sbjct: 1292 KSDDVDGRKLTYEAIVKGRPIPLGGVPESFNVLVKEMQALCLDVELLKDIRRK 1344


>gi|41017794|sp|Q9F3X8|RPOB_PORCN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|10637868|emb|CAC10563.1| DNA-dependent RNA polymerase subunit beta [Porphyromonas
            cangingivalis]
          Length = 1270

 Score = 1279 bits (3309), Expect = 0.0,   Method: Composition-based stats.
 Identities = 563/1363 (41%), Positives = 795/1363 (58%), Gaps = 119/1363 (8%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              R  F      ++  D ++VQ  S+  FL ++  P++R  EGL   F   FPI      
Sbjct: 7    TQRVNFASIKNPMEYADFLDVQLKSFKDFLQLDTPPEKRKKEGLYKVFAENFPIHDTRNN 66

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +LEF+ Y  DPP++ +D+C+ R LTY VPLK  ++L   D +       I     Q +Y
Sbjct: 67   FVLEFLDYYIDPPRYTLDECISRGLTYNVPLKAKMKLYCTDPEHEDFETVI-----QDVY 121

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G +P MT+ GTF+I G +R+VVSQ+HRSPG+ F         +G  L++ RIIP +G W
Sbjct: 122  LGPIPYMTESGTFIINGAERVVVSQMHRSPGVFFSES---VHPNGTKLFSARIIPFKGSW 178

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            ++   D  ++++  IDR++K+PVT+ L A+G +++ +IL+ F                  
Sbjct: 179  IEFATDINNVMYAYIDRKKKLPVTTLLRAIGFETDKDILNLFGIAEEVKVSKSTLKKYY- 237

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                      G+K+ + +L S  E  V                 
Sbjct: 238  --------------------------GRKIAARVLNSWIEDLVDEET------------G 259

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRNTLVTDKNK 368
            ++V+ E  ++ ++  +++ E ++++I  S  ++I I   DS     Y    NTL  D + 
Sbjct: 260  EVVSMERYDVIVDRDELLTEDNVDQIIESGAKNILITKDDSELGLDYSVTTNTLQKDPSN 319

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              K+A+  IY+ +R  D    + A  + N LFF   +YDL  VGR ++N +L ++  ++ 
Sbjct: 320  SEKEAVYHIYKQLRNQDPVDDASAREVINSLFFSEKRYDLGDVGRYRINKKLGINIDEET 379

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + +  EDI AII  LV+L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+++E
Sbjct: 380  KVLTTEDITAIIAHLVELMNSKQVVDDIDHLSNRRVRTVGEQLYNQFGIGLARMARTVRE 439

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DLINAK + S V  FF ++ LSQ  +  N L+ ITH RRLS+LG GG
Sbjct: 440  RMNVRDNEVFTPIDLINAKTISSVVNSFFGTNALSQFMDRTNPLAEITHKRRLSSLGPGG 499

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            ++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYRKV DG
Sbjct: 500  LSRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINDLGFISTPYRKVVDG 559

Query: 609  KV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            KV    N V Y +A  E+++ +AQ N+ LDE+G F ++ V+ R   +  +V   +ID +D
Sbjct: 560  KVDFSENGVEYYTAEAEDDKTVAQGNAPLDENGKFIKDAVYARYGSDFPVVSPSEIDLMD 619

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPL+ ++AP VGTG+E  +   S  
Sbjct: 620  VSPIQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLIHSDAPIVGTGVEQKLVHDSRT 679

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             IVA+ AG VE VDA  I IR     +         + IY L KF+++NQ+T ++ RP+ 
Sbjct: 680  QIVAEGAGTVEFVDASVIKIRYDRSEDDTFVSFEDNLKIYNLPKFRKTNQSTTIDLRPIC 739

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V + DI+ +G ST+ G+LALGRN+ VA+MPW GYN+ED+++++ERMV ED+FTS+
Sbjct: 740  RKGDRVEKGDILTEGYSTENGELALGRNVQVAYMPWKGYNYEDAIVLNERMVREDIFTSV 799

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H++E+ +  R+TK G EE+T DIPNVSEE  K++D+ GII VGA V+PGDIL+GKITPKG
Sbjct: 800  HVDEYILEVRETKRGLEELTSDIPNVSEEATKDLDDRGIIRVGARVHPGDILIGKITPKG 859

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ES  TPEEKLL AIFG+KA DV+D SL+    +SG V+   +F++    K +      RE
Sbjct: 860  ESDPTPEEKLLHAIFGDKAGDVKDASLKANPSLSGVVIKTHLFSKAMHSKKD--KGGVRE 917

Query: 963  QIELLARDKDDEQVILDRNIYSRL-----MEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             ++ L  + +++   L   +  +L      ++  G       +   K   L+  + S+  
Sbjct: 918  IVKKLDEEMEEKLAELRELMLKKLIQLTDNKLSNGIRNFEDTEIVPKGVKLTPAVCSKIE 977

Query: 1018 RSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
              +   F    DE     V  L   Y      +E  ++ K      GD++P G++++ KV
Sbjct: 978  FGEVAIFNWTGDEHTDELVAKLISNYLRKAKEIESEYRRKKFDATIGDELPNGIIQIAKV 1037

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +A KR IQ GDKMAGRHGNKGIVS+I+  EDMPF++DGTP+D+ LNPLGVPSRMN+GQI
Sbjct: 1038 LIAKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFMEDGTPMDLCLNPLGVPSRMNLGQI 1097

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE         L  K  + I D  +  D+                               
Sbjct: 1098 FE-LSSMGSRRLDVKFATPIFDGASLDDLDQWTD-------------------------- 1130

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                K+G+P                          G++ LYDG TGE FD+P TVG  Y 
Sbjct: 1131 ----KAGIP------------------------RYGKTYLYDGGTGEQFDQPATVGVTYF 1162

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+VLQEMLT
Sbjct: 1163 LKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHVLQEMLT 1222

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            IKSDDVVGR++ YE+IV G      G PES NVL+ E++ LGL
Sbjct: 1223 IKSDDVVGRSKAYEAIVKGAPMPTPGIPESLNVLLHELKGLGL 1265


>gi|262340957|ref|YP_003283812.1| DNA-directed RNA polymerase subunit beta [Blattabacterium sp.
            (Blattella germanica) str. Bge]
 gi|262272294|gb|ACY40202.1| DNA-directed RNA polymerase subunit beta [Blattabacterium sp.
            (Blattella germanica) str. Bge]
          Length = 1273

 Score = 1278 bits (3306), Expect = 0.0,   Method: Composition-based stats.
 Identities = 565/1372 (41%), Positives = 800/1372 (58%), Gaps = 119/1372 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                  R  F    + ++ PD +++Q  S+  F  ++  P+ R NEGL  AF   FPI+ 
Sbjct: 7    TEKISERITFSSVAKQVEYPDFLDIQIKSFKEFFQLDTKPENRKNEGLFKAFTENFPISD 66

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
               + +LEF  Y  D P++ +++C+ R LTY+VPLK  L+L   D +         +   
Sbjct: 67   ARNSFVLEFKGYSIDSPRYSIEECIERGLTYSVPLKAKLKLYCTDPEHEDF-----ETVY 121

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y+G  P MT  G+F+  G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 122  QDVYLGTCPYMTPSGSFIFNGAERVIVSQLHRSPGVFFGQSH---HANGTKLYSARIIPF 178

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+P+T+ L ++G + + +IL  F          +   
Sbjct: 179  KGSWIEFATDINNVMYAYIDRKKKLPMTTLLRSIGYERDKDILEIFDLAEEIKITDESKN 238

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                     +        VD DTGE                                   
Sbjct: 239  ILNRTLAARILRIWHEDFVDEDTGEV---------------------------------- 264

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTD 365
                  V+ E  EI I+   ++ E+ ++ + + EI+ + +        + + I NTL  D
Sbjct: 265  ------VSIEKNEILIDRDVLLKEEHIDLLKNHEIKTVLLHKEGGRKKDYSIIYNTLHKD 318

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 K+A+  IYR +R  +      A  + + LFF   +Y L  VGR ++N RL L+  
Sbjct: 319  PTNSEKEAVEYIYRQLRNTEPPDEETARGVIDKLFFSDTRYSLGPVGRYRLNKRLELNID 378

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             +   + K+DIIAI+  L  L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+
Sbjct: 379  PNHLVLTKKDIIAIVDHLNALFNSKREVDDIDHLSNRRVRTVGEQLYTQFSIGLARMART 438

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +  MP DLINAK + S +  FF ++QLSQ  +  N LS ITH RRLSALG
Sbjct: 439  IRERMNVRDNEVFMPVDLINAKTLSSVINTFFGTNQLSQFMDQTNPLSEITHKRRLSALG 498

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL+ FA++N  GF+ETPYR V
Sbjct: 499  PGGLSRERAGFEVRDVNYSHYGRLCPIETPEGPNIGLISSLSVFAKINNMGFVETPYRTV 558

Query: 606  CDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               KV   ++V YLSA EEE + IAQAN+ +D+ G+F  + +  R  G+  +V   ++D+
Sbjct: 559  FQKKVDLKSEVKYLSAEEEEGKIIAQANA-IDQYGNFLSDRIIAREDGDFPIVQSNQVDY 617

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            ID +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK +AP VGTG+E  VA+ S
Sbjct: 618  IDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPDAPIVGTGLEQQVARDS 677

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               I AK+ GIVE +D+ +I++R  +     L      V +Y L+KF+++NQNTC+N +P
Sbjct: 678  RILINAKKNGIVEYIDSKKIIVRYDKTDKEALVSFDDDVQVYDLIKFRKTNQNTCINLKP 737

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK G  + +  I+ +G +T+ G+LALGRN+  AF+P +GYNFED++LISE++VSED FT
Sbjct: 738  IVKKGMRIVKGQILCEGYATENGELALGRNLKAAFIPCNGYNFEDAVLISEKVVSEDWFT 797

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE GII VGAEV PGDIL+GKITP
Sbjct: 798  SIHIDEYSLDVRDTKLGMEELTNDIPNVSEEATKDLDENGIIRVGAEVKPGDILIGKITP 857

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGES  TPEEKLLRAIFG+KA +V+D SLR    + G V+D ++F R    K++++ + +
Sbjct: 858  KGESDPTPEEKLLRAIFGDKAGNVKDASLRAEPSLFGVVIDTKLFIR--SIKDKQTRTQD 915

Query: 961  REQIELLARDKDDEQVILDRNIYS-----RLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            + +IE L +  + + + L   +       +              +   K +  +   + +
Sbjct: 916  KIKIECLEKKYEKKFLDLRNLLIKIIFCFKWKLCNSSVFNEKNKEIIAKGSKFNIKKLEK 975

Query: 1016 YPRS--QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                   +      D +    +  +   Y+ +   L    K+K   I  GD++P G++++
Sbjct: 976  ISDYIGVFSNSWTDDPETNDLISEILHNYQIAVGDLTSILKHKKFSITVGDELPSGIIKM 1035

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             KV++A KR ++ GDKMAGRHGNKG+V+RIL  EDMPFL+DG+PVDIVLNPLGVPSRMN+
Sbjct: 1036 AKVYIAKKRKLKVGDKMAGRHGNKGVVARILRVEDMPFLEDGSPVDIVLNPLGVPSRMNI 1095

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI+ET LGWA   L +K  + I D      I       +                    
Sbjct: 1096 GQIYETVLGWAGQKLNRKFSTPIFDGATIDQICEYTDKAKI------------------- 1136

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                           P F                    G + L+DG TGE FD+P TVG 
Sbjct: 1137 ---------------PRF--------------------GTTYLFDGGTGEKFDQPATVGV 1161

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +L+E
Sbjct: 1162 IYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNILRE 1221

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +LT+KSDDVVGR + YE+IV G    E   PESFNVL  E++ LGL I LE 
Sbjct: 1222 ILTVKSDDVVGRAKTYEAIVKGEPMPEPNNPESFNVLCYELKGLGLDIRLEE 1273


>gi|189499299|ref|YP_001958769.1| DNA-directed RNA polymerase subunit beta [Chlorobium phaeobacteroides
            BS1]
 gi|189494740|gb|ACE03288.1| DNA-directed RNA polymerase, beta subunit [Chlorobium
            phaeobacteroides BS1]
          Length = 1302

 Score = 1277 bits (3305), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1419 (41%), Positives = 831/1419 (58%), Gaps = 181/1419 (12%)

Query: 6    VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
                   +   F K   I++ PDL++VQ  S+  F+  ++   +R ++GL+   +S FPI
Sbjct: 5    DKTQKKCI--AFSKIQSIVNPPDLLQVQLDSFKRFIQDSVPLAKRKDQGLEKVLRSAFPI 62

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            T   G  +LE++SY FD PK+ V++C+ R LTY V LK+ L+L   D  +    K     
Sbjct: 63   TDTRGLYLLEYISYTFDKPKYTVEECIERGLTYDVSLKVKLKLSYKDEPDEQDWKET--- 119

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
             +Q +Y+G +P MT  GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+
Sbjct: 120  IQQEVYLGRIPYMTDRGTFIVNGAERVVVAQLHRSPGVVFSE---AIHPNGKKMYSAKIV 176

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDF 244
            P +G W++ + D  + I+V ID+++   V++ L A+G   +E ILS F            
Sbjct: 177  PTRGSWIEFQTDINNQIYVYIDQKKNFLVSALLRAIGFTKDEDILSLF------------ 224

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                               L++    E  +++ KK                     + L 
Sbjct: 225  ------------------DLIE----EVPVKANKK---------------------EYLI 241

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN---AYIRNT 361
            G  +A DI++ +TGE+ + A   I E+ L++I  +  + + I+   +       + + NT
Sbjct: 242  GKNLASDIIDMQTGEV-VSARTAITEEILDQITAAGSKTVRIMKPGTGEKGLDKSVVTNT 300

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            ++ D +   ++AL  +Y  +R  +      A S     FF+  KYDL  VGR ++N +L 
Sbjct: 301  ILNDSSATEEEALEIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGDVGRYRINKKLG 360

Query: 422  LD------------------------------------TPDDVRHIRKEDIIAIIKILVD 445
             +                                      DD+  +   DIIA+I  L+ 
Sbjct: 361  KEHEAFKEFLSGQPELKALSDSIYEKILQTIQSYSDEPISDDIMVLTHYDIIAVINYLIK 420

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            L NG+  +DD+D+L NRRVR+VGE L  Q+ +GL RM ++++E+++S D D + P DLIN
Sbjct: 421  LVNGQAEVDDVDHLANRRVRTVGEQLAAQFVIGLARMGKNVREKLNSRDTDKIAPADLIN 480

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            A+ V S V  FF +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH TH
Sbjct: 481  ARTVSSVVSSFFATSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTH 540

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            YGR+CP ET EG NIGL+SSL+ +A +N  GFI+ PYR V  G VT+ V  LSA +EEN+
Sbjct: 541  YGRLCPIETPEGPNIGLISSLSVYAEINDKGFIQAPYRVVEKGIVTDKVEMLSAEDEENK 600

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                 +   DE+   T E V  R  G+  +V  E++D++D SP Q+VS AA+LIPFLE+D
Sbjct: 601  ITVPVSVKFDENRRITTETVQARTKGDYPVVDAEQVDYMDVSPIQIVSAAAALIPFLEHD 660

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D NR LMG NMQRQAVPLL A+AP VGTGME+ VA+ S A ++A+  G++E V A  I +
Sbjct: 661  DGNRALMGANMQRQAVPLLVADAPLVGTGMEAKVARDSRAVVLAEGDGVIESVTAESIRV 720

Query: 746  RSVEGDLDPS-------TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            R    + +           GV  Y L+KF+RSNQ+TC++Q+P+V+ G ++ + D++ADGP
Sbjct: 721  RYDMHEDEDDRMIMLDPDEGVKTYNLIKFKRSNQDTCISQKPVVRTGQKLEKGDVLADGP 780

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            ST+ G+LALG+N+LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G 
Sbjct: 781  STENGELALGKNVLVAFMPWRGYNFEDAIVLSERLVYDDVFTSIHIHEFEANVRDTKRGE 840

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E+ TRDI NVSE+ L+N+DE GII +GAEV   DILVGKITPKGES  TPEEKLLRAIFG
Sbjct: 841  EQFTRDIYNVSEDALRNLDENGIIRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFG 900

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
            +K+ DV+D S+ VP+G+ G V+  ++F+R      ++     RE+ E +    +     L
Sbjct: 901  DKSSDVKDASMHVPAGMKGIVIKTKLFSR-----KKKVGLDIRERQEAIDALFERRTADL 955

Query: 979  DRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISE------YPRSQWWQFAVQ 1027
                 + + ++  G+ +       G +     +VL ++ + +             +  V+
Sbjct: 956  RSRFNTWMNQLFEGKKSTGIYNLKGKEIVPAGSVLDAETLGKFAGPGFLESVDLSKGIVK 1015

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D K    +  L  +Y      +ED  +N+  K+  GD++PPG+  + KV++A KR IQ G
Sbjct: 1016 DAKANATLLRLCREYRLMLKDMEDERENEKYKLNIGDELPPGIEELAKVYIAQKRKIQVG 1075

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+V +ILP ED+PF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   
Sbjct: 1076 DKMAGRHGNKGVVGKILPIEDLPFMGDGTPVDIVLNPLGVPSRMNIGQLYETSLGWAARA 1135

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG + K+ I D     ++                                   K+G+P+ 
Sbjct: 1136 LGVQFKTPIFDGATYTEVQEQLE------------------------------KAGLPM- 1164

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G+  LYDG TGEPFD  VTVGYIYMLKL+H+V DK+
Sbjct: 1165 -----------------------HGKVRLYDGRTGEPFDDEVTVGYIYMLKLSHLVDDKI 1201

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDVVGR +
Sbjct: 1202 HARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVVGRNK 1261

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             YESIV G +  + GTPESFNVLV+E+Q LGL I ++N 
Sbjct: 1262 TYESIVKGQNLPDPGTPESFNVLVRELQGLGLEIRIDNK 1300


>gi|261749526|ref|YP_003257212.1| DNA-directed RNA polymerase subunit beta [Blattabacterium sp.
            (Periplaneta americana) str. BPLAN]
 gi|261497619|gb|ACX84069.1| DNA-directed RNA polymerase beta subunit [Blattabacterium sp.
            (Periplaneta americana) str. BPLAN]
          Length = 1272

 Score = 1275 bits (3298), Expect = 0.0,   Method: Composition-based stats.
 Identities = 575/1373 (41%), Positives = 810/1373 (58%), Gaps = 118/1373 (8%)

Query: 8    NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                  R  F    + ++ PD +++Q  S+  F  ++  P+ R NEGL  AF   FPI+ 
Sbjct: 3    TENVSERITFASVAKQVEYPDFLDIQIKSFKEFFQLDTKPENRKNEGLFKAFTENFPISD 62

Query: 68   FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
               + +LEF  Y  D P++ +++C+ R LTY+VPLK  L+L   D +         +   
Sbjct: 63   ARNSFVLEFKGYSIDTPRYSIEECIERGLTYSVPLKAKLKLYCTDPEHEDF-----ETVY 117

Query: 128  QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
            Q +Y+G  P MT  G+F+  G +R++VSQLHRSPG+ F         +G  LY+ RIIP 
Sbjct: 118  QDVYLGTYPYMTPSGSFIFNGAERVIVSQLHRSPGVFFGQSH---HANGTKLYSARIIPF 174

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            +G W++   D  ++++  IDR++K+P+T+ L A+G + + +IL  F              
Sbjct: 175  KGSWIEFATDINNVMYAYIDRKKKLPMTTLLRAIGYERDKDILEIFDLAEEVKITETEDT 234

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
              +                            + L + +L    E  V             
Sbjct: 235  KSIL--------------------------SRSLAARILNIWHEDFVDEDT--------- 259

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTD 365
                ++++ E  E+ I+    I ++ ++ +   EI+ I +   +    + + I NTL  D
Sbjct: 260  ---GEVISVEKNEVLIDRDVSITQEHIDLMIQHEIKTILLHKKEGKKKDYSIIYNTLQKD 316

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 K+A+  IYR +R  +      A  + + LFF   +Y L  VGR ++N RL L+  
Sbjct: 317  PTNSEKEAVEYIYRQLRNTEPPDEETARGVIDKLFFSDTRYSLGPVGRYRLNKRLGLNIN 376

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             D   + KEDIIAI++ L  L N K  +DDID+L NRRVR+VGE L  Q+ +GL RM R+
Sbjct: 377  PDYLVLTKEDIIAIVEHLNALFNSKREVDDIDHLSNRRVRTVGEQLYAQFSIGLARMART 436

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+ER++  D +  MP DLINAK + S +  FF ++QLSQ  +  N LS +TH RRLSALG
Sbjct: 437  IRERMNVRDNEVFMPVDLINAKTLSSVINTFFGTNQLSQFMDQTNPLSELTHKRRLSALG 496

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL+ FA++N  GF+ETPY+ +
Sbjct: 497  PGGLSRERAGFEVRDVNYSHYGRLCPIETPEGPNIGLISSLSVFAKINDMGFVETPYQSI 556

Query: 606  CDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
             DGKV   + V YLSA EEE + IAQAN+ +D+ G+F  + +  R  G+  +V  +K+D+
Sbjct: 557  HDGKVDLKSKVKYLSAEEEEGKIIAQANA-IDQYGNFISDRIIAREDGDFPIVTPKKVDY 615

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            ID +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK EAP VGTG+E  VA+ S
Sbjct: 616  IDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPEAPIVGTGLEKQVARDS 675

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               I A+  G+VE +DA +I+IR  +     L      V  Y L+KF+++NQNTC+  +P
Sbjct: 676  RILINAESNGLVEYLDARKIIIRYEKTEREALVSFEPKVKTYDLIKFRKTNQNTCITLKP 735

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK+G +V +  I+ +G +T+ G+LALGRN+  AF+P +GYNFED++LISE++VSED FT
Sbjct: 736  IVKMGMKVVKGQILCEGYATENGELALGRNLRAAFIPCNGYNFEDAVLISEKVVSEDWFT 795

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE GII VGAEV PGDIL+GKITP
Sbjct: 796  SIHIDEYSLDVRDTKLGMEELTNDIPNVSEEATKDLDENGIIRVGAEVRPGDILIGKITP 855

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGES  TPEEKLLRAIFG+KA +V+D SLR    + G V+D ++F R    K+++S   +
Sbjct: 856  KGESDPTPEEKLLRAIFGDKAGNVKDASLRAEPSLFGVVIDTKLFTR--SIKDKKSRVQD 913

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK------STVLSSDLIS 1014
            + Q+E + +  + +   L   +  +L  +L G+ +       KK       T  ++ L++
Sbjct: 914  KIQLERIEKKYEKKFSDLRNQLLQKLHTVLHGKISKKIIINEKKQEIIEEGTKFTAKLLN 973

Query: 1015 EYPRSQWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +              D +    V  +   Y+ S + L    K+K   I  GD++P G+++
Sbjct: 974  KISDYIEITPGDWTFDVETNNLVSEILHNYQISVNDLNSMLKHKKFSITVGDELPSGIIK 1033

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            + KV++A KR ++ GDKMAGRHGNKG+V+RIL  EDMPFL+DG+PVDIVLNPLGVPSRMN
Sbjct: 1034 MAKVYIAKKRKLKVGDKMAGRHGNKGVVARILREEDMPFLEDGSPVDIVLNPLGVPSRMN 1093

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI+ET LGWA   L  K  + I D      IS                          
Sbjct: 1094 IGQIYETVLGWAGYKLNIKFSTPIFDGATIEKISEFTDKANI------------------ 1135

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                            P F                    G + L+DG TGE FD+P TVG
Sbjct: 1136 ----------------PRF--------------------GTTYLFDGGTGERFDQPATVG 1159

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IYMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++A+GA+ +L+
Sbjct: 1160 VIYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASNILR 1219

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            E+LT+KSDDV GR + YESIV G+   E   PESFNVL  E++ LGL I+LE 
Sbjct: 1220 EILTVKSDDVTGRAKTYESIVKGDPMPEPNNPESFNVLCYELKGLGLDINLEE 1272


>gi|282858388|ref|ZP_06267568.1| DNA-directed RNA polymerase, beta subunit [Prevotella bivia
            JCVIHMP010]
 gi|282588836|gb|EFB93961.1| DNA-directed RNA polymerase, beta subunit [Prevotella bivia
            JCVIHMP010]
          Length = 1269

 Score = 1274 bits (3297), Expect = 0.0,   Method: Composition-based stats.
 Identities = 570/1367 (41%), Positives = 809/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFSDFLQLDTPPEERKNDGLYKVFTENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D    A    D     +++G
Sbjct: 68   LEFLDYFVDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFATVTDD-----VFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGSVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGFESDKDILQIFDLCEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+++   ++K+  E  V                 ++
Sbjct: 234  ---------------------AAIGRRIAGNVMKTWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   ++ +++++ I  S +  I +    D+ N  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETLVTDENVDVILESSVPTILLHKDEDAANKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L LDT  +VR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGLDTDSEVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKEDIIEIVKYLINLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFRPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIITPYRQVRDAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE + I Q N+ L+ DG+F    V CR   +  +VP   +  +D SP
Sbjct: 561  MDNKDVVFLTAEEEEEKIIGQGNAPLNADGTFIRTTVKCRQDADYPVVPPSNVKLMDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I+
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIM 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  ++ RP+ + G
Sbjct: 681  AEGEGVIEYVDATTIRILYDRTEDDEFVSFEPALKEYRIPKFRRTNQNMVIDLRPICEKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++NDI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKNDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTADIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  ++
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKAVLQ 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             L  +++ +   L   +  +LME+  G+        S  +   K +  +   +       
Sbjct: 919  RLDDEQEAKINDLKDILVDKLMELTEGKESQGVKDYSDAEIITKGSKFTVAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    D+     ++ L + +      ++   K +   I  GD++P GV+++ KV++A
Sbjct: 979  VQSNGWTDDDHTNSLIQKLIMNFIRKYKQMDAELKRRKFAITIGDELPSGVIQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLEDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTHIYDGE--------------------------TGERFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LT+
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTV 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|325269547|ref|ZP_08136163.1| DNA-directed RNA polymerase subunit beta [Prevotella multiformis DSM
            16608]
 gi|324988166|gb|EGC20133.1| DNA-directed RNA polymerase subunit beta [Prevotella multiformis DSM
            16608]
          Length = 1269

 Score = 1273 bits (3295), Expect = 0.0,   Method: Composition-based stats.
 Identities = 580/1367 (42%), Positives = 808/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYVDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGYETDRDILQIFDLCEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++K+  E  V                 ++
Sbjct: 234  ---------------------AAIGRKIAGNVMKTWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   VI E++++EI  S +  I +    ++ N  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETVITEENVDEILDSSVSTILLHKDEEAANKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNLDT  DVR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLDTDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIIEIIKYLISLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMNRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRCVKDSKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE++ I Q N+ L+ DG+F  + V CR   +  +V  E ++ ID SP
Sbjct: 561  MDNKDVVFLTAEEEEDQIIGQGNAPLNADGTFIRDTVKCRQDADYPVVSPEAVNLIDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ E +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTSDIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKATLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 919  KIDEEQEAKVNDLKDLLVDKLLELTEDKVSEGVKDYSDAEIITKGSKFTVAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + Y      ++   K K   I  GD++P GVL++ KV++A
Sbjct: 979  IQSNGWTDDEHTNLLIQKLIMNYIRKYKQMDAELKRKKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG+PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGSPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|307565738|ref|ZP_07628207.1| DNA-directed RNA polymerase, beta subunit [Prevotella amnii CRIS
            21A-A]
 gi|307345564|gb|EFN90932.1| DNA-directed RNA polymerase, beta subunit [Prevotella amnii CRIS
            21A-A]
          Length = 1269

 Score = 1273 bits (3293), Expect = 0.0,   Method: Composition-based stats.
 Identities = 573/1367 (41%), Positives = 810/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFSDFLQLDTPPEERKNDGLYKVFTENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +++CL R LTY+VPLK  ++L   D D    A    D     +++G
Sbjct: 68   LEFLDYFVDPPRYSIEECLERGLTYSVPLKAKMKLYCTDPDHEDFATVTDD-----VFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTGNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGSVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGFESDKDILQIFDLCEEIKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+++   ++K+  E  V                 ++
Sbjct: 234  ---------------------AAIGRRIAGNVMKTWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   +I E +++ I  S +  I +    D+ N  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETLITEDNIDIILGSSVPTILLHKDEDAANKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L ++T  +VR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLGIETDSEVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             KEDII I+K L++L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKEDIIEIVKYLINLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFRPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV   KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRKVSAAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               +DVVYL+A EEE + I Q N+ L++DG+F  E V CR   +  +V    +  +D SP
Sbjct: 561  MNNDDVVYLTAEEEEEKIIGQGNAPLNDDGTFIRETVKCRKDADYPVVLPSNVSLMDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I+
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIM 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G+VE VDA  I I   R+ E +       +  YR+ KF+R+NQN  ++ RP+ + G
Sbjct: 681  AEGDGVVEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMVIDLRPICEKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++NDI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV ED+ TS+H++
Sbjct: 741  QRVKKNDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDILTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTSDIPNVSEETTKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  ++
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--LKTRESKRQDKIFLQ 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             L ++++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 919  RLDKEQETKINDLKDILVDKLLELTEGKDSSGVKDYSDAEIITKGSKFTIAALKNLDYES 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                   +DE     ++ L + +      ++   K +   I  GD++P GVL++ KV++A
Sbjct: 979  IQSSGWTEDEHTNLLIQKLIMNFIRKYKQMDAELKRRKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLEDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTHIYDGE--------------------------TGERFDQPATVGVTYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|213609927|ref|ZP_03369753.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E98-2068]
          Length = 1144

 Score = 1272 bits (3292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 605/1162 (52%), Positives = 822/1162 (70%), Gaps = 18/1162 (1%)

Query: 99   AVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLH 158
            + PL++ LRL++++ +   G  ++KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLH
Sbjct: 1    SAPLRVKLRLVIYEREAPEG--TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLH 58

Query: 159  RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFL 218
            RSPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD KD + VRIDRRRK+P T  L
Sbjct: 59   RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIIL 118

Query: 219  MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
             AL   +E+IL  F+ K+V+  R +     L    L  G   S  +     G+  +E G+
Sbjct: 119  RALNYTTEQILDLFFEKVVFEIRDNKLQMELIPERL-RGETASFDIE--ANGKVYVEKGR 175

Query: 279  KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            ++T+  ++ L++  +K + +  + + G  V++D V+  TGE+   A   +    L ++  
Sbjct: 176  RITARHIRQLEKDDIKHIEVPVEYIAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQ 235

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            S  + I  L+ + +++  YI  T+  D   DR  AL++IYR+MRPG+  T   AES+F  
Sbjct: 236  SGHKRIETLFTNDLDHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFEN 295

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            LFF  D+YDLS VGR+K N  L  D  +    + K+DII ++K L+D+RNGKG +DDID+
Sbjct: 296  LFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDH 355

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF 
Sbjct: 356  LGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFG 415

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 416  SSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 475

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS+LD++G
Sbjct: 476  NIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEG 535

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
             F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQR
Sbjct: 536  HFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQR 595

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G
Sbjct: 596  QAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAG 655

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            +DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW
Sbjct: 656  IDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPW 715

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            +GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTKLGPEEIT DIPNV E  L  +DE
Sbjct: 716  NGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDE 775

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGT
Sbjct: 776  SGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGT 835

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            V+DV++F R G++K++R++ +E  Q++   +D  +E  IL+  ++SR+  +L        
Sbjct: 836  VIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV--- 892

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                       ++ + + PR +W +  + DE+ Q  +E L  QY+  K   E + + K  
Sbjct: 893  ----------EAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRR 942

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPV
Sbjct: 943  KITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPV 1002

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +++   +    +         +   
Sbjct: 1003 DIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGAD 1062

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  +S + DD VLR+AE  + G+P++TPVFDGA E  I  +L++ DL  SGQ  L+D
Sbjct: 1063 VRQKVDLSTFSDDEVLRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFD 1122

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TGE F+RPVTVGY+YMLKLN
Sbjct: 1123 GRTGEQFERPVTVGYMYMLKLN 1144


>gi|260592778|ref|ZP_05858236.1| DNA-directed RNA polymerase, beta subunit [Prevotella veroralis
            F0319]
 gi|260535309|gb|EEX17926.1| DNA-directed RNA polymerase, beta subunit [Prevotella veroralis
            F0319]
          Length = 1269

 Score = 1271 bits (3290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1367 (41%), Positives = 808/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +++CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYVDPPRYTIEECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGYESDRDILQIFDLCEEIKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++K+  E  V                 ++
Sbjct: 234  ---------------------AAIGRKIAGNVMKTWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  ++ +E   VI E++++EI  S +  I +    D+ N  + I NTL  D +    
Sbjct: 261  VSIERNKVVVERETVITEENVDEILDSSVSTILLHKDEDAANKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNLDT  D R +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLDTDMDTRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DI+ IIK L+ L N   T+DDID+L NRRVR++GE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIVEIIKYLISLVNSNATVDDIDHLSNRRVRTIGEQLANQFSIGLARMNRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRRVRDSKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE++ I Q N+ L++DG+F  + V CR   +  +V  + ++ ID SP
Sbjct: 561  MDNKDVVFLTAEEEEDQIIGQGNAPLNDDGTFVRDTVKCRQDADYPVVGPDSVNLIDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   I 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMIT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 681  AEGEGVIEYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTSDIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F R    K   S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFARA--IKTRESKRQDKITLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  ++  +       
Sbjct: 919  KIDEEQEAKVNDLKDLLVDKLLELTEDKVSEGVKDYSDAEIITKGSKFTAAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + +      ++   K K   I  GD++P GVL++ KV++A
Sbjct: 979  IQSNGWTDDEHTNLLIQKLIMNFIRKYKQMDAELKRKKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|313887243|ref|ZP_07820937.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas
            asaccharolytica PR426713P-I]
 gi|312923296|gb|EFR34111.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas
            asaccharolytica PR426713P-I]
 gi|332176995|gb|AEE12685.1| DNA-directed RNA polymerase subunit beta [Porphyromonas
            asaccharolytica DSM 20707]
          Length = 1280

 Score = 1271 bits (3290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 563/1367 (41%), Positives = 776/1367 (56%), Gaps = 109/1367 (7%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             RK F      ++ PD +EVQ  S+  F  +N   + R  EGL   F   FPI       
Sbjct: 8    TRKSFASIAHPMEYPDFLEVQLKSFQDFFQLNTPAESRKKEGLFKVFSENFPIEDTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L F  Y  DPPK+ +++CL R LTY+VPL+  L+L   D +      ++     Q +++
Sbjct: 68   KLLFEDYFVDPPKYSIEECLRRGLTYSVPLRAKLKLTCEDPEHEDFESTV-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GSIPYMTPAGTFVINGAERVVVSQLHRSPGVFFGSSL---HNNGTRLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D+ + ++  IDR++K+P+T+ L A+G +++ +IL  F          +        
Sbjct: 180  EFATDTNNELYAYIDRKKKLPITTLLRAIGYETDKDILDLFGIAEEIPVTLESLQANY-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYV 308
                                     G++L + ++    ++  +     ++       L  
Sbjct: 238  -------------------------GRQLAASVILKYYDEESEEETGETETFARYNTLVE 272

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               I++ +  ++ +E G     +++         D      + ++  + I NTL  D   
Sbjct: 273  QNAILDEDNAQVILENGI----ETILLRRDLATSDQESTDQEVMD-YSIIFNTLKRDSAN 327

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              + A   IY ++R         A+ +FN +FF   +YDL  VGR K+N +L LD   DV
Sbjct: 328  SEQAAYNFIYNLLRNSTPPDDQSAKEIFNNIFFSEKRYDLGDVGRYKINSKLGLDIDPDV 387

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + +  EDI+AII+ L+ L NGK  +DDID+L NRRVR+VGE L NQ+ +GL RM R++KE
Sbjct: 388  KILTAEDIVAIIRHLIKLVNGKAPVDDIDHLSNRRVRTVGEQLYNQFSIGLSRMARTVKE 447

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DL+N+K + S V  FF ++ LSQ  +  N LS ITH RRLSALG GG
Sbjct: 448  RMNVRDSEVFTPVDLVNSKTIASVVNSFFGTNALSQFMDQQNPLSEITHKRRLSALGPGG 507

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYR V DG
Sbjct: 508  LTRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINELGFITTPYRNVKDG 567

Query: 609  KV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             V    + + Y +A EEE++ +AQ N+ LD+DG F    V  R   +  +V  E++D +D
Sbjct: 568  TVDFEDSKLAYFTAEEEEDKTVAQGNAPLDDDGHFIRSRVKARYGADFPVVEPEEVDLMD 627

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL  EAP VGTG+E  +   S  
Sbjct: 628  VSPTQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLTPEAPIVGTGIERRLVSDSRT 687

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             I A   G+V  VDA +IV+      E +L         Y L K++++NQ+T ++  P+ 
Sbjct: 688  QIEAAGDGVVVYVDATKIVVDYDRTEEEELVSFEPSEVTYSLPKYRKTNQSTTIDLSPIC 747

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V +  I+++G ST  G+LALGRN+L A+MPW GYN+ED+++++ER+VSED+FTSI
Sbjct: 748  RKGDRVVKGQILSEGFSTQDGELALGRNILAAYMPWKGYNYEDAIVLNERVVSEDLFTSI 807

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H++E+ +  R+TK G EE T DIPNVSEE  K++D  GI+ VGA + PGDILVGKITPKG
Sbjct: 808  HVDEYSLDVRETKRGMEEFTADIPNVSEEATKDLDANGIVRVGARIVPGDILVGKITPKG 867

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH----GIDKNERSIS 958
            ES  TPEEKLL AIFG+KA DV+D SL+    + G V+D ++++R     GI    +   
Sbjct: 868  ESDPTPEEKLLLAIFGDKAGDVKDASLKASPSLKGVVIDTKLYSRANRKGGISATRKITQ 927

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
               E++  L     +E V   + I  +            G    K  T +S  L+ E   
Sbjct: 928  RYEEELSKLQAALKEELVSKLQIILKKHKTTATDFVDYIGVVKVKAGTRISKSLLLELDY 987

Query: 1019 SQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +         DE     V+     Y     I       +      GD++P G+++  K+ 
Sbjct: 988  NDLRMSDWTNDEHTNELVKQTIANYIKKDKITIAEVNRRKLDETLGDELPSGIIQTAKIL 1047

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR IQ GDKMAGRHGNKGIVS+I+  EDMP+L DGTPVDI LNPLGVPSRMN+GQIF
Sbjct: 1048 IAKKRKIQVGDKMAGRHGNKGIVSKIVRREDMPYLPDGTPVDICLNPLGVPSRMNLGQIF 1107

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L WA   LG K  + I D     D++                              A
Sbjct: 1108 EAVLAWAGRKLGVKFATPIFDGATLDDLN------------------------------A 1137

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               K+G+P                          GQ  LYDG TGEPFD+  TVG  Y L
Sbjct: 1138 WTDKAGLP------------------------RGGQMKLYDGGTGEPFDQEATVGVTYFL 1173

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGKSN GGQR GEMEVW ++A+GAA+VLQE+LTI
Sbjct: 1174 KLGHMVDDKMHARSIGPYSLITQQPLGGKSNFGGQRFGEMEVWALEAFGAAHVLQEILTI 1233

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G++    G PES NVL+ E++ L LS+ +E
Sbjct: 1234 KSDDVVGRSKAYEAIVRGDNMPTPGLPESLNVLLNELKGLALSVHIE 1280


>gi|78188335|ref|YP_378673.1| DNA-directed RNA polymerase subunit beta [Chlorobium chlorochromatii
            CaD3]
 gi|88909128|sp|Q3ATP5|RPOB_CHLCH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78170534|gb|ABB27630.1| DNA-directed RNA polymerase subunit beta [Chlorobium chlorochromatii
            CaD3]
          Length = 1300

 Score = 1271 bits (3289), Expect = 0.0,   Method: Composition-based stats.
 Identities = 587/1412 (41%), Positives = 831/1412 (58%), Gaps = 180/1412 (12%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F K   II+ PDL++VQ  S+ +F+  ++   +R ++GL+   +  FPIT   G  +
Sbjct: 8    RIDFSKIKSIINSPDLLKVQLDSFHNFIQDSVPLAKRKDQGLERVLRGAFPITDTRGLYL 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LE++SY FD PK+ V++C+ R LTY V LK+ L+L   D          K+  +Q +Y+G
Sbjct: 68   LEYISYAFDKPKYTVEECIERGLTYDVSLKVKLKLSYKD---EADEPDWKETIQQEVYLG 124

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +++ +I+P +G W++
Sbjct: 125  RIPYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMFSAKIVPTRGSWIE 181

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
             + D  + I V ID+++   VT+ L A+G    E+IL+ F                    
Sbjct: 182  FQTDINNQIFVYIDQKKNFLVTALLRAIGFARDEDILALF-------------------- 221

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                       LV+    E  +++ K+                     + L G Y+A DI
Sbjct: 222  ----------DLVE----EVSLKASKR---------------------EQLVGQYLASDI 246

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN----NNAYIRNTLVTDKNK 368
            V+ +TGE+   A   I E+  E+I  +  + I ++   S N    + + I NT++ D + 
Sbjct: 247  VDMQTGEVI-SARTAITEEIFEQILLAGYKSIKVMKSFSNNEKGMDKSVIINTILNDSSA 305

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-- 426
              ++AL  +Y  +R  +      A S     FF+  KYDL  VGR ++  +L  +  +  
Sbjct: 306  TEEEALEIVYEELRANEAPDIEAARSFLERTFFNQKKYDLGDVGRYRIKKKLRREFEELY 365

Query: 427  ----------------------------------DVRHIRKEDIIAIIKILVDLRNGKGT 452
                                              D+  +   DIIA+I  L+ L NG+  
Sbjct: 366  SFIGEKPELKALSDTIEEKILQTIQTYSDEPIGEDILVLTHYDIIAVIYYLIKLVNGQAE 425

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            +DD+D+L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S 
Sbjct: 426  VDDVDHLANRRVRSVGEQLAAQFVVGLARMGKNVREKLNSRDSDKIAPSDLINARTVSSV 485

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
            V  FF +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 486  VSSFFATSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPI 545

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG NIGL+SSL+ +A +N  GFI+TPYR V +G+VT+ VV LSA +EEN+     + 
Sbjct: 546  ETPEGPNIGLISSLSVYAEINDKGFIQTPYRLVDNGQVTDTVVMLSAEDEENKITVPVSI 605

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LDE+     E V  R  G+  +V    + ++D SP Q+VS AA+LIPFLE+DD NR LM
Sbjct: 606  PLDENNRIAVETVQARTKGDYPVVAATDVHYMDVSPVQIVSAAAALIPFLEHDDGNRALM 665

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQAVPLL ++AP VGTGME  VA+ S A IVA+  G V  V A  I +R      
Sbjct: 666  GANMQRQAVPLLTSDAPVVGTGMEGKVARDSRAVIVAEGPGEVVDVTADYIQVRYQLDAD 725

Query: 753  D-------PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            +           G+  Y+L+KF+RSNQ+TC++Q+PLV++GD+V +N ++AD  ST+ G+L
Sbjct: 726  NNLRLSMLDPDEGLKTYKLIKFKRSNQDTCISQKPLVRIGDKVEKNTVLADSSSTEYGEL 785

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ALG+N+LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G E+ TRDI
Sbjct: 786  ALGKNVLVAFMPWRGYNFEDAIILSERLVYDDVFTSIHIHEFEANVRDTKRGEEQFTRDI 845

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             NVSEE L+N+DE GI+  GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+
Sbjct: 846  YNVSEEALRNLDENGIVRCGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVK 905

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D S+ VP+G+ G ++  ++F+R    K +  + + +E+IELL +    ++  L +     
Sbjct: 906  DASMHVPAGMKGIIIKTKLFSR----KKKIGLDI-KEKIELLDKQFAAKEYDLRKRFAKW 960

Query: 986  LMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF------AVQDEKVQRN 1034
            L   L      G     G     + TV    +++++  +Q+ +        V  +K  +N
Sbjct: 961  LKHFLDGKTSTGVYNDKGKVVVPEGTVFEESVLAKFATAQFLESVDLSRGVVSSDKTNKN 1020

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V  L  ++      + D  +N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRH
Sbjct: 1021 VTRLIKEFRFLLKDIADERENEKYKVNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRH 1080

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+V +ILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+
Sbjct: 1081 GNKGVVGKILPVEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAAKKLGVKFKT 1140

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             I +     ++                                   ++G+P         
Sbjct: 1141 PIFNGATYEEVQRELE------------------------------RAGLP--------- 1161

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G+  L+DG TGE FD  VTVGYIYMLKL+H+V DK++ARSTG 
Sbjct: 1162 ---------------THGKVSLFDGRTGERFDDEVTVGYIYMLKLSHLVDDKIHARSTGP 1206

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+ +L+EMLT+KSDDVVGR + YE+IV 
Sbjct: 1207 YSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASNILREMLTVKSDDVVGRNKTYEAIVK 1266

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            G +  E G PESFNVLV+E+Q LGL I +++ 
Sbjct: 1267 GQNLPEPGIPESFNVLVRELQGLGLEIRIDDK 1298


>gi|228470322|ref|ZP_04055226.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas uenonis
            60-3]
 gi|228308065|gb|EEK16940.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas uenonis
            60-3]
          Length = 1280

 Score = 1270 bits (3286), Expect = 0.0,   Method: Composition-based stats.
 Identities = 554/1367 (40%), Positives = 775/1367 (56%), Gaps = 109/1367 (7%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             RK F      ++ PD +EVQ  S+  F  ++   + R  EGL   F   FPI       
Sbjct: 8    TRKSFASIAHPMEYPDFLEVQLKSFQDFFQLDTPAESRKKEGLFKVFSENFPIEDTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L F  Y  DPPK+ +++CL R LTY+VPL+  L+L   D +      ++     Q +++
Sbjct: 68   KLLFEDYFVDPPKYSIEECLRRGLTYSVPLRAKLKLTCEDPEHEDFESTV-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT  GTFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GSIPYMTPAGTFVINGAERVVVSQLHRSPGVFFGSSL---HNNGTRLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D+ + ++  IDR++K+P+T+ L A+G +++ +IL  F          +        
Sbjct: 180  EFATDTNNELYAYIDRKKKLPITTLLRAIGYETDKDILDLFGIAEEVPVTLETLQANY-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYV 308
                                     G++L + ++    ++  +     ++       L  
Sbjct: 238  -------------------------GRQLAASVILKYYDEESEEETGETETFARYNTLVE 272

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               I++ E  ++ +E G     +++         D      + ++  + I NTL  D   
Sbjct: 273  QNAILDEENAQVILENGI----ETILLRRDLSTSDQESTDQEVMD-YSIIFNTLKRDSAN 327

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              + A   IY ++R         A+ +FN +FF   +YDL  VGR K+N +L LD   D+
Sbjct: 328  SEQAAYNFIYNLLRNSTPPDDQSAKEIFNNIFFSEKRYDLGDVGRYKINSKLGLDIDPDI 387

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R +  EDI+AII+ L+ L NGK  +DDID+L NRRVR+VGE L NQ+ +GL RM R++KE
Sbjct: 388  RILTAEDIVAIIRHLIKLVNGKAPVDDIDHLSNRRVRTVGEQLYNQFSIGLSRMARTVKE 447

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            R++  D +   P DL+N+K + S V  FF ++ LSQ  +  N LS ITH RRLSALG GG
Sbjct: 448  RMNVRDSEVFTPVDLVNSKTIASVVNSFFGTNALSQFMDQQNPLSEITHKRRLSALGPGG 507

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A++N  GFI TPYR V  G
Sbjct: 508  LTRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKINELGFITTPYRNVDKG 567

Query: 609  KVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             V+   + + Y +A EEE++ +AQ N+ L EDG F    V  R   +  +V   ++D +D
Sbjct: 568  TVSFKDSQLGYYTAEEEEDKTVAQGNAPLSEDGHFVRSRVKARYGADFPVVEPSEVDLMD 627

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL  EAP VGTG+E  +   S  
Sbjct: 628  VSPTQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLTPEAPIVGTGIERRLVSDSRT 687

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
             + A+  G+V  VDA +IV+      E +L         Y+L K++++NQ+T ++  P+ 
Sbjct: 688  QVEAEGDGVVVYVDATKIVVDYDRTEEEELVSFEPSEVTYKLPKYRKTNQSTTIDLSPVC 747

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + GD V +  I+  G ST  G+LALGRN+L A+MPW GYN+ED+++++ER+V+ED+FTS+
Sbjct: 748  RKGDRVTKGQILTQGFSTQDGELALGRNILAAYMPWKGYNYEDAIVLNERVVAEDLFTSV 807

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            H++E+ +  R+TK G EE T DIPNVSEE  K++D  GI+ VGA + PGDILVGKITPKG
Sbjct: 808  HVDEYSLDVRETKRGMEEFTADIPNVSEEATKDLDTNGIVRVGARIVPGDILVGKITPKG 867

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH----GIDKNERSIS 958
            ES  TPEEKLL AIFG+KA DV+D SL+    + G V+D ++++R     GI    +   
Sbjct: 868  ESDPTPEEKLLLAIFGDKAGDVKDASLKASPSLKGVVIDTKLYSRANRKGGIVATRKINQ 927

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
               E++  L     +E V   + I  +            G    K  T ++  L+ E   
Sbjct: 928  RYEEELSKLQSALKEELVSKLQIILKKHKATATDFVDYIGIVKVKAGTRITKSLLLELDY 987

Query: 1019 SQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            +        +DE   + V+     Y     +       +      GD++P G+++  K+ 
Sbjct: 988  NDLRMSDWTKDEHTNQLVKQTIANYIKKDKVTIADVNRRKLDETLGDELPSGIIQTAKIL 1047

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR IQ GDKMAGRHGNKGIVS+I+  EDMP+L DGTPVDI LNPLGVPSRMN+GQIF
Sbjct: 1048 IAKKRKIQVGDKMAGRHGNKGIVSKIVRREDMPYLPDGTPVDICLNPLGVPSRMNLGQIF 1107

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L WA   LG K  + I D     D++                               
Sbjct: 1108 EAVLAWAGRKLGVKFATPIFDGATLDDLNEWTD--------------------------- 1140

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               K+G+P                          GQ  L+DG TGEPFD+  TVG  Y L
Sbjct: 1141 ---KAGLP------------------------RGGQMKLFDGGTGEPFDQEATVGVTYFL 1173

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGKSN GGQR GEMEVW ++A+GAA+VLQE+LTI
Sbjct: 1174 KLGHMVDDKMHARSIGPYSLITQQPLGGKSNFGGQRFGEMEVWALEAFGAAHVLQEILTI 1233

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G++    G PES NVL+ E++ L LS+ +E
Sbjct: 1234 KSDDVVGRSKAYEAIVRGDNMPTPGLPESLNVLLNELKGLALSVHIE 1280


>gi|325853552|ref|ZP_08171384.1| DNA-directed RNA polymerase, beta subunit [Prevotella denticola CRIS
            18C-A]
 gi|325484356|gb|EGC87284.1| DNA-directed RNA polymerase, beta subunit [Prevotella denticola CRIS
            18C-A]
          Length = 1289

 Score = 1269 bits (3283), Expect = 0.0,   Method: Composition-based stats.
 Identities = 577/1367 (42%), Positives = 810/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 28   RINFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 87

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +++CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 88   LEFLDYYVDPPRYSIEECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 142

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 143  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 199

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 200  FATDINNVMYAYIDRKKKLPVTTMLRAIGYETDRDILQIFDLCEEVKVNKKNMK------ 253

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++K+  E  V                 ++
Sbjct: 254  ---------------------AAIGRKIAGNVMKTWTEDFVDEDT------------GEV 280

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   VI E++++EI  S +  I +    ++ N  + I NTL  D +    
Sbjct: 281  VSIERNEVVVERETVITEENVDEILDSSVSTILLHKDEEAANKYSIIFNTLAKDPSHSEM 340

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNLDT  DVR +
Sbjct: 341  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLDTDMDVRVL 400

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 401  TKDDIIEIIKYLISLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMNRTIRERMN 460

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 461  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 520

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 521  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRRVKDSKVD 580

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE++ I Q N+ L++DG+F  E V CR   +  +V  + ++ ID SP
Sbjct: 581  MDNKDVVFLTAEEEEDQIIGQGNAPLNDDGTFIRETVKCRQDADYPVVGPDSVNLIDVSP 640

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 641  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 700

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  GI+E VDA  I I   R+ E +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 701  AEGDGIIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 760

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 761  QRVKKGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 820

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 821  EYSLEVRETKRGVEEFTSDIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 880

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 881  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKVTLA 938

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 939  KIDEEQEAKVNDLKDLLVDKLLELTADKVSEGVKDYSDAEIITKGSKFTVAALKNLDYEG 998

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + Y      ++   K +   I  GD++P GVL++ KV++A
Sbjct: 999  IQSNGWTDDEHTNLLIQKLIMNYIRKYKQMDAELKRRKFAITIGDELPSGVLQMAKVYIA 1058

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL++G+PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1059 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLENGSPVDLVLNPMGVPSRMNLGQIFEA 1118

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1119 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1149

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1150 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1182

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1183 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1242

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1243 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1289


>gi|327313175|ref|YP_004328612.1| DNA-directed RNA polymerase subunit beta [Prevotella denticola F0289]
 gi|326945816|gb|AEA21701.1| DNA-directed RNA polymerase, beta subunit [Prevotella denticola
            F0289]
          Length = 1269

 Score = 1268 bits (3282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1367 (42%), Positives = 810/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RINFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +++CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYVDPPRYSIEECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGYETDRDILQIFDLCEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++K+  E  V                 ++
Sbjct: 234  ---------------------AAIGRKIAGNVMKTWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   VI E++++EI  S +  I +    ++ N  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETVIAEENVDEILDSSVSTILLHKDEEAANKYSIIFNTLAKDPSHSEM 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNLDT  DVR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLDTDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIIEIIKYLISLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMNRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRRVKDSKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE++ I Q N+ L++DG+F  E V CR   +  +V  + ++ ID SP
Sbjct: 561  MDNKDVVFLTAEEEEDQIIGQGNAPLNDDGTFIRETVKCRQDADYPVVGPDSVNLIDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  GI+E VDA  I I   R+ E +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 681  AEGDGIIEYVDATTIRILYDRTEEEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTSDIPNVSEEATKDLDDNGIIRVGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKVTLA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 919  KIDEEQEAKVNDLKDLLVDKLLELTADKVSEGVKDYSDAEIITKGSKFTVAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + Y      ++   K +   I  GD++P GVL++ KV++A
Sbjct: 979  IQSNGWTDDEHTNLLIQKLIMNYIRKYKQMDAELKRRKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG+PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGSPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1269


>gi|189218816|ref|YP_001939457.1| DNA-directed RNA polymerase subunit beta [Methylacidiphilum
            infernorum V4]
 gi|226699420|sp|B3E163|RPOB_METI4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189185674|gb|ACD82859.1| DNA-directed RNA polymerase, beta subunit [Methylacidiphilum
            infernorum V4]
          Length = 1289

 Score = 1268 bits (3282), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1374 (43%), Positives = 837/1374 (60%), Gaps = 134/1374 (9%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  FGK  E + +P+LIE Q  SY  FL +++AP ER  EGL   F  VFPI ++ G
Sbjct: 4    KIQRINFGKIREGLSLPNLIEHQTKSYADFLQLSVAPQERKAEGLHGVFLEVFPIESYDG 63

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
               LE+V+YE    KF   DCL    TYA PL +T RL           K  + +KE+ +
Sbjct: 64   KVKLEYVNYEIGESKFSPIDCLRDGKTYAAPLYVTFRL-----------KDEEGVKEEKV 112

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMG+LP+MT  G+F+I G +R++V+QLHRSPGI F+        +GK LY+ RIIPD+G 
Sbjct: 113  YMGELPMMTPQGSFIINGAERVIVNQLHRSPGICFESSF---HSNGKTLYSFRIIPDRGS 169

Query: 191  WMDIEFDSKDIIHVRIDRR---RKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
            W+++ FD+ D+++V +DRR   RK  +T+                               
Sbjct: 170  WLEVAFDTNDLLYVYLDRRKKRRKFLITT------------------------------- 198

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                         + +         +   G +    L  +++E  +   GI  D +    
Sbjct: 199  ----------LLRALAAALSGPSSPLGSGGDEEIIRLFYTVEELNLSE-GIDEDKVATKV 247

Query: 308  VAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            +  ++ +      +   A + +    + ++    I+ I ++ V   +    +   L  D 
Sbjct: 248  LVSEVKDPHNPDVVLARAYEPVTRSVVRQLLDVGIQSISVVDVQYDDT---LIKCLKKDP 304

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             KD  +AL +IYR +RPGD  T S A+ +   L  D  +YDL  VGR K+N +LN+    
Sbjct: 305  TKDPVEALKEIYRRLRPGDPPTESNAKLLLKRLLLDPKRYDLGRVGRYKLNQKLNIQVDP 364

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            D+R +  ED++A  + L+ LR G+G  DDID+LG+RRVR+VGE++ NQ R+GL R ER +
Sbjct: 365  DIRILTWEDLVAATRYLIKLRKGEGITDDIDHLGSRRVRTVGELVANQCRMGLARTERLV 424

Query: 487  KERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            KER++  D   + + PQ LIN K + + + +FF  SQLSQL + +N LS +TH RRLSAL
Sbjct: 425  KERMTLFDVNTEGMTPQKLINPKALSATIRDFFARSQLSQLMDQINPLSELTHKRRLSAL 484

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVHP+HYGRICP ET EG NIGL++++ S++R N YG +ETPYRK
Sbjct: 485  GPGGLSRERAGFEVRDVHPSHYGRICPIETPEGPNIGLIATMASYSRFNDYGILETPYRK 544

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V +GKVTN++VY +A +EEN  IA AN+++ EDG+  ++ V  R   E + V REK++++
Sbjct: 545  VLNGKVTNEIVYFTADQEENYVIAMANTAVSEDGTILDQRVAVRFRREFMEVEREKVEYM 604

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D SPKQ+VS+AA LIPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTG+E  VA+   
Sbjct: 605  DVSPKQIVSVAAGLIPFLEHDDANRALMGSNMQRQAVPLIQPEAPIVGTGIEERVARDIQ 664

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDP--------STSGVDIYRLMKFQRSNQNTCV 776
            A IV++  G V  V    I++      ++         S     +Y+L KF RSN  TC+
Sbjct: 665  AVIVSEVDGTVSSVTGKEIIVTPTGSPVEQKKKKSKQGSEREGIVYKLNKFMRSNAGTCI 724

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ+P+VK G  V++ D++ADGPST  G+LALGRN+LVAFMPW+GYNFED++++SER+V E
Sbjct: 725  NQKPIVKKGQVVKKGDVLADGPSTQNGELALGRNLLVAFMPWNGYNFEDAIIVSERVVKE 784

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D+FTSI+I+EFE++ARDTKLGPEEITRDIPNV +E LKN+   GII VGAEV PGDILVG
Sbjct: 785  DLFTSIYIDEFEIVARDTKLGPEEITRDIPNVGDEALKNLGPDGIIRVGAEVKPGDILVG 844

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN-RHGIDKNER 955
            KITPK E+ + PEE+LLRAIFGEKA DV+D+SLRVPSG  G V+DVR+ +    + K + 
Sbjct: 845  KITPKSETELAPEERLLRAIFGEKAADVKDSSLRVPSGTYGIVMDVRVSSGTARVRKEKI 904

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL------S 1009
            + S  +++I+ +    D ++  L   +   L  IL  +         +   ++       
Sbjct: 905  NASEAKQKIKEIEERYDQKEEELREELTQALSNILLNEKIPLDVVNVETGEIIIPANRKI 964

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++       + +  +    ++  +  +   +E     L +  + ++++I+ G+D  PG
Sbjct: 965  TKVLLRKMAQAYDKIEIDPSPIRSKIFEIIGNFEAKFEQLRNDRELELDQIESGEDTEPG 1024

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            +++ VKVF+A KR +  GDKMAGRHGNKG+VS+I+P EDMP+L DGTPVDIVLNPLGVPS
Sbjct: 1025 IIKQVKVFIANKRKLSVGDKMAGRHGNKGVVSKIVPVEDMPYLPDGTPVDIVLNPLGVPS 1084

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMNVGQ+ ETHLG A   LG  + + + D      I                        
Sbjct: 1085 RMNVGQVLETHLGIAAKKLGFNVATPVFDGVKEEKIREFLVKA----------------- 1127

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                                   G DE+              G+SILYDG TGE F++ V
Sbjct: 1128 -----------------------GMDED--------------GKSILYDGRTGEMFNQRV 1150

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             VG IYM+KLNHMV+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1151 VVGMIYMMKLNHMVADKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWAMEAYGAAY 1210

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +LQE+LT+KSDDV GRTR+YESIV G +  ET TPESFNVL+KE+Q L L +++
Sbjct: 1211 ILQELLTVKSDDVQGRTRIYESIVKGENYLETTTPESFNVLIKELQGLCLEVNI 1264


>gi|187735536|ref|YP_001877648.1| DNA-directed RNA polymerase, beta subunit [Akkermansia muciniphila
            ATCC BAA-835]
 gi|187425588|gb|ACD04867.1| DNA-directed RNA polymerase, beta subunit [Akkermansia muciniphila
            ATCC BAA-835]
          Length = 1312

 Score = 1267 bits (3279), Expect = 0.0,   Method: Composition-based stats.
 Identities = 613/1388 (44%), Positives = 857/1388 (61%), Gaps = 149/1388 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R +FG   E+I+ P+LIE+Q  SY  FL  +     R N GLQ   K +FPI ++     
Sbjct: 4    RLYFGNIKEVIEPPNLIEIQLQSYFDFLQQDTPAAARKNIGLQGVLKEIFPIKSYDENIE 63

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            L+FVSY+ + PK    + +    TY+  L++T +L           KS  + KE+++YMG
Sbjct: 64   LDFVSYDIEQPKMSDYEAIRAGETYSAALQVTFKL-----------KSDNESKEETVYMG 112

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +LP+MT  GTFVI G +R++VSQLHRSPGI F+  +    L+GKLL++ RIIPD+G W++
Sbjct: 113  ELPMMTNRGTFVINGAERVIVSQLHRSPGICFESAQ---HLNGKLLHSFRIIPDRGSWLE 169

Query: 194  IEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            ++FD+ D+++V +DRRR   K   T+F+  LG  +         + + SQ  +    PLS
Sbjct: 170  VQFDTNDLLYVYLDRRRRRRKFLATTFMRYLGFKT--------DRDIVSQFYNIRTLPLS 221

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                                                            T + L  L   +
Sbjct: 222  EDM---------------------------------------------TEEDLHNLVAVD 236

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             I + +   +  +A + ++   + ++    I+ I ++     + +  +  TL  D   D 
Sbjct: 237  TIKDKDL--VLAKAFEQLNMGVVRQLLQFGIKKIDVID---QSEDDVLIKTLKKDPAHDE 291

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            + AL +IY+ +RPGD +T + A ++   LF D  KYDL+ VGR K+N +L LDT  D R 
Sbjct: 292  ESALKEIYKRLRPGDPATAAQARTLLKRLFDDPKKYDLTRVGRYKINQKLGLDTSLDQRL 351

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +  ED +A +K L+ L+ G+G +DDID+LG+RRVR+VGE++ NQ R+GL R ER +KER+
Sbjct: 352  MTAEDFLAALKYLLRLKKGEGMVDDIDHLGSRRVRAVGELMANQCRVGLARTERLVKERM 411

Query: 491  SSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            + +D  I+ V P  LIN K + + V +FF  SQLSQ  + +N L+ +TH RRLSALG GG
Sbjct: 412  TLIDQNIEGVTPSKLINPKALSAVVRDFFGRSQLSQFMDQINPLAELTHKRRLSALGPGG 471

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            + R RAG E+RDVHP+HYGRICP ET EG NIGL++S+ ++AR+N +GFIETPYRKV +G
Sbjct: 472  LNRDRAGFEVRDVHPSHYGRICPIETPEGPNIGLINSMCTYARINEFGFIETPYRKVENG 531

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            +VTN + Y++A +EE   IAQAN+ LDE G+FT   V  R  GE I V    + ++D SP
Sbjct: 532  RVTNTIEYVTADQEEGYLIAQANNPLDEQGNFTTSRVTAREKGEFIEVDPADVHYMDVSP 591

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            KQ+VSIAA LIPFLE+DD+NR LMG NMQRQ VPL+ AE+P+VGTG+E   A+ S + ++
Sbjct: 592  KQLVSIAAGLIPFLEHDDANRALMGSNMQRQGVPLMVAESPYVGTGIEGKCARDSRSVVL 651

Query: 729  AKRAGIVEQVDAI--------RIVIRSV------EGDLDPSTSGVDIYRLMKFQRSNQNT 774
            A+  GIV    A          + +R        +       +GV +Y L KF RSN  T
Sbjct: 652  AEADGIVASATAEVIITTKDGELPVRPEVFLSDPDSVRTDRDNGVYVYPLRKFMRSNAGT 711

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQRP+V+ GD+++  D++ADGP+TD G+LALGRN+LVA+MPW+GYNFED+++ISE+ V
Sbjct: 712  CINQRPIVRRGDKIKTGDVLADGPNTDQGELALGRNVLVAYMPWNGYNFEDAIVISEKTV 771

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FTSIHI EFEV ARDTKLGPEEITRDIPN  +E LKN+D  G+I +GAEV PGDIL
Sbjct: 772  KEDTFTSIHISEFEVQARDTKLGPEEITRDIPNAGDEALKNLDHDGVIRIGAEVKPGDIL 831

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI------FNRH 948
            VGKITPK E+ + PEE+LLRAIFGEKA +V+DTSLRVPSG +G V+DVRI       +R 
Sbjct: 832  VGKITPKSETELAPEERLLRAIFGEKAAEVKDTSLRVPSGCTGIVMDVRISSTGSGHHRG 891

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA-------VSGPKG 1001
             +  +    + +++Q + +  +   ++  L   +  +L +IL G+          +G   
Sbjct: 892  DLVVDS---AEKKKQFKKINDEHKKKKEQLIDQLTKKLSDILLGEKIPLDVVNEQTGEII 948

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
               +  ++  L+ +          ++   ++  +  +   +E   + L+D  ++++++++
Sbjct: 949  IPANRKITKTLLRKLAL-VHDHIEIEPSPIRNKILEIITSFEGRFTELDDEREHRLDQME 1007

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+  PG L+ VKV++A KR +  GDKMAGRHGNKG+V++I+P +DMPFL DGTPVDIV
Sbjct: 1008 SGDESEPGGLKEVKVYIAAKRKLGVGDKMAGRHGNKGVVAKIVPEQDMPFLADGTPVDIV 1067

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQ+ E HLG A   LG K+ + + D  +   I    S  +KV G    
Sbjct: 1068 LNPLGVPSRMNVGQVLEAHLGIAARALGFKVATPVFDGISEETIWNYMSEAKKVDGF--- 1124

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                      T + DG D                G+S LYDGLT
Sbjct: 1125 --------------------------TWIGDGKDGTV------------GGKSTLYDGLT 1146

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEPF  PV VG  YMLKLNH+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1147 GEPFHNPVVVGQTYMLKLNHLVADKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWA 1206

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQE+LT+KSDDV GRTR+YESIV G++T E GTPESFNVL+KEMQ+LGL++
Sbjct: 1207 LEAYGAAYTLQELLTVKSDDVQGRTRIYESIVKGDNTLEAGTPESFNVLMKEMQSLGLNV 1266

Query: 1362 DLENSRTK 1369
               +   +
Sbjct: 1267 RPGSKDEQ 1274


>gi|303237498|ref|ZP_07324063.1| DNA-directed RNA polymerase, beta subunit [Prevotella disiens
            FB035-09AN]
 gi|302482318|gb|EFL45348.1| DNA-directed RNA polymerase, beta subunit [Prevotella disiens
            FB035-09AN]
          Length = 1296

 Score = 1265 bits (3273), Expect = 0.0,   Method: Composition-based stats.
 Identities = 560/1365 (41%), Positives = 793/1365 (58%), Gaps = 117/1365 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD +++Q  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 35   RVNFASVQSPYPYPDFLDLQLKSFRDFLQLDTPPEERKNDGLYKVFTENFPITDTRNNFV 94

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ + +CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 95   LEFLDYYIDPPRYSISECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 149

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 150  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 206

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                L   
Sbjct: 207  FATDINNVMYAYIDRKKKLPVTTMLRAIGFESDKDILQIFDLCEEMKVNKKNMKAAL--- 263

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+KL   ++KS  E  V                 ++
Sbjct: 264  ------------------------GRKLAGNVMKSWNEDFVDEDT------------GEV 287

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E    I + +L+ I  S +  + +    D  N  + I NTL  D +    
Sbjct: 288  VSIERNEVVVERETEITDDNLDIILESGVSSVLLHKDEDVANKYSIIFNTLAKDPSHSEI 347

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +L L+T  DVR +
Sbjct: 348  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINRKLGLETDMDVRVL 407

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L++L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 408  TKDDIIEIIKYLINLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRTIRERMN 467

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 468  VRDNEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 527

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYRKV D KV 
Sbjct: 528  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCLYAKINDLGFIVTPYRKVVDSKVD 587

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               + VVY++A EEE+  + Q N+ L+ DG+F    V CR   +  +V   ++  +D +P
Sbjct: 588  LDNDHVVYMTAEEEEDLPVGQGNAPLNPDGTFIRSYVKCRQDADYPVVEPSQVTLMDVAP 647

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 648  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 707

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  Y++ KF+R+NQN  ++ RP+   G
Sbjct: 708  AEGDGVIEYVDATCIRILYDRTEDEEFVSFEPALKEYKISKFRRTNQNMVIDLRPICSKG 767

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V+  DI+ +G +T+ G+LALGRN+LVA+MPW GYN+ED+++ISERMV ED+ TS+H++
Sbjct: 768  QRVKAGDILTEGYATENGELALGRNLLVAYMPWKGYNYEDAVVISERMVREDILTSVHVD 827

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++DE G+I +GA V PGDI++GKI+PKGES 
Sbjct: 828  EYSLEVRETKRGVEEFTADIPNVSEEATKDLDENGVIRIGARVEPGDIMIGKISPKGESD 887

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F R    K   S   ++  + 
Sbjct: 888  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKMFARA--VKTRESKRHDKATLA 945

Query: 966  LLARDKDDEQVILDRNIYSRLM-----EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             L  +++ +   L   +  +L+     ++  G    S  +   K +  +   +       
Sbjct: 946  RLDEEQEAKINDLKDLLVDKLLELTEDKLSQGIKDYSNAEIITKGSKFTIAALKNLDYEG 1005

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + +      ++ + K K   I  GD++P GVL++ KV++A
Sbjct: 1006 IQSNGWTDDEHTNLLIQKLIMNFIRKYKQMDAQLKRKKFAITIGDELPSGVLQMAKVYIA 1065

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1066 RKRKIQVGDKLAGRHGNKGIVSKVVRAEDMPFLEDGRPVDLVLNPMGVPSRMNLGQIFEA 1125

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+               +                  
Sbjct: 1126 ILGAAGRNLGIKFATPIFDGAKLEDLKEWTDKAGLPPMCSRY------------------ 1167

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                      ++DG                            GE FD+P TVG  Y LKL
Sbjct: 1168 ----------IYDGET--------------------------GERFDQPATVGITYFLKL 1191

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTIKS
Sbjct: 1192 GHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTIKS 1251

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            DDV+GR++ YE+IV G      G PES NVL+ E++ LGLSI L+
Sbjct: 1252 DDVIGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSIKLD 1296


>gi|182412057|ref|YP_001817123.1| DNA-directed RNA polymerase subunit beta [Opitutus terrae PB90-1]
 gi|177839271|gb|ACB73523.1| DNA-directed RNA polymerase, beta subunit [Opitutus terrae PB90-1]
          Length = 1259

 Score = 1263 bits (3269), Expect = 0.0,   Method: Composition-based stats.
 Identities = 603/1373 (43%), Positives = 834/1373 (60%), Gaps = 141/1373 (10%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  FGK  E++  P+LIE+Q  SY  FL   +   +R  +GL+A F+ VFPI ++  
Sbjct: 6    HSERINFGKLREVLQPPNLIEIQITSYLDFLQKGVPEKQRKPQGLEAVFREVFPILSYDE 65

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
               LE+VSY    PK    +CL   +TY+VPL + LRL           +    IK++ I
Sbjct: 66   RLTLEYVSYTLGDPKNTEIECLREGITYSVPLYVKLRL-----------REEDFIKDEEI 114

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMG++P++T+ G+F+I G +R+VVSQLHRSPGI F+        +GK L++ RIIPD+G 
Sbjct: 115  YMGEIPMVTERGSFIINGAERVVVSQLHRSPGIAFE---VTPHPNGKPLHSFRIIPDRGT 171

Query: 191  WMDIEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
            W++++FD+ D+++V +DRRR   K  +T+ L A+G  S+ ++L+ FY             
Sbjct: 172  WLEVQFDNNDLLYVYLDRRRRRRKFLITTLLRAIGYSSDIDLLNLFY------------- 218

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                             + D+   +                          +  + +  L
Sbjct: 219  ----------------EIKDLKVSK-------------------------ALDMENVSTL 237

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             + ED ++ + G +   A + + +  +      +I  + ++   + +  A IR  L  D 
Sbjct: 238  VLVEDAIDAQKGVVLARAFEPLTKAIVRTFEKHDITTLRVIDT-AADEGAIIR-ALKKDP 295

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             ++ ++AL +IY+ +RPG+  T + A+++   LFFD  +YDL  VGR K+N +L L    
Sbjct: 296  TRNEEEALKEIYKRLRPGEPPTTANAKALLKRLFFDPKRYDLGRVGRYKVNQKLGLKVDL 355

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            + R +   D++A  K LV L+ G+G +DDID+LG+RRVR+VGE+L NQ R+GL R ER +
Sbjct: 356  EQRILESGDVVAATKYLVRLKKGEGVVDDIDHLGSRRVRTVGELLANQCRVGLSRTERLV 415

Query: 487  KERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            +ER++  D   DS+ PQ LIN K + + + +FF  SQLSQ  + +N L+ +TH RRLSAL
Sbjct: 416  RERMTMYDQSVDSITPQKLINPKALTTVIRDFFARSQLSQFMDQINPLAEVTHKRRLSAL 475

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL+++ARVN +GFIETPYR 
Sbjct: 476  GPGGLNRERAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLSTYARVNEFGFIETPYRT 535

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V DG+VT+ + YL+A +EE + IAQAN+ +DE G F    V  R  G  I VP   +  +
Sbjct: 536  VKDGRVTDKIEYLTADQEEGKIIAQANAEIDEKGHFIG-KVTSRQDGNFIEVPAADVHLM 594

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D SPKQV+SIAA +IPFLE+DD+NR LMG NMQRQ VPLL++EAPFVGTG+E  VA+ S 
Sbjct: 595  DVSPKQVISIAAGMIPFLEHDDANRALMGANMQRQGVPLLQSEAPFVGTGIEERVARDSK 654

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDL----DPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               VA+ AG+V  VDA RIVI               +GV +Y L KF RSN  TC NQ+P
Sbjct: 655  IVAVAEEAGVVASVDAKRIVITRDGEMPRNLKTDPKNGVHVYELRKFMRSNAGTCFNQKP 714

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK G +V+   +IADGPSTD G++ALGRN+LVAFMPW+GYNFED++LISE+++ ED+FT
Sbjct: 715  VVKQGQKVKTGQVIADGPSTDHGEMALGRNVLVAFMPWNGYNFEDAILISEKVLKEDIFT 774

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+EFEV ARDTKLGPEEITRDIPNV EE LKN+D  G+I +GAEV PGDILVGKITP
Sbjct: 775  SIHIQEFEVTARDTKLGPEEITRDIPNVGEEALKNLDHNGVIRIGAEVKPGDILVGKITP 834

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ + PEEKLLRAIFGEKA DV+DTSL VPSG +G V+DV++ +R   +K + S S  
Sbjct: 835  KSETELAPEEKLLRAIFGEKAADVKDTSLVVPSGAAGIVMDVKVSSRVDFEKEKLSPSDR 894

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL------SSDLIS 1014
            R Q++ +  +   +   L   +   L  IL G+         +   ++       +  + 
Sbjct: 895  RRQVKQIQEEYKTQMDKLREGLTEALSNILLGEKIPLDVINGETGEIIIPANRKITKTLL 954

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                +      +    V+  +  +   Y+T    LE   + KI  I+ G D   G ++ V
Sbjct: 955  RKLAAVSKHVQIDPSPVRIKIMEIIGSYQTKFDELETDRERKIGGIESGADAGDGAIKQV 1014

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A K+ ++ GDKMAGRHGNKG+V++I+  EDMPFL DGTP++I LNPLGVPSRMNVG
Sbjct: 1015 KVYIAEKQKLEVGDKMAGRHGNKGVVAKIVAEEDMPFLPDGTPIEICLNPLGVPSRMNVG 1074

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ ETHLGWAC  +G K+ + + D      +       +      S              
Sbjct: 1075 QVLETHLGWACKRIGLKVATPVFDGIPEKKVREYLKEAKLPSSGKSVLS----------- 1123

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                             DG   E                            D+ V VGYI
Sbjct: 1124 -----------------DGRTGE--------------------------RLDQEVVVGYI 1140

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YM+KLNH+VS K++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+
Sbjct: 1141 YMMKLNHLVSHKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWALEAYGAAHTLQEL 1200

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            LT+KSDDV GRT++YES+V G++T + GTPESFNVL+KE+Q+LGL I L  S 
Sbjct: 1201 LTVKSDDVQGRTKIYESLVKGDNTLQAGTPESFNVLIKEIQSLGLDIKLNKSD 1253


>gi|15606949|ref|NP_214331.1| RNA polymerase beta subunit [Aquifex aeolicus VF5]
 gi|6226042|sp|O67762|RPOB_AQUAE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|2984192|gb|AAC07723.1| RNA polymerase beta subunit [Aquifex aeolicus VF5]
          Length = 1468

 Score = 1263 bits (3268), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1477 (41%), Positives = 873/1477 (59%), Gaps = 144/1477 (9%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            RKFFG+  E+++ P L+ + K S+++F+ + + P +R N GL+  F++ FP        +
Sbjct: 8    RKFFGRRFEVLEPPYLLSIPKNSFENFVQLKVNPYKRKNVGLEHIFRTSFPFKDPDENFI 67

Query: 74   LEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAVP 101
            LE++ YE                                    KF  ++C  + LTY+ P
Sbjct: 68   LEYLGYEIGDWECNRCGYKPKDDLLGGWDVDCPQCGAKLVYKEKFTPEECKLKGLTYSAP 127

Query: 102  LKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSP 161
            L++ L+L     + +      ++   + +Y G++PLMT+ G+F+I G +RI+++QL RS 
Sbjct: 128  LRVMLQLKAKTKNGY------REFPPKKVYFGEIPLMTETGSFIINGTERIIINQLIRSS 181

Query: 162  GIHFDH--DKGRASLSGKLLYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFL 218
            G+ FD   +K + +   ++LY   IIPD+G  ++ E   + D+I  RIDR+ K+  T+ L
Sbjct: 182  GVFFDEKEEKQKDATITRILYRGSIIPDKGSRVEFELSGATDLISARIDRK-KLSATAVL 240

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS----SSLVDIDTGEQV 273
             A G+++  +IL  FY  +      D + +     +      +      +++        
Sbjct: 241  RAFGLETAYDILKYFYEDVRKFIVKDKYLYDAQTGEEFTPEDLEHHYIFAIIKFRGKLVG 300

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
              S K               +   I    +        +++ +  E+   +   +    +
Sbjct: 301  FASSK---------------ERDFIEERYIEEWEDLVRLLDDDRIEVL--SVTAVPRDVV 343

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA-LLDIYRVMRPGDVSTFSV- 391
             +        I  L  D+   +   R+ +        +D  L+++Y+ +R  +  T  + 
Sbjct: 344  IKSP-YGKSLIDTLANDTSPKDVDKRSPVKVPAEYTLRDYGLMEMYKRLRHIEAITMEID 402

Query: 392  -----AESMFNFLFFDSDKYDLSTVGRVKMNMRLNL------------------------ 422
                 A   FN  F D  +YDLS VGRVK+N +++                         
Sbjct: 403  SVIERARIFFNVFFRDLKRYDLSRVGRVKINAKVHRIPKVLKPADVDLLDQLPPLALAED 462

Query: 423  -----------------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                                          T D+ R I   D++ I+K L+DLR+G+   
Sbjct: 463  YGEYKAGTRVTKDLLKELFKQYKEIKVKDYTEDEARFILPIDLVNILKYLIDLRHGRVKK 522

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI--SSVDIDSVMPQDLINAKPVVS 511
            DDI +LGNRRVRSVGE+L+NQ RLG+ +ME+  ++R    + +   + PQD IN + V +
Sbjct: 523  DDIAHLGNRRVRSVGELLENQARLGIAKMEKVFRDRSAVINPEQPDLKPQDFINPRYVTT 582

Query: 512  AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
            A+ +F  + QLSQ  ++ N LS +TH RRLSALG GG+ R  A  E+RDVHP+HYGRICP
Sbjct: 583  AITDFLKTGQLSQYLDNTNPLSELTHKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICP 642

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             ET EG NIGLV+S T +ARVN YGF+ TPYRKV +GKVT+ + +L+A EEEN  IAQ +
Sbjct: 643  IETPEGQNIGLVTSPTVYARVNEYGFLITPYRKVENGKVTDKIEWLAAYEEENYVIAQ-S 701

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  DE+G    E +  R   +  LV  E++++ID SP+QV+S ++SLIPFLE+DD+NR L
Sbjct: 702  TPTDEEGRLKAEFILARHKNDIRLVKPEQVEYIDVSPRQVISPSSSLIPFLEHDDANRAL 761

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-- 749
            MG NMQRQAVPL+  +AP +GTGME  +A+ S A +VAKR G+VE+VD+ +I+IR     
Sbjct: 762  MGSNMQRQAVPLIFTQAPLIGTGMEKKIARDSHAVVVAKRGGVVEEVDSSKIIIRVNPEE 821

Query: 750  -GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                DP   G+DIY L KFQR+NQ TCVNQRP+V+ G++V +  IIADG STD G+LALG
Sbjct: 822  INFDDPLDIGIDIYELRKFQRTNQKTCVNQRPIVRKGEKVEKGQIIADGHSTDRGELALG 881

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +++LVAFMPW GYNFED+++ISER+V EDV+TSIHIEE EV AR+TK+G EEITR IP V
Sbjct: 882  KDVLVAFMPWRGYNFEDAIVISERLVKEDVYTSIHIEELEVEARETKVGEEEITRQIPGV 941

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
             E  L ++DE GI+ VG  V PGDILVGK+TPKGE+ +TPEEKLL+AIFGEK  DV+D S
Sbjct: 942  PERALAHLDEHGIVRVGTYVKPGDILVGKVTPKGETRLTPEEKLLQAIFGEKTRDVKDAS 1001

Query: 929  LRVPSGVSGTVVDVRIFNRHGI-DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
            LR P GV G V+DV++F R G   K+  +  VERE++E L ++ + ++ ++       L 
Sbjct: 1002 LRCPPGVEGIVIDVQVFTRKGTGKKDMLAEKVEREELEALEQELEKKKNLIITGRDKVLK 1061

Query: 988  EILCGQNAVS----GPKGFKKSTVLSSDLISEYPRSQWWQFA--VQDEKVQRNVESLKVQ 1041
             ++ G+        G K  KK TV+   +  E+      +     +DE + R +  +  +
Sbjct: 1062 GLVLGRKVEKDAKVGRKTVKKGTVIDEKVFEEFVNYILGRPENFFEDEDLIRKIREIAER 1121

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
              T   +L   ++ K E +    D+PPGV+ +VKVF+A KR I+ GDKMAGRHGNKG++S
Sbjct: 1122 TRTQIEMLNKVYEEKKETLLKRRDLPPGVITLVKVFIANKRKIKVGDKMAGRHGNKGVIS 1181

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             +LP EDMPFL DGTPVDIVLNPLGVPSRMNVGQI ETHLGWA   LGKKI  +I   + 
Sbjct: 1182 VVLPVEDMPFLPDGTPVDIVLNPLGVPSRMNVGQILETHLGWAAKELGKKIGEMIEKGRD 1241

Query: 1162 NGDISPLRSFL-----EKVIGTGSHTEKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGAD 1215
               I+     +     +         E ++   ++    V   + + G+P++TP F+GA+
Sbjct: 1242 RKAITEYLKEIFAIGDKDGENAKFIEEFLNSLSEEEFWSVVRDYAERGIPMATPAFEGAE 1301

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E+AI  +L+ A L E+G++ LYDG TGEPFD  VTVGY++MLKL HMV DK++AR+TG Y
Sbjct: 1302 EDAIKELLKKAGLPENGKTTLYDGRTGEPFDFEVTVGYMHMLKLIHMVDDKIHARATGPY 1361

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDDV GRT+VYE+IV G
Sbjct: 1362 SLVTQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDVEGRTKVYEAIVKG 1421

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
              T+  G PESF VLV+E++ALGL++   N   K   
Sbjct: 1422 KYTYTPGIPESFKVLVRELKALGLNVKCLNGEEKPCD 1458


>gi|225012654|ref|ZP_03703089.1| DNA-directed RNA polymerase, beta subunit [Flavobacteria bacterium
            MS024-2A]
 gi|225003187|gb|EEG41162.1| DNA-directed RNA polymerase, beta subunit [Flavobacteria bacterium
            MS024-2A]
          Length = 1269

 Score = 1261 bits (3264), Expect = 0.0,   Method: Composition-based stats.
 Identities = 568/1369 (41%), Positives = 803/1369 (58%), Gaps = 116/1369 (8%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
                R  F         PD +++Q  S+  F  +    DER  EGL   FK  FPIT   
Sbjct: 4    KQSQRTNFAGAKHTPMYPDFLDIQIKSFQDFFQLETKSDERNEEGLFNTFKENFPITDTR 63

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               +LEF+ Y  DPP++ + +C+ R LTY+VPLK  L+L   D +       +     Q 
Sbjct: 64   NQFVLEFLDYFVDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIV-----QD 118

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            +++G +P MT  GTFVI G +RIVVSQLHRSPG+ F         +G  LY+ R+IP +G
Sbjct: 119  VFLGTIPYMTPSGTFVINGAERIVVSQLHRSPGVFFGQSF---HANGTKLYSARVIPFKG 175

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
             W++   D   +++  IDR++K+PVT+   A+G + + +IL  F                
Sbjct: 176  SWIEFATDINSVMYAYIDRKKKLPVTTLFRAIGFEHDRDILEIF---------------- 219

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                       ++  +    TG + +  G+KL + +LK+  E  V               
Sbjct: 220  ----------DLAEEIKVSKTGIKKV-LGRKLAARVLKTWHEDFVDEDT----------- 257

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKN 367
              ++++ E  EI I+   V++++ +EEI  + ++ I +  VD  +++ A I NTL  D  
Sbjct: 258  -GEVISIERNEIIIDRDTVLEKEHIEEILEASVKTILLHKVDAHMSDYAIIYNTLQKDPT 316

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               K+A+  IYR +R  +      A  + + LFF   +Y+L  VGR +MN +L LD   D
Sbjct: 317  NSEKEAVEHIYRQLRNAEPPDEDTARGIIDKLFFSDQRYNLGEVGRYRMNKKLGLDVEMD 376

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             + + K DII IIK L++L N K  IDDID+L NRRVR+VGE L +Q+ +GL RM R+I+
Sbjct: 377  KQVLTKLDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSSQFGVGLARMARTIR 436

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG G
Sbjct: 437  ERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPG 496

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G++R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA+VN  GFIETPYRKV +
Sbjct: 497  GLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVFAKVNNLGFIETPYRKVEN 556

Query: 608  GKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            G +   + +YLSA EEEN+ I QAN + D+ G   +E V  R   +  +V  +K+++ D 
Sbjct: 557  GVINLKETIYLSAEEEENQLITQANINFDKAGKILDEKVIARDQADFPVVTPDKVNYTDV 616

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  S   
Sbjct: 617  APNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLEKQVASDSRVL 676

Query: 727  IVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            I A+  G+VE VDA +I I+     + DL         Y L+KF+++NQ TC+N +P+++
Sbjct: 677  INAENDGVVEYVDANKITIKYDFSEKDDLISFDGDTKSYNLIKFRKTNQGTCINLKPIIQ 736

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD V +  ++  G +T+ G+LALGRN+ VAFMPW GYNFED+++ISE++V +D+FTSIH
Sbjct: 737  KGDRVTKGQVLCQGYATEAGELALGRNLKVAFMPWKGYNFEDAIVISEKVVRQDIFTSIH 796

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E+ +  RDTKLG EE+T DIPNVSEE   ++DE G+I +GAEVNPGDIL+GKITPKGE
Sbjct: 797  IDEYSLDVRDTKLGTEELTNDIPNVSEEATSDLDENGMIRIGAEVNPGDILIGKITPKGE 856

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S  TPEEKLLRAIFG+KA DV+D SL+ P  + G V+D ++F R    K++R  + ++++
Sbjct: 857  SDPTPEEKLLRAIFGDKAGDVKDASLKAPPSLRGVVIDKKLFTR--SVKDKRKRNQDKQE 914

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPR 1018
            ++ L    D +   L   +  +L  I+ G+         G +   K    +  L+S    
Sbjct: 915  LDALEDAFDVKSEALKTVLVEKLFTIVNGKTCQGVQNDLGEEVLPKGKKYTLKLLSGVED 974

Query: 1019 SQWWQF--AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                         +    +  L   Y+  ++ L+   + +   I  GD++P G+ ++ K+
Sbjct: 975  YTHLTKGSWTTTSETNDLIADLIHNYKIKENDLQGALRREKFTISVGDELPAGIKKLAKI 1034

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A KR ++ GDKMAGRHGNKGIV+RI+  E+MPFL+DGTPVDIVLNPLGVPSRMN+GQI
Sbjct: 1035 YIAKKRKLKVGDKMAGRHGNKGIVARIVREEEMPFLEDGTPVDIVLNPLGVPSRMNIGQI 1094

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            +ET LGWA   LG+K  + I D      I+ L       +   S+       +       
Sbjct: 1095 YETVLGWAGQNLGEKYATPIFDGATIEQINALTEKGNVPLYGHSYLYDGGTGER------ 1148

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                          FD      +  ML++                          G++  
Sbjct: 1149 --------------FDQPATVGVIYMLKL--------------------------GHM-- 1166

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
                  V DK+++RS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+  LQE+LT
Sbjct: 1167 ------VDDKMHSRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASSTLQEILT 1220

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +KSDDV+GR + YE+IV G+   E G PESFNVL+ E++ LGL I LE 
Sbjct: 1221 VKSDDVIGRAKTYEAIVKGDTLPEPGLPESFNVLMHELKGLGLDIRLEE 1269


>gi|194333132|ref|YP_002014992.1| DNA-directed RNA polymerase subunit beta [Prosthecochloris aestuarii
            DSM 271]
 gi|194310950|gb|ACF45345.1| DNA-directed RNA polymerase, beta subunit [Prosthecochloris aestuarii
            DSM 271]
          Length = 1301

 Score = 1258 bits (3256), Expect = 0.0,   Method: Composition-based stats.
 Identities = 587/1411 (41%), Positives = 821/1411 (58%), Gaps = 172/1411 (12%)

Query: 11   GRVRK--FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
               RK   F K   I+D PDL++VQ  S++ F+  ++  ++R ++GL+   +S FPIT  
Sbjct: 6    KTPRKCIAFSKIQSIVDPPDLLQVQLDSFNTFIQDSVPLEKRKDQGLEKVLRSAFPITDT 65

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             G  +LE++SY FD PK+ V++C+ R LTY V LK+ L+L   D  + T  K      +Q
Sbjct: 66   RGLYLLEYISYSFDRPKYSVEECIERGLTYDVSLKVKLKLSYKDEPDETDWKET---IQQ 122

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +Y+G +P MT  GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +
Sbjct: 123  EVYLGRIPYMTGRGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTR 179

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCF 247
            G W++ + D  + I+V ID+++   V++ L A+G   +E IL  F        + +    
Sbjct: 180  GSWIEFQTDINNQIYVYIDQKKNFLVSALLRAIGFAKDEDILGLFDMVEEVPVKSNK--- 236

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                 D ++G  ++S ++D+ TGE  + +   +T  +L  +   G K + I         
Sbjct: 237  ----KDYLIGKNLASDIIDMQTGEV-VSARTAITEDILDQITAAGYKSVSIIR------- 284

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                                 DE  L++                    + I NT++ D +
Sbjct: 285  -------------------AADENGLDK--------------------SIITNTILNDSS 305

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD---- 423
               ++AL  +Y  +R  +      A S     FF+  KYDL  VGR ++N +L  +    
Sbjct: 306  ATEEEALEIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGDVGRYRINKKLGREQQEF 365

Query: 424  --------------------------------TPDDVRHIRKEDIIAIIKILVDLRNGKG 451
                                              +D+  +   DII++I  L+ L NG+ 
Sbjct: 366  MDYIGGNPELKQLSDAIYEKILLTIQSYSDEPVGEDIMVLTHYDIISVIYYLIKLVNGQA 425

Query: 452  TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
             +DD+D+L NRRVR+VGE L  Q+ +GL R+ ++++E+++S D D + P DLINA+ V S
Sbjct: 426  EVDDVDHLANRRVRTVGEQLAAQFVIGLARLGKNVREKLNSRDSDKIAPADLINARTVSS 485

Query: 512  AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
             V  FF +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP
Sbjct: 486  VVSSFFATSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCP 545

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             ET EG NIGL+SSL+ +A +N  GFI+TPYR V  G VT++V+ LSA +EEN+     N
Sbjct: 546  IETPEGPNIGLISSLSVYAEINDKGFIQTPYRVVTKGVVTDEVLMLSAEDEENKITVPVN 605

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              LDE+     E V  R  G+  +V  E++D++D SP Q+VS AA+LIPFLE+DD NR L
Sbjct: 606  VPLDENRKIASETVQARTKGDYPVVTAEEVDYMDVSPVQIVSAAAALIPFLEHDDGNRAL 665

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            MG NMQRQAVPLL A+AP VGTGME+ VA+ S + IVA+  G+VE V A  I +R     
Sbjct: 666  MGANMQRQAVPLLVADAPIVGTGMEAKVARDSRSVIVAEGPGVVESVTAESIRVRYDVEG 725

Query: 752  LDPS-------TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +         GV  Y L+KF+RSNQ+TC+ Q+P V  G  + + D+IADG ST+ G+
Sbjct: 726  QGDNHVVMLDPDEGVKTYTLIKFKRSNQDTCITQKPFVYEGQVLAKGDVIADGSSTESGE 785

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            LALG+N+LVAFMPW GYNFED++++SER+V +DV TSIHI EFE   RDTK G E+ TRD
Sbjct: 786  LALGKNVLVAFMPWRGYNFEDAIVLSERLVYDDVLTSIHIHEFEANVRDTKRGEEQFTRD 845

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I NVSE+ L+N+DE GII +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV
Sbjct: 846  IYNVSEDALRNLDENGIIRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDV 905

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRH---GIDKNERSISVEREQIELLARDKDDEQVILDRN 981
            +D S+ VP+G+ G V+  ++F+R    G+D  ERS ++E+   E    D         + 
Sbjct: 906  KDASMHVPAGMKGIVIKTKLFSRKKKVGMDVKERSEAIEK-LFERKEMDLRSRFSKWLKK 964

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP------RSQWWQFAVQDEKVQRNV 1035
            +     ++  G     G       ++  + L+S++            +  ++D KV  NV
Sbjct: 965  LLE--GKVSTGVFNDKGKAIIPPGSLYDAGLLSKFSGLGFLETVDLSKGFIEDTKVNANV 1022

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              L  +Y        D   N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRHG
Sbjct: 1023 VQLIKEYRLMLKDHADERDNEKYKLNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHG 1082

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+V +ILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG   K+ 
Sbjct: 1083 NKGVVGKILPIEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAGKSLGVNFKTP 1142

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            I D     ++    S                              K+G+P          
Sbjct: 1143 IFDGATYEEVQEQLS------------------------------KAGLP---------- 1162

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                            G+  LYDG TGE FD  VTVGYIYMLKL+H+V DK++ARSTG Y
Sbjct: 1163 --------------SHGKVRLYDGRTGEAFDDEVTVGYIYMLKLSHLVDDKIHARSTGPY 1208

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SL+TQQPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G
Sbjct: 1209 SLITQQPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKG 1268

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             +    GTPESFNVLV+E+Q LGL I +++ 
Sbjct: 1269 QNLPNPGTPESFNVLVRELQGLGLEIRIDDK 1299


>gi|46446238|ref|YP_007603.1| DNA-directed RNA polymerase subunit beta [Candidatus Protochlamydia
            amoebophila UWE25]
 gi|81627411|sp|Q6MDM1|RPOB_PARUW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|46399879|emb|CAF23328.1| probable DNA-directed RNA polymerase, beta chain [Candidatus
            Protochlamydia amoebophila UWE25]
          Length = 1254

 Score = 1257 bits (3252), Expect = 0.0,   Method: Composition-based stats.
 Identities = 604/1375 (43%), Positives = 845/1375 (61%), Gaps = 149/1375 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R+ F    EIID+P+LIE+Q  SY+ FL  +  PDER N GLQ  F  +FPI ++    +
Sbjct: 8    RESFNDKEEIIDLPNLIEIQIKSYNQFLQADKFPDERENIGLQEVFTEIFPIKSYDEKTI 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+SY    PK++ ++C+ R +TY V LK+  RL      + TG      IKE+ +YMG
Sbjct: 68   LEFLSYNLGVPKYNPEECIRRGITYNVTLKVKFRLT-----DETG------IKEEEVYMG 116

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P+MT  GTF++ G +R+VVSQLHRSPGI F+ ++      G ++Y+ RIIP +G W++
Sbjct: 117  TIPVMTDKGTFIVNGAERVVVSQLHRSPGICFEQER---HSRGNVIYSFRIIPYRGSWLE 173

Query: 194  IEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
              FD+ D+IH+ IDR   RRK+  T+F+ ALG  S  +I+  F+                
Sbjct: 174  GAFDTNDLIHIYIDRKKRRRKILATTFIRALGYSSNSDIIEEFF---------------- 217

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                           T+   K   EK           L G  +A
Sbjct: 218  -------------------------------TTRKYKIKNEKEFAK-------LVGKILA 239

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +D+V+ E+G ++ +A + +    L+ I  + I  I I   +  +  + +   L  D    
Sbjct: 240  QDVVDEESGLVFGKASEKLTTAMLKRIVDAGIDVIRI--AEDADETSPVIKMLAKDPTDS 297

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             + AL D YR +RPG+ +T S A S    LFFD  +Y+L  VGR K+N +L  +  D+  
Sbjct: 298  YESALKDFYRKIRPGEPATLSNARSAIMRLFFDPKRYNLGRVGRYKLNSKLGCEINDEKL 357

Query: 430  ---HIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                + KED+I  +K L+ L++G  + +IDDID+LGNRRVRSVGE+++NQ R+GL RME+
Sbjct: 358  QTVTLDKEDVIGALKYLIMLKSGSEEASIDDIDHLGNRRVRSVGELIQNQCRIGLARMEK 417

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             I+ER++  D   D++ P  +++AK +   + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 418  IIRERMNLFDFSSDTLTPGKIVSAKGLSGVLKDFFGRSQLSQFMDQTNPIAELTHKRRLS 477

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +LG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL+SFA++N +GFIETPY
Sbjct: 478  SLGPGGLNRDRAGFEVRDVHTSHYGRICPIETPEGPNIGLISSLSSFAKINEFGFIETPY 537

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +G VT+++ Y++A +EE   IAQA++ LDE   F E + + R  GE+     + + 
Sbjct: 538  RIVREGVVTDEIEYMTADQEEQCVIAQASAPLDEYHMFAEPICWARYKGEQFETDTKNVT 597

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQ VPLLK  AP VGTG+E+  A+ 
Sbjct: 598  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQGVPLLKPTAPIVGTGLEARAARD 657

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA ++A   G+V+ VD ++IVI   +  L+        Y L KF RSN  TC+NQRPL 
Sbjct: 658  SGAVLIAHEDGVVDYVDGLKIVISPDDNRLEK-----RTYLLKKFIRSNAGTCINQRPLC 712

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD+++  D+IADGP+TD G++ALGRN+LVAFMPW GYN+ED+++ISE+++ ED +TS+
Sbjct: 713  HVGDKIKAGDVIADGPATDKGEVALGRNVLVAFMPWFGYNYEDAIIISEKLLREDYYTSL 772

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L+N+++ GII +GAEV PGD LVGKITPK 
Sbjct: 773  YIEEFELTARDTKLGKEEITRDIPNVSEETLRNLNDDGIIRIGAEVKPGDTLVGKITPKS 832

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFG+KA DV+D SL  P G  G V+DV++F+R   + K +  +  E 
Sbjct: 833  ETELAPEERLLRAIFGDKASDVKDASLIAPPGTEGVVMDVKVFSRRDRLSKTDDELVEEA 892

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLIS 1014
             +++ + R+    Q  L    + R+  +L  + A               +  +++ DLI 
Sbjct: 893  SKLKDIQREYKSNQAQLRTEKHERVGALLLNETAPGNIVHRRTAEIIVDEGDLITQDLIE 952

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       + +  +   +  +   YE +   +E ++K ++E ++ GD D+ PGV+R 
Sbjct: 953  ALEKESVEDLLMPENDIYTTLRQILHDYEIALQTVETQYKTQLEFMRKGDTDLDPGVIRQ 1012

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL  G  ++I+LNPLGVPSRMN+
Sbjct: 1013 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLSTGQTIEIILNPLGVPSRMNM 1072

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+FETHLG A    G  +KS + +      I  +                         
Sbjct: 1073 GQLFETHLGIAAKHTGITVKSPVFEGFPEEKIWEMMK----------------------- 1109

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   K+G+P                        E G+  LYDG +GE FD  V VGY
Sbjct: 1110 -------KAGLP------------------------EDGKFFLYDGCSGERFDNSVVVGY 1138

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW  +AYGAA++LQE
Sbjct: 1139 IYMLKLSHLVADKIHARAVGPYSLVTQQPLGGKAQMGGQRFGEMEVWAAEAYGAAHLLQE 1198

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            MLT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL++  E    
Sbjct: 1199 MLTVKSDDVAGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLNVYTEAVDD 1253


>gi|119356080|ref|YP_910724.1| DNA-directed RNA polymerase subunit beta [Chlorobium phaeobacteroides
            DSM 266]
 gi|158512597|sp|A1BD23|RPOB_CHLPD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119353429|gb|ABL64300.1| DNA-directed RNA polymerase subunit beta [Chlorobium phaeobacteroides
            DSM 266]
          Length = 1312

 Score = 1256 bits (3251), Expect = 0.0,   Method: Composition-based stats.
 Identities = 582/1405 (41%), Positives = 819/1405 (58%), Gaps = 172/1405 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   +ID PDL++VQ  S+ +F+  ++   +R ++GL+   +S FPIT   G  +LE
Sbjct: 22   DFSKIQSVIDPPDLLKVQLDSFHNFIQDSVPLAKRRDQGLERVLRSAFPITDTRGLYLLE 81

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V+DC+ R LTY V LK+ L+L   D  +    K      +Q +Y+G +
Sbjct: 82   YISYSFDKPKYTVEDCIERGLTYDVSLKVKLKLSYKDEPDEADWKET---IQQEVYLGRI 138

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 139  PYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AIHPNGKKMYSAKIVPTRGSWIEFQ 195

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   VT+ L A+G   +E IL  F                    + 
Sbjct: 196  TDINNQIFVYIDQKKNFLVTALLRAIGFAKDEDILGLFDLVEEVKITSAK-------KEQ 248

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            ++G  ++S +VD+ TGE  + +   +T  ++  +   G K + +                
Sbjct: 249  LIGQYLASDIVDMQTGEV-VSARTAITEDIVDQIIAAGYKSVRVMKSF------------ 295

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                                               D   + + I NT++ D +   ++AL
Sbjct: 296  --------------------------------SGNDKGPDKSIIINTILNDNSATEEEAL 323

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-------- 426
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L+ +  +        
Sbjct: 324  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGDVGRYRIRKKLSKEFEELHGYLDGQ 383

Query: 427  ----------------------------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                        D+  +   DIIA+I  L+ L NG+  +DD+D+
Sbjct: 384  PELKKLSDTIYEKILHTIQSFSDEPIGGDILVLTHYDIIAVIYYLIKLVNGQAEVDDVDH 443

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 444  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDSDKIAPSDLINARTVSSVVSSFFA 503

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 504  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 563

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V +G VT+ V+ LSA +EEN+     +  LDE+ 
Sbjct: 564  NIGLISSLSVYAEINDKGFIQTPYRVVTNGVVTDTVLMLSAEDEENKITVPVSIPLDENM 623

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  LVP E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 624  KIAIESVQARTKGDYPLVPAEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 683

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-------D 751
            QAVPLL AEAP VGTGMES VA+ S + I+A+  GIV+ V A  I +R            
Sbjct: 684  QAVPLLTAEAPIVGTGMESKVARDSRSVILAEGDGIVDDVTAEYIKVRYDIDADTDVRLS 743

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            L     G+  Y+L+KF+RSNQ+TC++Q+PL+ +G  V + D++AD  ST+ G+LALG+N+
Sbjct: 744  LLDPDEGLKTYKLIKFKRSNQDTCISQKPLIHIGQRVSKGDVLADSSSTENGELALGKNV 803

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G E+ TRDI NVSE+
Sbjct: 804  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHIHEFEANVRDTKRGEEQFTRDIYNVSED 863

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 864  ALRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 923

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G+ G V+  ++F+R      ++     +E+IE+L +  D ++  L +    RL ++L 
Sbjct: 924  PAGMKGIVIKTKLFSR-----KKKVGLDIKEKIEILEKKYDYKEYDLRKKFLKRLKQLLE 978

Query: 992  GQNAVSGPKGFKKSTVLSSDLISE-----------YPRSQWWQFAVQDEKVQRNVESLKV 1040
            G+ +        K  V    +  +                + +   Q EKV  NV  L  
Sbjct: 979  GKTSTGIYSDKGKLLVAEDAVYDDSVLERFTAIPFLESIDFVKGVTQSEKVNENVMLLVK 1038

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      L D   N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1039 EFRLKLKDLNDERDNEKYKLNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1098

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +ILP EDMPF+++G PVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1099 GKILPIEDMPFMENGKPVDIVLNPLGVPSRMNIGQLYETSLGWAGKELGVKFKTPIFNGA 1158

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                                   K+G+P               
Sbjct: 1159 TYQEVQQELE------------------------------KAGLP--------------- 1173

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  LYDG TGE FD  VT+GYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1174 ---------SHGKVSLYDGRTGEQFDDEVTIGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1224

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E
Sbjct: 1225 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPE 1284

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
             GTPESFNVLV+E+Q LGL I +++
Sbjct: 1285 PGTPESFNVLVRELQGLGLEIRIDD 1309


>gi|282889742|ref|ZP_06298281.1| hypothetical protein pah_c004o107 [Parachlamydia acanthamoebae str.
            Hall's coccus]
 gi|281500316|gb|EFB42596.1| hypothetical protein pah_c004o107 [Parachlamydia acanthamoebae str.
            Hall's coccus]
          Length = 1251

 Score = 1256 bits (3251), Expect = 0.0,   Method: Composition-based stats.
 Identities = 610/1372 (44%), Positives = 846/1372 (61%), Gaps = 149/1372 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F +  EIID+P+LIE+Q  SY+ FL  N+ P+ER N GLQ  F  +FPI ++     
Sbjct: 8    RVSFVEKEEIIDLPNLIEIQVKSYNQFLQANLFPNERENIGLQEVFNEIFPIKSYDEKTT 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+SY    PK+  D+C+ R ++Y V LK+  RL      + TG      IKE+ +YMG
Sbjct: 68   LEFLSYSLGVPKYIPDECIRRGISYNVTLKVKFRLT-----DETG------IKEEEVYMG 116

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P+MT+ GTF+I G +R+VVSQLHRSPGI F+ ++    + G  +Y+ RIIP +G W++
Sbjct: 117  TIPVMTEKGTFIINGAERVVVSQLHRSPGICFEQER---HMRGNWIYSFRIIPYRGSWLE 173

Query: 194  IEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
              FDS D+IH+ IDR   RRK+  T+F+ ALG  +  +I+  F+                
Sbjct: 174  GAFDSNDLIHIYIDRKKRRRKILATTFIRALGYSTNADIIEEFFSTRKIKL--------- 224

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                     K    L D                                    L G  +A
Sbjct: 225  ---------KNDKDLSD------------------------------------LVGKILA 239

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +D+++ E+G ++ +AG+ +    L+ +  + I  I I   +  +  + I   L  D    
Sbjct: 240  QDVLDEESGTVFGKAGEKLTTAMLKRMIDAGIDVIRI--AEDADEASPIIKMLSKDPTDS 297

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             + AL D YR +RPG+ +T S A S    LFFD  +Y+L  VGR K+N +L L+  D+  
Sbjct: 298  YESALKDFYRKIRPGEPATLSNARSAIMRLFFDPKRYNLGRVGRYKLNSKLGLEIGDEQL 357

Query: 430  ---HIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                + KED+I  +K L+ L+  K    +DDID+LGNRRVRSVGE+++NQ R+GL RME+
Sbjct: 358  KTVTLTKEDVIGALKYLISLKQNKEDTYVDDIDHLGNRRVRSVGELIQNQCRIGLARMEK 417

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             I+ER++  D   D++ P  +++AK +   + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 418  IIRERMNLFDFSSDTLTPGKIVSAKGLSGVLKDFFGRSQLSQFMDQTNPIAELTHKRRLS 477

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +LG GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 478  SLGPGGLNRDRAGFEVRDVHPSHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 537

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              V +G VT+++ Y++A +EE   IAQA++ LDE   F E + + R  GE + +   KI 
Sbjct: 538  LIVREGVVTDEIEYMTADQEERCVIAQASAVLDEFKMFAEPICWARWRGEPLEIESSKIT 597

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQ VPLL+ +AP VGTG+E+  A+ 
Sbjct: 598  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQGVPLLRPQAPIVGTGLEARAARD 657

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA ++A   GIVE VD ++IVI   +  LD        Y L KF RSN  TC+NQ+PL 
Sbjct: 658  SGAVVIAHEDGIVEYVDGLKIVISPTDNRLDK-----KTYYLKKFLRSNAGTCINQQPLC 712

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +GDEV+  D+IADGP+TD G++ALGRN+LVAFMPW GYN+ED+++ISE+++ ED +TSI
Sbjct: 713  NIGDEVKAGDVIADGPATDKGEVALGRNVLVAFMPWFGYNYEDAIIISEKLLREDAYTSI 772

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVS+E L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 773  YIEEFELTARDTKLGKEEITRDIPNVSDEALLNLGEDGIIRIGAEVKPGDILVGKITPKS 832

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K +  +  E 
Sbjct: 833  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRRDRLSKTDDELVEEA 892

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
             +++ + ++   +Q  L      ++  +L  + A       K       +  +++ DLI 
Sbjct: 893  SRLKDIQKEFKQKQSELRTERREKIGALLLNETAPGTIVHRKTAEVVIEEGMLITQDLIE 952

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
            E  +       + D ++   ++     YE +   LE ++K ++E ++ GD D+ PG++R 
Sbjct: 953  ELEKENVEDLLMPDNQIYNALKQFLHDYEIATQTLETQYKTEVEFMRKGDTDLDPGIIRQ 1012

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VSRI+P  DMPFL +G  ++I+LNPLGVPSRMN+
Sbjct: 1013 VKVYVASKRKLQVGDKMAGRHGNKGVVSRIVPEADMPFLPNGESIEIILNPLGVPSRMNM 1072

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+FETHLG+A    G  +KS + +      I  +                         
Sbjct: 1073 GQLFETHLGFAAKKQGINVKSPVFEGFPENKIWEMME----------------------- 1109

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   K G+P                          G+  L+DG TG+ FD  V VGY
Sbjct: 1110 -------KQGMP------------------------SDGKFYLHDGCTGDRFDSSVVVGY 1138

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IY+LKL+H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW  +AYGAA++LQE
Sbjct: 1139 IYILKLSHLVADKIHARAVGPYSLVTQQPLGGKAQMGGQRFGEMEVWAAEAYGAAHLLQE 1198

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL I  E 
Sbjct: 1199 LLTVKSDDVSGRTRIYESIVKGENLLQSGTPESFNVLIKEMQGLGLDIRTET 1250


>gi|254442756|ref|ZP_05056232.1| DNA-directed RNA polymerase, beta subunit [Verrucomicrobiae bacterium
            DG1235]
 gi|198257064|gb|EDY81372.1| DNA-directed RNA polymerase, beta subunit [Verrucomicrobiae bacterium
            DG1235]
          Length = 1257

 Score = 1255 bits (3248), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1371 (43%), Positives = 835/1371 (60%), Gaps = 147/1371 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  FGK  ++I  P+LIE+Q  SY  FL  +    ER N+G++A F+ VFPI ++ G  +
Sbjct: 4    RINFGKLKDVITPPNLIEIQINSYLDFLQKDTPISERKNDGIEAVFREVFPIESYDGRLV 63

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEFVSY    PK    +C+   +TY+VPL + LRL           +   +IK++ IYMG
Sbjct: 64   LEFVSYTVGDPKASEIECIREGITYSVPLYVKLRL-----------REEDNIKDEEIYMG 112

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            ++P+++  G+F+I G +R+VVSQLHRSPGI ++        +GK L+A RIIPD+G W++
Sbjct: 113  EIPMVSSRGSFIINGAERVVVSQLHRSPGIAYE---VTPHTNGKPLHAFRIIPDRGTWLE 169

Query: 194  IEFDSKDIIHVRID---RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            ++FD+ D+++V +D   RRRK  +T+ L A+G  S+ +IL  FY         D      
Sbjct: 170  VQFDNNDLLYVYLDRRRRRRKFLITTLLRAVGYSSDVDILKLFYTIE------DISTSDA 223

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A D +    +    +D + G  +  + + LT  +++  +  G+  L +           
Sbjct: 224  LAKDNVSQYVLVEDAIDAEKGVVIARAFEPLTKAIVREFEGHGIPTLKV----------- 272

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                                   +D+  ++  I   +  D +++
Sbjct: 273  ---------------------------------------IDTTVDDGAIVRAMKKDTSQN 293

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             ++AL +IY+ +RPG+  T + A+++   LFFD  +YDL  VGR K+N +L +D   + R
Sbjct: 294  EEEALKEIYKRLRPGEPPTTANAKALLKRLFFDPKRYDLGRVGRYKINQKLEMDVDVETR 353

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             ++ EDI+   K L+ L+ G+G +DDID+LG+RRVR+VGE+L NQ RLGL R ER ++ER
Sbjct: 354  TLQGEDIVLATKYLIKLKAGEGYLDDIDHLGSRRVRTVGELLANQCRLGLARTERLVRER 413

Query: 490  ISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ++  D   DS+ PQ LIN K + + + +FF  SQLSQ  + +N L+ +TH RRLSALG G
Sbjct: 414  MTLYDQSVDSITPQKLINPKALTTVIRDFFARSQLSQFMDQINPLAELTHKRRLSALGPG 473

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL++++RVN +GFIETPYR V +
Sbjct: 474  GLNRERAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLSTYSRVNEFGFIETPYRIVDN 533

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            G+VT ++ YL+A  EE + IAQANS +DE+G+F    V  R +GE + V  +++ F+D S
Sbjct: 534  GRVTEEIKYLNADMEEGKIIAQANSEIDEEGNFIG-KVTVRQSGEFLEVDPDQVHFMDVS 592

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
             KQVVS+AA LIPFLE+DD+NR LMG NMQRQ VPLL+A++PFVGTG+E  VA+ S    
Sbjct: 593  TKQVVSVAAGLIPFLEHDDANRALMGSNMQRQGVPLLQADSPFVGTGIEERVARDSKTVC 652

Query: 728  VAKRAGIVEQVDAIRIVIRSVEG--------DLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            V+   GIV  VDA RIVI                   +G+ +Y L KF RSN  TC NQ+
Sbjct: 653  VSDIEGIVASVDARRIVISKDGELPANFERKPQTDVKAGIHVYELRKFMRSNAGTCFNQK 712

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+V  G  ++ + IIADGP T  G+LA+G+N+L+AFMPW+GYNFED++LISE+++ +D++
Sbjct: 713  PIVSKGQPIKADQIIADGPCTQDGELAIGKNILLAFMPWNGYNFEDAILISEKVLKDDIY 772

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHI EFEV ARDTKLGPEEITRDIPNV EE LK+++  G+I +GAEV PGDILVGKIT
Sbjct: 773  TSIHISEFEVTARDTKLGPEEITRDIPNVGEEALKHLNHDGVIRIGAEVKPGDILVGKIT 832

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PK E+ + PEEKLLRAIFGEKA DV+DTSL VPSGV G V+DV++ +R   ++   S S 
Sbjct: 833  PKSETELAPEEKLLRAIFGEKAADVKDTSLIVPSGVDGIVMDVKVSSRLDYERERLSPSD 892

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA-------VSGPKGFKKSTVLSSDL 1012
             R Q++ +  D   +   L   +   L  IL G+          +G      +  ++  L
Sbjct: 893  RRRQVKQINEDYKTQMDKLREGLTEALSNILLGEKIPLDVVNGQNGEIIIPANRKITKTL 952

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + +          +    V+  +  +   Y++    LE   + K   I+ G+D   GV++
Sbjct: 953  LRKLAAVS-KHVEIDPSPVRIKIMEIIGSYQSKFDELESDRERKTANIESGEDAGTGVIK 1011

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA K  ++ GDKMAGRHGNKG+V++I+P EDMP+L DGTP+ I LNPLGVPSRMN
Sbjct: 1012 QVKVYVATKEKLKVGDKMAGRHGNKGVVAKIVPEEDMPYLPDGTPIQICLNPLGVPSRMN 1071

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQ+ ETH+GWAC  LG K+ + + D      +    +         S            
Sbjct: 1072 VGQVLETHMGWACKMLGMKVSTPVFDGIPEKVVRQHLADAGLPTTGKSKL---------- 1121

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                              FDG                           TGE  D  V VG
Sbjct: 1122 ------------------FDG--------------------------RTGEQLDNEVVVG 1137

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            ++YMLKLNH+VS K++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1138 WVYMLKLNHLVSHKIHARAVGPYSLVTQQPLGGKAQYGGQRFGEMEVWALEAYGAAYTLQ 1197

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            E+LT+KSDDV GRT++YES+V G+ T + GTPESFNVL+KE+Q+LGL + L
Sbjct: 1198 ELLTVKSDDVQGRTKIYESLVKGDSTLQAGTPESFNVLIKEIQSLGLDVKL 1248


>gi|229497054|ref|ZP_04390758.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas endodontalis
            ATCC 35406]
 gi|229315979|gb|EEN81908.1| DNA-directed RNA polymerase, beta subunit [Porphyromonas endodontalis
            ATCC 35406]
          Length = 1273

 Score = 1255 bits (3248), Expect = 0.0,   Method: Composition-based stats.
 Identities = 554/1373 (40%), Positives = 772/1373 (56%), Gaps = 131/1373 (9%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA          +R+ F K    +  PD +EVQ  S+  F  +  A + R  EGL   F 
Sbjct: 1    MANTTD-----TIRENFSKIQNTLPYPDFLEVQLKSFQDFFQLQTATECRKQEGLYKVFA 55

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              FPI     +  LEF+ Y  DPPK+ +++C+ R LTY+VPLK  L+L   D +      
Sbjct: 56   ENFPIKDTRNSFTLEFIDYCVDPPKYSIEECISRGLTYSVPLKAKLKLSCNDPEHVDFET 115

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             +KD     +Y+G +P MT  GTFVI G +R+VVSQLHRSPG+ F  +      SG   +
Sbjct: 116  QVKD-----VYLGPIPYMTPSGTFVINGAERVVVSQLHRSPGVFFSSN---ILPSGVRTF 167

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
            + RIIP +G W++I  D  ++++  IDR++KVPV + L A+G  S+ +I S F    V  
Sbjct: 168  SARIIPFRGTWIEIATDPNNVLYAYIDRKKKVPVATLLRAIGYSSDRDIWSAFGIGEVVE 227

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
                        A+ +    +    +D   GE                            
Sbjct: 228  TSKLKNYIGRRVAERIGVRNLEEESLDAAAGEVTA------------------------- 262

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV------DSVN 353
                               E+ +E   ++ E+ +EEI   +   + I  V      D+ N
Sbjct: 263  ---------------QMRYELRVERDTLLTEEVVEEIQKLQEERLTIPDVLLFKESDNSN 307

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                +  TL  D      +A    Y + R         A+  FN LFF   +YDL  VGR
Sbjct: 308  VINLLVQTLSKDSTISEVEAWRQFYLIQRSVIAPDDLTAKESFNNLFFSDKRYDLGDVGR 367

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             ++N +LNLD   DVR + KEDI++I+  L+ L      +DDID+L NRRVR+VGE L  
Sbjct: 368  YRINSKLNLDVDPDVRVLTKEDIVSIVNHLLLLATTGANVDDIDHLSNRRVRTVGEQLAA 427

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
            Q+ +GL RM R+++ER++  D +   P DL+NAK + S V  FF ++QLSQ  +  N L+
Sbjct: 428  QFGVGLARMARTVRERMNVRDNEVFGPTDLVNAKTISSVVSSFFGTNQLSQFMDQTNPLA 487

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ITH RRLSALG GG+ R RAG  +RDVH THYGR+CP ET EG NIGL+SSL  +A+VN
Sbjct: 488  EITHKRRLSALGPGGLTRERAGFAVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKVN 547

Query: 594  AYGFIETPYRKVCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            + GFIETPYR V DGKV      + Y +A EEE   +AQ N+ L+ DG+F  + V  R A
Sbjct: 548  SLGFIETPYRAVKDGKVDFSEEGLKYYTAEEEEEMNVAQGNAPLNPDGTFVRDKVKSRYA 607

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +  +V   ++  +D SP Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPL++ EAP 
Sbjct: 608  ADFPIVAPNQVHLMDVSPSQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLIQPEAPI 667

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKF 767
            VGTG+E  + + S   ++A+ AG V  VDA +I +R     E         V  Y L K+
Sbjct: 668  VGTGVEGKLVRDSRTQVMAEGAGEVIYVDADQIKVRYDKTDEELFVSFEEPVVTYPLPKY 727

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            +++NQ+T ++ +P+ + GD V + DI+ +G +T  G+LALGRN+LVA+MPW GYN+ED++
Sbjct: 728  RKTNQSTTIDLKPICRKGDRVEKGDILTEGYATQNGELALGRNILVAYMPWKGYNYEDAI 787

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            +++ER+V ED FTS+H+EE ++  R+TK G EE+T DIPNVSE+  K++ E GI+ +GA 
Sbjct: 788  VLNERIVREDFFTSVHVEEQQLEVRETKRGLEELTSDIPNVSEDATKDLAENGIVRIGAH 847

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            + PGDILVGKITPKGES  TPEE+LLRAIFG+KA DV+D SL+    + G V+D ++F++
Sbjct: 848  IVPGDILVGKITPKGESDPTPEERLLRAIFGDKASDVKDASLKASPSLRGVVIDTKLFSK 907

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-----SGPKGF 1002
            +   K +    +     E +  +   ++  L +    +L+++  G  +      +  +  
Sbjct: 908  NLDKKRKDIKEI----TERIEGEYSKKKEQLRKVFIDKLLKLTDGHTSNLVEDFASLEII 963

Query: 1003 KKSTVLSSDLISEYPRSQWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +  ++         +     +D      + +L   Y      LE  F+ +I+  
Sbjct: 964  AAGKKFNRTMLESIDEYSNIKSSNWTEDAHTNELITTLIANYIRKDKELEAEFRRRIQDE 1023

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++  G+++  KV++A KR IQ GDKMAGRHGNKGIVS+I+  EDMPFL+DGTPVDI
Sbjct: 1024 TIGDELASGIVQTAKVYIAKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLEDGTPVDI 1083

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNPLGVPSRMN+GQ+FE  L  A   LGK+  S + D  +  DI               
Sbjct: 1084 CLNPLGVPSRMNLGQLFEAVLARAGRKLGKRFASPVFDGASPEDI--------------- 1128

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               EE I      A +D   ++ LYDG 
Sbjct: 1129 -----------------------------------EEYIKE----AGIDPGAKTQLYDGG 1149

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF +  TVG  Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1150 TGEPFKQRATVGVTYFLKLGHMVDDKMHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1209

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             ++A+GAA++LQE+LTIKSDD +GR+R YE+IV G      G PES NVL+ E
Sbjct: 1210 ALEAFGAAHILQEILTIKSDDTIGRSRAYEAIVKGTPMPTPGIPESLNVLMNE 1262


>gi|189345745|ref|YP_001942274.1| DNA-directed RNA polymerase subunit beta [Chlorobium limicola DSM
            245]
 gi|189339892|gb|ACD89295.1| DNA-directed RNA polymerase, beta subunit [Chlorobium limicola DSM
            245]
          Length = 1312

 Score = 1254 bits (3246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1405 (41%), Positives = 820/1405 (58%), Gaps = 172/1405 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   IID PDL++VQ  S+ +F+  ++   +R ++GL+   ++ FPIT   G  +LE
Sbjct: 22   DFSKIQSIIDPPDLLKVQLDSFHNFIQDSVPLAKRKDQGLERVLRNAFPITDTRGLYLLE 81

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V+DC+ R LTY V LK+ L+L   D  +    K      +Q +Y+G +
Sbjct: 82   YISYSFDKPKYTVEDCIERGLTYDVSLKVKLKLSYKDEPDEQDWKET---IQQEVYLGRI 138

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 139  PYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 195

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   V++ L A+G   +E IL  F                    D 
Sbjct: 196  TDINNQIFVYIDQKKNFLVSALLRAIGFAKDEDILGLFDLVEEIK-------MSAGKKDQ 248

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            ++G  ++S +VD+ TGE  + +   +T  + + +   G K + +                
Sbjct: 249  LIGKYLASDIVDMQTGEV-VSARTAITEDIFEQILAAGYKAVKVMKSY------------ 295

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                                               D   + + I NT++ D +   ++AL
Sbjct: 296  --------------------------------SGSDKGQDKSIIINTILNDSSATEEEAL 323

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------- 425
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L  +           
Sbjct: 324  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGDVGRYRIRKKLAREFEELVTYLSGK 383

Query: 426  ---------------------------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       DD+  +   DIIA+I  L+ L NG+  +DD+D+
Sbjct: 384  KELRELSDGIYQKILQTIQSFSDEPVGDDILVLTHFDIIAVINYLIKLVNGQAEVDDVDH 443

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 444  LANRRVRSVGEQLAAQFVVGLARMGKNVREKLNSRDSDKIAPADLINARTVSSVVSSFFA 503

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 504  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 563

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G+VT+ VV LSA +EEN+     +  LDE+ 
Sbjct: 564  NIGLISSLSVYAEINDKGFIQTPYRVVEKGQVTDKVVMLSAEDEENKITVPVSVPLDENR 623

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  LVP E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 624  KIALESVQARTKGDYPLVPAEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 683

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL +EAP VGTGME+ VA+ S + IVA+ AG VE+V A  I +R      +     
Sbjct: 684  QAVPLLTSEAPVVGTGMEAKVARDSRSVIVAEEAGTVEEVTADYIRVRYDIDTENEVHLS 743

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G+  Y+L+KF+RSNQ+TC++Q+ LV+    V + D++AD  ST+ G+LALG+N+
Sbjct: 744  MLDPDEGLKTYKLIKFKRSNQDTCISQKSLVRTAQRVAKGDVLADSSSTENGELALGKNV 803

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G E+ TRDI NVSE+
Sbjct: 804  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHIHEFEANVRDTKRGEEQFTRDIYNVSED 863

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 864  ALRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 923

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G+ G V+  ++F+R      ++     +++IE + +  D ++  L +     L ++L 
Sbjct: 924  PAGMKGIVIKTKLFSR-----KKKVGLDVKDRIEAVDKRYDQKEYDLRKRFAKWLNQLLD 978

Query: 992  GQN-----AVSGPKGFKKSTVLSSDLISEYP------RSQWWQFAVQDEKVQRNVESLKV 1040
            G+         G     + +V    +++ +          + +  V+ +KV  NV  L  
Sbjct: 979  GKKTTGIFNEKGKVLVAEGSVFDESVLARFSGLPFLESIDFSKGLVESKKVNENVVRLVK 1038

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      + D  +N+  KI  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1039 EFRFKLKDIADERENEKYKINVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1098

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +IL  EDMPF++DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1099 GKILSIEDMPFMEDGTPVDIVLNPLGVPSRMNIGQLYETSLGWAAKKLGVKFKTPIFNGA 1158

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                                   ++G+P+              
Sbjct: 1159 TYEEVQNELE------------------------------RAGLPM-------------- 1174

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  L+DG TGE FD  VTVGYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1175 ----------HGKVSLFDGRTGEKFDDEVTVGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1224

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E
Sbjct: 1225 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPE 1284

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
             GTPESFNVLV+E+Q LGL I ++ 
Sbjct: 1285 PGTPESFNVLVRELQGLGLEIRIDE 1309


>gi|225850728|ref|YP_002730962.1| DNA-directed RNA polymerase subunit beta [Persephonella marina EX-H1]
 gi|225645675|gb|ACO03861.1| DNA-directed RNA polymerase, beta subunit [Persephonella marina
            EX-H1]
          Length = 1491

 Score = 1254 bits (3246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 622/1481 (41%), Positives = 876/1481 (59%), Gaps = 109/1481 (7%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK   +  E+I  PDL+ VQK S++ F+  N  P +R N+GL+  F++ FP    +G  
Sbjct: 12   LRKNLSRRKEVISPPDLLHVQKKSFEDFVQFNKNPYKRENKGLENIFRTSFPFEDPNGQI 71

Query: 73   MLEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAV 100
             + +++YE                                    K  +++C ++ LTY+ 
Sbjct: 72   EIRYIAYEIGDWECGKCRKPLPEDVVGGPEIPCPNCGGVLIYKEKNSIEECKYKGLTYSA 131

Query: 101  PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            PL++ L LIV  VD  TG  + K IK   +Y GD+PL+T    F+I G +R+VVSQL RS
Sbjct: 132  PLRVLLELIVNHVDPSTGEITPKTIKRHKVYFGDIPLLTDKAYFIINGSERVVVSQLIRS 191

Query: 161  PGIHFDHDKGRA-SLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTSFL 218
             GI F+  + +   +  +++Y   IIP++G  ++ E  +  +I + RIDR RK+  T+ L
Sbjct: 192  SGIFFEAKEDKTKDILTRIIYKGSIIPEKGSRLEFEHATNVEIFNARIDR-RKLLGTTIL 250

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA-----ADLMVGAKVSSSLVDIDTGEQ 272
             A G+DS  +IL  FY  +    + D              D +V    +  +    T E+
Sbjct: 251  RAFGLDSAYKILKAFYSDVKRYVKKDNEYIDEKTGVVYNIDELVKELENDEIFITYTVEE 310

Query: 273  VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET---GEIYIEAGDVID 329
              E G  +T    K+++ + ++   +         VA   +       G I IE     +
Sbjct: 311  QDEKGNAVTIRHEKAVEPQNLEKYLLDDRLTIEEIVAISPLVFRKSPYGNIIIETLKKDE 370

Query: 330  EKSLEEIFHSEIRDIPIL------YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             +        +   + I           ++  A+++       +        D+ +V R 
Sbjct: 371  PQINAMFTFQDAARVDIYRKMRPTDTAVMDPKAFLKRANELFNSVFYDHQRYDLSKVGRV 430

Query: 384  GDVSTFSVAESMFNFLFFDS--DKYDLSTVGRVKM------------------------- 416
               +           L  D+  +KY    +G                             
Sbjct: 431  KINAKVHDIPKTIKPLDLDTLLEKYPPLALGEDVEIEGETLKAGTKIDQSVIEKLKTLKF 490

Query: 417  -NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
              +++     D+ R I   D+IAI+K L+++R GK  +DDI +LGNRRVR VGE+L+NQ 
Sbjct: 491  EEIKVEQYLDDEARFILLPDVIAIVKYLLEIRLGKKELDDIAHLGNRRVRPVGELLENQA 550

Query: 476  RLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
            RLGL+RM ++ ++R+++VDI+  ++   D++N + V  ++ EF    QLSQ  +  N L+
Sbjct: 551  RLGLVRMNKAFRDRVATVDIEDPNLKAADIVNPRYVTGSILEFLKGGQLSQFMDQANPLA 610

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             +TH RRLSALG GG+ R  A  E+RDVHPTHYGR+CP ET EG NIGL+SS+T ++ +N
Sbjct: 611  ELTHKRRLSALGPGGLTRDSAKFEIRDVHPTHYGRVCPIETPEGQNIGLISSMTVYSTIN 670

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
             +GF+ +PYRKV +GKVTN++ YL+A +EE   IAQAN+ +D++G+F  E V  R  G+ 
Sbjct: 671  EFGFLVSPYRKVKNGKVTNEIEYLAAYDEEKYVIAQANAPVDDEGNFLAERVLARAKGDI 730

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             LV  +++D++D SPKQVVS++ASLIPFLE+DD+NR LMG NMQRQAVPLLK E P VGT
Sbjct: 731  RLVDPKEVDYMDVSPKQVVSVSASLIPFLEHDDANRALMGSNMQRQAVPLLKTEYPLVGT 790

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRS 770
            GME +VAK+SGAA+VAKR G+VE V   RIVI+         DP   G+D+Y LMKF+ S
Sbjct: 791  GMEKIVAKNSGAAVVAKRGGVVESVSGNRIVIKVNPEEINQDDPLDIGLDVYELMKFKGS 850

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQ TC+NQRPLV+ GD+V    IIADG ST  G+LALG+N+LVAFMPW GYNFED+++IS
Sbjct: 851  NQATCMNQRPLVRRGDKVEAGAIIADGTSTYRGELALGKNVLVAFMPWRGYNFEDAIVIS 910

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+V +DVFTSIHIEEFE  AR+TKLG EEITR+I  VSE+ L N+DE GI+ VGA V P
Sbjct: 911  ERLVKDDVFTSIHIEEFECEARETKLGSEEITRNIVGVSEKALANLDEHGIVRVGAYVKP 970

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGK+TPKGE+  TPEEKLL AIFGEKA +V+D+SLRVP+GV G V+DV++F R   
Sbjct: 971  GDILVGKVTPKGETQPTPEEKLLLAIFGEKASEVKDSSLRVPAGVEGIVIDVQVFARKKT 1030

Query: 951  DK--NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
             K  +     +  E+I  L ++ ++++  +       + E++ GQ      K   K  V 
Sbjct: 1031 GKKEDRYLKQLAEEEINRLEKELEEKKRFIQARRDELVKELIIGQKVPRDIKVAGKVVVK 1090

Query: 1009 SSDLISEYPRSQWWQFAV-------QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              + I+E       +F V        D+KV  +VE +  + +    + E+ ++ +   +Q
Sbjct: 1091 KGEEITEKTVDAILRFIVVNPSGFLSDKKVAEDVEKIVSKAKLQIELWENIYEKQKAAVQ 1150

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G D+ PGV  +VKV++A KR IQ GDKMAGRHGNKG++S +LP EDMPF++DGTPVDIV
Sbjct: 1151 KGSDLKPGVNELVKVYIAQKRKIQVGDKMAGRHGNKGVISVVLPEEDMPFMEDGTPVDIV 1210

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKK--------------IKSLINDYKANGDISP 1167
            LNPLGVPSRMNVGQI ETHLG A   LG+K              I  +I  Y+   D + 
Sbjct: 1211 LNPLGVPSRMNVGQILETHLGLAAKKLGQKLYEELKKLNSKEALIDKIIEYYEIANDTAG 1270

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS-GVPVSTPVFDGADEEAINSMLRMA 1226
              +   +          +   DD+++  + +     G+PV TPVF+GA EE I +MLR A
Sbjct: 1271 ELAQKYREEDIRELRRYLESLDDETLKAIIKDLGEIGIPVRTPVFEGATEEDIKTMLRKA 1330

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
               E+G+  L DG TGEPFD  VT GY+YMLKL HMV DK++ARSTG YSL+TQQPLGG+
Sbjct: 1331 GFKETGKMKLIDGRTGEPFDLEVTAGYMYMLKLIHMVDDKIHARSTGPYSLITQQPLGGR 1390

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++A+GAAY LQEMLT+KSDD+ GR RVYESIV G   ++ G PES
Sbjct: 1391 AQFGGQRFGEMEVWALEAHGAAYTLQEMLTVKSDDIEGRKRVYESIVKGRYYYDIGVPES 1450

Query: 1347 FNVLVKEMQALGLSI--DLENSRTKNSAKMEEIPDFNKCEL 1385
            F VLV+E++AL L +  ++E    +   +++ +    K EL
Sbjct: 1451 FKVLVRELKALALDVQCNMEGGEKQACDQVDIVSKSKKKEL 1491


>gi|302345061|ref|YP_003813414.1| DNA-directed RNA polymerase, beta subunit [Prevotella melaninogenica
            ATCC 25845]
 gi|302149692|gb|ADK95954.1| DNA-directed RNA polymerase, beta subunit [Prevotella melaninogenica
            ATCC 25845]
          Length = 1269

 Score = 1254 bits (3245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 572/1367 (41%), Positives = 807/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYVDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +S+ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGYESDRDILQIFDLCEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++KS  E  V                 ++
Sbjct: 234  ---------------------AAIGRKIAGNVMKSWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   +I E ++++I  S +  I +    D+ +  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETIITEDNVDQILDSSVSSILLHKDEDAASKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNL+T  DVR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLETDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIIEIIKYLISLINSNATVDDIDHLSNRRVRTVGEQLANQFSVGLARMNRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRRVKDAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE + I Q N+ L+ DG+F  ++V CR   +  +V  + +  ID SP
Sbjct: 561  MDNKDVVFLTAEEEEEQIIGQGNAPLNADGTFIRDVVKCRQDADYPVVTPDSVALIDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTDDEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN++VA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLVVAYMPWKGYNYEDAIVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII +GA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTADIPNVSEEATKDLDDNGIIRIGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKNILA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 919  KIDEEQEAKINDLKDLLVDKLLELTEDKVSEGVKDYSDAEIITKGSKFTVAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + +      ++   K K   I  GD++P GVL++ KV++A
Sbjct: 979  IQSNGWTDDEHTNLLIQKLIMNFIRKYKQMDAEMKRKKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG+PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGSPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G      G PES NVL+ E++ LGLS+ L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPGIPESLNVLLHELRGLGLSVKLD 1269


>gi|78187804|ref|YP_375847.1| DNA-directed RNA polymerase subunit beta [Chlorobium luteolum DSM
            273]
 gi|109904624|sp|Q3B1H7|RPOB_PELLD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|78167706|gb|ABB24804.1| DNA-directed RNA polymerase subunit beta [Chlorobium luteolum DSM
            273]
          Length = 1301

 Score = 1254 bits (3245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 575/1405 (40%), Positives = 821/1405 (58%), Gaps = 172/1405 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   +I+ PDL++VQ  S+ +F+  ++   +R  +GL+   +S FPIT   G  +LE
Sbjct: 11   DFSKIQSVIEAPDLLKVQLDSFHNFIQDSVPLAKRREQGLEKVLRSAFPITDTRGLYLLE 70

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V+DC+ R LTY V LK+ L+L   D  + T  K      +Q +Y+G +
Sbjct: 71   YISYSFDKPKYTVEDCIERGLTYDVSLKVKLKLSYKDEADETDWKET---IQQEVYLGRI 127

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 128  PYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 184

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   VT+ L A+G   +E IL  F                 +  + 
Sbjct: 185  TDINNQIFVYIDQKKNFLVTALLRAIGFTRDEDILGLFDLVEEV-------PMKAAKRER 237

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            +VG  ++S +VD+ TGE  + +   +T  + + ++  G K + I                
Sbjct: 238  LVGQYLASDIVDMQTGEV-VSARTAITEEVFEQIQAAGYKSVKIMKSF------------ 284

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
               G                               D   + + + NT++ D +   ++AL
Sbjct: 285  --NG------------------------------SDKGQDKSIVINTILNDSSATEEEAL 312

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------- 425
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L+ +           
Sbjct: 313  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGEVGRYRIGKKLSREFSEMDEYLGGK 372

Query: 426  ---------------------------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       ++V  +   DIIA+I  L+ L NG+  +DD+D+
Sbjct: 373  GELKQLSDTIHQKILQTIQSFSDEPIGEEVLVLTHLDIIAVINYLIKLVNGQAEVDDVDH 432

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 433  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDSDKIAPADLINARTVSSVVSSFFA 492

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 493  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 552

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G VT+ VV LSA +EEN+     +  +D + 
Sbjct: 553  NIGLISSLSVYAEINDKGFIQTPYRVVEKGHVTDTVVMLSAEDEENKITVPVSIPIDANN 612

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +   E V  R  G+  LVP E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 613  NIAVESVQARTKGDYPLVPSEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 672

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL +EAP VGTGME+ VA+ S + I+ +  G VE+V +  I +R      +     
Sbjct: 673  QAVPLLVSEAPVVGTGMEAKVARDSRSVILGEGPGFVEEVTSEFIKVRYDIDTENNEHMS 732

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G+  YR++KF+RSNQ+TC++QRP+VK G +V +  ++AD  ST+ G+LALG+N+
Sbjct: 733  LLDPDEGLKTYRMIKFKRSNQDTCISQRPIVKNGQKVDKGTVLADSSSTEDGELALGKNV 792

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIH+ EFE   RDTK G E+ TRDI NVS+E
Sbjct: 793  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHVHEFEANVRDTKRGEEQFTRDIYNVSDE 852

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 853  ALRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 912

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G+ G V+  ++F+R      ++     +E++EL+    +  ++ L ++    L ++L 
Sbjct: 913  PAGMKGIVIKTKLFSR-----KKKVGMDVKEKLELIDARFERREIELRKSFEKWLRQMLQ 967

Query: 992  GQNAVS-----GPKGFKKSTVLSSDLISEYPRSQWWQFA------VQDEKVQRNVESLKV 1040
            G+         G     +       L++++    + +           +KV   V  L  
Sbjct: 968  GKKVKGLTSDKGKVLADEGAAFDDALLAKFSSQPFLESIDFTLGVTGTKKVDEAVIRLVK 1027

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      L D   N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1028 EFRFKLKDLADERDNEKYKVNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1087

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +ILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1088 GKILPIEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAAKKLGVKFKTPIFNGA 1147

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                               AE  ++G+P+              
Sbjct: 1148 TYEEVQ------------------------------AELERAGLPM-------------- 1163

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  LYDG TGE FD  VTVGYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1164 ----------HGKVRLYDGRTGEQFDDEVTVGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1213

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDVVGR + YE+IV G +  E
Sbjct: 1214 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVVGRNKTYEAIVKGQNLPE 1273

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
             G PESFNVL++E+Q LGL I +++
Sbjct: 1274 PGIPESFNVLIRELQGLGLEIRIDD 1298


>gi|281358737|ref|ZP_06245213.1| DNA-directed RNA polymerase, beta subunit [Victivallis vadensis ATCC
            BAA-548]
 gi|281314764|gb|EFA98801.1| DNA-directed RNA polymerase, beta subunit [Victivallis vadensis ATCC
            BAA-548]
          Length = 1274

 Score = 1254 bits (3244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 601/1376 (43%), Positives = 836/1376 (60%), Gaps = 124/1376 (9%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  FGK  +++D+PDLI +Q  SY +FL  ++ P ER N+GLQ  F  +FPI +F     
Sbjct: 4    RINFGKLRDVLDVPDLIGLQLDSYFNFLQRDVPPAERKNQGLQEVFNEIFPIESFDKQMS 63

Query: 74   LEFVSYEFDPP---KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            LEFVSYE       K DV DC+     Y  PL +   L V   +             + +
Sbjct: 64   LEFVSYEIGNSTDQKGDVVDCIKDGKIYDAPLYVDFLLKVNGTEIP-----------ERV 112

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGD+P+MT+ GTF+I G +R+++SQLHRSPGI F+  +     SG+ LY+ RIIPD+G 
Sbjct: 113  YMGDIPIMTEQGTFIINGAERVIISQLHRSPGICFEKTR---HTSGRTLYSYRIIPDRGS 169

Query: 191  WMDIEFDSKDIIHVRIDRRR---KVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWC 246
            WMD++FD  D I++ +DRRR   K  +T+FL A+G   + +IL+  Y    ++       
Sbjct: 170  WMDVQFDINDFIYIYLDRRRRRRKFYITTFLRAIGYPTNRDILAECYEVKKHT------- 222

Query: 247  FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                                              T+ LLK                L G 
Sbjct: 223  ----------------------------------TASLLKQ-------------KDLSGF 235

Query: 307  YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            Y  +DI   E   + I+    + E  L+++  + I+++ + Y+     + Y+   L  D 
Sbjct: 236  YTVDDIT-TEDDVLVIDELVQLTENHLKQLIDAGIKEVELAYI--AEGDNYLIGCLRKDP 292

Query: 367  NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             ++ +DAL +IYR MRPGD    + A+ +   LFFD+ +YDL  VGR K+N RL  D P 
Sbjct: 293  ARNEEDALKEIYRRMRPGDPPNINNAKLLIKRLFFDNRRYDLGAVGRYKLNERLKQDIPL 352

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             +R +  +D++A  K+L+ LR+  G +DDID+LG RRVR+VGE+L+NQ R GLLR ER +
Sbjct: 353  TLRVLDPKDLMAATKMLIKLRHSGGAVDDIDHLGARRVRTVGELLQNQCRAGLLRTERLV 412

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER++  D  +V P  L+N K     + +FF  SQLSQ  +  N LS +T+ RRLSALG 
Sbjct: 413  RERMTFDDQ-NVTPSKLVNPKAFAGVIRDFFARSQLSQFMDQTNPLSELTNKRRLSALGP 471

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+SS++ +A ++ YGF+ETPYRKV 
Sbjct: 472  GGLSRDRAGFEVRDVHSSHYGRICPIETPEGPNIGLISSMSLYAIIDEYGFLETPYRKVV 531

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
            DG+VT+ + YL+A +EE   IAQAN+ LDE+  F   ++  R  GE    PRE + ++D 
Sbjct: 532  DGQVTDQIDYLTADKEEQYVIAQANALLDENNRFVRPMIMSRYKGESEEHPREAVQYMDV 591

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            SPKQ++S AA +IPFLE+DD+NR LMG NMQRQAVPLL  E+P+VGTG+E+ +A+ S A 
Sbjct: 592  SPKQLISAAAGIIPFLEHDDANRALMGSNMQRQAVPLLMPESPYVGTGLEARIARDSRAV 651

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEG--DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            + AK  GIV +V +  I++         D        YRL K+ RSN  T VNQRP+V+ 
Sbjct: 652  VAAKADGIVAEVCSEHIIVTPDGNLPAPDADKKSYQYYRLYKYLRSNAGTSVNQRPIVEH 711

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ADG +T  G+LALGRN+LVA+MPW GYNFED++++SER+V EDV+TSIH+
Sbjct: 712  GQAVKKGDILADGAATQDGELALGRNVLVAYMPWCGYNFEDAIIVSERLVKEDVYTSIHV 771

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +EFE+ +R+TKLGPEEITRDIPNVSE+ L+N+D  G++  GAEV PGDILVGKITPK E+
Sbjct: 772  DEFEITSRETKLGPEEITRDIPNVSEDALRNLDSRGVVFEGAEVKPGDILVGKITPKSET 831

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             + PEE+LLRAIFGEKA DV+D+SL VPSG  G V+D+RI       ++  S S E+ Q 
Sbjct: 832  ELAPEERLLRAIFGEKAADVKDSSLTVPSGKGGIVMDIRIEYAKDPSRSSLSKSEEKRQQ 891

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG----------FKKSTVLSSDLIS 1014
            +++  D  D    L  ++ SRL +++ G                      +  ++   I 
Sbjct: 892  KMMKNDYRDIYNGLIDDLTSRLSDVMLGIKLPYPIFDMSPARENAVLISSNRKVTKSSIQ 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            +   + +  ++++D  +++ +  +   +       E++ +   + +  GD+   GV++ V
Sbjct: 952  KLA-AHYDCWSMEDCDLKKTLTEIIDSFIPQFEENEEKRRRMADNMDSGDNADLGVIKRV 1010

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV+V  KR +Q GDKMAGRHGNKGIVSRI+P EDMPFL+DGTPVDI+LNPLGVPSRMN+G
Sbjct: 1011 KVYVGCKRKLQVGDKMAGRHGNKGIVSRIVPVEDMPFLEDGTPVDIILNPLGVPSRMNIG 1070

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ ETHLGWA   LG K  + + D     +I  L              +    +  +   
Sbjct: 1071 QVLETHLGWAAKMLGFKAATPVFDGIGEQEIIDLMRKGNDAFTAKEGHDYHWGFKQNEAG 1130

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                 G++ +YDG TG  FD+ V VG +
Sbjct: 1131 EWV--------------------------------YDGKADVYDGRTGNKFDQRVMVGQV 1158

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V++K++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEM
Sbjct: 1159 YMLKLDHLVANKIHARAVGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAYGAAYNLQEM 1218

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LT+KSDDV GR R+YESIV G++  E G PESFNVL+KEMQ+LGL I      ++N
Sbjct: 1219 LTVKSDDVAGRARIYESIVKGHNVLEAGRPESFNVLLKEMQSLGLDIRTVKKTSEN 1274


>gi|291516062|emb|CBK65272.1| DNA-directed RNA polymerase subunit beta [Alistipes shahii WAL 8301]
          Length = 1249

 Score = 1254 bits (3244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 564/1351 (41%), Positives = 801/1351 (59%), Gaps = 131/1351 (9%)

Query: 43   MNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPL 102
            M+   + R NEGL   F+  FPIT      +LEF+ Y  DPP++ +++CL R LTY+VPL
Sbjct: 1    MDTTAENRKNEGLYKVFQENFPITDTRNNFVLEFIDYYIDPPRYSIEECLERGLTYSVPL 60

Query: 103  KITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPG 162
            K  L+L   D +       +     Q +Y G +P MT+ GTFVI G +R++VSQLHRSPG
Sbjct: 61   KAKLKLYCTDDEHEDFGVVV-----QDVYFGTIPYMTERGTFVINGAERVIVSQLHRSPG 115

Query: 163  IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
            + F         +G  LY+ RIIP +G W++   D  ++++  IDR++K+PVT+ L A+G
Sbjct: 116  VFFGQSM---HTNGTKLYSARIIPFKGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIG 172

Query: 223  MDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
             ++++ IL  F                             +  V ++        G+KL 
Sbjct: 173  YEADQQILEIF---------------------------DLADEVKVNKANLKKAVGRKLA 205

Query: 282  SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            + +L +  E  V                 ++V+ E   + ++   V++E+ +++I  S  
Sbjct: 206  ARVLSTWVEDFVDEDT------------GEVVSIERNNVIVDRETVLEEEHVDQILESGA 253

Query: 342  RDIPILYVDSVN-NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            + I +   +    + + I NTL  D     K+A++ IYR +R  +    + A  +   LF
Sbjct: 254  KTILLHKENLSGIDFSIIYNTLQKDPCNSEKEAVVYIYRQLRASEPPDEATARDVIEKLF 313

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F   +YDL  VGR ++N +L+LDT   +R + +EDIIAIIK L+ L N K  +DDID+L 
Sbjct: 314  FSDKRYDLGDVGRYRINKKLDLDTDPAIRTLTREDIIAIIKYLIQLINSKADVDDIDHLS 373

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVR+VGE L NQ+ +G +RM R+I+ER++  D +   P DLINAK + S +  FF +S
Sbjct: 374  NRRVRTVGEQLSNQFSVGFVRMARTIRERMNVRDNEVFTPVDLINAKTLSSVINSFFGTS 433

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  + +N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP E+ EG NI
Sbjct: 434  QLSQFMDQINPLAEITHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRLCPIESPEGPNI 493

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSSLDED 637
            GL+SSL  +A+++  GFIETPYR+V +GKV  D   + Y SA EEE+   AQAN+ +D +
Sbjct: 494  GLISSLCVYAKISPMGFIETPYRRVENGKVDMDNSHIHYYSAEEEEDLVAAQANTPIDGE 553

Query: 638  GSFTE-ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            G+F E + +  R   +  +V   ++D +D +P Q+ SIAASLIPFLE+DD+NR LMG NM
Sbjct: 554  GNFLEPDRIKAREGADFPVVTASEVDLMDVAPNQIASIAASLIPFLEHDDANRALMGSNM 613

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLD 753
             RQAVPL+ +EAP VGTG+E  +   S   IVA+  G V   DA +I I+     +  L 
Sbjct: 614  MRQAVPLVTSEAPIVGTGIEKDMISDSRIQIVAEGDGEVVFADATKIQIKYERTEDEILA 673

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                 V  Y L +++R+NQNT V  +P+V  GD+V +  I+ +G ST  G+LALGRN+ V
Sbjct: 674  SFAPEVTTYTLPRYRRTNQNTSVTLKPIVLTGDKVTKGQILTEGYSTQHGELALGRNLKV 733

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            AFMPW GYNFED+++ISER+  ED+FTS+H++E+ +  RDTK G EE+T DIPNVSE+  
Sbjct: 734  AFMPWKGYNFEDAIVISERIQREDIFTSVHVDEYIMEVRDTKRGVEELTSDIPNVSEDAT 793

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            K++D  GI+ VGA ++PGDIL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+   
Sbjct: 794  KDLDANGIVRVGANIHPGDILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKAQP 853

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             + G V+D R+++R   +  ++S S E+ Q++ L      E   L + +  +L  +L G+
Sbjct: 854  SLHGVVIDTRLYSRANKE-GKKSKSAEKAQLDKLDEKFAAEIAELTKRLVGKLWTLLQGK 912

Query: 994  NAVS-----GPKGFKKSTVLSSDLISEYPRSQWWQF--------------AVQDEKVQRN 1034
             +       G + +   T  S  ++ E  R    +                  D      
Sbjct: 913  TSTGVTDYFGVELYPAGTKFSQKMLEEIARKSTDEKTGVVMGYLNLGSCNWTGDAHTDAL 972

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGR 1093
            +E+    Y       +   K +   I  GD++P  GV+++ KV++A KR ++ GDKMAGR
Sbjct: 973  IEATINNYTIEWKKADAAIKREKYNITNGDELPQTGVIQMAKVYIAKKRKLKVGDKMAGR 1032

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGIV+RI+  EDMPFL+DGT VDI LNPLGVPSRMN+GQI+ET LGWA   LG K  
Sbjct: 1033 HGNKGIVARIVRDEDMPFLEDGTIVDICLNPLGVPSRMNLGQIYETVLGWAGRELGLKFA 1092

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + I D  +   I+   +                              ++G+P        
Sbjct: 1093 TPIFDGASLDQINEYTA------------------------------QAGIP-------- 1114

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                             SG++ LYDG TGE FD+P TVG IYMLKL HM+ DK++ARS G
Sbjct: 1115 ----------------HSGRTYLYDGGTGEMFDQPATVGVIYMLKLGHMIDDKMHARSIG 1158

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSL+TQQPLGGK+  GGQR GEMEVW ++ +GAA +LQE+LTIKSDDV+GR + YE+IV
Sbjct: 1159 PYSLITQQPLGGKAQFGGQRFGEMEVWALEGFGAANILQEILTIKSDDVMGRAKAYEAIV 1218

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             G +  + G PE+ NVL+ E++ L LS+ LE
Sbjct: 1219 KGENLPKPGIPEAMNVLLHELRGLALSVKLE 1249


>gi|110597684|ref|ZP_01385969.1| DNA-directed RNA polymerase, beta subunit [Chlorobium ferrooxidans
            DSM 13031]
 gi|110340804|gb|EAT59281.1| DNA-directed RNA polymerase, beta subunit [Chlorobium ferrooxidans
            DSM 13031]
          Length = 1300

 Score = 1253 bits (3241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 572/1405 (40%), Positives = 808/1405 (57%), Gaps = 172/1405 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   II+ PDL++VQ  S+ +FL  ++   +R ++GL+   +S FPIT   G  +LE
Sbjct: 10   DFSKIQSIIEPPDLLKVQLDSFHNFLQDSVPLAKRKDQGLERVLRSAFPITDTRGLYLLE 69

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V+DC+ R LTY V LK+ L+L   D  + T  K      +Q +Y+G +
Sbjct: 70   YISYSFDKPKYTVEDCIERGLTYDVSLKVKLKLSYKDEPDETDWKET---IQQEVYLGRI 126

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 127  PFMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 183

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   V++ L A+G   +E IL  F        +           + 
Sbjct: 184  TDINNQIFVYIDQKKNFLVSALLRAIGFTRDEDILGLFDLVEEVPLKAGK-------KEQ 236

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            +VG  ++S +VD+ TGE  + +   +T  + + +   G K + +      G         
Sbjct: 237  LVGQYLASDIVDMQTGEV-VSARTAITEEIFEQILAAGYKSVKVMKSFAGG--------- 286

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                                               D   + + I NT++ D +   ++AL
Sbjct: 287  -----------------------------------DKGKDKSIIINTILNDSSATEEEAL 311

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------- 425
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L  +           
Sbjct: 312  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGDVGRYRIKKKLGREFEELDTYLAGK 371

Query: 426  ---------------------------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       +D+  +   DII++I  L++L NG   +DD+D+
Sbjct: 372  PELKKLSDTIYDKILQTIQSFSDEPVGEDILVLTHYDIISVIYYLINLVNGLAEVDDVDH 431

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 432  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDSDKIAPADLINARTVSSVVSSFFA 491

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 492  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 551

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G+VT  V+ LSA +EEN+     +  LD + 
Sbjct: 552  NIGLISSLSVYAEINDKGFIQTPYRVVEKGQVTGTVLMLSAEDEENKITVPVSVPLDANN 611

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  +V  E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 612  RIALETVQARTKGDYPVVAAEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 671

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL +EAP VGTGME  VA+ S + IVA+  G+VE V A  + +R      +     
Sbjct: 672  QAVPLLTSEAPVVGTGMEGKVARDSRSVIVAEGTGVVEDVTAEYVQVRYDISVENDVRLS 731

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G+  Y+L+KF+RSNQ+TC++Q+P+V +G+ V +  ++AD  STD G+LALG+N+
Sbjct: 732  LLDPDEGLKTYKLIKFKRSNQDTCISQKPMVHIGNRVEKGSVLADSSSTDHGELALGKNV 791

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIH+ EFE   RDTK G E+ TRDI NVSE+
Sbjct: 792  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHVHEFEANVRDTKRGEEQFTRDIYNVSED 851

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 852  ALRNLDENGIVRLGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 911

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G+ G V+  ++F+R      ++     +E++E + +  D  +  L R     L + L 
Sbjct: 912  PAGMKGIVIKTKLFSR-----KKKVGMDVKEKLEAVDKRFDSREFDLRRRFAKWLKQHLE 966

Query: 992  GQNAV-----SGPKGFKKSTVLSSDLISEYPRSQWWQFA------VQDEKVQRNVESLKV 1040
            G  +V      G     + +     L++++    + +           EKV  NV  L  
Sbjct: 967  GAVSVAVNSDKGKVLIAEGSAFDDALLAKFSSMPFLESIDFTRGLTASEKVNDNVLRLVK 1026

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      L D  +N+  KI  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1027 EFRFKLKDLSDERENEKYKINVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1086

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +ILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1087 GKILPIEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAAKKLGVKFKTPIFNGA 1146

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                                             FD        
Sbjct: 1147 TYEEVQQQLEKAGLPAHGKVSL----------------------------FD-------- 1170

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                              G TGE FD  VTVGYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1171 ------------------GRTGERFDDEVTVGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1212

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E
Sbjct: 1213 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPE 1272

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
             G PESFNVL++E+Q LGL I +++
Sbjct: 1273 PGIPESFNVLIRELQGLGLEIRIDD 1297


>gi|288803792|ref|ZP_06409219.1| DNA-directed RNA polymerase, beta subunit [Prevotella melaninogenica
            D18]
 gi|288333699|gb|EFC72147.1| DNA-directed RNA polymerase, beta subunit [Prevotella melaninogenica
            D18]
          Length = 1269

 Score = 1252 bits (3239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 570/1367 (41%), Positives = 807/1367 (59%), Gaps = 121/1367 (8%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F         PD ++VQ  S+  FL ++  P+ER N+GL   F   FPIT      +
Sbjct: 8    RVNFASVKNPYPYPDFLDVQLKSFRDFLQLDTPPEERKNDGLYKVFAENFPITDTRNNFV 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LEF+ Y  DPP++ +D+CL R LTY+VPLK  ++L   D D       I     Q +++G
Sbjct: 68   LEFLDYYVDPPRYSIDECLERGLTYSVPLKAKMKLYCTDPDHEDFGTFI-----QDVFLG 122

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P MT +GTFVI G +R+VVSQLHRSPG+ F         +G +LY+ RIIP +G W++
Sbjct: 123  TIPYMTSNGTFVINGAERVVVSQLHRSPGVFFGQG---VHANGTVLYSARIIPFKGSWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
               D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                    
Sbjct: 180  FATDINNVMYAYIDRKKKLPVTTMLRAIGYETDRDILQIFDLCEEVKVNKKNMK------ 233

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                    G+K+   ++KS  E  V                 ++
Sbjct: 234  ---------------------AAIGRKIAGNVMKSWTEDFVDEDT------------GEV 260

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ E  E+ +E   +I E+++++I  S +  I +    D+ +  + I NTL  D +    
Sbjct: 261  VSIERNEVVVERETIITEENVDQILDSSVSSILLHKDEDAASKYSIIFNTLAKDPSHSEI 320

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A+  IYR +R  D +  + A  +F  LFF   +YDL  VGR ++N +LNL+T  DVR +
Sbjct: 321  EAVNYIYRQLRNADAADDASAREVFQNLFFSDKRYDLGEVGRYRINKKLNLETDMDVRVL 380

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K+DII IIK L+ L N   T+DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER++
Sbjct: 381  TKDDIIEIIKYLISLINSNATVDDIDHLSNRRVRTVGEQLANQFSIGLARMNRTIRERMN 440

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 441  VRDSEVFQPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALGPGGLSR 500

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV- 610
             RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A++N  GFI TPYR+V D KV 
Sbjct: 501  ERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCMYAKINDLGFIVTPYRRVKDAKVD 560

Query: 611  --TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                DVV+L+A EEE + I Q N+ L+ DG+F  ++V CR   +  +V  + +  ID SP
Sbjct: 561  MDNKDVVFLTAEEEEEQIIGQGNAPLNADGTFIRDVVKCRQDADYPVVTPDSVALIDVSP 620

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            +Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  +AP VGTG+E  V + S   + 
Sbjct: 621  QQIASVSAGLIPFLEHDDGHRALMGCNMMRQAVPLLHNDAPIVGTGLEKQVCEDSRTMVT 680

Query: 729  AKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  G++E VDA  I I   R+ + +       +  YR+ KF+R+NQN  V+ RP+   G
Sbjct: 681  AEGDGVIEYVDATTIRILYDRTDDEEFVSFEPALKEYRIPKFRRTNQNMVVDLRPICDKG 740

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++ DI+ +G +T+ G+LALGRN++VA+MPW GYN+ED+++ISERMV EDV TS+H++
Sbjct: 741  QRVKKGDILTEGYATENGELALGRNLVVAYMPWKGYNYEDAIVISERMVREDVLTSVHVD 800

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  R+TK G EE T DIPNVSEE  K++D+ GII +GA V PGDI++GKI+PKGES 
Sbjct: 801  EYSLEVRETKRGVEEFTADIPNVSEEATKDLDDNGIIRIGARVEPGDIMIGKISPKGESD 860

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PEEKLLRAIFG+KA DV+D+SL+    +SG V+D ++F+R    K   S   ++  + 
Sbjct: 861  PSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVVIDKKLFSRA--IKTRESKRQDKNILA 918

Query: 966  LLARDKDDEQVILDRNIYSRLMEIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             +  +++ +   L   +  +L+E+       G    S  +   K +  +   +       
Sbjct: 919  KIDEEQEAKINDLKDLLVDKLLELTEDKVSEGVKDYSDAEIITKGSKFTVAALKNLDYEG 978

Query: 1021 W-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE     ++ L + +      ++   K K   I  GD++P GVL++ KV++A
Sbjct: 979  IQSNGWTDDEHTNLLIQKLIMNFIRKYKQMDAEMKRKKFAITIGDELPSGVLQMAKVYIA 1038

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR IQ GDK+AGRHGNKGIVS+++  EDMPFL+DG+PVD+VLNP+GVPSRMN+GQIFE 
Sbjct: 1039 KKRKIQVGDKLAGRHGNKGIVSKVVRTEDMPFLEDGSPVDLVLNPMGVPSRMNLGQIFEA 1098

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             LG A   LG K  + I D     D+                                  
Sbjct: 1099 ILGAAGRKLGVKFATPIFDGAKLSDLKEWTD----------------------------- 1129

Query: 1200 WKSGVPV--STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             K+G+P   ST ++DG                           TGE FD+P TVG  Y L
Sbjct: 1130 -KAGLPNLCSTYIYDGE--------------------------TGEKFDQPATVGITYFL 1162

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTI
Sbjct: 1163 KLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTI 1222

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            KSDDVVGR++ YE+IV G        PES NVL+ E++ LGLS+ L+
Sbjct: 1223 KSDDVVGRSKAYEAIVKGEPMPTPDIPESLNVLLHELRGLGLSVKLD 1269


>gi|208435092|ref|YP_002266758.1| DNA-directed RNA polymerase, beta subunit [Helicobacter pylori G27]
 gi|208433021|gb|ACI27892.1| DNA-directed RNA polymerase, beta subunit [Helicobacter pylori G27]
          Length = 2805

 Score = 1251 bits (3238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 579/1327 (43%), Positives = 850/1327 (64%), Gaps = 44/1327 (3%)

Query: 92   LWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
            + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQSI++ ++PLMT+  +F+I G++
Sbjct: 1    MERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTERTSFIINGVE 60

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
            R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+G W+  E+DSKD+++ RI++RR
Sbjct: 61   RVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRR 119

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
            KVPVT    A+    ++I+  FYP +      D +  P ++ D     ++   L D   G
Sbjct: 120  KVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLD--ANQRMEFDLKDPQ-G 176

Query: 271  EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            + ++ +GKKLTS  +K LKE  ++++    D L   ++AE +      E+ ++    +D+
Sbjct: 177  KIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPV--MVGKEVLLDMLTQLDK 234

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK----------DRKDAL--LDIY 378
              LE+I    +++  I+   ++ ++A I ++ + D             D ++AL  + I+
Sbjct: 235  NRLEKIHDLGVQEFVIINDLALGHDASIIHSFLADYESLKLLKQTEKIDDENALAAIRIH 294

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            +VM+PGD  T  VA+     LFFD ++YDL+ VGR+KMN +L L  PD +  +  EDII 
Sbjct: 295  KVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIIT 354

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--ID 496
             +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+   GL++M+++IK++++++    D
Sbjct: 355  TVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFD 414

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            S+MP DL+N+K + S + EFF   QLSQ  +  N LS +TH RRLSALG+GG+ + R G 
Sbjct: 415  SLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGF 474

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            E RDVHPTHYGRICP ET EG NIGL+++L++F RVN  GFIE PY+KV DGKV  + +Y
Sbjct: 475  EARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIY 534

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            L+A++E++  IA A++ +DE+G+   +L+  R  GE +L  + K+  +D S   +V +AA
Sbjct: 535  LTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAA 594

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            SLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG+E ++A+ S  AI A RAG+VE
Sbjct: 595  SLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVE 654

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            ++D+  I I           + +D Y L K  R+NQNT  NQ P+VKVGD+V    IIAD
Sbjct: 655  KIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIAD 710

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GPS D G+LALG+N+ VAFMPW+GYNFED++++SE +  +DVFTS HI E EV AR+ K 
Sbjct: 711  GPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSECITKDDVFTSTHIYEKEVDARELKH 770

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G EE T DIP+V EE L ++DE GI+ VG  V+ G ILVGK +PKGE   TPEE+LLRAI
Sbjct: 771  GAEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAI 830

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FG+KA  V + SL  P  + GTV+DV++F + G +K+ R +S   E+   L  +  D   
Sbjct: 831  FGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLT 890

Query: 977  ILDRNIYSRLMEILCG----QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ-DEKV 1031
            +L+R    R+  +L      +      K +K+   +  + I+   R        +  ++V
Sbjct: 891  MLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEV 950

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q + E  K  +   K +L +  + K+  ++  D +P GV++ VK+++A KR ++ GDKMA
Sbjct: 951  QNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMA 1010

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGIVS I+P  DMP+  DG PVDIVLNPLGVPSRMN+GQI E HLG      GK+
Sbjct: 1011 GRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1070

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI-----SDYDDDSVLRVAEQWKSGVPV 1206
            I S++ D K       LR+ + ++    +  + +      +  D+ +L  A+ W  GV +
Sbjct: 1071 IASMLED-KTRDFAKELRAKMLEIANAINEKDPLTIHVLENCSDEELLEYAKDWSKGVKM 1129

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            + PVF+G  +E    +  +A +   G+  LYDG TGE     V VGY+YM+KL+H+V +K
Sbjct: 1130 AIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEK 1189

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            V+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++AYGAA+ L+EMLTIKSDD+ GR 
Sbjct: 1190 VHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRE 1249

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA-----KMEEIP--- 1378
              Y +I  G    E+  PE+F VL KE+Q+L L I++               ++E     
Sbjct: 1250 NAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDVDEDGAPKPIVIKEDDRPK 1309

Query: 1379 DFNKCEL 1385
            DF+  +L
Sbjct: 1310 DFSSFQL 1316



 Score = 39.3 bits (90), Expect = 5.0,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            G + +    + + G  + ED+++  T EI + A  +IDE+  +++  + I+ I I
Sbjct: 2108 GSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVIEAGIKSITI 2162


>gi|21672996|ref|NP_661061.1| DNA-directed RNA polymerase subunit beta [Chlorobium tepidum TLS]
 gi|41017753|sp|Q8KG15|RPOB_CHLTE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21646059|gb|AAM71403.1| DNA-directed RNA polymerase, beta subunit [Chlorobium tepidum TLS]
          Length = 1303

 Score = 1251 bits (3236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 579/1404 (41%), Positives = 811/1404 (57%), Gaps = 170/1404 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   II+ PDL++VQ  S+ +F+  ++  ++R ++GL+   +S FPIT   G  +LE
Sbjct: 13   DFSKIQSIINPPDLLKVQLDSFHNFIQDSVPLEKRKDQGLEKVLRSAFPITDTRGLYLLE 72

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V++C+ R LTY V LKI L+L   D          K+  +Q +Y+G +
Sbjct: 73   YISYSFDKPKYTVEECIERGLTYDVSLKIKLKLSYKD---EADEPDWKETIQQEVYLGRI 129

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT  GTF+I G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 130  PYMTDRGTFIINGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 186

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   VT+ L A+G   +E IL  F                    + 
Sbjct: 187  TDINNQIFVYIDQKKNFLVTALLRAIGFAKDEDILGLFDLVEEVEVSSKSSKR-----EQ 241

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            ++G  ++S ++D+ TGE  + +   +T  ++  +   G K + +               +
Sbjct: 242  LLGQYLASDIIDMTTGEV-VPARAAITEEIIDQIVAAGYKTVKVMK-----------TTS 289

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             E G                                   + + I NT++ D +   ++AL
Sbjct: 290  PEKGV----------------------------------DKSVIINTILNDSSATEEEAL 315

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD----------- 423
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L  +           
Sbjct: 316  EIVYEELRSNEAPDIDAARSFLERTFFNQKKYDLGDVGRYRIQKKLQNELAELSAYLEKR 375

Query: 424  -------------------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       +D+  +   DIIA+I  L+ L NG   +DD+D+
Sbjct: 376  PELKELSDAIYERILQTISTYSEEPIGEDILVLTHYDIIAVINYLIKLINGMAEVDDVDH 435

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 436  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDTDKIAPADLINARTVSSVVSSFFA 495

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 496  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 555

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V +G+VT+ VV LSA +EEN+     +  LDE+ 
Sbjct: 556  NIGLISSLSVYAEINDKGFIQTPYRVVENGQVTDKVVMLSAEDEENKITVPVSIELDENN 615

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  LV  E+++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 616  RIAAESVQARTKGDYPLVLAEEVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 675

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL +EAP VGTGME+ VA+ S A IVA+  G+V+ V A RI +R      +     
Sbjct: 676  QAVPLLVSEAPIVGTGMEAKVARDSRAVIVAEGPGVVQCVTADRIEVRYDLDPENNTVSL 735

Query: 754  -PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 GV +Y+L+KF+RSNQ+TC++QRPLV  G  V   D++AD  STD G+LALG+N+L
Sbjct: 736  LDPDEGVKVYKLIKFKRSNQDTCISQRPLVHNGQRVNAGDVLADSSSTDNGELALGKNVL 795

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW GYNFED++++SER+V +DVFTSIH+ EFE   RDTK G E+ TRDI NVSE+ 
Sbjct: 796  VAFMPWRGYNFEDAIVLSERLVYDDVFTSIHVHEFESSVRDTKRGEEQFTRDIYNVSEDA 855

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ VP
Sbjct: 856  LRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHVP 915

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G+ G V+  ++F+R      ++     +E++E + +  D ++  L       + + L G
Sbjct: 916  AGMKGIVIKTKLFSR-----KKKIGMDVKERMEAIDKQFDLKEADLRSRFAKWMKQYLNG 970

Query: 993  QNAV-----SGPKGFKKSTVLSSDLISEYP------RSQWWQFAVQDEKVQRNVESLKVQ 1041
            + +V      G     + TV+   L++++            +  V   K   NV  L  +
Sbjct: 971  KKSVAITSDKGKVLVPEGTVIDEALLAKFNGLPFLESIDLSKGIVSGAKTNENVVRLIRE 1030

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y      L D  +N+  KI  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V 
Sbjct: 1031 YRLKLKDLSDERENEKYKINVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVVG 1090

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP EDMPF++DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I     
Sbjct: 1091 KILPIEDMPFMEDGTPVDIVLNPLGVPSRMNIGQLYETSLGWAGKKLGVKFKTPIFSGAT 1150

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              ++                                             FD         
Sbjct: 1151 YTEVQEYLEKAGLPGHGKVKL----------------------------FD--------- 1173

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                             G TGE F   VTVGYIYMLKL+H+V DK++ARS G YSL+TQQ
Sbjct: 1174 -----------------GRTGEQFHDEVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQ 1216

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E 
Sbjct: 1217 PLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPEP 1276

Query: 1342 GTPESFNVLVKEMQALGLSIDLEN 1365
            GTPESFNVL++E+Q LGL I +++
Sbjct: 1277 GTPESFNVLIRELQGLGLEIRIDD 1300


>gi|193213522|ref|YP_001999475.1| DNA-directed RNA polymerase subunit beta [Chlorobaculum parvum NCIB
            8327]
 gi|193086999|gb|ACF12275.1| DNA-directed RNA polymerase, beta subunit [Chlorobaculum parvum NCIB
            8327]
          Length = 1301

 Score = 1250 bits (3234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1404 (41%), Positives = 812/1404 (57%), Gaps = 170/1404 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   II+ PDL++VQ  S+ +F+  ++   +R ++GL+   +S FPIT   G  +LE
Sbjct: 11   DFSKIQSIINPPDLLKVQLDSFHNFIQDSVPLAKRKDQGLEKVLRSAFPITDTRGLYLLE 70

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V++C+ R LTY V LKI L+L   D          K+  +Q +Y+G +
Sbjct: 71   YISYSFDKPKYTVEECIERGLTYDVSLKIKLKLSYKD---EADEPDWKETIQQEVYLGRI 127

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 128  PYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 184

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   VT+ L A+G   +E IL+ F                    + 
Sbjct: 185  TDINNQIFVYIDQKKNFLVTALLRAIGFAKDEDILALFDLVEEVEVSSKSAKR-----EQ 239

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            ++G  ++S ++D++TGE  + +   +T  +L  +   G K + +               +
Sbjct: 240  LLGQYLASDIIDMNTGEV-VSARSAITEDILDQIVAAGYKTIKVMK-----------TTS 287

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             E G                                   + + I NT++ D +   ++AL
Sbjct: 288  PEKGV----------------------------------DKSVIINTILNDSSATEEEAL 313

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD----------- 423
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L+ +           
Sbjct: 314  EIVYEELRSNEAPDIDAARSFLERTFFNQKKYDLGDVGRYRIQKKLHNELTELSSYLEER 373

Query: 424  -------------------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       +D+  +   DIIA+I  L+ L NG   +DD+D+
Sbjct: 374  PELKELSDAIYERILQTISTYSEEPIGEDILVLTHYDIIAVINYLIKLVNGMAEVDDVDH 433

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 434  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDTDKIAPADLINARTVSSVVSSFFA 493

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 494  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 553

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G VT+ V+ LSA +EEN+     +  LDE+ 
Sbjct: 554  NIGLISSLSVYAEINDKGFIQTPYRVVDKGLVTDKVLMLSAEDEENKITVPVSIELDENN 613

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  LV  E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 614  RIAAESVQARTKGDYPLVLAEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 673

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL ++AP VGTGME+ VA+ S A IVA+  G+V+ V A RI +R      +     
Sbjct: 674  QAVPLLVSDAPVVGTGMEAKVARDSRAVIVAEGPGVVQNVTAERIEVRYDLDPENNTVSL 733

Query: 754  -PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 GV +Y+L+KF+RSNQ+TC++QRPLV  G  V   D++AD  STD G+LALG+N+L
Sbjct: 734  LDPDEGVKVYKLIKFKRSNQDTCISQRPLVHNGQRVDAGDVLADSSSTDNGELALGKNVL 793

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW GYNFED++++SER+V +DVFTSIH+ EFE   RDTK G E+ TRDI NVSE+ 
Sbjct: 794  VAFMPWRGYNFEDAIVLSERLVYDDVFTSIHVHEFESNVRDTKRGEEQFTRDIYNVSEDA 853

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ VP
Sbjct: 854  LRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHVP 913

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G+ G V+  ++F+R      ++     +E++E + +  D ++  L       + + L G
Sbjct: 914  AGMKGIVIKTKLFSR-----KKKIGMDVKERMEAIDKQFDLKEADLRSRFAKWMKQHLNG 968

Query: 993  QNAV-----SGPKGFKKSTVLSSDLISEYP------RSQWWQFAVQDEKVQRNVESLKVQ 1041
            + +V      G     + TV+   L++++            +  V   K   NV  L  +
Sbjct: 969  KKSVAITSDKGKVLVPEGTVIDEALLAKFNGLPFLESIDVSKGIVSGAKTNENVVRLIRE 1028

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y      LED  +N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V 
Sbjct: 1029 YRLKLKDLEDERENEKYKVNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVVG 1088

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +   
Sbjct: 1089 KILPIEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAGKKLGVKFKTPIFNGAT 1148

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              ++                                             FD         
Sbjct: 1149 YKEVQENLEKAGLPGHGKVKL----------------------------FD--------- 1171

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                             G TGE F   VTVGYIYMLKL+H+V DK++ARS G YSL+TQQ
Sbjct: 1172 -----------------GRTGEQFHDEVTVGYIYMLKLSHLVDDKIHARSIGPYSLITQQ 1214

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E 
Sbjct: 1215 PLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPEP 1274

Query: 1342 GTPESFNVLVKEMQALGLSIDLEN 1365
            GTPESFNVLV+E+Q LGL I +++
Sbjct: 1275 GTPESFNVLVRELQGLGLEIRIDD 1298


>gi|194337661|ref|YP_002019455.1| DNA-directed RNA polymerase, beta subunit [Pelodictyon
            phaeoclathratiforme BU-1]
 gi|194310138|gb|ACF44838.1| DNA-directed RNA polymerase, beta subunit [Pelodictyon
            phaeoclathratiforme BU-1]
          Length = 1303

 Score = 1249 bits (3233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1406 (40%), Positives = 819/1406 (58%), Gaps = 172/1406 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   II+ PDL++VQ  S+ +F+  ++   +R ++GL+   +  FPIT   G  +LE
Sbjct: 13   DFSKIQSIIEPPDLLKVQLDSFHNFIQDSVPLAKRKDQGLERVLRGAFPITDTRGLYLLE 72

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ ++DC+ R LTY V LK+ L+L   D  + T  K      +Q +Y+G +
Sbjct: 73   YISYSFDKPKYTIEDCIERGLTYDVSLKVKLKLSYKDEADETDWKET---IQQEVYLGRI 129

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT  GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 130  PYMTNRGTFIVNGAERVVVAQLHRSPGVVFSE---AVHPNGKKMYSAKIVPTRGSWIEFQ 186

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   V++ L A+G    E+IL  F        +           + 
Sbjct: 187  TDINNQIFVYIDQKKNFLVSALLRAIGFARDEDILGLFDLVEELPLKSSK-------KEQ 239

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            +VG  ++S +VD+ TGE  + +   +T  + + +   G K + +      G         
Sbjct: 240  LVGQYLASDIVDMQTGEV-VSARTAITEDIFEQILAAGYKSVKVMKTFAGG--------- 289

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                                               D   + + I NT++ D +   ++AL
Sbjct: 290  -----------------------------------DKGVDKSIIINTILNDNSATEEEAL 314

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------- 425
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L  +           
Sbjct: 315  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGEVGRYRIKKKLAKEFDDLTAYLAEK 374

Query: 426  ---------------------------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       +D+  +   DII++I  L+ L NG   +DD+D+
Sbjct: 375  PELKQLSDTIYEKILQTIQSFSDEPTGEDILVLTHYDIISVIYYLIKLVNGLADVDDVDH 434

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 435  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDSDKIAPADLINARTVSSVVSSFFA 494

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 495  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 554

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G+VT+ V+ LSA +EEN+     +  LDE+ 
Sbjct: 555  NIGLISSLSVYAEINDKGFIQTPYRVVDKGQVTDTVLMLSAEDEENKITVPVSVPLDENR 614

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                E V  R  G+  +V  E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 615  KIAMETVQARTKGDYPVVAAEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 674

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----- 753
            QAVPLL +EAP VGTGME+ VA+ S + IVA+ AG++E V A  I +R      +     
Sbjct: 675  QAVPLLTSEAPVVGTGMEAKVARDSRSVIVAEGAGVLEDVTAEYIQVRYDLNPDNDVRLS 734

Query: 754  --PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                  G+  Y+L+KF+RSNQ+TC++Q+PLV +G  V +  ++AD  STD G+LALG+N+
Sbjct: 735  MLDPDEGLKTYKLIKFKRSNQDTCISQKPLVHIGQRVEKGTVLADSSSTDNGELALGKNV 794

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G E+ TRDI NVS+E
Sbjct: 795  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHIHEFEANVRDTKRGEEQFTRDIYNVSDE 854

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 855  ALRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 914

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL- 990
            P+G+ G V+  ++F+R      ++     +E++E++ +  D ++  L +     + ++L 
Sbjct: 915  PAGMKGIVIKTKLFSR-----KKKVGMDVKEKLEVVDKRFDSKEYDLRKRFAKWIKQLLG 969

Query: 991  ----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA------VQDEKVQRNVESLKV 1040
                 G     G +   + +V    L++++    + +           +KV  NV  L  
Sbjct: 970  GKSSVGVYNDKGKQLIAEGSVYDEILLAKFSAMPFLESIDFTKGLTDSKKVNDNVIRLVK 1029

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      L D   N+  KI  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1030 EFRFMLKDLADERDNEKYKINVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1089

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +IL  EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1090 GKILSIEDMPFMADGTPVDIVLNPLGVPSRMNIGQLYETSLGWAAKKLGVKFKTPIFNGA 1149

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                               AE  ++G+P               
Sbjct: 1150 TYEEVQ------------------------------AELERAGLPA-------------- 1165

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  L+DG TGE FD  VT+GYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1166 ----------HGKVSLFDGRTGERFDDEVTIGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1215

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  E
Sbjct: 1216 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPE 1275

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENS 1366
             G PESFNVLV+E+Q LGL I +++ 
Sbjct: 1276 PGIPESFNVLVRELQGLGLEIRIDDK 1301


>gi|255311116|ref|ZP_05353686.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis 6276]
 gi|255317417|ref|ZP_05358663.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            6276s]
 gi|296435831|gb|ADH18005.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            G/9768]
 gi|296437691|gb|ADH19852.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            G/11074]
 gi|297140190|gb|ADH96948.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            G/9301]
          Length = 1252

 Score = 1248 bits (3230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 598/1370 (43%), Positives = 825/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+  F+     S         
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEEFFSVEERSL-------- 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   L++  V         L G  +
Sbjct: 224  --------------------------------------RLEKDFVA--------LVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|76789037|ref|YP_328123.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            A/HAR-13]
 gi|88909129|sp|Q3KM47|RPOB_CHLTA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|76167567|gb|AAX50575.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis
            A/HAR-13]
          Length = 1252

 Score = 1248 bits (3229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 598/1370 (43%), Positives = 825/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+  F+     S         
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEEFFSVEERSL-------- 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   L++  V         L G  +
Sbjct: 224  --------------------------------------RLEKDFVA--------LVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLTKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|145220408|ref|YP_001131117.1| DNA-directed RNA polymerase subunit beta [Prosthecochloris
            vibrioformis DSM 265]
 gi|145206572|gb|ABP37615.1| DNA-directed RNA polymerase subunit beta [Chlorobium phaeovibrioides
            DSM 265]
          Length = 1301

 Score = 1247 bits (3226), Expect = 0.0,   Method: Composition-based stats.
 Identities = 571/1405 (40%), Positives = 817/1405 (58%), Gaps = 172/1405 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K   +I  PDL++VQ  S+ +F+  ++   +R ++GL+   +S FPIT   G  +LE
Sbjct: 11   DFSKIQSVIKAPDLLKVQLDSFHNFIQDSVPLAKRRDQGLERVLRSAFPITDTRGLYLLE 70

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            ++SY FD PK+ V+DC+ R LTY V LK+ L+L   D  + T  K       Q +Y+G +
Sbjct: 71   YISYSFDKPKYTVEDCIERGLTYDVSLKVKLKLSYKDEADETDWKETLQ---QEVYLGRI 127

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            P MT+ GTF++ G +R+VV+QLHRSPG+ F         +GK +Y+ +I+P +G W++ +
Sbjct: 128  PYMTERGTFIVNGAERVVVAQLHRSPGVVFSE---AIHPNGKKMYSAKIVPTRGSWIEFQ 184

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  + I V ID+++   VT+ L A+G    E+IL  F        +G          D 
Sbjct: 185  TDINNQIFVYIDQKKNFLVTALLRAIGFARDEDILGLFDLVEEVQLKG-------VKKDR 237

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            ++G  +++ +VD++TGE  + +   +T  +L+ +   G K + +      G         
Sbjct: 238  LIGQYLAADIVDMNTGEV-VSARTAITEEVLEQIIAAGQKSVKVMKTFNGG--------- 287

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                                               D   + + + NT++ D +   ++AL
Sbjct: 288  -----------------------------------DKGQDKSIVSNTILNDSSATEEEAL 312

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP--------- 425
              +Y  +R  +      A S     FF+  KYDL  VGR ++  +L+ +           
Sbjct: 313  EIVYEELRANEAPDIDAARSFLERTFFNQKKYDLGEVGRYRIRKKLSNEFSELESYLAGK 372

Query: 426  ---------------------------DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                                       +D   +   DII++I  L+ L NG+  +DD+D+
Sbjct: 373  GELKELSDAISAKINQTIQSFSDEPVGEDTLVLTHYDIISVINYLIKLVNGQAEVDDVDH 432

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L NRRVRSVGE L  Q+ +GL RM ++++E+++S D D + P DLINA+ V S V  FF 
Sbjct: 433  LANRRVRSVGEQLAAQFVIGLARMGKNVREKLNSRDSDKIAPSDLINARTVSSVVSSFFA 492

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 493  TSQLSQFMDQTNPLAEMTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETPEGP 552

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            NIGL+SSL+ +A +N  GFI+TPYR V  G VT++V+ LSA +EEN+     +  LD+  
Sbjct: 553  NIGLISSLSVYAEINDKGFIQTPYRVVNKGHVTDEVLMLSAEDEENKITVPVSIKLDDKN 612

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +  +E V  R  G+  LVP E ++++D SP Q+VS AA+LIPFLE+DD NR LMG NMQR
Sbjct: 613  TIVDESVQARTKGDYPLVPSEDVNYMDVSPVQIVSAAAALIPFLEHDDGNRALMGANMQR 672

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD------- 751
            QAVPLL +EAP VGTGME  VA+ S +  + + +G+VE+V A  I +R            
Sbjct: 673  QAVPLLTSEAPVVGTGMEEKVARDSRSVCLGEGSGVVEEVTAEYIKVRYDINPDSNEELS 732

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            L     G+  YR++KF+RSNQ+TC++Q+PLV  G +V +  ++AD  ST+ G+LALG+N+
Sbjct: 733  LLDPDEGLKTYRMIKFKRSNQDTCISQKPLVHNGQKVEKGTVLADSSSTENGELALGKNV 792

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED++++SER+V +DVFTSIH+ EFE   RDTK G E+ TRDI NVS+E
Sbjct: 793  LVAFMPWRGYNFEDAIILSERLVYDDVFTSIHVHEFEANVRDTKRGEEQFTRDIYNVSDE 852

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L+N+DE GI+ +GAEV   DILVGKITPKGES  TPEEKLLRAIFG+K+ DV+D S+ V
Sbjct: 853  ALRNLDENGIVRIGAEVKERDILVGKITPKGESDPTPEEKLLRAIFGDKSSDVKDASMHV 912

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G+ G V+  ++F+R      ++     +E++EL+    +  +  L  +    L +IL 
Sbjct: 913  PAGMKGIVIKTKLFSR-----KKKVGMDVKEKLELIDSRFERREQDLRISFEKWLHKILQ 967

Query: 992  GQNAVSGPKGFKKSTVLSSDL-----------ISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            G+          K+   +              +S      +       +KV  +V  L  
Sbjct: 968  GKETTGLQSDKGKTLAAAGAKFDAALISKFAGLSFLETVDFSNGITGTKKVDDSVIRLVK 1027

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++      L D  +N+  K+  GD++PPG+  + KV++A KR IQ GDKMAGRHGNKG+V
Sbjct: 1028 EFRFKLKDLADERENEKYKVNVGDELPPGIEELAKVYIAQKRKIQVGDKMAGRHGNKGVV 1087

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
             +ILP EDMPF+ DG PVDIVLNPLGVPSRMN+GQ++ET LGWA   LG K K+ I +  
Sbjct: 1088 GKILPIEDMPFMADGKPVDIVLNPLGVPSRMNIGQLYETSLGWAAKTLGVKFKTPIFNGA 1147

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                               AE  ++G+P               
Sbjct: 1148 TYEEVQ------------------------------AELERAGLPA-------------- 1163

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  LYDG TGE FD  VTVGYIYMLKL+H+V DK++ARSTG YSL+TQ
Sbjct: 1164 ----------HGKVSLYDGRTGERFDDEVTVGYIYMLKLSHLVDDKIHARSTGPYSLITQ 1213

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAA +L+EMLT+KSDDV+GR + YE+IV G +  +
Sbjct: 1214 QPLGGKAQFGGQRFGEMEVWALEAYGAANILREMLTVKSDDVIGRNKTYEAIVKGQNLPD 1273

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
             G PESFNVL++E+Q LGL + +++
Sbjct: 1274 PGIPESFNVLIRELQGLGLEVRIDD 1298


>gi|237802738|ref|YP_002887932.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            B/Jali20/OT]
 gi|231273972|emb|CAX10764.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis
            B/Jali20/OT]
          Length = 1252

 Score = 1246 bits (3225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 599/1370 (43%), Positives = 826/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+  F+     S         
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEEFFSVEERSL-------- 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   L++  V         L G  +
Sbjct: 224  --------------------------------------RLEKDFVA--------LVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++S +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPATIIHRRSADILVQESAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|15605036|ref|NP_219820.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            D/UW-3/CX]
 gi|290463293|sp|P0CE09|RPOB_CHLTR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|3328732|gb|AAC67908.1| RNA Polymerase Beta [Chlamydia trachomatis D/UW-3/CX]
 gi|297748444|gb|ADI50990.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis D-EC]
 gi|297749324|gb|ADI52002.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis D-LC]
          Length = 1252

 Score = 1246 bits (3225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1370 (43%), Positives = 825/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+  F+     S         
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEEFFSVEERSL-------- 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   L++  V         L G  +
Sbjct: 224  --------------------------------------RLEKDFVA--------LVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYDMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E G++ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGVVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|41017813|sp|Q9X6Y1|RPOB_AQUPY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|4753643|emb|CAA52957.1| DNA dependent RNA polymerase [Aquifex pyrophilus]
          Length = 1469

 Score = 1246 bits (3224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 616/1484 (41%), Positives = 880/1484 (59%), Gaps = 137/1484 (9%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            RKFFG+  EI++ P L+ + K S+++F+ + + P +R N GL+  F++ FP        +
Sbjct: 8    RKFFGRRTEILEPPYLLSIPKNSFENFVQLKVNPYKRKNVGLEHIFRTSFPFKDPDENFI 67

Query: 74   LEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAVP 101
            LE++ YE                                    KF  ++C  + LTY+ P
Sbjct: 68   LEYLGYEIGDWECNRCGYKPKDDLLGGWDVDCPECGAKLVYKEKFTPEECKLKGLTYSAP 127

Query: 102  LKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSP 161
            L++ L+L     + +      K      +Y G++PLMT +G+F+I G +RI+++QL RS 
Sbjct: 128  LRVMLQLKAKTKNGYRTFPPRK------VYFGEVPLMTDNGSFIINGTERIIINQLIRSS 181

Query: 162  GIHFDH--DKGRASLSGKLLYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFL 218
            G+ FD   +K + +   ++LY   IIPD+G  ++ E   + D+I  RIDR+ K+   S L
Sbjct: 182  GVFFDEKEEKQKDATITRILYRASIIPDKGSRVEFELSGATDLISARIDRK-KLSAISVL 240

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
             A G+++  +IL  FY  +      D + +     +      +    +       +++  
Sbjct: 241  RAFGLETAYDILKPFYEGVRKYIVKDKYLYDAETGEEFTPEDLEHHYIFA-----ILKFK 295

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             K+        +E   +      + L        I++ E  E+   +   +  +++ +  
Sbjct: 296  AKIAGFGTSKEREIIEERYIEEWEELV------RILDDERIEVL--SVTSVPRENVIKSP 347

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA-LLDIYRVMRPGDVSTFSV----- 391
                  +  L  D+   +A  R+ +        +D  L+++Y+ +R  +  T  +     
Sbjct: 348  -YGKSLVDTLATDTSPRDADRRSPVKVPAEYTLRDYGLMEMYKKLRHIEALTMEIDSIIE 406

Query: 392  -AESMFNFLFFDSDKYDLSTVGRVKMN--------------------------------- 417
             A   FN  F D  +YDLS VGRVK+N                                 
Sbjct: 407  RARVYFNVFFRDLKRYDLSRVGRVKINAKVHNIPKVLKPTDIDLLDNLPPLALAEDYGEY 466

Query: 418  --------------------MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                                +++   T D+ R +   D+I I+K L+DLR+G+   DDI 
Sbjct: 467  KAGTRITKELLKELFKNYKEIKVKDYTEDEARFLLPIDLINILKYLIDLRHGRVKKDDIA 526

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCE 515
            +LGNRRVRSVGE+L+NQ RLG+ +ME+  ++R      +   + PQD IN + V +A+ +
Sbjct: 527  HLGNRRVRSVGELLENQARLGIAKMEKVFRDRSATIHPEQPDLKPQDFINPRYVTNAIAD 586

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            F  + QLSQ  ++ N LS +TH RRLSALG GG+ R  A  E+RDVHP+HYGRICP ET 
Sbjct: 587  FLKTGQLSQYLDNTNPLSELTHKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIETP 646

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG NIGLV+S T +ARVN YGF+ TPYRKV +G+VT+ + +L+A EEEN  IAQ ++  D
Sbjct: 647  EGQNIGLVTSPTVYARVNEYGFLITPYRKVENGRVTDKIEWLAAYEEENYVIAQ-STPTD 705

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            E+G    E V  R   +  LV  E++D+ID SP+QV+S ++SLIPFLE+DD+NR LMG N
Sbjct: 706  EEGRIKAEFVLARHKNDIRLVKPEQVDYIDVSPRQVISPSSSLIPFLEHDDANRALMGSN 765

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD---L 752
            MQRQAVPL+  +AP VGTGME  +A+ S A +VAKR G+VE+VD  +I++R    +    
Sbjct: 766  MQRQAVPLIFTQAPLVGTGMEKKIARDSHAVVVAKRGGVVEEVDGSKIIVRVNPEEINLE 825

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            DP   G+DIY L KF+R+NQ TCVNQRP+VK G+ V +  IIADG STD G+LALG+++L
Sbjct: 826  DPLDIGIDIYELRKFERTNQKTCVNQRPIVKKGERVEKGQIIADGHSTDRGELALGKDVL 885

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAFMPW GYNFED+++ISER+V EDV+TSIHIEE EV AR+TK+G EEITR IP V E  
Sbjct: 886  VAFMPWRGYNFEDAIVISERLVKEDVYTSIHIEELEVEARETKVGDEEITRQIPGVPERA 945

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            L ++DE GI+ VG  V PGDILVGK+TPKGE+ +TPEEKLL+AIFGEK  DV+D SLR P
Sbjct: 946  LAHLDEHGIVRVGTYVKPGDILVGKVTPKGETRLTPEEKLLQAIFGEKTKDVKDASLRCP 1005

Query: 933  SGVSGTVVDVRIFNRHGID--KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
             GV G V+DV++F R G    K+  +  VERE++E L R+ + ++ +L   +   L  ++
Sbjct: 1006 PGVEGIVIDVQVFTRKGGKAAKDMLAQKVEREELEALERELEKKKNLLMSGVEKVLKGLI 1065

Query: 991  CGQNAVSGPKGFKKS----TVLSSDLISEYPRSQWWQFA--VQDEKVQRNVESLKVQYET 1044
             G+      K  KK     T ++ ++  EY +    +      DE++ + +  +  +  T
Sbjct: 1066 LGKKTDKDVKIGKKEIKKGTEITEEIFKEYSQYILARPENFFTDEELIKKIREIYTRSRT 1125

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
               +L+  ++ K E +    D+PPGV+ +VKVF+A KR I+ GDKMAGRHGNKG++S +L
Sbjct: 1126 QIDMLQKVYQEKKETLLKRRDLPPGVITLVKVFIANKRKIKVGDKMAGRHGNKGVISVVL 1185

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL DGTPVDIVLNPLGVPSRMNVGQI ETHLGWA   LGKKI  +I   +    
Sbjct: 1186 PVEDMPFLPDGTPVDIVLNPLGVPSRMNVGQILETHLGWAAKELGKKIGEMIEKGRDRKA 1245

Query: 1165 ISPLRSFLEKVIGTGSHT-----EKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGADEEA 1218
            I+     +  V            E ++   ++    V   + + G+P++TP F+GADE+A
Sbjct: 1246 ITEYLKEIYAVGDENGENAKFIEEFLNSLSEEEFWSVVRDYAQRGIPMATPAFEGADEKA 1305

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +  +L+ A L ESG++ LYDG TGEPFD  VTVGY++MLKL HMV DK++AR+TG YSLV
Sbjct: 1306 VKELLKKAGLPESGKTTLYDGRTGEPFDFEVTVGYMHMLKLIHMVDDKIHARATGPYSLV 1365

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDDV GR++VYE+IV G  T
Sbjct: 1366 TQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDVEGRSKVYEAIVKGKYT 1425

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +  G PESF VLV+E++ L L++   N   K   ++E   +  K
Sbjct: 1426 YTPGIPESFKVLVRELKGLSLNVKCMNGEEKPCDQVEIKEEEEK 1469


>gi|237804660|ref|YP_002888814.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            B/TZ1A828/OT]
 gi|231272960|emb|CAX09871.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis
            B/TZ1A828/OT]
          Length = 1252

 Score = 1245 bits (3222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 825/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY++ LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSITLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+  F+     S         
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEEFFSVEERSL-------- 223

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   L++  V         L G  +
Sbjct: 224  --------------------------------------RLEKDFVA--------LVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLTKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPN+SEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNISEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|269302960|gb|ACZ33060.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila pneumoniae
            LPCoLN]
          Length = 1252

 Score = 1244 bits (3220), Expect = 0.0,   Method: Composition-based stats.
 Identities = 593/1370 (43%), Positives = 826/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   VLEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +PLMT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPLMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+        ++         
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSDADIIE-----EFFTIEESSLRSE 226

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                                  L G  +
Sbjct: 227  KD-------------------------------------------------FALLVGRIL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A++I++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D   
Sbjct: 238  ADNIIDEASSLVYGKAGEKLSTAMLKRMLDAGIASVKIAVD--ADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFSMDDEA 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ L+ G  K  +DDID+L NRRVRSVGE+++NQ R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLKMGDEKACVDDIDHLANRRVRSVGELIQNQCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +++AK + S + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKVVSAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++SLDE   FTE + + R AGE        +
Sbjct: 536  YRIVRDGIVTDEIEYMTADVEEECVIAQASASLDEYNMFTEPVCWVRYAGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPVVGTGLECRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA +VA+  G+V+ VD  ++V+ +              Y L KF RSN  TC+NQ+PL
Sbjct: 656  DSGAIVVAEEDGVVDFVDGYKVVVAAKHNPTIK-----RTYHLKKFLRSNSGTCINQQPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD + + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ ED +TS
Sbjct: 711  CAVGDVITKGDVIADGPATDRGELALGKNVLVAFMPWYGYNFEDAIIISEKLIREDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVS+E L N+ E GII +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSDEVLANLGEDGIIRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLI 1013
               ++ L +   ++   L      +L  +L  + A +     +       +  +   + I
Sbjct: 891  AVHLKDLQKGYKNQVATLKTEYREKLGALLLNEKAPAAIIHRRTAEIVVHEGLLFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                +       + + ++   ++ L   YET+   LE  +K ++E I+ GD D+  GV+R
Sbjct: 951  ERIEQEDLVDLLMPNCEMYEVLKGLLSDYETALQRLEINYKTEVEHIREGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPEQRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S LYDG TGE FD  V +G
Sbjct: 1108 --------------------------IEQGLPEDG-----KSFLYDGKTGERFDNKVVIG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|294056237|ref|YP_003549895.1| DNA-directed RNA polymerase, beta subunit [Coraliomargarita
            akajimensis DSM 45221]
 gi|293615570|gb|ADE55725.1| DNA-directed RNA polymerase, beta subunit [Coraliomargarita
            akajimensis DSM 45221]
          Length = 1261

 Score = 1243 bits (3217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1382 (43%), Positives = 832/1382 (60%), Gaps = 142/1382 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  FG+  E+I  P+LIE Q  S+  FL M+ AP +R   GL+A F  VFPI ++    
Sbjct: 3    ERINFGQIKEVIQPPNLIENQINSFKEFLQMDTAPSQRQPVGLEAVFSEVFPIESYDSRC 62

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE+VSY    P+    + +   +TY+V L + LRL           +  + IK++ IYM
Sbjct: 63   HLEYVSYNVTAPRETEIEAIREGVTYSVSLYVKLRL-----------REEEHIKDEEIYM 111

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G+LP++T+ G+F+I G +R++VSQLHRSPGI F+        SGK+L+A RIIPD+G W+
Sbjct: 112  GELPMITERGSFIINGAERVIVSQLHRSPGIAFEES---VHTSGKILHAFRIIPDRGTWL 168

Query: 193  DIEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +++FD  D+++V +DRRR   K  +T+ L A+G  S+                D      
Sbjct: 169  EVQFDQNDLLYVYLDRRRRRRKFLLTTLLRAMGYSSD---------------ADILNLFY 213

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
               D+ V                                         +  + +  L + 
Sbjct: 214  ELEDITVED--------------------------------------ALKRESVSNLVLT 235

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            EDIV+ + G +   A + + +  +     + ++ +  +   +V++ A IR  L  D  ++
Sbjct: 236  EDIVDADKGVVLARAFEPLTKTIVRSFEQAGLKSVTAIDT-TVDDGAIIR-CLKKDPTQN 293

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             ++AL DIY+ +RPG+  T + A+++   LF D  +YDL  VGR K+N +L +DT  D R
Sbjct: 294  EEEALKDIYKRLRPGEPPTTANAKALLKRLFQDPRRYDLGRVGRYKLNQKLKMDTDLDFR 353

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +  +D++   K L  L+ G GT+DDID+LG+RRVR+VGE+L NQ R GL R ER +KER
Sbjct: 354  VVSADDVVEATKYLTRLKRGDGTLDDIDHLGSRRVRTVGELLANQCRTGLARTERLVKER 413

Query: 490  ISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ++  D   DS+ PQ LIN K + + + +FF  SQLSQ  + +N L+ +TH RRLSALG G
Sbjct: 414  MTLYDQSVDSITPQKLINPKALSTVIRDFFARSQLSQFMDQINPLAELTHKRRLSALGPG 473

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL++++R+N +GFIETPYRKV +
Sbjct: 474  GLNRERAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLSTYSRINEFGFIETPYRKVVE 533

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GKV  +V YL+A  EE   +AQANS +DE+G+     V CR   E I     ++D++D S
Sbjct: 534  GKVLEEVEYLNADMEEPFLVAQANSEMDEEGNLIG-RVTCRRQDEVIETEGTQVDYMDVS 592

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+VS+AA LIPFLE+DD+NR LMG NMQRQ VPLL+AEAPFVGTG+E+ VA  S    
Sbjct: 593  PKQLVSVAAGLIPFLEHDDANRALMGSNMQRQGVPLLQAEAPFVGTGIENRVAIDSKTVE 652

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDL-------DPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            ++   G+V  VDA R+++                   G+ +Y L KF RSN  TC NQ+P
Sbjct: 653  ISDIDGVVASVDARRVIVTEDGELPARAKQLKTDPKKGIYVYNLRKFMRSNAGTCFNQKP 712

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +V  G  V++  ++ADG ST+ GDLA+GRN+LVAFMPW+GYNFED++LISE++V ED+FT
Sbjct: 713  IVSKGQPVKKGQVLADGASTEDGDLAIGRNILVAFMPWNGYNFEDAILISEKIVKEDIFT 772

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIH++EFEV ARDTKLGPEEITRDIPNV EE LK+++  G+I VGAEV PGDILVGKITP
Sbjct: 773  SIHVDEFEVTARDTKLGPEEITRDIPNVGEEALKDLNHDGVIRVGAEVKPGDILVGKITP 832

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K E+ + PEEKLLRAIFGEKA DV+DTSL VPSGV G V+DV++  R   +  + S S  
Sbjct: 833  KSETELAPEEKLLRAIFGEKAADVKDTSLVVPSGVRGIVMDVKVSARVDGEPEQMSASDR 892

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL------SSDLIS 1014
            R QI+ +  +   +   L  ++   L  IL G+      K  +   V+       +  + 
Sbjct: 893  RRQIKKINEEYRSQSDRLREDLTEALSNILLGEKIPLDVKNGETDEVIIPANRKITKTLL 952

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                +      +    V+  +  +   Y+     L+   + KIE I+ G+D   GV++ V
Sbjct: 953  RRLAAVSKHIEIDPSPVKIKIMEIVNNYQGKFDELDYDRERKIEGIESGEDADQGVIKSV 1012

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A KR +Q GDKMAGRHGNKG+V++I+P EDMP+L DGTPV+I LNPLGVPSRMNVG
Sbjct: 1013 KVYIAKKRKMQVGDKMAGRHGNKGVVAKIVPEEDMPYLPDGTPVEICLNPLGVPSRMNVG 1072

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ ETHLGWAC  LG K+ + I D  +   +                             
Sbjct: 1073 QVLETHLGWACKKLGIKVATPIFDGISEKRVREYLDEAGLPSTG---------------- 1116

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                      SML        G++       GE   + V VGY+
Sbjct: 1117 -------------------------KSMLI------DGRT-------GEALHQEVVVGYM 1138

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKLNH+V+ K++AR+ G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+
Sbjct: 1139 YMLKLNHLVASKIHARAVGPYSLITQQPLGGKAQYGGQRFGEMEVWALEAYGAAYTLQEL 1198

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDDV GRTR+YES+V G+ + E GTP+SFNVL+KE+Q+L L + LE+    +    
Sbjct: 1199 LTVKSDDVAGRTRIYESLVKGDSSLEAGTPQSFNVLMKEIQSLCLDVQLESKDKFDMGLT 1258

Query: 1375 EE 1376
             +
Sbjct: 1259 AD 1260


>gi|255506893|ref|ZP_05382532.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            D(s)2923]
          Length = 1252

 Score = 1243 bits (3216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDVDSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|15835206|ref|NP_296965.1| DNA-directed RNA polymerase subunit beta [Chlamydia muridarum Nigg]
 gi|270285378|ref|ZP_06194772.1| DNA-directed RNA polymerase subunit beta [Chlamydia muridarum Nigg]
 gi|7388085|sp|P56869|RPOB_CHLMU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|7190626|gb|AAF39421.1| DNA-directed RNA polymerase, beta subunit [Chlamydia muridarum Nigg]
          Length = 1252

 Score = 1243 bits (3216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1369 (43%), Positives = 820/1369 (59%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  +                 D      
Sbjct: 172  EASFDINDLIYIHIDRKKRRRKILAMTFIRALGYST-----------------DADIIEE 214

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              A      +     V                                     L G  +A
Sbjct: 215  FFAVEEHSLRSEKDFV------------------------------------ALVGKVLA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D    
Sbjct: 239  DNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFDS +Y+L  VGR K+N +L     D+  
Sbjct: 297  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDSKRYNLGRVGRYKLNKKLGFPLDDETL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHSSHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE+  IAQA++ LDE   F + + + R  GE        + 
Sbjct: 537  RVVRDGIVTDEIEYMTADVEEDCVIAQASAELDEYNMFKDSVCWARYKGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK 
Sbjct: 597  HMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+VE VD+  IV+              D Y L KF RSN  TC+NQ PL 
Sbjct: 657  SGAIVVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DTYPLKKFLRSNSGTCINQTPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TSI
Sbjct: 712  SVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISEKLIKQDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLIS 1014
              ++ L ++   +   L      +L  +L  + A        S     ++  V   + I 
Sbjct: 892  VHLKDLQKEYKSQLAQLKMEHREKLGALLLNEKAPAAIIHRRSADILVQEGAVFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R 
Sbjct: 952  LLERESLVDLLMAPCDMYDVLKDILSNYETAVQRLEVNYKTEAEHIKEGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S L+DG TGE FD  V VGY
Sbjct: 1108 -------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|166154525|ref|YP_001654643.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            434/Bu]
 gi|166155400|ref|YP_001653655.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            L2b/UCH-1/proctitis]
 gi|226699385|sp|B0B7N1|RPOB_CHLT2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699386|sp|B0BBU6|RPOB_CHLTB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|51538993|gb|AAU06082.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis]
 gi|56544490|gb|AAV92910.1| RpoB [Chlamydia trachomatis]
 gi|165930513|emb|CAP04007.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis 434/Bu]
 gi|165931388|emb|CAP06961.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis
            L2b/UCH-1/proctitis]
          Length = 1252

 Score = 1243 bits (3215), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDTGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIVHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLIAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|255348675|ref|ZP_05380682.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis 70]
 gi|255503215|ref|ZP_05381605.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis 70s]
          Length = 1252

 Score = 1242 bits (3213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIRSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDVDSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGCVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|163783789|ref|ZP_02178773.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880942|gb|EDP74462.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
          Length = 1470

 Score = 1241 bits (3212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 602/1484 (40%), Positives = 865/1484 (58%), Gaps = 136/1484 (9%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            RKFFG+  EII+ P L+ V K+S+++F+ +  AP ER N GL+   ++ FP     G   
Sbjct: 8    RKFFGRRDEIIEPPYLLSVPKSSFENFIQLKKAPHERENIGLEYILRTSFPFVDPDGNIH 67

Query: 74   LEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAVP 101
            +E++ YE                                    K+  D+C  + LTY+ P
Sbjct: 68   MEYLGYEIGDWECNACGYKPESDFLAGWGVDCPKCGGKLVYKEKYTPDECRIKGLTYSAP 127

Query: 102  LKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSP 161
            L++  +L V   ++       ++   + +Y G++PLMT  G+F+I G +R++V+QL RS 
Sbjct: 128  LRVMFKLKVKSKEDGKE----RETPPKKVYFGEIPLMTDWGSFIINGSERVIVNQLIRST 183

Query: 162  GIHFDH--DKGRASLSGKLLYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFL 218
            G+ F+   +K + +   +++Y   IIPD+G  ++ E   + D  H R+DR+ K+   + L
Sbjct: 184  GVFFEEKEEKQKDATITRIIYRASIIPDKGSRIEFELSGTTDTFHARVDRK-KISGIAIL 242

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
             A G ++  EILS FY  +                +      +    +            
Sbjct: 243  RAWGFETAYEILSNFYEGVRKLTLQKGALIDTETGEEYRPEDLEHHYIFA---------- 292

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
                      L++   +   I    +      E ++  E   I +EA  ++  ++  +  
Sbjct: 293  ---ILRYRAKLEDSDKEKEFIEERYIEEWEGLELLLKDER--IKVEAVTILPNENAVKSP 347

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV------ 391
            +++I    +    +      +    V  +   +    ++IY+ +R  +  T  +      
Sbjct: 348  YAKIVVDTLANETTPREPDRMSVVKVPSEFTLKDYGYMEIYKKLRLVETMTMEIENLIER 407

Query: 392  AESMFNFLFFDSDKYDL------------------------------------STVGRVK 415
            A S F   F    +YDL                                      VG+ K
Sbjct: 408  ARSYFEVFFGHITRYDLSKVGRVKINAKVHKLPKTLKPADVDLLDKLPPVALAEDVGKYK 467

Query: 416  MNMRLNLDT-------------------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
               RL  +                     ++ R I   D+I I+K L+DLR  +   DDI
Sbjct: 468  EGTRLTKEVLKDIFKSKKVKEVKIKDYTEEEARFILPVDLINILKYLIDLRFRRERKDDI 527

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI--SSVDIDSVMPQDLINAKPVVSAVC 514
             +LGNRRVRSVGE+L+NQ R G+ +ME+  ++R+   + +  ++ PQDLIN + V +++ 
Sbjct: 528  AHLGNRRVRSVGELLENQVRTGIAKMEKVFRDRVAVINPEDPNIRPQDLINPRYVTNSIT 587

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EF    QLSQ  ++ N LS +TH RRLSALG GG+ R  A  E+RDVHP+HYGRICP ET
Sbjct: 588  EFLKGGQLSQYLDNANPLSALTHKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIET 647

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGLV+S+T +A+VN YGF+ TPYRKV +G VTND+ YL+A EEE+  IAQ ++  
Sbjct: 648  PEGQNIGLVTSMTVYAQVNEYGFLITPYRKVENGTVTNDIDYLAAYEEEDFVIAQ-STPT 706

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DE G    E V  R   +  +V  E++++ID SP+QV+S++ASLIPFLE+DD+NR LMG 
Sbjct: 707  DEKGKILTERVLARHKNDIRIVKPEQVNYIDVSPRQVISVSASLIPFLEHDDANRALMGS 766

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL+  +AP +GTGME  VA+ S + + AKR G+VE+V++ RIV+R    ++DP
Sbjct: 767  NMQRQAVPLIFTQAPLIGTGMEKKVARDSHSVLTAKRGGVVEEVNSARIVVRVNPEEIDP 826

Query: 755  STS---GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            +     G+DIY L KFQR+NQNTCVNQRPLV+ G E++  ++IADG ST  G+LALG+++
Sbjct: 827  NDPLDFGIDIYDLKKFQRTNQNTCVNQRPLVEKGQEIKAGEVIADGQSTFRGELALGKDV 886

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED+++ISER+V EDVFTSIHIEE EV AR+TKLG EEI+R IP V E+
Sbjct: 887  LVAFMPWRGYNFEDAIVISERLVKEDVFTSIHIEELEVEARETKLGEEEISRQIPGVPEK 946

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L ++DE GI+ VG  V PGDILVGK+TPKGE+ +TPEEKLL+AIFGEK+ DV+D+SLR 
Sbjct: 947  ALAHLDELGIVRVGTYVKPGDILVGKVTPKGETQLTPEEKLLQAIFGEKSKDVKDSSLRC 1006

Query: 932  PSGVSGTVVDVRIFNRH-GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
            P GV G V+DV+IF R  G  +N    +VERE++E L  + +  + ++       L  ++
Sbjct: 1007 PPGVEGVVIDVQIFTRRTGERRNMLVDTVEREEMEALKEELERRKNLIIDGRNKVLKGLV 1066

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA------VQDEKVQRNVESLKVQYET 1044
             G+         KK+    + +  ++  S             + +K+   +  +  + +T
Sbjct: 1067 LGKKIEKDVTLRKKTYKAGTKIDEKFLSSFLNFIISKPDNFFKSKKLINQITEVVNKAKT 1126

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
               +L   +  K + +    D+PPGV+ +VKV++A KR I+ GDKMAGRHGNKG++S +L
Sbjct: 1127 QMQMLTKIYDEKKKSLYRKGDLPPGVITLVKVYIAQKRKIKVGDKMAGRHGNKGVISVVL 1186

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL DGTPVD+VLNPLGVPSRMNVGQI ETHLGWA  GLG+KI  +I+       
Sbjct: 1187 PVEDMPFLPDGTPVDVVLNPLGVPSRMNVGQILETHLGWAARGLGRKIGDMISQGLDRKK 1246

Query: 1165 ISPLRSFLEKV-----IGTGSHTEKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGADEEA 1218
            ++     +  +            E ++   DD    + + + + GVP++TP F+GA+EEA
Sbjct: 1247 LTKWFKEIYAIGDITGENAKFIEEFLNSLSDDEFYALVKDYAEKGVPMATPAFEGAEEEA 1306

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  +L+ A L E+G+S LYDG TGEPFD  VTVGY++MLKL HMV DKV+ARSTG YSLV
Sbjct: 1307 IKKLLKRAGLPENGKSTLYDGRTGEPFDFEVTVGYMHMLKLIHMVDDKVHARSTGPYSLV 1366

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDD+ GR++VYE+IV G  T
Sbjct: 1367 TQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDIEGRSKVYEAIVKGRYT 1426

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +  G PESF VLV+E++AL L +   N       ++E   +  K
Sbjct: 1427 YSPGIPESFRVLVRELKALSLDVRCVNGENVGCDQVEMKEEEEK 1470


>gi|15618005|ref|NP_224289.1| DNA-directed RNA polymerase subunit beta [Chlamydophila pneumoniae
            CWL029]
 gi|33241416|ref|NP_876357.1| DNA-directed RNA polymerase subunit beta [Chlamydophila pneumoniae
            TW-183]
 gi|6647782|sp|Q9Z9A0|RPOB_CHLPN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|4376339|gb|AAD18234.1| RNA Polymerase Beta [Chlamydophila pneumoniae CWL029]
 gi|33235924|gb|AAP98014.1| DNA-directed RNA polymerase beta chain [Chlamydophila pneumoniae
            TW-183]
          Length = 1252

 Score = 1241 bits (3211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1369 (43%), Positives = 830/1369 (60%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDIPDLPNLIEIQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   VLEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +PLMT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPLMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+                       
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSD----------------------- 208

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                   +IE    +    L+S K+  +         L G  +A
Sbjct: 209  ---------------------ADIIEEFFTIGESSLRSEKDFAL---------LVGRILA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ++I++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D    
Sbjct: 239  DNIIDEASSLVYGKAGEKLSTAMLKRMLDAGIASVKIAVD--ADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     D+  
Sbjct: 297  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFSIDDEAL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ L+ G  K  +DDID+L NRRVRSVGE+++NQ R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLKMGDEKACVDDIDHLANRRVRSVGELIQNQCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +++AK + S + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKVVSAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA++SLDE   FTE + + R AGE        + 
Sbjct: 537  RIVRDGIVTDEIEYMTADVEEECVIAQASASLDEYNMFTEPVCWVRYAGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E   AK 
Sbjct: 597  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPVVGTGLECRAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+V+ VD  ++V+ +              Y L KF RSN  TC+NQ+PL 
Sbjct: 657  SGAIVVAEEDGVVDFVDGYKVVVAAKHNPTIK-----RTYHLKKFLRSNSGTCINQQPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD + + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ ED +TSI
Sbjct: 712  AVGDVITKGDVIADGPATDRGELALGKNVLVAFMPWYGYNFEDAIIISEKLIREDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVS+E L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSDEVLANLGEDGIIRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
              ++ L +   ++   L      +L  +L  + A +     +       +  +   + I 
Sbjct: 892  VHLKDLQKGYKNQVATLKTEYREKLGALLLNEKAPAAIIHRRTAEIVVHEGLLFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       + + ++   ++ L   YET+   LE  +K ++E I+ GD D+  GV+R 
Sbjct: 952  RIEQEDLVDLLMPNCEMYEVLKGLLSDYETALQRLEINYKTEVEHIREGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPEQRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S LYDG TGE FD  V +GY
Sbjct: 1108 -------------------------IEQGLPEDG-----KSFLYDGKTGERFDNKVVIGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|289525354|emb|CBJ14830.1| DNA-directed RNA polymerase beta chain [Chlamydia trachomatis
            Sweden2]
 gi|296434904|gb|ADH17082.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            E/150]
          Length = 1252

 Score = 1241 bits (3210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTHKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDVDSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGCVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|16753076|ref|NP_445236.1| DNA-directed RNA polymerase subunit beta [Chlamydophila pneumoniae
            AR39]
 gi|7189608|gb|AAF38502.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila pneumoniae
            AR39]
          Length = 1262

 Score = 1241 bits (3210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1369 (43%), Positives = 830/1369 (60%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 16   ERVSVKKKEDIPDLPNLIEIQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 75

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 76   VLEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 124

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +PLMT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 125  GTIPLMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 181

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+                       
Sbjct: 182  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSD----------------------- 218

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                   +IE    +    L+S K+  +         L G  +A
Sbjct: 219  ---------------------ADIIEEFFTIGESSLRSEKDFAL---------LVGRILA 248

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ++I++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D    
Sbjct: 249  DNIIDEASSLVYGKAGEKLSTAMLKRMLDAGIASVKIAVD--ADENHPIIKMLAKDPTDS 306

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     D+  
Sbjct: 307  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFSIDDEAL 366

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ L+ G  K  +DDID+L NRRVRSVGE+++NQ R GL RME+
Sbjct: 367  SQVTLRKEDVIGALKYLIRLKMGDEKACVDDIDHLANRRVRSVGELIQNQCRSGLARMEK 426

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +++AK + S + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 427  IVRERMNLFDFSSDTLTPGKVVSAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 487  ALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 546

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA++SLDE   FTE + + R AGE        + 
Sbjct: 547  RIVRDGIVTDEIEYMTADVEEECVIAQASASLDEYNMFTEPVCWVRYAGEAFEADTSTVT 606

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E   AK 
Sbjct: 607  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPVVGTGLECRAAKD 666

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+V+ VD  ++V+ +              Y L KF RSN  TC+NQ+PL 
Sbjct: 667  SGAIVVAEEDGVVDFVDGYKVVVAAKHNPTIK-----RTYHLKKFLRSNSGTCINQQPLC 721

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD + + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ ED +TSI
Sbjct: 722  AVGDVITKGDVIADGPATDRGELALGKNVLVAFMPWYGYNFEDAIIISEKLIREDAYTSI 781

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVS+E L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 782  YIEEFELTARDTKLGKEEITRDIPNVSDEVLANLGEDGIIRIGAEVKPGDILVGKITPKS 841

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 842  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 901

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
              ++ L +   ++   L      +L  +L  + A +     +       +  +   + I 
Sbjct: 902  VHLKDLQKGYKNQVATLKTEYREKLGALLLNEKAPAAIIHRRTAEIVVHEGLLFDQETIE 961

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       + + ++   ++ L   YET+   LE  +K ++E I+ GD D+  GV+R 
Sbjct: 962  RIEQEDLVDLLMPNCEMYEVLKGLLSDYETALQRLEINYKTEVEHIREGDADLDHGVIRQ 1021

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN+
Sbjct: 1022 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNL 1081

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1082 GQVLETHLGYAAKTAGIYVKTPVFEGFPEQRIWDMM------------------------ 1117

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S LYDG TGE FD  V +GY
Sbjct: 1118 -------------------------IEQGLPEDG-----KSFLYDGKTGERFDNKVVIGY 1147

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1148 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1207

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1208 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1256


>gi|296438624|gb|ADH20777.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            E/11023]
          Length = 1252

 Score = 1240 bits (3209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTHKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDVDSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGCVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNA-------VSGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKALAAIIHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|301335785|ref|ZP_07224029.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            L2tet1]
          Length = 1252

 Score = 1240 bits (3209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 595/1370 (43%), Positives = 822/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++ +I+                 F 
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTDADIIEE---------------FF 216

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                  +   K                                           L G  +
Sbjct: 217  SVEERSLRSEK---------------------------------------DFVALVGKVL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D   
Sbjct: 238  ADNVVDADSSLVYGKAGEKLSTAMLKRILDTGVQSLKIAV--GADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD+ +Y+L  VGR K+N +L     D+ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +T+ RRL
Sbjct: 416  KIVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTNKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        +
Sbjct: 536  YRVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK
Sbjct: 596  THMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL
Sbjct: 656  DSGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TS
Sbjct: 711  CSVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLI 1013
               ++ L ++   +   L      +L  +L  + A        S     ++  +   + I
Sbjct: 891  AVHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIVHRRSADILVQEGAIFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R
Sbjct: 951  ELLERESLVDLLIAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                      I   L         +S L+DG TGE FD  V VG
Sbjct: 1108 --------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|15835616|ref|NP_300140.1| DNA-directed RNA polymerase subunit beta [Chlamydophila pneumoniae
            J138]
 gi|8978454|dbj|BAA98291.1| RNA polymerase beta [Chlamydophila pneumoniae J138]
          Length = 1252

 Score = 1240 bits (3208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1369 (43%), Positives = 829/1369 (60%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDIPDLPNLIEIQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   VLEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +PLMT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPLMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+                       
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSD----------------------- 208

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                   +IE    +    L+S K+  +         L G  +A
Sbjct: 209  ---------------------ADIIEEFFTIGESSLRSEKDFAL---------LVGRILA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ++I++     +Y +AG+ +    L+ +  + I  + I      + N  I   L  D    
Sbjct: 239  DNIIDEACSLVYGKAGEKLSIAMLKRMLDAGIASVKIAVD--ADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     D+  
Sbjct: 297  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFSIDDEAL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ L+ G  K  +DDID+L NRRVRSVGE+++NQ R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLKMGDEKACVDDIDHLANRRVRSVGELIQNQCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +++AK + S + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKVVSAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA++SLDE   FTE + + R AGE        + 
Sbjct: 537  RIVRDGIVTDEIEYMTADVEEECVIAQASASLDEYNMFTEPVCWVRYAGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E   AK 
Sbjct: 597  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPVVGTGLECRAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+V+ VD  ++V+ +              Y L KF RSN  TC+NQ+PL 
Sbjct: 657  SGAIVVAEEDGVVDFVDGYKVVVAAKHNPTIK-----RTYHLKKFLRSNSGTCINQQPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD + + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ ED +TSI
Sbjct: 712  AVGDVITKGDVIADGPATDRGELALGKNVLVAFMPWYGYNFEDAIIISEKLIREDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVS+E L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSDEVLANLGEDGIIRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
              ++ L +   ++   L      +L  +L  + A +     +       +  +   + I 
Sbjct: 892  VHLKDLQKGYKNQVATLKTEYREKLGALLLNEKAPAAIIHRRTAEIVVHEGLLFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       + + ++   ++ L   YET+   LE  +K ++E I+ GD D+  GV+R 
Sbjct: 952  RIEQEDLVDLLMPNCEMYEVLKGLLSDYETALQRLEINYKTEVEHIREGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPEQRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S LYDG TGE FD  V +GY
Sbjct: 1108 -------------------------IEQGLPEDG-----KSFLYDGKTGERFDNKVVIGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|301336775|ref|ZP_07224977.1| DNA-directed RNA polymerase subunit beta [Chlamydia muridarum
            MopnTet14]
          Length = 1252

 Score = 1240 bits (3208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 595/1369 (43%), Positives = 819/1369 (59%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  +                 D      
Sbjct: 172  EASFDINDLIYIHIDRKKRRRKILAMTFIRALGYST-----------------DADIIEE 214

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              A      +     V                                     L G  +A
Sbjct: 215  FFAVEEHSLRSEKDFV------------------------------------ALVGKVLA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D    
Sbjct: 239  DNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFDS +Y+L  VGR K+N +L     D+  
Sbjct: 297  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDSKRYNLGRVGRYKLNKKLGFPLDDETL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +T  RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTDKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHSSHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE+  IAQA++ LDE   F + + + R  GE        + 
Sbjct: 537  RVVRDGIVTDEIEYMTADVEEDCVIAQASAELDEYNMFKDSVCWARYKGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK 
Sbjct: 597  HMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+VE VD+  IV+              D Y L KF RSN  TC+NQ PL 
Sbjct: 657  SGAIVVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DTYPLKKFLRSNSGTCINQTPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TSI
Sbjct: 712  SVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISEKLIKQDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GI+ +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIVRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLIS 1014
              ++ L ++   +   L      +L  +L  + A        S     ++  V   + I 
Sbjct: 892  VHLKDLQKEYKSQLAQLKMEHREKLGALLLNEKAPAAIIHRRSADILVQEGAVFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R 
Sbjct: 952  LLERESLVDLLMAPCDMYDVLKDILSNYETAVQRLEVNYKTEAEHIKEGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S L+DG TGE FD  V VGY
Sbjct: 1108 -------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|296436756|gb|ADH18926.1| DNA-directed RNA polymerase subunit beta [Chlamydia trachomatis
            G/11222]
          Length = 1252

 Score = 1239 bits (3206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 596/1369 (43%), Positives = 823/1369 (60%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+L+EVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSIKKKEDILDLPNLVEVQIKSYKQFLQIGKLAEERENIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  ++                D      
Sbjct: 172  EAVFDINDLIYIHIDRKKRRRKILAMTFIRALGYSTD---------------ADIIEEFF 216

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
            S  +  +                               L++  V         L G  +A
Sbjct: 217  SVEERSL------------------------------HLEKDFVA--------LVGKVLA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +++V+ ++  +Y +AG+ +    L+ I  + ++ + I      + N  I   L  D    
Sbjct: 239  DNVVDADSSLVYGKAGEKLSTAMLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T   A S    LFFD+ +Y+L  VGR K+N +L     D+  
Sbjct: 297  YEAALKDFYRRLRPGEPATLVNARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ LR G  K +IDDID+L NRRVRSVGE+++N  R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLRMGDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +I+AK +VS + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKIISAKGLVSVLKDFFSRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA++ LDE   F   + + R  GE        + 
Sbjct: 537  RVVRDGIVTDEIEYMTADVEEECVIAQASAELDEYDMFKTPVCWARYKGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VS+   LIPFLE+DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK 
Sbjct: 597  HMDVSPKQLVSVVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA IVA+  G+VE VD+  IV+              D Y+L KF RSN  TC+NQ PL 
Sbjct: 657  SGAIIVAQEDGVVEYVDSYEIVVAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V   D++ADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI
Sbjct: 712  SVGDVVTHGDVLADGPATDKGELALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E G++ +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGVVRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLIS 1014
              ++ L ++   +   L      +L  +L  + A        S     ++  +   + I 
Sbjct: 892  VHLKDLQKEYKSQLAQLKVEHREKLGALLLNEKAPAAIIHRRSADILVQEGAIFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               R       +    +   ++ +   YET+   LE  +K + E I+ GD D+  GV+R 
Sbjct: 952  LLERESLVDLLMAPCDMYDVLKDILSSYETAVQRLEVNYKTEAEHIKEGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMPFL +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPFLANGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I   L         +S L+DG TGE FD  V VGY
Sbjct: 1108 -------------------------IEQGLPEDG-----KSYLFDGKTGERFDSKVVVGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|298501290|ref|ZP_07011087.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MAK 757]
 gi|297539981|gb|EFH76045.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae MAK 757]
          Length = 1121

 Score = 1239 bits (3205), Expect = 0.0,   Method: Composition-based stats.
 Identities = 600/1140 (52%), Positives = 819/1140 (71%), Gaps = 21/1140 (1%)

Query: 229  LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
            +  F+ K+ +  +       L    L  G   +  +     G+  +E G+++T+  ++ L
Sbjct: 1    MDIFFEKVNFEVKDQTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQL 57

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            ++ GV F+ +  + + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+
Sbjct: 58   EKDGVNFIEVPVEYIVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLF 117

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
             + +++  ++  TL  D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDL
Sbjct: 118  TNDLDHGPFMSETLRVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDL 177

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            STVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVG
Sbjct: 178  STVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVG 237

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            EM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  + 
Sbjct: 238  EMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQ 297

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 298  NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSA 357

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R
Sbjct: 358  FARCNEYGFLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTAR 417

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              GE  L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E 
Sbjct: 418  QKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEK 477

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ 
Sbjct: 478  PLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYT 537

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L
Sbjct: 538  RSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSIL 597

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SER+V +D FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV
Sbjct: 598  VSERVVQDDRFTTIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEV 657

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R 
Sbjct: 658  KGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRD 717

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  
Sbjct: 718  GVEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------Y 764

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +   +    R +W +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ P
Sbjct: 765  TEAKLGSIERKKWLEQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAP 824

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVP
Sbjct: 825  GVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVP 884

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKIS 1186
            SRMN+GQI E HLG A  G+G KI  +I   K   +++ LR FL+KV   G       IS
Sbjct: 885  SRMNIGQILEVHLGLAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDIS 941

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
            +  D+ V  +A   ++G+PV+TPVFDGA E +I +ML +ADL  S Q  L+DG TG+ F+
Sbjct: 942  ELSDEDVRTLAHNLRAGLPVATPVFDGAPESSIKAMLELADLPASRQLTLFDGRTGDAFE 1001

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1002 RPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1061

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQEMLT+KSDDV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 1062 AAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 1121


>gi|297170771|gb|ADI21793.1| hypothetical protein [uncultured gamma proteobacterium HF0130_22O14]
          Length = 1198

 Score = 1239 bits (3205), Expect = 0.0,   Method: Composition-based stats.
 Identities = 601/1206 (49%), Positives = 843/1206 (69%), Gaps = 15/1206 (1%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK FGK    +D+PDL+ +Q  SY+ FL  ++ P++R N GLQA F ++
Sbjct: 1    MSFSFTEKKRIRKDFGKQKPALDVPDLLTLQVNSYEGFLQKDVDPEKRENVGLQATFNNL 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KS 121
            FPI +FS  A LEFVSY  + P+F+  +C  R L+Y+ PL++  +LI +D        K 
Sbjct: 61   FPIESFSKNARLEFVSYRLEEPEFNERECQLRGLSYSAPLRVKTKLITYDKTTEKETVKE 120

Query: 122  IKDIKEQ----SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
            +KDIK+      +Y G++PLMT+ GTF+I G  R++VSQLHRSPG+ FDHDKG    SGK
Sbjct: 121  VKDIKQTGDTTDVYFGEIPLMTEHGTFIINGTDRVIVSQLHRSPGVFFDHDKG-VQTSGK 179

Query: 178  LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            LL++ R+IP +G W+D EFD+KD I  RIDRRRK+P T  L AL    ++I+  F+ +  
Sbjct: 180  LLFSARVIPYRGSWLDFEFDAKDSIFARIDRRRKIPATILLHALDFTDQDIIDIFFDEDS 239

Query: 238  YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            Y          ++  D + G      +      + ++  GK++ +  +K + E   K+L 
Sbjct: 240  YRLSKKAIEVKIN-TDHLKGTIAEFDIKFGR--KLIVSKGKRINALHIKQILETKKKYLE 296

Query: 298  ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            I    L G  ++++IV+ +TGEI   A D +  + +E      ++DI  +Y++ V+   Y
Sbjct: 297  IEESDLLGKVLSQEIVDKKTGEIIANANDEVTTELIELFKEHGVKDINTIYINDVDQGPY 356

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I N+L  D + D++ AL++IYR+MRPG+  T   A+++F  LFF+ ++YDLS VGR+K N
Sbjct: 357  ISNSLRIDPSSDKESALIEIYRMMRPGEPPTKEAADNLFTNLFFNDERYDLSEVGRMKFN 416

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             R+ +D       + KEDII ++K L+++RNG  T+DDID+LGNRR+R+VGEM +N +R+
Sbjct: 417  RRVGIDKDVGSSVLSKEDIINVLKTLINIRNGSDTVDDIDHLGNRRIRTVGEMAENAFRV 476

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+R+ER+++ER+S V+ + +MP+DLIN+KPV +A+ EFF SSQLSQ  +  N LS I H
Sbjct: 477  GLIRVERAVRERLSLVEQEELMPRDLINSKPVSAAIKEFFGSSQLSQFMDQNNPLSEIAH 536

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +ARVN YGF
Sbjct: 537  KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMAIYARVNEYGF 596

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +ETPYR+V +GK TN + YLSA++E N  IAQAN++LD   +   EL+  R   E  L+P
Sbjct: 597  LETPYRQVSNGKATNKIKYLSAIDEGNFVIAQANTTLDSKNNLVNELISARYQNEFTLMP 656

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             + I+++D SPKQ+VSIAASLIPFLE+DD+NR LMG NMQRQAVP L A+ P VGTGME 
Sbjct: 657  PDSIEYMDVSPKQIVSIAASLIPFLEHDDANRALMGSNMQRQAVPTLLADKPLVGTGMER 716

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             VA  SG  IVA+R G V+ VDA R+VI   + +     SGVDIY L K+ RSNQNTC+N
Sbjct: 717  KVATDSGVTIVARRGGTVDSVDASRVVIAVNDDEAITGESGVDIYNLTKYTRSNQNTCIN 776

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QRPLVKVGD +++ D+IADG ST LG+LA+G+N+LVAFMPW+G+NFEDS+LISER+V ED
Sbjct: 777  QRPLVKVGDSIQKGDVIADGASTSLGELAIGQNLLVAFMPWNGFNFEDSILISERVVQED 836

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             FT+IHIEE + +ARDTKLG EE+T DIPNV +  L+ +DE GI  +GAEV  GDILVGK
Sbjct: 837  RFTTIHIEELQCIARDTKLGSEEVTADIPNVGDTALRKLDESGIAYIGAEVVAGDILVGK 896

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ITPKGES +TPEEKLLRAIFGEKA DV+DTSLRVPSG+ GTV+DVR+F+R G++K++RS 
Sbjct: 897  ITPKGESQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMDGTVIDVRVFSREGVEKDDRSN 956

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
             +E   I+ + +D  D+  I++ +I++RL ++L  +NA  G K  K    +   L+    
Sbjct: 957  EIEAADIDSVRKDLKDQLRIVESDIFNRLEKLLLNKNAKVGRKTVK----IDKALLESMQ 1012

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            + +W++  +Q++K+   +E+    ++  +   + + +   +KI+  D++PPGVL++VKVF
Sbjct: 1013 QHKWFEIKLQNQKLNNELETYYKAHKELEKEFKQKLEAARKKIEAFDELPPGVLKMVKVF 1072

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A+KR +Q GDK+AGRHGNKG++SRI+P EDMP+++DGTPVDIVLNPLGVPSRMNVGQI 
Sbjct: 1073 LAVKRRVQPGDKVAGRHGNKGVISRIVPVEDMPYMEDGTPVDIVLNPLGVPSRMNVGQIL 1132

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK--ISDYDDDSVLR 1195
            ETHLGWA  GLG K+K ++ + +    +  LR+FL+KV  T + +EK  ++   DD VL 
Sbjct: 1133 ETHLGWAAKGLGNKVKIMLKEKEGAARVKALRTFLDKVYNTNNLSEKVPLNKLKDDEVLE 1192

Query: 1196 VAEQWK 1201
            ++E  K
Sbjct: 1193 LSENLK 1198


>gi|289548398|ref|YP_003473386.1| DNA-directed RNA polymerase subunit beta [Thermocrinis albus DSM
            14484]
 gi|289182015|gb|ADC89259.1| DNA-directed RNA polymerase, beta subunit [Thermocrinis albus DSM
            14484]
          Length = 1469

 Score = 1238 bits (3203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 614/1486 (41%), Positives = 859/1486 (57%), Gaps = 140/1486 (9%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RKFFG+  E+++ P L+ + K S++ FL    AP ER  +GL+  F++ FP        
Sbjct: 8    LRKFFGRRNELVEPPYLLFLPKESFESFLQFRKAPHERELKGLEYLFRTSFPFKDPDEKI 67

Query: 73   MLEFVSYEFDP----------------------------------PKFDVDDCLWRDLTY 98
             +E++ YE                                      KF V++C  +  TY
Sbjct: 68   TIEYLGYEVGEWECNKCGYSASKDHSFLGGYGVACPKCGTPLVHKEKFSVEECKVKGFTY 127

Query: 99   AVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLH 158
            AVPL++ +RL             + + ++  +Y G++P+MT+ G+F+I G +R+VV+QL 
Sbjct: 128  AVPLRVMVRLRTKTKKGE----RVGEPRK--VYFGEIPMMTEWGSFIINGSERVVVNQLI 181

Query: 159  RSPGIHFDH--DKGRASLSGKLLYACRIIPDQGLWMDIEFDS-KDIIHVRIDRRRKVPVT 215
            RSPG+ F+   ++ + S   +++Y   IIPD+G  ++ E  +  D++  R+D ++KV  T
Sbjct: 182  RSPGVFFEEKEERPKESTVVRVIYRASIIPDKGSRIEFELSTTSDVLVTRVD-KKKVGST 240

Query: 216  SFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
              L A G++ S +IL  FYP+       D   F     +      +    +         
Sbjct: 241  FVLRAFGLENSYQILKAFYPETKGFIVRDGLLFHQETGEEFSIEDLEGHHLFA------- 293

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
                         L+ KG +   I    L  L   E ++  +   I ++    +  +S  
Sbjct: 294  ------IMRYRGVLEGKGTEEEFIEERYLEELSQLERLLKDDR--IKLDLVVAVPRESAL 345

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV--- 391
            +        +  L  +    +       +  K   R  AL+DIY+ +R  +     +   
Sbjct: 346  KSP-YGKVILETLIAECSPRDQGRSPMRIPSKFSLRDIALVDIYKKLRAVEPMVMELEHL 404

Query: 392  ---AESMFNFLFFDSDKYDLSTVGRVKMNMRLNL-------------------------- 422
               A + F+  F D  +YDLS VGRVK+N ++                            
Sbjct: 405  VSRARTHFSVYFGDLTRYDLSRVGRVKINAKVYKVPKVLKADDIGRLGELPPLALAESVG 464

Query: 423  ---------------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                                        T D  R +  +D++  +K L++LR G+   DD
Sbjct: 465  PYKEGQLVTEEILKEVFKEKAEVKVKDYTEDKARFLTAQDLVNTVKYLINLRYGREKKDD 524

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAV 513
            I  LGNRRVRSVGE+L+ Q R+G+ RME+  ++R +  + D  ++ PQDL+  + + S +
Sbjct: 525  IAYLGNRRVRSVGELLEGQARVGIARMEKYFRDRCTVVNPDDPNLKPQDLLQPRYLTSTI 584

Query: 514  CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
             EF     LSQ  ++ N LS  TH RRLSALG GG+ R  A  E+RDVHP+HYGRICP E
Sbjct: 585  YEFLKGGALSQYLDNTNPLSATTHKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIE 644

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG NIGLV+SLT +A+VN YGFI TPYRKV +GKVT+ V YL+A EEEN  IAQ  + 
Sbjct: 645  TPEGQNIGLVTSLTVYAQVNEYGFIITPYRKVVEGKVTDQVEYLAAYEEENYVIAQY-TP 703

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
              +DGS   + V+ R   +  +V  +++D++D SP+QVVS+++SLIPFLE+DD+NR LMG
Sbjct: 704  YSKDGSILADRVYARYKNDIQVVRPQQVDYMDVSPRQVVSVSSSLIPFLEHDDANRALMG 763

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG--- 750
             NMQRQAVPL+   AP VGTGME  VA  SGA ++AKR G+VE+VDA RIVIR       
Sbjct: 764  SNMQRQAVPLIFPRAPLVGTGMERKVAYDSGALVLAKRGGVVEEVDARRIVIRVNPDEID 823

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
              DP+  G+DIY L KF R+NQNTC+NQRPLV  G +V++ D+IADG ST  G+LALGR+
Sbjct: 824  MNDPTDIGIDIYLLEKFARTNQNTCINQRPLVTKGQKVKKGDVIADGQSTYKGELALGRD 883

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +LVAFMPW GYNFED+++ISER+V +DV+TSIHIEE EV AR+TKLG EEITR IP V E
Sbjct: 884  VLVAFMPWRGYNFEDAIVISERLVRDDVYTSIHIEELEVEARETKLGYEEITRSIPGVPE 943

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            + L ++DE GI+ +G  V PGDILVGK++PKGES +TPEEKLL+AIFGEK+ DV+DTSLR
Sbjct: 944  KALAHLDEFGIVKIGTYVKPGDILVGKVSPKGESQLTPEEKLLQAIFGEKSRDVKDTSLR 1003

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
             P GV G VVDVR+F R   ++                  + +++  L      R+++ L
Sbjct: 1004 CPPGVEGIVVDVRVFARKVGERRNYLAEAVERAEREELEKELEKKKRLIIEGRDRVIQGL 1063

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV-------QDEKVQRNVESLKVQYE 1043
                 +      KK T  +  ++ E   SQ   + +        DE +   +  ++ + +
Sbjct: 1064 VVGRKLDKDVTVKKKTYPAGTVVDERIFSQIINYVLTKPDNFFDDEDLCNKIREIRDRAK 1123

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                 +   ++ KI+ I    D+P GV+ +VKV++A KR I+ GDKMAGRHGNKG++S +
Sbjct: 1124 AQTEAITRIYEEKIKSIGSRTDLPQGVIALVKVYIAQKRKIKVGDKMAGRHGNKGVISVV 1183

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMPFL DGTPVDIVLNPLGVPSRMNVGQI ETHLGWA   LGKK+  L    +   
Sbjct: 1184 LPVEDMPFLPDGTPVDIVLNPLGVPSRMNVGQILETHLGWAARELGKKVGELFRRTRDRV 1243

Query: 1164 DISPLRSFLEKVIGTGSHTE------KISDYDDDSVLRVAEQWKS-GVPVSTPVFDGADE 1216
             +      +  V  T            I+   D+ +  V  Q++  G+P++TPVF+GA E
Sbjct: 1244 AVLEFLKKIYAVGDTEDGQNVRALEDFINSLSDEELEAVVSQYEEQGIPMATPVFEGASE 1303

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            E I  +LRMA L E G+++LYDG TGEPFD  VTVGY++MLKL HMV DK++ARSTG YS
Sbjct: 1304 EHIKELLRMAGLPEDGKTVLYDGRTGEPFDMRVTVGYMHMLKLIHMVDDKIHARSTGPYS 1363

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDD+ GR+ VYE+IV G 
Sbjct: 1364 LVTQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDIEGRSNVYEAIVKGR 1423

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             T+  G PESF VLV+E++ALGL +  EN  +    K+++  +   
Sbjct: 1424 YTYTPGIPESFRVLVRELKALGLDVKCENGGSAPCDKVQKQEEDET 1469


>gi|297620829|ref|YP_003708966.1| DNA-directed RNA polymerase beta chain [Waddlia chondrophila WSU
            86-1044]
 gi|297376130|gb|ADI37960.1| DNA-directed RNA polymerase beta chain [Waddlia chondrophila WSU
            86-1044]
          Length = 1256

 Score = 1237 bits (3200), Expect = 0.0,   Method: Composition-based stats.
 Identities = 595/1377 (43%), Positives = 841/1377 (61%), Gaps = 149/1377 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R  F ++ EIID+P+LIE+Q  S++ FL ++  P+ER N GLQ  +  +FPI ++    +
Sbjct: 8    RVSFKESKEIIDLPNLIEIQIKSFNQFLQIDKYPEERDNIGLQEVYNEIFPIKSYDEKTI 67

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            +EF+SY    PK+  D+C+ R ++Y V LK+  RL      + TG      IKE+ +YMG
Sbjct: 68   IEFLSYSLGVPKYPPDECIRRGISYNVTLKVKFRLT-----DETG------IKEEEVYMG 116

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P+MT  GTF+I G +R+VVSQLHRSPGI F+ ++      G +LY+ RIIP +G W++
Sbjct: 117  TIPIMTDKGTFIINGAERVVVSQLHRSPGICFEQER---HPRGNILYSFRIIPYRGSWLE 173

Query: 194  IEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
              FD+ D+IH+ IDR   RRK+  T+F+ +LG  +  +I+  F+                
Sbjct: 174  GAFDTNDMIHIYIDRKKRRRKILATTFIRSLGYSTNADIIEEFFST-------------- 219

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                               +K   EK         + L G  +A
Sbjct: 220  ---------------------------------RKMKIKSEKD-------FEKLVGKILA 239

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ED+++ E+G I+ +AG+ +    L+ +  S+I  + I   +  +  + I   L  D    
Sbjct: 240  EDVLDEESGLIFGKAGEKLTTAMLKRMADSDISMVRI--AEDADETSPIIKMLAKDPTDS 297

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             + AL D YR +RPG+ +T S A S    LFFD  +Y+L  VGR K+N +L  +  D+V 
Sbjct: 298  YETALKDFYRKIRPGEPATLSNARSAMMRLFFDPKRYNLGRVGRYKLNSKLGCEVNDEVL 357

Query: 430  ---HIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                + K+D+I  +K L+ LR+G     IDDID+LGNRRVRSVGE+++NQ R+GL RME+
Sbjct: 358  EVVTLSKDDVINAVKYLIRLRSGDENAYIDDIDHLGNRRVRSVGELIQNQCRIGLARMEK 417

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             I+ER++  D   D++ P  +++AK +   + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 418  IIRERMNLFDFTSDTLTPGKIVSAKGLSGVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 477

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +LG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 478  SLGPGGLNRDRAGFEVRDVHTSHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 537

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT ++ Y++A +EEN  IAQA+ SLDE   F +E+ + R  GE + +   ++ 
Sbjct: 538  RIVRDGVVTEEIEYMTADQEENCVIAQASVSLDEFNMFEDEICWARYRGEPLEIESSRVT 597

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQ VPLL  EAP VGTG+E+  A+ 
Sbjct: 598  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQGVPLLAPEAPIVGTGLEARAARD 657

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA ++A+  G V+ +D  +IVI   +  ++        Y L KF RSN  +C+NQ+PL 
Sbjct: 658  SGAVVIAEEDGTVQYIDGNKIVIAPKKNPMEK-----KTYLLKKFMRSNSGSCINQKPLC 712

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVG++++  D+IADGP+TD G++ALGRN+LVAFMPW GYN+ED+++ISE+++ ED +TSI
Sbjct: 713  KVGEKIKSGDVIADGPATDNGEIALGRNVLVAFMPWMGYNYEDAIIISEKLLREDAYTSI 772

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            ++EEFE+ ARDTKLG EEITRDIPNVSE+ L N+ + GII +GAEV PGDILVGKITPK 
Sbjct: 773  YVEEFELTARDTKLGKEEITRDIPNVSEDALINLGDDGIIRIGAEVKPGDILVGKITPKS 832

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K +  +  E 
Sbjct: 833  ETELAPEERLLRAIFGEKAADVKDASLVVPPGTEGVVMDVKVFSRRDRLSKTDEELVEEA 892

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
             +++ L R+   ++  L    + RL  +L    A       K       +  +L+ D+I 
Sbjct: 893  SRLKDLQREYKQKRSELKMERHERLGALLLNDKAPGTIVHRKTAEIVLEEGVLLTQDVIE 952

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
             +         + + +V + ++ +   Y+     LE  FK ++E ++ GD D+  GV+R 
Sbjct: 953  TFEDYNVDDLIMPENQVYQTLKQVLHDYDVKLQTLETHFKTQLEHLKKGDTDLEAGVIRQ 1012

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS I+P  DMPFL+ G  V+++LNPLGVPSRMN+
Sbjct: 1013 VKVYVASKRKLQVGDKMAGRHGNKGVVSNIVPEADMPFLESGQTVEMILNPLGVPSRMNM 1072

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+FETHLG+A    G KIK+ + +     +I  +              +          
Sbjct: 1073 GQLFETHLGFAAKLKGIKIKTPVFEGFPEEEIWKMMKEQGLPENGKFFLQ---------- 1122

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                                  G++       G  FD  V VGY
Sbjct: 1123 -------------------------------------DGRT-------GNRFDNTVVVGY 1138

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+V+DK++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW  +AYGAA++LQE
Sbjct: 1139 IYMLKLSHLVADKIHARAVGPYSLVTQQPLGGKAQMGGQRFGEMEVWAAEAYGAAHLLQE 1198

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ L L +  E+     
Sbjct: 1199 LLTVKSDDVTGRTRIYESIVKGENVLRSGTPESFNVLIKEMQGLCLDVRTESVEESE 1255


>gi|29840449|ref|NP_829555.1| DNA-directed RNA polymerase subunit beta [Chlamydophila caviae GPIC]
 gi|41017695|sp|Q822J1|RPOB_CHLCV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|29834798|gb|AAP05433.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila caviae GPIC]
          Length = 1252

 Score = 1233 bits (3191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 593/1370 (43%), Positives = 835/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERDNVGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R++VSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVIVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+                   
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAMTFIRALGYSSDADIIEE----------------- 214

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   ++E+ +K        L G  +
Sbjct: 215  ------------------------------------FFQIEERSLKSEK-DFTLLVGKIL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++++  +  +Y +AG+ +    L+ +  ++I  + I      + N  I   L  D   
Sbjct: 238  ADNVLDESSSLVYGKAGEKLSTAMLKRMLDADISTLKIAV--EADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFDS +Y+L  VGR K+N +L     ++ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDSKRYNLGRVGRYKLNRKLGFPMDEET 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ L+ G  + +IDDID+L NRRVRSVGE+++NQ R GL RME
Sbjct: 356  LSQVTLRKEDVIGALKYLIRLKMGDERASIDDIDHLANRRVRSVGELIQNQCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + ++ER++  D   D+++P  +I+AK + S + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIVRERMNLFDFSSDTLIPGKIISAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA+++LDE   F + + + RC GE        +
Sbjct: 536  YRIVRDGVVTDEIEYMTADVEEECVIAQASAALDEYNMFVDPVCWARCRGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E+  AK
Sbjct: 596  THMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIVGTGLEARAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA +VA+  G+V+ VD  ++VI                Y L KF RSN  TC+NQRPL
Sbjct: 656  DSGAIVVAEEDGVVDYVDGYKVVIAPKHNPTLK-----RTYDLKKFLRSNSGTCINQRPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD + + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TS
Sbjct: 711  CSVGDVIVKGDVIADGPATDQGELALGKNILVAFMPWYGYNFEDAIIISEKLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIIRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLI 1013
               ++ L +   ++  +L      +L  +L  + A +            ++ TV   + I
Sbjct: 891  AVHLKDLQKGYKNQVSVLKTEYREKLGALLLNEKAPASIIHRRTADILVQEGTVFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                +       +   ++   ++ L   YETS   LE  +K ++E I+ GD D+  GV+R
Sbjct: 951  ELLEQESLVDLLMPPCEMYDVLKGLLSDYETSLQRLEVNYKTEVEHIREGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIHVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    + G+P      DG                  G+       TGE FD  V +G
Sbjct: 1108 -------IEQGLPA-----DGKS------------YLYDGK-------TGERFDNTVVIG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVSGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLDVR 1246


>gi|193214890|ref|YP_001996089.1| DNA-directed RNA polymerase subunit beta [Chloroherpeton thalassium
            ATCC 35110]
 gi|193088367|gb|ACF13642.1| DNA-directed RNA polymerase, beta subunit [Chloroherpeton thalassium
            ATCC 35110]
          Length = 1295

 Score = 1232 bits (3188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 579/1410 (41%), Positives = 818/1410 (58%), Gaps = 174/1410 (12%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F K P++I+ PDL++VQ +SY  FL  ++  D+R ++GL+   +S FPIT   G  
Sbjct: 2    QRVSFAKIPKVIEPPDLLKVQLSSYRSFLQDDLPSDQRNDQGLERVLRSTFPITDTRGLF 61

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY  D PK+ V++C+ R LTY V LK  L+L   D  E    K       Q +Y+
Sbjct: 62   LLEYISYSIDKPKYTVEECIERGLTYDVSLKTRLKLSYKDEPEEVDWKET---IVQDVYL 118

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT+ GTF+I G +R++V+QLHRSPG+ F         +GK +Y+ +I+P +G W+
Sbjct: 119  GKIPYMTERGTFIINGAERVIVAQLHRSPGVVFSE---ATHPNGKKMYSAKIVPLRGSWI 175

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            + + D  + + V ID+++K   TS L A+G    E+IL  F               P S 
Sbjct: 176  EFQTDINNQLFVYIDQKKKFLATSLLRAIGFPRDEDILRVFDLVETLPVD------PNSE 229

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             + ++G  ++S ++D+ TGE +  +   +    ++ + E G++ + ++            
Sbjct: 230  NEHLIGRYLASDIIDMATGEVI-SARTSIGEDEVQKIIEAGIQRVKVSRTE--------- 279

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
                                                  ++  + + I  TL+ DK    +
Sbjct: 280  -------------------------------------KETKLDKSVITTTLLKDKASTEE 302

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD----- 426
            +AL  IY+ +R  +      A  +    FF+  KYDL  VGR ++N +L  +  D     
Sbjct: 303  EALEMIYQELRANEAPDIESARGLLERTFFNLKKYDLGDVGRYRINKKLRYELADIQKFV 362

Query: 427  -------------------------------DVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                                           DV  +   DII+II  L+ L NGK  +DD
Sbjct: 363  KQMPDLDEISKGIEDRIARLVYEVDGKPLDSDVTVLTHYDIISIILYLIKLLNGKTEVDD 422

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +D+L NRRVR+VGE L  Q+ +GL RM ++ KE++++ D + + P DL+NA+ V S +  
Sbjct: 423  VDHLANRRVRTVGEQLSAQFLVGLARMAKNAKEKLNARDAEKITPGDLVNARTVSSVISS 482

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF +SQLSQ  +  N L+ +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET 
Sbjct: 483  FFATSQLSQFMDQTNPLAELTNKRRVSALGPGGLTRERAGFEVRDVHYTHYGRLCPIETP 542

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG NIGL+SS   FA VN  GFIETPYR V +G+V ++V++LSA +EE++     N  LD
Sbjct: 543  EGPNIGLISSFCIFAEVNDKGFIETPYRPVKEGQVQDEVLFLSAEDEESKVTVPVNVKLD 602

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             +     E V  R  G+  +V  E++D+ID +P Q+VS AASLIPFLE+DD+NR LMG N
Sbjct: 603  ANNKIALETVQARRKGDYPVVEAEEVDYIDVAPNQIVSAAASLIPFLEHDDANRALMGSN 662

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPLL +++P+VGTG+E  VA+ S   IVA+  G+VE+V A  + IR  +   D +
Sbjct: 663  MQRQAVPLLISDSPYVGTGLEEKVARDSRTIIVAEGPGVVEKVTAHTVTIRYDKKVDDDN 722

Query: 756  TSG--------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
              G        +  Y ++KF RSNQ+TC+NQ+P+V  G  V++ D++ADG ST+ G+LAL
Sbjct: 723  IEGSLLDTEETIKSYPMIKFSRSNQDTCINQKPIVSKGQRVKKGDVLADGSSTEHGELAL 782

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            G+N+LVAFMPW GYNFED++++SER+V +DVFTSIHI EFE   RDTK G E+ TRDI N
Sbjct: 783  GKNVLVAFMPWRGYNFEDAIVLSERLVYDDVFTSIHIHEFEATVRDTKRGEEQFTRDIYN 842

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            VSEE L+N+DE GII VGAEV   DIL+GKITPKGE+  TPEEKLLRAIFGEK+ DV+D 
Sbjct: 843  VSEEALRNLDENGIIRVGAEVKEKDILIGKITPKGETDPTPEEKLLRAIFGEKSSDVKDA 902

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
            SL VP G+ G V+  ++F+R      ++     + ++E L +    ++  L     +RL 
Sbjct: 903  SLHVPPGMKGVVIKTKLFSR-----KKKVGVDNKVKLEKLEKFFARKENELKEKFLTRLE 957

Query: 988  EIL-----CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD------EKVQRNVE 1036
              L      G   +SG    ++  V S   +         +    D       K+   V+
Sbjct: 958  HYLGGKESIGVKTLSGDVEIRRGNVFSKANLEPLVSIPRLEKIDADHGFVEAAKLNGTVK 1017

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L  +Y      L+D + N+  K+  GD++ PG+  + KV++A KR IQ GDKMAGRHGN
Sbjct: 1018 RLIQEYRMRHKSLQDEYDNERYKLNVGDELQPGIEELAKVYIAQKRKIQVGDKMAGRHGN 1077

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V +++P EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ+FET LGWA   LG K  + I
Sbjct: 1078 KGVVGKVVPVEDMPFMADGTPVDIVLNPLGVPSRMNIGQLFETSLGWAASKLGVKFATPI 1137

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     ++                                     G+PV          
Sbjct: 1138 FDGATYAEVQQKLKDA------------------------------GLPV---------- 1157

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G+  L+DG TGEPFD  VTVGYIYM+KL+H+V DK++ARSTG YS
Sbjct: 1158 --------------HGKIKLHDGRTGEPFDDEVTVGYIYMMKLSHLVDDKIHARSTGPYS 1203

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            L+TQQPLGGK+  GGQR GEMEVW ++AYGA+++LQE+LT+KSDDV GRTR YE+IV G 
Sbjct: 1204 LITQQPLGGKAQFGGQRFGEMEVWALEAYGASHILQEVLTVKSDDVSGRTRTYEAIVKGQ 1263

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +  +   PESFNVL++E+Q LGL I +++ 
Sbjct: 1264 NLPDPNVPESFNVLIRELQGLGLEIRIDDK 1293


>gi|91228701|ref|ZP_01262614.1| DNA-directed RNA polymerase beta subunit [Vibrio alginolyticus 12G01]
 gi|91187727|gb|EAS74046.1| DNA-directed RNA polymerase beta subunit [Vibrio alginolyticus 12G01]
          Length = 1118

 Score = 1231 bits (3185), Expect = 0.0,   Method: Composition-based stats.
 Identities = 593/1135 (52%), Positives = 812/1135 (71%), Gaps = 21/1135 (1%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            ++ +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV 
Sbjct: 3    EVNFEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVD 59

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             + +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++
Sbjct: 60   HIEVPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDH 119

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              ++  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+
Sbjct: 120  GPFMSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRM 179

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 180  KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 239

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 240  FRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 299

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 300  VTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 359

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 360  YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 419

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG
Sbjct: 420  LHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTG 479

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNT
Sbjct: 480  IERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNT 539

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V
Sbjct: 540  CINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVV 599

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 600  QEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDIL 659

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++
Sbjct: 660  VGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDK 719

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S   + 
Sbjct: 720  RALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLD 766

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R +W +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++V
Sbjct: 767  TTDRKKWLELTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIV 826

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+G
Sbjct: 827  KVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIG 886

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDS 1192
            QI E HLG A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD 
Sbjct: 887  QILEVHLGLAAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDE 943

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            V  + +  + G+P++TPVFDGA EE+I ++L +ADL  SGQ  L+DG TG+ F+RPVTVG
Sbjct: 944  VRTLIKNLRGGLPIATPVFDGAPEESIKALLELADLPTSGQLTLFDGRTGDAFERPVTVG 1003

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1004 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 1063

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            EMLT+KSDDV GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 1064 EMLTVKSDDVNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 1118


>gi|288818171|ref|YP_003432519.1| DNA-directed RNA polymerase beta subunit [Hydrogenobacter
            thermophilus TK-6]
 gi|288787571|dbj|BAI69318.1| DNA-directed RNA polymerase beta subunit [Hydrogenobacter
            thermophilus TK-6]
 gi|308751772|gb|ADO45255.1| DNA-directed RNA polymerase, beta subunit [Hydrogenobacter
            thermophilus TK-6]
          Length = 1469

 Score = 1231 bits (3185), Expect = 0.0,   Method: Composition-based stats.
 Identities = 615/1483 (41%), Positives = 875/1483 (59%), Gaps = 139/1483 (9%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            RKFFG+  EI++ P L+ + K S++ FL    +P ER ++GL+  FK+ FP         
Sbjct: 9    RKFFGRRSEILEPPHLLFLPKESFESFLQFKKSPHERESKGLEYIFKTSFPFKDPDEKIT 68

Query: 74   LEFVSYEFDP----------------------------------PKFDVDDCLWRDLTYA 99
            +E++ YE                                      K+ V++C  +  TYA
Sbjct: 69   VEYLGYEVGEWECNRCGYKAYNDQSFLGGYGVKCPKCGTLLTYKEKYTVEECKTKGFTYA 128

Query: 100  VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHR 159
            VPL++ +RL V         K  K ++ + +Y G++P+MT+ G+FVI G +RIVVSQL R
Sbjct: 129  VPLRVLVRLKVK------TKKGEKALEPKKVYFGEIPMMTETGSFVINGSERIVVSQLIR 182

Query: 160  SPGIHFDH--DKGRASLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTS 216
            SPG+ F+   ++ + +   +++Y   IIPD+G  ++ E  S  DI+  R+D ++K+  + 
Sbjct: 183  SPGVFFEEKEERQKDTTIVRIIYRASIIPDKGSRIEFELSSTTDILTARVD-KKKISGSY 241

Query: 217  FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
               A G+++  +IL  FYP+           F     +      +S++ +          
Sbjct: 242  IFRAFGLETAYDILKYFYPETRAFFSEGGRLFDKQTGEEYRVEDLSNNYLFA-------- 293

Query: 276  SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
                        L+ KG +   +    +      + ++  E   I ++    +   S  +
Sbjct: 294  -----ILRYKGKLEGKGKEEEFLEERYIEDAEDLKRLLKDER--IRLDLLTAVPRDSAVK 346

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV---- 391
              + +I    ++   S  +       ++  +   R  AL+DIY+ +R  +     +    
Sbjct: 347  SPYGKIIIETLIAETSPRDPDKRSPIIIPARFTFRDIALVDIYKKLRAVEPMVMELEHLV 406

Query: 392  --AESMFNFLFFDSDKYDLSTVGRVKMN-------------------------------- 417
              A S F+  F D  +YDLS VGRVK+N                                
Sbjct: 407  SRARSHFSLYFEDITRYDLSRVGRVKINAKIHRPPKVLKPADVERLSVLPPLALAEKVSG 466

Query: 418  ---------------------MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                                 +R+   T    R +   D++  +K L+DLR G+   DDI
Sbjct: 467  YIEGELITEQMLKEVFKTKDQVRVRDYTEGAARFVLPVDLVNTVKYLIDLRFGREKKDDI 526

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVC 514
              LGNRRVRS+GE+L+NQ R+G+ RME+  ++R +  + +   + PQDL+N + + SA+ 
Sbjct: 527  AYLGNRRVRSIGELLENQARIGVARMEKFFRDRCTVANPEDPHLKPQDLLNPRYLTSALY 586

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EF     LSQ  ++ N LS +TH RRLSALG GG+ R  A  E+RDVHP+HYGRICP ET
Sbjct: 587  EFLKGGLLSQYLDNTNPLSALTHKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIET 646

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGLV+SLT +A++N +GFI TPYRKV DGKVT+++ YL+A EEEN  IAQ  +  
Sbjct: 647  PEGQNIGLVTSLTVYAQINEFGFIITPYRKVIDGKVTDEIEYLAAYEEENYVIAQY-TPT 705

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DE+G    + V  R   +  +V  ++++++D SP+QVVS++ASLIPFLE+DD+NR LMG 
Sbjct: 706  DEEGKINADRVLARYKNDIQIVKPQQVNYMDVSPRQVVSVSASLIPFLEHDDANRALMGS 765

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL+   +P VGTGME  VA  S A IVAKR GIVE+VD+ RI++R    ++DP
Sbjct: 766  NMQRQAVPLVFTSSPLVGTGMEKKVAYDSAAVIVAKRGGIVEEVDSKRIIVRVNPEEIDP 825

Query: 755  STS---GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            +     G+DIY L K QR+NQNTC+N+RPLV  G +V + D++ADG ST +G+LALG+++
Sbjct: 826  NDPTDIGIDIYELKKMQRTNQNTCINERPLVFKGQKVSKGDVLADGQSTQMGELALGKDV 885

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            LVAFMPW GYNFED+++ISER+V +DVFTSIHIEE EV AR+TK+G EEITR +P + E 
Sbjct: 886  LVAFMPWRGYNFEDAIVISERLVKDDVFTSIHIEELEVEARETKIGYEEITRSVPGIPER 945

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             L ++DE GI+ +G  V PGDILVGK+TPKGE  +TPEEKLL+AIFGEK+ DV+DTSLR 
Sbjct: 946  MLAHLDEFGIVRIGTYVKPGDILVGKVTPKGEQQLTPEEKLLQAIFGEKSRDVKDTSLRC 1005

Query: 932  PSGVSGTVVDVRIFNRH-GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
            P GV G VVDV++F R  G  +N  +  VER++ E L  + +  + +L       + +++
Sbjct: 1006 PPGVEGVVVDVQVFARKVGERRNYLTEHVERQEREALRNELEKRKKLLVEGRNRIIRDLV 1065

Query: 991  CGQNAVSGPKGFKK----STVLSSDLISEYPRSQWWQFA--VQDEKVQRNVESLKVQYET 1044
             G+         KK     TV+              +     +D+ +   +  ++ + + 
Sbjct: 1066 LGKKTDKDITVKKKTYKAGTVIDEKTFEVLLNYIVAKPENLFEDKDLCNRINEIRDRTKA 1125

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
               +LE  +K K E I    ++PPGV+ +VKV++A KR I+ GDKMAGRHGNKG++S +L
Sbjct: 1126 QVELLERIYKEKEESIGKRSELPPGVVTLVKVYIAQKRKIKVGDKMAGRHGNKGVISVVL 1185

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL DGTPVDIVLNPLGVPSRMNVGQI ETHLGWA   LGKK+  LI    +  +
Sbjct: 1186 PVEDMPFLPDGTPVDIVLNPLGVPSRMNVGQILETHLGWALKELGKKLGELIEHMASRQE 1245

Query: 1165 ISPLRSFL------EKVIGTGSHTEKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGADEE 1217
            I      +      +    T      ++   D+  ++V E + + G+PV+T VF+GA+EE
Sbjct: 1246 IVEFLKKVYSVGDTKDGENTKYIESFLNSLSDEDFIKVVESYAEKGIPVATSVFEGANEE 1305

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I  +L+MA L E G+  LYDG TGEPFD  VTVGY+YMLKL HMV DK++ARSTG YSL
Sbjct: 1306 HIKELLKMAGLPEDGRITLYDGRTGEPFDTKVTVGYMYMLKLIHMVDDKIHARSTGPYSL 1365

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDD+ GRT+VYE+IV G  
Sbjct: 1366 VTQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDIEGRTKVYEAIVKGKY 1425

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            T+  G PESF VLV+E++ALGL++  EN  +K   ++E   + 
Sbjct: 1426 TYTPGIPESFRVLVRELKALGLNVKCENGESKPCDQIEIEEEE 1468


>gi|89898127|ref|YP_515237.1| DNA-directed RNA polymerase subunit beta [Chlamydophila felis
            Fe/C-56]
 gi|123483622|sp|Q255E6|RPOB_CHLFF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|89331499|dbj|BAE81092.1| DNA-directed RNA polymerase beta chain [Chlamydophila felis Fe/C-56]
          Length = 1252

 Score = 1229 bits (3180), Expect = 0.0,   Method: Composition-based stats.
 Identities = 592/1369 (43%), Positives = 830/1369 (60%), Gaps = 147/1369 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERDNVGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+                +F+    
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAMTFIRALGYSSD-----------ADIIEEFFQIEE 220

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             +        V                                          L G  +A
Sbjct: 221  CSLKSEKDFSV------------------------------------------LVGKILA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +++++  +  +Y +AG+ +    L+ +  ++I  + I      + N  I   L  D    
Sbjct: 239  DNVLDEASSLVYGKAGEKLSTAMLKRMLDADISTLKI--ALEADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     ++  
Sbjct: 297  YEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFPMDEESL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ L+ G  K +IDDID+L NRRVRSVGE+++NQ R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLKMGDEKASIDDIDHLANRRVRSVGELIQNQCRSGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D+++P  +I+AK + S + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLIPGKIISAKGLTSVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA+++LDE   FT+ + + R  GE        + 
Sbjct: 537  RIVRDGVVTDEIEYMTADVEEECVIAQASANLDEYNMFTDPVCWARYRGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E+  AK 
Sbjct: 597  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIVGTGLEARAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +VA+  G+VE VD  ++V+ +              Y   KF RSN  TC+NQRPL 
Sbjct: 657  SGAIVVAEEDGVVEYVDGYKVVVAAKHNPTLK-----RTYEFKKFLRSNSGTCINQRPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TSI
Sbjct: 712  SVGDIVVKGDVIADGPATDQGELALGKNILVAFMPWYGYNFEDAVIISEKLIKQDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIIRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLIS 1014
              ++ L +   ++  +L      +L  +L  + A +            ++ TV   + I 
Sbjct: 892  VHLKDLQKGYKNQISVLKTEYREKLGALLLNEKAPASIIHRRTADILVQEGTVFDQETIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       +    +   +++L   YETS   LE  +K ++E I+ GD D+  GV+R 
Sbjct: 952  LLEQESLVDLLMPPCDMYDVLKNLLSDYETSLQRLEVNYKTEVEHIREGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  + ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLANGETIQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIHVKTPVFEGFPESRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   + G+P      DG                  G+       TGE FD  V +GY
Sbjct: 1108 ------IEQGLPA-----DGKS------------YLYDGK-------TGERFDNTVVIGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLDVR 1246


>gi|330444699|ref|YP_004377685.1| DNA-directed RNA polymerase subunit beta [Chlamydophila pecorum E58]
 gi|328807809|gb|AEB41982.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila pecorum E58]
          Length = 1252

 Score = 1228 bits (3178), Expect = 0.0,   Method: Composition-based stats.
 Identities = 592/1369 (43%), Positives = 829/1369 (60%), Gaps = 149/1369 (10%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            R    +  +++D+P+LIEVQ  SY  FL +    +ER N GL+  F+ +FPI +++ A +
Sbjct: 7    RVSVKQKEDVLDLPNLIEVQIKSYKQFLQIGKLAEERENVGLEEVFREIFPIKSYNEATI 66

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LE++SY    PK+  ++C+ R +TY+V LK+  RL      + TG      IKE+ +YMG
Sbjct: 67   LEYLSYNLGVPKYSPEECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYMG 115

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
             +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W++
Sbjct: 116  TIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGSILFSFRIIPYRGSWLE 172

Query: 194  IEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
              FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+  F+                
Sbjct: 173  AIFDVNDLIYIHIDRKKRRRKILAMTFIRALGYSSDADIIEEFFQIE------------- 219

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
               + +   K                                           L G  +A
Sbjct: 220  --ENSLRSEK---------------------------------------DFTLLVGKVLA 238

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            +++++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D    
Sbjct: 239  DNVIDETSSLVYGKAGEKLSTAMLKRMLDAGIASLKIAV--GADENHPIIKMLAKDPTDS 296

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD-- 427
             + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     D+  
Sbjct: 297  YESALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNCKLGFPIDDETL 356

Query: 428  -VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +RKED+I  +K L+ L+ G  K T+DDID+L NRRVRSVGE+++NQ R GL RME+
Sbjct: 357  SQVTLRKEDVIGALKYLIRLKMGDEKATVDDIDHLANRRVRSVGELIQNQCRAGLARMEK 416

Query: 485  SIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             ++ER++  D   D++ P  +++AK + S + +FF  SQLSQ  +  N ++ +TH RRLS
Sbjct: 417  IVRERMNLFDFSSDTLTPGKVVSAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRLS 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL++FA++N +GFIETPY
Sbjct: 477  ALGPGGLNRERAGFEVRDVHSSHYGRICPIETPEGPNIGLISSLSAFAKINEFGFIETPY 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V DG VT+++ Y++A  EE   IAQA++SLDE   FTE L + R  GE        + 
Sbjct: 537  RIVRDGVVTDEIEYMAANVEEECVIAQASASLDEFNMFTEPLCWARYRGEAFEADTSTVT 596

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK E P VGTG+E+  AK 
Sbjct: 597  HMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTETPIVGTGLEARAAKD 656

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA +V +  G+VE VD  ++V+ +              Y L KF RSN  TC+NQRPL 
Sbjct: 657  SGAIVVVEEDGVVEYVDGYKVVVAAKYNPTIK-----RTYHLKKFLRSNSGTCINQRPLC 711

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             VGD V + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++  D +TSI
Sbjct: 712  SVGDVVTKGDVIADGPATDRGELALGKNVLVAFMPWYGYNFEDAIIISEKLIKNDAYTSI 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK 
Sbjct: 772  YIEEFELTARDTKLGKEEITRDIPNVSEEILANLGEDGIIRIGAEVKPGDILVGKITPKS 831

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVER 961
            E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E 
Sbjct: 832  ETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELIEEA 891

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLIS 1014
              ++ L ++  ++   L      ++  +L  + A +     +       + T+   ++I 
Sbjct: 892  VHLKDLQKNYKNQVAALKTEYREKIGALLFNEKAPAAIIHRRTADVLVHEGTIFDQEIIE 951

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRV 1073
               +       +   ++   ++ +   YET+   LE  +K +IE I+ GD D+  GV+R 
Sbjct: 952  ILEKEALVDLLMPPCEIYDVLKGMLSDYETALQSLEVNYKTEIEHIREGDADLDHGVIRQ 1011

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN+
Sbjct: 1012 VKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNL 1071

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG+A    G  +K+ + +      I  +                         
Sbjct: 1072 GQVLETHLGYAAKTAGIYVKTPVFEGFPESRIWDMM------------------------ 1107

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   + G+P      DG                  G+       TGE FD  V +GY
Sbjct: 1108 ------IEQGLPA-----DGKS------------FLYDGK-------TGERFDNRVVIGY 1137

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQE
Sbjct: 1138 IYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHLLQE 1197

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +LT+KSDDV GRTR+YESIV G +   +GTPESFNVL+KEMQ LGL + 
Sbjct: 1198 ILTVKSDDVSGRTRIYESIVKGENLLRSGTPESFNVLIKEMQGLGLDVR 1246


>gi|213582505|ref|ZP_03364331.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E98-0664]
          Length = 1116

 Score = 1224 bits (3166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 583/1134 (51%), Positives = 797/1134 (70%), Gaps = 18/1134 (1%)

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            +FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  +
Sbjct: 1    MFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--T 58

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            +KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY 
Sbjct: 59   VKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYN 118

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R
Sbjct: 119  ARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIR 178

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
             +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  +
Sbjct: 179  DNKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVE 235

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T
Sbjct: 236  YIAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISET 295

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            +  D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L 
Sbjct: 296  VRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 355

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 356  RDEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 415

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 416  VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 476  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++
Sbjct: 536  YRRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 596  DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 656  DSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPC 715

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+
Sbjct: 716  VSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTT 775

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            IHI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 776  IHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 835

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E 
Sbjct: 836  GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEE 895

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             Q++   +D  +E  IL+  ++SR+  +L                   ++ + + PR +W
Sbjct: 896  MQLKQAKKDLSEELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRW 942

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+K
Sbjct: 943  LELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVK 1002

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHL
Sbjct: 1003 RRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHL 1062

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            G A  G+G KI +++   +    +         +         +S + DD VLR
Sbjct: 1063 GMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLR 1116


>gi|329943036|ref|ZP_08291810.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila psittaci
            Cal10]
 gi|313848192|emb|CBY17193.1| putative DNA-directed RNA polymerase beta chain [Chlamydophila
            psittaci RD1]
 gi|328814583|gb|EGF84573.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila psittaci
            Cal10]
          Length = 1252

 Score = 1220 bits (3157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1370 (43%), Positives = 831/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERDNIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  D+C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPDECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+                   
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSDADIIEE----------------- 214

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   ++E  +K        L G  +
Sbjct: 215  ------------------------------------FFQIEEHSLKSEK-DFSFLVGKIL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D   
Sbjct: 238  ADNVLDEASSLVYGKAGEKLSTAMLKRMLDANISTLKIAV--EADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     ++ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFPMDEES 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ L+ G  K +IDDID+L NRRVRSVGE+++NQ R GL RME
Sbjct: 356  LAQVTLRKEDVIGALKYLIRLKMGDEKASIDDIDHLANRRVRSVGELIQNQCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + I+ER++  D   D+++P  +I+AK + S + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIIRERMNLFDFSSDTLIPGKIISAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V  G VT+++ Y++A  EE   IAQA+++LDE   F + + + R  GE        +
Sbjct: 536  YRIVRGGVVTDEIEYMTADVEEECVIAQASANLDEYNMFVDPVCWARYRGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E+  AK
Sbjct: 596  THMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIVGTGLEARAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA +VA+  G+VE VD  ++VI +              Y L KF RSN  TC+NQRPL
Sbjct: 656  DSGAIVVAEEDGVVEYVDGYKVVIAAKHNPTLK-----RTYDLKKFLRSNSGTCINQRPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TS
Sbjct: 711  CSVGDVVVKGDVIADGPATDKGELALGKNILVAFMPWYGYNFEDAIIISEKLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIIRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLI 1013
               ++ L +   ++  +L      +L  +L  + A +            ++ TV   + I
Sbjct: 891  AVHLKDLQKGYKNQISVLKTEYREKLGALLLNEKAPASIIHRRTADILVQEGTVFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                +       +    +   ++SL   YETS   LE  +K ++E I+ GD D+  GV+R
Sbjct: 951  ELLEQESLVDLLMPPCDMYDVLKSLLSDYETSLQRLEVNYKTEVEHIREGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIHVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    + G+P      DG                  G+       TGE FD  V +G
Sbjct: 1108 -------IEQGLPA-----DGKS------------YLYDGK-------TGERFDNTVVIG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVTGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLDVR 1246


>gi|62185274|ref|YP_220059.1| DNA-directed RNA polymerase subunit beta [Chlamydophila abortus
            S26/3]
 gi|81312570|sp|Q5L5I3|RPOB_CHLAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|62148341|emb|CAH64108.1| putative DNA-directed RNA polymerase beta chain [Chlamydophila
            abortus S26/3]
          Length = 1252

 Score = 1220 bits (3156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 598/1370 (43%), Positives = 832/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERDNIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  D+C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPDECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+                   
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSDADIIEE----------------- 214

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   ++E  +K        L G  +
Sbjct: 215  ------------------------------------FFQIEEHSLKSEK-DFSFLVGKIL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D   
Sbjct: 238  ADNVLDEASSLVYGKAGEKLSTAMLKRMLDANISTLKIAV--EADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     ++ 
Sbjct: 296  SYEAALKDFYRRLRPGEPATLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFPMDEES 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ L+ G  K +IDDID+L NRRVRSVGE+++NQ R GL RME
Sbjct: 356  LAQVTLRKEDVIGALKYLIRLKMGDEKASIDDIDHLANRRVRSVGELIQNQCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + I+ER++  D   D+++P  +I+AK + S + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIIRERMNLFDFSSDTLIPGKIISAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V DG VT+++ Y++A  EE   IAQA+++LDE   F + + + R  GE        +
Sbjct: 536  YRIVRDGVVTDEIEYMTADVEEECVIAQASANLDEYNMFVDPVCWARYRGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E+  AK
Sbjct: 596  THMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIVGTGLEARAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA +VA+  G+VE VD  ++VI +              Y L KF RSN  TC+NQRPL
Sbjct: 656  DSGAIVVAEEDGVVEYVDGYKVVIAAKHHPTLK-----RTYDLKKFLRSNSGTCINQRPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TS
Sbjct: 711  CSVGDVVVKGDVIADGPATDKGELALGKNILVAFMPWYGYNFEDAIIISEKLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIIRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLI 1013
               ++ L +   ++  +L      +L  +L  + A +            ++ TV   + I
Sbjct: 891  AVHLKDLQKGYKNQISVLKIEYREKLGALLLNEKAPASIIHRRTADILVQEGTVFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                +       +    +   ++SL   YETS   LE  +K ++E I+ GD D+  GV+R
Sbjct: 951  ELLEQESLVDLLMPPCDMYDVLKSLLSDYETSLQRLEVNYKTEVEHIREGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIHVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    + G+P      DG                  G+       TGE FD  V +G
Sbjct: 1108 -------IEQGLPA-----DGKS------------YLYDGK-------TGERFDNTVVIG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVTGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLDVR 1246


>gi|195952636|ref|YP_002120926.1| DNA-directed RNA polymerase subunit beta [Hydrogenobaculum sp.
            Y04AAS1]
 gi|195932248|gb|ACG56948.1| DNA-directed RNA polymerase, beta subunit [Hydrogenobaculum sp.
            Y04AAS1]
          Length = 1470

 Score = 1220 bits (3156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 574/1481 (38%), Positives = 857/1481 (57%), Gaps = 138/1481 (9%)

Query: 10   LGRV-RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
               + RKFFG+  E++D+P L++V   S+++F+  N+ P +R  +GL+   ++ FP    
Sbjct: 5    KHAIPRKFFGRRSELLDLPFLVKVPTESFENFIQFNVPPTKRKEQGLEYILRTSFPFQDT 64

Query: 69   SGAAMLEFVSYEFD--------------------------------PPKFDVDDCLWRDL 96
            +    +E++ YE                                    K+  ++C  + +
Sbjct: 65   NKNITVEYIGYEIGNWECNKCGYKPETDFLAGADTECPKCKTILSYKEKYTPEECKEKGI 124

Query: 97   TYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQ 156
            TY+ P++I LRL              K      IY G++P+MT  GTFVI G +R+VV+Q
Sbjct: 125  TYSAPIRIMLRLRKKTKSGEFVDTPKK------IYFGEMPMMTPIGTFVINGSERVVVNQ 178

Query: 157  LHRSPGIHF--DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVP 213
            L RSPGI +    D+ +     + ++   I PD+G  ++ E  +  DII  RID++R + 
Sbjct: 179  LIRSPGIFYSDKEDRQKEGTVSRTIFTASIHPDKGSRIEFELSTNSDIISARIDKKR-IS 237

Query: 214  VTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
              S L A G+++  +ILS FY  +      D      +  ++     + S  +       
Sbjct: 238  AISILRAFGLETAYDILSQFYEDVKAFNVKDGLIIDKNTGEVYKPEDLESHYLFA----- 292

Query: 273  VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
                           ++    +   I    +  L V   ++  E   + IE    +  + 
Sbjct: 293  --------VLRYTAKIEGTEKEEEFIEERYIEDLNVLNRLIKDER--VKIELLTAVQSEK 342

Query: 333  LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD------V 386
              + F+ +I    ++      +           +   R   L DIY  +R  +       
Sbjct: 343  TTKSFYGKIILETLINDTKAKDQHGKSLVRTNSQFTLRDIGLRDIYVKLRSMEGLVQEMA 402

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-------------------- 426
                 + + F   F D  ++DLS VGRVK+N ++ +   +                    
Sbjct: 403  DIIQRSRAYFEAYFQDIARFDLSKVGRVKINAKIYIHKRELTEKDLEIFDELPVLELAKD 462

Query: 427  ---------------------------------DVRHIRKEDIIAIIKILVDLRNGKGTI 453
                                             + R +  +D++  IK L+ +R GK   
Sbjct: 463  YDNYKEGTILTKDIFEYILKSHKTIEVRDYTGLEARFLNHKDLVNAIKYLLKVRFGKEKK 522

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVS 511
            DDI +LGNRRVR +GE+L+NQ R+G+ RM +S ++++++++ +      QDL+N++ +VS
Sbjct: 523  DDIAHLGNRRVRPIGELLENQARIGIARMLKSFRDKVATINPEDPTIKAQDLVNSRYLVS 582

Query: 512  AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
            ++ EF    QLSQ  ++ N LS +TH RRLSALG GG+ R  A  E+RDVHP+HYGR+CP
Sbjct: 583  SMFEFLKGGQLSQYLDNSNPLSSLTHRRRLSALGPGGLTRESAKFEIRDVHPSHYGRLCP 642

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             ET EG NIGLV+S+T++A+ N YGF+ TPYRKV +G VT+ + +L+A EEEN  IAQ +
Sbjct: 643  IETPEGQNIGLVTSMTTYAQTNEYGFLVTPYRKVENGIVTDQIEFLAAYEEENFVIAQ-S 701

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  D+ G    + +  R   +  +V    +++ID SP+Q++S++ASLIPFLE+DD+NR L
Sbjct: 702  TPTDQKGKILGDRLIARYKNDIQIVKPSDVNYIDVSPRQIISVSASLIPFLEHDDANRAL 761

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            MG NMQRQAVPL+  +AP +GTGMES VA  SGAAI+AKR G+VE+VD+ RIVIR    +
Sbjct: 762  MGSNMQRQAVPLIFTQAPLIGTGMESKVAIDSGAAILAKRGGVVEEVDSNRIVIRVNPNE 821

Query: 752  ---LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                DP   G+D+Y+L+KF ++NQNT VNQRP+V  G ++++ D IADG ST +G+LALG
Sbjct: 822  INEKDPLDMGIDVYKLLKFTKTNQNTSVNQRPIVYKGQKIKKGDCIADGQSTFMGELALG 881

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +++LV FMPW GYNFED+++ISER+V EDV TS+HIEE +  AR+TK+G EEITR +P V
Sbjct: 882  KDLLVCFMPWRGYNFEDAIVISERLVKEDVLTSVHIEELKAEARETKIGDEEITRQVPGV 941

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            SE+ L  +DE GI+ VG  V PGDILVGK+TP GE+ +TPE+KLL+AIFGEK  DV+D+S
Sbjct: 942  SEKALAYLDEYGIVKVGTYVKPGDILVGKVTPIGETQLTPEQKLLQAIFGEKTRDVKDSS 1001

Query: 929  LRVPSGVSGTVVDVRIFNRHGID--KNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            LR P G+ G VVDV++F R   +  KN     VE+E+   + ++K+    ++       +
Sbjct: 1002 LRCPPGIEGVVVDVQVFTRKLSESKKNPLVEHVEQEEKNRIKKEKEFMLNLVIEKRNEIV 1061

Query: 987  MEILCGQNAVSGPKGFKK----STVLSSDLISEYPRSQWWQFA--VQDEKVQRNVESLKV 1040
             +++ G+      K  KK     TV+   L          +      D+K+ + +E ++ 
Sbjct: 1062 KDLVIGKVINKPIKLAKKTYEEGTVIDEALFDNIANFVITKPENFFSDKKLIKKIEEIRD 1121

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            + +  + +++  ++ KIE +    D+P GV+ +VKV++A KR I+ GDKMAGRHGNKG++
Sbjct: 1122 KAQAQRKVIDKIYEEKIENVGKQSDLPSGVITMVKVYIAQKRKIRVGDKMAGRHGNKGVI 1181

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            S +LP EDMPFL DGTPVD+VLNPLGVPSRMNVGQI ETHLG A   +GKK++ +I++Y 
Sbjct: 1182 SVVLPVEDMPFLPDGTPVDVVLNPLGVPSRMNVGQILETHLGMASKYIGKKVQEMIDEYF 1241

Query: 1161 ANGDISPLRSFL-----EKVIGTGSHTEKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGA 1214
               +I+   + +     +           +    D+    V     ++G+P++TP F+G 
Sbjct: 1242 NRDEITEYIASIYAIGDKNNENKNFIKNMLKSLSDEEFKNVVSFVAQNGIPIATPAFEGC 1301

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ + ++L+ A L E G+ +LYDG TGEPFD  VT GY++MLKL HMV DK++ARSTG 
Sbjct: 1302 SEDDLKTLLKEAGLPEDGKFVLYDGRTGEPFDFRVTTGYMHMLKLIHMVEDKIHARSTGP 1361

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQEMLT+KSDD+ GR R YESIV 
Sbjct: 1362 YSLVTQQPLGGRAQFGGQRLGEMEVWALEAHGAAYTLQEMLTVKSDDIEGRNRAYESIVK 1421

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            G   +  G PESF VLV+E+++LGL++  EN   K+   ++
Sbjct: 1422 GKYFYSPGIPESFKVLVRELKSLGLNVVCENGEAKSCDSVD 1462


>gi|56544492|gb|AAV92911.1| RpoB [Chlamydophila psittaci 6BC]
 gi|325507189|gb|ADZ18827.1| DNA-directed RNA polymerase subunit beta [Chlamydophila psittaci 6BC]
 gi|328914870|gb|AEB55703.1| DNA-directed RNA polymerase, beta subunit [Chlamydophila psittaci
            6BC]
          Length = 1252

 Score = 1220 bits (3156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 597/1370 (43%), Positives = 831/1370 (60%), Gaps = 149/1370 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R    K  +I+D+P+LIE+Q  SY  FL +    +ER N GL+  F+ +FPI +++ A 
Sbjct: 6    ERVSVKKKEDILDLPNLIEIQIKSYKQFLQIGKLAEERDNIGLEEVFREIFPIKSYNEAT 65

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LE++SY    PK+  D+C+ R +TY+V LK+  RL      + TG      IKE+ +YM
Sbjct: 66   ILEYLSYNLGVPKYSPDECIRRGITYSVTLKVRFRLT-----DETG------IKEEEVYM 114

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P+MT  GTF+I G +R+VVSQ+HRSPGI+F+ +K      G +L++ RIIP +G W+
Sbjct: 115  GTIPIMTDKGTFIINGAERVVVSQVHRSPGINFEQEK---HSKGNILFSFRIIPYRGSWL 171

Query: 193  DIEFDSKDIIHVRIDR---RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +  FD  D+I++ IDR   RRK+   +F+ ALG  S+ +I+                   
Sbjct: 172  EAIFDINDLIYIHIDRKKRRRKILAITFIRALGYSSDADIIEE----------------- 214

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                   ++E  +K        L G  +
Sbjct: 215  ------------------------------------FFQIEEHSLKSEK-DFSFLVGKIL 237

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+++++  +  +Y +AG+ +    L+ +  + I  + I      + N  I   L  D   
Sbjct: 238  ADNVLDEASSLVYGKAGEKLSTAMLKRMLDANISTLKIAV--EADENHPIIKMLAKDPTD 295

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD- 427
              + AL D YR +RPG+ +T + A S    LFFD  +Y+L  VGR K+N +L     ++ 
Sbjct: 296  SYEAALKDFYRRLRPGEPTTLANARSTIMRLFFDPKRYNLGRVGRYKLNRKLGFPMDEES 355

Query: 428  --VRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 +RKED+I  +K L+ L+ G  K +IDDID+L NRRVRSVGE+++NQ R GL RME
Sbjct: 356  LAQVTLRKEDVIGALKYLIRLKMGDEKASIDDIDHLANRRVRSVGELIQNQCRSGLARME 415

Query: 484  RSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + I+ER++  D   D+++P  +I+AK + S + +FF  SQLSQ  +  N ++ +TH RRL
Sbjct: 416  KIIRERMNLFDFSSDTLIPGKIISAKGLASVLKDFFGRSQLSQFMDQTNPVAELTHKRRL 475

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL+SFA++N +GFIETP
Sbjct: 476  SALGPGGLNRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETP 535

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            YR V  G VT+++ Y++A  EE   IAQA+++LDE   F + + + R  GE        +
Sbjct: 536  YRIVRGGVVTDEIEYMTADVEEECVIAQASANLDEYNMFVDPVCWARYRGEAFEADTSTV 595

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +D SPKQ+VSI   LIPFLE+DD+NR LMG NMQRQAVPLLK EAP VGTG+E+  AK
Sbjct: 596  THMDVSPKQLVSIVTGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIVGTGLEARAAK 655

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             SGA +VA+  G+VE VD  ++VI +              Y L KF RSN  TC+NQRPL
Sbjct: 656  DSGAIVVAEEDGVVEYVDGYKVVIAAKHNPTLK-----RTYDLKKFLRSNSGTCINQRPL 710

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
              VGD V + D+IADGP+TD G+LALG+N+LVAFMPW+GYNFED+++ISE+++ +D +TS
Sbjct: 711  CSVGDVVVKGDVIADGPATDKGELALGKNILVAFMPWYGYNFEDAIIISEKLIKQDAYTS 770

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I+IEEFE+ ARDTKLG EEITRDIPNVSEE L N+ E GII +GAEV PGDILVGKITPK
Sbjct: 771  IYIEEFELTARDTKLGKEEITRDIPNVSEEVLANLGEDGIIRIGAEVKPGDILVGKITPK 830

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNERSISVE 960
             E+ + PEE+LLRAIFGEKA DV+D SL VP G  G V+DV++F+R   + K++  +  E
Sbjct: 831  SETELAPEERLLRAIFGEKAADVKDASLTVPPGTEGVVMDVKVFSRKDRLSKSDDELVEE 890

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-------FKKSTVLSSDLI 1013
               ++ L +   ++  +L      +L  +L  + A +            ++ TV   + I
Sbjct: 891  AVHLKDLQKGYKNQISVLKTEYREKLGALLLNEKAPASIIHRRTADILVQEGTVFDQETI 950

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLR 1072
                +       +    +   ++SL   YETS   LE  +K ++E I+ GD D+  GV+R
Sbjct: 951  ELLEQESLVDLLMPPCDMYDVLKSLLSDYETSLQRLEVNYKTEVEHIREGDADLDHGVIR 1010

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN
Sbjct: 1011 QVKVYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLANGETVQMILNPLGVPSRMN 1070

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ ETHLG+A    G  +K+ + +      I  +                        
Sbjct: 1071 LGQVLETHLGYAAKTAGIHVKTPVFEGFPESRIWDMM----------------------- 1107

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    + G+P      DG                  G+       TGE FD  V +G
Sbjct: 1108 -------IEQGLPA-----DGKS------------YLYDGK-------TGERFDNTVVIG 1136

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            YIYMLKL+H+++DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG A++LQ
Sbjct: 1137 YIYMLKLSHLIADKIHARSIGPYSLVTQQPLGGKAQMGGQRFGEMEVWALEAYGVAHMLQ 1196

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            E+LT+KSDDV GRTR+YESIV G +  ++GTPESFNVL+KEMQ LGL + 
Sbjct: 1197 EILTVKSDDVTGRTRIYESIVKGENLLKSGTPESFNVLIKEMQGLGLDVR 1246


>gi|225849555|ref|YP_002729720.1| DNA-directed RNA polymerase subunit beta [Sulfurihydrogenibium
            azorense Az-Fu1]
 gi|225644617|gb|ACN99667.1| DNA-directed RNA polymerase, beta subunit [Sulfurihydrogenibium
            azorense Az-Fu1]
          Length = 1485

 Score = 1211 bits (3134), Expect = 0.0,   Method: Composition-based stats.
 Identities = 609/1470 (41%), Positives = 870/1470 (59%), Gaps = 109/1470 (7%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-NEGLQAAFKSVFPITAFSGAA 72
            RK   K  EII  PDL+ V + S+++F   ++ P +R  N+GL+  F++ FP    +G  
Sbjct: 13   RKSLSKRKEIITPPDLLSVIRESFENFTQFHVNPLKRDPNKGLENLFRTSFPFVDPNGQL 72

Query: 73   MLEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAV 100
             + +V YE                                    K  VD+C ++ LTY+ 
Sbjct: 73   EVRYVGYEIGDWECGKCGKSLPEEVLGGPEVDCPHCGSPLIYKEKLSVDECKYKGLTYSA 132

Query: 101  PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            PL++ L L++ +VD  TG    K I++Q +Y G+LPL+T    F+I G +R++VSQL RS
Sbjct: 133  PLRVLLELVINNVDPKTGEVVPKTIRKQKLYFGELPLLTDYAYFMINGSERVIVSQLIRS 192

Query: 161  PGIHFDHDKGRA-SLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTSFL 218
             GI F   + +   +  +++Y   +IP++G  +++++ +  +I + +IDR RK+  T+ +
Sbjct: 193  SGIFFSAKEDKTKDIITRIIYEGSVIPEKGSRVEVQYATNAEIFYAKIDR-RKILGTTLV 251

Query: 219  MALGMDSE-EILSTFYPK-IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
             A G D+  +IL TFY K   Y           +   + +    +  +      E++ + 
Sbjct: 252  RAFGCDTAYKILKTFYGKVEKYKVVNGELVEEKTGLPVSLEELANRDIFITYVTEEISDK 311

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA--------------------------- 309
            G+ ++    K +  + +              VA                           
Sbjct: 312  GQPVSIRYEKYVPAENLASYINDDRYKIEEIVAVEPQVCNKSPYQRIIVETLKKDEPKIN 371

Query: 310  --EDIVNGETGEIYIEAGDVID--------EKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                  +    EIY +               K   E+F +   D     +  V       
Sbjct: 372  AMFSFRDAALVEIYKKMRPTDTAVLDPKAFMKRARELFENTFEDYQKYDLSRVGRVKINA 431

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM-NM 418
                  K     D L D +    P  +                 D+  +  + +     +
Sbjct: 432  KVHNVPKTIKPLD-LEDFFEKFPPLMLDEDVKIRDTVYPAGTKIDRQLVEELKKHSFKEI 490

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++     ++ R ++  DIIAI+K L++LR GK T+DDI +LGNRRVR VGE+L+ Q R G
Sbjct: 491  KVKEYLDEEARTLQMADIIAIVKYLLELRYGKKTLDDIAHLGNRRVRPVGELLEVQARAG 550

Query: 479  LLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            + RM+++ K+R++ VDI+   + P +LIN + +V  + EF    QLSQ  +  N LS +T
Sbjct: 551  IARMQKAFKDRVAIVDIEDPQLKPSELINPRYLVGTIVEFLKGGQLSQFMDQTNPLSELT 610

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R  A  E+RDVHP+HYGR+CP ET EG NIGLVSS+T ++R+N +G
Sbjct: 611  HKRRLSALGPGGLTRDSAKFEIRDVHPSHYGRVCPIETPEGQNIGLVSSMTVYSRLNEFG 670

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+ TPYRKV DG VTN++ YL+A +EE   IAQAN+ +DE G FT + V  R  G+  LV
Sbjct: 671  FLITPYRKVVDGVVTNEIEYLTAYDEEKYVIAQANAEIDEKGRFTSDRVLARAYGDIRLV 730

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +++ ++D SPKQVVS +ASLIPFLE+DD+NR LMG NMQRQAVPL+K E P +GTGME
Sbjct: 731  DPKEVHYMDISPKQVVSPSASLIPFLEHDDANRALMGSNMQRQAVPLIKTEYPLIGTGME 790

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS---GVDIYRLMKFQRSNQN 773
             ++AK SG+A+VAKR G V +VD   I I+  E ++DP      G+DIY L KF+ SNQ 
Sbjct: 791  VIIAKDSGSAVVAKRGGEVVKVDGNSITIKVNEDEIDPHDPLDIGMDIYELKKFKGSNQA 850

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC+NQRPLV+VGD+V +  +IADG ST  G+LALG+N+LVAFMPW GYNFED+++ISER+
Sbjct: 851  TCINQRPLVRVGDKVEKGAVIADGTSTYKGELALGKNVLVAFMPWRGYNFEDAIVISERL 910

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V +DVFTSIHIEEFEV AR+TKLGPEEITR+IPNV E  L N+DE GI+ VG  V PGDI
Sbjct: 911  VKDDVFTSIHIEEFEVEARETKLGPEEITRNIPNVKERLLANLDEHGIVKVGTYVKPGDI 970

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGK+TPKGES  TPEEKLL AIFGEKA DV+DTSLRVP GV G VVDV+IF +   DK 
Sbjct: 971  LVGKVTPKGESTPTPEEKLLLAIFGEKASDVKDTSLRVPIGVEGVVVDVQIFAKKRKDKK 1030

Query: 954  ERSI----SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            E+      ++ +++IE L  + ++++  +       L  +L G       K   +  V  
Sbjct: 1031 EKREKYFDTLIKQEIEKLNTELEEKKKFILERRDENLKALLIGSKVSKDIKVGTEVIVKE 1090

Query: 1010 SDLISEYPRSQWWQFA-------VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             + ++E    +  +         ++D+KV    + +  + ++   + E  ++ K E ++ 
Sbjct: 1091 GEKLTEENIDKVIRIIAINPSNFIKDKKVSNLAKEISDKAKSQIELWEKIYQRKKEVLEE 1150

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G D+ PGV+ +VKV++A KR IQ GDKMAGRHGNKG++S +LP EDMPFL+DGTPVDIVL
Sbjct: 1151 GADLKPGVIELVKVYIAQKRKIQVGDKMAGRHGNKGVISVVLPVEDMPFLEDGTPVDIVL 1210

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKK--------------IKSLINDYKANGDISPL 1168
            NPLGVPSRMNVGQI ETHLG A   LG+K              I+ ++  Y    + +  
Sbjct: 1211 NPLGVPSRMNVGQILETHLGLAAKKLGEKLSKELENIFDKEKIIQKIVEYYSIVNETNDK 1270

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW-KSGVPVSTPVFDGADEEAINSMLRMAD 1227
                ++V  T    + + + DD+S+  + +   K G+P+ T +F+ A E+ I  ML+ A 
Sbjct: 1271 LLTKKRVEDTKELEKALRELDDESLRSLIKDLGKIGIPIETAIFESATEDDIRRMLQAAG 1330

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
              E+G+  L DG TGEPFD  VTVGY+YMLKL HMV DK++ARSTG YSL+TQQPLGG++
Sbjct: 1331 FKENGKVRLIDGRTGEPFDLEVTVGYMYMLKLIHMVDDKIHARSTGPYSLITQQPLGGRA 1390

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++A+GAAY L+EMLT+KSDD+ GR RVYE+I+ G   ++ G PESF
Sbjct: 1391 QFGGQRFGEMEVWALEAHGAAYTLREMLTVKSDDIEGRKRVYEAIIKGKHYYDIGVPESF 1450

Query: 1348 NVLVKEMQALGLSID-LENSRTKNSAKMEE 1376
             VLV+E++ALGL+++ + + ++++    EE
Sbjct: 1451 KVLVRELKALGLNVECITDGQSQSCDTSEE 1480


>gi|218960790|ref|YP_001740565.1| RNA polymerase, beta subunit [Candidatus Cloacamonas acidaminovorans]
 gi|167729447|emb|CAO80358.1| RNA polymerase, beta subunit [Candidatus Cloacamonas acidaminovorans]
          Length = 1258

 Score = 1211 bits (3132), Expect = 0.0,   Method: Composition-based stats.
 Identities = 542/1376 (39%), Positives = 815/1376 (59%), Gaps = 143/1376 (10%)

Query: 15   KFFGKN---------PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
            K + +          PE+ +IP+L+ +Q  S++ FL  +I P  R  +GLQA F+++FP+
Sbjct: 5    KSYSRISGRFAELGIPEV-EIPNLLAMQVDSFNDFLQKDIHPQRREKKGLQAVFENIFPL 63

Query: 66   TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
                G  +LEF+ Y     K+ +++C  R+L+Y  PLK  +RL VF+  E  G +  KD 
Sbjct: 64   EDTKGNFLLEFIEYNVLQEKYSLEECRERNLSYQAPLKAKMRLSVFENRE--GVREHKDT 121

Query: 126  KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
             EQ +++G++PL+T+ GTFVI G +R+++SQL RSPG+ F  +K     SGK LY+ ++I
Sbjct: 122  LEQEVFLGEIPLITEQGTFVINGAERVIISQLQRSPGVFFSEEK---HPSGKTLYSAKVI 178

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDF 244
            P  G W+D + D  D++ V ID+RRK+PVT+   A+G+ + E L  TFY     + +   
Sbjct: 179  PYSGSWLDFDIDIHDVMFVHIDKRRKLPVTTLFRAIGISTNEDLRKTFYKSEKLNLK--- 235

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                        G  + + + +    E +  + +++T  L+K L E+ +  + +      
Sbjct: 236  ---------EAKGRHLFADIYEKGNPEPIAMANEQITDSLIKFLSERKITKVEV------ 280

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
                                                      +  +       + NT+  
Sbjct: 281  ------------------------------------------IDYNYEIARKVLENTMAK 298

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D   ++++AL  IY ++RPG+ +    A+ + + +FF+  +Y+L  VGR K+N RL ++ 
Sbjct: 299  DPTTNQEEALKKIYNLIRPGEDAPLEAAKQLVDRMFFNEKRYNLGEVGRYKINSRLGINV 358

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               +  +  ED + I K L+++ + +  +DDIDNL NRRVR+VGE+L+ QY +G+  + R
Sbjct: 359  DPKIMTLTVEDFVYIFKTLINIYHDEDEVDDIDNLANRRVRTVGELLQEQYTIGMAMVAR 418

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             I+ER++  +ID V   DL+N+  ++S V  FF + QLSQ  E  N L+ + H R LSAL
Sbjct: 419  IIQERMAISNIDEVTVHDLVNSNALISVVQSFFLTGQLSQFMEQTNPLAALRHKRALSAL 478

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+AR RAG E+RDVH +HYGRICP ET EG NIGL+ S   ++R+N +GF+ETPYRK
Sbjct: 479  GPGGLARERAGFEVRDVHSSHYGRICPIETPEGPNIGLIVSPAIYSRINHFGFLETPYRK 538

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V DG +T++  YL A +EE   IAQ++  LD++   T+E++F R  GE + V    + ++
Sbjct: 539  VVDGCITDEYEYLDASQEEKYIIAQSDVHLDDNRRITDEMIFARDRGEFVQVSPNLVHYM 598

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D +P+Q+VS++A+LIPFLE+DD+NR LMG NMQRQAVPL+  +AP VGTGME + +  + 
Sbjct: 599  DVAPQQMVSVSAALIPFLEHDDANRALMGSNMQRQAVPLINPQAPLVGTGMEKIASMDTS 658

Query: 725  AAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            +  VA   GIV +V +  I ++   E D     S  +   L KF R+NQ+TC+NQRP+V+
Sbjct: 659  SIAVAPYDGIVTKVTSAFIDLKPLNEKDEAYYLSTGNRIHLKKFVRTNQDTCINQRPIVR 718

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD V++   I+DG   +   LALG N++VAFMPW+GYN+ED++++SE++  ED  TSI+
Sbjct: 719  VGDTVKKGQPISDGACVEDNRLALGTNLMVAFMPWYGYNYEDAVILSEKVAREDTLTSIY 778

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG- 902
            IEE EV+ R+ K G EE+  DIPNV  + L+N+D+ GII VG+ ++ GDI+VGK+TPK  
Sbjct: 779  IEELEVLVRNVKNGREELAYDIPNVPAQALRNLDKTGIIRVGSVIHAGDIIVGKVTPKSV 838

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E   +PEE L+RA+FG++A D  ++SL+   G+ G V+DV++F+R     +    + ++ 
Sbjct: 839  EIDPSPEENLMRALFGDRAGDFTNSSLKAKPGMEGVVIDVKVFSRLEEGSDLEEENEDK- 897

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------GPKGFKKSTVLSSDLISEY 1016
             IE L  +    +  ++     +L  +L GQ A +                ++   +   
Sbjct: 898  -IEKLKEELALRRSKIEEFKEEKLSAVLVGQIAKNIWDEKTNIPFIAPGKKITKQDLKRI 956

Query: 1017 PRSQWWQFA--VQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
               +       V+D +V   +   + ++ + S    ++ +K   E+I+ GD++  GV ++
Sbjct: 957  NFKKLDLDVELVEDREVNDYIYSQIVLKIKQSLEQSDNIYKKSRERIKHGDELQYGVRKM 1016

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV+VA KR I+ GDKMAGRHGNKG++S I P EDMPF++DGTPVDIVLNPLGVPSRMN+
Sbjct: 1017 VKVYVAKKRKIEVGDKMAGRHGNKGVISIIAPIEDMPFMEDGTPVDIVLNPLGVPSRMNI 1076

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI ETHLGWA   LG ++++ I D  +N DI                            
Sbjct: 1077 GQIMETHLGWAAKTLGFEVETPIFDGASNEDIVSELR----------------------- 1113

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   K+G+P                        E G+++LYDG +GEPF   VTVG 
Sbjct: 1114 -------KAGLP------------------------EDGKTVLYDGKSGEPFKERVTVGI 1142

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYM+KLNH+V+DK++ARSTG YSL+TQQPLGGK+  GGQRLGEMEVW ++AYGAA VL+E
Sbjct: 1143 IYMMKLNHLVADKMHARSTGPYSLITQQPLGGKAQHGGQRLGEMEVWALEAYGAASVLEE 1202

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            MLTIKSDDV GR   +++I  G++    G PESFNVL+ E+++LG  I+      K
Sbjct: 1203 MLTIKSDDVDGRNNAFKAITRGDNPPPPGVPESFNVLISELKSLGFDIEFIKEENK 1258


>gi|187251832|ref|YP_001876314.1| DNA-directed RNA polymerase subunit beta [Elusimicrobium minutum
            Pei191]
 gi|186971992|gb|ACC98977.1| DNA-directed RNA polymerase, beta subunit [Elusimicrobium minutum
            Pei191]
          Length = 1270

 Score = 1206 bits (3119), Expect = 0.0,   Method: Composition-based stats.
 Identities = 578/1395 (41%), Positives = 806/1395 (57%), Gaps = 177/1395 (12%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             FG+    + +PDL+++QK S+  FL +++AP +R  +GLQAAF+ VFPI A  G+  LE
Sbjct: 5    NFGQISSKLSLPDLLDMQKESFVDFLQLDVAPTKRELKGLQAAFEDVFPIEAPDGSMKLE 64

Query: 76   FVSYEFDPPKF-DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            FV YE   P++        RD TY+ P+K  +RL V   D       +K+  EQ + + D
Sbjct: 65   FVKYELGAPRYSTPQQAALRDGTYSAPMKAVMRLSVKKRDG-----KLKEASEQDVTLCD 119

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS-GKLLYACRIIPDQGLWMD 193
            LPLMT  G FV  G +R+VVSQLHRSPGI F+ D+ +   + GK LY  RIIP +G W++
Sbjct: 120  LPLMTDAGCFVFNGAERVVVSQLHRSPGIIFEEDEEKKQSTLGKKLYVARIIPYRGAWIE 179

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
              FD  + + VRIDR++KV  T+FL A G+++  +I+  FY       +        +  
Sbjct: 180  FSFDIMNALWVRIDRKKKVLATTFLRACGLETNAQIIQAFYDVEDVEVK-------PAEI 232

Query: 253  DLMVGAKVSSSLVDIDTGEQV----IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            D +VG   +  +VD  TGE +     ++   +   + K + E+ +K + I    + G   
Sbjct: 233  DNVVGRYAADDIVDPATGEVLWNLDDKAAMPMDDKIFKEMVERKIKKVKI----ISGNPR 288

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
             +D     T E                                             D+ +
Sbjct: 289  QDDPGILATLE------------------------------------------NRKDQIR 306

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS-DKYDLSTVGRVKMNMRL------- 420
              K+A  DIY+ MR  D      AE+  + L FD+  +YDLS VGR K+N +        
Sbjct: 307  TSKEAQADIYKKMRGQDFVVKEQAEAFLDNLIFDNIRRYDLSYVGRYKINKKFASLFDIV 366

Query: 421  -------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKG-----------TIDDIDNLGNR 462
                        D  R +  EDII  +K L+ L  G+              DDID+LGNR
Sbjct: 367  ENLKFKKFTKPTDKRRTLSAEDIIVTVKYLLALNAGEDAQKMYGEEIIFKTDDIDHLGNR 426

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVR +GE+L+NQ R+GL +M ++ ++R++  ++ S  P+ L+NA+PV + + +FF +SQL
Sbjct: 427  RVRGIGELLENQIRVGLSQMAKTARDRMNK-ELASHTPRALVNAQPVQAIIKKFFGTSQL 485

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  + +N LS +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 486  SQFMDQINPLSELTHKRRLSALGPGGLNRKRAGFEVRDVHHTHYGRVCPIETPEGPNIGL 545

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL  +++VN YG IETPYRKV  GKVT++  YL+A +E++  +AQ+N+ L + G    
Sbjct: 546  ITSLACYSKVNKYGLIETPYRKVNSGKVTDNFEYLTADQEDDLMVAQSNTPLTDSGKINT 605

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            ++V CR   +  +V   ++D++D SP QV+S++A+LIPFLE+DD+NR LMGCNMQRQ VP
Sbjct: 606  DMVSCRVRSDYPIVSPSEVDYMDVSPLQVISVSAALIPFLEHDDANRALMGCNMQRQGVP 665

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            LL  EAP VGTG+E  VA+ SGA I A + G V    A +I +  +EG         +IY
Sbjct: 666  LLLTEAPLVGTGIEHEVARDSGATISAAKPGRVVFAAADKIAVEPLEG------GAPEIY 719

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L+K++RSNQ+TC+NQRPLVK GD V++  ++ADGP+   G LALG+N+LV FM W GYN
Sbjct: 720  DLIKYKRSNQDTCINQRPLVKAGDIVKKGTVLADGPAMKDGFLALGKNLLVGFMSWEGYN 779

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +ED++L+S ++V EDVFTS+H+ EF + AR+TKLG EEITRDIPN+  E L ++D  GI+
Sbjct: 780  YEDAILVSHKLVKEDVFTSVHLHEFSIDARNTKLGAEEITRDIPNIGAEALAHLDADGIV 839

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                 V PGDILVGK+TPKGE  +TPEE+LL+ IFG+KA DV D SLRVP G SG V+  
Sbjct: 840  IPSTVVEPGDILVGKVTPKGEQQLTPEERLLKVIFGKKADDVVDASLRVPPGTSGKVIGT 899

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            R+F R    K + + + E+ +I+ L  +K      L       L  I       S  K  
Sbjct: 900  RVFVR----KEKLTKAEEKARIKALEDEKTTNLETLKEQRKLALTNI-----KDSNVKDA 950

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            KK                               E +   Y+  +  + + F+ ++E  + 
Sbjct: 951  KKEE-----------------------------ERINALYKKLEKRVLEDFEREMEFSKQ 981

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++   V + VKVF+A KR +  GDK++GRHGNKG+V++ILP EDMPFL DGTP+DIVL
Sbjct: 982  GDELAVTVNKSVKVFIASKRKLMVGDKLSGRHGNKGVVAKILPEEDMPFLPDGTPLDIVL 1041

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            +PLG+PSRMNVGQ+FET LGWA   LG    + + D      +       +K +      
Sbjct: 1042 SPLGIPSRMNVGQLFETMLGWAAKNLGYNAATPVFDGPTEETVREEIKKAKKAL------ 1095

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                              + GVP                       D+  +  LYDG TG
Sbjct: 1096 -----------------IEKGVP------------------EKHLPDDYCRITLYDGRTG 1120

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +PF+  VT+GY+Y++KL H+V DKV+ARSTG YSL+T+QPLGGK+  GGQR GEMEVW I
Sbjct: 1121 QPFEEKVTIGYMYIMKLIHLVEDKVHARSTGPYSLITRQPLGGKAQFGGQRFGEMEVWAI 1180

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            + YGA Y LQE LT+KSDD  GRT++YESIV G    + G PESF VLVKE+QALGLS++
Sbjct: 1181 EGYGATYTLQEFLTVKSDDFTGRTKMYESIVRGEAPQQPGVPESFKVLVKELQALGLSVE 1240

Query: 1363 LENSRTKNSAKMEEI 1377
            L       + +   +
Sbjct: 1241 LLKDNQGQAVEEMTV 1255


>gi|323182085|gb|EFZ67495.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli 1357]
          Length = 1028

 Score = 1202 bits (3110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 584/1041 (56%), Positives = 770/1041 (73%), Gaps = 13/1041 (1%)

Query: 326  DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
              +    L ++  S  + I  L+ + +++  YI  TL  D   DR  AL++IYR+MRPG+
Sbjct: 1    MELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGE 60

Query: 386  VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
              T   AES+F  LFF  D+YDLS VGR+K N  L  +  +    + K+DII ++K L+D
Sbjct: 61   PPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLID 120

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+IN
Sbjct: 121  IRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMIN 180

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            AKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTH
Sbjct: 181  AKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTH 240

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            YGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N 
Sbjct: 241  YGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNY 300

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+D
Sbjct: 301  VIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHD 360

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G+V+ VDA RIVI
Sbjct: 361  DANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVI 420

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            +  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+L
Sbjct: 421  KVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGEL 480

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTKLGPEEIT DI
Sbjct: 481  ALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADI 540

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            PNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+
Sbjct: 541  PNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVK 600

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +E  IL+  ++SR
Sbjct: 601  DSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSR 660

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
            +  +L                   ++ + + PR +W +  + DE+ Q  +E L  QY+  
Sbjct: 661  IRAVLVAGGV-------------EAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDEL 707

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
            K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P
Sbjct: 708  KHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINP 767

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +++   +    +
Sbjct: 768  IEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKL 827

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                     +         +S + D+ V+R+AE  + G+P++TPVFDGA E  I  +L++
Sbjct: 828  REFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKL 887

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
             DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGG
Sbjct: 888  GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGG 947

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   E G PE
Sbjct: 948  KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPE 1007

Query: 1346 SFNVLVKEMQALGLSIDLENS 1366
            SFNVL+KE+++LG++I+LE+ 
Sbjct: 1008 SFNVLLKEIRSLGINIELEDE 1028


>gi|189485077|ref|YP_001956018.1| DNA-directed RNA polymerase beta chain [uncultured Termite group 1
            bacterium phylotype Rs-D17]
 gi|170287036|dbj|BAG13557.1| DNA-directed RNA polymerase beta chain [uncultured Termite group 1
            bacterium phylotype Rs-D17]
          Length = 1257

 Score = 1201 bits (3107), Expect = 0.0,   Method: Composition-based stats.
 Identities = 569/1393 (40%), Positives = 818/1393 (58%), Gaps = 178/1393 (12%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
              FG+    ID P L+++QK S+  FL  N+AP++R  +GL++AF+ +FP+T   G  +L
Sbjct: 4    VNFGRIRIPIDPPSLLKMQKDSFSEFLQQNVAPEKRKLQGLESAFRDIFPLTNSDGNLVL 63

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+VSY F  PK+ V++ + RD TYA+PLK+ LRLI    D+       K++ EQ +Y GD
Sbjct: 64   EYVSYAFGEPKYSVEESITRDATYALPLKVKLRLIYKKEDDIE-----KELSEQEVYFGD 118

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS-GKLLYACRIIPDQGLWMD 193
            +PLMT   TF+I G +R+VVSQ+HRSPG+ F+ D+ +     GK LY  R+IP +G W++
Sbjct: 119  IPLMTDTATFIINGAERVVVSQIHRSPGVIFEEDEEKRVTVLGKPLYFARMIPYRGAWVE 178

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
             EFD   I++VRIDR+RK+ VT+FL +LG    EEIL+ F      S           A 
Sbjct: 179  FEFDQNGILYVRIDRKRKIFVTTFLRSLGFRTDEEILNLFKEVKEVSLDA--------AL 230

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
              + G  ++  + D +TGE + ++G++L   L+K L  KG   + +  D    L + +D 
Sbjct: 231  TSLTGEYIAEDISDENTGEIIADTGRELQEDLIKKLWAKGFTKVTVFKDVSILLTLKKDT 290

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            +                                    +      YI   L T +   ++ 
Sbjct: 291  I-----------------------------------KNQKEAINYIYKVLKTQEFVVQER 315

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL---------- 422
            A + +  ++                  F    +YDL+ +GR K+  +L            
Sbjct: 316  AQVFLEELL------------------FKSVRRYDLTKIGRYKILKKLAPIFKYYEKNFN 357

Query: 423  --DTPDDVRHIRKEDIIAIIKILVDLRNG-----------KGTIDDIDNLGNRRVRSVGE 469
                P+  R + KED++  +K L+ L +G           K  +DDID+LGNRRVRSVGE
Sbjct: 358  LNIPPETKRTLTKEDVVVTLKYLLMLYSGETEFTENGQTTKIVLDDIDHLGNRRVRSVGE 417

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +L+NQ R+GL++M R++KE +++ D  +V P+ LIN    ++ + +FF +SQLSQ  + +
Sbjct: 418  LLENQIRIGLVQMARTVKEHMNNQDKFNVTPRSLINITQFIAQIRKFFGTSQLSQFMDQI 477

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L+ +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++F
Sbjct: 478  NPLAELTHKRRLSALGPGGLNRKRAGFEVRDVHHTHYGRVCPIETPEGPNIGLITSLSAF 537

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            A VN YG IETPY+KV +G+ T+ + YL+A +E+  ++AQAN+ LD+ G+   +LV  R 
Sbjct: 538  ASVNPYGLIETPYKKVKNGRATDKIEYLTADKEDEFFVAQANTPLDDKGNILSDLVQGRK 597

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              + +     K+D++D SP QV+SI+A+LIPFLE+DD+NR LMGCNMQRQAVPLL AE P
Sbjct: 598  WDDFLFQSPAKVDYMDVSPMQVISISAALIPFLEHDDANRALMGCNMQRQAVPLLLAEVP 657

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             V TG+E  VA+ SG  +V+   G V  V +  I+I          +  +++Y L K+ R
Sbjct: 658  LVSTGIEKKVAEDSGVVVVSDSDGEVVSVSSDEIMIY-------SQSKKIEVYELKKYLR 710

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ+TC+NQ+PL+ +GD V++  IIADGP+T  G L+LG+N+LVA+MPW GYNFED+ML+
Sbjct: 711  SNQDTCINQKPLITLGDIVKKGQIIADGPATSDGQLSLGQNILVAYMPWDGYNFEDAMLL 770

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SE+++ +D FTSIHI EF+  AR+TK  PEEIT+DIPNV  E L ++DE GI+ VG+ V 
Sbjct: 771  SEKLIQDDKFTSIHIREFKTEARETKEHPEEITKDIPNVGAEDLLDLDEYGIVKVGSMVQ 830

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK  PKGE  MTPEE+LLR +FG+KA DV+D SLRVP G+SG V+ VR+F R  
Sbjct: 831  RGDILVGKTAPKGEQQMTPEERLLRVLFGKKAEDVQDVSLRVPPGISGKVIGVRVFIRLE 890

Query: 950  IDKNERSI-------SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
               ++          SV       L +DK ++  I  ++  +++  I             
Sbjct: 891  KITDQEKKKKQKEMYSVYEAAKAKLCKDKKEQLEIAKKSETAKIEAI------------- 937

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                                                   Y T + IL   ++++ EK++ 
Sbjct: 938  ---------------------------------------YATKEEILRQNYESEKEKLKK 958

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GDD+P  V + VKV++A K  +Q GDK+AGRHGNKG+V+RILP EDMP L DGTPVD VL
Sbjct: 959  GDDLPVSVNKTVKVYIAAKLKVQVGDKLAGRHGNKGVVARILPVEDMPHLPDGTPVDCVL 1018

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            +PL +PSRMNVGQ+ E  LGW+   LG ++ + + D  +   I       +  I      
Sbjct: 1019 SPLAIPSRMNVGQLLEIMLGWSGKELGVQMITPVFDGASEEQIKDYVEKAKAKILDKKKK 1078

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              I+   +   L                     EE+++     +      +  LYDG TG
Sbjct: 1079 LLIAHGLEGVEL---------------------EESLSKFADESLPTSDCKIKLYDGRTG 1117

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF   VT+G +Y++KLNH+V DK++ARSTG YSL+T+QPLGGK+  GGQR GEMEVW I
Sbjct: 1118 EPFMEKVTIGVMYVMKLNHLVEDKMHARSTGPYSLITRQPLGGKAQFGGQRFGEMEVWAI 1177

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            + YGAA++LQE LT+KSDDV GR ++Y+SI+ G    + G PESF VLV E+++L L+++
Sbjct: 1178 EGYGAAHILQEFLTVKSDDVEGRVKMYDSIIKGESISKPGVPESFKVLVSELKSLALNVE 1237

Query: 1363 LENSRTKNSAKME 1375
            L N + +     +
Sbjct: 1238 LFNGKRQKDNHEK 1250


>gi|320101660|ref|YP_004177251.1| DNA-directed RNA polymerase subunit beta [Isosphaera pallida ATCC
            43644]
 gi|319748942|gb|ADV60702.1| DNA-directed RNA polymerase subunit beta [Isosphaera pallida ATCC
            43644]
          Length = 1236

 Score = 1199 bits (3103), Expect = 0.0,   Method: Composition-based stats.
 Identities = 553/1357 (40%), Positives = 785/1357 (57%), Gaps = 141/1357 (10%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAAM 73
            KFFG+  +   IPDL ++Q  SY  FL  +  P++R ++GL+A F+ +FPI ++      
Sbjct: 16   KFFGRIRDDFPIPDLTQIQTESYARFLQEDTPPEQRKDQGLEAVFREIFPIESYGDKTLR 75

Query: 74   LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            LE++ YE   P++D D+C    LTY  PL + LRL   D           +  E  +Y+G
Sbjct: 76   LEYIKYELGKPRYDPDECRRLSLTYGRPLNVWLRLWKGD-----------ESIEDHVYLG 124

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            D+P+M   G F+I G +R+VVSQLHRSPG+ F  D        K L+ACRIIP++G W++
Sbjct: 125  DMPIMIGGGEFIINGAERVVVSQLHRSPGVDFVVD---TESGDKKLHACRIIPERGSWIE 181

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSEE-ILSTFYPKIVYSQRGDFWCFPLS 250
            ++ + KD + VRID+  K    + L A+     ++E IL                     
Sbjct: 182  LQVNKKDALEVRIDQSGKFSAMTLLRAMDPAYSTDEAIL--------------------- 220

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                    +       I T E+   +                          L       
Sbjct: 221  --------RAFYDTETIHTSEEGAAA-------------------------RLENKIACG 247

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D+V+ ETGE+  ++G  ID    +      +  I ++       +  I ++L  D   D 
Sbjct: 248  DVVDPETGEVLCDSGARIDRVRAQLFVDHNLGAIEVMV---EVKDPLILHSLQMDPTSDH 304

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            + ALL IY+ +RPG+      A  +F   F+D+++Y L  VGR ++N + NLD P+D   
Sbjct: 305  ESALLKIYQRLRPGNPPQLDKARDLFREKFYDTNRYRLGRVGRFRINRKFNLDLPEDKMT 364

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +   D +  I+ ++DLR  KG IDDID+LGNRR+R++ E+  ++ R G L++ R+++ER+
Sbjct: 365  LDAADYVHAIRYIIDLRRNKGHIDDIDHLGNRRLRTIDELAADEIRKGFLKLRRTVQERM 424

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D + + P+ LIN K + +A+  FF   +LSQ+ +  N L+++TH RRLSALG GG+ 
Sbjct: 425  TMKDAEDLNPRSLINQKSISAAIDYFFGRGELSQVVDQTNPLAQLTHERRLSALGPGGLN 484

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH +HYGRICP ET EG NIGL+SSL ++ARV+ YGF+  PYR V +GK 
Sbjct: 485  RKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLANYARVDEYGFLVCPYRVVENGKP 544

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            TN+V ++ A +E + Y+A A+  LDE G         R   +  ++P +K+ +ID SP+Q
Sbjct: 545  TNEVRWMRADDENDVYLAPADVPLDEHGRIKGPNTIARYQSDIHMIPSDKVQYIDISPRQ 604

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            VV ++A LIPFLE+DD+NR LMG NMQRQAVPLL AE P V TG+E  VA +SG  + A+
Sbjct: 605  VVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLVAEPPLVATGLEGAVAMNSGMVVRAR 664

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              G+V +VD+ ++VI            GV +Y+L K+   N+ TC+NQ+P+V VG +V++
Sbjct: 665  EDGVVTEVDSTKVVID-----------GVHVYKLRKYIGLNERTCLNQKPVVSVGQQVKK 713

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
             D++ADG ST  G+LALGRN+LVAFM W GYNFED++++SER+V EDV+TSIHIEEFE  
Sbjct: 714  GDLLADGASTYQGELALGRNVLVAFMSWDGYNFEDAIILSERLVKEDVYTSIHIEEFEAD 773

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R+TKLG EE TRDIPNVSE+ L+++DE GI+ VG  V PGDILVGK+ PK +S ++PEE
Sbjct: 774  IRETKLGREEFTRDIPNVSEKALRHLDENGIVAVGTYVKPGDILVGKVAPKSKSELSPEE 833

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
            KLL AIFG    DV++ SL VPSGV G V+  + F+R      E   + ++ +I+   + 
Sbjct: 834  KLLHAIFGRSGEDVKNDSLEVPSGVEGIVLSTQRFSRRTSLTEEERKAHDK-EIKDTEQA 892

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            +  +     R +   L E++ G                   L  E    +     +    
Sbjct: 893  ESIKIAEAYRQMIKELEEVIGGPVVHKETARPYGREKDPVALAEESQSFKLEHIDLHGPD 952

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            +      +  ++      L D  + K+  ++ GD++  GVL++VK++VA KR I  GDKM
Sbjct: 953  ILSKAREVHRRHAVRIDNLRDEKERKLNSLKLGDELQTGVLQMVKIYVATKRVISVGDKM 1012

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++++ILP EDMPFL DGTPV+I+LNPLGVPSRMNVGQI ETHLGWA   LG 
Sbjct: 1013 AGRHGNKGVIAKILPEEDMPFLADGTPVEILLNPLGVPSRMNVGQILETHLGWAAAKLGF 1072

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +    + D      I              +                              
Sbjct: 1073 RAICPVFDGADESVIRQHLKEAGLPENGKAQL---------------------------- 1104

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                                 G        TGEPFD+ VTVGY+YMLKL+H+V DK++AR
Sbjct: 1105 -------------------YDG-------RTGEPFDQKVTVGYMYMLKLHHLVDDKIHAR 1138

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            +TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GRT++YE
Sbjct: 1139 ATGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGRTKIYE 1198

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            S+V G +T E GTP SF+VL  E++ L L++ LE  R
Sbjct: 1199 SMVKGENTLEAGTPASFDVLTNEIRGLALNMQLEKKR 1235


>gi|168700810|ref|ZP_02733087.1| DNA-directed RNA polymerase beta chain [Gemmata obscuriglobus UQM
            2246]
          Length = 1254

 Score = 1194 bits (3088), Expect = 0.0,   Method: Composition-based stats.
 Identities = 550/1361 (40%), Positives = 790/1361 (58%), Gaps = 130/1361 (9%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            + FG+  + +++PDL +VQ  SYD FL ++ + D+R   GL+   + +FPI ++     L
Sbjct: 15   RDFGRFGDAVEVPDLTDVQTRSYDRFLQLDASYDKRTQTGLEGVLQEIFPIESYDKRIKL 74

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E++ YE   P++D D+C    LTY  P ++ LRL           K+  +  E+ +Y+GD
Sbjct: 75   EYLRYELGKPRYDPDECRQLRLTYGRPFRVWLRL----------RKTEGEPVEEEVYLGD 124

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +P+M   G F+I G +R+VVSQLHRSPG+ F         + K L++CRIIP++G W++I
Sbjct: 125  MPIMIGGGEFIINGAERVVVSQLHRSPGVDFV----VTREADKDLHSCRIIPERGSWIEI 180

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALG--MD-SEEILSTFY----PKIVYSQRGDFWCF 247
                KD + VRID+  K    + L A+      +E IL  F+     ++  S  G     
Sbjct: 181  NATKKDTLGVRIDQSGKFSAVTLLRAMDPMYSTTESILKEFFGEVIEQVNVSVAGSRLKL 240

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                    +       ++D +TGE  +++GK  TS     +    +K + +         
Sbjct: 241  VGDPEANQMPCIAVEDVIDPETGEVYLDAGKPFTSDKYDRVASSMIKTVQVM-------- 292

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                                           +  +D  IL     +           D  
Sbjct: 293  -------------------------------AYPKDPIILNAIHEDVGT------AGDSK 315

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               + ALL IY+ +RPG+      A+ +F   F D ++Y L  VGR ++N + N    + 
Sbjct: 316  DSHEGALLKIYQRLRPGNPPQLEKAKELFKEKFLDPNRYRLGRVGRFRINRKFNQTVAET 375

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
               +R  D +  +K L+DLR GKG +DDID+LGNRR+R++ E+  ++ R G L++ R+++
Sbjct: 376  EMTLRSVDFVNSVKYLLDLRAGKGHVDDIDHLGNRRLRTIDELAADELRKGFLKLRRTVQ 435

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER++  D   + P+ LIN K V +A+  FF  S+LSQ+ +  N L+++TH RRLSALG G
Sbjct: 436  ERMAIRDQQDMNPRTLINPKSVSAAIEYFFGRSELSQVVDQTNPLAQLTHERRLSALGPG 495

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL+ ++ ++ YGF+ TPY+KV +
Sbjct: 496  GLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLSIYSEIDEYGFLITPYKKVSN 555

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              +T +VV L A EE N  +  A++   E        V  R +GE +L+P EK+ +ID S
Sbjct: 556  KNLTEEVVRLRADEESNAVLVPADTP-FEGNKIATANVSGRQSGELMLIPAEKVQYIDVS 614

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            PKQ+V ++A LIPFLE+DD+NR LMG NMQRQAVPLL  E P VGTG+E  VAK SG  +
Sbjct: 615  PKQMVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLIPEPPLVGTGLEKDVAKHSGMLV 674

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VDA RI +   +         V  Y L K+   N+ TC+NQ+P+V++G +
Sbjct: 675  RAQEEGTVVFVDAERIRLEEKDKI-------VREYVLRKYHGLNERTCLNQKPIVRMGQK 727

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ +IIADG +T  G+LALGRN+LVAFM W GYNFED+++ISER+V  D +TSIHIEEF
Sbjct: 728  VKKGEIIADGAATKNGELALGRNVLVAFMSWEGYNFEDAIIISERLVKNDTYTSIHIEEF 787

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            ++  R+TKLG EE TRDIPNVS + L N+DE G++ +G  V PGDILVGK++PK  S +T
Sbjct: 788  DIEIRETKLGKEEFTRDIPNVSPKALANLDEHGVVQIGTYVRPGDILVGKVSPKSRSELT 847

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL AIFG    DV++ SL V SG  G V+    F+R      +    +++++ + +
Sbjct: 848  PEEKLLHAIFGRAGEDVKNDSLEVQSGTEGIVIAAHRFSRRAHMSEDEKKQIDKDR-KDI 906

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS-QWWQFAV 1026
                +       R     L ++L  +       G + ++     +++E  +  +  +  +
Sbjct: 907  ESTYNRRIAEQFREFVKALEDVLDKKELKDPNTGKQLASDKDDKVVAEQAKEFKLDKLDI 966

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +     +  + +  ++        D  + K+  +  GD++P GV ++VKV+VA KR I  
Sbjct: 967  RSPDSLKKAQKIHHRHWERIQFFIDEQERKLNSLNRGDELPSGVQQMVKVYVATKRVISV 1026

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++S++LP EDMPFLKDGTPVDI+LNPLGVPSRMNVGQI ETHLG+A  
Sbjct: 1027 GDKMAGRHGNKGVISKVLPEEDMPFLKDGTPVDILLNPLGVPSRMNVGQILETHLGYAAA 1086

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG K  + + D     +I                                         
Sbjct: 1087 KLGFKAVTPVFDGATEEEIR---------------------------------------- 1106

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                 D   E  I          E+G+S+LYDG TG+ FD+PVTVGYIYMLKL+H+V DK
Sbjct: 1107 -----DALKEAGI---------PETGKSVLYDGRTGDAFDQPVTVGYIYMLKLHHLVDDK 1152

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            V+AR+TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GRT
Sbjct: 1153 VHARATGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGRT 1212

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            ++YES+V G +T E GTP SF+VL  E++ LGL++ LE  R
Sbjct: 1213 KIYESMVKGENTLEAGTPASFDVLTHEIRGLGLNMCLEKKR 1253


>gi|237756130|ref|ZP_04584703.1| DNA-directed RNA polymerase, beta subunit [Sulfurihydrogenibium
            yellowstonense SS-5]
 gi|237691715|gb|EEP60750.1| DNA-directed RNA polymerase, beta subunit [Sulfurihydrogenibium
            yellowstonense SS-5]
          Length = 1488

 Score = 1192 bits (3084), Expect = 0.0,   Method: Composition-based stats.
 Identities = 614/1478 (41%), Positives = 874/1478 (59%), Gaps = 109/1478 (7%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-NEGLQAAFKSVFPITAFSGAA 72
            RK   K  EII  PDL+ V K S+++F+  +  P +R  N+GL++ F++ FP    +G  
Sbjct: 13   RKILSKRREIITPPDLLSVPKESFENFVQFHTNPLKRDPNKGLESLFRTSFPFVDPNGQL 72

Query: 73   MLEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAV 100
             + ++ YE                                    K  V++C ++ LTY  
Sbjct: 73   EVRYIGYEIGDWECGKCGKALPDEVLGGPEVDCPNCGGPLIYKEKLTVEECKFKGLTYGA 132

Query: 101  PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            PL++ L L++   D  TG    K IK+Q IY G++PL+T    F+I G +RI+VSQL RS
Sbjct: 133  PLRVLLELVINHTDPKTGEIIPKTIKKQKIYFGEIPLLTDYAYFMINGSERIIVSQLIRS 192

Query: 161  PGIHFDHDKGRA-SLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTSFL 218
             GI F   + +   +  +++Y   +IP++G  +++++ +  +I + +IDR RK+  T+ L
Sbjct: 193  SGIFFSGKEDKTKDIITRVIYEGSVIPEKGSRVEVQYATNSEIFYAKIDR-RKILGTTLL 251

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA-----DLMVGAKVSSSLVDIDTGE- 271
             A G+D+  +IL  FY K+      D      +       + +V   +  + V  +  E 
Sbjct: 252  RAFGLDTAYKILKNFYGKVDRYIVEDGKLVHENTKIPVNLEELVNRDIFVTYVYEEMSEK 311

Query: 272  -----------QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG-- 318
                         +ES +KL +     ++E       + +       + E +   E    
Sbjct: 312  GQPVPIKQEKYVSVESLEKLLNDDRIKIEEVVTVEPQVINKSSYQRVIVETLKKDEPKIN 371

Query: 319  -----------EIYIEAGDVID--------EKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                       EIY +               K  +E+F++   DI    +  V       
Sbjct: 372  ALFTFRDAALVEIYRKMRPTDTAVLDPKAFMKRAKELFNNTFTDIQRYDLSRVGRVKLNA 431

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM-NM 418
                  K     D L D +    P  +      +          D   L  +       +
Sbjct: 432  KVHNIPKTIKPLD-LEDFFEKFPPLALDEDIETKDGIIPKGTKIDPVVLEKLKETSFKEI 490

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++     ++ R ++  DIIAI+K L++LR GK  +DDI +LGNRRVR VGE+L+ Q R G
Sbjct: 491  KVKEYLDEEARTLQLADIIAIVKYLLELRFGKKNLDDIAHLGNRRVRPVGELLEAQARAG 550

Query: 479  LLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            + RM+++ ++R+++VD++  ++ P +LIN + + +++ EF  S QLSQ  +  N LS +T
Sbjct: 551  IARMQKAFRDRVATVDVEDPNLKPSELINPRYLTNSILEFLKSGQLSQFMDQTNPLSELT 610

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG GG+ R  A  E+RDVHP+HYGRICP ET EG NIGLVSS+T ++R+N +G
Sbjct: 611  HKRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIETPEGQNIGLVSSMTVYSRINEFG 670

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+ +PYRKV +G VTN++ YL+A EEE   IAQAN+ +DE G F  + V  R  G+  LV
Sbjct: 671  FLISPYRKVINGVVTNEIEYLTAYEEEKYVIAQANAEIDEKGRFLTDRVLARAYGDIRLV 730

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               ++ ++D SPKQVVS +ASLIPFLE+DD+NR LMG NMQRQAVPL++ E P VGTGME
Sbjct: 731  EPNEVHYMDVSPKQVVSPSASLIPFLEHDDANRALMGSNMQRQAVPLIRTEYPLVGTGME 790

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG---DLDPSTSGVDIYRLMKFQRSNQN 773
             V+AK SG+ IVAKR G V +VD   IVI+  E      DP   G+DIY+L KF+ SNQ 
Sbjct: 791  VVIAKDSGSVIVAKRGGEVIKVDGNTIVIKVNEDEINPHDPLDIGMDIYKLNKFKGSNQA 850

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC+NQRPLV+ GD V +   IADG ST  G+LALG+N+LVAFMPW GYNFED+++ISER+
Sbjct: 851  TCMNQRPLVRKGDIVEKGATIADGTSTYKGELALGKNVLVAFMPWRGYNFEDAIVISERL 910

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V +DVFTSIHIEEFE+ AR+TKLGPEEITR+IP ++E  L N+DE G++ VGA V PGDI
Sbjct: 911  VKDDVFTSIHIEEFEIEARETKLGPEEITRNIPGINERQLANLDEHGVVRVGAYVKPGDI 970

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGK+TPKGE+ +TPEEKLL AIFGEKA +V+D+SLRVP GV G VVDV+IF +   DK 
Sbjct: 971  LVGKVTPKGETALTPEEKLLFAIFGEKASEVKDSSLRVPVGVEGVVVDVQIFAKKKKDKK 1030

Query: 954  ERSI----SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            E+      ++ +++++ L  + ++++  +     ++L EIL G       K   +  +  
Sbjct: 1031 EKREKYLDTLIKQEVDKLNLELEEKKKFILDKRDAQLREILIGVKVAKDVKVAGEVIIPE 1090

Query: 1010 SDLISEYPRSQWWQFA-------VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             + ISE   SQ  +         ++D+K+ + VES+  + ++   + E  +  + E +Q 
Sbjct: 1091 GEYISENNVSQAIKIIAINPSNFIKDKKLLKKVESIIEKAKSQIELWEKIYDKRKEAVQE 1150

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G D+ PGV  +VKV++A KR IQ GDKMAGRHGNKG++S +LP EDMPF++DGTPVDIVL
Sbjct: 1151 GADLKPGVNELVKVYIAQKRKIQVGDKMAGRHGNKGVISVVLPVEDMPFMEDGTPVDIVL 1210

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKK--------------IKSLINDYKANGDISPL 1168
            NPLGVPSRMNVGQI ETHLG A   LG+K              I  ++  Y    D    
Sbjct: 1211 NPLGVPSRMNVGQILETHLGLAAKKLGEKLGKELEKIFDREKIIDKIVEYYSIVNDTDNK 1270

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS-GVPVSTPVFDGADEEAINSMLRMAD 1227
                ++   +    E +S  DD+S+  +       G+PV T +F+ A EE I  +L  A 
Sbjct: 1271 ILTAQRKKDSQELREVLSKLDDESLRELVRDLTKIGIPVETAIFESASEEDIKKLLNHAG 1330

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            + ++G+  L DG TGEPFD  VTVGY+YMLKL HMV DK++ARSTG YSL+TQQPLGG++
Sbjct: 1331 IKDNGKVKLIDGRTGEPFDLEVTVGYMYMLKLIHMVDDKIHARSTGPYSLITQQPLGGRA 1390

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++A+GAAY L+EMLT+KSDD+ GR RVYE+I+ G   ++ G PESF
Sbjct: 1391 QFGGQRFGEMEVWALEAHGAAYTLREMLTVKSDDIEGRKRVYEAIIKGKHYYDIGVPESF 1450

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             VLV+E++ALGL+++      +  A     P+  K EL
Sbjct: 1451 KVLVRELKALGLNVECIV-DGQPQACDTSEPEKKKPEL 1487


>gi|325108564|ref|YP_004269632.1| DNA-directed RNA polymerase subunit beta [Planctomyces brasiliensis
            DSM 5305]
 gi|324968832|gb|ADY59610.1| DNA-directed RNA polymerase subunit beta [Planctomyces brasiliensis
            DSM 5305]
          Length = 1238

 Score = 1190 bits (3078), Expect = 0.0,   Method: Composition-based stats.
 Identities = 555/1366 (40%), Positives = 789/1366 (57%), Gaps = 154/1366 (11%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            +  G      ++  L  +Q  SY  FL  ++    R   GL+   + +FP+ +F G   L
Sbjct: 15   RNTGVLQTDFEMSGLTRIQTDSYARFLQADVDTSRRKPVGLEELLREIFPVESFDGQYKL 74

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E++ Y+   P++   +C    LTY  PL++ LRL            + +   E+ +Y+GD
Sbjct: 75   EYIKYDLGKPRYSPMECRQLRLTYGRPLRLWLRL------------NKEQPIEEEVYLGD 122

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LP+M   G F+I G +R++VSQLHRSPG+ F  +        +  ++CRIIP++G W+++
Sbjct: 123  LPIMLGGGEFIINGSERVLVSQLHRSPGVDFVIN---VEPGERKTHSCRIIPERGSWIEL 179

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
                K+ + VRID+  K    + L A+     ++ E++  FYP                 
Sbjct: 180  LISKKETLGVRIDQSGKFSAMTLLRAMDKSHSTDSELVKMFYPTESL------------- 226

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             ++   +K                                         + L G  VA+D
Sbjct: 227  -EITRNSKA----------------------------------------EDLTGKVVADD 245

Query: 312  IVNG----ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            I+      + GEI +E    I E    E+  S I+ + ++   +  ++  I N+++ D  
Sbjct: 246  IIYPAGHEKCGEIIVECAHQIVETQAIELLESGIKTVEVV---TQVSDPLIINSILEDST 302

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               ++ALL IY+ +RPG+      A  +FN  FFD ++Y L  VGR ++N +   D  DD
Sbjct: 303  TSHEEALLRIYQRLRPGNPPQLDKAIDLFNEKFFDLNRYRLGRVGRFRINRKFKQDVSDD 362

Query: 428  VRHIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
               +R  D    I  L+ LR+G     IDDIDNLGNRR+R++ E+  ++ R G L++ R+
Sbjct: 363  EMTLRPIDFSNSIHYLLRLRSGDDSAHIDDIDNLGNRRLRTIDELASDEIRKGFLKLRRT 422

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            ++ER+S  D+D++ P+ LIN K + +A+  FF  S+LSQ+ +  N LS +TH RRLSALG
Sbjct: 423  VQERMSLKDVDTMTPRTLINPKSISAAIDFFFGRSELSQVVDQTNPLSMLTHERRLSALG 482

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL+ +++V+ YGF+ TPY+K+
Sbjct: 483  PGGLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLSVYSKVDDYGFLITPYKKI 542

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             DGKVT+++ +L A EE   Y+A A++   EDG      V  R   E +    E I++ D
Sbjct: 543  VDGKVTDEIEWLRADEEAKVYVAPADTP-TEDGKVAGTRVLARHHHEFVWTTPETIEYFD 601

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             SP Q+V ++A LIPFLE+DD+NR LMG NMQRQAVPLL  E P VGTGME VVA++SG 
Sbjct: 602  ISPCQMVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLITEQPIVGTGMEKVVAENSGM 661

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + A++AG V  VDA  I I                Y L K+   N+ TC+NQ+PLV+VG
Sbjct: 662  GVFAEKAGTVTFVDATVIEI------------DGKSYPLRKYMGLNERTCLNQKPLVRVG 709

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            ++V++  ++ D  +T  G+LALGRN+LVAFM W GYNFED++++SER+  EDV+TSIHI+
Sbjct: 710  EKVKKGQLLCDTAATRDGELALGRNVLVAFMSWEGYNFEDAIILSERLAKEDVYTSIHID 769

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            EF+V  R+TKLG EE TRDIPNVSE+ L+++D  GI+ +G  V+PGDILVGK+TPK +S 
Sbjct: 770  EFDVEIRETKLGREEFTRDIPNVSEKALRHLDNNGIVQIGTRVSPGDILVGKVTPKAKSE 829

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLL AIFG    DV++ SL VPSGV G V+    F+R          S E    E
Sbjct: 830  LTPEEKLLHAIFGRAGEDVKNESLEVPSGVEGIVIHTEKFSRRMSLTESEKKSYESGLKE 889

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
              A  + +E + +    + +  E   G   +S   G +  +V    ++++Y  +   +F 
Sbjct: 890  --AETEGNEAIAVAFKDFLKTFEAELG-KHLSDEDGIEWRSVEDPKMLAQYAENFLQKFE 946

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFK---NKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              D +  + +   K       SI+ED      +K+  ++ GD++P GVL++VKV+VA KR
Sbjct: 947  QLDIRSPQKIADCKKIISEHWSIVEDAIDARDSKLNTLKRGDELPSGVLQMVKVYVASKR 1006

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQI ET LG
Sbjct: 1007 QISVGDKMAGRHGNKGVISKILPVEDMPFLSDGTPVDIILNPLGVPSRMNVGQILETQLG 1066

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   LG +    + D      I                                     
Sbjct: 1067 WAAEKLGFRALCPVFDSIDEQGI------------------------------------- 1089

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                    FD         ++  A L   G+S L+DG TGE F++  TVG IYMLKL+H+
Sbjct: 1090 --------FD---------LMGEAGLPTDGKSQLFDGRTGEAFEQKTTVGQIYMLKLHHL 1132

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DKV+AR+TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV
Sbjct: 1133 VDDKVHARATGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDV 1192

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             GRT++YES+V G +T E GTP SF+VL  E++ L L++ LE +  
Sbjct: 1193 EGRTKIYESMVKGENTLEAGTPASFDVLNNEIRGLCLNMQLEKTTG 1238


>gi|188996246|ref|YP_001930497.1| DNA-directed RNA polymerase, beta subunit [Sulfurihydrogenibium sp.
            YO3AOP1]
 gi|188931313|gb|ACD65943.1| DNA-directed RNA polymerase, beta subunit [Sulfurihydrogenibium sp.
            YO3AOP1]
          Length = 1488

 Score = 1181 bits (3056), Expect = 0.0,   Method: Composition-based stats.
 Identities = 603/1470 (41%), Positives = 876/1470 (59%), Gaps = 106/1470 (7%)

Query: 14   RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-NEGLQAAFKSVFPITAFSGAA 72
            RK   +  EII  PDL+ V K S+++F+  +  P +R  N+GL++  ++ FP    +G  
Sbjct: 13   RKILSRRREIITPPDLLSVPKESFENFVQFHTNPLKRDPNKGLESLLRTSFPFVDPNGQL 72

Query: 73   MLEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAV 100
             + ++ YE                                    K  V++C ++ LTY  
Sbjct: 73   EVRYIGYEIGDWECGKCGKALPDEVLGGPEVDCPHCGGPLIYKEKLTVEECKFKGLTYGA 132

Query: 101  PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            PL++ L L++   D  TG    K IK+Q IY G++PL+T    F+I G +RI+VSQL RS
Sbjct: 133  PLRVLLELVINHTDPKTGEIIPKTIKKQKIYFGEIPLLTDYAYFMINGSERIIVSQLIRS 192

Query: 161  PGIHFDHDKGRA-SLSGKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTSFL 218
             GI F   + +   +  +++Y   +IP++G  +++++ +  +I + +IDR RK+  T+ L
Sbjct: 193  SGIFFSGKEDKTKDIITRVIYEGSVIPEKGSRVEVQYATNSEIFYAKIDR-RKILGTTLL 251

Query: 219  MALGMDSE-EILSTFYPKI-VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
             A G+D+  +IL  FY K+  Y           +   + +   ++  +      E++ E 
Sbjct: 252  RAFGLDTTYKILKNFYGKVDRYIVEDGKLVLENTKIPVNLEELMNRDIFVTYVYEEISEK 311

Query: 277  GKKLTSGLLKSLKEKGVKFLGITSD-CLCGLYVAED-IVNGETGEIYIEAGDVIDEKSLE 334
            G+ +     K +  + ++ L       +  +   E  ++N    +  I      DE  + 
Sbjct: 312  GQPVPIKQEKYVSVENLEKLLNDDRIRIEEVVTVEPQVINKSPYQRVIVETLKKDEPKIN 371

Query: 335  EIFHSEIRDIPILYVDS-------VNNNAYIRNTLVTDKNKDRKDALLDIYRV------- 380
             +F      +  +Y          ++  A+++       N        D+ RV       
Sbjct: 372  ALFTFRDAALVEIYRKMRPTDTAVLDPKAFMKRAKELFNNMFADIQRYDLSRVGRVKLNA 431

Query: 381  --------MRPGDVSTFSVAESMFNFLFFDSDKY---------DLSTVGRVKMNM----R 419
                    ++P D+  F     +         K          DL  + ++K       +
Sbjct: 432  KVHNVPKTIKPLDLEDFFEKFPLLALDEDVKTKNGVIPKGTKIDLVVLEKLKETSFKEIK 491

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            +     ++ R ++  DIIAI+K L++LR GK ++DDI +LGNRRVR VGE+L+ Q R+G+
Sbjct: 492  VKEYLDEEARTLQLADIIAIVKYLLELRYGKKSLDDIAHLGNRRVRPVGELLEAQARIGI 551

Query: 480  LRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             RM+++ ++R+++VD++  ++ P +LIN + + +++ EF  S QLSQ  +  N LS +TH
Sbjct: 552  ARMQKAFRDRVATVDVEDPNLKPSELINPRYLTNSILEFLKSGQLSQFMDQTNPLSELTH 611

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R  A  E+RDVHP+HYGRICP ET EG NIGLVSS+T ++R+N +GF
Sbjct: 612  KRRLSALGPGGLTRESAKFEIRDVHPSHYGRICPIETPEGQNIGLVSSMTVYSRINEFGF 671

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            + +PYRKV DG VTN++ YL+A EEE   IAQAN+ +DE G F  + V  R  G+  LV 
Sbjct: 672  LISPYRKVVDGVVTNEIEYLTAYEEEKYVIAQANAEIDEKGRFLTDRVLARAYGDIRLVE 731

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              ++ ++D SPKQVVS +ASLIPFLE+DD+NR LMG NMQRQAVPL++ E P VGTGME 
Sbjct: 732  PNEVHYMDISPKQVVSPSASLIPFLEHDDANRALMGSNMQRQAVPLVRTEYPLVGTGMEV 791

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG---DLDPSTSGVDIYRLMKFQRSNQNT 774
             +AK SG+ IVAKR G V +VD   IVI+  E      DP   G+DIY+L KF+ SNQ T
Sbjct: 792  SIAKDSGSVIVAKRGGEVVKVDGNTIVIKVNEDEINPHDPLDIGMDIYKLNKFKGSNQAT 851

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQRPLV+ GD V +   IADG ST  G+LALG+N+LVAFMPW GYNFED+++ISER+V
Sbjct: 852  CMNQRPLVRKGDIVEKGATIADGTSTYKGELALGKNVLVAFMPWRGYNFEDAIVISERLV 911

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +DVFTSIHIEEFE+ AR+TKLGPEEITR+IP ++E  L N+DE G+I VGA V PGDIL
Sbjct: 912  KDDVFTSIHIEEFEIEARETKLGPEEITRNIPGINERQLANLDEHGVIRVGAYVKPGDIL 971

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLL AIFGEKA +V+D+SLRVP GV G VVDV+IF +   DK E
Sbjct: 972  VGKVTPKGETALTPEEKLLFAIFGEKASEVKDSSLRVPVGVEGVVVDVQIFAKKKKDKKE 1031

Query: 955  RSI----SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +      ++ +++++ L  + ++++  +     + L EIL G       K   +  +   
Sbjct: 1032 KREKYLDTLIKQEVDKLNLELEEKKKFILDKRDAWLREILIGVKVAKDVKVAGEVIIPEG 1091

Query: 1011 DLISEYPRSQWWQFA-------VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            + I+E   SQ  +         ++D+K+ + VES+  + ++   + E  ++ + E +Q G
Sbjct: 1092 EYITENNVSQAIKIIAINPSNFIKDKKLIKKVESIIEKAKSQIELWEKIYEKRKEAVQEG 1151

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
             D+ PGV  +VKV++A KR IQ GDKMAGRHGNKG++S +LP EDMPF++DGTPVDIVLN
Sbjct: 1152 ADLKPGVNELVKVYIAQKRKIQVGDKMAGRHGNKGVISVVLPVEDMPFMEDGTPVDIVLN 1211

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKK--------------IKSLINDYKANGDISPLR 1169
            PLGVPSRMNVGQI ETHLG A   LG+K              I  ++  Y    D     
Sbjct: 1212 PLGVPSRMNVGQILETHLGLAAKKLGEKLGKELEKIFDREKIIDKIVEYYSIVNDTDNKI 1271

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS-GVPVSTPVFDGADEEAINSMLRMADL 1228
               ++   +    E +S  DD+S+  +       G+PV T +F+ A EE I  +L  A +
Sbjct: 1272 LTKQRKKDSQELREALSKLDDESLRDLVRDLTKIGIPVETAIFESASEEDIKKLLNYAGI 1331

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             ++G+  L DG +GE FD  VT GY+YMLKL HMV DK++ARSTG YSL+TQQPLGG++ 
Sbjct: 1332 KDNGKVKLIDGRSGEAFDLEVTAGYMYMLKLIHMVDDKIHARSTGPYSLITQQPLGGRAQ 1391

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++A+GAAY L+EMLT+KSDD+ GR RVYE+I+ G   ++ G PESF 
Sbjct: 1392 FGGQRFGEMEVWALEAHGAAYTLREMLTVKSDDIEGRKRVYEAIIKGKHYYDIGVPESFK 1451

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            VLV+E++ALGL+++        +    E+ 
Sbjct: 1452 VLVRELKALGLNVECIVEGEPQACDTSELE 1481


>gi|283780325|ref|YP_003371080.1| DNA-directed RNA polymerase subunit beta [Pirellula staleyi DSM 6068]
 gi|283438778|gb|ADB17220.1| DNA-directed RNA polymerase, beta subunit [Pirellula staleyi DSM
            6068]
          Length = 1240

 Score = 1180 bits (3053), Expect = 0.0,   Method: Composition-based stats.
 Identities = 543/1366 (39%), Positives = 787/1366 (57%), Gaps = 152/1366 (11%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R  + FG    +  +PDL  +Q ASY  FL  ++  ++R ++GL+   K +FPI ++   
Sbjct: 12   RESRRFGSGISVQTMPDLTVIQTASYAAFLQDDLPAEKRKDQGLEGVLKEIFPIESYDKT 71

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              L+++ Y+   P++  ++C    LTY  P +I LRL            + +   E+ +Y
Sbjct: 72   IKLDYLRYDLGKPRYTPEECRQLRLTYGRPFRIWLRL------------NKEQPIEEEVY 119

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +GD+P+M   G F+I G +R+VVSQLHRSPG+ F  ++     S + L +CRIIP++G W
Sbjct: 120  LGDIPIMLGGGEFIINGAERVVVSQLHRSPGVDFVMEQDGT--SDRKLPSCRIIPERGSW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--GMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            +++    ++ + +RID+  K    + L A+     ++ +++  FYP  +           
Sbjct: 178  IEVNVTKREALSIRIDQSGKFSALTLLRAMSPKYSTDSDLIRAFYPPTIEKITDGRSVVK 237

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            +                    G+  ++                                V
Sbjct: 238  IE-------------------GKIAVD-------------------------------DV 247

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
                 +   GEI +EAG  I + + E I  S +  + ++    V     I N+L  D   
Sbjct: 248  CYPSGSDRAGEIIVEAGHKITKNAAETICTSGVTKVEVI---PVPKVPVIFNSLAEDTTS 304

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              ++ALL IY+ +RPG+      A+++F   FFD ++Y L  VGR ++N +L L+T D  
Sbjct: 305  SHEEALLRIYQRLRPGNPPQLEKAKTLFAEKFFDVNRYRLGRVGRFRVNRKLKLETSDKE 364

Query: 429  RHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
              +  ED+IA I  L+DL  G G   IDDID+LGNRR+R++ E+  ++ R G L++ R++
Sbjct: 365  MTLNPEDLIASIAYLLDLMGGTGDAHIDDIDHLGNRRLRTIDELASDELRKGFLKLRRTV 424

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +ER+S  D++ + P+ L+N K + +A+  FF   +LSQ+ +  N LS++TH RRLSALG 
Sbjct: 425  QERMSLKDVEDMTPRSLVNPKSISAAIEYFFGRGELSQVVDQTNPLSQLTHERRLSALGP 484

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL  +A V+ YGF+  PYRKV 
Sbjct: 485  GGLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLAIYAGVDEYGFLVAPYRKVN 544

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
             GK+T +VV+L A EE + Y+A A++++ +        +  R   +  +V  +++ FID 
Sbjct: 545  KGKLTEEVVWLRADEEADAYVAPADTAVQDGKIVQSASLIARHRSDFEIVLPDQVQFIDV 604

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            +P Q+V ++A LIPFLE+DD+NR LMG NMQRQAVPLL  E P V TGME  VA++S   
Sbjct: 605  APSQMVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLVTEPPIVATGMEKDVARNSSMV 664

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            + AKRAG V   DA RI I            G DIY L K+Q  N+ TC+NQ+P++K+GD
Sbjct: 665  VRAKRAGKVTYCDATRIEI------------GSDIYHLKKYQGLNERTCLNQKPIIKLGD 712

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            +V +N ++ADG +T  G+LALGRN+LV FM + GYNFED+++IS+ +V  D +TSIHIEE
Sbjct: 713  KVEKNQVLADGAATYNGELALGRNVLVGFMSFDGYNFEDAIIISQELVQNDTYTSIHIEE 772

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            F+V  R+TKLG EE TRDIPNVSE+ L+N+DE GI+ +G  V PGDILVGK++PK ++ +
Sbjct: 773  FDVEIRETKLGREEFTRDIPNVSEKALRNLDENGIVRIGTFVKPGDILVGKVSPKSKTEL 832

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            TPEEKLL AIFG    DV++ SL VPSG+ G V+D + F+R      +     ER++ E 
Sbjct: 833  TPEEKLLHAIFGRAGEDVKNDSLEVPSGIEGIVIDTQKFSRRMSLSED-----ERKKFEK 887

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA- 1025
              +D + E        +  L+E L      +     ++ T L  D   ++   +   F  
Sbjct: 888  ELKDAETEGNKWIAQAFGTLVEELEAVVGKTLTD--EEGTPLVKDQDPKFVSERAANFQL 945

Query: 1026 ------VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                  ++ +      E +  Q+  +  +  D    K+  ++ GD++  GVL++VKV+++
Sbjct: 946  LKITSKLRSDDKIAEAEKVYKQHWPNVELAIDNRDRKLNSMKRGDELRSGVLQMVKVYIS 1005

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDKMAGRHGNKG++++ILP EDMPFL DGT V I+LNPLGVPSRMNVGQI ET
Sbjct: 1006 TKRVISVGDKMAGRHGNKGVIAKILPIEDMPFLPDGTSVQIMLNPLGVPSRMNVGQILET 1065

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA   LG +  + + D    GDI+                                 
Sbjct: 1066 HLGWAGAALGFQAVTPVFDGATEGDINDCLEAAG-------------------------- 1099

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                                   L         +  L+DG TGE   +  TVGY+YMLKL
Sbjct: 1100 -----------------------LPRHG-----KQRLFDGRTGEALQQETTVGYLYMLKL 1131

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DKV+ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KS
Sbjct: 1132 HHLVDDKVHARSTGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKS 1191

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            DDV GRT++YES+V G +T E GTP SF VL  E++ L L++ LE 
Sbjct: 1192 DDVEGRTKIYESMVKGENTLEAGTPASFEVLTNEIRGLALNMQLEK 1237


>gi|32473688|ref|NP_866682.1| DNA-directed RNA polymerase beta chain [Rhodopirellula baltica SH 1]
 gi|32444224|emb|CAD74221.1| DNA-directed RNA polymerase beta chain [Rhodopirellula baltica SH 1]
 gi|327540885|gb|EGF27445.1| DNA-directed RNA polymerase subunit beta [Rhodopirellula baltica
            WH47]
          Length = 1261

 Score = 1171 bits (3029), Expect = 0.0,   Method: Composition-based stats.
 Identities = 539/1358 (39%), Positives = 770/1358 (56%), Gaps = 139/1358 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK FG      D+PDL  +Q  SY  FL  + A + R + GL++  + +FPI ++ G  
Sbjct: 35   IRK-FGTGLGQFDLPDLTALQTVSYAAFLQEDAASNARKDHGLESVLREIFPIASYDGNT 93

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE++ YE   P++ + +C    LTY  PL+I LRL            + ++  E+ +Y+
Sbjct: 94   TLEYLYYELGKPRYTIQECRQLRLTYGRPLRIWLRL------------NREEPIEEEVYL 141

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            GDLP+M   G F+I G +R+VVSQLHRSPG+ F  ++     + + L +CR+IP++G W+
Sbjct: 142  GDLPIMLGGGEFIINGAERVVVSQLHRSPGVDFVLEQDTT--TDRKLPSCRVIPERGSWI 199

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            ++    KD + VRID+  K   T  L A+     ++ ++LS FY        G      +
Sbjct: 200  EVNVTKKDALTVRIDQSGKFAATMLLRAMDPKYSTDADLLSAFYETGTIKVNGGKDATKI 259

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                                          + +         V 
Sbjct: 260  E-------------------------------------------NKIAVDD-------VV 269

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                +   GEI +EAG  I  +  E I ++ +  +  + +  V     I NTL  D    
Sbjct: 270  YPSGHERAGEIIVEAGYKITTELSETICNAGVTSVEAMDLPKV---PLIFNTLADDNTAS 326

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             ++ALL IY+ +RPG+      A ++F   F+D ++Y L  VGR ++N +L L   + V 
Sbjct: 327  HEEALLRIYQRLRPGNPPQLEKARTLFQEKFYDDNRYRLGKVGRFRLNRKLGLGVEETVM 386

Query: 430  HIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +R +D+IA I+ L+DL +      IDDID+LGNRR+R++ E+   + R G L++ R+++
Sbjct: 387  TLRPDDMIAAIRYLIDLFDADSGAEIDDIDHLGNRRLRTIDELASEELRKGFLKLRRTVQ 446

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+S  D   + P+ LIN K V +A+  FF   +LSQ+ +  N LS++ H RRLSALG G
Sbjct: 447  ERMSVKDAQDMTPRSLINPKSVSAAIDFFFGRGELSQVVDQTNPLSQLAHERRLSALGPG 506

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL  +A V+ YGF+ TP+RKV D
Sbjct: 507  GLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLAIYAGVDDYGFLCTPFRKVID 566

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GK++++ V+L A EE   Y+A A++ + +        +  R   +  +V  E++ F+D +
Sbjct: 567  GKISDETVWLRADEEGESYVAPADTEVKDGALVPGPNMIARFRSDFEIVMPEQVSFMDVA 626

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+V ++A LIPFLE+DD+NR LMG NMQRQAVPLL  E P VGTGME  VAK+S   +
Sbjct: 627  PAQMVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLVTEPPIVGTGMEREVAKNSAMVV 686

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+RAG V   DA RI I            G D Y L K+Q  N+ TC NQ+PL+ VGD+
Sbjct: 687  RARRAGKVTYADATRIEI------------GSDHYPLKKYQGLNERTCQNQKPLITVGDK 734

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  IIADG +T  G+LALGRN+LV FM + G+N+ED+++ISE +V  D +TSIHIE+F
Sbjct: 735  VEKGQIIADGAATQKGELALGRNVLVGFMSFDGFNYEDAIIISEELVRNDTYTSIHIEDF 794

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            +V  R+TKLG EE TRDIPNVSE+ L+N+D+ GI+  G  V PGDILVGK++PK ++ +T
Sbjct: 795  DVEIRETKLGREEFTRDIPNVSEKALRNLDDTGIVQTGTYVKPGDILVGKVSPKSKTELT 854

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL AIFG    DV++ SL VPSG+ G V+D + F+R      +   + ERE  +  
Sbjct: 855  PEEKLLHAIFGRAGEDVKNDSLEVPSGIEGIVIDTQKFSRRMSLGEDERKAFERELKQHE 914

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                ++     +  I              +G               +   R +     ++
Sbjct: 915  TEGNEEIASTFESLIRDMEEASGVKLKDSTGTPLADGQDPKFVAERATSFRLELVLEQIE 974

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DE+ ++  E +      +     D    K+  ++ GD++  GVL++VK+++A KR I  G
Sbjct: 975  DEEKRKAAEKVHQTQWQNVEQAIDERDRKLNSMKRGDELRSGVLQMVKIYIATKRTISVG 1034

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++++ILP EDMPFL DGTP+ I+LNPLGVPSRMNVGQI ETHLGWA   
Sbjct: 1035 DKMAGRHGNKGVIAKILPIEDMPFLPDGTPIQIMLNPLGVPSRMNVGQILETHLGWAGAK 1094

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG +  + I D  +  +I+   +                                     
Sbjct: 1095 LGFQALTPIFDGASESEINDCLAEAGLPAHGKIRL------------------------- 1129

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G++       GEP ++  TVGYIYMLKL+H+V DKV
Sbjct: 1130 ----------------------TDGRT-------GEPMEQETTVGYIYMLKLHHLVDDKV 1160

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GRT+
Sbjct: 1161 HARSTGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGRTK 1220

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +YES+V G +T E GTP SF+VL  E++ L L++ LE 
Sbjct: 1221 IYESMVKGENTLEAGTPASFDVLTNEIRGLALNMQLEK 1258


>gi|41017927|sp|Q7URW6|RPOB_RHOBA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1240

 Score = 1169 bits (3024), Expect = 0.0,   Method: Composition-based stats.
 Identities = 539/1358 (39%), Positives = 770/1358 (56%), Gaps = 139/1358 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK FG      D+PDL  +Q  SY  FL  + A + R + GL++  + +FPI ++ G  
Sbjct: 14   IRK-FGTGLGQFDLPDLTALQTVSYAAFLQEDAASNARKDHGLESVLREIFPIASYDGNT 72

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             LE++ YE   P++ + +C    LTY  PL+I LRL            + ++  E+ +Y+
Sbjct: 73   TLEYLYYELGKPRYTIQECRQLRLTYGRPLRIWLRL------------NREEPIEEEVYL 120

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            GDLP+M   G F+I G +R+VVSQLHRSPG+ F  ++     + + L +CR+IP++G W+
Sbjct: 121  GDLPIMLGGGEFIINGAERVVVSQLHRSPGVDFVLEQDTT--TDRKLPSCRVIPERGSWI 178

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSE-EILSTFYPKIVYSQRGDFWCFPL 249
            ++    KD + VRID+  K   T  L A+     ++ ++LS FY        G      +
Sbjct: 179  EVNVTKKDALTVRIDQSGKFAATMLLRAMDPKYSTDADLLSAFYETGTIKVNGGKDATKI 238

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                                          + +         V 
Sbjct: 239  E-------------------------------------------NKIAVDD-------VV 248

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                +   GEI +EAG  I  +  E I ++ +  +  + +  V     I NTL  D    
Sbjct: 249  YPSGHERAGEIIVEAGYKITTELSETICNAGVTSVEAMDLPKV---PLIFNTLADDNTAS 305

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             ++ALL IY+ +RPG+      A ++F   F+D ++Y L  VGR ++N +L L   + V 
Sbjct: 306  HEEALLRIYQRLRPGNPPQLEKARTLFQEKFYDDNRYRLGKVGRFRLNRKLGLGVEETVM 365

Query: 430  HIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +R +D+IA I+ L+DL +      IDDID+LGNRR+R++ E+   + R G L++ R+++
Sbjct: 366  TLRPDDMIAAIRYLIDLFDADSGAEIDDIDHLGNRRLRTIDELASEELRKGFLKLRRTVQ 425

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            ER+S  D   + P+ LIN K V +A+  FF   +LSQ+ +  N LS++ H RRLSALG G
Sbjct: 426  ERMSVKDAQDMTPRSLINPKSVSAAIDFFFGRGELSQVVDQTNPLSQLAHERRLSALGPG 485

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            G+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL  +A V+ YGF+ TP+RKV D
Sbjct: 486  GLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLAIYAGVDDYGFLCTPFRKVID 545

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            GK++++ V+L A EE   Y+A A++ + +        +  R   +  +V  E++ F+D +
Sbjct: 546  GKISDETVWLRADEEGESYVAPADTEVKDGALVPGPNMIARFRSDFEIVMPEQVSFMDVA 605

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P Q+V ++A LIPFLE+DD+NR LMG NMQRQAVPLL  E P VGTGME  VAK+S   +
Sbjct: 606  PAQMVGVSAGLIPFLEHDDANRALMGSNMQRQAVPLLVTEPPIVGTGMEREVAKNSAMVV 665

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+RAG V   DA RI I            G D Y L K+Q  N+ TC NQ+PL+ VGD+
Sbjct: 666  RARRAGKVTYADATRIEI------------GSDHYPLKKYQGLNERTCQNQKPLITVGDK 713

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  IIADG +T  G+LALGRN+LV FM + G+N+ED+++ISE +V  D +TSIHIE+F
Sbjct: 714  VEKGQIIADGAATQKGELALGRNVLVGFMSFDGFNYEDAIIISEELVRNDTYTSIHIEDF 773

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            +V  R+TKLG EE TRDIPNVSE+ L+N+D+ GI+  G  V PGDILVGK++PK ++ +T
Sbjct: 774  DVEIRETKLGREEFTRDIPNVSEKALRNLDDTGIVQTGTYVKPGDILVGKVSPKSKTELT 833

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL AIFG    DV++ SL VPSG+ G V+D + F+R      +   + ERE  +  
Sbjct: 834  PEEKLLHAIFGRAGEDVKNDSLEVPSGIEGIVIDTQKFSRRMSLGEDERKAFERELKQHE 893

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                ++     +  I              +G               +   R +     ++
Sbjct: 894  TEGNEEIASTFESLIRDMEEASGVKLKDSTGTPLADGQDPKFVAERATSFRLELVLEQIE 953

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DE+ ++  E +      +     D    K+  ++ GD++  GVL++VK+++A KR I  G
Sbjct: 954  DEEKRKAAEKVHQTQWQNVEQAIDERDRKLNSMKRGDELRSGVLQMVKIYIATKRTISVG 1013

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++++ILP EDMPFL DGTP+ I+LNPLGVPSRMNVGQI ETHLGWA   
Sbjct: 1014 DKMAGRHGNKGVIAKILPIEDMPFLPDGTPIQIMLNPLGVPSRMNVGQILETHLGWAGAK 1073

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG +  + I D  +  +I+   +                                     
Sbjct: 1074 LGFQALTPIFDGASESEINDCLAEAGLPAHGKIRL------------------------- 1108

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G++       GEP ++  TVGYIYMLKL+H+V DKV
Sbjct: 1109 ----------------------TDGRT-------GEPMEQETTVGYIYMLKLHHLVDDKV 1139

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GRT+
Sbjct: 1140 HARSTGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGRTK 1199

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +YES+V G +T E GTP SF+VL  E++ L L++ LE 
Sbjct: 1200 IYESMVKGENTLEAGTPASFDVLTNEIRGLALNMQLEK 1237


>gi|149177090|ref|ZP_01855698.1| DNA-directed RNA polymerase beta chain [Planctomyces maris DSM 8797]
 gi|148844155|gb|EDL58510.1| DNA-directed RNA polymerase beta chain [Planctomyces maris DSM 8797]
          Length = 1238

 Score = 1165 bits (3014), Expect = 0.0,   Method: Composition-based stats.
 Identities = 536/1363 (39%), Positives = 770/1363 (56%), Gaps = 148/1363 (10%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            K FGK     ++ DL ++Q +SY  FL  + +P ER N+GL+   + VFPI ++ G   L
Sbjct: 15   KNFGKIEHGFELSDLTQIQTSSYASFLQADKSPRERKNQGLEEILREVFPIESYQGQYQL 74

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            E+V YE   P++   +C    +TY  P ++ LRL+             +   E+ +Y+GD
Sbjct: 75   EYVKYELGKPRYTPTECRQLRMTYGRPFRVWLRLV------------KEQPIEEEVYLGD 122

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            LP+M   G F+I G +R +VSQLHRSPG+ F      +    K  Y+CR+IP++G W+++
Sbjct: 123  LPVMIGGGEFIINGAERCIVSQLHRSPGVDFVLS---SEPGEKKEYSCRVIPERGSWIEL 179

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMAL--GMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
                KD + VRID+  K    + L A+     S+ +++  FY                  
Sbjct: 180  VVGKKDTLGVRIDQSGKFSAMTLLRAMSKDYSSDTDLVKLFYDT---------------- 223

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                      +K++S                  + L G  VAED
Sbjct: 224  ------------------------KSEKISSSNA--------------MEKLLGKIVAED 245

Query: 312  IVNG----ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            ++        GE+ ++    I E+ ++EI  + ++ + I+       +  +  ++  D  
Sbjct: 246  VIYPAGHDRCGEVILDCCGTITEELIDEIVDTGLKTVEIVD---EVTDVLVLQSIAEDPT 302

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               ++ALL IY  +RPG+      A  +F   FFD ++Y L  VGR ++N +   D PD 
Sbjct: 303  ATHEEALLRIYSRLRPGNPPQLERAIDLFKEKFFDVNRYRLGRVGRFRINRKFKQDVPDT 362

Query: 428  VRHIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
               +R ED I  I+ LV LR G+    +DDIDNLGNRR+R++ E+  ++ R G L++ R+
Sbjct: 363  EMTLRPEDFINSIRYLVRLRVGESSAYVDDIDNLGNRRLRTIDELASDEIRKGFLKLRRT 422

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            ++ER++  D++ + P+ LIN K V +A+  FF  S+LSQ+ +  N LS +TH RRLSALG
Sbjct: 423  VQERMTQKDVEEMSPRTLINPKSVSAAIDFFFGRSELSQVVDQTNPLSMLTHERRLSALG 482

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL+ F++V+ YGF+ TPYR V
Sbjct: 483  PGGLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLSIFSKVDDYGFLVTPYRYV 542

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             +GK+T++V ++ A EE   ++A A++ + E+G F E+ V  R   + + +    +D+ID
Sbjct: 543  KNGKLTDEVHWMRADEEAEVHVAPADTPV-ENGKFIEDRVMARHRDDVVWIAAGDVDYID 601

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
              P Q+V I+A LIPFLE+DD+NR LMG NMQRQAVPLL AE P VGTGME  VA++SG 
Sbjct: 602  VDPAQMVGISAGLIPFLEHDDANRALMGSNMQRQAVPLLIAEPPLVGTGMEVAVAQNSGM 661

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + A++AG V  VD   + +                YRL K++  N+ TC+NQ P V VG
Sbjct: 662  VVRAEKAGKVTYVDGNVVEVNG------------KKYRLRKYEGLNERTCLNQTPAVSVG 709

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D+V++  I+    +   G LALGRN+LV FM W GYNFED++++SER+V EDV+TSIHI+
Sbjct: 710  DQVKKGQILCHSAAAADGLLALGRNVLVGFMSWDGYNFEDAIILSERLVKEDVYTSIHID 769

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            EF+V  R+TKLG EE TRDIPNVSE+ L++I E GII VG  V  GDILVGK++PK ++ 
Sbjct: 770  EFDVEIRETKLGREEFTRDIPNVSEKALRHIGEDGIIKVGTRVRQGDILVGKVSPKAKAE 829

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLL AIFG    DV++ SL   SGV G V+    F R     +      + E  +
Sbjct: 830  LTPEEKLLHAIFGRAGEDVKNESLEASSGVEGIVIHTEKFARRMSLTDYERKQYDEELKK 889

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            +               + +    +        G K  +          +    S      
Sbjct: 890  VEEEGNHQIAEEFRDFLKTFENALGQPMVDDDGRKVREIPEDKFVSQYAHDFLSHLDDMD 949

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            ++  + + +  ++      +   + +    K+  ++ G+++P GVL++VKV+VA KR I 
Sbjct: 950  IRSPQKKADCRAVIEDLWPNVEDVIETCDQKVNSMKRGEELPNGVLQMVKVYVASKRQIS 1009

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG++S++LP EDMPF +DGTP+DI+LNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 1010 VGDKMAGRHGNKGVISKVLPIEDMPFTEDGTPIDIMLNPLGVPSRMNVGQILETHLGWAA 1069

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G +    + D      I                            L  A   K G  
Sbjct: 1070 EKHGFRAVCPVFDGAMESQIQ-------------------------EFLETAGLPKDG-- 1102

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                       ++ L+DG TGE +++  TVG IYMLKL+H+V D
Sbjct: 1103 ---------------------------KAQLFDGRTGEAYEQKTTVGQIYMLKLHHLVDD 1135

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            KV+ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GR
Sbjct: 1136 KVHARSTGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGR 1195

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            T++YES+V G +T E GTP SF+VL  E++ LGL++ LE +  
Sbjct: 1196 TKIYESMVNGENTLEAGTPASFDVLNNEIRGLGLNLQLEKNPG 1238


>gi|149198915|ref|ZP_01875956.1| DNA-directed RNA polymerase subunit beta [Lentisphaera araneosa
            HTCC2155]
 gi|149137910|gb|EDM26322.1| DNA-directed RNA polymerase subunit beta [Lentisphaera araneosa
            HTCC2155]
          Length = 1263

 Score = 1163 bits (3008), Expect = 0.0,   Method: Composition-based stats.
 Identities = 581/1380 (42%), Positives = 808/1380 (58%), Gaps = 145/1380 (10%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +R+ FGK  E+ID PDLI VQ  S+  FL     PD R  +GLQ AF  +FPI +F    
Sbjct: 3    IRQNFGKLEEVIDTPDLISVQLESFREFLQETTNPDSREKKGLQEAFNEIFPIKSFDENC 62

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +L FV YE   P  ++ DCL    +Y   L +T  L + D +  +      ++ E+ ++M
Sbjct: 63   ILNFVKYEIGTPNVNMYDCLKDGESYQAGLHVTFELEIKDENGKS------ELFEERVFM 116

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            GD+P+MT   TF+I G +R+++SQLHR+PGI F+  K     S K LY+ RIIPD+G WM
Sbjct: 117  GDIPVMTPRATFIINGAERVIISQLHRTPGICFEAGKS---TSNKTLYSFRIIPDRGSWM 173

Query: 193  DIEFDSKDIIHVRID---RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            ++++D+ D+I++ +D   RRRK  +++FL A+  +S  ++L   Y     +         
Sbjct: 174  EVQYDNHDLIYIFMDRRRRRRKFLISTFLRAVYSESNYDLLDCVYGVQNVTV------AS 227

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            L+  +  +  K+    +  + G  + ++ + L+S +L  +K+ GVK L            
Sbjct: 228  LAKDESTLAEKILVDDITDENGTLIAKTLEPLSSSILDLVKDAGVKKL------------ 275

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
              DIV+                             I  L  D                  
Sbjct: 276  --DIVDT---------------------HELGTTFITNLEKDP---------------TT 297

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN------- 421
            +R+DAL  IY+ MRPGD +    A+ + N LFFD   YDL  VGR K+  RL        
Sbjct: 298  NREDALKYIYKKMRPGDPANIENAQGLLNRLFFDLKSYDLGKVGRYKIQQRLRNAFDGDQ 357

Query: 422  -----LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                 L  P + R +   D++A    L+ ++N  G +DDID+LG+RRVRSVGE+++NQ+R
Sbjct: 358  FKSKDLPLPTEERTLTPSDMVAATITLMKIKNTHGRVDDIDHLGSRRVRSVGELVQNQFR 417

Query: 477  LGLLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             GL R ER I+ER++  D +S  +MP  LIN K + S V +FF  SQLSQ  +  N LS 
Sbjct: 418  SGLSRTERLIRERMTLYDKNSTAIMPSKLINPKALQSVVRDFFGRSQLSQFMDQTNPLSE 477

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            +T  RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+SSL  +A++N 
Sbjct: 478  LTAKRRLSALGPGGLSRERAGFEVRDVHSSHYGRICPIETPEGPNIGLISSLACYAKINP 537

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            YGF+ETPYRK  DGKVT ++ Y++   EE+  +AQAN+ L++D +  E  V  R  G+ +
Sbjct: 538  YGFLETPYRKFVDGKVTEEIEYVTGDIEEDFVVAQANTVLNDDNTVAEAYVLARTDGDSV 597

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             V ++KI  +D SPKQ++S A   IPF+E+DD+NR LMG NMQRQAVPLLK ++P VGTG
Sbjct: 598  EVEKDKITHMDVSPKQLISPATGCIPFIEHDDANRALMGSNMQRQAVPLLKPDSPLVGTG 657

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQN 773
            ME++VAK S A + AK  GIV    + +I+I       D      + IY L KF RSN +
Sbjct: 658  MEALVAKGSRAVLTAKADGIVASSVSDKIIITKDGVLKDEEDLKPENIYNLYKFMRSNSS 717

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC+NQ+PLVK GD V+  D+IADG  TD G+LALG+N+LVAFMPW GYNFED+++ISER+
Sbjct: 718  TCMNQKPLVKAGDVVKAGDVIADGFGTDNGELALGQNVLVAFMPWCGYNFEDAIIISERL 777

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V +DVFTSIHI E  + ARDTKLGPEEITRD PNV EE L+N+   G+I +G+EV PGDI
Sbjct: 778  VQDDVFTSIHIAEASIQARDTKLGPEEITRDTPNVGEEALRNLGPEGVIRLGSEVGPGDI 837

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGKITPK E+ + PEE+LLRAIFG+KA DV+D+SL V S  SG V+D+R+  +    K 
Sbjct: 838  LVGKITPKSETELAPEERLLRAIFGDKAADVKDSSLYVASSTSGIVMDIRVDRKIDPTKA 897

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL----- 1008
              + S  + + + +  +   +      ++  +L  IL G    +          +     
Sbjct: 898  AVTKSDLKRKRKEIDAEYKVQYNEFLEDLAEKLGAILLGSKLSNDIVSKDGKETIIVPAN 957

Query: 1009 --SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++     +Q   + + D   +  ++ +   ++   + +  R   KI+++   +  
Sbjct: 958  RKITKVLLRKLSAQHDNYTMVDSPAKAQIDEVMGNFKPRLNDIRLRNSEKIDQLADENSQ 1017

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              GV++ VKV++A KR I  GDKMAGRHGNKGI+S I+P  D+PF+KDGT VDI+LNPLG
Sbjct: 1018 ERGVIKSVKVYIASKRKISVGDKMAGRHGNKGIISNIVPKSDLPFMKDGTVVDIILNPLG 1077

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMNVGQI ETHLG A   +G KI + + D      I+ +   +       +      
Sbjct: 1078 VPSRMNVGQILETHLGMAANRMGIKIATPVFDGCPESIINDMLEEVGYDRDGKARL---- 1133

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                         G++       G+ FD
Sbjct: 1134 -------------------------------------------YDGRT-------GDSFD 1143

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            + +TVG IYMLKL+H+V +K++AR+ G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1144 QRITVGMIYMLKLDHLVVNKIHARAVGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAYG 1203

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQEMLT+KSDDV GRTR+YESIV G+++   G PESFNVL+KEM +L L I L   
Sbjct: 1204 AAYTLQEMLTVKSDDVEGRTRIYESIVRGDNSLVAGLPESFNVLMKEMMSLCLDIRLRKE 1263


>gi|296120714|ref|YP_003628492.1| DNA-directed RNA polymerase, subunit beta [Planctomyces limnophilus
            DSM 3776]
 gi|296013054|gb|ADG66293.1| DNA-directed RNA polymerase, beta subunit [Planctomyces limnophilus
            DSM 3776]
          Length = 1238

 Score = 1157 bits (2994), Expect = 0.0,   Method: Composition-based stats.
 Identities = 555/1367 (40%), Positives = 784/1367 (57%), Gaps = 149/1367 (10%)

Query: 9    GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
                 R  FG       I +L ++Q ASY  FL +   P ER ++GL+A  + VFPI ++
Sbjct: 10   ETHETRH-FGSIRGEFAISELTQIQTASYHRFLQLESEPRERADDGLEAILREVFPIESY 68

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                 LE++ YE   P++   +C    LTY  P ++ LRL+             +  +E+
Sbjct: 69   DQKYRLEYIKYELGKPRYTPLECRQLRLTYGRPFRVWLRLM------------KEQPQEE 116

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +Y+GDLP+M   G F+I G +R+VVSQLHRSPG+ F      A    K  ++CR+IP++
Sbjct: 117  EVYLGDLPIMIGGGEFIINGSERVVVSQLHRSPGVDFVMS---AEPGEKKTFSCRVIPER 173

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
            G W+++    +D ++VRID+  K    +FL A+                           
Sbjct: 174  GSWIELNIGKRDTLNVRIDQSGKFSAMTFLRAM--------------------------- 206

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                D   G   +  LV +       +                         + + G + 
Sbjct: 207  ----DPAYGR--TKDLVKLFHNVVTFKVSDS------------------HFVEHVAGKHA 242

Query: 309  AEDIVNG----ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
            A+DIV        GEI  EA  VI +   EEI  S I+ + +      +++  I ++L+ 
Sbjct: 243  ADDIVYPAGHERMGEIICEACHVITKPLAEEIKESGIKTVDVA---EKSDDPIIMDSLIE 299

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D     +DALL IY+ +RPG+      A  +F   FFD ++Y +  VGR ++N + + D 
Sbjct: 300  DSTASHEDALLRIYQRLRPGNPPQLEKAIELFKEKFFDVNRYRIGRVGRFRVNRKFDQDV 359

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            PD    +R EDII  I+ ++ LR G     +DDIDNLGNRR+R++ E+ + + R G L++
Sbjct: 360  PDTEMTLRPEDIINSIRYVMKLRTGDATAHVDDIDNLGNRRLRTIDELAQEELRKGFLKL 419

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             R+++ER+S  D++ + P+ LIN K V +A+  FF   +LSQ+ +  N L+ +TH RRLS
Sbjct: 420  RRTVQERMSLKDVEEMSPRSLINPKSVSAAIDFFFGRGELSQVVDQTNPLATLTHERRLS 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+SSL+ FA+V+ YGF+ TPY
Sbjct: 480  ALGPGGLNRKRAGFEVRDVHISHYGRICPIETPEGTNIGLISSLSIFAKVDDYGFLITPY 539

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            RKV D KVT ++V+L A EE + YIA A++ + +D    +E V CR   + + +P  +++
Sbjct: 540  RKVVDKKVTEEIVWLRADEESHVYIAPADTPVQDD-KMRDERVMCRHHNDFLWLPASQVN 598

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +ID +P Q+V ++A LIPFLE+DD+NR LMG NMQRQ VPLL AE P VGTG+E  VA++
Sbjct: 599  YIDVAPCQMVGVSAGLIPFLEHDDANRALMGSNMQRQGVPLLIAEPPLVGTGLEGPVAQN 658

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG  + A+++G V  VD   I I                  L K+   N+ TC+NQ P+V
Sbjct: 659  SGMVLRAEKSGKVTYVDGDCIEI------------DGKRTPLRKYTGLNERTCLNQTPVV 706

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            KVGD+V++ DI+ D  +   G+LALGRN+LVAFM W G+NFED++++SER+V EDV+TSI
Sbjct: 707  KVGDKVKKGDILVDSAAVGDGELALGRNVLVAFMSWEGFNFEDAIILSERLVKEDVYTSI 766

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+EF+V  R+TKLG EE TRDIPNVS++ L+++D+ G+I VG  V PGDILVGK++PK 
Sbjct: 767  HIDEFDVEVRETKLGREEFTRDIPNVSDKALRHLDDDGVIHVGTRVEPGDILVGKVSPKA 826

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            ++ +TPEEKLL AIFG    DV++ SL VPSGV G V+    F+R            E  
Sbjct: 827  KTELTPEEKLLHAIFGRAGEDVKNESLEVPSGVEGIVIHTEKFSRRMSLSETERKKFE-T 885

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             ++ +    +D      +   +     L     +    G     +  +  ++ Y  S   
Sbjct: 886  DLKRVEESGNDLIAAAFKTFLTHFETALE--KKLQDDDGRDLGKLDDAKFLATYAESFLH 943

Query: 1023 QFAVQD---EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +F   D    + + + +    ++        D    K+  ++ GD++P GVL++VKV+VA
Sbjct: 944  RFETMDLRSPQKKADCKKAIKEFWGPVEEAIDDRDRKLNTMKRGDELPSGVLQMVKVYVA 1003

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDKMAGRHGNKG++S++LP EDMPFL DGTPVDI+LNPLGVPSRMNVGQI ET
Sbjct: 1004 QKRQISVGDKMAGRHGNKGVISKVLPVEDMPFLADGTPVDIILNPLGVPSRMNVGQILET 1063

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA   LG + K  + D  A   I  L                               
Sbjct: 1064 HLGWAAAKLGFRAKCPVFDGPAEETIRELLKQA--------------------------- 1096

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                         G  E+    +L              DG TGEPF++  TVGYIYMLKL
Sbjct: 1097 -------------GLPEDGKAQLL--------------DGRTGEPFEQKTTVGYIYMLKL 1129

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DKV+AR+TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KS
Sbjct: 1130 HHLVEDKVHARATGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKS 1189

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DDV GRT++YES+V G +T E GTP SF VL  E++ L L++ LE S
Sbjct: 1190 DDVEGRTKIYESMVKGENTLEAGTPASFEVLNNEIRGLCLNMQLEKS 1236


>gi|87306545|ref|ZP_01088692.1| DNA-directed RNA polymerase beta chain [Blastopirellula marina DSM
            3645]
 gi|87290724|gb|EAQ82611.1| DNA-directed RNA polymerase beta chain [Blastopirellula marina DSM
            3645]
          Length = 1224

 Score = 1148 bits (2969), Expect = 0.0,   Method: Composition-based stats.
 Identities = 542/1349 (40%), Positives = 781/1349 (57%), Gaps = 135/1349 (10%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNE-GLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
            +  PDL  +Q  SY  FL   +  D R  E G+++  + +FPI ++ G   L++V YE  
Sbjct: 1    MSPPDLTTIQTHSYTKFLQEELDSDARDPEIGIESVLREIFPINSYDGTVQLDYVRYELG 60

Query: 83   PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
             P++   +C    LTY +P +I LRL            + ++  E+ +Y+GD+P+M   G
Sbjct: 61   KPRYTPQECKQLRLTYGLPFRIWLRL------------NKEEPIEEEVYLGDMPVMLGGG 108

Query: 143  TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
             F+I G +R+VVSQLHRSPG+ F  +      S + L +CRIIP++G W++I    KD  
Sbjct: 109  EFIINGAERVVVSQLHRSPGVDFVEEAETT--SDRRLPSCRIIPERGSWIEINITKKDSF 166

Query: 203  HVRIDRRRKVPVTSFLMAL--GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
             VRID+  K   T+ L A+   +  +  ++  FY                          
Sbjct: 167  TVRIDQSGKFAATTLLRAMSPELSDDASLIRAFYDTT----------------------- 203

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                       +  ++ G+ +T    K   +  V  +    D   G            GE
Sbjct: 204  -----------KVHVKDGRSIT----KIEGKIAVDDIVYPIDSDRG------------GE 236

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            I +EAG  I   + E I    I +   + V        I NTL+ D     ++ALL IY+
Sbjct: 237  IIVEAGQKISRNTAELICSVGITEE--IEVMDSPKIPIIFNTLIEDNTSSHEEALLRIYQ 294

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+      A+++F+  F+D ++Y L  VGR +MN +L ++  +  + +R  D+I  
Sbjct: 295  RLRPGNPPQLEKAKTLFDEKFYDDNRYRLGRVGRFRMNRKLGIEVNEGEQTLRPSDLINS 354

Query: 440  IKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            IK ++ + +G G    DDID+LGNRR+R++ E+  ++ R G L++ R+++ER+S  D + 
Sbjct: 355  IKYVMSILDGDGTARKDDIDHLGNRRLRTIDELACDELRKGFLKLRRTVQERMSLKDAED 414

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + P++LIN K + +A+  FF   +LSQ+ +  N LS +TH RRLSALG GG+ R RAG E
Sbjct: 415  MTPRNLINPKSISAAIEYFFGRGELSQVVDQTNPLSMLTHERRLSALGPGGLNRKRAGFE 474

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            +RDVH +HYGRICP ET EG NIGL+SSL  ++ V+ YGF+ TPYR + DGK+ +++V+L
Sbjct: 475  VRDVHISHYGRICPIETPEGTNIGLISSLAIYSAVDEYGFLITPYRVIRDGKIADEIVWL 534

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             A EE + Y+A A++  D  G    +L+  R   +  LV  + + +ID +P Q+V ++AS
Sbjct: 535  RADEESDAYVAPADTPTDAKGQLLGDLIIARYRSDFDLVEPKTVQYIDVAPCQMVGVSAS 594

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            LIPFLE+DD+NR LMG NMQRQAVPLL AE P V TG+E+ VA++S   I AKRAG++E 
Sbjct: 595  LIPFLEHDDANRALMGSNMQRQAVPLLIAEPPIVCTGLETEVARNSSMMIRAKRAGVIEY 654

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            VDA RIVI++ EG  D        Y L KF   N+ TC+NQRP++ VG EV    ++ADG
Sbjct: 655  VDAERIVIKTTEGRTD-------NYTLRKFVGLNERTCLNQRPIISVGQEVEVGTVLADG 707

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             +T  G LALGRN+LV FM + GYN+ED++++SE +V +DV+TS+HIEEF+V  R+TKLG
Sbjct: 708  AATHNGQLALGRNVLVGFMSFDGYNYEDAIILSEELVKQDVYTSLHIEEFDVEIRETKLG 767

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E+ TRDIPNVSE+ L+N+DE G++ VG  V PGDILVGK++PK ++ +TPEEKLL AIF
Sbjct: 768  REDFTRDIPNVSEKMLRNLDEGGVVQVGTFVKPGDILVGKVSPKSKTELTPEEKLLHAIF 827

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
            G    DV++ SL VPSG+ G V+    F R     ++   + E+   E+           
Sbjct: 828  GRAGEDVKNDSLEVPSGIEGIVIHTDKFARRMSLSDDERKAFEKRLKEVETEGNSKISEA 887

Query: 978  LDRNIYSRLMEILCGQNAVSG-PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                I      +        G P    +     ++   ++   +  +    DE++Q+  E
Sbjct: 888  FAAMIVEFERILGKTLTDEDGTPLTQDQDPKFIAEQAQQFRLKKIVEHLRSDERIQQIRE 947

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
            +    +   ++ L+ R    +  ++ GD++  GVL++VKV++A KR I  GDKMAGRHGN
Sbjct: 948  AYATSWPLVEAALDVR-DRVLNSMKRGDELRSGVLQMVKVYIATKRCISVGDKMAGRHGN 1006

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++++ILP EDMPFL DGTP+ I+LNPLGVPSRMNVGQI ETHLGWA   LG +  + +
Sbjct: 1007 KGVIAKILPVEDMPFLPDGTPIQIMLNPLGVPSRMNVGQILETHLGWAGAKLGFQSITPV 1066

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +  DI+                                                  
Sbjct: 1067 FDGASEEDINNCLEEAG------------------------------------------- 1083

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  L         +  L DG TGE   +  TVGYIYMLKL+H+V DKV+ARSTG YS
Sbjct: 1084 ------LPRHG-----KIRLKDGRTGELMHQETTVGYIYMLKLHHLVDDKVHARSTGPYS 1132

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            L+TQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQE+LT+KSDDV GRT++YE++V G 
Sbjct: 1133 LITQQPLGGKARFGGQRFGEMEVWALEAYGAAYILQELLTVKSDDVEGRTKIYEAMVKGE 1192

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +T E GTP SF+VL  E++ LGL++ LE 
Sbjct: 1193 NTLEAGTPASFDVLTNEIRGLGLNMQLEK 1221


>gi|307128566|ref|YP_003880596.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            CARI]
 gi|306483028|gb|ADM89898.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            CARI]
          Length = 1277

 Score = 1146 bits (2964), Expect = 0.0,   Method: Composition-based stats.
 Identities = 536/1364 (39%), Positives = 787/1364 (57%), Gaps = 122/1364 (8%)

Query: 10   LGRVRK-FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
               ++K  F      +  PD +E+Q  S+++FL ++   + R NEGL  AF   FPI+  
Sbjct: 4    KKEIKKINFASVKTKLKYPDFLEIQLKSFNNFLKIDSNFENRKNEGLYKAFIENFPISDA 63

Query: 69   SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                +LEF+ Y  DPP++ +++CL R LTY+V +K  L+L     +         +   Q
Sbjct: 64   KNKFILEFIDYIIDPPRYSLEECLKRGLTYSVSIKARLKLYCTKSEIQNF-----ETIYQ 118

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             +Y+G  P MT  G+F+  G +R+VVSQL RSPG+ FD        +G+  Y+ +IIP +
Sbjct: 119  DVYLGTCPYMTPSGSFIFNGSERVVVSQLQRSPGVFFDQS---YHSNGQKFYSAKIIPFK 175

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
            G W++   D  ++++V I++ +K+PVT+ L A+G   E +IL+ F            +  
Sbjct: 176  GSWIEFSTDIHNVMYVFIEKNKKIPVTTLLRAIGFSKERDILNLFEITETIKINKKNYKK 235

Query: 248  PLSAADLMVGAKV-SSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
             L         K+     +D D+GE + ++  K L +  +   K+   K +      +  
Sbjct: 236  ILGRTLGERILKIWYEDYIDEDSGEIISLKKSKILLNRNIILNKKNINKIIDNNIKYISL 295

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              + +  ++                                         + I+NT+  D
Sbjct: 296  YKLKKTSIDF----------------------------------------SIIQNTIQID 315

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                +K+A+  IY++++  D      A    N  FF   KY L  VGR ++N  L LD P
Sbjct: 316  PTNSKKEAIYYIYKILKNSDPIDEITAILFINKFFFSEYKYSLGEVGRYRLNKTLKLDFP 375

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
               + + KED+I+IIK L+ L N K  +DDID+L NRRV++VGE L  QY +GL RM R 
Sbjct: 376  LTYKVLSKEDLISIIKNLIILNNSKKEVDDIDHLANRRVKTVGEQLYTQYVIGLARMSRI 435

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+E++S  + +   P  LINA+ + S +  FF +SQLSQ  +  N L+ +TH RRLS+LG
Sbjct: 436  IREKMSIKENEVFSPIKLINARYLTSVINSFFGTSQLSQFMDQTNPLAEVTHKRRLSSLG 495

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL  FAR+N  GFIETPY KV
Sbjct: 496  PGGLSRDRAGFEVRDVNYSHYGRLCPIETPEGPNIGLISSLCVFARINDMGFIETPYLKV 555

Query: 606  CDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
              GKV   N  +YLSA +E  + IAQAN+ L+ +    +  +  R   +  +V  +K+++
Sbjct: 556  NKGKVILKNKPIYLSAEQEYGKIIAQANAILNYNTGVLKNQIIVRANADFPMVNSKKVNY 615

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            ID S  Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLLK + P VGTG+E  +A+ +
Sbjct: 616  IDISTNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLKPQVPIVGTGLEKKLAQDA 675

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
               I A++ GI+E VD+ +I I+     +  L      +  ++L+KF+++NQNTC+N +P
Sbjct: 676  RILIHAEKDGIIESVDSNKIRIKYFFSEKKKLLSFEEEIKSFKLIKFRKTNQNTCINIKP 735

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VK G  V +  ++ +G +T  G+LALGRN+ VAFMP+ GYNFED+++ISE++V ED+FT
Sbjct: 736  IVKKGMNVTKGQVLCEGYATKNGELALGRNIKVAFMPFKGYNFEDAIVISEKVVREDLFT 795

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHI+E+ +  R+TKLG EE++ DIPN+SE  L+ +D+ GII +G  V PGD+L+GK TP
Sbjct: 796  SIHIDEYSIEVRETKLGMEELSNDIPNMSERQLQKLDQNGIIQIGHYVKPGDLLIGKTTP 855

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            K +   T EEKLL+AIFGEKA+ ++D+SL+  S + G V+D +I+++    KN+      
Sbjct: 856  KKKKNPTSEEKLLKAIFGEKAISIKDSSLKANSSLFGVVIDTKIYSKKIKMKNKELEKEN 915

Query: 961  REQIELLARDKDD----EQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSD 1011
             +  ++  +  DD    +   L   + ++L  +L G+           K   K  +++  
Sbjct: 916  LKLEKMKLKKIDDKFTKKFKKLKNLLINKLNTVLEGEISEEVFDSFFKKKISKGQIINLK 975

Query: 1012 LISEYP--RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            +++     R+      +++      V  +   Y   K  L+ +   K   I  GD++P G
Sbjct: 976  ILNSIKNYRNIISNRWIKNNYKNYLVLKILKNYFFLKKKLKIKLILKKNNILIGDELPTG 1035

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            ++++ KVF+A KR ++ GDKM+GRHGNKGIV+RI+  EDMP+L+DGTPVD+VLNPLGVPS
Sbjct: 1036 IIKLAKVFIAKKRKLKVGDKMSGRHGNKGIVARIVREEDMPYLEDGTPVDLVLNPLGVPS 1095

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQI+ET LGWA   L +   + I D  +  +IS                       
Sbjct: 1096 RMNIGQIYETILGWAGEKLKRNFSTPIFDGASLEEISKYTDKANL--------------- 1140

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                               P F                    G + L+DG TGE FD+PV
Sbjct: 1141 -------------------PRF--------------------GSTYLFDGETGEKFDQPV 1161

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEMEVW ++++GAA 
Sbjct: 1162 TVGVIYMLKLNHMVDDKMHARSIGPYSLITQQPLGGKSQFGGQRFGEMEVWALESFGAAN 1221

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
            +L+E+LTIKSDD++GRTR YE+IV G    E G PESFNVL+ E
Sbjct: 1222 ILREILTIKSDDIIGRTRTYEAIVQGAKIPEPGIPESFNVLINE 1265


>gi|91200660|emb|CAJ73710.1| strongly similar to DNA-directed RNA polymerase, beta chain
            [Candidatus Kuenenia stuttgartiensis]
          Length = 1230

 Score = 1145 bits (2963), Expect = 0.0,   Method: Composition-based stats.
 Identities = 541/1362 (39%), Positives = 796/1362 (58%), Gaps = 150/1362 (11%)

Query: 15   KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            + + K  E+I++ +L ++Q  +Y  FL ++I   +R N G++A  + +FP++ + G   L
Sbjct: 4    RNYSKVDEVIELQNLTQIQTKAYMDFLQLDIPASKRKNVGIEAILREIFPVSNYDGNITL 63

Query: 75   EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
             +V YE   P++  D+C    LTY  P ++ LRL   D DE           E+ +Y+G+
Sbjct: 64   NYVKYELGKPRYSQDECRQLRLTYGRPFRVWLRL---DKDEP---------IEEEVYLGE 111

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +P++   G F+I G +R++V+QLHRSPG+ F  +      + K L++CRIIP++G W+++
Sbjct: 112  IPVVIGGGEFIINGTERVIVAQLHRSPGVDFIEEF----YAEKRLHSCRIIPERGSWIEL 167

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            E   KD++ VRID+  K+P T FL AL                Y+   D           
Sbjct: 168  EVGKKDVLTVRIDQSGKLPATCFLRAL-------------SAEYANDEDII--------- 205

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                                         L   ++   +    + +  L G + AE +VN
Sbjct: 206  ----------------------------RLFHEVETVKIADYDVAAK-LRGRFTAEQVVN 236

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             ETGEI ++AG    + +++ I   EI+ + ++       +  I N+L +D  K  +DAL
Sbjct: 237  PETGEILLDAGRQFSDSTVKAITDLEIKKVDVIK---KVEDNLILNSLESDFTKSHEDAL 293

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            L IY   RPG+      A  +F   FFD  +Y L  VGR ++N ++  D       ++KE
Sbjct: 294  LKIYARFRPGNPQQVEKARQLFYDKFFDEKRYRLGPVGRFRLNRKMGHDVDSSKMTLQKE 353

Query: 435  DIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            D +  I+ L+ LR G    +IDDIDNLGNRR+R++ E++  + R G L++ R+I+ER+S 
Sbjct: 354  DFVEAIRYLMKLRKGTPGASIDDIDNLGNRRLRTIDELVGEELRKGFLKLRRTIQERLSV 413

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             + + + P+ L+N+K + SA+  FF  S+LSQ+ +  N L+++TH RRLSALG GG+ R 
Sbjct: 414  KETEQLTPRSLVNSKTIFSAIDYFFSRSELSQVLDQTNPLAQLTHERRLSALGPGGLNRK 473

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVH +HYGR+CP ET EG NIGL++SL+ +A ++ YGF+ TPYR +  GK + 
Sbjct: 474  RAGFEVRDVHVSHYGRVCPIETPEGTNIGLIASLSIYATIDEYGFLITPYRLIEKGKPSK 533

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +++YL A EEE R IA A+  +    +  +  V CR  G+      + ++++D SPKQ+V
Sbjct: 534  NIIYLRADEEEGRLIAPADILISTKDTLGKTEVLCRHDGDFKHTAFKDVNYMDVSPKQMV 593

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
             ++ASLIPFLE+ D+NR LMG NMQRQAVPLLK E P + TGME VVAK+S   + +++ 
Sbjct: 594  GVSASLIPFLEHSDANRALMGSNMQRQAVPLLKTEPPIIATGMERVVAKNSSMTVQSEKN 653

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G V +V +  IVI + E           IY+L KF   N+ TC+NQ+P+V  G ++++ +
Sbjct: 654  GTVTKVSSNEIVIDNNE-----------IYKLRKFVGLNEGTCLNQKPIVTEGQKIKKGE 702

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADG +T  G+L+LG+N+LVAFM W GYNFED+M+ISE ++ +D FTSIH +EFEV  R
Sbjct: 703  VIADGAATHNGELSLGKNVLVAFMTWDGYNFEDAMVISEALLKDDRFTSIHRDEFEVEIR 762

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +TKLG EE TRDIPNVSE+ L+N+DE GII VG +V PGDILVGKI PK  S ++PEEKL
Sbjct: 763  ETKLGREEFTRDIPNVSEKALRNLDENGIIRVGTKVKPGDILVGKIAPKSRSELSPEEKL 822

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-------SVEREQIE 965
            L AIFG    DV++ SL VPSG+ G +++ ++F+R      E+          +E +  E
Sbjct: 823  LHAIFGRAGEDVKNESLEVPSGMEGIIINTQVFSRKSYISEEKRQKILGEVSEIESKYNE 882

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             +A++       ++  I   L++I  GQ   +     +K+      +++          A
Sbjct: 883  TIAKEFAKMLKAINAEIEEALVDIQTGQVYKTERAMSEKT------ILAMEDHFNIENIA 936

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               +K +     +  +Y+     L++    KI +++ GD++P GVL + KV +A KR + 
Sbjct: 937  FSSKKKKELALEISQEYKRKMEELKEERDGKINQLKRGDELPTGVLELAKVSIATKRKLS 996

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG++S+ILP EDMPFL DGT V+++LNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 997  VGDKMAGRHGNKGVISKILPEEDMPFLADGTRVEMLLNPLGVPSRMNVGQILETHLGWAA 1056

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG +  + I +     +I       +                                
Sbjct: 1057 KKLGFRAITPIFEGALEEEIRETLKEAKLP------------------------------ 1086

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                       E   ++L        G        TGE F + V VGY+YMLKL+H+V +
Sbjct: 1087 -----------EDGKAVL------YDG-------RTGESFGQKVAVGYMYMLKLHHLVDE 1122

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            KV+AR+TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1123 KVHARATGPYSLITQQPLGGKARFGGQRFGEMEVWALEAYGAAHNLQELLTVKSDDVEGR 1182

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            T++YES+V G +T E GTP SF VL  E+  LGL++ LE  +
Sbjct: 1183 TKIYESMVKGENTLEAGTPASFEVLSNEIAGLGLNLKLEKKK 1224


>gi|323155567|gb|EFZ41744.1| DNA-directed RNA polymerase, beta subunit [Escherichia coli EPECa14]
          Length = 951

 Score = 1145 bits (2962), Expect = 0.0,   Method: Composition-based stats.
 Identities = 556/964 (57%), Positives = 728/964 (75%), Gaps = 13/964 (1%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             D+YDLS VGR+K N  L  +  +    + K+DII ++K L+D+RNGKG +DDID+LGNR
Sbjct: 1    EDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNR 60

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQL
Sbjct: 61   RIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQL 120

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 121  SQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 180

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E
Sbjct: 181  INSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVE 240

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 241  DLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVP 300

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+A+ P VGTGME  VA  SG   VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY
Sbjct: 301  TLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIY 360

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 361  NLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 420

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            FEDS+L+SER+V ED FT+IHI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+
Sbjct: 421  FEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIV 480

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV
Sbjct: 481  YIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDV 540

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R G++K++R++ +E  Q++   +D  +E  IL+  ++SR+  +L            
Sbjct: 541  QVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGV------- 593

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                   ++ + + PR +W +  + DE+ Q  +E L  QY+  K   E + + K  KI  
Sbjct: 594  ------EAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQ 647

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++GTPVDIVL
Sbjct: 648  GDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVL 707

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQI ETHLG A  G+G KI +++   +    +         +       
Sbjct: 708  NPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQK 767

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +S + D+ V+R+AE  + G+P++TPVFDGA E  I  +L++ DL  SGQ  LYDG TG
Sbjct: 768  VDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTG 827

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 828  EQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWAL 887

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+
Sbjct: 888  EAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIE 947

Query: 1363 LENS 1366
            LE+ 
Sbjct: 948  LEDE 951


>gi|256370637|ref|YP_003108462.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            SMDSEM]
 gi|256009429|gb|ACU52789.1| DNA-directed RNA polymerase beta subunit [Candidatus Sulcia muelleri
            SMDSEM]
          Length = 1317

 Score = 1134 bits (2932), Expect = 0.0,   Method: Composition-based stats.
 Identities = 537/1365 (39%), Positives = 779/1365 (57%), Gaps = 119/1365 (8%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F          D +E+Q  S+  F  ++     R  EGL  AF   FPI+      
Sbjct: 50   ERINFSLVKTNSYYSDFLEIQIKSFKKFFQLDSTYMNRKKEGLYKAFLEYFPISDSKSQF 109

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +++CL R LTY+V +K+ L+    + +  T      +   Q IY+
Sbjct: 110  ILEFIDYLIDPPRYSLEECLQRGLTYSVSIKVRLKFYCTNPEYETF-----ETVYQDIYI 164

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G  P MT  G+F+  G +R++VSQL +SPGI F      +  +GK L   ++IP +G+WM
Sbjct: 165  GSCPYMTPTGSFIFNGSERVIVSQLQKSPGIFFGQ---YSHPNGKNLAYAKLIPSKGVWM 221

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  +++ V ID+ +K P+T+ L A+G   + +IL+ F     +          L  
Sbjct: 222  EFSIDINNVLSVSIDQSKKFPITTLLRAIGYSKDQDILNIFELADKFILTKKNSNQLLGK 281

Query: 252  ADLMVGAKVSS-SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                   K S    +D  TGE +                                     
Sbjct: 282  YMAANILKTSFEDWIDEKTGELI------------------------------------- 304

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
               + E  EI ++    +++  ++++   ++++I  LY       + I NTL  D    +
Sbjct: 305  ---SLEKNEILLKRNIFLNKNHIKKLLQCQMKEI-YLYKKKNFYYSIIHNTLQKDPTNYK 360

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+AL  IY+ ++  D  + S ++ + N L F    Y L  VGR K+N  L +D P     
Sbjct: 361  KEALDFIYKQVKNCDPPSHSSSKELMNKLIFSEINYSLGEVGRYKLNKTLKVDIPLTYNI 420

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KED+I+II+ L++L N    I+DID+L NRRV++VGE L  QY LG+ ++ R IKE+I
Sbjct: 421  LSKEDLISIIEHLIELNNSTKEIEDIDHLSNRRVKTVGEQLYTQYVLGIAKIARIIKEKI 480

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +     S+ P +LI AK + S +  FF ++ LSQ  +  N L+ ITH RRLS+LGQGG+ 
Sbjct: 481  NLKKKISITPLELIKAKTLTSVINTFFGTNPLSQFMDQTNPLAEITHKRRLSSLGQGGIL 540

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL  FA++N+ GFIETPY +V DGKV
Sbjct: 541  RERAGFEVRDVNSSHYGRLCPIETPEGPNIGLISSLCVFAKINSMGFIETPYLRVKDGKV 600

Query: 611  T--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                  +YLSA +E  + IAQAN+ L+      +  +  R   +  LV  +K+D+ID S 
Sbjct: 601  LLKKKPLYLSAEQETGKLIAQANAILNHKTGELKPKLIVREDSDFTLVNYKKVDYIDLST 660

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL  + P VGTG+E  +A  S   I 
Sbjct: 661  NQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLNPQVPIVGTGLEKHLAYDSRMLIY 720

Query: 729  AKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            A+  GIV+ VDA  I I+        L      +  Y+L+KF+++NQNTC+N RP+VK G
Sbjct: 721  AEADGIVDSVDANVIKIKYFMSETEKLLSFEKRIKKYKLIKFRKTNQNTCINLRPIVKKG 780

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
             +V +N ++ +G +T  G+LALG N+ VAFMP+ GYNFED+++ISE+++ ED FTSIHI+
Sbjct: 781  MKVVKNQVLCEGYATKNGELALGINLKVAFMPFKGYNFEDAIVISEKVLREDWFTSIHID 840

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E+ +  RDT+ G EE+T D+PN +EE LKN+DE G+I +G++V PGDI++GK+TPK +  
Sbjct: 841  EYSIEVRDTQFGMEELTNDLPNFNEEDLKNLDENGMIRIGSKVKPGDIIIGKLTPKIDKN 900

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
             +PE+KLL+AIFGE+AV++++ SL+    + G V+D ++++R      E     +  ++E
Sbjct: 901  PSPEKKLLKAIFGERAVNLKNVSLKADPSLFGVVIDKKLYSRSENT--EEYKIKKHLKLE 958

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQ-----NAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             L          L   +  +L  IL G         S  +   K   ++  ++ +     
Sbjct: 959  KLNFSFKKNLDKLKDLLIKKLNSILEGTISEGVRNSSNKEIILKGKKITLKVLKKIDNFS 1018

Query: 1021 --WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   V+D    + V  L   +   K+ L+ + K K  +I  GD++PPGV ++ KVF+
Sbjct: 1019 NIISPNWVKDNLKNKLVLKLINNFNLKKNQLKIKLKKKQNRILIGDELPPGVFKLAKVFI 1078

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR ++ GDKM+GRHGNKGIV+ IL  EDMP+L+DGTP+D+VLNPLGVPSRMN+GQI+E
Sbjct: 1079 AKKRKLKVGDKMSGRHGNKGIVAIILKEEDMPYLEDGTPIDLVLNPLGVPSRMNIGQIYE 1138

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            T LGWA   LG    + I D  +  +IS                                
Sbjct: 1139 TILGWAGEKLGINFSTPIFDGASLDEISKYTDKANL------------------------ 1174

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                      P F                    G + L+DG TGE F++PVTVG IYMLK
Sbjct: 1175 ----------PRF--------------------GNTYLFDGETGEKFEQPVTVGVIYMLK 1204

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            LNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEMEVW ++++GAA +L+E++TIK
Sbjct: 1205 LNHMVDDKLHARSIGPYSLITQQPLGGKSQFGGQRFGEMEVWALESFGAANILREIITIK 1264

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SDDV+GR   +E+IV G      G PESFNVL+ E++ LGL++ L
Sbjct: 1265 SDDVIGRANTFEAIVKGKKFPIPGVPESFNVLISELKGLGLNLSL 1309


>gi|213161404|ref|ZP_03347114.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E00-7866]
          Length = 920

 Score = 1124 bits (2906), Expect = 0.0,   Method: Composition-based stats.
 Identities = 543/933 (58%), Positives = 710/933 (76%), Gaps = 13/933 (1%)

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            +DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  
Sbjct: 1    DDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLG 60

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 61   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 120

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT++
Sbjct: 121  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDE 180

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 181  IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 240

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 241  VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 300

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 301  TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 360

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RD
Sbjct: 361  LADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD 420

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            TKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLL
Sbjct: 421  TKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLL 480

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            RAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +
Sbjct: 481  RAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSE 540

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  IL+  ++SR+  +L                   ++ + + PR +W +  + DE+ Q 
Sbjct: 541  ELQILEAGLFSRIRAVLVSGGV-------------EAEKLDKLPRDRWLELGLTDEEKQN 587

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGR
Sbjct: 588  QLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGR 647

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI 
Sbjct: 648  HGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKIN 707

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +++   +    +         +         +S + DD VLR+AE  + G+P++TPVFDG
Sbjct: 708  AMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRKGMPIATPVFDG 767

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTG
Sbjct: 768  AKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTG 827

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
            SYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV
Sbjct: 828  SYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV 887

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 888  DGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 920


>gi|153869212|ref|ZP_01998874.1| DNA-directed RNA polymerase, beta subunit [Beggiatoa sp. PS]
 gi|152074248|gb|EDN71124.1| DNA-directed RNA polymerase, beta subunit [Beggiatoa sp. PS]
          Length = 1118

 Score = 1119 bits (2895), Expect = 0.0,   Method: Composition-based stats.
 Identities = 565/1117 (50%), Positives = 759/1117 (67%), Gaps = 114/1117 (10%)

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            +  D      +A ++IYR+MRPG+  T   AES+FN LFF  ++YDLS VGR+K N R+ 
Sbjct: 1    MRIDSTTTTLEAQIEIYRMMRPGEPPTPEAAESLFNNLFFSEERYDLSAVGRMKFNRRIG 60

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D       +  +DI+ +++ L+++ NG G +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 61   RDEITGPGILTVDDILDVLRTLINIPNGIGGVDDIDHLGNRRIRSVGEMTENQFRIGLVR 120

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +ER++KER+S  +I++V+PQ+LINAKPV +++ EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 121  VERAVKERLSVAEIENVVPQELINAKPVSASIREFFGSSQLSQFMDQNNPLSEVTHKRRI 180

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+ETP
Sbjct: 181  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNDYGFLETP 240

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             R+V DG+VT+ V YLSA+EE    IAQAN++LDE+G F +++V  R   E  ++ ++K+
Sbjct: 241  CRRVEDGRVTDKVEYLSAIEEGGFVIAQANANLDENGYFKDDMVAARHENEFTVISKDKV 300

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            +++D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME +VA 
Sbjct: 301  NYMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAQKPLVGTGMERIVAI 360

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST--------------SGVDIYRLMKF 767
             SG  +VA+R GI++ VDA RIV+R  + ++                  SGVDIY L K+
Sbjct: 361  DSGVTVVAERGGIIDSVDAARIVVRINDDEVLKEGEDNSITPKFGTLLSSGVDIYNLTKY 420

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             RSNQNTC+NQ+PLVK  D ++R D++ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+
Sbjct: 421  VRSNQNTCINQKPLVKPDDLIKRGDVLADGPSTDLGELALGQNLFVAFMPWNGYNFEDSI 480

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISER+V E+ FTSIHI E   +ARDTKLG EEIT DIPNVSE  LKN+DE GII +GA+
Sbjct: 481  LISERVVEEERFTSIHIVELSCLARDTKLGAEEITADIPNVSESALKNLDEAGIISIGAQ 540

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG  GTV+DV++F R
Sbjct: 541  VMPGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGTMGTVIDVQVFTR 600

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------GPKG 1001
             G+DK  R+  +E+ ++  + +D  D   IL+ ++Y R+ ++L G    +      G +G
Sbjct: 601  DGVDKGARAGRIEQAELNRVKKDLQDTLRILEHDVYLRVEKLLVGNKVTNSSNGWEGWEG 660

Query: 1002 FKK--------------------------------STVLSSDLISEYPRSQWWQFAVQDE 1029
             KK                                +T+++S+++ E P  +W++F+++D+
Sbjct: 661  VKKLLVGNKVTNSSKDEDGIETNTIITSRSDDIETNTIITSEILGE-PSDKWFKFSLEDK 719

Query: 1030 KVQRNVE----------------------------------------------------- 1036
            K Q  +E                                                     
Sbjct: 720  KSQAQLESFAALKALHDLHQVEEDEKSQAQLESFKPALKALHDLPRTKLFELRVEDEKIQ 779

Query: 1037 SLKVQYETSKSILEDR----FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            +    +         R    ++ K +K+  GD++ PGVL++VKV++A+KR IQ GDKMAG
Sbjct: 780  AQIESFAQQLKDQRQRADALYEEKRQKLISGDELAPGVLKMVKVYLAIKRTIQPGDKMAG 839

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VS I+P EDMP+ KDG PVD+VLNPLGVPSRMN+GQ+ ETHLGWA   LG++I
Sbjct: 840  RHGNKGVVSMIVPVEDMPYTKDGRPVDLVLNPLGVPSRMNIGQVLETHLGWAAKALGEQI 899

Query: 1153 ----KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
                K +         I  LRS+L K+       E ++  ++  +L +A+    GVP++T
Sbjct: 900  EQKLKIINKSKIIAQSIEELRSYLTKIYNVSGKPEDLTVLNNAEILELAKNLSDGVPMAT 959

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             VFDGA E  I  ML +A L  +GQ+ LYDG TGE F R +TVGY+YMLKLNH+V DK++
Sbjct: 960  QVFDGASESEIKMMLELAGLPTNGQTTLYDGRTGEAFSRQITVGYMYMLKLNHLVDDKMH 1019

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT++
Sbjct: 1020 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDVNGRTQM 1079

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            Y++IV G+   E G PESFNVLVKE+++LG+ I+LE 
Sbjct: 1080 YKNIVDGDHRMEAGMPESFNVLVKEIRSLGIDIELEQ 1116


>gi|68171621|ref|ZP_00544989.1| DNA-directed RNA polymerase, beta subunit [Ehrlichia chaffeensis str.
            Sapulpa]
 gi|67998958|gb|EAM85641.1| DNA-directed RNA polymerase, beta subunit [Ehrlichia chaffeensis str.
            Sapulpa]
          Length = 1150

 Score = 1115 bits (2884), Expect = 0.0,   Method: Composition-based stats.
 Identities = 568/1143 (49%), Positives = 798/1143 (69%), Gaps = 27/1143 (2%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + K+ +I D + DLI++Q+ SY+ F+ ++    +    G++  F+S+FPI    G A
Sbjct: 20   RLSYAKSIDIKDSLTDLIKIQRDSYNAFIGID----QNTESGIKNIFQSMFPIQDLLGRA 75

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV------------DEFTGAK 120
            +LEFVSY    P++D  +C+ R +T++VP++I LR IV+ V            DE T  K
Sbjct: 76   VLEFVSYSIGEPQYDEYECIKRGITFSVPIRIVLRFIVWKVQEVSFKEVKYVVDEETSEK 135

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIK IKEQ + +GDLP MT  GTF+I GI+R++VSQ+HRSPG+ FD DKG+   SGKL+Y
Sbjct: 136  SIKYIKEQEVSIGDLPTMTSHGTFIINGIERVIVSQMHRSPGVFFDSDKGKTYSSGKLIY 195

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + RIIP +G W+D EFD KDI++ RIDR+RK+PV+  L ALG+ + +IL TFY KI Y +
Sbjct: 196  SARIIPYRGSWLDFEFDIKDILYFRIDRKRKLPVSLLLRALGLSNNDILDTFYDKIRYVK 255

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                W  P  A D   G ++S  L+D D G  ++++  ++T  + + L   G+    +  
Sbjct: 256  SEKGWVVPFVA-DRFRGVRLSHDLMDSD-GNVLVKANTRITLRMARKLANDGLTKYLVPF 313

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + + GL++A D+++     + I AG+ I  + + ++    I +I +L +D +    YI N
Sbjct: 314  NEIQGLFIANDLLDSTGNALIISAGENITSEHINKLELFNIEEIFVLNIDFLTVGPYILN 373

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TL  DKN   +DAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L
Sbjct: 374  TLFLDKNVSYEDALFEIYKVLRSGESPSLDTIKAFFDGLFFEKERYDLSTVGRIKLNDHL 433

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L+  +D+  + K+DII +IK LV LR+G+G++DDID+LGNRRVRSVGE ++NQ+R+G+L
Sbjct: 434  GLNVSEDITVLTKDDIIHVIKKLVLLRDGEGSVDDIDHLGNRRVRSVGEFIENQFRIGIL 493

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            R+ER I + +SSV+ D+ MP D +N K + + + +FF SSQLSQ  +  N LS +TH RR
Sbjct: 494  RLERMIMDYMSSVNFDNAMPCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRR 553

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  + R+N +GFIE+
Sbjct: 554  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYGRINKHGFIES 613

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKV  G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE+
Sbjct: 614  PYRKVDKGVVTDKVEYLLAMQESNYYIADASATLDENNQFVDDMLYCRHDGNFVMVKREE 673

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP +GTGMES+VA
Sbjct: 674  VDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLIGTGMESIVA 733

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG  ++AKR GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQRP
Sbjct: 734  AGSGTVVLAKRGGIVHRVDGLYIVIRAFDQEKNEY-LGVDIYNLRKFQRSNHNTCINQRP 792

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD V+ ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFT
Sbjct: 793  LVKPGDYVKANDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFT 852

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFE + RDT LGPE+I R +P+++E+ L ++D+ GI+ VGAEV+ GDILVGK+TP
Sbjct: 853  SIHIEEFECVVRDTTLGPEKIMRSVPDINEDSLSHLDDVGIVNVGAEVSAGDILVGKVTP 912

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            +    + PE KLL  IFGEK  D  D+SL +P  V GTVVDV +F R G+++N+RS+ ++
Sbjct: 913  RPPVSLPPETKLLVTIFGEKVFDCVDSSLYLPLDVEGTVVDVHVFVRRGVEENDRSLLIK 972

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            + +I    +++D E  ++    Y  L  +L          G + +     D ++  P+ +
Sbjct: 973  QNEINGFIKERDYEIDVVSEYFYDELKRVLVSS-------GVQYNNQNIDDYLASIPKKE 1025

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            WW   + DE +   V+ LK ++++       +F  KI+K+ +G D+P GVL +VKVFVA+
Sbjct: 1026 WWDINLSDEAMLLQVKDLKEKFDSMIQNAHSKFDQKIDKLNYGYDLPQGVLCIVKVFVAV 1085

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            K  +Q GDKMAGRHGNKG++SRI+P EDMP+L+DGTPVDI+LN LGVPSRMNVGQI ETH
Sbjct: 1086 KHNLQPGDKMAGRHGNKGVISRIVPVEDMPYLEDGTPVDIILNSLGVPSRMNVGQILETH 1145

Query: 1141 LGW 1143
            LGW
Sbjct: 1146 LGW 1148


>gi|269962521|ref|ZP_06176869.1| DNA-directed RNA polymerase beta subunit [Vibrio harveyi 1DA3]
 gi|269832716|gb|EEZ86827.1| DNA-directed RNA polymerase beta subunit [Vibrio harveyi 1DA3]
          Length = 914

 Score = 1100 bits (2846), Expect = 0.0,   Method: Composition-based stats.
 Identities = 536/930 (57%), Positives = 703/930 (75%), Gaps = 18/930 (1%)

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
            +K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++M
Sbjct: 1    MKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIM 60

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+R
Sbjct: 61   PQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVR 120

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            DVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA
Sbjct: 121  DVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSA 180

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            +EE    IAQAN++L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLI
Sbjct: 181  IEEGQFVIAQANAALTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLI 240

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            PFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  SG   VAKR G+++ VD
Sbjct: 241  PFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVD 300

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V  G+ V R D++ADGPS
Sbjct: 301  ASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPS 360

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
            TDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   +ARDTKLG E
Sbjct: 361  TDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELTCVARDTKLGSE 420

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            EIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGE
Sbjct: 421  EITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGE 480

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            KA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ Q++   +D  +E  IL+
Sbjct: 481  KASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKEAKKDLTEEFQILE 540

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              + +R+  +L                  S   +    R +W +  ++D+ +Q  +E L 
Sbjct: 541  GGLLNRVRAVLIDGG-------------YSEAKLDTTDRKKWLELTLEDDALQSQLEQLA 587

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG+
Sbjct: 588  EQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 647

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG A  G+G KI  ++   
Sbjct: 648  ISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGDKINQMV--- 704

Query: 1160 KANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            K   +++  R FL+KV   G       I+   DD V  + +  + G+P++TPVFDGA E 
Sbjct: 705  KEQQELAKFREFLQKVYDLGETRQKVDIASLSDDEVRTLIKNLRGGLPIATPVFDGAPEA 764

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +I ++L++ADL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSL
Sbjct: 765  SIKALLKLADLPESGQLKLFDGRTGDQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSL 824

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN 
Sbjct: 825  VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNH 884

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 885  SMEPGMPESFNVLLKEIRSLGINIELEDEE 914


>gi|189424403|ref|YP_001951580.1| DNA-directed RNA polymerase subunit beta [Geobacter lovleyi SZ]
 gi|226699410|sp|B3E7S8|RPOB_GEOLS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189420662|gb|ACD95060.1| DNA-directed RNA polymerase, beta subunit [Geobacter lovleyi SZ]
          Length = 1497

 Score = 1100 bits (2844), Expect = 0.0,   Method: Composition-based stats.
 Identities = 541/990 (54%), Positives = 728/990 (73%), Gaps = 12/990 (1%)

Query: 386  VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
              +F     +     +D ++  +  + R +M   L +   D V    + DI+ I++ L++
Sbjct: 513  PESFIKLMDLIEQGGYDENRRRIEGLRRNRM--LLEVAYGDSVECCNRNDILEIVRYLIE 570

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            L+NG+G IDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +++++MP DLIN
Sbjct: 571  LKNGRGAIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEVENLMPHDLIN 630

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTH
Sbjct: 631  SKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTH 690

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            YGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +G+VT++V + SA+EEE  
Sbjct: 691  YGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRLVREGQVTSEVKFFSALEEEGH 750

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             IAQAN+ +D+DG F  E V  R +GE +LV R++I+ +D +PKQ+VS+AA+LIPFLEND
Sbjct: 751  AIAQANALVDQDGRFINEYVSARKSGEFVLVQRDEIELMDVAPKQLVSVAAALIPFLEND 810

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+NR LMG NMQRQAVPLL+A++P VGTGME +VAK SG +++A+  G+V+ VDA RIVI
Sbjct: 811  DANRALMGSNMQRQAVPLLRADSPLVGTGMERIVAKDSGVSVIARHNGVVDAVDAGRIVI 870

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            +  E + D + +GVDIY L+KF RSNQNTC+NQ+P+VKVGD+V+R D+IADGPSTD+G+L
Sbjct: 871  KIDEEEYDETGTGVDIYNLVKFSRSNQNTCINQKPVVKVGDKVKRGDVIADGPSTDMGEL 930

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ALG+N++VAFMPW GYNFEDS+L+SER+  +D +TSIHIEEFE +ARDTKLG EEIT DI
Sbjct: 931  ALGQNIIVAFMPWGGYNFEDSILVSERLTKDDRYTSIHIEEFECVARDTKLGKEEITADI 990

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            PN+ EE LK++DE GII +GAEV PGDILVGKITPKGE+ ++PEEKLLRAIFGEKA DVR
Sbjct: 991  PNLGEEALKDLDESGIIRIGAEVKPGDILVGKITPKGETQLSPEEKLLRAIFGEKAGDVR 1050

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            DTSL +P GV GTV+  ++F+R G DK+ R+  +E+ + E L +D+ DE  I+  +   +
Sbjct: 1051 DTSLTIPPGVEGTVIGAKVFSRKGNDKDARTELIEKIEEEKLRKDEQDEVRIIRDSARGK 1110

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-EKVQRNVESL 1038
            L  +L G+ A        G     K   ++ +L+      +W   +V D   V+  V  +
Sbjct: 1111 LKRLLVGKTAGAKIEDRHGVTVLAKGKKITDELLESLTMDRWATISVSDGTDVEEKVAEV 1170

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              +      ++   F +K++K++ GDD+PPGV+++VKV+VA+KR +Q GDKMAGRHGNKG
Sbjct: 1171 LSKLNEQVELIRGVFDDKVQKLRRGDDLPPGVIKMVKVYVAIKRKLQVGDKMAGRHGNKG 1230

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VSRILP EDMP++ DG PV+IVLNPLGVPSRMNVGQI ETHLGWA  GLG KI+ ++ +
Sbjct: 1231 VVSRILPEEDMPYMDDGRPVEIVLNPLGVPSRMNVGQILETHLGWAAKGLGWKIQKMLEE 1290

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            + +      L+ F+ +        + +   D + +L VA +   GVP+++PVF+GA E  
Sbjct: 1291 HTSE---ENLKKFIRETYDNADFNKILDTMDREELLLVARRLSRGVPMASPVFEGAGEAK 1347

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  +L  A    +GQ  L+DG TGEPF   VTVG +Y+LKL+H+V DK++ARS G YSLV
Sbjct: 1348 IKELLTRAGFATNGQVTLFDGRTGEPFKHKVTVGIMYVLKLHHLVDDKIHARSIGPYSLV 1407

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQRLGEMEVW ++AYG +Y LQE LT+KSDDV GRTR+YE+IV G  T
Sbjct: 1408 TQQPLGGKAQFGGQRLGEMEVWAMEAYGCSYALQEFLTVKSDDVSGRTRMYEAIVKGKHT 1467

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             E G PESFNVL+KE+Q+L L ++L     
Sbjct: 1468 LEPGLPESFNVLIKELQSLCLDVELLEGDE 1497



 Score =  546 bits (1407), Expect = e-153,   Method: Composition-based stats.
 Identities = 253/1062 (23%), Positives = 422/1062 (39%), Gaps = 65/1062 (6%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                      +RK F     IIDIP+LI++QK SY  FL  ++  D R N GL+A F+SV
Sbjct: 1    MAYSIANNHLLRKNFATIKNIIDIPNLIDIQKNSYRRFLQSDVPLDLRKNIGLEAVFRSV 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI  FS  + LE+VSY    PK+DV++C  R +TYA P+K+ +RL+++D  + +G + +
Sbjct: 61   FPIKDFSETSSLEYVSYTLSKPKYDVEECHQRGMTYAAPMKVKVRLVIWDSGKESGVRGV 120

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            KDIKEQ +Y G++PLMT++GTF+I G +R++VSQLHRSPG+ FDHDKG+   SGK+LY+ 
Sbjct: 121  KDIKEQEVYFGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKVLYSA 180

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            R+IP +G W+D EFD KDI+ VRIDRRRK+P T  L ALG   E +L+ +Y         
Sbjct: 181  RVIPYRGSWLDFEFDHKDILFVRIDRRRKMPATVLLKALGYSVEHLLNYYYKSEQIYIAA 240

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                      +L+   K    + D   GE ++++ +K T   +K L + GV  +  +S+ 
Sbjct: 241  -GELRKGIEPELLTMQKAVVDVADA-NGEVIVKANRKFTKASIKKLLDHGVTSIPTSSES 298

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            + G Y + D+V+  TGEI +E    +    L+E+   E+    +LY+D +N  +  R+TL
Sbjct: 299  IIGRYASADVVDPVTGEILLECNQELTADKLDELRQKEVTTFNLLYIDGLNVTSSFRDTL 358

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            + DK     +AL++IYR +RPGD  T   + ++F+ LFF+ ++YDLS VGR+K+N +L L
Sbjct: 359  LADKISSSDEALIEIYRRLRPGDPPTLKSSLALFDNLFFNPERYDLSAVGRLKLNFKLGL 418

Query: 423  D------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     +    +   ++    +++  L NG   +D           +      +  +
Sbjct: 419  KVWPDCTILNGPTMLTAAELQNAEQLIGSLLNGTRPVDLALKDRLSSDLTKSLKKLDLKQ 478

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
                R+   + + ++S   ++   Q  + A         F     L +   +  +  RI 
Sbjct: 479  PVPERLLEQLADELNSAVANAEFFQRDLIAGL--ELPESFIKLMDLIEQGGYDENRRRIE 536

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
              RR   L +     +       D+      R      +    I  +  L +        
Sbjct: 537  GLRRNRMLLEVAYGDSVECCNRNDI--LEIVRYLIELKNGRGAIDDIDHLGNRRVRAVGE 594

Query: 597  FIETPYRK--------VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             +E  YR         + +     +V  L   +     I     S      F    +   
Sbjct: 595  LLENQYRIGLVRMERAIKERMSLQEVENLMPHD----LINSKPVSAVVKEFFGSSQLSQF 650

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                    P  ++                     E  D +    G               
Sbjct: 651  MDQTN---PLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG--RVCPIETPEGPNI 705

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI-RIVIRSVEGDLDPSTSGVDIYRLMKF 767
              + +          G      R     QV +  +      E     + +   + +  +F
Sbjct: 706  GLIASLSTYARINEHGFVETPYRLVREGQVTSEVKFFSALEEEGHAIAQANALVDQDGRF 765

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDI-------------------IADGPSTDLGDLALG 808
                 +   +   ++   DE+   D+                    A+            
Sbjct: 766  INEYVSARKSGEFVLVQRDEIELMDVAPKQLVSVAAALIPFLENDDANRALMGSNMQRQA 825

Query: 809  RNMLVAFMPWHGYNFEDSMLISE---------RMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              +L A  P  G   E  +              +V       I I+  E    +T  G +
Sbjct: 826  VPLLRADSPLVGTGMERIVAKDSGVSVIARHNGVVDAVDAGRIVIKIDEEEYDETGTGVD 885

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFG 918
                 +          I++  ++ VG +V  GD++  G  T  GE  +     +    +G
Sbjct: 886  IY-NLVKFSRSNQNTCINQKPVVKVGDKVKRGDVIADGPSTDMGELALGQNIIVAFMPWG 944

Query: 919  EKAVD----VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
                +    V +   +     S  + +     R      E   +      E   +D  DE
Sbjct: 945  GYNFEDSILVSERLTKDDRYTSIHIEEFECVARDTKLGKEEITADIPNLGEEALKDL-DE 1003

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
              I+      +  +IL G+    G         L   +  E 
Sbjct: 1004 SGIIRIGAEVKPGDILVGKITPKGETQLSPEEKLLRAIFGEK 1045


>gi|291334053|gb|ADD93726.1| DNA directed RNA polymerase beta subunit [uncultured marine bacterium
            MedDCM-OCT-S05-C114]
          Length = 1187

 Score = 1095 bits (2833), Expect = 0.0,   Method: Composition-based stats.
 Identities = 554/1288 (43%), Positives = 764/1288 (59%), Gaps = 162/1288 (12%)

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            E+ I+MG+LP++T+ G+F+I G +R+VVSQLHRSPG+ F+        SGK+L+  RIIP
Sbjct: 13   EEEIFMGELPIITERGSFIINGAERVVVSQLHRSPGVSFEES---THTSGKVLHGFRIIP 69

Query: 187  DQGLWMDIEFDSKDIIHVRID---RRRKVPVTSFLMALGM---------DSEEILSTFYP 234
            D+G W++ +FD  D+++V +D   RRRK  +T+FL AL M           ++I+  FY 
Sbjct: 70   DRGTWIEAQFDQHDLLYVYLDRRRRRRKFLITTFLRAL-MDWDPEKDKDSDQKIIELFYD 128

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
                          L A D +    +   + D   G  + ++ + LT   L+S  + G  
Sbjct: 129  IESLDIN------ELLAKDNVSNYVLVEPMFDRAKGAVLAKAFEPLTKTYLRSFVKAGEN 182

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             L                                                    +D+  +
Sbjct: 183  QLRA--------------------------------------------------IDTSVD 192

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            +  I   L  D  K++ +AL +IY+ +RPG+      AE++   LF DS +YDL+ VGR 
Sbjct: 193  DGAIIRCLKKDTTKNKDEALKEIYKKLRPGEPPDRVNAEALIKRLFLDSKRYDLAKVGRH 252

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNL 459
             +N++LN  TP +VR    ED++A  + L DL+ GK                 IDDID+L
Sbjct: 253  MLNLKLNQSTPLEVRVTTVEDLVAATRKLTDLKRGKSNEEKAREDAGSIFDMGIDDIDHL 312

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFF 517
            GNRRVR+VGE+L N  R GL R ER ++ER++  D   +S+ P  LIN K + + V +FF
Sbjct: 313  GNRRVRTVGELLANVCRSGLARTERVVRERMTLYDQGAESLTPGKLINPKALTTVVRDFF 372

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              SQLSQ ++ +N L+ +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG
Sbjct: 373  ARSQLSQFKDQINPLAEMTHKRRLSALGPGGLNRERAGFEVRDVHPTHYGRICPIETPEG 432

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSL 634
             NIGL+++L+++A+++ +GF+++PY  V DG V     +V YL+A EEE   IAQAN+ +
Sbjct: 433  PNIGLINTLSTYAKIDEFGFLQSPYHPVKDGVVDKNPKNVAYLNAFEEERFLIAQANTEI 492

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            D         V CR   +       +++++D SPKQVVS+AA LIPFLE+DD+NR LMG 
Sbjct: 493  DTKTGKLVGRVTCRYRDQVSEYEPSEVEYMDVSPKQVVSVAAGLIPFLEHDDANRALMGA 552

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV------ 748
            NMQRQAVPLL++++P VGTG+E  VA+ S    V++  G+V   D  RIV+         
Sbjct: 553  NMQRQAVPLLQSDSPLVGTGIEKKVAEDSRTVTVSESEGVVALADGKRIVVTDDGKLPPR 612

Query: 749  --EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              +        G+  Y + KF RSN  TC NQ+P+V+ GD V+    +ADG  TD G+LA
Sbjct: 613  FLKEPRSDHKRGIYCYEMRKFLRSNAGTCFNQKPIVRKGDTVKVGQALADGACTDNGELA 672

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            LGRN+LVAFMPW GYNFED++LISE++V ED++TSIHIEEFEV ARDTKLGPEEITRDIP
Sbjct: 673  LGRNILVAFMPWKGYNFEDAILISEKIVKEDIYTSIHIEEFEVTARDTKLGPEEITRDIP 732

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            N  EE L+N+D  GI+ +GAEV PGDILVGKITPK E+ + PEEKLLRAIFGEKA DV+D
Sbjct: 733  NAGEEALRNLDHLGIVRIGAEVKPGDILVGKITPKSETDLAPEEKLLRAIFGEKAADVKD 792

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            +SL+VPSG  G V+D+++ +R   ++ + S S  R Q++ +  D  ++   L   +   L
Sbjct: 793  SSLKVPSGTQGIVMDIKVSSRTDAEQEKLSPSDFRRQMKQIKEDFRNQTEDLRSQLTESL 852

Query: 987  MEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              IL G+          +G      +  ++  L+        +   +    V+  V  + 
Sbjct: 853  SNILLGEKIPLNVTNSETGDVIIPANRKITKTLLRRLAAVHRF-IEIPPSPVRIKVFEII 911

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
              YE+  + LED    KIE I+ GD +  G ++ V+VFVA K+ ++ GDKMAGRHGNKG+
Sbjct: 912  ESYESKFTDLEDDRDRKIEAIEQGDPIDQGAIKNVRVFVAKKQKMRVGDKMAGRHGNKGV 971

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V++I+  EDMPFL DGTP++I LNPLGVPSRMNVGQ+ ETHLGWAC  LG K+ + I D 
Sbjct: 972  VAKIVAEEDMPFLPDGTPIEICLNPLGVPSRMNVGQVLETHLGWACKKLGLKVATPIFDG 1031

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 I                                                  E  +
Sbjct: 1032 IPESRIQEYL---------------------------------------------KEAEL 1046

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                      E+G++ LYDG TGE F + + VGY+YMLKLNH+VS K++AR+ G YSL+T
Sbjct: 1047 ---------PETGKTFLYDGCTGEQFYQKIVVGYMYMLKLNHLVSSKIHARAVGPYSLIT 1097

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GRT++YES+V G+++ 
Sbjct: 1098 QQPLGGKAQYGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVSGRTKIYESLVKGDNSL 1157

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSR 1367
            + GTP+SFNVL+KEMQ+L L I +    
Sbjct: 1158 QAGTPQSFNVLMKEMQSLCLDIRVLGED 1185


>gi|118579112|ref|YP_900362.1| DNA-directed RNA polymerase, beta subunit [Pelobacter propionicus DSM
            2379]
 gi|158512559|sp|A1ALT4|RPOB_PELPD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|118501822|gb|ABK98304.1| DNA-directed RNA polymerase subunit beta [Pelobacter propionicus DSM
            2379]
          Length = 1499

 Score = 1092 bits (2825), Expect = 0.0,   Method: Composition-based stats.
 Identities = 537/973 (55%), Positives = 725/973 (74%), Gaps = 12/973 (1%)

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIR--KEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +   V  V    R+  +       +   K DI+ I++ L+DL+NG+G IDDID+LGNRR
Sbjct: 530  EENRRVIEVLRRNRMIFEDLYAPVVLTSPKNDILEIVRYLIDLKNGRGAIDDIDHLGNRR 589

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            VR+VGE+L+NQYR+GL+RMER+IKER+S  +++++MP DLIN+KPV + V EFF SSQLS
Sbjct: 590  VRAVGELLENQYRIGLVRMERAIKERMSLQEVENLMPHDLINSKPVSAVVKEFFGSSQLS 649

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 650  QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 709

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            +SL+++AR+N +GF+ETPYR V DGK+TN+V + SA+EEE   IAQAN+ +D +G F  +
Sbjct: 710  ASLSTYARINDHGFVETPYRIVLDGKLTNEVRFFSALEEEGHAIAQANAEVDAEGRFVND 769

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             V  R +GE ILV R++I+ +D +PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL
Sbjct: 770  YVSARKSGEFILVHRDEIELMDVAPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 829

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            L+A++P VGTGME +VAK SG +++A+  G+VE VDA RIV++  E ++D + +GVDIY 
Sbjct: 830  LRADSPLVGTGMERIVAKDSGVSVIARHNGVVESVDASRIVVKIDESEVDETGTGVDIYN 889

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+KF RSNQNTC+N +P+VKVGD V+R+D+IADGPSTD+G+LALG+N++VAFMPW GYNF
Sbjct: 890  LIKFARSNQNTCINNKPVVKVGDVVKRHDVIADGPSTDMGELALGQNIVVAFMPWGGYNF 949

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+L+SE++V +D +TSIHIEE+E +ARDTKLG EEIT DIPN+ EE LK++DE GII 
Sbjct: 950  EDSILVSEKLVKDDRYTSIHIEEYECVARDTKLGKEEITSDIPNLGEEALKDLDESGIIR 1009

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +GAEV PGDILVGKITPKGE+ ++PEEKLLRAIFGEKA DVRDTSL VP GV GTV+  +
Sbjct: 1010 IGAEVKPGDILVGKITPKGETQLSPEEKLLRAIFGEKAGDVRDTSLTVPPGVEGTVIGAK 1069

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS------ 997
            +F+R G DK+ R+  +E+ + E L +D+ DE  I+ ++   +L  +L G++         
Sbjct: 1070 VFSRKGADKDTRTELIEKAEEEKLRKDEQDEIRIIRQSAEGKLHRLLIGKSLSVKLEDGE 1129

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE-KVQRNVESLKVQYETSKSILEDRFKNK 1056
            G     K   ++++ +     +     +V D+ +   NV  +         +++  F++K
Sbjct: 1130 GNLILAKGKEITAEALKSLSINDMGAISVSDDGQTDDNVSKVIDTLNRQIELIQSVFEDK 1189

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I+K++ GDD+PPGV+++VKV++A+KR +Q GDKMAGRHGNKG+VSRILP EDMP+++DG 
Sbjct: 1190 IQKLRRGDDLPPGVIKMVKVYIAIKRKLQVGDKMAGRHGNKGVVSRILPEEDMPYMEDGR 1249

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PV+IVLNPLGVPSRMNVGQI ETHLGWA  G+G +I+ ++   +       L+++L+ V 
Sbjct: 1250 PVEIVLNPLGVPSRMNVGQILETHLGWAAKGIGWRIEEML---QKQTSAESLKAYLKDVY 1306

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
            G       I   D + ++ V  + + GV +++PVF+GA E+ I SML  A    SGQ  L
Sbjct: 1307 GDDEVGTFIDGMDQEELMLVCRRLQRGVSMASPVFEGASEDKIKSMLGKAGFHSSGQVTL 1366

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG +G+PF   VTVG +Y+LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGE
Sbjct: 1367 FDGRSGDPFKHKVTVGVMYVLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGE 1426

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE LT+KSDDV GRTR+YE+IV G  T E G PESFNVL+KE+Q+
Sbjct: 1427 MEVWAMEAYGAAYALQEFLTVKSDDVSGRTRMYEAIVKGKHTLEPGLPESFNVLIKELQS 1486

Query: 1357 LGLSIDLENSRTK 1369
            L L ++L     +
Sbjct: 1487 LCLDVELLEGEDE 1499



 Score =  544 bits (1401), Expect = e-152,   Method: Composition-based stats.
 Identities = 173/431 (40%), Positives = 271/431 (62%), Gaps = 1/431 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                     +RK F K   IIDIP+LI++QK SY  FL      + R N GL+A F+SV
Sbjct: 1   MAYSIANNHLLRKTFTKIKNIIDIPNLIDIQKNSYRRFLQQEGVSESRNNTGLEAVFRSV 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI  FS +A LE+VSY    PK+DV +C  R +T+A P+K+ +RL+++D  + +G ++I
Sbjct: 61  FPIKDFSESASLEYVSYSLSKPKYDVVECHQRGMTFAAPMKVKVRLVIWDTGKESGIRAI 120

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +Y G++PLMT +GTF+I G +R++VSQLHRSPG+ +DHDKG+   SGK+LY+ 
Sbjct: 121 KDIKEQEVYFGEIPLMTDNGTFIINGTERVIVSQLHRSPGVFYDHDKGKTHSSGKVLYSA 180

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           R+IP +G W+D EFD KDI++VRIDRRRK+P T  L ALG  +E++L+ +Y        G
Sbjct: 181 RVIPYRGSWLDFEFDHKDILYVRIDRRRKMPATVLLKALGYSAEQLLNYYYKSEEIFLTG 240

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     + A  L+   K    +VD  +GE ++++ +K T   ++ + E  +K + IT D 
Sbjct: 241 ETPSKSIDAE-LLTLQKALVDVVDPKSGEVIVKANRKFTKASIRKMVEHDIKAVPITFDS 299

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G Y + D+++  TGE+ +E  + +  +  +EI    +    +L++D+++  +  R+TL
Sbjct: 300 IIGRYASSDVIDPATGEVLLECNEEVTAEKFDEIKAKGVESFRLLFIDNLHITSSFRDTL 359

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
           + DK     +AL++IYR +RPGD  T   + ++F  LFF+ ++YDLS VGR+K+N +L L
Sbjct: 360 LMDKISTNDEALIEIYRRLRPGDPPTLKSSLALFENLFFNPERYDLSAVGRLKLNFKLGL 419

Query: 423 DTPDDVRHIRK 433
               +   +  
Sbjct: 420 KVWPECTVLNA 430


>gi|225629893|ref|YP_002726684.1| DNA-directed RNA polymerase, beta subunit [Wolbachia sp. wRi]
 gi|225591874|gb|ACN94893.1| DNA-directed RNA polymerase, beta subunit [Wolbachia sp. wRi]
          Length = 2837

 Score = 1092 bits (2823), Expect = 0.0,   Method: Composition-based stats.
 Identities = 547/1226 (44%), Positives = 800/1226 (65%), Gaps = 38/1226 (3%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ ++ D + DL++VQK SYD F      P  + NE L+  F ++FPI      A
Sbjct: 16   RVSYSRSIDLKDSLLDLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLRRA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTG 118
             +EF+S   D PK+D  +C+ R +T++  +  ++RL+V                 D    
Sbjct: 71   TIEFISCRVDDPKYDESECIKRGVTFSAQVIASIRLVVMQDGISLDEYKSIKESGDHSKL 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            A  +K I+EQ ++   LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL
Sbjct: 131  ATVVKSIEEQKVHFCGLPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            +Y+ RIIP +G W+DIEFD KD ++ R+DR+RK+P++  L ALG+ + +IL  FY KI Y
Sbjct: 191  IYSARIIPYRGSWLDIEFDVKDHLYFRVDRKRKLPISVLLKALGLSNNDILDRFYEKIKY 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
             +  D W  P    D   G ++   L+DI+ G  ++++  ++TS L K L +  +K   +
Sbjct: 251  VKHKDGWKVPFVP-DKFKGVRLPFDLMDIE-GNVLLKANVRITSRLAKKLYDNELKEYLV 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              + +CGL++AED+++  +    + AG+ I  + ++++    + +I +L +D++    YI
Sbjct: 309  PFNSICGLFLAEDLMDSASSTKILSAGESIKLEDIKKLELLSVDEISVLNIDNLFVGPYI 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D+N   +DAL +IYRV+RPG+V    + E  F  LFF  + YDLS +GR+K+N 
Sbjct: 369  LNTLFLDENMSYQDALYEIYRVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNS 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             L L+  +D+  +  EDII I+K +V LR+G+G++DDID+LGNRRVRSVGE ++NQ+R G
Sbjct: 429  YLGLNYDEDLTVLTHEDIIEIVKKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LL++ER+I + +S+  +D V P D IN K + + + +FF SSQLSQ  +  N LS ITH 
Sbjct: 489  LLKLERAIVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +AR+N YGFI
Sbjct: 549  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFI 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV +  VT+ + YLSA++E + +IA  +  LDE+  F +++++CR AG  ++V  
Sbjct: 609  ESPYRKVVNRVVTDQIEYLSAIDEGSHHIADTSVKLDENNCFVDDMLYCRYAGSFVMVSS 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++ +ID SPKQV+S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP V TGMES 
Sbjct: 669  DQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESF 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGA ++AKR GIV+  D+  IVIR+ + +   +   VDIY L KFQRSN NTC+NQ
Sbjct: 729  VASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQ 787

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLV VGD V++ D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+
Sbjct: 788  RPLVCVGDYVKKGDVIADGPAINSGELALGKNLLVAFMSWQGYNFEDSIIISSEVVKKDL 847

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEF+ +  DT LG E+ITR IP V+EE L ++D+ GI+ +G  V PG ILVGK+
Sbjct: 848  FTSIHIEEFDCVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKV 907

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPK    + PE KLL  IFGEK+ D  D+SL     V GTV+DV++F R G+++NER++ 
Sbjct: 908  TPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALL 967

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +++++I     ++D    +     Y  L ++L    +               +      R
Sbjct: 968  IKQKEINDFEEERDYIINVTSEYFYDELKKLLINSGSQ------------DREKFDSIER 1015

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
             QWW   ++++ +   V+SLK  ++   S    +FK K+EK+  G D+P GV   VKVF+
Sbjct: 1016 EQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFI 1075

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+K  +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMNVGQI E
Sbjct: 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            TH+GWAC  LG+K+ +++++             +  +         ++  D+  +  + +
Sbjct: 1136 THVGWACRKLGEKVSNILDEINKIKSA--FCKGIRSLNDDNFTQFAVAYLDNKKIENIDD 1193

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLR 1224
               +   ++TP    A  + +N ++ 
Sbjct: 1194 DEITASVLNTPN-KNALNDELNELVE 1218



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 118/226 (52%), Positives = 160/226 (70%), Gaps = 7/226 (3%)

Query: 1162 NGDISPLRSFLEKVIGTGSHT---EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                S LR+FL +V   GS+      I +  D++++  A + + GVPV+ PVF+G  +E 
Sbjct: 1225 KSSYSNLRNFLIEVYSYGSNVSICNDIRNISDNNLIEFARKLRDGVPVAAPVFEGPKDEQ 1284

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  +  +A LD SGQ++LYDG +GE FDR VTVGY+YMLKL+H+V  K++ARS G YSLV
Sbjct: 1285 IAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLV 1344

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+ GR ++YESI+ G+  
Sbjct: 1345 TQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSN 1404

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            FE G PESFNV++KE+++L L++DL     +N   +E+I   N  +
Sbjct: 1405 FECGIPESFNVMIKELRSLCLNVDL----KQNDVVIEDISHTNIAQ 1446


>gi|42519942|ref|NP_965857.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Drosophila melanogaster]
 gi|81652940|sp|Q73IW9|RPOBC_WOLPM RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|42409679|gb|AAS13791.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Drosophila melanogaster]
          Length = 2837

 Score = 1092 bits (2823), Expect = 0.0,   Method: Composition-based stats.
 Identities = 547/1226 (44%), Positives = 800/1226 (65%), Gaps = 38/1226 (3%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ ++ D + DL++VQK SYD F      P  + NE L+  F ++FPI      A
Sbjct: 16   RVSYSRSIDLKDSLLDLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLRRA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTG 118
             +EF+S   D PK+D  +C+ R +T++  +  ++RL+V                 D    
Sbjct: 71   TIEFISCRVDDPKYDESECIKRGVTFSAQVIASIRLVVMQDGISLDEYKSIKESGDHSKL 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            A  +K I+EQ ++   LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL
Sbjct: 131  ATVVKSIEEQKVHFCGLPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            +Y+ RIIP +G W+DIEFD KD ++ R+DR+RK+P++  L ALG+ + +IL  FY KI Y
Sbjct: 191  IYSARIIPYRGSWLDIEFDVKDHLYFRVDRKRKLPISVLLKALGLSNNDILDRFYEKIKY 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
             +  D W  P    D   G ++   L+DI+ G  ++++  ++TS L K L +  +K   +
Sbjct: 251  VKHKDGWKVPFVP-DKFKGVRLPFDLMDIE-GNVLLKANVRITSRLAKKLYDNELKEYLV 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              + +CGL++AED+++  +    + AG+ I  + ++++    + +I +L +D++    YI
Sbjct: 309  PFNSICGLFLAEDLMDSASSTKILSAGESIKLEDIKKLELLSVDEISVLNIDNLFVGPYI 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D+N   +DAL +IYRV+RPG+V    + E  F  LFF  + YDLS +GR+K+N 
Sbjct: 369  LNTLFLDENMSYQDALYEIYRVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNS 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             L L+  +D+  +  EDII I+K +V LR+G+G++DDID+LGNRRVRSVGE ++NQ+R G
Sbjct: 429  YLGLNYDEDLTVLTHEDIIEIVKKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LL++ER+I + +S+  +D V P D IN K + + + +FF SSQLSQ  +  N LS ITH 
Sbjct: 489  LLKLERAIVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +AR+N YGFI
Sbjct: 549  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFI 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV +  VT+ + YLSA++E + +IA  +  LDE+  F +++++CR AG  ++V  
Sbjct: 609  ESPYRKVVNRVVTDQIEYLSAIDEGSHHIADTSVKLDENNCFVDDMLYCRYAGSFVMVSS 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++ +ID SPKQV+S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP V TGMES 
Sbjct: 669  DQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESF 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGA ++AKR GIV+  D+  IVIR+ + +   +   VDIY L KFQRSN NTC+NQ
Sbjct: 729  VASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQ 787

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            RPLV VGD V++ D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+
Sbjct: 788  RPLVCVGDYVKKGDVIADGPAINSGELALGKNLLVAFMSWQGYNFEDSIIISSEVVKKDL 847

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEF+ +  DT LG E+ITR IP V+EE L ++D+ GI+ +G  V PG ILVGK+
Sbjct: 848  FTSIHIEEFDCVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKV 907

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPK    + PE KLL  IFGEK+ D  D+SL     V GTV+DV++F R G+++NER++ 
Sbjct: 908  TPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALL 967

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +++++I     ++D    +     Y  L ++L    +               +      R
Sbjct: 968  IKQKEINDFEEERDYIINVTSEYFYDELKKLLINSGSQ------------DREKFDSIER 1015

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
             QWW   ++++ +   V+SLK  ++   S    +FK K+EK+  G D+P GV   VKVF+
Sbjct: 1016 EQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFI 1075

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+K  +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMNVGQI E
Sbjct: 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            TH+GWAC  LG+K+ +++++             +  +         ++  D+  +  + +
Sbjct: 1136 THVGWACRKLGEKVSNILDEINKIKSA--FCKGIRSLNDDNFTQFAVAYLDNKKIENIDD 1193

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLR 1224
               +   ++TP    A  + +N ++ 
Sbjct: 1194 DEITASVLNTPN-KNALNDELNELVE 1218



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 118/226 (52%), Positives = 160/226 (70%), Gaps = 7/226 (3%)

Query: 1162 NGDISPLRSFLEKVIGTGSHT---EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                S LR+FL +V   GS+      I +  D++++  A + + GVPV+ PVF+G  +E 
Sbjct: 1225 KSSYSNLRNFLIEVYSYGSNVSICNDIRNISDNNLIEFARKLRDGVPVAAPVFEGPKDEQ 1284

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  +  +A LD SGQ++LYDG +GE FDR VTVGY+YMLKL+H+V  K++ARS G YSLV
Sbjct: 1285 IAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLV 1344

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+ GR ++YESI+ G+  
Sbjct: 1345 TQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSN 1404

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            FE G PESFNV++KE+++L L++DL     +N   +E+I   N  +
Sbjct: 1405 FECGIPESFNVMIKELRSLCLNVDL----KQNDVVIEDISHTNIAQ 1446


>gi|58584904|ref|YP_198477.1| DNA-directed RNA polymerase, fusion of beta and beta' subunits.
            RpoB/RpoC [Wolbachia endosymbiont strain TRS of Brugia
            malayi]
 gi|75497690|sp|Q5GRY9|RPOBC_WOLTR RecName: Full=Bifunctional DNA-directed RNA polymerase subunit
            beta-beta'; Includes: RecName: Full=DNA-directed RNA
            polymerase subunit beta; AltName: Full=RNA polymerase
            subunit beta; AltName: Full=Transcriptase subunit beta;
            Includes: RecName: Full=DNA-directed RNA polymerase
            subunit beta'; AltName: Full=RNA polymerase beta';
            AltName: Full=Transcriptase subunit beta'
 gi|58419220|gb|AAW71235.1| DNA-directed RNA polymerase, fusion of beta and beta' subunits.
            RpoB/RpoC [Wolbachia endosymbiont strain TRS of Brugia
            malayi]
          Length = 2839

 Score = 1088 bits (2815), Expect = 0.0,   Method: Composition-based stats.
 Identities = 541/1166 (46%), Positives = 785/1166 (67%), Gaps = 35/1166 (3%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ ++ D + DL++VQK SY  F      P    NE L++ F+SVFPI      A
Sbjct: 16   RISYSRSIDLKDSLLDLVKVQKESYKSF-----TPGNHGNERLESIFRSVFPINDPLHRA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTG 118
             +EF+S   D PK+D  +C+ R +T++  +  ++RL++                 D    
Sbjct: 71   TIEFISCRIDNPKYDESECIKRGITFSARVIASIRLVIMQDGISLDEYKSIKGSGDHSKL 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            +  IK I EQ ++  +LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL
Sbjct: 131  STIIKFIGEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            +Y+ R+IP +G W+DIEFD KD+++ RIDR+RK+P++  L ALG+ + +IL  FY KI Y
Sbjct: 191  IYSARVIPYRGSWLDIEFDVKDLLYFRIDRKRKLPISVLLKALGLSNSDILDRFYEKIKY 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
             +  + W  P    D   G ++   L+D++ G  + ++  ++TS L K L +  +K   +
Sbjct: 251  IKYKNSWKVPFVP-DKFKGVRLPFDLMDVE-GNVLFKANVRITSRLAKKLHDDELKEYLV 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D +CGL++AED+++  +    + AG+ I  + ++++    I +I +L +D+++   YI
Sbjct: 309  PFDSICGLFLAEDLIDSVSSTKILSAGESIKIEDVKKLELLSIGEISVLNIDNLSVGPYI 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D+N   +DAL +IY+V+RPG+V    + E  F+ LFF+ + YDLS +GR+K+N 
Sbjct: 369  LNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFHNLFFNPEYYDLSNIGRLKLNS 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             L LD  +D+  +  EDII I++ +V LR+G+G++DDID+LGNRRVRSVGE ++NQ+R G
Sbjct: 429  YLGLDYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRAG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LL++ER++ + +S+  +D V   D IN K + + + +FF SSQLSQ  +  N LS ITH 
Sbjct: 489  LLKLERAVIDSMSTSSLDKVSSPDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +ARVN YGFI
Sbjct: 549  RRLSALGPGGLTRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARVNKYGFI 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV +   T+ + YLSA++E   YIA A++ LD +  F +++++CR AG  ++V  
Sbjct: 609  ESPYRKVINRVATDQIEYLSAIDEGLYYIADASAKLDNNNRFIDDMLYCRYAGNFVMVSS 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +++ +ID SPKQV+S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP VGTG+ES 
Sbjct: 669  DQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVGTGIESF 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGA ++AKR GIV+  D+  IVIR+ + +   +  GVDIY L KFQRSN NTC+NQ
Sbjct: 729  VASGSGAVVLAKRDGIVDSSDSNSIVIRAFDEERV-NYLGVDIYHLKKFQRSNHNTCINQ 787

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLV++GD V+  D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+
Sbjct: 788  KPLVRIGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEIVKKDL 847

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFE +  DT LG E+ITR IP V+EE L ++D  GI+ +G  V PG ILVGKI
Sbjct: 848  FTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDNSGIVKIGTRVGPGYILVGKI 907

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPK    + PE KLL  IFGEK+ D  D+SL     V GTV+DV++F R G+++NER++ 
Sbjct: 908  TPKPSLLLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALL 967

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            ++++++  L +++D    +     Y  L ++L              S     + +    R
Sbjct: 968  IKQKEMNDLEKERDYIINVASEYFYDELKKLLV------------HSCSQDQEKLDAIER 1015

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
             QWW   +++  +   V++LK  ++   S    +FK K+EK+  G D+P GVL  VKVF+
Sbjct: 1016 EQWWGIGLKNRSISEQVKNLKKDFDKKVSNTIAQFKQKVEKLDEGYDLPQGVLMSVKVFI 1075

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+K  +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMNVGQI E
Sbjct: 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135

Query: 1139 THLGWACVGLGKKIKSLINDYKANGD 1164
            TH+GWAC  LG+++ +++++      
Sbjct: 1136 THVGWACKKLGERVGNILDEINKINS 1161



 Score =  355 bits (912), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 120/243 (49%), Positives = 167/243 (68%), Gaps = 9/243 (3%)

Query: 1147 GLGKKIKSLINDYKANGD--ISPLRSFLEKVIGTGSHT---EKISDYDDDSVLRVAEQWK 1201
             L  ++ +L+ +Y  +       LRSFL +V   GS       I D  + +++  A + +
Sbjct: 1208 LLNDELNALVENYLNSCKSAYDNLRSFLIEVYSCGSDVSICNNIRDISNSNLIEFAHKLR 1267

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +G+PV+ PVF+G  ++ I  +  +A LD SGQ+  YDG TGE FDR VTVGY+YMLKL+H
Sbjct: 1268 NGIPVAAPVFEGPKDKNIIKLFTLAGLDPSGQTEAYDGRTGEKFDRKVTVGYMYMLKLHH 1327

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD
Sbjct: 1328 LVDDKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDD 1387

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            + GR ++YESI+ G+  FE GTPESFNV++KE+++L L++ L     +N+  +E+I   N
Sbjct: 1388 INGRVKIYESIIKGDSNFECGTPESFNVMIKELRSLCLNVAL----KQNNVVIEDISHTN 1443

Query: 1382 KCE 1384
              +
Sbjct: 1444 IAQ 1446


>gi|255957888|dbj|BAH96858.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957908|dbj|BAH96876.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957918|dbj|BAH96885.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957938|dbj|BAH96903.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
          Length = 1018

 Score = 1085 bits (2807), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1017/1018 (99%), Positives = 1017/1018 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018


>gi|255957552|dbj|BAH96615.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957848|dbj|BAH96822.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957858|dbj|BAH96831.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957868|dbj|BAH96840.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957898|dbj|BAH96867.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
          Length = 1018

 Score = 1084 bits (2804), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1016/1018 (99%), Positives = 1016/1018 (99%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVYEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018


>gi|255957878|dbj|BAH96849.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957928|dbj|BAH96894.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957948|dbj|BAH96912.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957958|dbj|BAH96921.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957968|dbj|BAH96930.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957978|dbj|BAH96939.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957988|dbj|BAH96948.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255957998|dbj|BAH96957.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958008|dbj|BAH96966.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958018|dbj|BAH96975.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958028|dbj|BAH96984.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958038|dbj|BAH96993.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958048|dbj|BAH97002.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958058|dbj|BAH97011.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958068|dbj|BAH97020.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958078|dbj|BAH97029.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958088|dbj|BAH97038.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958098|dbj|BAH97047.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958108|dbj|BAH97056.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958118|dbj|BAH97065.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
 gi|255958128|dbj|BAH97074.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
          Length = 1018

 Score = 1083 bits (2802), Expect = 0.0,   Method: Composition-based stats.
 Identities = 1018/1018 (100%), Positives = 1018/1018 (100%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR
Sbjct: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET
Sbjct: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK
Sbjct: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA
Sbjct: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP
Sbjct: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT
Sbjct: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP
Sbjct: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE
Sbjct: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR
Sbjct: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018


>gi|161833684|ref|YP_001597880.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            GWSS]
 gi|182676574|sp|A8Z5T3|RPOB_SULMW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|152206174|gb|ABS30484.1| DNA-directed RNA polymerase beta subunit [Candidatus Sulcia muelleri
            GWSS]
          Length = 1328

 Score = 1083 bits (2800), Expect = 0.0,   Method: Composition-based stats.
 Identities = 514/1359 (37%), Positives = 765/1359 (56%), Gaps = 127/1359 (9%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
            F     +   F      I  PD +++Q  S+ +F  +N       N+G    F   FPI+
Sbjct: 14   FTKEKTI--NFASVRNKISYPDFLDIQIKSFTNFFCINYTYKNISNKGFYKVFIEYFPIS 71

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIK-- 123
                  +++F+SY+   P + +++C+ R LTY V ++   ++      + T   K  K  
Sbjct: 72   DSKNKFIIDFISYKIYDPLYSIEECIKRGLTYNVYIRARFKIYRTRKRKITIENKRTKYF 131

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            +   Q +Y G  P MT  G+F+  G +R++VSQLHRSPG+ F           K+ Y  R
Sbjct: 132  ETIYQDVYFGTCPYMTPSGSFIFNGSERVIVSQLHRSPGVFFGQYDIPNLP--KISY-AR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
            IIP +G W+++  D  +++++ +D ++++P+T+ L ALG   + +IL+ F      +   
Sbjct: 189  IIPLKGSWIELSTDINNVMYIYLDIKKRLPITTLLRALGYTRDIDILNIFNLAEEVNINK 248

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L                           G+ L + + K+  +K           
Sbjct: 249  VNYKKFL---------------------------GRTLAARIFKTSYQKF---------- 271

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN----NAYI 358
                         E  +I +E    + +  ++ I + +I+ I +   +  N      + I
Sbjct: 272  -------------EENDILLERNIKLKKYHIDIILYYKIKVISLYKKNEKNEKNLYYSII 318

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D    +K+A + IY+ ++         A+   N  FFD     L  VGR K+N 
Sbjct: 319  HNTLKKDPTNSQKEANIYIYKELKDSFPKNDKKAKLFINKFFFDET--HLGEVGRYKLNK 376

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             L LD P   + +  EDII+II+ L+ L N K  +DDIDNL NRRV++VGE L  QY +G
Sbjct: 377  TLKLDFPLKDQILNIEDIISIIENLIALCNNKKEVDDIDNLANRRVKTVGEQLYTQYTIG 436

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            + R+ R IKERI+  D +++ P +LIN+K + S +  FF + +LSQ  +  N L+ +TH 
Sbjct: 437  IARVSRIIKERINVKDNETLTPLELINSKTLTSVINSFFGTDELSQFMDQTNPLAEMTHK 496

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RR+S+LG GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL  FA++N+ GFI
Sbjct: 497  RRISSLGPGGLSRERAGFEIRDVNYSHYGRLCPIETPEGPNIGLISSLCVFAKINSMGFI 556

Query: 599  ETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            ETPY KV  GKV      +Y+S+ +E  + I QAN+ L+      +  +  R   +  +V
Sbjct: 557  ETPYFKVKKGKVVINEAPIYISSDQEYGKLITQANAILNYKTGVLKNNIIVRVNADFPMV 616

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +KI++ID S  Q+ SI+ASLIPFLE+DD+NR LMG NM RQ+VPLL  +AP VGTG+E
Sbjct: 617  NYKKINYIDVSTNQIASISASLIPFLEHDDANRALMGSNMMRQSVPLLNPKAPIVGTGLE 676

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQN 773
              +A+   A I A+  GIVE VDA  I ++     +  L      +  Y+L+KF+++NQN
Sbjct: 677  KHLAQYVNALIYAEGDGIVESVDANNIKVKYFNSEKEKLLSFEKRIKTYKLIKFRKTNQN 736

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC+N RP+VK G  V +  ++ +G +T  G LALGRN+ VAFMP+ GYNFED+++ISE++
Sbjct: 737  TCLNIRPIVKKGMYVTKGQVLCEGFATQNGKLALGRNIKVAFMPFKGYNFEDAIVISEKV 796

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V ED FTSIHI+E+ +  RDTKLG EE T DIPN +EE  K +D+ GII +G+EV PGD+
Sbjct: 797  VREDWFTSIHIDEYSLEVRDTKLGMEEFTFDIPNFNEENKKKLDKYGIIKIGSEVKPGDV 856

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L+G+ITPK E   + EE  L+AIFG+K   +++TSL+  S + G V+D +I+++    ++
Sbjct: 857  LIGRITPKKEGYPSSEENFLKAIFGKKVGTIKNTSLKADSSLFGVVIDTKIYSKFSSKED 916

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDL 1012
            E+     ++      ++    + +L   +   L   +  G    S  +   K  +L+   
Sbjct: 917  EQKQFQIKKLNNKFMKNLKLLRKLLINKLILVLEGSVSEGILNSSYKEIIPKGKILNKLN 976

Query: 1013 ISEYPRSQ--WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + +  ++Q   +Q  V ++     V  +   Y    + L+ + K K  ++  GD++  G+
Sbjct: 977  LKKLLKNQEIIYQNWVNNKYKNNLVFKIIKFYYLKINELKIKLKRKKNRLLIGDEITSGI 1036

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++ KV +A KR ++ GDKM+GRHGNKGIV+RI+  EDMP+L+DGT VD+VLNPLGVPSR
Sbjct: 1037 IKIAKVLIAKKRKLKVGDKMSGRHGNKGIVARIVKEEDMPYLEDGTSVDLVLNPLGVPSR 1096

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQI+ET LGWA   LG    + I D  +  +IS                        
Sbjct: 1097 MNLGQIYETILGWAGEKLGINFSTPIFDGASIEEIS------------------------ 1132

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                        I ++         G + L+DG TGE FD+PVT
Sbjct: 1133 ------------------------KYTDIANL------PSFGNTYLFDGETGEKFDQPVT 1162

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQRLGEMEVW ++A+GAA +
Sbjct: 1163 VGVIYMLKLNHMVDDKMHARSIGPYSLITQQPLGGKSKFGGQRLGEMEVWALEAFGAANI 1222

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            L+E+LT+KSDDV GRT+ YE+IV        G PESF+V
Sbjct: 1223 LREILTVKSDDVKGRTKTYEAIVKRETIPNPGIPESFHV 1261


>gi|269215187|ref|ZP_06159097.1| DNA-directed RNA polymerase, beta subunit [Neisseria lactamica ATCC
            23970]
 gi|269208103|gb|EEZ74558.1| DNA-directed RNA polymerase, beta subunit [Neisseria lactamica ATCC
            23970]
          Length = 1076

 Score = 1082 bits (2799), Expect = 0.0,   Method: Composition-based stats.
 Identities = 517/1079 (47%), Positives = 726/1079 (67%), Gaps = 27/1079 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++D+P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MSYSFTEKKRIRKSFAKRENVLDVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG  +E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYGNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDIANAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A D+++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+   R+ A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVVDGKVTEEIDYLSAIEEGCYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+V+R  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVVRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D  D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLSDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
               K + ++++ ++  P +  W+   + DE + + +E +K+  +  +   ++ ++ K +
Sbjct: 1017 KLAKGSEITTEYLAGLPSKHDWFDIRLADEDLAKQLELIKLSLQQKREEADELYEIKKK 1075


>gi|297250922|ref|ZP_06934377.1| DNA-directed RNA polymerase, beta subunit [Neisseria polysaccharea
            ATCC 43768]
 gi|296837683|gb|EFH21621.1| DNA-directed RNA polymerase, beta subunit [Neisseria polysaccharea
            ATCC 43768]
          Length = 1076

 Score = 1079 bits (2790), Expect = 0.0,   Method: Composition-based stats.
 Identities = 520/1079 (48%), Positives = 729/1079 (67%), Gaps = 27/1079 (2%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
                F    R+RK F K   ++++P L+  Q  SY  FL +  A D+R ++GLQAAF S+
Sbjct: 1    MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTDDGLQAAFNSI 60

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            FPI + +G A LEFV Y    P FD+ +C  R +TYA PL+  +RL++ D        ++
Sbjct: 61   FPIVSHNGYARLEFVHYTLGEPLFDIPECQLRGITYAAPLRARIRLVILDK--EASKPTV 118

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+++E  +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 119  KEVRENEVYMGEIPLMTPSGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 178

Query: 183  RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
            RIIP +G W+D EFD KD+++ RIDRRRK+PVT  L ALG ++E+IL  FY K  +    
Sbjct: 179  RIIPYRGSWLDFEFDPKDLLYFRIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSS 238

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +     L A  L  G      ++D   G  ++  GK++T+  ++ +   G+  L +  + 
Sbjct: 239  NGVQTDLVAGRL-KGETAKVDILD-KEGNVLVAKGKRITAKNIRDITNAGLTRLDVEPES 296

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L G  +A ++++ ETGE+   A D I E+ L +   + +++I  LY++ ++  AYI NTL
Sbjct: 297  LLGKALAAELIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGAYISNTL 356

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             TD+  DR  A + IYR+MRPG+  T    E +FN LFF  D YDLS VGR+K N R   
Sbjct: 357  RTDETADRPAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSYDLSRVGRMKFNTRTYE 416

Query: 423  DTPDDVR----------------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                + +                       +  EDI+A I  LV+LRNG G +DDID+LG
Sbjct: 417  QKLSEAQQNSWYGRLLNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLG 476

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            NRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SS
Sbjct: 477  NRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSS 536

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 537  QLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 596

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+ 
Sbjct: 597  GLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNL 656

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 657  IGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQA 716

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +      GVD
Sbjct: 717  VPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGEVGVD 776

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            IY L+KF RSNQ+T +NQRP VKVGD ++R D++ADG STDLG+LALG+NM +AFMPW+G
Sbjct: 777  IYNLVKFTRSNQSTNINQRPAVKVGDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNG 836

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE G
Sbjct: 837  YNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESG 896

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+
Sbjct: 897  IVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVI 956

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            DV++F R GI +++R+ S+   +++    D +D+  I D + + R+  ++ GQ A  GP 
Sbjct: 957  DVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFDRIERMIVGQKANGGPM 1016

Query: 1001 GFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
               K + ++++ ++  P R  W+   + DE + + +E +KV  +  +   ++ ++ K +
Sbjct: 1017 KLAKGSEITTEYLAGLPSRHDWFDIRLTDEDLAKQLELIKVSLQQKREEADELYEIKKK 1075


>gi|293977795|ref|YP_003543225.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            DMIN]
 gi|292667726|gb|ADE35361.1| DNA-directed RNA polymerase subunit beta [Candidatus Sulcia muelleri
            DMIN]
          Length = 1331

 Score = 1076 bits (2783), Expect = 0.0,   Method: Composition-based stats.
 Identities = 513/1356 (37%), Positives = 760/1356 (56%), Gaps = 126/1356 (9%)

Query: 7    FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
            F     +   F      I  PD +++Q  S+ +F  +N       N+G    F   FPI+
Sbjct: 14   FTKEKTI--NFASVRNKISYPDFLDIQIKSFTNFFCINYTYKNISNKGFYKVFIEYFPIS 71

Query: 67   AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIK-- 123
                  +++F+SY+   P + +++C+ R LTY V ++   ++      + T   K  K  
Sbjct: 72   DSKNKLIIDFISYKIYDPIYSIEECIKRGLTYNVYIRARFKIYRTRKRKITIENKRTKYF 131

Query: 124  DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            +   Q +Y G  P MT  G+F+  G +R++VSQLHRSPG+ F           K+ Y  R
Sbjct: 132  ETIYQDVYFGTCPYMTPSGSFIFNGSERVIVSQLHRSPGVFFGQYDIPNLP--KISY-AR 188

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
            IIP +G W+++  D  +++++ +D ++++P+T+ L ALG   + +IL+ F      +   
Sbjct: 189  IIPLKGSWIELSTDINNVMYIYLDIKKRLPITTLLRALGYTRDIDILNIFNLAEEVNINK 248

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
              +   L                           G+ L + + K+  +K           
Sbjct: 249  GNYKKFL---------------------------GRTLAARIFKTSYQKF---------- 271

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNT 361
                         E  +I +E    + +  ++ I   +I+ I +   +  N   + I NT
Sbjct: 272  -------------EENDILLERNIKLKKYHIDIILSYKIKVISLYKKNEKNLYYSIIHNT 318

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            L  D    +K+A + IY+ ++         A+   N  FF      L  VGR K+N  L 
Sbjct: 319  LKKDPTNSQKEANIYIYKELKDSFPKNDKKAKLFINQFFFYET--HLGEVGRYKLNKTLK 376

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            LD P   + +  EDII+II  L+ L N K  +DDIDNL NRRV++VGE L  QY +G+ R
Sbjct: 377  LDFPLKDQILNIEDIISIIDNLIALCNNKKEVDDIDNLANRRVKTVGEQLYTQYTIGIAR 436

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + R IKERI+  D +++ P +LIN+K + S +  FF + +LSQ  +  N L+ ITH RR+
Sbjct: 437  VSRIIKERINVKDNETLTPIELINSKTLTSVINSFFGTDELSQFMDQTNPLAEITHKRRI 496

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            S+LG GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL  FA++N+ GFIETP
Sbjct: 497  SSLGPGGLSRERAGFEIRDVNYSHYGRLCPIETPEGPNIGLISSLCVFAKINSMGFIETP 556

Query: 602  YRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            Y KV  GKV      +Y+S+ +E  + I QAN+ L+      +  +  R   +  +V  +
Sbjct: 557  YFKVKKGKVVINEAPIYISSDQEYGKLITQANAILNYKTGVLKNNIIVRVNADFPMVNYK 616

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            KI++ID S  Q+ SI+ASLIPFLE+DD+NR LMG NM RQ+VPLL  +AP VGTG+E  +
Sbjct: 617  KINYIDVSTNQIASISASLIPFLEHDDANRALMGSNMMRQSVPLLNPKAPIVGTGLEKHL 676

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            A+   A I A+  GIVE VDA  I ++     +  L      +  Y+L+KF+++NQNTC+
Sbjct: 677  AQYVNALIYAEGDGIVESVDANNIKVKYFNSEKEKLLSFEKRIKTYKLIKFRKTNQNTCI 736

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            N RP+VK G  V +  ++ +G +T  G LALGRN+ VAFMP+ GYNFED+++ISE++V E
Sbjct: 737  NIRPIVKKGMYVTKGQVLCEGFATQNGKLALGRNIKVAFMPFKGYNFEDAIVISEKVVRE 796

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTSIHI+E+ +  RDTKLG EE T DIPN +EE  K +D+ GII +G+EV PGD+L+G
Sbjct: 797  DWFTSIHIDEYSLEVRDTKLGMEEFTFDIPNFNEENKKKLDKYGIIKIGSEVKPGDVLIG 856

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            +ITPK E   + EE  L+AIFG+K   +++TSL+  S + G V+D +I+++    ++E+ 
Sbjct: 857  RITPKKEGYPSSEENFLKAIFGKKVGTIKNTSLKADSSLFGVVIDTKIYSKFSSKEDEQK 916

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                ++      ++    + +L   +   L   +  G    S  +   K  +L+   + +
Sbjct: 917  QLKIKKLNNKFIKNLKLLRKLLINKLILVLEGSVSEGILNSSYKEIIPKGKILNKLNLKK 976

Query: 1016 YPRSQ--WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
              ++Q   +Q  V ++     V  +   Y    + L+ + K K  ++  GD++    +++
Sbjct: 977  LLKNQEIIYQNWVNNKYKNNLVFKIIKFYYLKINELKIKLKRKKNRLLIGDEITS--IKI 1034

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             KV +A KR ++ GDKM+GRHGNKGIV+RI+  EDMP+L+DGT VD+VLNPLGVPSRMN+
Sbjct: 1035 AKVLIAKKRKLKVGDKMSGRHGNKGIVARIVKEEDMPYLEDGTSVDLVLNPLGVPSRMNL 1094

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI+ET LGWA   LG    + I D  +  +IS                           
Sbjct: 1095 GQIYETILGWAGEKLGINFSTPIFDGASIEEIS--------------------------- 1127

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                     I ++         G + L+DG TGE FD+PVTVG 
Sbjct: 1128 ---------------------KYTDIANL------PSFGNTYLFDGETGEKFDQPVTVGV 1160

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQRLGEMEVW ++A+GAA +L+E
Sbjct: 1161 IYMLKLNHMVDDKMHARSIGPYSLITQQPLGGKSKFGGQRLGEMEVWALEAFGAANILRE 1220

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            +LT+KSDDV GRT+ YE+IV        G PESF+V
Sbjct: 1221 ILTVKSDDVKGRTKTYEAIVKRETIPNPGIPESFHV 1256


>gi|226226261|ref|YP_002760367.1| DNA-directed RNA polymerase beta subunit [Gemmatimonas aurantiaca
            T-27]
 gi|226089452|dbj|BAH37897.1| DNA-directed RNA polymerase beta subunit [Gemmatimonas aurantiaca
            T-27]
          Length = 1522

 Score = 1070 bits (2768), Expect = 0.0,   Method: Composition-based stats.
 Identities = 512/1208 (42%), Positives = 745/1208 (61%), Gaps = 60/1208 (4%)

Query: 16   FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
             F K    +D+P L+++Q  +++  L ++ A  ER + GL+  FK +FPIT       LE
Sbjct: 5    SFAKLETGMDMPHLLDIQTRAFESLLQLDAASQEREDVGLERVFKDLFPITDVHENFSLE 64

Query: 76   FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            FV Y    PK+ V +C+ RD+TY+ PLK TL+L++F+       K  ++I E+ +Y+G+L
Sbjct: 65   FVRYSLGEPKYTVAECIERDMTYSAPLKATLQLVIFEDTGDG--KRPRNIIEKEVYLGEL 122

Query: 136  PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
            PL+T+ GTFVI G +R++VSQLHRSPG+ F+        +G+ L + RIIP +G W++  
Sbjct: 123  PLLTELGTFVINGAERVIVSQLHRSPGVVFEES---THPNGQRLLSSRIIPFRGSWVEFT 179

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D  D+I+V ID+++K P T+ L A G     +IL  F+ +              +    
Sbjct: 180  VDIHDVIYVHIDKKKKFPATALLRAFGYGENRDILRLFFAERDLDLTKK--RETRNDQRE 237

Query: 255  MVGAKVSSSLV----------------------DIDTGEQVIESGKKLTSGLLKSLKEKG 292
            ++GA ++  +                       +    E ++  G +LT  +L  L  +G
Sbjct: 238  VLGAIIAEDITLEGEVTAADAPKPKTKKAKAERERSEAELLVREGDELTEEVLNRLVRQG 297

Query: 293  VKFLGITS-----------------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            +K + + +                 +      +A D+++ +TGE+  E    + +  ++ 
Sbjct: 298  IKTVKMFASYTQIDLRDEQDAIDRGEREVRRMLARDVIDQDTGEVVAEKDTTLTDAVIKR 357

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
            I  ++I  + +        +  I+NTL  D  K  ++AL  IY ++RPGD      A+  
Sbjct: 358  IRKADIVKVFVFVASGRAESTLIKNTLAKDPTKAEEEALKQIYALLRPGDAPNRETAKQA 417

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
               LFF   +YDL  VGR K+N RL L+TP     + KED + I++ LV+L  G+G +DD
Sbjct: 418  LERLFFSPKRYDLGRVGRYKINQRLRLNTPMRTTVLTKEDFVEIMRQLVELHEGRGDVDD 477

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVC 514
            ID LGNRR+RSVGE++ NQ+ +GL RM R +KER+S   D + +   DL+NA+ V + + 
Sbjct: 478  IDQLGNRRIRSVGELIANQFSVGLSRMARLVKERMSINTDPEKISLDDLVNARTVSAVIQ 537

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
             FF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG E+RDVH + YGR+CP ET
Sbjct: 538  AFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSQYGRMCPIET 597

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG NIGL++SL  FA+VN  GFIETPYR V +G+VT ++V+L A  EE+  IAQANS L
Sbjct: 598  PEGPNIGLITSLACFAQVNDLGFIETPYRIVKEGRVTGEIVWLDANREEDAIIAQANSKL 657

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            + DG+F ++LV  R  G+  L P   ID++D +P+Q+VSIAA+LIPFLE+DD+NR LMG 
Sbjct: 658  NPDGTFVDDLVLSRKRGDLPLEPPMNIDYMDVAPEQLVSIAAALIPFLEHDDANRALMGS 717

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS------- 747
            NMQRQAVPLL    PFVGTG+E+ VA  SGA I+A+R G+V  V A  I+I +       
Sbjct: 718  NMQRQAVPLLNPATPFVGTGLEATVAVDSGAVIIARRPGVVTNVTADEIIIDAGLNQEAV 777

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             +G        +D YRL K+ R+NQ+T +NQRPLV++G  V + +++ADG +T++G LAL
Sbjct: 778  DDGRPLTRLGQLDRYRLKKYWRTNQDTAINQRPLVRMGQTVAKGEVLADGAATEMGQLAL 837

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            GRN+ VAFMPW+G+NFED++++SER+V  DVF+SIHI+E E+  RDTK G EEITR+IPN
Sbjct: 838  GRNVTVAFMPWYGHNFEDAIVLSERLVKFDVFSSIHIQELELHVRDTKRGQEEITREIPN 897

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V+EE L ++DE GI+ +GA V  GDILVGKITPKGE+ ++PEEKLL AIFGEKA DV+D+
Sbjct: 898  VAEESLVDLDERGIVRIGAAVKAGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDS 957

Query: 928  SLRVPSGVSGTVVDVRIFNR---HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
            SL+V  G+ G V+DV+IF+R     ++K+      E  ++E   + + +E    + +   
Sbjct: 958  SLKVSPGMEGVVIDVKIFSRVEDQVVEKDRGERIGEVRRLEGEEKIRVNEVRDAELSRLL 1017

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS--QWWQFAVQDEKVQRNVESLKVQY 1042
                +     A +  +     T L+ +++     +      F V+++K    V  +    
Sbjct: 1018 EGETVALALKAGTVEEAIGAGTTLTREILDGLRFATLDLKTFRVENKKANDRVRDILDAA 1077

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
               K+ +E+R +++I++I   D++PPGV+++VKV++A KR I  GDKMAGRHGNKGIV+R
Sbjct: 1078 AEEKARIEERAEDRIDRILQPDELPPGVIQLVKVYLAEKRKISVGDKMAGRHGNKGIVAR 1137

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+P EDMPFL +G PVDIVLNPLGVPSRMNVGQI ETHLGWA   L    K+ + +    
Sbjct: 1138 IVPEEDMPFLPNGRPVDIVLNPLGVPSRMNVGQILETHLGWAAKLLNFYAKTPVFEGANE 1197

Query: 1163 GDISPLRS 1170
             +I  L  
Sbjct: 1198 REIGLLMK 1205



 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 93/167 (55%), Positives = 120/167 (71%), Gaps = 4/167 (2%)

Query: 1213 GADEEAI----NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            G  +  +    + ++R+A L  +G+  L DG TGE F  PVTVG IYMLKL+H+V DK++
Sbjct: 1344 GGKDADVDAAASELIRLAGLTPTGKVRLRDGRTGETFTAPVTVGEIYMLKLSHLVDDKIH 1403

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YSLVTQQPL GK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR+RV
Sbjct: 1404 ARSIGPYSLVTQQPLAGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVNGRSRV 1463

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            YE+IV G +  E G PESFNVLVKE+QALG+ + L  +       ++
Sbjct: 1464 YEAIVKGQNLPEPGIPESFNVLVKELQALGIKVTLGATDGTGVELVD 1510


>gi|190570968|ref|YP_001975326.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Culex quinquefasciatus Pel]
 gi|213019484|ref|ZP_03335290.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Culex quinquefasciatus JHB]
 gi|190357240|emb|CAQ54662.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Culex quinquefasciatus Pel]
 gi|212994906|gb|EEB55548.1| DNA-directed RNA polymerase, beta/beta' subunits [Wolbachia
            endosymbiont of Culex quinquefasciatus JHB]
          Length = 2839

 Score = 1070 bits (2767), Expect = 0.0,   Method: Composition-based stats.
 Identities = 541/1225 (44%), Positives = 798/1225 (65%), Gaps = 42/1225 (3%)

Query: 14   RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  + ++ ++ D + DL++VQK SY+ F      P+   NE L+A F ++FPI+     A
Sbjct: 16   RVSYSRSIDLKDSLLDLVKVQKGSYNSF-----TPNNESNERLEAIFHTIFPISDPLHRA 70

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF--------------DVDEFTG 118
             +EF++   D  K+   +C+ R +T++  +  ++RL++               D D    
Sbjct: 71   TIEFLNCRVDDLKYSESECIKRGITFSAQVIASIRLVIMQDGVSLEKYQEIKEDDDHSKL 130

Query: 119  AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            A  IK  +EQ +   +LP+MT  GTF+I G+++++VSQ+HRSPG+ FD D+G+   SGKL
Sbjct: 131  ATVIKSAEEQEVRFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDRGKTYNSGKL 190

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            +Y+ R+IP +G W+DIEFD KD ++  IDR+RK+P++  L ALG+ + +IL+ FY KI Y
Sbjct: 191  IYSARVIPYRGSWLDIEFDVKDHLYFHIDRKRKLPISVLLKALGLSNNDILNKFYEKIEY 250

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
             +    W  P S  D   G ++   L +++ G  ++++  ++TS L K+L + G+K   I
Sbjct: 251  IKHKSGWRVPFSP-DKFKGVRLPFDLKNVE-GNVLLKANVRITSKLAKNLYDNGLKEYLI 308

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D +CGL++AED+++  +    + AG+ I  + ++++    I  I +L +D+V+   YI
Sbjct: 309  PYDSICGLFLAEDLIDSASSTKVLSAGESIKLEDIKKLELLSIDKISVLNIDNVSVGPYI 368

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D+N   ++AL +IY+V+RPG+V    + E  F  LFF S+ YDLS +GR+K+N 
Sbjct: 369  LNTLFLDENMSYENALYEIYKVLRPGEVPILKIVEEFFRNLFFSSEYYDLSNIGRLKLNS 428

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             L L+  +++  +  EDII II+ +V LR+G+G++DDID+L NRRVRSVGE ++NQ+R G
Sbjct: 429  CLGLNYEENLTTLTHEDIIEIIRKIVLLRDGQGSVDDIDHLANRRVRSVGEFIENQFRTG 488

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            LL++ R++ + +S+  +D V P D IN K + + + +FF SSQLSQ  +  N LS ITH 
Sbjct: 489  LLKLGRAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +AR+N YGFI
Sbjct: 549  RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFI 608

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            E+PYRKV +  VT+ + YLSA++E   YIA  ++ LDE+  F +++++CR AG  ++V  
Sbjct: 609  ESPYRKVVNKVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGTFVMVNS 668

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             ++ +ID SPKQV+S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP V TGMES 
Sbjct: 669  NQVSYIDLSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESF 728

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            VA  SGA ++AKR GIV+  D+  IVIR+ +     +   VDIY L KFQRSN NTC+NQ
Sbjct: 729  VASGSGAVVLAKRGGIVDSSDSNSIVIRAFDKGGI-NYLDVDIYHLRKFQRSNHNTCINQ 787

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            +PLV VGD V+  D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+
Sbjct: 788  KPLVHVGDCVKEGDVIADGPAINNGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDL 847

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            FTSIHIEEFE +  DT LG E+ITR IP V+EE L ++D+ GI+ VG  V PG ILVGK+
Sbjct: 848  FTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKVGTRVGPGYILVGKV 907

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            TPK    + PE KLL  IFGEK+ D  D+SL     + G V+DV++F R G ++NER+  
Sbjct: 908  TPKHSLSLPPETKLLMTIFGEKSFDCVDSSLYTSPDIEGIVIDVQVFTRRGEEENERAFL 967

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +++++     +++D    ++++  Y  L +IL    +               + I+   R
Sbjct: 968  IKQKEANDFEKERDHIINVINQYFYDELRKILINSGSQ------------DRESINFIER 1015

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
              WW   ++++ + + VESLK  ++   S     FK K+EK+  G D+P GV   VKVF+
Sbjct: 1016 EGWWDIGLKNQSISKQVESLKKDFDEKVSHAIANFKRKVEKLHEGYDLPQGVSMSVKVFI 1075

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+K  +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTP+DI+LNPLGVPSRMNVGQI E
Sbjct: 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPIDIILNPLGVPSRMNVGQILE 1135

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            TH+GWAC  LG+K+ +++++      I        + +      +  + Y D+       
Sbjct: 1136 THVGWACKKLGEKVGNILDE---INKIKRAFCEAIRSLSDDDFEKFAALYLDNKKFEDIN 1192

Query: 1199 QWKSGVPVSTPVFDGADEEAINSML 1223
              +    ++  + D  +++ +N+ L
Sbjct: 1193 DDE----ITASILDTPNKDELNNEL 1213



 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 116/222 (52%), Positives = 157/222 (70%), Gaps = 7/222 (3%)

Query: 1166 SPLRSFLEKVIGTGSHT---EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            S LR FL +V   GS+      I D +D+ ++  A + + G+PV+ PVF+G  +E I  +
Sbjct: 1229 SSLRHFLIEVYSCGSNLSICNNIRDINDNHLIEFAYKLRDGIPVTAPVFEGPKDEQIVKL 1288

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
              +A LD SGQ +LYDG +GE FDR VTVGY+YMLKL+H+V  K++ARS G YSLVTQQP
Sbjct: 1289 FELAGLDNSGQVVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQP 1348

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+ GR ++YES++ G+  FE G
Sbjct: 1349 LGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESVIKGDSNFECG 1408

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
             PESFNV++KE+++L  ++DL     +N   +E+I   N  +
Sbjct: 1409 IPESFNVMIKELRSLCFNVDL----KQNDIVIEDISHTNIAQ 1446


>gi|323144266|ref|ZP_08078891.1| DNA-directed RNA polymerase, beta subunit [Succinatimonas hippei YIT
            12066]
 gi|322415959|gb|EFY06668.1| DNA-directed RNA polymerase, beta subunit [Succinatimonas hippei YIT
            12066]
          Length = 1490

 Score = 1058 bits (2736), Expect = 0.0,   Method: Composition-based stats.
 Identities = 527/1012 (52%), Positives = 706/1012 (69%), Gaps = 21/1012 (2%)

Query: 363  VTDKNKDRKDALLDIYRV-MRPGDVSTFSVAESMFN----FLFFDSDKYDLSTVGRVKMN 417
              DK+     A   +++V +  GD         +F      L  +    +          
Sbjct: 493  KADKDPMAPAATRYLHKVKINVGDEVISFERAVIFPLSELNLNVNVKDLEAKVTDNRGKA 552

Query: 418  MRLNLDTPDDVR-HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            + L  + P++ R  +   DII +++ LV +RNGK  IDDID+LGNRR+RSVGEM +NQ+R
Sbjct: 553  LHLEPNQPEEERGTLSNNDIIKVMRYLVKIRNGKENIDDIDHLGNRRIRSVGEMAENQFR 612

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            +GL+R+ER++KER+S  D+D+  PQ+LINAKP+ +A+ EFF SSQLSQ  +  N LS +T
Sbjct: 613  IGLVRVERAVKERLSLGDLDNTTPQELINAKPISAAIKEFFGSSQLSQFMDQNNPLSEVT 672

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YG
Sbjct: 673  HKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLAVFARCNDYG 732

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+ETPYR+V DG+V+ D  YLSA++E    IAQAN+ LDE+G   ++ V CR  GE  + 
Sbjct: 733  FLETPYRRVKDGQVSEDFEYLSAIDEGQYVIAQANTDLDENGHIIDDYVQCRYKGESTVR 792

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                + F+D SP+QV+S+AA+LIPFLE+DD+NR LMG NMQRQAVP +++E PFVGTGME
Sbjct: 793  RSSDVQFMDVSPQQVISVAAALIPFLEHDDANRALMGANMQRQAVPTVRSEKPFVGTGME 852

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTC 775
              VA  SG +I+A+R G+V+ VD  RIVIR   +       +G+DIY L+K+ RSNQNTC
Sbjct: 853  RAVAVDSGVSIIARRGGVVDNVDGARIVIRVNPDEIEGSHDAGIDIYNLIKYTRSNQNTC 912

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +NQRP V + ++V   D++ADG STDLG+LALG+N+ VAFMPW+GYN+EDS+L+SER+ +
Sbjct: 913  INQRPCVSLHEKVVAGDVLADGSSTDLGELALGQNLRVAFMPWNGYNYEDSILVSERVAA 972

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +D  T+IHI+E   +ARDTKLGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILV
Sbjct: 973  KDRLTTIHIQELSCVARDTKLGPEEITADIPNVGEAALSKLDEAGIVYVGAEVVGGDILV 1032

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GK+TPKGE+ +TPEEKLLRAIFGEKA +V+D+SLRVP+GVSGTVVDV+IF R G++K++R
Sbjct: 1033 GKVTPKGETQLTPEEKLLRAIFGEKASEVKDSSLRVPNGVSGTVVDVQIFTRDGVEKDKR 1092

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            +  +E   I    +D D+E   L   +  ++   L            K         + +
Sbjct: 1093 AKEIEEMHIAKAKKDLDEEFAFLSAGLLRQVRAHL-----------IKNGMK--EKDVEK 1139

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
               ++     + D+  QR +E   V+    K   +++F+   +KI  GDD+ PGVL++VK
Sbjct: 1140 LSDTEVLAQRLDDDTAQRQLEEFAVRLTDYKKEYQEKFETARKKITEGDDLTPGVLKIVK 1199

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V++A+KR IQ GDKMAGRHGNKG++S+I P EDMPF ++G PVDIVLNPLGVPSRMN+GQ
Sbjct: 1200 VYLAVKRRIQPGDKMAGRHGNKGVISKICPIEDMPFDENGKPVDIVLNPLGVPSRMNIGQ 1259

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E HLG A  G+G  I  ++ + KA  +I  +   +  + G  S    I    D  V+ 
Sbjct: 1260 VLEVHLGLAAKGIGDMINKMLIEQKAIAEIRKVLQQIYDL-GNTSQKVDIDSMSDAEVMT 1318

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            +A   + G+ V+TPVFDGA EE+I  +L++A L ESGQ  LYDG TG PF+R VTVGY+Y
Sbjct: 1319 LANNLRDGLTVATPVFDGATEESIKELLKLAGLPESGQMTLYDGTTGLPFERKVTVGYMY 1378

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L+EML
Sbjct: 1379 MLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLREML 1438

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            T+KSDDV GRT++Y++IV G+   + G PESFNVL++E+++LG++IDL    
Sbjct: 1439 TVKSDDVNGRTKMYKNIVDGSYRMDAGIPESFNVLLREIRSLGINIDLVRKD 1490



 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 167/425 (39%), Positives = 248/425 (58%), Gaps = 19/425 (4%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK  +++D P L+ VQ  S+  F+  +     +   GL AAFKSV
Sbjct: 1   MVYSYTEQKRIRKDFGKRVKVLDTPYLLAVQLDSFKQFISSD----PKSENGLVAAFKSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG A L + S+    PKFDV +C+ R  TY+ PLK+ L L+ ++ D     K++
Sbjct: 57  FPIRSYSGNAELCYNSFHLGEPKFDVRECMIRGTTYSAPLKVKLSLVRYEKDAP---KTV 113

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K+  +Q +YMG++PLMT +GTFVI G +R+VVSQLHRSPG+ FD+DKG+    G++L++ 
Sbjct: 114 KERIDQDVYMGEIPLMTDNGTFVINGTERVVVSQLHRSPGVFFDNDKGKTHP-GRILFSA 172

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD +D + VRIDRRRK+P +  L ALG  +E+IL  F+  +    +G
Sbjct: 173 RIIPYRGSWLDFEFDHRDNMFVRIDRRRKLPASILLRALGYTTEQILDLFFDTVDIEFKG 232

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                 L    L  G   S  +      + ++E GKK+T+  ++ LK+  V  + I  + 
Sbjct: 233 TKINMELVPERL-RGETASFDIKL--NKKVLVEKGKKITARHIRELKKAEVTSIEIPQEY 289

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L    VA D    E G   + A  V++E  +  I  + I+ I ILY   V+   +I  TL
Sbjct: 290 LYDKIVAHDYATKE-GTPVVAANTVLNETVVNNIRDNGIKKISILYTSQVDEGPFIAETL 348

Query: 363 VTDKNK-------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             D ++       DR  AL +IY++MRPG+  T   AE++F+ LFF  ++YDLS+VGR+K
Sbjct: 349 RNDTSRDLTSPEADRLAALYEIYKMMRPGEPPTAEAAETLFHNLFFAEERYDLSSVGRMK 408

Query: 416 MNMRL 420
            N R 
Sbjct: 409 FNSRF 413


>gi|257137636|ref|ZP_05585898.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            E264]
          Length = 1052

 Score = 1047 bits (2708), Expect = 0.0,   Method: Composition-based stats.
 Identities = 524/1051 (49%), Positives = 732/1051 (69%), Gaps = 6/1051 (0%)

Query: 186  PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
            P +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   +  
Sbjct: 2    PYRGSWLDFEFDPKDVLYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMDEGA 61

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                    L  G      + D   G+ +++  K++ +  ++ L+    K++ +  D L G
Sbjct: 62   QMEFVPERL-RGEVARFDITD-REGKVIVQKDKRINAKHIRDLEAAKTKYISVPEDYLLG 119

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              +A+++V+G+TGE+   A D I E  L+++  ++I++I  LY + ++   YI +TL  D
Sbjct: 120  RVLAKNVVDGDTGEVIANANDEITEGVLDKLREAKIKEIQTLYTNDLDQGPYISSTLRVD 179

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            +  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  D  
Sbjct: 180  ETVDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGRDEI 239

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                 ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+ER+
Sbjct: 240  TGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA 299

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            +KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 300  VKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALG 359

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPYRKV
Sbjct: 360  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPYRKV 419

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             D KVT+ + YLSA+EE    IAQAN+++  DGS  +ELV  R AGE ++V  ++I ++D
Sbjct: 420  VDSKVTDQIDYLSAIEEGRYMIAQANAAISNDGSLVDELVSSREAGETMMVTPDRIQYMD 479

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  SG 
Sbjct: 480  VAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTVAVDSGT 539

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + A R G+V+ VDA RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+VK+G
Sbjct: 540  TVQALRGGVVDYVDAGRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMG 599

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D+V R D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+LISER+V++D +TSIHIE
Sbjct: 600  DKVARGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISERVVADDRYTSIHIE 659

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKGE+ 
Sbjct: 660  ELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKGETQ 719

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  ++++
Sbjct: 720  LTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDDELK 779

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
                D +D+  I++ + + RL  +L G+ A  GPK   K T +    + +     W+   
Sbjct: 780  RYRLDLNDQLRIVEGDAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWFDIR 839

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            + D++    +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR +Q
Sbjct: 840  LADDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKRRLQ 899

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLGWA 
Sbjct: 900  PGDKMAGRHGNKGVVSKIVPVEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLGWAA 959

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLG +I  ++        I  LR FL K+       E +  + DD +L +A+  + GVP
Sbjct: 960  KGLGWRIGEML---ARQTKIEELRVFLTKIYNESGRAEDLESFSDDEILELAKNLREGVP 1016

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +TPVFDGA EE ++ ML +A   +     L
Sbjct: 1017 FATPVFDGATEEEMSKMLDLA-FPDDIAEQL 1046


>gi|226328684|ref|ZP_03804202.1| hypothetical protein PROPEN_02579 [Proteus penneri ATCC 35198]
 gi|225201870|gb|EEG84224.1| hypothetical protein PROPEN_02579 [Proteus penneri ATCC 35198]
          Length = 943

 Score = 1046 bits (2704), Expect = 0.0,   Method: Composition-based stats.
 Identities = 500/952 (52%), Positives = 675/952 (70%), Gaps = 9/952 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQNGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG A L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNAELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L A+   +EEIL  F+ K ++    
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRAMNYSTEEILGLFFEKTLFEISN 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L+++ +  + +  + 
Sbjct: 235 NKLMMTLVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKEQIDRIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  VA D ++  TGE+   A   I    L  +  +  + I  L+ + +++ AYI  T+
Sbjct: 292 IAGKVVARDYIDEATGELICAANMEISLDVLARLSQAGHKTIETLFTNDLDHGAYISETV 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AE++F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352 RVDPTNDRLSALVEIYRMMRPGEPPTREAAENLFENLFFSEDRYDLSAVGRMKFNRSLGR 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D  +    + +EDII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412 DEVEGSGILSQEDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472 ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532 ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ 
Sbjct: 592 RVVENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQ 651

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  
Sbjct: 652 YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVD 711

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VAKR G+V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712 SGVTAVAKRGGVVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCV 771

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN+EDS+L+SER+V ED FT+I
Sbjct: 772 SLGEPVDRGDVLADGPSTDLGELALGQNMRVAFMPWNGYNYEDSILVSERVVQEDRFTTI 831

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HI+E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 832 HIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 891

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           E+ +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K  
Sbjct: 892 ETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKKR 943


>gi|41018108|sp|Q93MK7|RPOB_WOLPI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|15081478|gb|AAK83926.1|AF401090_1 RNA polymerase beta-subunit [Wolbachia pipientis]
          Length = 1436

 Score = 1040 bits (2690), Expect = 0.0,   Method: Composition-based stats.
 Identities = 529/1211 (43%), Positives = 780/1211 (64%), Gaps = 45/1211 (3%)

Query: 28   DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
            DL++VQK SY+ F      P+   NE L+A F ++FPI+     A +EF++   D  K+ 
Sbjct: 37   DLVKVQKGSYNSF-----TPNNESNERLEAIFHTIFPISDPLHRATIEFLNCRVDDLKYS 91

Query: 88   VDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTGAKSIKDIKEQSIYMG 133
              +C+ R +T++  +  ++RL++                 D    A  IK  +EQ +   
Sbjct: 92   ESECIKRGITFSAQVIASIRLVIMQDGVSLEKYQEIKEYDDHSKLATVIKSAEEQEVRFC 151

Query: 134  DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL+Y+ R+IP +G W+D
Sbjct: 152  ELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPYRGSWLD 211

Query: 194  IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            IEFD KD ++ RIDR+RK+P++  L ALG+ + +IL+ F    VY      W  P    D
Sbjct: 212  IEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILNKFMKNRVYK-HKSGWKVPFFP-D 269

Query: 254  LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
               G ++   L +++ G  ++++  ++TS L K+L + G+K   I  D +CGL++AED++
Sbjct: 270  KFKGVRLPFDLKNVE-GNVLLKANVRITSKLAKNLYDNGLKEYLIPYDSICGLFLAEDLI 328

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
            +  +    + AG+ I  + ++++    I  I +L +D+V+   YI NTL  D+N   ++A
Sbjct: 329  DSASSTKILSAGESIKLEDIKKLELLSIDKISVLNIDNVSVGPYILNTLFLDENMSYENA 388

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L +IY+V+RPG+V    + E  F  LFF  + YDLS +GR+K+N  L L+  +++  +  
Sbjct: 389  LYEIYKVLRPGEVPVLKIVEEFFRNLFFSPEYYDLSNIGRLKLNSCLGLNYEENLTTLTH 448

Query: 434  EDIIAIIKILVDLRNGKGTI-DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            EDII II+ +V LR+G+G++ DDID+L NRRVRSVGE ++NQ+R GLL++ R++ + +S+
Sbjct: 449  EDIIEIIRKIVLLRDGQGSVDDDIDHLANRRVRSVGEFIENQFRTGLLKLGRAVVDSMST 508

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
              +D V P D IN K + + + +FF SSQLSQ  +  N LS ITH RRLSALG GG+ R 
Sbjct: 509  SSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRE 568

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            RAG E+RDVHPTHYGRICP ET E +     +SL  +AR+N YGFIE+PYRKV +  VT+
Sbjct: 569  RAGFEVRDVHPTHYGRICPIETPEQNIAY--NSLAIYARINKYGFIESPYRKVVNKVVTD 626

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
             + YLSA++E   YIA  ++ LDE+  F +++++CR AG  ++V   ++ +ID SPKQV+
Sbjct: 627  QIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGTFVMVNSNQVSYIDLSPKQVI 686

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP V TGMES VA  SGA ++AKR 
Sbjct: 687  SVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRG 746

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            GIV+  D+  IVIR+ +     +   VDIY L KFQRSN NTC+NQ+PLV VGD V+  D
Sbjct: 747  GIVDSSDSNSIVIRAFDKGGI-NYLDVDIYHLRKFQRSNHNTCINQKPLVHVGDCVKEGD 805

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            +IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+FTSIHIEEFE +  
Sbjct: 806  VIADGPAINNGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVH 865

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            DT LG E+ITR IP V+EE L ++D+ GI+ VG  V PG ILVGK+TP+    + PE KL
Sbjct: 866  DTPLGSEKITRAIPGVNEENLYHLDDSGIVKVGTRVGPGYILVGKVTPRHSLSLPPETKL 925

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L  IFGEK+ D  D+SL     + G V+DV++F R G ++NER+  +++++     +++D
Sbjct: 926  LMTIFGEKSFDCVDSSLYTSPDIEGIVIDVQVFTRRGEEENERAFLIKQKEANDFEKERD 985

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                ++++  Y  L +IL    +               + I+   R  WW   ++++ + 
Sbjct: 986  HIINVINQYFYDELRKILINSGSQ------------DRESINFIEREGWWDIGLKNQSIS 1033

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            + VESLK  ++   S     FK K+EK+  G D+P GV   VKVF+A+K  +Q GDKMAG
Sbjct: 1034 KQVESLKKDFDEKVSHAITNFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAG 1093

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SR++P EDMP+L+DGTP+DI+LNPLGVPSRMNVGQ+ ETH+GWAC  LG+K+
Sbjct: 1094 RHGNKGVISRVVPVEDMPYLEDGTPIDIILNPLGVPSRMNVGQMLETHVGWACKKLGEKV 1153

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +++++      I        + +      +  + Y D+         +    ++  + D
Sbjct: 1154 GNILDE---INKIKRAFCEAIRSLSDDDFEKFAALYLDNKKFEDINDDE----ITASILD 1206

Query: 1213 GADEEAINSML 1223
              +++ +N+ L
Sbjct: 1207 TPNKDELNNEL 1217



 Score =  346 bits (888), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 112/201 (55%), Positives = 149/201 (74%), Gaps = 3/201 (1%)

Query: 1166 SPLRSFLEKVIGTGSHT---EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            S LR FL +V   GS+      I D +D+ ++  A + + G+PV+ PVF+G  +E I  +
Sbjct: 1233 SSLRHFLIEVYSCGSNLSICNNIRDINDNHLIEFAYKLRDGIPVTAPVFEGPKDEQIVKL 1292

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
              +A LD SGQ +LYDG +GE FDR VTVGY+YMLKL+H+V  K++ARS G YSLVTQQP
Sbjct: 1293 FELAGLDNSGQVVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQP 1352

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+ GR ++YES++ G+  FE G
Sbjct: 1353 LGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESVIKGDSNFECG 1412

Query: 1343 TPESFNVLVKEMQALGLSIDL 1363
             PESFNV++KE+++L  ++DL
Sbjct: 1413 IPESFNVMIKELRSLCFNVDL 1433


>gi|183221354|ref|YP_001839350.1| DNA-directed RNA polymerase subunit beta [Leptospira biflexa serovar
            Patoc strain 'Patoc 1 (Paris)']
 gi|73917872|sp|Q9KK59|RPOB_LEPBI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226699416|sp|B0SSI4|RPOB_LEPBP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|8132026|gb|AAF73184.1|AF150880_1 RNA polymerase beta subunit [Leptospira biflexa serovar Patoc]
 gi|167779776|gb|ABZ98074.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit;
            Transcriptase beta chain) (RNA polymerase beta subunit)
            [Leptospira biflexa serovar Patoc strain 'Patoc 1
            (Paris)']
          Length = 1228

 Score = 1039 bits (2686), Expect = 0.0,   Method: Composition-based stats.
 Identities = 499/1381 (36%), Positives = 728/1381 (52%), Gaps = 183/1381 (13%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA-PDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++  +P+LI VQK S+D FL   +  P +R N+GL+A F+  FPI + + 
Sbjct: 8    RNRVNFGKITDLNLLPNLIYVQKKSFDWFLQSEVKDPTKRLNQGLEAVFRESFPIESPNN 67

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              ++E+  Y    PK D  +C   D ++AVPLK  +RLI+ D           +I+EQ +
Sbjct: 68   DMVMEYGHYVLGEPKRDPQECKDTDSSFAVPLKAVIRLIIKD---------TGEIREQVV 118

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGDLP+MT  GTF+I G +R+VVSQLHRSPGI F +D+       +  ++ R+IP +G 
Sbjct: 119  YMGDLPVMTDHGTFIINGAERVVVSQLHRSPGIFFSYDQV------RDTFSARVIPYRGS 172

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E D+K I+  +IDR++K P T  + A+GM + EE+L  FY        G       
Sbjct: 173  WLEFEMDNKGILVAKIDRKKKFPATLLVKAMGMGTNEEVLRLFYGSSKMKIAG----ANP 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 ++G +  + +++++TGE ++++G K+    +  L+E  VK               
Sbjct: 229  KDLKRLIGRRTIADIINMETGEVMLDAGSKINEDNISILREMKVKE-------------- 274

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                              + ++      +N  + N L  D   D
Sbjct: 275  ----------------------------------VDVIEFPKGKDNPVLINCLEKDGVND 300

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--- 426
             +DA+   + +MRPG+ ST   AE+    LFF    +DL  VGR K+N +   + P    
Sbjct: 301  YEDAVKKFHTIMRPGEPSTIENAEAELKRLFFSPKTFDLGIVGRYKINSKFEFNNPKEFS 360

Query: 427  --DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
              D R +RK+DII  ++ LV L +       DDID+LGNRR+RSVGE++ NQ +LG  R+
Sbjct: 361  KADDRVLRKQDIIETVRYLVMLMSEAENYYPDDIDHLGNRRIRSVGELIANQLKLGFSRV 420

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER IKER++  + +   PQ LI+ KP+ + + EFF SSQLSQ  +  N L+ +TH RRL+
Sbjct: 421  ERVIKERMTVQEPEQQTPQLLISIKPITAVINEFFGSSQLSQFMDQTNPLAELTHKRRLN 480

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ S++SFARVN YGFIETPY
Sbjct: 481  ALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLILSMSSFARVNDYGFIETPY 540

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKV   V YL+A +EE  Y+AQ+NS++DE G FT +L+  R  G+       +I 
Sbjct: 541  RLVKNGKVQKQVEYLTADKEEYHYMAQSNSTVDEKGEFTSKLISTRHRGDFPFRSPAEIQ 600

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL  EAPFVGTGME+  A  
Sbjct: 601  YMDLAPLQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLTEEAPFVGTGMEARAAYD 660

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            +G  IVAK+ G+V +VDA  + I+  +      +  +  Y L+KF+++NQ TC NQ+P V
Sbjct: 661  AGVCIVAKKDGVVSKVDATGVWIKEDQ------SKEIVHYPLIKFKKTNQGTCFNQKPNV 714

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +              +T  G ++      V     +G      +L+S+ +    V    
Sbjct: 715  SM------------LHTTTGGKVSKVSKERVEVTTPNGEKETHELLLSDEVQFHAVVK-- 760

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
                     ++  +G     + I           D   I+  G  +  G           
Sbjct: 761  -------EGQEVGIGAPVAGQIIKGEKYG-----DFGQILQKGTVLANGPS-------TD 801

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +     +L A    +  +  D  L     +   V          I    R   + +E
Sbjct: 802  AGYLALGRNVLVAFMPWEGYNFEDAILISERIIKDDVFSSIHIEEFEIQ--ARETKLGQE 859

Query: 963  QIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            QI     +  D+    LD +   R+   +   + + G    K  T L+ +      +   
Sbjct: 860  QITRDIPNLSDKAFRDLDESGVIRVGAEVKPGDILVGMVTPKGETDLTPEY-----KLLH 914

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  + ++V+ +   +   +E +   +      K    + GD++  GV  +VKV+VA K
Sbjct: 915  SIFGEKAKEVRDSSLRMPNGFEGTVIDI------KRYSRETGDELAAGVEEMVKVYVARK 968

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +  GDKMAGRHGNKG+V+R++  EDMP+++DG+PVDIVLNPLGVPSRMN+GQIFET L
Sbjct: 969  RKLLVGDKMAGRHGNKGVVARVMAQEDMPYMEDGSPVDIVLNPLGVPSRMNLGQIFETQL 1028

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G+A   LG   ++ + D  + GD++           +                       
Sbjct: 1029 GFAAKKLGINFETPVFDGASEGDVNDFCKKAGLPENSKFQL------------------- 1069

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G        TGE F   V  GYIYMLKL H
Sbjct: 1070 ----------------------------YDG-------RTGEKFINQVFCGYIYMLKLAH 1094

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE+LTIKSDD
Sbjct: 1095 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASHTLQELLTIKSDD 1154

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            ++GR R+YE+IV G  + + G PESFNVLV+E++ L L I +++S        +   +F+
Sbjct: 1155 MLGRARIYEAIVKGIHSIKPGIPESFNVLVQELRGLALDIIIKDSEGLEVDISDYEDEFS 1214

Query: 1382 K 1382
            K
Sbjct: 1215 K 1215


>gi|325124256|gb|ADY83779.1| DNA-directed RNA polymerase beta chain [Acinetobacter calcoaceticus
            PHEA-2]
          Length = 842

 Score = 1036 bits (2680), Expect = 0.0,   Method: Composition-based stats.
 Identities = 474/846 (56%), Positives = 625/846 (73%), Gaps = 8/846 (0%)

Query: 526  EEHVNSLS---RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                N LS   + TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL
Sbjct: 1    MVQANYLSSWTKTTHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGL 60

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            ++SL+ +A+ N +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D+DG+ TE
Sbjct: 61   INSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTE 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  R  GE + +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 121  EFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+A+ P VGTGME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +GVDIY
Sbjct: 181  TLRADKPLVGTGMEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEAGVDIY 240

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L+K+ RSNQNTC+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM W+GYN
Sbjct: 241  NLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYN 300

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +EDS+L+SER++ ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+
Sbjct: 301  YEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIV 360

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  GTV+DV
Sbjct: 361  YIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDV 420

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            ++F R G++K++R++++E+ Q++   +D  +E  I +     R++ +L GQ +  G    
Sbjct: 421  QVFTRDGLEKDDRALAIEKAQLDAYRKDLKEEYKIFEEAARERVIRLLKGQESNGG-GST 479

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            K+   L  +++S        +    DE +   +  ++V  +   + ++++F  K  K+  
Sbjct: 480  KRGDKLVEEVLSGLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLAT 539

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G PVDIVL
Sbjct: 540  GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVL 599

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSH 1181
            NPLGVPSRMNVGQI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+    G  
Sbjct: 600  NPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYNKVGGE 656

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
             E +    D  VL ++   ++GVP++TPVFDGA+E  I  +L +A +  +GQ++L+DG T
Sbjct: 657  QEDLDSLTDAEVLALSGNLRAGVPLATPVFDGAEESQIKDLLELAGISRTGQTVLFDGRT 716

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 717  GEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWA 776

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV GN   + G PESFNVL KE+++LG++I
Sbjct: 777  LEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINI 836

Query: 1362 DLENSR 1367
            +L+N  
Sbjct: 837  ELKNGD 842


>gi|189911447|ref|YP_001963002.1| DNA-directed RNA polymerase subunit beta [Leptospira biflexa serovar
            Patoc strain 'Patoc 1 (Ames)']
 gi|226699415|sp|B0SAG1|RPOB_LEPBA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|167776123|gb|ABZ94424.1| DNA-directed RNA polymerase, beta subunit [Leptospira biflexa serovar
            Patoc strain 'Patoc 1 (Ames)']
          Length = 1228

 Score = 1036 bits (2680), Expect = 0.0,   Method: Composition-based stats.
 Identities = 498/1381 (36%), Positives = 727/1381 (52%), Gaps = 183/1381 (13%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA-PDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++  +P+LI VQK S+D FL   +  P +R N+GL+A F+  FPI + + 
Sbjct: 8    RNRVNFGKITDLNLLPNLIYVQKKSFDWFLQSEVKDPTKRLNQGLEAVFRESFPIESPNN 67

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              ++E+  Y    PK D  +C   D ++AVPLK  +RLI+ D           +I+EQ +
Sbjct: 68   DMVMEYGHYVLGEPKRDPQECKDTDSSFAVPLKAVIRLIIKD---------TGEIREQVV 118

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGDLP+MT  GTF+I G +R+VVSQLHRSPGI F +D+       +  ++ R+IP +G 
Sbjct: 119  YMGDLPVMTDHGTFIINGAERVVVSQLHRSPGIFFSYDQV------RDTFSARVIPYRGS 172

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E D+K I+  +IDR++  P T  + A+GM + EE+L  FY        G       
Sbjct: 173  WLEFEMDNKGILVAKIDRKKNFPATLLVKAMGMGTNEEVLRLFYGSSKMKIAG----ANP 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 ++G +  + +++++TGE ++++G K+    +  L+E  VK               
Sbjct: 229  KDLKRLIGRRTIADIINMETGEVMLDAGSKINEDNISILREMKVKE-------------- 274

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                              + ++      +N  + N L  D   D
Sbjct: 275  ----------------------------------VDVIEFPKGKDNPVLINCLEKDGVND 300

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--- 426
             +DA+   + +MRPG+ ST   AE+    LFF    +DL  VGR K+N +   + P    
Sbjct: 301  YEDAVKKFHTIMRPGEPSTIENAEAELKRLFFSPKTFDLGIVGRYKINSKFEFNNPKEFS 360

Query: 427  --DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
              D R +RK+DII  ++ LV L +       DDID+LGNRR+RSVGE++ NQ +LG  R+
Sbjct: 361  KADDRVLRKQDIIETVRYLVMLMSEAENYYPDDIDHLGNRRIRSVGELIANQLKLGFSRV 420

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER IKER++  + +   PQ LI+ KP+ + + EFF SSQLSQ  +  N L+ +TH RRL+
Sbjct: 421  ERVIKERMTVQEPEQQTPQLLISIKPITAVINEFFGSSQLSQFMDQTNPLAELTHKRRLN 480

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ S++SFARVN YGFIETPY
Sbjct: 481  ALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLILSMSSFARVNDYGFIETPY 540

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKV   V YL+A +EE  Y+AQ+NS++DE G FT +L+  R  G+       +I 
Sbjct: 541  RLVKNGKVQKQVEYLTADKEEYHYMAQSNSTVDEKGEFTSKLISTRHRGDFPFRSPAEIQ 600

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL  EAPFVGTGME+  A  
Sbjct: 601  YMDLAPLQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLTEEAPFVGTGMEARAAYD 660

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            +G  IVAK+ G+V +VDA  + I+  +      +  +  Y L+KF+++NQ TC NQ+P V
Sbjct: 661  AGVCIVAKKDGVVSKVDATGVWIKEDQ------SKEIVHYPLIKFKKTNQGTCFNQKPNV 714

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             +              +T  G ++      V     +G      +L+S+ +    V    
Sbjct: 715  SM------------LHTTTGGKVSKVSKERVEVTTPNGEKETHELLLSDEVQFHAVVK-- 760

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
                     ++  +G     + I           D   I+  G  +  G           
Sbjct: 761  -------EGQEVGIGAPVAGQIIKGEKYG-----DFGQILQKGTVLANGPS-------TD 801

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +     +L A    +  +  D  L     +   V          I    R   + +E
Sbjct: 802  AGYLALGRNVLVAFMPWEGYNFEDAILISERIIKDDVFSSIHIEEFEIQ--ARETKLGQE 859

Query: 963  QIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            QI     +  D+    LD +   R+   +   + + G    K  T L+ +      +   
Sbjct: 860  QITRDIPNLSDKAFRDLDESGVIRVGAEVKPGDILVGMVTPKGETDLTPEY-----KLLH 914

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  + ++V+ +   +   +E +   +      K    + GD++  GV  +VKV+VA K
Sbjct: 915  SIFGEKAKEVRDSSLRMPNGFEGTVIDI------KRYSRETGDELAAGVEEMVKVYVARK 968

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R +  GDKMAGRHGNKG+V+R++  EDMP+++DG+PVDIVLNPLGVPSRMN+GQIFET L
Sbjct: 969  RKLLVGDKMAGRHGNKGVVARVMAQEDMPYMEDGSPVDIVLNPLGVPSRMNLGQIFETQL 1028

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G+A   LG   ++ + D  + GD++           +                       
Sbjct: 1029 GFAAKKLGINFETPVFDGASEGDVNDFCKKAGLPENSKFQL------------------- 1069

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G        TGE F   V  GYIYMLKL H
Sbjct: 1070 ----------------------------YDG-------RTGEKFINQVFCGYIYMLKLAH 1094

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE+LTIKSDD
Sbjct: 1095 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASHTLQELLTIKSDD 1154

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            ++GR R+YE+IV G  + + G PESFNVLV+E++ L L I +++S        +   +F+
Sbjct: 1155 MLGRARIYEAIVKGIHSIKPGIPESFNVLVQELRGLALDIIIKDSEGLEVDISDYEDEFS 1214

Query: 1382 K 1382
            K
Sbjct: 1215 K 1215


>gi|153830719|ref|ZP_01983386.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 623-39]
 gi|148873799|gb|EDL71934.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae 623-39]
          Length = 816

 Score = 1034 bits (2673), Expect = 0.0,   Method: Composition-based stats.
 Identities = 478/832 (57%), Positives = 624/832 (75%), Gaps = 18/832 (2%)

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YG
Sbjct: 1    HKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYG 60

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            F+ETPYR+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L 
Sbjct: 61   FLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLH 120

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E
Sbjct: 121  PREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIE 180

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+
Sbjct: 181  RNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCI 240

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +
Sbjct: 241  NQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQD 300

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVG
Sbjct: 301  DRFTTIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVG 360

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R+
Sbjct: 361  KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRA 420

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            + +E+ Q++   +D  +E  IL+  + +R+  +L                  +   +   
Sbjct: 421  LEIEQMQLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSI 467

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             R +W +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV
Sbjct: 468  ERKKWLEQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKV 527

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI
Sbjct: 528  YLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQI 587

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVL 1194
             E HLG A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V 
Sbjct: 588  LEVHLGLAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVR 644

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
             +A   ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+
Sbjct: 645  TLAHNLRAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYM 704

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEM
Sbjct: 705  YMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 764

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            LT+KSDDV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 765  LTVKSDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 816


>gi|330969829|gb|EGH69895.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 935

 Score = 1032 bits (2668), Expect = 0.0,   Method: Composition-based stats.
 Identities = 502/939 (53%), Positives = 685/939 (72%), Gaps = 4/939 (0%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P L+ +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1   MDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61  PAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119 FLINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG+     L    L  G      
Sbjct: 179 VRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRGENLSLELVPQRL-RGEIAVLD 237

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           ++D D G+ ++E G+++T+  +  L++ G+K L +  D + G   A+ IV+  TGEI  E
Sbjct: 238 ILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDYVLGRTTAKVIVHPATGEIIAE 296

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
               ++ + L +I  +++  I  LY + ++   ++ +TL  D   ++ +AL++IYR+MRP
Sbjct: 297 CNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTLKIDSTSNQLEALVEIYRMMRP 356

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T   AE++FN LFF  ++YDLS VGR+K N R+     +    + KEDI+A++K L
Sbjct: 357 GEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTL 416

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417 VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           INAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 477 INAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHP 536

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+LSA+EE 
Sbjct: 537 THYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVFLSAIEEA 596

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE
Sbjct: 597 DHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RI
Sbjct: 657 HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRI 716

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
           V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G
Sbjct: 717 VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMG 776

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 777 ELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 836

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 837 DIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 896

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
           V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ 
Sbjct: 897 VKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKS 935


>gi|124514450|gb|EAY55963.1| DNA-directed RNA polymerase, beta subunit [Leptospirillum rubarum]
          Length = 1718

 Score = 1029 bits (2660), Expect = 0.0,   Method: Composition-based stats.
 Identities = 544/1199 (45%), Positives = 749/1199 (62%), Gaps = 114/1199 (9%)

Query: 217  FLMAL---GMDSEEI----LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            FL  L   G+ SE+I     + F P      +     F +      +GAK +  L+  D 
Sbjct: 588  FLRYLLSKGLSSEQITIALANRFLPYEEIVVQSKKRRFFV-----RIGAKATFKLIS-DD 641

Query: 270  GEQVIESGKKLTSGLLKSLKEKG-----------------------------VKFLGITS 300
            GE ++  G  +T  +  ++K  G                                  +  
Sbjct: 642  GEVLLAEGAVMTPEMASAIKSNGQAILVRGKNDEVSVSMQMESDILGEKLVLTSKDQVKP 701

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    +   +     G      G+  + + ++     +   +P++ V SV        
Sbjct: 702  EDLLSKVLLFPMGETRKGYPLRSVGESSEFEDIDLAKKGKHEILPLVTVSSVKMGELFWE 761

Query: 361  TLVTDKNKDRKD---ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
             +   K+  R +   A+++IY+ +RPG+V     A   F   FF++ +YDLS+VGR+K+N
Sbjct: 762  LVDLGKHPHRVESDPAVIEIYKKIRPGEVPHVETARQFFEQTFFNTKRYDLSSVGRLKIN 821

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +L +    + R + K D++ +I+ +V L   KG +DDID+LGNRRVRSVGE+L+NQ+R+
Sbjct: 822  SKLGIKENLNNRLLTKNDVVEVIRYMVGLLENKGEVDDIDHLGNRRVRSVGELLENQFRV 881

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+RMER+IKER++  D D+++  DLINAKPV + + EFF SSQLSQ  +  N L+ +TH
Sbjct: 882  GLVRMERAIKERLNLGDPDAIISTDLINAKPVSAIIKEFFGSSQLSQFMDQTNPLAEVTH 941

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL +FARVN +GF
Sbjct: 942  KRRLSALGPGGLTRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLATFARVNDFGF 1001

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IE+P RKV DGKV  +++YLSAM+ +   IAQAN+ +DE G F E  +  R  G+ + V 
Sbjct: 1002 IESPVRKVEDGKVLPEIIYLSAMDGDKYIIAQANTPVDETGKFIESHITARHKGDFVSVS 1061

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +++ FID +P+Q+VS+A ++IPFLE++D+NR LMG NMQRQAVPLL+A AP VGTGME 
Sbjct: 1062 VDRVQFIDVAPQQIVSVATAMIPFLEHNDANRALMGSNMQRQAVPLLRASAPVVGTGMER 1121

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            +VA+ SG  I A+  G V  VD  RI IR               Y L+KFQRSNQNTC+N
Sbjct: 1122 IVARDSGYVIYAEDDGQVTNVDGTRIAIRYQ------GHDKPKEYNLIKFQRSNQNTCLN 1175

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+ L+ VG +V++ D+IADGPSTD GDLA+G+N+LVAFMPW GYNFED++L+SER++ +D
Sbjct: 1176 QKALLAVGTKVKKGDVIADGPSTDRGDLAMGQNVLVAFMPWGGYNFEDAILVSERLIKDD 1235

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +FTSIHIEEFE+ AR+TK G EEITRDIPN+SEE L+N+DE GII +GAEV PGDILVGK
Sbjct: 1236 MFTSIHIEEFELEARETKQGKEEITRDIPNLSEEALRNLDESGIIRIGAEVKPGDILVGK 1295

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPK E+ +TPEE+LLRAIFG+K+ + +D SL VP+G+ G VVDVRI +R G++K E   
Sbjct: 1296 VTPKAETQLTPEERLLRAIFGDKSANWKDASLTVPAGIEGIVVDVRILSRKGVEKEEFPA 1355

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSS 1010
             +  + + +L +   D+   L+ +   ++ + L G+          +G    KK   L+ 
Sbjct: 1356 PMSNQDVTVLTKSYQDDLRELESSKNQKIRKFLIGKVIKEDILDSETGDVLLKKKRRLTQ 1415

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +++ +   S      + D K Q  + S++ + +     ++ R   +I +++ GD++PPGV
Sbjct: 1416 EILEKL--SDLSIITLSDPKEQDELLSIERETKEKIEAIQLRHDERIGRLKRGDELPPGV 1473

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L++VKV++AMKR +  GDKMAGRHGNKG+VSRILP EDMPFL DGTPVDIVLNPLGVPSR
Sbjct: 1474 LKLVKVYIAMKRKLSVGDKMAGRHGNKGVVSRILPMEDMPFLPDGTPVDIVLNPLGVPSR 1533

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETHLGWA   L     + + D  +  +I                         
Sbjct: 1534 MNVGQILETHLGWAGKMLDVHFATPVFDGASEAEIKEQLK-------------------- 1573

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                          + L  +      Q++LYDG TGEPF+RPVT
Sbjct: 1574 -----------------------------KAQLPESG-----QTVLYDGKTGEPFERPVT 1599

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +YMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW +QAYGAA  
Sbjct: 1600 VGVMYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALQAYGAAST 1659

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            LQE LT+KSDDV GR+R+YE+IV G +  E G PESFNVL+KE+Q+L L I+L  ++ K
Sbjct: 1660 LQEFLTVKSDDVSGRSRMYEAIVRGENYLEPGLPESFNVLIKELQSLALDIELLKTKEK 1718



 Score =  354 bits (908), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 137/555 (24%), Positives = 245/555 (44%), Gaps = 39/555 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R FFG   + +D+ DLIE+QK SYD FL +++ P++R + GLQ+AF SVFPI  ++G   
Sbjct: 9   RHFFGLGQQYLDVQDLIEIQKKSYDRFLQLDVDPEQREDWGLQSAFLSVFPIEDYNGNIR 68

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-----------SI 122
           ++F+ Y    PK++  + + R +T+A PLKI +R+ V + ++                ++
Sbjct: 69  IDFLEYSLGEPKYNEREAIERGMTHAAPLKIKVRIAVLEKNKENDRPKSFVSPHIQDSTV 128

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K ++EQ IY+GDLPLMT  GTF+I G +R+VVSQLHRSPG+ F HDK +  ++G  L+  
Sbjct: 129 KTLREQEIYLGDLPLMTSKGTFIINGTERVVVSQLHRSPGVFFSHDKTKTRVAGTPLFTS 188

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-- 240
           RIIP +G W+D E+D KD + VRIDR++K P T  L ALG+ +  I+  +Y         
Sbjct: 189 RIIPYRGSWVDFEYDPKDNLFVRIDRKKKFPATVMLKALGLTASNIIREYYSPETLFIEP 248

Query: 241 ------------------------RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                                    G  +      +DL    ++     D+       E+
Sbjct: 249 GVPQIVAFYPFAPGESLPFQLRDHEGPIFREETLPSDLAELNRILKDRTDLTIRFHSSET 308

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           G +L    +K   +     L I  + +       +  + E  ++  E  + + ++S    
Sbjct: 309 GSELHISDVKVHSDSKNLGLFIPLNSILTSIKKTEYASPELHKLLEELNNSLKKRSEFFS 368

Query: 337 FH-SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                 + +  L+      N  + +T++  ++K ++ ++     V R  ++S  +     
Sbjct: 369 GELLNAKALLSLFELHSKANENLLHTVIPFQSKTKEFSVYQPMTVFRCTELSADAPIPFR 428

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                   +   +  V    +N R  L   ++VR + K   I  I             +D
Sbjct: 429 IVSRTAKEEGDRIRFVDETVLNEREPLSK-ENVRLLLKSKNIGTIHHRSKKFYSISLRED 487

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +      + ++ E   ++Y      ++ S   +        +  +D    +  +  +  
Sbjct: 488 KNQNLFTLLEALPEKEIDEYYAAEEILDPSDFTKTLVTPTQPLGSKDFDKNRKPLLQILF 547

Query: 516 FFCSSQLSQLEEHVN 530
                +L      +N
Sbjct: 548 EKGVQKLEAYIVPLN 562


>gi|206602625|gb|EDZ39106.1| DNA-directed RNA polymerase, beta subunit [Leptospirillum sp. Group
            II '5-way CG']
          Length = 1718

 Score = 1026 bits (2652), Expect = 0.0,   Method: Composition-based stats.
 Identities = 543/1199 (45%), Positives = 747/1199 (62%), Gaps = 114/1199 (9%)

Query: 217  FLMAL---GMDSEEI----LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            FL  L   G+ SE+I     + F P      +     F +      +GAK +  L+  D 
Sbjct: 588  FLRYLLSKGLSSEQITIALANRFLPYEEIVLQSKKRRFYV-----RIGAKATFKLIS-DD 641

Query: 270  GEQVIESGKKLTSGLLKSLKEKGVKFLGI-----------------------------TS 300
            GE ++  G  +T  +  ++K  G   L                                 
Sbjct: 642  GEVLLTEGAVMTPEIASAIKSSGQAILVRGKNDEVSVSMQMESDMLGEKLVLTSKDQAKP 701

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
            + L    +   +     G      G+  + + ++     +   +P++ V S+        
Sbjct: 702  EDLLSKVLLFPMGETRKGYPLRSVGESSEFEDIDLAKKGKHEILPLVTVSSIKMGELFWE 761

Query: 361  TLVTDKNKDRKD---ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
             +   K+  R +   A+++IY+ +RPG+V     A   F   FF++ +YDLS+VGR+K+N
Sbjct: 762  LVDLGKHPHRVESDPAVIEIYKKIRPGEVPHVETARQFFEQTFFNTKRYDLSSVGRLKIN 821

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +L +    + R + K D++ +I+ +V L   KG +DDID+LGNRRVRSVGE+L+NQ+R+
Sbjct: 822  SKLGIKENLNNRLLTKNDVVEVIRYMVGLLENKGEVDDIDHLGNRRVRSVGELLENQFRV 881

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+RMER+IKER++  D D+++  DLINAKPV + + EFF SSQLSQ  +  N L+ +TH
Sbjct: 882  GLVRMERAIKERLNLGDPDAIISTDLINAKPVSAIIKEFFGSSQLSQFMDQTNPLAEVTH 941

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL++SL +FARVN +GF
Sbjct: 942  KRRLSALGPGGLTRERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLATFARVNDFGF 1001

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            IE+P RKV DGKV  +++YLSAM+ +   IAQAN+ +DE G F E  +  R  G+ + V 
Sbjct: 1002 IESPVRKVEDGKVLPEIIYLSAMDGDKYIIAQANTPVDETGKFIESHITARHKGDFVSVS 1061

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +++ FID +P+Q+VS+A ++IPFLE++D+NR LMG NMQRQAVPLL+A AP VGTGME 
Sbjct: 1062 VDRVQFIDVAPQQIVSVATAMIPFLEHNDANRALMGSNMQRQAVPLLRASAPVVGTGMER 1121

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            +VA+ SG  I A+  G V  VD  RI IR               Y L+KFQRSNQNTC+N
Sbjct: 1122 IVARDSGYVIYAEDDGQVTNVDGTRIAIRYQ------GHDKPTEYNLIKFQRSNQNTCLN 1175

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+ L+ VG +V++ D+IADGPSTD GDLA+G+N+LVAFMPW GYNFED++L+SER++ +D
Sbjct: 1176 QKALLAVGTKVKKGDVIADGPSTDRGDLAMGQNVLVAFMPWGGYNFEDAILVSERLIKDD 1235

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +FTSIHIEEFE+ AR+TK G EEITRDIPN+SEE L+N+DE GII +GAEV PGDILVGK
Sbjct: 1236 MFTSIHIEEFELEARETKQGKEEITRDIPNLSEEALRNLDESGIIRIGAEVKPGDILVGK 1295

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +TPK E+ +TPEE+LLRAIFG+K+ + +D SL VP+G+ G VVDVRI +R G++K E   
Sbjct: 1296 VTPKAETQLTPEERLLRAIFGDKSANWKDASLTVPAGIEGIVVDVRILSRKGVEKEEFPA 1355

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSS 1010
             +  + + +L +   D+   L+     ++ + L G+          +G    KK   L+ 
Sbjct: 1356 PMSNQDVTVLTKSYQDDLRELESTKNQKIRKFLIGKVIKEDILDSETGDVLLKKKRRLTQ 1415

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +++ +   S      + D K Q  + S++ + +     ++ R   +I +++ GD++PPGV
Sbjct: 1416 EILEKL--SDLSIITLSDPKEQDELLSIERETKEKIEAIQLRHDERIGRLKRGDELPPGV 1473

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L++VKV++AMKR +  GDKMAGRHGNKG+VSRILP EDMPFL DGTPVDIVLNPLGVPSR
Sbjct: 1474 LKLVKVYIAMKRKLSVGDKMAGRHGNKGVVSRILPTEDMPFLPDGTPVDIVLNPLGVPSR 1533

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETHLGWA   L     + + D  +  +I                         
Sbjct: 1534 MNVGQILETHLGWAGKMLDVHFATPVFDGASEAEIKEQLK-------------------- 1573

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                          + L  +      Q++LYDG TGE F+RPVT
Sbjct: 1574 -----------------------------KAQLPESG-----QTVLYDGKTGEAFERPVT 1599

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +YMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW +QAYGAA  
Sbjct: 1600 VGVMYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALQAYGAAST 1659

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            LQE LT+KSDDV GR+R+YE+IV G +  E G PESFNVL+KE+Q+L L I+L  ++ K
Sbjct: 1660 LQEFLTVKSDDVSGRSRMYEAIVRGENYLEPGLPESFNVLIKELQSLALDIELLKTKEK 1718



 Score =  350 bits (899), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 135/555 (24%), Positives = 243/555 (43%), Gaps = 39/555 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R FFG   + +D+ DLIE+QK SYD FL ++  P++R + GLQ+AF SVFPI  ++G   
Sbjct: 9   RHFFGLGQQYLDVQDLIEIQKKSYDRFLQLDADPEQREDWGLQSAFLSVFPIEDYNGNIR 68

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-----------SI 122
           ++F+ Y    PK++  + + R +T+A PLKI +R+ V + ++                ++
Sbjct: 69  IDFLEYSLGEPKYNEREAIERGMTHAAPLKIKVRIAVLEKNKENDRPKSFVSPHIQDSTV 128

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K ++EQ IY+GDLPLMT  GTF+I G +R+VVSQLHRSPG+ F HDK +  ++G  L+  
Sbjct: 129 KTLREQEIYLGDLPLMTSKGTFIINGTERVVVSQLHRSPGVFFSHDKTKTRVAGTPLFTS 188

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-- 240
           RIIP +G W+D E+D KD + VRIDR++K P T  L ALG+ +  ++  +Y         
Sbjct: 189 RIIPYRGSWVDFEYDPKDNLFVRIDRKKKFPATVMLKALGLTASNVIREYYSPETLFIEP 248

Query: 241 ------------------------RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                                    G  +      +DL    ++     D+       E+
Sbjct: 249 GVPQIVAFYPVVPGEALAFQLRDHEGPIFREETLPSDLAELNRILKDRTDLSIRFHNSET 308

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           G +L    +K   +     L I  + +       +  + E  ++  E  + + ++S    
Sbjct: 309 GSELHISDVKVHSDSKNLGLFIPLNSILTSTKKTEYASPELHKLLEELNNSLKKRSEFFS 368

Query: 337 FH-SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                 + +  L+      N  + +T++  + K ++ ++     V R  ++S  +     
Sbjct: 369 GELLNAKALLSLFELHSKANESLLHTVIPFQAKTKEFSVYQPMTVFRCTELSADAPIPFR 428

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                   +   +  V    +N R  L   ++VR + K   I  I             +D
Sbjct: 429 IVSRAAKEEGDRIRFVDETVLNEREPLSK-ENVRLLLKSKNIGTIHHRSKKFYSISLRED 487

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +      + ++ E   ++Y      ++ +   +        +  +D    +  +  +  
Sbjct: 488 KNQNLFTLLEALPEKEIDEYYAAEEILDPADFTKTLVTPTQPLGSKDFDKNRKPLLQILF 547

Query: 516 FFCSSQLSQLEEHVN 530
                +L      +N
Sbjct: 548 EKGVQKLEAYIVPLN 562


>gi|121728867|ref|ZP_01681876.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae V52]
 gi|121628835|gb|EAX61295.1| DNA-directed RNA polymerase, beta subunit [Vibrio cholerae V52]
          Length = 979

 Score = 1025 bits (2651), Expect = 0.0,   Method: Composition-based stats.
 Identities = 503/950 (52%), Positives = 684/950 (72%), Gaps = 9/950 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35  MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 91  FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 148

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 149 KDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 208

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  + 
Sbjct: 209 RIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEVKD 268

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                 L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  + 
Sbjct: 269 QTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEY 325

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 326 IVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETL 385

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +  
Sbjct: 386 RVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGR 445

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 446 EDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 505

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 506 ERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 565

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 566 ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 625

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R+V +G VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +D
Sbjct: 626 RRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVD 685

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L++E P VGTG+E  VA  
Sbjct: 686 YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVD 745

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 746 SGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCV 805

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 806 MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 865

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 866 HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 925

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K
Sbjct: 926 ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEK 975


>gi|116327516|ref|YP_797236.1| DNA-directed RNA polymerase subunit beta [Leptospira borgpetersenii
            serovar Hardjo-bovis L550]
 gi|116331871|ref|YP_801589.1| DNA-directed RNA polymerase subunit beta [Leptospira borgpetersenii
            serovar Hardjo-bovis JB197]
 gi|122280394|sp|Q04QI9|RPOB_LEPBJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|122284684|sp|Q054E2|RPOB_LEPBL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|116120260|gb|ABJ78303.1| DNA-directed RNA polymerase, beta subunit [Leptospira borgpetersenii
            serovar Hardjo-bovis L550]
 gi|116125560|gb|ABJ76831.1| DNA-directed RNA polymerase, beta subunit [Leptospira borgpetersenii
            serovar Hardjo-bovis JB197]
          Length = 1226

 Score = 1025 bits (2650), Expect = 0.0,   Method: Composition-based stats.
 Identities = 483/1380 (35%), Positives = 710/1380 (51%), Gaps = 182/1380 (13%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD-ERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK   +  +P+LI++QK S+D FL  ++  + +R ++GL+A F+  FPI + + 
Sbjct: 7    RKRVNFGKITNLDYLPNLIQIQKRSFDWFLQADVKDETKRKHQGLEAVFRETFPIESPNN 66

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              ++E+  Y    PK    +C   D T+A+PLK  +RLI+         K   +I+EQ++
Sbjct: 67   DMIMEYSHYILGEPKRSPQECKDTDATFAMPLKAVIRLII---------KETGEIREQTV 117

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGDLP+MT+ GTF+I G +R+VVSQLHRSPGI F +D        + +++ R+IP +G 
Sbjct: 118  YMGDLPVMTEQGTFIINGAERVVVSQLHRSPGIFFSYDME------RDVFSARVIPYRGS 171

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E D+K I+  +IDR++K P T  + +LG  + EE+L  FY        G       
Sbjct: 172  WLEFEMDNKGILIAKIDRKKKFPATLLIKSLGHGTNEEVLRLFYSSKKEKIAGATSK--- 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 ++G +  + +++++TGE ++E+G K+    +  LKE  VK               
Sbjct: 229  -DLKKILGRRTINDIINMETGEVMLEAGSKVNEDNISILKEMKVK--------------- 272

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                             ++ ++      +N  + N L  D   D
Sbjct: 273  ---------------------------------EVELIEFPKGKDNPILINALEKDGVND 299

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---- 425
             +DA+L  + +MR G+ ST   A +    LFF    +DL  VGR K+N +   + P    
Sbjct: 300  YEDAILKFHSLMRQGEPSTIENATTELTRLFFSPKTFDLGEVGRYKINSKFEFNNPKEFS 359

Query: 426  -DDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +  R +R  DII  ++ +++L +       DDID+LGNRR+RSVGE++ NQ + G  R+
Sbjct: 360  GEKARVLRPADIIETVRYILNLFSETENYYPDDIDHLGNRRIRSVGELISNQLKTGFSRV 419

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER IKER++  +I++  PQ LI+ KP+ + + EFF SSQLSQ  +  N L+ +TH RRL+
Sbjct: 420  ERVIKERMTVQEIETQTPQLLISIKPITAVINEFFGSSQLSQFMDQTNPLAELTHKRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ S++S+ARVN YGF+ETPY
Sbjct: 480  ALGPGGLSRDRAGMEVRDVHYSHYGRMCPIETPEGPNIGLILSMSSYARVNDYGFLETPY 539

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKVT  + +L+A +EE  YIAQA+  +DE G    +L+  R  G+       +I 
Sbjct: 540  RTVKNGKVTGQIEHLTADKEEYHYIAQASGVIDEKGELKNKLISTRHRGDFPFRNPSEIQ 599

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPFVGTGME+  A  
Sbjct: 600  YMDLAPLQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLREEAPFVGTGMETRAAYD 659

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S   IV K  G+V  VDA  IV+              D Y L KF+++NQ TC NQ+P+V
Sbjct: 660  SRICIVNKHDGVVTSVDAETIVVER------KGGKESDTYSLTKFKKTNQGTCFNQKPIV 713

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             V        +     S +  ++      L  ++   G      ++ S   V      + 
Sbjct: 714  GVVHSEINGKV--SKVSKEKIEVTGENGELKEYVLQIGSKQYAPIVSSGEEVKRGTTLAG 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             +   E                           +DE G I V   V      V       
Sbjct: 772  QVVVGE--------------------------KLDEMGNILVKGTVLADGPAVDNGVLAL 805

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +            E A+ + +  +R     S  + +  I  R      E+       
Sbjct: 806  GRNVLAAFMPWEGYNFEDAILISERIVRDDVFSSIHIEEFEIQARETKLGPEQITRDIPN 865

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              +   RD  DE  ++      +  +IL G     G         L   +  E  +    
Sbjct: 866  LSDKAFRDL-DETGVIRIGAEVKPGDILVGMVTPKGETDLTPEYKLLHSIFGEKAKD--- 921

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    V+ +   +   +E +   +      K    +  D++P GV  +VKVFVA KR
Sbjct: 922  --------VRDSSLRMPNGFEGTVIDI------KRFSRENQDELPAGVEEMVKVFVARKR 967

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+V+R++  EDMP+++DGTP+DIVLNPLGVPSRMN+GQIFET LG
Sbjct: 968  KLLVGDKMAGRHGNKGVVARVMAEEDMPYMEDGTPLDIVLNPLGVPSRMNLGQIFETQLG 1027

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            +A   LG   ++ + D     D+          + +                        
Sbjct: 1028 FAASKLGISFETPVFDGAEESDVDNFCKEANLPLNSKFKL-------------------- 1067

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                         G++       G PF   V  GYIY+LKL H+
Sbjct: 1068 ---------------------------YDGRT-------GLPFMNEVFCGYIYILKLAHL 1093

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE+LTIKSDD+
Sbjct: 1094 VEDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASHTLQELLTIKSDDM 1153

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +GR R+YE+IV G  + + G PESFNVLV+E++ L L I + +S        +   +++K
Sbjct: 1154 LGRARIYEAIVKGIHSIKPGIPESFNVLVQELRGLALDIIITDSEGNTVDISDYEDEYSK 1213


>gi|24216119|ref|NP_713600.1| DNA-directed RNA polymerase subunit beta [Leptospira interrogans
            serovar Lai str. 56601]
 gi|41017737|sp|Q8F0S2|RPOB_LEPIN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|24197362|gb|AAN50618.1| DNA-directed RNA polymerase subunit beta [Leptospira interrogans
            serovar Lai str. 56601]
          Length = 1226

 Score = 1022 bits (2643), Expect = 0.0,   Method: Composition-based stats.
 Identities = 482/1380 (34%), Positives = 711/1380 (51%), Gaps = 182/1380 (13%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD-ERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK   +  +P+LI++QK S+D FL  ++  + +R ++GL+A F+  FPI + + 
Sbjct: 7    RKRVNFGKITNLDYLPNLIQIQKRSFDWFLQADVKDETKRRHQGLEAVFRETFPIESPNN 66

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              ++E+  Y    PK    +C   D T+A+PLK  +RLI+         K   +I+EQ++
Sbjct: 67   DMIMEYSHYILGEPKRSPQECKDTDATFAMPLKAVIRLII---------KETGEIREQTV 117

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGDLP+MT+ GTF+I G +R+VVSQLHRSPGI F +D        + +++ R+IP +G 
Sbjct: 118  YMGDLPVMTEQGTFIINGAERVVVSQLHRSPGIFFSYDME------RDVFSARVIPYRGS 171

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E D+K I+  +IDR++K P T  + +LG  + EE+L  FY        G       
Sbjct: 172  WLEFEMDNKGILIAKIDRKKKFPATLLVKSLGHGTNEEVLRLFYSSKKEKIAGATSK--- 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 ++G +  + +++++TGE ++E+G K+    +  LKE  VK               
Sbjct: 229  -DLKKILGRRTINDIINMETGEVMLEAGSKINEDNISILKEMKVK--------------- 272

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                             ++ ++      +N  + N L  D   D
Sbjct: 273  ---------------------------------EVELIEFPKGKDNPILINALEKDGVND 299

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---- 425
             +DA+L  + +MR G+ ST   A +    LFF    +DL  VGR K+N +   + P    
Sbjct: 300  YEDAILKFHSLMRQGEPSTIENATTELTRLFFSPKTFDLGEVGRYKINSKFEFNNPKEFS 359

Query: 426  -DDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +  R +R  DII  ++ +++L +       DDID+LGNRR+RSVGE++ NQ + G  R+
Sbjct: 360  GEKARVLRPADIIETVRYILNLFSETENYYPDDIDHLGNRRIRSVGELISNQLKTGFSRV 419

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER IKER++  +I++  PQ LI+ KP+ + + EFF SSQLSQ  +  N L+ +TH RRL+
Sbjct: 420  ERVIKERMTVQEIETQTPQLLISIKPITAVINEFFGSSQLSQFMDQTNPLAELTHKRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ S++S+ARVN YGF+ETPY
Sbjct: 480  ALGPGGLSRDRAGMEVRDVHYSHYGRMCPIETPEGPNIGLILSMSSYARVNDYGFLETPY 539

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKVT  + +L+A +EE  YIAQA+  +DE G    +L+  R  G+       +I 
Sbjct: 540  RTVKNGKVTGQIEHLTADKEEYHYIAQASGVIDEKGELKNKLISTRHRGDFPFRNPSEIQ 599

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPFVGTGME+  A  
Sbjct: 600  YMDLAPLQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLREEAPFVGTGMETRAAYD 659

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S   IV K  G+V  VDA  IV+              D Y+L KF+++NQ TC NQ+P+V
Sbjct: 660  SRICIVNKHDGVVTSVDAENIVVER------KGGKESDTYQLTKFKKTNQGTCFNQKPIV 713

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             V        +     S +  ++      L  ++   G      ++ +   V      + 
Sbjct: 714  GVVHSEINGKV--SKVSKEKIEVTGENGELKEYVLQIGSKQYSPIVSAGEEVKRGSTLAG 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             +   E                           +DE G I V   V      V       
Sbjct: 772  QVVVGE--------------------------KLDEMGNILVKGTVLADGPAVDNGVLAL 805

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +            E A+ + +  +R     S  + +  I  R      E+       
Sbjct: 806  GRNVLAAFMPWEGYNFEDAILISERIVRDDVFSSIHIEEFEIQARETKLGPEQITRDIPN 865

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              +   RD  DE  ++      +  +IL G     G         L   +  E  +    
Sbjct: 866  LSDKAFRDL-DETGVIRIGAEVKPGDILVGMVTPKGETDLTPEYKLLHSIFGEKAKD--- 921

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    V+ +   +   +E +   +      K    +  D++P GV  +VKVFVA KR
Sbjct: 922  --------VRDSSLRMPNGFEGTVIDI------KRFSRENQDELPAGVEEMVKVFVARKR 967

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+V+R++  EDMP+++DGTP+DIVLNPLGVPSRMN+GQIFET LG
Sbjct: 968  KLLVGDKMAGRHGNKGVVARVMAEEDMPYMEDGTPLDIVLNPLGVPSRMNLGQIFETQLG 1027

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            +A   LG   ++ + D     D+          + +                        
Sbjct: 1028 FAASKLGISFETPVFDGAEESDVDNFCKEANLPLNSKFKL-------------------- 1067

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                         G++       G PF   V  GYIY+LKL H+
Sbjct: 1068 ---------------------------YDGRT-------GLPFMNEVFCGYIYILKLAHL 1093

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE+LTIKSDD+
Sbjct: 1094 VEDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASHTLQELLTIKSDDM 1153

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +GR R+YE+IV G  + + G PESFNVLV+E++ L L I + +S        +   +++K
Sbjct: 1154 LGRARIYEAIVKGIHSIKPGIPESFNVLVQELRGLALDIIITDSEGNTVDISDYEDEYSK 1213


>gi|45656647|ref|YP_000733.1| DNA-directed RNA polymerase subunit beta [Leptospira interrogans
            serovar Copenhageni str. Fiocruz L1-130]
 gi|73917873|sp|Q72UA8|RPOB_LEPIC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|45599883|gb|AAS69370.1| RNA polymerase beta subunit [Leptospira interrogans serovar
            Copenhageni str. Fiocruz L1-130]
          Length = 1226

 Score = 1022 bits (2643), Expect = 0.0,   Method: Composition-based stats.
 Identities = 482/1380 (34%), Positives = 711/1380 (51%), Gaps = 182/1380 (13%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD-ERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK   +  +P+LI++QK S+D FL  ++  + +R ++GL+A F+  FPI + + 
Sbjct: 7    RKRVNFGKITNLDYLPNLIQIQKRSFDWFLQADVKDETKRRHQGLEAVFRETFPIESPNN 66

Query: 71   AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              ++E+  Y    PK    +C   D T+A+PLK  +RLI+         K   +I+EQ++
Sbjct: 67   DMIMEYSHYILGEPKRSPQECKDTDATFAMPLKAVIRLII---------KETGEIREQTV 117

Query: 131  YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            YMGDLP+MT+ GTF+I G +R+VVSQLHRSPGI F +D        + +++ R+IP +G 
Sbjct: 118  YMGDLPVMTEQGTFIINGAERVVVSQLHRSPGIFFSYDME------RDVFSARVIPYRGS 171

Query: 191  WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E D+K I+  +IDR++K P T  + +LG  + EE+L  FY        G       
Sbjct: 172  WLEFEMDNKGILIAKIDRKKKFPATLLVKSLGHGTNEEVLRLFYSSKKEKIAGATSK--- 228

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 ++G +  + +++++TGE ++E+G K+    +  LKE  VK               
Sbjct: 229  -DLKKILGRRTINDIINMETGEVMLEAGSKINEDNISILKEMKVK--------------- 272

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
                                             ++ ++      +N  + N L  D   D
Sbjct: 273  ---------------------------------EVELIEFPKGKDNPILINALEKDGVND 299

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---- 425
             +DA+L  + +MR G+ ST   A +    LFF    +DL  VGR K+N +   + P    
Sbjct: 300  YEDAILKFHSLMRQGEPSTIENATTELTRLFFSPKTFDLGEVGRYKINSKFEFNNPKEFS 359

Query: 426  -DDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +  R +R  DII  ++ +++L +       DDID+LGNRR+RSVGE++ NQ + G  R+
Sbjct: 360  GEKSRVLRPADIIETVRYILNLFSETENYYPDDIDHLGNRRIRSVGELISNQLKTGFSRV 419

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ER IKER++  +I++  PQ LI+ KP+ + + EFF SSQLSQ  +  N L+ +TH RRL+
Sbjct: 420  ERVIKERMTVQEIETQTPQLLISIKPITAVINEFFGSSQLSQFMDQTNPLAELTHKRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            ALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ S++S+ARVN YGF+ETPY
Sbjct: 480  ALGPGGLSRDRAGMEVRDVHYSHYGRMCPIETPEGPNIGLILSMSSYARVNDYGFLETPY 539

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            R V +GKVT  + +L+A +EE  YIAQA+  +DE G    +L+  R  G+       +I 
Sbjct: 540  RTVKNGKVTGQIEHLTADKEEYHYIAQASGVIDEKGELKNKLISTRHRGDFPFRNPSEIQ 599

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++D +P QVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPFVGTGME+  A  
Sbjct: 600  YMDLAPLQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLREEAPFVGTGMETRAAYD 659

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S   IV K  G+V  VDA  IV+              D Y+L KF+++NQ TC NQ+P+V
Sbjct: 660  SRICIVNKHDGVVTSVDAENIVVER------KGGKESDTYQLTKFKKTNQGTCFNQKPIV 713

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             V        +     S +  ++      L  ++   G      ++ +   V      + 
Sbjct: 714  GVVHSEINGKV--SKVSKEKIEVTGENGELKEYVLQIGSKQYSPIVSAGEEVKRGSTLAG 771

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             +   E                           +DE G I V   V      V       
Sbjct: 772  QVVVGE--------------------------KLDEMGNILVKGTVLADGPAVDNGVLAL 805

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +            E A+ + +  +R     S  + +  I  R      E+       
Sbjct: 806  GRNVLAAFMPWEGYNFEDAILISERIVRDDVFSSIHIEEFEIQARETKLGPEQITRDIPN 865

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              +   RD  DE  ++      +  +IL G     G         L   +  E  +    
Sbjct: 866  LSDKAFRDL-DETGVIRIGAEVKPGDILVGMVTPKGETDLTPEYKLLHSIFGEKAKD--- 921

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    V+ +   +   +E +   +      K    +  D++P GV  +VKVFVA KR
Sbjct: 922  --------VRDSSLRMPNGFEGTVIDI------KRFSRENQDELPAGVEEMVKVFVARKR 967

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+V+R++  EDMP+++DGTP+DIVLNPLGVPSRMN+GQIFET LG
Sbjct: 968  KLLVGDKMAGRHGNKGVVARVMAEEDMPYMEDGTPLDIVLNPLGVPSRMNLGQIFETQLG 1027

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            +A   LG   ++ + D     D+          + +                        
Sbjct: 1028 FAASKLGISFETPVFDGAEESDVDNFCKEANLPLNSKFKL-------------------- 1067

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                         G++       G PF   V  GYIY+LKL H+
Sbjct: 1068 ---------------------------YDGRT-------GLPFMNEVFCGYIYILKLAHL 1093

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA++ LQE+LTIKSDD+
Sbjct: 1094 VEDKIHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASHTLQELLTIKSDDM 1153

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +GR R+YE+IV G  + + G PESFNVLV+E++ L L I + +S        +   +++K
Sbjct: 1154 LGRARIYEAIVKGIHSIKPGIPESFNVLVQELRGLALDIIITDSEGNTVDISDYEDEYSK 1213


>gi|171319359|ref|ZP_02908469.1| RNA polymerase Rpb2 domain 6 [Burkholderia ambifaria MEX-5]
 gi|171095430|gb|EDT40402.1| RNA polymerase Rpb2 domain 6 [Burkholderia ambifaria MEX-5]
          Length = 813

 Score = 1020 bits (2638), Expect = 0.0,   Method: Composition-based stats.
 Identities = 448/816 (54%), Positives = 603/816 (73%), Gaps = 13/816 (1%)

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +HPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+
Sbjct: 1    MHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAI 60

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            EE    IAQAN+++DE+G   +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIP
Sbjct: 61   EEGRYMIAQANAAIDENGQLVDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIP 120

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            FLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA
Sbjct: 121  FLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDA 180

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             RIVIR  + +      GVDIY L+K+ RSNQNT +NQRP+VK+GD+V R D++ADG ST
Sbjct: 181  GRIVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGAST 240

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            DLG+LALG+NML+AFMPW+GYNFEDS+LISE++V++D +TSIHIEE  V+ARDTKLGPEE
Sbjct: 241  DLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEE 300

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            ITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEK
Sbjct: 301  ITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEK 360

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
            A DV+DTSLRVPSG+SGTV+DV++F R GI +++R+  +  ++++    D +D+  I++ 
Sbjct: 361  ASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDDELKRYRLDLNDQLRIVEG 420

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            + + RL  +L G+ A  GPK   K T +    + +     W+   + D++    +E++K 
Sbjct: 421  DAFQRLARMLVGKVANGGPKKLAKGTKIDQAYLEDLDHYHWFDIRLADDEAAAQLEAIKN 480

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR +Q GDKMAGRHGNKG+V
Sbjct: 481  SIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVV 540

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            S+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQ+ E HLGWA  GLG +I  ++   +
Sbjct: 541  SKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLGWAAKGLGWRIGEML---Q 597

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                I  +R+FL K+       E +  + DD +L +A+  + GVP +TPVFDGA EE + 
Sbjct: 598  RQAKIEEMRAFLTKIYNDSGRKEDLESFTDDEILELAKNLREGVPFATPVFDGATEEEMG 657

Query: 1221 SMLRMA---------DLDES-GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
             ML +A          ++ S  Q  LYDG TGE F+R VT+GY++ LKL+H+V DK++AR
Sbjct: 658  KMLDLAFPDDIAEQLGMNPSKNQVRLYDGRTGEMFERRVTLGYMHYLKLHHLVDDKMHAR 717

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYE
Sbjct: 718  STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVNGRTKVYE 777

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            ++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 778  NLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 813


>gi|241068588|ref|XP_002408478.1| DNA-directed RNA polymerase beta chain, putative [Ixodes scapularis]
 gi|215492466|gb|EEC02107.1| DNA-directed RNA polymerase beta chain, putative [Ixodes scapularis]
          Length = 986

 Score = 1018 bits (2633), Expect = 0.0,   Method: Composition-based stats.
 Identities = 564/988 (57%), Positives = 763/988 (77%), Gaps = 6/988 (0%)

Query: 25   DIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
            DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A LEFV YEFD 
Sbjct: 2    DIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANLEFVKYEFDT 61

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
            PK+DV++C  R L+YA PLK+TLRL ++D+DE TGA+ IK IKEQ +YMGD+PLMTK+GT
Sbjct: 62   PKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGAREIKGIKEQEVYMGDIPLMTKNGT 121

Query: 144  FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            F+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G W+D+EFDSKD+I+
Sbjct: 122  FIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRGSWLDLEFDSKDVIY 181

Query: 204  VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ-RGDFWCFPLSAADLMVGAKVSS 262
             RIDR+RK+  T+ L A+GM +EEI+  +Y  + Y   +   W        +    +++S
Sbjct: 182  FRIDRKRKLYATTLLRAIGMSTEEIIKFYYNSVTYKLVKNKGWAVKFIPQHI-TAHRLTS 240

Query: 263  SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             LVD DTG  ++++G+K+T  L K    +G+  + +  + L G Y++ED+ +  + E+  
Sbjct: 241  DLVDADTGNVLLKAGQKITPRLAKKYFGEGLNNILVAHETLIGKYLSEDLRDPASDEVLA 300

Query: 323  EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
            + G++I    L  I   +I+++ +L ++   +  YIRNTL  DKN+DR+ AL DI+RV+R
Sbjct: 301  KIGEMITVDMLNVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQDREAALCDIFRVLR 359

Query: 383  PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            PG+ +    AES+F  LFFD+++Y+LS VGR+KMN RL L+  ++V  +  +DI  I+++
Sbjct: 360  PGEPANIEAAESLFYNLFFDAERYNLSEVGRIKMNSRLELNISEEVTVLTIDDIKNIVRV 419

Query: 443  LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
            LV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+RME+S+ ER+S+ D+D+VMP D
Sbjct: 420  LVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRMEKSVIERMSAGDVDTVMPHD 479

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            L+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG++R RAG E+RDVH
Sbjct: 480  LVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGGLSRDRAGFEVRDVH 539

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            PTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V +G VT++VVYLSA+EE
Sbjct: 540  PTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKNGHVTDEVVYLSAIEE 599

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                I QANS +D+DG    E + CR   G  ++V   ++DFID +P QVVS+AASLIPF
Sbjct: 600  GKYKIGQANSKVDKDGKLQGEFINCRVEGGNFVMVEPHEVDFIDVTPMQVVSVAASLIPF 659

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LENDD+NR LMG NMQRQAVPL+K +APFVGTG+E VVAK SGA+++A   GIVEQVD+ 
Sbjct: 660  LENDDANRALMGSNMQRQAVPLIKTDAPFVGTGVEGVVAKDSGASVLALHDGIVEQVDSN 719

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD
Sbjct: 720  RIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTD 778

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEFEV+ARDT+LGPEEI
Sbjct: 779  NGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEFEVIARDTRLGPEEI 838

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            TRDIPNVSEE L+++DE GII VGAEV  GDILVGK+TPK ESP+TPEEKLLRAIFGEKA
Sbjct: 839  TRDIPNVSEEALRHLDEVGIIYVGAEVKAGDILVGKVTPKSESPITPEEKLLRAIFGEKA 898

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             D++D+SL VPSGVSGTVV+VR+F+R G++K++R+I++E++QIE LA+D+DDE  I++  
Sbjct: 899  FDIKDSSLYVPSGVSGTVVEVRVFSRRGVEKDQRAIAIEKQQIEKLAKDRDDELEIIEHF 958

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++S L ++L GQ  ++GPK  K    ++
Sbjct: 959  VFSWLEKLLVGQVIINGPKQVKAGQTIT 986


>gi|313113553|ref|ZP_07799141.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium cf.
            prausnitzii KLE1255]
 gi|310624068|gb|EFQ07435.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium cf.
            prausnitzii KLE1255]
          Length = 1280

 Score = 1017 bits (2629), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/1392 (31%), Positives = 635/1392 (45%), Gaps = 196/1392 (14%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  F    E+I +P+LIEVQK SY  FL          +EGL+  F  +  I  ++G
Sbjct: 11   KTERMSFSHIDEVISMPNLIEVQKNSYQWFL----------DEGLKEVFHDIGTIEDYTG 60

Query: 71   AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               L FV +  D  PK+ + +C  RD+TYA PL++T RL+          K   ++K+Q 
Sbjct: 61   NLALSFVDFRLDKEPKYSIKECKERDVTYAAPLRVTARLL---------NKETGEVKDQE 111

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            I+MGD PLMT  GTFVI G +R +VSQL RSPG+ +   K +    G  LY+  + P++G
Sbjct: 112  IFMGDFPLMTDAGTFVINGAERAIVSQLVRSPGVFYGDAKDKV---GNDLYSATMNPNRG 168

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
             W++ E D+ D+ +VRID+ RK+PVT    ALG+ + E+IL+ F          +     
Sbjct: 169  AWLEYETDASDVFYVRIDKNRKLPVTVLCRALGLSTNEDILNFFGDDERILATLEKDTTK 228

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
                 L+           +  GE   +ES     + L    +   +   G          
Sbjct: 229  NQEEGLL------EVYRKLRPGEPPTVESATSQINMLFFDPRRYDLSRFGRYKMNKKLSL 282

Query: 301  -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               + G   AE++V   TGEI IEAG  I  +  E+  ++ +  + +   D +   +   
Sbjct: 283  ARRITGQVAAENVVAPLTGEILIEAGAKITRELAEKADNAGVNLVVLKLDDPMKEES--- 339

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
               +        DA       ++   ++     + +   L   SD  +   + R   +  
Sbjct: 340  -RKIKVITNGCVDAQGFFSFDVKECGINERCSFDEIKKILDTTSDVEEQKEMLRRNHDQL 398

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            +        R +   DI+A I  L  L +  GT DDID+LGNRR+RSVGE+L+NQ+R+G 
Sbjct: 399  IG-------RTVTVADILASINYLNGLGHNIGTTDDIDHLGNRRIRSVGELLQNQFRIGF 451

Query: 480  LRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             RMER I+ER++  S D   + PQ LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH
Sbjct: 452  SRMERVIRERMTLQSQDQSVITPQALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTH 511

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L S+A++N YGF
Sbjct: 512  KRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASYAKINEYGF 571

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +E PYRKV                             DE+G+  E++V            
Sbjct: 572  VEAPYRKVKKIY-------------------------DENGNLKEQVVT----------- 595

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             ++++++ A  +    +A +  P  E     R  +     R+   +L+ +A  V      
Sbjct: 596  -DEVEYMTADVEDEYVVAQANEPLDEGKHFIRPRVSA---RRRDEILEIDAEKVD---YM 648

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             V+     ++       +E  D  R ++ S                    QR      V 
Sbjct: 649  DVSPRMMVSVATACIPFLENDDCNRALMGSN------------------MQRQAVPLMVT 690

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+P+V  G E +         +TD G   L +N     +     N               
Sbjct: 691  QQPIVATGMEYKA--------ATDSGTAVLAKND--GIVEKMDANH-------------- 726

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                        +      G  E    +          I++  I+ VG  V  G +L   
Sbjct: 727  ------------VVVRNNKGELEDYPLVKFARSNAGTCINQRPIVEVGESVKAGQVLADG 774

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                    ++  +  L      +  +  D  L     V   V        +  +  +  +
Sbjct: 775  P-AMRNGEISLGKNALIGFMTWEGYNYEDAVLLNEKIVREDVYTSIHIEEYETESRDTKL 833

Query: 958  SVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              E          E   +D  DE+ I+      +  +IL G+    G         L   
Sbjct: 834  GPEEITRDIPNVSEDALKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRA 892

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E                   K+   +  D++ PGV 
Sbjct: 893  IFGEKAR-----------------EVRDTSLRVPHGAYGIIVDVKVFTPENSDELQPGVR 935

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             VV+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMP+L DGTP+DIVLNPLGVPSRM
Sbjct: 936  EVVRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPYLPDGTPLDIVLNPLGVPSRM 995

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E +LG+A    G K+ + + D     DI        ++    +     +     
Sbjct: 996  NIGQVLEVNLGYAAKACGIKVMTPVFDSARENDIGDTFDTAREMWHGENAPAYPTKL--- 1052

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                             P   G     I+      +LD  G++ +YDG TGE FD  VTV
Sbjct: 1053 -----------------PKIMGEKGHIID--FSKIELDRDGKTTVYDGRTGEKFDNRVTV 1093

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY+Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1094 GYMYYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1153

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT+KSDDV GR + YE+IV G    + G PESF V++KE+Q+LGL + +++      
Sbjct: 1154 QEILTVKSDDVEGRVKTYEAIVKGEPIPQPGIPESFRVMLKELQSLGLDVVVQDKDGNEI 1213

Query: 1372 AKMEEIPDFNKC 1383
               +   D    
Sbjct: 1214 DMRQNFDDEETG 1225


>gi|150015036|ref|YP_001307290.1| DNA-directed RNA polymerase subunit beta [Clostridium beijerinckii
            NCIMB 8052]
 gi|189043852|sp|A6LPQ4|RPOB_CLOB8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|149901501|gb|ABR32334.1| DNA-directed RNA polymerase, beta subunit [Clostridium beijerinckii
            NCIMB 8052]
          Length = 1236

 Score = 1016 bits (2626), Expect = 0.0,   Method: Composition-based stats.
 Identities = 454/1388 (32%), Positives = 646/1388 (46%), Gaps = 229/1388 (16%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             R R  FGK  ++ ++P+LIEVQ  SY+ FL           EGL   F  + PIT F+G
Sbjct: 9    KRTRMSFGKVNDVTEMPNLIEVQLDSYEWFLR----------EGLHEVFDDINPITNFTG 58

Query: 71   AAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              +LEFV Y+ D    K+ V++C  RD TYA PLK+++RL               +IKEQ
Sbjct: 59   NLVLEFVDYKLDMENIKYSVEECKERDATYAAPLKVSIRL---------QNNETGEIKEQ 109

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
             ++MGD PLMT+ GTFVI G +R++VSQL RSPG+++++   +   SGK LY+  +IP++
Sbjct: 110  EVFMGDFPLMTEQGTFVINGAERVIVSQLVRSPGVYYNYSIDK---SGKKLYSSTVIPNR 166

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
            G W++ E DS D+I+VRID+ RK+ ++    A+G+ S+ E+L  F  +  +    +    
Sbjct: 167  GAWLEYETDSNDVIYVRIDKTRKLSISILARAMGLGSDQELLDFFGEEERFRASIEKDNT 226

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                  L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227  KTKEEALLEIYK------RLRPGEPPTVDSAISLIDTLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302  ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A DIVN +TGEI +E G  I     EEI ++ ++ + +L  D V     I
Sbjct: 281  LNLRIANQVAATDIVNPQTGEIMVEKGQKISRLVAEEIQNAGVKSVDVLIEDKVIR--VI 338

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             N  V  K +   D        +   ++  +   + + +        +      + ++  
Sbjct: 339  SNNFVDLKKQVSFD-----ISDLGIKELVHYPTLKEILDN-------FSDEASIKEEIKK 386

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             ++   P   +HI ++DI A I   + L  G G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387  NISKLIP---KHIIRDDIFATISYELGLTYGIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
            L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444  LSRMERVVKERMTIQDQEAITPQMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFI
Sbjct: 504  RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFI 563

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            ETPYR V             A +E   + A                              
Sbjct: 564  ETPYRIVDKENG-------RATDEIRYFTA------------------------------ 586

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                      +    IA +  P  EN       +        + +   +   +      +
Sbjct: 587  --------DEEDQCLIAEAKEPMDENGHFINKKVRVRHLEDILVVPTTDVDLIDVSARQI 638

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                   ++       +E  DA R ++ S                    QR        Q
Sbjct: 639  ------VSVATAMIPFLENDDASRALMGSN------------------MQRQAVPLLSPQ 674

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
             P+V  G E +         + D G L   +N  V             +  SE  V  D 
Sbjct: 675  APIVGTGIEFKA--------AVDSGVLPKAKNAGVV----------TYVSGSEIRVKRDS 716

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
                 + +  +  + +  G     R I +  E   KN     +I  G   + G+I +GK 
Sbjct: 717  DGGTDVYKL-LKFKRSNSGTCINQRPIVDTGEIVYKN----QVIADGPSTDLGEIALGKN 771

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
               G                E A+ + +  +R     S  + +     R      E    
Sbjct: 772  IRMGFITWEGYNY-------EDAMLISEELVREDVFTSMHIEEYECEARDTKLGPEEITR 824

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
                  +   +D DD   I+      R  +IL G+    G         L   +  E  R
Sbjct: 825  DIPNVSDDALKDVDDR-GIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR 883

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                             E                   K+   + GD++ PGV  +V+ ++
Sbjct: 884  -----------------EVRDTSLRVPHGEAGIIVDIKVFTRENGDELNPGVNELVRCYI 926

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKG++SRILP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E
Sbjct: 927  AQKRKISVGDKMAGRHGNKGVISRILPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLE 986

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
             HLGWA   LG  I + + D     +I+                                
Sbjct: 987  VHLGWAASHLGWHIATPVFDGATQPEITECMIKA-------------------------- 1020

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                          G  E+A              ++ILYDG TGEPFD PVTVG +Y+LK
Sbjct: 1021 --------------GFREDA--------------KTILYDGRTGEPFDNPVTVGIMYILK 1052

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+K
Sbjct: 1053 LHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVK 1112

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            SDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L I + N        ++E  
Sbjct: 1113 SDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDIKVLN-DEHEEVTLKEFV 1171

Query: 1379 DFNKCELK 1386
            D +   L+
Sbjct: 1172 DEDMANLE 1179


>gi|295101752|emb|CBK99297.1| DNA-directed RNA polymerase subunit beta [Faecalibacterium
            prausnitzii L2-6]
          Length = 1275

 Score = 1014 bits (2621), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/1392 (30%), Positives = 625/1392 (44%), Gaps = 202/1392 (14%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  F    E+I +P+LIEVQK SY  FL          +EGL+  F  +  I  ++G
Sbjct: 11   KTERMSFSHIDEVISMPNLIEVQKNSYQWFL----------DEGLKEVFHDIGTIEDYTG 60

Query: 71   AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               L FV +  D  PK+ + +C  RD+TYA PL++T RL+          K   ++K+Q 
Sbjct: 61   NLALSFVDFRLDKEPKYSIKECKERDVTYAAPLRVTARLL---------NKETGEVKDQE 111

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            I+MGD PLMT  GTFVI G +R +VSQL RSPG+ + HD  +    G  LY+  + P++G
Sbjct: 112  IFMGDFPLMTDAGTFVINGAERAIVSQLVRSPGVFYGHDHDKV---GNDLYSATMNPNRG 168

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
             W++ E D+ ++ +VRID+ RK+PVT    ALG+ S E+IL+ F          +     
Sbjct: 169  AWLEYETDASNVFYVRIDKNRKLPVTVLCRALGLSSNEDILNYFGEDERILATLEKDTTK 228

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
             +   L+           +  GE   +ES     + L    +   +   G          
Sbjct: 229  NTEEGLL------EVYRKLRPGEPPTVESATSQLNMLFFDPRRYDLSRFGRYKMNKKLSL 282

Query: 301  -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               +     AE++V   TGE+ IE    I  +  E   ++ +  I +L ++         
Sbjct: 283  ARRIMNHVAAENVVAPLTGELLIEKDAKITRQLAEAADNAGVN-IVVLNIEGKKVKVITN 341

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              +              I       ++       S          +     +GR      
Sbjct: 342  GCVDAQGFFSFDVKECGINERCSFEEIRKILDTTSDVEEQKELLRRNHDQLIGR------ 395

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                       +   DI++ I  L  L +G GT DDID+LGNRR+RSVGE+L+NQ+R+G 
Sbjct: 396  ----------TVTVTDILSSINYLNGLGHGIGTTDDIDHLGNRRIRSVGELLQNQFRIGF 445

Query: 480  LRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             RMER I+ER++  S D   + PQ LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH
Sbjct: 446  SRMERVIRERMTLQSQDQSVITPQALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTH 505

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L S+A++N YGF
Sbjct: 506  KRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASYAKINEYGF 565

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +E PYRKV                             DE G   +++V            
Sbjct: 566  VEAPYRKVKKTY-------------------------DEKGRLIDQVVT----------- 589

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             ++++++ A  +    +A +  P  E     R  +     R+   +L+ +A  V      
Sbjct: 590  -DEVEYMTADVEDEYVVAQANEPLDETKHFKRARVSA---RRRDDILEIDAEKVD---YM 642

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             V+     ++       +E  D  R ++ S                    QR      V 
Sbjct: 643  DVSPRMMVSVATACIPFLENDDCNRALMGSN------------------MQRQAVPLMVT 684

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+P+V  G E +         +TD G   L +N                    + +V + 
Sbjct: 685  QQPIVATGMEYKA--------ATDSGTAVLAKN--------------------DGIVEKV 716

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                +              G  +    +          I++  I+ VG  V  G +L   
Sbjct: 717  DADHV--------EVRNAQGAVDNYSLVKFARSNAGTCINQRPIVEVGENVKAGQVLADG 768

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                    ++  +  L      +  +  D  L     V   V        +  +  +  +
Sbjct: 769  P-AMRNGEISLGKNALIGFMTWEGYNYEDAVLLNEKIVREDVYTSIHIEEYETESRDTKL 827

Query: 958  SVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              E          E   +D  DE+ I+      +  +IL G+    G         L   
Sbjct: 828  GPEEITRDIPNVSEDALKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRA 886

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E                   K+   +  D++ PGV 
Sbjct: 887  IFGEKAR-----------------EVRDTSLRVPHGEYGIIVDVKVFTPENSDELQPGVR 929

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             VV+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMP+L DGTP+DIVLNPLGVPSRM
Sbjct: 930  EVVRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPYLPDGTPLDIVLNPLGVPSRM 989

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E +LG+A    G K+ + + D     DI        ++    +     +     
Sbjct: 990  NIGQVLEVNLGYAAKACGIKVMTPVFDSAREADIGDTFDTAREMWHGENAPAYPTKL--- 1046

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                             P   G     I+      +LD  G++ +YDG TGE FD  VTV
Sbjct: 1047 -----------------PKLMGEKGHIID--FSKIELDRDGKTTVYDGRTGEKFDNRVTV 1087

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY+Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1088 GYMYYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1147

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT+KSDDV GR + YE+IV G    + G PESF V++KE+Q+LGL + +++      
Sbjct: 1148 QEILTVKSDDVEGRVKTYEAIVKGEPIPQPGIPESFRVMLKELQSLGLDVVVQDKEGNEI 1207

Query: 1372 AKMEEIPDFNKC 1383
               +   D    
Sbjct: 1208 DMRQNFDDEETG 1219


>gi|294627834|ref|ZP_06706413.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
 gi|292597748|gb|EFF41906.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
          Length = 980

 Score = 1010 bits (2612), Expect = 0.0,   Method: Composition-based stats.
 Identities = 493/974 (50%), Positives = 681/974 (69%), Gaps = 27/974 (2%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
              F    R+RK FGK   I+++P L+ +Q  SY  FL  ++ P++R + GL AA KSVF
Sbjct: 3   SYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVEPNKRKDLGLHAALKSVF 62

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI+++SG A LE+V Y+   P FD  +C  R ++Y  PL++T+RL+++D +  T  K+IK
Sbjct: 63  PISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESST--KAIK 120

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            +KEQ +Y+G++PLMT +GTF++ G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ R
Sbjct: 121 YVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSAR 180

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
           IIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EE+L+ F+    +    D
Sbjct: 181 IIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEMLAEFFEINTFHINPD 240

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                    + + G  ++  L D D  + ++E+GK++T+  +K L+  GV  L +  D L
Sbjct: 241 EGVQLELVPERLRGETLNFDLADGD--KVIVEAGKRITARHVKQLEAAGVAALAVPDDYL 298

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  ++ D+V+G TGE+   A D I+E  L     + +  +  L+V+ ++   Y+ NTL 
Sbjct: 299 VGRILSHDVVDGSTGELLANANDEINEDQLAAFRKAGVDAVGTLWVNDLDRGPYLSNTLR 358

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D  K + +AL++IYR+MRPG+  T   A+++F+ LFF  ++YDLSTVGR+K N R+   
Sbjct: 359 IDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRK 418

Query: 424 TPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDIDNLGN 461
                  +  +   A                      +IK+L ++RNG+G +DDID+LGN
Sbjct: 419 DVLGESVLYDKKYFAERNDEESKRLVAEHADTSDILEVIKVLTEIRNGRGVVDDIDHLGN 478

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EFF SSQ
Sbjct: 479 RRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQ 538

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NIG
Sbjct: 539 LSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIG 598

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     T
Sbjct: 599 LINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLT 658

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQAV
Sbjct: 659 EQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAV 718

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVD 760
           P L+++ P VGTG+E  VA+ SG  + A R G++EQ+DA RIV++  E      + +GVD
Sbjct: 719 PTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVD 778

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           IY L+K+ RSNQNTC+NQRPLV VGD + R D++ADGPSTD+G+LALG+NML+AFMPW+G
Sbjct: 779 IYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNG 838

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLGPEEI+ DIPNVSE+ L  +DE G
Sbjct: 839 YNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESG 898

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++ +GAEV  GDI+VGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G++GTV+
Sbjct: 899 VVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMTGTVI 958

Query: 941 DVRIFNRHGIDKNE 954
           +V++F      K +
Sbjct: 959 EVQVFTPRRHRKRQ 972


>gi|261415670|ref|YP_003249353.1| DNA-directed RNA polymerase, beta subunit [Fibrobacter succinogenes
            subsp. succinogenes S85]
 gi|261372126|gb|ACX74871.1| DNA-directed RNA polymerase, beta subunit [Fibrobacter succinogenes
            subsp. succinogenes S85]
 gi|302328065|gb|ADL27266.1| DNA-directed RNA polymerase, beta subunit [Fibrobacter succinogenes
            subsp. succinogenes S85]
          Length = 1429

 Score = 1008 bits (2607), Expect = 0.0,   Method: Composition-based stats.
 Identities = 485/1471 (32%), Positives = 737/1471 (50%), Gaps = 169/1471 (11%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
              RK +  N   +++P LIEVQKASY+ FL  +I  ++R N GL+  F+ +FPIT     
Sbjct: 3    TERKSYSSNKFHLELPYLIEVQKASYEQFLQKDIPQEKRMNVGLERVFRDIFPITDDKDL 62

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              L++  Y F  PK+ + +C  R LTY++ L  TL L VF+ D    +K  ++IK   + 
Sbjct: 63   YSLKYEGYYFGIPKYSIPECRERGLTYSMELFATLSLQVFEKDGE-ESKLKEEIK-NDVL 120

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            + DLP+MT++GTF+I G +R+VVSQLHRSPG+ FD +      +G+  Y  RIIP +G W
Sbjct: 121  VCDLPIMTENGTFIINGAERVVVSQLHRSPGVSFDEEM---QPNGRSDYKSRIIPHRGAW 177

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD------------SEEI------LSTFY 233
            ++   +  DI+++ IDR++K+  T+ L  +G +            ++EI       + F 
Sbjct: 178  VEFNTEG-DILYLIIDRKKKIAATAMLRCIGFETTQDILNLFYKKTDEIVLDDAAFNDFD 236

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT---------GEQVIESGKKLTSGL 284
             + V +         +   +       +++++D             +  + S ++    +
Sbjct: 237  KEGVCTLINRIIFNDVVDEETGEIILEANTVIDDKKLERLRESSVEKITVLSKEEDNLLI 296

Query: 285  LKSLKEKGVK--FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF----- 337
              +L     K     + +         E+  N +T E Y +   + D    +        
Sbjct: 297  HYTLAADKTKSREDALKAVYSVTHQQQEEAPNLQTAERYFDELFLNDPHKYDLGEVGRYR 356

Query: 338  -HSEIRDIPIL--------YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             ++++    IL          D VN       T +T    D    +  +  +    +  T
Sbjct: 357  LNAKVYTAAILAKVKEVAERFDRVNEFKMPSVTQMTMSKTDFLAIIEYMVGLFNGDEGYT 416

Query: 389  FSVAESMFNFLFFDSDKYDLSTVG------RVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
                + + N       +     +          +   L+L + ++    R+     ++  
Sbjct: 417  LDDIDHLGNRRTRSVGELLAGQISVGLSRMSRVIRENLSLHSEEEQTTPRELVNTRMVST 476

Query: 443  LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG-----LLRMERSIKERISSVDIDS 497
            +V    G+  +    +  N       +   +    G         E           +  
Sbjct: 477  VVQAFFGQSQLSQFMDQMNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHYTHYGRLCP 536

Query: 498  VMPQDLINAKPVVSAVCEFFCSS-----------QLSQLEE-HVNSLSRITHTRRLSALG 545
            +   +  N   + S       +             L + ++   N               
Sbjct: 537  IETPEGPNIGLINSLASYAVVNHFGFIETPYRIVGLVEFKDAQGNKCYFPEEKWHFGIFK 596

Query: 546  -----------------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                             +    R       R++      ++   + ++G+     +    
Sbjct: 597  GFVHDPHLFVELELTQKEIDTVRLNLDNRQRELFEGFVNKVFQLKDADGNVSYSKNGFAL 656

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE---LV 645
                    +++     V +  V++ + YL+A EE++  +A A++ LDE+  F  +    V
Sbjct: 657  DDFDGTPDYVQVG--DVVEQIVSDYISYLTADEEDSFKVAPASTELDENNRFKGDMDGYV 714

Query: 646  FCRCAGEEILVPR-----------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              R   E   + +           E+ID +D +P Q+VS+AA LIPFLE+DD+NR LMG 
Sbjct: 715  IVRDKSEYPHLMKQDSIAIGDTETERIDLMDVAPMQIVSVAAGLIPFLEHDDANRALMGS 774

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV------ 748
            NMQRQAVPLL+AEAP VGTG+E   A  SG  + AK  G V  VDA  I ++        
Sbjct: 775  NMQRQAVPLLRAEAPVVGTGLERRAALDSGTVVRAKHDGKVTFVDARNITVQRGKMVNGV 834

Query: 749  --------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                    E         +D Y L KF+RSNQ++C+NQ+P+V VGD V   D++ADG ST
Sbjct: 835  FEPLTGLGENYEFLGKDPIDEYTLRKFERSNQDSCINQKPIVNVGDFVEVGDVLADGVST 894

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            D G+LALG+N+L+ F+PW+GYN+ED+++ISE +  +D FTSIHIEE+E+  RDTK GPEE
Sbjct: 895  DHGELALGKNILIGFLPWNGYNYEDAVIISEELAIKDTFTSIHIEEYEMEVRDTKRGPEE 954

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            +TR+IPNV E+ L+N+DE G+I VGAEV P DILVGK+TPKGE+ +TPEE+LLRAIFGEK
Sbjct: 955  LTREIPNVGEDALRNLDENGVIRVGAEVGPDDILVGKVTPKGETELTPEERLLRAIFGEK 1014

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
            A DVRD+SL+ P G+ G V++ RIF++      + S   ++E IE + ++   +   +  
Sbjct: 1015 AGDVRDSSLKAPPGMKGVVLETRIFSKKDKADKK-SKEKDQETIEEIRQNFQSQIDRIKD 1073

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSD---------LISEYPRSQWWQFAVQDEKV 1031
                 L ++L G++A           ++            LI     S    F V D+ +
Sbjct: 1074 ACREHLFDLLAGKSAGKVMDNETHELLIREGQTYNEQNLRLIDVTKVSPLSTFVVDDDDL 1133

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q  V SL +    +   L    + +I+K+  GD++ PGVL+ VKV++A KR +  GDKMA
Sbjct: 1134 QDKVLSLVLVARDNLDTLTRTMEKEIDKVTKGDELKPGVLKSVKVYIAKKRCLSIGDKMA 1193

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRI+P EDMPF +DG P+ I+LNPLGVPSRMN+GQ+ E HLGWA   LG K
Sbjct: 1194 GRHGNKGVVSRIVPVEDMPFTEDGRPLQILLNPLGVPSRMNIGQVLEVHLGWAAKTLGFK 1253

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D     DI      LEK            D D++ ++                 
Sbjct: 1254 VTTPVFDGAKFEDIC---KELEKAYQKNPIVNYEMDPDNNKII----------------- 1293

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                                G++ LYDG TGE    PVT+GY+Y LKL H+V DK++ARS
Sbjct: 1294 --------------------GKAKLYDGKTGEALLNPVTIGYMYYLKLGHLVDDKIHARS 1333

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             GSY+LVTQQPLGGKS  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR++VY++
Sbjct: 1334 IGSYALVTQQPLGGKSQFGGQRFGEMEVWAMEAYGAAYTLQELLTVKSDDVQGRSKVYDA 1393

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            IV G +T + G PESFNV+++E+ +LGL I+
Sbjct: 1394 IVKGQNTPKPGIPESFNVMIREVHSLGLDIE 1424


>gi|160945277|ref|ZP_02092503.1| hypothetical protein FAEPRAM212_02796 [Faecalibacterium prausnitzii
            M21/2]
 gi|158443008|gb|EDP20013.1| hypothetical protein FAEPRAM212_02796 [Faecalibacterium prausnitzii
            M21/2]
 gi|295105510|emb|CBL03054.1| DNA-directed RNA polymerase subunit beta [Faecalibacterium
            prausnitzii SL3/3]
          Length = 1287

 Score =  999 bits (2583), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/1392 (30%), Positives = 628/1392 (45%), Gaps = 188/1392 (13%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
               R  F    E+I +P+LIEVQK SY  FL          +EGL+  F  +  I  ++G
Sbjct: 11   KTERMSFSHIDEVISMPNLIEVQKNSYQWFL----------DEGLKEVFHDIGTIEDYTG 60

Query: 71   AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               L FV +  D  PK+ + +C  RD+T+A PL++T RL+          K   ++K+Q 
Sbjct: 61   NLALSFVDFRLDKEPKYSIKECKERDVTFAAPLRVTARLL---------NKETGEVKDQE 111

Query: 130  IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
            I+MGD PLMT  GTFVI G +R +VSQL RSPG+ + H K +    G  LY+  + P++G
Sbjct: 112  IFMGDFPLMTDAGTFVINGAERAIVSQLVRSPGVFYGHAKDKV---GNDLYSATMNPNRG 168

Query: 190  LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
             W++ E D+ ++ +VRID+ RK+PVT    ALG+ S E+IL+ F          +     
Sbjct: 169  AWLEYETDAANVFYVRIDKNRKLPVTVLCRALGLSSNEDILNYFGEDERILATLEKDTTK 228

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
                 L+           +  GE   +ES       L    +   +   G          
Sbjct: 229  NREEGLL------EVYRKLRPGEPPTVESATSQIDMLFFDPRRYDLSRFGRYKMNKKLSL 282

Query: 301  -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
               +     AE++V+  TGEI +EA   ID K  E+I  + +  + +L +D    +   +
Sbjct: 283  ARRIMDHVAAENVVDPFTGEILVEADKKIDRKLAEQIDAAGVNLV-VLKIDDPMKDQPHK 341

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              ++T+   D +  +   Y   +  DV    + E             D ++     M   
Sbjct: 342  VKVITNGCVDAQAIIDSYYPAFKGVDVKECGINERCCLK--ELRKILDNASSAEEVMESL 399

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                     R +  +DI++ I  L  L  G GT DDID+LGNRR+RSVGE+L+NQ+R+G 
Sbjct: 400  KKDHDLLIGRTVTIDDILSSINYLNGLGYGIGTTDDIDHLGNRRIRSVGELLQNQFRIGF 459

Query: 480  LRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             RMER I+ER++  S D   + PQ LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH
Sbjct: 460  SRMERVIRERMTLQSQDQSVITPQALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTH 519

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L S+A++N    
Sbjct: 520  KRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASYAKIN---- 575

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                                    E     A              + ++         V 
Sbjct: 576  ------------------------EYGFVEAP---------YRKVKKIYDENNNLIEQVV 602

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             ++++++ A  +    +A +  P  E     R  +     R+   +L+ +A  V      
Sbjct: 603  TDEVEYMTADVEDEYVVAQANEPLDEGKHFIRPRVSA---RRRDEILEIDAEKVD---YM 656

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             V+     ++       +E  D  R ++ S                    QR      V 
Sbjct: 657  DVSPRMMVSVATACIPFLENDDCNRALMGSN------------------MQRQAVPLMVT 698

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+P+V  G E +         +TD G   L +                    S  +V + 
Sbjct: 699  QQPIVATGMEYKA--------ATDSGTAVLAK--------------------SNGVVEKV 730

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                + +          + G  E    I          I++  I+ VG  V  G +L   
Sbjct: 731  DADHVVV--------RNEQGALEDYSLIKFARSNAGTCINQRPIVEVGETVTAGQVLADG 782

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                    ++  +  L      +  +  D  L     V   V        +  +  +  +
Sbjct: 783  P-AMRNGEISLGKNALIGFMTWEGYNYEDAVLLNEKIVREDVYTSIHIEEYETESRDTKL 841

Query: 958  SVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              E          E   +D  DE+ I+      +  +IL G+    G         L   
Sbjct: 842  GPEEITRDIPNVSEDALKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRA 900

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E                   K+   +  D++ PGV 
Sbjct: 901  IFGEKAR-----------------EVRDTSLRVPHGAYGIIVDVKVFTPENSDELQPGVR 943

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             VV+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMP+L DGTP+DIVLNPLGVPSRM
Sbjct: 944  EVVRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPYLPDGTPLDIVLNPLGVPSRM 1003

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E +LG+A    G K+ + + D     DI        ++    +     +     
Sbjct: 1004 NIGQVLEVNLGYAAKACGIKVMTPVFDSARENDIGDTFDTAREMWHGENAPAYPTKL--- 1060

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                             P   G     I+      +LD  G++ +YDG TGE FD  VTV
Sbjct: 1061 -----------------PKIMGEKGHIID--FSKIELDRDGKTTVYDGRTGEKFDNRVTV 1101

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GY+Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1102 GYMYYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1161

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT+KSDDV GR + YE+IV G    + G PESF V++KE+Q+LG+ + +++      
Sbjct: 1162 QEILTVKSDDVEGRVKTYEAIVKGEPIPQPGIPESFRVMLKELQSLGMDVIVQDKDGNEI 1221

Query: 1372 AKMEEIPDFNKC 1383
               +   D    
Sbjct: 1222 DMRQNFDDEETG 1233


>gi|254495704|ref|ZP_05108620.1| DNA-directed RNA polymerase subunit beta [Legionella drancourtii
            LLAP12]
 gi|254355051|gb|EET13670.1| DNA-directed RNA polymerase subunit beta [Legionella drancourtii
            LLAP12]
          Length = 783

 Score =  995 bits (2573), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/786 (56%), Positives = 599/786 (76%), Gaps = 4/786 (0%)

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +++SL+ +AR N YGFIETP RKV DG+VT+D+ YLSA+EE ++YIAQ++ +LDEDG+  
Sbjct: 1    MINSLSVYARTNDYGFIETPCRKVIDGRVTDDIEYLSAIEEVDQYIAQSSVALDEDGNIL 60

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             +LV CR   E  L   +KI+++D SPKQ+VS+AASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 61   ADLVPCRHQNEFSLTTPDKINYMDVSPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAV 120

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            P L++E P VGTGME +VA  SG ++VAKR G+++ VDA RIV+R  + +     +GVDI
Sbjct: 121  PTLRSEKPLVGTGMERIVASDSGVSVVAKRGGVIDLVDASRIVVRVNDDETTAGETGVDI 180

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y L K+ RSNQ+TC+NQRP+V  GD+++R D++ADGP TD+G+LALG+N+LVAFMPW+GY
Sbjct: 181  YNLTKYFRSNQDTCINQRPIVSTGDKIQRGDVLADGPCTDMGELALGQNLLVAFMPWNGY 240

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFEDS+LISER+V ED FT+IHIEE   +ARDTKLG EEIT DIPNV E  L N+DE G+
Sbjct: 241  NFEDSILISERIVQEDRFTTIHIEELTCIARDTKLGTEEITSDIPNVGESALSNLDESGV 300

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +GAEVN GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG++GTV+D
Sbjct: 301  VYIGAEVNAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVID 360

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            V++F R G+DK+ R+ S+E E +  + +D  DE+ I + +IY R+  +L  + A  GP  
Sbjct: 361  VQVFTRDGLDKDARAKSIEEEHLARVRKDLVDERRIREEDIYHRVATLLLDKVATGGPAN 420

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K  + ++ D + +  R +W+   + ++ + + +E L  Q E     +E RF +  +KI 
Sbjct: 421  LKPGSTVTQDYLDKVERQRWFDIRLDNDALSQQLEQLSKQLEMLSKEMEKRFNDSRKKII 480

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S ++P EDMP ++DGT VDIV
Sbjct: 481  QGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTSVDIV 540

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG-TGS 1180
            LNPLGVPSRMN+GQ+ ETHLG A  GLG KI ++++  +   +I   +SFL K+    G 
Sbjct: 541  LNPLGVPSRMNIGQVLETHLGLAAKGLGHKIAAMLDTKQTATEI---KSFLTKIYNHDGV 597

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                +   +DD + R+A+  ++GVP++TPVFDGA EE I SML++A L   G++ L DG 
Sbjct: 598  QRVNLDCLNDDELFRLADNLRAGVPMATPVFDGASEEEIKSMLQLAGLSSDGKTTLIDGR 657

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG  FD  VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 658  TGSKFDNKVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVW 717

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   + G PESFNVL+KE++ALG+ 
Sbjct: 718  ALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGID 777

Query: 1361 IDLENS 1366
            I+L++ 
Sbjct: 778  IELDHD 783


>gi|293391585|ref|ZP_06635919.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952119|gb|EFE02238.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 914

 Score =  992 bits (2565), Expect = 0.0,   Method: Composition-based stats.
 Identities = 466/912 (51%), Positives = 642/912 (70%), Gaps = 10/912 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P++++IP L+ +Q  S++ F+  +        +GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLNIPYLLTIQIDSFEKFIKRD----PDGQQGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G   L++VSY+   P FDV +C  R  TYA PL++ LRL+ +D D   G  +I
Sbjct: 57  FPIVSTNGNTELQYVSYQLGEPVFDVRECQIRGTTYAAPLRVKLRLVSYDKDAAPG--TI 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD ++ RIDRRRK+P T  L ALG  +E+IL  F+ KI +  + 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALGYTTEQILDLFFYKITFEIKD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   +  +     G+  +E G+++T+  +K+L++  V  + + ++ 
Sbjct: 235 NKLLMTLVPERL-RGETAAFDIE--AKGKVYVERGRRITTRHIKALEKDKVTQVEVPTEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G   A+D V+ ETGE+   A   +  + L ++  +    +  L+ + ++   YI  TL
Sbjct: 292 IIGKVAAKDYVDLETGELICPANMELSLELLAKLAQAGYTTLETLFTNDLDYGPYISETL 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D + DR  AL++IYR+MRPG+  T   AE++F+ LFF SD+YDLS VGR+K N  L +
Sbjct: 352 RVDPSNDRLSALVEIYRMMRPGEPPTKEAAEALFDNLFFSSDRYDLSAVGRMKFNRSLGI 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           +       +  EDI++++K L+D+RNG+G +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412 EETTGGGTLSNEDIVSVMKKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRV 471

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+++V PQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472 ERAVKERLSLGDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPY
Sbjct: 532 ALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPY 591

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKI 661
           RKV +G+VT ++ YLSA+EE    IAQANS+LD+D  FT+  V CR   GE  L   E+I
Sbjct: 592 RKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFRFTDAFVTCRGEHGESGLYKPEEI 651

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            ++D S +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA 
Sbjct: 652 HYMDVSTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGIEKAVAL 711

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG A+VAKR G ++ VDA RIV++  E +     +G+DIY L+K+ RSNQNTC+NQ P 
Sbjct: 712 DSGVAVVAKRGGTIQYVDASRIVVKVNEDETVAGEAGIDIYNLIKYTRSNQNTCINQIPC 771

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V++GD V R +I+ADGPSTDLG+LALG+N+ VAFMPW+GYNFEDSML+SER+V +D FT+
Sbjct: 772 VELGDPVERGEILADGPSTDLGELALGQNIRVAFMPWNGYNFEDSMLVSERVVQQDRFTT 831

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPK
Sbjct: 832 IHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPK 891

Query: 902 GESPMTPEEKLL 913
           GE+ +    K++
Sbjct: 892 GETQLNAGRKII 903


>gi|71902420|ref|ZP_00684375.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Ann-1]
 gi|71727851|gb|EAO30093.1| DNA-directed RNA polymerase, beta subunit [Xylella fastidiosa Ann-1]
          Length = 1050

 Score =  988 bits (2553), Expect = 0.0,   Method: Composition-based stats.
 Identities = 517/1055 (49%), Positives = 716/1055 (67%), Gaps = 33/1055 (3%)

Query: 179  LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            LY+ RIIP +G W+D EFD KD +  RIDRRRK+PV+  L ALG  +EEIL  F+    +
Sbjct: 2    LYSARIIPCRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYSNEEILGEFFEINTF 61

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                D         + + G  +S +L D   G  ++E+GK++T+  +K L+  G+  L +
Sbjct: 62   HINPDKGVQLELVPERLRGEILSFNLTD--GGGVIVEAGKRITARHVKQLEASGISALAV 119

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D L G  ++ D+++  TGE+   A   ++E  +     + I  +  L+V+ ++  AY+
Sbjct: 120  PDDYLIGRILSHDVIDATTGELLASANSEVNEDRIVAFRKAGIESVGTLWVNDLDRGAYL 179

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             NTL  D  + + +A ++IYR+MRPG+  T   A+++F+ LFF  D+YDLS VGR+K N 
Sbjct: 180  SNTLRIDPTRTQLEAQVEIYRMMRPGEPPTKEAAQNLFHNLFFTFDRYDLSMVGRMKFNR 239

Query: 419  RLNLDTPDDVRHIRKEDIIA----------------------IIKILVDLRNGKGTIDDI 456
            R+          +  +   +                      +IK L ++RNG+G +DDI
Sbjct: 240  RVGRKEVAGEPVLYDKKYFSDRNDEESRRLVSKLGETSDILDVIKGLCEIRNGRGVVDDI 299

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            D+LGNRRVRSVGEM +N +R+GL+R+ER++KER+S  + + + PQ+LINAKPV +A+ EF
Sbjct: 300  DHLGNRRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEF 359

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
            F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVH +HYG +C  ET E
Sbjct: 360  FGSSQLSQFMDQNNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHLSHYGCLCTIETPE 419

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G NIGL++SL  FAR N YGF+ETPYRKV +G+VT++V YLSA+EE    IAQAN+  D+
Sbjct: 420  GPNIGLINSLAVFARTNQYGFLETPYRKVVEGRVTDEVEYLSAIEENQYVIAQANTLTDD 479

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +G  TE  V CR  GE +L P   + ++D SP Q VS+AA+L+PFLE+DD+NR LMG NM
Sbjct: 480  NGQLTESFVPCRFQGESLLKPPSYVHYMDVSPMQTVSVAAALVPFLEHDDANRALMGANM 539

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPS 755
            QRQAVP L+A+ P VGTG+E  VA  SG  + A+R G+++QVDA RIV++  E   +  +
Sbjct: 540  QRQAVPTLRAQKPLVGTGIERTVALDSGVTVNARRGGVIDQVDAGRIVVKVNESEIIGAT 599

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             +GVDIY L+K+ RSNQNTC+NQRPLV VGD +   D++ADGPSTD+G+LALG+NML+AF
Sbjct: 600  DAGVDIYGLIKYTRSNQNTCINQRPLVNVGDIIASGDVLADGPSTDIGELALGQNMLIAF 659

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW+GYNFEDS+L+SER+V ED +T+IHIEE   +ARDTKLG EEI+ DIPNVSE+ L  
Sbjct: 660  MPWNGYNFEDSILLSERVVEEDRYTTIHIEELTCIARDTKLGSEEISADIPNVSEQALNR 719

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +DE G++ +GAEV  GDILVGK+TPKGES +TPEEKLLRAIFGEKA DV+D+SLRVP G+
Sbjct: 720  LDESGVVYIGAEVRAGDILVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGM 779

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
             GTV+DV++F R GI+K++R+  +E  +I+ + +D DD+  IL+  IY+RL   + G+  
Sbjct: 780  DGTVIDVQVFTRDGIEKDKRAHQIEEYEIKRVKKDFDDQFRILEGAIYARLRSQIVGKVV 839

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             SG    KK  V++   +    +S W+   ++DE     ++  + Q +  +   + RF +
Sbjct: 840  NSGV-DIKKGEVITGPYLDGLKKSDWFALRMKDEVAVEAIDRAQKQIQAYQKEFDQRFSD 898

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  KI  GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG++S I+P EDMPF++DG
Sbjct: 899  KRSKITQGDDLAPGVLKMVKVFLAVKRCIQCGDKMAGRHGNKGVISNIVPVEDMPFMEDG 958

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDIVLNPLGVPSRMN+GQI E HLGWA  GLG +I+ ++   +AN  I+ LR FL ++
Sbjct: 959  TPVDIVLNPLGVPSRMNIGQILEVHLGWAAKGLGHRIQRML---EANAAIADLRKFLNEI 1015

Query: 1176 IGTG----SHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                         +S + DD +L +A+    GVP+
Sbjct: 1016 YNHDKSLVGERVDLSQFSDDELLNMAKNLTDGVPM 1050


>gi|251772649|gb|EES53213.1| DNA-directed RNA polymerase, beta subunit [Leptospirillum
            ferrodiazotrophum]
          Length = 1729

 Score =  973 bits (2514), Expect = 0.0,   Method: Composition-based stats.
 Identities = 504/1070 (47%), Positives = 700/1070 (65%), Gaps = 75/1070 (7%)

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-- 372
             + G  Y + G++ + + L+    S+  ++ ++Y  +  ++  +   L   KN  R +  
Sbjct: 723  PKKGNPYKKEGELFEFEDLDVAKKSKKNNVSLVYSATNKSHDLLLELLDLAKNPHRIESD 782

Query: 373  -ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             A+++IY+ +RPG+V     A   F+  FF+S +YDLS+VGR+K+N +L +      R +
Sbjct: 783  PAVVEIYKKIRPGEVPHVETARQFFDQSFFNSKRYDLSSVGRLKLNSKLGIRESLSNRLL 842

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             K DI+ +I+ +VDL   KG IDDID+LGNRRVRSVGE+L+NQ+R+GL+RMER+IKER++
Sbjct: 843  TKSDIVEVIRYMVDLLENKGEIDDIDHLGNRRVRSVGELLENQFRIGLVRMERAIKERLN 902

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              D +SV+  D IN KPV + + EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R
Sbjct: 903  LGDPESVISSDPINVKPVTAIIKEFFGSSQLSQFMDQTNPLAEVTHKRRLSALGPGGLTR 962

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             RAG E+RDVH +HYGRICP ET EG NIGL++SL +FARVN +GFIE+P R V +G   
Sbjct: 963  ERAGFEVRDVHASHYGRICPIETPEGPNIGLITSLATFARVNDFGFIESPVRVVENGIAK 1022

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             ++VYLSAM+ +   IAQA++ LD++G+ TE  V  R  G+ I V  +++ +ID +P+Q+
Sbjct: 1023 PEIVYLSAMDGDKYIIAQASTKLDQNGALTEPQVSARFKGDFISVSPDQVQYIDVAPQQI 1082

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+A +LIPFLE++D+NR LMG NMQRQAVPLL+  AP VGTGME VVA+ SG  I A  
Sbjct: 1083 VSVATALIPFLEHNDANRALMGSNMQRQAVPLLRPSAPLVGTGMEKVVARDSGYVIYATE 1142

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G V ++D     ++          +G+  Y L+KF+RSNQNTC+NQ+ L+    + ++ 
Sbjct: 1143 DGEVVKIDGTSFTVKYK-------NTGLKTYPLIKFRRSNQNTCLNQKVLLSPRTKFKKG 1195

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D++ DGPST+ GDLA+G+N+LVAFMPW GYNFED++LISER+V +D+FTSIHIEEFE+ A
Sbjct: 1196 DVLVDGPSTERGDLAMGQNVLVAFMPWGGYNFEDAILISERLVRDDMFTSIHIEEFELEA 1255

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R+TK G EEITRDIPN+S+E LKN+DE GI+ +GAEV PGDILVGK+TPK E+ +TPEE+
Sbjct: 1256 RETKQGKEEITRDIPNLSDEALKNLDEGGIVRIGAEVKPGDILVGKVTPKAETQLTPEER 1315

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV--EREQIELLAR 969
            LLRAIFG+K+ + +D SL VP+G+ G VVDV+I +R GI+K E  ++     + I  L  
Sbjct: 1316 LLRAIFGDKSANWKDASLTVPAGIEGIVVDVKILSRKGIEKEEAVMAAPMHGQDIGSLTH 1375

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQWW 1022
                E   ++     ++   L G+          +G    KK   L++D + +     + 
Sbjct: 1376 AYQGELRKVEEEKKEKIKAFLLGKVIKEDILDAETGDVILKKKRRLTTDTLEKLA--DYS 1433

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               + D+K Q  +++++ + +     ++ R   +I +++ GD++ PGVL++VKV+VAMKR
Sbjct: 1434 AITLSDQKEQDELQAIESRTKEKIEAIQMRHDERIGRLKKGDELAPGVLKLVKVYVAMKR 1493

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +  GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMNVGQI ETHLG
Sbjct: 1494 KLSVGDKMAGRHGNKGVVSRIVPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQILETHLG 1553

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D     +I  +           +                      
Sbjct: 1554 MAARALGLHVATPVFDGATEEEIKAMLKKGGISETGQTRLV------------------- 1594

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                         G+       TGE F+RPVTVG +YM KL+H+
Sbjct: 1595 ----------------------------DGK-------TGEVFERPVTVGVMYMFKLHHL 1619

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW +QAYGAA  LQE LT+KSDDV
Sbjct: 1620 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALQAYGAASTLQEFLTVKSDDV 1679

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
             GR+R+YE+IV G +  + G PESFNVL+KE+Q+L L I+L  ++ K + 
Sbjct: 1680 SGRSRMYEAIVRGENYLDPGLPESFNVLIKELQSLALDIELLKTQEKLND 1729



 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 104/238 (43%), Positives = 152/238 (63%), Gaps = 9/238 (3%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           VR  FG + + ID+ DLIE+QK SY+ FL +++ P  R + GLQ+AF SVFPI  ++G  
Sbjct: 8   VRHNFGGSQQFIDVQDLIEIQKRSYERFLQLDVPPSLREDSGLQSAFLSVFPIEDYNGNY 67

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS---------IK 123
            ++F+ Y    PK++  +CL R +TYA PLKI +R+   + ++     S         +K
Sbjct: 68  RIDFIEYSLGEPKYEEYECLERGMTYAAPLKIKIRIAALEQNKEIDKTSPLSKEPSFSVK 127

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
            +KE+  Y+GDLPLMT  GTF+I G +R+VVSQLHRSPG+ F HDK +  L+G  L+  R
Sbjct: 128 YMKEEEKYLGDLPLMTTKGTFIINGTERVVVSQLHRSPGVFFSHDKTKTRLTGTPLFTSR 187

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           IIP +G W+D E+D KD ++VRIDR++K P T  L A+GM S +++  +Y       +
Sbjct: 188 IIPYRGSWIDFEYDQKDNLYVRIDRKKKFPATILLKAMGMTSADVVKEYYNIETLQIK 245


>gi|294810204|ref|ZP_06768871.1| DNA-directed RNA polymerase, beta subunit [Bacteroides xylanisolvens
            SD CC 1b]
 gi|294442616|gb|EFG11416.1| DNA-directed RNA polymerase, beta subunit [Bacteroides xylanisolvens
            SD CC 1b]
          Length = 1070

 Score =  965 bits (2495), Expect = 0.0,   Method: Composition-based stats.
 Identities = 460/1112 (41%), Positives = 671/1112 (60%), Gaps = 63/1112 (5%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
             R  F      ++ PD +EVQ  S+  FL ++  P++R NEGL   F   FPI       
Sbjct: 8    QRVNFASTKNPLEYPDFLEVQLKSFQDFLQLDTPPEKRKNEGLYKVFAENFPIADTRNNF 67

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            +LEF+ Y  DPP++ +DDC+ R LTY+VPLK  L+L   D D       I     Q +++
Sbjct: 68   VLEFLDYYIDPPRYTIDDCIERGLTYSVPLKAKLKLYCTDPDHEDFDTVI-----QDVFL 122

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +P MT   TFVI G +R+VVSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 123  GPIPYMTDKATFVINGAERVVVSQLHRSPGVFFGQS---VHANGTKLYSARIIPFKGSWI 179

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            +   D  ++++  IDR++K+PVT+ L A+G +++ +IL  F                L  
Sbjct: 180  EFATDINNVMYAYIDRKKKLPVTTLLRAIGFENDKDILEIFDLAEDVKVNKTNLKKVL-- 237

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                                     G+KL + +LK+  E  V                 +
Sbjct: 238  -------------------------GRKLAARVLKTWIEDFVDEDT------------GE 260

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDR 370
            +V+ E  E+ I+   V++E+ ++EI  S +++I +   +   ++ + I NTL  D +   
Sbjct: 261  VVSIERNEVIIDRETVLEEEHIDEILESGVQNILLHKDEPNQSDFSIIYNTLQKDPSNSE 320

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            K+A+L IYR +R  D +  + A  + N LFF   +YDL  VGR ++N +LNL T  DVR 
Sbjct: 321  KEAVLYIYRQLRNADPADDASAREVINNLFFSEKRYDLGDVGRYRINKKLNLTTDMDVRV 380

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            + KEDII IIK L++L N K  +DDID+L NRRVR+VGE L NQ+ +GL RM R+I+ER+
Sbjct: 381  LTKEDIIEIIKYLIELINSKADVDDIDHLSNRRVRTVGEQLSNQFAVGLARMSRTIRERM 440

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ ITH RR+SALG GG++
Sbjct: 441  NVRDNEVFTPIDLINAKTISSVINSFFGTNALSQFMDQTNPLAEITHKRRMSALGPGGLS 500

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  FA++N  GFIETPYRKV +GKV
Sbjct: 501  RERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVFAKINELGFIETPYRKVENGKV 560

Query: 611  ---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N ++YL+A EEE + IAQ N+ L++DG+F    V  R   +  +V   ++D +D +
Sbjct: 561  DLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVLNRVKSRQDADFPVVEPSEVDLMDVA 620

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVPLL++EAP VGTG+E  + + S   I
Sbjct: 621  PQQIASIAASLIPFLEHDDANRALMGSNMMRQAVPLLRSEAPIVGTGIERQLVRDSRTQI 680

Query: 728  VAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             A+  G+V+ VDA  I I   R+ + +       +  YR+ KF+++NQN  ++ RP+   
Sbjct: 681  TAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPALKEYRIPKFRKTNQNMTIDLRPICDK 740

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW GYN+ED+++++ER+V ED+ TS+H+
Sbjct: 741  GQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWKGYNYEDAIVLNERVVREDLLTSVHV 800

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EE+ +  R+TK G EE+T DIPNVSEE  K++DE GI+ +GA + PGDI++GKITPKGES
Sbjct: 801  EEYSLEVRETKRGMEELTSDIPNVSEEATKDLDENGIVRIGARIEPGDIMIGKITPKGES 860

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              +PEEKLLRAIFG+KA DV+D SL+    + G V+D ++F+R  + KN  S   ++  +
Sbjct: 861  DPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVVIDKKLFSR--VIKNRSSKLADKALL 918

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-----GPKGFKKSTVLSSDLISEYPRS 1019
              +  + + +   L R +  +LM +  G+ +       G +   K +  S+        +
Sbjct: 919  PKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVKDYLGAEVIAKGSKFSASDFDSLDFT 978

Query: 1020 QW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+ +   +  L + +      L+   K K   I  GD++P G++++ KV++
Sbjct: 979  SIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAELKRKKFAITIGDELPAGIIQMAKVYI 1038

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
            A KR I  GDKMAGRHGNKGIVSR++  EDMP
Sbjct: 1039 AKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMP 1070


>gi|284097274|ref|ZP_06385416.1| DNA-directed RNA polymerase subunit beta [Candidatus Poribacteria sp.
            WGA-A3]
 gi|283831216|gb|EFC35184.1| DNA-directed RNA polymerase subunit beta [Candidatus Poribacteria sp.
            WGA-A3]
          Length = 836

 Score =  962 bits (2486), Expect = 0.0,   Method: Composition-based stats.
 Identities = 474/888 (53%), Positives = 614/888 (69%), Gaps = 65/888 (7%)

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++ +D+++V+P DLINAKP+V+A+ EFF  SQLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 1    MNLLDMETVLPHDLINAKPIVAAIKEFFAGSQLSQFMDQTNPLAEITHKRRLSALGPGGL 60

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R RAG E+RDVHP+HY RICP ET EG NIGL++SL ++AR+N +GFIE P+RKV  G+
Sbjct: 61   TRERAGFEVRDVHPSHYSRICPIETPEGPNIGLITSLATYARINEFGFIEAPFRKVQKGR 120

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            V  DV +LS +E E+  IAQANS +D  G    + V  R  GE I    +++D++D SPK
Sbjct: 121  VLRDVEFLSPLEGEHHVIAQANSQVDAAGRLLSDSVTARSEGEFIATTPDRVDYVDVSPK 180

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            QVVS+A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME+VVA+ SG    A
Sbjct: 181  QVVSVATALIPFLEHDDANRALMGSNMQRQAVPLVQSEAPLVGTGMEAVVARDSGYVEQA 240

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGV----DIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +R G+VE VDA RIV+R+  G  D          D Y L+KFQR+NQNTCV Q P+VKVG
Sbjct: 241  RRDGVVESVDARRIVVRTEGGKADEGKKKTGRFWDTYDLVKFQRTNQNTCVTQTPIVKVG 300

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              V++  ++ADGP+ D G+LALG+N+LV FMPW GYNFED++L+SER+V ED FTSIHIE
Sbjct: 301  QPVKKGQVLADGPAIDRGELALGKNILVGFMPWGGYNFEDAILLSERLVREDTFTSIHIE 360

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            EFEV ARDTKLG EEITRDIPN+ EE L+N+DE GI+ +GAEV  GDILVGK+TPKGE+ 
Sbjct: 361  EFEVEARDTKLGKEEITRDIPNLGEEALRNLDESGIVRIGAEVKAGDILVGKVTPKGETQ 420

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +TPEEKLLRAIFGEKA DV+DTSL+VP G+ G VVDV+IF+R GIDK+ERS ++E +   
Sbjct: 421  LTPEEKLLRAIFGEKAGDVKDTSLQVPPGIEGIVVDVKIFSRKGIDKDERSKNIESQDRL 480

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNA-------VSGPKGFKKSTVLSSDLISEYPR 1018
               R+  DE  I++     ++  +L GQ          SG    KK   ++++++ + P 
Sbjct: 481  KFERNYQDELHIIEDERNKKIRRLLLGQVVGRDLMDPESGEVILKKKGKITAEVLRKLPD 540

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                +  + D++ QR +E ++   +     L+  +  K+ +++ GD++PPGV+++VKV++
Sbjct: 541  DDVRRVILGDQEEQRKLEEVERAAKDHIESLQTFYDEKVGRLRRGDELPPGVIKLVKVYL 600

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR I  GDKMAGRHGNKG+VSRILP EDMP+L DGTP++IVLNPLGVPSRMNVGQI E
Sbjct: 601  AIKRKISVGDKMAGRHGNKGVVSRILPEEDMPYLPDGTPIEIVLNPLGVPSRMNVGQILE 660

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGW+   LG    S + D    G+I  L                              
Sbjct: 661  THLGWSARALGIYAASPVFDGATEGEIKELLRQAG------------------------- 695

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                                    L         QS++YDG TG+PF  PVTVGY+YM+K
Sbjct: 696  ------------------------LPENG-----QSVVYDGRTGDPFKSPVTVGYVYMMK 726

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQRLGEMEVW +QAYGAA  LQE LT+K
Sbjct: 727  LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALQAYGAASTLQEFLTVK 786

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            SDDV GR+R+YE+IV G +  E G PESFNVLVKE+Q+LGL ++L  S
Sbjct: 787  SDDVPGRSRMYEAIVKGENFLEPGLPESFNVLVKELQSLGLDVELIKS 834



 Score = 41.6 bits (96), Expect = 1.00,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 63/166 (37%), Gaps = 10/166 (6%)

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV-SSSLVDIDTGEQVIESGKKLTSGL 284
           E++L   + +     +      P     ++V  K+ S   +D D   + IES  +L    
Sbjct: 425 EKLLRAIFGEKAGDVKDTSLQVPPGIEGIVVDVKIFSRKGIDKDERSKNIESQDRLKFER 484

Query: 285 -----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                L  ++++  K +      L G  V  D+++ E+GE+ ++    I  + L ++   
Sbjct: 485 NYQDELHIIEDERNKKIRRL---LLGQVVGRDLMDPESGEVILKKKGKITAEVLRKLPDD 541

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           ++R + IL                 D  +  +    +    +R GD
Sbjct: 542 DVRRV-ILGDQEEQRKLEEVERAAKDHIESLQTFYDEKVGRLRRGD 586


>gi|154355|gb|AAA27215.1| RNA polymerase (EC 2.7.7.6) [Salmonella enterica subsp. enterica
            serovar Typhimurium]
          Length = 958

 Score =  959 bits (2480), Expect = 0.0,   Method: Composition-based stats.
 Identities = 506/973 (52%), Positives = 687/973 (70%), Gaps = 16/973 (1%)

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R +     L    L
Sbjct: 1    EFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRDNKLQMELIPERL 60

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
              G   S  +     G+  +E G+++T+  ++ L++  +K + +  + + G  V++D V+
Sbjct: 61   -RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEYIAGKVVSKDYVD 117

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+  D   DR  AL
Sbjct: 118  ESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETVRVDPTNDRLSAL 177

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR+MRPG+  T   AES+F  LFF  D+YDLS V R+K N  L  D  +    + K+
Sbjct: 178  VEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVARMKFNRSLLRDEIEGSGILSKD 237

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D
Sbjct: 238  DIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 297

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R  A
Sbjct: 298  LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRELA 357

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++
Sbjct: 358  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEI 417

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+
Sbjct: 418  HYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSV 477

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G 
Sbjct: 478  GASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGT 537

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++
Sbjct: 538  VQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVL 597

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDT
Sbjct: 598  ADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDT 657

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLR
Sbjct: 658  KLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLR 717

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +E
Sbjct: 718  AIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEE 777

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              IL+  ++SR+  +L                   ++ + + PR +W +  + DE+ Q  
Sbjct: 778  LQILEAGLFSRIRAVLVSSGV-------------EAEKLDKLPRDRWLELGLTDEEKQNQ 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRH
Sbjct: 825  LEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRH 884

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +
Sbjct: 885  GNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINA 944

Query: 1155 LINDYKANGDISP 1167
            ++   +    +  
Sbjct: 945  MLKQQQEVAKLRE 957


>gi|147728|gb|AAA24585.1| RNA polymerase beta subunit (EC 2.7.7.6) [Escherichia coli]
 gi|223201|prf||0607192A polymerase beta,RNA
          Length = 958

 Score =  959 bits (2479), Expect = 0.0,   Method: Composition-based stats.
 Identities = 510/973 (52%), Positives = 689/973 (70%), Gaps = 16/973 (1%)

Query: 195  EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
            EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R +     L    L
Sbjct: 1    EFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERL 60

Query: 255  MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
              G   S  +     G+  +E G+++T+  ++ L++  VK + +  + + G  VA+D ++
Sbjct: 61   -RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYID 117

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL  D   DR  AL
Sbjct: 118  ESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSAL 177

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            ++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  +  +    + K+
Sbjct: 178  VEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKD 237

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D
Sbjct: 238  DIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 297

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+SALG GG+ R RA
Sbjct: 298  LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRISALGPGGLTRERA 357

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            G E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++
Sbjct: 358  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEI 417

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+
Sbjct: 418  HYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSV 477

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G+
Sbjct: 478  GASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGV 537

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++
Sbjct: 538  VQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVL 597

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDT
Sbjct: 598  ADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDT 657

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            KLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLR
Sbjct: 658  KLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLR 717

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +E
Sbjct: 718  AIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEE 777

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              IL+  ++SR+  +L                   ++ + + PR +W +  + DE+ Q  
Sbjct: 778  LQILEAGLFSRIRAVLVAGGV-------------EAEKLDKLPRDRWLELGLTDEEKQNQ 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRH
Sbjct: 825  LEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRH 884

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +
Sbjct: 885  GNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINA 944

Query: 1155 LINDYKANGDISP 1167
            ++   +    +  
Sbjct: 945  MLKQQQEVAKLRE 957


>gi|57504730|ref|ZP_00370784.1| DNA-directed RNA polymerase beta chain , fragment [Campylobacter coli
            RM2228]
 gi|57019386|gb|EAL56084.1| DNA-directed RNA polymerase beta chain , fragment [Campylobacter coli
            RM2228]
          Length = 963

 Score =  959 bits (2479), Expect = 0.0,   Method: Composition-based stats.
 Identities = 463/968 (47%), Positives = 644/968 (66%), Gaps = 15/968 (1%)

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            +KMN +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N
Sbjct: 1    MKMNHKLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLAN 60

Query: 474  QYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +  LGL +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N 
Sbjct: 61   ELHLGLAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNP 120

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+
Sbjct: 121  LSEVTHKRRLSALGEGGLVKERAGFEVRDVHSTHYGRICPVETPEGQNIGLINTLSTYAK 180

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  G
Sbjct: 181  VNELGFVEAPYRKVANGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDG 240

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E IL  RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP V
Sbjct: 241  ETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIV 300

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTGME ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+N
Sbjct: 301  GTGMEQIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTN 356

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNT   Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SE
Sbjct: 357  QNTNYIQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSE 416

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R++ ED FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG
Sbjct: 417  RIIREDTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPG 476

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             ILVGK++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +
Sbjct: 477  MILVGKVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYE 536

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTV 1007
            K++R+I    ++   L ++  D  +++DR    R+  +L       +   G K +KK   
Sbjct: 537  KDDRAIKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKAPLNSDQKIGDKNYKKGQT 596

Query: 1008 LSSDLISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                 + +  R           +++Q+  + LK  ++  K  L+     K+E ++  D +
Sbjct: 597  ADISELEKINRFTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDIL 656

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            P GV+++VKV++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLG
Sbjct: 657  PSGVIKLVKVYIATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLG 716

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTE 1183
            VPSRMN+GQI E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E
Sbjct: 717  VPSRMNIGQILESHLGLVGLRLGDQIQEI-FDRKQKDFVKELRAKMLEICSIPRLVNEKE 775

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
             I +  D+ +L  A  W  GV  +TPVF+G + E    +  +A +D  G++ LYDG TGE
Sbjct: 776  FIKNLSDEELLNYARDWSKGVKFATPVFEGVNIEEFAKLFEIAKIDMDGKTELYDGRTGE 835

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
                 V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++
Sbjct: 836  KIAERVHVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALE 895

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAA+ L+EMLTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++
Sbjct: 896  AYGAAHTLREMLTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEI 955

Query: 1364 ENSRTKNS 1371
             +    N 
Sbjct: 956  FDKDEDNE 963


>gi|33339717|gb|AAQ14338.1|AF288479_1 P127-H5 [Helicobacter bilis]
          Length = 1122

 Score =  952 bits (2460), Expect = 0.0,   Method: Composition-based stats.
 Identities = 479/1124 (42%), Positives = 712/1124 (63%), Gaps = 32/1124 (2%)

Query: 12   RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R+R  F K+ E +D+P+L+ +QK SYD FL      ++    G++   KS+FPI   +G 
Sbjct: 10   RLRVDFSKSQEELDVPNLLMLQKDSYDSFL----YSNDSRESGIERVLKSIFPIQDSAGR 65

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              LE+   EF   K+ + + + R LTY++PLKI +RL+++D D+      +KDIKEQ+IY
Sbjct: 66   VTLEYAGCEFGKQKYTIAETMVRGLTYSIPLKIKIRLVLWDKDDKGEQVGVKDIKEQTIY 125

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            + ++PLMT   +F+I G++R+VV+QLHRSPG+ F  D+   S + KL+Y  +IIP+ G W
Sbjct: 126  VREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEDESNTSAN-KLIYTGQIIPNMGAW 184

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            +  E+D+KDI++VRI++RRK+PVT    ALG   ++I+   YP +  S + D +  P + 
Sbjct: 185  LYFEYDAKDIMYVRINKRRKMPVTILFRALGYSKQQIIQMLYPVLDVSVKKDKFYIPFNP 244

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD--CLCGLYVA 309
             D+     +   L++ + G+ V+ +GK+     ++ L E+ + +  +      L   Y+A
Sbjct: 245  NDI--EGSLEYDLIN-EKGQVVLSAGKRFNKKRIRDLNEQNISYDKVEFSTTNLLNTYLA 301

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK- 368
            E +++ ++GE+ ++    ++E + +++  ++I    I++  +   +  I N+ + D    
Sbjct: 302  EPVIDSKSGEVILDTLSPLNEANTKKLNDNKITKFKIIHDTAPGYDNSIINSFLADMESL 361

Query: 369  -----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                       +   A + IY+VMRP +  T  VA      LFFD  +YDL+ VGR+KMN
Sbjct: 362  KNIRQTEKIDDECDLAAIRIYKVMRPAEPVTREVAHKFIEQLFFDPSRYDLTGVGRMKMN 421

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +LNL  PD V  +  EDII  +K L+ +RNGKG IDD D+LGNRR+R++GE+L N+   
Sbjct: 422  HKLNLKVPDYVSVLTYEDIIETVKYLMQVRNGKGRIDDRDHLGNRRIRAIGELLANELHS 481

Query: 478  GLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            GL++M++SIK++++     ++VMP DLI++K + S + EFF S QLSQ  +  N LS IT
Sbjct: 482  GLVKMQKSIKDKLTQQTSFENVMPHDLISSKMITSTIMEFFASGQLSQFMDQTNPLSEIT 541

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F +VN  G
Sbjct: 542  HKRRLSALGEGGLVKERVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTKVNDLG 601

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIE PY+KV DGK TN+VVYL+A +E+ + IA A++ LD      E L+  RC GE  L 
Sbjct: 602  FIEAPYKKVVDGKTTNEVVYLTATQEDGKVIAPASTKLDSTNKIVEGLIETRCGGEISLR 661

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              E ++ ID S + +V +AASLIPFLE+DD+NR LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 662  KTEDVELIDLSARMLVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLKPDAPIVGTGIE 721

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            SV+A+ S AAI A++ G+VE+VD   I I         + + +D Y + K  R+NQNT  
Sbjct: 722  SVIARDSWAAIKARQGGVVEKVDGKNIYILGENE----NGAYIDSYSMQKNMRTNQNTSF 777

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             QRP+VKVGD+++   IIADG S D G+LALG+N+ VAFMPW+GYNFED++++SE ++ +
Sbjct: 778  TQRPIVKVGDKIKAGQIIADGASMDSGELALGKNIRVAFMPWYGYNFEDAIVVSENIIKD 837

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D FTS+HI E E+ AR+ K G EEIT DIPNV E+ + ++DE GI+ +G  V  G ILVG
Sbjct: 838  DAFTSVHIYEKEIEARELKHGIEEITADIPNVREDSIAHLDESGIVKIGTYVTGGMILVG 897

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKG+   TPEE+LLRAIFGEKA  V + SL  P  + G VVDV+IF + G +K+ R+
Sbjct: 898  KVTPKGDVKPTPEERLLRAIFGEKAGHVVNKSLYCPQSMEGYVVDVKIFXKKGYEKDARA 957

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ----NAVSGPKGFKKSTVLSSDL 1012
                 ++   L  +  +   +L++    R+  +L  +     A    K FKK   +    
Sbjct: 958  RQAYEDEKSDLDIEHHERLTMLNKEEMLRISYVLSKEPLSAEAKINDKVFKKGECIPKKE 1017

Query: 1013 ISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              +  R           +++Q   E +K  +   K +L    + K+  ++  D +P GV+
Sbjct: 1018 FDDINRFALNTLIKSYSKEIQNQYEQIKNNFLEQKRVLGVEHEEKLAILEKDDILPNGVV 1077

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+ KDG
Sbjct: 1078 KLVKIYIATKRKLKVGDKMAGRHGNKGIVSNIVPAVDMPYTKDG 1121


>gi|213418782|ref|ZP_03351848.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 837

 Score =  945 bits (2443), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/845 (51%), Positives = 596/845 (70%), Gaps = 9/845 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235 NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292 IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352 RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D  +    + K+DII ++K L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412 DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 472 ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 531

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 532 ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 591

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 592 RRVVDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 651

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 652 YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 711

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 712 SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 771

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 772 SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTI 831

Query: 843 HIEEF 847
           HI+E 
Sbjct: 832 HIQEL 836


>gi|312795764|ref|YP_004028686.1| DNA-directed RNA polymerase beta chain [Burkholderia rhizoxinica HKI
            454]
 gi|312167539|emb|CBW74542.1| DNA-directed RNA polymerase beta chain (EC 2.7.7.6) [Burkholderia
            rhizoxinica HKI 454]
          Length = 712

 Score =  918 bits (2373), Expect = 0.0,   Method: Composition-based stats.
 Identities = 400/713 (56%), Positives = 525/713 (73%), Gaps = 11/713 (1%)

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E   VGTG+E   A  S
Sbjct: 1    MDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKAVVGTGIERTTAVDS 60

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP+VK
Sbjct: 61   GTTVQAFRGGVVDYVDAGRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVK 120

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD V R D+IADG STDLG+LALG+NMLVAF PW+GYNFEDS+LISER+V++D +TSIH
Sbjct: 121  VGDRVARGDVIADGASTDLGELALGQNMLVAFTPWNGYNFEDSILISERVVADDRYTSIH 180

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI+ +GAEV  GD+LVGK+TPKGE
Sbjct: 181  IEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKGE 240

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+DTSLRVPSG++GTV+DV++F R GI +++R+  +  ++
Sbjct: 241  TQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMTGTVIDVQVFTREGIQRDKRAQQIIDDE 300

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            ++    D +D+  I++ + + RL  +L G+    GPK   K   ++ + + +     W+ 
Sbjct: 301  LKRYRLDLNDQLRIVEGDAFERLARMLDGKVVNGGPKKLAKGAKITREYLDDLDHYHWFD 360

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              + DE     +E++K   E  +   +  F+ K +K+  GD++PPGVL++VKV++A+KR 
Sbjct: 361  IRLADEDAAAQLEAIKESIEQKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKRR 420

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q GDKMAGRHGNKG+VS+I+P EDMP++ DG P D+VLNPLGVPSRMNVGQI ETHLGW
Sbjct: 421  LQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPCDVVLNPLGVPSRMNVGQILETHLGW 480

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A  GLG +I  ++   K    +  LRSFL KV     H E I +  DD V+ +A+  + G
Sbjct: 481  AAKGLGWRIGEML-QAKKATLVQDLRSFLTKVYNESGHPESIDEMSDDEVIELAQNLREG 539

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESG----------QSILYDGLTGEPFDRPVTVGY 1253
            VP +TPVFDGA E+ I+ ML +A  DE            Q  LYDG TGE F+RPVTVGY
Sbjct: 540  VPFATPVFDGAHEKEISRMLDLAFPDEVAQQLGMTKSKNQVALYDGRTGEAFERPVTVGY 599

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            ++MLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQE
Sbjct: 600  MHMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQE 659

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            MLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++LG+ IDL+ +
Sbjct: 660  MLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 712


>gi|254230351|ref|ZP_04923736.1| DNA-directed RNA polymerase, beta subunit [Vibrio sp. Ex25]
 gi|151937118|gb|EDN55991.1| DNA-directed RNA polymerase, beta subunit [Vibrio sp. Ex25]
          Length = 690

 Score =  895 bits (2313), Expect = 0.0,   Method: Composition-based stats.
 Identities = 398/706 (56%), Positives = 524/706 (74%), Gaps = 18/706 (2%)

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  S
Sbjct: 1    MDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVDS 60

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V 
Sbjct: 61   GVTAVAKRGGVIQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPCVM 120

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IH
Sbjct: 121  PGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIH 180

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE
Sbjct: 181  IQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGE 240

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ Q
Sbjct: 241  TQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQ 300

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            ++   +D  +E  IL+  + +R+  +L                  S   +    R +W +
Sbjct: 301  LKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDTTDRKKWLE 347

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR 
Sbjct: 348  LTLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKRR 407

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S+I P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG 
Sbjct: 408  IQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLGL 467

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWK 1201
            A  G+G KI  ++   K   +++  R FL+KV   G       I+   DD V  + +  +
Sbjct: 468  AAKGIGDKINQMV---KEQQELAKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNLR 524

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G+P++TPVFDGA EE+I ++L +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLNH
Sbjct: 525  GGLPIATPVFDGAPEESIKALLELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLNH 584

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 585  LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 644

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V GRT++Y++IV GN + E G PESFNVL+KE+++LG++I+LE+  
Sbjct: 645  VNGRTKMYKNIVDGNHSMEPGMPESFNVLLKEIRSLGINIELEDEE 690


>gi|2668777|gb|AAB88811.1| DNA-dependent RNA polymerase beta subunit [Rickettsia typhi]
          Length = 864

 Score =  891 bits (2302), Expect = 0.0,   Method: Composition-based stats.
 Identities = 476/850 (56%), Positives = 645/850 (75%), Gaps = 6/850 (0%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
            RVRK FG    + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S
Sbjct: 17  RRVRKNFGHINLVADIPNLIEIQKNSYERNFLQLNIKDSERKNKGLQSILNSIFPISDSS 76

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             A LEFV YEFD PK+DVD+C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ 
Sbjct: 77  NIANLEFVKYEFDTPKYDVDECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQE 136

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +YMGD+PLMTK+GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP +G
Sbjct: 137 VYMGDIPLMTKNGTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPYRG 196

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS-QRGDFWCFP 248
            W+D+EFD+KD+I+ RIDR+RK+  T+ L A+GM++EEI+  +Y  + Y   +   W   
Sbjct: 197 SWLDLEFDAKDVIYFRIDRKRKLYATTLLRAIGMNTEEIMKFYYNSVTYKCIKNKGWSVK 256

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                +    +++S L+D DTG  ++++G+K+T  L +     G+  + +T + L G Y+
Sbjct: 257 FIPQHI-TAHRLTSDLIDADTGNVLLKAGQKITPRLAQKYFSIGLNNILVTHETLIGKYL 315

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           +ED+ + E+ EI  + G++I    L+ I   +I+++ +L ++   +  YIRNTL  DKN+
Sbjct: 316 SEDLRDPESDEILAKIGEMITADMLQVINDLKIKNVNVLVINPQ-SGPYIRNTLFADKNQ 374

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           DR+ AL DI+RV+RPG+ +    AES+F  LFFD+++YDLS VGR+KMN RL L+  +++
Sbjct: 375 DREAALCDIFRVLRPGEPANIEAAESLFYNLFFDAERYDLSEVGRIKMNSRLELNISEEI 434

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             +  +DI  I++ILV+L++GKG IDDID+LGNRRVRSVGE+++NQ+R+GL+R+E+S+ E
Sbjct: 435 TVLTIDDIKNIVRILVELKDGKGIIDDIDHLGNRRVRSVGELIENQFRIGLVRIEKSVIE 494

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S+ D+D+VMP DL+N+K +VS V EFF +SQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 495 RMSAGDVDTVMPHDLVNSKILVSVVKEFFSTSQLSQFMDQTNPLSEITHKRRLSALGPGG 554

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++AR+N +GFIE+PYR+V DG
Sbjct: 555 LSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYARINKHGFIESPYRRVKDG 614

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDAS 667
            VT++VVYLSA+EE    I QANS +D+DG    E + CR   G  ++V   ++DFID +
Sbjct: 615 YVTDEVVYLSAIEEGKYKIGQANSKVDQDGKLQGEFINCRVEGGNFVMVEPYEVDFIDVT 674

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K EAPFVGTG+E VVAK SGA++
Sbjct: 675 PMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTEAPFVGTGVEGVVAKDSGASV 734

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +A   GIVE+VD+ RIVIR++E      +  VDIY L+KFQ+SN NTC+NQ+PLVKVG  
Sbjct: 735 LALHDGIVERVDSNRIVIRTLE-QKVDGSPSVDIYNLLKFQKSNHNTCINQKPLVKVGHY 793

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+LISER+V EDVFTSIHIEEF
Sbjct: 794 VKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSILISERIVKEDVFTSIHIEEF 853

Query: 848 EVMARDTKLG 857
           EV+ARDT+LG
Sbjct: 854 EVIARDTRLG 863


>gi|56418633|ref|YP_145951.1| DNA-directed RNA polymerase subunit beta [Geobacillus kaustophilus
           HTA426]
 gi|261417599|ref|YP_003251281.1| DNA-directed RNA polymerase subunit beta [Geobacillus sp. Y412MC61]
 gi|297528474|ref|YP_003669749.1| DNA-directed RNA polymerase subunit beta [Geobacillus sp. C56-T3]
 gi|319765257|ref|YP_004130758.1| DNA-directed RNA polymerase subunit beta [Geobacillus sp. Y412MC52]
 gi|81348402|sp|Q5L405|RPOB_GEOKA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|56378475|dbj|BAD74383.1| DNA-directed RNA polymerase beta subunit [Geobacillus kaustophilus
           HTA426]
 gi|261374056|gb|ACX76799.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp.
           Y412MC61]
 gi|297251726|gb|ADI25172.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp. C56-T3]
 gi|317110123|gb|ADU92615.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp.
           Y412MC52]
          Length = 1190

 Score =  890 bits (2300), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/964 (46%), Positives = 607/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGRLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 51  EISPIEDFSGNLSLEFIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L +      K         
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE I++ ET E+  EAG +ID ++L  +     + + +    
Sbjct: 273 YKINKKLHIKNRLFNQRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     T    +     D  +   ++  P D                         
Sbjct: 329 ---------QTYRPAEGVVDGDISVQTIKIYAPNDP------------------------ 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 DGEKVINVIGNGFIAEDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R
Sbjct: 536 KVNKFGFIETPYRRVDPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EA
Sbjct: 596 FRGENIVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF
Sbjct: 656 PIVGTGMEYVSAKDSGAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+VK GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVKKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V EDV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAE
Sbjct: 776 IMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 178/523 (34%), Positives = 246/523 (47%), Gaps = 77/523 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 705  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 763

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 764  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 823

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 824  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 882

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 883  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 926

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 927  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 986

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 987  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1018

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1019 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1052

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1053 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1112

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            IV G +  E G PESF VL+KE+Q+LG+ + +  S  +     
Sbjct: 1113 IVKGENIPEPGVPESFKVLIKELQSLGMDVTILTSDEQEVNME 1155


>gi|295401928|ref|ZP_06811891.1| DNA-directed RNA polymerase, beta subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109253|ref|YP_003987569.1| DNA-directed RNA polymerase subunit beta [Geobacillus sp. Y4.1MC1]
 gi|294976058|gb|EFG51673.1| DNA-directed RNA polymerase, beta subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214354|gb|ADP72958.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp. Y4.1MC1]
          Length = 1190

 Score =  889 bits (2297), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 604/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGRLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYKWFL----------DEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 51  EISPIEDFSGNLSLEFIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYSEKVDK---NGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   IE+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTIENAKNLLISRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGE+  E G ++D ++L  I       + +    
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEVIAEKGTIVDRRTLNRILPYLENGVGL---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               ++  L   ++  P D                         
Sbjct: 329 ---------RVHKPFGGVVEEEIALQSIKIYAPNDP------------------------ 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 DGEQVINVISNGYIAEDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R
Sbjct: 536 KVNKFGFIETPYRRVDPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EA
Sbjct: 596 FRGENIVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V A+ SGAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF
Sbjct: 656 PIVGTGMEYVSARDSGAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+VK GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVKKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V EDV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAE
Sbjct: 776 IMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 181/535 (33%), Positives = 251/535 (46%), Gaps = 79/535 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 705  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 763

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 764  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 823

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 824  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 882

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 883  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 926

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 927  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 986

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 987  IASPVFDGATEEDVWNILEEAGMPRDAK----------------------------TVLY 1018

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1019 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1052

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1053 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1112

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM--EEIPDFNKCE 1384
            IV G +  E G PESF VL+KE+Q+LG+ + +  S  K       +E  D +  +
Sbjct: 1113 IVKGENIPEPGVPESFKVLIKELQSLGMDVTILTSDEKEINMENFDEEDDVHSAD 1167


>gi|138893777|ref|YP_001124230.1| DNA-directed RNA polymerase subunit beta [Geobacillus
           thermodenitrificans NG80-2]
 gi|196251033|ref|ZP_03149715.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp. G11MC16]
 gi|158513825|sp|A4IJI1|RPOB_GEOTN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|134265290|gb|ABO65485.1| DNA-directed RNA polymerase beta subunit [Geobacillus
           thermodenitrificans NG80-2]
 gi|196209505|gb|EDY04282.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp. G11MC16]
          Length = 1190

 Score =  889 bits (2297), Expect = 0.0,   Method: Composition-based stats.
 Identities = 451/964 (46%), Positives = 605/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  FK
Sbjct: 1   MTGRLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 51  EISPIEDFSGNLSLEFIDYSLGEPKYSVEEAKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L +      K         
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTLENAKSLLASRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE I + ETGEI  EAG +ID ++L  +     +        
Sbjct: 273 YKINKKLHIKNRLFNQRLAETIADPETGEIIAEAGTMIDRRTLNRLLPYLEK-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y     V D         +   ++  P D     V                   
Sbjct: 325 GAGLQTYRPTEGVADGQIS-----VQTVKIYAPNDPDNEKV------------------- 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 361 -----INIIGNGFIAEDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDANTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R
Sbjct: 536 KVNKFGFIETPYRRVDPETGKVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVIAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EA
Sbjct: 596 FRGENIVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAAI+ K  GIVE+V+A  I +R  +E D       +D YRL+KF
Sbjct: 656 PIVGTGMEYVSAKDSGAAIICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+VK GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVKKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V EDV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAE
Sbjct: 776 IMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 178/523 (34%), Positives = 246/523 (47%), Gaps = 77/523 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 705  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 763

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 764  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 823

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 824  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 882

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 883  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 926

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 927  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 986

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 987  IASPVFDGATEEDVWNILEEAGMARDAK----------------------------TVLY 1018

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1019 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1052

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1053 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1112

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            IV G +  E G PESF VL+KE+Q+LG+ + +  S  +     
Sbjct: 1113 IVKGENIPEPGVPESFKVLIKELQSLGMDVTILTSDEQEINME 1155


>gi|239825685|ref|YP_002948309.1| DNA-directed RNA polymerase subunit beta [Geobacillus sp. WCH70]
 gi|239805978|gb|ACS23043.1| DNA-directed RNA polymerase, beta subunit [Geobacillus sp. WCH70]
          Length = 1185

 Score =  887 bits (2292), Expect = 0.0,   Method: Composition-based stats.
 Identities = 450/964 (46%), Positives = 605/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  FK
Sbjct: 1   MTGRLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYKWFL----------DEGLREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 51  EISPIEDFSGNLSLEFIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYSEKVDK---NGKRGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   IE+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTIENAKNLLISRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +VN ETGEI  E G +ID ++L  I       + +    
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVNPETGEIIAEKGTLIDRRTLNRILPYLENGVGL---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               ++  L   ++  P D                         
Sbjct: 329 ---------QVYKPVGGVVDEEFALQSIKIYSPND------------------------A 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 DGEKVINVISNGYIAEDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI+++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDINTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ + YL+A EE+N  IAQAN  L EDG+F EE V  R
Sbjct: 536 KVNKFGFIETPYRRVDPETGRVTDQIDYLTADEEDNYVIAQANVPLAEDGTFLEENVVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EA
Sbjct: 596 FRGENIVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF
Sbjct: 656 PIVGTGMEYVSAKDSGAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+VK GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVKKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V EDV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GI+ +GAE
Sbjct: 776 IMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALRNLDERGIVRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 181/530 (34%), Positives = 245/530 (46%), Gaps = 77/530 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 705  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 763

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 764  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALRN 823

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 824  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 870

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 871  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 926

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 927  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 986

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 987  IASPVFDGAMEEDVWNILEEAGMPRDAK----------------------------TVLY 1018

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1019 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1052

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1053 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1112

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            IV G +  E G PESF VL+KE+Q+LG+ + +  S  K         D +
Sbjct: 1113 IVKGENIPEPGVPESFKVLIKELQSLGMDVTILTSDEKEINMENFDEDDD 1162


>gi|212637946|ref|YP_002314466.1| DNA-directed RNA polymerase subunit beta [Anoxybacillus
           flavithermus WK1]
 gi|212559426|gb|ACJ32481.1| DNA-directed RNA polymerase beta subunit [Anoxybacillus
           flavithermus WK1]
          Length = 1189

 Score =  886 bits (2290), Expect = 0.0,   Method: Composition-based stats.
 Identities = 444/964 (46%), Positives = 609/964 (63%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEESKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIVDLLGDNEYIR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTESTEKALL------EIYERLRPGEPPTVENAKSLLISRFFDPKRYDLASVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L G  +AE +V+ ETGE+  E G V+D ++L+ I            + 
Sbjct: 276 YKINKKLHIKNRLFGQRLAETLVHPETGEVIAEKGTVLDRRTLDRI------------LP 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +     IR         + + AL  I ++  P D                         
Sbjct: 324 ELEKGIGIRKYQPLGGVVEDEFALQAI-KIYAPNDP------------------------ 358

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   + +  N   P+ V+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 359 DGEKVITVISNGYIPETVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 419 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 479 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 538

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVTN + YL+A EE+N  +AQAN  + EDG+F EE V  R
Sbjct: 539 KVNKFGFIETPYRRVDPETGKVTNQIDYLTADEEDNYVVAQANVPIAEDGTFLEENVVAR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 599 FRGENIVVKRDRVDYVDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF
Sbjct: 659 PIVGTGMEYVAAKDSGAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKF 718

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+VK GD V + +I+ADGPS + G+LALGRN+LVAFM W GYN+ED++
Sbjct: 719 VRSNQGTCYNQRPIVKAGDIVEKGEILADGPSMEKGELALGRNVLVAFMTWDGYNYEDAI 778

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GI+ +GAE
Sbjct: 779 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIVRIGAE 838

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++F R
Sbjct: 839 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFTR 898

Query: 948 HGID 951
              D
Sbjct: 899 EDGD 902



 Score =  503 bits (1295), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/535 (34%), Positives = 263/535 (49%), Gaps = 79/535 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 708  GDLDKYRLLKFVRSNQGTCYNQRPIVKAGDIVEKGEILADGPS-MEKGELALGRNVLVAF 766

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----D 972
                  +  D  +     +S  +V   ++    I++ E      +   E + RD     +
Sbjct: 767  MTWDGYNYEDAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 821

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEK 1030
            D    LD     R+   +   + + G    K  T L+++  L+      +  +      +
Sbjct: 822  DALRNLDERGIVRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLR 881

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V      +                 K+   + GD++PPGV ++V+V++  KR I  GDKM
Sbjct: 882  VPHGGGGIV-------------LDVKVFTREDGDELPPGVNQLVRVYIVQKRKISEGDKM 928

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG 
Sbjct: 929  AGRHGNKGVISRILPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARKLGL 988

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + S + D     D+                                             
Sbjct: 989  HVASPVFDGAREEDVW-------------------------------------------- 1004

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
               A  E        A +    +++LYDG TGEPFD  V+VG +YM+KL HMV DK++AR
Sbjct: 1005 ---ATLEE-------AGMARDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHAR 1054

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE
Sbjct: 1055 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYE 1114

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            +IV G +  E G PESF VL+KE+Q+LG+ + + +S  K  +      D +   +
Sbjct: 1115 AIVKGENVPEPGVPESFKVLIKELQSLGMDVTVLSSDEKEISMENFGEDDDVQPV 1169


>gi|20808668|ref|NP_623839.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter
           tengcongensis MB4]
 gi|41018079|sp|Q8R7U6|RPOB_THETN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|20517303|gb|AAM25443.1| DNA-directed RNA polymerase beta subunit/140 kD subunit (split gene
           in Mjan, Mthe, Aful) [Thermoanaerobacter tengcongensis
           MB4]
          Length = 1234

 Score =  877 bits (2267), Expect = 0.0,   Method: Composition-based stats.
 Identities = 462/953 (48%), Positives = 613/953 (64%), Gaps = 64/953 (6%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F K  E+++IPDLIEVQK SY  FL           EGL+  F+ + PI +F+G 
Sbjct: 10  RTRMSFAKIDEVLEIPDLIEVQKKSYQWFL----------EEGLKEVFQEISPIESFTGN 59

Query: 72  AMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             LEFV Y  +  PK+ V++C  RD TYA PLK+ +RL           +   +IKE  +
Sbjct: 60  LALEFVDYRLENNPKYSVEECKDRDTTYAAPLKVKVRLT---------NRETGEIKESEV 110

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGDLPLMT  GTF+I G +R++VSQL RSPG+++D    +    GK L    +IP++G 
Sbjct: 111 FMGDLPLMTDKGTFIINGAERVIVSQLVRSPGVYYDQQFDKF---GKKLIFATVIPNRGA 167

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E DS D+I+VRIDR RKVP+T  L A+G +++ +IL     +       D      
Sbjct: 168 WLEYEEDSNDVIYVRIDRTRKVPITVLLRAIGYNTDIQILDLLGEEEKLKATLDKDTTKS 227

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------- 301
               L+   K       +  GE   +ES + L + L    K   +  +G           
Sbjct: 228 EEEALIEIYK------RLRPGEPPTVESARSLFNALFFDPKRYDLAKVGRYKFNKKLALK 281

Query: 302 -CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             +     A+ IVN  TGE+ +E G+ I  +  EEI +  I ++ IL    V        
Sbjct: 282 ARIANHKSAKRIVNPITGEVLVEEGEKITREKAEEIQNCGINEVEILVDGKVVKVVGNNT 341

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                         +DI +   P DVS+ ++ E +   +    +  D  +     +N   
Sbjct: 342 --------------VDINKYPMPYDVSSLNIKELV--NVRVLREILDNFSDEEAVLNEIK 385

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           N       +HI K+DI+A I   ++L +G G +DDID+LGNRRVRSVGE+L+NQ+R+GL 
Sbjct: 386 NRMDELVPKHITKDDIVATISYQLNLTHGVGFVDDIDHLGNRRVRSVGELLQNQFRIGLA 445

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER +KER++  D++ V PQ+LIN +PVV+A+ EFF SSQLSQ  +  N LS +TH RR
Sbjct: 446 RLERVVKERMTIQDVNEVTPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLSELTHKRR 505

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL++SLT++ARVN YGFIET
Sbjct: 506 VSALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLITSLTTYARVNEYGFIET 565

Query: 601 PYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYRKV      VT+++VY++A EE+   IAQAN  LDE+  F  + V CR   E I VP 
Sbjct: 566 PYRKVDKATGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINDRVVCRLREEIISVPP 625

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            ++DF+D SPKQ+VS++ASLIPFLENDD+NR LMG NMQRQAVPLLK EAP VGTGME  
Sbjct: 626 TEVDFMDVSPKQIVSVSASLIPFLENDDANRALMGSNMQRQAVPLLKPEAPIVGTGMEYK 685

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SGA I+AK  GIVE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQ
Sbjct: 686 AAVDSGAVILAKNDGIVEKVTADKVVIRTKDGKRDE-------YHLLKFKRSNQGTCINQ 738

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GDEV++  +I DGPSTD G+LALG+N+LV FMPW GYN+ED++LISE +V +D 
Sbjct: 739 RPIVNEGDEVKKGQVICDGPSTDHGELALGKNVLVGFMPWEGYNYEDAILISEELVMDDS 798

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+
Sbjct: 799 LTSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVRAGDILVGKV 858

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 859 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 275/1142 (24%), Positives = 423/1142 (37%), Gaps = 134/1142 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            + G  + +G  + +  + V+  G+  D      G  +    V    G          ++ 
Sbjct: 120  DKGTFIINGAERVIVSQLVRSPGVYYDQQFDKFGKKLIFATVIPNRGAWLEYEEDSNDVI 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +   +  I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRAIGYNTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+FN LFFD  +YDL+ VGR K N +L L          +       K
Sbjct: 240  RPGEPPTVESARSLFNALFFDPKRYDLAKVGRYKFNKKLALKA--------RIANHKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N+  + +      +    +       MP 
Sbjct: 292  RIVNPITGEVLVEEGEKITREKAEEIQNCGINEVEILVDGKVVKVVGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG-VEMRD 560
            D+ +   +   V        L    +    L+ I    R+  L    + +          
Sbjct: 352  DVSSL-NIKELVNVRVLREILDNFSDEEAVLNEI--KNRMDELVPKHITKDDIVATISYQ 408

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            ++ TH           G+    V S+    +      +    R V +     DV  ++  
Sbjct: 409  LNLTHGVGFVDDIDHLGN--RRVRSVGELLQNQFRIGLARLERVVKERMTIQDVNEVTPQ 466

Query: 621  EEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDFIDA 666
               N    +A       +S L +    T  L           +        R   +  D 
Sbjct: 467  NLINIRPVVAAIREFFGSSQLSQFMDQTNPLSELTHKRRVSALGPGGLSRERAGFEVRDV 526

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF-VGTGMESVVAKSSGA 725
                   I     P   N      L       +   +          TG           
Sbjct: 527  HYSHYGRICPIETPEGPNIGLITSLTTYARVNEYGFIETPYRKVDKATG----TVTDEIV 582

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             + A          A   +  +     D        +I  +   +    +    Q   V 
Sbjct: 583  YMTADEEDEYIIAQANEPLDENNRFINDRVVCRLREEIISVPPTEVDFMDVSPKQIVSVS 642

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                    +  A+              +L    P  G   E    +    V       I 
Sbjct: 643  ASLIPFLENDDANRALMGSNMQRQAVPLLKPEAPIVGTGMEYKAAVDSGAVILAKNDGIV 702

Query: 844  -IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
                 + +   TK G  +    +          I++  I+  G EV  G ++    +   
Sbjct: 703  EKVTADKVVIRTKDGKRDEYHLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDGPST-D 761

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI----- 957
               +   + +L      +  +  D  L         V+D  + + H  + +  +      
Sbjct: 762  HGELALGKNVLVGFMPWEGYNYEDAILI----SEELVMDDSLTSIHIEEYDAEARDTKLG 817

Query: 958  -SVEREQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
                  +I  +  D     DE+ I+      R  +IL G+    G         L   + 
Sbjct: 818  PEEITREIPNVGEDALKDLDERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIF 877

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R                 E                   K+   + GD++PPGV ++
Sbjct: 878  GEKAR-----------------EVRDTSLRVPHGESGIVVDVKVYSRENGDELPPGVNQM 920

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN+
Sbjct: 921  VRVFVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLQICLNPLGVPSRMNI 980

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLG     LG  I S + D     DI  L +               S +  D  
Sbjct: 981  GQVLETHLGLVAKALGWYIASPVFDGATEKDIEELLAK--------------SGFSPDGK 1026

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            +++                                   G++       GEPFD  VTVGY
Sbjct: 1027 VQL---------------------------------YDGRT-------GEPFDNKVTVGY 1046

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE
Sbjct: 1047 MYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQE 1106

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            MLT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +    
Sbjct: 1107 MLTVKSDDVTGRVKAYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDGQEIPI 1166

Query: 1374 ME 1375
             E
Sbjct: 1167 KE 1168


>gi|229542212|ref|ZP_04431272.1| DNA-directed RNA polymerase, beta subunit [Bacillus coagulans 36D1]
 gi|229326632|gb|EEN92307.1| DNA-directed RNA polymerase, beta subunit [Bacillus coagulans 36D1]
          Length = 1186

 Score =  874 bits (2259), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/964 (45%), Positives = 601/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M+  +V  G  R R+ + +  EI+++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MSHQLVQYGRHRQRRSYARIKEILELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ +D+C  RD+TYA PL++ +RL+          K
Sbjct: 51  DISPIEDFAGNLSLEFIDYSLGEPKYSIDECKERDVTYAAPLRVKVRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F+    +   +GK  Y
Sbjct: 102 ETGEVKDQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFNSKMDK---NGKYGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+ +VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVAYVRIDRTRKLPITVLLRALGFGSDQEIIDLIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +E+ K L        K   +     
Sbjct: 219 NTLEKDNTESTEKALL------EIYERLRPGEPPTVENAKSLLISRFFDPKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE I + ETGEI  E G V+D ++L++I     + +      
Sbjct: 273 YKMNKKLHLKFRLFGQRLAESIADPETGEIIAEEGTVLDRRTLDKIVPFLEKGLK----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     T          D  L   ++  P D                         
Sbjct: 328 --------FETYSQTGGVVDDDVTLQSIKIYAPID------------------------- 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    + ++HI   DI+A I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 355 DNEKVINVIGNAYVDESIKHITPADIVASISYFFNLLHGVGNTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI+++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDINTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT  + YL+A EE+N  +AQAN+ LDE+G F ++ V+ R
Sbjct: 535 KVNRFGFIETPYRRVDPDTGRVTEHIDYLTADEEDNYVVAQANAQLDENGFFVDDEVYAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V  +++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 595 FRGENIVVKTDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPQA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE V+A  I +R  ++ D       +D YRL KF
Sbjct: 655 PIVGTGMEYVNAKDSGAALICKHDGIVEHVEAREIWVRRVIDVDGQEVKGDLDKYRLQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN   C+NQRP+VK GD V + +I+ADG S D G+LALG+N+LVAFM W GYN+ED++
Sbjct: 715 KRSNNGMCINQRPIVKKGDRVVKGEILADGQSMDHGELALGQNVLVAFMTWEGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SE++V EDV+TSIHIEE+E  ARDTKLGPEE+TRDIPNV E+ LKN+DE GI+ +GAE
Sbjct: 775 IMSEKLVKEDVYTSIHIEEYESEARDTKLGPEEMTRDIPNVGEDALKNLDERGIVRIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++F R
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFTR 894

Query: 948 HGID 951
              D
Sbjct: 895 EAGD 898



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 178/535 (33%), Positives = 250/535 (46%), Gaps = 79/535 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R            I++  I+  G  V  G+IL    +      +   + +L A 
Sbjct: 704  GDLDKYRLQKFKRSNNGMCINQRPIVKKGDRVVKGEILADGQS-MDHGELALGQNVLVAF 762

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE--QIELLARDKD-- 972
               +  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 763  MTWEGYNYEDAIIMSEKLVKEDVYTSIHIEEYESEARDTKLGPEEMTRDIPNVGEDALKN 822

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 823  LDERGIVRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 881

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 882  GGGI----------------VLDVKVFTREAGDELPPGVNQLVRVYIVQKRKIHQGDKMA 925

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTPV I+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 926  GRHGNKGVISRILPEEDMPFLPDGTPVQIMLNPLGVPSRMNIGQVLELHLGMAAKKLGLH 985

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D     D+                                          T ++
Sbjct: 986  VATPVFDGAREEDVWETIEEAGMARDAK----------------------------TVLY 1017

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1018 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1051

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1052 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1111

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            IV G +  E G PESF VL+KE+Q+LGL + + +   +      +E+  D N+ +
Sbjct: 1112 IVKGENVPEPGVPESFKVLIKELQSLGLDVKILSGDDEEIEMRDLEDDDDLNQAD 1166


>gi|311029041|ref|ZP_07707131.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. m3-13]
          Length = 1185

 Score =  874 bits (2258), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 602/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++D+P+LIE+Q +SY  FL          +EGL+  F 
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLDLPNLIEIQTSSYQWFL----------DEGLREMFH 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT  GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLLGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTESTEKALL------EIYERLRPGEPPTVENAKSLLESRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI +E G ++D ++L+ I  +    I +    
Sbjct: 273 YKINKKLHIKNRLFNQRIAETLVDPETGEIIVEKGTLLDRRTLDRILPNIEDGIGL---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     +          +  +   ++  P D                         
Sbjct: 329 ---------TSFHPHGGVVEDEVPMQSIKIYAPND------------------------A 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G  ++ +  N    + V+HI   DIIA I    DL +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEKEIVVLGNGFIEEKVKHIAPADIIASISYFFDLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ + YL+A EE+N  +AQAN+ L EDG+F +E V  R
Sbjct: 536 KVNKFGFIETPYRRVDPETGRVTDQIDYLTADEEDNYVVAQANARLGEDGTFLDENVVSR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V  E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ E+
Sbjct: 596 FRGENTVVVSERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLQPES 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R   E D       +D YR++KF
Sbjct: 656 PIVGTGMEHVSAKDSGAAVICKHPGVVERVEAREVWVRRMEEVDGQQVKGNLDKYRMLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD V + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 716 IRSNQGTCYNQRPIVSVGDVVTKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LKN+D+ GII VGAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDDRGIIRVGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  478 bits (1229), Expect = e-132,   Method: Composition-based stats.
 Identities = 175/574 (30%), Positives = 257/574 (44%), Gaps = 77/574 (13%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M         + +I +   +V       + +   E +      G  +  R +  +     
Sbjct: 662  MEHVSAKDSGAAVICKHPGVVERVEAREVWVRRMEEVDGQQVKGNLDKYRMLKFIRSNQG 721

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG  V  G+IL    +   +  +     ++         +  D  +    
Sbjct: 722  TCYNQRPIVSVGDVVTKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMS-- 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
                            + K++   S+  E+ E  ARD       + R+I +   E L   
Sbjct: 779  --------------ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNL 824

Query: 994  NAVSGPKG---FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
            +     +     K   +L   +  +       +  +           ++           
Sbjct: 825  DDRGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGG 884

Query: 1051 DR-FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                  K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDM
Sbjct: 885  GIVLDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDM 944

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+    
Sbjct: 945  PYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARTLGIHVASAVFDGAREEDVWSTL 1004

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                  T ++DG                
Sbjct: 1005 EEAGMARDAK----------------------------TVLYDG---------------- 1020

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
                       TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1021 ----------RTGEPFDSRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQF 1070

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF V
Sbjct: 1071 GGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKV 1130

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            L+KE+Q+LG+ + + +   +     +   D  + 
Sbjct: 1131 LIKELQSLGMDVKILSGDEEEIEMRDLEEDEEQA 1164


>gi|52078601|ref|YP_077392.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis
           ATCC 14580]
 gi|52783963|ref|YP_089792.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis
           ATCC 14580]
 gi|81667235|sp|Q65PB5|RPOB_BACLD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|52001812|gb|AAU21754.1| RNA polymerase (beta subunit) [Bacillus licheniformis ATCC 14580]
 gi|52346465|gb|AAU39099.1| RpoB [Bacillus licheniformis ATCC 14580]
          Length = 1193

 Score =  874 bits (2257), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 604/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENTDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGAILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 320 PYLENGIGFKKLYPNGGVVEDEVTLQSIKIYAPTD------------------------Q 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQTINVIGNAYIEEGVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L++DGSF ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLNDDGSFVDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +VP++++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+
Sbjct: 596 FRGENTVVPKDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPES 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ +  GIVE+V+A  I +R   E D       +D Y L+KF
Sbjct: 656 PIVGTGMEYVSAKDSGAAVICRHPGIVERVEAKNIWVRRYEEVDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVEKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 264/1179 (22%), Positives = 431/1179 (36%), Gaps = 137/1179 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D +  
Sbjct: 155  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-IDLIGE 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS----- 409
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+     
Sbjct: 214  NEYLRNTLDKDNTENTDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLASVGRY 273

Query: 410  ------TVGRVKMNMRL--NLDTPDDVRHIRKEDIIAIIKILVD----LRNGKGTIDDID 457
                   +     N RL   L  P+    + ++  I   + L      L NG G      
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGAILDRRTLDKVLPYLENGIGFKKLYP 333

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            N G        + +K  Y       E++I    ++   + V      +    +S      
Sbjct: 334  NGGVVEDEVTLQSIKI-YAPTDQEGEQTINVIGNAYIEEGVKNITPSDIIASISYFFNLL 392

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                 +   +H+ +    +    L    + G++R    V  R               +  
Sbjct: 393  HGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIR 452

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
              I  +      ++++ +               TN +  L+                   
Sbjct: 453  PVIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------H 482

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNM 696
                  L       E   +    + +        +       I  + +  S   +     
Sbjct: 483  KRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFGF 542

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAI----VAKRAGIVEQVDAIRIVIRSVEGDL 752
                   +  E   V   ++ + A      +     A+       VD   +     E  +
Sbjct: 543  IETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLNDDGSFVDDSIVARFRGENTV 602

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             P      +    K   S    C+           +  +D        ++   A+     
Sbjct: 603  VPKDRVDYMDVSPKQVVSAATACIP---------FLENDDSNRALMGANMQRQAVPLMQP 653

Query: 813  VAFMPWHGYNFEDS-------MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             + +   G  +  +       +     +V      +I +  +E +      G  +    +
Sbjct: 654  ESPIVGTGMEYVSAKDSGAAVICRHPGIVERVEAKNIWVRRYEEVDGQKVKGNLDKYSLL 713

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              V        ++  I+ VG EV  G+IL    +   +  +     ++         +  
Sbjct: 714  KFVRSNQGTCYNQRPIVSVGDEVEKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYE 772

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 773  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 827

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 828  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 886

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP
Sbjct: 887  I------LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILP 940

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+
Sbjct: 941  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDV 1000

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1001 WETLEEAGMSRDAK----------------------------TVLYDG------------ 1020

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1021 --------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1066

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PE
Sbjct: 1067 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPE 1126

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            SF VL+KE+Q+LG+ + + +S  +     +   D +  +
Sbjct: 1127 SFKVLIKELQSLGMDVKILSSDEEEIEMRDLEDDEDAKQ 1165


>gi|167036793|ref|YP_001664371.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320115215|ref|YP_004185374.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|254765313|sp|B0KCJ2|RPOB_THEP3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|166855627|gb|ABY94035.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319928306|gb|ADV78991.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 1238

 Score =  872 bits (2253), Expect = 0.0,   Method: Composition-based stats.
 Identities = 454/952 (47%), Positives = 612/952 (64%), Gaps = 64/952 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K  E++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G  
Sbjct: 11  TRMSFAKIDEVLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNL 60

Query: 73  MLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            LEFV Y  +  PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++
Sbjct: 61  ALEFVDYRLENNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W
Sbjct: 112 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E DS DI++VRIDR RKVP+T  L ALG  ++ +IL     +       D       
Sbjct: 169 LEYEEDSNDIVYVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD-------- 301
              L+   K       +  GE   +ES K L   L    K   +  +G            
Sbjct: 229 EEALIEIYK------RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKT 282

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I  + +L          I N 
Sbjct: 283 RIANLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLV--EGKVVKVIGNN 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        +DI +   P DVS+ ++ E++   L    +  D  +     +N   N
Sbjct: 341 T------------VDINKYPMPYDVSSLNIKEAV--NLSVLKEILDNFSDEEAVINEIKN 386

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                  +HI K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 387 RMDELVPKHITKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLAR 446

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER +KER++  D++ + PQ+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR+
Sbjct: 447 LERVVKERMTIQDVNEITPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRV 506

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++ARVN YGFIE P
Sbjct: 507 SALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAP 566

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YR+V      VT+++VY++A EE+   IAQAN  LDE+  F  E V CR   E I VP  
Sbjct: 567 YRRVDKTTGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPT 626

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K EAP +GTG+E   
Sbjct: 627 EVDFMDVSPKQIVSVATSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKA 686

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK  G+VE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQR
Sbjct: 687 AVDSGVVVLAKNDGVVEKVAADKVVIRTKDGRRDE-------YNLLKFKRSNQGTCINQR 739

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GDEV++  +I DGPSTD G+LALG+N+LV FMPW GYN+ED++LISE +V +D  
Sbjct: 740 PIVNEGDEVKKGQVICDGPSTDYGELALGKNVLVGFMPWEGYNYEDAILISEELVRDDSL 799

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+T
Sbjct: 800 TSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVT 859

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 860 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 266/1143 (23%), Positives = 437/1143 (38%), Gaps = 136/1143 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 120  EKGTFIINGAERVIVSQLVRSPGVYYEQQFDKFGKKLISATVIPNRGAWLEYEEDSNDIV 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A+S+   LFFD+ +YDL+ VGR K N +L L          +   +   K
Sbjct: 240  RPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALK--------TRIANLKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N   + +      +    +       MP 
Sbjct: 292  KIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVKVIGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARARAG-VEM 558
            D+ +       + E    S L ++ ++ +    + +    R+  L    + +        
Sbjct: 352  DVSSLN-----IKEAVNLSVLKEILDNFSDEEAVINEIKNRMDELVPKHITKDDIIATIS 406

Query: 559  RDVHPTH-YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
              ++ TH  G I   +      +  V  L    +      +    R V +     DV  +
Sbjct: 407  YQLNLTHGIGSIDDIDHLGNRRLRSVGELL---QNQFRIGLARLERVVKERMTIQDVNEI 463

Query: 618  SAMEEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDF 663
            +     N    +A       +S L +    T  L           +        R   + 
Sbjct: 464  TPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGGLSRERAGFEV 523

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D        I     P   N      L       +   +         T   +      
Sbjct: 524  RDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAPYRRVDKT---TGTVTDE 580

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               + A          A   +  +     +        +I  +   +    +    Q   
Sbjct: 581  IVYMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPTEVDFMDVSPKQIVS 640

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SED 837
            V         +  A+              ++    P  G   E    +   +V    ++ 
Sbjct: 641  VATSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKAAVDSGVVVLAKNDG 700

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            V   +  ++   +   TK G  +    +          I++  I+  G EV  G ++   
Sbjct: 701  VVEKVAADK---VVIRTKDGRRDEYNLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDG 757

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
             +      +   + +L      +  +  D  L         V D  + + H  + +  + 
Sbjct: 758  PST-DYGELALGKNVLVGFMPWEGYNYEDAILI----SEELVRDDSLTSIHIEEYDAEAR 812

Query: 958  SVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--L 1012
              +    E    +    +D    LD     R+   +   + + G    K  T L+++  L
Sbjct: 813  DTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVTPKGETELTAEERL 872

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +      +  +      +V      + V               K+   + GD++PPGV +
Sbjct: 873  LRAIFGEKAREVRDTSLRVPHGESGIVV-------------DVKVYSRENGDELPPGVNQ 919

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN
Sbjct: 920  MVRVFVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLQICLNPLGVPSRMN 979

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLG     LG +I + + D     DI  L +               S +  D 
Sbjct: 980  IGQVLEVHLGLVAKALGWQIATPVFDGATEEDIQELLAK--------------SGFSPDG 1025

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             +++                                   G++       GEPFD  VTVG
Sbjct: 1026 KVQL---------------------------------YDGRT-------GEPFDNKVTVG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQ
Sbjct: 1046 YMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ 1105

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +   
Sbjct: 1106 EILTVKSDDVSGRVKTYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDNQEIP 1165

Query: 1373 KME 1375
              E
Sbjct: 1166 LKE 1168


>gi|170293434|gb|ACB12770.1| DNA-directed RNA polymerase [Geobacillus thermocatenulatus]
          Length = 1075

 Score =  871 bits (2251), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/949 (46%), Positives = 600/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKSLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE IV+ ETGE+  EAG +ID ++L  +     + + +          Y     V D
Sbjct: 273 QRLAETIVDPETGEVIAEAGAMIDRRTLNRLLPYLEKGVGL--------QTYRPAEGVVD 324

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 D  +   ++  P D                          G   +N+  N    
Sbjct: 325 G-----DISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L  +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLVELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEK  +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKTREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  354 bits (908), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 146/458 (31%), Positives = 202/458 (44%), Gaps = 77/458 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKTRE-VRDTSLRVPHG 867

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 868  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATGEDVWNILEEAGLARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1075


>gi|319649124|ref|ZP_08003332.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. BT1B_CT2]
 gi|317388824|gb|EFV69643.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. BT1B_CT2]
          Length = 1196

 Score =  871 bits (2251), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/964 (45%), Positives = 604/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 105 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGENEYLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLDKDNTENTDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLASVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGAILDRRTLDK-------------VL 322

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 323 PYLENGIGFKKLYPNGGVVEDEVTLQSIKIYAPTD------------------------Q 358

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 359 EGEQTINVIGNAYIEEGVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 419 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 479 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 538

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L++DGSF ++ +  R
Sbjct: 539 KVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLNDDGSFVDDSIVAR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +VP++++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+
Sbjct: 599 FRGENTVVPKDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPES 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ +  GIVE+V+A  I +R   E D       +D Y L+KF
Sbjct: 659 PIVGTGMEYVSAKDSGAAVICRHPGIVERVEAKNIWVRRYEEVDGQKVKGNLDKYSLLKF 718

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 719 VRSNQGTCYNQRPIVSVGDEVEKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 778

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 779 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 838

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 839 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 898

Query: 948 HGID 951
              D
Sbjct: 899 EDGD 902



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 264/1179 (22%), Positives = 431/1179 (36%), Gaps = 137/1179 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D +  
Sbjct: 158  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-IDLIGE 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS----- 409
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+     
Sbjct: 217  NEYLRNTLDKDNTENTDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLASVGRY 276

Query: 410  ------TVGRVKMNMRL--NLDTPDDVRHIRKEDIIAIIKILVD----LRNGKGTIDDID 457
                   +     N RL   L  P+    + ++  I   + L      L NG G      
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGAILDRRTLDKVLPYLENGIGFKKLYP 336

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            N G        + +K  Y       E++I    ++   + V      +    +S      
Sbjct: 337  NGGVVEDEVTLQSIKI-YAPTDQEGEQTINVIGNAYIEEGVKNITPSDIIASISYFFNLL 395

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                 +   +H+ +    +    L    + G++R    V  R               +  
Sbjct: 396  HGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIR 455

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
              I  +      ++++ +               TN +  L+                   
Sbjct: 456  PVIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------H 485

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNM 696
                  L       E   +    + +        +       I  + +  S   +     
Sbjct: 486  KRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFGF 545

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAI----VAKRAGIVEQVDAIRIVIRSVEGDL 752
                   +  E   V   ++ + A      +     A+       VD   +     E  +
Sbjct: 546  IETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLNDDGSFVDDSIVARFRGENTV 605

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             P      +    K   S    C+           +  +D        ++   A+     
Sbjct: 606  VPKDRVDYMDVSPKQVVSAATACIP---------FLENDDSNRALMGANMQRQAVPLMQP 656

Query: 813  VAFMPWHGYNFEDS-------MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             + +   G  +  +       +     +V      +I +  +E +      G  +    +
Sbjct: 657  ESPIVGTGMEYVSAKDSGAAVICRHPGIVERVEAKNIWVRRYEEVDGQKVKGNLDKYSLL 716

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              V        ++  I+ VG EV  G+IL    +   +  +     ++         +  
Sbjct: 717  KFVRSNQGTCYNQRPIVSVGDEVEKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYE 775

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 776  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 830

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 831  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 889

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP
Sbjct: 890  I------LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILP 943

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+
Sbjct: 944  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDV 1003

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1004 WETLEEAGMSRDAK----------------------------TVLYDG------------ 1023

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1024 --------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1069

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PE
Sbjct: 1070 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPE 1129

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            SF VL+KE+Q+LG+ + + +S  +     +   D +  +
Sbjct: 1130 SFKVLIKELQSLGMDVKILSSDEEEIEMRDLEDDEDAKQ 1168


>gi|170293432|gb|ACB12769.1| DNA-directed RNA polymerase [Geobacillus vulcani]
          Length = 1076

 Score =  871 bits (2250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/949 (46%), Positives = 601/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYSVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKSLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I + ETGEI  EAG +ID ++L  +     + + +          Y     V D
Sbjct: 273 QRLAETIADPETGEIIAEAGAMIDRRTLNRLLPYLEKGVGL--------QTYRPAEGVVD 324

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 D  +   ++  P D                          G   +N+  N    
Sbjct: 325 G-----DISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 146/459 (31%), Positives = 202/459 (44%), Gaps = 77/459 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 867

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 868  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGMARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1076


>gi|326390669|ref|ZP_08212224.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993347|gb|EGD51784.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 1239

 Score =  871 bits (2250), Expect = 0.0,   Method: Composition-based stats.
 Identities = 454/952 (47%), Positives = 612/952 (64%), Gaps = 64/952 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K  E++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G  
Sbjct: 11  TRMSFAKIDEVLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNL 60

Query: 73  MLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            LEFV Y  +  PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++
Sbjct: 61  ALEFVDYRLENNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W
Sbjct: 112 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E DS DI++VRIDR RKVP+T  L ALG  ++ +IL     +       D       
Sbjct: 169 LEYEEDSNDIVYVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD-------- 301
              L+   K       +  GE   +ES K L   L    K   +  +G            
Sbjct: 229 EEALIEIYK------RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKT 282

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I  + +L          I N 
Sbjct: 283 RIANLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLV--EGKVVKVIGNN 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        +DI +   P DVS+ ++ E++   L    +  D  +     +N   N
Sbjct: 341 T------------VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKN 386

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                  +HI K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 387 RMDELVPKHITKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLAR 446

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER +KER++  D++ + PQ+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR+
Sbjct: 447 LERVVKERMTIQDVNEITPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRV 506

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++ARVN YGFIE P
Sbjct: 507 SALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAP 566

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YR+V      VT+++VY++A EE+   IAQAN  LDE+  F  E V CR   E I VP  
Sbjct: 567 YRRVDKTTGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPT 626

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K EAP +GTG+E   
Sbjct: 627 EVDFMDVSPKQIVSVATSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKA 686

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK  G+VE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQR
Sbjct: 687 AVDSGVVVLAKNDGVVEKVAADKVVIRTKDGRRDE-------YNLLKFKRSNQGTCINQR 739

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GDEV++  +I DGPSTD G+LALG+N+LV FMPW GYN+ED++LISE +V +D  
Sbjct: 740 PIVNEGDEVKKGQVICDGPSTDHGELALGKNVLVGFMPWEGYNYEDAILISEELVRDDSL 799

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+T
Sbjct: 800 TSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVT 859

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 860 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  528 bits (1360), Expect = e-147,   Method: Composition-based stats.
 Identities = 265/1141 (23%), Positives = 432/1141 (37%), Gaps = 132/1141 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 120  EKGTFIINGAERVIVSQLVRSPGVYYEQQFDKFGKKLISATVIPNRGAWLEYEEDSNDIV 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A+S+   LFFD+ +YDL+ VGR K N +L L          +   +   K
Sbjct: 240  RPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALK--------TRIANLKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N   + +      +    +       MP 
Sbjct: 292  KIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVKVIGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG-VEMRD 560
            D+ +     +          L    +    ++ I    R+  L    + +          
Sbjct: 352  DVSSLNIKEAVNLSILKEI-LDNFSDEEAVINEI--KNRMDELVPKHITKDDIIATISYQ 408

Query: 561  VHPTH-YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++ TH  G I   +      +  V  L    +      +    R V +     DV  ++ 
Sbjct: 409  LNLTHGIGSIDDIDHLGNRRLRSVGELL---QNQFRIGLARLERVVKERMTIQDVNEITP 465

Query: 620  MEEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDFID 665
                N    +A       +S L +    T  L           +        R   +  D
Sbjct: 466  QNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGGLSRERAGFEVRD 525

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
                    I     P   N      L       +   +         T   +        
Sbjct: 526  VHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAPYRRVDKT---TGTVTDEIV 582

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             + A          A   +  +     +        +I  +   +    +    Q   V 
Sbjct: 583  YMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPTEVDFMDVSPKQIVSVA 642

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVF 839
                    +  A+              ++    P  G   E    +   +V    ++ V 
Sbjct: 643  TSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKAAVDSGVVVLAKNDGVV 702

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              +  ++   +   TK G  +    +          I++  I+  G EV  G ++    +
Sbjct: 703  EKVAADK---VVIRTKDGRRDEYNLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDGPS 759

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   + +L      +  +  D  L         V D  + + H  + +  +   
Sbjct: 760  T-DHGELALGKNVLVGFMPWEGYNYEDAILI----SEELVRDDSLTSIHIEEYDAEARDT 814

Query: 960  E---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LIS 1014
            +    E    +    +D    LD     R+   +   + + G    K  T L+++  L+ 
Sbjct: 815  KLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVTPKGETELTAEERLLR 874

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                 +  +      +V      + V               K+   + GD++PPGV ++V
Sbjct: 875  AIFGEKAREVRDTSLRVPHGESGIVV-------------DVKVYSRENGDELPPGVNQMV 921

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            +VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN+G
Sbjct: 922  RVFVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLQICLNPLGVPSRMNIG 981

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLG     LG +I + + D     DI  L +               S +  D  +
Sbjct: 982  QVLEVHLGLVAKALGWQIATPVFDGATEEDIQELLAK--------------SGFSPDGKV 1027

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            ++                                   G++       GEPFD  VTVGY+
Sbjct: 1028 QL---------------------------------YDGRT-------GEPFDNKVTVGYM 1047

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+
Sbjct: 1048 YMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEI 1107

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +     
Sbjct: 1108 LTVKSDDVSGRVKTYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDNQEIPLK 1167

Query: 1375 E 1375
            E
Sbjct: 1168 E 1168


>gi|170293436|gb|ACB12771.1| DNA-directed RNA polymerase [Bacillus caldotenax]
          Length = 1083

 Score =  870 bits (2249), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/949 (46%), Positives = 601/949 (63%), Gaps = 71/949 (7%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYSVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKSLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I + ETGEI  EAG +ID ++   +  +  R +P L             T    
Sbjct: 273 QRLAETIADPETGEIIAEAGTMIDRRAEPSVALTLNRLLPYL------EKGVGLQTYRPA 326

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +     D  +   ++  P D                          G   +N+  N    
Sbjct: 327 EGVVDGDISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 362

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 363 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 422

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 423 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 482

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 483 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 542

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 543 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 602

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 603 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 662

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 663 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 722

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 723 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 782

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 783 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 842

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 843 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 891



 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 147/459 (32%), Positives = 199/459 (43%), Gaps = 77/459 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 697  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 755

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 756  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 815

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 816  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 862

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 863  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 918

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 919  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 978

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 979  IASPVFDGATEEDVWNILEEAGMARDAK----------------------------TVLY 1010

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1011 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1044

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1045 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1083


>gi|229917366|ref|YP_002886012.1| DNA-directed RNA polymerase subunit beta [Exiguobacterium sp. AT1b]
 gi|259494183|sp|C4KZQ4|RPOB_EXISA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|229468795|gb|ACQ70567.1| DNA-directed RNA polymerase, beta subunit [Exiguobacterium sp.
           AT1b]
          Length = 1182

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/964 (45%), Positives = 605/964 (62%), Gaps = 77/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ F +  E++++P+LIE+Q ASY+ FL           EGL+  F 
Sbjct: 1   MTGQLVQYGRHRQRRSFARISEVLELPNLIEIQTASYEWFLR----------EGLKEMFT 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ F+G  +LEF+ Y    PK+ +D+   RD+TY+ PL++ +RL           K
Sbjct: 51  DISPISDFTGNLVLEFIDYSLSEPKYSIDESKERDVTYSAPLRVKVRL---------QNK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++++    +   +GK  +
Sbjct: 102 ETGELKEQEVFMGDFPLMTESGTFIINGAERVIVSQLVRSPSVYYNAKLDK---NGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  ++ EI+          
Sbjct: 159 GATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGTDQEIIDLLGDDEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +E+ K L        K   +     
Sbjct: 219 NTLEKDNTESTEKALI------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE +V+ ETGE+  EAG ++D ++L+ I            + 
Sbjct: 273 YKMNKKLHLKNRLFGQKLAETLVDPETGEVLAEAGTILDRRNLDRI------------LP 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + N     +   T    + +   L   +V+ P D                         
Sbjct: 321 HLENGLGYIDAEPTGGVAEGEPFGLQSIKVISPDDP------------------------ 356

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +    V+HI   DIIA I    +L +  GT DDID+LGNRR+RSVGE+
Sbjct: 357 DGERILNIIGNGNIDRSVKHITPADIIASINYFFNLLHEVGTTDDIDHLGNRRLRSVGEL 416

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER +KER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 417 LQNQFRIGLSRMERVVKERMSIQDQNAITPQALINIRPVIASLKEFFGSSQLSQFMDQTN 476

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 477 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 536

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIE PYR+V    G VT D+ Y++A EE+   +AQAN  L EDG F +E V CR
Sbjct: 537 KVNEYGFIEAPYRRVDPETGLVTGDIQYMTADEEDLYVVAQANMPLTEDGHFADEQVLCR 596

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ + V   ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ ++
Sbjct: 597 FRGQNLSVEPSRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLQPDS 656

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG-VDIYRLMKF 767
           P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG +D Y+L K+
Sbjct: 657 PIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSGDLDRYKLQKY 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM W GYN+ED++
Sbjct: 717 VRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMTWDGYNYEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D+ GII +GAE
Sbjct: 777 IMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLDDRGIIRIGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G ++DV++F+R
Sbjct: 837 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDR 896

Query: 948 HGID 951
              D
Sbjct: 897 ENGD 900



 Score =  536 bits (1380), Expect = e-149,   Method: Composition-based stats.
 Identities = 267/1172 (22%), Positives = 426/1172 (36%), Gaps = 145/1172 (12%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCL 303
                 +         +    +  ++G  +I   ++ + S L++S        L       
Sbjct: 98   LQNKETGELKEQEVFMGDFPLMTESGTFIINGAERVIVSQLVRSPSVYYNAKLDKNGKRG 157

Query: 304  CGLYVAEDI-----VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             G  V  +      +  +  +I     D   +  +  +  +         +D + ++ Y+
Sbjct: 158  FGATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGTDQEIIDLLGDDEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  +  + AL++IY  +RPG+  T   A+S+    FFD  +YDL+ VGR KMN 
Sbjct: 218  RNTLEKDNTESTEKALIEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRYKMNK 277

Query: 419  RLNLD-------------TPDDVRHI----RKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            +L+L               P+    +       D   + +IL  L NG G ID     G 
Sbjct: 278  KLHLKNRLFGQKLAETLVDPETGEVLAEAGTILDRRNLDRILPHLENGLGYIDAEPTGGV 337

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G              ER +    +     SV      +    ++          
Sbjct: 338  AEGEPFGLQSIKVISPDDPDGERILNIIGNGNIDRSVKHITPADIIASINYFFNLLHEVG 397

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
             +   +H+ +    +    L    + G++R    V+ R            A  +    I 
Sbjct: 398  TTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVKERMSIQDQNAITPQALINIRPVIA 457

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
             +      ++++ +               TN +  L+                       
Sbjct: 458  SLKEFFGSSQLSQF------------MDQTNPLAELT------------------HKRRL 487

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 488  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNEYGFIEAP 547

Query: 701  VPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
               +  E   V   ++ + A  +       A      +   A   V+    G        
Sbjct: 548  YRRVDPETGLVTGDIQYMTADEEDLYVVAQANMPLTEDGHFADEQVLCRFRGQNLSVEPS 607

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               Y  +  ++                      +  ++              +L    P 
Sbjct: 608  RVDYMDVSPKQVVSAATAC---------IPFLENDDSNRALMGANMQRQAVPLLQPDSPI 658

Query: 819  HGYNFE---------DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             G   E           +     +V       I I     +      G  +  +    V 
Sbjct: 659  VGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSGDLDRYKLQKYVR 718

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                   ++  II  G  V  G+IL    +      +     ++ A       +  D  +
Sbjct: 719  SNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAFMTWDGYNYEDAII 777

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
                 V   V    I       ++  +     E    +    DD    LD     R+   
Sbjct: 778  MSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLDDRGIIRIGAE 836

Query: 990  LCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +   + + G    K  T L+++  L+      +  +      +V    + +         
Sbjct: 837  VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDGI--------- 887

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    K+   + GD++ PGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP E
Sbjct: 888  ----ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEE 943

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D     D+  
Sbjct: 944  DMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIKVATPVFDGAREEDVW- 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                          A  E        A 
Sbjct: 1003 ----------------------------------------------ATIEE-------AG 1009

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D+  ++ LYDG TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1010 MDKDAKTRLYDGRTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKA 1069

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDD VGR + YE+IV G    + G PESF
Sbjct: 1070 QFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDTVGRVKAYEAIVKGESVPKAGVPESF 1129

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KE+QALG+ + + ++  +     +E  D
Sbjct: 1130 RVLIKELQALGMEVKMMSADDEEVEMKDEDDD 1161


>gi|170293424|gb|ACB12765.1| DNA-directed RNA polymerase [Bacillus caldolyticus]
          Length = 1076

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/949 (46%), Positives = 600/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  ++ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSTDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I++ ET E+  EAG +ID ++L  +     + + +              T    
Sbjct: 273 QRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL-------------QTYRPA 319

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +     D  +   ++  P D                          G   +N+  N    
Sbjct: 320 EGVVDGDISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  355 bits (912), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 147/459 (32%), Positives = 199/459 (43%), Gaps = 77/459 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 855

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 856  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1076


>gi|402363|gb|AAB00972.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 1193

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 603/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD------------------------Q 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +++++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ LD++G+F ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 596 FRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF
Sbjct: 656 PFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 259/1174 (22%), Positives = 440/1174 (37%), Gaps = 125/1174 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D +  
Sbjct: 155  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+ VGR 
Sbjct: 214  NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E +    +IL      K      + +G R++  
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYP 333

Query: 467  VGEMLKNQYRLGLLRM--------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             G +++++  L  +++        E+ I    ++   + +      +    +S       
Sbjct: 334  NGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLH 393

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                +   +H+ +    +    L    + G++R    V  R               +   
Sbjct: 394  GVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRP 453

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             I  +      ++++ +               TN +  L+                    
Sbjct: 454  VIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------HK 483

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQ 697
                 L       E   +    + +        +       I  + +  S   +      
Sbjct: 484  RRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFI 543

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                  +  E   V   ++ + A      +VA+    +   D     I           +
Sbjct: 544  ETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARL---DDEGAFIDDSIVARFRGEN 600

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             V     + +   +    V+         E   ++    G +     + L +        
Sbjct: 601  TVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGT 660

Query: 818  WHGY---NFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               Y       + +I +   +V      ++ +  +E +      G  +    +  V    
Sbjct: 661  GMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQ 720

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     ++         +  D  +   
Sbjct: 721  GTCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII--- 776

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 777  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIG 833

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +          +   
Sbjct: 834  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV--- 890

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 891  ---KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 947

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 948  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 1007

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1008 GMSRDAK----------------------------TVLYDG------------------- 1020

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GG 
Sbjct: 1021 -------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGH 1073

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
              GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+K
Sbjct: 1074 GFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIK 1133

Query: 1353 EMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            E+Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1134 ELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQAD 1167


>gi|170293430|gb|ACB12768.1| DNA-directed RNA polymerase [Geobacillus lituanicus]
          Length = 1076

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/949 (46%), Positives = 600/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I++ ET E+  EAG +ID ++L  +     + + +              T    
Sbjct: 273 QRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL-------------QTYRPA 319

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +     D  +   ++  P D                          G   +N+  N    
Sbjct: 320 EGVVDGDISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  355 bits (912), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 147/459 (32%), Positives = 199/459 (43%), Gaps = 77/459 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 855

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 856  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1076


>gi|319654860|ref|ZP_08008935.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. 2_A_57_CT2]
 gi|317393423|gb|EFV74186.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. 2_A_57_CT2]
          Length = 1187

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 604/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F 
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFH 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RL+          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEESKERDVTYSAPLRVKVRLV---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 105 ETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFS---GKLDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYIR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTESTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L G  +AE +V+ ETGEI  E G  +D ++L+ I  +  +DI      
Sbjct: 276 YKINKKLHIKNRLFGQKLAETLVDPETGEIIAEKGVTLDRRTLDRILPNLEKDIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     T+         + LL   ++  P +                         
Sbjct: 331 --------FKTVSLLGGVVDDEVLLQSIKIYAPNE------------------------- 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + V++I   DIIA I    +L +  G  DDID+LGNRR+RSVGE+
Sbjct: 358 DGEKVINVIGNAYVEEAVKNISPSDIIASISYFFNLLHSVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQAN+ L +DGSF +E V  R
Sbjct: 538 KVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQANALLGDDGSFLDEEVVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 598 FKGENTVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKF 767
           P VGTGME V  K SGAA++ K  GIVE V+A  + +R ++  D       +D YR++KF
Sbjct: 658 PRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIQNVDGQEVKGDLDKYRMLKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAFM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII  GAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRTGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/533 (33%), Positives = 256/533 (48%), Gaps = 78/533 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  +        ++  I+ VG  V  G+IL    +      +     +L A 
Sbjct: 707  GDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPS-MELGELALGRNVLVAF 765

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 766  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 825

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 826  LDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 884

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 885  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 928

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 929  GRHGNKGVISRILPEEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIH 988

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + S + D     D+                                              
Sbjct: 989  VASPVFDGAREEDVW--------------------------------------------- 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A  E        A +    +++LYDG +GEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 --ATIEE-------AGMARDAKTVLYDGRSGEPFDNRVSVGVMYMIKLAHMVDDKLHARS 1054

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YES
Sbjct: 1055 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYES 1114

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            IV G +  E G PESF VL+KE+Q+LG+ + + +   +    M ++ D +  +
Sbjct: 1115 IVKGENVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIE-MRDLEDEDDVQ 1166


>gi|307267200|ref|ZP_07548706.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306917779|gb|EFN48047.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 1239

 Score =  870 bits (2247), Expect = 0.0,   Method: Composition-based stats.
 Identities = 454/952 (47%), Positives = 612/952 (64%), Gaps = 64/952 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K  E++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G  
Sbjct: 11  TRMSFAKIDEVLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNL 60

Query: 73  MLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            LEFV Y  +  PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++
Sbjct: 61  ALEFVDYRLENNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W
Sbjct: 112 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E DS DI++VRIDR RKVP+T  L ALG  ++ +IL     +       D       
Sbjct: 169 LEYEEDSNDIVYVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD-------- 301
              L+   K       +  GE   +ES K L   L    K   +  +G            
Sbjct: 229 EEALIEIYK------RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKM 282

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I  + +L          I N 
Sbjct: 283 RIANLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLV--EGKVVKVIGNN 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        +DI +   P DVS+ ++ E++   L    +  D  +     +N   N
Sbjct: 341 T------------VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKN 386

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                  +HI K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 387 RMDELVPKHITKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLAR 446

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER +KER++  D++ + PQ+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR+
Sbjct: 447 LERVVKERMTIQDVNEITPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRV 506

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++ARVN YGFIE P
Sbjct: 507 SALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAP 566

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YR+V      VT+++VY++A EE+   IAQAN  LDE+  F  E V CR   E I VP  
Sbjct: 567 YRRVDKTTGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPT 626

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K EAP +GTG+E   
Sbjct: 627 EVDFMDVSPKQIVSVATSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKA 686

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK  G+VE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQR
Sbjct: 687 AVDSGVVVLAKNDGVVEKVAADKVVIRTKDGRRDE-------YNLLKFKRSNQGTCINQR 739

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GDEV++  +I DGPSTD G+LALG+N+LV FMPW GYN+ED++LISE +V +D  
Sbjct: 740 PIVNEGDEVKKGQVICDGPSTDHGELALGKNVLVGFMPWEGYNYEDAILISEELVRDDSL 799

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+T
Sbjct: 800 TSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVT 859

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 860 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  526 bits (1354), Expect = e-146,   Method: Composition-based stats.
 Identities = 263/1141 (23%), Positives = 426/1141 (37%), Gaps = 132/1141 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 120  EKGTFIINGAERVIVSQLVRSPGVYYEQQFDKFGKKLISATVIPNRGAWLEYEEDSNDIV 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A+S+   LFFD+ +YDL+ VGR K N +L L          +   +   K
Sbjct: 240  RPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALK--------MRIANLKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N   + +      +    +       MP 
Sbjct: 292  KIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVKVIGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG-VEMRD 560
            D+ +     +          L    +    ++ I    R+  L    + +          
Sbjct: 352  DVSSLNIKEAVNLSILKEI-LDNFSDEEAVINEI--KNRMDELVPKHITKDDIIATISYQ 408

Query: 561  VHPTH-YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++ TH  G I   +      +  V  L    +      +    R V +     DV  ++ 
Sbjct: 409  LNLTHGIGSIDDIDHLGNRRLRSVGELL---QNQFRIGLARLERVVKERMTIQDVNEITP 465

Query: 620  MEEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDFID 665
                N    +A       +S L +    T  L           +        R   +  D
Sbjct: 466  QNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGGLSRERAGFEVRD 525

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
                    I     P   N      L       +   +         T   +        
Sbjct: 526  VHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAPYRRVDKT---TGTVTDEIV 582

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             + A          A   +  +     +        +I  +   +    +    Q   V 
Sbjct: 583  YMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPTEVDFMDVSPKQIVSVA 642

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVF 839
                    +  A+              ++    P  G   E    +   +V    ++ V 
Sbjct: 643  TSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKAAVDSGVVVLAKNDGVV 702

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              +  ++   +   TK G  +    +          I++  I+  G EV  G ++    +
Sbjct: 703  EKVAADK---VVIRTKDGRRDEYNLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDGPS 759

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   + +L      +  +  D  L         V D  + + H  + +  +   
Sbjct: 760  T-DHGELALGKNVLVGFMPWEGYNYEDAILI----SEELVRDDSLTSIHIEEYDAEARDT 814

Query: 960  E---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LIS 1014
            +    E    +    +D    LD     R+   +   + + G    K  T L+++  L+ 
Sbjct: 815  KLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVTPKGETELTAEERLLR 874

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                 +  +      +V      + V               K+   + GD++PPGV ++V
Sbjct: 875  AIFGEKAREVRDTSLRVPHGESGIVV-------------DVKVYSRENGDELPPGVNQMV 921

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            +VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN+G
Sbjct: 922  RVFVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLQICLNPLGVPSRMNIG 981

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLG     LG +I + + D     DI  L +                        
Sbjct: 982  QVLEVHLGLVAKALGWQIATPVFDGATEEDIQELLAKSGFSPDGKVQL------------ 1029

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                 G++       GEPFD  VTVGY+
Sbjct: 1030 -----------------------------------YDGRT-------GEPFDNKVTVGYM 1047

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+
Sbjct: 1048 YMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEI 1107

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +     
Sbjct: 1108 LTVKSDDVSGRVKTYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDNQEIPLK 1167

Query: 1375 E 1375
            E
Sbjct: 1168 E 1168


>gi|221307919|ref|ZP_03589766.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312240|ref|ZP_03594045.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317174|ref|ZP_03598468.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221321437|ref|ZP_03602731.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767022|ref|NP_387988.2| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|321313778|ref|YP_004206065.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis BSn5]
 gi|239938700|sp|P37870|RPOB_BACSU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|225184649|emb|CAB11883.2| RNA polymerase (beta subunit) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|320020052|gb|ADV95038.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis BSn5]
          Length = 1193

 Score =  869 bits (2246), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 603/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD------------------------Q 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +++++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ LD++G+F ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 596 FRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF
Sbjct: 656 PFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 261/1174 (22%), Positives = 442/1174 (37%), Gaps = 125/1174 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D +  
Sbjct: 155  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+ VGR 
Sbjct: 214  NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E +    +IL      K      + +G R++  
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYP 333

Query: 467  VGEMLKNQYRLGLLRM--------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             G +++++  L  +++        E+ I    ++   + +      +    +S       
Sbjct: 334  NGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLH 393

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                +   +H+ +    +    L    + G++R    V  R               +   
Sbjct: 394  GVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRP 453

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             I  +      ++++ +               TN +  L+                    
Sbjct: 454  VIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------HK 483

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQ 697
                 L       E   +    + +        +       I  + +  S   +      
Sbjct: 484  RRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFI 543

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                  +  E   V   ++ + A      +VA+    +   D     I           +
Sbjct: 544  ETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARL---DDEGAFIDDSIVARFRGEN 600

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             V     + +   +    V+         E   ++    G +     + L +        
Sbjct: 601  TVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGT 660

Query: 818  WHGY---NFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               Y       + +I +   +V      ++ +  +E +      G  +    +  V    
Sbjct: 661  GMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQ 720

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     ++         +  D  +   
Sbjct: 721  GTCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII--- 776

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 777  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIG 833

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +          +   
Sbjct: 834  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV--- 890

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 891  ---KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 947

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 948  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 1007

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1008 GMSRDAK----------------------------TVLYDG------------------- 1020

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1021 -------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1073

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+K
Sbjct: 1074 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIK 1133

Query: 1353 EMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            E+Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1134 ELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQAD 1167


>gi|170293428|gb|ACB12767.1| DNA-directed RNA polymerase [Geobacillus thermoleovorans]
          Length = 1075

 Score =  869 bits (2245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/949 (46%), Positives = 600/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I++ ET E+  EAG +ID ++L  +     + + +              T    
Sbjct: 273 QRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL-------------QTYRPA 319

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +     D  +   ++  P D                          G   +N+  N    
Sbjct: 320 EGVVDGDISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  353 bits (907), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 147/458 (32%), Positives = 199/458 (43%), Gaps = 77/458 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 855

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 856  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGMARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1075


>gi|296333104|ref|ZP_06875558.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305672806|ref|YP_003864477.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296149720|gb|EFG90615.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411049|gb|ADM36167.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 1193

 Score =  869 bits (2245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 603/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLVGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD------------------------Q 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    +++++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ LD++G+F ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 596 FRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF
Sbjct: 656 PFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 262/1174 (22%), Positives = 442/1174 (37%), Gaps = 125/1174 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D V  
Sbjct: 155  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLVGE 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+ VGR 
Sbjct: 214  NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E +    +IL      K      + +G R++  
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYP 333

Query: 467  VGEMLKNQYRLGLLRM--------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             G +++++  L  +++        E+ I    ++   + +      +    +S       
Sbjct: 334  NGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLH 393

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                +   +H+ +    +    L    + G++R    V  R               +   
Sbjct: 394  GVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRP 453

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             I  +      ++++ +               TN +  L+                    
Sbjct: 454  VIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------HK 483

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQ 697
                 L       E   +    + +        +       I  + +  S   +      
Sbjct: 484  RRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFI 543

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                  +  E   V   ++ + A      +VA+    +   D     I           +
Sbjct: 544  ETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARL---DDEGAFIDDSIVARFRGEN 600

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             V     + +   +    V+         E   ++    G +     + L +        
Sbjct: 601  TVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGT 660

Query: 818  WHGY---NFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               Y       + +I +   +V      ++ +  +E +      G  +    +  V    
Sbjct: 661  GMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQ 720

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     ++         +  D  +   
Sbjct: 721  GTCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII--- 776

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 777  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIG 833

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +          +   
Sbjct: 834  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV--- 890

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 891  ---KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 947

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 948  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 1007

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1008 GMSRDAK----------------------------TVLYDG------------------- 1020

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1021 -------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1073

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+K
Sbjct: 1074 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIK 1133

Query: 1353 EMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            E+Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1134 ELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQAD 1167


>gi|205372077|ref|ZP_03224894.1| DNA-directed RNA polymerase subunit beta [Bacillus coahuilensis
           m4-4]
          Length = 1185

 Score =  869 bits (2245), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 602/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F 
Sbjct: 1   MTGQLVQYGRHRQRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFH 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+   RD+T++ PL++ +RL+          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYPVDESKERDVTFSAPLRVKVRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  ++ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGTDQEIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +          L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTESIEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L G  +AE I + ETGEI  E G  +D ++L+ I     + I      
Sbjct: 273 YKINKKLHIKNRLFGQVLAETIADPETGEILAERGTTLDRRNLDRIIPYLEKGIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     T+         + ++   ++  P +                         
Sbjct: 328 --------FKTVHQGGGVIEDETVVQSIKIFAPNE------------------------- 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G  ++N+  N    +DV++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 355 DGEKEINVISNAYVTEDVKNISAADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  ++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTATITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR V    GKVT+ + YL+A EE+N  +AQAN+ L +DGSF +E V  R
Sbjct: 535 KVNRFGFIETPYRHVDPETGKVTDRIDYLTADEEDNYVVAQANARLGDDGSFLDEEVVVR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +  RE++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+
Sbjct: 595 FRGENTVAKRERVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKF 767
           P VGTGME V A+ SGAA++ K+ GIVE+V+A ++ +R +E  D       +D Y++ KF
Sbjct: 655 PIVGTGMEHVSARDSGAAVICKQRGIVERVEAKQVWVRRIEEIDGKKVKGDIDKYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V  GD V + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVAEGDLVEKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGEGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 177/576 (30%), Positives = 260/576 (45%), Gaps = 80/576 (13%)

Query: 816  MPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M         + +I ++  +V       + +   E +      G  +  +    +     
Sbjct: 661  MEHVSARDSGAAVICKQRGIVERVEAKQVWVRRIEEIDGKKVKGDIDKYKMQKFIRSNQG 720

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+  G  V  G+IL    +   +  +     ++         +  D  +    
Sbjct: 721  TCYNQRPIVAEGDLVEKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMSER 779

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      +  +
Sbjct: 780  LVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAEVKDGD 839

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L G+    G         L   +  E  R    +      +V    E +          
Sbjct: 840  LLVGKVTPKGVTELTAEERLLHAIFGEKAR----EVRDTSLRVPHGGEGI---------- 885

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                   K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP ED
Sbjct: 886  ---ILDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEED 942

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+   
Sbjct: 943  MPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHVASPVFDGANEEDVWST 1002

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                   T ++DG               
Sbjct: 1003 IEEAGMARDAK----------------------------TVLYDG--------------- 1019

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
                        TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1020 -----------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQ 1068

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1069 FGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFK 1128

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            VL+KE+Q+LG+ + + +        M ++ D  + +
Sbjct: 1129 VLIKELQSLGMDVKILSGDETEIE-MRDLEDEEEHQ 1163


>gi|289579153|ref|YP_003477780.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter
           italicus Ab9]
 gi|289528866|gb|ADD03218.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           italicus Ab9]
          Length = 1234

 Score =  869 bits (2244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 455/952 (47%), Positives = 612/952 (64%), Gaps = 64/952 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K  E++ +PDLIEVQK SY  FL           EGL+  F+ + PI +F+G  
Sbjct: 11  TRMSFAKIDEVLQMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNL 60

Query: 73  MLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            LEFV Y  +  PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++
Sbjct: 61  ALEFVDYRLENTPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W
Sbjct: 112 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKRLISATVIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E DS D+++VRIDR RKVP+T  L ALG  S+ +IL     +       D       
Sbjct: 169 LEYEEDSNDVVYVRIDRTRKVPITVLLRALGYSSDIQILDLLGEEEKLKATLDKDTTKSE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD-------- 301
              L+   K       +  GE   +ES K L   L    K   +  +G            
Sbjct: 229 EEALIEIYK------RLRPGEPPTVESAKSLLYTLFFDAKRYDLAKVGRYKFNKKLALKA 282

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I ++ +L          I N 
Sbjct: 283 RIANLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINEVEVLV--EGKVVKVIGNN 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        +DI +   P DVS+ ++ E++   L    +  D  +     +N   N
Sbjct: 341 T------------VDINKYPMPYDVSSLNIKEAV--NLSVLKEILDNFSDEEAVINEIKN 386

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                  +HI K+DIIA +   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 387 RIDELIPKHITKDDIIATVNYQLNLAHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLAR 446

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER +KER++  D++ + PQ+LIN +PVV+A+ EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 447 LERVVKERMTIQDVNEITPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLSELTHKRRV 506

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++ARVN YGFIE P
Sbjct: 507 SALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAP 566

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      VT+++VY++A EE+   IAQAN  LDE+  F  + V CR   E I VP  
Sbjct: 567 YRKVDKTTGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINDKVVCRLKEEIIAVPPT 626

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DF+D SPKQ+VS+A SLIPFLENDD+NR LMG NMQRQAVPL+K EAP +GTG+E   
Sbjct: 627 EVDFMDVSPKQIVSVATSLIPFLENDDANRALMGSNMQRQAVPLIKTEAPIIGTGIEYKA 686

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK  G+VE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQR
Sbjct: 687 AVDSGVVVLAKNDGVVEKVTADKVVIRTKDGRKDE-------YNLLKFKRSNQGTCINQR 739

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GDEV++  +I DGPSTD G+LALG+N+LV FMPW GYN+ED++LISE +V +D  
Sbjct: 740 PIVNEGDEVKKGQVICDGPSTDHGELALGKNVLVGFMPWEGYNYEDAILISEELVRDDSL 799

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+T
Sbjct: 800 TSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVT 859

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 860 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  526 bits (1355), Expect = e-146,   Method: Composition-based stats.
 Identities = 267/1154 (23%), Positives = 442/1154 (38%), Gaps = 138/1154 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          ++ 
Sbjct: 120  EKGTFIINGAERVIVSQLVRSPGVYYEQQFDKFGKRLISATVIPNRGAWLEYEEDSNDVV 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRALGYSSDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A+S+   LFFD+ +YDL+ VGR K N +L L          +   +   K
Sbjct: 240  RPGEPPTVESAKSLLYTLFFDAKRYDLAKVGRYKFNKKLALKA--------RIANLKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N+  + +      +    +       MP 
Sbjct: 292  KIVNPVTGEILVEEGEKISKEKAEEIQNCGINEVEVLVEGKVVKVIGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARARAG-VEM 558
            D+ +       + E    S L ++ ++ +    + +    R+  L    + +        
Sbjct: 352  DVSSLN-----IKEAVNLSVLKEILDNFSDEEAVINEIKNRIDELIPKHITKDDIIATVN 406

Query: 559  RDVHPTH-YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
              ++  H  G I   +      +  V  L    +      +    R V +     DV  +
Sbjct: 407  YQLNLAHGIGSIDDIDHLGNRRLRSVGELL---QNQFRIGLARLERVVKERMTIQDVNEI 463

Query: 618  SAMEEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDF 663
            +     N    +A       +S L +    T  L           +        R   + 
Sbjct: 464  TPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLSELTHKRRVSALGPGGLSRERAGFEV 523

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D        I     P   N      L       +   +         T   +      
Sbjct: 524  RDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAPYRKVDKT---TGTVTDE 580

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               + A          A   +  +     D        +I  +   +    +    Q   
Sbjct: 581  IVYMTADEEDEYIIAQANEPLDENNRFINDKVVCRLKEEIIAVPPTEVDFMDVSPKQIVS 640

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SED 837
            V         +  A+              ++    P  G   E    +   +V    ++ 
Sbjct: 641  VATSLIPFLENDDANRALMGSNMQRQAVPLIKTEAPIIGTGIEYKAAVDSGVVVLAKNDG 700

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            V   +  ++   +   TK G ++    +          I++  I+  G EV  G ++   
Sbjct: 701  VVEKVTADK---VVIRTKDGRKDEYNLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDG 757

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
             +      +   + +L      +  +  D  L         V D  + + H  + +  + 
Sbjct: 758  PST-DHGELALGKNVLVGFMPWEGYNYEDAILI----SEELVRDDSLTSIHIEEYDAEAR 812

Query: 958  SVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--L 1012
              +    E    +    +D    LD     R+   +   + + G    K  T L+++  L
Sbjct: 813  DTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVTPKGETELTAEERL 872

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +      +  +      +V      + V               K+   + GD++PPGV +
Sbjct: 873  LRAIFGEKAREVRDTSLRVPHGESGIVV-------------DVKVYSRENGDELPPGVNQ 919

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN
Sbjct: 920  MVRVFVAQKRKIAVGDKMAGRHGNKGVISRILPIEDMPFLPDGTPLQICLNPLGVPSRMN 979

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLG     LG +I + + D     DI  L +               S +  D 
Sbjct: 980  IGQVLEVHLGLVAKALGWEIITPVFDGATEDDIQELLTK--------------SGFSPDG 1025

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             +++                                   G++       GEPFD  VTVG
Sbjct: 1026 KVQL---------------------------------YDGRT-------GEPFDNKVTVG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQ
Sbjct: 1046 YMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQ 1105

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +   
Sbjct: 1106 EILTVKSDDVAGRVKTYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDNQEIP 1165

Query: 1373 KM--EEIPDFNKCE 1384
                EE  D +  +
Sbjct: 1166 LKEFEEDDDSDVPD 1179


>gi|170293438|gb|ACB12772.1| DNA-directed RNA polymerase [Geobacillus thermoglucosidasius]
          Length = 1075

 Score =  869 bits (2244), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/949 (46%), Positives = 597/949 (62%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYKWFL----------DEGLREMFREISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  ++  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYSEKVDK---NGKRGFSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   IE+ K L        K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTIENAKNLLISRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE +V+ ETGE+  E G ++D ++L  I       + +                   
Sbjct: 273 QRLAETLVDPETGEVIAEKGTIVDRRTLNRILPYLENGVGL-------------RVHKPF 319

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                ++  L   ++  P D                          G   +N+  N    
Sbjct: 320 GGVVEEEIALQSIKIYAPNDP------------------------DGEQVINVISNGYIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 536 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V A+ S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSARDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 146/458 (31%), Positives = 202/458 (44%), Gaps = 77/458 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 867

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 868  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGMPRDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1075


>gi|167039512|ref|YP_001662497.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter sp.
           X514]
 gi|256752779|ref|ZP_05493624.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300915237|ref|ZP_07132552.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter sp.
           X561]
 gi|307725161|ref|YP_003904912.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacter sp.
           X513]
 gi|254765314|sp|B0K5G8|RPOB_THEPX RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|166853752|gb|ABY92161.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter sp.
           X514]
 gi|256748340|gb|EEU61399.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300888961|gb|EFK84108.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter sp.
           X561]
 gi|307582222|gb|ADN55621.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacter sp.
           X513]
          Length = 1238

 Score =  868 bits (2243), Expect = 0.0,   Method: Composition-based stats.
 Identities = 453/952 (47%), Positives = 610/952 (64%), Gaps = 64/952 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K  E++ +PDLIEVQK SY  FL           EGL+  F+ + PI +F+G  
Sbjct: 11  TRMSFAKIDEVLQMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNL 60

Query: 73  MLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            LEFV Y  +  PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++
Sbjct: 61  ALEFVDYRLENNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W
Sbjct: 112 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E DS DI++VRIDR RKVP+T  L ALG  ++ +IL     +       D       
Sbjct: 169 LEYEEDSNDIVYVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD-------- 301
              L+   K       +  GE   +ES K L   L    K   +  +G            
Sbjct: 229 EEALIEIYK------RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKA 282

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I  + +L          I N 
Sbjct: 283 RIANLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLV--EGKVVKVIGNN 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        +DI +   P DVS+ ++ E++   L    +  D  +     +N   N
Sbjct: 341 T------------VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKN 386

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                  +HI K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 387 RMDELVPKHITKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLAR 446

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER +KER++  D++ + PQ+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR+
Sbjct: 447 LERVVKERMTIQDVNEITPQNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRV 506

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SLT++ARVN YGFIE P
Sbjct: 507 SALGPGGLSRERAGFEVRDVHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAP 566

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YR+V      VT+++VY++A EE+   IAQAN  LDE+  F  E V CR   E I VP  
Sbjct: 567 YRRVDKTTGTVTDEIVYMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPT 626

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K EAP +GTG+E   
Sbjct: 627 EVDFMDVSPKQIVSVATSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKA 686

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK  G+VE+V A ++VIR+ +G  D        Y L+KF+RSNQ TC+NQR
Sbjct: 687 AVDSGVVVLAKNDGVVEKVAADKVVIRTKDGRRDE-------YNLLKFKRSNQGTCINQR 739

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GDEV++  +I DGPSTD G+LALG+N+LV FM W GYN+ED++LISE +V +D  
Sbjct: 740 PIVNEGDEVKKGQVICDGPSTDHGELALGKNVLVGFMLWEGYNYEDAILISEELVRDDSL 799

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+T
Sbjct: 800 TSIHIEEYDAEARDTKLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVT 859

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++++R   D
Sbjct: 860 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVYSRENGD 911



 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 265/1141 (23%), Positives = 432/1141 (37%), Gaps = 132/1141 (11%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSD---CLCGLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 120  EKGTFIINGAERVIVSQLVRSPGVYYEQQFDKFGKKLISATVIPNRGAWLEYEEDSNDIV 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      I  +D +     ++ TL  D  K  ++AL++IY+ +
Sbjct: 180  YVRIDRTRKVPITVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A+S+   LFFD+ +YDL+ VGR K N +L L          +   +   K
Sbjct: 240  RPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKA--------RIANLKSAK 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V+   G+  +++ + +   +   +     N   + +      +    +       MP 
Sbjct: 292  KIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVKVIGNNTVDINKYPMPY 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG-VEMRD 560
            D+ +     +          L    +    ++ I    R+  L    + +          
Sbjct: 352  DVSSLNIKEAVNLSILKEI-LDNFSDEEAVINEI--KNRMDELVPKHITKDDIIATISYQ 408

Query: 561  VHPTH-YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++ TH  G I   +      +  V  L    +      +    R V +     DV  ++ 
Sbjct: 409  LNLTHGIGSIDDIDHLGNRRLRSVGELL---QNQFRIGLARLERVVKERMTIQDVNEITP 465

Query: 620  MEEENR--YIA-----QANSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDFID 665
                N    +A       +S L +    T  L           +        R   +  D
Sbjct: 466  QNLINIRPVVAAIREFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGGLSRERAGFEVRD 525

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
                    I     P   N      L       +   +         T   +        
Sbjct: 526  VHYSHYGRICPIETPEGPNIGLIGSLTTYARVNEYGFIEAPYRRVDKT---TGTVTDEIV 582

Query: 726  AIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             + A          A   +  +     +        +I  +   +    +    Q   V 
Sbjct: 583  YMTADEEDEYIIAQANEPLDENNRFINEKVVCRLKEEIIAVPPTEVDFMDVSPKQIVSVA 642

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVF 839
                    +  A+              ++    P  G   E    +   +V    ++ V 
Sbjct: 643  TSMIPFLENDDANRALMGSNMQRQAVPLIKPEAPIIGTGIEYKAAVDSGVVVLAKNDGVV 702

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              +  ++   +   TK G  +    +          I++  I+  G EV  G ++    +
Sbjct: 703  EKVAADK---VVIRTKDGRRDEYNLLKFKRSNQGTCINQRPIVNEGDEVKKGQVICDGPS 759

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   + +L      +  +  D  L         V D  + + H  + +  +   
Sbjct: 760  T-DHGELALGKNVLVGFMLWEGYNYEDAILI----SEELVRDDSLTSIHIEEYDAEARDT 814

Query: 960  E---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LIS 1014
            +    E    +    +D    LD     R+   +   + + G    K  T L+++  L+ 
Sbjct: 815  KLGPEEITREIPNVGEDALKDLDERGIIRIGAEVTAGDILVGKVTPKGETELTAEERLLR 874

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                 +  +      +V      + V               K+   + GD++PPGV ++V
Sbjct: 875  AIFGEKAREVRDTSLRVPHGESGIVV-------------DVKVYSRENGDELPPGVNQMV 921

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            +VFVA KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+ I LNPLGVPSRMN+G
Sbjct: 922  RVFVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLQICLNPLGVPSRMNIG 981

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLG     LG +I + + D     DI  L +               S +  D  +
Sbjct: 982  QVLEVHLGLVAKALGWQIATPVFDGATEEDIQELLAK--------------SGFSPDGKV 1027

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            ++                                   G++       GEPFD  VTVGY+
Sbjct: 1028 QL---------------------------------YDGRT-------GEPFDNKVTVGYM 1047

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+
Sbjct: 1048 YMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEI 1107

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDDV GR + YE+IV G +  E G PESF VLVKE+Q+L L + +     +     
Sbjct: 1108 LTVKSDDVSGRVKTYEAIVKGENIPEPGIPESFKVLVKELQSLALDVKVITEDNQEIPLK 1167

Query: 1375 E 1375
            E
Sbjct: 1168 E 1168


>gi|308171998|ref|YP_003918703.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens DSM 7]
 gi|307604862|emb|CBI41233.1| RNA polymerase (beta subunit) [Bacillus amyloliquefaciens DSM 7]
 gi|328551808|gb|AEB22300.1| DNA-directed RNA polymerase subunit beta [Bacillus
           amyloliquefaciens TA208]
          Length = 1193

 Score =  868 bits (2243), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 602/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      + +L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVMLQSIKIYAPTD------------------------A 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + +++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L +DGSF ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANAKLSDDGSFLDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 596 FRGENTVVARNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF
Sbjct: 656 PIVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           VN GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 836 VNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 183/573 (31%), Positives = 270/573 (47%), Gaps = 71/573 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V      ++ +  +E +      G  +    +  V     
Sbjct: 662  MEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKFVRSNQG 721

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     ++         +  D  +    
Sbjct: 722  TCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII---- 776

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 777  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIGA 834

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +          +    
Sbjct: 835  EVNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV---- 890

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L 
Sbjct: 891  --KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLP 948

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+        
Sbjct: 949  DGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAG 1008

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1009 MSRDAK----------------------------TVLYDG-------------------- 1020

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1021 ------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1074

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE
Sbjct: 1075 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKE 1134

Query: 1354 MQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            +Q+LG+ + + +S  +      +E+  D  + +
Sbjct: 1135 LQSLGMDVKILSSDEEEIEMRDLEDEEDAKQAD 1167


>gi|163938110|ref|YP_001642994.1| DNA-directed RNA polymerase subunit beta [Bacillus
           weihenstephanensis KBAB4]
 gi|226699370|sp|A9VP69|RPOB_BACWK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|163860307|gb|ABY41366.1| DNA-directed RNA polymerase, beta subunit [Bacillus
           weihenstephanensis KBAB4]
          Length = 1177

 Score =  868 bits (2242), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G V+D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               K A      V    ++ +                 Y   +
Sbjct: 328 -------------------FKTAKPMGGVVAGDVELQSI--------------KIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   D++HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERSINVIGNANITRDIKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E G F +E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLINPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K+ G+VE+V+A  + +R  V+ D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKQPGVVERVEAREVWVRRYVDVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD+V + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 253/1167 (21%), Positives = 428/1167 (36%), Gaps = 120/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            K+N +L++               P+    +  E  +   + L  +               
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIGFKTAKP 333

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G++     ++     E   +      + +       I    +++++  FF    
Sbjct: 334  MGGVVAGDVELQSIKIYAPESEGE-RSINVIGNANITRDIKHITPGDILASISYFFNL-- 390

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            L ++ +  +         R          R       R V      R+   +T+      
Sbjct: 391  LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITPQA 446

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++     A +  +       + +       ++ +                         
Sbjct: 447  LINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KRRL 485

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 486  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIETP 545

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDPSTSG 758
               +  E   V   ++ + A      +VA+    + +V       ++    G+   +   
Sbjct: 546  YRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVARFRGENIVTNKE 605

Query: 759  VDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               Y  +  ++  S    C+         D+  R  + A+     +  +     ++   M
Sbjct: 606  RIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLINPESPIVGTGM 661

Query: 817  PWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       + +I ++  +V       + +  +  +   T  G  +  +    +      
Sbjct: 662  EYVSAKDSGAAVICKQPGVVERVEAREVWVRRYVDVDGQTVKGDLDRYKMQKFIRSNQGT 721

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+ VG +V  G+IL    +      +     +L         +  D  +     
Sbjct: 722  CYNQRPIVSVGDQVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII----- 775

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G  
Sbjct: 776  MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGAE 834

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G     K T      ++   R     F  +  +V+     +                
Sbjct: 835  VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------LD 888

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L D
Sbjct: 889  VKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLPD 948

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+         
Sbjct: 949  GTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAGM 1008

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1009 ANDAK----------------------------TILYDG--------------------- 1019

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1020 -----RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 1074

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+KE+
Sbjct: 1075 GEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIKEL 1134

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFN 1381
            Q+LG+ + + +         +   D +
Sbjct: 1135 QSLGMDVKMMSINDTEIEMRDTEDDDD 1161


>gi|166162242|gb|ABY83465.1| DNA-directed RNA polymerase [Geobacillus kaustophilus]
          Length = 1085

 Score =  867 bits (2241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/949 (46%), Positives = 599/949 (63%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 6   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLE 55

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 56  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 106

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 107 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 163

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 164 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 223

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 224 I------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 277

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I++ ET E+  EAG +ID ++L  +     + + +          Y     V D
Sbjct: 278 QRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL--------QTYRPAEGVVD 329

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 D  +   ++  P D                          G   +N+  N    
Sbjct: 330 G-----DISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIA 360

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 361 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 420

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+   D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 421 VRERMPIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 480

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDV  +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V
Sbjct: 481 PGGLTRERAGFEVRDVQYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRV 540

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D+
Sbjct: 541 DPETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDY 600

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 601 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDS 660

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 661 GAAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 720

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 721 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 780

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 781 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 840

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 841 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 889



 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 148/461 (32%), Positives = 201/461 (43%), Gaps = 77/461 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 695  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 753

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 754  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 813

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 814  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 860

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 861  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 916

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 917  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 976

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 977  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1008

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1009 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1042

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L+
Sbjct: 1043 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLK 1083


>gi|328958739|ref|YP_004376125.1| DNA-directed RNA polymerase subunit beta [Carnobacterium sp. 17-4]
 gi|328675063|gb|AEB31109.1| DNA-directed RNA polymerase subunit beta [Carnobacterium sp. 17-4]
          Length = 1188

 Score =  867 bits (2241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 592/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  FK
Sbjct: 1   MAGHLVNYGKHRTRRSFSRIHEVLELPNLIEIQTDSYQWFL----------DEGLREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF  Y+   PK+ V++    D  Y+ P+ + LRLI          K
Sbjct: 51  DISPIDDFAGNLSLEFTDYQLQEPKYTVEEARSHDANYSAPIYVKLRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++ GD PLMT+ GTFVI G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ESGEVKEQEVFFGDFPLMTEMGTFVINGAERVIVSQLVRSPGVYFH---GKLDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S++ IL  F       
Sbjct: 159 GSTLIPNRGAWLEFETDAKDLSYVRIDRTRKIPLTVLVRALGFGSDDQILEIFGDNESLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 LTMEKD-LHKNAGDSRTEEALKDVYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +E+G  +D   ++++              
Sbjct: 278 YKVNKKLNLVTRLFNQTLAETLVDPETGEIIVESGTFLDRDQIDKL------------TP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N+         +D +   +   L + +V    D                         
Sbjct: 326 YLNDGLNSVTYYPSDDSVVPEPVELQVVKVFSQRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +NM  N    D+ ++    DI+A +    +L+ G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --ERVVNMIGNKVIADETKNATPADILASMSYFFNLQEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D+ +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDMATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V      VT+ + YL+A EE+N  +AQAN+ L+EDG+F  ++V  R
Sbjct: 540 KVNKFGFIETPYRRVNRETGLVTDQIDYLTADEEDNYVVAQANAPLNEDGTFANDIVLAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + VP  ++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  + 
Sbjct: 600 YVEENLEVPISRVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIHPQG 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME V A+ SGAA++ K  GIVE VDA +I +R   G L+        Y + KF+
Sbjct: 660 PLVGTGMEHVAARDSGAALICKNDGIVEYVDADQIRVRQENGALNK-------YAVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  TC NQRP+V+ GD V + +I+ADG S + G++ALG+N LVAFM W GYN+ED+++
Sbjct: 713 RSNSGTCYNQRPIVEKGDRVEKGEILADGSSMENGEMALGQNPLVAFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEEITR++PNV ++ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEITRELPNVGDDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  GTV DV+IF R 
Sbjct: 833 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGTVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 267/1085 (24%), Positives = 397/1085 (36%), Gaps = 185/1085 (17%)

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            S+ + + I   +        ++      +   ++AL D+Y  +RPG+  T   + S+   
Sbjct: 203  SDDQILEIFGDNESLRLTMEKDLHKNAGDSRTEEALKDVYERLRPGEPKTADSSRSLLTA 262

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTP--------------------DDVRHIRKEDIIA 438
             FFD  +YDL+ VGR K+N +LNL T                     +    + ++ I  
Sbjct: 263  RFFDPKRYDLANVGRYKVNKKLNLVTRLFNQTLAETLVDPETGEIIVESGTFLDRDQIDK 322

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   L D  N        D++    V      + +Q      R+   I  ++ + +  + 
Sbjct: 323  LTPYLNDGLNSVTYYPSDDSVVPEPVELQVVKVFSQRD--PERVVNMIGNKVIADETKNA 380

Query: 499  MPQD----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             P D    +     +   +        L                R   +  +  V    +
Sbjct: 381  TPADILASMSYFFNLQEGIGNVDDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMS 440

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK---------- 604
              +M  V P     I P   S     G         + N  G +    R           
Sbjct: 441  IQDMATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTR 500

Query: 605  ------VCDGKVTNDVVYLSAMEEENRYIAQANS--SLDEDGSFTEELVFCRCAGEEILV 656
                  V D   ++          E   I   NS  S  +   F       R    E  +
Sbjct: 501  DRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVNRETGL 560

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              ++ID++ A  +    +A +  P   N+D          +     L    +      + 
Sbjct: 561  VTDQIDYLTADEEDNYVVAQANAPL--NEDGTFANDIVLARYVEENLEVPISRVDYMDVS 618

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                     A+       +E  D+ R ++ +                    QR       
Sbjct: 619  PKQV----VAVATACIPFLENDDSNRALMGAN------------------MQRQAVPLIH 656

Query: 777  NQRPLVKVG-DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV  G + V   D  A     + G +       +     +G        +++  V 
Sbjct: 657  PQGPLVGTGMEHVAARDSGAALICKNDGIVEYVDADQIRVRQENG-------ALNKYAV- 708

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                            R +  G     R                 I+  G  V  G+IL 
Sbjct: 709  -------------TKFRRSNSGTCYNQRP----------------IVEKGDRVEKGEILA 739

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
               +      M   +  L A    +  +  D  +     V   V           +  + 
Sbjct: 740  DGSS-MENGEMALGQNPLVAFMTWEGYNYEDAIIMSERLVKDDVYTSIHIEEFESEARDT 798

Query: 956  SISVEREQIELLA------RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             +  E    EL        +D  DE  I+      +  ++L G+    G         L 
Sbjct: 799  KLGPEEITRELPNVGDDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLL 857

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              +  E  R                 E                   KI   + GD++ PG
Sbjct: 858  HAIFGEKAR-----------------EVRDTSLRVPHGGGGTVHDVKIFTREAGDELSPG 900

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V  +V+V++  KR I  GDKMAGRHGNKG+VS I+P EDMPF+ DGTPVDI+LNPLGVPS
Sbjct: 901  VNMLVRVYIVQKRKINEGDKMAGRHGNKGVVSLIMPEEDMPFMPDGTPVDIMLNPLGVPS 960

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E H+G A   LG  I + + D  ++ D                         
Sbjct: 961  RMNIGQVLELHIGMAARQLGIHIATPVFDGASDED------------------------- 995

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                                V+D   E         A +    +++LYDG TGEPFD  +
Sbjct: 996  --------------------VWDTVKE---------AGMAADAKTVLYDGRTGEPFDNRI 1026

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            +VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1027 SVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1086

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL + + N   +
Sbjct: 1087 TLQEILTYKSDDVVGRVKTYEAIVKGEKIPKPGVPESFRVLVKELQSLGLDMKVLNENDE 1146

Query: 1370 NSAKM 1374
                 
Sbjct: 1147 AIELR 1151


>gi|329925591|ref|ZP_08280432.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp. HGF5]
 gi|328939720|gb|EGG36062.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp. HGF5]
          Length = 1181

 Score =  867 bits (2241), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/967 (46%), Positives = 606/967 (62%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q+ SY+ FL           EGL+  F+
Sbjct: 1   MAGHLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYEWFL----------EEGLREMFQ 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 50  DISPIQDFTGNLVLEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  Y
Sbjct: 101 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKTTY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 158 TATVIPNRGAWLELEMDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIQ 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 218 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLENAKSLLVARFFDPKRYDLANVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++ +TGEI  EAG  +D + L+EI     + +      
Sbjct: 272 YKINKKLHIKNRLFNQRLAESLIDIDTGEIVAEAGQTVDRRLLDEIMPYLEKSVG----- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   +N  VT    D +D  L    V  P +                         
Sbjct: 327 -------FKNYHVTGGVMDSEDIPLQTIDVFSPIE----------------------DGK 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N     +    V+HI + DII+ I   +DL +G G  DDID+LGNRR+RSVGE+
Sbjct: 358 VVKIIAN----ANIDKSVKHITQADIISSISYFIDLLHGIGNTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FA
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V     KVT+ + YL+A EE+N  +AQAN+ L+EDG+F +E+V  R
Sbjct: 534 RINEYGFIEAPYRWVDPKTSKVTDQIDYLTADEEDNYIVAQANAELNEDGTFADEMVIVR 593

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P +++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 594 YNKQSDNILPMPSDRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 653

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRL 764
            +AP VGTGME   AK SG  IV+K  GI+E+  A  I +R VE  D       +  Y+L
Sbjct: 654 PKAPLVGTGMEHKSAKDSGVCIVSKYDGIIERSSANEIWLRRVENIDGQEVKGDIVKYKL 713

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+VK GD +++ DI+ADGPST++G+LALGRN++VAFM W GYN+E
Sbjct: 714 HKFMRSNQGTCINQRPIVKRGDVIKKGDILADGPSTEMGELALGRNVVVAFMTWEGYNYE 773

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LKN+DE GII +
Sbjct: 774 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDERGIIRI 833

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G +VDV++
Sbjct: 834 GAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGSDGIIVDVKV 893

Query: 945 FNRHGID 951
           F R   D
Sbjct: 894 FTRENGD 900



 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/529 (35%), Positives = 267/529 (50%), Gaps = 68/529 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  I+  G  +  GDIL    + +    +     ++ A 
Sbjct: 706  GDIVKYKLHKFMRSNQGTCINQRPIVKRGDVIKKGDILADGPSTE-MGELALGRNVVVAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 765  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 819

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 820  EALKNLDER-GIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 878

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 879  RVPHGSDGIIVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 932

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + S +
Sbjct: 933  KGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVASPV 992

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +  D                                             VFD    
Sbjct: 993  FDGASEYD---------------------------------------------VFD---- 1003

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G+++LYDG TGE F+R VTVG ++M+KL HMV DK++ARSTG YS
Sbjct: 1004 -----TMEEAGMQRNGKTVLYDGRTGERFEREVTVGVMHMIKLAHMVDDKIHARSTGPYS 1058

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1059 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1118

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +  E G PESF VL+KE+Q+LG+ + + +   +     E +  D  + +
Sbjct: 1119 NVPEPGVPESFKVLIKELQSLGMDVKILSENEEEIEMKELDDEDDAQGD 1167


>gi|163791691|ref|ZP_02186085.1| DNA-directed RNA polymerase subunit beta [Carnobacterium sp. AT7]
 gi|159873039|gb|EDP67149.1| DNA-directed RNA polymerase subunit beta [Carnobacterium sp. AT7]
          Length = 1188

 Score =  867 bits (2240), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  FK
Sbjct: 1   MAGHLVNYGKHRTRRSFSRIHEVLELPNLIEIQTDSYQWFL----------DEGLREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF  Y+   PK+ V++    D  Y+ P+ + LRLI          K
Sbjct: 51  DISPIDDFAGNLSLEFTDYQLQEPKYTVEEARSHDANYSAPIYVKLRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++ GD PLMT+ GTFVI G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ESGEVKEQEVFFGDFPLMTEMGTFVINGAERVIVSQLVRSPGVYFH---GKLDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S++ IL  F       
Sbjct: 159 GSTLIPNRGAWLEFETDAKDLSYVRIDRTRKIPLTVLVRALGFGSDDQILEIFGDNESLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 LTMEKD-LHKNASDSRTEEALKDVYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG  +D   + ++              
Sbjct: 278 YKVNKKLNLATRLFNQTLAETLVDPETGEIIVEAGTFLDRDQMNKL------------TP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +           ++ +   +   L + +V    D                         
Sbjct: 326 YLTAGLNSVTYYPSEDSVVPEPVELQVVKVFSQKDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +NM  N    D+ ++    DI+A +    +L+ G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --ERVVNMIGNKIIADETKNATPADILASMSYFFNLQEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D+ +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDMATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V      VT+ + YL+A EE+N  +AQAN+ L+EDG+FT ++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGVVTDQIDYLTADEEDNYVVAQANAPLNEDGTFTNDIVLAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + VP  ++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  + 
Sbjct: 600 YVEENLEVPISRVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIHPQG 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME V A+ SGAA++ K  GIVE VDA  I +R   G L+        Y + KF+
Sbjct: 660 PLVGTGMEHVAARDSGAALICKNDGIVEYVDANEIRVRQENGALNK-------YAVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  TC NQRP+V+ GD V + +I+ADG S + G++ALG+N LVAFM W GYN+ED+++
Sbjct: 713 RSNSGTCYNQRPIVEKGDRVEKGEILADGSSMENGEMALGQNPLVAFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEEITR++PNV ++ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEITRELPNVGDDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  GTV DV+IF R 
Sbjct: 833 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGTVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 266/1089 (24%), Positives = 403/1089 (37%), Gaps = 193/1089 (17%)

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            S+ + + I   +        ++      +   ++AL D+Y  +RPG+  T   + S+   
Sbjct: 203  SDDQILEIFGDNESLRLTMEKDLHKNASDSRTEEALKDVYERLRPGEPKTADSSRSLLTA 262

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTP--------------------DDVRHIRKEDIIA 438
             FFD  +YDL+ VGR K+N +LNL T                     +    + ++ +  
Sbjct: 263  RFFDPKRYDLANVGRYKVNKKLNLATRLFNQTLAETLVDPETGEIIVEAGTFLDRDQMNK 322

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   L    N        D++    V      + +Q      R+   I  +I + +  + 
Sbjct: 323  LTPYLTAGLNSVTYYPSEDSVVPEPVELQVVKVFSQ--KDPERVVNMIGNKIIADETKNA 380

Query: 499  MPQD----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             P D    +     +   +        L                R   +  +  V    +
Sbjct: 381  TPADILASMSYFFNLQEGIGNVDDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMS 440

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK---------- 604
              +M  V P     I P   S     G         + N  G +    R           
Sbjct: 441  IQDMATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTR 500

Query: 605  ------VCDGKVTNDVVYLSAMEEENRYIAQANS--SLDEDGSFTEELVFCRCAGEEILV 656
                  V D   ++          E   I   NS  S  +   F       R    E  V
Sbjct: 501  DRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDRETGV 560

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              ++ID++ A  +    +A +  P   N+D          +     L    +      + 
Sbjct: 561  VTDQIDYLTADEEDNYVVAQANAPL--NEDGTFTNDIVLARYVEENLEVPISRVDYMDVS 618

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                     A+       +E  D+ R ++ +                    QR       
Sbjct: 619  PKQV----VAVATACIPFLENDDSNRALMGAN------------------MQRQAVPLIH 656

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q PLV  G        +    + D G   + +N             +  +   +     
Sbjct: 657  PQGPLVGTG--------MEHVAARDSGAALICKN-------------DGIVEYVDANEIR 695

Query: 837  DVFTSIHIEEFEV-MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                +  + ++ V   R +  G     R                 I+  G  V  G+IL 
Sbjct: 696  VRQENGALNKYAVTKFRRSNSGTCYNQRP----------------IVEKGDRVEKGEILA 739

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
               +      M   +  L A    +  +  D  +                    + K++ 
Sbjct: 740  DGSS-MENGEMALGQNPLVAFMTWEGYNYEDAIIMS----------------ERLVKDDV 782

Query: 956  SISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKGFKKS 1005
              S+  E+ E  ARD       + R +             +  I  G     G     K 
Sbjct: 783  YTSIHIEEFESEARDTKLGPEEITRELPNVGDDALKDLDEMGIIRIGAEVKDGDLLVGKV 842

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T      +S   R     F  +  +V+     +      +   +      KI   + GD+
Sbjct: 843  TPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGTVHDV------KIFTREAGDE 896

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            + PGV  +V+V++  KR I  GDKMAGRHGNKG+VS I+P EDMPF+ DGTPVDI+LNPL
Sbjct: 897  LSPGVNMLVRVYIVQKRKINEGDKMAGRHGNKGVVSLIMPEEDMPFMPDGTPVDIMLNPL 956

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I + + D  ++ D                     
Sbjct: 957  GVPSRMNIGQVLELHIGMAARQLGIHIATPVFDGASDED--------------------- 995

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                    V+D   E         A +    +++LYDG TGEPF
Sbjct: 996  ------------------------VWDTVRE---------AGMAADAKTVLYDGRTGEPF 1022

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 1023 DNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1082

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            GAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL + + N
Sbjct: 1083 GAAYTLQEILTYKSDDVVGRVKTYEAIVKGEKIPKPGVPESFRVLVKELQSLGLDMKVLN 1142

Query: 1366 SRTKNSAKM 1374
               +     
Sbjct: 1143 ENDELIELR 1151


>gi|170293426|gb|ACB12766.1| DNA-directed RNA polymerase [Bacillus caldovelox]
          Length = 1072

 Score =  867 bits (2239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/948 (46%), Positives = 600/948 (63%), Gaps = 78/948 (8%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LEF
Sbjct: 2   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLEF 51

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD P
Sbjct: 52  IDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFP 102

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E 
Sbjct: 103 LMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYET 159

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L+
Sbjct: 160 DAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKALI 219

Query: 256 VGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGL 306
                      +  GE   +E+ K L +      K           +       + L   
Sbjct: 220 ------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFNQ 273

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            +AE I++ ET E+  EAG +ID ++L  +     + + +              T    +
Sbjct: 274 RLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL-------------QTYRPAE 320

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                D  +   ++  P D                          G   +N+  N    +
Sbjct: 321 GVVDGDISVQTIKIYAPNDP------------------------DGEKVINVIGNGFIAE 356

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER +
Sbjct: 357 DVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVV 416

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG 
Sbjct: 417 RERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGP 476

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV- 605
           GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V 
Sbjct: 477 GGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRVD 536

Query: 606 -CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
              G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D++
Sbjct: 537 PETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVVARFRGENIVVKRDRVDYM 596

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK SG
Sbjct: 597 DVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDSG 656

Query: 725 AAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           AA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+VK
Sbjct: 657 AAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIVK 716

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSIH
Sbjct: 717 KGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSIH 776

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG 
Sbjct: 777 IEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKGM 836

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 837 TELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  345 bits (886), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 144/455 (31%), Positives = 196/455 (43%), Gaps = 77/455 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 855

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 856  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGMARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1072


>gi|194017595|ref|ZP_03056206.1| DNA-directed RNA polymerase, beta subunit [Bacillus pumilus ATCC
           7061]
 gi|194010867|gb|EDW20438.1| DNA-directed RNA polymerase, beta subunit [Bacillus pumilus ATCC
           7061]
          Length = 1193

 Score =  867 bits (2239), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/958 (44%), Positives = 599/958 (62%), Gaps = 66/958 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V +   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGDPKYPVAESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI--V 237
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEILDLIGENEYLR 218

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFL 296
            +   D       A   +           ++  + +++S         L ++    +   
Sbjct: 219 NTLEKDNTENADKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKK 278

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + L    +AE +V+ ETGEI  E G ++D + L++             V     N 
Sbjct: 279 LHIKNRLFNQKLAETLVDPETGEILAEKGQILDRRVLDK-------------VLPYLENG 325

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                L  +      +  L   ++  P D                          G   +
Sbjct: 326 IGFRKLYPNGGVVEDEVELQSIKIYAPSD------------------------QEGEQVI 361

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N+  N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 362 NVIGNAYVEEAVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFR 421

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +T
Sbjct: 422 IGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELT 481

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +G
Sbjct: 482 HKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFG 541

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           FIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L EDGSF ++ +  R  GE  
Sbjct: 542 FIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANAILGEDGSFIDDNIIARFRGENT 601

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +VPR ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+P VGTG
Sbjct: 602 VVPRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPESPIVGTG 661

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           ME V  K SGAA++ +  G+VE+V+A  I +R   + D       +D Y L+KF RSNQ 
Sbjct: 662 MEYVSGKDSGAAVICRYPGVVERVEAKNIWVRRYEDVDGQQVKGNLDKYSLLKFVRSNQG 721

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++++SER+
Sbjct: 722 TCYNQRPIVSVGDEVVKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAIIMSERL 781

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  GD+
Sbjct: 782 VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDL 841

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 842 LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 899



 Score =  486 bits (1250), Expect = e-134,   Method: Composition-based stats.
 Identities = 181/560 (32%), Positives = 265/560 (47%), Gaps = 69/560 (12%)

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +     +V      +I +  +E +      G  +    +  V        ++  I+ VG 
Sbjct: 675  ICRYPGVVERVEAKNIWVRRYEDVDGQQVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGD 734

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  G+IL    +   +  +     ++         +  D  +     +S  +V   ++ 
Sbjct: 735  EVVKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAII-----MSERLVKDDVYT 788

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
               I++ E      +   E + RD  +      RN+  R   I  G     G     K T
Sbjct: 789  SIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRIGAEVKDGDLLVGKVT 847

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  ++   R     F  +  +V+     +          +      K+   + GD++
Sbjct: 848  PKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV------KVFNREDGDEL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPLG
Sbjct: 902  PPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E H+G A   LG  I S + D     D+                     
Sbjct: 962  VPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------- 1014

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 T ++DG                           TGEPFD
Sbjct: 1015 ---------------------TVLYDG--------------------------RTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE+Q+LG+ + + + 
Sbjct: 1088 AAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSG 1147

Query: 1367 RTKNSAK--MEEIPDFNKCE 1384
              +      +E+  +  K +
Sbjct: 1148 DEEEIEMRDLEDDEETKKAD 1167


>gi|116334277|ref|YP_795804.1| DNA-directed RNA polymerase subunit beta [Lactobacillus brevis ATCC
           367]
 gi|122269041|sp|Q03PU9|RPOB_LACBA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116099624|gb|ABJ64773.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Lactobacillus brevis ATCC 367]
          Length = 1203

 Score =  866 bits (2238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/963 (45%), Positives = 592/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ FL          +EGL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYSRIKEVLDLPNLIEIQTNSYNWFL----------DEGLRDMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIEDFQGNLSLEFVDYQLLEPKYSVDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++F+ D  +   +G+ +Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTAQGTFIINGAERVIVSQLVRSPGVYFNEDTDK---NGRTVY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+ EIL          
Sbjct: 159 GATVIPNRGAWLEFETDAKNVSYVRIDRTRKIPMTELVRALGFGSDDEILDILGDNESLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
           Q  +      +  D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 QTLEKDI-HKNTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGR 277

Query: 299 TSD--------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L GL +AE + + +TGEI    G V+D+  ++ +        P L  D
Sbjct: 278 YKTNKKLSLKTRLLGLTLAETLADPDTGEIIAAKGTVVDKDVMKSLA-------PFLDQD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 +  +    D+    +   L I +V  P D                   + ++  
Sbjct: 331 DFKMVTFQPS----DEAVVTEPLKLQIIKVQSPDDP------------------EQEVPV 368

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G   ++++L        +HIR  DIIA +    DL+ G G  DDID+LGNRR+RSVGE+
Sbjct: 369 IGNGNIDIKL--------KHIRPADIIASMNYFFDLQLGIGNTDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQAN+ L++DGSF  + +  R
Sbjct: 541 RVNKYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYVVAQANTPLNDDGSFNTDTIMAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E I    ++ID++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 601 AQSENIETSADRIDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLNPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++++  G VE VDA  I +R  +G LD        Y+LMKF+
Sbjct: 661 PLIGTGIEYKAAHDSGVALISQHDGTVEYVDAREIRVRREDGALD-------TYKLMKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++++ADGPS + G+LALG+N LVAFM W GYNFED++ 
Sbjct: 714 RSNGGKNYNQRPIVKVGDHVDNDEVLADGPSMENGELALGQNPLVAFMTWQGYNFEDAIG 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII VGAEV
Sbjct: 774 INERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNLDEDGIIRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G + DV+IF R 
Sbjct: 834 QDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLKVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 NGD 896



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 175/522 (33%), Positives = 250/522 (47%), Gaps = 67/522 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +      G KN ++  I+ VG  V+  ++L    +      +   +  
Sbjct: 698  RREDGALDTYKLMKFRRSNGGKNYNQRPIVKVGDHVDNDEVLADGPS-MENGELALGQNP 756

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D        V   V        +  +  +  +  E    E+    +D
Sbjct: 757  LVAFMTWQGYNFEDAIGINERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGED 816

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  I      I  G     G     K T      +S   R     F  +  +V+
Sbjct: 817  ALKNLDEDGI------IRVGAEVQDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVR 870

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI   + GD++ PGV  +V+V++A KR IQ GDKM+G
Sbjct: 871  DTSLKVPHGGGGIIQDV------KIFTRENGDELSPGVNMMVRVYIAQKRKIQVGDKMSG 924

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 925  RHGNKGTVSVVIPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARKLGVHM 984

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + DI+                                             D
Sbjct: 985  ATPVFDGAQDTDIA---------------------------------------------D 999

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E         A +    +++LYDG TGEPFD+ V VG ++ LKL HMV DK++ARS 
Sbjct: 1000 AVKE---------AGMAADAKTVLYDGRTGEPFDKRVAVGVMHYLKLAHMVDDKMHARSI 1050

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+I
Sbjct: 1051 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAI 1110

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            V G+   + G PESF VLVKE+Q+LGL + + N   +     
Sbjct: 1111 VKGDPIPKPGVPESFRVLVKELQSLGLDMKVLNGDKEEIELR 1152


>gi|47570395|ref|ZP_00241035.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus G9241]
 gi|47552937|gb|EAL11348.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus G9241]
          Length = 1177

 Score =  866 bits (2238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 182/568 (32%), Positives = 262/568 (46%), Gaps = 69/568 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 661  MEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 720

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 721  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 775

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 776  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 833

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 834  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 887

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 888  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLP 947

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+        
Sbjct: 948  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAG 1007

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1008 MANDAK----------------------------TILYDG-------------------- 1019

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1020 ------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1073

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1074 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1133

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +Q+LG+ + + +S        +   D +
Sbjct: 1134 LQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|253577171|ref|ZP_04854491.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
 gi|251843415|gb|EES71443.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
          Length = 1187

 Score =  866 bits (2238), Expect = 0.0,   Method: Composition-based stats.
 Identities = 447/967 (46%), Positives = 602/967 (62%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  EI+++P+LIE+Q+ SY+ FL           EGL+  F+
Sbjct: 7   LAGHLVQYGR-RTRRSYARINEILEVPNLIEIQQKSYEWFL----------EEGLREMFQ 55

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 56  DISPIQDFTGNLVLEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 106

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK +Y
Sbjct: 107 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKKMY 163

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 164 TATVIPNRGAWLELETDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIR 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 224 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLENAKSLLVARFFDPKRYDLANVGR 277

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++  TGEI  EAG ++D + L+EI            + 
Sbjct: 278 YKINKKLHIKNRLFNQRLAETLIDTTTGEIIAEAGQMVDRRLLDEI------------LP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + N    +N  V     D  D  L    V  P +                         
Sbjct: 326 YLENGVGFKNYHVAGGVLDVDDVPLQTIDVFSPIE----------------------DGK 363

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V +V  N     +    V+HI   DII+ I   ++L +G G+ DDID+LGNRR+RSVGE+
Sbjct: 364 VVKVIANR----NIDKSVKHITPADIISSISYFINLLHGIGSTDDIDHLGNRRLRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP ET EG NIGL++SL+++A
Sbjct: 480 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLINSLSTYA 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    G VT+ V YL+A EE+N  IAQAN+ L  D  F +E V  R
Sbjct: 540 RINEYGFIEAPYRWVDPKTGTVTDQVTYLTADEEDNYVIAQANAKLTPDNKFEDEFVIVR 599

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P  ++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 600 YNKQSDNILTMPSSRVDYMDISPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLV 659

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRL 764
            +AP VGTGME   AK SG  IV+K  GI+E+ +A +I +R +E          +  Y+L
Sbjct: 660 PKAPLVGTGMEHKAAKDSGVCIVSKYDGIIERSEANQIWLRRIEVVDGKEVKGDLVKYKL 719

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+VK GD V++ DI+ADGPST+LG+LALGRN++VAFM W GYN+E
Sbjct: 720 HKFMRSNQGTCINQRPIVKRGDIVKKGDILADGPSTELGELALGRNVVVAFMTWEGYNYE 779

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE L+N+DE GII V
Sbjct: 780 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDERGIIRV 839

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++
Sbjct: 840 GAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKV 899

Query: 945 FNRHGID 951
           F R   D
Sbjct: 900 FTRENGD 906



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 267/1172 (22%), Positives = 432/1172 (36%), Gaps = 125/1172 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 100  KVRLINKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFSTKVDKNG 159

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                T+  +       ++       IY+             +          + +D + N
Sbjct: 160  KKMYTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEI-LDLLGN 218

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            + YIRNTL  D     + AL++IY  +RPG+  T   A+S+    FFD          R 
Sbjct: 219  DEYIRNTLDKDNTDSTEKALIEIYERLRPGEPPTLENAKSLLVARFFDPK--------RY 270

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             +           +    +     + + L+D   G+   +    +  R +  +   L+N 
Sbjct: 271  DLANVGRYKINKKLHIKNRLFNQRLAETLIDTTTGEIIAEAGQMVDRRLLDEILPYLENG 330

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                     ++       +D+D V  Q +    P+           ++ ++  + N    
Sbjct: 331  VGF------KNYHVAGGVLDVDDVPLQTIDVFSPIED--------GKVVKVIANRNIDKS 376

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            + H      +                    H G        E         L+   RV  
Sbjct: 377  VKHITPADIISSISYFINLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR 436

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
               +      V   +   ++  + A  +E       +S L +    T  L          
Sbjct: 437  E-RMSIQDANVITPQALINIRPVIASIKE----FFGSSQLSQFMDQTNPLAELTHKRRLS 491

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             +    +       ++   +    +          +          +  L   A     G
Sbjct: 492  ALGPGGLT------RERAGMEVRDVHPSHYGRMCPIETPEGPNIGLINSLSTYARINEYG 545

Query: 715  MESVVAK--SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                  +        V  +   +   +    VI      L P     D + ++++ + + 
Sbjct: 546  FIEAPYRWVDPKTGTVTDQVTYLTADEEDNYVIAQANAKLTPDNKFEDEFVIVRYNKQSD 605

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDL-------------GDLALGRNMLVAFMPWH 819
            N        V   D   +  +                              +LV   P  
Sbjct: 606  NILTMPSSRVDYMDISPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLVPKAPLV 665

Query: 820  GYNFE-------DSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            G   E          ++S+   ++       I +   EV+      G     +    +  
Sbjct: 666  GTGMEHKAAKDSGVCIVSKYDGIIERSEANQIWLRRIEVVDGKEVKGDLVKYKLHKFMRS 725

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                 I++  I+  G  V  GDIL    + +    +     ++ A    +  +  D  L 
Sbjct: 726  NQGTCINQRPIVKRGDIVKKGDILADGPSTEL-GELALGRNVVVAFMTWEGYNYEDAIL- 783

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I 
Sbjct: 784  ----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDER-GIIR 838

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G    +G     K T      ++   R     F  +  +V+     +    +     + 
Sbjct: 839  VGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDV- 897

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMP
Sbjct: 898  -----KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMP 952

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F+ DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + +G  + + + D     D      
Sbjct: 953  FMPDGTPVQVVLNPLGVPSRMNIGQVLEIHLGMAALQMGIHVATPVFDGANEED------ 1006

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                   VFD          +  A +  
Sbjct: 1007 ---------------------------------------VFD---------TMEEAGMQR 1018

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
            +G++ILYDG TGEPF+R VTVG ++M+KL HMV DK++ARSTG YSLVTQQPLGGK+  G
Sbjct: 1019 NGKTILYDGRTGEPFEREVTVGVMHMIKLAHMVDDKIHARSTGPYSLVTQQPLGGKAQFG 1078

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G +  E G PESF VL
Sbjct: 1079 GQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGENVPEPGVPESFKVL 1138

Query: 1351 VKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +KE+Q+LG+ + +     +     E   + + 
Sbjct: 1139 IKELQSLGMDVKILTENEEEIEMKEIDDEDDA 1170


>gi|229170953|ref|ZP_04298554.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus MM3]
 gi|228612493|gb|EEK69714.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus MM3]
          Length = 1177

 Score =  866 bits (2237), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 594/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V      VT  V YL+A EE+N  +AQAN  L E+G F  E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPESGLVTGQVDYLTADEEDNYVVAQANMKLSEEGEFLSEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 183/568 (32%), Positives = 263/568 (46%), Gaps = 69/568 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 661  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 720

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 721  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 775

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 776  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 833

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 834  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 887

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 888  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLP 947

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+        
Sbjct: 948  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAG 1007

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1008 MANDAK----------------------------TILYDG-------------------- 1019

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1020 ------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1073

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1074 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1133

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +Q+LG+ + + +S  K     +   D +
Sbjct: 1134 LQSLGMDVKMMSSDDKEIEMRDTEDDDD 1161


>gi|324324092|gb|ADY19352.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 1177

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 333

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 334  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 390

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 391  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 444

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 445  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 483

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 484  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 543

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 544  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 603

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 604  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 659

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 660  GMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 719

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 720  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 775

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 776  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 832

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 833  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 886

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 887  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 946

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 947  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1006

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1007 GMANDAK----------------------------TILYDG------------------- 1019

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1020 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1072

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1073 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1132

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1133 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|165873341|ref|ZP_02217943.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0488]
 gi|254751215|ref|ZP_05203253.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Vollum]
 gi|164710921|gb|EDR16496.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0488]
          Length = 1177

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 263/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 333

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 334  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 390

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 391  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 444

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 445  QALINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 483

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 484  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 543

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 544  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 603

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 604  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 659

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 660  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 719

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 720  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 775

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 776  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 832

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 833  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 886

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SR+LP EDMP+L
Sbjct: 887  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRVLPEEDMPYL 946

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 947  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1006

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1007 GMANDAK----------------------------TILYDG------------------- 1019

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1020 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1072

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+K
Sbjct: 1073 RFGEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIK 1132

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1133 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|170293440|gb|ACB12773.1| DNA-directed RNA polymerase [Geobacillus thermodenitrificans]
          Length = 1076

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/949 (46%), Positives = 596/949 (62%), Gaps = 78/949 (8%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD 
Sbjct: 51  FIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E
Sbjct: 102 PLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L
Sbjct: 159 TDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKAL 218

Query: 255 MVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCG 305
           +           +  GE   +E+ K L +      K           +       + L  
Sbjct: 219 I------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFN 272

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AE I++ ET E+  EAG +ID ++L  +     +              Y     V D
Sbjct: 273 QRLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEK--------GAGLQTYRPTEGVAD 324

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                    +   ++  P D                              +N+  N    
Sbjct: 325 GQIS-----VQTVKIYAPNDPDN------------------------EKVINIIGNGFIA 355

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER 
Sbjct: 356 EDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERV 415

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +++ PQ LIN +PV++AV EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 416 VRERMSIQDANTITPQQLINIRPVIAAVKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 475

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH +HYGR+CP ET EG  IGL++SL+++A+VN +GFIETPYR+V
Sbjct: 476 PGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPTIGLINSLSTYAKVNKFGFIETPYRRV 535

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
               GKVT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V RE++D+
Sbjct: 536 DPETGKVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVIARFRGENIVVKRERVDY 595

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK S
Sbjct: 596 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLQPEAPIVGTGMEYVSAKDS 655

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           GAAI+ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+V
Sbjct: 656 GAAIICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSI
Sbjct: 716 KKGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSI 775

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 776 HIEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKG 835

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 MTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 884



 Score =  356 bits (914), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 147/459 (32%), Positives = 199/459 (43%), Gaps = 77/459 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 690  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 748

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 749  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 808

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 809  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 855

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 856  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 911

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 912  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 971

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 972  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1003

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1004 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1038 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1076


>gi|154684625|ref|YP_001419786.1| DNA-directed RNA polymerase subunit beta [Bacillus
           amyloliquefaciens FZB42]
 gi|182676553|sp|A7Z0M9|RPOB_BACA2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|154350476|gb|ABS72555.1| RpoB [Bacillus amyloliquefaciens FZB42]
          Length = 1196

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/964 (45%), Positives = 602/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 105 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 322

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      + +L   ++  P D                         
Sbjct: 323 PYLENGIGFRKLYPNGGVVEDEVMLQSIKIYAPTD------------------------A 358

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + +++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 359 EGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 419 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 479 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 538

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L +DGSF ++ +  R
Sbjct: 539 KVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANAKLSDDGSFLDDSIVAR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 599 FRGENTVVARNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF
Sbjct: 659 PIVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKF 718

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 719 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 778

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 779 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 838

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           VN GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 839 VNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 898

Query: 948 HGID 951
              D
Sbjct: 899 EDGD 902



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 182/573 (31%), Positives = 269/573 (46%), Gaps = 71/573 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V      ++ +  +E +      G  +    +  V     
Sbjct: 665  MEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKFVRSNQG 724

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     ++         +  D  +    
Sbjct: 725  TCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII---- 779

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 780  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIGA 837

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +          +    
Sbjct: 838  EVNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV---- 893

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L 
Sbjct: 894  --KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLP 951

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+        
Sbjct: 952  DGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAG 1011

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1012 MSRDAK----------------------------TVLYDG-------------------- 1023

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1024 ------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1077

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE
Sbjct: 1078 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKE 1137

Query: 1354 MQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            +Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1138 LQSLGMDVKILSGDEEEIEMRDLEDEEDAKQAD 1170


>gi|315649711|ref|ZP_07902795.1| DNA-directed RNA polymerase subunit beta [Paenibacillus vortex
           V453]
 gi|315274899|gb|EFU38275.1| DNA-directed RNA polymerase subunit beta [Paenibacillus vortex
           V453]
          Length = 1181

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/967 (45%), Positives = 605/967 (62%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q+ SY+ FL           EGL+  F+
Sbjct: 1   MAGHLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYEWFL----------EEGLREMFQ 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 50  DISPIQDFTGNLVLEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  Y
Sbjct: 101 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKTTY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 158 TATVIPNRGAWLELEMDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIQ 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 218 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLENAKSLLVARFFDPKRYDLANVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++ +TGEI  EAG  +D + L+EI     + +      
Sbjct: 272 YKINKKLHIKNRLFNQRLAESLIDTDTGEIVAEAGQTVDRRLLDEIMPYLEKSVG----- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   +N  V     D +D  L    V  P + +      +                
Sbjct: 327 -------FKNYHVAGGVMDSEDIPLQTIDVFSPTEDAKVVKVIA---------------- 363

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                     N +    V+HI + DII+ I   ++L +G G  DDID+LGNRR+RSVGE+
Sbjct: 364 ----------NANIDKSVKHITQADIISSISYFINLLHGIGNTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FA
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    GKVT  + YL+A EE+N  +AQAN+ L+EDG+FT+E+V  R
Sbjct: 534 RINEYGFIEAPYRWVDPKTGKVTEQIDYLTADEEDNYIVAQANAELNEDGTFTDEMVIVR 593

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P +++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 594 YNKQSDNILPMPSDRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 653

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRL 764
            +AP VGTGME   AK SG  IV+K  GI+E+  A  I +R VE  D       +  ++L
Sbjct: 654 PKAPLVGTGMEHKSAKDSGVCIVSKYDGIIERSSANEIWLRRVENVDGQEVKGDIVKHKL 713

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+VK G+ +++ DI+ADGPST++G+LALGRN++VAFM W GYN+E
Sbjct: 714 HKFMRSNQGTCINQRPIVKRGEVIKKGDILADGPSTEMGELALGRNVVVAFMTWEGYNYE 773

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LKN+DE GII +
Sbjct: 774 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDERGIIRI 833

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G +VDV++
Sbjct: 834 GAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGSDGIIVDVKV 893

Query: 945 FNRHGID 951
           F R   D
Sbjct: 894 FTRENGD 900



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/529 (35%), Positives = 267/529 (50%), Gaps = 68/529 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  I+  G  +  GDIL    + +    +     ++ A 
Sbjct: 706  GDIVKHKLHKFMRSNQGTCINQRPIVKRGEVIKKGDILADGPSTE-MGELALGRNVVVAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 765  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 819

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 820  EALKNLDER-GIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 878

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 879  RVPHGSDGIIVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 932

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + S +
Sbjct: 933  KGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVASPV 992

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +  D                                             VFD    
Sbjct: 993  FDGASEYD---------------------------------------------VFD---- 1003

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G+++LYDG TGE F+R VTVG ++M+KL HMV DK++ARSTG YS
Sbjct: 1004 -----TMEEAGMQRNGKTVLYDGRTGERFEREVTVGVMHMIKLAHMVDDKIHARSTGPYS 1058

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1059 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1118

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +  E G PESF VL+KE+Q+LG+ + + +   +     E +  D  + +
Sbjct: 1119 NVPEPGVPESFKVLIKELQSLGMDVKILSENEEEIEMKELDDEDDAQGD 1167


>gi|229083422|ref|ZP_04215770.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-44]
 gi|228699855|gb|EEL52492.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-44]
          Length = 1180

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G V+D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 DGERSINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGRVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y+++KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMLKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD+V + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 180/568 (31%), Positives = 263/568 (46%), Gaps = 69/568 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  + +  +     
Sbjct: 664  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMLKFIRSNQG 723

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG +V  G+IL    +      +     +L         +  D  +    
Sbjct: 724  TCYNQRPIVSVGDQVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 779  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 836

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 837  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 890

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 891  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLP 950

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+        
Sbjct: 951  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHVATPVFDGAREEDVWGTIEEAG 1010

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1011 MANDAK----------------------------TILYDG-------------------- 1022

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1023 ------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1076

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1077 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1136

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +Q+LG+ + + +S        +   D +
Sbjct: 1137 LQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|42779183|ref|NP_976430.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           10987]
 gi|49479286|ref|YP_034454.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|52145116|ref|YP_081713.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus E33L]
 gi|196036937|ref|ZP_03104318.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus W]
 gi|196042329|ref|ZP_03109604.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus
           NVH0597-99]
 gi|217957677|ref|YP_002336221.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH187]
 gi|222093872|ref|YP_002527922.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Q1]
 gi|225862154|ref|YP_002747532.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus 03BB102]
 gi|254720823|ref|ZP_05182615.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           A1055]
 gi|300119587|ref|ZP_07057131.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus SJ1]
 gi|301051839|ref|YP_003790050.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis CI]
 gi|81397480|sp|Q6HPR6|RPOB_BACHK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|81411363|sp|Q73FA4|RPOB_BACC1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|81689844|sp|Q63H98|RPOB_BACCZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158512711|sp|A0R8H2|RPOB_BACAH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|226699369|sp|B7HQT6|RPOB_BACC7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765271|sp|C1ET31|RPOB_BACC3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765272|sp|B9IZI6|RPOB_BACCQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|42735098|gb|AAS39038.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus ATCC
           10987]
 gi|49330842|gb|AAT61488.1| DNA-directed RNA polymerase, beta subunit [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|51978585|gb|AAU20135.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus E33L]
 gi|195990450|gb|EDX54437.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus W]
 gi|196026835|gb|EDX65467.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus
           NVH0597-99]
 gi|217065081|gb|ACJ79331.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH187]
 gi|221237920|gb|ACM10630.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus Q1]
 gi|225789287|gb|ACO29504.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus 03BB102]
 gi|298723059|gb|EFI63957.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus SJ1]
 gi|300374008|gb|ADK02912.1| DNA-directed RNA polymerase beta subunit [Bacillus cereus biovar
           anthracis str. CI]
          Length = 1177

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 333

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 334  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 390

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 391  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 444

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 445  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 483

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 484  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 543

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 544  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 603

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 604  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 659

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 660  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 719

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 720  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 775

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 776  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 832

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 833  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 886

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 887  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 946

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 947  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1006

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1007 GMANDAK----------------------------TILYDG------------------- 1019

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1020 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1072

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1073 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1132

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1133 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|30018372|ref|NP_830003.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           14579]
 gi|206972219|ref|ZP_03233166.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH1134]
 gi|218233125|ref|YP_002364951.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus B4264]
 gi|218895237|ref|YP_002443648.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus G9842]
 gi|228963202|ref|ZP_04124371.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|296500936|ref|YP_003662636.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           BMB171]
 gi|41017690|sp|Q81J48|RPOB_BACCR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|226699367|sp|B7IT11|RPOB_BACC2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|226699368|sp|B7HJ40|RPOB_BACC4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|29893912|gb|AAP07204.1| DNA-directed RNA polymerase beta chain [Bacillus cereus ATCC 14579]
 gi|206732793|gb|EDZ49968.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH1134]
 gi|218161082|gb|ACK61074.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus B4264]
 gi|218541792|gb|ACK94186.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus G9842]
 gi|228796460|gb|EEM43899.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|296321988|gb|ADH04916.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           BMB171]
 gi|326937896|gb|AEA13792.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar chinensis CT-43]
          Length = 1177

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 262/1176 (22%), Positives = 429/1176 (36%), Gaps = 138/1176 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 333

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 334  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 390

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 391  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 444

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 445  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 483

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 484  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 543

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                 +  E   V   ++ + A                 V A   +  S EG+       
Sbjct: 544  TPYRRVDPETGLVTGHVDYLTA-----------DEEDNYVVAQANMKLSDEGEFLSEDIV 592

Query: 759  VDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LAL 807
                         +   ++  P  +V             D     +G          +  
Sbjct: 593  ARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNP 652

Query: 808  GRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               ++   M +       + +I +   +V       + +  +  +   T  G  +  +  
Sbjct: 653  ESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQ 712

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  I+ VG EV  G+IL    +      +     +L         +  
Sbjct: 713  KFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYE 771

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 772  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 826

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 827  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 885

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 886  I------LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILP 939

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+
Sbjct: 940  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDV 999

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1000 WGTIEEAGMANDAK----------------------------TILYDG------------ 1019

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1020 --------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1065

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PE
Sbjct: 1066 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPE 1125

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            SF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1126 SFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|227438086|gb|ACP30541.1| RNA polymerase beta subunit [Neisseria sp. CSL 7565]
          Length = 777

 Score =  865 bits (2236), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/779 (54%), Positives = 571/779 (73%), Gaps = 16/779 (2%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +
Sbjct: 2    NPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVY 61

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR N YGF+ETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD DG+ T +L+ CR 
Sbjct: 62   ARTNEYGFLETPYRRVIDGKVTDEIDYLSAIEEGRYVIAQANAELDSDGNLTGDLITCRE 121

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P
Sbjct: 122  KGETIMATADRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKP 181

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E  VA  S  AIVA+R GIVE VDA RIV+R  + +      GVDIY LMKF R
Sbjct: 182  MVGTGIERSVAVDSATAIVARRGGIVEYVDANRIVVRVHDAEATAGEVGVDIYNLMKFTR 241

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQ+T +NQRP+VK GD ++R D++ADG STDLG+LALG+NM +AFMPW+GYN+EDS+LI
Sbjct: 242  SNQSTNINQRPVVKAGDVLQRGDVVADGASTDLGELALGQNMTIAFMPWNGYNYEDSILI 301

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SE++ ++D +TSIHIEE  V+ARDTKLG E+ITRDIPN+SE     +DE GI+ +GAEV 
Sbjct: 302  SEKVAADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESGIVYIGAEVE 361

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR+P+G+SGTV+DV++F R G
Sbjct: 362  AGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTGMSGTVIDVQVFTREG 421

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I +++R+ ++   +++   +D  D+  I D + +SR+  ++ GQ A  GP    K + ++
Sbjct: 422  IQRDKRAQAIIDSELKRYRQDLSDQLRIFDNDAFSRIERMIVGQKANGGPLKLAKDSDIT 481

Query: 1010 SDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            S+ ++  P +  W+   + DE + + +E +KV  +  ++  ++ ++ K +K+  GD++ P
Sbjct: 482  SEYLASLPSKHDWFDIRLADESLAKQLELIKVSLQQKRAEADELYEVKKKKLTQGDELQP 541

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDIVLNPLGVP
Sbjct: 542  GVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVP 601

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQI E HLGWA  G+G++I  ++ + +   DI   R+FL ++  +    E + D 
Sbjct: 602  SRMNIGQILEVHLGWAAKGIGERIDHMLAEQRKVSDI---RAFLNQLYNSSGKQENLDDL 658

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------G------QSIL 1236
             D+ +L +AE  K G   ++PVFDGA E  I  ML +A   E       G      Q  L
Sbjct: 659  SDEEILVLAENLKDGATFASPVFDGAKENEIYEMLNLAYPSEDPEIQKLGFNDSKTQITL 718

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            YDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 719  YDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKAQFGGQRFG 777


>gi|30260293|ref|NP_842670.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Ames]
 gi|49183136|ref|YP_026388.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Sterne]
 gi|50196908|ref|YP_052605.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           'Ames Ancestor']
 gi|167636697|ref|ZP_02394984.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0442]
 gi|167642037|ref|ZP_02400266.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0193]
 gi|170689707|ref|ZP_02880883.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0465]
 gi|170709438|ref|ZP_02899845.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0389]
 gi|177656134|ref|ZP_02937161.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0174]
 gi|190569397|ref|ZP_03022284.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|227812775|ref|YP_002812784.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           CDC 684]
 gi|229600646|ref|YP_002864753.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0248]
 gi|254684394|ref|ZP_05148254.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           CNEVA-9066]
 gi|254733743|ref|ZP_05191458.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Western North America USA6153]
 gi|254739412|ref|ZP_05197112.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Kruger B]
 gi|254756814|ref|ZP_05208842.1| DNA-directed RNA polymerase subunit beta [Bacillus anthracis str.
           Australia 94]
 gi|41017692|sp|Q81VT8|RPOB_BACAN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765269|sp|C3P9P7|RPOB_BACAA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765270|sp|C3LJ74|RPOB_BACAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|30253614|gb|AAP24156.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           Ames]
 gi|49177063|gb|AAT52439.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           Sterne]
 gi|50082970|gb|AAT70113.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           'Ames Ancestor']
 gi|167510003|gb|EDR85420.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0193]
 gi|167527871|gb|EDR90698.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0442]
 gi|170125655|gb|EDS94575.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0389]
 gi|170666332|gb|EDT17119.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0465]
 gi|172079854|gb|EDT64966.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0174]
 gi|190559490|gb|EDV13488.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|227006638|gb|ACP16381.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           CDC 684]
 gi|229265054|gb|ACQ46691.1| DNA-directed RNA polymerase, beta subunit [Bacillus anthracis str.
           A0248]
          Length = 1177

 Score =  865 bits (2235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 102 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 328 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 355 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 535 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 655 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 715 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 264/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 155  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 214  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 333

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 334  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 390

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 391  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 444

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 445  QALINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 483

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 484  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 543

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 544  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 603

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 604  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 659

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 660  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 719

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 720  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 775

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 776  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 832

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 833  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 886

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 887  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 946

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 947  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1006

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1007 GMANDAK----------------------------TILYDG------------------- 1019

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1020 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1072

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+K
Sbjct: 1073 RFGEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIK 1132

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1133 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1161


>gi|229003117|ref|ZP_04160964.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides
           Rock1-4]
 gi|228758132|gb|EEM07330.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides
           Rock1-4]
          Length = 1179

 Score =  865 bits (2235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 DGERSINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGRVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G VE+V+A  + +R  VE D       +D Y+++KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGTVERVEAREVWVRRYVEVDGQKVKGDLDRYKMLKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD+V + +I+ADGPS + G+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMEKGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 264/1167 (22%), Positives = 436/1167 (37%), Gaps = 124/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ERSI    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESDGERSINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 547  TPYRRVDPETGRVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 606

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 607  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 662

Query: 815  FMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +    V       + +  +  +      G  +  + +  +    
Sbjct: 663  GMEYVSAKDSGAAVICKHPGTVERVEAREVWVRRYVEVDGQKVKGDLDRYKMLKFIRSNQ 722

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG +V  G+IL    +   +  +     +L         +  D  +   
Sbjct: 723  GTCYNQRPIVSVGDQVVKGEILADGPS-MEKGELALGRNVLVGFMTWDGYNYEDAII--- 778

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 779  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 835

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 836  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 889

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 890  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 949

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 950  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1009

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1010 GMANDAK----------------------------TILYDG------------------- 1022

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1023 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1075

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1076 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1135

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPD 1379
            E+Q+LG+ + + +S        +   D
Sbjct: 1136 ELQSLGMDVKMMSSDDTEIEMRDTEDD 1162


>gi|229009611|ref|ZP_04166837.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides DSM
           2048]
 gi|229131109|ref|ZP_04260021.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST196]
 gi|229165090|ref|ZP_04292885.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH621]
 gi|228618353|gb|EEK75383.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH621]
 gi|228652322|gb|EEL08247.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST196]
 gi|228751633|gb|EEM01433.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides DSM
           2048]
          Length = 1180

 Score =  865 bits (2235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G V+D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               K A      V    ++ +                 Y   +
Sbjct: 331 -------------------FKTAKPMGGVVAGDVELQSI--------------KIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   D++HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERSINVIGNANITRDIKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLINPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K+ G+VE+V+A  + +R  V+ D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKQPGVVERVEAREVWVRRYVDVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD+V + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 253/1167 (21%), Positives = 428/1167 (36%), Gaps = 120/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            K+N +L++               P+    +  E  +   + L  +               
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIGFKTAKP 336

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G++     ++     E   +      + +       I    +++++  FF    
Sbjct: 337  MGGVVAGDVELQSIKIYAPESEGE-RSINVIGNANITRDIKHITPGDILASISYFFNL-- 393

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            L ++ +  +         R          R       R V      R+   +T+      
Sbjct: 394  LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITPQA 449

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++     A +  +       + +       ++ +                         
Sbjct: 450  LINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KRRL 488

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 489  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIETP 548

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDPSTSG 758
               +  E   V   ++ + A      +VA+    + +V       ++    G+   +   
Sbjct: 549  YRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVARFRGENIVTNKE 608

Query: 759  VDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               Y  +  ++  S    C+         D+  R  + A+     +  +     ++   M
Sbjct: 609  RIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLINPESPIVGTGM 664

Query: 817  PWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       + +I ++  +V       + +  +  +   T  G  +  +    +      
Sbjct: 665  EYVSAKDSGAAVICKQPGVVERVEAREVWVRRYVDVDGQTVKGDLDRYKMQKFIRSNQGT 724

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+ VG +V  G+IL    +      +     +L         +  D  +     
Sbjct: 725  CYNQRPIVSVGDQVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII----- 778

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G  
Sbjct: 779  MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGAE 837

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G     K T      ++   R     F  +  +V+     +                
Sbjct: 838  VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------LD 891

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L D
Sbjct: 892  VKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLPD 951

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+         
Sbjct: 952  GTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAGM 1011

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1012 ANDAK----------------------------TILYDG--------------------- 1022

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1023 -----RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 1077

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+KE+
Sbjct: 1078 GEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIKEL 1137

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFN 1381
            Q+LG+ + + +         +   D +
Sbjct: 1138 QSLGMDVKMMSINDTEIEMRDTEDDDD 1164


>gi|261409529|ref|YP_003245770.1| DNA-directed RNA polymerase subunit beta [Paenibacillus sp.
           Y412MC10]
 gi|261285992|gb|ACX67963.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp.
           Y412MC10]
          Length = 1187

 Score =  865 bits (2235), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/967 (46%), Positives = 606/967 (62%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q+ SY+ FL           EGL+  F+
Sbjct: 7   LAGHLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYEWFL----------EEGLREMFQ 55

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 56  DISPIQDFTGNLVLEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 106

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  Y
Sbjct: 107 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKTTY 163

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 164 TATVIPNRGAWLELEMDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIQ 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +E+ K L        K         
Sbjct: 224 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLENAKSLLVARFFDPKRYDLANVGR 277

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++ +TGEI  EAG  +D + L+EI     + +      
Sbjct: 278 YKINKKLHIKNRLFNQRLAESLIDIDTGEIVAEAGQTVDRRLLDEIMPYLEKSVG----- 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   +N  V     D +D  L    V  P +                         
Sbjct: 333 -------FKNYHVAGGVMDSEDIPLQTIDVFSPIE----------------------DGK 363

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V +V  N     +    V+HI + DII+ I   ++L +G G  DDID+LGNRR+RSVGE+
Sbjct: 364 VVKVIAN----ANIDKSVKHITQADIISSISYFINLLHGIGNTDDIDHLGNRRLRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FA
Sbjct: 480 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFA 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    GKVT+ + YL+A EE+N  +AQAN+ L+EDG+F +E+V  R
Sbjct: 540 RINEYGFIEAPYRWVDPKTGKVTDQIDYLTADEEDNYIVAQANAELNEDGTFADEMVIVR 599

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P +++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 600 YNKQSDNILPMPSDRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 659

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRL 764
            +AP VGTGME   AK SG  IV+K  GI+E+  A  I +R VE  D       +  Y+L
Sbjct: 660 PKAPLVGTGMEHKSAKDSGVCIVSKYDGIIERSSANEIWLRRVENIDGQEVKGDIVKYKL 719

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+VK GD +++ DI+ADGPST++G+LALGRN++VAFM W GYN+E
Sbjct: 720 HKFMRSNQGTCINQRPIVKRGDVIKKGDILADGPSTEMGELALGRNVVVAFMTWEGYNYE 779

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LKN+DE GII +
Sbjct: 780 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDERGIIRI 839

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G +VDV++
Sbjct: 840 GAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGSDGIIVDVKV 899

Query: 945 FNRHGID 951
           F R   D
Sbjct: 900 FTRENGD 906



 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/529 (35%), Positives = 267/529 (50%), Gaps = 68/529 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  I+  G  +  GDIL    + +    +     ++ A 
Sbjct: 712  GDIVKYKLHKFMRSNQGTCINQRPIVKRGDVIKKGDILADGPSTE-MGELALGRNVVVAF 770

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 771  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 825

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 826  EALKNLDER-GIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 884

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 885  RVPHGSDGIIVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 938

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + S +
Sbjct: 939  KGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVASPV 998

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +  D                                             VFD    
Sbjct: 999  FDGASEYD---------------------------------------------VFD---- 1009

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G+++LYDG TGE F+R VTVG ++M+KL HMV DK++ARSTG YS
Sbjct: 1010 -----TMEEAGMQRNGKTVLYDGRTGERFEREVTVGVMHMIKLAHMVDDKIHARSTGPYS 1064

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1065 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1124

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +  E G PESF VL+KE+Q+LG+ + + +   +     E +  D  + +
Sbjct: 1125 NVPEPGVPESFKVLIKELQSLGMDVKILSENEEEIEMKELDDEDDAQGD 1173


>gi|229053948|ref|ZP_04195382.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH603]
 gi|228721366|gb|EEL72887.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH603]
          Length = 1180

 Score =  865 bits (2234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G V+D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               K A      V    ++ +                 Y   +
Sbjct: 331 -------------------FKTAKPMGGVVAGDVELQSI--------------KIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   D++HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERSINVIGNANITRDIKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLINPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K+ G+VE+V+A  + +R  ++ D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKQPGVVERVEAREVWVRRYIDVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGD+V + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 253/1167 (21%), Positives = 428/1167 (36%), Gaps = 120/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            K+N +L++               P+    +  E  +   + L  +               
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIGFKTAKP 336

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G++     ++     E   +      + +       I    +++++  FF    
Sbjct: 337  MGGVVAGDVELQSIKIYAPESEGE-RSINVIGNANITRDIKHITPGDILASISYFFNL-- 393

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            L ++ +  +         R          R       R V      R+   +T+      
Sbjct: 394  LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITPQA 449

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++     A +  +       + +       ++ +                         
Sbjct: 450  LINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KRRL 488

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 489  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIETP 548

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDPSTSG 758
               +  E   V   ++ + A      +VA+    + +V       ++    G+   +   
Sbjct: 549  YRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEVGEFLDEDIVARFRGENIVTNKE 608

Query: 759  VDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               Y  +  ++  S    C+         D+  R  + A+     +  +     ++   M
Sbjct: 609  RIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLINPESPIVGTGM 664

Query: 817  PWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       + +I ++  +V       + +  +  +   T  G  +  +    +      
Sbjct: 665  EYVSAKDSGAAVICKQPGVVERVEAREVWVRRYIDVDGQTVKGDLDRYKMQKFIRSNQGT 724

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+ VG +V  G+IL    +      +     +L         +  D  +     
Sbjct: 725  CYNQRPIVSVGDQVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII----- 778

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G  
Sbjct: 779  MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGAE 837

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G     K T      ++   R     F  +  +V+     +                
Sbjct: 838  VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------LD 891

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L D
Sbjct: 892  VKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLPD 951

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+         
Sbjct: 952  GTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAGM 1011

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1012 ANDAK----------------------------TILYDG--------------------- 1022

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1023 -----RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 1077

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+KE+
Sbjct: 1078 GEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIKEL 1137

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFN 1381
            Q+LG+ + + +         +   D +
Sbjct: 1138 QSLGMDVKMMSINDTEIEMRDTEDDDD 1164


>gi|327438262|dbj|BAK14627.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Solibacillus silvestris StLB046]
          Length = 1181

 Score =  865 bits (2234), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 603/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ F +  E++++P+LIE+Q ASY+ FL           EGL+  F 
Sbjct: 1   MTGQLVQYGQHRQRRSFARISEVLELPNLIEIQTASYEWFL----------EEGLREMFH 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+DVD+C  RD+TYA PL++ +RL           K
Sbjct: 51  DISPIEDFTGNLSLEFVDYTLGEPKYDVDECKERDVTYAAPLRVKVRLH---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  +
Sbjct: 102 ETNEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFHE---KTDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 GATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDIIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +ES K L        K   +     
Sbjct: 219 NTLEKDNTEGTEKALL------EIYERLRPGEPPTVESAKNLLYSRFFDAKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ +TGEI +EAG ++D ++L+++            + 
Sbjct: 273 YKMNKKLHIKNRLFNQTIAETLVDPDTGEIIVEAGTLLDRRNLDKL------------IP 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +    R            D  +   ++  P D +                       
Sbjct: 321 YLESGVGFRTLNQV-GGVLEDDITIQSVKIFAPNDEAQK--------------------- 358

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N    ++V++I   D++A +    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 359 ----EINVISNAYVDEEVKNITPADVLASVSYFFNLLYDVGNTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +++PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSINDTAAIVPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT+++ YL+A EE+N  +AQANS L+EDG+F  E V  R
Sbjct: 535 KVNKFGFIETPYRRVDPETGAVTSEIHYLTADEEDNYVVAQANSILNEDGTFANEEVVGR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+  +  +++ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 595 FRGDNTVFSKDRIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLYPNA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKF 767
           PFVGTGME V A+ SGAA+VAK  GIVE V+A  I +R +E        G    Y+L KF
Sbjct: 655 PFVGTGMEHVDARDSGAAVVAKFDGIVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRP+VKVGD V+  DI+ADGPS + G+LALG+N+LVAFM W G+N+ED++
Sbjct: 715 IRSNQGTSYNQRPIVKVGDRVKPRDILADGPSMEKGELALGQNVLVAFMTWDGFNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAE
Sbjct: 775 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 835 VRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIILDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 188/555 (33%), Positives = 267/555 (48%), Gaps = 68/555 (12%)

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V      SIH+   EV+      G     +    +      + ++  I+ VG  V P D
Sbjct: 680  IVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKFIRSNQGTSYNQRPIVKVGDRVKPRD 739

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL    +   +  +   + +L A       +  D  +     +S  +V   ++    I++
Sbjct: 740  ILADGPS-MEKGELALGQNVLVAFMTWDGFNYEDAVI-----MSERLVKDDVYTSVHIEE 793

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             E      +   E + RD  +      RN+  R   I  G     G     K T      
Sbjct: 794  YESESRDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIGAEVRDGDILVGKVTPKGVTE 852

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            ++   R     F  +  +V+     +                 K+   + GD++PPGV +
Sbjct: 853  LTAEERLLHAIFGEKAREVRDTSLRVPHGAGGII------LDVKVFNREDGDELPPGVNQ 906

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGVPSRMN
Sbjct: 907  LVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGVPSRMN 966

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLG A   LG  + S + D     D+                           
Sbjct: 967  IGQVLELHLGMASRYLGIHMASPVFDGANEADVW-------------------------E 1001

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             +  A   + G                             ++ILYDG +GEPFD  V+VG
Sbjct: 1002 TMEEAGMNRDG-----------------------------KTILYDGRSGEPFDSRVSVG 1032

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1033 IMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 1092

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + +     +   
Sbjct: 1093 EILTVKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLTINDEEVE 1152

Query: 1373 KME-EIPDFNKCELK 1386
              + +  D     ++
Sbjct: 1153 LRDLDDEDEVAAPVE 1167


>gi|311070754|ref|YP_003975677.1| DNA-directed RNA polymerase subunit beta [Bacillus atrophaeus 1942]
 gi|310871271|gb|ADP34746.1| DNA-directed RNA polymerase subunit beta [Bacillus atrophaeus 1942]
          Length = 1194

 Score =  864 bits (2233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 603/964 (62%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI           
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      +  L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD------------------------A 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + +++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ LD++GSF ++ +  R
Sbjct: 536 KVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLDDEGSFVDDSIVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +VPR ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EA
Sbjct: 596 FRGENTVVPRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V  K SGAA++ K  GIVE+V+A  + +R   + D       +D Y L+KF
Sbjct: 656 PFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEDVDGQKVKGNLDKYSLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 776 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           VN GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR
Sbjct: 836 VNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 265/1181 (22%), Positives = 438/1181 (37%), Gaps = 139/1181 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 95   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  D +  
Sbjct: 155  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TDLIGE 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+ VGR 
Sbjct: 214  NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRY 273

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVD----LRNGKGTIDDID 457
            K+N +L++               P+    + ++  I   + L      L NG G      
Sbjct: 274  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYP 333

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            N G        + +K  +       E++I    ++   +++      +    +S      
Sbjct: 334  NGGVVEDEVTLQSIKI-FAPTDAEGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLL 392

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                 +   +H+ +    +    L    + G++R    V  R               +  
Sbjct: 393  HGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIR 452

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
              I  +      ++++ +               TN +  L+                   
Sbjct: 453  PVIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------H 482

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNM 696
                  L       E   +    + +        +       I  + +  S   +     
Sbjct: 483  KRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGF 542

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAI----VAKRAGIVEQVDAIRIVIRSVEGDL 752
                   +  E   V   ++ + A      +     A+       VD   +     E  +
Sbjct: 543  IETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLDDEGSFVDDSIVARFRGENTV 602

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             P      +    K   S    C+           +  +D        ++   A+     
Sbjct: 603  VPRNRVDYMDVSPKQVVSAATACIP---------FLENDDSNRALMGANMQRQAVPLMQP 653

Query: 813  VAFMPWHGYNF-----EDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             A     G  +       + +I +   +V      ++ +  +E +      G  +    +
Sbjct: 654  EAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEDVDGQKVKGNLDKYSLL 713

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              V        ++  I+ VG EV  G+IL    +      +     ++         +  
Sbjct: 714  KFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYE 772

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 773  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 827

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 828  -GIIRIGAEVNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 886

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               +      K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP
Sbjct: 887  IHDV------KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILP 940

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+
Sbjct: 941  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDV 1000

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1001 WETLEEAGMSRDAK----------------------------TVLYDG------------ 1020

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1021 --------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1066

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PE
Sbjct: 1067 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPE 1126

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            SF VL+KE+Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1127 SFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDDEDGKQAD 1167


>gi|157690891|ref|YP_001485353.1| DNA-directed RNA polymerase subunit beta [Bacillus pumilus
           SAFR-032]
 gi|182676554|sp|A8F976|RPOB_BACP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|157679649|gb|ABV60793.1| DNA-directed RNA polymerase subunit beta [Bacillus pumilus
           SAFR-032]
          Length = 1196

 Score =  864 bits (2233), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/958 (44%), Positives = 599/958 (62%), Gaps = 66/958 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V +   RD+TY+ PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGDPKYPVAESKERDVTYSAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 105 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI--V 237
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEILDLIGENEYLR 221

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFL 296
            +   D       A   +           ++  + +++S         L ++    +   
Sbjct: 222 NTLEKDNTENADKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKK 281

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + L    +AE +V+ ETGEI  E G ++D + L++             V     N 
Sbjct: 282 LHIKNRLFNQKLAETLVDPETGEILAEKGQILDRRVLDK-------------VLPYLENG 328

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                L  +      +  L   ++  P D                          G   +
Sbjct: 329 IGFRKLYPNGGVVEDEVELQSIKIYAPSD------------------------QEGEQVI 364

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N+  N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 365 NVIGNAYVEEAVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFR 424

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +T
Sbjct: 425 IGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELT 484

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +G
Sbjct: 485 HKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFG 544

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           FIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L +DGSF ++ +  R  GE  
Sbjct: 545 FIETPYRRVDPETGKVTPRIDYLTADEEDNYVVAQANALLADDGSFIDDNIIARFRGENT 604

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +VPR ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+P VGTG
Sbjct: 605 VVPRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPESPIVGTG 664

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           ME V  K SGAA++ +  G+VE+V+A  I +R   + D       +D Y L+KF RSNQ 
Sbjct: 665 MEYVSGKDSGAAVICRYPGVVERVEAKNIWVRRYEDVDGQQVKGNLDKYSLLKFVRSNQG 724

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++++SER+
Sbjct: 725 TCYNQRPIVSVGDEVVKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAIIMSERL 784

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  GD+
Sbjct: 785 VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDL 844

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 845 LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 902



 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 181/560 (32%), Positives = 265/560 (47%), Gaps = 69/560 (12%)

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +     +V      +I +  +E +      G  +    +  V        ++  I+ VG 
Sbjct: 678  ICRYPGVVERVEAKNIWVRRYEDVDGQQVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGD 737

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  G+IL    +   +  +     ++         +  D  +     +S  +V   ++ 
Sbjct: 738  EVVKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAII-----MSERLVKDDVYT 791

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
               I++ E      +   E + RD  +      RN+  R   I  G     G     K T
Sbjct: 792  SIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRIGAEVKDGDLLVGKVT 850

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  ++   R     F  +  +V+     +          +      K+   + GD++
Sbjct: 851  PKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV------KVFNREDGDEL 904

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPLG
Sbjct: 905  PPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLG 964

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E H+G A   LG  I S + D     D+                     
Sbjct: 965  VPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------- 1017

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 T ++DG                           TGEPFD
Sbjct: 1018 ---------------------TVLYDG--------------------------RTGEPFD 1030

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1031 NRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1090

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE+Q+LG+ + + + 
Sbjct: 1091 AAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSG 1150

Query: 1367 RTKNSAK--MEEIPDFNKCE 1384
              +      +E+  +  K +
Sbjct: 1151 DEEEIEMRDLEDDEETKKAD 1170


>gi|226309798|ref|YP_002769692.1| DNA-directed RNA polymerase subunit beta [Brevibacillus brevis NBRC
           100599]
 gi|254765275|sp|C0ZIH0|RPOB_BREBN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|226092746|dbj|BAH41188.1| DNA-directed RNA polymerase beta chain [Brevibacillus brevis NBRC
           100599]
          Length = 1179

 Score =  864 bits (2232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 444/964 (46%), Positives = 605/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  V+ +G  R R+ + +  E++ +P+LIE+Q+ SY  FL          +EGL+  F+
Sbjct: 1   MAGKVIQSGRHRQRRTYSRINEVLGLPNLIEIQQKSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+DVD+   RD+TYA PL++ +RL+          K
Sbjct: 51  DISPIQDFTGNLVLEFIDYSLGEPKYDVDESKERDVTYAAPLRVKVRLL---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++++    +   +GK  +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYN---TKVDKNGKQTF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KD+I+VRIDR RK+PVT  L ALG  S+ EIL+         
Sbjct: 159 TATVIPNRGAWLELETDAKDVIYVRIDRTRKIPVTVLLRALGFGSDIEILNLLGEDEYIK 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTVENAKSLLISRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +++  TGEI+ EAG +ID + LE I  +    I  + V 
Sbjct: 273 YKMNKKLHLKNRLYNQRLAETLIDTTTGEIFAEAGQMIDRRVLERIVPALEGSIGFIDVR 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           +                                G +   ++     N      D   +  
Sbjct: 333 THG------------------------------GVLEDEAIHLQSINIFSPIEDGKIIKV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G   ++           +HI   DI++ I   ++L +  G+ DDID+LGNRR+RSVGE+
Sbjct: 363 IGNGNVDKSF--------KHITPADIVSAINYFMNLLHSVGSTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDQNQITPQALINIRPVIASLKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETP RKV    G V  D+ YL+A EE+   +AQAN  LDEDG F  ++V CR
Sbjct: 535 RINDYGFIETPRRKVDPETGFVLTDISYLTADEEDVFNVAQANQPLDEDGRFVNDMVICR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE + VPR+K+DF+D SPKQVVS+A +LIPFLENDD+NR LMG NMQRQAVPLL  +A
Sbjct: 595 RKGEILSVPRDKVDFMDVSPKQVVSVATALIPFLENDDANRALMGSNMQRQAVPLLIPQA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME   A+ SG AIVAK  G VE+V A  I IR   E D       +D Y++ KF
Sbjct: 655 PFVGTGMEHKAAQDSGVAIVAKHPGQVERVTAREIWIRRYQEIDGRKVAGDLDKYKMHKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC+NQRP+V  GD + + DI+ DGPST+ G+LALGRN++VAFM W GYN+ED++
Sbjct: 715 IRSNQGTCINQRPIVSTGDWIEKGDIVGDGPSTEKGELALGRNVIVAFMTWEGYNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SE++V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAE
Sbjct: 775 LLSEKLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           +  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G SG +VDV++F R
Sbjct: 835 IQDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGSGIIVDVKVFTR 894

Query: 948 HGID 951
              D
Sbjct: 895 ENGD 898



 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 227/1149 (19%), Positives = 391/1149 (34%), Gaps = 104/1149 (9%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  + K     
Sbjct: 95   KVRLLNKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYNTKVDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI-RDIPILYVDSVN 353
                T+  +       ++       IY+             +       DI IL  + + 
Sbjct: 155  KQTFTATVIPNRGAWLELETDAKDVIYVRIDRTRKIPVTVLLRALGFGSDIEIL--NLLG 212

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
             + YI+NTL  D     + AL++IY  +RPG+  T   A+S+    FFD  +YDL++VGR
Sbjct: 213  EDEYIKNTLEKDNTDSTEKALIEIYERLRPGEPPTVENAKSLLISRFFDPKRYDLASVGR 272

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             KMN +L+L          +     + + L+D   G+   +    +  R +  +   L+ 
Sbjct: 273  YKMNKKLHLK--------NRLYNQRLAETLIDTTTGEIFAEAGQMIDRRVLERIVPALEG 324

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
                  +R    + E  +   + S+     I    ++  +           +       +
Sbjct: 325  SIGFIDVRTHGGVLEDEAIH-LQSINIFSPIEDGKIIKVIGNGNVDKSFKHITPADIVSA 383

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
                   L ++G            +R V      +     +     +    S+    ++ 
Sbjct: 384  INYFMNLLHSVGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDQNQIT 443

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                I    R V          +  + +           +          L       E 
Sbjct: 444  PQALI--NIRPVIASLK----EFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRER 497

Query: 654  ILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                   +          +       I  + +  S   +            +  E  FV 
Sbjct: 498  AGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSFARINDYGFIETPRRKVDPETGFVL 557

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            T +  + A       VA+    +             +  +      +      K    + 
Sbjct: 558  TDISYLTADEEDVFNVAQANQPL-----DEDGRFVNDMVICRRKGEILSVPRDKVDFMDV 612

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE-------- 824
            +    Q   V         +  A+              +L+   P+ G   E        
Sbjct: 613  SP--KQVVSVATALIPFLENDDANRALMGSNMQRQAVPLLIPQAPFVGTGMEHKAAQDSG 670

Query: 825  -DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
               +      V       I I  ++ +      G  +  +    +       I++  I+ 
Sbjct: 671  VAIVAKHPGQVERVTAREIWIRRYQEIDGRKVAGDLDKYKMHKFIRSNQGTCINQRPIVS 730

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             G  +  GD +VG      +  +     ++ A    +  +  D  L              
Sbjct: 731  TGDWIEKGD-IVGDGPSTEKGELALGRNVIVAFMTWEGYNYEDAILLS------------ 777

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
                  + K++   S+  E+ E  ARD       + R+I +   + L   +         
Sbjct: 778  ----EKLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERG------ 827

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                     I            +  +   + V  L  +     +I  ++ +   +     
Sbjct: 828  ---------IIRVGAEIQDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRV 878

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                 G++  VKVF         GD++       G+   +                    
Sbjct: 879  PHGGSGIIVDVKVFTREN-----GDELPP-----GVNQLV-------------------- 908

Query: 1124 PLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                  R+ + Q  +  +G       G K        + +    P  S +E V+      
Sbjct: 909  ------RVYIAQKRKISVGDKMAGRHGNKGVIARIMAEEDMPFLPDGSPVEIVLNPLGVP 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
             +++                G+ V+TPVFDGA +  +   L  A LD  G++IL+DG TG
Sbjct: 963  SRMNIGQVLETHLGMAAKLLGIHVATPVFDGARQAEVFETLAEAGLDRDGKTILFDGRTG 1022

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPFDR VTVG +YMLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1023 EPFDRRVTVGCVYMLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1082

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LG+ + 
Sbjct: 1083 EAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGMDVK 1142

Query: 1363 LENSRTKNS 1371
            + +   +  
Sbjct: 1143 ILSGDEQEI 1151


>gi|229074163|ref|ZP_04207209.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock4-18]
 gi|229094824|ref|ZP_04225829.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-29]
 gi|229100901|ref|ZP_04231705.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-28]
 gi|229113778|ref|ZP_04243213.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock1-3]
 gi|228669649|gb|EEL25056.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock1-3]
 gi|228682480|gb|EEL36553.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-28]
 gi|228688567|gb|EEL42440.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-29]
 gi|228708933|gb|EEL61060.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock4-18]
          Length = 1180

 Score =  864 bits (2232), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G V+D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                               K A      V    ++ +                 Y   +
Sbjct: 331 -------------------FKTAKPMGGVVAGDVELQSI--------------KIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   D++HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDIKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 258/1167 (22%), Positives = 426/1167 (36%), Gaps = 120/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            K+N +L++               P+    +  E  +   + L  +               
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTVLDRRTLDRILPYLEKNIGFKTAKP 336

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G++     ++     E   +      + +       I    +++++  FF    
Sbjct: 337  MGGVVAGDVELQSIKIYAPESEGE-RVINVIGNANITRDIKHITPGDILASISYFFNL-- 393

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            L ++ +  +         R          R       R V      R+   +T+      
Sbjct: 394  LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITPQA 449

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++     A +  +       + +       ++ +                         
Sbjct: 450  LINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KRRL 488

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 489  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIETP 548

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDPST 756
               +  E   V   ++ + A      +VA    K +   E +D   +     E  +    
Sbjct: 549  YRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTNKE 608

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                +    K   S    C+         D+  R  + A+     +  +     ++   M
Sbjct: 609  RIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGTGM 664

Query: 817  PWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       + +I +   +V       + +  +  +   T  G  +  +    +      
Sbjct: 665  EYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQGT 724

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+ VG EV  G+IL    +      +     +L         +  D  +     
Sbjct: 725  CYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII----- 778

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G  
Sbjct: 779  MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGAE 837

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G     K T      ++   R     F  +  +V+     +                
Sbjct: 838  VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------LD 891

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L D
Sbjct: 892  VKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLPD 951

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+         
Sbjct: 952  GTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAGM 1011

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1012 ANDAK----------------------------TILYDG--------------------- 1022

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1023 -----RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 1077

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+KE+
Sbjct: 1078 GEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIKEL 1137

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFN 1381
            Q+LG+ + + +S  K     +   D +
Sbjct: 1138 QSLGMDVKMMSSDDKEIEMRDTEDDDD 1164


>gi|288554717|ref|YP_003426652.1| DNA-directed RNA polymerase subunit beta [Bacillus pseudofirmus
           OF4]
 gi|288545877|gb|ADC49760.1| DNA-directed RNA polymerase subunit beta [Bacillus pseudofirmus
           OF4]
          Length = 1180

 Score =  864 bits (2231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 599/964 (62%), Gaps = 77/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARINEVLELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VD+   RD+T+A PL++ +RLI          K
Sbjct: 51  DISPIQDFTGNLVLEFIDYSLGEPKYPVDESKERDVTFAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++     +   +GK  +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSQ---KTDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGSDQEIIDLLGEDEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NSLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGE+  E G ++D ++L+ I  +   +I      
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEVIAEEGTLLDRRTLDRILPNLENNIG----- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   R    +    +  +  L   +V  P D                         
Sbjct: 328 -------FRTARASGGVVEDSEIDLQSIKVYAPDD------------------------Q 356

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   + +  N     +V+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 357 EGEQVIRIIGNGLVEREVKHITPADIIASINYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 416

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 417 LQNQFRIGLSRMERVVRERMSIQDPNMITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 476

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 477 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 536

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GF+ETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L +DGSF ++ +  R
Sbjct: 537 KVNEFGFMETPYRRVDPETGKVTAQIDYLTADEEDNYVVAQANARLADDGSFVDDNIIAR 596

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +VPRE++D++D SPKQVVS A S IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 597 FRGENTVVPRERLDYMDVSPKQVVSAATSCIPFLENDDSNRALMGANMQRQAVPLLIPEA 656

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRLMKF 767
           P VGTGME V AK SGAAIV+K  G+VE+V A  I +R  E          +D YRL KF
Sbjct: 657 PLVGTGMEHVSAKDSGAAIVSKHPGVVERVTAKEIWVRRTEEVDGKQVKGDLDKYRLQKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRP+V+ GD + + +I+ADGPS + G++ALGRN+LV FM W GYN+ED++
Sbjct: 717 IRSNQGTSYNQRPIVREGDVIEKREILADGPSMESGEMALGRNVLVGFMTWDGYNYEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAE
Sbjct: 777 ILSERLVKDDVYTSVHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR P G  G V+DV+IFNR
Sbjct: 837 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKIFNR 896

Query: 948 HGID 951
              D
Sbjct: 897 EDGD 900



 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 256/1052 (24%), Positives = 401/1052 (38%), Gaps = 108/1052 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D +  + Y+RN+L  D     + ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL
Sbjct: 208  IDLLGEDEYLRNSLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K+N +L++      + +              L + +      +       R++ 
Sbjct: 268  ANVGRYKINKKLHIKNRLFNQRL-----------AETLVDPETGEVIAEEGTLLDRRTLD 316

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             +L N       R  R+    +   +ID    +           V     +  + +  +H
Sbjct: 317  RILPNLENNIGFRTARASGGVVEDSEIDLQSIKVYAPDDQEGEQVIRIIGNGLVEREVKH 376

Query: 529  VNSLSRITHTRRL-SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +     I       + L   G       +  R +     G +   +   G +        
Sbjct: 377  ITPADIIASINYFFNLLHGVGDTDDIDHLGNRRLRS--VGELLQNQFRIGLSRMERVVRE 434

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              + +     I           + +   +  + +           +          L   
Sbjct: 435  RMS-IQDPNMITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPG 493

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                E        + +        +       I  + +  S   +            +  
Sbjct: 494  GLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNEFGFMETPYRRVDP 553

Query: 707  EAPFVGTGMESVVAKSSGAAI----VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            E   V   ++ + A      +     A+ A     VD   I     E  + P      + 
Sbjct: 554  ETGKVTAQIDYLTADEEDNYVVAQANARLADDGSFVDDNIIARFRGENTVVPRERLDYMD 613

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
               K   S   +C+           +  +D  ++              +L+   P  G  
Sbjct: 614  VSPKQVVSAATSCIP---------FLENDD--SNRALMGANMQRQAVPLLIPEAPLVGTG 662

Query: 823  FE-------DSMLISERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNVSEEGL 873
             E        + ++S+     +  T+  I        D K   G  +  R    +     
Sbjct: 663  MEHVSAKDSGAAIVSKHPGVVERVTAKEIWVRRTEEVDGKQVKGDLDKYRLQKFIRSNQG 722

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             + ++  I+  G  +   +IL    +      M     +L         +  D  +    
Sbjct: 723  TSYNQRPIVREGDVIEKREILADGPS-MESGEMALGRNVLVGFMTWDGYNYEDAII---- 777

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      +N+  R   I  G 
Sbjct: 778  -LSERLVKDDVYTSVHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDER-GIIRVGA 835

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+          +          
Sbjct: 836  EVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIV------L 889

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPFL 
Sbjct: 890  DVKIFNREDGDELPPGVNQLVRVYIVQKRKINQGDKMAGRHGNKGVISRILPEEDMPFLP 949

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+        
Sbjct: 950  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHVASPVFDGANEEDVWGTLEEAG 1009

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                  DG                    
Sbjct: 1010 MAR-----------------------------------DGKTV----------------- 1017

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1018 --LYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1075

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1076 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1135

Query: 1354 MQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +Q+LG+ + + +S  +     E +  D    E
Sbjct: 1136 LQSLGMDVKMLSSNEEEIEMRELDDEDEQTSE 1167


>gi|170293422|gb|ACB12764.1| DNA-directed RNA polymerase [Geobacillus stearothermophilus ATCC
           7953]
          Length = 1074

 Score =  864 bits (2231), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/948 (46%), Positives = 600/948 (63%), Gaps = 78/948 (8%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD P
Sbjct: 51  IDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W++ E 
Sbjct: 102 LMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAWLEYET 158

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             +      +   L+
Sbjct: 159 DAKDVVYVRIDRTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLRNTLEKDNTDSTEKALI 218

Query: 256 VGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGL 306
                      +  GE   +E+ K L +      K           +       + L   
Sbjct: 219 ------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGRYKINKKLHIKNRLFNQ 272

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            +AE I++ ET E+  EAG +ID ++L  +     + + +          Y     V D 
Sbjct: 273 RLAETIIDPETKEVIAEAGAMIDRRTLNRLLPYLEKGVGL--------RTYRPAEGVADG 324

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             +     +   ++  P D                              +N+  N    +
Sbjct: 325 PIE-----VQTVKIYAPNDPDN------------------------EKVINIIGNGFIAE 355

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER +
Sbjct: 356 DVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVV 415

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N L+ +TH RRLSALG 
Sbjct: 416 RERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGP 475

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV- 605
           GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIETPYR+V 
Sbjct: 476 GGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNKFGFIETPYRRVD 535

Query: 606 -CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
              G+VT+ + YL+A EE+N  +AQAN  L EDG+F EE V  R  GE I+V R+++D++
Sbjct: 536 PETGRVTDQIDYLTADEEDNYVVAQANVPLAEDGTFLEENVIARFRGENIVVKRDRVDYM 595

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+ EAP VGTGME V AK SG
Sbjct: 596 DVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPEAPIVGTGMEYVSAKDSG 655

Query: 725 AAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           AA++ K  GIVE+V+A  I +R  +E D       +D YRL+KF RSNQ TC NQRP+VK
Sbjct: 656 AAVICKHRGIVERVEAKEIWVRRLIEVDGKEVKGDLDKYRLLKFVRSNQGTCYNQRPIVK 715

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V + +I+ADGPS D G+LALGRN+LVAFM W GYN+ED++++SER+V EDV+TSIH
Sbjct: 716 KGDIVEKGEILADGPSMDKGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKEDVYTSIH 775

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IEE+E  +RDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GD+LVGK+TPKG 
Sbjct: 776 IEEYEAESRDTKLGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKDGDLLVGKVTPKGM 835

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 836 TELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 883



 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 147/458 (32%), Positives = 199/458 (43%), Gaps = 77/458 (16%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  V        ++  I+  G  V  G+IL    +   +  +     +L A 
Sbjct: 689  GDLDKYRLLKFVRSNQGTCYNQRPIVKKGDIVEKGEILADGPS-MDKGELALGRNVLVAF 747

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 748  MTWDGYNYEDAIIMSERLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEDALKN 807

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 808  LDERGIVRIGAEVKDGDLLVGKVTPKGMTELTAEERLLHAIFGEKAR------------- 854

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 855  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 910

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  
Sbjct: 911  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAAKKLGLH 970

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I S + D     D+  +                                       T ++
Sbjct: 971  IASPVFDGATEEDVWNILEEAGLARDAK----------------------------TVLY 1002

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 1003 DG--------------------------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1036

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1037 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1074


>gi|229159275|ref|ZP_04287299.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus R309803]
 gi|228624167|gb|EEK80969.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus R309803]
          Length = 1180

 Score =  863 bits (2230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   D++HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVISNANITRDIKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 254/1174 (21%), Positives = 411/1174 (35%), Gaps = 134/1174 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS----- 409
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+     
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 410  ------TVGRVKMNMRL--NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                   +     N RL   L  P+    +  E  I   + L  +               
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                  G++     ++     E   +      + +       I    +++++  FF    
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGE-RVINVISNANITRDIKHITPGDILASISYFFNL-- 393

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            L ++ +  +         R          R       R V      R+   +T+      
Sbjct: 394  LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITPQA 449

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L++     A +  +       + +       ++ +                         
Sbjct: 450  LINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KRRL 488

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQA 700
              L       E        + +        +       I  + +  S   +         
Sbjct: 489  SALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIETP 548

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
               +  E   V           +G             V A   +  S EG+         
Sbjct: 549  YRRVDPETGLV-----------TGQVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 761  IYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LALGR 809
                       +   ++  P  +V             D     +G          +    
Sbjct: 598  FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 810  NMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
             ++   M +       + +I +   +V       + +  +  +   T  G  +  +    
Sbjct: 658  PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +        ++  I+ VG EV  G+IL    +      +     +L         +  D 
Sbjct: 718  IRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDA 776

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R  
Sbjct: 777  II-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-G 830

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G     G     K T      ++   R     F  +  +V+     +         
Sbjct: 831  IIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII- 889

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP E
Sbjct: 890  -----LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEE 944

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+  
Sbjct: 945  DMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWG 1004

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                    T ++DG              
Sbjct: 1005 TIEEAGMANDAK----------------------------TILYDG-------------- 1022

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                         TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1023 ------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKA 1070

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF
Sbjct: 1071 QFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESF 1130

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
             VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1131 KVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|229027950|ref|ZP_04184103.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1271]
 gi|228733338|gb|EEL84167.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1271]
          Length = 1180

 Score =  863 bits (2230), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGQVDYLTADEEDNYVVAQANMKLSEEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 183/568 (32%), Positives = 263/568 (46%), Gaps = 69/568 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 664  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 723

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 724  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 779  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 836

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 837  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 890

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 891  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLP 950

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+        
Sbjct: 951  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAG 1010

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1011 MANDAK----------------------------TILYDG-------------------- 1022

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1023 ------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1076

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1077 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1136

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +Q+LG+ + + +S  K     +   D +
Sbjct: 1137 LQSLGMDVKMMSSDDKEIEMRDTEDDDD 1164


>gi|118475871|ref|YP_893022.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           str. Al Hakam]
 gi|228912841|ref|ZP_04076488.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228925355|ref|ZP_04088451.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228931604|ref|ZP_04094510.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228943908|ref|ZP_04106293.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228983357|ref|ZP_04143570.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|229089233|ref|ZP_04220514.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-42]
 gi|229119764|ref|ZP_04249025.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus 95/8201]
 gi|229136948|ref|ZP_04265575.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST26]
 gi|229182496|ref|ZP_04309747.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus BGSC 6E1]
 gi|229194492|ref|ZP_04321295.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus m1293]
 gi|118415096|gb|ABK83515.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           str. Al Hakam]
 gi|228588958|gb|EEK46973.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus m1293]
 gi|228600951|gb|EEK58520.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus BGSC 6E1]
 gi|228646486|gb|EEL02693.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST26]
 gi|228663665|gb|EEL19244.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus 95/8201]
 gi|228694072|gb|EEL47754.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock3-42]
 gi|228776347|gb|EEM24700.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228815741|gb|EEM61977.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228828032|gb|EEM73760.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228834277|gb|EEM79818.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228846777|gb|EEM91782.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
          Length = 1180

 Score =  863 bits (2229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 606

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 607  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 662

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 663  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 722

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 723  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 778

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 779  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 835

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 836  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 889

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 890  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 949

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 950  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1009

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1010 GMANDAK----------------------------TILYDG------------------- 1022

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1023 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1075

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1076 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1135

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1136 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|228919052|ref|ZP_04082431.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228937404|ref|ZP_04100050.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228950650|ref|ZP_04112784.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228970290|ref|ZP_04130949.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228976860|ref|ZP_04137272.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           Bt407]
 gi|229067867|ref|ZP_04201184.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus F65185]
 gi|229107788|ref|ZP_04237424.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock1-15]
 gi|229125619|ref|ZP_04254651.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-Cer4]
 gi|229142908|ref|ZP_04271349.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST24]
 gi|229148511|ref|ZP_04276767.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus m1550]
 gi|229176702|ref|ZP_04304106.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus 172560W]
 gi|229188387|ref|ZP_04315435.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           10876]
 gi|228595061|gb|EEK52832.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           10876]
 gi|228606745|gb|EEK64162.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus 172560W]
 gi|228634927|gb|EEK91500.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus m1550]
 gi|228640529|gb|EEK96918.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-ST24]
 gi|228657811|gb|EEL13617.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus
           BDRD-Cer4]
 gi|228675637|gb|EEL30845.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock1-15]
 gi|228715226|gb|EEL67085.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus F65185]
 gi|228782830|gb|EEM30996.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           Bt407]
 gi|228789399|gb|EEM37319.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228809001|gb|EEM55486.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228822237|gb|EEM68219.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228840577|gb|EEM85839.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
          Length = 1180

 Score =  863 bits (2229), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 262/1176 (22%), Positives = 429/1176 (36%), Gaps = 138/1176 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                 +  E   V   ++ + A                 V A   +  S EG+       
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTA-----------DEEDNYVVAQANMKLSDEGEFLSEDIV 595

Query: 759  VDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LAL 807
                         +   ++  P  +V             D     +G          +  
Sbjct: 596  ARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNP 655

Query: 808  GRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               ++   M +       + +I +   +V       + +  +  +   T  G  +  +  
Sbjct: 656  ESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQ 715

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  I+ VG EV  G+IL    +      +     +L         +  
Sbjct: 716  KFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYE 774

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 775  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 829

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 830  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 888

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 889  I------LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILP 942

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+
Sbjct: 943  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDV 1002

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1003 WGTIEEAGMANDAK----------------------------TILYDG------------ 1022

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1023 --------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1068

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PE
Sbjct: 1069 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPE 1128

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            SF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1129 SFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|299821074|ref|ZP_07052962.1| DNA-directed RNA polymerase subunit beta [Listeria grayi DSM 20601]
 gi|299816739|gb|EFI83975.1| DNA-directed RNA polymerase subunit beta [Listeria grayi DSM 20601]
          Length = 1181

 Score =  862 bits (2228), Expect = 0.0,   Method: Composition-based stats.
 Identities = 444/964 (46%), Positives = 604/964 (62%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M+   V  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MSGHDVKYGRHRTRRSYARISEVLELPNLIEIQTASYQWFL----------DEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K
Sbjct: 51  DISPIEDFAGNLSLEFIDYDLGEPKYSVEESKSRDANYAAPLRVKLRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+    +   +G+  +
Sbjct: 102 ETGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---DKIDKNGRTGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ +I+          
Sbjct: 159 GSTVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQDIIELVGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ + L        K         
Sbjct: 219 NTLEKDNTDNAEKALL------EIYERLRPGEPPTVENARNLLISRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    GD++D ++L++I       IP L   
Sbjct: 273 YKINKKLHLKNRLFNQRLAETLVDPETGEIIASKGDILDRRALDQI-------IPNLESG 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 +  N ++ D        ++   ++  P D                         
Sbjct: 326 VGFRTLHPSNGIMDDSV------VVQSIKIYAPND------------------------- 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N    +DV+HI   DI++ I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 355 -EEKEINIIGNAYIEEDVKHITPSDIVSSISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDMSTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 474 PLGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LD+DGSF EE V  R
Sbjct: 534 KVNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDDDGSFAEEEVMAR 593

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V +E++D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 594 FRSENLAVTKERVDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEA 653

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V AK SGAAI AK  GIVE V+A  I IR   + D    T G+D Y L KF
Sbjct: 654 PFVGTGMEHVSAKDSGAAITAKYDGIVEHVEAKEIWIRRVSDVDGTEVTGGIDKYTLRKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP V  GD V + +I+A+GPS D G+LALGRN+LVAFM W GYN+ED++
Sbjct: 714 VRSNQGTCYNQRPNVAEGDRVVKGEILANGPSMDSGELALGRNVLVAFMTWDGYNYEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAE
Sbjct: 774 IMSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V   D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R
Sbjct: 834 VKDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 EAGD 897



 Score =  511 bits (1315), Expect = e-142,   Method: Composition-based stats.
 Identities = 249/1048 (23%), Positives = 397/1048 (37%), Gaps = 114/1048 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++ V +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A ++    FFD  +YDL
Sbjct: 208  IELVGDNEYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVENARNLLISRFFDPKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 268  ASVGRYKINKKLHLK--------NRLFNQRLAETLVDPETGEIIASKGDILDRRALDQII 319

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L++   +G   +  S      SV + S+      + +  ++ +   +    +  +   
Sbjct: 320  PNLES--GVGFRTLHPSNGIMDDSVVVQSIKIYAPNDEEKEINIIGNAYIEEDVKHITPS 377

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 378  DIVSSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 437

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             + +     I    R V          +  + +                      L    
Sbjct: 438  MSTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 491

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 492  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDPE 551

Query: 708  APFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
               V   ++ + A  + +     A      +   A   V+     +    T     Y  +
Sbjct: 552  TNRVTDKIDYLTADEEDNYVVAQANSKLDDDGSFAEEEVMARFRSENLAVTKERVDYMDV 611

Query: 766  KFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              ++  S    C+           +  +D        ++   A+      A     G   
Sbjct: 612  SPKQVVSVATACIP---------FLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEH 662

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E+  R           G  +       V        
Sbjct: 663  VSAKDSGAAITAKYDGIVEHVEAKEIWIRRVSDVDGTEVTGGIDKYTLRKFVRSNQGTCY 722

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++   +  G  V  G+IL    +      +     +L A       +  D  +       
Sbjct: 723  NQRPNVAEGDRVVKGEILANGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SE 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
              V D    + H  +    +   +    E    +    +D    LD     R+   +   
Sbjct: 778  RLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDN 837

Query: 994  NAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            + + G    K  T L+++  L+      +  +      +V      +             
Sbjct: 838  DLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV------------ 885

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF
Sbjct: 886  -LDVKIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPF 944

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            + DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+      
Sbjct: 945  MPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEE 1004

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                                T ++DG                  
Sbjct: 1005 AGMARDAK----------------------------TILYDG------------------ 1018

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
                     TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GG
Sbjct: 1019 --------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGG 1070

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    + G PESF VL+
Sbjct: 1071 QRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPQPGVPESFKVLI 1130

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+LG+ + + ++  +     +   D
Sbjct: 1131 KELQSLGMDVKILSADEEEIEFRDLDDD 1158


>gi|65317559|ref|ZP_00390518.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Bacillus anthracis str. A2012]
          Length = 1180

 Score =  862 bits (2228), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 264/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 606

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 607  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 662

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 663  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 722

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 723  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 778

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 779  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 835

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 836  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 889

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 890  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 949

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 950  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1009

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1010 GMANDAK----------------------------TILYDG------------------- 1022

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1023 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1075

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+K
Sbjct: 1076 RFGEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIK 1135

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1136 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|228956543|ref|ZP_04118339.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228803108|gb|EEM49930.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           serovar pakistani str. T13001]
          Length = 1180

 Score =  862 bits (2228), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 262/1176 (22%), Positives = 429/1176 (36%), Gaps = 138/1176 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                 +  E   V   ++ + A                 V A   +  S EG+       
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTA-----------DEEDNYVVAQANMKLSDEGEFLSEDIV 595

Query: 759  VDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LAL 807
                         +   ++  P  +V             D     +G          +  
Sbjct: 596  ARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNP 655

Query: 808  GRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               ++   M +       + +I +   +V       + +  +  +   T  G  +  +  
Sbjct: 656  ESPIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQ 715

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  I+ VG EV  G+IL    +      +     +L         +  
Sbjct: 716  KFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYE 774

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 775  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 829

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 830  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 888

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 889  I------LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILP 942

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+
Sbjct: 943  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDV 1002

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1003 WGTIEEAGMANDAK----------------------------TILYDG------------ 1022

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1023 --------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1068

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PE
Sbjct: 1069 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPE 1128

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            SF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1129 SFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|229041007|ref|ZP_04189770.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH676]
 gi|228727304|gb|EEL78498.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH676]
          Length = 1180

 Score =  862 bits (2227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/964 (45%), Positives = 595/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQIVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 261/1176 (22%), Positives = 428/1176 (36%), Gaps = 138/1176 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                 +  E   V   ++ + A                 V A   +  S EG+       
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTA-----------DEEDNYVVAQANMKLSDEGEFLSEDIV 595

Query: 759  VDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LAL 807
                         +   ++  P  +V             D     +G          +  
Sbjct: 596  ARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNP 655

Query: 808  GRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               ++   M +       + +I +   +V       + +  +  +      G  +  +  
Sbjct: 656  ESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQIVKGDLDRYKMQ 715

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  I+ VG EV  G+IL    +      +     +L         +  
Sbjct: 716  KFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYE 774

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 775  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 829

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 830  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 888

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 889  I------LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILP 942

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+
Sbjct: 943  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDV 1002

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 1003 WGTIEEAGMANDAK----------------------------TILYDG------------ 1022

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1023 --------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1068

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PE
Sbjct: 1069 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPE 1128

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            SF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1129 SFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|172056132|ref|YP_001812592.1| DNA-directed RNA polymerase subunit beta [Exiguobacterium sibiricum
            255-15]
 gi|171988653|gb|ACB59575.1| DNA-directed RNA polymerase, beta subunit [Exiguobacterium sibiricum
            255-15]
          Length = 1185

 Score =  862 bits (2227), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/1015 (42%), Positives = 618/1015 (60%), Gaps = 78/1015 (7%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M   +V  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL+  F 
Sbjct: 1    MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTNSYEWFLR----------EGLREMFH 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
             + PI+ F+G  +LEF+ Y    PK+ +D+   RD+TY+ PL++ +RL           K
Sbjct: 51   DISPISDFTGNLVLEFIDYSLGEPKYSIDESKERDVTYSAPLRVKVRL---------QNK 101

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++++   +   +GK  +
Sbjct: 102  ETGELKEQEVFMGDFPLMTESGTFIINGAERVIVSQLVRSPSVYYNNKLDK---NGKRGF 158

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
            +  +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  ++ EI+          
Sbjct: 159  SATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGTDQEIIDLLGDDEYLR 218

Query: 240  QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
               +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219  NSLEKDNTETTEKALI------EIYERLRPGEPPTVENAKALLVSRFFDPKRYDLANVGR 272

Query: 292  -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              +       + L G  +AE +V+ ETGE+  E G V+D + L+++       +  +   
Sbjct: 273  CKINKKLHLKNRLFGQKLAETLVDPETGEVIAEEGTVLDRRMLDKVLPFLEGSVGYI--- 329

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                         T      +   L   +V  P D                         
Sbjct: 330  ---------EATPTGGVTQGEAFNLQSIKVFAPDD------------------------A 356

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             G   +N+  N +   D++HI   D+IA I    +L +  GT DDID+LGNRR+RSVGE+
Sbjct: 357  EGERIINIIGNGNIDRDIKHITPADMIAAINYFFNLLHEVGTTDDIDHLGNRRLRSVGEL 416

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            L+NQ+R+GL RMER +KER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 417  LQNQFRIGLSRMERVVKERMSIQDQNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 476

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             L+ +TH RRLSALG GG+ R RAG E+RDVH +HY R+CP ET EG NIGL++SL+SFA
Sbjct: 477  PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYSRMCPIETPEGPNIGLINSLSSFA 536

Query: 591  RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +VN YGFIE PYR+V    G VTN++ Y++A EE+   +AQAN  L E+ +F +  V  R
Sbjct: 537  KVNEYGFIEAPYRRVDPETGVVTNEIHYMTADEEDLYVVAQANMLLTEEKTFQDTHVLSR 596

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              G+ + V   ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+
Sbjct: 597  FRGQNLSVEPARVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLDPES 656

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
            P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +     +D Y++ KF
Sbjct: 657  PIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQGELDRYKIQKF 716

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV FM W GYN+ED++
Sbjct: 717  IRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAV 776

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            ++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D+ GII VGAE
Sbjct: 777  IMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAE 836

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV+IF+R
Sbjct: 837  VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDR 896

Query: 948  -HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
             +G + +     + R  I    +  + +++         +  IL  ++    P G
Sbjct: 897  DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDG 951



 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 258/1174 (21%), Positives = 437/1174 (37%), Gaps = 136/1174 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    S    I+  E+VI S    +  +  + K     
Sbjct: 95   KVRLQNKETGELKEQEVFMGDFPLMTESGTFIINGAERVIVSQLVRSPSVYYNNKLDKNG 154

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G ++  +       ++       +Y+             +          + +D + +
Sbjct: 155  KRGFSATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGTDQEI-IDLLGD 213

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            + Y+RN+L  D  +  + AL++IY  +RPG+  T   A+++    FFD  +YDL+ VGR 
Sbjct: 214  DEYLRNSLEKDNTETTEKALIEIYERLRPGEPPTVENAKALLVSRFFDPKRYDLANVGRC 273

Query: 415  KMNMRLNLD-------------TPDDVRHIRKEDIIAIIKILVD----LRNGKGTIDDID 457
            K+N +L+L               P+    I +E  +   ++L      L    G I+   
Sbjct: 274  KINKKLHLKNRLFGQKLAETLVDPETGEVIAEEGTVLDRRMLDKVLPFLEGSVGYIEATP 333

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
              G  +  +        +       ER I    +      +      +    ++      
Sbjct: 334  TGGVTQGEAFNLQSIKVFAPDDAEGERIINIIGNGNIDRDIKHITPADMIAAINYFFNLL 393

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                 +   +H+ +    +    L    + G++R    V+ R            A  +  
Sbjct: 394  HEVGTTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVKERMSIQDQNAITPQALINIR 453

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
              I  +      ++++ +               TN +  L+                   
Sbjct: 454  PVIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------H 483

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNM 696
                  L       E        + +   S    +       I  + +  S   +     
Sbjct: 484  KRRLSALGPGGLTRERAGFEVRDVHYSHYSRMCPIETPEGPNIGLINSLSSFAKVNEYGF 543

Query: 697  QRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                   +  E   V   +  + A  +       A      E+      V+    G    
Sbjct: 544  IEAPYRRVDPETGVVTNEIHYMTADEEDLYVVAQANMLLTEEKTFQDTHVLSRFRGQNLS 603

Query: 755  STSGVDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                   Y  +  ++  S    C+           +  +D        ++   A+     
Sbjct: 604  VEPARVDYMDVSPKQVVSAATACIP---------FLENDDSNRALMGANMQRQAVPLLDP 654

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDI 865
             + +   G  +  +      +V++    +  +   E++ R T         G  +  +  
Sbjct: 655  ESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQGELDRYKIQ 714

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  II VG  V+ G+IL    +      +     +L         +  
Sbjct: 715  KFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPS-MDGGELALGRNVLVGFMTWDGYNYE 773

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      +N+  R
Sbjct: 774  DAVI-----MSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDR 828

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +    +  
Sbjct: 829  -GIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGI 887

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      KI     GD++ PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 888  I------LDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILP 941

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP++ DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG K+ S + D     D+
Sbjct: 942  EEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAARQLGIKVASPVFDGAREEDV 1001

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                            A  E        
Sbjct: 1002 W-----------------------------------------------ATIEE------- 1007

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            A +D   ++ILYDG +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1008 AGMDRDAKTILYDGRSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1067

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD +GR + YE+IV G +  + G PE
Sbjct: 1068 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDTIGRVKAYEAIVKGENVPQPGVPE 1127

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            SF VL+KE+Q+LG+ + + ++  +     ++  D
Sbjct: 1128 SFRVLIKELQSLGMDVKMMSAEDEEIEMKDDDED 1161


>gi|295702342|ref|YP_003595417.1| DNA-directed RNA polymerase subunit beta [Bacillus megaterium DSM
           319]
 gi|294800001|gb|ADF37067.1| DNA-directed RNA polymerase, beta subunit [Bacillus megaterium DSM
           319]
          Length = 1187

 Score =  862 bits (2226), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 595/964 (61%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V +   RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIDDFTGNLSLEFIDYSLGEPKYSVGESKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  Y
Sbjct: 102 ETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKLDKNGKKGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYIR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTETTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +         L    +AE +V+ ETGEI  E G +ID + L+ +              
Sbjct: 273 YKINKKLHIKHRLFNQKLAETLVDPETGEIIAEKGAMIDRRLLDRLI------------- 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +        T          D  L   ++  P D                         
Sbjct: 320 PMLEGGVNFKTYSPVGGVVEDDVTLQSIKIYAPNDP------------------------ 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   + +  N    ++V++I   DI+A I    +L +  G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEKIITVSGNAYVTEEVKNITPADILASISYFFNLLHQVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLGELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++    GKVT  + YL+A EE+N  +AQAN+ L +DGSF +E V  R
Sbjct: 536 KVNKFGFIETPYRRIDPETGKVTERIDYLTADEEDNYVVAQANARLGDDGSFLDENVVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  ++ R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 596 FRGENTVIRRDRLDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V  K SGAA++ K  G+VE+V+A +I +R   E D       +D Y+L+KF
Sbjct: 656 PIVGTGMEYVSGKDSGAAVICKYPGVVERVEAKQIFVRRYEEVDGQKVKGNLDQYKLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 776 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 184/575 (32%), Positives = 269/575 (46%), Gaps = 79/575 (13%)

Query: 816  MPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       I +  +E +      G  +  + +  V     
Sbjct: 662  MEYVSGKDSGAAVICKYPGVVERVEAKQIFVRRYEEVDGQKVKGNLDQYKLLKFVRSNQG 721

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +   +  +     ++         +  D  +    
Sbjct: 722  TCYNQRPIVSVGDEVVKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMSER 780

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      +  +
Sbjct: 781  LVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGD 840

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L G+    G         L   +  E  R      +++       +             
Sbjct: 841  LLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI------------- 886

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                   K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP ED
Sbjct: 887  ---ILDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEED 943

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+   
Sbjct: 944  MPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHVASPVFDGAREEDVW-- 1001

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                         A  E        A +
Sbjct: 1002 ---------------------------------------------ATIEE-------AGM 1009

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
                +++LYDG TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1010 SRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQ 1069

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1070 FGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPESFK 1129

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            VL+KE+Q+LG+ + + ++  +    M+   D  + 
Sbjct: 1130 VLIKELQSLGMDVKMLSADEQEIDIMDSEEDHEQP 1164


>gi|294496975|ref|YP_003560675.1| DNA-directed RNA polymerase subunit beta [Bacillus megaterium QM
           B1551]
 gi|294346912|gb|ADE67241.1| DNA-directed RNA polymerase, beta subunit [Bacillus megaterium QM
           B1551]
          Length = 1187

 Score =  862 bits (2226), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 596/964 (61%), Gaps = 78/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V +   RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIDDFTGNLSLEFIDYSLGEPKYSVGESKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  Y
Sbjct: 102 ETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKLDKNGKKGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYIR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLEKDNTETTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +         L    +AE +V+ ETGEI  E G +ID + L+ +              
Sbjct: 273 YKINKKLHIKHRLFNQKLAETLVDPETGEIIAEKGAMIDRRLLDRLI------------- 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +        T          D  L   ++  P D                         
Sbjct: 320 PMLEGGVNFKTYSPVGGVVEDDVTLQSIKIYAPNDP------------------------ 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   + +  N    ++V++I   DI+A I    +L +  G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGEKIITVSGNAYVTEEVKNITPADILASISYFFNLLHQVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 476 PLGELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++    GKVT  + YL+A EE+N  +AQAN+ L +DGSF +E V  R
Sbjct: 536 KVNKFGFIETPYRRIDPETGKVTERIDYLTADEEDNYVVAQANARLGDDGSFLDENVVAR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  ++ R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 596 FRGENTVIRRDRLDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V  K SGAA++ K  G+VE+V+A +I++R   E D       +D Y+L+KF
Sbjct: 656 PIVGTGMEYVSGKDSGAAVICKYPGVVERVEAKQIIVRRYEEVDGQKVKGNLDQYKLLKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++
Sbjct: 716 VRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 776 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 836 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 895

Query: 948 HGID 951
              D
Sbjct: 896 EDGD 899



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 184/575 (32%), Positives = 269/575 (46%), Gaps = 79/575 (13%)

Query: 816  MPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       I +  +E +      G  +  + +  V     
Sbjct: 662  MEYVSGKDSGAAVICKYPGVVERVEAKQIIVRRYEEVDGQKVKGNLDQYKLLKFVRSNQG 721

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +   +  +     ++         +  D  +    
Sbjct: 722  TCYNQRPIVSVGDEVVKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMSER 780

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      +  +
Sbjct: 781  LVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGD 840

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L G+    G         L   +  E  R      +++       +             
Sbjct: 841  LLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI------------- 886

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                   K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP ED
Sbjct: 887  ---ILDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEED 943

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+   
Sbjct: 944  MPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHVASPVFDGAREEDVW-- 1001

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                         A  E        A +
Sbjct: 1002 ---------------------------------------------ATIEE-------AGM 1009

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
                +++LYDG TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1010 SRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQ 1069

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1070 FGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPESFK 1129

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            VL+KE+Q+LG+ + + ++  +    M+   D  + 
Sbjct: 1130 VLIKELQSLGMDVKMLSADEQEIDIMDSEEDHEQP 1164


>gi|229015504|ref|ZP_04172502.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1273]
 gi|229021713|ref|ZP_04178295.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1272]
 gi|228739581|gb|EEL89995.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1272]
 gi|228745791|gb|EEL95795.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus AH1273]
          Length = 1180

 Score =  862 bits (2226), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 4   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI          K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK  +
Sbjct: 105 ETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          S
Sbjct: 162 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYLS 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L        K         
Sbjct: 222 NTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGR 275

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I      
Sbjct: 276 YKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG----- 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                               +         +        Y   +
Sbjct: 331 ---------------------------------FKTAKPMGGVVEGDVELQSIKIYAPES 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 358 EGERSINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +  R
Sbjct: 538 KVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVAR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 598 FRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAA++ K  G+VE+V+A  I +R  VE D       +D Y++ KF
Sbjct: 658 PIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREIWVRRYVEVDGQIVKGDLDRYKMQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED++
Sbjct: 718 IRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 778 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 98   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 158  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 217  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 276

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 277  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 336

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ERSI    ++     V     I    +++++  FF  
Sbjct: 337  MGGVVEGDVELQSIKIYAPESEGERSINVIGNANITRDV---KHITPGDILASISYFFNL 393

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 394  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 447

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 448  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 486

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 487  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 546

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 547  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 606

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 607  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 662

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       I +  +  +      G  +  +    +    
Sbjct: 663  GMEYVSAKDSGAAVICKHPGVVERVEAREIWVRRYVEVDGQIVKGDLDRYKMQKFIRSNQ 722

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 723  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 778

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 779  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 835

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 836  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 889

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 890  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 949

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 950  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 1009

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 1010 GMANDAK----------------------------TILYDG------------------- 1022

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1023 -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1075

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE+IV G +  E G PESF VL+K
Sbjct: 1076 RFGEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKTYEAIVKGENVPEPGVPESFKVLIK 1135

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1136 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1164


>gi|257868143|ref|ZP_05647796.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC30]
 gi|257874582|ref|ZP_05654235.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC10]
 gi|257877752|ref|ZP_05657405.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC20]
 gi|257802257|gb|EEV31129.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC30]
 gi|257808746|gb|EEV37568.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC10]
 gi|257811918|gb|EEV40738.1| DNA directed RNA polymerase subunit beta [Enterococcus
           casseliflavus EC20]
          Length = 1208

 Score =  861 bits (2225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 591/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIEGFNGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRSLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETLGA------------ 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++     +   + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTEPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N       R +R  DIIA +    +L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EQEVNVIGNGYPDTATRTVRPADIIASMSYFFNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDGSF  ++V  R
Sbjct: 543 KVNKYGFIETPYRRVDRETGRVTDKIDYLTADTEDHYVVAQANSLLNEDGSFVNDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 ATSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  GIVE VDA  + +R   G LD       +Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGIVEYVDAAEVRVRRDNGALD-------VYSVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPLV +G++V + DI+ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPLVALGEKVEKGDILADGPSMEQGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 184/583 (31%), Positives = 259/583 (44%), Gaps = 82/583 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       ++    PW G   E                   I E+   A        
Sbjct: 646  MGANMQRQAVPLINPKAPWVGTGMEYKSAHDSGAALLCKHDG--IVEYVDAAEVRVRRDN 703

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  ++             + ++  ++ +G +V  GDIL    +   +  M   + +L A 
Sbjct: 704  GALDVYSVTKFRRSNSGTSYNQRPLVALGEKVEKGDILADGPS-MEQGEMALGQNVLVAF 762

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
               +  +  D  +     V   V        +  +  +  +  E    +I  +  D    
Sbjct: 763  MTWEGYNYEDAIIMSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKD 822

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      +  ++L G+    G         L   +  E  R           +V
Sbjct: 823  LDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EV 871

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +          +      KI   + GD++ PGV  +V+V++  KR I  GDKMA
Sbjct: 872  RDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMA 925

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 926  GRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIH 985

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D  ++ D+                                              
Sbjct: 986  VATPVFDGASDEDVW--------------------------------------------- 1000

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A           A +    +++LYDG TGEPFD  ++VG +YM+KL HMV DK++ARS
Sbjct: 1001 --ATVAE-------AGMASDAKTVLYDGRTGEPFDGRISVGVMYMIKLAHMVDDKLHARS 1051

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+
Sbjct: 1052 IGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEA 1111

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            IV G    + G PESF VLVKE+Q+LGL + + +         
Sbjct: 1112 IVKGEPIPKPGVPESFRVLVKELQSLGLDMRVLDIDDAEIELR 1154


>gi|301299456|ref|ZP_07205732.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852938|gb|EFK80546.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 1196

 Score =  861 bits (2225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/966 (44%), Positives = 593/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  RVR+ + +  E++D+P+LIEVQ  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVKYGKHRVRRSYSRIKEVLDLPNLIEVQTDSYKWFL----------DEGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRLI           
Sbjct: 51  DIMPIEDFQGKLSLEFVDYQLLEPKYTVEEARQHDANYSAPLHVTLRLI---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFNSELDK---NGRTNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE----EILSTFYPKI 236
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+    EIL +    +
Sbjct: 159 GTTVIPNRGAWLEYETDAKNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
           + +   D      +  D  V   +      +  GE    +S + L +      K   +  
Sbjct: 219 MLTLEKDVHK---NMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAP 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L  L VAE + + +TGEI +   +VID++ ++++     RD    
Sbjct: 276 VGRYKINKKLDLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKT 335

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           +    +    ++  +            L I +V  P D                      
Sbjct: 336 FTFHPSEEGVVQEPMT-----------LQIVKVYSPKDP--------------------- 363

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                   +N+  N +     +HI   DI+A +    +L+ G G+ DDID+LGNRR RSV
Sbjct: 364 -----EKVVNVIGNANVDIQFKHITPADIVASMNYFFNLQEGMGSTDDIDHLGNRRTRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  ++H RR SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 479 QTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 538

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+AR+N YGF+ETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF +++V
Sbjct: 539 SYARINKYGFVETPYRRVSWETHKVTDKIDYLTADEEDNYVIAQANSPLNDDGSFVDDVV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +++ +  EK+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+K
Sbjct: 599 MARKKDDDVEISTEKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIK 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++  G VE VDA  I +R  +G LD        Y+LM
Sbjct: 659 PHAPLVGTGIEYKAAHDSGVALISEHEGTVEYVDAREIRVRRDDGSLDK-------YKLM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN     NQ P+V+VGD V  ++++ADGP+ + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFHRSNGGKNYNQTPIVRVGDRVDADEVLADGPAMENGELALGQNPLIAFMTWDGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V EDV+TSIHIEE E  ARDTKLGPEEITR+IPNV E+ LKN+DE GII +G
Sbjct: 772 AIAINERLVKEDVYTSIHIEEHESEARDTKLGPEEITREIPNVGEDALKNLDEFGIIRIG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF
Sbjct: 832 AEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVQDVKIF 891

Query: 946 NRHGID 951
            R G D
Sbjct: 892 TREGGD 897



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 238/1083 (21%), Positives = 385/1083 (35%), Gaps = 120/1083 (11%)

Query: 306  LYVAEDIVNGETG----EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              VA   ++        E+    G   D + +E +  +    +  L  D           
Sbjct: 177  KNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSLMLTLEKDV---------- 226

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                 +   +++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L 
Sbjct: 227  HKNMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAPVGRYKINKKL- 285

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D    + ++   + +A       + N    ID           +  +     +      
Sbjct: 286  -DLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKTFTFHPSEEG 344

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + +               P+ ++N     +         Q   +       S        
Sbjct: 345  VVQEPMTLQIVKVYSPKDPEKVVNVIGNANVDI------QFKHITPADIVASMNYFFNLQ 398

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
              +G             R V      +     +     +    S+   + V     I   
Sbjct: 399  EGMGSTDDIDHLGNRRTRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLI--N 456

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             R V          +  + +                      L       +        +
Sbjct: 457  IRPVVASIK----EFFGSSQLSQFMDQTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDV 512

Query: 662  DFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
             +        +       I  + +  S   +            +  E   V   ++ + A
Sbjct: 513  HYTHYGRMCPIETPEGPNIGLINSLSSYARINKYGFVETPYRRVSWETHKVTDKIDYLTA 572

Query: 721  KSSGAAIVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                  ++A+           VD + +  +  +     +     +    K   +    C+
Sbjct: 573  DEEDNYVIAQANSPLNDDGSFVDDVVMARKKDDDVEISTEKVDYMDVSPKQVVAVATACI 632

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A +   G  ++ +      ++SE
Sbjct: 633  P---------FLENDDSNRALMGANMQRQAVPLIKPHAPLVGTGIEYKAAHDSGVALISE 683

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               T  +++  E+  R      ++      + S  G KN ++  I+ VG  V   D ++ 
Sbjct: 684  HEGTVEYVDAREIRVRRDDGSLDKYKLMKFHRSNGG-KNYNQTPIVRVGDRV-DADEVLA 741

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     +   +  L A       +  D        V   V        H  +  +  
Sbjct: 742  DGPAMENGELALGQNPLIAFMTWDGYNFEDAIAINERLVKEDVYTSIHIEEHESEARDTK 801

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  +  D     DE  I+      +  +IL G+    G         L   
Sbjct: 802  LGPEEITREIPNVGEDALKNLDEFGIIRIGAEVKDGDILVGKVTPKGVTELSAEERLLHA 861

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R           +V+     +          +      KI   + GD++ PGV 
Sbjct: 862  IFGEKAR-----------EVRDTSLRVPHGAGGIVQDV------KIFTREGGDELSPGVN 904

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +V+V++A KR +Q GDKMAGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRM
Sbjct: 905  MMVRVYIAQKRKLQVGDKMAGRHGNKGTVSVVIPEEDMPFMPDGTPIDIMLSPMGVPSRM 964

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ + HLG A   LG  + S + D   + DI                          
Sbjct: 965  NIGQVLDLHLGMAARKLGIHVASPVFDGARDEDIWSALQEAGLPGDGK------------ 1012

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                            T ++DG                           TGE FD  + V
Sbjct: 1013 ----------------TVLYDG--------------------------RTGEAFDNRIAV 1030

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1031 GVMYYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1090

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+QALG+ + + ++     
Sbjct: 1091 QEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGMDMKVLDADKNEI 1150

Query: 1372 AKM 1374
               
Sbjct: 1151 ELR 1153


>gi|300214103|gb|ADJ78519.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
           (Transcriptase subunit beta) (RNA polymerase subunit
           beta) [Lactobacillus salivarius CECT 5713]
          Length = 1196

 Score =  861 bits (2225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/966 (44%), Positives = 593/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  RVR+ + +  E++D+P+LIEVQ  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVKYGKHRVRRSYSRIKEVLDLPNLIEVQTDSYKWFL----------DEGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRLI           
Sbjct: 51  DIMPIEDFQGKLSLEFVDYQLLEPKYTVEEARQHDANYSAPLHVTLRLI---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFNSELDK---NGRTNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE----EILSTFYPKI 236
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+    EIL +    +
Sbjct: 159 GTTVIPNRGAWLEYETDAKNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
           + +   D      +  D  V   +      +  GE    +S + L +      K   +  
Sbjct: 219 MLTLEKDVHK---NMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAP 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L  L VAE + + +TGEI +   +VID++ ++++     RD    
Sbjct: 276 VGRYKINKKLDLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKT 335

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           +    +    ++  +            L I +V  P D                      
Sbjct: 336 FTFHPSEEGVVQEPMT-----------LQIVKVYSPKDP--------------------- 363

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                   +N+  N +     +HI   DI+A +    +L+ G G+ DDID+LGNRR RSV
Sbjct: 364 -----EKVVNVIGNANVDIQFKHITPADIVASMNYFFNLQEGMGSTDDIDHLGNRRTRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  ++H RR SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 479 QTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 538

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+AR+N YGF+ETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF +++V
Sbjct: 539 SYARINKYGFVETPYRRVSWETHKVTDKIDYLTADEEDNYVIAQANSPLNDDGSFVDDVV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +++ +  EK+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+K
Sbjct: 599 MARKKDDDVEISTEKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIK 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++  G VE VDA  I +R  +G LD        Y+LM
Sbjct: 659 PHAPLVGTGIEYKAAHDSGVALISEHEGTVEYVDAREIRVRRDDGSLDK-------YKLM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN     NQ P+V+VGD V  ++++ADGP+ + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFHRSNGGKNYNQTPIVRVGDRVDADEVLADGPAMENGELALGQNPLIAFMTWDGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V EDV+TSIHIEE E  ARDTKLGPEEITR+IPNV E+ LKN+DE GII +G
Sbjct: 772 AIAINERLVKEDVYTSIHIEEHESEARDTKLGPEEITREIPNVGEDALKNLDEFGIIRIG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF
Sbjct: 832 AEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVQDVKIF 891

Query: 946 NRHGID 951
            R G D
Sbjct: 892 TREGGD 897



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 237/1083 (21%), Positives = 384/1083 (35%), Gaps = 120/1083 (11%)

Query: 306  LYVAEDIVNGETG----EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              VA   ++        E+    G   D + +E +  +    +  L  D           
Sbjct: 177  KNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSLMLTLEKDV---------- 226

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                 +   +++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L 
Sbjct: 227  HKNMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAPVGRYKINKKL- 285

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D    + ++   + +A       + N    ID           +  +     +      
Sbjct: 286  -DLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKTFTFHPSEEG 344

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + +               P+ ++N     +         Q   +       S        
Sbjct: 345  VVQEPMTLQIVKVYSPKDPEKVVNVIGNANVDI------QFKHITPADIVASMNYFFNLQ 398

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
              +G             R V      +     +     +    S+   + V     I   
Sbjct: 399  EGMGSTDDIDHLGNRRTRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLI--N 456

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             R V          +  + +                      L       +        +
Sbjct: 457  IRPVVASIK----EFFGSSQLSQFMDQTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDV 512

Query: 662  DFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
             +        +       I  + +  S   +            +  E   V   ++ + A
Sbjct: 513  HYTHYGRMCPIETPEGPNIGLINSLSSYARINKYGFVETPYRRVSWETHKVTDKIDYLTA 572

Query: 721  KSSGAAIVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                  ++A+           VD + +  +  +     +     +    K   +    C+
Sbjct: 573  DEEDNYVIAQANSPLNDDGSFVDDVVMARKKDDDVEISTEKVDYMDVSPKQVVAVATACI 632

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A +   G  ++ +      ++SE
Sbjct: 633  P---------FLENDDSNRALMGANMQRQAVPLIKPHAPLVGTGIEYKAAHDSGVALISE 683

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               T  +++  E+  R      ++      + S  G KN ++  I+ VG  V   D ++ 
Sbjct: 684  HEGTVEYVDAREIRVRRDDGSLDKYKLMKFHRSNGG-KNYNQTPIVRVGDRV-DADEVLA 741

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     +   +  L A       +  D        V   V        H  +  +  
Sbjct: 742  DGPAMENGELALGQNPLIAFMTWDGYNFEDAIAINERLVKEDVYTSIHIEEHESEARDTK 801

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  +  D     DE  I+      +  +IL G+    G         L   
Sbjct: 802  LGPEEITREIPNVGEDALKNLDEFGIIRIGAEVKDGDILVGKVTPKGVTELSAEERLLHA 861

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R           +V+     +          +      KI   + GD++ PGV 
Sbjct: 862  IFGEKAR-----------EVRDTSLRVPHGAGGIVQDV------KIFTREGGDELSPGVN 904

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +V+V++A KR +Q GDKMAGRHGNKG VS ++P EDMPF+ DGT +DI+L+P+GVPSRM
Sbjct: 905  MMVRVYIAQKRKLQVGDKMAGRHGNKGTVSVVIPEEDMPFMPDGTSIDIMLSPMGVPSRM 964

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ + HLG A   LG  + S + D   + DI                          
Sbjct: 965  NIGQVLDLHLGMAARKLGIHVASPVFDGARDEDIWSALQEAGLPGDGK------------ 1012

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                            T ++DG                           TGE FD  + V
Sbjct: 1013 ----------------TVLYDG--------------------------RTGEAFDNRIAV 1030

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1031 GVMYYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1090

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+QALG+ + + ++     
Sbjct: 1091 QEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGMDMKVLDADKNEI 1150

Query: 1372 AKM 1374
               
Sbjct: 1151 ELR 1153


>gi|297582441|ref|YP_003698221.1| DNA-directed RNA polymerase subunit beta [Bacillus selenitireducens
           MLS10]
 gi|297140898|gb|ADH97655.1| DNA-directed RNA polymerase, beta subunit [Bacillus
           selenitireducens MLS10]
          Length = 1181

 Score =  861 bits (2225), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/964 (45%), Positives = 601/964 (62%), Gaps = 76/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++D+P+LIE+Q ASY  FL          +EG++  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLDLPNLIEIQTASYQWFL----------DEGIREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ F+G  +LEF+ Y    PK+ VD+   RD+TY+ PL++ +RLI          +
Sbjct: 51  DISPISDFTGNLVLEFIDYSLGDPKYPVDESKERDVTYSAPLRVKVRLI---------NQ 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTF+I G +R++VSQL RSP ++F+    +   +GK  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFIINGAERVIVSQLVRSPSVYFN---NKVDKNGKKGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KD+++VRIDR RK+P T  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLELETDAKDVVYVRIDRTRKIPATVLLRALGFGSDQEIIDLLGEDAYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      S   L+           +  GE   +ES K L        K   +  +G 
Sbjct: 219 NTLDKDNTDSSEKALL------EIYERLRPGEPPTVESAKSLLDSRFFDPKRYDLASVGR 272

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ +TGEI  E G VID + L+++      ++    ++
Sbjct: 273 YKMNKKLHIKNRLFNQKLAETLVDPDTGEILAEEGTVIDRRVLDKLMPYLENNLGFRRIN 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                    N  V D  +       +I  VM      T                      
Sbjct: 333 L--------NGGVVDDEET------EIQSVMIYSQEPTAEEG------------------ 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               K+ +  N    + V++I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 361 ---EKIKVIANGTVGEKVKNITPADIIASVSYFFNLLHGVGNTDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSIQDTNVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 537

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIE+PYRKV      V+  V YL+A EE+N  +AQAN+ L+EDG+FT+E + CR
Sbjct: 538 KVNPFGFIESPYRKVDHDTGIVSEQVDYLTADEEDNYIVAQANAKLNEDGTFTDENIICR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+  +
Sbjct: 598 FRGENIIVSRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLEPHS 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKF 767
           P VGTGME V AK SGAAIVA+  G VE+V A  + +R + + D   +   +  Y  MKF
Sbjct: 658 PLVGTGMEYVSAKDSGAAIVARARGRVEKVTAKFVDVRELADVDGKETEGDLKRYNFMKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ TC NQRP+V  G  V + +I+ADG S + G++ALG+N+LV FM W GYN+ED++
Sbjct: 718 ERSNQGTCYNQRPIVSEGMIVEKGEILADGSSMEKGEMALGQNVLVGFMTWDGYNYEDAI 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII  GAE
Sbjct: 778 ILSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRTGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR P G  G V+DV++FNR
Sbjct: 838 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 181/540 (33%), Positives = 259/540 (47%), Gaps = 67/540 (12%)

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            + E   +      G  +    +           ++  I+  G  V  G+IL    +   +
Sbjct: 694  VRELADVDGKETEGDLKRYNFMKFERSNQGTCYNQRPIVSEGMIVEKGEILADGSS-MEK 752

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              M   + +L         +  D  +     +S  +V   ++    I++ E      +  
Sbjct: 753  GEMALGQNVLVGFMTWDGYNYEDAII-----LSERLVKDDVYTSIHIEEYESEARDTKLG 807

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E + RD  +      RN+  R   I  G     G     K T      ++   R     
Sbjct: 808  PEEITRDIPNVGEDALRNLDER-GIIRTGAEVKDGDILVGKVTPKGVTELTAEERLLHAI 866

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            F  +  +V+          +            K+   + GD++PPGV ++V+V++  KR 
Sbjct: 867  FGEKAREVRDTSLRAPHGGDGIV------LDVKVFNREDGDELPPGVNQLVRVYIVQKRK 920

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I  GDKMAGRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E H+G 
Sbjct: 921  INEGDKMAGRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGM 980

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG  I + + D     D+                            +  A   + G
Sbjct: 981  AARQLGIHIATPVFDGAREEDVW-------------------------ETIEEAGMARDG 1015

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                         +++LYDG TGEPFD  V+VG +YM+KL HMV
Sbjct: 1016 -----------------------------KTVLYDGRTGEPFDSRVSVGVMYMIKLAHMV 1046

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD +
Sbjct: 1047 DDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDTI 1106

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            GR + YE+IV G +  E G PESF VL+KE+Q+LG+ + + +S  +    +E   D  + 
Sbjct: 1107 GRVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGMDVKMLSSNDEEIDMLEHEDDDEQT 1166


>gi|15612689|ref|NP_240992.1| DNA-directed RNA polymerase subunit beta [Bacillus halodurans
           C-125]
 gi|13124539|sp|Q9Z9M2|RPOB_BACHD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|4512396|dbj|BAA75263.1| rpoB homologue (identity of 87% to B. subtilis ) [Bacillus
           halodurans]
 gi|10172738|dbj|BAB03845.1| DNA-directed RNA polymerase beta subunit [Bacillus halodurans
           C-125]
          Length = 1180

 Score =  861 bits (2224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 600/964 (62%), Gaps = 77/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   ++  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MTGQLIQYGRHRQRRSYARINEVLELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VD+   RD+TYA PL++ +RLI          K
Sbjct: 51  DISPIQDFTGNLVLEFIDYSLGEPKYPVDESKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTF+I G +R++VSQL RSP +++     +   +GK  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFIINGAERVIVSQLVRSPSVYYSEKIDK---NGKKGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGSDQEIIDLLGEDEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +E+ K L        K   +     
Sbjct: 219 NTLEKDNTDSAEKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +++ ETGE+  E G +ID ++L+ I            + 
Sbjct: 273 YKVNKKLHIKNRLFNQRLAETLIDPETGEVIAEEGSIIDRRTLDRI------------LP 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + NN   R   ++    +  +  L   ++  P D                         
Sbjct: 321 YLENNVGFRTVRMSGGVVEEDEVRLQSVKIYAPDD------------------------Q 356

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   + +  N     +++HI   DIIA I    +L +  G  DDID+LGNRR+RSVGE+
Sbjct: 357 DGEHVIRVIGNGLVEKEIKHITPADIIASINYFFNLLHSVGGTDDIDHLGNRRLRSVGEL 416

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 417 LQNQFRIGLSRMERVVRERMSIQDPNSITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 476

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 477 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 536

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GF+ETPYR+V    GKVT  + YL+A EE+N  +AQAN  L EDGSF +E +  R
Sbjct: 537 KVNEFGFMETPYRRVDPETGKVTAQIDYLTADEEDNYVVAQANMKLAEDGSFIDENIIAR 596

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+V R+++D++D SPKQVVS A S IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 597 FRGENIVVSRDRVDYMDVSPKQVVSAATSCIPFLENDDSNRALMGANMQRQAVPLLVPEA 656

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRLMKF 767
           P VGTGME V AK SGAAIV+K  GIVE+V A  I +R +E          +D YRL KF
Sbjct: 657 PIVGTGMEHVSAKDSGAAIVSKHRGIVERVTAKEIWVRRLEEVDGKEIKGDLDKYRLQKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRP+VK GD V + +I+ADGPS + G++ALGRN+LV FM W GYN+ED++
Sbjct: 717 IRSNQGTSYNQRPIVKEGDVVEKREILADGPSMEKGEMALGRNVLVGFMTWEGYNYEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAE
Sbjct: 777 ILSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR P G  G V+DV+IFNR
Sbjct: 837 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKIFNR 896

Query: 948 HGID 951
              D
Sbjct: 897 EDGD 900



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 252/1052 (23%), Positives = 407/1052 (38%), Gaps = 108/1052 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D +  + Y+RNTL  D     + ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL
Sbjct: 208  IDLLGEDEYLRNTLEKDNTDSAEKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K+N +L++          +     + + L+D   G+   ++   +  R +  + 
Sbjct: 268  ANVGRYKVNKKLHIK--------NRLFNQRLAETLIDPETGEVIAEEGSIIDRRTLDRIL 319

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N      +RM   +   +   ++     +           V     +  + +  +H
Sbjct: 320  PYLENNVGFRTVRMSGGV---VEEDEVRLQSVKIYAPDDQDGEHVIRVIGNGLVEKEIKH 376

Query: 529  VNSLSRITHTRRL-SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +     I       + L   G       +  R +     G +   +   G +        
Sbjct: 377  ITPADIIASINYFFNLLHSVGGTDDIDHLGNRRLRS--VGELLQNQFRIGLSRMERVVRE 434

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              +  +           +     +    +  + +           +          L   
Sbjct: 435  RMSIQDPNSITPQALINIRPVIASIK-EFFGSSQLSQFMDQTNPLAELTHKRRLSALGPG 493

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                E        + +        +       I  + +  +   +            +  
Sbjct: 494  GLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKVNEFGFMETPYRRVDP 553

Query: 707  EAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            E   V   ++ + A      +VA    K A     +D   I     E  +        + 
Sbjct: 554  ETGKVTAQIDYLTADEEDNYVVAQANMKLAEDGSFIDENIIARFRGENIVVSRDRVDYMD 613

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
               K   S   +C+           +  +D  ++              +LV   P  G  
Sbjct: 614  VSPKQVVSAATSCIP---------FLENDD--SNRALMGANMQRQAVPLLVPEAPIVGTG 662

Query: 823  FE-------DSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             E        + ++S+   +V       I +   E +      G  +  R    +     
Sbjct: 663  MEHVSAKDSGAAIVSKHRGIVERVTAKEIWVRRLEEVDGKEIKGDLDKYRLQKFIRSNQG 722

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             + ++  I+  G  V   +IL    +   +  M     +L      +  +  D  +    
Sbjct: 723  TSYNQRPIVKEGDVVEKREILADGPS-MEKGEMALGRNVLVGFMTWEGYNYEDAII---- 777

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 778  -LSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 835

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+          +          
Sbjct: 836  EVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIV------L 889

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 890  DVKIFNREDGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYLP 949

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  +  D+        
Sbjct: 950  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGASEEDVWATLEEAG 1009

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1010 MARDGK----------------------------TILYDG-------------------- 1021

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1022 ------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1075

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1076 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1135

Query: 1354 MQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +Q+LG+ + + +S  +     E +  D    +
Sbjct: 1136 LQSLGMDVKMLSSTEEEIEMKELDDEDEQASD 1167


>gi|257871167|ref|ZP_05650820.1| DNA directed RNA polymerase subunit beta [Enterococcus gallinarum
           EG2]
 gi|257805331|gb|EEV34153.1| DNA directed RNA polymerase subunit beta [Enterococcus gallinarum
           EG2]
          Length = 1208

 Score =  861 bits (2224), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIEGFNGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSDSLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRSLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETLGA------------ 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++     +   + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTEPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      VR +R  DIIA +    +L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EQEVNVIGNGYPDTTVRTVRPADIIASMSYFFNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKYGFIETPYRRVDRETGRVTDQIDYLTADIEDHYVVAQANSLLNEDGTFVNDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  ++
Sbjct: 603 ATSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K+ GIVE VDA  I +R   G LD       +Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKQDGIVEYVDAAEIRVRRDNGALD-------VYSVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPLV +G++V + DI+ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPLVALGEKVEKGDILADGPSMENGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 176/499 (35%), Positives = 242/499 (48%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G +V  GDIL    +      M   + +L A    +  +  D  +     V   V 
Sbjct: 728  LVALGEKVEKGDILADGPS-MENGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D  ++ D+          
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGASDEDVW--------- 1000

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                  A           A +    +++
Sbjct: 1001 --------------------------------------ATVAE-------AGMASDAKTV 1015

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1016 LYDGRTGEPFDGRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIDDAEIELR 1154


>gi|218290023|ref|ZP_03494190.1| DNA-directed RNA polymerase, beta subunit [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239857|gb|EED07045.1| DNA-directed RNA polymerase, beta subunit [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 1176

 Score =  860 bits (2223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/964 (45%), Positives = 602/964 (62%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G    R+ + +  E++D+P+LIE+Q+ SY+ FL           EGL+  F 
Sbjct: 1   MQGHMVKYGW-AERRSYARIREVLDLPNLIEIQQKSYEWFLR----------EGLRETFA 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PIT F+G  +LEFV Y    PK+DV++   RD+TYA PL++ +RL+          K
Sbjct: 50  DISPITDFTGNLVLEFVDYSLGEPKYDVEESKERDVTYAAPLRVKVRLL---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ +++GD PLMT  GTF+I G +R++VSQL RSP +++     +   +GK  +
Sbjct: 101 ETGEVKEQEVFLGDFPLMTDTGTFIINGAERVIVSQLVRSPSVYYSSKIDK---NGKRTF 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           A  +IP++G W++ E D+KD+++VRIDR RK+P+T  L ALG+ S+ EI+          
Sbjct: 158 AATVIPNRGAWLEFETDAKDVVYVRIDRTRKLPITVLLRALGLSSDAEIIELLGEDEYLQ 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +         +      +  GE   +E+ + L +      K         
Sbjct: 218 NTLDKDTTDSTE------RALIEIYERLRPGEPPTVENARALLASRFFDPKRYDLAAVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  EAG V+D ++L+ I            + 
Sbjct: 272 YKINKKLHLKNRLLNQRLAETLVDEETGEIIAEAGTVLDRRTLDRI------------IP 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++          T    ++ +  L + ++  P +                         
Sbjct: 320 RLSGKVGRFTIRGTRDLFEQDEIPLQMVKIFSPAE------------------------- 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +++  N + P DV++I   DIIA +    +L  G GT DDID+LGNRR+RSVGE+
Sbjct: 355 -DGKVLHVISNGELPADVKYITPSDIIAAVSYFFNLLRGVGTTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  ++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDASAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN YGFIETPYR+V    G VT+ + YL+A EEEN  IAQAN  L EDG F  E +  R
Sbjct: 534 RVNEYGFIETPYRRVDPETGVVTDQIDYLTADEEENYLIAQANEPLTEDGHFVAEEITVR 593

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I V R++ID++D SPKQVVS+A +LIPFLENDD+NR LMG NMQRQAVPLL  ++
Sbjct: 594 SREDVITVSRDRIDYMDVSPKQVVSVATALIPFLENDDANRALMGSNMQRQAVPLLVTDS 653

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKF 767
           P VGTGME   AK SG  +V+K  G+VE+V A  I +R     D       V  Y+L+KF
Sbjct: 654 PLVGTGMEYQAAKDSGVCVVSKHNGVVERVTAREIWVREEAVVDGQVVKGNVHKYKLIKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQNTC+NQRP+V+ GD V+  DI+ADGP+T  G+LALGRN+LVAFM W GYN+ED++
Sbjct: 714 ARSNQNTCLNQRPIVREGDRVKVGDILADGPATQNGELALGRNVLVAFMTWEGYNYEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE+MV EDV+TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ LKN+DE GII +GAE
Sbjct: 774 LISEKMVKEDVYTSIHIEEYEIEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRIGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           +   DILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G +G VVDV++F R
Sbjct: 834 ITTNDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGAGIVVDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 199/576 (34%), Positives = 274/576 (47%), Gaps = 79/576 (13%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +         ++S+   +V       I + E  V+      G     + I        
Sbjct: 660  MEYQAAKDSGVCVVSKHNGVVERVTAREIWVREEAVVDGQVVKGNVHKYKLIKFARSNQN 719

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +++  I+  G  V  GDIL      +    +     +L A    +  +  D  L    
Sbjct: 720  TCLNQRPIVREGDRVKVGDILADGPATQN-GELALGRNVLVAFMTWEGYNYEDAILISEK 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        + I+  +  +  E     I  +  D     DE+ I+         +
Sbjct: 779  MVKEDVYTSIHIEEYEIEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRIGAEITTND 838

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R           +V+     +          
Sbjct: 839  ILVGKVTPKGVTELTAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGAGIVVD 887

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +      K+   + GD++P GV ++V+V+VA KR I  GDKMAGRHGNKG+V+RILP ED
Sbjct: 888  V------KVFTRENGDELPAGVNQLVRVYVAQKRKISEGDKMAGRHGNKGVVARILPEED 941

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPFL+DGTPV+IVLNPLGVPSRMN+GQ+ ETHLG A   LG K+ + + D     D    
Sbjct: 942  MPFLEDGTPVEIVLNPLGVPSRMNIGQVLETHLGMAAKVLGLKMATPVFDGAKPED---- 997

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                     VF           LR A L
Sbjct: 998  -----------------------------------------VF---------ETLREAGL 1007

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             E G+ +LYDG TGEPF+  VTVGY+YM+KL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1008 PEDGKQVLYDGRTGEPFENRVTVGYVYMMKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1067

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1068 FGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFK 1127

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            VL+KE+Q+LG+ + + +   +     E   D +  +
Sbjct: 1128 VLIKELQSLGMDVKILSGDEREIEMKEMDDDEDSPD 1163


>gi|258512678|ref|YP_003186112.1| DNA-directed RNA polymerase, beta subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257479404|gb|ACV59723.1| DNA-directed RNA polymerase, beta subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 1176

 Score =  860 bits (2223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 602/964 (62%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G    R+ + +  E++D+P+LIE+Q+ SY+ FL           EGL+  F 
Sbjct: 1   MQGHMVKYGW-AERRSYARIREVLDLPNLIEIQQKSYEWFLR----------EGLRETFA 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PIT F+G  +LEFV Y    PK+DV++   RD+TYA PL++ +RL+          K
Sbjct: 50  DISPITDFTGNLVLEFVDYSLGEPKYDVEESKERDVTYAAPLRVKVRLL---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ +++GD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  +
Sbjct: 101 ETGEVKEQEVFLGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYSSKIDK---NGKRTF 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           A  +IP++G W++ E D+KD+++VRIDR RK+P+T  L ALG+ S+ EI+          
Sbjct: 158 AATVIPNRGAWLEFETDAKDVVYVRIDRTRKLPITVLLRALGLSSDAEIIELLGEDEYLQ 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +         +      +  GE   +E+ + L +      K         
Sbjct: 218 NTLDKDTTDSTE------RALIEIYERLRPGEPPTVENARALLASRFFDPKRYDLAAVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  EAG V+D ++L+ I            + 
Sbjct: 272 YKINKKLHLKNRLLNQRLAETLVDEETGEIIAEAGTVLDRRTLDRI------------IP 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++          T    ++ +  L + ++  P +                         
Sbjct: 320 RLSGKVGRFTIRGTRDLFEQDEIPLQMVKIFSPAE------------------------- 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +++  N + P DV++I   DIIA +    +L  G GT DDID+LGNRR+RSVGE+
Sbjct: 355 -DGKVLHVISNGELPADVKYITPSDIIAAVSYFFNLLRGVGTTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  ++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDASAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V    G VT+ + YL+A EEEN  IAQAN  L EDG F  E +  R
Sbjct: 534 CVNEYGFIETPYRRVDPETGVVTDQIDYLTADEEENYLIAQANEPLTEDGHFVAEEITVR 593

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I V R++ID++D SPKQVVS+A +LIPFLENDD+NR LMG NMQRQAVPLL  ++
Sbjct: 594 SREDVITVSRDRIDYMDVSPKQVVSVATALIPFLENDDANRALMGSNMQRQAVPLLVTDS 653

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKF 767
           P VGTGME   AK SG  +V+K  G+VE+V A  I +R     D       V  Y+L+KF
Sbjct: 654 PLVGTGMEYQAAKDSGVCVVSKHNGVVERVTAREIWVREEAVVDGQVVKGNVHKYKLIKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQNTC+NQRP+V+ GD V+  DI+ADGP+T  G+LALGRN+LVAFM W GYN+ED++
Sbjct: 714 ARSNQNTCLNQRPIVREGDRVKVGDILADGPATQNGELALGRNVLVAFMTWEGYNYEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE+MV EDV+TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ LKN+DE GII +GAE
Sbjct: 774 LISEKMVKEDVYTSIHIEEYEIEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRIGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           +   DILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G +G VVDV++F R
Sbjct: 834 ITTNDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGAGIVVDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  535 bits (1378), Expect = e-149,   Method: Composition-based stats.
 Identities = 199/576 (34%), Positives = 274/576 (47%), Gaps = 79/576 (13%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +         ++S+   +V       I + E  V+      G     + I        
Sbjct: 660  MEYQAAKDSGVCVVSKHNGVVERVTAREIWVREEAVVDGQVVKGNVHKYKLIKFARSNQN 719

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +++  I+  G  V  GDIL      +    +     +L A    +  +  D  L    
Sbjct: 720  TCLNQRPIVREGDRVKVGDILADGPATQN-GELALGRNVLVAFMTWEGYNYEDAILISEK 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        + I+  +  +  E     I  +  D     DE+ I+         +
Sbjct: 779  MVKEDVYTSIHIEEYEIEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRIGAEITTND 838

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R           +V+     +          
Sbjct: 839  ILVGKVTPKGVTELTAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGAGIVVD 887

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +      K+   + GD++P GV ++V+V+VA KR I  GDKMAGRHGNKG+V+RILP ED
Sbjct: 888  V------KVFTRENGDELPAGVNQLVRVYVAQKRKISEGDKMAGRHGNKGVVARILPEED 941

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPFL+DGTPV+IVLNPLGVPSRMN+GQ+ ETHLG A   LG K+ + + D     D    
Sbjct: 942  MPFLEDGTPVEIVLNPLGVPSRMNIGQVLETHLGMAAKVLGLKMATPVFDGAKPED---- 997

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                     VF           LR A L
Sbjct: 998  -----------------------------------------VF---------ETLREAGL 1007

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             E G+ +LYDG TGEPF+  VTVGY+YM+KL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1008 PEDGKQVLYDGRTGEPFENRVTVGYVYMMKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1067

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1068 FGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFK 1127

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            VL+KE+Q+LG+ + + +   +     E   D +  +
Sbjct: 1128 VLIKELQSLGMDVKILSGDEREIEMKEMDDDEDSPD 1163


>gi|299541919|ref|ZP_07052242.1| DNA-directed RNA polymerase subunit beta [Lysinibacillus fusiformis
           ZC1]
 gi|298725657|gb|EFI66298.1| DNA-directed RNA polymerase subunit beta [Lysinibacillus fusiformis
           ZC1]
          Length = 1188

 Score =  860 bits (2223), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 602/964 (62%), Gaps = 76/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ F +  E++++P+LIE+Q ASY+ FL           EGL+  F+
Sbjct: 1   MTGQLVQYGQHRQRRSFARIKEVLELPNLIEIQTASYEWFL----------EEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+DVD+C  RD+TYA PL++ +RL           K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGEPKYDVDECKERDVTYAAPLRVKVRLY---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  +
Sbjct: 102 ETDEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFH---DKTDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 GATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDIIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +ES K L        K   +     
Sbjct: 219 NTLEKDNSESTEKALL------EIYERLRPGEPPTVESAKSLLYSRFFDAKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +E G V+D ++L++I          +   
Sbjct: 273 YKMNKKLHIKNRLFNQTIAETLVDPETGEILVEKGTVLDRRTLDKILPYLEDSSKGIGYR 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           +++    +             D  +   ++  P D +                       
Sbjct: 333 TLSQVGGVLE----------DDVTIQSIKIYAPKDEAQK--------------------- 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N    ++V++I   D+++ +    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 362 ----EINIIGNAYIDEEVKNITPADVLSSVSYFFNLLYQVGATDDIDHLGNRRLRSVGEL 417

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +++PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 418 LQNQFRIGLSRMERVVRERMSINDTAAIVPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 477

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 478 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 537

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++     +VT  + YL+A EE+N Y+AQANS L+ DG+F  + V  R
Sbjct: 538 KVNKFGFIETPYRRIDHETGRVTEQIDYLTADEEDNYYVAQANSPLNPDGTFANDEVVGR 597

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+  +  + ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 598 FRGDNTVFNKAQMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 657

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKF 767
           PFVGTGME V A+ SGAA+VAK  GIVE V+A  I +R +E        G    Y+L KF
Sbjct: 658 PFVGTGMEHVDARDSGAAVVAKYDGIVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKF 717

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRPLVKVG+ V+  DI+ADGPS + G+LALGRN+LVAFM W+G+N+ED++
Sbjct: 718 IRSNQGTSYNQRPLVKVGERVKPRDILADGPSMEKGELALGRNVLVAFMTWNGFNYEDAV 777

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 778 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 837

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 838 VRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIILDVKVFNR 897

Query: 948 HGID 951
              D
Sbjct: 898 EDGD 901



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 183/554 (33%), Positives = 260/554 (46%), Gaps = 77/554 (13%)

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V      SIH+   EV+      G     +    +      + ++  ++ VG  V P D
Sbjct: 683  IVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKFIRSNQGTSYNQRPLVKVGERVKPRD 742

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL    +   +  +     +L A       +  D  +     V   V        +  + 
Sbjct: 743  ILADGPS-MEKGELALGRNVLVAFMTWNGFNYEDAVIMSERLVKDDVYTSVHIEEYESES 801

Query: 953  NERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
             +  +  E     I  +  D     DE+ I+      R  +IL G+    G         
Sbjct: 802  RDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEER 861

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L   +  E  R      +++       +                    K+   + GD++P
Sbjct: 862  LLHAIFGEKARE-VRDTSLRVPHGAGGI----------------ILDVKVFNREDGDELP 904

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGV
Sbjct: 905  PGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGV 964

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D     D+                      
Sbjct: 965  PSRMNIGQVLELHLGMASRYLGVHMATPVFDGANEEDVW--------------------- 1003

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  +  A   + G                             ++ILYDG +GEPFD 
Sbjct: 1004 ----ETMEEAGMNRDG-----------------------------KTILYDGRSGEPFDN 1030

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1031 RVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1090

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + +    
Sbjct: 1091 AYTLQEILTVKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLTVN 1150

Query: 1368 TKNSAKMEEIPDFN 1381
             +     +   + +
Sbjct: 1151 DEEVELRDLDEEDD 1164


>gi|325567850|ref|ZP_08144400.1| DNA-directed RNA polymerase subunit beta [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158482|gb|EGC70631.1| DNA-directed RNA polymerase subunit beta [Enterococcus
           casseliflavus ATCC 12755]
          Length = 1208

 Score =  860 bits (2222), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIEGFNGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRSLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETLGA------------ 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++     +   + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTEPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N       R +R  DIIA +    +L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EQEVNVIGNGYPDTATRTVRPADIIASMSYFFNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF  SQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGYSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDGSF  ++V  R
Sbjct: 543 KVNKYGFIETPYRRVDRETGRVTDKIDYLTADTEDHYVVAQANSLLNEDGSFVNDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 ATSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  GIVE VDA  + +R   G LD       +Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGIVEYVDAAEVRVRRDNGALD-------VYSVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPLV +G++V + DI+ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPLVALGEKVEKGDILADGPSMEQGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 184/583 (31%), Positives = 259/583 (44%), Gaps = 82/583 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       ++    PW G   E                   I E+   A        
Sbjct: 646  MGANMQRQAVPLINPKAPWVGTGMEYKSAHDSGAALLCKHDG--IVEYVDAAEVRVRRDN 703

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  ++             + ++  ++ +G +V  GDIL    +   +  M   + +L A 
Sbjct: 704  GALDVYSVTKFRRSNSGTSYNQRPLVALGEKVEKGDILADGPS-MEQGEMALGQNVLVAF 762

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
               +  +  D  +     V   V        +  +  +  +  E    +I  +  D    
Sbjct: 763  MTWEGYNYEDAIIMSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKD 822

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      +  ++L G+    G         L   +  E  R           +V
Sbjct: 823  LDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EV 871

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +          +      KI   + GD++ PGV  +V+V++  KR I  GDKMA
Sbjct: 872  RDTSLRVPHGGGGIVHDV------KIFTREAGDELAPGVNMLVRVYIVQKRKIHEGDKMA 925

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 926  GRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIH 985

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D  ++ D+                                              
Sbjct: 986  VATPVFDGASDEDVW--------------------------------------------- 1000

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A           A +    +++LYDG TGEPFD  ++VG +YM+KL HMV DK++ARS
Sbjct: 1001 --ATVAE-------AGMASDAKTVLYDGRTGEPFDGRISVGVMYMIKLAHMVDDKLHARS 1051

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+
Sbjct: 1052 IGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEA 1111

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            IV G    + G PESF VLVKE+Q+LGL + + +         
Sbjct: 1112 IVKGEPIPKPGVPESFRVLVKELQSLGLDMRVLDIDDAEIELR 1154


>gi|229552693|ref|ZP_04441418.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
 gi|229313899|gb|EEN79872.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
          Length = 1253

 Score =  859 bits (2219), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 54  LAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 103

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 104 DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 154

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  + S   ++ Y
Sbjct: 155 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDKNS---RVTY 211

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 212 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 271

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 272 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 330

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 331 YKVNKKLSLKTRLLNQVLAETLADPDTGEVLAQKGTKVDRQVMDKLAPYL---------- 380

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G ++     +S+  +     DK     
Sbjct: 381 ------------------DRDDFKTVTYQPSDQGVMTDPIELQSIKVYSQVTPDKE---- 418

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+
Sbjct: 419 -----INLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGEL 473

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 474 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 533

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 534 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 593

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R
Sbjct: 594 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLAR 653

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 654 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHA 713

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+
Sbjct: 714 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFK 766

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 767 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 826

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 827 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 886

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 887 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 946

Query: 949 GID 951
             D
Sbjct: 947 AGD 949



 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 235/1073 (21%), Positives = 381/1073 (35%), Gaps = 104/1073 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 228  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 287

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 288  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 347

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 348  L-----------AETLADPDTGEVLAQKGTKVDRQVMDKLAPYLDRDDFKTVTYQPSDQG 396

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 397  VMTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTV 456

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 457  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 514

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 515  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 570

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 571  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 630

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 631  IVAQANSPLNDDGSFVDDTVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 685

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTS 841
                 +  +D  ++              ++    P  G   E      S   V  +   +
Sbjct: 686  ----FLENDD--SNRALMGANMQRQAVPLINPHAPLVGTGMEYKAAHDSGTAVLANNAGT 739

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   + + +    + G  +  + +        KN ++  I+ +G  V   D ++      
Sbjct: 740  VEYVDAKQIRVRREDGALDTYKLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAM 798

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + A       +  D  +         V D    + H  +    +   + 
Sbjct: 799  QNGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKL 854

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E+     +  +  L          +  G     G     K T      +S   R   
Sbjct: 855  GPEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLH 912

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  K
Sbjct: 913  AIFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQK 966

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HL
Sbjct: 967  RKIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHL 1026

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG  + + + D   + D+                                    
Sbjct: 1027 GMAARNLGIHVATPVFDGANDKDLW----------------------------------- 1051

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+H
Sbjct: 1052 ------------ATVKE-------AGMPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSH 1092

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD
Sbjct: 1093 MVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDD 1152

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VVGR + YE+IV G+   + G PESF VLVKE+QALGL + +  +  +     
Sbjct: 1153 VVGRVKTYEAIVKGDPIPKPGVPESFRVLVKELQALGLDMKVLGADKQEIELR 1205


>gi|199598822|ref|ZP_03212233.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
           HN001]
 gi|199590234|gb|EDY98329.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
           HN001]
          Length = 1253

 Score =  859 bits (2219), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 54  LAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 103

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 104 DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 154

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  + S   ++ Y
Sbjct: 155 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDKNS---RVTY 211

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 212 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 271

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 272 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 330

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 331 YKVNKKLSLKTRLLNQVLAETLADPDTGEVVAQKGTKVDRQVMDKLAPYL---------- 380

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G ++     +S+  +     DK     
Sbjct: 381 ------------------DRDDFKTATYQPSDQGVMTDPIELQSIKVYSQVTPDKE---- 418

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+
Sbjct: 419 -----INLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGEL 473

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 474 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 533

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 534 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 593

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R
Sbjct: 594 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLAR 653

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 654 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHA 713

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+
Sbjct: 714 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFK 766

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 767 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 826

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 827 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 886

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 887 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 946

Query: 949 GID 951
             D
Sbjct: 947 AGD 949



 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 264/1107 (23%), Positives = 402/1107 (36%), Gaps = 172/1107 (15%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 228  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 287

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 288  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 347

Query: 431  IR----KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            +       D   ++       + +        L     ++      +Q  +      +SI
Sbjct: 348  LAETLADPDTGEVVAQKGTKVDRQVMDKLAPYLDRDDFKTATYQPSDQGVMTDPIELQSI 407

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT-----RRL 541
            K          +      +    V  +      + ++        L  +        RR+
Sbjct: 408  KVYSQVTPDKEINLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRI 467

Query: 542  SALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVSSLT 587
             ++G+        G++R    V  R        V P     I P   S     G      
Sbjct: 468  RSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQ 527

Query: 588  SFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                 V D   T+          E   I   N
Sbjct: 528  FMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLIN 587

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            S            +            +  +KID++ A  +    +A +  P   NDD + 
Sbjct: 588  SLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPL--NDDGSF 645

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            V      + +   +  +        +          A+       +E  D+ R ++ +  
Sbjct: 646  VDDTVLARHKDNNIEISPDKVDYMDVSPKQV----VAVATACIPFLENDDSNRALMGAN- 700

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          PLV  G E +                A   
Sbjct: 701  -----------------MQRQAVPLINPHAPLVGTGMEYK----------------AAHD 727

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            +         G               +    +  + +F    + +  G     R I  + 
Sbjct: 728  SGTAVLANNAGTVEYVDAKQIRVRREDGALDTYKLMKF----KRSNAGKNYNQRPIVTIG 783

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +    ++D   II  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 784  D----HVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIVLSERLVKDDVY-- 837

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + +     R      E          E   +D  DE  ++      R  
Sbjct: 838  -------TSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDL-DEFGVVRVGAEVRDG 889

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R           +V+     +         
Sbjct: 890  DILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIIQ 938

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
             +      KI   + GD++ PGV  +V+V++  KR IQ GDKMAGRHGNKG VS ++P E
Sbjct: 939  DV------KIFTREAGDELSPGVNMMVRVYITQKRKIQVGDKMAGRHGNKGTVSVVVPEE 992

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + D+  
Sbjct: 993  DMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLGMAARNLGIHVATPVFDGANDKDLW- 1051

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                          A  +        A 
Sbjct: 1052 ----------------------------------------------ATVKE-------AG 1058

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +   G+S+LYDG TGEPF+  V+VG +Y +KL+HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1059 MPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSHMVDDKIHARSIGPYSLVTQQPLGGKA 1118

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G+   + G PESF
Sbjct: 1119 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGDPIPKPGVPESF 1178

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKM 1374
             VLVKE+QALGL + +  +  +     
Sbjct: 1179 RVLVKELQALGLDMKVLGADKQEIELR 1205


>gi|116871647|ref|YP_848428.1| DNA-directed RNA polymerase subunit beta [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|123460679|sp|A0AF63|RPOB_LISW6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116740525|emb|CAK19645.1| DNA-directed RNA polymerase beta subunit [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 1184

 Score =  859 bits (2219), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/963 (46%), Positives = 603/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 EEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDEEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TVLYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|258540692|ref|YP_003175191.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
           Lc 705]
 gi|257152368|emb|CAR91340.1| DNA-directed RNA polymerase, beta chain [Lactobacillus rhamnosus Lc
           705]
          Length = 1200

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 159 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 219 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 278 YKVNKKLSLKTRLLNQVLAETLADPDTGEVLAQKGTKVDRQVMDKLAPYL---------- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G ++     +S+  +     DK     
Sbjct: 328 ------------------DRDDFKTVTYQPSDQGVMTDPIELQSIKVYSQVTPDKE---- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+
Sbjct: 366 -----INLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R
Sbjct: 541 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+
Sbjct: 661 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFK 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 714 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 774 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 834 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 AGD 896



 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 235/1073 (21%), Positives = 381/1073 (35%), Gaps = 104/1073 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 175  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 234

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 235  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 294

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 295  L-----------AETLADPDTGEVLAQKGTKVDRQVMDKLAPYLDRDDFKTVTYQPSDQG 343

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 344  VMTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTV 403

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 404  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 461

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 462  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 517

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 518  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 577

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 578  IVAQANSPLNDDGSFVDDTVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 632

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTS 841
                 +  +D  ++              ++    P  G   E      S   V  +   +
Sbjct: 633  ----FLENDD--SNRALMGANMQRQAVPLINPHAPLVGTGMEYKAAHDSGTAVLANNAGT 686

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   + + +    + G  +  + +        KN ++  I+ +G  V   D ++      
Sbjct: 687  VEYVDAKQIRVRREDGALDTYKLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAM 745

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + A       +  D  +         V D    + H  +    +   + 
Sbjct: 746  QNGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKL 801

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E+     +  +  L          +  G     G     K T      +S   R   
Sbjct: 802  GPEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLH 859

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  K
Sbjct: 860  AIFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQK 913

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HL
Sbjct: 914  RKIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHL 973

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG  + + + D   + D+                                    
Sbjct: 974  GMAARNLGIHVATPVFDGANDKDLW----------------------------------- 998

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+H
Sbjct: 999  ------------ATVKE-------AGMPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSH 1039

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD
Sbjct: 1040 MVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDD 1099

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VVGR + YE+IV G+   + G PESF VLVKE+QALGL + +  +  +     
Sbjct: 1100 VVGRVKTYEAIVKGDPIPKPGVPESFRVLVKELQALGLDMKVLGADKQEIELR 1152


>gi|289433612|ref|YP_003463484.1| DNA-directed RNA polymerase beta subunit [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
 gi|289169856|emb|CBH26394.1| DNA-directed RNA polymerase beta subunit [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
          Length = 1184

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/963 (46%), Positives = 602/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R     D   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPADGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 EEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPGTNRVTDKIDYLTADEEDNYVVAQANSKLDEHGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 239/1048 (22%), Positives = 378/1048 (36%), Gaps = 114/1048 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD      
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPK---- 266

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
                R  +           +    +     + + LVD   G+      D L  R +  + 
Sbjct: 267  ----RYDLASVGRYKINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPADGVMEDSVLVQSIKIYAPNDEEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +   
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPG 554

Query: 708  APFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
               V   ++ + A      +VA    K        +   +     E           +  
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKLDEHGTFTEEEVMARFRSENLAVEKERIDYMDV 614

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K   S    C+           +  +D        ++   A+      A     G   
Sbjct: 615  SPKQVVSVATACIP---------FLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEH 665

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E+  R   L       G  +       V        
Sbjct: 666  VSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCY 725

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++   +  G  V  G+IL    +      +     +L A       +  D  +       
Sbjct: 726  NQRPNVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SE 780

Query: 937  GTVVDVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
              V D    + H  +    +   +    E    +    +D    LD     R+   +   
Sbjct: 781  RLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDN 840

Query: 994  NAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            + + G    K  T L+++  L+      +  +      +V      +             
Sbjct: 841  DLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV------------ 888

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF
Sbjct: 889  -LDVKIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPF 947

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            + DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+      
Sbjct: 948  MPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEE 1007

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                                T ++DG                  
Sbjct: 1008 AGMARDAK----------------------------TVLYDG------------------ 1021

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
                     +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GG
Sbjct: 1022 --------RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGG 1073

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+
Sbjct: 1074 QRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLI 1133

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+LG+ + + ++  +     +   D
Sbjct: 1134 KELQSLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|16799362|ref|NP_469630.1| DNA-directed RNA polymerase subunit beta [Listeria innocua
           Clip11262]
 gi|20139537|sp|Q92F22|RPOB_LISIN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|16412714|emb|CAC95518.1| RNA polymerase (beta subunit) [Listeria innocua Clip11262]
          Length = 1184

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/963 (46%), Positives = 603/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 DEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDDEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TVLYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|90961179|ref|YP_535095.1| DNA-directed RNA polymerase subunit beta [Lactobacillus salivarius
           UCC118]
 gi|227891884|ref|ZP_04009689.1| DNA-directed RNA polymerase subunit beta [Lactobacillus salivarius
           ATCC 11741]
 gi|122449388|sp|Q1WVA5|RPOB_LACS1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|90820373|gb|ABD99012.1| DNA-directed RNA polymerase beta chain [Lactobacillus salivarius
           UCC118]
 gi|227866347|gb|EEJ73768.1| DNA-directed RNA polymerase subunit beta [Lactobacillus salivarius
           ATCC 11741]
          Length = 1199

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/966 (44%), Positives = 593/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  RVR+ + +  E++D+P+LIEVQ  SY  FL          +EGL+  F 
Sbjct: 4   LAGHLVKYGKHRVRRSYSRIKEVLDLPNLIEVQTDSYKWFL----------DEGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRLI           
Sbjct: 54  DIMPIEDFQGKLSLEFVDYQLLEPKYTVEEARQHDANYSAPLHVTLRLI---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFNSELDK---NGRTNY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE----EILSTFYPKI 236
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+    EIL +    +
Sbjct: 162 GTTVIPNRGAWLEYETDAKNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSL 221

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
           + +   D      +  D  V   +      +  GE    +S + L +      K   +  
Sbjct: 222 MLTLEKDVHK---NMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAP 278

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L  L VAE + + +TGEI +   +VID++ ++++     RD    
Sbjct: 279 VGRYKINKKLDLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKT 338

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           +    +    ++  +            L I +V  P D                      
Sbjct: 339 FTFHPSEEGVVQEPMT-----------LQIVKVYSPKDP--------------------- 366

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                   +N+  N +     +HI   DI+A +    +L+ G G+ DDID+LGNRR RSV
Sbjct: 367 -----EKVVNVIGNANVDIQFKHITPADIVASMNYFFNLQEGMGSTDDIDHLGNRRTRSV 421

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 422 GELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 481

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  ++H RR SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 482 QTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 541

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+AR+N YGF+ETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF +++V
Sbjct: 542 SYARINKYGFVETPYRRVSWETHKVTDKIDYLTADEEDNYVIAQANSPLNDDGSFVDDVV 601

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +++ +  EK+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+K
Sbjct: 602 MARKKDDDVEISTEKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIK 661

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++  G VE VDA  I +R  +G LD        Y+LM
Sbjct: 662 PHAPLVGTGIEYKAAHDSGVALISEHEGTVEYVDAREIRVRRDDGSLDK-------YKLM 714

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN     NQ P+V+VGD V  ++++ADGP+ + G+LALG+N L+AFM W GYNFED
Sbjct: 715 KFHRSNGGKNYNQTPIVRVGDRVDADEVLADGPAMENGELALGQNPLIAFMTWDGYNFED 774

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V EDV+TSIHIEE E  ARDTKLGPEEITR+IPNV E+ LKN+DE GII +G
Sbjct: 775 AIAINERLVKEDVYTSIHIEEHESEARDTKLGPEEITREIPNVGEDALKNLDEFGIIRIG 834

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF
Sbjct: 835 AEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVQDVKIF 894

Query: 946 NRHGID 951
            R G D
Sbjct: 895 TREGGD 900



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 238/1083 (21%), Positives = 385/1083 (35%), Gaps = 120/1083 (11%)

Query: 306  LYVAEDIVNGETG----EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              VA   ++        E+    G   D + +E +  +    +  L  D           
Sbjct: 180  KNVAYVRIDRTRKIPLTELIRALGYGSDNEIVEILGSNSDSLMLTLEKDV---------- 229

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                 +   +++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L 
Sbjct: 230  HKNMDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAPVGRYKINKKL- 288

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             D    + ++   + +A       + N    ID           +  +     +      
Sbjct: 289  -DLKTRLLNLTVAETLADPDTGEIIVNKDEVIDKQVMDKLAPYLARDDFKTFTFHPSEEG 347

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + +               P+ ++N     +         Q   +       S        
Sbjct: 348  VVQEPMTLQIVKVYSPKDPEKVVNVIGNANVDI------QFKHITPADIVASMNYFFNLQ 401

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
              +G             R V      +     +     +    S+   + V     I   
Sbjct: 402  EGMGSTDDIDHLGNRRTRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLI--N 459

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             R V          +  + +                      L       +        +
Sbjct: 460  IRPVVASIK----EFFGSSQLSQFMDQTNPLGELSHKRRFSALGPGGLTRDRAGYEVRDV 515

Query: 662  DFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
             +        +       I  + +  S   +            +  E   V   ++ + A
Sbjct: 516  HYTHYGRMCPIETPEGPNIGLINSLSSYARINKYGFVETPYRRVSWETHKVTDKIDYLTA 575

Query: 721  KSSGAAIVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                  ++A+           VD + +  +  +     +     +    K   +    C+
Sbjct: 576  DEEDNYVIAQANSPLNDDGSFVDDVVMARKKDDDVEISTEKVDYMDVSPKQVVAVATACI 635

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A +   G  ++ +      ++SE
Sbjct: 636  P---------FLENDDSNRALMGANMQRQAVPLIKPHAPLVGTGIEYKAAHDSGVALISE 686

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               T  +++  E+  R      ++      + S  G KN ++  I+ VG  V   D ++ 
Sbjct: 687  HEGTVEYVDAREIRVRRDDGSLDKYKLMKFHRSNGG-KNYNQTPIVRVGDRV-DADEVLA 744

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     +   +  L A       +  D        V   V        H  +  +  
Sbjct: 745  DGPAMENGELALGQNPLIAFMTWDGYNFEDAIAINERLVKEDVYTSIHIEEHESEARDTK 804

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  +  D     DE  I+      +  +IL G+    G         L   
Sbjct: 805  LGPEEITREIPNVGEDALKNLDEFGIIRIGAEVKDGDILVGKVTPKGVTELSAEERLLHA 864

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R           +V+     +          +      KI   + GD++ PGV 
Sbjct: 865  IFGEKAR-----------EVRDTSLRVPHGAGGIVQDV------KIFTREGGDELSPGVN 907

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +V+V++A KR +Q GDKMAGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRM
Sbjct: 908  MMVRVYIAQKRKLQVGDKMAGRHGNKGTVSVVIPEEDMPFMPDGTPIDIMLSPMGVPSRM 967

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ + HLG A   LG  + S + D   + DI                          
Sbjct: 968  NIGQVLDLHLGMAARKLGIHVASPVFDGARDEDIWSALQEAGLPGDGK------------ 1015

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                            T ++DG                           TGE FD  + V
Sbjct: 1016 ----------------TVLYDG--------------------------RTGEAFDNRIAV 1033

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1034 GVMYYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1093

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+QALG+ + + ++     
Sbjct: 1094 QEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGMDMKVLDADKNEI 1153

Query: 1372 AKM 1374
               
Sbjct: 1154 ELR 1156


>gi|149183751|ref|ZP_01862157.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. SG-1]
 gi|148848537|gb|EDL62781.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. SG-1]
          Length = 1177

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/956 (45%), Positives = 603/956 (63%), Gaps = 79/956 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R+ F +  E++D+P+LIE+Q +SY  FL          +EGL+  F+ + PI  F
Sbjct: 1   GRHRQRRSFARISEVLDLPNLIEIQTSSYQWFL----------DEGLREMFRDISPIEDF 50

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           +G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RL+          K   ++K+Q
Sbjct: 51  TGNLSLEFIDYSLGEPKYSVEESKERDVTYSAPLRVKVRLL---------NKETGEVKDQ 101

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT  GTFVI G +R++VSQL RSP ++F    G+   +GK  +   +IP++
Sbjct: 102 DVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFS---GKMDKNGKKGFTATVIPNR 158

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+             +    
Sbjct: 159 GAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNEYIRNTLEKDNT 218

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--------FLGI 298
                 L+           +  GE   +E+ K L        K   +             
Sbjct: 219 EGIEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRYKMNKKLH 272

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + L G  +AE + + ETGEI  E G V+D ++L++I       IP L       N   
Sbjct: 273 IKNRLFGQTLAETLADPETGEIVAEKGTVLDRRALDKI-------IPYL------ENGIG 319

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             T         +D +L   ++  P +                          G  ++N+
Sbjct: 320 FKTYQQSGGVLEEDVVLQSIKIYSPNEE-------------------------GEKEINI 354

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             N    +++++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 355 ISNAFVEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIG 414

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH 
Sbjct: 415 LSRMERVVRERMSIQDANTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHK 474

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFI
Sbjct: 475 RRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFGFI 534

Query: 599 ETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR+V    GKVTN + YL+A EE+N  +AQAN+ L +DGSF ++ V  R  GE  +V
Sbjct: 535 ETPYRRVDPDTGKVTNRMDYLTADEEDNYVVAQANARLSDDGSFLDDEVIARFRGENTVV 594

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+P VGTGME
Sbjct: 595 KRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPIVGTGME 654

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKFQRSNQNTC 775
            V AK SGAA++ +  GIVE+V+A ++ +R ++  D       +D YR+ KF RSNQ TC
Sbjct: 655 HVSAKDSGAAVICRHEGIVERVEAKQVWVRQIKEIDGQEVKGDLDKYRMQKFIRSNQGTC 714

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQRP+V  GD V + +I+ADGPS + G+LALGRN++V FM W GYN+ED++++SER+V 
Sbjct: 715 YNQRPIVSEGDRVTKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAIIMSERLVK 774

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  GD+LV
Sbjct: 775 DDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDLLV 834

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 835 GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 890



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 178/533 (33%), Positives = 254/533 (47%), Gaps = 78/533 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R    +        ++  I+  G  V  G+IL    +   +  +     ++   
Sbjct: 696  GDLDKYRMQKFIRSNQGTCYNQRPIVSEGDRVTKGEILADGPS-MEKGELALGRNVMVGF 754

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 755  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 814

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 815  LDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 873

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +                    K+   + GD++PPGV ++V+ ++  KR I  GDKMA
Sbjct: 874  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMA 917

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 918  GRHGNKGVISRILPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIH 977

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + S + D     D+                                              
Sbjct: 978  VASPVFDGAREEDVW--------------------------------------------- 992

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A  E        A +    +++LYDG TGEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 993  --ATIEE-------AGMARDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARS 1043

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1044 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1103

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            IV G +  E G PESF VL+KE+Q+LG+ + + +S  +    M ++ D  + +
Sbjct: 1104 IVKGENVPEPGVPESFKVLIKELQSLGMDVKILSSNDEEIE-MRDLEDEEESQ 1155


>gi|217965646|ref|YP_002351324.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           HCC23]
 gi|255025581|ref|ZP_05297567.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J2-003]
 gi|290892599|ref|ZP_06555592.1| RNA polymerase [Listeria monocytogenes FSL J2-071]
 gi|254765293|sp|B8DEY8|RPOB_LISMH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|217334916|gb|ACK40710.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           HCC23]
 gi|290557908|gb|EFD91429.1| RNA polymerase [Listeria monocytogenes FSL J2-071]
 gi|307569805|emb|CAR82984.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           L99]
          Length = 1184

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/963 (46%), Positives = 603/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 DEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDDEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TILYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|258509493|ref|YP_003172244.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
           GG]
 gi|257149420|emb|CAR88393.1| DNA-directed RNA polymerase, beta chain [Lactobacillus rhamnosus
           GG]
          Length = 1200

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 159 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 219 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 278 YKVNKKLSLKTRLLNQVLAETLADPDTGEVVAQKGTKVDRQVMDKLAPYL---------- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G ++     +S+  +     DK     
Sbjct: 328 ------------------DRDDFKTATYQPSDQGVMTDPIELQSIKVYSQVTPDKE---- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+
Sbjct: 366 -----INLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R
Sbjct: 541 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+
Sbjct: 661 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFK 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 714 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 774 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 834 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 AGD 896



 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 235/1073 (21%), Positives = 380/1073 (35%), Gaps = 104/1073 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 175  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 234

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 235  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 294

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R           ++ 
Sbjct: 295  L-----------AETLADPDTGEVVAQKGTKVDRQVMDKLAPYLDRDDFKTATYQPSDQG 343

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 344  VMTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTV 403

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 404  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 461

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 462  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 517

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 518  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 577

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 578  IVAQANSPLNDDGSFVDDTVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 632

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTS 841
                 +  +D  ++              ++    P  G   E      S   V  +   +
Sbjct: 633  ----FLENDD--SNRALMGANMQRQAVPLINPHAPLVGTGMEYKAAHDSGTAVLANNAGT 686

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   + + +    + G  +  + +        KN ++  I+ +G  V   D ++      
Sbjct: 687  VEYVDAKQIRVRREDGALDTYKLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAM 745

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + A       +  D  +         V D    + H  +    +   + 
Sbjct: 746  QNGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKL 801

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E+     +  +  L          +  G     G     K T      +S   R   
Sbjct: 802  GPEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLH 859

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  K
Sbjct: 860  AIFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQK 913

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HL
Sbjct: 914  RKIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHL 973

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG  + + + D   + D+                                    
Sbjct: 974  GMAARNLGIHVATPVFDGANDKDLW----------------------------------- 998

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+H
Sbjct: 999  ------------ATVKE-------AGMPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSH 1039

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD
Sbjct: 1040 MVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDD 1099

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VVGR + YE+IV G+   + G PESF VLVKE+QALGL + +  +  +     
Sbjct: 1100 VVGRVKTYEAIVKGDPIPKPGVPESFRVLVKELQALGLDMKVLGADKQEIELR 1152


>gi|323705653|ref|ZP_08117227.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535130|gb|EGB24907.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 1237

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/951 (46%), Positives = 597/951 (62%), Gaps = 64/951 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F +  E++D+P+LIEVQK SY  FL           EGL+  F+ + PI +F+G   
Sbjct: 12  RMSFARIEEVLDMPNLIEVQKNSYKWFL----------EEGLREVFRDISPIESFTGNLS 61

Query: 74  LEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           LEF+ Y+ D  PK+ V++C  RD TYA P+K+ +RL           +   +IKE  ++M
Sbjct: 62  LEFLDYKLDDNPKYSVEECKDRDTTYAAPMKVKVRLT---------NRDTGEIKESEVFM 112

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT  GTF+I G +R++VSQL RSPG++++    +    GK L+   +IP++G W+
Sbjct: 113 GDFPLMTDKGTFIINGAERVIVSQLVRSPGVYYEQQFDKL---GKKLFFATVIPNRGAWL 169

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           + E DS DI  VRIDR RKVP+T FL ALG  ++ +IL  F          D        
Sbjct: 170 EYEEDSNDIFSVRIDRTRKVPITVFLRALGYGTDAQILDLFGEDERIKATLDKDTTKSEE 229

Query: 252 ADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD--------C 302
             L+           +  GE   +ES K L   L    K   +  +G             
Sbjct: 230 EGLL------EVYKRLRPGEPPTVESAKSLLYSLFFDPKRYDLAHVGRYKFNKKLALSSR 283

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L     A  IVN  TGEI +E G  I  ++ ++I    I ++ +L          I    
Sbjct: 284 LTNQKAATKIVNPLTGEIIVEEGQRISRETAKKIQDCGINEVEVL---VEGRPVKIIGNN 340

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D N+      +     ++  +    +V + + N    + +        + ++  RL+ 
Sbjct: 341 TVDINEYPLSFDV---SDLKIKEKVHLTVLKEILNNFSSEDEI-------KNEIRRRLDE 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI K+DIIA +   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHITKDDIIASVNYNLNLSYGVGFVDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER++  D+  +  Q+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 448 ERVVRERMTIQDVSEITAQNLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG+E+RDVH THY R+CP ET EG NIGL+ SL ++AR+N YGFIE PY
Sbjct: 508 ALGPGGLSRERAGMEVRDVHHTHYSRMCPIETPEGPNIGLIGSLATYARINEYGFIEAPY 567

Query: 603 RKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV     KV N++VY++A  E+   IAQA+  LDE+  F  E V  R   + + VPRE+
Sbjct: 568 RKVDKSTGKVLNEIVYMTADVEDEYVIAQADEPLDEENRFINERVTVRSKDDILSVPREE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +DF+D SPKQVVS+A ++IPFLENDD+NR LMG NM+RQAVPLL  +AP VGTG+E   A
Sbjct: 628 VDFMDVSPKQVVSVATAMIPFLENDDANRALMGSNMRRQAVPLLVPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG   +A+ +GIVE+V A +IVI++ +G  D        Y L+KF+RSNQ TC+N RP
Sbjct: 688 RDSGVVNIARNSGIVERVTADKIVIKTDDGRRDE-------YELLKFKRSNQGTCINCRP 740

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V +  +I+DGPST+LG++ALGRN+LV FMPW GYN+ED++LISE +V ED  T
Sbjct: 741 IVNEGDRVEKGQVISDGPSTELGEIALGRNVLVGFMPWEGYNYEDAILISEELVKEDALT 800

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 801 SIHIEEYESEARDTKLGPEEITRDIPNVGEEALKDLDERGIIRIGAEVTAGDILVGKVTP 860

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVDV+++ R   D
Sbjct: 861 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEGGIVVDVKVYTRENGD 911



 Score =  463 bits (1190), Expect = e-127,   Method: Composition-based stats.
 Identities = 241/1062 (22%), Positives = 380/1062 (35%), Gaps = 137/1062 (12%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D    +  I+ TL  D  K  ++ LL++Y+ +RPG+  T   A+S+   LFFD  +YDL+
Sbjct: 208  DLFGEDERIKATLDKDTTKSEEEGLLEVYKRLRPGEPPTVESAKSLLYSLFFDPKRYDLA 267

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L L          +         +V+   G+  +++   +     + + +
Sbjct: 268  HVGRYKFNKKLALS--------SRLTNQKAATKIVNPLTGEIIVEEGQRISRETAKKIQD 319

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
               N+  + +      I    +    +  +  D+ + K     + E    + L ++  + 
Sbjct: 320  CGINEVEVLVEGRPVKIIGNNTVDINEYPLSFDVSDLK-----IKEKVHLTVLKEILNNF 374

Query: 530  NSLSRITH--TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +S   I +   RRL  L    + +      +       YG     +     N  L  S+ 
Sbjct: 375  SSEDEIKNEIRRRLDELIPKHITKDDIIASVNYNLNLSYGVGFVDDIDHLGNRRLR-SVG 433

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR--YIA-----QANSSLDEDGSF 640
               +      +    R V +     DV  ++A    N    +A       +S L +    
Sbjct: 434  ELLQNQFRIGLSRMERVVRERMTIQDVSEITAQNLINIRPVVAAIKEFFGSSQLSQFMDQ 493

Query: 641  TEELVFCRCAG------------EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            T  L                   E   +    +     S    +         L    + 
Sbjct: 494  TNPLAELTHKRRLSALGPGGLSRERAGMEVRDVHHTHYSRMCPIETPEGPNIGLIGSLAT 553

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
               +           ++A    V      V+ +        +   ++ Q D         
Sbjct: 554  YARI------NEYGFIEAPYRKVDKSTGKVLNEIVYMTADVEDEYVIAQADEPLDEENRF 607

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
              +     S  DI  + + +    +    Q   V         +  A+            
Sbjct: 608  INERVTVRSKDDILSVPREEVDFMDVSPKQVVSVATAMIPFLENDDANRALMGSNMRRQA 667

Query: 809  RNMLVAFMPWHGYNFE---------DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              +LV   P  G   E          ++  +  +V       I I         T  G  
Sbjct: 668  VPLLVPQAPIVGTGIEYKAARDSGVVNIARNSGIVERVTADKIVI--------KTDDGRR 719

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +    +          I+   I+  G  V  G ++    + +    +     +L      
Sbjct: 720  DEYELLKFKRSNQGTCINCRPIVNEGDRVEKGQVISDGPSTEL-GEIALGRNVLVGFMPW 778

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKDD 973
            +  +  D  L     V    +       +  +  +  +  E          E   +D  D
Sbjct: 779  EGYNYEDAILISEELVKEDALTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKDL-D 837

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+         +IL G+    G         L   +  E  R               
Sbjct: 838  ERGIIRIGAEVTAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------------- 882

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E                   K+   + GD++PPGV  +V+VF+A KR I  GDKMAGR
Sbjct: 883  --EVRDTSLRVPHGEGGIVVDVKVYTRENGDELPPGVNEMVRVFIAQKRKISVGDKMAGR 940

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNK                            GV SR+                    ++
Sbjct: 941  HGNK----------------------------GVVSRI------------------LPVE 954

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +                L+  +       +++      V         G  ++TPVFDG
Sbjct: 955  DMPFLPDGTP--------LQICLNPLGVPSRMNIGQVLEVHLGLAAKALGWYMATPVFDG 1006

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A EE I  +L  A     G+  LYDG TGEPFD PVTVGY+YMLKL+H+V DK++ARSTG
Sbjct: 1007 AHEEDIQELLEKAGFSPDGKIQLYDGRTGEPFDHPVTVGYMYMLKLHHLVDDKMHARSTG 1066

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDD+ GR + YESIV
Sbjct: 1067 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDITGRVKTYESIV 1126

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             G +  E G PESF VLVKE+Q+L L + +     +  A  E
Sbjct: 1127 KGENIPEPGVPESFKVLVKELQSLCLDVKVLTEDNQEVALKE 1168


>gi|16802304|ref|NP_463789.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           EGD-e]
 gi|46906495|ref|YP_012884.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           str. 4b F2365]
 gi|47096519|ref|ZP_00234110.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|224498893|ref|ZP_03667242.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           Finland 1988]
 gi|224502448|ref|ZP_03670755.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL R2-561]
 gi|226222889|ref|YP_002756996.1| RNA polymerase (beta subunit) [Listeria monocytogenes Clip81459]
 gi|254825695|ref|ZP_05230696.1| RNA polymerase subunit beta [Listeria monocytogenes FSL J1-194]
 gi|254828718|ref|ZP_05233405.1| RNA polymerase [Listeria monocytogenes FSL N3-165]
 gi|254831920|ref|ZP_05236575.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           10403S]
 gi|254853472|ref|ZP_05242820.1| RNA polymerase [Listeria monocytogenes FSL R2-503]
 gi|254900554|ref|ZP_05260478.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           J0161]
 gi|254913495|ref|ZP_05263507.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           J2818]
 gi|254937924|ref|ZP_05269621.1| RNA polymerase subunit beta [Listeria monocytogenes F6900]
 gi|284800555|ref|YP_003412420.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           08-5578]
 gi|284993741|ref|YP_003415509.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           08-5923]
 gi|300764614|ref|ZP_07074606.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           FSL N1-017]
 gi|20139836|sp|Q9RLT9|RPOB_LISMO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|67461457|sp|Q724F0|RPOB_LISMF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|259494187|sp|C1KYJ3|RPOB_LISMC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|6002201|emb|CAB56706.1| DNA-dependent RNA polymerase subunit beta [Listeria monocytogenes]
 gi|16409623|emb|CAD00785.1| RNA polymerase (beta subunit) [Listeria monocytogenes EGD-e]
 gi|46879759|gb|AAT03061.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|47015110|gb|EAL06052.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|225875351|emb|CAS04048.1| RNA polymerase (beta subunit) [Listeria monocytogenes serotype 4b
           str. CLIP 80459]
 gi|258601123|gb|EEW14448.1| RNA polymerase [Listeria monocytogenes FSL N3-165]
 gi|258606844|gb|EEW19452.1| RNA polymerase [Listeria monocytogenes FSL R2-503]
 gi|258610533|gb|EEW23141.1| RNA polymerase subunit beta [Listeria monocytogenes F6900]
 gi|284056117|gb|ADB67058.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           08-5578]
 gi|284059208|gb|ADB70147.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           08-5923]
 gi|293591503|gb|EFF99837.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           J2818]
 gi|293594939|gb|EFG02700.1| RNA polymerase subunit beta [Listeria monocytogenes FSL J1-194]
 gi|300514721|gb|EFK41776.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           FSL N1-017]
          Length = 1184

 Score =  858 bits (2218), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/963 (46%), Positives = 603/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 EEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDEEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TILYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|47091392|ref|ZP_00229189.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|47020069|gb|EAL10805.1| DNA-directed RNA polymerase, beta subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|328467869|gb|EGF38909.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           1816]
          Length = 1184

 Score =  858 bits (2217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/963 (46%), Positives = 603/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 DEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDDEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TILYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|56961924|ref|YP_173646.1| DNA-directed RNA polymerase subunit beta [Bacillus clausii KSM-K16]
 gi|81367464|sp|Q5WLS0|RPOB_BACSK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|56908158|dbj|BAD62685.1| DNA-directed RNA polymerase beta subunit [Bacillus clausii KSM-K16]
          Length = 1180

 Score =  858 bits (2217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/958 (45%), Positives = 613/958 (63%), Gaps = 65/958 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   ++  G  R R+ + +  E++++P+LIE+Q ASY  FL          +EGL+  F+
Sbjct: 1   MTGQLIQYGRHRQRRSYARINEVLELPNLIEIQTASYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VD+   RD+T+A PL++ +RLI          K
Sbjct: 51  DISPIQDFTGNLVLEFIDYSLGEPKYPVDESKERDVTFAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYSQKLDK---NGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI--V 237
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 TATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGSDQEIVDLLGENEYLR 218

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFL 296
            +   D       A   +           ++  + ++ES         L ++    +   
Sbjct: 219 NTLEKDNTDSTDKALLEIYERLRPGEPPTVENAKSLLESRFFDPKRYDLANVGRYKINKK 278

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + L    +AE +V+ ETGE+  E G ++D ++L+++       IP L  +     A
Sbjct: 279 LHIKNRLFNQRLAEKLVDPETGEVLAEEGTLLDRRTLDKL-------IPHLEKNVGFRTA 331

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
             R +    +  D +   + IY                        +D Y+   V  V  
Sbjct: 332 --RTSGGVLEESDVEIQSVKIYV-----------------------ADDYEGERVISVIS 366

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N  +  D     +HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 367 NGMVERDV----KHIAPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFR 422

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +T
Sbjct: 423 IGLSRMERVVRERMSIQDPNVITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELT 482

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL+++L+S+A+VN +G
Sbjct: 483 HKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINTLSSYAKVNEFG 542

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           F+ETPYR+V    GKVT+ + YL+A EE+N  +AQAN+ L++DGSF ++ +  R  GE  
Sbjct: 543 FMETPYRRVDPETGKVTSRIDYLTADEEDNYVVAQANAKLNDDGSFVDDNIIARFRGENT 602

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +VP +++D++D SPKQVVS A S IPFLENDDSNR LMG NMQRQAVPLL  EAP VGTG
Sbjct: 603 VVPCDRVDYMDVSPKQVVSAATSCIPFLENDDSNRALMGANMQRQAVPLLVPEAPLVGTG 662

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKFQRSNQN 773
           ME V AK SGAA+V+K AGIVE+V A  I +R +E  D   +   +D Y+L KF RSNQ 
Sbjct: 663 MEHVSAKDSGAAVVSKYAGIVERVTAKEIWVRRIEEVDGKETKGDLDKYKLQKFVRSNQG 722

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           T  NQRP+V+ GD + + +I+ADGPS ++G++ALGRN+LVAFM W GYN+ED++++SER+
Sbjct: 723 TSYNQRPIVREGDRIEKREILADGPSMEMGEMALGRNVLVAFMTWDGYNYEDAIILSERL 782

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  GDI
Sbjct: 783 VKDDVYTSIHIEEYESDARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDI 842

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR P G  G V+DV+IFNR   D
Sbjct: 843 LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKIFNREDGD 900



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 255/1050 (24%), Positives = 404/1050 (38%), Gaps = 107/1050 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            VD +  N Y+RNTL  D       ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 208  VDLLGENEYLRNTLEKDNTDSTDKALLEIYERLRPGEPPTVENAKSLLESRFFDPKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K+N +L++      + +              L + +      +       R++ 
Sbjct: 268  ANVGRYKINKKLHIKNRLFNQRL-----------AEKLVDPETGEVLAEEGTLLDRRTLD 316

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            +++ +  +    R  R+    +   D++    +  +        V     +  + +  +H
Sbjct: 317  KLIPHLEKNVGFRTARTSGGVLEESDVEIQSVKIYVADDYEGERVISVISNGMVERDVKH 376

Query: 529  VNSLSRITHTRRL-SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +     I       + L   G       +  R +     G +   +   G +        
Sbjct: 377  IAPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRS--VGELLQNQFRIGLSRMERVVRE 434

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              + +     I           + +   +  + +           +          L   
Sbjct: 435  RMS-IQDPNVITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPG 493

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                E   +    + +        +       I  +    S   +            +  
Sbjct: 494  GLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINTLSSYAKVNEFGFMETPYRRVDP 553

Query: 707  EAPFVGTGMESVVAKSSGAAI----VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            E   V + ++ + A      +     AK       VD   I     E  + P      + 
Sbjct: 554  ETGKVTSRIDYLTADEEDNYVVAQANAKLNDDGSFVDDNIIARFRGENTVVPCDRVDYMD 613

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
               K   S   +C+           +  +D  ++              +LV   P  G  
Sbjct: 614  VSPKQVVSAATSCIP---------FLENDD--SNRALMGANMQRQAVPLLVPEAPLVGTG 662

Query: 823  FE-------DSMLISERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNVSEEGL 873
             E        + ++S+     +  T+  I    +   D K   G  +  +    V     
Sbjct: 663  MEHVSAKDSGAAVVSKYAGIVERVTAKEIWVRRIEEVDGKETKGDLDKYKLQKFVRSNQG 722

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             + ++  I+  G  +   +IL    +      M     +L A       +  D  +    
Sbjct: 723  TSYNQRPIVREGDRIEKREILADGPS-MEMGEMALGRNVLVAFMTWDGYNYEDAII---- 777

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 778  -LSERLVKDDVYTSIHIEEYESDARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRIGA 835

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+          +          
Sbjct: 836  EVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIV------L 889

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPFL 
Sbjct: 890  DVKIFNREDGDELPPGVNQLVRVYIVQKRKINQGDKMAGRHGNKGVISRILPEEDMPFLP 949

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  +  D+        
Sbjct: 950  DGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHVASPVFDGASEEDVWGTLEEAG 1009

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 1010 MARDGK----------------------------TILYDG-------------------- 1021

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1022 ------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 1075

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 1076 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 1135

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +Q+LG+ + + +S  +     E   + ++ 
Sbjct: 1136 LQSLGMDVKMLSSNEEEIEMRELDDEEDQT 1165


>gi|116495960|ref|YP_807694.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei ATCC
           334]
 gi|239630363|ref|ZP_04673394.1| DNA-directed RNA polymerase subunit beta [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|301067514|ref|YP_003789537.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei str.
           Zhang]
 gi|122262640|sp|Q034X0|RPOB_LACC3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116106110|gb|ABJ71252.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei ATCC
           334]
 gi|239527975|gb|EEQ66976.1| DNA-directed RNA polymerase subunit beta [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|300439921|gb|ADK19687.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Lactobacillus casei str. Zhang]
          Length = 1199

 Score =  858 bits (2217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 583/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 159 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 219 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 278 YKVNKKLSLKTRLLNQVLAETLADPDTGEVIAQKGTKVDRQVMDKLAPYL---------- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G V+     +S+  +     DK     
Sbjct: 328 ------------------DRDDFKTITYQPSDQGVVTDPIELQSIKVYSQVTPDKE---- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 -----INLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSIDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF +E V  R
Sbjct: 541 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDETVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVNPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y LMKF+
Sbjct: 661 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALDA-------YNLMKFK 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 714 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 774 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 834 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 AGD 896



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 236/1072 (22%), Positives = 385/1072 (35%), Gaps = 102/1072 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 175  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 234

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 235  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 294

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 295  L-----------AETLADPDTGEVIAQKGTKVDRQVMDKLAPYLDRDDFKTITYQPSDQG 343

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 344  VVTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSI 403

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 404  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 461

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 462  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 517

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 518  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 577

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 578  IVAQANSPLNDDGSFVDETVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 632

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                 +  +D        ++   A+      A +   G  ++ +      +++ +  T  
Sbjct: 633  ----FLENDDSNRALMGANMQRQAVPLVNPHAPLVGTGMEYKAAHDSGTAVLANNAGTVE 688

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +++  ++  R  + G  +    +        KN ++  I+ +G  V   D ++       
Sbjct: 689  YVDAKQIRVRR-EDGALDAYNLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAMQ 746

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + A       +  D  +         V D    + H  +    +   +  
Sbjct: 747  NGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKLG 802

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E+     +  +  L          +  G     G     K T      +S   R    
Sbjct: 803  PEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLHA 860

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  KR
Sbjct: 861  IFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKR 914

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG
Sbjct: 915  KIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLG 974

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D   + D+                                     
Sbjct: 975  MAARNLGIHVATPVFDGANDKDLW------------------------------------ 998

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                       A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+HM
Sbjct: 999  -----------ATVKE-------AGMASDGKSVLYDGRTGEPFENRVSVGIMYYMKLSHM 1040

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV
Sbjct: 1041 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDV 1100

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VGR + YE+IV G    + G PESF VLVKE+QALGL + +  +  K     
Sbjct: 1101 VGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGLDMKVLGADKKEIELR 1152


>gi|295694829|ref|YP_003588067.1| DNA-directed RNA polymerase, beta subunit [Bacillus tusciae DSM
           2912]
 gi|295410431|gb|ADG04923.1| DNA-directed RNA polymerase, beta subunit [Bacillus tusciae DSM
           2912]
          Length = 1175

 Score =  858 bits (2217), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 607/964 (62%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R  F +  E++ +P+LIE+Q+ SY  FL           EGL+  F+
Sbjct: 1   MRGQLVDYGR-RKRWSFARIHEVLPLPNLIEIQQNSYRWFL----------EEGLREMFQ 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PIT F+G  +LEFV Y    PK+ V++   RD+TYA PL++ +RLI          +
Sbjct: 50  DISPITDFTGNLVLEFVDYTLGEPKYSVEESKERDVTYAAPLRVKVRLI---------NR 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F+    +A  +GK  Y
Sbjct: 101 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFN---AKADKNGKRTY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KD+I+ RIDR RK+PVT  L ALG  ++ +I+          
Sbjct: 158 GATVIPNRGAWLELETDTKDVIYARIDRTRKIPVTVLLRALGFSTDADIVHLLGEDEYLR 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +          L+           +  GE   +E+ + L        K         
Sbjct: 218 NTLEKDNTDSVEKALL------EIYDRLRPGEPPTLENARALLKSRFFDPKRYDLANVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AED+V+  TGE+  E+G V+D + L+++  +           
Sbjct: 272 YKINKKLHLKNRLLNQRLAEDLVDPRTGEVVAESGRVLDRRLLDKVVPA----------- 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +     ++    +    +     L   R+  P                           
Sbjct: 321 -LEAGMNMKEYRKSSGVVEDDVIRLQEVRIFSP--------------------------L 353

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V    + +  N      V++I   DIIA +   ++L +G G IDDID+LGNRR+RSVGE+
Sbjct: 354 VEGQVIKVIGNGMVDKSVKYIVPADIIASVNYFLNLLHGVGDIDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDANAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSYA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETPYR+V    G VT+++ YL+A EE+N  IAQAN+ LDEDG FT+E V  R
Sbjct: 534 RINEYGFIETPYRRVDPETGVVTDEIHYLTADEEDNYVIAQANAELDEDGRFTQEQVIAR 593

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  + PR +ID++D SPKQVVS+A +LIPFLENDD+NR LMG NMQRQAVPLL  E+
Sbjct: 594 YKEEIGMFPRSRIDYMDVSPKQVVSVATALIPFLENDDANRALMGSNMQRQAVPLLVTES 653

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG-VDIYRLMKF 767
           PFVGTGME   AK SG   VAKR G+VE+V A  I IR  E       SG +D Y+L+KF
Sbjct: 654 PFVGTGMEYKAAKDSGVCTVAKRGGVVERVTADEIWIRVQEEVDGKVVSGDLDKYKLLKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ TC+NQRP+V+ G++V+  DIIADGP+TD G+LALGRN+LVAFM W GYN+ED++
Sbjct: 714 RRSNQGTCINQRPIVRKGEKVQAGDIIADGPATDQGELALGRNVLVAFMTWEGYNYEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+++D+ GII +GAE
Sbjct: 774 LLSEKLVKEDVYTSIHIEEYEAEARDTKLGPEEITRDIPNVGEDALRHLDDRGIIRIGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           +  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G +G VVDV++F R
Sbjct: 834 IYAGDILVGKVTPKGMTELTAEERLLHAIFGEKAREVRDTSLRVPHGGAGIVVDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  562 bits (1449), Expect = e-157,   Method: Composition-based stats.
 Identities = 277/1152 (24%), Positives = 432/1152 (37%), Gaps = 147/1152 (12%)

Query: 268  DTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI-----VNGETGEIY 321
            +TG  +I   ++ + S L++S                 G  V  +      +  +T ++ 
Sbjct: 120  ETGTFIINGAERVIVSQLVRSPSVYFNAKADKNGKRTYGATVIPNRGAWLELETDTKDVI 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         V  +  + Y+RNTL  D     + ALL+IY  +
Sbjct: 180  YARIDRTRKIPVTVLLRALGFSTDADIVHLLGEDEYLRNTLEKDNTDSVEKALLEIYDRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI--------RK 433
            RPG+  T   A ++    FFD  +YDL+ VGR K+N +L+L      + +          
Sbjct: 240  RPGEPPTLENARALLKSRFFDPKRYDLANVGRYKINKKLHLKNRLLNQRLAEDLVDPRTG 299

Query: 434  EDIIAIIKIL-VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +    ++L   L +      +         +S G +  +  RL  +R+   + E    
Sbjct: 300  EVVAESGRVLDRRLLDKVVPALEAGMNMKEYRKSSGVVEDDVIRLQEVRIFSPLVEGQVI 359

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS------ALGQ 546
              I + M    +        +        L      ++ +  + + R  S         +
Sbjct: 360  KVIGNGMVDKSVKYIVPADIIASVNYFLNLLHGVGDIDDIDHLGNRRLRSVGELLQNQFR 419

Query: 547  GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
             G++R    V  R        + P     I P   +     G         + N    + 
Sbjct: 420  IGLSRMERVVRERMSIQDANAITPQALINIRPVIAAIKEFFGSSQLSQFMDQTNPLAELT 479

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
               R             LSA                            R      +    
Sbjct: 480  HKRR-------------LSA---------------------LGPGGLTRERAGFEVRDVH 505

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
               +    P +        I  + +  S   +            +  E   V   +  + 
Sbjct: 506  HSHYGRMCPIET--PEGPNIGLINSLSSYARINEYGFIETPYRRVDPETGVVTDEIHYLT 563

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A      ++A+    +   D      +           G+     + +     +    Q 
Sbjct: 564  ADEEDNYVIAQANAEL---DEDGRFTQEQVIARYKEEIGMFPRSRIDYM----DVSPKQV 616

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE-------DSMLISER 832
              V         +  A+              +LV   P+ G   E           +++R
Sbjct: 617  VSVATALIPFLENDDANRALMGSNMQRQAVPLLVTESPFVGTGMEYKAAKDSGVCTVAKR 676

Query: 833  --MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              +V       I I   E +      G  +  + +          I++  I+  G +V  
Sbjct: 677  GGVVERVTADEIWIRVQEEVDGKVVSGDLDKYKLLKFRRSNQGTCINQRPIVRKGEKVQA 736

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDI+        +  +     +L A    +  +  D  L     V   V    I      
Sbjct: 737  GDIIADGP-ATDQGELALGRNVLVAFMTWEGYNYEDAILLSEKLVKEDV-YTSIHIEEYE 794

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
             +   +     E    +    +D    LD     R+     G    +G     K T    
Sbjct: 795  AEARDTKLGPEEITRDIPNVGEDALRHLDDRGIIRI-----GAEIYAGDILVGKVTPKGM 849

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              ++   R     F  +  +V+     +          +      K+   + GD++PPGV
Sbjct: 850  TELTAEERLLHAIFGEKAREVRDTSLRVPHGGAGIVVDV------KVFTRENGDELPPGV 903

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             ++V+V++A KR I  GDKMAGRHGNKG+++RILP EDMPFL DGTPV+IVLNPLGVPSR
Sbjct: 904  NQLVRVYIAQKRKISEGDKMAGRHGNKGVIARILPEEDMPFLPDGTPVEIVLNPLGVPSR 963

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ ETHLG     +G ++ + + D     DI                         
Sbjct: 964  MNIGQVLETHLGMVAKAMGLRMATPVFDGATEHDI------------------------- 998

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                FD          L  A LD  G+++LYDG TGEPFD  VT
Sbjct: 999  --------------------FD---------ALEEAGLDRDGKTVLYDGRTGEPFDDRVT 1029

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 1030 VGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1089

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+L + + + +   + 
Sbjct: 1090 LQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKELQSLAMDVKILSEDEQE 1149

Query: 1371 SAKMEEIPDFNK 1382
                E   D   
Sbjct: 1150 IIMRESDDDEED 1161


>gi|228475243|ref|ZP_04059968.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus hominis
           SK119]
 gi|314937153|ref|ZP_07844500.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus hominis
           subsp. hominis C80]
 gi|228270708|gb|EEK12117.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus hominis
           SK119]
 gi|313655772|gb|EFS19517.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus hominis
           subsp. hominis C80]
          Length = 1183

 Score =  858 bits (2216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 447/964 (46%), Positives = 603/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KDI++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDIVYVRIDRTRKLPLTVLLRALGFSSDQEIIDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDSTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IV+ ETGEI  E G V+D + L+EI +        +   
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVDSETGEIVAEEGTVLDRRKLDEIMN--------VLES 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D ++   + 
Sbjct: 325 NANSEVFELEGSVIDEPVEIQSIKVYV----------------------PNDEEERTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDIDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVSVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIIYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 162/440 (36%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP---KGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIIYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1148 HDNEIE-MADVDDEDATERK 1166


>gi|169830046|ref|YP_001700204.1| DNA-directed RNA polymerase subunit beta [Lysinibacillus sphaericus
           C3-41]
 gi|226699418|sp|B1HMZ6|RPOB_LYSSC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|168994534|gb|ACA42074.1| DNA-directed RNA polymerase beta chain [Lysinibacillus sphaericus
           C3-41]
          Length = 1191

 Score =  858 bits (2216), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 603/964 (62%), Gaps = 76/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ F +  E++++P+LIE+Q ASY+ FL           EGL+  F+
Sbjct: 4   LTGQLVQYGQHRQRRSFARIKEVLELPNLIEIQTASYEWFL----------EEGLREMFR 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+DVD+C  RD+TYA PL++ +RL           K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGDPKYDVDECKERDVTYAAPLRVKVRLY---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  +
Sbjct: 105 ETDEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFH---DKTDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 162 GATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDIIGDNEYLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +ES K L        K   +     
Sbjct: 222 NTLEKDNSESTEKALL------EIYERLRPGEPPTVESAKSLLYSRFFDAKRYDLANVGR 275

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +E G V+D ++L++I          +   
Sbjct: 276 YKMNKKLHIKNRLFNQTIAETLVDPETGEILVEKGTVLDRRTLDKILPYLEDSSKGIGFR 335

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           +++    +             D  +   ++  P D +                       
Sbjct: 336 TLSQVGGVLE----------DDVTIQSIKIYAPKDEAQK--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N    ++V++I   D+++ +    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 365 ----EINIISNAYIDEEVKNITPADVLSSVSYFFNLLYQVGATDDIDHLGNRRLRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +++PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSINDTAAIVPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 481 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 540

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++     +VT+ + YL+A EE+N Y+AQANS L+ DGSF  + V  R
Sbjct: 541 KVNKFGFIETPYRRIDHETGQVTDQIDYLTADEEDNYYVAQANSPLNPDGSFANDEVVGR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+  +  + ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 601 FRGDNTVFNKAQMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKF 767
           PFVGTGME V A+ SGAA+VAK  GIVE V+A  I +R +E        G    Y+L KF
Sbjct: 661 PFVGTGMEHVDARDSGAAVVAKYDGIVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKF 720

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRPLVKVG+ V+  DI+ADGPS + G+LALGRN+LVAFM W+G+N+ED++
Sbjct: 721 IRSNQGTSYNQRPLVKVGERVKPRDILADGPSMEKGELALGRNVLVAFMTWNGFNYEDAV 780

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 781 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 840

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 841 VRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIILDVKVFNR 900

Query: 948 HGID 951
              D
Sbjct: 901 EDGD 904



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 183/554 (33%), Positives = 260/554 (46%), Gaps = 77/554 (13%)

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V      SIH+   EV+      G     +    +      + ++  ++ VG  V P D
Sbjct: 686  IVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKFIRSNQGTSYNQRPLVKVGERVKPRD 745

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL    +   +  +     +L A       +  D  +     V   V        +  + 
Sbjct: 746  ILADGPS-MEKGELALGRNVLVAFMTWNGFNYEDAVIMSERLVKDDVYTSVHIEEYESES 804

Query: 953  NERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
             +  +  E     I  +  D     DE+ I+      R  +IL G+    G         
Sbjct: 805  RDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEER 864

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L   +  E  R      +++       +                    K+   + GD++P
Sbjct: 865  LLHAIFGEKARE-VRDTSLRVPHGAGGI----------------ILDVKVFNREDGDELP 907

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGV
Sbjct: 908  PGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGV 967

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D     D+                      
Sbjct: 968  PSRMNIGQVLELHLGMASRYLGVHMATPVFDGANEEDVW--------------------- 1006

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  +  A   + G                             ++ILYDG +GEPFD 
Sbjct: 1007 ----ETMEEAGMNRDG-----------------------------KTILYDGRSGEPFDN 1033

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1034 RVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1093

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + +    
Sbjct: 1094 AYTLQEILTVKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLTVN 1153

Query: 1368 TKNSAKMEEIPDFN 1381
             +     +   + +
Sbjct: 1154 DEEVELRDLDEEED 1167


>gi|313903159|ref|ZP_07836553.1| DNA-directed RNA polymerase subunit beta [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466661|gb|EFR62181.1| DNA-directed RNA polymerase subunit beta [Thermaerobacter
           subterraneus DSM 13965]
          Length = 1237

 Score =  857 bits (2215), Expect = 0.0,   Method: Composition-based stats.
 Identities = 454/951 (47%), Positives = 586/951 (61%), Gaps = 94/951 (9%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            VV +G  R R  FG+  E++D+P+LIEVQ  SY  FL          NEGL+  F+ + 
Sbjct: 3   HVVKSG-KRERLSFGRIHEVLDLPNLIEVQLNSYRWFL----------NEGLKETFQDIS 51

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  F+G  +LEFV Y    PK+ V +C  RD+TYA P+++ +RLI          K   
Sbjct: 52  PIQDFTGNLVLEFVDYSLGEPKYSVQECKDRDVTYAAPMRVRVRLI---------NKETG 102

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           ++KEQ ++MGD PLMT+ GTFVI G +R+VVSQL RSPG+++  D      +G  LY+  
Sbjct: 103 EVKEQEVFMGDFPLMTEHGTFVINGAERVVVSQLVRSPGVYYSVDYD---ANGNPLYSAT 159

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +IP++G W++ E D+  +++VR+DR RK P T  L ALG  ++ E+L             
Sbjct: 160 VIPNRGAWLEFETDASGVVYVRVDRTRKQPATVLLRALGYQTDAELLELLGDTEHVRATL 219

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD 301
           D       A  L+   K       +  GE    ES ++L   L    K   +        
Sbjct: 220 DKDNTDSQAEALIEIYK------RLRPGEPPTDESARQLLDNLFFDPKRYDLAA------ 267

Query: 302 CLCGLYVAEDIVNGETGEI-YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
              G Y     +N     I    A DV+D ++ E I  +  R    L             
Sbjct: 268 --VGRYKMNKKLNLRARLIGLYAAEDVVDPQTGERIVEAGQRFDRQLAQRVQAAGV---- 321

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                + +  +D  +    V+  G                                    
Sbjct: 322 --RRVRVRTPEDREV---VVLGNGQP---------------------------------- 342

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                  VR + +EDI AII     L  G GT DDID+LGNRR+RSVGE+L+NQ+R+GL 
Sbjct: 343 ----DTTVRTLTREDIAAIINYAFGLFAGVGTTDDIDHLGNRRLRSVGELLQNQFRIGLA 398

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER IKER+S  D D++ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 399 RMERVIKERMSIQDADAITPQALINIRPVVAAVKEFFGSSQLSQFMDQTNPLSELTHKRR 458

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG ++RDVH +HYGR+CP ET EG NIGL+ ++ ++ARVN YGFIET
Sbjct: 459 LSALGPGGLSRERAGFDVRDVHHSHYGRMCPIETPEGPNIGLIGAMATYARVNEYGFIET 518

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V  G+VT+DVVYL+A EE+   IAQAN+ LDE+G F E+ V  R   E  L   E+
Sbjct: 519 PYRRVEKGRVTDDVVYLTADEEDECVIAQANAELDENGYFKEKRVAVRFRDEVRLAAPEE 578

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ID++D SPKQV SIA +LIPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTG+E   A
Sbjct: 579 IDYMDVSPKQVFSIATALIPFLEHDDANRALMGANMQRQAVPLIRTEAPLVGTGVEYRTA 638

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  I A+RAG V +V A  IV+ + +G  D        Y LMKF+RSNQ TC NQRP
Sbjct: 639 VDSGVVITARRAGTVRRVTAREIVVETEDGQRD-------TYHLMKFERSNQGTCFNQRP 691

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ G  V + D++ADGPSTD G+LALGRN+LVAFMPW GYN+ED++LISER+V +DVFT
Sbjct: 692 LVRKGQRVEKGDVLADGPSTDHGELALGRNVLVAFMPWEGYNYEDAILISERLVKDDVFT 751

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+++DE GII +GAEV  GDILVGK+TP
Sbjct: 752 SIHIEEYECEARDTKLGPEEITRDIPNVGEDQLRDLDERGIIRIGAEVRAGDILVGKVTP 811

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 812 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVFSRENGD 862



 Score =  542 bits (1396), Expect = e-151,   Method: Composition-based stats.
 Identities = 200/532 (37%), Positives = 275/532 (51%), Gaps = 79/532 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +T+ G  +    +           ++  ++  G  V  GD+L    +      +     +
Sbjct: 664  ETEDGQRDTYHLMKFERSNQGTCFNQRPLVRKGQRVEKGDVLADGPST-DHGELALGRNV 722

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK- 971
            L A    +  +  D  L     +S  +V   +F    I++ E      +   E + RD  
Sbjct: 723  LVAFMPWEGYNYEDAIL-----ISERLVKDDVFTSIHIEEYECEARDTKLGPEEITRDIP 777

Query: 972  ---DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAV 1026
               +D+   LD     R+   +   + + G    K  T L+++  L+      +  +   
Sbjct: 778  NVGEDQLRDLDERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRD 837

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
               +V      + V               K+   + GD++ PGV ++V+V+VA KR I  
Sbjct: 838  TSLRVPHGESGIVV-------------DVKVFSRENGDELAPGVNQLVQVYVAQKRKISE 884

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+++RI+P EDMPFL DGTPVDIVLNPLGVPSRMN+GQI E        
Sbjct: 885  GDKMAGRHGNKGVIARIMPEEDMPFLPDGTPVDIVLNPLGVPSRMNIGQILE-------C 937

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG   K+L                                               G+ V
Sbjct: 938  HLGWAAKAL-----------------------------------------------GLWV 950

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDG  EE+I  +LR A L ESG+++LYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 951  ATPVFDGTGEESIRELLRKAGLPESGKTVLYDGRTGEPFDNEVTVGYVYMLKLAHLVDDK 1010

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1011 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRV 1070

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            + YE+IV G +  E G PESF VL+KEMQ+LGL + + +   +     E+  
Sbjct: 1071 KTYEAIVKGENVPEPGVPESFKVLIKEMQSLGLDVKILSEDNREIVLREDEE 1122


>gi|260585055|ref|ZP_05852797.1| DNA-directed RNA polymerase, beta subunit [Granulicatella elegans
           ATCC 700633]
 gi|260157251|gb|EEW92325.1| DNA-directed RNA polymerase, beta subunit [Granulicatella elegans
           ATCC 700633]
          Length = 1213

 Score =  857 bits (2214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/989 (43%), Positives = 608/989 (61%), Gaps = 89/989 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  RVR+ + +  E++++P+LIE+Q  SY  FL          +EG++  FK
Sbjct: 1   MAHHDVKYGKHRVRRSYARISEVLELPNLIEIQTDSYQWFL----------DEGIREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI   +G   LEF+ YE   PK+++ +    D  YA P+ + +RL+          K
Sbjct: 51  DISPIEDHTGNLSLEFLDYELHAPKYNLAEARNHDANYAAPIYVKMRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG +F     R   +GK LY
Sbjct: 102 ETGEVKDQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGSYFH---DRPDKNGKALY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E DSKDI +VRIDR RK+P+T  + ALG +S++ IL  F       
Sbjct: 159 GATLIPNRGAWLEYESDSKDISYVRIDRTRKIPLTVLVRALGFESDDTILEIFGESETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVD-IDTGEQ-VIESGKKLTSGLLKSLKEK------ 291
              D         D     +    + D +  GE    ES + L +      +        
Sbjct: 219 LTLDKDVHKRM--DESRTEEALKDIYDRLRPGEPKTAESSRNLLTARFFDPRRYDFAAVG 276

Query: 292 --GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
              V         L    +AE+IV+ ETGEI +EAG V++++ +E++  +          
Sbjct: 277 RYKVNKKLNLKTRLLNQTIAENIVHPETGEIVVEAGTVLEKEIMEKVAQA---------- 326

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
             +   A +     + +   ++   +   +V  P D                        
Sbjct: 327 --LEAGANLFTLYPSSEGVIQEPVTIQSVQVYSPQDP----------------------- 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N + PD+++ +   D++A I   ++L  G G+ DDID+LGNRR+RSVGE
Sbjct: 362 ---EKVIKVIGNANIPDEIKCVTAADVLATISYFLNLYEGIGSTDDIDHLGNRRIRSVGE 418

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D+ +V PQ L+N +PVV+A+ EFF SSQLSQ  +  
Sbjct: 419 LLQNQFRIGLSRMERVVRERMSIQDVATVTPQQLVNIRPVVAAIKEFFGSSQLSQFMDQT 478

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+
Sbjct: 479 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSY 538

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           A++N YGF+ETPYR+V     KVT+ + YL+A EE+   +AQANS L+EDGSF  ++V  
Sbjct: 539 AKINKYGFVETPYRRVDWKTHKVTDKIDYLTADEEDRYVVAQANSPLNEDGSFVNDVVMA 598

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + VP E++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL  +
Sbjct: 599 RYVSENLEVPVERVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLNPK 658

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           APF+GTGME V A  SG A++ KR GIVE VDA ++ +R+ +G LD        Y + KF
Sbjct: 659 APFIGTGMEYVTAHDSGVALLCKREGIVEFVDANQVRVRTADGSLDQ-------YNITKF 711

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             SN   C NQRP+V  GD+V   +I+ADGPS + G+LALG+N+LVAFM W GYN+ED++
Sbjct: 712 HGSNAGMCYNQRPIVSKGDKVEVGEILADGPSMEQGELALGQNVLVAFMTWEGYNYEDAV 771

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHI++++  ARDTKLGPEEITR+IPNV E+ LKN+DE GII +GAE
Sbjct: 772 IMSERLVKDDVYTSIHIDDYDSEARDTKLGPEEITREIPNVGEDALKNLDENGIIRIGAE 831

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG +  +PEE+LL AIFGEKA +VRDTSLRVP G  G V DVR+F R
Sbjct: 832 VKDGDILVGKVTPKGLTEQSPEERLLHAIFGEKAREVRDTSLRVPHGGGGIVRDVRVFTR 891

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   G++K  R   V++ +I    +
Sbjct: 892 AAGDELAPGVNKLVRVYIVQKRKINEGDK 920



 Score =  473 bits (1217), Expect = e-130,   Method: Composition-based stats.
 Identities = 179/536 (33%), Positives = 246/536 (45%), Gaps = 85/536 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +                ++  I+  G +V  G+IL    +   +  +   + +
Sbjct: 697  RTADGSLDQYNITKFHGSNAGMCYNQRPIVSKGDKVEVGEILADGPS-MEQGELALGQNV 755

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI------SVEREQIEL 966
            L A    +  +  D  +         V D    + H  D +  +            +I  
Sbjct: 756  LVAFMTWEGYNYEDAVIM----SERLVKDDVYTSIHIDDYDSEARDTKLGPEEITREIPN 811

Query: 967  LARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  D     DE  I+      +  +IL G+    G         L   +  E  R     
Sbjct: 812  VGEDALKNLDENGIIRIGAEVKDGDILVGKVTPKGLTEQSPEERLLHAIFGEKAR----- 866

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                  +V+     +          +      ++     GD++ PGV ++V+V++  KR 
Sbjct: 867  ------EVRDTSLRVPHGGGGIVRDV------RVFTRAAGDELAPGVNKLVRVYIVQKRK 914

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I  GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG 
Sbjct: 915  INEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGM 974

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG  I + + D   + D+    +                                 
Sbjct: 975  AARELGIYIATPVFDGAQDEDVWGTVAEAGMARDAK------------------------ 1010

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                T ++DG                           TGEPFD  V+VG +YM+KL HMV
Sbjct: 1011 ----TILYDG--------------------------RTGEPFDNRVSVGVMYMIKLAHMV 1040

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVV
Sbjct: 1041 DDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVV 1100

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            GR + YESIV G    + G PESF VLVKE+QALGL + + ++  +     +   D
Sbjct: 1101 GRVKTYESIVKGQQISKPGVPESFRVLVKELQALGLDMKVLDANDEEIKLEDMDDD 1156


>gi|227533947|ref|ZP_03963996.1| DNA-directed RNA polymerase subunit beta [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227188419|gb|EEI68486.1| DNA-directed RNA polymerase subunit beta [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 1231

 Score =  857 bits (2214), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 583/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 33  LAGHLVNYGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFD 82

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 83  DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 133

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  + S   ++ Y
Sbjct: 134 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDKNS---RVTY 190

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 191 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 250

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 251 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 309

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 310 YKVNKKLSLKTRLLNQVLAETLADPDTGEVIAQKGTKVDRQVMDKLAPYL---------- 359

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G V+     +S+  +     DK     
Sbjct: 360 ------------------DRDDFKTITYQPSDQGVVTDPIELQSIKVYSQVTPDKE---- 397

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 398 -----INLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSIDDIDHLGNRRIRSVGEL 452

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 453 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 512

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 513 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 572

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF +E V  R
Sbjct: 573 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDETVLAR 632

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 633 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVNPHA 692

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y LMKF+
Sbjct: 693 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALDA-------YNLMKFK 745

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 746 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 805

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 806 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 865

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 866 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 925

Query: 949 GID 951
             D
Sbjct: 926 AGD 928



 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 236/1072 (22%), Positives = 385/1072 (35%), Gaps = 102/1072 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 207  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 266

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 267  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 326

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 327  L-----------AETLADPDTGEVIAQKGTKVDRQVMDKLAPYLDRDDFKTITYQPSDQG 375

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 376  VVTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSI 435

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 436  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 493

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 494  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 549

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 550  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 609

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 610  IVAQANSPLNDDGSFVDETVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 664

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                 +  +D        ++   A+      A +   G  ++ +      +++ +  T  
Sbjct: 665  ----FLENDDSNRALMGANMQRQAVPLVNPHAPLVGTGMEYKAAHDSGTAVLANNAGTVE 720

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +++  ++  R  + G  +    +        KN ++  I+ +G  V   D ++       
Sbjct: 721  YVDAKQIRVRR-EDGALDAYNLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAMQ 778

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + A       +  D  +         V D    + H  +    +   +  
Sbjct: 779  NGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKLG 834

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E+     +  +  L          +  G     G     K T      +S   R    
Sbjct: 835  PEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLHA 892

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  KR
Sbjct: 893  IFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKR 946

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG
Sbjct: 947  KIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLG 1006

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D   + D+                                     
Sbjct: 1007 MAARNLGIHVATPVFDGANDKDLW------------------------------------ 1030

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                       A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+HM
Sbjct: 1031 -----------ATVKE-------AGMASDGKSVLYDGRTGEPFENRVSVGIMYYMKLSHM 1072

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV
Sbjct: 1073 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDV 1132

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VGR + YE+IV G    + G PESF VLVKE+QALGL + +  +  K     
Sbjct: 1133 VGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGLDMKVLGADKKEIELR 1184


>gi|121534751|ref|ZP_01666572.1| DNA-directed RNA polymerase, beta subunit [Thermosinus
           carboxydivorans Nor1]
 gi|121306771|gb|EAX47692.1| DNA-directed RNA polymerase, beta subunit [Thermosinus
           carboxydivorans Nor1]
          Length = 1276

 Score =  857 bits (2213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 450/952 (47%), Positives = 599/952 (62%), Gaps = 103/952 (10%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           RVR  + K  E++D+P+LIE+QK SY+ FL           EGLQ  F+ + PI  F+G 
Sbjct: 10  RVRYSYAKINEVLDMPNLIEIQKNSYNWFL----------KEGLQEIFRDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L F  +    PK+ V++C  RD+TY+ PL++++RLI          K   +IKEQ ++
Sbjct: 60  LVLSFEGFTLGEPKYSVEECKERDVTYSAPLRVSVRLI---------NKETGEIKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT++GTF+I G +R++VSQL RSPG ++         SGK LY   IIP++G W
Sbjct: 111 MGDFPLMTENGTFIINGAERVIVSQLVRSPGAYYGETID---TSGKKLYNATIIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           +++E D+ D++ VR+DR RK+PVT  + ALG  S   IL  F   +      +       
Sbjct: 168 LELETDANDVVSVRVDRTRKLPVTVLIRALGWASNGAILDLFNDDVRIRATLERDSTSSK 227

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------D 301
              L+   K       +  GE   +E+  +L   L    K   +  +G            
Sbjct: 228 EEALVEIYK------RLRPGEPPTVENATQLLESLFFDPKRYDLAAVGRYKLTKKLGWRR 281

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G  + E I+N ETGEI +  G V+DEK    I  S + +   L              
Sbjct: 282 RIMGKTLHEPIINKETGEIIVPEGTVVDEKVAARIEASGVFNHEGL-------------- 327

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                          I   +R  D                         V +V  N  L 
Sbjct: 328 ---------------IEFKIRQKD-----------------------GAVIKVIANPSL- 348

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
              P   R I +EDIIA I  L++L +G G +DDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 349 ---PYSHRTITREDIIAAISYLLNLMDGHGKVDDIDHLGNRRLRSVGELLQNQFRIGLSR 405

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER +KER++  DID + PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRL
Sbjct: 406 MERVVKERMTIQDIDVITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRL 465

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++FAR+N +GFIETP
Sbjct: 466 SALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTFARINEFGFIETP 525

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV   + +VT++V YL+A EE+   IAQAN  + EDG F +  V  R   + ++VP E
Sbjct: 526 YRKVDKENRRVTDEVHYLTADEEDEVVIAQANEEISEDGWFVQPRVTVRYKHDILVVPAE 585

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D++D SPKQVVSIA ++IPFLENDD+NR LMG NMQRQAVPLLK +AP VGTGME   
Sbjct: 586 QVDYMDVSPKQVVSIATAMIPFLENDDANRALMGANMQRQAVPLLKTQAPLVGTGMEYKA 645

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG  ++AK AG+VE+V A  I +R+ +G LD        Y+L+K+ RSNQ TC+NQ+
Sbjct: 646 ACDSGVVVLAKNAGVVEKVTATEIQVRTDKGSLD-------TYKLLKYMRSNQGTCINQK 698

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  G  V +   +ADGPST+ G+LALG N+LVAFMPW GYN+ED++L+SE +V ED+F
Sbjct: 699 PIVYKGQRVEKGQPLADGPSTNNGELALGYNVLVAFMPWEGYNYEDAILLSEELVKEDIF 758

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ L+++DE GII VGAEV PGDILVGK+T
Sbjct: 759 TSIHIEEYECDARDTKLGPEEITRDIPNVSEDVLRDLDERGIIRVGAEVRPGDILVGKVT 818

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 819 PKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFTRENGD 870



 Score =  570 bits (1469), Expect = e-160,   Method: Composition-based stats.
 Identities = 208/537 (38%), Positives = 276/537 (51%), Gaps = 46/537 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  + +  +       I++  I+  G  V  G  L    +      +     +
Sbjct: 672  RTDKGSLDTYKLLKYMRSNQGTCINQKPIVYKGQRVEKGQPLADGPST-NNGELALGYNV 730

Query: 913  LRAIFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L      +     S  + +     R      E          E 
Sbjct: 731  LVAFMPWEGYNYEDAILLSEELVKEDIFTSIHIEEYECDARDTKLGPEEITRDIPNVSED 790

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            + RD  DE+ I+      R  +IL G+    G         L   +  E  R        
Sbjct: 791  VLRDL-DERGIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 841

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E                   K+   + GD++PPGV ++V+V++A KR I  
Sbjct: 842  ---------EVRDTSLRVPHGEAGKIVDVKVFTRENGDELPPGVNQLVRVYIAQKRKISE 892

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSRI+P EDMPFL DG PV IVLNPLGVPSRMN+GQ+ ETHLGWA  
Sbjct: 893  GDKMAGRHGNKGVVSRIMPVEDMPFLPDGRPVQIVLNPLGVPSRMNIGQVLETHLGWAAH 952

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG +IK++                                  D     + +  ++GV +
Sbjct: 953  ALGLQIKNM---------------------DPNVEQRLREVGYDVDKHGMLKPGEAGVHL 991

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE +   L+MA L E+G+SILYDG TGEPFD PVTVGYIYMLKL H+V DK
Sbjct: 992  ATPVFDGAREEDVFKTLKMAGLPENGKSILYDGRTGEPFDNPVTVGYIYMLKLAHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1052 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            + YE+IV G +  E G PESF VL+KE+Q++GL + + +   +     E   D ++ 
Sbjct: 1112 KTYEAIVKGENVPEPGVPESFKVLIKELQSIGLDVKVLSEDAQEILIRESDEDIHET 1168


>gi|5726633|gb|AAD48492.1|AF172323_1 RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 1105

 Score =  857 bits (2213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/954 (45%), Positives = 600/954 (62%), Gaps = 78/954 (8%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G
Sbjct: 1   HRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTG 50

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q +
Sbjct: 51  NLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDV 101

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G 
Sbjct: 102 FMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGA 158

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+             D      
Sbjct: 159 WLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGENEYLRNTLDKDNTEN 218

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSDC------ 302
           +   L+           +  GE   +E+ K L        K   +  +G           
Sbjct: 219 TDQALL------EIYERLRPGEPPTVENAKSLLESRFFDPKRYDLASVGRYKINKKLHIK 272

Query: 303 --LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L    +AE +V+ ETGEI  E G ++D ++L++             V     N     
Sbjct: 273 SGLFNQRLAETLVDPETGEILAEKGAILDRRTLDK-------------VLPYLENGIGFK 319

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            L  +      +  L   ++  P D                          G   +N+  
Sbjct: 320 KLYPNGGVVEDEVTLQSIKIYAPTD------------------------QEGEQTINVIG 355

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL 
Sbjct: 356 NAYIEEGVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLS 415

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +T+ RR
Sbjct: 416 RMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTYKRR 475

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIET
Sbjct: 476 LSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFGFIET 535

Query: 601 PYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V    GKVT  + YL+A EE+N  +AQAN+ L++DGSF ++ +  R  GE  +VP+
Sbjct: 536 PYRRVDPETGKVTPRIDYLTADEEDNYVVAQANARLNDDGSFVDDSIVARFRGENTVVPK 595

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+P VGTGME V
Sbjct: 596 DRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPESPIVGTGMEYV 655

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            AK SGA ++ +  GIVE+V+A  I +R   E D       +D Y L+KF RSNQ TC N
Sbjct: 656 SAKDSGAVVICRHPGIVERVEAKNIWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYN 715

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+V VGDEV + +I+ADGPS + G+LALGRN++V FM W GYN+ED++++SER+V +D
Sbjct: 716 QRPIVSVGDEVEKGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDD 775

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAEV  GD+LVGK
Sbjct: 776 VYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGK 835

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 836 VTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNREDGD 889



 Score =  454 bits (1168), Expect = e-125,   Method: Composition-based stats.
 Identities = 247/1091 (22%), Positives = 414/1091 (37%), Gaps = 125/1091 (11%)

Query: 267  IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            I+  E+VI S    +  +  S K       G T+  +       +        +Y+    
Sbjct: 117  INGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDR 176

Query: 327  VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                     +          + +D +  N Y+RNTL  D  ++   ALL+IY  +RPG+ 
Sbjct: 177  TRKLPVTVLLRALGFGSDQEI-IDLIGENEYLRNTLDKDNTENTDQALLEIYERLRPGEP 235

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI--------RKEDIIA 438
             T   A+S+    FFD  +YDL++VGR K+N +L++ +    + +          E +  
Sbjct: 236  PTVENAKSLLESRFFDPKRYDLASVGRYKINKKLHIKSGLFNQRLAETLVDPETGEILAE 295

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM--------ERSIKERI 490
               IL      K      + +G +++   G +++++  L  +++        E++I    
Sbjct: 296  KGAILDRRTLDKVLPYLENGIGFKKLYPNGGVVEDEVTLQSIKIYAPTDQEGEQTINVIG 355

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            ++   + V      +    +S           +   +H+ +    +    L    + G++
Sbjct: 356  NAYIEEGVKNITPSDIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLS 415

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R    V  R         +   +T+      L++     A +  +       + +     
Sbjct: 416  RMERVVRER---------MSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNP 466

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              ++ Y                           L       E   +    + +       
Sbjct: 467  LAELTY---------------------KRRLSALGPGGLTRERAGMEVRDVHYSHYGRMC 505

Query: 671  VVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI-- 727
             +       I  + +  S   +            +  E   V   ++ + A      +  
Sbjct: 506  PIETPEGPNIGLINSLSSFAKVNRFGFIETPYRRVDPETGKVTPRIDYLTADEEDNYVVA 565

Query: 728  --VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
               A+       VD   +     E  + P      +    K   S    C+         
Sbjct: 566  QANARLNDDGSFVDDSIVARFRGENTVVPKDRVDYMDVSPKQVVSAATACIPFL----EN 621

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIH 843
            D+  R  + A+     +  +     ++   M +       +++I     +V      +I 
Sbjct: 622  DDSNRALMGANMQRQAVPLMQPESPIVGTGMEYVSAKDSGAVVICRHPGIVERVEAKNIW 681

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            +  +E +      G  +    +  V        ++  I+ VG EV  G+IL    +   +
Sbjct: 682  VRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGDEVEKGEILADGPS-MEK 740

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              +     ++         +  D  +     +S  +V   ++    I++ E      +  
Sbjct: 741  GELALGRNVMVGFMTWDGYNYEDAII-----MSERLVKDDVYTSIHIEEYESEARDTKLG 795

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E + RD  +      RN+  R   I  G     G     K T      ++   R     
Sbjct: 796  PEEITRDIPNVGEDALRNLDER-GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAI 854

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            F  +  +V+     +                 K+   + GD++PPGV ++V+V++  KR 
Sbjct: 855  FGEKAREVRDTSLRVPHGGGGII------LDVKVFNREDGDELPPGVNQLVRVYIVQKRK 908

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG 
Sbjct: 909  ISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGM 968

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG  + S + D     D+                                      
Sbjct: 969  AARRLGLHVASPVFDGAREEDVWETLEEAGMSRDAK------------------------ 1004

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                T ++DG                           TGEPFD  V+VG +YM+KL HMV
Sbjct: 1005 ----TVLYDG--------------------------RTGEPFDNRVSVGIMYMIKLAHMV 1034

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVV
Sbjct: 1035 DDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVV 1094

Query: 1324 GRTRVYESIVA 1334
            GR + YE+IV 
Sbjct: 1095 GRVKTYEAIVK 1105


>gi|191639439|ref|YP_001988605.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei BL23]
 gi|226699414|sp|B3WAM8|RPOB_LACCB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|190713741|emb|CAQ67747.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
           (Transcriptase subunit beta) (RNA polymerase subunit
           beta) [Lactobacillus casei BL23]
          Length = 1199

 Score =  857 bits (2213), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 583/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LI++Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVNYGKHRTRRSYARIKEVLDLPNLIKIQTNSYQWFL----------DEGLKEMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F       
Sbjct: 159 GTTVIPNRGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 219 LTLEKD-VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGE+  + G  +D + ++++              
Sbjct: 278 YKVNKKLSLKTRLLNQVLAETLADPDTGEVIAQKGTKVDRQVMDKLAPYL---------- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y+    G V+     +S+  +     DK     
Sbjct: 328 ------------------DRDDFKTITYQPSDQGVVTDPIELQSIKVYSQVTPDKE---- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+HI   D++A +   ++L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 -----INLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSIDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF +E V  R
Sbjct: 541 VVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDETVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 HKDNNIEISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVNPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A  AG VE VDA +I +R  +G LD        Y LMKF+
Sbjct: 661 PLVGTGMEYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALDA-------YNLMKFK 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED+++
Sbjct: 714 RSNAGKNYNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV
Sbjct: 774 LSERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 834 RDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 AGD 896



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 236/1072 (22%), Positives = 385/1072 (35%), Gaps = 102/1072 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 175  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 234

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 235  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 294

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 295  L-----------AETLADPDTGEVIAQKGTKVDRQVMDKLAPYLDRDDFKTITYQPSDQG 343

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 344  VVTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSI 403

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 404  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 461

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 462  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 517

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 518  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 577

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 578  IVAQANSPLNDDGSFVDETVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 632

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                 +  +D        ++   A+      A +   G  ++ +      +++ +  T  
Sbjct: 633  ----FLENDDSNRALMGANMQRQAVPLVNPHAPLVGTGMEYKAAHDSGTAVLANNAGTVE 688

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +++  ++  R  + G  +    +        KN ++  I+ +G  V   D ++       
Sbjct: 689  YVDAKQIRVRR-EDGALDAYNLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAMQ 746

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + A       +  D  +         V D    + H  +    +   +  
Sbjct: 747  NGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKLG 802

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E+     +  +  L          +  G     G     K T      +S   R    
Sbjct: 803  PEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLHA 860

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  KR
Sbjct: 861  IFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKR 914

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG
Sbjct: 915  KIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLG 974

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D   + D+                                     
Sbjct: 975  MAARNLGIHVATPVFDGANDKDLW------------------------------------ 998

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                       A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+HM
Sbjct: 999  -----------ATVKE-------AGMASDGKSVLYDGRTGEPFENRVSVGIMYYMKLSHM 1040

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV
Sbjct: 1041 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDV 1100

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VGR + YE+IV G    + G PESF VLVKE+QALGL + +  +  K     
Sbjct: 1101 VGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGLDMKVLGADKKEIELR 1152


>gi|317126848|ref|YP_004093130.1| DNA-directed RNA polymerase subunit beta [Bacillus cellulosilyticus
           DSM 2522]
 gi|315471796|gb|ADU28399.1| DNA-directed RNA polymerase, beta subunit [Bacillus
           cellulosilyticus DSM 2522]
          Length = 1179

 Score =  856 bits (2212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/959 (45%), Positives = 601/959 (62%), Gaps = 68/959 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++D+P+LIE+Q ASY  FL          +EG++  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARISEVLDLPNLIEIQTASYQWFL----------DEGIREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLVLEFIDYSLGEPKYSVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++++    +   +GK  +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYYNKKVDK---NGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI--V 237
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  ++ EI+          
Sbjct: 159 TATVIPNRGAWLELETDAKDIVYVRIDRTRKIPVTVLLRALGFGTDQEIIELLGEDEYLR 218

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +           ++  + ++ES         L    + K  K 
Sbjct: 219 NTLEKDNTDNSEKALLEIYERLRPGEPPTVENAKSLLESRFFDPKRYDLANVGRYKMNKK 278

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L I  D L    +AE +V+ +TGE+  E G VID + L+++      ++   +       
Sbjct: 279 LHI-KDRLFNQRLAETLVDPDTGEVLAEEGAVIDRRLLDKLIPYLENNVG--FKHYTLRG 335

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I                                  +S+        D+  +  +G   
Sbjct: 336 GVIEE---------------------------DEVELQSILITNPESVDEQPIRVLGNGV 368

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +           V++I   DIIA I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+
Sbjct: 369 VEKA--------VKNITVADIIASINYFFNLLHGVGNTDDIDHLGNRRLRSVGELLQNQF 420

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +
Sbjct: 421 RIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAEL 480

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +
Sbjct: 481 THKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEF 540

Query: 596 GFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GF+ETPYRKV     +VT+   YL+A EE+N  +AQAN+ LDE+G+F +E + CR  GE 
Sbjct: 541 GFMETPYRKVDHETGRVTSQFDYLTADEEDNYVVAQANAKLDENGAFMDENIICRFRGEN 600

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           I+V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLLK EAP VGT
Sbjct: 601 IIVSRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLKPEAPLVGT 660

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKFQRSNQ 772
           GME V AK SGAA+V+K  G VE+V A  + IR VE  D +     +  Y L KF+RSNQ
Sbjct: 661 GMEYVSAKDSGAAVVSKVRGRVERVSAKYVEIRRVETVDGNEVEGDIVRYNLQKFERSNQ 720

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V  G+ V   +I+ADGPS +LG++ALGRN++V FM W GYN+ED++++SER
Sbjct: 721 GTCYNQRPIVSEGNFVEIGEILADGPSMELGEMALGRNVMVGFMTWDGYNYEDAIILSER 780

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TS+HIEE+E  ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAEV  GD
Sbjct: 781 LVKDDVYTSVHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAEVKDGD 840

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR P G  G V+DV++FNR   D
Sbjct: 841 ILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKVFNREDGD 899



 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 165/424 (38%), Positives = 223/424 (52%), Gaps = 58/424 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   SV  E+ E  ARD       + R+I +   + L   +     +     K   +L
Sbjct: 783  KDDVYTSVHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAEVKDGDIL 842

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++     +    +      K+   + GD++P
Sbjct: 843  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRAPHGGDGIVLDVKVFNREDGDELP 902

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP+L DGTP+DI+LNPLGV
Sbjct: 903  PGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYLPDGTPIDIMLNPLGV 962

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + S + D     D+                      
Sbjct: 963  PSRMNIGQVLELHLGMAARNLGIHVASPVFDGAREEDVWGTLEEAGMAR----------- 1011

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                    DG                      LYDG TGEPFD 
Sbjct: 1012 ------------------------DGKTV-------------------LYDGRTGEPFDN 1028

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1029 RVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1088

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LG+ + + +S 
Sbjct: 1089 AYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGMDVKMLSSN 1148

Query: 1368 TKNS 1371
             +  
Sbjct: 1149 EEEI 1152


>gi|222152109|ref|YP_002561269.1| DNA-directed RNA polymerase beta subunit [Macrococcus caseolyticus
           JCSC5402]
 gi|254765294|sp|B9E8Q5|RPOB_MACCJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|222121238|dbj|BAH18573.1| DNA-directed RNA polymerase beta subunit [Macrococcus caseolyticus
           JCSC5402]
          Length = 1180

 Score =  856 bits (2212), Expect = 0.0,   Method: Composition-based stats.
 Identities = 444/964 (46%), Positives = 607/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   ++  G  R R+ + +  EI+++P+LIE+Q  SYD FL           EGL   FK
Sbjct: 1   MTGQLIQYGRHRKRRSYARISEILELPNLIEIQTKSYDWFL----------KEGLIEMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+D+D+   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYKLGEPKYDLDESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +GK+ +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFN---DKVDKNGKVSF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD++ VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 GATVIPNRGAWLEYETDAKDVVFVRIDRTRKLPITVLLRALGFSTDQEIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              D      + A L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NALDKDNTESTEAALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G ++D ++L++I       I +L  +
Sbjct: 273 YKMNKKLHLKHRLFNQVLAEPIVNTETGEIVAEEGTLLDRRNLDQI-------IDVLESN 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           +        N  V D +    D  ++I  V                         Y    
Sbjct: 326 A--------NQKVYDLDNGLLDEPIEIQSV-----------------------KVYVPGD 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             +    +  N    D+V+ I   DI++ +    +L  G G  DDID+LGNRR+RSVGE+
Sbjct: 355 EEKRTTTIIGNAFPDDEVKCITPADILSSVSYFFNLLAGVGFTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +SV PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSLQDTESVTPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      VT+ + YL+A EE+   +AQAN+ LD++G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDIETNTVTSQIDYLTADEEDAYVVAQANARLDDNGKFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+  ++ RE++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGDNTVMARERMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAA+VAK  G VE V+A +I +R + E       + +D+Y+L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAVVAKYKGRVEHVEARQIKVRRIVEEGGKEIETDLDVYKLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  TC NQRP+V+ G+ V + +I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 ARSNSGTCYNQRPIVEAGNIVTKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVS+  LKN+D+ GII VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSDNALKNLDDRGIIFVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGADGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 170/442 (38%), Positives = 229/442 (51%), Gaps = 71/442 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K++   S+  E+ E  ARD       + R+I                I  G     G   
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSDNALKNLDDRGIIFVGAEVRDGDIL 841

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +    +            K+   +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGADGIV------LDVKVFNRE 895

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++PPGV ++V+V++  KR I  GDKM GRHGNKG++SRILP EDMPF+ DGTP+DI+
Sbjct: 896  DGDELPPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISRILPEEDMPFMPDGTPIDIM 955

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+                
Sbjct: 956  LNPLGVPSRMNIGQVLELHLGMAAKNLGLHVASPVFDGANDEDVWST------------- 1002

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                        +  A   + G                             +++LYDG T
Sbjct: 1003 ------------IEEAGMARDG-----------------------------KTVLYDGRT 1021

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEPFD  V+VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1022 GEPFDNRVSVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1081

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQE+LT KSDD VGR + YE+IV G +    G PESF VL+KE+Q+LGL +
Sbjct: 1082 LEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENIPRPGVPESFRVLMKELQSLGLDV 1141

Query: 1362 DLENSRTKNSAKME-EIPDFNK 1382
             + +++ +     + E  DF  
Sbjct: 1142 KVMDNKDEEIEMRDLEDDDFVD 1163


>gi|148544705|ref|YP_001272075.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri DSM
           20016]
 gi|172048240|sp|A5VLL4|RPOB_LACRD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|148531739|gb|ABQ83738.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri DSM
           20016]
          Length = 1202

 Score =  856 bits (2211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/964 (43%), Positives = 588/964 (60%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+           +GL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------EKGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYSEENDK---NGRPNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 159 GATFIPNRGAWLEYETDAKNVSYVRIDRTRKLPMTELIRALGFGSDDEIIDMFGGDSETL 218

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 219 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVG 277

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD + ++ L ++        P L  
Sbjct: 278 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLE-------PYLDR 330

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D      Y              +A++     +           + +  +   D D+    
Sbjct: 331 DDFKTITY----------TPSDEAVVTEPVKL-----------QKILVYSKNDPDR---- 365

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE
Sbjct: 366 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGSTDDIDHLGNRRIRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 421 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 480

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 481 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 540

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L++DGSF ++ V  
Sbjct: 541 ARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQANTPLNDDGSFVDDQVMA 600

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E ID++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 601 RDKDDYIETSVENIDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 660

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 661 APLVSTGIDYKAAHDSGVAMIAKKPGTVEYVDAREVRVREEDGTLD-------TYKLMKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 714 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 774 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDENGIVRVGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R
Sbjct: 834 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 223/1067 (20%), Positives = 369/1067 (34%), Gaps = 172/1067 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A S+    FFD  +YD++ VGR K N 
Sbjct: 224  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVGRYKTNK 283

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 284  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLEPYLDRDDFKTITYTPSDE 343

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 344  AVVTEPVKLQKILVYS-KNDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 402

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 403  STDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 462

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 463  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 522

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 523  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQ 582

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E++                V 
Sbjct: 583  ANTPL---NDDGSFVDDQVMAR-------DKDDYIETSVENIDYMD-------VSPKQVV 625

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G           
Sbjct: 626  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGI---------- 668

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                                     +++ +      M+++   T  +++  EV  R+ + 
Sbjct: 669  -------------------------DYKAAHDSGVAMIAKKPGTVEYVDAREVRVRE-ED 702

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  L A 
Sbjct: 703  GTLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEQGELALGQNPLIAF 761

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 762  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 820

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD N   R+   +   + + G    K  T LS++                         
Sbjct: 821  DLDENGIVRVGAEVHDGDILVGKVTPKGMTELSAEE------------------------ 856

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                      +I  ++ +   +          G+++ VKVF         GD+++     
Sbjct: 857  ------RLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTREN-----GDELSP---- 901

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSL 1155
             G+ + +                          R+ + Q  +  +G       G K    
Sbjct: 902  -GVNTMV--------------------------RVYIAQKRKIQVGDKMSGRHGNKGTVS 934

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            I   + +    P  + ++ ++       +++      +       + G+ ++TPVFDGA 
Sbjct: 935  IVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAARRLGIHMATPVFDGAS 994

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            ++ +   +R +   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG Y
Sbjct: 995  DKDVWDAVRESGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPY 1054

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G
Sbjct: 1055 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIING 1114

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
                + G PESF VLVKE+QALGL + + +   K         D ++
Sbjct: 1115 QPIPKPGVPESFRVLVKELQALGLDMKVLDGNNKEIQLKNMDEDDDE 1161


>gi|304315932|ref|YP_003851077.1| DNA-directed RNA polymerase subunit beta [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777434|gb|ADL67993.1| DNA-directed RNA polymerase, beta subunit [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 1237

 Score =  856 bits (2211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/951 (46%), Positives = 592/951 (62%), Gaps = 64/951 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F +  E++++P+LIEVQK SY  FL           EGL+  F+ + PI +F+G   
Sbjct: 12  RMSFARIEEVLEMPNLIEVQKNSYKWFL----------EEGLREVFRDISPIESFTGNLS 61

Query: 74  LEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           LEF+ Y+ D  PK+ V++C  RD TYA P+K+ +RL           +   +IKE  ++M
Sbjct: 62  LEFLDYKLDDNPKYSVEECKDRDTTYAAPMKVKVRLT---------NRDTGEIKESEVFM 112

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT  GTF+I G +R++VSQL RSPG++++    +    GK L+   +IP++G W+
Sbjct: 113 GDFPLMTDKGTFIINGAERVIVSQLVRSPGVYYEQQFDKL---GKKLFFATVIPNRGAWL 169

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           + E DS DI  VRIDR RKVP+T FL ALG  ++ +IL  F          D        
Sbjct: 170 EYEEDSNDIFSVRIDRTRKVPITVFLRALGYGTDAQILDLFGEDERIKATLDKDTTKSEE 229

Query: 252 ADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD--------C 302
             L+           +  GE   ++S K L   L    K   + ++G             
Sbjct: 230 EGLL------EVYKRLRPGEPPTVDSAKSLLYSLFFDPKRYDLAYVGRYKFNKKLALSSR 283

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L     A +I N  TGEI +E G  I  ++ ++I    I  + +L          I N  
Sbjct: 284 LTNQKAATNIANPITGEIIVEEGQRISRETAKKIQDCGINVVEVLVEGRPIK--VIGNNT 341

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                       +DI     P DVS  ++ E +   L    +     T      N     
Sbjct: 342 ------------VDINEYPLPFDVSDLNIKEKV--QLGVLKEILSNFTNEDEIKNEIKRR 387

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 +HI K+DIIA I   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 388 MDELIPKHITKDDIIASINYNLNLSFGIGFVDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER++  D+  +  Q+LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 448 ERVVRERMTIQDVSEITAQNLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG+E+RDVH THY R+CP ET EG NIGL+ SL ++AR+N YGFIE PY
Sbjct: 508 ALGPGGLSRERAGMEVRDVHHTHYSRMCPIETPEGPNIGLIGSLATYARINEYGFIEAPY 567

Query: 603 RKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV     +V N++VY++A  E+   IAQA+  LDE+  F  E V  R   + + VPRE+
Sbjct: 568 RKVDKATGRVLNEIVYMTADVEDEYVIAQADEPLDEENRFVNERVTVRSKDDILSVPREE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +DF+D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPLL  +AP VGTG+E   A
Sbjct: 628 VDFMDVSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLVPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG   +AK +G+VE+V A +IVIR+ +G  D        Y L+KF+RSNQ TC+N RP
Sbjct: 688 RDSGVVNIAKNSGVVERVTADKIVIRTDDGRRDE-------YELLKFKRSNQGTCINCRP 740

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V +  +I+DGPST+LG++ALGRN+LV FMPW GYN+ED++LISE +V +D  T
Sbjct: 741 IVNEGDRVEKGQVISDGPSTELGEIALGRNVLVGFMPWEGYNYEDAILISEELVKDDALT 800

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 801 SIHIEEYESEARDTKLGPEEITRDIPNVGEEALKDLDERGIIRIGAEVTAGDILVGKVTP 860

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVDV+++ R   D
Sbjct: 861 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEGGIVVDVKVYTRENGD 911



 Score =  461 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 236/1059 (22%), Positives = 372/1059 (35%), Gaps = 133/1059 (12%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D    +  I+ TL  D  K  ++ LL++Y+ +RPG+  T   A+S+   LFFD  +YDL+
Sbjct: 208  DLFGEDERIKATLDKDTTKSEEEGLLEVYKRLRPGEPPTVDSAKSLLYSLFFDPKRYDLA 267

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L L          +         + +   G+  +++   +     + + +
Sbjct: 268  YVGRYKFNKKLALS--------SRLTNQKAATNIANPITGEIIVEEGQRISRETAKKIQD 319

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
               N   + +      +    +    +  +P D ++   +   V        LS      
Sbjct: 320  CGINVVEVLVEGRPIKVIGNNTVDINEYPLPFD-VSDLNIKEKVQLGVLKEILSNFTNED 378

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               + I   RR+  L    + +      +       +G     +     N  L  S+   
Sbjct: 379  EIKNEI--KRRMDELIPKHITKDDIIASINYNLNLSFGIGFVDDIDHLGNRRLR-SVGEL 435

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR--YIA-----QANSSLDEDGSFTE 642
             +      +    R V +     DV  ++A    N    +A       +S L +    T 
Sbjct: 436  LQNQFRIGLSRMERVVRERMTIQDVSEITAQNLINIRPVVAAIKEFFGSSQLSQFMDQTN 495

Query: 643  ELVFCRCAG------------EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
             L                   E   +    +     S    +         L    +   
Sbjct: 496  PLAELTHKRRLSALGPGGLSRERAGMEVRDVHHTHYSRMCPIETPEGPNIGLIGSLATYA 555

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
             +           ++A    V      V+ +        +   ++ Q D           
Sbjct: 556  RI------NEYGFIEAPYRKVDKATGRVLNEIVYMTADVEDEYVIAQADEPLDEENRFVN 609

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            +     S  DI  + + +    +    Q   V         +  A+              
Sbjct: 610  ERVTVRSKDDILSVPREEVDFMDVSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVP 669

Query: 811  MLVAFMPWHGYNFE---------DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            +LV   P  G   E          ++  +  +V       I I         T  G  + 
Sbjct: 670  LLVPQAPIVGTGIEYKAARDSGVVNIAKNSGVVERVTADKIVI--------RTDDGRRDE 721

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +          I+   I+  G  V  G ++    + +    +     +L      + 
Sbjct: 722  YELLKFKRSNQGTCINCRPIVNEGDRVEKGQVISDGPSTEL-GEIALGRNVLVGFMPWEG 780

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQ 975
             +  D  L     V    +       +  +  +  +  E          E   +D  DE+
Sbjct: 781  YNYEDAILISEELVKDDALTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKDL-DER 839

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         +IL G+    G         L   +  E  R                 
Sbjct: 840  GIIRIGAEVTAGDILVGKVTPKGETELTAEERLLRAIFGEKAR----------------- 882

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E                   K+   + GD++PPGV  +V+VF+A KR I  GDKMAGRHG
Sbjct: 883  EVRDTSLRVPHGEGGIVVDVKVYTRENGDELPPGVNEMVRVFIAQKRKISVGDKMAGRHG 942

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NK                            GV SR+                    ++ +
Sbjct: 943  NK----------------------------GVVSRI------------------LPVEDM 956

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                            L+  +       +++      V         G  ++TPVFDGA 
Sbjct: 957  PFLPDGTP--------LQICLNPLGVPSRMNIGQVLEVHLGLAAKALGWYMATPVFDGAH 1008

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            EE I  +L  A     G+  LYDG TGEPFD PVTVGY+YMLKL+H+V DK++ARSTG Y
Sbjct: 1009 EEDIQELLEKAGFSPDGKIQLYDGRTGEPFDHPVTVGYMYMLKLHHLVDDKMHARSTGPY 1068

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDD+ GR + YESIV G
Sbjct: 1069 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDITGRVKTYESIVKG 1128

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             +  E G PESF VLVKE+Q+L L + +     +  A  
Sbjct: 1129 ENIPEPGVPESFKVLVKELQSLCLDVKVLTEDNQEVALK 1167


>gi|154705562|gb|ABS84207.1| DNA-directed RNA polymerase beta subunit [Lactobacillus reuteri]
          Length = 1202

 Score =  856 bits (2211), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/964 (43%), Positives = 587/964 (60%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+           +GL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------EKGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYSEENDK---NGRPNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 159 GATFIPNRGAWLEYETDAKNVSYVRIDRTRKLPMTELIRALGFGSDDEIIDMFGGDSETL 218

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 219 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVG 277

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD + ++ L ++             
Sbjct: 278 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLEPY---------- 327

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
                    R+   T       +A++     +           + +  +   D D+    
Sbjct: 328 -------LHRDDFKTITPTPPDEAVVTEPVKL-----------QKILVYSKTDPDR---- 365

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE
Sbjct: 366 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGSTDDIDHLGNRRIRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 421 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 480

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 481 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 540

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L++DGSF ++ V  
Sbjct: 541 ARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQANTPLNDDGSFVDDQVMA 600

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E ID++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 601 RDKDDYIETSVENIDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 660

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 661 APLVSTGIDYKAAHDSGVAMIAKKPGTVEYVDAREVRVREEDGTLD-------TYKLMKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 714 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 774 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDENGIVRVGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R
Sbjct: 834 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 223/1067 (20%), Positives = 369/1067 (34%), Gaps = 172/1067 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A S+    FFD  +YD++ VGR K N 
Sbjct: 224  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVGRYKTNK 283

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 284  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLEPYLHRDDFKTITPTPPDE 343

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 344  AVVTEPVKLQKILVYS-KTDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 402

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 403  STDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 462

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 463  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 522

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 523  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQ 582

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E++                V 
Sbjct: 583  ANTPL---NDDGSFVDDQVMAR-------DKDDYIETSVENIDYMD-------VSPKQVV 625

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G           
Sbjct: 626  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGI---------- 668

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                                     +++ +      M+++   T  +++  EV  R+ + 
Sbjct: 669  -------------------------DYKAAHDSGVAMIAKKPGTVEYVDAREVRVRE-ED 702

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  L A 
Sbjct: 703  GTLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEQGELALGQNPLIAF 761

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 762  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 820

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD N   R+   +   + + G    K  T LS++                         
Sbjct: 821  DLDENGIVRVGAEVHDGDILVGKVTPKGMTELSAEE------------------------ 856

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                      +I  ++ +   +          G+++ VKVF         GD+++     
Sbjct: 857  ------RLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTREN-----GDELSP---- 901

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSL 1155
             G+ + +                          R+ + Q  +  +G       G K    
Sbjct: 902  -GVNTMV--------------------------RVYIAQKRKIQVGDKMSGRHGNKGTVS 934

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            I   + +    P  + ++ ++       +++      +       + G+ ++TPVFDGA 
Sbjct: 935  IVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAARRLGIHMATPVFDGAS 994

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            ++ +   +R +   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG Y
Sbjct: 995  DKDVWDAVRESGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPY 1054

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G
Sbjct: 1055 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIING 1114

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
                + G PESF VLVKE+QALGL + + +   K         D ++
Sbjct: 1115 QPIPKPGVPESFRVLVKELQALGLDMKVLDGNNKEIQLKNMDEDDDE 1161


>gi|126654238|ref|ZP_01726032.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. B14905]
 gi|126589296|gb|EAZ83453.1| DNA-directed RNA polymerase subunit beta [Bacillus sp. B14905]
          Length = 1191

 Score =  855 bits (2210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/964 (44%), Positives = 603/964 (62%), Gaps = 76/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ F +  E++++P+LIE+Q ASY+ FL           EGL+  F+
Sbjct: 4   LTGQLVQYGQHRQRRSFARIKEVLELPNLIEIQTASYEWFL----------EEGLREMFR 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+DVD+C  RD+TYA PL++ +RL           K
Sbjct: 54  DISPIEDFTGNLSLEFIDYSLGDPKYDVDECKERDVTYAAPLRVKVRLY---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  +
Sbjct: 105 ETDEVKEQDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFH---DKTDKNGKKGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 162 GATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDIIGDNEYLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +ES K L        K   +     
Sbjct: 222 NTLEKDNSESTEKALL------EIYERLRPGEPPTVESAKSLLYSRFFDAKRYDLANVGR 275

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +E G V+D ++L++I          +   
Sbjct: 276 YKMNKKLHIKNRLFNQTIAETLVDPETGEILVEKGTVLDRRTLDKILPYLEDSSKGIGFR 335

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           +++    +             D  +   ++  P D +                       
Sbjct: 336 TLSQVGGVLE----------DDVTIQSIKIYAPKDEAQK--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N    ++V++I   D+++ +    +L    G  DDID+LGNRR+RSVGE+
Sbjct: 365 ----EINIISNAYIDEEVKNITPADVLSSVSYFFNLLYQVGATDDIDHLGNRRLRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +++PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSINDTAAIVPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA
Sbjct: 481 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFA 540

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR++     +VT  + YL+A EE+N Y+AQANS L+ DGSF ++ V  R
Sbjct: 541 KVNKFGFIETPYRRIDHETGQVTEQIDYLTADEEDNYYVAQANSLLNPDGSFAKDEVVGR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+  +  + ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 601 FRGDNTVFNKAQMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKF 767
           PFVGTGME V A+ SGAA+VAK  GIVE V+A  I +R +E        G    Y+L KF
Sbjct: 661 PFVGTGMEHVDARDSGAAVVAKYDGIVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKF 720

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRPLVKVG+ V+  DI+ADGPS + G+LALGRN+LVAFM W+G+N+ED++
Sbjct: 721 IRSNQGTSYNQRPLVKVGERVKPRDILADGPSMEKGELALGRNVLVAFMTWNGFNYEDAV 780

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII +GAE
Sbjct: 781 IMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAE 840

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR
Sbjct: 841 VRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIILDVKVFNR 900

Query: 948 HGID 951
              D
Sbjct: 901 EDGD 904



 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 183/554 (33%), Positives = 260/554 (46%), Gaps = 77/554 (13%)

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V      SIH+   EV+      G     +    +      + ++  ++ VG  V P D
Sbjct: 686  IVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKFIRSNQGTSYNQRPLVKVGERVKPRD 745

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL    +   +  +     +L A       +  D  +     V   V        +  + 
Sbjct: 746  ILADGPS-MEKGELALGRNVLVAFMTWNGFNYEDAVIMSERLVKDDVYTSVHIEEYESES 804

Query: 953  NERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
             +  +  E     I  +  D     DE+ I+      R  +IL G+    G         
Sbjct: 805  RDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEER 864

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L   +  E  R      +++       +                    K+   + GD++P
Sbjct: 865  LLHAIFGEKARE-VRDTSLRVPHGAGGI----------------ILDVKVFNREDGDELP 907

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGV
Sbjct: 908  PGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGV 967

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D     D+                      
Sbjct: 968  PSRMNIGQVLELHLGMASRYLGVHMATPVFDGANEEDVW--------------------- 1006

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  +  A   + G                             ++ILYDG +GEPFD 
Sbjct: 1007 ----ETMEEAGMNRDG-----------------------------KTILYDGRSGEPFDN 1033

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1034 RVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1093

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + +    
Sbjct: 1094 AYTLQEILTVKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLTVN 1153

Query: 1368 TKNSAKMEEIPDFN 1381
             +     +   + +
Sbjct: 1154 DEEVELRDLDEEED 1167


>gi|194466962|ref|ZP_03072949.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus reuteri
           100-23]
 gi|227544410|ref|ZP_03974459.1| DNA-directed RNA polymerase [Lactobacillus reuteri CF48-3A]
 gi|300909336|ref|ZP_07126797.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri
           SD2112]
 gi|194453998|gb|EDX42895.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus reuteri
           100-23]
 gi|227185606|gb|EEI65677.1| DNA-directed RNA polymerase [Lactobacillus reuteri CF48-3A]
 gi|300893201|gb|EFK86560.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri
           SD2112]
          Length = 1202

 Score =  855 bits (2210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/964 (43%), Positives = 588/964 (60%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+           +GL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------EKGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYSEENDK---NGRPNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 159 GATFIPNRGAWLEYETDAKNVSYVRIDRTRKLPMTELIRALGFGSDDEIIDMFGGDSETL 218

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 219 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVG 277

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD + ++ L ++        P L  
Sbjct: 278 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLE-------PYLDR 330

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D      Y              +A++     +           + +  +   D D+    
Sbjct: 331 DDFKTITY----------TPSDEAVVTEPVKL-----------QKILVYSKTDPDR---- 365

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE
Sbjct: 366 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGSTDDIDHLGNRRIRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 421 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 480

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 481 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 540

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L++DGSF ++ V  
Sbjct: 541 ARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQANTPLNDDGSFVDDQVMA 600

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E ID++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 601 RDKDDYIETSVENIDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 660

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 661 APLVSTGIDYKAAHDSGVAMIAKKPGTVEYVDAREVRVREEDGTLD-------TYKLMKF 713

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 714 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAI 773

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 774 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDENGIVRVGAE 833

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R
Sbjct: 834 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTR 893

Query: 948 HGID 951
              D
Sbjct: 894 ENGD 897



 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 223/1067 (20%), Positives = 369/1067 (34%), Gaps = 172/1067 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A S+    FFD  +YD++ VGR K N 
Sbjct: 224  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVGRYKTNK 283

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 284  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLEPYLDRDDFKTITYTPSDE 343

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 344  AVVTEPVKLQKILVYS-KTDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 402

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 403  STDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 462

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 463  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 522

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 523  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQ 582

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E++                V 
Sbjct: 583  ANTPL---NDDGSFVDDQVMAR-------DKDDYIETSVENIDYMD-------VSPKQVV 625

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G           
Sbjct: 626  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGI---------- 668

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                                     +++ +      M+++   T  +++  EV  R+ + 
Sbjct: 669  -------------------------DYKAAHDSGVAMIAKKPGTVEYVDAREVRVRE-ED 702

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  L A 
Sbjct: 703  GTLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEQGELALGQNPLIAF 761

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 762  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 820

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD N   R+   +   + + G    K  T LS++                         
Sbjct: 821  DLDENGIVRVGAEVHDGDILVGKVTPKGMTELSAEE------------------------ 856

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                      +I  ++ +   +          G+++ VKVF         GD+++     
Sbjct: 857  ------RLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTREN-----GDELSP---- 901

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSL 1155
             G+ + +                          R+ + Q  +  +G       G K    
Sbjct: 902  -GVNTMV--------------------------RVYIAQKRKIQVGDKMSGRHGNKGTVS 934

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            I   + +    P  + ++ ++       +++      +       + G+ ++TPVFDGA 
Sbjct: 935  IVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAARRLGIHMATPVFDGAS 994

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            ++ +   +R +   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG Y
Sbjct: 995  DKDVWDAVRESGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPY 1054

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G
Sbjct: 1055 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIING 1114

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
                + G PESF VLVKE+QALGL + + +   K         D ++
Sbjct: 1115 QPIPKPGVPESFRVLVKELQALGLDMKVLDGNNKEIQLKNMDEDDDE 1161


>gi|27467224|ref|NP_763861.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis ATCC 12228]
 gi|57866134|ref|YP_187779.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis RP62A]
 gi|242241874|ref|ZP_04796319.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis W23144]
 gi|251809959|ref|ZP_04824432.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282875007|ref|ZP_06283882.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis SK135]
 gi|293367918|ref|ZP_06614556.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|41018015|sp|Q8CQ84|RPOB_STAES RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|81675386|sp|Q5HRL0|RPOB_STAEQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|27314767|gb|AAO03903.1|AE016745_2 RNA polymerase beta chain [Staphylococcus epidermidis ATCC 12228]
 gi|57636792|gb|AAW53580.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis RP62A]
 gi|242234652|gb|EES36964.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis W23144]
 gi|251806502|gb|EES59159.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281296335|gb|EFA88854.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis SK135]
 gi|291317947|gb|EFE58355.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319399709|gb|EFV87958.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis FRI909]
 gi|329734685|gb|EGG70992.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis VCU028]
 gi|329737853|gb|EGG74085.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis VCU045]
          Length = 1183

 Score =  855 bits (2210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 601/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI ++ G V+D + L+EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVVDEGTVLDRRKLDEIMDVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGSVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DI+A +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V +GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 162/440 (36%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1148 HDNEIE-MADVDDEDAAERK 1166


>gi|259502522|ref|ZP_05745424.1| DNA-directed RNA polymerase subunit beta [Lactobacillus antri DSM
           16041]
 gi|259169474|gb|EEW53969.1| DNA-directed RNA polymerase subunit beta [Lactobacillus antri DSM
           16041]
          Length = 1197

 Score =  855 bits (2210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/964 (43%), Positives = 590/964 (61%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+          ++GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------DKGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 162 GATFIPNRGAWLEYETDAKNISYVRIDRTRKLPMTELVRALGFGSDDEIIDMFGGDSETL 221

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 222 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARNLLTARFFDPKRYDMAPVG 280

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD + ++ L+++        P L  
Sbjct: 281 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKEVLKQLE-------PYLDR 333

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D      Y              +A++     +           + +  +   D D+    
Sbjct: 334 DDFKMVTY----------TPSDEAVVTEPVKL-----------QKILVYSKNDPDR---- 368

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G  DDID+LGNRR+RSVGE
Sbjct: 369 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGNTDDIDHLGNRRIRSVGE 423

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 424 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 483

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 484 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 543

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   D KVT+ + YL+A EE+N  IAQANS L++DGSF ++ V  
Sbjct: 544 ARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQANSPLNDDGSFVDDEVMA 603

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 604 RDKDDYIETSVENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 663

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 664 APLVSTGIDYKAAHDSGVALIAKKPGTVEYVDAREVRVREEDGSLD-------TYKLMKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 717 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEEGELALGQNPLIAFMTWQGYNFEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 777 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDEDGIVRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G V DV+IF R
Sbjct: 837 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIVQDVKIFTR 896

Query: 948 HGID 951
              D
Sbjct: 897 ENGD 900



 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 262/1066 (24%), Positives = 394/1066 (36%), Gaps = 170/1066 (15%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A ++    FFD  +YD++ VGR K N 
Sbjct: 227  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARNLLTARFFDPKRYDMAPVGRYKTNK 286

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 287  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKEVLKQLEPYLDRDDFKMVTYTPSDE 346

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 347  AVVTEPVKLQKILVYS-KNDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 405

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 406  NTDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 465

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 466  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 525

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 526  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQ 585

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E+V                V 
Sbjct: 586  ANSPL---NDDGSFVDDEVMAR-------DKDDYIETSVENVDYMD-------VSPKQVV 628

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G           
Sbjct: 629  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGI---------- 671

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                                     +++ +      ++++   T  +++  EV  R+ + 
Sbjct: 672  -------------------------DYKAAHDSGVALIAKKPGTVEYVDAREVRVRE-ED 705

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   E  +   +  L A 
Sbjct: 706  GSLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEEGELALGQNPLIAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 765  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 823

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+     G     G     K T      +S   R     F  +  +V+    
Sbjct: 824  DLDEDGIVRV-----GAEVHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSL 878

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +          +      KI   + GD++ PGV  +V+V++A KR IQ GDKM+GRHGN
Sbjct: 879  RVPHGGGGIVQDV------KIFTRENGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGN 932

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + +
Sbjct: 933  KGTVSIVIPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAAKRLGIHMATPV 992

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D   + D                                             V+D   E
Sbjct: 993  FDGATDKD---------------------------------------------VWDAVRE 1007

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                     A   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG YS
Sbjct: 1008 ---------AGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPYS 1058

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G 
Sbjct: 1059 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIINGE 1118

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
               + G PESF VLVKE+QALGL + + +   K         D  +
Sbjct: 1119 SIPKPGVPESFRVLVKELQALGLDMKVLDGNHKEVQLKNMDEDDAE 1164


>gi|73663522|ref|YP_302303.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
 gi|82581605|sp|Q49V52|RPOB_STAS1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|72496037|dbj|BAE19358.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 1183

 Score =  855 bits (2210), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 603/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQFVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------EEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TY+ PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDTTYSAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  +
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKLDK---NGRTNF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTETTDQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D ++L+EI          +   
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNTETGEIVAEEGTVLDRRNLDEIMD--------VLEA 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGTVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGN--------AFPDSEVKCITPADIIASMSYFFNLLSGIGFTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DSV PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSVTPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F  + V CR
Sbjct: 535 RVNEFGFIETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFIADEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAIVAKR G VE V++  I++R  +E D       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAIVAKRKGRVEHVESNEILVRQLIEEDGQEYEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V  GD V + +I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNTGTCYNQRPIVASGDVVTKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVS+  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSDSALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           VN GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 163/435 (37%), Positives = 231/435 (53%), Gaps = 63/435 (14%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +     L   +       +  + V   D
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSDSALKNLDDRG--IVYVGAEVNDGD 839

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILEDR----FKNKIEKIQWGDD 1065
            ++      +       +E++   +  E  +   +TS  +           K+   + GDD
Sbjct: 840  ILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDD 899

Query: 1066 -MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             + PGV ++V+V++  KR I  GDKM GRHGNKG++S+++P EDMP+L DGTP+DI+LNP
Sbjct: 900  TLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKLVPEEDMPYLPDGTPIDIMLNP 959

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMN+GQ+ E HLG A   LG  + S + D  ++ D+                   
Sbjct: 960  LGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWST---------------- 1003

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                     +  A   + G                             +++LYDG TGEP
Sbjct: 1004 ---------IEEAGMARDG-----------------------------KTVLYDGRTGEP 1025

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1026 FDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1085

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LT KSDD VGR + YESIV G +  + G PESF VL+KE+Q+LGL + + 
Sbjct: 1086 YGAAYTLQEILTYKSDDTVGRVKTYESIVKGENITKPGVPESFRVLMKELQSLGLDVKIM 1145

Query: 1365 NSRTKNSAKMEEIPD 1379
            +         +   +
Sbjct: 1146 DEHDNEIDMQDNEEE 1160


>gi|323339621|ref|ZP_08079894.1| DNA-directed RNA polymerase subunit beta [Lactobacillus ruminis
           ATCC 25644]
 gi|323092946|gb|EFZ35545.1| DNA-directed RNA polymerase subunit beta [Lactobacillus ruminis
           ATCC 25644]
          Length = 1194

 Score =  855 bits (2209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/963 (44%), Positives = 597/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  RVR+ + +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHLVKYGKHRVRRSYSRIKEVLELPNLIEIQTDSYKWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV+Y+   PK+ VD+    D  Y+ PL +TLRLI          K
Sbjct: 54  EIMPIEDFAGKLSLEFVNYQLLEPKYTVDEAREHDANYSAPLHVTLRLI---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFNSEMDK---NGRETY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  ++ EI+          
Sbjct: 162 GTTVIPNRGAWLEYETDAKNISYVRIDRTRKIPLTELVRALGYGTDSEIIEILGQNDCLM 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTLEKD-VHKNTEDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAAVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE + + ETGEI +E+G+V+ +  +E++     RD   ++  
Sbjct: 281 YKINKKLDLKTRLLGARLAETLADPETGEIIVESGEVVTKPIMEKLAPYLKRDDFKMFTF 340

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             +    ++  +            L I +V    +                         
Sbjct: 341 HPSEEGVVQEPMT-----------LQIIKVYSETNP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N + P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 --EEVINLIGNGNVPLEYKHITPSDILASMNYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLTRMERVVRERMSIQDIATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSTYA 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGF+ETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF + +V  R
Sbjct: 544 HVNKYGFVETPYRRVSWDTHKVTDKIDYLTADEEDNYVVAQANSPLNDDGSFVDPVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+K  A
Sbjct: 604 SKDENIEISVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIKPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTG+E   A  SG A++A+ AG +E VDA  I +R  +G LD        Y+LMKF+
Sbjct: 664 PFVGTGIEYKAAHDSGDALIAEHAGTIEYVDAREIRVRREDGALDS-------YKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P+V VGD V  ++++ADGPS + G+LALG+N L+AFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQTPIVHVGDHVDADEVLADGPSMEQGELALGQNPLIAFMTWDGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIEE E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII VGAEV
Sbjct: 777 INERLVKEDVYTSIHIEEHESEARDTKLGPEEMTREIPNVGEDALKNLDEFGIIRVGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 AGD 899



 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 241/1082 (22%), Positives = 399/1082 (36%), Gaps = 106/1082 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  N     I       + E      + ++   I IL  +    N   ++     ++   
Sbjct: 178  DAKNISYVRIDRTRKIPLTELVRALGYGTDSEIIEILGQNDCLMNTLEKDVHKNTEDSRV 237

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            +++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L T      
Sbjct: 238  EESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAAVGRYKINKKLDLKTRLLGAR 297

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +   + +A  +    +      +               +     +      + +      
Sbjct: 298  L--AETLADPETGEIIVESGEVVTKPIMEKLAPYLKRDDFKMFTFHPSEEGVVQEPMT-- 353

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
                +  +      N + V++ +       +   +       S          LG     
Sbjct: 354  ----LQIIKVYSETNPEEVINLIGNGNVPLEYKHITPSDILASMNYFFNLQEGLGSTDDI 409

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
                   +R V      +     T     +    S+   A V     I    R V     
Sbjct: 410  DHLGNRRIRSVGELLQNQFRIGLTRMERVVRERMSIQDIATVTPQQLI--NIRPVVASIK 467

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
                 +  + +                      L       +        + +       
Sbjct: 468  ----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMC 523

Query: 671  VVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
             +       I  + +  +   +            +  +   V   ++ + A      +VA
Sbjct: 524  PIETPEGPNIGLINSLSTYAHVNKYGFVETPYRRVSWDTHKVTDKIDYLTADEEDNYVVA 583

Query: 730  KRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +           VD + +     E           +    K   +    C+         
Sbjct: 584  QANSPLNDDGSFVDPVVMARSKDENIEISVDKVDYMDVSPKQVVAVATACIP-------- 635

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +  +D        ++   A+      A     G  ++ +    + +++E   T  +++
Sbjct: 636  -FLENDDSNRALMGANMQRQAVPLIKPHAPFVGTGIEYKAAHDSGDALIAEHAGTIEYVD 694

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
              E+  R  + G  +  + +      G KN ++  I+ VG  V+  ++L    +   +  
Sbjct: 695  AREIRVRR-EDGALDSYKLMKFRRSNGGKNYNQTPIVHVGDHVDADEVLADGPS-MEQGE 752

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE--Q 963
            +   +  L A       +  D        V   V        H  +  +  +  E    +
Sbjct: 753  LALGQNPLIAFMTWDGYNFEDAIAINERLVKEDVYTSIHIEEHESEARDTKLGPEEMTRE 812

Query: 964  IELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            I  +  D     DE  I+      +  +IL G+    G         L   +  E  R  
Sbjct: 813  IPNVGEDALKNLDEFGIIRVGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR-- 870

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                     +V+     +          +      KI   + GD++ PGV  +V+V++A 
Sbjct: 871  ---------EVRDTSLRVPHGGGGIVQDV------KIFTREAGDELAPGVNMMVRVYIAQ 915

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ + H
Sbjct: 916  KRKLQVGDKMAGRHGNKGTVSVVIPEEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLDLH 975

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG A   LG  + S + D   + DI                                   
Sbjct: 976  LGMAARKLGIHVTSPVFDGARDEDIWNALK------------------------------ 1005

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+P               S+L        G        TGEPFD  + VG +Y +KL 
Sbjct: 1006 EAGLP-----------SDGKSIL------YDG-------RTGEPFDNRIAVGVMYYMKLA 1041

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSD
Sbjct: 1042 HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSD 1101

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGR + YE+IV G    + G PESF VLVKE+QALGL + + +S+ +     +   + 
Sbjct: 1102 DVVGRVKTYEAIVKGEQIPQPGVPESFRVLVKELQALGLDMKVLDSKKQEIELRDMDEED 1161

Query: 1381 NK 1382
            ++
Sbjct: 1162 DE 1163


>gi|312868906|ref|ZP_07729091.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus oris
           PB013-T2-3]
 gi|311095580|gb|EFQ53839.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus oris
           PB013-T2-3]
          Length = 1197

 Score =  855 bits (2209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/964 (43%), Positives = 592/964 (61%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+          ++GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------DKGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 162 GATFIPNRGAWLEYETDAKNISYVRIDRTRKLPMTELVRALGFGSDDEIIDMFGGDSETL 221

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 222 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARNLLTARFFDPKRYDMAPVG 280

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD +D+++L+++        P L  
Sbjct: 281 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVDKETLKKLE-------PYLDR 333

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D      Y              +A++     +           + +  +   D D+    
Sbjct: 334 DDFKMVTY----------TPSDEAVVTEPVKL-----------QKILVYSKNDPDR---- 368

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G  DDID+LGNRR+RSVGE
Sbjct: 369 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGNTDDIDHLGNRRIRSVGE 423

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 424 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 483

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 484 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 543

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   + KVT+ + YL+A EE+N  IAQANS L++DGSF ++ V  
Sbjct: 544 ARVNKYGFIETPYRRVSWKEHKVTDKIDYLTADEEDNFIIAQANSPLNDDGSFVDDEVMA 603

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 604 RDKDDYIETSVENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 663

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 664 APLVSTGIDYKAAHDSGVALIAKKPGTVEYVDAREVRVREDDGSLD-------TYKLMKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 717 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEEGELALGQNPLIAFMTWQGYNFEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 777 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDEDGIVRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G V DV+IF R
Sbjct: 837 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIVQDVKIFTR 896

Query: 948 HGID 951
              D
Sbjct: 897 ENGD 900



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 264/1066 (24%), Positives = 389/1066 (36%), Gaps = 170/1066 (15%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A ++    FFD  +YD++ VGR K N 
Sbjct: 227  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARNLLTARFFDPKRYDMAPVGRYKTNK 286

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 287  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVDKETLKKLEPYLDRDDFKMVTYTPSDE 346

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 347  AVVTEPVKLQKILVYS-KNDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 405

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 406  NTDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 465

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 466  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 525

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 526  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKEHKVTDKIDYLTADEEDNFIIAQ 585

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E+V                V 
Sbjct: 586  ANSPL---NDDGSFVDDEVMAR-------DKDDYIETSVENVDYMD-------VSPKQVV 628

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G + +       
Sbjct: 629  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGIDYK------- 674

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                     A   + +       G    + +   E  V ED                   
Sbjct: 675  ---------AAHDSGVALIAKKPGT--VEYVDAREVRVRED------------------D 705

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   E  +   +  L A 
Sbjct: 706  GSLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEEGELALGQNPLIAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 765  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 823

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+     G     G     K T      +S   R     F  +  +V+    
Sbjct: 824  DLDEDGIVRV-----GAEVHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSL 878

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +          +      KI   + GD++ PGV  +V+V++A KR IQ GDKM+GRHGN
Sbjct: 879  RVPHGGGGIVQDV------KIFTRENGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGN 932

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + +
Sbjct: 933  KGTVSIVIPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAAKRLGIHMATPV 992

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D   + D                                             V+D   E
Sbjct: 993  FDGATDKD---------------------------------------------VWDAVRE 1007

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                     A   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG YS
Sbjct: 1008 ---------AGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPYS 1058

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G 
Sbjct: 1059 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIINGE 1118

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
               + G PESF VLVKE+QALGL + + +   K         D  +
Sbjct: 1119 SIPKPGVPESFRVLVKELQALGLDMKVLDGNQKEVQLKNMDEDDAE 1164


>gi|242372760|ref|ZP_04818334.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis M23864:W1]
 gi|242349533|gb|EES41134.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           epidermidis M23864:W1]
          Length = 1183

 Score =  855 bits (2209), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGDPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGESEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D + ++EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVAEEGTVLDRRKIDEIMDVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGSVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  +++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEVLVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVSVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  483 bits (1243), Expect = e-134,   Method: Composition-based stats.
 Identities = 162/440 (36%), Positives = 224/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
            +      M ++ D +  E K
Sbjct: 1148 QDNEIE-MADVDDEDATERK 1166


>gi|223042737|ref|ZP_03612785.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus capitis
           SK14]
 gi|314932766|ref|ZP_07840135.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus caprae
           C87]
 gi|222443591|gb|EEE49688.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus capitis
           SK14]
 gi|313654447|gb|EFS18200.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus caprae
           C87]
          Length = 1183

 Score =  855 bits (2208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/964 (46%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIIDLLGESEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D + ++EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVAEEGTVLDRRKIDEIMEVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGSVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESSEILVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNTGTCYNQRPIVSVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 248/1163 (21%), Positives = 428/1163 (36%), Gaps = 115/1163 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         +D +  + Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIIDLLGESEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+ +           + +      +  E+ + +  +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNSETGEIVAEEGTVLDRRKIDEIMEVLETNANSEVFELEGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLIN--AKPVVSAVCEFFCSSQLSQLEEHVN---SL 532
                +E    +     D +      + N      V  +      + +S     +N     
Sbjct: 338  IDEPVEIQSIKVYVPNDEEGRTTTVIGNALPDSEVKCITPADIIASMSYFFNLLNGIGYT 397

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
              I H         G + + +  + +  +      R+   +T       L++     A +
Sbjct: 398  DDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASI 457

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +       + +       ++ +                           L       E
Sbjct: 458  KEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSALGPGGLTRE 496

Query: 653  EILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
               +    + +        +       I  + +  S   +            +  +   +
Sbjct: 497  RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSI 556

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               ++ + A    + +VA+    +             +  +        +    K    +
Sbjct: 557  TDQIDYLTADEEDSYVVAQANSRL-----DENGRFLDDEVVCRFRGNNTVMAKEKMDYMD 611

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +              +  +D        ++   A+      A     G     +     
Sbjct: 612  VSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEAPFVGTGMEHVAARDSGA 671

Query: 832  RMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICV 884
             + ++      H+E  E++ R           G  +                ++  I+ V
Sbjct: 672  AITAKHRGRVEHVESSEILVRRLVEENGTEHEGELDRYPLAKFKRSNTGTCYNQRPIVSV 731

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V   +IL    +      M     ++         +  D  +     +S  +V   +
Sbjct: 732  GDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDV 785

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            +    I++ E      +   E + RD  +      +N+  R   +  G     G     K
Sbjct: 786  YTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYVGAEVKDGDILVGK 844

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             T      ++   R     F  +  +V+     +                 K+   + GD
Sbjct: 845  VTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGD 898

Query: 1065 D-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LN
Sbjct: 899  DTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLN 958

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+                  
Sbjct: 959  PLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST--------------- 1003

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                      +  A   + G                             +++LYDG TGE
Sbjct: 1004 ----------IEEAGMARDG-----------------------------KTVLYDGRTGE 1024

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            PFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 1025 PFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1084

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + +
Sbjct: 1085 AYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1144

Query: 1364 ENSRTKNSAKMEEIPDFNKCELK 1386
             + +      M ++ D +  E K
Sbjct: 1145 MDEQNNEIE-MADVDDEDATERK 1166


>gi|254932480|ref|ZP_05265839.1| RNA polymerase [Listeria monocytogenes HPB2262]
 gi|293584036|gb|EFF96068.1| RNA polymerase [Listeria monocytogenes HPB2262]
          Length = 1184

 Score =  855 bits (2208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/963 (46%), Positives = 602/963 (62%), Gaps = 80/963 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   + K  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNVKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK-------- 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +       + L    +AE +V+ ETGEI    GD++D ++L++I            + +
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQI------------IPN 324

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + N    R    TD   +    L+   ++  P D                          
Sbjct: 325 LENGVGFRTLRPTDGVME-DSVLVQSIKIYAPND-------------------------- 357

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
              ++N+  N    ++V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L
Sbjct: 358 EEKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELL 417

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 418 QNQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 477

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+
Sbjct: 478 LGELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAK 537

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R 
Sbjct: 538 VNKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARF 597

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V +E+ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 598 RSENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAP 657

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQ 768
           FVGTGME V AK SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF 
Sbjct: 658 FVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFV 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED+++
Sbjct: 718 RSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAII 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV
Sbjct: 778 MSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R 
Sbjct: 838 KDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 271  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 322

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 323  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDEEKEINIIGNAYIEENVKHITPS 380

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 381  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 440

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 441  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 494

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 495  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 554

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 555  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 609

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 610  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 669

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 670  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 729

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 730  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 784

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 785  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 844

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 845  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 891

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 892  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 952  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 1011

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1012 RDAK----------------------------TILYDG---------------------- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1138 SLGMDVKMLSADEEEIEMRDMDDD 1161


>gi|304385423|ref|ZP_07367768.1| DNA-directed RNA polymerase subunit beta [Pediococcus acidilactici
           DSM 20284]
 gi|304328630|gb|EFL95851.1| DNA-directed RNA polymerase subunit beta [Pediococcus acidilactici
           DSM 20284]
          Length = 1202

 Score =  855 bits (2208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 592/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFN 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ VD+    +  Y+ PL +TLRL            
Sbjct: 54  DIMPIEDFAGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++++ D  +   + + ++
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNLDVDK---NNRNIW 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+E I+  F       
Sbjct: 162 GATVIPNRGAWLEYETDAKEVSYVRIDRTRKIPMTELVRALGFGSDEEIIDIFGGSDSLD 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      +  D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 FTLDKD-VHKNPEDSRVAESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE + + +TGE+  + GDV+D+  ++++        P L   
Sbjct: 281 YKVNKKLSLKTRLLGQTLAETLADPDTGEVLAQKGDVVDKDVMKKLA-------PYLDRQ 333

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +    D+    +   + + ++  P D                   + +L  
Sbjct: 334 DFKMVTYQPS----DEAVVPEPMTIQVIKIQDPNDP------------------ERELKM 371

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G   ++++L        +HI   DIIA I     L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 372 IGNGNIDLKL--------KHITPADIIASINYFFLLQQGIGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+A  EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLARMERVVRERMSIQDAETVTPQQLINIRPVVAATKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L S+ 
Sbjct: 484 PLGELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLASYG 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++N YGFIETPYR+V   D KVT+ + YL+A EE+   IAQANS L++DGSF +++V  R
Sbjct: 544 KINRYGFIETPYRRVSWKDHKVTDRIDYLTADEEDQFVIAQANSPLNDDGSFVDDVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I    E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 HESDNIETSIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G+VE VDA  I +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGVALLCQHPGVVEYVDAREIRVRRDDGALD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+V D+V  +D++ADGPS +LG+LALG+N L+AFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQRPIVRVNDKVDADDVLADGPSMELGELALGQNPLIAFMTWQGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ L+N+D+ GI+ +GAEV
Sbjct: 777 INERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALRNLDQDGIVRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 837 QDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  460 bits (1183), Expect = e-127,   Method: Composition-based stats.
 Identities = 168/525 (32%), Positives = 242/525 (46%), Gaps = 73/525 (13%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  + +      G KN ++  I+ V  +V+  D+L    +      +   +  
Sbjct: 701  RRDDGALDTYKLMKFRRSNGGKNYNQRPIVRVNDKVDADDVLADGPS-MELGELALGQNP 759

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLAR 969
            L A    +  +  D            V D    + H  +    +   +    E    +  
Sbjct: 760  LIAFMTWQGYNFEDAIAIN----ERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPN 815

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +D    LD++   R+     G     G     K T      +S   R     F  +  
Sbjct: 816  VGEDALRNLDQDGIVRI-----GAEVQDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR 870

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V+     +          +      KI   + GD++ PGV  +V+V++A KR +Q GDK
Sbjct: 871  EVRDTSLRVPHGGGGIVQDV------KIFTRENGDELSPGVNMMVRVYIAQKRKLQVGDK 924

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG
Sbjct: 925  MAGRHGNKGTVSVVIPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARNLG 984

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + + + D   + DI    +                                       
Sbjct: 985  IHMTTPVFDGARDEDIWEAVAEAGM----------------------------------- 1009

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                  +    S+L        G++       GEPF++ V VG ++ +KL HMV DK++A
Sbjct: 1010 ------DSDAKSVL------YDGRT-------GEPFEQRVAVGVMHYMKLAHMVDDKIHA 1050

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD+VGR + Y
Sbjct: 1051 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDIVGRVKTY 1110

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            E+IV G      G PESF VLVKE+QALGL + +     +     
Sbjct: 1111 EAIVKGESIPRPGVPESFRVLVKELQALGLDMKVLGEDKQEVELR 1155


>gi|310644212|ref|YP_003948971.1| DNA-directed RNA polymerase subunit beta [Paenibacillus polymyxa
           SC2]
 gi|309249163|gb|ADO58730.1| DNA-directed RNA polymerase subunit beta [Paenibacillus polymyxa
           SC2]
          Length = 1181

 Score =  855 bits (2208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/967 (45%), Positives = 596/967 (61%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q+ SYD FL           EGL+  F+
Sbjct: 1   MAGHLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYDWFL----------EEGLREMFR 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 50  DISPIQDFTGNLILEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   + K  Y
Sbjct: 101 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNAKTTY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 158 TATVIPNRGAWLELEMDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIR 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +++ K L        K         
Sbjct: 218 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLDNAKSLLVARFFDPKRYDLANVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++  TGEI  EAG ++D + L+EI       +      
Sbjct: 272 YKINKKLHIKNRLFNQRLAETLIDTTTGEIIAEAGQMVDRRLLDEILAQLEESVG----- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   R   V     +  D  L    V  P +                         
Sbjct: 327 -------HRTYHVASGVLESNDIPLQTIDVFSPIE----------------------DGK 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N     +    V++I   DII+ I   ++L +G G+ DDID+LGNRR+RSVGE+
Sbjct: 358 VVKLIAN----GNIDKSVKNITPADIISSISYFINLLHGIGSTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP ET EG NIGL++SL++FA
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLINSLSTFA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    GKVT+ + YL+A EE+N  +AQAN+ L E+ +F +E+V  R
Sbjct: 534 RINEYGFIEAPYRWVDPKTGKVTDQIDYLTADEEDNYIVAQANAELTEENTFKDEIVIVR 593

Query: 649 CAGEEILVPR---EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              +   +      ++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 594 YNKQSDNIIPMASSRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 653

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRL 764
            +AP VGTGME   AK SG  +V+K  G++E+  A  I +R +E          +  Y+L
Sbjct: 654 PKAPLVGTGMEHKSAKDSGVCVVSKYNGVIERSSANEIWLRRIETVDGTEVKGDIVKYKL 713

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+V  GD V+  DI+ADGPST++G+LALGRN++VAFM W GYN+E
Sbjct: 714 HKFMRSNQGTCINQRPIVNRGDIVKVGDILADGPSTEMGELALGRNVVVAFMTWEGYNYE 773

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE L+N+DE GII +
Sbjct: 774 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDERGIIRI 833

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++
Sbjct: 834 GAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKV 893

Query: 945 FNRHGID 951
           F R   D
Sbjct: 894 FTRENGD 900



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 185/527 (35%), Positives = 264/527 (50%), Gaps = 67/527 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  I+  G  V  GDIL    + +    +     ++ A 
Sbjct: 706  GDIVKYKLHKFMRSNQGTCINQRPIVNRGDIVKVGDILADGPSTE-MGELALGRNVVVAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 765  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 819

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               RN+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 820  EALRNLDER-GIIRIGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 878

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 879  RVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 932

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + +
Sbjct: 933  KGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHLGMAAMRLGIHVATPV 992

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     D                                             VFD    
Sbjct: 993  FDGAKEYD---------------------------------------------VFD---- 1003

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G+++LYDG TG+ F+R VTVG ++M+KL HMV DK++ARSTG YS
Sbjct: 1004 -----TMEEAGMQRNGKTVLYDGRTGDRFEREVTVGVMHMIKLAHMVDDKIHARSTGPYS 1058

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1059 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1118

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +  E G PESF VL+KE+Q+LG+ + + +   +     E   + +  
Sbjct: 1119 NVPEPGVPESFKVLIKELQSLGMDVKILSEDEQEIEMRELDDEDDTT 1165


>gi|317123104|ref|YP_004103107.1| DNA-directed RNA polymerase subunit beta [Thermaerobacter
           marianensis DSM 12885]
 gi|315593084|gb|ADU52380.1| DNA-directed RNA polymerase subunit beta [Thermaerobacter
           marianensis DSM 12885]
          Length = 1244

 Score =  855 bits (2208), Expect = 0.0,   Method: Composition-based stats.
 Identities = 448/950 (47%), Positives = 586/950 (61%), Gaps = 92/950 (9%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            VV +G  R R  FG+  E++D+P+LIEVQ  SY  FL          NEGL+  F+ + 
Sbjct: 10  HVVKSG-KRERLSFGRIHEVLDLPNLIEVQLNSYRWFL----------NEGLKETFQDIS 58

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  F+G  +LEFV Y    PK+ V +C  RD+TYA P+++ +RLI          K   
Sbjct: 59  PIQDFTGNLVLEFVDYSLGEPKYSVQECKDRDVTYAAPMRVRVRLI---------NKETG 109

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           ++KEQ ++MGD PLMT+ GTFVI G +R+VVSQL RSPG+++  D      +G  LY+  
Sbjct: 110 EVKEQEVFMGDFPLMTEHGTFVINGAERVVVSQLVRSPGVYYSVDYD---ANGNPLYSAT 166

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +IP++G W++ E D+  +++VR+DR RK P T  L ALG  ++ E+L             
Sbjct: 167 VIPNRGAWLEFESDATGVVYVRVDRTRKQPATVLLRALGYQTDAELLELLGDNEHVRATL 226

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD 301
           D       A  L+   K       +  GE    ES ++L   L    K   +  +G    
Sbjct: 227 DKDNTDSQAEALIEIYK------RLRPGEPPTDESARQLLDNLFFDPKRYDLAAVGRYK- 279

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
                 + + +           A DV+D ++ E I  +  R    L              
Sbjct: 280 ------LNKKLNLRARLIGLYAAEDVVDPETGERIVEAGQRFDRQLAQRVQAAGV----- 328

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
               + +  +D  +    V+  G                                     
Sbjct: 329 -RRVRVRTPEDREV---VVLGNGQP----------------------------------- 349

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                 VR + +ED+ AI+     L  G GT DDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 350 ---DTSVRTLTREDVAAIVNYAFGLFAGVGTTDDIDHLGNRRLRSVGELLQNQFRIGLAR 406

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER IKER+S  D D++ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RRL
Sbjct: 407 MERVIKERMSIQDADAITPQALINIRPVVAAVKEFFGSSQLSQFMDQTNPLSELTHKRRL 466

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG ++RDVH +HYGR+CP ET EG NIGL+ ++ ++ARVN YGFIETP
Sbjct: 467 SALGPGGLSRERAGFDVRDVHHSHYGRMCPIETPEGPNIGLIGAMATYARVNEYGFIETP 526

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V +G+VT+DVVYL+A EE+   IAQAN+ LDE+G F  + V  R   +  L   E+I
Sbjct: 527 YRRVENGRVTDDVVYLTADEEDECVIAQANAELDENGYFKNKRVAVRFRDQVRLAAPEEI 586

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D SPKQV SIA +LIPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTG+E   A 
Sbjct: 587 DYMDVSPKQVFSIATALIPFLEHDDANRALMGANMQRQAVPLIRTEAPLVGTGVEYRTAV 646

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  + A+RAG V +V A  IVI + +G  D        Y LMKF+RSNQ TC NQRPL
Sbjct: 647 DSGVVLTARRAGTVRRVTAREIVIETDDGQRD-------TYTLMKFERSNQGTCFNQRPL 699

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+ G  V + ++IADGPSTD G+LALGRN+LVAFMPW GYN+ED++LISER+V EDVFTS
Sbjct: 700 VRKGQRVEKGEVIADGPSTDHGELALGRNVLVAFMPWEGYNYEDAILISERLVKEDVFTS 759

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNV E+ L+++DE GII +GAEV  GDILVGK+TPK
Sbjct: 760 IHIEEYECEARDTKLGPEEITRDIPNVGEDQLRDLDERGIIRIGAEVRAGDILVGKVTPK 819

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 820 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVFSRENGD 869



 Score =  539 bits (1388), Expect = e-150,   Method: Composition-based stats.
 Identities = 199/532 (37%), Positives = 274/532 (51%), Gaps = 79/532 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +T  G  +    +           ++  ++  G  V  G+++    +      +     +
Sbjct: 671  ETDDGQRDTYTLMKFERSNQGTCFNQRPLVRKGQRVEKGEVIADGPST-DHGELALGRNV 729

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK- 971
            L A    +  +  D  L     +S  +V   +F    I++ E      +   E + RD  
Sbjct: 730  LVAFMPWEGYNYEDAIL-----ISERLVKEDVFTSIHIEEYECEARDTKLGPEEITRDIP 784

Query: 972  ---DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAV 1026
               +D+   LD     R+   +   + + G    K  T L+++  L+      +  +   
Sbjct: 785  NVGEDQLRDLDERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRD 844

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
               +V      + V               K+   + GD++ PGV ++V+V+VA KR I  
Sbjct: 845  TSLRVPHGESGIVV-------------DVKVFSRENGDELAPGVNQLVQVYVAQKRKISE 891

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+++RI+P EDMPFL DGTPVDIVLNPLGVPSRMN+GQI E        
Sbjct: 892  GDKMAGRHGNKGVIARIMPEEDMPFLPDGTPVDIVLNPLGVPSRMNIGQILE-------C 944

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG   K+L                                               G+ V
Sbjct: 945  HLGWAAKAL-----------------------------------------------GLWV 957

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDG DEE+I  +LR A L ESG+++LYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 958  ATPVFDGTDEESIRELLRQAGLPESGKTVLYDGRTGEPFDNEVTVGYVYMLKLAHLVDDK 1017

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1018 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRV 1077

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            + YE+IV G +  E G PESF VL+KEMQ+LGL + +     +     +E  
Sbjct: 1078 KTYEAIVKGENVPEPGVPESFKVLIKEMQSLGLDVKILTEDNREIELRDEED 1129


>gi|224475691|ref|YP_002633297.1| DNA-directed RNA polymerase subunit beta [Staphylococcus carnosus
           subsp. carnosus TM300]
 gi|254765304|sp|B9DKV0|RPOB_STACT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|222420298|emb|CAL27112.1| RNA polymerase beta chain [Staphylococcus carnosus subsp. carnosus
           TM300]
          Length = 1183

 Score =  854 bits (2207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 594/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGKFVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKDQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E D+KDI++VRIDR RK+P+T  L ALG  +++ I+          
Sbjct: 159 DATVIPNRGAWLEFETDAKDIVYVRIDRTRKLPLTVLLRALGYSTDQSIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDSTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN +TGEI  E G V+D + L+EI      +  I    
Sbjct: 273 YKMNKKLHLKHRLFNQKLAEPIVNSDTGEIVAEEGTVLDRRKLDEIMDVLESNANI---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                         D +   +   +   +V  P D                         
Sbjct: 329 ---------EVDELDDSIVNEPVEIQSIKVYVPND------------------------E 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DI+A +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIVASMSYFFNLLHGIGQTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V CR
Sbjct: 535 RVNEFGFIETPYRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFISEEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ R+K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+
Sbjct: 595 FRGNNTMMDRDKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKF 767
           PFVGTGME   A+ SGAA++ K  G VE V++  I +R + E D       +D YRL KF
Sbjct: 655 PFVGTGMEHATARDSGAAVINKHFGRVEHVESNEIKVRRIIEEDGQQYDGELDTYRLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+VK GD V + +I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVKDGDIVSQGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV+E  LKN+DE GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVAESALKNLDERGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 253/1155 (21%), Positives = 426/1155 (36%), Gaps = 112/1155 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LINKETGEVKDQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  +I     D   +  L  +  +         +D + +N Y+
Sbjct: 158  YDATVIPNRGAWLEFETDAKDIVYVRIDRTRKLPLTVLLRALGYSTDQSIIDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          R  +  
Sbjct: 218  RNTLEKDSTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPK--------RYDLAS 269

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                     +    +     + + +V+   G+   ++   L  R++  + ++L++   + 
Sbjct: 270  VGRYKMNKKLHLKHRLFNQKLAEPIVNSDTGEIVAEEGTVLDRRKLDEIMDVLESNANIE 329

Query: 479  LLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +  ++ SI    +    I   +P D        + +   F  S++  +       S    
Sbjct: 330  VDELDDSIVNEPVEIQSIKVYVPNDEEGRT--TTVIGNAFPDSEVKCITPADIVASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               L  +GQ           +R V      +     +     +    S+     +     
Sbjct: 388  FNLLHGIGQTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +          L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  E   V   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLETNTVTDQID 561

Query: 717  SVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR--SNQ 772
             + A  + S     A      E       V+    G+          Y  +  ++  S  
Sbjct: 562  YLTADEEDSYVVAQANSRLDDEGHFISEEVVCRFRGNNTMMDRDKMDYMDVSPKQVVSAA 621

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
              C+           +  +D        ++   A+      +     G     +      
Sbjct: 622  TACIP---------FLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEHATARDSGAA 672

Query: 833  MVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECGIICVG 885
            ++++      H+E  E+  R           G  +  R             ++  I+  G
Sbjct: 673  VINKHFGRVEHVESNEIKVRRIIEEDGQQYDGELDTYRLAKFKRSNSGTCYNQRPIVKDG 732

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
              V+ G+IL    +      M     ++         +  D  +     +S  +V   ++
Sbjct: 733  DIVSQGEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVY 786

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
                I++ E      +   E + RD  +      +N+  R   +  G     G     K 
Sbjct: 787  TSIHIEEYESEARDTKLGPEEITRDIPNVAESALKNLDER-GIVYVGAEVKDGDILVGKV 845

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T      ++   R     F  +  +V+     +                 K+   + GDD
Sbjct: 846  TPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREDGDD 899

Query: 1066 -MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DGTP+DI+LNP
Sbjct: 900  SLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNP 959

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+                   
Sbjct: 960  LGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST---------------- 1003

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                     +  A   + G                             +++LYDG TGEP
Sbjct: 1004 ---------IEEAGMARDG-----------------------------KTVLYDGRTGEP 1025

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1026 FDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1085

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LT KSDD VGR + YE+IV G +  +   PESF VL+KE+Q+LGL + + 
Sbjct: 1086 YGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISKPSVPESFRVLMKELQSLGLDVKVM 1145

Query: 1365 NSRTKNSAKMEEIPD 1379
            +   K     +   D
Sbjct: 1146 DEDDKEIEMADVDED 1160


>gi|257897292|ref|ZP_05676945.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           Com12]
 gi|293378969|ref|ZP_06625124.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           PC4.1]
 gi|257833857|gb|EEV60278.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           Com12]
 gi|292642510|gb|EFF60665.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           PC4.1]
          Length = 1205

 Score =  854 bits (2207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPKDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|298693873|gb|ADI97095.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus ED133]
 gi|323439812|gb|EGA97529.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           O11]
 gi|323443086|gb|EGB00706.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           O46]
          Length = 1183

 Score =  854 bits (2207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------E 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 242/1158 (20%), Positives = 417/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD--------KYDLST 410
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          +Y  + 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +K  +         V     E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDEEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|269202165|ref|YP_003281434.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ED98]
 gi|296275788|ref|ZP_06858295.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MR1]
 gi|262074455|gb|ACY10428.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ED98]
          Length = 1183

 Score =  854 bits (2207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 242/1158 (20%), Positives = 417/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD--------KYDLST 410
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          +Y  + 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +K  +         V     E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|49482772|ref|YP_039996.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MRSA252]
 gi|257424656|ref|ZP_05601083.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257427324|ref|ZP_05603723.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257429960|ref|ZP_05606344.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257432662|ref|ZP_05609022.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257435566|ref|ZP_05611614.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|282903130|ref|ZP_06311021.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|282904920|ref|ZP_06312778.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282907870|ref|ZP_06315705.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282913375|ref|ZP_06321164.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282918330|ref|ZP_06326067.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282923292|ref|ZP_06330972.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|283957340|ref|ZP_06374793.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|293500421|ref|ZP_06666272.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|293509366|ref|ZP_06668077.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|293523953|ref|ZP_06670640.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|295427080|ref|ZP_06819716.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297590567|ref|ZP_06949206.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MN8]
 gi|56749585|sp|Q6GJC6|RPOB_STAAR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|49240901|emb|CAG39568.1| DNA-directed RNA polymerase beta chain protein [Staphylococcus
           aureus subsp. aureus MRSA252]
 gi|257272226|gb|EEV04349.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257275517|gb|EEV06990.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257279157|gb|EEV09758.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257282077|gb|EEV12212.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257284757|gb|EEV14876.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|282314160|gb|EFB44550.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|282317464|gb|EFB47836.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282322407|gb|EFB52729.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282328254|gb|EFB58532.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282331745|gb|EFB61256.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282596085|gb|EFC01046.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|283790791|gb|EFC29606.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|290920916|gb|EFD97977.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|291095426|gb|EFE25687.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|291467463|gb|EFF09978.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|295128868|gb|EFG58498.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297576866|gb|EFH95581.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MN8]
 gi|315193906|gb|EFU24300.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus CGS00]
          Length = 1183

 Score =  854 bits (2207), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 242/1158 (20%), Positives = 417/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD--------KYDLST 410
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          +Y  + 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +K  +         V     E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEFNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|15926220|ref|NP_373753.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus N315]
 gi|21282226|ref|NP_645314.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MW2]
 gi|49485407|ref|YP_042628.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus MSSA476]
 gi|82750250|ref|YP_415991.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           RF122]
 gi|150393049|ref|YP_001315724.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus JH1]
 gi|151220716|ref|YP_001331538.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156978871|ref|YP_001441130.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus Mu3]
 gi|161353532|ref|YP_499096.2| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus NCTC 8325]
 gi|161508782|ref|YP_001574441.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|162138570|ref|YP_493230.2| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|221141021|ref|ZP_03565514.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus str. JKD6009]
 gi|253315652|ref|ZP_04838865.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|253731147|ref|ZP_04865312.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253732550|ref|ZP_04866715.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|257795359|ref|ZP_05644338.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9781]
 gi|258408954|ref|ZP_05681235.1| RNA polymerase subunit beta [Staphylococcus aureus A9763]
 gi|258420408|ref|ZP_05683351.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9719]
 gi|258439329|ref|ZP_05690261.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus A9299]
 gi|258444069|ref|ZP_05692406.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           A8115]
 gi|258452725|ref|ZP_05700723.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A5948]
 gi|258453786|ref|ZP_05701760.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           A5937]
 gi|262049585|ref|ZP_06022454.1| DNA-directed RNA polymerase beta subunit [Staphylococcus aureus
           D30]
 gi|282894977|ref|ZP_06303200.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A8117]
 gi|282915865|ref|ZP_06323630.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282928879|ref|ZP_06336470.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A10102]
 gi|283769698|ref|ZP_06342590.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus H19]
 gi|284023552|ref|ZP_06377950.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus 132]
 gi|295406919|ref|ZP_06816722.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|297208744|ref|ZP_06925172.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297246257|ref|ZP_06930106.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|300912834|ref|ZP_07130276.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|304381859|ref|ZP_07364506.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|41017889|sp|P60278|RPOB_STAAN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|41017890|sp|P60279|RPOB_STAAW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|56749538|sp|Q6GBU5|RPOB_STAAS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|109914398|sp|Q2FJ98|RPOB_STAA3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|109914399|sp|Q2YSB9|RPOB_STAAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|110282991|sp|P47768|RPOB_STAA8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|166229308|sp|A7WYW7|RPOB_STAA1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|172048778|sp|A6QEJ4|RPOB_STAAE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|189043870|sp|A6TZ19|RPOB_STAA2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|189043872|sp|A8YZP0|RPOB_STAAT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|13700433|dbj|BAB41731.1| RNA polymerase beta chain [Staphylococcus aureus subsp. aureus
           N315]
 gi|21203662|dbj|BAB94362.1| RNA polymerase beta chain [Staphylococcus aureus subsp. aureus MW2]
 gi|49243850|emb|CAG42275.1| DNA-directed RNA polymerase beta chain protein [Staphylococcus
           aureus subsp. aureus MSSA476]
 gi|82655781|emb|CAI80181.1| DNA-dependent RNA polymerase beta subunit [Staphylococcus aureus
           RF122]
 gi|149945501|gb|ABR51437.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus JH1]
 gi|150373516|dbj|BAF66776.1| DNA-directed RNA polymerase beta chain [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156721006|dbj|BAF77423.1| RNA polymerase beta chain [Staphylococcus aureus subsp. aureus Mu3]
 gi|160367591|gb|ABX28562.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|253725112|gb|EES93841.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253729479|gb|EES98208.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|257789331|gb|EEV27671.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9781]
 gi|257840305|gb|EEV64768.1| RNA polymerase subunit beta [Staphylococcus aureus A9763]
 gi|257843598|gb|EEV68004.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9719]
 gi|257847666|gb|EEV71665.1| DNA-directed RNA polymerase subunit beta protein [Staphylococcus
           aureus A9299]
 gi|257850739|gb|EEV74684.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           A8115]
 gi|257859598|gb|EEV82448.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A5948]
 gi|257864042|gb|EEV86796.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           A5937]
 gi|259162325|gb|EEW46898.1| DNA-directed RNA polymerase beta subunit [Staphylococcus aureus
           D30]
 gi|269940115|emb|CBI48491.1| DNA-directed RNA polymerase beta chain protein [Staphylococcus
           aureus subsp. aureus TW20]
 gi|282320161|gb|EFB50506.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282589487|gb|EFB94576.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A10102]
 gi|282762659|gb|EFC02796.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A8117]
 gi|283459845|gb|EFC06935.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus H19]
 gi|283469834|emb|CAQ49045.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus ST398]
 gi|285816243|gb|ADC36730.1| DNA-directed RNA polymerase beta subunit [Staphylococcus aureus
           04-02981]
 gi|294968150|gb|EFG44176.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|296886689|gb|EFH25594.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297176855|gb|EFH36113.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|300885938|gb|EFK81141.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|302332255|gb|ADL22448.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus JKD6159]
 gi|302750433|gb|ADL64610.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus str. JKD6008]
 gi|304339645|gb|EFM05592.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|312829038|emb|CBX33880.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315128835|gb|EFT84834.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus CGS03]
 gi|315196646|gb|EFU26993.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus CGS01]
 gi|320141593|gb|EFW33432.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus MRSA131]
 gi|320141778|gb|EFW33606.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus MRSA177]
 gi|329731052|gb|EGG67425.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 21189]
 gi|329731972|gb|EGG68328.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 21193]
          Length = 1183

 Score =  854 bits (2206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 242/1158 (20%), Positives = 417/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD--------KYDLST 410
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          +Y  + 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +K  +         V     E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|319891506|ref|YP_004148381.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317161202|gb|ADV04745.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323465322|gb|ADX77475.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           pseudintermedius ED99]
          Length = 1184

 Score =  854 bits (2206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQFVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP ++F+    +   +G++ Y
Sbjct: 102 ETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDK---NGRVNY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELIGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDSTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D + L+EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNTETGEIVAEEGTVLDRRKLDEIMDVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                                +A   +Y +  P  +    V          + D+   +T
Sbjct: 325 ---------------------NANAQVYEL--PNSIIDEPVEIQSIKVYVPNDDEERTTT 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V         N     +V+ I   DI+A +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 362 V-------IGNAFPDSEVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR
Sbjct: 535 RVNEFGFIETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G    + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+
Sbjct: 595 FRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPES 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAA+++K  G VE V +  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAVISKYRGRVEHVQSSEILVRRLVEENGQEVDGTLDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP++  GD V + +I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIIAKGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 157/428 (36%), Positives = 217/428 (50%), Gaps = 59/428 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDSL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKM 1374
            +       
Sbjct: 1148 QDNEIEMR 1155


>gi|282910183|ref|ZP_06317987.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|282325575|gb|EFB55883.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|312439038|gb|ADQ78109.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus TCH60]
          Length = 1183

 Score =  854 bits (2206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V  GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAAGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 157/427 (36%), Positives = 217/427 (50%), Gaps = 59/427 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP---KGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAK 1373
            +      
Sbjct: 1148 QDNEIEM 1154


>gi|258422611|ref|ZP_05685517.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9635]
 gi|257847183|gb|EEV71191.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9635]
          Length = 1183

 Score =  854 bits (2206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 599/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI +            
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMN------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 247/1145 (21%), Positives = 417/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMNVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +          L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|167461257|ref|ZP_02326346.1| DNA-directed RNA polymerase subunit beta [Paenibacillus larvae
           subsp. larvae BRL-230010]
          Length = 1180

 Score =  854 bits (2206), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/959 (45%), Positives = 601/959 (62%), Gaps = 80/959 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E+++IP+LIE+Q+ SY  FL          +EGL+  F+
Sbjct: 3   LAGHLVQYGR-RKRRTYARINEVLEIPNLIEIQQKSYQWFL----------DEGLREMFQ 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 52  DISPIQDFTGNLVLEFIDYSLGEPKYTVDDSKERDVTYAAPLRVKVRLI---------NK 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD P+MT+ GTF+I G +R++VSQL RSP ++++    +   +GK  +
Sbjct: 103 ETGEVKEQEVFMGDFPIMTETGTFIINGAERVIVSQLVRSPSVYYN---TKVDKNGKKAF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 160 TATVIPNRGAWLELETDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGDDEYIR 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +++ + L        K         
Sbjct: 220 NTLDKDNTDSTDKALI------EIYERLRPGEPPTLDNARSLLYARFFDPKRYDLANVGR 273

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  EAG ++D + L+EI            + 
Sbjct: 274 YKINKKLHIKNRLFNQRLAETLVHPETGEIIAEAGQLVDRRLLDEI------------LP 321

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +      +   V +   +     +    V  P +                         
Sbjct: 322 CLEEGVGFKEYSVPNGVLESDHIPMQTIDVFSPIE----------------------DGK 359

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V +V  N  +      +V++I   DII+ I   ++L +G G  DDID+LGNRR+RSVGE+
Sbjct: 360 VVKVISNGVI----DKNVKNITPADIISSINYFINLLHGIGNTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FA
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFA 535

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR+V    G VT+++VY++A EE+N  +AQAN+ L+EDG+F  + V+ R
Sbjct: 536 RINEYGFIEAPYRRVDPKTGVVTDEIVYMTADEEDNYVVAQANAELNEDGTFAADNVYVR 595

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + +P+E++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL  +A
Sbjct: 596 YKDEILTLPKERVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLMPKA 655

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKF 767
           P VGTGME   AK SG  +VAK  GI+E+V    I +R  E       SG    ++L KF
Sbjct: 656 PLVGTGMEYKAAKDSGVCVVAKHDGIIEKVSGNEIWLRRQEEVDGRLVSGNITKFKLHKF 715

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC+NQRPLV  G  V+  DI+ADGPST+ G+LALGRN++VAFM W GYN+ED++
Sbjct: 716 MRSNQGTCINQRPLVLEGQRVKAGDILADGPSTEQGELALGRNVVVAFMTWEGYNYEDAI 775

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAE
Sbjct: 776 LLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAE 835

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           +  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++F 
Sbjct: 836 IGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKVFT 894



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/527 (35%), Positives = 267/527 (50%), Gaps = 68/527 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  ++  G  V  GDIL    + + +  +     ++ A 
Sbjct: 705  GNITKFKLHKFMRSNQGTCINQRPLVLEGQRVKAGDILADGPSTE-QGELALGRNVVVAF 763

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 764  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 818

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 819  DALKNLDER-GIIRVGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 877

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 878  RVPHGTDGIVVDV------KVFTHENGDELPPGVNQLVRVYIAQKRKISQGDKMAGRHGN 931

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+++RILP EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG  + + +
Sbjct: 932  KGVIARILPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMAAKQLGIHVATPV 991

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     D                                             VFD    
Sbjct: 992  FDGAHEYD---------------------------------------------VFD---- 1002

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G++ LYDG TGE F+R VTVG +YM+KL HMV DK++ARSTG YS
Sbjct: 1003 -----TMEEAGMQRNGKTKLYDGRTGEEFEREVTVGVMYMIKLAHMVDDKIHARSTGPYS 1057

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1058 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1117

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +  E G PESF VL+KE+Q+LG+ + + +   +    M+E+ D +  
Sbjct: 1118 NVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIE-MKELDDEDDA 1163


>gi|184154057|ref|YP_001842398.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri JCM
           1112]
 gi|227363828|ref|ZP_03847935.1| DNA-directed RNA polymerase [Lactobacillus reuteri MM2-3]
 gi|325683039|ref|ZP_08162555.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri
           MM4-1A]
 gi|183225401|dbj|BAG25918.1| DNA-directed RNA polymerase beta subunit [Lactobacillus reuteri JCM
           1112]
 gi|227071185|gb|EEI09501.1| DNA-directed RNA polymerase [Lactobacillus reuteri MM2-3]
 gi|324977389|gb|EGC14340.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri
           MM4-1A]
          Length = 1205

 Score =  853 bits (2205), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/964 (43%), Positives = 588/964 (60%), Gaps = 80/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q  SY+ F+           +GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLELPNLIEIQTDSYNWFM----------EKGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYSEENDK---NGRPNY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY-PKIVY 238
               IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG  S+ EI+  F       
Sbjct: 162 GATFIPNRGAWLEYETDAKNVSYVRIDRTRKLPMTELIRALGFGSDDEIIDMFGGDSETL 221

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--- 294
           S   D      +A D  V   +      +  GE    +S + L +      K   +    
Sbjct: 222 SLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVG 280

Query: 295 -----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                   +    L G  +AE + + +TGE+  + GD + ++ L ++        P L  
Sbjct: 281 RYKTNKKLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLE-------PYLDR 333

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D      Y              +A++     +           + +  +   D D+    
Sbjct: 334 DDFKTITY----------TPSDEAVVTEPVKL-----------QKILVYSKNDPDR---- 368

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N   P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE
Sbjct: 369 -----VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGSTDDIDHLGNRRIRSVGE 423

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  
Sbjct: 424 LLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQT 483

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+
Sbjct: 484 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSY 543

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L++DGSF ++ V  
Sbjct: 544 ARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQANTPLNDDGSFVDDQVMA 603

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E ID++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   
Sbjct: 604 RDKDDYIETSVENIDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPH 663

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG++   A  SG A++AK+ G VE VDA  + +R  +G LD        Y+LMKF
Sbjct: 664 APLVSTGIDYKAAHDSGVAMIAKKPGTVEYVDAREVRVREEDGTLD-------TYKLMKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 717 RRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE GI+ VGAE
Sbjct: 777 AINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDENGIVRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R
Sbjct: 837 VHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTR 896

Query: 948 HGID 951
              D
Sbjct: 897 ENGD 900



 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 223/1067 (20%), Positives = 369/1067 (34%), Gaps = 172/1067 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++     ++   ++AL DIY  +RPG+  T   A S+    FFD  +YD++ VGR K N 
Sbjct: 227  KDVHKNAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAPVGRYKTNK 286

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L L               PD    +        KE +  +   L        T    D 
Sbjct: 287  KLMLKYRLLGQTLAETLADPDTGEVLAQKGDTVTKELLNKLEPYLDRDDFKTITYTPSDE 346

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVC 514
                    + ++L    +    R+   I      ++   + P D+         +   + 
Sbjct: 347  AVVTEPVKLQKILVYS-KNDPDRVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIG 405

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  +   V P     I P   
Sbjct: 406  STDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVA 465

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLS 618
            S     G         + N  G +    R                 V D   T+      
Sbjct: 466  SIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCP 525

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA 
Sbjct: 526  IETPEGPNIGLINSLSSYARVNKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNFIIAQ 585

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P    +D    +    M R        +  ++ T +E++                V 
Sbjct: 586  ANTPL---NDDGSFVDDQVMAR-------DKDDYIETSVENIDYMD-------VSPKQVV 628

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V +  I     +                  QR          PLV  G           
Sbjct: 629  SVASACIPFLENDDSNRALMGA-------NMQRQAVPLINPHAPLVSTGI---------- 671

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                                     +++ +      M+++   T  +++  EV  R+ + 
Sbjct: 672  -------------------------DYKAAHDSGVAMIAKKPGTVEYVDAREVRVRE-ED 705

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  L A 
Sbjct: 706  GTLDTYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPS-MEQGELALGQNPLIAF 764

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D        V   V        +  +  E  +  E    E +    DD   
Sbjct: 765  MTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALK 823

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD N   R+   +   + + G    K  T LS++                         
Sbjct: 824  DLDENGIVRVGAEVHDGDILVGKVTPKGMTELSAEE------------------------ 859

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                      +I  ++ +   +          G+++ VKVF         GD+++     
Sbjct: 860  ------RLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTREN-----GDELSP---- 904

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSL 1155
             G+ + +                          R+ + Q  +  +G       G K    
Sbjct: 905  -GVNTMV--------------------------RVYIAQKRKIQVGDKMSGRHGNKGTVS 937

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            I   + +    P  + ++ ++       +++      +       + G+ ++TPVFDGA 
Sbjct: 938  IVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQLLELHLGMAARRLGIHMATPVFDGAS 997

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            ++ +   +R +   E G++ILYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG Y
Sbjct: 998  DKDVWDAVRESGFPEDGKTILYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPY 1057

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G
Sbjct: 1058 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIING 1117

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
                + G PESF VLVKE+QALGL + + +   K         D ++
Sbjct: 1118 QPIPKPGVPESFRVLVKELQALGLDMKVLDGNNKEIQLKNMDEDDDE 1164


>gi|257888773|ref|ZP_05668426.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,141,733]
 gi|257899845|ref|ZP_05679498.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           Com15]
 gi|293572776|ref|ZP_06683730.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E980]
 gi|257824827|gb|EEV51759.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,141,733]
 gi|257837757|gb|EEV62831.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           Com15]
 gi|291607126|gb|EFF36494.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E980]
          Length = 1205

 Score =  853 bits (2204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|257880397|ref|ZP_05660050.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,230,933]
 gi|257882393|ref|ZP_05662046.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,502]
 gi|257891725|ref|ZP_05671378.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,410]
 gi|257894064|ref|ZP_05673717.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,408]
 gi|258614170|ref|ZP_05711940.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecium DO]
 gi|260559360|ref|ZP_05831541.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium C68]
 gi|293553569|ref|ZP_06674193.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1039]
 gi|293564002|ref|ZP_06678408.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1162]
 gi|293569984|ref|ZP_06681064.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1071]
 gi|294616962|ref|ZP_06696682.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1636]
 gi|294623902|ref|ZP_06702729.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           U0317]
 gi|257814625|gb|EEV43383.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,230,933]
 gi|257818051|gb|EEV45379.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,502]
 gi|257828085|gb|EEV54711.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,410]
 gi|257830443|gb|EEV57050.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,408]
 gi|260074459|gb|EEW62780.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium C68]
 gi|291587356|gb|EFF19240.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1071]
 gi|291590116|gb|EFF21905.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1636]
 gi|291596664|gb|EFF27888.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           U0317]
 gi|291602144|gb|EFF32372.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1039]
 gi|291603920|gb|EFF33448.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1162]
          Length = 1205

 Score =  853 bits (2204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|257886148|ref|ZP_05665801.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,501]
 gi|257822004|gb|EEV49134.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium
           1,231,501]
          Length = 1205

 Score =  853 bits (2204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|258448430|ref|ZP_05696545.1| RNA polymerase subunit beta [Staphylococcus aureus A6224]
 gi|257858299|gb|EEV81186.1| RNA polymerase subunit beta [Staphylococcus aureus A6224]
          Length = 1183

 Score =  853 bits (2204), Expect = 0.0,   Method: Composition-based stats.
 Identities = 443/964 (45%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLDELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 249/1158 (21%), Positives = 428/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            +L+L      + +          E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +      +++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLDELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|70727464|ref|YP_254380.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           haemolyticus JCSC1435]
 gi|82581604|sp|Q4L3K3|RPOB_STAHJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|68448190|dbj|BAE05774.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           haemolyticus JCSC1435]
          Length = 1183

 Score =  853 bits (2203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/964 (46%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSNDQEIIDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D + L+EI              
Sbjct: 273 YKANKKLHLKHRLFNQRLAEPIVNSETGEIVAEEGTVLDRRKLDEIMEVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGTVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKYRGRVEHVESKEILVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNTGTCYNQRPIVSVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 248/1163 (21%), Positives = 429/1163 (36%), Gaps = 115/1163 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         +D + ++ Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSNDQEIIDLLGDSEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANK 277

Query: 419  RLNLDTPD-DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L     + R           +I+ +           + +      +  E+ + +  +
Sbjct: 278  KLHLKHRLFNQRLAEPIVNSETGEIVAEEGTVLDRRKLDEIMEVLETNANSEVFELEGTV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLIN--AKPVVSAVCEFFCSSQLSQLEEHVN---SL 532
                +E    +     D +      + N      V  +      + +S     +N     
Sbjct: 338  IDEPVEIQSIKVYVPNDEEGRTTTVIGNALPDSEVKCITPADIIASMSYFFNLLNGIGYT 397

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
              I H         G + + +  + +  +      R+   +T       L++     A +
Sbjct: 398  DDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASI 457

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +       + +       ++ +                           L       E
Sbjct: 458  KEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSALGPGGLTRE 496

Query: 653  EILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
               +    + +        +       I  + +  S   +            +  +   +
Sbjct: 497  RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSI 556

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               ++ + A    + +VA+    +             +  +        +    K    +
Sbjct: 557  TDQIDYLTADEEDSYVVAQANSRL-----DENGRFLDDEVVCRFRGNNTVMAKEKMDYMD 611

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +              +  +D        ++   A+      A     G     +     
Sbjct: 612  VSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEAPFVGTGMEHVAARDSGA 671

Query: 832  RMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICV 884
             + ++      H+E  E++ R           G  +                ++  I+ V
Sbjct: 672  AITAKYRGRVEHVESKEILVRRLVEENGTEHEGELDRYPLAKFKRSNTGTCYNQRPIVSV 731

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V   +IL    +      M     ++         +  D  +     +S  +V   +
Sbjct: 732  GDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDV 785

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            +    I++ E      +   E + RD  +      +N+  R   +  G     G     K
Sbjct: 786  YTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDR-GIVYVGAEVKDGDILVGK 844

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             T      ++   R     F  +  +V+     +                 K+   + GD
Sbjct: 845  VTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGD 898

Query: 1065 D-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LN
Sbjct: 899  DTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLN 958

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+                  
Sbjct: 959  PLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--------------- 1003

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                      +  A   + G                             +++LYDG TGE
Sbjct: 1004 ----------IEEAGMARDG-----------------------------KTVLYDGRTGE 1024

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            PFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 1025 PFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1084

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + +
Sbjct: 1085 AYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1144

Query: 1364 ENSRTKNSAKMEEIPDFNKCELK 1386
             + +      M ++ D +  E K
Sbjct: 1145 MDEQDNEIE-MADVDDEDATERK 1166


>gi|294617122|ref|ZP_06696783.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1679]
 gi|291596618|gb|EFF27850.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           E1679]
          Length = 1205

 Score =  853 bits (2203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLDELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|304405627|ref|ZP_07387286.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus
           curdlanolyticus YK9]
 gi|304345666|gb|EFM11501.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus
           curdlanolyticus YK9]
          Length = 1181

 Score =  853 bits (2203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/967 (45%), Positives = 601/967 (62%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q+ SY+ FL  +          L   F+
Sbjct: 1   MAGQLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYEKFLDAD----------LLELFQ 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+   RD+T+A PL++ +RL+          K
Sbjct: 50  DISPIQDFTGNLSLEFIDYSLGEPKYSVDESKERDVTFAAPLRVKVRLL---------NK 100

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  Y
Sbjct: 101 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKRTY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 158 TATVIPNRGAWLELETDAKDIIYVRIDRTRKIPVTVLLRALGFSTDAEILDLLGQDEYIR 217

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +++ K L        K         
Sbjct: 218 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLDNAKSLLVARFFDPKRYDLANVGR 271

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+  TGEI  EAG +ID + L+EI            + 
Sbjct: 272 YKINKKLHIKNRLFNQRLAETLVDPATGEIIAEAGQIIDRRLLDEI------------LP 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +N   +   V +   +     L    V  P                      Y+   
Sbjct: 320 RLESNVGFKTYHVANGVLNADSIPLQAINVFSP----------------------YEDGK 357

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +       V+HI   DII+ I   ++L +G G  DDID+LGNRR+RSVGE+
Sbjct: 358 VIKIVSNGII----DKTVKHITPADIISSINYFINLLHGIGNTDDIDHLGNRRLRSVGEL 413

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 414 LQNQFRIGLSRMERVVRERMSIQDANAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 473

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVHP+HYGR+CP ET EG NIGL++SL++FA
Sbjct: 474 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLINSLSTFA 533

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    G VT  + Y++A EE+N  +AQAN+ L E+G+F E++V  R
Sbjct: 534 RINEYGFIEAPYRWVDPKTGVVTEQIDYMTADEEDNYVVAQANAKLTEEGNFAEDVVLVR 593

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P E++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 594 YNKQRDNILTMPSERVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 653

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRL 764
            +AP VGTGME   AK SG  IV+K  G++E+V A  I +R +E       T  +  ++L
Sbjct: 654 PKAPLVGTGMEHKSAKDSGVCIVSKYDGVIERVSANEIWLRRIEMLDGKQVTGDLVKHKL 713

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRPLV  GD +R+ DI+ADGPST+ G+LALGRN++VAFM W GYN+E
Sbjct: 714 HKFMRSNQGTCINQRPLVNKGDIIRKGDIMADGPSTEQGELALGRNVVVAFMTWEGYNYE 773

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LKN+DE GII V
Sbjct: 774 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDERGIIRV 833

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++
Sbjct: 834 GAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKV 893

Query: 945 FNRHGID 951
           F R   D
Sbjct: 894 FTRENGD 900



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 172/440 (39%), Positives = 233/440 (52%), Gaps = 70/440 (15%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +   S+  E+ E  ARD       + R+I                I  G    +G   
Sbjct: 784  KEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNLDERGIIRVGAEISAGDIL 843

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +    +     +      K+   +
Sbjct: 844  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDV------KVFTRE 897

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++PPGV ++V+ ++A KR I  GDKMAGRHGNKG+++RI+P EDMPFL DGTPV++V
Sbjct: 898  NGDELPPGVNQLVRAYIAQKRKISEGDKMAGRHGNKGVIARIMPEEDMPFLPDGTPVEVV 957

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E HLG AC  LG    + + D     D                 
Sbjct: 958  LNPLGVPSRMNIGQVLEVHLGMACKRLGIHAATPVFDGAREYD----------------- 1000

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF         + +  A +  +G+++LYDG T
Sbjct: 1001 ----------------------------VF---------NAMEEAGMQRNGKTVLYDGRT 1023

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE F+R VTVG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1024 GEEFEREVTVGVMYMIKLAHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1083

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQE+LT+KSDDVVGR + YESIV G +  E G PESF VL+KE+Q+LG+ +
Sbjct: 1084 LEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGENVPEPGVPESFKVLIKELQSLGMDV 1143

Query: 1362 DLENSRTKNSAKMEEIPDFN 1381
             + +   +     E   D +
Sbjct: 1144 KILSEDEEEIELREADDDED 1163


>gi|259046407|ref|ZP_05736808.1| DNA-directed RNA polymerase, beta subunit [Granulicatella adiacens
           ATCC 49175]
 gi|259036952|gb|EEW38207.1| DNA-directed RNA polymerase, beta subunit [Granulicatella adiacens
           ATCC 49175]
          Length = 1212

 Score =  853 bits (2203), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/989 (43%), Positives = 603/989 (60%), Gaps = 89/989 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  RVR+ + +  E++++P+LIE+Q  SY  FL          +EG++  FK
Sbjct: 4   LAHHDVKYGRHRVRRSYARISEVLELPNLIEIQTDSYQWFL----------DEGIREMFK 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI   +G   LEF+ YE   PK+++ +    D  YA P+ + +RL+          K
Sbjct: 54  DISPIEDHTGNLSLEFLDYELHAPKYNLQEARNHDANYAAPIYVKMRLV---------NK 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG +F     R   +GK LY
Sbjct: 105 ETGEVKDQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGAYFH---DRPDKNGKQLY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E DSKDI +VRIDR RK+P+T  + ALG  S+E I   F       
Sbjct: 162 GSTLIPNRGAWLEYETDSKDISYVRIDRTRKIPLTVLVRALGFGSDELIQEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVD-IDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG 297
              D         D     +    + D +  GE    ES + L +      +   +  +G
Sbjct: 222 LTLDKDVHKRM--DESRTEEALKDIYDRLRPGEPKTAESSRNLLTARFFDPRRYDLAAVG 279

Query: 298 ITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                      + L    +AE++V+ ETGEI +E G V++   +E++     +   +  +
Sbjct: 280 RYKVNKKLNLKNRLLHQTIAENLVDPETGEIVVEKGTVLERDVMEKVVEVLEKGANLFTL 339

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
               +               ++  ++    V  P D                        
Sbjct: 340 HPSEDGVI------------KEPVIIQTVEVYSPADP----------------------- 364

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + +  N +  +DV+H+   DIIA I   ++L  G GT DDID+LGNRR+RSVGE
Sbjct: 365 ---ERVIKVIGNGNVTEDVKHVTASDIIATISYFLNLYEGIGTTDDIDHLGNRRIRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D  +V PQ L+N +PVV+A+ EFF SSQLSQ  +  
Sbjct: 422 LLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLVNIRPVVAAIKEFFGSSQLSQFMDQT 481

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++
Sbjct: 482 NPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTY 541

Query: 590 ARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           A++N YGFIETPYR+V     KVT+ + YL+A EE++  +AQANS L+EDGSF  ++V  
Sbjct: 542 AKINKYGFIETPYRRVDWNTHKVTDKIDYLTADEEDSFVVAQANSPLNEDGSFVNDVVMA 601

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + VP E++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL  +
Sbjct: 602 RYVSENLEVPVERVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLNPK 661

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           APF+GTGME V A  SG A++ KR G+VE VDA  + +R+ +G LD        Y + KF
Sbjct: 662 APFIGTGMEYVSAHDSGVALLCKRDGVVEFVDAKEVRVRTADGSLD-------TYHITKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             SN   C NQRP+V  GD+V + +I+ADGPS + G+LALG+N+LVAFM W GYN+ED++
Sbjct: 715 HGSNAGMCYNQRPIVAQGDKVVKGEILADGPSMEKGELALGQNVLVAFMTWEGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHI++++  ARDTKLGPEEITR+IPNV E+ LKN+D  GII +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIDDYDSEARDTKLGPEEITREIPNVGEDALKNLDADGIIRIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG +  +PEE+LL AIFGEKA +VRDTSLRVP G  G V DVR+F R
Sbjct: 835 VKDGDILVGKVTPKGLTEQSPEERLLHAIFGEKAREVRDTSLRVPHGGGGIVRDVRVFTR 894

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   G++K  R   V++ +I    +
Sbjct: 895 AAGDELAPGVNKLVRVYIVQKRKINEGDK 923



 Score =  469 bits (1207), Expect = e-129,   Method: Composition-based stats.
 Identities = 177/529 (33%), Positives = 242/529 (45%), Gaps = 67/529 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +                ++  I+  G +V  G+IL    +   +  +   + +
Sbjct: 700  RTADGSLDTYHITKFHGSNAGMCYNQRPIVAQGDKVVKGEILADGPS-MEKGELALGQNV 758

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +         V D    + H  D +  +   +    E+     +
Sbjct: 759  LVAFMTWEGYNYEDAVIM----SERLVKDDVYTSIHIDDYDSEARDTKLGPEEITREIPN 814

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              +  L          I  G     G     K T       S   R     F  +  +V+
Sbjct: 815  VGEDALKN--LDADGIIRIGAEVKDGDILVGKVTPKGLTEQSPEERLLHAIFGEKAREVR 872

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      ++     GD++ PGV ++V+V++  KR I  GDKMAG
Sbjct: 873  DTSLRVPHGGGGIVRDV------RVFTRAAGDELAPGVNKLVRVYIVQKRKINEGDKMAG 926

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 927  RHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARELGIYI 986

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D+    +                                     T ++D
Sbjct: 987  ATPVFDGAQDEDVWGTVAEAGMARDAK----------------------------TILYD 1018

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL HMV DK++ARS 
Sbjct: 1019 G--------------------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSI 1052

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YESI
Sbjct: 1053 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYESI 1112

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            V G      G PESF VLVKE+QALGL + + +++ +     +   D  
Sbjct: 1113 VKGQQISRPGVPESFRVLVKELQALGLDMKVLDAQDEEIKLEDMDEDEG 1161


>gi|167769915|ref|ZP_02441968.1| hypothetical protein ANACOL_01256 [Anaerotruncus colihominis DSM
           17241]
 gi|167667906|gb|EDS12036.1| hypothetical protein ANACOL_01256 [Anaerotruncus colihominis DSM
           17241]
          Length = 1251

 Score =  852 bits (2202), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/954 (45%), Positives = 578/954 (60%), Gaps = 56/954 (5%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
                 R  F    E++ +P+LIEVQK SY  FL          +EGL+  FK V PIT 
Sbjct: 8   TQGKTTRMSFSHIDEVLQMPNLIEVQKNSYQWFL----------DEGLKEVFKDVSPITD 57

Query: 68  FSGAAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           +    +L+F+ Y  D  PK+ +++C  RD TYA PL++   L+          K   ++K
Sbjct: 58  YQDNLVLDFIDYHLDDKPKYTIEECKERDATYAAPLRVRASLL---------NKETGEVK 108

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           EQ I+MGD PLMT  GTF+I G +R++VSQL RSPG+++     +   SGK LY   +IP
Sbjct: 109 EQDIFMGDFPLMTDSGTFIINGAERVIVSQLVRSPGVYYGSSHDK---SGKELYTTTVIP 165

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY--SQRGD 243
           ++G W++ E DS D+ +VRID+ RK+PVT+F+ ALG  S E I+  F        +   D
Sbjct: 166 NRGAWLEYETDSNDVFYVRIDKNRKLPVTTFVRALGFSSNESIIDFFGDDERIMATLEKD 225

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSD 301
                  A   +           +D+ +  I+S         L K  + K  K L IT  
Sbjct: 226 GTANTEEALLEVYRKLRPGEPPTVDSAQSHIDSLFFDPRRYDLSKVGRYKYNKKLAITP- 284

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   +  + +  TGE+   A  V+  +  E I  + +  + I   D           
Sbjct: 285 RILGRTTSRPVADPLTGELLAGADTVLTRELAERIGRAGVDTVYIRIGDDREMRVLSNGM 344

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +          A L I   +R             F  L    D  D     R  +  R +
Sbjct: 345 VDIKDFVGFDCAPLGINEKVR-------------FAVLREILDACDGEDALREAIAARRD 391

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
              P   +HI K+DI + I  L  L +G GT+DDID+LGNRR+RSVGE+L+NQ+R+G  R
Sbjct: 392 ELIP---KHIIKDDIFSSINYLCGLGHGIGTVDDIDHLGNRRIRSVGELLQNQFRIGFSR 448

Query: 482 MERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           MER I+ER+++   D+D V PQ LIN +PVV+++ EFF SS LSQ  +  N L+ +TH R
Sbjct: 449 MERVIRERMATQAQDMDVVTPQALINIRPVVASIKEFFGSSPLSQFMDQTNPLAELTHKR 508

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L +FA++N YGF+E
Sbjct: 509 RLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLATFAKINEYGFVE 568

Query: 600 TPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            PYR+V      V ++V Y++A  E+   +AQAN  L EDG F  E V  R     ++  
Sbjct: 569 APYRRVDKATGVVLDEVEYMTADIEDMYIVAQANEPLTEDGKFANEKVSVRYRDAVMVCE 628

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           REK+D++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP V TGME 
Sbjct: 629 REKVDYMDVSPKMVVSVATAMIPFLENDDANRALMGANMQRQAVPLLVPEAPIVATGMEY 688

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG A+V+K AG+VE V A  IVIR        S      Y L+KF RSNQ TC+N
Sbjct: 689 KSAVDSGVAVVSKHAGVVESVSANEIVIR-------DSRGESHSYHLIKFMRSNQGTCIN 741

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK G+E+    +IADGPST  G+++LGRNMLV FM W GYN+ED++LI+ER+V +D
Sbjct: 742 QRPIVKKGEEISVGQVIADGPSTAGGEISLGRNMLVGFMTWEGYNYEDAVLINERLVKDD 801

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           ++TSIHIEE+E+ +RDTKLGPEEITRDIPNV ++ L+ +DE GII VGAEV  GDILVGK
Sbjct: 802 IYTSIHIEEYEIESRDTKLGPEEITRDIPNVGDDALRELDERGIIRVGAEVRAGDILVGK 861

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +  EE+LLRAIFGEKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 862 VTPKGETELNAEERLLRAIFGEKAREVRDTSLRVPHGEYGIIVDVKVFTRENCD 915



 Score =  387 bits (994), Expect = e-105,   Method: Composition-based stats.
 Identities = 150/538 (27%), Positives = 217/538 (40%), Gaps = 77/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G       I  +       I++  I+  G E++ G ++    +  G   ++    +
Sbjct: 717  RDSRGESHSYHLIKFMRSNQGTCINQRPIVKKGEEISVGQVIADGPSTAG-GEISLGRNM 775

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L      +  +  D  L     V   +        + I+  +  +  E     I  +  D
Sbjct: 776  LVGFMTWEGYNYEDAVLINERLVKDDIYTSIHIEEYEIESRDTKLGPEEITRDIPNVGDD 835

Query: 971  ---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + DE+ I+      R  +IL G+    G         L   +  E  R         
Sbjct: 836  ALRELDERGIIRVGAEVRAGDILVGKVTPKGETELNAEERLLRAIFGEKAR--------- 886

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   K+   +  D++ PGV  VV+ ++A        
Sbjct: 887  --------EVRDTSLRVPHGEYGIIVDVKVFTRENCDELSPGVNMVVRCYIA-------- 930

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
                     K  +S                               VG             
Sbjct: 931  --------QKRKIS-------------------------------VG-------DKMAGR 944

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G K        + +    P    L+ V+       +++      V       + G  V 
Sbjct: 945  HGNKGVVSRVLPQEDMPYLPDGRPLDIVLNPLGVPSRMNIGQVLEVHLGRAAAELGWKVM 1004

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGADE  I   L  A L   G++ L+DG TGE FD PVTVGY+Y LKL+H+V DK+
Sbjct: 1005 TPVFDGADETDIADCLEQAGLSRDGKTWLHDGRTGELFDNPVTVGYMYYLKLHHLVDDKI 1064

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR +
Sbjct: 1065 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVK 1124

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             +ESIV G +  + G PESF VL+KE+Q+LGL + + +         +   D +   L
Sbjct: 1125 TFESIVKGKNVPQPGIPESFKVLIKELQSLGLDMRVLDKDNNEIDLKQTFDDDDNMGL 1182


>gi|330686247|gb|EGG97859.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis VCU121]
          Length = 1183

 Score =  852 bits (2202), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/964 (46%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKLDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + L+EI          +   
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVVEEGTVLDRRKLDEIMD--------VLEA 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGTVIDEPVEIQSIKVYV----------------------PNDDEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI A   G VE V++  I++R  VE D       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITANHRGRVEHVESNEILVRRLVEQDGQEYEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V  GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAAGDIVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+DE GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDERGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  483 bits (1243), Expect = e-134,   Method: Composition-based stats.
 Identities = 167/446 (37%), Positives = 226/446 (50%), Gaps = 72/446 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K++   S+  E+ E  ARD       + R+I                +  G     G   
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDERGIVYVGAEVKDGDIL 841

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +                 K+   +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNRE 895

Query: 1062 WGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
             GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI
Sbjct: 896  EGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDI 955

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+               
Sbjct: 956  MLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------ 1003

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +  A   + G                             +++LYDG 
Sbjct: 1004 -------------IEEAGMARDG-----------------------------KTVLYDGR 1021

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1022 TGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1081

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL 
Sbjct: 1082 ALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPNVPESFRVLMKELQSLGLD 1141

Query: 1361 IDLENSRTKNSAKMEEIPDFNKCELK 1386
            + + + +      M +I D +  E K
Sbjct: 1142 VKVMDEQDNEIE-MADIEDEDVTERK 1166


>gi|294779446|ref|ZP_06744845.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           PC1.1]
 gi|300861604|ref|ZP_07107688.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|294453484|gb|EFG21887.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           PC1.1]
 gi|300849065|gb|EFK76818.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|323479153|gb|ADX78592.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           62]
          Length = 1204

 Score =  852 bits (2202), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 324 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 362 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 600 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 784  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 844  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 887  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 991

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 992  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1133 SLGLDMRVLDIEEAEIELR 1151


>gi|57651418|ref|YP_185474.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus COL]
 gi|81695152|sp|Q5HID3|RPOB_STAAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|57285604|gb|AAW37698.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus COL]
          Length = 1183

 Score =  852 bits (2201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E   RDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEVRDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDT LRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTLLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 249/1158 (21%), Positives = 429/1158 (37%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            +L+L      + +          E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E  +   +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEVRDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+  +  +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTLLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|239636941|ref|ZP_04677939.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus warneri
           L37603]
 gi|239597489|gb|EEQ79988.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus warneri
           L37603]
          Length = 1183

 Score =  852 bits (2201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/964 (46%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + L+EI          +   
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVVEEGTVLDRRKLDEIMD--------VLEA 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGTVIDEPVEIQSIKVYV----------------------PNDDEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI A   G VE V++  I++R  VE D       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITANHRGRVEHVESNEILVRRLVEQDGQEYEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V  GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVATGDIVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+DE GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDERGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 167/446 (37%), Positives = 226/446 (50%), Gaps = 72/446 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K++   S+  E+ E  ARD       + R+I                +  G     G   
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDERGIVYVGAEVKDGDIL 841

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +                 K+   +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNRE 895

Query: 1062 WGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
             GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI
Sbjct: 896  EGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDI 955

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+               
Sbjct: 956  MLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------ 1003

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +  A   + G                             +++LYDG 
Sbjct: 1004 -------------IEEAGMARDG-----------------------------KTVLYDGR 1021

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1022 TGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1081

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL 
Sbjct: 1082 ALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLD 1141

Query: 1361 IDLENSRTKNSAKMEEIPDFNKCELK 1386
            + + + +      M +I D +  E K
Sbjct: 1142 VKVMDEQDNEIE-MADIEDEDVTERK 1166


>gi|307069542|ref|YP_003878019.1| putative DNA-directed RNA polymerase subunit beta [Candidatus
            Zinderia insecticola CARI]
 gi|306482802|gb|ADM89673.1| putative DNA-directed RNA polymerase subunit beta [Candidatus
            Zinderia insecticola CARI]
          Length = 1291

 Score =  852 bits (2201), Expect = 0.0,   Method: Composition-based stats.
 Identities = 447/1360 (32%), Positives = 744/1360 (54%), Gaps = 89/1360 (6%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +RK F K      IP+LI  Q  SY  F+        R N G+Q     +FPI + +   
Sbjct: 7    IRKSFSKIINNHKIPNLINHQIDSYKFFIQKKNKSFYRKNLGIQKEISKIFPIFSKNKNI 66

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L F +Y+   PK +   C  +DLTY+  +++ L+L+            I  I E  I +
Sbjct: 67   SLYFKNYKIIKPKNNKKKCFEKDLTYSYNIELNLKLVN-----------INKINEIKISI 115

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PL+ K+ +F+  G++R++V Q+ R  GI + ++K + +L+ + +Y  +I   +G  +
Sbjct: 116  GEIPLILKNASFIFNGMERVIVPQISRKFGIFYINEKKKNNLN-EYIYKVKINILKGYKI 174

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
             IEFD  + +  RI++++K+P+     +L +  ++I++ FY       +           
Sbjct: 175  IIEFDMNNNLFFRINKKKKIPLIILFKSLNISKKKIINFFYNNYKVYIKNKKIKIKFDFK 234

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            +     K   +L +    + +++  KK+    +K +  K +K+  I++  L    +A DI
Sbjct: 235  N-FYNYKFDYNLYNKKG-KLLLKKNKKINKKKIKKIFNKNIKYFYISNKHLIKKIIANDI 292

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                   +  +   +I++K ++ +  + I  I I  +   N N YI N L    N  + +
Sbjct: 293  Y--INNNLLFKKYTIINKKKIKILKKNNIYKIFIFNLGEKNKNNYIFNILKKYNNYSKFE 350

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            +   IY+ +     S   +   +F  +FF   K +         N             + 
Sbjct: 351  SKYLIYKYLNFKGNSKKKIDF-LFYNIFFKIRKKNNFIYKNSIKNK------------LS 397

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             + ++ IIK L+ L+N    + D+++L  ++V+++  +    + L +    ++I E+++ 
Sbjct: 398  TKYLLNIIKKLIILKNKNKKLKDLNSLYFKKVKNLEYLFNEIFFLSMEIFYKNIIEKLNF 457

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            ++ +     + +     +S++ +FF  S+ SQ  +  N LS ITH RRL++LG GG+ + 
Sbjct: 458  MEFNKNYKLNKLEYLNTLSSLKDFFSVSEFSQFLDSTNPLSEITHKRRLTSLGPGGLTKK 517

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI-ETPYRKVCDGKVT 611
             A  E RDVH THYGRICP ET EG +IGLV++L  + +++    + ++PY+KV    +T
Sbjct: 518  TANFESRDVHYTHYGRICPIETPEGPHIGLVNNLALYCKIDRKSRLLKSPYKKVKKSNLT 577

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            N + YL+   E+  YIAQ+N  L ++       +  R  G E  V ++KI +ID +P Q+
Sbjct: 578  NKIFYLNNFNEDKYYIAQSNI-LIKNKKIINNFISTRKYGNEKFVNKKKIKYIDINPNQI 636

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VSIA+SLIPFLE++D+NR LM  NMQRQ+VP + +E PFVGTG+E  V       I +K 
Sbjct: 637  VSIASSLIPFLEHNDANRALMAANMQRQSVPCINSEFPFVGTGIEKNVVFDLNYIIKSKT 696

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             GIV+ +D+  I+I +           ++ Y+L KF+R+NQNT +NQ+ +V + D +++N
Sbjct: 697  NGIVKYIDSKYILILNE-------NLKIEKYKLDKFKRTNQNTLINQKSIVNINDYIKKN 749

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             +IAD   +  G+LALG+N+L+AFM   GYNFEDS++ISE+++  + +TSIHI E ++  
Sbjct: 750  QVIADSSCSKFGELALGKNVLIAFMTLKGYNFEDSIIISEKLLKNNKYTSIHILELKIPL 809

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            +  + G E IT++I N+ +  + N+D+ GII +G  + PGDILV K  P           
Sbjct: 810  KFNEFGEEIITKNIKNIKKNKISNLDKLGIIKIGKYILPGDILVSKKLPINN-------- 861

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
                 F  K     +TS + P+GV G V+D++IF     + N    +  ++ I       
Sbjct: 862  -----FLNKKNKFINTSYKNPNGVYGKVIDIKIFKNKKNENNYNEYNNIKKIIFKKKNIY 916

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                    + IY   +  L                       +++   + + F       
Sbjct: 917  SFLLFFKKKIIYKYKLFFL---------------------YKNKFFFIKMFNFIKIFFLN 955

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            ++ + ++K + +    ++ + F+N  E +     +P G+ +++K+ +   + +Q GDKM+
Sbjct: 956  KKILLNIKNKIKKINKLIYNSFENFKENL-----LPFGISKIIKIKILTIKKLQPGDKMS 1010

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VS+ILP  ++P++ DGT +DI+LNPLGVPSRMNVGQ  E HLG A  GLG++
Sbjct: 1011 GRHGNKGVVSKILPIRNVPYMNDGTYIDIILNPLGVPSRMNVGQALEVHLGLASWGLGRR 1070

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I ++    K   +++ +++FL K+    S  + I +  D +   + +  K G+P STP+F
Sbjct: 1071 INNIF--KKNPKNLNKIKNFLYKIYNKPSEFKFIKNISDKNFYNLIKVLKKGIPFSTPIF 1128

Query: 1212 DGADEEAINSMLRMADL----------DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +   E+ IN ML +A             +  Q  LY+G T + FD+ +TVGY+Y LKLNH
Sbjct: 1129 ESIKEKYINKMLLLAFPEKIRKKLKMSSDRKQLTLYNGKTNKSFDKKITVGYMYYLKLNH 1188

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V+DK+++RSTG YSLVTQQPL GKSN GGQR GEMEVW ++AYGA+Y LQE+LT+KSDD
Sbjct: 1189 LVNDKIHSRSTGPYSLVTQQPLRGKSNIGGQRFGEMEVWALEAYGASYNLQEILTVKSDD 1248

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++GR  +Y+++V G + F    PESFNVL+KE+  L L +
Sbjct: 1249 ILGRNEIYKNLVKGINNFYPNLPESFNVLLKELNGLCLDL 1288


>gi|258446337|ref|ZP_05694495.1| RNA polymerase subunit beta [Staphylococcus aureus A6300]
 gi|257854931|gb|EEV77876.1| RNA polymerase subunit beta [Staphylococcus aureus A6300]
          Length = 1183

 Score =  852 bits (2200), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +T+ RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTNKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 247/1145 (21%), Positives = 418/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +   +      L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFMDQANPLAELTNKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|294850318|ref|ZP_06791052.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
 gi|294822830|gb|EFG39265.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
          Length = 1183

 Score =  852 bits (2200), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLS+  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSKFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 247/1145 (21%), Positives = 417/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +          L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSKFMDQANPLAELTHKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|227552789|ref|ZP_03982838.1| DNA-directed RNA polymerase subunit beta (RNA polymerase subunit
           beta) [Enterococcus faecium TX1330]
 gi|227178032|gb|EEI59004.1| DNA-directed RNA polymerase subunit beta (RNA polymerase subunit
           beta) [Enterococcus faecium TX1330]
          Length = 1208

 Score =  852 bits (2200), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1131 VKELQSLGLDMRVLDIEETEIELR 1154


>gi|81429387|ref|YP_396388.1| DNA-directed RNA polymerase subunit beta [Lactobacillus sakei
           subsp. sakei 23K]
 gi|88909140|sp|Q38UQ2|RPOB_LACSS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|78611030|emb|CAI56083.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 1197

 Score =  851 bits (2199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/963 (43%), Positives = 573/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++++P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVNYGKHRTRRSYARIKEVLELPNLIEIQSNSYQWFL----------DEGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ V++    D  Y+ PL +TL+L            
Sbjct: 51  DIMPIDDFAGNLSLEFVDYQLLEPKYTVEEARQHDANYSAPLHVTLKLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++F+    +   + +  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYFNSAIDK---NSRTTY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P++  + ALG  S+ EI+          
Sbjct: 159 GTTVIPNRGAWLEFETDAKDIAYVRIDRTRKIPMSVLVRALGYGSDQEIIDILGDNDSLM 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        K   +  +G 
Sbjct: 219 LTLEKDI-HKNTDDSRTEEALKDVYERLRPGEPKTADSSRSLLFARFFDAKRYDLASVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE + + +TGE+      V+D + ++ +              
Sbjct: 278 YKINKKLSLKTRLLGQTLAETLADPDTGEVIAAKDTVVDRQVMDALAPYL---------- 327

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             D +D     Y+    G +      + +  +     DK     
Sbjct: 328 ------------------DCEDFKAVTYQPSDEGVLPEPMTLQVIKVYSQKTPDKE---- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N      V+H+   DIIA +    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 -----INLIGNGHIDAKVKHVIPADIIASMNYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V      VT+ + YL+A EE+N  IAQANS L++DGSF +  V  R
Sbjct: 541 VVNRYGFIETPYRRVSWDTHDVTDKIDYLTADEEDNYVIAQANSPLNDDGSFVDNTVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I    +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 YKDDNIETSIDKLDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVNPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A++A+ AG VE VDA  I +R  +       S +D Y LMKF+
Sbjct: 661 PLVGTGMEYKAAHDSGIALLAQHAGTVEYVDAKVIRVRRED-------SSLDTYELMKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V  GD V  ++IIADGP+ + G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 714 RSNAGKNYNQRPIVAKGDHVDVDEIIADGPAMEKGELALGQNPLIAFMTWNMYNYEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V ED++TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV
Sbjct: 774 LSERLVKEDLYTSIHIEEYESEARDTKLGPEEITREIPNVGEDSLKDLDEFGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G + DV+IF R 
Sbjct: 834 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLKVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 AGD 896



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 260/1078 (24%), Positives = 399/1078 (37%), Gaps = 170/1078 (15%)

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            S+   I IL  +        ++      +   ++AL D+Y  +RPG+  T   + S+   
Sbjct: 203  SDQEIIDILGDNDSLMLTLEKDIHKNTDDSRTEEALKDVYERLRPGEPKTADSSRSLLFA 262

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID- 457
             FFD+ +YDL++VGR K+N +L+L T    + + +         ++  ++       +D 
Sbjct: 263  RFFDAKRYDLASVGRYKINKKLSLKTRLLGQTLAETLADPDTGEVIAAKDTVVDRQVMDA 322

Query: 458  -------------NLGNRRVRSVGEMLKNQY-----RLGLLRMERSIKERISSVDIDSVM 499
                                  + E +  Q      +    +    I        +  V+
Sbjct: 323  LAPYLDCEDFKAVTYQPSDEGVLPEPMTLQVIKVYSQKTPDKEINLIGNGHIDAKVKHVI 382

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR----ARAG 555
            P D+I +      + E   S+       +    S     +    +G   + R      + 
Sbjct: 383  PADIIASMNYFFNLQEGLGSTDDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSI 442

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----------- 604
             +   V P     I P   S     G         + N  G +    R            
Sbjct: 443  QDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRD 502

Query: 605  -----VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP-- 657
                 V D   T+          E   I   NS            +              
Sbjct: 503  RAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYAVVNRYGFIETPYRRVSWDTHDV 562

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +KID++ A  +    IA +  P   NDD + V      + +   +  +        +  
Sbjct: 563  TDKIDYLTADEEDNYVIAQANSPL--NDDGSFVDNTVLARYKDDNIETSIDKLDYMDVSP 620

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                    A+       +E  D+ R ++ +                    QR        
Sbjct: 621  KQV----VAVATACIPFLENDDSNRALMGAN------------------MQRQAVPLVNP 658

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
              PLV  G E +                A   + +       G      +   +  V   
Sbjct: 659  HAPLVGTGMEYK----------------AAHDSGIALLAQHAGT-----VEYVDAKVIRV 697

Query: 838  VFTSIHIEEFEVM-ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                  ++ +E+M  R +  G     R I    +    ++D   II  G  +  G++ +G
Sbjct: 698  RREDSSLDTYELMKFRRSNAGKNYNQRPIVAKGD----HVDVDEIIADGPAMEKGELALG 753

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                                  E A+ + +  ++     S  + +     R      E  
Sbjct: 754  -------QNPLIAFMTWNMYNYEDAIVLSERLVKEDLYTSIHIEEYESEARDTKLGPEEI 806

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
                    E   +D  DE  I+      +  +IL G+    G         L   +  E 
Sbjct: 807  TREIPNVGEDSLKDL-DEFGIVRVGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEK 865

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             R           +V+     +          +      KI   + GD++ PGV  +V+V
Sbjct: 866  AR-----------EVRDTSLKVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRV 908

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            ++  KR IQ GDKMAGRHGNKG VS ++P EDMP+  DGTPVDI+L+P+GVPSRMN+GQ+
Sbjct: 909  YITQKRKIQVGDKMAGRHGNKGTVSIVVPEEDMPYTPDGTPVDILLSPMGVPSRMNIGQV 968

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLG A   LG  + + + D   + D+                               
Sbjct: 969  LELHLGMAARNLGIHVATPVFDGAQDKDLW------------------------------ 998

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                           D   E          ++   G+SILYDG TGEPFD  V+VG +Y 
Sbjct: 999  ---------------DAVREA---------NMPSDGKSILYDGRTGEPFDTRVSVGVMYY 1034

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT
Sbjct: 1035 MKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILT 1094

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL + + +   +     
Sbjct: 1095 YKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQSLGLDMKVLDIDNQEIELR 1152


>gi|308180004|ref|YP_003924132.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           subsp. plantarum ST-III]
 gi|308045495|gb|ADN98038.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           subsp. plantarum ST-III]
          Length = 1204

 Score =  851 bits (2199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 586/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFAGKLSLEFVDYQLLEPKYTVEEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFNEELDK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+K++ +VRIDR RK+P+T  + ALG  S++ I+          
Sbjct: 162 GTTVIPNRGAWLELETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLM 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +  D  V   +      +  GE    +S + L +      K         
Sbjct: 222 LTLEKD-VHKNTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGR 280

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             V         L    +AE + + +TGE+  +   VID+  + ++     RD       
Sbjct: 281 YKVNKKLSMKTRLMDQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTY 340

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + ++ A + N +V           L + +V    D                         
Sbjct: 341 TPSDEAVVTNPMV-----------LQVVKVYSQNDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N +     +HI   DIIA I    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     KVT+ + YL+A EE+   IAQANS L++DGSF E+ V  R
Sbjct: 544 KVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPLNDDGSFVEDTVLAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +  P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 NKEENLETPIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G VE VDA  + +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++++ADGP+ + G+LALG+N LVAFM W+GYNFED+++
Sbjct: 717 RSNGGKNYNQRPIVKVGDHVDNDEVLADGPAMEGGELALGQNPLVAFMTWNGYNFEDAII 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 777 INERLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNLDEDGIIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 267/1108 (24%), Positives = 410/1108 (37%), Gaps = 168/1108 (15%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +  D  N     I       + E      + S+   I +L           ++      +
Sbjct: 175  LETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLMLTLEKDVHKNTDD 234

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +++L DIY  +RPG+  T   + S+    FFD  +YD + VGR K+N +L++ T   
Sbjct: 235  SRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGRYKVNKKLSMKTRLM 294

Query: 428  VRHIR----KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             + +       D   +I     + +          L     ++V     ++  +    + 
Sbjct: 295  DQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTYTPSDEAVVTNPMVL 354

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT----- 538
            + +K    +     V      N       +      + ++        L           
Sbjct: 355  QVVKVYSQNDPEKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGN 414

Query: 539  RRLSALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVS 584
            RR+ ++G+        G++R    V  R        V P     I P   S     G   
Sbjct: 415  RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQ 474

Query: 585  SLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIA 628
                  + N  G +    R                 V D   T+          E   I 
Sbjct: 475  LSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIG 534

Query: 629  QANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              NS  S  +   +       R          +KID++ A  +    IA +  P   NDD
Sbjct: 535  LINSLSSYAKVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPL--NDD 592

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             + V      + +   L           +          A+       +E  D+ R ++ 
Sbjct: 593  GSFVEDTVLARNKEENLETPIENVDYMDVSPKQV----VAVATACIPFLENDDSNRALMG 648

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +                    QR          PL+  G                  +  
Sbjct: 649  AN------------------MQRQAVPLLDPHAPLIGTGI-----------------EYK 673

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               +  +A +  H    E       R+  +D     +     +  R +  G     R I 
Sbjct: 674  AAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLDTYKL---MKFRRSNGGKNYNQRPIV 730

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             V +    ++D   ++  G  +  G++ +G                      E A+ + +
Sbjct: 731  KVGD----HVDNDEVLADGPAMEGGELALG-------QNPLVAFMTWNGYNFEDAIIINE 779

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              +R     S  + +     R      E          E   ++  DE  I+      + 
Sbjct: 780  RLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNL-DEDGIIRIGAEVKD 838

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   +  E  R           +V+     +        
Sbjct: 839  GDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGII 887

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      KI   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P 
Sbjct: 888  QDV------KIFTRENGDELSPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSIVVPE 941

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI 
Sbjct: 942  EDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHMATPVFDGAQDTDIW 1001

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                              EAI      A
Sbjct: 1002 --------------------------------------------------EAIRE----A 1007

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +D   +SI+YDG TGEPFD+ V VG ++ +KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1008 GVDSDAKSIVYDGRTGEPFDKRVAVGVMHYMKLSHMVDDKIHARSIGPYSLVTQQPLGGK 1067

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PES
Sbjct: 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPES 1127

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            F VLVKE+QALGL + + +S  K     
Sbjct: 1128 FRVLVKELQALGLDMKVLDSEDKEIELR 1155


>gi|300767813|ref|ZP_07077723.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
 gi|300494798|gb|EFK29956.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
          Length = 1204

 Score =  851 bits (2199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 586/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFAGKLSLEFVDYQLLEPKYTVEEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFNEELDK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+K++ +VRIDR RK+P+T  + ALG  S++ I+          
Sbjct: 162 GTTVIPNRGAWLELETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLM 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +  D  V   +      +  GE    +S + L +      K         
Sbjct: 222 LTLEKD-VHKNTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGR 280

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             V         L    +AE + + +TGE+  +   VID+  + ++     RD       
Sbjct: 281 YKVNKKLSMKTRLMDQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTY 340

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + ++ A + N +V           L + +V    D                         
Sbjct: 341 TPSDEAVVTNPMV-----------LQVVKVYSQNDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N +     +HI   DIIA I    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     KVT+ + YL+A EE+   IAQANS L++DGSF E+ V  R
Sbjct: 544 KVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPLNDDGSFVEDTVLAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +  P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 NKEENLETPIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G VE VDA  + +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++++ADGP+ + G+LALG+N LVAFM W+GYNFED+++
Sbjct: 717 RSNGGKNYNQRPIVKVGDHVDNDEVLADGPAMEGGELALGQNPLVAFMTWNGYNFEDAII 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 777 INERLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNLDEDGIIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 267/1108 (24%), Positives = 410/1108 (37%), Gaps = 168/1108 (15%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +  D  N     I       + E      + S+   I +L           ++      +
Sbjct: 175  LETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLMLTLEKDVHKNTDD 234

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +++L DIY  +RPG+  T   + S+    FFD  +YD + VGR K+N +L++ T   
Sbjct: 235  SRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGRYKVNKKLSMKTRLM 294

Query: 428  VRHIR----KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             + +       D   +I     + +          L     ++V     ++  +    + 
Sbjct: 295  DQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTYTPSDEAVVTNPMVL 354

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT----- 538
            + +K    +     V      N       +      + ++        L           
Sbjct: 355  QVVKVYSQNDPEKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGN 414

Query: 539  RRLSALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVS 584
            RR+ ++G+        G++R    V  R        V P     I P   S     G   
Sbjct: 415  RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQ 474

Query: 585  SLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIA 628
                  + N  G +    R                 V D   T+          E   I 
Sbjct: 475  LSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIG 534

Query: 629  QANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              NS  S  +   +       R          +KID++ A  +    IA +  P   NDD
Sbjct: 535  LINSLSSYAKVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPL--NDD 592

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             + V      + +   L           +          A+       +E  D+ R ++ 
Sbjct: 593  GSFVEDTVLARNKEENLETPIENVDYMDVSPKQV----VAVATACIPFLENDDSNRALMG 648

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +                    QR          PL+  G                  +  
Sbjct: 649  AN------------------MQRQAVPLLDPHAPLIGTGI-----------------EYK 673

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               +  +A +  H    E       R+  +D     +     +  R +  G     R I 
Sbjct: 674  AAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLDTYKL---MKFRRSNGGKNYNQRPIV 730

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             V +    ++D   ++  G  +  G++ +G                      E A+ + +
Sbjct: 731  KVGD----HVDNDEVLADGPAMEGGELALG-------QNPLVAFMTWNGYNFEDAIIINE 779

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              +R     S  + +     R      E          E   ++  DE  I+      + 
Sbjct: 780  RLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNL-DEDGIIRIGAEVKD 838

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   +  E  R           +V+     +        
Sbjct: 839  GDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGII 887

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      KI   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P 
Sbjct: 888  QDV------KIFTRENGDELSPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSIVVPE 941

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI 
Sbjct: 942  EDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHMATPVFDGAQDTDIW 1001

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                              EAI      A
Sbjct: 1002 --------------------------------------------------EAIRE----A 1007

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +D   +SI+YDG TGEPFD+ V VG ++ +KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1008 GVDSDAKSIVYDGRTGEPFDKRVAVGVMHYMKLSHMVDDKIHARSIGPYSLVTQQPLGGK 1067

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PES
Sbjct: 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPES 1127

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            F VLVKE+QALGL + + +S  K     
Sbjct: 1128 FRVLVKELQALGLDMKVLDSEDKEIELR 1155


>gi|15923532|ref|NP_371066.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|255005336|ref|ZP_05143937.2| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|41018107|sp|Q932F8|RPOB_STAAM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|14246310|dbj|BAB56704.1| RNA polymerase beta chain [Staphylococcus aureus subsp. aureus
           Mu50]
          Length = 1183

 Score =  851 bits (2199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 598/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +T+ RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTYKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 250/1158 (21%), Positives = 427/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            +L+L      + +          E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ Y                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTY---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 777

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 778  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 836

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 837  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 890

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 891  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 951  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1003

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1004 ------------------IEEAGMARDG-----------------------------KTV 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1076

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1077 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1136

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1137 SLGLDVKVMDEQDNEIEM 1154


>gi|329729422|gb|EGG65825.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus
           epidermidis VCU144]
          Length = 1183

 Score =  851 bits (2199), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 600/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYVRISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDSEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI ++ G V+D + L+EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVVDEGTVLDRRKLDEIMDVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGSVIDEPVEIQSIKVYV----------------------PNDEEGRTTTV 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DI+A +    +L NG G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI A   G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITANHRGRVEHVESNEILVRRLVEENGTEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V +GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 162/440 (36%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1148 HDNEIE-MADVDDEDAAERK 1166


>gi|329727935|gb|EGG64384.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus 21172]
          Length = 1183

 Score =  851 bits (2198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +T  RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTDKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 248/1145 (21%), Positives = 418/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +   D      L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFMDQANPLAELTDKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|289551658|ref|YP_003472562.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315659117|ref|ZP_07911982.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           lugdunensis M23590]
 gi|289181189|gb|ADC88434.1| DNA-directed RNA polymerase beta subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315495841|gb|EFU84171.1| DNA-directed RNA polymerase subunit beta [Staphylococcus
           lugdunensis M23590]
          Length = 1184

 Score =  851 bits (2198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/964 (45%), Positives = 599/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SYD FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RL++         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLVI---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  ++ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVELLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI  E G V+D + L+EI              
Sbjct: 273 YKANKKLHLKHRLFNQKLAEPIVNSETGEIVAEEGTVLDRRKLDEIMDVLET-------- 324

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + N+  +     V D+  + +   + +                        D +    + 
Sbjct: 325 NANSEVFELEGTVIDEPVEIQSIKVYV----------------------PNDEEGRTTTI 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G              +V+ I   DII+ +    +L  G G  DDID+LGNRR+RSVGE+
Sbjct: 363 IGNAL--------PDSEVKCITPADIISSMSYFFNLLAGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDIDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  +E +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRLIEENGKEYEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V +GD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 161/440 (36%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 782  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 842  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 901

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 902  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 961

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 962  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST------------------ 1003

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 1004 -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1027

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1028 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1087

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1088 AAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1148 HDNEIE-MADVEDEDTTERK 1166


>gi|299783535|gb|ADJ41533.1| DNA-directed RNA polymerase [Lactobacillus fermentum CECT 5716]
          Length = 1190

 Score =  851 bits (2198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/966 (44%), Positives = 596/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ F+          ++GL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYSRIKEVLDLPNLIEIQTDSYNWFM----------DKGLREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V +    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGKLSLEFVDYQLLEPKYTVAEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY---PKI 236
               IP++G W++ E D+K I +VRIDR RK+P+T  + ALG  S+ EI          +
Sbjct: 159 GANFIPNRGAWLEYETDAKGISYVRIDRTRKLPITELVRALGFGSDDEIWDMLGSESESL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D         D  V   +      +  GE    +S + L +      K   +  
Sbjct: 219 NATIEKDLHK---EPEDSRVEESLKDIYERLRPGEPKTADSARSLLTTRFFDPKRYDMAP 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L GL +AE + + ETGEI  + GDVI ++ L+E+        P+L
Sbjct: 276 VGRYKTNKKLQMKYRLLGLTLAETLADPETGEIIAKDGDVITKEVLKELE-------PVL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             D      Y              +A++     +           + +  +   D ++  
Sbjct: 329 EQDDFKMITY----------TPSDEAVVTAPVQL-----------QKIMVYSKNDPER-- 365

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                  K+ +  N     D++HI+  DI+A I   ++L+ G GT DDID+LGNRR+RSV
Sbjct: 366 -------KVPVVSNGHISLDLKHIQPADILASINYFLNLQEGIGTTDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  DI++V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLARMERVVRERMSIQDINTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 479 QTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVNAYGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L+EDGSF  + +
Sbjct: 539 SYARVNAYGFIETPYRRVSWADHKVTDRIDYLTADEEDNFIIAQANTPLNEDGSFVHDEI 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 599 MCRDKEDYIETAPENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLIN 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP +GTG+E   A  SG A++AK +G VE VDA  + +R  +G LD        Y+LM
Sbjct: 659 PHAPLIGTGIEYKAAHDSGVALIAKNSGTVEYVDAREVRVRQEDGTLD-------TYKLM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNVSE+  KN+DE G+I VG
Sbjct: 772 AIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSEDARKNLDESGVIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVF 891

Query: 946 NRHGID 951
            R   D
Sbjct: 892 TRENGD 897



 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 176/530 (33%), Positives = 254/530 (47%), Gaps = 67/530 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  
Sbjct: 699  RQEDGTLDTYKLMKFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPS-MEQGELALGQNP 757

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D        V   V        +  +  E  +  E    E+    +D
Sbjct: 758  LIAFMTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSED 817

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  +      I  G     G     K T      +S   R     F  +  +V+
Sbjct: 818  ARKNLDESGV------IRVGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVR 871

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GD++ PGV ++V+V++A KR IQ GDKM+G
Sbjct: 872  DTSLRVPHGGGGIIQDV------KVFTRENGDELAPGVNKMVRVYIAQKRKIQVGDKMSG 925

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 926  RHGNKGTVSIVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVIELHLGMAARELGIHI 985

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D                                             V+D
Sbjct: 986  ATPVFDGANDQD---------------------------------------------VWD 1000

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E         A L   G++ILYDG TGEPF++ V VG ++ LKL HMV DK++ARST
Sbjct: 1001 AVKE---------AGLPSDGKTILYDGRTGEPFEQRVAVGVMHYLKLAHMVDDKIHARST 1051

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR   Y++I
Sbjct: 1052 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVNTYQAI 1111

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G+   + G PESF VLVKE+Q+LGL + + + + +         D   
Sbjct: 1112 IDGDQIPKPGVPESFRVLVKELQSLGLDMKVLDDKHEEIQLKSMDEDVAD 1161


>gi|41017744|sp|Q8GCR4|RPOB2_ENTFC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|27372995|gb|AAO00730.1| DNA-dependent RNA polymerase subunit beta [Enterococcus faecium]
          Length = 1208

 Score =  851 bits (2198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R RK F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERKSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPESAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDASEIRVRRDNGALDK-------YAVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 237/504 (47%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTILYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + + +       
Sbjct: 1131 VKELQSLGLDMRVLDIKDSEIELR 1154


>gi|296116736|ref|ZP_06835345.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter hansenii
            ATCC 23769]
 gi|295976720|gb|EFG83489.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter hansenii
            ATCC 23769]
          Length = 606

 Score =  851 bits (2198), Expect = 0.0,   Method: Composition-based stats.
 Identities = 385/604 (63%), Positives = 485/604 (80%), Gaps = 1/604 (0%)

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            + K+ RSNQ+TC+NQRPLV+VGD+V   +IIADGPST+LG+LALGRN+LVAFMPW+GYNF
Sbjct: 1    MRKYMRSNQSTCINQRPLVRVGDQVSAGEIIADGPSTELGELALGRNVLVAFMPWNGYNF 60

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            EDS+LISER+  +DVFTSIHIEEFEVMARDTKLG EEITRDIPNV EE L+N+DE GI+ 
Sbjct: 61   EDSILISERIARDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALRNLDEAGIVY 120

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            VGAEVNPGDIL+GK+TPKGESPMTPEEKLLRAIFGEKA DVRDTSL++P G SGT+VDVR
Sbjct: 121  VGAEVNPGDILIGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLKLPPGTSGTIVDVR 180

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F+R G+DK+ER++++ER +IE LA+D+DDE+ I +R+ Y+RL E L GQ A +G KG +
Sbjct: 181  VFSRRGVDKDERAMAIERAEIERLAKDRDDERAIQERSFYNRLREHLIGQTAGAGFKGIR 240

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
              T ++ +++SE+PR  W    V  + V   +E L+ +++T+ S ++ RF NK+EK+Q G
Sbjct: 241  SGTPITDEVLSEHPRGAWRNVTVTSDAVMAELEVLRREFDTAVSRIQARFDNKVEKLQRG 300

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++PPGV+++VKVFVA+KR +Q GDKMAGRHGNKG+VSR++P EDMPFL+DGTPVD++LN
Sbjct: 301  DELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRVVPVEDMPFLEDGTPVDLLLN 360

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY-KANGDISPLRSFLEKVIGTGSHT 1182
            PLGVPSRMNVGQI ETHLGWAC  +G+ I  L++ Y K       L   L  V G  +  
Sbjct: 361  PLGVPSRMNVGQILETHLGWACANIGRGIGQLVDTYHKTGEKRQELLDELRSVYGEDAFA 420

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              I+D  D  +L ++   + GVP++TPVFDGA    I +ML  A LD+SGQS L DG TG
Sbjct: 421  ANIADMTDAQLLELSNNLRKGVPIATPVFDGASIPDIEAMLEKAGLDKSGQSQLIDGRTG 480

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF+R  TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 481  EPFERKTTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 540

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAAY LQEMLT+KSDDV GRT+VYE+IV   D FE G PESFNVL+KE+++LGL++D
Sbjct: 541  EAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVREQDDFEAGIPESFNVLIKELKSLGLNVD 600

Query: 1363 LENS 1366
            LE S
Sbjct: 601  LEQS 604


>gi|116493170|ref|YP_804905.1| DNA-directed RNA polymerase subunit beta [Pediococcus pentosaceus
           ATCC 25745]
 gi|122265366|sp|Q03EA9|RPOB_PEDPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116103320|gb|ABJ68463.1| DNA-directed RNA polymerase subunit beta [Pediococcus pentosaceus
           ATCC 25745]
          Length = 1202

 Score =  850 bits (2197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 413/963 (42%), Positives = 588/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQSDSYQWFL----------DEGLREMFN 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ VD+    +  Y+ PL +TLRL            
Sbjct: 51  DIMPIEDFAGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++++ D  +   + + ++
Sbjct: 102 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNLDTDK---NNRKIW 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  S+E I+  F       
Sbjct: 159 GTTVIPNRGAWLEYETDAKEISYVRIDRTRKIPMTELVRALGFGSDEEIIDIFGGSDSLD 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      +  D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 FTLDKD-VHKNPEDSRVAESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE + + +TGE+  + G+++++  ++++     R    +   
Sbjct: 278 YKVNKKLSLKTRLLGQTLAETLADPDTGEVIAQKGEMVNKDVMKKLAVFLDRPDFKMVTY 337

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             +  A +   +            + + +V  P D                         
Sbjct: 338 QPSEEAVVTEPMT-----------IQVIKVQDPNDP------------------------ 362

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +NM  N +    ++HI   DIIA +     L++G G+ DDID+LGNRR+RSVGE+
Sbjct: 363 --ERTLNMIGNGNIDAKLKHITPADIIASMNYFFLLQDGIGSTDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+A  EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDAETVTPQQLINIRPVVAATKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L S+ 
Sbjct: 481 PLGELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLASYG 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++N YGFIETPYR+V   D KVT+ + YL+A EE+   IAQANS L++DGSF +++V  R
Sbjct: 541 KINRYGFIETPYRRVSWEDHKVTDRIDYLTADEEDQFVIAQANSPLNDDGSFADDVVMAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I    E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   +
Sbjct: 601 HESDNIETSIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVDPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ + AG+VE VDA  + +R  +G LD        Y+LMKF+
Sbjct: 661 PLIGTGIEYKAAHDSGVALLCQHAGVVEYVDAREVRVRRDDGALD-------TYKLMKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+V D+V  ++++ADGPS + G+LALG+N L+AFM W GYNFED++ 
Sbjct: 714 RSNGGKNYNQRPIVRVNDKVDADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAIA 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPN+ E+ L+N+D+ GI+ VGAEV
Sbjct: 774 INERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNIGEDALRNLDQDGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 834 EDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 NGD 896



 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 260/1104 (23%), Positives = 411/1104 (37%), Gaps = 182/1104 (16%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
             I       + E      F S+   I I       +    ++     ++    ++L DIY
Sbjct: 183  RIDRTRKIPMTELVRALGFGSDEEIIDIFGGSDSLDFTLDKDVHKNPEDSRVAESLKDIY 242

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP----DDVRHIRKE 434
              +RPG+  T   + S+    FFD  +YD++ VGR K+N +L+L T          +   
Sbjct: 243  ERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGRYKVNKKLSLKTRLLGQTLAETLADP 302

Query: 435  DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            D   +I    ++ N          L     + V      +  +      + IK +  +  
Sbjct: 303  DTGEVIAQKGEMVNKDVMKKLAVFLDRPDFKMVTYQPSEEAVVTEPMTIQVIKVQDPNDP 362

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE---EHVNSLSRITHT--RRLSALGQ--- 546
              ++      N    +  +      + ++      + + S   I H   RR+ ++G+   
Sbjct: 363  ERTLNMIGNGNIDAKLKHITPADIIASMNYFFLLQDGIGSTDDIDHLGNRRIRSVGELLQ 422

Query: 547  ----GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
                 G++R    V  R        V P     I P   +     G         + N  
Sbjct: 423  NQFRIGLSRMERVVRERMSIQDAETVTPQQLINIRPVVAATKEFFGSSQLSQFMDQTNPL 482

Query: 596  GFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                 V D   T+          E   I   N  +S  + 
Sbjct: 483  GELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLASYGKI 542

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R    E     ++ID++ A  +    IA +  P   NDD +         
Sbjct: 543  NRYGFIETPYRRVSWEDHKVTDRIDYLTADEEDQFVIAQANSPL--NDDGSFADD----- 595

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKS-SG---AAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
               V + + E+  + T +E+V     S     A+       +E  D+ R ++ +      
Sbjct: 596  ---VVMARHESDNIETSIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGAN----- 647

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                          QR          PL+  G                  +     +  V
Sbjct: 648  -------------MQRQAVPLVDPHSPLIGTGI-----------------EYKAAHDSGV 677

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +        + +   E  V  D                   G  +  + +      G 
Sbjct: 678  ALLC-QHAGVVEYVDAREVRVRRD------------------DGALDTYKLMKFRRSNGG 718

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN ++  I+ V  +V+  ++L    +   +  +   +  L A    +  +  D       
Sbjct: 719  KNYNQRPIVRVNDKVDADEVLADGPS-MEQGELALGQNPLIAFMTWQGYNFEDAIAIN-- 775

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 V D    + H  +    +   +    E    +    +D    LD++   R+    
Sbjct: 776  --ERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNIGEDALRNLDQDGIVRV---- 829

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 830  -GAEVEDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV- 887

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++A KR +Q GDKMAGRHGNKG VS ++P EDMP
Sbjct: 888  -----KIFTRENGDELSPGVNMMVRVYIAQKRKLQVGDKMAGRHGNKGTVSVVIPQEDMP 942

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            ++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI    +
Sbjct: 943  YMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARNLGIHMTTPVFDGAQDKDIWEAVA 1002

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                         +    S+L       
Sbjct: 1003 EAGM-----------------------------------------DSDAKSVL------Y 1015

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G++       GEPF++ V VG ++ +KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1016 DGRT-------GEPFEQRVAVGVMHYMKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFG 1068

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G      G PESF VL
Sbjct: 1069 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPRPGVPESFRVL 1128

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+QALGL + +     +     
Sbjct: 1129 VKELQALGLDMKVLGGDDQEVELR 1152


>gi|314937431|ref|ZP_07844766.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133a04]
 gi|314942599|ref|ZP_07849431.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133C]
 gi|314952440|ref|ZP_07855444.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133A]
 gi|314993625|ref|ZP_07858976.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133B]
 gi|314998235|ref|ZP_07863108.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133a01]
 gi|313587799|gb|EFR66644.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133a01]
 gi|313591888|gb|EFR70733.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133B]
 gi|313595422|gb|EFR74267.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133A]
 gi|313598650|gb|EFR77495.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133C]
 gi|313643165|gb|EFS07745.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0133a04]
          Length = 1208

 Score =  850 bits (2197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1131 VKELQSLGLDMRVLDIEETEIELR 1154


>gi|256618015|ref|ZP_05474861.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           ATCC 4200]
 gi|256597542|gb|EEU16718.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           ATCC 4200]
          Length = 1207

 Score =  850 bits (2197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEAGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  473 bits (1217), Expect = e-130,   Method: Composition-based stats.
 Identities = 170/499 (34%), Positives = 233/499 (46%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +      M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEAGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+          
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGATDEDVWETVREAGMA 1009

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                +                                                   G++ 
Sbjct: 1010 SDAKTVL-----------------------------------------------HDGRT- 1021

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1022 ------GEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|261209106|ref|ZP_05923509.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium TC
           6]
 gi|260076933|gb|EEW64657.1| DNA directed RNA polymerase subunit beta [Enterococcus faecium TC
           6]
          Length = 1205

 Score =  850 bits (2197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +T+ RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTYKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|326802951|ref|YP_004320769.1| DNA-directed RNA polymerase, beta subunit [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326650257|gb|AEA00440.1| DNA-directed RNA polymerase, beta subunit [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 1200

 Score =  850 bits (2197), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/988 (43%), Positives = 600/988 (60%), Gaps = 87/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  RVR+ + +  E++++P+LIE+Q  SY   L          ++G++  F 
Sbjct: 1   MAGHNVEYGKHRVRRSYSRINEVLELPNLIEIQTESYRWLL----------DKGIREMFS 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI    G   LEFV Y F  PK+D+ +   +D  YA P+ + LRLI           
Sbjct: 51  DISPIEDHGGKLALEFVDYSFQEPKYDMSESRQQDTNYAAPMYVKLRLI---------NS 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK+Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++    +   +GKL Y
Sbjct: 102 ETGEIKDQEVFFGDFPLMTDSGTFIINGSERVIVSQLVRSPGVYYN---DKVDKNGKLSY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+ +T  + ALG  S++ I   F      S
Sbjct: 159 GATVIPNRGAWLEMETDAKDISYVRIDRTRKLQMTVLMRALGFGSDDQIRELFGDSETLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    ES + L +      +   +  +G 
Sbjct: 219 LTLEKD-VHKNPSDSRTEEALKDIYERLRPGEPKTAESSRNLLNTRFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG V   + L++I             D
Sbjct: 278 YKINKKLDLKSRLYKQTLAENLVDNETGEIVLEAGTVFTREVLDDI------------SD 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N   +      D         + + +++ P D                         
Sbjct: 326 KLDNGLGLVTVYPNDDAVITDPVDIQLIKIVAPKDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +++  N     D + +   D++  +   ++L  G GT DDID+LGNRR+RSVGE+
Sbjct: 362 --ERVVHVIGNAMQNSDYKSLTVADVLTAMNYFLNLYEGLGTTDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  DID+V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQLRIGLSRMERVVRERMSIQDIDTVTPQQLINIRPVVASIREFFGSSQLSQFMDQNN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A
Sbjct: 480 PLSELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++N +GFIETPYR+V     KVT+ + YL+A EE+   IAQ N+ L+EDGSF  + +  R
Sbjct: 540 KINDFGFIETPYRRVDWNTHKVTDKIDYLTADEEDRFVIAQGNTPLNEDGSFATDTIMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E I V  E++D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 600 KIEENIEVSPEEVDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLLNPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SGAA+  KRAG+V+ VDA  I +R+ EG LD        Y L+KF 
Sbjct: 660 PLVGTGMEYKAAHDSGAAVTCKRAGVVDYVDAREIRVRTEEGALDK-------YELVKFY 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN ++C NQ PLV+ GD+V +++I+A+GPS + G+LALG+N ++AFM W GYN+ED+++
Sbjct: 713 RSNASSCYNQTPLVRKGDQVDKDEILANGPSMEGGELALGQNPIIAFMTWDGYNYEDAVV 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHI+E E  ARDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 LSERLVKEDVYTSIHIDELESEARDTKLGPEEITREIPNVGEDALRNLDENGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++PEE LL AIFGEKA +VRDTSLRVP G  G V DV++F+R 
Sbjct: 833 TDGDILVGKVTPKGVTELSPEEHLLHAIFGEKAREVRDTSLRVPHGGGGIVNDVKVFHRE 892

Query: 949 GIDKNE-------RSISVEREQIELLAR 969
             D+ +       R   +++ +I++  +
Sbjct: 893 NGDELKPGVSMMVRVYIIQKRKIQVGDK 920



 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 169/437 (38%), Positives = 219/437 (50%), Gaps = 70/437 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +   S+  +++E  ARD       + R I                I  G     G   
Sbjct: 779  KEDVYTSIHIDELESEARDTKLGPEEITREIPNVGEDALRNLDENGIIRIGAEVTDGDIL 838

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      +S         F  +  +V+     +        + +      K+   +
Sbjct: 839  VGKVTPKGVTELSPEEHLLHAIFGEKAREVRDTSLRVPHGGGGIVNDV------KVFHRE 892

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++ PGV  +V+V++  KR IQ GDKMAGRHGNKG+VS +LP EDMP+L DGTPVDI 
Sbjct: 893  NGDELKPGVSMMVRVYIIQKRKIQVGDKMAGRHGNKGVVSIVLPEEDMPYLPDGTPVDIC 952

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + DI                
Sbjct: 953  LNPLGVPSRMNIGQVLELHLGMAARNLGIHVATPVFDGAQDEDIWETVKEAGMA------ 1006

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                               E   ++L             YDG T
Sbjct: 1007 -----------------------------------EDAKTVL-------------YDGRT 1018

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEPFD  V+VG +Y LKL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1019 GEPFDNRVSVGVMYYLKLSHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1078

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQE+LT KSDDVVGR + YE+IV G+   +   PESF VLVKE+Q+LGL I
Sbjct: 1079 LEAYGAAYTLQEILTYKSDDVVGRVQTYEAIVKGDPIPKPSVPESFRVLVKELQSLGLDI 1138

Query: 1362 DLENSRTKNSAKMEEIP 1378
             + +   K     +E P
Sbjct: 1139 QVLDESDKELDLRDEDP 1155


>gi|282924456|ref|ZP_06332128.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9765]
 gi|282592867|gb|EFB97871.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           A9765]
          Length = 1183

 Score =  850 bits (2196), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/964 (45%), Positives = 596/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ     N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMGQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH R LSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRHLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 246/1146 (21%), Positives = 421/1146 (36%), Gaps = 106/1146 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          R  +  
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPK--------RYDLAS 269

Query: 419  RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                 T   +    +     + + +V+   G+  +++   L  R++  + ++L++     
Sbjct: 270  VGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSE 329

Query: 479  LLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +  +  S+ +  +    I   +P D        + +   F  S++  +       S    
Sbjct: 330  VFELHGSVIDEPVEIQSIKVYVPNDDEGRT--TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD-EDGSFTEELVFCRCAGEEILV 656
            I    R V          +  + +       QAN   +         L       E   +
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFM-GQANPLAELTHKRHLSALGPGGLTRERAQM 500

Query: 657  PREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                + +        +       I  + +  S   +            +  +   +   +
Sbjct: 501  EVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQI 560

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            + + A    + +VA+    +             +  +        +    K    + +  
Sbjct: 561  DYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPK 615

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                        +  +D        ++   A+      A     G     +      + +
Sbjct: 616  QVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITA 675

Query: 836  EDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +      H+E  E++ R           G  +                ++  I+ VG  V
Sbjct: 676  KHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVV 735

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
               +IL    +      M     ++         +  D  +     +S  +V   ++   
Sbjct: 736  EYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSI 789

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
             I++ E      +   E + RD  +      +N+  R   +  G     G     K T  
Sbjct: 790  HIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPK 848

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MP 1067
                ++   R     F  +  +V+     +                 K+   + GDD + 
Sbjct: 849  GVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLS 902

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGV
Sbjct: 903  PGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGV 962

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + S + D   + D+                      
Sbjct: 963  PSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------- 1003

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  +  A   + G                             +++LYDG TGEPFD 
Sbjct: 1004 ------IEEAGMARDG-----------------------------KTVLYDGRTGEPFDN 1028

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1029 RISVGVMYMLKLVHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1088

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + +
Sbjct: 1089 AYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQ 1148

Query: 1368 TKNSAK 1373
                  
Sbjct: 1149 DNEIEM 1154


>gi|28377825|ref|NP_784717.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           WCFS1]
 gi|41017720|sp|Q88XZ3|RPOB_LACPL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|28270658|emb|CAD63564.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus plantarum
           WCFS1]
          Length = 1204

 Score =  850 bits (2196), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 585/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFAGKLSLEFVDYQLLEPKYTVEEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFNEELDK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+K++ +VRIDR RK+P+T  + ALG  S++ I+          
Sbjct: 162 GTTVIPNRGAWLELETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLM 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +  D  V   +      +  GE    +S + L +      K         
Sbjct: 222 LTLEKD-VHKNTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGR 280

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             V         L    +AE + + +TGE+  +   VID+  + ++     RD       
Sbjct: 281 YKVNKKLSMKTRLMDQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTY 340

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + ++ A + N +V           L + +V    D                         
Sbjct: 341 TPSDEAVVTNPMV-----------LQVVKVYSQNDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N +     +HI   DIIA I    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN  GFIETPYR+V     KVT+ + YL+A EE+   IAQANS L++DGSF E+ V  R
Sbjct: 544 KVNRSGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPLNDDGSFVEDTVLAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +  P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 NKEENLETPIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G VE VDA  + +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++++ADGP+ + G+LALG+N LVAFM W+GYNFED+++
Sbjct: 717 RSNGGKNYNQRPIVKVGDHVDNDEVLADGPAMEGGELALGQNPLVAFMTWNGYNFEDAII 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 777 INERLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNLDEDGIIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 267/1108 (24%), Positives = 409/1108 (36%), Gaps = 168/1108 (15%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +  D  N     I       + E      + S+   I +L           ++      +
Sbjct: 175  LETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDIIDMLGETDSLMLTLEKDVHKNTDD 234

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +++L DIY  +RPG+  T   + S+    FFD  +YD + VGR K+N +L++ T   
Sbjct: 235  SRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGRYKVNKKLSMKTRLM 294

Query: 428  VRHIR----KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             + +       D   +I     + +          L     ++V     ++  +    + 
Sbjct: 295  DQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTYTPSDEAVVTNPMVL 354

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT----- 538
            + +K    +     V      N       +      + ++        L           
Sbjct: 355  QVVKVYSQNDPEKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGN 414

Query: 539  RRLSALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVS 584
            RR+ ++G+        G++R    V  R        V P     I P   S     G   
Sbjct: 415  RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQ 474

Query: 585  SLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIA 628
                  + N  G +    R                 V D   T+          E   I 
Sbjct: 475  LSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIG 534

Query: 629  QANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              NS  S  +           R          +KID++ A  +    IA +  P   NDD
Sbjct: 535  LINSLSSYAKVNRSGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPL--NDD 592

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             + V      + +   L           +          A+       +E  D+ R ++ 
Sbjct: 593  GSFVEDTVLARNKEENLETPIENVDYMDVSPKQV----VAVATACIPFLENDDSNRALMG 648

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +                    QR          PL+  G                  +  
Sbjct: 649  AN------------------MQRQAVPLLDPHAPLIGTGI-----------------EYK 673

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               +  +A +  H    E       R+  +D     +     +  R +  G     R I 
Sbjct: 674  AAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLDTYKL---MKFRRSNGGKNYNQRPIV 730

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             V +    ++D   ++  G  +  G++ +G                      E A+ + +
Sbjct: 731  KVGD----HVDNDEVLADGPAMEGGELALG-------QNPLVAFMTWNGYNFEDAIIINE 779

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              +R     S  + +     R      E          E   ++  DE  I+      + 
Sbjct: 780  RLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNL-DEDGIIRIGAEVKD 838

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   +  E  R           +V+     +        
Sbjct: 839  GDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGII 887

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      KI   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P 
Sbjct: 888  QDV------KIFTRENGDELSPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSIVVPE 941

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI 
Sbjct: 942  EDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHMATPVFDGAQDTDIW 1001

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                              EAI      A
Sbjct: 1002 --------------------------------------------------EAIRE----A 1007

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +D   +SI+YDG TGEPFD+ V VG ++ +KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1008 GVDSDAKSIVYDGRTGEPFDKRVAVGVMHYMKLSHMVDDKIHARSIGPYSLVTQQPLGGK 1067

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PES
Sbjct: 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPES 1127

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            F VLVKE+QALGL + + +S  K     
Sbjct: 1128 FRVLVKELQALGLDMKVLDSEDKEIELR 1155


>gi|227517171|ref|ZP_03947220.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           TX0104]
 gi|257083106|ref|ZP_05577467.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           Fly1]
 gi|257417341|ref|ZP_05594335.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           AR01/DG]
 gi|227075394|gb|EEI13357.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           TX0104]
 gi|256991136|gb|EEU78438.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           Fly1]
 gi|257159169|gb|EEU89129.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           ARO1/DG]
          Length = 1207

 Score =  850 bits (2195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSVLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|270291141|ref|ZP_06197364.1| DNA-directed RNA polymerase, beta subunit [Pediococcus acidilactici
           7_4]
 gi|270280537|gb|EFA26372.1| DNA-directed RNA polymerase, beta subunit [Pediococcus acidilactici
           7_4]
          Length = 1202

 Score =  850 bits (2195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 591/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFN 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ VD+    +  Y+ PL +TLRL            
Sbjct: 54  DIMPIEDFAGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++++ D  +   + + ++
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNLDVDK---NNRNIW 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G  ++ E D+K++ +VRIDR RK+P+T  + ALG  S+E I+  F       
Sbjct: 162 GATVIPNRGARLEYETDAKEVSYVRIDRTRKIPMTELVRALGFGSDEEIIDIFGGSDSLD 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      +  D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 FTLDKD-VHKNPEDSRVAESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE + + +TGE+  + GDV+D+  ++++        P L   
Sbjct: 281 YKVNKKLSLKTRLLGQTLAETLADPDTGEVLAQKGDVVDKDVMKKLA-------PYLDRQ 333

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +    D+    +   + + ++  P D                   + +L  
Sbjct: 334 DFKMVTYQPS----DEAVVPEPMTIQVIKIQDPNDP------------------ERELKM 371

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G   ++++L        +HI   DIIA I     L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 372 IGNGNIDLKL--------KHITPADIIASINYFFLLQQGIGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+A  EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLARMERVVRERMSIQDAETVTPQQLINIRPVVAATKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L S+ 
Sbjct: 484 PLGELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLASYG 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++N YGFIETPYR+V   D KVT+ + YL+A EE+   IAQANS L++DGSF +++V  R
Sbjct: 544 KINRYGFIETPYRRVSWKDHKVTDRIDYLTADEEDQFVIAQANSPLNDDGSFVDDVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I    E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 HESDNIETSIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G+VE VDA  I +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGVALLCQHPGVVEYVDAREIRVRRDDGALD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+V D+V  +D++ADGPS +LG+LALG+N L+AFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQRPIVRVNDKVDADDVLADGPSMELGELALGQNPLIAFMTWQGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ L+N+D+ GI+ +GAEV
Sbjct: 777 INERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALRNLDQDGIVRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 837 QDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  460 bits (1183), Expect = e-127,   Method: Composition-based stats.
 Identities = 168/525 (32%), Positives = 242/525 (46%), Gaps = 73/525 (13%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  + +      G KN ++  I+ V  +V+  D+L    +      +   +  
Sbjct: 701  RRDDGALDTYKLMKFRRSNGGKNYNQRPIVRVNDKVDADDVLADGPS-MELGELALGQNP 759

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLAR 969
            L A    +  +  D            V D    + H  +    +   +    E    +  
Sbjct: 760  LIAFMTWQGYNFEDAIAIN----ERLVRDDVYTSIHIEEYESEARDTKLGPEEMTREIPN 815

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +D    LD++   R+     G     G     K T      +S   R     F  +  
Sbjct: 816  VGEDALRNLDQDGIVRI-----GAEVQDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR 870

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V+     +          +      KI   + GD++ PGV  +V+V++A KR +Q GDK
Sbjct: 871  EVRDTSLRVPHGGGGIVQDV------KIFTRENGDELSPGVNMMVRVYIAQKRKLQVGDK 924

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG
Sbjct: 925  MAGRHGNKGTVSVVIPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARNLG 984

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + + + D   + DI    +                                       
Sbjct: 985  IHMTTPVFDGARDEDIWEAVAEAGM----------------------------------- 1009

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                  +    S+L        G++       GEPF++ V VG ++ +KL HMV DK++A
Sbjct: 1010 ------DSDAKSVL------YDGRT-------GEPFEQRVAVGVMHYMKLAHMVDDKIHA 1050

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD+VGR + Y
Sbjct: 1051 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDIVGRVKTY 1110

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            E+IV G      G PESF VLVKE+QALGL + +     +     
Sbjct: 1111 EAIVKGESIPRPGVPESFRVLVKELQALGLDMKVLGEDKQEVELR 1155


>gi|29377682|ref|NP_816836.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           V583]
 gi|227555177|ref|ZP_03985224.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           HH22]
 gi|229547349|ref|ZP_04436074.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           TX1322]
 gi|229547924|ref|ZP_04436649.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           ATCC 29200]
 gi|255970583|ref|ZP_05421169.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T1]
 gi|255974167|ref|ZP_05424753.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T2]
 gi|256760947|ref|ZP_05501527.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T3]
 gi|256854893|ref|ZP_05560257.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T8]
 gi|256958498|ref|ZP_05562669.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           DS5]
 gi|256963053|ref|ZP_05567224.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           HIP11704]
 gi|257078189|ref|ZP_05572550.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           JH1]
 gi|257080348|ref|ZP_05574709.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           E1Sol]
 gi|257088388|ref|ZP_05582749.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis D6]
 gi|257091457|ref|ZP_05585818.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           CH188]
 gi|257418061|ref|ZP_05595055.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           T11]
 gi|257420330|ref|ZP_05597320.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           X98]
 gi|307267872|ref|ZP_07549263.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX4248]
 gi|307273722|ref|ZP_07554949.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0855]
 gi|307276540|ref|ZP_07557658.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX2134]
 gi|307284751|ref|ZP_07564907.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0860]
 gi|307288302|ref|ZP_07568298.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0109]
 gi|307292252|ref|ZP_07572115.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0411]
 gi|312899231|ref|ZP_07758568.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0470]
 gi|312905536|ref|ZP_07764650.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0635]
 gi|312953784|ref|ZP_07772613.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0102]
 gi|41017700|sp|Q82Z40|RPOB_ENTFA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|29345150|gb|AAO82906.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           V583]
 gi|227175695|gb|EEI56667.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           HH22]
 gi|229306945|gb|EEN72941.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           ATCC 29200]
 gi|229307498|gb|EEN73485.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           TX1322]
 gi|255961601|gb|EET94077.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T1]
 gi|255967039|gb|EET97661.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T2]
 gi|256682198|gb|EEU21893.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T3]
 gi|256710453|gb|EEU25497.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis T8]
 gi|256948994|gb|EEU65626.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           DS5]
 gi|256953549|gb|EEU70181.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           HIP11704]
 gi|256986219|gb|EEU73521.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           JH1]
 gi|256988378|gb|EEU75680.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           E1Sol]
 gi|256996418|gb|EEU83720.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis D6]
 gi|257000269|gb|EEU86789.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           CH188]
 gi|257159889|gb|EEU89849.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           T11]
 gi|257162154|gb|EEU92114.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           X98]
 gi|306496667|gb|EFM66221.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0411]
 gi|306500740|gb|EFM70061.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0109]
 gi|306503010|gb|EFM72267.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0860]
 gi|306506650|gb|EFM75802.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX2134]
 gi|306509589|gb|EFM78632.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0855]
 gi|306515806|gb|EFM84328.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX4248]
 gi|310628310|gb|EFQ11593.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0102]
 gi|310631265|gb|EFQ14548.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0635]
 gi|311293586|gb|EFQ72142.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0470]
 gi|315026471|gb|EFT38403.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX2137]
 gi|315031924|gb|EFT43856.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0017]
 gi|315034145|gb|EFT46077.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0027]
 gi|315144223|gb|EFT88239.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX2141]
 gi|315146440|gb|EFT90456.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX4244]
 gi|315152719|gb|EFT96735.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0031]
 gi|315154657|gb|EFT98673.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0043]
 gi|315161240|gb|EFU05257.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0645]
 gi|315163558|gb|EFU07575.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX1302]
 gi|315167096|gb|EFU11113.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX1341]
 gi|315171082|gb|EFU15099.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX1342]
 gi|315172932|gb|EFU16949.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX1346]
 gi|315574598|gb|EFU86789.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0309B]
 gi|315578503|gb|EFU90694.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0630]
          Length = 1207

 Score =  850 bits (2195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|256960563|ref|ZP_05564734.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           Merz96]
 gi|293385239|ref|ZP_06631055.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           R712]
 gi|293389749|ref|ZP_06634193.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           S613]
 gi|312906590|ref|ZP_07765590.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           DAPTO 512]
 gi|312910949|ref|ZP_07769784.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           DAPTO 516]
 gi|256951059|gb|EEU67691.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           Merz96]
 gi|291077439|gb|EFE14803.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           R712]
 gi|291080996|gb|EFE17959.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           S613]
 gi|310627238|gb|EFQ10521.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           DAPTO 512]
 gi|311288817|gb|EFQ67373.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           DAPTO 516]
          Length = 1207

 Score =  850 bits (2195), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 592/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRTTGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|18311395|ref|NP_563329.1| DNA-directed RNA polymerase subunit beta [Clostridium perfringens
           str. 13]
 gi|110799233|ref|YP_697102.1| DNA-directed RNA polymerase subunit beta [Clostridium perfringens
           ATCC 13124]
 gi|168208049|ref|ZP_02634054.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           E str. JGS1987]
 gi|168211996|ref|ZP_02637621.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           B str. ATCC 3626]
 gi|123049581|sp|Q0TMN8|RPOB_CLOP1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|124053360|sp|P0C2E7|RPOB_CLOPE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|15186724|dbj|BAB62884.1| RNA polymerase beta subunit [Clostridium perfringens]
 gi|18146079|dbj|BAB82119.1| RNA polymerase beta subunit [Clostridium perfringens str. 13]
 gi|110673880|gb|ABG82867.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           ATCC 13124]
 gi|170660657|gb|EDT13340.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           E str. JGS1987]
 gi|170710068|gb|EDT22250.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           B str. ATCC 3626]
          Length = 1234

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/955 (45%), Positives = 592/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  ++ ++P+LIE+Q  SY  FL          + GL   F  + PI+ F+G
Sbjct: 9   KRTRMSFAKVKDVAEMPNLIEIQLDSYKWFL----------DAGLYEVFDDINPISNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y  D    K+ V++C  RD TYA PLK+ +RL           K   +IKEQ
Sbjct: 59  NLVLEFVGYTLDMDNIKYSVEECKERDTTYAAPLKVAVRL---------QNKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG++++++  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNYNVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS D+I+VRID+ RK+P++    A+G  S+ E+L  F  +  +    +    
Sbjct: 167 GAWLEYETDSNDVIYVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     AEDIV+  TGE+ +  G+ I   + EEI +  I  + +L  D V     I
Sbjct: 281 IGLRIANQIAAEDIVDKLTGEVLVAKGEKISRANAEEIQNRGINSVDVLVEDRVIR---I 337

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                 D +K            +   ++  +     + +        Y      + ++  
Sbjct: 338 IGNHFVDIHKCVD----FDISDLNIRELVHYPTLREILDN-------YSDEETIKEEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +    P   +HI K+DI A I   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NMTRLIP---KHIIKDDIFATISYQIGLAYNIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEAITPQQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V     +VT ++ Y +A EE+   +AQAN  LDE+G F ++ V  R  GE ++V
Sbjct: 564 ETPYRVVDKAEGRVTGEIRYFTADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P + +D +D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E
Sbjct: 624 PSKDVDLMDVSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG V  V A  + ++           GVD YRL+KF+RSNQ TC+
Sbjct: 684 YKAAVDSGVLPKAKNAGEVVYVSANEVRVKRE------LDGGVDTYRLLKFKRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  GD V + +++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 738 NQRPIVAKGDWVLKGEVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 261/1155 (22%), Positives = 419/1155 (36%), Gaps = 140/1155 (12%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          ++ 
Sbjct: 121  EQGTFIINGAERVIVSQLVRSPGVYYNYNVDKTGKKLFSATVIPNRGAWLEYETDSNDVI 180

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         ++        + T+  D  K +++ALL+IY+ +
Sbjct: 181  YVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNTKTKEEALLEIYKRL 240

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L +      +   ++ +  +  
Sbjct: 241  RPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLAIGLRIANQIAAEDIVDKLTG 300

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             ++  +  K +  + + + NR + SV  ++++       R+ R I      +        
Sbjct: 301  EVLVAKGEKISRANAEEIQNRGINSVDVLVED-------RVIRIIGNHFVDIHKCVDFDI 353

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
              +N   +   V        L    +       I   + ++ L    + +      +   
Sbjct: 354  SDLN---IRELVHYPTLREILDNYSDEETIKEEI--KKNMTRLIPKHIIKDDIFATISYQ 408

Query: 562  HPTHY--GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
                Y  G +   +      +  V  L    +      +    R V +     D   ++ 
Sbjct: 409  IGLAYNIGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQEAITP 465

Query: 620  MEEENRY-IAQAN---------SSLDEDGSFTEELVFCRC---------AGEEILVPREK 660
             +  N   +A A          S   +  +   EL   R          + E        
Sbjct: 466  QQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 525

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +          +         L N  +    +      +    +  +A    TG      
Sbjct: 526  VHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFIETPYRVVDKAEGRVTGEIRYFT 585

Query: 721  KSSGA---AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                       A            + V    +G++    S               +    
Sbjct: 586  ADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVVPSK---------DVDLMDVSPR 636

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--S 835
            Q   V         +  A               +L  + P  G   E    +   ++  +
Sbjct: 637  QLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIEYKAAVDSGVLPKA 696

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    +++   EV  +    G  +  R +          I++  I+  G  V  G++L 
Sbjct: 697  KNAGEVVYVSANEVRVKRELDGGVDTYRLLKFKRSNQGTCINQRPIVAKGDWVLKGEVLA 756

Query: 896  GKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
               +         +   +  I       E A+ + +  +R     S  + +     R   
Sbjct: 757  DGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSIHIEEYECEARDTK 816

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
               E          E   +D  DE+ I+      R  +IL G+    G         L  
Sbjct: 817  LGPEEITRDIPNVSEDALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLR 875

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +  E  R                 E                   K+   + GDD+ PGV
Sbjct: 876  AIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKVFTRENGDDLSPGV 918

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSR
Sbjct: 919  NELVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSR 978

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLGWA   LG  I + + D     DI              +          
Sbjct: 979  MNIGQVLEVHLGWAASALGWHIATPVFDGATETDIEDCLEKAGYNRNGKTVL-------- 1030

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                                     G        TGE FD  VT
Sbjct: 1031 ---------------------------------------RDG-------RTGEEFDNEVT 1044

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ 
Sbjct: 1045 VGIMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHT 1104

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   + 
Sbjct: 1105 LQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDNNQE 1164

Query: 1371 SAKMEEIPDFNKCEL 1385
                E   D ++ E+
Sbjct: 1165 VKFKELAEDDDEIEV 1179


>gi|148267002|ref|YP_001245945.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus JH9]
 gi|189043871|sp|A5IQ96|RPOB_STAA9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|147740071|gb|ABQ48369.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus JH9]
          Length = 1183

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 444/964 (46%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ     N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMYQSN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLSDLTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 248/1145 (21%), Positives = 417/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           S          L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQLSQFMYQSNPLSDLTHKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|329313262|gb|AEB87675.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus
           subsp. aureus T0131]
          Length = 1183

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 597/964 (61%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQ SQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQSSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +T+ RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTNKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GAE
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EEGD 898



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 247/1145 (21%), Positives = 418/1145 (36%), Gaps = 104/1145 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+V+           + +      +  E+ +    +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                +E    +     D +              + +   F  S++  +       S    
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRT----------TTVIGNAFPDSEVKCITPADIIASMSYF 387

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
               LS +G            +R V      +     +     +    S+     +     
Sbjct: 388  FNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQL 447

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            I    R V          +  + +           +   +      L       E   + 
Sbjct: 448  I--NIRPVIASIK----EFFGSSQSSQFMDQANPLAELTNKRRLSALGPGGLTRERAQME 501

Query: 658  REKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + +        +       I  + +  S   +            +  +   +   ++
Sbjct: 502  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQID 561

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A    + +VA+    +             +  +        +    K    + +   
Sbjct: 562  YLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 616

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+      A     G     +      + ++
Sbjct: 617  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAK 676

Query: 837  DVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                  H+E  E++ R           G  +                ++  I+ VG  V 
Sbjct: 677  HRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVE 736

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              +IL    +      M     ++         +  D  +     +S  +V   ++    
Sbjct: 737  YNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MSERLVKDDVYTSIH 790

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            I++ E      +   E + RD  +      +N+  R   +  G     G     K T   
Sbjct: 791  IEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVKDGDILVGKVTPKG 849

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-MPP 1068
               ++   R     F  +  +V+     +                 K+   + GDD + P
Sbjct: 850  VTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGDDTLSP 903

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLGVP
Sbjct: 904  GVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A   LG  + S + D   + D+                       
Sbjct: 964  SRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST-------------------- 1003

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 +  A   + G                             +++LYDG TGEPFD  
Sbjct: 1004 -----IEEAGMARDG-----------------------------KTVLYDGRTGEPFDNR 1029

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1089

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + + 
Sbjct: 1090 YTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQD 1149

Query: 1369 KNSAK 1373
                 
Sbjct: 1150 NEIEM 1154


>gi|323490606|ref|ZP_08095811.1| DNA-directed RNA polymerase subunit beta [Planococcus donghaensis
           MPA1U2]
 gi|323395698|gb|EGA88539.1| DNA-directed RNA polymerase subunit beta [Planococcus donghaensis
           MPA1U2]
          Length = 1184

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/964 (45%), Positives = 599/964 (62%), Gaps = 79/964 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ F +  E++D+P+LIE+Q +SY+ FL           EGL+  F+
Sbjct: 1   MVGQLVQYGQHRQRRSFSRISEVLDLPNLIEIQSSSYEWFL----------EEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+ VD+   RD+TYA PL++ +RL           K
Sbjct: 51  DISPIEDFTGNLSLEFVDYSLAEPKYPVDESKERDVTYAAPLRVKVRLH---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP ++F     +   +GK  +
Sbjct: 102 ETDEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFH---DKTDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+          
Sbjct: 159 GATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLLGDNEYLQ 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK---- 294
              +      +   L+           +  GE   +ES K L        K   +     
Sbjct: 219 NTLEKDNTESTDKALL------EIYERLRPGEPPTVESAKSLLYSRFFDPKRYDLANVGR 272

Query: 295 ----FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + ETGEI +EAG +ID + L+ +            + 
Sbjct: 273 YKMNKKLHIKNRLFNQTIAETLADPETGEILVEAGTLIDRRVLDRL------------IP 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           ++ N              + +  L  I                            Y  + 
Sbjct: 321 NLENGVGFHTVSQVGGVLEGEVTLQSI--------------------------KIYAPNN 354

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             + ++ +  N    D ++H+   DII+ I    +L  G G  DDID+LGNRR+RSVGE+
Sbjct: 355 EDQKEITVISNAYIEDKIKHVTPADIISSISYFFNLLYGVGNTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +++PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSINDTQAIVPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL+++L++FA
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINTLSTFA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G VT  + YL+A EE+N  +AQANS L++DGSF EE +  R
Sbjct: 535 KVNKFGFIETPYRRVDAETGVVTKHIDYLTADEEDNYVVAQANSKLNDDGSFVEEGIVAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +  R  ID++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPLL  EA
Sbjct: 595 FRGENTIYKRGSIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLLNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKF 767
           PFVGTGME + A+ SGAA+VAK  GIVE V+A  I +R +E  D +     +D Y+L KF
Sbjct: 655 PFVGTGMEHLAARDSGAAVVAKNDGIVEFVEAKEIAVRRIEVVDGNEVRGDLDTYKLQKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T  NQRP+VKVGD V + DI+ADGPS + G++ALGRN+LVAFM W G+N+ED++
Sbjct: 715 VRSNQGTSYNQRPIVKVGDRVSKRDILADGPSMERGEMALGRNVLVAFMTWDGFNYEDAI 774

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+D+ GII VGAE
Sbjct: 775 IMSERLVKDDVYTSVHIEEYESDSRDTKLGPEEITRDIPNVGEDALRNLDDRGIIRVGAE 834

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IFNR
Sbjct: 835 VKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKIFNR 894

Query: 948 HGID 951
              D
Sbjct: 895 EDGD 898



 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 252/1059 (23%), Positives = 400/1059 (37%), Gaps = 131/1059 (12%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y++NTL  D  +    ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 208  IDLLGDNEYLQNTLEKDNTESTDKALLEIYERLRPGEPPTVESAKSLLYSRFFDPKRYDL 267

Query: 409  STVG----RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            + VG      K++++  L        +   +   I+     L + +     I NL N   
Sbjct: 268  ANVGRYKMNKKLHIKNRLFNQTIAETLADPETGEILVEAGTLIDRRVLDRLIPNLENGVG 327

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
                  +      G + ++       ++ D   +        +  +  V      S +S 
Sbjct: 328  FHTVSQVGGVLE-GEVTLQSIKIYAPNNEDQKEITVISNAYIEDKIKHVTPADIISSISY 386

Query: 525  LEEHVN---SLSRITHT--RRLSALGQ-------GGVARARAGVEMRDVHPTHYGRICPA 572
                +    +   I H   RRL ++G+        G++R    V  R         +   
Sbjct: 387  FFNLLYGVGNTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSINDTQAIVPQQ 446

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
              +    I  +      ++++ +               TN +  L+              
Sbjct: 447  LINIRPVIASIKEFFGSSQLSQF------------MDQTNPLAELT-------------- 480

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVL 691
                       L       E        + +        +       I  +    +   +
Sbjct: 481  ----HKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINTLSTFAKV 536

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                        + AE   V   ++ + A      +VA+    +    +        EG 
Sbjct: 537  NKFGFIETPYRRVDAETGVVTKHIDYLTADEEDNYVVAQANSKLNDDGS-----FVEEGI 591

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            +        IY+         +    Q   V         +  ++              +
Sbjct: 592  VARFRGENTIYKRGSID--YMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPL 649

Query: 812  LVAFMPWHGYNFE---------DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            L    P+ G   E           +  ++ +V       I +   EV+  +   G  +  
Sbjct: 650  LNPEAPFVGTGMEHLAARDSGAAVVAKNDGIVEFVEAKEIAVRRIEVVDGNEVRGDLDTY 709

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +    V      + ++  I+ VG  V+  DIL    +      M     +L A       
Sbjct: 710  KLQKFVRSNQGTSYNQRPIVKVGDRVSKRDILADGPS-MERGEMALGRNVLVAFMTWDGF 768

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+
Sbjct: 769  NYEDAII-----MSERLVKDDVYTSVHIEEYESDSRDTKLGPEEITRDIPNVGEDALRNL 823

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   I  G     G     K T      ++   R     F  +  +V+     +    
Sbjct: 824  DDR-GIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGA 882

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                         KI   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SR
Sbjct: 883  GGIV------LDVKIFNREDGDELPPGVNQLVRAYIVQKRKISVGDKMAGRHGNKGVISR 936

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMPF+ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D    
Sbjct: 937  ILPEEDMPFMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRSLGIHMASSVFDGANE 996

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             D+                                          T ++DG         
Sbjct: 997  EDVLETMEESGMPRDGK----------------------------TILYDG--------- 1019

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                              +GE FD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQP
Sbjct: 1020 -----------------RSGEAFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQP 1062

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G    E  
Sbjct: 1063 LGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGESVPEPS 1122

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
             PESF VL+KE+Q+LG+ + +     +     +   + +
Sbjct: 1123 VPESFKVLIKELQSLGMDVKMLTIDDEEIELRDLDEEED 1161


>gi|331702087|ref|YP_004399046.1| DNA-directed RNA polymerase subunit beta [Lactobacillus buchneri
           NRRL B-30929]
 gi|329129430|gb|AEB73983.1| DNA-directed RNA polymerase subunit beta [Lactobacillus buchneri
           NRRL B-30929]
          Length = 1202

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 582/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ FL           EGL+  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTNSYNWFLH----------EGLKETFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    +  Y+ PL ITL+L            
Sbjct: 51  GIMPIDDFQGKLSLEFVDYQLLTPKYTVDEAREHEANYSAPLHITLKLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  DK +   +G+  +
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYHADKDK---NGRDSF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  S+ EI+          
Sbjct: 159 GTTVIPNRGAWLEFETDAKNIAYVRIDRTRKIPLTELIRALGFGSDSEIIDILGDNDSLG 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +         D  V   +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 LTLEKD-VHKDTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE + + +TGE+  + G V+ +  ++++      D    Y  
Sbjct: 278 YKTNKKLSLKNRLLGLTLAETLADPDTGEVIAQKGTVVTKDVMKDLAPFLDNDEFKAYTF 337

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + ++ A +   +            + I +V    D                         
Sbjct: 338 TPSDEAVVTEPMT-----------VQIIKVQSVNDPDRV--------------------- 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N + P   +HI   DII+ +    +L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 -----VPLIGNDNIPLSFKHITPADIISAMNYFFNLQEGIGSIDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 481 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 540

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN YGFIETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF   +V  R
Sbjct: 541 RVNKYGFIETPYRRVDWTTHKVTDRIDYLTADEEDNFVIAQANSPLNDDGSFVNNIVMAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 601 HKSNNIEIGIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A++ K  G VE VDA  I +R  +  LD        Y+LMKF+
Sbjct: 661 PLVGTGIEYKAAHDSGVALICKNEGTVEYVDAREIRVRRDDKSLDK-------YKLMKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++I+ADGPS + G+LALG+N +VAFM W GYNFED++ 
Sbjct: 714 RSNGGKNYNQRPIVKVGDRVDADEILADGPSMEGGELALGQNPVVAFMTWQGYNFEDAIA 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V +DV+TSIHIEE+E   RDTKLGPEE+TR+IPNV E+ LKN+DE G + +GAEV
Sbjct: 774 ISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKNLDEDGTVRIGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV+IF R 
Sbjct: 834 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 NGD 896



 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 263/1107 (23%), Positives = 401/1107 (36%), Gaps = 172/1107 (15%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  N     I       + E      F S+   I IL  +        ++      +   
Sbjct: 175  DAKNIAYVRIDRTRKIPLTELIRALGFGSDSEIIDILGDNDSLGLTLEKDVHKDTDDSRV 234

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD------- 423
            +++L DIY  +RPG+  T   + S+    FFD  +YD++ VGR K N +L+L        
Sbjct: 235  EESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDMAPVGRYKTNKKLSLKNRLLGLT 294

Query: 424  -------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                                + K+ +  +   L +      T    D           ++
Sbjct: 295  LAETLADPDTGEVIAQKGTVVTKDVMKDLAPFLDNDEFKAYTFTPSDEAVVTEP-MTVQI 353

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLE 526
            +K Q      R+   I      +    + P D    +     +   +        L    
Sbjct: 354  IKVQSVNDPDRVVPLIGNDNIPLSFKHITPADIISAMNYFFNLQEGIGSIDDIDHLGNRR 413

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
                        R   +  +  V    +  +   V P     I P   S     G     
Sbjct: 414  IRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLS 473

Query: 587  TSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIAQA 630
                + N  G +    R                 V D   T+          E   I   
Sbjct: 474  QFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLI 533

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            NS            +       +    +  ++ID++ A  +    IA +  P    +D  
Sbjct: 534  NSLSSYARVNKYGFIETPYRRVDWTTHKVTDRIDYLTADEEDNFVIAQANSPL---NDDG 590

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              +    M R     ++     V       V+     A+       +E  D+ R ++ + 
Sbjct: 591  SFVNNIVMARHKSNNIEIGIDKVD---YMDVSPKQVVAVATACIPFLENDDSNRALMGAN 647

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                               QR          PLV  G                  +    
Sbjct: 648  ------------------MQRQAVPLIDPHAPLVGTGI-----------------EYKAA 672

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM-ARDTKLGPEEITRDIPN 867
             +  VA +  +    E       R+  +D       +++++M  R +  G     R I  
Sbjct: 673  HDSGVALICKNEGTVEYVDAREIRVRRDDKSL----DKYKLMKFRRSNGGKNYNQRPIVK 728

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V +     +D   I+  G  +  G++ +G                 +    E A+ + + 
Sbjct: 729  VGD----RVDADEILADGPSMEGGELALG-------QNPVVAFMTWQGYNFEDAIAISER 777

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             ++     S  + +     R      E          E   ++ D++             
Sbjct: 778  LVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKNLDED------------G 825

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G     G     K T      +S   R     F  +  +V+     +         
Sbjct: 826  TVRIGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQ 885

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
             +      KI   + GD++ PGV ++V+V++A KR IQ GDKM+GRHGNKG VS ++P E
Sbjct: 886  DV------KIFTRENGDELSPGVNKMVRVYIAQKRKIQVGDKMSGRHGNKGTVSVVIPEE 939

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPFL DGTPVDI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI  
Sbjct: 940  DMPFLPDGTPVDIMLSPMGVPSRMNIGQVLELHLGMAARRLGIHVATPVFDGARDKDIW- 998

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        D   E         A 
Sbjct: 999  --------------------------------------------DAVKE---------AG 1005

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +   G+ ILYDG TGEPFD+ + VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1006 MPSDGKYILYDGRTGEPFDKKIAVGVMHYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKA 1065

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1066 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESF 1125

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKM 1374
             VLVKE+Q+LGL + + ++  K     
Sbjct: 1126 RVLVKELQSLGLDMKVLDASHKEIELR 1152


>gi|110801957|ref|YP_699671.1| DNA-directed RNA polymerase subunit beta [Clostridium perfringens
           SM101]
 gi|123145886|sp|Q0SQD6|RPOB_CLOPS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|110682458|gb|ABG85828.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           SM101]
          Length = 1234

 Score =  849 bits (2194), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/955 (45%), Positives = 592/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  ++ ++P+LIE+Q  SY  FL          + GL   F  + PI+ F+G
Sbjct: 9   KRTRMSFAKVKDVAEMPNLIEIQLDSYKWFL----------DAGLYEVFDDINPISNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y  D    K+ V++C  RD TYA PLK+ +RL           K   +IKEQ
Sbjct: 59  NLVLEFVGYTLDMDNIKYSVEECKERDTTYAAPLKVAVRL---------QNKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG++++++  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNYNVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS D+I+VRID+ RK+P++    A+G  S+ E+L  F  +  +    +    
Sbjct: 167 GAWLEYETDSNDVIYVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     AEDIV+  TGE+ +  G+ I   + EEI +  I  + +L  D V     I
Sbjct: 281 IGLRIANQIAAEDIVDKLTGEVLVAKGEKISRANAEEIQNRGINSVDVLVEDRVIR---I 337

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                 D +K            +   ++  +     + +        Y      + ++  
Sbjct: 338 IGNHFVDIHKCVD----FDISDLNIRELVHYPTLREILDN-------YSDEETIKEEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +    P   +HI K+DI A I   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NMTRLIP---KHIIKDDIFATISYQIGLAYNIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEAITPQQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V     +VT ++ Y +A EE+   +AQAN  LDE+G F ++ V  R  GE ++V
Sbjct: 564 ETPYRVVDKSEGRVTGEIRYFTADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P + +D +D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E
Sbjct: 624 PSKDVDLMDVSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG V  V A  + ++           GVD YRL+KF+RSNQ TC+
Sbjct: 684 YKAAVDSGVLPKAKNAGEVVYVSANEVRVKRE------LDGGVDTYRLLKFKRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  GD V + +++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 738 NQRPIVAKGDWVLKGEVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 260/1155 (22%), Positives = 419/1155 (36%), Gaps = 140/1155 (12%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          ++ 
Sbjct: 121  EQGTFIINGAERVIVSQLVRSPGVYYNYNVDKTGKKLFSATVIPNRGAWLEYETDSNDVI 180

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         ++        + T+  D  K +++ALL+IY+ +
Sbjct: 181  YVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNTKTKEEALLEIYKRL 240

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L +      +   ++ +  +  
Sbjct: 241  RPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLAIGLRIANQIAAEDIVDKLTG 300

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             ++  +  K +  + + + NR + SV  ++++       R+ R I      +        
Sbjct: 301  EVLVAKGEKISRANAEEIQNRGINSVDVLVED-------RVIRIIGNHFVDIHKCVDFDI 353

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
              +N   +   V        L    +       I   + ++ L    + +      +   
Sbjct: 354  SDLN---IRELVHYPTLREILDNYSDEETIKEEI--KKNMTRLIPKHIIKDDIFATISYQ 408

Query: 562  HPTHY--GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
                Y  G +   +      +  V  L    +      +    R V +     D   ++ 
Sbjct: 409  IGLAYNIGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQEAITP 465

Query: 620  MEEENRY-IAQAN---------SSLDEDGSFTEELVFCRC---------AGEEILVPREK 660
             +  N   +A A          S   +  +   EL   R          + E        
Sbjct: 466  QQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 525

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +          +         L N  +    +      +    +  ++    TG      
Sbjct: 526  VHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFIETPYRVVDKSEGRVTGEIRYFT 585

Query: 721  KSSGA---AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                       A            + V    +G++    S               +    
Sbjct: 586  ADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVVPSK---------DVDLMDVSPR 636

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--S 835
            Q   V         +  A               +L  + P  G   E    +   ++  +
Sbjct: 637  QLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIEYKAAVDSGVLPKA 696

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    +++   EV  +    G  +  R +          I++  I+  G  V  G++L 
Sbjct: 697  KNAGEVVYVSANEVRVKRELDGGVDTYRLLKFKRSNQGTCINQRPIVAKGDWVLKGEVLA 756

Query: 896  GKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
               +         +   +  I       E A+ + +  +R     S  + +     R   
Sbjct: 757  DGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSIHIEEYECEARDTK 816

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
               E          E   +D  DE+ I+      R  +IL G+    G         L  
Sbjct: 817  LGPEEITRDIPNVSEDALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLR 875

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +  E  R                 E                   K+   + GDD+ PGV
Sbjct: 876  AIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKVFTRENGDDLSPGV 918

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSR
Sbjct: 919  NELVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSR 978

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLGWA   LG  I + + D     DI              +          
Sbjct: 979  MNIGQVLEVHLGWAASALGWHIATPVFDGATETDIEDCLEKAGYNRNGKTVL-------- 1030

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                                     G        TGE FD  VT
Sbjct: 1031 ---------------------------------------RDG-------RTGEEFDNEVT 1044

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ 
Sbjct: 1045 VGIMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHT 1104

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   + 
Sbjct: 1105 LQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDNNQE 1164

Query: 1371 SAKMEEIPDFNKCEL 1385
                E   D ++ E+
Sbjct: 1165 VKFKELAEDDDEIEV 1179


>gi|308070984|ref|YP_003872589.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
           [Paenibacillus polymyxa E681]
 gi|305860263|gb|ADM72051.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
           [Paenibacillus polymyxa E681]
          Length = 1187

 Score =  849 bits (2193), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/967 (44%), Positives = 595/967 (61%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q+ SYD FL           EGL+  F+
Sbjct: 7   LAGHLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYDWFL----------EEGLREMFR 55

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G  +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K
Sbjct: 56  DISPIQDFTGNLILEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NK 106

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   + K  Y
Sbjct: 107 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNAKTTY 163

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDII+VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 164 TATVIPNRGAWLELEMDAKDIIYVRIDRTRKIPVTVLLRALGFGTDAEILDLLGNDEYIR 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +++ K L        K         
Sbjct: 224 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLDNAKSLLVARFFDPKRYDLANVGR 277

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +++  TGEI  EAG ++D + L+EI       +      
Sbjct: 278 YKINKKLHIKNRLFNQRLAETLIDTTTGEIIAEAGQMVDRRLLDEILAQLEESVG----- 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                   R   V     +  D  L    V  P +                         
Sbjct: 333 -------HRTYHVASGVLESNDIPLQTIDVFSPIE----------------------DGK 363

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N     +    V++I   DII+ I   ++L +G G+ DDID+LGNRR+RSVGE+
Sbjct: 364 VVKLIAN----GNIDKSVKNITPADIISSISYFINLLHGIGSTDDIDHLGNRRLRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLS+  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSRFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP ET EG NIGL++SL++FA
Sbjct: 480 PLAELTHKRRLSALGPGGLTRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLINSLSTFA 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    GKVT  + YL+A EE+N  +AQAN+ L E+ +F +E+V  R
Sbjct: 540 RINEYGFIEAPYRWVDPKTGKVTEQIDYLTADEEDNYIVAQANAELTEENTFKDEVVIVR 599

Query: 649 CAGEEILVPR---EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              +   +      ++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 600 YNKQSDNIIPMASSRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 659

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRL 764
            ++P VGTGME   AK SG  +V+K  G++E+  A  I +R +E          +  Y+L
Sbjct: 660 PKSPLVGTGMEHKSAKDSGVCVVSKYNGVIERSSANEIWLRRIETVDGAEVKGDIVKYKL 719

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRP+V  GD V+  DI+ADGPST++G+LALGRN++VAFM W GYN+E
Sbjct: 720 HKFMRSNQGTCINQRPIVNRGDIVKVGDILADGPSTEMGELALGRNVVVAFMTWEGYNYE 779

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE L+N+DE GII +
Sbjct: 780 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDERGIIRI 839

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++
Sbjct: 840 GAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKV 899

Query: 945 FNRHGID 951
           F R   D
Sbjct: 900 FTRENGD 906



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 185/527 (35%), Positives = 264/527 (50%), Gaps = 67/527 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  I+  G  V  GDIL    + +    +     ++ A 
Sbjct: 712  GDIVKYKLHKFMRSNQGTCINQRPIVNRGDIVKVGDILADGPSTE-MGELALGRNVVVAF 770

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 771  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 825

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               RN+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 826  EALRNLDER-GIIRIGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 884

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 885  RVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 938

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + +
Sbjct: 939  KGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHLGMAAMRLGIHVATPV 998

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     D                                             VFD    
Sbjct: 999  FDGAKEYD---------------------------------------------VFD---- 1009

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G+++LYDG TG+ F+R VTVG ++M+KL HMV DK++ARSTG YS
Sbjct: 1010 -----TMEEAGMQRNGKTVLYDGRTGDRFEREVTVGVMHMIKLAHMVDDKIHARSTGPYS 1064

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1065 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1124

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +  E G PESF VL+KE+Q+LG+ + + +   +     E   + +  
Sbjct: 1125 NVPEPGVPESFKVLIKELQSLGMDVKILSEDEQEIEMRELDDEDDTT 1171


>gi|169344026|ref|ZP_02865015.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           C str. JGS1495]
 gi|169297850|gb|EDS79946.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           C str. JGS1495]
          Length = 1234

 Score =  849 bits (2193), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/955 (45%), Positives = 592/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  ++ ++P+LIE+Q  SY  FL          + GL   F  + PI+ F+G
Sbjct: 9   KRTRMSFAKVKDVAEMPNLIEIQLDSYKWFL----------DAGLYEVFDDINPISNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y  D    K+ V++C  RD TYA PLK+ +RL           K   +IKEQ
Sbjct: 59  NLVLEFVGYTLDMDNIKYSVEECKERDTTYAAPLKVAVRL---------QNKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG++++++  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNYNVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS D+I+VRID+ RK+P++    A+G  S+ E+L  F  +  +    +    
Sbjct: 167 GAWLEYETDSNDVIYVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLS 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     AEDIV+  TGE+ +  G+ I   + EEI +  I  + +L  D V     I
Sbjct: 281 IGLRIANQIAAEDIVDKLTGEVLVAKGEKISRANAEEIQNRGINSVDVLVEDRVIR---I 337

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                 D +K            +   ++  +     + +        Y      + ++  
Sbjct: 338 IGNHFVDIHKCVD----FDISDLNIRELVHYPTLREILDN-------YSDEETIKEEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +    P   +HI K+DI A I   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NMTRLIP---KHIIKDDIFATISYQIGLAYNIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEAITPQQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V     +VT ++ Y +A EE+   +AQAN  LDE+G F ++ V  R  GE ++V
Sbjct: 564 ETPYRVVDKSEGRVTGEIRYFTADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P + +D +D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E
Sbjct: 624 PSKDVDLMDVSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG V  V A  + ++           GVD YRL+KF+RSNQ TC+
Sbjct: 684 YKAAVDSGVLPKAKNAGEVVYVSANEVRVKRE------LDGGVDTYRLLKFKRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  GD V + +++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 738 NQRPIVAKGDWVLKGEVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 260/1155 (22%), Positives = 420/1155 (36%), Gaps = 140/1155 (12%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          ++ 
Sbjct: 121  EQGTFIINGAERVIVSQLVRSPGVYYNYNVDKTGKKLFSATVIPNRGAWLEYETDSNDVI 180

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         ++        + T+  D  K +++ALL+IY+ +
Sbjct: 181  YVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNTKTKEEALLEIYKRL 240

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L++      +   ++ +  +  
Sbjct: 241  RPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLSIGLRIANQIAAEDIVDKLTG 300

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             ++  +  K +  + + + NR + SV  ++++       R+ R I      +        
Sbjct: 301  EVLVAKGEKISRANAEEIQNRGINSVDVLVED-------RVIRIIGNHFVDIHKCVDFDI 353

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
              +N   +   V        L    +       I   + ++ L    + +      +   
Sbjct: 354  SDLN---IRELVHYPTLREILDNYSDEETIKEEI--KKNMTRLIPKHIIKDDIFATISYQ 408

Query: 562  HPTHY--GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
                Y  G +   +      +  V  L    +      +    R V +     D   ++ 
Sbjct: 409  IGLAYNIGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQEAITP 465

Query: 620  MEEENRY-IAQAN---------SSLDEDGSFTEELVFCRC---------AGEEILVPREK 660
             +  N   +A A          S   +  +   EL   R          + E        
Sbjct: 466  QQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 525

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            +          +         L N  +    +      +    +  ++    TG      
Sbjct: 526  VHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFIETPYRVVDKSEGRVTGEIRYFT 585

Query: 721  KSSGA---AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                       A            + V    +G++    S               +    
Sbjct: 586  ADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVVPSK---------DVDLMDVSPR 636

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--S 835
            Q   V         +  A               +L  + P  G   E    +   ++  +
Sbjct: 637  QLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIEYKAAVDSGVLPKA 696

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    +++   EV  +    G  +  R +          I++  I+  G  V  G++L 
Sbjct: 697  KNAGEVVYVSANEVRVKRELDGGVDTYRLLKFKRSNQGTCINQRPIVAKGDWVLKGEVLA 756

Query: 896  GKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
               +         +   +  I       E A+ + +  +R     S  + +     R   
Sbjct: 757  DGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSIHIEEYECEARDTK 816

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
               E          E   +D  DE+ I+      R  +IL G+    G         L  
Sbjct: 817  LGPEEITRDIPNVSEDALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLR 875

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +  E  R                 E                   K+   + GDD+ PGV
Sbjct: 876  AIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKVFTRENGDDLSPGV 918

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSR
Sbjct: 919  NELVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSR 978

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLGWA   LG  I + + D     DI              +          
Sbjct: 979  MNIGQVLEVHLGWAASALGWHIATPVFDGATETDIEDCLEKAGYNRNGKTVL-------- 1030

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                                     G        TGE FD  VT
Sbjct: 1031 ---------------------------------------RDG-------RTGEEFDNEVT 1044

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ 
Sbjct: 1045 VGIMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHT 1104

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   + 
Sbjct: 1105 LQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDNNQE 1164

Query: 1371 SAKMEEIPDFNKCEL 1385
                E   D ++ E+
Sbjct: 1165 VKFKELAEDDDEIEV 1179


>gi|306432036|emb|CBK13147.2| RNA polymerase beta subunit [Paenibacillus anaericanus]
 gi|306432038|emb|CBK13148.2| RNA polymerase beta subunit [Paenibacillus ginsengisoli]
          Length = 1114

 Score =  849 bits (2193), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/957 (45%), Positives = 598/957 (62%), Gaps = 82/957 (8%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R+ + +  E+++IP+LIE+Q+ SY+ FL           EGL+  F  + PI  F+G
Sbjct: 3   RRTRRSYARINEVLEIPNLIEIQQKSYEWFL----------EEGLREMFHDISPIQDFTG 52

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +LEF+ Y    PK+ VDD   RD+TYA PL++ +RLI          K   ++KEQ +
Sbjct: 53  NLVLEFIDYSLGEPKYTVDDAKERDVTYAAPLRVKVRLI---------NKETGEVKEQEV 103

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R++VSQL RSP ++F+    +   +GK  YA  +IP++G 
Sbjct: 104 FMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFN---TKVDKNGKKTYAATVIPNRGA 160

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+KDI++VRIDR RK+PVT  L +LG  ++ EIL             D      
Sbjct: 161 WLELETDAKDIVYVRIDRTRKIPVTVLLRSLGFGTDAEILDLLGNDEYIRNTLDKDNTDS 220

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK--------FLGITS 300
           +   L+           +  GE   +++ K L        K   +               
Sbjct: 221 TEKALI------EIYERLRPGEPPTLDNAKSLLVARFFDPKRYDLANVGRYKVNKKLHIK 274

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + L    +AE +++  TGEI  EAG ++D + L+EI            +  + N    +N
Sbjct: 275 NRLFNQRLAESLIDISTGEIIAEAGQMVDRRLLDEI------------LPYLENGVGFKN 322

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             V +   D  D  L    +  P +                         V +V  N   
Sbjct: 323 YHVANGVLDANDVPLQTIDIFSPIE----------------------DGKVVKVIANC-- 358

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             +    V+HI   DII+ I   ++L +G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL 
Sbjct: 359 --NIDKSVKHITPADIISSISYFLNLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLS 416

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+S  D + + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RR
Sbjct: 417 RMERVVRERMSIQDANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRR 476

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FAR+N YGFIE 
Sbjct: 477 LSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFARINEYGFIEA 536

Query: 601 PYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEIL 655
           PYR V     KVT+ + Y++A EE+N  IAQAN+ L+EDG+F +E V  R        + 
Sbjct: 537 PYRWVDPKTAKVTDQIAYVTADEEDNYIIAQANAILNEDGTFQDENVIVRYNKQADNILT 596

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +P +++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL  +AP VGTGM
Sbjct: 597 MPSDRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLIPKAPLVGTGM 656

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRLMKFQRSNQNT 774
           E   AK SG  IV+K  GI+E+  A  I +R +E          +  ++L KF RSNQ T
Sbjct: 657 EHKSAKDSGVCIVSKYDGIIERSAANEIWLRRIETVDGKEVKGDLVKHKLHKFMRSNQGT 716

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C+NQRP+VK GD V+  DI+ADGPST++G+LALGRN++VAFM W GYN+ED++L+SE++V
Sbjct: 717 CINQRPIVKHGDVVKAGDILADGPSTEMGELALGRNVVVAFMTWEGYNYEDAILLSEKLV 776

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV EE L+N+DE GII VGAE+  GDIL
Sbjct: 777 KEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDERGIIRVGAEIGAGDIL 836

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 837 VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKVFTRENGD 893



 Score =  463 bits (1190), Expect = e-127,   Method: Composition-based stats.
 Identities = 238/1015 (23%), Positives = 383/1015 (37%), Gaps = 126/1015 (12%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D + N+ YIRNTL  D     + AL++IY  +RPG+  T   A+S+    FFD       
Sbjct: 201  DLLGNDEYIRNTLDKDNTDSTEKALIEIYERLRPGEPPTLDNAKSLLVARFFDPK----- 255

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
               R  +           +    +     + + L+D+  G+   +    +  R +  +  
Sbjct: 256  ---RYDLANVGRYKVNKKLHIKNRLFNQRLAESLIDISTGEIIAEAGQMVDRRLLDEILP 312

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L+N        +   +               D  +       +       ++ ++  + 
Sbjct: 313  YLENGVGFKNYHVANGVL--------------DANDVPLQTIDIFSPIEDGKVVKVIANC 358

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N    + H      +                    H G        E         L+  
Sbjct: 359  NIDKSVKHITPADIISSISYFLNLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRM 418

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
             RV     +      V   +   ++  + A  +E       +S L +    T  L     
Sbjct: 419  ERVVRE-RMSIQDANVITPQALINIRPVIASIKE----FFGSSQLSQFMDQTNPLAELTH 473

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
                  +    +   + +  +V  +  S    +   ++        +   +      E  
Sbjct: 474  KRRLSALGPGGLTR-ERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFARINEYG 532

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR---IVIRSVEGDLDPSTSGVDIYRLMK 766
            F+      V  K       AK    +  V A      +I      L+   +  D   +++
Sbjct: 533  FIEAPYRWVDPK------TAKVTDQIAYVTADEEDNYIIAQANAILNEDGTFQDENVIVR 586

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-------------GDLALGRNMLV 813
            + +   N        V   D   +  +                              +L+
Sbjct: 587  YNKQADNILTMPSDRVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 646

Query: 814  AFMPWHGYNFE-------DSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
               P  G   E          ++S+   ++       I +   E +      G     + 
Sbjct: 647  PKAPLVGTGMEHKSAKDSGVCIVSKYDGIIERSAANEIWLRRIETVDGKEVKGDLVKHKL 706

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
               +       I++  I+  G  V  GDIL    + +    +     ++ A    +  + 
Sbjct: 707  HKFMRSNQGTCINQRPIVKHGDVVKAGDILADGPSTE-MGELALGRNVVVAFMTWEGYNY 765

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  L     +S  +V   ++    I++ E      +   E + RD  +      RN+  
Sbjct: 766  EDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALRNLDE 820

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R   I  G    +G     K T      ++   R     F  +  +V+     +    + 
Sbjct: 821  R-GIIRVGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDG 879

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RIL
Sbjct: 880  IVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARIL 933

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPF+ DGTPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D  +  D
Sbjct: 934  PEEDMPFMPDGTPVQVVLNPLGVPSRMNIGQVLEIHLGMAALRLGIHVATPVFDGASEYD 993

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                         VFD          + 
Sbjct: 994  ---------------------------------------------VFD---------AME 999

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A +  +G+++LYDG TG+ F+R VTVG ++M+KL HMV DK++ARSTG YSLVTQQPLG
Sbjct: 1000 EAGMQRNGKTVLYDGRTGDRFEREVTVGVMHMIKLAHMVDDKIHARSTGPYSLVTQQPLG 1059

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            GK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G +  
Sbjct: 1060 GKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGENVP 1114


>gi|41017746|sp|Q8GCR6|RPOB1_ENTFC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|27372991|gb|AAO00728.1| DNA-dependent RNA polymerase subunit beta [Enterococcus faecium]
          Length = 1208

 Score =  848 bits (2192), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +             +
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETLAP--------FIDN 332

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N+  Y  +              + + +V  P D                         
Sbjct: 333 GLNSGTYYPSEDGV----VTDPMTVQVIKVFSPRDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V +   +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGVTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 175/504 (34%), Positives = 235/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  G  L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGVTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1131 VKELQSLGLDMRVLDIEETEIELR 1154


>gi|315150845|gb|EFT94861.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0012]
          Length = 1207

 Score =  848 bits (2192), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFGIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEISVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1236), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|254556009|ref|YP_003062426.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           JDM1]
 gi|254044936|gb|ACT61729.1| DNA-directed RNA polymerase subunit beta [Lactobacillus plantarum
           JDM1]
          Length = 1204

 Score =  848 bits (2191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 586/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFAGKLSLEFVDYQLLEPKYTVEEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFNEELDK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+K++ +VRIDR RK+P+T  + ALG  S++ ++          
Sbjct: 162 GTTVIPNRGAWLELETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDVIDMLGETDSLM 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +  D  V   +      +  GE    +S + L +      K         
Sbjct: 222 LTLEKD-VHKNTDDSRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGR 280

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             V         L    +AE + + +TGE+  +   VID+  + ++     RD       
Sbjct: 281 YKVNKKLSMKTRLMDQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTY 340

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           + ++ A + N +V           L + +V    D                         
Sbjct: 341 TPSDEAVVTNPMV-----------LQVVKVYSQNDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N +     +HI   DIIA I    +L+ G G+ DDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     KVT+ + YL+A EE+   IAQANS L++DGSF E+ V  R
Sbjct: 544 KVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPLNDDGSFVEDTVLAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +  P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL   A
Sbjct: 604 NKEENLETPIENVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E   A  SG A++ +  G VE VDA  + +R  +G LD        Y+LMKF+
Sbjct: 664 PLIGTGIEYKAAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLD-------TYKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+VKVGD V  ++++ADGP+ + G+LALG+N LVAFM W+GYNFED+++
Sbjct: 717 RSNGGKNYNQRPIVKVGDHVDNDEVLADGPAMEGGELALGQNPLVAFMTWNGYNFEDAII 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 777 INERLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNLDEDGIIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 267/1108 (24%), Positives = 410/1108 (37%), Gaps = 168/1108 (15%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +  D  N     I       + E      + S+   I +L           ++      +
Sbjct: 175  LETDAKNVSYVRIDRTRKIPLTELVRALGYGSDDDVIDMLGETDSLMLTLEKDVHKNTDD 234

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +++L DIY  +RPG+  T   + S+    FFD  +YD + VGR K+N +L++ T   
Sbjct: 235  SRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDFAPVGRYKVNKKLSMKTRLM 294

Query: 428  VRHIR----KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             + +       D   +I     + +          L     ++V     ++  +    + 
Sbjct: 295  DQTLAETLADPDTGEVIAQKDTVIDKNVMAKLSPYLERDDFKTVTYTPSDEAVVTNPMVL 354

Query: 484  RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT----- 538
            + +K    +     V      N       +      + ++        L           
Sbjct: 355  QVVKVYSQNDPEKVVNVIGNGNIDLKFKHIVPADIIASINYFFNLQEGLGSTDDIDHLGN 414

Query: 539  RRLSALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVS 584
            RR+ ++G+        G++R    V  R        V P     I P   S     G   
Sbjct: 415  RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQ 474

Query: 585  SLTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIA 628
                  + N  G +    R                 V D   T+          E   I 
Sbjct: 475  LSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIG 534

Query: 629  QANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              NS  S  +   +       R          +KID++ A  +    IA +  P   NDD
Sbjct: 535  LINSLSSYAKVNRYGFIETPYRRVDWTTHKVTDKIDYLAADEEDQFVIAQANSPL--NDD 592

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             + V      + +   L           +          A+       +E  D+ R ++ 
Sbjct: 593  GSFVEDTVLARNKEENLETPIENVDYMDVSPKQV----VAVATACIPFLENDDSNRALMG 648

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +                    QR          PL+  G                  +  
Sbjct: 649  AN------------------MQRQAVPLLDPHAPLIGTGI-----------------EYK 673

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               +  +A +  H    E       R+  +D     +     +  R +  G     R I 
Sbjct: 674  AAHDSGIALICRHEGTVEYVDAREVRVRRDDGSLDTYKL---MKFRRSNGGKNYNQRPIV 730

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             V +    ++D   ++  G  +  G++ +G                      E A+ + +
Sbjct: 731  KVGD----HVDNDEVLADGPAMEGGELALG-------QNPLVAFMTWNGYNFEDAIIINE 779

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              +R     S  + +     R      E          E   ++  DE  I+      + 
Sbjct: 780  RLVREDVYTSIHIEEYESEARDTKLGPEEMTREIPNVGEDALKNL-DEDGIIRIGAEVKD 838

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   +  E  R           +V+     +        
Sbjct: 839  GDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGII 887

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      KI   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P 
Sbjct: 888  QDV------KIFTRENGDELSPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSIVVPE 941

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D   + DI 
Sbjct: 942  EDMPYMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHMATPVFDGAQDTDIW 1001

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                              EAI      A
Sbjct: 1002 --------------------------------------------------EAIRE----A 1007

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +D   +SI+YDG TGEPFD+ V VG ++ +KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1008 GVDSDAKSIVYDGRTGEPFDKRVAVGVMHYMKLSHMVDDKIHARSIGPYSLVTQQPLGGK 1067

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PES
Sbjct: 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPES 1127

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            F VLVKE+QALGL + + +S  K     
Sbjct: 1128 FRVLVKELQALGLDMKVLDSEDKEIELR 1155


>gi|259650771|dbj|BAI42933.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
           GG]
          Length = 1195

 Score =  848 bits (2191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/956 (43%), Positives = 580/956 (60%), Gaps = 79/956 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F  + PI  
Sbjct: 3   YGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFDDIMPIDD 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL               +IK 
Sbjct: 53  FQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NHETGEIKS 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y   +IP+
Sbjct: 104 QDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTYGTTVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
           +G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F          +   
Sbjct: 161 RGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKD- 219

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS----- 300
              +  D      +      +  GE    +S + L        K   +  +G        
Sbjct: 220 VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKL 279

Query: 301 ---DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                L    +AE + + +TGE+  + G  +D + ++++                     
Sbjct: 280 SLKTRLLNQVLAETLADPDTGEVVAQKGTKVDRQVMDKLAPYL----------------- 322

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                      DR D     Y+    G ++     +S+  +     DK          +N
Sbjct: 323 -----------DRDDFKTATYQPSDQGVMTDPIELQSIKVYSQVTPDKE---------IN 362

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +  N      V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 363 LIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGELLQNQFRI 422

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH
Sbjct: 423 GLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTH 482

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A VN YGF
Sbjct: 483 KRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYAVVNPYGF 542

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R     I 
Sbjct: 543 IETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLARHKDNNIE 602

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP VGTGM
Sbjct: 603 ISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHAPLVGTGM 662

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+RSN    
Sbjct: 663 EYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFKRSNAGKN 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED++++SER+V 
Sbjct: 716 YNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIVLSERLVK 775

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV  GDILV
Sbjct: 776 DDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEVRDGDILV 835

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R   D
Sbjct: 836 GKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTREAGD 891



 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 235/1073 (21%), Positives = 380/1073 (35%), Gaps = 104/1073 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 170  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 229

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 230  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 289

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R           ++ 
Sbjct: 290  L-----------AETLADPDTGEVVAQKGTKVDRQVMDKLAPYLDRDDFKTATYQPSDQG 338

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 339  VMTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHILPADVLASMNYFLNLQEGLGTV 398

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 399  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 456

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 457  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 512

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 513  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 572

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 573  IVAQANSPLNDDGSFVDDTVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 627

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTS 841
                 +  +D  ++              ++    P  G   E      S   V  +   +
Sbjct: 628  ----FLENDD--SNRALMGANMQRQAVPLINPHAPLVGTGMEYKAAHDSGTAVLANNAGT 681

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   + + +    + G  +  + +        KN ++  I+ +G  V   D ++      
Sbjct: 682  VEYVDAKQIRVRREDGALDTYKLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAM 740

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + A       +  D  +         V D    + H  +    +   + 
Sbjct: 741  QNGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKL 796

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E+     +  +  L          +  G     G     K T      +S   R   
Sbjct: 797  GPEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLH 854

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
              F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  K
Sbjct: 855  AIFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQK 908

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HL
Sbjct: 909  RKIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHL 968

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG  + + + D   + D+                                    
Sbjct: 969  GMAARNLGIHVATPVFDGANDKDLW----------------------------------- 993

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+H
Sbjct: 994  ------------ATVKE-------AGMPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSH 1034

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD
Sbjct: 1035 MVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDD 1094

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VVGR + YE+IV G+   + G PESF VLVKE+QALGL + +  +  +     
Sbjct: 1095 VVGRVKTYEAIVKGDPIPKPGVPESFRVLVKELQALGLDMKVLGADKQEIELR 1147


>gi|255527834|ref|ZP_05394683.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           carboxidivorans P7]
 gi|296187258|ref|ZP_06855654.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           carboxidivorans P7]
 gi|255508475|gb|EET84866.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           carboxidivorans P7]
 gi|296048129|gb|EFG87567.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           carboxidivorans P7]
          Length = 1232

 Score =  848 bits (2191), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/955 (44%), Positives = 588/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+ ++P+LIEVQ  SY+ FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSKLKEVGEMPNLIEVQLNSYNWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLNLEFVGYKLDMDNIKYTVEECKERDSTYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMSVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS DII+VRID+ RK+P+T    A+G  ++ EI   F          +    
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPITILARAMGYGTDAEITEFFGEDERLKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S + L   L    K   +  +G         
Sbjct: 227 KTREEALLEIYK------RLRPGEPPTVDSAQSLIESLFFDPKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A+DIVN +TGEI +E G+ I  +   EI +  +  + +   D V     I
Sbjct: 281 LNLRIANQISAQDIVNPQTGEILVEKGEKISREKALEIQNCGVNMVNVQLEDRVIK--II 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N  V   N      +      +   ++  +   + + +        Y      + ++  
Sbjct: 339 GNNFVNIHN-----FVDFNIDDLNIKELVHYPALKQILDN-------YSDEDSIKEQIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI ++DI   I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NIHALIP---KHIIRDDIYTTINYELGLPYDIGHTDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEVITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLAAYAKVNEYGFI 563

Query: 599 ETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V     T    +VY++A EE+   IAQAN  LDE+G F +  V  R   + ++V
Sbjct: 564 ETPYRIVDKKTGTVQKKIVYMTADEEDEYVIAQANEPLDEEGHFIDSKVTVRDQEDVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P + +D +D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 624 PAQDVDLMDISARQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG V  V A  + ++        S  G+D YRL+KF+RSNQ++C+
Sbjct: 684 FKAAVDSGVLPKAKNAGTVVYVSANEVRVKRD------SDGGIDTYRLLKFKRSNQSSCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  G++V +  +++DGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V +
Sbjct: 738 NQRPIVSKGEKVDKGTVLSDGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVKK 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYEAEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 179/538 (33%), Positives = 245/538 (45%), Gaps = 77/538 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV  +    G  +  R +          I++  I+  G +V+ G +L    +        
Sbjct: 709  EVRVKRDSDGGIDTYRLLKFKRSNQSSCINQRPIVSKGEKVDKGTVLSDGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +   +  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNIRMGFITWEGYNYEDAMLISEELVKKDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEDALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++  KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIVQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   +G  I + + D     DI                                     
Sbjct: 991  WAASEMGWHIATPVFDGATEEDIVQCLKDAGYDESGK----------------------- 1027

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                 T ++DG                           TG+ FD PVTVGY+Y+LKL H+
Sbjct: 1028 -----TVLYDG--------------------------RTGDAFDNPVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESVDEE 1174


>gi|251799653|ref|YP_003014384.1| DNA-directed RNA polymerase subunit beta [Paenibacillus sp. JDR-2]
 gi|247547279|gb|ACT04298.1| DNA-directed RNA polymerase, beta subunit [Paenibacillus sp. JDR-2]
          Length = 1187

 Score =  848 bits (2190), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/967 (45%), Positives = 597/967 (61%), Gaps = 83/967 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++++P+LIE+Q+ SY+ FL  +          L   F+
Sbjct: 7   LAGQLVQYGR-RTRRSYARINEVLEVPNLIEIQQKSYEKFLDND----------LLELFQ 55

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ VD+   RD+TYA PL++ +RL           K
Sbjct: 56  DISPIQDFTGNLSLEFIDYSLGEPKYSVDESKERDVTYAAPLRVKVRL---------FNK 106

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++F     +   +GK  Y
Sbjct: 107 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYFS---TKVDKNGKKTY 163

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W+++E D+KDI++VRIDR RK+PVT  L ALG  ++ EIL          
Sbjct: 164 TATVIPNRGAWLELETDAKDIMYVRIDRTRKIPVTVLLRALGFGTDAEILELLGHDEYIR 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              D      +   L+           +  GE   +++ K L        K         
Sbjct: 224 NTLDKDNTDSTEKALI------EIYERLRPGEPPTLDNAKSLLVARFFDPKRYDLANVGR 277

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+  TGEI  EAG +ID + L+EI            +D
Sbjct: 278 YKINKKLHIKNRLFNQRLAETLVDPGTGEIIAEAGQMIDRRLLDEI------------LD 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +  N   +   V +   D     L    V  P                       D + 
Sbjct: 326 KLEKNVGFKTYHVANGVLDADSIPLQAISVYSP----------------------LDDAK 363

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V +V  N  +       V+HI   DII+ I   ++L +G G  DDID+LGNRR+RSVGE+
Sbjct: 364 VIKVISNGVI----DKSVKHITPADIISSINYFINLLHGVGNTDDIDHLGNRRLRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDANAITPQALINIRPVIASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL++FA
Sbjct: 480 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFA 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIE PYR V    G VT  + YL+A EE+N  +AQAN+ L E+G+F ++ V  R
Sbjct: 540 RINEYGFIEAPYRWVDPKTGVVTEQISYLTADEEDNYVVAQANAKLTEEGNFVDDSVIVR 599

Query: 649 CA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   + +P E++D++D SPKQVVS+A +LIPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 600 YNKQADNILTMPSERVDYMDVSPKQVVSVATALIPFLENDDSNRALMGSNMQRQAVPLLI 659

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG-VDIYRL 764
            +AP VGTGME   AK SG  IV+K  G++E+  A  I +R  E        G +  ++L
Sbjct: 660 PKAPLVGTGMEHKSAKDSGVCIVSKYDGVIERASANEIWLRRTEILDGKQVVGDLVKHKL 719

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC+NQRPLV+ GD +++ DI+ADGPST+ G+LALGRN++VAFM W GYN+E
Sbjct: 720 HKFMRSNQGTCINQRPLVRKGDVIKKGDILADGPSTEQGELALGRNVVVAFMTWEGYNYE 779

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LKN+DE GII V
Sbjct: 780 DAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNLDERGIIRV 839

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G VVDV++
Sbjct: 840 GAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKV 899

Query: 945 FNRHGID 951
           F R   D
Sbjct: 900 FTRENGD 906



 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 185/529 (34%), Positives = 265/529 (50%), Gaps = 68/529 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  ++  G  +  GDIL    + + +  +     ++ A 
Sbjct: 712  GDLVKHKLHKFMRSNQGTCINQRPLVRKGDVIKKGDILADGPSTE-QGELALGRNVVVAF 770

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 771  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 825

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 826  DALKNLDER-GIIRVGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 884

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 885  RVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGN 938

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+++RI+P EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG AC  LG    + +
Sbjct: 939  KGVIARIMPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMACKRLGLHAATPV 998

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     D                                             VFD    
Sbjct: 999  FDGAREYD---------------------------------------------VFD---- 1009

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G++ILYDG TGE F+R VTVG +YM+KL HMV DK++ARSTG YS
Sbjct: 1010 -----TMEEAGMQRNGKTILYDGRTGESFEREVTVGVMYMIKLAHMVDDKIHARSTGPYS 1064

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1065 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1124

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
            +  E G PESF VL+KE+Q+LG+ + +     +     E +  D    +
Sbjct: 1125 NVPEPGVPESFKVLIKELQSLGMDVKILTENEEEIEMKEIDDEDDGTSD 1173


>gi|677851|emb|CAA45512.1| DNA-directed RNA polymerase beta chain [Staphylococcus aureus
           RN4220]
 gi|1094970|prf||2107219B RNA polymerase:SUBUNIT=beta
 gi|1096954|prf||2113202B RNA polymerase:SUBUNIT=beta
          Length = 1182

 Score =  848 bits (2190), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/965 (45%), Positives = 597/965 (61%), Gaps = 80/965 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ + +  E++++P+LIE+Q  SY+ FL           EGL   F+
Sbjct: 1   MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLR----------EGLIEMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+         K
Sbjct: 51  DISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII---------K 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+  Y
Sbjct: 102 ETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGRENY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+          
Sbjct: 159 DATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG- 297
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGR 272

Query: 298 -------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE IVN ETGEI +E G V+D + ++EI              
Sbjct: 273 YKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD------------ 320

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            V  +           +   +   +   +V  P D                         
Sbjct: 321 -VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND------------------------D 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 EGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGEL 414

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 415 LQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR
Sbjct: 535 RVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EA
Sbjct: 595 FRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKF 767
           PFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF
Sbjct: 655 PFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKF 714

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+ED++
Sbjct: 715 KRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAV 774

Query: 828 LISERMVSEDVFTSIHIEEFEV-MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++SER+V +DV+TSIHIEE+E    RDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +GA
Sbjct: 775 IMSERLVKDDVYTSIHIEEYESRRQRDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGA 834

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FN
Sbjct: 835 EVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFN 894

Query: 947 RHGID 951
           R   D
Sbjct: 895 REEGD 899



 Score =  516 bits (1329), Expect = e-144,   Method: Composition-based stats.
 Identities = 249/1158 (21%), Positives = 423/1158 (36%), Gaps = 129/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 98   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 157

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 158  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 217

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 218  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 277

Query: 419  RLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            +L+L      + +          E ++    +L   +  +       N  +      G +
Sbjct: 278  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 337

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 338  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 397

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 398  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 449

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 450  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 488

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 489  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 549  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 603

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 604  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 663

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 664  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 723

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +       
Sbjct: 724  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVIM----SE 778

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              V D    + H  +   R     +   E + RD  +      +N+  R   +  G    
Sbjct: 779  RLVKDDVYTSIHIEEYESRRQRDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 837

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 838  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 891

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 892  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 951

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 952  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 1004

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 1005 ------------------IEEAGMARDG-----------------------------KTV 1017

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1018 LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1077

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1078 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1137

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1138 SLGLDVKVMDEQDNEIEM 1155


>gi|327383528|gb|AEA55004.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei LC2W]
 gi|327386721|gb|AEA58195.1| DNA-directed RNA polymerase subunit beta [Lactobacillus casei
           BD-II]
          Length = 1194

 Score =  848 bits (2190), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/956 (43%), Positives = 579/956 (60%), Gaps = 79/956 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ + +  E++D+P+LIE+Q  SY  FL          +EGL+  F  + PI  
Sbjct: 3   YGKHRTRRSYARIKEVLDLPNLIEIQTNSYQWFL----------DEGLKEMFDDIMPIDD 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL               +IK 
Sbjct: 53  FQGKLSLEFVGYQLLEPKYTVEEARQHDANYSAPLHVTLRLT---------NHETGEIKS 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMTK GTF+I G +R++VSQL RSPG++F  +  +   + ++ Y   +IP+
Sbjct: 104 QDVFFGDFPLMTKQGTFIINGAERVIVSQLVRSPGVYFHSETDK---NSRVTYGTTVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
           +G W++ E D+KDI +VRIDR RK+P+T  + ALG  S+ +I++ F          +   
Sbjct: 161 RGAWLEYETDAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKD- 219

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS----- 300
              +  D      +      +  GE    +S + L        K   +  +G        
Sbjct: 220 VHKNTDDSRTDEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKL 279

Query: 301 ---DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                L    +AE + + +TGE+  + G  +D + ++++                     
Sbjct: 280 SLKTRLLNQVLAETLADPDTGEVIAQKGTKVDRQVMDKLAPYL----------------- 322

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                      DR D     Y+    G V+     +S+  +     DK          +N
Sbjct: 323 -----------DRDDFKTITYQPSDQGVVTDPIELQSIKVYSQVTPDKE---------IN 362

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +  N      V+HI   D++A +   ++L+ G G+IDDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 363 LIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSIDDIDHLGNRRIRSVGELLQNQFRI 422

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH
Sbjct: 423 GLSRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTH 482

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A VN YGF
Sbjct: 483 KRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYAVVNPYGF 542

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF +E V  R     I 
Sbjct: 543 IETPYRRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDETVLARHKDNNIE 602

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP VGTGM
Sbjct: 603 ISPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVNPHAPLVGTGM 662

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG A++A  AG VE VDA +I +R  +G LD        Y LMKF+RSN    
Sbjct: 663 EYKAAHDSGTAVLANNAGTVEYVDAKQIRVRREDGALDA-------YNLMKFKRSNAGKN 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQRP+V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED++++SER+V 
Sbjct: 716 YNQRPIVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIVLSERLVK 775

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TSIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV  GDILV
Sbjct: 776 DDVYTSIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEVRDGDILV 835

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R   D
Sbjct: 836 GKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTREAGD 891



 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 236/1072 (22%), Positives = 385/1072 (35%), Gaps = 102/1072 (9%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  +     I       + E      F S+   I +   +        ++      +   
Sbjct: 170  DAKDIAYVRIDRTRKIPLTELVRALGFGSDQDIINMFGDNDSLMLTLEKDVHKNTDDSRT 229

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
             +AL DIY  +RPG+  T   + S+    FFD  +YDL++VGR K+N +L+L T    + 
Sbjct: 230  DEALKDIYERLRPGEPKTADSSRSLLYARFFDPKRYDLASVGRYKVNKKLSLKTRLLNQV 289

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +              L +                + + ++     R     +     ++ 
Sbjct: 290  L-----------AETLADPDTGEVIAQKGTKVDRQVMDKLAPYLDRDDFKTITYQPSDQG 338

Query: 491  SSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
               D     S+     +     ++ +       ++  +       S          LG  
Sbjct: 339  VVTDPIELQSIKVYSQVTPDKEINLIGNGHIGKKVKHIVPADVLASMNYFLNLQEGLGSI 398

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                      +R V      +     +     +    S+   A V     I    R V  
Sbjct: 399  DDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTATVTPQQLI--NIRPVVA 456

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                    +  + +                      L       +        + +    
Sbjct: 457  SIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYG 512

Query: 668  PKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                +       I  + +  S  V+            +  +   V   ++ + A      
Sbjct: 513  RMCPIETPEGPNIGLINSLASYAVVNPYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNY 572

Query: 727  IVAKRA----GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            IVA+           VD   +                 +    K   +    C+      
Sbjct: 573  IVAQANSPLNDDGSFVDETVLARHKDNNIEISPDKVDYMDVSPKQVVAVATACIP----- 627

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                 +  +D        ++   A+      A +   G  ++ +      +++ +  T  
Sbjct: 628  ----FLENDDSNRALMGANMQRQAVPLVNPHAPLVGTGMEYKAAHDSGTAVLANNAGTVE 683

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +++  ++  R  + G  +    +        KN ++  I+ +G  V   D ++       
Sbjct: 684  YVDAKQIRVRR-EDGALDAYNLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAMQ 741

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + A       +  D  +         V D    + H  +    +   +  
Sbjct: 742  NGELALGQNPIIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKLG 797

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E+     +  +  L          +  G     G     K T      +S   R    
Sbjct: 798  PEEVTREIPNVGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLHA 855

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      KI   + GD++ PGV  +V+V++  KR
Sbjct: 856  IFGEKAREVRDTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKR 909

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG
Sbjct: 910  KIQVGDKMAGRHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLG 969

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D   + D+                                     
Sbjct: 970  MAARNLGIHVATPVFDGANDKDLW------------------------------------ 993

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                       A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+HM
Sbjct: 994  -----------ATVKE-------AGMASDGKSVLYDGRTGEPFENRVSVGIMYYMKLSHM 1035

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV
Sbjct: 1036 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDV 1095

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VGR + YE+IV G    + G PESF VLVKE+QALGL + +  +  K     
Sbjct: 1096 VGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQALGLDMKVLGADKKEIELR 1147


>gi|184155999|ref|YP_001844339.1| DNA-directed RNA polymerase subunit beta [Lactobacillus fermentum
           IFO 3956]
 gi|183227343|dbj|BAG27859.1| DNA-directed RNA polymerase beta subunit [Lactobacillus fermentum
           IFO 3956]
          Length = 1193

 Score =  847 bits (2189), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/966 (44%), Positives = 596/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ F+          ++GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLDLPNLIEIQTDSYNWFM----------DKGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V +    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLLEPKYTVAEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY---PKI 236
               IP++G W++ E D+K I +VRIDR RK+P+T  + ALG  S+ EI          +
Sbjct: 162 GANFIPNRGAWLEYETDAKGISYVRIDRTRKLPITELVRALGFGSDDEIWDMLGSESESL 221

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D         D  V   +      +  GE    +S + L +      K   +  
Sbjct: 222 NATIEKDLHK---EPEDSRVEESLKDIYERLRPGEPKTADSARSLLTTRFFDPKRYDMAP 278

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L GL +AE + + ETGEI  + GDVI ++ L+E+        P+L
Sbjct: 279 VGRYKTNKKLQMKYRLLGLTLAETLADPETGEIIAKDGDVITKEVLKELE-------PVL 331

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             D      Y              +A++     +           + +  +   D ++  
Sbjct: 332 EQDDFKMITY----------TPSDEAVVTAPVQL-----------QKIMVYSKNDPER-- 368

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                  K+ +  N     D++HI+  DI+A I   ++L+ G GT DDID+LGNRR+RSV
Sbjct: 369 -------KVPVVSNGHISLDLKHIQPADILASINYFLNLQEGIGTTDDIDHLGNRRIRSV 421

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  DI++V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 422 GELLQNQFRIGLARMERVVRERMSIQDINTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 481

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 482 QTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 541

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVNAYGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L+EDGSF  + +
Sbjct: 542 SYARVNAYGFIETPYRRVSWADHKVTDRIDYLTADEEDNFIIAQANTPLNEDGSFVHDEI 601

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 602 MCRDKEDYIETAPENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLIN 661

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP +GTG+E   A  SG A++AK +G VE VDA  + +R  +G LD        Y+LM
Sbjct: 662 PHAPLIGTGIEYKAAHDSGVALIAKNSGTVEYVDAREVRVRQEDGTLD-------TYKLM 714

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 715 KFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 774

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNVSE+  K++DE G+I VG
Sbjct: 775 AIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSEDARKDLDESGVIRVG 834

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F
Sbjct: 835 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVF 894

Query: 946 NRHGID 951
            R   D
Sbjct: 895 TRENGD 900



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 176/530 (33%), Positives = 254/530 (47%), Gaps = 67/530 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  
Sbjct: 702  RQEDGTLDTYKLMKFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPS-MEQGELALGQNP 760

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D        V   V        +  +  E  +  E    E+    +D
Sbjct: 761  LIAFMTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSED 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  +      I  G     G     K T      +S   R     F  +  +V+
Sbjct: 821  ARKDLDESGV------IRVGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVR 874

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GD++ PGV ++V+V++A KR IQ GDKM+G
Sbjct: 875  DTSLRVPHGGGGIIQDV------KVFTRENGDELAPGVNKMVRVYIAQKRKIQVGDKMSG 928

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 929  RHGNKGTVSIVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVIELHLGMAARELGIHI 988

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D                                             V+D
Sbjct: 989  ATPVFDGANDQD---------------------------------------------VWD 1003

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E         A L   G++ILYDG TGEPF++ V VG ++ LKL HMV DK++ARST
Sbjct: 1004 AVKE---------AGLPSDGKTILYDGRTGEPFEQRVAVGVMHYLKLAHMVDDKIHARST 1054

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR   Y++I
Sbjct: 1055 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVNTYQAI 1114

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G+   + G PESF VLVKE+Q+LGL + + + + +         D   
Sbjct: 1115 IDGDQIPKPGVPESFRVLVKELQSLGLDMKVLDDKHEEIQLKSMDEDVAD 1164


>gi|260662743|ref|ZP_05863637.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus fermentum
           28-3-CHN]
 gi|260552824|gb|EEX25823.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus fermentum
           28-3-CHN]
          Length = 1193

 Score =  847 bits (2189), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/966 (44%), Positives = 596/966 (61%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ F+          ++GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLDLPNLIEIQTDSYNWFM----------DKGLREMFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V +    D  Y+ PL +TLRL            
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLLEPKYTVAEAREHDANYSAPLHVTLRLT---------NH 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 105 ETGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY---PKI 236
               IP++G W++ E D+K I +VRIDR RK+P+T  + ALG  S+ EI          +
Sbjct: 162 GANFIPNRGAWLEYETDAKGISYVRIDRTRKLPITELVRALGFGSDDEIWDMLGSESESL 221

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D         D  V   +      +  GE    +S + L +      K   +  
Sbjct: 222 NATIEKDLHK---EPEDSRVEESLKDIYERLRPGEPKTADSARSLLTTRFFDPKRYDMAP 278

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L GL +AE + + ETGEI  + GDVI ++ L+E+        P+L
Sbjct: 279 VGRYKTNKKLQMKYRLLGLTLAETLADPETGEIIAKDGDVITKEVLKELE-------PVL 331

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             D      Y              +A++     +           + +  +   D ++  
Sbjct: 332 EQDDFKMITY----------TPSDEAVVTAPVQL-----------QKIMVYSKNDPER-- 368

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                  K+ +  N     D++HI+  DI+A I   ++L+ G GT DDID+LGNRR+RSV
Sbjct: 369 -------KVPVVSNGHISLDLKHIQPADILASINYFLNLQEGIGTTDDIDHLGNRRIRSV 421

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  DI++V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 422 GELLQNQFRIGLARMERVVRERMSIQDINTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 481

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 482 QTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 541

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVNAYGFIETPYR+V   D KVT+ + YL+A EE+N  IAQAN+ L+EDGSF  + +
Sbjct: 542 SYARVNAYGFIETPYRRVSWADHKVTDRIDYLTADEEDNFIIAQANTPLNEDGSFVHDEI 601

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 602 MCRDKEDYIETAPENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLIN 661

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP +GTG+E   A  SG A++AK +G VE VDA  + +R  +G LD        Y+LM
Sbjct: 662 PHAPLIGTGIEYKAAHDSGVALIAKNSGTVEYVDAREVRVRQEDGTLD-------TYKLM 714

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 715 KFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 774

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ I+ER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNVSE+  K++DE G+I VG
Sbjct: 775 AIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSEDARKDLDESGVIRVG 834

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F
Sbjct: 835 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVF 894

Query: 946 NRHGID 951
            R   D
Sbjct: 895 TRENGD 900



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 177/530 (33%), Positives = 255/530 (48%), Gaps = 67/530 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  
Sbjct: 702  RQEDGTLDTYKLMKFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPS-MEQGELALGQNP 760

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D        V   V        +  +  E  +  E    E+    +D
Sbjct: 761  LIAFMTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSED 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  +      I  G     G     K T      +S   R     F  +  +V+
Sbjct: 821  ARKDLDESGV------IRVGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVR 874

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GD++ PGV ++V+V++A KR IQ GDKM+G
Sbjct: 875  DTSLRVPHGGGGIIQDV------KVFTRENGDELAPGVNKMVRVYIAQKRKIQVGDKMSG 928

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 929  RHGNKGTVSIVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVIELHLGMAARELGIHI 988

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +L+ D   + D                                             V+D
Sbjct: 989  ATLVFDGANDQD---------------------------------------------VWD 1003

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E         A L   G++ILYDG TGEPF++ V VG ++ LKL HMV DK++ARST
Sbjct: 1004 AVKE---------AGLPSDGKTILYDGRTGEPFEQRVAVGVMHYLKLAHMVDDKIHARST 1054

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR   Y++I
Sbjct: 1055 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVNTYQAI 1114

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G+   + G PESF VLVKE+Q+LGL + + + + +         D   
Sbjct: 1115 IDGDQIPKPGVPESFRVLVKELQSLGLDMKVLDDKHEEIQLKSMDEDVAD 1164


>gi|41017743|sp|Q8GCR3|RPOB4_ENTFC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|27372997|gb|AAO00731.1| DNA-dependent RNA polymerase subunit beta [Enterococcus faecium]
          Length = 1208

 Score =  847 bits (2189), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/963 (43%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + N         ++         + + +V  P D                         
Sbjct: 329 FIENGLNSVTYYPSEDGVVTDPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPEAPVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRQTGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA +I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDASQIRVRRDNGALDK-------YDITKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+L   M W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLSVSMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 KDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 173/499 (34%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLSVSMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------SDEDVWETVREAGMASEAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTSKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + + +       
Sbjct: 1136 SLGLDMRVLDIKDAEIELR 1154


>gi|315580834|gb|EFU93025.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0309A]
          Length = 1207

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 592/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S + I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSYDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|41017745|sp|Q8GCR5|RPOB3_ENTFC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|27372993|gb|AAO00729.1| DNA-dependent RNA polymerase subunit beta [Enterococcus faecium]
          Length = 1208

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL   F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLGEMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E  +KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETSAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPKDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPESAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDASEIRVRRDNGALDK-------YAVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 237/504 (47%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTILYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + + +       
Sbjct: 1131 VKELQSLGLDMRVLDIKDSEIQLR 1154


>gi|227512857|ref|ZP_03942906.1| DNA-directed RNA polymerase subunit beta [Lactobacillus buchneri
           ATCC 11577]
 gi|227083857|gb|EEI19169.1| DNA-directed RNA polymerase subunit beta [Lactobacillus buchneri
           ATCC 11577]
          Length = 1205

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/963 (44%), Positives = 587/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ FL           +GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTNSYNWFL----------KDGLRETFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    +  Y+ PL ITL+L   + D      
Sbjct: 54  GIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHITLKLTNHETD------ 107

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  D  +   +G++ Y
Sbjct: 108 ---EIKTQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYHEDTDK---NGRISY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E DSK+I +VRIDR RK+P+T  + ALG  S+ EI           
Sbjct: 162 GTTVIPNRGAWLEFETDSKNISYVRIDRTRKIPLTELIRALGFGSDGEITDILGDNDSLE 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +         D  V   +      +  GE    ES + L +      K   +  +G 
Sbjct: 222 LTLEKD-VHKDTDDSRVEESLKDIYERLRPGEPKTAESSRSLLTARFFDPKRYDMAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE + + ETGE+ ++   V+ +  ++++           Y+D
Sbjct: 281 YKTNKKLSLKNRLLGLTLAETLADPETGEVIVQKDTVVTKDVMKKLSP---------YLD 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                AY  N   +D+    +   + I +V    D                         
Sbjct: 332 QKEFKAYTFNP--SDEAVVTEPMTVQIIKVYSANDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N + P   +HI   DIIA +    +L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVPLIGNDNIPLAFKHITPADIIASMNYFFNLQEGIGSIDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF   +V  R
Sbjct: 544 RINKYGFIETPYRRVDWTSHKVTDRIDYLTADEEDNFVIAQANSPLNDDGSFVNNVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 604 HKSNNIEISIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A++ K AG VE VDA  + IR  +G LD        Y+LMKF+
Sbjct: 664 PLVGTGIEYKAAHDSGVALICKFAGTVEYVDAREVRIRRDDGTLDK-------YKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+VGD V  ++++ADGPS + G+LALG+N +VAFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQRPIVRVGDHVDPDEVLADGPSMEGGELALGQNPIVAFMTWQGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V +DV+TSIHIEE+E   RDTKLGPEE+TR+IPNV E+ LKN+DE G I +GAEV
Sbjct: 777 ISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKNLDEGGTIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G V DV++F R 
Sbjct: 837 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIVQDVKVFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 257/1105 (23%), Positives = 398/1105 (36%), Gaps = 168/1105 (15%)

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            D  N     I       + E      F S+     IL  +        ++      +   
Sbjct: 178  DSKNISYVRIDRTRKIPLTELIRALGFGSDGEITDILGDNDSLELTLEKDVHKDTDDSRV 237

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV----KMNMRLNLDTPD 426
            +++L DIY  +RPG+  T   + S+    FFD  +YD++ VGR     K++++  L    
Sbjct: 238  EESLKDIYERLRPGEPKTAESSRSLLTARFFDPKRYDMAPVGRYKTNKKLSLKNRLLGLT 297

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
                +   +   +I     +            L  +  ++      ++  +      + I
Sbjct: 298  LAETLADPETGEVIVQKDTVVTKDVMKKLSPYLDQKEFKAYTFNPSDEAVVTEPMTVQII 357

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT-----RRL 541
            K   ++     V      N       +      + ++        +  I        RR+
Sbjct: 358  KVYSANDPEKVVPLIGNDNIPLAFKHITPADIIASMNYFFNLQEGIGSIDDIDHLGNRRI 417

Query: 542  SALGQ-------GGVARARAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVSSLT 587
             ++G+        G++R    V  R        V P     I P   S     G      
Sbjct: 418  RSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                 V D   T+          E   I   N
Sbjct: 478  FMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLIN 537

Query: 632  S--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            S  S      +       R          ++ID++ A  +    IA +  P    +D   
Sbjct: 538  SLSSYARINKYGFIETPYRRVDWTSHKVTDRIDYLTADEEDNFVIAQANSPL---NDDGS 594

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             +    M R     ++     V       V+     A+       +E  D+ R ++ +  
Sbjct: 595  FVNNVVMARHKSNNIEISIDKVD---YMDVSPKQVVAVATACIPFLENDDSNRALMGAN- 650

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          PLV  G                  +     
Sbjct: 651  -----------------MQRQAVPLVDPHAPLVGTGI-----------------EYKAAH 676

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            +  VA +       E       R+  +D                   G  +  + +    
Sbjct: 677  DSGVALICKFAGTVEYVDAREVRIRRDD-------------------GTLDKYKLMKFRR 717

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
              G KN ++  I+ VG  V+P ++L    + +G   +   +  + A    +  +  D   
Sbjct: 718  SNGGKNYNQRPIVRVGDHVDPDEVLADGPSMEG-GELALGQNPIVAFMTWQGYNFEDAI- 775

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               +     V D    + H  +    +   +    E+     +  +  L          I
Sbjct: 776  ---AISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKN--LDEGGTI 830

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G     G     K T      +S   R     F  +  +V+     +          +
Sbjct: 831  RIGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIVQDV 890

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                  K+   + GD++ PGV R+V+V++A KR IQ GDKM+GRHGNKG VS ++P EDM
Sbjct: 891  ------KVFTRENGDELSPGVNRMVRVYIAQKRKIQVGDKMSGRHGNKGTVSVVIPEEDM 944

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PFL DGTPVDI+L+P+GVPSRMN+GQ+ E HLG A   LG  + + + D  ++ DI    
Sbjct: 945  PFLPDGTPVDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHVATPVFDGASDKDIWNAV 1004

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                                        
Sbjct: 1005 KEAGMPKDGKYIL----------------------------------------------- 1017

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G++       GEPFD+P+ VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  
Sbjct: 1018 YDGRT-------GEPFDKPIAVGVMHYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQF 1070

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF V
Sbjct: 1071 GGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRV 1130

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKM 1374
            LVKE+Q+LGL + + +S  K     
Sbjct: 1131 LVKELQSLGLDMKVLDSSHKEIELR 1155


>gi|51894220|ref|YP_076911.1| DNA-directed RNA polymerase subunit beta [Symbiobacterium
           thermophilum IAM 14863]
 gi|81387938|sp|Q67JT3|RPOB_SYMTH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|51857909|dbj|BAD42067.1| RNA polymerase beta subunit [Symbiobacterium thermophilum IAM
           14863]
          Length = 1250

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/960 (45%), Positives = 593/960 (61%), Gaps = 110/960 (11%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +V  G  R R  F +  E++++P+LIE+Q+ SY  FL           EGLQ  F+ + 
Sbjct: 3   KIVQAGR-RQRLSFSRIDEVLEMPNLIELQRNSYQWFLR----------EGLQEMFQDIS 51

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  F+G  +LEF+ Y    PK+ +++C  RD+TYA PL++ +RLI          K   
Sbjct: 52  PIQDFTGNLVLEFIDYSLGEPKYSIEECKERDVTYAAPLRVRVRLI---------NKETG 102

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           ++KEQ ++MGD PLMT  GTF+I G +R++VSQL RSPG++F         SGK L+   
Sbjct: 103 EVKEQEVFMGDFPLMTPTGTFIINGAERVIVSQLVRSPGVYFSEQID---PSGKKLFFAT 159

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +IP++G W++ E D  D+I+VR+DR RK+P T  L ALG  S+ EIL          +  
Sbjct: 160 MIPNRGAWLEFESDVNDVIYVRVDRTRKLPATVLLRALGFGSDQEILDAVGDSEYIRRTL 219

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGIT-- 299
           +          L+   K       +  GE    ++ ++L   L    K   +  +G    
Sbjct: 220 EKDSTESEEEALIEIYK------RLRPGEPPAADNARQLLETLFFEPKRYDLMHVGRYRL 273

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                    + G    + +V+ ETGE+                                 
Sbjct: 274 NKKLALKRRIVGTSTVDRVVHPETGEVLA------------------------------- 302

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                             +A + I + +   +    +  +++       + +     + R
Sbjct: 303 ------------------EAGVQIDKRL--AEKIDEAGVDAL-------TVRLRDGGIVR 335

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           V  N R        V+ I ++DI+A+I  +V L  G G++DDID+LGNRRVRSVGE+L+N
Sbjct: 336 VVANGR----PDIRVKTIVRQDIVAVINYMVSLFKGLGSVDDIDHLGNRRVRSVGELLQN 391

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL RMER IKER++  D+D + PQ LIN +PVV+AV EFF SSQLSQ  +  N L+
Sbjct: 392 QFRIGLARMERVIKERMTIQDVDIITPQALINIRPVVAAVKEFFGSSQLSQFMDQTNPLA 451

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ +L +FAR+N
Sbjct: 452 ELTNKRRLSALGPGGLSRERAGYEVRDVHTSHYGRMCPIETPEGPNIGLIGALATFARIN 511

Query: 594 AYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            YGFIETPYRKV     +VT+++VYL+A EE+   IAQAN  L+ DG+F  + V CR   
Sbjct: 512 EYGFIETPYRKVDQESGRVTDEIVYLTADEEDENIIAQANEPLNPDGTFARDRVTCRYRD 571

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + VP  ++D++D SPKQVVSIA +LIPFLENDD++R LMG NMQRQAVPLL+ EAP+V
Sbjct: 572 EILQVPPSQVDYMDVSPKQVVSIATALIPFLENDDASRALMGSNMQRQAVPLLRTEAPYV 631

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+  G+V +  A  +V++  +         V  Y+L KF RSN
Sbjct: 632 GTGMEYRSAWDSGVCVIAENDGVVLRATASEVVVQYDDMQ-------VKKYKLTKFTRSN 684

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC+NQ+P+V+ GD VR+ D+IADGPSTD G+LALGRN+LVA+M + GYN+ED+++I+E
Sbjct: 685 QGTCMNQKPIVRAGDRVRKGDVIADGPSTDQGELALGRNVLVAYMCYEGYNYEDAIIINE 744

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V EDVFTSIHIEE E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV PG
Sbjct: 745 RLVREDVFTSIHIEEHECEARDTKLGPEEITRDIPNVGEDVLKDLDERGIIRIGAEVRPG 804

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++F R   D
Sbjct: 805 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKVFTRENGD 864



 Score =  394 bits (1013), Expect = e-107,   Method: Composition-based stats.
 Identities = 148/514 (28%), Positives = 219/514 (42%), Gaps = 81/514 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD++    +   +  +     +L A    +  +  D  +     V   V 
Sbjct: 694  IVRAGDRVRKGDVIADGPST-DQGELALGRNVLVAYMCYEGYNYEDAIIINERLVREDVF 752

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H  +  +  +  E          E + +D  DE+ I+      R  +IL G+ 
Sbjct: 753  TSIHIEEHECEARDTKLGPEEITRDIPNVGEDVLKDL-DERGIIRIGAEVRPGDILVGKV 811

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E                  
Sbjct: 812  TPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGESGIVVD 854

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+   + GD++ PGV  +V+V+            MA     K    R +   D      
Sbjct: 855  VKVFTRENGDELSPGVNELVRVY------------MA----QK----RKISQGD------ 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
                                              G K    +   + +    P  + ++ 
Sbjct: 889  ----------------------------KMAGRHGNKGVISVIVPEEDMPFMPDGTPIDI 920

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            ++       +++      +         G+ V++PVFDGA+E+ I  ML  A L  +G++
Sbjct: 921  ILTPLGVPSRMNIGQIMEIHLGWAAKTLGMYVASPVFDGANEQDIREMLLKAHLPPNGKT 980

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LYDG TGEPFD  VTVGY YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 981  VLYDGKTGEPFDNEVTVGYKYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1040

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+
Sbjct: 1041 GEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKEL 1100

Query: 1355 QALGLSIDLENSRTKNSAKME--EIPDFNKCELK 1386
            Q+L L + + +         E  +  D +  +L+
Sbjct: 1101 QSLALDVKVLDESGNEIELRELDDEMDLSDRDLE 1134


>gi|182627157|ref|ZP_02954870.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           D str. JGS1721]
 gi|177907460|gb|EDT70132.1| DNA-directed RNA polymerase, beta subunit [Clostridium perfringens
           D str. JGS1721]
          Length = 1234

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/955 (44%), Positives = 592/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  ++ ++P+LIE+Q  SY  FL          + GL   F  + PI+ F+G
Sbjct: 9   KRTRMSFAKVKDVAEMPNLIEIQLDSYKWFL----------DAGLYEVFDDINPISNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y  D    K+ V++C  RD TYA PLK+ +RL           K   +IKEQ
Sbjct: 59  NLVLEFVGYTLDMDNIKYSVEECKERDTTYAAPLKVAVRL---------QNKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG++++++  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNYNVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS D+I+VRID+ RK+P++    A+G  S+ E+L  F  +  +    +    
Sbjct: 167 GAWLEYETDSNDVIYVRIDKTRKLPISILGRAMGFGSDQELLEYFGEEERFKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     AEDIV+  TGE+ +  G+ I   + EEI +  I  + +L  D V     I
Sbjct: 281 IGLRIANQIAAEDIVDKLTGEVLVAKGEKISRANAEEIQNRGINSVDVLVEDRVIR---I 337

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                 D +K            +   ++  +     + +        Y      + ++  
Sbjct: 338 IGNHFVDIHKCVD----FDISDLNIRELVHYPTLREILDN-------YSDEETIKEEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +    P   +HI K+DI A I   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NMTRLIP---KHIIKDDIFATISYQIGLAYNIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEAITPQQLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDV+ +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVNHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V     +VT ++ Y +A EE+   +AQAN  LDE+G F ++ V  R  GE ++V
Sbjct: 564 ETPYRVVDKAEGRVTGEIRYFTADEEDQYLVAQANEPLDENGCFIDKKVTVRDKGEVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P + +D +D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E
Sbjct: 624 PSKDVDLMDVSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPYAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG V  V A  + ++           GVD YRL+KF+RSNQ TC+
Sbjct: 684 YKAAVDSGVLPKAKNAGEVVYVSANEVRVKRE------LDGGVDTYRLLKFKRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  GD V + +++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 738 NQRPIVAKGDWVLKGEVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 185/598 (30%), Positives = 257/598 (42%), Gaps = 79/598 (13%)

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMAR 852
            A               +L  + P  G   E    +   ++  +++    +++   EV  +
Sbjct: 654  ASRALMGSNMQRQAVPLLKPYAPIVGTGIEYKAAVDSGVLPKAKNAGEVVYVSANEVRVK 713

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  R +          I++  I+  G  V  G++L    +         +   
Sbjct: 714  RELDGGVDTYRLLKFKRSNQGTCINQRPIVAKGDWVLKGEVLADGPSTDLGEIALGKNIR 773

Query: 913  LRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            +  I       E A+ + +  +R     S  + +     R      E          E  
Sbjct: 774  MGFITWEGYNYEDAMLISEELVREDVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDA 833

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D  DE+ I+      R  +IL G+    G         L   +  E  R         
Sbjct: 834  LKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 883

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   K+   + GDD+ PGV  +V+ ++A KR I  G
Sbjct: 884  --------EVRDTSLRVPHGEAGIIVDVKVFTRENGDDLSPGVNELVRCYIAQKRKISVG 935

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   
Sbjct: 936  DKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAASA 995

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG  I + + D     DI              +                           
Sbjct: 996  LGWHIATPVFDGATETDIEDCLEKAGYNRNGKTVL------------------------- 1030

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G        TGE FD  VTVG +Y+LKL H+V DK+
Sbjct: 1031 ----------------------RDG-------RTGEEFDNEVTVGIMYILKLAHLVDDKI 1061

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR +
Sbjct: 1062 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVK 1121

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E   D ++ E+
Sbjct: 1122 TYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDNNQEVKFKELAEDDDEIEV 1179


>gi|227509924|ref|ZP_03939973.1| DNA-directed RNA polymerase subunit beta [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
 gi|227190530|gb|EEI70597.1| DNA-directed RNA polymerase subunit beta [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
          Length = 1205

 Score =  847 bits (2188), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/963 (44%), Positives = 587/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ FL           +GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTNSYNWFL----------KDGLRETFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    +  Y+ PL ITL+L   + D      
Sbjct: 54  GIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHITLKLTNHETD------ 107

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG+++  D  +   +G++ Y
Sbjct: 108 ---EIKTQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYHEDTDK---NGRISY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E DSK+I +VRIDR RK+P+T  + ALG  S+ EI           
Sbjct: 162 GTTVIPNRGAWLEFETDSKNISYVRIDRTRKIPLTELIRALGFGSDGEITDILGDNDSLE 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +         D  V   +      +  GE    ES + L +      K   +  +G 
Sbjct: 222 LTLEKD-VHKDTDDSRVEESLKDIYERLRPGEPKTAESSRSLLTARFFDPKRYDMAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE + + ETGE+ ++   V+ +  ++++           Y+D
Sbjct: 281 YKTNKKLSLKNRLLGLTLAETLADPETGEVIVQKDTVVTKDVMKKLSP---------YLD 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                AY  N   +D+    +   + I +V    D                         
Sbjct: 332 QKEFKAYTFNP--SDEAVVTEPMTVQIIKVYSANDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N + P   +HI   DIIA +    +L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVPLIGNDNIPLAFKHITPADIIASMNYFFNLQEGIGSIDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           RVN YGFIETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF   +V  R
Sbjct: 544 RVNKYGFIETPYRRVDWTSHKVTDRIDYLTADEEDNFVIAQANSPLNDDGSFVNNVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 604 HKSNNIEISIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A++ K AG VE VDA  + IR  +G LD        Y+LMKF+
Sbjct: 664 PLVGTGIEYKAAHDSGVALICKFAGTVEYVDAREVRIRRDDGTLDK-------YKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+VGD V  ++++ADGPS + G+LALG+N +VAFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQRPIVRVGDHVDPDEVLADGPSMEGGELALGQNPIVAFMTWQGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V +DV+TSIHIEE+E   RDTKLGPEE+TR+IPNV E+ LKN+DE G I +GAEV
Sbjct: 777 ISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKNLDEGGTIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R 
Sbjct: 837 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 172/522 (32%), Positives = 243/522 (46%), Gaps = 67/522 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  + +      G KN ++  I+ VG  V+P ++L    + +G   +   +  
Sbjct: 701  RRDDGTLDKYKLMKFRRSNGGKNYNQRPIVRVGDHVDPDEVLADGPSMEG-GELALGQNP 759

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + A    +  +  D      +     V D    + H  +    +   +    E+     +
Sbjct: 760  IVAFMTWQGYNFEDAI----AISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPN 815

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              +  L          I  G     G     K T      +S   R     F  +  +V+
Sbjct: 816  VGEDALKN--LDEGGTIRIGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVR 873

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GD++ PGV R+V+V++A KR IQ GDKM+G
Sbjct: 874  DTSLRVPHGGGGIIQDV------KVFTRENGDELSPGVNRMVRVYIAQKRKIQVGDKMSG 927

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMPFL DGTPVDI+L+P+GVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 928  RHGNKGTVSVVIPEEDMPFLPDGTPVDIMLSPMGVPSRMNIGQVLELHLGMAARKLGIHV 987

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ DI                                               
Sbjct: 988  ATPVFDGASDKDIWNAVKEAGMPKDGKYIL------------------------------ 1017

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G++       GEPFD+P+ VG ++ LKL HMV DK++ARS 
Sbjct: 1018 -----------------YDGRT-------GEPFDKPIAVGVMHYLKLAHMVDDKIHARSI 1053

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+I
Sbjct: 1054 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAI 1113

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            V G    + G PESF VLVKE+Q+LGL + + +S  K     
Sbjct: 1114 VKGEPIPKPGVPESFRVLVKELQSLGLDMKVLDSSHKEIELR 1155


>gi|315028694|gb|EFT40626.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX4000]
          Length = 1207

 Score =  847 bits (2187), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 593/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +T+ RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTYKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|23097567|ref|NP_691033.1| DNA-directed RNA polymerase subunit beta [Oceanobacillus iheyensis
           HTE831]
 gi|41017735|sp|Q8ETY8|RPOB_OCEIH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|22775790|dbj|BAC12068.1| DNA-directed RNA polymerase beta subunit [Oceanobacillus iheyensis
           HTE831]
          Length = 1179

 Score =  847 bits (2187), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/964 (44%), Positives = 595/964 (61%), Gaps = 75/964 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q ASYD FL           EGL+  F+
Sbjct: 1   MTGQLVQYGRHRQRRSYARINEVLELPNLIEIQTASYDWFL----------EEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV Y    PK+ VD+   RD+TY  PL++ +RLI           
Sbjct: 51  DISPIEDFTGNLSLEFVDYSLGDPKYPVDEAKERDVTYNAPLRVKVRLI---------NN 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSP ++++    +   +GK   
Sbjct: 102 ETGEVKEQEVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYNEKIDK---NGKRGI 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KDI +VRIDR RK+P+T  L ALG  ++ EI           
Sbjct: 159 GATVIPNRGAWLEFETDAKDIAYVRIDRTRKLPITVLLRALGFGTDQEITDLLGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +   L+           +  GE   +E+ K L        K   +  +G 
Sbjct: 219 NTLEKDNTENAEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAHVGR 272

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE IV+ ETGE+  E G+ ++ K L++I          L   
Sbjct: 273 YKMNKKLHMKNRLFNQILAEPIVDPETGEVIAEKGEKLERKLLDKI----------LPYL 322

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               + +  + L   +     +  +   +++ P D +                       
Sbjct: 323 ERAEDRFGESVLSPHEGVLEDEITIQSVKIIDPTDPN----------------------- 359

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G  ++ +  N    +DV++I   DI++ I    +L +  G  DDID+LGNRR+RSVGE+
Sbjct: 360 -GERELTVIGNGGVTNDVKNITPADILSSISYFFNLLHEVGGTDDIDHLGNRRLRSVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  SV PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 419 LQNQFRIGLSRMERVVRERMSIQDTSSVTPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 479 PLGELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 538

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIE+PYR+V    GKVTN + YL+A E++N  +AQANS LDED  F  E V  R
Sbjct: 539 KVNKFGFIESPYRRVDPETGKVTNKIDYLTADEQDNYIVAQANSPLDEDSRFQNEEVISR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + I+V R+KID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+K +A
Sbjct: 599 FQEDNIVVSRDKIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMKPQA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGVDIYRLMKF 767
           P VGTGME V  K SGAA++    G++E+V+A  + +R +           +D Y L K+
Sbjct: 659 PIVGTGMEYVNGKDSGAAVICHHDGVIERVEAKEVYVRRISIVDGKEVEGDLDRYGLQKY 718

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ TC NQRP+V  GD V + +++ADGPS + G+LALG+N+LV FM W GYN+ED++
Sbjct: 719 KRSNQGTCYNQRPIVSQGDRVTKGEVLADGPSMEDGELALGQNVLVGFMTWEGYNYEDAI 778

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEEFE  ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAE
Sbjct: 779 IMSERLVKDDVYTSIHIEEFESEARDTKLGPEEITRDIPNVGEDALKNLDEHGIIRVGAE 838

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IFNR
Sbjct: 839 VTDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFNR 898

Query: 948 HGID 951
              D
Sbjct: 899 EDGD 902



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 266/1086 (24%), Positives = 398/1086 (36%), Gaps = 183/1086 (16%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
             D +  N Y+RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 208  TDLLGENEYLRNTLEKDNTENAEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 267

Query: 409  STVGRVKMNMRLNLD--------------------TPDDVRHIRKEDIIAIIKILVDLRN 448
            + VGR KMN +L++                       +    + ++ +  I+  L    +
Sbjct: 268  AHVGRYKMNKKLHMKNRLFNQILAEPIVDPETGEVIAEKGEKLERKLLDKILPYLERAED 327

Query: 449  GKGTIDDIDNLGNRRVRSV--GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL-IN 505
              G      + G            + +       R    I     + D+ ++ P D+  +
Sbjct: 328  RFGESVLSPHEGVLEDEITIQSVKIIDPTDPNGERELTVIGNGGVTNDVKNITPADILSS 387

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHV--NSLSRITHTRRLSALGQGGVARAR-AGVEMRDVH 562
                 + + E   +  +  L      +    + +  R+       V R R +  +   V 
Sbjct: 388  ISYFFNLLHEVGGTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTSSVT 447

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------VC 606
            P     I P   S     G         + N  G +    R                 V 
Sbjct: 448  PQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRERAGFEVR 507

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            D   ++          E   I   NS  S  +   F       R    E      KID++
Sbjct: 508  DVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIESPYRRVDPETGKVTNKIDYL 567

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
             A  +    +A +  P  E             Q + V     E   V           S 
Sbjct: 568  TADEQDNYIVAQANSPLDE---------DSRFQNEEVISRFQEDNIVV----------SR 608

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              I        + V A    I         +            QR        Q P+V  
Sbjct: 609  DKIDYMDVSPKQVVSAATACI-----PFLENDDSNRALMGANMQRQAVPLMKPQAPIVGT 663

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G E                 +         ++          + I +    E       +
Sbjct: 664  GMEYVNGKDSGAAVICHHDGVIERVEAKEVYV--------RRISIVDGKEVEGDLDRYGL 715

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +++    + +  G     R                 I+  G  V  G++L    +   + 
Sbjct: 716  QKY----KRSNQGTCYNQRP----------------IVSQGDRVTKGEVLADGPS-MEDG 754

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   + +L      +  +  D  +                    + K++   S+  E+ 
Sbjct: 755  ELALGQNVLVGFMTWEGYNYEDAIIMS----------------ERLVKDDVYTSIHIEEF 798

Query: 965  ELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            E  ARD       + R+I                I  G     G     K T      +S
Sbjct: 799  ESEARDTKLGPEEITRDIPNVGEDALKNLDEHGIIRVGAEVTDGDILVGKVTPKGVTELS 858

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R     F  +  +V+     +                 KI   + GD++PPGV ++V
Sbjct: 859  AEERLLHAIFGEKAREVRDTSLRVPHGGGGIV------LDVKIFNREDGDELPPGVNQLV 912

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            + ++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPLGVPSRMN+G
Sbjct: 913  RAYIVQKRKIHEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIG 972

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+FE HLG A   LG  + S + D     D+                             
Sbjct: 973  QVFELHLGMAARQLGIHVASPVFDGAREEDVWETLEEAGMPRDAK--------------- 1017

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                         T ++DG                           TGE FD  V+VG +
Sbjct: 1018 -------------TVLYDG--------------------------RTGEAFDNRVSVGVM 1038

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+
Sbjct: 1039 YMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEI 1098

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDD VGR + YE+IV G++  E G PESF VL+KE+Q+LG+ + + +S        
Sbjct: 1099 LTVKSDDTVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKMLSSNEDEIDMR 1158

Query: 1375 EEIPDF 1380
            E   + 
Sbjct: 1159 ELEEEE 1164


>gi|327536346|gb|AEA95180.1| DNA-directed RNA polymerase subunit beta [Enterococcus faecalis
           OG1RF]
          Length = 1207

 Score =  847 bits (2187), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 592/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +T  RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTRKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|281419555|ref|ZP_06250566.1| DNA-directed RNA polymerase, beta subunit [Clostridium thermocellum
           JW20]
 gi|281406777|gb|EFB37044.1| DNA-directed RNA polymerase, beta subunit [Clostridium thermocellum
           JW20]
          Length = 1250

 Score =  847 bits (2187), Expect = 0.0,   Method: Composition-based stats.
 Identities = 458/955 (47%), Positives = 603/955 (63%), Gaps = 64/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + K  E+ID+P+LIE+QK SY+ FL           EG +  FK V PIT ++G
Sbjct: 9   RNVRMSYSKIDEVIDMPNLIEIQKNSYEQFL----------KEGFKEVFKDVNPITDYTG 58

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D P K+ VD+C  RD TYA PLK+ +RLI          K   ++KEQ 
Sbjct: 59  NLILEFVDYSLDEPPKYSVDECKERDATYAAPLKVKVRLI---------NKETGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTF+I G +R++VSQL RSPGI++     +   +GK L++  +IP++G
Sbjct: 110 IFMGDFPLMTETGTFIINGAERVIVSQLVRSPGIYYA---MKIDKAGKQLFSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D++ VRIDR RK+P+T  + ALG  ++ EI   F                
Sbjct: 167 AWLEYETDSNDVLSVRIDRTRKLPLTVLVRALGYGTDLEITELFGEDERILATIQKDSTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES K L  GL    K   +   G          
Sbjct: 227 TEEEGLLEIYK------RLRPGEPPTVESAKALLHGLFFDPKRYDLAKPGRFKFNKKLSI 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              + G    E+I + +TGEI +  G+ I  +  E I ++ +  + IL VD  N      
Sbjct: 281 AARIHGFIAGENIKDPDTGEIIVAEGETISREKAETIQNAGVNTV-ILRVDGKNVKVIGN 339

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           +             ++DI R +   D     + E +   +  +  +              
Sbjct: 340 D-------------MVDIKRYV-DFDPKEIGINEKVKRDVLMEILEEYKGKGDDAIKKAL 385

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI KEDII+ I  ++ L  G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 386 QERIDDLIPKHITKEDIISSISYIIGLSYGIGSTDDIDHLGNRRLRSVGELLQNQFRIGL 445

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER++  D+D   PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +TH R
Sbjct: 446 SRMERVVRERMTIQDLDVATPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHKR 505

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN YGFIE
Sbjct: 506 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIE 565

Query: 600 TPYRKVCDG---KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           TPYRKV      KVTN++VYL+A EE+   IAQAN  LDE+G F    V CR   E I V
Sbjct: 566 TPYRKVSKEEPGKVTNEIVYLTADEEDEYIIAQANEPLDEEGRFISNKVVCRYKEEFIEV 625

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              KIDF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K E+P VGTG+E
Sbjct: 626 DPSKIDFMDVSPKQIVSVATSMIPFLENDDANRALMGANMQRQAVPLIKTESPIVGTGIE 685

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A+ SG  I+AK  G+VE+V A  I+IR+ +G  D        Y+L+K+ RSNQ TC+
Sbjct: 686 YRAARDSGVVILAKNPGVVEKVTANEIIIRTKDGKRD-------TYKLLKYMRSNQGTCI 738

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+VK G+EV   D+IADGPSTD G++ALG+N+LV FM W GYN+ED++LISER+V +
Sbjct: 739 NQRPIVKKGEEVEAGDVIADGPSTDNGEIALGKNVLVGFMTWEGYNYEDAILISERLVKD 798

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPE+ITR+IPNVSE+ LK+++  GII +GAEV  GDILVG
Sbjct: 799 DVFTSIHIEEYEAEARDTKLGPEDITREIPNVSEDALKDLNSEGIIRIGAEVRAGDILVG 858

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+IF R   D
Sbjct: 859 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKIFTRENGD 913



 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 170/532 (31%), Positives = 236/532 (44%), Gaps = 77/532 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G  +  + +  +       I++  I+  G EV  GD++    +      +   + +
Sbjct: 715  RTKDGKRDTYKLLKYMRSNQGTCINQRPIVKKGEEVEAGDVIADGPSTDN-GEIALGKNV 773

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L      +  +  D  L     V   V        +  +  +  +  E    +I  ++ D
Sbjct: 774  LVGFMTWEGYNYEDAILISERLVKDDVFTSIHIEEYEAEARDTKLGPEDITREIPNVSED 833

Query: 971  KDDEQV---ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               +     I+      R  +IL G+    G         L   +  E  R         
Sbjct: 834  ALKDLNSEGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 884

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   KI   + GD++ PGV ++V+V+VA KR I  G
Sbjct: 885  --------EVRDTSLRVPHGESGIVVDVKIFTRENGDELAPGVNKLVRVYVAQKRKISVG 936

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNK                            GV SR+                
Sbjct: 937  DKMAGRHGNK----------------------------GVISRI---------------- 952

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
                ++ +                L+ V+       +++      V         G  V+
Sbjct: 953  --LPVEDMPFLPDGTP--------LDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWKVA 1002

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I   LR A L E G+SILYDG TGEPF+  VTVGY+YMLKL H+V DK+
Sbjct: 1003 TPVFDGATEEDIVQTLRKAGLAEDGKSILYDGRTGEPFENRVTVGYMYMLKLAHLVDDKI 1062

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR +
Sbjct: 1063 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVK 1122

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             YE+IV G +  E G PESF VL+KE+Q+L L + + +   +  A  E + D
Sbjct: 1123 TYEAIVKGENVPEPGIPESFKVLIKELQSLCLDVKVYSEEQEEIAIKESVED 1174


>gi|125975206|ref|YP_001039116.1| DNA-directed RNA polymerase subunit beta [Clostridium thermocellum
           ATCC 27405]
 gi|158513257|sp|A3DIZ4|RPOB_CLOTH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|125715431|gb|ABN53923.1| DNA-directed RNA polymerase subunit beta [Clostridium thermocellum
           ATCC 27405]
          Length = 1250

 Score =  847 bits (2187), Expect = 0.0,   Method: Composition-based stats.
 Identities = 459/955 (48%), Positives = 604/955 (63%), Gaps = 64/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + K  E+ID+P+LIE+QK SY+ FL           EG +  FK V PIT ++G
Sbjct: 9   RNVRMSYSKIDEVIDMPNLIEIQKNSYEQFL----------KEGFKEVFKDVNPITDYTG 58

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D P K+ VD+C  RD TYA PLK+ +RLI          K   ++KEQ 
Sbjct: 59  NLILEFVDYSLDEPPKYSVDECKERDATYAAPLKVKVRLI---------NKETGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTF+I G +R++VSQL RSPGI++     +   +GK L++  +IP++G
Sbjct: 110 IFMGDFPLMTETGTFIINGAERVIVSQLVRSPGIYYA---MKIDKAGKQLFSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D++ VRIDR RK+P+T  + ALG  ++ EI   F                
Sbjct: 167 AWLEYETDSNDVLSVRIDRTRKLPLTVLVRALGYGTDLEITELFGEDERILATIQKDSTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES K L  GL    K   +   G          
Sbjct: 227 TEEEGLLEIYK------RLRPGEPPTVESAKALLHGLFFDPKRYDLAKPGRFKFNKKLSI 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              + G    E+I + +TGEI +  G+ I  +  E I ++ +  + IL VD  N      
Sbjct: 281 AARIHGFIAGENIKDPDTGEIIVAEGETISREKAETIQNAGVNTV-ILRVDGKNVKVIGN 339

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           +             ++DI R +   D     + E +   +  +  +              
Sbjct: 340 D-------------MVDIKRYV-DFDPKEIGINEKVKRDVLMEILEEYKGKGDDAIKKAL 385

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI KEDII+ I  ++ L  G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 386 QERIDDLIPKHITKEDIISSISYIIGLSYGIGSTDDIDHLGNRRLRSVGELLQNQFRIGL 445

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER++  D+D V PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +TH R
Sbjct: 446 SRMERVVRERMTIQDLDVVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHKR 505

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN YGFIE
Sbjct: 506 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIE 565

Query: 600 TPYRKVCDG---KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           TPYRKV      KVTN++VYL+A EE+   IAQAN  LDE+G F    V CR   E I V
Sbjct: 566 TPYRKVSKEEPGKVTNEIVYLTADEEDEYIIAQANEPLDEEGRFISNKVVCRYKEEFIEV 625

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              KIDF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K E+P VGTG+E
Sbjct: 626 DPSKIDFMDVSPKQIVSVATSMIPFLENDDANRALMGANMQRQAVPLIKTESPIVGTGIE 685

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A+ SG  I+AK  G+VE+V A  I+IR+ +G  D        Y+L+K+ RSNQ TC+
Sbjct: 686 YRAARDSGVVILAKNPGVVEKVTANEIIIRTKDGKRD-------TYKLLKYMRSNQGTCI 738

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+VK G+EV   D+IADGPSTD G++ALG+N+LV FM W GYN+ED++LISER+V +
Sbjct: 739 NQRPIVKKGEEVEAGDVIADGPSTDNGEIALGKNVLVGFMTWEGYNYEDAILISERLVKD 798

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPE+ITR+IPNVSE+ LK+++  GII +GAEV  GDILVG
Sbjct: 799 DVFTSIHIEEYEAEARDTKLGPEDITREIPNVSEDALKDLNSEGIIRIGAEVRAGDILVG 858

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+IF R   D
Sbjct: 859 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKIFTRENGD 913



 Score =  437 bits (1125), Expect = e-120,   Method: Composition-based stats.
 Identities = 169/532 (31%), Positives = 235/532 (44%), Gaps = 77/532 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G  +  + +  +       I++  I+  G EV  GD++    +      +   + +
Sbjct: 715  RTKDGKRDTYKLLKYMRSNQGTCINQRPIVKKGEEVEAGDVIADGPSTDN-GEIALGKNV 773

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L      +  +  D  L     V   V        +  +  +  +  E    +I  ++ D
Sbjct: 774  LVGFMTWEGYNYEDAILISERLVKDDVFTSIHIEEYEAEARDTKLGPEDITREIPNVSED 833

Query: 971  KDDEQV---ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               +     I+      R  +IL G+    G         L   +  E  R         
Sbjct: 834  ALKDLNSEGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 884

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   KI   + GD++ PGV ++V+V+VA KR I  G
Sbjct: 885  --------EVRDTSLRVPHGESGIVVDVKIFTRENGDELAPGVNKLVRVYVAQKRKISVG 936

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNK                            GV SR+                
Sbjct: 937  DKMAGRHGNK----------------------------GVISRI---------------- 952

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
                ++ +                L+ V+       +++      V         G  V+
Sbjct: 953  --LPVEDMPFLPDGTP--------LDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWKVA 1002

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I   LR A L E G+SILYDG TGEPF+  VTVGY+YMLKL H+V DK+
Sbjct: 1003 TPVFDGATEEDIVQTLRKAGLAEDGKSILYDGRTGEPFENRVTVGYMYMLKLAHLVDDKI 1062

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR +
Sbjct: 1063 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVK 1122

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             YE+IV G +  E G PE F VL+KE+Q+L L + + +   +  A  E + D
Sbjct: 1123 TYEAIVKGENVPEPGIPECFKVLIKELQSLCLDVKVYSEEQEEIAIKESVED 1174


>gi|256003132|ref|ZP_05428124.1| DNA-directed RNA polymerase, beta subunit [Clostridium thermocellum
           DSM 2360]
 gi|255992823|gb|EEU02913.1| DNA-directed RNA polymerase, beta subunit [Clostridium thermocellum
           DSM 2360]
 gi|316939370|gb|ADU73404.1| DNA-directed RNA polymerase, beta subunit [Clostridium thermocellum
           DSM 1313]
          Length = 1250

 Score =  846 bits (2186), Expect = 0.0,   Method: Composition-based stats.
 Identities = 459/955 (48%), Positives = 604/955 (63%), Gaps = 64/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + K  E+ID+P+LIE+QK SY+ FL           EG +  FK V PIT ++G
Sbjct: 9   RNVRMSYSKIDEVIDMPNLIEIQKNSYEQFL----------KEGFKEVFKDVNPITDYTG 58

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D P K+ VD+C  RD TYA PLK+ +RLI          K   ++KEQ 
Sbjct: 59  NLILEFVDYSLDEPPKYSVDECKERDATYAAPLKVKVRLI---------NKETGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTF+I G +R++VSQL RSPGI++     +   +GK L++  +IP++G
Sbjct: 110 IFMGDFPLMTETGTFIINGAERVIVSQLVRSPGIYYA---MKIDKAGKQLFSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D++ VRIDR RK+P+T  + ALG  ++ EI   F                
Sbjct: 167 AWLEYETDSNDVLSVRIDRTRKLPLTVLVRALGYGTDLEITELFGEDERILATIQKDSTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES K L  GL    K   +   G          
Sbjct: 227 TEEEGLLEIYK------RLRPGEPPTVESAKALLHGLFFDPKRYDLAKPGRFKFNKKLSI 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              + G    E+I + +TGEI +  G+ I  +  E I ++ +  + IL VD  N      
Sbjct: 281 AARIHGFIAGENIKDPDTGEIIVAEGETISREKAETIQNAGVNTV-ILRVDGKNVKVIGN 339

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           +             ++DI R +   D     + E +   +  +  +              
Sbjct: 340 D-------------MVDIKRYV-DFDPKEIGINEKVKRDVLMEILEEYKGKGDDAIKKAL 385

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI KEDII+ I  ++ L  G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 386 QERIDDLIPKHITKEDIISSISYIIGLSYGIGSTDDIDHLGNRRLRSVGELLQNQFRIGL 445

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER++  D+D V PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +TH R
Sbjct: 446 SRMERVVRERMTIQDLDVVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHKR 505

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN YGFIE
Sbjct: 506 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIE 565

Query: 600 TPYRKVCDG---KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           TPYRKV      KVTN++VYL+A EE+   IAQAN  LDE+G F    V CR   E I V
Sbjct: 566 TPYRKVSKEEPGKVTNEIVYLTADEEDEYIIAQANEPLDEEGRFISNKVVCRYKEEFIEV 625

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              KIDF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL+K E+P VGTG+E
Sbjct: 626 DPSKIDFMDVSPKQIVSVATSMIPFLENDDANRALMGANMQRQAVPLIKTESPIVGTGIE 685

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A+ SG  I+AK  G+VE+V A  I+IR+ +G  D        Y+L+K+ RSNQ TC+
Sbjct: 686 YRAARDSGVVILAKNPGVVEKVTANEIIIRTKDGKRD-------TYKLLKYMRSNQGTCI 738

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+VK G+EV   D+IADGPSTD G++ALG+N+LV FM W GYN+ED++LISER+V +
Sbjct: 739 NQRPIVKKGEEVEAGDVIADGPSTDNGEIALGKNVLVGFMTWEGYNYEDAILISERLVKD 798

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPE+ITR+IPNVSE+ LK+++  GII +GAEV  GDILVG
Sbjct: 799 DVFTSIHIEEYEAEARDTKLGPEDITREIPNVSEDALKDLNSEGIIRIGAEVRAGDILVG 858

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+IF R   D
Sbjct: 859 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKIFTRENGD 913



 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 170/532 (31%), Positives = 236/532 (44%), Gaps = 77/532 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G  +  + +  +       I++  I+  G EV  GD++    +      +   + +
Sbjct: 715  RTKDGKRDTYKLLKYMRSNQGTCINQRPIVKKGEEVEAGDVIADGPSTDN-GEIALGKNV 773

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L      +  +  D  L     V   V        +  +  +  +  E    +I  ++ D
Sbjct: 774  LVGFMTWEGYNYEDAILISERLVKDDVFTSIHIEEYEAEARDTKLGPEDITREIPNVSED 833

Query: 971  KDDEQV---ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               +     I+      R  +IL G+    G         L   +  E  R         
Sbjct: 834  ALKDLNSEGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 884

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   KI   + GD++ PGV ++V+V+VA KR I  G
Sbjct: 885  --------EVRDTSLRVPHGESGIVVDVKIFTRENGDELAPGVNKLVRVYVAQKRKISVG 936

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNK                            GV SR+                
Sbjct: 937  DKMAGRHGNK----------------------------GVISRI---------------- 952

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
                ++ +                L+ V+       +++      V         G  V+
Sbjct: 953  --LPVEDMPFLPDGTP--------LDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWKVA 1002

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA EE I   LR A L E G+SILYDG TGEPF+  VTVGY+YMLKL H+V DK+
Sbjct: 1003 TPVFDGATEEDIVQTLRKAGLAEDGKSILYDGRTGEPFENRVTVGYMYMLKLAHLVDDKI 1062

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR +
Sbjct: 1063 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVK 1122

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             YE+IV G +  E G PESF VL+KE+Q+L L + + +   +  A  E + D
Sbjct: 1123 TYEAIVKGENVPEPGIPESFKVLIKELQSLCLDVKVYSEEQEEIAIKESVED 1174


>gi|289566323|ref|ZP_06446753.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           D344SRF]
 gi|289161899|gb|EFD09769.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           D344SRF]
          Length = 1205

 Score =  845 bits (2184), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 589/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  VV  G  R R+ F +  E++++ +LIE+Q  SY  FL          +EGL+  F+
Sbjct: 1   MAGHVVKYGKHRERRSFARISEVLELSNLIEIQTDSYQWFL----------DEGLREMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 51  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 102 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 159 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 219 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 278 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 325

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 326 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 362 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +T+ RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 480 PLGELTYKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 540 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 660 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 713 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 AGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 725  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 775

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 776  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 827

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 828  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 886

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 887  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 941

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 942  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 991

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 992  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1016

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1017 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1067

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1068 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1127

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1128 VKELQSLGLDMRVLDIEETEIELR 1151


>gi|315159665|gb|EFU03682.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX0312]
          Length = 1207

 Score =  845 bits (2183), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 592/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL  SPG++F    G+   +GK  +
Sbjct: 105 ETGEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVHSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTIEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL-------------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 YI N L +      +DA++         +  T  V + +               
Sbjct: 327 ----GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP---------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 365 --ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +
Sbjct: 603 LQSENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRS 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 786

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 787  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 846

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 847  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 889

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 890  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 949

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 950  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 995  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 1019

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1020 ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1075

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1076 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1135

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1136 SLGLDMRVLDIEEAEIELR 1154


>gi|314949429|ref|ZP_07852770.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0082]
 gi|313644260|gb|EFS08840.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium
           TX0082]
          Length = 1208

 Score =  844 bits (2180), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/963 (43%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V +    D  Y+ PL +TLRL           +
Sbjct: 54  DILPIDDFNGNLSLEFVDYELKEPKYTVAEARAHDANYSAPLHVTLRLT---------NR 104

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 105 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 162 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLR 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      K   +  +G 
Sbjct: 222 NTVEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G V+  + +E +              
Sbjct: 281 YKVNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQVMETL------------AP 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         ++         + + +V  P D                         
Sbjct: 329 FIDNGLNSVTYYPSEDGVVTDPMTVQVIKVFSPRDP------------------------ 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+
Sbjct: 365 --EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGEL 422

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 423 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 482

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +T  R LSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A
Sbjct: 483 PLGELTRKRCLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 542

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN +GFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F +++V  R
Sbjct: 543 KVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMAR 602

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 603 AQSENLEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 662

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 663 PWVGTGMEYKSAHDSGAALLCKHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFR 715

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LV FM W GYN+ED+++
Sbjct: 716 RSNSGTSYNQRPIVHLGEKVEKGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAII 775

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 776 MSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 835

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 836 QDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 895

Query: 949 GID 951
             D
Sbjct: 896 AGD 898



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 728  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 778

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 779  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 830

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 831  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 889

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 890  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 944

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 945  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 994

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 995  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 1019

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 1020 ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1070

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1071 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1130

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1131 VKELQSLGLDMRVLDIEETEIELR 1154


>gi|187932557|ref|YP_001884466.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum B
           str. Eklund 17B]
 gi|226699388|sp|B2TIG8|RPOB_CLOBB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|187720710|gb|ACD21931.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum B
           str. Eklund 17B]
          Length = 1249

 Score =  844 bits (2180), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/956 (46%), Positives = 602/956 (62%), Gaps = 67/956 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++ ++P+LIEVQ  SY  FL           EGL   F+ + PIT F+G
Sbjct: 9   KRTRMSFGKVKDVTEMPNLIEVQLDSYQWFLR----------EGLHEVFEDINPITNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y+ D    K+ V++C  RD TYA PLK+++RL               +IKEQ
Sbjct: 59  NLVLEFVDYKLDMDNIKYSVEECKERDATYAAPLKVSVRL---------QNNETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++++   +    GK LY+  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYNYSIDKT---GKKLYSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS DII+VRID+ RK+P+T    A+G  S+ E+L  F     +    +    
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPITILARAMGFGSDQELLDFFGEDERFRASIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTREEGLLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A D++N  TGEI +E G  I     E+I ++ I+ + IL  D +     I
Sbjct: 281 LNLRIANQIAAMDVINPSTGEIMVEKGQKISRLLAEDIQNAGIKSVDILVDDKLVR--VI 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKMN 417
            N              +DI + + P DVS   + E + +  L    D Y   T  + ++ 
Sbjct: 339 SNN------------FVDITKQV-PFDVSDLQIKELVHYPTLREILDNYSDETTIKEEIK 385

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             L+   P   +HI K+DI A I   + L  G G +DDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 386 KNLSRLIP---KHIIKDDIFATISYELGLPYGIGYVDDIDHLGNRRLRSVGELLQNQFRI 442

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER +KER++  D +S+ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH
Sbjct: 443 GLSRMERVVKERMTIQDQESITPQMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTH 502

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FARVN YGF
Sbjct: 503 KRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFARVNEYGF 562

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR V   + + T ++ Y +A EE+   IAQA   LDE+G F ++ V  R   + ++
Sbjct: 563 IETPYRIVDKENARATEEIRYFTADEEDQCLIAQAKEPLDENGYFVDKKVTVRYLEDVLV 622

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           VP   +D +D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+
Sbjct: 623 VPATDVDLMDVSARQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGI 682

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG    A+ AG+V  V A  I ++        S  G D YRL+KF+RSNQ++C
Sbjct: 683 EFKAAVDSGVLPKARNAGVVTFVSANEIRVKRD------SDGGTDNYRLLKFKRSNQSSC 736

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +NQRP+V  G+ V +N ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V 
Sbjct: 737 INQRPIVNKGEIVFKNQVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVR 796

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           EDVFTS+HIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+ID+ GII +GAEV  GDILV
Sbjct: 797 EDVFTSMHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDDRGIIRIGAEVRSGDILV 856

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VD+++F R   D
Sbjct: 857 GKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDIKVFTRENGD 912



 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 264/1141 (23%), Positives = 416/1141 (36%), Gaps = 122/1141 (10%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            E G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 121  EQGTFIINGAERVIVSQLVRSPGVYYNYSIDKTGKKLYSATVIPNRGAWLEYETDSNDII 180

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         +D    +   R ++  D  K R++ LL+IY+ +
Sbjct: 181  YVRIDKTRKLPITILARAMGFGSDQELLDFFGEDERFRASIEKDNTKTREEGLLEIYKRL 240

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L L+     +    + I     
Sbjct: 241  RPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLALNLRIANQIAAMDVINPSTG 300

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             ++  +  K +    +++ N  ++SV  ++ +       ++ R I    + VDI   +P 
Sbjct: 301  EIMVEKGQKISRLLAEDIQNAGIKSVDILVDD-------KLVRVIS--NNFVDITKQVPF 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            D ++   +   V        L    +       I   + LS L    + +      +   
Sbjct: 352  D-VSDLQIKELVHYPTLREILDNYSDETTIKEEI--KKNLSRLIPKHIIKDDIFATISYE 408

Query: 562  HPTHYGR--ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
                YG   +   +      +  V  L    +      +    R V +     D   ++ 
Sbjct: 409  LGLPYGIGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQESITP 465

Query: 620  MEEENRY-IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
                N   +A A          ++ +       E     R          ++        
Sbjct: 466  QMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 525

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK--SSGAAIVAKRAGIVE 736
            +          +          +  L   A     G      +      A   +      
Sbjct: 526  VHHSHYGRMCPIETPEGPNIGLINSLATFARVNEYGFIETPYRIVDKENARATEEIRYFT 585

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF----------QRSNQNTCVNQRPLVKVGD 786
              +  + +I   +  LD +   VD    +++               +    Q   V    
Sbjct: 586  ADEEDQCLIAQAKEPLDENGYFVDKKVTVRYLEDVLVVPATDVDLMDVSARQIVSVATAM 645

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHI 844
                 +  A               +L    P  G   E    +   ++  + +      +
Sbjct: 646  IPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEFKAAVDSGVLPKARNAGVVTFV 705

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
               E+  +    G  +  R +          I++  I+  G  V    +L    +     
Sbjct: 706  SANEIRVKRDSDGGTDNYRLLKFKRSNQSSCINQRPIVNKGEIVFKNQVLADGPSTDLGE 765

Query: 905  PMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                +   +  I       E A+ + +  +R     S  + +     R      E     
Sbjct: 766  IALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSMHIEEYECEARDTKLGPEEITRD 825

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
                 E   +D DD   I+      R  +IL G+    G         L   +  E  R 
Sbjct: 826  IPNVSEDALKDIDDR-GIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR- 883

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                            E                   K+   + GD++ PGV  +V+ ++ 
Sbjct: 884  ----------------EVRDTSLRVPHGEAGIIVDIKVFTRENGDELNPGVNELVRCYIV 927

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDKMAGRHGNKG++SRILP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E 
Sbjct: 928  QKRKISVGDKMAGRHGNKGVISRILPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEV 987

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA   LG  I + + D     +I                                  
Sbjct: 988  HLGWAASKLGWHISTPVFDGATENEIEECLEKAGYNANGK-------------------- 1027

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    T ++DG                           TGEPFD  VTVG +Y+LKL
Sbjct: 1028 --------TVLYDG--------------------------RTGEPFDNLVTVGIMYILKL 1053

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KS
Sbjct: 1054 AHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKS 1113

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +  +  E   D
Sbjct: 1114 DDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNENHQEVSLKEYTDD 1173

Query: 1380 F 1380
             
Sbjct: 1174 E 1174


>gi|225026546|ref|ZP_03715738.1| hypothetical protein EUBHAL_00795 [Eubacterium hallii DSM 3353]
 gi|224956160|gb|EEG37369.1| hypothetical protein EUBHAL_00795 [Eubacterium hallii DSM 3353]
          Length = 1302

 Score =  844 bits (2180), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/980 (44%), Positives = 606/980 (61%), Gaps = 66/980 (6%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G   +R  + +  +++D+P+LIEVQK SY  FL            GL+  F+ + PIT +
Sbjct: 37  GSKNIRMSYARQKDVLDMPNLIEVQKDSYKWFLTD----------GLKEVFEDISPITDY 86

Query: 69  SGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           SG   LEFV ++   +  K+ +++C  RD TYA PLK+ +RL           K   D K
Sbjct: 87  SGQLSLEFVDFQLCREDRKYSIEECKERDATYAAPLKVKVRLH---------NKETDDFK 137

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP
Sbjct: 138 QHDIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAISHDKI---GKKLYSCTVIP 194

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGD 243
           ++G W++ E DS D+ +VR+DR RKVPVT  + ALG+ +  EI   F    KI+ +   D
Sbjct: 195 NRGAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGIGTNAEIKELFGEEPKILKTLEKD 254

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSD 301
                      +         + +D+ E +I S         L K  + K  K L    +
Sbjct: 255 TATNYQEGLKKLYEKIRPGEPLSVDSAESLINSMFFDARRYDLAKVGRYKFNKKLMF-RN 313

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G  +A+D+++  TGEI  EAG  + ++  + I ++    +P +YV++      + ++
Sbjct: 314 RIAGHRLAQDVLDPSTGEILFEAGVRLTKEQADAIQNA---AVPYVYVETEEKEVKVLSS 370

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           ++ D               + P +V    +    +  L    ++YD     + ++   + 
Sbjct: 371 MMVDITSFVD---------VDPEEVGVTELVY--YPALEKILEEYDDIDEIKAQIRKNIT 419

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
              P   +HI +EDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R
Sbjct: 420 ELIP---KHITREDILASINYNIHLEYGVGNDDDIDHLGNRRIRAVGELLQNQYRIGLSR 476

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER ++ER+++ DI+S+ PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH RRL
Sbjct: 477 LERVVRERMTTQDIESISPQTLINIKPVTAAVKEFFGSSQLSQFMDQHNPLSELTHKRRL 536

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGF+E P
Sbjct: 537 SALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLATYARINEYGFVEAP 596

Query: 602 YRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           YRKV      +  VT+DVVYL+A EE+N  +AQAN  LDE+G F    V  R   E    
Sbjct: 597 YRKVDKSDPQNPVVTDDVVYLTADEEDNYTVAQANEPLDEEGHFIHTNVSGRYREETSEF 656

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            + +ID +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLLK E P VGTGME
Sbjct: 657 RKSRIDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLKTEVPVVGTGME 716

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
           +  A+ SG  I+A  AG VE   +  I+++  +G  D        Y ++KF RSNQ  C+
Sbjct: 717 AKAARDSGVCIIAHHAGTVEYSTSKEIIVKREDGIRD-------TYHVIKFSRSNQGNCM 769

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  GD V   DI+ADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V  
Sbjct: 770 NQRPIVNKGDHVEAGDILADGASTCGGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQN 829

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DV+TS+HIEE+E  ARDTKLG EEITRD+  +SE+ LK++DE GII +GAEV+ GDILVG
Sbjct: 830 DVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDENGIIRIGAEVHAGDILVG 889

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID----- 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V+D ++F R   D     
Sbjct: 890 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGAYGVVMDTKVFTRENGDELPPT 949

Query: 952 --KNERSISVEREQIELLAR 969
             K+ R    ++ +I +  +
Sbjct: 950 VNKSVRVYIAQKRKISVGDK 969



 Score =  540 bits (1390), Expect = e-151,   Method: Composition-based stats.
 Identities = 253/1055 (23%), Positives = 401/1055 (38%), Gaps = 67/1055 (6%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +       I  TL  D   + ++ L  +Y  +RPG+  +   AES+ N +FFD+ +YDL+
Sbjct: 239  ELFGEEPKILKTLEKDTATNYQEGLKKLYEKIRPGEPLSVDSAESLINSMFFDARRYDLA 298

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKED---IIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             VGR K N +L          + ++        I     +R  K   D I N     V  
Sbjct: 299  KVGRYKFNKKLMFRNRIAGHRLAQDVLDPSTGEILFEAGVRLTKEQADAIQNAAVPYVYV 358

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
              E             E+ +K   S +    V     ++  P    V E      L ++ 
Sbjct: 359  ETE-------------EKEVKVLSSMM----VDITSFVDVDPEEVGVTELVYYPALEKIL 401

Query: 527  EHVNSLSRITHTRRLSA--LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            E  + +  I    R +   L    + R      +       YG     +     N   + 
Sbjct: 402  EEYDDIDEIKAQIRKNITELIPKHITREDILASINYNIHLEYGVGNDDDIDHLGN-RRIR 460

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            ++    +      +    R V +   T D+  +S     N     A        S   + 
Sbjct: 461  AVGELLQNQYRIGLSRLERVVRERMTTQDIESISPQTLINIKPVTAAVKEFFGSSQLSQF 520

Query: 645  VFCRCAGEEILVPREKIDF------IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +       E+   R            D +  +V  +  S    +   ++        +  
Sbjct: 521  MDQHNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINS 580

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
             A      E  FV      V        +V      +   +     +      LD     
Sbjct: 581  LATYARINEYGFVEAPYRKVDKSDPQNPVVTDDVVYLTADEEDNYTVAQANEPLDEEGHF 640

Query: 759  VDIYRLMKFQRS--------NQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALG 808
            +      +++               V+ + +  V         +  A+            
Sbjct: 641  IHTNVSGRYREETSEFRKSRIDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQA 700

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFT-SIHIEEFEVMARDTKLGPEEITRDIPN 867
              +L   +P  G   E        +        ++     + +    + G  +    I  
Sbjct: 701  VPLLKTEVPVVGTGMEAKAARDSGVCIIAHHAGTVEYSTSKEIIVKREDGIRDTYHVIKF 760

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +++  I+  G  V  GDIL    +  G   M   +  L      +  +  D 
Sbjct: 761  SRSNQGNCMNQRPIVNKGDHVEAGDILADGASTCG-GEMALGKNPLIGFMTWEGYNYEDA 819

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             L +   +    V   +       +   +   + E    LA   +D    LD N   R+ 
Sbjct: 820  VL-LSERLVQNDVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDENGIIRIG 878

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
              +   + + G    K  T L+++      R+ + + A +       V            
Sbjct: 879  AEVHAGDILVGKVTPKGETELTAE--ERLLRAIFGEKAREVRDTSLRVPHG--------- 927

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    K+   + GD++PP V + V+V++A KR I  GDKMAGRHGNKG+VSR+LP E
Sbjct: 928  AYGVVMDTKVFTRENGDELPPTVNKSVRVYIAQKRKISVGDKMAGRHGNKGVVSRVLPVE 987

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + +     DI  
Sbjct: 988  DMPFLPNGRPLDIVLNPLGVPSRMNIGQVLELHLSLASKVLGFNVATPVFNGADENDIMD 1047

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                            +    D  +   +   W +                     +   
Sbjct: 1048 TLEMANDYANKTWEEFEERWGDKVNDDIMKYLWDN--------------RDHREEWKGVP 1093

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D +G+  L DG TG+ FD PV++G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1094 IDRTGKVQLRDGRTGQEFDSPVSIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1153

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF
Sbjct: 1154 QFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESF 1213

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VL+KE Q+L L + +           E     N+
Sbjct: 1214 KVLLKEFQSLALDVRVLKEDMTEIELQEGSETINE 1248


>gi|158319535|ref|YP_001512042.1| DNA-directed RNA polymerase subunit beta [Alkaliphilus oremlandii
           OhILAs]
 gi|182676550|sp|A8MLD2|RPOB_ALKOO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158139734|gb|ABW18046.1| DNA-directed RNA polymerase, beta subunit [Alkaliphilus oremlandii
           OhILAs]
          Length = 1241

 Score =  844 bits (2180), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/965 (44%), Positives = 595/965 (61%), Gaps = 65/965 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G    R  + +  E++++P+LI++QK SY  FL          +EGL+  F 
Sbjct: 1   MMPHPVQLGKK-TRMSYSQIDEVLEMPNLIDLQKDSYQWFL----------DEGLKEVFD 49

Query: 61  SVFPITAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            V PI  ++G  +LEFV Y  D  PK++++D   RD+TYA PLK+ +RLI          
Sbjct: 50  DVSPIEDYTGNLILEFVDYSLDENPKYNIEDSKERDVTYAAPLKVKVRLI---------N 100

Query: 120 KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
           K+  ++KEQ ++MGD PLMT  GTF+I G +R++V+QL RSPG+++  +  +    GK L
Sbjct: 101 KTTGEVKEQEVFMGDFPLMTDTGTFIINGAERVIVNQLVRSPGVYYSREFDKT---GKQL 157

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY 238
           ++  +IP++G W++ E DS DI+ VRIDR RK PVT  L ALG  S+ +I          
Sbjct: 158 FSATVIPNRGAWLEYETDSNDIVSVRIDRTRKQPVTVLLRALGYGSDAQIKELLGEDERL 217

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG 297
               +      +   L+   K       +  GE   +E+ K L   L    K   +  +G
Sbjct: 218 LATLEKDSTKTTDEALLEIYK------KLRPGEPPTVENAKSLLRTLFFDPKRYDLAKVG 271

Query: 298 ITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                      + + G   A +IV+  TGEI +E G  ID ++   +  S I ++ I Y 
Sbjct: 272 RYKFNKKLSLANRILGKKAAANIVDPSTGEILVEEGTKIDRETSIMVQDSGINEVFI-YA 330

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +       + N  V                 ++  D   + V + + +    + D  D  
Sbjct: 331 EDNKVIKVLGNHFVNINKHIP-----FNIEELKISDKVYYPVLKEILDTFSQEEDIRDAL 385

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                              +HI   DIIA I    +L +  G IDDID+LGNRR RSVGE
Sbjct: 386 K----------ERAKELSPKHIIIADIIASISYEFNLAHDTGNIDDIDHLGNRRSRSVGE 435

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER +KER++  D+D   PQ LIN +PV +A+ EFF SSQLSQ  +  
Sbjct: 436 LLQNQFRIGLSRMERVVKERMTIQDVDLATPQALINIRPVAAAIKEFFGSSQLSQFMDQN 495

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+++L+++
Sbjct: 496 NPLSELTHKRRLSALGPGGLSRERAGFEVRDVHNSHYGRMCPIETPEGPNIGLINTLSTY 555

Query: 590 ARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGFIE+PYRKV   +  VTN + YL+A EE+   IAQAN  LDE+G F  + + C
Sbjct: 556 ARVNEYGFIESPYRKVDKKRGVVTNVIEYLTADEEDLLVIAQANEPLDEEGRFVNKRIAC 615

Query: 648 RCAGEEILVPR-EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R     I +    ++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPLL  
Sbjct: 616 RMQFGAIDIAPANEVDYMDVSPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLLIT 675

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +AP +GTGME   AK SG  I+AK  G+++++ +  IVI+  +          D Y+L+K
Sbjct: 676 DAPIIGTGMEYQSAKDSGVVILAKHDGVIDRLSSNEIVIKRDK------DGQKDRYKLLK 729

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ TC+NQRP+V  G+ V+  D+IADGPST+ G++ALGRN L+ FM W GYN+ED+
Sbjct: 730 FKRSNQGTCINQRPIVSKGERVKAGDVIADGPSTNQGEIALGRNCLIGFMTWEGYNYEDA 789

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LI+E++V ED  TSIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++DE GII +GA
Sbjct: 790 ILINEKLVKEDSLTSIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDLDERGIIRIGA 849

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VD+++F+
Sbjct: 850 EVQSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDIKVFS 909

Query: 947 RHGID 951
           R   D
Sbjct: 910 RENGD 914



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 185/540 (34%), Positives = 254/540 (47%), Gaps = 79/540 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++ +  K G ++  + +          I++  I+  G  V  GD++    +   +  + 
Sbjct: 711  EIVIKRDKDGQKDRYKLLKFKRSNQGTCINQRPIVSKGERVKAGDVIADGPST-NQGEIA 769

Query: 908  PEEKLLRAIFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                 L      +  +  D  L      +  S  S  + +     R      E       
Sbjct: 770  LGRNCLIGFMTWEGYNYEDAILINEKLVKEDSLTSIHIEEYEAEARDTKLGPEEITRDIP 829

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E   +D  DE+ I+      +  +IL G+    G         L   +  E  R   
Sbjct: 830  NVGEEALKDL-DERGIIRIGAEVQSGDILVGKVTPKGETELTAEERLLRAIFGEKAR--- 885

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E      +            K+   + GD++PPGV  +V+ ++A K
Sbjct: 886  --------------EVRDTSLKVPHGESGIIVDIKVFSRENGDELPPGVNELVRAYIAQK 931

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I  GDKMAGRHGNKG++SR+LP EDMPFL DGTP++IVLNPLGVPSRMN+GQ+ E HL
Sbjct: 932  RKINVGDKMAGRHGNKGVISRVLPAEDMPFLADGTPLEIVLNPLGVPSRMNIGQVLEVHL 991

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG  + + + D     DI                            L +A   +
Sbjct: 992  GLAAKSLGWNVATPVFDGANEHDIM-------------------------DALEMAGFSR 1026

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            SG                             +  LYDG TGEPFD  VTVGY+YMLKL+H
Sbjct: 1027 SG-----------------------------KVKLYDGRTGEPFDNDVTVGYMYMLKLHH 1057

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDD
Sbjct: 1058 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDD 1117

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR + YE IV G +  E G PESF VL+KE+Q+L L + +           E + D +
Sbjct: 1118 VVGRVKTYECIVKGENIPEPGVPESFKVLIKELQSLCLDVKVLTEEDSEIEIKESVEDDS 1177


>gi|197303964|ref|ZP_03168996.1| hypothetical protein RUMLAC_02701 [Ruminococcus lactaris ATCC
           29176]
 gi|197296932|gb|EDY31500.1| hypothetical protein RUMLAC_02701 [Ruminococcus lactaris ATCC
           29176]
          Length = 1287

 Score =  843 bits (2178), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/953 (46%), Positives = 589/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 13  KSFRMSYSRQEEVLEMPNLIEVQKDSYKWFL----------DEGLKEVFDDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIDECKERDATYAAPLKVRVRLY---------NKENDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKF---GKKLYSATVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASFTKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ESYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLNL-KNRV 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGE+  E G  I  +    I +S    I +   D   N   + N +V
Sbjct: 290 TGQVLAEDVVSAVTGEVVAEKGTKITRELAGMIQNSAAPYIWVEGEDESRNIKVLSNLMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             ++                 D +   V E ++  +     +     V  +K  ++ +L 
Sbjct: 350 DLQSVVDI-------------DPAEVGVTEQVYYPVLAGIIEESAGDVDEMKRMIKRDLH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 397 -DLIPKHITKEDILASINYNMHLEYGMGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRME 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D D + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDQDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACYARINEYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           KV      +  VT++VVY++A EE+N ++AQAN+ LDE+G F  + V  R   E     R
Sbjct: 576 KVDKSDPMNPVVTDEVVYMTADEEDNYHVAQANTPLDEEGHFINKNVSGRYREETQDYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K D++D SPKQV S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 NKFDYMDVSPKQVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG A VA++AG+VE   +  I IR  +G           Y+L KFQRSNQ+ C NQ
Sbjct: 696 SAVDSGVAEVAEQAGVVESSTSTSITIRHDDGTK-------KTYKLTKFQRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV
Sbjct: 749 RPIVDKGERVEAGQVIADGPSTSGGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  555 bits (1430), Expect = e-155,   Method: Composition-based stats.
 Identities = 238/1067 (22%), Positives = 400/1067 (37%), Gaps = 79/1067 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D       I  +   D ++  ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 212  IDLFGEEPKILASFTKDTSESYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +LNL      + + ++ + A+         G+   +    +       + 
Sbjct: 272  AKVGRYKFNKKLNLKNRVTGQVLAEDVVSAVT--------GEVVAEKGTKITRELAGMIQ 323

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +      R+IK   + +     +         V   V     +  + +    
Sbjct: 324  NSAAPYIWVEGEDESRNIKVLSNLMVDLQSVVDIDPAEVGVTEQVYYPVLAGIIEESAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            V+ + R+   R L  L    + +      +       YG     +     N   + ++  
Sbjct: 384  VDEMKRMI-KRDLHDLIPKHITKEDILASINYNMHLEYGMGNDDDIDHLGN-RRIRAVGE 441

Query: 589  FARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED 637
              +      +    R V +   T D           +  ++A  +E    +Q +  +D++
Sbjct: 442  LLQNQYRIGLSRMERVVRERMTTQDQDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 501

Query: 638  G--------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                          L     + +        + +        +         L N  +  
Sbjct: 502  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACY 561

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +           ++A    V          +     +         V      +    
Sbjct: 562  ARI------NEYGFIEAPYRKVDKSDPMNPVVTDEVVYMTADEEDNYHVAQANTPLDEEG 615

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTC---VNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              ++ + SG        ++R+  +       Q   V         +  A+          
Sbjct: 616  HFINKNVSGRYREETQDYERNKFDYMDVSPKQVFSVATALIPFLQNDDANRALMGSNMQR 675

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGPEEITRDI 865
                +L    P  G   E    +   +        +        +      G ++  +  
Sbjct: 676  QAVPLLTTEAPVVGTGMEVKSAVDSGVAEVAEQAGVVESSTSTSITIRHDDGTKKTYKLT 735

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                       ++  I+  G  V  G ++    +  G   M   +  L      +  +  
Sbjct: 736  KFQRSNQSNCYNQRPIVDKGERVEAGQVIADGPSTSG-GEMALGKNPLIGFMTWEGYNYE 794

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILD 979
            D  L     V   V        +  +  +  +  E    +         +D  DE+ I+ 
Sbjct: 795  DAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIR 853

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 R  +IL G+    G         L   +  E  R                 E   
Sbjct: 854  IGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRD 896

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
               +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+
Sbjct: 897  TSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGV 956

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + +   
Sbjct: 957  VSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVSTPVFAG 1016

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                DI          +       +    ++     +    ++                 
Sbjct: 1017 ANENDIMDTLDLANDYVNLEWEEFEKKHGEELRPEVLQFLSENRAH-------------- 1062

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVT
Sbjct: 1063 RELWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVT 1122

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  
Sbjct: 1123 QQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIP 1182

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            E G PESF VL+KE+Q+L L + +          ME + D+ + +L+
Sbjct: 1183 EPGVPESFKVLLKELQSLALDVRVLRDDNTEVKIMESV-DYGETDLR 1228


>gi|302388106|ref|YP_003823928.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           saccharolyticum WM1]
 gi|302198734|gb|ADL06305.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           saccharolyticum WM1]
          Length = 1283

 Score =  843 bits (2177), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/953 (45%), Positives = 595/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F +  E++++P+LIE+QK SY  FL          +EGL+  F+ + PI  F+G
Sbjct: 8   KSLRMSFSRQKEVLEMPNLIEIQKNSYQWFL----------DEGLKEVFEDISPIADFAG 57

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV++    D  K+ +++C  RD TYA PLK+ +RL   D D         +I E 
Sbjct: 58  HLSLEFVNFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD---------EINEH 108

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++  +  +    GK LYAC +IP++
Sbjct: 109 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIEHDKV---GKELYACTVIPNR 165

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS DI +VR+DR RKVPVT  + ALG  +  EI+  F    K++ S   D  
Sbjct: 166 GAWLEYETDSNDIFYVRVDRTRKVPVTVLIRALGFGTNAEIIELFGEEPKLLASFGKDTS 225

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L    + +
Sbjct: 226 DNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKL-HFKNRI 284

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGEI  EAG  +D++   +I ++    +P ++++ V +   + + L+
Sbjct: 285 TGHVLAEDVVDTTTGEILAEAGTTVDKQLATDIQNA---AVPFVWLEGVEHKQKVLSNLM 341

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D +                 D     + E +F            S       N      
Sbjct: 342 VDLSTFV------------SFDPKEAGITELVFYPALEKILAEAGSEDEETLKNALHRNI 389

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L    GT DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 390 NELIPKHITKEDILASINYNMHLEEEVGTADDIDHLGNRRIRAVGELLQNQYRIGLSRME 449

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L+ +TH RRLSA
Sbjct: 450 RVVRERMTTQDMDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLSA 509

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGF+E PYR
Sbjct: 510 LGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFVEAPYR 569

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            V      +  VT++VVYL+A EE+N  +AQAN  LDEDG F  + +  R   E     R
Sbjct: 570 VVDKTNAQNPVVTDEVVYLTADEEDNFVVAQANEPLDEDGHFVHKNISGRFREETSEFQR 629

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           + ID +D SPK V S+A ++IPFLENDD+NR LMG NMQRQAVPLL  E P VGTGMES 
Sbjct: 630 KNIDLMDVSPKMVFSVATAMIPFLENDDANRALMGSNMQRQAVPLLTTETPVVGTGMESK 689

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+ AG+VE+  +  I+I+        S  G D+YRL KF+RSNQ+ C NQ
Sbjct: 690 AAVDSGVCVVARNAGVVERSASNEIIIKRD------SDGGKDVYRLTKFKRSNQSNCYNQ 743

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +P+V   + V + ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SE++V EDV
Sbjct: 744 KPIVYKNNHVEKGEVIADGPSTQNGEIALGKNPLIGFMTWEGYNYEDAVLLSEKLVQEDV 803

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK+
Sbjct: 804 YTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGKV 863

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 864 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 916



 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 179/595 (30%), Positives = 267/595 (44%), Gaps = 42/595 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E    +     +V+ +          E++ +    G
Sbjct: 663  MGSNMQRQAVPLLTTETPVVGTGMESKAAVDSGVCVVARNAGVVERSASNEIIIKRDSDG 722

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +++ R             ++  I+     V  G+++    + +    +   +  L    
Sbjct: 723  GKDVYRLTKFKRSNQSNCYNQKPIVYKNNHVEKGEVIADGPSTQN-GEIALGKNPLIGFM 781

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDK 971
              +  +  D  L     V   V        +  +  +  +  E          E   +D 
Sbjct: 782  TWEGYNYEDAVLLSEKLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDL 841

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 842  -DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 887

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+   + GD++ PGV + V++++A KR I  GDKMA
Sbjct: 888  ----EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNQTVRIYIAQKRKISVGDKMA 943

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  
Sbjct: 944  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAARALGFN 1003

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D     DI                 +    Y +     V       +       
Sbjct: 1004 VSTPVFDGANEIDIMDTLDVAND-YVNMEWKDFQEKYSETLKPEVIRYLGDHL------- 1055

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                      + +   ++  G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARS
Sbjct: 1056 ------DHKELWKGVPINRDGKVRLRDGRTGEFFDSPVTIGHMHYLKLHHLVDDKIHARS 1109

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE++T+KSDDVVGR + YE+
Sbjct: 1110 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEIMTVKSDDVVGRVKTYEA 1169

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            I+ G++  E G PESF VL+KE+Q+L L + +           E   DF + +L+
Sbjct: 1170 IIKGDNIPEPGIPESFKVLLKELQSLALDVRVLRDDNTEVQIAEST-DFEETDLR 1223


>gi|188588112|ref|YP_001919665.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum E3
           str. Alaska E43]
 gi|251780255|ref|ZP_04823175.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|226699387|sp|B2UYA3|RPOB_CLOBA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|188498393|gb|ACD51529.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum E3
           str. Alaska E43]
 gi|243084570|gb|EES50460.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 1241

 Score =  842 bits (2176), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/956 (46%), Positives = 599/956 (62%), Gaps = 67/956 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++ ++P+LIEVQ  SY  FL           EGL   F  + PIT F+G
Sbjct: 9   KRTRMSFGKVKDVTEMPNLIEVQLDSYQWFLR----------EGLHEVFDDINPITNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y+ D    K+ V++C  RD TYA PLK+++RL               +IKEQ
Sbjct: 59  NLVLEFVDYKLDMDNIKYSVEECKERDATYAAPLKVSVRL---------QNNETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT  GTF+I G +R++VSQL RSPG+++++   +    GK LY+  +IP++
Sbjct: 110 EVFMGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNYSIDKT---GKKLYSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS DII+VRID+ RK+P+T    A+G  S+ E+L  F     +    +    
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPITILARAMGFGSDQELLDFFGEDERFRASIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTREEGLLEIYK------RLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A D++N  TGEI +E G  I     E+I ++ I+ + IL  D +     I
Sbjct: 281 LNLRIANQIAAMDVINPSTGEIMVEKGQKISRLLSEDIQNAGIKSVDILVDDKLVR--VI 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKMN 417
            N              +DI + + P DVS   + E + +  L    D Y      + ++ 
Sbjct: 339 SNN------------FVDITKQV-PFDVSDLQIKELVHYPTLKEILDNYSDEATIKEEIK 385

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             L+   P   +HI K+DI A I   + L  G G +DDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 386 KNLSRLIP---KHIIKDDIFATISYELGLPYGIGYVDDIDHLGNRRLRSVGELLQNQFRI 442

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER +KER++  D +S+ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH
Sbjct: 443 GLSRMERVVKERMTIQDQESITPQMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTH 502

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FARVN YGF
Sbjct: 503 KRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFARVNEYGF 562

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR +   + + T ++ Y +A EE+   IAQA   LDE+G F ++ V  R   + ++
Sbjct: 563 IETPYRIIDKENARATEEIRYFTADEEDQCLIAQAKEPLDENGYFVDKKVTVRYLEDVLV 622

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           VP   +D +D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+
Sbjct: 623 VPATDVDLMDVSARQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGI 682

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG    AK AG+V  V A  I ++        S  G D YRL+KF+RSNQ++C
Sbjct: 683 EFKAAVDSGVLPKAKNAGVVTFVSANEIRVKRD------SDGGTDNYRLLKFKRSNQSSC 736

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +NQRP+V  G+ V +N ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V 
Sbjct: 737 INQRPIVNKGEIVFKNQVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVR 796

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           EDVFTS+HIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+ID+ GII +GAEV  GDILV
Sbjct: 797 EDVFTSMHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDDRGIIRIGAEVRSGDILV 856

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VD+++F R   D
Sbjct: 857 GKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDIKVFTRENGD 912



 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 268/1151 (23%), Positives = 420/1151 (36%), Gaps = 142/1151 (12%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            + G  + +G  + +  + V+  G+  +      G  +    V    G          +I 
Sbjct: 121  DQGTFIINGAERVIVSQLVRSPGVYYNYSIDKTGKKLYSATVIPNRGAWLEYETDSNDII 180

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         +D    +   R ++  D  K R++ LL+IY+ +
Sbjct: 181  YVRIDKTRKLPITILARAMGFGSDQELLDFFGEDERFRASIEKDNTKTREEGLLEIYKRL 240

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L L+     +    + I     
Sbjct: 241  RPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLALNLRIANQIAAMDVINPSTG 300

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             ++  +  K +    +++ N  ++SV  ++ +       ++ R I    + VDI   +P 
Sbjct: 301  EIMVEKGQKISRLLSEDIQNAGIKSVDILVDD-------KLVRVIS--NNFVDITKQVPF 351

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            D ++   +   V        L    +       I   + LS L    + +      +   
Sbjct: 352  D-VSDLQIKELVHYPTLKEILDNYSDEATIKEEI--KKNLSRLIPKHIIKDDIFATISYE 408

Query: 562  HPTHYGR--ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
                YG   +   +      +  V  L    +      +    R V +     D   ++ 
Sbjct: 409  LGLPYGIGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQESITP 465

Query: 620  MEEENRY-IAQAN---------SSLDEDGSFTEELVFCRC---------AGEEILVPREK 660
                N   +A A          S   +  +   EL   R          + E        
Sbjct: 466  QMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 525

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +          +         L N  +    +           ++  E       +    
Sbjct: 526  VHHSHYGRMCPIETPEGPNIGLINSLATFARVNEYGFIETPYRIIDKENARATEEIRYFT 585

Query: 720  AKSSGAAIVA---KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            A      ++A   +           ++ +R +E  L    + VD            +   
Sbjct: 586  ADEEDQCLIAQAKEPLDENGYFVDKKVTVRYLEDVLVVPATDVD----------LMDVSA 635

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q   V         +  A               +L    P  G   E    +   ++ +
Sbjct: 636  RQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEFKAAVDSGVLPK 695

Query: 837  DVFTSIHIEEF--EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 +       E+  +    G  +  R +          I++  I+  G  V    +L
Sbjct: 696  AKNAGVVTFVSANEIRVKRDSDGGTDNYRLLKFKRSNQSSCINQRPIVNKGEIVFKNQVL 755

Query: 895  VGKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                +         +   +  I       E A+ + +  +R     S  + +     R  
Sbjct: 756  ADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSMHIEEYECEARDT 815

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
                E          E   +D DD   I+      R  +IL G+    G         L 
Sbjct: 816  KLGPEEITRDIPNVSEDALKDIDDR-GIIRIGAEVRSGDILVGKVTPKGETELTAEERLL 874

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              +  E  R                 E                   K+   + GD++ PG
Sbjct: 875  RAIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDIKVFTRENGDELNPG 917

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V  +V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMPFL DG P+ I LNPLGVPS
Sbjct: 918  VNELVRCYIVQKRKISVGDKMAGRHGNKGVISRILPEEDMPFLPDGRPLQICLNPLGVPS 977

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGWA   LG  I + + D     +I                        
Sbjct: 978  RMNIGQVLEVHLGWAASKLGWHISTPVFDGATENEIEACLEKAGYNANGK---------- 1027

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                              T ++DG                           TGEPFD PV
Sbjct: 1028 ------------------TVLYDG--------------------------RTGEPFDNPV 1043

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVG +Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+
Sbjct: 1044 TVGIMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAH 1103

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +
Sbjct: 1104 TLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNENHQ 1163

Query: 1370 NSAKMEEIPDF 1380
              +  E   D 
Sbjct: 1164 EVSLKEYTDDE 1174


>gi|255654155|ref|ZP_05399564.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-23m63]
 gi|296449806|ref|ZP_06891574.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           NAP08]
 gi|296877870|ref|ZP_06901891.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           NAP07]
 gi|296261350|gb|EFH08177.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           NAP08]
 gi|296431124|gb|EFH16950.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           NAP07]
          Length = 1238

 Score =  842 bits (2176), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/955 (45%), Positives = 598/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY+ FL           EGL+  F  + PI  ++G
Sbjct: 9   KRTRMSFSKIKEIADVPNLIEIQVDSYEWFL----------KEGLKEVFDDISPIEDYTG 58

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 59  NLILEFVDYSLDDKPKYDIEECKERDATYCAPLKVKVRLI---------NKETGEIKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTFVI G +R++VSQL RSPG+++  ++ +    GK L +  +IP++G
Sbjct: 110 VFMGDFPLMTERGTFVINGAERVIVSQLVRSPGVYYAEERDKT---GKRLISSTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+I VR+DR RK PVT  L ALG+ ++ EI+         S   +     
Sbjct: 167 AWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGTDAEIIDLLGEDERLSATLEKDNTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 227 TVEEGLVEIYK------KLRPGEPPTVESASSLLNALFFDPKRYDLAKVGRYKFNKKLAL 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +     AEDI+N ETGE++++AG+ I     + I ++ I  + +L  D         
Sbjct: 281 CYRIMNKISAEDIINPETGEVFVKAGEKISYDLAKAIQNAGINVVNLLMDDDKKVRVIGN 340

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + D     L+I   +              +  L    D Y      +  +  R
Sbjct: 341 NFVDIKSHIDFDIDDLNIKEKVH-------------YPTLKEILDGYSDEEEIKEAIKSR 387

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           +    P   +HI  +DIIA I    ++    G IDDID+LGNRR+RSVGE+L+NQ R+GL
Sbjct: 388 IKELIP---KHILLDDIIASISYEFNIFYNIGNIDDIDHLGNRRIRSVGELLQNQVRIGL 444

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER IKER++  D++++ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 445 SRMERVIKERMTVQDMEAITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 504

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A++N +GFIE
Sbjct: 505 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLGTYAKINEFGFIE 564

Query: 600 TPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK       VT+++ YL+A EE+    AQAN  L EDG F    V CR   G   +V
Sbjct: 565 SPYRKFDKETSTVTDEIHYLTADEEDLFVRAQANEPLTEDGKFVNHRVVCRTVNGAVEMV 624

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P  ++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 625 PESRVDYMDISPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLVRREAPIIGTGIE 684

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VA+ +GI E+V A  I+I+  +G+ D        Y L+KF+RSN  TC+
Sbjct: 685 YRAAKDSGAVVVARNSGIAERVTADEIIIKREDGNRD-------RYNLLKFKRSNSGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P++  GD++ + D+IADGP+TDLG++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 738 NQTPIINKGDQIMKGDVIADGPATDLGEVALGRNCLIAFMTWEGYNYEDAILINERLVKE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV +  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 798 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVFTRENGD 912



 Score =  466 bits (1199), Expect = e-128,   Method: Composition-based stats.
 Identities = 158/441 (35%), Positives = 220/441 (49%), Gaps = 70/441 (15%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +R  ++  E+ E  ARD       + R+I                I  G    SG   
Sbjct: 796  KEDRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDIL 855

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +          +      K+   +
Sbjct: 856  VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDV------KVFTRE 909

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GDD+ PGV  +V+ ++A KR I+ GDKMAGRHGNKG++SR+LP EDMPF+++GTP+DI+
Sbjct: 910  NGDDLSPGVNELVRCYIAKKRKIKVGDKMAGRHGNKGVISRVLPEEDMPFMENGTPLDII 969

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP G+PSRMN+GQ+ E HLG A   LG  + + + D     DI                
Sbjct: 970  LNPQGIPSRMNIGQVLEVHLGLAAKTLGWYVATSVFDGANEYDIMDALEEAGYPRDGKLT 1029

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                              G++       
Sbjct: 1030 L-----------------------------------------------YDGRT------- 1035

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE FD  +TVGY+Y LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1036 GESFDNRITVGYMYYLKLHHLVDEKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1095

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAA++LQE+LT+KSDDVVGR R YE+IV G +  E G PESF VL+KE+Q+L L +
Sbjct: 1096 LEAYGAAHILQEILTVKSDDVVGRVRTYEAIVKGENIPEPGIPESFKVLIKELQSLCLDV 1155

Query: 1362 DLENSRTKNSAKMEEIPDFNK 1382
             +     +     E + + + 
Sbjct: 1156 KVLTDEDQEIEVRESVDEDDT 1176


>gi|167758507|ref|ZP_02430634.1| hypothetical protein CLOSCI_00847 [Clostridium scindens ATCC 35704]
 gi|167663703|gb|EDS07833.1| hypothetical protein CLOSCI_00847 [Clostridium scindens ATCC 35704]
          Length = 1291

 Score =  842 bits (2175), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/953 (44%), Positives = 586/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTSTGTFVINGAERVIVSQLVRSPGIYYAIAHDKV---GKKLYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + A+G  +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRAMGFGTNPEIVELFGEEPKIIASFEKDAA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 TNYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +A+D+ +  TGE+  EAG  +  +  ++I ++ +  + I   D   N   + N +V
Sbjct: 290 TGQILAQDVASPLTGEVIAEAGTKVTRELADQIQNAAVPYVWIEREDEERNIKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
              +             +   D     V E ++  +     +     +  +K  ++ ++ 
Sbjct: 350 DITS-------------IVDVDPKEVGVTELVYYPVLAGILEETAGDIDELKDAIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+RSVGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNIHLEYGLGNDDDIDHLGNRRIRSVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINQYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +VVY++A EE+N ++AQAN  LD +G F  + V  R   E     R
Sbjct: 576 KINHDDPANPVVTEEVVYMTADEEDNYHVAQANEPLDAEGHFIHKNVSGRYRDETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 RMFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLMTEAPVVGTGMEEK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++A+  G+VE+  +  I IR  +G        +  Y+L+KF RSNQ+ C NQ
Sbjct: 696 SAVDSGVCVIAETGGVVERSTSTEITIRQDDG-------NLKRYKLIKFLRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD V   D+IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV
Sbjct: 749 RPIVFKGDRVEAGDVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LKN+DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKNLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRDNGD 921



 Score =  560 bits (1442), Expect = e-157,   Method: Composition-based stats.
 Identities = 245/1100 (22%), Positives = 409/1100 (37%), Gaps = 79/1100 (7%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            ++ +++    D   +  +  +  +         V+       I  +   D   + ++ LL
Sbjct: 179  DSNDVFYVRVDRTRKVPITVLIRAMGFGTNPEIVELFGEEPKIIASFEKDAATNYQEGLL 238

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            ++Y+ +RPG+      AES+   +FFD  +YDL+ VGR K N +L L      + + ++ 
Sbjct: 239  ELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLALKNRITGQILAQDV 298

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +         G+   +    +       +         +     ER+IK   + +  
Sbjct: 299  ASPLT--------GEVIAEAGTKVTRELADQIQNAAVPYVWIEREDEERNIKVLSNMMVD 350

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
             + +         V   V     +  L +    ++ L      R +  L    + +    
Sbjct: 351  ITSIVDVDPKEVGVTELVYYPVLAGILEETAGDIDELKDAI-KRDIHDLIPKHITKEDIL 409

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
              +       YG     +     N   + S+    +      +    R V +   T D+ 
Sbjct: 410  ASINYNIHLEYGLGNDDDIDHLGN-RRIRSVGELLQNQYRIGLSRLERVVRERMTTQDLE 468

Query: 616  YLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC---------AGEEILV 656
             +S     N     A               +  +   EL   R          + +    
Sbjct: 469  GISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPGGLSRDRAGF 528

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQRQAVPLLKAEAPFVGTGM 715
                + +        +         L N  +    +            +  + P      
Sbjct: 529  EVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINQYGFIEAPYRKINHDDPANPVVT 588

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E           +         V      + +    +  + SG       +++R   +  
Sbjct: 589  EE-------VVYMTADEEDNYHVAQANEPLDAEGHFIHKNVSGRYRDETQEYERRMFDYM 641

Query: 776  -VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             V+ + +  V         +  A+              +L+   P  G   E+   +   
Sbjct: 642  DVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLMTEAPVVGTGMEEKSAVDSG 701

Query: 833  -MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
              V  +    +       +      G  +  + I  +        ++  I+  G  V  G
Sbjct: 702  VCVIAETGGVVERSTSTEITIRQDDGNLKRYKLIKFLRSNQSNCYNQRPIVFKGDRVEAG 761

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D++    +      M   +  L      +  +  D  L     V   V        +  +
Sbjct: 762  DVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAE 820

Query: 952  KNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
              +  +  E     I  +  D     DE+ I+      R  +IL G+    G        
Sbjct: 821  ARDTKLGPEEITRDIPGVGDDALKNLDERGIIRIGAEVRAGDILVGKVTPKGETELTAEE 880

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  E  R                 E      +            K+     GD++
Sbjct: 881  RLLRAIFGEKAR-----------------EVRDTSLKVPHGEYGIVVDAKVFTRDNGDEL 923

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLG
Sbjct: 924  SPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLG 983

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HL  A   LG  I + + D     DI              S  E  +
Sbjct: 984  VPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGADENDIMDTLDLAND-YVNLSWEEFEA 1042

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
             + ++ +  V +                       + +   +   G+  L DG TGE FD
Sbjct: 1043 KHKEELLPEVLQYLSD-------------NREHRKLWKGVPISRDGKVRLRDGRTGEYFD 1089

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
             PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1090 SPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1149

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+Y LQE+LT+KSDDV+GR + YE+I+ G +  E G PESF VL+KE+Q+LGL + +   
Sbjct: 1150 ASYTLQEILTVKSDDVIGRVKTYEAIIKGENIPEPGIPESFKVLLKELQSLGLDVRVLRD 1209

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   ME + D  + + +
Sbjct: 1210 DNTEVEIMETV-DMGETDFR 1228


>gi|254973724|ref|ZP_05270196.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-66c26]
 gi|255091114|ref|ZP_05320592.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile CIP
           107932]
 gi|255312768|ref|ZP_05354351.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-76w55]
 gi|255515528|ref|ZP_05383204.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-97b34]
 gi|255648622|ref|ZP_05395524.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-37x79]
 gi|260681839|ref|YP_003213124.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           CD196]
 gi|260685437|ref|YP_003216570.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           R20291]
 gi|306518745|ref|ZP_07405092.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-32g58]
 gi|260208002|emb|CBA60173.1| DNA-directed RNA polymerase beta chain [Clostridium difficile
           CD196]
 gi|260211453|emb|CBE01567.1| DNA-directed RNA polymerase beta chain [Clostridium difficile
           R20291]
          Length = 1238

 Score =  842 bits (2175), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/955 (45%), Positives = 598/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY+ FL           EGL+  F  + PI  ++G
Sbjct: 9   KRTRMSFSKIKEIADVPNLIEIQVDSYEWFL----------KEGLKEVFDDISPIEDYTG 58

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 59  NLILEFVDYSLDDKPKYDIEECKERDATYCAPLKVKVRLI---------NKETGEIKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTFVI G +R++VSQL RSPG+++  ++ +    GK L +  +IP++G
Sbjct: 110 VFMGDFPLMTERGTFVINGAERVIVSQLVRSPGVYYAEERDKT---GKRLISSTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+I VR+DR RK PVT  L ALG+ ++ EI+         S   +     
Sbjct: 167 AWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGTDAEIIDLLGEDERLSATLEKDNTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 227 TVEEGLVEIYK------KLRPGEPPTVESASSLLNALFFDPKRYDLAKVGRYKFNKKLAL 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +     AEDI+N ETGE++++AG+ I     + I ++ I  + +L  D         
Sbjct: 281 CYRIMNKISAEDIINPETGEVFVKAGEKISYDLAKAIQNAGINVVNLLMDDDKKVRVIGN 340

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + D     L+I   +              +  L    D Y      +  +  R
Sbjct: 341 NFVDIKSHIDFDIDDLNIKEKVH-------------YPTLKEILDGYSDEEEIKEAIKSR 387

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           +    P   +HI  +DIIA I    ++    G IDDID+LGNRR+RSVGE+L+NQ R+GL
Sbjct: 388 IKELIP---KHILLDDIIASISYEFNIFYNIGNIDDIDHLGNRRIRSVGELLQNQVRIGL 444

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER IKER++  D++++ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 445 SRMERVIKERMTVQDMEAITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 504

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A++N +GFIE
Sbjct: 505 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLGTYAKINEFGFIE 564

Query: 600 TPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK       VT+++ YL+A EE+    AQAN  L EDG F    V CR   G   +V
Sbjct: 565 SPYRKFDKETSTVTDEIHYLTADEEDLFVRAQANEPLTEDGKFVNHRVVCRTVNGAVEMV 624

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P  ++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 625 PESRVDYMDISPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLVRREAPIIGTGIE 684

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VA+ +GI E+V A  I+I+  +G+ D        Y L+KF+RSN  TC+
Sbjct: 685 YRAAKDSGAVVVARNSGIAERVTADEIIIKREDGNRD-------RYNLLKFKRSNSGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P++  GD++ + D+IADGP+TDLG++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 738 NQTPIINKGDQIIKGDVIADGPATDLGEVALGRNCLIAFMTWEGYNYEDAILINERLVKE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV +  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 798 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVFTRENGD 912



 Score =  464 bits (1193), Expect = e-128,   Method: Composition-based stats.
 Identities = 157/441 (35%), Positives = 220/441 (49%), Gaps = 70/441 (15%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +R  ++  E+ E  ARD       + R+I                I  G    SG   
Sbjct: 796  KEDRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDIL 855

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +          +      K+   +
Sbjct: 856  VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDV------KVFTRE 909

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GDD+ PGV  +V+ ++A KR I+ GDKMAGRHGNKG++SR+LP EDMPF+++GTP+DI+
Sbjct: 910  NGDDLSPGVNELVRCYIAKKRKIKVGDKMAGRHGNKGVISRVLPEEDMPFMENGTPLDII 969

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP G+PSRMN+GQ+ E HLG A   LG  + + + D     DI                
Sbjct: 970  LNPQGIPSRMNIGQVLEVHLGLAAKTLGWYVATSVFDGANEYDIMDALEEAGYPRDGKLT 1029

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                              G++       
Sbjct: 1030 L-----------------------------------------------YDGRT------- 1035

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ FD  +TVGY+Y LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1036 GQSFDNRITVGYMYYLKLHHLVDEKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1095

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAA++LQE+LT+KSDDVVGR R YE+IV G +  E G PESF VL+KE+Q+L L +
Sbjct: 1096 LEAYGAAHILQEILTVKSDDVVGRVRTYEAIVKGENIPEPGIPESFKVLIKELQSLCLDV 1155

Query: 1362 DLENSRTKNSAKMEEIPDFNK 1382
             +     +     E + + + 
Sbjct: 1156 KVLTDEDQEIEVRESVDEDDT 1176


>gi|126697633|ref|YP_001086530.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           630]
 gi|255099226|ref|ZP_05328203.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           QCD-63q42]
 gi|255305008|ref|ZP_05349180.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile
           ATCC 43255]
 gi|123363690|sp|Q18CF1|RPOB_CLOD6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|115249070|emb|CAJ66881.1| DNA-directed RNA polymerase subunit beta [Clostridium difficile]
          Length = 1238

 Score =  842 bits (2174), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/955 (45%), Positives = 598/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY+ FL           EGL+  F  + PI  ++G
Sbjct: 9   KRTRMSFSKIKEIADVPNLIEIQVDSYEWFL----------KEGLKEVFDDISPIEDYTG 58

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 59  NLILEFVDYSLDDKPKYDIEECKERDATYCAPLKVKVRLI---------NKETGEIKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTFVI G +R++VSQL RSPG+++  ++ +    GK L +  +IP++G
Sbjct: 110 VFMGDFPLMTERGTFVINGAERVIVSQLVRSPGVYYAEERDKT---GKRLISSTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+I VR+DR RK PVT  L ALG+ ++ EI+         S   +     
Sbjct: 167 AWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGTDAEIIDLLGEDERLSATLEKDNTK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 227 TVEEGLVEIYK------KLRPGEPPTVESASSLLNALFFDPKRYDLAKVGRYKFNKKLAL 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +     AEDI+N ETGE++++AG+ I     + I ++ I  + +L  D         
Sbjct: 281 CYRIMNKISAEDIINPETGEVFVKAGEKISYDLAKAIQNAGINVVNLLMDDDKKVRVIGN 340

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + D     L+I   +              +  L    D Y      +  +  R
Sbjct: 341 NFVDIKSHIDFDIDDLNIKEKVH-------------YPTLKEILDGYSDEEEIKEAIKSR 387

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           +    P   +HI  +DIIA I    ++    G IDDID+LGNRR+RSVGE+L+NQ R+GL
Sbjct: 388 IKELIP---KHILLDDIIASISYEFNIFYNIGNIDDIDHLGNRRIRSVGELLQNQVRIGL 444

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER IKER++  D++++ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 445 SRMERVIKERMTVQDMEAITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 504

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A++N +GFIE
Sbjct: 505 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLGTYAKINEFGFIE 564

Query: 600 TPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK       VT+++ YL+A EE+    AQAN  L EDG F    V CR   G   +V
Sbjct: 565 SPYRKFDKETSTVTDEIHYLTADEEDLFVRAQANEPLTEDGKFVNHRVVCRTVNGAVEMV 624

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P  ++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 625 PESRVDYMDISPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLVRREAPIIGTGIE 684

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VA+ +GI E+V A  I+I+  +G+ D        Y L+KF+RSN  TC+
Sbjct: 685 YRAAKDSGAVVVARNSGIAERVTADEIIIKREDGNRD-------RYNLLKFKRSNSGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P++  GD++ + D+IADGP+TDLG++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 738 NQTPIINKGDQIIKGDVIADGPATDLGEVALGRNCLIAFMTWEGYNYEDAILINERLVKE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV +  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 798 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVFTRENGD 912



 Score =  466 bits (1199), Expect = e-128,   Method: Composition-based stats.
 Identities = 158/441 (35%), Positives = 220/441 (49%), Gaps = 70/441 (15%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +R  ++  E+ E  ARD       + R+I                I  G    SG   
Sbjct: 796  KEDRLSTIHIEEYECEARDTKLGPEEITRDIPNVGDSAIKNLDDRGIIRIGAEVDSGDIL 855

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +          +      K+   +
Sbjct: 856  VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDV------KVFTRE 909

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GDD+ PGV  +V+ ++A KR I+ GDKMAGRHGNKG++SR+LP EDMPF+++GTP+DI+
Sbjct: 910  NGDDLSPGVNELVRCYIAKKRKIKVGDKMAGRHGNKGVISRVLPEEDMPFMENGTPLDII 969

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP G+PSRMN+GQ+ E HLG A   LG  + + + D     DI                
Sbjct: 970  LNPQGIPSRMNIGQVLEVHLGLAAKTLGWYVATSVFDGANEYDIMDALEEAGYPRDGKLT 1029

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                              G++       
Sbjct: 1030 L-----------------------------------------------YDGRT------- 1035

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE FD  +TVGY+Y LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1036 GESFDNRITVGYMYYLKLHHLVDEKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1095

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAA++LQE+LT+KSDDVVGR R YE+IV G +  E G PESF VL+KE+Q+L L +
Sbjct: 1096 LEAYGAAHILQEILTVKSDDVVGRVRTYEAIVKGENIPEPGIPESFKVLIKELQSLCLDV 1155

Query: 1362 DLENSRTKNSAKMEEIPDFNK 1382
             +     +     E + + + 
Sbjct: 1156 KVLTDEDQEIEVRESVDEDDT 1176


>gi|24380333|ref|NP_722288.1| DNA-directed RNA polymerase subunit beta [Streptococcus mutans
           UA159]
 gi|290579694|ref|YP_003484086.1| DNA-dependent RNA polymerase subunit beta [Streptococcus mutans
           NN2025]
 gi|41018032|sp|Q8DS46|RPOB_STRMU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|24378350|gb|AAN59594.1|AE015022_1 DNA-dependent RNA polymerase, beta subunit [Streptococcus mutans
           UA159]
 gi|254996593|dbj|BAH87194.1| DNA-dependent RNA polymerase beta subunit [Streptococcus mutans
           NN2025]
          Length = 1187

 Score =  842 bits (2174), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D  Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARAHDAHYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPLMTEMGTFIINGAERIIVSQLVRSPGVYFN---DKVDKNGKIGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPNDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQVIAENLVDPETGEILVEAGTEMTRSVIDSIADYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N          +  +L  ++VM P D                         
Sbjct: 332 --NKIVYTPNEYAVL----TEPVVLQKFKVMAPNDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D VRH+   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 362 --DRTVTVIGNASPDDKVRHLTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN++ +L+A EE+   +AQANS L+EDGSF EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRETGKVTNEIEWLTADEEDEFTVAQANSKLNEDGSFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   ++++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPASSVEYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAAI+A+  G V   DA +I +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAIIAQHNGKVVYSDADKIEVRREDGSLD-------VYHVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LV+VGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVRVGDSVEKGDFIADGPSMEKGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVCDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 239/1069 (22%), Positives = 397/1069 (37%), Gaps = 122/1069 (11%)

Query: 332  SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 195  LVRALGFSGDDEIIDIFGDSELVRNTIEKDIHKNPNDSRTDEALKEIYERLRPGEPKTAD 254

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             + S+    FFD+ +YDL+ VGR K+N +LN           +     I + LVD   G+
Sbjct: 255  SSRSLLIARFFDARRYDLAAVGRYKINKKLN--------VKTRLLNQVIAENLVDPETGE 306

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
              ++    +    + S+ + L          + + +    +  +   +    ++    V+
Sbjct: 307  ILVEAGTEMTRSVIDSIADYLDG-------DLNKIVY---TPNEYAVLTEPVVLQKFKVM 356

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +         +   +  + +   ++ H      L +       A    +     H G   
Sbjct: 357  APND----PDRTVTVIGNASPDDKVRHLTPADILAEMSYFLNLAEGLGKVDDIDHLGNRR 412

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
                 E         L    R N    +     +V   +   ++  ++A  +E    +Q 
Sbjct: 413  IRAVGELLANQFRIGLARMER-NVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQL 471

Query: 631  NSSLDEDG--------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPF 681
            +  +D+               L       +        + +        +       I  
Sbjct: 472  SQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGL 531

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVD 739
            + N  S   L      +     +  E   V   +E + A  +       A      +   
Sbjct: 532  INNLSSYGHLNKYGFIQTPYRKVDRETGKVTNEIEWLTADEEDEFTVAQANSKLNEDGSF 591

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A  IV+   +G+     +    Y          +    Q   V         +  ++   
Sbjct: 592  AEEIVMGRHQGNNQEFPASSVEY---------MDVSPKQVVAVATACIPFLENDDSNRAL 642

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   +       +   + + +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPFVGTGMEYQAAHDSGAAIIAQHNGKVVYSDADKIEVRREDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +   +  M   +  + A   
Sbjct: 703  LDVYHVTKFRRSNSGTAYNQRTLVRVGDSVEKGDFIADGPS-MEKGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  +     V   V           +  +  +  E    +I  +  D     D
Sbjct: 762  WEGYNFEDAVIMSERLVKDDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALKDLD 821

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+      +  +IL G+    G K       L   +  +  R           +V+ 
Sbjct: 822  EMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVRD 870

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAGR
Sbjct: 871  TSLRVPHGGDGVVCDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGR 924

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I 
Sbjct: 925  HGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIA 984

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D   + D+                                          T ++DG
Sbjct: 985  TPVFDGATSDDLWETVKEAGMDSDAK----------------------------TVLYDG 1016

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                                       TGEPFD  V+VG +YM+KL+HMV DK++ARS G
Sbjct: 1017 --------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVG 1050

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YS +TQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I 
Sbjct: 1051 PYSTITQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAIT 1110

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             G    + G PESF VLVKE+Q+LGL + + +   K     +     + 
Sbjct: 1111 KGKPIPKPGVPESFRVLVKELQSLGLDMRVLDKDDKEVDLRDLDEGEDD 1159


>gi|331007093|ref|ZP_08330316.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium
            IMCC1989]
 gi|330419088|gb|EGG93531.1| DNA-directed RNA polymerase beta subunit [gamma proteobacterium
            IMCC1989]
          Length = 643

 Score =  841 bits (2173), Expect = 0.0,   Method: Composition-based stats.
 Identities = 356/640 (55%), Positives = 484/640 (75%), Gaps = 1/640 (0%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
               VAKR G++E+VDA RIV+R+ + + +   +GVDIY L K+ RSNQNTC+NQ+P+V V
Sbjct: 1    MCGVAKRGGVIERVDAARIVVRASDSETEAGDAGVDIYNLTKYTRSNQNTCINQKPIVHV 60

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD + R DI+ADGPS D+G+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IHI
Sbjct: 61   GDTIVRGDILADGPSVDMGELALGQNMRIAFMPWNGYNFEDSILVSERVVKEDRFTTIHI 120

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV PGDILVGK+TPKGE+
Sbjct: 121  QELTCIARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVGPGDILVGKVTPKGET 180

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +TPEEKLLRAIFGEKA DV+DTS RVP+   GTV+DV++F R G++K+ RS ++E  Q+
Sbjct: 181  QLTPEEKLLRAIFGEKASDVKDTSSRVPTSTKGTVIDVQVFTRDGLEKDPRSKAIEEMQL 240

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E + +D ++E  I++   + RL  +L GQ   +G K  KK T L+++++++  + Q +  
Sbjct: 241  EKVRKDLNEEFRIVEAATFERLYSVLVGQKTSAG-KAVKKGTELTAEILADLDKDQLFNL 299

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             V D+ +   ++  + Q +  ++IL++RF++K  K+Q GDD+ PGVL++VKV++A+KR I
Sbjct: 300  RVSDDAINEQIDRAEEQLKERRAILDERFEDKKRKLQTGDDLAPGVLKIVKVYLAIKRRI 359

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG++S I+P EDMP+ + G P+DIVLNPLGVPSRMNVGQ+ E HLG A
Sbjct: 360  QPGDKMAGRHGNKGVISVIMPIEDMPYDEHGEPIDIVLNPLGVPSRMNVGQVLEMHLGLA 419

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
              GLG KI ++I   KA  ++      +    G     E + ++ D  ++ +A+  + GV
Sbjct: 420  AKGLGNKIDAMIRQQKAVKEVRGFLEDIYNKTGDIKDREDLKNFSDKELMDLAQNLRGGV 479

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P++T VFDGA E  I S+LR+ADL +SGQ  LYDG +G+ F RPVTVGY+Y+LKLNH+V 
Sbjct: 480  PMATRVFDGAKETEIKSLLRLADLPDSGQMTLYDGRSGDAFTRPVTVGYMYVLKLNHLVD 539

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV G
Sbjct: 540  DKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAG 599

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            RT++Y++IV G+   E G PESFNVLVKE+++LG++++LE
Sbjct: 600  RTKMYKNIVDGDHRMEPGMPESFNVLVKEIRSLGINMELE 639


>gi|227522985|ref|ZP_03953034.1| DNA-directed RNA polymerase subunit beta [Lactobacillus hilgardii
           ATCC 8290]
 gi|227089803|gb|EEI25115.1| DNA-directed RNA polymerase subunit beta [Lactobacillus hilgardii
           ATCC 8290]
          Length = 1205

 Score =  841 bits (2173), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 585/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ FL           +GL+  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYARIKEVLDLPNLIEIQTNSYNWFL----------KDGLRETFD 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    +  Y+ PL ITL+L   + D      
Sbjct: 54  GIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHEANYSAPLHITLKLTNHETD------ 107

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSP +++  D  +   +G++ Y
Sbjct: 108 ---EIKTQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPSVYYHEDTDK---NGRISY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E DSK+I +VRIDR RK+P+T  + A G  S+ EI           
Sbjct: 162 GTTVIPNRGAWLEFETDSKNISYVRIDRTRKIPLTELIRAFGFGSDGEITDILGDNDSLE 221

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +         D  V   +      +  GE    ES + L +      K   +  +G 
Sbjct: 222 LTLEKD-VHKDTDDSRVEESLKDIYERLRPGEPKTAESSRSLLTARFFDPKRYDMAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE + + ETGE+ ++   V+ +  ++++           Y+D
Sbjct: 281 YKTNKKLSLKNRLLGLTLAETLADPETGEVIVQKDTVVTKDVMKKLSP---------YLD 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                AY  N   +D+    +   + I +V    D                         
Sbjct: 332 QKEFKAYTFNP--SDEAVVTEPMTVQIIKVYSANDP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N + P   +HI   DIIA +    +L+ G G+IDDID+LGNRR+RSVGE+
Sbjct: 366 --EKVVPLIGNDNIPLAFKHITPADIIASMNYFFNLQEGIGSIDDIDHLGNRRIRSVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+A
Sbjct: 484 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYA 543

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETPYR+V     KVT+ + YL+A EE+N  IAQANS L++DGSF   +V  R
Sbjct: 544 RINKYGFIETPYRRVDWTSHKVTDRIDYLTADEEDNFVIAQANSPLNDDGSFVNNVVMAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I +  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 604 HKSNNIEISIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVDPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A++ K AG VE VDA  + IR  +G LD        Y+LMKF+
Sbjct: 664 PLVGTGIEYKAAHDSGVALICKFAGTVEYVDAREVRIRRDDGTLDK-------YKLMKFR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQRP+V+VGD V  ++++ADGPS + G+LALG+N +VAFM W GYNFED++ 
Sbjct: 717 RSNGGKNYNQRPIVRVGDHVDPDEVLADGPSMEGGELALGQNPIVAFMTWQGYNFEDAIA 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V +DV+TSIHIEE+E   RDTKLGPEE+TR+IPNV E+ LK++DE G I +GAEV
Sbjct: 777 ISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPNVGEDALKDLDEGGTIRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G V DV++F R 
Sbjct: 837 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIVQDVKVFTRE 896

Query: 949 GID 951
             D
Sbjct: 897 NGD 899



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 251/1072 (23%), Positives = 392/1072 (36%), Gaps = 170/1072 (15%)

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             IL  +        ++      +   +++L DIY  +RPG+  T   + S+    FFD  
Sbjct: 212  DILGDNDSLELTLEKDVHKDTDDSRVEESLKDIYERLRPGEPKTAESSRSLLTARFFDPK 271

Query: 405  KYDLSTVGRV----KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            +YD++ VGR     K++++  L        +   +   +I     +            L 
Sbjct: 272  RYDMAPVGRYKTNKKLSLKNRLLGLTLAETLADPETGEVIVQKDTVVTKDVMKKLSPYLD 331

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             +  ++      ++  +      + IK   ++     V      N       +      +
Sbjct: 332  QKEFKAYTFNPSDEAVVTEPMTVQIIKVYSANDPEKVVPLIGNDNIPLAFKHITPADIIA 391

Query: 521  QLSQLEEHVNSLSRITHT-----RRLSALGQ-------GGVARARAGVEMR-------DV 561
             ++        +  I        RR+ ++G+        G++R    V  R        V
Sbjct: 392  SMNYFFNLQEGIGSIDDIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTV 451

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----------------V 605
             P     I P   S     G         + N  G +    R                 V
Sbjct: 452  TPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEV 511

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
             D   T+          E   I   NS  S      +       R          ++ID+
Sbjct: 512  RDVHYTHYGRMCPIETPEGPNIGLINSLSSYARINKYGFIETPYRRVDWTSHKVTDRIDY 571

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            + A  +    IA +  P    +D    +    M R     ++     V       V+   
Sbjct: 572  LTADEEDNFVIAQANSPL---NDDGSFVNNVVMARHKSNNIEISIDKVD---YMDVSPKQ 625

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
              A+       +E  D+ R ++ +                    QR          PLV 
Sbjct: 626  VVAVATACIPFLENDDSNRALMGAN------------------MQRQAVPLVDPHAPLVG 667

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             G                  +     +  VA +       E       R+  +D      
Sbjct: 668  TGI-----------------EYKAAHDSGVALICKFAGTVEYVDAREVRIRRDD----GT 706

Query: 844  IEEFEVM-ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            ++++++M  R +  G     R I  V +    ++D   ++  G  +  G++ +G      
Sbjct: 707  LDKYKLMKFRRSNGGKNYNQRPIVRVGD----HVDPDEVLADGPSMEGGELALG------ 756

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
                       +    E A+ + +  ++     S  + +     R      E        
Sbjct: 757  -QNPIVAFMTWQGYNFEDAIAISERLVKDDVYTSIHIEEYESETRDTKLGPEEMTREIPN 815

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D D+   I              G     G     K T      +S   R    
Sbjct: 816  VGEDALKDLDEGGTI------------RIGAEVHDGDILVGKVTPKGVTELSAEERLLHA 863

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      K+   + GD++ PGV R+V+V++A KR
Sbjct: 864  IFGEKSREVRDTSLRVPHGGGGIVQDV------KVFTRENGDELSPGVNRMVRVYIAQKR 917

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKM+GRHGNKG VS ++P EDMPFL DGTPVDI+L+P+GVPSRMN+GQ+ E HLG
Sbjct: 918  KIQVGDKMSGRHGNKGTVSVVIPEEDMPFLPDGTPVDIMLSPMGVPSRMNIGQVLELHLG 977

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D  ++ DI                                     
Sbjct: 978  MAARKLGIHVATPVFDGASDKDIWNAVKEAGMPKDGKYIL-------------------- 1017

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                         G++       GEPFD+P+ VG ++ LKL HM
Sbjct: 1018 ---------------------------YDGRT-------GEPFDKPIAVGVMHYLKLAHM 1043

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV
Sbjct: 1044 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDV 1103

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            VGR + YE+IV G    + G PESF VLVKE+Q+LGL + + +S  K     
Sbjct: 1104 VGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQSLGLDMKVLDSSHKEIELR 1155


>gi|256847754|ref|ZP_05553199.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715443|gb|EEU30419.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 1196

 Score =  841 bits (2172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/966 (43%), Positives = 587/966 (60%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  +V  G  R R+ + +  E++D+P+LIE+Q  SY+ F+          ++G++  F 
Sbjct: 4   LAGHLVKYGKHRTRRSYSRIKEVLDLPNLIEIQTNSYNWFM----------DKGIREMFN 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL   +        
Sbjct: 54  DIMPIDDFQGKLSLEFVDYQLMEPKYTVDEAREHDANYSAPLHVTLRLTSHE-------- 105

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G   Y
Sbjct: 106 -TGEIKSQDVFFGDFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEETDK---NGWPSY 161

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFY---PKI 236
               IP++G W++ E D+K I +VRIDR RK+P+T  + ALG  S+ EI+         +
Sbjct: 162 GANFIPNRGAWLEYETDAKGISYVRIDRTRKLPLTELVRALGFGSDDEIIEMLGGNSDSL 221

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D       A D  V   +      +  GE    +S + L +      K   +  
Sbjct: 222 SATLDKDVHK---DAEDSRVEEALKDIYERLRPGEPKTADSARSLLTARFFDPKRYDMAP 278

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L G  +AE + + ETGEI    GDV+ ++ L+++  +   D    
Sbjct: 279 VGRYKTNKKLKMKYRLLGQTLAETLADPETGEILANKGDVVTKEVLKKLEPALESD---- 334

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                                   +A++     +                       K D
Sbjct: 335 -------------DFKMVTYTPSDEAVVTAPVKL----------------QKILVYSKKD 365

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              V  +  N  +    P +++HI+  DIIA +    +L+ G G+ DDID+LGNRR+RSV
Sbjct: 366 PERVVPIVSNGHI----PLELKHIQPADIIASVNYFFNLQEGIGSTDDIDHLGNRRIRSV 421

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  DI++V PQ LIN +PVV+++ EFF SSQLSQ  +
Sbjct: 422 GELLQNQFRIGLARMERVVRERMSIQDINTVTPQQLINIRPVVASIKEFFGSSQLSQFMD 481

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 482 QTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLS 541

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN YGFIETPYR+V     KVT+ + YL+A EE+N  IAQAN+ L++DGSF E+ +
Sbjct: 542 SYARVNKYGFIETPYRRVSWETHKVTDKIDYLTADEEDNYIIAQANTKLNDDGSFAEDEI 601

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 602 MCRDKDDYISTTAENVDYMDISPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLIN 661

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP +GTG+E   A  SG A++AK +G VE VDA  I +R  +  LD        Y+LM
Sbjct: 662 PHAPLIGTGIEYKAAHDSGVALIAKYSGTVEYVDAREIRVRRDDDTLD-------TYKLM 714

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQRP+VKVG+ V  +DI+ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 715 KFRRSNGGKNYNQRPIVKVGEHVDADDILADGPSMEQGELALGQNPLIAFMTWQGYNFED 774

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++ ISER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV  + LKN+DE G++ VG
Sbjct: 775 AIAISERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGADALKNLDENGVVRVG 834

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F
Sbjct: 835 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVF 894

Query: 946 NRHGID 951
            R   D
Sbjct: 895 TRENGD 900



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 248/1070 (23%), Positives = 407/1070 (38%), Gaps = 114/1070 (10%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            E+    G   D++ +E +  +       L  D               ++   ++AL DIY
Sbjct: 197  ELVRALGFGSDDEIIEMLGGNSDSLSATLDKDV----------HKDAEDSRVEEALKDIY 246

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
              +RPG+  T   A S+    FFD  +YD++ VGR K N +L            K     
Sbjct: 247  ERLRPGEPKTADSARSLLTARFFDPKRYDMAPVGRYKTNKKL------------KMKYRL 294

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            + + L +      T + + N G+   + V + L+        +M        + V     
Sbjct: 295  LGQTLAETLADPETGEILANKGDVVTKEVLKKLEPALESDDFKMVTYTPSDEAVVTAPVK 354

Query: 499  MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV-- 556
            + + L+ +K     V     +  +    +H+     I        L +G  +        
Sbjct: 355  LQKILVYSKKDPERVVPIVSNGHIPLELKHIQPADIIASVNYFFNLQEGIGSTDDIDHLG 414

Query: 557  --EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
               +R V      +           +    S+     V     I    R V         
Sbjct: 415  NRRIRSVGELLQNQFRIGLARMERVVRERMSIQDINTVTPQQLI--NIRPVVASIK---- 468

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             +  + +                      L       +        + +        +  
Sbjct: 469  EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIET 528

Query: 675  AAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                 I  + +  S   +            +  E   V   ++ + A      I+A+   
Sbjct: 529  PEGPNIGLINSLSSYARVNKYGFIETPYRRVSWETHKVTDKIDYLTADEEDNYIIAQANT 588

Query: 734  IVEQ--VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVR 789
             +      A   ++   + D   +T+    Y  +  ++  S  + C+           + 
Sbjct: 589  KLNDDGSFAEDEIMCRDKDDYISTTAENVDYMDISPKQVVSVASACIP---------FLE 639

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
             +D        ++   A+      A +   G  ++ +      ++++   T  +++  E+
Sbjct: 640  NDDSNRALMGANMQRQAVPLINPHAPLIGTGIEYKAAHDSGVALIAKYSGTVEYVDAREI 699

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
              R      +         S  G KN ++  I+ VG  V+  DIL    +   +  +   
Sbjct: 700  RVRRDDDTLDTYKLMKFRRSNGG-KNYNQRPIVKVGEHVDADDILADGPS-MEQGELALG 757

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  L A    +  +  D        V   V        +  +  E  +  E    E+   
Sbjct: 758  QNPLIAFMTWQGYNFEDAIAISERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNV 817

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              D  + + +  +         G     G     K T      +S   R     F  +  
Sbjct: 818  GADALKNLDENGVVR------VGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSR 871

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V+     +          +      K+   + GD++ PGV ++V+V++A KR IQ GDK
Sbjct: 872  EVRDTSLRVPHGGGGIIQDV------KVFTRENGDELSPGVNKMVRVYIAQKRKIQVGDK 925

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            M+GRHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG
Sbjct: 926  MSGRHGNKGTVSIVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVIELHLGMAARELG 985

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I + + D   + D                                             
Sbjct: 986  IHIATPVFDGATDQD--------------------------------------------- 1000

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            V+D   E         A L   G++ILYDG TGEPF++ V VG ++ LKL HMV DK++A
Sbjct: 1001 VWDAVKE---------AGLPSDGKTILYDGRTGEPFEQRVAVGVMHYLKLAHMVDDKIHA 1051

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR   Y
Sbjct: 1052 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVNTY 1111

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ++I+ G+   + G PESF VLVKE+Q+LGL + + ++  +         D
Sbjct: 1112 DAIINGDQIPKPGVPESFRVLVKELQSLGLDMKVLDNNHEEVQLKNMDED 1161


>gi|168178824|ref|ZP_02613488.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           NCTC 2916]
 gi|226950941|ref|YP_002806032.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum A2
           str. Kyoto]
 gi|254765283|sp|C1FMV9|RPOB_CLOBJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|182670035|gb|EDT82011.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           NCTC 2916]
 gi|226841129|gb|ACO83795.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum A2
           str. Kyoto]
 gi|322807814|emb|CBZ05389.1| DNA-directed RNA polymerase beta subunit [Clostridium botulinum
           H04402 065]
          Length = 1232

 Score =  841 bits (2172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/951 (46%), Positives = 601/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             + P D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVPFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELGLSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|153939112|ref|YP_001392842.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum F
           str. Langeland]
 gi|166229293|sp|A7GJ82|RPOB_CLOBL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|152935008|gb|ABS40506.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum F
           str. Langeland]
 gi|295320821|gb|ADG01199.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum F
           str. 230613]
          Length = 1234

 Score =  841 bits (2172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/951 (46%), Positives = 601/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             + P D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVPFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELGLSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|148381429|ref|YP_001255970.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum A
           str. ATCC 3502]
 gi|153933778|ref|YP_001385804.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum A
           str. ATCC 19397]
 gi|166229292|sp|A7FZ77|RPOB_CLOB1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|182676559|sp|A5I7L4|RPOB_CLOBH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|148290913|emb|CAL85049.1| DNA-directed RNA polymerase beta chain [Clostridium botulinum A
           str. ATCC 3502]
 gi|152929822|gb|ABS35322.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum A
           str. ATCC 19397]
          Length = 1232

 Score =  841 bits (2172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/951 (46%), Positives = 601/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             + P D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVPFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELALSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|288904307|ref|YP_003429528.1| RNA polymerase (beta subunit) [Streptococcus gallolyticus UCN34]
 gi|306830337|ref|ZP_07463507.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977303|ref|YP_004287019.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731032|emb|CBI12576.1| RNA polymerase (beta subunit) [Streptococcus gallolyticus UCN34]
 gi|304427362|gb|EFM30464.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177231|emb|CBZ47275.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 1190

 Score =  841 bits (2172), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DNGLREVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PIT F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPITNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIMDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQTIAENLVDAETGEILVEAGTVMTRDVIDSIAEQLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                         
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPVDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D  R +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 362 --NRVVTIVGNANPDDKARALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGVVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEFPSNIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYN+ED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWDGYNYEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 171/508 (33%), Positives = 236/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A       +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWDGYNYEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E    +I    E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLWDTVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGIMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|291549812|emb|CBL26074.1| DNA-directed RNA polymerase subunit beta [Ruminococcus torques
           L2-14]
          Length = 1287

 Score =  840 bits (2170), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 593/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          ++GL+  F  + PI  ++G
Sbjct: 13  KSFRMSYSRQQEVLEMPNLIEVQKDSYQWFL----------DKGLKEVFDDISPIADYNG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    +  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEEDAKYTIDECKERDATYAAPLKVRVRLY---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKF---GKKLYSATVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    K++ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGVGTNAEIIELFGEEPKLLASFGKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKL-LLKNRV 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED V+  TGE+  E G  I  +  + I ++ +  I +   ++  N   + N +V
Sbjct: 290 SGQILAEDAVSAITGEVVAEKGTKITREIADMIQNAAVPYIWVEGEETSRNIKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +      A++DI       D +   V E ++  +     +     V  +K  ++ +L 
Sbjct: 350 DLQ------AVVDI-------DPAEVGVTEQVYYPVLAGIIEESAGDVDEMKRLIKRDLH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDIFASINYNMHLEYGMGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D D + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDQDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACYARINEYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT++VVY++A EE+N ++AQAN+ LDE+G F  + V  R   E     R
Sbjct: 576 KIDKTDPMNPVVTDEVVYMTADEEDNYHVAQANTPLDEEGHFINKNVSGRYREETQDYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 NKFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG A VA++AG+VE   +  I IR  +G           Y+L KFQRSNQ+ C NQ
Sbjct: 696 TAVDSGVAEVAEQAGVVESSTSTSITIRHDDGTK-------KTYKLTKFQRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RPIVDKGERVEAGQVIADGPSTSGGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  551 bits (1420), Expect = e-154,   Method: Composition-based stats.
 Identities = 244/1067 (22%), Positives = 400/1067 (37%), Gaps = 79/1067 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++       +  +   D +++ ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 212  IELFGEEPKLLASFGKDTSENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L      + + ++ + AI         G+   +    +       + 
Sbjct: 272  AKVGRYKFNKKLLLKNRVSGQILAEDAVSAIT--------GEVVAEKGTKITREIADMIQ 323

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +      R+IK   + +     +         V   V     +  + +    
Sbjct: 324  NAAVPYIWVEGEETSRNIKVLSNMMVDLQAVVDIDPAEVGVTEQVYYPVLAGIIEESAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            V+ + R+   R L  L    + +      +       YG     +     N   + ++  
Sbjct: 384  VDEMKRLI-KRDLHDLIPKHITKEDIFASINYNMHLEYGMGNDDDIDHLGN-RRIRAVGE 441

Query: 589  FARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED 637
              +      +    R V +   T D           +  ++A  +E    +Q +  +D++
Sbjct: 442  LLQNQYRIGLSRLERVVRERMTTQDQDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 501

Query: 638  ---GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
               G  T +          +   R   +  D        +     P   N      L   
Sbjct: 502  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACY 561

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS----VEG 750
                +   +         T   + V       + A          A   +        + 
Sbjct: 562  ARINEYGFIEAPYRKIDKTDPMNPVVTDEVVYMTADEEDNYHVAQANTPLDEEGHFINKN 621

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                       Y   KF   + +  +     V         +  A+              
Sbjct: 622  VSGRYREETQDYERNKFDYMDVSPKMVFS--VATALIPFLQNDDANRALMGSNMQRQAVP 679

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGPEEITRDIPNVS 869
            +L    P  G   E    +   +        +        +      G ++  +      
Sbjct: 680  LLTTEAPVVGTGMEVKTAVDSGVAEVAEQAGVVESSTSTSITIRHDDGTKKTYKLTKFQR 739

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                   ++  I+  G  V  G ++    +  G   M   +  L      +  +  D  L
Sbjct: 740  SNQSNCYNQRPIVDKGERVEAGQVIADGPSTSG-GEMALGKNPLIGFMTWEGYNYEDAVL 798

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILD 979
                     V D    + H  +    +   +   E+I        +   +D  DE+ I+ 
Sbjct: 799  L----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIR 853

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 R  +IL G+    G         L   +  E  R                 E   
Sbjct: 854  IGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRD 896

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
               +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+
Sbjct: 897  TSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGV 956

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + +   
Sbjct: 957  VSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVSTPVFAG 1016

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                DI                 E    + ++    V +                     
Sbjct: 1017 ANENDIMDTLDLAND-YVNLEWDEFEKKHGEELRPEVLQFLSE-------------NRDH 1062

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVT
Sbjct: 1063 RELWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVT 1122

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  
Sbjct: 1123 QQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIP 1182

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            E G PESF VL+KE+Q+L L + +          ME + D+ + +L+
Sbjct: 1183 EPGVPESFKVLLKELQSLALDVRVLRDDNTEVKIMESV-DYGETDLR 1228


>gi|322390726|ref|ZP_08064238.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           parasanguinis ATCC 903]
 gi|321142553|gb|EFX38019.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           parasanguinis ATCC 903]
          Length = 1189

 Score =  840 bits (2170), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYSLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNIKNRLLNQTIAEPLVDAETGEILVEAGTVMTRDVIDSISEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DAAVLTEPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR I   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIITPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D D + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNDVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV    G VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEEDEYIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYHVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDAVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDAVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     + 
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGEDD 1159


>gi|322386310|ref|ZP_08059941.1| DNA-directed RNA polymerase subunit beta [Streptococcus cristatus
           ATCC 51100]
 gi|321269677|gb|EFX52606.1| DNA-directed RNA polymerase subunit beta [Streptococcus cristatus
           ATCC 51100]
          Length = 1190

 Score =  840 bits (2170), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNIKNRLLNQTLAEHLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTEPVELQKFKVVAPSDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + M  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTMIGNANPSDKVRTVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 238/1074 (22%), Positives = 395/1074 (36%), Gaps = 132/1074 (12%)

Query: 332  SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 195  LVRALGFSGDDEILDIFGDSDLVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 254

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             + S+    FFD  +YDL+ VGR     ++N       R + +     + + LVD   G+
Sbjct: 255  SSRSLLVARFFDPHRYDLAAVGRY----KINKKLNIKNRLLNQ----TLAEHLVDAETGE 306

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
              ++    +    + S+ E L N             K      D   +     +    VV
Sbjct: 307  ILVEAGTVMTRSVIDSIAEQLDNGLN----------KITYIPNDSAVLTEPVELQKFKVV 356

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +         ++  +  + N   ++        L +       A    R     H G   
Sbjct: 357  APSD----PDRVVTMIGNANPSDKVRTVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRR 412

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
                 E     +   L+   R N    +     +V   +   ++  ++A  +E       
Sbjct: 413  IRAVGELLANQVRLGLSRMER-NVRERMSVQDNEVLTPQQIINIRPVTAAIKE----FFG 467

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            +S L +       L           +    +       +         + +        +
Sbjct: 468  SSQLSQFMDQHNPLSELSHKRRLSALGPGGLT------RDRAGYEVRDVHYTHYGRMCPI 521

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAK--SSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                      +  L +       G      +     A +V      +   +    ++   
Sbjct: 522  ETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQA 581

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL------ 802
               L+      +   + + Q +NQ    +Q   V   D   +  +               
Sbjct: 582  NSKLNEKGGFAEPIVMGRHQGNNQEFPSDQ---VDYMDVSPKQVVAVATACIPFLENDDS 638

Query: 803  -------GDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARD 853
                           ++    P+ G   E          ++++      + +  +V  R 
Sbjct: 639  NRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRR 698

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                 +         S  G    ++  ++ VG  V  GD +    +      M   +  +
Sbjct: 699  EDGSLDVYHIQKFRRSNSGTAY-NQRTLVKVGDVVEKGDFIADGPS-MENGEMALGQNPI 756

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  +     V   V        +  +  +  +  E    +I  +  D 
Sbjct: 757  VAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDA 816

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE  I+      +  +IL G+    G K       L   +  +  R          
Sbjct: 817  LKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR---------- 866

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
             +V+     +    +     +      KI     GD++  GV  +V+V++A KR I+ GD
Sbjct: 867  -EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGD 919

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 920  KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 979

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  I + + D  ++ D+                                           
Sbjct: 980  GIHIATPVFDGASSEDLWSTVREAGM---------------------------------- 1005

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                   +    ++L        G        TGEPFD  V+VG +YM+KL+HMV DK++
Sbjct: 1006 -------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLHHMVDDKLH 1045

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YS VTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDD+ GR + 
Sbjct: 1046 ARSVGPYSTVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDINGRLKA 1105

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            YE+I  G    + G PESF VLVKE+Q+LGL + + +   +     +   D ++
Sbjct: 1106 YEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDQEVELRDLDEDMDE 1159


>gi|28212181|ref|NP_783125.1| DNA-directed RNA polymerase subunit beta [Clostridium tetani E88]
 gi|41017721|sp|Q890N4|RPOB_CLOTE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|28204625|gb|AAO37062.1| DNA-directed RNA polymerase beta chain [Clostridium tetani E88]
          Length = 1236

 Score =  840 bits (2169), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/955 (46%), Positives = 600/955 (62%), Gaps = 62/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+ ++ +LIEVQ  SY+ FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSKIKEVCEMSNLIEVQLDSYEWFLQ----------EGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+++RLI          K   +IKEQ
Sbjct: 59  NLSLEFVGYKLDMENIKYSVEECKERDATYAAPLKVSVRLI---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +   SGK L++  +IP++
Sbjct: 110 DVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDVSLDK---SGKELFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS DII+VRID+ RK+P++  + AL   S+ EI+  F          +    
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPISILIRALEYGSDLEIIDYFGEDERLKASIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAMSLIGSLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A+DIVN  TGEI ++ G+ ID     EI +S I  + I   D V      
Sbjct: 281 LHLRIANQISAQDIVNPATGEIVVQEGEKIDRDKAIEIQNSGINSVDIQLDDKVLRVIGN 340

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
               +    K   D L     V  P               L    D Y    + + ++  
Sbjct: 341 NFVDIKSFVKFDIDDLNIKEYVHYP--------------TLKEILDNYSDEEMIKEQIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +N+  P   +HI ++DI++ I   + L  G G  DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NINVLIP---KHIIRDDIMSTISYEIGLPYGIGYTDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D DS+ PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQDSITPQALINIRPVTASIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV      VT+D++Y++A EE++  IA+AN  L++DG+F ++ +  R   + ++V
Sbjct: 564 ETPYRKVDKATGVVTHDIIYMTADEEDHYLIAKANEILNDDGTFIDDKITVRDQEDVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P+E++DF+D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK EAP VGTG+E
Sbjct: 624 PKEEVDFMDVSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPEAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  S     AK+ G+V  V A  I ++  +     S   VD Y+L+KF+RSNQ TC+
Sbjct: 684 YKAAVDSAVLPKAKKPGVVTYVSASEIRVKKDKP---DSNGDVDKYKLLKFKRSNQGTCI 740

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ+PLV  GD+V    ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 741 NQKPLVSKGDKVDTKTVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 800

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK+IDE GII +GAEV  GDILVG
Sbjct: 801 DVFTSIHIEEYEAEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRSGDILVG 860

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 861 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 915



 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 163/414 (39%), Positives = 212/414 (51%), Gaps = 72/414 (17%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 841  DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------------- 886

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E                   K+   + GD++ PGV ++V+ ++A KR I  GDKMAG
Sbjct: 887  ---EVRDTSLRVPHGEAGIIVDVKVFTRENGDELSPGVNKLVRCYIAQKRKISVGDKMAG 943

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 944  RHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGLAASKLGWHV 1003

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     +I                                          T ++D
Sbjct: 1004 ATPVFDGATEPEIVECLEKAGYEGDGK----------------------------TVLYD 1035

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  VTVGY+Y+LKL H+V DK++ARST
Sbjct: 1036 G--------------------------RTGEPFDNRVTVGYMYILKLAHLVDDKIHARST 1069

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I
Sbjct: 1070 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAI 1129

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            V G +  E G PESF VL+KE+QAL L + + N   +  A  +E+ D +  EL+
Sbjct: 1130 VKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNEEIAI-KELADDDMVELE 1182


>gi|323353633|ref|ZP_08088166.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           VMC66]
 gi|322121579|gb|EFX93342.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           VMC66]
 gi|325697739|gb|EGD39623.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK160]
          Length = 1188

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTNTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|228478020|ref|ZP_04062631.1| DNA-directed RNA polymerase, beta subunit [Streptococcus salivarius
           SK126]
 gi|228250200|gb|EEK09453.1| DNA-directed RNA polymerase, beta subunit [Streptococcus salivarius
           SK126]
          Length = 1193

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/963 (44%), Positives = 589/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKEFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKVNKKLNIKTRLLGQTIAENLVDPETGEILVEAGTEMTRDVIDSIAEYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTTADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN+VV+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGKVTNEVVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEYPSHLVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVVYSDADKVEVRREDGSLD-------VYTIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEGGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/508 (33%), Positives = 237/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    + +G   M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPSMEG-GEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     +    ++L        G  
Sbjct: 1006 -----------------------------------------DSDAKTIL------YDG-- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ +LQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNILQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDYEVELRDLDEGEDD 1159


>gi|306832583|ref|ZP_07465722.1| DNA-directed RNA polymerase subunit beta [Streptococcus bovis ATCC
           700338]
 gi|304425191|gb|EFM28318.1| DNA-directed RNA polymerase subunit beta [Streptococcus bovis ATCC
           700338]
          Length = 1190

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 586/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DNGLREVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PIT F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPITNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQTIAENLVDTETGEILVEAGTVMTRDVIDSIAEQLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPVDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D  R +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKARALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRTTGVVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEFPSNIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYN+ED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWDGYNYEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 171/508 (33%), Positives = 236/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A       +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWDGYNYEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E    +I    E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLWDTVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGIMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|238922790|ref|YP_002936303.1| DNA-directed RNA polymerase subunit beta [Eubacterium rectale ATCC
           33656]
 gi|238874462|gb|ACR74169.1| DNA-directed RNA polymerase subunit beta [Eubacterium rectale ATCC
           33656]
 gi|291528829|emb|CBK94415.1| DNA-directed RNA polymerase subunit beta [Eubacterium rectale
           M104/1]
          Length = 1313

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/960 (45%), Positives = 592/960 (61%), Gaps = 64/960 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++ +P+LIEVQK SY  FL          +EGL+ AF  + PIT +SG
Sbjct: 13  KSMRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEAFADISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L+FV +    D  K+ + +C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  KLSLDFVDFTLCEDDVKYTIPECKERDATYAAPLKVKVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP++
Sbjct: 114 EIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKTLYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  L ALG+ + + IL  F    KI  S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLLRALGVGTNQAILDMFGDEPKIQASFSKDPA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS---- 300
                         +      I  GE + +ES + L + +    +   +  +G       
Sbjct: 231 ITEREPQGSYEAG-LLELYKKIRPGEPLSVESAESLITAMFFDPRRYDLAKVGRYKFNKK 289

Query: 301 ----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + + G  +AED+V+  TGE+  EAG V+D     +I ++    +P L++ +   N 
Sbjct: 290 LALKNRISGQVLAEDVVDPSTGEVIAEAGTVVDRALATQIQNA---AVPALWIQTETRNV 346

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            I ++++ D  +     L          D  +  V E ++  +     +   S   R++ 
Sbjct: 347 KILSSMMVD-IRSWIPELE---------DPKSIGVTELVYYPVLAQILEEYDSLEDRIEA 396

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             R   D     +HI KEDI A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 397 IKRDISDLI--PKHITKEDIFATINYNMHLEWGAGTDDDIDHLGNRRIRAVGELLQNQYR 454

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL R+ER ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +T
Sbjct: 455 IGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELT 514

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YG
Sbjct: 515 HKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLACYARINEYG 574

Query: 597 FIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           F+E PYRK+      +  VT +VVY++A EE+N ++AQAN  LD +G F    V  R   
Sbjct: 575 FVEAPYRKIDKTDPKNPVVTEEVVYMTADEEDNYHVAQANEKLDAEGHFVRNSVSGRYRE 634

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     +   D++D SPK V S+A +LIPFL+NDD  R LMG NMQRQAVPLL  EAP V
Sbjct: 635 ETQEYDKSAFDYMDVSPKMVFSVATALIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVV 694

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E+  A  SG  +VAK  G V   ++ RI+I+  +G+          Y L KF RSN
Sbjct: 695 GTGIETKAAVDSGVCVVAKADGEVLSSESNRIIIKETDGNKRE-------YILTKFSRSN 747

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+ C NQRP+V  GD+V+  D+IADGPST  G+LALG+N L+ FM W GYN+ED++L+SE
Sbjct: 748 QSNCYNQRPIVFKGDKVKAGDVIADGPSTSQGELALGKNPLIGFMTWEGYNYEDAVLLSE 807

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V  DV+TS+HIEE+EV +RDTKLGPEEITRD+P V ++ LK++DE GII VGAEV  G
Sbjct: 808 RLVEYDVYTSVHIEEYEVESRDTKLGPEEITRDVPGVGDDALKDLDERGIIRVGAEVRAG 867

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 868 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 927



 Score =  542 bits (1397), Expect = e-151,   Method: Composition-based stats.
 Identities = 249/1051 (23%), Positives = 415/1051 (39%), Gaps = 70/1051 (6%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +  LL++Y+ +RPG+  +   AES+   +FFD  +YDL+ VGR K N +L L      
Sbjct: 239  SYEAGLLELYKKIRPGEPLSVESAESLITAMFFDPRRYDLAKVGRYKFNKKLALKNRISG 298

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + + ++ +      ++     +        L  +   +    L  Q     +++  S+  
Sbjct: 299  QVLAEDVVDPSTGEVIA----EAGTVVDRALATQIQNAAVPALWIQTETRNVKILSSMMV 354

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQ 546
             I S   +   P+ +   + V   V        L+Q+ E  +SL        R +S L  
Sbjct: 355  DIRSWIPELEDPKSIGVTELVYYPV--------LAQILEEYDSLEDRIEAIKRDISDLIP 406

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + +      +       +G     +     N   + ++    +      +    R V 
Sbjct: 407  KHITKEDIFATINYNMHLEWGAGTDDDIDHLGN-RRIRAVGELLQNQYRIGLSRLERVVR 465

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC------- 649
            +   T D+  +S     N     A               +  +   EL   R        
Sbjct: 466  ERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPG 525

Query: 650  --AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQRQAVPLLKA 706
              + +        + +        V         L N  +    +            +  
Sbjct: 526  GLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLACYARINEYGFVEAPYRKIDK 585

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
              P      E VV  ++        A   E++DA    +R+              Y    
Sbjct: 586  TDPKNPVVTEEVVYMTADEEDNYHVAQANEKLDAEGHFVRN--SVSGRYREETQEYDKSA 643

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F   + +  +       +   ++ +D       +++   A+      A +   G   + +
Sbjct: 644  FDYMDVSPKMVFSVATALIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVVGTGIETKAA 703

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +     +V++     +  E   ++ ++T     E                ++  I+  G 
Sbjct: 704  VDSGVCVVAKADGEVLSSESNRIIIKETDGNKREYI-LTKFSRSNQSNCYNQRPIVFKGD 762

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            +V  GD++    +   +  +   +  L      +  +  D  L     V   V       
Sbjct: 763  KVKAGDVIADGPST-SQGELALGKNPLIGFMTWEGYNYEDAVLLSERLVEYDVYTSVHIE 821

Query: 947  RHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
             + ++  +  +  E    +         +D  DE+ I+      R  +IL G+    G  
Sbjct: 822  EYEVESRDTKLGPEEITRDVPGVGDDALKDL-DERGIIRVGAEVRAGDILVGKVTPKGET 880

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                   L   +  E  R                 E      +            K+   
Sbjct: 881  ELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGAYGIIVDAKVFTR 923

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DI
Sbjct: 924  ENGDELSPGVNQSVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDI 983

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI          +    
Sbjct: 984  VLNPLGVPSRMNIGQVLEIHLSLAAKALGFNISTPVFDGANEVDIEDTLELANDYVNLPF 1043

Query: 1181 HTEKISDYDDDSVLRVAEQWK--SGVPVSTPVFDG----ADEEAINSMLRMADLDESGQS 1234
              E++           +   +      V T   D     +   A  S+ +   + + G+ 
Sbjct: 1044 DKEELEKDLQAEHPYWSADAEIFYDKYVDTLREDVMEYLSTNRAHRSLWKGVPISKDGKV 1103

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG TGE FD   T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1104 QLRDGRTGECFDGKTTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1163

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+
Sbjct: 1164 GEMEVWALEAYGAAYTLQEILTMKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLLKEL 1223

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            QALGL + + +   +    +E   ++   ++
Sbjct: 1224 QALGLDVKVLDENREEVELIET-SEYGNTDI 1253


>gi|210623170|ref|ZP_03293620.1| hypothetical protein CLOHIR_01570 [Clostridium hiranonis DSM 13275]
 gi|210153783|gb|EEA84789.1| hypothetical protein CLOHIR_01570 [Clostridium hiranonis DSM 13275]
          Length = 1241

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/955 (46%), Positives = 600/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY  FL           EGL+  F  + PI  ++G
Sbjct: 13  KRKRMSFSKIKEIADVPNLIEIQVDSYKWFL----------EEGLKEVFDDISPIEDYTG 62

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 63  NLILEFVDYSLDENPKYDIEECKERDATYCAPLKVKVRLI---------NKETGEIKEQE 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTFVI G +R++VSQL RSP +++  ++ +    GK L +  +IP++G
Sbjct: 114 VFMGDFPLMTERGTFVINGAERVIVSQLVRSPSVYYAEERDKT---GKRLISSTVIPNRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+I VR+DR RK PVT  L ALG+ S+ EI+         S   +     
Sbjct: 171 AWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGSDAEIIELLGEDERLSATLEKDNTN 230

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 231 TVEEGLIEIYK------KLRPGEPPTVESASSLINALFFDPKRYDLAKVGRYKFNKKLAI 284

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +     A DIVN ETGE++++AG+ I     ++I ++ I  + +L  D         
Sbjct: 285 CYRIMNRVAARDIVNPETGEVFVKAGETIGYNVAKDIQNAGINVVHLLVDDEKEIKVIGN 344

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +  + + +   + L I   +              +  L    D YD     +  +  R
Sbjct: 345 NFVDIEAHVNFDISDLKIKEKVH-------------YPTLKEILDNYDDEEEIKEAIKSR 391

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           +    P   +HI  +DIIA I    +L  G GTIDDID+LGNRR+RSVGE+L+NQ R+GL
Sbjct: 392 MKELIP---KHILLDDIIASISYEFNLFYGVGTIDDIDHLGNRRIRSVGELLQNQVRIGL 448

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER IKER++  D++S+ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 449 SRMERVIKERMTVQDMESITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 508

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFIE
Sbjct: 509 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLGTYAKVNEYGFIE 568

Query: 600 TPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK      +VTN++ YL+A EE+    AQAN  L EDG F    + CR   G   L+
Sbjct: 569 SPYRKYDKETGRVTNEIHYLTADEEDLFVRAQANEPLTEDGEFINNRIACRTVNGALELL 628

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             +K+D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 629 SSDKVDYMDISPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLVRREAPIIGTGIE 688

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VAK  G+V++V A  I+I+  +G  D        Y+L+KF+RSN  TC+
Sbjct: 689 YRAAKDSGAVVVAKNGGVVDRVSADEIIIKKEDGTKDK-------YKLLKFKRSNAGTCI 741

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P+V  G+E++  D+IADGP+TDLG++ALGRN  +AFM W GYN+ED++LI+ER+V E
Sbjct: 742 NQTPIVSKGEEIKAGDVIADGPATDLGEIALGRNCFIAFMTWEGYNYEDAVLINERLVRE 801

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV E  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 802 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGESAIKNLDDRGIIRIGAEVDSGDILVG 861

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F R   D
Sbjct: 862 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVFTRENGD 916



 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 254/1175 (21%), Positives = 422/1175 (35%), Gaps = 117/1175 (9%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                         I+  E+VI S    +  +  + +     
Sbjct: 98   KVRLINKETGEIKEQEVFMGDFPLMTERGTFVINGAERVIVSQLVRSPSVYYAEERDKTG 157

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
               I+S  +       +        I +       +     +    I     + ++ +  
Sbjct: 158  KRLISSTVIPNRGAWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGSDAEI-IELLGE 216

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            +  +  TL  D     ++ L++IY+ +RPG+  T   A S+ N LFFD  +YDL+ VGR 
Sbjct: 217  DERLSATLEKDNTNTVEEGLIEIYKKLRPGEPPTVESASSLINALFFDPKRYDLAKVGRY 276

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L +      R           + +V+   G+  +   + +G    + +     N 
Sbjct: 277  KFNKKLAICYRIMNRV--------AARDIVNPETGEVFVKAGETIGYNVAKDIQNAGINV 328

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
              L +   E+ IK   ++     V  +  +N       + E      L ++ ++ +    
Sbjct: 329  VHLLVDD-EKEIKVIGNNF----VDIEAHVNFDISDLKIKEKVHYPTLKEILDNYDDEEE 383

Query: 535  ITH--TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            I      R+  L    +        +       YG     +     N   + S+    + 
Sbjct: 384  IKEAIKSRMKELIPKHILLDDIIASISYEFNLFYGVGTIDDIDHLGN-RRIRSVGELLQN 442

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLS------------AMEEE-------NRYIAQANSS 633
                 +    R + +     D+  ++            A++E                 S
Sbjct: 443  QVRIGLSRMERVIKERMTVQDMESITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLS 502

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLM 692
                      L     + E        +          +       I  + +  +   + 
Sbjct: 503  ELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLGTYAKVN 562

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA---KRAGIVEQVDAIRIVIRSVE 749
                          E   V   +  + A      + A   +      +    RI  R+V 
Sbjct: 563  EYGFIESPYRKYDKETGRVTNEIHYLTADEEDLFVRAQANEPLTEDGEFINNRIACRTVN 622

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            G L+  +S    Y          +    Q   V         +  A+             
Sbjct: 623  GALELLSSDKVDY---------MDISPKQVVSVATAMIPFLENDDANRALMGSNMQRQAV 673

Query: 810  NMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
             ++    P  G   E      S  +V       +     + +    + G ++  + +   
Sbjct: 674  PLVRREAPIIGTGIEYRAAKDSGAVVVAKNGGVVDRVSADEIIIKKEDGTKDKYKLLKFK 733

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                   I++  I+  G E+  GD++           +        A    +  +  D  
Sbjct: 734  RSNAGTCINQTPIVSKGEEIKAGDVIADGPATDL-GEIALGRNCFIAFMTWEGYNYEDAV 792

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            L         V + R+   H  +    +    +   E + RD  +      +N+  R   
Sbjct: 793  LIN----ERLVREDRLSTIHIEEYECEARDT-KLGPEEITRDIPNVGESAIKNLDDR-GI 846

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G    SG     K T      ++   R     F  +  +V+     +          
Sbjct: 847  IRIGAEVDSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVD 906

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +      K+   + GDD+ PGV  +V+ ++A KR I+ GDKMAGRHGNKG++SR+LP ED
Sbjct: 907  V------KVFTRENGDDLSPGVNELVRCYIAKKRKIKVGDKMAGRHGNKGVISRVLPEED 960

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF++DGTP+DIVLNP GVPSRMN+GQ+ E HLG A   LG  + + + D     DI   
Sbjct: 961  MPFMEDGTPMDIVLNPQGVPSRMNIGQVLEVHLGLAAKKLGWYVATSVFDGANEYDIMDA 1020

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                                        
Sbjct: 1021 LEEAGYPRDGKLTL---------------------------------------------- 1034

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G++       G+ FD  +TVGY+Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1035 -YDGRT-------GDSFDNRITVGYMYYLKLHHLVDDKLHARSTGPYSLVTQQPLGGKAQ 1086

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA++LQE+LT+KSDDVVGR R YE+IV G +  E G PESF 
Sbjct: 1087 FGGQRFGEMEVWALEAYGAAHILQEILTVKSDDVVGRVRTYEAIVKGENIPEPGIPESFK 1146

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            VL+KE+Q+L L + +  +  +     E +   +  
Sbjct: 1147 VLIKELQSLCLDVKVLTAEDQEIEVKESVDYEDDG 1181


>gi|322374094|ref|ZP_08048628.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. C150]
 gi|321277060|gb|EFX54131.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. C150]
          Length = 1193

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKVNKKLNIKTRLLGQTIAENLVDPETGEILVEAGTEMTRDVIDSIAEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTTADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN+VV+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGKVTNEVVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEYPSHLVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPRA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHDGKVVYSDADKVEVRREDGSLD-------VYTVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEGGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 175/508 (34%), Positives = 243/508 (47%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    + +G   M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPSMEG-GEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW-------- 997

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                 D   E           +D   ++
Sbjct: 998  -------------------------------------DTVREA---------GMDSDAKT 1011

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ILYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1012 ILYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ +LQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNILQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDHEVELRDLDEGEDD 1159


>gi|55821840|ref|YP_140282.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           thermophilus LMG 18311]
 gi|55823756|ref|YP_142197.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           thermophilus CNRZ1066]
 gi|81558888|sp|Q5LXV3|RPOB_STRT1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|81560075|sp|Q5M2F5|RPOB_STRT2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|55737825|gb|AAV61467.1| DNA-directed RNA polymerase beta subunit [Streptococcus
           thermophilus LMG 18311]
 gi|55739741|gb|AAV63382.1| DNA-directed RNA polymerase beta subunit [Streptococcus
           thermophilus CNRZ1066]
 gi|312279182|gb|ADQ63839.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           thermophilus ND03]
          Length = 1193

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/963 (44%), Positives = 591/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++ +P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLGLPNLIEIQTDSFKEFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKLNKKLNIKTRLLGQTIAENLVDPETGEILVEAGTEMTRDVIDSIAEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRRVR+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTTADILAEMSYFLNLAEGIGKVDDIDHLGNRRVRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D +++ PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEALTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFI+TPYRKV     KVTN+VV+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 RLNKYGFIQTPYRKVDRATGKVTNEVVWLTADEEDEYIVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPSHLVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAKHDGKVVYSDADKVEVRREDGSLD-------VYTIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEGGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR++PNVSEE LKN+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITRELPNVSEEALKNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 175/507 (34%), Positives = 242/507 (47%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    + +G   M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPSMEG-GEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    E       A    DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITRELPNVSEEALKNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E           +D   ++I
Sbjct: 998  ------------------------------------DTVREA---------GMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ +LQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNILQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDYEVELRDLDEGEDD 1159


>gi|225412293|ref|ZP_03761482.1| hypothetical protein CLOSTASPAR_05515 [Clostridium asparagiforme
           DSM 15981]
 gi|225042170|gb|EEG52416.1| hypothetical protein CLOSTASPAR_05515 [Clostridium asparagiforme
           DSM 15981]
          Length = 1080

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/951 (45%), Positives = 592/951 (62%), Gaps = 59/951 (6%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             + +  E++++P+LIE+QK SY  FL           EGL+ AF  + PI  F+G   L
Sbjct: 1   MSYSRQKEVLEMPNLIEIQKDSYQWFL----------KEGLKEAFDDISPIADFAGHLSL 50

Query: 75  EFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           EFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         ++ E  I+M
Sbjct: 51  EFVDFTLCKDDVKYTIEECKERDATYAAPLKVKVRLYNKDKD---------EMNEHEIFM 101

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GDLPLMT  G+FVI G +R++VSQL RSPGI++     +    GK L+ C +IP++G W+
Sbjct: 102 GDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIGHDKV---GKELFTCTVIPNRGAWL 158

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWCFPL 249
           + E DS D+ +VR+DR RKVPVT  + ALG  +  EIL  F    K++ S   D      
Sbjct: 159 EYETDSNDVFYVRVDRTRKVPVTVLVRALGYGTNAEILDLFGEEPKLLASFGKDTSDNYQ 218

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
                +         + +D+ E ++ S         L K  + K  K L    + L G  
Sbjct: 219 DGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKLSF-KNRLNGQT 277

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           +AED+V+  TGEI  EAG  +D+    EI ++    +P ++VD  N    + + ++ D  
Sbjct: 278 LAEDVVDTTTGEILAEAGTKVDKNKAAEIQNA---AVPFVWVDGPNRKQKVLSNMMVD-- 332

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                  L  Y    P +V        +  +    +   ++ T     +   L  +  D 
Sbjct: 333 -------LAAYVSFDPEEV----GVTELVYYPALSAILAEVGTDDTEALKEALRKNIHDL 381

Query: 428 V-RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           + +HI KEDIIA I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL RMER +
Sbjct: 382 IPKHITKEDIIASINYNMHLEEEVGNADDIDHLGNRRIRAVGELLQNQYRIGLSRMERVV 441

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L+ +TH RRLSALG 
Sbjct: 442 RERMTTQDMDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLSALGP 501

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGFIE PYR V 
Sbjct: 502 GGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIEAPYRVVD 561

Query: 607 ------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
                 + +VT++VVYL+A EE+N  +AQAN +LDEDG F    V  R   E     ++ 
Sbjct: 562 KTTDPANPRVTDEVVYLTADEEDNFVVAQANEALDEDGHFVHNNVSGRFRTETSEFQKKT 621

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ID +D SPK V S+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTG+E   A
Sbjct: 622 IDLMDVSPKMVFSVATAMIPFLENDDANRALMGSNMQRQAVPLLTTEAPAVGTGIEGKAA 681

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  ++A+ AG+V +  +  I+I+        S    D+Y L KF+RSNQ+ C NQ+P
Sbjct: 682 VDSGVCVLARNAGVVTRSASNEIIIKRD------SDGNKDVYHLTKFKRSNQSNCYNQKP 735

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V   ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV+T
Sbjct: 736 IVYKGDHVEAGEVIADGPSTSQGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYT 795

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 796 SIHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGKVTP 855

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 856 KGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 906



 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 110/461 (23%), Positives = 168/461 (36%), Gaps = 41/461 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E    +   +   + +          E++ +    G
Sbjct: 653  MGSNMQRQAVPLLTTEAPAVGTGIEGKAAVDSGVCVLARNAGVVTRSASNEIIIKRDSDG 712

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +++               ++  I+  G  V  G+++    +   +  +   +  L    
Sbjct: 713  NKDVYHLTKFKRSNQSNCYNQKPIVYKGDHVEAGEVIADGPST-SQGEIALGKNPLIGFM 771

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDK 971
              +  +  D  L     V   V        +  +  +  +  E          E   +D 
Sbjct: 772  TWEGYNYEDAVLLSERLVQEDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDL 831

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 832  -DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 877

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+   + GD++ PGV   V++++A KR I  GDKMA
Sbjct: 878  ----EVRDTSLKVPHGAYGIIVDAKVFTRENGDELAPGVNETVRIYIAQKRKISVGDKMA 933

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  
Sbjct: 934  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFN 993

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + I D     DI              S  E  + Y D     V +   S +       
Sbjct: 994  VSTPIFDGANENDIQDTLELAND-YVNLSWEEFETKYKDLIRPEVMDYLGSNL------- 1045

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                      + +   +   G+  L DG TGE FD  VT+G
Sbjct: 1046 ------EHRELWKGVPISRDGKVRLRDGRTGEFFDGSVTIG 1080


>gi|283798887|ref|ZP_06348040.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. M62/1]
 gi|291073346|gb|EFE10710.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. M62/1]
 gi|295092651|emb|CBK78758.1| DNA-directed RNA polymerase subunit beta [Clostridium cf.
           saccharolyticum K10]
          Length = 1289

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/953 (45%), Positives = 587/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F +  E++++P+LIE+QK SY  FL          +EGL+  F  + PI  F+G
Sbjct: 13  KGIRMSFSRQKEVLEMPNLIEIQKNSYQWFL----------DEGLREVFDDISPIADFAG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         +I E 
Sbjct: 63  HLSLEFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD---------EINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    G  LY+C +IP++
Sbjct: 114 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIGHDKI---GTELYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY--SQRGDFW 245
           G W++ E DS DI +VR+DR RKVPVT  + ALG  +  EI+  F  ++    S   D  
Sbjct: 171 GAWLEYETDSNDIFYVRVDRTRKVPVTVLIRALGYGTNAEIIDLFGDELKLEKSFEKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L    + +
Sbjct: 231 DNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKL-HFKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGEI  E G V+D++   +I ++    +P +++     N  + + ++
Sbjct: 290 AGHTLAEDVVDMSTGEILAEKGTVVDKELATKIQNA---AVPFVWIAGEKKNHKVLSNMM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D                   D +   V E +F  +  +    +                
Sbjct: 347 VDLAAYV------------SFDPAEIGVTELVFYPVLENILAENDGKGEDELKEAIRKNI 394

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDIIA I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 395 HELIPKHITKEDIIASINYNMHLEGGIGTPDDIDHLGNRRIRAVGELLQNQYRIGLSRME 454

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++++ PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 455 RVVRERMTTQDMENISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTHKRRLSA 514

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGF+E PYR
Sbjct: 515 LGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFVEAPYR 574

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            V      +  VT++VVYL+A EE+N  +AQAN  LDE+G F    V  R   E     +
Sbjct: 575 VVDKTDPSNPVVTDEVVYLTADEEDNFVVAQANEPLDEEGHFVHNNVSGRFREETSEFQK 634

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +ID +D SPK V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTG+E  
Sbjct: 635 RRIDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLTTEAPAVGTGIEGK 694

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++AK AG+VE+  +  I+++        S    D+YRL KF RSNQ+ C NQ
Sbjct: 695 AAVDSGVCVLAKNAGVVERSASNEIIVKRD------SDGQKDVYRLTKFTRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +P+V  GD V   ++IADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV
Sbjct: 749 KPIVYKGDHVEAGEVIADGASTCNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 921



 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 180/547 (32%), Positives = 259/547 (47%), Gaps = 44/547 (8%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++ +    G +++ R             ++  I+  G  V  G+++    +      + 
Sbjct: 718  EIIVKRDSDGQKDVYRLTKFTRSNQSNCYNQKPIVYKGDHVEAGEVIADGAST-CNGEIA 776

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--- 964
              +  L      +  +  D  L     V   V        +  +  +  +  E       
Sbjct: 777  LGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVP 836

Query: 965  ---ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E   +D  DE+ I+      R  +IL G+    G         L   +  E  R   
Sbjct: 837  GVGEDALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--- 892

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E      +            K+   + GD++ PGV   V++++A K
Sbjct: 893  --------------EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNETVRIYIAQK 938

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 939  RKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHL 998

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT--GSHTEKISDYDDDSVLRVAEQ 1199
              A   LG  + + I D     DI+         + T       K  D  D+ V+     
Sbjct: 999  SLAAKALGFNVSTPIFDGANENDIADTLEMANDYVNTSWEEFEAKYKDKVDEGVMEYLG- 1057

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                                  + +   +   G+  L DG TGE FD PVT+G+++ LKL
Sbjct: 1058 ---------------SHLEHRKLWKGVPISRDGKVRLRDGRTGEFFDSPVTIGHMHYLKL 1102

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KS
Sbjct: 1103 HHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKS 1162

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDVVGR + YE+I+ G +  E G PESF VL+KE+Q+LGL + +           E I D
Sbjct: 1163 DDVVGRVKTYEAIIKGENIPEPGVPESFKVLLKELQSLGLDVRVLREDGSEVELSENI-D 1221

Query: 1380 FNKCELK 1386
            +   +++
Sbjct: 1222 YGDTDIR 1228


>gi|168181856|ref|ZP_02616520.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           Bf]
 gi|237796950|ref|YP_002864502.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum Ba4
           str. 657]
 gi|259494176|sp|C3KVQ9|RPOB_CLOB6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|182674872|gb|EDT86833.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           Bf]
 gi|229262928|gb|ACQ53961.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           Ba4 str. 657]
          Length = 1241

 Score =  839 bits (2168), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/951 (46%), Positives = 600/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             +   D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LISFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELGLSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVAYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVREDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1286), Expect = e-139,   Method: Composition-based stats.
 Identities = 188/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  +R     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVREDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|116628547|ref|YP_821166.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           thermophilus LMD-9]
 gi|122266858|sp|Q03IK2|RPOB_STRTD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116101824|gb|ABJ66970.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Streptococcus thermophilus LMD-9]
          Length = 1193

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/963 (44%), Positives = 591/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++ +P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLGLPNLIEIQTDSFKEFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKLNKKLNIKTRLLGQTIAENLVDPETGEILVEAGTEMTRDVIDSIAEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTTADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D +++ PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEALTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFI+TPYRKV     KVTN+VV+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 RLNKYGFIQTPYRKVDRATGKVTNEVVWLTADEEDEYIVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPSHLVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAKHDGKVVYSDADKVEVRREDGSLD-------VYTIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEGGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR++PNVSEE LKN+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITRELPNVSEEALKNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  478 bits (1229), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/507 (33%), Positives = 236/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    + +G   M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPSMEG-GEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    E       A    DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITRELPNVSEEALKNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ +LQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNILQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDYEVELRDLDEGEDD 1159


>gi|158513702|sp|A3CKD3|RPOB_STRSV RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1188

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 581/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTNTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N              L  ++V+ P D                         
Sbjct: 330 GLNKITYIPNDSAVLTAPVD----LQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|291523709|emb|CBK89296.1| DNA-directed RNA polymerase subunit beta [Eubacterium rectale DSM
           17629]
          Length = 1313

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/960 (45%), Positives = 592/960 (61%), Gaps = 64/960 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++ +P+LIEVQK SY  FL          +EGL+ AF  + PIT +SG
Sbjct: 13  KSMRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEAFADISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L+FV +    D  K+ + +C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  KLSLDFVDFTLCEDDVKYTIPECKERDATYAAPLKVKVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP++
Sbjct: 114 EIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKTLYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  L ALG+ + + IL  F    KI  S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLLRALGVGTNQAILDMFGDEPKIQASFSKDPA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS---- 300
                         +      I  GE + +ES + L + +    +   +  +G       
Sbjct: 231 ITEREPQGSYEAG-LLELYKKIRPGEPLSVESAESLITAMFFDPRRYDLAKVGRYKFNKK 289

Query: 301 ----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + + G  +AED+V+  TGE+  EAG V+D     +I ++    +P L++ +   N 
Sbjct: 290 LALKNRISGQVLAEDVVDPSTGEVIAEAGTVVDRALATQIQNA---AVPALWIQTETRNV 346

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            I ++++ D  +     L          D  +  V E ++  +     +   S   R++ 
Sbjct: 347 KILSSMMVD-IRSWIPELE---------DPKSIGVTELVYYPVLAQILEEYDSLEDRIEA 396

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             R   D     +HI KEDI A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 397 IKRDISDLI--PKHITKEDIFATINYNMHLEWGAGTDDDIDHLGNRRIRAVGELLQNQYR 454

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL R+ER ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +T
Sbjct: 455 IGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELT 514

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL  +AR+N YG
Sbjct: 515 HKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLACYARINEYG 574

Query: 597 FIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           F+E PYRK+      +  VT +VVY++A EE+N ++AQAN  LD +G F    V  R   
Sbjct: 575 FVEAPYRKIDKTDPKNPVVTEEVVYMTADEEDNYHVAQANEKLDAEGHFIRNSVSGRYRE 634

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     +   D++D SPK V S+A +LIPFL+NDD  R LMG NMQRQAVPLL  EAP V
Sbjct: 635 ETQEYDKSAFDYMDVSPKMVFSVATALIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVV 694

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E+  A  SG  +VAK  G V   ++ RI+I+  +G+          Y L KF RSN
Sbjct: 695 GTGIETKAAVDSGVCVVAKADGEVLSSESNRIIIKETDGNKRE-------YILTKFSRSN 747

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+ C NQRP+V  GD+V+  D+IADGPST  G+LALG+N L+ FM W GYN+ED++L+SE
Sbjct: 748 QSNCYNQRPIVFKGDKVKAGDVIADGPSTSQGELALGKNPLIGFMTWEGYNYEDAVLLSE 807

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V  DV+TS+HIEE+EV +RDTKLGPEEITRD+P V ++ LK++DE GII VGAEV  G
Sbjct: 808 RLVEYDVYTSVHIEEYEVESRDTKLGPEEITRDVPGVGDDALKDLDERGIIRVGAEVRAG 867

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 868 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 927



 Score =  543 bits (1398), Expect = e-151,   Method: Composition-based stats.
 Identities = 250/1051 (23%), Positives = 415/1051 (39%), Gaps = 70/1051 (6%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +  LL++Y+ +RPG+  +   AES+   +FFD  +YDL+ VGR K N +L L      
Sbjct: 239  SYEAGLLELYKKIRPGEPLSVESAESLITAMFFDPRRYDLAKVGRYKFNKKLALKNRISG 298

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + + ++ +      ++     +        L  +   +    L  Q     +++  S+  
Sbjct: 299  QVLAEDVVDPSTGEVIA----EAGTVVDRALATQIQNAAVPALWIQTETRNVKILSSMMV 354

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQ 546
             I S   +   P+ +   + V   V        L+Q+ E  +SL        R +S L  
Sbjct: 355  DIRSWIPELEDPKSIGVTELVYYPV--------LAQILEEYDSLEDRIEAIKRDISDLIP 406

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + +      +       +G     +     N   + ++    +      +    R V 
Sbjct: 407  KHITKEDIFATINYNMHLEWGAGTDDDIDHLGN-RRIRAVGELLQNQYRIGLSRLERVVR 465

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC------- 649
            +   T D+  +S     N     A               +  +   EL   R        
Sbjct: 466  ERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPG 525

Query: 650  --AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQRQAVPLLKA 706
              + +        + +        V         L N  +    +            +  
Sbjct: 526  GLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLACYARINEYGFVEAPYRKIDK 585

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
              P      E VV  ++        A   E++DA    IR+              Y    
Sbjct: 586  TDPKNPVVTEEVVYMTADEEDNYHVAQANEKLDAEGHFIRN--SVSGRYREETQEYDKSA 643

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F   + +  +       +   ++ +D       +++   A+      A +   G   + +
Sbjct: 644  FDYMDVSPKMVFSVATALIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVVGTGIETKAA 703

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +     +V++     +  E   ++ ++T     E                ++  I+  G 
Sbjct: 704  VDSGVCVVAKADGEVLSSESNRIIIKETDGNKREYI-LTKFSRSNQSNCYNQRPIVFKGD 762

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            +V  GD++    +   +  +   +  L      +  +  D  L     V   V       
Sbjct: 763  KVKAGDVIADGPST-SQGELALGKNPLIGFMTWEGYNYEDAVLLSERLVEYDVYTSVHIE 821

Query: 947  RHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
             + ++  +  +  E    +         +D  DE+ I+      R  +IL G+    G  
Sbjct: 822  EYEVESRDTKLGPEEITRDVPGVGDDALKDL-DERGIIRVGAEVRAGDILVGKVTPKGET 880

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                   L   +  E  R                 E      +            K+   
Sbjct: 881  ELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGAYGIIVDAKVFTR 923

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DI
Sbjct: 924  ENGDELSPGVNQSVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDI 983

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI          +    
Sbjct: 984  VLNPLGVPSRMNIGQVLEIHLSLAAKALGFNISTPVFDGANEVDIEDTLELANDYVNLPF 1043

Query: 1181 HTEKISDYDDDSVLRVAEQWK--SGVPVSTPVFDG----ADEEAINSMLRMADLDESGQS 1234
              E++           +   +      V T   D     +   A  S+ +   + + G+ 
Sbjct: 1044 DKEELEKDLQAEHPYWSADAEIFYDKYVDTLREDVMEYLSTNRAHRSLWKGVPISKDGKV 1103

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG TGE FD   T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1104 QLRDGRTGECFDGKTTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1163

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+
Sbjct: 1164 GEMEVWALEAYGAAYTLQEILTMKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLLKEL 1223

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            QALGL + + +   +    +E   ++   ++
Sbjct: 1224 QALGLDVKVLDENREEVELIET-SEYGNTDI 1253


>gi|315640268|ref|ZP_07895385.1| DNA-directed RNA polymerase subunit beta [Enterococcus italicus DSM
           15952]
 gi|315483930|gb|EFU74409.1| DNA-directed RNA polymerase subunit beta [Enterococcus italicus DSM
           15952]
          Length = 1213

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 590/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 15  LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 64

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEFV YE   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 65  DILPIDDFNGNLSLEFVDYELKTPKYTVEEARAHDANYSAPLHVTLRLT---------NR 115

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +
Sbjct: 116 ETGEIKAQEVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGF 172

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F       
Sbjct: 173 GSTVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFDIFGESKSLR 232

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +A+D      +      +  GE    +S + L +      +   +  +G 
Sbjct: 233 NTIEKD-LHKNASDSRTEEGLKDVYERLRPGEPKTADSSRNLLNARFFDPRRYDLASVGR 291

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L  L +AE +V+ ETGEI +E G VI  + ++E               
Sbjct: 292 YKVNKKLDLRTRLLNLTLAETLVDPETGEIIVEKGTVITHQVMDE--------------- 336

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y+ N L        +D           G V+     + +  F   D ++     
Sbjct: 337 --TLGEYLTNGLNAVTYYPSED-----------GVVTDPMTVQVIKVFSPLDPERE---- 379

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N     +VR +R  DII+ +    +L    G +DDID+LGNRR+RSVGE+
Sbjct: 380 -----INVIGNGYPGPEVRTVRPADIISAMSYFFNLMESIGKVDDIDHLGNRRIRSVGEL 434

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 435 LQNQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 494

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+A
Sbjct: 495 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYA 554

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFIETPYR+V     +VT+ + YL+A  E++  +AQANS L+EDG+F   +V  R
Sbjct: 555 KVNKYGFIETPYRRVDRESGRVTDTIDYLTADIEDHYVVAQANSPLNEDGTFKNSVVMAR 614

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + +   K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  ++
Sbjct: 615 ATSENLEIDVNKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKS 674

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+
Sbjct: 675 PWVGTGMEYKSAHDSGAALLCKADGVVEYVDAKEIRVRRDNGTLD-------TYAITKFR 727

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPLV +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED+++
Sbjct: 728 RSNSGTSYNQRPLVGLGEQVEKGDTLADGPSMENGEMALGQNVLVAFMTWEGYNYEDAVI 787

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 788 MSRRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEV 847

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R 
Sbjct: 848 EDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRE 907

Query: 949 GID 951
             D
Sbjct: 908 AGD 910



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 173/499 (34%), Positives = 236/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G +V  GD L    +      M   + +L A    +  +  D  +     V   V 
Sbjct: 740  LVGLGEQVEKGDTLADGPS-MENGEMALGQNVLVAFMTWEGYNYEDAVIMSRRLVKDDVY 798

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+         ++L G+  
Sbjct: 799  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVEDGDLLVGKVT 858

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 859  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 901

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 902  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 961

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 962  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 1007 -------------SDEDVWETVREAGMAKDAKTILYDG---------------------- 1031

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1032 ----RTGEPFDGRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 1087

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 1088 EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1147

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +   +     
Sbjct: 1148 SLGLDMRVLDIDDQEIELR 1166


>gi|300857254|ref|YP_003782238.1| DNA-directed RNA polymerase subunit beta [Clostridium ljungdahlii
           DSM 13528]
 gi|300437369|gb|ADK17136.1| DNA-directed RNA polymerase beta chain [Clostridium ljungdahlii DSM
           13528]
          Length = 1242

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/951 (45%), Positives = 600/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  EI  +P+LIEVQ  SY+ FL           EGLQ  F  + PI  ++ 
Sbjct: 9   KRTRMSFSRLKEIGHMPNLIEVQLDSYNWFL----------KEGLQEVFDDINPIQDYTA 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RLI          K   ++KEQ
Sbjct: 59  NLNLEFVGYKLDMDNIKYSVEECKERDATYAAPLKVKVRLI---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDLSVDKT---GKNLFSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS ++I+VRID+ RK+P+T  + A+G  ++ EI + F            D  
Sbjct: 167 GAWLEYETDSNNVIYVRIDKTRKLPITILIRAMGYGTDAEITNFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ + +IES         L +  + K  K L +    +
Sbjct: 227 KTHEEALLEIYKRLRPGEPPTVDSAQSLIESLFFDAKRYDLSRVGRYKFNKKLSLHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                A+D+VN +TGEI I+ G+ I+ +   EI    I  + I   D V     I N  V
Sbjct: 286 ANQIAAQDVVNPDTGEILIQKGEKINREKAVEIQQCGINVVDIQIEDIVLR--VIGNNFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                          R     D+   ++ ES+ +  L    D Y      + ++   ++ 
Sbjct: 344 D-------------IRSFIDFDIDDLNIKESVHYPTLKKILDNYSDEESIKEQIRKNIHE 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI ++D+ A I   + L  G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIVRDDMYATISYELGLAYGVGHTDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV   + +VTN++VY++A EE+   I +AN  +DE+G+F +  +  R   + I+VP + 
Sbjct: 568 RKVDKENKRVTNEIVYMTADEEDEYLIGRANEPIDENGNFIDNKITVRDKEDVIVVPGQD 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VDYMDVSSRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    A+ AG+V  V A  + ++        S  G DIYRL+KFQRSNQ TC+NQRP
Sbjct: 688 VDSGVLPKARNAGVVSYVCANEVRVKRD------SDGGTDIYRLLKFQRSNQCTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V+ G+ V++  ++ADGPSTDLG++ALG+N+ + F  W GYN+ED+MLISE +V +DVFT
Sbjct: 742 IVEKGEVVKKGTVLADGPSTDLGEIALGKNIRMGFTTWEGYNYEDAMLISEELVKKDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIH+EE+E  ARDTKLGPEEITRDIPNV E+ LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHLEEYESEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRAGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/572 (32%), Positives = 261/572 (45%), Gaps = 77/572 (13%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G  ++ ++       + +     ++   EV  +    G  +I R +        
Sbjct: 675  APIVGTGIEYKAAVDSGVLPKARNAGVVSYVCANEVRVKRDSDGGTDIYRLLKFQRSNQC 734

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              I++  I+  G  V  G +L    +      +   + +       +  +  D  L    
Sbjct: 735  TCINQRPIVEKGEVVKKGTVLADGPSTDL-GEIALGKNIRMGFTTWEGYNYEDAMLISEE 793

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK---DDEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      R  +
Sbjct: 794  LVKKDVFTSIHLEEYESEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRAGD 853

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                 E            
Sbjct: 854  ILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGE 896

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                   K+   + GD++ PGV ++V+ ++A KR I  GDKMAGRHGNKG++SR+LP ED
Sbjct: 897  AGIIVDVKVFTRENGDELSPGVNKLVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEED 956

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPFL DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   LG  + + + D     DI   
Sbjct: 957  MPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAASKLGWHVATPVFDGATEEDILEC 1016

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                        G  E+           
Sbjct: 1017 LKKA----------------------------------------GYRED----------- 1025

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G++ILYDG TGE F+RPVTVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1026 ---GKTILYDGRTGEEFNRPVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1082

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1083 FGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPESFK 1142

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            VL+KE+QAL L + + N   +     E + + 
Sbjct: 1143 VLIKELQALCLDVKVLNDNKEEIKLKESVDEE 1174


>gi|320547856|ref|ZP_08042140.1| DNA-directed RNA polymerase subunit beta [Streptococcus equinus
           ATCC 9812]
 gi|320447616|gb|EFW88375.1| DNA-directed RNA polymerase subunit beta [Streptococcus equinus
           ATCC 9812]
          Length = 1190

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DNGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PIT F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPITNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIMDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQTIAENLVDAETGEILVEAGTVMTRDVIDSIADQLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D  R +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKARALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      +TN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGVITNEIVWLTADEEDEYTVAQANSKLNEDGTFAEDIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEFPASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQ  LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYN+ED+++
Sbjct: 713 RSNSGTAYNQHTLVKVGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWDGYNYEDAII 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 LSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 174/508 (34%), Positives = 243/508 (47%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A       +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWDGYNYEDAIILSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E    +I    E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLW-------- 997

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                 D  +E         A +    ++
Sbjct: 998  -------------------------------------DTVNE---------AGMASDAKT 1011

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1012 VLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|326203312|ref|ZP_08193177.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           papyrosolvens DSM 2782]
 gi|325986570|gb|EGD47401.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           papyrosolvens DSM 2782]
          Length = 1246

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/954 (45%), Positives = 605/954 (63%), Gaps = 65/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + K  E++++P+LIEVQK SY  FL          +EGL+  F+ + PIT ++G
Sbjct: 9   RNTRMSYSKMREVLEMPNLIEVQKNSYQWFL----------DEGLREVFRDISPITDYTG 58

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L+FV Y  D  PK+ V++C  RD TY+ PLK  +RLI          K   ++KEQ 
Sbjct: 59  NLILDFVDYSLDDTPKYSVEECKERDTTYSAPLKAKVRLI---------NKESGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT  GTF+I G +R++VSQL RSPGI++     R    GK LY+  +IP++G
Sbjct: 110 IFMGDFPLMTDTGTFIINGAERVIVSQLVRSPGIYYSMKFDRV---GKKLYSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS DI+ VRIDR RK+P+T  L ALG  ++ EI+                   
Sbjct: 167 AWLEYETDSNDILSVRIDRTRKLPLTVLLRALGYGTDFEIMQLLGEDERLLATIQKDNAK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +   L+   K       +  GE   ++S + L + L    K   +   G          
Sbjct: 227 TTEEGLLEIYK------RLRPGEPPTVDSARSLLNSLFFDPKRYDLAKFGRFKFNKKLAI 280

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + + G   AE+IV+ ETGE+ +  G++I+     E+ +S    + I+Y+     +  + 
Sbjct: 281 SNLISGQVAAENIVSAETGEVLVTEGELIERDKAVEVQNSG---VNIVYLSVEGKSIKVI 337

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                D +        DI  +     V    + E + N    +  K  L       +   
Sbjct: 338 GNNTVDIHAYVD---FDISDLNINEKVKYAVLKEILENTSGEEQIKKTLKERINDLI--- 391

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI  +DIIA I  +++L  G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 392 --------PKHITIDDIIASINYIINLDYGIGSIDDIDHLGNRRIRSVGELLQNQFRIGL 443

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER++  DID V PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +T+ R
Sbjct: 444 SRMERVVRERMTIQDIDIVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTNKR 503

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN YGFIE
Sbjct: 504 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIE 563

Query: 600 TPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            PYRKV   + +VTN++VYL+A  E+   +AQA   L +DG+F    V  R   E + V 
Sbjct: 564 APYRKVDRKNRRVTNEIVYLTADVEDPFVVAQATEPLSDDGTFVSNKVVARYRHEILEVE 623

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             KIDF+D SP+Q+VS+A ++IPFLENDD+NR LMG NMQRQAVPL+KA++P VGTG+E 
Sbjct: 624 SNKIDFMDVSPQQMVSVATAMIPFLENDDANRALMGSNMQRQAVPLIKADSPIVGTGIEF 683

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A+ SG  ++AK AG++++V A  IVI++  G  D        Y+L+K+ RSNQ TC+N
Sbjct: 684 KAARDSGVCVIAKNAGVIDKVSANEIVIKTNSGQKD-------TYKLLKYMRSNQGTCLN 736

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+V+ G+ + + +IIADGPSTD G++ALGRN+L+ FM W GYN+ED++LI+E++V ED
Sbjct: 737 QRPIVRKGEMIEKGEIIADGPSTDNGEIALGRNILIGFMTWEGYNYEDAILINEKLVKED 796

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TSIHIEE+E  +RDTKLGPEEITRDIPNV EE LK++D+ GII +GAEV  GDILVGK
Sbjct: 797 VYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEEALKDLDDRGIIRIGAEVRSGDILVGK 856

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG +VDV++F R   D
Sbjct: 857 VTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIIVDVKVFTRENGD 910



 Score =  531 bits (1369), Expect = e-148,   Method: Composition-based stats.
 Identities = 269/1215 (22%), Positives = 432/1215 (35%), Gaps = 143/1215 (11%)

Query: 213  PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
            P+T            IL      +  + +                 K    L++ ++GE 
Sbjct: 52   PIT------DYTGNLILDFVDYSLDDTPKYSVEECKERDTTYSAPLKAKVRLINKESGEV 105

Query: 273  V------------IESGKKLTSGLLKSLKEKGVKFLGIT---SDCLCGLYVAEDIVNGET 317
                          ++G  + +G  + +  + V+  GI         G  +  + V    
Sbjct: 106  KEQEIFMGDFPLMTDTGTFIINGAERVIVSQLVRSPGIYYSMKFDRVGKKLYSNTVIPNR 165

Query: 318  G----------EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            G          +I     D   +  L  +  +         +  +  +  +  T+  D  
Sbjct: 166  GAWLEYETDSNDILSVRIDRTRKLPLTVLLRALGYGTDFEIMQLLGEDERLLATIQKDNA 225

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            K  ++ LL+IY+ +RPG+  T   A S+ N LFFD  +YDL+  GR K N +L +     
Sbjct: 226  KTTEEGLLEIYKRLRPGEPPTVDSARSLLNSLFFDPKRYDLAKFGRFKFNKKLAISNLIS 285

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +    E+I++     V +  G+    D          ++  +      + ++       
Sbjct: 286  GQV-AAENIVSAETGEVLVTEGELIERDKAVEVQNSGVNIVYLSVEGKSIKVIGNNTVDI 344

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                  DI  +   + +    +   +       Q+ +               R++ L   
Sbjct: 345  HAYVDFDISDLNINEKVKYAVLKEILENTSGEEQIKKTL-----------KERINDLIPK 393

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
             +        +  +    YG     +     N   + S+    +      +    R V +
Sbjct: 394  HITIDDIIASINYIINLDYGIGSIDDIDHLGN-RRIRSVGELLQNQFRIGLSRMERVVRE 452

Query: 608  GKVTNDVVYLSAMEEENRY-IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
                 D+  ++     N   +A A          ++ +       E     R        
Sbjct: 453  RMTIQDIDIVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTNKRRLSALGPGG 512

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG--------MESV 718
              ++        +          +          +  L   A     G        ++  
Sbjct: 513  LSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIEAPYRKVDRK 572

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS----GVDIYRLMKFQRSNQNT 774
              + +   +          V A      S +G    +        +I  +   +    + 
Sbjct: 573  NRRVTNEIVYLTADVEDPFVVAQATEPLSDDGTFVSNKVVARYRHEILEVESNKIDFMDV 632

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE----DSMLIS 830
               Q   V         +  A+              ++ A  P  G   E        + 
Sbjct: 633  SPQQMVSVATAMIPFLENDDANRALMGSNMQRQAVPLIKADSPIVGTGIEFKAARDSGVC 692

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                +  V   +   E   +   T  G ++  + +  +       +++  I+  G  +  
Sbjct: 693  VIAKNAGVIDKVSANE---IVIKTNSGQKDTYKLLKYMRSNQGTCLNQRPIVRKGEMIEK 749

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            G+I+    +      +     +L      +  +  D  L     V   V        +  
Sbjct: 750  GEIIADGPSTDN-GEIALGRNILIGFMTWEGYNYEDAILINEKLVKEDVYTSIHIEEYEA 808

Query: 951  DKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            +  +  +  E          E   +D DD   I+      R  +IL G+    G      
Sbjct: 809  ESRDTKLGPEEITRDIPNVGEEALKDLDDR-GIIRIGAEVRSGDILVGKVTPKGETELTA 867

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
               L   +  E  R                 E                   K+   + GD
Sbjct: 868  EERLLRAIFGEKAR-----------------EVRDTSLRVPHGESGIIVDVKVFTRENGD 910

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            ++PPGV ++V+ ++A KR I  GDKMAGRHGNKG++SRILP EDMPFL DGTP++IVLNP
Sbjct: 911  ELPPGVNQLVRCYIAQKRKISVGDKMAGRHGNKGVISRILPEEDMPFLPDGTPLEIVLNP 970

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMN+GQ+ E HLG+A   LG KI + + D     DI        K          
Sbjct: 971  LGVPSRMNIGQVLEVHLGFAAKALGWKIATPVFDGATEEDIRDTLIQAGKDP-------- 1022

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                       DG                      LYDG TG+P
Sbjct: 1023 ---------------------------DGKTV-------------------LYDGRTGDP 1036

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD  VTVGY+Y LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1037 FDNRVTVGYMYYLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1096

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LT+KSDDVVGR + YESIV G +  E G PESF VL+KE+Q+L L + + 
Sbjct: 1097 YGAAYTLQEILTVKSDDVVGRVKTYESIVKGENIPEPGIPESFKVLIKELQSLALDVKVY 1156

Query: 1365 NSRTKNSAKMEEIPD 1379
            +   +  A  E + D
Sbjct: 1157 SEEQEEIAIKEYVED 1171


>gi|170761098|ref|YP_001788829.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum A3
           str. Loch Maree]
 gi|226699390|sp|B1KSN3|RPOB_CLOBM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|169408087|gb|ACA56498.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum A3
           str. Loch Maree]
          Length = 1239

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/951 (46%), Positives = 600/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  + ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGVNEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             +   D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LISFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELGLSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFMDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVAYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVREDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 188/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  +R     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVREDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDV 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|312134688|ref|YP_004002026.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           owensensis OL]
 gi|311774739|gb|ADQ04226.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           owensensis OL]
          Length = 1230

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/959 (45%), Positives = 600/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRRIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G  + + I   F          +
Sbjct: 164 IPNRGAWLEFETDTNELLSVRLDRTRKVSLTTLLKAFGLYNQQMIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L + +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLNNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+  TGEI ++ GD+I  +    I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPRTGEILVKNGDMITREIALNIQDAGINEVWVYADEERLF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  D           +   ++    V E + N         D+S + R+
Sbjct: 343 KVVGNNTVKLDRYVDFD------VSDLNIKELVYLPVLEEILNATN------DVSEIKRL 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       +  +DI A     + L+ G G  DDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 IKEK----ERELVPYCLTIDDIYAATSYFLGLKYGIGATDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT++VVYL+A EE+   IAQA   +D++G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATEPVDQEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLITESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE+V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVEKVSADEIVIRNNDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+VK G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVKKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  474 bits (1219), Expect = e-131,   Method: Composition-based stats.
 Identities = 249/1194 (20%), Positives = 424/1194 (35%), Gaps = 162/1194 (13%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCL 303
                 +         +    +  +TG  +I   ++ + S L++S        +      +
Sbjct: 99   LINKETGEIKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQGRRI 158

Query: 304  CGLYVAEDI-----VNGETGEIYIEAGDVIDEKSLEEIFHS-----EIRDIPILYVDSVN 353
                +  +         +T E+     D   + SL  +  +     +         D   
Sbjct: 159  FSGTLIPNRGAWLEFETDTNELLSVRLDRTRKVSLTTLLKAFGLYNQQMIFEKFGEDERL 218

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
              +  +     +     ++ALL++YR +RPG+      A ++ N +FFD  +YDL+ VGR
Sbjct: 219  KASLEKEANKGELGNPVENALLEVYRRLRPGEPPNVENARNLLNNMFFDPRRYDLAKVGR 278

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             K N +L+L         ++       + +VD R G+  + + D +      ++ +   N
Sbjct: 279  YKFNKKLSL--------WKRIFNKRAAQDVVDPRTGEILVKNGDMITREIALNIQDAGIN 330

Query: 474  QYRLG--LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +  +     R+ + +      +D         +N K +V           L  LEE +N+
Sbjct: 331  EVWVYADEERLFKVVGNNTVKLDRYVDFDVSDLNIKELVY----------LPVLEEILNA 380

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
             + ++  +RL    +  +      ++      +++  +       G             R
Sbjct: 381  TNDVSEIKRLIKEKERELVPYCLTIDDIYAATSYFLGLKY-----GIGATDDIDHLGNRR 435

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            V A G +     ++   ++   +        E   I   ++   +       +       
Sbjct: 436  VRAVGELLQNQFRIGLARMERVIR-------ERMNIHDIDTVTPQTLINIRPVTAAIK-- 486

Query: 652  EEILVPREKIDFIDASPKQVV----SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            E              +P   +     ++A     L  D +   +   +            
Sbjct: 487  EFFGSSPLSQFMDQVNPLAALTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIET 546

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                  G+ + +A  +             +VD     +      L               
Sbjct: 547  PEGPNIGLITSLATYARVNEYGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATE 606

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDII---------------------------ADGPST 800
                +   +NQR  V+ G+E+   D                             A+    
Sbjct: 607  PVDQEGRFINQRVTVRFGEEIIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALM 666

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTKL 856
                      +L+   P  G   E    +   +      + V   +  +E   +      
Sbjct: 667  GSNMQRQAVPLLITESPIIGTGVEYRAAVDSGVCILAKKDGVVEKVSADE---IVIRNND 723

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +++   +           ++  I+  G EV  G+++    +      +   + +L A 
Sbjct: 724  GTKDVYHLLKFKRTNQGTCFNQRPIVKKGQEVKAGEVIADGPST-DHGELALGKNVLVAF 782

Query: 917  FGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +  D  L            S  + +     R      E          E   +D
Sbjct: 783  MPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKD 842

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE+ I+      +  +IL G+    G         L   +  E  R            
Sbjct: 843  L-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------ 889

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 E+                  K+     GD++PPGV ++V+V+VA KR I  GDKM
Sbjct: 890  -----ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISVGDKM 944

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNK                            GV SR+                   
Sbjct: 945  AGRHGNK----------------------------GVISRI------------------L 958

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             ++ +                ++ V+       +++                G  V+TPV
Sbjct: 959  PVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKVATPV 1010

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FDGA EE I   L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK++AR
Sbjct: 1011 FDGAKEEDIEEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDKIHAR 1070

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR + YE
Sbjct: 1071 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRVKTYE 1130

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +IV G +  E G PESF VLVKE+Q+L L + L +   K     E + D  + +
Sbjct: 1131 AIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDDDEQPQ 1184


>gi|327467037|gb|EGF12551.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK330]
 gi|328945415|gb|EGG39568.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK1087]
          Length = 1188

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|303239015|ref|ZP_07325545.1| DNA-directed RNA polymerase, beta subunit [Acetivibrio
           cellulolyticus CD2]
 gi|302593353|gb|EFL63071.1| DNA-directed RNA polymerase, beta subunit [Acetivibrio
           cellulolyticus CD2]
          Length = 1251

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 445/954 (46%), Positives = 610/954 (63%), Gaps = 63/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + K  E+ID+P+LIE+Q+ SY  FL          ++GL+  F+ V PIT ++G
Sbjct: 9   RNVRMSYSKIDEVIDMPNLIEIQRNSYIQFL----------DDGLREVFRDVSPITDYTG 58

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L+FV Y  D  PK+ V++C  RD TY+ PLK+ +RLI          K   ++KEQ 
Sbjct: 59  NLILDFVDYSIDDNPKYSVEECKERDATYSAPLKVKVRLI---------NKETGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT +GTF+I G +R++VSQL RSPGI++     +    GK LY+  +IP++G
Sbjct: 110 IFMGDFPLMTDNGTFIINGAERVIVSQLVRSPGIYYAMKFDKI---GKQLYSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D++ VRIDR RK+P+T  L ALG  ++ EI                    
Sbjct: 167 AWLEYETDSNDVMSVRIDRTRKLPITVLLRALGYGTDLEITELLGEDERIIATIQKDSAK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES + L  GL    K   +   G          
Sbjct: 227 TEDEGLLEIYK------RLRPGEPPTVESARSLLFGLFFDPKRYDLAKFGRFKFNKKLSI 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              + G   AE+I++ ETGE+ +  G+ I  +  E I ++ +  +   Y++       + 
Sbjct: 281 ASRINGFLAAENIIDPETGEVIVAEGEKISRQKAEVIQNAGVNAV---YLNIEGKKLKVM 337

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              + D         L  Y    P ++      +        + +K   +   +  +  +
Sbjct: 338 GNGMVD---------LKSYVDFDPKEIGFNEKVKLSVLKTVLEENKDKDTEELKKAIKEK 388

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           ++   P   ++I  EDII+ I  ++ L  G G +DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 389 VDELIP---KYITVEDIISSINYIITLSYGVGQVDDIDHLGNRRLRSVGELLQNQFRIGL 445

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER++  DID V PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +TH R
Sbjct: 446 ARMERVVRERMTIQDIDIVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHKR 505

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++FARVN YGFIE
Sbjct: 506 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTFARVNEYGFIE 565

Query: 600 TPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            PYR+V     KVTN++VYL+A EE+   +AQAN  LDE+G F ++ V CR   E + V 
Sbjct: 566 APYRRVDKETLKVTNEIVYLTADEEDAFIVAQANEPLDEEGKFLDKKVVCRAREEFLEVE 625

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             K+DF+D SPKQ+VS+A S+IPFLENDD+NR LMG NMQRQAVPL++ ++P VGTG+E 
Sbjct: 626 PSKVDFMDVSPKQIVSVATSMIPFLENDDANRALMGANMQRQAVPLIRTDSPIVGTGIEY 685

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  ++AK  GI+E+V A  IVIR+ EG  D       IY+L+K+ RSNQ TC+N
Sbjct: 686 KAAKDSGVCVLAKNPGIIEKVSASEIVIRTKEGKRD-------IYKLLKYLRSNQGTCIN 738

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+V+ G+EV + D+IADGPSTD G++ LGRN+L+ FM W GYN+ED++LISE++V ED
Sbjct: 739 QKPIVRKGEEVEKGDVIADGPSTDKGEIGLGRNILIGFMTWEGYNYEDAILISEKLVKED 798

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           VFTSIHIEE+E  +RDTKLGPEEITR+IPNVSE+ LK++D+ GII VGAEV  GDILVGK
Sbjct: 799 VFTSIHIEEYEAESRDTKLGPEEITREIPNVSEDSLKDLDDRGIIRVGAEVRSGDILVGK 858

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG +VDV++F R   D
Sbjct: 859 VTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIIVDVKVFTRENGD 912



 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/533 (35%), Positives = 257/533 (48%), Gaps = 79/533 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G  +I + +  +       I++  I+  G EV  GD++    +   +  +     +
Sbjct: 714  RTKEGKRDIYKLLKYLRSNQGTCINQKPIVRKGEEVEKGDVIADGPST-DKGEIGLGRNI 772

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----EL 966
            L      +  +  D  L     V   V        +  +  +  +  E    +I    E 
Sbjct: 773  LIGFMTWEGYNYEDAILISEKLVKEDVFTSIHIEEYEAESRDTKLGPEEITREIPNVSED 832

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D DD   I+      R  +IL G+    G         L   +  E  R        
Sbjct: 833  SLKDLDDR-GIIRVGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 883

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E                   K+   + GD++ PGV ++V+V++A KR I  
Sbjct: 884  ---------EVRDTSLRVPHGESGIIVDVKVFTRENGDELSPGVNQLVRVYIAQKRKISV 934

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL DGTP+ IVLNPLGVPSRMN+GQ+ E HLG+A  
Sbjct: 935  GDKMAGRHGNKGVISRILPEEDMPFLPDGTPLQIVLNPLGVPSRMNIGQVLEVHLGFAAK 994

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG KI + + D     DI                                         
Sbjct: 995  ALGWKIATPVFDGATEEDIVETLKKA---------------------------------- 1020

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                  G  E+              G+++LYDG TG PF+  VTVGY+Y+LKL H+V DK
Sbjct: 1021 ------GLSED--------------GKTVLYDGRTGLPFENRVTVGYMYILKLAHLVDDK 1060

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1061 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRV 1120

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            + YE+IV G +  E G PESF VL+KE+Q+L L + + +   +  A  E + D
Sbjct: 1121 KTYEAIVKGENVPEPGIPESFKVLIKELQSLCLDVKVYSEEQEEIAIKESVED 1173


>gi|239628535|ref|ZP_04671566.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239518681|gb|EEQ58547.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 1296

 Score =  839 bits (2167), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/954 (45%), Positives = 597/954 (62%), Gaps = 58/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + +  E++++P+LIE+QK SY  FL          +EGL+ AF  + PI  F+G
Sbjct: 13  KSVRMSYSRQKEVLEMPNLIEIQKDSYQWFL----------DEGLREAFDDISPIADFAG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         ++ E 
Sbjct: 63  HLSLEFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLYNKDKD---------EMNEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    GK LY C +IP++
Sbjct: 114 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIGHDKV---GKELYTCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVPVT  + ALG  +  EIL  F    K++ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGFGTNAEILELFGEEPKLLASFGKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L      L
Sbjct: 231 DNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKLSF-KYRL 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGEI  EAG  +D++S  +I ++    +P ++VD  +    + + ++
Sbjct: 290 NGQILAEDVVDTTTGEILAEAGTKLDKESAMKIQNA---AVPFVWVDGPDRKQKVLSNMM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            + +               P D     V E ++        +   +    +K  +R N+ 
Sbjct: 347 VELSAHV------------PFDPEEVGVTELVYYPALSSILEEAGTDPEALKEAIRRNIH 394

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 395 -DLIPKHITKEDILASINYNMHLEGQVGNADDIDHLGNRRIRAVGELLQNQYRIGLSRME 453

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L+ +TH RRLSA
Sbjct: 454 RVVRERMTTQDMDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLSA 513

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGFIE PYR
Sbjct: 514 LGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIEAPYR 573

Query: 604 KVC------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            V       + +VT++VVYL+A EE+N  +AQAN +LDE+G F    V  R   E     
Sbjct: 574 VVDKTTDPANPRVTDEVVYLTADEEDNFVVAQANEALDEEGHFIHNNVSGRFRTETSEFQ 633

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           ++ ID +D SPK V S+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTG+ES
Sbjct: 634 KKTIDLMDVSPKMVFSVATAMIPFLENDDANRALMGSNMQRQAVPLLTTEAPAVGTGIES 693

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG  +VA+ AG+VE+  +  I+I+  +          D+Y L KF+RSNQ+ C N
Sbjct: 694 KAAVDSGVCVVARNAGVVERSASNEIIIKRDK------DGNRDVYHLTKFKRSNQSNCYN 747

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+V   D V   ++IADGPSTD G++ALG+N L+ FM W GYN+ED++L+SER+V ED
Sbjct: 748 QKPIVYKNDHVEAGEVIADGPSTDNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQED 807

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK
Sbjct: 808 VYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGK 867

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 868 VTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 921



 Score =  526 bits (1354), Expect = e-146,   Method: Composition-based stats.
 Identities = 185/595 (31%), Positives = 267/595 (44%), Gaps = 42/595 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E    +     +V+ +          E++ +  K G
Sbjct: 668  MGSNMQRQAVPLLTTEAPAVGTGIESKAAVDSGVCVVARNAGVVERSASNEIIIKRDKDG 727

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              ++               ++  I+     V  G+++    +      +   +  L    
Sbjct: 728  NRDVYHLTKFKRSNQSNCYNQKPIVYKNDHVEAGEVIADGPSTDN-GEIALGKNPLIGFM 786

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDK 971
              +  +  D  L     V   V        +  +  +  +  E          E   +D 
Sbjct: 787  TWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDL 846

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 847  -DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 892

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+   + GD++ PGV   V++++A KR I  GDKMA
Sbjct: 893  ----EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNETVRIYIAQKRKISVGDKMA 948

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  
Sbjct: 949  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFN 1008

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + I D     DI          +                      ++K  +  S   +
Sbjct: 1009 VSTPIFDGANENDIMDTLELANDYVNLP-------------WEEFEVKYKDLIKPSVMDY 1055

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             GA  E    + +   +   G+  L DG TGE FD  VT+G+++ LKL+H+V DK++ARS
Sbjct: 1056 LGAHLEH-RELWKGVPISRDGKVRLRDGRTGEFFDGAVTIGHMHYLKLHHLVDDKIHARS 1114

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE++T+KSDDVVGR + YE+
Sbjct: 1115 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEIMTVKSDDVVGRVKTYEA 1174

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            I+ G +  E G PESF VL+KEMQ+LGL + +           E I D+   EL+
Sbjct: 1175 IIKGENIPEPGVPESFKVLLKEMQSLGLDVQVLRDDGTEVEMAENI-DYGDTELR 1228


>gi|255282535|ref|ZP_05347090.1| DNA-directed RNA polymerase, beta subunit [Bryantella formatexigens
           DSM 14469]
 gi|255266828|gb|EET60033.1| DNA-directed RNA polymerase, beta subunit [Bryantella formatexigens
           DSM 14469]
          Length = 1282

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/966 (45%), Positives = 603/966 (62%), Gaps = 72/966 (7%)

Query: 9   GLGRVR---------KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+R           + +  E++++P+LIEVQK SY  FL          +EGL+  F
Sbjct: 2   EKNRIRPIKNGNSFRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
             + PI  +     LEFV ++   D  K+ +++C  RD TYA PLK+ +RL         
Sbjct: 52  DDISPIRDYGEKLSLEFVDFKLCEDDVKYSIEECKERDATYAAPLKVKVRLH-------- 103

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK
Sbjct: 104 -NKETDEINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIAHDKI---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP-- 234
            L++C +IP++G W++ E DS DI +VR+DR RKVP+T  + ALG+ +  EIL  F    
Sbjct: 160 RLFSCTVIPNRGAWLEYETDSNDIFYVRVDRTRKVPITVLVRALGISTNAEILELFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KIV +   D           +         + +++ E +I +         L K  + K 
Sbjct: 220 KIVATLAKDTATNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +  + + G  +AED+++  TGEI  EAG     +  + I ++    +P ++V + 
Sbjct: 280 NKKL-LLRNRIAGHVLAEDVIDPSTGEILAEAGTKATRELADTIQNA---AVPFVWVQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV--STFSVAESMFNFLFFDSDKYDLST 410
             N  + ++++ D            Y  + P +V  +      ++ + L  +SD  D+  
Sbjct: 336 ERNVKVLSSMMVDITN---------YVDIDPQEVGVTELVYYPALKSILEENSDIEDIKE 386

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             R  ++  +        +HI KEDI+A I   + L  G GT DDID+LGNRR+RSVGE+
Sbjct: 387 AIRRDIHDLIP-------KHITKEDILASINYNIHLEYGIGTDDDIDHLGNRRIRSVGEL 439

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQYR+GL R+ER ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N
Sbjct: 440 LQNQYRIGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNN 499

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+A
Sbjct: 500 PLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYA 559

Query: 591 RVNAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           R+N YGFIE PYR +      + +VT++VVY++A EE+N ++AQAN +LDE+G F  + V
Sbjct: 560 RINQYGFIEAPYRVIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANEALDEEGHFIRKTV 619

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E     R   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL 
Sbjct: 620 SGRYREETQEYDRAMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLT 679

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            EAP VGTGME+  A  SG  +VAK AG VE+V +  IVIR+ +G  D        Y L 
Sbjct: 680 TEAPVVGTGMETKTAVDSGVCVVAKHAGTVERVTSKDIVIRTDDGKRDE-------YHLT 732

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSNQ+ C NQ+P+V  G+ V+   +IADGPST  G++ALG+N L+ FM W GYN+ED
Sbjct: 733 KFLRSNQSNCYNQKPIVFKGNRVQEGQVIADGPSTSNGEIALGKNPLIGFMTWEGYNYED 792

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SER+V +DV+TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII VG
Sbjct: 793 AVLLSERLVMDDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRVG 852

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F
Sbjct: 853 AEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVF 912

Query: 946 NRHGID 951
            R   D
Sbjct: 913 TREAGD 918



 Score =  555 bits (1431), Expect = e-155,   Method: Composition-based stats.
 Identities = 248/1135 (21%), Positives = 421/1135 (37%), Gaps = 85/1135 (7%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            +  G+      K +    +  +   G ++  +    ++ +I+    D   +  +  +  +
Sbjct: 148  IYYGIAHDKIGKRLFSCTVIPNR--GAWLEYE---TDSNDIFYVRVDRTRKVPITVLVRA 202

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                     ++       I  TL  D   + ++ LL++Y+ +RPG+      AES+   +
Sbjct: 203  LGISTNAEILELFGEEPKIVATLAKDTATNYQEGLLELYKKIRPGEPLAVESAESLIMAM 262

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD  +YDL+ VGR K N +L L        + ++ I              G I      
Sbjct: 263  FFDPRRYDLAKVGRYKFNKKLLLRNRIAGHVLAEDVIDPST----------GEILAEAGT 312

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
               R  +          + +   ER++K   S +   +           V   V      
Sbjct: 313  KATRELADTIQNAAVPFVWVQTEERNVKVLSSMMVDITNYVDIDPQEVGVTELVYYPALK 372

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S L +  +  +    I   R +  L    + +      +       YG     +     N
Sbjct: 373  SILEENSDIEDIKEAI--RRDIHDLIPKHITKEDILASINYNIHLEYGIGTDDDIDHLGN 430

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS------ 633
               + S+    +      +    R V +   T D+  +S     N     A         
Sbjct: 431  -RRIRSVGELLQNQYRIGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSS 489

Query: 634  ----LDEDGSFTEELVFCRC---------AGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                  +  +   EL   R          + +        + +        +        
Sbjct: 490  QLSQFMDQNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNI 549

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             L N  ++   +           ++A    +          +     +         V  
Sbjct: 550  GLINSLASYARI------NQYGFIEAPYRVIDKSDPKNPRVTDEVVYMTADEEDNYHVAQ 603

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADG 797
                +      +  + SG       ++ R+  +   V+ + +  V         +  A+ 
Sbjct: 604  ANEALDEEGHFIRKTVSGRYREETQEYDRAMFDYMDVSPKMVFSVATALIPFLQNDDANR 663

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKL 856
                         +L    P  G   E    +     V      ++     + +   T  
Sbjct: 664  ALMGSNMQRQAVPLLTTEAPVVGTGMETKTAVDSGVCVVAKHAGTVERVTSKDIVIRTDD 723

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +       +        ++  I+  G  V  G ++    +         +  L+  +
Sbjct: 724  GKRDEYHLTKFLRSNQSNCYNQKPIVFKGNRVQEGQVIADGPSTSNGEIALGKNPLIGFM 783

Query: 917  --FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDK 971
               G    D    S R+      T V +  +     D       + R+     +   +D 
Sbjct: 784  TWEGYNYEDAVLLSERLVMDDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL 843

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 844  -DERGIIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 889

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+   + GD++ PGV + V++++A KR I  GDKMA
Sbjct: 890  ----EVRDTSLKVPHGEYGIVVDAKVFTREAGDELAPGVNQAVRIYIAQKRKISVGDKMA 945

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  
Sbjct: 946  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFN 1005

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + I D     DI          +       K    ++     +   +++         
Sbjct: 1006 VSTPIFDGANENDIMDTLDLANDYVNLEWEEFKAKHEEELLPEVLDYLYEN--------- 1056

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                      + +   +   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARS
Sbjct: 1057 -----RDHRKLWKGVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARS 1111

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDD++GR + YE+
Sbjct: 1112 TGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDIIGRVKTYEA 1171

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            I+ G +  E G PESF VL+KE+Q+LGL + +     K     E +  + + +++
Sbjct: 1172 IIKGENIPEPGIPESFKVLLKELQSLGLDVRVLGENQKEVEIKETVE-YGETDIR 1225


>gi|222528810|ref|YP_002572692.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           bescii DSM 6725]
 gi|254765268|sp|B9MQG5|RPOB_ANATD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|222455657|gb|ACM59919.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 1228

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/959 (44%), Positives = 600/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G+ +++ I   F          +
Sbjct: 164 IPNRGAWLEFETDASELLSVRLDRTRKVSLTTLLKAFGLYNQQLIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLYSMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+ +TGEI ++ G++I  +   +I  + + ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPKTGEILVKEGELITREIATQIQDAGVNEVWVYADEERPF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  +                  +    + +      D      + V  +
Sbjct: 343 KVVGNNTVKLDRYVEFD---------------VSDINIKELVYRPVLDDILNTTNDVLEI 387

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K  ++   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 388 KRLIK-ERERELVPYCLTIDDIFAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VTN+VVYL+A EE+   IAQA   +DE+G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTNEVVYLTADEEDTYKIAQATEPVDEEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLMTESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVENVSADEIVIRNNDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  449 bits (1154), Expect = e-123,   Method: Composition-based stats.
 Identities = 164/538 (30%), Positives = 234/538 (43%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +++   +           ++  I+  G EV  G+++    +      +   + +
Sbjct: 720  RNNDGTKDVYHLLKFKRTNQGTCFNQRPIVRKGQEVKAGEVIADGPST-DHGELALGKNV 778

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L            S  + +     R      E          E 
Sbjct: 779  LVAFMPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGED 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      +  +IL G+    G         L   +  E  R        
Sbjct: 839  AIKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+                  K+     GD++PPGV ++V+V+VA KR I  
Sbjct: 890  ---------ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                ++ V+       +++                G  V
Sbjct: 958  ---LPVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKV 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE I   L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 1007 ATPVFDGAKEEDIEEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YE+IV G +  E G PESF VLVKE+Q+L L + L +   K     E + +  + +
Sbjct: 1127 KTYEAIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDEDEQPQ 1184


>gi|154503742|ref|ZP_02040802.1| hypothetical protein RUMGNA_01566 [Ruminococcus gnavus ATCC 29149]
 gi|153795842|gb|EDN78262.1| hypothetical protein RUMGNA_01566 [Ruminococcus gnavus ATCC 29149]
          Length = 1285

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/953 (45%), Positives = 592/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI+ ++G
Sbjct: 13  KSSRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPISDYAG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           +   +I E 
Sbjct: 63  HFSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLY---------NRETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKELYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASFGKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  VAED+VN  TGEI  E G +I  +  + I +S    + +   D   N   + N +V
Sbjct: 290 KGQKVAEDVVNELTGEIVAEKGTLITAEIADAIQNSGAPFVWVEGEDESRNIKILSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +      A++DI       D     V E ++  +     +     V  +K  ++ ++ 
Sbjct: 350 DLQ------AVVDI-------DPEEVGVTEQVYYPVLAGLLEESAGDVEELKSLIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNIHLEYRMGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D D V PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDQDGVSPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT DVVY++A EE+N ++AQAN+ LDE+G F  + V  R   E     R
Sbjct: 576 KIDKTDPMNPIVTEDVVYMTADEEDNYHVAQANTPLDEEGHFLHKNVSGRYREETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K D++D SP+ V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 SKFDYMDVSPQMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPAVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+RAG+VE   +  I I+  +G           Y+L KF RSNQ+ C NQ
Sbjct: 696 AAVDSGVCMVAERAGVVESSTSTSITIKHDDGTK-------KTYKLTKFLRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            P+V  G+ V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V+EDV
Sbjct: 749 VPIVDKGERVEAGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVAEDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 921



 Score =  544 bits (1402), Expect = e-152,   Method: Composition-based stats.
 Identities = 243/1065 (22%), Positives = 404/1065 (37%), Gaps = 75/1065 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D       I  +   D  ++ ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 212  IDLFGEEPKILASFGKDTAENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR     + N       R   ++    ++  L     G+   +    +      ++ 
Sbjct: 272  AKVGRY----KFNKKLALKNRIKGQKVAEDVVNELT----GEIVAEKGTLITAEIADAIQ 323

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +      R+IK   + +     +         V   V     +  L +    
Sbjct: 324  NSGAPFVWVEGEDESRNIKILSNMMVDLQAVVDIDPEEVGVTEQVYYPVLAGLLEESAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVE-MRDVHPTH-YGRICPAETSEGHNIGLVSSL 586
            V  L  +   R +  L    + +         ++H  +  G     +      I  V  L
Sbjct: 384  VEELKSLI-KRDIHDLIPKHITKEDILASINYNIHLEYRMGNDDDIDHLGNRRIRAVGEL 442

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLD 635
                +      +    R V +   T D           +  ++A  +E    +Q +  +D
Sbjct: 443  L---QNQYRIGLSRLERVVRERMTTQDQDGVSPQSLINIKPVTAAVKEFFGSSQLSQFMD 499

Query: 636  ED---GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            ++   G  T +          +   R   +  D        +     P   N      L 
Sbjct: 500  QNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLA 559

Query: 693  GCNMQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                  +   +         T  M  +V +      +         V      +      
Sbjct: 560  TYARINEYGFIEAPYRKIDKTDPMNPIVTED--VVYMTADEEDNYHVAQANTPLDEEGHF 617

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALG 808
            L  + SG       +++RS  +   V+ + +  V         +  A+            
Sbjct: 618  LHKNVSGRYREETQEYERSKFDYMDVSPQMVFSVATALIPFLENDDANRALMGSNMQRQA 677

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
              +L    P  G   E    +   +    +    +       +      G ++  +    
Sbjct: 678  VPLLTTEAPAVGTGMEVKAAVDSGVCMVAERAGVVESSTSTSITIKHDDGTKKTYKLTKF 737

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +        ++  I+  G  V  G ++    +      M   +  L      +  +  D 
Sbjct: 738  LRSNQSNCYNQVPIVDKGERVEAGQVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDA 796

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRN 981
             L     V+  V        +  +  +  +  E    +         +D  DE+ I+   
Sbjct: 797  VLLSERLVAEDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIRIG 855

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 856  AEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 898

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VS
Sbjct: 899  LKVPHGEYGIIVDAKVFTRENGDELSPGVNQSVRIYIAQKRKISVGDKMAGRHGNKGVVS 958

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R+LP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + +     
Sbjct: 959  RVLPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVATPVFGGAN 1018

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              DI                 +    + ++ +  V +                      +
Sbjct: 1019 ENDIMDTLDLAND-YVNMEWEDFEKKHGEELLPEVLQYLSD-------------NREHRA 1064

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1065 LWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQ 1124

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E 
Sbjct: 1125 PLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEP 1184

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            G PESF VL+KE+Q+L L + +          ME + D+ + +L+
Sbjct: 1185 GIPESFKVLLKELQSLALDVRVLRDDNTEVEIMEAV-DYGETDLR 1228


>gi|317501870|ref|ZP_07960055.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088617|ref|ZP_08337528.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316896760|gb|EFV18846.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407574|gb|EGG87074.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 1287

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 587/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 13  KSFRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIDECKERDATYAAPLKVRVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKKLYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIVDLFGEEPKILASFTKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ESYQEGLLELYKKIRPGEPLAVDSAESLINSMFFDPRRYDLAKVGRYKFNKKL-MLKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED V+  TGEI  E G  I  +  ++I ++ +  + +   D   N   + N +V
Sbjct: 290 AGCILAEDAVSQLTGEIVAEKGTKITRELADKIQNNAVPYLWVEGEDEERNIKILSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +                  D     V E ++  +     +     +  +K  ++ ++ 
Sbjct: 350 DFQAVTDI-------------DPEEVGVTEQVYYPVLAGIIEESAGDIEEMKALIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNMHLEYGMGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D + + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGF+E PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINQYGFVEAPYR 575

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            +      +  VT  VVY++A EE+N ++AQAN+ LDE+G F  + V  R   E     R
Sbjct: 576 WIDKSDPENPVVTEKVVYMTADEEDNYHVAQANTPLDEEGHFIHKNVSGRYREETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 SKFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+RAG VE   +  IV+R  +G           Y+L KFQRSNQ+ C NQ
Sbjct: 696 AAVDSGVCVVAERAGTVESSTSKEIVVREEDGKKTS-------YKLTKFQRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RPIVNKGDVVAAGQVIADGPSTSGGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  555 bits (1429), Expect = e-155,   Method: Composition-based stats.
 Identities = 255/1066 (23%), Positives = 416/1066 (39%), Gaps = 77/1066 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            VD       I  +   D  +  ++ LL++Y+ +RPG+      AES+ N +FFD  +YDL
Sbjct: 212  VDLFGEEPKILASFTKDTAESYQEGLLELYKKIRPGEPLAVDSAESLINSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L        + ++ +  +   +V  +  K T +  D + N  V    
Sbjct: 272  AKVGRYKFNKKLMLKNRIAGCILAEDAVSQLTGEIVAEKGTKITRELADKIQNNAV---- 327

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +     ER+IK   + +     +         V   V     +  + +    
Sbjct: 328  ----PYLWVEGEDEERNIKILSNMMVDFQAVTDIDPEEVGVTEQVYYPVLAGIIEESAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            +  +  +   R +  L    + +      +       YG     +     N   + ++  
Sbjct: 384  IEEMKALI-KRDIHDLIPKHITKEDILASINYNMHLEYGMGTDDDIDHLGN-RRIRAVGE 441

Query: 589  FARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED 637
              +      +    R V +   T D           +  ++A  +E    +Q +  +D++
Sbjct: 442  LLQNQYRIGLSRLERVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 501

Query: 638  ---GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
               G  T +          +   R   +  D        +     P   N      L   
Sbjct: 502  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATY 561

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS----VEG 750
                Q   +         +  E+ V       + A          A   +        + 
Sbjct: 562  ARINQYGFVEAPYRWIDKSDPENPVVTEKVVYMTADEEDNYHVAQANTPLDEEGHFIHKN 621

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                       Y   KF   + +  +       +   +  +D       +++   A+   
Sbjct: 622  VSGRYREETQEYERSKFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLL 681

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
               A +   G   + ++     +V+E   T       E++ R+ + G +   +       
Sbjct: 682  TTEAPVVGTGMEVKAAVDSGVCVVAERAGTVESSTSKEIVVRE-EDGKKTSYKLTKFQRS 740

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                  ++  I+  G  V  G ++    +  G   M   +  L      +  +  D  L 
Sbjct: 741  NQSNCYNQRPIVNKGDVVAAGQVIADGPSTSG-GEMALGKNPLIGFMTWEGYNYEDAVLL 799

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDR 980
                    V D    + H  +    +   +   E+I        +   +D  DE+ I+  
Sbjct: 800  ----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIRI 854

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                R  +IL G+    G         L   +  E  R                 E    
Sbjct: 855  GAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDT 897

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+V
Sbjct: 898  SLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVV 957

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            SR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D  
Sbjct: 958  SRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNISTPVFDGA 1017

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               DI                 E    +  + +  V +                      
Sbjct: 1018 NEIDIMDTLDLAND-YVNLEWEEFEKKHGQELLPEVLQYLSD-------------NREHR 1063

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            ++ +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQ
Sbjct: 1064 NLWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQ 1123

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E
Sbjct: 1124 QPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPE 1183

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
             G PESF VL+KE+Q+L L + +          ME + D+ + +L+
Sbjct: 1184 PGIPESFKVLLKELQSLALDVRVLRDDNTEVEIMENV-DYGETDLR 1228


>gi|324994403|gb|EGC26317.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK678]
 gi|325688490|gb|EGD30507.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK72]
 gi|325689597|gb|EGD31602.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK115]
 gi|327473093|gb|EGF18520.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK408]
 gi|327490872|gb|EGF22653.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK1058]
          Length = 1188

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|77413372|ref|ZP_00789565.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           515]
 gi|77160542|gb|EAO71660.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           515]
          Length = 1191

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DAGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+   +LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMVLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+GETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNLKTRLLNQTIAENLVDGETGEILVEAGTVMTRDVIDSIAEHIDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVILQKFKVVAPTDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGNS--------NPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLD-------VYHVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 170/507 (33%), Positives = 236/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDLVEKGDFIADGPS-MENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMD 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1007 SDAK----------------------------TVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|325693918|gb|EGD35837.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK150]
          Length = 1188

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLDARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|160937581|ref|ZP_02084942.1| hypothetical protein CLOBOL_02472 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439650|gb|EDP17400.1| hypothetical protein CLOBOL_02472 [Clostridium bolteae ATCC
           BAA-613]
          Length = 1309

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/954 (45%), Positives = 593/954 (62%), Gaps = 58/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + +  E++++P+LIE+QK SY  FL           EGL+ AF  + PI  F+G
Sbjct: 28  KSVRMSYSRQKEVLEMPNLIEIQKDSYQWFL----------KEGLKEAFDDISPIADFAG 77

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         ++ E 
Sbjct: 78  HLSLEFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLYNKDKD---------EMNEH 128

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    GK LY C +IP++
Sbjct: 129 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIGHDKV---GKELYTCTVIPNR 185

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVPVT  + ALG  +  EIL  F    K++ S   D  
Sbjct: 186 GAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGFGTNAEILELFGEEPKLLASFGKDTS 245

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L      L
Sbjct: 246 DNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKLSF-KYRL 304

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGEI  EAG  +D++S   I ++    +P ++VD  +    + + ++
Sbjct: 305 NGQVLAEDVVDTATGEILAEAGTKLDKESAMRIQNA---AVPYVWVDGPDRKQKVLSNMM 361

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            + +               P D     V E ++        +   +    +K  +R N+ 
Sbjct: 362 VELSAYV------------PFDPEEVGVTELVYYPALASILEEAGTDEESLKEAVRRNIH 409

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 410 -DLIPKHITKEDILASINYNMHLEEQVGNADDIDHLGNRRIRAVGELLQNQYRIGLSRME 468

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L+ +TH RRLSA
Sbjct: 469 RVVRERMTTQDMDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLSA 528

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGFIE PYR
Sbjct: 529 LGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIEAPYR 588

Query: 604 KVCD------GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            V         +VT++VVYL+A EE+N  +AQAN +LDE+G F    V  R   E     
Sbjct: 589 VVDKTTDPSSPRVTDEVVYLTADEEDNFVVAQANEALDEEGHFIHNNVSGRFRTETSEFQ 648

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           ++ ID +D SPK V S+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTG+E+
Sbjct: 649 KKTIDLMDVSPKMVFSVATAMIPFLENDDANRALMGSNMQRQAVPLLTTEAPAVGTGIEA 708

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG  +VAK AG+VE+  +  I+IR        S    D+Y L KF+RSNQ+ C N
Sbjct: 709 KAAVDSGVCVVAKNAGVVERSASNEIIIRRD------SDGNRDVYHLTKFKRSNQSNCYN 762

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+V   D V   ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V ED
Sbjct: 763 QKPIVYKNDHVEAGEVIADGPSTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQED 822

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK
Sbjct: 823 VYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGK 882

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 883 VTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 936



 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 177/545 (32%), Positives = 255/545 (46%), Gaps = 40/545 (7%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++ R    G  ++               ++  I+     V  G+++    +      + 
Sbjct: 733  EIIIRRDSDGNRDVYHLTKFKRSNQSNCYNQKPIVYKNDHVEAGEVIADGPSTSN-GEIA 791

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--- 964
              +  L      +  +  D  L     V   V        +  +  +  +  E       
Sbjct: 792  LGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVP 851

Query: 965  ---ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E   +D  DE+ I+      R  +IL G+    G         L   +  E  R   
Sbjct: 852  GVGEDALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--- 907

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E      +            K+   + GD++ PGV + V++++A K
Sbjct: 908  --------------EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNQTVRIYIAQK 953

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 954  RKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHL 1013

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
              A   LG  + + I D     DI          +              + +L+ +    
Sbjct: 1014 SLAAKALGFNVSTPIFDGANENDIMDTLEVANDYVNLS---WDEFKAKYEDLLKPSVIDY 1070

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G  +               + +   +   G+  L DG TGE FD  VT+G+++ LKL+H
Sbjct: 1071 LGAHL-----------EHRELWKGVPISRDGKVRLRDGRTGEYFDGAVTIGHMHYLKLHH 1119

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE++T+KSDD
Sbjct: 1120 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEIMTVKSDD 1179

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR + YE+I+ G +  E G PESF VL+KEMQ+LGL + +           E I D+ 
Sbjct: 1180 VVGRVKTYEAIIKGENIPEPGVPESFKVLLKEMQSLGLDVQVLRDDGTEVEMNENI-DYG 1238

Query: 1382 KCELK 1386
              EL+
Sbjct: 1239 DTELR 1243


>gi|324990484|gb|EGC22422.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK353]
          Length = 1188

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDNDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|153935474|ref|YP_001389211.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum A
           str. Hall]
 gi|152931388|gb|ABS36887.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum A
           str. Hall]
          Length = 1232

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 440/951 (46%), Positives = 601/951 (63%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSTTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             + P D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVPFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELALSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|153815044|ref|ZP_01967712.1| hypothetical protein RUMTOR_01261 [Ruminococcus torques ATCC 27756]
 gi|145847612|gb|EDK24530.1| hypothetical protein RUMTOR_01261 [Ruminococcus torques ATCC 27756]
          Length = 1287

 Score =  838 bits (2166), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 587/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 13  KSFRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIDECKERDATYAAPLKVRVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKKLYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIVDLFGEEPKILASFTKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ESYQEGLLELYKKIRPGEPLAVDSAESLINSMFFDPRRYDLAKVGRYKFNKKL-MLKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED V+  TGEI  E G  I  +  ++I ++ +  + +   D   N   + N +V
Sbjct: 290 AGCILAEDAVSQLTGEIVAEKGTKITRELADKIQNNAVPYLWVEGEDEERNIKILSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +                  D     V E ++  +     +     +  +K  ++ ++ 
Sbjct: 350 DLQAVTDI-------------DPEEVGVTEQVYYPVLAGIIEESAGDIEEMKALIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNMHLEYGMGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D + + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGF+E PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINQYGFVEAPYR 575

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            +      +  VT  VVY++A EE+N ++AQAN+ LDE+G F  + V  R   E     R
Sbjct: 576 WIDKSDPENPVVTEKVVYMTADEEDNYHVAQANTPLDEEGHFIHKNVSGRYREETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 SKFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+RAG VE   +  IV+R  +G           Y+L KFQRSNQ+ C NQ
Sbjct: 696 AAVDSGVCVVAERAGTVESSTSKEIVVREEDGKKTS-------YKLTKFQRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RPIVNKGDVVAAGQVIADGPSTSGGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  554 bits (1428), Expect = e-155,   Method: Composition-based stats.
 Identities = 255/1066 (23%), Positives = 416/1066 (39%), Gaps = 77/1066 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            VD       I  +   D  +  ++ LL++Y+ +RPG+      AES+ N +FFD  +YDL
Sbjct: 212  VDLFGEEPKILASFTKDTAESYQEGLLELYKKIRPGEPLAVDSAESLINSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L        + ++ +  +   +V  +  K T +  D + N  V    
Sbjct: 272  AKVGRYKFNKKLMLKNRIAGCILAEDAVSQLTGEIVAEKGTKITRELADKIQNNAV---- 327

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +     ER+IK   + +     +         V   V     +  + +    
Sbjct: 328  ----PYLWVEGEDEERNIKILSNMMVDLQAVTDIDPEEVGVTEQVYYPVLAGIIEESAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            +  +  +   R +  L    + +      +       YG     +     N   + ++  
Sbjct: 384  IEEMKALI-KRDIHDLIPKHITKEDILASINYNMHLEYGMGTDDDIDHLGN-RRIRAVGE 441

Query: 589  FARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED 637
              +      +    R V +   T D           +  ++A  +E    +Q +  +D++
Sbjct: 442  LLQNQYRIGLSRLERVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 501

Query: 638  ---GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
               G  T +          +   R   +  D        +     P   N      L   
Sbjct: 502  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATY 561

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS----VEG 750
                Q   +         +  E+ V       + A          A   +        + 
Sbjct: 562  ARINQYGFVEAPYRWIDKSDPENPVVTEKVVYMTADEEDNYHVAQANTPLDEEGHFIHKN 621

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                       Y   KF   + +  +       +   +  +D       +++   A+   
Sbjct: 622  VSGRYREETQEYERSKFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLL 681

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
               A +   G   + ++     +V+E   T       E++ R+ + G +   +       
Sbjct: 682  TTEAPVVGTGMEVKAAVDSGVCVVAERAGTVESSTSKEIVVRE-EDGKKTSYKLTKFQRS 740

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                  ++  I+  G  V  G ++    +  G   M   +  L      +  +  D  L 
Sbjct: 741  NQSNCYNQRPIVNKGDVVAAGQVIADGPSTSG-GEMALGKNPLIGFMTWEGYNYEDAVLL 799

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDR 980
                    V D    + H  +    +   +   E+I        +   +D  DE+ I+  
Sbjct: 800  ----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIRI 854

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                R  +IL G+    G         L   +  E  R                 E    
Sbjct: 855  GAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDT 897

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+V
Sbjct: 898  SLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVV 957

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            SR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D  
Sbjct: 958  SRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNISTPVFDGA 1017

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               DI                 E    +  + +  V +                      
Sbjct: 1018 NEIDIMDTLDLAND-YVNLEWEEFEKKHGQELLPEVLQYLSD-------------NREHR 1063

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            ++ +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQ
Sbjct: 1064 NLWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQ 1123

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E
Sbjct: 1124 QPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPE 1183

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
             G PESF VL+KE+Q+L L + +          ME + D+ + +L+
Sbjct: 1184 PGIPESFKVLLKELQSLALDVRVLRDDNTEVEIMENV-DYGETDLR 1228


>gi|170757275|ref|YP_001783129.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum B1
           str. Okra]
 gi|226699389|sp|B1IGG2|RPOB_CLOBK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|169122487|gb|ACA46323.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum B1
           str. Okra]
          Length = 1232

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/951 (46%), Positives = 599/951 (62%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI    I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQSCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             +   D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVSFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELALSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|187776568|ref|ZP_02993041.1| hypothetical protein CLOSPO_00082 [Clostridium sporogenes ATCC
           15579]
 gi|187775227|gb|EDU39029.1| hypothetical protein CLOSPO_00082 [Clostridium sporogenes ATCC
           15579]
          Length = 1236

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/951 (46%), Positives = 599/951 (62%), Gaps = 57/951 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  E+  +P+LIEVQ  SYD FL           EGLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSRLKEVGQMPNLIEVQLDSYDWFL----------KEGLQEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   +IKEQ
Sbjct: 59  NLNLEFVGYKLDLDSIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D  
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+ E +IES         L +  + K  K L I    +
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNKKLAIHL-RI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                 +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V
Sbjct: 286 TNQIADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNL 422
              +             +   D+S  ++ E +F  +     D Y      + ++   +  
Sbjct: 344 DIHS-------------LVSFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYR 390

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 391 LIP---KHIIREDIYATINYELGLSYDIGYKDDIDHLGNRRLRSVGELLQNQFRIGLSRM 447

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLS
Sbjct: 448 ERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLS 507

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPY
Sbjct: 508 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPY 567

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R++   + + TND+VY++A EE+   IA+++  +DE G F ++ V  R   E ++VP  +
Sbjct: 568 RRIDPKNKRATNDIVYMTADEEDLYVIARSDEPIDEKGYFLDDKVTVRAKEEVLVVPVSE 627

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ++++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A
Sbjct: 628 VEYMDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAA 687

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP
Sbjct: 688 TDSGVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRP 741

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFT
Sbjct: 742 IVSKGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFT 801

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TP
Sbjct: 802 SIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTP 861

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 862 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 187/544 (34%), Positives = 253/544 (46%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 709  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E        
Sbjct: 769  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 991  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 1020

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 1021 ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L + + N   +     E + D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVLNDDNQEIKLKESV-DEDA 1175

Query: 1383 CELK 1386
             EL+
Sbjct: 1176 DELE 1179


>gi|291535404|emb|CBL08516.1| DNA-directed RNA polymerase subunit beta [Roseburia intestinalis
           M50/1]
 gi|291537953|emb|CBL11064.1| DNA-directed RNA polymerase subunit beta [Roseburia intestinalis
           XB6B4]
          Length = 1298

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/964 (44%), Positives = 601/964 (62%), Gaps = 68/964 (7%)

Query: 9   GLGRVR---------KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+R           + +  E++++P+LIEVQK SY  FL           EGL+  F
Sbjct: 2   EKNRIRPVKAGKGMRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------KEGLKEVF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
             + PI  +SG   LEFV +       K+ + +C  RD TYA PLK+ +RL         
Sbjct: 52  DDISPIADYSGHLSLEFVDFTLCESDVKYTIPECKERDATYAAPLKVKVRLH-------- 103

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK
Sbjct: 104 -NKETDEINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIAHDKV---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYP-- 234
            LY+C +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ + +EI+  F    
Sbjct: 160 KLYSCTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNQEIVDLFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KI+ S   D           +         + +++ E +I +         L K  + K 
Sbjct: 220 KILASFGKDVATNYEEGLLELYKKIRPGEPLTVESAESLISAMFFDPRRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +  + + G  +AED+VN  TGEI  EAG  +     ++I ++    +P +++ + 
Sbjct: 280 NKKL-MLKNRINGHVLAEDVVNLATGEIIAEAGTEVTRSLADDIQNA---AVPYVWIQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             N  + ++++ D             + +   ++  + V   +       +D  DL    
Sbjct: 336 TRNVKVLSSMMVDLRAYVD----CNPKDLGITELVYYPVLAQLME---EHTDIDDLKEAI 388

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  ++  +        +HI K+DI A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 389 KKNVHDLIP-------KHITKDDIFASINYNMHLEYGIGNDDDIDHLGNRRIRAVGELLQ 441

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER++++D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 442 NQYRIGLSRLERVVRERMTTLDLDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 501

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+
Sbjct: 502 GELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARI 561

Query: 593 NAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGF+E PYRK+      + +VT++VVY++A EE+N ++AQAN +LD +G F    V  
Sbjct: 562 NEYGFVEAPYRKIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANEALDAEGHFVRNSVSG 621

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E     +   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  +
Sbjct: 622 RYREETQEYEKTMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTD 681

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTGME+  A  SG  ++AK++GIVE  ++ +I+I+S EG  D       +Y+L KF
Sbjct: 682 APVVGTGMETKAAVDSGVCVIAKKSGIVESSESNQIIIKSDEGTRD-------VYKLTKF 734

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ+ C NQRP+V  GD V   ++IADGPST  G+LALG+N L+ FM W GYN+ED++
Sbjct: 735 SRSNQSNCYNQRPIVFKGDRVEAGEVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAV 794

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAE
Sbjct: 795 LLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAE 854

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R
Sbjct: 855 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTR 914

Query: 948 HGID 951
              D
Sbjct: 915 ENGD 918



 Score =  533 bits (1373), Expect = e-149,   Method: Composition-based stats.
 Identities = 184/592 (31%), Positives = 271/592 (45%), Gaps = 28/592 (4%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E    +     V       +   E   +   +  G 
Sbjct: 666  MGSNMQRQAVPLLTTDAPVVGTGMETKAAVDSGVCVIAKKSGIVESSESNQIIIKSDEGT 725

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI-- 916
             ++ +             ++  I+  G  V  G+++    +         +  L+  +  
Sbjct: 726  RDVYKLTKFSRSNQSNCYNQRPIVFKGDRVEAGEVIADGPSTSNGELALGKNPLIGFMTW 785

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDD 973
             G    D    S R+      T + +  +     D       + R+     +   +D  D
Sbjct: 786  EGYNYEDAVLLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-D 844

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 845  ERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------------- 889

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +            K+   + GD++ PGV + V++++A KR I  GDKMAGR
Sbjct: 890  --EVRDTSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGR 947

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I+
Sbjct: 948  HGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIE 1007

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     DI          +       +              +      V   + D 
Sbjct: 1008 TPVFDGAKEIDIQDTLELANDYVNMPFDAAEAEKEGKTESFEEKYKDILREDVMKYLSD- 1066

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                A  ++ +   +   G+  L DG TGEPFD PVT+G+++ LKL+H+V DK++ARSTG
Sbjct: 1067 --NRAHRALWKGVPISRDGKVQLRDGRTGEPFDSPVTIGHMHYLKLHHLVDDKIHARSTG 1124

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+
Sbjct: 1125 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAII 1184

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             G++  E G PESF VL+KE+Q+LGL + + +        ME   ++   +L
Sbjct: 1185 KGDNIPEPGIPESFKVLLKELQSLGLDVKVLDEDRNEVELMET-SEYGNTDL 1235


>gi|260437412|ref|ZP_05791228.1| DNA-directed RNA polymerase, beta subunit [Butyrivibrio crossotus
           DSM 2876]
 gi|292810044|gb|EFF69249.1| DNA-directed RNA polymerase, beta subunit [Butyrivibrio crossotus
           DSM 2876]
          Length = 1289

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/960 (45%), Positives = 589/960 (61%), Gaps = 63/960 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + +  E++D+P+LIEVQK SY  FL           +GL+  F+ + PIT +SG
Sbjct: 13  KNVRMSYSRQKEVLDMPNLIEVQKNSYKWFL----------EDGLKEVFEDISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +IKE 
Sbjct: 63  HLSLEFVDFMLCEDDKKYSIEECKERDATYAAPLKVKVRLY---------NKETDEIKEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI+++    +    GK LY+C +IP++
Sbjct: 114 DIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYEIGHDKI---GKTLYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+  VR+DR RKVPVT  + ALG  +  +I   F    KI  S   D  
Sbjct: 171 GAWLEYETDSNDVFSVRVDRTRKVPVTVLIRALGFGTNAQIRELFGDEPKIEASIAKDPS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS---- 300
               S  +      +      I  GE + ++S + L + +    +   +  +G       
Sbjct: 231 VTEKSP-NGGYEEGLLELYKKIRPGEPLSVDSAESLINAMFFDPRRYDLAKVGRYKFNKK 289

Query: 301 ----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + + G  +AED+V+  TGEI   AGD + + S   I ++ +               
Sbjct: 290 LNFRNRIWGHKLAEDVVDVTTGEIIASAGDTLTKDSALAIQNAAV--------------P 335

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           YI   +   K K   + ++DI + +   +    S+      +        + +T      
Sbjct: 336 YIWLAVEDRKVKVLSNMMVDITKHVDITEEEAKSLGIHEAVYYPVLKTILEENTSIDDIK 395

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                  +    +HI  +DIIA I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 396 EAIKKNASDLVPKHITVDDIIASINYNIHLEYGVGTKDDIDHLGNRRIRAVGELLQNQYR 455

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER+++ D++   PQ LIN KPV +AV EFF SSQLSQ  +  N LS IT
Sbjct: 456 IGLSRMERVVRERMTTQDVEGASPQTLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSEIT 515

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++AR+N YG
Sbjct: 516 HKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARINEYG 575

Query: 597 FIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           F+E PYR V      + +VT +V YL+A EE+N Y+AQAN+ LDE+G F +  V  R   
Sbjct: 576 FVEAPYRVVDKTDPKNPRVTEEVRYLTADEEDNYYVAQANAELDENGYFVKNSVSGRYRE 635

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     + KID +D SPK V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL  ++  V
Sbjct: 636 ETSEFEKSKIDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLTTDSAVV 695

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SGA +VA++ G+V++  +  IVI   +G+          Y+L KF RSN
Sbjct: 696 GTGMEYKTAVDSGACVVAEKGGLVDRATSTEIVILEDDGNRHS-------YQLTKFARSN 748

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+ C NQ+P+V  GD V   D+IADGPST  G++ALG+N L+ FM W GYN+ED++L+SE
Sbjct: 749 QSNCYNQKPIVTKGDRVEAGDVIADGPSTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSE 808

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TS+HIEE+E  ARDTKLGPEEITR++P V E+ LK++DE GII +GAEV  G
Sbjct: 809 RLVRDDVYTSVHIEEYEAEARDTKLGPEEITREVPGVGEDALKDLDERGIIRIGAEVRAG 868

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G +VD ++F R   D
Sbjct: 869 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGVIVDAKVFTRENGD 928



 Score =  525 bits (1353), Expect = e-146,   Method: Composition-based stats.
 Identities = 187/581 (32%), Positives = 268/581 (46%), Gaps = 51/581 (8%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            M +       + +++E+    D  TS  I   E        G     +            
Sbjct: 699  MEYKTAVDSGACVVAEKGGLVDRATSTEIVILEDD------GNRHSYQLTKFARSNQSNC 752

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPS 933
             ++  I+  G  V  GD++    +         +  L+  +   G    D    S R+  
Sbjct: 753  YNQKPIVTKGDRVEAGDVIADGPSTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVR 812

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLMEIL 990
                T V +  +     D       + RE     E   +D  DE+ I+      R  +IL
Sbjct: 813  DDVYTSVHIEEYEAEARDTKLGPEEITREVPGVGEDALKDL-DERGIIRIGAEVRAGDIL 871

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+    G         L   +  E  R                 E              
Sbjct: 872  VGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEYG 914

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 K+   + GDD+ PGV + V++++A KR I  GDKMAGRHGNKG+VSRILP EDMP
Sbjct: 915  VIVDAKVFTRENGDDLNPGVNQSVRIYIAQKRKISVGDKMAGRHGNKGVVSRILPVEDMP 974

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG KI + + D     DI     
Sbjct: 975  YLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAARALGFKISTPVFDGANEKDIMDTLD 1034

Query: 1171 FLEKVIGTG--SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                 +        EK     ++ ++    +                     +  +   +
Sbjct: 1035 LANDYVNLEWDEFKEKWDGKINEELMEYLGEHL----------------DHRAEWKGVPI 1078

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1079 SRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1138

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G++  E G PESF 
Sbjct: 1139 FGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGIPESFK 1198

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEI----PDFNKCEL 1385
            VL++E+++L L + + +         E I     D +  +L
Sbjct: 1199 VLLEELRSLALDVKVLDENGDEVDIKENIGYAESDTSHEDL 1239


>gi|312865581|ref|ZP_07725807.1| DNA-directed RNA polymerase, beta subunit [Streptococcus downei
           F0415]
 gi|311098909|gb|EFQ57127.1| DNA-directed RNA polymerase, beta subunit [Streptococcus downei
           F0415]
          Length = 1193

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/963 (44%), Positives = 594/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL            GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------ENGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTETMELEFVGYELKEPKYSLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADARTDEALKEIYERLRPGEPKTADSSRSLLTARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+GETGEI +EAG V+    ++ I  +          +
Sbjct: 278 YKINKKLNVKTRLLNQTLAENLVDGETGEILVEAGTVMTRDVIDSIAEALD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N+  Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 330 GLNSFVYTPN----DYAVVTEPVILQKFKVVSPLDADKV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGNS--------NPDDKVRALTPADILAEMSYFLNLAQGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D +++ PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLTRMERNVRERMSVQDNEALTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSTGKVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFAASTVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHPGRVTFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD+V + D IADGPS + G++ALGRN +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDQVEKGDFIADGPSMEKGEMALGRNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 833 EEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 172/508 (33%), Positives = 236/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V  GD +    +   +  M      + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDQVEKGDFIADGPS-MEKGEMALGRNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E    +I    E   +D  DE  I+         +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL-DEMGIIRIGAEVEEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +          +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGAGIVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLWETVEEAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|312622901|ref|YP_004024514.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203368|gb|ADQ46695.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 1228

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/959 (45%), Positives = 600/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G  + + I   F          +
Sbjct: 164 IPNRGAWLEFETDTSELLSVRLDRTRKVSLTTLLKAFGLYNQQMIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLYNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+ +TGEI ++ G++I  +   +I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPKTGEILVKEGELITREIATQIQDAGINEVWVYADEERPF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  +   + L I                 +      D      + V  +
Sbjct: 343 KVVGNNTVKLDRYVEFDVSDLHIK---------------ELVYKPVLDDILNTTNDVLEI 387

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K  +R   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 388 KRLIR-ERERELVPYCLTIDDIFAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VTN+VVYL+A EE+   IAQA   +DE+G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTNEVVYLTADEEDTYKIAQATEPVDEEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLMTESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE+V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVEKVSADEIVIRNNDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 163/538 (30%), Positives = 234/538 (43%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +++   +           ++  I+  G EV  G+++    +      +   + +
Sbjct: 720  RNNDGTKDVYHLLKFKRTNQGTCFNQRPIVRKGQEVKAGEVIADGPST-DHGELALGKNV 778

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L            S  + +     R      E          E 
Sbjct: 779  LVAFMPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGED 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      +  +IL G+    G         L   +  E  R        
Sbjct: 839  AIKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+                  K+     GD++PPGV ++V+V+VA KR I  
Sbjct: 890  ---------ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                ++ V+       +++                G  V
Sbjct: 958  ---LPVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKV 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE I   L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 1007 ATPVFDGAKEEDIEEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YE+IV G +  E G PESF VLVKE+Q+L L + L +   +     E + +  + +
Sbjct: 1127 KTYEAIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSENNEEIELKESVDEDEQPQ 1184


>gi|312862392|ref|ZP_07722635.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           vestibularis F0396]
 gi|322515918|ref|ZP_08068859.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           vestibularis ATCC 49124]
 gi|311102035|gb|EFQ60235.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           vestibularis F0396]
 gi|322125592|gb|EFX96922.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           vestibularis ATCC 49124]
          Length = 1193

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/963 (44%), Positives = 589/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKEFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AE++V+ ETGEI +EAG  +    ++ I      D+      
Sbjct: 278 YKVNKKLNIKTRLLGQTIAENLVDPETGEILVEAGTEMTRDVIDSIAEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVAPNDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTTADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN+VV+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGKVTNEVVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEYPSHLVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVVYSDADKVEVRREDGSLD-------VYTIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEGGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/508 (33%), Positives = 237/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    + +G   M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPSMEG-GEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITRELPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     +    ++L        G  
Sbjct: 1006 -----------------------------------------DSDAKTIL------YDG-- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ +LQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNILQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDHEVELRDLDEGEDD 1159


>gi|150392168|ref|YP_001322217.1| DNA-directed RNA polymerase subunit beta [Alkaliphilus
           metalliredigens QYMF]
 gi|182676549|sp|A6TWJ0|RPOB_ALKMQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|149952030|gb|ABR50558.1| DNA-directed RNA polymerase, beta subunit [Alkaliphilus
           metalliredigens QYMF]
          Length = 1246

 Score =  838 bits (2165), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/962 (45%), Positives = 601/962 (62%), Gaps = 66/962 (6%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G   VR  + +  E++D+P+LIE+QK +YD FL          +EGL+  F  + 
Sbjct: 3   HPVQLGKK-VRMSYSQINEVLDMPNLIELQKEAYDWFL----------DEGLREVFNDIS 51

Query: 64  PITAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           PI  ++G  +LEFV Y  D  PK+DV +   RD TYA PLK+ +RLI          K  
Sbjct: 52  PIQDYTGNLILEFVDYSLDENPKYDVGESKERDATYAAPLKVKVRLI---------NKET 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++MGD PLMT  GTF+I G +R++VSQL RSPG++++    +    GK LY+ 
Sbjct: 103 GEVKEQEVFMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYNRQFDKT---GKQLYSA 159

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E DS D++ VR+DR RK P T  L ALG  ++ +I             
Sbjct: 160 TVIPNRGAWLEYETDSNDVVSVRVDRTRKQPATVLLRALGYGTDQQIKDLLGEDERILAT 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      +   L+   K       +  GE   IES   L + L    K   +  +G   
Sbjct: 220 LEKDNTKTAEEGLLEIYK------KLRPGEPPTIESATSLINTLFFDAKRYDLAKVGRYK 273

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + +     AE++ + +TGEI +E G  ID +    I +S I ++ + Y +  
Sbjct: 274 FSKKLSLANRIMSHKAAENVSDPQTGEILVEEGTKIDREISLLIQNSGINEVHV-YSEEN 332

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I N  V  K     D      + ++  +   + V   +        D +D     
Sbjct: 333 KKIKVIGNHFVDIKTHIDFD-----IQDLKLRERVYYPVLREIL-------DTFDSEAEI 380

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  +  R     P   +HI K DI+A I    +L +  G +DDID+LGNRR+RSVGE+L+
Sbjct: 381 KEALKERKRELIP---KHILKSDIVASINYAFNLAHEIGNVDDIDHLGNRRLRSVGELLQ 437

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER +KER++  D+D V PQ LIN +PV +++ EFF SSQLSQ  +  N L
Sbjct: 438 NQFRIGLSRMERVVKERMTIQDVDLVTPQALINIRPVAASIKEFFGSSQLSQFMDQTNPL 497

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+AR+
Sbjct: 498 AELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSYARI 557

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           N YGFIE+PYRKV   +  VT D+ YL+A EE+   IAQAN  LDE+G F  + V  R  
Sbjct: 558 NEYGFIESPYRKVDKKRDVVTTDIEYLTADEEDLFIIAQANEPLDEEGKFGNKRVTSRTK 617

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +VP +++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPLL  +AP
Sbjct: 618 FGGIDVVPFDEVDYMDVSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLITDAP 677

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            +GTGME   AK SG  +VA+ +GIV+ V +  IV++  +G  D        Y+L+KF+R
Sbjct: 678 IIGTGMEYKAAKDSGVVVVARNSGIVDYVASNEIVVKLEDGQKD-------RYKLLKFKR 730

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ TC+NQ+P+V  G+ +   D+IADGPSTD G++ALGRN LV FM W GYNFED++LI
Sbjct: 731 SNQGTCINQKPIVSKGERIEAGDVIADGPSTDRGEIALGRNCLVGFMAWEGYNFEDAILI 790

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +E++V ED  T+IHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE G+I +GAEV 
Sbjct: 791 NEKLVKEDALTTIHIEEYESEARDTKLGPEEITRDIPNVGEDSLKDLDERGVIRIGAEVE 850

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G +G +VD+++F R  
Sbjct: 851 SGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGENGIIVDIKVFTREN 910

Query: 950 ID 951
            D
Sbjct: 911 GD 912



 Score =  430 bits (1106), Expect = e-118,   Method: Composition-based stats.
 Identities = 241/1209 (19%), Positives = 415/1209 (34%), Gaps = 143/1209 (11%)

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV--------- 273
                 IL      +  + + D        A      KV   L++ +TGE           
Sbjct: 56   YTGNLILEFVDYSLDENPKYDVGESKERDATYAAPLKVKVRLINKETGEVKEQEVFMGDF 115

Query: 274  ---IESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG--------- 318
                ++G  + +G  + +  + V+  G+  +      G  +    V    G         
Sbjct: 116  PLMTDTGTFIINGAERVIVSQLVRSPGVYYNRQFDKTGKQLYSATVIPNRGAWLEYETDS 175

Query: 319  -EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             ++     D   ++    +  +          D +  +  I  TL  D  K  ++ LL+I
Sbjct: 176  NDVVSVRVDRTRKQPATVLLRALGYGTDQQIKDLLGEDERILATLEKDNTKTAEEGLLEI 235

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            Y+ +RPG+  T   A S+ N LFFD+ +YDL+ VGR K + +L+L          +    
Sbjct: 236  YKKLRPGEPPTIESATSLINTLFFDAKRYDLAKVGRYKFSKKLSLA--------NRIMSH 287

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
               + + D + G+  +++   +       +     N+  +     ++        VDI +
Sbjct: 288  KAAENVSDPQTGEILVEEGTKIDREISLLIQNSGINEVHVYSEENKKIKVIGNHFVDIKT 347

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARARAG 555
             +  D+ + K     + E      L ++ +  +S + I      R   L    + ++   
Sbjct: 348  HIDFDIQDLK-----LRERVYYPVLREILDTFDSEAEIKEALKERKRELIPKHILKSDIV 402

Query: 556  VEMRDVHPT--HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              +          G +   +      +  V  L    +      +    R V +     D
Sbjct: 403  ASINYAFNLAHEIGNVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQD 459

Query: 614  VVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC---------AGEEI 654
            V  ++     N     A+              +  +   EL   R          + E  
Sbjct: 460  VDLVTPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERA 519

Query: 655  LVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                  +          +       I  + +  S   +            +  +   V T
Sbjct: 520  GFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSYARINEYGFIESPYRKVDKKRDVVTT 579

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
             +E + A      I+A+        +  +   + V          V  +  + +     +
Sbjct: 580  DIEYLTADEEDLFIIAQ--ANEPLDEEGKFGNKRVTSRTKFGGIDVVPFDEVDYM----D 633

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                Q   V         +  A+              +L+   P  G   E        +
Sbjct: 634  VSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLITDAPIIGTGMEYKAAKDSGV 693

Query: 834  VSEDVFTSIH-IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            V     + I        +    + G ++  + +          I++  I+  G  +  GD
Sbjct: 694  VVVARNSGIVDYVASNEIVVKLEDGQKDRYKLLKFKRSNQGTCINQKPIVSKGERIEAGD 753

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++    +      +      L      +  +  D  L     V    +       +  + 
Sbjct: 754  VIADGPSTDR-GEIALGRNCLVGFMAWEGYNFEDAILINEKLVKEDALTTIHIEEYESEA 812

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD- 1011
             +  +  E E    +    +D    LD     R+   +   + + G    K  T L+++ 
Sbjct: 813  RDTKLGPE-EITRDIPNVGEDSLKDLDERGVIRIGAEVESGDILVGKVTPKGETELTAEE 871

Query: 1012 -LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             L+      +  +      KV      + V               K+   + GD++PPGV
Sbjct: 872  RLLRAIFGEKAREVRDTSLKVPHGENGIIV-------------DIKVFTRENGDELPPGV 918

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +V+V++A K+ I                                              
Sbjct: 919  NELVRVYIAKKKKI---------------------------------------------- 932

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
             NVG              G K        + +       + LE V+       +++    
Sbjct: 933  -NVG-------DKMAGRHGNKGVISRILPQEDMPFLEDGTPLEIVLNPLGVPSRMNIGQI 984

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
              V         G  V+TPVFDGA+E  I   L  +     G+  L DG TGE FD PVT
Sbjct: 985  LEVHLGLAAKALGWKVATPVFDGANEFDIMDALEESGYPRGGKLKLQDGRTGEAFDNPVT 1044

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ 
Sbjct: 1045 VGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHT 1104

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LT+KSDDVVGR + YE IV G +  E G PESF VL+KE+Q+L L + +       
Sbjct: 1105 LQEILTVKSDDVVGRVKTYECIVKGENIPEPGVPESFKVLIKELQSLCLDVKVLTDDDHE 1164

Query: 1371 SAKMEEIPD 1379
                E I D
Sbjct: 1165 LEIKETIDD 1173


>gi|327459627|gb|EGF05973.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK1]
          Length = 1188

 Score =  838 bits (2164), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 581/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLDARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLN--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N              L  ++V+ P D                         
Sbjct: 330 GLNKITYIPNDSAVLTAPVE----LQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|289804191|ref|ZP_06534820.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. AG3]
          Length = 871

 Score =  838 bits (2164), Expect = 0.0,   Method: Composition-based stats.
 Identities = 473/878 (53%), Positives = 631/878 (71%), Gaps = 13/878 (1%)

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
              A   +    L ++  S  + I  L+ + +++  YI  T+  D   DR  AL++IYR+M
Sbjct: 1    CAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETVRVDPTNDRLSALVEIYRMM 60

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  D  +    + K+DII ++K
Sbjct: 61   RPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKDDIIDVMK 120

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             L+D+RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQ
Sbjct: 121  KLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 180

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            D+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDV
Sbjct: 181  DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDV 240

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            HPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+E
Sbjct: 241  HPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIE 300

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPF
Sbjct: 301  EGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPF 360

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA 
Sbjct: 361  LEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDAS 420

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTD
Sbjct: 421  RIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTD 480

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTKLGPEEI
Sbjct: 481  LGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEI 540

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            T DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA
Sbjct: 541  TADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKA 600

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +E  IL+  
Sbjct: 601  SDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAG 660

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            ++SR+  +L                   ++ + + PR +W +  + DE+ Q  +E L  Q
Sbjct: 661  LFSRIRAVLVSGGV-------------EAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQ 707

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S
Sbjct: 708  YDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVIS 767

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +I P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +++   + 
Sbjct: 768  KINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQE 827

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
               +         +         +S + DD VLR+A +
Sbjct: 828  VAKLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLARK 865


>gi|240146975|ref|ZP_04745576.1| DNA-directed RNA polymerase, beta subunit [Roseburia intestinalis
           L1-82]
 gi|257200890|gb|EEU99174.1| DNA-directed RNA polymerase, beta subunit [Roseburia intestinalis
           L1-82]
          Length = 1298

 Score =  838 bits (2164), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/964 (44%), Positives = 601/964 (62%), Gaps = 68/964 (7%)

Query: 9   GLGRVR---------KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+R           + +  E++++P+LIEVQK SY  FL           EGL+  F
Sbjct: 2   EKNRIRPVKAGKGMRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------KEGLKEVF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
             + PI  +SG   LEFV +       K+ + +C  RD TYA PLK+ +RL         
Sbjct: 52  DDISPIADYSGHLSLEFVDFTLCESDVKYTIPECKERDATYAAPLKVKVRLH-------- 103

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK
Sbjct: 104 -NKETDEINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIAHDKV---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYP-- 234
            LY+C +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ + +EI+  F    
Sbjct: 160 KLYSCTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNQEIVDLFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KI+ S   D           +         + +++ E +I +         L K  + K 
Sbjct: 220 KILASFGKDVATNYEEGLLELYKKIRPGEPLTVESAESLISAMFFDPRRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +  + + G  +AED+VN  TGEI  EAG  +     ++I ++    +P +++ + 
Sbjct: 280 NKKL-MLKNRINGHVLAEDVVNLATGEIIAEAGTEVTRSLADDIQNA---AVPYVWIQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             N  + ++++ D             + +   ++  + V   +       +D  DL    
Sbjct: 336 TRNVKVLSSMMVDLRAYVD----CNPKDLGITELVYYPVLAQLME---EHTDIDDLKEAI 388

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  ++  +        +HI K+DI A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 389 KKNVHDLIP-------KHITKDDIFASINYNMHLEYGIGNDDDIDHLGNRRIRAVGELLQ 441

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER++++D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 442 NQYRIGLSRLERVVRERMTTLDLDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 501

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+
Sbjct: 502 GELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARI 561

Query: 593 NAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGF+E PYRK+      + +VT++VVY++A EE+N ++AQAN +LD +G F    V  
Sbjct: 562 NEYGFVEAPYRKIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANEALDAEGHFVRNSVSG 621

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E     +   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  +
Sbjct: 622 RYREETQEYEKTMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTD 681

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTGME+  A  SG  ++AK++GIVE  ++ +I+I+S EG  D       +Y+L KF
Sbjct: 682 APVVGTGMETKAAVDSGVCVIAKKSGIVESSESNQIIIKSDEGTRD-------VYKLTKF 734

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ+ C NQRP+V  GD V   ++IADGPST  G+LALG+N L+ FM W GYN+ED++
Sbjct: 735 SRSNQSNCYNQRPIVFKGDRVEAGEVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAV 794

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAE
Sbjct: 795 LLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAE 854

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R
Sbjct: 855 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTR 914

Query: 948 HGID 951
              D
Sbjct: 915 ENGD 918



 Score =  533 bits (1372), Expect = e-148,   Method: Composition-based stats.
 Identities = 184/592 (31%), Positives = 271/592 (45%), Gaps = 28/592 (4%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E    +     V       +   E   +   +  G 
Sbjct: 666  MGSNMQRQAVPLLTTDAPVVGTGMETKAAVDSGVCVIAKKSGIVESSESNQIIIKSDEGT 725

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI-- 916
             ++ +             ++  I+  G  V  G+++    +         +  L+  +  
Sbjct: 726  RDVYKLTKFSRSNQSNCYNQRPIVFKGDRVEAGEVIADGPSTSNGELALGKNPLIGFMTW 785

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDD 973
             G    D    S R+      T + +  +     D       + R+     +   +D  D
Sbjct: 786  EGYNYEDAVLLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-D 844

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 845  ERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------------- 889

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +            K+   + GD++ PGV + V++++A KR I  GDKMAGR
Sbjct: 890  --EVRDTSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGR 947

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I+
Sbjct: 948  HGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIE 1007

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     DI          +       +              +      V   + D 
Sbjct: 1008 TPVFDGAKEIDIQDTLELANDYVNMPFDAAEAEKEGKTENFEEKYKDILREDVMKYLSD- 1066

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                A  ++ +   +   G+  L DG TGEPFD PVT+G+++ LKL+H+V DK++ARSTG
Sbjct: 1067 --NRAHRALWKGVPISRDGKVQLRDGRTGEPFDSPVTIGHMHYLKLHHLVDDKIHARSTG 1124

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+
Sbjct: 1125 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAII 1184

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             G++  E G PESF VL+KE+Q+LGL + + +        ME   ++   +L
Sbjct: 1185 KGDNIPEPGIPESFKVLLKELQSLGLDVKVLDEDRNEVELMET-SEYGNTDL 1235


>gi|312128088|ref|YP_003992962.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311778107|gb|ADQ07593.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 1230

 Score =  838 bits (2164), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/959 (44%), Positives = 602/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G  + + I   F          +
Sbjct: 164 IPNRGAWLEFETDASELLSVRLDRTRKVSLTTLLKAFGLYNQQMIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLYNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+  TGEI ++ G+VI  +   +I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPRTGEILVKEGEVITREIATQIQDAGINEVWVYADEEREF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  +   + L+I  ++    +       +            D+S + R+
Sbjct: 343 KVVGNNTVKLDRYVEFDVSDLNIKELVYKPVLEDILKTTN------------DVSEIKRL 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 IKER----ERELVPYCLTIDDIFAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT++VVYL+A EE+   IAQA   +DE+G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTDEVVYLTADEEDTYRIAQATEPVDEEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLTTESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE+V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVEKVSADEIVIRNNDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G E++  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEIKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 163/538 (30%), Positives = 233/538 (43%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +++   +           ++  I+  G E+  G+++    +      +   + +
Sbjct: 720  RNNDGTKDVYHLLKFKRTNQGTCFNQRPIVRKGQEIKAGEVIADGPST-DHGELALGKNV 778

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L            S  + +     R      E          E 
Sbjct: 779  LVAFMPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGED 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      +  +IL G+    G         L   +  E  R        
Sbjct: 839  AIKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+                  K+     GD++PPGV ++V+V+VA KR I  
Sbjct: 890  ---------ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                ++ V+       +++                G  V
Sbjct: 958  ---LPVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKV 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE I   L++A L  +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 1007 ATPVFDGAKEEDIEEALKLAGLKPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YE+IV G +  E G PESF VLVKE+Q+L L + L +   K     E + +  + +
Sbjct: 1127 KTYEAIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDEDEQPQ 1184


>gi|157150595|ref|YP_001451193.1| DNA-directed RNA polymerase subunit beta [Streptococcus gordonii
           str. Challis substr. CH1]
 gi|189043873|sp|A8AZI3|RPOB_STRGC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|157075389|gb|ABV10072.1| DNA-directed RNA polymerase, beta subunit [Streptococcus gordonii
           str. Challis substr. CH1]
          Length = 1188

 Score =  837 bits (2163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKIGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    ++ I             +
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDAETGEILVEAGTLMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTEPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRTVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E+G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEEGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWDTVREAGMD 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1007 SDAK----------------------------TVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|77410922|ref|ZP_00787278.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           CJB111]
 gi|77162977|gb|EAO73932.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           CJB111]
          Length = 1191

 Score =  837 bits (2163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DAGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+GETGEI  EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNLKTRLLNQTIAENLVDGETGEILAEAGTVMTRDVIDSIAEHIDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVILQKFKVVAPTDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGNS--------NPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLD-------VYHVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 170/507 (33%), Positives = 236/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDLVEKGDFIADGPS-MENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMD 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1007 SDAK----------------------------TVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|225573383|ref|ZP_03782138.1| hypothetical protein RUMHYD_01575 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039296|gb|EEG49542.1| hypothetical protein RUMHYD_01575 [Blautia hydrogenotrophica DSM
           10507]
          Length = 1284

 Score =  837 bits (2163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/953 (44%), Positives = 594/953 (62%), Gaps = 59/953 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  + G
Sbjct: 13  KSMRMSYQRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYGG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEF+ +    D  K+ ++ C  RD+TYA PLK+ +RLI          K   +I E 
Sbjct: 63  KLSLEFIDFTLCVDDAKYTIEQCKERDVTYAAPLKVRVRLI---------NKENDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP++
Sbjct: 114 EIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAISHDKV---GKKLYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG  +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGYGTNAEIIELFGEEPKILASFTKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +++ E +I S         L K  + K  K L +  + +
Sbjct: 231 ESYQEGLLELYKKIRPGEPLAVESAESLIMSMFFDPRRYDLAKVGRYKFNKKL-MLRNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+G TGEI  EAG V+ ++  ++I ++ +               Y+     
Sbjct: 290 AGQALAEDVVDGTTGEILAEAGTVVSKELADDIQNAAV--------------PYVWIQTE 335

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             K K     ++DI + +             +  +   +    +   +  +K  +  ++ 
Sbjct: 336 ERKVKVLSSMMVDIRKYVDAD--PKEMGVTELVYYPVLEKILEENDNLEEIKAAVHRDIH 393

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 394 -DLIPKHITKEDILASINYNMHLEYGLGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 452

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ DI+ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 453 RVVRERMTTQDIEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 512

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGF+E PYR
Sbjct: 513 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINQYGFVEAPYR 572

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      + +VT +V+Y++A EE+N ++AQAN  LDE+G F  + V  R   E     R
Sbjct: 573 KIDKSDPKNPRVTEEVIYMTADEEDNYHVAQANEPLDENGYFIRKNVSGRYREETQEYER 632

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +  D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME+ 
Sbjct: 633 QMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMETK 692

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++AK+AG+V++  +  I I++ +G  D        Y L KF RSNQ+ C NQ
Sbjct: 693 AAVDSGVCVLAKKAGVVQRATSTDISIKNDDGTRDD-------YHLTKFMRSNQSNCYNQ 745

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 746 RPIVVQGEHVEAGQVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 805

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 806 YTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 865

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 866 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 918



 Score =  559 bits (1441), Expect = e-156,   Method: Composition-based stats.
 Identities = 252/1139 (22%), Positives = 427/1139 (37%), Gaps = 94/1139 (8%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            +   +      K +    +  +   G ++  +    ++ +++    D   +  +  +  +
Sbjct: 148  IYYAISHDKVGKKLYSCTVIPNR--GAWLEYE---TDSNDVFYVRVDRTRKVPITVLIRA 202

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                     ++       I  +   D  +  ++ LL++Y+ +RPG+      AES+   +
Sbjct: 203  LGYGTNAEIIELFGEEPKILASFTKDTAESYQEGLLELYKKIRPGEPLAVESAESLIMSM 262

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD  +YDL+ VGR K N +L L      + + ++ +      ++       + +  D++
Sbjct: 263  FFDPRRYDLAKVGRYKFNKKLMLRNRIAGQALAEDVVDGTTGEILAEAGTVVSKELADDI 322

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
             N  V  V       +     R  + +   +       V  +  ++A P    V E    
Sbjct: 323  QNAAVPYV-------WIQTEERKVKVLSSMM-------VDIRKYVDADPKEMGVTELVYY 368

Query: 520  SQLSQLEEHVNSLSRI--THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              L ++ E  ++L  I     R +  L    + +      +       YG     +    
Sbjct: 369  PVLEKILEENDNLEEIKAAVHRDIHDLIPKHITKEDILASINYNMHLEYGLGNDDDIDHL 428

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS---- 633
             N   + ++    +      +    R V +   T D+  +S     N     A       
Sbjct: 429  GN-RRIRAVGELLQNQYRIGLSRLERVVRERMTTQDIEGISPQSLINIKPVTAAVKEFFG 487

Query: 634  ------LDEDGSFTEELVFCRC---------AGEEILVPREKIDFIDASPKQVVSIAASL 678
                    +  +   EL   R          + +        + +        +      
Sbjct: 488  SSQLSQFMDQNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGP 547

Query: 679  IPFLENDDSNRVLM-GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
               L N  ++   +            +    P      E V+  ++        A   E 
Sbjct: 548  NIGLINSLASYARINQYGFVEAPYRKIDKSDPKNPRVTEEVIYMTADEEDNYHVAQANEP 607

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +D     IR          +     ++  +   +     +    V         +  A+ 
Sbjct: 608  LDENGYFIRKNVSGRYREETQEYERQMFDYMDVSPKMVFS----VATALIPFLQNDDANR 663

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKL 856
                         +L    P  G   E    +     V       +       ++     
Sbjct: 664  ALMGSNMQRQAVPLLTTEAPVVGTGMETKAAVDSGVCVLAKKAGVVQRATSTDISIKNDD 723

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +       +        ++  I+  G  V  G ++    +      +   +  L   
Sbjct: 724  GTRDDYHLTKFMRSNQSNCYNQRPIVVQGEHVEAGQVIADGPSTSN-GELALGKNPLIGF 782

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------EL 966
               +  +  D  L         V D    + H  +    +   +   E+I        + 
Sbjct: 783  MTWEGYNYEDAVLL----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDD 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      R  +IL G+    G         L   +  E  R        
Sbjct: 839  ALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E      +            K+   + GD++ PGV + V++++A KR I  
Sbjct: 890  ---------EVRDTSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQSVRIYIAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A  
Sbjct: 941  GDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAK 1000

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  I + + D     DI          +      +    Y +     V E  ++ +  
Sbjct: 1001 ALGFNIATPVFDGANENDIMDTLDMANDYVNMEDFADFKEKYREVLAPDVMEYLENNL-- 1058

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                           + +   +   G+  L DG TGE FD PVT+G+++ LKL+H+V DK
Sbjct: 1059 -----------EHRKLWKGVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDK 1107

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR 
Sbjct: 1108 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRV 1167

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            + YE+I+ G++  E G PESF VL+KE+Q+LGL + + N        ME + D+   +L
Sbjct: 1168 KTYEAIIKGDNIPEPGIPESFKVLLKELQSLGLDVRVLNEDQTEVEIMESV-DYGDTDL 1225


>gi|262283748|ref|ZP_06061512.1| DNA-directed RNA polymerase subunit beta [Streptococcus sp.
           2_1_36FAA]
 gi|262260594|gb|EEY79296.1| DNA-directed RNA polymerase subunit beta [Streptococcus sp.
           2_1_36FAA]
          Length = 1190

 Score =  837 bits (2163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKIGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    ++ I             +
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDAETGEILVEAGTLMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTEPVELQKFKVVAPNDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRTVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E+G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEEGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWDTVREAGMD 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1007 SDAK----------------------------TVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|22536344|ref|NP_687195.1| DNA-directed RNA polymerase subunit beta [Streptococcus agalactiae
           2603V/R]
 gi|25010231|ref|NP_734626.1| DNA-directed RNA polymerase subunit beta [Streptococcus agalactiae
           NEM316]
 gi|76788022|ref|YP_328891.1| DNA-directed RNA polymerase subunit beta [Streptococcus agalactiae
           A909]
 gi|76798582|ref|ZP_00780812.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           18RS21]
 gi|77406339|ref|ZP_00783402.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           H36B]
 gi|77407917|ref|ZP_00784668.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           COH1]
 gi|41018037|sp|Q8E239|RPOB_STRA5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|41018040|sp|Q8E7J8|RPOB_STRA3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|88909642|sp|Q3K3L2|RPOB_STRA1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|22533169|gb|AAM99067.1|AE014199_3 DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           2603V/R]
 gi|23094583|emb|CAD45801.1| RNA polymerase beta-subunit [Streptococcus agalactiae NEM316]
 gi|76563079|gb|ABA45663.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           A909]
 gi|76586068|gb|EAO62596.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           18RS21]
 gi|77173464|gb|EAO76582.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           COH1]
 gi|77175044|gb|EAO77850.1| DNA-directed RNA polymerase, beta subunit [Streptococcus agalactiae
           H36B]
 gi|319744100|gb|EFV96475.1| DNA-directed RNA polymerase subunit beta [Streptococcus agalactiae
           ATCC 13813]
          Length = 1191

 Score =  837 bits (2163), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 589/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DAGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+GETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNLKTRLLNQTIAENLVDGETGEILVEAGTVMTRDVIDSIAEHIDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVILQKFKVVAPTDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGNS--------NPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLD-------VYHVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 170/507 (33%), Positives = 236/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDLVEKGDFIADGPS-MENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMD 1006

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 1007 SDAK----------------------------TVLYDG---------------------- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|15896392|ref|NP_349741.1| DNA-directed RNA polymerase subunit beta [Clostridium
           acetobutylicum ATCC 824]
 gi|20139600|sp|Q97EG9|RPOB_CLOAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|15026209|gb|AAK81081.1|AE007809_7 DNA-dependent RNA polymerase beta subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|325510548|gb|ADZ22184.1| DNA-directed RNA polymerase subunit beta [Clostridium
           acetobutylicum EA 2018]
          Length = 1241

 Score =  837 bits (2162), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/955 (45%), Positives = 603/955 (63%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI  +P+LIEVQ  SY  FL          + GLQ  F  + PI  ++G
Sbjct: 9   KRTRMSFSKLDEIGVMPNLIEVQLDSYQWFL----------DNGLQEIFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEF+ Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLILEFIGYKLDMDNIKYSVEECKERDTTYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG ++D+   +   +GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGAYYDYIVDK---NGKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS  +IHVRID+ RK+P+T  + A+G  S+ EI++ F  +       +    
Sbjct: 167 GAWLEYETDSNSVIHVRIDKTRKLPITILVRAMGFGSDAEIVNYFGEEERLKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L + L    K   +  +G         
Sbjct: 227 KTREEALLEIYK------RLRPGEPPTVDSAFSLINSLFFDPKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A+DIVN ETGEI +E G  I ++   EI +S I  + I   D++     I
Sbjct: 281 VSIRIANKTAAKDIVNPETGEIIVEKGQRISKEKALEIQNSGINSVDISVDDNIIR--VI 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N  V  K+  + D      R +              +  L    + Y      + ++  
Sbjct: 339 GNNFVDIKSYIKFDISDLNIREL------------VYYPVLKEILENYTDEEAIKEQLKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI K+D+ A +   + L  G G +DDID+LGNRRVRSVGE+L+NQ+R+G
Sbjct: 387 NVHKLVP---KHIIKDDMFATVSYELGLAYGIGNVDDIDHLGNRRVRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  + +N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQINPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGF+
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFV 563

Query: 599 ETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V   +  VT+++ Y++A EE+   IA+AN +LDE+G F ++ +  R   E ++V
Sbjct: 564 ETPYRTVDKEQGRVTDEIHYITADEEDRCLIARANEALDENGYFIDKKITVRAPDEVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P  ++D +D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 624 PANEVDLMDVSARQMVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPVVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    A+ AG+VE V A  + +R        S  GVD YRL+KF+RSNQ TC+
Sbjct: 684 HKAAVDSGILPKARNAGVVEYVSANEVRVRRD------SDGGVDTYRLLKFKRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V+  ++V +  ++ADG STDLG++ALGRN+ + F+ W GYN+ED+MLISE++V +
Sbjct: 738 NQRPIVEKNEKVEKGTVLADGQSTDLGEIALGRNIRMGFITWEGYNYEDAMLISEQLVRD 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK+IDE GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYEAEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  468 bits (1205), Expect = e-129,   Method: Composition-based stats.
 Identities = 253/1219 (20%), Positives = 407/1219 (33%), Gaps = 157/1219 (12%)

Query: 223  MDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-------- 273
                 IL    Y   + + +                 KV   L++ +TGE          
Sbjct: 56   YTGNLILEFIGYKLDMDNIKYSVEECKERDTTYAAPLKVKVRLLNKETGEVKEQEVFMGD 115

Query: 274  ----IESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG-------- 318
                 E G  + +G  + +  + V+  G   D +    G  +    V    G        
Sbjct: 116  FPLMTEQGTFIINGAERVIVSQLVRSPGAYYDYIVDKNGKKLFSATVIPNRGAWLEYETD 175

Query: 319  --EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               +     D   +  +  +  +         V+       ++ T+  D  K R++ALL+
Sbjct: 176  SNSVIHVRIDKTRKLPITILVRAMGFGSDAEIVNYFGEEERLKATIEKDNTKTREEALLE 235

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IY+ +RPG+  T   A S+ N LFFD  +YDLS VGR K N +L +      +       
Sbjct: 236  IYKRLRPGEPPTVDSAFSLINSLFFDPKRYDLSRVGRYKFNKKLAVSIRIANKT------ 289

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
                K +V+   G+  ++    +   +   +     N   + +      I+   ++    
Sbjct: 290  --AAKDIVNPETGEIIVEKGQRISKEKALEIQNSGINSVDISVDD--NIIRVIGNNFVDI 345

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
                +  I+   +   V        L    +      ++   + +  L    + +     
Sbjct: 346  KSYIKFDISDLNIRELVYYPVLKEILENYTDEEAIKEQL--KKNVHKLVPKHIIKDDMFA 403

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
             +       YG     +     N   V S+    +      +    R V +     D   
Sbjct: 404  TVSYELGLAYGIGNVDDIDHLGN-RRVRSVGELLQNQFRIGLSRMERVVKERMTIQDQEV 462

Query: 617  LSAMEEENRY-IA------QANSSLDEDGSFTEELVFCRCAG------------EEILVP 657
            ++     N   +A        +S L +       L                   E     
Sbjct: 463  ITPQALINIRPVAASIKEFFGSSQLSQFMDQINPLSELTHKRRLSALGPGGLSRERAGFE 522

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRV-LMGCNMQRQAVPLLKAEAPFVGTGME 716
               +          +         L N  +    +            +  E   V   + 
Sbjct: 523  VRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFVETPYRTVDKEQGRVTDEIH 582

Query: 717  SVVAKSSGAAIVAKRAG----IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
             + A      ++A+           +D    V    E  + P+            +    
Sbjct: 583  YITADEEDRCLIARANEALDENGYFIDKKITVRAPDEVLVVPAN-----------EVDLM 631

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +    Q   V         +  A               +L    P  G   E    +   
Sbjct: 632  DVSARQMVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPVVGTGIEHKAAVDSG 691

Query: 833  MVSEDVFTSIHIEEF----EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ++ +     +   E+    EV  R    G  +  R +          I++  I+    +V
Sbjct: 692  ILPKARNAGVV--EYVSANEVRVRRDSDGGVDTYRLLKFKRSNQGTCINQRPIVEKNEKV 749

Query: 889  NPGDILVGKITPKGE-----SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
              G +L    +           +            E A+ + +  +R     S  + +  
Sbjct: 750  EKGTVLADGQSTDLGEIALGRNIRMGFITWEGYNYEDAMLISEQLVRDDVFTSIHIEEYE 809

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               R      E          E   +D  DE+ I+      R  +IL G+    G     
Sbjct: 810  AEARDTKLGPEEITRDIPNVGEDALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELT 868

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                L   +  E  R                 E                   KI   + G
Sbjct: 869  AEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKIFTRENG 911

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++PPGV  +V+ ++A KR I  GDKM+GRHGNK                          
Sbjct: 912  DELPPGVNELVRCYIAQKRKISVGDKMSGRHGNK-------------------------- 945

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
              GV SR                             + +    P    L+  +       
Sbjct: 946  --GVISR--------------------------VLPEEDMPFLPDGRPLQICLNPLGVPS 977

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            +++      V         G  ++TPVFDGA E  I   L+ A   E G+++LYDG TGE
Sbjct: 978  RMNIGQVLEVHLGWAAANLGWHIATPVFDGALEPEIVECLKRAGYAEDGKTVLYDGRTGE 1037

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FD  VTVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 1038 AFDNRVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1097

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PE+F VL+KE+QAL L + +
Sbjct: 1098 AYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPEAFKVLIKELQALCLDVKV 1157

Query: 1364 ENSRTKNSAKMEEIPDFNK 1382
             +         E I D  +
Sbjct: 1158 LSDNNNEIELKESIEDETE 1176


>gi|317132039|ref|YP_004091353.1| DNA-directed RNA polymerase, beta subunit [Ethanoligenens
           harbinense YUAN-3]
 gi|315470018|gb|ADU26622.1| DNA-directed RNA polymerase, beta subunit [Ethanoligenens
           harbinense YUAN-3]
          Length = 1232

 Score =  837 bits (2162), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/957 (45%), Positives = 594/957 (62%), Gaps = 69/957 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  F    E++D+P+LIEVQK SY  FL          +EGL+  FK V  IT F+G
Sbjct: 11  KNVRMSFAHIDEVLDMPNLIEVQKNSYQWFL----------DEGLKEVFKDVSAITDFTG 60

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L+FV Y  +  PK+ +++C  RD TYA P+++  RLI          +   ++KEQ 
Sbjct: 61  NLVLDFVDYTIENQPKYGIEECKERDATYAAPMRVLARLI---------NRETGEVKEQE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT  GTFVI G +R++VSQL RSPG+++     +    GK L+   +IP++G
Sbjct: 112 IFMGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYGMQHDKT---GKKLFTATVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+ +VRID+ RK+PVT F+ ALG+ S+ EIL  F          +     
Sbjct: 169 AWLEYETDSNDVFYVRIDKNRKIPVTVFIRALGLGSDAEILDFFGDDDRIKSSIEKDNTK 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
                LM           +  GE   +ES +   + L    +   +  +G          
Sbjct: 229 SIEEGLM------EVYRKLRPGEPPTVESAQTHINALFFDPRRYDLSRVGRYKYNKKLAI 282

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + L G  ++  + N  TGEI  +AG+ +      EI  + +    +   D        R
Sbjct: 283 GNRLTGCTLSRPVANPLTGEILADAGETLSRARAHEIERAGVDTAFVQVFD--------R 334

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKMNM 418
              V        DA L       P D     + E + F+ L    + ++     +  +  
Sbjct: 335 EVKVISNGMVDADAFL-------PFDPEEVGIREKVRFSVLREILEAHEGEDDLKAAVEE 387

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           R++   P   +HI  +DI + I  L +L N  G IDDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 388 RMDDLIP---KHIIIDDIFSSINYLNNLANDIGVIDDIDHLGNRRIRSVGELLQNQFRIG 444

Query: 479 LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
             RMER I+ER++  S D+D++ PQ +IN++PV++++ EFF SS LSQ  +  N L+ +T
Sbjct: 445 FSRMERVIRERMNLQSQDLDTITPQSIINSRPVMASIKEFFGSSPLSQFMDQTNPLAELT 504

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+S L SFAR+N YG
Sbjct: 505 HKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLISYLASFARINDYG 564

Query: 597 FIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           FIE PYRKV      V+++VVY++A  E+   +AQAN  LDE+G F    V  R   E +
Sbjct: 565 FIEAPYRKVDKVTGIVSSEVVYMTADVEDEYTVAQANEPLDEEGRFARPKVAARHRDEIL 624

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            + REKID++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPLL+ ++P VGTG
Sbjct: 625 EIEREKIDYMDVSPKMVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLRTDSPIVGTG 684

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  SG  ++AK  G+VE+V A  ++IR+  G LD        Y L+KF RSNQ T
Sbjct: 685 MEYKAAVDSGVCVLAKEEGVVERVAADEVIIRTDSGRLD-------NYHLIKFLRSNQGT 737

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C NQ P+V  G+ V +  ++ADGPST  G++ALGRN+L+ FM W GYN+ED++L++E +V
Sbjct: 738 CFNQHPIVHHGERVVKGQVLADGPSTSQGEIALGRNVLIGFMTWEGYNYEDAVLLNEHLV 797

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L+++DE GII VGAEV+ GDIL
Sbjct: 798 MDDVYTSIHIEEYELEARDTKLGPEEITRDIPNVGEDALRDLDERGIIRVGAEVHAGDIL 857

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVDV++F R   +
Sbjct: 858 VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGIVVDVKVFTRENSE 914



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 188/580 (32%), Positives = 256/580 (44%), Gaps = 80/580 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L R           Y       +      E V   +  +E   +   T  
Sbjct: 663  GSNMQRQAVPLLRTDSPIVGTGMEYKAAVDSGVCVLAKEEGVVERVAADE---VIIRTDS 719

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +    I  +        ++  I+  G  V  G +L    +   +  +     +L   
Sbjct: 720  GRLDNYHLIKFLRSNQGTCFNQHPIVHHGERVVKGQVLADGPST-SQGEIALGRNVLIGF 778

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
               +  +  D  L     V   V        + ++  +  +  E     I  +  D    
Sbjct: 779  MTWEGYNYEDAVLLNEHLVMDDVYTSIHIEEYELEARDTKLGPEEITRDIPNVGEDALRD 838

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+         +IL G+    G         L   +  E  R             
Sbjct: 839  LDERGIIRVGAEVHAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 885

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   +  +++ PGV  VV+ ++A KR I  GDKMA
Sbjct: 886  ----EVRDTSLRVPHGEYGIVVDVKVFTRENSEELNPGVNMVVRCYIAQKRKISVGDKMA 941

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+A   LG K
Sbjct: 942  GRHGNKGVVSRVLPAEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWK 1001

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I + + D    GDI+                                             
Sbjct: 1002 IMTPVFDGAHEGDIAECLKEA--------------------------------------- 1022

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             G  E+              G+  LYDG TGE FD PVTVGY+Y LKL H+V DK++ARS
Sbjct: 1023 -GLRED--------------GKCCLYDGRTGEQFDNPVTVGYMYFLKLAHLVDDKIHARS 1067

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+ T+KSDDVVGR + YE+
Sbjct: 1068 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEIQTVKSDDVVGRVKTYEA 1127

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            IV G +    G PE+F VL+KE+Q+LGL + + +   +  
Sbjct: 1128 IVKGQNVPRPGVPEAFKVLIKELQSLGLDMKVLDKAGEEI 1167


>gi|312868034|ref|ZP_07728238.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           parasanguinis F0405]
 gi|311096438|gb|EFQ54678.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           parasanguinis F0405]
          Length = 1189

 Score =  837 bits (2162), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 586/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          N GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------NHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYSLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNIKNRLLNQTIAEPLVDAETGEILVEAGTVMTRDVIDSISEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DAAVLTEPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR I   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIITPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D D++ PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNDALTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN++V+L+A EE+   +AQANS L+ DG+F E++V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGKVTNEIVWLTADEEDEYTVAQANSKLNADGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPASSVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 133/507 (26%), Positives = 208/507 (41%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A                 K    R +   D       
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIA----------------QK----RKIRVGD------- 919

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                                             G K          +    P  + ++ +
Sbjct: 920  ---------------------------KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIM 952

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +       +++      +         G+ ++TPVFDGA  E +   ++ A +D   ++I
Sbjct: 953  LNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVKEAGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     + 
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGEDD 1159


>gi|331086364|ref|ZP_08335444.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406130|gb|EGG85653.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 1282

 Score =  837 bits (2161), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 595/953 (62%), Gaps = 58/953 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          +EGL+  F+ + PI  +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEVFRDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   + D         +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLYNKEKD---------EINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK L++  +IP++
Sbjct: 114 EIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKI---GKELFSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG  +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGFGTNAEIIELFGEEPKILASFGKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   AE +V+  TGE+ +E G +I  +  E I ++    +P ++V        + + ++
Sbjct: 290 SGQKAAETVVSPLTGEVLVEEGQLITRELAEAIQNA---AVPYVWVQGEERKIKVLSNMM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D       A++DI       D     V E++F  +     +     V  +K  +R N++
Sbjct: 347 VDLK-----AIVDI-------DPKEVGVTEAVFYPVLAGLLEETAGDVEELKDAIRKNIN 394

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 395 -ELIPKHITKEDILASINYNIHLEYGLGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 453

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 454 RVVRERMTTQDLDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 513

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 514 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYR 573

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +V+Y++A EE+N ++AQAN  LDE+G F  + V  R   E     R
Sbjct: 574 KIDKTDPANPVVTEEVIYMTADEEDNYHVAQANEPLDEEGHFLHKNVSGRYREETQEYER 633

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +  D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 634 KMFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 693

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA++AG VE+  +  I IR  +G           Y+L KF RSNQ+ C NQ
Sbjct: 694 AAVDSGVCVVAEQAGTVERSTSKEITIRHEDGTK-------KTYKLTKFLRSNQSNCYNQ 746

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G++V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 747 RPIVVKGEKVEAGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 806

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 807 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 866

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 867 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 919



 Score =  533 bits (1372), Expect = e-148,   Method: Composition-based stats.
 Identities = 185/597 (30%), Positives = 272/597 (45%), Gaps = 49/597 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E    +     V  +   ++     + +    + G 
Sbjct: 667  MGSNMQRQAVPLLTTEAPVVGTGMEVKAAVDSGVCVVAEQAGTVERSTSKEITIRHEDGT 726

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            ++  +    +        ++  I+  G +V  G ++    +      M   +  L     
Sbjct: 727  KKTYKLTKFLRSNQSNCYNQRPIVVKGEKVEAGQVIADGPSTSN-GEMALGKNPLIGFMT 785

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLA 968
             +  +  D  L         V D    + H  +    +   +   E+I        +   
Sbjct: 786  WEGYNYEDAVLL----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDAL 841

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D  DE+ I+      R  +IL G+    G         L   +  E  R          
Sbjct: 842  KDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR---------- 890

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E      +            K+   + GD++ PGV + V++++A KR I  GD
Sbjct: 891  -------EVRDTSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGD 943

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   L
Sbjct: 944  KMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKAL 1003

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  I + + D     DI                 E    + ++ +  V +          
Sbjct: 1004 GFNIATPVFDGANENDIMDTLDLAND-YVNLEWEEFEQKHKEELLPEVMQYLSD------ 1056

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                         + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++
Sbjct: 1057 -------NREHRKLWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIH 1109

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + 
Sbjct: 1110 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKT 1169

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            YE+I+ G++  E G PESF VL+KE+Q+LGL + +          ME I D+ + +L
Sbjct: 1170 YEAIIKGDNIPEPGIPESFKVLLKELQSLGLDVRVLREDQTEVEIMETI-DYGETDL 1225


>gi|160894090|ref|ZP_02074868.1| hypothetical protein CLOL250_01644 [Clostridium sp. L2-50]
 gi|156864123|gb|EDO57554.1| hypothetical protein CLOL250_01644 [Clostridium sp. L2-50]
          Length = 1310

 Score =  837 bits (2161), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/983 (43%), Positives = 605/983 (61%), Gaps = 66/983 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V +G G +R  + +  +++++P+ IEVQK SY  FL            GL+ AFK + PI
Sbjct: 40  VQSGKG-IRMSYSRQKDVLEMPNFIEVQKNSYQWFLTD----------GLKEAFKDISPI 88

Query: 66  TAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           T ++G   LEFV ++   D  K+ +++C  RD TYA PLK+ +RL   D          K
Sbjct: 89  TDYTGQLSLEFVDFQLCRDDVKYSIEECKERDATYAAPLKVKVRLHANDA---------K 139

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           ++ E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++D    +    GK LY+C 
Sbjct: 140 EMSEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYDIAHDKI---GKKLYSCT 196

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQ 240
           +IP++G W++ E DS D+ +VR+DR RKVP+T  + +LG+ +  EI+  F    KI+ S 
Sbjct: 197 VIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRSLGIGTNAEIIDLFGEEPKILASI 256

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +++ E +I +         L K  + K  K L  
Sbjct: 257 EKDPSETYQDGLLELYKKIRPGEPLAVESAENLINAMFFDPRRYDLAKVGRYKFNKKLAF 316

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + + G  +AED ++  TGE+  EAG  +     ++I  + +               Y+
Sbjct: 317 Q-NRITGQILAEDAIDPATGEVIAEAGTTLTRAQAKDIQDAAV--------------PYV 361

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                    K   + ++D+ + +   D +   + E ++  +                   
Sbjct: 362 MIQTEERNVKVLSNMVVDLSKYVG-FDPAEVGIHEGVYYPVLETLLNEYSDE--EELKAA 418

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                +    +HI KEDIIA I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+G
Sbjct: 419 IARDASDLVPKHITKEDIIASINYNIHLEYGIGTKDDIDHLGNRRIRAVGELLQNQYRIG 478

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L R+ER ++ER+++ D++++ PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH 
Sbjct: 479 LSRLERVVRERMTTQDVETITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTHK 538

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++AR+N YGF+
Sbjct: 539 RRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARINEYGFV 598

Query: 599 ETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           E PYRK+      +  VT++V+YL+A EE+N  +AQAN  LD DG F    V  R   + 
Sbjct: 599 EAPYRKLDKSDPANPVVTDEVIYLTADEEDNYRVAQANEPLDADGHFVNNNVSGRYREDT 658

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
              P+ ++D +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPL+  E+  VGT
Sbjct: 659 TEFPKSRVDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLMLTESAVVGT 718

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME+  A  SG  IVAKR G+VE   +  I I++ E          DIY ++KF RSNQ 
Sbjct: 719 GMEAKAAVDSGVCIVAKRDGVVEYSTSKEICIKADE------DGTKDIYHVIKFARSNQG 772

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            C+NQRP+V  G+ V+  ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+
Sbjct: 773 NCMNQRPIVFKGEHVKAGEVIADGPSTSGGEIALGKNPLIGFMTWEGYNYEDAVLLSERL 832

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRD+  +S + LK++DE GII +GAEV  GDI
Sbjct: 833 VKDDVYTSIHIEEYECEARDTKLGPEEITRDLAGLSNDALKDLDENGIIRIGAEVRAGDI 892

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR------ 947
           LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G ++D +IF R      
Sbjct: 893 LVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAFGVIMDTKIFTRENGDEL 952

Query: 948 -HGIDKNERSISVEREQIELLAR 969
             G++K+ R    ++ +I++  +
Sbjct: 953 SPGVNKSVRVYIAQKRKIQVGDK 975



 Score =  562 bits (1448), Expect = e-157,   Method: Composition-based stats.
 Identities = 254/1131 (22%), Positives = 424/1131 (37%), Gaps = 83/1131 (7%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            +   +      K +    +  +   G ++  +  + +   + ++    +    L  I   
Sbjct: 179  IYYDIAHDKIGKKLYSCTVIPNR--GAWLEYETDSNDVFYVRVDRTRKVPITVL--IRSL 234

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             I     + +D       I  ++  D ++  +D LL++Y+ +RPG+      AE++ N +
Sbjct: 235  GIGTNAEI-IDLFGEEPKILASIEKDPSETYQDGLLELYKKIRPGEPLAVESAENLINAM 293

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD  +YDL+ VGR K N +L        + + ++ I              G +      
Sbjct: 294  FFDPRRYDLAKVGRYKFNKKLAFQNRITGQILAEDAIDPAT----------GEVIAEAGT 343

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
               R ++          + +   ER++K   + V   S           +   V      
Sbjct: 344  TLTRAQAKDIQDAAVPYVMIQTEERNVKVLSNMVVDLSKYVGFDPAEVGIHEGVYYPVLE 403

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            + L++  +     + I   R  S L    + +      +       YG     +     N
Sbjct: 404  TLLNEYSDEEELKAAIA--RDASDLVPKHITKEDIIASINYNIHLEYGIGTKDDIDHLGN 461

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS------ 633
               + ++    +      +    R V +   T DV  ++     N     A         
Sbjct: 462  -RRIRAVGELLQNQYRIGLSRLERVVRERMTTQDVETITPQSLINIKPVTAAVKEFFGSS 520

Query: 634  ----LDEDGSFTEELVFCRC---------AGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                  +  +   EL   R          + +        + +        +        
Sbjct: 521  QLSQFMDQNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNI 580

Query: 681  FLENDDSNRVLM-GCNMQRQAVPLLK---AEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             L N  +    +            L       P V   +  + A          +A    
Sbjct: 581  GLINSLATYARINEYGFVEAPYRKLDKSDPANPVVTDEVIYLTA-DEEDNYRVAQANEPL 639

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
              D   +         + +T        +          V    +      +  +D    
Sbjct: 640  DADGHFVNNNVSGRYREDTTEFPKSRVDLMDVSPKMVFSVATSMI----PFLENDDANRA 695

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
               +++   A+   +  + +   G   + ++     +V++      +    E+  +  + 
Sbjct: 696  LMGSNMQRQAVPLMLTESAVVGTGMEAKAAVDSGVCIVAKRDGVVEYSTSKEICIKADED 755

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G ++I   I          +++  I+  G  V  G+++    +  G      +  L+  +
Sbjct: 756  GTKDIYHVIKFARSNQGNCMNQRPIVFKGEHVKAGEVIADGPSTSGGEIALGKNPLIGFM 815

Query: 917  --FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI---ELLARDK 971
               G    D    S R+      T + +  +     D       + R+         +D 
Sbjct: 816  TWEGYNYEDAVLLSERLVKDDVYTSIHIEEYECEARDTKLGPEEITRDLAGLSNDALKDL 875

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      R  +IL G+    G         L   +  E  R             
Sbjct: 876  -DENGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 921

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            KI   + GD++ PGV + V+V++A KR IQ GDKMA
Sbjct: 922  ----EVRDTSLKVPHGAFGVIMDTKIFTRENGDELSPGVNKSVRVYIAQKRKIQVGDKMA 977

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HLG A   LG K
Sbjct: 978  GRHGNKGVISRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLGLASQVLGFK 1037

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + D     DI                 +    Y D     V               
Sbjct: 1038 VSTPVFDGADEFDIMDTLEMAND-YANTEWEDFYEKYKDSVSEEVMNYLYE--------- 1087

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                        +   +D +G+  L DG TGE FD PVT+GY++ LKL+H+V DK++ARS
Sbjct: 1088 ----NRDHREEWKGVPIDRTGKVQLRDGRTGEEFDSPVTIGYMHYLKLHHLVDDKIHARS 1143

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+
Sbjct: 1144 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEA 1203

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            I+ G +    G PESF VL+KE Q+LGL + +           E I  +++
Sbjct: 1204 IIKGENIPTPGIPESFKVLLKEFQSLGLDVRVVKDDMTEVDLGETIEAYDE 1254


>gi|325662611|ref|ZP_08151211.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471108|gb|EGC74334.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 1282

 Score =  837 bits (2161), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 595/953 (62%), Gaps = 58/953 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          +EGL+  F+ + PI  +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEVFRDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   + D         +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLYNKEKD---------EINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK L++  +IP++
Sbjct: 114 EIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKI---GKELFSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG  +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGFGTNAEIIELFGEEPKILASFGKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   AE +V+  TGE+ +E G +I  +  E I ++    +P ++V        + + ++
Sbjct: 290 SGQKAAETVVSPLTGEVLVEEGQLITRELAEAIQNA---AVPYVWVQGEERKIKVLSNMM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D       A++DI       D     V E++F  +     +     V  +K  +R N++
Sbjct: 347 VDLK-----AIVDI-------DPKEVGVTEAVFYPVLAGLLEETAGDVEELKDAIRKNIN 394

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 395 -ELIPKHITKEDILASINYNIHLEYGLGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 453

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 454 RVVRERMTTQDLDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 513

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 514 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYR 573

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +V+Y++A EE+N ++AQAN  LDE+G F  + V  R   E     R
Sbjct: 574 KIDKTDPANPVVTEEVIYMTADEEDNYHVAQANEPLDEEGHFLHKNVSGRYREETQEYER 633

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +  D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 634 KMFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 693

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA++AG VE+  +  I IR  +G           Y+L KF RSNQ+ C NQ
Sbjct: 694 AAVDSGVCVVAEQAGTVERSTSKEITIRHEDGTK-------KTYKLTKFLRSNQSNCYNQ 746

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G++V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 747 RPIVVKGEKVEAGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 806

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 807 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 866

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 867 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 919



 Score =  532 bits (1371), Expect = e-148,   Method: Composition-based stats.
 Identities = 185/597 (30%), Positives = 272/597 (45%), Gaps = 49/597 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E    +     V  +   ++     + +    + G 
Sbjct: 667  MGSNMQRQAVPLLTTEAPVVGTGMEVKAAVDSGVCVVAEQAGTVERSTSKEITIRHEDGT 726

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            ++  +    +        ++  I+  G +V  G ++    +      M   +  L     
Sbjct: 727  KKTYKLTKFLRSNQSNCYNQRPIVVKGEKVEAGQVIADGPSTSN-GEMALGKNPLIGFMT 785

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLA 968
             +  +  D  L         V D    + H  +    +   +   E+I        +   
Sbjct: 786  WEGYNYEDAVLL----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDAL 841

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D  DE+ I+      R  +IL G+    G         L   +  E  R          
Sbjct: 842  KDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR---------- 890

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E      +            K+   + GD++ PGV + V++++A KR I  GD
Sbjct: 891  -------EVRDTSLKVPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGD 943

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   L
Sbjct: 944  KMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKAL 1003

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  I + + D     DI                 E    + ++ +  V +          
Sbjct: 1004 GFNIATPVFDGANENDIMDTLDLAND-YVNLEWEEFEQKHKEELLPEVMQYLSD------ 1056

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                         + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++
Sbjct: 1057 -------NREHRKLWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIH 1109

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + 
Sbjct: 1110 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKT 1169

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            YE+I+ G++  E G PESF VL+KE+Q+LGL + +          ME I D+ + +L
Sbjct: 1170 YEAIIKGDNIPEPGIPESFKVLLKELQSLGLDVRVLREDQTEVEIMETI-DYGETDL 1225


>gi|324992319|gb|EGC24241.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK405]
          Length = 1188

 Score =  837 bits (2161), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLSVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTD------------------------- 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 361 -SDRVVTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|171778937|ref|ZP_02919999.1| hypothetical protein STRINF_00860 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282583|gb|EDT48007.1| hypothetical protein STRINF_00860 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 1215

 Score =  836 bits (2160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 27  LAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DNGLREVFE 76

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PIT F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 77  DVLPITNFTDTMELEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 127

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 128 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 184

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 185 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIMDIFGDSELVR 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    +S + L        +   +  +G 
Sbjct: 245 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGR 303

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 304 YKINKKLNIKTRLLNQTIAENLVDAETGEILVEAGTVMTRDVIDSIADQLDGDL------ 357

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 358 --NKFVYTPN----DYAVVTEPVVLQKFKVISPVDPDRV------------------VTI 393

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D  R +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 394 VGN--------ANPDDKARALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 445

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 446 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 505

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+++ 
Sbjct: 506 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSTYG 565

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 566 HLNKYGFIQTPYRKVDRATGVVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEDIVMGR 625

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 626 HQGNNQEFPSNIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 685

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++AK  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 686 PYVGTGMEYQAAHDSGAAVIAKHDGRVVFSDAEKVEVRREDGSLD-------VYHITKFR 738

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQ  LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYN+ED+++
Sbjct: 739 RSNSGTAYNQHTLVKVGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWDGYNYEDAII 798

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 799 LSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 858

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 859 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 918

Query: 949 GID 951
             D
Sbjct: 919 NGD 921



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/508 (34%), Positives = 243/508 (47%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A       +  D  +     V   V 
Sbjct: 751  LVKVGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWDGYNYEDAIILSERLVKEDVY 809

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E    +I    E   +D  DE  I+      +  +IL G+ 
Sbjct: 810  TSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 868

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 869  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV----- 912

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P EDMP+L D
Sbjct: 913  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVEDMPYLPD 971

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 972  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLW-------- 1023

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                 D  +E         A +    ++
Sbjct: 1024 -------------------------------------DTVNE---------AGMASDAKT 1037

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1038 VLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1097

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1098 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1157

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1158 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1185


>gi|331091890|ref|ZP_08340722.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402789|gb|EGG82356.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 1276

 Score =  836 bits (2160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/953 (45%), Positives = 586/953 (61%), Gaps = 58/953 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          + GL+  F+ + PI  +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DAGLKEVFEDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVKVRLY---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYAIAHDKI---GKELYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG  +  EIL  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGFGTNAEILDLFGEEPKILASFGKDTA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ESYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   AEDIV+  TGE+ +E G VI  +  E I +     +P ++V     N  I + ++
Sbjct: 290 TGQVAAEDIVSAITGEVIVEEGQVITRELAEAIQN---GAVPFVWVKGEERNIKILSNMM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D                   D     +AE ++  +  D  +     +  +K  +R N+ 
Sbjct: 347 VDLESVVD------------VDAKELGIAELVYYPVLADLLEETGGDIDELKEEIRRNIH 394

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 395 -ELIPKHITKEDILASINYNIHLEYGIGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 453

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 454 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 513

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +AR+N YGF+E PYR
Sbjct: 514 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACYARINEYGFVEAPYR 573

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +VVY++A EE+N ++AQAN  LD +G F  + V  R   E     +
Sbjct: 574 KIDKTDPKNPVVTEEVVYMTADEEDNYHVAQANEPLDAEGHFIHKNVSGRYREETQEYEK 633

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              D++D SPK V S+A +LIPFLENDD  R LMG NMQRQAVPLL  EAP VGTGME+ 
Sbjct: 634 TAFDYMDVSPKMVFSVATALIPFLENDDPTRALMGSNMQRQAVPLLMTEAPVVGTGMETK 693

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  IVA++AG+V++  +  I ++  +G           Y+L KF RSNQ+ C NQ
Sbjct: 694 AAVDSGVCIVAEQAGVVDRSTSKEITVKHDDGTR-------KTYKLTKFLRSNQSNCYNQ 746

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 747 RPIVVKGERVEAGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 806

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIP V ++ LK++D+ GII +GAEV  GDILVGK+
Sbjct: 807 YTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDDRGIIRIGAEVRAGDILVGKV 866

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 867 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 919



 Score =  558 bits (1439), Expect = e-156,   Method: Composition-based stats.
 Identities = 261/1180 (22%), Positives = 432/1180 (36%), Gaps = 84/1180 (7%)

Query: 233  YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            Y K                     G  V      I+  E+VI S    + G+  ++    
Sbjct: 103  YNKETDEINEHEIFMGDLPLMTKTGTFV------INGAERVIVSQLVRSPGIYYAIAHDK 156

Query: 293  VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            +     +S  +     A      ++ +++    D   +  +  +  +         +D  
Sbjct: 157  IGKELYSSTVIPNRG-AWLEYETDSNDVFYVRVDRTRKVPITVLIRALGFGTNAEILDLF 215

Query: 353  NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                 I  +   D  +  ++ LL++Y+ +RPG+      AES+   +FFD+ +YDL+ VG
Sbjct: 216  GEEPKILASFGKDTAESYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVG 275

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            R K N +L L      +    EDI++ I   V +  G+    ++             +  
Sbjct: 276  RYKFNKKLALKNRITGQV-AAEDIVSAITGEVIVEEGQVITRELAEAIQNGAVPFVWVKG 334

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                      ER+IK   + +     +         +   V     +  L +    ++ L
Sbjct: 335  E---------ERNIKILSNMMVDLESVVDVDAKELGIAELVYYPVLADLLEETGGDIDEL 385

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
                  R +  L    + +      +       YG     +     N   + ++    + 
Sbjct: 386  KEEI-RRNIHELIPKHITKEDILASINYNIHLEYGIGTDDDIDHLGN-RRIRAVGELLQN 443

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 +    R V +   T D+  +S     N     A        S   + +       
Sbjct: 444  QYRIGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLG 503

Query: 653  EILVPREKIDF------IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            E+   R            D +  +V  +  S    +   ++        +   A      
Sbjct: 504  ELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACYARIN 563

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E  FV      +        +V +    +   +     +      LD     +      +
Sbjct: 564  EYGFVEAPYRKIDKTDPKNPVVTEEVVYMTADEEDNYHVAQANEPLDAEGHFIHKNVSGR 623

Query: 767  FQRSNQNT------CVNQRPL----VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            ++   Q         ++  P     V         +                  +L+   
Sbjct: 624  YREETQEYEKTAFDYMDVSPKMVFSVATALIPFLENDDPTRALMGSNMQRQAVPLLMTEA 683

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E    +   +        +      + +      G  +  +    +       
Sbjct: 684  PVVGTGMETKAAVDSGVCIVAEQAGVVDRSTSKEITVKHDDGTRKTYKLTKFLRSNQSNC 743

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+  G  V  G ++    +      M   +  L      +  +  D  L      
Sbjct: 744  YNQRPIVVKGERVEAGQVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDAVLL----S 798

Query: 936  SGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDRNIYSR 985
               V D    + H  +    +   +   E+I        +   +D DD   I+      R
Sbjct: 799  ERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDDR-GIIRIGAEVR 857

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
              +IL G+    G         L   +  E  R                 E      +  
Sbjct: 858  AGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVP 900

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP
Sbjct: 901  HGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLP 960

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI
Sbjct: 961  VEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANEVDI 1020

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                      +       +    ++     +    ++                   + + 
Sbjct: 1021 MDTLDLANDYVNLEWEEFEAKHKEELLPEVLEYLSEN--------------REHRKLWKG 1066

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGG
Sbjct: 1067 VPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1126

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E G PE
Sbjct: 1127 KAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPE 1186

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            SF VL+KE+Q+LGL + +          ME I D+ + +L
Sbjct: 1187 SFKVLLKELQSLGLDVRVLRDDNTEVEIMETI-DYGETDL 1225


>gi|118443602|ref|YP_877190.1| DNA-directed RNA polymerase subunit beta [Clostridium novyi NT]
 gi|158512396|sp|A0PXT8|RPOB_CLONN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|118134058|gb|ABK61102.1| DNA-directed RNA polymerase, beta subunit [Clostridium novyi NT]
          Length = 1241

 Score =  836 bits (2160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/950 (45%), Positives = 595/950 (62%), Gaps = 55/950 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+  +P+LIEVQ  SYD F            EGL   F  V PI  ++G
Sbjct: 9   KRTRMSFSKVKEMCPMPNLIEVQLNSYDWF----------WKEGLNEVFDDVNPIQDYTG 58

Query: 71  AAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEF+ Y  D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLILEFIDYNLDKDAIKYSVEECKERDATYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTFVI G +R++VSQL RSPG ++ +D  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTQQGTFVINGAERVIVSQLVRSPGAYYGYDVDKT---GKKLFSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS DII+VRID+ RK+P++  + ALG+ S+ EI+  F  +         D  
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPISILIRALGLGSDAEIVDWFGEEERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+   +I S         L +  + K  K L I    L
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSALSLINSLFFDAKRYDLSRVGRYKFNKKLAIYI-RL 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                AED+VN  TGEI ++ G+ ID +   EI +  I  + I   D V           
Sbjct: 286 LNQVAAEDVVNPFTGEIIVQKGETIDREKALEIQNCAINAVNIQVEDKV----------- 334

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
               K   +  +DI++ +              +  L    D Y      + ++   ++  
Sbjct: 335 ---IKVIGNNFVDIHKFIDFDISDLKIKEHVHYPTLKNILDNYTDEKSIKEEIKKNIHEL 391

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   +HI  +DI A I   + L    GTIDDID+LGNRR+RSVGE+L+NQ+R+GL RME
Sbjct: 392 IP---KHIVVDDIYATISYELGLPYEIGTIDDIDHLGNRRLRSVGELLQNQFRIGLSRME 448

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R +KER++  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 449 RVVKERMTIQDQEVITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 508

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +A+VN YGFIETPYR
Sbjct: 509 LGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLACYAKVNEYGFIETPYR 568

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V   + +VT+++VYL+A EE++  +AQA   LDE+G F +E +  R   + I+V ++++
Sbjct: 569 LVDKKEARVTDEIVYLTADEEDHYLVAQAKEPLDENGCFIDEKITVRDLEDVIVVSKDQV 628

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SP Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E   A 
Sbjct: 629 DLMDVSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIVGTGIEYKAAV 688

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG    A+  G++E V +  + IR        S  G+D ++L+K++RSNQ TC+NQRP+
Sbjct: 689 DSGVLPKAEHDGVIEYVSSTEVRIRRD------SDGGLDKHKLLKYKRSNQGTCINQRPI 742

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V  G++V+  D++ADGPSTD G++ALG+N+ + F+ W GYN+ED+ML+SE++V +D+FTS
Sbjct: 743 VSKGEKVKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDDIFTS 802

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNV E+ LKNIDE GI+ +GAEV  GDILVGK+TPK
Sbjct: 803 IHIEEYESEARDTKLGPEEITRDIPNVGEDALKNIDERGIVRIGAEVRSGDILVGKVTPK 862

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 863 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  506 bits (1302), Expect = e-140,   Method: Composition-based stats.
 Identities = 190/593 (32%), Positives = 269/593 (45%), Gaps = 80/593 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI--HIEEFEVMARDTKLG 857
                       +L    P  G   E    +   ++ +     +  ++   EV  R    G
Sbjct: 659  MGSNMQRQAVPLLKPAAPIVGTGIEYKAAVDSGVLPKAEHDGVIEYVSSTEVRIRRDSDG 718

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  + +          I++  I+  G +V  GD+L    +      +   + +     
Sbjct: 719  GLDKHKLLKYKRSNQGTCINQRPIVSKGEKVKAGDVLADGPST-DFGEIALGQNIRMGFI 777

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK---D 972
              +  +  D  L     V   +        +  +  +  +  E     I  +  D     
Sbjct: 778  TWEGYNYEDAMLVSEQLVRDDIFTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNI 837

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 838  DERGIVRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------------- 883

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E                   K+   + GD++PPGV  +V+ ++A KR I  GDKMAG
Sbjct: 884  ---EVRDTSLRVPHGEAGIIVDVKVFTRENGDELPPGVNELVRCYIAQKRKISVGDKMAG 940

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   +G  I
Sbjct: 941  RHGNKGVISRILPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAAGEMGWHI 1000

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + +     +I  L                                            
Sbjct: 1001 ATPVFNGAFEDEIVELLQEA---------------------------------------- 1020

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL+H+V DK++ARST
Sbjct: 1021 GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLHHLVDDKIHARST 1066

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I
Sbjct: 1067 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEVLTVKSDDVVGRVKTYEAI 1126

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            V G +  E G PESF VL+KE+QAL L + +  S T    K++E  + +  +L
Sbjct: 1127 VKGENIPEPGVPESFKVLIKELQALCLDVKVL-SDTNEEIKIKESSEEDMEDL 1178


>gi|327459246|gb|EGF05594.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK1057]
          Length = 1188

 Score =  836 bits (2160), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P ++ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFSTLVRALGFSGDDEILDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D         L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DSAVLTDPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|296877136|ref|ZP_06901176.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           parasanguinis ATCC 15912]
 gi|296431656|gb|EFH17463.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           parasanguinis ATCC 15912]
          Length = 1189

 Score =  836 bits (2159), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 586/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIRDPKYSLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI +EAG V+    ++ I             +
Sbjct: 278 YKINKKLNIKNRLLNQTIAEPLVDAETGEILVEAGTVMTRDVIDSISEQLD--------N 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +   L  ++V+ P D                         
Sbjct: 330 GLNKITYIPN----DAAVLTEPVELQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPSDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D D + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNDVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV    G VTN++V+L+A EE+   +AQANS L+E+G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEEDEYIVAQANSKLNEEGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 175/507 (34%), Positives = 245/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDETGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     + 
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGEDD 1159


>gi|302871396|ref|YP_003840032.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574255|gb|ADL42046.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 1230

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/959 (44%), Positives = 601/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G  + + I   F          +
Sbjct: 164 IPNRGAWLEFETDTSELLSVRLDRTRKVSLTTLLKAFGLYNQQMIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLYNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+ +TGEI ++ G+VI  +    I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPKTGEILVKEGEVITREVALNIQDAGINEVWVYADEERLF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  DK  D           +   ++    V + + +         D+S + R+
Sbjct: 343 KVVGNNTVKLDKYVDFD------VSDLNIKELVYLPVLKEILDTTS------DVSEIKRL 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 IKEK----ERELVPYCLTIDDIYAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT+++VYL+A EE+   IAQA   +DE+G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTDEIVYLTADEEDTYKIAQATEPVDEEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKYEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLMTESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+A++ G+VE+V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAEKDGVVEKVSADEIVIRNNDGTKD-------VYNLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 177/645 (27%), Positives = 261/645 (40%), Gaps = 86/645 (13%)

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                    G +I  + K++    +    Q   V         +  A+             
Sbjct: 616  NQRVTVRFGEEIIEVDKYEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAV 675

Query: 810  NMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             +L+   P  G   E    +   +      + V   +  +E   +      G +++   +
Sbjct: 676  PLLMTESPIIGTGVEYRAAVDSGVCILAEKDGVVEKVSADE---IVIRNNDGTKDVYNLL 732

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                       ++  I+  G EV  G+++    +      +   + +L A    +  +  
Sbjct: 733  KFKRTNQGTCFNQRPIVRKGQEVKAGEVIADGPST-DHGELALGKNVLVAFMPWEGYNYE 791

Query: 926  DTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            D  L            S  + +     R      E          E   +D  DE+ I+ 
Sbjct: 792  DAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDL-DERGIIR 850

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+    G         L   +  E  R                 E+  
Sbjct: 851  IGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------ETRD 893

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                            K+     GD++PPGV ++V+V+VA KR I  GDKMAGRHGNK  
Sbjct: 894  TSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISVGDKMAGRHGNK-- 951

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                                      GV SR+                    ++ +    
Sbjct: 952  --------------------------GVISRI------------------LPVEDMPFLP 967

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                        ++ V+       +++                G  V+TPVFDGA EE I
Sbjct: 968  DGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKVATPVFDGAKEEDI 1019

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK++ARSTG YSLVT
Sbjct: 1020 EEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDKIHARSTGPYSLVT 1079

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR + YE+IV G +  
Sbjct: 1080 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRVKTYEAIVKGENIP 1139

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            E G PESF VLVKE+Q+L L + L +   K     E + D  + +
Sbjct: 1140 EPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDDDEQPQ 1184


>gi|266620116|ref|ZP_06113051.1| DNA-directed RNA polymerase, beta subunit [Clostridium hathewayi
           DSM 13479]
 gi|288868345|gb|EFD00644.1| DNA-directed RNA polymerase, beta subunit [Clostridium hathewayi
           DSM 13479]
          Length = 1288

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/954 (45%), Positives = 597/954 (62%), Gaps = 58/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F +  E++++P+LIE+QK SY  FL          +EGL+  F+ + PI  F+G
Sbjct: 13  KSLRMSFSRQKEVLEMPNLIEIQKNSYQWFL----------DEGLKEVFEDISPIADFAG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         +I E 
Sbjct: 63  HLSLEFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD---------EINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    GK LY C +IP++
Sbjct: 114 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIGHDKV---GKELYTCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS DI +VR+DR RKVPVT  + ALG  +  EI+  F    K++ S   D  
Sbjct: 171 GAWLEYETDSNDIFYVRVDRTRKVPVTVLIRALGFGTNAEIIELFGEEPKLLASFGKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L    + +
Sbjct: 231 DNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKKL-HFKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  ++ED+V+  TGEI   AG  +D++   +I ++    +P ++V+ +     + + L+
Sbjct: 290 VGHVLSEDVVDTTTGEILATAGTTVDKQLAVDIQNA---AVPYVWVEGLERRQKVLSNLM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDV-STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            D         L  Y    P D   T  V   +   +  D    D   V +  ++  L  
Sbjct: 347 VD---------LGAYVSFDPKDAGVTELVFYPVLEKILEDVGTED-EEVLKSAIHRSLGE 396

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             P   +H+ KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL RM
Sbjct: 397 LIP---KHVTKEDILASINYNMHLEQQVGNADDIDHLGNRRIRAVGELLQNQYRIGLSRM 453

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 454 ERVVRERMTTQDMEGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLS 513

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN YGF+E PY
Sbjct: 514 ALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQYGFVEAPY 573

Query: 603 RKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           R V      +  VT++VVYL+A EE+N  +AQAN  LDE+G F  + +  R   E     
Sbjct: 574 RLVDKSDPNNPIVTDEVVYLTADEEDNFVVAQANEPLDEEGHFIHKNISGRFREETSEFQ 633

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+ ID +D SPK V S+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME+
Sbjct: 634 RKSIDLMDVSPKMVFSVATAMIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEA 693

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG  +VA+ AG+VE+  +  I+I+        +  G D+Y L KF+RSNQ+ C N
Sbjct: 694 KAAVDSGVCVVARNAGVVERSASNEIIIKRD------ADGGRDVYHLTKFKRSNQSNCYN 747

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+V   + V + ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V ED
Sbjct: 748 QKPIVYKNNHVEKGEVIADGPSTQNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQED 807

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK
Sbjct: 808 VYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGK 867

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 868 VTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENGD 921



 Score =  530 bits (1365), Expect = e-148,   Method: Composition-based stats.
 Identities = 182/595 (30%), Positives = 267/595 (44%), Gaps = 42/595 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E    +     +V+ +          E++ +    G
Sbjct: 668  MGSNMQRQAVPLLTTEAPVVGTGMEAKAAVDSGVCVVARNAGVVERSASNEIIIKRDADG 727

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              ++               ++  I+     V  G+++    + +    +   +  L    
Sbjct: 728  GRDVYHLTKFKRSNQSNCYNQKPIVYKNNHVEKGEVIADGPSTQN-GEIALGKNPLIGFM 786

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDK 971
              +  +  D  L     V   V        +  +  +  +  E          E   +D 
Sbjct: 787  TWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDL 846

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 847  -DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 892

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+   + GD++ PGV + V++++A KR I  GDKMA
Sbjct: 893  ----EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNQTVRIYIAQKRKISVGDKMA 948

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  
Sbjct: 949  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAARALGFN 1008

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I + + D     DI              +  E    Y+D     V E     +       
Sbjct: 1009 IATPVFDGANEIDIMDTLDVAND-YVNMTWEEFQDKYNDTLKPEVIEYLGEHL------- 1060

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                      + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARS
Sbjct: 1061 ------DHRELWKGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARS 1114

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE++T+KSDDVVGR + YE+
Sbjct: 1115 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEIMTVKSDDVVGRVKTYEA 1174

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            I+ G +  E G PESF VL+KE+Q+L L + +           E + D+ + +L+
Sbjct: 1175 IIKGENIPEPGIPESFKVLLKELQSLALDVRVLRDDNTEVQIAESM-DYEETDLR 1228


>gi|225569775|ref|ZP_03778800.1| hypothetical protein CLOHYLEM_05869 [Clostridium hylemonae DSM
           15053]
 gi|225161245|gb|EEG73864.1| hypothetical protein CLOHYLEM_05869 [Clostridium hylemonae DSM
           15053]
          Length = 1287

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/953 (44%), Positives = 584/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTSTGTFVINGAERVIVSQLVRSPGIYYAIAHDKV---GKKLYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLVRALGIGTNPEIVDLFGEEPKILASFEKDAA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 TNYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+ +  TGE+  E G  +  ++ + I ++    + I   D   N   + N +V
Sbjct: 290 TGQVLAEDVKSALTGEVVAEKGTKVTRETADAIQNAAAPFVWIERPDEERNIKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
              +                 D     V E ++  +     +     +  +K  ++ ++ 
Sbjct: 350 DLASVVDI-------------DPKEVGVTELVYYPVLETLLEETAGDIDELKDAIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNIHLEYGLGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGF+E PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINQYGFVEAPYR 575

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           ++      +  VT+ VVY++A EE+N ++AQAN  LD++G F  + V  R   E     R
Sbjct: 576 EISHEDPDNPVVTDKVVYMTADEEDNYHVAQANEPLDDEGHFVHKNVSGRYREETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            + D++D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 TRFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLMTEAPVVGTGMEEK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+  G+VE+  +  I IR  +  L         Y+L KF RSNQ+ C NQ
Sbjct: 696 AAVDSGVCMVAEAGGVVERSTSNEITIRQDDNSL-------KRYKLTKFLRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD V   D+IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RPIVFKGDRVEAGDVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LKN+DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKNLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  555 bits (1429), Expect = e-155,   Method: Composition-based stats.
 Identities = 244/1060 (23%), Positives = 397/1060 (37%), Gaps = 67/1060 (6%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            VD       I  +   D   + ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 212  VDLFGEEPKILASFEKDAATNYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L      + + ++   A+         G+   +    +      ++ 
Sbjct: 272  AKVGRYKFNKKLALKNRITGQVLAEDVKSALT--------GEVVAEKGTKVTRETADAIQ 323

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +     ER+IK   + +   + +         V   V      + L +    
Sbjct: 324  NAAAPFVWIERPDEERNIKVLSNMMVDLASVVDIDPKEVGVTELVYYPVLETLLEETAGD 383

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            ++ L      R +  L    + +      +       YG     +     N   + ++  
Sbjct: 384  IDELKDAI-KRDIHDLIPKHITKEDILASINYNIHLEYGLGNDDDIDHLGN-RRIRAVGE 441

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDG 638
              +      +    R V +   T D+  +S     N     A               +  
Sbjct: 442  LLQNQYRIGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 501

Query: 639  SFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +   EL   R             R   +  D        +     P   N      L   
Sbjct: 502  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATY 561

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                Q   +            ++ V       + A          A    +      +  
Sbjct: 562  ARINQYGFVEAPYREISHEDPDNPVVTDKVVYMTADEEDNYHVAQANE-PLDDEGHFVHK 620

Query: 755  STSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            + SG       +++R+  +   V+ + +  V         +  A+              +
Sbjct: 621  NVSGRYREETQEYERTRFDYMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPL 680

Query: 812  LVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            L+   P  G   E+   +   +    +    +       +         +  +    +  
Sbjct: 681  LMTEAPVVGTGMEEKAAVDSGVCMVAEAGGVVERSTSNEITIRQDDNSLKRYKLTKFLRS 740

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                  ++  I+  G  V  GD++    +      M   +  L      +  +  D  L 
Sbjct: 741  NQSNCYNQRPIVFKGDRVEAGDVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDAVLL 799

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSR 985
                V   V        +  +  +  +  E     I  +  D     DE+ I+      R
Sbjct: 800  SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKNLDERGIIRIGAEVR 859

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
              +IL G+    G         L   +  E  R                 E      +  
Sbjct: 860  AGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVP 902

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP
Sbjct: 903  HGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLP 962

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI
Sbjct: 963  VEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANEIDI 1022

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                      +       +    +D     +                 +D      + + 
Sbjct: 1023 MDTLDLANDYVNLSWEEFEKKHKEDLLPEVLQYL--------------SDNREHRKLWKG 1068

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              +   G+  L DG +GE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGG
Sbjct: 1069 VPISRDGKVRLRDGRSGEFFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1128

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G +  E G PE
Sbjct: 1129 KAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEAIIKGENIPEPGIPE 1188

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            SF VL+KE+Q+LGL + +          ME + D  + + 
Sbjct: 1189 SFKVLLKELQSLGLDVRVLRDDNTEVEIMETV-DMGETDF 1227


>gi|291521812|emb|CBK80105.1| DNA-directed RNA polymerase subunit beta [Coprococcus catus GD/7]
          Length = 1285

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/960 (44%), Positives = 592/960 (61%), Gaps = 70/960 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++++P+LIEVQK SYD FL           +GL+  F+ + PIT +SG
Sbjct: 13  RNIRMSYSRQKEVLEMPNLIEVQKNSYDWFL----------KKGLKEVFEDISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEF  +    +  K+ +++C  RD TYA PLK+ +RLI  + D F+         E 
Sbjct: 63  HLSLEFTDFSLCEEEAKYSIEECKERDATYAAPLKVKVRLINKETDSFS---------EH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYGVGHDKL---GKELYSATVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYP--KIVYSQRGDFW 245
           G W++ E DS DI +VR+DR RKVPVT  + ALG+ + +EI+  F    KI+ +   +  
Sbjct: 171 GAWLEYETDSNDIYYVRVDRTRKVPVTVLIRALGVGTNQEIIDLFGEEPKIMATLSSNKD 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS---- 300
                       + +      I  GE + +ES + L + +    +   +  +G       
Sbjct: 231 VSD------SYQSGLLELYKKIRPGEPLAVESAESLINAMFFDPRRYDLAKVGRYKFNKK 284

Query: 301 ----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + + G  +AED+V+  TGEI  EA  ++ E   ++I ++    +  +YV +     
Sbjct: 285 LALKNRITGFALAEDVVDETTGEIIAEADTMVTEDLAQKIQNAG---VAAVYVQTEERVE 341

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            + + ++ +                   D  T  + E    +        +   +  +K 
Sbjct: 342 KVLSNMMVELTSFVD------------VDPETLGITEKYVYYPVLRQILDENEDIEDIKD 389

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            ++ N        HI KEDI A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 390 AIKKNA-ADLVPMHITKEDIFASINYNMHLEYGVGNADDIDHLGNRRIRAVGELLQNQYR 448

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER+++ D++ V  Q LIN KPV +AV EFF SSQLSQ  +  N LS +T
Sbjct: 449 IGLSRMERVVRERMTTQDLEGVSAQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELT 508

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL SFAR+N YG
Sbjct: 509 HKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLASFARINQYG 568

Query: 597 FIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           FIE PYR +      + +VT++V YL+A EE+   +AQAN  +DE+G F  + V  R   
Sbjct: 569 FIEAPYRILDKTDPKNPRVTDEVAYLTADEEDKFRVAQANEPIDENGYFVNKTVSGRYRE 628

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     R ++D +D SP+ V S+A S+IPFL+NDD+NR LMG NMQRQAVPL+  ++P V
Sbjct: 629 ETTSFQRSQVDLMDVSPRMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLMLTDSPVV 688

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME+  A  SG  +VAKR G+VE+  +  ++I++ +G  D        Y+L+KF  SN
Sbjct: 689 GTGMEAKAAVDSGVCVVAKRGGVVERSASNEVIIKADDGTRD-------TYKLLKFSGSN 741

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q  C NQRP+V  GD V + D++ADGPST  G+LALG+N L+ FM W GYNFED++L+SE
Sbjct: 742 QGACYNQRPIVFRGDRVEKGDVLADGPSTSQGELALGKNPLIGFMTWEGYNFEDAVLLSE 801

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V EDV+TSIHI E+E  ARDTKLGPEEITRD+P V ++ LKN+DE GII VGAEV  G
Sbjct: 802 RLVQEDVYTSIHISEYEAEARDTKLGPEEITRDVPGVGDDALKNLDERGIIRVGAEVRAG 861

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G ++D ++F R   D
Sbjct: 862 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIILDAKVFTRENGD 921



 Score =  549 bits (1414), Expect = e-153,   Method: Composition-based stats.
 Identities = 260/1072 (24%), Positives = 409/1072 (38%), Gaps = 79/1072 (7%)

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             +  I+ +           +   D +   +  LL++Y+ +RPG+      AES+ N +FF
Sbjct: 207  TNQEIIDLFGEEPKIMATLSSNKDVSDSYQSGLLELYKKIRPGEPLAVESAESLINAMFF 266

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            D  +YDL+ VGR K N +L L        + ++ +      ++   +   T D    + N
Sbjct: 267  DPRRYDLAKVGRYKFNKKLALKNRITGFALAEDVVDETTGEIIAEADTMVTEDLAQKIQN 326

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              V +V       Y     R+E+ +   +  V++ S +  D          V        
Sbjct: 327  AGVAAV-------YVQTEERVEKVLSNMM--VELTSFVDVDPETLGITEKYVYYPV---- 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH----YGRICPAETSEG 577
            L Q+ +    +  I    + +A     +   +  +     +  H     G     +    
Sbjct: 374  LRQILDENEDIEDIKDAIKKNAADLVPMHITKEDIFASINYNMHLEYGVGNADDIDHLGN 433

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS---- 633
              I  V  L    +      +    R V +   T D+  +SA    N     A       
Sbjct: 434  RRIRAVGELL---QNQYRIGLSRMERVVRERMTTQDLEGVSAQSLINIKPVTAAVKEFFG 490

Query: 634  ------LDEDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLE 683
                    +  +   EL   R             R   +  D        +     P   
Sbjct: 491  SSQLSQFMDQNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPVETPEGP 550

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            N      L       Q   +         T  ++       A + A          A   
Sbjct: 551  NIGLINSLASFARINQYGFIEAPYRILDKTDPKNPRVTDEVAYLTADEEDKFRVAQANE- 609

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPST 800
             I      ++ + SG        FQRS  +   V+ R +  V         +  A+    
Sbjct: 610  PIDENGYFVNKTVSGRYREETTSFQRSQVDLMDVSPRMVFSVATSMIPFLQNDDANRALM 669

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPE 859
                      +++   P  G   E    +     V       +       +      G  
Sbjct: 670  GSNMQRQAVPLMLTDSPVVGTGMEAKAAVDSGVCVVAKRGGVVERSASNEVIIKADDGTR 729

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  + +           ++  I+  G  V  GD+L    +   +  +   +  L      
Sbjct: 730  DTYKLLKFSGSNQGACYNQRPIVFRGDRVEKGDVLADGPST-SQGELALGKNPLIGFMTW 788

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDD 973
            +  +  D  L     V   V      + +  +  +  +  E    +         ++  D
Sbjct: 789  EGYNFEDAVLLSERLVQEDVYTSIHISEYEAEARDTKLGPEEITRDVPGVGDDALKNL-D 847

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 848  ERGIIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------------- 892

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +            K+   + GD++ PGV + V+V++A KR I  GDKMAGR
Sbjct: 893  --EVRDTSLKVPHGEYGIILDAKVFTRENGDELSPGVNQCVRVYIAQKRKISVGDKMAGR 950

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRILP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HLG A   LG KI+
Sbjct: 951  HGNKGVVSRILPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLGLAARALGFKIE 1010

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + +     DI          + T    E+ S    D++      +             
Sbjct: 1011 TPVFNGADENDIMDTLELANDYVNTS--WEEFSAKWKDTLDEKVYNYLD----------- 1057

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             + +A     +   +  +G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG
Sbjct: 1058 -ENKAYREEWKGVPISRTGKVQLRDGRTGEEFDSPVTIGFMHYLKLHHLVDDKIHARSTG 1116

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             Y+LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR + YE+I+
Sbjct: 1117 PYALVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTFKSDDVTGRVKAYEAII 1176

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             G +  E G PESF VL+KE+Q+L L + +           E + D+   + 
Sbjct: 1177 KGENISEPGIPESFKVLLKELQSLALDVRVLRDDQTEVELGETV-DYGDDDF 1227


>gi|319945775|ref|ZP_08020026.1| DNA-directed RNA polymerase subunit beta [Streptococcus australis
           ATCC 700641]
 gi|319748135|gb|EFW00378.1| DNA-directed RNA polymerase subunit beta [Streptococcus australis
           ATCC 700641]
          Length = 1189

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/963 (43%), Positives = 581/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I      D+  +   
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDAETGEILVEAGTVMTRDVIDSISEHLDGDLNKIV-- 335

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                         D     +  +L  ++V+ P D                         
Sbjct: 336 ----------YTPNDSAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV    G VTN++V+L+A EE+   +AQANS L+E G F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEEDEYIVAQANSKLNEAGGFAEPIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHGGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/507 (33%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   K     +     + 
Sbjct: 1133 SLGLDMRVLDEDDKEVELRDLDEGEDD 1159


>gi|291562244|emb|CBL41060.1| DNA-directed RNA polymerase subunit beta [butyrate-producing
           bacterium SS3/4]
          Length = 1282

 Score =  835 bits (2158), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/953 (45%), Positives = 582/953 (61%), Gaps = 57/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  F +  E++++P+LIE+QK SY  FL          +EGL+  F  + PI  F+G
Sbjct: 8   KSVRMSFSRQKEVLEMPNLIEIQKDSYQWFL----------DEGLKEVFDDISPIADFAG 57

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         +I E 
Sbjct: 58  HLSLEFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD---------EINEH 108

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++  D  +    GK LY+C +IP++
Sbjct: 109 EIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIDHDKI---GKELYSCTVIPNR 165

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVPVT  + ALG  +  EI+  F    K++ S   D  
Sbjct: 166 GAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGYGTNAEIIDLFGEEPKLLASFGKDTS 225

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++           L K  + K  K L    + +
Sbjct: 226 DNYQDGLLELYKKIRPGEPLSVDSAESLLNGMFFDPRRYDLAKVGRYKFNKKL-HMKNRI 284

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   +EDIV+  TGEI  EAG  I +     I ++    IP +++ +      + + L+
Sbjct: 285 VGQIPSEDIVDTSTGEILAEAGKAITKDQAIAIQNA---AIPYVWIQTEERVEKVLSNLM 341

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D         L  Y    P +V        +  +                         
Sbjct: 342 VD---------LSAYVTFDPAEV----GITELVYYPVLKEILEKAGDDEEALKAELHRNI 388

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                + I KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 389 HELVPKCITKEDILASINYNMHLEYGIGVKDDIDHLGNRRIRAVGELLQNQYRIGLSRME 448

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ DID + PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 449 RVVRERMTTQDIDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTHKRRLSA 508

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A+VN YGF+E PYR
Sbjct: 509 LGPGGLSRERAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLASYAKVNQYGFVEAPYR 568

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
            V      + +VT++VVY++A EE+N  +AQAN  LDE+G F    V  R   E     +
Sbjct: 569 VVDKTDPANPRVTDEVVYMTADEEDNYIVAQANEPLDENGYFIHNNVSGRFREETSSFQK 628

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +ID +D SP+ V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTG+E  
Sbjct: 629 RQIDLMDVSPRMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLSTEAPVVGTGIEGK 688

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VAK AG+VE+  +  IVI+        S    D+Y L+KF RSNQ+   NQ
Sbjct: 689 AAVDSGVCVVAKNAGVVERSASNEIVIKRD------SDGNRDVYCLIKFSRSNQSNSYNQ 742

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +P+V  GD V + ++IADGPST  G++ALG+N L+ FM W GYN+ED++L+SE++V  DV
Sbjct: 743 KPIVYKGDHVEKGEVIADGPSTKDGEIALGKNPLIGFMTWEGYNYEDAVLLSEKLVMNDV 802

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  +RDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  GDILVGK+
Sbjct: 803 YTSVHIEEYECESRDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRAGDILVGKV 862

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  GT++D ++F R   D
Sbjct: 863 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGTIIDAKLFTRENGD 915



 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 259/1171 (22%), Positives = 431/1171 (36%), Gaps = 78/1171 (6%)

Query: 243  DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS--LKEKGVKFLGITS 300
            +     ++  ++ +G       +  DTG  VI   +++    L        G+    I  
Sbjct: 99   NKDKDEINEHEIFMGD----LPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIDHDKIGK 154

Query: 301  DCLCGLYVAED----IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
            +      +           ++ +++    D   +  +  +  +         +D      
Sbjct: 155  ELYSCTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGYGTNAEIIDLFGEEP 214

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
             +  +   D + + +D LL++Y+ +RPG+  +   AES+ N +FFD  +YDL+ VGR K 
Sbjct: 215  KLLASFGKDTSDNYQDGLLELYKKIRPGEPLSVDSAESLLNGMFFDPRRYDLAKVGRYKF 274

Query: 417  NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            N +L++     V  I  EDI+      +    GK    D                   + 
Sbjct: 275  NKKLHMKNRI-VGQIPSEDIVDTSTGEILAEAGKAITKDQAIAIQNAAIPYV------WI 327

Query: 477  LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
                R+E+ +    + +   S           +   V        L +  +   +L    
Sbjct: 328  QTEERVEKVLS---NLMVDLSAYVTFDPAEVGITELVYYPVLKEILEKAGDDEEALKAEL 384

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H      + +             ++H  +   +       G+    + ++    +     
Sbjct: 385  HRNIHELVPKCITKEDILASINYNMHLEYGIGVKDDIDHLGN--RRIRAVGELLQNQYRI 442

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVF 646
             +    R V +   T D+  ++     N     A               +  +   EL  
Sbjct: 443  GLSRMERVVRERMTTQDIDGITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTH 502

Query: 647  CRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             R             R   +  D        +     P   N      L       Q   
Sbjct: 503  KRRLSALGPGGLSRERAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLASYAKVNQYGF 562

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            +         T   +         + A          A   +  +     +  +      
Sbjct: 563  VEAPYRVVDKTDPANPRVTDEVVYMTADEEDNYIVAQANEPLDENGYFIHNNVSGRFREE 622

Query: 763  RLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                 +R      V+ R +  V         +  A+              +L    P  G
Sbjct: 623  TSSFQKRQIDLMDVSPRMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLSTEAPVVG 682

Query: 821  YNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
               E    +     +V+++          E++ +    G  ++   I         + ++
Sbjct: 683  TGIEGKAAVDSGVCVVAKNAGVVERSASNEIVIKRDSDGNRDVYCLIKFSRSNQSNSYNQ 742

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPSGVS 936
              I+  G  V  G+++    + K       +  L+  +   G    D    S ++     
Sbjct: 743  KPIVYKGDHVEKGEVIADGPSTKDGEIALGKNPLIGFMTWEGYNYEDAVLLSEKLVMNDV 802

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             T V +  +     D       + R+     E   +D  DE+ I+      R  +IL G+
Sbjct: 803  YTSVHIEEYECESRDTKLGPEEITRDVPGVGEDALKDL-DERGIIRIGAEVRAGDILVGK 861

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G         L   +  E  R                 E      +          
Sbjct: 862  VTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGAYGTII 904

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++ PGV   V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL 
Sbjct: 905  DAKLFTRENGDELAPGVNETVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLP 964

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + D     DI        
Sbjct: 965  NGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVSTPVFDGADENDIQDTLELAN 1024

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
              +                +LR       G  +              ++ +   +  +G+
Sbjct: 1025 DYVN---MEWDAFQEKYKDILRPDAMEYLGEHL-----------DHRALWKGVPISRTGK 1070

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L DG TGE FD P T+G+++ LKL+H+V DK++ARSTG Y+LVTQQPLGGK+  GGQR
Sbjct: 1071 VQLRDGRTGEYFDGPTTIGHMHYLKLHHLVDDKIHARSTGPYALVTQQPLGGKAQFGGQR 1130

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE
Sbjct: 1131 FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLLKE 1190

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +Q+LGL + +     +     E I D++   
Sbjct: 1191 LQSLGLDVRVLRDNGEEVDMSENI-DYSDTN 1220


>gi|295397945|ref|ZP_06808002.1| DNA-directed RNA polymerase subunit beta [Aerococcus viridans ATCC
           11563]
 gi|294973830|gb|EFG49600.1| DNA-directed RNA polymerase subunit beta [Aerococcus viridans ATCC
           11563]
          Length = 1193

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 411/963 (42%), Positives = 576/963 (59%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  RVR+ + +  E++++P+LIE+Q  SY  FL          ++G++  F+
Sbjct: 1   MTGHNVNFGKHRVRRSYSRINEVLELPNLIEIQTDSYKWFL----------DQGMKEMFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI   +G   LEFV Y F   K+++ +    D  Y+ P+ + LRL+          K
Sbjct: 51  DISPIEDHAGKLALEFVDYSFKEAKYNLAEARAHDTNYSAPIYVKLRLM---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK+Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++F     +   +G+  +
Sbjct: 102 ETGEIKDQEVFFGDFPLMTDGGTFIINGAERVIVSQLVRSPGVYFH---DKLDKNGRQSF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              +IP++G W+++E D+K+I +VRIDR RKVP++  + ALG  S++ I   F       
Sbjct: 159 GTTVIPNRGAWLEMETDAKNISYVRIDRTRKVPMSVLMRALGFSSDDQIREIFGESETLE 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +        +D      +      +  GE    +S + L +      +   +  +G 
Sbjct: 219 LTLEKD-VHKDLSDSRTEEALKEIYERLRPGEPKTADSSRNLLTARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE +V+ ETGEI  + G  ++ + ++++              
Sbjct: 278 YKVNKKLDIKNRLFNQILAETLVDPETGEILADKGTELNREIMDKL-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  N L         DA+L         +     +             K     
Sbjct: 324 ----EPYFDNGLNVTTLYPNDDAVL--------TEPVDVQI------------IKIQAPK 359

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                +N+  N     + R +   D++A +   + L  G G  DDID+LGNRR+RSVGE+
Sbjct: 360 DADRVINVIGNASPGREARALTIADVLASLNYFLGLYEGIGKTDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI+ V PQ LIN +PVV+++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQFRIGLSRMERVVRERMSIQDIEKVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL+++L S+A
Sbjct: 480 PLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINNLASYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++N +GFIETPYR+V     KVT+ + YL+A EE+N  IAQ NS L+EDGSF EE+V  R
Sbjct: 540 KINEFGFIETPYRRVDWNTHKVTDRIDYLTADEEDNFVIAQGNSILNEDGSFAEEIVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E I V  E++D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPLL+  A
Sbjct: 600 YVEENIEVKPERVDYMDVSPKQVVSVATASIPFLENDDSNRALMGANMQRQAVPLLQPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SGAA+VA+  G+VE VDA  I +R  +G LD        Y L+K+ 
Sbjct: 660 PLVGTGMEHKAAADSGAAVVAQFDGVVEYVDAREIRVRREDGALDK-------YPLIKYH 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P V +G+ V   +I+A+GPS + G++ALG+N L+AFM W GYN+ED+++
Sbjct: 713 RSNASASYNQTPNVTIGESVTAGEILANGPSMENGEMALGQNPLIAFMTWDGYNYEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHI+E E  ARDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSIHIDELESEARDTKLGPEEITREIPNVGEDSLRNLDERGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE LL AIFGEKA +VRDTSLRVP G  G V DV++F R 
Sbjct: 833 KDGDILVGKVTPKGVTELSAEEHLLHAIFGEKAREVRDTSLRVPHGGGGIVNDVKVFYRE 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  508 bits (1307), Expect = e-141,   Method: Composition-based stats.
 Identities = 245/1098 (22%), Positives = 387/1098 (35%), Gaps = 175/1098 (15%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  + EIF         L  D                +   ++AL +IY 
Sbjct: 194  VLMRALGFSSDDQIREIFGESETLELTLEKDV----------HKDLSDSRTEEALKEIYE 243

Query: 380  VMRPGDVSTFSVAESMFNFLFFDS--------------------DKYDLSTVGRVKMNMR 419
             +RPG+  T   + ++    FFD                     ++     +    ++  
Sbjct: 244  RLRPGEPKTADSSRNLLTARFFDPRRYDLAAVGRYKVNKKLDIKNRLFNQILAETLVDPE 303

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                  D    + +E +  +     +  N      + D +    V    +++K Q     
Sbjct: 304  TGEILADKGTELNREIMDKLEPYFDNGLNVTTLYPNDDAVLTEPVDV--QIIKIQAPKDA 361

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R+   I       +  ++   D+         +   + +      L             
Sbjct: 362  DRVINVIGNASPGREARALTIADVLASLNYFLGLYEGIGKTDDIDHLGNRRIRSVGELLQ 421

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   +  +  V    +  ++  V P     I P   S     G         + N  
Sbjct: 422  NQFRIGLSRMERVVRERMSIQDIEKVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPL 481

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             LSA                        L       +   
Sbjct: 482  GELTHKRR-------------LSA------------------------LGPGGLTRDRAG 504

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQRQAVPLLKAEAPFVGTG 714
                 + +        +         L N+ ++   +            +      V   
Sbjct: 505  YEVRDVHYSHYGRMCPIETPEGPNIGLINNLASYAKINEFGFIETPYRRVDWNTHKVTDR 564

Query: 715  MESVVAKSSGAAIVAKRAGIVEQ--VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            ++ + A      ++A+   I+ +    A  IV+     +          Y          
Sbjct: 565  IDYLTADEEDNFVIAQGNSILNEDGSFAEEIVMARYVEENIEVKPERVDY---------M 615

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLIS 830
            +    Q   V         +  ++              +L    P  G   E   +    
Sbjct: 616  DVSPKQVVSVATASIPFLENDDSNRALMGANMQRQAVPLLQPHAPLVGTGMEHKAAADSG 675

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              +V++      +++  E+  R  + G  +    I         + ++   + +G  V  
Sbjct: 676  AAVVAQFDGVVEYVDAREIRVRR-EDGALDKYPLIKYHRSNASASYNQTPNVTIGESVTA 734

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            G+IL    +      M   +  L A       +  D  +                    +
Sbjct: 735  GEILANGPS-MENGEMALGQNPLIAFMTWDGYNYEDAVIMS----------------ERL 777

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPK 1000
             K++   S+  +++E  ARD       + R I                I  G     G  
Sbjct: 778  VKDDVYTSIHIDELESEARDTKLGPEEITREIPNVGEDSLRNLDERGIIRIGAEVKDGDI 837

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S         F  +  +V+     +        + +      K+   
Sbjct: 838  LVGKVTPKGVTELSAEEHLLHAIFGEKAREVRDTSLRVPHGGGGIVNDV------KVFYR 891

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++  KR IQ GDKMAGRHGNKG+VSRILP EDMP++ DGTPVDI
Sbjct: 892  ENGDELSPGVSMLVRVYIIQKRKIQVGDKMAGRHGNKGVVSRILPQEDMPYMPDGTPVDI 951

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   +G  I + + D     D+               
Sbjct: 952  MLNPLGVPSRMNIGQVLELHLGMAAREMGIHIATPVFDGANEEDVW-------------- 997

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                E I      A +    +++LYDG 
Sbjct: 998  ------------------------------------ETIKE----AGMASDAKTVLYDGR 1017

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD  V+VG +Y LKL+HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1018 TGEPFDNRVSVGVMYYLKLSHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1077

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1078 ALEAYGAAYTLQEILTYKSDDVVGRVQTYEAIVKGEPIPKPGVPESFRVLVKELQSLGLD 1137

Query: 1361 IDLENSRTKNSAKMEEIP 1378
            I++ +S  K     +   
Sbjct: 1138 IEVLDSDKKAVDLRDMDE 1155


>gi|94987714|ref|YP_595815.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS9429]
 gi|94541222|gb|ABF31271.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS9429]
          Length = 961

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ IR  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  105 bits (261), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 106/314 (33%), Gaps = 26/314 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPC 1106
            RHGNKG+VSRI+P 
Sbjct: 924  RHGNKGVVSRIVPR 937


>gi|229830154|ref|ZP_04456223.1| hypothetical protein GCWU000342_02261 [Shuttleworthia satelles DSM
           14600]
 gi|229791452|gb|EEP27566.1| hypothetical protein GCWU000342_02261 [Shuttleworthia satelles DSM
           14600]
          Length = 1326

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/967 (44%), Positives = 599/967 (61%), Gaps = 66/967 (6%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +V +G G VR  + ++ E++++P+ I VQ+ SY  FL          +EG++ AF  + 
Sbjct: 7   HLVKSGKG-VRMSYKRSKEVLEMPNFIAVQRDSYKWFL----------DEGMKEAFDDIS 55

Query: 64  PITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           PI+ FSG   LEFV +    D  K+ + +C  RD TY+ PLK+ +RL           K 
Sbjct: 56  PISDFSGHLSLEFVGFRLCTDEIKYTIPECKARDTTYSAPLKVKVRLY---------NKE 106

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++  D  +    GK L+ 
Sbjct: 107 TDEINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIDHDKI---GKELFT 163

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYP--KIVY 238
             +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+  ++EI+  F    KI+ 
Sbjct: 164 ATVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGLGSNQEIIEMFGEEPKILA 223

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLG 297
           S   D      +      G  +      I  GE + +ES + L SG+    +   +  +G
Sbjct: 224 SFEKDTSITEQAPQGSYEGG-LLELYKKIRPGEPLTVESAESLISGMFFDPRRYDLAKVG 282

Query: 298 ITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                        +    +AED+V+  TGEI   AG  +D++  + I ++ +        
Sbjct: 283 RYKFNKKLALRKRINKQVLAEDVVDQSTGEILASAGSRVDQELADRIQNAGV-------- 334

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
                  ++     T   K   + ++DI   +   D   + + E ++  +     + + +
Sbjct: 335 ------PFVWIQTETRNVKVLSNLMVDIRAHVDIDDPRAYGINEKVYYPVLEQLMRENPN 388

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
               ++   R   D     RHI ++DI A I   + L  G G  DDID+LGNRR+R+VGE
Sbjct: 389 REDLLEAIRRDAHDLI--PRHITRDDIFASINYNMHLEYGLGNDDDIDHLGNRRIRAVGE 446

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQYR+GL RMER ++ER+S+ D++++ PQ LIN KPV +AV EFF SSQLSQ  +  
Sbjct: 447 LLQNQYRIGLSRMERVVRERMSTQDVETISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 506

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+
Sbjct: 507 NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLASY 566

Query: 590 ARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           AR+N YGFIE PYR +      + +VT +VVY++A EE+N ++AQAN  LD DG F  + 
Sbjct: 567 ARINEYGFIEAPYRVIDKSDADNPRVTEEVVYMAADEEDNYHVAQANEPLDADGHFVHKQ 626

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E     R   D++D SP+ V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL
Sbjct: 627 VSGRFRDETQTYDRGAFDYMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLL 686

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
             EAP VGTGME   A  SG  ++A+ AG VE  ++ RI+I++ +G       G D Y L
Sbjct: 687 TTEAPVVGTGMEPKTAVDSGVCVLARAAGTVEAAESNRIIIKTDDG-------GRDEYLL 739

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF+RSNQ+ C NQRP+V  GD V   ++IADGPST  G+LALG+N L+ FM W GYN+E
Sbjct: 740 TKFERSNQSNCYNQRPIVFKGDRVEAGEVIADGPSTSRGELALGKNPLIGFMTWEGYNYE 799

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SE +V  DV+TSIHIEE+E  +RDTKLGPEEITRD+P V +E LK++DE GII +
Sbjct: 800 DAVLLSENLVENDVYTSIHIEEYETESRDTKLGPEEITRDVPGVGDEALKDLDENGIIRI 859

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GDILVGK+TPKGE+ +T EEKLLRAIFGEKA +VRDTSL+VP G  G VVD +I
Sbjct: 860 GAEVRSGDILVGKVTPKGETELTAEEKLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKI 919

Query: 945 FNRHGID 951
           F R   D
Sbjct: 920 FTRENGD 926



 Score =  542 bits (1397), Expect = e-151,   Method: Composition-based stats.
 Identities = 244/1040 (23%), Positives = 395/1040 (37%), Gaps = 82/1040 (7%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +  LL++Y+ +RPG+  T   AES+ + +FFD  +YDL+ VGR K N +L L    + 
Sbjct: 239  SYEGGLLELYKKIRPGEPLTVESAESLISGMFFDPRRYDLAKVGRYKFNKKLALRKRINK 298

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            + + ++ +      ++     +   +  D + N  V  V       +     R  + +  
Sbjct: 299  QVLAEDVVDQSTGEILASAGSRVDQELADRIQNAGVPFV-------WIQTETRNVKVLS- 350

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR-LSALGQG 547
                VDI + +  D   A  +   V           + E+ N    +   RR    L   
Sbjct: 351  -NLMVDIRAHVDIDDPRAYGINEKVYYPVLE---QLMRENPNREDLLEAIRRDAHDLIPR 406

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
             + R      +       YG     +     N   + ++    +      +    R V +
Sbjct: 407  HITRDDIFASINYNMHLEYGLGNDDDIDHLGN-RRIRAVGELLQNQYRIGLSRMERVVRE 465

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC-------- 649
               T DV  +S     N     A               +  +   EL   R         
Sbjct: 466  RMSTQDVETISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPGG 525

Query: 650  -AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             + +        + +        V         L N  ++   +           ++A  
Sbjct: 526  LSRDRAGFEVRDVHYTHYGRMCPVETPEGPNIGLINSLASYARI------NEYGFIEAPY 579

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              +          +     +A        V      + +    +    SG        + 
Sbjct: 580  RVIDKSDADNPRVTEEVVYMAADEEDNYHVAQANEPLDADGHFVHKQVSGRFRDETQTYD 639

Query: 769  RSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            R   +   V+ R +  V         +  A+              +L    P  G   E 
Sbjct: 640  RGAFDYMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEP 699

Query: 826  SMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
               +     V      ++   E   +   T  G  +                ++  I+  
Sbjct: 700  KTAVDSGVCVLARAAGTVEAAESNRIIIKTDDGGRDEYLLTKFERSNQSNCYNQRPIVFK 759

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V  G+++    +      +   +  L      +  +  D  L   + V   V     
Sbjct: 760  GDRVEAGEVIADGPSTSR-GELALGKNPLIGFMTWEGYNYEDAVLLSENLVENDVYTSIH 818

Query: 945  FNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
               +  +  +  +  E    +         +D  DE  I+      R  +IL G+    G
Sbjct: 819  IEEYETESRDTKLGPEEITRDVPGVGDEALKDL-DENGIIRIGAEVRSGDILVGKVTPKG 877

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                     L   +  E  R                 E      +            KI 
Sbjct: 878  ETELTAEEKLLRAIFGEKAR-----------------EVRDTSLKVPHGEYGIVVDAKIF 920

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+
Sbjct: 921  TRENGDELNPGVNKAVRIYIAQKRKIGPGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPL 980

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I++ + D  +  +I          +  
Sbjct: 981  DIVLNPLGVPSRMNIGQVLEIHLSLAAKALGLNIETPVFDGASEREIGDTLEMANDYVNE 1040

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 K    +      +    ++    +              + +   +   G+  L D
Sbjct: 1041 PWEDFKNKYQEILDQKTMDYLSENRGHRA--------------LWKGVPISRDGKVQLRD 1086

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+PFD P T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEME
Sbjct: 1087 GRTGQPFDGPTTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1146

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I+ G +  + GTPESF V++KE+QAL 
Sbjct: 1147 VWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIIKGENIPDPGTPESFKVMLKELQALA 1206

Query: 1359 LSIDLENSRTKNSAKMEEIP 1378
            L +++ +   +    ME   
Sbjct: 1207 LDVNVLDDSGREVKLMESTE 1226


>gi|330940876|gb|EGH43834.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            pisi str. 1704B]
          Length = 621

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 350/624 (56%), Positives = 473/624 (75%), Gaps = 5/624 (0%)

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G
Sbjct: 2    VVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMG 61

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
             LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEIT 
Sbjct: 62   GLALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITA 121

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 122  DIPNVGEAALNKLDEAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 181

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+DTSLRVP+G  GTV+DV++F R G++++ R++S+E+ Q++ + +D ++E  I++   +
Sbjct: 182  VKDTSLRVPTGTKGTVIDVQVFTRDGVERDARALSIEKSQLDEIRKDLNEEFRIVEGATF 241

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             RL   L G+ A  G  G KK   ++++++      QW++  + ++ +   +E  +    
Sbjct: 242  ERLRSALVGRVAEGG-AGLKKGQEITNEVLDGLEHGQWFKLRMAEDALNEQLEKAQAYIV 300

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I
Sbjct: 301  DRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVI 360

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 361  MPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRK-- 418

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++ LR FL ++    G   E + D  D+ +L +A+  ++GVP++TPVFDGA E  I +M
Sbjct: 419  -VAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLRNGVPMATPVFDGAKESEIKAM 477

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 478  LKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 537

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 538  LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPG 597

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
             PESFNVL+KE+++LG+ IDLE  
Sbjct: 598  MPESFNVLIKEIRSLGIDIDLETE 621


>gi|312794076|ref|YP_004026999.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181216|gb|ADQ41386.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 1230

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/959 (44%), Positives = 601/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   K + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLKEISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G+ +++ I   F          +
Sbjct: 164 IPNRGAWLEFETDASELLSVRLDRTRKVSLTTLLKAFGLYNQQLIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARNLLYNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+ +TGEI ++ G+VI  +    I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPKTGEILVKEGEVITREIALNIQDAGINEVWVYADEERTF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  +           +   ++    V + +           D+S + R+
Sbjct: 343 KVVGNNTVKLDRYVEFD------VSDLNIKELVYKPVLDDILKTTN------DVSEIKRL 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 IKEK----ERELVPYCLTIDDIYAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT++VVYL+A EE+   IAQA   +DE+G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATEPVDEEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D ID SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  EAP +G
Sbjct: 627 IIEVDKHEVDLIDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLTTEAPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE+V +  IVIR+ +G  D        Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVEKVSSDEIVIRNNDGTKDA-------YHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 164/538 (30%), Positives = 233/538 (43%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G ++    +           ++  I+  G EV  G+++    +      +   + +
Sbjct: 720  RNNDGTKDAYHLLKFKRTNQGTCFNQRPIVRKGQEVKAGEVIADGPST-DHGELALGKNV 778

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L            S  + +     R      E          E 
Sbjct: 779  LVAFMPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGED 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      +  +IL G+    G         L   +  E  R        
Sbjct: 839  AIKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+                  K+     GD++PPGV ++V+V+VA KR I  
Sbjct: 890  ---------ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                ++ V+       +++                G  V
Sbjct: 958  ---LPVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKV 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE I   L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 1007 ATPVFDGAKEEDIEEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YE+IV G +  E G PESF VLVKE+Q+L L + L +   K     E + +  + +
Sbjct: 1127 KTYEAIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDEDEQPQ 1184


>gi|210611077|ref|ZP_03288719.1| hypothetical protein CLONEX_00909 [Clostridium nexile DSM 1787]
 gi|210152173|gb|EEA83180.1| hypothetical protein CLONEX_00909 [Clostridium nexile DSM 1787]
          Length = 1313

 Score =  835 bits (2157), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/953 (45%), Positives = 595/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SY  FL          + GL+  F+ + PI+ +SG
Sbjct: 44  KSSRMSYARQKEVLQMPNLIEVQKDSYQWFL----------DAGLKEVFEDISPISDYSG 93

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 94  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLY---------NKETDEINEH 144

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 145 EIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKV---GKELYSSTVIPNR 201

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EIL  F    KI+ S   D  
Sbjct: 202 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNPEILELFGEEPKILASFGKDVA 261

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 262 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVGRYKFNKKLALQ-NRI 320

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+VN  TGE+  E G+ +  +    I ++ +  + I  VD    N  + + ++
Sbjct: 321 TGQVLAEDVVNAITGEVIAEKGEKLSREKATAIQNAAVPYVWI-DVDGEERNIKVLSNMM 379

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D       A++DI       D     V E+++  +     +     +  +K  +  N+ 
Sbjct: 380 VDLG-----AVVDI-------DPEEVGVTEAVYYPVLAGLLEETAGDIDELKEEIHKNIH 427

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 428 -ELIPKHITKEDILASINYNIHLEYGMGTDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 486

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ V PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 487 RVVRERMTTQDLEGVSPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 546

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 547 LGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLATYARINEYGFIEAPYR 606

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT++VVY++A EE+N ++AQAN  LDE+G F  + V  R   E     R
Sbjct: 607 KIDKADPKNPVVTDEVVYMTADEEDNYHVAQANEPLDEEGHFIHKNVAGRYREETQEYER 666

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              D++D SPK V S+A +LIPFLENDD  R LMG NMQRQAVPL+  EAP VGTG+E+ 
Sbjct: 667 TAFDYMDVSPKMVFSVATALIPFLENDDPTRALMGSNMQRQAVPLMMTEAPVVGTGIETT 726

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  IVA++AG++E+  +  IV++  +G           Y+L KF RSNQ+ C NQ
Sbjct: 727 AAVDSGVCIVAEQAGVIERSTSKEIVVKHDDGTK-------KTYKLTKFLRSNQSNCYNQ 779

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G++V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 780 RPIVVKGEKVEAGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 839

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIP V ++ LK++D+ GII +GAEV  GDILVGK+
Sbjct: 840 YTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDDRGIIRIGAEVRAGDILVGKV 899

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 900 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 952



 Score =  565 bits (1457), Expect = e-158,   Method: Composition-based stats.
 Identities = 267/1182 (22%), Positives = 441/1182 (37%), Gaps = 86/1182 (7%)

Query: 233  YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            Y K                     G  V      I+  E+VI S    + G+  ++    
Sbjct: 134  YNKETDEINEHEIFMGDLPLMTATGTFV------INGAERVIVSQLVRSPGIYYAIAHDK 187

Query: 293  VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            V     +S  +       +         Y+             I    I   P + ++  
Sbjct: 188  VGKELYSSTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNPEI-LELF 246

Query: 353  NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                 I  +   D  ++ ++ LL++Y+ +RPG+      AES+   +FFD+ +YDL+ VG
Sbjct: 247  GEEPKILASFGKDVAENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDARRYDLAKVG 306

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            R K N +L L      + + ++ + AI         G+   +  + L   +  ++     
Sbjct: 307  RYKFNKKLALQNRITGQVLAEDVVNAIT--------GEVIAEKGEKLSREKATAIQNAAV 358

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                + +   ER+IK   + +     +         V  AV     +  L +    ++ L
Sbjct: 359  PYVWIDVDGEERNIKVLSNMMVDLGAVVDIDPEEVGVTEAVYYPVLAGLLEETAGDIDEL 418

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTH-YGRICPAETSEGHNIGLVSSLTSFAR 591
                H      + +             ++H  +  G     +      I  V  L    +
Sbjct: 419  KEEIHKNIHELIPKHITKEDILASINYNIHLEYGMGTDDDIDHLGNRRIRAVGELL---Q 475

Query: 592  VNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED--- 637
                  +    R V +   T D           +  ++A  +E    +Q +  +D++   
Sbjct: 476  NQYRIGLSRLERVVRERMTTQDLEGVSPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 535

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G  T +          +   R   +  D        +     P   N      L      
Sbjct: 536  GELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLATYARI 595

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS----VEGDLD 753
             +   +            ++ V       + A          A   +        +    
Sbjct: 596  NEYGFIEAPYRKIDKADPKNPVVTDEVVYMTADEEDNYHVAQANEPLDEEGHFIHKNVAG 655

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                    Y    F   + +  +       +   +  +D       +++   A+   M  
Sbjct: 656  RYREETQEYERTAFDYMDVSPKMVFSVATALIPFLENDDPTRALMGSNMQRQAVPLMMTE 715

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G     ++     +V+E           E++ +    G ++  +    +     
Sbjct: 716  APVVGTGIETTAAVDSGVCIVAEQAGVIERSTSKEIVVKHD-DGTKKTYKLTKFLRSNQS 774

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+  G +V  G ++    +      M   +  L      +  +  D  L    
Sbjct: 775  NCYNQRPIVVKGEKVEAGQVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDAVLL--- 830

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDRNIY 983
                 V D    + H  +    +   +   E+I        +   +D DD   I+     
Sbjct: 831  -SERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDDR-GIIRIGAE 888

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             R  +IL G+    G         L   +  E  R                 E      +
Sbjct: 889  VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLK 931

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                        K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+
Sbjct: 932  VPHGEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRV 991

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     
Sbjct: 992  LPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANEI 1051

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            DI                 E    +  + +  V +                       + 
Sbjct: 1052 DIMDTLDLAND-YVNLEWEEFEKKHGAELLPEVLQYLSD-------------NREHRKLW 1097

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPL
Sbjct: 1098 KGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPL 1157

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G++  E G 
Sbjct: 1158 GGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGI 1217

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            PESF VL+KE+Q+LGL + +          ME I D+ + +L
Sbjct: 1218 PESFKVLLKELQSLGLDVRVLREDQTEVEIMETI-DYGETDL 1258


>gi|313891110|ref|ZP_07824729.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313120473|gb|EFR43593.1| DNA-directed RNA polymerase, beta subunit [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 1188

 Score =  835 bits (2156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 587/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DTGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKIGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQVIAENLVDSETGEILVEAGTEMTRDVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N  AY  N    D     +  +L  ++V+ P D                         
Sbjct: 332 --NKFAYTPN----DYAVVTEPVVLQKFKVVSPLDP------------------------ 361

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 362 --DKVVTIVGNASPDDRVRALTPADILAEMSYFLNLSEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV    G VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSKGVVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFAASTVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHDGKVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD + + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/508 (33%), Positives = 234/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  +  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIIEKGDFIADGPS-MENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGIVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  +  D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEDLWETVEEAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|146317779|ref|YP_001197491.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis
           05ZYH33]
 gi|146319971|ref|YP_001199682.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis
           98HAH33]
 gi|223933064|ref|ZP_03625057.1| DNA-directed RNA polymerase, beta subunit [Streptococcus suis
           89/1591]
 gi|253751036|ref|YP_003024177.1| DNA-directed RNA polymerase beta chain [Streptococcus suis SC84]
 gi|253752937|ref|YP_003026077.1| DNA-directed RNA polymerase beta chain [Streptococcus suis P1/7]
 gi|253754761|ref|YP_003027901.1| DNA-directed RNA polymerase beta chain [Streptococcus suis BM407]
 gi|158514126|sp|A4VSK2|RPOB_STRSY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158514143|sp|A4VYU3|RPOB_STRS2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|145688585|gb|ABP89091.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Streptococcus suis 05ZYH33]
 gi|145690777|gb|ABP91282.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Streptococcus suis 98HAH33]
 gi|223898251|gb|EEF64619.1| DNA-directed RNA polymerase, beta subunit [Streptococcus suis
           89/1591]
 gi|251815325|emb|CAZ50895.1| DNA-directed RNA polymerase beta chain [Streptococcus suis SC84]
 gi|251817225|emb|CAZ54951.1| DNA-directed RNA polymerase beta chain [Streptococcus suis BM407]
 gi|251819182|emb|CAR44349.1| DNA-directed RNA polymerase beta chain [Streptococcus suis P1/7]
 gi|292557579|gb|ADE30580.1| DNA-directed RNA polymerase, beta subunit [Streptococcus suis GZ1]
 gi|319757288|gb|ADV69230.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis JS14]
          Length = 1190

 Score =  835 bits (2156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/963 (43%), Positives = 586/963 (60%), Gaps = 81/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DYGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V P++ F+    LEFV YE   PK+ +++    D  Y+ P+ +T RL+          K
Sbjct: 51  DVLPVSNFTDTMELEFVGYELKEPKYTLEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGEFPIMTEMGTFIINGAERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    ES + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTAESSRSLLTARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE ++NGETGEI +EAG V+    LE++             D
Sbjct: 278 YKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTVLSRDVLEKVEAQ---------FD 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  LL  ++++ P D                         
Sbjct: 329 ELNLVEYIPN----DNAVLLEPVLLQKFKIVAPKDP------------------------ 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  ++VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 361 --ERVVTVIGNANPAENVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ R+GL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 419 LANQVRIGLTRMERNLRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 479 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 538

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRK+    G VTN++V+L+A EE+   +AQ+ S LDE+  F +++V  R
Sbjct: 539 HLNKYGFIQTPYRKIDRATGTVTNEIVWLTADEEDAYIVAQSTSPLDENNRFVDKIVMGR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +  DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 599 HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 659 PYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVEVRREDGSLD-------VYHISKFR 711

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK+GD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 712 RSNSGTAYNQRTLVKLGDIVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 771

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 772 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 831

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 832 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 891

Query: 949 GID 951
             D
Sbjct: 892 NGD 894



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 251/1096 (22%), Positives = 393/1096 (35%), Gaps = 177/1096 (16%)

Query: 332  SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 195  LVRALGFSGDDEIFDIFGDSELVRNTIEKDIHKNPADSRTDEALKEIYERLRPGEPKTAE 254

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA------------ 438
             + S+    FFD  +YDL+ VGR K+N +LNL T    + + +  I              
Sbjct: 255  SSRSLLTARFFDPRRYDLAPVGRYKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTV 314

Query: 439  -IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG----LLRMERSIKERISSV 493
                +L  +      ++ ++ + N     +  +L  ++++       R+   I     + 
Sbjct: 315  LSRDVLEKVEAQFDELNLVEYIPNDNAVLLEPVLLQKFKIVAPKDPERVVTVIGNANPAE 374

Query: 494  DIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++ +V P D    +     +   +        L                R      +  +
Sbjct: 375  NVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRIGLTRMERNL 434

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----- 604
                +  +   + P     I P   +     G         + N    +    R      
Sbjct: 435  RERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGP 494

Query: 605  -----------VCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAG 651
                       V D   T+          E   I   N  SS      +       R   
Sbjct: 495  GGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKID 554

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                    +I ++ A  +    +A S  P  EN+   R +    M R             
Sbjct: 555  RATGTVTNEIVWLTADEEDAYIVAQSTSPLDENN---RFVDKIVMGR------------- 598

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              G        S   +      +V    A    + + + +     + +            
Sbjct: 599  HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANM------------ 646

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                  QR        V   D  A    T +   A   +         G          E
Sbjct: 647  ------QR------QAVPLIDPKAPYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVE 694

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                +      HI +F    R +  G     R                 ++ +G  V  G
Sbjct: 695  VRREDGSLDVYHISKF----RRSNSGTAYNQRT----------------LVKLGDIVEKG 734

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D +    +      M   +  + A    +  +  D  +     V   V        +  +
Sbjct: 735  DFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLEEYESE 793

Query: 952  KNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
              +  +  E    +I  +  D     DE  I+      +  +IL G+    G K      
Sbjct: 794  TRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEE 853

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  +  R           +V+     +    +     +      KI     GD++
Sbjct: 854  RLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------KIFTRANGDEL 896

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLG
Sbjct: 897  QSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLG 956

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+                     
Sbjct: 957  VPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWSTVKEAGM------------ 1004

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                         +    ++L        G        TGEPFD
Sbjct: 1005 -----------------------------DSDAKTIL------YDG-------RTGEPFD 1022

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1023 NRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1082

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q+LGL + + + 
Sbjct: 1083 ASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDE 1142

Query: 1367 RTKNSAKMEEIPDFNK 1382
                    +     + 
Sbjct: 1143 DNNEVELRDLDEGEDD 1158


>gi|153952853|ref|YP_001393618.1| DNA-directed RNA polymerase subunit beta [Clostridium kluyveri DSM
           555]
 gi|219853518|ref|YP_002470640.1| hypothetical protein CKR_0175 [Clostridium kluyveri NBRC 12016]
 gi|189043853|sp|A5N4N9|RPOB_CLOK5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765284|sp|B9DYA1|RPOB_CLOK1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|146345734|gb|EDK32270.1| RpoB [Clostridium kluyveri DSM 555]
 gi|219567242|dbj|BAH05226.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 1234

 Score =  835 bits (2156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/955 (45%), Positives = 591/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F +  EI  +P+LIEVQ  SY+ FL           EGLQ  F+ + PI  ++ 
Sbjct: 9   KRTRMSFSRLKEIGHMPNLIEVQLDSYNWFL----------KEGLQEVFEDINPIQDYTA 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV Y+ D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLNLEFVGYKLDMDNIKYSVEECKERDSTYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDVSVDKT---GKNLFSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS +II+VRID+ RK+P+T  + A+G  ++ EI + F          +    
Sbjct: 167 GAWLEYETDSNNIIYVRIDKTRKLPITILVRAMGHGTDTEITNFFGEDERLKATIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S + L   L    K   +  +G         
Sbjct: 227 KTHEEALLEIYK------RLRPGEPPTVDSARSLIESLFFDPKRYDLSRVGRYKFNKKLS 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +       D+VN ETGEI ++ G+ ID +   +I    I  + I   D+       
Sbjct: 281 LHLRIVNQISTGDVVNPETGEILVQKGEKIDREKAVQIQQCGINSVDIEIEDTTLRVIGN 340

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
               + +      D L     V  P               L    D Y      R ++  
Sbjct: 341 NFVNINNFIDFNIDDLNIKESVYYPA--------------LKQILDNYSSEESIREQIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI ++DI A +   + L  G G  DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NIHNLIP---KHIIRDDIYATVSYELGLAYGVGHTDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFI 563

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV   +  VTN++VY++A EE+   I +AN  +DE+G F +  +  R   + I+V
Sbjct: 564 ETPYRKVNKKEKIVTNEIVYMTADEEDEYLIGRANEPIDENGKFVDSKITVRDKEDVIVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P E +D++D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 624 PAEDVDYMDLSPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPVVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    A+ AG+V  V A  I +R        S  G DIYRL+KFQRSNQ TC+
Sbjct: 684 YKAAVDSGVLPKARNAGVVSYVCANEIRVRRD------SDGGTDIYRLLKFQRSNQGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V+ G+ V++  ++ADGPSTDLG++ALG+N+ + F  W GYN+ED+MLISE +V +
Sbjct: 738 NQRPIVEKGEIVQQGTVLADGPSTDLGEIALGKNIRMGFTTWEGYNYEDAMLISEELVKK 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK+ID+ GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKDIDDRGIIKIGAEVRAGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRKNGD 912



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 188/572 (32%), Positives = 261/572 (45%), Gaps = 77/572 (13%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G  ++ ++       + +     ++   E+  R    G  +I R +        
Sbjct: 675  APVVGTGIEYKAAVDSGVLPKARNAGVVSYVCANEIRVRRDSDGGTDIYRLLKFQRSNQG 734

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGE-----SPMTPEEKLLRAIFGEKAVDVRDTS 928
              I++  I+  G  V  G +L    +           +            E A+ + +  
Sbjct: 735  TCINQRPIVEKGEIVQQGTVLADGPSTDLGEIALGKNIRMGFTTWEGYNYEDAMLISEEL 794

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            ++     S  + +     R      E          E   +D DD   I+      R  +
Sbjct: 795  VKKDVFTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKDIDDR-GIIKIGAEVRAGD 853

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                 E            
Sbjct: 854  ILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGE 896

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                   K+   + GD++ PGV ++V+ ++A KR I  GDKMAGRHGNKG++SR+LP ED
Sbjct: 897  AGIIVDVKVFTRKNGDELSPGVNKLVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEED 956

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPFL DG P++I LNPLGVPSRMN+GQ+ E HLGWA   LG  I + + D     DI   
Sbjct: 957  MPFLPDGRPLEICLNPLGVPSRMNIGQVLEVHLGWAASELGWHIATPVFDGATEEDIIEC 1016

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                        G  E+           
Sbjct: 1017 LKKA----------------------------------------GYRED----------- 1025

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G++ILYDG TGEPF+RPVTVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 1026 ---GKTILYDGRTGEPFNRPVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1082

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF 
Sbjct: 1083 FGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFK 1142

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            VL+KE+QAL L + + N   +     E + + 
Sbjct: 1143 VLIKELQALCLDVKVLNDDNQEIKLKESVDEE 1174


>gi|19745277|ref|NP_606413.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS8232]
 gi|94989594|ref|YP_597694.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS10270]
 gi|41018073|sp|Q8P2Y3|RPOB_STRP8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158564190|sp|Q1JJ23|RPOB_STRPD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|19747374|gb|AAL96912.1| putative DNA-dependent RNA polymerase subunit beta [Streptococcus
           pyogenes MGAS8232]
 gi|94543102|gb|ABF33150.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS10270]
          Length = 1188

 Score =  835 bits (2156), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 587/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGTVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ IR  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 178/590 (30%), Positives = 255/590 (43%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|158564250|sp|Q1JNX8|RPOB_STRPC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1197

 Score =  834 bits (2155), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ IR  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 166/599 (27%), Positives = 249/599 (41%), Gaps = 89/599 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILP---------CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            RHGNKG+VSRI+P          EDMP+L      D                        
Sbjct: 924  RHGNKGVVSRIVPKGVVSRIVPVEDMPYL-----PD------------------------ 954

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                 G  +  ++N       ++                  I    +  +   A     G
Sbjct: 955  -----GTPVDIMLNPLGVPSRMN------------------IGQVMELHLGMAARNL--G 989

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            + ++TPVFDGA  E +   +R A +D   +++LYDG TGEPFD  V+VG +YM+KL+HMV
Sbjct: 990  IHIATPVFDGASSEDLWDTVREAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMV 1049

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV 
Sbjct: 1050 DDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVT 1109

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            GR + YE+I  G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 GRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1168


>gi|330831972|ref|YP_004400797.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis ST3]
 gi|329306195|gb|AEB80611.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis ST3]
          Length = 1190

 Score =  834 bits (2155), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/963 (43%), Positives = 586/963 (60%), Gaps = 81/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DYGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V P++ F+    LEFV YE   PK+ +++    D  Y+ P+ +T RL+          K
Sbjct: 51  DVLPVSNFTDTMELEFVGYELKEPKYTLEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGEFPIMTEMGTFIINGAERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    ES + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTAESSRSLLTARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE ++NGETGEI +EAG V+    LE++             D
Sbjct: 278 YKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTVLSRDVLEKVEAQ---------FD 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  LL  ++++ P D                         
Sbjct: 329 ELNLVEYIPN----DNAVLLEPVLLQKFKIVAPKDP------------------------ 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  ++VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 361 --ERVVTVIGNANPAENVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ R+GL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 419 LANQVRIGLTRMERNLRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 479 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 538

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRK+    G VTN++V+L+A EE+   +AQ+ S LDE+  F +++V  R
Sbjct: 539 HLNKYGFIQTPYRKIDRATGTVTNEIVWLTADEEDAYIVAQSTSPLDENNRFVDKIVMGR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +  DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 599 HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 659 PYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVEVRREDGSLD-------VYHISKFR 711

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK+GD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 712 RSNSGTAYNQRTLVKLGDIVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 771

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 772 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 831

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 832 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 891

Query: 949 GID 951
             D
Sbjct: 892 NGD 894



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 251/1096 (22%), Positives = 393/1096 (35%), Gaps = 177/1096 (16%)

Query: 332  SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 195  LVRALGFSGDDEIFDIFGDSELVRNTIEKDIHKNPADSRTDEALKEIYERLRPGEPKTAE 254

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA------------ 438
             + S+    FFD  +YDL+ VGR K+N +LNL T    + + +  I              
Sbjct: 255  SSRSLLTARFFDPRRYDLAPVGRYKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTV 314

Query: 439  -IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG----LLRMERSIKERISSV 493
                +L  +      ++ ++ + N     +  +L  ++++       R+   I     + 
Sbjct: 315  LSRDVLEKVEAQFDELNLVEYIPNDNAVLLEPVLLQKFKIVAPKDPERVVTVIGNANPAE 374

Query: 494  DIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++ +V P D    +     +   +        L                R      +  +
Sbjct: 375  NVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRIGLTRMERNL 434

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----- 604
                +  +   + P     I P   +     G         + N    +    R      
Sbjct: 435  RERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGP 494

Query: 605  -----------VCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAG 651
                       V D   T+          E   I   N  SS      +       R   
Sbjct: 495  GGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKID 554

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                    +I ++ A  +    +A S  P  EN+   R +    M R             
Sbjct: 555  RATGTVTNEIVWLTADEEDAYIVAQSTSPLDENN---RFVDKIVMGR------------- 598

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              G        S   +      +V    A    + + + +     + +            
Sbjct: 599  HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANM------------ 646

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                  QR        V   D  A    T +   A   +         G          E
Sbjct: 647  ------QR------QAVPLIDPKAPYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVE 694

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                +      HI +F    R +  G     R                 ++ +G  V  G
Sbjct: 695  VRREDGSLDVYHISKF----RRSNSGTAYNQRT----------------LVKLGDIVEKG 734

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D +    +      M   +  + A    +  +  D  +     V   V        +  +
Sbjct: 735  DFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLEEYESE 793

Query: 952  KNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
              +  +  E    +I  +  D     DE  I+      +  +IL G+    G K      
Sbjct: 794  TRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEE 853

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  +  R           +V+     +    +     +      KI     GD++
Sbjct: 854  RLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------KIFTRANGDEL 896

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLG
Sbjct: 897  QSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLG 956

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+                     
Sbjct: 957  VPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWSTVKEAGM------------ 1004

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                         +    ++L        G        TGEPFD
Sbjct: 1005 -----------------------------DSDAKTIL------YDG-------RTGEPFD 1022

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1023 NRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1082

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q+LGL + + + 
Sbjct: 1083 ASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDE 1142

Query: 1367 RTKNSAKMEEIPDFNK 1382
                    +     + 
Sbjct: 1143 DNNEVELRDLDEGEDD 1158


>gi|21909611|ref|NP_663879.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS315]
 gi|28894988|ref|NP_801338.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           SSI-1]
 gi|50913477|ref|YP_059449.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS10394]
 gi|56808832|ref|ZP_00366545.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Streptococcus pyogenes M49 591]
 gi|71902747|ref|YP_279550.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS6180]
 gi|94991583|ref|YP_599682.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS2096]
 gi|94993486|ref|YP_601584.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS10750]
 gi|139472961|ref|YP_001127676.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           str. Manfredo]
 gi|209558663|ref|YP_002285135.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           NZ131]
 gi|306828222|ref|ZP_07461483.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           ATCC 10782]
 gi|41018064|sp|Q8K8W3|RPOB_STRP3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|73917874|sp|Q5XE97|RPOB_STRP6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|88909643|sp|Q48VR1|RPOB_STRPM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158512770|sp|A2RC51|RPOB_STRPG RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158564171|sp|Q1J8X1|RPOB_STRPF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158564180|sp|Q1JE20|RPOB_STRPB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|226699454|sp|B5XJ72|RPOB_STRPZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|21903792|gb|AAM78682.1| putative DNA-dependent RNA polymerase subunit beta [Streptococcus
           pyogenes MGAS315]
 gi|28810233|dbj|BAC63171.1| putative DNA-dependent RNA polymerase subunit beta [Streptococcus
           pyogenes SSI-1]
 gi|50902551|gb|AAT86266.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS10394]
 gi|71801842|gb|AAX71195.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS6180]
 gi|94545091|gb|ABF35138.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS2096]
 gi|94546994|gb|ABF37040.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS10750]
 gi|134271207|emb|CAM29423.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes str.
           Manfredo]
 gi|209539864|gb|ACI60440.1| DNA-directed RNA polymerase beta subunit [Streptococcus pyogenes
           NZ131]
 gi|304429600|gb|EFM32648.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           ATCC 10782]
          Length = 1188

 Score =  834 bits (2155), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ IR  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 178/590 (30%), Positives = 255/590 (43%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEIRRQDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|323126355|gb|ADX23652.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 1188

 Score =  834 bits (2155), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 177/590 (30%), Positives = 253/590 (42%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLINPKAPFVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKD 972
             +  +  D  +     V   V           +  +  +  E          E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|270293428|ref|ZP_06199637.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. M143]
 gi|270278277|gb|EFA24125.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. M143]
          Length = 1203

 Score =  834 bits (2154), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYGGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 175/507 (34%), Positives = 245/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDLVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR R YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLRAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|325261309|ref|ZP_08128047.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. D5]
 gi|324032763|gb|EGB94040.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. D5]
          Length = 1291

 Score =  834 bits (2154), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/953 (45%), Positives = 593/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++++P+LIEVQK SY  FL          +EG++  F  + PI+ FSG
Sbjct: 19  KSSRMSYSRQKEVLEMPNLIEVQKDSYQWFL----------DEGMKEVFADISPISDFSG 68

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL   D D         +I E 
Sbjct: 69  HLSLEFVDFTLCEDDVKYTIEECKERDATYAAPLKVRVRLYNKDND---------EINEH 119

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 120 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKELYSATVIPNR 176

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 177 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASFGKDTA 236

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S    +    L K  + K  K L +  + +
Sbjct: 237 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDSRRYDLAKVGRYKFNKKLAL-KNRI 295

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  VAED+V+  TGEI  E G VI     + I ++    +P L+V+    +   RN  +
Sbjct: 296 KGQRVAEDVVSPLTGEIVAEKGTVISRDLADTIQNA---AVPYLWVEGEEES---RNIKI 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                    A++DI       D     V E ++  +     +     +  +K  +R +L 
Sbjct: 350 LSNMMVDLQAVVDI-------DPKEVGVTEQVYYPVLEGLLEETGGDIEELKDLIRRDLH 402

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 403 -DLIPKHITKEDILASINYNIHLEYRMGNEDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 461

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D + + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 462 RVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 521

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR
Sbjct: 522 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYR 581

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +VVY++A EE+N ++AQAN  LD++G F    V  R   E     R
Sbjct: 582 KIDKENPENPIVTEEVVYMTADEEDNYHVAQANEPLDDEGHFIHRNVSGRYREETQEYER 641

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K DF+D SPK V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 642 SKFDFMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 701

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  IVA++AG++E+  +  I I+  +G           Y+L KF RSNQ+ C NQ
Sbjct: 702 AAVDSGVCIVAEKAGVIERSTSTDITIKHDDGTK-------KTYKLTKFLRSNQSNCYNQ 754

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V    +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 755 RPIVDKGERVEEGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 814

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 815 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 874

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 875 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 927



 Score =  548 bits (1411), Expect = e-153,   Method: Composition-based stats.
 Identities = 246/1066 (23%), Positives = 409/1066 (38%), Gaps = 79/1066 (7%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D       I  +   D  ++ ++ LL++Y+ +RPG+      AES+   +FFDS +YDL
Sbjct: 218  IDLFGEEPKILASFGKDTAENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDSRRYDL 277

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L      + + ++ +  +   +V  +    + D  D + N  V    
Sbjct: 278  AKVGRYKFNKKLALKNRIKGQRVAEDVVSPLTGEIVAEKGTVISRDLADTIQNAAV---- 333

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                    +      R+IK   + +     +         V   V        L +    
Sbjct: 334  ----PYLWVEGEEESRNIKILSNMMVDLQAVVDIDPKEVGVTEQVYYPVLEGLLEETGGD 389

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVE-MRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +  L  +   R L  L    + +         ++H  +  R+   +  +      + ++ 
Sbjct: 390  IEELKDLI-RRDLHDLIPKHITKEDILASINYNIHLEY--RMGNEDDIDHLGNRRIRAVG 446

Query: 588  SFARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDE 636
               +      +    R V +   T D           +  ++A  +E    +Q +  +D+
Sbjct: 447  ELLQNQYRIGLSRLERVVRERMTTQDQEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQ 506

Query: 637  D---GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +   G  T +          +   R   +  D        +     P   N      L  
Sbjct: 507  NNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLAT 566

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE---- 749
                 +   +            E+ +       + A          A   +         
Sbjct: 567  YARINEYGFIEAPYRKIDKENPENPIVTEEVVYMTADEEDNYHVAQANEPLDDEGHFIHR 626

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                        Y   KF   + +  +       +   +  +D       +++   A+  
Sbjct: 627  NVSGRYREETQEYERSKFDFMDVSPKMVFSVATALIPFLENDDANRALMGSNMQRQAVPL 686

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
                A +   G   + ++     +V+E     I       +      G ++  +    + 
Sbjct: 687  LTTEAPVVGTGMEVKAAVDSGVCIVAEKAGV-IERSTSTDITIKHDDGTKKTYKLTKFLR 745

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                   ++  I+  G  V  G ++    +      M   +  L      +  +  D  L
Sbjct: 746  SNQSNCYNQRPIVDKGERVEEGQVIADGPSTSN-GEMALGKNPLIGFMTWEGYNYEDAVL 804

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILD 979
                     V D    + H  +    +   +   E+I        +   +D  DE+ I+ 
Sbjct: 805  L----SERLVQDDVYTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDL-DERGIIR 859

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 R  +IL G+    G         L   +  E  R                 E   
Sbjct: 860  IGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRD 902

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
               +            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+
Sbjct: 903  TSLKVPHGEYGIIVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGV 962

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSR+LP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D 
Sbjct: 963  VSRVLPAEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNISTPVFDG 1022

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                DI          +            ++     +     +                 
Sbjct: 1023 ANEIDIMDTLDLANDYVNLEWEEFVKKHGEELLPEVLEYLLAN--------------REH 1068

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              + +   L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVT
Sbjct: 1069 RKLWKGVPLTRDGKVRLRDGRTGEFFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVT 1128

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  
Sbjct: 1129 QQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIP 1188

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            E G PESF VL+KE+Q+L L + +          ME + D+ + +L
Sbjct: 1189 EPGIPESFKVLLKELQSLALDVRVLRDDNTEVEIMETV-DYGETDL 1233


>gi|312876381|ref|ZP_07736366.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796875|gb|EFR13219.1| DNA-directed RNA polymerase, beta subunit [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 1230

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/959 (44%), Positives = 602/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   K + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLKEISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYSETLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  +
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTL 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G+ +++ I   F          +
Sbjct: 164 IPNRGAWLEFETDASELLSVRLDRTRKVSLTTLLKAFGLYNQQLIFEKFGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ + L   +    +   +  +G     
Sbjct: 224 KEANKGELGNPVENA-LLEVYRRLRPGEPPNVENARSLLYNMFFDPRRYDLAKVGRYKFN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     A+D+V+  TGEI ++ G+VI  +    I  + I ++ +   +    
Sbjct: 283 KKLSLWKRIFNKRAAQDVVDPMTGEILVKEGEVITREIALNIQDAGINEVWVYADEERPF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  +   + L+I  ++    +       +            D+S + R+
Sbjct: 343 KVVGNNTVKLDRYVEFDVSDLNIKELVYKPVLDDILKITN------------DVSEIKRL 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       +  +DI A     + L+ G GT DDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 IKEK----ERELVPYCLTIDDIYAATSYFLGLKYGIGTTDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DID+V PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMNIHDIDTVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT++VVYL+A EE+   IAQA   +D +G F  + V  R   E
Sbjct: 567 YGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATEPVDVEGRFINQRVTVRFGEE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D +D SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  EAP +G
Sbjct: 627 IIEVDKHEVDLVDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLTTEAPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  I+AK+ G+VE+V A  IVIR+ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCILAKKDGVVEKVSADEIVIRNNDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKAGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  444 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 165/538 (30%), Positives = 234/538 (43%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +++   +           ++  I+  G EV  G+++    +      +   + +
Sbjct: 720  RNNDGTKDVYHLLKFKRTNQGTCFNQRPIVRKGQEVKAGEVIADGPST-DHGELALGKNV 778

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L            S  + +     R      E          E 
Sbjct: 779  LVAFMPWEGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNVGED 838

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      +  +IL G+    G         L   +  E  R        
Sbjct: 839  AIKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 889

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+                  K+     GD++PPGV ++V+V+VA KR I  
Sbjct: 890  ---------ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                ++ V+       +++                G  V
Sbjct: 958  ---LPVEDMPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKV 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TPVFDGA EE I   L++A L+ +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK
Sbjct: 1007 ATPVFDGAKEEDIEEALKLAGLNPTGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW I+AYGAAY LQE+LT+KSDDV GR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAIEAYGAAYTLQELLTVKSDDVTGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YE+IV G +  E G PESF VLVKE+Q+L L + L +   K     E + +  + +
Sbjct: 1127 KTYEAIVKGENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESVDEDEQPQ 1184


>gi|302023207|ref|ZP_07248418.1| DNA-directed RNA polymerase subunit beta [Streptococcus suis
           05HAS68]
          Length = 1190

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/963 (43%), Positives = 586/963 (60%), Gaps = 81/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+L+E+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLVEIQTDSFQDFL----------DYGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V P++ F+    LEFV YE   PK+ +++    D  Y+ P+ +T RL+          K
Sbjct: 51  DVLPVSNFTDTMELEFVGYELKEPKYTLEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGEFPIMTEMGTFIINGAERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD      +      +  GE    ES + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNPADSRTDEALKEIYERLRPGEPKTAESSRSLLTARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE ++NGETGEI +EAG V+    LE++             D
Sbjct: 278 YKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTVLSRDVLEKVEAQ---------FD 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  LL  ++++ P D                         
Sbjct: 329 ELNLVEYIPN----DNAVLLEPVLLQKFKIVAPKDP------------------------ 360

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  ++VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 361 --ERVVTVIGNANPAENVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 418

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ R+GL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 419 LANQVRIGLTRMERNLRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 478

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 479 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 538

Query: 591 RVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRK+    G VTN++V+L+A EE+   +AQ+ S LDE+  F +++V  R
Sbjct: 539 HLNKYGFIQTPYRKIDRATGTVTNEIVWLTADEEDAYIVAQSTSPLDENNRFVDKIVMGR 598

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +  DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 599 HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 658

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 659 PYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVEVRREDGSLD-------VYHISKFR 711

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK+GD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 712 RSNSGTAYNQRTLVKLGDIVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 771

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV
Sbjct: 772 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEV 831

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 832 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 891

Query: 949 GID 951
             D
Sbjct: 892 NGD 894



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 251/1096 (22%), Positives = 392/1096 (35%), Gaps = 177/1096 (16%)

Query: 332  SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 195  LVRALGFSGDDEIFDIFGDSELVRNTIEKDIHKNPADSRTDEALKEIYERLRPGEPKTAE 254

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA------------ 438
             + S+    FFD  +YDL+ VGR K+N +LNL T    + + +  I              
Sbjct: 255  SSRSLLTARFFDPRRYDLAPVGRYKINKKLNLRTRLLNQTLAEHVINGETGEIVLEAGTV 314

Query: 439  -IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG----LLRMERSIKERISSV 493
                +L  +      ++ ++ + N     +  +L  ++++       R+   I     + 
Sbjct: 315  LSRDVLEKVEAQFDELNLVEYIPNDNAVLLEPVLLQKFKIVAPKDPERVVTVIGNANPAE 374

Query: 494  DIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++ +V P D    +     +   +        L                R      +  +
Sbjct: 375  NVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRIGLTRMERNL 434

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----- 604
                +  +   + P     I P   +     G         + N    +    R      
Sbjct: 435  RERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGP 494

Query: 605  -----------VCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAG 651
                       V D   T+          E   I   N  SS      +       R   
Sbjct: 495  GGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKID 554

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                    +I ++ A  +    +A S  P  EN+   R +    M R             
Sbjct: 555  RATGTVTNEIVWLTADEEDAYIVAQSTSPLDENN---RFVDKIVMGR------------- 598

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              G        S   +      +V    A    + + + +     + +            
Sbjct: 599  HQGNNQEFPADSADFMDVSPKQVVAVATACIPFLENDDSNRALMGANM------------ 646

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                  QR        V   D  A    T +   A   +         G          E
Sbjct: 647  ------QR------QAVPLIDPKAPYVGTGMEYQAAHDSGAAIIAQHDGKVVYADADKVE 694

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                +      HI +F    R +  G     R                 ++ +G  V  G
Sbjct: 695  VRREDGSLDVYHISKF----RRSNSGTAYNQRT----------------LVKLGDIVEKG 734

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D +    +      M   +  + A    +  +  D  +     V   V        +  +
Sbjct: 735  DFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLEEYESE 793

Query: 952  KNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
              +  +  E    +I  +  D     DE  I+      +  +IL G+    G K      
Sbjct: 794  TRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEE 853

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  +  R           +V+     +    +     +      KI     GD++
Sbjct: 854  RLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------KIFTRANGDEL 896

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              GV   V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLG
Sbjct: 897  QSGVNMFVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLG 956

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+                     
Sbjct: 957  VPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWSTVKEAGM------------ 1004

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                         +    ++L        G        TGEPFD
Sbjct: 1005 -----------------------------DSDAKTIL------YDG-------RTGEPFD 1022

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1023 NRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1082

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q+LGL + + + 
Sbjct: 1083 ASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDE 1142

Query: 1367 RTKNSAKMEEIPDFNK 1382
                    +     + 
Sbjct: 1143 DNNEVELRDLDEGEDD 1158


>gi|251781562|ref|YP_002995863.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390190|dbj|BAH80649.1| DNA-directed RNA polymerase beta subunit [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 1188

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 177/590 (30%), Positives = 253/590 (42%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKD 972
             +  +  D  +     V   V           +  +  +  E          E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|160881805|ref|YP_001560773.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           phytofermentans ISDg]
 gi|160430471|gb|ABX44034.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           phytofermentans ISDg]
          Length = 1278

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 590/953 (61%), Gaps = 57/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + K  E++++P+LIEVQK SY  FL           EGL   F  + PI  +S 
Sbjct: 13  KGVRMSYSKQKEVLEMPNLIEVQKDSYQWFL----------EEGLNEVFDDISPIEDYSD 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFVS++   D  K+ +++C  RD TYA PLK+ +RL           K  ++I E 
Sbjct: 63  HLSLEFVSFQLCEDDVKYSIEECKERDATYAAPLKVKVRL---------RNKETEEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK L++  +IP++
Sbjct: 114 DIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAIQHDKV---GKTLHSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  L A+G+ S  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRNRKVPITVLLRAMGIGSNAEIVEMFGEEPKILASFSKDPS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +++ E +I S         L K  + K  K L +  + +
Sbjct: 231 DNYQDGLLELYKKLRPGEPLSVESAESLINSMFFDPRRYDLAKVGRFKFNKKLAL-KNRV 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+ ETGEI  EAG +I E     I +  ++ I  L      N   + N +V
Sbjct: 290 LGFPLAEDVVDTETGEILAEAGTIITEALAIRIQNRAVKSI--LVQAEERNVVVLSNMMV 347

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +     D   +    +   +   +     + +      +  D        +   +   
Sbjct: 348 DFEEYATLDCDKE---ELGITEEVYYPALRMILDSCSSQEEIKD-------AVAKHITDL 397

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   +HI K+DI A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 398 IP---KHITKDDIYASINYNMHLEYGIGNEDDIDHLGNRRIRAVGELLQNQYRIGLSRME 454

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 455 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 514

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGFIE PYR
Sbjct: 515 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINQYGFIEAPYR 574

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           KV      + +VT +VVYL+A EE+   +AQAN  LDE G F  + V  R   E     +
Sbjct: 575 KVDRTDPENPRVTEEVVYLTADEEDKYVVAQANEPLDETGYFVNQSVSGRYREETSSYQK 634

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K+D +D SPK V S+A ++IPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 635 RKVDLMDVSPKMVFSVATAMIPFLQNDDANRALMGSNMQRQAVPLLFTEAPVVGTGMELK 694

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +V+K+AG VE+  +  ++I++ +G           YRL+KF RSNQ TC+NQ
Sbjct: 695 TAVDSGVCVVSKKAGTVEKSTSREVIIKNDDGTKSS-------YRLVKFARSNQGTCINQ 747

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD+V   ++IADGPST  G+LALG++ L+ FM W GYN+ED++L+SER+V EDV
Sbjct: 748 RPIVVKGDKVEAGEVIADGPSTANGELALGKSPLIGFMTWEGYNYEDAVLLSERLVQEDV 807

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 808 YTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 867

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G +VD ++F R   D
Sbjct: 868 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGIIVDAKVFTRENGD 920



 Score =  550 bits (1416), Expect = e-153,   Method: Composition-based stats.
 Identities = 258/1176 (21%), Positives = 422/1176 (35%), Gaps = 73/1176 (6%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +              +     +    I+  E+VI S    + G+  +++   V 
Sbjct: 99   KVRLRNKETEEINEHDIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAIQHDKVG 158

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                +S  +     A      ++ +++    D   +  +  +  +         V+    
Sbjct: 159  KTLHSSTVIPNRG-AWLEYETDSNDVFYVRVDRNRKVPITVLLRAMGIGSNAEIVEMFGE 217

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               I  +   D + + +D LL++Y+ +RPG+  +   AES+ N +FFD  +YDL+ VGR 
Sbjct: 218  EPKILASFSKDPSDNYQDGLLELYKKLRPGEPLSVESAESLINSMFFDPRRYDLAKVGRF 277

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L L      R +       ++         +      + L  R      + +  Q
Sbjct: 278  KFNKKLAL----KNRVLGFPLAEDVVDTETGEILAEAGTIITEALAIRIQNRAVKSILVQ 333

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                 +     +      VD +     D    +     + E      L  + +  +S   
Sbjct: 334  AEERNV-----VVLSNMMVDFEEYATLDCDKEEL---GITEEVYYPALRMILDSCSSQEE 385

Query: 535  ITHT--RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            I     + ++ L    + +      +       YG     +     N   + ++    + 
Sbjct: 386  IKDAVAKHITDLIPKHITKDDIYASINYNMHLEYGIGNEDDIDHLGN-RRIRAVGELLQN 444

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTE 642
                 +    R V +   T D+  +S     N     A               +  +   
Sbjct: 445  QYRIGLSRMERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLG 504

Query: 643  ELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            EL   R             R   +  D        +     P   N      L       
Sbjct: 505  ELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARIN 564

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            Q   +         T  E+         + A          A   +  +        +  
Sbjct: 565  QYGFIEAPYRKVDRTDPENPRVTEEVVYLTADEEDKYVVAQANEPLDETGYFVNQSVSGR 624

Query: 759  VDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                     +R      V+ + +  V         +  A+              +L    
Sbjct: 625  YREETSSYQKRKVDLMDVSPKMVFSVATAMIPFLQNDDANRALMGSNMQRQAVPLLFTEA 684

Query: 817  PWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E    +     V      ++       +      G +   R +          
Sbjct: 685  PVVGTGMELKTAVDSGVCVVSKKAGTVEKSTSREVIIKNDDGTKSSYRLVKFARSNQGTC 744

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            I++  I+  G +V  G+++    +      +   +  L      +  +  D  L     V
Sbjct: 745  INQRPIVVKGDKVEAGEVIADGPSTAN-GELALGKSPLIGFMTWEGYNYEDAVLLSERLV 803

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEI 989
               V        +  +  +  +  E    +         +D  DE+ I+      R  +I
Sbjct: 804  QEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEVRAGDI 862

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                 E             
Sbjct: 863  LVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEY 905

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                  K+   + GD++ PGV + V+V++A KR IQ GDKMAGRHGNKG+VSR+LP EDM
Sbjct: 906  GIIVDAKVFTRENGDELSPGVNQTVRVYIAQKRKIQVGDKMAGRHGNKGVVSRVLPAEDM 965

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + D     DI    
Sbjct: 966  PFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLASRVLGFNVSTPVFDGANEYDIMDTL 1025

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                  +       +    D      +                    E          ++
Sbjct: 1026 ELANDYVNAPLDKFEAKYKDILDPEVMDYL--------------VSNEDYRKQWEGVPIN 1071

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G+  L DG TGE FD  VTVG+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 1072 RDGKVRLRDGRTGEYFDSAVTVGFMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQF 1131

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA++LQE+LT+KSDDV GR + YE+I+ G++  E G PESF V
Sbjct: 1132 GGQRFGEMEVWALEAYGAAHILQEILTVKSDDVTGRVKTYEAIIKGDNISEPGIPESFKV 1191

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            L+KE+Q+L L + + +         E I D+ + E 
Sbjct: 1192 LLKELQSLALDVTVLDENGDEVKMTENI-DYGETEF 1226


>gi|15674321|ref|NP_268495.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes M1
           GAS]
 gi|71909897|ref|YP_281447.1| DNA-directed RNA polymerase subunit beta [Streptococcus pyogenes
           MGAS5005]
 gi|41018125|sp|Q9A1U1|RPOB_STRP1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|13621404|gb|AAK33216.1| putative DNA-dependent RNA polymerase subunit beta [Streptococcus
           pyogenes M1 GAS]
 gi|71852679|gb|AAZ50702.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
           MGAS5005]
          Length = 1188

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGTVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A++ G V   DA ++ IR  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQQNGKVVFSDAEKVEIRRQDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 178/590 (30%), Positives = 255/590 (43%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQQNGKVVFSDAEKVEIRRQDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|306825906|ref|ZP_07459245.1| DNA-directed RNA polymerase subunit beta [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304432267|gb|EFM35244.1| DNA-directed RNA polymerase subunit beta [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 1223

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 21  LAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 70

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 71  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 121

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 122 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 178

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 179 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 238

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 239 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 297

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E I      D+      
Sbjct: 298 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIESIESYLDGDL------ 351

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 352 --NKIVYIPN----DAAVLTEPVVLQKFKVVAPMDPDRV--------------------- 384

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 385 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 439

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 440 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 499

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 500 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 559

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 560 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 619

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 620 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 679

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 680 PYVGTGMEYQAAHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 732

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 733 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 792

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LKN+DE GII +GAEV
Sbjct: 793 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEV 852

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 853 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 912

Query: 949 GID 951
             D
Sbjct: 913 NGD 915



 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 175/507 (34%), Positives = 245/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 745  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 803

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 804  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVKEGDILVGKVT 863

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 864  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 906

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 907  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 966

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 967  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 1017

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 1018 ------------------------------------DTVKE---------AGMDSDAKTI 1032

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1033 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1092

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR R YE+I  G    + G PESF VLVKE+Q
Sbjct: 1093 EMEVWALEAYGASNVLQEILTYKSDDINGRLRAYEAITKGKPIPKPGVPESFRVLVKELQ 1152

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1153 SLGLDMRVLDEDDQEVELRDLDEGMDE 1179


>gi|307709965|ref|ZP_07646412.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK564]
 gi|307619336|gb|EFN98465.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK564]
          Length = 1203

 Score =  833 bits (2153), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIESIESYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 332 --NKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1226), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|293375382|ref|ZP_06621663.1| DNA-directed RNA polymerase, beta subunit [Turicibacter sanguinis
           PC909]
 gi|325844451|ref|ZP_08168178.1| DNA-directed RNA polymerase, beta subunit [Turicibacter sp. HGF1]
 gi|292645935|gb|EFF63964.1| DNA-directed RNA polymerase, beta subunit [Turicibacter sanguinis
           PC909]
 gi|325489125|gb|EGC91509.1| DNA-directed RNA polymerase, beta subunit [Turicibacter sp. HGF1]
          Length = 1177

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/966 (44%), Positives = 595/966 (61%), Gaps = 78/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +    +++P+LIE+Q ASY  FL          ++G++  FK
Sbjct: 1   MAGKIVQYGKKRQRRNYSRINVALELPNLIEIQTASYQWFL----------DQGIREMFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI   +G   LEFV Y    PK+ V +   RD  YA PL++ +RL + D +     +
Sbjct: 51  DISPIEDNNGNLALEFVDYNLGEPKYTVLEAKERDANYAAPLRVKVRLHIKDEE----TQ 106

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           +IK++KE  +YMGD PLMT  GTFVI G +R++VSQL RS G++++ +  +   SGK  Y
Sbjct: 107 AIKEVKESEVYMGDFPLMTPTGTFVINGSERVIVSQLVRSSGVYYNKETDKK--SGKEKY 164

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPK--IV 237
           A ++IP++G W++ E D+KDI++VR+DR RK+P+T  L ALG+ + E+I+  F     I+
Sbjct: 165 AAQVIPNRGAWLEYELDAKDIVYVRVDRTRKIPITVLLRALGLSTKEQIIEMFGENAYIL 224

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +           ID    +  S         L    + K  K 
Sbjct: 225 NTLEKDQTVNSDEALMEIFQKLRQGEHATIDGARTLFVSRFFDPKRYDLAHVGRYKFNKK 284

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L    + L    +A DI + ETGE+ +E G VI  +  E++   +I  + I  V+ VN  
Sbjct: 285 LS-AQERLLNQKLASDIFDSETGEVLVEEGTVITRRIFEDVLADKIDRLNIKKVELVN-- 341

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  + ++    ++  +   RV     V                             
Sbjct: 342 ------PLEERETYVQEFEVYSPRVNEGDQVV---------------------------- 367

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
              R+  +  D+ +HI   DI A I    +L +  G +DDID+LGNRR+R VGE+L+NQ+
Sbjct: 368 ---RIIGNVEDECKHITTSDIFASISYFFNLLDSVGYLDDIDHLGNRRLRLVGELLQNQF 424

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER +KER+S  + + + P  LIN +PV +A+ EFF SSQLSQ  +  N LS +
Sbjct: 425 RIGLSRMERVVKERMSIQETEGITPSSLINIRPVTAAIKEFFGSSQLSQFMDQTNPLSEL 484

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+VN +
Sbjct: 485 THKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKF 544

Query: 596 GFIETPYRKVC----------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           GFIETPYRKV              VT+++ YL+A EE+   +AQA   LDE G+   E V
Sbjct: 545 GFIETPYRKVVPVIDEETKQPKMHVTDEIRYLTADEEDRYVVAQAGLDLDEKGN-LPEKV 603

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE ++VP E++DF+D SPKQ+VS+A + IPFLE+DD+NR LMG NMQRQA+PLL 
Sbjct: 604 IVRHRGENLIVPAERVDFVDVSPKQIVSVATACIPFLEHDDANRALMGANMQRQAIPLLI 663

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            EAPFVGTGME V AK SG A+VA  +G VE VD+  I +R        +   +D Y L+
Sbjct: 664 PEAPFVGTGMEYVAAKDSGQAVVAYNSGTVEYVDSKVIKLRRD------ADGQIDKYPLI 717

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN +T +NQRP+VK+GD +   +++AD  S + G+LALGRN++VAFM W+GYN+ED
Sbjct: 718 KFVRSNSSTVLNQRPIVKLGDHINAGEVLADSSSMESGELALGRNVVVAFMTWNGYNYED 777

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE+E+ ARDTKLGPEEITRDIP V E+ LKN+D+ GII +G
Sbjct: 778 AIIMSERLVKDDVYTSIHIEEYELEARDTKLGPEEITRDIPGVGEDALKNLDDRGIIRIG 837

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV   DILVGK+T KG++ +T EE+LL AIFGEKA +VRDTSLRVP G  G V DV+ F
Sbjct: 838 AEVKEDDILVGKVTAKGQTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIVHDVKYF 897

Query: 946 NRHGID 951
           +R   D
Sbjct: 898 SRRNGD 903



 Score =  508 bits (1307), Expect = e-141,   Method: Composition-based stats.
 Identities = 238/1083 (21%), Positives = 421/1083 (38%), Gaps = 126/1083 (11%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            +  +I     D   +  +  +  +         ++    NAYI NTL  D+  +  +AL+
Sbjct: 181  DAKDIVYVRVDRTRKIPITVLLRALGLSTKEQIIEMFGENAYILNTLEKDQTVNSDEALM 240

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT----------- 424
            +I++ +R G+ +T   A ++F   FFD  +YDL+ VGR K N +L+              
Sbjct: 241  EIFQKLRQGEHATIDGARTLFVSRFFDPKRYDLAHVGRYKFNKKLSAQERLLNQKLASDI 300

Query: 425  --PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               +    + +E  +   +I  D+   K    +I  +         E    ++ +   R+
Sbjct: 301  FDSETGEVLVEEGTVITRRIFEDVLADKIDRLNIKKVELVNPLEERETYVQEFEVYSPRV 360

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                +      +++       I    + +++  FF         + V  L  I H     
Sbjct: 361  NEGDQVVRIIGNVEDE--CKHITTSDIFASISYFFNL------LDSVGYLDDIDHLGNRR 412

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
                G + + +  + +  +      R+   ET       L++     A +  +       
Sbjct: 413  LRLVGELLQNQFRIGLSRMERVVKERMSIQETEGITPSSLINIRPVTAAIKEFFGSSQLS 472

Query: 603  RKVCDGKVTNDVVY---LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV--P 657
            + +      +++ +   LSA+        +A   + +        +      E   +   
Sbjct: 473  QFMDQTNPLSELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLI 532

Query: 658  REKIDFIDASPKQVV-SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                 +   +    + +    ++P ++ +     +   +  R      +        G++
Sbjct: 533  NSLSSYAKVNKFGFIETPYRKVVPVIDEETKQPKMHVTDEIRYLTADEEDRYVVAQAGLD 592

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                 +    ++ +  G    V A R+    V      S +   I               
Sbjct: 593  LDEKGNLPEKVIVRHRGENLIVPAERVDFVDVSPKQIVSVATACI--------------- 637

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                       +  +D        ++   A+   +  A     G  +  +    + +V+ 
Sbjct: 638  ---------PFLEHDDANRALMGANMQRQAIPLLIPEAPFVGTGMEYVAAKDSGQAVVAY 688

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            +  T  +++   +  R    G  +    I  V       +++  I+ +G  +N G++L  
Sbjct: 689  NSGTVEYVDSKVIKLRRDADGQIDKYPLIKFVRSNSSTVLNQRPIVKLGDHINAGEVLAD 748

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
              +      +     ++ A       +  D  +                    + K++  
Sbjct: 749  SSS-MESGELALGRNVVVAFMTWNGYNYEDAIIMS----------------ERLVKDDVY 791

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVLSSDLI 1013
             S+  E+ EL ARD       + R+I     + L   +     +     K+  +L   + 
Sbjct: 792  TSIHIEEYELEARDTKLGPEEITRDIPGVGEDALKNLDDRGIIRIGAEVKEDDILVGKVT 851

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMPPGVLR 1072
            ++       +  +           ++          +      K    + GDD+ PGV  
Sbjct: 852  AKGQTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIVHDVKYFSRRNGDDLSPGVNE 911

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            V+++++  KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGTPVDI+LNPLGVPSRMN
Sbjct: 912  VIRIYIVQKRKISEGDKMAGRHGNKGVISKILPQEDMPYMPDGTPVDIMLNPLGVPSRMN 971

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI E HLG A   LG  + + + D     D+  + +                      
Sbjct: 972  IGQILEIHLGMAAKKLGIHVATPVFDGVKTEDLEAIIAEAGMDKDAK------------- 1018

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                           T ++DG                           TGE FD  ++VG
Sbjct: 1019 ---------------TVLYDG--------------------------RTGEKFDNRISVG 1037

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1038 VMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 1097

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDD+ GR + YE+IV G +  E G PESF VLVKE+Q+LGL + + ++      
Sbjct: 1098 EILTVKSDDITGRVKTYEAIVRGENVPEPGIPESFRVLVKELQSLGLDVKILSNEKDEIE 1157

Query: 1373 KME 1375
              +
Sbjct: 1158 IRD 1160


>gi|153852611|ref|ZP_01994048.1| hypothetical protein DORLON_00021 [Dorea longicatena DSM 13814]
 gi|149754253|gb|EDM64184.1| hypothetical protein DORLON_00021 [Dorea longicatena DSM 13814]
          Length = 1292

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/953 (45%), Positives = 585/953 (61%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQ  SY  FL           EGL   F  + PIT +SG
Sbjct: 13  KSSRMSYARQKEVVQMPNLIEVQTDSYKWFL----------EEGLNEVFDDISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L+FV +    D  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  KLSLDFVDFTLCEDEVKYTIDECKERDATYAAPLKVKVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTRTGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKKLYSATVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNPEIIELFGEEPKILASFEKDAA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 TNYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLAL-KNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+ +  TGE+  EAG  I  +    I ++ +  + I   ++      + N +V
Sbjct: 290 SGHVLAEDVASPMTGEVLAEAGTKITRELASTIQNNAVPYVWISVEETERPIKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                                D     V E ++  +     +     +  +K  ++ ++ 
Sbjct: 350 DLDAVVDV-------------DPEEVGVTEQVYYPVLAGILEETAGDIDELKDAIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G GT DDID+LGNRR+RSVGE+L+NQYR+GL R+E
Sbjct: 397 -DLIPKHITKEDILASINYNMHLEYGIGTDDDIDHLGNRRIRSVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDMEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLASYARINEYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT++VVY++A EE+N ++AQAN  LD++G F  + V  R   E     R
Sbjct: 576 KINHDDPTNPVVTDEVVYMTADEEDNYHVAQANEQLDKEGHFVRKNVSGRYREETQEYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 RMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLFTEAPVVGTGMEEK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+  G VE+  +  I +R  +G        +  Y+L KFQRSNQ+ C NQ
Sbjct: 696 AAVDSGVCVVAEEGGTVERSTSTEITVRQDDG-------KLKKYKLTKFQRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  GD V + ++IADGPST  G+L LG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RPIVFKGDRVEKGEVIADGPSTSNGELGLGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIP V ++ LKN+DE GII VGAEV  GDILVGK+
Sbjct: 809 YTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKNLDERGIIRVGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R G D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTREGGD 921



 Score =  560 bits (1442), Expect = e-157,   Method: Composition-based stats.
 Identities = 252/1142 (22%), Positives = 415/1142 (36%), Gaps = 66/1142 (5%)

Query: 267  IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            I+  E+VI S    + G+  ++    +     ++  +       +         Y+    
Sbjct: 131  INGAERVIVSQLVRSPGIYYAIAHDKLGKKLYSATVIPNRGAWLEYETDSNDVFYVRVDR 190

Query: 327  VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                     I    I   P + ++       I  +   D   + ++ LL++Y+ +RPG+ 
Sbjct: 191  TRKVPITVLIRALGIGTNPEI-IELFGEEPKILASFEKDAATNYQEGLLELYKKIRPGEP 249

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                 AES+   +FFD  +YDL+ VGR K N +L L        + ++    +       
Sbjct: 250  LAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLALKNRISGHVLAEDVASPMT------ 303

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
              G+   +    +      ++         + +   ER IK   + +     +       
Sbjct: 304  --GEVLAEAGTKITRELASTIQNNAVPYVWISVEETERPIKVLSNMMVDLDAVVDVDPEE 361

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
              V   V     +  L +    ++ L      R +  L    + +      +       Y
Sbjct: 362  VGVTEQVYYPVLAGILEETAGDIDELKDAI-KRDIHDLIPKHITKEDILASINYNMHLEY 420

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G     +     N   + S+    +      +    R V +   T D+  +S     N  
Sbjct: 421  GIGTDDDIDHLGN-RRIRSVGELLQNQYRIGLSRLERVVRERMTTQDMEGISPQSLINIK 479

Query: 627  IAQANSS----------LDEDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVV 672
               A               +  +   EL   R             R   +  D       
Sbjct: 480  PVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYG 539

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
             +     P   N      L       +   +             + V       + A   
Sbjct: 540  RMCPVETPEGPNIGLINSLASYARINEYGFIEAPYRKINHDDPTNPVVTDEVVYMTADEE 599

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRR 790
                   A   + +         +           +R      V+ + +  V        
Sbjct: 600  DNYHVAQANEQLDKEGHFVRKNVSGRYREETQEYERRMFDYMDVSPKMVFSVATALIPFL 659

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEV 849
             +  A+              +L    P  G   E+   +     V  +   ++       
Sbjct: 660  QNDDANRALMGSNMQRQAVPLLFTEAPVVGTGMEEKAAVDSGVCVVAEEGGTVERSTSTE 719

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            +      G  +  +             ++  I+  G  V  G+++    +         +
Sbjct: 720  ITVRQDDGKLKKYKLTKFQRSNQSNCYNQRPIVFKGDRVEKGEVIADGPSTSNGELGLGK 779

Query: 910  EKLLRAI--FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE---QI 964
              L+  +   G    D    S R+      T + +  +     D       + R+     
Sbjct: 780  NPLIGFMTWEGYNYEDAVLLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDIPGVG 839

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            +   ++  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 840  DDALKNL-DERGIIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 892

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E      +            K+   + GD+M PGV + V++++A KR I
Sbjct: 893  -----------EVRDTSLKVPHGEYGIVVDAKVFTREGGDEMSPGVNQSVRIYIAQKRKI 941

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A
Sbjct: 942  SVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLA 1001

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D     DI              S  E  + + ++ +  V +      
Sbjct: 1002 AKALGFNIATPVFDGANEIDIMDTLDLAND-YVNLSWEEFEAKHKEELLPEVLQYLSD-- 1058

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                             + +   +   G+  L DG TGE FD PVT+G+++ LKL+H+V 
Sbjct: 1059 -----------NREHRKLWKGVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVD 1107

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+G
Sbjct: 1108 DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIG 1167

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            R + YE+I+ G +  E G PESF VL+KE+Q+LGL + +          ME   D  + +
Sbjct: 1168 RVKTYEAIIKGENIPEPGIPESFKVLLKELQSLGLDVRVLRDDNTEVEIMET-SDMGETD 1226

Query: 1385 LK 1386
             +
Sbjct: 1227 FR 1228


>gi|322410928|gb|EFY01836.1| DNA-directed RNA polymerase subunit beta [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 1188

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/963 (44%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQIIAENLVDAETGEILVEAGTEMTRSVIESIEEHLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFIYTPN----DYAVITEPVVLQKFKVVSPIDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR+IPNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 178/590 (30%), Positives = 255/590 (43%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLIDPKAPFVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAEKVEVRREDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++ VG  V  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKVGDIVEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKD 972
             +  +  D  +     V   V           +  +  +  E    +I    E   +D  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 984  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|222152310|ref|YP_002561485.1| DNA-directed RNA polymerase subunit beta [Streptococcus uberis
           0140J]
 gi|254765309|sp|B9DSZ5|RPOB_STRU0 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|222113121|emb|CAR40524.1| DNA-directed RNA polymerase beta chain [Streptococcus uberis 0140J]
          Length = 1188

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 585/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRINEVLDLPNLIEIQTDSFQDFL----------DTGLREVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EIL  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++V+ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQIIAENLVDSETGEILVEAGTEMTRDVIESIEAHIDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V  P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVVLQKFKVQSPLDPDKV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG             D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ATPDDKVRALTPADILAEMSYFLNLSEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRATGVVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFAASTVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQHDGKVVFSDAEKVEVRREDGSLD-------VYHVTKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDIVEKGDFIADGPSMEKGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 170/508 (33%), Positives = 235/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDIVEKGDFIADGPS-MEKGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   RD  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREVPNVGEEALRDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGIVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+    +    
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATAEDLWDTVAEAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     +    ++L        G  
Sbjct: 1006 -----------------------------------------DSDAKTIL------YDG-- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|253681374|ref|ZP_04862171.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum D
           str. 1873]
 gi|253561086|gb|EES90538.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum D
           str. 1873]
          Length = 1241

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/950 (44%), Positives = 591/950 (62%), Gaps = 55/950 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+  +P+LIEVQ  SYD F            EGL   F  + PI  ++G
Sbjct: 9   KRTRMSFSKVKEMCPMPNLIEVQLNSYDWF----------WKEGLNEVFDDINPIQDYTG 58

Query: 71  AAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEF+ Y  D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLILEFIDYNLDRDAIKYSVEECKERDATYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTFVI G +R++VSQL RSPG ++ +D  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTQQGTFVINGAERVIVSQLVRSPGAYYGYDVDKT---GKKLFSATVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS DII+VRID+ RK+P++  + ALG+ S+ EI+  F  +         D  
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPISILIRALGLGSDAEIIEWFGEEERLKSTIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+   +I S         L +  + K  K L I    L
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAVSLINSLFFDAKRYDLSRVGRYKFNKKLAIYI-RL 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                AED+VN  TGEI ++ G+ I+     EI +  I  + I   D +     I N  V
Sbjct: 286 LNQVAAEDVVNPFTGEIIVQKGETIERDKALEIQNCAINAVNIQVEDKIIK--VIGNNFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
              N    D        ++  +   +   + + +        Y      + ++   ++  
Sbjct: 344 DIHNFVDFD-----ISDLKIKEHVHYPTLKKILDN-------YTDEESIKEEIRKNIHEL 391

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   +HI  +DI A +   + L    GTIDDID+LGNRR+RSVGE+L+NQ+R+GL RME
Sbjct: 392 IP---KHIVVDDIYATVSYELGLPYSVGTIDDIDHLGNRRLRSVGELLQNQFRIGLSRME 448

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R +KER++  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 449 RVVKERMTIQDQEVITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 508

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +A+VN YGFIETPYR
Sbjct: 509 LGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLACYAKVNEYGFIETPYR 568

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V   D +V  ++VYL+A EE++  +AQA   LDE+G F E+ +  R   + I+V + ++
Sbjct: 569 LVDKKDARVKEEIVYLTADEEDHYLVAQAKEPLDEEGHFLEDKITVRTLEDVIVVSKHQV 628

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SP Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E   A 
Sbjct: 629 DLMDVSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIVGTGIEFKAAV 688

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG    A+  G+VE V +  + IR        +  G+D  +L+K++RSNQ TC+NQRP+
Sbjct: 689 DSGVLPKAEHDGVVEYVSSTEVRIRRD------ADGGLDRCKLLKYKRSNQGTCINQRPI 742

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V  G++++  D++ADGPSTD G++ALG+N+ + F+ W GYN+ED+ML+SE++V +D+FTS
Sbjct: 743 VSKGEKLKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDDIFTS 802

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNV E+ LKNIDE GI+ +GAEV  GDILVGK+TPK
Sbjct: 803 IHIEEYESEARDTKLGPEEITRDIPNVGEDALKNIDERGIVRIGAEVRSGDILVGKVTPK 862

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 863 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 192/628 (30%), Positives = 269/628 (42%), Gaps = 79/628 (12%)

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            D+  + K Q    +   +Q   V         +  A               +L    P  
Sbjct: 619  DVIVVSKHQVDLMDVSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIV 678

Query: 820  GYNFEDSMLISERMVSEDVFTSI--HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            G   E    +   ++ +     +  ++   EV  R    G  +  + +          I+
Sbjct: 679  GTGIEFKAAVDSGVLPKAEHDGVVEYVSSTEVRIRRDADGGLDRCKLLKYKRSNQGTCIN 738

Query: 878  ECGIICVGAEVNPGDILVGKITPK-----GESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            +  I+  G ++  GD+L    +           +            E A+ V +  +R  
Sbjct: 739  QRPIVSKGEKLKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDD 798

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
               S  + +     R      E          E   ++  DE+ I+      R  +IL G
Sbjct: 799  IFTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNI-DERGIVRIGAEVRSGDILVG 857

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E                
Sbjct: 858  KVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGII 900

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV  +V+ ++A KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 901  VDVKVFTRENGDELPPGVNELVRCYIAQKRKISVGDKMAGRHGNKGVISRILPEEDMPFL 960

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   +G  I + + +     +I  L    
Sbjct: 961  PDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAAGEMGWHIATPVFNGAFEDEIVDLLKEA 1020

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                   DG                   
Sbjct: 1021 GYNA-----------------------------------DGKTV---------------- 1029

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               LYDG TGEPFD  VTVGY+Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1030 ---LYDGRTGEPFDNRVTVGYMYILKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQ 1086

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1087 RFGEMEVWALEAYGAAHTLQEVLTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIK 1146

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            E+QAL L + + +   +     E + + 
Sbjct: 1147 ELQALCLDVKVLSGDNEEITIRESVDEE 1174


>gi|254517462|ref|ZP_05129518.1| RNA polymerase subunit beta [Clostridium sp. 7_2_43FAA]
 gi|226911211|gb|EEH96412.1| RNA polymerase subunit beta [Clostridium sp. 7_2_43FAA]
          Length = 1235

 Score =  833 bits (2152), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/950 (45%), Positives = 594/950 (62%), Gaps = 55/950 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++ ++P+LIEVQ  SY  FL           EGL   F+ + PIT F+G
Sbjct: 9   KRTRMSFGKVKDVTEMPNLIEVQLDSYQWFL----------KEGLHEVFEDINPITNFTG 58

Query: 71  AAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y+ D    K+ V+ C  RD TYA PLK+++RL               +IKEQ
Sbjct: 59  NLVLEFVDYKLDMDNIKYSVEKCKERDATYAAPLKVSVRL---------QNNETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++  +  +    G+ LY+  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYSFNVDKT---GEKLYSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS DII+VRID+ RK+P++    A+G  S+ E+L  F     +      D  
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPISILARAMGFGSDQELLDYFGEDERFKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+   +I+S         L +  + K  K L +    L
Sbjct: 227 KTKEEALLEIYKRLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLALNL-RL 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                A DIVN +TGEI +E G  I     EEI +  I  + IL  D V     I N  V
Sbjct: 286 VNQVAATDIVNPQTGEIMVEQGKKISRSLAEEIQNVGINSVDILVEDRVVR--VIGNHFV 343

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                D K+ +      +   ++  +   + + +        YD     + ++   LN  
Sbjct: 344 -----DIKNFVSFNIEDLNIRELVHYPTLKEILDN-------YDDEDTIKEEIKKNLNRL 391

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   +HI ++DI A I   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+GL RME
Sbjct: 392 IP---KHIIRDDIFATISYELGLPYSVGYVDDIDHLGNRRLRSVGELLQNQFRIGLSRME 448

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  + VN LS +TH RRLSA
Sbjct: 449 RVVKERMTIQDQEAITPQMLINIRPVAAAIKEFFGSSQLSQFMDQVNPLSELTHKRRLSA 508

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFIETPYR
Sbjct: 509 LGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFIETPYR 568

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            +    G +T+++ Y +A EE+   +AQA   + ED  F +  V  R   + ++V  +++
Sbjct: 569 VIDKEKGIITDEIRYFTADEEDLYLVAQAKEPIGEDRKFVDSRVTVRSKHDILVVNADEV 628

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D ID SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A 
Sbjct: 629 DLIDVSPRQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPVVGTGIEFKAAV 688

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG    AK AG V  V +  I I+           G+D Y L+KF+RSNQ TC+NQRPL
Sbjct: 689 DSGVLPKAKNAGKVVYVSSNEIRIKRD------VDGGIDTYNLLKFKRSNQGTCINQRPL 742

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V  G+ V +N ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V EDVFTS
Sbjct: 743 VDKGEIVFKNQVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTS 802

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK+ID+ GII +GAEV  GDILVGK+TPK
Sbjct: 803 IHIEEYECEARDTKLGPEEITRDIPNVSEDALKDIDDRGIIRIGAEVRSGDILVGKVTPK 862

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 863 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 253/1104 (22%), Positives = 403/1104 (36%), Gaps = 132/1104 (11%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            ++ +I     D   +  +  +  +         +D    +   + T+  D  K +++ALL
Sbjct: 175  DSNDIIYVRIDKTRKLPISILARAMGFGSDQELLDYFGEDERFKATIEKDNTKTKEEALL 234

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +IY+ +RPG+  T   A S+ + LFFD+ +YDLS VGR K N +L L+     +      
Sbjct: 235  EIYKRLRPGEPPTVDSAISLIDSLFFDAKRYDLSRVGRYKFNKKLALNLRLVNQV----- 289

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
                   +V+ + G+  ++    +       +  +  N   + +    R ++   +    
Sbjct: 290  ---AATDIVNPQTGEIMVEQGKKISRSLAEEIQNVGINSVDILVED--RVVRVIGNHFVD 344

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
                    I    +   V        L   ++       I   + L+ L    + R    
Sbjct: 345  IKNFVSFNIEDLNIRELVHYPTLKEILDNYDDEDTIKEEI--KKNLNRLIPKHIIRDDIF 402

Query: 556  VEMRDVH--PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              +      P   G +   +      +  V  L    +      +    R V +     D
Sbjct: 403  ATISYELGLPYSVGYVDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQD 459

Query: 614  VVYLSAMEEENRY-IA------QANSSLDEDGSFTEELVFCRCAG------------EEI 654
               ++     N   +A        +S L +       L                   E  
Sbjct: 460  QEAITPQMLINIRPVAAAIKEFFGSSQLSQFMDQVNPLSELTHKRRLSALGPGGLSRERA 519

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV-LMGCNMQRQAVPLLKAEAPFVGT 713
                  +          +         L N  +    +           ++  E   +  
Sbjct: 520  GFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNEYGFIETPYRVIDKEKGIITD 579

Query: 714  GMESVVA--KSSGAAIVAKRA--GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             +    A  +       AK       + VD+ R+ +RS    L  +   VD+  +     
Sbjct: 580  EIRYFTADEEDLYLVAQAKEPIGEDRKFVDS-RVTVRSKHDILVVNADEVDLIDVSP--- 635

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                    Q   V         +  A               +L    P  G   E    +
Sbjct: 636  -------RQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPVVGTGIEFKAAV 688

Query: 830  SERMV--SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
               ++  +++    +++   E+  +    G  +    +          I++  ++  G  
Sbjct: 689  DSGVLPKAKNAGKVVYVSSNEIRIKRDVDGGIDTYNLLKFKRSNQGTCINQRPLVDKGEI 748

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDV 942
            V    +L    +         +   +  I       E A+ + +  +R     S  + + 
Sbjct: 749  VFKNQVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVREDVFTSIHIEEY 808

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
                R      E          E   +D DD   I+      R  +IL G+    G    
Sbjct: 809  ECEARDTKLGPEEITRDIPNVSEDALKDIDDR-GIIRIGAEVRSGDILVGKVTPKGETEL 867

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                 L   +  E  R                 E                   K+   + 
Sbjct: 868  TAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKVFTREN 910

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++ PGV  +V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I L
Sbjct: 911  GDELNPGVNELVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICL 970

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA   LG  I + + D     DI                 
Sbjct: 971  NPLGVPSRMNIGQVLEVHLGWAASQLGWHIATPVFDGATEKDIEDCLEKAGYNANGK--- 1027

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                     T ++DG                           TG
Sbjct: 1028 -------------------------TVLYDG--------------------------RTG 1036

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD  VTVG +Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1037 EAFDNEVTVGIMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1096

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + 
Sbjct: 1097 EAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVK 1156

Query: 1363 LENSRTKNSAKMEEIPDFNKCELK 1386
            + N       +++E  + +  +L+
Sbjct: 1157 VLN-DENEEVRLKEFAEEDMEDLE 1179


>gi|307704126|ref|ZP_07641054.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK597]
 gi|307622348|gb|EFO01357.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK597]
          Length = 1203

 Score =  833 bits (2151), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|291459928|ref|ZP_06599318.1| DNA-directed RNA polymerase, beta subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
 gi|291417269|gb|EFE90988.1| DNA-directed RNA polymerase, beta subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
          Length = 1351

 Score =  833 bits (2151), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/961 (45%), Positives = 601/961 (62%), Gaps = 55/961 (5%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G   VR  F ++ E++++P+LIE+QK SY  FL           EGL+ AF  +
Sbjct: 30  MRPVRTG-KNVRMTFSQSKEVLEMPNLIEIQKDSYRWFL----------KEGLREAFDDI 78

Query: 63  FPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            PI  F+G   LEFV+++   +  K+ +++C  RD TYA PLK+ +RLI  D D      
Sbjct: 79  SPIQDFAGHMSLEFVNFKLCEEEKKYTIEECKERDATYAAPLKVKVRLINKDKD------ 132

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +I E  I+MGDLPLMT+ G+FVI G +R++VSQL RSPGI++  D+ +    GK LY
Sbjct: 133 ---EINEHEIFMGDLPLMTETGSFVINGAERVIVSQLVRSPGIYYSIDRDKL---GKELY 186

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIV 237
           +C +IP++G W++ E DS D+  VR+DR RKVPVT F+ ALG+ S  EI+  F    K++
Sbjct: 187 SCTVIPNRGAWIEYETDSNDVFFVRVDRTRKVPVTVFIRALGIGSNAEIIELFGEEPKLL 246

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            S   D           +         + +D+ E ++ S         L K  + K  K 
Sbjct: 247 ASFEKDPSDNYQDGLLELYKKIRPGEPLSVDSAESLLRSMFFDPRRYDLAKVGRYKFNKK 306

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L    + + GL +AED+ +  TGE+  EAG V+  +  EEI ++    +P +++D  +  
Sbjct: 307 L-HFKNRIRGLSLAEDVADPATGELLAEAGTVLSREKAEEIQNAG---VPYVWIDGPSRK 362

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             + ++L  D +    +        +R  ++  +    ++ + +   S+        R  
Sbjct: 363 EKVLSSLQVDASSYFPEDFDLASLGIR--ELVYYPALRALLDEMEGASEAE-----LREA 415

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +   ++   P   +HI +EDI A I   ++L    G  DDID+LGNRR+R+VGE+L+NQY
Sbjct: 416 VKKHIHELVP---KHITREDIFASINYCMNLEEEIGNPDDIDHLGNRRIRAVGELLQNQY 472

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+S+ DI+ + PQ LIN KPV ++V EFF SSQLSQ  +  N LS +
Sbjct: 473 RIGLSRMERVVRERMSTQDIEEITPQSLINIKPVTASVKEFFGSSQLSQFMDQNNPLSEL 532

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+AR+N Y
Sbjct: 533 THKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYARINEY 592

Query: 596 GFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           GFIE+PYR V      D  VT+ VVYL+A EE+N  +AQAN  +D +G F  + V  R  
Sbjct: 593 GFIESPYRVVDKSDPKDPVVTDRVVYLAADEEDNYRVAQANEPIDSEGHFVNDSVSGRYR 652

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 P+  ID +D SPK V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL  E   
Sbjct: 653 ELTSAFPKASIDMMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLVTEPAV 712

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TGM +  A  SGA +VA+ +G V    + RIVI+  +         +D Y+LMKF RS
Sbjct: 713 VDTGMSAKAAVDSGACVVAENSGEVLVSASNRIVIKRDK------DGVLDEYKLMKFVRS 766

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N + C NQ+P+V   + V + DIIADGPST  G++ALG+N L+ FM W GYN+ED++L+S
Sbjct: 767 NPSNCYNQKPIVSPHEHVEKGDIIADGPSTSAGEIALGKNPLIGFMTWEGYNYEDAVLLS 826

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +DV+TS+HIEE+E  ARDTKLGPEEIT D+P V EE LKN+DE GII +GAEV  
Sbjct: 827 ERLVQQDVYTSVHIEEYECEARDTKLGPEEITSDVPGVGEEALKNLDERGIIRIGAEVRA 886

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  GTV++  +F R   
Sbjct: 887 GDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGTVINTMVFTRENS 946

Query: 951 D 951
           D
Sbjct: 947 D 947



 Score =  536 bits (1381), Expect = e-150,   Method: Composition-based stats.
 Identities = 251/1183 (21%), Positives = 423/1183 (35%), Gaps = 89/1183 (7%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +              +     +    I+  E+VI S    + G+  S+    + 
Sbjct: 123  KVRLINKDKDEINEHEIFMGDLPLMTETGSFVINGAERVIVSQLVRSPGIYYSIDRDKLG 182

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                +   +       +         ++             I    I     + ++    
Sbjct: 183  KELYSCTVIPNRGAWIEYETDSNDVFFVRVDRTRKVPVTVFIRALGIGSNAEI-IELFGE 241

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               +  +   D + + +D LL++Y+ +RPG+  +   AES+   +FFD  +YDL+ VGR 
Sbjct: 242  EPKLLASFEKDPSDNYQDGLLELYKKIRPGEPLSVDSAESLLRSMFFDPRRYDLAKVGRY 301

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L+    + +R +   + +A       L      +        +            
Sbjct: 302  KFNKKLHFK--NRIRGLSLAEDVADPATGELLAEAGTVLSREKAEEIQNAGVP-----YV 354

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +  G  R E+ +      VD  S  P+D          + E      L  L + +   S 
Sbjct: 355  WIDGPSRKEKVLS--SLQVDASSYFPEDF---DLASLGIRELVYYPALRALLDEMEGASE 409

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN------IGLVSSLTS 588
                R         +       E  D+  +    +   E     +         + ++  
Sbjct: 410  -AELREAVKKHIHELVPKHITRE--DIFASINYCMNLEEEIGNPDDIDHLGNRRIRAVGE 466

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDG 638
              +      +    R V +   T D+  ++     N     A+              +  
Sbjct: 467  LLQNQYRIGLSRMERVVRERMSTQDIEEITPQSLINIKPVTASVKEFFGSSQLSQFMDQN 526

Query: 639  SFTEELVFCRC---------AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            +   EL   R          + +        + +        +         L N  ++ 
Sbjct: 527  NPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASY 586

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +           +++    V          +     +A       +V      I S  
Sbjct: 587  ARI------NEYGFIESPYRVVDKSDPKDPVVTDRVVYLAADEEDNYRVAQANEPIDSEG 640

Query: 750  GDLDPSTSGVDIYRLMKFQR-SNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLA 806
              ++ S SG        F + S     V+ + +  V         +  A+          
Sbjct: 641  HFVNDSVSGRYRELTSAFPKASIDMMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQR 700

Query: 807  LGRNMLVA--FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                +LV    +   G + + ++     +V+E+    +      ++ +  K G  +  + 
Sbjct: 701  QAVPLLVTEPAVVDTGMSAKAAVDSGACVVAENSGEVLVSASNRIVIKRDKDGVLDEYKL 760

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +  V        ++  I+     V  GDI+    +      +   +  L      +  + 
Sbjct: 761  MKFVRSNPSNCYNQKPIVSPHEHVEKGDIIADGPST-SAGEIALGKNPLIGFMTWEGYNY 819

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILD 979
             D  L     V   V        +  +  +  +  E    +       A    DE+ I+ 
Sbjct: 820  EDAVLLSERLVQQDVYTSVHIEEYECEARDTKLGPEEITSDVPGVGEEALKNLDERGIIR 879

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 R  +IL G+    G         L   +  E  R                 E   
Sbjct: 880  IGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRD 922

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
               +             +   +  D++ PGV   V++++A KR I  GDKMAGRHGNKG+
Sbjct: 923  TSLKVPHGAYGTVINTMVFTRENSDELAPGVSESVRIYIAQKRKIGVGDKMAGRHGNKGV 982

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSR+LP EDMP+L +G  +DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + I D 
Sbjct: 983  VSRVLPVEDMPYLPNGRSLDIVLNPLGVPSRMNIGQVLELHLSLAAKALGLDVSTPIFDG 1042

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                DI          +            ++          K                  
Sbjct: 1043 ADENDIQQTLILANDYVNESWEDFSKKHKEELDPAVYDYLGKHL--------------EH 1088

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                +   +   G+  L DG TGE FD P  +G+++ LKL+H+V DK++ARSTG YSLVT
Sbjct: 1089 REEWKGVTISVDGKVQLRDGRTGEMFDGPTAIGFMHYLKLHHLVDDKIHARSTGPYSLVT 1148

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR + YE+I+ G +  
Sbjct: 1149 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTMKSDDVAGRVKTYEAIIKGQNIP 1208

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G PESF VL+KEMQAL L + + + +       E++ D N+
Sbjct: 1209 APGVPESFKVLLKEMQALCLDMRVLDEKKNEVEITEDLYDANQ 1251


>gi|195977259|ref|YP_002122503.1| DNA-directed RNA polymerase subunit beta [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|225869575|ref|YP_002745522.1| DNA-directed RNA polymerase beta chain [Streptococcus equi subsp.
           equi 4047]
 gi|226699450|sp|B4U047|RPOB_STREM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765305|sp|C0M7C8|RPOB_STRE4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|195973964|gb|ACG61490.1| DNA-directed RNA polymerase beta chain RpoB [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
 gi|225698979|emb|CAW92040.1| DNA-directed RNA polymerase beta chain [Streptococcus equi subsp.
           equi 4047]
          Length = 1188

 Score =  833 bits (2151), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNQSDSRTDEALKEIYERLRPGEPKTADSSRSLLTARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++++ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQIIAENLIDSETGEILVEAGTEMTRSVIESIEEQLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVILQKFKVVSPVDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+ DG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRVIGRVTNEIVWLTADEEDEFTVAQANSKLNPDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P  ++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPASQVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA R+ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAERVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK+GD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKIGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/508 (33%), Positives = 235/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKIGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGIVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLWETVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|225867707|ref|YP_002743655.1| DNA-directed RNA polymerase beta chain [Streptococcus equi subsp.
           zooepidemicus]
 gi|259494193|sp|C0MEE3|RPOB_STRS7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|225700983|emb|CAW97721.1| DNA-directed RNA polymerase beta chain [Streptococcus equi subsp.
           zooepidemicus]
          Length = 1188

 Score =  833 bits (2151), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 590/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFL----------DSGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIIDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L +      +   +  +G 
Sbjct: 219 NTIEKDI-HKNQSDSRTDEALKEIYERLRPGEPKTADSSRSLLTARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++++ ETGEI +EAG  +    +E I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQIIAENLIDSETGEILVEAGTEMTRSVIESIEEQLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   Y  N    D     +  +L  ++V+ P D                      ++ 
Sbjct: 332 --NKFVYTPN----DYAVVTEPVILQKFKVVSPVDPDRV------------------VTI 367

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VG          +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 368 VGN--------ANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     +VTN++V+L+A EE+   +AQANS L+ DG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRVIGRVTNEIVWLTADEEDEFTVAQANSKLNPDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P  ++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGNNQEFPASQVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA R+ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQHNGKVVFSDAERVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK+GD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKIGDIVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE LK++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 169/508 (33%), Positives = 235/508 (46%), Gaps = 79/508 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKIGDIVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKEDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                      +  +  +  E          E   +D  DE  I+      +  +IL G+ 
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKV 842

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G K       L   +  +  R           +V+     +    +     +     
Sbjct: 843  TPKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGDGIVRDV----- 886

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L D
Sbjct: 887  -KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPD 945

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+         
Sbjct: 946  GTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLWETVREAGM 1005

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                             T ++DG                     
Sbjct: 1006 DSDAK----------------------------TVLYDG--------------------- 1016

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1017 -----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRF 1071

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+
Sbjct: 1072 GEMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKEL 1131

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+LGL + + +         +     + 
Sbjct: 1132 QSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|194396940|ref|YP_002038544.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           G54]
 gi|226699452|sp|B5E2F3|RPOB_STRP4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|194356607|gb|ACF55055.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           G54]
          Length = 1203

 Score =  833 bits (2151), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYNGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|225859717|ref|YP_002741227.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           70585]
 gi|254765307|sp|C1CA06|RPOB_STRP7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|225721911|gb|ACO17765.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           70585]
          Length = 1198

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|116516435|ref|YP_817182.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           D39]
 gi|148989960|ref|ZP_01821235.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP6-BS73]
 gi|148998490|ref|ZP_01825931.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP11-BS70]
 gi|168484260|ref|ZP_02709212.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC1873-00]
 gi|168487101|ref|ZP_02711609.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC1087-00]
 gi|168492064|ref|ZP_02716207.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC0288-04]
 gi|168576638|ref|ZP_02722504.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           MLV-016]
 gi|225857535|ref|YP_002739046.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           P1031]
 gi|225861777|ref|YP_002743286.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298229974|ref|ZP_06963655.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           str. Canada MDR_19F]
 gi|298254765|ref|ZP_06978351.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           str. Canada MDR_19A]
 gi|298503732|ref|YP_003725672.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           TCH8431/19A]
 gi|303254114|ref|ZP_07340229.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS455]
 gi|303260335|ref|ZP_07346305.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP-BS293]
 gi|303262483|ref|ZP_07348425.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP14-BS292]
 gi|303265113|ref|ZP_07351026.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS397]
 gi|303266025|ref|ZP_07351920.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS457]
 gi|303268043|ref|ZP_07353844.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS458]
 gi|307068570|ref|YP_003877536.1| DNA-directed RNA polymerase subunit beta/140 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|122277972|sp|Q04IK6|RPOB_STRP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158518627|sp|Q8DNF0|RPOB_STRR6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765311|sp|C1CMQ8|RPOB_STRZP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765312|sp|C1CTL4|RPOB_STRZT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116077011|gb|ABJ54731.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           D39]
 gi|147755683|gb|EDK62729.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP11-BS70]
 gi|147924620|gb|EDK75706.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP6-BS73]
 gi|172042457|gb|EDT50503.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC1873-00]
 gi|183569961|gb|EDT90489.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC1087-00]
 gi|183573741|gb|EDT94269.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC0288-04]
 gi|183577612|gb|EDT98140.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           MLV-016]
 gi|225726024|gb|ACO21876.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           P1031]
 gi|225728394|gb|ACO24245.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298239327|gb|ADI70458.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           TCH8431/19A]
 gi|301802640|emb|CBW35406.1| DNA-directed RNA polymerase beta chain [Streptococcus pneumoniae
           INV200]
 gi|302598947|gb|EFL65978.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS455]
 gi|302636383|gb|EFL66876.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP14-BS292]
 gi|302638501|gb|EFL68966.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP-BS293]
 gi|302642403|gb|EFL72749.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS458]
 gi|302644466|gb|EFL74718.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS457]
 gi|302645330|gb|EFL75564.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           BS397]
 gi|306410107|gb|ADM85534.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|327389125|gb|EGE87471.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           GA04375]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|67550160|gb|AAY68426.1| RNA polymerase subunit B [Pseudomonas fluorescens]
          Length = 714

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/718 (54%), Positives = 534/718 (74%), Gaps = 5/718 (0%)

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             N+GL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA+++++E+
Sbjct: 1    PNVGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNEE 60

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 61   KVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 120

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +
Sbjct: 121  RQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEA 180

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L K+ RSNQ+TC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM 
Sbjct: 181  GVDIYNLTKYTRSNQDTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMA 240

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEEI  DIPNV E  L  +D
Sbjct: 241  WNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEIPADIPNVGEAALNKLD 300

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+G  G
Sbjct: 301  EAGIVYVGAEVGAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKG 360

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R G++++ R++S+E+ Q++ + +D ++   I++   + RL   L G  A  
Sbjct: 361  TVIDVQVFTRDGVERDARALSIEKTQLDGIRKDLNEGFRIVEGATFERLRSALVGHKAEG 420

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G  G KK    + +++      QW++  + ++ +   +E  +      + +L+D+F++K 
Sbjct: 421  G-AGLKKGQDFTDEVLDGLEHGQWFKLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKK 479

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
             K+Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I+P EDMP   +GTP
Sbjct: 480  RKLQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTP 539

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VD+VLNPLGVPSRMNVGQI ETHLG A  GLG+KI  +I + +    ++ LR FL ++  
Sbjct: 540  VDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMIEEQR---KVADLRKFLHEIYN 596

Query: 1178 T-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G   E++  + D  +L +A+  + GVP++TPVFDGA E  I +ML++ADL ESGQ  L
Sbjct: 597  EIGGRKEELDTFSDQEILDLAKNLRGGVPMATPVFDGAKESEIKAMLKLADLPESGQMQL 656

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +DG TG  F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR 
Sbjct: 657  FDGRTGNKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRF 714


>gi|148985540|ref|ZP_01818729.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP3-BS71]
 gi|148993179|ref|ZP_01822745.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP9-BS68]
 gi|149012450|ref|ZP_01833481.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP19-BS75]
 gi|149021911|ref|ZP_01835898.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP23-BS72]
 gi|168489966|ref|ZP_02714165.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           SP195]
 gi|168494799|ref|ZP_02718942.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC3059-06]
 gi|221232687|ref|YP_002511841.1| DNA-directed RNA polymerase beta chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|307128161|ref|YP_003880192.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           670-6B]
 gi|254765308|sp|B8ZNW7|RPOB_STRPJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|147763506|gb|EDK70442.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP19-BS75]
 gi|147922260|gb|EDK73381.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP3-BS71]
 gi|147928153|gb|EDK79171.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           SP9-BS68]
 gi|147929949|gb|EDK80937.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP23-BS72]
 gi|183571598|gb|EDT92126.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           SP195]
 gi|183575332|gb|EDT95860.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           CDC3059-06]
 gi|220675149|emb|CAR69733.1| DNA-directed RNA polymerase beta chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|301800724|emb|CBW33372.1| DNA-directed RNA polymerase beta chain [Streptococcus pneumoniae
           OXC141]
 gi|306485223|gb|ADM92092.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           670-6B]
 gi|332072043|gb|EGI82530.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           GA17570]
 gi|332072149|gb|EGI82635.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           GA41301]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVIAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|322391275|ref|ZP_08064746.1| DNA-directed RNA polymerase subunit beta [Streptococcus peroris
           ATCC 700780]
 gi|321145879|gb|EFX41269.1| DNA-directed RNA polymerase subunit beta [Streptococcus peroris
           ATCC 700780]
          Length = 1200

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 580/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRTLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +E G V+    +E I      D+  +   
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDPETGEILVEKGTVMTRDVIESIEDHLDGDLNKIV-- 335

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                         D     +  +L  ++V+ P D                         
Sbjct: 336 ----------YTPNDSAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR I   DI+A +   ++L  G G IDDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTITPADILAEMSYFLNLAEGIGRIDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN++V+L+A EE+   +AQANS L+ DG+F E++V  R
Sbjct: 540 HLNIYGFIQTPYRKVDRATGKVTNEIVWLTADEEDEYTVAQANSKLNADGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPSSSVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAIIAQYDGKVTYADADKVEVRREDGSLD-------VYHVQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|149003618|ref|ZP_01828483.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP14-BS69]
 gi|237650981|ref|ZP_04525233.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           CCRI 1974]
 gi|237821634|ref|ZP_04597479.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           CCRI 1974M2]
 gi|147758350|gb|EDK65350.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP14-BS69]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  475 bits (1223), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIYIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|307708109|ref|ZP_07644577.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis NCTC
           12261]
 gi|307615894|gb|EFN95099.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis NCTC
           12261]
          Length = 1201

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDAVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDAVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|307710994|ref|ZP_07647416.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK321]
 gi|307616956|gb|EFN96134.1| DNA-directed RNA polymerase, beta subunit [Streptococcus mitis
           SK321]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|166030466|ref|ZP_02233295.1| hypothetical protein DORFOR_00127 [Dorea formicigenerans ATCC
           27755]
 gi|166029718|gb|EDR48475.1| hypothetical protein DORFOR_00127 [Dorea formicigenerans ATCC
           27755]
          Length = 1290

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/953 (45%), Positives = 592/953 (62%), Gaps = 56/953 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + +  E++ +P+LIEVQK SYD FL            GL+  F+ + PIT +SG
Sbjct: 13  KSSRMSYSRQKEVLQMPNLIEVQKDSYDWFL----------KSGLKEVFEDISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LE V +    D  K+ +D+C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  KLSLELVDFTLCEDDVKYSIDECRDRDATYAAPLKVRVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++
Sbjct: 114 EIFMGDLPLMTRTGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKKLYSSTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNPEIIELFGEEPKIMASFEKDAA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 TNYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKL-LLKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED V+  TGE+  EAG  +  +  + I +  +  + I   +   N   + N +V
Sbjct: 290 SGHVLAEDAVSPITGEVIAEAGTKVTREIADRIQNGAVPYVWIDRPEEERNVKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                          + +   D     V E ++  +  +  +     +  +K  ++ ++ 
Sbjct: 350 DL-------------KEVVDIDPEEVGVTELVYYPVLANLLEETAGDIDELKAAIKRDIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 397 -DLIPKHITKEDIMASINYNMHLEYGLGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRME 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINEYGFIEAPYR 575

Query: 604 KV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      + +VT++VVY++A EE+N ++AQAN +LDE+G F  + V  R   E     R
Sbjct: 576 KIDHSDPENPRVTDEVVYMTADEEDNYHVAQANETLDEEGHFVHKNVSGRYREETQAYER 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +  D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 KAFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLMTEAPVVGTGMEEK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+ AG+VE+  +  I IR  +G L         Y+L KF RSNQ+ C NQ
Sbjct: 696 AAVDSGVCVVAEEAGVVERSTSAEIQIRQDDGKLKK-------YKLTKFLRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           R +V  GD V + D+IADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+V +DV
Sbjct: 749 RAIVFKGDRVEKGDVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIP V ++ LKN+D+ GII VGAEV  GDILVGK+
Sbjct: 809 YTSIHIEEYEAEARDTKLGPEEITRDIPGVGDDALKNLDDRGIIRVGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 869 TPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRSNGD 921



 Score =  557 bits (1436), Expect = e-156,   Method: Composition-based stats.
 Identities = 255/1144 (22%), Positives = 422/1144 (36%), Gaps = 70/1144 (6%)

Query: 267  IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            I+  E+VI S    + G+  ++    +     +S  +       +         Y+    
Sbjct: 131  INGAERVIVSQLVRSPGIYYAIAHDKLGKKLYSSTVIPNRGAWLEYETDSNDVFYVRVDR 190

Query: 327  VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                     I    I   P + ++       I  +   D   + ++ LL++Y+ +RPG+ 
Sbjct: 191  TRKVPITVLIRALGIGTNPEI-IELFGEEPKIMASFEKDAATNYQEGLLELYKKIRPGEP 249

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                 AES+   +FFD  +YDL+ VGR K N +L L        + ++ +  I       
Sbjct: 250  LAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKLLLKNRISGHVLAEDAVSPIT------ 303

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
              G+   +    +       +         +     ER++K   + +     +       
Sbjct: 304  --GEVIAEAGTKVTREIADRIQNGAVPYVWIDRPEEERNVKVLSNMMVDLKEVVDIDPEE 361

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
              V   V     ++ L +    ++ L      R +  L    + +      +       Y
Sbjct: 362  VGVTELVYYPVLANLLEETAGDIDELKAAI-KRDIHDLIPKHITKEDIMASINYNMHLEY 420

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G     +     N   + ++    +      +    R V +   T D+  +S     N  
Sbjct: 421  GLGNDDDIDHLGN-RRIRAVGELLQNQYRIGLSRMERVVRERMTTQDLEGISPQSLINIK 479

Query: 627  IAQANSS----------LDEDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVV 672
               A               +  +   EL   R             R   +  D       
Sbjct: 480  PVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYG 539

Query: 673  SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
             +     P   N      L       +   +         +  E+         + A   
Sbjct: 540  RMCPIETPEGPNIGLINSLASYARINEYGFIEAPYRKIDHSDPENPRVTDEVVYMTADEE 599

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVR 789
                   A    +      +  + SG        ++R   +   V+ + +  V       
Sbjct: 600  DNYHVAQANE-TLDEEGHFVHKNVSGRYREETQAYERKAFDYMDVSPKMVFSVATALIPF 658

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEF 847
              +  A+              +L+   P  G   E+   +     +V+E+          
Sbjct: 659  LQNDDANRALMGSNMQRQAVPLLMTEAPVVGTGMEEKAAVDSGVCVVAEEAGVVERSTSA 718

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  +    +        ++  I+  G  V  GD++    +        
Sbjct: 719  EIQIRQD-DGKLKKYKLTKFLRSNQSNCYNQRAIVFKGDRVEKGDVIADGPSTSNGELAL 777

Query: 908  PEEKLLRAI--FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE--- 962
             +  L+  +   G    D    S R+      T + +  +     D       + R+   
Sbjct: 778  GKNPLIGFMTWEGYNYEDAVLLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDIPG 837

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              +   ++ DD   I+      R  +IL G+    G         L   +  E  R    
Sbjct: 838  VGDDALKNLDDR-GIIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 892

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E      +            K+     GD+M PGV + V++++A KR
Sbjct: 893  -------------EVRDTSLKVPHGEYGIVVDAKVFTRSNGDEMSPGVNQSVRIYIAQKR 939

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL 
Sbjct: 940  KISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLS 999

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI          +       +    ++     +   +++
Sbjct: 1000 LAAKALGFNISTPVFDGANEIDIMDTLDLANDYVNLSWEEFEKKHKEELLPEVLDYLYEN 1059

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                               + +   +   G+  L DG TGE FD PVT+G+++ LKL+H+
Sbjct: 1060 --------------RDHRKLWKGVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHL 1105

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV
Sbjct: 1106 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDV 1165

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +GR + YE+I+ G +  E G PESF VL+KE+Q+LGL + +          ME   D  +
Sbjct: 1166 IGRVKTYEAIIKGENIPEPGIPESFKVLLKELQSLGLDVRVLRDDNTEVEIMET-SDMGE 1224

Query: 1383 CELK 1386
               +
Sbjct: 1225 TSFR 1228


>gi|315612444|ref|ZP_07887357.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           ATCC 49296]
 gi|315315425|gb|EFU63464.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           ATCC 49296]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIEHHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQFDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|331267074|ref|YP_004326704.1| DNA-dependent RNA Polymerase, beta subunit [Streptococcus oralis
           Uo5]
 gi|326683746|emb|CBZ01364.1| DNA-dependent RNA Polymerase, beta subunit [Streptococcus oralis
           Uo5]
          Length = 1203

 Score =  832 bits (2150), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTETMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYGGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|301794905|emb|CBW37366.1| DNA-directed RNA polymerase beta chain [Streptococcus pneumoniae
           INV104]
          Length = 1203

 Score =  832 bits (2149), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLKEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|322374982|ref|ZP_08049496.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. C300]
 gi|321280482|gb|EFX57521.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. C300]
          Length = 1203

 Score =  832 bits (2149), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIEHHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSHLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|293364291|ref|ZP_06611017.1| DNA-directed RNA polymerase subunit beta [Streptococcus oralis ATCC
           35037]
 gi|307702743|ref|ZP_07639695.1| DNA-directed RNA polymerase, beta subunit [Streptococcus oralis
           ATCC 35037]
 gi|291317137|gb|EFE57564.1| DNA-directed RNA polymerase subunit beta [Streptococcus oralis ATCC
           35037]
 gi|307623859|gb|EFO02844.1| DNA-directed RNA polymerase, beta subunit [Streptococcus oralis
           ATCC 35037]
          Length = 1203

 Score =  832 bits (2149), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNVTTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNTNPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 997

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 998  ------------------------------------DTVKE---------AGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|306828840|ref|ZP_07462032.1| DNA-directed RNA polymerase subunit beta [Streptococcus mitis ATCC
           6249]
 gi|304429018|gb|EFM32106.1| DNA-directed RNA polymerase subunit beta [Streptococcus mitis ATCC
           6249]
          Length = 1203

 Score =  832 bits (2149), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 584/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTETMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVLTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRVVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P E +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 239/507 (47%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|322377182|ref|ZP_08051674.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. M334]
 gi|321281895|gb|EFX58903.1| DNA-directed RNA polymerase, beta subunit [Streptococcus sp. M334]
          Length = 1203

 Score =  832 bits (2148), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E I      D+      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIESIESYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   YI N    D        +L  ++V+ P D                         
Sbjct: 332 --NKIVYIPN----DAAVVTDPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRIVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  474 bits (1219), Expect = e-131,   Method: Composition-based stats.
 Identities = 166/507 (32%), Positives = 237/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   L   I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLDIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|163813884|ref|ZP_02205278.1| hypothetical protein COPEUT_00037 [Coprococcus eutactus ATCC 27759]
 gi|158450754|gb|EDP27749.1| hypothetical protein COPEUT_00037 [Coprococcus eutactus ATCC 27759]
          Length = 1293

 Score =  832 bits (2148), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/989 (43%), Positives = 605/989 (61%), Gaps = 73/989 (7%)

Query: 9   GLGRV---------RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+         R  + K  +++D+P+ IEVQK SY+ FL            GL+ AF
Sbjct: 2   EKNRISPVKSGKGYRMSYAKQKDVLDMPNFIEVQKNSYNWFLTD----------GLREAF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           + + PIT +SG   LEFV ++F     K+ +++C  RD TYA PL++ +RL V D     
Sbjct: 52  RDISPITDYSGQYSLEFVDFQFCKNDLKYSIEECKERDATYAAPLRVKVRLRVKDAP--- 108

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 D+ E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++D    +    GK
Sbjct: 109 ------DMPEYEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYDITHDKV---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP-- 234
            LYAC +IP++G W++ E DS D+ +VR+DR RKVPVT  + ALG+ ++ EI+  F    
Sbjct: 160 KLYACTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGLGTDQEIIDLFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KI+ S   D           +           ++  E +I +         L K  + K 
Sbjct: 220 KIMESLNKDPAKSYSEGVVELYKKIRPDEPSVVENAESLINAMFFDARRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +    + G  +AED ++  TGE+  EAG V+ E+  + I  +    +P + + + 
Sbjct: 280 NKKLAL-KARIAGHVLAEDAIDPSTGEVIAEAGTVVSEELADTIQDA---AVPYVMIQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             N  + + ++ +                   D +   + E ++  +     +       
Sbjct: 336 ERNVKVLSNMMVNIANYVD------------FDPAELGIVERVYYPVLEGLLEEYGDDTE 383

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           ++K  +  ++ +    +HI KEDI A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 384 KLKAAVERDM-SDLVPKHITKEDIFASINYNIHLEYGIGFDDDIDHLGNRRIRAVGELLQ 442

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER+++ D +S+ PQ LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 443 NQYRIGLSRLERVVRERMTTQDAESITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 502

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++AR+
Sbjct: 503 SELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARI 562

Query: 593 NAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGF+E PYR++      +  VT++VVYL+A EE+   + QAN  +D DG F    V  
Sbjct: 563 NEYGFVEAPYRRLDKTDPKNPVVTDEVVYLTADEEDRYRVVQANEPIDADGHFVRNNVSG 622

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   +    P+ K+D +D SPK V S+A S+IPFL+NDD+NR LMG NMQRQAVPL+  E
Sbjct: 623 RFRADTTEFPKSKVDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLMMTE 682

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +  VGTGME+  A  SG  +VAKR G+VE  ++  I IR+ E          D+Y ++KF
Sbjct: 683 SAVVGTGMEAKAAVDSGVCVVAKRDGVVEYSNSTEICIRADE------DGKKDVYHVIKF 736

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ  C+NQRP+V  GD V+  D+IADGPST  G++ALG+N L+ FM W GYN+ED++
Sbjct: 737 ARSNQGNCMNQRPIVFKGDHVKAGDVIADGPSTSGGEIALGKNPLIGFMTWEGYNYEDAV 796

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TSIHIE++E  ARDTKLG EEITRD+  +S + LK++DE GII +GAE
Sbjct: 797 LLSERLVRDDVYTSIHIEKYECEARDTKLGKEEITRDLAGLSNDVLKDLDENGIIRIGAE 856

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G V+D ++F R
Sbjct: 857 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAFGIVIDAKVFTR 916

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   G+DK  R    ++ +I++  +
Sbjct: 917 ADGDDLPAGVDKKVRVYIAQKRKIQVGDK 945



 Score =  558 bits (1437), Expect = e-156,   Method: Composition-based stats.
 Identities = 256/1133 (22%), Positives = 419/1133 (36%), Gaps = 83/1133 (7%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            +   +      K +    +  +   G ++  +  + +   + ++    +    L      
Sbjct: 148  IYYDITHDKVGKKLYACTVIPNR--GAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGL 205

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                  I   D       I  +L  D  K   + ++++Y+ +RP + S    AES+ N +
Sbjct: 206  GTDQEII---DLFGEEPKIMESLNKDPAKSYSEGVVELYKKIRPDEPSVVENAESLINAM 262

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD+ +YDL+ VGR K N +L L        + ++ I              G +      
Sbjct: 263  FFDARRYDLAKVGRYKFNKKLALKARIAGHVLAEDAIDPST----------GEVIAEAGT 312

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                  +          + +   ER++K   + +   +           +V  V      
Sbjct: 313  VVSEELADTIQDAAVPYVMIQTEERNVKVLSNMMVNIANYVDFDPAELGIVERVYYPVLE 372

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L +  +    L +    R +S L    + +      +       YG     +     N
Sbjct: 373  GLLEEYGDDTEKL-KAAVERDMSDLVPKHITKEDIFASINYNIHLEYGIGFDDDIDHLGN 431

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS------ 633
               + ++    +      +    R V +   T D   ++     N     A         
Sbjct: 432  -RRIRAVGELLQNQYRIGLSRLERVVRERMTTQDAESITPQSLINIKPVTAAVKEFFGSS 490

Query: 634  ----LDEDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLEND 685
                  +  +   EL   R             R   +  D        +     P   N 
Sbjct: 491  QLSQFMDQNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNI 550

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                 L       +   +         T  ++ V       + A        V A   + 
Sbjct: 551  GLINSLATYARINEYGFVEAPYRRLDKTDPKNPVVTDEVVYLTADEEDRYRVVQANEPID 610

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLG 803
                   +  +           +       V+ + +  V         +  A+       
Sbjct: 611  ADGHFVRNNVSGRFRADTTEFPKSKVDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSN 670

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                   +++      G   E    +     +V++      +    E+  R  + G +++
Sbjct: 671  MQRQAVPLMMTESAVVGTGMEAKAAVDSGVCVVAKRDGVVEYSNSTEICIRADEDGKKDV 730

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I          +++  I+  G  V  GD++    +  G   +   +  L      + 
Sbjct: 731  YHVIKFARSNQGNCMNQRPIVFKGDHVKAGDVIADGPSTSG-GEIALGKNPLIGFMTWEG 789

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--------- 972
             +  D  L     +S  +V   ++    I+K E      +   E + RD           
Sbjct: 790  YNYEDAVL-----LSERLVRDDVYTSIHIEKYECEARDTKLGKEEITRDLAGLSNDVLKD 844

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      R  +IL G+    G         L   +  E  R             
Sbjct: 845  LDENGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------- 891

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E      +            K+     GDD+P GV + V+V++A KR IQ GDKMA
Sbjct: 892  ----EVRDTSLKVPHGAFGIVIDAKVFTRADGDDLPAGVDKKVRVYIAQKRKIQVGDKMA 947

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HLG A   LG K
Sbjct: 948  GRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLGLASQVLGFK 1007

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + + + +     DI             G+  +  + Y D     V +             
Sbjct: 1008 VSTPVFNGATEFDIMDTLEMAND-YANGTWEDFEAKYKDTVKPEVMDFLY---------- 1056

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                     +  +   ++ +G+  L DG TGE FD PVT+GY++ LKL+H+V DK++ARS
Sbjct: 1057 ---KNRDHRAEWKGVPINRTGKVQLRDGRTGENFDAPVTIGYMHYLKLHHLVDDKIHARS 1113

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+
Sbjct: 1114 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEA 1173

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP-DFNKC 1383
            I+ G +    G PESF VL+KE QALGL + +           + +  D ++ 
Sbjct: 1174 IIKGENIPAPGVPESFKVLLKEFQALGLDVRVVREEDDEDGNKKMVEVDLSET 1226


>gi|164686520|ref|ZP_02210548.1| hypothetical protein CLOBAR_00087 [Clostridium bartlettii DSM
           16795]
 gi|164604389|gb|EDQ97854.1| hypothetical protein CLOBAR_00087 [Clostridium bartlettii DSM
           16795]
          Length = 1240

 Score =  831 bits (2147), Expect = 0.0,   Method: Composition-based stats.
 Identities = 438/955 (45%), Positives = 597/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY  FL           EGL+  F  + PI  ++G
Sbjct: 9   KRKRMSFSKIKEIADLPNLIEIQVDSYKWFL----------EEGLKEVFNDISPIEDYTG 58

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 59  NLILEFVDYSLDDKPKYDIEECKERDATYCAPLKVKVRLI---------NKETGEIKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R++VSQL RSPG+++  ++ +    GK L +  +IP++G
Sbjct: 110 VFMGDFPLMTDRGTFVINGAERVIVSQLVRSPGVYYALERDKT---GKKLISSTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+I VR+DR RK PVT  L ALG+ +  EI+             +     
Sbjct: 167 AWLEYETDSNDVISVRVDRTRKQPVTVLLRALGIGTNAEIIELLGEDERLMATLEKDNTT 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 227 NVEEGLVEIYK------KLRPGEPPTVESASSLINALFFDAKRYDLAKVGRYKFNKKLAL 280

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +      +DI+N ETGE++++A + I      +I +S I  + I   +         
Sbjct: 281 AYRIMNRVAYDDIINPETGEVFVKADEKISYDDAWKIQNSGINAVTIKTDEDRKVKVIGN 340

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + D     L+I   +              +  L    D+Y      +  + +R
Sbjct: 341 NFVDIKAHIDFDIDDLNIKEKVH-------------YPTLKEILDEYSDEEEIKESIKIR 387

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           +    P   +HI  +DIIA I    +L  G G IDDID+LGNRR+RSVGE+L+NQ R+GL
Sbjct: 388 IKELVP---KHILLDDIIASISYEFNLFFGIGNIDDIDHLGNRRIRSVGELLQNQVRIGL 444

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER I+ER++  D++S+ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 445 SRMERVIRERMTVQDMESITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 504

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A++N YGFIE
Sbjct: 505 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTYAKINEYGFIE 564

Query: 600 TPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK      K+T+++ YL+A EE+     QAN  L+ DGSF    V CR   G   LV
Sbjct: 565 SPYRKYDKETGKMTDEIHYLTADEEDLFIRVQANEPLNSDGSFVNSKVVCRTVNGAVELV 624

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P E++DF+D SPKQVVSIA ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 625 PTERVDFMDISPKQVVSIATAMIPFLENDDANRALMGANMQRQAVPLMRREAPIIGTGVE 684

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VAK +GI E+V A  IVI+  +G+ D        Y+L+KF+RSN  TC+
Sbjct: 685 YRAAKDSGAVVVAKNSGIAERVTADEIVIKREDGNRD-------RYKLLKFKRSNHGTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P++  G+ ++  D+IADGP+TDLG++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 738 NQTPIINKGEMIKAGDVIADGPATDLGEIALGRNCLIAFMTWEGYNYEDAVLINERLVKE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEIT+DIPNV E  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 798 DRLSTIHIEEYECEARDTKLGPEEITKDIPNVGESAIKNLDDRGIIRIGAEVDSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVFTRENGD 912



 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 169/536 (31%), Positives = 247/536 (46%), Gaps = 69/536 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +          I++  II  G  +  GD++           +      
Sbjct: 714  KREDGNRDRYKLLKFKRSNHGTCINQTPIINKGEMIKAGDVIADGPATDL-GEIALGRNC 772

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L         V + R+   H  +    +    +   E + +D  
Sbjct: 773  LIAFMTWEGYNYEDAVLIN----ERLVKEDRLSTIHIEEYECEARDT-KLGPEEITKDIP 827

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +      +N+  R   I  G    SG     K T      ++   R     F  +  +V+
Sbjct: 828  NVGESAIKNLDDR-GIIRIGAEVDSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVR 886

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GDD+ PGV  +V+ ++A KR I+ GDKMAG
Sbjct: 887  DTSLKVPHGESGIIVDV------KVFTRENGDDLSPGVNELVRCYIAKKRKIKVGDKMAG 940

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SR+LP EDMPF++DGTP+DIVLNP G+PSRMN+GQ+ E HLG A   LG  +
Sbjct: 941  RHGNKGVISRVLPEEDMPFMEDGTPMDIVLNPQGIPSRMNIGQVLEMHLGLAAKKLGWHV 1000

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     DI                                               
Sbjct: 1001 ATSVFDGAKETDIMDALEEAGYPRDGKLTL------------------------------ 1030

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G++       G+ FD  +TVGY+Y LKL+H+V +K++ARST
Sbjct: 1031 -----------------YDGRT-------GDTFDNRITVGYMYYLKLHHLVDEKLHARST 1066

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA++LQE+LT+KSDDVVGR R YE+I
Sbjct: 1067 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHILQEILTVKSDDVVGRVRTYEAI 1126

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME--EIPDFNKCELK 1386
            V G +  E G PESF VL+KE+Q+L L + + +   +     E  ++ D      +
Sbjct: 1127 VKGENIPEPGIPESFKVLIKELQSLCLDVKVLSEEDEELEVRESTDLDDEVDGNFE 1182


>gi|313884740|ref|ZP_07818495.1| DNA-directed RNA polymerase, beta subunit [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620001|gb|EFR31435.1| DNA-directed RNA polymerase, beta subunit [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 1206

 Score =  831 bits (2147), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/961 (43%), Positives = 572/961 (59%), Gaps = 80/961 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G    R+ + +  E++++P+LIE+Q  SY  FL          +EGLQ  F  +
Sbjct: 4   HHIVKYGKKAERRSYSRIHEVLEMPNLIEIQTDSYQWFL----------DEGLQLMFDDI 53

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI   S    L FV Y     K+DV++    D  Y+ P+ +TLRLI          K  
Sbjct: 54  SPIVDHSENLELHFVGYSLKEAKYDVNEARSHDANYSRPIYVTLRLI---------NKET 104

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++ GD P+MT+ GTF+I G +R++VSQL RSP ++F     R     +  +  
Sbjct: 105 GEVKEQEVFFGDFPMMTEMGTFIINGAERVIVSQLVRSPSVYFH---DRVDKKNRHTFTT 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W++ E D+K + + RIDR RK+P+T  + ALG +S+E I+  F    +    
Sbjct: 162 TVIPNRGAWLEFETDAKGVAYTRIDRTRKLPMTELIRALGFESDEEIIDIFTESDLLEAT 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            D      + AD  +   +      +  GE    ES + L        +   +  +G   
Sbjct: 222 LDKD-VHKNIADSRIEESLKDIYERLRPGEPKTAESSRNLLIARFFDPRRYDLAPVGRYK 280

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                     L GL +AE++ + ETGEI    G  +    ++ +      +I ++ +   
Sbjct: 281 INKKLNLKYRLQGLTLAENLADPETGEIIFPEGTELTHDKMDTLIPYLENNINLVTLYPS 340

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                             +   + I +V  P D                           
Sbjct: 341 EEGVL------------GEPVDVQIIKVYSPRDP-------------------------- 362

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              +N+  N +   DVR +   DIIA     + L  G G  DDID+LGNRR+RSVGE+L+
Sbjct: 363 EKVINIIGNGNITPDVRSLTPADIIASANYYLFLDYGIGVSDDIDHLGNRRIRSVGELLQ 422

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  D  S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L
Sbjct: 423 NQFRIGLSRMERVVRERMSLQDTSSMTPQQLINIRPVVAAIKEFFGSSQLSQFMDQSNPL 482

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L S+A++
Sbjct: 483 GELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLASYAKI 542

Query: 593 NAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYRKV     K T+ + YL+A EE+   +AQANS L+EDGSF  E V  R  
Sbjct: 543 NEYGFIETPYRKVDKATHKPTDQIDYLTADEEDYYVVAQANSKLNEDGSFANETVMARYV 602

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E + +P E++D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPLLK  APF
Sbjct: 603 DENLEIPIERVDYMDVSPKQVVSVATASIPFLENDDSNRALMGANMQRQAVPLLKPHAPF 662

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SGAA++ KR G V  VDA  + ++  +G +D        Y L KF RS
Sbjct: 663 VGTGIEYQAAHDSGAALLCKRDGQVIYVDANEVKVQLEDGSVDS-------YHLTKFARS 715

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N  TC NQRPLV+ G++V + DI+ADGPS   G+++LG+N LVAFM W GYN+ED++++S
Sbjct: 716 NAGTCYNQRPLVRTGEQVEKGDILADGPSMQNGEMSLGQNPLVAFMTWDGYNYEDAIIMS 775

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +DV+TSIHIEE+E  ARDTKLGPEEITR+IPNVSE+ LK +D+ GII +GAEV  
Sbjct: 776 ERLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVSEDALKYLDKDGIIAIGAEVRD 835

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   
Sbjct: 836 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTRENG 895

Query: 951 D 951
           D
Sbjct: 896 D 896



 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 256/1087 (23%), Positives = 384/1087 (35%), Gaps = 151/1087 (13%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
             I       + E      F S+   I I     +      ++      +   +++L DIY
Sbjct: 184  RIDRTRKLPMTELIRALGFESDEEIIDIFTESDLLEATLDKDVHKNIADSRIEESLKDIY 243

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TP 425
              +RPG+  T   + ++    FFD  +YDL+ VGR K+N +LNL               P
Sbjct: 244  ERLRPGEPKTAESSRNLLIARFFDPRRYDLAPVGRYKINKKLNLKYRLQGLTLAENLADP 303

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL-----L 480
            +    I  E        +  L        ++  L       +GE +  Q           
Sbjct: 304  ETGEIIFPEGTELTHDKMDTLIPYLENNINLVTLYPSEEGVLGEPVDVQIIKVYSPRDPE 363

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            ++   I     + D+ S+ P D+I +      +      S       +    S     + 
Sbjct: 364  KVINIIGNGNITPDVRSLTPADIIASANYYLFLDYGIGVSDDIDHLGNRRIRSVGELLQN 423

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
               +G   + R                R+   +TS      L++     A +  +     
Sbjct: 424  QFRIGLSRMERVVRE------------RMSLQDTSSMTPQQLINIRPVVAAIKEFFGSSQ 471

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
              + +       ++ +                           L       +        
Sbjct: 472  LSQFMDQSNPLGELTH---------------------KRRLSALGPGGLTRDRAGYEVRD 510

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG---MES 717
            + +        +         L N+ ++   +      +       +A    T      +
Sbjct: 511  VHYTHYGRMCPIETPEGPNIGLINNLASYAKINEYGFIETPYRKVDKATHKPTDQIDYLT 570

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
               +       A      +   A   V+     +          Y          +    
Sbjct: 571  ADEEDYYVVAQANSKLNEDGSFANETVMARYVDENLEIPIERVDY---------MDVSPK 621

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V         +  ++              +L    P+ G   E             
Sbjct: 622  QVVSVATASIPFLENDDSNRALMGANMQRQAVPLLKPHAPFVGTGIEYQAAHDSGAALLC 681

Query: 838  VFTSIHIEEFEVMAR-DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                  I       +   + G  +                ++  ++  G +V  GDIL  
Sbjct: 682  KRDGQVIYVDANEVKVQLEDGSVDSYHLTKFARSNAGTCYNQRPLVRTGEQVEKGDILAD 741

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
              +      M+  +  L A       +  D  +                    + K++  
Sbjct: 742  GPS-MQNGEMSLGQNPLVAFMTWDGYNYEDAIIMS----------------ERLVKDDVY 784

Query: 957  ISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKGFKKST 1006
             S+  E+ E  ARD       + R I            +   I  G     G     K T
Sbjct: 785  TSIHIEEYESEARDTKLGPEEITREIPNVSEDALKYLDKDGIIAIGAEVRDGDILVGKVT 844

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  +S   R     F  +  +V+     +          +      KI   + GD++
Sbjct: 845  PKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV------KIFTRENGDEL 898

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV  +V+VF+  KR IQ GDKMAGRHGNKG+VS I+P EDMPFL DGTPVDI+LNPLG
Sbjct: 899  SPGVNMLVRVFIVQKRKIQVGDKMAGRHGNKGVVSLIVPEEDMPFLPDGTPVDIMLNPLG 958

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+FE HLG A   LG  I + + D     D                      
Sbjct: 959  VPSRMNIGQVFELHLGMAARSLGINIATPVFDGANEND---------------------- 996

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                   V++   E           + E  ++ILYDG TGEPFD
Sbjct: 997  -----------------------VWETVKEA---------GMAEDAKTILYDGRTGEPFD 1024

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            R V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1025 RKVSVGVMYMMKLGHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1084

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDDVVGR + YE+IV G      G PESF VLVKE+QALGL + + + 
Sbjct: 1085 AAYTLQEILTYKSDDVVGRVKTYEAIVKGEQIPRPGVPESFRVLVKELQALGLDLKVLDQ 1144

Query: 1367 RTKNSAK 1373
              +    
Sbjct: 1145 DDQEIDL 1151


>gi|15901784|ref|NP_346388.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           TIGR4]
 gi|111658849|ref|ZP_01409470.1| hypothetical protein SpneT_02000020 [Streptococcus pneumoniae
           TIGR4]
 gi|149007435|ref|ZP_01831078.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP18-BS74]
 gi|225855453|ref|YP_002736965.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           JJA]
 gi|41018113|sp|Q97NQ7|RPOB_STRPN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|254765310|sp|C1CGP4|RPOB_STRZJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|14973467|gb|AAK76028.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           TIGR4]
 gi|147761007|gb|EDK67976.1| DNA-directed RNA polymerase beta subunit [Streptococcus pneumoniae
           SP18-BS74]
 gi|225722523|gb|ACO18376.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           JJA]
 gi|332071939|gb|EGI82427.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           GA17545]
          Length = 1203

 Score =  831 bits (2146), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETSEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVIAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|289168678|ref|YP_003446947.1| DNA-dependent RNA Polymerase, beta subunit [Streptococcus mitis B6]
 gi|288908245|emb|CBJ23087.1| DNA-dependent RNA Polymerase, beta subunit [Streptococcus mitis B6]
          Length = 1202

 Score =  831 bits (2146), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +++ RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSNKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDEQEVELRDLDEGMDE 1159


>gi|42518422|ref|NP_964352.1| DNA-directed RNA polymerase subunit beta [Lactobacillus johnsonii
           NCC 533]
 gi|81668275|sp|Q74L95|RPOB_LACJO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|41582707|gb|AAS08318.1| DNA-directed RNA polymerase beta chain [Lactobacillus johnsonii NCC
           533]
          Length = 1209

 Score =  831 bits (2146), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/988 (42%), Positives = 593/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 102 ETGEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ EI   F       
Sbjct: 159 GATVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEIADMFGESDSIR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 219 FTLEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + GDV+  + L+++              
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHELLDKL-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               + Y+          DR D  +  Y   + G +      + +  +   D ++     
Sbjct: 324 ----SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER----- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    DDV+H+   D++A I    DL++  GT DDID+LGNRR+R VGE+
Sbjct: 365 ----VVKLMSNGHIADDVKHLTPADVLASINYFFDLQDNIGTTDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R
Sbjct: 541 IVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNEDGSFKDKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A
Sbjct: 601 HKEDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+
Sbjct: 661 PIVGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R 
Sbjct: 834 QDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELPPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 263/1082 (24%), Positives = 398/1082 (36%), Gaps = 179/1082 (16%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRK-----DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            D    +  IR TL  D +K+       +AL DIY  +RPG+  T   + S+    FFD  
Sbjct: 209  DMFGESDSIRFTLEKDIHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPR 268

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHI--------------------RKEDIIAIIKILV 444
            +YDL+ VGR K+N +L+L      + +                      E +  +   L 
Sbjct: 269  RYDLAPVGRYKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHELLDKLSPYLD 328

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD-- 502
                   T +           +V E +K   ++   R+ + +     + D+  + P D  
Sbjct: 329  RDDFKMVTYEPSKEGVLPDPVTVQE-IKVYSKVDPERVVKLMSNGHIADDVKHLTPADVL 387

Query: 503  --LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
              +     +   +        L                R   A  +  V    +  ++  
Sbjct: 388  ASINYFFDLQDNIGTTDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQDIST 447

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR----------------K 604
            V P     I P   S     G         + N  G +    R                +
Sbjct: 448  VTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPLGELTHKRRMSALGPGGLSRDRAGYE 507

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            V D   T+          E   I   N  ++      +       R    +     +KID
Sbjct: 508  VRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIVNKYGFIETPYRRVSWDTHKVTDKID 567

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            ++ A  +    IA +     E D S +  +     ++    +  +       +       
Sbjct: 568  YLTADVEDNYIIAGANARLNE-DGSFKDKIVLARHKEDNLEVTPDK-IDYMDVIPKQV-- 623

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
               ++ +     +E  D+ R ++ +                    QR          P+V
Sbjct: 624  --VSVTSACIPFLENDDSNRALMGAN------------------HQRQAVPLINPHAPIV 663

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G               +        + LVA  P       + +  +E  +  D  T  
Sbjct: 664  GTG--------------MEYRAAHDSGDALVAKAPG----VVEYVDANEIRIRRDDDTLD 705

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--KITP 900
                  V+ +  +    +     P V +      DE  +I  G  +  G++ +G   I  
Sbjct: 706  KY----VLEKFRRSNATKNYNQTPAVKQGERVVADE--VIADGPAMENGELALGQNPIIA 759

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 M   E  +         DV           S  + D     R      E      
Sbjct: 760  FLTWNMYNYEDAVMISERMVKDDVY---------TSIHIEDYESEARDTKLGPEEITREI 810

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
                E   +D D+E  I+      +  +IL G+    G         L   +  E  R  
Sbjct: 811  PNVGEDALKDLDEE-GIVRIGAEVQDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR-- 867

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              +      +V      +                 ++   + GD++PPGV ++V+V++  
Sbjct: 868  --EVRDTSLRVPHGGGGIVQNV-------------QVFTREAGDELPPGVNKMVRVYIVQ 912

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKM+GRHGNKG ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E H
Sbjct: 913  KRKIQVGDKMSGRHGNKGTIALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLELH 972

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG A   LG  + + + D  +  D+  +                                
Sbjct: 973  LGIAAKQLGIHVATPVFDGASEDDMWNM-------------------------------- 1000

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                           E  I            G+++LYDG TGEPF   V+VG +Y LKL 
Sbjct: 1001 -------------VREAGIGK---------DGKTVLYDGRTGEPFHNRVSVGIMYYLKLT 1038

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSD
Sbjct: 1039 HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSD 1098

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K     +   D 
Sbjct: 1099 DVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIKVLDMDHKEIELRDMDDDS 1158

Query: 1381 NK 1382
            N 
Sbjct: 1159 ND 1160


>gi|315222771|ref|ZP_07864658.1| DNA-directed RNA polymerase, beta subunit [Streptococcus anginosus
           F0211]
 gi|315188134|gb|EFU21862.1| DNA-directed RNA polymerase, beta subunit [Streptococcus anginosus
           F0211]
          Length = 1188

 Score =  830 bits (2145), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 579/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE    K+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKESKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDPETGEILVEAGTVMTRSVIDSIAEYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   YI N    D        +L  ++V+ P D                         
Sbjct: 332 --NKITYIPN----DAAVLTDPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D V  I   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPGDRVHTITPADILAEMNYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L EDG F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRETGLVTNEIVWLTADEEDEFIVAQANSKLTEDGRFAEAIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEFPSDQVDFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAIIAQHDGKVVYSDAAKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 133/507 (26%), Positives = 205/507 (40%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDTVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +          +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGAGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A                 K    R +   D       
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIA----------------QK----RKIRVGD------- 919

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                                             G K          +    P  + ++ +
Sbjct: 920  ---------------------------KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIM 952

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +       +++      +         G+ ++TPVFDGA  + +   +R A +D   ++I
Sbjct: 953  LNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWDTVREAGMDSDAKTI 1012

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1013 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR R YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLRAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGMDD 1159


>gi|291544240|emb|CBL17349.1| DNA-directed RNA polymerase subunit beta [Ruminococcus sp. 18P13]
          Length = 1291

 Score =  830 bits (2145), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/959 (43%), Positives = 584/959 (60%), Gaps = 55/959 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  FGK  E++++P+LIEVQK SY  F            EGL+  F+ V  IT ++G
Sbjct: 13  KNTRMSFGKINEVLEMPNLIEVQKNSYKWF----------KEEGLKEVFRDVAAITDYNG 62

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L FV Y+ D  PK+ + +C  RD+TYA PL++   L           K   D+KE  
Sbjct: 63  NLVLNFVDYKIDDTPKYTIAECKERDVTYAAPLRVKATL---------WNKETGDVKESE 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTFVI G +R++VSQL RSPG+++  +K +    GK L+   +IP++G
Sbjct: 114 IFMGDFPLMTESGTFVINGAERVIVSQLVRSPGVYYAFEKDKT---GKDLFKATVIPNRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+ +VRID+ RK+P+T+F+ ALG+ ++E I   F       Q        
Sbjct: 171 AWLEYEMDSNDVAYVRIDKNRKIPLTTFIRALGIGTDEEIAEMFGNDERLRQTILQKDGT 230

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            + +D ++          +  GE   +ES  +    L    K   +   G          
Sbjct: 231 KNNSDALIDV-----YKKLRPGEPPTVESAIQHLDNLFFDAKRYDLSRFGRYKYNKKLGI 285

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              L G  ++  + N  TGE+  +AGD +  +   EI  + + +    Y++      Y  
Sbjct: 286 GSRLVGHILSRPVANELTGELLADAGDRLSFEKAMEIEQAGVYE---AYLNVETKEYYTN 342

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPG---DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
               T      K+  +    ++      D        +         +  + S   +   
Sbjct: 343 EQNETAIRMVEKEVKVIGNGMVDLSGYVDFDVLEYGINEKVSFKVLKEILESSADAQELE 402

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                       +HI  +DI A I    +L  G GT+DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 403 EQVKKRADELVPKHIILDDIYATISYFCNLCEGVGTVDDIDHLGNRRIRSVGELLQNQFR 462

Query: 477 LGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +G  RMER I+ER++    D+D + PQ L+N +P+ +A+ EFF SS LSQ  +  N L+ 
Sbjct: 463 IGFSRMERVIRERMNIQAQDMDVITPQALVNIRPITAAIKEFFGSSPLSQFMDQTNPLAE 522

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L +FAR+N 
Sbjct: 523 LTHKRRLSALGSGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLATFARINE 582

Query: 595 YGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGFIE PYRKV      VT++VVY++A  E+N  +AQAN  L E+G F  + V CR   +
Sbjct: 583 YGFIEAPYRKVDKATGVVTDEVVYMTADVEDNFIVAQANEPLTEEGKFARQRVNCRYREK 642

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            +   R+++D++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPLLK E PFVG
Sbjct: 643 ILECDRDQVDYMDVSPKMVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLKTERPFVG 702

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  SG  IV    G+VE V A  ++++  +G           Y+L KF+RSNQ
Sbjct: 703 TGMEYKAAVDSGVCIVCNADGVVESVCADEVIVKQEDGTKQK-------YKLTKFKRSNQ 755

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC+NQRP+V VG+ V++  ++ADGP+T  G+++LG+N L+ FM W GYN+ED++L++ER
Sbjct: 756 GTCINQRPIVSVGEAVKKGQVLADGPATADGEISLGKNALIGFMTWEGYNYEDAVLLNER 815

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDVFTS+HIEE+E+  RDTKLGPEEITRDIPNVS++ LK++DE GII +GAEV+ GD
Sbjct: 816 LVREDVFTSVHIEEYEIECRDTKLGPEEITRDIPNVSDDALKDLDEKGIIRIGAEVHSGD 875

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRD SL+VP G +G +VDV+IF R   D
Sbjct: 876 ILVGKVTPKGETELTAEERLLRAIFGEKAREVRDNSLKVPHGEAGVIVDVKIFTRDNCD 934



 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 104/265 (39%), Positives = 139/265 (52%), Gaps = 30/265 (11%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K        + +    P  + L+ V+       +++      V         
Sbjct: 959  KMAGRHGNKGVVSRILPEEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGMAAKAL 1018

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD------------------------------LDESG 1232
            G  + TPVFDGA E+ I + L  A+                              + E G
Sbjct: 1019 GWHIMTPVFDGAHEDDIRACLNAANEKNKKIQAEATEQYFTLNTMDKVINPNALEMCEDG 1078

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  LYDG TGE FD  VTVGY+Y LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQ
Sbjct: 1079 KFTLYDGRTGEKFDNRVTVGYMYYLKLHHLVDDKIHARSVGPYSLVTQQPLGGKAQFGGQ 1138

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDD VGR   YE+IV G +  + G PESF VL+K
Sbjct: 1139 RFGEMEVWALEAYGAAYTLQEILTVKSDDTVGRVNTYEAIVKGQNVPKPGIPESFKVLIK 1198

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEI 1377
            E+Q+LGL + + +   +     +  
Sbjct: 1199 ELQSLGLDVRVLDENQEEIDLKQNF 1223


>gi|319940287|ref|ZP_08014639.1| DNA-directed RNA polymerase subunit beta [Streptococcus anginosus
           1_2_62CV]
 gi|319810589|gb|EFW06925.1| DNA-directed RNA polymerase subunit beta [Streptococcus anginosus
           1_2_62CV]
          Length = 1188

 Score =  830 bits (2145), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/963 (43%), Positives = 579/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE    K+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKESKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    +S + L            +  +G 
Sbjct: 219 NTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTADSSRSLLVARFFDPHRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG V+    ++ I      D+      
Sbjct: 278 YKINKKLNIKTRLLNQTIAEPLVDPETGEILVEAGTVMTRNVIDSIAEYLDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N   YI N    D        +L  ++V+ P D                         
Sbjct: 332 --NKITYIPN----DAAVLTDPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D V  I   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPGDRVHTITPADILAEMNYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L EDG F E +V  R
Sbjct: 540 HLNKYGFIQTPYRKVNRETGLVTNEIVWLTADEEDEFIVAQANSKLTEDGRFAEAIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P +++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HQGNNQEFPSDQVDFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAIIAQHDGKVVYSDAAKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EEFE   RDTKLGPEEITR+IPNV E+ L+++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  473 bits (1217), Expect = e-131,   Method: Composition-based stats.
 Identities = 168/507 (33%), Positives = 235/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDTVEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEFESETRDTKLGPEEITREIPNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +          +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGGAGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWETVREAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR R YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLRAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1133 SLGLDMRVLDEDDNEVELRDLDEGMDD 1159


>gi|255029117|ref|ZP_05301068.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           LO28]
          Length = 1161

 Score =  830 bits (2144), Expect = 0.0,   Method: Composition-based stats.
 Identities = 441/944 (46%), Positives = 595/944 (63%), Gaps = 80/944 (8%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYE 80
            E++++P+LIE+Q ASY  FL          +EGL+  F+ + PI  F+G   LEF+ Y+
Sbjct: 1   SEVLELPNLIEIQTASYQWFL----------DEGLREMFRDISPIEDFAGNLSLEFIDYD 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              PK+ V++   RD  YA PL++ LRLI          K   ++K+Q ++MGD PLMT+
Sbjct: 51  LGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKETGEVKDQEVFMGDFPLMTE 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I G +R++VSQL RSPG++F+   G+   +GK  +   +IP++G W++ E D+KD
Sbjct: 102 MGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFGSTVIPNRGAWLEYETDAKD 158

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           ++HVRIDR RK+PVT  L ALG  S+ EI+             +      +   L+    
Sbjct: 159 VVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRNTLEKDNTDNAEKALL---- 214

Query: 260 VSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAE 310
                  +  GE   +++ + L        K           +       + L    +AE
Sbjct: 215 --EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRYKINKKLHLKNRLFNQTLAE 272

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            +V+ ETGEI    GD++D ++L++I            + ++ N    R    TD   + 
Sbjct: 273 TLVDPETGEIIASKGDILDRRNLDQI------------IPNLENGVGFRTLRPTDGVME- 319

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
              L+   ++  P D                             ++N+  N    ++V+H
Sbjct: 320 DSVLVQSIKIYAPND--------------------------EEKEINIIGNAYIEENVKH 353

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+
Sbjct: 354 ITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERM 413

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ 
Sbjct: 414 SIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLT 473

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDG 608
           R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V     
Sbjct: 474 RERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPETN 533

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R   E + V +E+ID++D SP
Sbjct: 534 RVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERIDYMDVSP 593

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK SGAA+ 
Sbjct: 594 KQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGAAVT 653

Query: 729 AKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           AK  GIVE V+A  I +R V   D    T G+D Y L KF RSNQ TC NQRP V  GD 
Sbjct: 654 AKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAEGDR 713

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+TSIHIEEF
Sbjct: 714 VVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEF 773

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           E  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TPKG + +T
Sbjct: 774 ESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTELT 833

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R   D
Sbjct: 834 AEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGD 877



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 246/1044 (23%), Positives = 392/1044 (37%), Gaps = 106/1044 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 188  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 247

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 248  ASVGRYKINKKLHLK--------NRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQII 299

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L+N   +G   +  +      SV + S+      + +  ++ +   +    +  +   
Sbjct: 300  PNLEN--GVGFRTLRPTDGVMEDSVLVQSIKIYAPNDEEKEINIIGNAYIEENVKHITPS 357

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 358  DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 417

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               +     I    R V          +  + +                      L    
Sbjct: 418  MTTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 471

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 472  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPE 531

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V   ++ + A      +VA+    +           + E  +    S        + 
Sbjct: 532  TNRVTDKIDYLTADEEDNYVVAQANSKL-----DEQGTFTEEEVMARFRSENLAVEKERI 586

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
               + +              +  +D        ++   A+      A     G     + 
Sbjct: 587  DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 646

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNIDECG 880
                 + ++      H+E  E+  R   L       G  +       V        ++  
Sbjct: 647  DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 706

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  V  G+IL    +      +     +L A       +  D  +         V 
Sbjct: 707  NVAEGDRVVKGEILGNGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SERLVK 761

Query: 941  DVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            D    + H  +    +   +    E    +    +D    LD     R+   +   + + 
Sbjct: 762  DDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLV 821

Query: 998  GPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            G    K  T L+++  L+      +  +      +V      +                 
Sbjct: 822  GKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV-------------LDV 868

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DG
Sbjct: 869  KIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDG 928

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+          
Sbjct: 929  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMA 988

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 989  RDAK----------------------------TILYDG---------------------- 998

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 999  ----RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1054

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q
Sbjct: 1055 EMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQ 1114

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +LG+ + + ++  +     +   D
Sbjct: 1115 SLGMDVKMLSADEEEIEMRDMDDD 1138


>gi|295425659|ref|ZP_06818346.1| DNA-directed RNA polymerase subunit beta [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064675|gb|EFG55596.1| DNA-directed RNA polymerase subunit beta [Lactobacillus
           amylolyticus DSM 11664]
          Length = 1210

 Score =  830 bits (2144), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/963 (41%), Positives = 581/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   V+  G  R R+ F K  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVLNYGKHRTRRSFSKIKEVLKLPNLTDVQTQSYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPIGDFSGKLSLEYVGYKLQKPKYTVDEARDHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+  +
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYSGDFDK---NGRQTF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VR+DR RK+P+T  + A+G+ S+ EIL  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSYVRVDRTRKLPLTVLIRAMGLGSDGEILDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLATVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  + G V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKGTVVTHEVMDKLEKYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +S     + +  +   + ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLSDPITVQEIKVYSKVNPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D+++ I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLISNGHIGSDVKHLTPADVLSSINYFFALQDQIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E+L+  R
Sbjct: 542 IINKYGFIETPYRRVSWKTHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKEKLILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 HKEDNVEVSPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK  G VE VD   I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALLAKAPGTVEYVDGNEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK GD+V  +DIIA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKKGDKVDASDIIANGPAMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEDGIVRIGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  468 bits (1204), Expect = e-129,   Method: Composition-based stats.
 Identities = 176/532 (33%), Positives = 244/532 (45%), Gaps = 81/532 (15%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             +  +    +     PNV +     +D   II  G  ++ G++ +G              
Sbjct: 711  EKYRRSNNSKSYNQTPNVKKG--DKVDASDIIANGPAMDHGELALG-------QNPLIAF 761

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
                    E A+ + +  ++     S ++ D     R      E          E   +D
Sbjct: 762  MTWNMYNYEDAIMLSERLVKDDVYTSISIEDYESEARDTKLGPEEITREIPNVGEDALKD 821

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+         +IL G+    G         L   +  E  R           +
Sbjct: 822  L-DEDGIVRIGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------E 869

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +          +      K+   + GD++ PGV  +V+V++A KR IQ GDKM
Sbjct: 870  VRDTSLRVPHGGGGIVQDV------KVYTREAGDELSPGVNTMVRVYIAQKRKIQVGDKM 923

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            +GRHGNKG V+ ++P EDMP+L DGTPVDI LNP+GVPSRMN+GQ+ E HLG A   LG 
Sbjct: 924  SGRHGNKGTVAAVVPEEDMPYLPDGTPVDICLNPMGVPSRMNIGQLLELHLGAAARQLGI 983

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + + + D     ++                            +R A   K G    T +
Sbjct: 984  HVATPVFDGANEDEVWNT-------------------------VRQAGVDKDG---KTVI 1015

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +DG                           +GEPF   V+VG ++ LKL HMV DK++AR
Sbjct: 1016 YDG--------------------------RSGEPFHNRVSVGVMHYLKLTHMVDDKIHAR 1049

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            S G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR R YE
Sbjct: 1050 SIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVRAYE 1109

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +IV G    + G PESF VLVKE+Q+LGL I + +         +   D N+
Sbjct: 1110 AIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMNHNEIELRDMDDDSNE 1161


>gi|169833177|ref|YP_001695315.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           Hungary19A-6]
 gi|226699453|sp|B1I8R4|RPOB_STRPI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|168995679|gb|ACA36291.1| DNA-directed RNA polymerase, beta subunit [Streptococcus pneumoniae
           Hungary19A-6]
          Length = 1203

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 582/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 159 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 219 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 278 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 329

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 330 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RL L RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQVRLELSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 539

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 540 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 600 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 773 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 725  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 783

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 784  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 843

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 844  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 887  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 946

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 947  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1005

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1006 ----------------------------------------DSDAKTIL------YDG--- 1016

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1017 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1072

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1073 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1132

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1133 SLGLDMRVLDEDDQEVELRDLDEGMDE 1159


>gi|329117465|ref|ZP_08246182.1| DNA-directed RNA polymerase, beta subunit [Streptococcus parauberis
           NCFD 2020]
 gi|326907870|gb|EGE54784.1| DNA-directed RNA polymerase, beta subunit [Streptococcus parauberis
           NCFD 2020]
          Length = 1192

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 588/963 (61%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 1   MAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQEFL----------DAGLKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YEF  PK+ +++    D +Y+ P+ +T RL+          K
Sbjct: 51  DVLPISNFTDTMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 102 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKIGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E D+KDI + RIDR RK+P T+ + ALG    +EI+  F    +  
Sbjct: 159 GSTVIPNRGAWLELETDAKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + +D      +      +  GE    +S + L        +   +  +G 
Sbjct: 219 NTIEKDI-HKNPSDSRTDEALKEIYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE++++ ETGEI +E+G V+  + +E I      D+      
Sbjct: 278 YKVNKKLNIKTRLLNQTIAENLIDAETGEILVESGTVMTREVIESIEEHIDGDL------ 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             N  AY  N    D     +  +L  ++V+ P D                         
Sbjct: 332 --NKFAYTPN----DYAVVTEPVILQKFKVVSPIDPDRV--------------------- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 365 -----VTLIGNAAPDDKVRALTPADILAEMSYFLNLSEGIGKVDDIDHLGNRRIRAVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ+R+GL RMER+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 420 LANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF 
Sbjct: 480 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFG 539

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV      VT+++V+L+A EE+   +AQANS L+EDG+F EE+V  R
Sbjct: 540 HLNKYGFIQTPYRKVDRSTGIVTSEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G         +DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  ++
Sbjct: 600 HQGNNQEFSASIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPKS 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+ +G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 660 PFVGTGMEYQAAHDSGAAVIAQYSGKVVFSDAEKVEVRREDGSLD-------VYHITKFR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVK GD + + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 713 RSNSGTAYNQRTLVKAGDIIEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TS+H+EEFE   RDTKLGPEEITR++PNV EE L+++DE GII +GAEV
Sbjct: 773 MSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALRDLDEMGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 833 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 176/590 (29%), Positives = 250/590 (42%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P+ G   E      S   V       +   + E +    + G 
Sbjct: 643  MGANMQRQAVPLINPKSPFVGTGMEYQAAHDSGAAVIAQYSGKVVFSDAEKVEVRREDGS 702

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++               ++  ++  G  +  GD +    +      M   +  + A   
Sbjct: 703  LDVYHITKFRRSNSGTAYNQRTLVKAGDIIEKGDFIADGPS-MENGEMALGQNPVVAYMT 761

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKD 972
             +  +  D  +     V   V           +  +  +  E          E   RD  
Sbjct: 762  WEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALRDL- 820

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 821  DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 869

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 870  DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 923

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 924  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 983

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+                                          T ++D
Sbjct: 984  ATPVFDGATADDLWETVIEAGMDSDAK----------------------------TVLYD 1015

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGEPFD  V+VG +YM+KL+HMV DK++ARS 
Sbjct: 1016 G--------------------------RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSV 1049

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I
Sbjct: 1050 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAI 1109

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
              G    + G PESF VLVKE+Q+LGL + + +         +     + 
Sbjct: 1110 TKGKPIPKPGVPESFRVLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 1159


>gi|323483088|ref|ZP_08088481.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14163]
 gi|323403628|gb|EGA95933.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14163]
          Length = 1284

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/961 (45%), Positives = 596/961 (62%), Gaps = 59/961 (6%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G G VR  F +  E++++P+LIE+QK SY  FL          +EGL+  F  +
Sbjct: 1   MRPVKAGKG-VRMTFSRQKEVLEMPNLIEIQKNSYQWFL----------DEGLREVFADI 49

Query: 63  FPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            PI  F+G   L+FV +    D  K+ +++C  RD TYA PLK+ +RL   D D      
Sbjct: 50  SPIADFAGHLSLDFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD------ 103

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +I E  I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    G  LY
Sbjct: 104 ---EINEHEIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIAHDKI---GTELY 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY- 238
           +C +IP++G W++ E DS DI +VR+DR RKVPVT  + ALG  +  EI+  F  ++   
Sbjct: 158 SCTVIPNRGAWLEYETDSNDIFYVRVDRTRKVPVTVLIRALGYGTNAEIIELFGEELKLE 217

Query: 239 -SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            S   D           +         + +D+ E ++ S         L K  + K  K 
Sbjct: 218 KSFEKDPSSNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKK 277

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L    + + G  +AED+V+  TGEI  E G  +D++   +I ++    IP +++     N
Sbjct: 278 L-HFKNRIAGHTLAEDVVDMSTGEILAEKGTEVDKQLATDIQNA---AIPYVWIQGERKN 333

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             + + ++ D         L  Y    P +V        +  +   +    +  +   +K
Sbjct: 334 HKVLSNMMVD---------LASYVDFDPEEV----GVTELVYYPVLEGILAEAGSDEELK 380

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             ++ ++      +HI KEDIIA I   + L  G GT DDID+LGNRR+R+VGE+L+NQY
Sbjct: 381 EVIKRDIH-DLIPKHITKEDIIASINYNMHLEGGIGTQDDIDHLGNRRIRAVGELLQNQY 439

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+++ D++ V  Q LIN KPV +AV EFF SSQLSQ  +  N L+ +
Sbjct: 440 RIGLSRMERVVRERMTTQDMEGVSAQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAEL 499

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN Y
Sbjct: 500 THKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQY 559

Query: 596 GFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           GF+E PYR V      +  VT +VVYL+A EE+N  +AQAN  LD++G F    V  R  
Sbjct: 560 GFVEAPYRVVDKSDPHNPVVTEEVVYLTADEEDNFVVAQANEPLDDEGHFIHNNVSGRFR 619

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E     +++ID +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLLK EA  
Sbjct: 620 EETSEFQKKRIDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLKTEAAV 679

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SG  +VAK AG+VE+  +  I+I+        S    D+Y L KF+RS
Sbjct: 680 VGTGIEGKAAVDSGVCMVAKNAGVVERSASNEIIIKRD------SDGNRDVYHLTKFKRS 733

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+ C NQ+P+V  GD V   ++IADGPSTD G++ALG+N L+ FM W GYN+ED++L+S
Sbjct: 734 NQSNCYNQKPIVYKGDHVEVGEVIADGPSTDNGEIALGKNPLIGFMTWEGYNYEDAVLLS 793

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V EDV+TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  
Sbjct: 794 ERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRA 853

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   
Sbjct: 854 GDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENG 913

Query: 951 D 951
           D
Sbjct: 914 D 914



 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 180/545 (33%), Positives = 257/545 (47%), Gaps = 40/545 (7%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++ +    G  ++               ++  I+  G  V  G+++    +      + 
Sbjct: 711  EIIIKRDSDGNRDVYHLTKFKRSNQSNCYNQKPIVYKGDHVEVGEVIADGPSTDN-GEIA 769

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--- 964
              +  L      +  +  D  L     V   V        +  +  +  +  E       
Sbjct: 770  LGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVP 829

Query: 965  ---ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E   +D  DE+ I+      R  +IL G+    G         L   +  E  R   
Sbjct: 830  GVGEDALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--- 885

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E      +            K+   + GD++ PGV   V++++A K
Sbjct: 886  --------------EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNETVRIYIAQK 931

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 932  RKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHL 991

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
              A   LG  + + I D     DI              S  E    Y D +  ++ E   
Sbjct: 992  SLAARALGFNVSTPIFDGANEIDIQDTLELAND-YVNTSWEEFEEKYRDKADPKLMEYLG 1050

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                               ++ +   L   G+  L DG TGE FD PVT+G+++ LKL+H
Sbjct: 1051 -------------SHLEHRALWKGVPLGRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHH 1097

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDD
Sbjct: 1098 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDD 1157

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR + YE+I+ G +  E G PESF VL+KE+Q+LGL + +           E I D+ 
Sbjct: 1158 VVGRVKTYEAIIKGENIPEPGIPESFKVLLKELQSLGLDVRVLKEDGSEVELAETI-DYG 1216

Query: 1382 KCELK 1386
              +++
Sbjct: 1217 DTDIR 1221


>gi|253579269|ref|ZP_04856539.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849367|gb|EES77327.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 1286

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/960 (44%), Positives = 592/960 (61%), Gaps = 61/960 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G   +R  + +  E++++P+LIEVQ+ SY  FL          +EGL+  F  + PI
Sbjct: 9   VKTG-KSMRMSYQRQEEVLEMPNLIEVQRDSYKWFL----------DEGLREVFDDISPI 57

Query: 66  TAFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             +SG   LEF+ + FD    K+ ++ C  RD TYA PLK+ +RLI          K  +
Sbjct: 58  ADYSGKLSLEFIDFTFDEKDAKYTIEQCKERDATYAAPLKVRVRLI---------NKETE 108

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I E  I+MGDLP+MT  GTFVI G +R++VSQL RSPGI++     +    GK L++  
Sbjct: 109 EINEHEIFMGDLPIMTVTGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKRLFSST 165

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQ 240
           +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ S  EI+  F    KI+ S 
Sbjct: 166 VIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGVGSNAEIIDLFGEEPKILASF 225

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +++ E +I +         L K  + K  K L  
Sbjct: 226 TKDTSTNYQEGLLELYKKIRPGEPLAVESAESLINAMFFDPRRYDLAKVGRYKFNKKL-H 284

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            +  + G  +AED+V+  TGEI  E G V+ ++    I +S +               Y+
Sbjct: 285 LNRRIVGHRLAEDVVDASTGEILAEEGTVVTKEMANTIQNSAV--------------PYV 330

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 D+       L+   R   P   D  +  V E+++  +  +  + + +   R+  
Sbjct: 331 WILGEEDRRIKVLSNLMVDIRHYLPEIEDPKSIGVTEAVYYPVLENILEENDTLEDRIAA 390

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             R   D     +HI KEDI A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 391 IHRDIHDLI--PKHITKEDIFASINYNMHLEYGLGNADDIDHLGNRRIRAVGELLQNQYR 448

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL R+ER ++ER+++ D +++ PQ LIN KPV +AV EFF SSQLSQ  +  N L  +T
Sbjct: 449 IGLSRLERVVRERMTTQDTENISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELT 508

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YG
Sbjct: 509 HKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLASYARINQYG 568

Query: 597 FIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           FIE PYRK+      + +VT++VVY++A EE+N ++AQAN  LDE+G F  + V  R   
Sbjct: 569 FIEAPYRKIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANEPLDEEGYFIHKNVSGRFRE 628

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     R   D++D SP+ V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP V
Sbjct: 629 ETQEYERHMFDYMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVV 688

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  +VAK++G V +  +  I I++ +G  D        Y L K+ RSN
Sbjct: 689 GTGMEVKTAVDSGVCVVAKKSGTVLRSTSTDISIKNDDGTKDD-------YHLTKYLRSN 741

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+ C NQ+P+V  G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SE
Sbjct: 742 QSNCYNQKPIVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLLSE 801

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  G
Sbjct: 802 RLVMDDVYTSVHIEEYECEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAG 861

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 862 DILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 921



 Score =  560 bits (1442), Expect = e-157,   Method: Composition-based stats.
 Identities = 254/1062 (23%), Positives = 405/1062 (38%), Gaps = 68/1062 (6%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D       I  +   D + + ++ LL++Y+ +RPG+      AES+ N +FFD  +YDL
Sbjct: 212  IDLFGEEPKILASFTKDTSTNYQEGLLELYKKIRPGEPLAVESAESLINAMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L+L+       + ++ + A    ++    G     ++ N          
Sbjct: 272  AKVGRYKFNKKLHLNRRIVGHRLAEDVVDASTGEILA-EEGTVVTKEMANTIQNSAVPYV 330

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             +L  + R   +++  ++   I     +   P+ +   + V   V E       +  +  
Sbjct: 331  WILGEEDR--RIKVLSNLMVDIRHYLPEIEDPKSIGVTEAVYYPVLENILEENDTLEDRI 388

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH-YGRICPAETSEGHNIGLVSSLT 587
                  I          +   A          +H  +  G     +      I  V  L 
Sbjct: 389  AAIHRDIHDLIPKHITKEDIFASINYN-----MHLEYGLGNADDIDHLGNRRIRAVGELL 443

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDED 637
               +      +    R V +   T D   +S     N     A               + 
Sbjct: 444  ---QNQYRIGLSRLERVVRERMTTQDTENISPQSLINIKPVTAAVKEFFGSSQLSQFMDQ 500

Query: 638  GSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             +   EL   R             R   +  D        +     P   N      L  
Sbjct: 501  NNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLAS 560

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                 Q   +         +  ++         + A          A    +      + 
Sbjct: 561  YARINQYGFIEAPYRKIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANE-PLDEEGYFIH 619

Query: 754  PSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
             + SG       +++R   +   V+ R +  V         +  A+              
Sbjct: 620  KNVSGRFREETQEYERHMFDYMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVP 679

Query: 811  MLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            +L    P  G   E    +     V      ++       ++     G ++       + 
Sbjct: 680  LLTTEAPVVGTGMEVKTAVDSGVCVVAKKSGTVLRSTSTDISIKNDDGTKDDYHLTKYLR 739

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDT 927
                   ++  I+  G  V  G ++    +         +  L+  +   G    D    
Sbjct: 740  SNQSNCYNQKPIVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLL 799

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYS 984
            S R+      T V +  +     D       + R+     +   +D  DE+ I+      
Sbjct: 800  SERLVMDDVYTSVHIEEYECEARDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEV 858

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R  +IL G+    G         L   +  E  R                 E      + 
Sbjct: 859  RAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKV 901

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                       K+   + GD+M PGV + V++++A KR I  GDKMAGRHGNKG+VSR+L
Sbjct: 902  PHGEYGIIVDAKVFTRENGDEMSPGVNQSVRIYIAQKRKISVGDKMAGRHGNKGVVSRVL 961

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + I       D
Sbjct: 962  PVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVATPIFQGANEHD 1021

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            I          + T    E    Y D     V +                  +A  ++ +
Sbjct: 1022 IQDTLELANDYVNTEDFEEFREKYKDILAPDVMQYLDE-------------NKAHRALWK 1068

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLG
Sbjct: 1069 GVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLG 1128

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G++  E G P
Sbjct: 1129 GKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGIP 1188

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            ESF VL+KE+Q+LGL + +          +E + D+   +L+
Sbjct: 1189 ESFKVLLKELQSLGLDVKVLKDDNTEVHLLESV-DYGDTDLR 1229


>gi|256849190|ref|ZP_05554623.1| DNA-directed RNA polymerase subunit beta [Lactobacillus crispatus
           MV-1A-US]
 gi|262047206|ref|ZP_06020164.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|312978421|ref|ZP_07790163.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           CTV-05]
 gi|256713966|gb|EEU28954.1| DNA-directed RNA polymerase subunit beta [Lactobacillus crispatus
           MV-1A-US]
 gi|260572451|gb|EEX29013.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|310894764|gb|EFQ43836.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           CTV-05]
          Length = 1212

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/963 (41%), Positives = 587/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARNHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  + G V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIVAKKGTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPIAVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D+V+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIADNVKHLTPADVLASINYFFALQDEIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V   D KVT+ + YL+A EE+N  IA AN+ L++DGSF E+L+  R
Sbjct: 542 IINKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKEKLILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVSPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG+VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGVVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V ++D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDKSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 237/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDKSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGADENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T V+D                          G 
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVVYD--------------------------GR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|295692153|ref|YP_003600763.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           ST1]
 gi|295030259|emb|CBL49738.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           ST1]
          Length = 1212

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/963 (41%), Positives = 587/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARNHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  + G V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIVAKKGTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D+V+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIADNVKHLTPADVLASINYFFALQDEIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V   D KVT+ + YL+A EE+N  IA AN+ L++DGSF E+L+  R
Sbjct: 542 IINKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKEKLILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVSPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG+VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGVVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V ++D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDKSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 237/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDKSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGADENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T V+D                          G 
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVVYD--------------------------GR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|15903819|ref|NP_359369.1| DNA-directed RNA polymerase subunit beta [Streptococcus pneumoniae
           R6]
 gi|15459460|gb|AAL00580.1| DNA-dependent RNA polymerase subunit beta [Streptococcus pneumoniae
           R6]
          Length = 1216

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/963 (43%), Positives = 583/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 14  LAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 63

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 64  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 114

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 115 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 171

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 172 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 231

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 232 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 290

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E         I      
Sbjct: 291 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDG 342

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +N   YI N    D     +  +L  ++V+ P D                         
Sbjct: 343 DLNKIVYIPN----DAAVVTEPVVLQKFKVVAPTDPDRV--------------------- 377

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+
Sbjct: 378 -----VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGEL 432

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N
Sbjct: 433 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHN 492

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 493 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 552

Query: 591 RVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R
Sbjct: 553 HLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGR 612

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 613 HQGVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQA 672

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 673 PYVGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFR 725

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 726 RSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVI 785

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 786 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 845

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 846 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 905

Query: 949 GID 951
             D
Sbjct: 906 NGD 908



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 738  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 796

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 797  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 856

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 857  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 899

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 900  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 959

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 960  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 1018

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 1019 ----------------------------------------DSDAKTIL------YDG--- 1029

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1030 ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1085

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1086 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1145

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1146 SLGLDMRVLDEDDQEVELRDLDEGMDE 1172


>gi|168187822|ref|ZP_02622457.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum C
           str. Eklund]
 gi|169294357|gb|EDS76490.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum C
           str. Eklund]
          Length = 1241

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/950 (45%), Positives = 591/950 (62%), Gaps = 55/950 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+  +P+LIEVQ  SYD F            EGL   F  V PI  ++G
Sbjct: 9   KRTRMSFSKVKEMCPMPNLIEVQLNSYDWF----------WKEGLNEVFDDVNPIQDYTG 58

Query: 71  AAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEF+ Y  D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ
Sbjct: 59  NLILEFIDYNLDKDAIKYSVEECKERDATYAAPLKVKVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTFVI G +R++VSQL RSPG ++ +D  +    GK L++  +IP++
Sbjct: 110 EVFMGDFPLMTQQGTFVINGAERVIVSQLVRSPGAYYGYDVDKT---GKKLFSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFW 245
           G W++ E DS DII+VRID+ RK+P++  + ALG+ S+ E++  F  +         D  
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPISILIRALGLGSDAEVVDWFGEEERLKATIEKDNT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+   +I S         L +  + K  K L I    L
Sbjct: 227 KTREEALLEIYKRLRPGEPPTVDSAVSLINSLFFDAKRYDLSRVGRYKFNKKLAIYI-RL 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                AED+VN  TGEI ++ G+ ID +   EI    I  + I   D V           
Sbjct: 286 LNQVAAEDVVNPFTGEIIVQKGETIDREKALEIQDCAINAVNIQVEDKV----------- 334

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
               K   +  +DI++ +              +  L    D Y      + ++   ++  
Sbjct: 335 ---IKVIGNNFVDIHKFIDFDISDLKIKEHVHYPTLKNILDNYTDEESIKEEIKKNIHEL 391

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   +HI  +DI A I   + L    GTIDDID+LGNRR+RSVGE+L+NQ+R+GL RME
Sbjct: 392 IP---KHIVVDDIYATISYELGLPYEIGTIDDIDHLGNRRLRSVGELLQNQFRIGLSRME 448

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R +KER++  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 449 RVVKERMTIQDQEVITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 508

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +A+VN YGFIETPYR
Sbjct: 509 LGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLACYAKVNEYGFIETPYR 568

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V   + +VT  +VYL+A EE++  +AQA   +DE+G F +E +  R   + I+V R ++
Sbjct: 569 LVDKKEARVTEKIVYLTADEEDHYLVAQAKEPVDENGCFIDEKITVRDLEDVIVVSRNQV 628

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SP Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E   A 
Sbjct: 629 DLMDVSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIVGTGIEYKAAV 688

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG    A+  G++E V +  + IR        +  G+D ++L+K++RSNQ TC+NQRP+
Sbjct: 689 DSGVLPKAEHDGVIEYVSSTEVRIRRD------ADGGLDKHKLLKYKRSNQGTCINQRPI 742

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V  G++V+  D++ADGPSTD G++ALG+N+ + F+ W GYN+ED+ML+SE++V +D+FTS
Sbjct: 743 VGKGEKVKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDDIFTS 802

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNV E+ LKNIDE GI+ +GAEV  GDILVGK+TPK
Sbjct: 803 IHIEEYESEARDTKLGPEEITRDIPNVGEDALKNIDERGIVRIGAEVRSGDILVGKVTPK 862

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 863 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 912



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 254/1099 (23%), Positives = 396/1099 (36%), Gaps = 124/1099 (11%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            ++ +I     D   +  +  +  +         VD       ++ T+  D  K R++ALL
Sbjct: 175  DSNDIIYVRIDKTRKLPISILIRALGLGSDAEVVDWFGEEERLKATIEKDNTKTREEALL 234

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +IY+ +RPG+  T   A S+ N LFFD+         R  ++          +    +  
Sbjct: 235  EIYKRLRPGEPPTVDSAVSLINSLFFDAK--------RYDLSRVGRYKFNKKLAIYIRLL 286

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
                 + +V+   G+  +   + +   +   + +   N   + +    + IK   ++   
Sbjct: 287  NQVAAEDVVNPFTGEIIVQKGETIDREKALEIQDCAINAVNIQVED--KVIKVIGNNFVD 344

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
                    I+   +   V      + L    +  +    I             V    A 
Sbjct: 345  IHKFIDFDISDLKIKEHVHYPTLKNILDNYTDEESIKEEIKKNIHELIPKHIVVDDIYAT 404

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            +      P   G I   +      +  V  L    +      +    R V +     D  
Sbjct: 405  ISYELGLPYEIGTIDDIDHLGNRRLRSVGELL---QNQFRIGLSRMERVVKERMTIQDQE 461

Query: 616  YLS------------AMEEE-------NRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             ++            A++E                 S          L     + E    
Sbjct: 462  VITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGF 521

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-- 714
                +          +         L N  +    +      +    L  +     T   
Sbjct: 522  EVRDVHHSHYGRMCPIETPEGPNIGLINSLACYAKVNEYGFIETPYRLVDKKEARVTEKI 581

Query: 715  -MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
               +   +       AK       VD     I       D     V        Q    +
Sbjct: 582  VYLTADEEDHYLVAQAKEP-----VDENGCFIDEKITVRDLEDVIVVSRN----QVDLMD 632

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               +Q   V         +  A               +L    P  G   E    +   +
Sbjct: 633  VSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIVGTGIEYKAAVDSGV 692

Query: 834  VSEDVFTSI--HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            + +     +  ++   EV  R    G  +  + +          I++  I+  G +V  G
Sbjct: 693  LPKAEHDGVIEYVSSTEVRIRRDADGGLDKHKLLKYKRSNQGTCINQRPIVGKGEKVKAG 752

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D+L    +      +   + +       +  +  D  L     V   +        +  +
Sbjct: 753  DVLADGPST-DFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDDIFTSIHIEEYESE 811

Query: 952  KNERSISVER--EQIELLARDK---DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
              +  +  E     I  +  D     DE+ I+      R  +IL G+    G        
Sbjct: 812  ARDTKLGPEEITRDIPNVGEDALKNIDERGIVRIGAEVRSGDILVGKVTPKGETELTAEE 871

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  E  R                 E                   K+   + GD++
Sbjct: 872  RLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKVFTRENGDEL 914

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV  +V+ ++A KR I  GDKMAGRHGNKG++SRILP EDMPFL DG P+ I LNPLG
Sbjct: 915  PPGVNELVRCYIAQKRKISVGDKMAGRHGNKGVISRILPEEDMPFLPDGRPLQICLNPLG 974

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLGWA   +G  I + + +     +I  L                  
Sbjct: 975  VPSRMNIGQVLEVHLGWAAGEMGWHIATPVFNGAFEDEIVDLLKEA-------------- 1020

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                      G  E+              G++ LYDG TGEPFD
Sbjct: 1021 --------------------------GYSED--------------GKTTLYDGRTGEPFD 1040

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              VTVGY+Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1041 NRVTVGYMYILKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1100

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + +  S
Sbjct: 1101 AAHTLQEVLTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDVKVL-S 1159

Query: 1367 RTKNSAKMEEIPDFNKCEL 1385
             T    K++E  + +  +L
Sbjct: 1160 DTNEEIKIKESSEEDTEDL 1178


>gi|302876542|ref|YP_003845175.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           cellulovorans 743B]
 gi|307687215|ref|ZP_07629661.1| DNA-directed RNA polymerase subunit beta [Clostridium cellulovorans
           743B]
 gi|302579399|gb|ADL53411.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           cellulovorans 743B]
          Length = 1239

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/955 (44%), Positives = 591/955 (61%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  E+  +P+LIE+Q  SY  FL          +EGLQ  F  V PI  ++G
Sbjct: 9   KRTRMSFSKQVEVGKMPNLIEIQVDSYKWFL----------DEGLQEIFDDVNPIQDYTG 58

Query: 71  AAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y+ D    K+ V++C  RD TYA PLK+T+RL+          K   ++KEQ
Sbjct: 59  NLVLEFVGYKLDMENIKYSVEECKERDATYAAPLKVTVRLL---------NKETGEVKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R+VVSQL RSPG ++++   +    GK LY+  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFIINGAERVVVSQLVRSPGTYYNYTVDKT---GKKLYSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS  +I+VRID+ RK+P+T  + A+G  ++ E++     +       +    
Sbjct: 167 GAWLEYETDSNSVIYVRIDKTRKLPITMLVRAMGYGTDAEVIDFLGEEERLKATMEKDSV 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                       +      +  GE   +ES  +L + L    K   +  +G         
Sbjct: 227 K------SREDALLEIYKRLRPGEPPTVESAVELINTLFFDPKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     AEDIVN ETGEI +E G  I+ +   EI +  I ++ I   D       I
Sbjct: 281 LSLRIANQTAAEDIVNPETGEILVEKGTKIEREKAVEIQNLGINEVIIQVED--KTLKVI 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N  V  K+    D      + +              +  L    D+Y      + ++  
Sbjct: 339 GNNFVDIKSHVNFDPTKINVKELVH------------YPTLREILDQYTDEEEQKAEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI K+DI+A +   + L  G G +DDID+LGNRR+R+VGE+L+NQ+R+G
Sbjct: 387 NIHKLIP---KHIVKDDILATVNYEIGLPYGVGNVDDIDHLGNRRLRAVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N L  +TH 
Sbjct: 444 LSRMERVVKERMTVQDQEAITPQALINTRPVAAAIKEFFGSSQLSQFMDQTNPLGELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++A+VN YGFI
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNDYGFI 563

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ET YR V   +G+VT ++ Y +A EE+   +AQAN  LDE+G F    +  R   + ++V
Sbjct: 564 ETCYRVVDKKEGRVTEEIRYFTADEEDALVVAQANEQLDENGYFVNSKITVRDGEDVLVV 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            +  +D +D S +Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E
Sbjct: 624 SKHDVDLMDVSSRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    A  AG V  V A  + ++  E         +D Y+L+KF+R+NQ+TC+
Sbjct: 684 YKAAVDSGVLPKAIHAGEVVYVSADLVKVKRDE------DGKLDSYKLLKFKRTNQSTCI 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  G++V    ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE++V +
Sbjct: 738 NQRPIVVKGEKVEAGAVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEQLVRD 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK+ID+ GII +GAEV  GDILVG
Sbjct: 798 DVFTSIHIEEYECEARDTKLGPEEITRDIPNVGEDALKDIDDSGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 912



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 261/1100 (23%), Positives = 409/1100 (37%), Gaps = 124/1100 (11%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            ++  +     D   +  +  +  +         +D +     ++ T+  D  K R+DALL
Sbjct: 175  DSNSVIYVRIDKTRKLPITMLVRAMGYGTDAEVIDFLGEEERLKATMEKDSVKSREDALL 234

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +IY+ +RPG+  T   A  + N LFFD  +YDLS VGR K N +L L          +  
Sbjct: 235  EIYKRLRPGEPPTVESAVELINTLFFDPKRYDLSRVGRYKFNKKLALSL--------RIA 286

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
                 + +V+   G+  ++    +   +   +  +  N+  + +    +++K   ++   
Sbjct: 287  NQTAAEDIVNPETGEILVEKGTKIEREKAVEIQNLGINEVIIQVED--KTLKVIGNNFVD 344

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
                         V   V        L Q  +     + I   + +  L    + +    
Sbjct: 345  IKSHVNFDPTKINVKELVHYPTLREILDQYTDEEEQKAEI--KKNIHKLIPKHIVKDDIL 402

Query: 556  VEMRDVHPTHYGR--ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              +       YG   +   +      +  V  L    +      +    R V +     D
Sbjct: 403  ATVNYEIGLPYGVGNVDDIDHLGNRRLRAVGELL---QNQFRIGLSRMERVVKERMTVQD 459

Query: 614  VVYLSAMEEENRY-IAQAN---------SSLDEDGSFTEELVFCRC---------AGEEI 654
               ++     N   +A A          S   +  +   EL   R          + E  
Sbjct: 460  QEAITPQALINTRPVAAAIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLSRERA 519

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV-LMGCNMQRQAVPLLKAEAPFVGT 713
                  +          +         L N  +    +           ++  +   V  
Sbjct: 520  GFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYAKVNDYGFIETCYRVVDKKEGRVTE 579

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
             +    A    A +VA+     EQ+D     + S     D    G D+  + K      +
Sbjct: 580  EIRYFTADEEDALVVAQ---ANEQLDENGYFVNSKITVRD----GEDVLVVSKHDVDLMD 632

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                Q   V         +  A               +L    P  G   E    +   +
Sbjct: 633  VSSRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAAVDSGV 692

Query: 834  VSEDVFTS--IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            + + +     +++    V  +  + G  +  + +          I++  I+  G +V  G
Sbjct: 693  LPKAIHAGEVVYVSADLVKVKRDEDGKLDSYKLLKFKRTNQSTCINQRPIVVKGEKVEAG 752

Query: 892  DILVGKITPKGESPMTPEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             +L    +         +   +  I       E A+ + +  +R     S  + +     
Sbjct: 753  AVLADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEQLVRDDVFTSIHIEEYECEA 812

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R      E          E   +D DD   I+      R  +IL G+    G        
Sbjct: 813  RDTKLGPEEITRDIPNVGEDALKDIDD-SGIIRIGAEVRSGDILVGKVTPKGETELTAEE 871

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   +  E  R                 E                   KI   + GD++
Sbjct: 872  RLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDEL 914

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV ++V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLG
Sbjct: 915  PPGVNQLVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLG 974

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLGWA    G  I + + D     +I                     
Sbjct: 975  VPSRMNIGQVLEVHLGWAAANKGWHIATPVFDGATEEEIEDQLEEAGYARDGK------- 1027

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 T ++DG                           TGEPFD
Sbjct: 1028 ---------------------TVLYDG--------------------------RTGEPFD 1040

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              VTVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1041 NRVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1100

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+QAL L + +  S
Sbjct: 1101 AAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGLPESFKVLIKELQALCLDVRVLTS 1160

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
              +     E + D    +L+
Sbjct: 1161 DNEEIQLKESV-DEELEDLE 1179


>gi|58336623|ref|YP_193208.1| DNA-directed RNA polymerase subunit beta [Lactobacillus acidophilus
           NCFM]
 gi|75358070|sp|Q5FM97|RPOB_LACAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|58253940|gb|AAV42177.1| RNA-polymerase DNA-directed beta subunit [Lactobacillus acidophilus
           NCFM]
          Length = 1213

 Score =  830 bits (2143), Expect = 0.0,   Method: Composition-based stats.
 Identities = 402/963 (41%), Positives = 585/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARDHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VR+DR RK+P+T  + A+G+ S+ EI+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSYVRVDRTRKLPLTVLIRAMGIGSDSEIIEMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI ++   V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIVKKDTVVTHEIMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIDADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF E+++  R
Sbjct: 542 IINKYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKEDIILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+   +
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHS 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDADEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDESDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  473 bits (1218), Expect = e-131,   Method: Composition-based stats.
 Identities = 172/502 (34%), Positives = 237/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDESDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVMPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T ++DG                           
Sbjct: 1000 -----------DTVRQAGMDKDG---KTVIYDG--------------------------R 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMDHNEIELRDMDEDSSE 1161


>gi|329666685|gb|AEB92633.1| DNA-directed RNA polymerase beta chain [Lactobacillus johnsonii DPC
           6026]
          Length = 1212

 Score =  829 bits (2142), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/986 (42%), Positives = 592/986 (60%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREIFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++  
Sbjct: 107 GEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ EI   F         
Sbjct: 164 TVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEIADMFGESDSLRFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        +   +  +G   
Sbjct: 224 LEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + GDV+  + L+++                
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHELLDKL---------------- 326

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + Y+          DR D  +  Y   + G +      + +  +   D ++       
Sbjct: 327 --SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER------- 367

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              + +  N    DDV+H+   D++A I    DL++  GT DDID+LGNRR+R VGE+L+
Sbjct: 368 --VVKLMSNGHIADDVKHLTPADVLASINYFFDLQDNIGTTDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R  
Sbjct: 546 NKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNEDGSFKDKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP 
Sbjct: 606 EDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPI 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RS
Sbjct: 666 VGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R   
Sbjct: 839 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELPPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 256/1055 (24%), Positives = 391/1055 (37%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 239  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 298

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 299  AETLADPDTGEIIAKKGDVVTHELLDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 357

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D    +     +   +        L     
Sbjct: 358  KVYSKVDPERVVKLMSNGHIADDVKHLTPADVLASINYFFDLQDNIGTTDDIDHLGNRRI 417

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 418  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 478  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 537

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +     E D S +
Sbjct: 538  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNE-DGSFK 596

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +       +          ++ +     +E  D+ R ++ +  
Sbjct: 597  DKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLENDDSNRALMGAN- 650

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 651  -----------------HQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 679

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T    +++ V+ +  +    +     P V 
Sbjct: 680  DALVAKAPG----VVEYVDANEIRIRRDDDTL---DKY-VLEKFRRSNATKNYNQTPAVK 731

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 732  QGERVVADE--VIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 787

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          E   +D D+E  I+      +  
Sbjct: 788  -------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE-GIVRIGAEVQDG 839

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 840  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 891  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 942

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 943  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 1003 M---------------------------------------------VREAGIGK------ 1011

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1012 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1068

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1069 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1128

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1129 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1163


>gi|268318844|ref|YP_003292500.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus johnsonii
           FI9785]
 gi|262397219|emb|CAX66233.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus johnsonii
           FI9785]
          Length = 1212

 Score =  829 bits (2142), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/986 (42%), Positives = 592/986 (60%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++  
Sbjct: 107 GEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ EI   F         
Sbjct: 164 TVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEIADMFGESDSLRFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        +   +  +G   
Sbjct: 224 LEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + GDV+  + L+++                
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHELLDKL---------------- 326

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + Y+          DR D  +  Y   + G +      + +  +   D ++       
Sbjct: 327 --SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER------- 367

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              + +  N    DDV+H+   D++A I    DL++  GT DDID+LGNRR+R VGE+L+
Sbjct: 368 --VVKLMSNGHIADDVKHLTPADVLASINYFFDLQDNIGTTDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R  
Sbjct: 546 NKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNEDGSFKDKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP 
Sbjct: 606 EDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPI 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RS
Sbjct: 666 VGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P+VK G+ V  +++IADGP+   G+LALG+N ++AF+ W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPVVKQGERVVADEVIADGPAMKNGELALGQNPIIAFLTWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R   
Sbjct: 839 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELPPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 256/1055 (24%), Positives = 388/1055 (36%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 239  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 298

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 299  AETLADPDTGEIIAKKGDVVTHELLDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 357

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D    +     +   +        L     
Sbjct: 358  KVYSKVDPERVVKLMSNGHIADDVKHLTPADVLASINYFFDLQDNIGTTDDIDHLGNRRI 417

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 418  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 478  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 537

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +     E D S +
Sbjct: 538  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNE-DGSFK 596

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +       +          ++ +     +E  D+ R ++ +  
Sbjct: 597  DKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLENDDSNRALMGAN- 650

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 651  -----------------HQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 679

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T        V+ +  +    +     P V 
Sbjct: 680  DALVAKAPG----VVEYVDANEIRIRRDDDTLDKY----VLEKFRRSNATKNYNQTPVVK 731

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 732  QGERVVADE--VIADGPAMKNGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 787

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          E   +D D+E  I+      +  
Sbjct: 788  -------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE-GIVRIGAEVQDG 839

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 840  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 891  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 942

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 943  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 1003 M---------------------------------------------VREAGIGK------ 1011

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1012 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1068

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1069 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1128

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1129 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1163


>gi|238853490|ref|ZP_04643868.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus gasseri
           202-4]
 gi|238833930|gb|EEQ26189.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus gasseri
           202-4]
          Length = 1209

 Score =  829 bits (2142), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/988 (42%), Positives = 593/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 102 ETGEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ E+   F       
Sbjct: 159 GATVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEVADMFGESDSLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 219 FTLEKDI-HKNPADSRVVEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + GDV+  + L+++              
Sbjct: 278 YKINKKLSLKNRLLRQNLAETLADPDTGEIIAKKGDVVTHEILDKL-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               + Y+          DR D  +  Y   + G +      + +  +   D ++     
Sbjct: 324 ----SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER----- 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    DDV+H+   D++A I    +L++  GT DDID+LGNRR+R VGE+
Sbjct: 365 ----VIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R
Sbjct: 541 IVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNEDGSFKDKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A
Sbjct: 601 HKEDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHA 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+
Sbjct: 661 PIVGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R 
Sbjct: 834 QDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELPPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 260/1068 (24%), Positives = 393/1068 (36%), Gaps = 174/1068 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++      +    +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N 
Sbjct: 223  KDIHKNPADSRVVEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINK 282

Query: 419  RLNLD-------------TPDDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L+L               PD    I         E +  +   L        T +    
Sbjct: 283  KLSLKNRLLRQNLAETLADPDTGEIIAKKGDVVTHEILDKLSPYLDRDDFKMVTYEPSKE 342

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVC 514
                   +V E +K   ++   R+ + +     + D+  + P D    +     +   + 
Sbjct: 343  GVLPDPVTVQE-IKVYSKVDPERVIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIG 401

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   L                R   A  +  V    +  ++  V P     I P   
Sbjct: 402  TTDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVA 461

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLS 618
            S     G         + N  G +    R                +V D   T+      
Sbjct: 462  SVKEFFGSSQLSQFMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCP 521

Query: 619  AMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
                E   I   N  ++      +       R    +     +KID++ A  +    IA 
Sbjct: 522  IETPEGPNIGLINSLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAG 581

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P  E D S +  +     ++    +  +       +          ++ +     +E
Sbjct: 582  ANAPLNE-DGSFKDKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLE 635

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
              D+ R ++ +                    QR          P+V  G           
Sbjct: 636  NDDSNRALMGAN------------------HQRQAVPLINPHAPIVGTG----------- 666

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                +        + LVA  P       + +  +E  +  D  T        V+ +  + 
Sbjct: 667  ---MEYRAAHDSGDALVAKAPG----VVEYVDANEIRIRRDDDTLDKY----VLEKFRRS 715

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLR 914
               +     P V +      DE  +I  G  +  G++ +G   I       M   E  + 
Sbjct: 716  NATKNYNQTPAVKQGERVVADE--VIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVM 773

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
                    DV           S  + D     R      E          E   +D D+E
Sbjct: 774  ISERMVKDDVY---------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE 824

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I+      +  +IL G+    G         L   +  E  R    +      +V   
Sbjct: 825  -GIVRIGAEVQDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHG 879

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +                 ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRH
Sbjct: 880  GGGIVQNV-------------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRH 926

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + +
Sbjct: 927  GNKGTIALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVAT 986

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D  +  D+  +                                              
Sbjct: 987  PVFDGASEDDMWNM---------------------------------------------V 1001

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E  I            G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G 
Sbjct: 1002 REAGIGK---------DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGP 1052

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV 
Sbjct: 1053 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVK 1112

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            G    + G PESF VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1113 GERIPKPGVPESFRVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1160


>gi|302388704|ref|YP_003824525.1| DNA-directed RNA polymerase subunit beta [Thermosediminibacter
           oceani DSM 16646]
 gi|302199332|gb|ADL06902.1| DNA-directed RNA polymerase subunit beta [Thermosediminibacter
           oceani DSM 16646]
          Length = 1209

 Score =  829 bits (2141), Expect = 0.0,   Method: Composition-based stats.
 Identities = 446/949 (46%), Positives = 598/949 (63%), Gaps = 94/949 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F K  E+ D+P L+E+QK SY+ FL           EGL+   +   PI  F+G 
Sbjct: 10  RTRWSFAKIEEVRDLPYLLEIQKNSYEWFL----------KEGLREVLQEFSPIEDFTGN 59

Query: 72  AMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            +LEF+ Y  D  PK+ VD+C  RD+TYAVPLK+ +RLI          K   ++KEQ +
Sbjct: 60  MVLEFLDYSLDNNPKYSVDECKERDVTYAVPLKVRVRLI---------NKETGEVKEQDV 110

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT++GTF+I G +R++VSQL RSPG++FD    +   +G+ LY   IIP++G 
Sbjct: 111 FMGDFPLMTENGTFIINGAERVIVSQLVRSPGVYFDRQIDK---NGRALYMGTIIPNRGA 167

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E DS ++I+VR+DR RK+P+T  L ALG  +  +I+          +  +      
Sbjct: 168 WLEMETDSNEVIYVRVDRTRKIPITVLLRALGYGTNAQIIELLGEDEKILRTLEKDNTEN 227

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               L+   K       +  GE   +E+ + L   L    K   +  +G           
Sbjct: 228 QEEALLEIYK------RLRPGEPPTVENARALLESLFFDPKRYDLANVGRYKF------- 274

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
                                      + +  +  I    V+  N    I          
Sbjct: 275 ----------------------NKKLRLRNRIVGKIAAENVEDPNTGEII---------- 302

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFN-FLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
                       ++ G+  T   AE++ +  +       D   V +V  N   + D PD 
Sbjct: 303 ------------LKKGEKITRKTAETLESLRINEIKVMVDEDRVVKVIANGYNDGDGPDV 350

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               ++I  EDI+A I  L++L  G G +DDID+LGNRRVRSVGE+L+NQ+R+GL RMER
Sbjct: 351 FPTEKYITVEDIVASINYLLNLSYGIGDVDDIDHLGNRRVRSVGELLQNQFRIGLARMER 410

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            +KER++  D+D++ PQ LIN +P+V+A+ EFF SSQLSQ  +  N L+ +T+ RRLSAL
Sbjct: 411 VVKERMTIQDVDAITPQGLINIRPLVAAIKEFFGSSQLSQFMDQTNPLAELTNKRRLSAL 470

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL+++ARVN YGFIETPYRK
Sbjct: 471 GPGGLSRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLISSLSTYARVNQYGFIETPYRK 530

Query: 605 VCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           V   +  VTN+V YL+A EEE   IAQAN  LDE+G F ++ V  R   + ++VP E++D
Sbjct: 531 VDKERGVVTNEVEYLTADEEEEFIIAQANVPLDEEGRFVQKRVTARYKDDIVVVPAEEVD 590

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQ+VS+A +LIPFLE+DD+NR LMG NMQRQAVPL+  EAP VGTG+E   A  
Sbjct: 591 YMDVSPKQLVSVATALIPFLEHDDANRALMGANMQRQAVPLITTEAPLVGTGIEWKAALD 650

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  IVAK +G+VE+V A  IVIR        S +G+D+Y++ KF RSNQ TC+NQRP+V
Sbjct: 651 SGVMIVAKNSGVVERVTAREIVIRRD------SDNGLDVYKVHKFMRSNQGTCINQRPIV 704

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K GD V     IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER+V +DVFTSI
Sbjct: 705 KKGDRVEAGQPIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISERLVRDDVFTSI 764

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIE++E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV  GDILVGK+TPKG
Sbjct: 765 HIEQYEAEARDTKLGPEEITRDIPNVGEDALKDLDERGIIRIGAEVRAGDILVGKVTPKG 824

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVDV++F+R   D
Sbjct: 825 ETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGIVVDVKVFSRENGD 873



 Score =  558 bits (1439), Expect = e-156,   Method: Composition-based stats.
 Identities = 267/1145 (23%), Positives = 445/1145 (38%), Gaps = 161/1145 (14%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETG----------EIY 321
            E+G  + +G  + +  + V+  G+  D      G  +    +    G          E+ 
Sbjct: 120  ENGTFIINGAERVIVSQLVRSPGVYFDRQIDKNGRALYMGTIIPNRGAWLEMETDSNEVI 179

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +         ++ +  +  I  TL  D  +++++ALL+IY+ +
Sbjct: 180  YVRVDRTRKIPITVLLRALGYGTNAQIIELLGEDEKILRTLEKDNTENQEEALLEIYKRL 239

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   A ++   LFFD  +YDL+ VGR K N +L L      +           +
Sbjct: 240  RPGEPPTVENARALLESLFFDPKRYDLANVGRYKFNKKLRLRNRIVGKI--------AAE 291

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG--LLRMERSIKERISSVDIDSVM 499
             + D   G+  +   + +  +   ++  +  N+ ++     R+ + I    +  D   V 
Sbjct: 292  NVEDPNTGEIILKKGEKITRKTAETLESLRINEIKVMVDEDRVVKVIANGYNDGDGPDVF 351

Query: 500  PQ-DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-------GGVAR 551
            P    I  + +V+++      S      + ++ L      RR+ ++G+        G+AR
Sbjct: 352  PTEKYITVEDIVASINYLLNLSYGIGDVDDIDHLG----NRRVRSVGELLQNQFRIGLAR 407

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                V+ R               +    +  +      ++++ +               T
Sbjct: 408  MERVVKERMTIQDVDAITPQGLINIRPLVAAIKEFFGSSQLSQF------------MDQT 455

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            N +  L+                  +      L     + E        + +        
Sbjct: 456  NPLAELT------------------NKRRLSALGPGGLSRERAGFEVRDVHYSHYGRMCP 497

Query: 672  VSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +       I  + +  +   +            +  E   V   +E + A      I+A+
Sbjct: 498  IETPEGPNIGLISSLSTYARVNQYGFIETPYRKVDKERGVVTNEVEYLTADEEEEFIIAQ 557

Query: 731  ---RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                     +    R+  R  +  +      VD   +             Q   V     
Sbjct: 558  ANVPLDEEGRFVQKRVTARYKDDIVVVPAEEVDYMDVSP----------KQLVSVATALI 607

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIE 845
                   A+              ++    P  G   E   ++     +V+++      + 
Sbjct: 608  PFLEHDDANRALMGANMQRQAVPLITTEAPLVGTGIEWKAALDSGVMIVAKNSGVVERVT 667

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
              E++ R       ++ +    +       I++  I+  G  V  G  +    +      
Sbjct: 668  AREIVIRRDSDNGLDVYKVHKFMRSNQGTCINQRPIVKKGDRVEAGQPIADGPST-DHGE 726

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER---- 961
            +   + +L A    +  +  D  L     V   V       ++  +  +  +  E     
Sbjct: 727  LALGKNVLVAFMPWEGYNYEDAILISERLVRDDVFTSIHIEQYEAEARDTKLGPEEITRD 786

Query: 962  --EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
                 E   +D  DE+ I+      R  +IL G+    G         L   +  E  R 
Sbjct: 787  IPNVGEDALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR- 844

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                            E                   K+   + GD++PPGV ++V+V++A
Sbjct: 845  ----------------EVRDTSLRVPHGEYGIVVDVKVFSRENGDELPPGVNQLVRVYIA 888

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDKMAGRHGNKG++SRILP EDMP+L DGTPVDIVLNPLGVPSRMN+GQ+ ET
Sbjct: 889  QKRKISEGDKMAGRHGNKGVISRILPVEDMPYLPDGTPVDIVLNPLGVPSRMNIGQVLET 948

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA   LG  + + + D     +I                                  
Sbjct: 949  HLGWAAKALGWHVATPVFDGATEEEIFECLR----------------------------- 979

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K+G+P                        E G+  L DG TGEPFD+ VTVGY+YMLKL
Sbjct: 980  -KAGLP------------------------EDGKIELRDGRTGEPFDKKVTVGYMYMLKL 1014

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KS
Sbjct: 1015 AHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQELLTVKS 1074

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV+GR + YE+IV G +  E G PESF VL+KE+Q+L L + + +   +     ++  +
Sbjct: 1075 DDVMGRVKTYEAIVKGENVPEPGIPESFKVLIKELQSLCLDVKILSEDAQEIEI-KDADE 1133

Query: 1380 FNKCE 1384
            + + E
Sbjct: 1134 YEETE 1138


>gi|256844422|ref|ZP_05549908.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           125-2-CHN]
 gi|256613500|gb|EEU18703.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           125-2-CHN]
          Length = 1212

 Score =  829 bits (2141), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/963 (41%), Positives = 588/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARNHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  + G V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIVAKKGTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D+V+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIADNVKHLTPADVLASINYFFALQDEIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V   D KVT+ + YL+A EE+N  IA AN+ L++DGSF E+L+  R
Sbjct: 542 IINKYGFIETPYRRVSWKDHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKEKLILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVSPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG+VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGVVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD+V ++D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDQVDKSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 174/502 (34%), Positives = 239/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G +V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDQVDKSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV R+V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNRMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGADENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T V+D                          G 
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVVYD--------------------------GR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|261367092|ref|ZP_05979975.1| DNA-directed RNA polymerase, beta subunit [Subdoligranulum
           variabile DSM 15176]
 gi|282571215|gb|EFB76750.1| DNA-directed RNA polymerase, beta subunit [Subdoligranulum
           variabile DSM 15176]
          Length = 1276

 Score =  828 bits (2140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/969 (42%), Positives = 572/969 (59%), Gaps = 77/969 (7%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V NG    R  F +  E+ID+P+LIE+QK SY+ FL           EGL   F  +  I
Sbjct: 7   VQNGR-TTRMSFSRINEVIDMPNLIEIQKNSYNWFLQ----------EGLHEVFHDIAAI 55

Query: 66  TAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             ++G  +LEFV Y  D  PK+ + +C  RD TYA PL +T RL           K   +
Sbjct: 56  EDYTGNLVLEFVDYRLDKNPKYSIKECKERDATYAAPLYVTARL---------FNKQTGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           +KEQ I+MGD PLMT  GTF+  G +R +VSQL RSPG+ +   K R    GK L+   +
Sbjct: 107 VKEQEIFMGDFPLMTDSGTFISNGAERAIVSQLVRSPGVFYGSSKDRT---GKDLFTATM 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY----PKIVYSQ 240
            P++G W++ E DS+D+ +VRID+ RK+PVT+ + ALG+ ++E +  F+    PKI  S 
Sbjct: 164 NPNRGAWLEYETDSQDVFYVRIDKNRKLPVTTLIRALGLGTDEQIRQFFGNSEPKINASL 223

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGIT 299
             D                +      +  GE   +E+ +   + L    +   +   G  
Sbjct: 224 EKDITHSTEEG--------LLEVYRKLRPGEPPTVENSRSHLNSLFFDPRRYDLARFGRY 275

Query: 300 S--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                      + G   AEDI+   TGE+ +  G+ I+     EI  + +  + +L    
Sbjct: 276 KMNNKLALARRIAGYKAAEDIIAPLTGELLVAKGEKINTAKANEIDAAGVTRVVVLVERK 335

Query: 352 VNNNA---YIRNTLVT--DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
              +     I N  V          DA   I       ++     A S         D  
Sbjct: 336 GEESTPVIVISNGCVDAQPFFSFDVDAECGINERANFAEIRKILDATS---------DPE 386

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
           +   + R   ++ +        R +  +DI A I  L+ L +G G  D+ID+LGNRRVRS
Sbjct: 387 EQKELLRQNHDVLI-------SRTVTVDDIFASINYLIGLDHGIGVTDEIDHLGNRRVRS 439

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           VGE+L+NQ+R+G  RMER I+ER++  + ++  + PQ L+N +PVV+A+ EF  SS LSQ
Sbjct: 440 VGELLQNQFRIGFSRMERVIRERMTLQNQENGEITPQSLVNIRPVVAAIKEFIGSSPLSQ 499

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N L+ +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+S
Sbjct: 500 FMDQNNPLAELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRLCPIETPEGPNIGLIS 559

Query: 585 SLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L ++A++N YGF+E PYR+V      VT++VVY++A  E+   +AQAN  LDE+  F  
Sbjct: 560 YLATYAKINKYGFVEAPYRRVDKATGVVTDEVVYMTADVEDEYIVAQANEPLDENNRFVR 619

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             V  R   +       ++DF+D SP+ +VS+A + IPFLENDD NR LMG NMQRQAVP
Sbjct: 620 PRVSGRHRNDIQEFEASQVDFMDVSPRMMVSVATACIPFLENDDCNRALMGSNMQRQAVP 679

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L+  + P V TGME   A  SG  I+A   G VE VDA +IV+R  +G  D        Y
Sbjct: 680 LMVTQQPIVATGMEYKAATDSGVCILAAHDGTVEYVDAEKIVVRCADGSAD-------TY 732

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+KF RSNQ  C NQRP+V+VGD V+  D++ADGP+T  G+++LG+N LV FM W GYN
Sbjct: 733 ELIKFMRSNQGNCNNQRPIVQVGDAVKTGDVLADGPATKNGEISLGKNALVGFMTWEGYN 792

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++L++E++V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPNV ++ LK++D+ GII
Sbjct: 793 YEDAVLLNEKLVREDVYTSIHIEEYETEARDTKLGPEEITRDIPNVGDDALKDLDDRGII 852

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVD+
Sbjct: 853 RIGAEVKTGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGAYGIVVDI 912

Query: 943 RIFNRHGID 951
           ++F     D
Sbjct: 913 KVFTPENSD 921



 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 119/317 (37%), Positives = 157/317 (49%), Gaps = 47/317 (14%)

Query: 1110 PFLKDGTPVDI-VLNPL-------GVPSRMN----VGQIFETHLG-WACVGLGKKIKSLI 1156
            P    G  VDI V  P        GV  RM     + Q  +  +G       G K     
Sbjct: 902  PHGAYGIVVDIKVFTPENSDELQPGV--RMCVRCYIAQKRKISVGDKMAGRHGNKGVVSR 959

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
               + +    P  + L+ V+       +++      V         G  V TPVFDGA E
Sbjct: 960  ILPQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVNLGYVAKALGWKVQTPVFDGAHE 1019

Query: 1217 EAINSMLRMA--------------------------------DLDESGQSILYDGLTGEP 1244
              +      A                                DL + G++ +YDG TGE 
Sbjct: 1020 SDLRDCFAEARTKWHGENAPEYPTKLDRLMGEKGHIIDFSKIDLTDDGKTTVYDGRTGEQ 1079

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   VTVGY+Y LKL+H+V DK++ARSTG YS+VTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 1080 FPNKVTVGYMYYLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGGQRFGEMEVWALEA 1139

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LTIKSDDVVGR + YE+IV G+     G PESF V++KE+Q+LGL I ++
Sbjct: 1140 YGAAYTLQEILTIKSDDVVGRVKTYEAIVKGDPIPRPGIPESFRVMLKELQSLGLDIVVQ 1199

Query: 1365 NSRTKNSAKMEEIPDFN 1381
            +         +E  D +
Sbjct: 1200 DKEGNPVDMRQEFDDDD 1216


>gi|300362396|ref|ZP_07058572.1| DNA-directed RNA polymerase subunit beta [Lactobacillus gasseri
           JV-V03]
 gi|300353387|gb|EFJ69259.1| DNA-directed RNA polymerase subunit beta [Lactobacillus gasseri
           JV-V03]
          Length = 1212

 Score =  828 bits (2140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/986 (42%), Positives = 592/986 (60%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++  
Sbjct: 107 GEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ E+   F         
Sbjct: 164 TVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEVADMFGESDSLRFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        +   +  +G   
Sbjct: 224 LEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + GDV+  + L+++                
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHEILDKL---------------- 326

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + Y+          DR D  +  Y   + G +      + +  +   D ++       
Sbjct: 327 --SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER------- 367

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              + +  N    DDV+H+   D++A I    +L++  GT DDID+LGNRR+R VGE+L+
Sbjct: 368 --VIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R  
Sbjct: 546 NKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNEDGSFKDKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP 
Sbjct: 606 EDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPI 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RS
Sbjct: 666 VGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R   
Sbjct: 839 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELPPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 257/1055 (24%), Positives = 392/1055 (37%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 239  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 298

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 299  AETLADPDTGEIIAKKGDVVTHEILDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 357

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D    +     +   +        L     
Sbjct: 358  KVYSKVDPERVIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRI 417

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 418  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 478  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 537

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +  P  E D S +
Sbjct: 538  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNE-DGSFK 596

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +       +          ++ +     +E  D+ R ++ +  
Sbjct: 597  DKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLENDDSNRALMGAN- 650

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 651  -----------------HQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 679

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T    +++ V+ +  +    +     P V 
Sbjct: 680  DALVAKAPG----VVEYVDANEIRIRRDDDTL---DKY-VLEKFRRSNATKNYNQTPAVK 731

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 732  QGERVVADE--VIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 787

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          E   +D D+E  I+      +  
Sbjct: 788  -------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE-GIVRIGAEVQDG 839

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 840  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 891  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 942

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 943  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 1003 M---------------------------------------------VREAGIGK------ 1011

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1012 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1068

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1069 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1128

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1129 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1163


>gi|146295985|ref|YP_001179756.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|166229291|sp|A4XI30|RPOB_CALS8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|145409561|gb|ABP66565.1| DNA-directed RNA polymerase subunit beta [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 1229

 Score =  828 bits (2140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/959 (44%), Positives = 600/959 (62%), Gaps = 60/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R  +GK  E++D+P L+E+QK S+  FL          +EGL+   + + PI
Sbjct: 7   VQYG-KVQRMSYGKVKEVLDLPYLLEIQKKSFQWFL----------DEGLREVLREISPI 55

Query: 66  TAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             ++   +LEFV Y F  PPK+   +C  RD TYA PLK+ +RLI          K   +
Sbjct: 56  KDYTENLLLEFVDYYFDGPPKYSEQECKERDATYARPLKVKVRLI---------NKETGE 106

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ IYMG+ P+MT+ GTF+I G +R++VSQL RSPG +F     +    G+ +++  I
Sbjct: 107 IKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQ---GRKIFSGTI 163

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGD 243
           IP++G W++ E D+ +++ VR+DR RKV +T+ L A G+ +++ I +            +
Sbjct: 164 IPNRGAWLEFETDTSELLSVRLDRTRKVSLTTLLKAFGLYNQQLIFNKLGEDERLKASLE 223

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                    + +  A +      +  GE   +E+ K L   +    +   +  +G     
Sbjct: 224 KEANKGEIGNPVENA-LLEIYRRLRPGEPPNVENAKNLLERMYFDPRGYDLAKVGRYKLN 282

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                   +     AEDIV+  TGEI ++ G++I  ++   I  + I ++ +   D    
Sbjct: 283 KKLSLWKRIFNKRAAEDIVDKRTGEILVKEGEIISREAALNIQDAGINEVLVYVEDDKVF 342

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                NT+  D+  D           +   ++    V   + +     ++   L      
Sbjct: 343 KVVGNNTVKLDRYVDFD------VSDLNIKELVYLPVLNEILSTTNDVNEIKQL------ 390

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +       + ++D+ A     + L+ G G IDDID+LGNRRVR+VGE+L+NQ
Sbjct: 391 ----IKERERELVPYCLTRDDVFAATSYFLGLKYGIGHIDDIDHLGNRRVRAVGELLQNQ 446

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL RMER I+ER++  DIDSV PQ LIN +PV +A+ EFF SS LSQ  + VN L+ 
Sbjct: 447 FRIGLARMERVIRERMTIQDIDSVTPQTLINIRPVTAAIKEFFGSSPLSQFMDQVNPLAA 506

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++ARVN 
Sbjct: 507 LTNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRMCPIETPEGPNIGLITSLATYARVNE 566

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGF+ETPYRKV   + +VT++VVYL+A EE+   IAQA   +DE+G F  + +  R   +
Sbjct: 567 YGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATEPVDEEGRFINQRITVRFGED 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V + ++D +D SPKQ+VS++ SLIPFLENDD+NR LMG NMQRQAVPLL  E+P +G
Sbjct: 627 IIEVDKHEVDLVDISPKQIVSVSTSLIPFLENDDANRALMGSNMQRQAVPLLTTESPIIG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG  ++AK+ GIVE+V A  IVI++ +G  D       +Y L+KF+R+NQ
Sbjct: 687 TGVEYRAAVDSGVCVLAKKDGIVEKVSADEIVIQNHDGTKD-------VYHLLKFKRTNQ 739

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G EV+  ++IADGPSTD G+LALG+N+LVAFMPW GYN+ED++LISER
Sbjct: 740 GTCFNQRPIVRKGQEVKTGEVIADGPSTDHGELALGKNVLVAFMPWEGYNYEDAILISER 799

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V EDV+TSIHIEE+E  ARDTKLGPEEITRDIPN+ E+ +K++DE GII +GAEV  GD
Sbjct: 800 LVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNIGEDAIKDLDERGIIRIGAEVKSGD 859

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA + RDTSLRVP G  G VVDV++F+R   D
Sbjct: 860 ILVGKVTPKGETELTAEERLLRAIFGEKARETRDTSLRVPHGEGGIVVDVKVFSRDKGD 918



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 252/1190 (21%), Positives = 422/1190 (35%), Gaps = 154/1190 (12%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  +TG  +I   ++ + S L++S        +      I
Sbjct: 99   LINKETGEIKEQDIYMGEFPIMTETGTFIINGAERVIVSQLIRSPGCYFASSIDKQGRKI 158

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS-----EIRDIPILYVDSVN 353
             S  +     A      +T E+     D   + SL  +  +     +      L  D   
Sbjct: 159  FSGTIIPNRGAWLEFETDTSELLSVRLDRTRKVSLTTLLKAFGLYNQQLIFNKLGEDERL 218

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
              +  +     +     ++ALL+IYR +RPG+      A+++   ++FD   YDL+ VGR
Sbjct: 219  KASLEKEANKGEIGNPVENALLEIYRRLRPGEPPNVENAKNLLERMYFDPRGYDLAKVGR 278

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAII-KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
                 +LN       R   K     I+ K   ++   +G I   +   N +   + E+L 
Sbjct: 279  Y----KLNKKLSLWKRIFNKRAAEDIVDKRTGEILVKEGEIISREAALNIQDAGINEVL- 333

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                +   ++ + +      +D         +N K +V         +++      VN +
Sbjct: 334  --VYVEDDKVFKVVGNNTVKLDRYVDFDVSDLNIKELVYLPV----LNEILSTTNDVNEI 387

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVSSLTSFA 590
             ++    R   L    + R              YG   I   +      +  V  L    
Sbjct: 388  KQLI-KERERELVPYCLTRDDVFAATSYFLGLKYGIGHIDDIDHLGNRRVRAVGELL--- 443

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            +      +    R + +     D+  ++     N  I    +++ E    +         
Sbjct: 444  QNQFRIGLARMERVIRERMTIQDIDSVTPQTLIN--IRPVTAAIKEFFGSS----PLSQF 497

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +++       +    S      ++     F   D      +  +   +  P+   E P 
Sbjct: 498  MDQVNPLAALTNKRRLSALGPGGLSRDRAGFEVRD------VHHSHYGRMCPIETPEGPN 551

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            +  G+ + +A  +             +VD     +      L                  
Sbjct: 552  I--GLITSLATYARVNEYGFLETPYRKVDKKEARVTDEVVYLTADEEDTYKIAQATEPVD 609

Query: 771  NQNTCVNQRPLVKVGDEVRRNDII---------------------------ADGPSTDLG 803
             +   +NQR  V+ G+++   D                             A+       
Sbjct: 610  EEGRFINQRITVRFGEDIIEVDKHEVDLVDISPKQIVSVSTSLIPFLENDDANRALMGSN 669

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTKLGPE 859
                   +L    P  G   E    +   +      + +   +  +E   +      G +
Sbjct: 670  MQRQAVPLLTTESPIIGTGVEYRAAVDSGVCVLAKKDGIVEKVSADE---IVIQNHDGTK 726

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            ++   +           ++  I+  G EV  G+++    +      +   + +L A    
Sbjct: 727  DVYHLLKFKRTNQGTCFNQRPIVRKGQEVKTGEVIADGPST-DHGELALGKNVLVAFMPW 785

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DE 974
            +  +  D  L     V   V        +  +  +  +  E     I  +  D     DE
Sbjct: 786  EGYNYEDAILISERLVKEDVYTSIHIEEYECEARDTKLGPEEITRDIPNIGEDAIKDLDE 845

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            + I+      +  +IL G+    G         L   +  E  R                
Sbjct: 846  RGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---------------- 889

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             E+                  K+     GD++PPGV ++V+V+VA KR I  GDKMAGRH
Sbjct: 890  -ETRDTSLRVPHGEGGIVVDVKVFSRDKGDELPPGVNQLVRVYVAQKRKISVGDKMAGRH 948

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNK                            GV SR+                    ++ 
Sbjct: 949  GNK----------------------------GVISRI------------------LPVED 962

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +                ++ V+       +++                G  V+TPVFDGA
Sbjct: 963  MPFLPDGTP--------VDIVLNPLGVPSRMNIGQILETHLGYAAKALGWKVATPVFDGA 1014

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             EE I   L +A L  +G++ILYDG TGEPFD  VTVGY+YMLKL H+V DK++ARSTG 
Sbjct: 1015 KEEDIEEALNLAGLSPNGKTILYDGRTGEPFDNEVTVGYMYMLKLVHLVDDKIHARSTGP 1074

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR + YE+IV 
Sbjct: 1075 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVTGRVKTYEAIVK 1134

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            G +  E G PESF VLVKE+Q+L L + L +   K     E I +  + +
Sbjct: 1135 GENIPEPGIPESFKVLVKELQSLCLDVKLLSEDNKEIELKESIDEDEQPQ 1184


>gi|227888860|ref|ZP_04006665.1| DNA-directed RNA polymerase subunit beta [Lactobacillus johnsonii
           ATCC 33200]
 gi|227850697|gb|EEJ60783.1| DNA-directed RNA polymerase subunit beta [Lactobacillus johnsonii
           ATCC 33200]
          Length = 1212

 Score =  828 bits (2140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/986 (42%), Positives = 591/986 (59%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++  
Sbjct: 107 GEIKTQDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ EI   F         
Sbjct: 164 TVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEIADMFGESDSLRFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        +   +  +G   
Sbjct: 224 LEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + GDV+  + L+++                
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHELLDKL---------------- 326

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + Y+          DR D  +  Y   + G +      + +  +   D ++       
Sbjct: 327 --SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER------- 367

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              + +  N    DDV+H+   D++A +    DL++  GT DDID+LGNRR+R VGE+L+
Sbjct: 368 --VVKLMSNGHIADDVKHLTPADVLASLNYFFDLQDNIGTTDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R  
Sbjct: 546 NKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNEDGSFKDKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP 
Sbjct: 606 EDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPI 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RS
Sbjct: 666 VGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P VK G+ V  +++IADGP+   G+LALG+N ++AF+ W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPAVKQGERVVADEVIADGPAMKNGELALGQNPIIAFLTWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV ++ LK++DE GI+ +GAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGDDALKDLDEEGIVRIGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R   
Sbjct: 839 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELPPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 255/1055 (24%), Positives = 391/1055 (37%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 239  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 298

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 299  AETLADPDTGEIIAKKGDVVTHELLDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 357

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D+         +   +        L     
Sbjct: 358  KVYSKVDPERVVKLMSNGHIADDVKHLTPADVLASLNYFFDLQDNIGTTDDIDHLGNRRI 417

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 418  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 478  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 537

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +     E D S +
Sbjct: 538  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANARLNE-DGSFK 596

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +       +          ++ +     +E  D+ R ++ +  
Sbjct: 597  DKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLENDDSNRALMGAN- 650

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 651  -----------------HQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 679

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T    +++ V+ +  +    +     P V 
Sbjct: 680  DALVAKAPG----VVEYVDANEIRIRRDDDTL---DKY-VLEKFRRSNATKNYNQTPAVK 731

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 732  QGERVVADE--VIADGPAMKNGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 787

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          +   +D D+E  I+      +  
Sbjct: 788  -------TSIHIEDYESEARDTKLGPEEITREIPNVGDDALKDLDEE-GIVRIGAEVQDG 839

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 840  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 891  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 942

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 943  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 1003 M---------------------------------------------VREAGIGK------ 1011

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1012 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1068

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1069 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1128

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1129 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1163


>gi|154499823|ref|ZP_02037861.1| hypothetical protein BACCAP_03480 [Bacteroides capillosus ATCC
           29799]
 gi|150271421|gb|EDM98678.1| hypothetical protein BACCAP_03480 [Bacteroides capillosus ATCC
           29799]
          Length = 1270

 Score =  828 bits (2140), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/966 (43%), Positives = 576/966 (59%), Gaps = 70/966 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V+ G   +RK + ++ EI+ +P+L+EVQK SY  FL          + GL+  FK
Sbjct: 32  MMVKDVYYG-KTLRKSYARHEEILSMPNLLEVQKNSYQWFL----------DTGLREVFK 80

Query: 61  SVFPITAFSGAAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            V  IT ++G   L F+ Y  D P K+ +++C  RD TYA P+K+ +RL           
Sbjct: 81  DVASITDYAGNLELSFIDYSMDEPPKYSIEECKARDATYAAPIKVRVRL---------RN 131

Query: 120 KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
           K  ++IKEQ I+MGD PLMT  G+FVI G +R++VSQ+ RSPG+++   + +   +G + 
Sbjct: 132 KETEEIKEQEIFMGDFPLMTDSGSFVINGAERVIVSQIVRSPGVYYARTEDK---AGNVT 188

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPK--I 236
           YA  +IP +G W++ E D  D+ +VRID+ RK+P+T F+ A+G  ++ EI+  F     I
Sbjct: 189 YATTVIPYRGAWLEYETDLSDVFYVRIDKNRKLPITCFIRAVGPRTDAEIIDMFGEDPRI 248

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
           V +   D       A        +      +  GE   ++S + L + L    +   +  
Sbjct: 249 VATLEKDACKTYEDA--------LLEVYRKLRPGEPPTVDSAESLLNALFFDPRRYDLSA 300

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +A  I +  TGE+  EAG+VI  +   E+    + +  I 
Sbjct: 301 VGRYKFNKKLALWHRLVNQKLALPIADPMTGELLAEAGEVISREKAHELDDHGVNEAVIQ 360

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      +  N +   K  D   A   I   +R   +       S             
Sbjct: 361 LENGTLVKMFSNNMVDMSKFVDFDPAECGITERVRFSVLQDLMNQYS------------- 407

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               G                +HI  +D++A I  L  L NG GT DDID+LGNRR+R V
Sbjct: 408 ----GEELKEAIAEHADDLVPKHIIVDDMMATINYLNCLANGAGTPDDIDHLGNRRLRCV 463

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+G  RMER I+ER++  D+D V PQ LIN +PV +A+ EFF SS LSQ  +
Sbjct: 464 GELLQNQFRIGFSRMERVIRERMTIQDLDIVTPQSLINIRPVTAAIKEFFGSSPLSQFMD 523

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RR+SALG GG++R RA  ++RDVH +HYGR+CP ET EG NIGL+S L 
Sbjct: 524 QTNPLAELTHKRRMSALGPGGLSRDRASFDVRDVHYSHYGRLCPIETPEGPNIGLISYLA 583

Query: 588 SFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+AR+N YGFIE PYRKV    G +T+ V Y++A  E+   IAQA   LDE+     + +
Sbjct: 584 SYARINRYGFIEAPYRKVDKATGCLTDQVDYMTADIEDQFIIAQATEPLDENKRLVNDRI 643

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   E I V R+++D+ID SP+ + SIA + IPFLENDD+NR LMG NMQRQAVPLL+
Sbjct: 644 TCRHRNEIIEVDRDQVDYIDVSPQMMFSIATAQIPFLENDDANRALMGANMQRQAVPLLR 703

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            EAP V TG E      SG AI+A+  G V +  A  I +R   G +         Y+L 
Sbjct: 704 PEAPIVATGQEHKNCIDSGVAILAEEDGEVLKSSAQYITVRYDSGRVVD-------YKLT 756

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN  TC+NQRP+V  G  V + ++IADGPST  G++ALG+N+L+ FM W GYN+ED
Sbjct: 757 KFMRSNHTTCINQRPIVNAGQRVEKGEVIADGPSTSNGEIALGKNILMGFMTWEGYNYED 816

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L++ERMV +DVFTSIHIEE+E  +RDTKLGPEEITRDIPNV E+ LK++DE GII VG
Sbjct: 817 AILLNERMVKDDVFTSIHIEEYETESRDTKLGPEEITRDIPNVGEDALKDLDERGIIRVG 876

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VDV++F
Sbjct: 877 AEVRSGDILVGKVTPKGETDLTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKVF 936

Query: 946 NRHGID 951
            R G D
Sbjct: 937 TREGGD 942



 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 187/538 (34%), Positives = 252/538 (46%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +    +       I++  I+  G  V  G+++    +      +   + +
Sbjct: 744  RYDSGRVVDYKLTKFMRSNHTTCINQRPIVNAGQRVEKGEVIADGPSTSN-GEIALGKNI 802

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIEL 966
            L      +  +  D  L     V   V        +  +  +  +  E          E 
Sbjct: 803  LMGFMTWEGYNYEDAILLNERMVKDDVFTSIHIEEYETESRDTKLGPEEITRDIPNVGED 862

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE+ I+      R  +IL G+    G         L   +  E  R        
Sbjct: 863  ALKDL-DERGIIRVGAEVRSGDILVGKVTPKGETDLTAEERLLRAIFGEKAR-------- 913

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E      +            K+   + GD++ PGV +VV+V++A KR I  
Sbjct: 914  ---------EVRDTSLKVPHGESGIIVDVKVFTREGGDELSPGVNQVVRVYIAQKRKISV 964

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSRILP EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+A  
Sbjct: 965  GDKMAGRHGNKGVVSRILPQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYAAK 1024

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG K+ + I +     DI+                           L++A     G   
Sbjct: 1025 TLGWKVATPIFNGADEKDIA-------------------------ETLQMAGLSPDG--- 1056

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                          S L             YDG TGE FD  VTVGY+Y LKL+H+V DK
Sbjct: 1057 -------------KSWL-------------YDGRTGERFDNRVTVGYVYFLKLHHLVDDK 1090

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD  GR 
Sbjct: 1091 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDTTGRV 1150

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            R YE+IV G++  + G PESF VLVKE+QAL L I + ++  +     +E  D    +
Sbjct: 1151 RTYEAIVKGHNVPKPGVPESFKVLVKELQALCLDIKVLDAEGQEIELKDEDEDNYTPD 1208


>gi|323691464|ref|ZP_08105736.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
 gi|323504510|gb|EGB20300.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
          Length = 1293

 Score =  828 bits (2139), Expect = 0.0,   Method: Composition-based stats.
 Identities = 437/961 (45%), Positives = 596/961 (62%), Gaps = 59/961 (6%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G G VR  F +  E++++P+LIE+QK SY  FL          +EGL+  F  +
Sbjct: 10  MRPVKAGKG-VRMTFSRQKEVLEMPNLIEIQKNSYQWFL----------DEGLREVFADI 58

Query: 63  FPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            PI  F+G   L+FV +    D  K+ +++C  RD TYA PLK+ +RL   D D      
Sbjct: 59  SPIADFAGHLSLDFVDFTLCKDDIKYTIEECKERDATYAAPLKVKVRLCNKDKD------ 112

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +I E  I+MGDLPLMT  G+FVI G +R++VSQL RSPGI++     +    G  LY
Sbjct: 113 ---EINEHEIFMGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYGIAHDKI---GTELY 166

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY- 238
           +C +IP++G W++ E DS DI +VR+DR RKVPVT  + ALG  +  EI+  F  ++   
Sbjct: 167 SCTVIPNRGAWLEYETDSNDIFYVRVDRTRKVPVTVLIRALGYGTNAEIIELFGEELKLE 226

Query: 239 -SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            S   D           +         + +D+ E ++ S         L K  + K  K 
Sbjct: 227 KSFEKDPSSNYQDGLLELYKKIRPGEPLSVDSAESLLNSMFFDPRRYDLAKVGRYKFNKK 286

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L    + + G  +AED+V+  TGEI  E G  +D++   +I ++    IP +++     N
Sbjct: 287 L-HFKNRIAGHTLAEDVVDMSTGEILAEKGTEVDKQLATDIQNA---AIPYVWIQGERKN 342

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             + + ++ D         L  Y    P +V        +  +   +    +  +   +K
Sbjct: 343 HKVLSNMMVD---------LASYVDFDPEEV----GVTELVYYPVLEGILAEAGSDEELK 389

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             ++ ++      +HI KEDIIA I   + L  G GT DDID+LGNRR+R+VGE+L+NQY
Sbjct: 390 EVIKRDIH-DLIPKHITKEDIIASINYNMHLEGGIGTQDDIDHLGNRRIRAVGELLQNQY 448

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+++ D++ V  Q LIN KPV +AV EFF SSQLSQ  +  N L+ +
Sbjct: 449 RIGLSRMERVVRERMTTQDMEGVSAQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLAEL 508

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++ARVN Y
Sbjct: 509 THKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARVNQY 568

Query: 596 GFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           GF+E PYR V      +  VT +VVYL+A EE+N  +AQAN  LD++G F    V  R  
Sbjct: 569 GFVEAPYRVVDKSDPHNPVVTEEVVYLTADEEDNFVVAQANEPLDDEGHFIHNNVSGRFR 628

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E     +++ID +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLLK EA  
Sbjct: 629 EETSEFQKKRIDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLKTEAAV 688

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SG  +VAK AG+VE+  +  I+I+        S    D+Y L KF+RS
Sbjct: 689 VGTGIEGKAAVDSGVCMVAKNAGVVERSASNEIIIKRD------SDGNRDVYHLTKFKRS 742

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+ C NQ+P+V  GD V   ++IADGPSTD G++ALG+N L+ FM W GYN+ED++L+S
Sbjct: 743 NQSNCYNQKPIVYKGDHVEVGEVIADGPSTDNGEIALGKNPLIGFMTWEGYNYEDAVLLS 802

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V EDV+TS+HIEE+E  ARDTKLGPEEITRD+P V E+ LK++DE GII +GAEV  
Sbjct: 803 ERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGEDALKDLDERGIIRIGAEVRA 862

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   
Sbjct: 863 GDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIIVDAKVFTRENG 922

Query: 951 D 951
           D
Sbjct: 923 D 923



 Score =  530 bits (1364), Expect = e-147,   Method: Composition-based stats.
 Identities = 180/545 (33%), Positives = 257/545 (47%), Gaps = 40/545 (7%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++ +    G  ++               ++  I+  G  V  G+++    +      + 
Sbjct: 720  EIIIKRDSDGNRDVYHLTKFKRSNQSNCYNQKPIVYKGDHVEVGEVIADGPSTDN-GEIA 778

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--- 964
              +  L      +  +  D  L     V   V        +  +  +  +  E       
Sbjct: 779  LGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYTSVHIEEYEAEARDTKLGPEEITRDVP 838

Query: 965  ---ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               E   +D  DE+ I+      R  +IL G+    G         L   +  E  R   
Sbjct: 839  GVGEDALKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--- 894

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E      +            K+   + GD++ PGV   V++++A K
Sbjct: 895  --------------EVRDTSLKVPHGAYGIIVDAKVFTRENGDELSPGVNETVRIYIAQK 940

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL
Sbjct: 941  RKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHL 1000

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
              A   LG  + + I D     DI              S  E    Y D +  ++ E   
Sbjct: 1001 SLAARALGFNVSTPIFDGANEIDIQDTLELAND-YVNTSWEEFEEKYRDKADPKLMEYLG 1059

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                               ++ +   L   G+  L DG TGE FD PVT+G+++ LKL+H
Sbjct: 1060 -------------SHLEHRALWKGVPLGRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHH 1106

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDD
Sbjct: 1107 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDD 1166

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR + YE+I+ G +  E G PESF VL+KE+Q+LGL + +           E I D+ 
Sbjct: 1167 VVGRVKTYEAIIKGENIPEPGIPESFKVLLKELQSLGLDVRVLKEDGSEVELAETI-DYG 1225

Query: 1382 KCELK 1386
              +++
Sbjct: 1226 DTDIR 1230


>gi|322381134|ref|ZP_08055137.1| DNA-directed RNA polymerase subunit beta-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
 gi|321154710|gb|EFX46981.1| DNA-directed RNA polymerase subunit beta-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
          Length = 1157

 Score =  828 bits (2138), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/936 (45%), Positives = 589/936 (62%), Gaps = 79/936 (8%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           ++IP+LIE+Q+ SY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y    
Sbjct: 2   LEIPNLIEIQQKSYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLGE 51

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VDD   RD+TYA PL++ +RLI          K   ++KEQ ++MGD P+MT+ GT
Sbjct: 52  PKYTVDDSKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPIMTETGT 102

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQL RSP ++++    +   +GK  +   +IP++G W+++E D+KDII+
Sbjct: 103 FIINGAERVIVSQLVRSPSVYYN---TKVDKNGKKAFTATVIPNRGAWLELETDAKDIIY 159

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VRIDR RK+PVT  L ALG  ++ EIL             D      +   L+       
Sbjct: 160 VRIDRTRKIPVTVLLRALGFGTDAEILDLLGDDEYIRNTLDKDNTDSTDKALI------E 213

Query: 263 SLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAEDIV 313
               +  GE   +++ + L        K           +       + L    +AE +V
Sbjct: 214 IYERLRPGEPPTLDNARSLLYARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLV 273

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           + ETGEI  EAG ++D + L+EI            +  +      +   V +   +    
Sbjct: 274 HPETGEIIAEAGQLVDRRLLDEI------------LPCLEEGVGFKEYSVPNGVLESDHI 321

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            +    V  P +                         V +V  N  +      +V++I  
Sbjct: 322 PMQTIDVFSPIE----------------------DGKVVKVISNGVI----DKNVKNITP 355

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            DII+ I   ++L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  
Sbjct: 356 ADIISSINYFINLLHGIGNTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQ 415

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D + + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R R
Sbjct: 416 DANVITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRER 475

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVT 611
           AG E+RDVH +HYGR+CP ET EG NIGL++SL++FAR+N YGFIE PYR+V    G VT
Sbjct: 476 AGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTFARINEYGFIEAPYRRVDPKTGVVT 535

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++VY++A EE+N  +AQAN+ L+EDG+F  + V+ R   E + +P+E++D++D SPKQV
Sbjct: 536 DEIVYMTADEEDNYVVAQANAELNEDGTFAADNVYVRYKDEILTLPKERVDYMDVSPKQV 595

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+A +LIPFLENDDSNR LMG NMQRQAVPLL  +AP VGTGME   AK SG  +VAK 
Sbjct: 596 VSVATALIPFLENDDSNRALMGSNMQRQAVPLLMPKAPLVGTGMEYKAAKDSGVCVVAKH 655

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            GI+E+V    I +R  E       SG    ++L KF RSNQ TC+NQRPLV  G  V+ 
Sbjct: 656 DGIIEKVSGNEIWLRRQEEVDGRLVSGNITKFKLHKFMRSNQGTCINQRPLVLEGQRVKA 715

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            DI+ADGPST+ G+LALGRN++VAFM W GYN+ED++L+SE++V EDV+TSIHIEE+E  
Sbjct: 716 GDILADGPSTEQGELALGRNVVVAFMTWEGYNYEDAILLSEKLVKEDVYTSIHIEEYESE 775

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           ARDTKLGPEEITRDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T EE
Sbjct: 776 ARDTKLGPEEITRDIPNVGEDALKNLDERGIIRVGAEIGAGDILVGKVTPKGVTELTAEE 835

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           +LL AIFGEKA +VRDTSLRVP G  G VVDV++F 
Sbjct: 836 RLLHAIFGEKAREVRDTSLRVPHGTDGIVVDVKVFT 871



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/527 (35%), Positives = 267/527 (50%), Gaps = 68/527 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G     +    +       I++  ++  G  V  GDIL    + + +  +     ++ A 
Sbjct: 682  GNITKFKLHKFMRSNQGTCINQRPLVLEGQRVKAGDILADGPSTE-QGELALGRNVVVAF 740

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 741  MTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGE 795

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               +N+  R   I  G    +G     K T      ++   R     F  +  +V+    
Sbjct: 796  DALKNLDER-GIIRVGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 854

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGN
Sbjct: 855  RVPHGTDGIVVDV------KVFTHENGDELPPGVNQLVRVYIAQKRKISQGDKMAGRHGN 908

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+++RILP EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG  + + +
Sbjct: 909  KGVIARILPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMAAKQLGIHVATPV 968

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     D                                             VFD    
Sbjct: 969  FDGAHEYD---------------------------------------------VFD---- 979

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  +  A +  +G++ LYDG TGE F+R VTVG +YM+KL HMV DK++ARSTG YS
Sbjct: 980  -----TMEEAGMQRNGKTKLYDGRTGEEFEREVTVGVMYMIKLAHMVDDKIHARSTGPYS 1034

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G 
Sbjct: 1035 LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYESIVKGE 1094

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +  E G PESF VL+KE+Q+LG+ + + +   +    M+E+ D +  
Sbjct: 1095 NVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIE-MKELDDEDDA 1140


>gi|315037523|ref|YP_004031091.1| DNA-directed RNA polymerase subunit beta [Lactobacillus amylovorus
           GRL 1112]
 gi|312275656|gb|ADQ58296.1| DNA-directed RNA polymerase subunit beta [Lactobacillus amylovorus
           GRL 1112]
 gi|327182819|gb|AEA31266.1| DNA-directed RNA polymerase subunit beta [Lactobacillus amylovorus
           GRL 1118]
          Length = 1213

 Score =  828 bits (2138), Expect = 0.0,   Method: Composition-based stats.
 Identities = 401/963 (41%), Positives = 582/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARDHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGISSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  +   V++ + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKDTVVNHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIAADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF E ++  R
Sbjct: 542 IINKYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKENIILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  469 bits (1206), Expect = e-129,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 238/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T ++DG                           
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVIYDG--------------------------R 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR R YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVRAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +   K     +   + ++
Sbjct: 1140 IRVLDMNHKEIELRDMDGESSE 1161


>gi|325955995|ref|YP_004286605.1| DNA-directed RNA polymerase subunit beta [Lactobacillus acidophilus
           30SC]
 gi|325332560|gb|ADZ06468.1| DNA-directed RNA polymerase subunit beta [Lactobacillus acidophilus
           30SC]
          Length = 1213

 Score =  828 bits (2138), Expect = 0.0,   Method: Composition-based stats.
 Identities = 401/963 (41%), Positives = 583/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARDHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGISSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  +   V++ + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKDTVVNHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +    + + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPIIVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIAADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF E ++  R
Sbjct: 542 IINKYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKENIILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  469 bits (1206), Expect = e-129,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 238/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T ++DG                           
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVIYDG--------------------------R 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR R YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVRAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +   K     +   + ++
Sbjct: 1140 IRVLDMNHKEIELRDMDGESSE 1161


>gi|322387029|ref|ZP_08060642.1| DNA-directed RNA polymerase subunit beta [Streptococcus infantis
           ATCC 700779]
 gi|321142173|gb|EFX37665.1| DNA-directed RNA polymerase subunit beta [Streptococcus infantis
           ATCC 700779]
          Length = 1228

 Score =  827 bits (2137), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/963 (43%), Positives = 580/963 (60%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 29  LAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKDFL----------DYGLKEVFE 78

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 79  DVLPISNFTETMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 129

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 130 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 186

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 187 GSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 246

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 247 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRTLLVARFFDPRRYDLAAVGR 305

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +E G V+    +E I      D+  +   
Sbjct: 306 YKINKKLNNKTRLLNQTIAEPLVDPETGEILVEKGTVMTRDVIESIESHLDGDLNKIV-- 363

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                         D     +  +L  ++V+ P D                         
Sbjct: 364 ----------YTPNDSAVLTEPVVLQKFKVVAPTDPDRV--------------------- 392

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +  D VR I   DI+A +   ++L  G G IDDID+LGNRR+R+VGE+
Sbjct: 393 -----VTIIGNANPDDKVRTITPADILAEMSYFLNLAEGIGRIDDIDHLGNRRIRAVGEL 447

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L NQ RLGL RMER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N
Sbjct: 448 LANQVRLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHN 507

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+ 
Sbjct: 508 PLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYG 567

Query: 591 RVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFI+TPYRKV     KVTN++V+L+A EE+   +AQANS L+ DG+F E++V  R
Sbjct: 568 HLNKYGFIQTPYRKVDRATGKVTNEIVWLTADEEDEYTVAQANSKLNADGTFAEKVVMGR 627

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +A
Sbjct: 628 HQGVNQEYPASSVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKA 687

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+
Sbjct: 688 PFVGTGMEYQAAHDSGAAVIAQHGGKVTYADADKVEVRREDGSLD-------VYHIQKFR 740

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQR LV+VGD + + D IADGPS + G++ALG+N +VA+M W GYNFED+++
Sbjct: 741 RSNSGTAYNQRTLVRVGDVIEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAVI 800

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TS+H+EE+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 801 MSERLVKDDVYTSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEV 860

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 861 KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 920

Query: 949 GID 951
             D
Sbjct: 921 NGD 923



 Score =  496 bits (1278), Expect = e-137,   Method: Composition-based stats.
 Identities = 173/507 (34%), Positives = 246/507 (48%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  +  GD +    +   +  M   +  + A    +  +  D  +     V   V 
Sbjct: 753  LVRVGDVIEKGDFIADGPS-MEKGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 811

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 812  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 871

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 872  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 914

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 915  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 974

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 975  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLW--------- 1025

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E         A +D   ++I
Sbjct: 1026 ------------------------------------DTVKE---------AGMDSDAKTI 1040

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 1041 LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 1100

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1101 EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1160

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 1161 SLGLDMRVLDEDDQEVELRDLDEGMDE 1187


>gi|220927770|ref|YP_002504679.1| DNA-directed RNA polymerase subunit beta [Clostridium
           cellulolyticum H10]
 gi|219998098|gb|ACL74699.1| DNA-directed RNA polymerase, beta subunit [Clostridium
           cellulolyticum H10]
          Length = 1246

 Score =  827 bits (2136), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/955 (46%), Positives = 609/955 (63%), Gaps = 67/955 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + K  E++++P+LIEVQK SY  FL          +EGL+  F+ + PIT ++G
Sbjct: 9   RNTRMSYSKIREVLEMPNLIEVQKNSYQWFL----------DEGLREVFRDISPITDYTG 58

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L+FV Y  D  PK+ V++C  RD TY+ PLK  +RLI          K   ++KEQ 
Sbjct: 59  NLILDFVDYSLDDTPKYSVEECKERDTTYSAPLKAKVRLI---------NKESGEVKEQE 109

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT  GTF+I G +R++VSQL RSPGI++     R    GK LY+  +IP++G
Sbjct: 110 IFMGDFPLMTDTGTFIINGAERVIVSQLVRSPGIYYSMKFDRV---GKKLYSNTVIPNRG 166

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS DI+ VRIDR RK+P+T  L ALG  ++  I                    
Sbjct: 167 AWLEYETDSNDILSVRIDRTRKLPLTVLLRALGYGTDFAITQLLGEDERILATIQKDNAK 226

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +   L+   K       +  GE   ++S + L + L    K   +   G          
Sbjct: 227 TTEEGLLEIYK------RLRPGEPPTVDSARSLLNSLFFDPKRYDLAKFGRFKFNKKLSV 280

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + + G   AE+IV+ ETGEI +  G++I+ +   E+ +S    + ++++     +  + 
Sbjct: 281 ANLITGQVAAENIVSAETGEILVTEGELIEREKAVEVQNSG---VNVVHLSVEGKSIKVV 337

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                D        + DI          T +V  ++   +         ST G V++   
Sbjct: 338 GNNTVDIRAFIDFDVSDIG--------ITENVQYAVLKEILE-------STSGEVQIKKA 382

Query: 420 LNLDTPDDV-RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           L     D + +HI  EDII+ I  +++L  G G+IDDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 383 LGERINDLIPKHITVEDIISSINYIINLDYGIGSIDDIDHLGNRRLRSVGELLQNQFRIG 442

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER++  DID V PQ LIN +PV +A+ EFF SSQLSQ  +  N L+ +TH 
Sbjct: 443 LSRMERVVRERMTIQDIDIVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHK 502

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN YGFI
Sbjct: 503 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFI 562

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           E P+RKV   + KVTN++VYL+A  E+   +AQA   LDE+G F    V  R   E + V
Sbjct: 563 EAPFRKVDKKNRKVTNEIVYLTADVEDPFVVAQATEPLDEEGKFISNKVVARIRHEILEV 622

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              KIDF+D SPKQ+VS+A ++IPFLENDD+NR LMG NMQRQAVPL+KA++P +GTG+E
Sbjct: 623 ESNKIDFMDVSPKQMVSVATAMIPFLENDDANRALMGSNMQRQAVPLIKADSPIIGTGIE 682

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A+ SG  ++A+ +G+V++V A  IVI++  G  D        Y+L+K+ RSNQ TC+
Sbjct: 683 YKAARDSGVCVIARTSGVVDKVSASEIVIKTKSGQKDS-------YKLLKYMRSNQGTCL 735

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V+ G+ V + DIIADGPSTD G++ALGRN+L+ FM W GYN+ED++LI+E++V E
Sbjct: 736 NQRPIVRKGEVVEKGDIIADGPSTDNGEIALGRNVLIGFMTWEGYNYEDAILINEKLVKE 795

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV EE LK++D+ GII +GAEV  GDILVG
Sbjct: 796 DVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEEALKDLDDRGIIRIGAEVRSGDILVG 855

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG +VDV++F R   D
Sbjct: 856 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIIVDVKVFTRENGD 910



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/533 (35%), Positives = 250/533 (46%), Gaps = 79/533 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G ++  + +  +       +++  I+  G  V  GDI+    +      +     +
Sbjct: 712  KTKSGQKDSYKLLKYMRSNQGTCLNQRPIVRKGEVVEKGDIIADGPSTDN-GEIALGRNV 770

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIEL 966
            L      +  +  D  L     V   V        +  +  +  +  E          E 
Sbjct: 771  LIGFMTWEGYNYEDAILINEKLVKEDVYTSIHIEEYEAESRDTKLGPEEITRDIPNVGEE 830

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D DD   I+      R  +IL G+    G         L   +  E  R        
Sbjct: 831  ALKDLDDR-GIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 881

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E                   K+   + GD++PPGV ++V+ ++A KR I  
Sbjct: 882  ---------EVRDTSLRVPHGESGIIVDVKVFTRENGDELPPGVNQLVRCYIAQKRKISV 932

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL DGTP++IVLNPLGVPSRMN+GQ+ E HLG+A  
Sbjct: 933  GDKMAGRHGNKGVISRILPEEDMPFLPDGTPLEIVLNPLGVPSRMNIGQVLEVHLGYAAK 992

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG KI + + D     DI        K                                
Sbjct: 993  ALGWKIATPVFDGATEEDIRETLIKAGKDP------------------------------ 1022

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                 DG                      LYDG TGEPFD  VTVGY+Y LKL H+V DK
Sbjct: 1023 -----DGKTV-------------------LYDGRTGEPFDNRVTVGYMYYLKLAHLVDDK 1058

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1059 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRV 1118

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            + YESIV G +  E G PESF VL+KE+Q+L L + + +   +  A  E + D
Sbjct: 1119 KTYESIVKGENVPEPGIPESFKVLIKELQSLALDVKVYSEEQEEIAIKEYVED 1171


>gi|238916249|ref|YP_002929766.1| DNA-directed RNA polymerase [Eubacterium eligens ATCC 27750]
 gi|238871609|gb|ACR71319.1| DNA-directed RNA polymerase [Eubacterium eligens ATCC 27750]
          Length = 1325

 Score =  827 bits (2135), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/959 (43%), Positives = 584/959 (60%), Gaps = 59/959 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F +  E++++P+LIEVQK SY  FL          NEGL+  F  + PI  ++G
Sbjct: 13  KAMRMSFSRQKEVLEMPNLIEVQKDSYQWFL----------NEGLKEVFDDISPIADYNG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+T+RL           K  + I E 
Sbjct: 63  RLSLEFVDFALCEDEVKYSIEECKERDATYAAPLKVTVRLH---------NKETESISEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL-LYACRIIPD 187
            I+MGDLPLMTK GTFVI G +R++VSQL RSPGI++D  K +    GK+ LY+C++IP+
Sbjct: 114 EIFMGDLPLMTKTGTFVINGAERVIVSQLVRSPGIYYDIQKDKY---GKIFLYSCQVIPN 170

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
           +G W++ E D+ DI +V++DR +KVP+T  + ALG  +  EIL  F  +       +   
Sbjct: 171 RGAWLEYETDANDIFYVKVDRNKKVPITVLIRALGFGTNAEILDIFGEEPKLLATMEKDT 230

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITSD---- 301
                        +      +  GE + +ES + L SG+    +   +  +G        
Sbjct: 231 STN------YQEGILELYKKLRPGEPLSVESAEALISGMFFDPRRYDLAHVGRYKFNKKL 284

Query: 302 ----CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                + G  +AED+V+ E G +   AG+ +  +S + I  + +  + I       +   
Sbjct: 285 SFKSRITGQVLAEDVVD-ENGTVIATAGEKLTRESAQAIQDAAVPSVFITVEVKAADGTV 343

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
               +    N+      +DI + +   +     +  + + +    +     +        
Sbjct: 344 SDRVVKILSNRA-----VDITKWVDISEEEAKELGVTEYVYYPVLAQILAENESLEDIKE 398

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                      +HI  EDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQ+R+
Sbjct: 399 AITKNIADLIPKHITVEDILASINYNMHLEYGVGTKDDIDHLGNRRIRAVGELLQNQFRI 458

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G+ RMER ++ER+S+ D+  + PQ LIN KPV +A+ EFF SSQLSQ  +  N LS ITH
Sbjct: 459 GISRMERVVRERMSTQDLSGISPQSLINIKPVTAAIKEFFGSSQLSQFMDQNNPLSEITH 518

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+AR+N YGF
Sbjct: 519 KRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYARINEYGF 578

Query: 598 IETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           +E PYR V      + +VT++V Y +A EE++ ++AQAN+ +DE+G F    V  R   E
Sbjct: 579 VEAPYRIVDKSDPKNPRVTDEVRYFTADEEDDFHVAQANAEIDENGYFVRNTVSGRYREE 638

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                + +ID +D SPK V S+A S+IPFL+NDD  R LMG NMQRQAVPLL  EAP +G
Sbjct: 639 TSQFDKSQIDLMDVSPKMVFSVATSMIPFLQNDDCTRALMGSNMQRQAVPLLMTEAPVIG 698

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E+  A  SG  +VA+  G+V   ++ +IVIR  +G           Y+L KF RSNQ
Sbjct: 699 TGIENKTAVDSGVCVVAEADGVVLSSESNKIVIREKDGKARE-------YKLTKFSRSNQ 751

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           + C NQRP+V  GDEV+  D+IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER
Sbjct: 752 SNCYNQRPIVFKGDEVKAGDVIADGPSTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSER 811

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TSIHIEE+E  ARDTKLGPEEITRD+P+   + +K++DE GII VGAEV  GD
Sbjct: 812 LVRDDVYTSIHIEEYETEARDTKLGPEEITRDLPSTGSDAVKDLDENGIIRVGAEVRAGD 871

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VV V+ F R   D
Sbjct: 872 ILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGIVVAVKTFTRENGD 930



 Score =  531 bits (1369), Expect = e-148,   Method: Composition-based stats.
 Identities = 188/621 (30%), Positives = 274/621 (44%), Gaps = 36/621 (5%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V         +                  +L+   P  G   E+   +   +        
Sbjct: 660  VATSMIPFLQNDDCTRALMGSNMQRQAVPLLMTEAPVIGTGIENKTAVDSGVCVVAEADG 719

Query: 842  IHIE-EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            + +  E   +    K G     +             ++  I+  G EV  GD++    + 
Sbjct: 720  VVLSSESNKIVIREKDGKAREYKLTKFSRSNQSNCYNQRPIVFKGDEVKAGDVIADGPST 779

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +   +  L      +  +  D  L     V   V        +  +  +  +  E
Sbjct: 780  SN-GEIALGKNPLIGFMTWEGYNYEDAVLLSERLVRDDVYTSIHIEEYETEARDTKLGPE 838

Query: 961  REQIELLA------RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                +L +      +D  DE  I+      R  +IL G+    G         L   +  
Sbjct: 839  EITRDLPSTGSDAVKDL-DENGIIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFG 897

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            E  R                 E      +            K    + GD++ PGV + V
Sbjct: 898  EKAR-----------------EVRDTSLKVPHGAYGIVVAVKTFTRENGDELSPGVNKSV 940

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            ++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+G
Sbjct: 941  RIYIAQKRKIGVGDKMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIG 1000

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HL  A   LG  I + + D     DI                 E+++    ++  
Sbjct: 1001 QVLEIHLSLAAKVLGFNISTPVFDGADENDIMDTLDMANAYANHPFDDEELAAQKAEAEK 1060

Query: 1195 RVAEQWKSGVPVST--------PVFDGADE-EAINSMLRMADLDESGQSILYDGLTGEPF 1245
               E  +  V  +          VFD   E     +  +   +   G+  L DG TGE F
Sbjct: 1061 NGEEYPEDMVTFTAQYKDVLNKEVFDYLSEHRDHRAEWKGVPIGRDGKVRLRDGRTGEYF 1120

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 1121 DSPVTIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1180

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            GAAY LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+Q+L L + + +
Sbjct: 1181 GAAYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGVPESFKVLLKELQSLALDVRVLD 1240

Query: 1366 SRTKNSAKMEEIPDFNKCELK 1386
                    +E   ++   + K
Sbjct: 1241 QDNNEVRLLES-SEYEVTDFK 1260


>gi|161506866|ref|YP_001576820.1| DNA-directed RNA polymerase subunit beta [Lactobacillus helveticus
           DPC 4571]
 gi|182676566|sp|A8YXJ8|RPOB_LACH4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|160347855|gb|ABX26529.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus helveticus
           DPC 4571]
          Length = 1213

 Score =  827 bits (2135), Expect = 0.0,   Method: Composition-based stats.
 Identities = 399/963 (41%), Positives = 582/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+  Y+   PK+ VD+    D TYA P+++TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYEGYKLQKPKYTVDEARDHDATYAAPMRVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEAIKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  +   V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKDTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIAEDVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPLTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF  +++  R
Sbjct: 542 IINKYGFIETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKSDVILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAEPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  489 bits (1258), Expect = e-135,   Method: Composition-based stats.
 Identities = 172/502 (34%), Positives = 240/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + +       D                
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFAGANEND---------------- 997

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+D   +  I         D+ G++++YDG 
Sbjct: 998  -----------------------------VWDTVRQAGI---------DKDGKTVIYDGR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|241895219|ref|ZP_04782515.1| DNA-directed RNA polymerase beta subunit [Weissella
           paramesenteroides ATCC 33313]
 gi|241871525|gb|EER75276.1| DNA-directed RNA polymerase beta subunit [Weissella
           paramesenteroides ATCC 33313]
          Length = 1212

 Score =  826 bits (2133), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/966 (43%), Positives = 585/966 (60%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  RVR+ + +  E++D+P+LIE+Q  SY+ FL          +EGL+  F 
Sbjct: 13  LVGTLVKYGKHRVRRSYARIKEVLDLPNLIEIQTDSYNWFL----------DEGLREMFM 62

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LEFV Y+   PK+ V++    D  Y+ PL +TLRL           +
Sbjct: 63  DILPIEDFQGKLSLEFVDYKLMEPKYTVEEARNHDANYSAPLHVTLRLT---------NQ 113

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y
Sbjct: 114 ETGEIKSQDVFFGDFPLMTPSGTFIINGAERVIVSQLVRSPGVYYNEELDK---NGRPNY 170

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
               IP +G W++ E D+K + +VRIDR RK+P+T  + ALG  S+ EIL      Y  I
Sbjct: 171 GTTFIPSRGAWLEFETDAKGLSYVRIDRTRKLPITELVRALGYGSDSEILQMLGDQYDSI 230

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D         D  V   +      +  GE    +S + L +      K   +  
Sbjct: 231 SLTLDKDVHK---DIEDSRVEEALKDIYERLRPGEPKTADSARALLTARFFDPKRYDLAP 287

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L GL + E + + +TGEI  E G +ID+K +  +        P L
Sbjct: 288 VGRYKINKKLSLKSRLMGLTLGETLADPDTGEIIAEKGTLIDKKVMSALS-------PYL 340

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      +              DA++           +   V +++      D +K  
Sbjct: 341 DREDFKRTTF----------TPSDDAVV-----------TEPMVLQTILVENPEDPEK-T 378

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L  +G  + +  +        R ++  DIIA +   ++L  G GT DDID+LGNRR+R V
Sbjct: 379 LPIIGNGQFDPAI--------RTVKPADIIAGMNYFLNLPLGVGTTDDIDHLGNRRIRRV 430

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+N +R+GL RMER ++ER+S  D D+V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 431 GELLQNTFRIGLSRMERVVRERMSIQDPDTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 490

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  +T+ RRLSALG GG+ R RAG E+RDVH THYGR+ P ET EG NIGL++SL 
Sbjct: 491 QTNPLGELTNKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMDPIETPEGPNIGLINSLA 550

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ RVN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQ NS L+EDGSF  + V
Sbjct: 551 TYGRVNKYGFIETPYRRVDWTTHKVTDRIDYLTADEEDNFVVAQGNSVLNEDGSFATDTV 610

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R + E + VP +++D++D SPKQ+V++A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 611 LARKSDENVEVPIDQVDYMDVSPKQIVAVATAAIPFLENDDSNRALMGANMQRQAVPLID 670

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP +GTG+E   A  +G AI+++  G+VE VD   I +R  +G LD        Y LM
Sbjct: 671 PHAPLIGTGIEYKAAHDAGVAIISQYPGVVEYVDGREIRVRREDGSLDK-------YALM 723

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQRP+VKVGD+V  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 724 KFRRSNAGKNYNQRPIVKVGDKVDADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 783

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++I+ER++ +DV+TSIHIEE+E  ARDTKLGPEE TR+IPN  E+ LKN+DE GII +G
Sbjct: 784 AIIINERLIRDDVYTSIHIEEYESEARDTKLGPEEFTREIPNTGEDQLKNLDERGIIRIG 843

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G V DVRIF
Sbjct: 844 AEVEDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLKVPHGGGGVVQDVRIF 903

Query: 946 NRHGID 951
            R   D
Sbjct: 904 TRENGD 909



 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 172/536 (32%), Positives = 252/536 (47%), Gaps = 73/536 (13%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +        KN ++  I+ VG +V+  ++L    +   +  +   +  
Sbjct: 711  RREDGSLDKYALMKFRRSNAGKNYNQRPIVKVGDKVDADEVLADGPS-MEQGELALGQNP 769

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLAR 969
            L A    +  +  D  +         + D    + H  +    +   +    E    +  
Sbjct: 770  LIAFMTWQGYNFEDAIIIN----ERLIRDDVYTSIHIEEYESEARDTKLGPEEFTREIPN 825

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +D+   LD     R+     G     G     K T      +S   R     F  +  
Sbjct: 826  TGEDQLKNLDERGIIRI-----GAEVEDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR 880

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V+     +          +      +I   + GD++ PGV  +V+V++A +R IQ GDK
Sbjct: 881  EVRDTSLKVPHGGGGVVQDV------RIFTRENGDELSPGVNMMVRVYIAQRRKIQVGDK 934

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG VS I+P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG
Sbjct: 935  MAGRHGNKGTVSVIVPSEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARELG 994

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + S + D   + DI                                   ++G+P    
Sbjct: 995  IHVASPVFDGARDTDIWDAIQ------------------------------EAGLP---- 1020

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                       S+L        G        TGE FD+ V+VG ++ +KL HMV DK++A
Sbjct: 1021 -------ADGKSIL------YDG-------RTGEAFDKRVSVGIMHYMKLAHMVDDKIHA 1060

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT KSDDVVGR + Y
Sbjct: 1061 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTYKSDDVVGRVKTY 1120

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            E+IV G    + G PESF VLVKE+QALGL + + ++  +     +   D +   +
Sbjct: 1121 EAIVKGEQIPKPGVPESFRVLVKELQALGLDMKVLDADEREIELRDMDEDDSVLNI 1176


>gi|328463472|gb|EGF35123.1| DNA-directed RNA polymerase subunit beta [Lactobacillus helveticus
           MTCC 5463]
          Length = 1213

 Score =  826 bits (2133), Expect = 0.0,   Method: Composition-based stats.
 Identities = 399/963 (41%), Positives = 580/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+  Y+   PK+ VD+    D TYA P+++TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYEGYKLQKPKYTVDEARDHDATYAAPMRVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  +   V+  + + ++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKDTVVTHEVMNKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIAADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF  +++  R
Sbjct: 542 IINKYGFIETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKSDVILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAEPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDANGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 175/502 (34%), Positives = 240/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD N   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDANGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + +       D                
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFAGANEND---------------- 997

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+D   +  I         D+ G++ILYDG 
Sbjct: 998  -----------------------------VWDTVRQAGI---------DKDGKTILYDGR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|182418863|ref|ZP_02950121.1| DNA-directed RNA polymerase, beta subunit [Clostridium butyricum
           5521]
 gi|237666463|ref|ZP_04526448.1| DNA-directed RNA polymerase, beta subunit [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|182377288|gb|EDT74855.1| DNA-directed RNA polymerase, beta subunit [Clostridium butyricum
           5521]
 gi|237657662|gb|EEP55217.1| DNA-directed RNA polymerase, beta subunit [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 1235

 Score =  825 bits (2132), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/955 (44%), Positives = 595/955 (62%), Gaps = 65/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  FGK  ++ ++P+LIE+Q  SY  FL           EGL   F  + PIT F+G
Sbjct: 9   KRTRMSFGKVNDVTEMPNLIEIQLDSYQWFLR----------EGLHEVFDDINPITNFTG 58

Query: 71  AAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             +LEFV Y+ D    K+ V++C  RD TYA PLK+++RL               +IKEQ
Sbjct: 59  NLVLEFVDYKLDMENIKYSVEECKDRDATYAAPLKVSVRL---------QNNETGEIKEQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT+ GTF+I G +R++VSQL RSPG+++ +   +   SGK LY+  +IP++
Sbjct: 110 EVFMGDFPLMTEQGTFLINGAERVIVSQLVRSPGVYYSYTIDK---SGKKLYSSTVIPNR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
           G W++ E DS DII+VRID+ RK+P+T    A+G+ S+ E++  F  +  +    +    
Sbjct: 167 GAWLEYETDSNDIIYVRIDKTRKLPITVLARAMGIGSDQELIDFFGEEERFRASIEKDNT 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD----- 301
                 L+   K       +  GE   ++S   L   L    K   +  +G         
Sbjct: 227 KTKEEALLEIYK------RLRPGEPPTVDSAISLIDTLFFDAKRYDLSRVGRYKFNKKLA 280

Query: 302 ---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +     A DI+N +TGE+ +E G  I     E+I +S I+ + +L  D V     I
Sbjct: 281 LALRIANQVAATDIINPQTGEVMVEEGQKISRLMAEDIQNSGIKSVDLLVEDKVIK--VI 338

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N  V    +   D      + +   ++  +   + + +        +      + ++  
Sbjct: 339 SNNFVDLSKQVSFD-----VKGLGIKELVHYPTLKEILDN-------FSDEDTIKKEIKK 386

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI ++DI A I   + L  G G +DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 387 NIHRLIP---KHIIRDDIFATISYELGLAYGIGYVDDIDHLGNRRLRSVGELLQNQFRIG 443

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D +++ PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 444 LSRMERVVKERMTIQDQEAITPQMLINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHK 503

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGF+
Sbjct: 504 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFM 563

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR V   + + T ++ Y +A EE+   IAQA + +DE G F E+ V  R   + + +
Sbjct: 564 ETPYRIVDKENARATEEIRYFTADEEDQYLIAQAKTPMDETGKFLEDKVMVRYLEDVLFI 623

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P  ++D ID S +Q+VS+A ++IPFLENDD+ R LMG NMQRQAVPLLK EAP VGTG+E
Sbjct: 624 PSNQVDLIDVSARQMVSVATAMIPFLENDDATRALMGSNMQRQAVPLLKTEAPVVGTGIE 683

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG    AK AG+V  V    I I+        S  G D+Y+L+KF+R+N  TC 
Sbjct: 684 FKAAVDSGVLPKAKNAGVVSYVSGSEIRIKRD------SDGGTDVYKLLKFKRTNAGTCA 737

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+V  G+ V +N +IADGPSTDLG++ALG+N+ + F+ W GYN+ED+MLISE +V E
Sbjct: 738 NQRPIVDKGEVVFKNQVIADGPSTDLGEIALGKNIRMGFITWEGYNYEDAMLISEELVRE 797

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTS+HIEE+E  ARDTKLGPEEITRDIPNVS++ LK++D+ GII +GAEV  GDILVG
Sbjct: 798 DVFTSMHIEEYECEARDTKLGPEEITRDIPNVSDDALKDVDDRGIIRIGAEVRSGDILVG 857

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VD+++F R   D
Sbjct: 858 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDIKVFTRENGD 912



 Score =  489 bits (1258), Expect = e-135,   Method: Composition-based stats.
 Identities = 179/544 (32%), Positives = 246/544 (45%), Gaps = 78/544 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  +    G  ++ + +           ++  I+  G  V    ++    +        
Sbjct: 709  EIRIKRDSDGGTDVYKLLKFKRTNAGTCANQRPIVDKGEVVFKNQVIADGPSTDLGEIAL 768

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +   +  I       E A+ + +  +R     S  + +     R      E        
Sbjct: 769  GKNIRMGFITWEGYNYEDAMLISEELVREDVFTSMHIEEYECEARDTKLGPEEITRDIPN 828

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              +   +D DD   I+      R  +IL G+    G         L   +  E  R    
Sbjct: 829  VSDDALKDVDDR-GIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   K+   + GDD+ PGV  +V+ ++A KR
Sbjct: 884  -------------EVRDTSLRVPHGEAGIIVDIKVFTRENGDDLNPGVNELVRCYIAQKR 930

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SRILP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 931  KISVGDKMAGRHGNKGVISRILPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 990

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            WA   LG  I + + D     +I+                                    
Sbjct: 991  WAASNLGWHISTPVFDGATQDEITECMLKAGFNANAK----------------------- 1027

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                 T ++DG                           TGEPFD  VTVG +YMLKL+H+
Sbjct: 1028 -----TILYDG--------------------------RTGEPFDNEVTVGIMYMLKLHHL 1056

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV
Sbjct: 1057 VDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDV 1116

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VGR + YE+IV G +  E G PESF VL+KE+QAL L I + N       +++E  D + 
Sbjct: 1117 VGRVKTYEAIVKGENIPEPGVPESFKVLIKELQALCLDIKVLN-DDNEEVELKEFADGDV 1175

Query: 1383 CELK 1386
             +L+
Sbjct: 1176 ADLE 1179


>gi|293380370|ref|ZP_06626441.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           214-1]
 gi|290923053|gb|EFD99984.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus crispatus
           214-1]
          Length = 1212

 Score =  825 bits (2132), Expect = 0.0,   Method: Composition-based stats.
 Identities = 402/963 (41%), Positives = 588/963 (61%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFN 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+V Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYVGYKLQKPKYTVDEARNHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G++R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGVERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGLGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  + G V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIVAKKGTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    D+V+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIADNVKHLTPADVLASINYFFALQDEIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V   D KV + + YL+A EE+N  +A AN+ L++DGSF E+L+  R
Sbjct: 542 IINKYGFIETPYRRVSWKDHKVIDKIDYLTADEEDNYIVAGANTPLNDDGSFKEKLILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVSPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAAPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG+VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGVVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD+V ++D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDQVDKSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 238/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G +V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDQVDKSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGADENDVW-------------- 999

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T V+D                          G 
Sbjct: 1000 -----------DTVRQAGVDKDG---KTVVYD--------------------------GR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|225376345|ref|ZP_03753566.1| hypothetical protein ROSEINA2194_01986 [Roseburia inulinivorans DSM
           16841]
 gi|225211721|gb|EEG94075.1| hypothetical protein ROSEINA2194_01986 [Roseburia inulinivorans DSM
           16841]
          Length = 918

 Score =  825 bits (2132), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/968 (43%), Positives = 596/968 (61%), Gaps = 72/968 (7%)

Query: 9   GLGRVR---------KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+R           + +  E++++P+LIEVQK SY  FL          +EGL+  F
Sbjct: 2   EKNRIRPVKAGKGMRMSYSRQKEVLEMPNLIEVQKDSYKWFL----------DEGLKEVF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
             + PI  +SG   LEFV +    D  K+ + +C  RD TYA PLK+ +RL         
Sbjct: 52  DDISPIADYSGHLSLEFVDFTLCEDDVKYTIPECKERDATYAAPLKVKVRLH-------- 103

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK
Sbjct: 104 -NKETDEINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGISHDKV---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYP-- 234
            LY+C +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+  ++EI+  F    
Sbjct: 160 QLYSCTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGVGSNQEIIDLFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KIV S   D           +         + +++ E +I +         L K  + K 
Sbjct: 220 KIVASFGKDVATNYEEGLLELYKKIRPGEPLSVESAESLINAMFFDPRRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +  + + G  +AED+V+  TGEI  EAG  +     ++I ++    +P +++ + 
Sbjct: 280 NKKLAL-KNRINGHVLAEDVVDVTTGEIIAEAGTEVTRSLADDIQNA---AVPYVWIQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             N  + ++++ D             + +   ++  + +   +      + D  DL    
Sbjct: 336 TRNVKVLSSMMVDLRHYVD----CDPKELGITELVYYPILAQLME---ENPDVEDLKEAI 388

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  ++  +        +HI K+DI A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 389 KKNVHDLIP-------KHITKDDIFASINYNMHLEYGIGHDDDIDHLGNRRIRAVGELLQ 441

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER++++D+D + PQ LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 442 NQYRIGLSRLERVVRERMTTLDLDGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 501

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+
Sbjct: 502 GELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARI 561

Query: 593 NAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGFIE PYRK+      + +VT++VVY++A EE+N ++AQAN +LD +G F    V  
Sbjct: 562 NEYGFIEAPYRKIDKSDPKNPRVTDEVVYMTADEEDNYHVAQANEALDAEGHFVRNSVSG 621

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E     +   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  E
Sbjct: 622 RYLDETQEYEKTMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTE 681

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTGME+  A  SG  +VAK+AG +E  ++ +I++++ +G  D       +Y+L KF
Sbjct: 682 APVVGTGMETKAAVDSGVCVVAKKAGTIESSESNQIIVKNDDGTRD-------VYKLTKF 734

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ+ C NQRP+V  GD V   ++IADGPST  G+L LG+N L+ FM W GYN+ED++
Sbjct: 735 SRSNQSNCYNQRPIVFKGDHVEVGEVIADGPSTSNGELGLGKNPLIGFMTWEGYNYEDAV 794

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAE
Sbjct: 795 LLSERLVQDDVYTSIHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAE 854

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+     S   +  R  ++
Sbjct: 855 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLK----SSSRRIWYRCGSQ 910

Query: 948 HGIDKNER 955
               +  R
Sbjct: 911 SIYKRKRR 918


>gi|160935065|ref|ZP_02082451.1| hypothetical protein CLOLEP_03941 [Clostridium leptum DSM 753]
 gi|156866518|gb|EDO59890.1| hypothetical protein CLOLEP_03941 [Clostridium leptum DSM 753]
          Length = 1243

 Score =  825 bits (2132), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/951 (44%), Positives = 592/951 (62%), Gaps = 59/951 (6%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            VR  F +  E++++P+LIEVQK SY  FL          +EGL+  FK V  IT ++G 
Sbjct: 12  TVRMSFSRIDEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFKDVSGITDYTGN 61

Query: 72  AMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            +L+FV Y+ D   P + V++C  RD TYA  L++T RL+          K   +IKE  
Sbjct: 62  LVLDFVDYKLDVDKPNYTVEECKERDTTYAAALRVTARLL---------NKESGEIKESE 112

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R++VSQL RSPG+++  +  +    GK L++  +IP++G
Sbjct: 113 VFMGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYKMEYDKT---GKELFSSTVIPNRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPK--IVYSQRGDFWC 246
            W++ E D+ D+ +VRID+ RK+P+T F+ ALG+ ++ E+L  F     I  +   D   
Sbjct: 170 AWLEYENDANDVFYVRIDKNRKIPITVFIRALGLGTDGELLDYFGNDQRIKATIEKDPCK 229

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +      S    I++ +  I +         L +  + K  K LGI+ + L 
Sbjct: 230 TTEEALLEVYRKLRPSEPPTIESAQSHINALFFDARRYDLSRVGRYKYNKKLGIS-NRLQ 288

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A  I N  TGE+  + G V+  +   ++ ++ +    ++          I N +V 
Sbjct: 289 GQKLAAPIANPLTGEVMFDEGKVLSREEAVQVENAGVTVAYVMAEGQEEPVKIISNGMVD 348

Query: 365 DKNKDRKDALLD--IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                  DA  +  I   +R   ++    A              +L    R + +  +  
Sbjct: 349 ISCYVDFDAKKECGINEKVRFSVLAEILEAAR---------TPEELKDALREREDELIP- 398

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 +HI  +DI A I  +  L  G G+ DDID+LGNRR+RSVGE+L+NQ+R+G  R+
Sbjct: 399 ------KHIIVDDIFASINYMNCLACGIGSTDDIDHLGNRRIRSVGELLQNQFRIGFSRL 452

Query: 483 ERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           ER I+ER++    D++ + P  LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH RR
Sbjct: 453 ERVIRERMTLQAQDLEVLTPHALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTHKRR 512

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LS+LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L +FAR+N YGFIE 
Sbjct: 513 LSSLGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLATFARINEYGFIEA 572

Query: 601 PYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           P+RKV   +  VTN+VVY++A  E++  +AQAN  LDE+G F    V  R   E + V R
Sbjct: 573 PFRKVDKVNHVVTNEVVYMTADMEDDYIVAQANEPLDENGYFLHAKVNGRFRDEFVEVER 632

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           ++ D++D SP+ VVS+A ++IPFLENDD+NR LMG NMQRQAVPLLK EAP VGTGME  
Sbjct: 633 DRADYMDVSPRMVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLKTEAPIVGTGMEYK 692

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               SG  I+AK+ G+VE V A  I +++ +G  D        Y ++KF RSNQ TCVNQ
Sbjct: 693 AGVDSGVCILAKKDGVVEAVSADEIRMKNDDGTTD-------TYHVIKFMRSNQGTCVNQ 745

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            P+V  G  V++N ++ADGP+T  G+++LG+N L+ FM W GYN+ED++LI+E++V +DV
Sbjct: 746 VPVVSKGQRVKKNAVLADGPATCNGEISLGKNALIGFMTWEGYNYEDAVLINEKIVRDDV 805

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEIT DIPNV+E+ LK++DE GII VGAEV  GDILVGK+
Sbjct: 806 YTSIHIEEYETEARDTKLGPEEITCDIPNVNEDLLKDLDENGIIHVGAEVRAGDILVGKV 865

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G VVDV++F R  
Sbjct: 866 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGIVVDVKVFTREN 916



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 192/588 (32%), Positives = 262/588 (44%), Gaps = 83/588 (14%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +           Y       +      + V  ++  +E   +      
Sbjct: 667  GSNMQRQAVPLLKTEAPIVGTGMEYKAGVDSGVCILAKKDGVVEAVSADE---IRMKNDD 723

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +    I  +       +++  ++  G  V    +L           ++  +  L   
Sbjct: 724  GTTDTYHVIKFMRSNQGTCVNQVPVVSKGQRVKKNAVLADGP-ATCNGEISLGKNALIGF 782

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARD 970
               +  +  D  L     V   V        +  +  +  +  E          E L +D
Sbjct: 783  MTWEGYNYEDAVLINEKIVRDDVYTSIHIEEYETEARDTKLGPEEITCDIPNVNEDLLKD 842

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      R  +IL G+    G         L   +  E  R            
Sbjct: 843  L-DENGIIHVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------ 889

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIE-KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 E                   K+  +    D++PPGV +VV+ +VA KR I  GDK
Sbjct: 890  -----EVRDTSLRVPHGEYGIVVDVKVFTRENSHDELPPGVNKVVRCYVAQKRKISVGDK 944

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRILP EDMP+L DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+A   LG
Sbjct: 945  MAGRHGNKGVVSRILPQEDMPYLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYAAKALG 1004

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             KI + + D     DI                                            
Sbjct: 1005 WKIMTPVFDGANEEDI-------------------------------------------- 1020

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F+   E         A L E G++ L DG TG+ FD PVTVGY+Y LKL+H+V DK++A
Sbjct: 1021 -FECFRE---------AGLSEDGKTWLRDGRTGQLFDNPVTVGYMYYLKLHHLVDDKIHA 1070

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + Y
Sbjct: 1071 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTY 1130

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            ESIV G +  E G PESF VL+KE+Q+LGL + + +   +     +  
Sbjct: 1131 ESIVKGQNIPEPGIPESFKVLIKELQSLGLDVKVLDKDEQEIDLKQNF 1178


>gi|302671724|ref|YP_003831684.1| DNA directed RNA polymerase beta subunit RpoB [Butyrivibrio
           proteoclasticus B316]
 gi|302396197|gb|ADL35102.1| DNA directed RNA polymerase beta subunit RpoB [Butyrivibrio
           proteoclasticus B316]
          Length = 1290

 Score =  825 bits (2131), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/956 (45%), Positives = 592/956 (61%), Gaps = 59/956 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  +SG
Sbjct: 15  KNIRMSFQRQKEVLEMPNLIEVQKNSYQWFL----------DEGLKEVFDDISPIEDYSG 64

Query: 71  AAMLEFVSYEF-----DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
              LEFV ++      D  K  ++ C  RD T+A PLK+ +RL   + D         +I
Sbjct: 65  KLSLEFVDFKLCEDEIDKNKNTIEKCKERDATFAAPLKVKVRLHNKEKD---------EI 115

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
            E  I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++D    +    GK L AC +I
Sbjct: 116 TEHEIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYDITYDKI---GKELMACTVI 172

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYP--KIVYSQRG 242
           P++G W++ E D  D+ + R+DR RKVPVT  + ALG+  +EEIL  F    KI  S   
Sbjct: 173 PNRGAWLEYETDPNDVFYARVDRTRKVPVTVLIRALGIGSNEEILELFGDEPKIQGSFSK 232

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D      S    +         + +++ E +I +         L K  + K  K L    
Sbjct: 233 DSSTDYQSGLLELYRKIRPGEPLSVESAESLINAMFFDPRRYDLAKVGRYKFNKKL-HFK 291

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + + G  +AED+V+  TGE+   AG  +D     EI ++    IP + +     N  + +
Sbjct: 292 NRINGHVLAEDVVDETTGEMIASAGTKVDRALATEIQNA---AIPYVLLQEEERNVKVLS 348

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            ++ D     +         +   +   + V + + +     +D   L+   + +++  +
Sbjct: 349 NMMVDITHFIE----CDPAELGINENVYYPVLKEILDEYTAKNDPEGLAETIKKRVHELI 404

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                   +HI KEDIIA I   + L  G G  DDID+LGNRR+R VGE+L+NQYR+GL 
Sbjct: 405 P-------KHITKEDIIASINYNIHLEYGIGNDDDIDHLGNRRIRCVGELLQNQYRIGLS 457

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER ++ER+++ D + V PQ LIN KPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 458 RLERVVRERMTTHDTEEVSPQTLINIKPVQAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 517

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+ARVN YGF+E 
Sbjct: 518 LSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYARVNDYGFVEA 577

Query: 601 PYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           PYR V      + +VT++V YL+A EE+N ++AQAN+ LDE+G F ++ V  R   E   
Sbjct: 578 PYRVVDRTDPENPRVTDEVEYLTADEEDNYHVAQANTPLDEEGHFVKKTVSGRFREETSE 637

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            P+  ++++D SP+ V S+A +LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGM
Sbjct: 638 YPKTAVEYMDVSPRMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLMTEAPAVGTGM 697

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG  +VA++AG ++ VD+  I I   +G+ +          L+KFQRSNQ+ C
Sbjct: 698 EKKAAVDSGVCVVARKAGTIDFVDSKLIQITYDDGEKEEF-------HLIKFQRSNQSNC 750

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQRP+V  GD V    +IADGPST  G+L LG+N L+ FM W GYN+ED++L+SER+V 
Sbjct: 751 YNQRPIVFKGDHVEAGQVIADGPSTSQGELGLGKNPLIGFMTWEGYNYEDAVLLSERLVR 810

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TS+HIEE+E  AR+TKLGPEEITRD+P V ++ LK++D+ GII +GAEV  GDILV
Sbjct: 811 DDVYTSVHIEEYEAEARETKLGPEEITRDVPGVGDDALKDLDDRGIIRIGAEVRAGDILV 870

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 871 GKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRDNGD 926



 Score =  556 bits (1433), Expect = e-155,   Method: Composition-based stats.
 Identities = 254/1176 (21%), Positives = 418/1176 (35%), Gaps = 70/1176 (5%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +              +    ++    I+  E+VI S    + G+   +    + 
Sbjct: 104  KVRLHNKEKDEITEHEIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYDITYDKIG 163

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
               +    +       +         Y              I    I     + ++   +
Sbjct: 164  KELMACTVIPNRGAWLEYETDPNDVFYARVDRTRKVPVTVLIRALGIGSNEEI-LELFGD 222

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               I+ +   D + D +  LL++YR +RPG+  +   AES+ N +FFD  +YDL+ VGR 
Sbjct: 223  EPKIQGSFSKDSSTDYQSGLLELYRKIRPGEPLSVESAESLINAMFFDPRRYDLAKVGRY 282

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L+     +   + ++ +              G +         R  +        
Sbjct: 283  KFNKKLHFKNRINGHVLAEDVVDETT----------GEMIASAGTKVDRALATEIQNAAI 332

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
              + L   ER++K   + +   +   +       +   V        L +     +    
Sbjct: 333  PYVLLQEEERNVKVLSNMMVDITHFIECDPAELGINENVYYPVLKEILDEYTAKNDPEGL 392

Query: 535  ITH-TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
                 +R+  L    + +      +       YG     +     N   +  +    +  
Sbjct: 393  AETIKKRVHELIPKHITKEDIIASINYNIHLEYGIGNDDDIDHLGN-RRIRCVGELLQNQ 451

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEE 643
                +    R V +   T+D   +S     N    QA               +  +   E
Sbjct: 452  YRIGLSRLERVVRERMTTHDTEEVSPQTLINIKPVQAAVKEFFGSSQLSQFMDQNNPLSE 511

Query: 644  LVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            +   R             R   +  D        +     P   N      L        
Sbjct: 512  ITHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYARVND 571

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
               +         T  E+         + A          A   +           +   
Sbjct: 572  YGFVEAPYRVVDRTDPENPRVTDEVEYLTADEEDNYHVAQANTPLDEEGHFVKKTVSGRF 631

Query: 760  DIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                    + + +   V+ R +  V         +  A+              +L+   P
Sbjct: 632  REETSEYPKTAVEYMDVSPRMVFSVATALIPFLENDDANRALMGSNMQRQAVPLLMTEAP 691

Query: 818  WHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G   E    +     V      +I   + +++      G +E    I           
Sbjct: 692  AVGTGMEKKAAVDSGVCVVARKAGTIDFVDSKLIQITYDDGEKEEFHLIKFQRSNQSNCY 751

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+  G  V  G ++    +   +  +   +  L      +  +  D  L     V 
Sbjct: 752  NQRPIVFKGDHVEAGQVIADGPST-SQGELGLGKNPLIGFMTWEGYNYEDAVLLSERLVR 810

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEIL 990
              V        +  +  E  +  E    +         +D DD   I+      R  +IL
Sbjct: 811  DDVYTSVHIEEYEAEARETKLGPEEITRDVPGVGDDALKDLDDR-GIIRIGAEVRAGDIL 869

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+    G         L   +  E  R                 E      +       
Sbjct: 870  VGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEYG 912

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 K+     GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMP
Sbjct: 913  IVVDAKVFTRDNGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPIEDMP 972

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + I D     DI     
Sbjct: 973  YLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPIFDGANEIDIQDTLE 1032

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                 + +     +    D      +   +++                   + +   +  
Sbjct: 1033 LANDYVNSTWDEFQAKYKDLVHPEIMDYLYEN--------------RDHRELWKGVPIRS 1078

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+  L DG TG+ FD P T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  G
Sbjct: 1079 DGKVQLRDGRTGQKFDSPTTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1138

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G++  E G PESF VL
Sbjct: 1139 GQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGVPESFKVL 1198

Query: 1351 VKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            +KE+Q+LGL I +          ME + D+   + +
Sbjct: 1199 LKELQSLGLDIKVLREDNTEVEIMESV-DYTDSDYR 1233


>gi|291547338|emb|CBL20446.1| DNA-directed RNA polymerase subunit beta [Ruminococcus sp. SR1/5]
          Length = 1269

 Score =  825 bits (2131), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/949 (43%), Positives = 593/949 (62%), Gaps = 57/949 (6%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI  + G   L
Sbjct: 1   MSYQRQKEVLEMPNLIEVQKDSYQWFL----------DEGLKEVFDDISPIADYGGKLSL 50

Query: 75  EFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           EF+ + +D    K+ ++ C  RD+TYA PLK+ +RLI          K  ++I E  I+M
Sbjct: 51  EFIDFTYDEKDAKYSIEQCKERDVTYAAPLKVRVRLI---------NKETEEINEHEIFM 101

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK L++  +IP++G W+
Sbjct: 102 GDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKRLFSSTVIPNRGAWL 158

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWCFPL 249
           + E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D      
Sbjct: 159 EYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASFTKDTSTNYQ 218

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
                +         + +++ E +I +         L K  + K  K L      + G  
Sbjct: 219 EGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDLAKVGRYKFNKKLHFNK-RIVGHK 277

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           +++D+V+  TGEI  EA  ++ ++  + + +S    +P +++        + ++L+ D  
Sbjct: 278 LSQDVVDTTTGEILAEAETLVTKELADTLQNS---AVPYVWIQGEEREIKVLSSLMVDIR 334

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +  L+  + +   ++  + V E +        D+ D   + R   ++         
Sbjct: 335 HYLPE--LEDPKSLGVTELVYYPVLEKILEENDTFEDRCD--AIKRDIHDLI-------- 382

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R+ER ++
Sbjct: 383 PKHITKEDILASINYNMHLEYGLGNDDDIDHLGNRRIRAVGELLQNQYRIGLSRLERVVR 442

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+++ D +S+ PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSALG G
Sbjct: 443 ERMTTQDTESISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSALGPG 502

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC- 606
           G++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGF+E PYRK+  
Sbjct: 503 GLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINQYGFVEAPYRKIDK 562

Query: 607 ----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
               + +VT++VVY++A EE+N ++AQAN  LDE+G F  + V  R   E     +   D
Sbjct: 563 TDPSNPRVTDEVVYMTADEEDNYHVAQANEPLDEEGHFIHKNVSGRYREETQEYEQHMFD 622

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SP+ V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME+  A  
Sbjct: 623 YMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMETKTAVD 682

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA++AG V +  +  I I++ +G  D        Y L KF RSNQ+ C NQRP+V
Sbjct: 683 SGVCVVARKAGTVLRSTSTDISIKNDDGTKDD-------YHLTKFMRSNQSNCYNQRPIV 735

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SE++V  DV+TS+
Sbjct: 736 FQGEHVEAGQVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAVLLSEKLVQNDVYTSV 795

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E  +RDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDILVGK+TPKG
Sbjct: 796 HIEEYEAESRDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDILVGKVTPKG 855

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 856 ETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 904



 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 248/1062 (23%), Positives = 403/1062 (37%), Gaps = 69/1062 (6%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D       I  +   D + + ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 196  IDLFGEEPKILASFTKDTSTNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDL 255

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L+ +       + ++ +      ++       T +  D L N  V  V 
Sbjct: 256  AKVGRYKFNKKLHFNKRIVGHKLSQDVVDTTTGEILAEAETLVTKELADTLQNSAVPYVW 315

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               + +    L  +   I+  +  ++    +    +   PV+  + E   +      E+ 
Sbjct: 316  IQGEEREIKVLSSLMVDIRHYLPELEDPKSLGVTELVYYPVLEKILEENDT-----FEDR 370

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +++      R +  L    + +      +       YG     +     N   + ++  
Sbjct: 371  CDAI-----KRDIHDLIPKHITKEDILASINYNMHLEYGLGNDDDIDHLGN-RRIRAVGE 424

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDG 638
              +      +    R V +   T D   +S     N     A               +  
Sbjct: 425  LLQNQYRIGLSRLERVVRERMTTQDTESISPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 484

Query: 639  SFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +   EL   R             R   +  D        +     P   N      L   
Sbjct: 485  NPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASY 544

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                Q   +         T   +         + A          A    +      +  
Sbjct: 545  ARINQYGFVEAPYRKIDKTDPSNPRVTDEVVYMTADEEDNYHVAQANE-PLDEEGHFIHK 603

Query: 755  STSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            + SG       ++++   +   V+ R +  V         +  A+              +
Sbjct: 604  NVSGRYREETQEYEQHMFDYMDVSPRMVFSVATALIPFLQNDDANRALMGSNMQRQAVPL 663

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSE 870
            L    P  G   E    +   +          +             G ++       +  
Sbjct: 664  LTTEAPVVGTGMETKTAVDSGVCVVARKAGTVLRSTSTDISIKNDDGTKDDYHLTKFMRS 723

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                  ++  I+  G  V  G ++    +      +   +  L      +  +  D  L 
Sbjct: 724  NQSNCYNQRPIVFQGEHVEAGQVIADGPSTSN-GELALGKNPLIGFMTWEGYNYEDAVLL 782

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYS 984
                V   V        +  +  +  +  E    +         +D  DE+ I+      
Sbjct: 783  SEKLVQNDVYTSVHIEEYEAESRDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEV 841

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R  +IL G+    G         L   +  E  R                 E      + 
Sbjct: 842  RAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKV 884

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                       K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+L
Sbjct: 885  PHGEYGIIVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVL 944

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     D
Sbjct: 945  PVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANEVD 1004

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            I          + T    E    Y D     V +                  +A  ++ +
Sbjct: 1005 IQDTLELANDYVNTEDFEEFREKYKDILAPDVMQYLDE-------------NKAHRALWK 1051

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLG
Sbjct: 1052 GVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLG 1111

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G++  E G P
Sbjct: 1112 GKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEAIIKGDNIPEPGIP 1171

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            ESF VL+KE+Q+LGL + + +        ME   D+   +L+
Sbjct: 1172 ESFKVLLKELQSLGLDVRVLSEDGSEVHIMET-SDYGDTDLR 1212


>gi|331268405|ref|YP_004394897.1| DNA-directed RNA polymerase subunit beta [Clostridium botulinum
           BKT015925]
 gi|329124955|gb|AEB74900.1| DNA-directed RNA polymerase, beta subunit [Clostridium botulinum
           BKT015925]
          Length = 1231

 Score =  825 bits (2131), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/946 (44%), Positives = 589/946 (62%), Gaps = 55/946 (5%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F K  E+  +P+LIEVQ  SYD F            EGL   F  + PI  ++G  +L
Sbjct: 1   MSFSKVKEMCPMPNLIEVQLNSYDWF----------WKEGLNEVFDDINPIQDYTGNLIL 50

Query: 75  EFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           EF+ Y  D    K+ V++C  RD TYA PLK+ +RL+          K   ++KEQ ++M
Sbjct: 51  EFIDYNLDKDAIKYSVEECKERDATYAAPLKVKVRLL---------NKETGEVKEQEVFM 101

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT+ GTFVI G +R++VSQL RSPG ++ +D  +    GK L++  +IP++G W+
Sbjct: 102 GDFPLMTQQGTFVINGAERVIVSQLVRSPGAYYGYDVDKT---GKKLFSATVIPNRGAWL 158

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFWCFPL 249
           + E DS DII+VRID+ RK+P++  + ALG+ S+ EI+  F  +         D      
Sbjct: 159 EYETDSNDIIYVRIDKTRKLPISILIRALGLGSDAEIIEWFGEEERLKSTIEKDNTKTRE 218

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
            A   +           +D+   +I S         L +  + K  K L I    L    
Sbjct: 219 EALLEIYKRLRPGEPPTVDSAVSLINSLFFDAKRYDLSRVGRYKFNKKLAIYI-RLLNQV 277

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            AED+VN  TGEI ++ G+ I+     EI +  I  + I   D V     I N  V   N
Sbjct: 278 AAEDVVNPFTGEIIVQKGETIERDKALEIQNCAINAVNIQVEDKVIK--VIGNNFVDIHN 335

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               D        ++  +   +   + + +        Y      + ++   ++   P  
Sbjct: 336 FVDFD-----ISDLKIKEHVHYPTLKKILDN-------YTDEESIKEEIRKNIHELIP-- 381

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            +HI  +DI A +   + L    GTIDDID+LGNRR+RSVGE+L+NQ+R+GL RMER +K
Sbjct: 382 -KHIVVDDIYATVSYELGLPYSIGTIDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVK 440

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER++  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH RRLSALG G
Sbjct: 441 ERMTIQDQEVITPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPG 500

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV-- 605
           G++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +A+VN YGFIETPYR V  
Sbjct: 501 GLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLACYAKVNEYGFIETPYRLVDK 560

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            D +V  ++VYL+A EE++  +AQA   LD++G F E+ +  R   + I+V + ++D +D
Sbjct: 561 KDARVKEELVYLTADEEDHYLVAQAKEPLDKEGHFLEDKITVRTLEDVIVVSKHQVDLMD 620

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SP Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK  AP VGTG+E   A  SG 
Sbjct: 621 VSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIVGTGIEFKAAVDSGV 680

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
              A+  G+VE V +  + IR        +  G+D  +L+K++RSNQ TC+NQRP+V  G
Sbjct: 681 LPKAEHDGVVEYVSSTEVRIRRD------ADGGLDRCKLLKYKRSNQGTCINQRPIVSKG 734

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           ++++  D++ADGPSTD G++ALG+N+ + F+ W GYN+ED+ML+SE++V +D+FTSIHIE
Sbjct: 735 EKLKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDDIFTSIHIE 794

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           E+E  ARDTKLGPEEITRDIPNV E+ LKNIDE GI+ +GAEV  GDILVGK+TPKGE+ 
Sbjct: 795 EYESEARDTKLGPEEITRDIPNVGEDALKNIDERGIVRIGAEVRSGDILVGKVTPKGETE 854

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 855 LTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGD 900



 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 191/622 (30%), Positives = 266/622 (42%), Gaps = 79/622 (12%)

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            D+  + K Q    +   +Q   V         +  A               +L    P  
Sbjct: 607  DVIVVSKHQVDLMDVSPSQIVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPAAPIV 666

Query: 820  GYNFEDSMLISERMVSEDVFTSI--HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            G   E    +   ++ +     +  ++   EV  R    G  +  + +          I+
Sbjct: 667  GTGIEFKAAVDSGVLPKAEHDGVVEYVSSTEVRIRRDADGGLDRCKLLKYKRSNQGTCIN 726

Query: 878  ECGIICVGAEVNPGDILVGKITPK-----GESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            +  I+  G ++  GD+L    +           +            E A+ V +  +R  
Sbjct: 727  QRPIVSKGEKLKAGDVLADGPSTDFGEIALGQNIRMGFITWEGYNYEDAMLVSEQLVRDD 786

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
               S  + +     R      E          E   ++  DE+ I+      R  +IL G
Sbjct: 787  IFTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALKNI-DERGIVRIGAEVRSGDILVG 845

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E                
Sbjct: 846  KVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGEAGII 888

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV  +V+ ++A KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 889  VDVKVFTRENGDELPPGVNELVRCYIAQKRKISVGDKMAGRHGNKGVISRILPEEDMPFL 948

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   +G  I + + +     +I  L    
Sbjct: 949  PDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAAGEMGWHIATPVFNGAFEDEIVDLLKEA 1008

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                   DG                   
Sbjct: 1009 GYNA-----------------------------------DGKTV---------------- 1017

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               LYDG TGEPFD  VTVGY+Y+LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 1018 ---LYDGRTGEPFDNRVTVGYMYILKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQ 1074

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1075 RFGEMEVWALEAYGAAHTLQEVLTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIK 1134

Query: 1353 EMQALGLSIDLENSRTKNSAKM 1374
            E+QAL L + + +   +     
Sbjct: 1135 ELQALCLDVKVLSGDNEEITIK 1156


>gi|154484472|ref|ZP_02026920.1| hypothetical protein EUBVEN_02186 [Eubacterium ventriosum ATCC
           27560]
 gi|149734320|gb|EDM50237.1| hypothetical protein EUBVEN_02186 [Eubacterium ventriosum ATCC
           27560]
          Length = 1276

 Score =  825 bits (2131), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/959 (44%), Positives = 587/959 (61%), Gaps = 61/959 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V +G G +R  + +  E++ +P+LIEVQ+ SY+ FL            GL+   + + PI
Sbjct: 9   VKSGKG-IRMSYSRQKEVLGMPNLIEVQRDSYEWFLS----------TGLKEVLEDISPI 57

Query: 66  TAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             ++    LEFV ++   D  K+ +++C  RD TY+ PLK+ +RL           K   
Sbjct: 58  EDYAQNLSLEFVDFKLCEDEKKYTIEECKERDATYSAPLKVKVRLH---------NKETG 108

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +  E  I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY  +
Sbjct: 109 EFTEHDIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYVIGHDKV---GKELYTSQ 165

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--Q 240
           +IP++G W++ E DS DI +VR+DR RK+PVT  + ALG+ +  EI   F  +   +   
Sbjct: 166 VIPNRGAWLEYETDSNDIFYVRVDRTRKLPVTVLIRALGIGTNAEITELFGEEEKLTATF 225

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +D+ E ++           L +  + K  K L  
Sbjct: 226 EKDPSTSYEEGLLELYKKIRPGEPLSVDSAESIVAGMFFDARRYDLARVGRYKYNKKLA- 284

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + + GL +AED+V+  TGE+  EAG V+ E+   +I ++ +  + I           I
Sbjct: 285 YKNRIKGLPLAEDVVDMTTGEVLAEAGTVVTEELAIKIQNAAVPSVMI--------QTDI 336

Query: 359 RNTLVTDKNKDRKDALLDI-YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +N  V        +A +D   + +   +   + V   +      + +  D   + R    
Sbjct: 337 KNEKVLSNLAVDINAYVDFDCKELGINEEVYYPVLAEILAENETEEELKD--AIKRNVHE 394

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +          +HI KEDI A I   +++  G G+ DDID+LGNRR+R+VGE+L+NQYR+
Sbjct: 395 LI--------PKHITKEDIFATINYCMNIEYGIGSEDDIDHLGNRRIRAVGELLQNQYRI 446

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+++ D++ V PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH
Sbjct: 447 GLSRMERVVRERMTTQDLEGVSPQTLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTH 506

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S  SFAR+N YGF
Sbjct: 507 KRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSFASFARLNEYGF 566

Query: 598 IETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           +E PYR V      + +VT++VVYL+A EE+N  +AQAN  LD +G F    V  R   E
Sbjct: 567 VEAPYRVVDKSDPENPRVTDEVVYLTADEEDNYTVAQANEPLDAEGHFVHNNVSGRYREE 626

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                +++ID +D SP+ V S+A S+IPFL+NDDSNR LMG NMQRQAVPL+  EAP VG
Sbjct: 627 TSQFDKKRIDLMDVSPRMVFSVATSMIPFLQNDDSNRALMGSNMQRQAVPLITTEAPVVG 686

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME+  A  SG  +VAKRAG++E+  +  I IR  +          + Y+L+KFQRSNQ
Sbjct: 687 TGMEAKAAVDSGVCVVAKRAGVIERSTSKEITIRYDDN------GEKETYKLLKFQRSNQ 740

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           + C NQR +V  GD V   ++IADG ST  G++ALG+N L+ FM W GYN+ED++L+SER
Sbjct: 741 SNCYNQRSIVFKGDHVEAGEVIADGASTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSER 800

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TSIHIEE+E  ARDTKLGPEEIT D+P V +E  K++DE GII +GAEV  GD
Sbjct: 801 LVQDDVYTSIHIEEYETEARDTKLGPEEITNDVPGVGDEARKDLDERGIIRIGAEVRAGD 860

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 861 ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEQGIIVDAKVFKRENGD 919



 Score =  553 bits (1424), Expect = e-154,   Method: Composition-based stats.
 Identities = 236/1052 (22%), Positives = 391/1052 (37%), Gaps = 53/1052 (5%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
             +       +  T   D +   ++ LL++Y+ +RPG+  +   AES+   +FFD+ +YDL
Sbjct: 212  TELFGEEEKLTATFEKDPSTSYEEGLLELYKKIRPGEPLSVDSAESIVAGMFFDARRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L        R         ++ +       +      + L  +   +  
Sbjct: 272  ARVGRYKYNKKLAY----KNRIKGLPLAEDVVDMTTGEVLAEAGTVVTEELAIKIQNAAV 327

Query: 469  EMLKNQYRLGLLRMERSIKERIS---SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
              +  Q  +   ++  ++   I+     D   +   + +    +   + E     +L   
Sbjct: 328  PSVMIQTDIKNEKVLSNLAVDINAYVDFDCKELGINEEVYYPVLAEILAENETEEELKDA 387

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +         H  +                   +    H G        E         
Sbjct: 388  IKRNVHELIPKHITKEDIFATINYCMNIEYGIGSEDDIDHLGNRRIRAVGELLQNQYRIG 447

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED---GSFTE 642
            L+   RV            V   +   ++  ++A  +E    +Q +  +D++   G  T 
Sbjct: 448  LSRMERVVRERMTTQDLEGVS-PQTLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTH 506

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +          +   R   +  D        +     P   N              +   
Sbjct: 507  KRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSFASFARLNEYGF 566

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            +         +  E+         + A          A   +        +  +      
Sbjct: 567  VEAPYRVVDKSDPENPRVTDEVVYLTADEEDNYTVAQANEPLDAEGHFVHNNVSGRYREE 626

Query: 763  RLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                 ++      V+ R +  V         +  ++              ++    P  G
Sbjct: 627  TSQFDKKRIDLMDVSPRMVFSVATSMIPFLQNDDSNRALMGSNMQRQAVPLITTEAPVVG 686

Query: 821  YNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
               E    +     +V++           E+  R    G +E  + +           ++
Sbjct: 687  TGMEAKAAVDSGVCVVAKRAGVIERSTSKEITIRYDDNGEKETYKLLKFQRSNQSNCYNQ 746

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPSGVS 936
              I+  G  V  G+++    +         +  L+  +   G    D    S R+     
Sbjct: 747  RSIVFKGDHVEAGEVIADGASTSNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDV 806

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             T + +  +     D       +  +     +   +D  DE+ I+      R  +IL G+
Sbjct: 807  YTSIHIEEYETEARDTKLGPEEITNDVPGVGDEARKDL-DERGIIRIGAEVRAGDILVGK 865

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G         L   +  E  R                 E      +          
Sbjct: 866  VTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEQGIIV 908

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+ K + GD++ PGV   V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL 
Sbjct: 909  DAKVFKRENGDELAPGVNESVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLP 968

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI        
Sbjct: 969  NGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKVLGFNIATPVFDGADEYDIMDTLEMAN 1028

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                     +  + Y D     V E     +                   +   +   G+
Sbjct: 1029 D-YANTEWEDFQAKYQDKLNPEVMEYLGEHL-------------DHREEWKGVPIARDGK 1074

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L DG TG+ FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 1075 VRLRDGRTGDYFDNPVTIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQR 1134

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  + G PESF VL+KE
Sbjct: 1135 FGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPQPGIPESFKVLIKE 1194

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            +Q+L L + + +         E I D+ +   
Sbjct: 1195 LQSLALDVKVLDENDNEVELKESI-DYGETNF 1225


>gi|323465815|gb|ADX69502.1| DNA-directed RNA polymerase subunit beta [Lactobacillus helveticus
           H10]
          Length = 1213

 Score =  825 bits (2130), Expect = 0.0,   Method: Composition-based stats.
 Identities = 399/963 (41%), Positives = 580/963 (60%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F 
Sbjct: 2   LNGHVVNYGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LE+  Y+   PK+ VD+    D TYA P+ +TL+L           +
Sbjct: 52  DIMPISDFSGKLSLEYEGYKLQKPKYTVDEARDHDATYAAPMHVTLKLT---------NQ 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F       
Sbjct: 160 GTTVIPNRGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQ 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 FTLDKD-VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGEI  +   V+  + ++++              
Sbjct: 279 YKINKKLSLKNRLYGQTLAETLADPDTGEIIAKKDTVVTHEVMDKLAPYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D  +  Y+  + G +      + +  +   D ++     
Sbjct: 329 ------------------DRDDFKMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+
Sbjct: 367 -----VKLMSNGHIAADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQFRIGLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A
Sbjct: 482 PLGELTHKRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYA 541

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF  +++  R
Sbjct: 542 IINKYGFIETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKSDVILAR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+    
Sbjct: 602 QKEDNVEVTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAEPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++
Sbjct: 662 SLVGTGMEYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +   NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 715 RSNNSKSYNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV
Sbjct: 775 LSERLVKDDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R 
Sbjct: 835 HDGDILVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDVKVYTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 241/502 (48%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 728  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 784

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 785  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 839

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 840  LVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDV------KVYTR 893

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 894  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 953

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D                
Sbjct: 954  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANEND---------------- 997

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+D   +  I         D+ G++++YDG 
Sbjct: 998  -----------------------------VWDTVRQAGI---------DKDGKTVIYDGR 1019

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1020 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1079

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1080 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1139

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1140 IRVLDMNHNEIELRDMDEDSSE 1161


>gi|116628956|ref|YP_814128.1| DNA-directed RNA polymerase subunit beta [Lactobacillus gasseri
           ATCC 33323]
 gi|122274046|sp|Q046D2|RPOB_LACGA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116094538|gb|ABJ59690.1| DNA-directed RNA polymerase subunit beta [Lactobacillus gasseri
           ATCC 33323]
          Length = 1212

 Score =  825 bits (2130), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/986 (42%), Positives = 592/986 (60%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ G+ PLMT  GTFVI G +RI+VSQL RSPG+++  D  +   +G+ ++  
Sbjct: 107 GEIKTQDVFFGEFPLMTDSGTFVINGAERIIVSQLVRSPGVYYHSDFDK---NGRQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ E+   F         
Sbjct: 164 TVIPNRGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEVADMFGESDSLRFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        +   +  +G   
Sbjct: 224 LEKDI-HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + GDV+  + L+++                
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHEILDKL---------------- 326

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + Y+          DR D  +  Y   + G +      + +  +   D ++       
Sbjct: 327 --SPYL----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER------- 367

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              + +  N    DDV+H+   D++A I    +L++  GT DDID+LGNRR+R VGE+L+
Sbjct: 368 --VIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R  
Sbjct: 546 NKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNEDGSFKDKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP 
Sbjct: 606 EDNLEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPI 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RS
Sbjct: 666 VGTGMEYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R   
Sbjct: 839 GDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELPPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 258/1055 (24%), Positives = 386/1055 (36%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 239  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 298

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 299  AETLADPDTGEIIAKKGDVVTHEILDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 357

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D    +     +   +        L     
Sbjct: 358  KVYSKVDPERVIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRI 417

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 418  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 477

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 478  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 537

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +  P  E D S +
Sbjct: 538  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNE-DGSFK 596

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +                   I       V  V +  I     +
Sbjct: 597  DKIVLARHKEDNLEVTPDK------------IDYMDVI----PKQVVSVTSACIPFLEND 640

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 641  DSNRALMGA-------NHQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 679

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T    +++ V+ +  +    +     P V 
Sbjct: 680  DALVAKAPG----VVEYVDANEIRIRRDDDTL---DKY-VLEKFRRSNATKNYNQTPAVK 731

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 732  QGERVVADE--VIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 787

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          E   +D D+E  I+      +  
Sbjct: 788  -------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE-GIVRIGAEVQDG 839

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 840  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 891  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 942

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 943  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 1002

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 1003 M---------------------------------------------VREAGIGK------ 1011

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1012 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1068

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1069 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1128

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1129 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1163


>gi|260886395|ref|ZP_05897658.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sputigena
           ATCC 35185]
 gi|330838838|ref|YP_004413418.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sputigena
           ATCC 35185]
 gi|260863916|gb|EEX78416.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sputigena
           ATCC 35185]
 gi|329746602|gb|AEB99958.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sputigena
           ATCC 35185]
          Length = 1245

 Score =  825 bits (2130), Expect = 0.0,   Method: Composition-based stats.
 Identities = 436/955 (45%), Positives = 595/955 (62%), Gaps = 102/955 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++D+P L+++Q+ SY+ FL           EGL+  F+ + PI  F+G
Sbjct: 9   KRNRYTYARIKEVMDMPHLLDIQRNSYEWFL----------KEGLREIFQDISPIQDFTG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+++D+C  RD+T A PL++ +RLI          +   +IKEQ +
Sbjct: 59  NLVLSFEDFSLGEPKYELDECKERDVTLAAPLRVNVRLI---------NRETGEIKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++         +GK LY   IIP++G 
Sbjct: 110 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGAYYGETID---TTGKKLYNATIIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY--SQRGDFWCF 247
           W+++E D+ D+I VRIDR RK+PVT  + ALG  S   I   F        +   D    
Sbjct: 167 WIELETDANDVISVRIDRTRKLPVTILVRALGYSSNSAIAELFNYDERIQATLERDGASS 226

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------ 300
              A        +      +  GE   +++ ++L   L    K   +  +G         
Sbjct: 227 KEEA--------LVEIYKRLRPGEPPTVDNAQQLLDSLFFDPKRYDLAMVGRYKLTKKLG 278

Query: 301 --DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               + G  +A+ IV+ ETGE+ + A  V+DE  LE I                      
Sbjct: 279 WKRRILGRVLAQPIVDKETGEVVVPADVVVDESMLENI---------------------- 316

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                     +++DAL    +              ++F       D   +  +       
Sbjct: 317 --------TAEQEDALFGEDK-------------PAVFFARTQTGDGKSMKVL------- 348

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             +   P + R I   D++A I  L++L +G GT DDID+LGNRRVRSVGE+L+NQ+R+G
Sbjct: 349 -CSRTLPYNHRTITCNDVMASINYLLNLMDGVGTTDDIDHLGNRRVRSVGELLQNQFRIG 407

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER +KER++  D+D + PQ LIN +PVV+A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 408 LSRMERVVKERMTIQDVDVITPQALINIRPVVAAIKEFFGSSQLSQFMDQHNPLSELTHK 467

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++ARVN +GF+
Sbjct: 468 RRLSALGPGGLSRERAGFEVRDVHNSHYGRMCPIETPEGPNIGLIGSLSNYARVNQFGFM 527

Query: 599 ETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV     +VT+DV YL+A EE    IAQAN  LDE+G F  E V  R   E +LV
Sbjct: 528 ETPYRKVDKAAHRVTDDVRYLTADEENKIVIAQANEPLDENGWFVNERVTARYNEETVLV 587

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            R+++D++D SPKQVVSIA ++IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME
Sbjct: 588 ARDRVDYMDVSPKQVVSIATAMIPFLENDDANRALMGANMQRQAVPLLRTQAPLVGTGME 647

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG  I+AKRAG++E+V A +I +R+ EG        +DIY+L K+QRSNQ TC+
Sbjct: 648 YKAACDSGVMILAKRAGVIEKVTADQIQVRTHEG-------DLDIYKLQKYQRSNQGTCI 700

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P+V+ G+EV     IADGP+TD G+LALG N++VA+MPW GYN+ED++L+SE +V  
Sbjct: 701 NQVPIVEKGEEVFEKQPIADGPATDHGELALGYNIIVAYMPWEGYNYEDAILLSENLVKR 760

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D++TSIHIEE+E  ARDTKLG EEITRDIPNVS + LK++DE G+I +GA+V PGDILVG
Sbjct: 761 DLYTSIHIEEYECDARDTKLGSEEITRDIPNVSGDALKDLDENGVISIGADVLPGDILVG 820

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+ F+R   D
Sbjct: 821 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKSFSRENND 875



 Score =  545 bits (1403), Expect = e-152,   Method: Composition-based stats.
 Identities = 189/521 (36%), Positives = 264/521 (50%), Gaps = 34/521 (6%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +I +            I++  I+  G EV     +           +     +
Sbjct: 677  RTHEGDLDIYKLQKYQRSNQGTCINQVPIVEKGEEVFEKQPIADGP-ATDHGELALGYNI 735

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + A    +  +  D  L   + V   +        +  D  +  +  E    ++     D
Sbjct: 736  IVAYMPWEGYNYEDAILLSENLVKRDLYTSIHIEEYECDARDTKLGSEEITRDIPNVSGD 795

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  + S   ++L G   V       ++ + + + +      +  +         
Sbjct: 796  ALKDLDENGVISIGADVLPGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 846

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E                   K    +  D++PPGV  +V+V++A KR I  GDKM+G
Sbjct: 847  ---EVRDTSLRVPHGEAGKIVDVKSFSRENNDELPPGVNHLVRVYIAQKRKISVGDKMSG 903

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI ETHLG A   LG +I
Sbjct: 904  RHGNKGVVSRIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQILETHLGMAVRALGMQI 963

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K+                               S   D     V +   +G+ ++TPVFD
Sbjct: 964  KAG---------------------DPTVGERLRSIGYDVEAHGVPKPDVAGIHIATPVFD 1002

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA +  +   +R A L E G++ILYDG TGEPF+  VTVG +YMLKL+H+V DK++ARST
Sbjct: 1003 GAGDAEVFGTIRAAGLPEDGKTILYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARST 1062

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I
Sbjct: 1063 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAI 1122

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            V G +  E G PESF VL+KE+Q++GL I +     +    
Sbjct: 1123 VKGENIPEPGVPESFKVLIKELQSIGLDIKVLTEDAQEIVI 1163


>gi|282852643|ref|ZP_06261985.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus gasseri
           224-1]
 gi|282556385|gb|EFB62005.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus gasseri
           224-1]
          Length = 1204

 Score =  825 bits (2130), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/981 (42%), Positives = 591/981 (60%), Gaps = 86/981 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E++ +P+L +VQ  SY  FL          NEG++  F  + PI+ 
Sbjct: 3   YGSHRTRRSFSRIKEVLKLPNLTDVQTQSYKWFL----------NEGIREMFDDIMPISD 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG   LEFV Y+   PK+ +++    D  Y+ PL +TL+L               +IK 
Sbjct: 53  FSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLKLT---------NHETGEIKT 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ G+ PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ ++   +IP+
Sbjct: 104 QDVFFGEFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHSDFDK---NGRQIFGATVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
           +G W++ E D+KD+ +VRIDR RK+P+T  + ALG  S+ E+   F          +   
Sbjct: 161 RGAWLEYETDAKDLAYVRIDRTRKLPLTVLIRALGFGSDSEVADMFGESDSLRFTLEKDI 220

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS----- 300
              + AD  V   +      +  GE    +S + L        +   +  +G        
Sbjct: 221 -HKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKL 279

Query: 301 ---DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              + L    +AE + + +TGEI  + GDV+  + L+++                  + Y
Sbjct: 280 SLKNRLLRQTLAETLADPDTGEIIAKKGDVVTHEILDKL------------------SPY 321

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +          DR D  +  Y   + G +      + +  +   D ++          + 
Sbjct: 322 L----------DRDDFKMVTYEPSKEGVLPDPVTVQEIKVYSKVDPER---------VIK 362

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +  N    DDV+H+   D++A I    +L++  GT DDID+LGNRR+R VGE+L+NQ+R+
Sbjct: 363 LMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRIRRVGELLQNQFRI 422

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L  +TH
Sbjct: 423 GLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPLGELTH 482

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++A VN YGF
Sbjct: 483 KRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLATYAIVNKYGF 542

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF +++V  R   + + 
Sbjct: 543 IETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNEDGSFKDKIVLARHKEDNLE 602

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   AP VGTGM
Sbjct: 603 VTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAPIVGTGM 662

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG A+VAK  G+VE VDA  I IR  +  LD        Y L KF+RSN    
Sbjct: 663 EYRAAHDSGDALVAKAPGVVEYVDANEIRIRRDDDTLDK-------YVLEKFRRSNATKN 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQ P VK G+ V  +++IADGP+ + G+LALG+N ++AF+ W+ YN+ED+++ISERMV 
Sbjct: 716 YNQTPAVKQGERVVADEVIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMISERMVK 775

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  GDILV
Sbjct: 776 DDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEEGIVRIGAEVQDGDILV 835

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------H 948
           GK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V++F R        
Sbjct: 836 GKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVQVFTREAGDELPP 895

Query: 949 GIDKNERSISVEREQIELLAR 969
           G++K  R   V++ +I++  +
Sbjct: 896 GVNKMVRVYIVQKRKIQVGDK 916



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 257/1055 (24%), Positives = 389/1055 (36%), Gaps = 174/1055 (16%)

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +AL DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L      + +
Sbjct: 231  EALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLLRQTL 290

Query: 432  --------------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                                  E +  +   L        T +           +V E +
Sbjct: 291  AETLADPDTGEIIAKKGDVVTHEILDKLSPYLDRDDFKMVTYEPSKEGVLPDPVTVQE-I 349

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFFCSSQLSQLEE 527
            K   ++   R+ + +     + D+  + P D    +     +   +        L     
Sbjct: 350  KVYSKVDPERVIKLMSNGHIADDVKHLTPADVLASINYFFNLQDNIGTTDDIDHLGNRRI 409

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       R   A  +  V    +  ++  V P     I P   S     G      
Sbjct: 410  RRVGELLQNQFRIGLARMERVVRERMSIQDISTVTPQQLINIRPVVASVKEFFGSSQLSQ 469

Query: 588  SFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               + N  G +    R                +V D   T+          E   I   N
Sbjct: 470  FMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLIN 529

Query: 632  --SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              ++      +       R    +     +KID++ A  +    IA +  P  E D S +
Sbjct: 530  SLATYAIVNKYGFIETPYRRVSWDTHKVTDKIDYLTADVEDNYIIAGANAPLNE-DGSFK 588

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              +     ++    +  +       +          ++ +     +E  D+ R ++ +  
Sbjct: 589  DKIVLARHKEDNLEVTPDK-IDYMDVIPKQV----VSVTSACIPFLENDDSNRALMGAN- 642

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                              QR          P+V  G               +        
Sbjct: 643  -----------------HQRQAVPLINPHAPIVGTG--------------MEYRAAHDSG 671

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            + LVA  P       + +  +E  +  D  T        V+ +  +    +     P V 
Sbjct: 672  DALVAKAPG----VVEYVDANEIRIRRDDDTLDKY----VLEKFRRSNATKNYNQTPAVK 723

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +      DE  +I  G  +  G++ +G   I       M   E  +         DV   
Sbjct: 724  QGERVVADE--VIADGPAMENGELALGQNPIIAFLTWNMYNYEDAVMISERMVKDDVY-- 779

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + D     R      E          E   +D D+E  I+      +  
Sbjct: 780  -------TSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEE-GIVRIGAEVQDG 831

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R    +      +V      +         
Sbjct: 832  DILVGKVTPKGVTELSAEERLLHAIFGEKAR----EVRDTSLRVPHGGGGIVQNV----- 882

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    ++   + GD++PPGV ++V+V++  KR IQ GDKM+GRHGNKG ++ + P E
Sbjct: 883  --------QVFTREAGDELPPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGTIALVCPEE 934

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D+  
Sbjct: 935  DMPYLPDGRPVDICLNPMGVPSRMNIGQVLELHLGIAAKQLGIHVATPVFDGASEDDMWN 994

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                               E  I        
Sbjct: 995  M---------------------------------------------VREAGIGK------ 1003

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++LYDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+
Sbjct: 1004 ---DGKTVLYDGRTGEPFHNRVSVGIMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKA 1060

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF
Sbjct: 1061 QFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESF 1120

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             VLVKE+Q+LGL I + +   K     +   D N 
Sbjct: 1121 RVLVKELQSLGLDIKVLDMDHKEIELRDMDDDSND 1155


>gi|295108945|emb|CBL22898.1| DNA-directed RNA polymerase subunit beta [Ruminococcus obeum
           A2-162]
          Length = 1285

 Score =  824 bits (2128), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/958 (43%), Positives = 594/958 (62%), Gaps = 58/958 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G   +R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI
Sbjct: 9   VKTG-KSMRMSYQRQKEVLEMPNLIEVQKDSYKWFL----------DEGLKEVFDDISPI 57

Query: 66  TAFSGAAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             + G   LEF+ + +D    K+ ++ C  RD+TYA PLK+ +RLI          K  +
Sbjct: 58  ADYGGKFSLEFIDFTYDAKDAKYTIEQCKERDVTYAAPLKVRVRLI---------NKETE 108

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK L++  
Sbjct: 109 EINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAIAHDKI---GKRLFSST 165

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQ 240
           +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S 
Sbjct: 166 VIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIVELFGEEPKILASF 225

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +++ E +I +         L K  + K  K L  
Sbjct: 226 AKDTSTNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDLAKVGRYKFNKKLHF 285

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               + G  + E +V+  TGEI  E G  +  +  ++I ++    +P +++        +
Sbjct: 286 NK-RIVGHKLGETVVDPSTGEILAEEGTNVTVELADKIQNA---AVPFVWIQGEERKIKV 341

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++++ D        L    + +   ++  + V E +        ++ D     +  +  
Sbjct: 342 LSSMMVDITAHVD--LDCDPKDLGVTELVYYPVLEKIL-------EENDNLEDIKAAVQR 392

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI KEDI+A I   + L  G G  DDID+LGNRR+RSVGE+L+NQYR+G
Sbjct: 393 DIHDLIP---KHITKEDILASINYNMHLEYGIGNDDDIDHLGNRRIRSVGELLQNQYRIG 449

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L R+ER ++ER+++ D +SV PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH 
Sbjct: 450 LSRLERVVRERMTTQDTESVSPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHK 509

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGFI
Sbjct: 510 RRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINEYGFI 569

Query: 599 ETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           E PYR++      +  VT++VVY++A EE+N ++AQAN  LDE+G F  + V  R   E 
Sbjct: 570 EAPYRRIDKADPANPVVTDEVVYMTADEEDNYHVAQANEPLDEEGHFLHKNVSGRFREET 629

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
               +   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGT
Sbjct: 630 QEYEKRMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGT 689

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME+  A  SG  ++AK++G V +  +  I I++ +G  D        Y L+KF RSNQ+
Sbjct: 690 GMETKTAVDSGVCVLAKKSGTVLRSTSTDITIKNDDGTKDD-------YHLIKFLRSNQS 742

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            C NQ+P+V  G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+
Sbjct: 743 NCYNQKPIVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLLSERL 802

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V  DV+TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDI
Sbjct: 803 VMNDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDI 862

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 863 LVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 920



 Score =  559 bits (1440), Expect = e-156,   Method: Composition-based stats.
 Identities = 272/1231 (22%), Positives = 456/1231 (37%), Gaps = 107/1231 (8%)

Query: 192  MDIEFDSKDIIHVRID--RRRKV----PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
            +D  +D+KD  +  I+  + R V    P+   +  +  ++EEI             GD  
Sbjct: 69   IDFTYDAKDAKY-TIEQCKERDVTYAAPLKVRVRLINKETEEI------NEHEIFMGDLP 121

Query: 246  CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                +   ++ G             E+VI S    + G+  ++    +     +S  +  
Sbjct: 122  LMTETGTFVING------------AERVIVSQLVRSPGIYYAIAHDKIGKRLFSSTVIPN 169

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
                 +         Y+             I    I     + V+       I  +   D
Sbjct: 170  RGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEI-VELFGEEPKILASFAKD 228

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             + + ++ LL++Y+ +RPG+      AES+   +FFD  +YDL+ VGR K N +L+ +  
Sbjct: 229  TSTNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDLAKVGRYKFNKKLHFNKR 288

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                 + +  +      ++       T++  D + N  V  V       +  G  R  + 
Sbjct: 289  IVGHKLGETVVDPSTGEILAEEGTNVTVELADKIQNAAVPFV-------WIQGEERKIKV 341

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI--THTRRLSA 543
            +   +       +     ++  P    V E      L ++ E  ++L  I     R +  
Sbjct: 342  LSSMMV-----DITAHVDLDCDPKDLGVTELVYYPVLEKILEENDNLEDIKAAVQRDIHD 396

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            L    + +      +       YG     +     N   + S+    +      +    R
Sbjct: 397  LIPKHITKEDILASINYNMHLEYGIGNDDDIDHLGN-RRIRSVGELLQNQYRIGLSRLER 455

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC---- 649
             V +   T D   +S     N     A               +  +   EL   R     
Sbjct: 456  VVRERMTTQDTESVSPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSAL 515

Query: 650  -----AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                 + +        + +        +         L N  ++   +           +
Sbjct: 516  GPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARI------NEYGFI 569

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            +A    +     +    +     +         V      +      L  + SG      
Sbjct: 570  EAPYRRIDKADPANPVVTDEVVYMTADEEDNYHVAQANEPLDEEGHFLHKNVSGRFREET 629

Query: 765  MKF-QRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             ++ +R      V+ + +  V         +  A+              +L    P  G 
Sbjct: 630  QEYEKRMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGT 689

Query: 822  NFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
              E    +     V      ++       +      G ++    I  +        ++  
Sbjct: 690  GMETKTAVDSGVCVLAKKSGTVLRSTSTDITIKNDDGTKDDYHLIKFLRSNQSNCYNQKP 749

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPSGVSGT 938
            I+  G  V  G ++    +         +  L+  +   G    D    S R+      T
Sbjct: 750  IVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLLSERLVMNDVYT 809

Query: 939  VVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
             V +  +     D       + R+     +   +D  DE+ I+      R  +IL G+  
Sbjct: 810  SVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEVRAGDILVGKVT 868

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 869  PKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEYGIIVDA 911

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL +G
Sbjct: 912  KVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLPNG 971

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + D  +  DI          
Sbjct: 972  RPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVATPVFDGASEVDIQDTLELANDY 1031

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +      E  + Y D     V E                  +    + +   +   G+  
Sbjct: 1032 VNIEDFEEFRAKYQDTLAPDVMEYLDE-------------HKDHRELWKGVPISRDGKVQ 1078

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGE FD  VT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 1079 LRDGRTGEYFDGRVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 1138

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G++  E G PESF VL+KE+Q
Sbjct: 1139 EMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGIPESFKVLLKELQ 1198

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            +LGL + +          +E + D+   +L+
Sbjct: 1199 SLGLDVKVLKDDNTEVHLLESV-DYGDTDLR 1228


>gi|167768221|ref|ZP_02440274.1| hypothetical protein CLOSS21_02777 [Clostridium sp. SS2/1]
 gi|317497822|ref|ZP_07956133.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709745|gb|EDS20324.1| hypothetical protein CLOSS21_02777 [Clostridium sp. SS2/1]
 gi|291560239|emb|CBL39039.1| DNA-directed RNA polymerase subunit beta [butyrate-producing
           bacterium SSC/2]
 gi|316894894|gb|EFV17065.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 1265

 Score =  823 bits (2125), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/989 (43%), Positives = 601/989 (60%), Gaps = 75/989 (7%)

Query: 9   GLGRV---------RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+         R  + +  +++++P+LIE+QK SYD FL           EGL   F
Sbjct: 2   EKNRIQPIKSGTGMRISYARQDDVLEVPNLIEIQKDSYDWFLR----------EGLAEVF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           + + PI  +S    LEFV Y+   D  K+ +++C  RD TYA PLK+ +RL         
Sbjct: 52  EDISPIEDYSDQLSLEFVDYQLCKDDVKYSIEECKERDATYAAPLKVKVRLH-------- 103

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   +IK+  I+MGDLPLMT  GTF+I G +R++VSQL RSPGI++     +    GK
Sbjct: 104 -NKETDEIKQHEIFMGDLPLMTATGTFIINGAERVIVSQLVRSPGIYYGIAHDKI---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP-- 234
            LY+  +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI   F    
Sbjct: 160 ELYSSTVIPNRGAWLEYETDSNDVFNVRVDRTRKVPITVLIRALGIGTNAEIKELFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KI+ S   D           +         + +D+ E +I S         L K  + K 
Sbjct: 220 KILASIEKDPSDNYEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +  + + G  +AED+++  TGE+  EAG  +D +  ++I ++ +  +        
Sbjct: 280 NKKLAL-RNRISGFILAEDVLDPTTGEVLAEAGTNVDMELADKIQNAAVASVM------- 331

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I+      K     +  L  Y    P ++         +  L    ++       
Sbjct: 332 -----IQTEEGATKILSNMEVNLAEYVDFNPEEIGVHEDV--FYPVLEKILEEGYEGEEL 384

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  +   ++   P   +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 385 KEALKKNIHELIP---KHITKEDILASINYNIHLEYGIGHDDDIDHLGNRRIRAVGELLQ 441

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER+++ DI+S+ PQ LIN KPV +AV EFF SSQLSQ  +H N L
Sbjct: 442 NQYRIGLSRLERVVRERMTTQDIESISPQSLINIKPVTAAVKEFFGSSQLSQFMDHNNPL 501

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL ++AR+
Sbjct: 502 SELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYARI 561

Query: 593 NAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGFIE PYR +      +  VT+ VVYL+A EE+N  +AQAN  +DEDG F    V  
Sbjct: 562 NEYGFIEAPYRVLDKSDPENPVVTDKVVYLTADEEDNYVVAQANEPVDEDGHFVNTHVSG 621

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   +     +  +D +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLL  E
Sbjct: 622 RFREDTSEFDKVNLDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLSTE 681

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTGMES  A  SG  I A+  G+VE+  + +IV+R+ +G  D        Y ++KF
Sbjct: 682 APVVGTGMESKAAYDSGVCITARNGGVVERSTSTKIVVRNDDGQRDE-------YNVIKF 734

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ  C+NQRP+V VGD V + DI+ADG ST  G++ALG+N L+ FM W GYN+ED++
Sbjct: 735 ARSNQGNCMNQRPIVFVGDRVEKGDILADGASTSNGEMALGKNPLIGFMTWEGYNYEDAV 794

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TS+HIEE+E  ARDTKLG EEITRD+  +SE+ LK++D+ GII +GAE
Sbjct: 795 LLSERLVQDDVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDDNGIIRIGAE 854

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V+D +IF R
Sbjct: 855 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGAYGVVMDTKIFTR 914

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   G++K+ R    ++ +I +  +
Sbjct: 915 ENGDELPPGVNKSVRVYIAQKRKISVGDK 943



 Score =  557 bits (1436), Expect = e-156,   Method: Composition-based stats.
 Identities = 251/1056 (23%), Positives = 396/1056 (37%), Gaps = 77/1056 (7%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +       I  ++  D + + +D LL++Y+ +RPG+  +   AES+ N +FFD  +YDL+
Sbjct: 213  ELFGEEPKILASIEKDPSDNYEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLA 272

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L L        + ++ +      ++        ++  D + N  V SV  
Sbjct: 273  KVGRYKFNKKLALRNRISGFILAEDVLDPTTGEVLAEAGTNVDMELADKIQNAAVASVMI 332

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
              +      L  ME ++ E +   + + +   + +    +   + E +   +L +  +  
Sbjct: 333  QTEEGATKILSNMEVNLAEYV-DFNPEEIGVHEDVFYPVLEKILEEGYEGEELKEALKKN 391

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
                   H  +   L               D    H G               + ++   
Sbjct: 392  IHELIPKHITKEDILASINYNIHLEYGIGHDDDIDHLGN------------RRIRAVGEL 439

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGS 639
             +      +    R V +   T D+  +S     N     A               +  +
Sbjct: 440  LQNQYRIGLSRLERVVRERMTTQDIESISPQSLINIKPVTAAVKEFFGSSQLSQFMDHNN 499

Query: 640  FTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
               EL   R             R   +  D        +     P   N      L    
Sbjct: 500  PLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLATYA 559

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
               +   +         +  E+ V       + A          A   V           
Sbjct: 560  RINEYGFIEAPYRVLDKSDPENPVVTDKVVYLTADEEDNYVVAQANEPVDEDGHFVNTHV 619

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +           + +     V+ + +  V         +  A+              +L 
Sbjct: 620  SGRFREDTSEFDKVNLDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLS 679

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               P  G   E        +        +        +      G  +    I       
Sbjct: 680  TEAPVVGTGMESKAAYDSGVCITARNGGVVERSTSTKIVVRNDDGQRDEYNVIKFARSNQ 739

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +++  I+ VG  V  GDIL    +      M   +  L      +  +  D  L   
Sbjct: 740  GNCMNQRPIVFVGDRVEKGDILADGASTSN-GEMALGKNPLIGFMTWEGYNYEDAVLL-- 796

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDRNI 982
                  V D    + H  +    +   +  +E+I        E + +D DD   I+    
Sbjct: 797  --SERLVQDDVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDDN-GIIRIGA 853

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R  +IL G+    G         L   +  E  R                 E      
Sbjct: 854  EVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSL 896

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                         KI   + GD++PPGV + V+V++A KR I  GDKMAGRHGNKG++SR
Sbjct: 897  RVPHGAYGVVMDTKIFTRENGDELPPGVNKSVRVYIAQKRKISVGDKMAGRHGNKGVISR 956

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + +    
Sbjct: 957  ILPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKVLGFNVATPVFNGADE 1016

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             DI+           T          D  +   +   +++                    
Sbjct: 1017 NDIADTLRMANDYANTSWEEFDAKWRDKVNDDVMDYLYEN--------------RDHRKE 1062

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
             +   +D +G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQP
Sbjct: 1063 WQGVPIDTTGKVRLRDGRTGEEFDSPVTIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQP 1122

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+I+ G++  E G
Sbjct: 1123 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTFKSDDVVGRVKAYEAIIKGDNIPEPG 1182

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             PESF VL+KE Q+L L + + +   +     E++ 
Sbjct: 1183 VPESFKVLLKEFQSLALDVKILDENAEEVELREDVD 1218


>gi|260588979|ref|ZP_05854892.1| DNA-directed RNA polymerase, beta subunit [Blautia hansenii DSM
           20583]
 gi|331083299|ref|ZP_08332412.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540758|gb|EEX21327.1| DNA-directed RNA polymerase, beta subunit [Blautia hansenii DSM
           20583]
 gi|330404380|gb|EGG83925.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 1281

 Score =  823 bits (2125), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/958 (44%), Positives = 595/958 (62%), Gaps = 56/958 (5%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
                  +R  + +  E++++P+LIEVQK SY  FL          +EGL   F+ + PI
Sbjct: 8   SVTNGKAMRMSYQRQKEVLEMPNLIEVQKDSYQWFL----------DEGLNEVFEDISPI 57

Query: 66  TAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             +SG   LEFV +    D  K+ ++ C  RD TYA PLK+ +RL           K   
Sbjct: 58  ADYSGKLSLEFVGFTLCEDEKKYTIEQCKERDATYAAPLKVKVRLH---------NKENG 108

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I    I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  
Sbjct: 109 EITTHEIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKTLYSST 165

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQ 240
           +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S 
Sbjct: 166 VIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASF 225

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +++ E +I S         L K  + K  K L +
Sbjct: 226 TKDTSESYQEGLLELYKKIRPGEPLAVESAESLITSMFFDARRYDLAKVGRYKFNKKL-L 284

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + + G  +AE++V+  TGEI  EAG V+ ++  + I ++    +P +++     N  +
Sbjct: 285 LRNRIAGHMLAEEVVDVTTGEIIAEAGTVVSQELADTIQNA---AVPYVWIQGEERNIKV 341

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            +++  D       +  ++ + +   ++  + V   +        D  D   + R    +
Sbjct: 342 LSSMAVDLKNYVDLSDEEL-KELGVTELVYYPVLAKILEENEELDDIKD--AIKREIHEL 398

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                     +HI KEDI+A I   + L  G GT DDID+LGNRR+R+VGE+L+NQYR+G
Sbjct: 399 I--------PKHITKEDILASINYNMHLEYGLGTDDDIDHLGNRRIRAVGELLQNQYRIG 450

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L R+ER ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH 
Sbjct: 451 LSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHK 510

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGF+
Sbjct: 511 RRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINEYGFV 570

Query: 599 ETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           E PYRK+      + +VT++VVY++A EE+  ++AQAN  LDE+G F  + V  R   E 
Sbjct: 571 EAPYRKIDRTDPKNPRVTDEVVYMTADEEDIYHVAQANEPLDEEGHFIHKNVSGRYREET 630

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
               R+  +++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGT
Sbjct: 631 QEYERQMFEYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGT 690

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GMES  A  SG  +VAK++G +E   +  I++++ +G  D       +Y L KF RSNQ+
Sbjct: 691 GMESKAAVDSGVCVVAKKSGTIECAASKEIIMKNDDGTKD-------VYHLTKFMRSNQS 743

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            C NQRP+V  G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+
Sbjct: 744 NCYNQRPIVVKGEHVEAGQVIADGPSTSNGELALGKNPLIGFMTWEGYNYEDAVLLSERL 803

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDI
Sbjct: 804 VMDDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDI 863

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 864 LVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENGD 921



 Score =  563 bits (1452), Expect = e-158,   Method: Composition-based stats.
 Identities = 266/1180 (22%), Positives = 438/1180 (37%), Gaps = 77/1180 (6%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    + +            +    ++    I+  E+VI S    + G+  ++    + 
Sbjct: 99   KVRLHNKENGEITTHEIFMGDLPLMTATGTFVINGAERVIVSQLVRSPGIYYAIAHDKLG 158

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                +S  +       +         Y+             I    I     + +D    
Sbjct: 159  KTLYSSTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEI-IDLFGE 217

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               I  +   D ++  ++ LL++Y+ +RPG+      AES+   +FFD+ +YDL+ VGR 
Sbjct: 218  EPKILASFTKDTSESYQEGLLELYKKIRPGEPLAVESAESLITSMFFDARRYDLAKVGRY 277

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L L        + +E +      ++       + +  D + N  V  V       
Sbjct: 278  KFNKKLLLRNRIAGHMLAEEVVDVTTGEIIAEAGTVVSQELADTIQNAAVPYV------- 330

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +  G  R  + +      +     +  + +    V   V     +  L + EE  +    
Sbjct: 331  WIQGEERNIKVLSSMAVDLKNYVDLSDEELKELGVTELVYYPVLAKILEENEELDDIKDA 390

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            I   R +  L    + +      +       YG     +     N   + ++    +   
Sbjct: 391  I--KREIHELIPKHITKEDILASINYNMHLEYGLGTDDDIDHLGN-RRIRAVGELLQNQY 447

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFTEEL 644
               +    R V +   T D+  +S     N     A               +  +   EL
Sbjct: 448  RIGLSRLERVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGEL 507

Query: 645  VFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
               R             R   +  D        +     P   N      L       + 
Sbjct: 508  THKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINEY 567

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
              +         T  ++         + A    I     A    +      +  + SG  
Sbjct: 568  GFVEAPYRKIDRTDPKNPRVTDEVVYMTADEEDIYHVAQANE-PLDEEGHFIHKNVSGRY 626

Query: 761  IYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                 +++R       V+ + +  V         +  A+              +L    P
Sbjct: 627  REETQEYERQMFEYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAP 686

Query: 818  WHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G   E    +     V      +I     + +      G +++      +        
Sbjct: 687  VVGTGMESKAAVDSGVCVVAKKSGTIECAASKEIIMKNDDGTKDVYHLTKFMRSNQSNCY 746

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+  G  V  G ++    +      +   +  L      +  +  D  L       
Sbjct: 747  NQRPIVVKGEHVEAGQVIADGPSTSN-GELALGKNPLIGFMTWEGYNYEDAVLL----SE 801

Query: 937  GTVVDVRIFNRHGIDKNERSISVE--REQI--------ELLARDKDDEQVILDRNIYSRL 986
              V+D    + H  +    +   +   E+I        +   +D  DE+ I+      R 
Sbjct: 802  RLVMDDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEVRA 860

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   +  E  R                 E      +   
Sbjct: 861  GDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPH 903

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                     K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP 
Sbjct: 904  GEYGIVVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPV 963

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI 
Sbjct: 964  EDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANENDIQ 1023

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                     + T    E    Y+D     V +                  +A   + +  
Sbjct: 1024 DTLELANDYVNTEDFEEFRKKYEDTLRPEVMQFLDE-------------NKAHRELWKGV 1070

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             L   G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK
Sbjct: 1071 PLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1130

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G++  E G PES
Sbjct: 1131 AQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEAIIKGDNIPEPGIPES 1190

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+LGL + +          ME I D+   +++
Sbjct: 1191 FKVLLKELQSLGLDVRVLREDMTEVEIMENI-DYGDTDMR 1229


>gi|153812149|ref|ZP_01964817.1| hypothetical protein RUMOBE_02546 [Ruminococcus obeum ATCC 29174]
 gi|149831804|gb|EDM86890.1| hypothetical protein RUMOBE_02546 [Ruminococcus obeum ATCC 29174]
          Length = 1285

 Score =  823 bits (2125), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/958 (43%), Positives = 592/958 (61%), Gaps = 58/958 (6%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G   +R  + +  E++++P+LIEVQK SY  FL          +EGL+  F  + PI
Sbjct: 9   VKTG-KSMRMSYQRQKEVLEMPNLIEVQKDSYKWFL----------DEGLKEVFDDISPI 57

Query: 66  TAFSGAAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             + G   LEF+ + +D    K+ +  C  RD+TYA PLK+ +RLI          K  +
Sbjct: 58  ADYGGKFSLEFIDFTYDAKDAKYTIAQCKERDVTYAAPLKVRVRLI---------NKETE 108

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I E  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK L++  
Sbjct: 109 EINEHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYAIAHDKL---GKRLFSST 165

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQ 240
           +IP++G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S 
Sbjct: 166 VIPNRGAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIVELFGEEPKILASF 225

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
             D           +         + +++ E +I +         L K  + K  K L  
Sbjct: 226 TKDTSTNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDLAKVGRYKFNKKLHF 285

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               + G  + E +V+  TGEI  E G  +  +  ++I ++    +P +++        +
Sbjct: 286 NK-RIVGHKLGEAVVDPSTGEILAEEGTNVTIELADKIQNA---AVPFVWIQGEERKIKV 341

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++++ D        L    + +   ++  + V E +        ++ D     +  +  
Sbjct: 342 LSSMMVDITAHVD--LDCDPKELGVTELVYYPVLEKIL-------EENDNLEDIKAAIKR 392

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            ++   P   +HI KEDI+A I   + L  G G  DDID+LGNRR+RSVGE+L+NQYR+G
Sbjct: 393 DIHDLIP---KHITKEDILASINYNMHLEYGIGNDDDIDHLGNRRIRSVGELLQNQYRIG 449

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L R+ER ++ER+++ D +S+ PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH 
Sbjct: 450 LSRLERVVRERMTTQDTESISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHK 509

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGFI
Sbjct: 510 RRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLASYARINEYGFI 569

Query: 599 ETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           E PYRK+      +  VT+DVVY++A EE+N ++AQAN  LDE+G F  + V  R   E 
Sbjct: 570 EAPYRKIDKTDPSNPIVTDDVVYMTADEEDNYHVAQANEPLDEEGHFLHKNVSGRFREET 629

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
               +   D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGT
Sbjct: 630 QEYEKRMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGT 689

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME+  A  SG  ++AK++G V +  +  I I++ +G  D        Y L KF RSNQ+
Sbjct: 690 GMETKAAVDSGVCVLAKKSGTVLRSTSTDISIKNDDGTKDD-------YHLTKFLRSNQS 742

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            C NQ+P+V  G+ V    +IADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+
Sbjct: 743 NCYNQKPIVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLLSERL 802

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V  DV+TS+HIEE+E  ARDTKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDI
Sbjct: 803 VQNDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDI 862

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G +VD ++F R   D
Sbjct: 863 LVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIIVDAKVFTRENGD 920



 Score =  561 bits (1446), Expect = e-157,   Method: Composition-based stats.
 Identities = 250/1062 (23%), Positives = 400/1062 (37%), Gaps = 69/1062 (6%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            V+       I  +   D + + ++ LL++Y+ +RPG+      AES+   +FFD  +YDL
Sbjct: 212  VELFGEEPKILASFTKDTSTNYQEGLLELYKKIRPGEPLAVESAESLIMAMFFDPRRYDL 271

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L+ +       + +  +      ++       TI+  D + N  V  V 
Sbjct: 272  AKVGRYKFNKKLHFNKRIVGHKLGEAVVDPSTGEILAEEGTNVTIELADKIQNAAVPFV- 330

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                  +  G  R  + +   +       +     ++  P    V E      L ++ E 
Sbjct: 331  ------WIQGEERKIKVLSSMMV-----DITAHVDLDCDPKELGVTELVYYPVLEKILEE 379

Query: 529  VNSLSRITH--TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
             ++L  I     R +  L    + +      +       YG     +     N   + S+
Sbjct: 380  NDNLEDIKAAIKRDIHDLIPKHITKEDILASINYNMHLEYGIGNDDDIDHLGN-RRIRSV 438

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDE 636
                +      +    R V +   T D   +S     N     A               +
Sbjct: 439  GELLQNQYRIGLSRLERVVRERMTTQDTESISPQSLINIKPVTAAVKEFFGSSQLSQFMD 498

Query: 637  DGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              +   EL   R             R   +  D        +     P   N      L 
Sbjct: 499  QNNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLA 558

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
                  +   +         T   + +       + A          A   +        
Sbjct: 559  SYARINEYGFIEAPYRKIDKTDPSNPIVTDDVVYMTADEEDNYHVAQANEPLDEEGHFLH 618

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               +           +R      V+ + +  V         +  A+              
Sbjct: 619  KNVSGRFREETQEYEKRMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVP 678

Query: 811  MLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            +L    P  G   E    +     V      ++       ++     G ++       + 
Sbjct: 679  LLTTEAPVVGTGMETKAAVDSGVCVLAKKSGTVLRSTSTDISIKNDDGTKDDYHLTKFLR 738

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRDT 927
                   ++  I+  G  V  G ++    +         +  L+  +   G    D    
Sbjct: 739  SNQSNCYNQKPIVFQGEHVEAGQVIADGPSTANGELALGKNPLIGFMTWEGYNYEDAVLL 798

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYS 984
            S R+      T V +  +     D       + R+     +   +D  DE+ I+      
Sbjct: 799  SERLVQNDVYTSVHIEEYEAEARDTKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEV 857

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R  +IL G+    G         L   +  E  R                 E      + 
Sbjct: 858  RAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKV 900

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                       K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+L
Sbjct: 901  PHGEYGIIVDAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVL 960

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + D  +  D
Sbjct: 961  PVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVSTPVFDGASEID 1020

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            I          +      E  + Y D     V E                  +    + +
Sbjct: 1021 IQDTLELANDYVNIEDFEEFRAKYQDTLAPDVMEYLDE-------------HKDHRELWK 1067

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +   G+  L DG TGE FD  VT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLG
Sbjct: 1068 GVPISRDGKVQLRDGRTGEYFDGRVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLG 1127

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G++  E G P
Sbjct: 1128 GKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGIP 1187

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            ESF VL+KE+Q+LGL + +          +E + D+   +L+
Sbjct: 1188 ESFKVLLKELQSLGLDVKVLRDDNTEVHLLETV-DYGDTDLR 1228


>gi|229824570|ref|ZP_04450639.1| hypothetical protein GCWU000282_01914 [Catonella morbi ATCC 51271]
 gi|229785941|gb|EEP22055.1| hypothetical protein GCWU000282_01914 [Catonella morbi ATCC 51271]
          Length = 1228

 Score =  823 bits (2125), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/987 (43%), Positives = 593/987 (60%), Gaps = 90/987 (9%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +V  G    R+ + +  E++++P+LIE+Q  SY  FL          +EGL+  F+ + 
Sbjct: 15  HIVKYGKKAERRSYARIDEVLELPNLIEIQTDSYKWFL----------DEGLKVMFEDIS 64

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI   S    L FV YEF   K+ +++    D  Y+ P+ +TLRL           K   
Sbjct: 65  PIVDHSENLELHFVDYEFKEAKYSLEEARSHDANYSKPIYVTLRL---------FNKETG 115

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           ++KEQ ++ GD P+MT+ GTF+I G +R++VSQL RSPG++F     +    G+  Y   
Sbjct: 116 EVKEQEVFFGDFPIMTEMGTFIINGAERVIVSQLVRSPGVYFHDRMDKK---GRHSYTST 172

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +IP++G W++ E D+K I +VRIDR RK+P+T  + ALG  S+ EI   F    +     
Sbjct: 173 VIPNRGAWLEFESDAKGIAYVRIDRTRKIPLTVLMRALGFGSDDEIYDIFGQSELLDLTI 232

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GV 293
           +      +  D      +      +  GE    ES + L        +           +
Sbjct: 233 EKD-VHKNIQDSRTEEALKDIYERLRPGEPKTAESSRNLLVARFFDPRRYDLAPVGRYKI 291

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                  + L GL +AE +VN ETGE+  E G V+D++ ++ +       IP L      
Sbjct: 292 NKKLHLKNRLVGLTLAETLVNPETGEVLFEEGTVLDQERVQAL-------IPYLEAGLNK 344

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
              Y     V  +  D     L I +V  P +                            
Sbjct: 345 VTLYPSEDSVVAQPID-----LQIIKVYSPKNA--------------------------- 372

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            ++   +     + ++ +   DIIA +   + L  G G  DDID+L NRR+RSVGE+L+N
Sbjct: 373 EQVINIIGNGNIEKIKCLTPADIIASMNYYLYLDQGIGVTDDIDHLANRRIRSVGELLQN 432

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL RMER ++ER+S  D+ ++ PQ LIN +PVV+A+ EFF SSQLSQ  + VN L 
Sbjct: 433 QFRIGLSRMERVVRERMSLQDVATITPQQLINIRPVVAAIKEFFGSSQLSQFMDQVNPLG 492

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A++N
Sbjct: 493 ELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKIN 552

Query: 594 AYGFIETPYRKVCD----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            YGFIETPYRKV       +VT ++ YL+A EE+   +AQANS L+EDG+F  +LV  R 
Sbjct: 553 KYGFIETPYRKVDKSVTPHRVTTEIDYLAADEEDLYVVAQANSKLNEDGTFANDLVMARF 612

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + I V  +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  ++P
Sbjct: 613 RSQNIEVNVDQVDYMDVSPKQVVAVATASIPFLENDDSNRALMGANMQRQAVPLINPQSP 672

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            +GTGME   A  SGAA++ KRAG V  VDA ++ +R+ EG        VD YRL KF R
Sbjct: 673 LIGTGMEYKAAHDSGAALLCKRAGEVVYVDANKVRVRTPEG-------EVDEYRLTKFAR 725

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQRP+V++GD+V   +I+ADGPS   G++ALG+N LVAFM W GYN+ED++++
Sbjct: 726 SNAGTCYNQRPIVELGDQVDALEILADGPSMQNGEMALGQNPLVAFMTWEGYNYEDAVIM 785

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV+TSIHIEE+E  +RDTKLGPEEITR+IPNVSE+ LK +D+ GIIC+GAEV 
Sbjct: 786 SERLVKDDVYTSIHIEEYESESRDTKLGPEEITREIPNVSEDALKYLDKDGIICIGAEVK 845

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-- 947
            GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R  
Sbjct: 846 DGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREA 905

Query: 948 -----HGIDKNERSISVEREQIELLAR 969
                 G++K  R   V++ +I    +
Sbjct: 906 GDELAPGVNKLVRVYIVQKRKINEGDK 932



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 233/1049 (22%), Positives = 371/1049 (35%), Gaps = 148/1049 (14%)

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM--------------------F 396
              ++     ++   ++AL DIY  +RPG+  T   + ++                     
Sbjct: 232  IEKDVHKNIQDSRTEEALKDIYERLRPGEPKTAESSRNLLVARFFDPRRYDLAPVGRYKI 291

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
            N      ++    T+    +N        ++   + +E + A+I  L    N        
Sbjct: 292  NKKLHLKNRLVGLTLAETLVNPETGEVLFEEGTVLDQERVQALIPYLEAGLNKVTLYPSE 351

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            D++  + +           ++   +    +   I + +I+ +      +    ++     
Sbjct: 352  DSVVAQPIDL------QIIKVYSPKNAEQVINIIGNGNIEKIKCLTPADIIASMNYYLYL 405

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 ++   +H+ +    +    L    + G++R    V  R               + 
Sbjct: 406  DQGIGVTDDIDHLANRRIRSVGELLQNQFRIGLSRMERVVRERMSLQDVATITPQQLINI 465

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
               +  +      ++++ +                + V  L  +  + R  A     L  
Sbjct: 466  RPVVAAIKEFFGSSQLSQF---------------MDQVNPLGELTHKRRLSALGPGGLTR 510

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            D          R   E   V       +             +         N+       
Sbjct: 511  D----------RAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKINKYGFIETP 560

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
             R+    +            +   +       A      +   A  +V+           
Sbjct: 561  YRKVDKSVTPHRVTTEIDYLAADEEDLYVVAQANSKLNEDGTFANDLVMARFRSQNIEVN 620

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y          +    Q   V         +  ++              ++    
Sbjct: 621  VDQVDY---------MDVSPKQVVAVATASIPFLENDDSNRALMGANMQRQAVPLINPQS 671

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR-DTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E                   +       R  T  G  +  R            
Sbjct: 672  PLIGTGMEYKAAHDSGAALLCKRAGEVVYVDANKVRVRTPEGEVDEYRLTKFARSNAGTC 731

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+ +G +V+  +IL    +      M   +  L A    +  +  D  +      
Sbjct: 732  YNQRPIVELGDQVDALEILADGPS-MQNGEMALGQNPLVAFMTWEGYNYEDAVIMS---- 786

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSR 985
                          + K++   S+  E+ E  +RD       + R I            +
Sbjct: 787  ------------ERLVKDDVYTSIHIEEYESESRDTKLGPEEITREIPNVSEDALKYLDK 834

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      +S   R     F  +  +V+     +       
Sbjct: 835  DGIICIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 894

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               +      KI   + GD++ PGV ++V+V++  KR I  GDKMAGRHGNKG+VS I+P
Sbjct: 895  VHDV------KIFTREAGDELAPGVNKLVRVYIVQKRKINEGDKMAGRHGNKGVVSLIMP 948

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   +G KI + + D  +  D 
Sbjct: 949  EEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAREMGIKIATPVFDGASEED- 1007

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                        V++   E         
Sbjct: 1008 --------------------------------------------VWETVKEA-------- 1015

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              L+   ++ILYDG TGEPFDR V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1016 -GLEADAKTILYDGRTGEPFDRKVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1074

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G      G PE
Sbjct: 1075 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGQPIPRPGVPE 1134

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            SF VLVKE+QALGL + + +   +     
Sbjct: 1135 SFRVLVKELQALGLDLKVLDEHDQEIELR 1163


>gi|330940874|gb|EGH43833.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
           pisi str. 1704B]
          Length = 715

 Score =  822 bits (2124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 362/719 (50%), Positives = 502/719 (69%), Gaps = 4/719 (0%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P L+ +Q  SY  FL      D+  + GL AAFKSVFPI ++SG A LE+V Y    
Sbjct: 1   MDVPYLLAIQLDSYREFLQAGATKDQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGE 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P FDV +C+ R +TYAVPL++ +RLI+FD    +  K+IKDIKEQ +YMG++PLMT++GT
Sbjct: 61  PAFDVKECVLRGVTYAVPLRVKVRLIIFDK--ESSNKAIKDIKEQEVYMGEIPLMTENGT 118

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FVI G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ RIIP +G W+D EFD KD + 
Sbjct: 119 FVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVF 178

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRIDRRRK+P +  L ALG  +E++L  FY   V+  RG+     L    L  G      
Sbjct: 179 VRIDRRRKLPASVLLRALGYTTEQVLDAFYTTNVFHVRGENLSLELVPQRL-RGEIAVLD 237

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           ++D D G+ ++E G+++T+  +  L++ G+K L +  D + G   A+ IV+  TGEI  E
Sbjct: 238 ILD-DKGKVIVEQGRRITARHINQLEKAGIKELEVPLDYVLGRTTAKVIVHPATGEIIAE 296

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
               ++ + L +I  +++  I  LY + ++   ++ +TL  D   ++ +AL++IYR+MRP
Sbjct: 297 CNTELNTEILAKIAKAQVVRIETLYTNDIDCGPFVSDTLKIDSTSNQLEALVEIYRMMRP 356

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T   AE++FN LFF  ++YDLS VGR+K N R+     +    + KEDI+A++K L
Sbjct: 357 GEPPTKDAAETLFNNLFFSPERYDLSAVGRMKFNRRIGRTEIEGSGVLCKEDIVAVLKTL 416

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDL
Sbjct: 417 VDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDL 476

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           INAKPV +AV EFF SSQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHP
Sbjct: 477 INAKPVAAAVKEFFGSSQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHP 536

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+LSA+EE 
Sbjct: 537 THYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVFLSAIEEA 596

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE
Sbjct: 597 DHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLE 656

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA R
Sbjct: 657 HDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASR 715


>gi|310829727|ref|YP_003962084.1| DNA-directed RNA polymerase subunit beta [Eubacterium limosum
           KIST612]
 gi|308741461|gb|ADO39121.1| DNA-directed RNA polymerase subunit beta [Eubacterium limosum
           KIST612]
          Length = 1229

 Score =  822 bits (2124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/957 (44%), Positives = 590/957 (61%), Gaps = 59/957 (6%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ F K  E++++P+L+EVQ  SY  F+           +GLQ  F  +  IT ++G 
Sbjct: 12  RTRQSFSKIKEVLEMPNLLEVQLDSYKWFI----------EKGLQEVFDDIHEITDYTGN 61

Query: 72  AMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            +L+FV Y     PK+ +++C  RD TY VPLK+ +RLI          K   ++KEQ +
Sbjct: 62  LVLQFVDYAIEGEPKYSIEECKERDQTYYVPLKVRVRLI---------NKEKNEVKEQKV 112

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           YM DL  MT  GTF++ G +R++VSQL RSPG ++   + +    GK LY+ ++IP++G 
Sbjct: 113 YMADLHKMTDTGTFIVNGAERVIVSQLVRSPGAYYTLTRDKL---GKKLYSAQVIPNRGA 169

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           W++ E DS DI++V+IDR RK+P+T+ L A G+  +EEIL  F       +         
Sbjct: 170 WLEYESDSNDIMYVKIDRTRKLPITALLRAFGLGSNEEILEVFGDDYRLLETIKKDETAG 229

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------- 301
              +      +      +  GE   +ES + L + +    +   +  +G           
Sbjct: 230 MKDER---DGLLEIYKRLRPGEPPTVESAQSLLNSMFFDDRRYDLARVGRYKYNKKLSLA 286

Query: 302 -CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR--DIPILYVDSVNNNAYI 358
             + G   AED+++ ETGE+  E G +  +    +I ++ I   ++ +L+         I
Sbjct: 287 TRITGQVAAEDVIDPETGEVLAEEGQIFKKDVAWQIQNAGINVVNVKVLHQGEEKIVRVI 346

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N              +DI+    P D+S   +   +           +       K + 
Sbjct: 347 GNG------------FVDIHTQDIPFDISDLEIK-ELVCREALMQILDNDEMTDEEKHDE 393

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             N       +HI + D+ A +   + +  G G  DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 394 IKNHMERLVPKHILQSDLFATVSYFIGIDYGIGNTDDIDHLGNRRLRSVGELLQNQFRIG 453

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER+S  D + + PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH 
Sbjct: 454 LSRMERVVRERMSVQDDEILTPQGLINTRPVNAALKEFFGSSQLSQFMDQNNPLSELTHK 513

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL +FARVN YGFI
Sbjct: 514 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLATFARVNEYGFI 573

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILV 656
           E+PYRKV DG VT+++ YLSA EE    IAQAN  LDE+  F  E +  R     + + V
Sbjct: 574 ESPYRKVIDGVVTDEIHYLSADEEGQYAIAQANEPLDENNRFVNEQITGRAGSSRDFVTV 633

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             +++DF+D SPKQVVS+A +LIPFLENDD+NR LMG NMQRQAVPLL  +AP VGTGME
Sbjct: 634 APDRVDFMDISPKQVVSVATALIPFLENDDANRALMGANMQRQAVPLLIPKAPVVGTGME 693

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SG   +A  AG VE VDA  I IR        S   ++ ++L+KF+RSNQ TCV
Sbjct: 694 HKAAKDSGVCAIAGEAGTVEFVDADHIRIRRD------SDGSLEKHKLLKFKRSNQGTCV 747

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ+PLV  G  V+  +IIADGPST++G+LALGRN L+ FM W GYN+ED++LI+E M+  
Sbjct: 748 NQKPLVVQGQRVKAGEIIADGPSTEMGELALGRNALIGFMTWEGYNYEDAVLINENMLKT 807

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D +TSIHIEEFE  AR+TKLGPEEITRDIPNV E+ L+N+DE GI+ VGAEV   DILVG
Sbjct: 808 DKYTSIHIEEFECEARETKLGPEEITRDIPNVGEDALRNLDERGIVFVGAEVKSEDILVG 867

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           K+TPKGE+ ++ EEKLLRAIFGEKA ++RDTSL+VP G +G VVDV++F+R   D++
Sbjct: 868 KVTPKGETDLSAEEKLLRAIFGEKAREIRDTSLKVPHGEAGIVVDVKVFSRANKDED 924



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/542 (32%), Positives = 242/542 (44%), Gaps = 76/542 (14%)

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +  R    G  E  + +          +++  ++  G  V  G+I+    + +    +  
Sbjct: 720  IRIRRDSDGSLEKHKLLKFKRSNQGTCVNQKPLVVQGQRVKAGEIIADGPSTE-MGELAL 778

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIEL 966
                L      +  +  D  L   + +               +  E  +  E     I  
Sbjct: 779  GRNALIGFMTWEGYNYEDAVLINENMLKTDKYTSIHIEEFECEARETKLGPEEITRDIPN 838

Query: 967  LARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            +  D     DE+ I+      +  +IL G+    G         L   +  E  R     
Sbjct: 839  VGEDALRNLDERGIVFVGAEVKSEDILVGKVTPKGETDLSAEEKLLRAIFGEKARE-IRD 897

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
             +++    +  +      +  +    +               + PGV  +V+V++A KR 
Sbjct: 898  TSLKVPHGEAGIVVDVKVFSRANKDED---------------LKPGVNTMVRVYIATKRK 942

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I  GDKMAGRHGNKG+VSR+LP EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG 
Sbjct: 943  ISVGDKMAGRHGNKGVVSRVLPQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGM 1002

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG  I + + D     DI  L    +                              
Sbjct: 1003 AVKALGWHIATPVFDPANEEDIEELLEKADLPSDGKIKL--------------------- 1041

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                        G++       GEPFD PVTVGY+Y LKL+H+V
Sbjct: 1042 --------------------------YDGRT-------GEPFDNPVTVGYMYYLKLHHLV 1068

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVV
Sbjct: 1069 DDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTIKSDDVV 1128

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            GR   YE+IV G +  + G PESF VL+KE Q+L L + + N          +  D    
Sbjct: 1129 GRVAAYEAIVKGENIPKPGIPESFKVLMKEFQSLALDVQILNDDEVVEILDGDFADDPVE 1188

Query: 1384 EL 1385
            EL
Sbjct: 1189 EL 1190


>gi|260880967|ref|ZP_05403288.2| DNA-directed RNA polymerase, beta subunit [Mitsuokella multacida
           DSM 20544]
 gi|260850069|gb|EEX70076.1| DNA-directed RNA polymerase, beta subunit [Mitsuokella multacida
           DSM 20544]
          Length = 1240

 Score =  822 bits (2124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 439/955 (45%), Positives = 588/955 (61%), Gaps = 102/955 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++++P L+++Q+ SY  FL          ++GLQ  F  + PI  FSG
Sbjct: 9   KRTRYSYARIKEVMEMPHLLDIQRNSYQWFL----------DKGLQEIFHDISPIQDFSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+T A PL++ +RLI          +   +IKEQ +
Sbjct: 59  NLVLSFESFSLGEPKYDLDECKERDVTLAAPLRVNVRLI---------NRETGEIKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +       GK LY   +IP++G 
Sbjct: 110 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGAYYGEEIDPT---GKHLYNATVIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIV--YSQRGDFWCF 247
           W+++E D+ D++ VRIDR RK+PVT F+ ALG D++E I+  F        +   D    
Sbjct: 167 WIELETDTNDVVSVRIDRTRKMPVTYFIRALGFDTDEKIIELFGDDPRMLNTIERDG--- 223

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS------ 300
                    G  V      +  GE   E +  +L + L    K   +  +G         
Sbjct: 224 ---EEVKSQGKAVIEIYKRLRPGEPANEDNATQLLNSLFFDPKRYDLATVGRYKLTKKLG 280

Query: 301 --DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               + G  +AE IV+ ETGEI I  G+V+ E  L                         
Sbjct: 281 WKRRILGKVLAEPIVDHETGEIVIPQGEVVTEDML------------------------- 315

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                                     D       + +F      +         +V++  
Sbjct: 316 --------------------------DAVDVEREKQIFGEGNLITLFLLKKDGTKVRLLC 349

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
              LD  D  R I K DI+A I  L++L +G GT DDID+LGNRRVR+VGE+L+NQ+R+G
Sbjct: 350 SPTLDIHD--RTITKNDILASISYLLNLMDGFGTTDDIDHLGNRRVRAVGELLQNQFRIG 407

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER++  D+D + PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH 
Sbjct: 408 LSRMERVVRERMTIQDVDVITPQALINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHK 467

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+
Sbjct: 468 RRLSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLATYARVNQFGFM 527

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYR+V   + +VT++V YL+A EE+   IAQAN  LDE+  F  E V  R   E  L 
Sbjct: 528 ETPYRRVDKENHRVTDEVRYLTADEEDELVIAQANEPLDENEWFVNERVTARYNEETGLH 587

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            RE +D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME
Sbjct: 588 TRETVDYMDVSPRQVFSIATTMIPFLENDDANRALMGANMQRQAVPLLRTQAPLVGTGME 647

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  SG  ++AKRAG+VE+V A  I +R+  G+LD        Y+L KF RSNQ TC+
Sbjct: 648 YKAACDSGVMVLAKRAGVVEEVTADYINVRTESGELD-------HYKLQKFLRSNQGTCI 700

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P+V  GDEV     IADGP+TD G+LALG N++VA+MPW GYN+ED++L+SE +V  
Sbjct: 701 NQVPIVYKGDEVEEKQPIADGPATDHGELALGYNIIVAYMPWEGYNYEDAVLLSENLVKR 760

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D++TSIHIEE+E  ARDTKLGPEEITRDIPNV+EE LK++DE GII +GA+V PGDILVG
Sbjct: 761 DIYTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEEGIISIGADVRPGDILVG 820

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G +VDV+IF+R   D
Sbjct: 821 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEQGKIVDVKIFSRENND 875



 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 197/529 (37%), Positives = 272/529 (51%), Gaps = 50/529 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T+ G  +  +    +       I++  I+  G EV     +           +     +
Sbjct: 677  RTESGELDHYKLQKFLRSNQGTCINQVPIVYKGDEVEEKQPIADGP-ATDHGELALGYNI 735

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            + A    +  +  D  L   + V   +      +    + + R   +  E+I        
Sbjct: 736  IVAYMPWEGYNYEDAVLLSENLVKRDI--YTSIHIEEYECDARDTKLGPEEITRDIPNVA 793

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D D+E  I+      R  +IL G+    G         L   +  E  R      
Sbjct: 794  EEALKDLDEE-GIISIGADVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 846

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI   +  D++PPGV R+V+V++A KR I
Sbjct: 847  -----EVRDTSLRVPHGEQGKIVDV------KIFSRENNDELPPGVNRLVRVYIAQKRKI 895

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQI E HLG A
Sbjct: 896  SVGDKMAGRHGNKGVVSRIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQILEAHLGRA 955

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
             + +GK+IK                                    D   L + +   +G+
Sbjct: 956  VLEIGKQIKE---------------------HNPTIEQRLRDLGYDVDRLGMPKPDVAGL 994

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             ++TPVFDGA +E +   ++ A L   G+++LYDG TGEPF+  VTVG  Y LKL+H+V 
Sbjct: 995  HIATPVFDGASDEEVFGTIKAAGLPVDGKTVLYDGRTGEPFENRVTVGCTYFLKLHHLVD 1054

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVG
Sbjct: 1055 DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVG 1114

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            R + YE+IV G +  E G PESF VL+KE+Q++GL I + N   K    
Sbjct: 1115 RVKAYEAIVKGENIPEPGVPESFKVLIKELQSIGLDIKVLNEDAKEITI 1163


>gi|291518238|emb|CBK73459.1| DNA-directed RNA polymerase subunit beta [Butyrivibrio fibrisolvens
           16/4]
          Length = 1301

 Score =  822 bits (2124), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/960 (44%), Positives = 587/960 (61%), Gaps = 65/960 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++++P+LIEVQK SYD F+           +GL+ AF  + PI     
Sbjct: 13  KNLRMSYSRQKEVLEMPNLIEVQKDSYDWFV----------KDGLKEAFADISPIQDRGN 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L FV +    D  K+ +  C  RD TYA PLK+ +RL+          K   D++E 
Sbjct: 63  QLELHFVDFTLCKDEVKYTIPQCKERDATYAAPLKVKVRLV---------NKESGDMQEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP++
Sbjct: 114 EIFMGDLPLMTDTGTFVINGAERVIVSQLVRSPGIYYAIGHDKI---GKELYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVPVT  + ALG+ + +EI+  F    KI+ +   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRNRKVPVTVLIRALGLGTNQEIIDVFGEEPKILATFAKDPA 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS---- 300
               +      G  +      +  GE + + S + L  G+    +   +  +G       
Sbjct: 231 ITEKNPQGSYEGG-LLELYRRLRPGEPLAKDSAESLIHGMFFDPRRYDLAKVGRYKFNKK 289

Query: 301 ----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
               + + G  +AED+++  TGEI  +AGD +  +  EEI ++ +  +   ++ +   N 
Sbjct: 290 LMLKNRITGHVLAEDVIDTTTGEIIAKAGDKVTLEMAEEIQNAAVTHV---FIQTETRNV 346

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            + + ++ D  K          + +   ++  + V E +        D  D         
Sbjct: 347 KVLSNMMVDITKFVD----CDAKALGITELVYYPVLERILEENTTKEDIEDAIA------ 396

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                       +HI  EDI A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR
Sbjct: 397 ----RSVADLIPKHITVEDIFASINYNMHLEYGIGKEDDIDHLGNRRIRAVGELLQNQYR 452

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL R+E+ ++ER+++ D++ + PQ+LIN KPV +A+ EFF SSQLSQ     N LS +T
Sbjct: 453 IGLSRLEKVVRERMTTRDLEDISPQNLINIKPVTAAIKEFFGSSQLSQFMVQNNPLSELT 512

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YG
Sbjct: 513 HKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARINEYG 572

Query: 597 FIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           F+E PYR++      + +VT++VVY++A EE+N ++AQAN  LDE+G F  + V  R   
Sbjct: 573 FVEAPYRRIDKSDPQNPRVTDEVVYMTADEEDNYHVAQANVKLDEEGHFMRKNVSGRFRE 632

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E     +   D++D SPK V S+A + IPFL+NDD  R LMG NMQRQAVPLL  EAP V
Sbjct: 633 ETQEYDKTMFDYMDVSPKMVFSVATASIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVV 692

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  +VAKRAGIVE  +  RI++++ E          D Y L KF RSN
Sbjct: 693 GTGMEPKTAVDSGVCVVAKRAGIVEMSETNRIIVKADE------DGTRDEYTLFKFTRSN 746

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+ C NQRP+V  GD V   ++IADGPST  G+LALG+N L+ FM W GYN+ED++L+SE
Sbjct: 747 QSNCYNQRPIVFKGDHVEAGEVIADGPSTKNGELALGKNPLIGFMTWEGYNYEDAVLLSE 806

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE+E+ ARDTKLGPEEITRD+  V ++ LK++DE GII +GAEV  G
Sbjct: 807 RLVQDDVYTSIHIEEYEIDARDTKLGPEEITRDVAGVGDDALKDLDESGIIRIGAEVRAG 866

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+  TPEE+LL AIFGEKA +VRDTSLRVP G  G VVD ++F R   D
Sbjct: 867 DILVGKVTPKGETERTPEERLLLAIFGEKAREVRDTSLRVPHGAYGIVVDAKVFTRENGD 926



 Score =  544 bits (1401), Expect = e-152,   Method: Composition-based stats.
 Identities = 240/1055 (22%), Positives = 405/1055 (38%), Gaps = 90/1055 (8%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +  LL++YR +RPG+      AES+ + +FFD  +YDL+ VGR K N +L L      
Sbjct: 239  SYEGGLLELYRRLRPGEPLAKDSAESLIHGMFFDPRRYDLAKVGRYKFNKKLMLKNRITG 298

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              + ++ I      ++     K T++  + + N  V  V       +     R  + +  
Sbjct: 299  HVLAEDVIDTTTGEIIAKAGDKVTLEMAEEIQNAAVTHV-------FIQTETRNVKVLSN 351

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQ 546
             +       V     ++       + E      L ++ E   +   I     R ++ L  
Sbjct: 352  MM-------VDITKFVDCDAKALGITELVYYPVLERILEENTTKEDIEDAIARSVADLIP 404

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              +        +       YG     +     N   + ++    +      +    + V 
Sbjct: 405  KHITVEDIFASINYNMHLEYGIGKEDDIDHLGN-RRIRAVGELLQNQYRIGLSRLEKVVR 463

Query: 607  DGKVTNDVVYLS------------AMEEE-------NRYIAQANSSLDEDGSFTEELVFC 647
            +   T D+  +S            A++E           +     S          L   
Sbjct: 464  ERMTTRDLEDISPQNLINIKPVTAAIKEFFGSSQLSQFMVQNNPLSELTHKRRLSALGPG 523

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              + +        + +        +         L N  ++   +           ++A 
Sbjct: 524  GLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLASYARI------NEYGFVEAP 577

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               +          +     +         V    + +      +  + SG       ++
Sbjct: 578  YRRIDKSDPQNPRVTDEVVYMTADEEDNYHVAQANVKLDEEGHFMRKNVSGRFREETQEY 637

Query: 768  QRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             ++  +   V+ + +  V         +                  +L    P  G   E
Sbjct: 638  DKTMFDYMDVSPKMVFSVATASIPFLQNDDPTRALMGSNMQRQAVPLLTTEAPVVGTGME 697

Query: 825  DSMLISERMVSEDVFTSIHIEEFE----VMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
                +   +    V     I E      ++ +  + G  +                ++  
Sbjct: 698  PKTAVDSGVC--VVAKRAGIVEMSETNRIIVKADEDGTRDEYTLFKFTRSNQSNCYNQRP 755

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G+++    + K    +   +  L      +  +  D  L         V 
Sbjct: 756  IVFKGDHVEAGEVIADGPSTKN-GELALGKNPLIGFMTWEGYNYEDAVLL----SERLVQ 810

Query: 941  DVRIFNRH--GIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEIL 990
            D    + H    + + R   +  E+I        +   +D  DE  I+      R  +IL
Sbjct: 811  DDVYTSIHIEEYEIDARDTKLGPEEITRDVAGVGDDALKDL-DESGIIRIGAEVRAGDIL 869

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+    G         L   +  E  R                 E              
Sbjct: 870  VGKVTPKGETERTPEERLLLAIFGEKAR-----------------EVRDTSLRVPHGAYG 912

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMP
Sbjct: 913  IVVDAKVFTRENGDELSPGVNKSVRIYIAQKRKIGVGDKMAGRHGNKGVVSRVLPVEDMP 972

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I++ + D     DI     
Sbjct: 973  YLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFDIETPVFDGAKEIDIQDTLE 1032

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                 +      E+  + ++    +  +  +  V             A  ++ +   +  
Sbjct: 1033 LANDYVNMPFDKEEAENGEETFYDKYVDILREDVMEYLS-----TNRAHRALWKGVPISR 1087

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+  L DG TG+PFD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  G
Sbjct: 1088 DGKVQLRDGRTGQPFDGPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1147

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G +  E G PESF VL
Sbjct: 1148 GQRFGEMEVWALEAYGASYTLQEILTMKSDDVIGRVKTYEAIIKGENIPEPGIPESFKVL 1207

Query: 1351 VKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            +KE+Q+LGL + + +   +    ME   ++   +L
Sbjct: 1208 LKELQSLGLDVRVLDENREEVELMET-SEYGNTDL 1241


>gi|317472305|ref|ZP_07931633.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
 gi|316900262|gb|EFV22248.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
          Length = 1258

 Score =  822 bits (2123), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/951 (45%), Positives = 589/951 (61%), Gaps = 58/951 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           +R  + +  +++++P+LIE+QK SY+ FL           EGL+  F+ + PI  +S   
Sbjct: 7   IRMSYARQDDVLEVPNLIEIQKDSYNWFLG----------EGLKEVFEDISPIGDYSDQL 56

Query: 73  MLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            LEF+ ++   D  K+ +++C  RD TYA P+K+ +RL           K   +IK+  I
Sbjct: 57  SLEFIDFKLCRDDIKYSIEECKERDATYAAPMKVKVRLH---------NKETDEIKQHDI 107

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++G 
Sbjct: 108 FMGDLPLMTDTGTFVINGAERVIVSQLVRSPGIYYGIAHDKI---GKKLYSATVIPNRGA 164

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWCF 247
           W++ E DS DI +VR+DR RKVP+T  + ALG+ +  EI   F    KI+ S   D    
Sbjct: 165 WLEYETDSNDIFNVRVDRTRKVPITVLIRALGIGTNAEIKELFGEEPKILASMEKDPSDN 224

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCG 305
                  +         + +D+ E +I S         L K  + K  K L    + + G
Sbjct: 225 YEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLAKVGRYKFNKKLAF-RNRITG 283

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AED+++  TGEI  EAG  +  +  ++I ++ ++   +L      N   + N  V  
Sbjct: 284 HMLAEDVIDTSTGEILAEAGTEVTLELADKIQNAAVQS--VLIQTEFGNTKVLSNMTVNL 341

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                              D     + E++F  +        LS         +   D  
Sbjct: 342 AEYVD-------------FDPEELGIHENVFYPVLEKILAEGLSGDELKAAVKKNIHDLI 388

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL R+ER 
Sbjct: 389 --PKHITKEDILASINYNMHLEYNIGNHDDIDHLGNRRIRAVGELLQNQYRIGLSRLERV 446

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+++ DI+++ PQ LIN KPV +AV EFF SSQLSQ  +H N LS +TH RRLSALG
Sbjct: 447 VRERMTTQDIETITPQSLINIKPVTAAVKEFFGSSQLSQFMDHNNPLSELTHKRRLSALG 506

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR +
Sbjct: 507 PGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYRVL 566

Query: 606 -----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
                 +  VT++VVYL+A EE+N  +AQAN  LDEDG F    V  R   +     +  
Sbjct: 567 DKTDPENPVVTDNVVYLTADEEDNFVVAQANEPLDEDGHFVHAHVSGRFREDTSEFDKAN 626

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGMES  A
Sbjct: 627 LDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLSTEAPVVGTGMESKAA 686

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  IVAK  G+VE+  + +IV+R        S  G DIY ++KF RSNQ  C+NQRP
Sbjct: 687 FDSGVCIVAKNDGVVEKSTSTKIVVRRD------SDGGKDIYNVIKFARSNQGNCMNQRP 740

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V+++DI+ADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV+T
Sbjct: 741 IVFEGDRVKKDDILADGASTKSGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYT 800

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           S+HIEE+E  ARDTKLG EEITRD+  +SE+ LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 801 SVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDENGIIRIGAEVRAGDILVGKVTP 860

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V+D +IF R   D
Sbjct: 861 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGAYGVVMDTKIFTRENGD 911



 Score =  559 bits (1441), Expect = e-156,   Method: Composition-based stats.
 Identities = 254/1057 (24%), Positives = 412/1057 (38%), Gaps = 78/1057 (7%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +       I  ++  D + + +D LL++Y+ +RPG+  +   AES+ N +FFD  +YDL+
Sbjct: 205  ELFGEEPKILASMEKDPSDNYEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLA 264

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L          + ++ I      ++     + T++  D + N  V+SV  
Sbjct: 265  KVGRYKFNKKLAFRNRITGHMLAEDVIDTSTGEILAEAGTEVTLELADKIQNAAVQSV-- 322

Query: 470  MLKNQYRLGLLRMERSIKERISSV---DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +++ ++  G  ++  ++   ++     D + +   + +    +   + E     +L    
Sbjct: 323  LIQTEF--GNTKVLSNMTVNLAEYVDFDPEELGIHENVFYPVLEKILAEGLSGDELKAAV 380

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY-GRICPAETSEGHNIGLVSS 585
            +         H  +   L                +H  +  G     +      I  V  
Sbjct: 381  KKNIHDLIPKHITKEDILASINYN----------MHLEYNIGNHDDIDHLGNRRIRAVGE 430

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LD 635
            L    +      +    R V +   T D+  ++     N     A               
Sbjct: 431  LL---QNQYRIGLSRLERVVRERMTTQDIETITPQSLINIKPVTAAVKEFFGSSQLSQFM 487

Query: 636  EDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +   EL   R             R   +  D        +     P   N      L
Sbjct: 488  DHNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSL 547

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                   +   +         T  E+ V   +   + A          A   +       
Sbjct: 548  ATYARINEYGFIEAPYRVLDKTDPENPVVTDNVVYLTADEEDNFVVAQANEPLDEDGHFV 607

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGR 809
                +           + +     V+ + +  V         +  A+             
Sbjct: 608  HAHVSGRFREDTSEFDKANLDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAV 667

Query: 810  NMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
             +L    P  G   E          +V+++          +++ R    G ++I   I  
Sbjct: 668  PLLSTEAPVVGTGMESKAAFDSGVCIVAKNDGVVEKSTSTKIVVRRDSDGGKDIYNVIKF 727

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +++  I+  G  V   DIL    + K    M   +  L      +  +  D 
Sbjct: 728  ARSNQGNCMNQRPIVFEGDRVKKDDILADGASTK-SGEMALGKNPLIGFMTWEGYNYEDA 786

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRN 981
             L     V   V        +  +  +  +  E          E + +D  DE  I+   
Sbjct: 787  VLLSERLVQEDVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDL-DENGIIRIG 845

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 846  AEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 888

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                          KI   + GD++PPGV + V+V++A KR I  GDKMAGRHGNKG++S
Sbjct: 889  LRVPHGAYGVVMDTKIFTRENGDELPPGVNKTVRVYIAQKRKISVGDKMAGRHGNKGVIS 948

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RILP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + +   
Sbjct: 949  RILPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKVLGFNVATPVFNGAD 1008

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              DI+                E  +D+ + S      +WK  V  +   F   + +    
Sbjct: 1009 EDDIAVTL-------------EMANDFANTSWEDFEAKWKDRVDGNVIEFLREN-QDHKK 1054

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                  +D +G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1055 DWEGVPIDSTGKVRLRDGRTGEEFDSPVTIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQ 1114

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G++  E 
Sbjct: 1115 PLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEAIIKGDNIPEP 1174

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            G PESF VL+KE Q+L L + + +   +     E + 
Sbjct: 1175 GIPESFKVLLKEFQSLALDVKVLDENAEEVEIKENVD 1211


>gi|313904457|ref|ZP_07837834.1| DNA-directed RNA polymerase, beta subunit [Eubacterium
           cellulosolvens 6]
 gi|313470793|gb|EFR66118.1| DNA-directed RNA polymerase, beta subunit [Eubacterium
           cellulosolvens 6]
          Length = 1300

 Score =  822 bits (2123), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/964 (43%), Positives = 588/964 (60%), Gaps = 69/964 (7%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  + +  E++++P+LIEVQK SYD FL           +GL+ AF  + PI  + G
Sbjct: 13  RNVRMTYQRQKEVLEMPNLIEVQKNSYDWFL----------KDGLKEAFDDISPIEDYGG 62

Query: 71  AAMLEFVSYEF--------DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
              LEFV +E         +  K+ +++C  RD TYA PLK+ +RL   + ++       
Sbjct: 63  KFSLEFVDFELCDGTRGTKNETKYSIEECKQRDATYAAPLKVKVRLCNHEKND------- 115

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +I E +I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C
Sbjct: 116 -EISEHTIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYGIGHDKL---GKELYSC 171

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E DS D+  VR+DR RKVP+T  L ALG+ +  EI+  F  +      
Sbjct: 172 TVIPNRGAWLEYETDSNDVFWVRVDRTRKVPITVLLRALGLGTNAEIVEYFGEEPKILAS 231

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
                       L+           I  GE + +ES + L  G+    +   +  +G   
Sbjct: 232 FGKDTATNYQEGLL------ELYKKIRPGEPLAVESAESLIRGMFFDARRYDLAKVGRYK 285

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + + G  +AED+VN  TGEI  EAG VID    +EI +S    + I   +  
Sbjct: 286 FNKKLALRNRISGKVLAEDVVNAATGEIVAEAGQVIDRALADEIQYSGAPFVWIKQEEDD 345

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            N   + N  V        D   +    +   +   +     +        ++Y      
Sbjct: 346 RNVKVMSNMFVD--ITRWVDISKEEAESIGITEEVYYPALAELM-------EQYPDEEEL 396

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +  +  R++   P   +HI +E+I A I   + L    G  DDID+LGNRR+R VGE+L+
Sbjct: 397 KEVLASRVHELIP---KHITREEIFASINYNMHLEYHIGNDDDIDHLGNRRIRCVGELLQ 453

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER+++ D+D++  Q LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 454 NQYRIGLSRLERVVRERMTTQDMDTISAQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 513

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG++R RAG+E+RD+H THYGR+CP ET EG NIGL++SL S+AR+
Sbjct: 514 GELTHKRRLSALGPGGLSRDRAGMEVRDIHYTHYGRMCPVETPEGPNIGLINSLASYARI 573

Query: 593 NAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           N YGF+E PYR++      +  VT +VVY++A EE+N ++AQAN  LDE+G F  + V  
Sbjct: 574 NEYGFVEAPYRRIDKTDPANPIVTKEVVYMTADEEDNYHVAQANEPLDEEGHFIHKNVSG 633

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E     +   D++D SP+ V S+A +L+PFL+NDD  R LMG NMQRQAVPLL  E
Sbjct: 634 RFREETQAYEKSMFDYMDVSPRMVFSVATALVPFLQNDDPTRALMGSNMQRQAVPLLFTE 693

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTGME   A  SG  +VA+++G++    +  I + + +G  D       +Y LMKF
Sbjct: 694 APAVGTGMEEKTAVDSGVCVVARKSGVITYSTSYEIRMDNDDGTRD-------VYHLMKF 746

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ+ C NQRP+V  GD V   ++IADGPST  G+LALG+N L+ FM W GYN+ED++
Sbjct: 747 ERSNQSNCYNQRPIVDKGDHVEAGEVIADGPSTCGGELALGKNPLIGFMTWEGYNYEDAV 806

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V +DV+TSIH+EE+E  ARDTKLGPEEIT+D+P V +E LK++DE GII +GAE
Sbjct: 807 LLSERLVQDDVYTSIHVEEYECEARDTKLGPEEITKDVPGVGDEALKDLDERGIIRIGAE 866

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD R+F R
Sbjct: 867 VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDARVFTR 926

Query: 948 HGID 951
              D
Sbjct: 927 ENGD 930



 Score =  559 bits (1441), Expect = e-156,   Method: Composition-based stats.
 Identities = 253/1063 (23%), Positives = 405/1063 (38%), Gaps = 69/1063 (6%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            V+       I  +   D   + ++ LL++Y+ +RPG+      AES+   +FFD+ +YDL
Sbjct: 219  VEYFGEEPKILASFGKDTATNYQEGLLELYKKIRPGEPLAVESAESLIRGMFFDARRYDL 278

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N +L L      + + ++ + A    +V            D +         
Sbjct: 279  AKVGRYKFNKKLALRNRISGKVLAEDVVNAATGEIVAEAGQVIDRALADEIQYSGA-PFV 337

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             + + +      R  + +      +     + ++   +  +   V     +  + Q  + 
Sbjct: 338  WIKQEE----DDRNVKVMSNMFVDITRWVDISKEEAESIGITEEVYYPALAELMEQYPDE 393

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVE-MRDVHPT-HYGRICPAETSEGHNIGLVSSL 586
                  +    R+  L    + R         ++H   H G     +      I  V  L
Sbjct: 394  EELKEVLAS--RVHELIPKHITREEIFASINYNMHLEYHIGNDDDIDHLGNRRIRCVGEL 451

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                +      +    R V +   T D+  +SA    N     A        S   + + 
Sbjct: 452  L---QNQYRIGLSRLERVVRERMTTQDMDTISAQSLINIKPVTAAVKEFFGSSQLSQFMD 508

Query: 647  CRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL- 704
                 GE     R          +    +    I +        V          +  L 
Sbjct: 509  QNNPLGELTHKRRLSALGPGGLSRDRAGMEVRDIHYTHYGRMCPVETPEGPNIGLINSLA 568

Query: 705  ----KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
                  E  FV      +        IV K    +   +     +      LD     + 
Sbjct: 569  SYARINEYGFVEAPYRRIDKTDPANPIVTKEVVYMTADEEDNYHVAQANEPLDEEGHFIH 628

Query: 761  IYRLMKFQRSNQNT------CVNQRPL----VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                 +F+   Q         ++  P     V         +                  
Sbjct: 629  KNVSGRFREETQAYEKSMFDYMDVSPRMVFSVATALVPFLQNDDPTRALMGSNMQRQAVP 688

Query: 811  MLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +L    P  G   E+   +     +V+       +   +E+   D   G  ++   +   
Sbjct: 689  LLFTEAPAVGTGMEEKTAVDSGVCVVARKSGVITYSTSYEIRM-DNDDGTRDVYHLMKFE 747

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEKAVDVRD 926
                    ++  I+  G  V  G+++    +  G      +  L+  +   G    D   
Sbjct: 748  RSNQSNCYNQRPIVDKGDHVEAGEVIADGPSTCGGELALGKNPLIGFMTWEGYNYEDAVL 807

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIY 983
             S R+      T + V  +     D       + ++     +   +D  DE+ I+     
Sbjct: 808  LSERLVQDDVYTSIHVEEYECEARDTKLGPEEITKDVPGVGDEALKDL-DERGIIRIGAE 866

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             R  +IL G+    G         L   +  E  R                 E      +
Sbjct: 867  VRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLK 909

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                        ++   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+
Sbjct: 910  VPHGEYGIVVDARVFTRENGDELSPGVNQSVRIYIAQKRKISIGDKMAGRHGNKGVVSRV 969

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMP+L +G P+DIVLNPLGVPSRMN+GQI E HL  A + LG  I + + D     
Sbjct: 970  LPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQILEIHLSLAAMALGFNISTPVFDGANEV 1029

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            DI                 E    Y D  +  V +                      ++ 
Sbjct: 1030 DIQDTLELAND-YVNMEWDEFYEKYKDTLLPEVMQYLSD-------------NRDHRALW 1075

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +   +  +G+  L DG TGEPFD P T+G+++ LKL+H+V DK++ARSTG YSLVTQQPL
Sbjct: 1076 KGVPISRTGKVQLRDGRTGEPFDGPTTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPL 1135

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G +  E G 
Sbjct: 1136 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGI 1195

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            PESF VL+KE+Q+L L I + +   +    ME + D+     +
Sbjct: 1196 PESFKVLLKELQSLALDIQVLDENGEEVKIMESV-DYGNTSFR 1237


>gi|227871693|ref|ZP_03990104.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
 gi|227842449|gb|EEJ52668.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
          Length = 1311

 Score =  822 bits (2122), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/967 (43%), Positives = 587/967 (60%), Gaps = 67/967 (6%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G   +R  F ++ E++++P+LIE+QK SY+ FL           EGL+ AF  +
Sbjct: 18  MHPVQTG-KNLRMTFSRSKEVLEMPNLIEIQKDSYEWFLH----------EGLREAFDDI 66

Query: 63  FPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            PI  F+G   LEFV+++   +  K+ +++C  RD TYA PLK+ +RL   D +      
Sbjct: 67  SPIQDFAGHLSLEFVNFKLAKEEAKYSIEECKERDATYAAPLKVKVRLFNKDKE------ 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +I E  I+MGDLPLMT++G+FVI G +R++VSQL RSPGI++  D  +    GK LY
Sbjct: 121 ---EINEHEIFMGDLPLMTENGSFVINGAERVIVSQLVRSPGIYYGVDHDKV---GKELY 174

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYS 239
           +  +IP++G W++ E DS D+  VR+DR RKVPVT F+ ALG+  +++IL  F       
Sbjct: 175 SSTVIPNRGAWIEYETDSNDVFFVRVDRTRKVPVTVFIRALGVGSNKDILDLFGEDPKLL 234

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGI 298
              D          L+           I  GE + ++S + L + +    +   +  +G 
Sbjct: 235 ASIDKDPSENYQEGLL------ELYKKIRPGEPLSVDSAQSLLNSMFFDPRRYDLAKVGR 288

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + + G  +AE +   ETGE   EAG  + ++  E+I ++    +P +++D
Sbjct: 289 YKFNKKLHFKNRIKGHVLAEAVYAPETGEQLAEAGATVSQELAEQIQNA---AVPFVWID 345

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  + +++  D           I   +             +  +         +  
Sbjct: 346 GPTRTEKVLSSMQVD-----------IKEWIPASINPEECGINELVFYPALKELLASVEG 394

Query: 411 VGRVKMNMRLNLDT-PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G   +   +  +      +HI KEDI A I  L++L    GT+DDID+LGNRR+R+VGE
Sbjct: 395 QGEDALRDGIRKNIHSLIPKHITKEDIFASINYLLNLDEEIGTVDDIDHLGNRRIRAVGE 454

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQYR+GL RMER ++ER+S+ DID + PQ LIN KPV +AV EFF SSQLSQ  +  
Sbjct: 455 LLQNQYRIGLSRMERVVRERMSTQDIDEITPQSLINIKPVTAAVKEFFGSSQLSQFMDQN 514

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+
Sbjct: 515 NPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASY 574

Query: 590 ARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           AR+N YGFIE PY  V      +  VTN  VYL+A EE+   +AQAN  LDE+G F  + 
Sbjct: 575 ARINEYGFIEAPYLVVDKTDPANPVVTNQAVYLAADEEDQFVVAQANEPLDEEGHFKHDN 634

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   +    P+  ID +D SPK V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL
Sbjct: 635 VSGRYRDQTSAFPKTSIDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLL 694

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
             E+  V TGM S  A  SGA +VAK +G V    + RI+I+  +        G+D Y+L
Sbjct: 695 ITESAVVDTGMSSKAAVDSGACVVAKNSGEVTLSSSARILIKRDK------DGGIDEYKL 748

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           MKF RSN + C NQ+P+V   D V   D+IADGPST  G++ALG+N L+ FM W GYN+E
Sbjct: 749 MKFMRSNPSNCYNQKPIVNTHDRVEAGDVIADGPSTKDGEIALGKNPLIGFMTWEGYNYE 808

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++L+SER+V  DV+TS+HIEE+E  ARDTKLGPEEIT D+P V ++ LKN+DE GII +
Sbjct: 809 DAVLLSERLVQNDVYTSVHIEEYECEARDTKLGPEEITSDVPGVGDDALKNLDERGIIRI 868

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GDILVG++TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  GTV++  +
Sbjct: 869 GAEVRAGDILVGRVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGTVINTMV 928

Query: 945 FNRHGID 951
           + R   D
Sbjct: 929 YTRENSD 935



 Score =  532 bits (1371), Expect = e-148,   Method: Composition-based stats.
 Identities = 235/1064 (22%), Positives = 410/1064 (38%), Gaps = 80/1064 (7%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            D    +  +  ++  D +++ ++ LL++Y+ +RPG+  +   A+S+ N +FFD  +YDL+
Sbjct: 225  DLFGEDPKLLASIDKDPSENYQEGLLELYKKIRPGEPLSVDSAQSLLNSMFFDPRRYDLA 284

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L+         +      A+       +  +        L  +   +   
Sbjct: 285  KVGRYKFNKKLHFKNRIKGHVL----AEAVYAPETGEQLAEAGATVSQELAEQIQNAAVP 340

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             +   +  G  R E+ +      VDI   +P  +   +  ++ +  +    +L    E  
Sbjct: 341  FV---WIDGPTRTEKVLSSMQ--VDIKEWIPASINPEECGINELVFYPALKELLASVEGQ 395

Query: 530  NSLSRITHTRRL-SALGQGGVARARAGVEMRDVHP--THYGRICPAETSEGHNIGLVSSL 586
               +     R+   +L    + +      +  +       G +   +      I  V  L
Sbjct: 396  GEDALRDGIRKNIHSLIPKHITKEDIFASINYLLNLDEEIGTVDDIDHLGNRRIRAVGEL 455

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDE 636
                +      +    R V +   T D+  ++     N     A               +
Sbjct: 456  L---QNQYRIGLSRMERVVRERMSTQDIDEITPQSLINIKPVTAAVKEFFGSSQLSQFMD 512

Query: 637  DGSFTEELVFCRC---------AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
              +   EL   R          + +        + +        +         L N  +
Sbjct: 513  QNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLA 572

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            +   +           ++A    V     +    ++ A  +A        V      +  
Sbjct: 573  SYARI------NEYGFIEAPYLVVDKTDPANPVVTNQAVYLAADEEDQFVVAQANEPLDE 626

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGD 804
                   + SG    +   F +++ +   V+ + +  V         +  A+        
Sbjct: 627  EGHFKHDNVSGRYRDQTSAFPKTSIDLMDVSPKMVFSVATSMIPFLQNDDANRALMGSNM 686

Query: 805  LALGRNMLV--AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  +L+  + +   G + + ++     +V+++           ++ +  K G  +  
Sbjct: 687  QRQAVPLLITESAVVDTGMSSKAAVDSGACVVAKNSGEVTLSSSARILIKRDKDGGIDEY 746

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI--FGEK 920
            + +  +        ++  I+     V  GD++    + K       +  L+  +   G  
Sbjct: 747  KLMKFMRSNPSNCYNQKPIVNTHDRVEAGDVIADGPSTKDGEIALGKNPLIGFMTWEGYN 806

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--DEQVIL 978
              D    S R+      T V +  +     D       +  +   +        DE+ I+
Sbjct: 807  YEDAVLLSERLVQNDVYTSVHIEEYECEARDTKLGPEEITSDVPGVGDDALKNLDERGII 866

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  R  +IL G+    G         L   +  E  R                 E  
Sbjct: 867  RIGAEVRAGDILVGRVTPKGETELTAEERLLRAIFGEKAR-----------------EVR 909

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                +             +   +  D++ PGV + V++++A KR I  GDKMAGRHGNKG
Sbjct: 910  DTSLKVPHGAYGTVINTMVYTRENSDELAPGVSQSVRIYIAQKRKIGVGDKMAGRHGNKG 969

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VSR+LP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + I D
Sbjct: 970  VVSRVLPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLELHLSLAAKALGIDVSTPIFD 1029

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                 DI          +            ++      A   +                 
Sbjct: 1030 GATEVDIQQTLLLANDYVNLSWEEFSEKHKEELDPEVYAYLGEHL--------------D 1075

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                 +   +   G+  L DG TGE FD P ++G+++ LKL+H+V DK++ARSTG YS+V
Sbjct: 1076 HRKEWQGVPIGIDGKIQLRDGRTGEKFDSPTSIGFMHYLKLHHLVDDKIHARSTGPYSMV 1135

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR + YE+I+ G + 
Sbjct: 1136 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTMKSDDVAGRVKTYEAIIKGQNI 1195

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
               G PESF VL+KEMQAL L + + +   +     E++ D N+
Sbjct: 1196 PAPGVPESFKVLLKEMQALCLDMRVLDENQQVVEITEDLYDANQ 1239


>gi|167748163|ref|ZP_02420290.1| hypothetical protein ANACAC_02907 [Anaerostipes caccae DSM 14662]
 gi|167652155|gb|EDR96284.1| hypothetical protein ANACAC_02907 [Anaerostipes caccae DSM 14662]
          Length = 1300

 Score =  821 bits (2121), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/951 (45%), Positives = 589/951 (61%), Gaps = 58/951 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           +R  + +  +++++P+LIE+QK SY+ FL           EGL+  F+ + PI  +S   
Sbjct: 49  IRMSYARQDDVLEVPNLIEIQKDSYNWFLG----------EGLKEVFEDISPIGDYSDQL 98

Query: 73  MLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            LEF+ ++   D  K+ +++C  RD TYA P+K+ +RL           K   +IK+  I
Sbjct: 99  SLEFIDFKLCRDDIKYSIEECKERDATYAAPMKVKVRLH---------NKETDEIKQHDI 149

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGDLPLMT  GTFVI G +R++VSQL RSPGI++     +    GK LY+  +IP++G 
Sbjct: 150 FMGDLPLMTDTGTFVINGAERVIVSQLVRSPGIYYGIAHDKI---GKKLYSATVIPNRGA 206

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWCF 247
           W++ E DS DI +VR+DR RKVP+T  + ALG+ +  EI   F    KI+ S   D    
Sbjct: 207 WLEYETDSNDIFNVRVDRTRKVPITVLIRALGIGTNAEIKELFGEEPKILASMEKDPSDN 266

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCG 305
                  +         + +D+ E +I S         L K  + K  K L    + + G
Sbjct: 267 YEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLAKVGRYKFNKKLAF-RNRITG 325

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +AED+++  TGEI  EAG  +  +  ++I ++ ++   +L      N   + N  V  
Sbjct: 326 HMLAEDVIDTSTGEILAEAGTEVTLELADKIQNAAVQS--VLIQTEFGNTKVLSNMTVNL 383

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                              D     + E++F  +        LS         +   D  
Sbjct: 384 AEYVD-------------FDPEELGIHENVFYPVLEKILAEGLSGDELKAAVKKNIHDLI 430

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              +HI KEDI+A I   + L    G  DDID+LGNRR+R+VGE+L+NQYR+GL R+ER 
Sbjct: 431 --PKHITKEDILASINYNMHLEYNIGNHDDIDHLGNRRIRAVGELLQNQYRIGLSRLERV 488

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+++ DI+++ PQ LIN KPV +AV EFF SSQLSQ  +H N LS +TH RRLSALG
Sbjct: 489 VRERMTTQDIETITPQSLINIKPVTAAVKEFFGSSQLSQFMDHNNPLSELTHKRRLSALG 548

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL ++AR+N YGFIE PYR +
Sbjct: 549 PGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATYARINEYGFIEAPYRVL 608

Query: 606 -----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
                 +  VT++VVYL+A EE+N  +AQAN  LDEDG F    V  R   +     +  
Sbjct: 609 DKTDPENPVVTDNVVYLTADEEDNFVVAQANEPLDEDGHFVHAHVSGRFREDTSEFDKAN 668

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPK V S+A S+IPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGMES  A
Sbjct: 669 LDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLLSTEAPVVGTGMESKAA 728

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  IVAK  G+VE+  + +IV+R        S  G DIY ++KF RSNQ  C+NQRP
Sbjct: 729 FDSGVCIVAKNDGVVEKSTSTKIVVRRD------SDGGKDIYNVIKFARSNQGNCMNQRP 782

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V+++DI+ADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V EDV+T
Sbjct: 783 IVFEGDRVKKDDILADGASTKSGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQEDVYT 842

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           S+HIEE+E  ARDTKLG EEITRD+  +SE+ LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 843 SVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDLDENGIIRIGAEVRAGDILVGKVTP 902

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V+D +IF R   D
Sbjct: 903 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGAYGVVMDTKIFTRENGD 953



 Score =  559 bits (1440), Expect = e-156,   Method: Composition-based stats.
 Identities = 254/1057 (24%), Positives = 412/1057 (38%), Gaps = 78/1057 (7%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +       I  ++  D + + +D LL++Y+ +RPG+  +   AES+ N +FFD  +YDL+
Sbjct: 247  ELFGEEPKILASMEKDPSDNYEDGLLELYKKIRPGEPLSVDSAESLINSMFFDPRRYDLA 306

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L          + ++ I      ++     + T++  D + N  V+SV  
Sbjct: 307  KVGRYKFNKKLAFRNRITGHMLAEDVIDTSTGEILAEAGTEVTLELADKIQNAAVQSV-- 364

Query: 470  MLKNQYRLGLLRMERSIKERISSV---DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +++ ++  G  ++  ++   ++     D + +   + +    +   + E     +L    
Sbjct: 365  LIQTEF--GNTKVLSNMTVNLAEYVDFDPEELGIHENVFYPVLEKILAEGLSGDELKAAV 422

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY-GRICPAETSEGHNIGLVSS 585
            +         H  +   L                +H  +  G     +      I  V  
Sbjct: 423  KKNIHDLIPKHITKEDILASINYN----------MHLEYNIGNHDDIDHLGNRRIRAVGE 472

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LD 635
            L    +      +    R V +   T D+  ++     N     A               
Sbjct: 473  LL---QNQYRIGLSRLERVVRERMTTQDIETITPQSLINIKPVTAAVKEFFGSSQLSQFM 529

Query: 636  EDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +   EL   R             R   +  D        +     P   N      L
Sbjct: 530  DHNNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSL 589

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                   +   +         T  E+ V   +   + A          A   +       
Sbjct: 590  ATYARINEYGFIEAPYRVLDKTDPENPVVTDNVVYLTADEEDNFVVAQANEPLDEDGHFV 649

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGR 809
                +           + +     V+ + +  V         +  A+             
Sbjct: 650  HAHVSGRFREDTSEFDKANLDLMDVSPKMVFSVATSMIPFLENDDANRALMGSNMQRQAV 709

Query: 810  NMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
             +L    P  G   E          +V+++          +++ R    G ++I   I  
Sbjct: 710  PLLSTEAPVVGTGMESKAAFDSGVCIVAKNDGVVEKSTSTKIVVRRDSDGGKDIYNVIKF 769

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +++  I+  G  V   DIL    + K    M   +  L      +  +  D 
Sbjct: 770  ARSNQGNCMNQRPIVFEGDRVKKDDILADGASTK-SGEMALGKNPLIGFMTWEGYNYEDA 828

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRN 981
             L     V   V        +  +  +  +  E          E + +D  DE  I+   
Sbjct: 829  VLLSERLVQEDVYTSVHIEEYEAEARDTKLGQEEITRDLAGLSEDVLKDL-DENGIIRIG 887

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 888  AEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 930

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                          KI   + GD++PPGV + V+V++A KR I  GDKMAGRHGNKG++S
Sbjct: 931  LRVPHGAYGVVMDTKIFTRENGDELPPGVNKTVRVYIAQKRKISVGDKMAGRHGNKGVIS 990

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RILP EDMP+L +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + +   
Sbjct: 991  RILPVEDMPYLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKVLGFNVATPVFNGAD 1050

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              DI+                E  +D+ + S      +WK  V  +   F   + +    
Sbjct: 1051 EDDIAVTL-------------EMANDFANTSWEDFEAKWKDRVDGNVIEFLREN-QDHKK 1096

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                  +D +G+  L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1097 DWEGVPIDSTGKVRLRDGRTGEEFDSPVTIGFMHYLKLHHLVDDKIHARSTGPYSLVTQQ 1156

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+GR + YE+I+ G++  E 
Sbjct: 1157 PLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIGRVKTYEAIIKGDNIPEP 1216

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            G PESF VL+KE Q+L L + + +   +     E + 
Sbjct: 1217 GIPESFKVLLKEFQSLALDVKVLDENAEEVEIKENVD 1253


>gi|313887928|ref|ZP_07821607.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312846094|gb|EFR33476.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 1247

 Score =  821 bits (2120), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/955 (44%), Positives = 598/955 (62%), Gaps = 46/955 (4%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G  R R  F +  E++ +P+L++VQ +SY   +           EGL+  F  V 
Sbjct: 3   HPVKYG-KRERMSFSRVDEVMSLPNLLDVQTSSYKWLI----------EEGLKEVFDDVS 51

Query: 64  PITAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           PI  +SG  +LEFV Y      K+D+D+   RD  Y+ PLK  +RLI             
Sbjct: 52  PIEDYSGNLILEFVDYHLSEDIKYDIDESKQRDTNYSAPLKAKVRLI---------NSET 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++MGDLPLMT  GTFVI G +R+VVSQL RSPG ++  ++ +    GK +Y+ 
Sbjct: 103 GEVKEQEVFMGDLPLMTPTGTFVINGAERVVVSQLVRSPGAYYKEERDKT---GKKIYSA 159

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY--S 239
            +IP++G W++ E D++ +I+VRIDR RK+P+T  L ALG++S +EI+           +
Sbjct: 160 TLIPNRGAWLEFETDAQGVINVRIDRTRKIPITILLRALGVESNQEIMDVIGESEAVLKT 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +           ID+ + + E+         L K  + K  K LG
Sbjct: 220 LEKDTTTNKSEALLEIYKKLRPGEPPTIDSAQSLFENMFFDDRRYDLAKVGRYKFNKKLG 279

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           I++  L G   AEDIV+  TGEI  EAG++++    E+I  + +  + +   ++  + + 
Sbjct: 280 ISA-RLEGNIPAEDIVDPMTGEILAEAGELLNRAKAEKIEAAGVNQVLVKTDENYEHASE 338

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
               +  +        L      +   +     + + ++     D++K+    V   K  
Sbjct: 339 NTIVIGNNFTFVDAYELDFDMEELGFKEKVYRPLFDELYEEYSEDTEKFKEELVKAHK-- 396

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                      ++I  +DIIA I     L N  G++DDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 397 -------ELSPKNILIDDIIAGINYQFGLMNNVGSVDDIDHLGNRRIRSVGELLQNQFRI 449

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G+ RMER I+ER++  D+D+  PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH
Sbjct: 450 GISRMERVIRERMTVQDVDATTPQSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLSELTH 509

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SLT++AR+N YGF
Sbjct: 510 KRRLSALGPGGLSRDRAGFEVRDVHNSHYGRMCPIETPEGPNIGLITSLTTYARINDYGF 569

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           IETPYRKV +G VT+ + YL+A  E  + IAQA+  LDE+  F E+ +  R   G   + 
Sbjct: 570 IETPYRKVVNGVVTDQIDYLTADVEYEQIIAQADERLDENNRFVEDRIAARGHGGNADIF 629

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             + ++++D SP+Q+V++  S+IPFLENDD+NR LMG NMQRQAVPLLK EAP VGTG+E
Sbjct: 630 DIKDVNYMDVSPQQIVAVGTSMIPFLENDDANRALMGANMQRQAVPLLKTEAPVVGTGIE 689

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SG  IV+K  G +++VD++ I +         S  G+D Y+L KF   NQ T +
Sbjct: 690 YRAAKDSGVVIVSKNKGKIKKVDSVHIEVERE------SDKGIDTYKLHKFMGGNQGTTI 743

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+VK GD V   +IIADGPSTD G++ALG+N+L+AFM W GYN+ED+ML+S+ +V +
Sbjct: 744 NQRPIVKEGDLVEAGEIIADGPSTDQGEMALGKNILIAFMNWEGYNYEDAMLVSQELVID 803

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DV TS+HIEE+E  ARDTKLGPEE+TRDIPNV E+ LK++D+ GII +GAEV PGDILVG
Sbjct: 804 DVLTSLHIEEYESEARDTKLGPEEVTRDIPNVGEDMLKDLDDRGIIRIGAEVKPGDILVG 863

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ ++ EE+LLR+IFGEKA +VRDTSLR+P G  G VVDV+ FNR   D
Sbjct: 864 KVTPKGETELSAEERLLRSIFGEKAREVRDTSLRLPHGEQGIVVDVKTFNRSDGD 918



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 187/575 (32%), Positives = 265/575 (46%), Gaps = 84/575 (14%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            + +        +++S+         S+HIE    + R++  G +   +    +       
Sbjct: 688  IEYRAAKDSGVVIVSKNKGKIKKVDSVHIE----VERESDKGID-TYKLHKFMGGNQGTT 742

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            I++  I+  G  V  G+I+    +   +  M   + +L A    +  +  D  L     V
Sbjct: 743  INQRPIVKEGDLVEAGEIIADGPST-DQGEMALGKNILIAFMNWEGYNYEDAMLVSQELV 801

Query: 936  SGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEI 989
               V+       +  +  +  +  E          E + +D DD   I+      +  +I
Sbjct: 802  IDDVLTSLHIEEYESEARDTKLGPEEVTRDIPNVGEDMLKDLDDR-GIIRIGAEVKPGDI 860

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                 E             
Sbjct: 861  LVGKVTPKGETELSAEERLLRSIFGEKAR-----------------EVRDTSLRLPHGEQ 903

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                  K      GD++ PGV  +V+VFVA KR IQ GDKM GRHGNKG++SR++P EDM
Sbjct: 904  GIVVDVKTFNRSDGDELQPGVNEMVRVFVATKRKIQVGDKMCGRHGNKGVISRVMPKEDM 963

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P++ DGTP+ IVLNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     DI    
Sbjct: 964  PYMPDGTPIQIVLNPLGVPSRMNLGQVLEVHLGLAAKKLGWHVATPVFDGANENDI---- 1019

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                     FD          L  A   
Sbjct: 1020 -----------------------------------------FD---------TLEEAGYS 1029

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G+  L DG TGE FD PVTVGY+YMLKL+H+V +K++ARSTG YSLVTQQPLGGK+  
Sbjct: 1030 RDGKIQLRDGRTGEEFDHPVTVGYMYMLKLHHLVDEKIHARSTGPYSLVTQQPLGGKAQF 1089

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA++ LQEMLT+KSDD+VGR + YE+IV G +  + G PESF V
Sbjct: 1090 GGQRFGEMEVWALEAYGASHTLQEMLTVKSDDIVGRVKTYEAIVKGENIPQPGVPESFKV 1149

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            L+KE+QAL L I + + +        +  +  K +
Sbjct: 1150 LIKELQALALEIQVLDEKGNEVDLEVDEDELTKID 1184


>gi|309807024|ref|ZP_07701006.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|312872517|ref|ZP_07732585.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2062A-h1]
 gi|325913090|ref|ZP_08175460.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners UPII
           60-B]
 gi|308166644|gb|EFO68841.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|311091879|gb|EFQ50255.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2062A-h1]
 gi|325477511|gb|EGC80653.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners UPII
           60-B]
          Length = 1223

 Score =  820 bits (2119), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/988 (42%), Positives = 594/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S
Sbjct: 159 GTTVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        K   +  +G 
Sbjct: 219 FTLEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + G V+  + ++++          L  D
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +          ++A+L         D  T    +           K D   
Sbjct: 331 DFKTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPER 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+
Sbjct: 365 VVKLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E++V  R
Sbjct: 541 VVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +
Sbjct: 601 HKEENLEVSPDKLDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG AI+AK AG+VE VDA  I +R  +  LD        Y L K++
Sbjct: 661 PLVGTGMEYRAAHDSGDAILAKAAGVVEYVDANVIKVRRDDKTLDE-------YVLEKYR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P V  G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPNVHCGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R 
Sbjct: 834 QDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELAPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  472 bits (1215), Expect = e-130,   Method: Composition-based stats.
 Identities = 166/523 (31%), Positives = 234/523 (44%), Gaps = 79/523 (15%)

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    KN ++   +  G +V  G+++           +   +  + A       +  
Sbjct: 711  KYRRSNATKNYNQTPNVHCGEKVVEGEVIADGP-AMENGELALGQNPIIAFATWNMYNYE 769

Query: 926  DTSLRVPSGVSG------TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            D  +     V         + D    +R      E          E   +D  DE  I+ 
Sbjct: 770  DAVMISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DEDGIVR 828

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+    G         L   +  E  R    +      +V      + 
Sbjct: 829  VGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHGGGGII 884

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                             +   + GD++ PGV ++V+V++  KR IQ GDKM+GRHGNKG 
Sbjct: 885  QNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGT 931

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D 
Sbjct: 932  IALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVATPVFDG 991

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                          ++ +  +  +   G    T ++DG      
Sbjct: 992  A----------------------------SEEDMWNMVREAGLGKDGKTVLYDG------ 1017

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                 TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVT
Sbjct: 1018 --------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGPYSLVT 1057

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    
Sbjct: 1058 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIP 1117

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 1118 KPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 1160


>gi|302190543|ref|ZP_07266797.1| DNA-directed RNA polymerase subunit beta [Lactobacillus iners AB-1]
 gi|309803787|ref|ZP_07697873.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|309804709|ref|ZP_07698774.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|309808789|ref|ZP_07702675.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|309809578|ref|ZP_07703435.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners SPIN
           2503V10-D]
 gi|312871529|ref|ZP_07731622.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           3008A-a]
 gi|308164196|gb|EFO66457.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|308166101|gb|EFO68319.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|308168025|gb|EFO70157.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|308170059|gb|EFO72095.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners SPIN
           2503V10-D]
 gi|311092924|gb|EFQ51275.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           3008A-a]
          Length = 1224

 Score =  820 bits (2119), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/988 (42%), Positives = 594/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S
Sbjct: 159 GTTVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        K   +  +G 
Sbjct: 219 FTLEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + G V+  + ++++          L  D
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +          ++A+L         D  T    +           K D   
Sbjct: 331 DFKTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPER 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+
Sbjct: 365 VVKLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E++V  R
Sbjct: 541 VVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +
Sbjct: 601 HKEENLEVSPDKLDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG AI+AK AG+VE VDA  I +R  +  LD        Y L K++
Sbjct: 661 PLVGTGMEYRAAHDSGDAILAKAAGVVEYVDANVIKVRRDDKTLDE-------YVLEKYR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P V  G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPNVHCGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R 
Sbjct: 834 QDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELAPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  472 bits (1215), Expect = e-130,   Method: Composition-based stats.
 Identities = 166/523 (31%), Positives = 234/523 (44%), Gaps = 79/523 (15%)

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    KN ++   +  G +V  G+++           +   +  + A       +  
Sbjct: 711  KYRRSNATKNYNQTPNVHCGEKVVEGEVIADGP-AMENGELALGQNPIIAFATWNMYNYE 769

Query: 926  DTSLRVPSGVSG------TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            D  +     V         + D    +R      E          E   +D  DE  I+ 
Sbjct: 770  DAVMISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DEDGIVR 828

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+    G         L   +  E  R    +      +V      + 
Sbjct: 829  VGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHGGGGII 884

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                             +   + GD++ PGV ++V+V++  KR IQ GDKM+GRHGNKG 
Sbjct: 885  QNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGT 931

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D 
Sbjct: 932  IALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVATPVFDG 991

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                          ++ +  +  +   G    T ++DG      
Sbjct: 992  A----------------------------SEEDMWNMVREAGLGKDGKTVLYDG------ 1017

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                 TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVT
Sbjct: 1018 --------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGPYSLVT 1057

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    
Sbjct: 1058 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIP 1117

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 1118 KPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 1160


>gi|218133821|ref|ZP_03462625.1| hypothetical protein BACPEC_01710 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991196|gb|EEC57202.1| hypothetical protein BACPEC_01710 [Bacteroides pectinophilus ATCC
           43243]
          Length = 1290

 Score =  820 bits (2118), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/961 (45%), Positives = 597/961 (62%), Gaps = 71/961 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           VR  + +  E++++P+LIEVQK SY  FL          +EGL  AF  + PI  +SG  
Sbjct: 15  VRMSYSRQKEVLEMPNLIEVQKNSYQWFL----------DEGLNEAFNDISPIGDYSGRW 64

Query: 73  MLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            L+F  +    D  K+ +++C  RD TYA PL++ +RL           K   ++K+  I
Sbjct: 65  SLDFTGFRLCTDEAKYTIEECKERDATYAAPLRVKVRL---------QDKQTGEMKDHEI 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGDLPLMT+ GTFVI G +R++VSQL RSPGI++D    +    GK LY+C +IP++G 
Sbjct: 116 FMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYDIQHDKI---GKELYSCTVIPNRGA 172

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-----------GMDSEEILSTFYP--KIV 237
           W++ E DS DI +VR+DR RKVPVT  + AL           G  +E+I++ F    K++
Sbjct: 173 WLEYETDSNDIFYVRVDRTRKVPVTVLIRALLTPTKDNAMING-SNEDIINIFGDEPKLL 231

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D           +         V +D  E +I++         L K  + K  K 
Sbjct: 232 ATIEKDVSTDHEKGLTELYKKIRPGEPVSVDNAESLIQAMFFDPRRYDLAKVGRYKFNKK 291

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L      + G  +AED+V  +TGE    AG V+  +  + I  +    +P +Y+ +    
Sbjct: 292 LNF-RTRIAGQTLAEDVVIEQTGE-TFPAGTVVTREIGQTIQDA---AVPYVYIQTEERK 346

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             + + L+ D  K   D   D  + +   +   F V +++        ++ D+ T+ +  
Sbjct: 347 VKVLSNLMVDVTK-WVDITEDEAKELGIVEPVYFPVLKTLLEN-----EEDDIKTLLKKN 400

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N  +        +HI  EDI A I   + L  G GT DDID+LGNRR+R+VGE+L+NQY
Sbjct: 401 VNDLIP-------KHITIEDIFASINYNLHLEYGIGTKDDIDHLGNRRIRAVGELLQNQY 453

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+ + D   +  Q+LIN KPV +AV EFF SSQLSQ  +  N L  +
Sbjct: 454 RIGLSRMERVVRERMQTQDQSGLSAQNLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGEL 513

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+AR+N Y
Sbjct: 514 THKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYARINEY 573

Query: 596 GFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           GFIE PYR +      + +VT++V YL+A EE++ Y+AQAN+ LDEDG F +  V  R  
Sbjct: 574 GFIEAPYRLIDKSDPQNPRVTDEVRYLTADEEDDFYVAQANAELDEDGHFVKNSVSGRYR 633

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E    P+ K+D +D SP+ V S+A S+IPFL+NDD+NR LMG NMQRQAVPLL  EAP 
Sbjct: 634 EETSEFPKSKLDLMDVSPRMVFSVATSMIPFLQNDDANRALMGSNMQRQAVPLLTTEAPV 693

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG  +VAK AG+VE   +  I +++ +        G D+YRL KF RS
Sbjct: 694 VGTGMEYKAAVDSGVCVVAKEAGVVEYSTSKEIAVKTKD--------GRDVYRLTKFARS 745

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+ C NQRP+V  GD+V +  +IADGPST  G++ALG+N L+ FM W GYN+ED++L+S
Sbjct: 746 NQSNCYNQRPIVFKGDKVEKGQVIADGPSTKNGEIALGKNPLIGFMTWEGYNYEDAVLLS 805

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +DV+TS+HIEE+E  ARDTKLGPEEITRD+P V  + LK++DE GII +GAEV  
Sbjct: 806 ERLVQDDVYTSVHIEEYETEARDTKLGPEEITRDVPGVGNDVLKDLDERGIIRIGAEVRA 865

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   
Sbjct: 866 GDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEYGIVVDAKVFTRENG 925

Query: 951 D 951
           D
Sbjct: 926 D 926



 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 182/542 (33%), Positives = 265/542 (48%), Gaps = 45/542 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             TK G + + R             ++  I+  G +V  G ++    + K       +  L
Sbjct: 729  KTKDGRD-VYRLTKFARSNQSNCYNQRPIVFKGDKVEKGQVIADGPSTKNGEIALGKNPL 787

Query: 913  LRAI--FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELL 967
            +  +   G    D    S R+      T V +  +     D       + R+       +
Sbjct: 788  IGFMTWEGYNYEDAVLLSERLVQDDVYTSVHIEEYETEARDTKLGPEEITRDVPGVGNDV 847

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D  DE+ I+      R  +IL G+    G         L   +  E  R         
Sbjct: 848  LKDL-DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 897

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E      +            K+   + GD++ PGV + V++++A KR I  G
Sbjct: 898  --------EVRDTSLKVPHGEYGIVVDAKVFTRENGDELGPGVNQTVRIYIAQKRKISVG 949

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   
Sbjct: 950  DKMAGRHGNKGVVSRILPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKA 1009

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIG---TGSHTEKISDYDDDSVLRVAEQWKSGV 1204
            LG  I + + D     DI          +         ++    DD+    + E      
Sbjct: 1010 LGFNISTPVFDGADEHDIMDTLDLANDYVNLEWDEFVAKRKGKIDDELFAYLEEN----- 1064

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                        +   +  +   +   G+  L DG TGE FD PVT+G+++ LKL+H+V 
Sbjct: 1065 ------------KDHRAEWKGVPISRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHLVD 1112

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV+G
Sbjct: 1113 DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVIG 1172

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            R + YE+I+ G++  E G PESF VL+KE+Q+L L + + +   +    ME + D+++ +
Sbjct: 1173 RVKTYEAIIKGDNIPEPGIPESFKVLLKELQSLALDVKVLDENGEEVDIMENV-DYSEGD 1231

Query: 1385 LK 1386
             K
Sbjct: 1232 FK 1233


>gi|289450656|ref|YP_003474536.1| DNA-directed RNA polymerase subunit beta [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289185203|gb|ADC91628.1| DNA-directed RNA polymerase, beta subunit [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 1254

 Score =  820 bits (2117), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/979 (44%), Positives = 595/979 (60%), Gaps = 55/979 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  + K  E+ID+PDL+EVQK SY  FL          +EGL    + V PIT FSG
Sbjct: 9   RTERMTYSKLREVIDMPDLVEVQKKSYQWFL----------DEGLMEVLQDVSPITDFSG 58

Query: 71  AAMLEFVS--YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L F+   ++ D P +D+ +C  RD  YA PL++ +RL     D          IK+Q
Sbjct: 59  DIELSFIDKEFDIDHPTYDIPECKDRDANYAAPLRVKVRLHNRRDDV---------IKDQ 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            IY+G+ P+MT  GTF+I G +R+++SQL RSPG +F + K     + K LY  ++IP++
Sbjct: 110 VIYVGEFPIMTDTGTFIINGAERVIISQLIRSPGAYFANLKDPK--TDKELYTSQLIPNR 167

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCF 247
           G W++ E D+ D ++VRIDR RK P+T FL +LGM + EEI+  F  +   +        
Sbjct: 168 GAWLEYETDANDTLYVRIDRTRKFPLTVFLRSLGMGTNEEIIEVFGDETPITATLAKDTC 227

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------ 300
                       ++     +  GE V IE  + L   +    K   +  +GI        
Sbjct: 228 ------RSQEEGLAELYRKLRPGEPVSIEGAETLLHNMFFDPKRYDLARIGIYKLNKKLG 281

Query: 301 --DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               L G   AE+IV+   GE+   AGD+++ +  +EI ++ I  +P+  +  +  +   
Sbjct: 282 LAARLVGHKAAENIVDA-NGEVLAMAGDILNAEVAKEIQNAGINVVPVHAIVVIGESVME 340

Query: 359 RNTLVTDKNKDRKDALLDIYRVM-----RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
              +      +R DA L + RV+        D+S  +            ++      V  
Sbjct: 341 DEKVFKIIGNNRVDARLYLQRVLGAAKAAQVDLSPLNEMVRTSVLAELLAEAEASDDVVA 400

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
              +           +H+  EDIIA I   + L +G G  DDID+LGNRR+RSVGE+L+N
Sbjct: 401 TLSSSIKARKNDLMPKHLTIEDIIASISYFLGLDHGIGGTDDIDHLGNRRIRSVGELLQN 460

Query: 474 QYRLGLLRMERSIKERI-SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           Q R+G  RMER ++ER+ +  D +S  PQ L+N +P+ +A+ EFF SSQLSQ  +  N+L
Sbjct: 461 QVRIGFARMERVVRERMGTLADAESATPQMLVNTRPISAAIKEFFGSSQLSQFMDQPNAL 520

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RA  E+RDVH +HYGR+CP ET EG NIGL++SL ++ARV
Sbjct: 521 AELTHKRRLSALGPGGLSRDRANFEVRDVHSSHYGRMCPIETPEGPNIGLINSLATYARV 580

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR     +  VT++V Y++A EE+N YIAQAN+ LDE+G FT   V  R  
Sbjct: 581 NEYGFIETPYRVYDKERGVVTDEVRYMTADEEDNYYIAQANAPLDEEGHFTCNKVTVRLL 640

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            + + V    +D +D SPKQ+VS+A SLIPFL NDD+NR LMG NMQRQAVPL+K EAP 
Sbjct: 641 DKFLEVEPSMVDLMDVSPKQLVSVATSLIPFLGNDDANRALMGSNMQRQAVPLIKPEAPI 700

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           +GTGME   AK SG   VAK  G V+ V A +IV+       +      D Y L K++RS
Sbjct: 701 IGTGMEYRTAKDSGVCAVAKHDGTVDYVSANKIVV-------NGGPGIADTYNLAKYRRS 753

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC+NQRPLV  GD+V+  DIIADGPST+ G+LALG+N+L+ FM W GYN+ED++L++
Sbjct: 754 NQSTCINQRPLVAKGDKVKAGDIIADGPSTENGELALGKNVLIGFMTWEGYNYEDAVLLN 813

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED++TSIHIEE+E  ARDTKLG EEITR+IPNV ++ LK++DE GI+ +GAEV  
Sbjct: 814 ERLVKEDIYTSIHIEEYECEARDTKLGSEEITREIPNVGDDSLKDLDEHGIVRIGAEVRT 873

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+L RAIFGEK  +VRDTS+RVP G SG VVDV++F+R   
Sbjct: 874 GDILVGKVTPKGETELTAEERLYRAIFGEKVREVRDTSVRVPHGESGIVVDVKVFDREKD 933

Query: 951 DKNERSISVEREQIELLAR 969
           D       + R  I    +
Sbjct: 934 DLKHGVNRLVRVYIAQKRK 952



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 179/537 (33%), Positives = 251/537 (46%), Gaps = 79/537 (14%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
              G  +               I++  ++  G +V  GDI+    + +    +   + +L 
Sbjct: 738  GPGIADTYNLAKYRRSNQSTCINQRPLVAKGDKVKAGDIIADGPSTEN-GELALGKNVLI 796

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD 972
                 +  +  D  L     V   +        +  +  +  +  E    +I  +  D  
Sbjct: 797  GFMTWEGYNYEDAVLLNERLVKEDIYTSIHIEEYECEARDTKLGSEEITREIPNVGDDSL 856

Query: 973  ---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
               DE  I+      R  +IL G+    G         L   +  E  R      +V+  
Sbjct: 857  KDLDEHGIVRIGAEVRTGDILVGKVTPKGETELTAEERLYRAIFGEKVRE-VRDTSVRVP 915

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              +  +      ++  K                 DD+  GV R+V+V++A KR I  GDK
Sbjct: 916  HGESGIVVDVKVFDREK-----------------DDLKHGVNRLVRVYIAQKRKISVGDK 958

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG++SRILP EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG A   LG
Sbjct: 959  MAGRHGNKGVISRILPEEDMPFLPDGTPLDIVLNPLGVPSRMNIGQLLEVHLGRAARELG 1018

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K+ + + D     D+S                                       ++  
Sbjct: 1019 WKVATPVFDGATEEDVSEA-----------------------------------FKMAGI 1043

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
              DG                      LYDG TGEPFD  +T+G +Y LKL+H+V DK++A
Sbjct: 1044 DPDGKTV-------------------LYDGRTGEPFDGRITIGIMYYLKLHHLVDDKIHA 1084

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L+EMLT+KSDD+ GRT+ Y
Sbjct: 1085 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALKAYGAAYTLREMLTVKSDDITGRTKTY 1144

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK-NSAKMEEIPDFNKCEL 1385
            E+IV G    E+G PESF VLVKE+Q+L L + +     + ++  + E  D    + 
Sbjct: 1145 EAIVKGESVPESGVPESFKVLVKELQSLCLDVKIFMQDQEVSAQNLPEDDDDVSFDF 1201


>gi|307244725|ref|ZP_07526827.1| DNA-directed RNA polymerase, beta subunit [Peptostreptococcus
           stomatis DSM 17678]
 gi|306491902|gb|EFM63953.1| DNA-directed RNA polymerase, beta subunit [Peptostreptococcus
           stomatis DSM 17678]
          Length = 1248

 Score =  820 bits (2117), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/955 (45%), Positives = 594/955 (62%), Gaps = 59/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY  FL           EGL+  F  + PI  ++G
Sbjct: 10  KRERMSFSKIKEIADVPNLIEIQVDSYKWFL----------EEGLKEVFTDISPIEDYTG 59

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 60  NLILEFVDYSLDEKPKYDIEECKERDTTYCAPLKVKVRLI---------NKETGEIKEQE 110

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R++VSQL RSPG+++  ++ +    G  L +  +IP++G
Sbjct: 111 VFMGDFPLMTDRGTFVINGAERVIVSQLVRSPGVYYAEERDKT---GNRLISSTVIPNRG 167

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS  +I VR+DR RK PVT  L ALG+ ++ EI++            +     
Sbjct: 168 AWLEYETDSTGVISVRVDRTRKQPVTVLLRALGIGTDAEIINLLGEDERVLSTLEKDNTT 227

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   ++S   L + L    K   +  +G          
Sbjct: 228 NVDEGLIEIYK------KLRPGEPPTVDSASSLLNSLFFDPKRYDLAKVGRYKFNKKLAL 281

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +     + +I+N +TGE + +AGD I  +   EI +S I  + I   D         
Sbjct: 282 CYRIMDKVASREIINPDTGEKFADAGDKISLELAREIQNSGINAVWIAIDDDKEIKVIGN 341

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + +   + L+I       DV   ++ E M  +      +  L++  +  +   
Sbjct: 342 NFVDIKSHINFDISDLNI-----KEDVHYPTLKEFMETYQDEAQLREVLASNSKKLVPKH 396

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           + LD       I        +  L+D ++  G IDDID+LGNRR+R VGE+L+NQ R+G 
Sbjct: 397 ILLDD-----IIASISYEFGLFYLIDGKDRVGNIDDIDHLGNRRIRCVGELLQNQVRIGF 451

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER I+ER++  D+D++ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 452 SRMERVIRERMTVQDMDTITPQALVNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 511

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A++N YGFIE
Sbjct: 512 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTYAKINEYGFIE 571

Query: 600 TPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK    +  VT+++ YL+A EE+    AQAN  LDE+G F    V CR   G   +V
Sbjct: 572 SPYRKYDKVNKVVTDEIHYLTADEEDLYVRAQANEQLDEEGHFVNSRVICRTVLGAVEMV 631

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           P +++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 632 PEDRVDYMDISPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLVRREAPIIGTGIE 691

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +VAK  GIV++V A  I+I+   GD D        Y+L+KF+RSN  TCV
Sbjct: 692 YRAAKDSGAVVVAKNDGIVDRVSADEIIIKKENGDKD-------RYKLLKFKRSNSGTCV 744

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P+V   +EV+  D+IADGP+TD G++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 745 NQAPIVSKNEEVKAGDVIADGPATDHGEIALGRNCLIAFMTWEGYNYEDAVLINERLVKE 804

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV E  +KN+D+ GII +GAEV+ GDILVG
Sbjct: 805 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGENAIKNLDDRGIIRIGAEVDSGDILVG 864

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VD+RIF R   D
Sbjct: 865 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDIRIFTRENGD 919



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 176/541 (32%), Positives = 250/541 (46%), Gaps = 87/541 (16%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G ++  + +          +++  I+    EV  GD++           +      
Sbjct: 721  KKENGDKDRYKLLKFKRSNSGTCVNQAPIVSKNEEVKAGDVIADGP-ATDHGEIALGRNC 779

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L                    + K +R  ++  E+ E  ARD  
Sbjct: 780  LIAFMTWEGYNYEDAVLIN----------------ERLVKEDRLSTIHIEEYECEARDTK 823

Query: 973  DEQVILDRNI----------YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
                 + R+I                I  G    SG     K T      ++   R    
Sbjct: 824  LGPEEITRDIPNVGENAIKNLDDRGIIRIGAEVDSGDILVGKVTPKGETELTAEERLLRA 883

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      +I   + GDD+ PGV  +V+ ++A KR
Sbjct: 884  IFGEKAREVRDTSLKVPHGESGIIVDI------RIFTRENGDDLSPGVNELVRCYIAKKR 937

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I+ GDKMAGRHGNKG++SR+LP EDMPF+ DGTP+DIVLNP G+PSRMN+GQ+ E HLG
Sbjct: 938  KIKVGDKMAGRHGNKGVISRVLPEEDMPFMDDGTPMDIVLNPQGIPSRMNIGQVLEMHLG 997

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D     DI                            L +A   + 
Sbjct: 998  LAAKKLGWYVATSVFDGANEYDIM-------------------------DALEMAGYPRD 1032

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G                             +  LYDG TGE FD  +TVGY+Y LKL+H+
Sbjct: 1033 G-----------------------------KLTLYDGRTGESFDNRITVGYMYYLKLHHL 1063

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+++LQE+LT+KSDDV
Sbjct: 1064 VDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHILQEILTVKSDDV 1123

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             GR   YE+IV G +  E G PESF VL+KE+Q+L L +   + +       E + D  +
Sbjct: 1124 KGRVETYEAIVKGENIPEPGMPESFRVLMKELQSLCLDVSALDQKGLAIDIKESVDDEEE 1183

Query: 1383 C 1383
             
Sbjct: 1184 A 1184


>gi|289422567|ref|ZP_06424410.1| DNA-directed RNA polymerase, beta subunit [Peptostreptococcus
           anaerobius 653-L]
 gi|289157139|gb|EFD05761.1| DNA-directed RNA polymerase, beta subunit [Peptostreptococcus
           anaerobius 653-L]
          Length = 1245

 Score =  820 bits (2117), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/955 (44%), Positives = 590/955 (61%), Gaps = 59/955 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  EI D+P+LIE+Q  SY  FL           EGL+  F  + PI  ++G
Sbjct: 13  KRERMSFSKIKEIADVPNLIEIQVDSYKWFLA----------EGLKEVFIDMSPIEDYTG 62

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+D+++C  RD TY  PLK+ +RLI          K   +IKEQ 
Sbjct: 63  NLILEFVDYSLDEKPKYDIEECKERDTTYCAPLKVKVRLI---------NKETGEIKEQE 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTF+I G +R++VSQL RSPG+++  ++ +   +G  L +  +IP++G
Sbjct: 114 VFMGDFPLMTDRGTFIINGAERVIVSQLVRSPGVYYAEERDK---AGNRLISSTVIPNRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS  +I VR+DR RK PVT  L ALG+ S+ EIL             +     
Sbjct: 171 AWLEYETDSTGVISVRVDRTRKQPVTVLLRALGIGSDAEILELLGDDERLRLTLEKDNTT 230

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSD------ 301
                L+   K       +  GE   +ES   L + L    K   +  +G          
Sbjct: 231 NVEEGLVEIYK------KLRPGEPPTVESASSLLNSLFFDPKRYDLAKVGRYKFNKKLAL 284

Query: 302 --CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              +       D+VN ETGE++++ G+ I  ++   I +S I  + +   +         
Sbjct: 285 RYRIMDKIATRDVVNEETGEVFVKQGENISFETATAIQNSGINAVWVSVAEDKEIKVIGN 344

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +    + D       I  +    +V   ++ E +  +   +  K  +    +V     
Sbjct: 345 NFVDIRAHVDFD-----IDELGIKPEVHYPTLKEILDKYEDDEELKEVIKANHKVLSPKH 399

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           + LD       I        +  ++D +   G IDDID+LGNRR+R VGE+L+NQ R+G 
Sbjct: 400 ILLDD-----IIASISYEFGLFYIIDGKERVGNIDDIDHLGNRRIRCVGELLQNQVRIGF 454

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER IKE+++  D++S+ PQ L+N +PV +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 455 SRMERVIKEKMTVQDMESMTPQALLNIRPVSAAIKEFFGSSQLSQFMDQTNPLSELTHKR 514

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A++N YGFIE
Sbjct: 515 RLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSTYAKINEYGFIE 574

Query: 600 TPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           +PYRK    +  VT+++ YL+A EE+    AQAN  L+EDG F    V CR   G   LV
Sbjct: 575 SPYRKYDKVNKVVTDEIHYLTADEEDLYVRAQANEPLNEDGGFINNRVICRTVLGAVELV 634

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             +++D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GTG+E
Sbjct: 635 SEDRVDYMDISPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLVRREAPIIGTGIE 694

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SGA +V+K  G+V++V A  IVI+   GD D        Y+L+KF+RSN  TCV
Sbjct: 695 YRAAKDSGAVVVSKNDGVVDRVSADEIVIKKNNGDKD-------RYKLLKFKRSNSGTCV 747

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ P+V  G+ V+  D+IADGP+TDLG++ALGRN L+AFM W GYN+ED++LI+ER+V E
Sbjct: 748 NQTPIVTKGELVKAGDVIADGPATDLGEIALGRNCLIAFMTWEGYNYEDAVLINERLVKE 807

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D  ++IHIEE+E  ARDTKLGPEEITRDIPNV E  +KN+DE GII +GAEV+ GDILVG
Sbjct: 808 DRLSTIHIEEYECEARDTKLGPEEITRDIPNVGENAIKNLDERGIIRIGAEVDSGDILVG 867

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G SG +VD+RIF R   D
Sbjct: 868 KVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDIRIFTRENGD 922



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 176/544 (32%), Positives = 250/544 (45%), Gaps = 87/544 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G ++  + +          +++  I+  G  V  GD++           +      
Sbjct: 724  KKNNGDKDRYKLLKFKRSNSGTCVNQTPIVTKGELVKAGDVIADGPATDL-GEIALGRNC 782

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L                    + K +R  ++  E+ E  ARD  
Sbjct: 783  LIAFMTWEGYNYEDAVLIN----------------ERLVKEDRLSTIHIEEYECEARDTK 826

Query: 973  DEQVILDRNI----------YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
                 + R+I                I  G    SG     K T      ++   R    
Sbjct: 827  LGPEEITRDIPNVGENAIKNLDERGIIRIGAEVDSGDILVGKVTPKGETELTAEERLLRA 886

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
             F  +  +V+     +          +      +I   + GDD+ PGV  +V+ ++A KR
Sbjct: 887  IFGEKAREVRDTSLKVPHGESGIIVDI------RIFTRENGDDLSPGVNELVRCYIAKKR 940

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I+ GDKMAGRHGNKG++SR+LP EDMPF+ DGTP+DIVLNP G+PSRMN+GQ+ E HLG
Sbjct: 941  KIKVGDKMAGRHGNKGVISRVLPEEDMPFMADGTPMDIVLNPQGIPSRMNIGQVLEMHLG 1000

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  + + + D     DI                            L +A   + 
Sbjct: 1001 LAAKKLGWHVATSVFDGANEYDIM-------------------------DALEMAGYPRD 1035

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G                             +  L+DG TGE FD  +TVGY+Y LKL+H+
Sbjct: 1036 G-----------------------------KLQLFDGRTGETFDNRITVGYMYYLKLHHL 1066

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+++LQE+LT+KSDDV
Sbjct: 1067 VDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHILQEILTVKSDDV 1126

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             GR   YE+IV G +  E G PESF VL+KE+Q+L L +   +   K     E + +   
Sbjct: 1127 KGRVETYEAIVKGENIPEPGMPESFRVLMKELQSLCLDVSALDQDGKIIDIKESVDEEIP 1186

Query: 1383 CELK 1386
             + K
Sbjct: 1187 EDFK 1190


>gi|325912433|ref|ZP_08174828.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners UPII
           143-D]
 gi|325475775|gb|EGC78946.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners UPII
           143-D]
          Length = 1223

 Score =  819 bits (2116), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/988 (42%), Positives = 594/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S
Sbjct: 159 GTTVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        K   +  +G 
Sbjct: 219 FTLEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + G V+  + ++++          L  D
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +          ++A+L         D  T    +           K D   
Sbjct: 331 DFKTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPER 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+
Sbjct: 365 VVKLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E++V  R
Sbjct: 541 VVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +
Sbjct: 601 HKEENLEVSPDKLDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG AI+AK AG+VE VDA  I +R  +  LD        Y L K++
Sbjct: 661 PLVGTGMEYRAAHDSGDAILAKAAGVVEYVDANVIKVRRADKTLDE-------YVLEKYR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P V  G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPNVHCGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R 
Sbjct: 834 QDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELAPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 259/1068 (24%), Positives = 397/1068 (37%), Gaps = 174/1068 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++      +    ++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N 
Sbjct: 223  KDMHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGRYKINK 282

Query: 419  RLNLD--------------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L+L                            +  E +  + K L        T    + 
Sbjct: 283  KLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKYLDRDDFKTVTYQPSEE 342

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                   +V E +K   ++   R+ + I       D+  + P D++++     A+ +   
Sbjct: 343  AVLPDPITVQE-IKVFSKVDPERVVKLISNGHIGEDVKHITPADVLSSINYFFALQDGLG 401

Query: 519  S----SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            S      L                R   A  +  V    +  ++  V P     I P   
Sbjct: 402  SIDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVA 461

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLS 618
            S     G         + N  G +    R                +V D   T+      
Sbjct: 462  SVKEFFGSSQLSQFMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCP 521

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA+
Sbjct: 522  IETPEGPNIGLINSMATYAVVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIAS 581

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P  E D S +  +     ++    +  +       +          ++ +     +E
Sbjct: 582  ANAPLNE-DGSFKEKIVLARHKEENLEVSPDK-LDYMDVIPKQV----VSVTSACIPFLE 635

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
              D+ R ++ +                    QR          PLV  G E R       
Sbjct: 636  NDDSNRALMGAN------------------HQRQAVPLINPHSPLVGTGMEYRAAH---- 673

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                D GD  L +   V         + D+ +I  R   + +      +E+ V+ +  + 
Sbjct: 674  ----DSGDAILAKAAGVV-------EYVDANVIKVRRADKTL------DEY-VLEKYRRS 715

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLR 914
               +     PNV       + E  +I  G  +  G++ +G   I       M   E  + 
Sbjct: 716  NATKNYNQTPNVHCGE--KVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
                    DV           S  + D    +R      E          E   +D  DE
Sbjct: 774  ISERMVKDDVY---------TSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DE 823

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I+      +  +IL G+    G         L   +  E  R    +      +V   
Sbjct: 824  DGIVRVGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHG 879

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +                  +   + GD++ PGV ++V+V++  KR IQ GDKM+GRH
Sbjct: 880  GGGIIQNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRH 926

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + +
Sbjct: 927  GNKGTIALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVAT 986

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D                               ++ +  +  +   G    T ++DG 
Sbjct: 987  PVFDGA----------------------------SEEDMWNMVREAGLGKDGKTVLYDG- 1017

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                                      TGEPF   V+VG +Y LKL HMV DK++ARS G 
Sbjct: 1018 -------------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGP 1052

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV 
Sbjct: 1053 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVK 1112

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            G    + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 1113 GEKIPKPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 1160


>gi|312874293|ref|ZP_07734325.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2052A-d]
 gi|329920551|ref|ZP_08277283.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners SPIN
           1401G]
 gi|311090166|gb|EFQ48578.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2052A-d]
 gi|328936227|gb|EGG32680.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners SPIN
           1401G]
          Length = 1224

 Score =  819 bits (2116), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/988 (42%), Positives = 594/988 (60%), Gaps = 86/988 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S
Sbjct: 159 GTTVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        K   +  +G 
Sbjct: 219 FTLEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + G V+  + ++++          L  D
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +          ++A+L         D  T    +           K D   
Sbjct: 331 DFKTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPER 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+
Sbjct: 365 VVKLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            VN YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E++V  R
Sbjct: 541 VVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEKIVLAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + V  +K+D++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +
Sbjct: 601 HKEENLEVSPDKLDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTGME   A  SG AI+AK AG+VE VDA  I +R  +  LD        Y L K++
Sbjct: 661 PLVGTGMEYRAAHDSGDAILAKAAGVVEYVDANVIKVRRADKTLDE-------YVLEKYR 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P V  G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++
Sbjct: 714 RSNATKNYNQTPNVHCGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV
Sbjct: 774 ISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVGK+TPKG + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R 
Sbjct: 834 QDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSRE 893

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G++K  R   V++ +I++  +
Sbjct: 894 AGDELAPGVNKMVRVYIVQKRKIQVGDK 921



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 259/1068 (24%), Positives = 397/1068 (37%), Gaps = 174/1068 (16%)

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            ++      +    ++L DIY  +RPG+  T   + S+    FFD  +YDL+ VGR K+N 
Sbjct: 223  KDMHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGRYKINK 282

Query: 419  RLNLD--------------------TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            +L+L                            +  E +  + K L        T    + 
Sbjct: 283  KLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKYLDRDDFKTVTYQPSEE 342

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                   +V E +K   ++   R+ + I       D+  + P D++++     A+ +   
Sbjct: 343  AVLPDPITVQE-IKVFSKVDPERVVKLISNGHIGEDVKHITPADVLSSINYFFALQDGLG 401

Query: 519  S----SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            S      L                R   A  +  V    +  ++  V P     I P   
Sbjct: 402  SIDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVA 461

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYR----------------KVCDGKVTNDVVYLS 618
            S     G         + N  G +    R                +V D   T+      
Sbjct: 462  SVKEFFGSSQLSQFMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCP 521

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAA 676
                E   I   NS            +            +  +KID++ A  +    IA+
Sbjct: 522  IETPEGPNIGLINSMATYAVVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIAS 581

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +  P  E D S +  +     ++    +  +       +          ++ +     +E
Sbjct: 582  ANAPLNE-DGSFKEKIVLARHKEENLEVSPDK-LDYMDVIPKQV----VSVTSACIPFLE 635

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
              D+ R ++ +                    QR          PLV  G E R       
Sbjct: 636  NDDSNRALMGAN------------------HQRQAVPLINPHSPLVGTGMEYRAAH---- 673

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                D GD  L +   V         + D+ +I  R   + +      +E+ V+ +  + 
Sbjct: 674  ----DSGDAILAKAAGVV-------EYVDANVIKVRRADKTL------DEY-VLEKYRRS 715

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--KITPKGESPMTPEEKLLR 914
               +     PNV       + E  +I  G  +  G++ +G   I       M   E  + 
Sbjct: 716  NATKNYNQTPNVHCGE--KVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVM 773

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
                    DV           S  + D    +R      E          E   +D  DE
Sbjct: 774  ISERMVKDDVY---------TSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DE 823

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I+      +  +IL G+    G         L   +  E  R    +      +V   
Sbjct: 824  DGIVRVGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHG 879

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +                  +   + GD++ PGV ++V+V++  KR IQ GDKM+GRH
Sbjct: 880  GGGIIQNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRH 926

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + +
Sbjct: 927  GNKGTIALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVAT 986

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D                               ++ +  +  +   G    T ++DG 
Sbjct: 987  PVFDGA----------------------------SEEDMWNMVREAGLGKDGKTVLYDG- 1017

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                                      TGEPF   V+VG +Y LKL HMV DK++ARS G 
Sbjct: 1018 -------------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGP 1052

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV 
Sbjct: 1053 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVK 1112

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            G    + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 1113 GEKIPKPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 1160


>gi|260102348|ref|ZP_05752585.1| DNA-directed RNA polymerase subunit beta [Lactobacillus helveticus
           DSM 20075]
 gi|260083857|gb|EEW67977.1| DNA-directed RNA polymerase subunit beta [Lactobacillus helveticus
           DSM 20075]
          Length = 1207

 Score =  819 bits (2115), Expect = 0.0,   Method: Composition-based stats.
 Identities = 397/956 (41%), Positives = 577/956 (60%), Gaps = 79/956 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E++ +P+L +VQ  SY  FL          ++G++  F  + PI+ 
Sbjct: 3   YGKHRTRRSFSRIKEVLKLPNLTDVQTESYKWFL----------DKGIKEVFDDIMPISD 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG   LE+  Y+   PK+ VD+    D TYA P+++TL+L           +   +IK 
Sbjct: 53  FSGKLSLEYEGYKLQKPKYTVDEARDHDATYAAPMRVTLKLT---------NQETGEIKT 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GDLPLMT+ G+F++ G +R++VSQL RSPG+++  D  +   +G+ ++   +IP+
Sbjct: 104 QDVFFGDLPLMTESGSFIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIFGTTVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
           +G W++ E D+K++  VR+DR RK+P+T  + A+G+ S+ +I+  F          D   
Sbjct: 161 RGAWLEYETDAKNVSFVRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQFTLDKD- 219

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS----- 300
              + AD  V   +      +  GE    +S + L        +   +  +G        
Sbjct: 220 VHKNPADSRVAEALKDIYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKL 279

Query: 301 ---DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              + L G  +AE + + +TGEI  +   V+  + + ++                     
Sbjct: 280 SLKNRLYGQTLAETLADPDTGEIIAKKDTVVTHEVMNKLAPYL----------------- 322

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                      DR D  +  Y+  + G +      + +  +   D ++          + 
Sbjct: 323 -----------DRDDFKMVTYQPSKEGVLQDPITVQEIKVYSKVDPERE---------VK 362

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +  N     DV+H+   D++A I     L++  GT DDID+LGNRR+R VGE+L+NQ+R+
Sbjct: 363 LMSNGHIAADVKHLTPADVLASINYFFALQDKIGTTDDIDHLGNRRIRRVGELLQNQFRI 422

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+S  D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N L  +TH
Sbjct: 423 GLARMERVVRERMSIQDPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHNPLGELTH 482

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A +N YGF
Sbjct: 483 KRRMSALGPGGLTRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYAIINKYGF 542

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYR+V     KVT+ + YL+A EE+N  IA AN+ L++DGSF  +++  R   + + 
Sbjct: 543 IETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAGANTPLNDDGSFKSDVILARQKEDNVE 602

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V  +KID++D  PKQVVS+A++ IPFLENDDSNR LMG N QRQA PL+      VGTGM
Sbjct: 603 VTPDKIDYMDVIPKQVVSVASACIPFLENDDSNRALMGANQQRQAEPLINPHGSLVGTGM 662

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SGAA++AK AG VE VDA  I IR  +G LD        Y L K++RSN +  
Sbjct: 663 EYRAAHDSGAALIAKAAGTVEYVDANEIRIRREDGTLDK-------YTLEKYRRSNNSKS 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQ P VK+GD V  +D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED++++SER+V 
Sbjct: 716 YNQTPNVKLGDHVDVSDVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVK 775

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +DV+TSI IE++E  ARDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV+ GDILV
Sbjct: 776 DDVYTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDANGIVRVGAEVHDGDILV 835

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+++ R   D
Sbjct: 836 GKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDVKVYTREAGD 891



 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 175/502 (34%), Positives = 240/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 722  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 778

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD N   R+     G     G  
Sbjct: 779  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDANGIVRV-----GAEVHDGDI 833

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 834  LVGKVTPKGVTELSAEERLLHAIFGEKAHEVRDTSLRVPHGGGGIVQDV------KVYTR 887

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 888  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 947

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + +       D                
Sbjct: 948  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFAGANEND---------------- 991

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+D   +  I         D+ G++ILYDG 
Sbjct: 992  -----------------------------VWDTVRQAGI---------DKDGKTILYDGR 1013

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1014 TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1073

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1074 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1133

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1134 IRVLDMNHNEIELRDMDEDSSE 1155


>gi|330719434|ref|ZP_08314034.1| DNA-directed RNA polymerase subunit beta [Leuconostoc fallax KCTC
           3537]
          Length = 1202

 Score =  819 bits (2115), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/966 (42%), Positives = 579/966 (59%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ + +  E++D+P+LIE+Q ASY  FL          +EG++  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYARIKEVLDVPNLIEIQTASYKWFL----------DEGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LE+V Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGTLSLEYVDYKLMEPKYTIEEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ PLMT  GTF+I G +R++VSQL RSPGI+++ +  +   +G+  +
Sbjct: 102 ETGEIKSQDVFFGEFPLMTDQGTFIINGAERVIVSQLVRSPGIYYNQETDK---NGRPHF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +IL  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDILEIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        +   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEESLKDIYERLRPGEPKTADSSRALLVARFFDPRRYDLAN 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L G  +AE + + ++GEI  E G V+D+  + E+        P L
Sbjct: 276 VGRYKINKKLSLKTRLLGQTLAETLADPDSGEIIAEKGTVVDKTVMSELA-------PFL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      Y  +     +          I + ++         A  +            
Sbjct: 329 EREDFKTTTYTPSGDAVLQEPV-------ILQKIKIESPEDPEKALVLIGN--------- 372

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                                R +R  DI+A +   ++L+ G G++DDID+LGNRR+RSV
Sbjct: 373 --------------GHIEAANRTVRPADILAGMNYFLNLQEGIGSVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGELNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++AR+N YGF+ETPYR+V      VT+ + YL+A EE+N  +AQANS L++DGSF  + V
Sbjct: 539 TYARINKYGFVETPYRRVDWTTHNVTDKIDYLTADEEDNFIVAQANSPLNDDGSFVNDTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P +KID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPVDKIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             +P VGTG+E   A  +G A++++ AG VE VD  +I IR  +G LD        Y LM
Sbjct: 659 PHSPLVGTGIEYKAAHDAGVALISRAAGEVEYVDGRQIRIRREDGQLD-------TYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P+VKVG+ +  + +IADGPS +LG+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIVKVGEHIDDDQVIADGPSMELGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  EE L+++DE GII +G
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEEQLRDLDENGIIRIG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 259/1095 (23%), Positives = 417/1095 (38%), Gaps = 172/1095 (15%)

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            + +  +      DI  ++ D  +       ++      +   +++L DIY  +RPG+  T
Sbjct: 194  ELVRALGFGSDSDILEIFSDQYDALNMTLEKDVHKDMSDSRVEESLKDIYERLRPGEPKT 253

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP----DDVRHIRKEDIIAIIKILV 444
               + ++    FFD  +YDL+ VGR K+N +L+L T          +   D   II    
Sbjct: 254  ADSSRALLVARFFDPRRYDLANVGRYKINKKLSLKTRLLGQTLAETLADPDSGEIIAEKG 313

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
             + +     +    L     ++          L    + + IK         +++     
Sbjct: 314  TVVDKTVMSELAPFLEREDFKTTTYTPSGDAVLQEPVILQKIKIESPEDPEKALVLIGNG 373

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT-----RRLSALGQ-------GGVARA 552
            + +     V      + ++        +  +        RR+ ++G+        G+ R 
Sbjct: 374  HIEAANRTVRPADILAGMNYFLNLQEGIGSVDDIDHLGNRRIRSVGELLQNQFRIGLTRM 433

Query: 553  RAGVEMR-------DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK- 604
               V  R        V P     I P   +     G         + N  G +    R  
Sbjct: 434  ERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMDQTNPLGELNHKRRLS 493

Query: 605  ---------------VCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                           V D   T    +  +   E  N  +  + ++      +       
Sbjct: 494  ALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLATYARINKYGFVETPY 553

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R          +KID++ A  +    +A +  P    +D    +    M R     ++  
Sbjct: 554  RRVDWTTHNVTDKIDYLTADEEDNFIVAQANSPL---NDDGSFVNDTVMARFGEENIETP 610

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               +       V+     ++       +E  D+ R ++ +                    
Sbjct: 611  VDKID---YMDVSPKQVVSVGTAAIPFLENDDSNRALMGAN------------------M 649

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QR          PLV  G                  +     +  VA +       E   
Sbjct: 650  QRQAVPLLDPHSPLVGTGI-----------------EYKAAHDAGVALISRAAGEVEYVD 692

Query: 828  LISERMVSEDVFTSIHIEEFEVM-ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
                R+  ED      ++ +E+M  R +  G     + I  V E    +ID+  +I  G 
Sbjct: 693  GRQIRIRRED----GQLDTYELMKFRRSNGGKNYNQKPIVKVGE----HIDDDQVIADGP 744

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             +  G++ +G             +  L A    +  +  D  +     V   V       
Sbjct: 745  SMELGELALG-------------QNPLIAFMTWQGYNFEDAIVLNERLVREDVYTSIHIE 791

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
             +  +  +  +  E    E +    +++   LD N   R+     G     G     K T
Sbjct: 792  EYDSEARDTKLGPEEMTRE-IPNTGEEQLRDLDENGIIRI-----GAEVHDGDILVGKVT 845

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  +S   R     F  +  +V+     +          +      +I   + GD++
Sbjct: 846  PKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNV------RIYTPENGDEL 899

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P EDMP++ DGTP+DI+L+P+G
Sbjct: 900  APGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMG 959

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG+A   LG  + S + D   + +I                     
Sbjct: 960  VPSRMNIGQVLELHLGFAARNLGIHVASPVFDGATDDEI--------------------- 998

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                         E+A+      A L   G+S++YDG +G+ FD
Sbjct: 999  -----------------------------EDALRE----AGLPVDGKSVVYDGRSGDAFD 1025

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            + V VG ++ +KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1026 KRVAVGVMHYMKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1085

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDDV GR +VYESIV G+     G PESF VLVKE+QALGL + + + 
Sbjct: 1086 AAYTLQEILTYKSDDVAGRVKVYESIVKGDSIPRPGVPESFRVLVKELQALGLDMRVLDV 1145

Query: 1367 RTKNSAKMEEIPDFN 1381
                    +   D +
Sbjct: 1146 AGDEVELRQMDEDDS 1160


>gi|304438181|ref|ZP_07398123.1| DNA-directed RNA polymerase subunit beta [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
 gi|304368788|gb|EFM22471.1| DNA-directed RNA polymerase subunit beta [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
          Length = 1251

 Score =  819 bits (2115), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/953 (44%), Positives = 575/953 (60%), Gaps = 98/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++++P L+++Q+ SY  FL            GL   F+ + PI  FSG
Sbjct: 13  RRTRYSYARIKEVMEMPHLLDIQRESYRWFL----------EVGLAEIFRDISPIQDFSG 62

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+TYA PL++ +RL+          +   +IKEQ +
Sbjct: 63  NLILSFESFALGEPKYDLDECKERDVTYAAPLRVNVRLV---------NRETGEIKEQEV 113

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +      +GK LY   +IP++G 
Sbjct: 114 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGTYYGVEID---TTGKELYNATMIPNRGA 170

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ DI+ VRIDR RK+PVT  + ALG +++ EI + F          +      
Sbjct: 171 WIELETDANDIVSVRIDRTRKMPVTYLIRALGYETDAEIRALFGDDPRMLATIERDT--- 227

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS-------- 300
                     V      +  GE   E + ++L   L    +   +  +G           
Sbjct: 228 -DEVKTRSRAVIEIYRRLRPGEPANEDNARQLLETLFFDPRRYDLATVGRYKLTKKLGWR 286

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L G  +AE +V+ ETGEI    G+ I    ++ +       +         +   I  
Sbjct: 287 RRLLGKVLAEPVVDVETGEIVFPKGEPITPAMVDAVSEERETALF-------GDGELIAF 339

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +             DIYR++                                       
Sbjct: 340 QVQKPDG--------DIYRML--------------------------------------C 353

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                   R + +EDI+A I  L+ L +  G  DDID+LGNRRVR+VGE+L+NQ+R+GL 
Sbjct: 354 APTRDYQYRTVTREDIMAAISYLLGLMDSFGNTDDIDHLGNRRVRAVGELLQNQFRIGLS 413

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+S  + +S+ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 414 RMERVVRERMSIQETESITPQGLINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHKRR 473

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+ET
Sbjct: 474 LSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYARVNRFGFMET 533

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V     +VT DV YL+A EE++  IAQAN  LD +  F  E V  R   E  L PR
Sbjct: 534 PYRRVDKEHHRVTEDVRYLTADEEDDLIIAQANEPLDANEYFVNERVTARFHEETGLHPR 593

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           E++D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME  
Sbjct: 594 ERVDYMDVSPRQVFSIATAMIPFLENDDANRALMGANMQRQAVPLLRTQAPLVGTGMEYK 653

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++AK AG V  V A  I +RS EG  D        Y+L KF RSNQ TC+NQ
Sbjct: 654 AACDSGVMVLAKHAGEVTDVTADAITVRSDEGAFD-------TYKLQKFIRSNQATCINQ 706

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +PLV  GD V     IADGPSTD G+LALG N++VA+MPW GYN+ED++L+SE +V  D+
Sbjct: 707 KPLVYAGDRVTEGQPIADGPSTDNGELALGYNIIVAYMPWEGYNYEDAILLSENLVKRDL 766

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV+EE LK++DE GII +GA+V PGDILVGK+
Sbjct: 767 YTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEDGIISIGADVRPGDILVGKV 826

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G ++DV+IF R   D
Sbjct: 827 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIIDVKIFTRENND 879



 Score =  588 bits (1517), Expect = e-165,   Method: Composition-based stats.
 Identities = 273/1062 (25%), Positives = 424/1062 (39%), Gaps = 92/1062 (8%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    +I  L+ D     A I     TD+ K R  A+++IYR +RPG+ +    
Sbjct: 197  LIRALGYETDAEIRALFGDDPRMLATI--ERDTDEVKTRSRAVIEIYRRLRPGEPANEDN 254

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            A  +   LFFD  +YDL+TVGR K+  +L        + + +  +      +V  +    
Sbjct: 255  ARQLLETLFFDPRRYDLATVGRYKLTKKLGWRRRLLGKVLAEPVVDVETGEIVFPKGEPI 314

Query: 452  TIDDIDNLGNRRVRS---VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            T   +D +   R  +    GE++  Q +     + R +          +V  +D      
Sbjct: 315  TPAMVDAVSEERETALFGDGELIAFQVQKPDGDIYRMLCAPTRDYQYRTVTRED------ 368

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            +++A+             +   +   I H         G + + +  + +  +      R
Sbjct: 369  IMAAISYLLGL------MDSFGNTDDIDHLGNRRVRAVGELLQNQFRIGLSRMERVVRER 422

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +   ET      GL++     A V  +             +  +    LS +  + R  A
Sbjct: 423  MSIQETESITPQGLINIRPVVAAVKEFFGSSQL------SQFMDQHNPLSELTHKRRLSA 476

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                 L             R      +       +    P +        +     + + 
Sbjct: 477  LGPGGL------------SRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYAR 524

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G          +  E   V   +  + A      I+A+    +   DA    +   
Sbjct: 525  VNRFGF--METPYRRVDKEHHRVTEDVRYLTADEEDDLIIAQANEPL---DANEYFVNER 579

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                    +G+     + +   +     +    +         +  A+            
Sbjct: 580  VTARFHEETGLHPRERVDYMDVSPRQVFS----IATAMIPFLENDDANRALMGANMQRQA 635

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE-EFEVMARDTKLGPEEITRDIPN 867
              +L    P  G   E        ++          +   + +   +  G  +  +    
Sbjct: 636  VPLLRTQAPLVGTGMEYKAACDSGVMVLAKHAGEVTDVTADAITVRSDEGAFDTYKLQKF 695

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +       I++  ++  G  V  G  +    +      +     ++ A    +  +  D 
Sbjct: 696  IRSNQATCINQKPLVYAGDRVTEGQPIADGPSTDN-GELALGYNIIVAYMPWEGYNYEDA 754

Query: 928  SLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             L   +        S  + +     R      E          E   +D  DE  I+   
Sbjct: 755  ILLSENLVKRDLYTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDL-DEDGIISIG 813

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 814  ADVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 856

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                          KI   +  D++PPGV R+V+V++A KR I  GDKM+GRHGNKG+VS
Sbjct: 857  LRVPHGEAGKIIDVKIFTRENNDELPPGVNRLVRVYIAQKRKISVGDKMSGRHGNKGVVS 916

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ+ ETHLG AC  LG++IK        
Sbjct: 917  RIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQVLETHLGMACRVLGQRIKDG------ 970

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                 +  +   D     +     +G+ ++TPVFDGA ++ +  
Sbjct: 971  ---------------DPTVEGDLRAAGYDFDKNGMPVPDVAGIHIATPVFDGAGDDDVFG 1015

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             +R A L   G+++LYDG TGEPF+  VTVG +YMLKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1016 TIRAAGLPSDGKTVLYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARSTGPYSLVTQQ 1075

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G++  E 
Sbjct: 1076 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYESIVKGDNIPEP 1135

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKM-EEIPDFNK 1382
            G PESF VL+KE+QA+GL I + N   K  A   EE  D N+
Sbjct: 1136 GVPESFKVLIKELQAIGLDIKVLNEDAKEIAIRDEEDEDINE 1177


>gi|313895344|ref|ZP_07828901.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|312976239|gb|EFR41697.1| DNA-directed RNA polymerase, beta subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
          Length = 1284

 Score =  819 bits (2115), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/953 (44%), Positives = 584/953 (61%), Gaps = 98/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++++P L+++Q+ SY  FL          + GL   F+ + PI  FSG
Sbjct: 43  RRTRYSYARIKEVMEMPHLLDIQRTSYRWFL----------DVGLGEIFRDISPIQDFSG 92

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+TYA PL++ +RL+          +   +IKEQ +
Sbjct: 93  NLILSFESFALGAPKYDLDECKERDVTYAAPLRVNVRLV---------NRETGEIKEQEV 143

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +      +GK LY   +IP++G 
Sbjct: 144 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGAYYGVEID---TTGKELYNATVIPNRGA 200

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ D++ VRIDR RK+PVT  + ALG +++ +I + F          +      
Sbjct: 201 WIELETDANDVVSVRIDRTRKMPVTYLIRALGYETDSDIRALFGDDPRILATIERDT--- 257

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS-------- 300
                  G  V      +  GE   E + ++L   L    +   +  +G           
Sbjct: 258 -DEVKTRGKAVIEIYRRLRPGEPANEDNARQLLEVLFFDPRRYDLATVGRYKLTKKLGWR 316

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L G  +AE +++ E+GEI    G+ I +  ++ +     +   +L+ D    +  I+ 
Sbjct: 317 RRLLGKVLAEPVIDKESGEIVFPKGEAITQDMVDAVSEEREK---VLFGDGELVSLSIQK 373

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                       A  ++YR++                                       
Sbjct: 374 ------------ADGEVYRML--------------------------------------C 383

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                   R I +ED++A I  L+ L +G G  DDID+LGNRRVR+VGE+L+NQ+R+GL 
Sbjct: 384 APTRDYQYRTITREDVMASISYLLGLMDGFGNTDDIDHLGNRRVRAVGELLQNQFRIGLS 443

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER++  + DS+ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 444 RMERVVRERMTIQETDSITPQGLINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHKRR 503

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+ET
Sbjct: 504 LSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYARVNRFGFMET 563

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V     +VT+DV YL+A EE+   IAQAN  LDE+  F  E V  R   E  L  R
Sbjct: 564 PYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPLDENEYFINERVTARFHEETGLHHR 623

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLLK +AP VGTGME  
Sbjct: 624 DRVDYMDVSPRQVFSIATAMIPFLENDDANRALMGANMQRQAVPLLKTQAPLVGTGMEYK 683

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++A+R G+V  V A  + I++ EG  D        Y+L KF RSNQ TC+NQ
Sbjct: 684 AACDSGVMVLARRGGVVTDVAANAVTIKTDEGTFD-------NYKLQKFVRSNQATCINQ 736

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV  G+ V     IADGPSTD G+LALG N++VA+MPW GYN+ED++L+SE +V  D+
Sbjct: 737 RPLVYEGERVVEGQPIADGPSTDNGELALGYNIIVAYMPWEGYNYEDAILLSENLVKRDL 796

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV+EE LK++DE GI+ +GA+V PGDILVGK+
Sbjct: 797 YTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEEGIVSIGADVRPGDILVGKV 856

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G ++DV+IF R   D
Sbjct: 857 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEGGKIIDVKIFTRENND 909



 Score =  586 bits (1511), Expect = e-165,   Method: Composition-based stats.
 Identities = 273/1058 (25%), Positives = 425/1058 (40%), Gaps = 91/1058 (8%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    DI  L+ D     A I     TD+ K R  A+++IYR +RPG+ +    
Sbjct: 227  LIRALGYETDSDIRALFGDDPRILATI--ERDTDEVKTRGKAVIEIYRRLRPGEPANEDN 284

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            A  +   LFFD  +YDL+TVGR K+  +L        + + +  I      +V  +    
Sbjct: 285  ARQLLEVLFFDPRRYDLATVGRYKLTKKLGWRRRLLGKVLAEPVIDKESGEIVFPKGEAI 344

Query: 452  TIDDIDNLGNRRVR---SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            T D +D +   R +     GE++    +     + R +          ++  +D      
Sbjct: 345  TQDMVDAVSEEREKVLFGDGELVSLSIQKADGEVYRMLCAPTRDYQYRTITRED------ 398

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            V++++             +   +   I H         G + + +  + +  +      R
Sbjct: 399  VMASISYLLGL------MDGFGNTDDIDHLGNRRVRAVGELLQNQFRIGLSRMERVVRER 452

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +   ET      GL++     A V  +             +  +    LS +  + R  A
Sbjct: 453  MTIQETDSITPQGLINIRPVVAAVKEFFGSSQL------SQFMDQHNPLSELTHKRRLSA 506

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                 L             R      +       +    P +        +     + + 
Sbjct: 507  LGPGGL------------SRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYAR 554

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G          +  E   V   +  + A      I+A+    +   D     I   
Sbjct: 555  VNRFGF--METPYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPL---DENEYFINER 609

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                    +G+     + +   +     +    +         +  A+            
Sbjct: 610  VTARFHEETGLHHRDRVDYMDVSPRQVFS----IATAMIPFLENDDANRALMGANMQRQA 665

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEEITRDIPN 867
              +L    P  G   E        ++       +  +     +   T  G  +  +    
Sbjct: 666  VPLLKTQAPLVGTGMEYKAACDSGVMVLARRGGVVTDVAANAVTIKTDEGTFDNYKLQKF 725

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V       I++  ++  G  V  G  +    +      +     ++ A    +  +  D 
Sbjct: 726  VRSNQATCINQRPLVYEGERVVEGQPIADGPSTDN-GELALGYNIIVAYMPWEGYNYEDA 784

Query: 928  SLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             L   +        S  + +     R      E          E   +D D+E  I+   
Sbjct: 785  ILLSENLVKRDLYTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEE-GIVSIG 843

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 844  ADVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 886

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                          KI   +  D++PPGV R+V+V++A KR I  GDKM+GRHGNKG+VS
Sbjct: 887  LRVPHGEGGKIIDVKIFTRENNDELPPGVNRLVRVYIAQKRKISVGDKMSGRHGNKGVVS 946

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ+ ETHLG AC  LG++IK        
Sbjct: 947  RIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQVLETHLGMACRVLGQRIKDG------ 1000

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                 +  +   +  V  + +  ++G+ ++TPVFDGA ++ +  
Sbjct: 1001 ---------------DPTVEGDLRAAGYNFDVNGMPKPDEAGIHIATPVFDGAGDDDVFG 1045

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             +R A L   G+++LYDG TGEPF+  VTVG +YMLKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1046 TIRAAGLPADGKTVLYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARSTGPYSLVTQQ 1105

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G++  E 
Sbjct: 1106 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYESIVKGDNIPEP 1165

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            G PESF VL+KE+QA+GL I + N   K  A  +E  +
Sbjct: 1166 GVPESFKVLIKELQAIGLDIKVLNEDAKEIAIRDEEDE 1203


>gi|259501008|ref|ZP_05743910.1| DNA-directed RNA polymerase subunit beta [Lactobacillus iners DSM
           13335]
 gi|315653932|ref|ZP_07906848.1| DNA-directed RNA polymerase subunit beta [Lactobacillus iners ATCC
           55195]
 gi|259167702|gb|EEW52197.1| DNA-directed RNA polymerase subunit beta [Lactobacillus iners DSM
           13335]
 gi|315488628|gb|EFU78274.1| DNA-directed RNA polymerase subunit beta [Lactobacillus iners ATCC
           55195]
          Length = 1227

 Score =  818 bits (2113), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/986 (42%), Positives = 593/986 (60%), Gaps = 86/986 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F  +
Sbjct: 6   GHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFDDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL              
Sbjct: 56  MPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y  
Sbjct: 107 GEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIYGT 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S  
Sbjct: 164 TVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLSFT 223

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      + AD  V   +      +  GE    +S + L        K   +  +G   
Sbjct: 224 LEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGRYK 282

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    +AE + + +TGEI  + G V+  + ++++          L  D  
Sbjct: 283 INKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRDDF 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
               Y  +          ++A+L         D  T    +           K D   V 
Sbjct: 336 KTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPERVV 369

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+L+
Sbjct: 370 KLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGELLQ 425

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N L
Sbjct: 426 NQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNNPL 485

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A V
Sbjct: 486 GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAVV 545

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E++V  R  
Sbjct: 546 NKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEKIVLARHK 605

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E + V  +K+D++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +P 
Sbjct: 606 EENLEVSPDKLDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHSPL 665

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SG AI+AK AG+VE VDA  I +R  +  LD        Y L K++RS
Sbjct: 666 VGTGMEYRAAHDSGDAILAKAAGVVEYVDANVIKVRRDDKTLDE-------YVLEKYRRS 718

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N     NQ P V  G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++IS
Sbjct: 719 NATKNYNQTPNVHCGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVMIS 778

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ERMV +DV+TSIHIE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV  
Sbjct: 779 ERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEVQD 838

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR--- 947
           GDILVGK+TPKG + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R   
Sbjct: 839 GDILVGKVTPKGVTDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSREAG 898

Query: 948 ----HGIDKNERSISVEREQIELLAR 969
                G++K  R   V++ +I++  +
Sbjct: 899 DELAPGVNKMVRVYIVQKRKIQVGDK 924



 Score =  472 bits (1215), Expect = e-130,   Method: Composition-based stats.
 Identities = 166/523 (31%), Positives = 234/523 (44%), Gaps = 79/523 (15%)

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    KN ++   +  G +V  G+++           +   +  + A       +  
Sbjct: 714  KYRRSNATKNYNQTPNVHCGEKVVEGEVIADGP-AMENGELALGQNPIIAFATWNMYNYE 772

Query: 926  DTSLRVPSGVSG------TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            D  +     V         + D    +R      E          E   +D  DE  I+ 
Sbjct: 773  DAVMISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DEDGIVR 831

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+    G         L   +  E  R    +      +V      + 
Sbjct: 832  VGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHGGGGII 887

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                             +   + GD++ PGV ++V+V++  KR IQ GDKM+GRHGNKG 
Sbjct: 888  QNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGT 934

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D 
Sbjct: 935  IALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVATPVFDG 994

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                          ++ +  +  +   G    T ++DG      
Sbjct: 995  A----------------------------SEEDMWNMVREAGLGKDGKTVLYDG------ 1020

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                 TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVT
Sbjct: 1021 --------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGPYSLVT 1060

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    
Sbjct: 1061 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIP 1120

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 1121 KPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 1163


>gi|320529705|ref|ZP_08030784.1| DNA-directed RNA polymerase, beta subunit [Selenomonas artemidis
           F0399]
 gi|320138066|gb|EFW29969.1| DNA-directed RNA polymerase, beta subunit [Selenomonas artemidis
           F0399]
          Length = 1250

 Score =  818 bits (2112), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/953 (44%), Positives = 582/953 (61%), Gaps = 98/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++++P L+++Q+ SY  FL          + GL   F+ + PI  FSG
Sbjct: 9   RRTRYSYARIKEVMEMPHLLDIQRTSYRWFL----------DVGLGEIFRDISPIQDFSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+TYA PL++ +RL+          +   +IKEQ +
Sbjct: 59  NLILSFESFALGAPKYDLDECKERDVTYAAPLRVNVRLV---------NRETGEIKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +      +GK LY   +IP++G 
Sbjct: 110 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGAYYGVEID---TTGKELYNATVIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ D++ VRIDR RK+PVT  + ALG +++ EI + F          +      
Sbjct: 167 WIELETDANDVVSVRIDRTRKMPVTYLIRALGYETDAEIRALFGDDPRILATIERDT--- 223

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS-------- 300
                  G  V      +  GE   E + ++L   L    +   +  +G           
Sbjct: 224 -DEVKTRGKAVIEIYRRLRPGEPANEDNARQLLEVLFFDPRRYDLATVGRYKLTKKLGWR 282

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L G  +AE +++ ETGE+    G+ I +  ++ +     +   +L+ D          
Sbjct: 283 RRLLGKVLAEPVIDKETGEVVFPKGEAITQDMVDAVSEEREK---VLFGDGE-------- 331

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                     + A  ++YR++                                       
Sbjct: 332 ----LVALSVQKADGEVYRML--------------------------------------C 349

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                   R I +ED++A I  L+ L +G G  DDID+LGNRRVR+VGE+L+NQ+R+GL 
Sbjct: 350 APTRDYQYRTITREDVMASISYLLGLMDGFGNTDDIDHLGNRRVRAVGELLQNQFRIGLS 409

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER++  + DS+ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 410 RMERVVRERMTIQETDSITPQGLINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHKRR 469

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+ET
Sbjct: 470 LSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYARVNRFGFMET 529

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V     +VT+DV YL+A EE+   IAQAN  LDE+  F  E V  R   E  L  R
Sbjct: 530 PYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPLDENEYFINERVTARFHEETGLHHR 589

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLLK +AP VGTGME  
Sbjct: 590 DRVDYMDVSPRQVFSIATAMIPFLENDDANRALMGANMQRQAVPLLKTQAPLVGTGMEYK 649

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++A+R G+V  V A  + I++ EG  D        Y+L KF RSNQ TC+NQ
Sbjct: 650 AACDSGVMVLARRGGVVTDVAANAVTIKTDEGTFD-------NYKLQKFVRSNQATCINQ 702

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV  G+ V     IADGPSTD G+LALG N++VA+MPW GYN+ED++L+SE +V  D+
Sbjct: 703 RPLVYEGERVVEGQPIADGPSTDNGELALGYNIIVAYMPWEGYNYEDAILLSENLVKRDL 762

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV+EE LK++DE GI+ +GA+V PGDILVGK+
Sbjct: 763 YTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEEGIVSIGADVRPGDILVGKV 822

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G ++DV+IF R   D
Sbjct: 823 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEGGKIIDVKIFTRENND 875



 Score =  585 bits (1508), Expect = e-164,   Method: Composition-based stats.
 Identities = 272/1058 (25%), Positives = 426/1058 (40%), Gaps = 91/1058 (8%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    +I  L+ D     A I     TD+ K R  A+++IYR +RPG+ +    
Sbjct: 193  LIRALGYETDAEIRALFGDDPRILATI--ERDTDEVKTRGKAVIEIYRRLRPGEPANEDN 250

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            A  +   LFFD  +YDL+TVGR K+  +L        + + +  I      +V  +    
Sbjct: 251  ARQLLEVLFFDPRRYDLATVGRYKLTKKLGWRRRLLGKVLAEPVIDKETGEVVFPKGEAI 310

Query: 452  TIDDIDNLGNRRVR---SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            T D +D +   R +     GE++    +     + R +          ++  +D      
Sbjct: 311  TQDMVDAVSEEREKVLFGDGELVALSVQKADGEVYRMLCAPTRDYQYRTITRED------ 364

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            V++++             +   +   I H         G + + +  + +  +      R
Sbjct: 365  VMASISYLLGL------MDGFGNTDDIDHLGNRRVRAVGELLQNQFRIGLSRMERVVRER 418

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +   ET      GL++     A V  +             +  +    LS +  + R  A
Sbjct: 419  MTIQETDSITPQGLINIRPVVAAVKEFFGSSQL------SQFMDQHNPLSELTHKRRLSA 472

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                 L             R      +       +    P +        +     + + 
Sbjct: 473  LGPGGL------------SRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYAR 520

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G          +  E   V   +  + A      I+A+    +   D     I   
Sbjct: 521  VNRFGF--METPYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPL---DENEYFINER 575

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                    +G+     + +   +     +    +         +  A+            
Sbjct: 576  VTARFHEETGLHHRDRVDYMDVSPRQVFS----IATAMIPFLENDDANRALMGANMQRQA 631

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEEITRDIPN 867
              +L    P  G   E        ++       +  +     +   T  G  +  +    
Sbjct: 632  VPLLKTQAPLVGTGMEYKAACDSGVMVLARRGGVVTDVAANAVTIKTDEGTFDNYKLQKF 691

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V       I++  ++  G  V  G  +    +      +     ++ A    +  +  D 
Sbjct: 692  VRSNQATCINQRPLVYEGERVVEGQPIADGPSTDN-GELALGYNIIVAYMPWEGYNYEDA 750

Query: 928  SLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             L   +        S  + +     R      E          E   +D D+E  I+   
Sbjct: 751  ILLSENLVKRDLYTSIHIEEYECDARDTKLGPEEITRDIPNVAEEALKDLDEE-GIVSIG 809

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R  +IL G+    G         L   +  E  R                 E     
Sbjct: 810  ADVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTS 852

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                          KI   +  D++PPGV R+V+V++A KR I  GDKM+GRHGNKG+VS
Sbjct: 853  LRVPHGEGGKIIDVKIFTRENNDELPPGVNRLVRVYIAQKRKISVGDKMSGRHGNKGVVS 912

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ+ ETHLG AC  LG++IK        
Sbjct: 913  RIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQVLETHLGMACRVLGQRIKDG------ 966

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                            +    +  +   +  V  + +  ++G+ ++TPVFDGA ++ +  
Sbjct: 967  ---------------DSTVEGDLRAAGYNFDVNGMPKPDEAGIHIATPVFDGAGDDDVFG 1011

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             +R A L   G+++LYDG TGEPF+  VTVG +YMLKL+H+V DK++ARSTG YSLVTQQ
Sbjct: 1012 TIRAAGLPADGKTVLYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARSTGPYSLVTQQ 1071

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G++  E 
Sbjct: 1072 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYESIVKGDNIPEP 1131

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            G PESF VL+KE+QA+GL I + N   K  A  +E  +
Sbjct: 1132 GVPESFKVLIKELQAIGLDIKVLNEDAKEIAIRDEEDE 1169


>gi|313123100|ref|YP_004033359.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. bulgaricus ND02]
 gi|312279663|gb|ADQ60382.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. bulgaricus ND02]
          Length = 1220

 Score =  818 bits (2112), Expect = 0.0,   Method: Composition-based stats.
 Identities = 402/963 (41%), Positives = 571/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 5   LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 54

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 55  DILPISDASGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 105

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 106 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 162

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 163 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 222

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 223 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 281

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGE+    G V++ + ++ +              
Sbjct: 282 YKVNKKLSLKNRLLGYTLAETLADPDTGEVLAAKGTVVNNEVMDVLKDYL---------- 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 332 ------------------DRDDFKTVTYTPSDEGVIPEPVTVQEIKVFSREIPDRE---- 369

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 370 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 424

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 425 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 484

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 485 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 544

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 545 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 604

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 605 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 664

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME   A  SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 665 PLVATGMEYRAAHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 718 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 778 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDENGIIRIGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV++F R 
Sbjct: 838 HDGDILVGKVTPKGITELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQDVQVFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 269/1106 (24%), Positives = 402/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 198  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 247

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 248  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 307

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 308  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 366

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 367  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 426

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 427  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 486

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 487  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 546

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 547  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 606

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 607  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 651

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV                +T +   A   +       
Sbjct: 652  ---------HQRQAVPLINPHGPLV----------------ATGMEYRAAHDSGDALLAE 686

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 687  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 737

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 738  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 790

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 791  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 849

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 850  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGVVQDVQ------ 892

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 893  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 952

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 953  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 1000

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 1001 ---------------------------------VWDFVRE---------AGVDSDGKTVL 1018

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1019 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1078

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1079 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1138

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1139 LGLDLRVLDSDENEVELRDMDEDSNE 1164


>gi|238927722|ref|ZP_04659482.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
 gi|238884438|gb|EEQ48076.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
          Length = 1246

 Score =  817 bits (2111), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/953 (45%), Positives = 580/953 (60%), Gaps = 98/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  +    E++++P L+++Q+ASY  FL            GL   F+ + PI  FSG
Sbjct: 9   RRTRYSYAHIKEVMEMPHLLDIQRASYQWFL----------EVGLAEIFRDISPIQDFSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+TYA PL++ +RL+          +   +IKEQ +
Sbjct: 59  NLILSFESFALGEPKYDLDECKERDVTYAAPLRVNVRLV---------NRETGEIKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +      +GK LY   +IP++G 
Sbjct: 110 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGTYYGVEID---TTGKELYNATMIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ D+I VRIDR RK+PVT  + ALG +++ EI + F          +      
Sbjct: 167 WIELETDANDVISVRIDRTRKMPVTYLIRALGYETDAEIRALFGDDPRILATIERDT--- 223

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS-------- 300
                  G  V      +  GE   E + ++L   L    +   +  +G           
Sbjct: 224 -DEVKTRGRAVIEIYRRLRPGEPANEDNARQLLEVLFFDPRRYDLATVGRYKLTKKLGWR 282

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L G  +AE IV+ ETGEI    G+ I  + ++ +       I         +   I  
Sbjct: 283 RRLLGKVLAEPIVDKETGEIVFPKGEPITPEMVDAVSAERETAIF-------GDGELISF 335

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +                                + + L   +  Y   TV R       
Sbjct: 336 DVQKPDG--------------------------EIHHMLCAPTRDYQFRTVTR------- 362

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                        EDI+A I  L+ L NG G  DDID+LGNRRVR+VGE+L+NQ+R+GL 
Sbjct: 363 -------------EDIMAAISYLLGLMNGFGNTDDIDHLGNRRVRAVGELLQNQFRIGLS 409

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+S  + +S+ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 410 RMERVVRERMSIQETESITPQGLINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHKRR 469

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+ET
Sbjct: 470 LSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLANYARVNQFGFMET 529

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V     +VT+DV YL+A EE+   IAQAN  LDE+  F  E V  R   E  L PR
Sbjct: 530 PYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPLDENEYFVNERVTARFHEETGLHPR 589

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           E++D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLLK +AP VGTGME  
Sbjct: 590 ERVDYMDVSPRQVFSIATAMIPFLENDDANRALMGANMQRQAVPLLKTQAPLVGTGMEYK 649

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++AK +G V +V A  I +RS EG  D        Y+L KF RSNQ TC+NQ
Sbjct: 650 AACDSGVMVLAKHSGEVTEVSADAITVRSDEGAFD-------TYKLQKFIRSNQATCINQ 702

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +PLV VGD V     IADGPSTD G+LALG N++VA+MPW GYN+ED++L+SE +V  D+
Sbjct: 703 KPLVYVGDRVTEGQPIADGPSTDNGELALGYNIIVAYMPWEGYNYEDAVLLSENLVKRDL 762

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV+E+ LK++DE GII +GA+V PGDILVGK+
Sbjct: 763 YTSIHIEEYECDARDTKLGPEEITRDIPNVAEDALKDLDEDGIISIGADVRPGDILVGKV 822

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G ++DV+IF R   D
Sbjct: 823 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIIDVKIFTRENND 875



 Score =  582 bits (1500), Expect = e-163,   Method: Composition-based stats.
 Identities = 273/1059 (25%), Positives = 417/1059 (39%), Gaps = 93/1059 (8%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    +I  L+ D     A I     TD+ K R  A+++IYR +RPG+ +    
Sbjct: 193  LIRALGYETDAEIRALFGDDPRILATI--ERDTDEVKTRGRAVIEIYRRLRPGEPANEDN 250

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGK 450
            A  +   LFFD  +YDL+TVGR K+  +L        + +          +I+       
Sbjct: 251  ARQLLEVLFFDPRRYDLATVGRYKLTKKLGWRRRLLGKVLAEPIVDKETGEIVFPKGEPI 310

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                       R     G+     + +     +   +                +  + ++
Sbjct: 311  TPEMVDAVSAERETAIFGDGELISFDVQ----KPDGEIHHMLCAPTRDYQFRTVTREDIM 366

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGR 568
            +A+             + ++ L      RR+ A+G+      R       R V      R
Sbjct: 367  AAISYLLGLMNGFGNTDDIDHLG----NRRVRAVGELLQNQFRIGLSRMERVVRE----R 418

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +   ET      GL++     A V  +             +  +    LS +  + R  A
Sbjct: 419  MSIQETESITPQGLINIRPVVAAVKEFFGSSQL------SQFMDQHNPLSELTHKRRLSA 472

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                 L             R      +       +    P +        I  + +  + 
Sbjct: 473  LGPGGL------------SRERAGFEVRDVHNSHYGRMCPVES--PEGPNIGLIGSLANY 518

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              +            +  E   V   +  + A      I+A+    +   D     +   
Sbjct: 519  ARVNQFGFMETPYRRVDKEHHRVTDDVRYLTADEEDELIIAQANEPL---DENEYFVNER 575

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                    +G+     + +   +     +    +         +  A+            
Sbjct: 576  VTARFHEETGLHPRERVDYMDVSPRQVFS----IATAMIPFLENDDANRALMGANMQRQA 631

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR--DTKLGPEEITRDIP 866
              +L    P  G   E      +  V      S  + E    A    +  G  +  +   
Sbjct: 632  VPLLKTQAPLVGTGME-YKAACDSGVMVLAKHSGEVTEVSADAITVRSDEGAFDTYKLQK 690

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             +       I++  ++ VG  V  G  +    +      +     ++ A    +  +  D
Sbjct: 691  FIRSNQATCINQKPLVYVGDRVTEGQPIADGPSTDN-GELALGYNIIVAYMPWEGYNYED 749

Query: 927  TSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              L   +        S  + +     R      E          E   +D  DE  I+  
Sbjct: 750  AVLLSENLVKRDLYTSIHIEEYECDARDTKLGPEEITRDIPNVAEDALKDL-DEDGIISI 808

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                R  +IL G+    G         L   +  E  R                 E    
Sbjct: 809  GADVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDT 851

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                           KI   +  D++PPGV R+V+V++A KR I  GDKM+GRHGNKG+V
Sbjct: 852  SLRVPHGEAGKIIDVKIFTRENNDELPPGVNRLVRVYIAQKRKISVGDKMSGRHGNKGVV 911

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            SRI+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ+ ETHLG AC  LG++IK      +
Sbjct: 912  SRIMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQVLETHLGMACRVLGQRIKDGDPTVE 971

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            A+   +                       D     +     +G+ ++TPVFDGA ++ + 
Sbjct: 972  ADLRAAGY---------------------DFDKNGMPVPDVAGIHIATPVFDGAGDDDVF 1010

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              +R A L   G+++LYDG TGEPF+  VTVG +YMLKL+H+V DK++ARSTG YSLVTQ
Sbjct: 1011 GTIRAAGLPADGKTVLYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARSTGPYSLVTQ 1070

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G++  E
Sbjct: 1071 QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYESIVKGDNIPE 1130

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             G PESF VL+KE+QA+GL I + N   K  A  +E  +
Sbjct: 1131 PGVPESFKVLIKELQAIGLDIKVLNEDAKEIAIRDEEEE 1169


>gi|325125168|gb|ADY84498.1| RNA-polymerase DNA-directed beta subunit [Lactobacillus delbrueckii
           subsp. bulgaricus 2038]
          Length = 1224

 Score =  817 bits (2111), Expect = 0.0,   Method: Composition-based stats.
 Identities = 401/963 (41%), Positives = 570/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 5   LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 54

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 55  DILPISDTSGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 105

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 106 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 162

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 163 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 222

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 223 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 281

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGE+    G V++ + ++ +              
Sbjct: 282 YKVNKKLSLKNRLLGYTLAETLADPDTGEVLAAKGTVVNNEVMDVLKDYL---------- 331

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 332 ------------------DRDDFKTVTYTPSDEGVIPEPVTVQEIKVFSREIPDRE---- 369

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 370 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 424

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 425 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 484

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 485 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 544

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 545 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 604

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 605 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 664

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME      SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 665 PLVATGMEYRAGHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 717

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 718 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 777

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 778 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDENGIIRIGAEV 837

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV++F R 
Sbjct: 838 HDGDILVGKVTPKGITELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQDVQVFTRE 897

Query: 949 GID 951
             D
Sbjct: 898 AGD 900



 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 270/1106 (24%), Positives = 401/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 198  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 247

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 248  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 307

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 308  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 366

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 367  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 426

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 427  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 486

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 487  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 546

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 547  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 606

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 607  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 651

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV  G E R                    +       
Sbjct: 652  ---------HQRQAVPLINPHGPLVATGMEYRAG----------------HDSGDALLAE 686

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 687  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 737

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 738  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 790

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 791  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 849

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 850  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGVVQDVQ------ 892

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 893  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 952

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 953  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 1000

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 1001 ---------------------------------VWDFVRE---------AGVDSDGKTVL 1018

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1019 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1078

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1079 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1138

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1139 LGLDLRVLDSDENEVELRDMDEDSNE 1164


>gi|188584828|ref|YP_001916373.1| DNA-directed RNA polymerase, beta subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179349515|gb|ACB83785.1| DNA-directed RNA polymerase, beta subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 1174

 Score =  817 bits (2110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/967 (43%), Positives = 591/967 (61%), Gaps = 116/967 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           +R+ + K  E+ ++PDLIE+QK+SY  FL          +EGL+  F  + PI  F+G  
Sbjct: 9   LRRSYSKLDEVFELPDLIEIQKSSYQWFL----------DEGLKEMFDDISPIEDFTGGL 58

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           +LEFV Y    PK+ V+DC  RD+TY+VPLK+ +RL+          +   ++KEQ ++M
Sbjct: 59  VLEFVDYSLGEPKYSVEDCKERDVTYSVPLKVKVRLV---------NQETGEVKEQEVFM 109

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT++GTF+I G +R++VSQL RSPG++F  +      +G  LY+  IIP++G W+
Sbjct: 110 GDFPLMTENGTFIINGAERVIVSQLVRSPGVYFSSEID---SNGNTLYSGTIIPNRGAWL 166

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSA 251
           + E +++++I VR+DR RK+PVT  + ALG  +++ I   F          +        
Sbjct: 167 EFEMNAQNVISVRVDRTRKLPVTVLIRALGYGTDDDIFHLFGEDPRIKATLEKDHTDSYE 226

Query: 252 ADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS--------DC 302
           A ++   K       +  GE + +E+ K L   L    K   +  +G           D 
Sbjct: 227 AGILEIYK------RLRPGEPLNVENAKSLFESLFFDPKRYDLAKVGRHKINQKLELGDR 280

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G    E I +               +++ E I       I    ++ +  +      +
Sbjct: 281 LLGKTARETITD---------------DETGEVIIEEG-TVIDTQDLEKLEQSGITSIRI 324

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D  +DR   +L                                               
Sbjct: 325 GKDDQEDRDCVVLTN--------------------------------------------G 340

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D   +V+++ + DI+A I  +++L +G G +DDID+LGNRR+R VGE+L+NQ+R+GL RM
Sbjct: 341 DVDKNVKNLTRNDIVASIGYMLNLLDGLGFVDDIDHLGNRRLRCVGELLQNQFRIGLSRM 400

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER++  D+DS+ P  LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 401 ERVVRERMTIQDVDSITPSALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 460

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL+S+ +VN +GFIETPY
Sbjct: 461 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLISSLSSYGKVNEFGFIETPY 520

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV   +G VT  + YLSA EE+   IAQAN+ LD DG F+ + +  R   E ++   +K
Sbjct: 521 RKVDKENGLVTEKIEYLSAHEEDKYVIAQANTPLDSDGYFSSDRITARYRHETLITTPDK 580

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ID++D SP+Q+VS+A + IPFLENDD+NR LMG NMQRQAVPLL+ E+P VGTGME   A
Sbjct: 581 IDYMDVSPRQLVSVATAQIPFLENDDANRALMGSNMQRQAVPLLQTESPLVGTGMEYRTA 640

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVE----------------GDLDPSTSGVDIYRL 764
             SGA + ++  G V++V +  I +R  +                G+     +G DIY+L
Sbjct: 641 YDSGAVVKSRADGTVDKVQSNEIWVRRNDNAKGRVVNGRTGEVFEGETGEVRAGYDIYKL 700

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KFQRSNQ TC+NQ P+V+ G ++  N I+ADGPSTD G++ALG+N+LV FMPW GYN+E
Sbjct: 701 QKFQRSNQGTCMNQVPIVEEGQQITENQILADGPSTDNGEIALGQNVLVGFMPWEGYNYE 760

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++LISE++V +D FTSIHIEE+E  ARD KLGPEEITRDIPNV E+ LKN+DE GI+ +
Sbjct: 761 DAILISEKLVKDDTFTSIHIEEYEAEARDAKLGPEEITRDIPNVGEDALKNLDERGIVRI 820

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVDV++
Sbjct: 821 GAEVKSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGEHGIVVDVKV 880

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 881 FNRDDGD 887



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 245/1067 (22%), Positives = 396/1067 (37%), Gaps = 136/1067 (12%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    DI  L+      +  I+ TL  D     +  +L+IY+ +RPG+      
Sbjct: 191  LIRALGYGTDDDIFHLF----GEDPRIKATLEKDHTDSYEAGILEIYKRLRPGEPLNVEN 246

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            A+S+F  LFFD  +YDL+ VGR K+N +L L      +           + + D   G+ 
Sbjct: 247  AKSLFESLFFDPKRYDLAKVGRHKINQKLELGDRLLGKT--------ARETITDDETGEV 298

Query: 452  TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
             I++   +  + +  + +      R+G    E      +++ D+D  +     N   +V+
Sbjct: 299  IIEEGTVIDTQDLEKLEQSGITSIRIGKDDQEDRDCVVLTNGDVDKNVKNLTRN--DIVA 356

Query: 512  AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-------GGVARARAGVEMRDVHPT 564
            ++             + ++ L      RRL  +G+        G++R    V  R     
Sbjct: 357  SIGYMLNLLDGLGFVDDIDHLG----NRRLRCVGELLQNQFRIGLSRMERVVRERMTIQD 412

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                   A  +    I  +      ++++ +               TN +  L+      
Sbjct: 413  VDSITPSALINIRPVIASIKEFFGSSQLSQF------------MDQTNPLAELT------ 454

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLE 683
                               L     + E        +          +       I  + 
Sbjct: 455  ------------HKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIS 502

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDA 740
            +  S   +            +  E   V   +E + A      ++A+            +
Sbjct: 503  SLSSYGKVNEFGFIETPYRKVDKENGLVTEKIEYLSAHEEDKYVIAQANTPLDSDGYFSS 562

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             RI  R     L  +   +D   +             Q   V         +  A+    
Sbjct: 563  DRITARYRHETLITTPDKIDYMDVSP----------RQLVSVATAQIPFLENDDANRALM 612

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISE----RMVSEDVFTSIHIEEFEVMARDTKL 856
                      +L    P  G   E           +  ++     +   E  V   D   
Sbjct: 613  GSNMQRQAVPLLQTESPLVGTGMEYRTAYDSGAVVKSRADGTVDKVQSNEIWVRRNDNAK 672

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK-GESPMTPEEKLLRA 915
            G     R       E  +      I  +               P   E     E ++L  
Sbjct: 673  GRVVNGRTGEVFEGETGEVRAGYDIYKLQKFQRSNQGTCMNQVPIVEEGQQITENQILAD 732

Query: 916  IFGEKAVDVR---DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
                   ++    +  +           D  + +   + K++   S+  E+ E  ARD  
Sbjct: 733  GPSTDNGEIALGQNVLVGFMPWEGYNYEDAILIS-EKLVKDDTFTSIHIEEYEAEARDAK 791

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
                 + R+I +   + L   +     +     K   +L   +  +       +  +   
Sbjct: 792  LGPEEITRDIPNVGEDALKNLDERGIVRIGAEVKSGDILVGKVTPKGETELTAEERLLRA 851

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                    ++               + K+     GD++PPGV ++V+V++A KR I  GD
Sbjct: 852  IFGEKAREVRDTSLKVPHGEHGIVVDVKVFNRDDGDELPPGVNQLVRVYIAQKRKISEGD 911

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++++ILP EDMPFL           P G P         E  L    V  
Sbjct: 912  KMAGRHGNKGVIAKILPEEDMPFL-----------PDGTP--------LEIILSPLGV-- 950

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
                                                +    +  +   A+    G+ +++
Sbjct: 951  -------------------------------PSRMNLGQVLETHLGWAAKAL--GLKMAS 977

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            PVFDGADE+ I   L+ A L E+G++ L DG TGEPFD  VTVGYIYMLKL H+V DK++
Sbjct: 978  PVFDGADEDEILETLKEAGLPENGKTQLVDGRTGEPFDNEVTVGYIYMLKLAHLVDDKIH 1037

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + 
Sbjct: 1038 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYSLQELLTVKSDDVVGRVKT 1097

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            YESIV G++  E G PESF VL+KE+Q+LG+ + + N      +  +
Sbjct: 1098 YESIVKGDNVPEPGIPESFKVLIKELQSLGMDVKVLNEEQGLVSIKD 1144


>gi|331004055|ref|ZP_08327537.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae oral
           taxon 107 str. F0167]
 gi|330411641|gb|EGG91049.1| DNA-directed RNA polymerase subunit beta [Lachnospiraceae oral
           taxon 107 str. F0167]
          Length = 1285

 Score =  817 bits (2110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/951 (44%), Positives = 584/951 (61%), Gaps = 58/951 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F    E++++P+LIE+QK SY  FL          + GL+  F+ +FPI  F+G   
Sbjct: 2   RMSFQTQKEVLEMPNLIEIQKDSYQWFL----------DAGLKEVFRDIFPIEDFAGHFS 51

Query: 74  LEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
           L+FV+++   D  K+ +++C  RD TYA PLK+ +RL+  D D         +I E  I+
Sbjct: 52  LDFVNFKLARDEVKYSIEECKDRDTTYAAPLKVKIRLVNKDKD---------EINEHEIF 102

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +GDLPLMT  G+FVI G +R++VSQL RSPGI++  D  +    GK L+  ++IP++G W
Sbjct: 103 LGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYTIDHDKI---GKELFMSQVIPNRGAW 159

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWCFP 248
           ++ E DS DI + R+DR RKVP+T  L A G+ +  +I+  F    KI+ S   D     
Sbjct: 160 LEYETDSNDIFYARVDRTRKVPITVLLRAFGLGTNTQIIDMFGEEPKIMASFAKDPSENY 219

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
                 +         + +D+ E ++ +         L K  + K  K L    + + G 
Sbjct: 220 QDGLLELYKKIRPGEPLSVDSAESLLRAMFFDARRYDLAKVGRYKFNKKL-HFKNRIKGH 278

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            +A D+V+  TGE+  +A  V+D +    I ++    IP +++  V     + + ++ D 
Sbjct: 279 TLARDVVDENTGEVLAQADTVVDAQIATTIQNA---AIPAVWIKGVEREVKVLSNMMVDI 335

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                +            D  +  V E ++        +      G   +          
Sbjct: 336 ESYVPE----------LTDPKSIGVTEQVYYPK---LQQLMEENEGEELIKAIEKNINEL 382

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             +HI KEDI A +   + +    G  DDID+LGNRR+R+VGE+L+NQYR+GL RMER +
Sbjct: 383 IPKHITKEDIFATVNYNMHIEEHIGNRDDIDHLGNRRIRAVGELLQNQYRIGLTRMERVV 442

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+++ DIDS+ PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH RRLSALG 
Sbjct: 443 RERMTTQDIDSITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTHKRRLSALGP 502

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV- 605
           GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL SFARVN YGF+E PYR V 
Sbjct: 503 GGLSRERAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASFARVNEYGFVEAPYRVVD 562

Query: 606 -----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
                 + +VT +VVYL+A EE+N  +AQAN  LD +G F    V  R   E     ++ 
Sbjct: 563 KSQDPENPRVTEEVVYLTADEEDNFTVAQANEPLDAEGHFVNNNVSGRYRDETSEFKKKN 622

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ID +D SP+ V S+A S+IPFLENDD+NR LMG NMQRQAVPL+  +AP VGTGME+  A
Sbjct: 623 IDLMDVSPRMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLMITDAPVVGTGMETKAA 682

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  +VAK +G V +  + +IVI+  +  +      +D Y+L+KF RSNQ+   NQ+P
Sbjct: 683 VDSGVCVVAKNSGTVMECSSDKIVIKRDDDAV------LDTYKLIKFARSNQSNSYNQKP 736

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V   ++IADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V  DV+T
Sbjct: 737 IVFKGNHVNAGEVIADGASTYNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVEYDVYT 796

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  AR+TKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDILVGK+TP
Sbjct: 797 SIHIEEYECAARETKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDILVGKVTP 856

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 857 KGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGVVVDAKVFTREAGD 907



 Score =  552 bits (1422), Expect = e-154,   Method: Composition-based stats.
 Identities = 262/1173 (22%), Positives = 441/1173 (37%), Gaps = 79/1173 (6%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            KI    +              +     +    I+  E+VI S    + G+  ++    + 
Sbjct: 85   KIRLVNKDKDEINEHEIFLGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYTIDHDKIG 144

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                 S  +     A      ++ +I+    D   +  +  +  +         +D    
Sbjct: 145  KELFMSQVIPNRG-AWLEYETDSNDIFYARVDRTRKVPITVLLRAFGLGTNTQIIDMFGE 203

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               I  +   D +++ +D LL++Y+ +RPG+  +   AES+   +FFD+ +YDL+ VGR 
Sbjct: 204  EPKIMASFAKDPSENYQDGLLELYKKIRPGEPLSVDSAESLLRAMFFDARRYDLAKVGRY 263

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            K N +L+         + ++ +      ++   +          + N  + +V       
Sbjct: 264  KFNKKLHFKNRIKGHTLARDVVDENTGEVLAQADTVVDAQIATTIQNAAIPAV------- 316

Query: 475  YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +  G+ R  + +   +  ++       D  +       V E     +L QL E       
Sbjct: 317  WIKGVEREVKVLSNMMVDIESYVPELTDPKSIG-----VTEQVYYPKLQQLMEENEGEEL 371

Query: 535  ITHTRRLSA-LGQGGVARARAG-VEMRDVHPT-HYGRICPAETSEGHNIGLVSSLTSFAR 591
            I    +    L    + +         ++H   H G     +      I  V  L    +
Sbjct: 372  IKAIEKNINELIPKHITKEDIFATVNYNMHIEEHIGNRDDIDHLGNRRIRAVGELL---Q 428

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS----------LDEDGSFT 641
                  +    R V +   T D+  ++     N     A               +  +  
Sbjct: 429  NQYRIGLTRMERVVRERMTTQDIDSITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 488

Query: 642  EELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             EL   R             R   +  D        +     P   N      L      
Sbjct: 489  SELTHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASFARV 548

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
             +   +         +        +     +         V      + +    ++ + S
Sbjct: 549  NEYGFVEAPYRVVDKSQDPENPRVTEEVVYLTADEEDNFTVAQANEPLDAEGHFVNNNVS 608

Query: 758  GVDIYRLMKFQRSNQNTC-VNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            G       +F++ N +   V+ R +  V         +  A+              +++ 
Sbjct: 609  GRYRDETSEFKKKNIDLMDVSPRMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLMIT 668

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
              P  G   E    +     +V+++  T +     +++ +       +  + I       
Sbjct: 669  DAPVVGTGMETKAAVDSGVCVVAKNSGTVMECSSDKIVIKRDDDAVLDTYKLIKFARSNQ 728

Query: 873  LKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLR 930
              + ++  I+  G  VN G+++  G  T  GE  +     +    + G    D    S R
Sbjct: 729  SNSYNQKPIVFKGNHVNAGEVIADGASTYNGEIALGKNPLIGFMTWEGYNYEDAVLLSER 788

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLM 987
            +      T + +  +     +       + R+     +   +D  DE+ I+      R  
Sbjct: 789  LVEYDVYTSIHIEEYECAARETKLGPEEITRDVPGVGDDALKDL-DERGIIRIGAEVRAG 847

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+    G         L   +  E  R                 E      +    
Sbjct: 848  DILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSLKVPHG 890

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP E
Sbjct: 891  AYGVVVDAKVFTREAGDELAPGVTQNVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVE 950

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  + + + D     DI  
Sbjct: 951  DMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNVATPVFDGANENDIMD 1010

Query: 1168 LRSFLEKVIGTG--SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            +       + +       K  D  D  V+                           +   
Sbjct: 1011 MLEVANDYVNSEWSDFENKYKDVLDPGVIEYLG----------------SHPENRKLWEG 1054

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              L   G+  L DG TGE FD PVT+G+++ LKL+HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 1055 VPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHMVDDKIHARSTGPYSLVTQQPLGG 1114

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV GR + YE+++ G +  + G PE
Sbjct: 1115 KAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVTGRVKTYEAVIKGENIPDAGIPE 1174

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            SF VL+KE+Q+LGL I +     +     E   
Sbjct: 1175 SFKVLLKELQSLGLDISVLGEDGREVELKENTE 1207


>gi|158564067|sp|Q04C22|RPOB_LACDB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1221

 Score =  817 bits (2110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 401/963 (41%), Positives = 570/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 2   LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 52  DILPISDTSGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 160 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGE+    G V++ + ++ +              
Sbjct: 279 YKVNKKLSLKNRLLGYTLAETLADPDTGEVLAAKGTVVNNEVMDVLKDYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 329 ------------------DRDDFKTVTYTPSDEGVIPEPVTVQEIKVFSREIPDRE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 367 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 482 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 541

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 542 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 602 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME      SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 662 PLVATGMEYRAGHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 715 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 775 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDENGIIRIGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV++F R 
Sbjct: 835 HDGDILVGKVTPKGITELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQDVQVFTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 270/1106 (24%), Positives = 401/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 195  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 244

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 245  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 304

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 305  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 363

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 364  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 423

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 424  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 483

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 484  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 543

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 544  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 603

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 604  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 648

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV  G E R                    +       
Sbjct: 649  ---------HQRQAVPLINPHGPLVATGMEYRAG----------------HDSGDALLAE 683

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 684  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 734

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 735  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 787

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 788  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 846

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 847  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGVVQDVQ------ 889

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 890  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 949

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 950  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 997

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 998  ---------------------------------VWDFVRE---------AGVDSDGKTVL 1015

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1016 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1075

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1076 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1135

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1136 LGLDLRVLDSDENEVELRDMDEDSNE 1161


>gi|291531030|emb|CBK96615.1| DNA-directed RNA polymerase subunit beta [Eubacterium siraeum 70/3]
          Length = 1261

 Score =  817 bits (2110), Expect = 0.0,   Method: Composition-based stats.
 Identities = 410/952 (43%), Positives = 576/952 (60%), Gaps = 55/952 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K  E+  +P+LIE+QK SY  FL          +EG++  FK +  IT  +G
Sbjct: 11  RNTRMSFSKINEVQKMPNLIEIQKDSYKWFL----------DEGIKEVFKDISSITDANG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L FV Y  D  PK+ +++C  RD TYA PL++  +L               ++ E  
Sbjct: 61  KLVLSFVDYRLDEDPKYSIEECKERDTTYAAPLRVKAQL---------RNNETGEVVENE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTFVI G +R++VSQL RSPG+++  D  +    GK L+   +IP++G
Sbjct: 112 IFMGDFPLMTESGTFVINGAERVIVSQLVRSPGVYYGFDYDKT---GKKLFKSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY---SQRGDFW 245
            W++ E DS DI +VRID+ RK+P T+F+ ALG+ S++ ++  F          Q  D  
Sbjct: 169 AWLEYEMDSNDIFYVRIDKNRKIPATTFIRALGISSDDDLIDLFGEDPRIVQTIQEKDAT 228

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+    I +         L +  + K  K LG+ +  +
Sbjct: 229 KNTEEALLEVYRKLRPGEPPTVDSANTHINNLFFDAKRYDLARFGRYKYNKKLGV-ASRI 287

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   A+ I++  TGEI ++  + I+ +  + +  + +++  I   + +          +
Sbjct: 288 AGHKAAQPIIDPTTGEILVDENEFINAEKAQAVEQAGVKECVIFSEEKIAKVLGNGMVDI 347

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                +  DA       +   +   FSV   + +    D +        RV         
Sbjct: 348 AGYIPESIDA-----ESLGINEKVCFSVLREILDKCGDDVEALTAELSNRV--------- 393

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI  +DI A +   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+G  RME
Sbjct: 394 EDLIPKHITLDDIFATVSYFINLCEGVGEVDDIDHLGNRRIRSVGELLQNQFRIGFARME 453

Query: 484 RSIKERI--SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           R I+ER+   S + D V P  LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH RRL
Sbjct: 454 RVIRERMGLQSQEGDKVTPNALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTHKRRL 513

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RA  E+RDVH +HYGR+CP ET EG NIGL+S L SFA++N YGFIE P
Sbjct: 514 SALGPGGLSRDRASFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASFAKINKYGFIEAP 573

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      V ++V Y++A  E+N  +AQAN  LDE G F  + V  R   E + V R+
Sbjct: 574 YRKVDKETGVVLDEVTYMTADMEDNYVVAQANEPLDEQGKFARKRVNARFREEILEVDRD 633

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPL+  + P VGTGME   
Sbjct: 634 RVDYMDVSPKMVVSVATAMIPFLENDDANRALMGANMQRQAVPLMVTQNPIVGTGMEYKA 693

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGA +VAK  G+V +  A  IV+    G           Y+L+KF+RSNQ TCVNQR
Sbjct: 694 AVDSGAVVVAKEDGVVTKCSADEIVVTDNNGVEHS-------YKLIKFKRSNQGTCVNQR 746

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V  G E++  D++ADGP+T  G+++LG+N L+ FM W GYN+ED++LI+E++V  DV+
Sbjct: 747 PAVSKGMEIKTGDVLADGPATSQGEISLGKNALIGFMTWEGYNYEDAVLINEKLVYNDVY 806

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE+E+  RDTKLGPEEITR+IPNVSE+ LK++DE GII +GAEV+ GDI+VGK+T
Sbjct: 807 TSIHIEEYELECRDTKLGPEEITREIPNVSEDALKDLDERGIIRIGAEVHSGDIMVGKVT 866

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFG+KA +VRD SLRVP G SG +VDV++F R   D
Sbjct: 867 PKGETELTAEERLLRAIFGDKAREVRDNSLRVPHGESGIIVDVKVFTRQNCD 918



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 184/530 (34%), Positives = 261/530 (49%), Gaps = 47/530 (8%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   + I          +++   +  G E+  GD+L        +  ++  +  L
Sbjct: 721  DNNGVEHSYKLIKFKRSNQGTCVNQRPAVSKGMEIKTGDVLADGP-ATSQGEISLGKNAL 779

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                  +  +  D  L     V   V        + ++  +  +  E    E +    +D
Sbjct: 780  IGFMTWEGYNYEDAVLINEKLVYNDVYTSIHIEEYELECRDTKLGPEEITRE-IPNVSED 838

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD     R+   +   + + G    K  T L+++        +  +    D+  + 
Sbjct: 839  ALKDLDERGIIRIGAEVHSGDIMVGKVTPKGETELTAE-------ERLLRAIFGDKAREV 891

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               SL+V +  S  I++     K+   Q  D++ PGV  VV+ ++A KR I  GDKMAGR
Sbjct: 892  RDNSLRVPHGESGIIVD----VKVFTRQNCDELSPGVNMVVRCYIAQKRKISVGDKMAGR 947

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRIL  EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+AC  L  +I 
Sbjct: 948  HGNKGVVSRILKQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYACKALDWQIM 1007

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     DI       E                                      D 
Sbjct: 1008 TPVFDGAHEADIRACFEKAEAERENYKDK-----------------------------DS 1038

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A  +          +    ++ L DG TGE FD PVTVGY+Y LKL+H+V DK++ARSTG
Sbjct: 1039 ARID-----FSKIPMRSDCKTQLTDGRTGEKFDSPVTVGYMYYLKLHHLVDDKIHARSTG 1093

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+VGR + YE+IV
Sbjct: 1094 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDIVGRVKTYEAIV 1153

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             G+   + G PESF VL KE+Q+LGL I + ++        +   + ++ 
Sbjct: 1154 KGDPVPKAGVPESFKVLFKELQSLGLDIKVLDADKNEIDLRQTYEEDDEY 1203


>gi|104773535|ref|YP_618515.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|122397386|sp|Q1GBM5|RPOB_LACDA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|103422616|emb|CAI97221.1| DNA-directed RNA polymerase beta chain [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
          Length = 1221

 Score =  816 bits (2108), Expect = 0.0,   Method: Composition-based stats.
 Identities = 401/963 (41%), Positives = 569/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 2   LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 51

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 52  DILPISDTSGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 102

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 103 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 160 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 220 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + +  TGE+    G V++ + ++ +              
Sbjct: 279 YKVNKKLSLKNRLLGYTLAETLADPGTGEVLAAKGTVVNNEVMDVLKDYL---------- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 329 ------------------DRDDFKTVTYTPSDEGVIPEPVTVQEIKVFSREIPDRE---- 366

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 367 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 421

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 422 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 481

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 482 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 541

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 542 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 601

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 602 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 661

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME      SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 662 PLVATGMEYRAGHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 714

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 715 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 774

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 775 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDENGIIRIGAEV 834

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV++F R 
Sbjct: 835 HDGDILVGKVTPKGITELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQDVQVFTRE 894

Query: 949 GID 951
             D
Sbjct: 895 AGD 897



 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 268/1106 (24%), Positives = 399/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 195  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 244

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD------------- 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L                 
Sbjct: 245  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPG 304

Query: 427  -------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                       +  E +  +   L        T    D        +V E +K   R   
Sbjct: 305  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 363

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 364  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 423

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 424  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 483

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 484  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 543

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 544  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 603

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 604  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 648

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV  G E R                    +       
Sbjct: 649  ---------HQRQAVPLINPHGPLVATGMEYRAG----------------HDSGDALLAE 683

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 684  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 734

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 735  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 787

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 788  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 846

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 847  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGVVQDVQ------ 889

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 890  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 949

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 950  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 997

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 998  ---------------------------------VWDFVRE---------AGVDSDGKTVL 1015

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1016 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1075

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1076 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1135

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1136 LGLDLRVLDSDENEVELRDMDEDSNE 1161


>gi|291541681|emb|CBL14791.1| DNA-directed RNA polymerase subunit beta [Ruminococcus bromii
           L2-63]
          Length = 1241

 Score =  816 bits (2108), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/951 (44%), Positives = 585/951 (61%), Gaps = 56/951 (5%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R  FGK  E+ID+P+LI++QKASY   L          +EGL+  FK V  IT +   
Sbjct: 12  TERMSFGKIDEVIDMPNLIDIQKASYKWLL----------DEGLKEVFKDVSGITDYQDN 61

Query: 72  AMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            +L+F+ Y  D   P + V +C  RD TY+  L++T RL+          KS  +IKE +
Sbjct: 62  LVLDFIDYTLDVDHPNYSVIECKVRDATYSAALRVTARLL---------NKSTGEIKESN 112

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R++VSQL RSPG+++  D  +    GK LY+  +IP++G
Sbjct: 113 VFMGDFPLMTASGTFVINGAERVIVSQLVRSPGVYYKMDHDKT---GKELYSTTVIPNRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIV--YSQRGDFWC 246
            W++ E D  D+ +VRID+ RK+PVTSF+ ALG+ ++ EIL  F        +   D   
Sbjct: 170 AWLEYETDVNDVFYVRIDKNRKLPVTSFIRALGLGTDAEILDYFGDDERMRATIEKDAAS 229

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                   +      S    +D+ +  I +         + +  + K  K LGI ++ L 
Sbjct: 230 NVEEGLIEVYKKLRPSEPPTVDSAQTHINNLFFDPGRYDMSRVGRYKYNKKLGI-ANRLE 288

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +AE I N  TGE+     + I ++   EI ++ ++ I  +          I N +V 
Sbjct: 289 GQVLAEPIANPRTGEVMALRDEKITKEKAFEIENAGVK-IAYVKAADETIVKVISNGMVD 347

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                  DA  +        D+      + +   L    ++ DL  + R + +       
Sbjct: 348 IACYVDFDAEAEC-------DIKENVRFDVLCEILDSCENEDDLKEMLRSRAD------- 393

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                HI  +DI A I  L  + +G G  DDID+LGNRR+R VGE+L+NQ+R+G  R+ER
Sbjct: 394 ELVPNHITVDDIFATINYLNCVAHGVGNTDDIDHLGNRRIRCVGELLQNQFRIGFSRLER 453

Query: 485 SIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ++ER+++   D++S+ P  LIN +PV +A+ EFF SS LSQ  +  N L+ +TH RRLS
Sbjct: 454 VVRERMTTQSQDMESLSPNSLINIRPVTAAIKEFFGSSPLSQFMDQGNPLAELTHKRRLS 513

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+S L SFAR+N YGFIE PY
Sbjct: 514 ALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLISYLASFARINKYGFIEAPY 573

Query: 603 RKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RK+      VT++VVY++A  E+N  +AQAN  LDE+G F    V  R   E +    E+
Sbjct: 574 RKIDKETGVVTDEVVYMTADVEDNYAVAQANEPLDENGRFVHSRVVGRYRDEFVEYSPER 633

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            DF+D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPLL++EAP VGTGME    
Sbjct: 634 FDFMDVSPKMVVSVATAMIPFLENDDANRALMGANMQRQAVPLLRSEAPIVGTGMEYKAG 693

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  I+A+  GIV  VDA  I ++   G +           ++KF RSNQ TC+NQRP
Sbjct: 694 TDSGVCILAEEDGIVMSVDARNIRVQYDSGRVQDFE-------VIKFLRSNQGTCINQRP 746

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G  V++ +++ADGP+T+ G++ALG+N L+ FM W GYN+ED++LI+E++V +DV+T
Sbjct: 747 IVSRGQRVKKGEVLADGPATENGEVALGKNALIGFMTWEGYNYEDAVLINEKIVRDDVYT 806

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE++  ARDTKLGPEEITRDIPNV E+ LK +DE GII +G+EV  GDILVGK+TP
Sbjct: 807 SIHIEEYDTEARDTKLGPEEITRDIPNVGEDVLKYLDEDGIIQIGSEVKAGDILVGKVTP 866

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  GTVVDV++F R    
Sbjct: 867 KGETELTAEERLLRAIFGEKAREVRDTSLRVPHGECGTVVDVKVFTRADSR 917



 Score =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 156/536 (29%), Positives = 225/536 (41%), Gaps = 78/536 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +    I  +       I++  I+  G  V  G++L      +    +   +  
Sbjct: 719  QYDSGRVQDFEVIKFLRSNQGTCINQRPIVSRGQRVKKGEVLADGPATEN-GEVALGKNA 777

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L      +  +  D  L     V   V        +  +  +  +  E     I  +  D
Sbjct: 778  LIGFMTWEGYNYEDAVLINEKIVRDDVYTSIHIEEYDTEARDTKLGPEEITRDIPNVGED 837

Query: 971  ---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE  I+      +  +IL G+    G         L   +  E  R         
Sbjct: 838  VLKYLDEDGIIQIGSEVKAGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 888

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIE-KIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                    E                   K+  +    +++ PGV +VV+V++A+KR I  
Sbjct: 889  --------EVRDTSLRVPHGECGTVVDVKVFTRADSRNELQPGVNKVVRVYLALKRKISV 940

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNK                            GV SR+               
Sbjct: 941  GDKMAGRHGNK----------------------------GVISRI--------------- 957

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 ++ +                L+ V+       +++      V         G  +
Sbjct: 958  ---LPMEDMPFLPDGTP--------LDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWKI 1006

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TPVFDGA E+ I   L+ A   E G++ L DG TGE FD PVTVGY+Y LKL+H+V +K
Sbjct: 1007 MTPVFDGAHEQDIFQCLKDAGYSEDGKTWLVDGRTGERFDNPVTVGYMYYLKLHHLVDEK 1066

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR 
Sbjct: 1067 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRV 1126

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + YE+IV G +    G PESF VL+KE+Q+L L + + NS  +     ++  +   
Sbjct: 1127 KTYEAIVKGQNIPAPGIPESFRVLIKELQSLSLDVRVLNSDGEEIDIKQKFDEDED 1182


>gi|315925264|ref|ZP_07921477.1| DNA-directed RNA polymerase subunit beta [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315621435|gb|EFV01403.1| DNA-directed RNA polymerase subunit beta [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 1260

 Score =  816 bits (2108), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/956 (43%), Positives = 589/956 (61%), Gaps = 57/956 (5%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ F K  E++++P+L+EVQ  SY  FL           +GLQ  F  +  IT ++G 
Sbjct: 12  RTRQSFSKIKEVLEMPNLLEVQLDSYKWFL----------EKGLQEVFDDIHEITDYTGN 61

Query: 72  AMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            +L+FV Y     PK+ +++C  RD TY  PLK+ +RLI          K   ++KEQ +
Sbjct: 62  LVLQFVDYAIDGEPKYSIEECKERDQTYYQPLKVRVRLI---------NKEKNEVKEQKV 112

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           Y+ DL  MT+ GTFV+ G +R++VSQL RSPG ++   + +    GK L+A ++IP++G 
Sbjct: 113 YLADLHKMTETGTFVVNGAERVIVSQLVRSPGAYYTMSRDKV---GKRLWASQVIPNRGA 169

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E DS D+++V+IDR RK+ +TS L A G+ ++ EIL  F       +         
Sbjct: 170 WLEYESDSNDLLYVKIDRTRKLSLTSMLRAFGLGTDAEILGVFGEDPRLVETLKKDA--- 226

Query: 250 SAADLMVGAKVSSSLVD-IDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            + D          +   +  GE   ++S + L + +    +   +  +G          
Sbjct: 227 -SNDTTTQVDGLLDIYRRLRPGEPPTVDSAESLLNSMFFDDRRYDLAKVGRYKYNKKLSI 285

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + L G   AED+++  TGE+  EAG   D ++   + ++ +  + +    +     +  
Sbjct: 286 ANRLMGQVAAEDVIDPATGEVLAEAGQKFDRETAWAVQNAGVNVVEVACQYNGEETTF-- 343

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                   +   +  +DI+    P D+S     + + +    D    D S     K    
Sbjct: 344 --------RVIGNGFVDIHTQELPFDISDI-EFDELVSKEALDEFLADDSLTDAEKHTAL 394

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI + D+ A +   + L    G +DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 395 KRNKYRLIPKHILQSDLFASVNYFLGLEYEIGEVDDIDHLGNRRLRSVGELLQNQFRIGL 454

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+S  D + + PQ LIN +P+ +A+ EFF SSQLSQ  +  N LS +TH R
Sbjct: 455 SRMERVVRERMSVQDDEILTPQSLINTRPINAALKEFFGSSQLSQFMDQNNPLSELTHKR 514

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL ++AR+N YGFIE
Sbjct: 515 RLSALGPGGLSRERAGFEVRDVHDSHYGRMCPIETPEGPNIGLIGSLATYARINEYGFIE 574

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR--CAGEEILVP 657
           +PYRKV +G  T++VVYL+A EE    IAQAN  LDE+  F  + V  R     + + + 
Sbjct: 575 SPYRKVVNGVATDEVVYLAADEEGEYAIAQANEPLDENSHFVNKQVTGRAGKNRDFVSIR 634

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           +E +DF+D SPKQV+S+AA+LIPFLENDD+NR LMG NMQRQAVPLL  EAP VGTGME+
Sbjct: 635 QEDVDFMDVSPKQVISVAAALIPFLENDDANRALMGANMQRQAVPLLIPEAPLVGTGMEA 694

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG   VA+  G V  V A  I IR  +         +D Y+L KF+R+NQ  C+N
Sbjct: 695 KAAKDSGNCQVARYDGEVVYVSADTIRIRRDD------VQDIDEYKLHKFERTNQGNCMN 748

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP V  G  V+  D+I+DGP+T++G+LALGRN L+ FM W GYN+ED++L++E ++ ED
Sbjct: 749 QRPRVDQGQHVKAGDVISDGPATEMGELALGRNALIGFMTWEGYNYEDAVLLNENLLKED 808

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +TSIHI EFE  AR+TKLGPEEITRDIPNV E+ LKN+DE GII VGAEV   DILVGK
Sbjct: 809 RYTSIHIAEFECEARETKLGPEEITRDIPNVGEDALKNLDENGIIYVGAEVKSEDILVGK 868

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           +TPKGE+ ++PEEKLLRAIFGEKA ++RDTSL+VP G +G VVDV++F+R   D++
Sbjct: 869 VTPKGETDLSPEEKLLRAIFGEKAREIRDTSLKVPHGEAGIVVDVKVFSRANKDED 924



 Score =  470 bits (1209), Expect = e-129,   Method: Composition-based stats.
 Identities = 173/597 (28%), Positives = 245/597 (41%), Gaps = 84/597 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L+   P  G   E                   +++    +  R   + 
Sbjct: 669  MGANMQRQAVPLLIPEAPLVGTGMEAKAAKDSGNCQVARYDGEVVYVSADTIRIRRDDVQ 728

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  +            +++   +  G  V  GD++      +    +      L    
Sbjct: 729  DIDEYKLHKFERTNQGNCMNQRPRVDQGQHVKAGDVISDGPATE-MGELALGRNALIGFM 787

Query: 918  GEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
              +  +  D  L   +        S  + +     R      E          E   ++ 
Sbjct: 788  TWEGYNYEDAVLLNENLLKEDRYTSIHIAEFECEARETKLGPEEITRDIPNVGEDALKNL 847

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      +  +IL G+    G         L   +  E  R      +++    
Sbjct: 848  -DENGIIYVGAEVKSEDILVGKVTPKGETDLSPEEKLLRAIFGEKARE-IRDTSLKVPHG 905

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +  +      +  +    +               + PGV  +V+V++A KR I  GDKMA
Sbjct: 906  EAGIVVDVKVFSRANKDED---------------LKPGVNTMVRVYIATKRKISVGDKMA 950

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMPFL DGTP+DI LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 951  GRHGNKGVISRILPQEDMPFLPDGTPLDICLNPLGVPSRMNIGQVLEVHLGMALRALGMH 1010

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I + + D    GDI  L                                           
Sbjct: 1011 IATPVFDAANEGDIQELLGKAGLPQDGKIQL----------------------------- 1041

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                                G++       GEPFD  VTVG +Y LKL+HMV +K++ARS
Sbjct: 1042 ------------------YDGRT-------GEPFDGRVTVGVMYYLKLHHMVDEKMHARS 1076

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+ TIKSDDVVGR + YE+
Sbjct: 1077 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEIQTIKSDDVVGRVKAYEA 1136

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK----NSAKMEEIPDFNKCE 1384
            IV G +  E G PE+F VL+KE Q+L L + +     K         +E  D  + +
Sbjct: 1137 IVKGENIPEPGLPEAFKVLIKEFQSLALDVTVYGEDNKMDVLELDLAQEALDNGEFD 1193


>gi|290968253|ref|ZP_06559796.1| DNA-directed RNA polymerase, beta subunit [Megasphaera genomosp.
           type_1 str. 28L]
 gi|290781735|gb|EFD94320.1| DNA-directed RNA polymerase, beta subunit [Megasphaera genomosp.
           type_1 str. 28L]
          Length = 1238

 Score =  815 bits (2106), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/953 (43%), Positives = 576/953 (60%), Gaps = 102/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E++ +P L+++Q  SY+ FL           +GL+  FK + PI   +G
Sbjct: 9   KRTRYTYAKINEVLKMPHLLDLQNKSYEWFL----------EKGLKDIFKDISPIEDAAG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F +++   PK+D+ +C  RD TYA PL++ +RL+              ++ ++ I
Sbjct: 59  NLSLSFENFKLGEPKYDIRECKERDTTYAAPLRVQVRLV---------NHETGEVNDKDI 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL+T  GTF+I G +R++VSQL RSPG+++  +       G  LY   +IP++G 
Sbjct: 110 FMGDFPLITDTGTFIINGAERVIVSQLVRSPGVYYGREID---PMGIRLYTSTVIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ DI++ RIDR RK+PVT  + ALG  +  EIL  F+         +      
Sbjct: 167 WIELETDANDIVYARIDRNRKIPVTVLIRALGWSTNAEILDLFFDDKRLKATFEKDTTES 226

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-------- 300
               L+   K       +   E   +ES + L  GL    +   +  +G           
Sbjct: 227 QEEALVEIYK------KLRPAEPPTVESARNLFEGLFFDARRYDMARVGRYKAAKKLGWE 280

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L GL + E IV+ ETGEI +EA   I  + +++I  S +     L             
Sbjct: 281 RRLFGLTLHEPIVDRETGEIIVEAHTEIGSEEVKKIRDSRVFSGEGLV------------ 328

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                      +AL++                                   G V   +  
Sbjct: 329 -----------EALVE--------------------------------KVDGSVYKIICN 345

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           N + P + R I +EDIIA I  L++L +G GT+DDID+LGNRR+R VGE+L+NQ+R+GL 
Sbjct: 346 NSNLPYEHRTITREDIIAHIDYLLNLMDGFGTVDDIDHLGNRRLRCVGELLQNQFRIGLT 405

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+++ D ++V  Q LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR
Sbjct: 406 RMERVVRERMTTQDAETVEAQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRR 465

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL  F +VN +GFIE 
Sbjct: 466 LSALGPGGLSRERAGFEVRDVHHSHYGRMCPVETPEGPNIGLISSLACFGKVNEFGFIEA 525

Query: 601 PYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V      VTN+V Y++A EEE   IAQAN  L EDG F  E V CR   +      
Sbjct: 526 PYRRVDKETGVVTNEVSYITADEEEQYIIAQANEPLTEDGHFVHERVACRHGEDTREFKA 585

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++DF+D SPK+V+S+  S+IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME  
Sbjct: 586 DRVDFMDVSPKEVISVGTSMIPFLENDDANRALMGANMQRQAVPLLRTQAPLVGTGMEYK 645

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  I+AK  G+V +V    I ++S           VD Y+L+KF RSNQ+TC+NQ
Sbjct: 646 AACDSGVCILAKHDGVVTRVTGDEIEVQSD-------AGSVDTYKLIKFVRSNQSTCINQ 698

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV   + V    ++ADG +TD G+LALG N+LVA+MPW GYN+ED++L+SE +   D+
Sbjct: 699 RPLVYKNEHVTAGQVLADGMATDGGELALGYNILVAYMPWEGYNYEDAVLLSEDLPKNDL 758

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLG EEITR+IPNVSEE  KN+DE GII +GA+V PGD+LVGK+
Sbjct: 759 YTSIHIEEYECDARDTKLGAEEITREIPNVSEESTKNLDENGIIMIGADVVPGDVLVGKV 818

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VV+VR+F+R   D
Sbjct: 819 TPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVNVRVFSRENND 871



 Score =  546 bits (1406), Expect = e-152,   Method: Composition-based stats.
 Identities = 211/573 (36%), Positives = 291/573 (50%), Gaps = 39/573 (6%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L R           Y       +      + V T +  +E EV    +  
Sbjct: 620  GANMQRQAVPLLRTQAPLVGTGMEYKAACDSGVCILAKHDGVVTRVTGDEIEVQ---SDA 676

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  + I  V       I++  ++     V  G +L   +   G   +     +L A 
Sbjct: 677  GSVDTYKLIKFVRSNQSTCINQRPLVYKNEHVTAGQVLADGMATDG-GELALGYNILVAY 735

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVD-VRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
               +  +  D  L           D     +    + + R   +  E+I     +  +E 
Sbjct: 736  MPWEGYNYEDAVLL---SEDLPKNDLYTSIHIEEYECDARDTKLGAEEITREIPNVSEES 792

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                         I+ G + V G     K T      +   P  +  +    D++ +   
Sbjct: 793  T----KNLDENGIIMIGADVVPGDVLVGKVTPKGETEL--TPEERLLRAIFGDKEREVRD 846

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V +  S  ++  R    +   +  D++PPGV R+V+V++A KR I  GDKM+GRHG
Sbjct: 847  TSLRVPHGESGKVVNVR----VFSRENNDELPPGVNRLVRVYIAQKRKIHEGDKMSGRHG 902

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQI ETHLGWA   +G +IK++
Sbjct: 903  NKGVVSRVMRQEDMPFLPDGTPVQIVLNPLGVPSRMNIGQILETHLGWAMHEMGLQIKAM 962

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                       +      D     + +  K+GV ++TPVFDGA 
Sbjct: 963  ---------------------DPKLEAKLKEAGYDVDAYGMPKPDKAGVHIATPVFDGAQ 1001

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             E +   L++A L E G+S+LYDG TGEP DR VTVGY Y LKL+H+V DK++ARSTG Y
Sbjct: 1002 AEDVFEALKIAGLPEDGKSVLYDGRTGEPMDRRVTVGYTYFLKLHHLVDDKIHARSTGPY 1061

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLTIKSDDVVGR + YE IV G
Sbjct: 1062 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTIKSDDVVGRVKAYEKIVKG 1121

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             +  E G PESF VL+KE+QA+GL + + N   
Sbjct: 1122 ENIPEPGVPESFKVLLKELQAIGLDVQILNEDG 1154


>gi|323141130|ref|ZP_08076033.1| DNA-directed RNA polymerase, beta subunit [Phascolarctobacterium
           sp. YIT 12067]
 gi|322414396|gb|EFY05212.1| DNA-directed RNA polymerase, beta subunit [Phascolarctobacterium
           sp. YIT 12067]
          Length = 1282

 Score =  815 bits (2106), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/947 (44%), Positives = 580/947 (61%), Gaps = 92/947 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  EI+ +P LI++Q+ SY+ F+           +GL      + PI  F+G 
Sbjct: 21  RTRYSYARINEILAMPHLIDIQRKSYEWFVQ----------KGLMEILHDISPIKDFAGN 70

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F S+E   PK+ V++C  RD +Y+ P+ +  RLI  D       K   +IKE S++
Sbjct: 71  LELSFESFELGTPKYSVEECKERDESYSAPMNVKARLIFKD-------KEKGEIKESSVF 123

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTFVI G +R++VSQL RSPG+++         SGK +Y   +IP++G W
Sbjct: 124 MGDFPLMTDTGTFVINGAERVIVSQLVRSPGVYYSVTMD---PSGKKIYGTTVIPNRGAW 180

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPK--IVYSQRGDFWCFP 248
           ++ E D  DII  R+DR RKVP T  L ALG+ S +EIL+ F     ++ +   D     
Sbjct: 181 IEYETDINDIISARVDRTRKVPATVLLRALGLSSNDEILACFGNHPALLATLEKDTTTNR 240

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
             A   +         V ++   Q+IE+    +    L    + K  K LG   + L G 
Sbjct: 241 DEAMLELYKKLRPGEPVILENAVQLIENTFFDSKRYDLANVGRYKLNKKLGW-RNRLSGT 299

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            +AE I + ETGEI + AG  + +++L++I  S I +   L                   
Sbjct: 300 VLAEAIADEETGEIILPAGTKMTDENLDKIAESGIYNERGL--------------RAVKV 345

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
               ++ LL                                                  +
Sbjct: 346 QNHEEEMLL-------------------------------------------MFTTGIDE 362

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            +  +  ED+ A    L++L +G GT DDID+LGNRRVR VGE+L+NQ+R+GL RMER +
Sbjct: 363 KMHTVTNEDVFASFNYLLNLMDGHGTGDDIDHLGNRRVRCVGELLQNQFRIGLSRMERVV 422

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER++  D + + PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG 
Sbjct: 423 KERMTIQDNEVITPQALINIRPVVAAIKEFFGSSQLSQFMDQNNPLAELTHKRRLSALGP 482

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV- 605
           GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++A +N YGF+ETPYR V 
Sbjct: 483 GGLSRERAGYEVRDVHNSHYGRMCPIETPEGPNIGLIGSLSTYAVINEYGFMETPYRVVD 542

Query: 606 -CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             + +VT ++ Y++A EE+   +AQAN  LD+DG F  E V  R   + + +  +K+D +
Sbjct: 543 KENKRVTEEIRYMTADEEDKYIVAQANEPLDDDGYFLGERVTARAKDDVLSITPDKVDLM 602

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVSIA +LIPFLENDD+NR LMG NMQRQAVPLL  +AP +GTGME  VA  SG
Sbjct: 603 DVSPKQVVSIATALIPFLENDDANRALMGANMQRQAVPLLCTQAPIIGTGMEYKVASDSG 662

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             ++AKRAG V +V    I +R+  G        VD+Y L+KF+RSNQ TCVNQRP+V  
Sbjct: 663 VCVLAKRAGEVIRVVGNEIRVRAENG-------EVDVYPLLKFKRSNQGTCVNQRPIVFK 715

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V    I+ADGP+TD G+LALG N++VA+MPW GYN+ED++L++E +V  D+FTSIHI
Sbjct: 716 GDKVTEKQILADGPATDHGELALGHNVIVAYMPWEGYNYEDAVLLNEDLVKADIFTSIHI 775

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE++  ARDTKLG EEITR+IPNVS+E LK++DE GII +GAEV PGDILVGK+TPKGE+
Sbjct: 776 EEYDCDARDTKLGKEEITREIPNVSDEALKDLDERGIIRIGAEVRPGDILVGKVTPKGET 835

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +T EE+LLRAIFGEKA +VRD+SLRVP G +G +V V++F+R   D
Sbjct: 836 ELTAEERLLRAIFGEKAREVRDSSLRVPHGEAGKIVSVKVFSRENGD 882



 Score =  545 bits (1405), Expect = e-152,   Method: Composition-based stats.
 Identities = 204/607 (33%), Positives = 280/607 (46%), Gaps = 48/607 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR-DTKLGP 858
                       +L    P  G   E  +     +          I       R   + G 
Sbjct: 630  MGANMQRQAVPLLCTQAPIIGTGMEYKVASDSGVCVLAKRAGEVIRVVGNEIRVRAENGE 689

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             ++   +          +++  I+  G +V    IL           +     ++ A   
Sbjct: 690  VDVYPLLKFKRSNQGTCVNQRPIVFKGDKVTEKQILADGP-ATDHGELALGHNVIVAYMP 748

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--------ELLARD 970
             +  +  D  L     V   +        +  D + R   + +E+I        +   +D
Sbjct: 749  WEGYNYEDAVLLNEDLVKADIFTSIHIEEY--DCDARDTKLGKEEITREIPNVSDEALKD 806

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE+ I+      R  +IL G+    G         L   +  E  R            
Sbjct: 807  L-DERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------ 853

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 E                   K+   + GDD+PPGV   V+V +A KR I  GDKM
Sbjct: 854  -----EVRDSSLRVPHGEAGKIVSVKVFSRENGDDLPPGVNEQVRVHIAQKRKISEGDKM 908

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG+VSRI+  EDMPFL  G PV IVLNPLGVPSRMN+GQ+ E HLGWA   LG 
Sbjct: 909  AGRHGNKGVVSRIMAREDMPFLPTGEPVHIVLNPLGVPSRMNIGQVLENHLGWAARALGM 968

Query: 1151 KIK------------------SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +I                          A  +        +K+   G   EK    +   
Sbjct: 969  EIDTTNLAAKLNAVEKTGAAEGTPEFEAAFKEELANSETAKKLEHYGYDYEKYGMPETVE 1028

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            + +   +    V +S PVFDGA E+ I   L +A +D++ ++ LYDG TGEPFD PVTVG
Sbjct: 1029 IDKFGGKSVKAVQISVPVFDGAHEQDIADALELAGIDKTAKTTLYDGRTGEPFDNPVTVG 1088

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1089 LTYYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 1148

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDDVVGR + YE+IV G +  + G PESF VLVKE+Q++GL I + N   +  +
Sbjct: 1149 EILTVKSDDVVGRVKTYEAIVKGENVPDPGIPESFKVLVKELQSIGLDIKVLNEDEEEVS 1208

Query: 1373 KMEEIPD 1379
              ++  D
Sbjct: 1209 LRDDEDD 1215


>gi|69246466|ref|ZP_00603961.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium DO]
 gi|68195269|gb|EAN09722.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecium DO]
          Length = 1182

 Score =  815 bits (2106), Expect = 0.0,   Method: Composition-based stats.
 Identities = 412/940 (43%), Positives = 578/940 (61%), Gaps = 80/940 (8%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +++P+LIE+Q  SY  FL          +EGL+  F+ + PI  F+G   LEFV YE   
Sbjct: 1   MELPNLIEIQTDSYQWFL----------DEGLREMFEDILPIDDFNGNLSLEFVDYELKE 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V +    D  Y+ PL +TLRL           +   +IK Q ++ GD PLMT+ GT
Sbjct: 51  PKYTVAEARAHDANYSAPLHVTLRLT---------NRETGEIKAQEVFFGDFPLMTEQGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQL RSPG++F    G+   +GK  +   +IP++G W+++E D+KDI +
Sbjct: 102 FIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGFGSTVIPNRGAWLEMETDAKDISY 158

Query: 204 VRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VRIDR RK+P+T  + ALG  S++ I   F          +      +A+D      +  
Sbjct: 159 VRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSETLRNTVEKD-LHKNASDSRTEEGLKD 217

Query: 263 SLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIV 313
               +  GE    +S + L +      K   +  +G             L  L +AE +V
Sbjct: 218 VYERLRPGEPKTADSSRNLLNARFFDPKRYDLANVGRYKVNKKLDLKTRLLNLTLAETLV 277

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           + ETGEI +E G V+  + +E +               ++N         ++        
Sbjct: 278 DPETGEIIVEKGTVLTHQVMETL------------APFIDNGLNSVTYYPSEDGVVTDPM 325

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            + + +V  P D                             ++N+  N      V+ +R 
Sbjct: 326 TVQVIKVFSPRDP--------------------------EREVNVIGNGYPEAAVKTVRP 359

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            DIIA +   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  
Sbjct: 360 ADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERMSIQ 419

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ R R
Sbjct: 420 DTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDR 479

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KVT 611
           AG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+VN +GFIETPYR+V     +VT
Sbjct: 480 AGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDRETGRVT 539

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YL+A  E++  +AQANS L+EDG+F +++V  R   E + V  +K+D++D SPKQV
Sbjct: 540 DQIDYLTADIEDHYIVAQANSPLNEDGTFAQDVVMARAQSENLEVSIDKVDYMDVSPKQV 599

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           V++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++ K 
Sbjct: 600 VAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPWVGTGMEYKSAHDSGAALLCKH 659

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V + 
Sbjct: 660 DGVVEYVDASEIRVRRDNGALDK-------YDVTKFRRSNSGTSYNQRPIVHLGEKVEKG 712

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E  A
Sbjct: 713 DTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEA 772

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+
Sbjct: 773 RDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEER 832

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 833 LLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 872



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 176/504 (34%), Positives = 236/504 (46%), Gaps = 87/504 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 702  IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 752

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 753  --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 804

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 805  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 863

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 864  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 918

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 919  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 968

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 969  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 993

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 994  ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 1044

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VL
Sbjct: 1045 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVL 1104

Query: 1351 VKEMQALGLSIDLENSRTKNSAKM 1374
            VKE+Q+LGL + + +         
Sbjct: 1105 VKELQSLGLDMRVLDIEETEIELR 1128


>gi|170017897|ref|YP_001728816.1| DNA-dependent RNA polymerase subunit beta [Leuconostoc citreum
           KM20]
 gi|226699417|sp|B1MVW8|RPOB_LEUCK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|169804754|gb|ACA83372.1| DNA-dependent RNA polymerase subunit beta [Leuconostoc citreum
           KM20]
          Length = 1204

 Score =  815 bits (2105), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/966 (42%), Positives = 583/966 (60%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ +    E++D+P+LIE+Q ASY  FL          +EG++  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYASIKEVLDVPNLIEIQTASYQWFL----------DEGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LE+V Y+   PK+++D+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGTLSLEYVDYQLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ G+ PLMT+ GTF+I G +R++VSQL RSPGI+++ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGEFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQENDK---NGRPRY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +I+  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDIIDIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        K   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLAS 275

Query: 296 LGIT--------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE + + ++GE+  E G ++D+  + ++        P L
Sbjct: 276 VGRYKINKKLSLKTRLLNQTLAETLADPDSGEVIAEKGTLVDKTVMSKLS-------PFL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      Y  +           DA+L+        +  T             ++ +  
Sbjct: 329 DREDFKTTTYTPSG----------DAVLE--------EPVTLQK----IKIESPENPEKT 366

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L  +G             ++ R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSV
Sbjct: 367 LLLIGN--------GHIDENDRTVRPADILAGMNYFLNLQEGIGNVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ R+N YGFIETPYR+V      VT+ + YL+A EE+N  +AQANS L++DGSF  + V
Sbjct: 539 TYGRINKYGFIETPYRRVDWTTHMVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVHDTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++ AG+VE VD  +I +R  +G LD        Y LM
Sbjct: 659 PHAPLVGTGIEYKAAHDSGVAMISRAAGVVEYVDGRQIRVRREDGQLD-------TYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P+V  G+ V  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIVHEGEHVEADEVLADGPSMEKGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VG
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 175/529 (33%), Positives = 252/529 (47%), Gaps = 67/529 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +      G KN ++  I+  G  V   ++L    +   +  +   +  
Sbjct: 699  RREDGQLDTYELMKFRRSNGGKNYNQKPIVHEGEHVEADEVLADGPS-MEKGELALGQNP 757

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     V   V        +  +  +  +  E    E +    +
Sbjct: 758  LIAFMTWQGYNFEDAIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGE 816

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+   LD +   R+     G     G     K T      +S   R     F  +  +V+
Sbjct: 817  DQLKDLDADGIIRV-----GAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVR 871

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      +I   + GD++ PGV  +V+V++A KR IQ GDKMAG
Sbjct: 872  DTSLRVPHGGGGVVQNV------RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAG 925

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  +
Sbjct: 926  RHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHV 985

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S + D  ++ +I                         ++ LR A   + G  V   V+D
Sbjct: 986  ASPVFDGASDDEI-------------------------EAALREAGLPQDGKSV---VYD 1017

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGE FD+ V VG ++ +KL HMV DK++ARS 
Sbjct: 1018 G--------------------------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSI 1051

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +VYESI
Sbjct: 1052 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVYESI 1111

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            + G      G PESF VLVKE+QALGL + + ++        +   D +
Sbjct: 1112 IKGEPIPRPGVPESFRVLVKELQALGLDMQVLDNAGDEVELRQMDEDDS 1160


>gi|300812109|ref|ZP_07092557.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300496948|gb|EFK32022.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 1252

 Score =  815 bits (2105), Expect = 0.0,   Method: Composition-based stats.
 Identities = 400/963 (41%), Positives = 570/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 29  LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 78

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 79  DILPISDASGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 129

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 130 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 186

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 187 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 246

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 247 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 305

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGE+    G V++ + ++ +              
Sbjct: 306 YKVNKKLSLKNRLLGYTLAETLADPDTGEVLAAKGTVVNNEVMDVLKDYL---------- 355

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 356 ------------------DRDDFKTVTYTPSDEGAIPEPVTVQEIKVFSREIPDRE---- 393

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 394 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 448

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 449 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 508

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 509 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 568

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 569 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 628

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 629 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 688

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME      SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 689 PLVATGMEYRAGHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 741

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 742 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 801

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 802 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDESGIIRIGAEV 861

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G V DV++F R 
Sbjct: 862 HDGDILVGKVTPKGITELSAEERLLHAIFGEKAREVRDTSLKVPHGGGGVVQDVQVFTRE 921

Query: 949 GID 951
             D
Sbjct: 922 AGD 924



 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 269/1106 (24%), Positives = 401/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 222  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 271

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 272  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 331

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 332  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGAIPEPVTVQE-IKVFSREIP 390

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 391  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 450

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 451  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 510

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 511  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 570

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 571  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 630

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 631  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 675

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV  G E R                    +       
Sbjct: 676  ---------HQRQAVPLINPHGPLVATGMEYRAG----------------HDSGDALLAE 710

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 711  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 761

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 762  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 814

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 815  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DESGIIRIGAEVHDGDILVGKVTP 873

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 874  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLKVPHGGGGVVQDVQ------ 916

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ + P EDMP+L DGT
Sbjct: 917  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALVAPVEDMPYLPDGT 976

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 977  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 1024

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 1025 ---------------------------------VWDFVRE---------AGVDSDGKTVL 1042

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1043 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1102

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1103 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1162

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1163 LGLDLRVLDSDENEVELRDMDEDSNE 1188


>gi|326693589|ref|ZP_08230594.1| DNA-directed RNA polymerase subunit beta [Leuconostoc argentinum
           KCTC 3773]
          Length = 1204

 Score =  815 bits (2105), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/966 (43%), Positives = 577/966 (59%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ +    E++D+P+LIE+Q ASY  FL          +EG++  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYASIKEVLDVPNLIEIQTASYQWFL----------DEGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LE+V Y+   PK+++D+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGNLSLEYVDYKLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPGI+++ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQENDK---NGRPRY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +I+  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDIIDIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        K   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEEALKDIYERLRPGEPKTADSSRALLVARFFDPKRYDLAS 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE + + ++GEI  E G ++D+  + ++        P L
Sbjct: 276 VGRYKINKKLSLKTRLLNQILAETLADPDSGEIIAEKGTLVDKTVMSKLS-------PYL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                    Y  +                        +  T             ++ +  
Sbjct: 329 DRPDFKTTTYTPSGDAVLN------------------EPVTLQK----IKIESPENPEKT 366

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L  +G             +D R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSV
Sbjct: 367 LLLIGN--------GHIGEDDRTVRPADILAGMNYFLNLQEGVGNVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV++V EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVASVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ R+N YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L+EDGSF  + V
Sbjct: 539 TYGRINKYGFIETPYRRVDWTTHKVTDKIDYLTADEEDNYIVAQANSPLNEDGSFVHDTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++ AG+VE VD   I +R  +G LD        Y LM
Sbjct: 659 PHAPLVGTGIEYKAAHDSGVAMISRAAGVVEYVDGREIRVRREDGQLD-------TYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P+V  G+ V  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIVHEGEHVEADEVLADGPSMEKGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEEITR+IPN  E+ LK++D  GII VG
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEITREIPNTGEDQLKDLDANGIIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 175/532 (32%), Positives = 254/532 (47%), Gaps = 73/532 (13%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +      G KN ++  I+  G  V   ++L    +   +  +   +  
Sbjct: 699  RREDGQLDTYELMKFRRSNGGKNYNQKPIVHEGEHVEADEVLADGPS-MEKGELALGQNP 757

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLAR 969
            L A    +  +  D  +         V +    + H  + +  +   +    E    +  
Sbjct: 758  LIAFMTWQGYNFEDAIVLN----ERLVREDVYTSIHIEEYDSEARDTKLGPEEITREIPN 813

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +D+   LD N   R+     G     G     K T      +S   R     F  +  
Sbjct: 814  TGEDQLKDLDANGIIRV-----GAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR 868

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V+     +          +      +I   + GD++ PGV  +V+V++A KR IQ GDK
Sbjct: 869  EVRDTSLRVPHGGGGVVQNV------RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDK 922

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG
Sbjct: 923  MAGRHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMGVPSRMNIGQVLELHLGYAAKELG 982

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + S + D  ++ +I                         ++ LR A   + G      
Sbjct: 983  IHVASPVFDGASDDEI-------------------------EAALREAGLPRDG------ 1011

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                   +S++YDG TGE FD+ V VG ++ +KL HMV DK++A
Sbjct: 1012 -----------------------KSVVYDGRTGEAFDKRVGVGVMHYMKLAHMVDDKIHA 1048

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +VY
Sbjct: 1049 RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVY 1108

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            ESI+ G      G PESF VLVKE+QALGL + + +         +   D +
Sbjct: 1109 ESIIKGEPIPRPGVPESFRVLVKELQALGLDMQVLDGAGDEVELRQMDEDDS 1160


>gi|167749850|ref|ZP_02421977.1| hypothetical protein EUBSIR_00818 [Eubacterium siraeum DSM 15702]
 gi|167657162|gb|EDS01292.1| hypothetical protein EUBSIR_00818 [Eubacterium siraeum DSM 15702]
          Length = 1261

 Score =  815 bits (2104), Expect = 0.0,   Method: Composition-based stats.
 Identities = 409/952 (42%), Positives = 575/952 (60%), Gaps = 55/952 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K  E+  +P+LIE+QK SY  FL          +EG++  FK +  IT  +G
Sbjct: 11  RNTRMSFSKINEVQKMPNLIEIQKDSYKWFL----------DEGIKEVFKDISSITDANG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L FV Y  D  PK+ +++C  RD TYA PL++  +L               ++ E  
Sbjct: 61  KLVLSFVDYRLDENPKYSIEECKERDTTYAAPLRVKAQL---------RNNETGEVVENE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTFVI G +R++VSQL RSPG+++  D  +    GK L+   +IP++G
Sbjct: 112 IFMGDFPLMTESGTFVINGAERVIVSQLVRSPGVYYGFDYDKT---GKKLFKSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY---SQRGDFW 245
            W++ E DS DI +VRID+ RK+P T+F+ ALG+ S++ ++  F          Q  D  
Sbjct: 169 AWLEYEMDSNDIFYVRIDKNRKIPATTFIRALGISSDDDLIDLFGEDPRIVQTIQEKDAT 228

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+    I +         L +  + K  K LG+ +  +
Sbjct: 229 KNTEEALLEVYRKLRPGEPPTVDSANTHINNLFFDAKRYDLARFGRYKYNKKLGV-ASRI 287

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   A+ I++  TGEI ++  + I+ +  + +  + +++  I   + +          +
Sbjct: 288 AGHKAAQPIIDPTTGEILVDENEFINAEKAQAVEQAGVKECVIFSEEKIAKVLGNGMVDI 347

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                +  DA       +   +   FSV   + +    D +        RV         
Sbjct: 348 AGYIPESIDA-----ESLGINEKVCFSVLREILDKCGDDVEALTAELSNRV--------- 393

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI  +DI A +   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+G  RME
Sbjct: 394 EDLIPKHITLDDIFATVSYFINLCEGVGEVDDIDHLGNRRIRSVGELLQNQFRIGFARME 453

Query: 484 RSIKERI--SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           R I+ER+   S + D V P  LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH RRL
Sbjct: 454 RVIRERMGLQSQEGDKVTPNALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTHKRRL 513

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RA  E+RDVH +HYGR+CP ET EG NIGL+S L SFA++N YGFIE P
Sbjct: 514 SALGPGGLSRDRASFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASFAKINKYGFIEAP 573

Query: 602 YRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      V ++V Y++A  E+N  +AQAN  LDE G F  + V  R   E + V R+
Sbjct: 574 YRKVDKETGVVLDEVTYMTADMEDNYVVAQANEPLDEQGKFARKRVNARFREEILEVDRD 633

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPL+  + P VGTGME   
Sbjct: 634 RVDYMDVSPKMVVSVATAMIPFLENDDANRALMGANMQRQAVPLMVTQNPIVGTGMEYKA 693

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGA +VAK  G+V +  A  IV+                Y+L+KF+RSNQ TCVNQR
Sbjct: 694 AVDSGAVVVAKEDGVVTKCSADEIVV-------TDGNGVEHSYKLIKFKRSNQGTCVNQR 746

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V  G E++  D++ADGP+T  G+++LG+N L+ FM W GYN+ED++LI+E++V  DV+
Sbjct: 747 PAVTKGMEIKTGDVLADGPATSQGEISLGKNALIGFMTWEGYNYEDAVLINEKLVYNDVY 806

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE+E+  RDTKLGPEEITR+IPNVSE+ LK++DE GII +GAEV+ GDI+VGK+T
Sbjct: 807 TSIHIEEYELECRDTKLGPEEITREIPNVSEDALKDLDERGIIRIGAEVHSGDIMVGKVT 866

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFG+KA +VRD SLRVP G SG +VDV++F R   D
Sbjct: 867 PKGETELTAEERLLRAIFGDKAREVRDNSLRVPHGESGIIVDVKVFTRQNCD 918



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 184/530 (34%), Positives = 261/530 (49%), Gaps = 47/530 (8%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   + I          +++   +  G E+  GD+L        +  ++  +  L
Sbjct: 721  DGNGVEHSYKLIKFKRSNQGTCVNQRPAVTKGMEIKTGDVLADGP-ATSQGEISLGKNAL 779

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                  +  +  D  L     V   V        + ++  +  +  E    E +    +D
Sbjct: 780  IGFMTWEGYNYEDAVLINEKLVYNDVYTSIHIEEYELECRDTKLGPEEITRE-IPNVSED 838

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD     R+   +   + + G    K  T L+++        +  +    D+  + 
Sbjct: 839  ALKDLDERGIIRIGAEVHSGDIMVGKVTPKGETELTAE-------ERLLRAIFGDKAREV 891

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               SL+V +  S  I++     K+   Q  D++ PGV  VV+ ++A KR I  GDKMAGR
Sbjct: 892  RDNSLRVPHGESGIIVD----VKVFTRQNCDELSPGVNMVVRCYIAQKRKISVGDKMAGR 947

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRIL  EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+AC  L  +I 
Sbjct: 948  HGNKGVVSRILKQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYACKALDWQIM 1007

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     DI       E                                      D 
Sbjct: 1008 TPVFDGAHEADIRACFEKAEAERENYKDK-----------------------------DS 1038

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A  +          +    ++ L DG TGE FD PVTVGY+Y LKL+H+V DK++ARSTG
Sbjct: 1039 AKID-----FSKIPMRPDCKTQLTDGRTGEKFDSPVTVGYMYYLKLHHLVDDKIHARSTG 1093

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+VGR + YE+IV
Sbjct: 1094 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDIVGRVKTYEAIV 1153

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             G+   + G PESF VL KE+Q+LGL I + ++        +   + ++ 
Sbjct: 1154 KGDPVPKAGVPESFKVLFKELQSLGLDIKVLDADKNEIDLRQTYEEDDEY 1203


>gi|325684711|gb|EGD26865.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. lactis DSM 20072]
          Length = 1244

 Score =  814 bits (2102), Expect = 0.0,   Method: Composition-based stats.
 Identities = 400/963 (41%), Positives = 570/963 (59%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   VV  G  R R+ F +  EI+ +P+L +VQ  SY  FL          +EG++  F 
Sbjct: 29  LNGHVVNYGQHRTRRSFSRIKEILPLPNLTDVQTESYKWFL----------DEGVKEVFD 78

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+  SG   LE+V Y+   PK+ VD+    D TY+ P+ +TL+L            
Sbjct: 79  DILPISDASGRLTLEYVDYKLQEPKYTVDESRKHDATYSAPMHVTLKLT---------NH 129

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GDLPLMTK G+F++ G +R++VSQL RSPG+++  +  +   +G+ ++
Sbjct: 130 ETGEIKTQDVFFGDLPLMTKSGSFIVNGAERVIVSQLVRSPGVYYSGEFDK---NGRQIF 186

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K+I +VR+DR RK+P++  + ALG  S+ EI   F       
Sbjct: 187 GTTVIPNRGAWLEFETDAKNISYVRVDRTRKLPLSVLVRALGFGSDSEIKEIFGDSDTLD 246

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 247 LTLDKD-VHKNPADSRVAEALKDIYDRLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGR 305

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L G  +AE + + +TGE+    G V++ + ++ +              
Sbjct: 306 YKVNKKLSLKNRLLGYTLAETLADPDTGEVLAAKGTVVNNEVMDVLKDYL---------- 355

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                             DR D     Y     G +      + +  F     D+     
Sbjct: 356 ------------------DRDDFKTVTYTPSDEGVIPEPVTVQEIKVFSREIPDRE---- 393

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N    +DV+ I   DIIA +   ++L+ G G IDDID+LGNRR+R VGE+
Sbjct: 394 -----IKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGEL 448

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER ++ER+S  D  +V PQ LIN +P+V ++ EFF SSQLSQ  +  N
Sbjct: 449 LQNQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNN 508

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 509 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 568

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGF+ETPYR+V     KVT+ + YL+A EE+N  IA AN+ L+EDGSF ++++ CR
Sbjct: 569 IINKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCR 628

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  ++ID+ID  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+    
Sbjct: 629 HREDNVEVSPDRIDYIDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHG 688

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TGME   A  SG A++A+  G VE VDA  I +R  +  LD        Y L K++
Sbjct: 689 PLVATGMEYRAAHDSGDALLAEADGEVEYVDANEIRVRREDQTLD-------TYTLEKYR 741

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P VK GD+V    +IA+GPS   G+LALG+N ++AF  W+ YNFED+++
Sbjct: 742 RSNATKNYNQTPNVKRGDKVVDGQVIANGPSMADGELALGQNPVIAFTTWNMYNFEDAIM 801

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHIE+++  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV
Sbjct: 802 LSERLVKEDVYTSIHIEDYDSEARDTKLGPEEITREIPNVGEDALKDLDENGIIRIGAEV 861

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVGK+TPKG + ++ EE+LL AIF EKA +VRDTSL+VP G  G V DV++F R 
Sbjct: 862 HDGDILVGKVTPKGITELSAEERLLHAIFVEKAREVRDTSLKVPHGGGGVVQDVQVFTRE 921

Query: 949 GID 951
             D
Sbjct: 922 AGD 924



 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 269/1106 (24%), Positives = 402/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 222  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 271

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 272  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 331

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 332  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 390

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 391  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 450

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 451  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 510

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 511  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 570

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 571  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 630

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 631  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 675

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV                +T +   A   +       
Sbjct: 676  ---------HQRQAVPLINPHGPLV----------------ATGMEYRAAHDSGDALLAE 710

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 711  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 761

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 762  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 814

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 815  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 873

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 874  KGITELSAEERLLHAIFVEKAR-----------EVRDTSLKVPHGGGGVVQDVQ------ 916

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 917  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 976

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 977  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 1024

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 1025 ---------------------------------VWDFVRE---------AGVDSDGKTVL 1042

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1043 YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1102

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1103 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1162

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1163 LGLDLRVLDSDENEVELRDMDEDSNE 1188


>gi|307693321|ref|ZP_07635558.1| DNA-directed RNA polymerase subunit beta [Ruminococcaceae bacterium
           D16]
          Length = 1297

 Score =  813 bits (2101), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/954 (43%), Positives = 576/954 (60%), Gaps = 57/954 (5%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V+ G   +RK F +  EI+++P+L+EVQK SY  FL          + GL+  FK V  I
Sbjct: 20  VYYGR-TLRKSFARYQEILEMPNLLEVQKKSYQWFL----------DTGLREVFKDVAAI 68

Query: 66  TAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           T ++G   L F+ Y  D  PK+DV++C  RD TYA P+K+ +RL           K  ++
Sbjct: 69  TDYAGNLELSFIDYSMDEKPKYDVEECKARDATYAAPIKVKVRL---------RNKETEE 119

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKEQ I+MGD P+MT  GTFVI G +R++VSQ+ RSPG+++     +   +  L +A  +
Sbjct: 120 IKEQEIFMGDFPIMTNSGTFVINGAERVIVSQIVRSPGMYYTRTADK---ADNLTFATTV 176

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY--SQR 241
           IP +G W++ E D  DI +VRID+ RK+P+T  + A+G  ++ EIL  F        +  
Sbjct: 177 IPYRGAWLEYETDLSDIFYVRIDKNRKLPITCLIRAVGPKTDAEILEMFGEDERIVATME 236

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGIT 299
            D       A   +           +D+ E ++ +         L    + K  K + + 
Sbjct: 237 KDSCKTYEEALLEIYRKLRPGEPPTLDSAESLLNATFYDPRRYDLSAVGRYKFNKKMNL- 295

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
           +  + G  +A  + +  TGEI  EAG+ +  +   E+    + ++ +L  D      +  
Sbjct: 296 ATRISGHTLAMPVADPRTGEIIAEAGESLSRERARELAAKGVNEV-VLDDDGKQVKVFSN 354

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N +      D       I       ++  F V   + +              G       
Sbjct: 355 NMVDMKNFVDFDPEECGI------SEMVFFPVLCQLMDQFS-----------GEELKEQI 397

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI KEDI+A I  L  L +  GT DDID+LGNRR+R VGE+++NQ+R+G 
Sbjct: 398 AAHVDDLVPKHIIKEDIMASINYLNGLAHNIGTPDDIDHLGNRRLRCVGELIQNQFRIGF 457

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER I+ER+++ D+D V PQ LIN +PV +A+ EFF SS LSQ  +  N L+ +TH R
Sbjct: 458 SRMERVIRERMTTQDLDVVTPQSLINIRPVTAAIKEFFGSSPLSQFMDQTNPLAELTHKR 517

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RA  ++RDVH +HYGR+CP ET EG NIGL+S L S+AR+N YGFIE
Sbjct: 518 RLSALGPGGLSRDRASFDVRDVHYSHYGRLCPIETPEGPNIGLISYLASYARINRYGFIE 577

Query: 600 TPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           TPYRKV    G+VT+++ Y++A  E+   I QA   +DE+  F  E + CR   E I VP
Sbjct: 578 TPYRKVDKATGQVTDEIEYMTADVEDEYTICQATEPVDENNCFVNERITCRRRNEIISVP 637

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             ++D++D SPK +VSIA ++IPFL+NDD+NR LMG NMQRQAVPLL+ EAP V TG E 
Sbjct: 638 AAQVDYVDVSPKMMVSIATAMIPFLQNDDANRALMGANMQRQAVPLLRPEAPVVATGQEH 697

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                S  AI+A+  G V +V A  I ++   G           YRL K+ RSN  TC+N
Sbjct: 698 KNCIDSEVAILAEGPGTVTKVSARYITVKYDNGQT-------KEYRLTKYLRSNHGTCIN 750

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+V +G  V   D++ADGPSTD G++ALGRN+L+ FM W GYN+ED++L++ERMV ED
Sbjct: 751 QRPIVNIGQRVEFQDVLADGPSTDRGEIALGRNILMGFMTWEGYNYEDAILLNERMVKED 810

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           VFTSIHIEE+E+ ARDTKLGPE ITRDIPNV E+ L+++DE GII VGAEV+ GD LVGK
Sbjct: 811 VFTSIHIEEYELEARDTKLGPETITRDIPNVGEDALRDLDEHGIIRVGAEVHAGDYLVGK 870

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + PKGE+  T EEKLLRAIFGEKA +VRDTSL+VP G SGT+VDV+IF R   D
Sbjct: 871 VAPKGEAEATAEEKLLRAIFGEKAREVRDTSLKVPHGESGTIVDVKIFTRENGD 924



 Score =  567 bits (1460), Expect = e-159,   Method: Composition-based stats.
 Identities = 264/1092 (24%), Positives = 417/1092 (38%), Gaps = 83/1092 (7%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            I+    D   +  +  +  +         ++    +  I  T+  D  K  ++ALL+IYR
Sbjct: 193  IFYVRIDKNRKLPITCLIRAVGPKTDAEILEMFGEDERIVATMEKDSCKTYEEALLEIYR 252

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   AES+ N  F+D  +YDLS VGR K N ++NL T               
Sbjct: 253  KLRPGEPPTLDSAESLLNATFYDPRRYDLSAVGRYKFNKKMNLATRISGHT--------- 303

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME-RSIKERISSVDIDSV 498
                  L          + +         E  +     G+  +      +++     + V
Sbjct: 304  ------LAMPVADPRTGEIIAEAGESLSRERARELAAKGVNEVVLDDDGKQVKVFSNNMV 357

Query: 499  MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA-LGQGGVARARAGVE 557
              ++ ++  P    + E      L QL +  +              L    + +      
Sbjct: 358  DMKNFVDFDPEECGISEMVFFPVLCQLMDQFSGEELKEQIAAHVDDLVPKHIIKEDIMAS 417

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            +  ++   +    P +     N  L   +    +           R + +   T D+  +
Sbjct: 418  INYLNGLAHNIGTPDDIDHLGNRRLRC-VGELIQNQFRIGFSRMERVIRERMTTQDLDVV 476

Query: 618  SAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC---------AGEEILVPR 658
            +     N     A               +  +   EL   R          + +      
Sbjct: 477  TPQSLINIRPVTAAIKEFFGSSPLSQFMDQTNPLAELTHKRRLSALGPGGLSRDRASFDV 536

Query: 659  EKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              + +        +       I  +    S   +            +      V   +E 
Sbjct: 537  RDVHYSHYGRLCPIETPEGPNIGLISYLASYARINRYGFIETPYRKVDKATGQVTDEIEY 596

Query: 718  VVA--KSSGAAIVAKRA--GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            + A  +       A          V+      R  E    P+     +    K   S   
Sbjct: 597  MTADVEDEYTICQATEPVDENNCFVNERITCRRRNEIISVPAAQVDYVDVSPKMMVSIAT 656

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              +           ++ +D        ++   A+      A +   G   ++ +     +
Sbjct: 657  AMIP---------FLQNDDANRALMGANMQRQAVPLLRPEAPVVATGQEHKNCIDSEVAI 707

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            ++E   T   +    +  +    G  +  R    +       I++  I+ +G  V   D+
Sbjct: 708  LAEGPGTVTKVSARYITVK-YDNGQTKEYRLTKYLRSNHGTCINQRPIVNIGQRVEFQDV 766

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L    +      +     +L      +  +  D  L     V   V        + ++  
Sbjct: 767  LADGPSTDR-GEIALGRNILMGFMTWEGYNYEDAILLNERMVKEDVFTSIHIEEYELEAR 825

Query: 954  ERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            +  +  E     I  +  D     DE  I+         + L G+ A  G         L
Sbjct: 826  DTKLGPETITRDIPNVGEDALRDLDEHGIIRVGAEVHAGDYLVGKVAPKGEAEATAEEKL 885

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               +  E  R                 E      +            KI   + GD++ P
Sbjct: 886  LRAIFGEKAR-----------------EVRDTSLKVPHGESGTIVDVKIFTRENGDELSP 928

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV +VV+V++A KR I  GDKMAGRHGNKG+VSRILP EDMPFL DGTP+DIVLNPLGVP
Sbjct: 929  GVNQVVRVYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPFLPDGTPLDIVLNPLGVP 988

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG+A   LG K+ + I +  +  DI             G +   I   
Sbjct: 989  SRMNIGQVLEVHLGYAAKTLGWKVATPIFNGASEADIQECLKMAGLAREVGKNEPLIGKQ 1048

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD-ESGQSILYDGLTGEPFDR 1247
               +      Q  S   ++       D   IN   +   L    G++ LYDG TGE FD 
Sbjct: 1049 LYLADEDGELQTLSAEEMA-------DTAQINQWQQEGRLRLVDGKNWLYDGRTGERFDN 1101

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY+Y LKL+H+V DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1102 PVTVGYVYFLKLHHLVDDKIHARATGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1161

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDV GR + YE+IV G++  + G PESF VL+KE+Q+L L + + +++
Sbjct: 1162 AYTLQEILTVKSDDVTGRVKTYEAIVKGHNVPKPGVPESFKVLIKELQSLCLDMKVLDAQ 1221

Query: 1368 TKNSAKMEEIPD 1379
                   +E  D
Sbjct: 1222 GNEIELKDEDED 1233


>gi|325681100|ref|ZP_08160630.1| DNA-directed RNA polymerase, beta subunit [Ruminococcus albus 8]
 gi|324107022|gb|EGC01308.1| DNA-directed RNA polymerase, beta subunit [Ruminococcus albus 8]
          Length = 1303

 Score =  813 bits (2100), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/956 (43%), Positives = 579/956 (60%), Gaps = 49/956 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              RK F K  E++++P+LIEVQK SY  FL          +EGL+  F+ V  IT ++G
Sbjct: 11  KNTRKSFAKINEVLEMPNLIEVQKNSYQWFL----------DEGLKEVFRDVSSITDYNG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              L FV Y FD   K+ + +C  RD TYAVPL++T RL               +IKE  
Sbjct: 61  NLELTFVGYRFDENSKYTIAECKARDATYAVPLRVTARL---------NNLETGEIKESE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MG+ P MT  GTFVI G +R++VSQL RSPG+++  DK +    GK L+   +IP++G
Sbjct: 112 VFMGEFPKMTDSGTFVINGAERVIVSQLVRSPGVYYAFDKDKT---GKDLFKTTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+++VRID+ RK+P+T+F+ ALG  + EEI +TF      +Q        
Sbjct: 169 AWLEYEMDSNDVVYVRIDKNRKIPITTFIRALGFGTNEEIEATFGVDERLTQTIMQKDQT 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +  + ++          +  GE   +ES +   + L    K   +   G          
Sbjct: 229 ANREEALLQV-----YQKLRPGEPPTVESSETHLNNLFFDAKRYDLSRFGRYKYNKKLGV 283

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              L G  +   +V   TGE+  E GD+I+ +   EI  + +++  +         A   
Sbjct: 284 GSRLVGHKLTRAVVAPMTGEVLAEEGDLINYEKAMEIETAGVKEAFVSVEVKEYETAPTG 343

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            T+    +K+ K     +  +    D        +         +  + +          
Sbjct: 344 ETVTRMVDKEVKIIGSGMVDMQAYVDFDPAECGINEKVSFAVLKEILESTDDEEELKETI 403

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    +HI  +DI+A +   ++L +G GT+DDID+LGNRR+RSVGE+L+NQ+R+G 
Sbjct: 404 RTRADELVPKHIVIDDIVATVSYFLNLCDGVGTVDDIDHLGNRRIRSVGELLQNQFRIGF 463

Query: 480 LRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            RMER I+ER++    D + V P  LIN +P+ +A+ EFF SS LSQ  +  N L+ +TH
Sbjct: 464 TRMERVIRERMNIQSQDSEVVTPAALINIRPITAAIREFFGSSPLSQFMDQNNPLAELTH 523

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+S L SFAR+N YGF
Sbjct: 524 KRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLISYLASFARINKYGF 583

Query: 598 IETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IE PYR+V      VT++VVY++A  E+N  +AQAN  L ED  F    V  R   + + 
Sbjct: 584 IEAPYRRVDKETGVVTDEVVYMTADVEDNFMVAQANEPLTEDHKFARAKVNGRYRDQILE 643

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +  EKIDF+D SPK VVS+A + IPFLENDD+NR LMG NMQRQAVPLLK E+P VGTGM
Sbjct: 644 IENEKIDFMDVSPKMVVSVATACIPFLENDDANRALMGSNMQRQAVPLLKTESPIVGTGM 703

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E      SG A+V+ +AG+VE VDA +IV+R  +G        +  Y L KF+RSN  TC
Sbjct: 704 EYKACIDSGVAVVSTKAGVVESVDADKIVVREDDG-------NMHTYELTKFKRSNAGTC 756

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQRP+V  G+ +  + II DGP+T  G+L+LG+N L+ FM W GYN+ED++L++E +V 
Sbjct: 757 TNQRPIVDKGERIEAHQIIGDGPATSNGELSLGKNALIGFMTWEGYNYEDAVLLNENLVK 816

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +D +TSIHIE+ E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV  GDILV
Sbjct: 817 QDKYTSIHIEDLETEARDTKLGPEEITRDIPNVGEDALKDLDENGIIRIGAEVRSGDILV 876

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +T EE+LLRAIFGEKA +VRD SL+VP G +GT+++VR+F R   D
Sbjct: 877 GKVTPKGETELTAEERLLRAIFGEKAREVRDNSLKVPHGEAGTIIEVRVFTRENCD 932



 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 176/508 (34%), Positives = 241/508 (47%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+  G  +     ++G         ++  +  L      +  +  D  L   +       
Sbjct: 762  IVDKGERIEAHQ-IIGDGPATSNGELSLGKNALIGFMTWEGYNYEDAVLLNENLVKQDKY 820

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + D+    R      E          E   +D  DE  I+      R  +IL G+ 
Sbjct: 821  TSIHIEDLETEARDTKLGPEEITRDIPNVGEDALKDL-DENGIIRIGAEVRSGDILVGKV 879

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +          +
Sbjct: 880  TPKGETELTAEERLLRAIFGEKAR-----------------EVRDNSLKVPHGEAGTIIE 922

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++ PGV  +V+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMPFL+D
Sbjct: 923  VRVFTRENCDELSPGVNMLVRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPFLED 982

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI LNPLGVPSRMN+GQ+ E HLG A   LG KI + + D     DI       ++
Sbjct: 983  GTPLDICLNPLGVPSRMNIGQVLEVHLGMAAKALGWKIMTPVFDGAHEADIRECFKMAQQ 1042

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                    E      D+ +   A                              + E G+ 
Sbjct: 1043 NYLEHKDDEFEIHPMDEVINPNALS----------------------------MSEDGKF 1074

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             +YDG TGE FD  VTVGY+Y LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1075 TVYDGRTGEKFDNRVTVGYMYYLKLHHLVDDKIHARSVGPYSLVTQQPLGGKAQFGGQRF 1134

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDD+ GR + YE+IV G +    G PE+F VL+KE+
Sbjct: 1135 GEMEVWALEAYGAAYTLQEILTVKSDDLNGRVKTYEAIVKGQNVPNPGVPEAFKVLIKEL 1194

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+L L I + N   +     ++  D + 
Sbjct: 1195 QSLCLDIKVLNINNEEIDLKQKFDDDDD 1222


>gi|116618914|ref|YP_819285.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|122270886|sp|Q03V60|RPOB_LEUMM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116097761|gb|ABJ62912.1| DNA-directed RNA polymerase subunit beta [Leuconostoc mesenteroides
           subsp. mesenteroides ATCC 8293]
          Length = 1202

 Score =  813 bits (2099), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/966 (42%), Positives = 582/966 (60%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ +    E++D+P+LIE+Q ASY  FL          N+G++  F 
Sbjct: 1   MVGHLVKYGKHRTRRSYASIKEVLDVPNLIEIQTASYQWFL----------NDGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LE+V Y+   PK+++D+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGTLSLEYVDYQLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPGI+++    +   +G+  +
Sbjct: 102 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQTTDK---NGRPHF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +I+  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDIIDIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        K   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLAS 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE + + ++GEI  E G ++D++ + ++        P L
Sbjct: 276 VGRYKINKKLSLKTRLLNQTLAETLADPDSGEIIAEKGTLVDKEVISKLT-------PYL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      Y  +           DA+L+        +  T             ++ +  
Sbjct: 329 DREDFKTTTYTPSG----------DAVLE--------EPVTLQK----IKIESPENPEKT 366

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L  +G             +D R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSV
Sbjct: 367 LLLIGN--------GHIDEDDRTVRPADILAGMNYFLNLQEGVGHVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ R+N YGF+ETPYR+V     KVT+ + YL+A EE+N  +AQANS L+EDGSF    V
Sbjct: 539 TYGRINKYGFVETPYRRVDWTTHKVTDKIDYLTADEEDNYIVAQANSPLNEDGSFVHNTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             +P VGTG+E   A  SG A++A+ +G VE VD  +I +R  +G LD        Y LM
Sbjct: 659 PHSPLVGTGIEYKAAHDSGVAMIARASGEVEYVDGRQIRVRREDGQLD-------TYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P+V VG+ +  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIVHVGEHIEADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VG
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 175/529 (33%), Positives = 251/529 (47%), Gaps = 67/529 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +      G KN ++  I+ VG  +   ++L    +   +  +   +  
Sbjct: 699  RREDGQLDTYELMKFRRSNGGKNYNQKPIVHVGEHIEADEVLADGPS-MEQGELALGQNP 757

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     V   V        +  +  +  +  E    E +    +
Sbjct: 758  LIAFMTWQGYNFEDAIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGE 816

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+   LD +   R+     G     G     K T      +S   R     F  +  +V+
Sbjct: 817  DQLKDLDADGIIRV-----GAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVR 871

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      +I   + GD++ PGV  +V+V++A KR IQ GDKMAG
Sbjct: 872  DTSLRVPHGGGGVVQNV------RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAG 925

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  +
Sbjct: 926  RHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHV 985

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S + D  ++ +I                         +  LR A   + G  V   V+D
Sbjct: 986  ASPVFDGASDDEI-------------------------EMALREAGLPQDGKSV---VYD 1017

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGE FD+ V VG ++ +KL HMV DK++ARS 
Sbjct: 1018 G--------------------------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSI 1051

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +VYESI
Sbjct: 1052 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVYESI 1111

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            + G      G PESF VLVKE+QALGL + + +         +   D +
Sbjct: 1112 IKGEPIPRPGVPESFRVLVKELQALGLDMQVLDGAGDEVELRQMDEDDS 1160


>gi|226322722|ref|ZP_03798240.1| hypothetical protein COPCOM_00494 [Coprococcus comes ATCC 27758]
 gi|225208883|gb|EEG91237.1| hypothetical protein COPCOM_00494 [Coprococcus comes ATCC 27758]
          Length = 892

 Score =  813 bits (2099), Expect = 0.0,   Method: Composition-based stats.
 Identities = 409/923 (44%), Positives = 564/923 (61%), Gaps = 56/923 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  + +  E++ +P+LIEVQ  SY  FL          +EGL+  F  + PIT +SG
Sbjct: 13  KSMRMSYSRQKEVLQMPNLIEVQTDSYKWFL----------DEGLKEVFDDISPITDYSG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              LEFV +    D  K+ +++C  RD TYA PLK+ +RL           K   +I E 
Sbjct: 63  HLSLEFVDFTLCTDETKYTIEECKERDATYAAPLKVKVRLH---------NKETDEINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I+MGDLP+MT+ GTFVI G +R++VSQL RSPGI++     +    GK LY+C +IP++
Sbjct: 114 EIFMGDLPIMTRTGTFVINGAERVIVSQLVRSPGIYYGIAHDKL---GKELYSCTVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS D+ +VR+DR RKVP+T  + ALG+ +  EI+  F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDVFYVRVDRTRKVPITVLIRALGIGTNAEIIDLFGEEPKILASFTKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E +I S         L K  + K  K L +  + +
Sbjct: 231 ENYQEGLLELYKKIRPGEPLAVDSAESLITSMFFDPRRYDLAKVGRYKFNKKL-MLKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  +AED+V+  TGE+  EAG V+D +  + I ++ +  + I   +S  N   + N +V
Sbjct: 290 TGHTLAEDVVSPMTGEVIAEAGAVVDRELADAIQNAAVPYVWIAREESDRNIKVLSNMMV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             K                  D     V E ++  +  +  +     +  +K  +  N+ 
Sbjct: 350 DLKAVCGI-------------DPEEVGVTELVYYPVLAELLEETAGDIDELKEAIHKNIH 396

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI+A I   + L  G G  DDID+LGNRR+R+VGE+L+NQYR+GL R+E
Sbjct: 397 -ELIPKHITKEDIMASINYNMHLEYGIGKDDDIDHLGNRRIRAVGELLQNQYRIGLSRLE 455

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D++ + PQ LIN KPV +AV EFF SSQLSQ  +  N L  +TH RRLSA
Sbjct: 456 RVVRERMTTQDLEGISPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLGELTHKRRLSA 515

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL  +AR+N YGFIE PYR
Sbjct: 516 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLACYARINEYGFIEAPYR 575

Query: 604 KVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           K+      +  VT +VVY++A EE+N ++AQAN  LDE+G F  + V  R   E     +
Sbjct: 576 KIDKTDPQNPVVTEEVVYMTADEEDNYHVAQANEPLDEEGHFIHKNVSGRYRDETQEYEK 635

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              D++D SPK V S+A +LIPFL+NDD+NR LMG NMQRQAVPLL  EAP VGTGME  
Sbjct: 636 RMFDYMDVSPKMVFSVATALIPFLQNDDANRALMGSNMQRQAVPLLTTEAPVVGTGMEVK 695

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  +VA+  GIVE+  +  I I+  +                 F RSNQ+ C NQ
Sbjct: 696 SAVDSGVCVVAEEGGIVERSTSTEITIKQDDKTKKTYKLTK-------FLRSNQSNCYNQ 748

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G+ V +  +IADGPST  G++ALG+N L+ FM W GYN+ED++L+SER+V  DV
Sbjct: 749 RPIVVKGERVEKGQVIADGPSTSNGEMALGKNPLIGFMTWEGYNYEDAVLLSERLVQNDV 808

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TS+HIEE+E  ARDTKLGPEEITRDIP V ++ LK++DE GII +GAEV  GDILVGK+
Sbjct: 809 YTSVHIEEYEAEARDTKLGPEEITRDIPGVGDDALKDLDERGIIRIGAEVRAGDILVGKV 868

Query: 899 TPKGESPMTPEEKLLRAIFGEKA 921
           TPKGE+ +T EE+LLRAIFGEK+
Sbjct: 869 TPKGETELTAEERLLRAIFGEKS 891


>gi|67550153|gb|AAY68423.1| RNA polymerase subunit B [Acinetobacter lwoffii]
          Length = 709

 Score =  812 bits (2098), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/713 (54%), Positives = 523/713 (73%), Gaps = 5/713 (0%)

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL+ +A+ N +GF+ETPYRKV DG+VT++V YLSA+EE    IAQA+S++D+D
Sbjct: 1    PNIGLINSLSVYAKCNNFGFLETPYRKVVDGRVTDEVEYLSAIEEVGTVIAQADSAMDKD 60

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G+ TEE V  R  G+ + +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 61   GNLTEEFVSVRHQGDFVRIPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQ 120

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L A+ P VGTGME+ VA  SG  ++A+R G +E VDA R+VIR  E ++    +
Sbjct: 121  RQAVPTLIADKPLVGTGMEANVAHDSGVCVIAQRGGRIEFVDASRVVIRVNEDEMIAGGA 180

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+K+ RSNQNTC+NQ+ LV +GD+V R D++ADGPSTD G+LALG+NM VAFM 
Sbjct: 181  GVDIYNLIKYTRSNQNTCINQKVLVNLGDKVGRGDVLADGPSTDGGELALGQNMRVAFMT 240

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYN+EDS+L+SER++ ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +D
Sbjct: 241  WNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLD 300

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  G
Sbjct: 301  ESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKG 360

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R G++K+ER+ ++E+ Q++   +D  +E  I +     R++ +L GQ +  
Sbjct: 361  TVIDVQVFTRDGLEKDERAQAIEKAQLDAYRKDLKEEFKIFEEAARERVIRLLNGQESNG 420

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G    K+   LS D++S        +    DE +   +  ++V  +     ++++F  K 
Sbjct: 421  GGTT-KRGDKLSEDVLSGLELVDLLEIQPVDEAIAERLTQIQVFLKEKSFEIDEKFAEKK 479

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
             K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G P
Sbjct: 480  RKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVP 539

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMNVGQI ETHLG A  GLG +I  ++ + +    +  LR FL+K+  
Sbjct: 540  VDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDKMMKEQRT---VLELRDFLDKIYN 596

Query: 1178 T-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G   E +    D+ +L+++   ++GVP++TPVFDGA+E  I  +L++A L  +GQ++L
Sbjct: 597  KVGGEQEDLDSLTDEEILKLSGNLRAGVPLATPVFDGAEEGQIKELLQLAGLSSTGQTVL 656

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            YDG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  
Sbjct: 657  YDGRTGERFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 709


>gi|299143783|ref|ZP_07036863.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
 gi|298518268|gb|EFI42007.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
          Length = 1251

 Score =  812 bits (2097), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/957 (44%), Positives = 593/957 (61%), Gaps = 47/957 (4%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G  R R  F +  E++ +P+LIEVQ  S++  L           EGL+  F  V 
Sbjct: 3   HPVKYG-KRERMSFSRIDEVLSLPNLIEVQTDSFEWLL----------KEGLKEVFDDVS 51

Query: 64  PITAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           PI  +SG  +LEFV Y   D  K+D+D+   RD  Y  PLK+ +RLI             
Sbjct: 52  PIEDYSGNLILEFVDYYISDEIKYDIDESKQRDTNYCAPLKVKVRLI---------NTET 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++MGD+PLMT +GTF+I G +R+VVSQL RSPG ++  +  +    GK LY+ 
Sbjct: 103 GEVKEQEVFMGDIPLMTPNGTFIINGAERVVVSQLVRSPGAYYKVETDKT---GKKLYSS 159

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY--S 239
            +IP++G W++ E D++ +++VRIDR RK+PVT  L A+G++S  EI            +
Sbjct: 160 TLIPNRGAWIEFETDAQGVVNVRIDRTRKIPVTILLRAIGIESNLEIKQMLGESESLLKT 219

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +           ID+ + + E+         L    + K  K LG
Sbjct: 220 FEKDTTSNKNEALLEIYKKLRPGEPPTIDSAKSLFENMFFDNRRYDLAHVGRYKFNKKLG 279

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           I++  +   Y +EDIVN ETGEI +  G++I+E+    I    I  + +      +  A 
Sbjct: 280 ISA-RILNHYASEDIVNPETGEILVSEGELINEEMASAIERCGINRLTVTIKSQHDGEAD 338

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
               ++ +      D  L       P D+      E ++  LF    + +   V  +K  
Sbjct: 339 RDVIVIGNNFAYADDFEL-------PFDLRELGYREKIYYPLFKQIVEENSEDVETLKNE 391

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           ++ N++     +HI  +DIIA +     L  G G +DDID+LGNRR+RSVGE+L+NQ+R+
Sbjct: 392 LKKNINL-LSPKHIIVDDIIAAVSYEFGLFEGVGVVDDIDHLGNRRIRSVGELLQNQFRI 450

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G+ RMER I+ER++  D D+  PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +TH
Sbjct: 451 GISRMERVIRERMTIQDSDATTPQSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLSELTH 510

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SLT++AR+N YGF
Sbjct: 511 KRRLSALGPGGLSRDRAGFEVRDVHNSHYGRMCPIETPEGPNIGLITSLTTYARINEYGF 570

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEI 654
           IE PYRKV   +G VTN++ Y++A  E  + IAQ+N  LDE+G F  + V  R   G   
Sbjct: 571 IEAPYRKVKLGEGIVTNEIEYITADVEYEQIIAQSNEPLDENGKFINDRVVARGHEGIVD 630

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +   + +  +D SP+Q+V++  ++IPFLENDD+NR LMG NMQRQAVPLL  EAP +GTG
Sbjct: 631 IYDAKSVTCMDVSPQQIVAVGTAMIPFLENDDANRALMGANMQRQAVPLLTTEAPIIGTG 690

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   AK SG  IVA   G + +VDA  I ++            VD Y+L KF   NQ T
Sbjct: 691 IEYRAAKDSGVVIVATDDGEIVKVDATEIHLKR------SGDGVVDKYKLHKFVGGNQGT 744

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +NQRP+V+ G  V++ +IIADGPSTD G++ALG+N+L+AFM W GYN+ED++L+++ +V
Sbjct: 745 TINQRPIVEKGQMVKKGEIIADGPSTDQGEMALGKNILIAFMNWEGYNYEDAILVNQELV 804

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +D  TS+HIEE+E  ARDTKLGPEEITRDIPNV ++ L+++DE GII +GAEVNPG+IL
Sbjct: 805 IKDTLTSLHIEEYESEARDTKLGPEEITRDIPNVGDDMLRDLDERGIIRIGAEVNPGNIL 864

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKGE+ ++ EE+LLRAIFGEKA +VRDTSLR+P G SG VVDV+ F R G D
Sbjct: 865 VGKVTPKGETELSAEERLLRAIFGEKAREVRDTSLRLPHGESGIVVDVKTFTRKGGD 921



 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 275/1219 (22%), Positives = 453/1219 (37%), Gaps = 172/1219 (14%)

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV--------- 273
                 IL      I    + D         +     KV   L++ +TGE           
Sbjct: 56   YSGNLILEFVDYYISDEIKYDIDESKQRDTNYCAPLKVKVRLINTETGEVKEQEVFMGDI 115

Query: 274  ---IESGKKLTSGLLK----SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE--- 323
                 +G  + +G  +     L      +  + +D   G  +    +    G        
Sbjct: 116  PLMTPNGTFIINGAERVVVSQLVRSPGAYYKVETDK-TGKKLYSSTLIPNRGAWIEFETD 174

Query: 324  -------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
                     D   +  +  +  +   +  +     +  +  +  T   D   ++ +ALL+
Sbjct: 175  AQGVVNVRIDRTRKIPVTILLRAIGIESNLEIKQMLGESESLLKTFEKDTTSNKNEALLE 234

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            IY+ +RPG+  T   A+S+F  +FFD+ +YDL+ VGR K N +L +      R +     
Sbjct: 235  IYKKLRPGEPPTIDSAKSLFENMFFDNRRYDLAHVGRYKFNKKLGI----SARILNHYAS 290

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              I+             +  + L +       EM     R G+ R+  +IK +       
Sbjct: 291  EDIVN-----------PETGEILVSEGELINEEMASAIERCGINRLTVTIKSQHDGEADR 339

Query: 497  SVMP--------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT----RRLSAL 544
             V+          D      +            L +     NS    T      + ++ L
Sbjct: 340  DVIVIGNNFAYADDFELPFDLRELGYREKIYYPLFKQIVEENSEDVETLKNELKKNINLL 399

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                +        +        G     +     N   + S+    +      I    R 
Sbjct: 400  SPKHIIVDDIIAAVSYEFGLFEGVGVVDDIDHLGN-RRIRSVGELLQNQFRIGISRMERV 458

Query: 605  VCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDEDG-----------SFTE 642
            + +     D           +  ++A  +E    +Q +  +D++            S   
Sbjct: 459  IRERMTIQDSDATTPQSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLSELTHKRRLSALG 518

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQ-----VVSIAASLIPFLENDDSNRVLMGCNMQ 697
                 R      +       +    P +      + +  SL  +   ++   +       
Sbjct: 519  PGGLSRDRAGFEVRDVHNSHYGRMCPIETPEGPNIGLITSLTTYARINEYGFIEAPYRKV 578

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            +    ++  E  ++   +E         A   +      +    R+V R  EG +D   +
Sbjct: 579  KLGEGIVTNEIEYITADVEYEQI----IAQSNEPLDENGKFINDRVVARGHEGIVDIYDA 634

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGD----EVRRNDIIADGPSTDLGDLALGRNMLV 813
                   +  Q+           +V VG      +  +D        ++   A+      
Sbjct: 635  KSVTCMDVSPQQ-----------IVAVGTAMIPFLENDDANRALMGANMQRQAVPLLTTE 683

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G  +  +      +V+ D    + ++  E+  + +  G  +  +    V     
Sbjct: 684  APIIGTGIEYRAAKDSGVVIVATDDGEIVKVDATEIHLKRSGDGVVDKYKLHKFVGGNQG 743

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              I++  I+  G  V  G+I+    +   +  M   + +L A    +  +  D  L V  
Sbjct: 744  TTINQRPIVEKGQMVKKGEIIADGPST-DQGEMALGKNILIAFMNWEGYNYEDAIL-VNQ 801

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +       +   +     E    +    DD    LD     R+   +   
Sbjct: 802  ELVIKDTLTSLHIEEYESEARDTKLGPEEITRDIPNVGDDMLRDLDERGIIRIGAEVNPG 861

Query: 994  NAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            N + G    K  T LS++  L+      +  +      ++      + V           
Sbjct: 862  NILVGKVTPKGETELSAEERLLRAIFGEKAREVRDTSLRLPHGESGIVV----------- 910

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                K    + GD++ PGV  +V+VFVA KR IQ GDKM GRHGNKG++SR+LP EDMP+
Sbjct: 911  --DVKTFTRKGGDELQPGVNEMVRVFVATKRKIQVGDKMCGRHGNKGVISRVLPKEDMPY 968

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            + DGTP+ IVLNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     DI+     
Sbjct: 969  MPDGTPIQIVLNPLGVPSRMNLGQVLEVHLGLAAKKLGWHVATPVFDGANEKDITDALDL 1028

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                           G P+     DG                  
Sbjct: 1029 A------------------------------GYPI-----DG------------------ 1035

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             +  L DG TGE FD PVTVGY+YMLKL+H+V +K++ARSTG YSLVTQQPLGGK+  GG
Sbjct: 1036 -KIQLRDGRTGEEFDHPVTVGYMYMLKLHHLVDEKIHARSTGPYSLVTQQPLGGKAQFGG 1094

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGA+Y LQEMLT+KSDD+VGR + YESIV G +  + G PESF VL+
Sbjct: 1095 QRFGEMEVWALEAYGASYTLQEMLTVKSDDIVGRVKTYESIVKGENIPQPGIPESFKVLI 1154

Query: 1352 KEMQALGLSIDLENSRTKN 1370
            KE+++L L I + +     
Sbjct: 1155 KELESLALEIKVLDDEGNE 1173


>gi|296111484|ref|YP_003621866.1| DNA-directed RNA polymerase beta subunit [Leuconostoc kimchii IMSNU
           11154]
 gi|295833016|gb|ADG40897.1| DNA-directed RNA polymerase beta subunit [Leuconostoc kimchii IMSNU
           11154]
          Length = 1200

 Score =  812 bits (2097), Expect = 0.0,   Method: Composition-based stats.
 Identities = 413/966 (42%), Positives = 579/966 (59%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ +    E++D+P+LIE+Q ASY  FL          + G++  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYASIKEVLDVPNLIEIQTASYQWFL----------DAGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F     LE+V Y+   PK+++D+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQDTLSLEYVDYQLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPGI+++ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQENDK---NGRPRY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +IL  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDILDIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        K   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLAS 275

Query: 296 LGIT--------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE + + ++GE+  E G ++D+  + ++        P L
Sbjct: 276 VGRYKINKKLSLKTRLLNQTLAETLADPDSGEVLAEKGTIVDKTVMSKLS-------PFL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             D      Y  +     +    +  +L   ++  P +                      
Sbjct: 329 ERDDFKTTTYTPSGDAVLE----EPIMLQKIKIESPENP--------------------- 363

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                   + +  N    ++ R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSV
Sbjct: 364 -----EKTLLLIGNGHIDENDRTVRPADILAGMNYFLNLQEGIGNVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ R+N YGFIETPYR+V      VTN + YL+A EE+N  +AQANS L+EDGSF ++ V
Sbjct: 539 TYGRINKYGFIETPYRRVDWTTHMVTNKIDYLTADEEDNYIVAQANSPLNEDGSFVKDTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             +P VGTG+E   A  SG A++++ AG+VE VD   I +R  +G LD        Y LM
Sbjct: 659 PHSPLVGTGIEYKAAHDSGVAMISRAAGVVEYVDGHEIRVRREDGQLD-------NYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P+V  G+ V  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIVHEGEYVAADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VG
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 180/568 (31%), Positives = 266/568 (46%), Gaps = 68/568 (11%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +   G  ++ +      M+S       +++  E+  R  + G  +    +      G 
Sbjct: 661  SPLVGTGIEYKAAHDSGVAMISRAAGVVEYVDGHEIRVRR-EDGQLDNYELMKFRRSNGG 719

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN ++  I+  G  V   ++L    +   +  +   +  L A    +  +  D  +    
Sbjct: 720  KNYNQKPIVHEGEYVAADEVLADGPS-MEQGELALGQNPLIAFMTWQGYNFEDAIVLNER 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V   V        +  +  +  +  E    E +    +D+   LD +   R+     G 
Sbjct: 779  LVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGEDQLKDLDADGIIRV-----GA 832

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      +S   R     F  +  +V+     +          +    
Sbjct: 833  EVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNV---- 888

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              +I   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P EDMP++ 
Sbjct: 889  --RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSVVVPEEDMPYMP 946

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  + S + D  ++ +I        
Sbjct: 947  DGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHVASPVFDGASDDEI-------- 998

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                             ++ LR A   + G  V   V+DG                    
Sbjct: 999  -----------------EAALREAGLPQDGKSV---VYDG-------------------- 1018

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGE FD+ V VG ++ +KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 1019 ------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQR 1072

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT KSDDV GR +VYESI+ G      G PESF VLVKE
Sbjct: 1073 FGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVYESIIKGEPIPRPGVPESFRVLVKE 1132

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +QALGL + + +         +   D +
Sbjct: 1133 LQALGLDMQVLDGAGSEVELRQMDEDDS 1160


>gi|315650863|ref|ZP_07903909.1| DNA-directed RNA polymerase subunit beta [Eubacterium saburreum DSM
           3986]
 gi|315486890|gb|EFU77226.1| DNA-directed RNA polymerase subunit beta [Eubacterium saburreum DSM
           3986]
          Length = 1317

 Score =  811 bits (2096), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/954 (44%), Positives = 585/954 (61%), Gaps = 58/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             +R  F    E++++P+LIE+QK SY  FL          + GL+  F+ +FPI  F+G
Sbjct: 13  KSMRMSFQTQKEVLEMPNLIEIQKNSYQWFL----------DAGLKEVFRDIFPIEDFAG 62

Query: 71  AAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              L+FV+++   D  K+ +++C  RD TYA PLK+ +RLI  D D         +I E 
Sbjct: 63  HFSLDFVNFKLARDEVKYSIEECKDRDTTYAAPLKVKIRLINKDKD---------EINEH 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I++GDLPLMT  G+FVI G +R++VSQL RSPGI++  +  +    GK L+ C++IP++
Sbjct: 114 EIFLGDLPLMTDTGSFVINGAERVIVSQLVRSPGIYYTIEHDKI---GKELFMCQVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS DI + R+DR RKVP+T  L A G+ +  +I   F    KI+ S   D  
Sbjct: 171 GAWLEYETDSNDIFYARVDRTRKVPITVLLRAFGLGTNTQITDMFGEEPKIMASFAKDPS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    +         + +D+ E ++ S         L K  + K  K L    + +
Sbjct: 231 ENYQDGLLELYKKIRPGEPLSVDSAESLLRSMFFDARRYDLAKVGRYKFNKKL-HFKNRI 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  ++ D+V+  TGEI  +A  V+D      I ++    IP +++  V     + + L+
Sbjct: 290 KGHTLSRDVVDENTGEIIAQAEIVVDADIATAIQNA---AIPAVWIHGVEREVKVLSNLM 346

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D      +            D  +  + E ++  +     K      G   +       
Sbjct: 347 VDIESYVPE----------LTDPKSIGITEQVYYPV---LKKLIEENKGEELIKAIEKNV 393

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI KEDI A +   + +    G  DDID+LGNRR+R+VGE+L+NQYR+GL RME
Sbjct: 394 NELIPKHITKEDIFATVNYNMHIEEHIGNKDDIDHLGNRRIRAVGELLQNQYRIGLTRME 453

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ DIDS+ PQ LIN KPV +AV EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 454 RVVRERMTTQDIDSITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPLSELTHKRRLSA 513

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL SFARVN YGF+E PYR
Sbjct: 514 LGPGGLSRERAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLASFARVNEYGFVEAPYR 573

Query: 604 KVC------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            V       +  VT++V+YL+A EE+N  +AQAN  LD +G F    V  R   E     
Sbjct: 574 VVDKSTDPSNPVVTDNVIYLTADEEDNFTVAQANEPLDAEGHFVRNNVSGRYRDETSEFA 633

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           ++ ID +D SP+ V S+A S+IPFLENDD+NR LMG NMQRQAVPL+  +AP VGTGME+
Sbjct: 634 KKNIDLMDVSPRMVFSVATSMIPFLENDDANRALMGSNMQRQAVPLMITDAPVVGTGMET 693

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG  +VAK +G V +  + +IVI+  +  +      +D Y+L+KF RSNQ+   N
Sbjct: 694 KAAVDSGVCVVAKNSGTVTECSSDKIVIKRDDDAV------LDTYKLIKFARSNQSNSYN 747

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+V  G+ V   ++IADG ST  G++ALG+N L+ FM W GYN+ED++L+SER+V  D
Sbjct: 748 QKPIVFKGNHVNAGEVIADGASTYNGEIALGKNPLIGFMTWEGYNYEDAVLLSERLVEYD 807

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V+TSIHIEE+E  AR+TKLGPEEITRD+P V ++ LK++DE GII +GAEV  GDILVGK
Sbjct: 808 VYTSIHIEEYECAARETKLGPEEITRDVPGVGDDALKDLDERGIIRIGAEVRAGDILVGK 867

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP G  G VVD ++F R   D
Sbjct: 868 VTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPHGAYGVVVDAKVFTREAGD 921



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 184/586 (31%), Positives = 271/586 (46%), Gaps = 39/586 (6%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +++   P  G   E    +     +V+++  T       +++ +     
Sbjct: 668  MGSNMQRQAVPLMITDAPVVGTGMETKAAVDSGVCVVAKNSGTVTECSSDKIVIKRDDDA 727

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAI 916
              +  + I         + ++  I+  G  VN G+++  G  T  GE  +     +    
Sbjct: 728  VLDTYKLIKFARSNQSNSYNQKPIVFKGNHVNAGEVIADGASTYNGEIALGKNPLIGFMT 787

Query: 917  F-GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ---IELLARDKD 972
            + G    D    S R+      T + +  +     +       + R+     +   +D  
Sbjct: 788  WEGYNYEDAVLLSERLVEYDVYTSIHIEEYECAARETKLGPEEITRDVPGVGDDALKDL- 846

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 847  DERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------------- 892

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E      +            K+   + GD++ PGV + V++++A KR I  GDKMAG
Sbjct: 893  ---EVRDTSLKVPHGAYGVVVDAKVFTREAGDELAPGVTQNVRIYIAQKRKISVGDKMAG 949

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  +
Sbjct: 950  RHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNV 1009

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     DI  +       +             DD   +  +    GV     V  
Sbjct: 1010 ATPVFDGANENDIMDMLEVANDYVNGDW---------DDFKDKYKDVLDPGV-----VEY 1055

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                     +     L   G+  L DG TGE FD PVT+G+++ LKL+HMV DK++ARST
Sbjct: 1056 LGSHLENRKLWEGVPLSRDGKVRLRDGRTGEYFDSPVTIGHMHYLKLHHMVDDKIHARST 1115

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDV GR + YE++
Sbjct: 1116 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVTGRVKTYEAV 1175

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            + G +  + G PESF VL+KE+Q+LGL I +     +     E   
Sbjct: 1176 IKGENIPDAGIPESFKVLLKELQSLGLDISVLGENGEEVELKENTE 1221


>gi|300173979|ref|YP_003773145.1| DNA-directed RNA polymerase subunit beta [Leuconostoc gasicomitatum
           LMG 18811]
 gi|299888358|emb|CBL92326.1| DNA-directed RNA polymerase, beta subunit [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 1204

 Score =  811 bits (2095), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/966 (42%), Positives = 579/966 (59%), Gaps = 84/966 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +V  G  R R+ +    E++D+P+LIE+Q ASY  FL          ++G++  F 
Sbjct: 1   MAGHLVKYGKHRTRRSYASIKEVLDVPNLIEIQTASYQWFL----------DDGIKEMFG 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F G   LE+V Y+   PK+++D+    D  Y+ PL +TLRL            
Sbjct: 51  DIMPIDDFQGTLSLEYVDYQLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPGI+++ +  +   +G+  Y
Sbjct: 102 ETGEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQENDK---NGRPRY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKI 236
              +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +IL  F   Y  +
Sbjct: 159 GTTVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDILDIFSDQYDAL 218

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
             +   D        +D  V   +      +  GE    +S + L        K   +  
Sbjct: 219 NMTLEKDVHK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLAS 275

Query: 296 LGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE + + ++GEI  E G  +D+  + ++        P L
Sbjct: 276 VGRYKINKKLSLKTRLLNHTLAETLADPDSGEIIAEKGTTVDKTVMSKLM-------PFL 328

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +      Y  +     +    +  +L   ++  P D                      
Sbjct: 329 EREDFKTTTYTPSGDAVLE----EPVVLQKIKIESPEDP--------------------- 363

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                   + +  N    ++ R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSV
Sbjct: 364 -----EKTLVLIGNGHIDENDRTVRPADILAGMNYFLNLQEGIGNVDDIDHLGNRRIRSV 418

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +
Sbjct: 419 GELLQNQFRIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMD 478

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL 
Sbjct: 479 QTNPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLA 538

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++ R+N YGFIETPYR+V      VT+ + YL+A EE+N  +AQANS L++DGSF  + V
Sbjct: 539 TYGRINKYGFIETPYRRVDWTTHMVTDKIDYLTADEEDNFIVAQANSPLNDDGSFVHDTV 598

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL 
Sbjct: 599 MARFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLD 658

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             AP VGTG+E   A  SG A++++ AG+VE VD   I IR  +G LD        Y LM
Sbjct: 659 PHAPLVGTGIEYKAAHDSGVAMISRAAGMVEYVDGREIRIRREDGQLD-------HYELM 711

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF+RSN     NQ+P++  G+ V  ++++ADGPS + G+LALG+N L+AFM W GYNFED
Sbjct: 712 KFRRSNGGKNYNQKPIIHEGEHVEADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFED 771

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VG
Sbjct: 772 AIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVG 831

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+
Sbjct: 832 AEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIY 891

Query: 946 NRHGID 951
                D
Sbjct: 892 TPENGD 897



 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 174/508 (34%), Positives = 246/508 (48%), Gaps = 67/508 (13%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN ++  II  G  V   ++L    +   +  +   +  L A    +  +  D  +    
Sbjct: 720  KNYNQKPIIHEGEHVEADEVLADGPS-MEQGELALGQNPLIAFMTWQGYNFEDAIVLNER 778

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V   V        +  +  +  +  E    E +    +D+   LD +   R+     G 
Sbjct: 779  LVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGEDQLKDLDADGIIRV-----GA 832

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      +S   R     F  +  +V+     +          +    
Sbjct: 833  EVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNV---- 888

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              +I   + GD++ PGV  +V+V++A KR IQ GDKMAGRHGNKG VS ++P EDMP++ 
Sbjct: 889  --RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAGRHGNKGTVSVVVPEEDMPYMP 946

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  + S + D  ++ +I        
Sbjct: 947  DGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHVASPVFDGASDDEI-------- 998

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                             ++ LR A   + G  V   V+DG                    
Sbjct: 999  -----------------EAALREAGLPQDGKSV---VYDG-------------------- 1018

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGE FD+ V VG ++ +KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 1019 ------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQR 1072

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT KSDDV GR +VYESI+ G      G PESF VLVKE
Sbjct: 1073 FGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVYESIIKGEPIPRPGVPESFRVLVKE 1132

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +QALGL + + +         +   D +
Sbjct: 1133 LQALGLDMQVLDGDGDEVELRQMDEDDS 1160


>gi|259157297|gb|ACV96840.1| DNA-directed RNA polymerase beta subunit [Paenibacillus elgii]
          Length = 1060

 Score =  811 bits (2095), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/930 (45%), Positives = 578/930 (62%), Gaps = 79/930 (8%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            SY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y    PK+ VD+   R
Sbjct: 2   KSYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLGEPKYSVDESKER 51

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
           D+T+A PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF+I G +R++V
Sbjct: 52  DVTFAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIV 102

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSP ++F     +   +GK  Y   +IP++G W+++E D+KDII+VRIDR RK+PV
Sbjct: 103 SQLVRSPSVYFS---TKVDKNGKKTYTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPV 159

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T  L ALG  ++ EI+             D      +   L+           +  GE  
Sbjct: 160 TVLLRALGFGTDAEIIDLLGDNEYIRNTLDKDNTDSTDKALI------EIYERLRPGEPP 213

Query: 273 VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            +++ + L        K           +       + L    +AE +V+  TGEI  EA
Sbjct: 214 TLDNARSLLVARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDTNTGEIVAEA 273

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
           G ++D + L+ I            +  +  +       V +   +     L    V  P 
Sbjct: 274 GQLLDRRLLDTI------------IPYLEESVGFTEYNVVNGVTESDKIPLQCVSVYSPL 321

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           +                         V +V  N ++       V++I   DII+ I   +
Sbjct: 322 E----------------------DGKVVKVIANGKI----DKTVKNITPADIISSINYFI 355

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
           +L +G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D++++ PQ LI
Sbjct: 356 NLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDVNTITPQQLI 415

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 416 NIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHHS 475

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL++SL++FARVN +GFIE PYR+V      VT+++ YL+A EE
Sbjct: 476 HYGRMCPIETPEGPNIGLINSLSTFARVNEFGFIEAPYRRVDPHTDVVTDEISYLTADEE 535

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +N  +AQAN+ L E+G F  + V  R   + + +P+E++D++D SPKQVVS+A +LIPFL
Sbjct: 536 DNYVVAQANAELTEEGKFANDSVIVRYKDDILTLPKERVDYMDVSPKQVVSVATALIPFL 595

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           ENDDSNR LMG NMQRQAVPLL  ++P VGTGME   AK SG  IV+K  G+VE+V A  
Sbjct: 596 ENDDSNRALMGSNMQRQAVPLLIPKSPLVGTGMEHKSAKDSGVCIVSKVNGVVERVSANE 655

Query: 743 IVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           I +R  E       +G +  ++L KF RSNQ TC+NQRP+   G++VR  DI+ADGPST+
Sbjct: 656 IWVRRQEMVDGRLVNGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE 715

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALGRN++VAFM W GYN+ED++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEI
Sbjct: 716 QGELALGRNVVVAFMTWEGYNYEDAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEI 775

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TRDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA
Sbjct: 776 TRDIPNVGEDALKNLDERGIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKA 835

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 836 REVRDTSLRVPHGTDGIVVDVKVFTRENGD 865



 Score =  395 bits (1014), Expect = e-107,   Method: Composition-based stats.
 Identities = 155/458 (33%), Positives = 220/458 (48%), Gaps = 67/458 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     +    +       I++  I   G +V  GDIL    + + +  +     ++ A
Sbjct: 670  NGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE-QGELALGRNVVVA 728

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +  
Sbjct: 729  FMTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVG 783

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                +N+  R   I  G    +G     K T      ++   R     F  +  +V+   
Sbjct: 784  EDALKNLDER-GIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTS 842

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 843  LRVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHG 896

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+++RILP EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG    + 
Sbjct: 897  NKGVIARILPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMAAKYLGIHTATP 956

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D     D                                             VFD   
Sbjct: 957  VFDGAREYD---------------------------------------------VFD--- 968

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   +  A +  +G+++LYDG TGE F+R VTVG +YM+KL HMV DK++ARSTG Y
Sbjct: 969  ------TMEEAGMQRNGKTMLYDGRTGEAFEREVTVGVMYMIKLAHMVDDKIHARSTGPY 1022

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1023 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1060


>gi|169335208|ref|ZP_02862401.1| hypothetical protein ANASTE_01616 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257946|gb|EDS71912.1| hypothetical protein ANASTE_01616 [Anaerofustis stercorihominis DSM
           17244]
          Length = 1244

 Score =  811 bits (2095), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/954 (45%), Positives = 598/954 (62%), Gaps = 59/954 (6%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K  +++++P+LI +Q  SY  F+           EGL+ AF  VFPI+  S 
Sbjct: 9   RRERMSFSKIKDVMEMPNLISIQTDSYKWFI----------EEGLREAFLDVFPISDPSE 58

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y  D  PK+DV++C  R   Y+  LK+ +RL+V +  E      IKD++EQ 
Sbjct: 59  NLILEFVDYILDDTPKYDVEECKERKTNYSASLKVKVRLVVKEDGE------IKDVREQH 112

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++M D PLMT+ GTF+I G +R++VSQL RSPG +F  ++ +    GK LY  +IIP++G
Sbjct: 113 VFMADFPLMTRTGTFIINGAERVIVSQLIRSPGAYFSVERDKY---GKELYNGQIIPNRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
            W++ E D+ D ++ R+DR +KVP+T  + ALG+ + EEI++ F  +       +     
Sbjct: 170 AWLEYETDASDCLYARVDRTKKVPITVLIRALGLGTNEEIINFFGEEKRLMTTFEKDSSS 229

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
                L+   K       +  GE   ++S K L   +    +   +  +G          
Sbjct: 230 SVDEGLIEIYK------KLRPGEPESVDSAKGLFIPMFFDQRRYDLMMVGRFKLNKKLAL 283

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
              + G Y  +DIVN  TGEI +   ++IDEK+  EI +  I  + +             
Sbjct: 284 STRITGQYAFKDIVNPLTGEILVSKDEIIDEKTAWEIQNCGINTVEV------------- 330

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                   K   + ++DI +   P DVS  ++ E +       S+  D       K    
Sbjct: 331 KVSEDRGFKIIGNGVVDINKYELPFDVSDLNIDEMV--NFRVLSEILDTDLSNEEKKEQI 388

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            +  +    +HI  EDI A I   +   +G GT+DDID+LGNRR+RSVGE+L+NQ+R+GL
Sbjct: 389 KDRMSELLPKHITVEDIYASISYNLGFDHGIGTLDDIDHLGNRRIRSVGELLQNQFRIGL 448

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ER++KER+ S D + V P  L+N KPV +A+ EFF SSQLSQ  +  N L  +TH R
Sbjct: 449 SRLERTVKERMISFDPEEVTPSSLVNVKPVNAALKEFFGSSQLSQFMDQTNPLGELTHKR 508

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R SALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL +F+RVN YGFIE
Sbjct: 509 RYSALGPGGLSRDRAGFEVRDVHHSHYGRVCPIETPEGPNIGLIGSLATFSRVNKYGFIE 568

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE--EILVP 657
           TPYR+V DG VT D+ Y+ A EE    IAQAN  L E+GSF    V  R   E   + V 
Sbjct: 569 TPYRRVKDGAVTGDIDYIPADEEGKYTIAQANEPLMENGSFEHSKVTGRAGFERDFVTVE 628

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           ++K+D++D SPKQVVS+A S+IPFLENDD+NR LMG NMQRQAVPLLK +AP V TG+E 
Sbjct: 629 KDKVDYMDISPKQVVSVATSMIPFLENDDANRALMGANMQRQAVPLLKPQAPMVATGIEH 688

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +V++  G+V++V A  I+I       D +T     Y+L+K++R+NQNTC+N
Sbjct: 689 RAAKDSGVCVVSEVDGVVKRVTATEIII------TDDATKQNVKYKLLKYKRTNQNTCIN 742

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q P+VK+GD +++ ++IADGPST+ GDL+LGRN+L+ FM W GYN+ED+++I+E++V ED
Sbjct: 743 QIPIVKLGDRIKKGEVIADGPSTENGDLSLGRNILIGFMTWEGYNYEDAIIINEKLVKED 802

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             TSIHIEEF+  A++TKLG EEITRDIPNV E+ L+N+DE G+I VGAEV   DILVGK
Sbjct: 803 ALTSIHIEEFDCEAKETKLGSEEITRDIPNVGEDALRNLDERGVIRVGAEVKSDDILVGK 862

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGES  T EEKLLRAIFGEKA +VRDTSL+VP G  G VVDV+++ +   D
Sbjct: 863 VTPKGESDPTAEEKLLRAIFGEKAREVRDTSLKVPHGEKGVVVDVKVYTKENGD 916



 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 161/493 (32%), Positives = 240/493 (48%), Gaps = 77/493 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G  +  G+++    + +    ++    +L      +  +  D  +     V    +
Sbjct: 746  IVKLGDRIKKGEVIADGPSTEN-GDLSLGRNILIGFMTWEGYNYEDAIIINEKLVKEDAL 804

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                      +  E  +  E     I  +  D     DE+ ++      +  +IL G+  
Sbjct: 805  TSIHIEEFDCEAKETKLGSEEITRDIPNVGEDALRNLDERGVIRVGAEVKSDDILVGKVT 864

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +    +     +      
Sbjct: 865  PKGESDPTAEEKLLRAIFGEKAR-----------EVRDTSLKVPHGEKGVVVDV------ 907

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++ P V ++V+V++A+KR IQ GDKMAGRHGNKG++SR++P EDMPFL DG
Sbjct: 908  KVYTKENGDELKPNVNKLVRVYIAIKRKIQVGDKMAGRHGNKGVISRVVPEEDMPFLPDG 967

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP++I+L+P+GVPSRMN+GQ+ E HLG AC  LG +I + + D     DI  L       
Sbjct: 968  TPLEILLSPMGVPSRMNIGQVLEVHLGLACKALGIEIATPVFDGAKEEDIMELLEQSGYS 1027

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    G++ 
Sbjct: 1028 ADGKIQL-----------------------------------------------YDGRT- 1039

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD  VTVGY+YML+L+H+V +K++AR+TG YSLVTQQPLGGK+  GGQR G
Sbjct: 1040 ------GEPFDNRVTVGYMYMLRLHHIVDEKMHARATGPYSLVTQQPLGGKAQMGGQRFG 1093

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDDV GR + YESI+ G +  + G PESF VL+KE Q
Sbjct: 1094 EMEVWALEAYGAAHTLQEILTVKSDDVSGRVKTYESIIKGENIPKAGVPESFKVLIKEFQ 1153

Query: 1356 ALGLSIDLENSRT 1368
            +L L +++   R 
Sbjct: 1154 SLCLDVNVLGERN 1166


>gi|17225232|gb|AAL37309.1| RNA polymerase B-subunit [Staphylococcus saccharolyticus]
          Length = 1156

 Score =  811 bits (2095), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/937 (46%), Positives = 583/937 (62%), Gaps = 79/937 (8%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +LIE+Q  SYD FL           EGL   F+ + PI  F+G   LEFV Y    P +D
Sbjct: 1   NLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPNYD 50

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
           +++   RD TYA PL++ +RLI+         K   ++KEQ ++MGD PLMT  GTFVI 
Sbjct: 51  LEESKNRDATYAAPLRVKVRLII---------KETGEVKEQEVFMGDFPLMTDTGTFVIN 101

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQL RSP ++F+    +   +G+  Y   IIP++G W++ E D+KD+++VRID
Sbjct: 102 GAERVIVSQLVRSPSVYFNEKIDK---NGRENYDATIIPNRGAWLEYETDAKDVVYVRID 158

Query: 208 RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R RK+P+T  L ALG  ++ EI+             +      +   L+           
Sbjct: 159 RTRKLPLTVLLRALGFSTDQEIVDLIGDSEYLRNTLEKDGTENTEQALL------EIYER 212

Query: 267 IDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG--------ITSDCLCGLYVAEDIVNGET 317
           +  GE   +E+ K L        K   +  +G             L    +AE IVN ET
Sbjct: 213 LRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKHRLFNQKLAEPIVNSET 272

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           GEI  E G V+D + L+EI              + N+  +     V D+  + +   + +
Sbjct: 273 GEIVAEEGTVLDRRKLDEIMDVLET--------NANSEVFELEGSVIDEPVEIQSIKVYV 324

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                                   D +    + +G              +V+ I   DII
Sbjct: 325 ----------------------PNDEEGRTTTVIGNAL--------PDSEVKCITPADII 354

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +    +L NG G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D DS
Sbjct: 355 ASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS 414

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E
Sbjct: 415 ITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 474

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVV 615
           +RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + 
Sbjct: 475 VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQID 534

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A
Sbjct: 535 YLTADEEDSYVVAQANSRLDENGCFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAA 594

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI AK  G V
Sbjct: 595 TACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRV 654

Query: 736 EQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           E V++  +++R  VE +       +D Y L KF+RSN  TC NQRP+V VGD V  N+I+
Sbjct: 655 EHVESNEVLVRRLVEENGIEHEGELDRYPLAKFKRSNSGTCYNQRPIVSVGDVVEYNEIL 714

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPS +LG++ALGRN++V FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDT
Sbjct: 715 ADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDT 774

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL 
Sbjct: 775 KLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLH 834

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 835 AIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGD 871



 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 163/440 (37%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 755  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 814

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 815  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 874

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 875  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 934

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  I S + D   + D+                     
Sbjct: 935  VPSRMNIGQVLELHLGMAAKNLGIHIASPVFDGANDDDVWST------------------ 976

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 977  -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1000

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1001 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1060

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1061 AAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1120

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1121 HDNEIE-MADVDDEDATERK 1139


>gi|227515478|ref|ZP_03945527.1| DNA-directed RNA polymerase RpoB [Lactobacillus fermentum ATCC
           14931]
 gi|227086164|gb|EEI21476.1| DNA-directed RNA polymerase RpoB [Lactobacillus fermentum ATCC
           14931]
          Length = 1167

 Score =  811 bits (2094), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/943 (44%), Positives = 584/943 (61%), Gaps = 84/943 (8%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P+LIE+Q  SY+ F+          ++GL+  F  + PI  F G   LEFV Y+   
Sbjct: 1   MDLPNLIEIQTDSYNWFM----------DKGLREMFDDIMPIDDFQGKLSLEFVDYQLLE 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V +    D  Y+ PL +TLRL               +IK Q ++ GD PLMT  GT
Sbjct: 51  PKYTVAEAREHDANYSAPLHVTLRLT---------NHETGEIKSQDVFFGDFPLMTDQGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQL RSPG++++ +  +   +G+  Y    IP++G W++ E D+K I +
Sbjct: 102 FIINGAERVIVSQLVRSPGVYYNEEADK---NGRPSYGANFIPNRGAWLEYETDAKGISY 158

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFY---PKIVYSQRGDFWCFPLSAADLMVGAK 259
           VRIDR RK+P+T  + ALG  S+ EI          +  +   D         D  V   
Sbjct: 159 VRIDRTRKLPITELVRALGFGSDDEIWDMLGSESESLNATIEKDLHK---EPEDSRVEES 215

Query: 260 VSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAE 310
           +      +  GE    +S + L +      K   +  +G             L GL +AE
Sbjct: 216 LKDIYERLRPGEPKTADSARSLLTTRFFDPKRYDMAPVGRYKTNKKLQMKYRLLGLTLAE 275

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            + + ETGEI  + GDVI ++ L+E+        P+L  D      Y             
Sbjct: 276 TLADPETGEIIAKDGDVITKEVLKELE-------PVLEQDDFKMITY----------TPS 318

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            +A++     +           + +  +   D ++         K+ +  N     D++H
Sbjct: 319 DEAVVTAPVQL-----------QKIMVYSKNDPER---------KVPVVSNGHISLDLKH 358

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I+  DI+A I   ++L+ G GT DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+
Sbjct: 359 IQPADILASINYFLNLQEGIGTTDDIDHLGNRRIRSVGELLQNQFRIGLARMERVVRERM 418

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  DI++V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ 
Sbjct: 419 SIQDINTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLT 478

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DG 608
           R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+ARVNAYGFIETPYR+V   D 
Sbjct: 479 RDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYARVNAYGFIETPYRRVSWADH 538

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT+ + YL+A EE+N  IAQAN+ L+EDGSF  + + CR   + I    E +D++D SP
Sbjct: 539 KVTDRIDYLTADEEDNFIIAQANTPLNEDGSFVHDEIMCRDKEDYIETAPENVDYMDVSP 598

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+   AP +GTG+E   A  SG A++
Sbjct: 599 KQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINPHAPLIGTGIEYKAAHDSGVALI 658

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AK +G VE VDA  + +R  +G LD        Y+LMKF+RSN     NQRP+VKVG+ V
Sbjct: 659 AKNSGTVEYVDAREVRVRQEDGTLD-------TYKLMKFRRSNGGKNYNQRPIVKVGEWV 711

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             +D++ADGPS + G+LALG+N L+AFM W GYNFED++ I+ER+V +DV+TSIHIE +E
Sbjct: 712 DADDVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAIAINERLVKDDVYTSIHIESYE 771

Query: 849 VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             AR+TKLGPEE+TR+IPNVSE+  KN+DE G+I VGAEV+ GDILVGK+TPKG + ++ 
Sbjct: 772 SEARETKLGPEEMTREIPNVSEDARKNLDESGVIRVGAEVHDGDILVGKVTPKGVTELSA 831

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EE+LL AIFGEK+ +VRDTSLRVP G  G + DV++F R   D
Sbjct: 832 EERLLHAIFGEKSREVRDTSLRVPHGGGGIIQDVKVFTRENGD 874



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 176/530 (33%), Positives = 254/530 (47%), Gaps = 67/530 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +      G KN ++  I+ VG  V+  D+L    +   +  +   +  
Sbjct: 676  RQEDGTLDTYKLMKFRRSNGGKNYNQRPIVKVGEWVDADDVLADGPS-MEQGELALGQNP 734

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D        V   V        +  +  E  +  E    E+    +D
Sbjct: 735  LIAFMTWQGYNFEDAIAINERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVSED 794

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              + + +  +      I  G     G     K T      +S   R     F  +  +V+
Sbjct: 795  ARKNLDESGV------IRVGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKSREVR 848

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      K+   + GD++ PGV ++V+V++A KR IQ GDKM+G
Sbjct: 849  DTSLRVPHGGGGIIQDV------KVFTRENGDELAPGVNKMVRVYIAQKRKIQVGDKMSG 902

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 903  RHGNKGTVSIVVPEEDMPYMPDGTPIDIMLSPMGVPSRMNIGQVIELHLGMAARELGIHI 962

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D                                             V+D
Sbjct: 963  ATPVFDGANDQD---------------------------------------------VWD 977

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E         A L   G++ILYDG TGEPF++ V VG ++ LKL HMV DK++ARST
Sbjct: 978  AVKE---------AGLPSDGKTILYDGRTGEPFEQRVAVGVMHYLKLAHMVDDKIHARST 1028

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD VGR   Y++I
Sbjct: 1029 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVNTYQAI 1088

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G+   + G PESF VLVKE+Q+LGL + + + + +         D   
Sbjct: 1089 IDGDQIPKPGVPESFRVLVKELQSLGLDMKVLDDKHEEIQLKSMDEDVAD 1138


>gi|67550151|gb|AAY68422.1| RNA polymerase subunit B [Acinetobacter baumannii]
          Length = 709

 Score =  810 bits (2091), Expect = 0.0,   Method: Composition-based stats.
 Identities = 395/713 (55%), Positives = 526/713 (73%), Gaps = 5/713 (0%)

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL+ +A+ N +GF+ETPYRKV DG+VT+DV YLSA+EE    IAQA+S++D+D
Sbjct: 1    PNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDDVEYLSAIEEVGTVIAQADSAVDKD 60

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G+ TEE V  R  GE + +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 61   GNLTEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQ 120

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+A  P VGTGME+ VA+ SG  ++A R G++E VDA RIVIR  E ++    +
Sbjct: 121  RQAVPTLRANKPLVGTGMEANVARDSGVCVIANRGGVIEYVDASRIVIRVNEDEMVAGEA 180

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+K+ RSNQNTC+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM 
Sbjct: 181  GVDIYNLIKYTRSNQNTCINQNVIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMT 240

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYN+EDS+L+SER++ ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +D
Sbjct: 241  WNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLD 300

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  G
Sbjct: 301  ESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKG 360

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R G++K++R++++E+ Q++   +D  +E  I +     R++ +L GQ +  
Sbjct: 361  TVIDVQVFTRDGLEKDDRALAIEKAQLDSYRKDLKEEYKIFEEAARERVIRLLKGQESNG 420

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G    K+   LS DL+S        +    DE +   +  ++V  +   + ++++F  K 
Sbjct: 421  G-GSTKRGDKLSEDLLSGLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKK 479

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
             K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G P
Sbjct: 480  RKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVP 539

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+  
Sbjct: 540  VDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYN 596

Query: 1178 T-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G   E +    D+ +L +A   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L
Sbjct: 597  KVGGEQEDLDSLTDEEILALAGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVL 656

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            +DG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  
Sbjct: 657  FDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 709


>gi|317057552|ref|YP_004106019.1| DNA-directed RNA polymerase subunit beta [Ruminococcus albus 7]
 gi|315449821|gb|ADU23385.1| DNA-directed RNA polymerase, beta subunit [Ruminococcus albus 7]
          Length = 1301

 Score =  810 bits (2091), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/959 (44%), Positives = 587/959 (61%), Gaps = 55/959 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              RK F K  E++++P+LIEVQK SY  FL          +EGL+  F+ V  IT ++G
Sbjct: 11  KNTRKSFAKINEVLEMPNLIEVQKNSYQWFL----------DEGLKEVFRDVSSITDYNG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              L FV Y FD   K+ + +C  RD TYAVPL++T RL               +IKE  
Sbjct: 61  NLELTFVGYRFDENSKYTIAECKARDATYAVPLRVTARL---------NNLETGEIKESE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MG+ P MT  GTFVI G +R++VSQL RSPG+++  DK +    GK L+   +IP++G
Sbjct: 112 VFMGEFPKMTDSGTFVINGAERVIVSQLVRSPGVYYAFDKDKT---GKDLFKTTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
            W++ E DS D+++VRID+ RK+P+T+F+ ALG  + EEI +TF      +Q        
Sbjct: 169 AWLEYEMDSNDVVYVRIDKNRKIPITTFIRALGFGTNEEIEATFGVDERLTQTIMQKDQT 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +  + ++          +  GE   +ES +   + L    K   +   G          
Sbjct: 229 ANREEALLQV-----YQKLRPGEPPTVESSETHLNNLFFDAKRYDLSRFGRYKYNKKLGV 283

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD--IPILYVDSVNNNAY 357
              L G  +   I+   TGE+  E GD+ID     EI  + +++  + +   +       
Sbjct: 284 GSRLVGHKITRPIIAPMTGEVLAEEGDLIDYDKAMEIETAGVKEAYVTVEVKEYETAPTG 343

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKM 416
              T + DK      + +   +     D +   + E + F  L    +  D     + ++
Sbjct: 344 ETITRMVDKEVKIIGSGMVDLQAYVDFDPAECGINEKVSFAVLKEILESTDDPEEIKEEI 403

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             R +   P   +HI  +DI+A +   ++L +G G +DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 404 RNRADDLVP---KHIIIDDIVATVSYFLNLCDGVGQVDDIDHLGNRRIRSVGELLQNQFR 460

Query: 477 LGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +G  RMER I+ER++    D + + P  LIN +P+ +A+ EFF SS LSQ  +  N L+ 
Sbjct: 461 IGFTRMERVIRERMNIQSQDSEVITPTALINIRPITAAIREFFGSSPLSQFMDQNNPLAE 520

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+S L SFAR+N 
Sbjct: 521 LTHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLISYLASFARINK 580

Query: 595 YGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGFIE PYR+V      VT++VVY++A  E+N  +AQAN  L ED  F    V  R   +
Sbjct: 581 YGFIEAPYRRVDKETGVVTDEVVYMTADVEDNFMVAQANEPLTEDHKFARPKVNGRYRDQ 640

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +   KIDF+D SPK VVS+A + IPFLENDD+NR LMG NMQRQAVPLLK E+P VG
Sbjct: 641 ILEIENSKIDFMDVSPKMVVSVATACIPFLENDDANRALMGSNMQRQAVPLLKTESPIVG 700

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME      SG A+V+ +AG+VE VDA +IVIR  +G        +  Y L KF+RSN 
Sbjct: 701 TGMEYKACIDSGVAVVSTKAGVVESVDADKIVIREDDG-------NMHTYELTKFKRSNA 753

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+V+ G+ +  + II DGP+T  G+L+LG+N L+ FM W GYN+ED++L++E 
Sbjct: 754 GTCTNQRPIVEKGERIEAHQIIGDGPATSNGELSLGKNALIGFMTWEGYNYEDAVLLNEN 813

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +D +TSIHIE+ E  ARDTKLGPEEITRDIPNV ++ LK++DE GII +GAEV  GD
Sbjct: 814 LVKQDKYTSIHIEDLETEARDTKLGPEEITRDIPNVGDDALKDLDENGIIRIGAEVRSGD 873

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRD SL+VP G +GT+++VR+F R   D
Sbjct: 874 ILVGKVTPKGETELTAEERLLRAIFGEKAREVRDNSLKVPHGEAGTIIEVRVFTRENCD 932



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 175/508 (34%), Positives = 241/508 (47%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+  G  +     ++G         ++  +  L      +  +  D  L   +       
Sbjct: 762  IVEKGERIEAHQ-IIGDGPATSNGELSLGKNALIGFMTWEGYNYEDAVLLNENLVKQDKY 820

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + D+    R      E          +   +D  DE  I+      R  +IL G+ 
Sbjct: 821  TSIHIEDLETEARDTKLGPEEITRDIPNVGDDALKDL-DENGIIRIGAEVRSGDILVGKV 879

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +          +
Sbjct: 880  TPKGETELTAEERLLRAIFGEKAR-----------------EVRDNSLKVPHGEAGTIIE 922

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++ PGV  +V+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMPFL+D
Sbjct: 923  VRVFTRENCDELSPGVNMLVRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPFLED 982

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI LNPLGVPSRMN+GQ+ E HLG A   LG KI + + D     DI       ++
Sbjct: 983  GTPLDICLNPLGVPSRMNIGQVLEVHLGMAAKALGWKIMTPVFDGAHEADIRECFKMAQQ 1042

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                    E      D+ +   A                              + E G+ 
Sbjct: 1043 NYLEHKDDEFEIHPMDEVINPNALS----------------------------MSEDGKF 1074

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             +YDG TGE FD  VTVGY+Y LKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1075 TVYDGRTGEKFDNRVTVGYMYYLKLHHLVDDKIHARSVGPYSLVTQQPLGGKAQFGGQRF 1134

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAAY LQE+LT+KSDD+ GR + YE+IV G +    G PE+F VL+KE+
Sbjct: 1135 GEMEVWALEAYGAAYTLQEILTVKSDDLNGRVKTYEAIVKGQNVPNPGVPEAFKVLIKEL 1194

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            Q+L L I + N   +     ++  D + 
Sbjct: 1195 QSLCLDIKVLNINNEEIDLKQKFDDDDD 1222


>gi|259157295|gb|ACV96839.1| DNA-directed RNA polymerase beta subunit [Paenibacillus ehimensis]
          Length = 1060

 Score =  810 bits (2091), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/930 (45%), Positives = 576/930 (61%), Gaps = 79/930 (8%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            SY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y    PK+ VD+   R
Sbjct: 2   KSYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLGEPKYSVDESKER 51

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
           D+T+A PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF+I G +R++V
Sbjct: 52  DVTFAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIV 102

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSP ++F     +   +GK  Y   +IP++G W+++E D+KDII+VRIDR RK+PV
Sbjct: 103 SQLVRSPSVYFS---TKVDKNGKKTYTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPV 159

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T  L ALG  ++ EI+             D      +   L+           +  GE  
Sbjct: 160 TVLLRALGFGTDAEIIDLLGDNEYIRNTLDKDNTDSTDKALI------EIYERLRPGEPP 213

Query: 273 VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            +++ + L        K           +       + L    +AE +V+  TGEI  EA
Sbjct: 214 TLDNARSLLVARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDTNTGEIVAEA 273

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
           G ++D + L+ I            +  +  +       VT+   +     L    V  P 
Sbjct: 274 GQLLDRRLLDTI------------IPYLEESVGFTEYSVTNGVTESDKIPLQCVSVYSPL 321

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           +                         V +V  N ++       V++I   DII+ I   +
Sbjct: 322 E----------------------DGKVVKVIANGKI----DKTVKNITPADIISSINYFI 355

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
           +L +G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D++++ PQ LI
Sbjct: 356 NLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDVNTITPQQLI 415

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 416 NIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHHS 475

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL++SL++FARVN +GFIE PYR+V      VT ++ YL+A EE
Sbjct: 476 HYGRMCPTETPEGPNIGLINSLSTFARVNEFGFIEAPYRRVDPNTGVVTEEIAYLTADEE 535

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +N  +AQAN+ L EDG F  + V  R   + + +P++++D++D SPKQVVS+A +LIPFL
Sbjct: 536 DNYVVAQANAELTEDGKFANDSVIVRYKDDILTLPKDRVDYMDVSPKQVVSVATALIPFL 595

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           ENDDSNR LMG NMQRQAVPLL  +AP VGTGME   AK SG  IV+K  G+VE+V A  
Sbjct: 596 ENDDSNRALMGSNMQRQAVPLLIPKAPLVGTGMEHKSAKDSGVCIVSKVNGVVERVSANE 655

Query: 743 IVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           I +R  E       +G +  ++L KF RSNQ TC+NQRP+   G++VR  DI+ADGPST+
Sbjct: 656 IWVRRQEMVDGRLVNGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE 715

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALGRN++VAFM W GYN+ED++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEI
Sbjct: 716 QGELALGRNVVVAFMTWEGYNYEDAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEI 775

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TRDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T  E+LL AIFGEKA
Sbjct: 776 TRDIPNVGEDALKNLDERGIIRVGAEIAAGDILVGKVTPKGVTELTAGERLLHAIFGEKA 835

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +VRDTSLRVP G  G VVDV++  R   D
Sbjct: 836 REVRDTSLRVPHGTDGIVVDVKVSTRENGD 865



 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 155/458 (33%), Positives = 220/458 (48%), Gaps = 67/458 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     +    +       I++  I   G +V  GDIL    + + +  +     ++ A
Sbjct: 670  NGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE-QGELALGRNVVVA 728

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +  
Sbjct: 729  FMTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVG 783

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                +N+  R   I  G    +G     K T      ++   R     F  +  +V+   
Sbjct: 784  EDALKNLDER-GIIRVGAEIAAGDILVGKVTPKGVTELTAGERLLHAIFGEKAREVRDTS 842

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 843  LRVPHGTDGIVVDV------KVSTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHG 896

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+++RILP EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG    + 
Sbjct: 897  NKGVIARILPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMAAKYLGIHTATP 956

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D     D                                             VFD   
Sbjct: 957  VFDGAREYD---------------------------------------------VFD--- 968

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   +  A +  +G+++LYDG TGEPF+R VTVG +YM+KL HMV DK++ARSTG Y
Sbjct: 969  ------TMEEAGMQRNGKTLLYDGRTGEPFEREVTVGVMYMIKLAHMVDDKIHARSTGPY 1022

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            SLVTQQPLGGK+  GGQR G MEVW ++AYGAAY LQE
Sbjct: 1023 SLVTQQPLGGKAQFGGQRFGGMEVWALEAYGAAYTLQE 1060


>gi|259157299|gb|ACV96841.1| DNA-directed RNA polymerase beta subunit [Paenibacillus koreensis]
          Length = 1060

 Score =  808 bits (2088), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/930 (45%), Positives = 577/930 (62%), Gaps = 79/930 (8%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            SY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y    PK+ VD+   R
Sbjct: 2   KSYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLGEPKYSVDESKER 51

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
           D+T+A PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF+I G +R++V
Sbjct: 52  DVTFAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIV 102

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSP ++F     +   +GK  Y   +IP++G W+++E D+KDII+VRIDR RK+PV
Sbjct: 103 SQLVRSPSVYFS---TKVDKNGKKTYTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPV 159

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T  L ALG  ++ EI+             D      +   L+           +  GE  
Sbjct: 160 TVLLRALGFGTDAEIIDLLGDNEYIRNTLDKDNTDSTDKALI------EIYERLRPGEPP 213

Query: 273 VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            +++ + L        K           +       + L    +AE +V+  TGEI  EA
Sbjct: 214 TLDNARSLLVARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDTNTGEIVAEA 273

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
           G ++D + L+ I            +  +  +       VT+   +     L    V  P 
Sbjct: 274 GQLLDRRLLDTI------------IPYLEESVGFTEYSVTNGVTESDKIPLQCVSVYSPL 321

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           +                         V +V  N ++       V++I   DII+ I   +
Sbjct: 322 E----------------------DGKVVKVIANGKI----DKTVKNITPADIISSINYFI 355

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
           +L +G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D++++ PQ LI
Sbjct: 356 NLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDVNTITPQQLI 415

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG E+R+VH +
Sbjct: 416 NIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRNVHHS 475

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL++SL++FARVN +GFIE PYR+V      VT ++ YL+A E 
Sbjct: 476 HYGRMCPIETPEGPNIGLINSLSTFARVNEFGFIEAPYRRVDPNTGVVTEEIAYLTADEG 535

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +N  +AQAN+ L EDG F  + V  R   + + +P++++D++D SPKQVVS+A +LIPFL
Sbjct: 536 DNYVVAQANAELTEDGKFANDSVIVRYKDDILTLPKDRVDYMDVSPKQVVSVATALIPFL 595

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           ENDDSNR LMG NMQRQAVPLL  +AP VGTGME   AK SG  IV+K  G+VE+V A  
Sbjct: 596 ENDDSNRALMGSNMQRQAVPLLIPKAPLVGTGMEHKSAKDSGVCIVSKVNGVVERVSANE 655

Query: 743 IVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           I +R  E       +G +  ++L KF RSNQ TC+NQRP+   G++VR  DI+ADGPST+
Sbjct: 656 IWVRRQEMVDGRLVNGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE 715

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALGRN++VAFM W GYN+ED++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEI
Sbjct: 716 QGELALGRNVVVAFMTWEGYNYEDAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEI 775

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TRDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA
Sbjct: 776 TRDIPNVGEDALKNLDERGIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKA 835

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 836 REVRDTSLRVPHGTDGIVVDVKVFTRENGD 865



 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 156/458 (34%), Positives = 221/458 (48%), Gaps = 67/458 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     +    +       I++  I   G +V  GDIL    + + +  +     ++ A
Sbjct: 670  NGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE-QGELALGRNVVVA 728

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +  
Sbjct: 729  FMTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVG 783

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                +N+  R   I  G    +G     K T      ++   R     F  +  +V+   
Sbjct: 784  EDALKNLDER-GIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTS 842

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 843  LRVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHG 896

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+++RILP EDMPFL DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG    + 
Sbjct: 897  NKGVIARILPEEDMPFLPDGTPVEVVLNPLGVPSRMNIGQVLEAHLGMAAKYLGIHTATP 956

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D     D                                             VFD   
Sbjct: 957  VFDGAREYD---------------------------------------------VFD--- 968

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   +  A +  +G+++LYDG TGEPF+R VTVG +YM+KL HMV DK++ARSTG Y
Sbjct: 969  ------TMEEAGMQRNGKTLLYDGRTGEPFEREVTVGVMYMIKLAHMVDDKIHARSTGPY 1022

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1023 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1060


>gi|259157293|gb|ACV96838.1| DNA-directed RNA polymerase beta subunit [Paenibacillus sp. B27]
 gi|291586762|gb|ADE19120.1| DNA-directed RNA polymerase beta subunit [Paenibacillus sp. B27]
          Length = 1059

 Score =  808 bits (2086), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/930 (45%), Positives = 576/930 (61%), Gaps = 80/930 (8%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            SY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y    PK+ VD+   R
Sbjct: 2   KSYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLGEPKYSVDESKER 51

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
           D+T+A PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF+I G +R++V
Sbjct: 52  DVTFAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTETGTFIINGAERVIV 102

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSP ++F     +   +GK  Y   +IP++G W+++E D+KDII+VRIDR RK+PV
Sbjct: 103 SQLVRSPSVYFS---TKVDKNGKKTYTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPV 159

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T  L ALG  ++ EI+             D      +   L+           +  GE  
Sbjct: 160 TVLLRALGFGTDAEIIDLLGDNEYIRNTLDKDNTDSTDKALI------EIYERLRPGEPP 213

Query: 273 VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            +++ + L        K           +       + L    +AE +V+  TGEI  EA
Sbjct: 214 TLDNARSLLVARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDTNTGEIVAEA 273

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
           G ++D + L+ I       +                  VT+   +     L    V  P 
Sbjct: 274 GQLLDRRLLDTIIPYLEESVG-------------FTEYVTNGVTESDKIPLQCVSVYSPL 320

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           +                         V +V  N ++       V++I   DII+ I   +
Sbjct: 321 E----------------------DGKVVKVIANGKI----DKTVKNITPADIISSINYFI 354

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
           +L +G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D++++ PQ LI
Sbjct: 355 NLLHGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDVNTITPQQLI 414

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG E++DVH +
Sbjct: 415 NIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVQDVHHS 474

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL++SL++FARVN +GFIE PYR+V      VT ++ YL+A EE
Sbjct: 475 HYGRMCPIETPEGPNIGLINSLSTFARVNEFGFIEAPYRRVDPNTDMVTEEIAYLTADEE 534

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +N  +AQAN+ L EDG F  + V  R   + + +P++++D++D SPKQVVS+A +LIPFL
Sbjct: 535 DNYVVAQANAELTEDGKFANDSVIVRYKDDILTLPKDRVDYMDVSPKQVVSVATALIPFL 594

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           ENDDSNR LMG NMQRQAVPLL  ++P VGTGME   AK SG  IV+K  G+VE+V A  
Sbjct: 595 ENDDSNRALMGSNMQRQAVPLLIPKSPLVGTGMEHKSAKDSGVCIVSKVNGVVERVSANE 654

Query: 743 IVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           I +R  E       +G +  ++L KF RSNQ TC+NQRP+   G++VR  DI+ADGPST+
Sbjct: 655 IWVRRQEMVDGRLVNGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE 714

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALGRN++VAFM W GYN+ED++L+SE++V EDV+TSIHIEE+E  ARDTKLGPEEI
Sbjct: 715 QGELALGRNVVVAFMTWEGYNYEDAILLSEKLVKEDVYTSIHIEEYESEARDTKLGPEEI 774

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TRDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA
Sbjct: 775 TRDIPNVGEDALKNLDERGIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKA 834

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 835 REVRDTSLRVPHGTDGIVVDVKVFTRENGD 864



 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 154/458 (33%), Positives = 220/458 (48%), Gaps = 67/458 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     +    +       I++  I   G +V  GDIL    + + +  +     ++ A
Sbjct: 669  NGDIIKHKLHKFLRSNQGTCINQRPICHKGEQVRVGDILADGPSTE-QGELALGRNVVVA 727

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     +S  +V   ++    I++ E      +   E + RD  +  
Sbjct: 728  FMTWEGYNYEDAIL-----LSEKLVKEDVYTSIHIEEYESEARDTKLGPEEITRDIPNVG 782

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                +N+  R   I  G    +G     K T      ++   R     F  +  +V+   
Sbjct: 783  EDALKNLDER-GIIRVGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTS 841

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +    +     +      K+   + GD++PPGV ++V+ ++A KR I  GDKMAGRHG
Sbjct: 842  LRVPHGTDGIVVDV------KVFTRENGDELPPGVNQLVRAYIAQKRKISEGDKMAGRHG 895

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+++RILP EDMPF+ DGTPV++VLNPLGVPSRMN+GQ+ E HLG A   LG    + 
Sbjct: 896  NKGVIARILPEEDMPFMPDGTPVEVVLNPLGVPSRMNIGQVLEVHLGMAAKYLGLHTATP 955

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D     D                                             VFD   
Sbjct: 956  VFDGAREYD---------------------------------------------VFD--- 967

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   +  A +  +G+++LYDG TGEPF+R VTVG +YM+KL HMV DK++ARSTG Y
Sbjct: 968  ------TMEEAGMQRNGKTMLYDGRTGEPFEREVTVGVMYMIKLAHMVDDKIHARSTGPY 1021

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            SLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1022 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1059


>gi|310659515|ref|YP_003937236.1| DNA-directed RNA polymerase subunit beta [Clostridium sticklandii
           DSM 519]
 gi|308826293|emb|CBH22331.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
           (Transcriptase subunit beta) (RNA polymerase subunit
           beta) [Clostridium sticklandii]
          Length = 1223

 Score =  807 bits (2084), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/951 (45%), Positives = 588/951 (61%), Gaps = 59/951 (6%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F +  E+ ++P+LIE+Q  SY+ FL           EGL+  F+ VFPI  ++G   L
Sbjct: 1   MSFSQITEVAELPNLIEIQLESYEWFLR----------EGLREVFEEVFPIEDYTGNIKL 50

Query: 75  EFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           EF+ Y  +  PK+DV++   RD+TY+ PLK+ +RL V D D   G+K IK+   + +++G
Sbjct: 51  EFLDYFIEETPKYDVEESKERDVTYSAPLKVRVRLTVPDED---GSKIIKNESGEPVFLG 107

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D PLMT  GTF+I G +R++VSQL RSPG++F  +  +   SGK L +  +IP++G W++
Sbjct: 108 DFPLMTDKGTFIINGAERVIVSQLVRSPGVYFSQEMDK---SGKRLISSTVIPNRGAWLE 164

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
            E DS DI+ VRIDR RK PVT  L ALG  S+ EI                     +  
Sbjct: 165 YETDSNDIVSVRIDRNRKQPVTMLLRALGYGSDQEIRELLGDDERLEATILKDSSKSTDE 224

Query: 253 DLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCL 303
            L+   K       +  GE   +ES   L + +    K   +  +G           + +
Sbjct: 225 GLIEIYK------KLRPGEPPTLESATSLINSMFFDHKRYDLAKVGRYKFNKKLALSNRI 278

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
               ++ D+V+  TGE+ + +G  +  +  + +    I  + + Y +       I N  V
Sbjct: 279 YSRVLSRDVVDPSTGEVVLTSGIKLSVEQAKMLDDIGISHVYV-YGEEEKEVKVIGNCFV 337

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                D K  +      +   +   + V   + +    + +               +   
Sbjct: 338 -----DIKKHIAFSIDDLNIKEKVRYKVLREILDNFSTEEE----------IKAQLIERK 382

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI +EDIIA I    +L +  G IDDID+LGNRRVRSVGE+L+NQ+R+GL RME
Sbjct: 383 RELVPKHITEEDIIASISYQFNLFHSIGNIDDIDHLGNRRVRSVGELLQNQFRIGLSRME 442

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R IKER++  D   + P  L+N +PV +A+ EFF SSQLSQ  +  N LS +TH RRLSA
Sbjct: 443 RVIKERMTVQDAIDLTPNSLMNIRPVTAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 502

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+ +AR+N YGFIE+PYR
Sbjct: 503 LGPGGLSRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSVYARINEYGFIESPYR 562

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREK 660
           +V   + KVT  + YL+A EE+     QAN  L ED  F    V  R       LVP E 
Sbjct: 563 RVDNENNKVTEIIDYLTADEEDLYIRVQANEPLSEDSWFVNSKVASRTKMGTVELVPTEL 622

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GT +E   A
Sbjct: 623 VDYVDVSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLVRREAPIIGTAIEYRAA 682

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           K SGA IVA+  G+VE+V A  I+I+  +G  D        YRL+KF+RSNQ TC+NQ P
Sbjct: 683 KDSGAVIVARHDGVVEKVSAKEIIIKREDGQKD-------RYRLLKFKRSNQGTCINQTP 735

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD +++ D+IADGPSTDLG++ALGRN LVAFM W GYN+ED++LI+ER+V ED  +
Sbjct: 736 LVNKGDVMKKGDVIADGPSTDLGEIALGRNCLVAFMTWEGYNYEDAILINERLVKEDRLS 795

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           +IHIEE+E  ARDTKLGPEEITRDIPNV ++ +KN+DE GII +GAEV  GDILVGK+TP
Sbjct: 796 TIHIEEYEAEARDTKLGPEEITRDIPNVGDDAIKNLDERGIIRIGAEVESGDILVGKVTP 855

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSLRVP G SG +VDVRIF R   D
Sbjct: 856 KGETEITPEERLLRAIFGEKAREVRDTSLRVPHGESGIIVDVRIFTRENGD 906



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 166/443 (37%), Positives = 222/443 (50%), Gaps = 70/443 (15%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K +R  ++  E+ E  ARD       + R+I                I  G    SG   
Sbjct: 790  KEDRLSTIHIEEYEAEARDTKLGPEEITRDIPNVGDDAIKNLDERGIIRIGAEVESGDIL 849

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      I+   R     F  +  +V+     +          +      +I   +
Sbjct: 850  VGKVTPKGETEITPEERLLRAIFGEKAREVRDTSLRVPHGESGIIVDV------RIFTRE 903

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++ PGV  +V+ ++A KR I  GDKMAGRHGNKG++SRILP EDMPF+ DGTPV+IV
Sbjct: 904  NGDELSPGVNELVRCYIAKKRKINVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVEIV 963

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E H+G A   LG  + + + D     DI               H
Sbjct: 964  LNPLGVPSRMNIGQVLEIHMGLAAKALGWHVATPVFDGAVEEDIFQALDKAGYPKSGKIH 1023

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
             +                                                G++       
Sbjct: 1024 LQ-----------------------------------------------DGRT------- 1029

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ FD PVTVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 1030 GDYFDNPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1089

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAA+ LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+L L +
Sbjct: 1090 LEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGIPESFKVLIKELQSLCLDV 1149

Query: 1362 DLENSRTKNSAKMEEIPDFNKCE 1384
             +     +     E I +    +
Sbjct: 1150 KVLTETDEEIEVRESIEEAALVD 1172


>gi|282849085|ref|ZP_06258473.1| DNA-directed RNA polymerase, beta subunit [Veillonella parvula ATCC
           17745]
 gi|282581203|gb|EFB86598.1| DNA-directed RNA polymerase, beta subunit [Veillonella parvula ATCC
           17745]
          Length = 1386

 Score =  806 bits (2083), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/969 (43%), Positives = 580/969 (59%), Gaps = 109/969 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E+I +P L+++Q+ SY+ FL            GLQ  F  + PI   SG
Sbjct: 9   KRTRYTYAKINEVIKMPHLLDIQRKSYEWFL----------ESGLQNIFNDISPIKDNSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+D+++C  RD TYA PL++ +RL+  D +         DIKEQ +
Sbjct: 59  NLVLSFEGFSLGEPKYDINECKNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEV 111

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G 
Sbjct: 112 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGA 168

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWC 246
           W+++E D+ +++ VRIDR RK+P T  + ALG D+ E IL  F+            D   
Sbjct: 169 WIELETDASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERI 228

Query: 247 FPLSAADLMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                 D        +      +  GE   +ES + L   L    +   +  +G      
Sbjct: 229 VRTLEKDTTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNK 288

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  + G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++       
Sbjct: 289 KLGWRQRMLGQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAE 342

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            YI N    +      +  L                              YD  TV R  
Sbjct: 343 FYIVNNDGVESKVICNNCNL-----------------------------PYDHRTVTR-- 371

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                             ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+
Sbjct: 372 ------------------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQF 413

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +
Sbjct: 414 RIGLTRMERVVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAEL 473

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +
Sbjct: 474 THKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEF 533

Query: 596 GFIETPYRKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           GFIE PYRKV                 V++ VVY++A EEE   IAQANS LD +G FT 
Sbjct: 534 GFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTT 593

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E V CR   + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVP
Sbjct: 594 EHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVP 653

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL+A+AP VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y
Sbjct: 654 LLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTY 707

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L KF RSNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN
Sbjct: 708 HLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYN 767

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++L+SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GII
Sbjct: 768 YEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGII 827

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           C+GAEV+PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV
Sbjct: 828 CIGAEVHPGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDV 887

Query: 943 RIFNRHGID 951
           ++F R   D
Sbjct: 888 KVFTRENGD 896



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 104/220 (47%), Positives = 143/220 (65%), Gaps = 5/220 (2%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        ++         D     + +   +G+ ++TPVFDGA
Sbjct: 1101 EELEAISKVKNTLNNIHSAEEKRVELRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1160

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1161 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1220

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV 
Sbjct: 1221 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKAYEKIVK 1280

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            G +  E G PESF VL+KE+Q++GL + + N   +     
Sbjct: 1281 GENIPEPGVPESFKVLLKELQSIGLDVKILNEDQEEVVMK 1320



 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 103/360 (28%), Positives = 155/360 (43%), Gaps = 19/360 (5%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L A  P  G   E   +      +++ +    +     E+       G
Sbjct: 643  MGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRDSDG 702

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +       +        ++  I+  G  V  G +L       G   +     +L A  
Sbjct: 703  RVDTYHLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELALGYNVLVAFM 761

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-ELLARDKDDEQ 975
              +  +  D  L           D+    +    + + R   +  E+I   L    DD  
Sbjct: 762  PWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTL 818

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD +       I  G     G     K+T      +   P  +  +    D++ +   
Sbjct: 819  KNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFGDKEREVRD 871

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 872  TSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEGDKMAGRHG 927

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  GLG KIK+ 
Sbjct: 928  NKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQGLGMKIKAT 987


>gi|304439652|ref|ZP_07399555.1| DNA-directed RNA polymerase subunit beta [Peptoniphilus duerdenii
           ATCC BAA-1640]
 gi|304371892|gb|EFM25495.1| DNA-directed RNA polymerase subunit beta [Peptoniphilus duerdenii
           ATCC BAA-1640]
          Length = 1260

 Score =  806 bits (2083), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/962 (43%), Positives = 590/962 (61%), Gaps = 56/962 (5%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G  R R  F +  E++ +P+LIEVQ +SY   L          +EGL+  F+ V 
Sbjct: 3   HPVKYG-KRERMSFSRIEEVLSLPNLIEVQTSSYKWLL----------DEGLKEVFEDVS 51

Query: 64  PITAFSGAAMLEFVSYEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           PI  ++G  +LEFV Y+      K+D+D+   RD  YA PLK+ +RLI            
Sbjct: 52  PIEDYAGNLILEFVDYKLHEEQAKYDIDESKARDTNYAAPLKVMVRLI---------NTK 102

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KEQ ++MGDLPLMT  GTF+I G +R+VVSQL RSPG ++  +  +    G+ L +
Sbjct: 103 TGEVKEQEVFMGDLPLMTPTGTFIINGAERVVVSQLVRSPGAYYKQETDKV---GRKLIS 159

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--- 238
             +IP++G W++ E DS+ +I+VRIDR RK+P+T  L A+G++S E ++ F  +      
Sbjct: 160 ATLIPNRGAWLEYETDSQSVINVRIDRTRKIPITVLLRAIGLESNEEITEFLGESELLLR 219

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFL 296
           +   D       A   +           +D+ + + E+         L    + K  K L
Sbjct: 220 TFEKDLTTNKEEALIEIYKKLRPGEPPTLDSAQSLFENMFFDYKRYDLAHVGRYKFNKKL 279

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL----YVDSV 352
            I +  + G +VAEDI++  TGEI  +AGD +  +    I ++ +  + +L    +    
Sbjct: 280 SI-ASRIEGQFVAEDIIDTLTGEILAKAGDKLTREDAFRIENAGVNTVTVLIKAIHAGDE 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           +    +     +         L    + +   +     V E ++N    D + +    + 
Sbjct: 339 DRKVIVHGNNFSIPKNYD---LPFDLKDLGFKEKIYLPVFEEIYNEFSNDEEAFKAELIK 395

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R               +HI  +D++A +     L  G GT DDID+LGNRR+RSVGE+L+
Sbjct: 396 R---------KFDLSPKHILVDDMLASVSYEFGLSQGVGTTDDIDHLGNRRIRSVGELLQ 446

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+G+ RMER IKER++  D D+  PQ LIN +PV +A+ EFF SSQLSQ  +  N L
Sbjct: 447 NQFRIGISRMERVIKERMTVQDADTTTPQSLINIRPVTAAIKEFFGSSQLSQFMDQNNPL 506

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SLT++AR+
Sbjct: 507 SELTHKRRLSALGPGGLSRDRAGFEVRDVHNSHYGRMCPIETPEGPNIGLITSLTTYARI 566

Query: 593 NAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIE PYRKV   +G VT+++ YL+A  E  + IAQ+N  LDEDG F    +  R  
Sbjct: 567 NEYGFIEAPYRKVKLGEGIVTDEIEYLTADVEYEQIIAQSNEILDEDGKFVNSRIVARGP 626

Query: 651 GEEI-LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              +     +K+ ++D SPKQ+V++  ++IPFLENDD+NR LMG NMQRQAVPLLK EAP
Sbjct: 627 EGVVDFFDSDKVTYMDVSPKQIVAVGTAMIPFLENDDANRALMGANMQRQAVPLLKTEAP 686

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            +GTG+E   AK SG  IVA   G++E+VD+  I ++  E         V  ++L KF  
Sbjct: 687 IIGTGIEYRAAKDSGVVIVATDDGVIEKVDSKSITLKRDE------DGKVINFKLHKFVG 740

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            NQ T +NQRP+VK G +V+  ++IADGPSTD+G++ALG+N+L+AFM W GYN+ED+ML+
Sbjct: 741 GNQGTTINQRPIVKEGQKVKAGEVIADGPSTDMGEMALGKNILIAFMNWEGYNYEDAMLV 800

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++ +V  DV TS+HIEE+E  ARDTKLGPEEITRDIPNV ++ LK++DE GII VGAEV 
Sbjct: 801 NKDLVINDVLTSLHIEEYESEARDTKLGPEEITRDIPNVGDDMLKDLDERGIIRVGAEVK 860

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGDILVGK+TPKGE   +PEE+LLRAIFGEK+ +VRDTSLR+P G  G VVDV+ F R  
Sbjct: 861 PGDILVGKVTPKGEGDQSPEERLLRAIFGEKSREVRDTSLRLPHGEQGIVVDVKTFRRST 920

Query: 950 ID 951
            D
Sbjct: 921 GD 922



 Score =  471 bits (1213), Expect = e-130,   Method: Composition-based stats.
 Identities = 172/543 (31%), Positives = 244/543 (44%), Gaps = 79/543 (14%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  +  + G     +    V       I++  I+  G +V  G+++    +      M 
Sbjct: 719  SITLKRDEDGKVINFKLHKFVGGNQGTTINQRPIVKEGQKVKAGEVIADGPST-DMGEMA 777

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------ 961
              + +L A    +  +  D  L     V   V+       +  +  +  +  E       
Sbjct: 778  LGKNILIAFMNWEGYNYEDAMLVNKDLVINDVLTSLHIEEYESEARDTKLGPEEITRDIP 837

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
               + + +D  DE+ I+      +  +IL G+    G         L   +  E  R   
Sbjct: 838  NVGDDMLKDL-DERGIIRVGAEVKPGDILVGKVTPKGEGDQSPEERLLRAIFGEKSR--- 893

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                          E                   K  +   GD++ PGV  +V+VF+A K
Sbjct: 894  --------------EVRDTSLRLPHGEQGIVVDVKTFRRSTGDELQPGVQEMVRVFIATK 939

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKM GRHGNKG++SR++P EDMP++ DGTP+ IVLNPLGVPSRMN+GQ+ E HL
Sbjct: 940  RKIQVGDKMCGRHGNKGVISRVMPAEDMPYMPDGTPIQIVLNPLGVPSRMNLGQVLEVHL 999

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG K+ + + D     DI                                    
Sbjct: 1000 GLAARKLGWKVATPVFDGANEQDIIDSLEKAGLPADGKIQL------------------- 1040

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G        TGE FD PVTVG +YMLKL+H
Sbjct: 1041 ----------------------------RDG-------RTGEEFDHPVTVGIMYMLKLHH 1065

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDD
Sbjct: 1066 LVDEKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDD 1125

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +VGR + YE+IV G +  + G PESF VL+KE++AL L I + +          +  D  
Sbjct: 1126 IVGRVKTYEAIVKGENIQKPGVPESFKVLIKELEALALEIQVLDEDKNLVDLQVDEEDLA 1185

Query: 1382 KCE 1384
            + +
Sbjct: 1186 RID 1188


>gi|329770373|ref|ZP_08261755.1| DNA-directed RNA polymerase subunit beta [Gemella sanguinis M325]
 gi|328836496|gb|EGF86156.1| DNA-directed RNA polymerase subunit beta [Gemella sanguinis M325]
          Length = 1269

 Score =  806 bits (2082), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/974 (43%), Positives = 584/974 (59%), Gaps = 79/974 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ + +  E+ID+PDLIE+Q  SY+ FL            GL+  F+ V
Sbjct: 1   MQKVKFGKHRERRSYARISEVIDLPDLIEIQTLSYEKFL----------ETGLKDVFRDV 50

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI   +    LEF+ Y+   PK++VD+   RD TY+ PL++ +RLI  + D        
Sbjct: 51  SPIEGNNDKLSLEFIDYKLGTPKYNVDESKERDATYSAPLRVRVRLINKERD-------- 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IKEQ ++MG+LPLMT+ GTF+I G +R++VSQL RSP ++F  D      +    Y  
Sbjct: 103 -EIKEQEVFMGELPLMTETGTFIINGAERVIVSQLVRSPSVYFTEDDKLKVKNIPNAYKT 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W++ E D K +++ RIDR RK+P+T+ + ALG +S+E I+  F         
Sbjct: 162 TVIPNRGAWLEFEKDIKGLVYARIDRTRKIPLTTLIRALGFESDESIVKLFGEDTELLNT 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +         +L  G  +      +  GE   +E+ K    G     +   +  +G   
Sbjct: 222 LEKD------ENLDTGTALKVIYDKLRPGEPANVETAKATLYGRFFDPRRYDLAKVGRYK 275

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    + E IV+ ETGEI +E G  +  + ++EI+        ++  +  
Sbjct: 276 LNNKLHVGERLENQILVEPIVDTETGEILVEKGTKLTREIIDEIYEELGTSANVVEFEMN 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +                    L +++V+    V      + +            L  +G
Sbjct: 336 ESLD------------GSDSLKLQLFKVVNQVKVGNDFNVDELLEDQV-------LHIIG 376

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-----------GTIDDIDNLGN 461
               N         D+  +   DI+A I   + L   +           G +DDID+LGN
Sbjct: 377 NGAPNK--------DILTLTIADIVASINYYLLLIRNRRNSDGFEYELIGRVDDIDHLGN 428

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R +GE+L+NQ R+G+ RMER ++ER+S  D + + PQ LIN +PV + + EFF SSQ
Sbjct: 429 RRLRCIGELLQNQIRVGISRMERVVRERMSIQDTNEITPQQLINVRPVTAIIKEFFGSSQ 488

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIG
Sbjct: 489 LSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIG 548

Query: 582 LVSSLTSFARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           L++SL+SFAR+N +GFI TPYRKV         VT +V YL+A +E+   +AQ+NS++DE
Sbjct: 549 LINSLSSFARINEFGFIMTPYRKVEVDAEGRPYVTENVQYLTADQEDKYVVAQSNSNVDE 608

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            G F ++ V CR  G+  + PRE ++++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 609 KGYFLDDEVVCRFRGDNTVKPREMMNYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
           QRQAVPL+  EAPFVGTGME + A+ SGAA++AK  GIVE VD  +I +R +E       
Sbjct: 669 QRQAVPLMVTEAPFVGTGMEHLAARDSGAAVIAKYPGIVEYVDGAKIKVRRIETLDGKEI 728

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +D Y + KF RSN +T  NQ+P+VKVGD V + DI+ADGPS D G+LALG+N++VAF
Sbjct: 729 EGDLDTYVIHKFVRSNHSTSYNQKPIVKVGDRVEKKDILADGPSMDKGELALGKNLVVAF 788

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + W GYN+ED++++SER+V +DV+TSIH+EE+E  ARDTKLGPEEITR+IPNV E  L+N
Sbjct: 789 VNWDGYNYEDAVIMSERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRN 848

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRVP G 
Sbjct: 849 LDSRGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGA 908

Query: 936 SGTVVDVRIFNRHG 949
            G V DV+IF R  
Sbjct: 909 DGVVADVKIFKRED 922



 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 166/497 (33%), Positives = 235/497 (47%), Gaps = 75/497 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V   DIL    +   +  +   + L+ A       +  D  +           
Sbjct: 754  IVKVGDRVEKKDILADGPS-MDKGELALGKNLVVAFVNWDGYNYEDAVIMS--------- 803

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                     + K++   S+  E+ E  ARD       + R I +     L   ++    +
Sbjct: 804  -------ERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRNLDSRGIIR 856

Query: 1001 G---FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-K 1056
                 K   +L   +  +    Q  +  +         + ++          +    + K
Sbjct: 857  IGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGADGVVADVK 916

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I K + G ++  GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DGT
Sbjct: 917  IFKREDGAELANGVNELVRVFIIQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDGT 976

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D  ++ D+    +      
Sbjct: 977  PVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGASDDDVWSTVAEAGMAK 1036

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                           T ++DG                       
Sbjct: 1037 DAK----------------------------TVLYDG----------------------- 1045

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
                TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1046 ---RTGEPFDSRVSVGVMYMIKLSHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1102

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDD  GR + YE+IV G +    G PESF VL+KE+QA
Sbjct: 1103 MEVWALEAYGAAYTLQEILTYKSDDTNGRVKTYEAIVKGENIPRPGVPESFRVLMKELQA 1162

Query: 1357 LGLSIDLENSRTKNSAK 1373
            LG+   + +        
Sbjct: 1163 LGMDFRVMDKDDNEVDM 1179


>gi|227432704|ref|ZP_03914676.1| DNA-directed RNA polymerase, beta subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227351542|gb|EEJ41796.1| DNA-directed RNA polymerase, beta subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 1205

 Score =  806 bits (2081), Expect = 0.0,   Method: Composition-based stats.
 Identities = 413/964 (42%), Positives = 580/964 (60%), Gaps = 84/964 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G    R+ +    E++D+P+LIE+Q ASY  FL          N+G++  F  +
Sbjct: 6   GHLVKYGKHCTRRSYASIKEVLDVPNLIEIQTASYQWFL----------NDGIKEMFGDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  F G   LE+V Y+   PK+++D+    D  Y+ PL +TLRL              
Sbjct: 56  MPIDDFQGTLSLEYVDYQLMEPKYNIDEAREHDANYSAPLHVTLRLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPGI+++    +   +G+  +  
Sbjct: 107 GEIKSQDVFFGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQTTDK---NGRPHFGT 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKIVY 238
            +IP++G W++ E D+K I +VRIDR RK+ +T  + ALG  S+ +I+  F   Y  +  
Sbjct: 164 TVIPNRGAWLEYETDAKGIANVRIDRTRKLLMTELVRALGFGSDSDIIDIFSDQYDALNM 223

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG 297
           +   D        +D  V   +      +  GE    +S + L        K   +  +G
Sbjct: 224 TLEKDVHK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLASVG 280

Query: 298 IT--------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                        L    +AE + + ++GEI  E G ++D++ + ++        P L  
Sbjct: 281 RYKIDKKLSLKTRLLNQTLAETLADPDSGEIIAEKGTLVDKEVISKLT-------PYLDR 333

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +      Y  +           DA+L+        +  T             ++ +  L 
Sbjct: 334 EDFKTTTYTPSG----------DAVLE--------EPVTLQK----IKIESPENPEKTLL 371

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            +G             +D R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSVGE
Sbjct: 372 LIGN--------GHIDEDDRTVRPADILAGMNYFLNLQEGVGHVDDIDHLGNRRIRSVGE 423

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +  
Sbjct: 424 LLQNQFRIGLSRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMDQT 483

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  + H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL ++
Sbjct: 484 NPLGEMNHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLATY 543

Query: 590 ARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            R+N YGF+ETPYR+V     KVT+ + YL+A EE+N  +AQANS L+EDGSF    V  
Sbjct: 544 GRINKYGFVETPYRRVDWTTHKVTDKIDYLTADEEDNYIVAQANSPLNEDGSFVHNTVMA 603

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL   
Sbjct: 604 RFGEENIETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLDPH 663

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A  SG A++A+ +G VE VD  +I +R  +G LD        Y LMKF
Sbjct: 664 SPLVGTGIEYKAAHDSGVAMIARASGEVEYVDGRQIRVRREDGQLD-------TYELMKF 716

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN     NQ+P+V VG+ +  ++++ADGPS + G+LALG+N L+AFM W GYNFED++
Sbjct: 717 RRSNGGKNYNQKPIVHVGEHIEADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAI 776

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +++ER+V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VGAE
Sbjct: 777 VLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVGAE 836

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +VRI+  
Sbjct: 837 VHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIYTP 896

Query: 948 HGID 951
              D
Sbjct: 897 ENGD 900



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 174/526 (33%), Positives = 249/526 (47%), Gaps = 67/526 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +      G KN ++  I+ VG  +   ++L    +   +  +   +  
Sbjct: 702  RREDGQLDTYELMKFRRSNGGKNYNQKPIVHVGEHIEADEVLADGPS-MEQGELALGQNP 760

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     V   V        +  +  +  +  E    E +    +
Sbjct: 761  LIAFMTWQGYNFEDAIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGE 819

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+   LD +   R+     G     G     K T      +S   R     F  +  +V+
Sbjct: 820  DQLKDLDADGIIRV-----GAEVHDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVR 874

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      +I   + GD++ PGV  +V+V++A KR IQ GDKMAG
Sbjct: 875  DTSLRVPHGGGGVVQNV------RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAG 928

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  +
Sbjct: 929  RHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHV 988

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S + D  ++ +I                         +  LR A   + G  V   V+D
Sbjct: 989  ASPVFDGASDDEI-------------------------EMALREAGLPQDGKSV---VYD 1020

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGE FD+ V VG ++ +KL HMV DK++ARS 
Sbjct: 1021 G--------------------------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSI 1054

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +VYESI
Sbjct: 1055 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVAGRVKVYESI 1114

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            + G      G PESF VLVKE+QALGL + + +         +   
Sbjct: 1115 IKGEPIPRPGVPESFRVLVKELQALGLDMQVLDGAGGEVELRQMDE 1160


>gi|282882624|ref|ZP_06291241.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus lacrimalis
           315-B]
 gi|300814500|ref|ZP_07094760.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|281297535|gb|EFA90014.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus lacrimalis
           315-B]
 gi|300511384|gb|EFK38624.1| DNA-directed RNA polymerase, beta subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 1265

 Score =  806 bits (2081), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/956 (43%), Positives = 591/956 (61%), Gaps = 47/956 (4%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G  R R  F +  E++ +P+L++VQ +S+D F+           EGL+  F  V 
Sbjct: 3   HPVKYG-KRERMSFSRVEEVMSLPNLLDVQTSSFDWFI----------KEGLKEVFDDVS 51

Query: 64  PITAFSGAAMLEFVSYEF-DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           PI  +SG  +LEFV Y   D  K+D+D+   RD  Y  PLK+ +RLI             
Sbjct: 52  PIEDYSGKLILEFVDYYISDDIKYDIDESKQRDTNYCAPLKVKVRLI---------NTET 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++MGDLPLMT  GTFVI G +R+VVSQL RSPG +F  ++ +    GK LY+ 
Sbjct: 103 GEVKEQEVFMGDLPLMTPTGTFVINGAERVVVSQLVRSPGAYFKEERDKT---GKKLYSS 159

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ- 240
            +IP++G W++ E D+  +I+VRIDR RK+P+T    A+G++S  EI          ++ 
Sbjct: 160 TLIPNRGAWLEFETDAAGVINVRIDRTRKIPITILARAIGVESNREITDILGESEALTKT 219

Query: 241 -RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +           +D+ + + E+         L +  + K  K LG
Sbjct: 220 FEKDTTSNKTEALLEIYKKLRPGEPPTLDSAKSLFENMFFDDRRYDLARVGRYKFNKKLG 279

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           I +  +    +AED VN  TGEI  E G+ +D     EI ++ I  I +  ++  + +  
Sbjct: 280 IEA-RIENNILAEDAVNPLTGEIIAEKGETLDRAKAFEIENAGINRILLKVLNPFDESES 338

Query: 358 IRNTLVTDKNKDRKDA-LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
               ++ +         L      +   +   F + +S++     D +        R   
Sbjct: 339 REVIVIGNNFCIPSSFGLNFTLEELGFREKIYFPLFQSIYEEFGSDEEALKEELKKRHN- 397

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                       +HI  +DI+A I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 398 --------ELSPKHIVVDDIVAAINYEFNLMDGVGYTDDIDHLGNRRIRSVGELLQNQFR 449

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +G+ RMER I+ER++  D+++  PQ LIN +PV +A+ EFF SSQLSQ  +  N LS +T
Sbjct: 450 IGISRMERVIRERMTVQDVEATTPQSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLSELT 509

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SLT++AR+N YG
Sbjct: 510 HKRRLSALGPGGLSRDRAGFEVRDVHNSHYGRMCPIETPEGPNIGLITSLTTYARINEYG 569

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEIL 655
           FIETPYRKV DG VT+ + YL+A  E  + IAQ+   LDEDG F E+ + CR   G   +
Sbjct: 570 FIETPYRKVVDGVVTDKIEYLTADVEYEQIIAQSYEKLDEDGRFLEKRIACRGHEGIVDI 629

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              + + ++D SP+Q+V++  S+IPFLENDD+NR LMG NMQRQAVPLL  +AP VGTG+
Sbjct: 630 FDVKDVTYMDVSPQQIVAVGTSMIPFLENDDANRALMGANMQRQAVPLLSTQAPIVGTGI 689

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   AK SG  IV+   G++E+VDA  I +R  +  +      +D Y+L KF   NQ T 
Sbjct: 690 EYRAAKDSGVVIVSTDDGVIEKVDATHIELRRDKDKV------LDTYKLHKFVGGNQGTT 743

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +NQRP+V  G +V++ +IIADGPSTD+G++ALG+N+L+AFM W GYN+ED++L+++ +V 
Sbjct: 744 INQRPIVNEGQKVKKGEIIADGPSTDMGEMALGKNILIAFMNWEGYNYEDAVLVNQELVI 803

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            D  TS+HIEE+E  ARDTKLGPEEITRDIPNV ++ LK++DE G++ +GAEV PGDILV
Sbjct: 804 NDTLTSLHIEEYESEARDTKLGPEEITRDIPNVGDDMLKDLDELGVVRIGAEVKPGDILV 863

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ ++ EE+LLR+IFGEKA +VRDTSLR+P G  G VVDV+ F R   D
Sbjct: 864 GKVTPKGETELSAEERLLRSIFGEKAREVRDTSLRLPHGEHGIVVDVKTFKRSEGD 919



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 177/536 (33%), Positives = 247/536 (46%), Gaps = 67/536 (12%)

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +  R  K    +  +    V       I++  I+  G +V  G+I+    +      M  
Sbjct: 717  IELRRDKDKVLDTYKLHKFVGGNQGTTINQRPIVNEGQKVKKGEIIADGPST-DMGEMAL 775

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             + +L A    +  +  D  L V   +        +       +   +     E    + 
Sbjct: 776  GKNILIAFMNWEGYNYEDAVL-VNQELVINDTLTSLHIEEYESEARDTKLGPEEITRDIP 834

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
               DD    LD     R+   +   + + G    K  T LS++      RS + + A + 
Sbjct: 835  NVGDDMLKDLDELGVVRIGAEVKPGDILVGKVTPKGETELSAE--ERLLRSIFGEKAREV 892

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                  +   +                K  K   GD++ PGV  +V+VFVA KR IQ GD
Sbjct: 893  RDTSLRLPHGEHGI---------VVDVKTFKRSEGDELQPGVNEMVRVFVATKRKIQVGD 943

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KM GRHGNKG++SR+LP EDMP++ DGTP+ IVLNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 944  KMCGRHGNKGVISRVLPKEDMPYMPDGTPIQIVLNPLGVPSRMNLGQVLEVHLGLAAKKL 1003

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  + + + D     DI                                           
Sbjct: 1004 GWHVATPVFDGANESDIFESLEKAGYPHDGKIQL-------------------------- 1037

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                   G        TGE FD PVTVGY+YMLKL+H+V +K++
Sbjct: 1038 ---------------------RDG-------RTGEEFDHPVTVGYMYMLKLHHLVDEKIH 1069

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQEMLT+KSDD+VGR + 
Sbjct: 1070 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEMLTVKSDDIVGRVKT 1129

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            YE+IV G +  +   PESF VL+KE+Q+L L I++ +          E  D ++ +
Sbjct: 1130 YEAIVKGENIPQPSIPESFKVLIKELQSLALEIEVLDDDGNPVDLEAEEDDLSRID 1185


>gi|329767188|ref|ZP_08258715.1| DNA-directed RNA polymerase subunit beta [Gemella haemolysans M341]
 gi|328836855|gb|EGF86502.1| DNA-directed RNA polymerase subunit beta [Gemella haemolysans M341]
          Length = 1273

 Score =  805 bits (2080), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/974 (43%), Positives = 584/974 (59%), Gaps = 79/974 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ + +  E+ID+PDLIE+Q  SYD FL            GL+  FK V
Sbjct: 1   MQKVKFGKHRQRRSYARISEVIDLPDLIEIQTLSYDKFL----------ETGLKDVFKDV 50

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI   +    LEF+ Y+   PK+DVD+   RD TY+ PL++ +RLI  + D        
Sbjct: 51  SPIEGNNDKLSLEFIDYKLGTPKYDVDESKERDATYSAPLRVRVRLINKERD-------- 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IKEQ ++MG+LPLMT+ GTF+I G +R++VSQL RSP ++F  D      +    Y  
Sbjct: 103 -EIKEQEVFMGELPLMTETGTFIINGAERVIVSQLVRSPSVYFTEDDKLKVKNIPNAYKT 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W++ E D K +++ RIDR RK+P+T+ + ALG +S+E I+  F         
Sbjct: 162 TVIPNRGAWLEFEKDIKGLVYARIDRTRKIPLTTLIRALGFESDESIIKLFGEDAELLNT 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +         +L  G  +      +  GE   +E+ K    G     +   +  +G   
Sbjct: 222 LEKD------ENLDTGTALKVIYDKLRPGEPANVETAKATLHGRFFDPRRYDLAKVGRYK 275

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    + E IV+ ETGEI +E G  +  + ++ I+        ++  D  
Sbjct: 276 LNNKLHVGERLENQILVEPIVDTETGEILVEKGTKLTREIIDGIYEELGTTANVVEFDMN 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +                    L +++V+    V      + +       +D   L  +G
Sbjct: 336 ESLD------------GSDSLKLQLFKVVNQVKVGNDFDIDEL-------TDDQVLHVIG 376

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-----------GTIDDIDNLGN 461
               N         DV  +   DI+A I   + L   +           G +DDID+LGN
Sbjct: 377 NGAPNK--------DVLTLTISDIVASINYYLLLIKNRRNNDGFEFELIGRVDDIDHLGN 428

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R +GE+L+NQ R+G+ RMER ++ER+S  D + + PQ LIN +PV + + EFF SSQ
Sbjct: 429 RRLRCIGELLQNQIRVGISRMERVVRERMSIQDTNEITPQQLINVRPVTAIIKEFFGSSQ 488

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  + VN LS +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIG
Sbjct: 489 LSQFMDQVNPLSELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIG 548

Query: 582 LVSSLTSFARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           L++SL+SFAR+N +GFI TPYRKV         VT +V YL+A +E+   +AQ+ +++DE
Sbjct: 549 LINSLSSFARINEFGFIMTPYRKVEFDAKGRPYVTENVQYLTADQEDKYVVAQSTANVDE 608

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            G F ++ V CR  G+  + PRE ++F+D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 609 KGYFVDDEVVCRFRGDNTVKPREMMNFMDVSPKQVVSAATACIPFLENDDSNRALMGANM 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
           QRQAVPL+  EAPFVGTGME + A+ SGAA++AK  GIVE VD  +I +R +E       
Sbjct: 669 QRQAVPLMITEAPFVGTGMEHLAARDSGAAVIAKYPGIVEYVDGAKIKVRRIETLEGKEI 728

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +D Y + KF RSN +T  NQ+P+VKVGD V   DI+ADGPS D G+LALG+N++VAF
Sbjct: 729 KGDLDTYVIHKFVRSNHSTAYNQKPIVKVGDRVEPKDILADGPSMDKGELALGKNLVVAF 788

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + W GYN+ED++++SER+V +DV+TSIH+EE+E  ARDTKLGPEEITR+IPNV E  L+N
Sbjct: 789 VNWDGYNYEDAVIMSERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRN 848

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRVP G 
Sbjct: 849 LDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGA 908

Query: 936 SGTVVDVRIFNRHG 949
            G V DV+IF R  
Sbjct: 909 DGVVADVKIFKRED 922



 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 169/497 (34%), Positives = 236/497 (47%), Gaps = 75/497 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V P DIL    +   +  +   + L+ A       +  D  +           
Sbjct: 754  IVKVGDRVEPKDILADGPS-MDKGELALGKNLVVAFVNWDGYNYEDAVIMS--------- 803

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                     + K++   S+  E+ E  ARD       + R I +     L   +A    +
Sbjct: 804  -------ERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRNLDARGIIR 856

Query: 1001 G---FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-K 1056
                 K   +L   +  +    Q  +  +         + ++          +    + K
Sbjct: 857  IGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGADGVVADVK 916

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DGT
Sbjct: 917  IFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDGT 976

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +      
Sbjct: 977  PVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDVWSTVAEAGMAK 1036

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                           T ++DG                       
Sbjct: 1037 DAK----------------------------TVLYDG----------------------- 1045

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
                TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 1046 ---RTGEPFDSRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1102

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDD  GR + YE+IV G +    G PESF VL+KE+QA
Sbjct: 1103 MEVWALEAYGAAYTLQEILTYKSDDTNGRVKTYEAIVKGENIPRPGVPESFRVLMKELQA 1162

Query: 1357 LGLSIDLENSRTKNSAK 1373
            LG+   + ++       
Sbjct: 1163 LGMDFRVMDNEDNEVDM 1179


>gi|269798559|ref|YP_003312459.1| DNA-directed RNA polymerase subunit beta [Veillonella parvula DSM
           2008]
 gi|269095188|gb|ACZ25179.1| DNA-directed RNA polymerase, beta subunit [Veillonella parvula DSM
           2008]
          Length = 1386

 Score =  805 bits (2078), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/969 (43%), Positives = 581/969 (59%), Gaps = 109/969 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E+I +P L+++Q+ SY+ FL            GLQ  F  + PI   SG
Sbjct: 9   KRTRYTYAKINEVIKMPHLLDIQRKSYEWFL----------ESGLQNIFNDISPIKDNSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+D+++C  RD TYA PL++ +RL+  D +         DIKEQ +
Sbjct: 59  NLVLSFEGFSLGEPKYDINECKNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEV 111

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G 
Sbjct: 112 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGA 168

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWC 246
           W+++E D+ +++ VRIDR RK+P T  + ALG D+ E IL  F+            D   
Sbjct: 169 WIELETDASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERI 228

Query: 247 FPLSAADLMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                 D        +      +  GE   +ES + L   L    +   +  +G      
Sbjct: 229 VRTLEKDTTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNK 288

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  + G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++       
Sbjct: 289 KLGWRQRMLGQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAE 342

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            YI N    +      +  L                              YD  TV R  
Sbjct: 343 FYIVNNDGVESKVICNNCNL-----------------------------PYDHRTVTR-- 371

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                             ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+
Sbjct: 372 ------------------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQF 413

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +
Sbjct: 414 RIGLTRMERVVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAEL 473

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +
Sbjct: 474 THKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEF 533

Query: 596 GFIETPYRKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           GFIE PYRKV                 V++ VVY++A EEE   IAQANS LD +G FT 
Sbjct: 534 GFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTT 593

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E V CR   + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVP
Sbjct: 594 EHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVP 653

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL+A+AP VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y
Sbjct: 654 LLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTY 707

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           RL KF RSNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN
Sbjct: 708 RLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYN 767

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++L+SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GII
Sbjct: 768 YEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGII 827

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           C+GAEV+PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV
Sbjct: 828 CIGAEVHPGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDV 887

Query: 943 RIFNRHGID 951
           ++F R   D
Sbjct: 888 KVFTRENGD 896



 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 105/220 (47%), Positives = 143/220 (65%), Gaps = 5/220 (2%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        +I         D     + +   +G+ ++TPVFDGA
Sbjct: 1101 EELEAISKVKNTLNNIHSAEEKRVEIRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1160

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1161 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1220

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV 
Sbjct: 1221 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKAYEKIVK 1280

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            G +  E G PESF VL+KE+Q++GL + + N   +     
Sbjct: 1281 GENIPEPGVPESFKVLLKELQSIGLDVKILNEDQEEVVMK 1320



 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 104/360 (28%), Positives = 156/360 (43%), Gaps = 19/360 (5%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L A  P  G   E   +      +++ +    +     E+       G
Sbjct: 643  MGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRDSDG 702

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  R    +        ++  I+  G  V  G +L       G   +     +L A  
Sbjct: 703  RVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELALGYNVLVAFM 761

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-ELLARDKDDEQ 975
              +  +  D  L           D+    +    + + R   +  E+I   L    DD  
Sbjct: 762  PWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTL 818

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD +       I  G     G     K+T      +   P  +  +    D++ +   
Sbjct: 819  KNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFGDKEREVRD 871

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 872  TSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEGDKMAGRHG 927

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  GLG KIK+ 
Sbjct: 928  NKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQGLGMKIKAT 987


>gi|320120541|gb|ADW16180.1| hypothetical protein HMPREF0389_01735 [Filifactor alocis ATCC
           35896]
          Length = 1244

 Score =  804 bits (2076), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/958 (45%), Positives = 594/958 (62%), Gaps = 52/958 (5%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
             V  G    R  F +  E+ ++P+LIE+Q  SY+ F+          NEGL+  F+ VF
Sbjct: 5   HPVKIGRK-TRMSFSQIDEVAELPNLIELQLDSYNWFV----------NEGLREVFEEVF 53

Query: 64  PITAFSGAAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-S 121
           PI  ++G   LEFV Y+ +   K+DV++   RD+ YA PLK+ +RL V D D     K  
Sbjct: 54  PIEDYTGNIKLEFVDYKLENDSKYDVEESKERDVNYAAPLKVQVRLTVPDEDGSRIVKNE 113

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             D     +++GD PLMT+ GTF+I G +R++VSQL RSPG+++  +  +   SGK L +
Sbjct: 114 TGDP----VFLGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYAQEIDK---SGKQLIS 166

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY-- 238
             +IP++G W++ E DS D++ VRIDR RK P+T  L A G  ++E I+           
Sbjct: 167 STVIPNRGAWLEYETDSNDVVSVRIDRDRKQPITMLLRAFGYGTDEQIIQLLGDDERIQA 226

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFL 296
           +   D           +           +++ E ++      +    L K  + K  K L
Sbjct: 227 TLAKDNTNSREEGIIEIYKKMRPGEPPTLESAESLLHMMFFDSKRYDLAKVGRYKFNKKL 286

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
            I++    G  +AED+VN  TGE+ +E G  +  ++   I       + +   D+ +   
Sbjct: 287 AISA-RAIGRVLAEDVVNPYTGELVMETGTKVTYQNAHLIDDCGCEYVYVQIDDTKSVKV 345

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                +      D   + L I + +R      +++ + + +    D +  DL        
Sbjct: 346 IGNRFVDIHNFIDIDISDLKIKQKVR------YNILKEILDEATNDEELKDL-------- 391

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                       +HI  EDI+A I    +L  G G +DDID+LGNRRVRSVGE+L+NQ+R
Sbjct: 392 --IKRRKRELVPKHIVIEDIVASISYQFNLFYGLGNVDDIDHLGNRRVRSVGELLQNQFR 449

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER I+ER++  D   + P  LIN +PV +A+ EFF SSQLSQ  +  N L+ +T
Sbjct: 450 IGLSRMERVIRERMTVQDTMELTPNSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLAELT 509

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+ FA++N YG
Sbjct: 510 HKRRLSALGPGGLSRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSVFAKINEYG 569

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-EE 653
           FIE+PYR V   + +VT+++ YL+A EE+    AQAN  LDE+  F  + V CR      
Sbjct: 570 FIESPYRVVDKENQRVTDEIRYLTADEEDLYIRAQANEPLDENQCFVNDRVACRTTQGNL 629

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           +LV  + +DF+D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPLL+ EAP VGT
Sbjct: 630 LLVEPKNVDFMDVSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLRREAPVVGT 689

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            +E   A  SGA +VAK  G+VE+V A ++VIR  +G        VD Y L+KF+RSNQ 
Sbjct: 690 AIEYRAAVDSGAVVVAKNDGVVEKVSARQVVIRREDG-------EVDNYSLLKFKRSNQG 742

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC+NQ  +V  GD V++ D IADGPSTDLG++ALGRN LVAFM W GYN+ED++LI+ER+
Sbjct: 743 TCINQTVIVNKGDVVKKGDAIADGPSTDLGEIALGRNCLVAFMTWEGYNYEDAILINERL 802

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED  +SIHIEE+E  ARDTKLGPEEITRDIPNV E+ +K++DE GII +GAEV  GDI
Sbjct: 803 VKEDRLSSIHIEEYEAEARDTKLGPEEITRDIPNVGEDAIKDLDENGIIRIGAEVESGDI 862

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG +VDV+IF R   D
Sbjct: 863 LVGKVTPKGETEITPEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDVKIFRRENGD 920



 Score =  419 bits (1077), Expect = e-114,   Method: Composition-based stats.
 Identities = 225/1102 (20%), Positives = 377/1102 (34%), Gaps = 130/1102 (11%)

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            ++ ++     D   ++ +  +  +         +  + ++  I+ TL  D    R++ ++
Sbjct: 182  DSNDVVSVRIDRDRKQPITMLLRAFGYGTDEQIIQLLGDDERIQATLAKDNTNSREEGII 241

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +IY+ MRPG+  T   AES+ + +FFDS +YDL+ VGR K N +L +      R + ++ 
Sbjct: 242  EIYKKMRPGEPPTLESAESLLHMMFFDSKRYDLAKVGRYKFNKKLAISARAIGRVLAEDV 301

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +     +L    GT     N  +       E +  Q       ++      +   + 
Sbjct: 302  ---VNPYTGELVMETGTKVTYQN-AHLIDDCGCEYVYVQIDDT-KSVKVIGNRFVDIHNF 356

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARAR 553
              +   DL   + V   +        L ++ +   +   +     RR   L    +    
Sbjct: 357  IDIDISDLKIKQKVRYNI--------LKEILDEATNDEELKDLIKRRKRELVPKHIVIED 408

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                +       YG +   +  +      V S+    +      +    R + +     D
Sbjct: 409  IVASISYQFNLFYG-LGNVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERVIRERMTVQD 467

Query: 614  VVYLSAMEEENRYIAQANSS----------LDEDGSFTEELVFCRC---------AGEEI 654
             + L+     N     A               +  +   EL   R          + E  
Sbjct: 468  TMELTPNSLINIRPVTAAIKEFFGSSQLSQFMDQNNPLAELTHKRRLSALGPGGLSRERA 527

Query: 655  LVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                  + +        +       I  + +      +           ++  E   V  
Sbjct: 528  GFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSVFAKINEYGFIESPYRVVDKENQRVTD 587

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
             +  + A      I A+    +             +     +T G  +    K      +
Sbjct: 588  EIRYLTADEEDLYIRAQANEPL-----DENQCFVNDRVACRTTQGNLLLVEPK-NVDFMD 641

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                Q   V         +  A+              +L    P  G   E    +    
Sbjct: 642  VSPKQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLLRREAPVVGTAIEYRAAVDSGA 701

Query: 834  VSEDVFTSIH-IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            V       +        +    + G  +    +          I++  I+  G  V  GD
Sbjct: 702  VVVAKNDGVVEKVSARQVVIRREDGEVDNYSLLKFKRSNQGTCINQTVIVNKGDVVKKGD 761

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +    +      +      L A    +  +  D  L                    + K
Sbjct: 762  AIADGPSTDL-GEIALGRNCLVAFMTWEGYNYEDAILIN----------------ERLVK 804

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKGF 1002
             +R  S+  E+ E  ARD       + R+I                I  G    SG    
Sbjct: 805  EDRLSSIHIEEYEAEARDTKLGPEEITRDIPNVGEDAIKDLDENGIIRIGAEVESGDILV 864

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K T      I+   R     F  +  +V+     +          +      KI + + 
Sbjct: 865  GKVTPKGETEITPEERLLRAIFGEKAREVRDTSLKVPHGESGIIVDV------KIFRREN 918

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD++  GV  +V+ ++A KR I                                      
Sbjct: 919  GDELAAGVNELVRCYIAQKRKI-------------------------------------- 940

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                     NVG              G K        + +    P  + LE V+      
Sbjct: 941  ---------NVG-------DKMAGRHGNKGVISRILPEEDMPFLPDGTPLEIVLNPLGVP 984

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
             +++      V       K G  V+TPVFDGA+E+ +   L+ A   + G+  L DG TG
Sbjct: 985  SRMNIGQVLEVHMGLAAKKLGWNVATPVFDGANEQDVFEALKQAGYPQDGKIQLQDGRTG 1044

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD  VTVGY+YM+KL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 1045 EFFDGRVTVGYMYMMKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1104

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAA+ LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+Q+L L I 
Sbjct: 1105 EAYGAAHTLQEILTVKSDDVVGRVQTYEAIIKGKNVPEPGIPESFKVLIKELQSLCLDIK 1164

Query: 1363 LENSRTKNSAKMEEIPDFNKCE 1384
            L +   +     E   +    +
Sbjct: 1165 LLSEFDEEIKVAESQDEMTIED 1186


>gi|225175682|ref|ZP_03729676.1| DNA-directed RNA polymerase, beta subunit [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169011|gb|EEG77811.1| DNA-directed RNA polymerase, beta subunit [Dethiobacter
           alkaliphilus AHT 1]
          Length = 1264

 Score =  804 bits (2076), Expect = 0.0,   Method: Composition-based stats.
 Identities = 432/971 (44%), Positives = 582/971 (59%), Gaps = 123/971 (12%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ + +  E++D+P+LIE+Q+ SY  FL           EGLQ  F  + PI  F+G 
Sbjct: 10  RKRRTYARIDEVLDLPNLIEIQQFSYRWFLS----------EGLQEMFNEISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK+ VD+C  RD T++VPL++ +RLI          K   ++KEQ ++
Sbjct: 60  LVLEFIGYSLGEPKYSVDECKERDATFSVPLRVRVRLI---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT++GTF+I G +R++VSQL RSPG++F+         GK L+A  IIP++G W
Sbjct: 111 MGDFPLMTENGTFIINGAERVIVSQLVRSPGVYFNSQID---FVGKTLFAGTIIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D+I+VR+DR RKVPVT  L A+G  +  +IL  +          +       
Sbjct: 168 LEFETDVNDVIYVRVDRTRKVPVTVLLRAIGYGTNNDILGLYDHDPRILATLEKDHTDTF 227

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS--------D 301
            A ++   K       +  GE + +E+ + L   L    K      +G            
Sbjct: 228 EAGILEIYK------RLRPGEPLNVENARSLFESLFFEPKRYDFAHVGRYKVNKKLSFVP 281

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +    +A+++++ E G +   AG+ +            +  I I               
Sbjct: 282 RVLHRNLADNVLDPE-GNVLARAGETVTVDMARSFEEKGVSRIRI--------------- 325

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                  D K+ ++     + PG                    + D+       +N+   
Sbjct: 326 -----TADDKEIVVLNNERITPG---------------VKHLTREDIVAAIGYILNLMDG 365

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
           +   DD+ H+                            GNRR+RSVGE+L+NQ+R+GL R
Sbjct: 366 VGHTDDIDHL----------------------------GNRRLRSVGELLQNQFRIGLSR 397

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER ++ER++  D++++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRL
Sbjct: 398 MERVVRERMTIQDVEAITPQALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRL 457

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+SF R+N YGFIETP
Sbjct: 458 SALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSSFGRINEYGFIETP 517

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV    G+VT ++VYL+A +E+N  +AQAN+ LDE+G F  E + CR   E +L P  
Sbjct: 518 YRKVDKEKGRVTEEIVYLTADDEDNYTVAQANALLDENGHFLAERITCRYRHETVLRPPS 577

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            IDF+D SPKQ+VS+A +LIPFLENDD+NR LMG NMQRQAVPLLKAEAP VGTGME   
Sbjct: 578 NIDFMDVSPKQLVSVATALIPFLENDDANRALMGANMQRQAVPLLKAEAPLVGTGMEYKT 637

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS-------------------GVD 760
           A+ SG  ++AK  G +  V A  I+IR  +    P+                     G D
Sbjct: 638 ARDSGVVVLAKNGGEIVFVSADSIMIRRDDDPEAPNRHINGRTGETFPGEPREGFPRGCD 697

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           IY L KF+RSNQ TC+NQRP V  G +V    +IADGPSTD G+LALGRN+LVAFMPW G
Sbjct: 698 IYTLQKFKRSNQGTCMNQRPTVTHGQKVAAGAVIADGPSTDHGELALGRNILVAFMPWEG 757

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YN+ED++L+SE+MV EDVFTSIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++DE G
Sbjct: 758 YNYEDAILLSEKMVKEDVFTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKDLDERG 817

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II VGAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VV
Sbjct: 818 IIRVGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGMVV 877

Query: 941 DVRIFNRHGID 951
           DV++F+R   D
Sbjct: 878 DVKVFSRENGD 888



 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/507 (37%), Positives = 245/507 (48%), Gaps = 79/507 (15%)

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G +V  G ++    +      +     +L A    +  +  D  L     V   V     
Sbjct: 722  GQKVAAGAVIADGPST-DHGELALGRNILVAFMPWEGYNYEDAILLSEKMVKEDVFTSIH 780

Query: 945  FNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
               +  +  +  +  E          E   +D  DE+ I+      R  +IL G+    G
Sbjct: 781  IEEYESEARDTKLGPEEITRDIPNVGEEALKDL-DERGIIRVGAEVRAGDILVGKVTPKG 839

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                     L   +  E  R                 E                   K+ 
Sbjct: 840  ETELTAEERLLRAIFGEKAR-----------------EVRDTSLRVPHGESGMVVDVKVF 882

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              + GD++PPGV ++V+ +VA KR I  GDKMAGRHGNKG+++RI+P EDMPFL DGTPV
Sbjct: 883  SRENGDELPPGVNQLVRAYVAQKRKISEGDKMAGRHGNKGVIARIMPEEDMPFLPDGTPV 942

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
             IVLNPLGVPSRMN+GQI ETHLGWA   +G  I S + D     D              
Sbjct: 943  QIVLNPLGVPSRMNIGQILETHLGWAAKTMGIHIASPVFDGAREED-------------- 988

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                           VFD           + A L E+G++ L+D
Sbjct: 989  -------------------------------VFD---------AFKEAGLPENGKTTLFD 1008

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TGE FD  VTVGY+YMLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEME
Sbjct: 1009 GRTGEAFDNTVTVGYVYMLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1068

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VLVKE+Q+LG
Sbjct: 1069 VWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLVKELQSLG 1128

Query: 1359 LSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            + + + +         E   D    +L
Sbjct: 1129 MDVKVVDEEVGELEIKEADEDGEVRDL 1155


>gi|241889577|ref|ZP_04776875.1| DNA-directed RNA polymerase, beta subunit [Gemella haemolysans ATCC
           10379]
 gi|241863199|gb|EER67583.1| DNA-directed RNA polymerase, beta subunit [Gemella haemolysans ATCC
           10379]
          Length = 1267

 Score =  804 bits (2076), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/974 (43%), Positives = 584/974 (59%), Gaps = 79/974 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ + +  E+ID+PDLIE+Q  SYD FL            GL+  FK V
Sbjct: 1   MQKVKFGKHRQRRSYARISEVIDLPDLIEIQTLSYDKFL----------ETGLKDVFKDV 50

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI   +    LEF+ Y+   PK+DVD+   RD TY+ PL++ +RLI  + D        
Sbjct: 51  SPIEGNNDKLSLEFIDYKLGTPKYDVDESKERDATYSAPLRVRVRLINKERD-------- 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IKEQ ++MG+LPLMT+ GTF+I G +R++VSQL RSP ++F  D      +    Y  
Sbjct: 103 -EIKEQEVFMGELPLMTETGTFIINGAERVIVSQLVRSPSVYFTEDDKLKVKNIPNAYKT 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W++ E D K +++ RIDR RK+P+T+ + ALG +S+E I+  F         
Sbjct: 162 TVIPNRGAWLEFEKDIKGLVYARIDRTRKIPLTTLIRALGFESDESIIKLFGEDTELLNT 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +         +L  G  +      +  GE   +E+ K    G     +   +  +G   
Sbjct: 222 LEKD------ENLDTGTALKVIYDKLRPGEPANVETAKATLHGRFFDPRRYDLAKVGRYK 275

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    + E IV+ ETGEI +E G  +  + ++ I+        ++  D  
Sbjct: 276 LNNKLHVGERLENQILVEPIVDTETGEILVEKGTKLTREIIDGIYEELGTTANVVEFDMN 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +                    L +++++    V      + +       +D   L  +G
Sbjct: 336 ESLD------------GSDSLKLQLFKIVNQVKVGNDYDIDEL-------TDDQVLHVIG 376

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-----------GTIDDIDNLGN 461
               N         DV  +   DI+A I   + L   +           G +DDID+LGN
Sbjct: 377 NGAPNK--------DVLTLTIADIVASINYYLLLIRTRRNNDGFEFELIGRVDDIDHLGN 428

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R +GE+L+NQ R+G+ RMER ++ER+S  D + + PQ LIN +PV + + EFF SSQ
Sbjct: 429 RRLRCIGELLQNQIRVGISRMERVVRERMSIQDTNEITPQQLINVRPVTAIIKEFFGSSQ 488

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  + VN LS +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIG
Sbjct: 489 LSQFMDQVNPLSELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIG 548

Query: 582 LVSSLTSFARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           L++SL+SFAR+N +GFI TPYRKV         VT +V YL+A +E+   +AQ+ +++DE
Sbjct: 549 LINSLSSFARINEFGFIMTPYRKVEFDGEGRPYVTENVQYLTADQEDKYVVAQSTANVDE 608

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            G F +E V CR  G+  + PRE ++F+D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 609 KGYFVDEEVVCRFRGDNTVKPREMMNFMDVSPKQVVSAATACIPFLENDDSNRALMGANM 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
           QRQAVPL+  EAPFVGTGME + A+ SGAA++AK  GIVE VD  +I +R +E       
Sbjct: 669 QRQAVPLMITEAPFVGTGMEHLAARDSGAAVIAKYPGIVEYVDGAKIKVRRIETLEGKEI 728

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +D Y + KF RSN +T  NQ+P+VKVGD V   DI+ADGPS D G+LALG+N++VAF
Sbjct: 729 KGDLDTYVIHKFVRSNHSTAYNQKPIVKVGDRVEPKDILADGPSMDKGELALGKNLVVAF 788

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + W GYN+ED++++SER+V +DV+TSIH+EE+E  ARDTKLGPEEITR+IPNV E  L+N
Sbjct: 789 VNWDGYNYEDAVIMSERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRN 848

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRVP G 
Sbjct: 849 LDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGA 908

Query: 936 SGTVVDVRIFNRHG 949
            G V DV+IF R  
Sbjct: 909 DGVVADVKIFKRED 922



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 253/1174 (21%), Positives = 425/1174 (36%), Gaps = 135/1174 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSL-----KEKGVKFLGI 298
                           +    +  +TG  +I   ++ + S L++S      ++  +K   I
Sbjct: 96   LINKERDEIKEQEVFMGELPLMTETGTFIINGAERVIVSQLVRSPSVYFTEDDKLKVKNI 155

Query: 299  TSDC----LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             +      +       +      G +Y              I          + +     
Sbjct: 156  PNAYKTTVIPNRGAWLEFEKDIKGLVYARIDRTRKIPLTTLIRALGFESDESI-IKLFGE 214

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            +  + NTL  D+N D   AL  IY  +RPG+ +    A++  +  FFD  +YDL+ VGR 
Sbjct: 215  DTELLNTLEKDENLDTGTALKVIYDKLRPGEPANVETAKATLHGRFFDPRRYDLAKVGRY 274

Query: 415  KM-NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            K+ N     +  ++   +         +ILV+              G +  R + + +  
Sbjct: 275  KLNNKLHVGERLENQILVEPIVDTETGEILVE-------------KGTKLTREIIDGIYE 321

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC-EFFCSSQLSQLEEHVNSL 532
            +       +E  + E +   D   +    ++N   V +    +     Q+  +  +    
Sbjct: 322  ELGTTANVVEFDMNESLDGSDSLKLQLFKIVNQVKVGNDYDIDELTDDQVLHVIGNGAPN 381

Query: 533  SRITHTRRLSALGQGG--VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              +        +      +   R             GR+   +      +  +  L    
Sbjct: 382  KDVLTLTIADIVASINYYLLLIRTRRNNDGFEFELIGRVDDIDHLGNRRLRCIGELLQNQ 441

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVVY--------LSAMEEENRYIAQANSSLDEDGSFTE 642
                   +E   R+    + TN++          ++A+ +E       +S L +      
Sbjct: 442  IRVGISRMERVVRERMSIQDTNEITPQQLINVRPVTAIIKE----FFGSSQLSQFMDQVN 497

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             L           +    +   + +  +V  +  S    +   ++        +   +  
Sbjct: 498  PLSELTHKRRLSALGPGGLTR-ERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSF 556

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
                E  F+ T    V     G   V +    +      + V+     ++D     VD  
Sbjct: 557  ARINEFGFIMTPYRKVEFDGEGRPYVTENVQYLTADQEDKYVVAQSTANVDEKGYFVDEE 616

Query: 763  RLMKFQRSN--QNTCVNQRPLVKVGDEVRRNDII--------ADGPSTDLGDLALGRNML 812
             + +F+  N  +   +     V     V              ++              ++
Sbjct: 617  VVCRFRGDNTVKPREMMNFMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLM 676

Query: 813  VAFMPWHGYNFEDSMLIS---------ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +   P+ G   E                 +V       I +   E +      G  +   
Sbjct: 677  ITEAPFVGTGMEHLAARDSGAAVIAKYPGIVEYVDGAKIKVRRIETLEGKEIKGDLDTYV 736

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                V        ++  I+ VG  V P DIL    +   +  +   + L+ A       +
Sbjct: 737  IHKFVRSNHSTAYNQKPIVKVGDRVEPKDILADGPS-MDKGELALGKNLVVAFVNWDGYN 795

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D  +                    + K++   S+  E+ E  ARD       + R I 
Sbjct: 796  YEDAVIMS----------------ERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIP 839

Query: 984  SRLMEILCGQNAVSGPKG---FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +     L   +A    +     K   +L   +  +    Q  +  +         + ++ 
Sbjct: 840  NVGENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRD 899

Query: 1041 QYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                     +    + KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG+
Sbjct: 900  TSLRVPHGADGVVADVKIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGV 959

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S ILP EDMP+L DGTPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D 
Sbjct: 960  ISNILPEEDMPYLPDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDG 1019

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
              + D+    +                                     T ++DG      
Sbjct: 1020 ATDEDVWSTVAEAGMAKDAK----------------------------TVLYDG------ 1045

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                 TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVT
Sbjct: 1046 --------------------RTGEPFDSRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVT 1085

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDD  GR + YE+IV G +  
Sbjct: 1086 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTNGRVKTYEAIVKGENIP 1145

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
              G PESF VL+KE+QALG+   + ++       
Sbjct: 1146 RPGVPESFRVLMKELQALGMDFRVMDNEDNEVDM 1179


>gi|268610263|ref|ZP_06143990.1| DNA-directed RNA polymerase subunit beta [Ruminococcus flavefaciens
           FD-1]
          Length = 1306

 Score =  803 bits (2075), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/957 (44%), Positives = 576/957 (60%), Gaps = 50/957 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
             VR  FGK  E +++P+LIEVQK SY  F            EGL+  F+ +  IT ++G
Sbjct: 11  KNVRMSFGKITEPLEMPNLIEVQKNSYQWF----------REEGLREVFRDMTAITDYNG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L F  Y FD  PK+ + +C  R  TY V ++ T  L           K    + E  
Sbjct: 61  NLVLNFKDYRFDDTPKYTLAECKSRGATYQVAMRATATL---------ANKETGAVSESE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           IYMGD PLMT  GTFVI G +R++VSQL RSPG+++  +K +    GK L+   +IP++G
Sbjct: 112 IYMGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYAFEKDKT---GKDLFNTTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E DS D+++VRID+ RK+P+T+F+ ALG     EEI +TF       Q       
Sbjct: 169 AWLEYEMDSNDVVYVRIDKNRKIPITTFIRALGEEGTDEEIYATFGEDDRLKQTILQKDQ 228

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS------ 300
             + +D ++          +  GE   +ES     + L    K   +   G         
Sbjct: 229 TKNKSDALIDV-----YKKLRPGEPPTVESSLTHLNNLFFDAKRYDLCRFGRYKYNKKLG 283

Query: 301 --DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               L G  +A+ ++N  TGEI  +AG+ I      EI  + + +  +            
Sbjct: 284 IASRLSGHVLAQPVINEMTGEILADAGETITYDKACEIEQAGVYEAFVTVEAKEYYTDDR 343

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             T +    K  K     +  +    D        +         +  + +        M
Sbjct: 344 GETSIRMVEKTVKIIGNGMVDIKGYVDFDAEKYGINEKVSFKVLKNILETAADADELEEM 403

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
              +      +HI  +DIIA I   ++L  G GT+DDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 404 VKKMADDLVPKHIILDDIIATISYFINLCEGVGTVDDIDHLGNRRIRSVGELLQNQFRIG 463

Query: 479 LLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
             RMERSI+ER++    D++++ PQ LIN +P+ SA+ EFFCSS LSQ  +    L+ +T
Sbjct: 464 YARMERSIRERMNIQTQDVNTLTPQMLINIRPISSAMKEFFCSSPLSQFMDQNTPLAELT 523

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L +FAR+N YG
Sbjct: 524 HKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLATFARINEYG 583

Query: 597 FIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           FIE PYRKV      VTN+VVY++A  E+N  +AQAN  L ED  F    V  R   + +
Sbjct: 584 FIEAPYRKVDKATGVVTNEVVYMTADVEDNFIVAQANEPLTEDSKFARPRVNARYRDQIL 643

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
              REK+D++D SPK VVS+A ++IPFLENDD+NR LMG NMQRQAVPLLK E PFVGTG
Sbjct: 644 ECEREKVDYMDVSPKMVVSVATAMIPFLENDDANRALMGANMQRQAVPLLKTERPFVGTG 703

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  SG  +VA   G V  VDA +I +         +T     Y L+KF+RSNQ T
Sbjct: 704 MEYKAAVDSGVCVVADCDGKVTYVDADKIHV-------VDTTGIEHKYELIKFKRSNQGT 756

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           CVNQRP+V VG+E+++  ++ADGP+T  G+++LG+N L+ FM W GYN+ED++L++ER+V
Sbjct: 757 CVNQRPIVAVGEEIKKGQVLADGPATADGEISLGKNALIGFMTWEGYNYEDAVLLNERLV 816

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            EDVFTS+HIEE+E+  RDTKLGPEEITRDIPNV ++ L N+DE GII +G+EVN GDIL
Sbjct: 817 REDVFTSVHIEEYEIECRDTKLGPEEITRDIPNVGDDALANLDENGIIRIGSEVNSGDIL 876

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKGE+ +T EE+LLRAIFGEKA +VRD SL+VP G SG +VDV++F R   D
Sbjct: 877 VGKVTPKGETELTAEERLLRAIFGEKAREVRDNSLKVPHGESGVIVDVKVFTRENCD 933



 Score =  513 bits (1321), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/565 (32%), Positives = 264/565 (46%), Gaps = 46/565 (8%)

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             G  ++ ++     +V++      +++  ++   DT  G E     I          +++
Sbjct: 702  TGMEYKAAVDSGVCVVADCDGKVTYVDADKIHVVDT-TGIEHKYELIKFKRSNQGTCVNQ 760

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              I+ VG E+  G +L        +  ++  +  L      +  +  D  L     V   
Sbjct: 761  RPIVAVGEEIKKGQVLADGP-ATADGEISLGKNALIGFMTWEGYNYEDAVLLNERLVRED 819

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            V        + I+  +  +  E E    +    DD    LD N   R+   +   + + G
Sbjct: 820  VFTSVHIEEYEIECRDTKLGPE-EITRDIPNVGDDALANLDENGIIRIGSEVNSGDILVG 878

Query: 999  PKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                K  T L+++  L+      +  +      KV      + V               K
Sbjct: 879  KVTPKGETELTAEERLLRAIFGEKAREVRDNSLKVPHGESGVIV-------------DVK 925

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   +  D++  GV   V  ++A KR I  GDKMAGRHGNKG+VSRILP EDMPFL DGT
Sbjct: 926  VFTRENCDELSAGVNMRVICYIAQKRKITVGDKMAGRHGNKGVVSRILPEEDMPFLPDGT 985

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+DIVLNPLGVPSRMN+GQ+ E HLG AC  LG  I + + D     DI        +  
Sbjct: 986  PLDIVLNPLGVPSRMNIGQVLEVHLGMACKALGWHIMTPVFDGAHEDDIRECFKQANEHA 1045

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                         D  +   A +                              E  +  L
Sbjct: 1046 QEHKDDMFELKAMDKVINPNALE----------------------------FTEDCKFTL 1077

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGE FD  VTVGY+Y LKL+H+V DK++ARS G Y+LVTQQPLGGK+  GGQR GE
Sbjct: 1078 YDGRTGEKFDNRVTVGYMYYLKLHHLVDDKIHARSVGPYALVTQQPLGGKAQFGGQRFGE 1137

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT+KSDD +GR   YE+IV G +    G PESF VL+KEMQ+
Sbjct: 1138 MEVWALEAYGAAYTLQEILTVKSDDTIGRVNTYEAIVKGQNVPTPGIPESFKVLIKEMQS 1197

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFN 1381
            L L + + +   +     +   D +
Sbjct: 1198 LCLDVKVLDINQEEIDLKQNFDDED 1222


>gi|225018161|ref|ZP_03707353.1| hypothetical protein CLOSTMETH_02098 [Clostridium methylpentosum
           DSM 5476]
 gi|224949158|gb|EEG30367.1| hypothetical protein CLOSTMETH_02098 [Clostridium methylpentosum
           DSM 5476]
          Length = 1259

 Score =  803 bits (2075), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/974 (43%), Positives = 592/974 (60%), Gaps = 85/974 (8%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F +  E++++P+LIEVQK SY+ F           NEGL+  F+    I+  +G
Sbjct: 22  KNTRMSFARINEVLEMPNLIEVQKDSYEWF----------RNEGLKEVFRDAAYISDHTG 71

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y FD  PK+DV +C  RD+TYA PL++  RLI          K   ++KEQ 
Sbjct: 72  NLVLEFVDYRFDDKPKYDVIECKERDVTYAAPLRVKTRLI---------NKETGEVKEQE 122

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTFVI G +R++VSQL RSPG+++  +  +    GK  ++  +IP++G
Sbjct: 123 IFMGDFPLMTESGTFVINGAERVIVSQLVRSPGVYYGSEYDKT---GKKKFSSTVIPNRG 179

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-----------------GMDSE-EILST 231
            W++ E DS DI +VRID+ RK+P+T F+ AL                    ++ EI   
Sbjct: 180 AWLEYETDSNDIFYVRIDKNRKIPITVFIRALLRIKDNVVPGDTDVFTEKYGTDPEIFEI 239

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKE 290
           F       Q         +  + ++          +  GE   ++S       L    + 
Sbjct: 240 FGEDKRLIQTITEKDSTKNGEEALLEV-----YRKLRPGEPPTLDSAVTHLRNLFFDDRR 294

Query: 291 KGVKFLGITSD--------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
             +  +G             L G  +AE +VN  TGE+  + G+V+      EI  +   
Sbjct: 295 YDLSRVGRYKYNKKLAIGARLTGQMLAEPVVNELTGEVLGDKGEVLTHARAMEIERAG-- 352

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            I   YVD       + +  + D                   D   + + E +   +  D
Sbjct: 353 -IDTAYVDVEGEIVKVISNGMVDLTDFVD------------IDPHEYGIHEKVRYRVLRD 399

Query: 403 -SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             +        +  +  R++   P   +H+ K+DI A I  + +L  G G IDDID+LGN
Sbjct: 400 ILESASDEEEVKELIKQRVDALVP---KHVIKDDIFATINYINNLACGVGNIDDIDHLGN 456

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
           RR+RSVGE+L+NQ+R+G  RMER I+ER++    D+D V PQ LIN +PVV+A+ EFF S
Sbjct: 457 RRIRSVGELLQNQFRIGFSRMERVIRERMTLQAQDMDVVTPQALINIRPVVAAIKEFFGS 516

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S LSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG N
Sbjct: 517 SPLSQFMDQTNPLAELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPN 576

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL+S L SFAR+N YGFIE PYRKV     KV ++VVY++A  E+N  +AQAN  L E+
Sbjct: 577 IGLISYLASFARLNEYGFIEAPYRKVDKETGKVLDEVVYMTADVEDNYVVAQANEPLTEE 636

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G+F    V  RC  + + + RE +DF+D SPK VVS+A ++IPFLENDD+NR LMG NMQ
Sbjct: 637 GTFARPKVNARCRDQILEIEREAVDFMDVSPKMVVSVATAMIPFLENDDANRALMGANMQ 696

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPLLK ++P VGTGME   A  SG  +VAK +G+V++V A  IVI   +G       
Sbjct: 697 RQAVPLLKTQSPIVGTGMEYKAAVDSGVCVVAKESGVVKKVSADEIVITDEQGVNHS--- 753

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               Y+L+K+ RSNQ+TCVNQ+P+V  G++V +  +IADGP+TD G+++LG+N L+ FM 
Sbjct: 754 ----YKLIKYMRSNQSTCVNQKPIVDKGEKVTKGQVIADGPATDNGEVSLGKNALIGFMT 809

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++L++E++V EDV+TSIH+EE+EV ARDTKLGPEEITR+IPNV E+ LK++D
Sbjct: 810 WEGYNYEDAVLLNEKLVREDVYTSIHVEEYEVEARDTKLGPEEITREIPNVGEDALKDLD 869

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GII VGAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G
Sbjct: 870 ERGIIRVGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYG 929

Query: 938 TVVDVRIFNRHGID 951
            + D+++F R   D
Sbjct: 930 IIQDIKVFTRENSD 943



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 181/539 (33%), Positives = 242/539 (44%), Gaps = 79/539 (14%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             + G     + I  +       +++  I+  G +V  G ++           ++  +  L
Sbjct: 746  DEQGVNHSYKLIKYMRSNQSTCVNQKPIVDKGEKVTKGQVIADGPATDN-GEVSLGKNAL 804

Query: 914  RAIFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
                  +  +  D  L      R     S  V +  +  R      E          E  
Sbjct: 805  IGFMTWEGYNYEDAVLLNEKLVREDVYTSIHVEEYEVEARDTKLGPEEITREIPNVGEDA 864

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +D  DE+ I+      R  +IL G+    G         L   +  E  R         
Sbjct: 865  LKDL-DERGIIRVGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR--------- 914

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E                   K+   +  D++ PGV  VV+ ++  KR I  G
Sbjct: 915  --------EVRDTSLRVPHGEYGIIQDIKVFTRENSDELSPGVNMVVRCYIIQKRKISVG 966

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSRILP EDMPFL DG P+DIVLNPLGVPSRMN+GQ+ E HLG A   
Sbjct: 967  DKMAGRHGNKGVVSRILPQEDMPFLPDGRPLDIVLNPLGVPSRMNIGQVLEVHLGMAAKA 1026

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG KI + + D     DI                                          
Sbjct: 1027 LGWKIMTPVFDGAHEADIRECFKEAGMAE------------------------------- 1055

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                DG                      LYDG TGEPFD  VTVGY+Y LKL+H+V DK+
Sbjct: 1056 ----DGKTV-------------------LYDGRTGEPFDNRVTVGYMYFLKLHHLVDDKI 1092

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD VGR +
Sbjct: 1093 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDTVGRVK 1152

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
             YE+IV G +  + G PE+F VL+KE+Q+L L + + +   +     +   D +   L+
Sbjct: 1153 TYEAIVKGQNVPKPGAPEAFKVLIKELQSLALDVKVLDKNNEEIDLQQTFDDDDDLGLQ 1211


>gi|67550162|gb|AAY68427.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
          Length = 709

 Score =  803 bits (2074), Expect = 0.0,   Method: Composition-based stats.
 Identities = 390/713 (54%), Positives = 523/713 (73%), Gaps = 5/713 (0%)

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             NIGL++SL+ +A+ N +GF+ETPYRKV DG+VT+ V YLSA+EE    IAQA+S++D+D
Sbjct: 1    PNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAIDKD 60

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            G+ TE+ V  R  G+ + +P EK+  +D S +QVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 61   GNLTEDFVSVRHQGDFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQ 120

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            RQAVP L+A+ P VGTGME+ VA+ SG  ++A R G +E VDA RIVIR  E ++    +
Sbjct: 121  RQAVPTLRADKPLVGTGMEANVARDSGVCVIANRGGAIEYVDASRIVIRVNEDEMIAGEA 180

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            GVDIY L+K+ RSNQNTC+NQ  +V +GD+V R DI+ADGPSTD+G+LALG+NM VAFM 
Sbjct: 181  GVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMT 240

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W+GYN+EDS+L+SER++ ED  TSIHI+E   +ARDTKLG EEIT DIPNV E  L  +D
Sbjct: 241  WNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLD 300

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVPSG  G
Sbjct: 301  ESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKG 360

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            TV+DV++F R G++K++R++++E+ Q++   +D  +E  I +     R++ +L GQ +  
Sbjct: 361  TVIDVQVFTRDGLEKDDRAMAIEKAQLDAYRKDLKEEYKIFEEAARERVIRLLNGQESNG 420

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G    K+   L  D++S        +    DE +   +  ++V  +   + ++++F  K 
Sbjct: 421  G-GSTKRGDELVEDMLSGLELVDLLEIQPTDEAIAERLSQIQVFLKEKSAEIDEKFAEKK 479

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
             K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G P
Sbjct: 480  RKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVP 539

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+  
Sbjct: 540  VDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKIYN 596

Query: 1178 T-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G   E +    D  VL ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ++L
Sbjct: 597  KVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQTVL 656

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            +DG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  
Sbjct: 657  FDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 709


>gi|326792617|ref|YP_004310438.1| DNA-directed RNA polymerase subunit beta [Clostridium lentocellum
           DSM 5427]
 gi|326543381|gb|ADZ85240.1| DNA-directed RNA polymerase, beta subunit [Clostridium lentocellum
           DSM 5427]
          Length = 1283

 Score =  803 bits (2074), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/952 (43%), Positives = 589/952 (61%), Gaps = 56/952 (5%)

Query: 11  GRVRKFFGKNPE-IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
            ++R  + +  + +++IP+L+E+Q++SY+ FL          NEGL+  F+ + PIT F+
Sbjct: 13  KQIRMSYARTEDGVLEIPNLVELQRSSYEWFL----------NEGLKEVFEDISPITDFN 62

Query: 70  GAAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           G  +LEFV +  D  PK+ +++C  RD TY  PLK+  RL           K      + 
Sbjct: 63  GNLILEFVDFYLDSKPKYTIEECRERDATYCAPLKVKARLH---------NKETGTSVDS 113

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT++ TF+I G +R++VSQL RSPGI++D    +    GK L++  +IP++
Sbjct: 114 EVFMGDFPLMTENATFIINGAERVIVSQLVRSPGIYYDIAFDKT---GKKLFSASVIPNR 170

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFW 245
           G W++ E DS DI +VR+DR RKVP+T  L +LG+ S+ EI+  F    KI+ + + D  
Sbjct: 171 GAWLEYETDSNDIFYVRVDRTRKVPITVLLRSLGLGSDAEIIEKFGEEPKILETIQKDTS 230

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                    M           +D+ E ++ +         L K  + K  K L +  + +
Sbjct: 231 KTYEEGLLEMYKRIRPGEPPTVDSAETLLRNMFFDPKRYDLAKVGRYKFNKKLAL-RNRV 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            GL +A+++++  TGEI    GD I       I ++ I  I +   +S      I N  V
Sbjct: 290 MGLTLADNVIDPFTGEIVASEGDKITVALANAIQNTGIEAIHVNVANSDKPIKIITNRTV 349

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                      L+ +  + P ++         +  L    ++Y      + ++  R    
Sbjct: 350 E----------LNHFVDVNPEELGIKDTVY--YPVLEEILEQYHDIEEIKAEIKARKADL 397

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
            P   + I  +DI A I   + L    G  DDID+LGNRR+R VGE+ +NQ+R+GL RME
Sbjct: 398 IP---KCITLDDIFASINYNMHLEYEIGNTDDIDHLGNRRIRGVGELFQNQFRIGLSRME 454

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER++  D ++V PQ  IN +PV SA+ EFF SSQLSQ  +H N L+ +TH RRLSA
Sbjct: 455 RVVRERMTIQDQEAVSPQAFINIRPVSSAIKEFFGSSQLSQFMDHNNPLAELTHKRRLSA 514

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FAR+N YGFIE PYR
Sbjct: 515 LGLGGLSRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATFARINEYGFIEAPYR 574

Query: 604 KVCD----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +       ++T++V+Y++A EEE   + QA    DE+G F  + V  R A + +    +
Sbjct: 575 VIDKSGPEPRLTDEVIYITADEEEKYTVCQATEQFDEEGYFINKRVTARHAEDILDYDYK 634

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           KID +D S KQ+VS+A +LIPFLENDD+NR LMG NMQRQAVPL+   +P V TGME  +
Sbjct: 635 KIDLMDVSTKQIVSVATALIPFLENDDANRALMGANMQRQAVPLIATNSPIVATGMEYKI 694

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
              SGA  VA+  GIV++  A  IV++  EG           Y+L KF+RSN  TC+NQR
Sbjct: 695 GIDSGALAVAREDGIVDKCTAKEIVVKDNEGKKHS-------YKLEKFERSNAGTCINQR 747

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GD V++ D++ADGPST  G+LALG+N L+ FM W GYN+ED++L+SER+V +D++
Sbjct: 748 PVVNKGDIVKKGDVLADGPSTQNGELALGQNPLIGFMTWEGYNYEDAILLSERLVQDDIY 807

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE+EV ARDTK+GPEEITRDIPNV E+ LK++DE GII +GAEV  GDILVG++T
Sbjct: 808 TSIHIEEYEVEARDTKVGPEEITRDIPNVGEDTLKDLDERGIIRIGAEVRSGDILVGRVT 867

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEK  +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 868 PKGETELTAEERLLRAIFGEKVREVRDTSLRVPHGEAGIIVDVKIFTRENGD 919



 Score =  553 bits (1424), Expect = e-154,   Method: Composition-based stats.
 Identities = 260/1127 (23%), Positives = 408/1127 (36%), Gaps = 81/1127 (7%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            +   +      K +    +  +   G ++  +    ++ +I+    D   +  +  +  S
Sbjct: 148  IYYDIAFDKTGKKLFSASVIPNR--GAWLEYE---TDSNDIFYVRVDRTRKVPITVLLRS 202

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                     ++       I  T+  D +K  ++ LL++Y+ +RPG+  T   AE++   +
Sbjct: 203  LGLGSDAEIIEKFGEEPKILETIQKDTSKTYEEGLLEMYKRIRPGEPPTVDSAETLLRNM 262

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FFD  +YDL+ VGR K N +L L        +           ++D   G+    + D +
Sbjct: 263  FFDPKRYDLAKVGRYKFNKKLALRNRVMGLTL--------ADNVIDPFTGEIVASEGDKI 314

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                  ++         + +   ++ IK   +     +           +   V      
Sbjct: 315  TVALANAIQNTGIEAIHVNVANSDKPIKIITNRTVELNHFVDVNPEELGIKDTVYYPVLE 374

Query: 520  SQLSQLEEHVNSLSRITHTR-----RLSALGQGGVARARAGVEMRDVHPT----HYGRIC 570
              L Q  +     + I   +     +   L     +         ++  T    H G   
Sbjct: 375  EILEQYHDIEEIKAEIKARKADLIPKCITLDDIFASINYNMHLEYEIGNTDDIDHLGNRR 434

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
                 E         L+   RV            V      N     SA++E        
Sbjct: 435  IRGVGELFQNQFRIGLSRMERVVRERMTIQDQEAVSPQAFINIRPVSSAIKEF-----FG 489

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILV-------PREKIDFIDASPKQVVSIAASLIPFLE 683
            +S L +       L           +        R   +  D        +     P   
Sbjct: 490  SSQLSQFMDHNNPLAELTHKRRLSALGLGGLSRERAGFEVRDVHYSHYGRMCPIETPEGP 549

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            N      L       +   +         +G E  +       I A          A   
Sbjct: 550  NIGLINSLATFARINEYGFIEAPYRVIDKSGPEPRL-TDEVIYITADEEEKYTVCQATEQ 608

Query: 744  VIR--SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                         +    DI      +    +    Q   V         +  A+     
Sbjct: 609  FDEEGYFINKRVTARHAEDILDYDYKKIDLMDVSTKQIVSVATALIPFLENDDANRALMG 668

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGPEE 860
                     ++    P      E  + I    ++      I      + +      G + 
Sbjct: 669  ANMQRQAVPLIATNSPIVATGMEYKIGIDSGALAVAREDGIVDKCTAKEIVVKDNEGKKH 728

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              +            I++  ++  G  V  GD+L    + +    +   +  L      +
Sbjct: 729  SYKLEKFERSNAGTCINQRPVVNKGDIVKKGDVLADGPSTQN-GELALGQNPLIGFMTWE 787

Query: 921  AVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
              +  D  L            S  + +  +  R      E          E   +D  DE
Sbjct: 788  GYNYEDAILLSERLVQDDIYTSIHIEEYEVEARDTKVGPEEITRDIPNVGEDTLKDL-DE 846

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            + I+      R  +IL G+    G         L   +  E  R                
Sbjct: 847  RGIIRIGAEVRSGDILVGRVTPKGETELTAEERLLRAIFGEKVR---------------- 890

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             E                   KI   + GD++ PGV ++V+ ++A KR I  GDKMAGRH
Sbjct: 891  -EVRDTSLRVPHGEAGIIVDVKIFTRENGDELDPGVNKMVRCYIAQKRKISVGDKMAGRH 949

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++SR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HLG A   LG KI++
Sbjct: 950  GNKGVISRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEVHLGLAAKALGFKIET 1009

Query: 1155 LINDYKANGDISPLRSFLEKVIGT--GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + +     DI          +         K S   D+SV++     +           
Sbjct: 1010 PVFNGATEQDIMSTLEMANDYVNWSWEEFEAKWSQRVDESVIKYLSDNR----------- 1058

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                    +  +   LD +G+  L DG TGE FD PVTVGY++ LKL+H+V DK++ARST
Sbjct: 1059 -----DHRAEWKGVPLDRTGKIRLRDGRTGEEFDNPVTVGYMHYLKLHHLVDDKMHARST 1113

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G Y+ +TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YESI
Sbjct: 1114 GPYATITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYESI 1173

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            V G +  E G PESF VL+KE+Q+L L I +  S        E + +
Sbjct: 1174 VKGENIPEPGIPESFKVLLKELQSLSLDIRVLTSNMTEIDIKESVDE 1220


>gi|291533531|emb|CBL06644.1| DNA-directed RNA polymerase subunit beta [Megamonas hypermegale
           ART12/1]
          Length = 1204

 Score =  802 bits (2072), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/934 (44%), Positives = 576/934 (61%), Gaps = 87/934 (9%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P L+++Q+ SYD F+           EGLQ  F  + PI  F+G  +L F  +    
Sbjct: 1   MDMPHLLDIQRNSYDWFM----------KEGLQEIFHDISPIQGFTGNLVLSFEGFSLGK 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+D+D C  RD TY+ PL++ +RL+  D           ++KEQ ++MGD PLMT+ GT
Sbjct: 51  PKYDIDKCKERDATYSAPLRVNVRLVNND---------TGEVKEQEVFMGDFPLMTETGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQL RSPG ++  +       GK LY   +IP++G W++ E D  D+I 
Sbjct: 102 FIINGAERVIVSQLVRSPGAYYGENIDPT---GKRLYNATVIPNRGAWIEFETDLNDVIS 158

Query: 204 VRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKV 260
           VR+DR RK+P T  + ALG  + + I+S F        +   D       A   +   + 
Sbjct: 159 VRLDRNRKLPATVLIRALGYGTNDAIMSLFDNDERIRNTIDRDNTVTKEEALVEIYKRQR 218

Query: 261 SSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                 +D  +Q++E          L ++    +         L G  +AE +V+ ETGE
Sbjct: 219 PGDPPTVDNAKQLLEQLLFDPKRYDLATVGRYKLTKKLGWKRRLLGKQLAEPLVDKETGE 278

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A   I+   +E+I   +  +I                          + A++ I  
Sbjct: 279 VLVPADVTIEASMVEDITIEQENNIFGED----------------------EHAIVYIKD 316

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                                              ++ M  +   P + R I   DIIA 
Sbjct: 317 K-------------------------------NNNRIKMICSRTLPYNHRTITINDIIAS 345

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I  L++L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER I+ER+++ D D + 
Sbjct: 346 ISYLLNLMDGHGHKDDIDHLGNRRIRSVGELLQNQFRIGLSRMERVIRERMNTQDNDVIT 405

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           PQ L+N +PVV+A+ EFF SSQLSQ  +  N LS +TH RRLSALG GG++R RAG E+R
Sbjct: 406 PQALVNIRPVVAAIKEFFGSSQLSQFMDQNNPLSELTHKRRLSALGPGGLSRERAGFEVR 465

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYL 617
           DVH +HYGR+CP ET EG NIGL+ SL ++AR+N +GF+ETPYRKV   + +VT DV YL
Sbjct: 466 DVHNSHYGRMCPIETPEGPNIGLIGSLATYARINEFGFMETPYRKVDKVNKQVTTDVRYL 525

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE++  IAQAN  LDE+  F  + V  R   E +LV  + +D++D SPKQ+VSIA +
Sbjct: 526 TADEEDDLVIAQANEPLDENNWFKAQRVTARVHEETMLVDADSVDYMDVSPKQIVSIATA 585

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLENDD+NR LMG NMQRQAVPL + +AP VGTGME   A  SG  ++AKRAG V +
Sbjct: 586 MIPFLENDDANRALMGANMQRQAVPLFRTQAPLVGTGMEYKAACDSGVMVLAKRAGEVVR 645

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I +R+ E      T  +D Y+L K+ RSNQ TC+NQ P+V  GD V   + IADG
Sbjct: 646 VTADYIEVRADE------TGEIDHYKLQKYLRSNQGTCMNQVPIVYKGDHVEAKEPIADG 699

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+TD G+LALG N++VA+MPW GYN+ED++L+SE++V ED++TSIHIEE+E  ARDTKLG
Sbjct: 700 PATDHGELALGYNVIVAYMPWEGYNYEDAILLSEKLVKEDIYTSIHIEEYECDARDTKLG 759

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEIT+DIPNV+E+ L+++D  GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIF
Sbjct: 760 PEEITQDIPNVAEDALRDLDADGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIF 819

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSLRVP G +G +VDV+IFNR   D
Sbjct: 820 GEKAREVRDTSLRVPHGEAGRIVDVKIFNRAKND 853



 Score =  545 bits (1404), Expect = e-152,   Method: Composition-based stats.
 Identities = 190/536 (35%), Positives = 286/536 (53%), Gaps = 36/536 (6%)

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +  R  + G  +  +    +       +++  I+  G  V   + +           +  
Sbjct: 651  IEVRADETGEIDHYKLQKYLRSNQGTCMNQVPIVYKGDHVEAKEPIADGP-ATDHGELAL 709

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELL 967
               ++ A    +  +  D  L     V   +      +    + + R   +  E+I + +
Sbjct: 710  GYNVIVAYMPWEGYNYEDAILLSEKLVKEDI--YTSIHIEEYECDARDTKLGPEEITQDI 767

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                +D    LD +   R+   +   + + G    K  T L+++        +  +    
Sbjct: 768  PNVAEDALRDLDADGIIRIGAEVRAGDILVGKVTPKGETELTAE-------ERLLRAIFG 820

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            ++  +    SL+V +  +  I++     KI      D++PPGV ++V+V++A KR I  G
Sbjct: 821  EKAREVRDTSLRVPHGEAGRIVD----VKIFNRAKNDELPPGVNQLVRVYIAQKRKISVG 876

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSR++  EDMPFL DGTPV+IVLNPLGVPSRMN+GQ+ ETHLG A   
Sbjct: 877  DKMAGRHGNKGVVSRVMREEDMPFLPDGTPVNIVLNPLGVPSRMNIGQVLETHLGMAVRE 936

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG +IK+                           +   +   D     + +   +G+ ++
Sbjct: 937  LGMQIKAG---------------------DPTVESRLRAIGYDFDKNGMPKPDVAGIHIA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TPVFDGA    +   L+ +   ++G++ILYDG TGEPF+ PVTVG +YMLKL+H+V DK+
Sbjct: 976  TPVFDGAKGNEVFETLKASGFSDNGKTILYDGRTGEPFENPVTVGCVYMLKLHHLVDDKI 1035

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR +
Sbjct: 1036 HARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVK 1095

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             YE+IV G +  E G PESF VL+KE+Q++GL I + +   +     +   D N+ 
Sbjct: 1096 TYEAIVKGENIPEPGVPESFKVLIKELQSIGLDIKVLSEDAQEIMINDIEDDINET 1151


>gi|317495085|ref|ZP_07953456.1| DNA-directed RNA polymerase [Gemella moribillum M424]
 gi|316914792|gb|EFV36267.1| DNA-directed RNA polymerase [Gemella moribillum M424]
          Length = 1272

 Score =  802 bits (2071), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/974 (42%), Positives = 582/974 (59%), Gaps = 79/974 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R+ + +  E+ID+PDLIE+Q  SY+ FL            G++  F+ V
Sbjct: 1   MQKVKFGKHRQRRSYARISEVIDLPDLIEIQTLSYEKFL----------ETGIKEVFRDV 50

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI   +    LEF+ Y+   PK+ VD+   RD TY+ PL++ +RLI  + D        
Sbjct: 51  SPIEGNNDKLSLEFIDYKLGTPKYSVDESKERDATYSAPLRVRVRLINKERD-------- 102

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IKEQ ++MG+LPLMT+ GTF+I G +R++VSQL RSP ++F  D      +    Y  
Sbjct: 103 -EIKEQEVFMGELPLMTETGTFIINGAERVIVSQLVRSPSVYFTEDDKLKIKNIPNAYKT 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W++ E D K + + RIDR RK+P+T+ + ALG +S+E I+  F         
Sbjct: 162 TVIPNRGAWLEFEKDIKGLAYARIDRTRKIPLTTLIRALGFESDEAIVKLFGEDTELLNT 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +         +L  G  +      +  GE   +E+ K    G     +   +  +G   
Sbjct: 222 LEKD------ENLDTGTALKVIYDKLRPGEPANVETAKATLHGRFFDPRRYDLAKVGRYK 275

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                   + L    + E IV+ ETGEI +E G  +  + ++ I+        ++  D  
Sbjct: 276 LNNKLHVGERLENQILVEPIVDTETGEILVEKGTKLTREIIDGIYEELGTTANVVEFDMN 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +                    L +++V+    V      + + N          L  +G
Sbjct: 336 ESLD------------GTDSLKLQLFKVVNQVKVGNEFNIDELTNDQI-------LHVIG 376

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-----------GTIDDIDNLGN 461
               N         D+  +   DI+A I   + L   +           G +DDID+LGN
Sbjct: 377 NGAPNK--------DILTLTIADIVASINYYLLLIRNRRNSDGFEYELIGRVDDIDHLGN 428

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R +GE+L+NQ R+G+ RMER ++ER+S  D + + PQ LIN +PV + + EFF SSQ
Sbjct: 429 RRLRCIGELLQNQIRVGISRMERVVRERMSIQDTNEITPQQLINVRPVTAIIKEFFGSSQ 488

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIG
Sbjct: 489 LSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIG 548

Query: 582 LVSSLTSFARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           L++SL+SFAR+N +GFI TPYRKV         VT +V YL+A +E+   +AQ+NS++D+
Sbjct: 549 LINSLSSFARINEFGFIMTPYRKVEVDKDGRPYVTENVQYLTADQEDKYVVAQSNSNIDK 608

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +G F ++ V CR  G+  + P+E ++++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 609 NGYFLDDEVVCRFRGDNTVKPKEMMNYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
           QRQAVPL+  EAPFVGTGME + A+ SGAA++AK  GIVE VD  +I +R +E       
Sbjct: 669 QRQAVPLMLTEAPFVGTGMEHLAARDSGAAVIAKYPGIVEYVDGAKIKVRRIETLDGKEI 728

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +D Y + KF RSN +T  NQ+P+VKVGD V   DI+ADGPS D G+LALG+N++VAF
Sbjct: 729 QGDLDTYVVHKFVRSNHSTSYNQKPIVKVGDRVEPKDILADGPSMDKGELALGKNLVVAF 788

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + W GYN+ED++++SER+V +DV+TSIH+EE+E  ARDTKLGPEEITR+IPNV E  L+N
Sbjct: 789 VNWDGYNYEDAVIMSERLVKDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRN 848

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRVP G 
Sbjct: 849 LDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGA 908

Query: 936 SGTVVDVRIFNRHG 949
            G V DV+IF R  
Sbjct: 909 DGVVADVKIFKRED 922



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 238/1086 (21%), Positives = 402/1086 (37%), Gaps = 122/1086 (11%)

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  L  +  +   +     V     +  + NTL  D+N D   AL  IY  +
Sbjct: 182  YARIDRTRKIPLTTLIRALGFESDEAIVKLFGEDTELLNTLEKDENLDTGTALKVIYDKL 241

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+ +    A++  +  FFD          R  +         + +    + +   +++
Sbjct: 242  RPGEPANVETAKATLHGRFFDPR--------RYDLAKVGRYKLNNKLHVGERLENQILVE 293

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +VD   G+  ++     G +  R + + +  +       +E  + E +   D   +   
Sbjct: 294  PIVDTETGEILVEK----GTKLTREIIDGIYEELGTTANVVEFDMNESLDGTDSLKLQLF 349

Query: 502  DLINAKPVVSAVC-EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG--VARARAGVEM 558
             ++N   V +    +   + Q+  +  +      I        +      +   R     
Sbjct: 350  KVVNQVKVGNEFNIDELTNDQILHVIGNGAPNKDILTLTIADIVASINYYLLLIRNRRNS 409

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY-- 616
                    GR+   +      +  +  L           +E   R+    + TN++    
Sbjct: 410  DGFEYELIGRVDDIDHLGNRRLRCIGELLQNQIRVGISRMERVVRERMSIQDTNEITPQQ 469

Query: 617  ------LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
                  ++A+ +E       +S L +    T  L           +    +   + +  +
Sbjct: 470  LINVRPVTAIIKE----FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTR-ERAGME 524

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            V  +  S    +   ++        +   +      E  F+ T    V     G   V +
Sbjct: 525  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSFARINEFGFIMTPYRKVEVDKDGRPYVTE 584

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN--QNTCVNQRPLVKVGDEV 788
                +      + V+     ++D +   +D   + +F+  N  +   +     V     V
Sbjct: 585  NVQYLTADQEDKYVVAQSNSNIDKNGYFLDDEVVCRFRGDNTVKPKEMMNYMDVSPKQVV 644

Query: 789  RRNDII--------ADGPSTDLGDLALGRNMLVAFMPWHGYNFE---------DSMLISE 831
                          ++              +++   P+ G   E           +    
Sbjct: 645  SAATACIPFLENDDSNRALMGANMQRQAVPLMLTEAPFVGTGMEHLAARDSGAAVIAKYP 704

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             +V       I +   E +      G  +       V      + ++  I+ VG  V P 
Sbjct: 705  GIVEYVDGAKIKVRRIETLDGKEIQGDLDTYVVHKFVRSNHSTSYNQKPIVKVGDRVEPK 764

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DIL    +   +  +   + L+ A       +  D  +                    + 
Sbjct: 765  DILADGPS-MDKGELALGKNLVVAFVNWDGYNYEDAVIMS----------------ERLV 807

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  ARD       + R I +     L   +A    +     K   +L
Sbjct: 808  KDDVYTSIHVEEYETDARDTKLGPEEITREIPNVGENALRNLDARGIIRIGAEVKDGDIL 867

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMP 1067
               +  +    Q  +  +         + ++          +    + KI K + G ++ 
Sbjct: 868  VGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGADGVVADVKIFKREDGAELA 927

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
             GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DGTPVD++LNPLGV
Sbjct: 928  NGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDGTPVDVMLNPLGV 987

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D   + D+    +                 
Sbjct: 988  PSRMNIGQVLELHLGMAAKQLGIHVATPVFDGANDDDVWATIAEAGMAKDAK-------- 1039

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                T ++DG                           TGEPFD 
Sbjct: 1040 --------------------TVLYDG--------------------------RTGEPFDS 1053

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1054 RVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1113

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT KSDD  GR + YE+IV G +    G PESF VL+KE+QALG+   + +  
Sbjct: 1114 AYTLQEILTYKSDDTNGRVKTYEAIVKGENIPRPGVPESFRVLMKELQALGMDFRVMDKD 1173

Query: 1368 TKNSAK 1373
                  
Sbjct: 1174 DNEVDM 1179


>gi|297179988|gb|ADI16213.1| hypothetical protein [uncultured bacterium HF0010_16H03]
          Length = 701

 Score =  800 bits (2067), Expect = 0.0,   Method: Composition-based stats.
 Identities = 386/700 (55%), Positives = 519/700 (74%), Gaps = 10/700 (1%)

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            KV +GKVT++++YLSA++E    IAQAN +LD++  F ++LV  R A E  L+  +++D 
Sbjct: 11   KVINGKVTDEIMYLSAIDEAEHVIAQANVALDKNNKFVDDLVAVRHASEFELMSPDRVDL 70

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +D SP+QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP+L+AE P VGTG+ESVVA+ S
Sbjct: 71   MDVSPQQVVSIAASLIPFLEHDDANRALMGSNMQRQAVPVLRAEKPLVGTGLESVVARDS 130

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            G  IVAK +G+VE VDA RIV+R  +     S S  D+Y L+K+ RSNQNTC+NQRP+VK
Sbjct: 131  GVCIVAKNSGVVESVDASRIVVRVTDK---KSKSASDVYNLVKYTRSNQNTCINQRPIVK 187

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            +GD V+  D++ADGPS D G+LALG+N+ +AFMPW+GYNFEDS+LISE++  ED FTSIH
Sbjct: 188  IGDTVKVGDVLADGPSVDNGELALGQNIRIAFMPWNGYNFEDSILISEKVAREDRFTSIH 247

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I+E   +ARDTKLG EEIT DIPNV E  L  +D+CGI+ VGAEV PGDILVGKITPKGE
Sbjct: 248  IQEIVCVARDTKLGSEEITADIPNVGEGSLNKLDDCGIVYVGAEVVPGDILVGKITPKGE 307

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + ++PEEKLLRAIFGEKA DV+DTS R  S   GTV+ V +F R G++K+ER+ ++E++ 
Sbjct: 308  TQLSPEEKLLRAIFGEKASDVKDTSQR--SSSKGTVIGVEVFTRDGVEKDERTQAIEQDH 365

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            ++   +D DDE +++++   +RL E+L G+ A+ G  G KK   L+ D +     +  + 
Sbjct: 366  LDQSKKDADDEAMVVEQATKTRLCELLKGKKAIKG-NGVKKGETLTQDKLESLELNDIFS 424

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                 + V   +E  +  Y      ++ RF+ K  KI  G D+ PGV+++VKV++A+KR 
Sbjct: 425  IRTDADNVNDVIEDTEKSYNEYVKDIKTRFEEKKAKIIRGHDLAPGVIKIVKVYLAIKRR 484

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKG++S I+P EDMP+  +G PVDIVLNPLGVPSRMNVGQ+ ETH+G 
Sbjct: 485  IQPGDKMAGRHGNKGVISEIMPVEDMPYDDNGNPVDIVLNPLGVPSRMNVGQVLETHMGC 544

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS-HTEKISDYDDDSVLRVAEQWKS 1202
            A  G+G+KI S++   KAN   + L+ +L+++    + + E IS ++++ +L +A   K 
Sbjct: 545  AAKGIGEKIDSML---KANAKPAELKDYLDQLYNKNAANKEDISSFNNNEILELANNLKD 601

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+P++TPVFDGA E  +  +L++ADL ESGQ  LYDG TG  FDRPVTVGY+Y++KLNH+
Sbjct: 602  GLPIATPVFDGAKESEVKDLLKLADLPESGQFTLYDGRTGTKFDRPVTVGYMYIIKLNHL 661

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW +
Sbjct: 662  VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWAL 701


>gi|238018615|ref|ZP_04599041.1| hypothetical protein VEIDISOL_00450 [Veillonella dispar ATCC 17748]
 gi|237865086|gb|EEP66376.1| hypothetical protein VEIDISOL_00450 [Veillonella dispar ATCC 17748]
          Length = 1376

 Score =  800 bits (2067), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/966 (44%), Positives = 585/966 (60%), Gaps = 107/966 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E+I +P L+++Q+ SY+ FL            GLQ  F  + PI   SG
Sbjct: 9   KRTRYTYAKINEVIKMPHLLDIQRKSYEWFL----------ESGLQNIFNDISPIKDNSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+D+++C  RD TYA PL++ +RL+  D +         DIKEQ +
Sbjct: 59  NLVLSFEGFSLGEPKYDINECKNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEV 111

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G 
Sbjct: 112 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGA 168

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWC 246
           W+++E D+ +++ VRIDR RK+P T  + ALG D+ E IL  F+            D   
Sbjct: 169 WIELETDASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERI 228

Query: 247 FPLSAADLMV--GAKVSSSLVDIDTGE-QVIESGKKL-----TSGLLKSLKEKGVKFLGI 298
                 D        +      +  GE   +ES + L        L +  + K  K LG 
Sbjct: 229 VRTLEKDTTQSADEALVEIYKKLRPGEPPTVESARNLFFDARRYDLARVGRYKLNKKLGW 288

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               + G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI
Sbjct: 289 -RQRMLGQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYI 341

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N    +      +  L                              YD  TV R     
Sbjct: 342 VNNDGVESKVICNNCNL-----------------------------PYDHRTVTR----- 367

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                          ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+G
Sbjct: 368 ---------------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIG 412

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH 
Sbjct: 413 LTRMERVVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHK 472

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFI
Sbjct: 473 RRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFI 532

Query: 599 ETPYRKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           E PYRKV                 VT+ VVY++A EEE   IAQANS +D +G FT E V
Sbjct: 533 EAPYRKVEKIYGTGADADKVVKVRVTDSVVYMTADEEEGMTIAQANSPIDAEGYFTNEHV 592

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR   + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+
Sbjct: 593 ACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLR 652

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           A+AP VGTGME   A  SG  ++A+ AG V +     I +         S   VD+YR+ 
Sbjct: 653 AQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDVYRMN 706

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED
Sbjct: 707 KFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYED 766

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+G
Sbjct: 767 AILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEEGIICIG 826

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV+PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F
Sbjct: 827 AEVHPGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVF 886

Query: 946 NRHGID 951
            R   D
Sbjct: 887 TRENGD 892



 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 104/193 (53%), Positives = 140/193 (72%), Gaps = 1/193 (0%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E+ +   L +A   + G+++LYDG TGEP D  V
Sbjct: 1132 DYETYGMPKPDVAGIHIATPVFDGAHEKDVFETLGIAGRSDDGKTVLYDGRTGEPMDNRV 1191

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1192 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1251

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT+KSDDVVGR + YE IV G +  E G PESF VL+KE+Q++GL + + N   +
Sbjct: 1252 TLQELLTVKSDDVVGRVKAYEKIVKGENIPEPGVPESFKVLLKELQSIGLDVKILNED-Q 1310

Query: 1370 NSAKMEEIPDFNK 1382
                M+E+ D ++
Sbjct: 1311 EEVVMKELDDEDE 1323



 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 173/847 (20%), Positives = 293/847 (34%), Gaps = 68/847 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 194  VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 249

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F    FD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 250  KLRPGEPPTVESARNLF----FDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 305

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 306  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 364

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQGGVARARAGVE 557
                     +            L  L +       I H   RRL  +G+           
Sbjct: 365  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGEL-------LQN 407

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
               +  T   R+      E   I  + S+T  A +N         R V          + 
Sbjct: 408  QFRIGLTRMERVV----RERMTIQEIESITPQALINI--------RPVVAAIK----EFF 451

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             + +           +          L     + E        +          +     
Sbjct: 452  GSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG 511

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV-----VAKSSGAAIVAKRA 732
              P +   +S       N         +      GTG ++          S   + A   
Sbjct: 512  --PNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGTGADADKVVKVRVTDSVVYMTADEE 569

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
              +    A   +        +          L           V+ + +V +G       
Sbjct: 570  EGMTIAQANSPIDAEGYFTNEHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFL 629

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 630  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 689

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  ++ R    +        ++  I+  G  V  G +L       G   +  
Sbjct: 690  IHVLRDSDGRVDVYRMNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 748

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
               +L A    +  +  D  L         +        +  D  +  +  E    EL  
Sbjct: 749  GYNVLVAFMPWEGYNYEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPN 808

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
               D  + + +  I      I  G     G     K+T      +   P  +  +    D
Sbjct: 809  TGDDTLKNLDEEGI------ICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFGD 860

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            ++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  GD
Sbjct: 861  KEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEGD 916

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  GL
Sbjct: 917  KMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQGL 976

Query: 1149 GKKIKSL 1155
            G KIK+ 
Sbjct: 977  GMKIKAT 983


>gi|303231251|ref|ZP_07317989.1| DNA-directed RNA polymerase, beta subunit [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514158|gb|EFL56162.1| DNA-directed RNA polymerase, beta subunit [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 1382

 Score =  800 bits (2066), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/969 (43%), Positives = 574/969 (59%), Gaps = 109/969 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E+I +P L+++Q+ SY+ FL            GLQ  F  + PI   SG
Sbjct: 9   KRTRYTYAKINEVIKMPHLLDIQRKSYEWFL----------ESGLQNIFNDISPIKDNSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+D+++C  RD TYA PL++ +RL+  D +         DIKEQ +
Sbjct: 59  NLVLSFEGFSLGEPKYDINECKNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEV 111

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG+++  +       G  LY   +IP++G 
Sbjct: 112 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYGKEID---TMGNRLYESTVIPNRGA 168

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWC 246
           W+++E D+ +++ VRIDR RK+P T  + ALG D+ E IL  F+            D   
Sbjct: 169 WIELETDASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGQTDEDGLPVYDERI 228

Query: 247 FPLSAADLMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                 D        +      +  GE   +ES + L   L    +   +  +G      
Sbjct: 229 VRTLEKDTTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNK 288

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  + G  +A+ IV+ ETGEI ++AG  + E+ L+ +  S       ++       
Sbjct: 289 KLGWRQRMLGQTLAQPIVDTETGEIILDAGVQVGEEQLDIVAKSG------VFSGEGFAE 342

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            YI N+          +  L+                                       
Sbjct: 343 FYITNSDGVVSKIICNNCNLEFNHR----------------------------------- 367

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                          + +ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+
Sbjct: 368 --------------TVTREDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQF 413

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +
Sbjct: 414 RIGLTRMERVVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAEL 473

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +
Sbjct: 474 THKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEF 533

Query: 596 GFIETPYRKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           GFIE PYRKV                 V+  V Y++A EEE   IAQANS LD DG F  
Sbjct: 534 GFIEAPYRKVEKIYGEGADVDKVVKVRVSESVAYMTADEEEGMTIAQANSPLDADGCFAN 593

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           + V CR   + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVP
Sbjct: 594 DHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVP 653

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL+A+AP VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y
Sbjct: 654 LLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTY 707

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           RL KF RSNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN
Sbjct: 708 RLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGFNVLVAFMPWEGYN 767

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++L+SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GII
Sbjct: 768 YEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGII 827

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           C+GAEV+PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV
Sbjct: 828 CIGAEVHPGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGECGKVVDV 887

Query: 943 RIFNRHGID 951
           ++F R   D
Sbjct: 888 KVFTRENGD 896



 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 104/193 (53%), Positives = 140/193 (72%), Gaps = 1/193 (0%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E+ +   L +A   + G+++LYDG TGEP D  V
Sbjct: 1136 DYDTYGMPKPDVAGIHIATPVFDGAHEKDVFETLDIAGRPDDGKTVLYDGRTGEPMDNRV 1195

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1196 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1255

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT+KSDDVVGR + YE IV G +  E G PESF VL+KE+Q++GL + + N   +
Sbjct: 1256 TLQELLTVKSDDVVGRVKAYEKIVKGENIPEPGVPESFKVLLKELQSIGLDVKILNED-Q 1314

Query: 1370 NSAKMEEIPDFNK 1382
                M+E+ D ++
Sbjct: 1315 EEVVMKELDDEDE 1327



 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 103/379 (27%), Positives = 158/379 (41%), Gaps = 19/379 (5%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L A  P  G   E   +      +++ +    +     E+       G
Sbjct: 643  MGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRDSDG 702

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  R    +        ++  I+  G  V  G +L       G   +     +L A  
Sbjct: 703  RVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELALGFNVLVAFM 761

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-ELLARDKDDEQ 975
              +  +  D  L           D+    +    + + R   +  E+I   L    DD  
Sbjct: 762  PWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTL 818

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD +       I  G     G     K+T      +   P  +  +    D++ +   
Sbjct: 819  KNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFGDKEREVRD 871

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V +     +++     K+   + GD++ PGV ++V+V++A KR I  GDKMAGRHG
Sbjct: 872  TSLRVPHGECGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEGDKMAGRHG 927

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  GLG KIK+ 
Sbjct: 928  NKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQGLGMKIKAT 987

Query: 1156 INDYKANGDISPLRSFLEK 1174
                +     +       +
Sbjct: 988  DLHIQNVLKEARTDESYWE 1006


>gi|17225228|gb|AAL37307.1| RNA polymerase B-subunit [Staphylococcus intermedius]
          Length = 1156

 Score =  800 bits (2066), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/937 (45%), Positives = 579/937 (61%), Gaps = 79/937 (8%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +LIE+   SYD FL           EGL   F+ + PI  F+G   LEFV Y    PK+D
Sbjct: 1   NLIEIXTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYD 50

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
           +++   RD TYA PL++ +RLI+         K   ++K+Q ++MGD PLMT+ GTFVI 
Sbjct: 51  LEESKNRDATYAAPLRVKVRLII---------KETGEVKDQEVFMGDFPLMTETGTFVIN 101

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQL RSP ++F+    +   +G + Y   +IP++G W++ E D+KD+++VRID
Sbjct: 102 GAERVIVSQLVRSPSVYFNEKLDK---NGCVNYDATVIPNRGAWLEYETDAKDVVYVRID 158

Query: 208 RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R RK+P+T  L ALG  ++ EI+             +      +   L+           
Sbjct: 159 RTRKLPLTVLLRALGYSTDQEIIELIGDNEYLRNTLEKDSTENTEQALL------EIYER 212

Query: 267 IDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG--------ITSDCLCGLYVAEDIVNGET 317
           +  GE   +E+ K L        K   +  +G             L    +AE IVN ET
Sbjct: 213 LRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKHRLFNQKLAEPIVNTET 272

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           GEI  E G V+D + L+EI                            D  +   +A +  
Sbjct: 273 GEIVAEEGTVLDRRKLDEIM---------------------------DVLETNANAQVYE 305

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           +      +        S+  ++  D ++   + +G              +V+ I   DI+
Sbjct: 306 HSKRIIDEPVEIQ---SIKVYVPNDDEERTTTVIGN--------AFPDSEVKCITPADIV 354

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D DS
Sbjct: 355 ASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS 414

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E
Sbjct: 415 ITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 474

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVV 615
           +RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + 
Sbjct: 475 VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIETNTITDQID 534

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +EK+D++D SPKQVVS A
Sbjct: 535 YLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAA 594

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            + IPFLENDDSNR LMG NMQRQAVPLL  E+PFVGTGME V A+ SGAA+++K  G V
Sbjct: 595 TACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGAAVISKYRGRV 654

Query: 736 EQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           E V +  I++R  VE +       +D Y L KF+RSN  TC NQRP++  GD V + +I+
Sbjct: 655 EHVQSSEILVRRLVEENGQEVDGTLDRYPLAKFKRSNSGTCYNQRPIIAKGDIVEKGEIL 714

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPS +LG++ALG+     FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDT
Sbjct: 715 ADGPSMELGEMALGQKRSSWFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDT 774

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL 
Sbjct: 775 KLGPEEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLH 834

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 835 AIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGD 871



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 157/428 (36%), Positives = 217/428 (50%), Gaps = 59/428 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 755  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDIL 814

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 815  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDSL 874

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 875  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 934

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 935  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------------------ 976

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 977  -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 1000

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1001 NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1060

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1061 AAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1120

Query: 1367 RTKNSAKM 1374
            +       
Sbjct: 1121 QDNEIEMR 1128


>gi|256852028|ref|ZP_05557415.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260661403|ref|ZP_05862316.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           115-3-CHN]
 gi|256615440|gb|EEU20630.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260547858|gb|EEX23835.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           115-3-CHN]
          Length = 1212

 Score =  800 bits (2065), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/963 (42%), Positives = 571/963 (59%), Gaps = 83/963 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G  R R+ F    E++ +P+L +VQ  SY  FL          NEG+   F+ +
Sbjct: 6   GHLVNYGQHRTRRSFSHIKEVVKLPNLTDVQTESYKWFL----------NEGISEVFEDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG   L+FV Y+    K  +D+    D  YA PL++TL+L              
Sbjct: 56  MPINDFSGKLSLDFVGYKLQDAKSTIDEARNHDANYAAPLRVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ GDLPLMT+ G+FVI G +R++VSQL RSPG++++ D  +   + + ++  
Sbjct: 107 GEIKTQDVFFGDLPLMTRSGSFVINGAERVIVSQLVRSPGVYYNCDVDK---NARQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYS 239
            +IP++G W++ E D+K+I +VRIDR RK+P++  + ALG  S+  +   Y     + ++
Sbjct: 164 TVIPNRGAWLEYETDAKNISYVRIDRTRKLPISVLIRALGFGSDSEIQDIYGTNDTLQFT 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 224 LEKD---VHNNPADSRVAEALKEIYERLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGEI  + G ++    +E +          L  D
Sbjct: 281 YKINKKLSLKSRLLNQTLAETLADPDTGEIIAKKGTIVTHAVMETLEKY-------LDRD 333

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +    D+   +    +   +V    +                         
Sbjct: 334 DFKMVTYTPS----DEGVMQDPITVQEIKVFSKVNP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++ +  N     DV+ I   DI+A I     L++  G+ DDID+LGNRR+R VGE+
Sbjct: 366 --EREVKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +P+V++V EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 484 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E L+  R
Sbjct: 544 IINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKENLILAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A
Sbjct: 604 HKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SG A+VA+ AG+VE VDA +I IR  +G LD        Y L K++
Sbjct: 664 ALVGTGMEYRAAHDSGDALVAEAAGVVEYVDADQIRIRREDGTLDK-------YELEKYR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN N   NQ P VK G+++   ++IA+GPS   G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 717 RSNANKNYNQTPNVKKGEKIVEGEVIANGPSMAEGELALGQNPLIAFMTWNMYNYEDAIM 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 777 ISERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEQGIVRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V +F R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVEVFTRE 896

Query: 949 GID 951
           G D
Sbjct: 897 GGD 899



 Score =  503 bits (1294), Expect = e-139,   Method: Composition-based stats.
 Identities = 253/1089 (23%), Positives = 391/1089 (35%), Gaps = 148/1089 (13%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + I A     +  +++I+ +       L  D  NN A          +    +AL +IY 
Sbjct: 197  VLIRALGFGSDSEIQDIYGTNDTLQFTLEKDVHNNPA----------DSRVAEALKEIYE 246

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-------- 431
             +RPG+  T   + S+    FFDS +YDL+ VGR K+N +L+L +    + +        
Sbjct: 247  RLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINKKLSLKSRLLNQTLAETLADPD 306

Query: 432  ------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                            +  + K L        T    D    +   +V E +K   ++  
Sbjct: 307  TGEIIAKKGTIVTHAVMETLEKYLDRDDFKMVTYTPSDEGVMQDPITVQE-IKVFSKVNP 365

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I       D+  + P D+         +   +        L             
Sbjct: 366  EREVKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGELLQ 425

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 426  NQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPL 485

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             +SA+        +A   + +        +      E   
Sbjct: 486  GELTHKRR-------------MSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPN 532

Query: 656  V--PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +        +   +    +      + +  +  ++++            +  A  P    
Sbjct: 533  IGLINSMATYAIINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNED 592

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G            I+A+      +V   +I    V      S +   I  L     +   
Sbjct: 593  G------SFKENLILARHKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRAL 646

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               N +        V   +  A    T +   A   +         G           R+
Sbjct: 647  MGANHQ-----RQAVPLINPHAALVGTGMEYRAAHDSGDALVAEAAGVVEYVDAD-QIRI 700

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              ED      ++++E+  +  +    +     PNV +     I E  +I  G  +  G++
Sbjct: 701  RRED----GTLDKYEL-EKYRRSNANKNYNQTPNVKKGE--KIVEGEVIANGPSMAEGEL 753

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G                      E A+ + +  ++     S  + D     R      
Sbjct: 754  ALG-------QNPLIAFMTWNMYNYEDAIMISERMVKDDVYTSIHIEDYESEARDTKLGP 806

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DEQ I+      +  +IL G+    G         L   + 
Sbjct: 807  EEITREIPNVGEDALKDL-DEQGIVRIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIF 865

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R    +      +V      +    E             +   + GD++ PGV  +
Sbjct: 866  GEKAR----EVRDTSLRVPHGGGGIVQNVE-------------VFTREGGDELSPGVNTM 908

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++  KR IQ GDKMAGRHGNKG ++ ++P EDMPFL DG PVDI LNP+GVPSRMN+
Sbjct: 909  VRVYICQKRKIQVGDKMAGRHGNKGTIAVVVPEEDMPFLPDGRPVDICLNPMGVPSRMNI 968

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  + + + D     ++                            
Sbjct: 969  GQVLELHLGMAARQLGIHVATPVFDGADEDEVYNTLREAGMSKDGK-------------- 1014

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPF   V+VG 
Sbjct: 1015 --------------TVIYDG--------------------------RTGEPFHNRVSVGV 1034

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +  LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1035 MNYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1094

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K    
Sbjct: 1095 ILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMDHKEIEL 1154

Query: 1374 MEEIPDFNK 1382
             +   D ++
Sbjct: 1155 RDMDEDSSE 1163


>gi|284047725|ref|YP_003398064.1| DNA-directed RNA polymerase, beta subunit [Acidaminococcus
           fermentans DSM 20731]
 gi|283951946|gb|ADB46749.1| DNA-directed RNA polymerase, beta subunit [Acidaminococcus
           fermentans DSM 20731]
          Length = 1244

 Score =  799 bits (2064), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/976 (43%), Positives = 585/976 (59%), Gaps = 104/976 (10%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R+R  + +  E++ +P LI++Q+ SY+ F+           EGL   FK V PI  F+  
Sbjct: 10  RIRYSYARIKEVLKMPHLIDLQRKSYEWFIR----------EGLHDVFKDVSPIKDFTDN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F ++    PK+D++ C  +D TYA PL + +RL+  D           +IKE +++
Sbjct: 60  LELSFENFTIGDPKYDIETCKEKDATYAAPLNVDVRLLYKD---------TGEIKESTVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTFVI G +R++VSQL RSPG+++  D       GK LY   +IP++G W
Sbjct: 111 MGDFPLMTDTGTFVINGAERVIVSQLVRSPGVYYAKDMD---PMGKFLYGTTVIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY--SQRGDFWCFP 248
           ++ E D  DII+ R+DR RK+P T+ L  +G+  +++I+ TF        +   D     
Sbjct: 168 IEYETDLNDIIYARVDRTRKLPATALLRVMGLPTNDDIIQTFGEHPFLMATLAKDTTKNE 227

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
             A   +          +++   Q+I++         L    + K  K LG     L G 
Sbjct: 228 EDALLEIYRKLRPGEPANLENAAQLIKNIFSDNRRYDLANVGRYKVNKKLGW-RQRLLGK 286

Query: 307 YV----AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +    A +  +G  GE+ + AG +I              +I  +    + +        
Sbjct: 287 ELTSPIAFENPDGTRGEVVLPAGTII-----------GDEEIDKIEQSGIYSQPGYAEVW 335

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
           V  + K  +                                              M +  
Sbjct: 336 VKYQEKPEQ----------------------------------------------MIVTK 349

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D    VR I   D+IA    L+++ +G    DDID+LGNRRVR VGE+L+NQ+R+GL RM
Sbjct: 350 DIDSSVRVITPADVIASFAYLLNVIDGMEGKDDIDHLGNRRVRCVGELLQNQFRIGLSRM 409

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER I+ER++  D D + PQ LIN +PVV+AV EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 410 ERVIRERMTLQDADVITPQALINIRPVVAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLS 469

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL ++  VN YGFIETPY
Sbjct: 470 ALGPGGLSRERAGYEVRDVHVSHYGRMCPIETPEGPNIGLIGSLAAYGVVNRYGFIETPY 529

Query: 603 RKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV     KVTN++VY++A EE+N  +AQAN  L++DG+F    V CR   + + +P  +
Sbjct: 530 RKVDKKTGKVTNEIVYMTADEEDNYIVAQANEPLNDDGTFVNSHVTCRERNDVLSIPPSR 589

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +DF+D SPKQV+SIAA+LIPFLENDD+NR LMG NMQRQAVPLL  +AP VGTGME  VA
Sbjct: 590 VDFMDVSPKQVMSIAAALIPFLENDDANRALMGANMQRQAVPLLNPKAPVVGTGMEYKVA 649

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  I+AK AG V+ V   +I++   +G      +G+D Y ++KF+RSNQ+TCVNQRP
Sbjct: 650 VDSGVCILAKHAGTVKYVSGDKIIVTRADG------AGIDEYNVLKFKRSNQSTCVNQRP 703

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD+V    ++ADGP+TD G+LALGRN + A+MPW GYN+ED++L+SE +V EDVFT
Sbjct: 704 IVFKGDKVEEGQVLADGPATDHGELALGRNAIAAYMPWEGYNYEDAVLLSEDLVKEDVFT 763

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+   ARDTKLGPEEITRDIPNVSEE LK++DE GII +GAEV PGDILVGK+TP
Sbjct: 764 SIHIEEYNCDARDTKLGPEEITRDIPNVSEEALKDLDEDGIIRIGAEVRPGDILVGKVTP 823

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKN 953
           KGE+ ++ EE+L+RAIF EKA +VRD+SLRVP G SG +V V+IF R        G+ K 
Sbjct: 824 KGETELSAEERLIRAIFAEKAREVRDSSLRVPHGESGIIVSVQIFTRENGDELPPGVSKQ 883

Query: 954 ERSISVEREQIELLAR 969
            R   V++ +I    +
Sbjct: 884 VRVHIVQKRKISEGDK 899



 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 207/573 (36%), Positives = 275/573 (47%), Gaps = 50/573 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE---FEVMARDTKL 856
                       +L    P  G   E  + +   +                  ++ R    
Sbjct: 621  MGANMQRQAVPLLNPKAPVVGTGMEYKVAVDSGVCILAKHAGTVKYVSGDKIIVTRADGA 680

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +E        S +    +++  I+  G +V  G +L           +      + A 
Sbjct: 681  GIDEYNVLKFKRSNQS-TCVNQRPIVFKGDKVEEGQVLADGP-ATDHGELALGRNAIAAY 738

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARD 970
               +  +  D  L     V   V        +  D  +  +  E          E   +D
Sbjct: 739  MPWEGYNYEDAVLLSEDLVKEDVFTSIHIEEYNCDARDTKLGPEEITRDIPNVSEEALKD 798

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      R  +IL G+    G         L   + +E  R    +      +
Sbjct: 799  L-DEDGIIRIGAEVRPGDILVGKVTPKGETELSAEERLIRAIFAEKAR----EVRDSSLR 853

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V      + V               +I   + GD++PPGV + V+V +  KR I  GDKM
Sbjct: 854  VPHGESGIIVSV-------------QIFTRENGDELPPGVSKQVRVHIVQKRKISEGDKM 900

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG+VSRI+P EDMPFL +G PV IVLNPLGVPSRMN+GQI E HLGWA   LG 
Sbjct: 901  AGRHGNKGVVSRIMPREDMPFLPNGEPVQIVLNPLGVPSRMNIGQILEAHLGWAACALGM 960

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +I+S                            E      D     + E     VPV+ PV
Sbjct: 961  RIESG---------------------DPKLAGELKEAGYDVDKYGMPETVDHAVPVAVPV 999

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FD A E+ +   L++A +D SG++ LYDG TGEPFD PVTVG IY LKL+H+V+DK++AR
Sbjct: 1000 FDSAREDDMEKTLQLAGVDPSGKTTLYDGRTGEPFDNPVTVGCIYYLKLHHLVADKIHAR 1059

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE
Sbjct: 1060 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYE 1119

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +IV G +  E G PESF VLVKEMQ++GL I +
Sbjct: 1120 AIVKGENIPEPGVPESFKVLVKEMQSIGLDIQV 1152


>gi|260664845|ref|ZP_05865696.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           SJ-7A-US]
 gi|260561328|gb|EEX27301.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           SJ-7A-US]
          Length = 1212

 Score =  799 bits (2063), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/963 (42%), Positives = 571/963 (59%), Gaps = 83/963 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G  R R+ F    E++ +P+L +VQ  SY  FL          NEG+   F+ +
Sbjct: 6   GHLVNYGQHRTRRSFSHIKEVVKLPNLTDVQTESYKWFL----------NEGISEVFEDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG   L+FV Y+    K  +D+    D  YA PL++TL+L              
Sbjct: 56  MPINDFSGKLSLDFVGYKLQDAKSTIDEARNHDANYAAPLRVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ GDLPLMT+ G+FVI G +R++VSQL RSPG++++ D  +   + + ++  
Sbjct: 107 GEIKTQDVFFGDLPLMTRSGSFVINGAERVIVSQLVRSPGVYYNCDVDK---NARQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYS 239
            +IP++G W++ E D+K+I +VRIDR RK+P++  + ALG  S+  +   Y     + ++
Sbjct: 164 TVIPNRGAWLEYETDAKNISYVRIDRTRKLPISVLIRALGFGSDSEIQDIYGTNDTLQFT 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 224 LEKD---VHNNPADSRVAEALKEIYERLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGEI  + G ++    +E +          L  D
Sbjct: 281 YKINKKLSLKSRLLNQTLAETLADPDTGEIIAKKGTIVTHAVMETLEKY-------LDRD 333

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +    D+   +    +   +V    +                         
Sbjct: 334 DFKMVTYTPS----DEGVMQDPITVQEIKVFSKVNP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++ +  N     DV+ I   DI+A I     L++  G+ DDID+LGNRR+R VGE+
Sbjct: 366 --EREVKLISNGHINADVKCITPADILASINYFFALQDEIGSTDDIDHLGNRRIRRVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +P+V++V EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 484 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E L+  R
Sbjct: 544 IINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKENLILAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A
Sbjct: 604 HKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SG A+VA+ AG+VE VDA +I IR  +G LD        Y L K++
Sbjct: 664 ALVGTGMEYRAAHDSGDALVAEAAGVVEYVDADQIRIRREDGTLDK-------YELEKYR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN N   NQ P VK G+++   ++IA+GPS   G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 717 RSNANKNYNQTPNVKKGEKIVEGEVIANGPSMAEGELALGQNPLIAFMTWNMYNYEDAIM 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 777 ISERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEQGIVRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V +F R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVEVFTRE 896

Query: 949 GID 951
           G D
Sbjct: 897 GGD 899



 Score =  503 bits (1294), Expect = e-139,   Method: Composition-based stats.
 Identities = 253/1089 (23%), Positives = 392/1089 (35%), Gaps = 148/1089 (13%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + I A     +  +++I+ +       L  D  NN A          +    +AL +IY 
Sbjct: 197  VLIRALGFGSDSEIQDIYGTNDTLQFTLEKDVHNNPA----------DSRVAEALKEIYE 246

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-------- 431
             +RPG+  T   + S+    FFDS +YDL+ VGR K+N +L+L +    + +        
Sbjct: 247  RLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINKKLSLKSRLLNQTLAETLADPD 306

Query: 432  ------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                            +  + K L        T    D    +   +V E +K   ++  
Sbjct: 307  TGEIIAKKGTIVTHAVMETLEKYLDRDDFKMVTYTPSDEGVMQDPITVQE-IKVFSKVNP 365

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   +        L             
Sbjct: 366  EREVKLISNGHINADVKCITPADILASINYFFALQDEIGSTDDIDHLGNRRIRRVGELLQ 425

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 426  NQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPL 485

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             +SA+        +A   + +        +      E   
Sbjct: 486  GELTHKRR-------------MSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPN 532

Query: 656  V--PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +        +   +    +      + +  +  ++++            +  A  P    
Sbjct: 533  IGLINSMATYAIINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNED 592

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G            I+A+      +V   +I    V      S +   I  L     +   
Sbjct: 593  G------SFKENLILARHKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRAL 646

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               N +        V   +  A    T +   A   +         G           R+
Sbjct: 647  MGANHQ-----RQAVPLINPHAALVGTGMEYRAAHDSGDALVAEAAGVVEYVDAD-QIRI 700

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              ED      ++++E+  +  +    +     PNV +     I E  +I  G  +  G++
Sbjct: 701  RRED----GTLDKYEL-EKYRRSNANKNYNQTPNVKKGE--KIVEGEVIANGPSMAEGEL 753

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G                      E A+ + +  ++     S  + D     R      
Sbjct: 754  ALG-------QNPLIAFMTWNMYNYEDAIMISERMVKDDVYTSIHIEDYESEARDTKLGP 806

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DEQ I+      +  +IL G+    G         L   + 
Sbjct: 807  EEITREIPNVGEDALKDL-DEQGIVRIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIF 865

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R    +      +V      +    E             +   + GD++ PGV  +
Sbjct: 866  GEKAR----EVRDTSLRVPHGGGGIVQNVE-------------VFTREGGDELSPGVNTM 908

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++  KR IQ GDKMAGRHGNKG ++ ++P EDMPFL DG PVDI LNP+GVPSRMN+
Sbjct: 909  VRVYICQKRKIQVGDKMAGRHGNKGTIAVVVPEEDMPFLPDGRPVDICLNPMGVPSRMNI 968

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  + + + D     ++                            
Sbjct: 969  GQVLELHLGMAARQLGIHVATPVFDGADEDEVYNTLREAGMSKDGK-------------- 1014

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPF   V+VG 
Sbjct: 1015 --------------TVIYDG--------------------------RTGEPFHNRVSVGI 1034

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +  LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1035 MNYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1094

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K    
Sbjct: 1095 ILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMDHKEIEL 1154

Query: 1374 MEEIPDFNK 1382
             +   D ++
Sbjct: 1155 RDMDEDSSE 1163


>gi|15673782|ref|NP_267957.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           lactis Il1403]
 gi|281492393|ref|YP_003354373.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           lactis KF147]
 gi|41017790|sp|Q9CEN6|RPOB_LACLA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|12724825|gb|AAK05898.1|AE006409_8 DNA-directed RNA polymerase beta chain [Lactococcus lactis subsp.
           lactis Il1403]
 gi|281376057|gb|ADA65548.1| DNA-directed RNA polymerase, beta chain [Lactococcus lactis subsp.
           lactis KF147]
          Length = 1196

 Score =  799 bits (2063), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 576/963 (59%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK
Sbjct: 1   MAGHDVKYGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            +FPI  F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K
Sbjct: 51  EMFPIDNFAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +A  +G   +
Sbjct: 102 ETGELKTQEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKADKNGLESF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
               IP++G W +++ D+K I +VRIDR RK+  T+ L ALG  S+E IL       + +
Sbjct: 159 GHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDEEILELLGETQLLT 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                     + AD  V   +      +  GE    +S + L        K      +G 
Sbjct: 219 DTIAKD-VHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPKRYDFAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE IV+ ETGEI +    ++    L+ I              
Sbjct: 278 YKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPL----------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         +D     +   L   +V  P D        S                
Sbjct: 327 -LDNGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDPERVVTLLS---------------- 369

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                     N +   + R +   D+I+ I   + L  G G +DDID+LGNRR+RSVGE+
Sbjct: 370 ----------NGNPDAECRVLTPADVISNISYWLGLAEGIGKVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER I+ER+SS + +++ PQ LIN +PV +++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQVRIGLSRMERVIRERMSSSENENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RR SALG GG++R RA  E+RDVH THYGR+CP ET EG NIGL+++L+S+A
Sbjct: 480 PLSELSHKRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFI +PYR+V   +G VT++V YL+A EE+N  +AQANS L ED  F  E V  R
Sbjct: 540 KVNEYGFIMSPYRRVDRVNGVVTDEVEYLTADEEDNYTVAQANSPLTEDSRFANETVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G  I V     D++D SPKQV+++AA+ IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HTGNNIEVEASTADYMDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P++GTGME   A+ SGAA++AK AG+VE VD   I +R   G+LD       IY + K++
Sbjct: 660 PWIGTGMEHQTARDSGAALIAKHAGVVEYVDGNEIRVRRTSGELD-------IYNITKYR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPL ++G++V + DIIADGPS + G++ALG+N LVA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRPLARLGEKVEKGDIIADGPSMENGEMALGQNPLVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER++ +DV+TSI IEE+E   RDTKLGPEEITR+IPNV +E LKN+DE GII +GAEV
Sbjct: 773 MSERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGDEALKNLDESGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKGE+  TPEE+LLRAIFGEKA +VRDTSLRVP G  G V DVR+F R 
Sbjct: 833 KDGDLLVGKVTPKGETDPTPEERLLRAIFGEKAREVRDTSLRVPHGGGGIVHDVRVFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 216/1114 (19%), Positives = 388/1114 (34%), Gaps = 125/1114 (11%)

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI--FHSEIRDI 344
               + G++  G T+    G +   D      G + I+    +   ++     F S+   +
Sbjct: 149  KADKNGLESFGHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDEEIL 208

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             +L    +  +   ++      +   ++AL DIY  +RPG+  T   +  +    FFD  
Sbjct: 209  ELLGETQLLTDTIAKDVHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPK 268

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YD + VGR K N +L L        + +  +      ++   +   T D +D +     
Sbjct: 269  RYDFAPVGRYKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPLLD 328

Query: 465  RSVGEMLKNQYRLGLLRME---RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              +G  +       ++      +SIK          V      N       +      S 
Sbjct: 329  NGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDPERVVTLLSNGNPDAECRVLTPADVISN 388

Query: 522  LSQLEEHVNSLSRITHT-----RRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAET 574
            +S        + ++        RR+ ++G+    + R G+    R +      R+  +E 
Sbjct: 389  ISYWLGLAEGIGKVDDIDHLGNRRIRSVGELLQNQVRIGLSRMERVIRE----RMSSSEN 444

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                  GL++     A +  +       + +      +++ +                  
Sbjct: 445  ENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHNPLSELSH------------------ 486

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMG 693
                     L     + +        + +        +       I  + N  S   +  
Sbjct: 487  ---KRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYAKVNE 543

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                      +      V   +E + A  + +     A      +   A   V+    G+
Sbjct: 544  YGFIMSPYRRVDRVNGVVTDEVEYLTADEEDNYTVAQANSPLTEDSRFANETVMARHTGN 603

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                 +    Y          +    Q   V         +  ++              +
Sbjct: 604  NIEVEASTADY---------MDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPL 654

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF----EVMARDTKLGPEEITRDIPN 867
            +    PW G   E                 +   E+    E+  R T  G  +I      
Sbjct: 655  IDPHAPWIGTGMEHQTARDSGAALIAKHAGVV--EYVDGNEIRVRRT-SGELDIYNITKY 711

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                   + ++  +  +G +V  GDI+    +      M   +  L A    +  +  D 
Sbjct: 712  RRSNSGTSYNQRPLARLGEKVEKGDIIADGPS-MENGEMALGQNPLVAYMTWEGYNFEDA 770

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +                    + K++   S+  E+ E   RD       + R I +   
Sbjct: 771  VIMS----------------ERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGD 814

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            E L   +     +      V   DL+         +   + E      E L       ++
Sbjct: 815  EALKNLDESGIIRIGA--EVKDGDLL-------VGKVTPKGETDPTPEERLL------RA 859

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            I  ++ +   +          G++  V+VF         GD++       G+   +    
Sbjct: 860  IFGEKAREVRDTSLRVPHGGGGIVHDVRVFTREN-----GDELPS-----GVNKLV---- 905

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDIS 1166
                                  R+ + Q  + H+G       G K          +    
Sbjct: 906  ----------------------RVFIAQKRKIHVGDKMAGRHGNKGVVSNIVPMEDMPYL 943

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P  + ++ ++       +++      +         G+ ++TPVFDGA +E I   ++ A
Sbjct: 944  PDGTPIDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASDEDIWDTVKEA 1003

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             + +  +++LYDG TGEPFD  ++VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1004 GMADDAKTVLYDGRTGEPFDNRISVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 1063

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA VLQE+LT KSDDV+GRTR YE+IV G    + G PES
Sbjct: 1064 AQFGGQRFGEMEVWALEAYGAANVLQEILTYKSDDVIGRTRAYEAIVKGERIPKPGLPES 1123

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VLVKE+Q+LGL + + ++        E   D 
Sbjct: 1124 FRVLVKELQSLGLDMKVLDADRNVLDLRELDEDE 1157


>gi|125624760|ref|YP_001033243.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|158512802|sp|A2RML9|RPOB_LACLM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|124493568|emb|CAL98553.1| DNA-directed RNA polymerase beta chain [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|300071560|gb|ADJ60960.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           cremoris NZ9000]
          Length = 1196

 Score =  798 bits (2062), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/963 (44%), Positives = 577/963 (59%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK
Sbjct: 1   MAGHDVKYGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            +FPI  F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K
Sbjct: 51  EMFPIDNFAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +   +G   +
Sbjct: 102 ETGELKTQEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
               IP++G W +++ D+K I +VRIDR RK+  T+ L ALG  S+ EIL       + +
Sbjct: 159 GHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDDEILELLGETQLLT 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                     + AD  V   +      +  GE    +S + L        K      +G 
Sbjct: 219 DTIAKD-VHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPKRYDFAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE IV+ ETGEI +    ++    L+ I              
Sbjct: 278 YKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLI-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  + N L     +   DA++         +  T                K     
Sbjct: 324 ----EPLLDNGLGNFVVEPSDDAVI--------PEPITLQS------------IKVYSPK 359

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +   + R +   D+I+ I   + L  G G +DDID+LGNRR+RSVGE+
Sbjct: 360 DSERVVTLLSNGNPDSECRVLTPADVISNISYWLGLAEGIGKVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER I+ER+SS + +++ PQ LIN +PV +++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQVRIGLSRMERVIRERMSSSENENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RR SALG GG++R RA  E+RDVH THYGR+CP ET EG NIGL+++L+S+A
Sbjct: 480 PLSELSHKRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFI +PYR+V   +G VT++V YL+A EE+N  +AQANS L +D  F  E V  R
Sbjct: 540 KVNEYGFIMSPYRRVDRVNGIVTDEVEYLTADEEDNYTVAQANSPLTDDSRFANETVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G  I V     D++D SPKQV+++AA+ IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HTGNNIEVEASTADYMDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P++GTGME   A+ SGAA++AK AG+VE VD   I +R   G+LD       IY + K++
Sbjct: 660 PWIGTGMEHQTARDSGAALLAKHAGVVEYVDGNEIRVRRTSGELD-------IYNITKYR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPL ++G++V +NDIIADGPS + G++ALG+N LVA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRPLARLGEKVEKNDIIADGPSMENGEMALGQNPLVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER++ +DV+TSI IEE+E   RDTKLGPEEITR+IPNV +E LKN+DE GII +GAEV
Sbjct: 773 MSERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGDEALKNLDESGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKGE+  TPEE+LLRAIFGEKA +VRDTSLRVP G  G V DVR+F R 
Sbjct: 833 KDGDLLVGKVTPKGETDPTPEERLLRAIFGEKAREVRDTSLRVPHGGGGIVHDVRVFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 215/1114 (19%), Positives = 386/1114 (34%), Gaps = 125/1114 (11%)

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI--FHSEIRDI 344
               + G++  G T+    G +   D      G + I+    +   ++     F S+   +
Sbjct: 149  KTDKNGLESFGHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDDEIL 208

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             +L    +  +   ++      +   ++AL DIY  +RPG+  T   +  +    FFD  
Sbjct: 209  ELLGETQLLTDTIAKDVHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPK 268

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YD + VGR K N +L L        + +  +      ++   +   T D +D +     
Sbjct: 269  RYDFAPVGRYKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPLLD 328

Query: 465  RSVGEMLKNQYRLGLLRME---RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              +G  +       ++      +SIK          V      N       +      S 
Sbjct: 329  NGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDSERVVTLLSNGNPDSECRVLTPADVISN 388

Query: 522  LSQLEEHVNSLSRITHT-----RRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAET 574
            +S        + ++        RR+ ++G+    + R G+    R +      R+  +E 
Sbjct: 389  ISYWLGLAEGIGKVDDIDHLGNRRIRSVGELLQNQVRIGLSRMERVIRE----RMSSSEN 444

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                  GL++     A +  +       + +      +++ +                  
Sbjct: 445  ENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHNPLSELSH------------------ 486

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMG 693
                     L     + +        + +        +       I  + N  S   +  
Sbjct: 487  ---KRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYAKVNE 543

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                      +      V   +E + A  + +     A      +   A   V+    G+
Sbjct: 544  YGFIMSPYRRVDRVNGIVTDEVEYLTADEEDNYTVAQANSPLTDDSRFANETVMARHTGN 603

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                 +    Y          +    Q   V         +  ++              +
Sbjct: 604  NIEVEASTADY---------MDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPL 654

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF----EVMARDTKLGPEEITRDIPN 867
            +    PW G   E                 +   E+    E+  R T  G  +I      
Sbjct: 655  IDPHAPWIGTGMEHQTARDSGAALLAKHAGVV--EYVDGNEIRVRRT-SGELDIYNITKY 711

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                   + ++  +  +G +V   DI+    +      M   +  L A    +  +  D 
Sbjct: 712  RRSNSGTSYNQRPLARLGEKVEKNDIIADGPS-MENGEMALGQNPLVAYMTWEGYNFEDA 770

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +                    + K++   S+  E+ E   RD       + R I +   
Sbjct: 771  VIMS----------------ERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGD 814

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            E L   +     +      V   DL+         +   + E      E L       ++
Sbjct: 815  EALKNLDESGIIRIGA--EVKDGDLL-------VGKVTPKGETDPTPEERLL------RA 859

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            I  ++ +   +          G++  V+VF         GD++       G+   +    
Sbjct: 860  IFGEKAREVRDTSLRVPHGGGGIVHDVRVFTREN-----GDELPS-----GVNKLV---- 905

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDIS 1166
                                  R+ + Q  + H+G       G K          +    
Sbjct: 906  ----------------------RVFIAQKRKIHVGDKMAGRHGNKGVVSNIVPVEDMPYL 943

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P  + ++ ++       +++      +         G+ ++TPVFDGA +E I   ++ A
Sbjct: 944  PDGTPIDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASDEDIWDTVKEA 1003

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +    +++LYDG TGEPFD  ++VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1004 GMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 1063

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA VLQE+LT KSDDV+GRTR YE+IV G    + G PES
Sbjct: 1064 AQFGGQRFGEMEVWALEAYGAANVLQEILTYKSDDVIGRTRAYEAIVKGERIPKPGLPES 1123

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VLVKE+Q+LGL + + ++        E   D 
Sbjct: 1124 FRVLVKELQSLGLDMKVLDADRNVLDLRELDEDE 1157


>gi|297205099|ref|ZP_06922495.1| DNA-directed RNA polymerase subunit beta [Lactobacillus jensenii
           JV-V16]
 gi|297149677|gb|EFH29974.1| DNA-directed RNA polymerase subunit beta [Lactobacillus jensenii
           JV-V16]
          Length = 1212

 Score =  798 bits (2062), Expect = 0.0,   Method: Composition-based stats.
 Identities = 405/963 (42%), Positives = 570/963 (59%), Gaps = 83/963 (8%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G  R R+ F    E++ +P+L +VQ  SY  FL          NEG+   F+ +
Sbjct: 6   GHLVNYGQHRTRRSFSHIKEVVKLPNLTDVQTESYKWFL----------NEGISEVFEDI 55

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG   L+FV Y+    K  +D+    D  YA PL++TL+L              
Sbjct: 56  MPINDFSGKLSLDFVGYKLQDAKSTIDEARNHDANYAAPLRVTLKLT---------NHET 106

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q ++ GDLPLMT+ G+FVI G +R++VSQL RSPG++++ D  +   + + ++  
Sbjct: 107 GEIKTQDVFFGDLPLMTRSGSFVINGAERVIVSQLVRSPGVYYNCDVDK---NARQIFGA 163

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYS 239
            +IP++G W++ E D+K+I +VRIDR RK+P++  + ALG  S+  +   Y     + ++
Sbjct: 164 TVIPNRGAWLEYETDAKNISYVRIDRTRKLPISVLIRALGFGSDSEIQDIYGTNDTLQFT 223

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D      + AD  V   +      +  GE    +S + L        +   +  +G 
Sbjct: 224 LEKD---VHNNPADSRVAEALKEIYERLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGR 280

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE + + +TGEI  + G ++    +E +          L  D
Sbjct: 281 YKINKKLSLKSRLLNQTLAETLADPDTGEIIAKKGTIVTHAVMETLEKY-------LDRD 333

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +    D+   +    +   +V    +                         
Sbjct: 334 DFKMVTYTPS----DEGVMQDPITVQEIKVFSKVNP------------------------ 365

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               ++ +  N     DV+ I   DI+A I     L++  G+ DDID+LGNRR+R VGE+
Sbjct: 366 --EREVKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGEL 423

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +P+V++V EFF SSQLSQ  +  N
Sbjct: 424 LQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNN 483

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 484 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 543

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E L+  R
Sbjct: 544 IINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKENLILAR 603

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A
Sbjct: 604 HKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHA 663

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTGME   A  SG A+VA+ AG+VE VDA +I IR  +G LD        Y L K++
Sbjct: 664 ALVGTGMEYRAAHDSGDALVAEAAGVVEYVDADQIRIRREDGTLDK-------YELEKYR 716

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN N   NQ P VK G+++   ++IA+G S   G+LALG+N L+AFM W+ YN+ED+++
Sbjct: 717 RSNANKNYNQTPNVKKGEKIVEGEVIANGSSMAEGELALGQNPLIAFMTWNMYNYEDAIM 776

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISERMV +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV
Sbjct: 777 ISERMVKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEQGIVRIGAEV 836

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V +F R 
Sbjct: 837 KDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVEVFTRE 896

Query: 949 GID 951
           G D
Sbjct: 897 GGD 899



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 253/1089 (23%), Positives = 392/1089 (35%), Gaps = 148/1089 (13%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + I A     +  +++I+ +       L  D  NN A          +    +AL +IY 
Sbjct: 197  VLIRALGFGSDSEIQDIYGTNDTLQFTLEKDVHNNPA----------DSRVAEALKEIYE 246

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-------- 431
             +RPG+  T   + S+    FFDS +YDL+ VGR K+N +L+L +    + +        
Sbjct: 247  RLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINKKLSLKSRLLNQTLAETLADPD 306

Query: 432  ------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                            +  + K L        T    D    +   +V E +K   ++  
Sbjct: 307  TGEIIAKKGTIVTHAVMETLEKYLDRDDFKMVTYTPSDEGVMQDPITVQE-IKVFSKVNP 365

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I       D+  + P D+         +   +        L             
Sbjct: 366  EREVKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGELLQ 425

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 426  NQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPL 485

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             +SA+        +A   + +        +      E   
Sbjct: 486  GELTHKRR-------------MSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPN 532

Query: 656  V--PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +        +   +    +      + +  +  ++++            +  A  P    
Sbjct: 533  IGLINSMATYAIINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNED 592

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G            I+A+      +V   +I    V      S +   I  L     +   
Sbjct: 593  G------SFKENLILARHKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRAL 646

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               N +        V   +  A    T +   A   +         G           R+
Sbjct: 647  MGANHQ-----RQAVPLINPHAALVGTGMEYRAAHDSGDALVAEAAGVVEYVDAD-QIRI 700

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              ED      ++++E+  +  +    +     PNV +     I E  +I  G+ +  G++
Sbjct: 701  RRED----GTLDKYEL-EKYRRSNANKNYNQTPNVKKGE--KIVEGEVIANGSSMAEGEL 753

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G                      E A+ + +  ++     S  + D     R      
Sbjct: 754  ALG-------QNPLIAFMTWNMYNYEDAIMISERMVKDDVYTSIHIEDYESEARDTKLGP 806

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DEQ I+      +  +IL G+    G         L   + 
Sbjct: 807  EEITREIPNVGEDALKDL-DEQGIVRIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIF 865

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R    +      +V      +    E             +   + GD++ PGV  +
Sbjct: 866  GEKAR----EVRDTSLRVPHGGGGIVQNVE-------------VFTREGGDELSPGVNTM 908

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++  KR IQ GDKMAGRHGNKG ++ ++P EDMPFL DG PVDI LNP+GVPSRMN+
Sbjct: 909  VRVYICQKRKIQVGDKMAGRHGNKGTIAVVVPEEDMPFLPDGRPVDICLNPMGVPSRMNI 968

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  + + + D     ++                            
Sbjct: 969  GQVLELHLGMAARQLGIHVATPVFDGADEDEVYNTLREAGMSKDGK-------------- 1014

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPF   V+VG 
Sbjct: 1015 --------------TVIYDG--------------------------RTGEPFHNRVSVGV 1034

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +  LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1035 MNYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1094

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K    
Sbjct: 1095 ILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMDHKEIEL 1154

Query: 1374 MEEIPDFNK 1382
             +   D ++
Sbjct: 1155 RDMDEDSSE 1163


>gi|326407288|gb|ADZ64359.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           lactis CV56]
          Length = 1196

 Score =  798 bits (2061), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/963 (44%), Positives = 575/963 (59%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   V  G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK
Sbjct: 1   MAGHDVKYGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            +FPI  F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K
Sbjct: 51  EMFPIDNFAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +A  +G   +
Sbjct: 102 ETGELKTQEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKADKNGLESF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
               IP++G W +++ D+K I +VRIDR RK+  T+ L ALG  S+E IL       + +
Sbjct: 159 GHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDEEILELLGETQLLT 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                     + AD  V   +      +  GE    +S + L        K      +G 
Sbjct: 219 DTIAKD-VHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPKRYDFAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE IV+ ETGEI +    ++    L+ I              
Sbjct: 278 YKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPL----------- 326

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++N         +D     +   L   +V  P D        S                
Sbjct: 327 -LDNGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDPERVVTLLS---------------- 369

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                     N +   + R +   D+I+ I   + L  G G +DDID+LGNRR+RSVGE+
Sbjct: 370 ----------NGNPDAECRVLTPADVISNISYWLGLAEGIGKVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER I+ER+SS + +++ PQ LIN +PV +++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQVRIGLSRMERVIRERMSSSENENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RR SALG GG++R RA  E+RDVH THYGR+CP ET EG NIGL+++L+S+A
Sbjct: 480 PLSELSHKRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFI +PYR+V   +G VT++V YL+A EE+N  +AQANS L ED  F  E V  R
Sbjct: 540 KVNEYGFIMSPYRRVDRVNGVVTDEVEYLTADEEDNYTVAQANSPLTEDSRFANETVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G  I V     D++D SPKQV+++AA+ IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HTGNNIEVEASTADYMDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P++GTGME   A+ SGAA++AK AG+VE VD   I +R   G+LD       IY + K++
Sbjct: 660 PWIGTGMEHQTARDSGAALIAKHAGVVEYVDGNEIRVRRTSGELD-------IYNITKYR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPL ++G++V + DIIADGPS   G++ALG+N LVA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRPLARLGEKVEKGDIIADGPSMVNGEMALGQNPLVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER++ +DV+TSI IEE+E   RDTKLGPEEITR+IPNV +E LKN+DE GII +GAEV
Sbjct: 773 MSERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGDEALKNLDESGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKGE+  TPEE+LLRAIFGEKA +VRDTSLRVP G  G V DVR+F R 
Sbjct: 833 KDGDLLVGKVTPKGETDPTPEERLLRAIFGEKAREVRDTSLRVPHGGGGIVHDVRVFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 216/1114 (19%), Positives = 388/1114 (34%), Gaps = 125/1114 (11%)

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI--FHSEIRDI 344
               + G++  G T+    G +   D      G + I+    +   ++     F S+   +
Sbjct: 149  KADKNGLESFGHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDEEIL 208

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             +L    +  +   ++      +   ++AL DIY  +RPG+  T   +  +    FFD  
Sbjct: 209  ELLGETQLLTDTIAKDVHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPK 268

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YD + VGR K N +L L        + +  +      ++   +   T D +D +     
Sbjct: 269  RYDFAPVGRYKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPLLD 328

Query: 465  RSVGEMLKNQYRLGLLRME---RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              +G  +       ++      +SIK          V      N       +      S 
Sbjct: 329  NGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDPERVVTLLSNGNPDAECRVLTPADVISN 388

Query: 522  LSQLEEHVNSLSRITHT-----RRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAET 574
            +S        + ++        RR+ ++G+    + R G+    R +      R+  +E 
Sbjct: 389  ISYWLGLAEGIGKVDDIDHLGNRRIRSVGELLQNQVRIGLSRMERVIRE----RMSSSEN 444

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                  GL++     A +  +       + +      +++ +                  
Sbjct: 445  ENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHNPLSELSH------------------ 486

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMG 693
                     L     + +        + +        +       I  + N  S   +  
Sbjct: 487  ---KRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYAKVNE 543

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                      +      V   +E + A  + +     A      +   A   V+    G+
Sbjct: 544  YGFIMSPYRRVDRVNGVVTDEVEYLTADEEDNYTVAQANSPLTEDSRFANETVMARHTGN 603

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                 +    Y          +    Q   V         +  ++              +
Sbjct: 604  NIEVEASTADY---------MDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPL 654

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF----EVMARDTKLGPEEITRDIPN 867
            +    PW G   E                 +   E+    E+  R T  G  +I      
Sbjct: 655  IDPHAPWIGTGMEHQTARDSGAALIAKHAGVV--EYVDGNEIRVRRT-SGELDIYNITKY 711

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                   + ++  +  +G +V  GDI+    +      M   +  L A    +  +  D 
Sbjct: 712  RRSNSGTSYNQRPLARLGEKVEKGDIIADGPS-MVNGEMALGQNPLVAYMTWEGYNFEDA 770

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +                    + K++   S+  E+ E   RD       + R I +   
Sbjct: 771  VIMS----------------ERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGD 814

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            E L   +     +      V   DL+         +   + E      E L       ++
Sbjct: 815  EALKNLDESGIIRIGA--EVKDGDLL-------VGKVTPKGETDPTPEERLL------RA 859

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            I  ++ +   +          G++  V+VF         GD++       G+   +    
Sbjct: 860  IFGEKAREVRDTSLRVPHGGGGIVHDVRVFTREN-----GDELPS-----GVNKLV---- 905

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDIS 1166
                                  R+ + Q  + H+G       G K          +    
Sbjct: 906  ----------------------RVFIAQKRKIHVGDKMAGRHGNKGVVSNIVPMEDMPYL 943

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P  + ++ ++       +++      +         G+ ++TPVFDGA +E I   ++ A
Sbjct: 944  PDGTPIDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASDEDIWDTVKEA 1003

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             + +  +++LYDG TGEPFD  ++VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1004 GMADDAKTVLYDGRTGEPFDNRISVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 1063

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA VLQE+LT KSDDV+GRTR YE+IV G    + G PES
Sbjct: 1064 AQFGGQRFGEMEVWALEAYGAANVLQEILTYKSDDVIGRTRAYEAIVKGERIPKPGLPES 1123

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VLVKE+Q+LGL + + ++        E   D 
Sbjct: 1124 FRVLVKELQSLGLDMKVLDADRNVLDLRELDEDE 1157


>gi|116512669|ref|YP_811576.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           cremoris SK11]
 gi|123025227|sp|Q02X59|RPOB_LACLS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116108323|gb|ABJ73463.1| DNA-directed RNA polymerase subunit beta [Lactococcus lactis subsp.
           cremoris SK11]
          Length = 1196

 Score =  797 bits (2058), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/963 (44%), Positives = 577/963 (59%), Gaps = 80/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA   +  G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK
Sbjct: 1   MAGHDIKYGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            +FPI  F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K
Sbjct: 51  EMFPIDNFAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +   +G   +
Sbjct: 102 ETGELKTQEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
               IP++G W +++ D+K I +VRIDR RK+  T+ L ALG  S+ EIL       + +
Sbjct: 159 GHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDDEILELLGETQLLT 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                     + AD  V   +      +  GE    +S + L        K      +G 
Sbjct: 219 DTIAKD-VHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPKRYDFAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L GL +AE IV+ ETGEI +    ++    L+ I              
Sbjct: 278 YKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLI-------------- 323

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  + N L     +   DA++         +  T                K     
Sbjct: 324 ----EPLLDNGLGNFVVEPSDDAVI--------PEPITLQS------------IKVYSPK 359

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + +  N +   + R +   D+I+ I   + L  G G +DDID+LGNRR+RSVGE+
Sbjct: 360 DSERVVTLLSNGNPDSECRVLTPADVISNISYWLGLAEGIGKVDDIDHLGNRRIRSVGEL 419

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL RMER I+ER+SS + +++ PQ LIN +PV +++ EFF SSQLSQ  +  N
Sbjct: 420 LQNQVRIGLSRMERVIRERMSSSENENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHN 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ++H RR SALG GG++R RA  E+RDVH THYGR+CP ET EG NIGL+++L+S+A
Sbjct: 480 PLSELSHKRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYA 539

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +VN YGFI +PYR+V   +G VT++V YL+A EE+N  +AQANS L +D  F  E V  R
Sbjct: 540 KVNEYGFIMSPYRRVDRVNGIVTDEVEYLTADEEDNYTVAQANSPLTDDSRFANETVMAR 599

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G  I V     D++D SPKQV+++AA+ IPFLENDDSNR LMG NMQRQAVPL+   A
Sbjct: 600 HTGNNIEVEASTADYMDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPLIDPHA 659

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P++GTGME   A+ SGAA++AK AG+VE VD   I +R   G+LD       IY + K++
Sbjct: 660 PWIGTGMEHQTARDSGAALLAKHAGVVEYVDGNEIRVRRTSGELD-------IYNITKYR 712

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQRPL ++G++V +NDIIADGPS + G++ALG+N LVA+M W GYNFED+++
Sbjct: 713 RSNSGTSYNQRPLARLGEKVEKNDIIADGPSMENGEMALGQNPLVAYMTWEGYNFEDAVI 772

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER++ +DV+TSI IEE+E   RDTKLGPEEITR+IPNV +E LKN+DE GII +GAEV
Sbjct: 773 MSERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGDEALKNLDESGIIRIGAEV 832

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKGE+  TPEE+LLRAIFGEKA +VRDTSLRVP G  G V DVR+F R 
Sbjct: 833 KDGDLLVGKVTPKGETDPTPEERLLRAIFGEKAREVRDTSLRVPHGGGGIVHDVRVFTRE 892

Query: 949 GID 951
             D
Sbjct: 893 NGD 895



 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 215/1114 (19%), Positives = 386/1114 (34%), Gaps = 125/1114 (11%)

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI--FHSEIRDI 344
               + G++  G T+    G +   D      G + I+    +   ++     F S+   +
Sbjct: 149  KTDKNGLESFGHTTIPNRGAWFELDTDAKGIGYVRIDRTRKLTFTTMLRALGFGSDDEIL 208

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             +L    +  +   ++      +   ++AL DIY  +RPG+  T   +  +    FFD  
Sbjct: 209  ELLGETQLLTDTIAKDVHKNPADTRVEEALKDIYDRLRPGEPKTADSSRGLLVARFFDPK 268

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +YD + VGR K N +L L        + +  +      ++   +   T D +D +     
Sbjct: 269  RYDFAPVGRYKFNKKLALKNRLLGLTLAEPIVDPETGEILVNTDTLVTRDVLDLIEPLLD 328

Query: 465  RSVGEMLKNQYRLGLLRME---RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              +G  +       ++      +SIK          V      N       +      S 
Sbjct: 329  NGLGNFVVEPSDDAVIPEPITLQSIKVYSPKDSERVVTLLSNGNPDSECRVLTPADVISN 388

Query: 522  LSQLEEHVNSLSRITHT-----RRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAET 574
            +S        + ++        RR+ ++G+    + R G+    R +      R+  +E 
Sbjct: 389  ISYWLGLAEGIGKVDDIDHLGNRRIRSVGELLQNQVRIGLSRMERVIRE----RMSSSEN 444

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                  GL++     A +  +       + +      +++ +                  
Sbjct: 445  ENITPQGLINIRPVTASIKEFFGSSQLSQFMDQHNPLSELSH------------------ 486

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMG 693
                     L     + +        + +        +       I  + N  S   +  
Sbjct: 487  ---KRRFSALGPGGISRDRASYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYAKVNE 543

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                      +      V   +E + A  + +     A      +   A   V+    G+
Sbjct: 544  YGFIMSPYRRVDRVNGIVTDEVEYLTADEEDNYTVAQANSPLTDDSRFANETVMARHTGN 603

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                 +    Y          +    Q   V         +  ++              +
Sbjct: 604  NIEVEASTADY---------MDVSPKQVIAVAAACIPFLENDDSNRALMGANMQRQAVPL 654

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF----EVMARDTKLGPEEITRDIPN 867
            +    PW G   E                 +   E+    E+  R T  G  +I      
Sbjct: 655  IDPHAPWIGTGMEHQTARDSGAALLAKHAGVV--EYVDGNEIRVRRT-SGELDIYNITKY 711

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                   + ++  +  +G +V   DI+    +      M   +  L A    +  +  D 
Sbjct: 712  RRSNSGTSYNQRPLARLGEKVEKNDIIADGPS-MENGEMALGQNPLVAYMTWEGYNFEDA 770

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +                    + K++   S+  E+ E   RD       + R I +   
Sbjct: 771  VIMS----------------ERLIKDDVYTSIAIEEYESETRDTKLGPEEITREIPNVGD 814

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            E L   +     +      V   DL+         +   + E      E L       ++
Sbjct: 815  EALKNLDESGIIRIGA--EVKDGDLL-------VGKVTPKGETDPTPEERLL------RA 859

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            I  ++ +   +          G++  V+VF         GD++       G+   +    
Sbjct: 860  IFGEKAREVRDTSLRVPHGGGGIVHDVRVFTREN-----GDELPS-----GVNKLV---- 905

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDIS 1166
                                  R+ + Q  + H+G       G K          +    
Sbjct: 906  ----------------------RVFIAQKRKIHVGDKMAGRHGNKGVVSNIVPVEDMPYL 943

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P  + ++ ++       +++      +         G+ ++TPVFDGA +E I   ++ A
Sbjct: 944  PDGTPIDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASDEDIWDTVKEA 1003

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +    +++LYDG TGEPFD  ++VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK
Sbjct: 1004 GMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 1063

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA VLQE+LT KSDDV+GRTR YE+IV G    + G PES
Sbjct: 1064 AQFGGQRFGEMEVWALEAYGAANVLQEILTYKSDDVIGRTRAYEAIVKGERIPKPGLPES 1123

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VLVKE+Q+LGL + + ++        E   D 
Sbjct: 1124 FRVLVKELQSLGLDMKVFDADRNVLDLRELDEDE 1157


>gi|89100358|ref|ZP_01173223.1| DNA-directed RNA polymerase beta subunit [Bacillus sp. NRRL
           B-14911]
 gi|89084979|gb|EAR64115.1| DNA-directed RNA polymerase beta subunit [Bacillus sp. NRRL
           B-14911]
          Length = 1139

 Score =  797 bits (2058), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/907 (45%), Positives = 575/907 (63%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RL+        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGDPKYSVEESKERDVTYSAPLRVKVRLV-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++K+Q ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK
Sbjct: 53  -NKETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKLDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             ++  +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI+       
Sbjct: 109 RGFSATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
                 +      +   L+           +  GE   +E+ K L        K      
Sbjct: 169 YIRNTLEKDNTESTDKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI  E G ++D ++L+ I  +   +I   
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEIIAEKGTMLDRRNLDRIIPNLENNIG-- 280

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                        T          + LL   +V  P +                      
Sbjct: 281 -----------FRTAAPSGGVVEDEVLLQSIKVYAPNE---------------------- 307

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               G  ++N+  N    + V++I   DIIA I    +L +G G  DDID+LGNRR+RSV
Sbjct: 308 ---DGEKEINIIGNAYVEEAVKNIAPSDIIASIGYFFNLLHGVGDTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           SFA+VN +GFIETPYR++    G+VT+ + YL+A EE+N  +AQAN+ L +DG+F ++ V
Sbjct: 485 SFAKVNRFGFIETPYRRINPETGRVTDQIDYLTADEEDNYVVAQANARLGDDGTFLDDEV 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  +VP++++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL+
Sbjct: 545 VARFRGENTVVPKDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLQ 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRL 764
            EAP VGTGME V  K SGAA++ K  GIVE V+A  + +R +   +       +D YR+
Sbjct: 605 PEAPRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRISEVNGQEVKGDLDKYRM 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           +KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAFM W GYN+E
Sbjct: 665 LKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII  
Sbjct: 725 DAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRT 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++
Sbjct: 785 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREDGD 851



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 177/535 (33%), Positives = 246/535 (45%), Gaps = 77/535 (14%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  +        ++  I+ VG  V  G+IL    +      +     +L A 
Sbjct: 657  GDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPS-MELGELALGRNVLVAF 715

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 716  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 775

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 776  LDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR------------- 822

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                E                   K+   + GD++PPGV ++V+V++  KR I  GDKMA
Sbjct: 823  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMA 878

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++SRILP EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  
Sbjct: 879  GRHGNKGVISRILPEEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIH 938

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + S + D     D+                                          T ++
Sbjct: 939  VASPVFDGAREEDVWSTIEEAGMARDAK----------------------------TVLY 970

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG                           +GEPFD  V+VG +YM+KL HMV DK++ARS
Sbjct: 971  DG--------------------------RSGEPFDNRVSVGVMYMIKLAHMVDDKLHARS 1004

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+
Sbjct: 1005 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEA 1064

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            IV G +  E G PESF VL+KE+Q+LG+ + + +   K     +   D +  + +
Sbjct: 1065 IVKGENVPEPGVPESFRVLMKELQSLGMDVKILSGDEKEIEMRDLEDDDDVQQAE 1119


>gi|17225226|gb|AAL37306.1| RNA polymerase B-subunit [Staphylococcus caprae]
          Length = 1157

 Score =  796 bits (2057), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/938 (45%), Positives = 575/938 (61%), Gaps = 80/938 (8%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +LIE+Q  SYD FL           EGL   F+ + PI  F+G   LEFV Y    PK+D
Sbjct: 1   NLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGDPKYD 50

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
           +++   RD TYA PL++ +RLI+         K   ++KEQ ++MGD PLMT  GTFVI 
Sbjct: 51  LEESKNRDATYAAPLRVKVRLII---------KETGEVKEQEVFMGDFPLMTDTGTFVIN 101

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQL RSP ++F+    +   +G+  Y   IIP++G W++ E D+KD+++VRID
Sbjct: 102 GAERVIVSQLVRSPSVYFNEKIDK---NGRENYDATIIPNRGAWLEYETDAKDVVYVRID 158

Query: 208 RRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R RK+P+T  L AL   ++ EI+             +      +   L+           
Sbjct: 159 RTRKLPLTVLLRALDFSTDQEIVDLLGESEYLRNTLEKDGTENTEQALL------EIYER 212

Query: 267 IDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLG--------ITSDCLCGLYVAEDIVNGET 317
           +  GE   +E+ K L        K   +  +G             L    +AE IVN ET
Sbjct: 213 LRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKHRLFNQKLAEPIVNSET 272

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           GEI  E G V+D + ++EI              + N+  +     V D+  + +   + +
Sbjct: 273 GEIVAEEGTVLDRRKIDEIMDVLET--------NANSEVFELEGSVIDEPVEIQSIKVYV 324

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                                   D +    + +G              +V+ I   DII
Sbjct: 325 ----------------------PNDEEGRTTTVIGNAL--------PDSEVKCITPADII 354

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +    +L NG G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D DS
Sbjct: 355 ASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS 414

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E
Sbjct: 415 ITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 474

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVV 615
           +RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + 
Sbjct: 475 VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQID 534

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A
Sbjct: 535 YLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAA 594

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI AK  G V
Sbjct: 595 TACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRV 654

Query: 736 EQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           E V++  +++R  VE +       +D Y L KF+RSN  TC NQRP+V VGD V  N+I+
Sbjct: 655 EHVESNEVLVRRLVEENGTEHEGELDRYPLAKFKRSNSGTCYNQRPIVSVGDVVEYNEIL 714

Query: 795 ADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           ADGPS +L         +LV FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARD
Sbjct: 715 ADGPSMELRLKWHRDVTLLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARD 774

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           TKLGPEEITRDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL
Sbjct: 775 TKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLL 834

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 835 HAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGD 872



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 251/1163 (21%), Positives = 429/1163 (36%), Gaps = 114/1163 (9%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 71   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 130

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD +  + Y+
Sbjct: 131  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALDFSTDQEIVDLLGESEYL 190

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD  +YDL++VGR K N 
Sbjct: 191  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANK 250

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +L+L      + +          +I+ +           + +      +  E+ + +  +
Sbjct: 251  KLHLKHRLFNQKLAEPIVNSETGEIVAEEGTVLDRRKIDEIMDVLETNANSEVFELEGSV 310

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLIN--AKPVVSAVCEFFCSSQLSQLEEHVN---SL 532
                +E    +     D +      + N      V  +      + +S     +N     
Sbjct: 311  IDEPVEIQSIKVYVPNDEEGRTTTVIGNALPDSEVKCITPADIIASMSYFFNLLNGIGYT 370

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
              I H         G + + +  + +  +      R+   +T       L++     A +
Sbjct: 371  DDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASI 430

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +       + +       ++ +                           L       E
Sbjct: 431  KEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSALGPGGLTRE 469

Query: 653  EILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
               +    + +        +       I  + +  S   +            +  +   +
Sbjct: 470  RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSI 529

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               ++ + A    + +VA+    +             +  +        +    K    +
Sbjct: 530  TDQIDYLTADEEDSYVVAQANSRL-----DENGRFLDDEVVCRFRGNNTVMAKEKMDYMD 584

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +              +  +D        ++   A+      A     G     +     
Sbjct: 585  VSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGA 644

Query: 832  RMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNIDECGIICV 884
             + ++      H+E  EV+ R           G  +                ++  I+ V
Sbjct: 645  AITAKHRGRVEHVESNEVLVRRLVEENGTEHEGELDRYPLAKFKRSNSGTCYNQRPIVSV 704

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V   +IL    + +       +  LL         +  D  +     +S  +V   +
Sbjct: 705  GDVVEYNEILADGPSMELRLKWHRDVTLLVGFMTWDGYNYEDAVI-----MSERLVKDDV 759

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            +    I++ E      +   E + RD  +      +N+  R   +  G     G     K
Sbjct: 760  YTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYVGAEVKDGDILVGK 818

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             T      ++   R     F  +  +V+     +                 K+   + GD
Sbjct: 819  VTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVKVFNREEGD 872

Query: 1065 D-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LN
Sbjct: 873  DTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLN 932

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+                  
Sbjct: 933  PLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--------------- 977

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                      +  A   + G                             +++LYDG TGE
Sbjct: 978  ----------IEEAGMARDG-----------------------------KTVLYDGRTGE 998

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            PFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 999  PFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1058

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LT KSDD VGR + YESIV G +      PESF VL+KE+Q+LGL + +
Sbjct: 1059 AYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1118

Query: 1364 ENSRTKNSAKMEEIPDFNKCELK 1386
             + +      M ++ D +  E K
Sbjct: 1119 MDEQDNEIE-MADVDDEDATERK 1140


>gi|296126983|ref|YP_003634235.1| DNA-directed RNA polymerase, beta subunit [Brachyspira murdochii
           DSM 12563]
 gi|296018799|gb|ADG72036.1| DNA-directed RNA polymerase, beta subunit [Brachyspira murdochii
           DSM 12563]
          Length = 1173

 Score =  796 bits (2057), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/1003 (43%), Positives = 613/1003 (61%), Gaps = 83/1003 (8%)

Query: 4   GVVFNGLGRV---RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           GV F    R+   R  F ++  +I+ PDL+ +QK SY+ FL  ++  ++R NEGLQ    
Sbjct: 16  GVEFAKKYRIENGRVNFSRSASVIEPPDLLAIQKESYESFLQKDVPENKRKNEGLQEVLT 75

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           S+FPI A +    +EF+SY    PK    +   RD TYA P KI ++L V D +      
Sbjct: 76  SIFPIVASNEKMQIEFISYSIGEPKITEKEARRRDKTYAYPFKIKVQLTVRDPER----- 130

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               I EQ I++GD+P MT  GTF+I G +R+VVSQ+HRSPG+ F             ++
Sbjct: 131 ----IIEQEIFVGDIPAMTDRGTFIINGAERVVVSQIHRSPGVVF------NRSDRDAMF 180

Query: 181 ACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY 238
             +IIPD+G W++ E D  KDI++VRIDR++K+PVT FL A+G+ + EEIL  FY     
Sbjct: 181 VAKIIPDRGTWLEFELDTKKDIMYVRIDRKKKLPVTVFLRAIGITTNEEILKLFYEVDNI 240

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDID-TGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           S           A + ++G +  S++ D +   E ++  G+ +   L + L   G+K + 
Sbjct: 241 SLEK---LSDEDAKEALIGRRSYSTVFDTENPDEIILNPGELINPNLAERLLMSGIKEIS 297

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +                                                L ++++ +N  
Sbjct: 298 V------------------------------------------------LNMEAIKDNVT 309

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I NTL  D  K++++A   IY V+RPG+ +         N L FD   Y L  VGR K+N
Sbjct: 310 IINTLDKDTTKNQEEACTKIYNVIRPGEPALIENVVRTCNDLVFDPKLYALGDVGRYKIN 369

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RLN    +  + +R +DII  I+ L+ +   +  +DDID+LGNRRVRSVGE+L  Q + 
Sbjct: 370 KRLNFPESEQDKVLRHKDIIETIRFLIKVFINEEQLDDIDHLGNRRVRSVGELLAIQIKA 429

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G  RMER  KER+   D+++V PQ L++ K + + + EF+ +SQLSQ  +  N LS ITH
Sbjct: 430 GFTRMERIAKERMQMQDMEAVTPQSLVSIKLIQAVIKEFYGTSQLSQFMDQNNPLSEITH 489

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRL+ALG GG+ R RAG E+RDVH THYG+ICP ET EG NIGL+ SL ++A++N +GF
Sbjct: 490 KRRLNALGPGGLTRDRAGFEVRDVHHTHYGKICPIETPEGPNIGLIVSLATYAKINKHGF 549

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYRKV DGKVT+++ YL+A +EE  +IA AN+ L+EDG+F E L+  R   E     
Sbjct: 550 LETPYRKVIDGKVTDEIEYLTAHDEERYHIADANAPLNEDGTFKENLISTRYRSEFPYSS 609

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            +++ ++D SP+Q+VS+++SLIPFLE+DD+NR LMG NMQRQ+VPLL  EAP VGTG+E+
Sbjct: 610 PDQVQYMDVSPQQIVSLSSSLIPFLEHDDANRALMGSNMQRQSVPLLYPEAPIVGTGVEA 669

Query: 718 VVAKS-SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            + +  +G A+ AKRAG V +V    I+I+  + + D      D+Y L+K+QR+NQ+T  
Sbjct: 670 KICQPGTGIAVHAKRAGKVIKVVHDEIIIKPTKQNSDD---DFDVYELVKYQRTNQDTNY 726

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +QRP+V VGD V+   ++ADGP+TD G+LALGRN+L AFM + GYNFED++L+S R+V E
Sbjct: 727 HQRPVVNVGDVVKAGGLLADGPATDHGELALGRNVLAAFMIFEGYNFEDAILLSRRLVQE 786

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEEF V AR+TKL  E ITRDIPNVS+   KN+DE GI+ +GA+V  GDILVG
Sbjct: 787 DVFTSIHIEEFSVEARETKLDKENITRDIPNVSDSAFKNLDERGIVRIGAKVKAGDILVG 846

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K+TPKGE+ +TPE +LL +IFGEKA DV+DTSLRVP G  GTV+DVR+++R   D     
Sbjct: 847 KVTPKGETEITPEYRLLHSIFGEKARDVKDTSLRVPHGKEGTVIDVRVYSRENGD----- 901

Query: 957 ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
               +  +E + +    ++ I+             G  A   P
Sbjct: 902 --ELKPGVEEVVKVFLAKKRIIQEGDKMAGRHGNKGVVARIMP 942



 Score =  334 bits (856), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 132/444 (29%), Positives = 192/444 (43%), Gaps = 57/444 (12%)

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR--NIYSRLMEILCG 992
                  D  + +R  + ++  +     E        K D++ I     N+     + L  
Sbjct: 769  EGYNFEDAILLSRRLVQEDVFTSIHIEEFSVEARETKLDKENITRDIPNVSDSAFKNLDE 828

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +  V      K   +L   +  +       ++ +           +K          E  
Sbjct: 829  RGIVRIGAKVKAGDILVGKVTPKGETEITPEYRLLHSIFGEKARDVKDTSLRVPHGKEGT 888

Query: 1053 FKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
              + ++   + GD++ PGV  VVKVF+A K                    RI+   D   
Sbjct: 889  VIDVRVYSRENGDELKPGVEEVVKVFLAKK--------------------RIIQEGD--- 925

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                                                 G K          +       + 
Sbjct: 926  -------------------------------KMAGRHGNKGVVARIMPIEDMPFLEDGTP 954

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            ++  +       +++      +L      K G+  + PVF+G  EEA+      + ++ +
Sbjct: 955  VDICLNPLGVPSRMNIGQVIEMLLGWSGHKMGLKYACPVFEGPKEEALREAFVTSGMNPN 1014

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  LYDG TGEPF   V VGY+YMLKLNH+V DKV+ARSTG YSLVTQQPLGGKS  GG
Sbjct: 1015 GKVRLYDGRTGEPFKNEVAVGYMYMLKLNHLVEDKVHARSTGPYSLVTQQPLGGKSQFGG 1074

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QRLGEMEVW ++AYGAA +LQE LT+KSDD+ GR R+YESIV G+     G PESFNVLV
Sbjct: 1075 QRLGEMEVWALEAYGAANMLQEFLTVKSDDMTGRARIYESIVKGDVISSPGIPESFNVLV 1134

Query: 1352 KEMQALGLSIDLENSRTKNSAKME 1375
            +E++ LGL+I + +         E
Sbjct: 1135 QELRGLGLNITIHDEEGNQLPSTE 1158


>gi|227879236|ref|ZP_03997106.1| DNA-directed RNA polymerase subunit beta [Lactobacillus crispatus
           JV-V01]
 gi|227861130|gb|EEJ68779.1| DNA-directed RNA polymerase subunit beta [Lactobacillus crispatus
           JV-V01]
          Length = 1188

 Score =  795 bits (2054), Expect = 0.0,   Method: Composition-based stats.
 Identities = 397/940 (42%), Positives = 576/940 (61%), Gaps = 79/940 (8%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           + +P+L +VQ  SY  FL          ++G++  F  + PI+ FSG   LE+V Y+   
Sbjct: 1   MKLPNLTDVQTESYKWFL----------DKGIKEVFDDIMPISDFSGKLSLEYVGYKLQK 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+    D TYA P+ +TL+L           +   +IK Q ++ GDLPLMT+ G+
Sbjct: 51  PKYTVDEARNHDATYAAPMHVTLKLT---------NQETGEIKTQDVFFGDLPLMTESGS 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ G +R++VSQL RSPG+++  D  +   +G+ ++   +IP++G W++ E D+K++  
Sbjct: 102 FIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIFGTTVIPNRGAWLEYETDAKNVSF 158

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VR+DR RK+P+T  + A+G+ S+ +I+  F          D      + AD  V   +  
Sbjct: 159 VRVDRTRKLPLTVLIRAMGIGSDSDIIDMFGQSDTLQFTLDKD-VHKNPADSRVAEALKD 217

Query: 263 SLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIV 313
               +  GE    +S + L        +   +  +G           + L G  +AE + 
Sbjct: 218 IYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLYGQTLAETLA 277

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           + +TGEI  + G V+  + ++++                                DR D 
Sbjct: 278 DPDTGEIVAKKGTVVTHEVMDKLAPYL----------------------------DRDDF 309

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            +  Y+  + G +      + +  +   D ++          + +  N    D+V+H+  
Sbjct: 310 KMVTYQPSKEGVLPDPIAVQEIKVYSKVDPERE---------VKLMSNGHIADNVKHLTP 360

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            D++A I     L++  GT DDID+LGNRR+R VGE+L+NQ+R+GL RMER ++ER+S  
Sbjct: 361 ADVLASINYFFALQDEIGTTDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQ 420

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N L  +TH RR+SALG GG+ R R
Sbjct: 421 DPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHNPLGELTHKRRMSALGPGGLTRDR 480

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVT 611
           AG E+RDVH THYGR+CP ET EG NIGL++SL S+A +N YGFIETPYR+V   D KVT
Sbjct: 481 AGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYAIINKYGFIETPYRRVSWKDHKVT 540

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YL+A EE+N  IA AN+ L++DGSF E+L+  R   + + V  +KID++D  PKQV
Sbjct: 541 DKIDYLTADEEDNYIIAGANTPLNDDGSFKEKLILARQKEDNVEVSPDKIDYMDVIPKQV 600

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+A++ IPFLENDDSNR LMG N QRQA PL+      VGTGME   A  SGAA++AK 
Sbjct: 601 VSVASACIPFLENDDSNRALMGANQQRQAAPLINPHGSLVGTGMEYRAAHDSGAALIAKA 660

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG+VE VDA  I IR  +G LD        Y L K++RSN +   NQ P VK+GD V ++
Sbjct: 661 AGVVEYVDANEIRIRREDGTLDK-------YTLEKYRRSNNSKSYNQTPNVKLGDHVDKS 713

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED++++SER+V +DV+TSI IE++E  A
Sbjct: 714 DVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDVYTSISIEDYESEA 773

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV+ GDILVGK+TPKG + ++ EE+
Sbjct: 774 RDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEVHDGDILVGKVTPKGVTELSAEER 833

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL AIFGEKA +VRDTSLRVP G  G V DV+++ R   D
Sbjct: 834 LLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTREAGD 873



 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 173/502 (34%), Positives = 237/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 704  VKLGDHVDKSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 760

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 761  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 815

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 816  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 869

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 870  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 929

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 930  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGADENDVW-------------- 975

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T V+D                          G 
Sbjct: 976  -----------DTVRQAGVDKDG---KTVVYD--------------------------GR 995

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 996  TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1055

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1056 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIPKPGVPESFRVLVKELQSLGLD 1115

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1116 IRVLDMNHNEIELRDMDEDSSE 1137


>gi|257065958|ref|YP_003152214.1| DNA-directed RNA polymerase, beta subunit [Anaerococcus prevotii
           DSM 20548]
 gi|256797838|gb|ACV28493.1| DNA-directed RNA polymerase, beta subunit [Anaerococcus prevotii
           DSM 20548]
          Length = 1235

 Score =  795 bits (2054), Expect = 0.0,   Method: Composition-based stats.
 Identities = 422/954 (44%), Positives = 601/954 (62%), Gaps = 56/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              RK F K P+++D+P+L++VQK SY+ FL           EGL    + + PI  ++G
Sbjct: 11  RTKRKSFSKFPQVLDLPNLLKVQKDSYEWFL----------KEGLGEILEDISPIEDYNG 60

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEF+ YEFD   K+ V +  ++D TYA  LK+  RLI          K  +++KEQ 
Sbjct: 61  NLILEFIGYEFDEETKYSVKESKYKDATYARDLKVKARLI---------NKETEEVKEQE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG  +Y+  +IP++G
Sbjct: 112 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYAEETDK---SGDKMYSSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +++E I++            +     
Sbjct: 169 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFETDEEIINAIGDTKHLRNTLEKENSE 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +   L+   +       +  G+   +ES   L + LL   +   +  +G          
Sbjct: 229 TADEALIEIYR------KLKPGDPASVESATNLINNLLFDDRRYDLAKVGRYKYNLKLAL 282

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            D + GL   +D+++ ETGE+++ AG++IDE++ + I ++ I  + ++  D    +  +R
Sbjct: 283 ADRIEGLVSKDDVIDPETGEVFVSAGEIIDEETAKAIENAGIVTVDVIKKDEYEEDKTLR 342

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                  + +  + L D+               +  F  +    ++ +     +  M  R
Sbjct: 343 VVGNNFVDFNSFEELKDV------DVTVDDFSEKVYFPVMKEIIEEANSPEEIKSLMERR 396

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                P   +HI K DI+AI+    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+GL
Sbjct: 397 KKELCP---KHITKADILAIVNYQFNLFEGIGYVDDIDHLGNRRVRGVGELLQNQFRVGL 453

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH R
Sbjct: 454 ARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKR 513

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++ARVN YGFIE
Sbjct: 514 RLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARVNKYGFIE 573

Query: 600 TPYRKVCDG-KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           TPYR V +G  VT+++ YL+A  E+N  IAQAN  LDE+  F  E V  R   GE  + P
Sbjct: 574 TPYRLVKEGGYVTDEIDYLTADIEDNFIIAQANEPLDENDRFVNERVSGRGIKGENDIYP 633

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           REKI ++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPL+K EAP V TG+E 
Sbjct: 634 REKIQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLIKTEAPIVATGIEH 693

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +V++  G V  V    I ++        S   ++ Y L+KF+R+NQ T +N
Sbjct: 694 RAAKDSGVCVVSRSKGEVVYVGDDHIKVKR------ASDGEIEDYELLKFERANQGTTIN 747

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK GD+V  N+I+ADGPSTD G+LALG+N+L+AF  W GYNFED+ML++E +V +D
Sbjct: 748 QRPIVKRGDKVEANEILADGPSTDNGELALGKNILIAFTTWEGYNFEDAMLLNEELVMDD 807

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TS+HIEE E  AR+TKLG EEIT+DIPNV E+  K++DE GII +GAEV  GDILVGK
Sbjct: 808 VLTSVHIEEHECEARETKLGAEEITKDIPNVGEDMKKDLDENGIIRIGAEVKSGDILVGK 867

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL+VP G SG VVDV+ +N+   D
Sbjct: 868 VSPKGETELSPEERLLRAIFGEKAREVRDTSLKVPHGESGIVVDVKEYNKKDGD 921



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 259/1066 (24%), Positives = 409/1066 (38%), Gaps = 114/1066 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++++ +  ++RNTL  + ++   +AL++IYR ++PGD ++   A ++ N L FD  +YDL
Sbjct: 209  INAIGDTKHLRNTLEKENSETADEALIEIYRKLKPGDPASVESATNLINNLLFDDRRYDL 268

Query: 409  STVGRVKMNMRLNL--------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            + VGR K N++L L              D       +   +II           G  T+D
Sbjct: 269  AKVGRYKYNLKLALADRIEGLVSKDDVIDPETGEVFVSAGEIIDEETAKAIENAGIVTVD 328

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
             I        +++  +  N          + +   +         P        +   + 
Sbjct: 329  VIKKDEYEEDKTLRVVGNNFVDFNSFEELKDVDVTVDDFSEKVYFP-------VMKEIIE 381

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            E     ++  L E         H  +   L                    H G       
Sbjct: 382  EANSPEEIKSLMERRKKELCPKHITKADILAIVNYQFNLFEGIGYVDDIDHLGNRRVRGV 441

Query: 575  SEGHNIGLVSSLTSFARV------NAYGFIETPYRKVCDGKVTNDV-VYLSAMEEENRYI 627
             E         L    RV           + TP   +    VT  +  +  + +      
Sbjct: 442  GELLQNQFRVGLARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMD 501

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                 S          L     + +   V    +          +         L    +
Sbjct: 502  QTNPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLT 561

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                +      +    L  E  +V   ++ + A      I+A+    +++ D       +
Sbjct: 562  TYARVNKYGFIETPYRLVKEGGYVTDEIDYLTADIEDNFIIAQANEPLDEND----RFVN 617

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG----DEVRRNDIIADGPSTDLG 803
                        DIY   K     Q   V+ + +V VG      +  +D        ++ 
Sbjct: 618  ERVSGRGIKGENDIYPREK----IQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQ 673

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
              A+      A +   G     +      +VS      +++ +  +  +    G  E   
Sbjct: 674  RQAVPLIKTEAPIVATGIEHRAAKDSGVCVVSRSKGEVVYVGDDHIKVKRASDGEIEDYE 733

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +          I++  I+  G +V   +IL    +      +   + +L A    +  +
Sbjct: 734  LLKFERANQGTTINQRPIVKRGDKVEANEILADGPSTDN-GELALGKNILIAFTTWEGYN 792

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVI 977
              D  L     V   V+       H  +  E  +  E          E + +D  DE  I
Sbjct: 793  FEDAMLLNEELVMDDVLTSVHIEEHECEARETKLGAEEITKDIPNVGEDMKKDL-DENGI 851

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            +      +  +IL G+ +  G         L   +  E  R      +++    +  +  
Sbjct: 852  IRIGAEVKSGDILVGKVSPKGETELSPEERLLRAIFGEKARE-VRDTSLKVPHGESGIVV 910

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
               +Y                    GD++ PGV +V++V+VA KR I  GDKM GRHGNK
Sbjct: 911  DVKEYNKK----------------DGDELAPGVNKVIRVYVAAKRKIMVGDKMCGRHGNK 954

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+VSRILP EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A   +G KI + + 
Sbjct: 955  GVVSRILPREDMPFLPDGTPLQICLNPLGIPSRMNLGQVLEVHMGLAARTMGWKIATPVF 1014

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D   + +I  +    +K     + T KI                                
Sbjct: 1015 DGALDTEIEEVLEEAKKTAPYVNKTGKI-------------------------------- 1042

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                              L DG TG PF  PVTVG +YMLKL+HMV +K++ARS G YSL
Sbjct: 1043 -----------------TLRDGRTGLPFQNPVTVGVMYMLKLHHMVEEKIHARSIGPYSL 1085

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQE+LT+KSDDV GR + YESIV G +
Sbjct: 1086 VTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEILTVKSDDVTGRVKTYESIVKGEN 1145

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
              E GTPESF VLVKE+Q+L L ++L +   +     E I + ++ 
Sbjct: 1146 IPEPGTPESFKVLVKELQSLALDVELLDEEGEVIELKENIDEQDRF 1191


>gi|225621225|ref|YP_002722483.1| DNA-directed RNA polymerase subunit beta [Brachyspira
           hyodysenteriae WA1]
 gi|225216045|gb|ACN84779.1| DNA-directed RNA polymerase beta subunit [Brachyspira
           hyodysenteriae WA1]
          Length = 1173

 Score =  795 bits (2053), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/1003 (42%), Positives = 615/1003 (61%), Gaps = 83/1003 (8%)

Query: 4   GVVFNGLGRV---RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           GV F    R+   R  F +   +I+ PDL+ +QK SY+ FL  ++  ++R NEGLQ    
Sbjct: 16  GVEFAKKYRMENGRVNFSRTASVIEPPDLLAIQKESYESFLQKDVPENKRKNEGLQEVLT 75

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           S+FPI A +    +EF+SY    PK    +   RD TYA P KI ++L V D +      
Sbjct: 76  SIFPIVASNEKMQIEFISYSIGEPKITEKEARRRDKTYAYPFKIKVQLTVRDPER----- 130

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               I EQ I++GD+P MT  GTF++ G +R++VSQ+HRSPG+ F             ++
Sbjct: 131 ----IIEQEIFVGDIPAMTDRGTFIVNGAERVIVSQIHRSPGVVF------NRSDRDAMF 180

Query: 181 ACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY 238
             +IIPD+G W++ E D  KDI++VRIDR++K+PVT FL A+G+ + EEIL  FY     
Sbjct: 181 VAKIIPDRGTWLEFELDTKKDIMYVRIDRKKKLPVTVFLRAIGITTNEEILKLFYEVDNI 240

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDID-TGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           S          ++ + ++G +  S++ D +   E ++  G+ +   L + L   G+K + 
Sbjct: 241 SLEK---LSDENSKEALIGRRSYSTVYDTENPDEIILNPGELINPNLAERLLMSGIKEIS 297

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +                                                L ++++ +N  
Sbjct: 298 V------------------------------------------------LNMEAIKDNVT 309

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I NTL  D  K++++A   IY V+RPG+ +         N L FD   Y L  VGR K+N
Sbjct: 310 IINTLDKDTTKNQEEACTKIYNVIRPGEPALIENVVRTCNDLVFDPKSYALGDVGRYKLN 369

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RLN    +  + +R +DII  I+ L+ +   +  +DDID+LGNRRVRSVGE+L  Q + 
Sbjct: 370 KRLNFPESEQDKVLRHKDIIETIRFLIKVFINEEQLDDIDHLGNRRVRSVGELLSIQIKA 429

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G  RMER  KER+   D+++V PQ L++ K + + + EFF ++QLSQ  +  N LS ITH
Sbjct: 430 GFTRMERIAKERMQMQDMEAVTPQSLVSIKLIQAVIKEFFGTNQLSQFMDQNNPLSEITH 489

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRL+ALGQGG+ R RAG E+RDVH THYG+ICP ET EG NIGL+ SL ++A++N +GF
Sbjct: 490 KRRLNALGQGGLTRDRAGFEVRDVHHTHYGKICPIETPEGPNIGLIVSLATYAKINKHGF 549

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYRKV DGKVT+++ YL+A +EE  +IA AN+ L+EDG+F + L+  R   E     
Sbjct: 550 LETPYRKVVDGKVTDEIEYLTAHDEEKYHIADANAPLNEDGTFKDNLISTRFRSEFPYSS 609

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            +++ ++D SP+Q+VS+++SLIPFLE+DD+NR LMG NMQRQ+VPLL  EAP VGTG+E+
Sbjct: 610 PDQVQYMDVSPQQIVSLSSSLIPFLEHDDANRALMGSNMQRQSVPLLYPEAPIVGTGVEA 669

Query: 718 VVAKS-SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            + +  +G A+ AKRAG V +V    IVI+  + + D     +D+Y L+K+QR+NQ+T  
Sbjct: 670 KICQPGTGIAVHAKRAGKVIKVVHNEIVIKPTKQNSDD---DLDVYELVKYQRTNQDTNY 726

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +QRP+V VGD V+   ++ADGP+TD G+LALGRN+L AFM + GYNFED++L+S R+V E
Sbjct: 727 HQRPVVNVGDVVKAGGLLADGPATDHGELALGRNVLAAFMIFEGYNFEDAILLSRRLVQE 786

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEEF V AR+TKL  E ITRDIPNVS+   KN+DE GI+ +GA+V  GDILVG
Sbjct: 787 DVFTSIHIEEFSVEARETKLDKENITRDIPNVSDAAFKNLDERGIVRIGAKVKAGDILVG 846

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K+TPKGE+ +TPE +LL +IFGEKA DV+DTSLRVP G  GTV+DVR+++R   D     
Sbjct: 847 KVTPKGETEITPEYRLLHSIFGEKARDVKDTSLRVPHGKDGTVIDVRVYSRENGD----- 901

Query: 957 ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
               +  +E + +    ++ I+             G  A   P
Sbjct: 902 --ELKPGVEEVVKVFLAKKRIIQEGDKMAGRHGNKGVVARIMP 942



 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 162/444 (36%), Positives = 217/444 (48%), Gaps = 57/444 (12%)

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR--NIYSRLMEILCG 992
                  D  + +R  + ++  +     E        K D++ I     N+     + L  
Sbjct: 769  EGYNFEDAILLSRRLVQEDVFTSIHIEEFSVEARETKLDKENITRDIPNVSDAAFKNLDE 828

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +  V      K   +L   +  +       ++ +           +K          +  
Sbjct: 829  RGIVRIGAKVKAGDILVGKVTPKGETEITPEYRLLHSIFGEKARDVKDTSLRVPHGKDGT 888

Query: 1053 FKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
              + ++   + GD++ PGV  VVKVF+A KR IQ GDKMAGRHGNKG+V+RI+P EDMPF
Sbjct: 889  VIDVRVYSRENGDELKPGVEEVVKVFLAKKRIIQEGDKMAGRHGNKGVVARIMPIEDMPF 948

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L+DGTPVDI LNPLGVPSRMN+GQ+ E  LGW+   +G K    + +      +      
Sbjct: 949  LEDGTPVDICLNPLGVPSRMNIGQVIEMLLGWSGHKMGLKYACPVFEGPKEEALREAFVA 1008

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                                                        
Sbjct: 1009 SGMNPNGKVRL-----------------------------------------------YD 1021

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++       GEPF   V VGY+YMLKLNH+V DKV+ARSTG YSLVTQQPLGGKS  GG
Sbjct: 1022 GRT-------GEPFKNDVAVGYMYMLKLNHLVEDKVHARSTGPYSLVTQQPLGGKSQFGG 1074

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QRLGEMEVW ++AYGAA +LQE LT+KSDD+ GR R+YESIV G+     G PESFNVLV
Sbjct: 1075 QRLGEMEVWALEAYGAANMLQEFLTVKSDDMTGRARIYESIVKGDVISSPGIPESFNVLV 1134

Query: 1352 KEMQALGLSIDLENSRTKNSAKME 1375
            +E++ LGL+I + +         E
Sbjct: 1135 QELRGLGLNITIHDEEGNQLPSTE 1158


>gi|282933700|ref|ZP_06339058.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           208-1]
 gi|281302190|gb|EFA94434.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           208-1]
          Length = 1204

 Score =  795 bits (2052), Expect = 0.0,   Method: Composition-based stats.
 Identities = 405/958 (42%), Positives = 569/958 (59%), Gaps = 83/958 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F    E++ +P+L +VQ  SY  FL          NEG+   F+ + PI  
Sbjct: 3   YGQHRTRRSFSHIKEVVKLPNLTDVQTESYKWFL----------NEGISEVFEDIMPIND 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG   L+FV Y+    K  +D+    D  YA PL++TL+L               +IK 
Sbjct: 53  FSGKLSLDFVGYKLQDAKSTIDEARNHDANYAAPLRVTLKLT---------NHETGEIKT 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GDLPLMT+ G+FVI G +R++VSQL RSPG++++ D  +   + + ++   +IP+
Sbjct: 104 QDVFFGDLPLMTRSGSFVINGAERVIVSQLVRSPGVYYNCDVDK---NARQIFGATVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYSQRGDF 244
           +G W++ E D+K+I +VRIDR RK+P++  + ALG  S+  +   Y     + ++   D 
Sbjct: 161 RGAWLEYETDAKNISYVRIDRTRKLPISVLIRALGFGSDSEIQDIYGTNDTLQFTLEKD- 219

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                + AD  V   +      +  GE    +S + L        +   +  +G      
Sbjct: 220 --VHNNPADSRVAEALKEIYERLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINK 277

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  L    +AE + + +TGEI  + G ++    +E +          L  D     
Sbjct: 278 KLSLKSRLLNQTLAETLADPDTGEIIAKKGTIVTHAVMETLEKY-------LDRDDFKMV 330

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            Y  +    D+   +    +   +V    +                             +
Sbjct: 331 TYTPS----DEGVMQDPITVQEIKVFSKVNP--------------------------ERE 360

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           + +  N     DV+ I   DI+A I     L++  G+ DDID+LGNRR+R VGE+L+NQ+
Sbjct: 361 VKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGELLQNQF 420

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+S  D D+V PQ LIN +P+V++V EFF SSQLSQ  +  N L  +
Sbjct: 421 RIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPLGEL 480

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A +N Y
Sbjct: 481 THKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAIINKY 540

Query: 596 GFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E L+  R   + 
Sbjct: 541 GFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKENLILARHKDDN 600

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A  VGT
Sbjct: 601 VEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAALVGT 660

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME   A  SG A+VA+ AG+VE VDA +I IR  +G LD        Y L K++RSN N
Sbjct: 661 GMEYRAAHDSGDALVAEAAGVVEYVDADQIRIRREDGTLDK-------YELEKYRRSNAN 713

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ P VK G+++   ++IA+GPS   G+LALG+N L+AFM W+ YN+ED+++ISERM
Sbjct: 714 KNYNQTPNVKKGEKIVEGEVIANGPSMAEGELALGQNPLIAFMTWNMYNYEDAIMISERM 773

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  GDI
Sbjct: 774 VKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEQGIVRIGAEVKDGDI 833

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V +F R G D
Sbjct: 834 LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVEVFTREGGD 891



 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 253/1089 (23%), Positives = 391/1089 (35%), Gaps = 148/1089 (13%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + I A     +  +++I+ +       L  D  NN A          +    +AL +IY 
Sbjct: 189  VLIRALGFGSDSEIQDIYGTNDTLQFTLEKDVHNNPA----------DSRVAEALKEIYE 238

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-------- 431
             +RPG+  T   + S+    FFDS +YDL+ VGR K+N +L+L +    + +        
Sbjct: 239  RLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINKKLSLKSRLLNQTLAETLADPD 298

Query: 432  ------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                            +  + K L        T    D    +   +V E +K   ++  
Sbjct: 299  TGEIIAKKGTIVTHAVMETLEKYLDRDDFKMVTYTPSDEGVMQDPITVQE-IKVFSKVNP 357

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I       D+  + P D+         +   +        L             
Sbjct: 358  EREVKLISNGHIDADVKCITPADILASINYFFVLQDEIGSTDDIDHLGNRRIRRVGELLQ 417

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 418  NQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPL 477

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             +SA+        +A   + +        +      E   
Sbjct: 478  GELTHKRR-------------MSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPN 524

Query: 656  V--PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +        +   +    +      + +  +  ++++            +  A  P    
Sbjct: 525  IGLINSMATYAIINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNED 584

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G            I+A+      +V   +I    V      S +   I  L     +   
Sbjct: 585  G------SFKENLILARHKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRAL 638

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               N +        V   +  A    T +   A   +         G           R+
Sbjct: 639  MGANHQ-----RQAVPLINPHAALVGTGMEYRAAHDSGDALVAEAAGVVEYVDAD-QIRI 692

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              ED      ++++E+  +  +    +     PNV +     I E  +I  G  +  G++
Sbjct: 693  RRED----GTLDKYEL-EKYRRSNANKNYNQTPNVKKGE--KIVEGEVIANGPSMAEGEL 745

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G                      E A+ + +  ++     S  + D     R      
Sbjct: 746  ALG-------QNPLIAFMTWNMYNYEDAIMISERMVKDDVYTSIHIEDYESEARDTKLGP 798

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DEQ I+      +  +IL G+    G         L   + 
Sbjct: 799  EEITREIPNVGEDALKDL-DEQGIVRIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIF 857

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R    +      +V      +    E             +   + GD++ PGV  +
Sbjct: 858  GEKAR----EVRDTSLRVPHGGGGIVQNVE-------------VFTREGGDELSPGVNTM 900

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++  KR IQ GDKMAGRHGNKG ++ ++P EDMPFL DG PVDI LNP+GVPSRMN+
Sbjct: 901  VRVYICQKRKIQVGDKMAGRHGNKGTIAVVVPEEDMPFLPDGRPVDICLNPMGVPSRMNI 960

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  + + + D     ++                            
Sbjct: 961  GQVLELHLGMAARQLGIHVATPVFDGADEDEVYNTLREAGMSKDGK-------------- 1006

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPF   V+VG 
Sbjct: 1007 --------------TVIYDG--------------------------RTGEPFHNRVSVGV 1026

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +  LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1027 MNYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1086

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K    
Sbjct: 1087 ILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMDHKEIEL 1146

Query: 1374 MEEIPDFNK 1382
             +   D ++
Sbjct: 1147 RDMDEDSSE 1155


>gi|17225230|gb|AAL37308.1| RNA polymerase B-subunit [Staphylococcus lugdunensis]
          Length = 1149

 Score =  795 bits (2052), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/929 (45%), Positives = 577/929 (62%), Gaps = 79/929 (8%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FL           EGL   F+ + PI  F+G   LEFV Y    PK+D+++   RD
Sbjct: 1   SYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRD 50

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
            TYA PL++ +RL++         K   ++KEQ ++MGD PLMT  GTFVI G +R++VS
Sbjct: 51  ATYAAPLRVKVRLVI---------KETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVS 101

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           QL RSP ++F+    +   +G+  Y   IIP++G W++ E D+KD+++VRIDR RK+P+T
Sbjct: 102 QLVRSPSVYFNEKIDK---NGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLT 158

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-V 273
             L ALG  ++ EI+             +      +   L+           +  GE   
Sbjct: 159 VLLRALGFSTDQEIVELLGDNEYLRNTLEKDGTENTEQALL------EIYERLRPGEPPT 212

Query: 274 IESGKKLTSGLLKSLKEKGVKFLG--------ITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+ K L        K   +  +G             L    +AE IVN ETGEI  E G
Sbjct: 213 VENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKHRLFNQKLAEPIVNSETGEIVAEEG 272

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
            V+D + L+EI              + N+  +     V D+  + +   + +        
Sbjct: 273 TVLDRRKLDEIMDVLET--------NANSEVFELEGTVIDEPVEIQSIKVYV-------- 316

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                           D +    + +G              +V+ I   DII+ +    +
Sbjct: 317 --------------PNDEEGCTTTIIGNAL--------PDSEVKCITPADIISSMSYFFN 354

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L  G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN
Sbjct: 355 LLAGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLIN 414

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +H
Sbjct: 415 IRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSH 474

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEE 623
           YGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE+
Sbjct: 475 YGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDTNAITDQIDYLTADEED 534

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           +  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLE
Sbjct: 535 SYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLE 594

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           NDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI AK  G VE V++  I
Sbjct: 595 NDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEI 654

Query: 744 VIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           ++R  +E +       +D Y L KF+RSN  TC NQRP+V +GD V  N+I+ADGPS +L
Sbjct: 655 LVRRLIEENGKEYEGELDRYPLAKFKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMEL 714

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
           G++ALGRN++V FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEIT
Sbjct: 715 GEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEIT 774

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 775 RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 834

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 835 EVRDTSLRVPHGAGGIVLDVKVFNREEGD 863



 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 161/440 (36%), Positives = 223/440 (50%), Gaps = 60/440 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS---GPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +     L   +           K   +L
Sbjct: 747  KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDIL 806

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 807  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTL 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG P+DI+LNPLG
Sbjct: 867  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLG 926

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + S + D   + D+                     
Sbjct: 927  VPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST------------------ 968

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   +  A   + G                             +++LYDG TGEPFD
Sbjct: 969  -------IEEAGMARDG-----------------------------KTVLYDGRTGEPFD 992

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 993  NRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1052

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LGL + + + 
Sbjct: 1053 AAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1112

Query: 1367 RTKNSAKMEEIPDFNKCELK 1386
                   M ++ D +  E K
Sbjct: 1113 HDNEIE-MADVEDEDTTERK 1131


>gi|238855060|ref|ZP_04645388.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           269-3]
 gi|282934604|ref|ZP_06339849.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           208-1]
 gi|238832304|gb|EEQ24613.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           269-3]
 gi|281301324|gb|EFA93623.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus jensenii
           208-1]
          Length = 1204

 Score =  794 bits (2051), Expect = 0.0,   Method: Composition-based stats.
 Identities = 405/958 (42%), Positives = 569/958 (59%), Gaps = 83/958 (8%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F    E++ +P+L +VQ  SY  FL          NEG+   F+ + PI  
Sbjct: 3   YGQHRTRRSFSHIKEVVKLPNLTDVQTESYKWFL----------NEGISEVFEDIMPIND 52

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG   L+FV Y+    K  +D+    D  YA PL++TL+L               +IK 
Sbjct: 53  FSGKLSLDFVGYKLQDAKSTIDEARNHDANYAAPLRVTLKLT---------NHETGEIKT 103

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GDLPLMT+ G+FVI G +R++VSQL RSPG++++ D  +   + + ++   +IP+
Sbjct: 104 QDVFFGDLPLMTRSGSFVINGAERVIVSQLVRSPGVYYNCDVDK---NARQIFGATVIPN 160

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYSQRGDF 244
           +G W++ E D+K+I +VRIDR RK+P++  + ALG  S+  +   Y     + ++   D 
Sbjct: 161 RGAWLEYETDAKNISYVRIDRTRKLPISVLIRALGFGSDSEIQDIYGTNDTLQFTLEKD- 219

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                + AD  V   +      +  GE    +S + L        +   +  +G      
Sbjct: 220 --VHNNPADSRVAEALKEIYERLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINK 277

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  L    +AE + + +TGEI  + G ++    +E +          L  D     
Sbjct: 278 KLSLKSRLLNQTLAETLADPDTGEIIAKKGTIVTHAVMETLEKY-------LDRDDFKMV 330

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            Y  +    D+   +    +   +V    +                             +
Sbjct: 331 TYTPS----DEGVMQDPITVQEIKVFSKVNP--------------------------ERE 360

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           + +  N     DV+ I   DI+A I     L++  G+ DDID+LGNRR+R VGE+L+NQ+
Sbjct: 361 VKLISNGHINADVKCITPADILASINYFFALQDEIGSTDDIDHLGNRRIRRVGELLQNQF 420

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+S  D D+V PQ LIN +P+V++V EFF SSQLSQ  +  N L  +
Sbjct: 421 RIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPLGEL 480

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A +N Y
Sbjct: 481 THKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAIINKY 540

Query: 596 GFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GFIETPYR+V     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E L+  R   + 
Sbjct: 541 GFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNEDGSFKENLILARHKDDN 600

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           + V  +KID++D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   A  VGT
Sbjct: 601 VEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHAALVGT 660

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME   A  SG A+VA+ AG+VE VDA +I IR  +G LD        Y L K++RSN N
Sbjct: 661 GMEYRAAHDSGDALVAEAAGVVEYVDADQIRIRREDGTLDK-------YELEKYRRSNAN 713

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ P VK G+++   ++IA+GPS   G+LALG+N L+AFM W+ YN+ED+++ISERM
Sbjct: 714 KNYNQTPNVKKGEKIVEGEVIANGPSMAEGELALGQNPLIAFMTWNMYNYEDAIMISERM 773

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIE++E  ARDTKLGPEEITR+IPNV E+ LK++DE GI+ +GAEV  GDI
Sbjct: 774 VKDDVYTSIHIEDYESEARDTKLGPEEITREIPNVGEDALKDLDEQGIVRIGAEVKDGDI 833

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V +V +F R G D
Sbjct: 834 LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQNVEVFTREGGD 891



 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 253/1089 (23%), Positives = 392/1089 (35%), Gaps = 148/1089 (13%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + I A     +  +++I+ +       L  D  NN A          +    +AL +IY 
Sbjct: 189  VLIRALGFGSDSEIQDIYGTNDTLQFTLEKDVHNNPA----------DSRVAEALKEIYE 238

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-------- 431
             +RPG+  T   + S+    FFDS +YDL+ VGR K+N +L+L +    + +        
Sbjct: 239  RLRPGEPKTTDSSRSLLFARFFDSRRYDLAPVGRYKINKKLSLKSRLLNQTLAETLADPD 298

Query: 432  ------------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                            +  + K L        T    D    +   +V E +K   ++  
Sbjct: 299  TGEIIAKKGTIVTHAVMETLEKYLDRDDFKMVTYTPSDEGVMQDPITVQE-IKVFSKVNP 357

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   +        L             
Sbjct: 358  EREVKLISNGHINADVKCITPADILASINYFFALQDEIGSTDDIDHLGNRRIRRVGELLQ 417

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 418  NQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPIVASVKEFFGSSQLSQFMDQNNPL 477

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            G +    R             +SA+        +A   + +        +      E   
Sbjct: 478  GELTHKRR-------------MSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPN 524

Query: 656  V--PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +        +   +    +      + +  +  ++++            +  A  P    
Sbjct: 525  IGLINSMATYAIINKYGFIETPYRRVSWETHKVTDKIDYLTADVEDNYIIAGANTPLNED 584

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G            I+A+      +V   +I    V      S +   I  L     +   
Sbjct: 585  G------SFKENLILARHKDDNVEVTPDKIDYMDVIPKQVVSVTSACIPFLENDDSNRAL 638

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               N +        V   +  A    T +   A   +         G           R+
Sbjct: 639  MGANHQ-----RQAVPLINPHAALVGTGMEYRAAHDSGDALVAEAAGVVEYVDAD-QIRI 692

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              ED      ++++E+  +  +    +     PNV +     I E  +I  G  +  G++
Sbjct: 693  RRED----GTLDKYEL-EKYRRSNANKNYNQTPNVKKGE--KIVEGEVIANGPSMAEGEL 745

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G                      E A+ + +  ++     S  + D     R      
Sbjct: 746  ALG-------QNPLIAFMTWNMYNYEDAIMISERMVKDDVYTSIHIEDYESEARDTKLGP 798

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DEQ I+      +  +IL G+    G         L   + 
Sbjct: 799  EEITREIPNVGEDALKDL-DEQGIVRIGAEVKDGDILVGKVTPKGVTELSAEERLLHAIF 857

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R    +      +V      +    E             +   + GD++ PGV  +
Sbjct: 858  GEKAR----EVRDTSLRVPHGGGGIVQNVE-------------VFTREGGDELSPGVNTM 900

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++  KR IQ GDKMAGRHGNKG ++ ++P EDMPFL DG PVDI LNP+GVPSRMN+
Sbjct: 901  VRVYICQKRKIQVGDKMAGRHGNKGTIAVVVPEEDMPFLPDGRPVDICLNPMGVPSRMNI 960

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  + + + D     ++                            
Sbjct: 961  GQVLELHLGMAARQLGIHVATPVFDGADEDEVYNTLREAGMSKDGK-------------- 1006

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPF   V+VG 
Sbjct: 1007 --------------TVIYDG--------------------------RTGEPFHNRVSVGI 1026

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +  LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 1027 MNYLKLAHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1086

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL I + +   K    
Sbjct: 1087 ILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLDIRVLDMDHKEIEL 1146

Query: 1374 MEEIPDFNK 1382
             +   D ++
Sbjct: 1147 RDMDEDSSE 1155


>gi|227498760|ref|ZP_03928902.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
 gi|226904214|gb|EEH90132.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
          Length = 1247

 Score =  794 bits (2050), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/976 (43%), Positives = 586/976 (60%), Gaps = 104/976 (10%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  E++ +P LI++Q+ SY+ F+           EGL  AF+ V PI   + +
Sbjct: 15  RKRYSYARIKEVLKMPHLIDLQRKSYEWFIR----------EGLHDAFQDVSPIKDATNS 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F ++    PK+D++ C  +D TYA PL + +RL+  D           +IKE +++
Sbjct: 65  LELSFENFTIGDPKYDIETCKEKDATYAAPLNVDVRLLYKD---------TGEIKESTVF 115

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTFVI G +R++VSQL RSPG+++  D       GK LY   +IP++G W
Sbjct: 116 MGDFPLMTDTGTFVINGAERVIVSQLVRSPGVYYAKDMD---PMGKFLYGTTVIPNRGAW 172

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPK--IVYSQRGDFWCFP 248
           ++ E D   II+ R+DR RK+  T+ L  +G+  +++I+S F     +V +   D     
Sbjct: 173 IEYETDLNSIIYARVDRTRKLSATALLRVMGLPTNDDIISVFGEHPYLVATLAKDTTKNE 232

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
             A   +          +++  EQ+I +         L    + K  K LG     L G 
Sbjct: 233 DDALLEIYRKLRPGEPANLENAEQLIYNLFSDNRRYDLANVGRYKINKKLGW-RHRLHGK 291

Query: 307 YVAEDIV----NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +AED+     +G  G + + AG  I +  ++ I  S I               +     
Sbjct: 292 TLAEDLCAENPDGTKGAVVLPAGTKIGDAEIDTIEKSGI---------------FADEGY 336

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                K ++ A   I                                          +  
Sbjct: 337 AIVYVKFQEHAERMI------------------------------------------VTK 354

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D    VR I   D+IA    L+++ +G    DDID+LGNRRVR VGE+L+NQ+R+GL RM
Sbjct: 355 DIEASVRTITPADVIASFGYLLNVIDGMEGKDDIDHLGNRRVRCVGELLQNQFRIGLSRM 414

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER I+ER++  D D + PQ LIN +PVV+AV EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 415 ERVIRERMTIQDADVITPQALINIRPVVAAVKEFFGSSQLSQFMDQNNPLAELTHKRRLS 474

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL ++  +N YGFIETPY
Sbjct: 475 ALGPGGLSRERAGYEVRDVHPSHYGRMCPIETPEGPNIGLIGSLAAYGVINRYGFIETPY 534

Query: 603 RKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV   + +VT+++VYL+A EE+N  +AQAN  L ED  F    V CR   E + +P E+
Sbjct: 535 RKVDKVNKRVTDEIVYLTADEEDNYVVAQANEPLTEDNHFVNTHVTCRDKNEVLAIPPER 594

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +DF+D SPKQV+SIAA+LIPFLENDD+NR LMG NMQRQAVPLL  +AP VGTGME  +A
Sbjct: 595 VDFMDVSPKQVMSIAAALIPFLENDDANRALMGANMQRQAVPLLNPKAPVVGTGMEYKIA 654

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  I+AK AG V+ V   +I+I   +G       G+D Y ++KF+RSNQ+TCVNQRP
Sbjct: 655 VDSGVCILAKHAGTVKYVSGDKILITRDDGK------GIDEYNVLKFKRSNQSTCVNQRP 708

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD+V    ++ADGP+TD G+LALGRN + A+MPW GYN+ED++L+SE +V EDVFT
Sbjct: 709 IVFKGDKVEEGQVLADGPATDHGELALGRNAIAAYMPWEGYNYEDAVLLSEDLVKEDVFT 768

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+   ARDTKLGPEEITRDIPNVSE+ LK++DE GII VGAEV PGDILVGK+TP
Sbjct: 769 SIHIEEYNCDARDTKLGPEEITRDIPNVSEDALKDLDEDGIIRVGAEVRPGDILVGKVTP 828

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKN 953
           KGE+ ++ EE+L+RAIF EKA +VRD+SLRVP G  G ++ V++F R        G++K 
Sbjct: 829 KGETELSAEERLIRAIFAEKAREVRDSSLRVPHGEFGIIISVKVFTRENGDELPPGVNKQ 888

Query: 954 ERSISVEREQIELLAR 969
            R   V++ +I    +
Sbjct: 889 VRVSIVQKRKIGEGDK 904



 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 207/573 (36%), Positives = 271/573 (47%), Gaps = 50/573 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE---FEVMARDTKL 856
                       +L    P  G   E  + +   +                  ++ RD   
Sbjct: 626  MGANMQRQAVPLLNPKAPVVGTGMEYKIAVDSGVCILAKHAGTVKYVSGDKILITRDDGK 685

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +E        S +    +++  I+  G +V  G +L           +      + A 
Sbjct: 686  GIDEYNVLKFKRSNQS-TCVNQRPIVFKGDKVEEGQVLADGP-ATDHGELALGRNAIAAY 743

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARD 970
               +  +  D  L     V   V        +  D  +  +  E          E   +D
Sbjct: 744  MPWEGYNYEDAVLLSEDLVKEDVFTSIHIEEYNCDARDTKLGPEEITRDIPNVSEDALKD 803

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      R  +IL G+    G         L   + +E  R            
Sbjct: 804  L-DEDGIIRVGAEVRPGDILVGKVTPKGETELSAEERLIRAIFAEKAR------------ 850

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 E                   K+   + GD++PPGV + V+V +  KR I  GDKM
Sbjct: 851  -----EVRDSSLRVPHGEFGIIISVKVFTRENGDELPPGVNKQVRVSIVQKRKIGEGDKM 905

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG+VSRILP EDMPFL +G PV IVLNPLGVPSRMN+GQI E HLGWA   LG 
Sbjct: 906  AGRHGNKGVVSRILPREDMPFLPNGEPVQIVLNPLGVPSRMNIGQILEAHLGWAATALGM 965

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +I +                            +      D   L + E     VPV+ PV
Sbjct: 966  RIDN---------------------HDPNVEADLRKAGYDFDELGMPETVDGAVPVAVPV 1004

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FD A ++ +   L  A +D SG+++LYDG TGEPFD PVTVG IY LKL+H+V+DK++AR
Sbjct: 1005 FDSARQDDMARTLEAAGVDPSGKTVLYDGRTGEPFDNPVTVGCIYYLKLHHLVADKIHAR 1064

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE
Sbjct: 1065 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYE 1124

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            SIV G +  E G PESF VLVKEMQA+GL + +
Sbjct: 1125 SIVKGENIPEPGVPESFKVLVKEMQAIGLDVSV 1157


>gi|306821197|ref|ZP_07454811.1| DNA-directed RNA polymerase subunit beta [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550709|gb|EFM38686.1| DNA-directed RNA polymerase subunit beta [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 1233

 Score =  793 bits (2048), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/954 (44%), Positives = 600/954 (62%), Gaps = 52/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  F K P +  +P+LIE+Q  SY  F+           EGL+  F+ +FPI  +SG
Sbjct: 11  RRTRMSFSKIPSVAQLPNLIELQVDSYKWFIQ----------EGLREVFEEIFPIENYSG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           +  LEF+ Y  +  PK+ +++   RD+TYA P+KI +RL V D D   G + +K+   + 
Sbjct: 61  SVKLEFLDYIIEDIPKYTIEESKERDVTYATPIKIRVRLTVKDED---GTEIVKNENAEP 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +++GD PLMT  GTF+I G +R++VSQ+ RSPG+++  +  +    G  L +  +IP++G
Sbjct: 118 VFLGDFPLMTDSGTFIINGAERVIVSQIVRSPGVYYAQEMDKT---GNRLISSTVIPNRG 174

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            W++ E DS DI+ VRIDR RK P+T  L ALG  S+E +     K +  +         
Sbjct: 175 AWLEYETDSSDIVSVRIDRNRKQPITVLLRALGYSSDEEI-----KDLLMEEELLLPTLQ 229

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-------- 300
             A       +      +  GE   IES  +L + +    K   +  +G           
Sbjct: 230 KDATKNKDEALIDIYRKLRPGEPPTIESATQLINMMFFEHKRYDLAKVGRYKYNKKLALS 289

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + + G ++AED+V+  TGE+  E G  + E+    + ++ +  + I   + +N    ++ 
Sbjct: 290 NRITGKHLAEDVVDQLTGEVLFEKGHRLTEQDAITVDNTGLSHVFIEIREGINEGKVVK- 348

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            ++ +   D K  +      ++  D   +SV   + +    + +      + R ++  + 
Sbjct: 349 -VIGNTFVDIKAHIDFDISDLKFNDKVKYSVLREILDSCETEEEIRKQLKLRRNELYPK- 406

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                    HI  EDIIA I    +L +G G++DDID+LGNRR+R+VGE+L+NQ+R+G+ 
Sbjct: 407 ---------HITLEDIIASISYQFNLLHGVGSVDDIDHLGNRRIRTVGELLQNQFRIGMA 457

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER I+ER+++ D+  + P +LIN +PV SA+ EFF SSQLSQ  +  N LS +T+ RR
Sbjct: 458 RMERVIRERMTTQDVLEMTPNNLINIRPVTSAIREFFGSSQLSQFMDQTNPLSELTNKRR 517

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A++N YGFIE+
Sbjct: 518 LSALGPGGLSRERAGFEVRDVHYTHYGRMCPIETPEGPNIGLINSLSVYAKINEYGFIES 577

Query: 601 PYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           PYR+V   + KVT+ + YLSA EE+     QAN  + EDG F  + V CR   G   LV 
Sbjct: 578 PYRRVDKENKKVTDIIDYLSADEEDKYIRVQANEPIGEDGWFKNKKVACRVEKGALELVD 637

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + +D++D SP QVVS+A ++IPFLENDD+NR LMG NMQRQAVPL++ EAP +GT +E 
Sbjct: 638 ADLVDYVDVSPMQVVSVATAMIPFLENDDANRALMGSNMQRQAVPLVRREAPIIGTSIEY 697

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SGA +VAK  G+V++V A  I+I+        S   +D YRL+KF+RSN  TCVN
Sbjct: 698 RAAKDSGAVVVAKNDGVVDKVSADEILIKRD------SDGKIDRYRLLKFKRSNSGTCVN 751

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q PLV  GD ++  D+IADGP+T+LG++ALGRN L+AFM W GYN+ED++LI+ER+V ED
Sbjct: 752 QTPLVDKGDVLKVGDVIADGPATELGEIALGRNSLIAFMTWDGYNYEDAILINERLVKED 811

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +SIHIEE++  ARDTKLGPE ITRDIPNV  + +K++DE G+I +GAEV  GDILVGK
Sbjct: 812 RLSSIHIEEYDSEARDTKLGPEIITRDIPNVGADAIKDLDENGVIRIGAEVKSGDILVGK 871

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+  TPEE+LLRAIFGEKA DV+DTSLRVP G SG +VDV+ F R   D
Sbjct: 872 VSPKGETDTTPEERLLRAIFGEKARDVKDTSLRVPHGESGIIVDVKEFTRDNCD 925



 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 160/431 (37%), Positives = 219/431 (50%), Gaps = 58/431 (13%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K +R  S+  E+ +  ARD      I+ R+I +   + +   +     +     K   +L
Sbjct: 809  KEDRLSSIHIEEYDSEARDTKLGPEIITRDIPNVGADAIKDLDENGVIRIGAEVKSGDIL 868

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMP 1067
               +  +       +  +           +K               + K       D++ 
Sbjct: 869  VGKVSPKGETDTTPEERLLRAIFGEKARDVKDTSLRVPHGESGIIVDVKEFTRDNCDELS 928

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV R+V+V++A KR IQ GDKMAGRHGNKG++SR+LP EDMPFL DGTP++IVLNPLGV
Sbjct: 929  PGVNRMVRVYIAKKRKIQVGDKMAGRHGNKGVISRVLPEEDMPFLPDGTPLEIVLNPLGV 988

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D     DI                      
Sbjct: 989  PSRMNIGQVLEVHLGLAAKALGWHVATPVFDGAIEEDIFNALKLAGYPESGKLML----- 1043

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                                        G++       GE FD 
Sbjct: 1044 ------------------------------------------RDGRT-------GEYFDN 1054

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 1055 PVTVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1114

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            A+ LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE+Q+L L + +    
Sbjct: 1115 AHTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGIPESFKVLIKELQSLSLDVKVLTET 1174

Query: 1368 TKNSAKMEEIP 1378
             +     E+  
Sbjct: 1175 DEEIKVDEDTE 1185


>gi|291482479|dbj|BAI83554.1| DNA-directed RNA polymerase subunit beta [Bacillus subtilis subsp.
           natto BEST195]
          Length = 1146

 Score =  793 bits (2048), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/907 (45%), Positives = 572/907 (63%), Gaps = 68/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK
Sbjct: 53  -NKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL       
Sbjct: 109 KGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
                 D      S   L+           +  GE   +E+ K L        K      
Sbjct: 169 YLRNTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI  E G ++D ++L++            
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK------------ 270

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
            V     N      L  +      +  L   ++  P D                      
Sbjct: 271 -VLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD---------------------- 307

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               G   +N+  N    +++++I   DII+ I    +L +G G  DDID+LGNRR+RSV
Sbjct: 308 --QEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSV 365

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 366 GELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMD 425

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 426 QTNPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 485

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+A+VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ LD++G+F ++ +
Sbjct: 486 SYAKVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSI 545

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  +V R ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++
Sbjct: 546 VARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQ 605

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRL 764
            EAPFVGTGME V  K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L
Sbjct: 606 PEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSL 665

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           +KF RSNQ TC NQRP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+E
Sbjct: 666 LKFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYE 725

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +
Sbjct: 726 DAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRI 785

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++
Sbjct: 786 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKV 845

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 846 FNREDGD 852



 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 261/1174 (22%), Positives = 442/1174 (37%), Gaps = 125/1174 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 48   KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 107

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          + +D +  
Sbjct: 108  KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 166

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL+ VGR 
Sbjct: 167  NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRY 226

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E +    +IL      K      + +G R++  
Sbjct: 227  KINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYP 286

Query: 467  VGEMLKNQYRLGLLRM--------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             G +++++  L  +++        E+ I    ++   + +      +    +S       
Sbjct: 287  NGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLH 346

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                +   +H+ +    +    L    + G++R    V  R               +   
Sbjct: 347  GVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRP 406

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             I  +      ++++ +               TN +  L+                    
Sbjct: 407  VIASIKEFFGSSQLSQF------------MDQTNPLAELT------------------HK 436

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQ 697
                 L       E   +    + +        +       I  + +  S   +      
Sbjct: 437  RRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFI 496

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                  +  E   V   ++ + A      +VA+    +   D     I           +
Sbjct: 497  ETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARL---DDEGAFIDDSIVARFRGEN 553

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             V     + +   +    V+         E   ++    G +     + L +        
Sbjct: 554  TVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGT 613

Query: 818  WHGY---NFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               Y       + +I +   +V      ++ +  +E +      G  +    +  V    
Sbjct: 614  GMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQ 673

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     ++         +  D  +   
Sbjct: 674  GTCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII--- 729

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 730  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIG 786

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +          +   
Sbjct: 787  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV--- 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 844  ---KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 900

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 901  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 960

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 961  GMSRDAK----------------------------TVLYDG------------------- 973

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 974  -------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1026

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+K
Sbjct: 1027 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIK 1086

Query: 1353 EMQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            E+Q+LG+ + + +   +      +E+  D  + +
Sbjct: 1087 ELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQAD 1120


>gi|227903180|ref|ZP_04020985.1| DNA-directed RNA polymerase subunit beta [Lactobacillus acidophilus
           ATCC 4796]
 gi|227868985|gb|EEJ76406.1| DNA-directed RNA polymerase subunit beta [Lactobacillus acidophilus
           ATCC 4796]
          Length = 1189

 Score =  793 bits (2047), Expect = 0.0,   Method: Composition-based stats.
 Identities = 394/940 (41%), Positives = 573/940 (60%), Gaps = 79/940 (8%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           + +P+L +VQ  SY  FL          ++G++  F  + PI+ FSG   LE+V Y+   
Sbjct: 1   MKLPNLTDVQTESYKWFL----------DKGIKEVFDDIMPISDFSGKLSLEYVGYKLQK 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+    D TYA P+ +TL+L           +   +IK Q ++ GDLPLMT+ G+
Sbjct: 51  PKYTVDEARDHDATYAAPMHVTLKLT---------NQETGEIKTQDVFFGDLPLMTESGS 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ G +R++VSQL RSPG+++  D  +   +G+ ++   +IP++G W++ E D+K++ +
Sbjct: 102 FIVNGAERVIVSQLVRSPGVYYTGDYDK---NGRQIFGTTVIPNRGAWLEYETDAKNVSY 158

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VR+DR RK+P+T  + A+G+ S+ EI+  F          D      + AD  V   +  
Sbjct: 159 VRVDRTRKLPLTVLIRAMGIGSDSEIIEMFGQSDTLQFTLDKD-VHKNPADSRVAEALKD 217

Query: 263 SLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIV 313
               +  GE    +S + L        +   +  +G           + L G  +AE + 
Sbjct: 218 IYERLRPGEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLYGQTLAETLA 277

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           + +TGEI ++   V+  + ++++                                DR D 
Sbjct: 278 DPDTGEIIVKKDTVVTHEIMDKLAPYL----------------------------DRDDF 309

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            +  Y+  + G +      + +  +   D ++          + +  N     DV+H+  
Sbjct: 310 KMVTYQPSKEGVLPDPITVQEIKVYSKVDPERE---------VKLMSNGHIDADVKHLTP 360

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            D++A I     L++  GT DDID+LGNR +R VGE+L+NQ+R+GL RMER ++ER+S  
Sbjct: 361 ADVLASINYFFALQDKIGTTDDIDHLGNRCIRRVGELLQNQFRIGLARMERVVRERMSIQ 420

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D  +V PQ LIN +P+V+++ EFF SSQLSQ  +  N L  +TH RR+SALG GG+ R R
Sbjct: 421 DPSTVTPQQLINIRPIVASIKEFFGSSQLSQFMDQHNPLGELTHKRRMSALGPGGLTRDR 480

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVT 611
           AG E+RDVH THYGR+CP ET EG NIGL++SL S+A +N YGFIETPYR+V     KVT
Sbjct: 481 AGYEVRDVHYTHYGRLCPIETPEGPNIGLINSLASYAIINKYGFIETPYRRVSWDTHKVT 540

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YL+A EE+N  IA AN+ L++DGSF E+++  R   + + V  +KID++D  PKQV
Sbjct: 541 DKIDYLTADEEDNYIIAGANTPLNDDGSFKEDIILARQKEDNVEVTPDKIDYMDVIPKQV 600

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+A++ IPFLENDDSNR LMG N QRQA PL+   +  VGTGME   A  SGAA++AK 
Sbjct: 601 VSVASACIPFLENDDSNRALMGANQQRQAAPLINPHSSLVGTGMEYRAAHDSGAALIAKA 660

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG VE VDA  I IR  +G LD        Y L K++RSN +   NQ P VK+GD V  +
Sbjct: 661 AGTVEYVDADEIRIRREDGTLDK-------YTLEKYRRSNNSKSYNQTPNVKLGDHVDES 713

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D+IA+GP+ D G+LALG+N L+AFM W+ YN+ED++++SER+V +DV+TSI IE++E  A
Sbjct: 714 DVIANGPTMDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDVYTSISIEDYESEA 773

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLGPEEITR++PN+ E+ LK++D  GI+ VGAEV+ GDILVGK+TPKG + ++ EE+
Sbjct: 774 RDTKLGPEEITRELPNIGEDALKDLDADGIVRVGAEVHDGDILVGKVTPKGVTELSAEER 833

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL AIFGEKA +VRDTSLRVP G  G V DV+++ R   D
Sbjct: 834 LLHAIFGEKAREVRDTSLRVPHGGGGIVQDVKVYTREAGD 873



 Score =  474 bits (1220), Expect = e-131,   Method: Composition-based stats.
 Identities = 172/502 (34%), Positives = 237/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 704  VKLGDHVDESDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 760

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 761  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRV-----GAEVHDGDI 815

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 816  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 869

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 870  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVMPEEDMPYLPDGTPVDI 929

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 930  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANENDVW-------------- 975

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T ++DG                           
Sbjct: 976  -----------DTVRQAGMDKDG---KTVIYDG--------------------------R 995

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 996  TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1055

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1056 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1115

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   D ++
Sbjct: 1116 IRVLDMDHNEIELRDMDEDSSE 1137


>gi|292670073|ref|ZP_06603499.1| DNA-directed RNA polymerase subunit beta [Selenomonas noxia ATCC
           43541]
 gi|292648261|gb|EFF66233.1| DNA-directed RNA polymerase subunit beta [Selenomonas noxia ATCC
           43541]
          Length = 1246

 Score =  793 bits (2047), Expect = 0.0,   Method: Composition-based stats.
 Identities = 402/953 (42%), Positives = 561/953 (58%), Gaps = 98/953 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++++P L+++Q+ SY  FL            GL   F+ + PI  FSG
Sbjct: 9   RRTRYSYARIKEVMEMPHLLDIQRRSYQWFL----------EVGLAEIFRDISPIQDFSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F S+    PK+D+D+C  RD+TYA PL++ +RL+          +   +IKEQ +
Sbjct: 59  NLILSFESFALGEPKYDLDECKERDVTYAAPLRVNVRLV---------NRETGEIKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG ++  +      +GK LY   +IP++G 
Sbjct: 110 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGAYYGVEID---TTGKELYNATMIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ D++ VRIDR RK+PVT  + ALG +++ EI + F          +      
Sbjct: 167 WIELETDANDVVSVRIDRTRKMPVTYLIRALGYETDAEIRALFGDDPHILATIERDT--- 223

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITS-------- 300
                  G  V      +  GE   E + ++L   L    +   +  +G           
Sbjct: 224 -DEVKTRGKAVIEIYRRLRPGEPANEDNARQLLEVLFFDPRRYDLATVGRYKLTKKLGWR 282

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L G  +AE I++ ETGEI    G+ I  + ++ +       +                
Sbjct: 283 RRLLGKVLAEPIIDKETGEIVFPKGERITSEMVDAVSPERETAL---------------- 326

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                      +  L  + V +        +     ++ +    + D+       + +  
Sbjct: 327 ---------FGEGELVAFDVQKKDGEVHRMLCAPTRDYQYRTITREDVMAAISYLLGLMD 377

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                DD+ H+    + A+                            GE+L+NQ+R+GL 
Sbjct: 378 GFGYTDDIDHLGNRRVRAV----------------------------GELLQNQFRIGLS 409

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+S  + +S+ PQ LIN +PVV+AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 410 RMERVVRERMSIQETESITPQGLINIRPVVAAVKEFFGSSQLSQFMDQHNPLSELTHKRR 469

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP E+ EG NIGL+ SL ++ARVN +GF+ET
Sbjct: 470 LSALGPGGLSRERAGFEVRDVHNSHYGRMCPVESPEGPNIGLIGSLATYARVNQFGFMET 529

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V     +VT +V YL+A EE+   IAQAN  LDE+  F  E V  R   E  L  R
Sbjct: 530 PYRRVDKEHHRVTEEVRYLTADEEDELIIAQANEPLDENEFFVNERVTARFHEETGLHHR 589

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           + +D++D SP+QV SIA ++IPFLENDD+NR LMG NMQRQAVPLLK +AP VGTGME  
Sbjct: 590 DSVDYMDVSPRQVFSIATAMIPFLENDDANRALMGANMQRQAVPLLKTQAPLVGTGMEYK 649

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  SG  ++AK +G V +V A  I IR+ EG  D        Y+L KF RSNQ TC+NQ
Sbjct: 650 AACDSGVMVLAKHSGEVTEVSADAITIRTDEGAFD-------NYKLQKFVRSNQATCINQ 702

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +PLV  G+ +     IADGPSTD G+LALG N++VA+MPW GYN+ED++L+SE +V  D+
Sbjct: 703 KPLVYEGEHIAEGQPIADGPSTDNGELALGYNIIVAYMPWEGYNYEDAILLSENLVKRDL 762

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV+E+ LK++DE GI+ +GA+V PGDILVGK+
Sbjct: 763 YTSIHIEEYECDARDTKLGPEEITRDIPNVAEDALKDLDEDGIVSIGADVRPGDILVGKV 822

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G ++DV+IF R   D
Sbjct: 823 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIIDVKIFTRENND 875



 Score =  587 bits (1512), Expect = e-165,   Method: Composition-based stats.
 Identities = 274/1061 (25%), Positives = 416/1061 (39%), Gaps = 90/1061 (8%)

Query: 332  SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +  + +    +I  L+ D  +  A I     TD+ K R  A+++IYR +RPG+ +    
Sbjct: 193  LIRALGYETDAEIRALFGDDPHILATI--ERDTDEVKTRGKAVIEIYRRLRPGEPANEDN 250

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGK 450
            A  +   LFFD  +YDL+TVGR K+  +L        + +          +I+       
Sbjct: 251  ARQLLEVLFFDPRRYDLATVGRYKLTKKLGWRRRLLGKVLAEPIIDKETGEIVFPKGERI 310

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +         R     GE     + +     E        + D            + V+
Sbjct: 311  TSEMVDAVSPERETALFGEGELVAFDVQKKDGEVHRMLCAPTRDYQYRTIT----REDVM 366

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +A+             +       I H         G + + +  + +  +      R+ 
Sbjct: 367  AAISYLLGL------MDGFGYTDDIDHLGNRRVRAVGELLQNQFRIGLSRMERVVRERMS 420

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
              ET      GL++     A V  +             +  +    LS +  + R  A  
Sbjct: 421  IQETESITPQGLINIRPVVAAVKEFFGSSQL------SQFMDQHNPLSELTHKRRLSALG 474

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
               L             R      +       +    P +        I  + +  +   
Sbjct: 475  PGGL------------SRERAGFEVRDVHNSHYGRMCPVES--PEGPNIGLIGSLATYAR 520

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            +            +  E   V   +  + A      I+A+    +   D     +     
Sbjct: 521  VNQFGFMETPYRRVDKEHHRVTEEVRYLTADEEDELIIAQANEPL---DENEFFVNERVT 577

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                  +G+     + +   +     +    +         +  A+              
Sbjct: 578  ARFHEETGLHHRDSVDYMDVSPRQVFS----IATAMIPFLENDDANRALMGANMQRQAVP 633

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR--DTKLGPEEITRDIPNV 868
            +L    P  G   E      +  V      S  + E    A    T  G  +  +    V
Sbjct: 634  LLKTQAPLVGTGME-YKAACDSGVMVLAKHSGEVTEVSADAITIRTDEGAFDNYKLQKFV 692

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                   I++  ++  G  +  G  +    +      +     ++ A    +  +  D  
Sbjct: 693  RSNQATCINQKPLVYEGEHIAEGQPIADGPSTDN-GELALGYNIIVAYMPWEGYNYEDAI 751

Query: 929  LRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            L   +        S  + +     R      E          E   +D  DE  I+    
Sbjct: 752  LLSENLVKRDLYTSIHIEEYECDARDTKLGPEEITRDIPNVAEDALKDL-DEDGIVSIGA 810

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R  +IL G+    G         L   +  E  R                 E      
Sbjct: 811  DVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EVRDTSL 853

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                         KI   +  D++PPGV R+V+V++A KR I  GDKM+GRHGNKG+VSR
Sbjct: 854  RVPHGEAGKIIDVKIFTRENNDELPPGVNRLVRVYIAQKRKISVGDKMSGRHGNKGVVSR 913

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+  EDMPFL DGTPVDIVLNPLGVPSRMN+GQ+ ETHLG AC  LG++IK         
Sbjct: 914  IMRQEDMPFLPDGTPVDIVLNPLGVPSRMNIGQVLETHLGMACRVLGQRIKDG------- 966

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                +  +   D     +    ++G+ ++TPVFDGA ++ +   
Sbjct: 967  --------------DPTVEGDLRTAGYDFDKNGMPLPDEAGIHIATPVFDGASDDDVFGT 1012

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +R A L + G+++LYDG TGEPF+  VTVG +YMLKL+H+V DK++ARSTG YSLVTQQP
Sbjct: 1013 IRAAGLPDDGKTVLYDGRTGEPFENRVTVGCVYMLKLHHLVDDKIHARSTGPYSLVTQQP 1072

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YESIV G++  E G
Sbjct: 1073 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYESIVKGDNIPEPG 1132

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKM-EEIPDFNK 1382
             PESF VL+KE+QA+GL I + N   K  A   EE  D N+
Sbjct: 1133 VPESFKVLIKELQAIGLDIKVLNEDAKEIAIRDEEDEDINE 1173


>gi|302379630|ref|ZP_07268115.1| DNA-directed RNA polymerase, beta subunit [Finegoldia magna
           ACS-171-V-Col3]
 gi|303234539|ref|ZP_07321176.1| DNA-directed RNA polymerase, beta subunit [Finegoldia magna
           BVS033A4]
 gi|302312537|gb|EFK94533.1| DNA-directed RNA polymerase, beta subunit [Finegoldia magna
           ACS-171-V-Col3]
 gi|302494373|gb|EFL54142.1| DNA-directed RNA polymerase, beta subunit [Finegoldia magna
           BVS033A4]
          Length = 1184

 Score =  793 bits (2047), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/947 (43%), Positives = 593/947 (62%), Gaps = 53/947 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F +N  ++ +P+LI +Q  S+D F+           +G++  F+ + PI  ++G+ +
Sbjct: 11  RVSFSRNKNVLGLPNLIGIQTDSFDWFV----------KKGIKEVFEDISPIKDYAGSLV 60

Query: 74  LEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           LEFV Y F+  PK+ + +   RD  Y+ PLK+ +RLI  D +         ++KEQ ++M
Sbjct: 61  LEFVDYYFEENPKYTIQEAKDRDTNYSCPLKVKVRLINTDTE---------EVKEQEVFM 111

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT  GTF+I G +R++VSQL RSPG++F  +  +   SG   +A  +IP++G W+
Sbjct: 112 GDFPLMTDSGTFIINGAERVIVSQLVRSPGVYFAEEIDK---SGNSNFASTVIPNRGAWL 168

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +++ D+  ++++RIDR RK+PVT+ L AL  D++ EI+       +  +  +        
Sbjct: 169 EMDTDASGVVNIRIDRTRKLPVTTLLRALLFDTDDEIIEAMGDSEILRKTLEKEISKDRE 228

Query: 252 ADLMVGAKV--SSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
           + L+   K         +++ E +I +    +    L K  + K  K L +  D +    
Sbjct: 229 SALIEIYKKLKPGDPASLESAEPLINNMFFDSRRYDLAKVGRYKFNKKLSL-RDRITNQK 287

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             ED+V+  TGEI   AGD+I E+   EI ++ I  + ++  +  +    I N  V   +
Sbjct: 288 AKEDVVDTSTGEILATAGDLITEEMAIEIENAGINVVDVVGHEGQSV-RVIGNHFVDLDS 346

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 L D    +   +   + + E +        ++ D     R  +   ++  +P  
Sbjct: 347 FGLDMDLSD----LNLSEKVYYPIMEKIL-------EENDDEKSIRRAIEENVHQLSPI- 394

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             HI   DI+A I    +L  G G+ DDID+LGNRRVR++GE+L+NQ+R+GL RMER ++
Sbjct: 395 --HIIHSDILASINYEFNLFFGIGSTDDIDHLGNRRVRTIGELLQNQFRIGLSRMERVVR 452

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+S+ D D   PQ LIN +PV +A+ EFF SSQLSQ  E  N L+ +TH RRLSALG G
Sbjct: 453 ERMSTQDPDLATPQSLINVRPVTAAIKEFFGSSQLSQFMEQTNPLAELTHKRRLSALGPG 512

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAGVE+RDVH +HYGRICP ET EG NIGL++S+T+++  N YGF+ETPYR+V  
Sbjct: 513 GLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSMTTYSTTNEYGFLETPYRRVDK 572

Query: 608 GK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFI 664
               VT D+VYL+A EE+   IAQAN  LDE+  F  E V  R   GE  + PRE ID++
Sbjct: 573 ETGEVTEDIVYLTADEEDKYIIAQANEPLDENSRFINERVSGRGINGENDIYPRELIDYM 632

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q+VS+  ++IPFLENDD+ R LMG NMQRQAVPLL  +AP +GTG+E   AK SG
Sbjct: 633 DVSPQQIVSVGTAMIPFLENDDATRALMGSNMQRQAVPLLATQAPIIGTGIEHKAAKDSG 692

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AK  G V +V +  I I   E         VD Y + KF+++NQ T  NQRP+V  
Sbjct: 693 VVVKAKHKGTVTKVSSDIIEITRDEDRK------VDKYTIRKFKKANQGTTFNQRPIVNK 746

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V  +DIIADGPST +G++ALG+N+L+AFM W GYN+ED+ML++E++V +DV TS+HI
Sbjct: 747 GDKVDVDDIIADGPSTHMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVLTSVHI 806

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE E  AR+TKLG EEIT+DIPN+ E+  KN+D+ GII +GAEV  GDILVGK+TPKGE+
Sbjct: 807 EEHESEARETKLGAEEITKDIPNIGEDMRKNLDDEGIIRIGAEVKSGDILVGKVTPKGET 866

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++ EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+ ++R   D
Sbjct: 867 ELSAEERLLRAIFGEKAREVRDTSLRVPHGESGVVVDVKTYSRANGD 913



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 185/509 (36%), Positives = 254/509 (49%), Gaps = 79/509 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V+  DI+    +      M   + +L A    +  +  D  L     V   V+
Sbjct: 743  IVNKGDKVDVDDIIADGPST-HMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVL 801

Query: 941  DVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H  +  E  +  E          E + ++ DDE  I+      +  +IL G+ 
Sbjct: 802  TSVHIEEHESEARETKLGAEEITKDIPNIGEDMRKNLDDE-GIIRIGAEVKSGDILVGKV 860

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R      +++    +  V      Y  +         
Sbjct: 861  TPKGETELSAEERLLRAIFGEKARE-VRDTSLRVPHGESGVVVDVKTYSRA--------- 910

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                    GD++ PGV +VV+VFVA KR I  GDKM GRHGNKG+VSRI+P EDMP+L D
Sbjct: 911  -------NGDELSPGVNKVVRVFVATKRKIMVGDKMCGRHGNKGVVSRIMPEEDMPYLPD 963

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPV +VLNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D  ++ +I         
Sbjct: 964  GTPVQVVLNPLGVPSRMNIGQVLEVHLGLAASKLGWKVATPVFDGASDLEI--------- 1014

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                            +  L  A   K+G                   L        G++
Sbjct: 1015 ----------------EDALEEAGYPKTG----------------KIWL------RDGRT 1036

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   GE FD PVTVGY+YMLKL+HMV++K++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1037 -------GEYFDNPVTVGYMYMLKLHHMVAEKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1089

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+
Sbjct: 1090 GEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLIKEL 1149

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            Q+L L + L +   +    +EE  D N+ 
Sbjct: 1150 QSLSLDVKLLDENNEEVELIEEDDDSNEF 1178


>gi|169824815|ref|YP_001692426.1| DNA-directed RNA polymerase subunit beta [Finegoldia magna ATCC
           29328]
 gi|167831620|dbj|BAG08536.1| DNA-directed RNA polymerase beta subunit [Finegoldia magna ATCC
           29328]
          Length = 1184

 Score =  793 bits (2047), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/947 (43%), Positives = 593/947 (62%), Gaps = 53/947 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F +N  ++ +P+LI +Q  S+D F+           +G++  F+ + PI  ++G+ +
Sbjct: 11  RVSFSRNKNVLGLPNLIGIQTDSFDWFV----------KKGIKEVFEDISPIKDYAGSLV 60

Query: 74  LEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           LEFV Y F+  PK+ + +   RD  Y+ PLK+ +RLI  D +         ++KEQ ++M
Sbjct: 61  LEFVDYYFEENPKYTIQEAKDRDTNYSCPLKVKVRLINTDTE---------EVKEQEVFM 111

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT  GTF+I G +R++VSQL RSPG++F  +  +   SG   +A  +IP++G W+
Sbjct: 112 GDFPLMTDSGTFIINGAERVIVSQLVRSPGVYFAEEIDK---SGNSNFASTVIPNRGAWL 168

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +++ D+  ++++RIDR RK+PVT+ L AL  D++ EI+       +  +  +        
Sbjct: 169 EMDTDASGVVNIRIDRTRKLPVTTLLRALLFDTDDEIIEAMGDSEILRKTLEKEISKDRE 228

Query: 252 ADLMVGAKV--SSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
           + L+   K         +++ E +I +    +    L K  + K  K L +  D +    
Sbjct: 229 SALIEIYKKLKPGDPASLESAEPLINNMFFDSRRYDLAKVGRYKFNKKLSL-RDRITNQK 287

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             ED+V+  TGEI   AGD+I E+   EI ++ I  + ++  +  +    I N  V   +
Sbjct: 288 AKEDVVDTSTGEILATAGDLITEEMAIEIENAGINVVDVVGHEGQSV-RVIGNHFVDLDS 346

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 L D    +   +   + + E +        ++ D     R  +   ++  +P  
Sbjct: 347 FGLDMDLSD----LNLSEKVYYPIMEKIL-------EENDDEKSIRRAIEENVHQLSPI- 394

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             HI   DI+A I    +L  G G+ DDID+LGNRRVR++GE+L+NQ+R+GL RMER ++
Sbjct: 395 --HIIHSDILASINYEFNLFFGIGSTDDIDHLGNRRVRTIGELLQNQFRIGLSRMERVVR 452

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+S+ D D   PQ LIN +PV +A+ EFF SSQLSQ  E  N L+ +TH RRLSALG G
Sbjct: 453 ERMSTQDPDLATPQSLINVRPVTAAIKEFFGSSQLSQFMEQTNPLAELTHKRRLSALGPG 512

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAGVE+RDVH +HYGRICP ET EG NIGL++S+T+++  N YGF+ETPYR+V  
Sbjct: 513 GLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSMTTYSTTNEYGFLETPYRRVDK 572

Query: 608 GK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFI 664
               VT D+VYL+A EE+   IAQAN  LDE+  F  E V  R   GE  + PRE ID++
Sbjct: 573 ETGEVTEDIVYLTADEEDKYIIAQANEPLDENSRFINERVSGRGINGENDIYPRELIDYM 632

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q+VS+  ++IPFLENDD+ R LMG NMQRQAVPLL  +AP +GTG+E   AK SG
Sbjct: 633 DVSPQQIVSVGTAMIPFLENDDATRALMGSNMQRQAVPLLATQAPIIGTGIEHKAAKDSG 692

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AK  G V +V +  I I   E         VD Y + KF+++NQ T  NQRP+V  
Sbjct: 693 VVVKAKHKGTVTKVSSDIIEITRDEDRK------VDKYTIRKFKKANQGTTFNQRPIVNK 746

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V  +DIIADGPST +G++ALG+N+L+AFM W GYN+ED+ML++E++V +DV TS+HI
Sbjct: 747 GDKVDVDDIIADGPSTHMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVLTSVHI 806

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE E  AR+TKLG EEIT+DIPN+ E+  KN+D+ GII +GAEV  GDILVGK+TPKGE+
Sbjct: 807 EEHESEARETKLGAEEITKDIPNIGEDMRKNLDDEGIIRIGAEVKSGDILVGKVTPKGET 866

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++ EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+ ++R   D
Sbjct: 867 ELSAEERLLRAIFGEKAREVRDTSLRVPHGESGVVVDVKTYSRANGD 913



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 187/509 (36%), Positives = 257/509 (50%), Gaps = 79/509 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V+  DI+    +      M   + +L A    +  +  D  L     V   V+
Sbjct: 743  IVNKGDKVDVDDIIADGPST-HMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVL 801

Query: 941  DVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H  +  E  +  E          E + ++ DDE  I+      +  +IL G+ 
Sbjct: 802  TSVHIEEHESEARETKLGAEEITKDIPNIGEDMRKNLDDE-GIIRIGAEVKSGDILVGKV 860

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R      +++    +  V      Y  +         
Sbjct: 861  TPKGETELSAEERLLRAIFGEKARE-VRDTSLRVPHGESGVVVDVKTYSRA--------- 910

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                    GD++ PGV +VV+VFVA KR I  GDKM GRHGNKG+VSRI+P EDMP+L D
Sbjct: 911  -------NGDELSPGVNKVVRVFVATKRKIMVGDKMCGRHGNKGVVSRIMPEEDMPYLPD 963

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPV +VLNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D  ++ +I         
Sbjct: 964  GTPVQVVLNPLGVPSRMNIGQVLEVHLGLAASKLGWKVATPVFDGASDLEI--------- 1014

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     E+A+      A   ++G+ 
Sbjct: 1015 -----------------------------------------EDALKE----AGYPKTGKI 1029

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG TGE FD PVTVGY+YMLKL+HMV++K++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1030 WLRDGRTGEYFDNPVTVGYMYMLKLHHMVAEKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1089

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+
Sbjct: 1090 GEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLIKEL 1149

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            Q+L L + L +   +    +EE  D N+ 
Sbjct: 1150 QSLSLDVKLLDENNEEVELIEEDDDSNEF 1178


>gi|297587198|ref|ZP_06945843.1| DNA-directed RNA polymerase subunit beta [Finegoldia magna ATCC
           53516]
 gi|297575179|gb|EFH93898.1| DNA-directed RNA polymerase subunit beta [Finegoldia magna ATCC
           53516]
          Length = 1184

 Score =  792 bits (2046), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/947 (43%), Positives = 594/947 (62%), Gaps = 53/947 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F +N  ++ +P+LI +Q  S+D F+           +G++  F+ + PI  ++G+ +
Sbjct: 11  RVSFSRNKNVLGLPNLIGIQTDSFDWFV----------KKGIKEVFEDISPIKDYAGSLV 60

Query: 74  LEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           LEFV Y F+  PK+ + +   RD  Y+ PLK+ +RLI  D +         ++KEQ ++M
Sbjct: 61  LEFVDYYFEENPKYTIQEAKDRDTNYSCPLKVKVRLINTDTE---------EVKEQEVFM 111

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT  GTF+I G +R++VSQL RSPG++F  +  +   SG   +A  +IP++G W+
Sbjct: 112 GDFPLMTDSGTFIINGAERVIVSQLVRSPGVYFAEEIDK---SGNSNFASTVIPNRGAWL 168

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSA 251
           +++ D+  ++++RIDR RK+PVT+ L AL  D++E I+       +  +  +        
Sbjct: 169 EMDTDASGVVNIRIDRTRKLPVTTLLRALLFDTDEEIIEAMGDSEILRKTLEKEISKDRE 228

Query: 252 ADLMVGAKV--SSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLY 307
           + L+   K         +++ E +I +    +    L K  + K  K L +  D +    
Sbjct: 229 SALIEIYKKLKPGDPASLESAEPLINNMFFDSRRYDLAKVGRYKFNKKLSL-RDRITNQK 287

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             ED+V+  TGEI   AGD+I E+   EI ++ I  + ++  +  +    I N  V   +
Sbjct: 288 AKEDVVDTSTGEILATAGDLITEEMAIEIENAGINVVDVIGHEGQSV-RVIGNHFVDLDS 346

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 L D    +   +   + + E +        ++ D     R  +   ++  +P  
Sbjct: 347 FGLDMDLSD----LNLSEKVYYPIMEKIL-------EENDDEKSIRRAIEENVHQLSPI- 394

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             HI   DI+A I    +L  G G+ DDID+LGNRRVR++GE+L+NQ+R+GL RMER ++
Sbjct: 395 --HIIHSDILASINYEFNLFFGIGSTDDIDHLGNRRVRTIGELLQNQFRIGLSRMERVVR 452

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+S+ D D   PQ LIN +PV +A+ EFF SSQLSQ  E  N L+ +TH RRLSALG G
Sbjct: 453 ERMSTQDPDLATPQSLINVRPVTAAIKEFFGSSQLSQFMEQTNPLAELTHKRRLSALGPG 512

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAGVE+RDVH +HYGRICP ET EG NIGL++S+T+++  N YGF+ETPYR+V  
Sbjct: 513 GLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSMTTYSTTNEYGFLETPYRRVDK 572

Query: 608 GK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFI 664
               VT D+VYL+A EE+   IAQAN  LDE+  F  E V  R   GE  + PRE ID++
Sbjct: 573 ETGEVTEDIVYLTADEEDKYIIAQANEPLDENSRFINERVSGRGINGENDIYPRELIDYM 632

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q+VS+  ++IPFLENDD+ R LMG NMQRQAVPLL  +AP +GTG+E   AK SG
Sbjct: 633 DVSPQQIVSVGTAMIPFLENDDATRALMGSNMQRQAVPLLATQAPIIGTGIEHKAAKDSG 692

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AK  G V +V +  I I   E         VD Y + KF+++NQ T  NQRP+V  
Sbjct: 693 VVVKAKHKGTVTKVSSDIIEITRDEDRK------VDKYTIRKFKKANQGTTFNQRPIVNK 746

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V  +DIIADGPST++G++ALG+N+L+AFM W GYN+ED+ML++E++V +DV TS+HI
Sbjct: 747 GDKVDVDDIIADGPSTNMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVLTSVHI 806

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE E  AR+TKLG EEIT+DIPN+ E+  KN+D+ GII +GAEV  GDILVGK+TPKGE+
Sbjct: 807 EEHESEARETKLGAEEITKDIPNIGEDMRKNLDDEGIIRIGAEVKSGDILVGKVTPKGET 866

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++ EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV+ ++R   D
Sbjct: 867 ELSAEERLLRAIFGEKAREVRDTSLRVPHGESGVVVDVKTYSRANGD 913



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 184/509 (36%), Positives = 254/509 (49%), Gaps = 79/509 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V+  DI+    +      M   + +L A    +  +  D  L     V   V+
Sbjct: 743  IVNKGDKVDVDDIIADGPST-NMGEMALGKNILIAFMTWEGYNYEDAMLLNEKLVVDDVL 801

Query: 941  DVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H  +  E  +  E          E + ++ DDE  I+      +  +IL G+ 
Sbjct: 802  TSVHIEEHESEARETKLGAEEITKDIPNIGEDMRKNLDDE-GIIRIGAEVKSGDILVGKV 860

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R      +++    +  V      Y  +         
Sbjct: 861  TPKGETELSAEERLLRAIFGEKARE-VRDTSLRVPHGESGVVVDVKTYSRA--------- 910

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                    GD++ PGV +VV+VFVA KR I  GDKM GRHGNKG+VSRI+P EDMP+L D
Sbjct: 911  -------NGDELSPGVNKVVRVFVATKRKIMVGDKMCGRHGNKGVVSRIMPEEDMPYLPD 963

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPV +VLNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D  ++ +I         
Sbjct: 964  GTPVQVVLNPLGVPSRMNIGQVLEVHLGLAASKLGWKVATPVFDGASDIEI--------- 1014

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                            +  L  A   K+G                   L        G++
Sbjct: 1015 ----------------EDALEEAGYPKTG----------------KIWL------RDGRT 1036

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   GE FD PVTVGY+YMLKL+HMV++K++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 1037 -------GEYFDNPVTVGYMYMLKLHHMVAEKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1089

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE+
Sbjct: 1090 GEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLIKEL 1149

Query: 1355 QALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            Q+L L + L +   +    +EE  D ++ 
Sbjct: 1150 QSLSLDVKLLDENNEEVELIEEDDDSSEF 1178


>gi|228989311|ref|ZP_04149302.1| DNA-directed RNA polymerase subunit beta [Bacillus pseudomycoides
           DSM 12442]
 gi|228995492|ref|ZP_04155160.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides
           Rock3-17]
 gi|228764221|gb|EEM13100.1| DNA-directed RNA polymerase subunit beta [Bacillus mycoides
           Rock3-17]
 gi|228770389|gb|EEM18962.1| DNA-directed RNA polymerase subunit beta [Bacillus pseudomycoides
           DSM 12442]
          Length = 1129

 Score =  791 bits (2043), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/907 (45%), Positives = 565/907 (62%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGEPKYSVEECKERDVTYAAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK
Sbjct: 53  -NKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI        
Sbjct: 109 RGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
             S   +      +   L+           +  GE   +E+ K L        K      
Sbjct: 169 YLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I   
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG-- 280

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                                                  +         +        Y 
Sbjct: 281 ------------------------------------FKTAKPMGGVVEGDVELQSIKIYA 304

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSV
Sbjct: 305 PESDGERSINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           SFA+VN +GFIETPYR+V    G+VT  V YL+A EE+N  +AQAN  L E+G F +E +
Sbjct: 485 SFAKVNEFGFIETPYRRVDPETGRVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDI 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 545 VARFRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMN 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRL 764
            E+P VGTGME V AK SGAA++ K  G VE+V+A  + +R  VE D       +D Y++
Sbjct: 605 PESPIVGTGMEYVSAKDSGAAVICKHPGTVERVEAREVWVRRYVEVDGQKVKGDLDRYKM 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           +KF RSNQ TC NQRP+V VGD+V + +I+ADGPS + G+LALGRN+LV FM W GYN+E
Sbjct: 665 LKFIRSNQGTCYNQRPIVSVGDQVVKGEILADGPSMEKGELALGRNVLVGFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII V
Sbjct: 725 DAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRV 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++
Sbjct: 785 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREDGD 851



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 264/1167 (22%), Positives = 436/1167 (37%), Gaps = 124/1167 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 48   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 107

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 108  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 166

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 167  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 226

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 227  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 286

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ERSI    ++     V     I    +++++  FF  
Sbjct: 287  MGGVVEGDVELQSIKIYAPESDGERSINVIGNANITRDV---KHITPGDILASISYFFNL 343

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 344  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 397

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 398  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 436

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 437  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 496

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 497  TPYRRVDPETGRVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 556

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 557  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 612

Query: 815  FMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +    V       + +  +  +      G  +  + +  +    
Sbjct: 613  GMEYVSAKDSGAAVICKHPGTVERVEAREVWVRRYVEVDGQKVKGDLDRYKMLKFIRSNQ 672

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG +V  G+IL    +   +  +     +L         +  D  +   
Sbjct: 673  GTCYNQRPIVSVGDQVVKGEILADGPS-MEKGELALGRNVLVGFMTWDGYNYEDAII--- 728

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 729  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 785

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 786  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 839

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 840  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 899

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 900  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 959

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 960  GMANDAK----------------------------TILYDG------------------- 972

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 973  -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1025

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1026 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1085

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPD 1379
            E+Q+LG+ + + +S        +   D
Sbjct: 1086 ELQSLGMDVKMMSSDDTEIEMRDTEDD 1112


>gi|168334900|ref|ZP_02693021.1| DNA-directed RNA polymerase, beta subunit [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 1420

 Score =  791 bits (2043), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/952 (44%), Positives = 589/952 (61%), Gaps = 55/952 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            +VR  +  + EI +IP+LIE+Q  SY  FL           EGL   FK + PI  F+G
Sbjct: 13  KQVRMSYALSNEIFEIPNLIEIQTDSYKWFL----------EEGLDEVFKDISPIVDFNG 62

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             MLEF+++  DP  K+ V++   +D+ YA  LK+ +RL           K   +  +  
Sbjct: 63  NLMLEFINFSLDPHSKYTVEEAKEKDVNYAASLKVKVRLY---------NKETGESMDND 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGDLPLMT+ G+F+I G +R++VSQL RSPGI+++ +  +    GK L++  +IP++G
Sbjct: 114 VFMGDLPLMTETGSFIINGAERVIVSQLVRSPGIYYNREFDKF---GKRLFSATVIPNRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP--KIVYSQRGDFWC 246
            W++ E DS DI +VR+DR RKVPVT  + AL + +  EI+  F    KI+ S   D   
Sbjct: 171 AWLEYETDSNDIFYVRVDRTRKVPVTVLMRALRLGTNVEIIDMFGEEPKILASIEKDGSN 230

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
                   +           +++ E ++ +    +    L K  + K  K L +  + + 
Sbjct: 231 SYEEGLIEIYKRVRPGEPPTVESAETLLANMFFDSRRYDLAKVGRYKFNKKLAL-KNRVK 289

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +AED+VN  TGE+  EAGD I E+  + I ++   ++ I   D       + N +V 
Sbjct: 290 GFTLAEDVVNMVTGEVVAEAGDKISEELADIIQNTGTSNVKIEISDLDRPVVVLTNQMVD 349

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                  D +    +     +   + V   +      +SD  ++  + + +MN  +    
Sbjct: 350 ITQFVDIDKVEFGIK-----ENVYYPVLAEIIEN---NSDIDEIKELIKQRMNELIP--- 398

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               +HI  EDI A +  +++L  G G  DDID+LGNRR+R+VGE+L+NQ+R+GL RMER
Sbjct: 399 ----KHITSEDIFASMNYVINLEYGIGARDDIDHLGNRRIRAVGELLQNQFRIGLTRMER 454

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           S++ER+++   +   PQ  IN +PV +A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 455 SVRERMTTQTDEPANPQTFINIRPVTAAIKEFFGSSQLSQFMDQNNPLAELTHKRRLSAL 514

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FAR+N YGFIE PYR 
Sbjct: 515 GPGGLSRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLATFARINEYGFIEAPYRI 574

Query: 605 VCD-----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           V         VT +  Y++A EEE+  I QA   L  D  F  + +  R   E +    +
Sbjct: 575 VKKDENGEPVVTEEFRYVTADEEESYTICQATEELTNDMHFVRKKITARRREEILEFDYK 634

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +ID +D S +Q+VS+A ++IPFLENDD+NR LMG NMQRQAVPL+K  +P VGTGME+  
Sbjct: 635 EIDMMDISSRQIVSVATAMIPFLENDDANRALMGANMQRQAVPLIKTNSPIVGTGMEAKA 694

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           AK +G  I+AK  G+ E V +  I+IR  E           +Y L KF RSNQ TC+NQR
Sbjct: 695 AKDAGVLIIAKEDGVAESVTSREIIIREDETMR------RRVYTLTKFTRSNQGTCINQR 748

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL+  GD VR+ +IIADGPST+ G+LALG+N L+ FM W GYNFED++L+SER+V EDV+
Sbjct: 749 PLISRGDFVRKGEIIADGPSTENGELALGQNPLIGFMTWEGYNFEDAILLSERLVKEDVY 808

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS+HIEE+EV ARDTK+G EEITRDIPN +EE LK++DE GII +GAEV  GDILVG++T
Sbjct: 809 TSVHIEEYEVEARDTKVGTEEITRDIPNTNEESLKDLDERGIIRIGAEVRAGDILVGRVT 868

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +T EE+LLRAIFGEK  +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 869 PKGETELTAEERLLRAIFGEKVREVRDTSLRVPHGEAGIIVDVKIFTRENDD 920



 Score =  545 bits (1404), Expect = e-152,   Method: Composition-based stats.
 Identities = 257/1147 (22%), Positives = 432/1147 (37%), Gaps = 91/1147 (7%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDC---LCGLYVAEDIVNGETG----------EIY 321
            E+G  + +G  + +  + V+  GI  +      G  +    V    G          +I+
Sbjct: 124  ETGSFIINGAERVIVSQLVRSPGIYYNREFDKFGKRLFSATVIPNRGAWLEYETDSNDIF 183

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                D   +  +  +  +      +  +D       I  ++  D +   ++ L++IY+ +
Sbjct: 184  YVRVDRTRKVPVTVLMRALRLGTNVEIIDMFGEEPKILASIEKDGSNSYEEGLIEIYKRV 243

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
            RPG+  T   AE++   +FFDS +YDL+ VGR K N +L L        + ++       
Sbjct: 244  RPGEPPTVESAETLLANMFFDSRRYDLAKVGRYKFNKKLALKNRVKGFTLAED------- 296

Query: 442  ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             +V++  G+   +  D +       +     +  ++ +  ++R +    + +   +    
Sbjct: 297  -VVNMVTGEVVAEAGDKISEELADIIQNTGTSNVKIEISDLDRPVVVLTNQMVDITQFVD 355

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                   +   V     +  +    +       I   +R++ L    +        M  V
Sbjct: 356  IDKVEFGIKENVYYPVLAEIIENNSDIDEIKELI--KQRMNELIPKHITSEDIFASMNYV 413

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN--------- 612
                YG     +     N   + ++    +      +    R V +   T          
Sbjct: 414  INLEYGIGARDDIDHLGN-RRIRAVGELLQNQFRIGLTRMERSVRERMTTQTDEPANPQT 472

Query: 613  --DVVYLSAMEEENRYIAQANSSLDEDG--------SFTEELVFCRCAGEEILVPREKID 662
              ++  ++A  +E    +Q +  +D++              L     + E        + 
Sbjct: 473  FINIRPVTAAIKEFFGSSQLSQFMDQNNPLAELTHKRRLSALGPGGLSRERAGFEVRDVH 532

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +        +         L N  +    +      +A   +  +      G   V  + 
Sbjct: 533  YSHYGRMCPIETPEGPNIGLINSLATFARINEYGFIEAPYRIVKKDE---NGEPVVTEEF 589

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                   + +  + Q                 +    +I      +    +    Q   V
Sbjct: 590  RYVTADEEESYTICQATEELTNDMHFVRKKITARRREEILEFDYKEIDMMDISSRQIVSV 649

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDV 838
                     +  A+              ++    P  G   E        ++     + V
Sbjct: 650  ATAMIPFLENDDANRALMGANMQRQAVPLIKTNSPIVGTGMEAKAAKDAGVLIIAKEDGV 709

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              S+   E  ++ R+ +     +              I++  +I  G  V  G+I+    
Sbjct: 710  AESVTSRE--IIIREDETMRRRVYTLTKFTRSNQGTCINQRPLISRGDFVRKGEIIADGP 767

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            + +    +   +  L      +  +  D  L     V   V        + ++  +  + 
Sbjct: 768  STEN-GELALGQNPLIGFMTWEGYNFEDAILLSERLVKEDVYTSVHIEEYEVEARDTKVG 826

Query: 959  VER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             E          E   +D  DE+ I+      R  +IL G+    G         L   +
Sbjct: 827  TEEITRDIPNTNEESLKDL-DERGIIRIGAEVRAGDILVGRVTPKGETELTAEERLLRAI 885

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              E  R                 E                   KI   +  D++ PGV R
Sbjct: 886  FGEKVR-----------------EVRDTSLRVPHGEAGIIVDVKIFTRENDDELSPGVNR 928

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+ ++A KR I  GDKMAGRHGNKG++SR+LP EDMPFL +G P+DIVLNPLGVPSRMN
Sbjct: 929  MVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPAEDMPFLPNGRPLDIVLNPLGVPSRMN 988

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLG A   LG KI + + D     DI          +      +    + D  
Sbjct: 989  IGQVLEVHLGLAAKALGFKIATPVFDGANEQDIMQTLEMANDYVNLEDFEDFRDLWADKL 1048

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                 +  +  +                   +   +D +G+  L DG TGE FD PVTVG
Sbjct: 1049 KPSALQYLEDNL-------------EHRQEWQGVPIDRTGKIRLRDGRTGEEFDNPVTVG 1095

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y++ LKL+H+V DK++ARSTG Y+ +TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1096 YMHYLKLHHLVDDKMHARSTGPYATITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 1155

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LTIKSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL I +         
Sbjct: 1156 EILTIKSDDVVGRVKAYEAIVKGENIPEPGIPESFKVLLKELQSLGLDIKVMTDDI-EIE 1214

Query: 1373 KMEEIPD 1379
              E I D
Sbjct: 1215 IKENIYD 1221


>gi|227500329|ref|ZP_03930396.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
 gi|227217615|gb|EEI82927.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
          Length = 1235

 Score =  791 bits (2043), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/954 (44%), Positives = 596/954 (62%), Gaps = 55/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              RK F K P+++D+P+L++VQK SY+ FL           EGL    + + PI  ++G
Sbjct: 11  RTKRKSFSKFPQVLDLPNLLKVQKDSYEWFL----------KEGLGEILEDISPIEDYNG 60

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEF+ YEFD   K+ V +  ++D TYA  LK+  RLI          K  +++KEQ 
Sbjct: 61  NLILEFIGYEFDDETKYSVKESKYKDATYARDLKVKARLI---------NKETEEVKEQE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG  +Y+  +IP++G
Sbjct: 112 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYAEETDK---SGDKMYSSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +S+E I++            +     
Sbjct: 169 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFESDEEIINAIGDTEHLRNTLEKENSE 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            +   L+   +       +  G+   +ES   L + LL   +   +  +G          
Sbjct: 229 TAEEALIEIYR------KLKPGDPASVESATNLINNLLFDDRRYDLAKVGRYKYNLKLAL 282

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + + GL   +D+++ ETGE+++ AG++I E+    I ++ I  + ++  D  +    I 
Sbjct: 283 ANRIAGLRAKDDVIDAETGELFVSAGELITEEIANAIENAGIVTVDVIKKDDYSEEDKI- 341

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              V   N    +A  ++  +    D       +  F  +    ++       +  M  R
Sbjct: 342 -LRVVGNNFVDINAFDELKDLDINVD---DFSEKVYFPVMKEIIEEAASIDEIKTLMERR 397

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                P   +HI K DI+AI+    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+GL
Sbjct: 398 KKELCP---KHITKSDILAIVNYQFNLFEGIGHVDDIDHLGNRRVRGVGELLQNQFRVGL 454

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH R
Sbjct: 455 ARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKR 514

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++ARVN YGFIE
Sbjct: 515 RLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARVNKYGFIE 574

Query: 600 TPYRKVCDG-KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           TPYR V +G  VT+++ YL+A  E++  IAQAN  LD D  F    V  R   GE  + P
Sbjct: 575 TPYRLVKEGGYVTDEIDYLTADIEDDFIIAQANEPLDSDNRFVNARVSGRGIKGENDIYP 634

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           REKI ++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPL+K+EAP V TG+E 
Sbjct: 635 REKIQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLIKSEAPIVATGIEH 694

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +++K  G V  V    I ++        S   ++ Y L+KF+R+NQ T +N
Sbjct: 695 RAAKDSGVCVLSKSKGEVVYVGDEHIKVKRD------SDGKIEDYELLKFERANQGTTIN 748

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK GD V  N+I+ADGPST+ G+LALG+N+L+AF  W GYNFED+ML++E +V +D
Sbjct: 749 QRPIVKKGDRVEANEILADGPSTENGELALGKNILIAFTTWEGYNFEDAMLLNEELVMDD 808

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TS+HIEE E  AR+TKLG EEIT+DIPNV E+  K++DE GII +GAEV  GDILVGK
Sbjct: 809 VLTSVHIEEHECEARETKLGAEEITKDIPNVGEDMKKDLDENGIIRIGAEVKSGDILVGK 868

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL+VP G SG VVDV+ +N+   D
Sbjct: 869 VSPKGETELSPEERLLRAIFGEKAREVRDTSLKVPHGESGIVVDVKEYNKKDGD 922



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 260/1060 (24%), Positives = 421/1060 (39%), Gaps = 101/1060 (9%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++++ +  ++RNTL  + ++  ++AL++IYR ++PGD ++   A ++ N L FD  +YDL
Sbjct: 209  INAIGDTEHLRNTLEKENSETAEEALIEIYRKLKPGDPASVESATNLINNLLFDDRRYDL 268

Query: 409  STVGRVKMNMRLN--------LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            + VGR K N++L             D +     E  ++  +++ +          I  + 
Sbjct: 269  AKVGRYKYNLKLALANRIAGLRAKDDVIDAETGELFVSAGELITEEIANAIENAGIVTVD 328

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              +     E  K    +G   ++ +  + +  +DI+     + +    +   + E     
Sbjct: 329  VIKKDDYSEEDKILRVVGNNFVDINAFDELKDLDINVDDFSEKVYFPVMKEIIEEAASID 388

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            ++  L E         H  +   L                    H G        E    
Sbjct: 389  EIKTLMERRKKELCPKHITKSDILAIVNYQFNLFEGIGHVDDIDHLGNRRVRGVGELLQN 448

Query: 581  GLVSSLTSFARV------NAYGFIETPYRKVCDGKVTNDV-VYLSAMEEENRYIAQANSS 633
                 L    RV           + TP   +    VT  +  +  + +           S
Sbjct: 449  QFRVGLARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMS 508

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                      L     + +   V    +          +         L    +    + 
Sbjct: 509  ELTHKRRLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARVN 568

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                 +    L  E  +V   ++ + A      I+A+           R V   V G   
Sbjct: 569  KYGFIETPYRLVKEGGYVTDEIDYLTADIEDDFIIAQ--ANEPLDSDNRFVNARVSGRGI 626

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG----DEVRRNDIIADGPSTDLGDLALGR 809
               +  DIY   K     Q   V+ + +V VG      +  +D        ++   A+  
Sbjct: 627  KGEN--DIYPREK----IQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPL 680

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
                A +   G     +      ++S+     +++ +  +  +    G  E    +    
Sbjct: 681  IKSEAPIVATGIEHRAAKDSGVCVLSKSKGEVVYVGDEHIKVKRDSDGKIEDYELLKFER 740

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                  I++  I+  G  V   +IL    + +    +   + +L A    +  +  D  L
Sbjct: 741  ANQGTTINQRPIVKKGDRVEANEILADGPSTEN-GELALGKNILIAFTTWEGYNFEDAML 799

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIY 983
                 V   V+       H  +  E  +  E          E + +D  DE  I+     
Sbjct: 800  LNEELVMDDVLTSVHIEEHECEARETKLGAEEITKDIPNVGEDMKKDL-DENGIIRIGAE 858

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +  +IL G+ +  G         L   +  E  R      +++    +  +     +Y 
Sbjct: 859  VKSGDILVGKVSPKGETELSPEERLLRAIFGEKARE-VRDTSLKVPHGESGIVVDVKEYN 917

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                               GD++ PGV +V++V+VA KR I  GDKM GRHGNKG+VSRI
Sbjct: 918  KK----------------DGDELAPGVNKVIRVYVAAKRKIMVGDKMCGRHGNKGVVSRI 961

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A   +G KI + + D   + 
Sbjct: 962  LPREDMPFLPDGTPLQICLNPLGIPSRMNLGQVLEVHMGLAARTMGWKIATPVFDGALDT 1021

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            +I  +    +KV    + T KI+  D                                  
Sbjct: 1022 EIEEVLEEAKKVAPYVNKTGKITLRD---------------------------------- 1047

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                           G TG PF+ PVTVG +YMLKL+HMV +K++ARS G YSLVTQQPL
Sbjct: 1048 ---------------GRTGLPFENPVTVGVMYMLKLHHMVEEKIHARSIGPYSLVTQQPL 1092

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGA++ LQE+LT+KSDDV GR + YESIV G +  E GT
Sbjct: 1093 GGKAQFGGQRFGEMEVWALEAYGASHTLQEILTVKSDDVTGRVKTYESIVKGENIPEPGT 1152

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            PESF VLVKE+Q+L L ++L +S  +     E I + ++ 
Sbjct: 1153 PESFKVLVKELQSLALDVELLDSEGEVIELKENIDEQDRF 1192


>gi|212695871|ref|ZP_03303999.1| hypothetical protein ANHYDRO_00404 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212677125|gb|EEB36732.1| hypothetical protein ANHYDRO_00404 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 1236

 Score =  790 bits (2041), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/954 (44%), Positives = 605/954 (63%), Gaps = 56/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K P+++D+P+L++VQK SY  F+           EGL    + + PI  ++G
Sbjct: 10  KTERVSFSKFPQVLDLPNLLKVQKDSYRWFI----------EEGLGEILEDISPIEDYNG 59

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y+FD   K+ +++  ++D TY+  LK+  RLI          K  +++KEQ 
Sbjct: 60  NLILEFVGYDFDDETKYTIEEAKYKDTTYSRDLKVKARLI---------NKETEEVKEQE 110

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG  +Y+  +IP++G
Sbjct: 111 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYASELDK---SGNKMYSSTVIPNRG 167

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +++E I+             +     
Sbjct: 168 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFENDEEIIEALGDTEHLRNTLEKENSE 227

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            S   L+   K       +  G+   +ES + L + LL   +   +  +G          
Sbjct: 228 TSEEALIEIYK------KLKPGDPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLAL 281

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            D L     A+D+++ ETGE++++AG++ID ++   I +S I  + ++      ++  +R
Sbjct: 282 HDRLIDQISAKDVIDDETGELFVKAGEMIDRQTALNIENSGINVVDVIVKQENGDDKELR 341

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                    D  + L +I       D+S   ++E ++  +    +  D +      +N  
Sbjct: 342 ICGNHFVYLDSFEELEEI-------DLSNIELSEKVYYPVM--REILDDNEDEESIINEI 392

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    ++I K DI+A +    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+GL
Sbjct: 393 ERRKKELCPKNIVKSDILAAVNYQFNLFEGIGDVDDIDHLGNRRVRGVGELLQNQFRIGL 452

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH R
Sbjct: 453 ARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKR 512

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++AR+N YGFIE
Sbjct: 513 RLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARINKYGFIE 572

Query: 600 TPYRKV-CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           TPYRKV  DG VT+++ YL+A  E+N  IAQAN  LDE+  F  + V  R   GE  + P
Sbjct: 573 TPYRKVGKDGYVTDEIDYLTADIEDNFIIAQANEPLDENNRFINDRVSGRGINGENDIYP 632

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           RE ++++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPLLK++AP V TG+E 
Sbjct: 633 RESVEYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEH 692

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +V+K AG V  V   +I I+        S   +D YRL+KF+R+NQ T +N
Sbjct: 693 RAAKDSGVCVVSKNAGEVVYVGDEKIRIKRD------SDGEIDYYRLLKFRRANQGTTIN 746

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK+GD V  N+IIADGPST+ G+LALG+N+L+AF  W GYN+ED+ML++E++V +D
Sbjct: 747 QRPIVKLGDHVDANEIIADGPSTEQGELALGKNILIAFTTWEGYNYEDAMLLNEQLVMDD 806

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TS+HIEE E  AR+TKLG EEIT+DIPNV ++  KN+DE G+I +GAEV  GDILVGK
Sbjct: 807 VLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGK 866

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL VP G SG VVDV+ +N+   D
Sbjct: 867 VSPKGETELSPEERLLRAIFGEKAREVRDTSLTVPHGESGIVVDVKEYNKKDGD 920



 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 280/1198 (23%), Positives = 477/1198 (39%), Gaps = 110/1198 (9%)

Query: 222  GMDSEE-----ILSTFYPKIVYSQRGD---FWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            G D ++     I    Y    YS+            +         +    +  D+   V
Sbjct: 67   GYDFDDETKYTIEEAKYKDTTYSRDLKVKARLINKETEEVKEQEVFMGDFPMMTDSATFV 126

Query: 274  IESGKKLTSG---------LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            I   +++                L + G K    T     G ++  D     T  + ++ 
Sbjct: 127  INGAERVIVSQLVRSPGVYYASELDKSGNKMYSSTVIPNRGAWIEFDTDASHTVNVRLDR 186

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
               +   +L      E  +  I   +++ +  ++RNTL  + ++  ++AL++IY+ ++PG
Sbjct: 187  TRKLPATTLVRALLFENDEEII---EALGDTEHLRNTLEKENSETSEEALIEIYKKLKPG 243

Query: 385  DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            D ++   A+++ N L FD  +YDL+ VGR K N +L L      +   K+ I      L 
Sbjct: 244  DPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLALHDRLIDQISAKDVIDDETGELF 303

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
             ++ G+               +V +++  Q   G  +  R        +D    + +  +
Sbjct: 304  -VKAGEMIDRQTALNIENSGINVVDVIVKQ-ENGDDKELRICGNHFVYLDSFEELEEIDL 361

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
            +   +   V        L   E+  + ++ I   RR   L    + ++     +      
Sbjct: 362  SNIELSEKVYYPVMREILDDNEDEESIINEIE--RRKKELCPKNIVKSDILAAVNYQFNL 419

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND----------- 613
              G     +     N  +   +    +      +    R V +   T D           
Sbjct: 420  FEGIGDVDDIDHLGNRRVRG-VGELLQNQFRIGLARMERVVRERMTTQDPDLATPQGLIN 478

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQ 670
            +  ++A+ +E    +Q +  +D+    +E   +          +   R  ++  D     
Sbjct: 479  IKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSH 538

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
               I     P   N      L       +   +          G            + A 
Sbjct: 539  YGRICPIETPEGPNIGLITSLTTYARINKYGFIETPYRKVGKDGY----VTDEIDYLTAD 594

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDP-STSGVDIYRLMKFQRSNQNTCVNQRPLVKVG---- 785
                     A   +  +     D  S  G++    +  + S +   V+ + +V VG    
Sbjct: 595  IEDNFIIAQANEPLDENNRFINDRVSGRGINGENDIYPRESVEYMDVSPQQIVSVGASLI 654

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +  +D        ++   A+      A +   G     +      +VS++    +++ 
Sbjct: 655  PFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEHRAAKDSGVCVVSKNAGEVVYVG 714

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            + ++  +    G  +  R +          I++  I+ +G  V+  +I+    + + +  
Sbjct: 715  DEKIRIKRDSDGEIDYYRLLKFRRANQGTTINQRPIVKLGDHVDANEIIADGPSTE-QGE 773

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   + +L A    +  +  D  L     V   V+       H  +  E  +  E E  +
Sbjct: 774  LALGKNILIAFTTWEGYNYEDAMLLNEQLVMDDVLTSVHIEEHECEARETKLGAE-EITK 832

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             +    DD +  LD N   R+   +   + + G    K  T LS +        +  +  
Sbjct: 833  DIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGKVSPKGETELSPE-------ERLLRAI 885

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              ++  +    SL V +  S  +++ +  NK +    GD++ PGV +V++VFVA KR I 
Sbjct: 886  FGEKAREVRDTSLTVPHGESGIVVDVKEYNKKD----GDELSPGVNKVIRVFVATKRKIM 941

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKM GRHGNKG+VSRI+P EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A 
Sbjct: 942  VGDKMCGRHGNKGVVSRIMPREDMPFLPDGTPIQICLNPLGIPSRMNIGQVLEVHMGLAA 1001

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +G KI + + D   + +I       +K     + T KI                    
Sbjct: 1002 RTMGWKIATPVFDGALDTEIEEALEEAKKTAPYVNKTGKIRL------------------ 1043

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                      G++       GE F  PVTVG +YMLKL+HMV +
Sbjct: 1044 ------------------------RDGRT-------GEEFQNPVTVGVMYMLKLHHMVEE 1072

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLT+KSDDV GR
Sbjct: 1073 KIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTVKSDDVTGR 1132

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             + YESIV G +  E GTPESF VLVKE+Q+L L ++L +         E I + +K 
Sbjct: 1133 VKTYESIVKGENVPEPGTPESFKVLVKELQSLALDVELLDEDGNVIELKENIDEQDKF 1190


>gi|315186337|gb|EFU20098.1| DNA-directed RNA polymerase subunit beta [Spirochaeta thermophila
           DSM 6578]
          Length = 1164

 Score =  790 bits (2041), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/940 (45%), Positives = 594/940 (63%), Gaps = 70/940 (7%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNI--APDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            PE++D+P+L+EVQ +SY+ FL        +    +GL+  F+S FPI + +G   LE+ 
Sbjct: 17  RPEVMDLPNLLEVQFSSYEKFLQAEKIRKGEPLAVQGLEEVFRSSFPIESPNGDMRLEYD 76

Query: 78  SYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            Y  D    K+  ++C  + LTYAVPLK  + LI  +           +I+++ IY+GD+
Sbjct: 77  FYTLDFEAIKYSEEECKRKGLTYAVPLKAQINLIFLE---------TGEIRQKMIYLGDI 127

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT  GTF+I G +R+VVSQ+HRSPG+ F H+KG        +Y  RIIP +G W++ E
Sbjct: 128 PLMTDRGTFIINGAERVVVSQIHRSPGVIFSHEKG--------VYGARIIPYRGSWLEFE 179

Query: 196 FDSK-DIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            D+K D+I+ +IDR++++  T FL ALG D+ E+I+S FY     +   +         D
Sbjct: 180 VDAKKDLIYAKIDRKKRILGTLFLRALGFDTREKIISAFYETKEVTVSSET-------KD 232

Query: 254 LMVGAKVSSSLVDIDTG--EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +VG  ++  +   +    ++++ +G K+    +  L   GV+ + +  D          
Sbjct: 233 EVVGRVLARDVYTGEGSDQKKLLRAGAKIHPHEMDELLHAGVERVWVIDDE--------- 283

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +    E+ +   D                              Y R    TD    ++
Sbjct: 284 HPDSLHSEVILNCFDR-------------------------EEAKYTREEEGTD-EPTKE 317

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           DA++ +Y  + PGD  T   AE     +FF   +YDL  VGR K+N + + D P     +
Sbjct: 318 DAIIAVYSAIMPGDPITIENAEKDLQAMFFSERRYDLGDVGRYKLNKKFDYDPPLSSTVL 377

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  ++ L+ +  G+  +DDID+LGNRRVRSVGE+L  + +    RMER  KER+S
Sbjct: 378 TLDDIVNTMRHLIKVYIGEEPVDDIDHLGNRRVRSVGELLTAELKTAFSRMERIAKERMS 437

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + D++ PQDLI+ KP+V+A+ EFF SSQLSQ  + VN LS +TH RRL+ALG GG++R
Sbjct: 438 LKESDTIKPQDLISIKPIVAAIKEFFGSSQLSQFMDQVNPLSELTHKRRLNALGPGGLSR 497

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL  +ARVN YGF+E PYRKV DG+VT
Sbjct: 498 ERAGFEVRDVHYTHYGRMCPIETPEGPNIGLILSLALYARVNEYGFLEAPYRKVKDGRVT 557

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           N++ YL+AM+EE  +IAQAN+ +DE+G F  + V  R  G+    P E I ++D SP+Q 
Sbjct: 558 NEIEYLTAMDEEKYFIAQANAPIDEEGRFLTDQVSVRKGGDYTTRPPETIQYMDVSPRQT 617

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS +ASLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTGME   A  SG  + A+R
Sbjct: 618 VSASASLIPFLEHDDANRALMGSNMQRQAVPLIFPEPPRVGTGMERRCAYDSGVVVKARR 677

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG+VE V + ++VI+             DIY L K+QR+NQ+TC NQRP+V  G  V + 
Sbjct: 678 AGVVEYVSSTKVVIKPD---GVTDERERDIYFLQKYQRTNQDTCFNQRPIVNKGQRVEKG 734

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D++ADGPST  G+LALGRN+LVAF+PW+GYNFED++LISER++ +DVFTSIHI+EF +  
Sbjct: 735 DVLADGPSTFKGELALGRNVLVAFVPWYGYNFEDAILISERLLKQDVFTSIHIKEFSIEV 794

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE+ITRDIPNVSE+ L+++DE GI+ +GA+V  G ILVGKITPK ++ +TPE K
Sbjct: 795 RETKLGPEKITRDIPNVSEKHLEHLDEEGIVRIGAKVKSGSILVGKITPKSDAELTPEFK 854

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL +IFGEKA DVRDTSLRVP G  GTV+DV+   R   D
Sbjct: 855 LLNSIFGEKAKDVRDTSLRVPHGAEGTVIDVQRLRRSEGD 894



 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 200/590 (33%), Positives = 276/590 (46%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E        +V        +       +        
Sbjct: 638  MGSNMQRQAVPLIFPEPPRVGTGMERRCAYDSGVVVKARRAGVVEYVSSTKVVIKPDGVT 697

Query: 859  EEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLL 913
            +E  RDI  + +    N D    +  I+  G  V  GD+L  G  T KGE  +     + 
Sbjct: 698  DERERDIYFLQKYQRTNQDTCFNQRPIVNKGQRVEKGDVLADGPSTFKGELALGRNVLVA 757

Query: 914  RAIF-GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR--D 970
               + G    D    S R+      T + ++ F+    +       + R+   +  +  +
Sbjct: 758  FVPWYGYNFEDAILISERLLKQDVFTSIHIKEFSIEVRETKLGPEKITRDIPNVSEKHLE 817

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE+ I+      +   IL G+              L + +  E  +            
Sbjct: 818  HLDEEGIVRIGAKVKSGSILVGKITPKSDAELTPEFKLLNSIFGEKAKD----------- 866

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +    E +   ++        +   GD++PPGV  VVKV VA KR +Q GDKM
Sbjct: 867  VRDTSLRVPHGAEGTVIDVQ------RLRRSEGDELPPGVEEVVKVLVASKRKLQEGDKM 920

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SR+LP EDMPFL DGTPVDI LNPLGVPSRMN+GQI ET LGWA V L +
Sbjct: 921  AGRHGNKGVISRVLPEEDMPFLADGTPVDICLNPLGVPSRMNLGQILETELGWAAVALDE 980

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               + + +  +   I                                             
Sbjct: 981  WYATPVFESASPEMI--------------------------------------------- 995

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                 EE +      A L E+ ++ LYDG TGE F +PV VGY+YMLKLNH+V DK++AR
Sbjct: 996  -----EEKLRE----AGLPETSKTTLYDGRTGEAFHQPVMVGYMYMLKLNHLVDDKMHAR 1046

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA  LQE+LTIKSDD+ GRT++YE
Sbjct: 1047 STGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQELLTIKSDDMEGRTKIYE 1106

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            SIV G  +   G PESFNVLV+E++ L L I +++++ K     E   + 
Sbjct: 1107 SIVKGEPSTSPGIPESFNVLVQELRGLALDITVQDTKGKPVPLTERDEEL 1156


>gi|312898065|ref|ZP_07757468.1| DNA-directed RNA polymerase, beta subunit [Megasphaera
           micronuciformis F0359]
 gi|310620835|gb|EFQ04392.1| DNA-directed RNA polymerase, beta subunit [Megasphaera
           micronuciformis F0359]
          Length = 1233

 Score =  790 bits (2041), Expect = 0.0,   Method: Composition-based stats.
 Identities = 408/945 (43%), Positives = 562/945 (59%), Gaps = 86/945 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E++ +P L+++Q  SY  FL           +GL+  FK + PI   SG
Sbjct: 9   KRTRYTYAKINEVLKMPHLLDLQTKSYKWFL----------EKGLKDIFKDISPIEDASG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F  +    PK+D+ +C  RD TY+ PL++ + L+          +   + + Q +
Sbjct: 59  NLSLSFEDFSLGEPKYDIRECKERDTTYSAPLRVQISLL---------DRGTGERRSQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL+T  GTF+I G +R++VSQL RSPG+++  +       G  LY+  IIP++G 
Sbjct: 110 FMGDFPLITDTGTFIINGAERVIVSQLVRSPGVYYGREID---PMGIRLYSSTIIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+  I++ RIDR RK+P T  + ALG   + +I+  FY         +      
Sbjct: 167 WIELETDTNGIVYARIDRNRKIPATVLIRALGWPTNNDIMELFYNDPRLQATFEKDTTES 226

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               L+   K       +  GE   +ES + L  GL    +   +  +G           
Sbjct: 227 QEEALVEIYK------KLRPGEPPTVESARSLFEGLFFDPRRYDMARVGRYK-------- 272

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
                                  +  ++          L+   VN+              
Sbjct: 273 -----------------------AARKLGWEHRLFGITLHEPIVNSETGELVLPAQTVIG 309

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             + A +    V     +                         G V   +  N + P D 
Sbjct: 310 AEEIAKIKESGVFNFDGLIEVFAE----------------KQDGTVAKIICNNSNLPYDH 353

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R I KEDIIA I  L++L +G G +DDID+LGNRR+R VGE+L+NQ+R+GL RMER ++E
Sbjct: 354 RTITKEDIIANIGYLLNLMDGFGNVDDIDHLGNRRLRCVGELLQNQFRIGLTRMERVVRE 413

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R++  D +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG
Sbjct: 414 RMTVQDAESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG 473

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD- 607
           ++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL  +++VN +GFIE PYR+V   
Sbjct: 474 LSRERAGFEVRDVHHSHYGRMCPVETPEGPNIGLISSLACYSKVNEFGFIEAPYRRVDKT 533

Query: 608 -GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
              VT+DV Y++A EEE   IAQAN  L EDG+F  E V CR     + V R+++DF+D 
Sbjct: 534 THVVTDDVHYITADEEEQYIIAQANEPLAEDGTFVNERVACRHGEAVLEVARDRVDFMDV 593

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SP++VVS+  S+IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME   A  SG  
Sbjct: 594 SPREVVSVGTSMIPFLENDDANRALMGANMQRQAVPLLRTQAPLVGTGMEYKAACDSGVC 653

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I+AK AG V +V    I+I + EG       G D Y+L+KF RSNQ+TC+NQRPLV  G+
Sbjct: 654 ILAKHAGKVARVTGDEIIITTDEG-------GTDTYKLIKFVRSNQSTCINQRPLVYKGE 706

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V R+ ++ADG +TD G+LALG N+LVA+MPW GYN+ED++L+SE +   D++TSIH+EE
Sbjct: 707 RVERDQVLADGMATDGGELALGYNILVAYMPWEGYNYEDAVLLSEELPKNDIYTSIHVEE 766

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +E  ARDTKLG EEITR+IPNVSE+  K++DE GII VGA+V PGD+LVGK+TPKGE+ +
Sbjct: 767 YECDARDTKLGAEEITREIPNVSEDSTKDLDEGGIIRVGADVVPGDVLVGKVTPKGETEL 826

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPEE+LLRAIFG+K  +VRDTSLRVP G SG +V VR+F+R   D
Sbjct: 827 TPEERLLRAIFGDKEREVRDTSLRVPHGESGKIVAVRVFSRENND 871



 Score =  551 bits (1420), Expect = e-154,   Method: Composition-based stats.
 Identities = 203/535 (37%), Positives = 287/535 (53%), Gaps = 41/535 (7%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T  G  +  + I  V       I++  ++  G  V   D ++          +     +L
Sbjct: 674  TDEGGTDTYKLIKFVRSNQSTCINQRPLVYKGERVER-DQVLADGMATDGGELALGYNIL 732

Query: 914  RAIFGEKAVDVRDT---SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
             A    +  +  D    S  +P     T + V  +     D    +  + RE   +    
Sbjct: 733  VAYMPWEGYNYEDAVLLSEELPKNDIYTSIHVEEYECDARDTKLGAEEITREIPNVSEDS 792

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              D    LD     R+   +   + + G    K  T L+ +        +  +    D++
Sbjct: 793  TKD----LDEGGIIRVGADVVPGDVLVGKVTPKGETELTPE-------ERLLRAIFGDKE 841

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             +    SL+V +  S  I+  R    +   +  D++PPGV ++V+V++A KR I  GDKM
Sbjct: 842  REVRDTSLRVPHGESGKIVAVR----VFSRENNDELPPGVNQLVRVYIAQKRKIHEGDKM 897

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG+VSR++  EDMPFL DGT V IVLNPLGVPSRMN+GQI ETHLGWA   +G 
Sbjct: 898  AGRHGNKGVVSRVMRQEDMPFLPDGTSVQIVLNPLGVPSRMNIGQILETHLGWAMHEIGV 957

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +I +                            +      D     + +  ++GV ++TPV
Sbjct: 958  QILNP---------------------DNHLADKLKEIGYDIDKYGMIQPDEAGVHIATPV 996

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FDGA  E +   LR+A L + G+++LYDG TGEP DR VTVGY Y LKL+H+V DK++AR
Sbjct: 997  FDGAHAEDVFEALRVAGLPDDGKTVLYDGRTGEPMDRRVTVGYTYFLKLHHLVDDKIHAR 1056

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE
Sbjct: 1057 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKAYE 1116

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             IV G +  E G PESF VL+KE+QA+GL++ + N  ++     +E+ D ++ E+
Sbjct: 1117 KIVKGENIPEPGVPESFKVLLKELQAIGLNVQILNEDSEEVVI-KELDDEDELEV 1170


>gi|262190049|ref|ZP_06048347.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae CT 5369-93]
 gi|262034067|gb|EEY52509.1| DNA-directed RNA polymerase beta subunit [Vibrio cholerae CT 5369-93]
          Length = 570

 Score =  790 bits (2040), Expect = 0.0,   Method: Composition-based stats.
 Identities = 326/586 (55%), Positives = 436/586 (74%), Gaps = 18/586 (3%)

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
              G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V +D FT+I
Sbjct: 1    MPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTI 60

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 61   HIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKG 120

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G++K++R++ +E+ 
Sbjct: 121  ETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQM 180

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++   +D  +E  IL+  + +R+  +L                  +   +    R +W 
Sbjct: 181  QLKEAKKDLTEEFQILEGGLLARVRSVLLAGG-------------YTEAKLGSIERKKWL 227

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR
Sbjct: 228  EQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKR 287

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG
Sbjct: 288  RIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLG 347

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQW 1200
             A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A   
Sbjct: 348  LAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNL 404

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLN
Sbjct: 405  RAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLN 464

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSD
Sbjct: 465  HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 524

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            DV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 525  DVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE 570


>gi|325849595|ref|ZP_08170833.1| DNA-directed RNA polymerase, beta subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325480076|gb|EGC83153.1| DNA-directed RNA polymerase, beta subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 1236

 Score =  790 bits (2039), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/954 (43%), Positives = 604/954 (63%), Gaps = 56/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K P+++D+P+L++VQK SY  F+           EGL    + + PI  ++G
Sbjct: 10  KTERVSFSKFPQVLDLPNLLKVQKDSYRWFI----------EEGLGEILEDISPIEDYNG 59

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y+FD   K+ +++  ++D TY+  LK+  RLI          K  +++KEQ 
Sbjct: 60  NLILEFVGYDFDDETKYTIEEAKYKDTTYSRDLKVKARLI---------NKETEEVKEQE 110

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG  +Y+  +IP++G
Sbjct: 111 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYASELDK---SGNKMYSSTVIPNRG 167

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +++E I+             +     
Sbjct: 168 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFENDEEIIEALGDTEHLRNTLEKENSE 227

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            S   L+   K       +  G+   +ES + L + LL   +   +  +G          
Sbjct: 228 TSEEALIEIYK------KLKPGDPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLAL 281

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            D L     A+D+++ ETGE++++AG++ID ++   I +S I  + ++       +  +R
Sbjct: 282 HDRLIDQISAKDVIDDETGELFVKAGEMIDRQTALNIENSGINVVDVIVKQENGEDKELR 341

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                    D  + L +I       D+S   ++E ++  +    +  D +      +N  
Sbjct: 342 ICGNHFVYLDSFEELEEI-------DLSNIELSEKVYYPVM--REILDDNEDKESIINEI 392

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    ++I K DI+A +    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+GL
Sbjct: 393 ERRKKELCPKNIVKSDILAAVNYQFNLFEGIGDVDDIDHLGNRRVRGVGELLQNQFRIGL 452

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH R
Sbjct: 453 ARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKR 512

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++AR+N YGFIE
Sbjct: 513 RLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARINKYGFIE 572

Query: 600 TPYRKV-CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           TPYRKV  DG VT+++ YL+A  E++  IAQAN  LDE+  F  + V  R   GE  + P
Sbjct: 573 TPYRKVGKDGYVTDEIDYLTADIEDDFIIAQANEPLDENNRFINDRVSGRGINGENDIYP 632

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           RE ++++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPLLK++AP V TG+E 
Sbjct: 633 RESVEYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEH 692

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +V+K AG V  V   +I I+        S   +D YRL+KF+R+NQ T +N
Sbjct: 693 RAAKDSGVCVVSKNAGEVVYVGDEKIRIKRD------SDGEIDYYRLLKFRRANQGTTIN 746

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK+GD V  N+IIADGPST+ G+LALG+N+L+AF  W GYN+ED+ML++E++V +D
Sbjct: 747 QRPIVKLGDHVDANEIIADGPSTEQGELALGKNILIAFTTWEGYNYEDAMLLNEQLVMDD 806

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TS+HIEE E  AR+TKLG EEIT+DIPNV ++  KN+DE G+I +GAEV  GDILVGK
Sbjct: 807 VLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGK 866

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL VP G SG VVDV+ +N+   D
Sbjct: 867 VSPKGETELSPEERLLRAIFGEKAREVRDTSLTVPHGESGIVVDVKEYNKKDGD 920



 Score =  510 bits (1312), Expect = e-141,   Method: Composition-based stats.
 Identities = 280/1198 (23%), Positives = 477/1198 (39%), Gaps = 110/1198 (9%)

Query: 222  GMDSEE-----ILSTFYPKIVYSQRGD---FWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            G D ++     I    Y    YS+            +         +    +  D+   V
Sbjct: 67   GYDFDDETKYTIEEAKYKDTTYSRDLKVKARLINKETEEVKEQEVFMGDFPMMTDSATFV 126

Query: 274  IESGKKLTSG---------LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            I   +++                L + G K    T     G ++  D     T  + ++ 
Sbjct: 127  INGAERVIVSQLVRSPGVYYASELDKSGNKMYSSTVIPNRGAWIEFDTDASHTVNVRLDR 186

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
               +   +L      E  +  I   +++ +  ++RNTL  + ++  ++AL++IY+ ++PG
Sbjct: 187  TRKLPATTLVRALLFENDEEII---EALGDTEHLRNTLEKENSETSEEALIEIYKKLKPG 243

Query: 385  DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            D ++   A+++ N L FD  +YDL+ VGR K N +L L      +   K+ I      L 
Sbjct: 244  DPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLALHDRLIDQISAKDVIDDETGELF 303

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
             ++ G+               +V +++  Q   G  +  R        +D    + +  +
Sbjct: 304  -VKAGEMIDRQTALNIENSGINVVDVIVKQ-ENGEDKELRICGNHFVYLDSFEELEEIDL 361

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
            +   +   V        L   E+  + ++ I   RR   L    + ++     +      
Sbjct: 362  SNIELSEKVYYPVMREILDDNEDKESIINEIE--RRKKELCPKNIVKSDILAAVNYQFNL 419

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND----------- 613
              G     +     N  +   +    +      +    R V +   T D           
Sbjct: 420  FEGIGDVDDIDHLGNRRVRG-VGELLQNQFRIGLARMERVVRERMTTQDPDLATPQGLIN 478

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQ 670
            +  ++A+ +E    +Q +  +D+    +E   +          +   R  ++  D     
Sbjct: 479  IKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSH 538

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
               I     P   N      L       +   +          G            + A 
Sbjct: 539  YGRICPIETPEGPNIGLITSLTTYARINKYGFIETPYRKVGKDGY----VTDEIDYLTAD 594

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDP-STSGVDIYRLMKFQRSNQNTCVNQRPLVKVG---- 785
                     A   +  +     D  S  G++    +  + S +   V+ + +V VG    
Sbjct: 595  IEDDFIIAQANEPLDENNRFINDRVSGRGINGENDIYPRESVEYMDVSPQQIVSVGASLI 654

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +  +D        ++   A+      A +   G     +      +VS++    +++ 
Sbjct: 655  PFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEHRAAKDSGVCVVSKNAGEVVYVG 714

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            + ++  +    G  +  R +          I++  I+ +G  V+  +I+    + + +  
Sbjct: 715  DEKIRIKRDSDGEIDYYRLLKFRRANQGTTINQRPIVKLGDHVDANEIIADGPSTE-QGE 773

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   + +L A    +  +  D  L     V   V+       H  +  E  +  E E  +
Sbjct: 774  LALGKNILIAFTTWEGYNYEDAMLLNEQLVMDDVLTSVHIEEHECEARETKLGAE-EITK 832

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             +    DD +  LD N   R+   +   + + G    K  T LS +        +  +  
Sbjct: 833  DIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGKVSPKGETELSPE-------ERLLRAI 885

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              ++  +    SL V +  S  +++ +  NK +    GD++ PGV +V++VFVA KR I 
Sbjct: 886  FGEKAREVRDTSLTVPHGESGIVVDVKEYNKKD----GDELSPGVNKVIRVFVATKRKIM 941

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKM GRHGNKG+VSRI+P EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A 
Sbjct: 942  VGDKMCGRHGNKGVVSRIMPREDMPFLPDGTPIQICLNPLGIPSRMNIGQVLEVHMGLAA 1001

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +G KI + + D   + +I       +K     + T KI                    
Sbjct: 1002 RTMGWKIATPVFDGALDTEIEEALEEAKKTAPYVNKTGKIRL------------------ 1043

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                      G++       GE F  PVTVG +YMLKL+HMV +
Sbjct: 1044 ------------------------RDGRT-------GEEFQNPVTVGVMYMLKLHHMVEE 1072

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLT+KSDDV GR
Sbjct: 1073 KIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTVKSDDVTGR 1132

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             + YESIV G +  E GTPESF VLVKE+Q+L L ++L +         E I + +K 
Sbjct: 1133 VKTYESIVKGENVPEPGTPESFKVLVKELQSLALDVELLDEDGNVIELKENIDEQDKF 1190


>gi|325478927|gb|EGC82035.1| DNA-directed RNA polymerase, beta subunit [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 1239

 Score =  789 bits (2038), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/955 (44%), Positives = 601/955 (62%), Gaps = 57/955 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              RK F K P+++D+P+L++VQK SY+ FL           EGL    + + PI  ++G
Sbjct: 11  RTKRKSFSKFPQVLDLPNLLKVQKDSYEWFL----------KEGLGEILEDISPIEDYNG 60

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEF+ YEFD   K+ V +  ++D TYA  LK+  RLI          K  +++KEQ 
Sbjct: 61  NLILEFIGYEFDEETKYSVKESKYKDATYARDLKVKARLI---------NKETEEVKEQE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG ++Y+  +IP++G
Sbjct: 112 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYAEETDK---SGDMMYSSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +S+E I++            +     
Sbjct: 169 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFESDEEIINALGDTKHLRNTLEKENSE 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            S   L+   +       +  G+   +ES   L + LL   +   +  +G          
Sbjct: 229 TSEEALIEIYR------KLKPGDPASVESATNLINNLLFDDRRYDLARVGRYKYNLKLAL 282

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            + + GL   +DI++ ETGE ++ AG+VID+ + + I ++ +  + ++  D  +    + 
Sbjct: 283 ANRIEGLRAKDDIIDPETGEFFVAAGEVIDKDTAQAIENAGVVTVDVIKKDEYSGEDKVL 342

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDV-STFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
             +  +         L  +  ++  DV       +  F  +    D+       +  M  
Sbjct: 343 RVVGNNFV------DLYSFEELKDVDVSVDDFSEKVYFPVMREIIDEASSPEEIKTLMER 396

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           R     P   +HI K DI+A++    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+G
Sbjct: 397 RKKELCP---KHITKSDILAVVNYQFNLFEGIGYVDDIDHLGNRRVRGVGELLQNQFRVG 453

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH 
Sbjct: 454 LARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHK 513

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++ARVN YGFI
Sbjct: 514 RRLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARVNKYGFI 573

Query: 599 ETPYRKVCDG-KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILV 656
           ETPYR V +G  VT+++ YL+A  E+N  IAQAN  LDE+  F  + V  R   GE  + 
Sbjct: 574 ETPYRVVKEGGVVTDEIDYLTADIEDNFIIAQANEPLDENNRFINDRVSGRGLKGENDIY 633

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PREKI ++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPL+K+EAP V TG+E
Sbjct: 634 PREKIQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLIKSEAPIVATGIE 693

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              AK SG  +V++  G V  V    I ++        S   ++ Y L+KF+R+NQ T +
Sbjct: 694 HRAAKDSGVCVVSRSKGEVVYVGDEHIKVKRD------SDGEIEDYELLKFERANQGTTI 747

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQRP+VK GD+V  N+I+ADGPSTD G+LALG+N+L+AF  W GYNFED+ML++E +V +
Sbjct: 748 NQRPIVKRGDKVEANEILADGPSTDNGELALGKNILIAFTTWEGYNFEDAMLLNEELVMD 807

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DV TS+HIEE E  AR+TKLG EEIT+DIPNV ++  K++DE GII +GAEV  GDILVG
Sbjct: 808 DVLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKDLDENGIIRIGAEVKSGDILVG 867

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL+VP G SG VVDV+ +N+   D
Sbjct: 868 KVSPKGETELSPEERLLRAIFGEKAREVRDTSLKVPHGESGIVVDVKEYNKKDGD 922



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 257/1064 (24%), Positives = 425/1064 (39%), Gaps = 109/1064 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++++ +  ++RNTL  + ++  ++AL++IYR ++PGD ++   A ++ N L FD  +YDL
Sbjct: 209  INALGDTKHLRNTLEKENSETSEEALIEIYRKLKPGDPASVESATNLINNLLFDDRRYDL 268

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + VGR K N++L L    +    + + I                 D    + N  V +V 
Sbjct: 269  ARVGRYKYNLKLALANRIEGLRAKDDIIDPETGEFFVAAGEVIDKDTAQAIENAGVVTVD 328

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             + K++Y  G  ++ R +      +     +    ++       V           + + 
Sbjct: 329  VIKKDEYS-GEDKVLRVVGNNFVDLYSFEELKDVDVSVDDFSEKVYFPVMRE----IIDE 383

Query: 529  VNSLSRITHT--RRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
             +S   I     RR   L    + ++     +        G   +   +      +  V 
Sbjct: 384  ASSPEEIKTLMERRKKELCPKHITKSDILAVVNYQFNLFEGIGYVDDIDHLGNRRVRGVG 443

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSS 633
             L    +      +    R V +   T D           +  ++A+ +E    +Q +  
Sbjct: 444  ELL---QNQFRVGLARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQF 500

Query: 634  LDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            +D+    +E   +          +   R  ++  D        I     P   N      
Sbjct: 501  MDQTNPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITS 560

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            L       +   +          G+           + A          A   +  +   
Sbjct: 561  LTTYARVNKYGFIETPYRVVKEGGV----VTDEIDYLTADIEDNFIIAQANEPLDENNRF 616

Query: 751  DLDP-STSGVDIYRLMKFQRSNQNTCVNQRPLVKVG----DEVRRNDIIADGPSTDLGDL 805
              D  S  G+     +  +   Q   V+ + +V VG      +  +D        ++   
Sbjct: 617  INDRVSGRGLKGENDIYPREKIQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQ 676

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            A+      A +   G     +      +VS      +++ +  +  +    G  E    +
Sbjct: 677  AVPLIKSEAPIVATGIEHRAAKDSGVCVVSRSKGEVVYVGDEHIKVKRDSDGEIEDYELL 736

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      I++  I+  G +V   +IL    +      +   + +L A    +  +  
Sbjct: 737  KFERANQGTTINQRPIVKRGDKVEANEILADGPSTDN-GELALGKNILIAFTTWEGYNFE 795

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILD 979
            D  L     V   V+       H  +  E  +  E    +       + +D  DE  I+ 
Sbjct: 796  DAMLLNEELVMDDVLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKDL-DENGIIR 854

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+ +  G         L   +  E  R      +++    +  +    
Sbjct: 855  IGAEVKSGDILVGKVSPKGETELSPEERLLRAIFGEKARE-VRDTSLKVPHGESGIVVDV 913

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +Y                    GD++ PGV +V++V+VA KR I  GDKM GRHGNKG+
Sbjct: 914  KEYNKK----------------DGDELSPGVNKVIRVYVAAKRKIMVGDKMCGRHGNKGV 957

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSRILP EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A   +G KI + + D 
Sbjct: 958  VSRILPREDMPFLPDGTPLQICLNPLGIPSRMNLGQVLEVHMGLAARTMGWKIATPVFDG 1017

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
              + +I  +    +K     + T KI+  D                              
Sbjct: 1018 ALDTEIEEVLEEAKKTAPFVNKTGKITLRD------------------------------ 1047

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                               G TG PF+ PVTVG +YMLKL+HMV +K++ARS G YSLVT
Sbjct: 1048 -------------------GRTGLPFENPVTVGVMYMLKLHHMVEEKIHARSIGPYSLVT 1088

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGA++ LQE+LT+KSDDV GR + YESIV G +  
Sbjct: 1089 QQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEILTVKSDDVTGRVKTYESIVKGENIP 1148

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            E GTPESF VLVKE+Q+L L ++L ++  +     E I + ++ 
Sbjct: 1149 EPGTPESFKVLVKELQSLALDVELLDNEGEVIELKENIDEQDRF 1192


>gi|262038203|ref|ZP_06011597.1| DNA-directed RNA polymerase, beta subunit [Leptotrichia
           goodfellowii F0264]
 gi|261747784|gb|EEY35229.1| DNA-directed RNA polymerase, beta subunit [Leptotrichia
           goodfellowii F0264]
          Length = 1148

 Score =  789 bits (2037), Expect = 0.0,   Method: Composition-based stats.
 Identities = 434/970 (44%), Positives = 621/970 (64%), Gaps = 76/970 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK  +  ++P  +E Q  SY+ FL   + P +R N+GL+  F  +FPI + +G  
Sbjct: 6   ERYSFGKIVDRGEMPHFLEFQINSYEDFLQAKVPPQKRENKGLEGIFNEIFPIESSNGLL 65

Query: 73  MLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE    D P  D  +C  R  TY+  LK+ L+L           K  ++I+E  
Sbjct: 66  KLEYLWYEIHDNDEPLNDELECKKRGKTYSGQLKVRLKLT---------NKRTQEIQETL 116

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++ GD+PLMT+  TFVI G +R+VVSQLHRSPG+ F+ +      +GK ++  +IIP +G
Sbjct: 117 VHFGDIPLMTEQATFVINGAERVVVSQLHRSPGVTFNKEL--NIQTGKDMFIGKIIPYKG 174

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  DI++V+IDRR+KV  T FL A+    ++ EI+  F+ +     +  +  +
Sbjct: 175 TWLEFETDKNDILNVKIDRRKKVLSTVFLKAVDFFANNAEIMDEFFEEKEVDLKPLYKKY 234

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +                                            +  + L G +
Sbjct: 235 KDEELE-------------------------------------------DVLKNRLEGSF 251

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             EDI++ ETGE  +E+ ++ID   +E++  ++I  I I  V   +    I N+L+ D  
Sbjct: 252 NKEDILDEETGEFIVESEELIDNIVIEKLIENKIDKITIWEVKPEDR--IIANSLIHDNT 309

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           K   +A++++++ +RPGD+ T   A S+   +FF+  +YDL+ VGR K+N RL LD P+D
Sbjct: 310 KTNDEAVIEVFKKLRPGDLVTVESARSLVKQMFFNPQRYDLANVGRYKINKRLKLDLPED 369

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
              + KED++  I  + +L NG+G  DDIDNL NRRVR VGE+L  Q + G+L+M + +K
Sbjct: 370 EIVLTKEDVLQTINYVRNLVNGEGFTDDIDNLSNRRVRGVGELLSIQVKGGMLKMAKMVK 429

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           E+++  DI ++ PQ L+N KP+ + + EFF S QLSQ  +  N L+ +TH RR+SALG G
Sbjct: 430 EKMTIQDITTLTPQSLLNTKPLNALILEFFGSGQLSQFMDQSNPLAELTHKRRISALGPG 489

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL+++ +VN YGFIETP+ K+ +
Sbjct: 490 GLSRERAGFEVRDVHNSHYGRICPIETPEGPNIGLIGSLSTYGKVNKYGFIETPFVKIEN 549

Query: 608 GKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           GK   +++ YL A EEE  +IAQA++ +DEDG+F  + V CR   E + + + K+D +D 
Sbjct: 550 GKANFDEIEYLGADEEEGLFIAQADTLIDEDGNFLTDEVVCRYGEEIVHIDKSKVDLLDV 609

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS++A LIPFLE+DD+NR LMG NMQRQAVPLLK EAP+VGTG+E  VA  SGA 
Sbjct: 610 SPKQLVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPYVGTGLERKVAIDSGAV 669

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I +K  G V  VDA RI++          +    ++RL+ F++SNQ+ C++Q+P++ +GD
Sbjct: 670 ITSKATGKVTYVDANRIIV-------TDKSEKEFVHRLLNFEKSNQSMCLHQKPIIDLGD 722

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           +V++ D+IADGPST  GDLALG+N+L+AFMPW GYNFED++LISER+  +DVFTS+HIEE
Sbjct: 723 KVKKGDVIADGPSTAGGDLALGKNILLAFMPWEGYNFEDAILISERLRKDDVFTSLHIEE 782

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           F++ AR TKLG EEITR+IPNVSEE L+N+DE GII +GA VNP DILVGK+TPKGES  
Sbjct: 783 FDIEARTTKLGDEEITREIPNVSEEALRNLDENGIIRIGAHVNPDDILVGKVTPKGESEP 842

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISV 959
             EEKLLRAIFGEKA DVRDTSLR+P GV GTVVDV + ++        G++K  R    
Sbjct: 843 PAEEKLLRAIFGEKAKDVRDTSLRLPHGVKGTVVDVLVLSKENGDDLKAGVNKLVRVYIA 902

Query: 960 EREQIELLAR 969
           E+ +I +  +
Sbjct: 903 EKRKIMVGDK 912



 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 169/603 (28%), Positives = 246/603 (40%), Gaps = 78/603 (12%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT- 840
            V  G         A+              +L    P+ G   E  + I    V     T 
Sbjct: 617  VSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPYVGTGLERKVAIDSGAVITSKATG 676

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             +   +   +    K   E + R +          + +  II +G +V  GD++    + 
Sbjct: 677  KVTYVDANRIIVTDKSEKEFVHRLLNFEKSNQSMCLHQKPIIDLGDKVKKGDVIADGPST 736

Query: 901  KGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGIDKNER 955
             G      +  LL  +   G    D    S R+       S  + +  I  R     +E 
Sbjct: 737  AGGDLALGKNILLAFMPWEGYNFEDAILISERLRKDDVFTSLHIEEFDIEARTTKLGDEE 796

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                     E   R+  DE  I+    +    +IL G+    G         L   +  E
Sbjct: 797  ITREIPNVSEEALRNL-DENGIIRIGAHVNPDDILVGKVTPKGESEPPAEEKLLRAIFGE 855

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              +            V+     L    + +   +       +   + GDD+  GV ++V+
Sbjct: 856  KAKD-----------VRDTSLRLPHGVKGTVVDVL------VLSKENGDDLKAGVNKLVR 898

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V++A KR I  GDKM+GRHGNK                            GV SR     
Sbjct: 899  VYIAEKRKIMVGDKMSGRHGNK----------------------------GVVSR----- 925

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                               L  +   + +           +G  S        +    L 
Sbjct: 926  ------------------VLPIEDMPHLENGTPIDVCINPLGVPSRMNIGQVLEVHLGLA 967

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            + +  K    ++TPVFDGA E+ +   L  A    +G+  L DG TGEPFD PVTVG +Y
Sbjct: 968  IGDIDKY---IATPVFDGAKEDDVKDYLEEAGYSRTGKVKLIDGRTGEPFDNPVTVGRMY 1024

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +LQEML
Sbjct: 1025 MLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNILQEML 1084

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDD+ GRT+ YE+IV G    E   PESF VL+KE Q+LGL + L +   +     +
Sbjct: 1085 TVKSDDIGGRTKTYEAIVKGQSMPEADAPESFRVLIKEFQSLGLDVTLYDREGEAIELDK 1144

Query: 1376 EIP 1378
             + 
Sbjct: 1145 NVD 1147


>gi|218901306|ref|YP_002449140.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH820]
 gi|218534906|gb|ACK87304.1| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH820]
          Length = 1130

 Score =  789 bits (2037), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/907 (46%), Positives = 565/907 (62%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK
Sbjct: 53  -NKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI        
Sbjct: 109 RGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
             S   +      +   L+           +  GE   +E+ K L        K      
Sbjct: 169 YLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I   
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG-- 280

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                                                  +         +        Y 
Sbjct: 281 ------------------------------------FKTAKPMGGVVEGDVELQSIKIYA 304

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSV
Sbjct: 305 PESEGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +
Sbjct: 485 SFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDI 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 545 VARFRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMN 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRL 764
            E+P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++
Sbjct: 605 PESPIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKM 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+E
Sbjct: 665 QKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII V
Sbjct: 725 DAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRV 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++
Sbjct: 785 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREDGD 851



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 48   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 107

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 108  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 166

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 167  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 226

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 227  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 286

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 287  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 343

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 344  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 397

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 398  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 436

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 437  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 496

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 497  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 556

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 557  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 612

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 613  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 672

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 673  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 728

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 729  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 785

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 786  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 839

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 840  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 899

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 900  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 959

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 960  GMANDAK----------------------------TILYDG------------------- 972

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 973  -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1025

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1026 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1085

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1086 ELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1114


>gi|229153880|ref|ZP_04282010.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           4342]
 gi|228629561|gb|EEK86258.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus ATCC
           4342]
          Length = 1130

 Score =  789 bits (2037), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/907 (46%), Positives = 565/907 (62%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK
Sbjct: 53  -NKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI        
Sbjct: 109 RGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
             S   +      +   L+           +  GE   +E+ K L        K      
Sbjct: 169 YLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I   
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG-- 280

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                                                  +         +        Y 
Sbjct: 281 ------------------------------------FKTAKPMGGVVEGDVELRSIKIYA 304

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSV
Sbjct: 305 PESEGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G F +E +
Sbjct: 485 SFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDI 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 545 VARFRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMN 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRL 764
            E+P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       +D Y++
Sbjct: 605 PESPIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKM 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+E
Sbjct: 665 QKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII V
Sbjct: 725 DAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRV 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++
Sbjct: 785 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREDGD 851



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 265/1169 (22%), Positives = 436/1169 (37%), Gaps = 124/1169 (10%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 48   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 107

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 108  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 166

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 167  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 226

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 227  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 286

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 287  MGGVVEGDVELRSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 343

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 344  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 397

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 398  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 436

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 437  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 496

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVA----KRAGIVEQVDAIRIVIRSVEGDLDP 754
                 +  E   V   ++ + A      +VA    K +   E +D   +     E  +  
Sbjct: 497  TPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGEFLDEDIVARFRGENIVTN 556

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    K   S    C+         D+  R  + A+     +  +     ++  
Sbjct: 557  KERIDYMDVSPKQVVSAATACIPFL----ENDDSNRALMGANMQRQAVPLMNPESPIVGT 612

Query: 815  FMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             M +       + +I +   +V       + +  +  +   T  G  +  +    +    
Sbjct: 613  GMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQ 672

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                ++  I+ VG EV  G+IL    +      +     +L         +  D  +   
Sbjct: 673  GTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII--- 728

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G
Sbjct: 729  --MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVG 785

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                 G     K T      ++   R     F  +  +V+     +              
Sbjct: 786  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------ 839

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 840  LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 899

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 900  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 959

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 960  GMANDAK----------------------------TILYDG------------------- 972

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 973  -------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 1025

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+K
Sbjct: 1026 RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIK 1085

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            E+Q+LG+ + + +S        +   D +
Sbjct: 1086 ELQSLGMDVKMVSSDDTEIEMRDTEDDDD 1114


>gi|228898855|ref|ZP_04063137.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           IBL 4222]
 gi|228905899|ref|ZP_04069796.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           IBL 200]
 gi|228853714|gb|EEM98474.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           IBL 200]
 gi|228860755|gb|EEN05133.1| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis
           IBL 4222]
          Length = 1130

 Score =  789 bits (2037), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/907 (46%), Positives = 564/907 (62%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ VD+C  RD+TYA PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGEPKYSVDECKERDVTYAAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++KEQ ++MGD PLMT+ GTFVI G +R++VSQL RSP +++    G+   +GK
Sbjct: 53  -NKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI        
Sbjct: 109 RGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK---- 291
             S   +      +   L+           +  GE   +E+ K L        K      
Sbjct: 169 YLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLAN 222

Query: 292 ----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I   
Sbjct: 223 VGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIG-- 280

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                                                  +         +        Y 
Sbjct: 281 ------------------------------------FKTAKPMGGVVEGDVELQSIKIYA 304

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + G   +N+  N +   DV+HI   DI+A I    +L    G  DDID+LGNRR+RSV
Sbjct: 305 PESEGERVINVIGNANITRDVKHITPGDILASISYFFNLLYKVGDTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTNAITPQALINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +
Sbjct: 485 SFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDI 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 545 VARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMN 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRL 764
            E+P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++
Sbjct: 605 PESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKM 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+E
Sbjct: 665 QKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII V
Sbjct: 725 DAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRV 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++
Sbjct: 785 GAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREDGD 851



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 262/1176 (22%), Positives = 429/1176 (36%), Gaps = 138/1176 (11%)

Query: 235  KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
            K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 48   KVRLINKETGEVKEQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYSGKVDKNG 107

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G T+  +       +        +Y+             +          +  + + +
Sbjct: 108  KRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-TELLGD 166

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 167  NEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 226

Query: 415  KMNMRLNLDTPDDVRHI--------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            K+N +L++      + +          E + A   IL      +       N+G +  + 
Sbjct: 227  KINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNIGFKTAKP 286

Query: 467  VGEMLKNQYRLGLLRM-------ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +G +++    L  +++       ER I    ++     V     I    +++++  FF  
Sbjct: 287  MGGVVEGDVELQSIKIYAPESEGERVINVIGNANITRDV---KHITPGDILASISYFFNL 343

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              L ++ +  +         R          R       R V      R+   +T+    
Sbjct: 344  --LYKVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTNAITP 397

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              L++     A +  +       + +       ++ +                       
Sbjct: 398  QALINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTH---------------------KR 436

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L       E        + +        +       I  + +  S   +       
Sbjct: 437  RLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNEFGFIE 496

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                 +  E   V   ++ + A                 V A   +  S EG+       
Sbjct: 497  TPYRRVDPETGLVTGHVDYLTA-----------DEEDNYVVAQANMKLSDEGEFLSEDIV 545

Query: 759  VDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGD---------LAL 807
                         +   ++  P  +V             D     +G          +  
Sbjct: 546  ARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNP 605

Query: 808  GRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               ++   M +       + +I +   +V       + +  +  +   T  G  +  +  
Sbjct: 606  ESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQ 665

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +        ++  I+ VG EV  G+IL    +      +     +L         +  
Sbjct: 666  KFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYE 724

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     +S  +V   ++    I++ E      +   E + RD  +      RN+  R
Sbjct: 725  DAII-----MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER 779

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G     G     K T      ++   R     F  +  +V+     +       
Sbjct: 780  -GIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 838

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                      K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP
Sbjct: 839  I------LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILP 892

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+
Sbjct: 893  EEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDV 952

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                      T ++DG            
Sbjct: 953  WGTIEEAGMANDAK----------------------------TILYDG------------ 972

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                           TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGG
Sbjct: 973  --------------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGG 1018

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PE
Sbjct: 1019 KAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPE 1078

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            SF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 1079 SFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 1114


>gi|160946992|ref|ZP_02094195.1| hypothetical protein PEPMIC_00954 [Parvimonas micra ATCC 33270]
 gi|158447376|gb|EDP24371.1| hypothetical protein PEPMIC_00954 [Parvimonas micra ATCC 33270]
          Length = 1252

 Score =  789 bits (2037), Expect = 0.0,   Method: Composition-based stats.
 Identities = 405/961 (42%), Positives = 581/961 (60%), Gaps = 61/961 (6%)

Query: 8   NGLG--RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
                   R  + K   ++D+P+LI +Q  SYD F+           +G++  F  + PI
Sbjct: 4   TEKYGITERVSYSKIQNVLDLPNLIAIQTDSYDWFI----------KQGIRDVFDDISPI 53

Query: 66  TAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
             +S A  LEF++Y  +  PK+   +C  RD+ Y+  LK+ +RL            +  +
Sbjct: 54  RDYSEAMKLEFLNYRLENAPKYSEQECKDRDMNYSTLLKVDVRLT---------NNNTGE 104

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           +KEQ ++MG++PLMT +GTF+I G +R++VSQL RSPG+++  +  +   SG  L++  +
Sbjct: 105 VKEQEVFMGEIPLMTDNGTFIINGAERVIVSQLVRSPGVYYGEEIDK---SGNKLFSSTV 161

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGD 243
           IP++G W++ + D+  ++ VRIDR RK+P+T+ + AL  ++ EE++  F          +
Sbjct: 162 IPNRGAWLEYDTDTNGVVSVRIDRTRKLPITTMIRALLYETNEEMVENFGDIKELHTTLE 221

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-- 300
                     ++   +       +  G+   +ESG+ L   LL   +   +  +G     
Sbjct: 222 KDITKSYQEAILEIYR------KLKPGDPATVESGESLLHNLLFDPRRYDLAKVGRYKFN 275

Query: 301 ------DCLCGLYVAEDIVNGETG---EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                 + L G  +AEDI   +     E     GD I E+  E+I ++  + +   +V  
Sbjct: 276 KKLALRNRLIGTILAEDIFKTDKFGEMEKIASVGDYISEELAEKIENAGYKRV---HVKV 332

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +    +      D         +    +    +   + V   +         +   + V
Sbjct: 333 EDKEIIVVGNHFVDIGAFELGFDISCNGL---SEKVYYPVMMEILESASEYEGEEYETQV 389

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            R   N            HI ++DI A +    +L  G G  DDID+LGNRRVR+VGE+L
Sbjct: 390 KRAVRNRV----KELSPTHIIRDDIEATVSYEFNLFYGLGICDDIDHLGNRRVRAVGELL 445

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL RMER ++ER+S+ D D   PQ LIN +P+V+++ EFF SSQLSQ  +  N 
Sbjct: 446 QNQFRIGLSRMERVVRERMSTQDPDLATPQGLINIRPLVASLKEFFGSSQLSQFMDQNNP 505

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L+ +TH RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL++SLT++AR
Sbjct: 506 LAELTHKRRLSALGPGGLSRDRAGYEVRDVHESHYGRICPIETPEGPNIGLITSLTTYAR 565

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           V+ YGFIETPYR V +G  T D+VYL+A EE+   IAQAN  LDE+G F  E V  R   
Sbjct: 566 VDQYGFIETPYRVVNNGIATKDIVYLTADEEDEVIIAQANEPLDENGRFVNERVSGRGIN 625

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           GE  + PR+ I  +D SP+Q+VS+  ++IPFLENDD+ R LMG NMQRQAVPLL  EAP 
Sbjct: 626 GENDIYPRDTIQLMDVSPQQIVSVGTAMIPFLENDDATRALMGSNMQRQAVPLLVTEAPI 685

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A+ SG  I+AK +GIV +VD+  I I+          + VD YRL+KF+RS
Sbjct: 686 VGTGIEHKAARDSGVVIIAKNSGIVTKVDSDEIHIKRD------LDNVVDKYRLLKFKRS 739

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T +NQRP+V   D +   DIIADGPST+ G++ALG+N+L+AFM W GYN+ED+ML++
Sbjct: 740 NQGTTINQRPIVNENDRINAGDIIADGPSTENGEIALGKNILMAFMNWEGYNYEDAMLLN 799

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           E++V +DV TS+HIEE E  AR+ KLG EEITRD+ N+ E+  KN+DE GII +GAEVN 
Sbjct: 800 EQLVIDDVLTSLHIEEHECEAREIKLGSEEITRDVINIGEDMRKNLDENGIIRIGAEVNS 859

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK++PKGE+ ++ EE+LLRAIFGEKA +VRDTSLRVP G +G VVDV+ ++R   
Sbjct: 860 GDILVGKVSPKGETELSAEERLLRAIFGEKAREVRDTSLRVPHGETGIVVDVKCYSRKNG 919

Query: 951 D 951
           D
Sbjct: 920 D 920



 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 233/1096 (21%), Positives = 401/1096 (36%), Gaps = 108/1096 (9%)

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             + +T  +     D   +  +  +  + + +     V++  +   +  TL  D  K  ++
Sbjct: 171  YDTDTNGVVSVRIDRTRKLPITTMIRALLYETNEEMVENFGDIKELHTTLEKDITKSYQE 230

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A+L+IYR ++PGD +T    ES+ + L FD  +YDL+ VGR K N +L L        + 
Sbjct: 231  AILEIYRKLKPGDPATVESGESLLHNLLFDPRRYDLAKVGRYKFNKKLALRNRLIGTILA 290

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERI 490
            ++         ++     G     +           ++    Y+   +++E    I    
Sbjct: 291  EDIFKTDKFGEMEKIASVGDYISEE--------LAEKIENAGYKRVHVKVEDKEIIVVGN 342

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCS----SQLSQLEEHVNSLSRITHTRRLSALGQ 546
              VDI +      I+   +   V          S      E   +  +     R+  L  
Sbjct: 343  HFVDIGAFELGFDISCNGLSEKVYYPVMMEILESASEYEGEEYETQVKRAVRNRVKELSP 402

Query: 547  GGVARARAGVEMRDVHPTHYG--RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
              + R      +       YG       +      +  V  L    +      +    R 
Sbjct: 403  THIIRDDIEATVSYEFNLFYGLGICDDIDHLGNRRVRAVGELL---QNQFRIGLSRMERV 459

Query: 605  VCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCA 650
            V +   T D           +  L A  +E    +Q +  +D++      T +       
Sbjct: 460  VRERMSTQDPDLATPQGLINIRPLVASLKEFFGSSQLSQFMDQNNPLAELTHKRRLSALG 519

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
               +   R   +  D        I     P   N      L       Q    ++     
Sbjct: 520  PGGLSRDRAGYEVRDVHESHYGRICPIETPEGPNIGLITSLTTYARVDQ-YGFIETPYRV 578

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            V  G+ +       A    +                  E     S  G++    +  + +
Sbjct: 579  VNNGIATKDIVYLTADEEDEVIIAQANEPLDENGRFVNERV---SGRGINGENDIYPRDT 635

Query: 771  NQNTCVNQRPLVKVGD----EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             Q   V+ + +V VG      +  +D       +++   A+   +  A +   G   + +
Sbjct: 636  IQLMDVSPQQIVSVGTAMIPFLENDDATRALMGSNMQRQAVPLLVTEAPIVGTGIEHKAA 695

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
                  +++++      ++  E+  +       +  R +          I++  I+    
Sbjct: 696  RDSGVVIIAKNSGIVTKVDSDEIHIKRDLDNVVDKYRLLKFKRSNQGTTINQRPIVNEND 755

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             +N GDI+    + +    +   + +L A    +  +  D  L         V+D  + +
Sbjct: 756  RINAGDIIADGPSTEN-GEIALGKNILMAFMNWEGYNYEDAMLLN----EQLVIDDVLTS 810

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
             H  +    +  + +   E + RD  +    + +N+      I  G    SG     K +
Sbjct: 811  LHIEEHECEAREI-KLGSEEITRDVINIGEDMRKNLDEN-GIIRIGAEVNSGDILVGKVS 868

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  +S   R     F  +  +V+     +          +      K    + GD++
Sbjct: 869  PKGETELSAEERLLRAIFGEKAREVRDTSLRVPHGETGIVVDV------KCYSRKNGDEL 922

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            PPGV  VV+V+VA KR I                                          
Sbjct: 923  PPGVNEVVRVYVATKRKI------------------------------------------ 940

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
                 NVG          C   G K        + +    P  + L+ V+       +++
Sbjct: 941  -----NVG-------DKMCGRHGNKGVISRIMPQEDMPFLPDGTPLQIVLNPLGVPSRMN 988

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  V       + G  V+TPVFDGA +  +   L++A   ESG+  L DG TG+ FD
Sbjct: 989  IGQVLEVHLGLAAKRLGWKVATPVFDGASDIDVLDALKLAGCPESGKIKLRDGRTGDEFD 1048

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
             PVTVGY+YMLKL+H+V +K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG
Sbjct: 1049 NPVTVGYMYMLKLHHLVDEKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1108

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A++ LQEMLT+KSDD+VGR + YESIV G +  E G PESF VL+KE+Q+L L + L + 
Sbjct: 1109 ASHTLQEMLTVKSDDIVGRVKTYESIVKGVNIPEPGIPESFKVLMKELQSLCLDVKLIDE 1168

Query: 1367 RTKNSAKMEEIPDFNK 1382
              +     E   +   
Sbjct: 1169 EGEEIKLRENSDEIKA 1184


>gi|307718200|ref|YP_003873732.1| DNA-directed RNA polymerase subunit beta [Spirochaeta thermophila
           DSM 6192]
 gi|306531925|gb|ADN01459.1| DNA-directed RNA polymerase, beta subunit [Spirochaeta thermophila
           DSM 6192]
          Length = 1164

 Score =  788 bits (2036), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/940 (45%), Positives = 592/940 (62%), Gaps = 70/940 (7%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNI--APDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            PE++D+P+L+EVQ +SY+ FL        +    +GL+  F+S FPI + +G   LE+ 
Sbjct: 17  RPEVMDLPNLLEVQFSSYEKFLQAEKIRKGEPLAVQGLEEVFRSSFPIESPNGDMRLEYD 76

Query: 78  SYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
            Y  D    K+  ++C  + LTYAVPLK  + LI  +           +I+++ IY+GD+
Sbjct: 77  FYTLDFEAIKYSEEECKRKGLTYAVPLKAQINLIFLE---------TGEIRQKMIYLGDI 127

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT  GTF+I G +R+VVSQ+HRSPG+ F H+KG        +Y  RIIP +G W++ E
Sbjct: 128 PLMTDRGTFIINGAERVVVSQIHRSPGVIFSHEKG--------VYGARIIPYRGSWLEFE 179

Query: 196 FDS-KDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            D+ KD+I+ +IDR++++  T FL ALG D+ E+I+S FY     +             D
Sbjct: 180 VDAKKDLIYAKIDRKKRILGTLFLRALGFDTREKIISAFYETKEVAVS-------PETKD 232

Query: 254 LMVGAKVSSSLVDID--TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +VG  ++  +   +    ++++ +G K+    +  L   GV+ + +  D          
Sbjct: 233 AVVGRVLARDVCTGEGPDQKKLLRAGAKIHPHEMDELLHAGVERVWVIDDE--------- 283

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +    E+ +   D                              Y R     D    ++
Sbjct: 284 HPDSLHSEVILNCFDR-------------------------EEAKYTREEEGID-EPTKE 317

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           DA++ +Y  + PGD  T   AE     +FF   +YDL  VGR K+N + + D P     +
Sbjct: 318 DAIIAVYSAIMPGDPITIENAEKDLQAMFFSERRYDLGDVGRYKLNKKFDYDPPLSTTVL 377

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  ++ L+ +  G+  +DDID+LGNRRVRSVGE+L  + +    RMER  KER+S
Sbjct: 378 TLDDIVNTMRHLIKVYIGEEPVDDIDHLGNRRVRSVGELLTAELKTAFSRMERIAKERMS 437

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + D++ PQDLI+ KP+V+A+ EFF SSQLSQ  + VN LS +TH RRL+ALG GG++R
Sbjct: 438 LKESDTIKPQDLISIKPIVAAIKEFFGSSQLSQFMDQVNPLSELTHKRRLNALGPGGLSR 497

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL  +ARVN YGF+E PYRKV DG+VT
Sbjct: 498 ERAGFEVRDVHYTHYGRMCPIETPEGPNIGLILSLALYARVNEYGFLEAPYRKVKDGRVT 557

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           N++ YL+AM+EE  +IAQAN+ +DE G F  + V  R  G+    P E I ++D SP+Q+
Sbjct: 558 NEIEYLTAMDEEKYFIAQANAPIDEKGRFLTDQVSVRKGGDYTTRPPEAIQYMDVSPRQI 617

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS +ASLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTGME   A  SG  + A+R
Sbjct: 618 VSASASLIPFLEHDDANRALMGSNMQRQAVPLIFPEPPRVGTGMERRCAYDSGVVVKARR 677

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG+VE V + ++VI+             DIY L K+QR+NQ+TC NQRP+V  G  V + 
Sbjct: 678 AGVVEYVSSTKVVIKPD---GVTDERERDIYFLQKYQRTNQDTCFNQRPIVNKGQRVEKG 734

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D++ADGPST  G+LALGRN+LVAF+PW+GYNFED++LISER++ +DVFTSIHI+EF +  
Sbjct: 735 DVLADGPSTFKGELALGRNVLVAFVPWYGYNFEDAILISERLLKQDVFTSIHIKEFSIEV 794

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE+ITRDIPNVSE+ L+++DE GI+ +GA+V  G ILVGKITPK ++ +TPE K
Sbjct: 795 RETKLGPEKITRDIPNVSEKHLEHLDEEGIVRIGAKVKSGSILVGKITPKSDAELTPEFK 854

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL +IFGEKA DVRDTSLRVP G  GTV+DV+   R   D
Sbjct: 855 LLNSIFGEKAKDVRDTSLRVPHGAEGTVIDVQRLRRSEGD 894



 Score =  487 bits (1253), Expect = e-135,   Method: Composition-based stats.
 Identities = 200/590 (33%), Positives = 276/590 (46%), Gaps = 80/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E        +V        +       +        
Sbjct: 638  MGSNMQRQAVPLIFPEPPRVGTGMERRCAYDSGVVVKARRAGVVEYVSSTKVVIKPDGVT 697

Query: 859  EEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLL 913
            +E  RDI  + +    N D    +  I+  G  V  GD+L  G  T KGE  +     + 
Sbjct: 698  DERERDIYFLQKYQRTNQDTCFNQRPIVNKGQRVEKGDVLADGPSTFKGELALGRNVLVA 757

Query: 914  RAIF-GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR--D 970
               + G    D    S R+      T + ++ F+    +       + R+   +  +  +
Sbjct: 758  FVPWYGYNFEDAILISERLLKQDVFTSIHIKEFSIEVRETKLGPEKITRDIPNVSEKHLE 817

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE+ I+      +   IL G+              L + +  E  +            
Sbjct: 818  HLDEEGIVRIGAKVKSGSILVGKITPKSDAELTPEFKLLNSIFGEKAKD----------- 866

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +    E +   ++        +   GD++PPGV  VVKV VA KR +Q GDKM
Sbjct: 867  VRDTSLRVPHGAEGTVIDVQ------RLRRSEGDELPPGVEEVVKVLVASKRKLQEGDKM 920

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SR+LP EDMPFL DGTPVDI LNPLGVPSRMN+GQI ET LGWA V L +
Sbjct: 921  AGRHGNKGVISRVLPEEDMPFLADGTPVDICLNPLGVPSRMNLGQILETELGWAAVALDE 980

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               + + +  +   I                                             
Sbjct: 981  WYATPVFESASPEMI--------------------------------------------- 995

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                 EE +      A L E+ ++ LYDG TGE F +PV VGY+YMLKLNH+V DK++AR
Sbjct: 996  -----EEKLRE----AGLPETSKTTLYDGRTGEAFHQPVMVGYMYMLKLNHLVDDKMHAR 1046

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA  LQE+LTIKSDD+ GRT++YE
Sbjct: 1047 STGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQELLTIKSDDMEGRTKIYE 1106

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            SIV G  +   G PESFNVLV+E++ L L I +++++ K     E   + 
Sbjct: 1107 SIVKGEPSTSPGIPESFNVLVQELRGLALDITVQDTKGKPVPLTERDEEL 1156


>gi|58697027|ref|ZP_00372494.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
            endosymbiont of Drosophila simulans]
 gi|58536712|gb|EAL59988.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
            endosymbiont of Drosophila simulans]
          Length = 940

 Score =  786 bits (2031), Expect = 0.0,   Method: Composition-based stats.
 Identities = 448/933 (48%), Positives = 635/933 (68%), Gaps = 15/933 (1%)

Query: 233  YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            Y KI Y +  D W  P    D   G ++   L+DI+ G  ++++  ++TS L K L +  
Sbjct: 1    YEKIKYVKHKDGWKVPFVP-DKFKGVRLPFHLMDIE-GNVLLKANVRITSRLAKKLYDNE 58

Query: 293  VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            +K   +  + +CGL++A+ +++  +    + AG+ I  + ++++    + +I +L +D++
Sbjct: 59   LKEYLVPFNSICGLFLAKYLMDSASSTKILSAGESIKLEDIKKLELLSVDEISVLNIDNL 118

Query: 353  NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                YI NTL  D+N   +DAL +IYRV+RPG+V    + E  F  LFF  + YDLS +G
Sbjct: 119  FVGPYILNTLFLDENMSYQDALYEIYRVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIG 178

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            R+K+N  L L+  +D+  +  EDII I+K +V LR+G+G++DDID+LGNRRVRSVGE ++
Sbjct: 179  RLKLNSYLGLNYDEDLTVLTHEDIIEIVKKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIE 238

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            NQ+R GLL++ER+I + +S+  +D V P D IN K + + + +FF SSQLSQ  +  N L
Sbjct: 239  NQFRTGLLKLERAIVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPL 298

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +AR+
Sbjct: 299  SEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 358

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            N YGFIE+PYRKV +  VT+ + YLSA++E + +IA  +  LDE+  F +++++CR AG 
Sbjct: 359  NKYGFIESPYRKVVNRVVTDQIEYLSAIDEGSHHIADTSVKLDENNCFVDDMLYCRYAGS 418

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             ++V  +++ +ID SPKQV+S+AASLIPFLENDD+NR LMG NMQRQAVPLLK  AP V 
Sbjct: 419  FVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVA 478

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TGMES VA  SGA ++AKR GIV+  D+  IVIR+ + +   +   VDIY L KFQRSN 
Sbjct: 479  TGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNH 537

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC+NQRPLV VGD V++ D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  
Sbjct: 538  NTCINQRPLVCVGDYVKKGDVIADGPAINSGELALGKNLLVAFMSWQGYNFEDSIIISSE 597

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V +D+FTSIHIEEF+ +  DT LG E+ITR IP V+EE L ++D+ GI+ +G  V PG 
Sbjct: 598  VVKKDLFTSIHIEEFDCVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGY 657

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ILVGK+TPK    + PE KLL  IFGEK+ D  D+SL     V GTV+DV++F R G+++
Sbjct: 658  ILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEE 717

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            NER++ +++++I     ++D    +     Y  L ++L    +               + 
Sbjct: 718  NERALLIKQKEINDFEEERDYIINVTSEYFYDELKKLLINSGSQ------------DREK 765

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                 R QWW   ++++ +   V+SLK  ++   S    +FK K+EK+  G D+P GV  
Sbjct: 766  FDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSM 825

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKVF+A+K  +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMN
Sbjct: 826  SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMN 885

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VGQI ETH+GWAC  LG+K+ +++++       
Sbjct: 886  VGQILETHVGWACRKLGEKVSNILDEINKIKSA 918


>gi|256544549|ref|ZP_05471922.1| DNA-directed RNA polymerase subunit beta [Anaerococcus vaginalis
           ATCC 51170]
 gi|256399874|gb|EEU13478.1| DNA-directed RNA polymerase subunit beta [Anaerococcus vaginalis
           ATCC 51170]
          Length = 1236

 Score =  786 bits (2030), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/954 (44%), Positives = 603/954 (63%), Gaps = 56/954 (5%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K P+++D+P+L++VQK SY  F+           EGL    + + PI  ++G
Sbjct: 10  KTERVSFSKFPQVLDLPNLLKVQKDSYRWFV----------EEGLGEILEDISPIEDYNG 59

Query: 71  AAMLEFVSYEFDPP-KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +LEFV Y+FD   K+ +++  ++D TY+  LK+  RLI          K  +++KEQ 
Sbjct: 60  NLILEFVGYDFDDETKYTIEEAKYKDTTYSRDLKVKARLI---------NKETEEVKEQE 110

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG  +Y+  +IP++G
Sbjct: 111 VFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYASELDK---SGNKMYSSTVIPNRG 167

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ + D+   ++VR+DR RK+P T+ + AL  +++E I+             +     
Sbjct: 168 AWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFENDEEIIEALGDTEHLRNTLEKENSE 227

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS------- 300
            S   L+   K       +  G+   +ES + L + LL   +   +  +G          
Sbjct: 228 TSEEALIEIYK------KLKPGDPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLAL 281

Query: 301 -DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            D L     A+D+V+ ETGE++++AG++ID ++   I +S I  + I+       +  +R
Sbjct: 282 HDRLIDQISAKDVVSDETGELFVKAGEMIDRQTALNIENSGINVVDIIVKQENGEDKELR 341

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                          LD +  +   D+    ++E ++  +    +  D +      +N  
Sbjct: 342 ICGNHFV-------YLDSFEELEGFDLEDLELSEKVYYPVM--REILDENEDKESIINEI 392

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                    ++I K DI+A +    +L  G G +DDID+LGNRRVR VGE+L+NQ+R+GL
Sbjct: 393 ERRKKELCPKNIVKSDILAAVNYQFNLFEGIGDVDDIDHLGNRRVRGVGELLQNQFRIGL 452

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  N +S +TH R
Sbjct: 453 ARMERVVRERMTTQDPDLATPQGLINIKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKR 512

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++AR+N YGFIE
Sbjct: 513 RLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTYARINKYGFIE 572

Query: 600 TPYRKV-CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVP 657
           TPYRKV  DG VT+++ YL+A  E+N  IAQAN  LDE+  F  + V  R   GE  + P
Sbjct: 573 TPYRKVGKDGHVTDEIDYLTADVEDNFIIAQANEPLDENNRFINDRVSGRGINGENDIYP 632

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           REK++++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPLLK++AP V TG+E 
Sbjct: 633 REKVEYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEH 692

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             AK SG  +V+K AG V  V   +I I+        S   +D YRL+KF+R+NQ T +N
Sbjct: 693 RAAKDSGVCVVSKNAGEVVYVGDEKIRIKRD------SDGEIDYYRLLKFRRANQGTTIN 746

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+VK+G+ V  N+IIADGPST+ G+LALG+N+L+AF  W GYN+ED+ML++E++V +D
Sbjct: 747 QRPIVKLGEHVDANEIIADGPSTEQGELALGKNILIAFTTWEGYNYEDAMLLNEQLVMDD 806

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TS+HIEE E  AR+TKLG EEIT+DIPNV ++  KN+DE G+I +GAEV  GDILVGK
Sbjct: 807 VLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGK 866

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL VP G SG VVDV+ +N+   D
Sbjct: 867 VSPKGETELSPEERLLRAIFGEKAREVRDTSLTVPHGESGIVVDVKEYNKKDGD 920



 Score =  511 bits (1315), Expect = e-142,   Method: Composition-based stats.
 Identities = 277/1199 (23%), Positives = 471/1199 (39%), Gaps = 112/1199 (9%)

Query: 222  GMDSEE-----ILSTFYPKIVYSQRGD---FWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            G D ++     I    Y    YS+            +         +    +  D+   V
Sbjct: 67   GYDFDDETKYTIEEAKYKDTTYSRDLKVKARLINKETEEVKEQEVFMGDFPMMTDSATFV 126

Query: 274  IESGKKLTSG---------LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
            I   +++                L + G K    T     G ++  D     T  + ++ 
Sbjct: 127  INGAERVIVSQLVRSPGVYYASELDKSGNKMYSSTVIPNRGAWIEFDTDASHTVNVRLDR 186

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
               +   +L      E  +  I   +++ +  ++RNTL  + ++  ++AL++IY+ ++PG
Sbjct: 187  TRKLPATTLVRALLFENDEEII---EALGDTEHLRNTLEKENSETSEEALIEIYKKLKPG 243

Query: 385  DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            D ++   A+++ N L FD  +YDL+ VGR K N +L L      +   K+ +      L 
Sbjct: 244  DPASLESAQNLINNLLFDDRRYDLAKVGRYKYNKKLALHDRLIDQISAKDVVSDETGELF 303

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
             ++ G+               +V +++  Q   G  +  R        +D    +    +
Sbjct: 304  -VKAGEMIDRQTALNIENSGINVVDIIVKQ-ENGEDKELRICGNHFVYLDSFEELEGFDL 361

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
                +   V        L + E+  + ++ I   RR   L    + ++     +      
Sbjct: 362  EDLELSEKVYYPVMREILDENEDKESIINEIE--RRKKELCPKNIVKSDILAAVNYQFNL 419

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND----------- 613
              G     +     N  +   +    +      +    R V +   T D           
Sbjct: 420  FEGIGDVDDIDHLGNRRVRG-VGELLQNQFRIGLARMERVVRERMTTQDPDLATPQGLIN 478

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQ 670
            +  ++A+ +E    +Q +  +D+    +E   +          +   R  ++  D     
Sbjct: 479  IKPVTAVIKEFFGSSQLSQFMDQTNPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSH 538

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
               I     P   N      L       +   +          G            + A 
Sbjct: 539  YGRICPIETPEGPNIGLITSLTTYARINKYGFIETPYRKVGKDGH----VTDEIDYLTAD 594

Query: 731  RAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--- 785
                     A   +  +     D            +   ++        Q+ +V VG   
Sbjct: 595  VEDNFIIAQANEPLDENNRFINDRVSGRGINGENDIYPREKVEYMDVSPQQ-IVSVGASL 653

Query: 786  -DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
               +  +D        ++   A+      A +   G     +      +VS++    +++
Sbjct: 654  IPFLENDDSTRALMGANMQRQAVPLLKSQAPIVATGIEHRAAKDSGVCVVSKNAGEVVYV 713

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             + ++  +    G  +  R +          I++  I+ +G  V+  +I+    + + + 
Sbjct: 714  GDEKIRIKRDSDGEIDYYRLLKFRRANQGTTINQRPIVKLGEHVDANEIIADGPSTE-QG 772

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   + +L A    +  +  D  L     V   V+       H  +  E  +  E E  
Sbjct: 773  ELALGKNILIAFTTWEGYNYEDAMLLNEQLVMDDVLTSVHIEEHECEARETKLGAE-EIT 831

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            + +    DD +  LD N   R+   +   + + G    K  T LS +        +  + 
Sbjct: 832  KDIPNVGDDMKKNLDENGVIRIGAEVKSGDILVGKVSPKGETELSPE-------ERLLRA 884

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               ++  +    SL V +  S  +++ +  NK +    GD++ PGV +V++VFVA KR I
Sbjct: 885  IFGEKAREVRDTSLTVPHGESGIVVDVKEYNKKD----GDELSPGVNKVIRVFVATKRKI 940

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKM GRHGNKG+VSRI+P EDMPFL DGTP+ I LNPLG+PSRMN+GQ+ E H+G A
Sbjct: 941  MVGDKMCGRHGNKGVVSRIMPREDMPFLPDGTPIQICLNPLGIPSRMNIGQVLEVHMGLA 1000

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               +G KI + + D   + +I       +K     + T KI                   
Sbjct: 1001 ARTMGWKIATPVFDGALDTEIEEALEQAQKTAPYVNKTGKIRL----------------- 1043

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                       G++       GE FD PVTVG +YMLKL+HMV 
Sbjct: 1044 -------------------------RDGRT-------GEEFDNPVTVGVMYMLKLHHMVE 1071

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            +K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLT+KSDDV G
Sbjct: 1072 EKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTVKSDDVTG 1131

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            R + YESIV G +  E GTPESF VLVKE+Q+L L ++L +         E I + +K 
Sbjct: 1132 RVKTYESIVKGENVPEPGTPESFKVLVKELQSLALDVELLDEDGNVIEIKENIDEQDKF 1190


>gi|269792802|ref|YP_003317706.1| DNA-directed RNA polymerase, beta subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100437|gb|ACZ19424.1| DNA-directed RNA polymerase, beta subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 1201

 Score =  786 bits (2030), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/942 (45%), Positives = 607/942 (64%), Gaps = 84/942 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R++ GK  ++I++PDL+EVQ+ SY+ F   +  P+ R  +GLQ  FK VFPI ++ G   
Sbjct: 12  RRYLGKQKDLIELPDLVEVQRHSYEWFFQADEDPNFRRLQGLQELFKEVFPIESYDGNFA 71

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           LEFV Y  DPP   +++   RDLT++ P++ T+RL+          +S  +IKE+ +Y+G
Sbjct: 72  LEFVRYYVDPPTISIEEARERDLTWSRPIRATIRLV---------NRSNGEIKEEEVYLG 122

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D P+MT  GTF+I G +R+VVSQL RS G++F  D       G+  YA ++IPD+G W++
Sbjct: 123 DFPVMTDRGTFIINGTERVVVSQLARSAGVYFSADLS---SPGQETYAAKLIPDRGAWLE 179

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            +    + + V+ID R+K+PVT FL ALG+   +E+L  F   +                
Sbjct: 180 FDLTPSEFLSVKIDNRKKIPVTMFLKALGVPTDDELLRLFGATVEEVD---------VVE 230

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           + + G  ++  +V  D G  +     ++T   L  L ++G   + +              
Sbjct: 231 EDVRGMLLAEPIVGSD-GRVIFHKNDRITKEHLDELWKQGRTRVAVW------------- 276

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                        D    ++LE+                             D      +
Sbjct: 277 -----------RVDHSVAETLEK-----------------------------DPTSSTDE 296

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           A+L+I+R ++P +      A    + LFFDS +Y+L  VGR K+N RL L   D+ R + 
Sbjct: 297 AMLEIFRRLKPNEPPRMENAREHMHSLFFDSRRYNLGRVGRYKLNRRLGLQVDDEQRLLT 356

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI-S 491
            ED++AI+  L+ LR+G    DDID+LGNRRVR++GE+L+NQ R+GLLRMER  KER+ +
Sbjct: 357 VEDVVAIVNGLLKLRDGLEREDDIDHLGNRRVRAIGELLQNQVRIGLLRMERIAKERMTT 416

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             D+ S   +DLIN +P+ +A+ EFF S QLSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 417 IPDLSSATAKDLINVRPISAALREFFGSGQLSQFMDQTNPLAELTHRRRLSALGPGGLSR 476

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E RDVH THYGRICP ET EG NIGLV+SL ++A++N YGF+ TP R+V DG+VT
Sbjct: 477 ERAGFEARDVHYTHYGRICPIETPEGSNIGLVTSLATYAKINEYGFLVTPRRRVVDGRVT 536

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            +VVYLSA +E+   +  A++ + EDGS   + V  R  G+  +VP++++DF+D SPKQ+
Sbjct: 537 GEVVYLSADDEDEYNVGMASTPVGEDGSILIDEVHVRHRGDIRMVPKDQVDFLDVSPKQI 596

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS++  LIPFLE+DD+NR LMG NMQRQAVPL++AEAP VGTG+E+ +A+ SG+ I+A+R
Sbjct: 597 VSVSTGLIPFLEHDDANRALMGSNMQRQAVPLVRAEAPLVGTGIEAKIARDSGSCILARR 656

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G VE VDA R+VIR+ +G L+        YRL+KF+RSNQ T ++QRPLV+ GD V+  
Sbjct: 657 SGTVEFVDADRVVIRAEDGTLNQ-------YRLVKFRRSNQGTVIHQRPLVRKGDPVKAG 709

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D+IADG +   G+LALGRN+LVAF+ W GYNFED++L+S+R+V ED +TSIHIEE+EV A
Sbjct: 710 DVIADGQACQGGELALGRNVLVAFVSWEGYNFEDAILLSQRVVKEDYYTSIHIEEYEVEA 769

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLGPEEITRDIPNV ++ LKN+DE GI+ +GAEV  GDILVGK+TPKGES  +PEE+
Sbjct: 770 RDTKLGPEEITRDIPNVGDDALKNLDENGIVRIGAEVRAGDILVGKVTPKGESDQSPEER 829

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           LLRAIFGEKA +VRD+SLRVP G  G VV ++  +R    ++
Sbjct: 830 LLRAIFGEKAREVRDSSLRVPHGEGGKVVAIKRLSREHNSED 871



 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 181/610 (29%), Positives = 266/610 (43%), Gaps = 71/610 (11%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              ++ A  P  G   E  +   S   +  
Sbjct: 595  QIVSVSTGLIPFLEHDDANRALMGSNMQRQAVPLVRAEAPLVGTGIEAKIARDSGSCILA 654

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                ++   + + +    + G     R +          I +  ++  G  V  GD++  
Sbjct: 655  RRSGTVEFVDADRVVIRAEDGTLNQYRLVKFRRSNQGTVIHQRPLVRKGDPVKAGDVIAD 714

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                +G   +     +L A    +  +  D  L     V            + ++  +  
Sbjct: 715  GQACQG-GELALGRNVLVAFVSWEGYNFEDAILLSQRVVKEDYYTSIHIEEYEVEARDTK 773

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E     I  +  D     DE  I+      R  +IL G+    G         L   
Sbjct: 774  LGPEEITRDIPNVGDDALKNLDENGIVRIGAEVRAGDILVGKVTPKGESDQSPEERLLRA 833

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R           +V+ +   +          ++     ++ +    +D+ PGV 
Sbjct: 834  IFGEKAR-----------EVRDSSLRVPHGEGGKVVAIK-----RLSREHNSEDLSPGVN 877

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             VVKV+VA  R I  GDKMAGRHGNKG+VS+ILP EDMPFL DGTPVD+VLNPLGVPSRM
Sbjct: 878  EVVKVYVAQFRKITEGDKMAGRHGNKGVVSKILPEEDMPFLSDGTPVDVVLNPLGVPSRM 937

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+FET +G+  +  G K+ + + +     +I  L   + +                 
Sbjct: 938  NLGQVFETVMGFVAMHNGWKVATPVFEGADQEEIFQLVDKIRENKYPE------------ 985

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                L    +  LYDG TGEP D+ VTV
Sbjct: 986  ------------------------------------LTRDCKITLYDGRTGEPMDKKVTV 1009

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL H+V DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++ YGAA++L
Sbjct: 1010 GVMYMLKLIHLVDDKIHARSTGPYSLITQQPLGGKTQFGGQRFGEMEVWALEGYGAAHML 1069

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LT+KSDD+ GR + YE IV G +  + G PESF VL+KE+Q LG+ +++        
Sbjct: 1070 QEILTVKSDDIRGRLKTYERIVKGQNLAKPGVPESFRVLIKELQGLGVDVEIVYEDGTVG 1129

Query: 1372 AKMEEIPDFN 1381
              +    +  
Sbjct: 1130 ELVMGDDEDE 1139


>gi|227530194|ref|ZP_03960243.1| DNA-directed RNA polymerase [Lactobacillus vaginalis ATCC 49540]
 gi|227349869|gb|EEJ40160.1| DNA-directed RNA polymerase [Lactobacillus vaginalis ATCC 49540]
          Length = 1165

 Score =  785 bits (2027), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/913 (44%), Positives = 566/913 (61%), Gaps = 70/913 (7%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
           ++GL+  F  + PI  F G   LEFV Y+   PK+ VD+    D  Y+ PL +TLRL   
Sbjct: 2   DKGLREMFDDIMPIDDFQGKLSLEFVDYQLLEPKYTVDEAREHDANYSAPLHVTLRLT-- 59

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
                       +IK Q ++ G+ PLMT  GTF+I G +R++VSQL RSPG++++ + G+
Sbjct: 60  -------NHETGEIKSQDVFFGEFPLMTDQGTFIINGAERVIVSQLVRSPGVYYNEEAGK 112

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILS 230
              +G+  Y    IP++G W++ E D+K+I +VRIDR RK+P+T  + ALG  S+ EI+ 
Sbjct: 113 ---NGRPSYGATFIPNRGAWLEYETDAKNISYVRIDRTRKLPMTELIRALGFGSDDEIID 169

Query: 231 TFY-PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSL 288
            F       S   D      +A D  V   +      +  GE    +S + L +      
Sbjct: 170 MFGGNSETLSLTLDKD-VHKNAEDSRVEEALKDIYERLRPGEPKTADSARNLLTARFFDP 228

Query: 289 KEKGVK--------FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           K   +            +    L G  +AE + + +TGE+  + GD + ++ L+++    
Sbjct: 229 KRYDMAPVGRYKTNKKLMLKYRLLGETLAETLADPDTGEVLAQKGDKVTKEVLKKLE--- 285

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
               P L  D      Y              +A++     +           + +  +  
Sbjct: 286 ----PYLDRDDFKMITY----------TPSDEAVVTEPVKL-----------QKVLVYSH 320

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            D ++          + +  N   P + +HI   DI+A +    +L+ G GT DDID+LG
Sbjct: 321 EDPER---------VVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGTTDDIDHLG 371

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+++ EFF SS
Sbjct: 372 NRRIRSVGELLQNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIREFFGSS 431

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 432 QLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNI 491

Query: 581 GLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GL++SL+S+ARVN YGFIETPYR+V     KVT+ + YL+A EE+N  IAQAN+ L++DG
Sbjct: 492 GLINSLSSYARVNKYGFIETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAQANTPLNDDG 551

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           SF ++ V CR   + I    E +D++D SPKQVVS+A++ IPFLENDDSNR LMG NMQR
Sbjct: 552 SFAQDQVMCRDKDDYIETSVENVDYMDVSPKQVVSVASACIPFLENDDSNRALMGANMQR 611

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL   AP V TG++   A  SG A++AK++G VE VDA  + +R  +G LD     
Sbjct: 612 QAVPLLNPHAPLVSTGIDYKAAHDSGVAMIAKKSGTVEYVDAREVRVREEDGTLD----- 666

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y+LMKF+RSN     NQRP+VKVG+ V  +D++ADGPS + G+LALG+N L+AFM W
Sbjct: 667 --TYKLMKFRRSNGGKNYNQRPIVKVGEHVDADDVLADGPSMEQGELALGQNPLIAFMTW 724

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++ ISER+V +DV+TSIHIE +E  AR+TKLGPEE+TR+IPNV ++ LK++DE
Sbjct: 725 QGYNFEDAIAISERLVKDDVYTSIHIESYESEARETKLGPEEMTREIPNVGDDALKDLDE 784

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +GAEV+ GDILVGK+TPKG + ++ EE+LL AIFGEK+ +VRDTSLRVP G  G 
Sbjct: 785 NGIVRIGAEVHDGDILVGKVTPKGMTELSAEERLLHAIFGEKSREVRDTSLRVPHGGGGI 844

Query: 939 VVDVRIFNRHGID 951
           + DV++F R   D
Sbjct: 845 IQDVKVFTRENGD 857



 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 228/1107 (20%), Positives = 376/1107 (33%), Gaps = 182/1107 (16%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            E+    G   D++ ++    +       L  D               ++   ++AL DIY
Sbjct: 154  ELIRALGFGSDDEIIDMFGGNSETLSLTLDKDV----------HKNAEDSRVEEALKDIY 203

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TP 425
              +RPG+  T   A ++    FFD  +YD++ VGR K N +L L               P
Sbjct: 204  ERLRPGEPKTADSARNLLTARFFDPKRYDMAPVGRYKTNKKLMLKYRLLGETLAETLADP 263

Query: 426  DDVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            D    +        KE +  +   L        T    D         + ++L       
Sbjct: 264  DTGEVLAQKGDKVTKEVLKKLEPYLDRDDFKMITYTPSDEAVVTEPVKLQKVLVYS-HED 322

Query: 479  LLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
              R+   I      ++   + P D+         +   +        L            
Sbjct: 323  PERVVPIIGNGHIPLEYKHIEPADILASLNYFFNLQEGIGTTDDIDHLGNRRIRSVGELL 382

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
                R   A  +  V    +  +   V P     I P   S     G         + N 
Sbjct: 383  QNQFRIGLARMERVVRERMSIQDPDTVTPQQLINIRPVVASIREFFGSSQLSQFMDQTNP 442

Query: 595  YGFIETPYRK----------------VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             G +    R                 V D   T+          E   I   NS      
Sbjct: 443  LGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYAR 502

Query: 639  SFTEELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                  +            +  +KID++ A  +    IA +  P   NDD +        
Sbjct: 503  VNKYGFIETPYRRVSWKTHKVTDKIDYLTADEEDNYIIAQANTPL--NDDGSFA------ 554

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              Q   + + +  ++ T +E+V                V  V +  I     +       
Sbjct: 555  --QDQVMCRDKDDYIETSVENVDYMD-------VSPKQVVSVASACIPFLENDDSNRALM 605

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                       QR          PLV  G + +                           
Sbjct: 606  GA-------NMQRQAVPLLNPHAPLVSTGIDYKA-------------------------- 632

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                ++   +M+  +    E V         EV  R+ + G  +  + +      G KN 
Sbjct: 633  ---AHDSGVAMIAKKSGTVEYVDAR------EVRVRE-EDGTLDTYKLMKFRRSNGGKNY 682

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V+  D+L    +   +  +   +  L A    +  +  D        V 
Sbjct: 683  NQRPIVKVGEHVDADDVLADGPS-MEQGELALGQNPLIAFMTWQGYNFEDAIAISERLVK 741

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              V        +  +  E  +  E    E +    DD    LD N   R+   +   + +
Sbjct: 742  DDVYTSIHIESYESEARETKLGPEEMTRE-IPNVGDDALKDLDENGIVRIGAEVHDGDIL 800

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G    K  T LS++                                   +I  ++ +  
Sbjct: 801  VGKVTPKGMTELSAEE------------------------------RLLHAIFGEKSREV 830

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
             +          G+++ VKVF         GD+++      G+ + +             
Sbjct: 831  RDTSLRVPHGGGGIIQDVKVFTREN-----GDELSP-----GVNTMV------------- 867

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                         R+ + Q  +  +G       G K    I   + +    P  + ++ +
Sbjct: 868  -------------RVYIAQKRKIQVGDKMSGRHGNKGTVSIVVPEEDMPYMPDGTPIDIM 914

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +       +++      +       + G+ ++TPVFDGA ++ +   ++ +   E G++I
Sbjct: 915  LSPMGVPSRMNIGQLLELHLGMAAKRLGIHMATPVFDGATDKDVWDAVKESGFPEDGKTI 974

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  + VG ++ LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 975  LYDGRTGEPFENRIAVGSMHYLKLAHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 1034

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR R Y++I+ G    + G PESF VLVKE+Q
Sbjct: 1035 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVRTYDAIINGEPIPKPGVPESFRVLVKELQ 1094

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            ALGL + + +             D ++
Sbjct: 1095 ALGLDMKVLDGNHNEVQLKNMDEDDDE 1121


>gi|300871176|ref|YP_003786048.1| DNA directed RNA polymerase subunit beta [Brachyspira pilosicoli
           95/1000]
 gi|300688876|gb|ADK31547.1| DNA directed RNA polymerase beta subunit [Brachyspira pilosicoli
           95/1000]
          Length = 1173

 Score =  785 bits (2027), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/1002 (42%), Positives = 604/1002 (60%), Gaps = 81/1002 (8%)

Query: 4   GVVFNGLGRV---RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           GV F    R+   R  F ++  +I+ PDL+ +QK SY+ FL  ++  ++R NEGLQ    
Sbjct: 16  GVEFAKKYRMENGRVNFSRSASVIEPPDLLAIQKESYESFLQKDVPENKRKNEGLQEVLT 75

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           S+FPI A +    +EF+SY    PK    +   RD TYA   KI ++L V D +      
Sbjct: 76  SIFPIVATNEKMQIEFISYSIGEPKISEKEARRRDKTYAYQFKIKVQLTVRDPER----- 130

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               I EQ I++G++P MT  GTF+I G +R+VVSQ+HRSPG+ F             ++
Sbjct: 131 ----IIEQEIFVGEIPAMTDRGTFIINGAERVVVSQIHRSPGVVF------NRSDRDAMF 180

Query: 181 ACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY 238
             +IIPD+G W++ E D  KDI++VRIDR++K+PVT FL A+G+ + EEIL  FY     
Sbjct: 181 VAKIIPDRGTWLEFELDTKKDIMYVRIDRKKKLPVTVFLRAIGITTNEEILKLFYEIDKI 240

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           S          +A                +  E ++  G+ +   L + L   G+  + +
Sbjct: 241 SLAKLSDEEKKAALIGRRSYSTVFD--KENPEEIILNPGELINQNLAERLLMSGIDEIEV 298

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                                                           L ++++ +N  I
Sbjct: 299 ------------------------------------------------LNMEAIKDNVTI 310

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            NTL  D  K++K+A   IY V+RPG+ +         N L FD   Y L  VGR K+N 
Sbjct: 311 INTLDKDTTKNQKEACTKIYNVIRPGEPALIENVVKTCNDLVFDPKLYALGDVGRYKINK 370

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           RLN    +  + +R +DII  I+ L+ +   +  +DDID+LGNRR+RSVGE+L  Q + G
Sbjct: 371 RLNFPESEQDKVLRHKDIIETIRFLIKVFINEEQLDDIDHLGNRRIRSVGELLAMQIKTG 430

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
             RMER+ KER+   D+++V PQ L++ K + + + EF+ +SQLSQ  +  N LS ITH 
Sbjct: 431 FTRMERAAKERMQMQDMEAVTPQSLVSIKVIQAVIKEFYGTSQLSQFMDQNNPLSEITHK 490

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRL+ALG GG+ R RAG E+RDVH THYG+ICP ET EG NIGL+ SL ++A++N +GF+
Sbjct: 491 RRLNALGPGGLTRDRAGFEVRDVHHTHYGKICPIETPEGPNIGLIVSLATYAKINKHGFL 550

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           ETPYRKV +GKVT+++ YL+A +EE  +IA AN+ L+EDG+F E L+  R   E      
Sbjct: 551 ETPYRKVVNGKVTDEIEYLTAHDEERYHIADANAPLNEDGTFKENLISTRYRSEFPYSTP 610

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++ ++D SP+Q+VS+++SLIPFLE+DD+NR LMG NMQRQ+VPLL  E+P VGTG+E+ 
Sbjct: 611 DQVQYMDVSPQQIVSLSSSLIPFLEHDDANRALMGSNMQRQSVPLLFPESPIVGTGVEAK 670

Query: 719 VAKS-SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
           + +  +G A+ AKRAG V +V    IVI+  + + D      D+Y L+K+QR+NQ+T  +
Sbjct: 671 ICQPGTGIAVHAKRAGKVIKVVHDEIVIKPTKQNSDD---DYDVYELIKYQRTNQDTNYH 727

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP+V VGD V+   ++ADGP+TD G+LALGRN+L AFM + GYNFED++L+S+R+V ED
Sbjct: 728 QRPVVNVGDTVKAGGLLADGPATDHGELALGRNVLAAFMIFEGYNFEDAILLSKRLVQED 787

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           VFTSIHIEEF V AR+TKL  E ITRDIPNV +   KN+DE GI+ +GA+V  GDILVGK
Sbjct: 788 VFTSIHIEEFSVEARETKLDKENITRDIPNVPDSAFKNLDERGIVRIGAKVKAGDILVGK 847

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
           +TPKGE+ +TPE +LL +IFGEK+ DV+DTSLRVP G  GTV+DVR+++R   D      
Sbjct: 848 VTPKGETEVTPEYRLLHSIFGEKSRDVKDTSLRVPHGKDGTVIDVRVYSRENGD------ 901

Query: 958 SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
              +  +E + +    ++ I+             G  A   P
Sbjct: 902 -ELKPGVEEVVKVFLAKKRIIQEGDKMAGRHGNKGVVARIMP 942



 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 144/523 (27%), Positives = 217/523 (41%), Gaps = 67/523 (12%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
              +       ++   I         N  +  ++ VG  V  G +L           +   
Sbjct: 700  PTKQNSDDDYDVYELIKYQRTNQDTNYHQRPVVNVGDTVKAGGLLADGP-ATDHGELALG 758

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L A    +  +  D  L     +S  +V   +F    I++        +   E + R
Sbjct: 759  RNVLAAFMIFEGYNFEDAIL-----LSKRLVQEDVFTSIHIEEFSVEARETKLDKENITR 813

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +N+  R   +  G    +G     K T      ++   R     F  +  
Sbjct: 814  DIPNVPDSAFKNLDER-GIVRIGAKVKAGDILVGKVTPKGETEVTPEYRLLHSIFGEKSR 872

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             V+     +    + +   +      ++   + GD++ PGV  VVKVF+A K        
Sbjct: 873  DVKDTSLRVPHGKDGTVIDV------RVYSRENGDELKPGVEEVVKVFLAKK-------- 918

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
                        RI+   D                                        G
Sbjct: 919  ------------RIIQEGD----------------------------------KMAGRHG 932

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K          +       + ++  +       +++      +L      K G+  + P
Sbjct: 933  NKGVVARIMPIEDMPYLEDGTPVDICLNPLGVPSRMNIGQVIEMLLGWTGHKMGLKYACP 992

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF+G  E+ +   +  A L+ +G+  L+DG TGEPF   V VGY+YMLKLNH+V DKV+A
Sbjct: 993  VFEGPKEDELKEAMISAGLNPTGKVKLFDGRTGEPFKNDVAVGYMYMLKLNHLVEDKVHA 1052

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGKS  GGQRLGEMEVW ++AYGAA +LQE LT+KSDD+ GR R+Y
Sbjct: 1053 RSTGPYSLVTQQPLGGKSQFGGQRLGEMEVWALEAYGAANMLQEFLTVKSDDMTGRARIY 1112

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            ESIV G+     G PESFNVLV+E++ LGL+I + +       
Sbjct: 1113 ESIVKGDVISSPGIPESFNVLVQELRGLGLNITIHDEEGNQLP 1155


>gi|227894513|ref|ZP_04012318.1| DNA-directed RNA polymerase subunit beta [Lactobacillus ultunensis
           DSM 16047]
 gi|227863672|gb|EEJ71093.1| DNA-directed RNA polymerase subunit beta [Lactobacillus ultunensis
           DSM 16047]
          Length = 1184

 Score =  784 bits (2025), Expect = 0.0,   Method: Composition-based stats.
 Identities = 389/933 (41%), Positives = 564/933 (60%), Gaps = 79/933 (8%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           +VQ  SY  FL          ++G++  F  + PI+ FSG   LE+V Y+   PK+ VD+
Sbjct: 3   DVQTESYKWFL----------DKGIKEVFDDIMPISDFSGKLSLEYVDYKLQKPKYTVDE 52

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
               D TYA P+ +TL+L           +   +IK Q ++ GDLPLMT+ G+F++ G +
Sbjct: 53  ARDHDATYAAPMHVTLKLT---------NQETGEIKTQDVFFGDLPLMTESGSFIVNGAE 103

Query: 151 RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
           R++VSQL RSPG+++  D  +   +G+ ++   +IP++G W++ E D+K++ +VR+DR R
Sbjct: 104 RVIVSQLVRSPGVYYTGDYDK---NGRQIFGTTVIPNRGAWLEYETDAKNVSYVRVDRTR 160

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           K+P+T  + A+G+ S+ +I+  F          D      + AD  V   +      +  
Sbjct: 161 KLPLTVLIRAMGIGSDSDIIDMFGQSDTLQFTLDKD-VHKNPADSRVAEALKDIYERLRP 219

Query: 270 GEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEI 320
           GE    +S + L        +   +  +G           + L G  +AE + + +TGEI
Sbjct: 220 GEPKTTDSSRSLLYARFFDPRRYDLAPVGRYKINKKLSLKNRLYGQTLAETLADPDTGEI 279

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             +   V+  + ++++                                DR D  +  Y+ 
Sbjct: 280 IAKKDTVVTHEVMDKLAPYL----------------------------DRDDFKMVTYQP 311

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
            + G +      + +  +   D ++          + +  N      V+H+   D++A I
Sbjct: 312 SKEGVLPDPITVQEIKVYSKVDPERE---------VKLISNGHIDAKVKHLTPADVLASI 362

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
               DL+   G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER ++ER+S  D  +V P
Sbjct: 363 NYFFDLQEKIGATDDIDHLGNRRIRRVGELLQNQFRIGLARMERVVRERMSIQDPSTVTP 422

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +P+V+++ EFF SSQLSQ  +  N L  +TH RR+SALG GG+ R RAG E+RD
Sbjct: 423 QQLINIRPIVASIKEFFGSSQLSQFMDQHNPLGELTHKRRMSALGPGGLTRDRAGYEVRD 482

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLS 618
           VH THYGR+CP ET EG NIGL++SL S+A +N YGFIETPYR+V     KVT+ + YL+
Sbjct: 483 VHYTHYGRLCPIETPEGPNIGLINSLASYAIINKYGFIETPYRRVSWKTHKVTDKIDYLT 542

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+N  IA AN+ L++DGSF ++L+  R   + + V  +KID++D  PKQVVS+A++ 
Sbjct: 543 ADEEDNYIIAGANTRLNDDGSFKDDLILARQKEDNVEVTPDKIDYMDVIPKQVVSVASAC 602

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDDSNR LMG N QRQA PL+      VGTGME   A   GAA++AK AG VE V
Sbjct: 603 IPFLENDDSNRALMGANQQRQAAPLINPHGSLVGTGMEYRAAHDLGAALIAKAAGTVEYV 662

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA  I IR  +G LD        Y L K++RSN +   NQ P VK+GD V  +D+IA+GP
Sbjct: 663 DANEIRIRREDGTLDK-------YTLEKYRRSNNSKSYNQTPNVKLGDHVDVSDVIANGP 715

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           + D G+LALG+N L+AFM W+ YN+ED++++SER+V +DV+TSI IE++E  ARDTKLGP
Sbjct: 716 TMDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDVYTSISIEDYESEARDTKLGP 775

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR++PN+ E+ LK++D  GI+ +GAEV+ GDILVGK+TPKG + ++ EE+LL AIFG
Sbjct: 776 EEITRELPNIGEDALKDLDADGIVRIGAEVHDGDILVGKVTPKGVTELSAEERLLHAIFG 835

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G V DV+++ R   D
Sbjct: 836 EKAREVRDTSLRVPHGGGGIVQDVKVYTREAGD 868



 Score =  472 bits (1214), Expect = e-130,   Method: Composition-based stats.
 Identities = 171/502 (34%), Positives = 236/502 (47%), Gaps = 69/502 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G  V+  D++    T      +   +  L A       +  D  +     V   V  
Sbjct: 699  VKLGDHVDVSDVIANGPT-MDHGELALGQNPLIAFMTWNMYNYEDAIMLSERLVKDDV-- 755

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                +    +   R   +  E+I     +  +D    LD +   R+     G     G  
Sbjct: 756  YTSISIEDYESEARDTKLGPEEITRELPNIGEDALKDLDADGIVRI-----GAEVHDGDI 810

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   R     F  +  +V+     +          +      K+   
Sbjct: 811  LVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVQDV------KVYTR 864

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++ PGV  +V+V++A KR IQ GDKM+GRHGNKG V+ ++P EDMP+L DGTPVDI
Sbjct: 865  EAGDELSPGVNTMVRVYIAQKRKIQVGDKMSGRHGNKGTVAAVVPEEDMPYLPDGTPVDI 924

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D     D+               
Sbjct: 925  CLNPMGVPSRMNIGQLLELHLGAAARQLGIHVATPVFDGANENDVW-------------- 970

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                         +R A   K G    T ++DG                           
Sbjct: 971  -----------DTVRQAGVDKDG---KTVIYDG--------------------------R 990

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPF   V+VG ++ LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 991  TGEPFHNRVSVGVMHYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1050

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+LGL 
Sbjct: 1051 ALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERIPKPGVPESFRVLVKELQSLGLD 1110

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            I + +         +   + + 
Sbjct: 1111 IRVLDMNHNEIELRDMDEESSD 1132


>gi|167757656|ref|ZP_02429783.1| hypothetical protein CLORAM_03206 [Clostridium ramosum DSM 1402]
 gi|167702653|gb|EDS17232.1| hypothetical protein CLORAM_03206 [Clostridium ramosum DSM 1402]
          Length = 1223

 Score =  784 bits (2024), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/959 (42%), Positives = 578/959 (60%), Gaps = 65/959 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +        R+ + +    +++P+L+E+Q  SY  F             G++  F+
Sbjct: 1   MENKITEAKSKITRRNYSRISGSLELPNLVEIQTNSYKWF----------KEVGIKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            ++PIT F+    LEFV   FD  K+ V++   RD  YA P++ +LRL+           
Sbjct: 51  DIYPITNFNETLSLEFVDCTFDEAKYSVEESKDRDANYAAPIRASLRLV---------NS 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IKEQ ++MGD PLMT  GTF+I G +R++VSQL RSPG +F     +   SGK ++
Sbjct: 102 GTGEIKEQEVFMGDFPLMTDSGTFIINGAERVIVSQLVRSPGAYFADALDK---SGKTVF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY- 238
              IIP +G W++ E D+KD+++VRIDR RK+P T  L ALG+ S +EI+  F       
Sbjct: 159 NGSIIPSRGTWLEFETDAKDVLNVRIDRNRKMPGTVLLRALGLSSNDEIIDVFGEHEYII 218

Query: 239 -SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +           ++    ++ +         L K+ + K  K 
Sbjct: 219 NTLAKDNTTNTEEALIEIYNKLRPGEPATLEGANNLLYTRFFDCKRYDLAKAGRFKFRKK 278

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE--KSLEEIFHSEIRDIPILYVDSVN 353
           L +  D + G  +AED+V+ +   +Y E   V  E   +++ IF +      +     + 
Sbjct: 279 LSLL-DRIAGRILAEDLVDVDGNVVYPEGTVVTQEVSDTIKPIFEAGAHTRELDTNPRLE 337

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +N  I+   V   +   K   +    +       T S   + ++++F   D YD      
Sbjct: 338 SNGVIQVLDVYVDDTKTKKMRVIGTDLSLDSKFVTISDMMAAYSYMFNLVDIYD------ 391

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                   LD   + R               +L    G +DDID+LGNRRVRSVGE+++N
Sbjct: 392 -------ALDLTAEDRV--------------NLMARIGLLDDIDHLGNRRVRSVGELIQN 430

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL RMER +KER+S  ++DS+ PQ L N +P+ +A+ EFF SSQLSQ  + +N L+
Sbjct: 431 QFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIKEFFSSSQLSQFMDQINPLA 490

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +T+ RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+S+L S+A++N
Sbjct: 491 ELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIETPEGPNIGLISTLASYAKIN 550

Query: 594 AYGFIETPYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            YGFIETPYRKV +  +   DV YL+A EE+N  IAQAN   D+DG+  +  V  R  GE
Sbjct: 551 QYGFIETPYRKVNNCVIDEHDVRYLTADEEKNYIIAQANVRTDKDGTILDAQVIARHLGE 610

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I+  RE++D+ID SPKQ+VS+A S IPFLENDD+ R LMG NMQRQAVPLL    PFVG
Sbjct: 611 NIMAKREEVDYIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQAVPLLNPHTPFVG 670

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A+ SGAA+V++  GIV  VDA ++++   EG           YRL KF+ SN 
Sbjct: 671 TGMEHQAARDSGAAVVSREDGIVTYVDAKKVIVEDNEGVE-------HRYRLSKFKISNN 723

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC+N +P+VK G++V +  ++ADGP+ + G+LALG+N+LV FM W+GYN+ED++++SER
Sbjct: 724 GTCINHKPIVKTGEKVLKGQVLADGPAMEQGELALGQNVLVGFMEWNGYNYEDAVIMSER 783

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TS+HI+E+ +  RDTKLGPEEITRDIPNV +E  KN++  GII +GAEV  GD
Sbjct: 784 LVKDDVYTSVHIDEYAIECRDTKLGPEEITRDIPNVGDEARKNLNSDGIIMIGAEVKEGD 843

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKG++ ++ EEKLL AIFGEK+ +V+D SLRVP G +G V D+++F R   D
Sbjct: 844 ILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAGIVHDIKVFERKNGD 902



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 241/1067 (22%), Positives = 383/1067 (35%), Gaps = 137/1067 (12%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D    + YI NTL  D   + ++AL++IY  +RPG+ +T   A ++    FFD  +YDL
Sbjct: 208  IDVFGEHEYIINTLAKDNTTNTEEALIEIYNKLRPGEPATLEGANNLLYTRFFDCKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKE---------------DIIAIIKILVDLRNGKGTI 453
            +  GR K   +L+L      R + ++                   +   +  +       
Sbjct: 268  AKAGRFKFRKKLSLLDRIAGRILAEDLVDVDGNVVYPEGTVVTQEVSDTIKPIFEAGAHT 327

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
             ++D         V ++L         +  R I         D  +    +    +++A 
Sbjct: 328  RELDTNPRLESNGVIQVLDVYVDDTKTKKMRVI-------GTDLSLDSKFVTISDMMAAY 380

Query: 514  CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
               F    +    +       +T   R++ + + G+      +  R V            
Sbjct: 381  SYMFNLVDIYDALD-------LTAEDRVNLMARIGLLDDIDHLGNRRVR----------- 422

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                       S+    +      +    R V +    ++V  ++     N     A   
Sbjct: 423  -----------SVGELIQNQFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIK 471

Query: 634  LDEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                 S   + +       E     R          +         +          +  
Sbjct: 472  EFFSSSQLSQFMDQINPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIET 531

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
                    +  L + A     G      +     ++ +        D  +  I +     
Sbjct: 532  PEGPNIGLISTLASYAKINQYGFIETPYRKVNNCVIDEHDVRYLTADEEKNYIIAQANVR 591

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL---------- 802
                  +         R      + +R  V   D   +  +                   
Sbjct: 592  TDKDGTIL--DAQVIARHLGENIMAKREEVDYIDISPKQIVSVATSCIPFLENDDATRAL 649

Query: 803  ---GDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P+ G   E          +VS +     +++  +V+  D   G
Sbjct: 650  MGANMQRQAVPLLNPHTPFVGTGMEHQAARDSGAAVVSREDGIVTYVDAKKVIVEDN-EG 708

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E   R            I+   I+  G +V  G +L        +  +   + +L    
Sbjct: 709  VEHRYRLSKFKISNNGTCINHKPIVKTGEKVLKGQVLADGP-AMEQGELALGQNVLVGFM 767

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D  +     V   V      + + I+  +  +  E  +I     +  DE   
Sbjct: 768  EWNGYNYEDAVIMSERLVKDDVYTSVHIDEYAIECRDTKLGPE--EITRDIPNVGDEAR- 824

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
                  +    I+ G     G     K T      +S   +     F  +  +V+ N   
Sbjct: 825  ---KNLNSDGIIMIGAEVKEGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLR 881

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +          +      K+ + + GD++ PGV +VVKV++  KR I  GDKMAGRHGNK
Sbjct: 882  VPHGGAGIVHDI------KVFERKNGDELQPGVNKVVKVYIVQKRKISEGDKMAGRHGNK 935

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMP L+DGTP+DI+LNPLGVPSRMN+GQ+ E HLG+A   LG  I +   
Sbjct: 936  GVISKILPIEDMPHLEDGTPLDIMLNPLGVPSRMNIGQVLELHLGYAARQLGLYIATPAF 995

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D     D+  + +                                      PV       
Sbjct: 996  DGLHPSDLEDIMAEAGMSKDGKQ----------------------------PV------- 1020

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                                 G TGE FD  ++VG +YM+KL HMV DK++ARS G YSL
Sbjct: 1021 -------------------ISGRTGEYFDNNISVGIMYMIKLAHMVDDKLHARSVGPYSL 1061

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGGK+  GGQR GEMEVW ++AYGAAY L+E+LT+KSDDVVGR + YE+IV G  
Sbjct: 1062 VTQQPLGGKAQNGGQRFGEMEVWALEAYGAAYTLREILTVKSDDVVGRVKTYEAIVKGQP 1121

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
              E G PESF VL KE+QAL L I L +             + ++  
Sbjct: 1122 LPEPGLPESFRVLKKELQALALDIRLLDENDNEVDMRNIEEEEHRFP 1168


>gi|313893097|ref|ZP_07826674.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. oral
           taxon 158 str. F0412]
 gi|313442450|gb|EFR60865.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. oral
           taxon 158 str. F0412]
          Length = 1384

 Score =  783 bits (2023), Expect = 0.0,   Method: Composition-based stats.
 Identities = 417/969 (43%), Positives = 572/969 (59%), Gaps = 109/969 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + K  E+I +P L+++Q+ SY+ FL            GLQ  F  + PI   SG
Sbjct: 9   KRTRYTYAKINEVIKMPHLLDIQRKSYEWFL----------ESGLQNIFNDISPIKDNSG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +L F  +    PK+D+++C  RD TYA PL++ +RL+  D +         DIKEQ +
Sbjct: 59  NLVLSFEGFSLGEPKYDINECKNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEV 111

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G 
Sbjct: 112 FMGDFPLMTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGA 168

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWC 246
           W+++E D+ +I+ VRIDR RK+P T  + ALG D+ E IL  F+            D   
Sbjct: 169 WIELETDASEIVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPIYDERI 228

Query: 247 FPLSAADLMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
                 D        +      +  GE   +ES + L   L    +   +  +G      
Sbjct: 229 VRTLEKDTTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNK 288

Query: 301 -----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  + G  +A+ IV+ ETGE+ ++AG  + E+ L+ + +S       ++       
Sbjct: 289 KLGWRQRMLGHTLAQPIVDPETGEVILDAGVQVGEEQLDIVANSH------VFDGEGFAE 342

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            YI N    +      +  L       P D  T                + D+       
Sbjct: 343 FYIVNNDGVESKVICNNCNL-------PFDHRTV--------------TREDMIANISYL 381

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N+       DD+ H+                            GNRR+R VGE+L+NQ+
Sbjct: 382 LNLMDGAGHTDDIDHL----------------------------GNRRLRCVGELLQNQF 413

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +
Sbjct: 414 RIGLTRMERVVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAEL 473

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL +SL+++A+VN +
Sbjct: 474 THKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLSNSLSNYAKVNEF 533

Query: 596 GFIETPYRKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           GFIE PYRKV                 V++ VVY++A EEE   IAQANS LDE+G FT 
Sbjct: 534 GFIEAPYRKVEKVYGKGADADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDEEGYFTT 593

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E V CR   + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVP
Sbjct: 594 EHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVP 653

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL+A+AP VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y
Sbjct: 654 LLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTY 707

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           RL KF RSNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN
Sbjct: 708 RLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYN 767

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++L+SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GII
Sbjct: 768 YEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEEGII 827

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           C+GAEV+PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV
Sbjct: 828 CIGAEVHPGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDV 887

Query: 943 RIFNRHGID 951
           ++F R   D
Sbjct: 888 KVFTRENGD 896



 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 108/228 (47%), Positives = 150/228 (65%), Gaps = 6/228 (2%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    I+ +++ L  +        +I         D     +     +G+ ++TPVFDGA
Sbjct: 1101 EELEAINKVKNTLNNIHSAEEKRIEIRKELEGLGYDFKKYGMPTPDVAGIHIATPVFDGA 1160

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   E+G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1161 HEKDVFETLEIAGRPENGKTVLYDGRTGEPMDNHVTVGYVYMLKLHHLVDDKIHARSTGP 1220

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV 
Sbjct: 1221 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKAYEKIVK 1280

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            G +  E G PESF VL+KE+Q++GL + + N   +    M+E+ D ++
Sbjct: 1281 GENIPEPGVPESFKVLLKELQSIGLDVKILNED-QEEVVMKELDDEDE 1327



 Score =  230 bits (586), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 181/867 (20%), Positives = 310/867 (35%), Gaps = 66/867 (7%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L +        I  TL  D  +   +AL++IY+
Sbjct: 194  VLVRALGWDTNESILDLFWNGKTDEDGLPIYDER----IVRTLEKDTTQSADEALVEIYK 249

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L          + +  +   
Sbjct: 250  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGHTLAQPIVDPE 309

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 310  TGEVI-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPFDHRT 368

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQGGVARARAGVE 557
                     +            L  L +       I H   RRL  +G+           
Sbjct: 369  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGEL-------LQN 411

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF---IETPYRKVCDGKVTNDV 614
               +  T   R+      E   I  + S+T  A +N       I+  +      +  +  
Sbjct: 412  QFRIGLTRMERVV----RERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQT 467

Query: 615  VYLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
              L+ +  + R  A     L  +   F    V     G    +   +   I  S      
Sbjct: 468  NPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLSNSLSNY 527

Query: 674  IAASLIPFLE--NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
               +   F+E       +V        + V +  +++    T  E      + A      
Sbjct: 528  AKVNEFGFIEAPYRKVEKVYGKGADADKVVKVRVSDSVVYMTADEEEGMTIAQAN---SP 584

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVR 789
                       +  R     L+ +   VD   +              + +V +G      
Sbjct: 585  LDEEGYFTTEHVACRRGHDVLEVTPDKVDYMDVSP------------KEVVSIGTAMIPF 632

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEF 847
              +  A+              +L A  P  G   E   +      +++ +    +     
Sbjct: 633  LENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGN 692

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+       G  +  R    +        ++  I+  G  V  G +L       G   + 
Sbjct: 693  EIHVLRDSDGRVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELA 751

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
                +L A    +  +  D  L         +        +  D  +  +  E    EL 
Sbjct: 752  LGYNVLVAFMPWEGYNYEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELP 811

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                D  + + +  I      I  G     G     K+T      +   P  +  +    
Sbjct: 812  NTGDDTLKNLDEEGI------ICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFG 863

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  G
Sbjct: 864  DKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEG 919

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  G
Sbjct: 920  DKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQG 979

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEK 1174
            LG KIK+     K     +   +   +
Sbjct: 980  LGMKIKATDLHIKNVLKEARTDASYWE 1006


>gi|237735203|ref|ZP_04565684.1| NA-directed RNA polymerase subunit beta-beta [Mollicutes bacterium
           D7]
 gi|229381979|gb|EEO32070.1| NA-directed RNA polymerase subunit beta-beta [Coprobacillus sp. D7]
          Length = 1223

 Score =  783 bits (2023), Expect = 0.0,   Method: Composition-based stats.
 Identities = 403/959 (42%), Positives = 577/959 (60%), Gaps = 65/959 (6%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +        R+ + +    +++P+L+E+Q  SY  F             G++  F+
Sbjct: 1   MENKITEAKSKITRRNYSRISGSLELPNLVEIQTNSYKWF----------KEVGIKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            ++PIT F+    LEFV   FD  K+ V++   RD  YA P++ +LRL+           
Sbjct: 51  DIYPITNFNETLSLEFVDCTFDEAKYSVEESKDRDANYAAPIRASLRLV---------NS 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IKEQ ++MGD PLMT  GTF+I G +R++VSQL RSPG +F     +   SGK ++
Sbjct: 102 GTGEIKEQEVFMGDFPLMTDSGTFIINGAERVIVSQLVRSPGAYFADALDK---SGKTVF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY- 238
              IIP +G W++ E D+KD+++VRIDR RK+P T  L ALG+ S +EI+  F       
Sbjct: 159 NGSIIPSRGTWLEFETDAKDVLNVRIDRNRKMPGTVLLRALGLSSNDEIIDVFGEHEYII 218

Query: 239 -SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +           ++    ++ +         L K+ + K  K 
Sbjct: 219 NTLAKDNTTNTEEALIEIYNKLRPGEPATLEGANNLLYTRFFDCKRYDLAKAGRFKFRKK 278

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE--KSLEEIFHSEIRDIPILYVDSVN 353
           L +  D + G  +AED+V+ +   +Y E   V  E   +++ I  +      +     + 
Sbjct: 279 LSLL-DRIAGRILAEDLVDVDGNVVYPEGTVVTQEVSDTIKPILEAGAHTRELDTNPRLE 337

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +N  I+   V   +   K   +    +       T S   + ++++F   D YD      
Sbjct: 338 SNGVIQVLDVYVDDTKTKKMRVIGTDLSLDSKFVTISDMMAAYSYMFNLVDIYD------ 391

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                   LD   + R               +L    G +DDID+LGNRRVRSVGE+++N
Sbjct: 392 -------ALDLTAEDRV--------------NLMARIGLLDDIDHLGNRRVRSVGELIQN 430

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL RMER +KER+S  ++DS+ PQ L N +P+ +A+ EFF SSQLSQ  + +N L+
Sbjct: 431 QFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIKEFFSSSQLSQFMDQINPLA 490

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +T+ RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+S+L S+A++N
Sbjct: 491 ELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIETPEGPNIGLISTLASYAKIN 550

Query: 594 AYGFIETPYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            YGFIETPYRKV +  +   DV YL+A EE+N  IAQAN   D+DG+  +  V  R  GE
Sbjct: 551 QYGFIETPYRKVNNCVIDEHDVRYLTADEEKNYIIAQANVRTDKDGTILDAQVIARHLGE 610

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I+  RE++D+ID SPKQ+VS+A S IPFLENDD+ R LMG NMQRQAVPLL    PFVG
Sbjct: 611 NIMAKREEVDYIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQAVPLLNPHTPFVG 670

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A+ SGAA+V++  GIV  VDA ++++   EG           YRL KF+ SN 
Sbjct: 671 TGMEHQAARDSGAAVVSREDGIVTYVDAKKVIVEDNEGVE-------HRYRLSKFKISNN 723

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC+N +P+VK G++V +  ++ADGP+ + G+LALG+N+LV FM W+GYN+ED++++SER
Sbjct: 724 GTCINHKPIVKTGEKVLKGQVLADGPAMEQGELALGQNVLVGFMEWNGYNYEDAVIMSER 783

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TS+HI+E+ +  RDTKLGPEEITRDIPNV +E  KN++  GII +GAEV  GD
Sbjct: 784 LVKDDVYTSVHIDEYAIECRDTKLGPEEITRDIPNVGDEARKNLNSDGIIMIGAEVKEGD 843

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKG++ ++ EEKLL AIFGEK+ +V+D SLRVP G +G V D+++F R   D
Sbjct: 844 ILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAGIVHDIKVFERKNGD 902



 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 237/1060 (22%), Positives = 389/1060 (36%), Gaps = 123/1060 (11%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +D    + YI NTL  D   + ++AL++IY  +RPG+ +T   A ++    FFD  +YDL
Sbjct: 208  IDVFGEHEYIINTLAKDNTTNTEEALIEIYNKLRPGEPATLEGANNLLYTRFFDCKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV--------DLRNGKGTIDDIDNLG 460
            +  GR K   +L+L      R + ++ +     ++         ++ +    I +     
Sbjct: 268  AKAGRFKFRKKLSLLDRIAGRILAEDLVDVDGNVVYPEGTVVTQEVSDTIKPILEAGAHT 327

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 +         ++  + ++ +  +++  +  D  +    +    +++A    F   
Sbjct: 328  RELDTNPRLESNGVIQVLDVYVDDTKTKKMRVIGTDLSLDSKFVTISDMMAAYSYMFNLV 387

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +    +       +T   R++ + + G+      +  R V                   
Sbjct: 388  DIYDALD-------LTAEDRVNLMARIGLLDDIDHLGNRRVR------------------ 422

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                S+    +      +    R V +    ++V  ++     N     A        S 
Sbjct: 423  ----SVGELIQNQFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIKEFFSSSQ 478

Query: 641  TEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              + +       E     R          +         +          +         
Sbjct: 479  LSQFMDQINPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIETPEGPNIG 538

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             +  L + A     G      +     ++ +        D  +  I +           +
Sbjct: 539  LISTLASYAKINQYGFIETPYRKVNNCVIDEHDVRYLTADEEKNYIIAQANVRTDKDGTI 598

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-------------GDLA 806
                     R      + +R  V   D   +  +                          
Sbjct: 599  L--DAQVIARHLGENIMAKREEVDYIDISPKQIVSVATSCIPFLENDDATRALMGANMQR 656

Query: 807  LGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                +L    P+ G   E          +VS +     +++  +V+  D   G E   R 
Sbjct: 657  QAVPLLNPHTPFVGTGMEHQAARDSGAAVVSREDGIVTYVDAKKVIVEDN-EGVEHRYRL 715

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                       I+   I+  G +V  G +L        +  +   + +L         + 
Sbjct: 716  SKFKISNNGTCINHKPIVKTGEKVLKGQVLADGP-AMEQGELALGQNVLVGFMEWNGYNY 774

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +     V   V      + + I+  +  +  E  +I     +  DE         +
Sbjct: 775  EDAVIMSERLVKDDVYTSVHIDEYAIECRDTKLGPE--EITRDIPNVGDEAR----KNLN 828

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I+ G     G     K T      +S   +     F  +  +V+ N   +      
Sbjct: 829  SDGIIMIGAEVKEGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAG 888

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                +      K+ + + GD++ PGV +VVKV++  KR I  GDKMAGRHGNKG++S+IL
Sbjct: 889  IVHDI------KVFERKNGDELQPGVNKVVKVYIVQKRKISEGDKMAGRHGNKGVISKIL 942

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP L+DGTP+DI+LNPLGVPSRMN+GQ+ E HLG+A   LG  I +   D     D
Sbjct: 943  PIEDMPHLEDGTPLDIMLNPLGVPSRMNIGQVLELHLGYAARQLGLYIATPAFDGLHPSD 1002

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +  + +                                      PV              
Sbjct: 1003 LEDIMAEAGMSKDGKQ----------------------------PV-------------- 1020

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                          G TGE FD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLG
Sbjct: 1021 ------------ISGRTGEYFDNNISVGIMYMIKLAHMVDDKLHARSVGPYSLVTQQPLG 1068

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY L+E+LT+KSDDVVGR + YE+IV G    E G P
Sbjct: 1069 GKAQNGGQRFGEMEVWALEAYGAAYTLREILTVKSDDVVGRVKTYEAIVKGQPLPEPGLP 1128

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            ESF VL KE+QAL L I L +             + ++  
Sbjct: 1129 ESFRVLKKELQALALDIRLLDENDNEVDMRNIEEEEHRFP 1168


>gi|237738816|ref|ZP_04569297.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 2_1_31]
 gi|229423919|gb|EEO38966.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 2_1_31]
          Length = 1186

 Score =  782 bits (2020), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/972 (44%), Positives = 606/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R ++G + AFK VFPI + +G  
Sbjct: 6   ERLDFGKIKARGSMPHFLEFQLNSYEDFLQTNMSPNKREDKGFELAFKEVFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKRRGKTYSNSLKVRLRLINK--------KMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT+  TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTERATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D++EI+  F               
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNKEIIEHF--------------- 220

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                                     +E+ +     L K   ++  + L +    L G  
Sbjct: 221 --------------------------LEAKELNLKSLYKKYSKEPEELLNVLKQELEGSL 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E   +I E+ +  +  ++I  I   +V   +    + NTL  D+ 
Sbjct: 255 VKEDILDEETGEFIAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDET 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
              + A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  DD
Sbjct: 313 LTEEQAVVEVFKKLRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADD 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  +K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTMKYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KE++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VKEKMTTQDIETVSPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVHYLAADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K AG V  VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVAGKVIYVDGKKIVI-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V+  DIIADGP+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHI
Sbjct: 725 GDVVKAGDIIADGPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARATKLGDEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/602 (31%), Positives = 270/602 (44%), Gaps = 76/602 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 677  KVAGKVIYVDGKKIVIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    ++  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPDSDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AK 1373
              
Sbjct: 1147 NV 1148


>gi|294781912|ref|ZP_06747244.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           1_1_41FAA]
 gi|294481723|gb|EFG29492.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           1_1_41FAA]
          Length = 1186

 Score =  781 bits (2018), Expect = 0.0,   Method: Composition-based stats.
 Identities = 429/972 (44%), Positives = 607/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R ++G ++AFK VFPI + +G  
Sbjct: 6   ERLDFGKIKARGSMPHFLEFQLNSYEDFLQTNMSPNKREDKGFESAFKEVFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKRRGKTYSNSLKVRLRLINK--------KMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT+  TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTERATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D++EI+  F               
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNKEIIEHF--------------- 220

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                                     +E+ +     L K   ++  + + +    L G  
Sbjct: 221 --------------------------LEAKELNLKSLYKKYSKEPEELVNVLKQELEGSL 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           + EDI++ ETGE   E   +I E+ +  +  ++I  I   +V   +    + NTL  D+ 
Sbjct: 255 LKEDILDEETGEFIAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDET 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
              + A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  D+
Sbjct: 313 STEEQAVVEVFKKLRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADN 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  +K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTMKYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KE++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VKEKMTTQDIETVSPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ L +D    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVRYLAADEEDGLFIAQADTKLGKDNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K AG V  VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVAGKVIYVDGKKIVI-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V+  DIIADGP+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHI
Sbjct: 725 GDIVKAGDIIADGPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARATKLGDEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 193/602 (32%), Positives = 271/602 (45%), Gaps = 76/602 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 677  KVAGKVIYVDGKKIVIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDIVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GVMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AK 1373
              
Sbjct: 1147 NV 1148


>gi|87125958|gb|ABD20472.1| DNA-directed RNA polymerase, beta subunit [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|87201862|gb|ABD29672.1| RNA polymerase beta chain, putative [Staphylococcus aureus subsp.
           aureus NCTC 8325]
          Length = 1136

 Score =  781 bits (2016), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/907 (46%), Positives = 568/907 (62%), Gaps = 69/907 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEFV Y    PK+D+++   RD TYA PL++ +RLI+       
Sbjct: 1   MFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLII------- 53

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++KEQ ++MGD PLMT  GTFVI G +R++VSQL RSP ++F+    +   +G+
Sbjct: 54  --KETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK---NGR 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKI 236
             Y   IIP++G W++ E D+KD+++VRIDR RK+P+T  L ALG  S+ EI+       
Sbjct: 109 ENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNE 168

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKF 295
                 +      +   L+           +  GE   +E+ K L        K   +  
Sbjct: 169 YLRNTLEKDGTENTEQALL------EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLAS 222

Query: 296 LG--------ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +G             L    +AE IVN ETGEI +E G V+D + ++EI           
Sbjct: 223 VGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMD--------- 273

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
               V  +           +   +   +   +V  P D                      
Sbjct: 274 ----VLESNANSEVFELHGSVIDEPVEIQSIKVYVPND---------------------- 307

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               GR    +  N     +V+ I   DIIA +    +L +G G  DDID+LGNRR+RSV
Sbjct: 308 --DEGRT-TTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSV 364

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ+R+GL RMER ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +
Sbjct: 365 GELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMD 424

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 425 QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 484

Query: 588 SFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 485 SYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEV 544

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+ 
Sbjct: 545 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMN 604

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRL 764
            EAPFVGTGME V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L
Sbjct: 605 PEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPL 664

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            KF+RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++ALGRN++V FM W GYN+E
Sbjct: 665 AKFKRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYE 724

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNVSE  LKN+D+ GI+ +
Sbjct: 725 DAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYI 784

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++
Sbjct: 785 GAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKV 844

Query: 945 FNRHGID 951
           FNR   D
Sbjct: 845 FNREEGD 851



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 242/1158 (20%), Positives = 417/1158 (36%), Gaps = 130/1158 (11%)

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFL-----GI 298
                 +         +    +  DTG  VI   ++ + S L++S      + +       
Sbjct: 51   LIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGREN 110

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                +     A      +  ++     D   +  L  +  +         VD + +N Y+
Sbjct: 111  YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYL 170

Query: 359  RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD--------KYDLST 410
            RNTL  D  ++ + ALL+IY  +RPG+  T   A+S+    FFD          +Y  + 
Sbjct: 171  RNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNK 230

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +K  +         V     E ++    +L   +  +       N  +      G +
Sbjct: 231  KLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSV 290

Query: 471  LKNQYRLGLLRME----RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +     +  +++        +      +         I    +++++  FF         
Sbjct: 291  IDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYT 350

Query: 527  EHVNSLSRITHTRRLSALGQG--GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            + ++ L      RRL ++G+      R       R V      R+   +T       L++
Sbjct: 351  DDIDHLG----NRRLRSVGELLQNQFRIGLSRMERVVRE----RMSIQDTESITPQQLIN 402

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                 A +  +       + +       ++ +                           L
Sbjct: 403  IRPVIASIKEFFGSSQLSQFMDQANPLAELTH---------------------KRRLSAL 441

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPL 703
                   E   +    + +        +       I  + +  S   +            
Sbjct: 442  GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 501

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +  +   +   ++ + A    + +VA+    +             +  +        +  
Sbjct: 502  VDLDTHAITDQIDYLTADEEDSYVVAQANSKL-----DENGRFMDDEVVCRFRGNNTVMA 556

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              K    + +              +  +D        ++   A+      A     G   
Sbjct: 557  KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEH 616

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDT-------KLGPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E++ R           G  +                
Sbjct: 617  VAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCY 676

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG  V   +IL    +      M     ++         +  D  +     +S
Sbjct: 677  NQRPIVAVGDVVEYNEILADGPS-MELGEMALGRNVVVGFMTWDGYNYEDAVI-----MS 730

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   ++    I++ E      +   E + RD  +      +N+  R   +  G    
Sbjct: 731  ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDR-GIVYIGAEVK 789

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G     K T      ++   R     F  +  +V+     +                 K
Sbjct: 790  DGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIV------LDVK 843

Query: 1057 IEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+L DG
Sbjct: 844  VFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 903

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+          
Sbjct: 904  RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST------- 956

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              +  A   + G                             +++
Sbjct: 957  ------------------IEEAGMARDG-----------------------------KTV 969

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  ++VG +YMLKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR G
Sbjct: 970  LYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFG 1029

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q
Sbjct: 1030 EMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQ 1089

Query: 1356 ALGLSIDLENSRTKNSAK 1373
            +LGL + + + +      
Sbjct: 1090 SLGLDVKVMDEQDNEIEM 1107


>gi|313892041|ref|ZP_07825641.1| DNA-directed RNA polymerase, beta subunit [Dialister
           microaerophilus UPII 345-E]
 gi|313119555|gb|EFR42747.1| DNA-directed RNA polymerase, beta subunit [Dialister
           microaerophilus UPII 345-E]
          Length = 1263

 Score =  781 bits (2016), Expect = 0.0,   Method: Composition-based stats.
 Identities = 416/978 (42%), Positives = 586/978 (59%), Gaps = 109/978 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + ++ E++++P L+++Q  SYD F            EGL+  F  + PI   + 
Sbjct: 18  KRKRYTYARSQEVLEMPHLLDLQTRSYDWF----------KAEGLKDVFADISPIEDGAH 67

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F SY F   K+++++C  RD TY  PL + +RL+          K   +IKE  +
Sbjct: 68  KWALYFGSYSFGKEKYNIEECKSRDATYCAPLHVQVRLV---------NKESGEIKEHEL 118

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD P+MT  GTF+I G +R++VSQL RSPG+++  +       GK +Y  +IIP++G 
Sbjct: 119 FMGDFPIMTDTGTFIINGAERVIVSQLVRSPGVYYKKELD---TFGKEIYNAQIIPNRGA 175

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+  +I VRIDR RK+PVT  + ALG  S +EIL+ F   I   +  +      
Sbjct: 176 WIELETDAGGVISVRIDRNRKMPVTVLVRALGYSSNDEILNLFDHDIHIIKTLEKDSTTS 235

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-------- 300
           +   L+   +       +  GE   +ESG  L +      +   +  +G           
Sbjct: 236 TEEALLEIYR------KLRPGEPATVESGTTLLNNFFYDPRRYDLAKVGRYKLNKKLSWK 289

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + L G      IVN ETGEI I+A   ID++++E +                + +    N
Sbjct: 290 NRLLGNRTEGPIVNTETGEIVIDADSYIDKEAIELL----------------DKSGVFAN 333

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           T   +    ++D                                       G     +  
Sbjct: 334 TDQVEVMTQKED---------------------------------------GTPVKVICS 354

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           + +  D+ R + + DIIA I  L+++  G G++DDID+LGNRRVR VGE+L+NQ+R+GL 
Sbjct: 355 SGNREDNFRILERADIIAYIDYLLNMMQGYGSVDDIDHLGNRRVRCVGELLQNQFRIGLS 414

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+++ D D + PQ L+N +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR
Sbjct: 415 RMERVVRERMTTQDQDKMTPQVLVNIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRR 474

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL+++  +N YG IET
Sbjct: 475 LSALGPGGLSRERAGFEVRDVHYSHYGRMCPVETPEGPNIGLISSLSNYGIINKYGLIET 534

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR +     +VTN+  Y +A  E++  IAQA+  LDE+G F  + V  R   + +    
Sbjct: 535 PYRLIDKKAHRVTNECKYYTADVEDSLVIAQASEPLDEEGRFVHKNVASRHGADVLEADS 594

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            ++D +D SPKQVVSI  SLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTGME V
Sbjct: 595 AEVDLMDVSPKQVVSIGTSLIPFLEHDDTNRALMGANMQRQAVPLLRPEAPLVGTGMEWV 654

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A+ SG  ++AKR+G+VE+V   +IV+R+  G+LD        Y L KF RSNQ+TC+NQ
Sbjct: 655 AAQDSGVCLLAKRSGVVERVTGKKIVVRADNGELD-------TYELTKFLRSNQSTCINQ 707

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV  GD V     +ADG +TD G+LALG N+LVAF+ W GYN ED++LISER+  +D+
Sbjct: 708 RPLVYKGDRVETGSTLADGMATDGGELALGHNVLVAFVSWEGYNHEDAVLISERLCKDDL 767

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLG EEITR + +VSE+ ++ +DE GII VGA+V PGDILVGK+
Sbjct: 768 YTSIHIEEYECDARDTKLGEEEITRQLSSVSEDAVRYLDENGIIMVGADVRPGDILVGKV 827

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGID 951
           TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV++F R        G++
Sbjct: 828 TPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGEFGKVVDVKVFTRENGDELAPGVN 887

Query: 952 KNERSISVEREQIELLAR 969
           K  R    ++ +I    +
Sbjct: 888 KLVRVYIAQKRKIREGDK 905



 Score =  542 bits (1397), Expect = e-151,   Method: Composition-based stats.
 Identities = 193/527 (36%), Positives = 268/527 (50%), Gaps = 38/527 (7%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +       +       I++  ++  G  V  G  L   +   G   +     +L A
Sbjct: 685  NGELDTYELTKFLRSNQSTCINQRPLVYKGDRVETGSTLADGMATDG-GELALGHNVLVA 743

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVD-VRIFNRHGIDKNER-SISVEREQIELLARDKDD 973
                +  +  D  L           D     +    + + R +   E E    L+   +D
Sbjct: 744  FVSWEGYNHEDAVLI---SERLCKDDLYTSIHIEEYECDARDTKLGEEEITRQLSSVSED 800

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD N       I+ G +   G     K T      +   P  +  +    D++   
Sbjct: 801  AVRYLDEN-----GIIMVGADVRPGDILVGKVTPKGETEL--TPEERLLRAIFGDKER-- 851

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E                   K+   + GD++ PGV ++V+V++A KR I+ GDKMAGR
Sbjct: 852  --EVRDTSLRVPHGEFGKVVDVKVFTRENGDELAPGVNKLVRVYIAQKRKIREGDKMAGR 909

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNK + SRILP EDMPF  DG PVD+VLNPLGVPSRMN+GQI E HL WAC  LG++IK
Sbjct: 910  HGNKCVCSRILPVEDMPFTPDGRPVDLVLNPLGVPSRMNIGQILEIHLSWACHMLGEEIK 969

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                + +                             D     + E  +SG+ ++TPVFDG
Sbjct: 970  KNPKEVEKRLRALGY---------------------DFDKYGMPEPDESGIHIATPVFDG 1008

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
              +E + + L+ A L E+G+S++YDG TGE  D PVT+G+ YMLKL+H+V DK++ARSTG
Sbjct: 1009 CRDEDLAATLKAAGLPETGKSVIYDGRTGEKLDGPVTIGWKYMLKLHHLVDDKIHARSTG 1068

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV
Sbjct: 1069 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYEKIV 1128

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
             G +    G PESF VL+KE+Q++GL + + N    +    E   + 
Sbjct: 1129 KGQNIPSPGVPESFKVLMKELQSIGLDVRVLNENGDDVILKELDENE 1175


>gi|218462360|ref|ZP_03502451.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli Kim 5]
          Length = 634

 Score =  780 bits (2015), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/635 (67%), Positives = 518/635 (81%), Gaps = 1/635 (0%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1   MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAK
Sbjct: 61  SVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+
Sbjct: 121 SIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLF 180

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
           A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y +
Sbjct: 181 AARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKR 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    
Sbjct: 241 DGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAGD 299

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIRN
Sbjct: 300 DDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILANGFDEIPVLGIDHINVGAYIRN 359

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           TL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMRL
Sbjct: 360 TLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMRL 419

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGLL
Sbjct: 420 DLTVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGLL 479

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH RR
Sbjct: 480 RMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKRR 539

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 540 LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 599

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           PYR++ DGKVTNDV+YLSAMEE   Y+AQAN+ ++
Sbjct: 600 PYRRIVDGKVTNDVLYLSAMEEAKYYVAQANAEMN 634


>gi|329121576|ref|ZP_08250197.1| DNA-directed RNA polymerase subunit beta [Dialister micraerophilus
           DSM 19965]
 gi|327468731|gb|EGF14208.1| DNA-directed RNA polymerase subunit beta [Dialister micraerophilus
           DSM 19965]
          Length = 1259

 Score =  780 bits (2015), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/978 (42%), Positives = 586/978 (59%), Gaps = 109/978 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + ++ E++++P L+++Q  SYD F            EGL+  F  + PI   + 
Sbjct: 14  KRKRYTYARSQEVLEMPHLLDLQTRSYDWF----------KAEGLKDVFADISPIEDGAH 63

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F SY F   K+++++C  RD TY  PL + +RL+          K   +IKE  +
Sbjct: 64  KWALYFGSYSFGEEKYNIEECKSRDATYCAPLHVQVRLV---------NKESGEIKEHEL 114

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD P+MT  GTF+I G +R++VSQL RSPG+++  +       GK +Y  +IIP++G 
Sbjct: 115 FMGDFPIMTDTGTFIINGAERVIVSQLVRSPGVYYKKELD---TFGKEIYNAQIIPNRGA 171

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+  +I VRIDR RK+PVT  + ALG  S +EIL+ F   I   +  +      
Sbjct: 172 WIELETDAGGVISVRIDRNRKMPVTVLVRALGYSSNDEILNLFDHDIHIIKTLEKDSTTS 231

Query: 250 SAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-------- 300
           +   L+   +       +  GE   +ESG  L +      +   +  +G           
Sbjct: 232 TEEALLEIYR------KLRPGEPATVESGTTLLNNFFYDPRRYDLAKVGRYKLNKKLSWK 285

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + L G      IVN ETGEI I+A   ID++++E +                + +    N
Sbjct: 286 NRLLGNRTEGPIVNTETGEIVIDADSYIDKEAIELL----------------DKSGVFAN 329

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           T   +    ++D                                       G     +  
Sbjct: 330 TDQVEVMTQKED---------------------------------------GTPVKVICS 350

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           + +  D+ R + + DIIA I  L+++  G G++DDID+LGNRRVR VGE+L+NQ+R+GL 
Sbjct: 351 SGNREDNFRILERADIIAYIDYLLNMMQGYGSVDDIDHLGNRRVRCVGELLQNQFRIGLS 410

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+++ D D + PQ L+N +PVV+A+ EFF SSQLSQ  +  N L+ +TH RR
Sbjct: 411 RMERVVRERMTTQDQDKMTPQVLVNIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRR 470

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL+++  +N YG IET
Sbjct: 471 LSALGPGGLSRERAGFEVRDVHYSHYGRMCPVETPEGPNIGLISSLSNYGIINKYGLIET 530

Query: 601 PYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR +     +VTN+  Y +A  E++  IAQA+  LDE+G F  + V  R   + +    
Sbjct: 531 PYRLIDKKAHRVTNECKYYTADVEDSLVIAQASEPLDEEGRFVHKNVASRHGADVLEADS 590

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            ++D +D SPKQVVSI  SLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTGME V
Sbjct: 591 AEVDLMDVSPKQVVSIGTSLIPFLEHDDTNRALMGANMQRQAVPLLRPEAPLVGTGMEWV 650

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A+ SG  ++AKR+G+VE+V   +I++R+  G+LD        Y L KF RSNQ+TC+NQ
Sbjct: 651 AAQDSGVCLLAKRSGVVEKVTGKKIIVRADNGELD-------TYELTKFLRSNQSTCINQ 703

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV  GD V     +ADG +TD G+LALG N+LVAF+ W GYN ED++LISER+  +D+
Sbjct: 704 RPLVYKGDRVETGSTLADGMATDGGELALGHNVLVAFVSWEGYNHEDAVLISERLCKDDL 763

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLG EEITR + +VSE+ ++ +DE GII VGA+V PGDILVGK+
Sbjct: 764 YTSIHIEEYECDARDTKLGEEEITRQLSSVSEDAVRYLDENGIIMVGADVRPGDILVGKV 823

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGID 951
           TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV++F R        G++
Sbjct: 824 TPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGEFGKVVDVKVFTRENGDELAPGVN 883

Query: 952 KNERSISVEREQIELLAR 969
           K  R    ++ +I    +
Sbjct: 884 KLVRVYIAQKRKIREGDK 901



 Score =  542 bits (1397), Expect = e-151,   Method: Composition-based stats.
 Identities = 193/527 (36%), Positives = 268/527 (50%), Gaps = 38/527 (7%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +       +       I++  ++  G  V  G  L   +   G   +     +L A
Sbjct: 681  NGELDTYELTKFLRSNQSTCINQRPLVYKGDRVETGSTLADGMATDG-GELALGHNVLVA 739

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVD-VRIFNRHGIDKNER-SISVEREQIELLARDKDD 973
                +  +  D  L           D     +    + + R +   E E    L+   +D
Sbjct: 740  FVSWEGYNHEDAVLI---SERLCKDDLYTSIHIEEYECDARDTKLGEEEITRQLSSVSED 796

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD N       I+ G +   G     K T      +   P  +  +    D++   
Sbjct: 797  AVRYLDEN-----GIIMVGADVRPGDILVGKVTPKGETEL--TPEERLLRAIFGDKER-- 847

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E                   K+   + GD++ PGV ++V+V++A KR I+ GDKMAGR
Sbjct: 848  --EVRDTSLRVPHGEFGKVVDVKVFTRENGDELAPGVNKLVRVYIAQKRKIREGDKMAGR 905

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNK + SRILP EDMPF  DG PVD+VLNPLGVPSRMN+GQI E HL WAC  LG++IK
Sbjct: 906  HGNKCVCSRILPVEDMPFTPDGRPVDLVLNPLGVPSRMNIGQILEIHLSWACHMLGEEIK 965

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                + +                             D     + E  +SG+ ++TPVFDG
Sbjct: 966  KNPKEVEKRLRALGY---------------------DFDKYGMPEPDESGIHIATPVFDG 1004

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
              +E + + L+ A L E+G+S++YDG TGE  D PVT+G+ YMLKL+H+V DK++ARSTG
Sbjct: 1005 CRDEDLAATLKAAGLPETGKSVIYDGRTGEKLDGPVTIGWKYMLKLHHLVDDKIHARSTG 1064

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV
Sbjct: 1065 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKAYEKIV 1124

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
             G +    G PESF VL+KE+Q++GL + + N    +    E   + 
Sbjct: 1125 KGQNIPSPGVPESFKVLMKELQSIGLDVRVLNENGDDVILKELDENE 1171


>gi|262067333|ref|ZP_06026945.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium
           periodonticum ATCC 33693]
 gi|291378896|gb|EFE86414.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium
           periodonticum ATCC 33693]
          Length = 1186

 Score =  780 bits (2014), Expect = 0.0,   Method: Composition-based stats.
 Identities = 428/972 (44%), Positives = 604/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R ++G + AFK VFPI + +G  
Sbjct: 6   ERLDFGKIKARGSMPHFLEFQLNSYEDFLQTNMSPNKREDKGFELAFKEVFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKRRGKTYSNSLKVRLRLINK--------KMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT+  TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTERATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D++EI+  F      + +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNKEIIEHFLATKELNLKSLYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         + +    L G  
Sbjct: 236 AKEPEEL-----------------------------------------INVLKQELEGSL 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I E+ +  +  ++I +I   +V   +    + NTL  D+ 
Sbjct: 255 VKEDILDEETGEFIAETEATITEELINILIENKIENITYWFVGPEDK--LLANTLANDET 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
              + A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  DD
Sbjct: 313 LTEEQAVVEVFKKLRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADD 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  ++ + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTMRYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KE++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VKEKMTTQDIETVSPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVRYLAADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K AG V  VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVAGKVVYVDGKKIVI-------EDTDKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V+  DIIADGP+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHI
Sbjct: 725 GDVVKAGDIIADGPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARATKLGDEEITREIPNVSESALRNLDENGIIIIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1295), Expect = e-139,   Method: Composition-based stats.
 Identities = 193/602 (32%), Positives = 271/602 (45%), Gaps = 76/602 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 677  KVAGKVVYVDGKKIVIEDTDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIIIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AK 1373
              
Sbjct: 1147 NV 1148


>gi|260495676|ref|ZP_05815799.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_33]
 gi|260196741|gb|EEW94265.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_33]
          Length = 1184

 Score =  780 bits (2014), Expect = 0.0,   Method: Composition-based stats.
 Identities = 427/972 (43%), Positives = 606/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AF+ VFPI + +G  
Sbjct: 6   ERLDFGKIKSRGKMPHFLEFQLNSYEDFLQTNMSPNKREEKGFELAFREVFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT+  TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTERATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +      
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATIFLKAVDFFKDNNEIRDYFLETKELNLK------ 229

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                                               L K   ++  + L I    L G  
Sbjct: 230 -----------------------------------ALYKKYSKEPEELLNILKQELEGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I+E+ +  +  +++  I   +V     +  I NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +   + +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVAIVDDVHYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  499 bits (1286), Expect = e-138,   Method: Composition-based stats.
 Identities = 195/606 (32%), Positives = 274/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EE+
Sbjct: 1147 NVDEEV 1152


>gi|290890923|ref|ZP_06553987.1| hypothetical protein AWRIB429_1377 [Oenococcus oeni AWRIB429]
 gi|290479322|gb|EFD87982.1| hypothetical protein AWRIB429_1377 [Oenococcus oeni AWRIB429]
          Length = 1197

 Score =  780 bits (2014), Expect = 0.0,   Method: Composition-based stats.
 Identities = 411/963 (42%), Positives = 566/963 (58%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V       R+ +    E+++IP L EVQ ASY  F+          ++G++  F 
Sbjct: 1   MVTHNVKINKHVTRRSYSSAKEVLEIPPLTEVQTASYKWFM----------DKGIKEMFN 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LE+V Y    PK+ + +   + + YA PL +TLRL           K
Sbjct: 51  DIMPIEDFAGKLSLEYVDYSLGEPKYSLKESREQGVNYAAPLHVTLRLT---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q +Y G+ PLMT+ G+FVI G +R+VVSQL RSPGI+++ D  +    G+++Y
Sbjct: 102 ETGEIKSQDVYFGEFPLMTEYGSFVINGAERVVVSQLVRSPGIYYNEDTDKT---GRVVY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++++ D+K + ++RIDR RK+P+T  + + G  S+ EI   F  +I   
Sbjct: 159 GTTVIPNRGAWLELDTDAKGVANIRIDRTRKLPITELIRSFGFGSDSEIQDIFGDEIDSL 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                       +   VG  +      +  GE   I+S + L +      K   +  +G 
Sbjct: 219 NLAIEKDVHKDPSMSRVGEALEDIYERLRPGEPKTIDSSRSLLAARFFDPKRYDLGNVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AEDI+N + GE+ +     ID+KS++ I      +   +   
Sbjct: 279 YKVNKKLSLKSRLLGQTLAEDILNSD-GEVVVPKDTKIDKKSMKLISPLLDEEDFHVENL 337

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             +    + + +     K        I+  + P  V                        
Sbjct: 338 QPDEEGVLPDPIKVQTIK--------IFSQVDPTKVIKLIG------------------- 370

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                     N    + + HI   DIIA +    +L+ G G  DDID+LGNRR+RSVGE+
Sbjct: 371 ----------NGHIDESIHHILPADIIAGMNYFFNLQEGVGATDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+ V EFF SSQLSQ  +  N
Sbjct: 421 LENQFRIGLTRMERVVRERMSIQDSDTVTPQQLINIRPVVATVKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  + H RRLSALG GG+ R RAG E+RDVH +HYGRI P ET EG NIGL++SL  + 
Sbjct: 481 PLGELNHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRIDPIETPEGPNIGLITSLAVYG 540

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETPYR+V     KVT+ + YL+A  E+N  IAQANS L++DGSFT   V  R
Sbjct: 541 RINEYGFIETPYRRVDWDTHKVTDKIDYLTADVEDNYTIAQANSPLNDDGSFTNPTVTAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I  P E +D++D SPKQVV+++ + IPFLENDDSNR LMG NMQRQAVPL+   +
Sbjct: 601 HGDNNIETPIEDVDYMDVSPKQVVAVSTAAIPFLENDDSNRALMGANMQRQAVPLVAPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A +A+  G VE VD   I +R  +G L         Y LMKFQ
Sbjct: 661 PIVGTGIEYRAAVDSGLAQIAEEKGTVEYVDGRTIKVREEDGTL-------HEYPLMKFQ 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P+VKVG+++ + +++ADGP+ + G+LALG+N ++AFM WHGYNFED+++
Sbjct: 714 RSNGGKNYNQTPIVKVGEKIEKGEVLADGPAMENGELALGQNPVIAFMTWHGYNFEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DV+TSIHIEE E  ARDTKLGPEEITR+IPNV E+ LK++D+ GII +GAEV
Sbjct: 774 LNERLVRDDVYTSIHIEEHESEARDTKLGPEEITREIPNVGEDQLKDLDDSGIIRIGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGKITPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV IF R 
Sbjct: 834 EDGDILVGKITPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVEIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 NGD 896



 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 254/1073 (23%), Positives = 405/1073 (37%), Gaps = 125/1073 (11%)

Query: 331  KSLEEIFHSEIRDIPILYVDSVN--NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            + +         +I  ++ D ++  N A  ++           +AL DIY  +RPG+  T
Sbjct: 194  ELIRSFGFGSDSEIQDIFGDEIDSLNLAIEKDVHKDPSMSRVGEALEDIYERLRPGEPKT 253

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
               + S+    FFD  +YDL  VGR K+N +L+L +    + + ++ + +         +
Sbjct: 254  IDSSRSLLAARFFDPKRYDLGNVGRYKVNKKLSLKSRLLGQTLAEDILNS---------D 304

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            G+  +     +  + ++ +  +L           E          D + V+P      K 
Sbjct: 305  GEVVVPKDTKIDKKSMKLISPLLD----------EEDFHVENLQPDEEGVLP---DPIKV 351

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                +      +++ +L  + +    I H      +                    H G 
Sbjct: 352  QTIKIFSQVDPTKVIKLIGNGHIDESIHHILPADIIAGMNYFFNLQEGVGATDDIDHLGN 411

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                   E         LT   RV            V   +   ++  + A  +E     
Sbjct: 412  RRIRSVGELLENQFRIGLTRMERVVRERMSIQDSDTV-TPQQLINIRPVVATVKE----F 466

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              +S L +    T  L           +    +   D +  +V  +  S    ++  ++ 
Sbjct: 467  FGSSQLSQFMDQTNPLGELNHKRRLSALGPGGLTR-DRAGYEVRDVHYSHYGRIDPIETP 525

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                   +   AV     E  F+ T     V   +      K    ++ + A      ++
Sbjct: 526  EGPNIGLITSLAVYGRINEYGFIET-PYRRVDWDTH-----KVTDKIDYLTADVEDNYTI 579

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL------ 802
                 P              R   N        V   D   +  +     +         
Sbjct: 580  AQANSPLNDDGSFTNPTVTARHGDNNIETPIEDVDYMDVSPKQVVAVSTAAIPFLENDDS 639

Query: 803  -------GDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARD 853
                           ++    P  G   E    +   +    E+  T  +++   +  R+
Sbjct: 640  NRALMGANMQRQAVPLVAPHSPIVGTGIEYRAAVDSGLAQIAEEKGTVEYVDGRTIKVRE 699

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E        S  G KN ++  I+ VG ++  G++L           +   +  +
Sbjct: 700  EDGTLHEYPLMKFQRSNGG-KNYNQTPIVKVGEKIEKGEVLADGP-AMENGELALGQNPV 757

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLARD 970
             A       +  D  +         V D    + H  +    +   +    E    +   
Sbjct: 758  IAFMTWHGYNFEDAIVLN----ERLVRDDVYTSIHIEEHESEARDTKLGPEEITREIPNV 813

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
             +D+   LD +   R+     G     G     K T      +S   R     F  +  +
Sbjct: 814  GEDQLKDLDDSGIIRI-----GAEVEDGDILVGKITPKGVTELSAEERLLHAIFGEKARE 868

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +          +E      I   + GD++ PGV  +V+VF+A KR IQ GDKM
Sbjct: 869  VRDTSLRVPHGGGGIIQDVE------IFTRENGDELAPGVNMMVRVFIAQKRKIQVGDKM 922

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPF+ DG P+DI+L+P+GVPSRMN+GQI E HLG A   LG 
Sbjct: 923  AGRHGNKGTVSVVVPEEDMPFMPDGRPIDILLSPMGVPSRMNIGQILELHLGMAAKKLGI 982

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            KI + + D  ++ +I                                             
Sbjct: 983  KIMTPVFDGASDDEIIDALKEA-------------------------------------- 1004

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
              G DE+              G+++LYDG TGE FD  ++VG ++ +KL HMV DK++AR
Sbjct: 1005 --GLDED--------------GKTVLYDGQTGEAFDNRISVGVMHYMKLAHMVDDKIHAR 1048

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            S G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +V+E
Sbjct: 1049 SIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVRGRNKVFE 1108

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            SIV G    + G PESF VLVKE+QALGL + + N + +     +   D N  
Sbjct: 1109 SIVKGQAIPKPGVPESFRVLVKELQALGLDMKVLNGKGQEVKMAQMDEDDNVA 1161


>gi|237743074|ref|ZP_04573555.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 7_1]
 gi|256028506|ref|ZP_05442340.1| DNA-directed RNA polymerase beta chain [Fusobacterium sp. D11]
 gi|289766426|ref|ZP_06525804.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. D11]
 gi|229433370|gb|EEO43582.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 7_1]
 gi|289717981|gb|EFD81993.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. D11]
          Length = 1184

 Score =  780 bits (2014), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/972 (43%), Positives = 606/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AF+ VFPI + +G  
Sbjct: 6   ERLDFGKIKSRGKMPHFLEFQLNSYEDFLQTNMSPNKREEKGFELAFREVFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT+  TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTERATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +      
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATIFLKAVDFFKDNNEIRDYFLETKELNLK------ 229

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                                               L K   ++  + L I    L G  
Sbjct: 230 -----------------------------------ALYKKYSKEPEELLNILKQELEGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I+E+ +  +  +++  I   +V     +  I NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  I+ ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIRYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +   + +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVAIVDDVHYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  499 bits (1286), Expect = e-138,   Method: Composition-based stats.
 Identities = 195/606 (32%), Positives = 274/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EE+
Sbjct: 1147 NVDEEV 1152


>gi|19705327|ref|NP_602822.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
 gi|41017765|sp|Q8RHI6|RPOB_FUSNN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|19713302|gb|AAL94121.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
          Length = 1184

 Score =  780 bits (2013), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/972 (43%), Positives = 607/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK     ++P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKARGEMPHFLEFQLNSYEDFLQTNMSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F        +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLEVKELKLKALYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   EA   I+E+ + ++  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAEAEAFINEEVINKLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVRYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGVIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1294), Expect = e-139,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGVIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|296329153|ref|ZP_06871655.1| DNA-directed RNA polymerase subunit beta [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153727|gb|EFG94543.1| DNA-directed RNA polymerase subunit beta [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 1184

 Score =  779 bits (2012), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/972 (43%), Positives = 607/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK     ++P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKARGEMPHFLEFQLNSYEDFLQTNMSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F        +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLEVKELKLKALYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   EA   I+E+ + ++  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAEAEAFINEEVINKLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVRYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKTGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSENALRNLDENGVIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKTGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSENALRNLDENGVIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|319937657|ref|ZP_08012060.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
 gi|319807092|gb|EFW03706.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
          Length = 1220

 Score =  778 bits (2010), Expect = 0.0,   Method: Composition-based stats.
 Identities = 413/952 (43%), Positives = 578/952 (60%), Gaps = 69/952 (7%)

Query: 10  LGRV-RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
             R+ R+ + +    +++P+L+E+Q  SY+ F           NEG++  F  V+PI+ F
Sbjct: 9   KSRINRRNYSRISGSLELPNLVEIQTNSYEWF----------KNEGIKEVFNDVYPISNF 58

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           +    LEFV   FD PK+ VD+   RD  Y+ P++ TLRLI              +IKE 
Sbjct: 59  NETLTLEFVDCRFDEPKYSVDEAKDRDANYSAPIRATLRLI---------NNGTGEIKEN 109

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD PLMT  GTF+I G +R++VSQL RSPG +F     +   SGK ++   +IP +
Sbjct: 110 EVFMGDFPLMTDSGTFIINGAERVIVSQLVRSPGAYFADAMDK---SGKTVFTGSVIPSR 166

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY--SQRGDFW 245
           G W++ E D+KDI++VRIDR RK+P T  L ALG+ S+ EI+           +   D  
Sbjct: 167 GTWLEFENDAKDILNVRIDRTRKIPGTILLRALGLSSDEEIIEVLGDHEFIRNTLAKDPT 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           ++    ++ +         L ++ + K  K L +  D +
Sbjct: 227 HNTDEALIEIYNKLRPGEPATLEGANTLLYTRFFDAKRYDLARAGRFKFGKKLSLL-DRI 285

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI---FHSEIRDIPILYVDSVNNNAYIRN 360
               +A+DIV+ + G + ++ G V+ +  ++ +   F +    + +   D + +N  I+ 
Sbjct: 286 TNRVLAQDIVDVD-GHVVMKEGTVLTKDKVDLLKPVFEAGAHTVDVKTNDFLKSNGKIQV 344

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             V       K   +    +       T S   + ++++    D YD             
Sbjct: 345 VEVYVDESQSKKMKVVGTDLSLDCKFVTISDMLAAYSYMLNLVDIYD------------- 391

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +LD   D R                L +  G +DDID+LGNRRVRSVGE+++NQ+R+GL 
Sbjct: 392 SLDLASDDRV--------------SLMSRIGLLDDIDHLGNRRVRSVGELIQNQFRIGLS 437

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER +KER+S  ++DSV PQ L N +P+ +A+ EFF SSQLSQ  + +N L+ +T+ RR
Sbjct: 438 RMERVVKERMSLSEVDSVTPQSLTNIRPLTAAMKEFFSSSQLSQFMDQINPLAELTNKRR 497

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVHP+HYGRICP ET EG NIGL+S+L S+A++N YGFIET
Sbjct: 498 LSALGPGGLSRDRAGYEVRDVHPSHYGRICPIETPEGPNIGLISTLASYAKINKYGFIET 557

Query: 601 PYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PYRKV +  +   DV YL+A EE+N  IAQA   + E+    +E V  R  GE I+    
Sbjct: 558 PYRKVNNSIIDESDVRYLTADEEKNYIIAQAKVQIGENNEILDEQVISRHLGENIMAKPS 617

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++DFID SPKQ+VS+A S IPFLENDD+ R LMG NMQRQAVPLL    P VGTGME   
Sbjct: 618 EVDFIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQAVPLLNPHTPLVGTGMEYQA 677

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SGAAIVAK  GIV  VDA +IV+   +G  +        YRL KF  SN  TC+N R
Sbjct: 678 ARDSGAAIVAKADGIVTYVDARKIVVEENDGPRN--------YRLTKFAISNAGTCINHR 729

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P++K GD+V +  ++ADGPS +LG+LALG+N+LV FM W+GYN+ED++++SER+V EDV+
Sbjct: 730 PIIKTGDKVLKGQVLADGPSMELGELALGQNVLVGFMTWNGYNYEDAVIMSERLVKEDVY 789

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE+ +  RDTKLGPEEITRDIPNV EE  KN++  GII +GAEV  GDILVGK+T
Sbjct: 790 TSIHIEEYSIECRDTKLGPEEITRDIPNVGEEARKNLNSEGIIMIGAEVKEGDILVGKVT 849

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKG++ ++ EEKLL AIFGEK+ +V+D SLRVP G +G V D+++F R   D
Sbjct: 850 PKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAGIVHDIKVFERKKGD 901



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 241/1060 (22%), Positives = 388/1060 (36%), Gaps = 124/1060 (11%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++ + ++ +IRNTL  D   +  +AL++IY  +RPG+ +T   A ++    FFD+ +YDL
Sbjct: 208  IEVLGDHEFIRNTLAKDPTHNTDEALIEIYNKLRPGEPATLEGANTLLYTRFFDAKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            +  GR K   +L+L      R + ++    I+ +   +   +GT+   D     +V  + 
Sbjct: 268  ARAGRFKFGKKLSLLDRITNRVLAQD----IVDVDGHVVMKEGTVLTKD-----KVDLLK 318

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             + +       ++    +K       ++  + +       V            +      
Sbjct: 319  PVFEAGAHTVDVKTNDFLKSNGKIQVVEVYVDESQSKKMKV------------VGTDLSL 366

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                  I+      +     V    +     D   +   RI   +  +      V S+  
Sbjct: 367  DCKFVTISDMLAAYSYMLNLVDIYDSLDLASDDRVSLMSRIGLLDDIDHLGNRRVRSVGE 426

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVV-----------YLSAMEEENRYIAQANSSLDED 637
              +      +    R V +    ++V             L+A  +E    +Q +  +D+ 
Sbjct: 427  LIQNQFRIGLSRMERVVKERMSLSEVDSVTPQSLTNIRPLTAAMKEFFSSSQLSQFMDQI 486

Query: 638  G---SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  T +          +   R   +  D  P     I     P    +      +  
Sbjct: 487  NPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHPSHYGRICPIETP-EGPNIGLISTLAS 545

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
              +      ++     V   +                      + A   V      ++  
Sbjct: 546  YAKINKYGFIETPYRKVNNSII-----DESDVRYLTADEEKNYIIAQAKVQIGENNEILD 600

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRN--DIIADGPSTDLGDLALGRN 810
                          + ++   ++  P  +V V         +  A               
Sbjct: 601  EQVISRHLGENIMAKPSEVDFIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQAVP 660

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +L    P  G   E                 I            +       R       
Sbjct: 661  LLNPHTPLVGTGMEYQAARDSGAAIVAKADGIVTYVDARKIVVEENDGPRNYRLTKFAIS 720

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                 I+   II  G +V  G +L    +      +   + +L         +  D  + 
Sbjct: 721  NAGTCINHRPIIKTGDKVLKGQVLADGPS-MELGELALGQNVLVGFMTWNGYNYEDAVIM 779

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYS 984
                V   V        + I+  +  +  E          E   ++ + E +I       
Sbjct: 780  SERLVKEDVYTSIHIEEYSIECRDTKLGPEEITRDIPNVGEEARKNLNSEGII------- 832

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                 + G     G     K T      +S   +     F  +  +V+ N   +      
Sbjct: 833  -----MIGAEVKEGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAG 887

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++  F+ K      GD++ PGV +VVKV++  KR I  GDKMAGRHGNKG++SRIL
Sbjct: 888  IVHDIK-VFERKK-----GDELQPGVNKVVKVYIVQKRKISEGDKMAGRHGNKGVISRIL 941

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP L+DGT +DI+LNPLGVPSRMN+GQ+ E HLG+A   LG    +   D   + D
Sbjct: 942  PVEDMPHLEDGTVLDIMLNPLGVPSRMNIGQVLELHLGYAARELGLYYATPAFDGINSKD 1001

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +  +                                ++G+PV                  
Sbjct: 1002 LENIMK------------------------------EAGMPV------------------ 1013

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G+  +  G TGE FD  V VG +YM+KL HMV DK++ARS G YSLVTQQPLG
Sbjct: 1014 ------DGKQPVISGRTGEYFDSNVCVGIMYMIKLAHMVDDKLHARSVGPYSLVTQQPLG 1067

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY L+E+LT+KSDDVVGR + YE+IV G    E G P
Sbjct: 1068 GKAQNGGQRFGEMEVWALEAYGAAYTLREILTVKSDDVVGRVKTYEAIVKGQKLPEPGLP 1127

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            ESF VL KE+QAL L I + +       + +   +  +  
Sbjct: 1128 ESFRVLKKELQALALDIQMLDEDGNELDERKIEDEERRFP 1167


>gi|254302290|ref|ZP_04969648.1| DNA-directed RNA polymerase subunit beta [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
 gi|148322482|gb|EDK87732.1| DNA-directed RNA polymerase subunit beta [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
          Length = 1184

 Score =  778 bits (2010), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/972 (43%), Positives = 605/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKPRGQMPHFLEFQLNSYEDFLQTNMSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK +++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDIFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +      
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLETKELNLK------ 229

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                                               L K   ++  + L +    L G  
Sbjct: 230 -----------------------------------ALYKKYSKEPEELLNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I+E+ + ++  +++  I   YV     +  I NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPED 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVHYLAADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVVYVDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 196/606 (32%), Positives = 276/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMRT-------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 975  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|269121546|ref|YP_003309723.1| DNA-directed RNA polymerase subunit beta [Sebaldella termitidis
           ATCC 33386]
 gi|268615424|gb|ACZ09792.1| DNA-directed RNA polymerase, beta subunit [Sebaldella termitidis
           ATCC 33386]
          Length = 1148

 Score =  777 bits (2007), Expect = 0.0,   Method: Composition-based stats.
 Identities = 433/969 (44%), Positives = 612/969 (63%), Gaps = 76/969 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  FGK  +  ++P  +E Q  SY+ F+   I P +R N+GL+  F+ +FPI + +G   
Sbjct: 7   RFSFGKIVDRGEMPHFLEFQLNSYEDFIQAGIPPQKRENQGLENIFQEIFPIESSNGQLK 66

Query: 74  LEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           LE++ YE    D P  D  +C  R  TYA  LK+ LRLI             ++I+E  +
Sbjct: 67  LEYIWYEIHENDKPLNDELECKKRRKTYAGQLKVRLRLI---------NLKTEEIQETLV 117

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           Y G++PLMT   TF+I G +R+VVSQLHRSPG+ F+ +   +  +GK ++  +IIP +G 
Sbjct: 118 YFGEIPLMTDKATFIINGAERVVVSQLHRSPGVTFNKEL--SIQTGKDIFIGKIIPYKGT 175

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFP 248
           W++ E D  DI++V+IDRR+KV  T FL ++    ++ EI+  F+          +    
Sbjct: 176 WLEFETDKNDILNVKIDRRKKVLSTIFLKSVDFFTNNREIMDQFFESKELELNKLYEK-- 233

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                                     KG     +  + L G + 
Sbjct: 234 -----------------------------------------YKGDDLQEVIKNRLEGSFN 252

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            EDI++ +TGE  +E+ ++IDE  +E++  +++  I   Y +    +  I N+L+ D  K
Sbjct: 253 KEDILDEKTGEFVLESEELIDEIGIEKLIENKVEKIY--YWEVKPEDRIIANSLIHDHTK 310

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +A++++++ +RPGD+ T   A S+   +FF+  +YDL+ VGR K+N RL LD P++ 
Sbjct: 311 TSDEAVVEVFKKLRPGDLVTVDSARSLLKQMFFNPQRYDLANVGRYKINKRLKLDLPENE 370

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             + KED++  I  + +L N  G  DDIDNL NRRVR VGE+L  Q + G+++M + +KE
Sbjct: 371 ITLTKEDVMQTINYVRNLYNDDGYTDDIDNLSNRRVRGVGELLAIQVKGGMMKMAKMVKE 430

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           +++  DI ++ PQ L+N KP+ + + EFF S QLSQ  +  N L+ +TH RR+SALG GG
Sbjct: 431 KMTIQDITTLTPQSLLNTKPLNALILEFFGSGQLSQFMDQSNPLAELTHKRRISALGPGG 490

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD- 607
           ++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++ +VN YGFIETP+ KV + 
Sbjct: 491 LSRERAGFEVRDVHNSHYGRICPIETPEGPNIGLIGSLATYGKVNKYGFIETPFAKVENG 550

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             + + V YL A EEE  +IAQA++ +DE G+   E V CR   E + + +EK+ ++D S
Sbjct: 551 KALLDKVNYLGADEEEGLFIAQADTPVDEKGNILVEEVVCRYGEEIVHIVKEKVHYLDVS 610

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAP+VGTG+E  VA  SGA +
Sbjct: 611 PKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYVGTGLERKVAVDSGAVM 670

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
            +K  G V  VDA +I++               ++RL+ F+RSNQ  C++Q+P++ + DE
Sbjct: 671 TSKANGRVTSVDAKQIIVTDENNKE-------HVHRLLNFERSNQAMCLHQKPIINLDDE 723

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V+R DIIADGPST  GDLALGRN+L+AFMPW GYNFED++LISER+  +DVFTSIHIEEF
Sbjct: 724 VKRGDIIADGPSTAGGDLALGRNILLAFMPWEGYNFEDAILISERLRKDDVFTSIHIEEF 783

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           ++ AR TKLG EEITR+IPNVSEE LKN+DE GII +GA+VNPGDILVGK+TPKGE+   
Sbjct: 784 DIEARTTKLGDEEITREIPNVSEETLKNLDESGIIRIGAQVNPGDILVGKVTPKGETEPP 843

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVE 960
            EEKLLRAIFGEKA DVRDTSLR+P G  GTVVDV +  +        G++K  R    E
Sbjct: 844 AEEKLLRAIFGEKAKDVRDTSLRLPHGTKGTVVDVLVLTKDDGDDLKAGVNKVVRVYIAE 903

Query: 961 REQIELLAR 969
           + +I +  +
Sbjct: 904 KRKITVGDK 912



 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 177/608 (29%), Positives = 250/608 (41%), Gaps = 78/608 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V  G         A+              +L    P+ G   E  + +    V   
Sbjct: 613  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYVGTGLERKVAVDSGAVMTS 672

Query: 838  VFT-SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +   + + +    +   E + R +          + +  II +  EV  GDI+  
Sbjct: 673  KANGRVTSVDAKQIIVTDENNKEHVHRLLNFERSNQAMCLHQKPIINLDDEVKRGDIIAD 732

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
              +  G         LL  +   G    D    S R+       S  + +  I  R    
Sbjct: 733  GPSTAGGDLALGRNILLAFMPWEGYNFEDAILISERLRKDDVFTSIHIEEFDIEARTTKL 792

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   ++  DE  I+         +IL G+    G         L   
Sbjct: 793  GDEEITREIPNVSEETLKNL-DESGIIRIGAQVNPGDILVGKVTPKGETEPPAEEKLLRA 851

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  +            V+     L    + +   +    K+       GDD+  GV 
Sbjct: 852  IFGEKAKD-----------VRDTSLRLPHGTKGTVVDVLVLTKD------DGDDLKAGVN 894

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            +VV+V++A KR I  GDKM+GRHGNKG+VSRILP EDM              P       
Sbjct: 895  KVVRVYIAEKRKITVGDKMSGRHGNKGVVSRILPVEDM--------------PH------ 934

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                  E                   D   N    P R  + +V+         +     
Sbjct: 935  -----LE--------------DGTPIDVAVNPLGVPSRMNIGQVLEVHLGLAIGNIDQY- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                          ++TPVFDGA E  +   L     + +G+  L DG TGEPFD PVTV
Sbjct: 975  --------------IATPVFDGASENDVKDYLEKVGFERNGKVKLIDGRTGEPFDNPVTV 1020

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1021 GRMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1080

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+IV G    E   PESF VL+KE Q+LGL I+L +   +  
Sbjct: 1081 QEMLTVKSDDISGRTKTYEAIVKGQGMPEADAPESFKVLIKEFQSLGLDINLFDKDGQVI 1140

Query: 1372 AKMEEIPD 1379
               +   +
Sbjct: 1141 ELDKNNEN 1148


>gi|237740923|ref|ZP_04571404.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 4_1_13]
 gi|229430967|gb|EEO41179.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 4_1_13]
          Length = 1184

 Score =  777 bits (2006), Expect = 0.0,   Method: Composition-based stats.
 Identities = 426/972 (43%), Positives = 604/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKPRGQMPHFLEFQLNSYEDFLQTNVSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLETKELNLKTLYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I+E+ +  +  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPED 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVHYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMR--------------------------------------------- 973

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 974  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|116491358|ref|YP_810902.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Oenococcus oeni PSU-1]
 gi|122276460|sp|Q04E85|RPOB_OENOB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|116092083|gb|ABJ57237.1| DNA-directed RNA polymerase subunit beta [Oenococcus oeni PSU-1]
          Length = 1197

 Score =  777 bits (2006), Expect = 0.0,   Method: Composition-based stats.
 Identities = 411/963 (42%), Positives = 566/963 (58%), Gaps = 79/963 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V       R+ +    E+++IP L EVQ ASY  F+          ++G++  F 
Sbjct: 1   MVTHNVKINKHVTRRSYSSAKEVLEIPPLTEVQTASYKWFM----------DKGIKEMFN 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LE+V Y    PK+ + +   + + YA PL +TLRL           K
Sbjct: 51  DIMPIEDFAGKLSLEYVDYSLGEPKYSLKESREQAVNYAAPLHVTLRLT---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q +Y G+ PLMT+ G+FVI G +R+VVSQL RSPGI+++ D  +    G+++Y
Sbjct: 102 ETGEIKSQDVYFGEFPLMTEYGSFVINGAERVVVSQLVRSPGIYYNEDTDKT---GRVVY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++++ D+K + ++RIDR RK+P+T  + + G  S+ EI   F  +I   
Sbjct: 159 GTTVIPNRGAWLELDTDAKGVANIRIDRTRKLPITELIRSFGFGSDSEIQDIFGDEIDSL 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
                       +   VG  +      +  GE   I+S + L +      K   +  +G 
Sbjct: 219 NLAIEKDVHKDPSMSRVGEALEDIYERLRPGEPKTIDSSRSLLAARFFDPKRYDLGNVGR 278

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L G  +AEDI+N + GE+ +     ID+KS++ I      +   +   
Sbjct: 279 YKVNKKLSLKSRLLGQTLAEDILNSD-GEVVVPKDTKIDKKSMKLISPLLDEEDFHVENL 337

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             +    + + +     K        I+  + P  V                        
Sbjct: 338 QPDEEGVLPDPIKVQTIK--------IFSQVDPTKVIKLIG------------------- 370

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                     N    + + HI   DIIA +    +L+ G G  DDID+LGNRR+RSVGE+
Sbjct: 371 ----------NGHIDESIHHILPADIIAGMNYFFNLQEGVGATDDIDHLGNRRIRSVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D D+V PQ LIN +PVV+ V EFF SSQLSQ  +  N
Sbjct: 421 LENQFRIGLTRMERVVRERMSIQDSDTVTPQQLINIRPVVAVVKEFFGSSQLSQFMDQTN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  + H RRLSALG GG+ R RAG E+RDVH +HYGRI P ET EG NIGL++SL  + 
Sbjct: 481 PLGELNHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRIDPIETPEGPNIGLITSLAVYG 540

Query: 591 RVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           R+N YGFIETPYR+V     KVT+ + YL+A  E+N  IAQANS L++DGSFT   V  R
Sbjct: 541 RINEYGFIETPYRRVDWDTHKVTDKIDYLTADVEDNYTIAQANSPLNDDGSFTNPTVTAR 600

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I  P E +D++D SPKQVV+++ + IPFLENDDSNR LMG NMQRQAVPL+   +
Sbjct: 601 HGDNNIETPIEDVDYMDVSPKQVVAVSTAAIPFLENDDSNRALMGANMQRQAVPLVAPHS 660

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A  SG A +A+  G VE VD   I +R  +G L         Y LMKFQ
Sbjct: 661 PIVGTGIEYRAAVDSGLAQIAEEKGTVEYVDGRTIKVREEDGTL-------HEYPLMKFQ 713

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN     NQ P+VKVG+++ + +++ADGP+ + G+LALG+N ++AFM WHGYNFED+++
Sbjct: 714 RSNGGKNYNQTPIVKVGEKIEKGEVLADGPAMENGELALGQNPVIAFMTWHGYNFEDAIV 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DV+TSIHIEE E  ARDTKLGPEEITR+IPNV E+ LK++D+ GII +GAEV
Sbjct: 774 LNERLVRDDVYTSIHIEEHESEARDTKLGPEEITREIPNVGEDQLKDLDDSGIIRIGAEV 833

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGKITPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV IF R 
Sbjct: 834 EDGDILVGKITPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVEIFTRE 893

Query: 949 GID 951
             D
Sbjct: 894 NGD 896



 Score =  503 bits (1295), Expect = e-139,   Method: Composition-based stats.
 Identities = 254/1073 (23%), Positives = 406/1073 (37%), Gaps = 125/1073 (11%)

Query: 331  KSLEEIFHSEIRDIPILYVDSVN--NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            + +         +I  ++ D ++  N A  ++           +AL DIY  +RPG+  T
Sbjct: 194  ELIRSFGFGSDSEIQDIFGDEIDSLNLAIEKDVHKDPSMSRVGEALEDIYERLRPGEPKT 253

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
               + S+    FFD  +YDL  VGR K+N +L+L +    + + ++ + +         +
Sbjct: 254  IDSSRSLLAARFFDPKRYDLGNVGRYKVNKKLSLKSRLLGQTLAEDILNS---------D 304

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            G+  +     +  + ++ +  +L           E          D + V+P      K 
Sbjct: 305  GEVVVPKDTKIDKKSMKLISPLLD----------EEDFHVENLQPDEEGVLP---DPIKV 351

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                +      +++ +L  + +    I H      +                    H G 
Sbjct: 352  QTIKIFSQVDPTKVIKLIGNGHIDESIHHILPADIIAGMNYFFNLQEGVGATDDIDHLGN 411

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                   E         LT   RV            V   +   ++  + A+ +E     
Sbjct: 412  RRIRSVGELLENQFRIGLTRMERVVRERMSIQDSDTV-TPQQLINIRPVVAVVKE----F 466

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              +S L +    T  L           +    +   D +  +V  +  S    ++  ++ 
Sbjct: 467  FGSSQLSQFMDQTNPLGELNHKRRLSALGPGGLTR-DRAGYEVRDVHYSHYGRIDPIETP 525

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                   +   AV     E  F+ T     V   +      K    ++ + A      ++
Sbjct: 526  EGPNIGLITSLAVYGRINEYGFIET-PYRRVDWDTH-----KVTDKIDYLTADVEDNYTI 579

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL------ 802
                 P              R   N        V   D   +  +     +         
Sbjct: 580  AQANSPLNDDGSFTNPTVTARHGDNNIETPIEDVDYMDVSPKQVVAVSTAAIPFLENDDS 639

Query: 803  -------GDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARD 853
                           ++    P  G   E    +   +    E+  T  +++   +  R+
Sbjct: 640  NRALMGANMQRQAVPLVAPHSPIVGTGIEYRAAVDSGLAQIAEEKGTVEYVDGRTIKVRE 699

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E        S  G KN ++  I+ VG ++  G++L           +   +  +
Sbjct: 700  EDGTLHEYPLMKFQRSNGG-KNYNQTPIVKVGEKIEKGEVLADGP-AMENGELALGQNPV 757

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLARD 970
             A       +  D  +         V D    + H  +    +   +    E    +   
Sbjct: 758  IAFMTWHGYNFEDAIVLN----ERLVRDDVYTSIHIEEHESEARDTKLGPEEITREIPNV 813

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
             +D+   LD +   R+     G     G     K T      +S   R     F  +  +
Sbjct: 814  GEDQLKDLDDSGIIRI-----GAEVEDGDILVGKITPKGVTELSAEERLLHAIFGEKARE 868

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +          +E      I   + GD++ PGV  +V+VF+A KR IQ GDKM
Sbjct: 869  VRDTSLRVPHGGGGIIQDVE------IFTRENGDELAPGVNMMVRVFIAQKRKIQVGDKM 922

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPF+ DG P+DI+L+P+GVPSRMN+GQI E HLG A   LG 
Sbjct: 923  AGRHGNKGTVSVVVPEEDMPFMPDGRPIDILLSPMGVPSRMNIGQILELHLGMAAKKLGI 982

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            KI + + D  ++ +I                                             
Sbjct: 983  KIMTPVFDGASDDEIIDALKEA-------------------------------------- 1004

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
              G DE+              G+++LYDG TGE FD  ++VG ++ +KL HMV DK++AR
Sbjct: 1005 --GLDED--------------GKTVLYDGQTGEAFDNRISVGVMHYMKLAHMVDDKIHAR 1048

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            S G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDV GR +V+E
Sbjct: 1049 SIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVRGRNKVFE 1108

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            SIV G    + G PESF VLVKE+QALGL + + N + +     +   D N  
Sbjct: 1109 SIVKGQAIPKPGVPESFRVLVKELQALGLDMKVLNGKGQEVKMAQMDEDDNVA 1161


>gi|260425105|ref|ZP_05734194.2| DNA-directed RNA polymerase, beta subunit [Dialister invisus DSM
           15470]
 gi|260404155|gb|EEW97702.1| DNA-directed RNA polymerase, beta subunit [Dialister invisus DSM
           15470]
          Length = 1263

 Score =  777 bits (2006), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/950 (42%), Positives = 567/950 (59%), Gaps = 102/950 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  + +  E++ +P L+++Q  SY+ F            EGL+  F  + PI   +    
Sbjct: 17  RYTYARAQEVLGMPHLLDLQTKSYEWF----------CKEGLRDVFADISPIEDSAHKWA 66

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           L F  Y F   K+ +D+C  RD TY+ PL++ ++L+          K   +IKE  ++MG
Sbjct: 67  LHFGEYYFKKEKYSIDECKTRDATYSAPLQVKVQLV---------NKETGEIKEHDLFMG 117

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D P+MT  GTF+I G +R++VSQL RSPG+++  +       GK +Y+ ++IP++G W++
Sbjct: 118 DFPIMTDTGTFIINGAERVIVSQLVRSPGVYYKKEMD---TFGKEIYSAQLIPNRGAWIE 174

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAA 252
           +E D+  ++ VRIDR RK+PVT  + ALG  S EEI+  F   I   +         +  
Sbjct: 175 LETDANGVVSVRIDRNRKMPVTYLIRALGFSSNEEIMELFNNDIHIEETLKKDETQNTKE 234

Query: 253 DLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCL 303
            L+   K       +  GE    ESG  L        +   +  +G           + L
Sbjct: 235 ALIAIYK------KLRPGEPATEESGTTLLRNFFYDPRRYDLAKVGRYKLNKKLSWENRL 288

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G      IV+ ETGEI I+   +IDE+++  +  S                        
Sbjct: 289 KGHRTEGPIVDTETGEIIIQGNALIDEEAIAILKKSG----------------------- 325

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                           V    ++                  K D + V  +  N      
Sbjct: 326 ----------------VFSKVEMVEVMT------------QKEDGTPVKVICSNGM---- 353

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             D  R + + DIIA +  L+++  G G  DDID+LGNRRVR VGE+L+NQ+R+GL RME
Sbjct: 354 RDDSYRILDRADIIAAVDYLLNMIQGYGRPDDIDHLGNRRVRCVGELLQNQFRIGLSRME 413

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D D +  Q L+N +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSA
Sbjct: 414 RVVRERMTTQDQDKMTAQALVNIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSA 473

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+SSL+++  VN YG IETPYR
Sbjct: 474 LGPGGLSRERAGFEVRDVHYSHYGRMCPVETPEGPNIGLISSLSNYGIVNKYGLIETPYR 533

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           ++     +VTN+ +Y++A  EEN+ IAQA+  L + G+F    V CR   + +    E++
Sbjct: 534 RINPKTHEVTNECLYVTADIEENKVIAQASEPLSDTGAFLNRYVACRRGPDVLEASPEEV 593

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQVVSI  SLIPFLE+DD+NR LMG NMQRQAVPLL+ EAP VGTGME V  +
Sbjct: 594 DLMDVSPKQVVSIGTSLIPFLEHDDTNRALMGANMQRQAVPLLRPEAPLVGTGMEWVAGQ 653

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  ++AKR+G+V  V+  +I++R+  G+ D        Y L+KF RSNQ+TC+NQ P+
Sbjct: 654 DSGVCVLAKRSGVVTSVNGKQIIVRADNGEYD-------TYDLIKFLRSNQSTCINQHPI 706

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V  GD+V     +ADG STD G+LALG N+LVAF+ W GYN ED++LISER+  +D++TS
Sbjct: 707 VYKGDKVEAGQTLADGMSTDGGELALGHNVLVAFVSWEGYNHEDAVLISERLCKDDLYTS 766

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLG EEITR++ +VS++ LKN+DE GII +GA+V PGDILVGK+TPK
Sbjct: 767 IHIEEYECDARDTKLGEEEITRELASVSDDALKNLDENGIIRIGADVRPGDILVGKVTPK 826

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV+ F R   D
Sbjct: 827 GETELTPEERLLRAIFGDKEREVRDTSLRVPHGEFGKVVDVKEFTRENGD 876



 Score =  533 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 196/531 (36%), Positives = 268/531 (50%), Gaps = 33/531 (6%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +    I  +       I++  I+  G +V  G  L   ++  G   +     +L A
Sbjct: 681  NGEYDTYDLIKFLRSNQSTCINQHPIVYKGDKVEAGQTLADGMSTDG-GELALGHNVLVA 739

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVD-VRIFNRHGIDKNER-SISVEREQIELLARDKDD 973
                +  +  D  L           D     +    + + R +   E E    LA   DD
Sbjct: 740  FVSWEGYNHEDAVLI---SERLCKDDLYTSIHIEEYECDARDTKLGEEEITRELASVSDD 796

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD N   R+   +   + + G    K  T L+ +        +  +    D++   
Sbjct: 797  ALKNLDENGIIRIGADVRPGDILVGKVTPKGETELTPE-------ERLLRAIFGDKER-- 847

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E                   K    + GD++ PGV ++V+V+VA KR ++ GDKMAGR
Sbjct: 848  --EVRDTSLRVPHGEFGKVVDVKEFTRENGDELAPGVNKLVRVYVAQKRKLREGDKMAGR 905

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNK + SRILP EDMPF  DG PVD+VLNPLGVPSRMN+GQI E HL WAC  LG++IK
Sbjct: 906  HGNKCVCSRILPVEDMPFTPDGRPVDLVLNPLGVPSRMNIGQILEIHLSWACHMLGEEIK 965

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                D      +            T    E                   GV ++TPVFDG
Sbjct: 966  EAKTDPVKAKALEKRLREAGYDFDTYGMPESTES---------------GVHIATPVFDG 1010

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
              +E + + L  A L  + +S LYDG TGE  D  VT+G+ YMLKL+H+V DK++ARSTG
Sbjct: 1011 CRDEDLAATLAAAGLPVNAKSDLYDGRTGEKLDGQVTIGWKYMLKLHHLVDDKIHARSTG 1070

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV+GR + YE IV
Sbjct: 1071 PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVIGRVKAYEKIV 1130

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
             G +    G PESF VL+KE+Q++GL + + N   K    M+E+ + +   
Sbjct: 1131 KGENIPSPGVPESFKVLMKELQSIGLDVRVLNED-KEEVVMKELDESDLEP 1180


>gi|255994396|ref|ZP_05427531.1| DNA-directed RNA polymerase, beta subunit [Eubacterium saphenum
           ATCC 49989]
 gi|255993109|gb|EEU03198.1| DNA-directed RNA polymerase, beta subunit [Eubacterium saphenum
           ATCC 49989]
          Length = 1246

 Score =  777 bits (2006), Expect = 0.0,   Method: Composition-based stats.
 Identities = 414/962 (43%), Positives = 585/962 (60%), Gaps = 42/962 (4%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R+ F K  E  ++P+LI++Q  SY  FL           +GLQ  F+   PI    G
Sbjct: 9   RRERQTFSKINEKSEMPNLIQIQTDSYKWFL----------EKGLQEIFEDFSPIVDHPG 58

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              L F SY  D   K+D  +C  RD TY   + + +RL+    +E          K + 
Sbjct: 59  NLELYFDSYRIDKNSKYDEQECKERDKTYEAAIYVKVRLVDKKTNEIME-------KGEE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +++G+ PLMT  GTF+  G +R+VV+QL RSPG +F  +  +   S   LY   +IP++G
Sbjct: 112 VFLGNFPLMTDKGTFIYNGAERVVVTQLVRSPGAYFASELDK---SNTTLYNLTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY--SQRGDFWC 246
            W++   DS  I++V+IDR RK+P+T+ L A+G +S+ EIL  F        +   D   
Sbjct: 169 AWLEYVTDSSKILYVKIDRNRKLPMTALLRAIGYESDKEILGMFGEDKRLLNTLEKDETR 228

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDCLC 304
               A   +            ++   + ES         L K  + K  K LGI +D + 
Sbjct: 229 NKNEAIKAIYRKMRPGEAATEESATSLFESTYFDPSRYDLAKVGRYKINKKLGI-ADRVV 287

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G    ED++  +TGEI +E+G  I ++   EI ++ +  + +   DS +  A + N  V 
Sbjct: 288 GTIAHEDVIAPDTGEILLESGQEISKEKALEIQNAGVFSVKVSLPDSEDVVAVVGNQFV- 346

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-NLD 423
                  D   D    +  G+   +   + +           +L+   + K+     +  
Sbjct: 347 -NITTHVDMTEDEADELGLGEGVYYPAFQELVEDELKGIKLDNLTKKNKEKVFEIFKDYK 405

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                R +   DI+A +  ++ L +G G +DDID+LGNRR+R+VGE+L+NQ+R+G+ RME
Sbjct: 406 RVLAPRQLMSGDILASVSYILGLDHGIGKLDDIDHLGNRRLRTVGELLQNQFRVGIARME 465

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+++ER+++ D D + P  LIN KPV + + EFF SSQLSQ  +  N L+ ITH RRLSA
Sbjct: 466 RTVRERMTTSDEDKIKPNKLINIKPVTAVIREFFGSSQLSQFMDQNNPLAEITHKRRLSA 525

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SLT++A +N YGFIETPYR
Sbjct: 526 LGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLIGSLTTYAIINKYGFIETPYR 585

Query: 604 KVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREK 660
            V  GK  VT+ + Y+SA +EE   IAQAN  LD  G F  + V  R   GE  L  R+ 
Sbjct: 586 VVKKGKGEVTDKIEYISADQEEEVIIAQANEPLDSKGKFVNKKVAARSANGEIDLEDRDN 645

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D SPKQVVS+A ++IPFLENDD+NR LMG NMQRQAVPLL  EAP +GTGME   A
Sbjct: 646 VDYMDVSPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLLITEAPIIGTGMEHKAA 705

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           K SG  ++AK  G+VE VDA RI+I+  +G+        D Y+L+KF+RSNQ T +NQ+P
Sbjct: 706 KDSGVVVIAKEPGVVEYVDADRIIIKRNKGNEK------DEYKLLKFKRSNQGTSINQKP 759

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +VKVG+EV   ++IADGPST  G+++LG+N+L+ FM W GYN+ED+++++E+++  DV T
Sbjct: 760 IVKVGEEVEAGEVIADGPSTSNGEISLGKNLLIGFMTWEGYNYEDAIILNEKLIMNDVLT 819

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           S+HIE++EV ARDTKLGP+EITRDIPN SEE LK +DE GII VGAEV+  DILVG++TP
Sbjct: 820 SVHIEKYEVEARDTKLGPQEITRDIPNCSEEKLKRLDENGIIHVGAEVSSSDILVGRVTP 879

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
           KGE+  TP E L+R +F EKA D+RD S +VP G +G VVDVR F R   DK+E +  + 
Sbjct: 880 KGETEPTPIENLMRHVFSEKARDIRDESKKVPHGENGIVVDVRTFER---DKDELAPGIN 936

Query: 961 RE 962
           + 
Sbjct: 937 KM 938



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 257/1221 (21%), Positives = 468/1221 (38%), Gaps = 131/1221 (10%)

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE--ILSTFYPKIVYSQRGDFWCFPL 249
            +++ FDS      RID+  K            D +E       Y   +Y +         
Sbjct: 60   LELYFDSY-----RIDKNSK-----------YDEQECKERDKTYEAAIYVKVRLVDKKTN 103

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLT-SGLLKSLKEKGVKFLGITSDCLCGLYV 308
               +      + +  +  D G  +    +++  + L++S        L  ++  L  L V
Sbjct: 104  EIMEKGEEVFLGNFPLMTDKGTFIYNGAERVVVTQLVRSPGAYFASELDKSNTTLYNLTV 163

Query: 309  AEDI-----VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
              +         ++ +I     D   +  +  +  +   +     +     +  + NTL 
Sbjct: 164  IPNRGAWLEYVTDSSKILYVKIDRNRKLPMTALLRAIGYESDKEILGMFGEDKRLLNTLE 223

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             D+ +++ +A+  IYR MRPG+ +T   A S+F   +FD  +YDL+ VGR K+N +L + 
Sbjct: 224  KDETRNKNEAIKAIYRKMRPGEAATEESATSLFESTYFDPSRYDLAKVGRYKINKKLGI- 282

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGT-----IDDIDNLGNRRVRSVGEMLKNQYRLG 478
                V  I  ED+IA     + L +G+       ++  +        S+ +       +G
Sbjct: 283  ADRVVGTIAHEDVIAPDTGEILLESGQEISKEKALEIQNAGVFSVKVSLPDSEDVVAVVG 342

Query: 479  LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
               +  +    ++  + D +   + +        V +     +L  L +           
Sbjct: 343  NQFVNITTHVDMTEDEADELGLGEGVYYPAFQELVEDELKGIKLDNLTKKNKEKVFEIFK 402

Query: 539  RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
                 L    +        +  +    +G     +     N  L + +    +      I
Sbjct: 403  DYKRVLAPRQLMSGDILASVSYILGLDHGIGKLDDIDHLGNRRLRT-VGELLQNQFRVGI 461

Query: 599  ETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDEDG--------S 639
                R V +   T+D           +  ++A+  E    +Q +  +D++          
Sbjct: 462  ARMERTVRERMTTSDEDKIKPNKLINIKPVTAVIREFFGSSQLSQFMDQNNPLAEITHKR 521

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQR 698
                L     + +        + +        +       I  + +  +  ++       
Sbjct: 522  RLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLIGSLTTYAIINKYGFIE 581

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                ++K     V   +E + A      I+A+    ++         + V   +   ++ 
Sbjct: 582  TPYRVVKKGKGEVTDKIEYISADQEEEVIIAQANEPLDSKG------KFVNKKVAARSAN 635

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +I    +      +    Q   V         +  A+              +L+   P 
Sbjct: 636  GEIDLEDRDNVDYMDVSPKQVVSVATAMIPFLENDDANRALMGANMQRQAVPLLITEAPI 695

Query: 819  HGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
             G   E        +V  +++     +++   ++ +  K   ++  + +         +I
Sbjct: 696  IGTGMEHKAAKDSGVVVIAKEPGVVEYVDADRIIIKRNKGNEKDEYKLLKFKRSNQGTSI 755

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++  I+ VG EV  G+++    +      ++  + LL      +  +  D  +     + 
Sbjct: 756  NQKPIVKVGEEVEAGEVIADGPSTSN-GEISLGKNLLIGFMTWEGYNYEDAIILNEKLIM 814

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              V+      ++ ++  + +    +E    +    +++   LD N    +   +   + +
Sbjct: 815  NDVLTSVHIEKYEVEARD-TKLGPQEITRDIPNCSEEKLKRLDENGIIHVGAEVSSSDIL 873

Query: 997  SGPKGFKKSTVLS--SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             G    K  T  +   +L+      +      + +KV      + V   T        F+
Sbjct: 874  VGRVTPKGETEPTPIENLMRHVFSEKARDIRDESKKVPHGENGIVVDVRT--------FE 925

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                     D++ PG+ ++V+ +VA KR I  GDKMAGRHGNKG++S+ILP EDMPFL+D
Sbjct: 926  RDK------DELAPGINKMVRCYVATKRKISVGDKMAGRHGNKGVISKILPEEDMPFLED 979

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+ ++LNPLGVPSRMNVGQ+ E HLG A    G  I + + D     DI  L      
Sbjct: 980  GTPLQVMLNPLGVPSRMNVGQVLEVHLGLAAKKKGWHIATPVFDGATENDIIELLG--SN 1037

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                     G++
Sbjct: 1038 GYDESGKVWL---------------------------------------------RDGRT 1052

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   GE F  PVT+GY+YMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR 
Sbjct: 1053 -------GERFHSPVTIGYMYMLKLHHLVDDKIHARSMGPYSLVTQQPLGGKAQFGGQRF 1105

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ LQE+LTIKSDD+ GR R +E+IV G +  + G PESF VLVKE+
Sbjct: 1106 GEMEVWALEAYGAAHSLQEILTIKSDDMEGRVRTHEAIVKGTNIPKPGLPESFRVLVKEL 1165

Query: 1355 QALGLSIDLENSRTKNSAKME 1375
            Q+LG+ +   +      +  +
Sbjct: 1166 QSLGIDVKAYDEMDNEVSIRD 1186


>gi|294784287|ref|ZP_06749581.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_27]
 gi|294488043|gb|EFG35395.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_27]
          Length = 1184

 Score =  776 bits (2005), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/972 (43%), Positives = 604/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKPRGQMPHFLEFQLNSYEDFLQTNVSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLETKELNLKTLYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V +DI++ ETGE   E    I+E+ +  +  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKDDILDEETGEFIAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPED 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVHYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMR--------------------------------------------- 973

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 974  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|34762883|ref|ZP_00143866.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|27887447|gb|EAA24534.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
          Length = 1184

 Score =  776 bits (2004), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/972 (43%), Positives = 604/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKPRGQMPHFLEFQLNSYEDFLQTNVSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLETKELNLKTLYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V +DI++ ETGE   E    I+E+ +  +  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKDDILDEETGEFIAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVHYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMR--------------------------------------------- 973

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 974  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|256846762|ref|ZP_05552218.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_36A2]
 gi|256717982|gb|EEU31539.1| DNA-directed RNA polymerase, beta subunit [Fusobacterium sp.
           3_1_36A2]
          Length = 1184

 Score =  776 bits (2003), Expect = 0.0,   Method: Composition-based stats.
 Identities = 424/972 (43%), Positives = 604/972 (62%), Gaps = 76/972 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK      +P  +E Q  SY+ FL  N++P++R  +G + AFK +FPI + +G  
Sbjct: 6   ERLDFGKIKPRGQMPHFLEFQLNSYEDFLQTNVSPNKREEKGFELAFKEIFPIESSNGDV 65

Query: 73  MLEFVSYEFDP---PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE      P  D  +C  R  TY+  LK+ LRLI          K   +I+E  
Sbjct: 66  RLEYIGYELHEAEAPLNDELECKKRGKTYSNSLKVRLRLIN--------KKMGNEIQESL 117

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           +Y G++P MT   TF+I G +R+VVSQLHRSPG+ F  +    + +GK L++ +IIP +G
Sbjct: 118 VYFGEVPKMTDRATFIINGAERVVVSQLHRSPGVSFSKEV--NTQTGKDLFSGKIIPYKG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  D + V+IDR++KV  T FL A+    D+ EI   F      + +  +  +
Sbjct: 176 TWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNNEIRDYFLETKELNLKTLYKKY 235

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                +L                                         L +    L G  
Sbjct: 236 SKEPEEL-----------------------------------------LNVLKQELDGSI 254

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   E    I+E+ +  +  +++  I   YV     +  + NTL+ D  
Sbjct: 255 VKEDILDEETGEFIAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTT 312

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
               +A++++++ +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++
Sbjct: 313 LTEDEAVVEVFKKLRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEE 372

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + KED++  IK +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + 
Sbjct: 373 QISLTKEDVLGTIKYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKM 432

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++E++++ DI++V PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG
Sbjct: 433 VREKMTTQDIETVTPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALG 492

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV
Sbjct: 493 PGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKV 552

Query: 606 CDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +G    +DV YL+A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++
Sbjct: 553 ENGVALVDDVRYLAADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYM 611

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SG
Sbjct: 612 DVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSG 671

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A +  K +G V  VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +
Sbjct: 672 AVVTTKVSGKVTYVDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDL 724

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V+  DIIADGP+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHI
Sbjct: 725 GDKVKAGDIIADGPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHI 784

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+E+ AR TKLG EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+
Sbjct: 785 EEYEIDARTTKLGDEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGET 844

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSI 957
               EEKLLRAIFGEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +
Sbjct: 845 EPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVL 904

Query: 958 SVEREQIELLAR 969
             E+ +I +  +
Sbjct: 905 VAEKRKITVGDK 916



 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 198/606 (32%), Positives = 277/606 (45%), Gaps = 76/606 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 617  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 676

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 677  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 736

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 737  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 796

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 797  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 855

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 856  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 898

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 899  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 958

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 959  NIGQVLEVHLGMAMR--------------------------------------------- 973

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 974  -------SLNEGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 1026

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1027 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1086

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDD+ GRT+ YE+I+ G    E+  PESF VL+KE QAL L I+L +      
Sbjct: 1087 QEMLTVKSDDITGRTKTYEAIIKGEAMPESDLPESFKVLLKEFQALALDIELCDEEDNVI 1146

Query: 1372 AKMEEI 1377
               EEI
Sbjct: 1147 NVDEEI 1152


>gi|302337471|ref|YP_003802677.1| DNA-directed RNA polymerase subunit beta [Spirochaeta smaragdinae
           DSM 11293]
 gi|301634656|gb|ADK80083.1| DNA-directed RNA polymerase, beta subunit [Spirochaeta smaragdinae
           DSM 11293]
          Length = 1166

 Score =  775 bits (2002), Expect = 0.0,   Method: Composition-based stats.
 Identities = 413/937 (44%), Positives = 597/937 (63%), Gaps = 64/937 (6%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMN--IAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
            E++++PDL+++Q  SYD FL  +  +A  +   +GL+  F++VFPI + +G   LE+  
Sbjct: 18  QEVMELPDLVDIQLTSYDRFLQRSKLLAGQDLAEQGLEEVFQTVFPIESPNGDMSLEYTQ 77

Query: 79  YEFDPP--KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           Y  D    KF  ++C  + LTYAVP+K  + L+  +           +I+++ IY+GD+P
Sbjct: 78  YTLDEENIKFSQEECKRKGLTYAVPVKAKINLVFHE---------TGEIRQKDIYVGDIP 128

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LMT+ GTF+I G +R+VVSQ+HRSPG+ F H+KG        +++ RIIP +G W++ E 
Sbjct: 129 LMTERGTFIINGAERVVVSQIHRSPGVIFSHEKG--------IFSSRIIPYRGSWLEFEI 180

Query: 197 D-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAADL 254
           D  K++I+ +IDR++++  + FL ALG D+ E+++  FY K +     +         + 
Sbjct: 181 DQKKELIYAKIDRKKRILGSLFLRALGFDTREKMIDLFYKKTLEHVSEEREK-----KEQ 235

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
           +V   ++ ++     GE              + L   G K      D L           
Sbjct: 236 LVNKVLARAVFVERDGET-------------RKLYRAGEKLHPHDVDELLH--------- 273

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            E  EI          + ++      +    IL          +++    D    ++DAL
Sbjct: 274 SEVREI----------EVIDFSHPESLHSQIILNCFEREEVKIVKDDPNVD-EPTKEDAL 322

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           + +Y V+ PG+  T   AE   + +FF S +YDL  VGR K+N + + + PDD   + K 
Sbjct: 323 IAVYSVLMPGEPITLEAAEKDLHSMFFSSRRYDLGRVGRYKLNKKFDYENPDDSHVLSKM 382

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           DI+  +  L+ +  G+  +DDID+LGNRR+RSVGE+L NQ +    RMER  KER+S  +
Sbjct: 383 DIVNTMLFLIKVYIGEAYVDDIDHLGNRRIRSVGELLANQLKTAFARMERIAKERMSLKE 442

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            D+V PQDLI+ KPVV+A+ EFF SSQLSQ  + VN L+ +TH RRL+ALG GG++R RA
Sbjct: 443 TDTVRPQDLISIKPVVAAIKEFFGSSQLSQFMDQVNPLAELTHKRRLNALGPGGLSRDRA 502

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVH THYGR+CP ET EG NIGL+ SL ++ +VN+YGF+E PYRKV DG  T D+
Sbjct: 503 GFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLANYTKVNSYGFLEAPYRKVVDGHATRDI 562

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YLSAM+EE   IAQAN+ +D++G+F +E++  R  G+    P   I ++D SPKQV+S+
Sbjct: 563 EYLSAMDEEKYNIAQANAKIDKNGTFLDEMISIRKGGDYTTKPPSDIQYMDVSPKQVISV 622

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A SLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTGME+  A  SG  + AKR+G+
Sbjct: 623 ATSLIPFLEHDDANRALMGSNMQRQAVPLVFPEPPRVGTGMEAKTAYDSGVLLKAKRSGV 682

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           VEQV ++ +VI+      D      D+Y + KFQR+NQ+TC NQ+P+V +G ++ +  ++
Sbjct: 683 VEQVTSLEVVIKPDNPKDDH---DRDVYHIQKFQRTNQDTCFNQKPVVSLGQKIDKGQVL 739

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+T  G+LALG+NM+V F+PW+GYN+ED++LISE++V ED +TSIHI+EF V  R+T
Sbjct: 740 ADGPATRAGELALGQNMIVGFVPWNGYNYEDAILISEKVVKEDSYTSIHIKEFTVDVRET 799

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPE++TRDIPN +E+ L+ +DE GII +GA+V  G ILVGK+TPK E+  TPE KLL 
Sbjct: 800 KLGPEKLTRDIPNTNEKSLEQLDEEGIIRIGAKVKSGYILVGKVTPKSETETTPEFKLLN 859

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +IFGEKA +VRDTSL+VP G+ GTV+DV+   R   D
Sbjct: 860 SIFGEKAKEVRDTSLKVPHGIEGTVIDVQRLRRSEGD 896



 Score =  429 bits (1104), Expect = e-117,   Method: Composition-based stats.
 Identities = 152/401 (37%), Positives = 210/401 (52%), Gaps = 55/401 (13%)

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            N   + +E L  +  +      K   +L   +  +       +F + +       + ++ 
Sbjct: 812  NTNEKSLEQLDEEGIIRIGAKVKSGYILVGKVTPKSETETTPEFKLLNSIFGEKAKEVRD 871

Query: 1041 QYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                    +E    + +  +   GDD+PPGV  VVKV +A KR ++ GDKMAGRHGNKG+
Sbjct: 872  TSLKVPHGIEGTVIDVQRLRRSEGDDLPPGVEEVVKVLIATKRKLRQGDKMAGRHGNKGV 931

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V+R+LP EDMP++ DGTP+D+ LNPLGVPSRMN+GQI ET LGWA + L K   + +   
Sbjct: 932  VARVLPEEDMPYMADGTPLDLCLNPLGVPSRMNLGQILETELGWAALALDKWFSTPVFQS 991

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
             +   I          +G                  V    ++G+P    VF        
Sbjct: 992  ASTDQIEQKMKEAGLPVGGK---------------TVLRDGRTGIPFENSVF-------- 1028

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                           VG +YMLKL+H+V DK++ARSTG YSLVT
Sbjct: 1029 -------------------------------VGVMYMLKLHHLVDDKMHARSTGPYSLVT 1057

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQRLGEMEVW ++AYGAA  LQE+LTIKSDD+ GR ++YESIV G  + 
Sbjct: 1058 QQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQELLTIKSDDMNGRAKIYESIVKGEPST 1117

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
              G PESFNVLV+E++ L L + + +S+ K     E   + 
Sbjct: 1118 AAGVPESFNVLVQELRGLALDMSIYDSKGKRIPLTERDEEL 1158


>gi|289523377|ref|ZP_06440231.1| DNA-directed RNA polymerase, beta subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503069|gb|EFD24233.1| DNA-directed RNA polymerase, beta subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 1183

 Score =  773 bits (1997), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/946 (45%), Positives = 606/946 (64%), Gaps = 82/946 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R FFG + E++ +P L+E+Q  SY  FL  + APD R ++GLQ   + +FPI ++
Sbjct: 8   GRKRERLFFGPSKELVALPYLVELQHQSYKWFLQPDEAPDYRKSQGLQELLEEIFPIESY 67

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            G+ ++EFV Y  DPP    ++   +DLT+++PL+ T++LI          +   +IKE+
Sbjct: 68  DGSFVIEFVRYYIDPPTLTEEEARQKDLTWSMPLRATVQLI---------NRGSGEIKEE 118

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I++GD P+MT  G+F+I G +R+VV+QL RS G++F  +     + G+ +Y  +IIPD+
Sbjct: 119 EIFLGDFPVMTDRGSFIINGTERVVVNQLARSAGVYFSIE---TGVPGQEVYKAKIIPDR 175

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G W++ +    D++ V ID RRKVP T+            L  F                
Sbjct: 176 GAWLEFDLTPGDVLSVNIDNRRKVPATAL-----------LKAF---------------- 208

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                   G + ++ L+    G +      +                         G  +
Sbjct: 209 --------GIRDNTELLRTFGGVEEEVDIVEEEIR---------------------GRLI 239

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           AEDI++   G + I   D + ++ +E +++S    + +  VD          TL  D   
Sbjct: 240 AEDIIDSA-GHVVIPKNDRLTKEHVEVLWNSGRTKVRLWNVD-----PVFAATLERDGTD 293

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             ++A+L+I+R MRP +      A+     LFFD+ +Y+L  VGR K+N RL L+  ++V
Sbjct: 294 TPEEAMLEIFRRMRPNEPLRVENAKDYVYSLFFDTRRYNLGRVGRYKLNRRLGLNISEEV 353

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R +  +D++ I+K +++LR+G    DDID+L NRRVRSVGE+L+NQ R+GLLRMER  K+
Sbjct: 354 RLLTIDDLVTIVKGILNLRDGLEREDDIDHLANRRVRSVGELLQNQIRIGLLRMERIAKD 413

Query: 489 RIS-SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           R++   D+ +    DLIN +P+ +A+ EFF SSQLSQ  +  N L+ +TH RRLSA+G G
Sbjct: 414 RMTTIPDLSTATAHDLINIRPISAAIREFFGSSQLSQFMDQTNPLADVTHRRRLSAMGPG 473

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+ R RAG E RDVHP+HYGRICP ET EG NIGLV+SL ++ARVN YGF+ +P R V +
Sbjct: 474 GLTRERAGFEARDVHPSHYGRICPIETPEGPNIGLVTSLANYARVNEYGFLMSPKRVVRN 533

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             VT++VVYL A EE+  ++A+AN  LDE+G   EE V  R  G  ++VP E+++++D +
Sbjct: 534 RYVTDEVVYLPADEEDEAFVARANIPLDEEGRICEEEVHVRHRGSIVIVPPEQVNYVDVT 593

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQ+VS++A+LIPFLE+DD+NR LMG NMQRQAVPL+++E+P VGTGME  VA+ SGA I
Sbjct: 594 PKQIVSVSAALIPFLEHDDANRALMGSNMQRQAVPLVQSESPLVGTGMEEKVARDSGACI 653

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +AKR G V  VDA +I + + +G        VD Y L+KF+RSNQ T ++QRP+V+ GD 
Sbjct: 654 LAKRPGTVTYVDANKIQVTTEDGL-------VDTYTLIKFRRSNQGTVIHQRPIVRKGDF 706

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V   D +ADG + D G+LALGRN+LVAFM W GYNFED++L+SER+V EDV+TSIHIEE+
Sbjct: 707 VNEGDFLADGQAVDHGELALGRNVLVAFMGWEGYNFEDAILLSERLVKEDVYTSIHIEEY 766

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           E+ ARDTKLGPEEITRDIPNV E+ LKN+DE GI+ +GAEV  GDILVGK++PKGE+  T
Sbjct: 767 EIDARDTKLGPEEITRDIPNVGEDQLKNLDERGIVRIGAEVRAGDILVGKVSPKGETDQT 826

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           PEEKLLRAIFGEKA +VRDTSLRVP G  G VV V+  +R     +
Sbjct: 827 PEEKLLRAIFGEKAREVRDTSLRVPHGEGGKVVAVKRLSRDEYSDD 872



 Score =  357 bits (916), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 154/534 (28%), Positives = 218/534 (40%), Gaps = 82/534 (15%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T+ G  +    I          I +  I+  G  VN GD L           +     +L
Sbjct: 673  TEDGLVDTYTLIKFRRSNQGTVIHQRPIVRKGDFVNEGDFLAD-GQAVDHGELALGRNVL 731

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A  G +  +  D  L     V   V        + ID  +  +  E     I  +  D+
Sbjct: 732  VAFMGWEGYNFEDAILLSERLVKEDVYTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDQ 791

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE+ I+      R  +IL G+ +  G         L   +  E  R          
Sbjct: 792  LKNLDERGIVRIGAEVRAGDILVGKVSPKGETDQTPEEKLLRAIFGEKAR---------- 841

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
             +V+     +          ++     ++ + ++ DD+PPGV  VVKVF+A  R I    
Sbjct: 842  -EVRDTSLRVPHGEGGKVVAVK-----RLSRDEYSDDLPPGVNEVVKVFLAQIRKI---- 891

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
                                                        VG              
Sbjct: 892  -------------------------------------------TVG-------DKMAGRH 901

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G K          +    P  + ++ V+       +++       +     + +G  V+T
Sbjct: 902  GNKGVVSRILPVEDMPYLPDGTPVDVVLNPLGVPSRMNLGQVLETILGFVAYHNGWSVAT 961

Query: 1209 PVFDGADEEAINSMLRM------ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            PVF+GA  + I   +         DL   G  +LYDG TGEPF+  VTVGY+YMLKL H+
Sbjct: 962  PVFEGASVDEIFKYMEEIRDRKLPDLTRDGSIVLYDGRTGEPFENKVTVGYMYMLKLIHL 1021

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARS G YSL+TQQPLGGKS  GGQR GEMEVW ++ YGA+++LQEMLTIKSDDV
Sbjct: 1022 VDDKIHARSVGPYSLITQQPLGGKSQFGGQRFGEMEVWALEGYGASHILQEMLTIKSDDV 1081

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
             GR + +ESIV G +    G PESF VLVKE+Q LGL + +           EE
Sbjct: 1082 QGRLKTFESIVKGQNIGNPGVPESFRVLVKELQGLGLDVQVLYDDDSVGYVEEE 1135


>gi|116513532|ref|YP_812438.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
 gi|116092847|gb|ABJ58000.1| DNA-directed RNA polymerase subunit beta [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
          Length = 1192

 Score =  773 bits (1996), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/933 (41%), Positives = 554/933 (59%), Gaps = 79/933 (8%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           +VQ  SY  FL          +EG++  F  + PI+  SG   LE+V Y+   PK+ VD+
Sbjct: 3   DVQTESYKWFL----------DEGVKEVFDDILPISDTSGRLTLEYVDYKLQEPKYTVDE 52

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
               D TY+ P+ +TL+L               +IK Q ++ GDLPLMTK G+F++ G +
Sbjct: 53  SRKHDATYSAPMHVTLKLT---------NHETGEIKTQDVFFGDLPLMTKSGSFIVNGAE 103

Query: 151 RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
           R++VSQL RSPG+++  +  +   +G+ ++   +IP++G W++ E D+K+I +VR+DR R
Sbjct: 104 RVIVSQLVRSPGVYYSGEFDK---NGRQIFGTTVIPNRGAWLEFETDAKNISYVRVDRTR 160

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           K+P++  + ALG  S+ EI   F          D      + AD  V   +      +  
Sbjct: 161 KLPLSVLVRALGFGSDSEIKEIFGDSDTLDLTLDKD-VHKNPADSRVAEALKDIYDRLRP 219

Query: 270 GEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEI 320
           GE    +S + L        +   +  +G           + L G  +AE + + +TGE+
Sbjct: 220 GEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPDTGEV 279

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
               G V++ + ++ +                                DR D     Y  
Sbjct: 280 LAAKGTVVNNEVMDVLKDYL----------------------------DRDDFKTVTYTP 311

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
              G +      + +  F     D+          + +  N    +DV+ I   DIIA +
Sbjct: 312 SDEGVIPEPVTVQEIKVFSREIPDRE---------IKLISNGHIAEDVKCITPADIIASV 362

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
              ++L+ G G IDDID+LGNRR+R VGE+L+NQ R+GL RMER ++ER+S  D  +V P
Sbjct: 363 NYFLELQEGVGNIDDIDHLGNRRIRRVGELLQNQMRIGLARMERVVRERMSIQDAATVTP 422

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +P+V ++ EFF SSQLSQ  +  N L  +TH RR+SALG GG++R RAG E+RD
Sbjct: 423 QQLINIRPIVGSIKEFFGSSQLSQFMDQNNPLGELTHKRRMSALGPGGLSRDRAGYEVRD 482

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLS 618
           VH THYGR+CP ET EG NIGL++S+ ++A +N YGF+ETPYR+V     KVT+ + YL+
Sbjct: 483 VHYTHYGRLCPIETPEGPNIGLINSMATYAIINKYGFLETPYRRVSWATHKVTDKIDYLT 542

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+N  IA AN+ L+EDGSF ++++ CR   + + V  ++ID+ID  PKQVVS+ ++ 
Sbjct: 543 ADEEDNYIIAGANTPLNEDGSFVDDVILCRHREDNVEVSPDRIDYIDVIPKQVVSVTSAC 602

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDDSNR LMG N QRQAVPL+    P V TGME      SG A++A+  G VE V
Sbjct: 603 IPFLENDDSNRALMGANHQRQAVPLINPHGPLVATGMEYRAGHDSGDALLAEADGEVEYV 662

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA  I +R  +  LD        Y L K++RSN     NQ P VK GD+V    +IA+GP
Sbjct: 663 DANEIRVRREDQTLD-------TYTLEKYRRSNATKNYNQTPNVKRGDKVVDGQVIANGP 715

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           S   G+LALG+N ++AF  W+ YNFED++++SER+V EDV+TSIHIE+++  ARDTKLGP
Sbjct: 716 SMADGELALGQNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTSIHIEDYDSEARDTKLGP 775

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNV E+ LK++DE GII +GAEV+ GDILVGK+TPKG + ++ EE+LL AIFG
Sbjct: 776 EEITREIPNVGEDALKDLDENGIIRIGAEVHDGDILVGKVTPKGITELSAEERLLHAIFG 835

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G V DV++F R   D
Sbjct: 836 EKAREVRDTSLRVPHGGGGVVQDVQVFTREAGD 868



 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 270/1106 (24%), Positives = 401/1106 (36%), Gaps = 182/1106 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A     +  ++EIF         L  D                +    +AL DIY 
Sbjct: 166  VLVRALGFGSDSEIKEIFGDSDTLDLTLDKDV----------HKNPADSRVAEALKDIYD 215

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD-------------TPD 426
             +RPG+  T   + S+    FFD  +YDL+ VGR K+N +L+L               PD
Sbjct: 216  RLRPGEPKTTDSSRSLLVSRFFDPRRYDLAAVGRYKVNKKLSLKNRLLGYTLAETLADPD 275

Query: 427  DVRHI-------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +         E +  +   L        T    D        +V E +K   R   
Sbjct: 276  TGEVLAAKGTVVNNEVMDVLKDYLDRDDFKTVTYTPSDEGVIPEPVTVQE-IKVFSREIP 334

Query: 480  LRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             R  + I     + D+  + P D+         +   V        L             
Sbjct: 335  DREIKLISNGHIAEDVKCITPADIIASVNYFLELQEGVGNIDDIDHLGNRRIRRVGELLQ 394

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               R   A  +  V    +  +   V P     I P   S     G         + N  
Sbjct: 395  NQMRIGLARMERVVRERMSIQDAATVTPQQLINIRPIVGSIKEFFGSSQLSQFMDQNNPL 454

Query: 596  GFIETPYR----------------KVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDED 637
            G +    R                +V D   T+          E   I   N  ++    
Sbjct: 455  GELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYAII 514

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              +       R          +KID++ A  +    IA +  P  E+      ++ C  +
Sbjct: 515  NKYGFLETPYRRVSWATHKVTDKIDYLTADEEDNYIIAGANTPLNEDGSFVDDVILCRHR 574

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               V +      ++   +          ++ +     +E  D+ R ++ +          
Sbjct: 575  EDNVEVSPDRIDYID--VIPKQV----VSVTSACIPFLENDDSNRALMGAN--------- 619

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                      QR          PLV  G E R                    +       
Sbjct: 620  ---------HQRQAVPLINPHGPLVATGMEYRAG----------------HDSGDALLAE 654

Query: 818  WHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              G    + +  +E R+  ED     +  E     +  +    +     PNV       +
Sbjct: 655  ADG--EVEYVDANEIRVRREDQTLDTYTLE-----KYRRSNATKNYNQTPNVKRG--DKV 705

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +  +I  G  +  G++ +G                      E A+ + +  ++     S
Sbjct: 706  VDGQVIANGPSMADGELALG-------QNPVIAFTTWNMYNFEDAIMLSERLVKEDVYTS 758

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D     R      E          E   +D  DE  I+         +IL G+   
Sbjct: 759  IHIEDYDSEARDTKLGPEEITREIPNVGEDALKDL-DENGIIRIGAEVHDGDILVGKVTP 817

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R           +V+     +          ++      
Sbjct: 818  KGITELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGVVQDVQ------ 860

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +   + GD++ PGV  +V+V++  KR IQ GDKM+GRHGNKG V+ I P EDMP+L DGT
Sbjct: 861  VFTREAGDELAPGVNTLVRVYIVQKRKIQVGDKMSGRHGNKGTVALIAPVEDMPYLPDGT 920

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D  +  D            
Sbjct: 921  PVDICLNPMGVPSRMNIGQLLEIHLGRAARALGIHVATPVFDGASEDD------------ 968

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                             V+D   E         A +D  G+++L
Sbjct: 969  ---------------------------------VWDFVRE---------AGVDSDGKTVL 986

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            YDG TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVTQQPLGGK+  GGQR GE
Sbjct: 987  YDGRTGEPFHNRVSVGVMYYLKLTHMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGE 1046

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q+
Sbjct: 1047 MEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGERITKPGVPESFRVLVKELQS 1106

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDFNK 1382
            LGL + + +S        +   D N+
Sbjct: 1107 LGLDLRVLDSDENEVELRDMDEDSNE 1132


>gi|257126634|ref|YP_003164748.1| DNA-directed RNA polymerase subunit beta [Leptotrichia buccalis
           C-1013-b]
 gi|257050573|gb|ACV39757.1| DNA-directed RNA polymerase, beta subunit [Leptotrichia buccalis
           C-1013-b]
          Length = 1148

 Score =  772 bits (1993), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/945 (45%), Positives = 608/945 (64%), Gaps = 69/945 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK  +  ++P  +E Q  SY+ FL   + P +R N+G +A F  +FPI + +G  
Sbjct: 6   ERYSFGKIVDRGEMPHFLEFQLNSYEDFLQTKVPPQKRENKGFEAIFNEIFPIESSNGLL 65

Query: 73  MLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE    D P  D  +C  R  TY+  LK+ L+L           K   +I+E  
Sbjct: 66  KLEYLWYEIHDNDEPLNDELECKKRGKTYSGQLKVRLKLT---------NKRTGEIQETL 116

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++ GD+PLMT   TF+I G +R+V+SQLHRSPGI F+ +      +GK ++  +IIP +G
Sbjct: 117 VHFGDIPLMTDKATFIINGAERVVISQLHRSPGITFNKEL--NIQTGKDVFIGKIIPYKG 174

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  DI++V+IDRR+KV +  FL A+    ++ EI++ F+ +        +  +
Sbjct: 175 TWLEFETDKNDILNVKIDRRKKVLLPVFLKAVDFFPNNAEIMNHFFEEKEVEVSELYEKY 234

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
             +  +                                            +    L G +
Sbjct: 235 RDTELEE-------------------------------------------VLRSRLEGSF 251

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   EA ++ID   ++ I  +++  + I  V   +    I N LV D  
Sbjct: 252 VKEDILDEETGEFVAEAEEIIDMPVIQRIIDAKVPVLSIWEVKPEDR--IIANALVHDST 309

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           K+  +A+++++R +RPGD+ T   A S+   +FF+  +YDL+ VGR K+N RL LD P D
Sbjct: 310 KNSDEAVIEVFRKLRPGDLVTVDSARSLVKQMFFNPQRYDLADVGRYKVNKRLKLDVPAD 369

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           V  + KED++  I+ + +L +G+G  DDIDNL NRRVR VGE+L  Q + G+L+M + ++
Sbjct: 370 VIVLTKEDVLQTIEYVKNLVSGEGFTDDIDNLSNRRVRGVGELLSIQIKGGMLKMSKMVR 429

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           E+++  DI ++ PQ L+N KP+ + + EFF S QLSQ  +  N LS +TH RR+SALG G
Sbjct: 430 EKMTIQDITTLTPQSLLNTKPLNALILEFFGSGQLSQFMDQSNPLSELTHKRRISALGPG 489

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAG E+RDVH +HYGRICP ET EG NIGL++SL+++ +VN YGFIETP+ K+ D
Sbjct: 490 GLSRDRAGFEVRDVHNSHYGRICPIETPEGPNIGLIASLSTYGKVNKYGFIETPFVKIND 549

Query: 608 GKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           GK   ND+ YL+A EEE  +IAQA++ +D+DG+F  + V CR   E + + + K+D +D 
Sbjct: 550 GKADFNDIRYLAADEEEGLFIAQADTPIDKDGNFLTDEVVCRYGDEIVHIDKSKVDILDV 609

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS++A LIPFLE+DD+NR LMG NMQRQAVPLLK +AP+VGTG+E  VA  SGA 
Sbjct: 610 SPKQLVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTQAPYVGTGLERKVAVDSGAV 669

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I +K  G V  VDA +I++   +G           +RL+ F++SNQ+ C++Q+P++ +GD
Sbjct: 670 ITSKATGTVTFVDARKIIVTDEDGKD-------YYHRLLNFEKSNQSMCLHQKPIIDLGD 722

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           +V++ DIIADGPST  GDLALG+N+L+AFMPW GYNFED +LISER+  +DVFTSIHIEE
Sbjct: 723 KVKKGDIIADGPSTAGGDLALGKNILLAFMPWEGYNFEDGILISERLRKDDVFTSIHIEE 782

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           F++ AR TKLG EEITR+IPNVSEE L+N+DE GII +GA V P DILVGK+TPKGE+  
Sbjct: 783 FDIEARTTKLGDEEITREIPNVSEEALRNLDENGIIRIGAHVTPDDILVGKVTPKGETEP 842

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             EEKLLRAIFGEKA DVRDTSLR+P GV GTVVDV   ++   D
Sbjct: 843 PAEEKLLRAIFGEKAKDVRDTSLRLPHGVKGTVVDVLELSKENGD 887



 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 170/606 (28%), Positives = 247/606 (40%), Gaps = 84/606 (13%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  G         A+              +L    P+ G   E  + +    V     T 
Sbjct: 617  VSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTQAPYVGTGLERKVAVDSGAVITSKATG 676

Query: 842  IHIEEFEVMARD----TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                   V AR      + G +   R +          + +  II +G +V  GDI+   
Sbjct: 677  TVTF---VDARKIIVTDEDGKDYYHRLLNFEKSNQSMCLHQKPIIDLGDKVKKGDIIADG 733

Query: 898  ITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGIDK 952
             +  G      +  LL  +   G    D    S R+       S  + +  I  R     
Sbjct: 734  PSTAGGDLALGKNILLAFMPWEGYNFEDGILISERLRKDDVFTSIHIEEFDIEARTTKLG 793

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            +E          E   R+  DE  I+    +    +IL G+    G         L   +
Sbjct: 794  DEEITREIPNVSEEALRNL-DENGIIRIGAHVTPDDILVGKVTPKGETEPPAEEKLLRAI 852

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              E  +            V+     L    + +   + +  K        GDD+  GV +
Sbjct: 853  FGEKAKD-----------VRDTSLRLPHGVKGTVVDVLELSKE------NGDDLKAGVNK 895

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++++++A KR I  GDKM+GRHGNK                            GV SR  
Sbjct: 896  LIRIYIAEKRKIMVGDKMSGRHGNK----------------------------GVISR-- 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                                  L  +   + +           +G  S        +   
Sbjct: 926  ---------------------VLPVEDMPHLENGTPIDVCLNPLGVPSRMNIGQVLEVHL 964

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             L + +  K    ++TPVFDGA EE + + L  A    +G+  L DG TG+PFD PVTVG
Sbjct: 965  GLAIGDIDKY---IATPVFDGASEEDVKNYLEEAGYSRTGKVKLIDGRTGQPFDNPVTVG 1021

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +LQ
Sbjct: 1022 RMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNILQ 1081

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            EMLT+KSDD+ GRT+ YE+IV G    E   PESF VL+KE Q+LGL + L +   +   
Sbjct: 1082 EMLTVKSDDISGRTKTYEAIVKGQAMPEADAPESFRVLIKEFQSLGLDVALYDKDGEQIE 1141

Query: 1373 KMEEIP 1378
              + + 
Sbjct: 1142 LDKNVD 1147


>gi|237736031|ref|ZP_04566512.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium mortiferum ATCC 9817]
 gi|229421845|gb|EEO36892.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium mortiferum ATCC 9817]
          Length = 1166

 Score =  771 bits (1992), Expect = 0.0,   Method: Composition-based stats.
 Identities = 421/955 (44%), Positives = 589/955 (61%), Gaps = 80/955 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FG+  E   +P  +E Q  SY+ FL    AP+ R ++GL++AF+ +FP+ + 
Sbjct: 2   GKLVERLNFGRIKERGSMPHFLEFQLDSYEDFLQAKEAPNNRKDKGLESAFREIFPVESS 61

Query: 69  SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           +G   LE+V+YE    +PP  D  +C  R  TY+  LK+ LRLI          KS  +I
Sbjct: 62  NGDIKLEYVAYELHEAEPPLNDELECKKRGKTYSASLKVRLRLIN--------KKSGNEI 113

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           +E  +Y G++PLMT+ GTFVI G +R+VVSQLHRSPG+ F+ +      +GK L++ +II
Sbjct: 114 QESLVYFGEIPLMTERGTFVINGAERVVVSQLHRSPGVSFNKEI--NIQTGKDLFSGKII 171

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGD 243
           P +G W++ E D  D + V+IDR++KV  T FL A+    ++ EI   F           
Sbjct: 172 PYKGTWLEFETDKNDFLSVKIDRKKKVLATVFLKAIDFFENNTEIKDYFLETKELELTPI 231

Query: 244 FWCFPLSAAD------LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           F  +               G+ +   + D +TGE + E    +   L++++ +  V  + 
Sbjct: 232 FQKYKNREELVSVLRTKFEGSFIKEDIYDEETGEIIAEVDAVIDEALIETIIDAKVDKVV 291

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                     +A  ++N                                           
Sbjct: 292 YWEVKPEDKLLANTVLN------------------------------------------- 308

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                  D    ++DA+ ++++ +RPGD+ T   A+S+   +FF+  +YDL  VGR KMN
Sbjct: 309 -------DTTLTKEDAVTEVFKKLRPGDLVTIESAKSLIRQMFFNPQRYDLEPVGRYKMN 361

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RL L+ PDD   + KEDIIA +K +++L NG G  DDIDNL NRRVR VGE+L  Q + 
Sbjct: 362 KRLKLNVPDDEILLTKEDIIATMKYVINLNNGNGHTDDIDNLSNRRVRGVGELLLMQIKA 421

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL +M + ++E+++  D +++ PQ L+N +P+ + + +FF S QLSQ  +  N LS +TH
Sbjct: 422 GLSKMGKMVREKMTIQDSETLTPQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLSELTH 481

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGF
Sbjct: 482 KRRISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINKYGF 541

Query: 598 IETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           IETPY KV DGK   + + YL+A EEE  +IAQA++ + E+     E V CR   E + +
Sbjct: 542 IETPYIKVVDGKADFDRIEYLAADEEEGLFIAQADTKIGENNELLGE-VVCRFGHEIVNI 600

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             EK+D++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAP++GTG+E
Sbjct: 601 TGEKVDYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLE 660

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SGA +V+K  G V  VDA +I+I    G           YRL+ ++RSN + C+
Sbjct: 661 RKVAVDSGALVVSKVDGKVVYVDASKIIIEDENGKEHK-------YRLLNYERSNASMCL 713

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +Q PLV +G+EV+   I+ADGP+T  GDLALGRN+L+AFMPW GYN+ED++LIS+R+  +
Sbjct: 714 HQTPLVSLGEEVKVGSILADGPATKGGDLALGRNILMAFMPWEGYNYEDAILISDRLRKD 773

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIHIEE+E+ AR+TKLG EEITR+IPN+SEE L+ +D  GII +G+EV PGDILVG
Sbjct: 774 DVFTSIHIEEYEIEARNTKLGDEEITREIPNISEEALRKLDANGIITIGSEVGPGDILVG 833

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K  PKGE+    EEKLLRAIFGEKA DVRDTSLR+P G  GTVV++   +R   D
Sbjct: 834 KTAPKGETEPPAEEKLLRAIFGEKARDVRDTSLRMPHGSKGTVVEILELSRENGD 888



 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 200/607 (32%), Positives = 277/607 (45%), Gaps = 78/607 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V  
Sbjct: 614  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLERKVAVDSGALVVS 673

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   +   +  + + G E   R +          + +  ++ +G EV  G IL  
Sbjct: 674  KVDGKVVYVDASKIIIEDENGKEHKYRLLNYERSNASMCLHQTPLVSLGEEVKVGSILAD 733

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                KG   +     +L A    +  +  D  L              I +R   D    S
Sbjct: 734  GPATKG-GDLALGRNILMAFMPWEGYNYEDAIL--------------ISDRLRKDDVFTS 778

Query: 957  ISVEREQIELLARDKDDEQ------VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            I +E  +IE       DE+       I +  +       +    +  GP           
Sbjct: 779  IHIEEYEIEARNTKLGDEEITREIPNISEEALRKLDANGIITIGSEVGPGDILVGKTAPK 838

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
                     +  + A+  EK +   ++       SK  + +  +   E    GD++  GV
Sbjct: 839  GETEPPAEEKLLR-AIFGEKARDVRDTSLRMPHGSKGTVVEILELSRE---NGDELKAGV 894

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             + +K+ VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSR
Sbjct: 895  NKAIKILVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSR 954

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLG A                                              
Sbjct: 955  MNIGQVLEVHLGMAM--------------------------------------------- 969

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                     +  G  ++TPVFDGA EE +   L       SG+  LYDG TG+ FD PVT
Sbjct: 970  -------GNYNGGTHIATPVFDGASEEQVKDYLEKLGFPRSGKVDLYDGRTGDKFDNPVT 1022

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +
Sbjct: 1023 VGRMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNI 1082

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQEMLT+KSDDV GRT+ YE+I+ G +  E   PESF VL+KE QAL L ++L +S    
Sbjct: 1083 LQEMLTVKSDDVTGRTKTYEAIIKGEEMPEADLPESFKVLLKEFQALALDVELFDSEDNI 1142

Query: 1371 SAKMEEI 1377
                EE+
Sbjct: 1143 INVDEEL 1149


>gi|257452907|ref|ZP_05618206.1| DNA-directed RNA polymerase beta chain [Fusobacterium sp. 3_1_5R]
 gi|317059449|ref|ZP_07923934.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 3_1_5R]
 gi|313685125|gb|EFS21960.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. 3_1_5R]
          Length = 1184

 Score =  771 bits (1992), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/977 (43%), Positives = 603/977 (61%), Gaps = 77/977 (7%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FGK  E   +P  +E Q  SY+ FL M +AP+ R N+GL++AF+ +FPI + 
Sbjct: 2   GKLVERLNFGKIKERGIMPHFLEFQLNSYEDFLQMKVAPNNRENKGLESAFREIFPIESS 61

Query: 69  -SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            +G   LE+VSYE    +PP  D  +C  R  TY+  LK+ LRL           KS  +
Sbjct: 62  SNGEIRLEYVSYELHAAEPPLNDELECKKRGKTYSDSLKVRLRL--------FNKKSGNE 113

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           I+E  +Y G++P MT+ GTF+I G +R+VVSQLHRSPG+ F+ +      +GK L++ +I
Sbjct: 114 IQESLVYFGEVPKMTERGTFIINGAERVVVSQLHRSPGVSFNKEV--NIQTGKDLFSGKI 171

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE--EILSTFYPKIVYSQRG 242
           IP +G W++ E D  D + V+IDR++KV  T FL A+    +  EI   F+         
Sbjct: 172 IPYKGTWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNTEIKEHFFEVKELDLTE 231

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +  +     +L+   +                                           
Sbjct: 232 FYEKYANDTEELLSVVRTK----------------------------------------- 250

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           +   ++ E I + ETGEI  E   VI E  + +I  ++I    + Y +    +  I NT+
Sbjct: 251 IESSFLKEAIYDEETGEIIAEEDAVISEALISKIIENKIAV--LSYWEVKPEDLLIANTI 308

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D  K+  +A+ ++++ +RPGD+ T   A S+   +FF+  +YDL  VGR KMN RL L
Sbjct: 309 ANDTTKNSDEAVTEVFKKLRPGDLVTVDSARSLIKQMFFNVQRYDLEPVGRYKMNKRLKL 368

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +  ++   +  ED++  I+ ++DL NG+  +   DIDNL NRRVR VGE+L  Q + GLL
Sbjct: 369 EIDENEVLLTPEDVLGTIQYVIDLNNGESHVHTDDIDNLSNRRVRGVGELLLMQIKTGLL 428

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +M + ++E+++  DI+++ PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR
Sbjct: 429 KMSKMVREKMTIQDIETLTPQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLAELTHKRR 488

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGFIET
Sbjct: 489 ISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINQYGFIET 548

Query: 601 PYRKVCDGK-VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY  V DG    ND+ YL+A EEE  +IAQA++ L E+    E  V CR   E + V  +
Sbjct: 549 PYVAVKDGVADLNDIRYLAADEEEGMFIAQADTKLGENNELLEP-VTCRIGPEILDVEAK 607

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++ ++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ +APF+GTG+E  V
Sbjct: 608 RVHYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTQAPFIGTGLERKV 667

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGA +  K  G V  VD  +IVI + +            YRL+ F+RSNQ+ C++Q 
Sbjct: 668 AVDSGAVVTTKVDGTVSYVDGKKIVIETEDKRE-------YTYRLLNFERSNQSMCLHQS 720

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV +GD+V+  DIIADGP+T  GDLALG+N+L+ FM W GYN+ED++LIS+R+  +DVF
Sbjct: 721 PLVNLGDKVKAGDIIADGPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVF 780

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIH+EE+E+ AR+TKLG EEITR+IPNVSE  L+N+D  GII VG+EV PGDILVGK +
Sbjct: 781 TSIHVEEYEIEARNTKLGDEEITREIPNVSEAALRNLDANGIIMVGSEVEPGDILVGKTS 840

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDK 952
           PKGE+    EEKLLRAIFGEKA DVRD+SLR+P G  GTVV++   +R        G++K
Sbjct: 841 PKGETEPPAEEKLLRAIFGEKARDVRDSSLRMPHGSKGTVVEILELSRENGDELKAGVNK 900

Query: 953 NERSISVEREQIELLAR 969
             R +  E+ +I +  +
Sbjct: 901 AIRVLVAEKRKITVGDK 917



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 193/612 (31%), Positives = 280/612 (45%), Gaps = 76/612 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 618  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTQAPFIGTGLERKVAVDSGAVVTT 677

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V  ++   + + +  +T+   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 678  KVDGTVSYVDGKKIVIETEDKREYTYRLLNFERSNQSMCLHQSPLVNLGDKVKAGDIIAD 737

Query: 897  KITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                        +  L+  +   G    D    S R+       S  V +  I  R+   
Sbjct: 738  GPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVFTSIHVEEYEIEARNTKL 797

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D   +I+  +      +IL G+ +  G         L   
Sbjct: 798  GDEEITREIPNVSEAALRNLDANGIIMVGSEVE-PGDILVGKTSPKGETEPPAEEKLLRA 856

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+ +   +    + +   + +  +        GD++  GV 
Sbjct: 857  IFGEKARD-----------VRDSSLRMPHGSKGTVVEILELSRE------NGDELKAGVN 899

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 900  KAIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 959

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 960  NIGQVLEVHLGMAMRT-------------------------------------------- 975

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE I   L       SG+  LYDG TG+ FD  +TV
Sbjct: 976  --------LNGGTHIATPVFDGATEEQIKDYLENQGYPRSGKVTLYDGRTGDKFDNKITV 1027

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1028 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1087

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+ YE+I+ G +  ++  PESF VL+KE QAL L ++L +      
Sbjct: 1088 QEMLTVKSDDVTGRTKTYEAIIKGEEMPDSDLPESFKVLLKEFQALALDVELCDENDNVI 1147

Query: 1372 AKMEEIPDFNKC 1383
               EE+   +  
Sbjct: 1148 NVDEELNKEDTT 1159


>gi|260890613|ref|ZP_05901876.1| DNA-directed RNA polymerase, beta subunit [Leptotrichia hofstadii
           F0254]
 gi|260859658|gb|EEX74158.1| DNA-directed RNA polymerase, beta subunit [Leptotrichia hofstadii
           F0254]
          Length = 1148

 Score =  771 bits (1992), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/945 (45%), Positives = 609/945 (64%), Gaps = 69/945 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  FGK  +  ++P  +E Q  SY+ FL   + P +R N+G +A F  +FPI + +G  
Sbjct: 6   ERYSFGKIVDRGEMPHFLEFQLNSYEDFLQTKVPPQKRENKGFEAIFNEIFPIESSNGLL 65

Query: 73  MLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
            LE++ YE    D P  D  +C  R  TY+  LK+ L+L           K   +I+E  
Sbjct: 66  KLEYLWYEIHDNDEPLNDELECKKRGKTYSGQLKVRLKLT---------NKRTGEIQETL 116

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++ GD+PLMT   TF+I G +R+V+SQLHRSPGI F+ +      +GK ++  +IIP +G
Sbjct: 117 VHFGDIPLMTDKATFIINGAERVVISQLHRSPGITFNKEL--NIQTGKDVFIGKIIPYKG 174

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCF 247
            W++ E D  DI++V+IDRR+KV +  FL A+    ++ EI+  F+ +        +  +
Sbjct: 175 TWLEFETDKNDILNVKIDRRKKVLLPVFLKAVDFFQNNAEIMGHFFEEKEVELSELYEKY 234

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
             +  +                                            +    L G +
Sbjct: 235 RDTELEE-------------------------------------------VLRSRLEGSF 251

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V EDI++ ETGE   EA +++D   +++I  +++  + I  V   +    I N LV D  
Sbjct: 252 VKEDILDEETGEFVAEAEEIVDMPVIQKIIDAKVPVLSIWEVKPEDR--IIANALVHDST 309

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           K+  +A+++++R +RPGD+ T   A S+   +FF+  +YDL+ VGR K+N RL LD P D
Sbjct: 310 KNSDEAVIEVFRKLRPGDLVTVDSARSLVKQMFFNPQRYDLADVGRYKVNKRLKLDVPAD 369

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +  + KED++  I+ + +L +G+G  DDIDNL NRRVR VGE+L  Q + G+L+M + ++
Sbjct: 370 IIVLTKEDVLQTIEYVKNLVSGEGFTDDIDNLSNRRVRGVGELLSIQIKGGMLKMSKMVR 429

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           E+++  DI ++ PQ L+N KP+ + + EFF S QLSQ  +  N LS +TH RR+SALG G
Sbjct: 430 EKMTIQDITTLTPQSLLNTKPLNALILEFFGSGQLSQFMDQSNPLSELTHKRRISALGPG 489

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAG E+RDVH +HYGRICP ET EG NIGL++SL+++ +VN YGFIETP+ K+ D
Sbjct: 490 GLSRDRAGFEVRDVHNSHYGRICPIETPEGPNIGLIASLSTYGKVNKYGFIETPFVKIND 549

Query: 608 GKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           GK   ND+ YL+A EEE  +IAQA++ +D+DG+F  + V CR   E + + + K+D +D 
Sbjct: 550 GKADFNDIRYLAADEEEGLFIAQADTPIDKDGNFLTDEVVCRYGDEIVHIDKSKVDILDV 609

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS++A LIPFLE+DD+NR LMG NMQRQAVPLLK +AP+VGTG+E  VA  SGA 
Sbjct: 610 SPKQLVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTQAPYVGTGLERKVAVDSGAV 669

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I +K AG V  VDA +I++   +G           +RL+ F++SNQ+ C++Q+P++ +GD
Sbjct: 670 ITSKAAGTVTFVDARKIIVTDEDGKE-------HYHRLLNFEKSNQSMCLHQKPIIDLGD 722

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           +V++ DIIADGPST  GDLALG+N+L+AFMPW GYNFED +LISER+  +DVFTSIHIEE
Sbjct: 723 KVKKGDIIADGPSTAGGDLALGKNILLAFMPWEGYNFEDGILISERLRKDDVFTSIHIEE 782

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           F++ AR TKLG EEITR+IPNVSEE L+N+DE GII +GA V P DILVGK+TPKGE+  
Sbjct: 783 FDIEARTTKLGDEEITREIPNVSEEALRNLDENGIIRIGAHVTPDDILVGKVTPKGETEP 842

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             EEKLLRAIFGEKA DVRDTSLR+P GV GTVVDV   ++   D
Sbjct: 843 PAEEKLLRAIFGEKAKDVRDTSLRLPHGVKGTVVDVLELSKENGD 887



 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 170/606 (28%), Positives = 246/606 (40%), Gaps = 84/606 (13%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  G         A+              +L    P+ G   E  + +    V       
Sbjct: 617  VSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTQAPYVGTGLERKVAVDSGAVITSKAAG 676

Query: 842  IHIEEFEVMARD----TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                   V AR      + G E   R +          + +  II +G +V  GDI+   
Sbjct: 677  TVTF---VDARKIIVTDEDGKEHYHRLLNFEKSNQSMCLHQKPIIDLGDKVKKGDIIADG 733

Query: 898  ITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGIDK 952
             +  G      +  LL  +   G    D    S R+       S  + +  I  R     
Sbjct: 734  PSTAGGDLALGKNILLAFMPWEGYNFEDGILISERLRKDDVFTSIHIEEFDIEARTTKLG 793

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            +E          E   R+  DE  I+    +    +IL G+    G         L   +
Sbjct: 794  DEEITREIPNVSEEALRNL-DENGIIRIGAHVTPDDILVGKVTPKGETEPPAEEKLLRAI 852

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              E  +            V+     L    + +   + +  K        GDD+  GV +
Sbjct: 853  FGEKAKD-----------VRDTSLRLPHGVKGTVVDVLELSKE------NGDDLKAGVNK 895

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++++++A KR I  GDKM+GRHGNK                            GV SR  
Sbjct: 896  LIRIYIAEKRKIMVGDKMSGRHGNK----------------------------GVISR-- 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                                  L  +   + +           +G  S        +   
Sbjct: 926  ---------------------VLPVEDMPHLENGTPIDVCLNPLGVPSRMNIGQVLEVHL 964

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             L + +  K    ++TPVFDGA EE + + L  A    +G+  L DG TG+PFD PVTVG
Sbjct: 965  GLAIGDIDKY---IATPVFDGASEEDVKNYLEEAGYSRTGKVKLIDGRTGQPFDNPVTVG 1021

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +LQ
Sbjct: 1022 RMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNILQ 1081

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            EMLT+KSDD+ GRT+ YE+IV G    E   PESF VL+KE Q+LGL + L +   +   
Sbjct: 1082 EMLTVKSDDISGRTKTYEAIVKGQAMPEADAPESFRVLIKEFQSLGLDVALYDKDGEQIE 1141

Query: 1373 KMEEIP 1378
              + + 
Sbjct: 1142 LDKNVD 1147


>gi|294101620|ref|YP_003553478.1| DNA-directed RNA polymerase, beta subunit [Aminobacterium
           colombiense DSM 12261]
 gi|293616600|gb|ADE56754.1| DNA-directed RNA polymerase, beta subunit [Aminobacterium
           colombiense DSM 12261]
          Length = 1206

 Score =  771 bits (1991), Expect = 0.0,   Method: Composition-based stats.
 Identities = 442/948 (46%), Positives = 604/948 (63%), Gaps = 90/948 (9%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R  FG+  ++++IPD+IEVQ+ SYD F   +  PD R  +GL+     VFPI ++
Sbjct: 8   GRKRQRLTFGRARDLVEIPDMIEVQRNSYDWFYQKDCDPDSRKLQGLEELLHEVFPIESY 67

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            GA  LEFV +  D P  D ++   RDLT++ P++ T+RL+          +  K+IKE+
Sbjct: 68  DGAFALEFVHFFVDNPSGDEEEARQRDLTWSQPIRATIRLV---------NRKTKEIKEE 118

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I++GD P+MT  GTF+I G +R+VV+QL RS G++F  ++    + G+  Y+ +IIPD+
Sbjct: 119 EIFLGDFPIMTDRGTFIINGTERVVVNQLARSAGVYFHKEE---QIPGQEAYSAKIIPDR 175

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCF 247
           G W++      D++ V ID R+K+P T  L A G+ S EEIL  F  K            
Sbjct: 176 GAWLEFSLSPGDVLSVNIDNRKKLPATILLKAFGVSSNEEILDMFGAKP----------I 225

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            +   +  V  ++ +  V  D G +++    +LT   L+ L  KG   L +         
Sbjct: 226 EIDLTEEEVRGRLVAESVVDDEGNEIVSRNGRLTKDNLEILWSKGRTKLHV--------- 276

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                                                        + +  I  TL  D  
Sbjct: 277 --------------------------------------------WDVDPAIAATLERDNT 292

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           K   DA+L+++R +RP + +    A      LFFD+ +Y+L  VGR KMN RL +  P++
Sbjct: 293 KGSDDAVLEMFRRLRPNEPARVENAREYVYSLFFDTRRYNLGRVGRYKMNRRLGIPVPEN 352

Query: 428 V----RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           +    R +  EDI  II+ ++DLRN +   DDID+LGNRRVRSVGE+L+NQ R+GLLRME
Sbjct: 353 ITEHNRLLTLEDICKIIQGVIDLRNPESEGDDIDHLGNRRVRSVGELLQNQIRIGLLRME 412

Query: 484 RSIKERI-SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           R  KER+ +  D+++ M +DLIN +P+ +A+ EFF S QLSQ  +  N L+ +TH RRLS
Sbjct: 413 RIAKERMTTIPDLEAAMARDLINVRPIAAAIREFFGSGQLSQFMDQTNPLAEVTHRRRLS 472

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E RDVH THYGRICP ET EG NIGLV+SL +++RVN YGF+ TP 
Sbjct: 473 ALGPGGLSRERAGFEARDVHHTHYGRICPIETPEGPNIGLVTSLATYSRVNEYGFLMTPR 532

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RKV  G+V N++VYLSA EE++ YIA+AN+ +DE+G + E+    R  G+   +PRE++D
Sbjct: 533 RKVEKGRVLNEIVYLSADEEDDLYIARANTPIDENG-YLEKECHTRYRGDIEYIPREEVD 591

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQ+VS++ +LIPFLE+DD+NR LMG NMQRQAVPL++  AP VGTG+E  +AK 
Sbjct: 592 YLDVSPKQIVSVSTALIPFLEHDDANRALMGSNMQRQAVPLIQPAAPVVGTGIEYRIAKD 651

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG+ +VA   G V  VDA RI IR        S  GV  Y L+KF+RSNQ T ++QRP V
Sbjct: 652 SGSCVVATDDGEVVYVDADRIEIR--------SKRGVRAYPLVKFRRSNQGTIIHQRPSV 703

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + G+ +++ DIIADG S D G+LALGRN+LVAF+PW G+N+ED++L+SER+V ED +TSI
Sbjct: 704 EKGELIKKGDIIADGQSVDNGELALGRNVLVAFLPWEGFNYEDAILLSERLVKEDFYTSI 763

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E+ ARDTKLGPEEITRDIPNV E+ LKN+DE GI+ VGAEVN GDILVGK+TPKG
Sbjct: 764 HIEEYEIEARDTKLGPEEITRDIPNVGEDMLKNLDEDGIVRVGAEVNAGDILVGKVTPKG 823

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ES  +PEEKLLRAIFGEKA +VRDTSL+VP G  G +V V+   R   
Sbjct: 824 ESDQSPEEKLLRAIFGEKAREVRDTSLKVPHGARGKIVAVKRMTRENN 871



 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 123/415 (29%), Positives = 177/415 (42%), Gaps = 76/415 (18%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+         +IL G+    G         L   +  E  R           +V+
Sbjct: 798  DEDGIVRVGAEVNAGDILVGKVTPKGESDQSPEEKLLRAIFGEKAR-----------EVR 846

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          ++     ++ +    D + PGV  VVK++VA  R I        
Sbjct: 847  DTSLKVPHGARGKIVAVK-----RMTRENNPDALSPGVNEVVKIYVAQLRKI-------- 893

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
                                                    VG              G K 
Sbjct: 894  ---------------------------------------TVG-------DKMAGRHGNKG 907

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                     +    P  +  + V+       +++       +       +G  V+TPVF+
Sbjct: 908  VVSKILPVEDMPYLPDGTPCDIVLNPLGVPSRMNLGQVLETIMGFVAVHNGWKVATPVFE 967

Query: 1213 GADEEAINS---MLRMADLDE---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            GA E+ I      LR  +  +    G   L+DG TGEP ++ VTVGY+YMLKL H+V DK
Sbjct: 968  GAQEKEIFENLAELRKGNYPDLTADGMITLFDGRTGEPMEKKVTVGYMYMLKLIHLVDDK 1027

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++ YGAA++LQEMLT+KSDD+ GR 
Sbjct: 1028 IHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHILQEMLTVKSDDIRGRL 1087

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            + YE IV G +  + G PESF VLVKE+Q L L ++++ S       + +  D  
Sbjct: 1088 KTYEKIVKGQNLAKPGVPESFRVLVKELQGLVLDVEIKYSDGTVGELVMDEEDEE 1142


>gi|257466712|ref|ZP_05631023.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917864|ref|ZP_07914104.1| DNA-directed RNA polymerase subunit beta [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691739|gb|EFS28574.1| DNA-directed RNA polymerase subunit beta [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 1184

 Score =  771 bits (1990), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/977 (43%), Positives = 602/977 (61%), Gaps = 77/977 (7%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FGK  E   +P  +E Q  SY+ FL M +AP+ R N+GL++AF+ +FPI + 
Sbjct: 2   GKLVERLNFGKIKERGIMPHFLEFQLNSYEDFLQMKVAPNNRENKGLESAFREIFPIESS 61

Query: 69  -SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            +G   LE+VSYE    +PP  D  +C  R  TY+  LK+ LRL           KS  +
Sbjct: 62  SNGEIRLEYVSYELHAAEPPLNDELECKKRGKTYSDSLKVRLRL--------FNKKSGNE 113

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           I+E  +Y G++P MT+ GTF+I G +R+VVSQLHRSPG+ F+ +      +GK L++ +I
Sbjct: 114 IQESLVYFGEVPKMTERGTFIINGAERVVVSQLHRSPGVSFNKEV--NIQTGKDLFSGKI 171

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE--EILSTFYPKIVYSQRG 242
           IP +G W++ E D  D + V+IDR++KV  T FL A+    +  EI   F+         
Sbjct: 172 IPYKGTWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNTEIKEHFFEVKELDLTE 231

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +  +     +L+   +                                           
Sbjct: 232 FYEKYANDTEELLSVVRTK----------------------------------------- 250

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           +   ++ E I + ETGEI  E   VI E  + +I  ++I    + Y +    +  I NT+
Sbjct: 251 IESSFLKEAIYDEETGEIIAEEDAVISEALISKIIENKIAV--LSYWEVKPEDLLIANTI 308

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D  K+  +A+ ++++ +RPGD+ T   A S+   +FF+  +YDL  VGR KMN RL L
Sbjct: 309 ANDTTKNSDEAVTEVFKKLRPGDLVTVDSARSLIKQMFFNVQRYDLEPVGRYKMNKRLKL 368

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +  ++   +  ED++  I+ ++DL NG+  +   DIDNL NRRVR VGE+L  Q + GLL
Sbjct: 369 EIDENEVLLTPEDVLGTIQYVIDLNNGESHVHTDDIDNLSNRRVRGVGELLLMQIKTGLL 428

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +M + ++E+++  DI+++ PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR
Sbjct: 429 KMSKMVREKMTIQDIETLTPQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLAELTHKRR 488

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGFIET
Sbjct: 489 ISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINQYGFIET 548

Query: 601 PYRKVCDGK-VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY  V DG    ND+ YL+A EEE  +IAQA++ L E     E  V CR   E + V  +
Sbjct: 549 PYVAVKDGVADLNDIRYLAADEEEGMFIAQADTKLGEHNELLEP-VTCRIGPEILDVEAK 607

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++ ++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ +APF+GTG+E  V
Sbjct: 608 RVHYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTQAPFIGTGLERKV 667

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGA +  K  G V  VD  +IVI + +            YRL+ F+RSNQ+ C++Q 
Sbjct: 668 AVDSGAVVTTKVDGTVSYVDGKKIVIETEDKRE-------YTYRLLNFERSNQSMCLHQS 720

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV +GD+V+  DIIADGP+T  GDLALG+N+L+ FM W GYN+ED++LIS+R+  +DVF
Sbjct: 721 PLVNLGDKVKAGDIIADGPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVF 780

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIH+EE+E+ AR+TKLG EEITR+IPNVSE  L+N+D  GII VG+EV PGDILVGK +
Sbjct: 781 TSIHVEEYEIEARNTKLGDEEITREIPNVSEAALRNLDANGIIMVGSEVEPGDILVGKTS 840

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDK 952
           PKGE+    EEKLLRAIFGEKA DVRD+SLR+P G  GTVV++   +R        G++K
Sbjct: 841 PKGETEPPAEEKLLRAIFGEKARDVRDSSLRMPHGSKGTVVEILELSRENGDELKAGVNK 900

Query: 953 NERSISVEREQIELLAR 969
             R +  E+ +I +  +
Sbjct: 901 AIRVLVAEKRKITVGDK 917



 Score =  501 bits (1290), Expect = e-139,   Method: Composition-based stats.
 Identities = 193/612 (31%), Positives = 280/612 (45%), Gaps = 76/612 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 618  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTQAPFIGTGLERKVAVDSGAVVTT 677

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V  ++   + + +  +T+   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 678  KVDGTVSYVDGKKIVIETEDKREYTYRLLNFERSNQSMCLHQSPLVNLGDKVKAGDIIAD 737

Query: 897  KITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                        +  L+  +   G    D    S R+       S  V +  I  R+   
Sbjct: 738  GPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVFTSIHVEEYEIEARNTKL 797

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D   +I+  +      +IL G+ +  G         L   
Sbjct: 798  GDEEITREIPNVSEAALRNLDANGIIMVGSEVE-PGDILVGKTSPKGETEPPAEEKLLRA 856

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+ +   +    + +   + +  +        GD++  GV 
Sbjct: 857  IFGEKARD-----------VRDSSLRMPHGSKGTVVEILELSRE------NGDELKAGVN 899

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 900  KAIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 959

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 960  NIGQVLEVHLGMAMRT-------------------------------------------- 975

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE I   L       SG+  LYDG TG+ FD  +TV
Sbjct: 976  --------LNGGTHIATPVFDGATEEQIKDYLENQGHPRSGKVTLYDGRTGDKFDNKITV 1027

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1028 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1087

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+ YE+I+ G +  ++  PESF VL+KE QAL L ++L +      
Sbjct: 1088 QEMLTVKSDDVTGRTKTYEAIIKGEEMPDSDLPESFKVLLKEFQALALDVELCDENDNVI 1147

Query: 1372 AKMEEIPDFNKC 1383
               EE+   +  
Sbjct: 1148 NVDEELNKEDTT 1159


>gi|310777983|ref|YP_003966316.1| DNA-directed RNA polymerase subunit beta [Ilyobacter polytropus DSM
           2926]
 gi|309747306|gb|ADO81968.1| DNA-directed RNA polymerase subunit beta [Ilyobacter polytropus DSM
           2926]
          Length = 1165

 Score =  771 bits (1990), Expect = 0.0,   Method: Composition-based stats.
 Identities = 431/950 (45%), Positives = 597/950 (62%), Gaps = 80/950 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  FG+  E   +P  +E Q  SY+ FL    AP+ R ++GL++AF+ +FPI + +G   
Sbjct: 7   RMNFGRIKERGAMPHFLEFQLNSYEDFLQAKKAPNTREDKGLESAFREIFPIESSNGDIK 66

Query: 74  LEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           LE++SYE    +PP  D  +C  R  TY+  LK+ LRLI          KS  +I+E  +
Sbjct: 67  LEYLSYELHEAEPPMNDELECKKRGKTYSASLKVRLRLIN--------KKSGNEIQETLV 118

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           Y G+LP MT+ GTF+I G +R+VVSQLHRSPG+ F+ ++     +GK L++ +IIP +G 
Sbjct: 119 YFGELPRMTERGTFIINGAERVVVSQLHRSPGVSFNKEQ--NIQTGKDLFSGKIIPYKGT 176

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE--EILSTFYPKIVYSQRGDFWCFP 248
           W++ E D  D + V+IDR++KV  T FL ++    +  EI+  F+          +  + 
Sbjct: 177 WLEFETDKNDFLSVKIDRKKKVLATVFLKSVDFFQDNLEIMEEFFKIKELDLTKYYEKYK 236

Query: 249 LSAAD------LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                         G+ V   + D +TGE + E    +   L++ + +  ++ +      
Sbjct: 237 EREELVSILRTKFEGSFVKEDIFDEETGEILAEEQTVIDEELIEKIVDMKLESINYWEVR 296

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
                +A                                                  NTL
Sbjct: 297 PEEKILA--------------------------------------------------NTL 306

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
           + D ++++ +A+ ++++ +RPGD+ T   A S+   +FF+  +YDL++VGR KMN RL L
Sbjct: 307 LADTSENKDEAVTEVFKKLRPGDLVTVDSARSLIRQMFFNPQRYDLASVGRYKMNKRLRL 366

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D PDD   + +ED++A IK ++ L NG G  DDIDNL NRRVR VGE+L  Q R GL++M
Sbjct: 367 DLPDDQVVLTREDLVASIKYVLGLHNGAGHTDDIDNLSNRRVRGVGELLLMQIRSGLVKM 426

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            + +KE+++  D  ++ PQ L+N +P+ + V +FF S QLSQ  +  N L+ +TH RR+S
Sbjct: 427 GKMVKEKMTVQDAGTLTPQSLLNTRPLNALVLDFFGSGQLSQFMDQSNPLAELTHKRRIS 486

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A+VN YGFIETPY
Sbjct: 487 ALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKVNKYGFIETPY 546

Query: 603 RKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             V DGK   +D+ YL+A EEE  +IAQA++ + EDG+   E V CR   E + V  EK+
Sbjct: 547 ITVKDGKADFDDIKYLAADEEEGLFIAQADTVVGEDGNLVGE-VVCRFGHEIVHVSGEKV 605

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           DF+D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLLKAEAPF+GTG+E  VA 
Sbjct: 606 DFLDVSPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKAEAPFIGTGLERKVAV 665

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SGA +V+K  G V  VDA ++V+   +            YRL+ F+RSNQ  C++Q+PL
Sbjct: 666 DSGAVVVSKVKGKVVTVDANKVVVLDEDKKEHS-------YRLLNFERSNQAMCLHQKPL 718

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V +G+EV    I+ADGP+T  GDLALGRN+L+AFMPW GYNFED++LIS+R+  +DVFTS
Sbjct: 719 VDLGEEVEVGTILADGPATKGGDLALGRNILMAFMPWEGYNFEDAILISDRLRKDDVFTS 778

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E+ AR TKLG EEITR+IPNVSEE L+N+D+ G+I VGAEV PGDILVGK TPK
Sbjct: 779 IHIEEYEIEARSTKLGDEEITREIPNVSEEALRNLDDRGVIRVGAEVGPGDILVGKTTPK 838

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+    EEKLLRAIFGEKA DVRDTSL++P G  GT+V++   +R   D
Sbjct: 839 GETEPPAEEKLLRAIFGEKARDVRDTSLKMPHGAKGTIVEILELSRENGD 888



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 187/540 (34%), Positives = 257/540 (47%), Gaps = 81/540 (15%)

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E   R +          + +  ++ +G EV  G IL      KG         L+  + 
Sbjct: 695  KEHSYRLLNFERSNQAMCLHQKPLVDLGEEVEVGTILADGPATKGGDLALGRNILMAFMP 754

Query: 918  --GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
              G    D    S R+       S  + +  I  R     +E          E   R+ D
Sbjct: 755  WEGYNFEDAILISDRLRKDDVFTSIHIEEYEIEARSTKLGDEEITREIPNVSEEALRNLD 814

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D  VI          +IL G+    G         L   +  E  R            V+
Sbjct: 815  DRGVIRVGAEVG-PGDILVGKTTPKGETEPPAEEKLLRAIFGEKARD-----------VR 862

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    + +   + +  +        GD++  GV +++++FVA KR I  GDKM+G
Sbjct: 863  DTSLKMPHGAKGTIVEILELSRE------NGDELKAGVNKLIRIFVAEKRKITVGDKMSG 916

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL +GT +D+V+NPLGVPSRMN+GQ+ E HLG A        
Sbjct: 917  RHGNKGVVSRVLPAEDMPFLANGTHLDVVINPLGVPSRMNIGQVLEVHLGLAM------- 969

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  ++TPVFD
Sbjct: 970  ---------------------------------------------GDLDGGTYIATPVFD 984

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G +E  +   L  +    +G+  L+DG TG+ FD PVTVG +YMLKL+H+V DK++AR+ 
Sbjct: 985  GGNEAQVKDYLESSGFSRTGKVTLFDGRTGDKFDNPVTVGRMYMLKLHHLVEDKMHARAI 1044

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA +LQEMLT+KSDDV GRT+ YE+I
Sbjct: 1045 GPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANILQEMLTVKSDDVAGRTKTYEAI 1104

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK------NSAKMEEIPDFNKCELK 1386
            V G +  E   PESF VL+KE QAL L ++L ++            K E I +F+  +LK
Sbjct: 1105 VKGEEMPEPDLPESFKVLLKEFQALALDVELFDTDKNIINVNEELNKEETITEFSLADLK 1164


>gi|169351744|ref|ZP_02868682.1| hypothetical protein CLOSPI_02525 [Clostridium spiroforme DSM 1552]
 gi|169291966|gb|EDS74099.1| hypothetical protein CLOSPI_02525 [Clostridium spiroforme DSM 1552]
          Length = 1224

 Score =  770 bits (1989), Expect = 0.0,   Method: Composition-based stats.
 Identities = 410/963 (42%), Positives = 580/963 (60%), Gaps = 73/963 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +        R+ + +    +++P+L+E+Q  SY  F             G++  F+
Sbjct: 1   MENKITKAKSKINRRNYSRISGSLELPNLVEIQTNSYKWF----------KEVGIKEVFE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            ++PIT F+    LEFV   FD  K  V++   RD  YA P++ +LRL+           
Sbjct: 51  DIYPITNFNETLSLEFVDCVFDEAKHSVEESKDRDANYAAPIRASLRLV---------NS 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           +  +IKEQ ++MGD PLMT  GTF+I G +R++VSQL RSPG +F     +   SGK ++
Sbjct: 102 TTGEIKEQEVFMGDFPLMTDSGTFIINGAERVIVSQLVRSPGAYFADALDK---SGKTVF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY- 238
              IIP +G W++ E D+KD+++VRIDR RK+P T  L ALG+ S +EI+  F       
Sbjct: 159 NGSIIPSRGTWLEFENDAKDVLNVRIDRNRKMPGTVLLRALGLSSNDEIIKVFGEHEFIL 218

Query: 239 -SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +           ++    ++ +         L K+ + K  K 
Sbjct: 219 NTLAKDNTTNMEEALIEIYNKLRPGEPATLEGANNLLFAKFFDCKRYDLAKAGRFKFKKK 278

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF---HSEIRDIPILYVDSV 352
           L +  D + G  +AED+++ + G +    G  I ++ ++ I     +      I     +
Sbjct: 279 LSLL-DRISGRVLAEDLIDID-GNVIYPEGTYITQEVIDVIKPVLEAGAHTREIKTNPRL 336

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY---DLS 409
            +N  I+   V   +   K   +    +       T S   + ++++F   D Y   DL+
Sbjct: 337 ESNGVIQILDVYVDDTKSKKMRVIGTDLSLDSKFVTISDMIAAYSYMFNLVDIYNSLDLT 396

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
              RV    R+                              G +DDID+LGNRRVRSVGE
Sbjct: 397 AEDRVNFMSRI------------------------------GLLDDIDHLGNRRVRSVGE 426

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ+R+GL RMER +KER+S  ++DS+ PQ L N +P+ +A+ EFF SSQLSQ  + +
Sbjct: 427 LIQNQFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIKEFFSSSQLSQFMDQI 486

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T+ RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+++L S+
Sbjct: 487 NPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIETPEGPNIGLITTLASY 546

Query: 590 ARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A++N YGFIETPYRKV +  +  NDV YL+A EE+N  IAQ+N   DE+G+  +E V  R
Sbjct: 547 AKINEYGFIETPYRKVNNCIIDENDVRYLTADEEKNYIIAQSNVKTDENGTILDEQVIAR 606

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE I+  RE+IDFID SPKQ+VS+A S IPFLENDD+ R LMG NMQRQAVPLL    
Sbjct: 607 HLGENIMAKREEIDFIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQAVPLLNPHT 666

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A+ SGAA+VA+  GIV+ VDA +I+I   EG           YRL KF+
Sbjct: 667 PFVGTGMEHQAARDSGAAVVAREDGIVKYVDAKKIIIEDNEGVE-------HRYRLAKFK 719

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            SN  TC+NQ+P+VK G+ V +  +IADGP+ + G+LALG+N+LV FM W+GYN+ED+++
Sbjct: 720 ISNAGTCINQKPIVKDGEAVLKGQVIADGPAMEQGELALGQNVLVGFMEWNGYNYEDAVI 779

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V EDV+TSIHI+E+ +  RDTKLGPEEITRDIPNV ++  KN++  GII +GAEV
Sbjct: 780 MSERLVKEDVYTSIHIDEYAIECRDTKLGPEEITRDIPNVGDDARKNLNSDGIIMIGAEV 839

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG++ ++ EEKLL AIFGEK+ +V+D SLRVP G +G V D+++F R 
Sbjct: 840 KEGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAGIVHDIKVFERK 899

Query: 949 GID 951
             D
Sbjct: 900 NGD 902



 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 233/1059 (22%), Positives = 385/1059 (36%), Gaps = 121/1059 (11%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +     + +I NTL  D   + ++AL++IY  +RPG+ +T   A ++    FFD  +YDL
Sbjct: 208  IKVFGEHEFILNTLAKDNTTNMEEALIEIYNKLRPGEPATLEGANNLLFAKFFDCKRYDL 267

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK-------ILVDLRNGKGTIDDIDNLGN 461
            +  GR K   +L+L      R + ++ I             +                  
Sbjct: 268  AKAGRFKFKKKLSLLDRISGRVLAEDLIDIDGNVIYPEGTYITQEVIDVIKPVLEAGAHT 327

Query: 462  RRVRSVGEMLKN-QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R +++   +  N   ++  + ++ +  +++  +  D  +    +    +++A    F   
Sbjct: 328  REIKTNPRLESNGVIQILDVYVDDTKSKKMRVIGTDLSLDSKFVTISDMIAAYSYMFNLV 387

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +    +       +T   R++ + + G+      +  R V                   
Sbjct: 388  DIYNSLD-------LTAEDRVNFMSRIGLLDDIDHLGNRRVR------------------ 422

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                S+    +      +    R V +    ++V  ++     N     A        S 
Sbjct: 423  ----SVGELIQNQFRIGLSRMERVVKERMSLSEVDSITPQSLTNIRPLTAAIKEFFSSSQ 478

Query: 641  TEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              + +       E     R          +         +          +         
Sbjct: 479  LSQFMDQINPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHASHYGRICPIETPEGPNIG 538

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             +  L + A     G      +     I+ +        D  +  I +           +
Sbjct: 539  LITTLASYAKINEYGFIETPYRKVNNCIIDENDVRYLTADEEKNYIIAQSNVKTDENGTI 598

Query: 760  DIY---------RLMKFQRSNQNTCVNQRPLVKVGDEVRRN--DIIADGPSTDLGDLALG 808
                         +M  +       ++ + +V V         +  A             
Sbjct: 599  LDEQVIARHLGENIMAKREEIDFIDISPKQIVSVATSCIPFLENDDATRALMGANMQRQA 658

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKLGPEEITRDI 865
              +L    P+ G   E             V     I ++    +   +   G E   R  
Sbjct: 659  VPLLNPHTPFVGTGMEHQAARDSGAA--VVAREDGIVKYVDAKKIIIEDNEGVEHRYRLA 716

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      I++  I+  G  V  G ++        +  +   + +L         +  
Sbjct: 717  KFKISNAGTCINQKPIVKDGEAVLKGQVIADGP-AMEQGELALGQNVLVGFMEWNGYNYE 775

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +     V   V      + + I+  +  +  E    ++     D  + +    I   
Sbjct: 776  DAVIMSERLVKEDVYTSIHIDEYAIECRDTKLGPEEITRDIPNVGDDARKNLNSDGI--- 832

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I+ G     G     K T      +S   +     F  +  +V+ N   +       
Sbjct: 833  ---IMIGAEVKEGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGAGI 889

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               +      K+ + + GD++ PGV +VVKV++  KR I  GDKMAGRHGNKG++S+ILP
Sbjct: 890  VHDI------KVFERKNGDELQPGVNKVVKVYIVQKRKISEGDKMAGRHGNKGVISKILP 943

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP L+DGTP+DI+LNPLGVPSRMN+GQ+ E HLG+A   LG  I +   D     D+
Sbjct: 944  IEDMPHLEDGTPLDIMLNPLGVPSRMNIGQVLELHLGYAARQLGLYIATPAFDGLHPSDL 1003

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
              + +                                      PV               
Sbjct: 1004 EDIMAEAGMSKDGKQ----------------------------PV--------------- 1020

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                         G TGE FD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGG
Sbjct: 1021 -----------ISGRTGEYFDNNISVGIMYMIKLAHMVDDKLHARSVGPYSLVTQQPLGG 1069

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY L+E+LT+KSDDVVGR + YE+IV G    E G PE
Sbjct: 1070 KAQNGGQRFGEMEVWALEAYGAAYTLREILTVKSDDVVGRVKTYEAIVKGQPLPEPGLPE 1129

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            SF VL KE+QAL L + L +             + ++  
Sbjct: 1130 SFRVLKKELQALALDVRLLDENDNEVDMRNIEEEEHRFP 1168


>gi|303230152|ref|ZP_07316921.1| DNA-directed RNA polymerase, beta subunit [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302515213|gb|EFL57186.1| DNA-directed RNA polymerase, beta subunit [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 1353

 Score =  770 bits (1987), Expect = 0.0,   Method: Composition-based stats.
 Identities = 412/948 (43%), Positives = 562/948 (59%), Gaps = 109/948 (11%)

Query: 32  VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDC 91
           +Q+ SY+ FL            GLQ  F  + PI   SG  +L F  +    PK+D+++C
Sbjct: 1   IQRKSYEWFL----------ESGLQNIFNDISPIKDNSGNLVLSFEGFSLGEPKYDINEC 50

Query: 92  LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQR 151
             RD TYA PL++ +RL+  D +         DIKEQ ++MGD PLMT  GTF+I G +R
Sbjct: 51  KNRDATYAAPLRVNIRLVNNDPENM-------DIKEQEVFMGDFPLMTDTGTFIINGAER 103

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK 211
           ++VSQL RSPG+++  +       G  LY   +IP++G W+++E D+ +++ VRIDR RK
Sbjct: 104 VIVSQLVRSPGVYYGKEID---TMGNRLYESTVIPNRGAWIELETDASEVVAVRIDRNRK 160

Query: 212 VPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLMV--GAKVSSSLV 265
           +P T  + ALG D+ E IL  F+            D         D        +     
Sbjct: 161 LPATVLVRALGWDTNESILDLFWNGQTDEDGLPVYDERIVRTLEKDTTQSADEALVEIYK 220

Query: 266 DIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGE 316
            +  GE   +ES + L   L    +   +  +G             + G  +A+ IV+ E
Sbjct: 221 KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDTE 280

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           TGEI ++AG  + E+ L+ +  S       ++        YI N+          +  L+
Sbjct: 281 TGEIILDAGVQVGEEQLDIVAKSG------VFSGEGFAEFYITNSDGVVSKIICNNCNLE 334

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
                                                                 + +ED+
Sbjct: 335 FNHR-------------------------------------------------TVTREDM 345

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER ++ER++  +I+
Sbjct: 346 IANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMERVVRERMTIQEIE 405

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG 
Sbjct: 406 SITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGF 465

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK------- 609
           E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRKV           
Sbjct: 466 EVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGEGADAD 525

Query: 610 ------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 V+  V Y++A EEE   IAQANS LD DG F  + V CR   + + V  +K+D+
Sbjct: 526 KVVKVRVSESVAYMTADEEEGMTIAQANSPLDADGCFANDHVACRRGHDVLEVTPDKVDY 585

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP VGTGME   A  S
Sbjct: 586 MDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDS 645

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  ++A+ AG V +     I +         S   VD YRL KF RSNQ+TC NQ+P+V 
Sbjct: 646 GVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYRLNKFLRSNQSTCFNQKPIVN 699

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE +  ED++TSIH
Sbjct: 700 RGDHVVKGQVLADGPATDGGELALGFNVLVAFMPWEGYNYEDAILLSEELCKEDIYTSIH 759

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+PGDILVGK TPKGE
Sbjct: 760 IEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVHPGDILVGKATPKGE 819

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 820 TELTPEERLLRAIFGDKEREVRDTSLRVPHGECGKVVDVKVFTRENGD 867



 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 104/193 (53%), Positives = 140/193 (72%), Gaps = 1/193 (0%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E+ +   L +A   + G+++LYDG TGEP D  V
Sbjct: 1107 DYDTYGMPKPDVAGIHIATPVFDGAHEKDVFETLDIAGRPDDGKTVLYDGRTGEPMDNRV 1166

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 1167 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 1226

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT+KSDDVVGR + YE IV G +  E G PESF VL+KE+Q++GL + + N   +
Sbjct: 1227 TLQELLTVKSDDVVGRVKAYEKIVKGENIPEPGVPESFKVLLKELQSIGLDVKILNED-Q 1285

Query: 1370 NSAKMEEIPDFNK 1382
                M+E+ D ++
Sbjct: 1286 EEVVMKELDDEDE 1298



 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 170/872 (19%), Positives = 296/872 (33%), Gaps = 76/872 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 165  VLVRALGWDTNESILDLFWNGQTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 220

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + +  + I+  
Sbjct: 221  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTL-AQPIVDT 279

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                + L  G    ++  ++  +     GE     Y      +   I     +++ +   
Sbjct: 280  ETGEIILDAGVQVGEEQLDIVAKSGVFSGEGFAEFYITNSDGVVSKIICNNCNLEFNHRT 339

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
                   + +++ +         +   + ++ L       R          R       R
Sbjct: 340  VT----REDMIANISYLLNLMDGAGHTDDIDHLG--NRRLRCVGELLQNQFRIGLTRMER 393

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             V              E   I  + S+T  A +N         R V          +  +
Sbjct: 394  VVR-------------ERMTIQEIESITPQALINI--------RPVVAAIK----EFFGS 428

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             +           +          L     + E        +          +       
Sbjct: 429  SQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG-- 486

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P +   +S       N         +      G G        +   +  + +  V  + 
Sbjct: 487  PNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGEG------ADADKVVKVRVSESVAYMT 540

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN-----TCVNQRPLVKVGDEVRRNDII 794
            A      ++     P  +           R   +             V   + V     +
Sbjct: 541  ADEEEGMTIAQANSPLDADGCFANDHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAM 600

Query: 795  --------ADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHI 844
                    A+              +L A  P  G   E   +      +++ +    +  
Sbjct: 601  IPFLENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRC 660

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
               E+       G  +  R    +        ++  I+  G  V  G +L       G  
Sbjct: 661  WGNEIHVLRDSDGRVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-G 719

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQ 963
             +     +L A    +  +  D  L           D+    +    + + R   +  E+
Sbjct: 720  ELALGFNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEE 776

Query: 964  I-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            I   L    DD    LD +       I  G     G     K+T      +   P  +  
Sbjct: 777  ITRELPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLL 829

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D++ +    SL+V +     +++     K+   + GD++ PGV ++V+V++A KR
Sbjct: 830  RAIFGDKEREVRDTSLRVPHGECGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKR 885

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLG
Sbjct: 886  KIHEGDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLG 945

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            WA  GLG KIK+     +     +       +
Sbjct: 946  WAVQGLGMKIKATDLHIQNVLKEARTDESYWE 977


>gi|229825621|ref|ZP_04451690.1| hypothetical protein GCWU000182_00983 [Abiotrophia defectiva ATCC
           49176]
 gi|229790184|gb|EEP26298.1| hypothetical protein GCWU000182_00983 [Abiotrophia defectiva ATCC
           49176]
          Length = 1306

 Score =  769 bits (1985), Expect = 0.0,   Method: Composition-based stats.
 Identities = 399/984 (40%), Positives = 592/984 (60%), Gaps = 73/984 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           +R  + +  E++++P+LIEVQK SY   L            GL+  F  +  I  +SG  
Sbjct: 28  IRMSYARQEEVLEMPNLIEVQKNSYQWLLTD----------GLREVFDDISMIVDYSGRY 77

Query: 73  MLEFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            L FV +  D PK    ++ C  RD TY+  LK+T+ L+          K ++  +++ +
Sbjct: 78  GLRFVDFSLD-PKENHTIEVCKERDGTYSAALKVTVELV------DLKEKKVRS-QQKGV 129

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           ++G+LPLMT  G+F+I G +R++VSQL RSPGI++     +    GK LY  ++IP++G 
Sbjct: 130 FLGELPLMTDTGSFIINGAERVIVSQLVRSPGIYYSIAHDKT---GKELYTSQVIPNRGA 186

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPL 249
           W++ E DS ++ +V++DR RKVP+T  + ALG+  +++I   F  +              
Sbjct: 187 WLEYETDSNNVFYVKVDRNRKVPITVLVRALGVSLNKDIEELFGDEPKLQASLAKDVATN 246

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS-------- 300
           S   L+           +  GE + +E+     + +L   K   +  +G           
Sbjct: 247 SDEGLL------ELYKKLRPGEPLLVENAANYINNMLFDPKRYDLAKVGRYKFNKKLAFR 300

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + +    +AED+++  TGEI  E G  I  +  +++ ++    +P +++   + N  + +
Sbjct: 301 NRIVRHVLAEDVMDKSTGEIIGEKGTEITVELADKMQNA---AVPYVWIQGEDRNVKVLS 357

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            L+ D N    +        +   ++  +     +      D    D     +  +N  +
Sbjct: 358 NLMVDINTYLPE---LNKEEVGITELVYYPKLMDVMELANGDYTGDDFKRELKNYVNDLI 414

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                   +HI +EDI A I  + +L NG G  DDID+LGNRR+R+VGE+L+NQYR+GL 
Sbjct: 415 P-------KHITREDIFASINYVFNLENGIGNEDDIDHLGNRRIRAVGELLQNQYRIGLS 467

Query: 481 RMERSIKERISSVDIDSV---MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           RMER++++++S+   D +    P D IN KPV +A+ EFF SSQLSQ  +  N L  +TH
Sbjct: 468 RMERTVRDKMSNTGSDVIDDSNPGDFINCKPVTAAIKEFFGSSQLSQFMDQHNPLGELTH 527

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL S+AR+N YGF
Sbjct: 528 KRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPVETPEGPNIGLINSLASYARINEYGF 587

Query: 598 IETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           IE PYRK+      + +VT++VVYL+A EE+   +AQAN  LDE+G F    V  R   E
Sbjct: 588 IEAPYRKLDKTDPNNPRVTDEVVYLTADEEDPFIVAQANEPLDENGYFINNSVSGRFRDE 647

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                ++ ++ +D SPK V S A ++IPFL+NDD+NR LMG NMQRQAVPLL  ++  VG
Sbjct: 648 TSTYDKKNVELMDVSPKMVFSAATAMIPFLQNDDANRALMGSNMQRQAVPLLFTDSAVVG 707

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME+ VA  SG  ++A++AG+VE     RI++R+ + +       +  Y L+KF RSNQ
Sbjct: 708 TGMEAKVAVDSGVCVLAEKAGVVESACGDRILVRNDDDNR------ITEYPLLKFARSNQ 761

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC+NQRP+V  GD V    +IADGPST  G++ LG++ L+ FM W GYN+ED++L+SER
Sbjct: 762 GTCINQRPIVNKGDHVEAKQVIADGPSTKGGEIGLGKSPLIGFMTWEGYNYEDAVLLSER 821

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TSIHIEE+E  ARDTKLG EEITRD+P V ++ LK+++E GII +GAEV  GD
Sbjct: 822 LVRDDVYTSIHIEEYECEARDTKLGDEEITRDVPGVGDDALKDLNEDGIIRIGAEVRAGD 881

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR----- 947
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G +VD + F R     
Sbjct: 882 ILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEYGIIVDAKKFEREKGDE 941

Query: 948 --HGIDKNERSISVEREQIELLAR 969
             HG+ K+ R    ++ +I++  +
Sbjct: 942 LAHGVKKSVRVYIAQKRKIQVGDK 965



 Score =  538 bits (1385), Expect = e-150,   Method: Composition-based stats.
 Identities = 250/1137 (21%), Positives = 414/1137 (36%), Gaps = 83/1137 (7%)

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFH 338
            +   +      K +    +  +   G ++  +  +     + ++    +    L   +  
Sbjct: 162  IYYSIAHDKTGKELYTSQVIPNR--GAWLEYETDSNNVFYVKVDRNRKVPITVLVRALGV 219

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            S  +DI  L+ D       ++ +L  D   +  + LL++Y+ +RPG+      A +  N 
Sbjct: 220  SLNKDIEELFGD----EPKLQASLAKDVATNSDEGLLELYKKLRPGEPLLVENAANYINN 275

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            + FD  +YDL+ VGR K N +L          + ++ +      ++  +  + T++  D 
Sbjct: 276  MLFDPKRYDLAKVGRYKFNKKLAFRNRIVRHVLAEDVMDKSTGEIIGEKGTEITVELADK 335

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            + N  V  V       +  G  R  + +      VDI++ +P+       +   V     
Sbjct: 336  MQNAAVPYV-------WIQGEDRNVKVLS--NLMVDINTYLPELNKEEVGITELVYYP-- 384

Query: 519  SSQLSQLEEHVNSLSRITHTRR-----LSALGQGGVARARAGVEMRDVHPTHYGRIC--P 571
              +L  + E  N        +R     ++ L    + R      +  V     G      
Sbjct: 385  --KLMDVMELANGDYTGDDFKRELKNYVNDLIPKHITREDIFASINYVFNLENGIGNEDD 442

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             +      I  V  L           +E   R       ++ +   +  +  N     A 
Sbjct: 443  IDHLGNRRIRAVGELLQNQYRIGLSRMERTVRDKMSNTGSDVIDDSNPGDFINCKPVTAA 502

Query: 632  SS----------LDEDGSFTEELVFCRCAGEEIL----VPREKIDFIDASPKQVVSIAAS 677
                          +  +   EL   R             R   +  D        +   
Sbjct: 503  IKEFFGSSQLSQFMDQHNPLGELTHKRRLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPV 562

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
              P   N      L       +   +         T   +         + A        
Sbjct: 563  ETPEGPNIGLINSLASYARINEYGFIEAPYRKLDKTDPNNPRVTDEVVYLTADEEDPFIV 622

Query: 738  VDAIRIVIRS----VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
              A   +  +                  Y     +  + +  +       +   ++ +D 
Sbjct: 623  AQANEPLDENGYFINNSVSGRFRDETSTYDKKNVELMDVSPKMVFSAATAMIPFLQNDDA 682

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                  +++   A+      + +   G   + ++     +++E            ++ R+
Sbjct: 683  NRALMGSNMQRQAVPLLFTDSAVVGTGMEAKVAVDSGVCVLAEKAGVVESACGDRILVRN 742

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE-----SPMTP 908
                       +          I++  I+  G  V    ++    + KG           
Sbjct: 743  DDDNRITEYPLLKFARSNQGTCINQRPIVNKGDHVEAKQVIADGPSTKGGEIGLGKSPLI 802

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
                      E AV + +  +R     S  + +     R     +E          +   
Sbjct: 803  GFMTWEGYNYEDAVLLSERLVRDDVYTSIHIEEYECEARDTKLGDEEITRDVPGVGDDAL 862

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D + E  I+      R  +IL G+    G         L   +  E  R          
Sbjct: 863  KDLN-EDGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR---------- 911

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E                   K  + + GD++  GV + V+V++A KR IQ GD
Sbjct: 912  -------EVRDTSLRVPHGEYGIIVDAKKFEREKGDELAHGVKKSVRVYIAQKRKIQVGD 964

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   L
Sbjct: 965  KMAGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAATVL 1024

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G K+ + I D     DI          I       +    +D     +            
Sbjct: 1025 GVKVSTPIFDGANEEDIGDTLELANDYINMPLDEFEQKYREDLGDEVMDYLL-------- 1076

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                        +  +   +   G+  L DG TG+ FD P TVG++  LKL+H+V DK++
Sbjct: 1077 ------THLESRNDWKGVKIGRDGKVWLKDGRTGQYFDSPATVGFMNYLKLHHLVDDKIH 1130

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + 
Sbjct: 1131 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKT 1190

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            YE+I+ G +  E G PESF VL+KE+Q+L L + + +        ME +  +   +L
Sbjct: 1191 YEAIIKGENISEPGIPESFKVLLKELQSLALDVTVLDEDGNEIKMMENVE-YGDEDL 1246


>gi|257462557|ref|ZP_05626968.1| DNA-directed RNA polymerase beta chain [Fusobacterium sp. D12]
 gi|317060210|ref|ZP_07924695.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. D12]
 gi|313685886|gb|EFS22721.1| DNA-directed RNA polymerase subunit beta [Fusobacterium sp. D12]
          Length = 1184

 Score =  768 bits (1984), Expect = 0.0,   Method: Composition-based stats.
 Identities = 425/977 (43%), Positives = 601/977 (61%), Gaps = 77/977 (7%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FGK  E   +P  +E Q  SY+ FL M +AP+ R N+GL++AF+ +FPI + 
Sbjct: 2   GKLVERLNFGKIKERGIMPHFLEFQLNSYEDFLQMKVAPNNRENKGLESAFREIFPIESS 61

Query: 69  -SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            +G   LE+VSYE    +PP  D  +C  R  TY+  LK+ LRL           KS  +
Sbjct: 62  SNGEIRLEYVSYELHAAEPPLNDELECKKRGKTYSDSLKVRLRL--------FNKKSGNE 113

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           I+E  +Y G++P MT  GTF+I G +R+VVSQLHRSPG+ F+ +      +GK L++ +I
Sbjct: 114 IQESLVYFGEVPKMTDRGTFIINGAERVVVSQLHRSPGVSFNKEV--NIQTGKDLFSGKI 171

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE--EILSTFYPKIVYSQRG 242
           IP +G W++ E D  D + V+IDR++KV  T FL A+    +  EI   F+ +   +   
Sbjct: 172 IPYKGTWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNIEIKEHFFEEKELNLSE 231

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
            +  +     +L+   +                                           
Sbjct: 232 FYEKYTHDPGELLSVVRTK----------------------------------------- 250

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           +   +V E I + ETGEI  E   VI E  + ++  +++  I   Y +    +  I NT+
Sbjct: 251 IENSFVKEAIFDEETGEIIAEEDAVISEALISKMIENKVSTIS--YWEVKPEDILIANTI 308

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D  K+  +A+ +++R +RPGD+ T   A S+   +FF+  +YDL  VGR KMN RL L
Sbjct: 309 ANDTTKNSDEAVTEVFRKLRPGDLVTVDSARSLIKQMFFNVQRYDLEPVGRYKMNKRLKL 368

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +  ++   +  ED++  I+ ++DL NG      DDIDNL NRRVR VGE+L  Q + GLL
Sbjct: 369 EIDENEVLLTPEDVLGTIQYVIDLNNGEYHVHTDDIDNLSNRRVRGVGELLLMQIKTGLL 428

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +M + ++E+++  DI+++ PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR
Sbjct: 429 KMSKMVREKMTIQDIETLTPQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLAELTHKRR 488

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGFIET
Sbjct: 489 ISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINQYGFIET 548

Query: 601 PYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY  V D     ND+ YL+A EEE  +IAQA++ L E      E V CR   E + V  +
Sbjct: 549 PYIAVKDGIADLNDIRYLAADEEEGMFIAQADTKLGEHNELL-EPVTCRIGPEILDVDAK 607

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++ ++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  V
Sbjct: 608 RVHYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPFIGTGLERKV 667

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGA +  K  G V  VD  +IVI + +            YRL+ F+RSNQ+ C++Q 
Sbjct: 668 AVDSGAVVTTKVDGKVSYVDGKKIVIETEDKRE-------YTYRLLNFERSNQSMCLHQS 720

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV +GDEV+  DIIADGP+T  GDLALG+N+L+ FM W GYN+ED++LIS+R+  +DVF
Sbjct: 721 PLVNLGDEVKAGDIIADGPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVF 780

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS+H+EE+E+ AR+TKLG EEITR+IPNVSE  L+N+D  G+I +G+EV PGDILVGK +
Sbjct: 781 TSVHVEEYEIEARNTKLGDEEITREIPNVSEAALRNLDANGVIMIGSEVEPGDILVGKTS 840

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDK 952
           PKGE+    EEKLLRAIFGEKA DVRD+SLR+P G  GTVV++   +R        G++K
Sbjct: 841 PKGETEPPAEEKLLRAIFGEKARDVRDSSLRMPHGSKGTVVEILELSRENGDELKAGVNK 900

Query: 953 NERSISVEREQIELLAR 969
             R +  E+ +I +  +
Sbjct: 901 AIRVLVAEKRKITVGDK 917



 Score =  499 bits (1286), Expect = e-139,   Method: Composition-based stats.
 Identities = 195/612 (31%), Positives = 278/612 (45%), Gaps = 76/612 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 618  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPFIGTGLERKVAVDSGAVVTT 677

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +T+   E   R +          + +  ++ +G EV  GDI+  
Sbjct: 678  KVDGKVSYVDGKKIVIETEDKREYTYRLLNFERSNQSMCLHQSPLVNLGDEVKAGDIIAD 737

Query: 897  KITPKGESPMTPEEKLLRAI--FGEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                        +  L+  +   G    D    S R+       S  V +  I  R+   
Sbjct: 738  GPATSKGDLALGKNILMGFMTWEGYNYEDAILISDRLRKDDVFTSVHVEEYEIEARNTKL 797

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D   VI+  +      +IL G+ +  G         L   
Sbjct: 798  GDEEITREIPNVSEAALRNLDANGVIMIGSEVE-PGDILVGKTSPKGETEPPAEEKLLRA 856

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+ +   +    + +   + +  +        GD++  GV 
Sbjct: 857  IFGEKARD-----------VRDSSLRMPHGSKGTVVEILELSRE------NGDELKAGVN 899

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 900  KAIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 959

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 960  NIGQVLEVHLGMAMR--------------------------------------------- 974

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE I   L       SG+  LYDG TG+ FD  +TV
Sbjct: 975  -------SLNGGTHIATPVFDGATEEQIKDYLENQGHPRSGKVTLYDGRTGDKFDNKITV 1027

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1028 GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1087

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+ YE+I+ G +  ++  PESF VL+KE QAL L ++L +      
Sbjct: 1088 QEMLTVKSDDVTGRTKTYEAIIKGEEMPDSDLPESFKVLLKEFQALALDVELCDENDNVI 1147

Query: 1372 AKMEEIPDFNKC 1383
               EE+      
Sbjct: 1148 NVDEELNKEETT 1159


>gi|224542340|ref|ZP_03682879.1| hypothetical protein CATMIT_01519 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524722|gb|EEF93827.1| hypothetical protein CATMIT_01519 [Catenibacterium mitsuokai DSM
           15897]
          Length = 1311

 Score =  767 bits (1981), Expect = 0.0,   Method: Composition-based stats.
 Identities = 408/977 (41%), Positives = 583/977 (59%), Gaps = 67/977 (6%)

Query: 6   VFNGLGRV-RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP 64
           V     R+ R+ + +    + +P+L+E+Q  S+  F            +G++  F+ ++P
Sbjct: 57  VRTAESRIKRRNYSRISGSLKLPNLVEIQTDSFKWF----------QEKGIREVFEDIYP 106

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           IT F+    LEFV   FD PK+D D+   RD  YA PL+ TLRL+          K   +
Sbjct: 107 ITNFNDTLSLEFVDCRFDEPKYDADESKERDAVYAAPLRATLRLV---------NKKTGE 157

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK   ++MGD PLMT  GTFV+ G +R++VSQL RSPG +F +   +    GK ++  ++
Sbjct: 158 IKTSEVFMGDFPLMTDSGTFVVNGAERVIVSQLVRSPGAYFGNGTDKI---GKTVFNGQV 214

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY--SQR 241
           IP +G W++ E D+KD+++VRIDR++K+P T  L ALG+ S E+I+  F        +  
Sbjct: 215 IPSRGTWLEFENDAKDVLNVRIDRQKKIPGTILLRALGLSSNEDIIEVFGEHQFLYNTFE 274

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGIT 299
            D       A   +           +D    ++ +         L K+ + K  K L + 
Sbjct: 275 KDPTHNTDDALMEIYSKLRPGEPATLDGANSLLFARFFDPKRYDLAKAGRFKLRKKLSLL 334

Query: 300 SDCLCGLYVAEDIVNGETGEIYIE--AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            D +    +AED+V+ +   +  E         + L+ +F +      I   +++++N  
Sbjct: 335 -DRIADRVLAEDVVDVDGNVVMTEGTKITKDKLEILKPVFEAGAHTREIKTNENMHSNHT 393

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I+   V           +    +       T S   + ++++    D YD          
Sbjct: 394 IQVLDVYTDESKSIKMRVIGTDLSLDSKFVTISDFIAAYSYMLNLVDIYD---------- 443

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
              + D   + R                L +  G +DDID+LGNRRVR+VGE+++NQ+R+
Sbjct: 444 ---SQDLAAEDRV--------------SLMSRIGLLDDIDHLGNRRVRTVGELVQNQFRI 486

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER +KER+S  + DS+ PQ L N +P+ +A+ EFF SSQLSQ  + +N L+ +T+
Sbjct: 487 GLSRMERVVKERMSLAEDDSMTPQSLTNIRPLTAAIKEFFASSQLSQFMDQINPLAELTN 546

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG++R RAG E+RDVHP+HYGRICP ET EG NIGL+S+L S+A+VN YGF
Sbjct: 547 KRRLSALGPGGLSRDRAGYEVRDVHPSHYGRICPIETPEGPNIGLISTLASYAKVNEYGF 606

Query: 598 IETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           IETPYRKV +  +  +D+ YL+A EE+N  IAQA    DE+    +E V  R  GE I+ 
Sbjct: 607 IETPYRKVNNCVIDEDDIRYLTADEEKNYIIAQAKVKTDENDRIIDEQVISRHLGENIMA 666

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             E+IDFID SPKQ+VS+A+S IPFLENDD+ R LMGCNMQRQAVPLL   AP+VGTGME
Sbjct: 667 KPEEIDFIDISPKQIVSVASSCIPFLENDDATRALMGCNMQRQAVPLLNPHAPYVGTGME 726

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A+ SGAA+VAK  G V+ VDA +I++           SG   Y+L+KF  SN  TC+
Sbjct: 727 FQAARDSGAAVVAKEEGTVKYVDAKKIIV--------EGESGEKTYKLLKFTVSNAGTCI 778

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           N RP+V  GD V +  ++ADGP+ + G+LALG+N+LV FM W+GYN+ED+++++E++V E
Sbjct: 779 NHRPIVMAGDHVLKGQVLADGPAMEQGELALGQNVLVGFMTWNGYNYEDAVIMNEKLVKE 838

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D +TSIHI+E+ +  RDTKLGPEEITRDIPNV E+   N+DE GII VGAEV  GDILVG
Sbjct: 839 DYYTSIHIQEYTIECRDTKLGPEEITRDIPNVGEDARSNLDENGIIRVGAEVKEGDILVG 898

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K+TPKG++ ++ EEKLL AIFGEK+ +V+D SLRVP G SG V  +R+F R G D+   +
Sbjct: 899 KVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGSGIVHRIRVFTRRGKDRKTEN 958

Query: 957 ISVEREQIELLARDKDD 973
              E   +     ++DD
Sbjct: 959 KYGEANSLAYKEVERDD 975



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 248/1059 (23%), Positives = 383/1059 (36%), Gaps = 109/1059 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++    + ++ NT   D   +  DAL++IY  +RPG+ +T   A S+    FFD  +YDL
Sbjct: 260  IEVFGEHQFLYNTFEKDPTHNTDDALMEIYSKLRPGEPATLDGANSLLFARFFDPKRYDL 319

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            +  GR K+  +L+L      R   +     ++ +  ++   +GT    D L         
Sbjct: 320  AKAGRFKLRKKLSLL----DRIADRVLAEDVVDVDGNVVMTEGTKITKDKL--------- 366

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E+LK  +  G     R IK   +         Q L        ++      + LS   + 
Sbjct: 367  EILKPVFEAGAH--TREIKTNENMHSNH--TIQVLDVYTDESKSIKMRVIGTDLSLDSKF 422

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            V     I     +  L     +      E R    +  G +   +      +  V  L  
Sbjct: 423  VTISDFIAAYSYMLNLVDIYDS-QDLAAEDRVSLMSRIGLLDDIDHLGNRRVRTVGEL-- 479

Query: 589  FARVNAYGFIETPYRKVCDGKVTND-----------VVYLSAMEEENRYIAQANSSLDED 637
              +      +    R V +     +           +  L+A  +E    +Q +  +D+ 
Sbjct: 480  -VQNQFRIGLSRMERVVKERMSLAEDDSMTPQSLTNIRPLTAAIKEFFASSQLSQFMDQI 538

Query: 638  G---SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  T +          +   R   +  D  P     I     P   N      L   
Sbjct: 539  NPLAELTNKRRLSALGPGGLSRDRAGYEVRDVHPSHYGRICPIETPEGPNIGLISTLASY 598

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                +   +                                  + A   V       +  
Sbjct: 599  AKVNEYGFIETPYRKVNN------CVIDEDDIRYLTADEEKNYIIAQAKVKTDENDRIID 652

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRN--DIIADGPSTDLGDLALGRN 810
                          +  +   ++  P  +V V         +  A               
Sbjct: 653  EQVISRHLGENIMAKPEEIDFIDISPKQIVSVASSCIPFLENDDATRALMGCNMQRQAVP 712

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +L    P+ G   E                                  E+  + +     
Sbjct: 713  LLNPHAPYVGTGMEFQAARDSGAAVVAKEEGTVKYVDAKKIIVEGESGEKTYKLLKFTVS 772

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                 I+   I+  G  V  G +L        +  +   + +L         +  D  + 
Sbjct: 773  NAGTCINHRPIVMAGDHVLKGQVLADGP-AMEQGELALGQNVLVGFMTWNGYNYEDAVIM 831

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSR 985
                V            + I+  +  +  E     I  +  D     DE  I+      +
Sbjct: 832  NEKLVKEDYYTSIHIQEYTIECRDTKLGPEEITRDIPNVGEDARSNLDENGIIRVGAEVK 891

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR---SQWWQFAVQDEKVQRNVESLKVQY 1042
              +IL G+    G         L   +  E  R       +       +   +     + 
Sbjct: 892  EGDILVGKVTPKGQAELSAEEKLLLAIFGEKSREVKDNSLRVPHGGSGIVHRIRVFTRRG 951

Query: 1043 ETSKSILE-DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +  K+  +     +   K    DD+ PGV +V+KV++  KR I  GDKM+GRHGNKG++S
Sbjct: 952  KDRKTENKYGEANSLAYKEVERDDLQPGVNKVIKVYIVQKRKISEGDKMSGRHGNKGVIS 1011

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP EDMP L+DGTP+DI+LNPLGVPSRMN+GQ+ E H                     
Sbjct: 1012 KILPTEDMPHLQDGTPLDIMLNPLGVPSRMNIGQVLELH--------------------- 1050

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                            L  A +   G   +TP FDG + + + +
Sbjct: 1051 --------------------------------LGYAARQLGGQYFATPAFDGINSKDLEN 1078

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +++ A + E+G+  +  G TGE FD  V+VG +YM+KL HMV DK++ARS G YSLVTQQ
Sbjct: 1079 IMKEAGMPENGKQKVISGKTGEYFDNEVSVGIMYMIKLCHMVDDKLHARSVGPYSLVTQQ 1138

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW ++AYGAAY L+E+LT+KSDDVVGR + YE+IV G    E 
Sbjct: 1139 PLGGKAQNGGQRFGEMEVWALEAYGAAYTLREILTVKSDDVVGRVKTYEAIVKGQKLPEP 1198

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAK-MEEIPD 1379
            G PESF VL KE+QAL L I L +           E  D
Sbjct: 1199 GLPESFRVLKKELQALALDIRLLDDEGNEINVGNIEDED 1237


>gi|253581641|ref|ZP_04858865.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium varium ATCC 27725]
 gi|251835990|gb|EES64527.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium varium ATCC 27725]
          Length = 1166

 Score =  767 bits (1981), Expect = 0.0,   Method: Composition-based stats.
 Identities = 418/980 (42%), Positives = 601/980 (61%), Gaps = 87/980 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FG+  E   +P  +E Q  SY+ FL    AP+ R ++GL++AF+ +FP+ + 
Sbjct: 2   GKLVERLNFGRIKERGTMPHFLEFQLDSYEDFLQAKEAPNNRKDKGLESAFREIFPVESS 61

Query: 69  SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           +G   LE+VSYE    +PP  D  +C  R  TY+  LK+ LRLI          KS  +I
Sbjct: 62  NGDIKLEYVSYELHEAEPPLNDELECKKRGKTYSTSLKVRLRLIN--------KKSGNEI 113

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           +E  +Y G++P+MT+ GTF+I G +R+VVSQLHRSPG+ F+ +      +GK L++ +II
Sbjct: 114 QESLVYFGEVPMMTERGTFIINGAERVVVSQLHRSPGVSFNKEI--NIQTGKDLFSGKII 171

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIV------ 237
           P +G W++ E D  D + ++IDR++KV  T FL A+    ++ EI   F           
Sbjct: 172 PYKGTWLEFETDKNDFLSIKIDRKKKVLATVFLKAIDFFNNNTEIKDYFLETKELDLASI 231

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           + +  +             G+ +   + D +TGE + E+   +   L++ + E  ++ + 
Sbjct: 232 FQKYKNKDELLSVIRTRFEGSFIKEDIYDDETGEVIAEADAVIDEALIEKMIEFKIEKVV 291

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                     +A  ++N  T                                        
Sbjct: 292 YWEVKPEDKLLANTVLNDST---------------------------------------- 311

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                       +++A+ ++++ +RPGD+ T   A S+   +FF+  +YDL  VGR KMN
Sbjct: 312 ----------LTKEEAVTEVFKKLRPGDLVTVESARSLIRQMFFNPQRYDLEPVGRYKMN 361

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RL L+ P+D   + K+DII  +K +++L NG G  DDIDNL NRRVR VGE+L  Q + 
Sbjct: 362 KRLKLNVPEDEILLTKDDIIGTMKYVINLNNGNGHTDDIDNLSNRRVRGVGELLLMQIKA 421

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL +M + +KE+++  D +++  Q L+N +P+ + + +FF S QLSQ  +  N L+ +TH
Sbjct: 422 GLSKMGKMVKEKMTVQDSETLTSQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLAELTH 481

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGF
Sbjct: 482 KRRISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINKYGF 541

Query: 598 IETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           IETPY KV DGK   + + YL+A EEE  +IAQA++ + EDGS   + V CR   E + +
Sbjct: 542 IETPYVKVVDGKADFDQIDYLAADEEEGLFIAQADTKIGEDGSLLGD-VVCRFGHEIVSI 600

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             EK+D++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAP++GTG+E
Sbjct: 601 SGEKVDYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLE 660

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SGA +++K  G V  VDA +I+I       +        YRL+ F+RSNQ+ C+
Sbjct: 661 RKVAVDSGAVVISKTDGKVVYVDAQKIII-------EDPEGKEHKYRLLNFERSNQSMCL 713

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +Q PLV  G+EV+   +IADGP+T  GDLALGRN+L+AFMPW GYN+ED++LIS+R+  +
Sbjct: 714 HQTPLVSPGEEVKAGGVIADGPATKGGDLALGRNILMAFMPWEGYNYEDAILISDRLRKD 773

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIH+EE+E+ AR+TKLG EEITR+IPN+SEE L+ +D  GII +G+EV PGDILVG
Sbjct: 774 DVFTSIHVEEYEIEARNTKLGDEEITREIPNISEEALRKLDSKGIITIGSEVGPGDILVG 833

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------G 949
           K  PKGE+    EEKLLRAIFGEKA DVRDTSLR+P G  GTVV++   +R        G
Sbjct: 834 KTAPKGETEPPAEEKLLRAIFGEKARDVRDTSLRMPHGSKGTVVEILELSRENGDELKAG 893

Query: 950 IDKNERSISVEREQIELLAR 969
           ++K  R +  E+ +I +  +
Sbjct: 894 VNKAIRVLVAEKRKITVGDK 913



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 200/612 (32%), Positives = 276/612 (45%), Gaps = 76/612 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V  
Sbjct: 614  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLERKVAVDSGAVVIS 673

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +   + + +  +   G E   R +          + +  ++  G EV  G ++  
Sbjct: 674  KTDGKVVYVDAQKIIIEDPEGKEHKYRLLNFERSNQSMCLHQTPLVSPGEEVKAGGVIAD 733

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                KG         L+  +   G    D    S R+       S  V +  I  R+   
Sbjct: 734  GPATKGGDLALGRNILMAFMPWEGYNYEDAILISDRLRKDDVFTSIHVEEYEIEARNTKL 793

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E  I+ E   I   A  K D + I+         +IL G+ A  G         L   
Sbjct: 794  GDEE-ITREIPNISEEALRKLDSKGIITIGSEVGPGDILVGKTAPKGETEPPAEEKLLRA 852

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+     +    + +   + +  +        GD++  GV 
Sbjct: 853  IFGEKARD-----------VRDTSLRMPHGSKGTVVEILELSRE------NGDELKAGVN 895

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 896  KAIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 955

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 956  NIGQVLEVHLGMAM---------------------------------------------- 969

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                    +  G  ++TPVFDGA EE +   L       SG+  LYDG TGE FD PVTV
Sbjct: 970  ------GNYNGGTHIATPVFDGASEEQVKDYLEKLGFPRSGKVDLYDGRTGEKFDNPVTV 1023

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1024 GRMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1083

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+ YE+I+ G +  E   PESF VL+KE QAL L ++L +      
Sbjct: 1084 QEMLTVKSDDVTGRTKTYEAIIKGEEMPEPDLPESFKVLLKEFQALALDVELFDKDDNVI 1143

Query: 1372 AKMEEIPDFNKC 1383
               EE+   +  
Sbjct: 1144 NVDEELNKEDMT 1155


>gi|257470023|ref|ZP_05634115.1| DNA-directed RNA polymerase beta chain [Fusobacterium ulcerans ATCC
           49185]
 gi|317064248|ref|ZP_07928733.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium ulcerans ATCC 49185]
 gi|313689924|gb|EFS26759.1| bifunctional DNA-directed RNA polymerase subunit beta
           [Fusobacterium ulcerans ATCC 49185]
          Length = 1166

 Score =  767 bits (1981), Expect = 0.0,   Method: Composition-based stats.
 Identities = 419/980 (42%), Positives = 601/980 (61%), Gaps = 87/980 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R  FG+  E   +P  +E Q  SY+ FL    AP+ R ++GL++AF+ +FP+ + 
Sbjct: 2   GKLVERLNFGRIKERGTMPHFLEFQLDSYEDFLQAKEAPNNRKDKGLESAFREIFPVESS 61

Query: 69  SGAAMLEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           +G   LE+VSYE    +PP  D  +C  R  TY+  LK+ LRLI          KS  +I
Sbjct: 62  NGDIKLEYVSYELHEAEPPLNDELECKKRGKTYSTSLKVRLRLIN--------KKSGNEI 113

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           +E  +Y G++P+MT+ GTF+I G +R+VVSQLHRSPG+ F+ +      +GK L++ +II
Sbjct: 114 QESLVYFGEVPMMTERGTFIINGAERVVVSQLHRSPGVSFNKEI--NIQTGKDLFSGKII 171

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIV------ 237
           P +G W++ E D  D + ++IDR++KV  T FL A+    ++ EI   F           
Sbjct: 172 PYKGTWLEFETDKNDFLSIKIDRKKKVLATVFLKAIDFFNNNTEIKDYFLETKELDLASI 231

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           + +  +             G+ +   + D +TGE + E+   +   L++ + E  ++ + 
Sbjct: 232 FQKYKNKDELLSVIRTRFEGSFIKEDIYDDETGEVIAEADAVIDEALIEKMIEFKIEKVT 291

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                     +A  ++N  T                                        
Sbjct: 292 YWEVKPEDKLLANTVLNDST---------------------------------------- 311

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                       +++A+ ++++ +RPGD+ T   A S+   +FF+  +YDL  VGR KMN
Sbjct: 312 ----------LTKEEAVTEVFKKLRPGDLVTVESARSLIRQMFFNPQRYDLEPVGRYKMN 361

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RL L+ P+D   + K+DII  +K +++L NG G  DDIDNL NRRVR VGE+L  Q + 
Sbjct: 362 KRLKLNVPEDEILLTKDDIIGTMKYVINLNNGNGHTDDIDNLSNRRVRGVGELLLMQIKA 421

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL +M + +KE+++  D +++  Q L+N +P+ + + +FF S QLSQ  +  N L+ +TH
Sbjct: 422 GLSKMGKMVKEKMTVQDSETLTSQSLLNTRPLNALILDFFGSGQLSQFMDQSNPLAELTH 481

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ SL  +A++N YGF
Sbjct: 482 KRRISALGPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLAIYAKINKYGF 541

Query: 598 IETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           IETPY KV DGK   N + YL+A EEE  +IAQA++ + EDGS   + V CR   E + +
Sbjct: 542 IETPYVKVIDGKADFNQIDYLAADEEEGLFIAQADTKIGEDGSLLGD-VVCRFGHEIVGI 600

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             EK+D++D SPKQVVS++A LIPFLE+DD+NR LMG NMQRQAVPLL+ EAP++GTG+E
Sbjct: 601 SGEKVDYLDISPKQVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLE 660

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SGA +++K  G V  VDA +IVI       +        YR++ F+RSNQ+ C+
Sbjct: 661 RKVAVDSGAVVISKTDGKVVYVDAQKIVI-------EDPEGKEHKYRMLNFERSNQSMCL 713

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +Q PLV  G+EV+   +IADGP+T  GDLALGRN+L+AFMPW GYN+ED++LIS+R+  +
Sbjct: 714 HQTPLVSPGEEVKAGGVIADGPATRGGDLALGRNILMAFMPWEGYNYEDAILISDRLRKD 773

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DVFTSIH+EE+E+ AR+TKLG EEITR+IPN+SEE L+ +D  GII +G+EV PGDILVG
Sbjct: 774 DVFTSIHVEEYEIEARNTKLGDEEITREIPNISEEALRKLDSKGIITIGSEVGPGDILVG 833

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------G 949
           K  PKGE+    EEKLLRAIFGEKA DVRDTSLR+P G  GTVV++   +R        G
Sbjct: 834 KTAPKGETEPPAEEKLLRAIFGEKARDVRDTSLRMPHGSKGTVVEILELSRENGDELKAG 893

Query: 950 IDKNERSISVEREQIELLAR 969
           ++K  R +  E+ +I +  +
Sbjct: 894 VNKAIRVLVAEKRKITVGDK 913



 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 198/610 (32%), Positives = 276/610 (45%), Gaps = 76/610 (12%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V  
Sbjct: 614  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPYIGTGLERKVAVDSGAVVIS 673

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +   + + +  +   G E   R +          + +  ++  G EV  G ++  
Sbjct: 674  KTDGKVVYVDAQKIVIEDPEGKEHKYRMLNFERSNQSMCLHQTPLVSPGEEVKAGGVIAD 733

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +G         L+  +   G    D    S R+       S  V +  I  R+   
Sbjct: 734  GPATRGGDLALGRNILMAFMPWEGYNYEDAILISDRLRKDDVFTSIHVEEYEIEARNTKL 793

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E  I+ E   I   A  K D + I+         +IL G+ A  G         L   
Sbjct: 794  GDEE-ITREIPNISEEALRKLDSKGIITIGSEVGPGDILVGKTAPKGETEPPAEEKLLRA 852

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+     +    + +   + +  +        GD++  GV 
Sbjct: 853  IFGEKARD-----------VRDTSLRMPHGSKGTVVEILELSRE------NGDELKAGVN 895

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 896  KAIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 955

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 956  NIGQVLEVHLGMAM---------------------------------------------- 969

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                    +  G  ++TPVFDGA E+ +   L       SG+  LYDG TGE FD PVTV
Sbjct: 970  ------GNYNGGTHIATPVFDGASEDQVKDYLEKLGFPRSGKVDLYDGRTGEKFDNPVTV 1023

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +L
Sbjct: 1024 GRMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNIL 1083

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QEMLT+KSDDV GRT+ YE+I+ G +  E   PESF VL+KE QAL L ++L +      
Sbjct: 1084 QEMLTVKSDDVTGRTKTYEAIIKGEEMPEPDLPESFKVLLKEFQALALDVELFDQEDNVI 1143

Query: 1372 AKMEEIPDFN 1381
               EE+   +
Sbjct: 1144 NVDEELNKED 1153


>gi|269123261|ref|YP_003305838.1| DNA-directed RNA polymerase, beta subunit [Streptobacillus
           moniliformis DSM 12112]
 gi|268314587|gb|ACZ00961.1| DNA-directed RNA polymerase, beta subunit [Streptobacillus
           moniliformis DSM 12112]
          Length = 1152

 Score =  764 bits (1972), Expect = 0.0,   Method: Composition-based stats.
 Identities = 423/971 (43%), Positives = 607/971 (62%), Gaps = 77/971 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  FGK  +  ++P+ +E Q  SY+ FL    + D R  +GL+A F+  FPI + +G   
Sbjct: 8   RYSFGKIKDRGEMPNFLEFQLDSYEDFLQTKRSYDVRELKGLEAIFQETFPIESANGTLK 67

Query: 74  LEFVSYEF---DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           LE+  YE    + P  D  +C  R  TY+  LK+ LRL               +IKE  +
Sbjct: 68  LEYFGYEIHDSEAPLNDELECKKRGKTYSGQLKVRLRLT---------NNKTGEIKETLV 118

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT   TF+I G +R+VVSQLHRSPGI F+ +      +GK ++  +IIP +G 
Sbjct: 119 HFGDIPLMTDKATFIINGAERVVVSQLHRSPGITFNKEL--NMQTGKDMFIGKIIPYKGT 176

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFP 248
           W++ E D  D+++V+IDR++KV  + FL A+    ++ EI+  F+               
Sbjct: 177 WLEFETDKNDVLNVKIDRKKKVLASVFLKAIKFFENNSEIMDEFFEIKTIEL-------- 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                                 E + +  K +                 +    + G +V
Sbjct: 229 ----------------------EPIYKKYKNIE------------DAKSVIRTEIEGSFV 254

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            EDIVN +TGEI IE+   IDE +++++    I +I I  V   +    I  ++  D  K
Sbjct: 255 NEDIVNEKTGEIVIESESFIDEITVDKLIEYNIPEITIWEVKPEDR--MIAKSIKDDHTK 312

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPD 426
              +A++++++ ++PGD+ T   A ++   +FF+  +YD + VGR K+N RL L+    +
Sbjct: 313 SSDEAVVEVFKKIKPGDIVTVESAYNLIIPMFFNPQRYDFAPVGRYKINKRLKLEGEINE 372

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
               + K+D+IA I  L  L NG G+ DDIDNL NRRVR VGE+L  Q + G+ +M + +
Sbjct: 373 QDIVLTKKDVIATINYLKVLYNGGGSTDDIDNLSNRRVRGVGELLSIQIKGGVAKMSKMV 432

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KE++ + DI+++ PQ L+N KP+ + + EFF S QLSQ  +  N L+ +TH RR+SALG 
Sbjct: 433 KEKMQTQDINTLTPQSLLNTKPLNALILEFFGSGQLSQFMDQSNPLAELTHKRRISALGP 492

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++ +VN YGFIETP+ KV 
Sbjct: 493 GGLSRDRAGFEVRDVHNSHYGRVCPIETPEGPNIGLIASLSTYGKVNKYGFIETPFVKVK 552

Query: 607 DGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
           DG    ND+ YL+A EEE  +IAQA++++DE G   +  V CR   E + V +E++D +D
Sbjct: 553 DGVADFNDISYLAADEEEGLFIAQADTNIDEKGRLLDNDVTCRYGDEIVHVKKEQVDLMD 612

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS++A LIPFLE+DD+NR LMG NMQRQAVPLLK EAP+VGTG+E  VA  SGA
Sbjct: 613 VSPKQIVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPYVGTGLERKVAIDSGA 672

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +V+K  G V  VDA +I++               ++RL+ F++SNQ+ C++Q+P++ +G
Sbjct: 673 VLVSKVKGEVTYVDASKIIV-------TDKKGDEHLHRLLNFEKSNQSMCLHQKPIIDLG 725

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D+V + DI+ADGPST  GDL+LG+N+L+AFMPW GYNFED +LISER+  +DVFTS+HIE
Sbjct: 726 DKVNKGDILADGPSTSGGDLSLGKNILLAFMPWEGYNFEDGILISERLRKDDVFTSLHIE 785

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           EF++ AR TKLG EEITR+IPNVSEE L+N+D+ GI+ +GA V P DILVGK+TPKGES 
Sbjct: 786 EFDIEARTTKLGEEEITREIPNVSEEALRNLDKDGIVRIGAYVEPDDILVGKVTPKGESE 845

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD-------VRIFNRHGIDKNERSIS 958
              EE+LLRAIFGEKA DVRDTSLR+P GV GTVVD        +   + G++K  R   
Sbjct: 846 PPAEERLLRAIFGEKAKDVRDTSLRLPHGVKGTVVDVLVLSKENKDDLKAGVNKVVRVYV 905

Query: 959 VEREQIELLAR 969
            E+ +I +  +
Sbjct: 906 AEKRKIMVGDK 916



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 203/653 (31%), Positives = 298/653 (45%), Gaps = 74/653 (11%)

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            +    + Q D        +  +      G +I  + K Q    +    Q   V  G    
Sbjct: 569  EEGLFIAQADTNIDEKGRLLDNDVTCRYGDEIVHVKKEQVDLMDVSPKQIVSVSAGLIPF 628

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFE 848
                 A+              +L    P+ G   E  + I    V    V   +   +  
Sbjct: 629  LEHDDANRALMGSNMQRQAVPLLKTEAPYVGTGLERKVAIDSGAVLVSKVKGEVTYVDAS 688

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +    K G E + R +          + +  II +G +VN GDIL    +  G   ++ 
Sbjct: 689  KIIVTDKKGDEHLHRLLNFEKSNQSMCLHQKPIIDLGDKVNKGDILADGPSTSG-GDLSL 747

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN--ERSISVEREQIEL 966
             + +L A    +  +  D  L           D    + H  + +   R+  +  E+I  
Sbjct: 748  GKNILLAFMPWEGYNFEDGILI----SERLRKDDVFTSLHIEEFDIEARTTKLGEEEITR 803

Query: 967  LARDKDDE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               +  +E    LD++   R+   +   + + G    K  +   ++        +  +  
Sbjct: 804  EIPNVSEEALRNLDKDGIVRIGAYVEPDDILVGKVTPKGESEPPAE-------ERLLRAI 856

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              ++       SL++ +    ++++    +K  K    DD+  GV +VV+V+VA KR I 
Sbjct: 857  FGEKAKDVRDTSLRLPHGVKGTVVDVLVLSKENK----DDLKAGVNKVVRVYVAEKRKIM 912

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKM+GRHGNKG++SR+LP EDMP L+DGTPVD+ LNPLGVPSRMN+GQ+ E H     
Sbjct: 913  VGDKMSGRHGNKGVISRVLPVEDMPHLEDGTPVDVCLNPLGVPSRMNIGQVLEVH----- 967

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG  I  +                                                  
Sbjct: 968  --LGLAIGDMNK-----------------------------------------------Y 978

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            ++TPVFDGA EE + + L  A    +G+  L DG TGE FD PVTVG +YMLKL+H+V D
Sbjct: 979  IATPVFDGATEEDVKNYLEEAGYPRTGKVKLIDGRTGEYFDNPVTVGRMYMLKLHHLVED 1038

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+ +LQEMLT+KSDD+ GR
Sbjct: 1039 KMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGASNILQEMLTVKSDDINGR 1098

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            T+ YESI+ G    E   PESF VL+KE Q+LGL ++L N   +         
Sbjct: 1099 TKTYESIIKGQSMPEADAPESFKVLIKEFQSLGLDVNLYNKEGEKIELDNNFE 1151


>gi|1840152|gb|AAB47279.1| DNA-directed RNA polymerase homolog [Helicobacter pylori]
          Length = 880

 Score =  763 bits (1970), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/887 (44%), Positives = 585/887 (65%), Gaps = 29/887 (3%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+R  F K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI    
Sbjct: 8   KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEH 63

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IKDIKEQ 128
               LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IKDIKEQ
Sbjct: 64  NRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTRSGEKNGIKDIKEQ 123

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           SI++ ++PLMT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+
Sbjct: 124 SIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDR 182

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P
Sbjct: 183 GSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++    D L   ++
Sbjct: 243 FASLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILINRHL 299

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           AE +      E+ ++    +D+  LE+I    +++  I+   ++ ++A I ++ + D   
Sbjct: 300 AEPV--MVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFLADYES 357

Query: 369 ----------DRKDAL--LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                     D ++AL  + I++VM+PGD  T  VA+     LFFD ++YDL+ VGR+KM
Sbjct: 358 LKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKM 417

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N +L L  PD +  +  EDII  +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+  
Sbjct: 418 NHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477

Query: 477 LGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            GL++M+++IK++++++    DS+MP DL+N+K + S + EFF   QLSQ  +  N LS 
Sbjct: 478 SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSE 537

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN 
Sbjct: 538 VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            GFIE PY+KV DGKV  + +YL+A++E++  IA A++ +DE+G+   +L+  R  GE +
Sbjct: 598 LGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIV 657

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L  + K+  +D S   +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG
Sbjct: 658 LNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E ++A+ S  AI A RAG+VE++D+  I I           + +D Y L K  R+NQNT
Sbjct: 718 IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNT 773

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
             NQ P+VKVGD+V    IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ 
Sbjct: 774 SFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERIT 833

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            +D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI
Sbjct: 834 KDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGI 880


>gi|227486350|ref|ZP_03916666.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235761|gb|EEI85776.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
          Length = 1226

 Score =  761 bits (1965), Expect = 0.0,   Method: Composition-based stats.
 Identities = 415/964 (43%), Positives = 592/964 (61%), Gaps = 57/964 (5%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA+          R  F K PE++D+P+L++VQK SY+ F+           EGL    +
Sbjct: 1   MAQYHKKLYGKTERMSFSKFPEVLDLPNLLKVQKDSYEWFI----------KEGLGEILE 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            + PI  ++G   LEF  +EF+  PK+ + +  ++DLTYA  LK+   L           
Sbjct: 51  DISPIEDYNGKLSLEFTGFEFEEEPKYSLKEAKYKDLTYARDLKVMAIL---------FN 101

Query: 120 KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
           K   +IK Q ++MGD P+MT   TFVI G +R++VSQL RSPG+++  +  +   SG   
Sbjct: 102 KETGEIKRQEVFMGDFPMMTDSATFVINGAERVIVSQLVRSPGVYYAEETDK---SGDKQ 158

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVY 238
           Y+  +IP++G W++ + D+   ++VR+DR RK+P T+ + AL  D++E I+         
Sbjct: 159 YSSTVIPNRGAWIEFDTDASHTVNVRLDRTRKLPATTLVRALLFDTDEEIIKALGDTPHL 218

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLG 297
               +      S   L+   +       +  G+   +ES   L + LL   +   +  +G
Sbjct: 219 RNTLEKENSENSEEALIEIYR------KLKPGDPASLESATTLINNLLFDDRRYDLARVG 272

Query: 298 ITSD--------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                        + G   AEDIV+ ETGEI+++AG+VI E   + I +S I  + I  +
Sbjct: 273 RYKYNLKLALAPRIAGEIAAEDIVDTETGEIFVKAGEVISEDIAKAIENSGIVSVDIRKL 332

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +S      +R       +    + L  +       D+     +E ++  +   ++  D +
Sbjct: 333 NSEEEEIVLRIVGNNFVDIHAFERLEGL-------DIDFDEFSEKVYYPVM--TEIIDEA 383

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 + M          +HI K DI+A++    +L  G G  DDID+LGNRRVR VGE
Sbjct: 384 ETDEELIKMMQKRKKELSPKHITKSDILAVVNYQFNLFEGVGDTDDIDHLGNRRVRGVGE 443

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER+++ D D   PQ LIN KPV + + EFF SSQLSQ  +  
Sbjct: 444 LLQNQFRVGLARMERVVRERMTTQDPDIATPQGLINIKPVTAVIKEFFGSSQLSQFMDQT 503

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N +S +TH RRLSALG GG++R RAGVE+RDVH +HYGRICP ET EG NIGL++SLT++
Sbjct: 504 NPMSELTHKRRLSALGPGGLSRDRAGVEVRDVHDSHYGRICPIETPEGPNIGLITSLTTY 563

Query: 590 ARVNAYGFIETPYRKVCDG-KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           AR+N YGFIETPYR V +G  VT+++ YL+A  E++  IAQAN  LDE+  F  E V  R
Sbjct: 564 ARINKYGFIETPYRVVKEGGVVTDEIDYLTADIEDDYIIAQANEPLDENNRFVNERVSGR 623

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              GE  + PR+ I ++D SP+Q+VS+ ASLIPFLENDDS R LMG NMQRQAVPL+K++
Sbjct: 624 GYRGENDIYPRDSIQYMDVSPQQIVSVGASLIPFLENDDSTRALMGANMQRQAVPLIKSQ 683

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E   AK SG  +V+K  G V  V A +I +++           V  Y L+KF
Sbjct: 684 APIVATGIEHRAAKDSGVCVVSKTDGKVVYVAADKIKVKT-------PKGEVITYELLKF 736

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +R+NQ T +NQRP+VK+ ++V+   ++ADGPSTD G+LALG+N+L+AF  W GYNFED+M
Sbjct: 737 ERANQGTTINQRPIVKLDEDVKEGQVLADGPSTDNGELALGKNILIAFTTWEGYNFEDAM 796

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L++E +V  DV TS+HIEE E  AR+TKLG EEIT+DIPNV ++  K++DE G+I +GAE
Sbjct: 797 LLNEELVINDVLTSVHIEEHECEARETKLGAEEITKDIPNVGDDMKKDLDENGVIRIGAE 856

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK++PKGE+ ++PEE+LLRAIFGEKA +VRDTSL+VP G  G VVDV+ +N+
Sbjct: 857 VASGDILVGKVSPKGETELSPEERLLRAIFGEKAREVRDTSLKVPHGEKGIVVDVKEYNK 916

Query: 948 HGID 951
              D
Sbjct: 917 KDGD 920



 Score =  475 bits (1223), Expect = e-131,   Method: Composition-based stats.
 Identities = 182/503 (36%), Positives = 257/503 (51%), Gaps = 62/503 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +  +V  G +L    +      +   + +L A    +  +  D  L     V   V+
Sbjct: 750  IVKLDEDVKEGQVLADGPSTDN-GELALGKNILIAFTTWEGYNFEDAMLLNEELVINDVL 808

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   H  +  E  +  E E  + +    DD +  LD N   R+   +   + + G  
Sbjct: 809  TSVHIEEHECEARETKLGAE-EITKDIPNVGDDMKKDLDENGVIRIGAEVASGDILVGKV 867

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K  T LS +        +  +    ++  +    SLKV +     +++ +  NK +  
Sbjct: 868  SPKGETELSPE-------ERLLRAIFGEKAREVRDTSLKVPHGEKGIVVDVKEYNKKD-- 918

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++ PGV +V++V+VA KR I  GDKM GRHGNKG+VSRILP EDMPFL DGTP+ I
Sbjct: 919  --GDELSPGVNKVIRVYVATKRKIMVGDKMCGRHGNKGVVSRILPREDMPFLPDGTPIQI 976

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNPLG+PSRMN+GQ+ E H+G A   LG KI + + D   + +I  +    +KV    +
Sbjct: 977  CLNPLGIPSRMNLGQVLEVHMGLAARTLGWKIATPVFDGAMDTEIEDVLEEAKKVAPFVN 1036

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
             T KI                                              G++      
Sbjct: 1037 KTGKIRL------------------------------------------RDGRT------ 1048

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
             G  F  PVTVG +YMLKL+HMV +K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 1049 -GLEFQNPVTVGVMYMLKLHHMVEEKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1107

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGA++ LQE+LT+KSDDV GR + YESIV G +  E GTPESF VLVKE+Q+L L 
Sbjct: 1108 ALEAYGASHTLQEILTVKSDDVTGRVKTYESIVKGENIPEPGTPESFKVLVKELQSLALD 1167

Query: 1361 IDLENSRTKNSAKMEEIPDFNKC 1383
            ++L +   +     E I D ++ 
Sbjct: 1168 VELLDEDGQVVELKENIDDQDRF 1190


>gi|15639233|ref|NP_218681.1| DNA-directed RNA polymerase subunit beta [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025474|ref|YP_001933246.1| DNA-directed RNA polymerase subunit beta [Treponema pallidum subsp.
           pallidum SS14]
 gi|6094125|sp|O83269|RPOB_TREPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|3322511|gb|AAC65229.1| DNA-directed RNA polymerase, beta subunit (rpoB) [Treponema
           pallidum subsp. pallidum str. Nichols]
 gi|189018049|gb|ACD70667.1| DNA-directed RNA polymerase, beta subunit [Treponema pallidum
           subsp. pallidum SS14]
 gi|291059645|gb|ADD72380.1| DNA-directed RNA polymerase, beta subunit [Treponema pallidum
           subsp. pallidum str. Chicago]
          Length = 1178

 Score =  759 bits (1959), Expect = 0.0,   Method: Composition-based stats.
 Identities = 402/958 (41%), Positives = 580/958 (60%), Gaps = 73/958 (7%)

Query: 11  GRVRKFFGK-NPEIIDIPDLIEVQKASYDHFLM---------MNIAPDERPNEGLQAAFK 60
              R + G+     +DIPDLIE+Q  SYD FL            +    R   GL+  FK
Sbjct: 7   KTHRVYVGRDVRNFMDIPDLIEIQLRSYDTFLHGARNTPSGADTLISGTREELGLEDVFK 66

Query: 61  SVFPITAFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           + FPI + +G   LE+ SY  D    KF   +C  + LTYA+PLK  + L   +      
Sbjct: 67  TTFPIESSTGDMTLEYQSYSLDEKNIKFSEAECKQKGLTYAIPLKALVDLRFNN------ 120

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                +I+ + IYMGD+P MT+ GTF+I G +R+VVSQ+HRSPG+ F H+K +    G+ 
Sbjct: 121 ---TGEIRRKDIYMGDIPKMTERGTFIINGAERVVVSQIHRSPGVVFSHEKDKE---GRE 174

Query: 179 LYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKI 236
           +++ RIIP +G W++ E D  KD+I+ ++D++R++  T FL AL  ++ E+I+  FY   
Sbjct: 175 VFSSRIIPYRGSWLEFEIDQKKDLIYAKLDKKRRILGTVFLRALHYETREQIIEAFY--- 231

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSL-VDIDTGE--QVIESGKKLTSGLLKSLKEKGV 293
             +      C   +  +L+ G  ++ S+ V+ + GE   + ++G+K+   ++  L + G+
Sbjct: 232 --AIEKTPVCQDRAEYELLTGKILARSVTVENEQGETRVLYKAGEKIHPHVIDDLLQNGI 289

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
             + I +    G   +  ++N                                     + 
Sbjct: 290 CEVYIINLEAEGSLRSAVVIN------------------------------------CLE 313

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                 +         R++AL  +Y  +RP D  T   AE     +FF   +YDL  VGR
Sbjct: 314 REEMKFSKSGAQDELSREEALCIVYSALRPSDPMTMDAAEKDLQTMFFSPRRYDLGRVGR 373

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            K+N +   D+P     +  +DI+  +K L+ + +G    DDID+LGNRR+RSVGE++ N
Sbjct: 374 YKLNKKFRSDSPTTECTLTLDDIVNTMKFLIRMYSGDAQEDDIDHLGNRRIRSVGELMTN 433

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
             +   LRMER  KER+SS + +++ PQDLI+ KP+++A+ EFF +SQLSQ  + VN L+
Sbjct: 434 TLKTAFLRMERIAKERMSSKETETIKPQDLISIKPIMAAIKEFFGASQLSQFMDQVNPLA 493

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRL+ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ S+ ++ARVN
Sbjct: 494 ELTHKRRLNALGPGGLSRERAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSMANYARVN 553

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            YGF+E PY +V DG VT ++ YL AM+E+  YI Q ++++  DG    + V CR  G+ 
Sbjct: 554 GYGFLEVPYVRVRDGVVTKEIEYLDAMDEDRYYIGQDSTAVGPDGVIRVDHVSCRHRGDY 613

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                + I ++D SPKQ++S++ASLIPFLE+DD+NR LMG NMQRQ VPL+  E P VGT
Sbjct: 614 STRSPKDIQYMDVSPKQIISVSASLIPFLEHDDANRALMGSNMQRQGVPLIFPEPPRVGT 673

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME   A  SG  + AK+ G V  V + +IV+ S             +Y L+K+QR+NQ+
Sbjct: 674 GMEEKCAYDSGVLVKAKQDGTVAYVSSEKIVVCS---AAASGEEQEVVYPLLKYQRTNQD 730

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC +QRP+V VGD V+  D +ADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS R+
Sbjct: 731 TCYHQRPIVHVGDRVQVGDALADGPATYRGELALGRNILVGFVPWNGYNYEDAILISHRV 790

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED+FTS+HI+EF    R+TKLG E +T DIPN SE+ L N+D  GII +G++V  GD+
Sbjct: 791 VKEDMFTSVHIKEFSTEVRETKLGSERMTNDIPNKSEKNLDNLDAEGIIRIGSKVRAGDV 850

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           L+GKITPK ES  TPE +LL +IFGEKA +VRD+SLRVP GV GTV+DV+   R   D
Sbjct: 851 LIGKITPKSESETTPEFRLLNSIFGEKAKEVRDSSLRVPHGVEGTVIDVQRLRRSEGD 908



 Score =  426 bits (1094), Expect = e-116,   Method: Composition-based stats.
 Identities = 165/501 (32%), Positives = 232/501 (46%), Gaps = 71/501 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD L           +     +L         +  D  L     V   + 
Sbjct: 738  IVHVGDRVQVGDALADGPATYR-GELALGRNILVGFVPWNGYNYEDAILISHRVVKEDMF 796

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                      +  E  +  ER   ++  + + +    LD     R+   +   + + G  
Sbjct: 797  TSVHIKEFSTEVRETKLGSERMTNDIPNKSEKN-LDNLDAEGIIRIGSKVRAGDVLIGKI 855

Query: 1001 GFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
              K  +  + +  L++     +  +      +V   VE                   +  
Sbjct: 856  TPKSESETTPEFRLLNSIFGEKAKEVRDSSLRVPHGVEGTV-------------IDVQRL 902

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            +   GDD+ PGV  VVKV +A KR ++ GDKMAGRHGNKGIV+RILP EDMP+L DGTP+
Sbjct: 903  RRSEGDDLNPGVSEVVKVLIATKRKLREGDKMAGRHGNKGIVARILPEEDMPYLDDGTPL 962

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+ LNPLGVPSRMN+GQI E+ LG A + L +  +S +    +N  I            +
Sbjct: 963  DVCLNPLGVPSRMNIGQILESELGLAGLRLDEWYESPVFQSPSNEQIGEKLMQAGFPTNS 1022

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                             +    ++G     PVF                           
Sbjct: 1023 KV---------------MLRDGRTGDYFQNPVF--------------------------- 1040

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
                        VG IY +KL H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEME
Sbjct: 1041 ------------VGVIYFMKLAHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGEME 1088

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAA  LQE+LTIKSDD+ GR+++YE+IV G  +  TG PESFNVLV+E++ L 
Sbjct: 1089 VWALEAYGAANTLQELLTIKSDDMHGRSKIYEAIVKGEASSPTGIPESFNVLVQELRGLA 1148

Query: 1359 LSIDLENSRTKNSAKMEEIPD 1379
            L   + +++ K     E   +
Sbjct: 1149 LDFTIYDAKGKQIPLTERDEE 1169


>gi|257458178|ref|ZP_05623332.1| DNA-directed RNA polymerase, beta subunit [Treponema vincentii ATCC
           35580]
 gi|257444472|gb|EEV19561.1| DNA-directed RNA polymerase, beta subunit [Treponema vincentii ATCC
           35580]
          Length = 1165

 Score =  759 bits (1959), Expect = 0.0,   Method: Composition-based stats.
 Identities = 403/950 (42%), Positives = 579/950 (60%), Gaps = 66/950 (6%)

Query: 10  LGRVRKFF-GK-NPEIIDIPDLIEVQKASYDHFLMMNIAPDER--PNEGLQAAFKSVFPI 65
              V + + GK     +++P+LI++Q +SY+ FL              GL+  F++ FPI
Sbjct: 4   RKTVNRQYIGKNIQNFMELPNLIDIQLSSYEKFLRRGTHQSGNTSEEVGLEDVFRTTFPI 63

Query: 66  TAFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            + +G   LE+ SY  D    KF   +C  + LTYA+PLK  + L+              
Sbjct: 64  ESPNGDMTLEYQSYTLDENDIKFSEYECKQKGLTYAIPLKAQIDLVFN---------QTG 114

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I+ +SIYMGD+PLMT+ GTF+I G +R+VVSQ+HRSPG+ F HDKG        +Y+ R
Sbjct: 115 EIRRKSIYMGDIPLMTERGTFIINGAERVVVSQIHRSPGVIFSHDKG--------VYSSR 166

Query: 184 IIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQR 241
           IIP +G W++ E D  KD+I+ ++D+++++  T FL ALG ++ E+I+  FY   V    
Sbjct: 167 IIPYRGSWLEFEIDQKKDLIYAKLDKKKRILGTLFLRALGYETREQIIDFFYKTEVLPVS 226

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                +      +       +      T   + ++G+K+   ++  L++  +  + +   
Sbjct: 227 EGATEYDKLVGRVFAKRITVADESGERT---LYQAGEKIHPHVVDELRQNHISEVTVIDF 283

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              G   +  I+N    E    A     ++                              
Sbjct: 284 KKEGSLDSPVIINCFEREEIRFADAAKGQE------------------------------ 313

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                   +++AL  +Y  ++PGD  T   AE     +FF S +YDL  VGR K+N + +
Sbjct: 314 ------PTKEEALSVVYAALKPGDPMTVEAAEKDLTSMFFSSRRYDLGRVGRYKLNKKFD 367

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            + P +   +  +DI+  +K L+ +  G  +IDDID+LGNRRVRSVGE++ N  +   LR
Sbjct: 368 YEHPVEECTLILDDIVNTMKYLIQVYIGDASIDDIDHLGNRRVRSVGELMTNTLKTAFLR 427

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER  +ER+ S +I+++ PQ+LI+ KP+V+ + EFF +SQLSQ  + VN L+ +TH RRL
Sbjct: 428 MERIARERMGSKEIETIKPQELISIKPIVATIKEFFGASQLSQFMDQVNPLAELTHKRRL 487

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           +ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ S+ S+A VN YGF+E P
Sbjct: 488 NALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSMASYAHVNDYGFLEAP 547

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           Y KV +G  T +V YLSAM+E+  YIAQ ++++  DG+ T E + CR  G+      +++
Sbjct: 548 YVKVVNGVATREVEYLSAMDEDKYYIAQVSTAVQSDGTITAEQIACRHQGDYTTRSSKEV 607

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            ++D SPKQ++S++ASLIPFLE+DD+NR LMG NMQRQ VPL+  E P VGTGME   A 
Sbjct: 608 QYMDVSPKQIISVSASLIPFLEHDDANRALMGSNMQRQGVPLVFPEPPRVGTGMEGKCAY 667

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  I AKR+G V+ V + +I I       + + + V  Y L+K+QR+NQ+TC +QRP+
Sbjct: 668 DSGVLIKAKRSGTVKFVSSEKISI--ESDAPEGTEAKVRDYTLLKYQRTNQDTCYHQRPV 725

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V VG  V   D+IADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS R++ ED+FTS
Sbjct: 726 VAVGQHVEVGDVIADGPATYQGELALGRNILVGFVPWNGYNYEDAILISRRVLKEDMFTS 785

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +HI+EF    R+TKLG E IT DIPN SE+ L N+D  GII +GA+V  GDIL+GKITPK
Sbjct: 786 VHIKEFTTEVRETKLGAERITSDIPNKSEKSLDNLDAEGIIRIGAQVRSGDILIGKITPK 845

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ES  TPE KLL +IFGEKA DVRD+SLRVP GV GTV+DV+   R   D
Sbjct: 846 NESETTPEFKLLNSIFGEKAKDVRDSSLRVPHGVEGTVIDVQRLKRSQGD 895



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 148/591 (25%), Positives = 216/591 (36%), Gaps = 81/591 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV---SEDVFTSIHIEEFEVMARDTKL 856
                    G  ++    P  G   E        ++              E   +  D   
Sbjct: 638  MGSNMQRQGVPLVFPEPPRVGTGMEGKCAYDSGVLIKAKRSGTVKFVSSEKISIESDAPE 697

Query: 857  GPEEITRD---IPNVSEEGLKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKL 912
            G E   RD   +            +  ++ VG  V  GD++  G  T +GE  +     +
Sbjct: 698  GTEAKVRDYTLLKYQRTNQDTCYHQRPVVAVGQHVEVGDVIADGPATYQGELALGRNILV 757

Query: 913  LRAIF-GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
                + G    D    S RV      T V ++ F     +    +  +  +      +  
Sbjct: 758  GFVPWNGYNYEDAILISRRVLKEDMFTSVHIKEFTTEVRETKLGAERITSDIPNKSEKSL 817

Query: 972  D--DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  D + I+      R  +IL G+         +  T     L++     +         
Sbjct: 818  DNLDAEGIIRIGAQVRSGDILIGKITPKN----ESETTPEFKLLNSIFGEKAKDVRDSSL 873

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V   VE                   +  K   GDD+ PGV   +KV +A KR +     
Sbjct: 874  RVPHGVEGTV-------------IDVQRLKRSQGDDLNPGVDEFIKVLIATKRKL----- 915

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
               R G+K                                 M                 G
Sbjct: 916  ---REGDK---------------------------------M-------------AGRHG 926

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K        + +       + L+  +       +++              +       P
Sbjct: 927  NKGIVARILPEEDMPYMEDGTPLDICLNPLGVPSRMNIGQILESELGLAGLRLDEWYEAP 986

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF     E I   L  A +  + +  L DG TG PF   V VG IY +KL H+V DK++A
Sbjct: 987  VFQSPTNEQIEKKLVEAGIPANSKVKLRDGRTGMPFQNDVFVGVIYFMKLAHLVDDKMHA 1046

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA  LQE+LTIKSDD+ GR+++Y
Sbjct: 1047 RSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQELLTIKSDDMHGRSKIY 1106

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            ESIV G      G PESFNVLV+E++ L L   + + + K     E   + 
Sbjct: 1107 ESIVKGQAATAAGIPESFNVLVQELRGLALDFMIYDEKGKQIPLTERDEEL 1157


>gi|325474853|gb|EGC78039.1| DNA-directed RNA polymerase subunit beta [Treponema denticola
           F0402]
          Length = 1167

 Score =  757 bits (1954), Expect = 0.0,   Method: Composition-based stats.
 Identities = 407/948 (42%), Positives = 589/948 (62%), Gaps = 62/948 (6%)

Query: 9   GLGRVRKFFGK-NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
           G    R+++GK  P  +++P+LI++Q  SY+ FL      DE   EGL++ F + FPI +
Sbjct: 5   GQKIDRRYYGKDVPNFMELPNLIDIQIQSYNKFLNKEKKTDETEIEGLESVFHTTFPIES 64

Query: 68  FSGAAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            +    L+++SY  D    KF   +C  + LTY+VPLK  + L           K  K+I
Sbjct: 65  TNEDMALQYLSYSLDYDSIKFSEIECKQKGLTYSVPLKAEIDL---------FFKETKEI 115

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           + ++IYMGD+PLMT+ GTF+I G +R+VVSQ+HRSPG+ F H+KG        +Y+ RII
Sbjct: 116 RRKNIYMGDIPLMTERGTFIINGAERVVVSQIHRSPGVIFSHEKG--------VYSSRII 167

Query: 186 PDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGD 243
           P +G W++ E D  K++I+ ++D ++++  T FL ALG D+ E+I+  FY         D
Sbjct: 168 PYRGTWLEFEIDQKKELIYAKLDSKKRILGTIFLRALGYDTREKIIDLFYKTKTAKISPD 227

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
              +     +L+         V  + GE+             + + + G K      D L
Sbjct: 228 RTEY----EELIGQVLARDVYVKGEDGEK-------------RKMHQAGEKIHPHNIDDL 270

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
               V +  +    G+  +++  +I+    EEI ++                        
Sbjct: 271 IQNDVKKITIIDFKGKDSLDSQIIINCFEREEIKYTPD--------------------PA 310

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            +     +DAL  +Y V+RPGD  T+  A+   + +FF + +YD+  VGR K+N + +  
Sbjct: 311 VNDEPTVEDALNAVYSVIRPGDPITYENAKEDLHNMFFTARRYDIGKVGRYKLNKKFDYS 370

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                  + +EDI   +K L+ +  G+ +IDDID+LGNRR+RSVGE++ +  +    RME
Sbjct: 371 DDVKGTTLIEEDIFKTMKFLIKVYIGEESIDDIDHLGNRRIRSVGEIMTDVLKKAFSRME 430

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R  ++R+SS ++D++ PQDLI+ KP+V+A+ EFF +SQLSQ  + VN L+ +TH RRL+A
Sbjct: 431 RIARDRMSSKEMDTIKPQDLISIKPIVAAIKEFFGASQLSQFMDQVNPLAELTHKRRLNA 490

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+R+VH THYGR+CP ET EG NIGL+ S+ ++ARVN YGF+E PY 
Sbjct: 491 LGPGGLSRDRAGFEVREVHYTHYGRMCPIETPEGPNIGLIVSMANYARVNEYGFLEAPYV 550

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV +G  T ++ YLSAM+E+  +I Q +S++ +DG    + V CR  G+   +  + I +
Sbjct: 551 KVVNGVATREIEYLSAMDEDKYFIGQVSSAIGKDGKINTDQVSCRKLGDYTSISPKDIQY 610

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ++S++ASLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTGME   A  S
Sbjct: 611 MDVSPKQIISVSASLIPFLEHDDANRALMGSNMQRQAVPLVFPEPPRVGTGMEKKCAYDS 670

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  + AKR+G VE V +  I+I   +G    +    D Y L+K+QR+NQ TC +QRP+V 
Sbjct: 671 GVLVKAKRSGKVEFVSSDTIIIAPEKG---KNKEDKDEYTLLKYQRTNQETCYHQRPIVN 727

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           VGD V+    IADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS R+V ED+FTSIH
Sbjct: 728 VGDTVKAGQPIADGPATYNGELALGRNILVGFVPWNGYNYEDAILISRRVVKEDMFTSIH 787

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           I+E     R+TKLG E++T DIPN SE+ L ++D  GII +G++V PGDILVGK+TPK E
Sbjct: 788 IKELSTDVRETKLGAEKMTCDIPNKSEKSLDDLDSEGIIRIGSKVKPGDILVGKVTPKSE 847

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           S  TPE KLL +IFGEKA +VRDTSLRVP G  GTV+DV+   R   D
Sbjct: 848 SDTTPEFKLLNSIFGEKAKEVRDTSLRVPHGTEGTVIDVQRLKRDQGD 895



 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 130/505 (25%), Positives = 197/505 (39%), Gaps = 69/505 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  G  +           +     +L         +  D  L     V   + 
Sbjct: 725  IVNVGDTVKAGQPIADGPATYN-GELALGRNILVGFVPWNGYNYEDAILISRRVVKEDMF 783

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                      D  E  +  E+   ++  +               + ++ L  +  +    
Sbjct: 784  TSIHIKELSTDVRETKLGAEKMTCDIPNK-------------SEKSLDDLDSEGIIRIGS 830

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEK 1059
              K   +L   +  +       +F + +       + ++          E    + +  K
Sbjct: 831  KVKPGDILVGKVTPKSESDTTPEFKLLNSIFGEKAKEVRDTSLRVPHGTEGTVIDVQRLK 890

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
               GDD+ PGV  VVKV +A KR +        R G+K                      
Sbjct: 891  RDQGDDLSPGVDEVVKVLIATKRKL--------REGDK---------------------- 920

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                                         G K        + +       + L+  +   
Sbjct: 921  ------------------------MAGRHGNKGLVARILPEEDMPYMEDGTPLDICLNPL 956

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                +++              K      +PVF+    E I + L+ A    S +  L DG
Sbjct: 957  GVPSRMNIGQILESELGLAGLKLNEWYESPVFESPSMEQIEAKLKEAGYPTSSKVKLRDG 1016

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            LTG  F+  V VG IY LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEV
Sbjct: 1017 LTGRLFENEVFVGVIYFLKLAHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEV 1076

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAA  LQE++TIKSDD+ GR+++YESIV G  +   G PESFNVLV+E++ L L
Sbjct: 1077 WALEAYGAANTLQELITIKSDDMHGRSKIYESIVKGEPSSSAGIPESFNVLVQELRGLAL 1136

Query: 1360 SIDLENSRTKNSAKMEEIPDFNKCE 1384
               + +++ +     E   +  K E
Sbjct: 1137 DFTIYDAKGQQIPLTERDEELIKRE 1161


>gi|42527922|ref|NP_973020.1| DNA-directed RNA polymerase subunit beta [Treponema denticola ATCC
           35405]
 gi|81411477|sp|Q73JJ7|RPOB_TREDE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|41818967|gb|AAS12939.1| DNA-directed RNA polymerase, beta subunit [Treponema denticola ATCC
           35405]
          Length = 1167

 Score =  755 bits (1950), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/948 (42%), Positives = 589/948 (62%), Gaps = 62/948 (6%)

Query: 9   GLGRVRKFFGK-NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
           G    R+++GK  P  +++P+LI++Q  SY+ FL      DE   EGL++ F + FPI +
Sbjct: 5   GQKIDRRYYGKDVPNFMELPNLIDIQIQSYNKFLNKEKKTDETEIEGLESVFHTTFPIES 64

Query: 68  FSGAAMLEFVSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            +    L+++SY  D    KF   +C  + LTY+VPLK  + L           K  K+I
Sbjct: 65  TNEDMALQYLSYSLDYDSIKFSEIECKQKGLTYSVPLKAEIDL---------FFKETKEI 115

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           + ++IYMGD+PLMT+ GTF+I G +R+VVSQ+HRSPG+ F H+KG        +Y+ RII
Sbjct: 116 RRKNIYMGDIPLMTERGTFIINGAERVVVSQIHRSPGVIFSHEKG--------VYSSRII 167

Query: 186 PDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGD 243
           P +G W++ E D  K++I+ ++D ++++  T FL ALG D+ E+I+  FY         D
Sbjct: 168 PYRGTWLEFEIDQKKELIYAKLDSKKRILGTIFLRALGYDTREKIIDLFYKTKTAKISPD 227

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
              +     +L+         V  + GE+             + + + G K      D L
Sbjct: 228 RTEY----EELIGQVLARDVYVKGEDGEK-------------RKMHQAGEKIHPHNIDDL 270

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
               V +  +    G+  +++  +I+    EEI ++                        
Sbjct: 271 IQNDVKKITIIDFKGKDSLDSQIIINCFEREEIKYTPD--------------------PA 310

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            +     +DAL  +Y V+RPGD  T+  A+   + +FF + +YD+  VGR K+N + +  
Sbjct: 311 VNDEPTVEDALNAVYSVIRPGDPITYENAKEDLHNMFFTARRYDIGKVGRYKLNKKFDYS 370

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                  + +EDI   +K L+ +  G+ +IDDID+LGNRR+RSVGE++ +  +    RME
Sbjct: 371 DDVKGTTLIEEDIFKTMKFLIKVYIGEESIDDIDHLGNRRIRSVGEIMTDVLKKAFSRME 430

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R  ++R+SS ++D++ P+DLI+ KP+V+A+ EFF +SQLSQ  + VN L+ +TH RRL+A
Sbjct: 431 RIARDRMSSKEMDTIKPKDLISIKPIVAAIKEFFGASQLSQFMDQVNPLAELTHKRRLNA 490

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG++R RAG E+R+VH THYGR+CP ET EG NIGL+ S+ ++ARVN YGF+E PY 
Sbjct: 491 LGPGGLSRDRAGFEVREVHYTHYGRMCPIETPEGPNIGLIVSMANYARVNEYGFLEAPYV 550

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV +G  T ++ YLSAM+E+  +I Q +S++ +DG    + V CR  G+   +  + I +
Sbjct: 551 KVVNGVATREIEYLSAMDEDKYFIGQVSSAIGKDGKINTDQVSCRKLGDYTSISPKDIQY 610

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ++S++ASLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTGME   A  S
Sbjct: 611 MDVSPKQIISVSASLIPFLEHDDANRALMGSNMQRQAVPLVFPEPPRVGTGMEKKCAYDS 670

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  + AKR+G VE V +  I+I   +G    +    D Y L+K+QR+NQ TC +QRP+V 
Sbjct: 671 GVLVKAKRSGKVEFVSSDTIIIAPEKG---KNKEDKDEYTLLKYQRTNQETCYHQRPIVN 727

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           VGD V+    IADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS R+V ED+FTSIH
Sbjct: 728 VGDTVKAGQPIADGPATYNGELALGRNILVGFVPWNGYNYEDAILISRRVVKEDMFTSIH 787

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           I+E     R+TKLG E++T DIPN SE+ L ++D  GII +G++V PGDILVGK+TPK E
Sbjct: 788 IKELSTDVRETKLGAEKMTCDIPNKSEKSLDDLDSEGIIRIGSKVKPGDILVGKVTPKSE 847

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           S  TPE KLL +IFGEKA +VRDTSLRVP G  GTV+DV+   R   D
Sbjct: 848 SDTTPEFKLLNSIFGEKAKEVRDTSLRVPHGTEGTVIDVQRLKRDQGD 895



 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 130/505 (25%), Positives = 197/505 (39%), Gaps = 69/505 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  G  +           +     +L         +  D  L     V   + 
Sbjct: 725  IVNVGDTVKAGQPIADGPATYN-GELALGRNILVGFVPWNGYNYEDAILISRRVVKEDMF 783

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                      D  E  +  E+   ++  +               + ++ L  +  +    
Sbjct: 784  TSIHIKELSTDVRETKLGAEKMTCDIPNK-------------SEKSLDDLDSEGIIRIGS 830

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEK 1059
              K   +L   +  +       +F + +       + ++          E    + +  K
Sbjct: 831  KVKPGDILVGKVTPKSESDTTPEFKLLNSIFGEKAKEVRDTSLRVPHGTEGTVIDVQRLK 890

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
               GDD+ PGV  VVKV +A KR +        R G+K                      
Sbjct: 891  RDQGDDLSPGVDEVVKVLIATKRKL--------REGDK---------------------- 920

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                                         G K        + +       + L+  +   
Sbjct: 921  ------------------------MAGRHGNKGLVARILPEEDMPYMEDGTPLDICLNPL 956

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                +++              K      +PVF+    E I + L+ A    S +  L DG
Sbjct: 957  GVPSRMNIGQILESELGLAGLKLNEWYESPVFESPSMEQIEAKLKEAGYPTSSKVKLRDG 1016

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            LTG  F+  V VG IY LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEV
Sbjct: 1017 LTGRLFENEVFVGVIYFLKLAHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGEMEV 1076

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAA  LQE++TIKSDD+ GR+++YESIV G  +   G PESFNVLV+E++ L L
Sbjct: 1077 WALEAYGAANTLQELITIKSDDMHGRSKIYESIVKGEPSSSAGIPESFNVLVQELRGLAL 1136

Query: 1360 SIDLENSRTKNSAKMEEIPDFNKCE 1384
               + +++ +     E   +  K E
Sbjct: 1137 DFTIYDAKGQQIPLTERDEELIKRE 1161


>gi|312880380|ref|ZP_07740180.1| DNA-directed RNA polymerase subunit beta [Aminomonas paucivorans
           DSM 12260]
 gi|310783671|gb|EFQ24069.1| DNA-directed RNA polymerase subunit beta [Aminomonas paucivorans
           DSM 12260]
          Length = 1213

 Score =  754 bits (1946), Expect = 0.0,   Method: Composition-based stats.
 Identities = 435/949 (45%), Positives = 618/949 (65%), Gaps = 82/949 (8%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R+ FG+  ++I++PDL+EVQ+ SYD F         RP++GLQ  F  +FPI ++ G+ 
Sbjct: 11  TRRIFGRAKDLIELPDLVEVQRHSYDWFFEHEADRGPRPSQGLQDLFDEIFPIESYDGSF 70

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            LEFV Y  DPP   +D+   RDLT+++P++ T+RL+          +   +IKE+ IY+
Sbjct: 71  ALEFVRYYVDPPSTSLDEARSRDLTWSMPVRATIRLV---------NRKSGEIKEEEIYL 121

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD P+MT  GTF+I G +R+VVSQL RS G++F  + G   + G+  Y  ++IPD+G W+
Sbjct: 122 GDFPVMTDRGTFIINGTERVVVSQLARSAGVYFSSEVG---VPGQESYLAKVIPDRGAWL 178

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
           + +    D++ V+ID R+K+PVT  L             F                    
Sbjct: 179 EFDLTPGDLLSVKIDNRKKIPVTMLL-----------KAFG------------------- 208

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                                + SG ++       L +     L +  + + G  +AE +
Sbjct: 209 ---------------------VGSGDEILR-----LFDAKEVELDLVEEEIKGRLLAETV 242

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           VN + G++ +   + I ++ LE +++     + +  VD       +  T+  D  +   +
Sbjct: 243 VNPD-GQVLLRKNERITKEHLETLWNQGRTKVWVWDVD-----PGLAATMEKDNTQSGDE 296

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           A L+++R +RP + +    A+   + LFFD+ +Y+L  VGR K+N RL LD P+  R + 
Sbjct: 297 ATLELFRRLRPNEPARMENAKEYIHGLFFDTRRYNLGRVGRYKVNRRLGLDIPEAARLLT 356

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             D++AI+K L+ LR+G    DDID+LGNRRVR+VGE+L+NQ R+GLLRMER  KER+++
Sbjct: 357 VGDVVAIVKGLLGLRDGMERDDDIDHLGNRRVRAVGELLQNQVRIGLLRMERIAKERMTT 416

Query: 493 -VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             D+ +   +DLIN +P+ +A+ EFF S QLSQ  +  N L+ +TH RRLSALG GG++R
Sbjct: 417 TPDLAAATAKDLINVRPISAALREFFGSGQLSQFMDQTNPLAELTHRRRLSALGPGGLSR 476

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E RDVH THYGR+CP ET EG NIGLV+SL++FAR+N YGF+ TP R+V +G+V 
Sbjct: 477 ERAGFEARDVHYTHYGRVCPIETPEGANIGLVTSLSTFARLNEYGFLVTPRRRVVEGRVG 536

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           ++VVYL+A EE+  Y+ +AN+ +D+DG+ +E+ V+ R  G  + V R+++DF+D SPKQ+
Sbjct: 537 DEVVYLAADEEDEFYVGRANTPVDDDGNLSEQEVYVRYRGNILTVERDRVDFLDVSPKQI 596

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VSI+ +LIPFLE+DD+NR LMG NMQRQAVPL+ AEAP+VGTG+E  +A+ SG+ ++++R
Sbjct: 597 VSISTALIPFLEHDDANRALMGSNMQRQAVPLVMAEAPYVGTGIEGCIARDSGSCVLSRR 656

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+VE VDA RIVIR  +G  D S       RL+KF+RSNQ T ++Q+PLV  G+ V R 
Sbjct: 657 DGVVEFVDADRIVIRGDDGARDES-------RLIKFRRSNQGTVIHQKPLVHQGERVDRG 709

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            IIADG S D G+LALGRN+LVAF+ W GYNFED++L+S+R+V ED +TSIHIEE+EV A
Sbjct: 710 RIIADGQSCDGGELALGRNVLVAFVSWEGYNFEDAILLSQRLVKEDFYTSIHIEEYEVEA 769

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLGPEEITRDIPNV E+ LKN+DE G++ VGAEV  GDILVGK+TPKGES  +PEEK
Sbjct: 770 RDTKLGPEEITRDIPNVGEDALKNLDESGVVRVGAEVKAGDILVGKVTPKGESDQSPEEK 829

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
           LLRAIFGEKA +VRDT LRVP G  G VV V+  +R    ++  +   E
Sbjct: 830 LLRAIFGEKAREVRDTCLRVPHGEGGKVVAVKRLSREENSEDLSAGVNE 878



 Score =  465 bits (1196), Expect = e-128,   Method: Composition-based stats.
 Identities = 148/327 (45%), Positives = 194/327 (59%), Gaps = 50/327 (15%)

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++ + +  +D+  GV  VVKV+VA  R I  GDKMAGRHGNKG+VS+ILP EDMPFL D
Sbjct: 861  KRLSREENSEDLSAGVNEVVKVYVAQFRKITEGDKMAGRHGNKGVVSKILPEEDMPFLSD 920

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD+VLNPLGVPSRMN+GQ+FET +G+  +  G K+ + + +     DI  L      
Sbjct: 921  GTPVDVVLNPLGVPSRMNLGQVFETIMGFVAMHKGWKVSTPVFEGAQEDDIFRL------ 974

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                      E I +  +  +L    + 
Sbjct: 975  -----------------------------------------VEEIQAE-KYPELTRDCKI 992

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             LYDG TGEP D+ VTVG +YMLKL H+V DK++ARS G YSL+TQQPLGGK+  GGQR 
Sbjct: 993  TLYDGRTGEPMDKKVTVGVMYMLKLIHLVDDKIHARSIGPYSLITQQPLGGKTQFGGQRF 1052

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++ YGA+++LQEMLT+KSDD+ GR + YE IV G +    G PESF VL+KE+
Sbjct: 1053 GEMEVWALEGYGASHMLQEMLTVKSDDIRGRLKTYERIVKGQNLAHPGVPESFRVLIKEL 1112

Query: 1355 QALGLSIDLENSRT--KNSAKMEEIPD 1379
            Q LGL ++++            +E  D
Sbjct: 1113 QGLGLDVEIQYEDGSFGELTLGDEDED 1139


>gi|332182022|gb|AEE17710.1| DNA-directed RNA polymerase subunit beta [Treponema brennaborense
           DSM 12168]
          Length = 1173

 Score =  754 bits (1946), Expect = 0.0,   Method: Composition-based stats.
 Identities = 410/956 (42%), Positives = 582/956 (60%), Gaps = 65/956 (6%)

Query: 7   FNGLGRVRKFF-GK-NPEIIDIPDLIEVQKASYDHFLMMNI--APDERPNEGLQAAFKSV 62
           F     + + + GK     +++P+LI++Q +SY++FL        +    +GLQ  F S 
Sbjct: 2   FAKSRTINRQYIGKNIQNFMELPNLIDIQLSSYENFLQKEKLDNREPLAEQGLQEVFSST 61

Query: 63  FPITAFSGAAMLEFVSYEFD-----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           FPI + +G     F+ YE+        KF   +C  + LTY+VPLK  + L         
Sbjct: 62  FPIESPNGDM---FLEYEYYELDEENIKFSELECKQKGLTYSVPLKARINL--------- 109

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             +   +I+++ IYMGD+PLMT  GTF+I G +R+VVSQ+HRSPG+ F H+KG       
Sbjct: 110 NFQQTGEIRQKDIYMGDIPLMTDRGTFIINGAERVVVSQIHRSPGVIFSHEKG------- 162

Query: 178 LLYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPK 235
            +Y+ RIIP +G W++ E D  K++I+ +IDR++++  T FL ALG  + EEI+  FY  
Sbjct: 163 -IYSSRIIPYRGSWLEFEIDQKKELIYAKIDRKKRILGTIFLRALGYSTREEIIRCFYDT 221

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
                             ++  A  +      +  +++  +G+KL    +  L   G+K 
Sbjct: 222 EKVVVGDSREEKEALVGKVLADAVYAVDAESGEN-KKIFRAGEKLHPHNIDELLLHGIKE 280

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L +                     I    GD  ++ SL            I+        
Sbjct: 281 LTV---------------------IRFAKGDDENDTSL--------SSQMIINCFEREEI 311

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            + +    +D    + DAL  +Y V+ PG+  T   AE     +FF   +YDL  VGR K
Sbjct: 312 RFTKEGSGSD-EPTKDDALSAVYSVLMPGEPITVDAAEKDLTTMFFSMRRYDLGRVGRYK 370

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N + +   P +   + K+DIIA +K L+ + +G   IDDID+LGNRRVRSVGE++ NQ 
Sbjct: 371 LNKKFDYAEPVEEHTLVKQDIIATMKFLIKVYSGVENIDDIDHLGNRRVRSVGELMTNQL 430

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           +    RMER  KER+   + +++ PQDLI+ KP+V+A+ EFF SSQLSQ  + VN L+ +
Sbjct: 431 KTAFSRMERIAKERMGLKETETMKPQDLISIKPIVAAIKEFFGSSQLSQFMDQVNPLAEL 490

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRL+ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ SL  + RVN Y
Sbjct: 491 THKRRLNALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLAIYTRVNEY 550

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+E PYRK+  GK T+ V YLSAM+E+  YI Q + ++ EDGSF  E + CR  G+   
Sbjct: 551 GFLEAPYRKIDAGKATDQVDYLSAMDEDKYYIGQVSVNMKEDGSFATEQISCRRHGDYTT 610

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              + + ++D SPKQ++S++A+L+PFLE+DD+NR LMG NMQRQAVPLL  E P VGTGM
Sbjct: 611 RDPKDVQYMDVSPKQIISVSAALVPFLEHDDANRALMGSNMQRQAVPLLFPEPPHVGTGM 670

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG  + AKR G V  V +  + ++            +D Y L+K+QR+NQ+TC
Sbjct: 671 EGKCAYDSGVLVKAKRPGEVVWVTSDVVKVKPTAPRRPD---DIDEYPLLKYQRTNQDTC 727

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +QRP+V++G +V +  ++ADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS+R+V 
Sbjct: 728 YHQRPVVELGQKVEKGTVLADGPATFNGELALGRNILVGFVPWNGYNYEDAILISQRVVK 787

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           ED+FTSIHI+EF    R+TKLGPE+ITRDIPN SE+ L N+D  GII +GA+V  GDILV
Sbjct: 788 EDMFTSIHIKEFMTEIRETKLGPEKITRDIPNTSEKTLDNLDAEGIIRIGAKVRSGDILV 847

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPK E+  TPE KLL +IFGEKA +VRD+SLRVP GV GT++DV+   R   D
Sbjct: 848 GKVTPKSETETTPEFKLLNSIFGEKAKEVRDSSLRVPHGVEGTIIDVQRLRRTEGD 903



 Score =  451 bits (1161), Expect = e-124,   Method: Composition-based stats.
 Identities = 172/504 (34%), Positives = 236/504 (46%), Gaps = 75/504 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPSGVSGT 938
            ++ +G +V  G +L                 L+  +   G    D    S RV      T
Sbjct: 733  VVELGQKVEKGTVLADGPATFNGELALGRNILVGFVPWNGYNYEDAILISQRVVKEDMFT 792

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKD--DEQVILDRNIYSRLMEILCGQNAV 996
             + ++ F     +       + R+      +  D  D + I+      R  +IL G+   
Sbjct: 793  SIHIKEFMTEIRETKLGPEKITRDIPNTSEKTLDNLDAEGIIRIGAKVRSGDILVGKVTP 852

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                     T     L++     +  +      +V   VE                   +
Sbjct: 853  KSET----ETTPEFKLLNSIFGEKAKEVRDSSLRVPHGVEG-------------TIIDVQ 895

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              +   GDD+ PGV  VVKV +A KR ++ GDKMAGRHGNKGIV+RILP EDMP+L DGT
Sbjct: 896  RLRRTEGDDLNPGVDEVVKVLIATKRKLREGDKMAGRHGNKGIVARILPVEDMPYLADGT 955

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
             +DI LNPLGVPSRMN+GQI                           ++     +L +  
Sbjct: 956  ALDICLNPLGVPSRMNIGQIM------------------------ESELGLAGMYLNEWY 991

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                            PVF     E I+  L  A  + + ++ L
Sbjct: 992  EA------------------------------PVFQSPSNEQISQKLVEAGFNANSKATL 1021

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
             DG TGEPF   V VG IY +KL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGE
Sbjct: 1022 RDGRTGEPFLNDVFVGVIYFMKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGE 1081

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAA  LQE+LTIKSDD+ GR+++YESIV G  +   G PESFNVLV+E++ 
Sbjct: 1082 MEVWALEAYGAANTLQELLTIKSDDMNGRSKIYESIVKGEPSTAAGVPESFNVLVQELRG 1141

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDF 1380
            L L   + +++ K     E   + 
Sbjct: 1142 LALDFTIYDAKGKQIPLTERDDEL 1165


>gi|328949283|ref|YP_004366620.1| DNA-directed RNA polymerase subunit beta [Treponema succinifaciens
           DSM 2489]
 gi|328449607|gb|AEB15323.1| DNA-directed RNA polymerase subunit beta [Treponema succinifaciens
           DSM 2489]
          Length = 1185

 Score =  749 bits (1934), Expect = 0.0,   Method: Composition-based stats.
 Identities = 411/976 (42%), Positives = 586/976 (60%), Gaps = 62/976 (6%)

Query: 10  LGRVRKFFGK-NPEIIDIPDLIEVQKASYDHFLMMN--IAPDERPNEGLQAAFKSVFPIT 66
              VR++ GK   + +++P+LI++Q +SY+ F+        +   N+GLQ  F S FPI 
Sbjct: 6   KKIVRQYIGKDIQDFMELPNLIDIQLSSYEEFIQKGRIEKGEPLLNQGLQEVFTSTFPIE 65

Query: 67  AFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           + +G   LE+  YE D    KF   +C  + ++YAVPLK  + L           K    
Sbjct: 66  SPAGDMSLEYEFYELDYDGMKFTEQECKKKGVSYAVPLKARINL---------NFKETGA 116

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           I ++ IYMGD+PLMT  GTFVI G +R+VVSQ+HRSPG+ F  DKG        + + RI
Sbjct: 117 ILQKDIYMGDVPLMTDRGTFVINGAERVVVSQIHRSPGVIFQRDKG--------VLSSRI 168

Query: 185 IPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRG 242
           IP +G W++ E D  K++I+ +IDR++K+  T FL ALG  + EEI++ FY         
Sbjct: 169 IPYRGSWLEFEIDQKKELIYAKIDRKKKILGTIFLRALGYSTREEIINCFYVTEDVKIPS 228

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           D       A  ++        + D +TGE  ++  +G KL    +  L   G+K + +  
Sbjct: 229 DLEKRDELAGRVLGK---PVIIKDEETGEEKKLFRAGDKLHPHDIDDLVANGIKEINVIK 285

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             +      ++  N                          +    I+         + + 
Sbjct: 286 FNMKKRPDDKEEKNPS------------------------LDSEMIVNCFEREEIVFSKE 321

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
              T     +++ L  +Y V+ PG+  T   AE     +FF   +YDL  VGR K+N + 
Sbjct: 322 GSSTADEPTKEECLSKVYAVLMPGEPITVEAAERDLTTMFFSVRRYDLGRVGRYKLNKKF 381

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +   P +   + KEDII  +K L+++  G   +DDID+LG RRVRSVGE+L NQ++    
Sbjct: 382 DYKEPVEDVTLTKEDIINTMKHLIEVYIGDEPLDDIDHLGRRRVRSVGELLTNQFKTAFA 441

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER  K+R++  + +++ P DLI+ KP++S++ EFF SSQLSQ  +  N L+ +TH RR
Sbjct: 442 RMERIAKDRMNLKETETLKPGDLISIKPIISSIREFFGSSQLSQFMDQCNPLAELTHKRR 501

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           L+ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ SL  F RVN YGF+E 
Sbjct: 502 LNALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLAIFTRVNEYGFLEE 561

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRKV +GK TN+V YL  M+E+  YI Q    +  DGSF  +LV CR  G+      + 
Sbjct: 562 PYRKVVNGKATNEVEYLDPMDEDKYYIGQVTEGMKADGSFPTDLVSCRHRGDYTSRSPKD 621

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           I ++D SP+QV+S++ASL+PFLE+DD+NR LMGCNMQRQAVPLL  E P VGTGME   A
Sbjct: 622 IQYMDVSPRQVISVSASLVPFLEHDDANRALMGCNMQRQAVPLLFPEPPHVGTGMEQKTA 681

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG    A+RAG V+ V++  I I+      D      D Y L+K+Q++N +T  +QRP
Sbjct: 682 YDSGVLTKARRAGTVKWVESDLIKIKPDGVKGDVF----DEYPLLKYQKTNSDTVNHQRP 737

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            V+VG+ V    +IADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS+R+V ED++T
Sbjct: 738 TVQVGEHVEAGGVIADGPATFNGELALGRNILVGFVPWNGYNYEDAVLISQRVVKEDMYT 797

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           S+HI EF+   R+TKLGPE ITRDIPN SE+ L N+D  GI+ +GA+V  GDILVGK+TP
Sbjct: 798 SVHIHEFQTEIRETKLGPERITRDIPNTSEKILDNLDSEGIVRIGAKVRSGDILVGKVTP 857

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK-----NER 955
           K E+  TPE KLL +IFGEKA +VRD+SL++P GV G V+D++   R   D+     +E+
Sbjct: 858 KSETETTPEFKLLNSIFGEKAKEVRDSSLKLPHGVQGVVIDIQRLKRSEGDELQPGVDEQ 917

Query: 956 SISVEREQIELLARDK 971
              +  ++ +L+  DK
Sbjct: 918 VKVIIADKRKLVVGDK 933



 Score =  330 bits (847), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 142/591 (24%), Positives = 214/591 (36%), Gaps = 83/591 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +L    P  G   E        ++++             + +    G +
Sbjct: 653  MGCNMQRQAVPLLFPEPPHVGTGMEQKTAYDSGVLTKARRAGTVKWVESDLIKIKPDGVK 712

Query: 860  EITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                D   + +    N D    +   + VG  V  G ++           +     +L  
Sbjct: 713  GDVFDEYPLLKYQKTNSDTVNHQRPTVQVGEHVEAGGVIADGPATFN-GELALGRNILVG 771

Query: 916  IFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                   +  D  L      +     S  + + +   R      ER         E +  
Sbjct: 772  FVPWNGYNYEDAVLISQRVVKEDMYTSVHIHEFQTEIRETKLGPERITRDIPNTSEKILD 831

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            + D E  I+      R  +IL G+            T     L++     +  +      
Sbjct: 832  NLDSE-GIVRIGAKVRSGDILVGKVTPKSET----ETTPEFKLLNSIFGEKAKEVRDSSL 886

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            K+   V+ +                 +  K   GD++ PGV   VKV +A KR +     
Sbjct: 887  KLPHGVQGVV-------------IDIQRLKRSEGDELQPGVDEQVKVIIADKRKL----- 928

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
                     +V                  D                             G
Sbjct: 929  ---------VVG-----------------D-----------------------KMAGRHG 939

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K          +       + L+  +       +++                    ++P
Sbjct: 940  NKGVVARILPVEDMPYLEDGTPLDVCLNPLGVPSRMNIGQIMESELGRAGLVLNEWYNSP 999

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F    +E I   L  A L    + I++DG TGEPF  P+ VG IY +KL+H+V DK++A
Sbjct: 1000 AFQTPSQEQIAEKLVQAGLSPDCKQIVHDGFTGEPFLNPIFVGVIYFMKLHHLVDDKMHA 1059

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA  LQEM+TIKSDD+ GR++VY
Sbjct: 1060 RSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQEMMTIKSDDMNGRSKVY 1119

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            ESIV G  T   G PESFNVLV+E++ L L   + + + K  A  E   + 
Sbjct: 1120 ESIVKGEPTAPIGVPESFNVLVQELRGLALDFTIYDDKGKQIALTERDQEL 1170


>gi|312795763|ref|YP_004028685.1| DNA-directed RNA polymerase beta chain [Burkholderia rhizoxinica
           HKI 454]
 gi|312167538|emb|CBW74541.1| DNA-directed RNA polymerase beta chain (EC 2.7.7.6) [Burkholderia
           rhizoxinica HKI 454]
          Length = 680

 Score =  748 bits (1930), Expect = 0.0,   Method: Composition-based stats.
 Identities = 305/657 (46%), Positives = 434/657 (66%), Gaps = 3/657 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1   MHYSFTEKKRIRKSFAKRPIVHPVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSV 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G A LEFVSY    P FDV +C  R LTY   L+  +RL++ D +  T    +
Sbjct: 61  FPIVSHNGFARLEFVSYALSSPAFDVKECQQRGLTYCSALRAKVRLVILDKESPT-KPVV 119

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120 KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180 RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMN 239

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +          L  G      + D   G+ ++   K++ +  ++ L+    K++ +  D 
Sbjct: 240 EGAQMEFVPERL-RGEVARFDIAD-RDGKVIVPKDKRINAKHIRDLENAKTKYISVPEDY 297

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G  +A+++++ +TGE+   A D I E  LE++  + +++I  LY + ++   Y+ +TL
Sbjct: 298 LIGRVLAKNVIDVDTGEVIANANDEITEGVLEKLREASVKEIQTLYTNDLDQGPYMSSTL 357

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D+  D+  A + IYR+MRPG+  T    E++FN LF+  D YDLS VGR+K N R+  
Sbjct: 358 RIDETIDKTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEDAYDLSKVGRMKFNRRVGR 417

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       +  +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +NQ+R GL+R+
Sbjct: 418 DEIHGPMTLTDDDILAAIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRV 477

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 478 ERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVS 537

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +A +N YGF+ETPY
Sbjct: 538 ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPY 597

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           RKV DGKVT+ + YLSA+EE    IAQAN+++D++G   +ELV  R AGE ++V  E
Sbjct: 598 RKVIDGKVTDQIDYLSAIEEGRYVIAQANAAIDDEGKLIDELVSAREAGETLMVTPE 654


>gi|125717055|ref|YP_001034188.1| DNA-directed RNA polymerase subunit beta [Streptococcus sanguinis
           SK36]
 gi|125496972|gb|ABN43638.1| DNA-directed RNA polymerase I, beta chain (140 kDa subunit),
           putative [Streptococcus sanguinis SK36]
          Length = 1127

 Score =  744 bits (1921), Expect = 0.0,   Method: Composition-based stats.
 Identities = 395/892 (44%), Positives = 544/892 (60%), Gaps = 70/892 (7%)

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K   +IK Q ++
Sbjct: 1   MELEFVGYEIREPKYTLEEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVF 51

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W
Sbjct: 52  FGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAW 108

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLS 250
           +++E DSKDI + RIDR RK+P T+ + ALG    +EIL  F    +     +      +
Sbjct: 109 LELETDSKDIAYTRIDRTRKIPFTTLVRALGFSGDDEILDIFGDSDLVRNTIEKDI-HKN 167

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------D 301
             D      +      +  GE    ES + L            +  +G            
Sbjct: 168 PMDSRTDEALKEIYERLRPGEPKTAESSRSLLEARFFDPHRYDLAAVGRYKINKKLSVKT 227

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            L    +AE +V+ ETGEI +EAG V+    ++ I             + +N   YI N 
Sbjct: 228 RLLNQTIAEPLVDAETGEILVEAGTVMTRSVIDSIAEQLD--------NGLNKITYIPND 279

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                        L  ++V+ P D                              + +  N
Sbjct: 280 SAVLTAPVD----LQKFKVVAPTDPDRV--------------------------VTIIGN 309

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL R
Sbjct: 310 ANPSDKVRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGELLANQVRLGLSR 369

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+++ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N LS ++H RRL
Sbjct: 370 MERNVRERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRL 429

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGFI+TP
Sbjct: 430 SALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTP 489

Query: 602 YRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R  G     P +
Sbjct: 490 YRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGRHQGNNQEFPSD 549

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   
Sbjct: 550 QVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQA 609

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SGAA++A+  G V   DA ++ +R  +G LD       +Y++ KF+RSN  T  NQR
Sbjct: 610 AHDSGAAVIAQHDGKVTYADADKVEVRREDGSLD-------VYQIQKFRRSNSGTAYNQR 662

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++++SER+V +DV+
Sbjct: 663 TLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 722

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS+H+EE+E   RDTKLGPEEITR+IPNV E+ L+N+DE GII +GAEV  GDILVGK+T
Sbjct: 723 TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 782

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 783 PKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRANGD 834



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 174/507 (34%), Positives = 243/507 (47%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 664  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 722

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 723  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVT 782

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 783  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 825

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 826  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 885

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 886  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW--------- 936

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E           +D   ++I
Sbjct: 937  ------------------------------------DTVREA---------GMDSDAKTI 951

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS+VTQQPLGGK+  GGQR G
Sbjct: 952  LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSMVTQQPLGGKAQFGGQRFG 1011

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 1012 EMEVWALEAYGASNVLQEILTYKSDDVNGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 1071

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +         +     + 
Sbjct: 1072 SLGLDMRVLDEDDNEVELRDLDEGEDD 1098


>gi|49065923|gb|AAT49052.1| RNA polymerase beta subunit [Capnocytophaga canimorsus]
 gi|49065927|gb|AAT49054.1| RNA polymerase beta subunit [Capnocytophaga canimorsus]
          Length = 733

 Score =  744 bits (1920), Expect = 0.0,   Method: Composition-based stats.
 Identities = 375/788 (47%), Positives = 498/788 (63%), Gaps = 67/788 (8%)

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 2    QFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLI 61

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            SSL  F++VN  GFIETPYR+V DGKV   D+ YLSA EEE + I  AN ++D++G   +
Sbjct: 62   SSLAVFSKVNGMGFIETPYRRVVDGKVDLTDMTYLSAEEEEGKMIGMANINMDDNGVILD 121

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  +  G+  ++   ++DFID +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 122  EKVVVKEEGDFPVIDPNQVDFIDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVP 181

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LLK E+P VGTG+E  VA  S   + A+  G V+ VDA +I+I   R+ +  L       
Sbjct: 182  LLKPESPIVGTGLERRVASDSRVLMNAEGEGTVDYVDADKIIITYDRTDDQRLVSFEEDA 241

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y L+KF+++NQ TC+N +P+V+ GD V +  ++ +G +T  G+LALGRNM VAFMPW 
Sbjct: 242  KTYDLIKFRKTNQGTCINLKPIVRKGDRVTKGQVLCEGYATQQGELALGRNMKVAFMPWK 301

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFED+++ISER+V ED+FTSIHI+E+ +  RDTKLG EE+T DIPNVSE+  K++DE 
Sbjct: 302  GYNFEDAIVISERVVREDIFTSIHIDEYSMDVRDTKLGAEELTNDIPNVSEDATKDLDEN 361

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G+I +GAEV PGDIL+GKITPKGES  TPEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 362  GMIRIGAEVRPGDILIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLHGVV 421

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R   DK +R    E  +I  L      +  +L   +  +L  ++ G+ A    
Sbjct: 422  IDKKLFSRAIKDKRKRGKDKE--EIATLEASYSAKFQVLKDKLVDKLFTLVNGKTAQGVV 479

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
               G +   K    +  ++                D++    ++ L   Y+   + L+  
Sbjct: 480  NDLGEEIIPKGKKYTQKMLHGIEDYAHLVSGGWTSDDRANALIDDLLHNYKIKLNDLQGA 539

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
             +     I  GD++P GV+++ K+++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL
Sbjct: 540  LRRDKFTISVGDELPAGVMKLAKIYIAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFL 599

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDIVLNPLGVPSRMN+GQI+ET LGWA   LG+K  + I D  +   I+ L    
Sbjct: 600  EDGTPVDIVLNPLGVPSRMNIGQIYETVLGWAGQKLGQKYATPIFDGASLEQINELTD-- 657

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                        K+GVP                          G
Sbjct: 658  ----------------------------KAGVP------------------------RFG 665

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
             + LYDG TGE FD+P TVG IYM+KL HM+ DK++ARS G YSL+TQQPLGGK+  GGQ
Sbjct: 666  HTYLYDGGTGERFDQPATVGVIYMIKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQ 725

Query: 1293 RLGEMEVW 1300
            R GEMEVW
Sbjct: 726  RFGEMEVW 733


>gi|223982605|ref|ZP_03632840.1| hypothetical protein HOLDEFILI_00114 [Holdemania filiformis DSM
            12042]
 gi|223965442|gb|EEF69719.1| hypothetical protein HOLDEFILI_00114 [Holdemania filiformis DSM
            12042]
          Length = 1382

 Score =  741 bits (1914), Expect = 0.0,   Method: Composition-based stats.
 Identities = 318/1451 (21%), Positives = 542/1451 (37%), Gaps = 194/1451 (13%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +   G    R+ + K    +D+PDL+EVQ  S++ F+           EG++  F+ +
Sbjct: 10   YRIEKLGKKAERRNYSKVSGNLDLPDLVEVQTQSFEWFIR----------EGIREVFEDI 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            +PI  + G   L+FV YEF  PK+ V++C +R+  +A PLK  + L + D        + 
Sbjct: 60   YPIQNYGGNIRLKFVDYEFGTPKYTVNECKYREANFAAPLKAKMELEMVDN-------TT 112

Query: 123  KDI--KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             ++  K + +++G+ P+MT+ GTF+I G +R++VSQ+ RSPG +F  D      +GK  Y
Sbjct: 113  GEVLTKWEDVFLGEFPMMTETGTFIINGAERVIVSQIVRSPGAYF--DIASEDKTGKDSY 170

Query: 181  ACRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMD----------- 224
             C +IP +G W++   D K      I+++ +DR+RK+  T    A+GM            
Sbjct: 171  NCELIPSRGTWLEFMTDGKKAALGRIVNMSVDRKRKILSTILFKAIGMSLNLEKSEDGFD 230

Query: 225  SEEI--------LSTF--------------------------YPKIVYSQRGDFWCFPLS 250
            + EI        L  F                          Y +I  +   D       
Sbjct: 231  TAEIRRFLKALGLEVFEENIVEGEPREFLNLYMLLYTSFFGNYEEIRNTLAADKIKTSNE 290

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVA 309
            A   +   + S  +  ID    ++ +         L       +      +D + G Y+A
Sbjct: 291  ALLAIYENQRSDEVPTIDGSVNLMNAKFFDHRRYDLTKAGRYKLNKKLSLTDRMEGTYLA 350

Query: 310  EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            ED+++GE G++  E G  + +K         +  + +L    V    ++      D +  
Sbjct: 351  EDVLSGE-GKVLFEKGTFVTKK------ERNVLRVEMLKGSHVTAFPFVHEFSHPDTSMM 403

Query: 370  RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
                 L +   +   DV      + +F      ++K D+  + +    +R+         
Sbjct: 404  DTSWSLGLIGRILANDVEC---GDRLFEKGTVLTEK-DIEALAKEVKEVRVYSGLVAKPV 459

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             +  E+  A++            +       N  + + GE++ ++Y      +      +
Sbjct: 460  ALTAENASAVLNYGHRFF-----VIGRLTANNEDMTNNGELVVDRY------IPDEDYSK 508

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +S+ +   ++ +   N       V     + Q+S   +  N +  +     +  + Q   
Sbjct: 509  LSASEQQVIIERAHQNQAITAWLVGAAVQTIQVSTSADCSNPIKIVA----IDPINQKKT 564

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                               +   +  +      + ++    +      +    R V +  
Sbjct: 565  ITISDMYAFYSYELNMMDGVGSVDDIDMLGNRRIRTVGELIQNQFRIGLSRMERVVKERM 624

Query: 610  -----------VTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEIL 655
                          ++  L+A  +E    +Q +  +D+       T +          + 
Sbjct: 625  SIAEAAGLTPKQLTNIRPLTAAIKEFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGLT 684

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              R   +  D        I     P    +      +    +      ++     V    
Sbjct: 685  RERAGFEVRDVHNSHYGRICPIETP-EGPNIGLISNLTTYAKINEYGFIETPYRLVKEDG 743

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E          + A          A  +    +  D+  +    +     + Q    +  
Sbjct: 744  EVTEDY---VYLSADEENDYVIAQANEVHEGRLINDMVVARKAGETIMAHRNQVELADVS 800

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              Q   V         +  A               +L    P+ G   E  +        
Sbjct: 801  PKQIVSVATACIPFLENDDASRALMGANMQRQAVPLLNPHSPYVGTGMEHRIARDSGSAC 860

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                  +           T+   E+   ++           I++  I+  G  V  GDIL
Sbjct: 861  ICTGNGVVTYVDANKIVVTEDEGEQRVYELQKFRRSNAGTCINQRPIVKHGERVERGDIL 920

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
                +   +  +   + +  A       +  D  +     V   V        + I+  E
Sbjct: 921  ADGPS-MEKGELALGQNVTIAFMTWHGYNYEDAIIMSERMVRDDVYTSIHIEEYDIECRE 979

Query: 955  RSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
              +  E     I  ++ +     D + I+      +  +IL G+    G         L 
Sbjct: 980  TKLGPEEITRDIPNVSENACRHLDGRGIVMVGAEVKEGDILVGKVTPKGQSEISPEEKLL 1039

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              +  E  R    +      KV      +                  I K   G D+PPG
Sbjct: 1040 LAIFGEKSR----EVRDNSLKVPHGGAGIVHSIR-------------IFKRNEGHDLPPG 1082

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            V  VVKV++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNP GVPS
Sbjct: 1083 VNEVVKVYIVQKRKISEGDKMAGRHGNKGVISKILPIEDMPYLPDGTPIDIMLNPFGVPS 1142

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG A   LG K  + + D  +N ++  +    +                
Sbjct: 1143 RMNIGQVLEIHLGMAAKTLGVKFATPVFDGISNDELKSIMEEAQTSQDGKLVL------- 1195

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                                                      G+       TGEP+D  +
Sbjct: 1196 ----------------------------------------HDGK-------TGEPYDERI 1208

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            +VG +YM+KL HMV DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+
Sbjct: 1209 SVGVMYMIKLAHMVDDKLHARATGPYSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGAAH 1268

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             LQE+LT+KSDD+VGRT+ YE+I+ G D  E G PESF VL  E+QAL + + + +    
Sbjct: 1269 TLQEILTVKSDDIVGRTKTYEAIIKGKDLPEPGIPESFRVLKHELQALAIDVKMLDEEGL 1328

Query: 1370 NSAKMEEIPDF 1380
                 +   D 
Sbjct: 1329 EVDMKKMEADE 1339


>gi|320536845|ref|ZP_08036840.1| DNA-directed RNA polymerase, beta subunit [Treponema phagedenis
           F0421]
 gi|320146304|gb|EFW37925.1| DNA-directed RNA polymerase, beta subunit [Treponema phagedenis
           F0421]
          Length = 1174

 Score =  740 bits (1910), Expect = 0.0,   Method: Composition-based stats.
 Identities = 404/959 (42%), Positives = 578/959 (60%), Gaps = 77/959 (8%)

Query: 10  LGRVRKFFGK-NPEIIDIPDLIEVQKASYDHFL----------MMNIAPDERPNEGLQAA 58
               R + GK     +++PDLI++Q  SYD FL            +         GL+  
Sbjct: 6   RKIKRTYIGKNIQNFMELPDLIDIQLKSYDTFLHCGNSANKAENPDDNTISSEETGLEDV 65

Query: 59  FKSVFPITAFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
           F++ FPI + +G   LE+ SY  D    KF   +C  + LTYA+PLK+ + L   +    
Sbjct: 66  FRTTFPIESPTGDMTLEYQSYTLDEKEIKFSEIECKQKGLTYAIPLKVQVDLRFNE---- 121

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                  +I+ + IY+GD+P MT+ GTF+I G +R+VVSQ+HRSPG+ F  +KG      
Sbjct: 122 -----TGEIRRKDIYLGDIPKMTERGTFIINGAERVVVSQIHRSPGVIFSKEKG------ 170

Query: 177 KLLYACRIIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYP 234
             +++ RIIP +G W++ E D  KD+I+ ++D+++++  T FL A+G  S EEI+  FY 
Sbjct: 171 --IFSSRIIPYRGSWLEFEIDQKKDLIYAKLDKKKRILGTIFLRAVGYSSREEIIDAFYK 228

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKG 292
                   D          L+      S +V  + GE  ++ ++G+K+   ++  L +  
Sbjct: 229 TENVEVLPDRA----EHEHLVGKILAKSVIVKDEEGEERKLYKAGEKVHPHVIDDLLQNN 284

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           V  + + +    G   +  I+N              + + ++ +  SE  DI        
Sbjct: 285 VGEISVINFEAEGSLNSPVIINC------------FEREEMKYLDSSEGDDI-------- 324

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                            ++ AL  +Y  ++PGD  T   AE     +FF + +YDL  VG
Sbjct: 325 ----------------SKETALSVVYTALKPGDPMTVEAAEKDLQTMFFSARRYDLGRVG 368

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R K+N + +   P     +  EDII  +K L+ + +G  ++DDID+LGNRR+RSVGE+L 
Sbjct: 369 RYKLNKKFDYQPPLKECTLVVEDIINTMKYLIQVYDGDESVDDIDHLGNRRIRSVGELLT 428

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           N  +   LRMER  KER+S+ +++++ PQDLI+ KP+V A+ +FF  SQLSQ  + VN L
Sbjct: 429 NILKSAFLRMERIAKERMSAKELETIKPQDLISIKPIVIALKDFFGGSQLSQFMDQVNPL 488

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRL+ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ S+ ++ RV
Sbjct: 489 AELTHKRRLNALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSMANYTRV 548

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+E PY KV DG VT +V YL AM+E+  YI Q + +++ DG+ + + + CR  G+
Sbjct: 549 NEYGFLEAPYVKVKDGVVTREVEYLDAMDEDRYYIGQDSIAVNADGTISIDQISCRHQGD 608

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                 + I ++D SPKQ++S++ASLIPFLE+DD+NR LMG NMQRQ VPL+  E P VG
Sbjct: 609 YTTRSPKDIQYMDVSPKQIISVSASLIPFLEHDDANRALMGSNMQRQGVPLVFPEPPRVG 668

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  SG  I AK AG V    + +I+++      D        YRL+K+QR+NQ
Sbjct: 669 TGMEGKCAYDSGVLIKAKEAGTVVYTSSDKIIVKPKGAKSDDENME---YRLLKYQRTNQ 725

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           +TC +QRP+V VGD V   D +ADGP+T  G+LALGRN+LV F+PW+GYN+ED++LIS R
Sbjct: 726 DTCYHQRPIVSVGDTVEVGDALADGPATYHGELALGRNILVGFVPWNGYNYEDAILISRR 785

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           ++ ED+FTS+HI+EF    R+TKLG E +T DIPN SE+ L N+D  GII +GA+V  GD
Sbjct: 786 VIKEDMFTSVHIKEFSTEVRETKLGAERMTSDIPNRSEKSLDNLDSEGIIRIGAKVRSGD 845

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IL+GKITPK ES  TPE KLL +IFGEKA DVRD+SLRVP GV GTV+DV+   R   D
Sbjct: 846 ILIGKITPKSESETTPEFKLLNSIFGEKAKDVRDSSLRVPHGVEGTVIDVQRLKRSEGD 904



 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 139/590 (23%), Positives = 208/590 (35%), Gaps = 82/590 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG-- 857
                    G  ++    P  G   E        ++ +       +            G  
Sbjct: 648  MGSNMQRQGVPLVFPEPPRVGTGMEGKCAYDSGVLIKAKEAGTVVYTSSDKIIVKPKGAK 707

Query: 858  ---PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                    R +            +  I+ VG  V  GD L           +     +L 
Sbjct: 708  SDDENMEYRLLKYQRTNQDTCYHQRPIVSVGDTVEVGDALADGPATYH-GELALGRNILV 766

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE---LLARDK 971
                    +  D  L     +   +           +  E  +  ER   +      +  
Sbjct: 767  GFVPWNGYNYEDAILISRRVIKEDMFTSVHIKEFSTEVRETKLGAERMTSDIPNRSEKSL 826

Query: 972  D--DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  D + I+      R  +IL G+         +  T     L++     +         
Sbjct: 827  DNLDSEGIIRIGAKVRSGDILIGKITPKS----ESETTPEFKLLNSIFGEKAKDVRDSSL 882

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +V   VE                   +  K   GDD+ PGV  VVKV +A KR +     
Sbjct: 883  RVPHGVEGTV-------------IDVQRLKRSEGDDLSPGVSEVVKVLIATKRKL----- 924

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
               R G+K                                                   G
Sbjct: 925  ---REGDK----------------------------------------------MAGRHG 935

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             K        + +       + L+  +       +++              +      +P
Sbjct: 936  NKGIVARILPEEDMPYLDDGTPLDICLNPLGVPSRMNIGQILESELGLAGLRLDEWYESP 995

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF     E I   L+ A    + + +L DG TG  F  PV VG IY +KL H+V DK++A
Sbjct: 996  VFQSPTNEQIEEKLKEAGFPANSKVMLRDGRTGNYFQNPVFVGVIYFMKLAHLVDDKMHA 1055

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGAA  LQE+LTIKSDD+ GR+++Y
Sbjct: 1056 RSTGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAANTLQELLTIKSDDMHGRSKIY 1115

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            E+IV G  +   G PE+FNVLV+E++ L L   + +++ K     E   +
Sbjct: 1116 EAIVKGEASSPAGIPEAFNVLVQELRGLALDFTIYDAKGKQIPLTERDEE 1165


>gi|187918255|ref|YP_001883818.1| DNA-directed RNA polymerase subunit beta [Borrelia hermsii DAH]
 gi|226699374|sp|B2S092|RPOB_BORHD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|119861103|gb|AAX16898.1| DNA-directed RNA polymerase beta chain [Borrelia hermsii DAH]
          Length = 1155

 Score =  739 bits (1909), Expect = 0.0,   Method: Composition-based stats.
 Identities = 396/940 (42%), Positives = 594/940 (63%), Gaps = 66/940 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           GK  EI+D+P+LIE+Q  SY+ FL +      RP  NEGL++ F+ VFP+ + +G   LE
Sbjct: 10  GKAEEILDLPNLIEIQLNSYEKFLQLERLKTNRPLLNEGLESVFRDVFPMKSSNGEVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LKI L L            +  +I+++ +YMG
Sbjct: 70  YEKYYIEYNSLSFTEKECKRKGQSYEAVLKIRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT  GTF++ G +R++VSQ+HRSPG+ F  +K         LY  RIIP +G W++
Sbjct: 121 TIPLMTDRGTFIVNGAERVIVSQIHRSPGVVFYKEKD--------LYYARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ VT FL ALG+++ E I+ TFY         D        
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILVTLFLRALGLNTRERIIETFYKIRKIEVNEDT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++++++  +       +G K+T   ++   + GVK + +         +  D
Sbjct: 226 KREITGQYLATNIIIKEN--MTYRAGDKITLQDIEDFLQNGVKEIDL---------IDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +   G+ +I +  +++    E+ + S       L                      R+
Sbjct: 275 GYDSVPGKHFISSDVILNCFEKEDAYFSLKDGFKEL---------------------SRE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y V+ PG+  +   AES    +FF   +YDL  VGR K++ +  LD       +
Sbjct: 314 SVMLAVYSVLLPGEPISIDNAESDLRNVFFSEKRYDLGHVGRYKLSKKFGLD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ + +G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMTDIVNTISHLLRIYDGHDVLDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL ++A+VN YGF+ETPYRKV DGKVT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYAKVNDYGFLETPYRKVVDGKVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++++ +G++ ++L+  R +G+   +  + ID++D SP+Q+
Sbjct: 553 DEIEYLSAIDEEKKCIAQANAAVNAEGNYIDDLISVRVSGDYTTMIPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGME +VAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPQPPIVGTGMERIVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +GIV    + +IVIR  +   D     +D Y L K++R+NQ+T  N   LVK G  V + 
Sbjct: 673 SGIVVLATSKKIVIRPEDAADDH---DLDEYELAKYERTNQDTSFNHSVLVKEGQVVNKG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G++ALG N+LV F+PW+G+N+ED++LISER++ ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGEVALGNNLLVGFIPWNGFNYEDAILISERIIKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVS + L  +DE GI+ +G  V PGDIL+GK+TPK E  +TPE K
Sbjct: 790 RETKLGPEKVTADIPNVSGKILNKLDENGIVRIGTYVKPGDILIGKVTPKSEGDITPEFK 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  + 
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKDDVS 889



 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 160/411 (38%), Positives = 227/411 (55%), Gaps = 71/411 (17%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            +K DE  I+    Y +  +IL G+              L + +  E  +           
Sbjct: 812  NKLDENGIVRIGTYVKPGDILIGKVTPKSEGDITPEFKLLTSIFGEKAKD---------- 861

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             V+ N   +    E +   ++   K+ +       ++PPGV  ++KV++A KR ++ GDK
Sbjct: 862  -VKNNSLKVPHGTEGTVIDVQRITKDDV------SNLPPGVDEILKVYIAKKRKLKEGDK 914

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+V++ILP EDMP+L DGTP+DI LNPLGVPSRMN+GQ+ E+ LG A     
Sbjct: 915  MAGRHGNKGVVAKILPVEDMPYLADGTPLDICLNPLGVPSRMNIGQLMESQLGLAG---- 970

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                                 +L +                                  P
Sbjct: 971  --------------------KYLGEYYDV------------------------------P 980

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF+ A  E I   L+ A  +E+ +++LYDG TGEPF+  V VG IYMLKL+H+V DK++A
Sbjct: 981  VFESATNECIQEKLKKAGFNETSKAVLYDGYTGEPFENEVMVGIIYMLKLHHLVDDKMHA 1040

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLV+QQPLGGK+  GGQRLGEMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++Y
Sbjct: 1041 RSTGPYSLVSQQPLGGKAQFGGQRLGEMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIY 1100

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            E+IV G  T  +G PESFNVL++E++ LG  + + + +       E+  + 
Sbjct: 1101 ENIVKGIPTNVSGIPESFNVLMQELRGLGFDLSIYDDKGNQIPLTEKEEEL 1151


>gi|116335064|ref|YP_802559.1| RNA polymerase beta subunit [Candidatus Carsonella ruddii PV]
 gi|123025703|sp|Q05FH8|RPOB_CARRP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|116235345|dbj|BAF35193.1| RNA polymerase beta subunit [Candidatus Carsonella ruddii PV]
          Length = 1267

 Score =  738 bits (1904), Expect = 0.0,   Method: Composition-based stats.
 Identities = 396/1356 (29%), Positives = 679/1356 (50%), Gaps = 102/1356 (7%)

Query: 14   RKFFGKNP--EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R  F K       ++P L+  Q  SY+ FL             ++   K  FP+   +  
Sbjct: 9    RFCFSKKKFFHKCNLPYLLHNQIGSYNSFLSSKYNSLFS----IKKVLKQYFPLICNNKN 64

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              ++    E   P         R+L     L + + + V + +     K         I+
Sbjct: 65   IFIKLKKIELLEPCNTEKYTKIRNLHLFSTLYMYISIYVINKNLNVYKK---------IF 115

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G++P MTK G F+I GI RI++SQ  +S GI+F  +K +          C IIP +G W
Sbjct: 116  LGNIPSMTKKGNFIINGIDRILISQFTKSYGIYFYTEKKKK--------KCIIIPLKGSW 167

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            ++    + + + V  D++    +  FL+ LG                 +    + F    
Sbjct: 168  LEFII-TNNFLIV-FDKKINFEINVFLICLG--------------YNKKYFFNFFFFKIK 211

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              ++ G K    L++                   K   +   K++ I+   + G    ++
Sbjct: 212  IKIIRGKKRIFFLLNKK-----------------KYFYKIYNKYICISIKKILGKLFGKN 254

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
                +   +     ++ID   +  I +  I    I+++  + N  Y+       K K  K
Sbjct: 255  YFLKKNTFLKF---NIIDINKVNLILNYPIYFFFIIFLKKIINLNYLIYIYKNFKLKINK 311

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + L      +              F    F   KY  S +G  ++  RL L   + +   
Sbjct: 312  ELLQYKKGYIIN------------FFRNLFYKKKYFYSLIGAKRIFKRLFLKKNNKLTIY 359

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +     +  I  +++N     D+ DNL N+ + + G++L  ++     ++ + I  +++
Sbjct: 360  LEIIKKILKFIKFNIQN-----DNFDNLENKLILNCGKLLSIKFDFLFKKVIKFINYKMN 414

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            +      +   ++N+  +   + ++FC+++LSQ  +  N L+ I+H R++S +   G+ +
Sbjct: 415  NFKKYKDL-DFIVNSDIITIGLKDYFCNNELSQFLDQNNPLAEISHNRKISLISGIGIEK 473

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
               G ++RD+H +HY ++CP +T EGHNIGL++SL   ++VN Y FI T Y+    GK+ 
Sbjct: 474  ENCGFDIRDIHYSHYCKVCPIDTPEGHNIGLINSLAYLSKVNKYNFISTIYKISILGKIL 533

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFT--EELVFCRCAGEEILVPREKIDFIDASPK 669
              + +L    +++++I   NS+++              R            ID I+    
Sbjct: 534  G-ITFLDNKFDKHKFIVNFNSTIETIYGEIFRSPYFEARKTNYYYYKKFLNIDLIEICGD 592

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q++S+ ASLIPFL ++D+NR LMG NMQRQAVPL+ +E P VGTG E  +  +S   I++
Sbjct: 593  QIISVGASLIPFLSHNDANRCLMGSNMQRQAVPLIDSENPIVGTGNELEIGLNSNYNILS 652

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               G V   D  +I+I++         + +  Y L K+ R+NQNT +NQ   V  GD V+
Sbjct: 653  DLNGYVLYSDNYKIIIKNN--------NFIKTYFLEKYTRTNQNTILNQYTKVLKGDFVK 704

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              +IIAD  ST  G+++LG+N+ VAFM W+GYNFEDS+L+S  +++++ F SIHI EF  
Sbjct: 705  VGNIIADSNSTKNGEISLGKNLRVAFMSWYGYNFEDSILLSSSILNKNNFNSIHIYEFIT 764

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + +  + G E ++ +    S E +KN  + GII +G  V   D++VGK+ PK +   +PE
Sbjct: 765  VLKYNENGFEIVSNEC-FGSNEKIKNKVKNGIIKIGEFVFSKDVIVGKMIPKKKRKFSPE 823

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKL + +F E   +  +  L VP  + GT++ V  F +    KN+    ++ EQ+    +
Sbjct: 824  EKLFKIVFSESNFNYYEQPLTVPKNIKGTIIAVNDF-KIFYFKNKIFKLLKFEQLNYTCK 882

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            + ++          +++ ++L         K      +  +++      ++   F +   
Sbjct: 883  NINNFFYETFNYYLTKIKKLLFNNKITIKKKRINSYNININNIFKIKCFNKKINFKLNIF 942

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            K   + E LK          ++ F  K       DD    ++R++K+ +A+K+ I  GDK
Sbjct: 943  KNIISNELLKK---------KNIFVYKKINFIKHDDFENSIIRIIKIKIAVKKQIAIGDK 993

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            M+GRHGNKG+VS I+  E+MP+ K G  +D++LNPLGVPSRMNVGQ+ E  L  A     
Sbjct: 994  MSGRHGNKGVVSNIIDYENMPYDKFGNKIDLILNPLGVPSRMNVGQLLEVFL--AGSLNL 1051

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRVAEQWKSGVPVST 1208
             K   L            ++ F++ +          ++ +++  VL++ +  K+ + V  
Sbjct: 1052 IKSFFLKIKNLNKISYFKMKLFIKIIFKCIYDKNINLNIFNNSLVLKIFKNIKNQLNVCV 1111

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
              F   +   +N++++   ++++ + +L+DG+TG+ + + V VGYIY +KLNH+V DK+Y
Sbjct: 1112 HNFYNFNVNKVNNIIKTIGINKNCELLLFDGITGKRYLQLVNVGYIYFMKLNHLVIDKIY 1171

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RS G YS+VTQQPLGGKSN GGQRLGEMEVW ++AYGAA++L+EMLTIKSDD++GR  +
Sbjct: 1172 SRSIGPYSIVTQQPLGGKSNLGGQRLGEMEVWALEAYGAAFLLKEMLTIKSDDILGRIEL 1231

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            Y++I+ G +   +G PESF VL+KE+Q+L   I + 
Sbjct: 1232 YKNIIKGINDANSGIPESFQVLMKEIQSLCFDIKIL 1267


>gi|119953180|ref|YP_945389.1| DNA-directed RNA polymerase subunit beta [Borrelia turicatae
           91E135]
 gi|254765274|sp|A1QZH7|RPOB_BORT9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|119861951|gb|AAX17719.1| DNA-directed RNA polymerase beta chain [Borrelia turicatae 91E135]
          Length = 1155

 Score =  735 bits (1897), Expect = 0.0,   Method: Composition-based stats.
 Identities = 393/939 (41%), Positives = 592/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           GK  EI+D+P+LIE+Q  SY+ FL ++   + +P  NEGL++ F+ VFP+ + +G   LE
Sbjct: 10  GKAEEILDLPNLIEIQLNSYEKFLQLDRLKNNKPLLNEGLESVFRDVFPMKSSNGEVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LKI L L            +  +I+++ +YMG
Sbjct: 70  YEKYYVEYDSLSFTEKECKRKGQSYEAVLKIRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT  GTF++ G +R++VSQ+HRSPG+ F  +K         LY  RIIP +G W++
Sbjct: 121 TIPLMTDRGTFIVNGAERVIVSQIHRSPGVVFYKEKD--------LYYARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ VT FL ALG+D+ E+I+ TFY         D        
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILVTLFLRALGLDTREKIIETFYKIKKIEVNEDT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ ++   +       +G K+T   ++   + GVK + +         +  D
Sbjct: 226 KREITGQYLAVNITIKEN--MTYRAGDKITLQDIEDFLQNGVKEIDL---------IDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +   G+ +I +  +++    E+ + S       L                      R+
Sbjct: 275 GYDSVPGKHFISSDVILNCFEKEDAYFSLKDGFKEL---------------------SRE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y V+ PG+  +   AE+    +FF   +YDL  VGR K++ +  L+       +
Sbjct: 314 SVMLAVYSVLLPGEPISIDNAENDLRTVFFSEKRYDLGHVGRYKLSKKFGLN-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ + +G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMTDIVNTISHLLRIYDGHDVLDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL ++A+VN YGF+ETPYRKV +GKVT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYAKVNDYGFLETPYRKVINGKVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++++ + ++ ++L+  R +G+   +  + ID++D SP+Q+
Sbjct: 553 DEIEYLSAIDEEKKCIAQANAAVNAESNYIDDLISVRVSGDYTTMIPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGME +VAK SG  I AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPQPPIVGTGMERIVAKDSGVVIKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + RIVIR            +D Y L K++R+NQ+T  N   L+K G  V + 
Sbjct: 673 SGTVVLATSKRIVIRPD---NADDEHDLDEYELAKYERTNQDTSFNHSVLIKEGQVVNKG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+LV F+PW+G+N+ED++LISER+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVS + L  +DE GI+ +G  V PGDIL+GK+TPK E  +TPE K
Sbjct: 790 RETKLGPEKVTADIPNVSGKILNKLDENGIVRIGTYVKPGDILIGKVTPKSEGDITPEFK 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   ++ +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKNDV 888



 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 178/505 (35%), Positives = 252/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +I  G  VN G+I+      +    +     LL         +  D  L     V   + 
Sbjct: 719  LIKEGQVVNKGEIIADGPATR-YGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLY 777

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLA-----RDKDDEQVILDRNIYSRLMEILCGQNA 995
                     I+  E  +  E+   ++        +K DE  I+    Y +  +IL G+  
Sbjct: 778  TSIHIKEFSIEVRETKLGPEKVTADIPNVSGKILNKLDENGIVRIGTYVKPGDILIGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   KN
Sbjct: 838  PKSEGDITPEFKLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKN 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++PPGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLPPGVDEILKVYVAKKRRLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAGK------------------------YLSEY 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  +E+ ++I
Sbjct: 977  YDV------------------------------PVFESATNECIQEKLKKAGFNETSKAI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGIIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAYTLQELLTVKSDDMSGRVKIYENIVKGIPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LG  + + +         E+  + 
Sbjct: 1127 GLGFDLSIYDDNGNQIPLTEKEEEL 1151


>gi|203284301|ref|YP_002222041.1| DNA-directed RNA polymerase beta chain [Borrelia duttonii Ly]
 gi|226699373|sp|B5RLU9|RPOB_BORDL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|201083744|gb|ACH93335.1| DNA-directed RNA polymerase beta chain [Borrelia duttonii Ly]
          Length = 1155

 Score =  734 bits (1894), Expect = 0.0,   Method: Composition-based stats.
 Identities = 400/939 (42%), Positives = 592/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           GK  EI+++P+LIE+Q  SY+ FL +    + +P  NEGL++ F+ VFP+ + +G   LE
Sbjct: 10  GKAEEILNLPNLIEIQLNSYEKFLQLERLKNNKPLLNEGLESVFRDVFPMKSSNGEVALE 69

Query: 76  FVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y    D   F   +C  +  +Y   LKI L L            +  +I+++ +YMG
Sbjct: 70  YEKYYIEYDSISFTEKECKRKGQSYEAVLKIRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT  GTF++ G +R++VSQ+HRSPG+ F  +K         LY  RIIP +G W++
Sbjct: 121 TIPLMTDRGTFIVNGAERVIVSQIHRSPGVVFYKEKD--------LYYARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ VT FL ALG+D+ E+I+ TFY         D        
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILVTLFLRALGLDTREKIIETFYKIRKIEVNDDT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  +++++   +       +G K+T   ++   + GVK + +         +  D
Sbjct: 226 KREITGQYLATNITIKEN--MTYRAGDKITLQDIEDFLQNGVKEINL---------IDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +   G+ +I +  +++    E+ + +       L                      R+
Sbjct: 275 GYDSVPGKHFISSDVILNCFEKEDAYFALKDGFKEL---------------------SRE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y V+ PG+  +   AE+    +FF   +YDL  VGR K++ +  LD       +
Sbjct: 314 SVMLAVYSVLLPGEPISIDNAENDLRTVFFSEKRYDLGHVGRYKLSKKFGLD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ + +G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMTDIVNTISHLLRIYDGHDVLDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KPVVSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPVVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL ++++VN YGF+ETPYRKV DGKVT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSKVNDYGFLETPYRKVIDGKVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D+ YLSA++EE + IAQAN+S+  DG++T++LV  R +G+   +  + ID++D SP+Q+
Sbjct: 553 DDIEYLSAIDEEKKCIAQANASVSSDGNYTDDLVSVRISGDYTTMMPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGME +VAK SG  I AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPQPPIVGTGMERIVAKDSGVVIKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G V      +IVI+        S   +D Y L K++R+NQ+T  N   LVK G  V ++
Sbjct: 673 PGRVVLATNKKIVIKPD---NATSERDLDEYELYKYERTNQDTSFNHSVLVKNGQIVNKD 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+LV F+PW+G+N+ED++LISER+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVS + L  +DE GI+ +G  V PGDIL+GK+TPK E  +TPE K
Sbjct: 790 RETKLGPEKVTADIPNVSGKILSKLDENGIVRIGTYVKPGDILIGKVTPKSEGDITPEFK 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKDDV 888



 Score =  459 bits (1180), Expect = e-126,   Method: Composition-based stats.
 Identities = 172/505 (34%), Positives = 249/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D ++          +     LL         +  D  L     V   + 
Sbjct: 719  LVKNGQIV-NKDEIIADGPATRYGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLY 777

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                     I+  E  +  E+    I  ++     K DE  I+    Y +  +IL G+  
Sbjct: 778  TSIHIKEFSIEVRETKLGPEKVTADIPNVSGKILSKLDENGIVRIGTYVKPGDILIGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K+
Sbjct: 838  PKSEGDITPEFKLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKD 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++PPGV  ++KV++A KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLPPGVDEILKVYIAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGEY 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  +E+ +++
Sbjct: 977  YDV------------------------------PVFESATNECIQEKLKKAGFNETSKAV 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGIPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LG  + + +         E+  + 
Sbjct: 1127 GLGFDLSIYDDNGNQIPLTEKEEEL 1151


>gi|203287837|ref|YP_002222852.1| DNA-directed RNA polymerase beta chain [Borrelia recurrentis A1]
 gi|226699376|sp|B5RRJ7|RPOB_BORRA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|201085057|gb|ACH94631.1| DNA-directed RNA polymerase beta chain [Borrelia recurrentis A1]
          Length = 1155

 Score =  734 bits (1894), Expect = 0.0,   Method: Composition-based stats.
 Identities = 400/939 (42%), Positives = 592/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           GK  EI+++P+LIE+Q  SY+ FL +    + +P  NEGL++ F+ VFP+ + +G   LE
Sbjct: 10  GKAEEILNLPNLIEIQLNSYEKFLQLERLKNNKPLLNEGLESVFRDVFPMKSSNGEVALE 69

Query: 76  FVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y    D   F   +C  +  +Y   LKI L L            +  +I+++ +YMG
Sbjct: 70  YEKYYIEYDSISFTEKECKRKGQSYEAVLKIRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT  GTF++ G +R++VSQ+HRSPG+ F  +K         LY  RIIP +G W++
Sbjct: 121 TIPLMTDRGTFIVNGAERVIVSQIHRSPGVVFYKEKD--------LYYARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ VT FL ALG+D+ E+I+ TFY         D        
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILVTLFLRALGLDTREKIIETFYKIRKIEVNDDT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  +++++   +       +G K+T   ++   + GVK + +         +  D
Sbjct: 226 KREITGQYLATNITIKEN--MTYRAGDKITLQDIEDFLQNGVKEINL---------IDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +   G+ +I +  +++    E+ + +       L                      R+
Sbjct: 275 GYDSVPGKHFISSDVILNCFEKEDAYFALKDGFKEL---------------------SRE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y V+ PG+  +   AE+    +FF   +YDL  VGR K++ +  LD       +
Sbjct: 314 SVMLAVYSVLLPGEPISIDNAENDLRTIFFSEKRYDLGHVGRYKLSKKFGLD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ + +G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMTDIVNTISHLLRIYDGHDVLDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KPVVSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPVVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL ++++VN YGF+ETPYRKV DGKVT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSKVNDYGFLETPYRKVIDGKVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D+ YLSA++EE + IAQAN+S+  DG++T++LV  R +G+   +  + ID++D SP+Q+
Sbjct: 553 DDIEYLSAIDEEKKCIAQANASVSSDGNYTDDLVSVRISGDYTTMMPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGME +VAK SG  I AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPQPPIVGTGMERIVAKDSGVVIKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G V      +IVI+        S   +D Y L K++R+NQ+T  N   LVK G  V ++
Sbjct: 673 PGRVVLATNKKIVIKPD---NATSERDLDEYELYKYERTNQDTSFNHSVLVKNGQIVNKD 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+LV F+PW+G+N+ED++LISER+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVS + L  +DE GI+ +G  V PGDIL+GK+TPK E  +TPE K
Sbjct: 790 RETKLGPEKVTADIPNVSGKILSKLDENGIVRIGTYVKPGDILIGKVTPKSEGDITPEFK 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKDDV 888



 Score =  459 bits (1180), Expect = e-126,   Method: Composition-based stats.
 Identities = 172/505 (34%), Positives = 249/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D ++          +     LL         +  D  L     V   + 
Sbjct: 719  LVKNGQIV-NKDEIIADGPATRYGELALGNNLLVGFIPWNGFNYEDAILISERIVKEDLY 777

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                     I+  E  +  E+    I  ++     K DE  I+    Y +  +IL G+  
Sbjct: 778  TSIHIKEFSIEVRETKLGPEKVTADIPNVSGKILSKLDENGIVRIGTYVKPGDILIGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K+
Sbjct: 838  PKSEGDITPEFKLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKD 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++PPGV  ++KV++A KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLPPGVDEILKVYIAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGEY 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  +E+ +++
Sbjct: 977  YDV------------------------------PVFESATNECIQEKLKKAGFNETSKAV 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGIPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LG  + + +         E+  + 
Sbjct: 1127 GLGFDLSIYDDNGNQIPLTEKEEEL 1151


>gi|55846638|gb|AAV67337.1| RNA polymerase beta subunit [Bacteroides fragilis]
          Length = 731

 Score =  733 bits (1892), Expect = 0.0,   Method: Composition-based stats.
 Identities = 357/787 (45%), Positives = 488/787 (62%), Gaps = 68/787 (8%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SS
Sbjct: 1    MDQTNPLAEITHKRRMSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  FA++N  GFIETPYRKV +GKV    N +VYL+A EEE + IAQ N+ L++DG+F  
Sbjct: 61   LCVFAKINDLGFIETPYRKVDNGKVDLSENGLVYLTAEEEEAKIIAQGNAPLNDDGTFIR 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
              V  R   +  +V   +++ +D +P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 121  NKVKSRQDADYPVVEPSEVELMDVAPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LL++EAP VGTG+E  + + S   I A+  G+++ VDA  I I   R+ + +       +
Sbjct: 181  LLRSEAPIVGTGIERQLVRDSRTQIAAEGDGVIDFVDATTIRILYDRTEDEEFVSFEPAL 240

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YR+ KF+++NQN  ++ RP    GD V +  I+ +G ST+ G+LALG+N+LVA+MPW 
Sbjct: 241  KEYRIPKFRKTNQNMTIDLRPTCNKGDRVTKGQILTEGYSTENGELALGKNLLVAYMPWK 300

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN+ED+++++ER+V ED+ TS+H+EE+ +  R+TK G EE+T DIPNVSEE  K++DE 
Sbjct: 301  GYNYEDAIVLNERVVREDLLTSVHVEEYSLEVRETKRGMEELTSDIPNVSEEATKDLDEN 360

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ VGA + PGDIL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G +
Sbjct: 361  GIVRVGARIQPGDILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVI 420

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R  + KN  S   ++  +  +  + + +   L R +  +LM +  G+ +    
Sbjct: 421  IDKKLFSR--VIKNRSSKLADKALLPKIDDEFESKVADLKRILVKKLMVLTEGKVSQGVK 478

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               G +   K +  S+        +         D+     +  L + +      L+   
Sbjct: 479  DYLGAEVIAKGSKFSASDFDSLDFTAIQLSDWTNDDHANGMIRDLILNFIKKYKELDAEL 538

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            K K   I  GD++P G++++ KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL+
Sbjct: 539  KRKKFAITIGDELPAGIIQMAKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLE 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMN+GQIFE  LG A   LG K  + I D     D++       
Sbjct: 599  DGTPVDIVLNPLGVPSRMNIGQIFEAVLGRAGKNLGVKFATPIFDGATLDDLNEWTD--- 655

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       K+G+P                           +
Sbjct: 656  ---------------------------KAGLP------------------------RYCK 664

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            + L DG TGE FD+P TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR
Sbjct: 665  TYLCDGGTGERFDQPATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQR 724

Query: 1294 LGEMEVW 1300
             GEMEVW
Sbjct: 725  FGEMEVW 731


>gi|55846634|gb|AAV67335.1| RNA polymerase beta subunit [Bacteroides sp. Smarlab 3301643]
          Length = 731

 Score =  732 bits (1890), Expect = 0.0,   Method: Composition-based stats.
 Identities = 356/787 (45%), Positives = 488/787 (62%), Gaps = 68/787 (8%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SS
Sbjct: 1    MDQTNPLAEITHKRRMSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  FA++N  GFIETPYRKV +GKV    N ++YL+A EEE + IAQ N+ L++DG+F  
Sbjct: 61   LCVFAKINELGFIETPYRKVENGKVDLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVL 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
              V  R   +  +V   ++D +D +P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 121  NRVKSRQDADFPVVEPSEVDLMDVAPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LL++EAP VGTG+E  + + S   I A+  G+V+ VDA  I I   R+ + +       +
Sbjct: 181  LLRSEAPIVGTGIERQLVRDSRTQITAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPAL 240

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YR+ KF+++NQN  ++ RP+   G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW 
Sbjct: 241  KEYRIPKFRKTNQNMTIDLRPICDKGQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWK 300

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN+ED+++++ER+V ED+ TS+H+EE+ +  R+TK G EE+T DIPNVSEE  K++DE 
Sbjct: 301  GYNYEDAIVLNERVVREDLLTSVHVEEYSLEVRETKRGMEELTSDIPNVSEEATKDLDEN 360

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GA + PGDI++GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 361  GIVRIGARIEPGDIMIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVV 420

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R  + KN  S   ++  +  +  + + +   L R +  +LM +  G+ +    
Sbjct: 421  IDKKLFSR--VIKNRSSKLADKALLPKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVK 478

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               G +   K +  S+        +         D+ +   +  L + +      L+   
Sbjct: 479  DYLGAEVIAKGSKFSASDFDSLDFTSIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAEL 538

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            K K   I  GD++P G++++ KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL 
Sbjct: 539  KRKKFAITIGDELPAGIIQMAKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLA 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMN+GQIFE  LG A   LG K  + I D     D+        
Sbjct: 599  DGTPVDIVLNPLGVPSRMNIGQIFEAVLGRAGKTLGVKFATPIFDGATMEDLDQWTD--- 655

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       K+G+P                           +
Sbjct: 656  ---------------------------KAGLP------------------------RYCK 664

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            + L DG TGE FD+  TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR
Sbjct: 665  TYLCDGGTGEQFDQAATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQR 724

Query: 1294 LGEMEVW 1300
             GEMEVW
Sbjct: 725  FGEMEVW 731


>gi|55846640|gb|AAV67338.1| RNA polymerase beta subunit [Bacteroides ovatus]
          Length = 731

 Score =  732 bits (1889), Expect = 0.0,   Method: Composition-based stats.
 Identities = 357/787 (45%), Positives = 488/787 (62%), Gaps = 68/787 (8%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SS
Sbjct: 1    MDQTNPLAEITHKRRMSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  FA++N  GFIETPYRKV +GKV    N ++YL+A EEE + IAQ N+ L++DG+F  
Sbjct: 61   LCVFAKINDLGFIETPYRKVENGKVDLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVR 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
              V  R   +  +V   ++D +D SP+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 121  NKVKSRQDADFPVVEPTEVDLMDVSPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LL++EAP VGTG+E  + + S   I A+  G+V+ VDA  I I   R+ + +       +
Sbjct: 181  LLRSEAPIVGTGIERQLVRDSRTQITAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPAL 240

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YR+ KF+++NQN  ++ RP+   G  V++ DI+ +G ST+ G+LALG+N+LVA+MPW 
Sbjct: 241  KEYRIPKFRKTNQNMTIDLRPICDRGQRVKKGDILTEGYSTEKGELALGKNLLVAYMPWK 300

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN+ED+++++ER+V ED+ TS+H+EE+ +  R+TK G EE+T DIPNVSEE  K++DE 
Sbjct: 301  GYNYEDAIVLNERVVREDLLTSVHVEEYSLEVRETKRGMEELTSDIPNVSEEATKDLDEN 360

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GA + PGDI++GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 361  GIVRIGARIEPGDIMIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVV 420

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R  + KN  S   ++  +  +  + + +   L R +  +LM +  G+ +    
Sbjct: 421  IDKKLFSR--VIKNRSSKLADKALLPKIDDEFESKVAXLKRILVKKLMTLTEGKVSQGVK 478

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               G +   K +  S+        +         D+ +   +  L + +      L+   
Sbjct: 479  DYLGAEVIAKGSKFSASDFDSLDFTSIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAEL 538

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            K K   I  GD++P G++++ KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL 
Sbjct: 539  KRKKFAITIGDELPAGIIQMAKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLA 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMN+GQIFE  LG A   LG K  + I D     D+        
Sbjct: 599  DGTPVDIVLNPLGVPSRMNIGQIFEAVLGRAGKTLGVKFATPIFDGATMEDLDQWTD--- 655

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       K+G+P                           +
Sbjct: 656  ---------------------------KAGLP------------------------RYCK 664

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            + L DG TGE FD+  TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR
Sbjct: 665  TYLCDGGTGEQFDQAATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQR 724

Query: 1294 LGEMEVW 1300
             GEMEVW
Sbjct: 725  FGEMEVW 731


>gi|13272292|gb|AAK17075.1|AF274444_5 beta subunit of RNA polymerase [Candidatus Carsonella ruddii]
          Length = 1267

 Score =  731 bits (1887), Expect = 0.0,   Method: Composition-based stats.
 Identities = 394/1356 (29%), Positives = 675/1356 (49%), Gaps = 102/1356 (7%)

Query: 14   RKFFGKNP--EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            R  F K       ++P L+  Q  SY+ FL             ++   K  FP+   +  
Sbjct: 9    RFCFSKKKFFHKCNLPYLLHNQIGSYNSFLSSKYNSLFS----IKKVLKQYFPLICNNKN 64

Query: 72   AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              ++    E   P         R+L     L + + + V + +     K         I+
Sbjct: 65   IFIKLKKIELLEPCNTEKYTKIRNLHLFSTLYMYISIYVINKNLNVYKK---------IF 115

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
            +G++P MTK G F+I GI RI++SQ  +S GI+F  +K +          C IIP +G W
Sbjct: 116  LGNIPSMTKKGNFIINGIDRILISQFTKSYGIYFYTEKKKK--------KCIIIPLKGSW 167

Query: 192  MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            ++    + + + V  D++    +  FL+ LG                 +    + F    
Sbjct: 168  LEFII-TNNFLIV-FDKKINFEINVFLICLG--------------YNKKYFFNFFFFKIK 211

Query: 252  ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              ++ G K    L++                   K   +   K++ I+   + G    ++
Sbjct: 212  IKIIRGKKRIFFLLNKK-----------------KYFYKIYNKYICISIKKILGKLFGKN 254

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
                +   +     ++ID   +  I +  I    I+++  + N  Y+       K K  K
Sbjct: 255  YFLKKNTFLKF---NIIDINKVNLILNYPIYFFFIIFLKKIINLNYLIYIYKNFKLKINK 311

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + L      +              F    F   KY  S +G  ++  RL L   + +   
Sbjct: 312  ELLQYKKGYIIN------------FFRNLFYKKKYFYSLIGAKRIFKRLFLKKNNKLTIY 359

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +     +  I  +++N     D+ DNL N+ + + G++L  ++     ++ + I  +++
Sbjct: 360  LEIIKKILKFIKFNIQN-----DNFDNLENKLILNCGKLLSIKFDFLFKKVIKFINYKMN 414

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            +      +   ++N+  +   + ++FC+++LSQ  +  N L+ I+H R++S +   G+ +
Sbjct: 415  NFKKYKDL-DFIVNSDIITIGLKDYFCNNELSQFLDQNNPLAEISHNRKISLISGIGIEK 473

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
               G ++RD+H +HY ++CP +T EGHNIGL++SL   ++VN Y FI T Y K       
Sbjct: 474  ENCGFDIRDIHYSHYCKVCPIDTPEGHNIGLINSLAYLSKVNKYNFISTIY-KYQFLGKI 532

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFT--EELVFCRCAGEEILVPREKIDFIDASPK 669
              + +L    +++++I   NS+++              R            ID I+    
Sbjct: 533  LGITFLDNKFDKHKFIVNFNSTIETIYGEIFRSPYFEARKTNYYYYKKFLNIDLIEICGD 592

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            Q++S+ ASLIPFL ++D+NR LMG NMQRQAVPL+ +E P VGTG E  +  +S   I++
Sbjct: 593  QIISVGASLIPFLSHNDANRCLMGSNMQRQAVPLIDSENPIVGTGNELEIGLNSNYNILS 652

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               G V   D  +I+I++         + +  Y L K+ R+NQNT +NQ   V  GD V+
Sbjct: 653  DLNGYVLYSDNYKIIIKNN--------NFIKTYFLEKYTRTNQNTILNQYTKVLKGDFVK 704

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              +IIAD  ST  G+++LG+N+ VAFM W+GYNFEDS+L+S  +++++ F SIHI EF  
Sbjct: 705  VGNIIADSNSTKNGEISLGKNLRVAFMSWYGYNFEDSILLSSSILNKNNFNSIHIYEFIT 764

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + +  + G E ++ +    S E +KN  + GII +G  V   D++VGK+ PK +   +PE
Sbjct: 765  VLKYNENGFEIVSNEC-FGSNEKIKNKVKNGIIKIGEFVFSKDVIVGKMIPKKKRKFSPE 823

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            EKL + +F E   +  +  L VP  + GT++ V  F +    KN+    ++ EQ+    +
Sbjct: 824  EKLFKIVFSESNFNYYEQPLTVPKNIKGTIIAVNDF-KIFYFKNKIFKLLKFEQLNYTCK 882

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            + ++          +++ ++L         K      +  +++      ++   F +   
Sbjct: 883  NINNFFYETFNYYLTKIKKLLFNNKITIKKKRINSYNININNIFKIKCFNKKINFKLNIF 942

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            K   + E LK          ++ F  K       DD    ++R++K+ +A+K+ I  GDK
Sbjct: 943  KNIISNELLKK---------KNIFVYKKINFIKHDDFENSIIRIIKIKIAVKKQIAIGDK 993

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            M+G HGNKG+VS I+  E+MP+ K G  +D++LNPLGVPSRMNVGQ+ E  L  A     
Sbjct: 994  MSGGHGNKGVVSNIIDYENMPYDKFGNKIDLILNPLGVPSRMNVGQLLEVFL--AGSLNL 1051

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRVAEQWKSGVPVST 1208
             K   L            ++ F++ +          ++ +++  VL++ +  K+ + V  
Sbjct: 1052 IKSFFLKIKNLNKISYFKMKLFIKIIFKCIYDKNINLNIFNNSLVLKIFKNIKNQLNVCV 1111

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
              F   +   +N++++   ++++ + +L+DG+TG+ + + V VGYIY +KLNH+V DK+Y
Sbjct: 1112 HNFYNFNVNKVNNIIKTIGINKNCELLLFDGITGKRYLQLVNVGYIYFMKLNHLVIDKIY 1171

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RS G YS+VTQQPLGGKSN GGQRLGEMEVW ++AYGAA++L+EMLTIKSDD++GR  +
Sbjct: 1172 SRSIGPYSIVTQQPLGGKSNLGGQRLGEMEVWALEAYGAAFLLKEMLTIKSDDILGRIEL 1231

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            Y++I+ G +   +G PESF VL+KE+Q+L   I + 
Sbjct: 1232 YKNIIKGINDANSGIPESFQVLMKEVQSLCFDIKIL 1267


>gi|55846636|gb|AAV67336.1| RNA polymerase beta subunit [Bacteroides sp. Smarlab 3302996]
          Length = 731

 Score =  731 bits (1886), Expect = 0.0,   Method: Composition-based stats.
 Identities = 356/787 (45%), Positives = 486/787 (61%), Gaps = 68/787 (8%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SS
Sbjct: 1    MDQTNPLAEITHKRRMSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  FA++N  GFIETPYRKV +GKV    N ++YL+A EEE + IAQ N+ L++DG+F  
Sbjct: 61   LCVFAKINELGFIETPYRKVENGKVDLSDNGLIYLTAEEEEEKVIAQGNAPLNDDGTFVL 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
              V  R   +  +V   ++D +D +P+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 121  NRVKSRQDADFPVVEPSEVDLMDVAPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LL++EAP VGTG+E  + + S   I A+  G+V+ VDA  I I   R+ + +       +
Sbjct: 181  LLRSEAPIVGTGIERQLVRDSRTQITAEGDGVVDYVDATTIRILYDRTEDEEFVSFEPAL 240

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YR+ KF+++NQN  ++ RP+   G  V   DI+ +G ST+ G+LALG+N+LVA+MPW 
Sbjct: 241  KEYRIPKFRKTNQNMTIDLRPICDKGQRVNNGDILTEGYSTEKGELALGKNLLVAYMPWK 300

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN+ED+++++ER+V ED+ TS+H+EE+ +  R+TK G EE+T DIPNVSEE  K++DE 
Sbjct: 301  GYNYEDAIVLNERVVREDLLTSVHVEEYSLEVRETKRGMEELTSDIPNVSEEATKDLDEN 360

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +GA + PGDI++GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 361  GIVRIGARIEPGDIMIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLKGVV 420

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R  + KN  S   ++  +  +  + + +   L R +  +LM +  G+ +    
Sbjct: 421  IDKKLFSR--VIKNRSSKLADKALLPKIDDEFESKVADLKRILVKKLMTLTEGKVSQGVK 478

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               G +   K +  S+        +         D+ +   +  L + +      L+   
Sbjct: 479  DYLGAEVIAKGSKFSASDFDSLDFTSIQLSNWTSDDHINGMIRDLVMNFIKKYKELDAEL 538

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            K K   I  GD++P G++++ KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL 
Sbjct: 539  KRKKFAITIGDELPAGIIQMAKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLA 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMN+GQIFE  LG A   LG K  + I D     D+        
Sbjct: 599  DGTPVDIVLNPLGVPSRMNIGQIFEAVLGRAGKTLGVKFATPIFDGATMEDLDQWTD--- 655

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       K+G+P                           +
Sbjct: 656  ---------------------------KAGLP------------------------RYCK 664

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            + L DG TGE FD+  TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR
Sbjct: 665  TYLCDGGTGEQFDQAATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQR 724

Query: 1294 LGEMEVW 1300
             GEMEVW
Sbjct: 725  FGEMEVW 731


>gi|49065925|gb|AAT49053.1| RNA polymerase beta subunit [Capnocytophaga cynodegmi]
          Length = 733

 Score =  730 bits (1885), Expect = 0.0,   Method: Composition-based stats.
 Identities = 377/788 (47%), Positives = 498/788 (63%), Gaps = 67/788 (8%)

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 2    QFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLI 61

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            SSL  F++VNA GFIETPY KV  GKV   D+ YLSA EEE   I  AN SLD +G+ TE
Sbjct: 62   SSLAVFSKVNAMGFIETPYHKVTKGKVDLKDMTYLSAEEEEGLKIGMANISLDAEGNITE 121

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  +  G+  ++   +++FID +P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 122  ERVVVKEDGDFPVIEPNQVEFIDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVP 181

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LLK E+P VGTG+E  VA  S   + A+  G VE VDA +I+I   R+    L       
Sbjct: 182  LLKPESPIVGTGLERRVASDSRVLMNAEGDGTVEYVDAEKIIITYDRTENQKLVSFDEDE 241

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
             +Y L+KFQ++NQ TC+N +P+V+ GD V +  ++ +G +T  G+LALGRNM VAFMPW 
Sbjct: 242  TVYNLIKFQKTNQGTCINLKPIVRKGDRVTKGQVLCEGYATQQGELALGRNMKVAFMPWK 301

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFED+++ISER+V ED+FTSIHI+E+ +  RDTKLG EE+T DIPNVSEE  K++DE 
Sbjct: 302  GYNFEDAIVISERVVREDIFTSIHIDEYSLEVRDTKLGAEELTNDIPNVSEEATKDLDEN 361

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G+I +GAE+ PGDIL+GKITPKGES  TPEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 362  GMIRIGAEIGPGDILIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLYGVV 421

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R   DK +R    E   I ++  + +     L   +  +L  ++ G+ +    
Sbjct: 422  IDKKLFSRVVKDKRKRGKDKED--IAVVEANFNSNFQSLKDKLVKKLFSLVDGKTSQGVL 479

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQWW--QFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
               G +   K    ++ ++                +++    ++ L   Y    + L+  
Sbjct: 480  NDLGEEIIAKGRKFTTKMLDSIEDYAHLVSDGWTDEKETNSLIDDLLHNYRIKLNDLQGA 539

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
             + +   I  GD++P G+L++ KV++A KR ++ GDKMAGRHGNKGIV+RI+  EDMPFL
Sbjct: 540  LRREKFTISVGDELPAGILKLAKVYIAKKRKLKVGDKMAGRHGNKGIVARIVRDEDMPFL 599

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDIVLNPLGVPSRMN+GQI+ET LGWA   LG+K  + I D  +   I+ L    
Sbjct: 600  EDGTPVDIVLNPLGVPSRMNIGQIYETVLGWAGQKLGQKYATPIFDGASLEQINELTD-- 657

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                        K+G+P                          G
Sbjct: 658  ----------------------------KAGIP------------------------RFG 665

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
             + LYDG TGE FD+P TVG IYM+KL HM+ DK++ARS G YSL+TQQPLGGK+  GGQ
Sbjct: 666  HTYLYDGGTGERFDQPATVGVIYMIKLGHMIDDKMHARSIGPYSLITQQPLGGKAQFGGQ 725

Query: 1293 RLGEMEVW 1300
            R GEMEVW
Sbjct: 726  RFGEMEVW 733


>gi|219685446|ref|ZP_03540264.1| DNA-directed RNA polymerase, beta subunit [Borrelia garinii Far04]
 gi|219673002|gb|EED30023.1| DNA-directed RNA polymerase, beta subunit [Borrelia garinii Far04]
          Length = 1155

 Score =  729 bits (1883), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/939 (41%), Positives = 592/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKNINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDAISGKCFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++ + +G + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 DELEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVVLATSNKIVVKPFES---KNAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  464 bits (1193), Expect = e-128,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLAPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDENGNQVPLTEKEEEL 1151


>gi|295112261|emb|CBL29011.1| DNA-directed RNA polymerase subunit beta [Synergistetes bacterium
           SGP1]
          Length = 1222

 Score =  729 bits (1881), Expect = 0.0,   Method: Composition-based stats.
 Identities = 411/942 (43%), Positives = 575/942 (61%), Gaps = 83/942 (8%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R R  FG+  ++ID+PD+IEVQ+ SY  F   ++ PD R  +GLQ   + +FPI ++ 
Sbjct: 9   RTRQRYTFGRAHDLIDMPDMIEVQRDSYQWFYQDDVEPDARRAQGLQELLQEIFPIESYD 68

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           G   LEFV Y  DPP+   ++   +DLT++ P++ T+ L               + KE+ 
Sbjct: 69  GQFSLEFVRYYIDPPERSEEEARQKDLTWSRPIRATIGLT---------NTKTGESKEKD 119

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I++G+ P+MT  GTF++ G +R+V++QL RS G++F      + + G    + ++IPD+G
Sbjct: 120 IFLGEFPVMTDRGTFIVNGTERVVINQLARSAGVYFT----YSGVPGSDSCSAKLIPDRG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            W+D    S DI+ V ID RRK+PVT             L  F           F   P 
Sbjct: 176 AWLDFSMASGDIVSVNIDNRRKLPVTLL-----------LKAFGVADNDEILSMFAAAPY 224

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                                                             SD + G   A
Sbjct: 225 FME----------------------------------------------YSDEMRGKLAA 238

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
           ED+   + G   +  G  I  + L+E++H        + V  ++ +  +  TL  D  + 
Sbjct: 239 EDVTGPD-GAAIVRRGRPITRELLDELYHKNPGGRGGIEVIGLDLSLAL--TLERDGTRS 295

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             +A+ +I+R +RP + +    A      LFFDS +Y L  VGR K+N RL ++  +DVR
Sbjct: 296 PDEAMQEIFRRLRPNEPARVENARDYIRSLFFDSRRYTLGRVGRYKLNRRLGMNLSEDVR 355

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +  +DI+AII+ +  +R      DDID+LGNRR+RS+GE+L+NQ R+GLLRMER ++ER
Sbjct: 356 LLTLDDIVAIIREMFAMRAEGKKSDDIDHLGNRRIRSIGELLQNQIRIGLLRMERIVRER 415

Query: 490 ISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           +++  D++ V P DLIN +P+ +A+ EF+ S QLSQ  +  N L+ +TH RRLSALG GG
Sbjct: 416 MTTTPDLNKVTPPDLINVRPIAAALREFYGSGQLSQFMDQTNPLAEVTHRRRLSALGPGG 475

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R RAG E RDVH THYGR+CP ET EG NIGLVSSLT++AR+N +GF+ TP RKV +G
Sbjct: 476 LSRERAGFEARDVHYTHYGRVCPIETPEGPNIGLVSSLTTYARLNEHGFLITPRRKVTNG 535

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKIDFIDAS 667
           K+T+ + +LSA EE+  Y+A AN+ L+EDG     +    R   +   +P EK++++D S
Sbjct: 536 KLTDKIEFLSADEEDQYYVAMANTPLEEDGVTIAGDSCPTRHQDDIDTIPVEKVNYMDVS 595

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQ+VS + +LIPFLE+DD+NR LMG NMQRQAVPL+  EAP VGTG+E  VA+ SG+ +
Sbjct: 596 PKQIVSPSTALIPFLEHDDANRALMGSNMQRQAVPLIMPEAPMVGTGIEHRVARDSGSCV 655

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           VA        VDA  +V          S  G   Y L+KF+RSNQ T ++QRP V  GD 
Sbjct: 656 VA--------VDAGEVVYVDSREIRIRSRRGERKYPLIKFRRSNQGTVIHQRPTVAKGDR 707

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V + +IIADG S + G+LALG+N+LVAF+PW GYNFED++L+SE +V ED F+SIHIEE+
Sbjct: 708 VDKGEIIADGQSIENGELALGQNVLVAFVPWEGYNFEDAILLSENLVKEDKFSSIHIEEY 767

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           E+ AR+TKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GDILVGK+TPKGES  T
Sbjct: 768 EIDARETKLGPEEITRDIPNVGEDMLRNLDDSGIIRIGAEVNAGDILVGKVTPKGESDQT 827

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PEEKLLRAIFGEKA +VRD SL++P G  G VV ++   R+ 
Sbjct: 828 PEEKLLRAIFGEKAREVRDNSLKLPHGSRGKVVAIKHMERND 869



 Score =  341 bits (875), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 150/596 (25%), Positives = 222/596 (37%), Gaps = 82/596 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +++   P  G   E  +          V     +       R      E
Sbjct: 620  MGSNMQRQAVPLIMPEAPMVGTGIEHRVARDSGSCVVAVDAGEVVYVDSREIRIRSRRGE 679

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          I +   +  G  V+ G+I+    + +    +   + +L A    
Sbjct: 680  RKYPLIKFRRSNQGTVIHQRPTVAKGDRVDKGEIIADGQSIEN-GELALGQNVLVAFVPW 738

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DE 974
            +  +  D  L   + V            + ID  E  +  E     I  +  D     D+
Sbjct: 739  EGYNFEDAILLSENLVKEDKFSSIHIEEYEIDARETKLGPEEITRDIPNVGEDMLRNLDD 798

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I+         +IL G+    G         L   +  E  R           +V+ N
Sbjct: 799  SGIIRIGAEVNAGDILVGKVTPKGESDQTPEEKLLRAIFGEKAR-----------EVRDN 847

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               L          ++      +E+    + M  G++R VKV+VA  R I          
Sbjct: 848  SLKLPHGSRGKVVAIK-----HMERNDAPNTMSAGIIRTVKVYVAQWRKI---------- 892

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
                                                  VG              G K   
Sbjct: 893  -------------------------------------TVG-------DKMAGRHGNKGVV 908

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                   +    P  + ++ V+       +++       +       +G  V+TPVF+GA
Sbjct: 909  SRILPVEDMPYLPDGTPVDVVLNPLGVPSRMNLGQVLETIMGFVAVNNGWHVATPVFEGA 968

Query: 1215 DEEAINSMLRMA------DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             E  I   ++        DL E G  +L DG TGEP ++ VT+G +YMLKLNH+V DK++
Sbjct: 969  QETEIFERMKELADEKYPDLTEDGMIVLRDGRTGEPMEKKVTIGCMYMLKLNHLVDDKIH 1028

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++ YGAA VLQEMLT+KSDD+ GR + 
Sbjct: 1029 ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAANVLQEMLTVKSDDIRGRDKT 1088

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            YE IV G    + G PESF VLVKE+Q LGL +++E           +  +    E
Sbjct: 1089 YERIVKGQSLVKPGMPESFRVLVKELQGLGLDVEVEYDDGTIGGIPLDEDEEKLPE 1144


>gi|207721917|ref|YP_002252355.1| dna-directed rna polymerase beta chain (partial sequence protein
            [Ralstonia solanacearum MolK2]
 gi|206587087|emb|CAQ17671.1| probable dna-directed rna polymerase beta chain (partial sequence
            protein [Ralstonia solanacearum MolK2]
          Length = 820

 Score =  729 bits (1881), Expect = 0.0,   Method: Composition-based stats.
 Identities = 358/675 (53%), Positives = 484/675 (71%), Gaps = 15/675 (2%)

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREK 660
            RKV + K+T++V YLSA+EE    +AQAN+++D+DG+  +ELV  R     E  +V  ++
Sbjct: 149  RKVENSKLTDEVHYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSERETRMVTPDR 208

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            + +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA
Sbjct: 209  VQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPLVGTGIERTVA 268

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
              SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RSNQNT +NQRP
Sbjct: 269  VDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRP 328

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            +VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LISER+V+ED +T
Sbjct: 329  MVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISERVVAEDRYT 388

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            SIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  GD+LVGK+TP
Sbjct: 389  SIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEAGDVLVGKVTP 448

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+ +++R+ S+ 
Sbjct: 449  KGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGVTRDKRAQSII 508

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ + +++  +  
Sbjct: 509  DEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLSKGTALTKEYLADLDKWH 568

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV+++VKV++A+
Sbjct: 569  WFDIRPSDEEVAAQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGVIKMVKVYLAV 628

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSRMNVGQI ETH
Sbjct: 629  KRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSRMNVGQILETH 688

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWA  GLG++I +++   KA    + LR  L ++       E +    D  VL +AE  
Sbjct: 689  LGWAARGLGERIGNML---KAQAKAAELRKLLGQIYNESGKVEDLDSLTDAEVLELAENL 745

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQS----------ILYDGLTGEPFDRPVT 1250
            K GVP +TPVFDGA E+ I  ML +A   +  +            L+DG TGE F+RPVT
Sbjct: 746  KKGVPFATPVFDGAHEDEIRRMLDLAYPADIAKEKGLTASKQQVTLFDGRTGEAFERPVT 805

Query: 1251 VGYIYMLKLNHMVSD 1265
            +G ++MLKL+H+V D
Sbjct: 806  LGVMHMLKLHHLVDD 820


>gi|219684654|ref|ZP_03539597.1| DNA-directed RNA polymerase, beta subunit [Borrelia garinii PBr]
 gi|219672016|gb|EED29070.1| DNA-directed RNA polymerase, beta subunit [Borrelia garinii PBr]
          Length = 1155

 Score =  728 bits (1879), Expect = 0.0,   Method: Composition-based stats.
 Identities = 390/939 (41%), Positives = 593/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNVKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKNINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDAISGKCFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++ + +G + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 DELEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMES+VAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESIVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     ++  +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVVLATSNKIVVKPFES---ENSKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRDGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRDGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLAPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPIEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQVPLTEKEEEL 1151


>gi|111115218|ref|YP_709836.1| DNA-directed RNA polymerase subunit beta [Borrelia afzelii PKo]
 gi|123341351|sp|Q0SNB8|RPOB_BORAP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|110890492|gb|ABH01660.1| DNA-directed RNA polymerase [Borrelia afzelii PKo]
          Length = 1155

 Score =  728 bits (1878), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/939 (41%), Positives = 593/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDTLNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R++VSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVIVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY                  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNI-------KKIKVEEGT 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +         V  D
Sbjct: 226 KRDLPGQYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDVSGKYFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGSD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           N++ YLSA++EE + IAQAN++ + DG + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 NELEYLSAIDEEKKCIAQANAAFNSDGKYLEDLVSVRISGDYTTTNPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E +       +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSNKIVVKPFESENVK---DLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAGK------------------------YLSES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQVPLTEKEEEL 1151


>gi|224531803|ref|ZP_03672435.1| DNA-directed RNA polymerase, beta subunit [Borrelia valaisiana
           VS116]
 gi|224511268|gb|EEF81674.1| DNA-directed RNA polymerase, beta subunit [Borrelia valaisiana
           VS116]
          Length = 1155

 Score =  728 bits (1878), Expect = 0.0,   Method: Composition-based stats.
 Identities = 395/939 (42%), Positives = 589/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRAEEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALDFTEKECKRKGQSYEAVLKVRLNLQFL---------ATGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D        
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITFFLRALGFDTREKIIETFYNIKKIKVEDDT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +             
Sbjct: 226 KRDLPGKYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIEL------------- 270

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            V+ +          V     L                + +             K   ++
Sbjct: 271 -VDFDGYNDVFGKYFVSSNVIL----------------NCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+ F  +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDFKTIFFSERRYDLGRVGRYKLSKKFGFD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMNDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++ D +G + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 DELEYLSAIDEEKKCIAQANAAFDSNGKYLEDLVSVRISGDYTTTNPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  I AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVIKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IVI+  E     +   +D Y+++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSNKIVIKPFES---ENAKDLDEYQIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAGK------------------------YLNES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGIPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQVPLTEKEEEL 1151


>gi|218249452|ref|YP_002374906.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           ZS7]
 gi|226321704|ref|ZP_03797230.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           Bol26]
 gi|226699372|sp|B7J1W1|RPOB_BORBZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|218164640|gb|ACK74701.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           ZS7]
 gi|226232893|gb|EEH31646.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           Bol26]
 gi|312149116|gb|ADQ29187.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           N40]
          Length = 1155

 Score =  727 bits (1876), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/939 (41%), Positives = 589/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYSSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|195941261|ref|ZP_03086643.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi 80a]
          Length = 1155

 Score =  727 bits (1876), Expect = 0.0,   Method: Composition-based stats.
 Identities = 390/939 (41%), Positives = 590/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY                  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVENGT------- 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +         V  D
Sbjct: 226 KRDLPGQYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|216264883|ref|ZP_03436875.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           156a]
 gi|215981356|gb|EEC22163.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           156a]
          Length = 1155

 Score =  727 bits (1876), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/939 (41%), Positives = 588/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYSSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGVVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|51598646|ref|YP_072834.1| DNA-directed RNA polymerase subunit beta [Borrelia garinii PBi]
 gi|81610031|sp|Q661M9|RPOB_BORGA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|51573217|gb|AAU07242.1| DNA-directed RNA polymerase [Borrelia garinii PBi]
          Length = 1155

 Score =  726 bits (1875), Expect = 0.0,   Method: Composition-based stats.
 Identities = 390/939 (41%), Positives = 592/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY                S 
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVED-------ST 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +         V  D
Sbjct: 226 KRDLPGQYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDAISGKCFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMYDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++ + +G + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 DELEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTNPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V   
Sbjct: 673 SGEVILATSSKIVVKPFES---ENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVESG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVESGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQVPLTEKEEEL 1151


>gi|312148478|gb|ADQ31137.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           JD1]
          Length = 1155

 Score =  726 bits (1875), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/939 (41%), Positives = 588/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGSLFPGEPISIDNAENDLRTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGVVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|15594734|ref|NP_212523.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi B31]
 gi|221217800|ref|ZP_03589268.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           72a]
 gi|224533726|ref|ZP_03674314.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225549089|ref|ZP_03770064.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           94a]
 gi|225550207|ref|ZP_03771167.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           118a]
 gi|3915861|sp|Q59191|RPOB_BORBU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|2688293|gb|AAB91501.1| DNA-directed RNA polymerase (rpoB) [Borrelia burgdorferi B31]
 gi|221192477|gb|EEE18696.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           72a]
 gi|224513019|gb|EEF83382.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225369319|gb|EEG98772.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           118a]
 gi|225370315|gb|EEG99753.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           94a]
          Length = 1155

 Score =  726 bits (1875), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/939 (41%), Positives = 588/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGVVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|223888904|ref|ZP_03623495.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           64b]
 gi|223885720|gb|EEF56819.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
           64b]
          Length = 1155

 Score =  726 bits (1875), Expect = 0.0,   Method: Composition-based stats.
 Identities = 390/939 (41%), Positives = 589/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   +       +
Sbjct: 314 SVMLAVYSSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFN-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|216263864|ref|ZP_03435858.1| DNA-directed RNA polymerase, beta subunit [Borrelia afzelii ACA-1]
 gi|215979908|gb|EEC20730.1| DNA-directed RNA polymerase, beta subunit [Borrelia afzelii ACA-1]
          Length = 1155

 Score =  726 bits (1873), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/939 (41%), Positives = 593/939 (63%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDTLNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R++VSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVIVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY                  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNI-------KKIKVEEGT 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +         V  D
Sbjct: 226 KRDLPGQYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDVSGKYFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGSD-DLSTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           N++ YLSA++EE + IAQAN++ + DG + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 NELEYLSAIDEEKKCIAQANAAFNSDGKYLEDLVSVRISGDYTTTNPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSNKIVVKPFES---ENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GI+ +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIMRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  462 bits (1189), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIMRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAGK------------------------YLSES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQVPLTEKEEEL 1151


>gi|225552230|ref|ZP_03773170.1| DNA-directed RNA polymerase, beta subunit [Borrelia sp. SV1]
 gi|225371228|gb|EEH00658.1| DNA-directed RNA polymerase, beta subunit [Borrelia sp. SV1]
          Length = 1155

 Score =  726 bits (1873), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/939 (41%), Positives = 589/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDVLNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLINIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E +       +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVVLATSSKIVVKPFEAENVK---DLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  460 bits (1184), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDAGNQVPLTEKEEEL 1151


>gi|325972668|ref|YP_004248859.1| DNA-directed RNA polymerase subunit beta [Spirochaeta sp. Buddy]
 gi|324027906|gb|ADY14665.1| DNA-directed RNA polymerase subunit beta [Spirochaeta sp. Buddy]
          Length = 1172

 Score =  726 bits (1873), Expect = 0.0,   Method: Composition-based stats.
 Identities = 391/957 (40%), Positives = 565/957 (59%), Gaps = 78/957 (8%)

Query: 11  GRVRKFF--GKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNEGLQAAFKSVFPI 65
             + + +   +  E+ ++P+LI +Q  SY+ FL +           + GL+  F+S FPI
Sbjct: 6   KSITRTYIGSELHEVCELPNLIGIQLDSYERFLQLERCKQGLGPDSSYGLEEVFQSTFPI 65

Query: 66  TAFSGAAMLEFVSYE--FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            + +G   L +  Y    D  KF   +C  +  +++VP+K+T+ L            S  
Sbjct: 66  DSPNGEMRLAYKGYTIDLDNIKFSETECKKKGRSFSVPIKVTISL----------EFSNG 115

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +++E+ I+ GD+PLMT  GTF+I G +R+VVSQ+HRSPG+ F         + K +Y+ R
Sbjct: 116 EMREKEIFFGDIPLMTDRGTFIINGAERVVVSQIHRSPGVIF--------SNEKDVYSSR 167

Query: 184 IIPDQGLWMDIEF-DSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQR 241
           IIP +G W++ E  D K +I  +IDR++++  T FL A+G D+ E+IL  FY        
Sbjct: 168 IIPYRGSWLEFEIDDKKHLIFTKIDRKKRILGTLFLRAIGFDTREKILEQFYSSETVELA 227

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            D           +     +       T ++V+ +G  L +  +  L +  V  + + + 
Sbjct: 228 DDSDLKSNLENRYLFKDVYAQV---EKTEKKVLRAGDMLHAHEIDELLKLNVHEVQLVNL 284

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              G                                   +    IL    + +  Y R  
Sbjct: 285 RGEGT----------------------------------LHSDMILNCFEIEDAKYTREG 310

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL- 420
                   ++D L  I+ V+ PG++     AE     +FF + +YDL +VGR K N +  
Sbjct: 311 C---DEPTKEDVLSPIFSVLMPGEMIAIERAEKDLPDMFFSNRRYDLGSVGRYKFNKKFG 367

Query: 421 ------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
                   +   D+  +  +DI+  +  L+ +   +  +DDID+LGNRRVRSVGE+L+N 
Sbjct: 368 TGTEEEEENASTDLTVLTPQDIVNTMDFLIKVFIREHNVDDIDHLGNRRVRSVGELLQNA 427

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            +    RMER  KER++  +  SV PQDLI+ KP+V+A+ EFF SSQLSQ  + VN L+ 
Sbjct: 428 LKSAFARMERIAKERMNL-ETGSVKPQDLISIKPIVAAIKEFFGSSQLSQFMDQVNPLAE 486

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRL+ALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+ SL ++ R+N 
Sbjct: 487 LTHKRRLNALGPGGLSRDRAGFEVRDVHYTHYGRICPIETPEGPNIGLIVSLANYTRINQ 546

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           +GF+ETPYRKV +G V+    YL A +EE  +IAQA++ LD DG+F E+ V  R +G+  
Sbjct: 547 HGFLETPYRKVVNGVVSKQYRYLDANDEEKFFIAQASAKLDTDGNFQEKEVPVRRSGDYS 606

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
             P  +I ++D  PKQV+S+AASLIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTG
Sbjct: 607 TKPPVEIKYMDVDPKQVISVAASLIPFLEHDDANRALMGSNMQRQAVPLVFPETPRVGTG 666

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME+  A  SG  + AKR+G +  V + R+VI+     +      +D Y + K+QR+NQ+T
Sbjct: 667 MEAKTAYDSGVLVKAKRSGTITYVSSDRVVIQPDSAQI---QGQLDTYEIQKYQRTNQDT 723

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C NQ+P+V  G  V    ++ADGP+T   +LALGRN+LV F+PW+GYN+ED++LISER+V
Sbjct: 724 CFNQKPIVSFGQHVEAGAVLADGPATQSAELALGRNILVGFVPWNGYNYEDAVLISERVV 783

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +D+FTS+HI+EF    R+TKLGPE++TRDIPN SE+ L+ +DE GI+ +G  V PG IL
Sbjct: 784 KDDIFTSVHIKEFTTDIRETKLGPEKLTRDIPNTSEKMLEQLDEDGIVRIGTAVRPGSIL 843

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPK ES  TPE KLL +IFGEKA +VRDTSL+VP G  GTV+D++   R   D
Sbjct: 844 VGKVTPKSESDTTPEFKLLNSIFGEKAKEVRDTSLKVPHGTEGTVIDIQRLKRSNND 900



 Score =  341 bits (875), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 143/504 (28%), Positives = 204/504 (40%), Gaps = 75/504 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPSGVSGT 938
            I+  G  V  G +L      +          L+  +   G    D    S RV      T
Sbjct: 730  IVSFGQHVEAGAVLADGPATQSAELALGRNILVGFVPWNGYNYEDAVLISERVVKDDIFT 789

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCGQNAV 996
             V ++ F     +       + R+      +  ++ DE  I+      R   IL G+   
Sbjct: 790  SVHIKEFTTDIRETKLGPEKLTRDIPNTSEKMLEQLDEDGIVRIGTAVRPGSILVGKVTP 849

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                  +  T     L++     +  +      KV    E                   +
Sbjct: 850  KS----ESDTTPEFKLLNSIFGEKAKEVRDTSLKVPHGTEGTV-------------IDIQ 892

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              K    D++PPGV   VKV +A KR +        R G+K                   
Sbjct: 893  RLKRSNNDELPPGVEETVKVLIATKRKL--------RQGDK------------------- 925

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
                          M                 G K        + +       + L+  +
Sbjct: 926  --------------M-------------AGRHGNKGVVSRILAEEDMPYMADGTPLDVCL 958

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                   +++              K     STPVF  A    I   +R A L E+ +++L
Sbjct: 959  NPLGVPSRMNIGQLMETQLGWAAVKLDKWYSTPVFQSASMAQIEEKMREAGLPENSKTVL 1018

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y+GLTG PF  PV  GYIY LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGE
Sbjct: 1019 YNGLTGVPFVNPVFCGYIYYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRLGE 1078

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGAA  LQE+LTIKSDD+ GR ++YESIV G      G PE+FNVLV+E++ 
Sbjct: 1079 MEVWALEAYGAANTLQELLTIKSDDMNGRVKIYESIVKGEPATTAGMPEAFNVLVQEIRG 1138

Query: 1357 LGLSIDLENSRTKNSAKMEEIPDF 1380
            L L + + +S+ +     E   + 
Sbjct: 1139 LALDMSVYDSKGRQVPLTERDEEL 1162


>gi|55846642|gb|AAV67339.1| RNA polymerase beta subunit [Bacteroides vulgatus]
          Length = 731

 Score =  725 bits (1872), Expect = 0.0,   Method: Composition-based stats.
 Identities = 355/787 (45%), Positives = 484/787 (61%), Gaps = 68/787 (8%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+SS
Sbjct: 1    MDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  +A++N  GFI TPYRKV DGKV      + YL+A EEE++ IAQ N+ LD++G F  
Sbjct: 61   LCVYAKINELGFISTPYRKVADGKVDISDEGIEYLTAEEEEDKIIAQGNAPLDDEGKFVR 120

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  R   +  +V  ++++ +D SP+Q+ SIAASLIPFLE+DD+NR LMG NM RQAVP
Sbjct: 121  EKVKARRDADYPVVTPDQVELMDVSPQQIASIAASLIPFLEHDDANRALMGSNMMRQAVP 180

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGV 759
            LL+ EAP VGTG+E  + + S   I A+  G+VE VDA  I I   R+ + +       +
Sbjct: 181  LLRTEAPIVGTGIEKQLVEDSRTQIAAEGDGVVEYVDATTIRILYDRNEDEEFVSFEPAL 240

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YR+ KF+++NQ+  ++ RP    G  V++ DI+ +G ST  G+LALG+N+LVA+MPW 
Sbjct: 241  KEYRIPKFRKTNQSMTIDLRPTCDKGQRVKKGDILTEGYSTQGGELALGKNLLVAYMPWK 300

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN+ED+++++ER+V ED+ TS+H++E+ +  R+TK G EE+T DIPNVSEE  K++DE 
Sbjct: 301  GYNYEDAIVLNERVVREDLLTSVHVDEYILEVRETKRGMEELTSDIPNVSEEATKDLDEN 360

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ VGA + PGDIL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G V
Sbjct: 361  GIVRVGARIEPGDILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKASPSLRGVV 420

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS-- 997
            +D ++F+R  + K+    + ++  +  L  + +++   L   +  +L+ +  G+ +    
Sbjct: 421  IDKKLFSR--VIKSRSEKNADKAILPKLNDEFEEKAAKLKDILIEKLLVLTNGKVSQGVK 478

Query: 998  ---GPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               G +   K    +   +     +         D      +  L + Y      L+   
Sbjct: 479  DYLGTEVIAKGAKFTKRDLESLDYTIIQLSKWTADAHKNDMIRDLVMNYLKKYKELDAEL 538

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            K K   I  GD++P G++++ KV++A KR I  GDKMAGRHGNKGIVSR++  EDMPFL 
Sbjct: 539  KRKKFAITIGDELPAGIIQMAKVYIAKKRKIGVGDKMAGRHGNKGIVSRVVRQEDMPFLA 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMN+GQIFE  LG A   LG K  + I D  +  D++       
Sbjct: 599  DGTPVDIVLNPLGVPSRMNIGQIFEAVLGRAGKELGVKFATPIFDGASMDDLNEWTD--- 655

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       K+G+P                           +
Sbjct: 656  ---------------------------KAGLP------------------------RYCK 664

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            + L DG TGE FD+P TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR
Sbjct: 665  TYLCDGGTGERFDQPATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQR 724

Query: 1294 LGEMEVW 1300
             GEMEVW
Sbjct: 725  FGEMEVW 731


>gi|309778358|ref|ZP_07673283.1| DNA-directed RNA polymerase, beta subunit [Erysipelotrichaceae
            bacterium 3_1_53]
 gi|308913889|gb|EFP59704.1| DNA-directed RNA polymerase, beta subunit [Erysipelotrichaceae
            bacterium 3_1_53]
          Length = 1403

 Score =  724 bits (1868), Expect = 0.0,   Method: Composition-based stats.
 Identities = 323/1445 (22%), Positives = 542/1445 (37%), Gaps = 172/1445 (11%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +V +G    R+ + K    +++P+L+E+Q  S++ F           NEG+   F  +
Sbjct: 7    YRIVASGKKAERRDYSKVSGHLELPNLVEIQTDSFEWF----------KNEGIGEVFNEI 56

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            +PI  + G   L+F  YEF  PKF+ ++ ++R+  +A PLK  + L + D        + 
Sbjct: 57   YPIQNYGGNIKLKFAGYEFGEPKFNAEESMYRECNFAAPLKARMELEITDN-------TT 109

Query: 123  KDI--KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             ++  K + +++GD PLMT+ GTF+I G +R++VSQ+ RSPG +F    G    +GK  +
Sbjct: 110  GEVINKWEDVFLGDFPLMTETGTFIINGAERVIVSQIVRSPGAYF--STGYEEKTGKESF 167

Query: 181  ACRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMD-----SEEI-- 228
            AC +IP +G W++   + K      ++++ IDR+RK+  +    A+GM      SE+   
Sbjct: 168  ACELIPSRGTWLEFLTEVKKASTGRVLNMSIDRKRKMLSSILFKAIGMSVDLDRSEDAHD 227

Query: 229  ---LSTF-----------------------------------YPKIVYSQRGDFWCFPLS 250
               + TF                                   Y +I  +   D       
Sbjct: 228  TMQIKTFLKAMGRDIVEDVAIDDEDREFMNLYLTLYASFFGKYEEIENTLMADKVKTTQE 287

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLGITSDCLCGLYV 308
            A   +   + S  +  +D G   + + K        L       ++      + +   ++
Sbjct: 288  ALLSIYENQRSDEIPTLD-GSITLMNAKFFDPRRYDLTKAGRYKLRKKLNAINRIDKHHL 346

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+DI++ + G +++ +G +++      +         +     VN   +       DK  
Sbjct: 347  AQDILDAD-GNVFMPSGTMVNRDERNALRK------ELEKGMHVNAFPFNPLFNHPDKVY 399

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                  L +   +  GDV       +++          D+  + +    + ++       
Sbjct: 400  VPSSNHLGLVGRVLAGDV--ELEDGTLYEGSILSEQ--DVEAIVKGVEKVAVHGGIIAKK 455

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--MERSI 486
              + +E++ A++     +          D  G   V   G+   + Y        +  + 
Sbjct: 456  VALTRENVNAVLNYGQRMY---AFARLTDTNGEDVVNEEGDFFVDGYTPRHKPEALNVTA 512

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
             + I +   +  +    +    +   +      + +  L     +         + A   
Sbjct: 513  VDEIKAKVNNGAVLYAWLVGAAIQEVLVRDHDGAVVKVLGNDPYADKHTITISDMYAFYA 572

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              +       +  D+      RI      E         L+   RV            + 
Sbjct: 573  YNLNNMEGVGDTDDIDMLGNRRIRSVG--ELIQNQFRIGLSRMERVVKERMSIADIATLT 630

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEILVPREKIDF 663
              K+TN +  L+A  +E    +Q +  +D+       T +          I   R   + 
Sbjct: 631  PKKLTN-IRPLTAAIKEFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGITRDRASYEV 689

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D        I     P   N      L       +   +          G      +  
Sbjct: 690  RDVHSSHYGRICPIETPEGPNIGLISNLTTYGKINEYGFIQTPYRIVNADG----TVQEE 745

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
               + A          A  +V   +  +   +    D     + +    +    Q   V 
Sbjct: 746  AIYLSADEEADYVIAQANEVVEGRLINEHVVARKAGDTIIARREEVELADVSPKQIVSVA 805

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                    +  A               +L    P+ G   E  +     +        + 
Sbjct: 806  TACVPFLENDDASRALMGANMQRQAVPLLQPHSPYVGTGVEYKIAKDSGVGIVAKENGVV 865

Query: 844  IEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
              E+    R       G     R           NI++  II  G  +  GDIL    + 
Sbjct: 866  --EYVDSQRIIVSENDGNRREYRLRKFQRSNNGTNINQSPIISKGERIEKGDILADGPS- 922

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
              +  +   + +  A       +  D  +         V D    + H  + +       
Sbjct: 923  MEKGELALGQNVTIAYMTWYGYNYEDAIIM----SERLVRDDVYTSIHIEEYDIDCRET- 977

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +   E + RD  +      RN+ SR   I+ G   + G     K T      IS   +  
Sbjct: 978  KLGPEEITRDIPNVSENACRNLDSR-GIIMVGAEVMEGDILVGKVTPKGQSEISPEEKLL 1036

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
               F  +  +V+ N   +          +      ++ K   G D+PPGV   VKV++  
Sbjct: 1037 LAIFGEKSREVRDNSLKVPHGGAGIVHSI------RVFKRSEGHDLPPGVNETVKVYIVQ 1090

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGTPVDI+LNP GVPSRMN+GQ+ E H
Sbjct: 1091 KRKISEGDKMAGRHGNKGVISKILPVEDMPYMPDGTPVDIMLNPFGVPSRMNIGQVLEIH 1150

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG+A   LG K  + + D   N ++S +    E  +                        
Sbjct: 1151 LGYAAKKLGVKFSTPVFDGINNTELSDIMKEAEMTVDGKQVL------------------ 1192

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                           G        TGEPFD  ++VG +YM+KL 
Sbjct: 1193 -----------------------------YDG-------RTGEPFDERISVGVMYMIKLA 1216

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSD
Sbjct: 1217 HMVDDKLHARATGPYSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLQEILTVKSD 1276

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            D+VGRT+ YE+I+ G D  E G PESF VL  E+QAL + + + +         +E    
Sbjct: 1277 DIVGRTKTYEAIIKGKDIPEPGIPESFRVLKHELQALAIDVKMLDEDGNEVDISKEDNSE 1336

Query: 1381 NKCEL 1385
                L
Sbjct: 1337 AAATL 1341


>gi|258513632|ref|YP_003189854.1| DNA-directed RNA polymerase subunit beta [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777337|gb|ACV61231.1| DNA-directed RNA polymerase, beta subunit [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 1227

 Score =  722 bits (1864), Expect = 0.0,   Method: Composition-based stats.
 Identities = 384/953 (40%), Positives = 523/953 (54%), Gaps = 119/953 (12%)

Query: 5   VVFNGL--GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
           +V+      R R  FGK  E++D+P+LIEVQ+ SY  FL            GL+  F  +
Sbjct: 4   MVYAEKLGTRERLNFGKFKEVLDLPNLIEVQRNSYKWFL----------KNGLREVFHDI 53

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  F+G  +LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K  
Sbjct: 54  SPIQDFTGNLVLEFLDYTLGEPKYFVEECKERDVTYAAPLRVKVRLI---------NKET 104

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++KEQ ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F         SGK L++ 
Sbjct: 105 GEVKEQEVFMGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYFAEQID---PSGKKLFSA 161

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI-LSTFYPKIVYSQR 241
            IIP++G W++ E D  D + VRIDR RK+P T  + ALG  S+ + +  F       + 
Sbjct: 162 TIIPNRGAWLEFETDVNDHVFVRIDRTRKIPATVLIRALGYSSDAMVMEEFGEDKNIQET 221

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                       L+   K       +  GE   +ES + L   L    K   +  +G   
Sbjct: 222 LSRDNTGSEEDALVEIYK------RLRPGEPPTVESARTLLETLFFDPKRYDLANVGRYK 275

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                  +   ++     E                    +I    IL  +      +IR 
Sbjct: 276 ---LHKKLQHGVLYRYPEE-----------------QSGKIEYDEILKQELPVEREFIRE 315

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
               D     K  L  +  +    D    ++  ++ +     + +  L +VG +  N   
Sbjct: 316 LTPKDILDTIKYLLRLVQGITEEKDPLGRNIEYTVDDIDHLGNRR--LRSVGELLQNQ-- 371

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
                                         G       +  R      +++  Q  + + 
Sbjct: 372 ---------------------------FRIGLSRMERVVRERMTIQDVDVITPQVLINIR 404

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            +  SIKE   S  +   M Q    A+                                 
Sbjct: 405 PVVASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPG-------------------- 444

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
                  G++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++AR+N +GFIET
Sbjct: 445 -------GLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARINQFGFIET 497

Query: 601 PYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           PYR+V      VTN++ YL+A  E+   IAQAN+ L+++G FTE+ V  R   E + VP 
Sbjct: 498 PYRRVDKEKRIVTNEIEYLTADVEDRNIIAQANAPLNKEGFFTEQAVNARHGHEILKVPG 557

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           EKIDF+D SPKQV SIA +LIPFLE+DD+NR LMG NMQRQAVPL+KA+AP VGTG+E  
Sbjct: 558 EKIDFMDVSPKQVFSIATALIPFLEHDDANRALMGANMQRQAVPLVKAQAPVVGTGVEYK 617

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A+ SG   +A+++GIVE+V A  I+IRS +G  D        ++L+KF RSNQ TC+NQ
Sbjct: 618 AARDSGVVPLARKSGIVEKVTANDIMIRSDDGTSD-------YHKLLKFTRSNQGTCINQ 670

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V  G  V   DIIADGP+TD G+LALGRN+LVAFMPW GYN+ED++LISE+ V ED 
Sbjct: 671 RPIVTKGQRVDEGDIIADGPATDNGELALGRNILVAFMPWDGYNYEDAILISEKAVKEDF 730

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           FTSIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++D+ GII VGAEV PGDI+VGK+
Sbjct: 731 FTSIHIEEYECDARDTKLGPEEITRDIPNVGEEILKDLDDRGIIRVGAEVRPGDIMVGKV 790

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F+R   D
Sbjct: 791 TPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFSRDNGD 843



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 179/525 (34%), Positives = 245/525 (46%), Gaps = 83/525 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             +  G  +  + +          I++  I+  G  V+ GDI+           +     +
Sbjct: 645  RSDDGTSDYHKLLKFTRSNQGTCINQRPIVTKGQRVDEGDIIADGPATDN-GELALGRNI 703

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A       +  D  L     V            +  + + R   +  E+I        
Sbjct: 704  LVAFMPWDGYNYEDAILISEKAVKEDFFTSIHIEEY--ECDARDTKLGPEEITRDIPNVG 761

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E + +D DD   I+      R  +I+ G+    G         L   +  E  R      
Sbjct: 762  EEILKDLDDR-GIIRVGAEVRPGDIMVGKVTPKGETELTAEERLLRAIFGEKAR------ 814

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   K+     GD++PPGV  +V+V++A KR I
Sbjct: 815  -----------EVRDTSLRVPHGEAGKIVDVKVFSRDNGDELPPGVNHLVRVYIAQKRKI 863

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+V+RI+P EDMPFL DGTP++IVLNPLGVPSRMN+GQ+ ETHLGWA
Sbjct: 864  SVGDKMAGRHGNKGVVARIMPEEDMPFLPDGTPIEIVLNPLGVPSRMNIGQVLETHLGWA 923

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + +     DI       +                               
Sbjct: 924  ARKLGCYVSTPVFNGATESDILEFLRKADLPDTAK------------------------- 958

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               T + DG   E                          PFD P+TVGY+YMLKL+H+V 
Sbjct: 959  ---TTLHDGRTGE--------------------------PFDNPITVGYVYMLKLHHLVD 989

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYG+AY LQE+LT+KSDDVVG
Sbjct: 990  DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGSAYTLQEILTVKSDDVVG 1049

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            R + YE+IV G +  E G PESF VL+KE+Q+LGL + + +   +
Sbjct: 1050 RVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGLDVKVLSEDDR 1094


>gi|224534641|ref|ZP_03675215.1| DNA-directed RNA polymerase, beta subunit [Borrelia spielmanii
           A14S]
 gi|224514110|gb|EEF84430.1| DNA-directed RNA polymerase, beta subunit [Borrelia spielmanii
           A14S]
          Length = 1155

 Score =  722 bits (1863), Expect = 0.0,   Method: Composition-based stats.
 Identities = 389/939 (41%), Positives = 590/939 (62%), Gaps = 66/939 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++   +++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKNKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R++VSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVIVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL  LG D+ E+I+ TFY                  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRVLGFDTREKIIETFYNI-------KKIKVEEIT 225

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              + G  ++ S+   +       +G K+T   ++   + GV  + +         V  D
Sbjct: 226 KRDLPGQYLAKSINIKEN--MYYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYNDISGKYFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYGALFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DI+  I  L+ +  G    DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMSDIVNTISHLLRIYEGHDIFDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVINGEVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++ YLSA++EE + IAQAN++ + +G + E+LV  R +G+      + ID++D SP+Q+
Sbjct: 553 DELEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTNPKNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E +       +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSNKIVVKPFESENVK---DLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEV 789

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +
Sbjct: 790 RETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFR 849

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           LL +IFGEKA DV++ SL+VP G  GTV+DV+   +  +
Sbjct: 850 LLTSIFGEKAKDVKNNSLKVPHGTEGTVIDVQRITKEDV 888



 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 719  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 778

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 779  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 837

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 838  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 886

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 887  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAGK------------------------YLSEF 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKKAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 1067 EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGIPTNVSGIPESFNVLMQELR 1126

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 1127 GLGLDLSIYDDNGNQFPLTEKEEEL 1151


>gi|330837661|ref|YP_004412302.1| DNA-directed RNA polymerase subunit beta [Spirochaeta coccoides DSM
           17374]
 gi|329749564|gb|AEC02920.1| DNA-directed RNA polymerase subunit beta [Spirochaeta coccoides DSM
           17374]
          Length = 1172

 Score =  721 bits (1861), Expect = 0.0,   Method: Composition-based stats.
 Identities = 405/959 (42%), Positives = 578/959 (60%), Gaps = 80/959 (8%)

Query: 11  GRVRKFF--GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---GLQAAFKSVFPI 65
             + + +      E+ D+P+LI +Q  SY+ FL  +   +    +   GL+  F S FPI
Sbjct: 6   KAITRTYIGSDFEEVCDLPNLIGIQLDSYEKFLQFDRMRNGLKPDPALGLEDVFTSTFPI 65

Query: 66  TAFSGAAMLEFVSYEFDP--PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            + +G   L +  YE D    KF   +C  +  TY+VP+K T+ L + +           
Sbjct: 66  ESANGEMRLVYDHYEVDMDGIKFSETECKRKGRTYSVPIKATISLEMPN----------G 115

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +++E+ I+ GD+PLMT+ GTF+I G +R+VVSQ+HRSPG+ F         + K +Y+ R
Sbjct: 116 ELREKEIFFGDIPLMTERGTFIINGAERVVVSQIHRSPGVIF--------SNEKDIYSAR 167

Query: 184 IIPDQGLWMDIEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQR 241
           IIP +G W++ E D  K +I+ +IDR++++  T FL A+G D+ E+I++ FY K   +  
Sbjct: 168 IIPYRGSWLEFEIDEKKHLIYTKIDRKKRILGTLFLRAIGFDTREKIIARFYAKQTVTLS 227

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            D         + +VG  + S +  +  GE  +V+ +G  L    +  L    V  + + 
Sbjct: 228 NDA-----DVKESLVGKYLYSDVYVLKEGEEYKVLRAGDILHPHEIDQLMNDKVTSVDVI 282

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                                              ++         I+       +A   
Sbjct: 283 -----------------------------------DLKAEGYLHSEIILNCFEIEDAKYT 307

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           N         +KD L  IY V+ PG++     AE     +FF   +YDL  VGR K N +
Sbjct: 308 NAEAGFDEPQKKDVLDPIYDVLMPGEMIPIERAEKELPDMFFSGRRYDLGNVGRYKFNKK 367

Query: 420 LNLDTPD-------DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
               T D       D+  +  +DI+  +  L+ +   +  +DDID+LGNRRVRSVGE+L+
Sbjct: 368 FGNGTDDNDEQMSTDLTVLTPDDIVNTMGFLIKVFIREENVDDIDHLGNRRVRSVGELLQ 427

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           N  +    RMER  +ER++  +  SV PQDLI+ KP+V+AV EFF SSQLSQ  + VN L
Sbjct: 428 NAMKSAFARMERIARERMNL-EGGSVRPQDLISIKPIVAAVKEFFGSSQLSQFMDQVNPL 486

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRL+ALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+ SL ++ RV
Sbjct: 487 AELTHKRRLNALGPGGLSRDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLANYTRV 546

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N +GF+ETPYRKV DGK T    YL A +EE  YIAQA+++LD+DG+F +  V  R +G+
Sbjct: 547 NEHGFLETPYRKVVDGKATKQYRYLDANDEERYYIAQASAALDQDGAFVDADVPVRRSGD 606

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                 + I ++D SPKQV+S+AASLIPFLE+DD+NR LMG NMQRQ+VPL+  EAP VG
Sbjct: 607 YSTRHPQDIRYMDVSPKQVISVAASLIPFLEHDDANRALMGSNMQRQSVPLVFPEAPRVG 666

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  SG  + A+ AG VE V + +I++R  + ++      V++Y + K+QR+NQ
Sbjct: 667 TGMEGRTAYDSGVLVKARHAGTVEYVSSTKIIVRLDKAEI---EGDVEVYEVQKYQRTNQ 723

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           +TC  QR +V +GD V    ++ADGP+T  G+LALGRN+LV F+PW+GYN+ED++LISER
Sbjct: 724 DTCFTQRVIVSIGDHVDVGAVLADGPATQKGELALGRNILVGFVPWNGYNYEDAVLISER 783

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +D++TSIHI+EF    R+TKLGPE++TRDIPN+SE+ L+ +DE GI+ +GA V PG 
Sbjct: 784 VVKDDIYTSIHIKEFTTDIRETKLGPEKLTRDIPNISEKMLEQLDEDGIVRIGASVKPGS 843

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPK ES  TPE KLL AIFGEKA +VRDTSL+VP G  GTV+D++   R   D
Sbjct: 844 ILVGKVTPKSESDTTPEFKLLNAIFGEKAKEVRDTSLKVPHGTEGTVIDIQRLKRSEGD 902



 Score =  426 bits (1095), Expect = e-116,   Method: Composition-based stats.
 Identities = 150/401 (37%), Positives = 207/401 (51%), Gaps = 55/401 (13%)

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            NI  +++E L     V      K  ++L   +  +       +F + +       + ++ 
Sbjct: 818  NISEKMLEQLDEDGIVRIGASVKPGSILVGKVTPKSESDTTPEFKLLNAIFGEKAKEVRD 877

Query: 1041 QYETSKSILEDR-FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                     E      +  K   GD++PPGV   VKV +A KR ++ GDKMAGRHGNKG+
Sbjct: 878  TSLKVPHGTEGTVIDIQRLKRSEGDELPPGVEETVKVLIATKRKLRQGDKMAGRHGNKGV 937

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VSRILP EDMP+++DGT +D+ LNPLGVPSRMN+GQ+ ET LGWA V L +   + +   
Sbjct: 938  VSRILPMEDMPYMEDGTSLDVCLNPLGVPSRMNIGQLLETQLGWAAVNLEEWYSTPVFQS 997

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
             +   I                         ++        ++GVP   PVF        
Sbjct: 998  GSMEQIEAKMREAG---------------LPENSKTTLYDGRTGVPFVNPVF-------- 1034

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                            GYIY LKL+H+V DK++ARSTG YSLVT
Sbjct: 1035 -------------------------------CGYIYYLKLHHLVDDKMHARSTGPYSLVT 1063

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQRLGEMEVW +QAYGAA  LQE+LTIKSDD+ GR ++Y++IV G    
Sbjct: 1064 QQPLGGKAQFGGQRLGEMEVWALQAYGAANTLQELLTIKSDDMNGRVQIYKNIVNGEPAT 1123

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
              G PE+FNVLV+E++ L L + + +++ K     E   + 
Sbjct: 1124 TAGMPEAFNVLVQEIRGLALDMSVYDTKGKQVPLTERDEEL 1164


>gi|160914579|ref|ZP_02076794.1| hypothetical protein EUBDOL_00587 [Eubacterium dolichum DSM 3991]
 gi|158433737|gb|EDP12026.1| hypothetical protein EUBDOL_00587 [Eubacterium dolichum DSM 3991]
          Length = 1395

 Score =  721 bits (1861), Expect = 0.0,   Method: Composition-based stats.
 Identities = 319/1438 (22%), Positives = 536/1438 (37%), Gaps = 172/1438 (11%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +V +G    R+ + K    +++P+L+E+Q  S+  F           + G++  F  +
Sbjct: 10   YRIVASGKKAQRRDYSKVSGDLELPNLVEIQTDSFAWF----------KDYGIEEVFNEI 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            +PI  + G   L+F  YEF  PKF+ ++ ++R+  +A PLK  + L + D        + 
Sbjct: 60   YPIQNYGGNIKLKFSGYEFGEPKFNAEESMFRECNFAAPLKAKMELEITDN-------TT 112

Query: 123  KDI--KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             ++  K + +++GD P+MT+ GTF+I G +R++VSQ+ RSPG +F    G    +GK+ Y
Sbjct: 113  GEVINKWEDVFLGDFPMMTETGTFIINGAERVIVSQIVRSPGAYF--STGYEEKTGKISY 170

Query: 181  ACRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMD-----SEEI-- 228
            AC +IP +G W++   + K      +++V IDR+RK+  +    A+GM      SE+   
Sbjct: 171  ACELIPSRGTWLEFLTELKKTSTGRVLNVSIDRKRKMLSSVLFKAIGMSVDLDRSEDAHD 230

Query: 229  ---LSTF-----------------------------------YPKIVYSQRGDFWCFPLS 250
               + TF                                   Y +I  +   D       
Sbjct: 231  TTQIKTFLQAMGRNLVDDVAIDDEDREFMNLYLTLYTSFFGKYEEIENTLLSDKVKTTQE 290

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLGITSDCLCGLYV 308
            A   +   + S  +  +D G   + + K        L       +       + +    +
Sbjct: 291  ALLSIYENQRSDEIPTLD-GSITLMNAKFFDPRRYDLTKAGRYKLTKKLNAINRIDRHRL 349

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            A+DI+  +   +++E+G +I+           +    +     VN   +       D   
Sbjct: 350  AQDIMAADGSGVFMESGKMINRD------ERNVLRGELAKGMYVNAFPFNPLFNHPDSVS 403

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                  L +   +   DV       ++F          D+  +      + ++       
Sbjct: 404  VPVSNRLGLIGRVLAQDV--EMGDITLFEGTILSEQ--DVEALQGEVERIYVHGGIIAKK 459

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY--RLGLLRMERSI 486
              +   ++ A++     L          D  G+  V   G++    Y  R+    +    
Sbjct: 460  VQLTGTNVNAVLNYGQRLY---ALGRLTDANGSDLVDEDGDLYVEGYTPRVKPDALSSVA 516

Query: 487  KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
               I     ++      +    V   +      + +  +     +         + A   
Sbjct: 517  MSEIKEKVHNNADVFAWLVGAAVQEILVRDENENVVKIMGNDPYANKHTITISDMYAFYS 576

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              +       E  D+      RI        +   +  S             E       
Sbjct: 577  YNLNVMEGVGETDDIDMLGNRRIRSVGELIQNQFRIGLSRMERVVKERMSIAEVA---TL 633

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEILVPREKIDF 663
              K   ++  L+A  +E    +Q +  +D+       T +          +   R   + 
Sbjct: 634  TPKKLTNIRPLTAAIKEFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGLTRDRAGFEV 693

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-MESVVAKS 722
             D        I     P   N      L       +   +          G +E      
Sbjct: 694  RDVHSSHYGRICPIETPEGPNIGLISNLTSYGKINEYGFIQTPYRIVEPDGTVEDKTIYL 753

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S     A          A  +V   +  +   +  G D     + +    +    Q   V
Sbjct: 754  S-----ADEEADYVIAQANEVVNGRLINERVVARKGGDTIIAHRDKVELADVSPKQIVSV 808

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFT 840
                     +  A               +L    P+ G   E  +       +V+++   
Sbjct: 809  ATACVPFLENDDASRALMGANMQRQAVPLLQPHSPFVGTGIEYKIAKDSGVGIVAKEDGI 868

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
              +++   ++  + +   E   R           NI++  I+  G  +  GDIL    + 
Sbjct: 869  VQYVDSQRIVVSEAEGNREYRLR--KFQRSNNGTNINQKPIVAKGERIEKGDILADGPS- 925

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +   + +  A       +  D  +     V   V        + ID  E  +  E
Sbjct: 926  MENGELALGQNVTIAYMTWYGYNYEDAIIMSERLVRDDVYTSVHIEEYDIDCRETKLGPE 985

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
                  + RD  +      RN+ SR   I+ G   + G     K T      IS   +  
Sbjct: 986  E-----ITRDIPNVSENACRNLDSR-GIIMVGAEVMEGDILVGKVTPKGQSEISPEEKLL 1039

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
               F  +  +V+ N   +          +      ++ K   G D+PPGV   VKV++  
Sbjct: 1040 LAIFGEKSREVRDNSLKVPHGGAGIVHSI------RVFKRSEGHDLPPGVNETVKVYIVQ 1093

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGTPVDI+LNP GVPSRMN+GQ+ E H
Sbjct: 1094 KRKISEGDKMAGRHGNKGVISKILPVEDMPYMPDGTPVDIMLNPFGVPSRMNIGQVLEIH 1153

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LG+A   LG K  + + D   N ++S +                                
Sbjct: 1154 LGYAAKKLGVKFSTPVFDGINNAELSDIMKEANMTSDGKQVL------------------ 1195

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                           G        TGEPFD  ++VG +YM+KL 
Sbjct: 1196 -----------------------------YDG-------RTGEPFDERISVGVMYMIKLA 1219

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSD
Sbjct: 1220 HMVDDKLHARATGPYSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLQEILTVKSD 1279

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            D+VGRT+ YE+I+ G D  E G PESF VL  E+QAL + + + +   +     ++  
Sbjct: 1280 DIVGRTKTYEAIIKGKDIPEAGIPESFRVLKHELQALAIDVKMLDENGEEVDINKDDS 1337


>gi|288574654|ref|ZP_06393011.1| DNA-directed RNA polymerase, beta subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570395|gb|EFC91952.1| DNA-directed RNA polymerase, beta subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 1272

 Score =  718 bits (1854), Expect = 0.0,   Method: Composition-based stats.
 Identities = 430/958 (44%), Positives = 591/958 (61%), Gaps = 99/958 (10%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R  FG+  ++++IPD++EVQ+ SY  F   ++ PD+R + GLQ     +FPI ++
Sbjct: 8   GKKRSRLTFGRVRDLVEIPDMVEVQRDSYRSFFQEDVDPDKRDSVGLQELLDEIFPIESY 67

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            G+  LEFV Y  D P    ++   +D T+  P++ T+RL+          +   +IKE+
Sbjct: 68  DGSFALEFVRYYLDRPATTQEESQQKDCTWHRPVRATIRLV---------NRKNLEIKEE 118

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            I++GD P+MT+ GTF+I G +R+VV+QL RS GI+F  D           +  +IIPD+
Sbjct: 119 EIFLGDFPMMTERGTFIINGTERVVVNQLTRSAGIYFKVDYSAPVA---ETFTAKIIPDR 175

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G W++    S D ++V ID R+K+P T             L  F                
Sbjct: 176 GAWLEFAMGSGDALYVNIDNRKKLPGTLL-----------LKAF---------------- 208

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                   G   +  ++ +  GE                     ++ + I+ + L G  +
Sbjct: 209 --------GVSSNEEMLRLFGGE---------------------IEEVDISEELLIGRLL 239

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            E +++ E G + +   + I ++ LE ++      + +      N N     TL  D   
Sbjct: 240 GETVLD-EGGNVVVRKEERIGKEELERLWDIGRTRVKV-----WNVNPVFAATLEKDFTN 293

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           +R +A+L+I+R +RP D +    A    + LFFDS +Y L  VGR K+N RL LD PD  
Sbjct: 294 NRDEAMLEIFRRLRPNDPARIENAREYIDSLFFDSRRYTLGRVGRYKLNRRLKLDLPDRE 353

Query: 429 RHIRKEDIIAIIKILVDLRNGKGT-------------IDDIDNLGNRRVRSVGEMLKNQY 475
             +  +D++ I+K ++ LR+ +                DDID+LGNRRVRSVGE+L+NQ 
Sbjct: 354 YLLTIDDLVRIVKGIIVLRDTEEQRDVVSFPDVTEEFPDDIDHLGNRRVRSVGELLQNQV 413

Query: 476 RLGLLRMERSIKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           R+GLLRMER  KER+++  D+   M +DLIN +P+ +A+ EFF S QLSQ  +  N LS 
Sbjct: 414 RIGLLRMERIAKERMTTVADLTKAMARDLINVRPISAALREFFGSGQLSQYMDQNNPLSE 473

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG GG++R RAG E RDVH THYGRICP ET EG NIGLV+SL+++++VN 
Sbjct: 474 LTHRRRLSALGPGGLSRERAGFEARDVHYTHYGRICPIETPEGPNIGLVTSLSTYSKVNQ 533

Query: 595 YGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCRCA 650
           YGF+ TP R V +G V+    DVVYL+A EE+N Y+ +AN+  DE  G  +EE  + R  
Sbjct: 534 YGFLVTPRRPVVEGVVSLNPEDVVYLAADEEDNSYVGRANTPYDESTGRLSEEYCYARYR 593

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G  + VP++KID++D SPKQ+VS + +LIPFLE+DD+NR LMG NMQRQAVPLL  EAP 
Sbjct: 594 GRIVEVPQDKIDYLDISPKQIVSASTALIPFLEHDDANRALMGSNMQRQAVPLLLPEAPR 653

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME  +AK SG+ +VA   G+V  VDA RI IRS  G             L KF+RS
Sbjct: 654 VGTGMEGRIAKDSGSCVVAPEDGVVTYVDADRIEIRSDLGVYRSM-------SLQKFKRS 706

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T ++QRP+V  GD V + +I+ADG S D  +LALGRN+L+AF+PW GYN+ED++L+S
Sbjct: 707 NQGTIIHQRPIVSKGDVVSKGEIMADGQSVDQAELALGRNVLIAFIPWEGYNYEDAILLS 766

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED FTSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ LK++DE G++ VGAEVN 
Sbjct: 767 ERLVKEDFFTSIHIEEYEMDARDTKLGPEEITRDIPNVGEDALKDLDEFGVVRVGAEVNA 826

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           GDILVGK+TPKGES  +PEEKLLRAIFGEKA +VRDTSL VP G  G VV V+  N+ 
Sbjct: 827 GDILVGKVTPKGESDQSPEEKLLRAIFGEKAREVRDTSLHVPHGARGKVVAVKKLNKD 884



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 165/597 (27%), Positives = 237/597 (39%), Gaps = 87/597 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L+   P  G   E  +   S   V       +   + + +   + LG 
Sbjct: 635  MGSNMQRQAVPLLLPEAPRVGTGMEGRIAKDSGSCVVAPEDGVVTYVDADRIEIRSDLGV 694

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                             I +  I+  G  V+ G+I+    +   ++ +     +L A   
Sbjct: 695  YRSMSLQKFKRSNQGTIIHQRPIVSKGDVVSKGEIMADGQS-VDQAELALGRNVLIAFIP 753

Query: 919  EKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
             +  +  D  L      +     S  + +  +  R      E          E   +D  
Sbjct: 754  WEGYNYEDAILLSERLVKEDFFTSIHIEEYEMDARDTKLGPEEITRDIPNVGEDALKDL- 812

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  ++         +IL G+    G         L   +  E  R           +V+
Sbjct: 813  DEFGVVRVGAEVNAGDILVGKVTPKGESDQSPEEKLLRAIFGEKAR-----------EVR 861

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          ++     K+ K +  D + PGV  VVKV+VA  R I  GDKM+G
Sbjct: 862  DTSLHVPHGARGKVVAVK-----KLNKDENSDSLSPGVNEVVKVYVAQLRKITVGDKMSG 916

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNK                            GV SR+                     
Sbjct: 917  RHGNK----------------------------GVVSRI--------------------- 927

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
               + D     D +P+   L  +                + + VA  W     V+TPVF+
Sbjct: 928  -LPVEDMPYLPDGTPVDVCLNPLGVPSRMNLGQVLETILATVAVANDW----HVATPVFE 982

Query: 1213 GADEEAINSMLRM--------ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            GA EE I  +L          + L   G   L DG TGEP +   TVG++YMLKLNH+V 
Sbjct: 983  GAQEEEIYDLLDKLSQENPDYSTLTRGGTMQLIDGRTGEPMEYKTTVGHMYMLKLNHLVD 1042

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW +Q YGAA+VLQEMLT+KSDD+ G
Sbjct: 1043 DKLHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALQGYGAAHVLQEMLTVKSDDIHG 1102

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            R + YE IV G +    G PESF VLVKE++ LGL +D+E +       + +  D  
Sbjct: 1103 RLKTYEKIVKGQNLTRPGVPESFKVLVKELEGLGLGVDIEYNDGTIGPLLPDEDDEQ 1159


>gi|282857671|ref|ZP_06266884.1| DNA-directed RNA polymerase, beta subunit [Pyramidobacter piscolens
           W5455]
 gi|282584495|gb|EFB89850.1| DNA-directed RNA polymerase, beta subunit [Pyramidobacter piscolens
           W5455]
          Length = 1229

 Score =  718 bits (1853), Expect = 0.0,   Method: Composition-based stats.
 Identities = 420/953 (44%), Positives = 577/953 (60%), Gaps = 102/953 (10%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
            GR R  FG   ++I +PD++EVQ+ SY  F     AP++R + GLQ     + PI+ F 
Sbjct: 9   KGRQRLIFGSGHDVIPLPDMVEVQRESYRSFFQEGAAPEDRESVGLQELLDEISPISNFD 68

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           G+  LEF+ YE D P    ++   RD T+  P++  +RL              ++++E+ 
Sbjct: 69  GSFRLEFLGYEIDEPSMSQEEAKRRDCTWHRPIRAKVRLHNDRA---------QEVREEE 119

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           IY+GD P+MT  GTF+I G +R+VV+QL RS G++F  + G    SG   Y+ +IIP++G
Sbjct: 120 IYLGDFPVMTPRGTFIINGTERVVVNQLARSAGVYFKSEPG---ASGAQNYSAKIIPERG 176

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFP 248
            W++    + D + V ID RRK+P T  L A G+ + EE+L  F   +      D     
Sbjct: 177 AWVEF-VMAGDSLSVNIDSRRKLPATLLLKAFGLGTNEELLKAFGGVVE-----DLDIVT 230

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             AA    G  ++ S+ D   G+ ++  G +L    L+ L E+G   L +          
Sbjct: 231 EEAA----GRLLAESVTDSR-GQVLLHEGTRLDKDGLELLWEQGRTSLKV---------- 275

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
                                                       N      + L  +   
Sbjct: 276 -------------------------------------------WNVAPIFVSALEKENAN 292

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              +ALL+I R MRP +      A   F+ LF D  +Y L  VGR K+N RL L    D 
Sbjct: 293 STDEALLEILRRMRPNEPVRIEGAREYFDELFLDVRRYTLGRVGRYKLNRRLGLSLKKDE 352

Query: 429 RHIRKEDIIAIIKILVDLRN-------------GKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             +  +D++ I+K LV LR+             G+  +DDID+LGNRRVRS+GE+L++Q 
Sbjct: 353 YLLTLDDLVRIVKGLVALRDTEEQRDDMTFPEIGEERVDDIDHLGNRRVRSIGELLQSQL 412

Query: 476 RLGLLRMERSIKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           R+G+LR+ER  KER+++  D+   M +DLIN +P+ +A+ EFF S QLSQ  +  N LS 
Sbjct: 413 RIGMLRLERIAKERMTTVADLSKAMARDLINVRPLAAALREFFGSGQLSQFMDQNNPLSE 472

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG GG++R RAG E RDVH THYGRICP ET EG NIGLV+SL ++AR+N 
Sbjct: 473 LTHRRRLSALGPGGLSRERAGFEARDVHYTHYGRICPIETPEGPNIGLVTSLGTYARLNE 532

Query: 595 YGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCRCA 650
           YGF+ TP R V +G V+    DVVYLSA EE+N Y+ +AN+  D   G  TE+ V+ R  
Sbjct: 533 YGFLITPRRPVKNGVVSTKAEDVVYLSADEEDNYYVGRANTPFDPQTGRLTEDAVYARYK 592

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+ + +  E++DF+D S KQVVS +A+LIPFLE+DD+NR LMG NMQRQAVPLL  +APF
Sbjct: 593 GDIVKIAPEQVDFLDVSSKQVVSASAALIPFLEHDDANRALMGSNMQRQAVPLLLPKAPF 652

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E  VA+ SG  + +   G V  VD+ RI +    G       G   + L KF RS
Sbjct: 653 VGTGIEERVARDSGCCVYSSCDGSVTYVDSDRIEVTDDNG-------GRHEFELDKFLRS 705

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T ++QRP V VGD V+ ++++ADG S D G+LALGRN+L+AF+PW GYN+ED++L+S
Sbjct: 706 NQGTIIHQRPTVDVGDRVKTDELLADGQSVDGGELALGRNVLIAFVPWEGYNYEDAILLS 765

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           E++V ED F+SIHIEE+E+ +RDTKLGPEEITRDIPNV E+ L+N+DE G++ +GAEVNP
Sbjct: 766 EKLVKEDYFSSIHIEEYEIDSRDTKLGPEEITRDIPNVGEDALRNLDEDGVVRIGAEVNP 825

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           GDILVGK+TPKGE+  +PEEKLLRAIFGEKA +VRDTSL +P G  G VV V+
Sbjct: 826 GDILVGKVTPKGEADHSPEEKLLRAIFGEKAGEVRDTSLHLPHGTRGKVVSVK 878



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 147/581 (25%), Positives = 221/581 (38%), Gaps = 80/581 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L+   P+ G   E+ +       + S    +  +++   +   D   G
Sbjct: 634  MGSNMQRQAVPLLLPKAPFVGTGIEERVARDSGCCVYSSCDGSVTYVDSDRIEVTDDNGG 693

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              E   D   +       I +   + VG  V   D L+          +     +L A  
Sbjct: 694  RHEFELD-KFLRSNQGTIIHQRPTVDVGDRVKT-DELLADGQSVDGGELALGRNVLIAFV 751

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDEQV 976
              +  +  D  L     V            +  + + R   +  E+I   +    +D   
Sbjct: 752  PWEGYNYEDAILLSEKLVKEDYFSSIHIEEY--EIDSRDTKLGPEEITRDIPNVGEDALR 809

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+     G     G     K T       S   +     F  +  +V+    
Sbjct: 810  NLDEDGVVRI-----GAEVNPGDILVGKVTPKGEADHSPEEKLLRAIFGEKAGEVRDTSL 864

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L          ++     ++  +   + + PGV  V+KV+VA  R I            
Sbjct: 865  HLPHGTRGKVVSVK-----RLNHVDNPESLSPGVNEVIKVYVAQWRKI------------ 907

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
                                                VG              G K     
Sbjct: 908  -----------------------------------TVG-------DKMSGRHGNKGVVSR 925

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                 +    P  + ++  +       +++      V+      K+G  V TPVF+GA E
Sbjct: 926  VLPVEDMPYLPDGTPVDVCLNPLGVPSRMNLGQVLEVILGFVALKNGWNVGTPVFEGATE 985

Query: 1217 EAINSMLRM---------ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            E I  ML+            L   G   L DG TG+    P TVG +YMLKLNH+V DK+
Sbjct: 986  EEIYKMLQEISDRDPDLRGKLSSGGTIRLRDGRTGDLMAEPSTVGVMYMLKLNHLVDDKL 1045

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARS G YSL+TQQPLGGK+  GGQR GEMEVW +Q YGAA+VLQEMLT+KSDD+ GR +
Sbjct: 1046 HARSVGPYSLITQQPLGGKAQFGGQRFGEMEVWALQGYGAAHVLQEMLTVKSDDIRGRLK 1105

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             YE I+ G +  + G PESF VLVKE++ LGL++ ++ S  
Sbjct: 1106 TYEKIIKGQNLTKPGVPESFKVLVKELEGLGLTVSIDYSDG 1146


>gi|55846630|gb|AAV67333.1| RNA polymerase beta subunit [Alistipes finegoldii DSM 17242]
          Length = 747

 Score =  717 bits (1851), Expect = 0.0,   Method: Composition-based stats.
 Identities = 360/802 (44%), Positives = 488/802 (60%), Gaps = 82/802 (10%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             + +N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP E+ EG NIGL+SS
Sbjct: 1    MDQINPLAEITHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRLCPIESPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCD---GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  +A+++  GFIETPYRKV +       +D+ Y SA EEE + +AQAN  +D++G F +
Sbjct: 61   LCVYAKISPMGFIETPYRKVENGQIDMNNDDIRYYSAEEEEGKIVAQANMPIDDEGHFLQ 120

Query: 643  -ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             + +  R   +  +V  E+++ +D +P Q+ SIAASLIPFLE+DD+NR LMG NM RQAV
Sbjct: 121  PDRIKAREGADFPVVTAEEVNLMDVAPNQIASIAASLIPFLEHDDANRALMGSNMMRQAV 180

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSG 758
            PL+  +AP VGTG+E  +   S   IVA+  G V   DA +I IR     +  L      
Sbjct: 181  PLVTTDAPIVGTGIEKDMISDSRIQIVAEGDGEVTFADATKIQIRYERTEDEILASFEPE 240

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            V  Y L +++R+NQNT +  +P+V  GD+V +  I+ +G ST  G+LALGRN+ VAFMPW
Sbjct: 241  VTTYELPRYRRTNQNTSITLKPIVLTGDKVVKGQILTEGYSTQHGELALGRNLKVAFMPW 300

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             GYNFED+++ISER+  ED+FTS+H++E+ +  RDTK G EE+T DIPNVSE+  K++D 
Sbjct: 301  KGYNFEDAIVISERIQREDIFTSVHVDEYIMEVRDTKRGVEELTSDIPNVSEDATKDLDA 360

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GII +GA V+PGDIL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G 
Sbjct: 361  NGIIRIGANVHPGDILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKAQPSLHGV 420

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS- 997
            V+D ++++R   +  ++  S E+ QIE L      E   L + + ++L  +L G+     
Sbjct: 421  VIDTKLYSRANKE-GKKGKSAEKVQIEKLDEKFAAEIAELTKRLVAKLWTLLQGKTTTGV 479

Query: 998  ----GPKGFKKSTVLSSDLISEYPRSQWWQ--------------FAVQDEKVQRNVESLK 1039
                G + +   T  S  ++ E  R    +                  D      +E+  
Sbjct: 480  TDYFGVELYPAGTKFSQKMLEEIARKTTDEKTGVVMGYLNLGTCKWTGDAHTDALIEATI 539

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Y       +   K +   I  GD++P  GV+++ KV++A KR ++ GDKMAGRHGNKG
Sbjct: 540  NNYTIEWKKADAAIKREKYNITNGDELPQTGVIQMAKVYIAKKRKLKVGDKMAGRHGNKG 599

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IV+RI+  EDMPFL+DGT VDI LNPLGVPSRMN+GQI+ET LGWA   LG K  + I D
Sbjct: 600  IVARIVRDEDMPFLEDGTIVDICLNPLGVPSRMNLGQIYETVLGWAGRELGLKFATPIFD 659

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
              +   I+   +                              K+G+P             
Sbjct: 660  GASLDQINEYTA------------------------------KAGIP------------- 676

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                        SG++ LYDG TGE FD+P TVG IYMLKL HM+ DK++ARS G YSL+
Sbjct: 677  -----------HSGRTYLYDGGTGEMFDQPATVGVIYMLKLGHMIDDKMHARSIGPYSLI 725

Query: 1279 TQQPLGGKSNRGGQRLGEMEVW 1300
            TQQPLGGK+  GGQR GEMEVW
Sbjct: 726  TQQPLGGKAQFGGQRFGEMEVW 747


>gi|254230350|ref|ZP_04923735.1| DNA-directed RNA polymerase, beta subunit [Vibrio sp. Ex25]
 gi|151937117|gb|EDN55990.1| DNA-directed RNA polymerase, beta subunit [Vibrio sp. Ex25]
          Length = 621

 Score =  714 bits (1844), Expect = 0.0,   Method: Composition-based stats.
 Identities = 291/620 (46%), Positives = 423/620 (68%), Gaps = 9/620 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57  FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  + 
Sbjct: 175 RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVNFEVKD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                 L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235 QTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL
Sbjct: 292 IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETL 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352 RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+
Sbjct: 412 EDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRV 471

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 472 ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 531

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 532 ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 591

Query: 603 RKVCDGKVTNDVVYLSAMEE 622
           R+V DG VT++V YLSA+EE
Sbjct: 592 RRVVDGVVTDEVDYLSAIEE 611


>gi|55846632|gb|AAV67334.1| RNA polymerase beta subunit [Alistipes putredinis]
          Length = 748

 Score =  713 bits (1841), Expect = 0.0,   Method: Composition-based stats.
 Identities = 355/802 (44%), Positives = 486/802 (60%), Gaps = 81/802 (10%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             + +N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP E+ EG NIGL+SS
Sbjct: 1    MDQINPLAEITHKRRLSALGPGGLSRDRAGFEVRDVHYTHYGRLCPIESPEGPNIGLISS 60

Query: 586  LTSFARVNAYGFIETPYRKVCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            L  +A+++  GFIETPYR V +G+V     D+ Y SA EEE + +AQ+N  +D++G F +
Sbjct: 61   LCVYAKISDMGFIETPYRTVTNGQVDLNNADIKYYSAEEEEGQVVAQSNVPIDDEGHFLQ 120

Query: 643  -ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             + +  R   +  +V  +++  +D +P Q+ SIAASLIPFLE+DD+NR LMG NM RQAV
Sbjct: 121  PDRIKAREGADFPVVTAQEVTLMDVAPNQIASIAASLIPFLEHDDANRALMGSNMMRQAV 180

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS---VEGDLDPSTSG 758
            PL+  E+P VGTG+E  +   S   I+A+  G V   DA +I I+     E  +      
Sbjct: 181  PLVTCESPIVGTGIEKDMISDSRIQIIAEGDGEVVFADATKIQIKYQRTEEEVICSFEPE 240

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            +  Y L +++R+NQNT +  +P V  GD+V +  I+ +G ST  G+LALGRN+ VAFMPW
Sbjct: 241  ITTYELPRYRRTNQNTSITLKPAVLTGDKVTKGQILTEGYSTQKGELALGRNLKVAFMPW 300

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             GYNFED+++ISER+  ED+FTS+H++E+ +  RDTK G EE+T DIPNVSE+  K++D 
Sbjct: 301  KGYNFEDAIVISERIQREDIFTSVHVDEYIMEVRDTKRGVEELTSDIPNVSEDATKDLDA 360

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GII +GA V+PGDIL+GKITPKGES  +PEEKLLRAIFG+KA DV+D SL+    + G 
Sbjct: 361  NGIIRIGANVHPGDILIGKITPKGESDPSPEEKLLRAIFGDKAGDVKDASLKAQPSLHGV 420

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS- 997
            V+D ++++R G +      S E+ QIE L      +   L + + ++L  +L G+     
Sbjct: 421  VIDTKLYSRAGKENKRAGKSSEKLQIEKLDEKFAAQVADLTKQLVNKLYTLLQGKTTTGI 480

Query: 998  ----GPKGFKKSTVLSSDLISEYPRSQWWQ--------------FAVQDEKVQRNVESLK 1039
                G + +   T  +  L+ E  R    +                  D  +   VE   
Sbjct: 481  TDYFGVELYPAGTKFTQKLLDELSRKVTDEKSGVAMGYLNLGTCKWTGDSHLDALVEKTI 540

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Y       +   K +   +  GD++P  GV+++ KV++A KR ++ GDKMAGRHGNKG
Sbjct: 541  NNYTIEWKKADAAIKREKYNLTNGDELPQTGVIQMAKVYIAKKRKLKVGDKMAGRHGNKG 600

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IV+R++  EDMPFL+DGT VDI LNPLGVPSRMN+GQI+ET LGWA   LG K  + I D
Sbjct: 601  IVARVVRDEDMPFLEDGTIVDICLNPLGVPSRMNLGQIYETVLGWAGKELGLKFATPIFD 660

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
              +   I+   +                              K+G+P             
Sbjct: 661  GASLDQINEYTA------------------------------KAGIP------------- 677

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                        SG++ LYDG TGE FD+P TVG IYMLKL HM+ DK++ARS G YSL+
Sbjct: 678  -----------RSGRTYLYDGGTGEKFDQPATVGVIYMLKLGHMIDDKMHARSIGPYSLI 726

Query: 1279 TQQPLGGKSNRGGQRLGEMEVW 1300
            TQQPLGGK+  GGQR GEMEVW
Sbjct: 727  TQQPLGGKAQFGGQRFGEMEVW 748


>gi|293399719|ref|ZP_06643865.1| DNA-directed RNA polymerase, beta subunit [Erysipelotrichaceae
            bacterium 5_2_54FAA]
 gi|291306119|gb|EFE47362.1| DNA-directed RNA polymerase, beta subunit [Erysipelotrichaceae
            bacterium 5_2_54FAA]
          Length = 1398

 Score =  706 bits (1822), Expect = 0.0,   Method: Composition-based stats.
 Identities = 320/1435 (22%), Positives = 529/1435 (36%), Gaps = 166/1435 (11%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +V +G    R+ + K    +++P+L+E+Q  S++ F           NEG+   F  +
Sbjct: 10   YRIVASGKKAERRDYSKVSGHLELPNLVEIQTDSFEWF----------KNEGIGEVFNEI 59

Query: 63   FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            +PI  + G   L+F  YEF  PK++ ++ ++R+  YA PLK  + L + D        + 
Sbjct: 60   YPIQNYGGNIKLKFAGYEFGEPKYNAEESMYRECNYAAPLKARMELEITDN-------TT 112

Query: 123  KDI--KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
             ++  K + +++GD PLMT+ GTF+I G +R++VSQ+ RSPG +F    G    +GK+ Y
Sbjct: 113  GEVINKWEDVFLGDFPLMTETGTFIINGAERVIVSQIVRSPGAYF--STGYDEKTGKVSY 170

Query: 181  ACRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVP---------------------- 213
            AC +IP +G W++   ++K      ++++ IDR+RK+                       
Sbjct: 171  ACELIPSRGTWLEYMTETKKASTGRVLNMSIDRKRKMLSSVLFKAVGMSIDLDHSEDAHD 230

Query: 214  ---VTSFLMALGMD------SEEILSTF--------------YPKIVYSQRGDFWCFPLS 250
               + +FL A+G D       ++    F              Y +I  +   D       
Sbjct: 231  TTQIKTFLKAMGRDVIEDVAQDDEDREFMNLYLTLYASYFGKYEEIENTLLADKVKTTQE 290

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A   +   + S  +  +D G   + + K          +   +   G          +  
Sbjct: 291  ALLSIYENQRSDEIPTLD-GSITLMNAK------FFDPRRYDLTKAGRFKLRKKLNAINR 343

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
               N    +I    G V        I   E   +       ++ +A+  N L    +K  
Sbjct: 344  IYGNRLAMDILASDGSVFMPSG-TMIHRDERNTLREELEKGMHVHAFPFNPLFNHPDKVE 402

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
              A   +  V R           ++F          D+  + +    + ++         
Sbjct: 403  VPASNHLGLVGRVLAEDVELSDATLFEGTVLTQK--DVDAIAKECETISVHGGIIAKQVA 460

Query: 431  IRKEDIIAIIKI-LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            + K ++ A++         G+ T    ++L N       E      R     +  + +E 
Sbjct: 461  LEKGNVNAVLNYGQRMYALGRVTDAQGNDLENEEGDFYAE--GYLPRHKPDTLSANDQEA 518

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            + +   +       +    V   +        +  +     +         + A     +
Sbjct: 519  LRNKVNNGETVYAWLVGAAVQEVLVRTGDEQVVKVIGNDPYANKHTITISDMYAFYTYNL 578

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                   E  D+      RI        +   +  S             ET        K
Sbjct: 579  NVMEGVGETDDIDMLGNRRIRSVGELIQNQFRIGLSRMERVVKERMSIAETA---TLTPK 635

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEILVPREKIDFIDA 666
               ++  L+A  +E    +Q +  +D+       T +          +   R   +  D 
Sbjct: 636  KLTNIRPLTAAIKEFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGLTRDRAGFEVRDV 695

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
                   I     P   N      L       +   +          G      +     
Sbjct: 696  HSSHYGRICPIETPEGPNIGLISNLTSYGKINEYGFIQTPYRIVKKDG----TVEDEAIY 751

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            + A          A  +V   +  +   +    +     + +    +    Q   V    
Sbjct: 752  LSADEEADYVIAQANEVVEGRLINENVVARKAGETIIAKREEVELADVSPKQIVSVATAC 811

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                 +  A               +L    P+ G   E  +     +    V     I E
Sbjct: 812  VPFLENDDASRALMGANMQRQAVPLLQPHSPYVGTGIEYKIAKDSGVGI--VAKENGIVE 869

Query: 847  FEVMARDT---KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            +    R       G     R           NI++  I+  G  ++ GDIL    +   +
Sbjct: 870  YVDSQRIIVSGDDGERHEYRLRKFQRSNNGTNINQSPIVKKGERIDKGDILADGPS-MEK 928

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              +   + +  A       +  D  +         V D    + H  + +       +  
Sbjct: 929  GELALGQNVTIAYMTWYGYNYEDAIIM----SERLVRDDVYTSIHIEEYDIDCRET-KLG 983

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E + RD  +      RN+ SR   I+ G     G     K T      IS   +     
Sbjct: 984  PEEITRDIPNVSEAACRNLDSR-GIIMVGAEVREGDILVGKVTPKGQSEISPEEKLLLAI 1042

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            F  +  +V+ N   +          +      +I K   G D+PPGV   VKV++  KR 
Sbjct: 1043 FGEKSREVRDNSLKVPHGGAGIVHSI------RIFKRSEGHDLPPGVNETVKVYIVQKRK 1096

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I  GDKMAGRHGNKG++S+ILP EDMP++ DGTP+DI+LNP GVPSRMN+GQ+ E HLG+
Sbjct: 1097 ISEGDKMAGRHGNKGVISKILPVEDMPYMPDGTPIDIMLNPFGVPSRMNIGQVLEIHLGY 1156

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG K  + + D   N ++S +    +  +                           
Sbjct: 1157 AAKKLGVKFSTPVFDGINNQELSDIMKEADMTVDGKQVL--------------------- 1195

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                        G        TGEPFD  ++VG +YM+KL HMV
Sbjct: 1196 --------------------------YDG-------RTGEPFDERISVGVMYMIKLAHMV 1222

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDD+V
Sbjct: 1223 DDKLHARATGPYSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDIV 1282

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            GRT+ YE+I+ G D  E G PESF VL  E+QAL + + + +         +E  
Sbjct: 1283 GRTKTYEAIIKGKDIPEPGIPESFRVLKHELQALAIDVKMLDEDGNEVDINKEES 1337


>gi|260655390|ref|ZP_05860878.1| DNA-directed RNA polymerase, beta subunit [Jonquetella anthropi
           E3_33 E1]
 gi|260629838|gb|EEX48032.1| DNA-directed RNA polymerase, beta subunit [Jonquetella anthropi
           E3_33 E1]
          Length = 1231

 Score =  702 bits (1813), Expect = 0.0,   Method: Composition-based stats.
 Identities = 406/962 (42%), Positives = 583/962 (60%), Gaps = 100/962 (10%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R  FG+  ++I IPD+++VQ+ SY  F   ++ P++R   GLQ     +FPI   
Sbjct: 8   GKNRQRLTFGRAHDLIPIPDMVDVQRVSYRSFFQEDVDPEQREKTGLQELLTEIFPIENH 67

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            G   LEFV Y+ D P    ++   RD  ++ P+++T+RL+          +  ++I  +
Sbjct: 68  DGTFALEFVKYDIDEPSMTEEEAERRDSNWSRPVRLTVRLV---------NRKTQEIAVE 118

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            +++GD P+MT  GTF+I G +R+VV+QL RS G ++   K  +S+SG   Y+ +IIP++
Sbjct: 119 QVFLGDFPVMTPRGTFIINGTERVVVNQLARSAGCYY---KIESSVSGNDNYSAKIIPER 175

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIV-YSQRGDFWC 246
           G W++    + D + V +D R+K+P T  L A G+   E ++  F       S  GD   
Sbjct: 176 GAWLEF-VMTGDKLMVNVDSRKKLPATLLLKAFGLGDNETLIKAFGGSEEMVSLTGDGLS 234

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                       ++S+  V    G ++I SG+ LT   ++ L ++G   L +        
Sbjct: 235 -----------GRLSAETVTDSEGNELISSGETLTQEKIQRLFDQGRTALKV-------- 275

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
                                                    +       A I       +
Sbjct: 276 -----------------------------------------WHVCPVIAASIATEREKGQ 294

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             + + A+L+I+R+MRP + +    A   FN  F D ++Y L  VGR K+N RL L  P+
Sbjct: 295 ADNIEGAMLEIFRLMRPSEPARIESARDYFNKTFADPNRYTLGRVGRYKVNRRLGLKIPE 354

Query: 427 DVRHIRKEDIIAIIKILVDLRNGK-------------GTIDDIDNLGNRRVRSVGEMLKN 473
             R +  ED+I I+K +V LR+ +                DDID+LGNRRVRSVGE+L++
Sbjct: 355 TNRLLTLEDLILIVKGIVALRDKEEQRDDPWFPEITDAHTDDIDHLGNRRVRSVGELLQS 414

Query: 474 QYRLGLLRMERSIKERISS-VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + R G+LRMER++KER+++  D+     +DLIN +PV S + EFF S QLSQ  +  N L
Sbjct: 415 ELRKGMLRMERNVKERMTTVPDLYKATARDLINVRPVTSEIREFFGSGQLSQYMDQNNPL 474

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG+ R RAG E RDVH THYGRICP ET EG NIGLV+SL ++A+V
Sbjct: 475 AGLTHRRRLSALGPGGLTRDRAGFEARDVHATHYGRICPIETPEGPNIGLVTSLGTYAKV 534

Query: 593 NAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFCR 648
           N YGF+ TP R V +G V    + VVYL+A EE+N Y+ +AN+  D   G   E  V+ R
Sbjct: 535 NEYGFLMTPRRPVKNGYVELGADKVVYLAADEEDNCYVGRANTPHDPKTGKLLESTVYAR 594

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ + VPRE+I+++D S KQVVS + +LIPFLE+DD+NR LMG NMQRQAVPLL  EA
Sbjct: 595 YQGQIVEVPREQINYLDVSSKQVVSASTALIPFLEHDDANRALMGSNMQRQAVPLLLPEA 654

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VG+G+E  +A+ SG  I+++  G++  VDA RI +R        ++  +  Y+++KF+
Sbjct: 655 PRVGSGIEGRIARDSGRCILSEIDGVISYVDADRIEVRG-------ASGQIKSYKMLKFR 707

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T ++QRPLV  G+ V+  D++ADG + D G+LALGRN+LVAF+PW GYN+ED++L
Sbjct: 708 RSNQGTIIHQRPLVSQGEAVKAGDVLADGQAVDQGELALGRNVLVAFVPWEGYNYEDAIL 767

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V ED F+S+HIEE+ + +RDTKLGPEEITRDIPNV ++ LKNID+ G++ +GA+V
Sbjct: 768 LSERLVKEDYFSSVHIEEYSIESRDTKLGPEEITRDIPNVGDDALKNIDDDGVVRIGADV 827

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK++PKGE+  TP+EKLLRAIFGEKA +VRDTSLR+P G  G VV ++  NR 
Sbjct: 828 EAGDILVGKVSPKGEADNTPQEKLLRAIFGEKAGEVRDTSLRLPHGTRGKVVGIKRLNRE 887

Query: 949 GI 950
             
Sbjct: 888 NN 889



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 138/589 (23%), Positives = 228/589 (38%), Gaps = 75/589 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L+   P  G   E  +   S R +  ++   I   + + +      G 
Sbjct: 638  MGSNMQRQAVPLLLPEAPRVGSGIEGRIARDSGRCILSEIDGVISYVDADRIEVRGASGQ 697

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +  + +          I +  ++  G  V  GD+L        +  +     +L A   
Sbjct: 698  IKSYKMLKFRRSNQGTIIHQRPLVSQGEAVKAGDVLAD-GQAVDQGELALGRNVLVAFVP 756

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V            + I+  +  +  E E    +    DD    +
Sbjct: 757  WEGYNYEDAILLSERLVKEDYFSSVHIEEYSIESRDTKLGPE-EITRDIPNVGDDALKNI 815

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D +   R+     G +  +G     K +       +   +     F  +  +V+     L
Sbjct: 816  DDDGVVRI-----GADVEAGDILVGKVSPKGEADNTPQEKLLRAIFGEKAGEVRDTSLRL 870

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                      ++     ++ +    + + PGV  V+KV+VA  R I              
Sbjct: 871  PHGTRGKVVGIK-----RLNRENNPESLSPGVDEVIKVYVAQLRKI-------------- 911

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                                              VG              G K       
Sbjct: 912  ---------------------------------TVG-------DKMSGRHGNKGVVSRIL 931

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
               +    P  + ++  +       +++      V+      ++   V+TPVF+GA+E  
Sbjct: 932  PVEDMPYLPDGTPVDVCLNPLGVPSRMNLGQVLEVILGFVAVQNDWFVATPVFEGAEEHE 991

Query: 1219 INSMLRM--------ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            I   +          A + +     L DG TG+  + P TVG +YMLKL+H+V DK++AR
Sbjct: 992  IYEQVHKITSTNPDYATMSDGATIRLRDGRTGDLMEYPSTVGVMYMLKLHHLVDDKLHAR 1051

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            S G YS++TQQPLGGK+  GGQRLGEMEVW +Q YGAA+VLQEMLT+KSDD+ GR + YE
Sbjct: 1052 SVGPYSMITQQPLGGKAQFGGQRLGEMEVWALQGYGAAHVLQEMLTVKSDDIKGRLKTYE 1111

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             IV G +  + G PESF VLVKE++ LGL++ ++ S   +   +++   
Sbjct: 1112 KIVKGENLTQPGVPESFKVLVKELEGLGLTVQIDYSDGTSGPLVDDEDH 1160


>gi|315929770|gb|EFV08940.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 781

 Score =  701 bits (1810), Expect = 0.0,   Method: Composition-based stats.
 Identities = 340/788 (43%), Positives = 499/788 (63%), Gaps = 30/788 (3%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R+R  F    + I+IP+L+++QK S+D+FL ++         G++  FKS+FPI      
Sbjct: 9   RLRVDFSNISKQIEIPNLLQLQKKSFDYFLNLD-----NGESGIEKVFKSIFPIHDPQNR 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
             LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  +KDIKEQ I
Sbjct: 64  LSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGVKDIKEQEI 123

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           Y+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++     + KL+Y  +IIPD+G 
Sbjct: 124 YIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVAN-KLVYTAQIIPDRGS 182

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
           W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +    +
Sbjct: 183 WLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTEFN 242

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             D M   ++   + D + G+ V ++GK+LT    + L + G+K++    + L   Y+A 
Sbjct: 243 PNDFM--DRIEYDIKD-EKGKIVHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYLAN 299

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-- 368
            I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D     
Sbjct: 300 PIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFDIANDLANGVDAAIINSFAQDGETLK 357

Query: 369 ----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                     +   A + IY+VMRPG+      A++  N LFF+ ++YDL+ VGR+KMN 
Sbjct: 358 LLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFNPERYDLTKVGRMKMNH 417

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNRR+RS+GE+L N+  LG
Sbjct: 418 KLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNRRIRSIGELLANELHLG 477

Query: 479 LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           L +M+++I+++ +  + D+D VMP DLIN K + + + EFF   QLSQ  +  N LS +T
Sbjct: 478 LAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGGQLSQFMDQTNPLSEVT 537

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++A+VN  G
Sbjct: 538 HKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTYAKVNELG 597

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           F+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R  GE IL 
Sbjct: 598 FVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQDGETILA 657

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            RE++  ID     VV +AASLIPFLE+DD+NR LMG NMQRQAVPLL A AP VGTGME
Sbjct: 658 RREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMGSNMQRQAVPLLTASAPIVGTGME 717

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            ++A+ +  A+ AKR G+VE+VD   I I   +         +D Y + K  R+NQNT  
Sbjct: 718 QIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFIDHYTMEKNLRTNQNTNY 773

Query: 777 NQRPLVKV 784
            Q P+VK 
Sbjct: 774 IQHPIVKK 781


>gi|1369760|gb|AAC37118.1| RNA polymerase beta subunit [Borrelia burgdorferi]
          Length = 1154

 Score =  699 bits (1805), Expect = 0.0,   Method: Composition-based stats.
 Identities = 386/965 (40%), Positives = 587/965 (60%), Gaps = 73/965 (7%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP---NEGLQAAFKSVFPITAFSGAAML 74
           G+  EI+D+P+LIE+Q  SY+ FL ++     +    NEGL++ F+++FPI + +G   L
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLEKVKKPLLNEGLESVFRNIFPIKSGNGDVAL 69

Query: 75  EFVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           E+  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YM
Sbjct: 70  EYERYYIENVALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYM 120

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G +PLMT+  TF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W+
Sbjct: 121 GTIPLMTERATFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWL 172

Query: 193 DIEFDSKDIIHV-RIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLS 250
           + E DSK II + +IDR+++  +T FL ALG D+ E+I+ TFY         D     L 
Sbjct: 173 EFEIDSKKIIFIEKIDRKKEYVITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLP 231

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              L     +  ++           +G K+T   ++   + GV  + +         V  
Sbjct: 232 GQYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDF 274

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           D  N  +G+ ++ +                      + ++ +             K   +
Sbjct: 275 DGYNDISGKRFVSSN---------------------VILNCLEKEDAFFALKDASKELPK 313

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           +   L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       
Sbjct: 314 ESVSLAVYGSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSV 372

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           +  +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+
Sbjct: 373 LTMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRM 432

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S+ ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++
Sbjct: 433 SNKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLS 492

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G V
Sbjct: 493 RDRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGVV 552

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ + YLSA++EE   IAQAN   + +G+  E+LV  R +G+        ID++D SP+Q
Sbjct: 553 TDQLEYLSAIDEEKNVIAQANRRFNSNGNDLEDLVSVRISGDYTTTSPTNIDYMDVSPRQ 612

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AK
Sbjct: 613 LISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAK 672

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R+G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R
Sbjct: 673 RSGEVILATSSKIVVKPFE---AENAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVER 729

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            +IIADGP+T  G+LALG N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF + 
Sbjct: 730 GEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIE 789

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            R+TKLGPE++T DIPNVSE+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE 
Sbjct: 790 VRETKLGPEKVTGDIPNVSEKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEF 849

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR------HGIDKNERSISVEREQI 964
           +LL +IFGEKA DV++ SL+    +   ++  +   +       G+++N  S++ ++ ++
Sbjct: 850 RLLTSIFGEKAKDVKNNSLKFLMVLKVLLLMFKGLPKRILVSSPGVEENLSSLAAKKRKL 909

Query: 965 ELLAR 969
           +   +
Sbjct: 910 KEGDK 914



 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 168/508 (33%), Positives = 241/508 (47%), Gaps = 85/508 (16%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 720  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 779

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 780  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 838

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E                 ++V++  +++     +L   FK 
Sbjct: 839  PKSEGDITPEFRLLTSIFGE---------------KAKDVKNNSLKFLMVLKVLLLMFKG 883

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
              ++I       PGV   +    A KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 884  LPKRILVS---SPGVEENLSSLAAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 940

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 941  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 976

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 977  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 1006

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 1007 LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 1066

Query: 1296 EMEVWCIQAYG---AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            EMEVW ++AYG    +  L    T+KSDD+ GR ++YE+IV G  T  +G PESFNVL++
Sbjct: 1067 EMEVWALEAYGRRTPSRTL----TVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQ 1122

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            E++ LGL + + +         E+  + 
Sbjct: 1123 ELRGLGLDLSIYDDAGNQVPLTEKEEEL 1150


>gi|298243975|ref|ZP_06967782.1| DNA-directed RNA polymerase, beta subunit [Ktedonobacter racemifer
            DSM 44963]
 gi|297557029|gb|EFH90893.1| DNA-directed RNA polymerase, beta subunit [Ktedonobacter racemifer
            DSM 44963]
          Length = 1163

 Score =  697 bits (1799), Expect = 0.0,   Method: Composition-based stats.
 Identities = 364/1112 (32%), Positives = 542/1112 (48%), Gaps = 117/1112 (10%)

Query: 276  SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET--GEIYIEAGDVIDEKSL 333
            +GKKL +  L   +   ++F     + L      +  +   T    I   A +    + L
Sbjct: 156  TGKKLFAAKLIPGRGAWLEFETSNKNLLTVKIDRKRKLPITTLLRAISRLAKEHWHVEDL 215

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            +      I D     VD+     YI+ TL  D  K  ++ALL++Y+ +RPGD +T   A 
Sbjct: 216  DLSTDQGILD-AFAGVDNDPVIRYIQATLDRDPVKKEEEALLELYKKLRPGDPATLDNAR 274

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            S+   LFF+  +YDL  VGR K+N +L+L  P   R + ++D++AII+ LV L NG+G  
Sbjct: 275  SLVKNLFFNPRRYDLGNVGRYKLNRKLDLSIPQSQRILTQDDLVAIIRRLVSLNNGRGRK 334

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
            DDID+LGNRRVR VGE++++Q+R+GLLRMER +KER+S  +     P  LIN +PVV+A+
Sbjct: 335  DDIDHLGNRRVRCVGELIQSQFRVGLLRMERVVKERMSIQEPGQATPNALINIRPVVAAM 394

Query: 514  CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
             EFF  SQLSQ  + VN+L+ I H RRLSALG GG++R RAG ++RDVH +HYGRICP E
Sbjct: 395  KEFFGGSQLSQFMDQVNALAEIGHKRRLSALGPGGLSRDRAGFDVRDVHESHYGRICPIE 454

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG NIGL+ +L ++ ++N YGFIETPYR V       D   L    E   Y  +    
Sbjct: 455  TPEGPNIGLIGNLATYGQINPYGFIETPYRHVIKRLAATDGRLL--GRELRGYYGRREDI 512

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            + EDG    +        EE+    EK+ F+  +P  +       + +   DD     + 
Sbjct: 513  VTEDGEVLLKRNNPVRVDEELF---EKLAFLGDTPLSIKPFVTDEVDYQTADDEENFYIA 569

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                        A+A                  ++A+  G   +V +  I    V     
Sbjct: 570  QANAVLTDNNEFADAR-----------------VLARYQGEFTEVPSESIDYMDVSPRQT 612

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             S +   I                          +  +D+       ++   A+      
Sbjct: 613  VSVATALI------------------------PFLEHDDVNRALMGANMQRQAVPLLRPQ 648

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +   G   + ++   + +V++     +     ++   D   G          V     
Sbjct: 649  SPICGTGIERQVAVDSGQVIVAQTTGEVVSSTSRKIEIMDQH-GQLYSHALRKFVRSNNG 707

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              I++  I+  G  V  G ++    + +    +   + +L A    +  +  D  L    
Sbjct: 708  TCINQRPIVKKGDYVTKGQVVADSSSTEL-GELALGQNILVAFMSWEGGNFEDAILISER 766

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V   +       ++  + + R   +  E+I        D   + +  + +     +   
Sbjct: 767  IVREDLFTSIHIEKY--EVDARDTKLGPEEITR------DIPNVGEEGLRNLDERGIIYV 818

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             A  GP+      +            +  +    ++  +    SL+V +     ++    
Sbjct: 819  GAEVGPQDILVGKITPKGETELTAEEKLLRAIFGEKAREVKDTSLRVPHGERGKVV---- 874

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + K+   + GD++ PGV ++V+V +A KR I +GDKMAGRHGNKG++SR+LP EDMPFL 
Sbjct: 875  EVKVFSREAGDELSPGVNQLVRVSIAQKRKIGAGDKMAGRHGNKGVISRVLPIEDMPFLP 934

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DG+PVDI+LNPLGVP RMN+GQI ETHLGWA   LG KI + + D     DI  +     
Sbjct: 935  DGSPVDIILNPLGVPHRMNIGQIMETHLGWAASVLGFKIATPVFDGATEEDIEEMLR--- 991

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       ++G+P                        ESG+
Sbjct: 992  ---------------------------RAGLP------------------------ESGK 1000

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG TGEPFD P+TVGY YMLKL H+V DKV+ARSTG YSL+TQQPLGGK+  GGQR
Sbjct: 1001 VQLYDGRTGEPFDHPITVGYTYMLKLAHLVEDKVHARSTGPYSLITQQPLGGKAQFGGQR 1060

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAA +LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VLVKE
Sbjct: 1061 FGEMEVWALEAYGAANILQEILTVKSDDVVGRVKTYEAIVKGENIMEPGVPESFKVLVKE 1120

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            +Q+LG+++++ N   +    +E+  +    EL
Sbjct: 1121 LQSLGINVEVLNEDEQKIQFVEDTSNDVMPEL 1152



 Score =  592 bits (1526), Expect = e-166,   Method: Composition-based stats.
 Identities = 331/961 (34%), Positives = 472/961 (49%), Gaps = 109/961 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-A 71
            R  FG+ P+I  +P LI++Q  S++ F            EGL+  F+ + PI  F+G  
Sbjct: 12  ERVSFGRIPDIRPMPGLIQIQLDSFEWF----------KKEGLRELFEEISPIEDFTGKN 61

Query: 72  AMLEFV--SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             LEF+     F  PK+D D+C  RD T+A PL +  RLI          K   +I E+ 
Sbjct: 62  LSLEFIVPPEPFGKPKYDEDECRDRDATHAAPLNVKARLI---------NKETGEIIEKD 112

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMTK GTF+I G +R+VVSQL RSPG++F  D+     +GK L+A ++IP +G
Sbjct: 113 IFMGDFPLMTKAGTFIINGAERVVVSQLVRSPGVYFTVDEDAT--TGKKLFAAKLIPGRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA-------------LGMDSEE-ILSTFYPK 235
            W++ E  +K+++ V+IDR+RK+P+T+ L A             L + +++ IL  F   
Sbjct: 171 AWLEFETSNKNLLTVKIDRKRKLPITTLLRAISRLAKEHWHVEDLDLSTDQGILDAFAGV 230

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK 294
                                   +      +  G+   +++ + L   L  + +   + 
Sbjct: 231 DNDPVIRYIQATLDRDPVKKEEEALLELYKKLRPGDPATLDNARSLVKNLFFNPRRYDLG 290

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            +G                                     ++  S  +   IL  D +  
Sbjct: 291 NVGRYK-------------------------------LNRKLDLSIPQSQRILTQDDLVA 319

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                 +L   + +      L   RV   G++        +        ++  +   G+ 
Sbjct: 320 IIRRLVSLNNGRGRKDDIDHLGNRRVRCVGELIQSQFRVGLLRMERVVKERMSIQEPGQA 379

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             N  +N+        +           L    +    + +I +         G + ++ 
Sbjct: 380 TPNALINIRP-----VVAAMKEFFGGSQLSQFMDQVNALAEIGHKRRLSALGPGGLSRD- 433

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                           +  D+  V         P+ +                 +N    
Sbjct: 434 ---------------RAGFDVRDVHESHYGRICPIETPEGPNIGLIGNLATYGQINPYGF 478

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           I    R              G E+R     +YGR     T +G  +   ++     RV+ 
Sbjct: 479 IETPYRHVIKRLAATDGRLLGRELRG----YYGRREDIVTEDGEVLLKRNNP---VRVDE 531

Query: 595 YGFIETPYR----KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
             F +  +           VT++V Y +A +EEN YIAQAN+ L ++  F +  V  R  
Sbjct: 532 ELFEKLAFLGDTPLSIKPFVTDEVDYQTADDEENFYIAQANAVLTDNNEFADARVLARYQ 591

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           GE   VP E ID++D SP+Q VS+A +LIPFLE+DD NR LMG NMQRQAVPLL+ ++P 
Sbjct: 592 GEFTEVPSESIDYMDVSPRQTVSVATALIPFLEHDDVNRALMGANMQRQAVPLLRPQSPI 651

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            GTG+E  VA  SG  IVA+  G V    + +I I    G L         + L KF RS
Sbjct: 652 CGTGIERQVAVDSGQVIVAQTTGEVVSSTSRKIEIMDQHGQLYS-------HALRKFVRS 704

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N  TC+NQRP+VK GD V +  ++AD  ST+LG+LALG+N+LVAFM W G NFED++LIS
Sbjct: 705 NNGTCINQRPIVKKGDYVTKGQVVADSSSTELGELALGQNILVAFMSWEGGNFEDAILIS 764

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV EEGL+N+DE GII VGAEV P
Sbjct: 765 ERIVREDLFTSIHIEKYEVDARDTKLGPEEITRDIPNVGEEGLRNLDERGIIYVGAEVGP 824

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DILVGKITPKGE+ +T EEKLLRAIFGEKA +V+DTSLRVP G  G VV+V++F+R   
Sbjct: 825 QDILVGKITPKGETELTAEEKLLRAIFGEKAREVKDTSLRVPHGERGKVVEVKVFSREAG 884

Query: 951 D 951
           D
Sbjct: 885 D 885


>gi|289152661|gb|ADC84227.1| RNA polymerase beta subunit [Prevotella nigrescens ATCC 33563]
          Length = 839

 Score =  694 bits (1792), Expect = 0.0,   Method: Composition-based stats.
 Identities = 377/888 (42%), Positives = 543/888 (61%), Gaps = 57/888 (6%)

Query: 107 RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           +L   D +       I     Q +++G +P MT +GTF+I G +R+VVSQLHRSPG+ F 
Sbjct: 1   KLYCTDPEHEDFGTFI-----QDVFLGTIPYMTDNGTFIINGAERVVVSQLHRSPGVFFG 55

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
                   +G +LY+ RIIP +G W++   D  ++++  IDR++K+PVT+ L A+G +S+
Sbjct: 56  QG---VHANGTVLYSARIIPFKGSWIEFATDINNVMYAYIDRKKKLPVTTMLRAIGFESD 112

Query: 227 -EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +IL  F                L                           G+KL   ++
Sbjct: 113 KDILQIFDLCEEIKVNKKNLKSAL---------------------------GRKLAGNVM 145

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           KS  E  V                 ++V+ E  E+ +E    I E++++ I  S +  I 
Sbjct: 146 KSWNEDFVDEDT------------GEVVSIERNEVVVERETEITEENVDTILESGVSSIL 193

Query: 346 ILYVDSV-NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           +   +SV N  + I NTL  D +    +A+  IYR +R  D +  + A  +F  LFF   
Sbjct: 194 LHKDESVANKFSIIFNTLAKDPSHSEIEAVNYIYRQLRNADAADDASAREVFQNLFFSDK 253

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           +YDL  VGR ++N +L LDT  DVR + K+DIIAIIK L++L N   T+DDID+L NRRV
Sbjct: 254 RYDLGEVGRYRINRKLGLDTDMDVRVLTKDDIIAIIKYLINLVNSNATVDDIDHLSNRRV 313

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           R+VGE L NQ+ +GL RM R+I+ER++  D +   P DLINAK + S +  FF ++ LSQ
Sbjct: 314 RTVGEQLANQFSIGLARMSRTIRERMNVRDNEVFQPTDLINAKTISSVINSFFGTNPLSQ 373

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N L+ +TH RRLSALG GG++R RAG E+RDVH THYGR+CP E+ EG NIGL+S
Sbjct: 374 FMDQTNPLAEVTHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIESPEGPNIGLIS 433

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SL  +A++N  GFI TPYRKV D KV    + VVY++A EEE+  + Q N+ L+ DG+F 
Sbjct: 434 SLCLYAKINDLGFIVTPYRKVTDSKVDLNNDHVVYMTAEEEEDLPVGQGNAPLNPDGTFI 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            + V CR   +  +V   ++  +D +P+Q+ S++A LIPFLE+DD +R LMGCNM RQAV
Sbjct: 494 RDNVKCRQDADYPVVEPSQVALMDVAPQQIASVSAGLIPFLEHDDGHRALMGCNMMRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSG 758
           PLL  +AP VGTG+E  V + S   + A+  G+++ VDA  I I   R+ + +       
Sbjct: 554 PLLHNDAPIVGTGLEKQVCEDSRTMVTAEGDGVIDYVDATTIRILYDRTEDEEFVSFEPA 613

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +  YR+ KF+R+NQN  V+ RP+   G  V++ DI+ +G +T+ G+LALGRN+LVA+MPW
Sbjct: 614 LKEYRISKFRRTNQNMVVDLRPICNKGQRVKKGDILTEGYATENGELALGRNLLVAYMPW 673

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++ISERMV EDV TS+H++E+ +  R+TK G EE T DIPNVSEE  K++DE
Sbjct: 674 KGYNYEDAVVISERMVREDVLTSVHVDEYSLEVRETKRGVEEFTSDIPNVSEEATKDLDE 733

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII +GA V PGDI++GKI+PKGES  +PEEKLLRAIFG+KA DV+D+SL+    +SG 
Sbjct: 734 NGIIRIGARVEPGDIMIGKISPKGESDPSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGV 793

Query: 939 VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
           V+D R+F R    K   S   ++  +  L  +++ +   L   +  +L
Sbjct: 794 VIDKRLFARA--LKTRESKRHDKATLARLDEEQEAKINDLRSLLVDKL 839


>gi|269837059|ref|YP_003319287.1| DNA-directed RNA polymerase, beta subunit [Sphaerobacter thermophilus
            DSM 20745]
 gi|269786322|gb|ACZ38465.1| DNA-directed RNA polymerase, beta subunit [Sphaerobacter thermophilus
            DSM 20745]
          Length = 1159

 Score =  692 bits (1787), Expect = 0.0,   Method: Composition-based stats.
 Identities = 361/1062 (33%), Positives = 509/1062 (47%), Gaps = 149/1062 (14%)

Query: 332  SLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             L  I   +  +I  L+ D  +  + +I +TL  D  K R++A +++YR +RPGD  T  
Sbjct: 208  LLRAIGIVDDDEIRELFADVDDPEHRFIESTLERDTTKTREEAQVELYRRLRPGDPPTRE 267

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             A S+ + LFF+  +YDL+ VGR K+N RL LD   D R + +ED++ +++ L+ +  G+
Sbjct: 268  NAASLLDGLFFNPRRYDLAKVGRYKLNKRLGLDIGLDTRVLTREDLVEVVRTLIRVNTGQ 327

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD-LINAKPV 509
               DDID+LGNRRVR+VGE+++   R GL R+ER I+ER++  DI++V P   +   +PV
Sbjct: 328  DQPDDIDHLGNRRVRAVGELIQMHVRTGLQRLERGIRERMTIQDIETVTPNGLISTTRPV 387

Query: 510  VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            ++AV EFF  SQLSQ  +  N L+ +T+ RRLSALG GG++R RAG ++RDVH +HYGRI
Sbjct: 388  MAAVREFFGGSQLSQFMDQTNPLAELTNKRRLSALGPGGLSRDRAGFDVRDVHYSHYGRI 447

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CP ET EG NIGL+ SL ++ R+NAYGFIETPYR+V           L+  E+    +  
Sbjct: 448  CPIETPEGPNIGLIGSLATYGRINAYGFIETPYRRVYRQ--------LNPQEDHELIL-- 497

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                    G      V     GE +     +ID      +   +    +       D   
Sbjct: 498  --------GRIVAVDVKHPETGEVLAAAGTQID-EALRARLAEAGITMVRIVPFVSDQIE 548

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             L      +  +    A        +E  V+   G   V+     ++ +D     + SV 
Sbjct: 549  YLSADREDQFVIAQANAPLNERAEFIEERVSARYGDGFVSAPPERIDYMDVSPKQLVSVA 608

Query: 750  GDLDPSTSGVDIYRLMK---FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              L P     D  R +     QR        Q P+V  G                     
Sbjct: 609  AALIPFLEHDDANRALMGANMQRQAVPLLRPQAPIVGTG--------------------- 647

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                     + +        ++++E      V TS+      V   D   G E + +   
Sbjct: 648  ---------VEYQAARDSGQVVVAE---KAGVVTSVTARAITVREDD---GTERVYKLRK 692

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             +       I++   +  G  V PG I+    +      +   + +L A    +  +  D
Sbjct: 693  FIRSNQDTCINQRPSVNKGDRVEPGQIIADSSSTDN-GELALGQNVLAAFMSWEGGNFED 751

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD----------DEQV 976
              L     +S  +V   ++    I+K E      +   E + RD            DE  
Sbjct: 752  AIL-----ISERLVRDDVYTSIHIEKYETEARDTKLGPEEITRDIPNVGEDSLANLDENG 806

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            I+      R  +IL G+    G         L   +  E  R           +V+    
Sbjct: 807  IIRIGAEVRPNDILVGKVTPRGETELSAEERLLRAIFGEKAR-----------EVKDTSL 855

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDD--MPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             +          +      K  K + G D  +P GV  +V+V +A KR I  GDKMAGRH
Sbjct: 856  RVPHGVHGKVIDV------KRFKREEGSDHELPAGVNEMVRVMIAQKRKISEGDKMAGRH 909

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++SRILP EDMP+L DGTPVDIVLNP+GVPSRMN+GQ+ ETHLGWA   LG KI S
Sbjct: 910  GNKGVISRILPIEDMPYLPDGTPVDIVLNPIGVPSRMNIGQVLETHLGWAAAALGLKIAS 969

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D      I  +                                ++G+P         
Sbjct: 970  PVFDGAKEYQIREMLE------------------------------RAGLP--------- 990

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G+  LYDG TGE FDRPVTVG +YM+KL H+V DK++ARSTG 
Sbjct: 991  ---------------SDGKVDLYDGRTGEKFDRPVTVGVMYMMKLAHLVEDKIHARSTGP 1035

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+IV 
Sbjct: 1036 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKTYEAIVK 1095

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            G    E G PESF VLVKE+++LGLS+++ N   +     E+
Sbjct: 1096 GEPIVEAGVPESFKVLVKELRSLGLSVEVINEDEETIDFAED 1137



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 93/468 (19%), Positives = 191/468 (40%), Gaps = 36/468 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F   P ++++P+L+++Q  S++ F            EG++   + + PI  ++G   
Sbjct: 26  RVSFASIPTVLEMPNLVQLQIESFEWF----------KTEGMRELLEEISPIVDYNGKME 75

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           L F+ + FD P++D + C  RD+TYA PL+I ++L++         +   +IKE  +++G
Sbjct: 76  LRFLEHRFDEPRYDEETCRERDMTYAAPLRIRVQLLI---------RETGEIKESDVFLG 126

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D P+MT  GTF+I G +R+VVSQL RSPG++FD        +G+ L   ++IP +G W++
Sbjct: 127 DFPIMTPHGTFLINGAERVVVSQLVRSPGVYFDLTTDPT--TGRQLAGAKLIPSRGAWLE 184

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            E  +K+++ V++DR+RK+PVT  L A+G+  ++ +   +  +   +             
Sbjct: 185 FETSNKNVLSVKVDRKRKLPVTVLLRAIGIVDDDEIRELFADVDDPEHRFIESTLERDTT 244

Query: 254 LMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDC--------LC 304
                        +  G+    E+   L  GL  + +   +  +G             L 
Sbjct: 245 KTREEAQVELYRRLRPGDPPTRENAASLLDGLFFNPRRYDLAKVGRYKLNKRLGLDIGLD 304

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
              +  + +      +            ++ + +  +R +  L    V          + 
Sbjct: 305 TRVLTREDLVEVVRTLIRVNTGQDQPDDIDHLGNRRVRAVGELIQMHVRTGLQRLERGIR 364

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           ++   +    +    ++        +V    F            + +  +    RL+   
Sbjct: 365 ERMTIQDIETVTPNGLISTTRPVMAAV-REFFGGSQLSQFMDQTNPLAELTNKRRLSALG 423

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           P  +   R    +  +       +  G I  I+      +  +G +  
Sbjct: 424 PGGLSRDRAGFDVRDVHY-----SHYGRICPIETPEGPNIGLIGSLAT 466


>gi|218673595|ref|ZP_03523264.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli GR56]
          Length = 761

 Score =  692 bits (1785), Expect = 0.0,   Method: Composition-based stats.
 Identities = 539/758 (71%), Positives = 647/758 (85%), Gaps = 1/758 (0%)

Query: 300  SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
             D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N  AYIR
Sbjct: 5    DDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILSNGFDEIPVLGIDHINVGAYIR 64

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            NTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRVKMNMR
Sbjct: 65   NTLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLSAVGRVKMNMR 124

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L+L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQYRLGL
Sbjct: 125  LDLTVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQYRLGL 184

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            LRMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  + VN LS ITH R
Sbjct: 185  LRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQVNPLSEITHKR 244

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE
Sbjct: 245  RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIE 304

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            +PYR++ DG+VTNDV+YLSAMEE   Y+AQAN+ ++ DGSF +E V CR AGE +L PR+
Sbjct: 305  SPYRRIVDGRVTNDVLYLSAMEEAKYYVAQANAEMNPDGSFVDEFVVCRHAGEVMLAPRD 364

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAPFVGTGME VV
Sbjct: 365  SMNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEPVV 424

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGAAI A+R G+V+QVDA RIVIR+ E  L+   SGVDIYRL KFQRSNQNTCVNQR
Sbjct: 425  ARDSGAAIGARRGGVVDQVDATRIVIRATED-LEAGKSGVDIYRLQKFQRSNQNTCVNQR 483

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLV VGD V R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVF
Sbjct: 484  PLVTVGDVVNRGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVF 543

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKIT
Sbjct: 544  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKIT 603

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++
Sbjct: 604  PKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAI 663

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            ERE+IE LA+D+DDEQ ILDRN+Y RL+++L GQ +++GPKGFKK T LS+ ++SEYPRS
Sbjct: 664  EREEIERLAKDRDDEQAILDRNVYGRLIDMLRGQVSIAGPKGFKKGTELSNAVVSEYPRS 723

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            QWW FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+
Sbjct: 724  QWWMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKV 761


>gi|94502266|ref|ZP_01308749.1| DNA-directed RNA polymerase beta chain [Candidatus Sulcia muelleri
            str. Hc (Homalodisca coagulata)]
 gi|94451173|gb|EAT14115.1| DNA-directed RNA polymerase beta chain [Candidatus Sulcia muelleri
            str. Hc (Homalodisca coagulata)]
          Length = 951

 Score =  691 bits (1782), Expect = 0.0,   Method: Composition-based stats.
 Identities = 385/1006 (38%), Positives = 587/1006 (58%), Gaps = 68/1006 (6%)

Query: 138  MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
            MT  G+F+  G +R++VSQLHRSPG+ F           K+ Y  RIIP +G W+++  D
Sbjct: 1    MTPSGSFIFNGSERVIVSQLHRSPGVFFGQYDIPNLP--KISY-ARIIPLKGSWIELSTD 57

Query: 198  SKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
              +++++ +D ++++P+T+ L ALG   + +IL+ F      +     +   L       
Sbjct: 58   INNVMYIYLDIKKRLPITTLLRALGYTRDIDILNIFNLAEEVNINKVNYKKFL------- 110

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                                G+ L + + K+  +K                        E
Sbjct: 111  --------------------GRTLAARIFKTSYQKF-----------------------E 127

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN----NAYIRNTLVTDKNKDRKD 372
              +I +E    + +  ++ I + +I+ I +   +  N      + I NTL  D    +K+
Sbjct: 128  ENDILLERNIKLKKYHIDIILYYKIKVISLYKKNEKNEKNLYYSIIHNTLKKDPTNSQKE 187

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            A + IY+ ++         A+   N  FFD     L  VGR K+N  L LD P   + + 
Sbjct: 188  ANIYIYKELKDSFPKNDKKAKLFINKFFFDET--HLGEVGRYKLNKTLKLDFPLKDQILN 245

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             EDII+II+ L+ L N K  +DDIDNL NRRV++VGE L  QY +G+ R+ R IKERI+ 
Sbjct: 246  IEDIISIIENLIALCNNKKEVDDIDNLANRRVKTVGEQLYTQYTIGIARVSRIIKERINV 305

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             D +++ P +LIN+K + S +  FF + +LSQ  +  N L+ +TH RR+S+LG GG++R 
Sbjct: 306  KDNETLTPLELINSKTLTSVINSFFGTDELSQFMDQTNPLAEMTHKRRISSLGPGGLSRE 365

Query: 553  RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV-- 610
            RAG E+RDV+ +HYGR+CP ET EG NIGL+SSL  FA++N+ GFIETPY KV  GKV  
Sbjct: 366  RAGFEIRDVNYSHYGRLCPIETPEGPNIGLISSLCVFAKINSMGFIETPYFKVKKGKVVI 425

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
                +Y+S+ +E  + I QAN+ L+      +  +  R   +  +V  +KI++ID S  Q
Sbjct: 426  NEAPIYISSDQEYGKLITQANAILNYKTGVLKNNIIVRVNADFPMVNYKKINYIDVSTNQ 485

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + SI+ASLIPFLE+DD+NR LMG NM RQ+VPLL  +AP VGTG+E  +A+   A I A+
Sbjct: 486  IASISASLIPFLEHDDANRALMGSNMMRQSVPLLNPKAPIVGTGLEKHLAQYVNALIYAE 545

Query: 731  RAGIVEQVDAIRIVIRS---VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              GIVE VDA  I ++     +  L      +  Y+L+KF+++NQNTC+N RP+VK G  
Sbjct: 546  GDGIVESVDANNIKVKYFNSEKEKLLSFEKRIKTYKLIKFRKTNQNTCLNIRPIVKKGMY 605

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  ++ +G +T  G LALGRN+ VAFMP+ GYNFED+++ISE++V ED FTSIHI+E+
Sbjct: 606  VTKGQVLCEGFATQNGKLALGRNIKVAFMPFKGYNFEDAIVISEKVVREDWFTSIHIDEY 665

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             +  RDTKLG EE T DIPN +EE  K +D+ GII +G+EV PGD+L+G+ITPK E   +
Sbjct: 666  SLEVRDTKLGMEEFTFDIPNFNEENKKKLDKYGIIKIGSEVKPGDVLIGRITPKKEGYPS 725

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
             EE  L+AIFG+K   +++TSL+  S + G V+D +I+++    ++E+     ++     
Sbjct: 726  SEENFLKAIFGKKVGTIKNTSLKADSSLFGVVIDTKIYSKFSSKEDEQKQFQIKKLNNKF 785

Query: 968  ARDKDDEQVILDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ--WWQF 1024
             ++    + +L   +   L   +  G    S  +   K  +L+   + +  ++Q   +Q 
Sbjct: 786  MKNLKLLRKLLINKLILVLEGSVSEGILNSSYKEIIPKGKILNKLNLKKLLKNQEIIYQN 845

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             V ++     V  +   Y    + L+ + K K  ++  GD++  G++++ KV +A KR +
Sbjct: 846  WVNNKYKNNLVFKIIKFYYLKINELKIKLKRKKNRLLIGDEITSGIIKIAKVLIAKKRKL 905

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            + GDKM+GRHGNKGIV+RI+  EDMP+L+DGT VD+VLNPLGVPSR
Sbjct: 906  KVGDKMSGRHGNKGIVARIVKEEDMPYLEDGTSVDLVLNPLGVPSR 951


>gi|328910069|gb|AEB61665.1| RNA polymerase (beta subunit) [Bacillus amyloliquefaciens LL3]
          Length = 1081

 Score =  689 bits (1777), Expect = 0.0,   Method: Composition-based stats.
 Identities = 393/833 (47%), Positives = 530/833 (63%), Gaps = 59/833 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W
Sbjct: 1   MGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAW 57

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S
Sbjct: 58  LEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENS 117

Query: 251 AADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSD 301
              L+           +  GE   +E+ K L        K           +       +
Sbjct: 118 DKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKN 171

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            L    +AE +V+ ETGEI  E G ++D ++L++             V     N      
Sbjct: 172 RLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VLPYLENGIGFRK 218

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  +      + +L   ++  P D                          G   +N+  N
Sbjct: 219 LYPNGGVVEDEVMLQSIKIYAPTD------------------------AEGEQTINVIGN 254

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
               + +++I   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL R
Sbjct: 255 AYIEEAIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSR 314

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRL
Sbjct: 315 MERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRL 374

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETP
Sbjct: 375 SALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNRFGFIETP 434

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YR+V    GKVT  + YL+A EE+N  +AQAN+ L +DGSF ++ +  R  GE  +V R 
Sbjct: 435 YRRVDPETGKVTPRIDYLTADEEDNYVVAQANAKLSDDGSFLDDSIVARFRGENTVVARN 494

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EAP VGTGME V 
Sbjct: 495 RVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPIVGTGMEYVS 554

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            K SGAA++ K  GIVE+V+A  + +R   E D       +D Y L+KF RSNQ TC NQ
Sbjct: 555 GKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKFVRSNQGTCYNQ 614

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RP+V VGDEV + +I+ADGPS +LG+LALGRN++V FM W GYN+ED++++SER+V +DV
Sbjct: 615 RPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDV 674

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+LVGK+
Sbjct: 675 YTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDLLVGKV 734

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 735 TPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 787



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 183/573 (31%), Positives = 270/573 (47%), Gaps = 71/573 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V      ++ +  +E +      G  +    +  V     
Sbjct: 550  MEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEIDGQKVKGNLDKYSLLKFVRSNQG 609

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     ++         +  D  +    
Sbjct: 610  TCYNQRPIVSVGDEVVKGEILADGPS-MELGELALGRNVMVGFMTWDGYNYEDAII---- 664

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 665  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDR-GIIRIGA 722

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +          +    
Sbjct: 723  EVNDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV---- 778

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L 
Sbjct: 779  --KVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLP 836

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+        
Sbjct: 837  DGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAG 896

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 897  MSRDAK----------------------------TVLYDG-------------------- 908

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 909  ------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 962

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G++  E G PESF VL+KE
Sbjct: 963  FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKE 1022

Query: 1354 MQALGLSIDLENSRTKNSAK--MEEIPDFNKCE 1384
            +Q+LG+ + + +S  +      +E+  D  + +
Sbjct: 1023 LQSLGMDVKILSSDEEEIEMRDLEDEEDAKQAD 1055


>gi|239618202|ref|YP_002941524.1| DNA-directed RNA polymerase, beta subunit [Kosmotoga olearia TBF
           19.5.1]
 gi|259494186|sp|C5CGD9|RPOB_KOSOT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|239507033|gb|ACR80520.1| DNA-directed RNA polymerase, beta subunit [Kosmotoga olearia TBF
           19.5.1]
          Length = 1173

 Score =  689 bits (1777), Expect = 0.0,   Method: Composition-based stats.
 Identities = 379/976 (38%), Positives = 579/976 (59%), Gaps = 114/976 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---- 66
            R R  FGK  E ++IP+LIE+Q  S+  FL           EGL    K   PI     
Sbjct: 8   KRERWVFGKVIEPLEIPNLIEIQLKSFKWFL----------EEGLLDVLKKYSPIKSQIQ 57

Query: 67  --AFSGA---AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFV      PK+++ +C  + LTY+VPL +T+R+             
Sbjct: 58  RPDSRKNEKGFSLEFVRTRIGNPKYNIQECKDKGLTYSVPLYVTVRITDL---------Y 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IKE+  + G LP MT + +F+I G +R++V+QL RSPG++F  +  +AS     +  
Sbjct: 109 SGEIKEEEAFFGYLPYMTDNASFIINGAERVIVNQLVRSPGVYFVDEPTKASSGSLPILV 168

Query: 182 CRIIPDQGLWMDIEFDS-KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +P +G W++I  +  K ++ VRIDRRRK+ +   L  LG + + E+L  F   +   
Sbjct: 169 AHFLPVKGAWLEILLNPNKKVLQVRIDRRRKMNLFLLLKTLGYEDDLELLDLFVHDV--- 225

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
                                     D +    ++E    +    +K+            
Sbjct: 226 --------------------------DANDEYVLLEHVGSIILSDVKT------------ 247

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                              E+  E G V+ E   ++I  S++  I +     +  +    
Sbjct: 248 -----------------RNELIAERGAVLTEALAKKIAESDVDVIKL--PMPIAMSTLKA 288

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                 +N   +DA ++I+R +RPG++   + A++  + L+F  D++D S VGR K+N R
Sbjct: 289 FHRTYGENIKSEDAYIEIFRKLRPGEIPRINAAKNYLHNLYFSPDRFDFSEVGRHKINSR 348

Query: 420 LN------------------LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           L                   ++  ++   + + DI+   + L  L +    +D  D+LGN
Sbjct: 349 LRKVYKEYLKEVKKTEVPEDIEYAEESTVLTELDIVLAARHLAQLESHPELLDTKDHLGN 408

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSS 520
           +RVR+VGE+++N++    +++ + ++E+++     D V  Q+L+N + +++ + +FF +S
Sbjct: 409 KRVRTVGELMQNEFEKAFVKIHKLLEEKLTIYTSFDKVTVQNLVNVRTLMTTLHQFFATS 468

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + VN L+ +TH RRLSA+G GG+ R  A  E+RDVH +HYGR+CP ET EG NI
Sbjct: 469 QLSQFMDQVNPLAELTHKRRLSAIGPGGLKREHARFEVRDVHHSHYGRMCPIETPEGANI 528

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+++A ++ YGF+ TPYRKV +GKVT+++VYL+A EEE   IAQ+   +D++G+ 
Sbjct: 529 GLMTSLSTYATIDKYGFLLTPYRKVKNGKVTDEIVYLAADEEELYNIAQSTIEVDDNGNI 588

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            E +V  R AGE   V +EK+D +  SPKQ+VS++ SLIPFLE+DD+NR LMG NMQRQA
Sbjct: 589 VESVVEVRHAGEIKYVEKEKVDLMAISPKQIVSVSTSLIPFLEHDDANRALMGSNMQRQA 648

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD-----LDPS 755
           VP++K EAP VGTG+E++ A+ SG  ++AK  GIV++VD+ +I+I  ++ D      +  
Sbjct: 649 VPVIKPEAPIVGTGVEAIAARDSGYVVLAKHRGIVKKVDSRKIIIERIDEDGNPILSESG 708

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
               D+Y L KF R+NQ+T +NQRP+V  G+ V + D IADGPSTD+G+LALG+N+ VAF
Sbjct: 709 EPIQDVYTLHKFIRTNQDTTINQRPIVSQGETVEKGDPIADGPSTDMGELALGKNIFVAF 768

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           +PW GYNFED++L+S+ ++ E+ FT+IHIE +E +ARDT+LGPEEIT DIPNVS+E LKN
Sbjct: 769 LPWEGYNFEDAILVSQELLEEETFTTIHIEMYETVARDTQLGPEEITADIPNVSKELLKN 828

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+ VGA V+ GDILVGK+TPKGES  TPEEK++R++FG++  DV+DTSLRVP GV
Sbjct: 829 LDENGIVRVGAYVSSGDILVGKVTPKGESDTTPEEKIIRSVFGDRGRDVKDTSLRVPHGV 888

Query: 936 SGTVVDVRIFNRHGID 951
            G V+DV++F++  I 
Sbjct: 889 EGRVIDVKVFDKEEIS 904



 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 128/511 (25%), Positives = 201/511 (39%), Gaps = 88/511 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVD----VRDTSLRVPSGV 935
            I+  G  V  GD +  G  T  GE  +     +    +     +    V    L   +  
Sbjct: 734  IVSQGETVEKGDPIADGPSTDMGELALGKNIFVAFLPWEGYNFEDAILVSQELLEEETFT 793

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            +  +       R      E   +      + L ++  DE  I+    Y    +IL G+  
Sbjct: 794  TIHIEMYETVARDTQLGPEEITADIPNVSKELLKNL-DENGIVRVGAYVSSGDILVGKVT 852

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         +   +  +  R            V+     +    E     +      
Sbjct: 853  PKGESDTTPEEKIIRSVFGDRGRD-----------VKDTSLRVPHGVEGRVIDV------ 895

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   +   ++  GV ++VKV+VA  R                                 
Sbjct: 896  KVFDKEEISELGSGVNKLVKVYVAC-RK-------------------------------- 922

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             P+D+                            G K        K +    P  + ++ V
Sbjct: 923  -PLDV--------------------GDKLAGRHGNKGVVSNIIPKEDMPFLPDGTPVQIV 961

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML----RMADLD-- 1229
            +       +++               +    +TP+FDGA E+ I   L    + A +D  
Sbjct: 962  LSPLGVPSRMNVGQVLETHLGWLGQLTNRYFATPIFDGAKEDEIMEELYKARKAAGIDVG 1021

Query: 1230 -----ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                 ++G+ +L DG +G PFD PV VG +YMLKL H+  DK++ARSTG YSL+ QQPLG
Sbjct: 1022 DSKKEKNGKVLLRDGRSGLPFDYPVVVGVMYMLKLVHIAKDKIHARSTGPYSLIHQQPLG 1081

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK++ GGQR GEMEVW ++A+GAA+ L E+LT+KSDD+ GR  VY++I+ G +    G P
Sbjct: 1082 GKAHFGGQRFGEMEVWALEAHGAAHTLNEVLTVKSDDIKGRNEVYKAILKGLNVPGPGIP 1141

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            ESF VL+KE+Q L L I + +         +
Sbjct: 1142 ESFKVLIKELQGLALDIRVYDQNGNELDVDK 1172


>gi|329568270|gb|EGG50085.1| DNA-directed RNA polymerase, beta subunit [Enterococcus faecalis
           TX1467]
          Length = 1103

 Score =  688 bits (1776), Expect = 0.0,   Method: Composition-based stats.
 Identities = 382/841 (45%), Positives = 533/841 (63%), Gaps = 61/841 (7%)

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           ++IK Q ++ GD PLMT+ GTF+I G +R++VSQL RSPG++F    G+   +GK  +  
Sbjct: 3   QEIKSQEVFFGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFH---GKVDKNGKEGFGS 59

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQR 241
            +IP++G W+++E D+KDI +VRIDR RK+P+T  + ALG  S++ I   F         
Sbjct: 60  TVIPNRGAWLEMETDAKDISYVRIDRTRKIPLTVLVRALGFGSDDTIFEIFGDSESLRNT 119

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      +A+D      +      +  GE    +S + L +      K   +  +G   
Sbjct: 120 IEKD-LHKNASDSRTEEGLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLANVGRYK 178

Query: 301 --------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
                     L  L +AE +V+ ETGEI +E G V+  + +E +                
Sbjct: 179 VNKKLDLKTRLLNLTLAETLVDPETGEIIVEKGTVLTHQIMETL---------------- 222

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
               YI N L +      +DA++         +  T  V + +                 
Sbjct: 223 --GEYIDNGLNSVTYYPSEDAVV--------TEPMTIQVIQVLSPKDP------------ 260

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              +N+  N    D V+ +R  DI+A +    +L    G +DDID+LGNRR+RSVGE+L+
Sbjct: 261 ERIVNVIGNGYPDDSVKTVRPADIVASMSYFFNLMEDIGNVDDIDHLGNRRIRSVGELLQ 320

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L
Sbjct: 321 NQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPL 380

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+V
Sbjct: 381 GELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKV 440

Query: 593 NAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N +GFIETPYR+V    G+VT+ V YL+A  E++  +AQANS L+EDG+F  ++V  R  
Sbjct: 441 NKFGFIETPYRRVDRATGRVTDQVDYLTADIEDHYIVAQANSLLNEDGTFANDVVMARLQ 500

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E + V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  +P+
Sbjct: 501 SENLEVAVDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPRSPW 560

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y + KF+RS
Sbjct: 561 VGTGMEYKSAHDSGAALLCKHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFRRS 613

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N  T  NQRP+V +G++V + D +ADGPS + G++ALG+N+LVAFM W GYN+ED++++S
Sbjct: 614 NSGTSYNQRPIVHLGEKVEKGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAIIMS 673

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            R+V +DV+TS+HIEE+E  ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  
Sbjct: 674 RRLVKDDVYTSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQD 733

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   
Sbjct: 734 GDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAG 793

Query: 951 D 951
           D
Sbjct: 794 D 794



 Score =  480 bits (1236), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/499 (35%), Positives = 237/499 (47%), Gaps = 77/499 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 624  IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 682

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 683  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 742

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V+     +          +      
Sbjct: 743  PKGVTELSAEERLLHAIFGEKAR-----------EVRDTSLRVPHGGGGIVHDV------ 785

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 786  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 845

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 846  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 890

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 891  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 915

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 916  ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 971

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    + G PESF VLVKE+Q
Sbjct: 972  EMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAIVKGEPIPKPGVPESFRVLVKELQ 1031

Query: 1356 ALGLSIDLENSRTKNSAKM 1374
            +LGL + + +         
Sbjct: 1032 SLGLDMRVLDIEEAEIELR 1050


>gi|162447041|ref|YP_001620173.1| DNA-directed RNA polymerase subunit beta [Acholeplasma laidlawii
           PG-8A]
 gi|189043846|sp|A9NEL7|RPOB_ACHLI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|161985148|gb|ABX80797.1| DNA-directed RNA polymerase, subunit beta [Acholeplasma laidlawii
           PG-8A]
          Length = 1271

 Score =  687 bits (1773), Expect = 0.0,   Method: Composition-based stats.
 Identities = 379/1027 (36%), Positives = 561/1027 (54%), Gaps = 104/1027 (10%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M+   V  G    R+ + K    +++P+LIE+Q  S++ F+            G+    K
Sbjct: 1   MSYKTVKYGKKAERRDYSKMLHQVELPNLIEIQTKSFEEFV----------ETGIDELLK 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI   +G   L F       PK+   +   RDL Y+  L   ++L            
Sbjct: 51  DISPIEGHNGDLKLYFEESSLSEPKYSTIETKIRDLNYSRQLSARVKL---------ENA 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +++E ++ M DLP+MT  GTF+I G +R+VVSQ+ RS G+++  +  +     K  Y
Sbjct: 102 ITGEVRESTVLMTDLPMMTPSGTFIINGAERVVVSQIVRSSGVYYTSELDKKINQIK--Y 159

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPK--IV 237
           + ++IP +G W++ E  SK+I++ ++DR +KVP+T+F+ ALG  + ++I  TF     I 
Sbjct: 160 SAQVIPTRGAWIEFEQGSKEILYAKLDRSKKVPLTTFIRALGFTTKKDIEETFGRSSLIT 219

Query: 238 YSQRGDFWCFPLSA-----ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            +   D    P  A     + L  G KV +         ++ ++ +     L K  + K 
Sbjct: 220 NTFEKDETKSPNEAVIDLYSKLRQGEKVPADAAREFIRMRLFDARR---YDLAKVGRYKF 276

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           +K L + +    G Y+A DI+    GE+ +     + ++ ++ +  +       L     
Sbjct: 277 IKKLDVLA-RAEGTYLANDIILD--GEVLVAKDTHLTKEVIQILAQNRDAFRKQLITKEN 333

Query: 353 N--------------------------------------NNAYIRNTLVTDKNKDRKDAL 374
           N                                       N  I   ++T+  K+R    
Sbjct: 334 NLQNETADEILATTLPEGGNTLYAKENVVNLKTGEVLVKKNEAITEEVLTNLRKNRHSID 393

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             + +     DV               D   YD     +  +   +  D  +D   +   
Sbjct: 394 EKVIKYFLTEDVYKKESLRQGVISEILDVYVYD-DAGDKSNVIRIIGSDQREDRIFVAVS 452

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           DI+A I   ++L +G G +DDID+LGNRR+R +GE+LKNQ+R+GL R E++IK+++S+ +
Sbjct: 453 DIVASISYFLNLYDGLGNVDDIDHLGNRRLRLIGELLKNQFRIGLARAEKNIKDKMSTTN 512

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +   P ++IN  P+V A+  FF SSQLSQ  + +N L+ +T  RR+SALG GG+AR RA
Sbjct: 513 FNDATPANVINMTPLVGAIKTFFGSSQLSQFMDQINPLAELTQKRRVSALGTGGIARDRA 572

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC----DGKV 610
           GVE+RDVH +HYGR+CP ET EG +IGL+SSL ++A+V+ YGFI+TP+ KV     +  V
Sbjct: 573 GVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATYAKVDEYGFIKTPFLKVVQNGNETSV 632

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T +V+YL+A EE +  IA A + +DE G F E  V  R  GE  +    +I  +D SPKQ
Sbjct: 633 TKEVIYLTADEESDHVIASAATPMDEHGLFIESRVIARRNGETGIYDANEITAMDVSPKQ 692

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+A S IPFLE+DD++R LMG NMQRQAVPLL+  +P VGTG+E   AK SGA ++AK
Sbjct: 693 VVSVATSSIPFLEHDDASRALMGANMQRQAVPLLQPTSPIVGTGVEYRAAKDSGAVVIAK 752

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGV------------------------DIYRLMK 766
            +G V  VD  +I+I     D   S S                          D Y L++
Sbjct: 753 NSGYVTYVDGKKIIITPEPTDTIKSGSKTLYKVGGEFDYGIAKKLYETKSVQNDQYDLVQ 812

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ+T + Q+P+V  G+ V   D+IADGPST+ G+LALGRN+ VAFM W GYN+ED+
Sbjct: 813 FFRSNQDTLILQKPIVMQGEYVDAGDVIADGPSTENGELALGRNVTVAFMTWEGYNYEDA 872

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTK--LGPEEITRDIPNVSEEGLKNIDECGIICV 884
           +++SE +V  DV+TSIHI+E+E+  RD K   G EEITR+IPNV +E +K +DE GII  
Sbjct: 873 VIMSEDLVKHDVYTSIHIDEYEIETRDLKQANGKEEITREIPNVGQEAIKFLDERGIIVP 932

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+EV  GDILVGKITPKG    TP EKL+ A+ G+KA + RD+SLRVP G  G V  V+ 
Sbjct: 933 GSEVKEGDILVGKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQY 992

Query: 945 FNRHGID 951
           F++   D
Sbjct: 993 FSKKNGD 999



 Score =  459 bits (1181), Expect = e-126,   Method: Composition-based stats.
 Identities = 166/501 (33%), Positives = 250/501 (49%), Gaps = 65/501 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V+ GD++    + +    +     +  A    +  +  D  +     V   V 
Sbjct: 827  IVMQGEYVDAGDVIADGPSTEN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 885

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   +  +E+I     +   E +            I+ G     G  
Sbjct: 886  TSIHIDEYEIETRDLKQANGKEEITREIPNVGQEAI----KFLDERGIIVPGSEVKEGDI 941

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 942  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 997

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGT VDI
Sbjct: 998  --GDQLPTGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYLADGTYVDI 1055

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ S + D   N ++               
Sbjct: 1056 MLNPLGVPSRMNIGQILEIHLGISAQKLGIKVASPVFDGVTNDEL--------------- 1100

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                            GA  E        A +   G++ LYDG 
Sbjct: 1101 --------------------------------GAIMEE-------AGIAPDGKTTLYDGR 1121

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP++  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR GEMEVW
Sbjct: 1122 TGEPYNNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQRFGEMEVW 1181

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             + AYGAA+ LQEMLTIKSDD++GR +VY +I  G +  +   PESF VL +E+QALGL 
Sbjct: 1182 ALYAYGAAHTLQEMLTIKSDDMIGRNKVYYAITHGQEIPKASIPESFRVLTRELQALGLY 1241

Query: 1361 IDLENSRTKNSAKMEEIPDFN 1381
            ++L ++    +  ++ + D +
Sbjct: 1242 VELIDANKGENEAIKSLVDNS 1262


>gi|222099189|ref|YP_002533757.1| DNA-directed RNA polymerase subunit beta [Thermotoga neapolitana DSM
            4359]
 gi|221571579|gb|ACM22391.1| DNA-directed RNA polymerase subunit beta [Thermotoga neapolitana DSM
            4359]
          Length = 1267

 Score =  685 bits (1768), Expect = 0.0,   Method: Composition-based stats.
 Identities = 338/1408 (24%), Positives = 537/1408 (38%), Gaps = 197/1408 (13%)

Query: 11   GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
             R R  FGK  E + +PDL+E+QK+SY  FL           +GL    K   PI +   
Sbjct: 13   RRTRVSFGKTHEPLPVPDLVEIQKSSYQKFL----------EKGLLEVLKKFSPIYSQST 62

Query: 68   ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                        LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 63   RSDLKRSDKGFALEFVSTRVGDPTVDPLECKAKGLTYSVPVYATARLTDL---------K 113

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
              ++KE+ +++G +P MT+ GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 114  SGEMKEEEVFLGYIPYMTERGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 168

Query: 182  CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
               +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 169  GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTFLDAD 227

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              D          L VG+ +   + D D   ++ E    LT  L +              
Sbjct: 228  DEDSLL-------LHVGSIILEDIYDGD--RKIAEKWDILTKDLAE-------------- 264

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                               I + +     +       ++  + + IL     +     R 
Sbjct: 265  ------------------RILMSSNIEQIKIVHPIAQNTFEKMLEILSTGEESETEEERT 306

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             +         DA L+I+R +RP ++   + A+   + LFF+S++YDLS VGR K+N RL
Sbjct: 307  KVYGLNEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLFFNSERYDLSEVGRYKVNERL 366

Query: 421  NL-----------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                         + P++ R     +   I+K L  +   +   D  +            
Sbjct: 367  KNAYIRYLIEVEGEDPEEARKKTYSETATILKPLDIVLASRILFDYFERRYINDFEIDSY 426

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA--VCEFFCSSQLSQLEE 527
             LK+  R+   + E   K + +  D+  ++     N                S +++   
Sbjct: 427  ELKSLIRI--FKEEYLSKRKTAPYDLRKLITTFRRNYDVTSDIGVFAAIRYVSNINKELP 484

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             +   ++     +        V R    +  R            +  S+     L++  +
Sbjct: 485  SIPFDTKDHLGNKRVRSVGELVQREFERLFARAQKAIQERLTLISSLSKVSIQSLINIKS 544

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              + VN +  +          +  + V  LS +  + R  A     L  +    E     
Sbjct: 545  IISTVNQFFAMNQL------SQFMDQVNPLSELTHKRRVSAVGPGGLRRESKVFEAR--- 595

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                             +    Q   +     P   N      L       +   L+   
Sbjct: 596  -----------------NVHYSQYGRLCPIETPEGANIGFITSLAIYAKVDEYGFLMTPY 638

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS--VEGDLDPSTSGVDIYRLM 765
               V   +           + A      + V A   V     +  +   +  G DI  + 
Sbjct: 639  RKVVNGKV-----TDEIVYLRANEEEEYKIVPATTPVDEEGNIIPERVVARMGEDIRLVP 693

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            + +    +    Q   V            A               +L    P  G   E 
Sbjct: 694  REEVDLMDVSTKQPFSVSASLIPFLEHDDASRALMGSNMQRQAVPLLKTEAPLVGTGMEW 753

Query: 826  SMLISERMVSEDVFTSIH-------IEEFEVMARDTKLGPE------EITRDIPNVSEEG 872
                +   V       I        I           +  E      +  R +  V    
Sbjct: 754  EAAKNSGYVVLARHNGIVKEVDASKIVIHRTDENGNPMYDENGNPVLDEYRLLKFVRSNQ 813

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               I++  I+  G  V  GD +           +     +L A    +  +  D  L   
Sbjct: 814  DTTINQKPIVNEGDFVKEGDPIADGP-ATDMGELALGRNILVAFMPWEGYNYEDAILVSQ 872

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLM 987
              +   V        +     E  +  E     I  ++++     DE  I+    Y  + 
Sbjct: 873  ELLEEDVFTSVHIEVYETQARETRLGPEEITADIPNVSKELLKNLDENGIIRVGAYV-VS 931

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +   G  A+   K   K    ++    E      +    +D  V+     L    E    
Sbjct: 932  DYGVGSQAILVGKVTPKGEGDTTP--EEKIIRSVFGERGRD--VKDTSLRLPHGVEGRVI 987

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
             ++   +N I       D+  GVL++V+V+VA ++ +  GDK+AGRHGNKG+VS ILP E
Sbjct: 988  RVDVYDQNDIA------DLGSGVLKLVRVYVATRKTLDIGDKLAGRHGNKGVVSNILPKE 1041

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPFL DGTPV +VLNPLG+PSRMNVGQI ETHLGW     GK   + + +     +I  
Sbjct: 1042 DMPFLPDGTPVQMVLNPLGIPSRMNVGQILETHLGWLAKLTGKWFATPVFEGAKEDEILK 1101

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                          E+ K G+ +      G DE           
Sbjct: 1102 PL--------------------------YEERKKRGLHL------GDDEN---------- 1119

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
             + +G+ IL DG TGEPFD PV VGY+YMLKL H+  +K++ARSTG YSL+ QQPLGGKS
Sbjct: 1120 -NPTGKVILRDGRTGEPFDNPVVVGYMYMLKLVHIAKEKIHARSTGPYSLIHQQPLGGKS 1178

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
            + GGQRLGEMEVW ++AYGAA+ L EMLTIKSDD+ GR   Y++I+   +  E G PESF
Sbjct: 1179 HFGGQRLGEMEVWALEAYGAAHTLAEMLTIKSDDIKGRNETYKAILKNMNIPEPGVPESF 1238

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME 1375
             VL+KE++ L L + L +         +
Sbjct: 1239 RVLIKELRGLALDVRLYDENGNEIDIDK 1266


>gi|296116738|ref|ZP_06835346.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295976706|gb|EFG83476.1| DNA-directed RNA polymerase subunit beta [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 595

 Score =  679 bits (1752), Expect = 0.0,   Method: Composition-based stats.
 Identities = 327/596 (54%), Positives = 420/596 (70%), Gaps = 28/596 (4%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           A    F G  R+RK FG+ PEI  +P+LI+VQ+ASY+ FL MN++PD R   GLQ  F+S
Sbjct: 3   AITKSFTGRKRIRKSFGRIPEIAPMPNLIDVQRASYEAFLQMNVSPDSRTPTGLQEVFRS 62

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           VFPI  F+G   LEFVSYE + PK+DV++C+ R LT+A PLK+ LRLIV+DVDE TG++S
Sbjct: 63  VFPINDFAGRGRLEFVSYELEEPKYDVEECIQRGLTFAAPLKVILRLIVWDVDEDTGSRS 122

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
           I+DIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A
Sbjct: 123 IRDIKEQPVYMGDMPLMTDNGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFA 182

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-------------------- 221
            R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                    
Sbjct: 183 ARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGEESRAAREAKAAEGGDVD 242

Query: 222 -----GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
                GM  +EIL  FY ++ + + G  W       D   G K+   LVD DTGE V + 
Sbjct: 243 SMEIQGMSPDEILGYFYGQVEFIKSGKGWARRFDP-DAFRGQKLLEPLVDADTGEIVAQV 301

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
             KLT+ +++ + E   K + +    L G ++A D+VN +TGEI+ EAGD + E  LE +
Sbjct: 302 DTKLTARMVRKIAET-TKDVLVGPAGLIGRFIAFDMVNPDTGEIFAEAGDELTETRLEAL 360

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
               +  +  L +D+ N   +IRNTL  DKN  R DAL DIYRVMRPG+  T   AE+MF
Sbjct: 361 EADGVTKLVTLAIDATN-GPWIRNTLAIDKNTSRDDALTDIYRVMRPGEPPTPETAEAMF 419

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           + LFFD D+YDLS VGRVKMNMRL +D PD VR +RKEDI+  +KI+ +L++G+G IDDI
Sbjct: 420 SGLFFDPDRYDLSAVGRVKMNMRLGVDVPDTVRVLRKEDILRTVKIMCELKDGRGAIDDI 479

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           DNLGNRRVRSVGE+++NQYR+GLLRMER+I+ER+ SVDID+VMP DLINAKP  +AV EF
Sbjct: 480 DNLGNRRVRSVGELMENQYRVGLLRMERAIRERMGSVDIDTVMPHDLINAKPAAAAVREF 539

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           F SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP 
Sbjct: 540 FGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPI 595


>gi|315930620|gb|EFV09648.1| DNA-directed RNA polymerase subunit beta [Campylobacter jejuni subsp.
            jejuni 305]
          Length = 596

 Score =  677 bits (1748), Expect = 0.0,   Method: Composition-based stats.
 Identities = 272/597 (45%), Positives = 386/597 (64%), Gaps = 9/597 (1%)

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD V+   IIADGPS D G+LA+G+N L+AFMPW+GYN+ED++++SER++ ED FTS+
Sbjct: 1    KKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNGYNYEDAIVVSERIIREDTFTSV 60

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI E E+ AR+ K G EEIT+DIPNV EE + ++DE GI  +G  + PG ILVGK++PKG
Sbjct: 61   HIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESGIAKIGTHIKPGMILVGKVSPKG 120

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E   TPEE+LLRAIFGEKA  V + SL   + + G VVDV+IF + G +K++R+I    +
Sbjct: 121  EVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVVDVKIFTKKGYEKDDRAIKSYDK 180

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +   L ++  D  +++DR    R+  +L       +   G K +KK        + +  R
Sbjct: 181  EKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQKIGDKNYKKGQTADISELEKINR 240

Query: 1019 SQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       +++Q+  + LK  ++  K  L+     K+E ++  D +P GV+++VKV+
Sbjct: 241  FTLTTLIKAYSKEIQKEYDDLKNHFQNEKKKLKAEHDEKLEILEKDDILPSGVIKLVKVY 300

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +A KR ++ GDKMAGRHGNKGIVS I+P  DMP+L +G  VDI LNPLGVPSRMN+GQI 
Sbjct: 301  IATKRKLKVGDKMAGRHGNKGIVSTIVPEVDMPYLPNGKSVDIALNPLGVPSRMNIGQIL 360

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG---SHTEKISDYDDDSVL 1194
            E+HLG   + LG +I+ +  D K    +  LR+ + ++       +  E I    D+ +L
Sbjct: 361  ESHLGLVGLRLGDQIQEI-FDRKQKDFLKELRAKILEICSIPRLANEKEFIKSLSDEELL 419

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
              A  W  GV  STPVF+G + E  + + +MA +D  G++ LYDG TGE     V VG +
Sbjct: 420  NYARDWSKGVKFSTPVFEGVNIEEFSKLFKMAKIDMDGKTELYDGRTGEKIAERVHVGCM 479

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKL+H+V +KV+ARSTG YSLVTQQP+GGK+  GGQR GEMEVW ++AYGAA+ L+EM
Sbjct: 480  YMLKLHHLVDEKVHARSTGPYSLVTQQPVGGKALFGGQRFGEMEVWALEAYGAAHTLREM 539

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            LTIKSDDV GR   Y+++  G +   TG PE+F VL  E+++L L +++ +    N 
Sbjct: 540  LTIKSDDVEGRFSAYKALTKGENVPATGIPETFFVLTNELKSLALDVEIFDKDEDNE 596


>gi|257438253|ref|ZP_05614008.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium
            prausnitzii A2-165]
 gi|257199330|gb|EEU97614.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium
            prausnitzii A2-165]
          Length = 998

 Score =  676 bits (1745), Expect = 0.0,   Method: Composition-based stats.
 Identities = 333/1090 (30%), Positives = 480/1090 (44%), Gaps = 163/1090 (14%)

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             + G   AE+IV   TGEI +EA   I  +  E+   + +  + IL +D           
Sbjct: 10   RITGFVAAENIVAPLTGEIIVEAKGKITRELAEKADAAGVDTV-ILSIDGKKVKVITNGC 68

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            +              I       ++       S          +     +GR        
Sbjct: 69   VDAQGFFSFDVKECGINERCSFDEIKKILDTTSDVEEQKEMLRRNHDQLIGR-------- 120

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                     +  +DI++ I  L  L +G GT DDID+LGNRR+RSVGE+L+NQ+R+G  R
Sbjct: 121  --------TVTVKDILSSINYLNGLGHGVGTTDDIDHLGNRRIRSVGELLQNQFRIGFSR 172

Query: 482  MERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            MER I+ER++  S D   + PQ LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH R
Sbjct: 173  MERVIRERMTLQSQDQSVITPQALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTHKR 232

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            RLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+S L S+A++N YGF+E
Sbjct: 233  RLSALGPGGLSRDRAGFEVRDVHYSHYGRMCPIETPEGPNIGLISYLASYAKINEYGFVE 292

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
             PYRKV                             DE+G   +++V             +
Sbjct: 293  APYRKVKKTY-------------------------DENGKLIDQVVT------------D 315

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +++++ A  +    +A +  P  E     R  +     R+   +L+ +A  V       V
Sbjct: 316  EVEYMTADVEDEYVVAQANEPLDETKHFIRPRVSA---RRRDDILEIDADKVD---YMDV 369

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            +     ++       +E  D  R ++ S                    QR      V Q+
Sbjct: 370  SPRMMVSVATACIPFLENDDCNRALMGSN------------------MQRQAVPLMVTQQ 411

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+V  G E +         +TD G   L +N     +     +                 
Sbjct: 412  PIVATGMEYKA--------ATDSGTAVLAKND--GIVEKMDADHVTV------------- 448

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                             G  +    +          I++  I+ VG  V  G +L     
Sbjct: 449  -------------RNAQGGVDNYPLVKFARSNAGTCINQRPIVEVGESVKAGQVLADGP- 494

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  ++  +  L      +  +  D  L     V   V        +  +  +  +  
Sbjct: 495  AMRNGEISLGKNALIGFMTWEGYNYEDAVLLNEKIVREDVYTSIHIEEYETESRDTKLGP 554

Query: 960  ER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E          E   +D  DE+ I+      +  +IL G+    G         L   + 
Sbjct: 555  EEITRDIPNVSEDALKDL-DERGIIRIGAEVKSGDILVGKVTPKGETELTAEERLLRAIF 613

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             E  R                 E                   K+   +  D++ PGV  V
Sbjct: 614  GEKAR-----------------EVRDTSLRVPHGEYGIIVDVKVFTPENSDELQPGVREV 656

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+ ++A KR I  GDKMAGRHGNKG+VSRILP EDMP+L DGTP+DIVLNPLGVPSRMN+
Sbjct: 657  VRCYIAQKRKISVGDKMAGRHGNKGVVSRILPQEDMPYLPDGTPLDIVLNPLGVPSRMNI 716

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E +LG+A    G K+ + + D     DI        ++    +     +       
Sbjct: 717  GQVLEVNLGYAAKACGIKVMTPVFDSARENDIGDTFDTARELWHGENAPAYPTKL----- 771

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                           P   G     I+      +LD  G++ +YDG TGE FD  VTVGY
Sbjct: 772  ---------------PKIMGEKGHIID--FSKIELDRDGKTTVYDGRTGEKFDNRVTVGY 814

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +Y LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 815  MYYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 874

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT+KSDDV GR + YE+IV G    + G PESF V++KE+Q+LG+ + +++        
Sbjct: 875  ILTVKSDDVEGRVKTYEAIVKGEPIPQPGIPESFRVMLKELQSLGMDVVVQDKDGNEIDM 934

Query: 1374 MEEIPDFNKC 1383
             +   D    
Sbjct: 935  RQNFDDEETG 944


>gi|207744569|ref|YP_002260961.1| hypothetical dna-directed rna polymerase beta chain protein
            [Ralstonia solanacearum IPO1609]
 gi|206595975|emb|CAQ62902.1| hypothetical dna-directed rna polymerase beta chain protein
            [Ralstonia solanacearum IPO1609]
          Length = 655

 Score =  675 bits (1741), Expect = 0.0,   Method: Composition-based stats.
 Identities = 346/644 (53%), Positives = 467/644 (72%), Gaps = 5/644 (0%)

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-- 650
            + YGF+ETPYRKV + K+T++V YLSA+EE    +AQAN+++D+DG+  +ELV  R    
Sbjct: 4    SDYGFLETPYRKVENSKLTDEVHYLSAIEEGKYVVAQANATVDKDGNLVDELVSAREGSE 63

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP L+A+ P 
Sbjct: 64   RETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPCLRADKPL 123

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E  VA  SG A+ A R G+V+ VDA R+VIR  + +      GVDIY L+K+ RS
Sbjct: 124  VGTGIERTVAVDSGTAVQATRGGVVDYVDANRVVIRVNDDEAVAGEVGVDIYNLIKYTRS 183

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNT +NQRP+VKVGD V R D+IADG STD+G+LALG+NMLVAFMPW+GYNFEDS+LIS
Sbjct: 184  NQNTNINQRPMVKVGDIVARGDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILIS 243

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+V+ED +TSIHIEE  V+ARDTKLGPEEITRDI N++E  L  +DE GI  +GAEV  
Sbjct: 244  ERVVAEDRYTSIHIEELSVVARDTKLGPEEITRDISNLAEAQLARLDESGITYIGAEVEA 303

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVPSG+SGTV+DV++F R G+
Sbjct: 304  GDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGV 363

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
             +++R+ S+  E+++    D +D+  I++ + + RL  +L G+ A  GPK   K T L+ 
Sbjct: 364  TRDKRAQSIIDEELKRYRLDLNDQLRIVEGDAFQRLERLLVGKVANGGPKKLSKGTALTK 423

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + +++  +  W+     DE+V   +E++K   E  +   +  F+ K +K+  GD++PPGV
Sbjct: 424  EYLADLDKWHWFDIRPSDEEVAAQLEAVKEAIEQKRHDFDLAFEEKRKKLTQGDELPPGV 483

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +++VKV++A+KR +Q GDKMAGRHGNKG+VS+I P EDMP++ DGTP DIVLNPLGVPSR
Sbjct: 484  IKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKITPIEDMPYMADGTPADIVLNPLGVPSR 543

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MNVGQI ETHLGWA  GLG++I +++   KA    + LR  L ++       E +    D
Sbjct: 544  MNVGQILETHLGWAARGLGERIGNML---KAQAKAAELRKLLGQIYNESGKVEDLDSLTD 600

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
              VL +AE  K GVP +TPVFDGA E+ I  ML +A   +  + 
Sbjct: 601  AEVLELAENLKKGVPFATPVFDGAHEDEIRRMLDLAYPADIAKE 644


>gi|157363341|ref|YP_001470108.1| DNA-directed RNA polymerase subunit beta [Thermotoga lettingae TMO]
 gi|182676576|sp|A8F4G0|RPOB_THELT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|157313945|gb|ABV33044.1| DNA-directed RNA polymerase, beta subunit [Thermotoga lettingae
           TMO]
          Length = 1172

 Score =  674 bits (1739), Expect = 0.0,   Method: Composition-based stats.
 Identities = 382/993 (38%), Positives = 572/993 (57%), Gaps = 129/993 (12%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              V  G  R R  FG+  + + +P+LI +Q  SY  FL            GL    K  
Sbjct: 1   MRTVCYG-KRERLTFGRIHDAVKVPNLISIQIDSYKDFL----------ENGLIEVLKKF 49

Query: 63  FPITA--FSGA-------AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
            PIT+    G         +LEFVS +   P   V++C  + LTY VP+  T+R+     
Sbjct: 50  SPITSQPHKGDLKKGEKGFVLEFVSTKVGQPNAPVEECKQKGLTYTVPVYTTVRIT---- 105

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                  +  +++E+  ++G +P MT++GTF+I G +R++VSQL R+PG++F  +  +  
Sbjct: 106 -----DVNTGEMREEEAFLGSIPHMTENGTFIINGAERVIVSQLVRAPGVYFVDEIPKTQ 160

Query: 174 LSGKLLYACRIIPDQGLWMD-IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILST 231
           +    +Y    +P +G W++ + + + ++ + RIDR+R++ +     ALG   + EIL  
Sbjct: 161 VVS-PIYVAHFLPVRGAWLELLYYSADNMFYARIDRKRRINLFLLFKALGFTDDLEILDL 219

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID---TGEQVIESGKKLTSGLLKSL 288
           F               P+ A D     K   S++  D    G++++E G  LT    +++
Sbjct: 220 FPD-------------PIDADDEYTMEKAVGSIILHDVVLDGKKIVERGGVLTKAASQAI 266

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            E  +  +                                 +K+LE++            
Sbjct: 267 LESKIATVV--------------------------RAHPAAQKTLEKMVD---------- 290

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                          T    D   A ++I+R ++PG++   + A++    L+F +++++L
Sbjct: 291 ---------------TYGEVDSSKAYVEIFRKLKPGEIPRVNTAKAYLTSLYFSTERFEL 335

Query: 409 STVGRVKMNMRLNL--------------------DTPDDVRHIRKEDIIAIIKILVDLRN 448
           S VGR K+N RL                      +   +   +   DI+   + L+D+  
Sbjct: 336 SDVGRYKINKRLTQAYRRYLAQVKGLPEEEVESVEYNPEDPVLTPMDIVLASRYLLDVSK 395

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAK 507
               +D  D+LGN+RVR+VGE++K ++     R +R I+ER++    +D +  Q LIN K
Sbjct: 396 NPEIMDTKDHLGNKRVRTVGELIKLEFERAFARAQRLIQERLTLYASLDKISIQSLINVK 455

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            +++ + +FF +S LSQ  E VN L+ +TH RRL+A+G GG+ R RA  E+RDVH +HYG
Sbjct: 456 TIIAGINQFFATSPLSQFMEQVNPLAELTHKRRLTAVGPGGLKRERARFEVRDVHHSHYG 515

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL  +A ++ +GF+ TPYRKV +G VT+++VYL+A EEE+  I
Sbjct: 516 RMCPIETPEGANIGLITSLAVYANIDKFGFLTTPYRKVVNGVVTSEIVYLTADEEEHYNI 575

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +D+DG   +E V  R       V + K+ F+D S KQ+VS++ SLIPFLE+DD+
Sbjct: 576 APCTIKIDKDGRILDERVPVRFMERLQFVEKNKVQFMDVSTKQIVSVSTSLIPFLEHDDA 635

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL+K EAPFV TG+E   A  SG  + AK +G V++VD+ +IVI  
Sbjct: 636 NRALMGSNMQRQAVPLVKPEAPFVATGVEYDAALYSGYVVQAKYSGRVKKVDSRKIVIER 695

Query: 748 VEGDLDP----STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
           ++ +  P        +D YRLMKF R+NQ+T VNQRP+V +GD V+  D+IADGP+TD+G
Sbjct: 696 MDENGKPVLKNGKPVLDEYRLMKFMRTNQDTTVNQRPIVDIGDIVKAGDVIADGPATDMG 755

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +LALG+N+LVAFMPW GYNFED++L+SE ++ ED FTSIHIE +E  ARDT+LGPEEIT 
Sbjct: 756 ELALGKNVLVAFMPWEGYNFEDAILVSEELLEEDTFTSIHIEVYETQARDTRLGPEEITV 815

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNVS+E L+N+DE GI+ VGA V P DILVGK+TPKGE   TPEEK++R++FGE+  D
Sbjct: 816 DIPNVSKEALRNLDENGIVRVGAYVGPQDILVGKVTPKGEGETTPEEKIIRSVFGERGKD 875

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           V+DTSLR+P G  G V+DV++F     DK+E +
Sbjct: 876 VKDTSLRLPHGTDGRVIDVKVF-----DKDEET 903



 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 184/604 (30%), Positives = 263/604 (43%), Gaps = 98/604 (16%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +           Y+         +         +   +  V+ R  + 
Sbjct: 641  GSNMQRQAVPLVKPEAPFVATGVEYDAALYSGYVVQAKYSGRVKKVDSRK-IVIERMDEN 699

Query: 857  GPEEITRDIPNVSEEGLKNI---------DECGIICVGAEVNPGDILVGKITPKGESPMT 907
            G   +    P + E  L            ++  I+ +G  V  GD++           + 
Sbjct: 700  GKPVLKNGKPVLDEYRLMKFMRTNQDTTVNQRPIVDIGDIVKAGDVIADGP-ATDMGELA 758

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSG-VSGTVVDVRIFNRHGIDKNERSISVE-REQIE 965
              + +L A    +  +  D  L         T   + I       ++ R    E    I 
Sbjct: 759  LGKNVLVAFMPWEGYNFEDAILVSEELLEEDTFTSIHIEVYETQARDTRLGPEEITVDIP 818

Query: 966  LLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             ++++     DE  I+    Y    +IL G+    G         +   +  E       
Sbjct: 819  NVSKEALRNLDENGIVRVGAYVGPQDILVGKVTPKGEGETTPEEKIIRSVFGE------- 871

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                + + V+     L    +     +      K+       D+  GV ++VKV+VA ++
Sbjct: 872  ----RGKDVKDTSLRLPHGTDGRVIDV------KVFDKDEETDLGAGVNKLVKVYVACRK 921

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             ++ GDK+AGRHGNKG+VS+ILP EDMPFL DGTPV +VL+PLGVPSRMNVGQI ETHLG
Sbjct: 922  TLEVGDKLAGRHGNKGVVSKILPKEDMPFLPDGTPVQLVLSPLGVPSRMNVGQILETHLG 981

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            W                                                    +   W  
Sbjct: 982  WLAK-------------------------------------------------LTRNW-- 990

Query: 1203 GVPVSTPVFDGADEEAINSML----RMADLDE-------SGQSILYDGLTGEPFDRPVTV 1251
                +TPVFDGA E  I   L    R   L+E       SG+ +L DG TGE F  P+ V
Sbjct: 991  ---FATPVFDGAKENEILPWLYEERRAVGLEEGDSDNEPSGKVVLRDGRTGESFAEPIVV 1047

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GYIYM+KL H+  DK++ARSTG YSL+ QQPLGGK+  GGQR GEMEVW ++A+GAA+ L
Sbjct: 1048 GYIYMMKLVHIAKDKIHARSTGPYSLIHQQPLGGKAQFGGQRFGEMEVWALEAHGAAHTL 1107

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
             EMLTIKSDD+ GR  VY++I+ G +  E G PESF VL+KE++ L L I + +      
Sbjct: 1108 NEMLTIKSDDIKGRNEVYKAILKGKNIPEPGIPESFRVLIKELRGLALDIRVYDENGNEI 1167

Query: 1372 AKME 1375
                
Sbjct: 1168 DIDR 1171


>gi|300087845|ref|YP_003758367.1| DNA-directed RNA polymerase subunit beta [Dehalogenimonas
            lykanthroporepellens BL-DC-9]
 gi|299527578|gb|ADJ26046.1| DNA-directed RNA polymerase, beta subunit [Dehalogenimonas
            lykanthroporepellens BL-DC-9]
          Length = 1252

 Score =  674 bits (1738), Expect = 0.0,   Method: Composition-based stats.
 Identities = 369/1086 (33%), Positives = 532/1086 (48%), Gaps = 129/1086 (11%)

Query: 333  LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD---ALLDIYRVMRPGDVSTF 389
            L  I +S+  ++  L+ D  ++  ++      DK+   +D   AL+D+Y  +RPGD +  
Sbjct: 202  LRAIGYSDDNELLNLFADVDDSTDHMYIQSSIDKDPLIRDTAGALIDLYGRLRPGDPANV 261

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLR 447
              A  + N +FF  D YDL  VGR K+N RL LD     + R + +EDIIAIIK L+ + 
Sbjct: 262  DNASRLVNDMFFSPDHYDLGEVGRYKVNRRLGLDDNVGGENRALTREDIIAIIKRLIRVN 321

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            NG+   DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V +D V P  L+N +
Sbjct: 322  NGREHGDDIDHLGNRRIRTVGELIQNQFRIGLVRLERVARERMSIVPLDQVTPSGLVNIR 381

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            PVV+AV EFF  SQLSQ  +  N L+ +TH RRLSA+G GG++R RAG ++RDVH +HYG
Sbjct: 382  PVVAAVREFFGGSQLSQFMDQTNPLAELTHKRRLSAMGPGGLSRDRAGFDVRDVHFSHYG 441

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV------CDGKVTNDVVYLSAME 621
            RICP ET EG NIGL+ SL ++ RVN YGFIETPYRKV       D ++   VV    ++
Sbjct: 442  RICPIETPEGPNIGLIGSLAAYGRVNRYGFIETPYRKVYHELANHDLRLVGQVVIEDIVD 501

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
               + +  A S +D+    +   +    + +      ++I ++ A  +    IA +    
Sbjct: 502  SAGKPLLSAGSVVDDKTFKSIAKLP-ETSIKIEPFVSDEIYYLAADEEDKHVIAQAH--- 557

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA-AIVAKRAGIVEQVDA 740
             + DD  R L      R     L        T +E +        ++ A     +E  DA
Sbjct: 558  AKLDDRGRFLDERIESRFGESYLYEPP----TKIEYMDISPKQIFSVAASLIPFLEHDDA 613

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             R ++ +                    QR        Q PLV                +T
Sbjct: 614  NRALMGAN------------------MQRQAVPLLRPQAPLV----------------AT 639

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             +   A+  +  V F    G       + SER+V E                 T  G E+
Sbjct: 640  GMEKEAVRYSSHVIFARRDGKVSS---VTSERIVVE-----------------TAGGEED 679

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + + +  +       I++  ++  G +V  G +L G  +      +   + L+ A     
Sbjct: 680  VYKLVKFMRTNQGTCINQRPVVKRGEQVKIGQVL-GDSSATENGELALGQNLVCAFMSWH 738

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQ 975
              +  D  +     V    +      R+ ++  +  + +E     I  +  +   + DE 
Sbjct: 739  GYNYEDAIILNERLVKDDRLTSLHITRYELEARDTKLGIEEITRDIPNVGEESLRELDED 798

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         +IL G+    G         L   +  E  R                 
Sbjct: 799  GIIRVGAEVGPDDILVGKITPKGETELSAEEKLLRAIFGEKAR----------------- 841

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E                   KI   + GDD+P  V + V+V+VA KR I  GDK+AGRHG
Sbjct: 842  EVKDTSLRMPHGEWGKVINVKIFSREEGDDLPARVNKWVQVWVAQKRKISVGDKLAGRHG 901

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGIVS I P EDMP+L DGTPVD++LNP+GVPSRMN+GQI E HLGWA   +G ++K+ 
Sbjct: 902  NKGIVSIIAPSEDMPYLPDGTPVDVILNPIGVPSRMNLGQILELHLGWAGHLMGFRVKTP 961

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDG- 1213
            + D   + DI    +        G         + + ++  A+ W +        VFD  
Sbjct: 962  VFDGATDVDIEDDLARAAIAQMAGLIRLDYESRNTEEIIAAAKAWVNDRGYDGDKVFDDR 1021

Query: 1214 ----ADEEAINSMLRMAD--------------------------LDESGQSILYDGLTGE 1243
                A E  +   L                              L   G++ L DG TG+
Sbjct: 1022 TVGFAREVCLRIWLEDQGVDGAAKIPMGELFEKAFQLARELNVPLPIDGKAKLRDGKTGD 1081

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FD+PVTVG +Y+LKL H+V DKV+ARSTG YSL++QQPLGGK+  GGQR GEMEVW ++
Sbjct: 1082 YFDQPVTVGNMYILKLIHLVEDKVHARSTGPYSLISQQPLGGKAQFGGQRFGEMEVWTLE 1141

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQEMLTIKSDDV GR + YESIV G D  + G PESF VLVKE+Q+LGL++++
Sbjct: 1142 AYGAAYNLQEMLTIKSDDVTGRAKAYESIVKGEDVSQPGVPESFKVLVKELQSLGLAVEV 1201

Query: 1364 ENSRTK 1369
             N   +
Sbjct: 1202 INEEER 1207



 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 94/358 (26%), Positives = 168/358 (46%), Gaps = 36/358 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
            RK + + PE+++IP+LI++Q AS+   +           +GL+A  + + P+  F+G  
Sbjct: 16  TRKSYSRIPEVVNIPNLIDIQLASFRWLM----------EDGLKALVEEITPVRDFNGNR 65

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+   ++C  RD  Y++PL I  RL++         K+  +IKE   +
Sbjct: 66  MELEFMGYEFREPRMSEEECQHRDKDYSIPLYIKARLVI---------KATGEIKEPFEL 116

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GDLPLMT +GTF+  G +R+VVSQL RSPG++F       + +G+ L    +IP +G 
Sbjct: 117 FFGDLPLMTANGTFITSGTERVVVSQLLRSPGVYFKAQDD--TATGRPLCQANLIPSRGA 174

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PVT+FL A+G   + E+L+ F      +          
Sbjct: 175 WLEFETSNRDVISVKIDGRRKIPVTTFLRAIGYSDDNELLNLFADVDDSTDHMYIQSSID 234

Query: 250 SAADLMVGAKVSSSLV-DIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS-DCLCG- 305
               +   A     L   +  G+   +++  +L + +  S     +  +G    +   G 
Sbjct: 235 KDPLIRDTAGALIDLYGRLRPGDPANVDNASRLVNDMFFSPDHYDLGEVGRYKVNRRLGL 294

Query: 306 --------LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                     +  + +      +            ++ + +  IR +  L  +     
Sbjct: 295 DDNVGGENRALTREDIIAIIKRLIRVNNGREHGDDIDHLGNRRIRTVGELIQNQFRIG 352


>gi|323703910|ref|ZP_08115542.1| DNA-directed RNA polymerase, beta subunit [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531126|gb|EGB21033.1| DNA-directed RNA polymerase, beta subunit [Desulfotomaculum
           nigrificans DSM 574]
          Length = 1149

 Score =  673 bits (1737), Expect = 0.0,   Method: Composition-based stats.
 Identities = 350/942 (37%), Positives = 484/942 (51%), Gaps = 125/942 (13%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           RVR  +GK  E++++P+LIEVQ+ SY+ FL           EGL+  F+ + PI  F+G 
Sbjct: 13  RVRWNYGKLREVLELPNLIEVQRNSYEWFLQ----------EGLREVFQDISPIQDFTGN 62

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 63  LILEFLDYTLGDPKYSVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVF 113

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG++F     +   SGK L+   IIP++G W
Sbjct: 114 MGDFPLMTDKGTFIINGAERVIVSQLVRSPGVYFA---DQIDTSGKRLFTSTIIPNRGAW 170

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           ++ E D  D I VRIDR RK+P T  + ALG  S  +++  +    + Q         S 
Sbjct: 171 LEFETDVNDHIFVRIDRTRKIPATVLIRALGYGSNAMIAELFNNNKFVQETLTRDNTDSE 230

Query: 252 ADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            + +V          +  GE   +ES + L + L    K   +  +G             
Sbjct: 231 EEALVEI-----YKRLRPGEPPTVESARSLLNTLFFDPKRYDLAHVGRYK---------- 275

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
                                                    + +    R     D  K+ 
Sbjct: 276 -------------------------------------LQKKLKHGILYRYPKGEDGPKEW 298

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
                   R +             +         K D+    R  + +       DD+ H
Sbjct: 299 D-------RYLNKEVPVEREFIREL--------TKEDIIATFRYLLGLMEGQGVVDDIDH 343

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           +    + ++ ++L +     G       +  R      +++  Q  + +  +  +IKE  
Sbjct: 344 LGNRRLRSVGELLQNQFR-IGLSRMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFF 402

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE-EHVNSLSRITHTRRLSALGQGGV 549
            S  +   M Q    A+              LS+            +H  R+  +     
Sbjct: 403 GSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG 462

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                   +     + Y RI      E                  Y  ++   ++V D  
Sbjct: 463 PNIGLIGSL-----STYARINSFGFIE----------------TPYRKVDKANKRVTDEI 501

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           V     YL+A EEE   IAQAN+ LDE+G F EE V  R   + ++VP +++DF+D SPK
Sbjct: 502 V-----YLTADEEEGLIIAQANAPLDENGYFVEERVNARHGHDTLIVPADRVDFMDVSPK 556

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           QV S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG+E   AK SG  +VA
Sbjct: 557 QVFSVATSLIPFLEHDDANRALMGANMQRQAVPLLRCQAPLVGTGIEYRAAKDSGVVVVA 616

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K AG V +V A  IVIR+ EG  D        Y+L+KF RSNQ TC+NQ+P+V  G+ V 
Sbjct: 617 KNAGEVTRVTANEIVIRTDEGHTD-------TYKLLKFTRSNQGTCINQKPIVNKGERVE 669

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              +IADGP+TD G+LALGRN+LVAFM W G N+ED++LISE+ V ED FTSIHIEE+E 
Sbjct: 670 AGQVIADGPATDKGELALGRNILVAFMTWEGNNYEDAILISEKAVKEDFFTSIHIEEYEC 729

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITRDIPNV E+ LK++DE GII VGAEV PGDILVGK+TPKGE+ +T E
Sbjct: 730 DARDTKLGPEEITRDIPNVGEDILKDLDERGIIRVGAEVRPGDILVGKVTPKGETELTAE 789

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R   D
Sbjct: 790 ERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFTRENGD 831



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/539 (35%), Positives = 261/539 (48%), Gaps = 83/539 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  + +          I++  I+  G  V  G ++        +  +     +
Sbjct: 633  RTDEGHTDTYKLLKFTRSNQGTCINQKPIVNKGERVEAGQVIADGP-ATDKGELALGRNI 691

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    +  +  D  L     V            +  + + R   +  E+I        
Sbjct: 692  LVAFMTWEGNNYEDAILISEKAVKEDFFTSIHIEEY--ECDARDTKLGPEEITRDIPNVG 749

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E + +D  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 750  EDILKDL-DERGIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 802

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   K+   + GD++PPGV ++V+V++A KR I
Sbjct: 803  -----------EVRDTSLRVPHGEAGKIVDVKVFTRENGDELPPGVNQLVRVYIAQKRKI 851

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+V+RILP EDMPF++DGTPV+IVLNPLGVPSRMN+GQ+ ETHLGWA
Sbjct: 852  SEGDKMAGRHGNKGVVARILPEEDMPFMEDGTPVEIVLNPLGVPSRMNIGQVLETHLGWA 911

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + +  +  DI                                   ++G+
Sbjct: 912  AKALGFHVATPVFNGASEEDIWESLK------------------------------RAGL 941

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P                        E G+  LYDG TGEPFD  VTVGY+YM+KL+H+V 
Sbjct: 942  P------------------------EDGKMTLYDGRTGEPFDNKVTVGYVYMIKLHHLVD 977

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVG
Sbjct: 978  DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVG 1037

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            R + YE+IV G +  E G PESF VL+KE+Q+LGL + + +   +     E   D  + 
Sbjct: 1038 RVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGLDVKVLSENEEEIEIKELEEDVTET 1096


>gi|10636178|emb|CAC10529.1| DNA-dependent RNA polymerase subunit beta [Clostridium botulinum]
          Length = 961

 Score =  673 bits (1736), Expect = 0.0,   Method: Composition-based stats.
 Identities = 389/828 (46%), Positives = 533/828 (64%), Gaps = 36/828 (4%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG+++D    +    G  L++  +IP++G W
Sbjct: 1   MGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDMTVDKT---GSKLFSATVIPNRGAW 57

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS--QRGDFWCFP 248
           ++ E DS +II+VRID+ RK+P+T    ALG  ++ EI+  F            D     
Sbjct: 58  LEYETDSNNIIYVRIDKTRKLPITILARALGYGTDAEIIEFFGEDERLKATIEKDNTKTR 117

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
             A   +           +D+ E +IES         L +  + K  + L I    +   
Sbjct: 118 EEALLEIYKRLRPGEPPTVDSAESLIESLFFDAKRYDLSRVGRYKFNQKLAIHL-RITNQ 176

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
              +DIVN +TGEI ++ G+ ID+    EI +  I ++ I   D   +   I N  V   
Sbjct: 177 IADQDIVNPQTGEILVQKGEKIDKDKAIEIQNCGINEVYIKIDD--KSFKVIGNHFVDIH 234

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +             + P D+S  ++ E +F  +     D Y      + ++   +    P
Sbjct: 235 S-------------LVPFDISDLNIKEYVFYPVLKEILDNYADEESIKEEIRKNIYRLIP 281

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              +HI +EDI A I   + L    G  DDID+LGNRR+RSVGE+L+    LGL RMER 
Sbjct: 282 ---KHIIREDIYATINYELALSYDIGYKDDIDHLGNRRLRSVGELLQINLELGLSRMERV 338

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER++  D + + PQ LIN +PV +++ EFF SSQLSQ  +  N LS +TH RRLSALG
Sbjct: 339 VKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALG 398

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL +FA+VN YGFIETPYR++
Sbjct: 399 PGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATFAKVNEYGFIETPYRRI 458

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
              + + TND+VY++A EE+   IA+++  +DE+G F ++ V  R   E ++VP  ++++
Sbjct: 459 DPKNKRATNDIVYMTADEEDLYVIARSDEPIDENGYFIDDKVTVRAKEEVLVVPVSEVEY 518

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SP+Q+VS+A ++IPFLENDD++R LMG NMQRQAVPLLK +AP VGTG+E   A  S
Sbjct: 519 MDISPRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAATDS 578

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G    AK AG V  V A  I +R        S  G+D Y+L+KF+RSNQ TC+NQRP+V 
Sbjct: 579 GVLPKAKNAGTVVYVSADEIRVRRD------SDGGIDKYKLLKFKRSNQGTCINQRPIVS 632

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            G+ V +  ++ADGPSTDLG++ALG+N+L+ F+ W GYN+ED+MLISE++V EDVFTSIH
Sbjct: 633 KGEVVAKETLLADGPSTDLGEIALGKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIH 692

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IEE+E  ARDTKLGPEEITRDIP+V EE LK+IDE GII +GAEV  GDILVGK+TPKGE
Sbjct: 693 IEEYEAEARDTKLGPEEITRDIPDVGEEALKDIDERGIIRIGAEVRSGDILVGKVTPKGE 752

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV+IF R   D
Sbjct: 753 TELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKIFTRENGD 800



 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 128/437 (29%), Positives = 178/437 (40%), Gaps = 77/437 (17%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+  R    G  +  + +          I++  I+  G  V    +L    +        
Sbjct: 597  EIRVRRDSDGGIDKYKLLKFKRSNQGTCINQRPIVSKGEVVAKETLLADGPSTDLGEIAL 656

Query: 908  PEEKLLRAI-----FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
             +  L+  I       E A+ + +  ++     S  + +     R      E       +
Sbjct: 657  GKNILMGFITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPD 716

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +D  DE+ I+      R  +IL G+    G         L   +  E  R    
Sbjct: 717  VGEEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR---- 771

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E                   KI   + GD++PPGV ++V+ ++A KR
Sbjct: 772  -------------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIAQKR 818

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLG
Sbjct: 819  KISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLG 878

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG  I + + D     DI                                     
Sbjct: 879  LAASKLGWHIATPVFDGAIESDIVDCLRKA------------------------------ 908

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                      G  E+              G+++LYDG TGEPFD  VTVGY+Y+LKL H+
Sbjct: 909  ----------GYSED--------------GKTVLYDGRTGEPFDNRVTVGYMYILKLAHL 944

Query: 1263 VSDKVYARSTGSYSLVT 1279
            V DK++ARSTG YSLVT
Sbjct: 945  VDDKIHARSTGPYSLVT 961


>gi|170761945|ref|YP_001752269.1| DNA-directed RNA polymerase subunit beta [Ureaplasma parvum serovar 3
            str. ATCC 27815]
 gi|183508740|ref|ZP_02689961.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            14 str. ATCC 33697]
 gi|186702007|ref|ZP_02554365.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            6 str. ATCC 27818]
 gi|189043874|sp|B1AIH5|RPOB_UREP2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|168827522|gb|ACA32784.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            3 str. ATCC 27815]
 gi|182675670|gb|EDT87575.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            14 str. ATCC 33697]
 gi|186700787|gb|EDU19069.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            6 str. ATCC 27818]
          Length = 1434

 Score =  671 bits (1730), Expect = 0.0,   Method: Composition-based stats.
 Identities = 337/1445 (23%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +         +R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVMRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                S+FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISSIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNTKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   VT+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSVTTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWC-----FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +           ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEIEKYAPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  + +            +  EI     +  D +    I +++
Sbjct: 290  KEEYIEQGSPLLSKLKQLIFNYV-----------EKNDEIDALLHENKDVEDASFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNIETLRHLGKASYQIA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I  + I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIANDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTKKINLLPTALESE-----IEQFLEYESIAVYKDNDLRDETTEIVGLASGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R++ +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREIEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEDYKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      N+   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPNE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + R+     ++  + I           ++  I+ VG  V+  +  +G         +   
Sbjct: 855  IIRNDNDKLDDY-KLIKYRKSNQDTCNNQIPIVKVGQRVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSSDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ V    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYENISNLIKHKQAKQAKDIDLIDVTIILK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I S++  A++D     G+ +LYDG TGEPFD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVSIMNEANIDIENNKGKQVLYDGRTGEPFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 VDINE 1387


>gi|217077413|ref|YP_002335131.1| DNA-directed RNA polymerase subunit beta [Thermosipho africanus
           TCF52B]
 gi|226699455|sp|B7ICR3|RPOB_THEAB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|217037268|gb|ACJ75790.1| DNA-directed RNA polymerase, beta subunit [Thermosipho africanus
           TCF52B]
          Length = 1172

 Score =  671 bits (1730), Expect = 0.0,   Method: Composition-based stats.
 Identities = 372/1000 (37%), Positives = 567/1000 (56%), Gaps = 120/1000 (12%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS- 69
            R R  FG+    I +P+L+E+Q  SY  FL            G+    K   PIT+   
Sbjct: 8   KRTRFSFGRVQAPIPVPNLVEIQTKSYQDFL----------ENGILKVLKKFSPITSSKS 57

Query: 70  -----GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                    LEFVS     P+  V +C  R LTY VP+  T+R+            S  +
Sbjct: 58  DLRKEKGFSLEFVSVRVGEPQNTVQECKERLLTYTVPVYTTVRITDN---------STNE 108

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           + E+  ++G LP MT   TF+I G +R+VV+QL RSPGI+F  +  +     + +Y    
Sbjct: 109 MIEEEAFLGYLPYMTPRTTFIINGAERVVVNQLVRSPGIYFVEEPRKT-SGTRPIYVAHF 167

Query: 185 IPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +P +G W++I  +  D + + RIDR+R+V +   L ALG   + ++LS F   I      
Sbjct: 168 LPVRGAWLEILLNLNDEVFYARIDRKRRVNLFLLLKALGYSDDLKLLSLFPQWIDVDDEY 227

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                      +     V    V   +GE + + G  +T GL++ L    ++ + +    
Sbjct: 228 ---------TLMHSEGLVVLEDVKTKSGELIAKRGDVITQGLIEKLANSEIEKIKVAHRY 278

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
                                        +LE++ H+   D+                  
Sbjct: 279 AVN--------------------------TLEKLKHTYGDDVE----------------- 295

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                     A ++I+R +RPG++   + A+   N L+F+ ++++LS VGR KMN RL  
Sbjct: 296 -------ENRAYIEIFRKLRPGELPRINAAKIFLNNLYFNEERFELSEVGRFKMNNRLEE 348

Query: 423 --------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
                                  +    +   DI+   + L+++    GT+D  D+LGN+
Sbjct: 349 AYRKYLIDVEGKSPEEVEGVKYTETSNVLTPMDIVLASRNLIEIDKHPGTMDTKDHLGNK 408

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RVR+VGE+++ ++     +    I+E+  +   +D +  Q LIN + +++ +  FF ++ 
Sbjct: 409 RVRTVGELIRIEFERAFSKAVFMIQEKLATYTSLDKISVQSLINVRSIIATINSFFATNP 468

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +TH RRL+A+G GG+ R RA  E+RDVH +HYGR+CP ET EG NIG
Sbjct: 469 LSQFMDQTNPLAELTHKRRLTAVGPGGLKRERARFEVRDVHHSHYGRMCPIETPEGANIG 528

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ ++ ++ YGF+ TPY KV  GKVT+++VYL+A EEEN  IA + + +DE+G+  
Sbjct: 529 LITSLSVYSTIDKYGFLITPYVKVVKGKVTDEIVYLTADEEENYKIAPSTTPVDEEGNII 588

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V  R   + + V +  + F+D +P Q+VS++ SLIPFLE+DD+NR LMG NMQRQ V
Sbjct: 589 PENVTVRYEEKVLYVSKYDVQFLDVAPNQIVSVSTSLIPFLEHDDANRALMGSNMQRQGV 648

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP-----ST 756
           PL++ EAP VGTGME   AK SG  ++AK  GIV++VDA +I+I  ++ +          
Sbjct: 649 PLIETEAPRVGTGMEWEAAKYSGTLVLAKHDGIVKKVDANKIIIHRIDENGKEMYDSMGN 708

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +D Y L+KF R+NQ+TC+NQRP+V VG+ V+++D IADGP+TD+G+LALG+N+LVAF+
Sbjct: 709 PVLDTYELLKFTRTNQDTCINQRPIVNVGEVVKKDDPIADGPATDMGELALGKNVLVAFV 768

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW GYNFED++LISE ++ ++ +TS+HIE +E  ARDT+LGPEEIT DIPNVS+E L+N+
Sbjct: 769 PWEGYNFEDAILISEELLEKETYTSVHIEVYETTARDTRLGPEEITPDIPNVSKEKLRNL 828

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GA V   DILVGK+TPK ES  TPEEK++R++FGEK  +V+D+SLRVP G+ 
Sbjct: 829 DEDGIIRIGAYVQETDILVGKVTPKSESDTTPEEKIIRSVFGEKGKEVKDSSLRVPHGIE 888

Query: 937 GTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           G V+ V +F++        G++K  R     R+ +E+  +
Sbjct: 889 GRVIAVHVFDKEKDGDLGPGVNKLIRVYVAIRKPLEVGDK 928



 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 165/500 (33%), Positives = 244/500 (48%), Gaps = 66/500 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG-VSGTV 939
            I+ VG  V   D +           +   + +L A    +  +  D  L         T 
Sbjct: 733  IVNVGEVVKKDDPIADGP-ATDMGELALGKNVLVAFVPWEGYNFEDAILISEELLEKETY 791

Query: 940  VDVRIFNRHGIDKNERSISVE-REQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
              V I       ++ R    E    I  ++++K    DE  I+    Y +  +IL G+  
Sbjct: 792  TSVHIEVYETTARDTRLGPEEITPDIPNVSKEKLRNLDEDGIIRIGAYVQETDILVGKVT 851

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        +   +  E           + ++V+ +   +    E     +    K 
Sbjct: 852  PKSESDTTPEEKIIRSVFGE-----------KGKEVKDSSLRVPHGIEGRVIAVHVFDKE 900

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      GD + PGV ++++V+VA+++P++ GDK+AGRHGNKG+VS+ILP EDMPFL DG
Sbjct: 901  K-----DGD-LGPGVNKLIRVYVAIRKPLEVGDKLAGRHGNKGVVSKILPKEDMPFLPDG 954

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VL+PLGVPSRMNVGQI ET LGW  +   K   + + D     DI P      K 
Sbjct: 955  TPVQVVLSPLGVPSRMNVGQILETSLGWLAMLTNKWFATPVFDGAKEKDILPELYKARKK 1014

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +G     ++                                            + +G+  
Sbjct: 1015 LGLEVGDDEN-------------------------------------------NPTGKVT 1031

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TG  FD P+ VGY+Y++KL H+  DK++ARSTG YSL+ QQPLGGK+  GGQR G
Sbjct: 1032 LRDGRTGLEFDHPILVGYMYVMKLIHIARDKIHARSTGPYSLIHQQPLGGKAQFGGQRFG 1091

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ L EMLT+KSDD++GR  VY++I+ G +  + G PESF VLV+E++
Sbjct: 1092 EMEVWALEAYGAAHTLNEMLTVKSDDIMGRNEVYKAIMKGKNIPDPGLPESFKVLVRELR 1151

Query: 1356 ALGLSIDLENSRTKNSAKME 1375
             + L + + +S        +
Sbjct: 1152 GIALDVRVYDSEGNEIDIEK 1171


>gi|13357745|ref|NP_078019.1| DNA-directed RNA polymerase subunit beta [Ureaplasma parvum serovar 3
            str. ATCC 700970]
 gi|14195189|sp|Q9PQV6|RPOB_UREPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|11261129|pir||C82923 DNA-directed RNA polymerase beta subunit UU187 [imported] -
            Ureaplasma urealyticum
 gi|6899151|gb|AAF30594.1|AE002118_4 DNA-directed RNA polymerase beta subunit [Ureaplasma parvum serovar 3
            str. ATCC 700970]
          Length = 1434

 Score =  670 bits (1729), Expect = 0.0,   Method: Composition-based stats.
 Identities = 337/1445 (23%), Positives = 573/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +         +R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVMRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                S+FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISSIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNTKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   VT+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSVTTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWC-----FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +           ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEIEKYAPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  + +            +  EI     +  D +    I +++
Sbjct: 290  KEEYIEQGSPLLSKLKQLIFNYV-----------EKNDEIDALLHENKDVEDASFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNIETLRHLGKASYQIA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I  + I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIANDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTKKINLLPTALESE-----IEQFLEYESIAVYKDNDLRDETTEIVGLASGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R++ +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREIEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +    +
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHS 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEDYKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      N+   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPNE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + R+     ++  + I           ++  I+ VG  V+  +  +G         +   
Sbjct: 855  IIRNDNDKLDDY-KLIKYRKSNQDTCNNQIPIVKVGQRVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSSDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ V    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYENISNLIKHKQAKQAKDIDLIDVTIILK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I S++  A++D     G+ +LYDG TGEPFD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVSIMNEANIDIENNKGKQVLYDGRTGEPFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 VDINE 1387


>gi|171920550|ref|ZP_02931821.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 13 str. ATCC 33698]
 gi|185178845|ref|ZP_02554816.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 5 str. ATCC 27817]
 gi|188024155|ref|ZP_02570055.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 7 str. ATCC 27819]
 gi|188518528|ref|ZP_02556765.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 11 str. ATCC 33695]
 gi|195867734|ref|ZP_03079735.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 9 str. ATCC 33175]
 gi|209554116|ref|YP_002284583.1| DNA-directed RNA polymerase subunit beta [Ureaplasma urealyticum
            serovar 10 str. ATCC 33699]
 gi|225551333|ref|ZP_03772279.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 8 str. ATCC 27618]
 gi|226699457|sp|B5ZAZ3|RPOB_UREU1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|171903247|gb|EDT49536.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 13 str. ATCC 33698]
 gi|184209481|gb|EDU06524.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 5 str. ATCC 27817]
 gi|188018786|gb|EDU56826.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 7 str. ATCC 27819]
 gi|188997915|gb|EDU67012.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 11 str. ATCC 33695]
 gi|195660589|gb|EDX53845.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 9 str. ATCC 33175]
 gi|209541617|gb|ACI59846.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 10 str. ATCC 33699]
 gi|225379148|gb|EEH01513.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 8 str. ATCC 27618]
          Length = 1434

 Score =  670 bits (1728), Expect = 0.0,   Method: Composition-based stats.
 Identities = 332/1445 (22%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +          R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVTRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                 +FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISGIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNAKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   +T+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSITTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWCFP-----LSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +   +       ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEVEKYSPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  D +            ++ EI     +  D +    I +++
Sbjct: 290  REEYIEQGSPLLSKLKELIFDYV-----------EKSDEIDALLHENKDVEDANFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNVETLRHLGKASYQLA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I ++ I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIARDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTRKINLLPIALETE-----IEQFLEYESIAVYKDNDLRDETTEIVGLAPGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R+V +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREVEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEECKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      ++   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPHE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + ++     +E  + I           ++  I+ +G +V+  +  +G         +   
Sbjct: 855  VIKNDNDKLDEY-KLIKYRKSNQDTCNNQIPIVKIGQKVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSTDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ +    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYEKITNLIKHKQAKQPKDIDLIDITIVLK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I  ++  A++D     G+ +LYDG TGE FD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVDIMNEANIDIENNKGKQVLYDGRTGEAFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 IDINE 1387


>gi|225550765|ref|ZP_03771714.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 2 str. ATCC 27814]
 gi|225379919|gb|EEH02281.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 2 str. ATCC 27814]
          Length = 1434

 Score =  669 bits (1727), Expect = 0.0,   Method: Composition-based stats.
 Identities = 332/1445 (22%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +          R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVTRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LR 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                 +FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISGIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNAKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   +T+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSITTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWCFP-----LSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +   +       ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEVEKYSPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  D +            ++ EI     +  D +    I +++
Sbjct: 290  REEYIEQGSPLLSKLKELIFDYV-----------EKSDEIDALLHENKDVEDANFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNVETLRHLGKASYQLA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I ++ I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIARDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTRKINLLPIALETE-----IEQFLEYESIAVYKDNDLRDETTEIVGLAPGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R+V +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREVEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEECKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      ++   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPHE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + ++     +E  + I           ++  I+ +G +V+  +  +G         +   
Sbjct: 855  VIKNDNDKLDEY-KLIKYRKSNQDTCNNQIPIVKIGQKVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSTDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ +    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYEKITNLIKHKQAKQPKDIDLIDITIVLK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I  ++  A++D     G+ +LYDG TGE FD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVDIMNEANIDIENNKGKQVLYDGRTGEAFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 IDINE 1387


>gi|171920404|ref|ZP_02931726.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            1 str. ATCC 27813]
 gi|171902844|gb|EDT49133.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma parvum serovar
            1 str. ATCC 27813]
          Length = 1434

 Score =  669 bits (1727), Expect = 0.0,   Method: Composition-based stats.
 Identities = 336/1445 (23%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +         +R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVMRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                S+FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISSIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNTKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   VT+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSVTTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWC-----FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +           ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEIEKYAPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  + +            +  EI     +  D +    I +++
Sbjct: 290  KEEYIEQGSPLLSKLKQLIFNYV-----------EKNDEIDALLHENKDVEDASFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNIETLRHLGKASYQIA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I  + I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIANDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTKKINLLPTALESE-----IEQFLEYESIAVYKDNDLRDETTEIVGLASGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R++ +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREIEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEEYKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      ++   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPHE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + R+     ++  + I           ++  I+ VG  V+  +  +G         +   
Sbjct: 855  IIRNDNDKLDDY-KLIKYRKSNQDTCNNQIPIVKVGQRVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSSDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ V    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYENISNLIKHKQAKQAKDIDLIDVTIILK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I S++  A++D     G+ +LYDG TGEPFD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVSIMNEANIDIENNKGKQVLYDGRTGEPFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 VDINE 1387


>gi|294668294|ref|ZP_06733398.1| hypothetical protein NEIELOOT_00207 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291309748|gb|EFE50991.1| hypothetical protein NEIELOOT_00207 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 726

 Score =  669 bits (1726), Expect = 0.0,   Method: Composition-based stats.
 Identities = 309/654 (47%), Positives = 434/654 (66%), Gaps = 25/654 (3%)

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                P FD+ +C  R +TYA PL+  +RL++ D +       IK+++E  +YMG++PLM
Sbjct: 43  IFLGEPLFDIPECQLRGITYAAPLRARIRLVILDKESSKQD-VIKEVRENEVYMGEIPLM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ RIIP +G W+D EFD 
Sbjct: 102 TPSGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARIIPYRGSWLDFEFDP 161

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           KD+++ RIDRRRK+PVT  L ALG + E+IL TFY K  +    D     L A  L  G 
Sbjct: 162 KDLLYFRIDRRRKMPVTILLKALGYNDEQILDTFYDKETFYFLKDGVETSLVAGRL-KGE 220

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
                +VD   G  ++ +GK++T+  ++ +++ G++ L +  + L G  +A+D+++  TG
Sbjct: 221 TAKFDIVD-KEGNVLVAAGKRITAKNIRDIEKSGLERLRVDPESLVGRTLAKDVISANTG 279

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           E+   A   I E+ L +   +++++I  LY++ ++   YI  TL TD+  D+  A + IY
Sbjct: 280 EVLAVANIEITEELLAQFDINDVQEIQTLYINDLDQGGYISATLRTDETADQHAARVAIY 339

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR--------- 429
           R+MRPG+  T    E +FN LFF+ D YDLS VGR+K N R         +         
Sbjct: 340 RMMRPGEPPTEEAVELLFNRLFFNEDSYDLSRVGRMKFNTRTYEQKLTSEQKASWYGRLL 399

Query: 430 -------------HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                         +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+R
Sbjct: 400 NETFAGAAEKGGFVLGVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELAENQFR 459

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS IT
Sbjct: 460 SGLSRVERAVKERLNQAESENLMPTDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEIT 519

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YG
Sbjct: 520 HKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYG 579

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           F+ETPYR+V DGKVT+D+ YLSA+EE    IAQAN++LD +G   ++LV CR  GE I+ 
Sbjct: 580 FLETPYRRVVDGKVTDDIEYLSAIEEGRFVIAQANAALDAEGHLVDDLVTCREKGETIMA 639

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +++ ++D +  Q VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE  +
Sbjct: 640 TTDRVQYMDVATGQAVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRAENRW 693


>gi|198273552|ref|ZP_03206088.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 4 str. ATCC 27816]
 gi|198250072|gb|EDY74852.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 4 str. ATCC 27816]
          Length = 1434

 Score =  669 bits (1726), Expect = 0.0,   Method: Composition-based stats.
 Identities = 332/1445 (22%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +          R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVTRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                 +FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISGIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNAKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   +T+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSITTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWCFP-----LSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +   +       ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEVEKYSPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  D +            ++ EI     +  D +    I +++
Sbjct: 290  REEYIEQGSPLLSKLKELIFDYV-----------EKSDEIDALLHENKDVEDANFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNVETLRHLGKASYQLA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I ++ I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIARDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTRKINLLPIALETE-----IEQFLEYESIAVYKDNDLRDETTEIVGLAPGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R+V +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREVEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHYHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEEYKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      ++   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPHE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + ++     +E  + I           ++  I+ +G +V+  +  +G         +   
Sbjct: 855  VIKNDNDKLDEY-KLIKYRKSNQDTCNNQIPIVKIGQKVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSTDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ +    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYEKITNLIKHKQAKQPKDIDLIDITIVLK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I  ++  A++D     G+ +LYDG TGE FD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVDIMNEANIDIENNKGKQVLYDGRTGEAFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 IDINE 1387


>gi|188524077|ref|ZP_02557312.2| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 12 str. ATCC 33696]
 gi|195660012|gb|EDX53392.1| DNA-directed RNA polymerase, beta subunit [Ureaplasma urealyticum
            serovar 12 str. ATCC 33696]
          Length = 1434

 Score =  669 bits (1726), Expect = 0.0,   Method: Composition-based stats.
 Identities = 332/1445 (22%), Positives = 572/1445 (39%), Gaps = 128/1445 (8%)

Query: 1    MAKGVVFNGL----GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M     +          R+ + K     + P+L+E+Q  S+  F+  +          L+
Sbjct: 1    MQNNKNYTEKFITDKVTRRDYSKIKSNFEGPNLLEIQVESFKRFMEKD----------LK 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                 +FP+ +  G   L F   +   P  D   C     T+  P+ I L L      E 
Sbjct: 51   EVISGIFPLKSPQGKYTLAFKGLKIKQPTKDESACRDEGKTFETPIYIDLELTDNYTGEV 110

Query: 117  TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLS 175
              A+      E  IY+G +P MT+ GTFVI GI++ V+SQ+ RSPGI+       + + S
Sbjct: 111  KRAQRNAKTGEDGIYLGAIPKMTEKGTFVINGIEKFVISQIVRSPGIYVLGKSSIKLNGS 170

Query: 176  GKLLY---ACRIIPDQGLWMDIEFDSKDIIHVRI-------DRRRKVPVTSFLMALGMDS 225
             K L+    C I P +G  + + +  KD  +++I       D  +   +T+ L A G+ S
Sbjct: 171  RKRLFEGKICEIYPSKGT-LMLGYIPKDRHNIQIVARDSSGDNAQTFSITTLLKAFGLTS 229

Query: 226  EEILSTFYPKIVYSQRGDFWCFP-----LSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
             EIL  F  +    +  +   +       ++ +  +  K+ S   DI       ES  KL
Sbjct: 230  AEILKIFNNEKEIRESLEVEKYSPEYIFENSQENEIIFKIYSDAHDIHEKADRRESNNKL 289

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                ++       K   +  D +            ++ EI     +  D +    I +++
Sbjct: 290  REEYIEQGSPLLSKLKELIFDYV-----------EKSDEIDALLHENKDVEDANFIKNNK 338

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                  LY +       I +        +     +     +R    +++ +A       F
Sbjct: 339  K-----LYDEREEIINCIISEKAAKDIVELLGINIKNVETLRHLGKASYQLA---LQQHF 390

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
            F+   YD+S+ GR K   +L L      + I ++ I     IL+                
Sbjct: 391  FNKRLYDISSAGRYKFEKKLLLSERLYQKVIARDIIDKKNNILIPKDTLITKEHIELIKK 450

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              R +++    K       L  E         ++ +S+      + +   + +       
Sbjct: 451  ESRDKNIKWTRKINLLPIALETE-----IEQFLEYESIAVYKDNDLRDETTEIVGLAPGC 505

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-----CPAETS 575
            +L  L       +          +G+           ++ +H     RI        +  
Sbjct: 506  KLQTLTVADLVATTSYIYNLNYEIGEFDDIDHLGNKRLKLIHELLRARIATSMARIEKFI 565

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-- 633
                     S  +   VN  G      R+V +  +++        EE+ + I+  +    
Sbjct: 566  NEKLAISDGSSNNITNVNDKGIDTELDREVEESDMSD--------EEKKKAISVKSIINT 617

Query: 634  -----LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP----KQVVSIAASLIPFLEN 684
                 L +D   + +L+        +     K       P    ++  ++    +     
Sbjct: 618  KQFQSLVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHHSHY 677

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                 +     M    +  L + A     G            +V +    +   +    +
Sbjct: 678  SRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYYVVEDGVVKEEYKYLTAHEDDNYI 737

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL-- 802
            I      LD +   +D   + +++ S      ++   V   D V +  +     +     
Sbjct: 738  IAESSVQLDENKRILDEQVVARYRGSTGLFSPHE---VDFIDIVPKQVVSIAASAIPFIE 794

Query: 803  -----------GDLALGRNMLVAFMPWHGYNFEDSMLISERM--VSEDVFTSIHIEEFEV 849
                               ++  + P  G   E  +     M  V+++      ++  ++
Sbjct: 795  NDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVVAKNDGVVEFVDSQKI 854

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            + ++     +E  + I           ++  I+ +G +V+  +  +G         +   
Sbjct: 855  VIKNDNDKLDEY-KLIKYRKSNQDTCNNQIPIVKIGQKVHKSET-IGDGPAMQNGELALG 912

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              +L      +  +  D  +     +S  +VD  +F    ID++       +   E + R
Sbjct: 913  RNILVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITR 967

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +      +        +L G     G     K+T   +  +   P  +  Q    D+
Sbjct: 968  DMPN-VSDTAKRFLDNQGIVLVGAEVHEGDVLVGKTTPRGN--VETAPEDRLLQTIFGDK 1024

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
               + V+   ++ +  +  +    K      + G ++P  V+ ++KV++  KR IQ GDK
Sbjct: 1025 --SKTVKDSSLKVKHGQEGIVAAVKRIKSTDENGSELPDDVIEIIKVYIVQKRKIQVGDK 1082

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +G
Sbjct: 1083 MAGRHGNKGIVSKVVPIQDMPFLKDGTPLDIMLNPLGVPSRMNIGQILELHLGYAAAEIG 1142

Query: 1150 KK--IKSLINDYKANGDISP------LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            KK  I+  I+       IS       +   L + I      ++     D  ++ +    K
Sbjct: 1143 KKQLIQIAIDQLGYEKYISLFGINEIIAKKLYEKITNLIKHKQAKQPKDIDLIDITIVLK 1202

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                     G+ +STPVFDGA+ + I  ++  A++D     G+ +LYDG TGE FD  ++
Sbjct: 1203 ELGLSYDDIGIKISTPVFDGANHDDIVDIMNEANIDIENNKGKQVLYDGRTGEAFDGLIS 1262

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1263 VGLTYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1322

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            L E+LTIKSDDV GR + Y +I+ G+D    G PESF +L K+MQ LGL I +E    + 
Sbjct: 1323 LLEILTIKSDDVQGRNQAYNAIIKGHDVVADGMPESFKLLTKQMQGLGLCITVETKDDRM 1382

Query: 1371 SAKME 1375
                E
Sbjct: 1383 IDINE 1387


>gi|150020400|ref|YP_001305754.1| DNA-directed RNA polymerase subunit beta [Thermosipho melanesiensis
           BI429]
 gi|182676577|sp|A6LKB8|RPOB_THEM4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|149792921|gb|ABR30369.1| DNA-directed RNA polymerase, beta subunit [Thermosipho
           melanesiensis BI429]
          Length = 1172

 Score =  668 bits (1724), Expect = 0.0,   Method: Composition-based stats.
 Identities = 374/1000 (37%), Positives = 561/1000 (56%), Gaps = 120/1000 (12%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS- 69
            R R  F +    I +P+L+E+Q  SY  FL            G+    K   PIT+   
Sbjct: 8   KRTRYSFERVQTPIPVPNLVEIQTKSYQDFL----------ENGILKVLKKFSPITSSKS 57

Query: 70  -----GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                    LEFVS     P+  V +C  R LTY VP+  T+R+            S  +
Sbjct: 58  DLRKEKGFSLEFVSVRIGEPQNTVQECKERLLTYTVPVYTTVRITDN---------STNE 108

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           + E+  ++G +P MT   TF+I G +R+VV+QL RSPGI+F  +  +     K +Y    
Sbjct: 109 MIEEEAFLGYIPYMTPRTTFIINGAERVVVNQLVRSPGIYFVEEAKKT-SGTKPIYVAHF 167

Query: 185 IPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +P +G W++I  +  D + + RIDR+R++ +   L ALG   + E+LS F   I      
Sbjct: 168 LPVRGAWLEILLNLNDEVFYARIDRKRRINLFLLLKALGYSEDLELLSLFPYWIDVEDEY 227

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                            +    V    G  + + G  +T GL++ L+   ++ + +    
Sbjct: 228 ---------TLQHSEGLIILEDVKTKNGGLIAKRGDVITQGLIEKLENSDIQKIKVAHRY 278

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
                                        +LE++ H    +I                  
Sbjct: 279 AVN--------------------------TLEKLNHVYGENIE----------------- 295

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                     A ++I+R +RPG++   + A+     L+F+ ++++LS VGR KMN RL  
Sbjct: 296 -------ENRAYIEIFRKLRPGELPRINAAKIFLRNLYFNEERFELSEVGRFKMNNRLEE 348

Query: 423 --------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
                                  +    +   DI+   + L+++    GT+D  D+LGN+
Sbjct: 349 AYRKYLIEVEGKDPQGVEEVKYDETSNVLTPMDIVLASRNLIEIDKHPGTMDTKDHLGNK 408

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RVR+VGE+++ ++     +    I+E+  +   +D +  Q LIN K +++ +  FF ++ 
Sbjct: 409 RVRTVGELIRIEFERAFSKAVFMIQEKLATYTSLDKISVQSLINVKSIIATINSFFATNP 468

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +TH RRL+A+G GG+ R RA  E+RDVH +HYGR+CP ET EG NIG
Sbjct: 469 LSQFMDQTNPLAELTHKRRLTAVGPGGLKRERARFEVRDVHHSHYGRMCPIETPEGANIG 528

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ ++ ++ +GF+ TPY KV  GKVTN++VYL+A EEEN  IA +   +DE G+  
Sbjct: 529 LITSLSVYSSIDKFGFLITPYVKVVKGKVTNEIVYLTADEEENYKIAPSTIPIDEKGNII 588

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V  R   + + V +  + FID +P Q+VS++ SLIPFLE+DD+NR LMG NMQRQ V
Sbjct: 589 PENVTVRYEEKVLYVNKNNVQFIDVAPNQIVSVSTSLIPFLEHDDANRALMGSNMQRQGV 648

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP-----ST 756
           PL++ EAP VGTGME   AK SG  I+AK  GIV++VDA +IVI  ++ +          
Sbjct: 649 PLIETEAPRVGTGMEWEAAKYSGTLILAKHDGIVKKVDAQKIVIHRIDENGKEMYDSMGN 708

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +DIY L+KF R+NQ+TC+NQRP+V VG+ V++++ IADGP+TD+G+LALG+N+LVAF+
Sbjct: 709 PMLDIYELLKFTRTNQDTCINQRPIVNVGEIVKKDEPIADGPATDMGELALGKNVLVAFV 768

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW GYNFED++LISE ++ ++ +TSIHIE +E  ARDT+LGPEEIT DIPNVS+E L+N+
Sbjct: 769 PWEGYNFEDAILISEELLEKETYTSIHIEVYETTARDTRLGPEEITPDIPNVSKEKLRNL 828

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GA V   DILVGK+TPK ES  TPEEK++R++FGEK  +V+DTSLRVP G+ 
Sbjct: 829 DEDGIIRIGAYVQETDILVGKVTPKSESDTTPEEKIIRSVFGEKGKEVKDTSLRVPHGIE 888

Query: 937 GTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           G V+ V +F++        G++K  R     R+ +E+  +
Sbjct: 889 GRVIAVHVFDKEKDGDLGPGVNKLIRVYVAIRKPLEVGDK 928



 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 177/571 (30%), Positives = 268/571 (46%), Gaps = 72/571 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M W    +  ++++++   +V +     I I   +   ++          DI  + +   
Sbjct: 662  MEWEAAKYSGTLILAKHDGIVKKVDAQKIVIHRIDENGKEMYDSMGNPMLDIYELLKFTR 721

Query: 874  KNID----ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
             N D    +  I+ VG  V   D  +          +   + +L A    +  +  D  L
Sbjct: 722  TNQDTCINQRPIVNVGEIVK-KDEPIADGPATDMGELALGKNVLVAFVPWEGYNFEDAIL 780

Query: 930  RVPSG-VSGTVVDVRIFNRHGIDKNERSISVE-REQIELLARDKD---DEQVILDRNIYS 984
                     T   + I       ++ R    E    I  ++++K    DE  I+    Y 
Sbjct: 781  ISEELLEKETYTSIHIEVYETTARDTRLGPEEITPDIPNVSKEKLRNLDEDGIIRIGAYV 840

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +  +IL G+              +   +  E           + ++V+     +    E 
Sbjct: 841  QETDILVGKVTPKSESDTTPEEKIIRSVFGE-----------KGKEVKDTSLRVPHGIEG 889

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                +    K K      GD + PGV ++++V+VA+++P++ GDK+AGRHGNKG+VS+IL
Sbjct: 890  RVIAVHVFDKEK-----DGD-LGPGVNKLIRVYVAIRKPLEVGDKLAGRHGNKGVVSKIL 943

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL DGTP+ +VL+PLGVPSRMNVGQI ET LGW  +   +   + + D    GD
Sbjct: 944  PKEDMPFLPDGTPIQVVLSPLGVPSRMNVGQILETSLGWLAMLTNRWFATPVFDGAKEGD 1003

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            I P      K  G                                   G  EE       
Sbjct: 1004 ILPELYKARKKFGLEM--------------------------------GDFEE------- 1024

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                + SG+ IL DG TG+ FD P+ VGY+Y++KL H+  DK++ARSTG YSL+ QQPLG
Sbjct: 1025 ----NPSGKVILRDGRTGKEFDHPILVGYMYVMKLIHIARDKIHARSTGPYSLIHQQPLG 1080

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAA+ L EMLT+KSDD+ GR  VY++I+ G +  E G P
Sbjct: 1081 GKAQFGGQRFGEMEVWALEAYGAAHTLNEMLTVKSDDIRGRNEVYKAIMKGKNIPEPGLP 1140

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            ESF VLV+E++ + L + + +         +
Sbjct: 1141 ESFKVLVRELRGIALDVRVYDDEGNEIDIEK 1171


>gi|10637863|emb|CAC10557.1| DNA-dependent RNA polymerase subunit beta [Listeria grayi]
          Length = 1062

 Score =  666 bits (1718), Expect = 0.0,   Method: Composition-based stats.
 Identities = 392/824 (47%), Positives = 526/824 (63%), Gaps = 61/824 (7%)

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
           +G F+I G +R++VSQL RSPG++F+    +   +G+  +   +IP++G W++ E D+KD
Sbjct: 2   NGYFIINGAERVIVSQLVRSPGVYFN---DKIDKNGRTGFGSTVIPNRGAWLEYETDAKD 58

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           ++HVRIDR RK+PVT  L ALG  S+ +I+             +      +   L+    
Sbjct: 59  VVHVRIDRTRKLPVTVLLRALGFGSDQDIIELVGDNEYLRNTLEKDNTDNAEKALL---- 114

Query: 260 VSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLYVAE 310
                  +  GE   +E+ + L        K           +       + L    +AE
Sbjct: 115 --EIYERLRPGEPPTVENARNLLISRFFDPKRYDLASVGRYKINKKLHLKNRLFNQRLAE 172

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            +V+ ETGEI    GD++D ++L++I       IP L      +  +  N ++ D     
Sbjct: 173 TLVDPETGEIIASKGDILDRRALDQI-------IPNLESGVGFHTLHPSNGIMDDSV--- 222

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
              ++   ++  P D                             ++N+  N    +DV+H
Sbjct: 223 ---VVQSIKIYAPND--------------------------EEKEINIIGNAYIEEDVKH 253

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I   DI++ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+
Sbjct: 254 ITPSDIVSSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERM 313

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ 
Sbjct: 314 SIQDMSTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLT 373

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDG 608
           R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+VN +GFIETPYR+V     
Sbjct: 374 RERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDPETN 433

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+ + YL+A EE+N  +AQANS LD+DGSF EE V  R   E + V +E++D++D SP
Sbjct: 434 RVTDKIDYLTADEEDNYVVAQANSKLDDDGSFAEEEVMARFRSENLAVTKERVDYMDVSP 493

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK SGAAI 
Sbjct: 494 KQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGAAIT 553

Query: 729 AKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           AK  GIVE V+A  I IR   + D    T G+D Y L KF RSNQ TC NQRP V  GD 
Sbjct: 554 AKYDGIVEHVEAKEIWIRRVSDVDGTEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAEGDR 613

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V + +I+A+GPS D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+TSIHIEEF
Sbjct: 614 VVKGEILANGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEF 673

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           E  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TPKG + +T
Sbjct: 674 ESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTELT 733

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R   D
Sbjct: 734 AEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGD 777



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 219/1048 (20%), Positives = 375/1048 (35%), Gaps = 114/1048 (10%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++ V +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A ++    FFD  +YDL
Sbjct: 88   IELVGDNEYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVENARNLLISRFFDPKRYDL 147

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            ++VGR K+N +L+L          +     + + LVD   G+      D L  R +  + 
Sbjct: 148  ASVGRYKINKKLHLK--------NRLFNQRLAETLVDPETGEIIASKGDILDRRALDQII 199

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
              L++   +G   +  S      SV + S+      + +  ++ +   +    +  +   
Sbjct: 200  PNLES--GVGFHTLHPSNGIMDDSVVVQSIKIYAPNDEEKEINIIGNAYIEEDVKHITPS 257

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S       L  +G            +R V      +     +     +    S+  
Sbjct: 258  DIVSSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 317

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             + +     I    R V          +  + +                      L    
Sbjct: 318  MSTITPQQLI--NIRPVVASIK----EFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGG 371

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E        + +        +       I  + +  S   +            +  E
Sbjct: 372  LTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDPE 431

Query: 708  APFVGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
               V   ++ + A  + +     A      +   A   V+     +    T     Y  +
Sbjct: 432  TNRVTDKIDYLTADEEDNYVVAQANSKLDDDGSFAEEEVMARFRSENLAVTKERVDYMDV 491

Query: 766  KFQR--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              ++  S    C+           +  +D        ++   A+      A     G   
Sbjct: 492  SPKQVVSVATACIP---------FLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEH 542

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-------GPEEITRDIPNVSEEGLKNI 876
              +      + ++      H+E  E+  R           G  +       V        
Sbjct: 543  VSAKDSGAAITAKYDGIVEHVEAKEIWIRRVSDVDGTEVTGGIDKYTLRKFVRSNQGTCY 602

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            ++   +  G  V  G+IL    +      +     +L A       +  D  +       
Sbjct: 603  NQRPNVAEGDRVVKGEILANGPS-MDSGELALGRNVLVAFMTWDGYNYEDAIIM----SE 657

Query: 937  GTVVDVRIFNRHGIDKNERSISVE---REQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
              V D    + H  +    +   +    E    +    +D    LD     R+   +   
Sbjct: 658  RLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDN 717

Query: 994  NAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            + + G    K  T L+++  L+      +  +      +V      +             
Sbjct: 718  DLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV------------ 765

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                KI   + GD++PPGV ++V+V++  KR I  G                        
Sbjct: 766  -LDVKIFTREAGDELPPGVNQLVRVYIVQKRKIHEG------------------------ 800

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             S+M                 G K        + +    P  + 
Sbjct: 801  -----------------SKM-------------AGRHGNKGVISRILPEEDMPFMPDGTP 830

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            ++ ++       +++      +         G+ V+TPVFDGA+EE + S +  A +   
Sbjct: 831  VDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARD 890

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ILYDG TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GG
Sbjct: 891  AKTILYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGG 950

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    + G PESF VL+
Sbjct: 951  QRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPQPGVPESFKVLI 1010

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+LG+ + + ++  +     +   D
Sbjct: 1011 KELQSLGMDVKILSADEEEIEFRDLDDD 1038


>gi|163846452|ref|YP_001634496.1| DNA-directed RNA polymerase subunit beta [Chloroflexus aurantiacus
            J-10-fl]
 gi|222524227|ref|YP_002568698.1| DNA-directed RNA polymerase subunit beta [Chloroflexus sp. Y-400-fl]
 gi|182676557|sp|A9WH12|RPOB_CHLAA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765282|sp|B9LL91|RPOB_CHLSY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|163667741|gb|ABY34107.1| DNA-directed RNA polymerase, beta subunit [Chloroflexus aurantiacus
            J-10-fl]
 gi|222448106|gb|ACM52372.1| DNA-directed RNA polymerase, beta subunit [Chloroflexus sp. Y-400-fl]
          Length = 1227

 Score =  666 bits (1717), Expect = 0.0,   Method: Composition-based stats.
 Identities = 373/1210 (30%), Positives = 534/1210 (44%), Gaps = 121/1210 (10%)

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            + E   +D+ +    R R       L  L   + EI  +      +    D   F  + A
Sbjct: 96   EFECRERDLTYAAPLRVR-----VELRIL--TTGEIKESEIFLGDFPIMTDNGTFVYNGA 148

Query: 253  DLMVGAKVSSSLVDIDTGEQVIESGKKL-TSGLLKS----LKEKGVKFLGITSDCLCGLY 307
            + +V +++  S       E+   SG+ L T+ L+ +    L+ +  K   I+        
Sbjct: 149  ERVVVSQLIRSPGVYFKDEKEPTSGRSLHTAKLIPNRGAWLEFETNKRDVISVKVDRKRK 208

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL---YVDSVNNNAYIRNTLVT 364
            +   I+         E           E+      D  I    +VD+V  + YI  TL  
Sbjct: 209  IPVTILLRAITAWIAEENGNGRWVPDNELDKFGHNDQIIELFRHVDTVPEHPYIHATLDK 268

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL---- 420
            D +++ K+ALL++Y+ +RPGD  T   A S+   L F   +YDL+ VGR K+N  L    
Sbjct: 269  DPSRNAKEALLELYKRLRPGDPPTLENARSLIESLLFSPRRYDLAKVGRYKLNKNLWERD 328

Query: 421  -----NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                        VR +   DI  I++ L+ L NG G  DDID+LGNRRVR+VGE+++ Q+
Sbjct: 329  VRRDGAKAPDLSVRVLLPRDIFRIVEQLILLNNGHGRPDDIDHLGNRRVRTVGELIQQQF 388

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            R+GLLR+ER +KER+S  D  S  P  LIN +PVV+A+ EFF  SQLSQ  +  N L+ +
Sbjct: 389  RVGLLRLERVVKERMSLQDPASATPNGLINIRPVVAAMREFFGGSQLSQFMDQTNPLAEL 448

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            T+ RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ ++++FARVN  
Sbjct: 449  TNKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRICPVETPEGPNIGLIGTMSTFARVNEM 508

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            GF+ETPYRKV          Y S            N  + ++       V     G+ I 
Sbjct: 509  GFLETPYRKV----------YNSVD----------NVQVWKEKGILLRDVRDLRTGDLIA 548

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                +++  + + +  + +    I   +  D +   +      +    L      +    
Sbjct: 549  AKGTRVN-DEIARQITIGLLRGQILREDIVDPDTDELIAEAGTEINRALAERIVELPIKH 607

Query: 716  ESVVAKSSGAAIV--AKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSN 771
              +    S       A        V A   + +       +     G D       +   
Sbjct: 608  IKIRPVVSQEVDYLSADEEDRFVIVQANAPLDQHNRFLDTIVSCRFGEDFVSERVERVDY 667

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +    Q   V            A+              +L    P  G   E       
Sbjct: 668  MDVSPKQVVSVSTSLIPFLEHDDANRALMGSNMQRQAVPLLRPDAPIVGTGMEYRAARDS 727

Query: 832  RMV---SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
              V     D        E  V+  D     E   R    +       I++   +  G  V
Sbjct: 728  GQVIVARRDGVVVSTTSERIVIEEDDGNQTEYRLR--KFMRSNQDTCINQRPAVVRGQRV 785

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              GD++    +   +  +   + +L A    +  +  D  L     VS  +V   IF   
Sbjct: 786  KAGDVIADSSST-DQGELALGQNVLVAYMPWEGGNFEDAIL-----VSERLVREDIFTSI 839

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
             I+K E      +   E + RD  +      RN+  R   I  G           K T  
Sbjct: 840  HIEKYEVEARDTKLGPEEITRDIPNVGQESLRNLDER-GIIYIGAEVQPNDILVGKITPK 898

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
                ++   R     F  +  +V+ +   +          +      K+     G ++P 
Sbjct: 899  GETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVRGKVIDV------KVFSRSEGAELPV 952

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV + V+V +  KR I +GDKMAGRHGNKG+VSR+LP EDMPFL DG PVDI+LNP+GVP
Sbjct: 953  GVNQTVRVLLCQKRKISAGDKMAGRHGNKGVVSRVLPIEDMPFLPDGRPVDIILNPIGVP 1012

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQI ETHLGWA   LG ++ + + D      I  L                    
Sbjct: 1013 SRMNIGQILETHLGWAAARLGFRVATPVFDGAHEDQIKDLLVQAGLPADGKVTL------ 1066

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                                       G++       GE FD P
Sbjct: 1067 -----------------------------------------YDGRT-------GERFDNP 1078

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVGY YMLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA
Sbjct: 1079 VTVGYAYMLKLAHLVEDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAA 1138

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            Y LQEMLT+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LGLS+++ ++  
Sbjct: 1139 YTLQEMLTVKSDDVVGRVKTYEAIVKGEPIQEAGVPESFKVLIKELQSLGLSVEVLSADE 1198

Query: 1369 KNSAKMEEIP 1378
            K     +++ 
Sbjct: 1199 KPVELSDDLD 1208



 Score =  605 bits (1559), Expect = e-170,   Method: Composition-based stats.
 Identities = 332/971 (34%), Positives = 494/971 (50%), Gaps = 100/971 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLE 75
           F +  + ID+P LIE Q  S++ F            EGL+  F  + PIT F+G    L 
Sbjct: 34  FARIKDAIDLPLLIETQLKSFEWF----------KREGLRELFDEISPITDFTGKNLELH 83

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F  Y F  P++D  +C  RDLTYA PL++ + L +          +  +IKE  I++GD 
Sbjct: 84  FRDYTFGEPRYDEFECRERDLTYAAPLRVRVELRIL---------TTGEIKESEIFLGDF 134

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           P+MT +GTFV  G +R+VVSQL RSPG++F  +K     SG+ L+  ++IP++G W++ E
Sbjct: 135 PIMTDNGTFVYNGAERVVVSQLIRSPGVYFKDEKEPT--SGRSLHTAKLIPNRGAWLEFE 192

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMAL--------GMD-------------SEEILSTF-- 232
            + +D+I V++DR+RK+PVT  L A+        G               +++I+  F  
Sbjct: 193 TNKRDVISVKVDRKRKIPVTILLRAITAWIAEENGNGRWVPDNELDKFGHNDQIIELFRH 252

Query: 233 ------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES---------- 276
                 +P I  +   D       A   +           ++    +IES          
Sbjct: 253 VDTVPEHPYIHATLDKDPSRNAKEALLELYKRLRPGDPPTLENARSLIESLLFSPRRYDL 312

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
            K     L K+L E+ V+  G  +  L    +    +     ++ +          ++ +
Sbjct: 313 AKVGRYKLNKNLWERDVRRDGAKAPDLSVRVLLPRDIFRIVEQLILLNNGHGRPDDIDHL 372

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            +  +R +  L              +V ++   +  A      ++    +     A   F
Sbjct: 373 GNRRVRTVGELIQQQFRVGLLRLERVVKERMSLQDPASATPNGLIN---IRPVVAAMREF 429

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                 S   D +       N R    +      + ++     ++ +     G+  I  +
Sbjct: 430 FGGSQLSQFMDQTNPLAELTNKR--RLSALGPGGLSRDRAGFEVRDVHHSHYGR--ICPV 485

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           +      +  +G M        +  +E   ++  +SVD   V  +  I  + V       
Sbjct: 486 ETPEGPNIGLIGTMSTFARVNEMGFLETPYRKVYNSVDNVQVWKEKGILLRDVRDLRTGD 545

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             +++ +++ + +     I            G+ R +   E           + P     
Sbjct: 546 LIAAKGTRVNDEIARQITI------------GLLRGQILRED---------IVDPDTDEL 584

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
               G   +     R+          R V    V+ +V YLSA EE+   I QAN+ LD+
Sbjct: 585 IAEAGTEINRALAERIVELPIKHIKIRPV----VSQEVDYLSADEEDRFVIVQANAPLDQ 640

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
              F + +V CR   + +    E++D++D SPKQVVS++ SLIPFLE+DD+NR LMG NM
Sbjct: 641 HNRFLDTIVSCRFGEDFVSERVERVDYMDVSPKQVVSVSTSLIPFLEHDDANRALMGSNM 700

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPLL+ +AP VGTGME   A+ SG  IVA+R G+V    + RIVI   +G+     
Sbjct: 701 QRQAVPLLRPDAPIVGTGMEYRAARDSGQVIVARRDGVVVSTTSERIVIEEDDGNQTE-- 758

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                YRL KF RSNQ+TC+NQRP V  G  V+  D+IAD  STD G+LALG+N+LVA+M
Sbjct: 759 -----YRLRKFMRSNQDTCINQRPAVVRGQRVKAGDVIADSSSTDQGELALGQNVLVAYM 813

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW G NFED++L+SER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV +E L+N+
Sbjct: 814 PWEGGNFEDAILVSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQESLRNL 873

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV P DILVGKITPKGE+ +T EE+LLRAIFGEKA +V+D+SLRVP+GV 
Sbjct: 874 DERGIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVR 933

Query: 937 GTVVDVRIFNR 947
           G V+DV++F+R
Sbjct: 934 GKVIDVKVFSR 944


>gi|57234592|ref|YP_181345.1| DNA-directed RNA polymerase subunit beta [Dehalococcoides ethenogenes
            195]
 gi|88909133|sp|Q3Z8V4|RPOB_DEHE1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|57225040|gb|AAW40097.1| DNA-directed RNA polymerase, beta subunit [Dehalococcoides
            ethenogenes 195]
          Length = 1272

 Score =  663 bits (1711), Expect = 0.0,   Method: Composition-based stats.
 Identities = 355/1090 (32%), Positives = 530/1090 (48%), Gaps = 125/1090 (11%)

Query: 332  SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
             L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 200  LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYSRLRPGDPPN 259

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
               A  + N +FFD   YDL  VGR K+N RL L   +  D R + +EDI+AIIK ++ +
Sbjct: 260  ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPDREVGDNRALTREDIVAIIKRIIMV 319

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
             NG+ T DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 320  NNGQDTPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEVVTPSALVNI 379

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 380  RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 439

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-----VVYLSAME 621
            GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV      ND     +   +A+ 
Sbjct: 440  GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNNDKKLVGLKLAAAVS 499

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            ++++ +A A S + E+       +   C  + +     ++ ++ A  +    IA +    
Sbjct: 500  DKDKVLASAGSVVSEENFKLISKLP-ECDIQVMPFVSAEVKYMPADEEDRYIIAQANTRL 558

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             EN       +   +  + V  ++         +          ++ A     +E  DA 
Sbjct: 559  DENGYFLDERIEARLAERYV--IEPPEKIDYMDVSPKQIF----SVAASLIPFLEHDDAN 612

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            R ++ +                    QR        + P+V  G                
Sbjct: 613  RALMGAN------------------MQRQAVPLLRAEAPMVATG---------------- 638

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                          M      +   ++ ++R     V  S+     E +   T  G ++ 
Sbjct: 639  --------------MEREAARYSGQVIFAKRA---GVAASV---TSEKIIIRTAEGQDDE 678

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                  V       I++  +I  G ++  G +L      +    +   +  + A    + 
Sbjct: 679  YLLKKFVRTNQGTCINQHAVINKGQKIEAGQVLADSSATEN-GELALGQNCVVAFMSWQG 737

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQV 976
             +  D  +     V           +H ++ ++  +  E     I  +  +   + DE  
Sbjct: 738  FNYEDAIILSERLVREDAFTSIHITKHELEAHDTKLGGEEITRDIPNVGEESLRELDEDG 797

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            I+         +IL G+    G         L   +  E  R                 E
Sbjct: 798  IIRIGAEVGPDDILVGKITPKGETELSAEEKLLRAIFGEKAR-----------------E 840

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                               ++   + GDD+P  V + V+V+VA KR +  GDK+AGRHGN
Sbjct: 841  VKDTSLRMPHGEWGKVINVRVFSRENGDDLPARVNKWVQVWVAQKRKVSVGDKLAGRHGN 900

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGWA   LG ++ + +
Sbjct: 901  KGVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGWAGHLLGFRVATPV 960

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDG-- 1213
             D   +  I    +        G+      +    +    A +W          VFD   
Sbjct: 961  FDGADDTAIEDALARSWLSAKAGATDMSPENKRPSTDTAKAVEWIKQQGFDGKKVFDERH 1020

Query: 1214 ---ADEEAINSMLRMADLDES-------------------------GQSILYDGLTGEPF 1245
               A E ++   L+   +D S                         G+S+L DG TGE F
Sbjct: 1021 PGLAKEVSLKLWLKDMGVDASSLSGAELEKKAYEVSSQSRLPSPIVGKSVLRDGRTGETF 1080

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQR GEMEVW + AY
Sbjct: 1081 DQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQRFGEMEVWAMYAY 1140

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            G A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVKE+Q+LGL++++ N
Sbjct: 1141 GTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVIQPGVPESFKVLVKELQSLGLAVEVIN 1200

Query: 1366 SRTKNSAKME 1375
               K +   +
Sbjct: 1201 EEVKIAPSEK 1210



 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 101/361 (27%), Positives = 168/361 (46%), Gaps = 42/361 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
            RK + + PE++++P+LIE+Q  S+  F            EGL+   + + PI  F G  
Sbjct: 15  TRKSYAQLPEVVNVPNLIEMQLQSFVWF----------QEEGLRELIEEISPIKDFVGNR 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+    +C  RD TY+VPL +  RLIV         K+  +IKE   +
Sbjct: 65  LELEFIGYEFREPRLSEYECTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDL 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT  GTF+  G +R+VVSQL RSPG++F         +G+ L    +IP +G 
Sbjct: 116 FFGDIPLMTALGTFITSGTERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGA 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PV++ L A+G   + +IL+ F    V     +      
Sbjct: 174 WLEFETSNRDVISVKIDGRRKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQS 230

Query: 250 SAADLMVGAKVSSSLVDI----DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS---- 300
           S     +     S+L+DI      G+    ++ +KL + +    +   +  +G       
Sbjct: 231 SIDRDPLIKDEISALIDIYSRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRR 290

Query: 301 ----DCLCG--LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
               D   G    +  + +      I +          ++ + +  IR +  L  +    
Sbjct: 291 LELPDREVGDNRALTREDIVAIIKRIIMVNNGQDTPDDIDHLGNRRIRTVGELVQNQFRI 350

Query: 355 N 355
            
Sbjct: 351 G 351


>gi|320527676|ref|ZP_08028850.1| DNA-directed RNA polymerase, beta subunit [Solobacterium moorei
            F0204]
 gi|320131997|gb|EFW24553.1| DNA-directed RNA polymerase, beta subunit [Solobacterium moorei
            F0204]
          Length = 1386

 Score =  660 bits (1702), Expect = 0.0,   Method: Composition-based stats.
 Identities = 286/1435 (19%), Positives = 516/1435 (35%), Gaps = 152/1435 (10%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
               VV  G    R+ + K    +D+PDL+E+Q A++D FL            G++  F  
Sbjct: 6    TYHVVHYGNKATRRDYSKVSSGLDLPDLVEIQTAAFDWFLRD----------GIKEVFND 55

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            V+PI+ ++G   L+F+ YEF  PK+ + +C +R++ Y+ PLK  + L V D    TG   
Sbjct: 56   VYPISNYAGNIRLKFLDYEFGEPKYSISECKYREVNYSAPLKGKMELEVMDP--ETGEVI 113

Query: 122  IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
                K + +++GD PLMT  GTF+I G +RI+VSQ+ RSPG +FD +      +G+  Y 
Sbjct: 114  T---KNEEVFLGDFPLMTPTGTFIINGAERIIVSQIVRSPGAYFDIESE--ERTGRDTYK 168

Query: 182  CRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
            C +IP +G W++   D K      I++V IDRRRKV  +    A+G+     L+    + 
Sbjct: 169  CELIPSRGTWLEFMSDDKKAALGRILNVSIDRRRKVLSSILFKAIGLS----LNLERGEN 224

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS---LKEKGV 293
             +               +     V     +      ++ +        +++     +   
Sbjct: 225  AFDTTNMKKFLKALNLPVHSDVIVPEEEREFQNDYMLLYTAIFGNYEEVRNTLAADKTKT 284

Query: 294  KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS-- 351
            K   + +            ++G    +  +  D       +   +   + + IL      
Sbjct: 285  KNEALLTVYENQRADEIATIDGAVTLMDAKFFDYRRYDLTKAGRYKVHKKLSILDRMEGL 344

Query: 352  --------VNNNAYIRNTLVTDKNKDRK---DALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                          ++  +V DK    +   +    I     P   +    + ++ +  +
Sbjct: 345  SLEKDLVSAEGKTLVKKGVVIDKELRNELRAEIDKGINCRALPFTHTFSHPSTAVMDTSW 404

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
             +S    +  +  V ++ +    T +    + +ED+ AI K    +    G I     + 
Sbjct: 405  KNSL---VGRILAVDLDGKTERTTLEMGTVLTEEDVKAIAKEFKQVTVYAGIIASPVKVT 461

Query: 461  NRRVRSVGEMLKNQYRLGLLRM----------ERSIKERISSVDIDSVMPQDLINAKPVV 510
            N  V +V +     + +G + +          E      +  V++  +   D        
Sbjct: 462  NDNVNAVLDYGSRMFEIGRVTLNGEDLTNADGEVMCPTYLPDVEVTKLSTTDQETIVSEA 521

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            +          +    + V  +    H   L  +            +M  ++        
Sbjct: 522  TNHSGDVIVWLVGACVQEVTVMQE-GHPVNLIGIDPLNDRHTITMSDMYALYNYELTMFD 580

Query: 571  PAETSEGHNI---GLVSSLTSFARVNAYGFIETPYRKVCDGK-----------VTNDVVY 616
               + +  ++     + ++    +      +    R V +                ++  
Sbjct: 581  GVGSQDDIDMLGNRRIRTVGELIQNQFRIGLSRMERVVKERMSIADTANLTPKQLTNIRP 640

Query: 617  LSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            L+A  +E    +Q +  +D++      + +          +   R   +  D        
Sbjct: 641  LTAAIKEFFSSSQLSQFMDQENPLAELSNKRRISALGPGGLTRERAGFEVRDIHNSHYGR 700

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I     P   N      L       +   +       V   +   +       + A    
Sbjct: 701  ICPIETPEGPNIGLISYLTTYAKVNEYGFIETPYRKVVDGKVTDEIKY-----MPADEEN 755

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                  A  I    + GD   +    +   + + Q    +    Q   V         + 
Sbjct: 756  DHVIAQANEIKDGHLVGDKIIARIKGETVMVDRSQVDYADVSPRQIVSVATACVPFLEND 815

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMA 851
                             ++    P+ G   E  +        V+       +++  +V+ 
Sbjct: 816  DCTRALMGANMQRQAVPLMNPHSPFVGTGMEHVIARDSGSACVATGPGVVTYVDATKVVV 875

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
             +   G E+               +++  I+  G  V  G IL           +   + 
Sbjct: 876  AED-NGNEKTYELTKYRRSNASTCLNQRPIVWDGERVERGTILADGP-AMENGELALGQN 933

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE-LLARD 970
            +  A       +  D  +           D              S+ +E   IE    + 
Sbjct: 934  VTIAFMTWHGYNYEDAIIM---SEKMQSQDYYT-----------SVHIEEYDIECRETKL 979

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              +E      N+       L G+  V      K+  +L   +  +    Q  +  +    
Sbjct: 980  GPEEITRDIPNVAESACRNLDGRGIVMVGAEVKEGDILVGKVTPKGQTDQTPEEKLLMAI 1039

Query: 1031 VQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                   ++                 ++ K +   ++PPGV  VVKV++  KR I  GDK
Sbjct: 1040 FGEKSREVRDNSLKVPHGGAGIVHSIRVFKRKEDHELPPGVNEVVKVYIVQKRKISEGDK 1099

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNK                            GV SR+N                 
Sbjct: 1100 MAGRHGNK----------------------------GVISRIN----------------- 1114

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                        +       + ++ ++       +++      V       + GV  +TP
Sbjct: 1115 ---------PVEDMPYMSDGTPIDIMLNPFGVPSRMNIGQVLEVHLGFAAKQLGVKFATP 1165

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDG     +  +++ ++    G+ +LYDG TGE +D  ++VG +YM+KL HMV DK++A
Sbjct: 1166 VFDGVSNTDLRDIMKESNSSPDGKYVLYDGRTGEAYDDRISVGVMYMIKLAHMVDDKLHA 1225

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            R+TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA++VLQE+LT+KSDD+ GRT+ Y
Sbjct: 1226 RATGPYSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGASHVLQEILTVKSDDIAGRTKTY 1285

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            E+IV G D  E G PESF VLV E+QAL + + + +         +   +  K E
Sbjct: 1286 EAIVKGKDMPEAGIPESFRVLVHELQALAIDVRMMDDAGNEMDLKQMEQEELKEE 1340


>gi|284930472|gb|ADC30411.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
            [Mycoplasma gallisepticum str. R(high)]
          Length = 1389

 Score =  659 bits (1701), Expect = 0.0,   Method: Composition-based stats.
 Identities = 305/1434 (21%), Positives = 535/1434 (37%), Gaps = 121/1434 (8%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A          VR+ + K     +  +L  +Q  +Y  FL             L+    S
Sbjct: 6    AFHNTQYSPKVVRRDYSKVHNKYNPLNLPGIQVNAYKQFLEKE----------LEEIIGS 55

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
             FPI + +G   +EF   +   P+   ++      TY   L + L L+            
Sbjct: 56   YFPIKSPNGKYSVEFHGMKILDPQITKEEASAESKTYDASLYVNLSLVNHQTGTVKKISK 115

Query: 122  IKDIKEQS-IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF-DHDKGRASLSGKLL 179
                 +   IY  D+PLMT++G F++ GI++ VV+Q+ RSPG +  +  + + S S K  
Sbjct: 116  KSAKSKAEGIYFADIPLMTENGAFIVNGIEKFVVAQIVRSPGAYILNKSQVKLSNSRKRN 175

Query: 180  ---YACRIIPDQGLWMDIEF-DSKDIIHVRI-----DRRRKVPVTSFLMALGMDSEEILS 230
               Y C + P +G  M     ++KD +   +     +  +   +T+ L A G+   +I  
Sbjct: 176  QEGYICEVFPSKGTLMLFYIAENKDFVQAVVRDVGGESAKVFSITTLLKAFGLSEIKIKE 235

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             F          D+    L +        ++ + +                + L++ ++ 
Sbjct: 236  IF-------NNNDYILRSLESEFYNEKQILNEADI----------------AQLIRDIES 272

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              +    + S  +   +              +     ++++  E +  S      I  ++
Sbjct: 273  DRISK--VKSLPIDQKWKN-----------LVLDWYKLNQEKQELLNSSNPNPTKIESLN 319

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +    +R  +     K     L    R +           +S+    FF   +YDLS+
Sbjct: 320  T-HIGVVLRKLICEKAAKHVIQELSISTRSLDNVSQKEEISYQSILLQHFFQKKRYDLSS 378

Query: 411  VGRVKMNMRLNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             GR K   +L +      R I    K+    ++     L   +           +R+  +
Sbjct: 379  AGRHKFVRKLRVSERLYQRTIAQDIKDLDGNVVIKQGTLMLKEQLDLFKRLSKEKRLDII 438

Query: 468  GEM------LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             ++      L  Q+       E  I       +  + +     + + + +       S  
Sbjct: 439  KQIDFINPELNTQFTDVNTYEEVQIYVNNDLRNETTQIIGIDGSNESIETLTLADLISIV 498

Query: 522  LSQLEEHVNS--LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
               +    N      I H           + +++    M  +    Y +         + 
Sbjct: 499  SYIVNLPFNIGLYDDIDHLGNKRLKLINELLKSKVQTGM--MRIEKYIKDKLQTADGNNK 556

Query: 580  IGLVSSLTS-FARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDE 636
            +    +     + +      +   + V + K    V+  + +  +       Q   S   
Sbjct: 557  LADQDAENDPDSDLGTKSSNDLTVKSVINPKPFQIVIKDFFNTHQLTQFLDQQNPLSELT 616

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +      +     + E+  +    + +        +     +   L    +    +  N 
Sbjct: 617  NKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIETPEGMNIGLIMSLAFYATIDKNG 676

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                 P LK E   +   +E + A      I+A+ +     +D  +    + E  +    
Sbjct: 677  F-LMTPYLKVENGKITDKVEHLTALREDEYIIAEASS---YMDVAKDGTINNEKIIARYR 732

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            S  D+Y     Q    +    Q   V         +  +               +L  + 
Sbjct: 733  SSQDLYDPK--QVDYIDVSPKQVVSVAASLIPFLENDDSSRALMGANMQRQATPLLKPYS 790

Query: 817  PWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E  +   S  +V+     ++   +   +    +         +  V       
Sbjct: 791  PLVGTGVEYKIAQDSGMLVTAKNPGTVTYVDASKITVKGEDNKSTDYNLLKFVKSNKNTC 850

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+ VG ++     L    + K    +   + +L         +  D  +      
Sbjct: 851  YNQSPIVAVGDKIETNQALADGPSMKN-GELALGQNVLVGFTTWSGYNYEDAVI------ 903

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQN 994
                    I +R   D    SI ++   IE L  ++ D+E      NI       L  + 
Sbjct: 904  --------ISDRLFKDDVYSSIHIDEYTIECLRTKNGDEEITRDIPNISESAKRYLDEEG 955

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             +      K+  +L      +       +  +    +   V+ ++       +  +    
Sbjct: 956  VIMVGAEVKEGDILVGKTSPKGQVELTPEEKLIQAILGDKVKQVRESSLKVPNGGDGIVA 1015

Query: 1055 -NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K   I  GD++   VL +VKV+V  KR IQ GDK+AGRHGNKGI+S+I+  EDMP L+
Sbjct: 1016 GIKRFSIANGDELEDDVLELVKVYVVQKRKIQIGDKVAGRHGNKGIISKIVAQEDMPHLE 1075

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   L K         K   D       LE
Sbjct: 1076 DGTPLDILLNPLGVPSRMNIGQIFELHLGYAARELAKAKLIEACFDKKLADQLDTVFGLE 1135

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKS--------------------GVPVSTPVFDG 1213
            K          +       V  +A+                           ++TPVF+G
Sbjct: 1136 KSKTQSLIKNLVEHMKSIGVTSLAQTKNRVRTIDIDIVLKQLGLTYDDLAFKIATPVFEG 1195

Query: 1214 ADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
             + E + +++  A +D     G+  L DG TGEPF++P++VG +YMLKL+HMV DK++AR
Sbjct: 1196 VNMEDLKAIMSEAGIDPDKTEGKFKLIDGRTGEPFEKPISVGIMYMLKLDHMVDDKIHAR 1255

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            + G YS +TQQPLGGKS  GGQR GEMEVW +QAYGAA+ L+E+LTIKSDDV GR   Y 
Sbjct: 1256 AVGPYSKITQQPLGGKSQNGGQRFGEMEVWALQAYGAAHNLREILTIKSDDVRGRNMTYN 1315

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +IV G    E G PESF +L KE+Q LG+++++    +  +     + D +   
Sbjct: 1316 AIVKGLSIPEPGVPESFKLLTKELQGLGMTLNVLYDDSIENINNISVVDESLEP 1369


>gi|182676595|sp|A5FRK5|RPOB_DEHSB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1273

 Score =  659 bits (1701), Expect = 0.0,   Method: Composition-based stats.
 Identities = 369/1102 (33%), Positives = 541/1102 (49%), Gaps = 130/1102 (11%)

Query: 332  SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
             L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 200  LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYSRLRPGDPPN 259

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
               A  + N +FFD   YDL  VGR K+N RL L + +  + R + +EDI+AII+ ++ +
Sbjct: 260  ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPSREVGENRALTREDIVAIIQRIIMV 319

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
             NG+ T DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 320  NNGQDTPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEMVTPSALVNI 379

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 380  RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 439

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-----VVYLSAME 621
            GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV      ND     +   + + 
Sbjct: 440  GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNNDKKLVGLKLKTEIS 499

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+ + +A A S++ ED       +                   D S    VS     +P 
Sbjct: 500  EKGKVLAAAGSTISEDSFKIISKLPE----------------CDISVMPFVSAEVKYMPA 543

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             E D   R ++     R        +        E  V          +    ++ +D  
Sbjct: 544  DEED---RYIIAQANTRLDEKGYFLDDRIEARSAERYVV---------EPPDKIDYMDVS 591

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMK---FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               I SV   L P     D  R +     QR        + P+V  G             
Sbjct: 592  PKQIFSVAASLIPFLEHDDANRALMGANMQRQAVPLLRAEAPMVATG------------- 638

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                             M      +   ++ ++      V +S+     E +   T  G 
Sbjct: 639  -----------------MEREAARYSGQVIFAKHA---GVASSV---TSEKIIIRTAEGG 675

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +       V       I++  II  G ++  G +L      +    +   +  + A   
Sbjct: 676  HDEYLLKKFVRTNQGTCINQHAIINKGQKIAAGQVLADSSATEN-GELALGQNCVVAFMS 734

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDE 974
             +  +  D  +     +S  +V    F    I K+E      +  +E + RD     ++ 
Sbjct: 735  WQGFNYEDAII-----LSERLVREDAFTSIHITKHELEARDTKLGVEEITRDIPNVGEES 789

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD +   R+   +   + + G    K  T LS++   +  R+ + + A + +     
Sbjct: 790  LRELDEDGIIRIGAEVGPDDILVGKITPKGETELSAE--EKLLRAIFGEKAREVKDT--- 844

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                                 +I     GDD+P  V + V+V+VA KR +  GDK+AGRH
Sbjct: 845  ------SLRMPHGEWGKVINVRIFSRDSGDDLPARVNKWVQVWVAQKRKVSVGDKLAGRH 898

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGWA   LG ++ +
Sbjct: 899  GNKGVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGWAGHLLGFRVAT 958

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDG 1213
             + D   +  I    +        G+      +    +    A +W          +FD 
Sbjct: 959  PVFDGADDTVIEDALARSWLSAKAGAIDMSPENKRPSADAHKAIEWIKQQGFDGKKIFDE 1018

Query: 1214 -----ADEEAINSMLRMADLDES-------------------------GQSILYDGLTGE 1243
                 A E ++   L+   +D S                         G+S+L DG TGE
Sbjct: 1019 KHPGLAKEVSLKLWLKDMGVDASALSGAELEKKAYDVSSQSRLPSPIVGKSVLRDGRTGE 1078

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FD+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQR GEMEVW + 
Sbjct: 1079 TFDQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQRFGEMEVWAMY 1138

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYG A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVKE+Q+LGL++++
Sbjct: 1139 AYGTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVLQPGVPESFKVLVKELQSLGLAVEV 1198

Query: 1364 ENSRTKNSAKMEEIPDFNKCEL 1385
             N   K  A  E++   N+  L
Sbjct: 1199 INEEVK-IAPSEKVSSLNEGNL 1219



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 99/361 (27%), Positives = 168/361 (46%), Gaps = 42/361 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
           +RK + + PE++++P+LIE+Q  S+  F            EGL+   + + PI  F G  
Sbjct: 15  IRKSYAQLPEVVNVPNLIEMQLQSFVWF----------QEEGLRELIEEISPIKDFVGNR 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+    +C  RD TY+VPL +  RLIV         K+  +IKE   +
Sbjct: 65  LELEFIGYEFREPRLSEYECTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDL 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT  GTF+  G +R+VVSQL RSPG++F         +G+ L    +IP +G 
Sbjct: 116 FFGDIPLMTALGTFITSGTERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGA 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PV++ L A+G   + +IL+ F    V     +      
Sbjct: 174 WLEFETSNRDVISVKIDGRRKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQS 230

Query: 250 SAADLMVGAKVSSSLVDI----DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS---- 300
           S     +     S+L+DI      G+    ++ +KL + +    +   +  +G       
Sbjct: 231 SIDRDPLIKDEISALIDIYSRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRR 290

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                 +      +  + +      I +          ++ + +  IR +  L  +    
Sbjct: 291 LELPSREVGENRALTREDIVAIIQRIIMVNNGQDTPDDIDHLGNRRIRTVGELVQNQFRI 350

Query: 355 N 355
            
Sbjct: 351 G 351


>gi|307297335|ref|ZP_07577141.1| DNA-directed RNA polymerase, beta subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916595|gb|EFN46977.1| DNA-directed RNA polymerase, beta subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 1174

 Score =  659 bits (1700), Expect = 0.0,   Method: Composition-based stats.
 Identities = 369/973 (37%), Positives = 564/973 (57%), Gaps = 113/973 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  FG+  E ++IP+LIE+Q  S++ F+          NEGL    K   PI +   
Sbjct: 8   KRERWVFGRVYEPLEIPNLIEIQTRSFEWFI----------NEGLLNVLKKYSPIKSQIQ 57

Query: 71  A---------AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       L+FV+      K  + +C  + LTY+VPL +T+R+             
Sbjct: 58  RSDLKKGEKGFSLDFVATRIGEAKHSIQECKDKGLTYSVPLYVTVRITDL---------Y 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IKE+  + G LP MT + +F+I G +R++V+QL RSPG++F  +  +A      +Y 
Sbjct: 109 TGEIKEEEAFFGYLPYMTDNASFIINGAERVIVNQLVRSPGVYFVDEPTKAVSGSLPIYV 168

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +P +G W +I  +    I+  RIDRRRK+    FL ALG +++ ++L  F  +  Y 
Sbjct: 169 AHFLPVKGAWYEILLNPNKQIMQARIDRRRKLNFFVFLKALGYENDLDLLRLF--ENEYD 226

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +        + ++   K          G+ + E G  LT  ++    E  VK + + 
Sbjct: 227 GSDEDELLANVGSMILEDVKTPG-------GDLIAEKGTLLTEEIIARAIEADVKTIKMP 279

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                                      +    +L++ +   + +                
Sbjct: 280 LP-----------------------IAMKTFNALQKTYGEGMTE---------------- 300

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                       DA ++++R +RPG++   + A+S    L+F  D++D S VGR K+N R
Sbjct: 301 -----------DDAYIELFRKLRPGEIPRINAAKSYIANLYFSPDRFDFSDVGRYKVNSR 349

Query: 420 LNL------------------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           L                    D  ++   +   D++   + L ++ +    +D  D+LGN
Sbjct: 350 LKKVYQDYLKEVEGKKVSKDTDYSEESSILTVLDVVLAARHLTEIESRPELLDTKDHLGN 409

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSS 520
           +RVR+VGE+++ ++    +++ + ++E+++     D +  Q L+N + +++ + +FF +S
Sbjct: 410 KRVRTVGELMETEFEKAFIKIHKLLEEKLTIYTSFDKISVQSLVNVRTLMTTLHQFFATS 469

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + VN L+ +T+ RRLSA+G GG+ R  A  E+RDVH +HYGR+CP ET EG NI
Sbjct: 470 QLSQFMDQVNPLAELTNKRRLSAIGPGGLKREHARFEVRDVHHSHYGRMCPIETPEGANI 529

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL +FA+++ YGF+ TPYRKV  G VTND+VYL+A EEE   IA +   +DE G+ 
Sbjct: 530 GLMTSLATFAKIDKYGFLLTPYRKVQKGAVTNDIVYLAADEEERYNIAHSTVDMDEKGNI 589

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E V  R AGE   V RE++D++  SPKQ+VSI+ SLIPFLENDD+NR LMG NMQRQA
Sbjct: 590 VDENVEIRYAGEVRYVNREEVDYMSVSPKQIVSISTSLIPFLENDDANRALMGSNMQRQA 649

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP-----S 755
           VP++KAEAP VGTG+E V A+ SG  +++K  G V  VD  RI+++ ++    P      
Sbjct: 650 VPVVKAEAPIVGTGVEGVAARDSGYVVLSKHRGKVVSVDGRRIIVQRIDEKGKPELDERG 709

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
               D+Y L KF R+NQ+T VNQRP+V VG+ V+    IADGPST++G+LALG+N+LVAF
Sbjct: 710 KPIEDVYTLHKFVRTNQDTAVNQRPIVSVGEIVQTGTPIADGPSTEMGELALGKNVLVAF 769

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++L+++ ++ +D FT+IH+E +E +ARDT+LGPEEIT DIPNVS+E LKN
Sbjct: 770 MPWEGYNFEDAILVNQELLEDDTFTTIHVEMYETIARDTQLGPEEITADIPNVSKESLKN 829

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+ +GA V   DILVGK+TPKGES  TPEEK++R++FG++  DV+D+SL++P GV
Sbjct: 830 LDESGIVRIGAYVTSQDILVGKVTPKGESETTPEEKIIRSVFGDRGRDVKDSSLKLPHGV 889

Query: 936 SGTVVDVRIFNRH 948
            G V+DV++F + 
Sbjct: 890 EGRVIDVKVFEKE 902



 Score =  434 bits (1115), Expect = e-119,   Method: Composition-based stats.
 Identities = 164/501 (32%), Positives = 237/501 (47%), Gaps = 68/501 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV------PSG 934
            I+ VG  V  G  +    + +    +   + +L A    +  +  D  L         + 
Sbjct: 735  IVSVGEIVQTGTPIADGPSTE-MGELALGKNVLVAFMPWEGYNFEDAILVNQELLEDDTF 793

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             +  V       R      E   +      +   ++  DE  I+    Y    +IL G+ 
Sbjct: 794  TTIHVEMYETIARDTQLGPEEITADIPNVSKESLKNL-DESGIVRIGAYVTSQDILVGKV 852

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         +   +  +  R            V+ +   L    E     +     
Sbjct: 853  TPKGESETTPEEKIIRSVFGDRGRD-----------VKDSSLKLPHGVEGRVIDV----- 896

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+ + +   ++  G+ ++VKVFV +++P+  GDK+AGRHGNKG+VS I+P EDMPFL D
Sbjct: 897  -KVFEKEEVSELGSGINKLVKVFVGIRKPLDVGDKLAGRHGNKGVVSNIIPKEDMPFLPD 955

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+ +VL+PLGVPSRMNVGQ+ ETHLGW      +   + I D     +I        K
Sbjct: 956  GTPIQLVLSPLGVPSRMNVGQVLETHLGWLGKLTNRYFATPIFDGATEEEIMTELYEARK 1015

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
              G                                  DG  E+     L+      +G+ 
Sbjct: 1016 RFGLE--------------------------------DGDSED-----LK------TGKV 1032

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L DG +G PFD P+ VG +YMLKL H+  DK++ARSTG YSL+ QQPLGGK++ GGQR 
Sbjct: 1033 TLRDGRSGNPFDYPIVVGVMYMLKLVHIAKDKIHARSTGPYSLIHQQPLGGKAHFGGQRF 1092

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ L EMLTIKSDD+ GR  VY++I+ G +  E G PESF VL+KE+
Sbjct: 1093 GEMEVWALEAYGAAHTLNEMLTIKSDDIKGRNDVYKAILKGINIPEPGIPESFKVLIKEL 1152

Query: 1355 QALGLSIDLENSRTKNSAKME 1375
            Q L L + + +         +
Sbjct: 1153 QGLSLDVKVFDQNNVELDVDK 1173


>gi|219849578|ref|YP_002464011.1| DNA-directed RNA polymerase subunit beta [Chloroflexus aggregans DSM
            9485]
 gi|254765281|sp|B8G4U9|RPOB_CHLAD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|219543837|gb|ACL25575.1| DNA-directed RNA polymerase, beta subunit [Chloroflexus aggregans DSM
            9485]
          Length = 1227

 Score =  659 bits (1700), Expect = 0.0,   Method: Composition-based stats.
 Identities = 346/1066 (32%), Positives = 488/1066 (45%), Gaps = 108/1066 (10%)

Query: 330  EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            +  L++  H+E       +VD+V  + YI+ T+  D + + K+ALL++Y+ +RPGD  T 
Sbjct: 234  DNELDKYGHNEHLIELFRHVDTVAEHLYIQATIDKDPSHNAKEALLELYKRLRPGDPPTL 293

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRL---------NLDTPDDVRHIRKEDIIAII 440
              A ++   L F+  +YDL+ VGR K+N  L                VR +   DI  I+
Sbjct: 294  ENARTLIESLLFNPRRYDLAKVGRYKLNKNLWERDARRDGPKAPDLSVRVLLPRDIFRIV 353

Query: 441  KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
            + ++ L NG G  DDID+LGNRRVR+VGE+++ Q+R+GLLR+ER +KER+S  D  S  P
Sbjct: 354  EQMILLNNGYGRPDDIDHLGNRRVRTVGELIQQQFRVGLLRLERVVKERMSLQDPASATP 413

Query: 501  QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
              LIN +PVV+A+ EFF  SQLSQ  +  N L+ +T+ RRLSALG GG++R RAG E+RD
Sbjct: 414  NGLINIRPVVAAMREFFGGSQLSQFMDQTNPLAELTNKRRLSALGPGGLSRDRAGFEVRD 473

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            VH +HYGRICP ET EG NIGL+ ++++FARVN  GF+ETPYRKV +             
Sbjct: 474  VHHSHYGRICPVETPEGPNIGLIGTMSTFARVNEMGFLETPYRKVYNSID---------- 523

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                      N+ +  +       V     G+ I     ++D    + +  + +    I 
Sbjct: 524  ----------NAQVWREKGILLRDVRDLRTGDLIAAKGTRVDDQ-IARQITIGLLRGQIL 572

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV--AKRAGIVEQV 738
              +  D N   +      +    L      +      +    S       A        V
Sbjct: 573  REDVVDPNTGELIAEAGTEINRALAERIVNLPMKQIKIRPVVSQEVDYLSADEEDRFVIV 632

Query: 739  DAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             A   +               G D       +    +    Q   V            A+
Sbjct: 633  QANAPLDEHNRFLDTTVSCRFGEDFVTERVERVDYMDVSPKQVVSVSTSLIPFLEHDDAN 692

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMAR 852
                          +L    P  G   E         V     + V  S       V   
Sbjct: 693  RALMGSNMQRQAVPLLRPDAPIVGTGMEYRTARDSGQVVVARRDGVVVSATGNRIIVEED 752

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            D   G     R    +       I++   +  G +V  GD++    +   +  +   + +
Sbjct: 753  D---GKRTEYRLRKFMRSNQDTCINQRPSVVRGQQVRAGDVIADSSST-DQGELALGQNV 808

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L     VS  +V   IF    I+K E      +   E + RD  
Sbjct: 809  LVAYMPWEGGNFEDAIL-----VSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIP 863

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +      RN+  R   I  G           K T      ++   R     F  +  +V+
Sbjct: 864  NVGQDSLRNLDER-GIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVK 922

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             +   +          +      K+     G ++P GV + V+V +  KR I +GDKMAG
Sbjct: 923  DSSLRVPNGVRGKVIDV------KVFSRSEGAELPVGVNQTVRVLLCQKRKISAGDKMAG 976

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL DG PVDI+LNP+GVPSRMN+GQI ETHLGWA   LG ++
Sbjct: 977  RHGNKGVVSRVLPMEDMPFLPDGRPVDIILNPIGVPSRMNIGQILETHLGWAAARLGFRV 1036

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D      I  L                                            
Sbjct: 1037 ATPVFDGAHEDQIKDLLVQAGLPADGKVTL------------------------------ 1066

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G++       GE FD PVTVGY YMLKL H+V DK++ARST
Sbjct: 1067 -----------------YDGRT-------GEKFDHPVTVGYAYMLKLAHLVEDKIHARST 1102

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+I
Sbjct: 1103 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKTYEAI 1162

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G    E G PESF VL+KE+Q+LGLS+++ ++  K     +++ 
Sbjct: 1163 VKGEPIQEAGVPESFKVLIKELQSLGLSVEVLSADEKPVELSDDLD 1208



 Score =  597 bits (1538), Expect = e-168,   Method: Composition-based stats.
 Identities = 320/971 (32%), Positives = 485/971 (49%), Gaps = 100/971 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLE 75
           F +  + ID+P LIE Q  S++ F            EGL+  F  + PIT F+G    L 
Sbjct: 34  FARIKDAIDLPLLIETQLKSFEWF----------KREGLRELFDEISPITDFTGKNLELH 83

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F  Y F  P++D  +C  RDLTYA PL++ + L +          +  +IKE  I++GD 
Sbjct: 84  FREYTFGEPRYDEFECRDRDLTYAAPLRVKVELRIL---------TTGEIKESEIFLGDF 134

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           P+MT +GTFV  G +R+VVSQL RSPG++F  +K     SG+ L+  ++IP++G W++ E
Sbjct: 135 PMMTDNGTFVYNGAERVVVSQLIRSPGVYFKDEKDPT--SGRALHTAKLIPNRGAWLEFE 192

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMAL--------------------GMDSEE-ILSTFYP 234
            + +D+I V++DR+RK+PVT  L A+                         E ++  F  
Sbjct: 193 TNKRDVISVKVDRKRKIPVTILLRAISAWIANEDGSGRWAPDNELDKYGHNEHLIELFRH 252

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV 293
               ++                   +      +  G+   +E+ + L   LL + +   +
Sbjct: 253 VDTVAEHLYIQATIDKDPSHNAKEALLELYKRLRPGDPPTLENARTLIESLLFNPRRYDL 312

Query: 294 KFLGITS-----------------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
             +G                      L    +    +     ++ +          ++ +
Sbjct: 313 AKVGRYKLNKNLWERDARRDGPKAPDLSVRVLLPRDIFRIVEQMILLNNGYGRPDDIDHL 372

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            +  +R +  L              +V ++   +  A      ++    +     A   F
Sbjct: 373 GNRRVRTVGELIQQQFRVGLLRLERVVKERMSLQDPASATPNGLIN---IRPVVAAMREF 429

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                 S   D +       N R    +      + ++     ++ +     G+  I  +
Sbjct: 430 FGGSQLSQFMDQTNPLAELTNKR--RLSALGPGGLSRDRAGFEVRDVHHSHYGR--ICPV 485

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           +      +  +G M        +  +E   ++  +S+D   V  +  I  + V       
Sbjct: 486 ETPEGPNIGLIGTMSTFARVNEMGFLETPYRKVYNSIDNAQVWREKGILLRDVRDLRTGD 545

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             +++ +++++ +     I            G+ R +   E           + P     
Sbjct: 546 LIAAKGTRVDDQIARQITI------------GLLRGQILRED---------VVDPNTGEL 584

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
               G   +     R+      +   R V    V+ +V YLSA EE+   I QAN+ LDE
Sbjct: 585 IAEAGTEINRALAERIVNLPMKQIKIRPV----VSQEVDYLSADEEDRFVIVQANAPLDE 640

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
              F +  V CR   + +    E++D++D SPKQVVS++ SLIPFLE+DD+NR LMG NM
Sbjct: 641 HNRFLDTTVSCRFGEDFVTERVERVDYMDVSPKQVVSVSTSLIPFLEHDDANRALMGSNM 700

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPLL+ +AP VGTGME   A+ SG  +VA+R G+V      RI++   +G      
Sbjct: 701 QRQAVPLLRPDAPIVGTGMEYRTARDSGQVVVARRDGVVVSATGNRIIVEEDDGKRTE-- 758

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                YRL KF RSNQ+TC+NQRP V  G +VR  D+IAD  STD G+LALG+N+LVA+M
Sbjct: 759 -----YRLRKFMRSNQDTCINQRPSVVRGQQVRAGDVIADSSSTDQGELALGQNVLVAYM 813

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW G NFED++L+SER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV ++ L+N+
Sbjct: 814 PWEGGNFEDAILVSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQDSLRNL 873

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV P DILVGKITPKGE+ +T EE+LLRAIFGEKA +V+D+SLRVP+GV 
Sbjct: 874 DERGIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVR 933

Query: 937 GTVVDVRIFNR 947
           G V+DV++F+R
Sbjct: 934 GKVIDVKVFSR 944


>gi|147669223|ref|YP_001214041.1| DNA-directed RNA polymerase subunit beta [Dehalococcoides sp. BAV1]
 gi|146270171|gb|ABQ17163.1| DNA-directed RNA polymerase subunit beta [Dehalococcoides sp. BAV1]
          Length = 1240

 Score =  659 bits (1699), Expect = 0.0,   Method: Composition-based stats.
 Identities = 369/1102 (33%), Positives = 541/1102 (49%), Gaps = 130/1102 (11%)

Query: 332  SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
             L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 167  LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYSRLRPGDPPN 226

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
               A  + N +FFD   YDL  VGR K+N RL L + +  + R + +EDI+AII+ ++ +
Sbjct: 227  ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPSREVGENRALTREDIVAIIQRIIMV 286

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
             NG+ T DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 287  NNGQDTPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEMVTPSALVNI 346

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 347  RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 406

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-----VVYLSAME 621
            GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV      ND     +   + + 
Sbjct: 407  GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNNDKKLVGLKLKTEIS 466

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+ + +A A S++ ED       +                   D S    VS     +P 
Sbjct: 467  EKGKVLAAAGSTISEDSFKIISKLPE----------------CDISVMPFVSAEVKYMPA 510

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             E D   R ++     R        +        E  V          +    ++ +D  
Sbjct: 511  DEED---RYIIAQANTRLDEKGYFLDDRIEARSAERYVV---------EPPDKIDYMDVS 558

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMK---FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               I SV   L P     D  R +     QR        + P+V  G             
Sbjct: 559  PKQIFSVAASLIPFLEHDDANRALMGANMQRQAVPLLRAEAPMVATG------------- 605

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                             M      +   ++ ++      V +S+     E +   T  G 
Sbjct: 606  -----------------MEREAARYSGQVIFAKHA---GVASSV---TSEKIIIRTAEGG 642

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +       V       I++  II  G ++  G +L      +    +   +  + A   
Sbjct: 643  HDEYLLKKFVRTNQGTCINQHAIINKGQKIAAGQVLADSSATEN-GELALGQNCVVAFMS 701

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDE 974
             +  +  D  +     +S  +V    F    I K+E      +  +E + RD     ++ 
Sbjct: 702  WQGFNYEDAII-----LSERLVREDAFTSIHITKHELEARDTKLGVEEITRDIPNVGEES 756

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD +   R+   +   + + G    K  T LS++   +  R+ + + A + +     
Sbjct: 757  LRELDEDGIIRIGAEVGPDDILVGKITPKGETELSAE--EKLLRAIFGEKAREVKDT--- 811

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                                 +I     GDD+P  V + V+V+VA KR +  GDK+AGRH
Sbjct: 812  ------SLRMPHGEWGKVINVRIFSRDSGDDLPARVNKWVQVWVAQKRKVSVGDKLAGRH 865

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGWA   LG ++ +
Sbjct: 866  GNKGVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGWAGHLLGFRVAT 925

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDG 1213
             + D   +  I    +        G+      +    +    A +W          +FD 
Sbjct: 926  PVFDGADDTVIEDALARSWLSAKAGAIDMSPENKRPSADAHKAIEWIKQQGFDGKKIFDE 985

Query: 1214 -----ADEEAINSMLRMADLDES-------------------------GQSILYDGLTGE 1243
                 A E ++   L+   +D S                         G+S+L DG TGE
Sbjct: 986  KHPGLAKEVSLKLWLKDMGVDASALSGAELEKKAYDVSSQSRLPSPIVGKSVLRDGRTGE 1045

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FD+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQR GEMEVW + 
Sbjct: 1046 TFDQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQRFGEMEVWAMY 1105

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYG A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVKE+Q+LGL++++
Sbjct: 1106 AYGTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVLQPGVPESFKVLVKELQSLGLAVEV 1165

Query: 1364 ENSRTKNSAKMEEIPDFNKCEL 1385
             N   K  A  E++   N+  L
Sbjct: 1166 INEEVK-IAPSEKVSSLNEGNL 1186



 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 91/342 (26%), Positives = 152/342 (44%), Gaps = 42/342 (12%)

Query: 32  VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-AMLEFVSYEFDPPKFDVDD 90
           +Q  S+  F            EGL+   + + PI  F G    LEF+ YEF  P+    +
Sbjct: 1   MQLQSFVWF----------QEEGLRELIEEISPIKDFVGNRLELEFIGYEFREPRLSEYE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SIYMGDLPLMTKDGTFVIKGI 149
           C  RD TY+VPL +  RLIV         K+  +IKE   ++ GD+PLMT  GTF+  G 
Sbjct: 51  CTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDLFFGDIPLMTALGTFITSGT 101

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R+VVSQL RSPG++F         +G+ L    +IP +G W++ E  ++D+I V+ID R
Sbjct: 102 ERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGAWLEFETSNRDVISVKIDGR 159

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI- 267
           RK+PV++ L A+G   + +IL+ F    V     +      S     +     S+L+DI 
Sbjct: 160 RKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQSSIDRDPLIKDEISALIDIY 216

Query: 268 ---DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS----------DCLCGLYVAEDIV 313
                G+    ++ +KL + +    +   +  +G             +      +  + +
Sbjct: 217 SRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPSREVGENRALTREDI 276

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                 I +          ++ + +  IR +  L  +     
Sbjct: 277 VAIIQRIIMVNNGQDTPDDIDHLGNRRIRTVGELVQNQFRIG 318


>gi|294660312|ref|NP_852995.2| DNA-directed RNA polymerase subunit beta [Mycoplasma gallisepticum
            str. R(low)]
 gi|33860205|sp|P47715|RPOB_MYCGA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|284811968|gb|AAP56563.2| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
            [Mycoplasma gallisepticum str. R(low)]
          Length = 1390

 Score =  658 bits (1698), Expect = 0.0,   Method: Composition-based stats.
 Identities = 307/1436 (21%), Positives = 535/1436 (37%), Gaps = 124/1436 (8%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A          VR+ + K     +  +L  +Q  +Y  FL             L+    S
Sbjct: 6    AFHNTQYSPKVVRRDYSKVHNKYNPLNLPGIQVNAYKQFLEKE----------LEEIIGS 55

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
             FPI + +G   +EF   +   P+   ++      TY   L + L L+            
Sbjct: 56   YFPIKSPNGKYSVEFHGMKILDPQITKEEASAESKTYDASLYVNLSLVNHQTGTVKKISK 115

Query: 122  IKDIKEQS-IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF-DHDKGRASLSGKLL 179
                 +   IY  D+PLMT++G F++ GI++ VV+Q+ RSPG +  +  + + S S K  
Sbjct: 116  KSAKSKAEGIYFADIPLMTENGAFIVNGIEKFVVAQIVRSPGAYILNKSQVKLSNSRKRN 175

Query: 180  ---YACRIIPDQGLWMDIEF-DSKDIIHVRI-----DRRRKVPVTSFLMALGMDSEEILS 230
               Y C + P +G  M     ++KD +   +     +  +   +T+ L A G+   +I  
Sbjct: 176  QEGYICEVFPSKGTLMLFYIAENKDFVQAVVRDVGGESAKVFSITTLLKAFGLSEIKIKE 235

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             F          D+    L +        ++ + +                + L++ ++ 
Sbjct: 236  IF-------NNNDYILRSLESEFYNEKQILNEADI----------------AQLIRDIES 272

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              +    + S  +   +              +     ++++  E +  S      I  ++
Sbjct: 273  DRISK--VKSLPIDQKWKN-----------LVLDWYKLNQEKQELLNSSNPNPTKIESLN 319

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +    +R  +     K     L    R +           +S+    FF   +YDLS+
Sbjct: 320  T-HIGVVLRKLICEKAAKHVIQELSISTRSLDNVSQKEEISYQSILLQHFFQKKRYDLSS 378

Query: 411  VGRVKMNMRLNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             GR K   +L +      R I    K+    ++     L   +           +R+  +
Sbjct: 379  AGRHKFVRKLRVSERLYQRTIAQDIKDLDGNVVIKQGTLMLKEQLDLFKRLSKEKRLDII 438

Query: 468  GEM------LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             ++      L  Q+       E  I       +  + +     + + + +       S  
Sbjct: 439  KQIDFINPELNTQFTDVNTYEEVQIYVNNDLRNETTQIIGIDGSNESIETLTLADLISIV 498

Query: 522  LSQLEEHVNS--LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
               +    N      I H           + +++    M  +    Y +         + 
Sbjct: 499  SYIVNLPFNIGLYDDIDHLGNKRLKLINELLKSKVQTGM--MRIEKYIKDKLQTADGNNK 556

Query: 580  IGLVSSLTS-FARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDE 636
            +    +     + +      +   + V + K    V+  + +  +       Q   S   
Sbjct: 557  LADQDAENDPDSDLGTKSSNDLTVKSVINPKPFQIVIKDFFNTHQLTQFLDQQNPLSELT 616

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +      +     + E+  +    + +        +     +   L    +    +  N 
Sbjct: 617  NKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIETPEGMNIGLIMSLAFYATIDKNG 676

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                 P LK E   +   +E + A      I+A+ +     +D  +    + E  +    
Sbjct: 677  F-LMTPYLKVENGKITDKVEHLTALREDEYIIAEASS---YMDVAKDGTINNEKIIARYR 732

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            S  D+Y     Q    +    Q   V         +  +               +L  + 
Sbjct: 733  SSQDLYDPK--QVDYIDVSPKQVVSVAASLIPFLENDDSSRALMGANMQRQATPLLKPYS 790

Query: 817  PWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E  +   S  +V+     ++   +   +    +         +  V       
Sbjct: 791  PLVGTGVEYKIAQDSGMLVTAKNPGTVTYVDASKITVKGEDNKSTDYNLLKFVKSNKNTC 850

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+ VG ++     L    + K    +   + +L         +  D  +      
Sbjct: 851  YNQSPIVAVGDKIETNQALADGPSMKN-GELALGQNVLVGFTTWSGYNYEDAVI------ 903

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQN 994
                    I +R   D    SI ++   IE L  ++ D+E      NI       L  + 
Sbjct: 904  --------ISDRLFKDDVYSSIHIDEYTIECLRTKNGDEEITRDIPNISESAKRYLDEEG 955

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             +      K+  +L      +       +  +    +   V+ ++       +  +    
Sbjct: 956  VIMVGAEVKEGDILVGKTSPKGQVELTPEEKLIQAILGDKVKQVRESSLKVPNGGDGIVA 1015

Query: 1055 -NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K   I  GD++   VL +VKV+V  KR IQ GDK+AGRHGNKGI+S+I+  EDMP L+
Sbjct: 1016 GIKRFSIANGDELEDDVLELVKVYVVQKRKIQIGDKVAGRHGNKGIISKIVAQEDMPHLE 1075

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   L K         K   D       LE
Sbjct: 1076 DGTPLDILLNPLGVPSRMNIGQIFELHLGYAARELAKAKLIEACFDKKLADQLDTVFGLE 1135

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKS--------------------GVPVSTPVFDG 1213
            K          +       V  +A+                           ++TPVF+G
Sbjct: 1136 KSKTQSLIKNLVEHMKSIGVTSLAQTKNRVRTIDIDIVLKQLGLTYDDLAFKIATPVFEG 1195

Query: 1214 ADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
             + E + +++  A +D     G+  L DG TGEPF++P++VG +YMLKL+HMV DK++AR
Sbjct: 1196 VNMEDLKAIMSEAGIDPDKTEGKFKLIDGRTGEPFEKPISVGIMYMLKLDHMVDDKIHAR 1255

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            + G YS +TQQPLGGKS  GGQR GEMEVW +QAYGAA+ L+E+LTIKSDDV GR   Y 
Sbjct: 1256 AVGPYSKITQQPLGGKSQNGGQRFGEMEVWALQAYGAAHNLREILTIKSDDVRGRNMTYN 1315

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALG--LSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +IV G    E G PESF +L KE+Q LG  L++ L +  +  +     + D +   
Sbjct: 1316 AIVKGLSIPEPGVPESFKLLTKELQGLGMTLNV-LYDDDSIENINNISVVDESLEP 1370


>gi|270307965|ref|YP_003330023.1| DNA-directed RNA polymerase beta subunit [Dehalococcoides sp. VS]
 gi|270153857|gb|ACZ61695.1| DNA-directed RNA polymerase beta subunit [Dehalococcoides sp. VS]
          Length = 1272

 Score =  657 bits (1696), Expect = 0.0,   Method: Composition-based stats.
 Identities = 356/1094 (32%), Positives = 540/1094 (49%), Gaps = 133/1094 (12%)

Query: 332  SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
             L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 200  LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYNRLRPGDPPN 259

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
               A  + N +FFD   YDL  VGR K+N RL L   +  + R + +EDI+AII+ ++ +
Sbjct: 260  ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPAREVGENRALTREDIVAIIQRIIMV 319

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
             NG+ T DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 320  NNGQDTPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEMVTPSALVNI 379

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 380  RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 439

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-----VVYLSAME 621
            GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV      +D     +   + + 
Sbjct: 440  GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNSDKKLVGLKLKTEVS 499

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+ + +A A + + ED       +   C  + +     ++ ++ A  +    IA +    
Sbjct: 500  EKGKVLAAAGTIITEDSFKLISKLP-ECDIQVMPFVSAEVKYMPADEEDRYIIAQANTRL 558

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             +        +   +  + V  ++         +          ++ A     +E  DA 
Sbjct: 559  DDKGYFLDERIEARLAERYV--IEPPEKIDYMDVSPKQIF----SVAASLIPFLEHDDAN 612

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            R ++ +                    QR        + P+V  G                
Sbjct: 613  RALMGAN------------------MQRQAVPLLRAEAPMVATG---------------- 638

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                          M      +   ++ ++R     V TS+     E +   T  G  + 
Sbjct: 639  --------------MEREAARYSGQVIFAKRA---GVATSV---TSEKIIIRTANGGHDE 678

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                  V       I++  +I  G ++  G +L      +    +   +  + A    + 
Sbjct: 679  YLLKKFVRTNQGTCINQHAVINKGQKIEVGQVLADSSATEN-GELALGQNCVVAFMSWQG 737

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDEQVI 977
             +  D  +     +S  +V    F    I K+E      +  +E + RD     ++    
Sbjct: 738  FNYEDAII-----LSERLVREDAFTSIHITKHELEARDTKLGVEEITRDIPNVGEESLRE 792

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +   R+   +   + + G    K  T LS++   +  R+ + + A + +        
Sbjct: 793  LDEDGIIRIGAEVGPDDILVGKITPKGETELSAE--EKLLRAIFGEKAREVKDT------ 844

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                              ++     GDD+P  V + V+V+VA KR +  GDK+AGRHGNK
Sbjct: 845  ---SLRMPHGEWGKVINVRVFSRDSGDDLPARVNKWVQVWVAQKRKVSVGDKLAGRHGNK 901

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGWA   LG ++ + + 
Sbjct: 902  GVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGWAGHLLGFRVATPVF 961

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG---- 1213
            D   +  I    +         S      D   ++    A+  K+   +    FDG    
Sbjct: 962  DGADDTAIEDALARSWL-----STKAGAIDMSPENKRPSADNAKAIEWIKQQGFDGKKIF 1016

Query: 1214 -------ADEEAINSMLRMADLDES-------------------------GQSILYDGLT 1241
                   A E ++   L+   +D S                         G+S+L DG T
Sbjct: 1017 DEKHPGLAKEVSLKLWLKDMGVDASALSGAELEKRAYEVSSQNRLPSPIVGKSVLRDGRT 1076

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE FD+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQR GEMEVW 
Sbjct: 1077 GETFDQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQRFGEMEVWA 1136

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            + AYG A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVKE+Q+LGL++
Sbjct: 1137 MYAYGTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVLQPGVPESFKVLVKELQSLGLAV 1196

Query: 1362 DLENSRTKNSAKME 1375
            ++ N   K +   +
Sbjct: 1197 EVINEEVKIAPSEK 1210



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 99/361 (27%), Positives = 168/361 (46%), Gaps = 42/361 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
           +RK + + PE++++P+LIE+Q  S+  F            EGL+   + + PI  F G  
Sbjct: 15  IRKSYAQLPEVVNVPNLIEMQLQSFVWF----------QEEGLRELIEEISPIKDFVGNR 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+    +C  RD TY+VPL +  RLIV         K+  +IKE   +
Sbjct: 65  LELEFIGYEFREPRLSEYECTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDL 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT  GTF+  G +R+VVSQL RSPG++F         +G+ L    +IP +G 
Sbjct: 116 FFGDIPLMTALGTFITSGTERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGA 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PV++ L A+G   + +IL+ F    V     +      
Sbjct: 174 WLEFETSNRDVISVKIDGRRKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQS 230

Query: 250 SAADLMVGAKVSSSLVDI----DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS---- 300
           S     +     S+L+DI      G+    ++ +KL + +    +   +  +G       
Sbjct: 231 SIDRDPLIKDEISALIDIYNRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRR 290

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                 +      +  + +      I +          ++ + +  IR +  L  +    
Sbjct: 291 LELPAREVGENRALTREDIVAIIQRIIMVNNGQDTPDDIDHLGNRRIRTVGELVQNQFRI 350

Query: 355 N 355
            
Sbjct: 351 G 351


>gi|600226|gb|AAB40951.1| RNA polymerase beta subunit [Mycoplasma gallisepticum]
          Length = 1390

 Score =  657 bits (1696), Expect = 0.0,   Method: Composition-based stats.
 Identities = 309/1443 (21%), Positives = 536/1443 (37%), Gaps = 138/1443 (9%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A          VR+ + K     +  +L  +Q  +Y  FL             L+    S
Sbjct: 6    AFHNTQYSPKVVRRDYSKVHNKYNPLNLPGIQVNAYKQFLEKE----------LEEIIGS 55

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
             FPI + +G   +EF   +   P+   ++      TY   L + L L+            
Sbjct: 56   YFPIKSPNGKYSVEFHGMKILDPQITKEEASAESKTYDASLYVNLSLVNHQTGTVKKISK 115

Query: 122  IKDIKEQS-IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF-DHDKGRASLSGKLL 179
                 +   IY  D+PLMT++G F++ GI++ VV+Q+ RSPG +  +  + + S S K  
Sbjct: 116  KSAKSKAEGIYFADIPLMTENGAFIVNGIEKFVVAQIVRSPGAYILNKSQVKLSNSRKRN 175

Query: 180  ---YACRIIPDQGLWMDIEF-DSKDIIHVRI-----DRRRKVPVTSFLMALGMDSEEILS 230
               Y C + P +G  M     ++KD +   +     +  +   +T+ L A G+   +I  
Sbjct: 176  QEGYICEVFPSKGTLMLFYIAENKDFVQAVVRDVGGESAKVFSITTLLKAFGLSEIKIKE 235

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             F          D+    L +        ++ + +                + L++ ++ 
Sbjct: 236  IF-------NNNDYILRSLESEFYNEKQILNEADI----------------AQLIRDIES 272

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              +    + S  +   +              +     ++++  E +  S      I  ++
Sbjct: 273  DRISK--VKSLPIDQKWKN-----------LVLDWYKLNQEKQELLNSSNPNPTKIESLN 319

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +    +R  +     K     L    R +           +S+    FF   +YDLS+
Sbjct: 320  T-HIGVVLRKLICEKAAKHVIQELSISTRSLDNVAQKEEISYQSILLQHFFQKKRYDLSS 378

Query: 411  VGRVKMNMRLNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             GR K   +L +      R I    K+    ++     L   +           +R+  +
Sbjct: 379  AGRHKFVRKLRVSERLYQRTIAQDIKDLDGNVVIKQGTLMLKEQLDLFKRLSKEKRLDII 438

Query: 468  GEM------LKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             ++      L  Q+  +      +         +   ++  D  N       + +     
Sbjct: 439  KQIDFINPELNTQFTHVNTYEEVQIYVNNDLRNETTQIIGIDGSNESIETLTLADLISIV 498

Query: 521  QLSQLEE-HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
                    ++     I H           + +++    M  +    Y +         + 
Sbjct: 499  SYIVNLPFNIGLYDDIDHLGNKRLKLINELLKSKVQTGM--MRIEKYIKDKLQTADGNNK 556

Query: 580  IGLVSSLTS-FARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDE 636
            +    +     + +      +   + V + K    V+  + +  +       Q   S   
Sbjct: 557  LADQDAENDPDSDLGTKSGNDLTVKSVINPKPFQIVIKDFFNTHQLTQFLDQQNPLSELT 616

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +      +     + E+  +    + +        +     +   L    +    +  N 
Sbjct: 617  NKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIETPEGMNIGLIMSLAFYATIDKNG 676

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                 P LK E   +   +E + A +    I+A+ +     +D  +    + E  +    
Sbjct: 677  F-LMTPYLKVENGKITDKVEHLTALTEDEYIIAEASS---YMDVAKDGTINNEKIIARYR 732

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            S  D+Y     Q         Q   V         +  +               +L  + 
Sbjct: 733  SSQDLYDPK--QVDYIVVSPKQVVSVAASLIPFLENDDSSRALMGANMQRQATPLLKPYS 790

Query: 817  PWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E  +   S  +V+     ++   +   +    +         +  V       
Sbjct: 791  PLVGTGVEYKIAQDSGMLVTAKNPGTVTYVDASKITVKGEDNKSTDYNLLKFVKSNKNTC 850

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+ VG ++     L    + K    +   + +L         +  D  +      
Sbjct: 851  YNQSPIVAVGDKIETNQALADGPSMKN-GELALGQNVLVGFTTWSGYNYEDAVI------ 903

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD--------RNIYSRLM 987
                    I +R   D    SI ++   IE L     DE++I D        +       
Sbjct: 904  --------ISDRLFKDDVYSSIHIDEYTIECLRTKNGDEEIIRDIPNISESAKRYLDEEG 955

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I+ G     G     K++      +   P  +  Q  + D      V+ ++       +
Sbjct: 956  VIMVGAEVKEGDILVGKTSPKGQVEL--TPEEKLIQVILGD-----KVKQVRESSLKVPN 1008

Query: 1048 ILEDRFK-NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      K   I  GD++   VL +VKV+V  KR IQ GDK+AGRHGNKGI+S+I+  
Sbjct: 1009 GGDGIVAGIKRFSIANGDELEDDVLELVKVYVVQKRKIQIGDKVAGRHGNKGIISKIVAQ 1068

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP L+DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   L K         K   D  
Sbjct: 1069 EDMPHLEDGTPLDILLNPLGVPSRMNIGQIFELHLGYAARELAKAKLIEACFDKKLADQL 1128

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS--------------------GVPV 1206
                 LEK          +       V  +A+                           +
Sbjct: 1129 DTVFGLEKSKTQSLIKNLVEHMKSIGVTSLAQTKNRVRTIDIDIVLKQLGLTYDDLAFKI 1188

Query: 1207 STPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +TPVF+G + E + +++  A +D     G+  L DG TGEPF++P++VG +YMLKL+HMV
Sbjct: 1189 ATPVFEGVNMEDLKAIMSEAGIDPDKTEGKFKLIDGRTGEPFEKPISVGIMYMLKLDHMV 1248

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++AR+ G YS +TQQPLGGKS  GGQR GEMEVW +QAYGAA+ L+E+LTIKSDDV 
Sbjct: 1249 DDKIHARAVGPYSKITQQPLGGKSQNGGQRFGEMEVWALQAYGAAHNLREILTIKSDDVR 1308

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG--LSIDLENSRTKNSAKMEEIPDFN 1381
            GR   Y +IV G    E G PESF +L KE+Q LG  L++ L +  +  +     + D +
Sbjct: 1309 GRNMTYNAIVKGLSIPEPGVPESFKLLTKELQGLGMTLNV-LYDDDSIENINNISVVDES 1367

Query: 1382 KCE 1384
               
Sbjct: 1368 LEP 1370


>gi|73748443|ref|YP_307682.1| DNA-directed RNA polymerase subunit beta [Dehalococcoides sp. CBDB1]
 gi|88909134|sp|Q3ZX01|RPOB_DEHSC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|73660159|emb|CAI82766.1| DNA-directed RNA polymerase, beta subunit [Dehalococcoides sp. CBDB1]
          Length = 1273

 Score =  657 bits (1694), Expect = 0.0,   Method: Composition-based stats.
 Identities = 369/1102 (33%), Positives = 540/1102 (49%), Gaps = 130/1102 (11%)

Query: 332  SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
             L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 200  LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYSRLRPGDPPN 259

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
               A  + N +FFD   YDL  VGR K+N RL L + +  + R + +EDI+AII+ ++ +
Sbjct: 260  ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPSREVGENRALTREDIVAIIQRIIMV 319

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
             NG+ T DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 320  NNGQDTPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEMVTPSALVNI 379

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 380  RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 439

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-----VVYLSAME 621
            GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV      ND     +     + 
Sbjct: 440  GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNNDKKLVGLKLKIEIS 499

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+ + +A A S++ ED       +                   D S    VS     +P 
Sbjct: 500  EKGKVLAAAGSTISEDSFKLISKLPE----------------CDISVMPFVSAEVKYMPA 543

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             E D   R ++     R        +        E  V          +    ++ +D  
Sbjct: 544  DEED---RYIIAQANTRLDEKGYFLDDRIEARSAERYVV---------EPPDKIDYMDVS 591

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMK---FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               I SV   L P     D  R +     QR        + P+V  G             
Sbjct: 592  PKQIFSVAASLIPFLEHDDANRALMGANMQRQAVPLLRAEAPMVATG------------- 638

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                             M      +   ++ ++      V +S+     E +   T  G 
Sbjct: 639  -----------------MEREAARYSGQVIFAKHA---GVASSV---TSEKIIIRTAEGG 675

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +       V       I++  II  G ++  G +L      +    +   +  + A   
Sbjct: 676  HDEYLLKKFVRTNQGTCINQHAIINKGQKIAAGQVLADSSATEN-GELALGQNCVVAFMS 734

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDE 974
             +  +  D  +     +S  +V    F    I K+E      +  +E + RD     ++ 
Sbjct: 735  WQGFNYEDAII-----LSERLVREDAFTSIHITKHELEARDTKLGVEEITRDIPNVGEES 789

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD +   R+   +   + + G    K  T LS++   +  R+ + + A + +     
Sbjct: 790  LRELDEDGIIRIGAEVGPDDILVGKITPKGETELSAE--EKLLRAIFGEKAREVKDT--- 844

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                                 +I     GDD+P  V + V+V+VA KR +  GDK+AGRH
Sbjct: 845  ------SLRMPHGEWGKVINVRIFSRDSGDDLPARVNKWVQVWVAQKRKVSVGDKLAGRH 898

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGWA   LG ++ +
Sbjct: 899  GNKGVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGWAGHLLGFRVAT 958

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDG 1213
             + D   +  I    +        G+      +    +    A +W          +FD 
Sbjct: 959  PVFDGADDTVIEDALARSWLSAKAGAIDMSPENKRPSADAHKAIEWIKQQGFDGKKIFDE 1018

Query: 1214 -----ADEEAINSMLRMADLDES-------------------------GQSILYDGLTGE 1243
                 A E ++   L+   +D S                         G+S+L DG TGE
Sbjct: 1019 KHPGLAKEVSLKLWLKDMGVDASALSGAELEKKAYDVSSQSRLPSPIVGKSVLRDGRTGE 1078

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FD+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQR GEMEVW + 
Sbjct: 1079 TFDQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQRFGEMEVWAMY 1138

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYG A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVKE+Q+LGL++++
Sbjct: 1139 AYGTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVLQPGVPESFKVLVKELQSLGLAVEV 1198

Query: 1364 ENSRTKNSAKMEEIPDFNKCEL 1385
             N   K  A  E++   N+  L
Sbjct: 1199 INEEVK-IAPSEKVSSLNEGNL 1219



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 99/361 (27%), Positives = 168/361 (46%), Gaps = 42/361 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
           +RK + + PE++++P+LIE+Q  S+  F            EGL+   + + PI  F G  
Sbjct: 15  IRKSYAQLPEVVNVPNLIEMQLQSFVWF----------QEEGLRELIEEISPIKDFVGNR 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+    +C  RD TY+VPL +  RLIV         K+  +IKE   +
Sbjct: 65  LELEFIGYEFREPRLSEYECTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDL 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT  GTF+  G +R+VVSQL RSPG++F         +G+ L    +IP +G 
Sbjct: 116 FFGDIPLMTALGTFITSGTERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGA 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PV++ L A+G   + +IL+ F    V     +      
Sbjct: 174 WLEFETSNRDVISVKIDGRRKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQS 230

Query: 250 SAADLMVGAKVSSSLVDI----DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS---- 300
           S     +     S+L+DI      G+    ++ +KL + +    +   +  +G       
Sbjct: 231 SIDRDPLIKDEISALIDIYSRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRR 290

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                 +      +  + +      I +          ++ + +  IR +  L  +    
Sbjct: 291 LELPSREVGENRALTREDIVAIIQRIIMVNNGQDTPDDIDHLGNRRIRTVGELVQNQFRI 350

Query: 355 N 355
            
Sbjct: 351 G 351


>gi|284931614|gb|ADC31552.1| DNA-directed RNA polymerase subunit beta (RNAP subunit beta)
            [Mycoplasma gallisepticum str. F]
          Length = 1390

 Score =  655 bits (1691), Expect = 0.0,   Method: Composition-based stats.
 Identities = 306/1436 (21%), Positives = 535/1436 (37%), Gaps = 124/1436 (8%)

Query: 2    AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            A          VR+ + K     +  +L  +Q  +Y  FL             L+    S
Sbjct: 6    AFHNTQYSPKVVRRDYSKVHNKYNPLNLPGIQVNAYKQFLEKE----------LEEIIGS 55

Query: 62   VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
             FPI + +G   +EF   +   P+   ++      TY   L + L L+            
Sbjct: 56   YFPIKSPNGKYSVEFHGMKILDPQITKEEASAESKTYDASLYVNLSLVNHQTGTVKKISK 115

Query: 122  IKDIKEQS-IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF-DHDKGRASLSGKLL 179
                 +   IY  D+PLMT++G F++ GI++ VV+Q+ RSPG +  +  + + S S K  
Sbjct: 116  KSAKSKAEGIYFADIPLMTENGAFIVNGIEKFVVAQIVRSPGAYILNKSQVKLSNSRKRN 175

Query: 180  ---YACRIIPDQGLWMDIEF-DSKDIIHVRI-----DRRRKVPVTSFLMALGMDSEEILS 230
               Y C + P +G  M     ++KD +   +     +  +   +T+ L A G+   +I  
Sbjct: 176  QEGYICEVFPSKGTLMLFYIAENKDFVQAVVRDVGGESAKVFSITTLLKAFGLSEIKIKE 235

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             F          D+    L +        ++ + +                + L++ ++ 
Sbjct: 236  IF-------NNNDYILRSLESEFYNEKQILNEADI----------------AQLIRDIES 272

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              +    + S  +   +              +     ++++  E +  S      I  ++
Sbjct: 273  DRISK--VKSLPIDQKWKN-----------LVLDWYKLNQEKQELLNSSNPNPTKIESLN 319

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + +    +R  +     K     L    R +           +S+    FF   +YDLS+
Sbjct: 320  T-HIGVVLRKLICEKAAKHVIQELSISTRSLDNVSQKEEISYQSILLQHFFQKKRYDLSS 378

Query: 411  VGRVKMNMRLNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             GR K   +L +      R I    K+    ++     L   +           +R+  +
Sbjct: 379  AGRHKFVRKLRVSERLYQRTIAQDIKDLDGNVVIKQGTLMLKEQLDLFKRLSKEKRLDII 438

Query: 468  GEM------LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             ++      L  Q+       E  I       +  + +     + + + +       S  
Sbjct: 439  KQIDFINPELNTQFTDVNTYEEVQIYVNNDLRNETTQIIGIDGSNESIETLTLADLISIV 498

Query: 522  LSQLEEHVNS--LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
               +    N      I H           + +++    M  +    Y +         + 
Sbjct: 499  SYIVNLPFNIGLYDDIDHLGNKRLKLINELLKSKVQTGM--MRIEKYIKDKLQTADGNNK 556

Query: 580  IGLVSSLTS-FARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDE 636
            +    +     + +      +   + V + K    V+  + +  +       Q   S   
Sbjct: 557  LADQDAENDPDSDLGTKSSNDLTVKSVINPKPFQIVIKDFFNTHQLTQFLDQQNPLSELT 616

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +      +     + E+  +    + +        +     +   L    +    +  N 
Sbjct: 617  NKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIETPEGMNIGLIMSLAFYATIDKNG 676

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                 P LK E   +   +E + A      I+A+ +     +D  +    + E  +    
Sbjct: 677  F-LMTPYLKVENGKITDKVEHLTALREDEYIIAEASS---YMDVAKDGTINNEKIIARYR 732

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            S  D+Y     Q    +    Q   V         +  +               +L  + 
Sbjct: 733  SSQDLYDPK--QVDYIDVSPKQVVSVAASLIPFLENDDSSRALMGANMQRQATPLLKPYS 790

Query: 817  PWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            P  G   E  +   S  +V+     ++   +   +    +         +  V       
Sbjct: 791  PLVGTGVEYKIAQDSGMLVTAKNPGTVTYVDASKITVKGEDNKSTDYNLLKFVKSNKNTC 850

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             ++  I+ VG ++     L    + K    +   + +L         +  D  +      
Sbjct: 851  YNQSPIVAVGDKIETNQALADGPSMKN-GELALGQNVLVGFTTWSGYNYEDAVI------ 903

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQN 994
                    I +R   D    SI ++   IE L  ++ D+E      NI       L  + 
Sbjct: 904  --------ISDRLFKDDVYSSIHIDEYTIECLRTKNGDEEITRDIPNISESAKRYLDEEG 955

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
             +      K+  +L      +       +  +    +   V+ ++       +  +    
Sbjct: 956  VIMVGAEVKEGDILVGKTSPKGQVELTPEEKLIQAILGDKVKRVRESSLKVPNGGDGIVA 1015

Query: 1055 -NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K   I  GD++   VL +VKV+V  KR IQ GDK+AGRHGNKGI+S+I+  EDMP L+
Sbjct: 1016 GIKRFSIANGDELEDDVLELVKVYVVQKRKIQIGDKVAGRHGNKGIISKIVAQEDMPHLE 1075

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   L K         K   D       LE
Sbjct: 1076 DGTPLDILLNPLGVPSRMNIGQIFELHLGYAARELAKAKLIEACFDKKLADQLDTVFGLE 1135

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKS--------------------GVPVSTPVFDG 1213
            K          +       V  +A+                           ++TPVF+G
Sbjct: 1136 KSKTQSLIKNLVEHMKSIGVTSLAQTKNRVRTIDIDIVLKQLGLTYDDLAFKIATPVFEG 1195

Query: 1214 ADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
             + E + +++  A +D     G+  L DG TGEPF++P++VG +Y+LKL+HMV DK++AR
Sbjct: 1196 VNMEDLKAIMSEAGIDPDKTEGKFKLIDGRTGEPFEKPISVGIMYILKLDHMVDDKIHAR 1255

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            + G YS +TQQPLGGKS  GGQR GEMEVW +QAYGAA+ L+E+LTIKSDDV GR   Y 
Sbjct: 1256 AVGPYSKITQQPLGGKSQNGGQRFGEMEVWALQAYGAAHNLREILTIKSDDVRGRNMTYN 1315

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALG--LSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +IV G    E G PESF +L KE+Q LG  L++ L +  +  +     + D +   
Sbjct: 1316 AIVKGLSIPEPGVPESFKLLTKELQGLGMTLNV-LYDDDSIENINNISVVDESLEP 1370


>gi|309798965|ref|ZP_07693223.1| DNA-directed RNA polymerase, beta subunit [Streptococcus infantis
           SK1302]
 gi|308117419|gb|EFO54837.1| DNA-directed RNA polymerase, beta subunit [Streptococcus infantis
           SK1302]
          Length = 973

 Score =  654 bits (1687), Expect = 0.0,   Method: Composition-based stats.
 Identities = 374/826 (45%), Positives = 512/826 (61%), Gaps = 61/826 (7%)

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E D
Sbjct: 1   MTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESD 57

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           SKDI + RIDR RK+P T+ + ALG    +EI   F    +     +      +  D   
Sbjct: 58  SKDIAYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSDLVRNTVEKDI-HKNPMDSRT 116

Query: 257 GAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLY 307
              +      +  GE    ES + L        +   +  +G             L    
Sbjct: 117 DEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQT 176

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           +AE +V+ ETGEI +EAG ++    +E         I       +N   YI N    D  
Sbjct: 177 IAEPLVDPETGEILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DAA 224

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
              +  +L  ++V+ P D                              + +  N +  D 
Sbjct: 225 VVTEPVVLQKFKVVAPTDPDRV--------------------------VTIIGNANPDDK 258

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++
Sbjct: 259 VRIVTPADILAEMSYFLNLAEGIGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVR 318

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+S  D + + PQ +IN +PV +A+ EFF SSQLSQ  +  N LS ++H RRLSALG G
Sbjct: 319 ERMSVQDNEVLTPQQIINIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPG 378

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV  
Sbjct: 379 GLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDR 438

Query: 608 G--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
              KVTN++V+L+A EE+   +AQANS L+ DG+F E++V  R  G     P   +D++D
Sbjct: 439 ETGKVTNEIVWLTADEEDEYTVAQANSKLNADGTFAEKVVMGRHQGVNQEYPASSVDYMD 498

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGA
Sbjct: 499 VSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGA 558

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
           A++A+  G V   DA ++ +R  +G LD       +Y + KF+RSN  T  NQR LVKVG
Sbjct: 559 AVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRSNSGTAYNQRTLVKVG 611

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D V + D IADGPS + G++ALG+N +VA+M W GYNFED++++SER+V +DV+TS+H+E
Sbjct: 612 DVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLE 671

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           E+E   RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  
Sbjct: 672 EYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKD 731

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 732 LSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRANGD 777



 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 121/409 (29%), Positives = 174/409 (42%), Gaps = 77/409 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 607  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 665

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 666  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 725

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 726  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 768

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 769  KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 828

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 829  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 887

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 888  ----------------------------------------DSDAKTIL------YDG--- 898

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLG
Sbjct: 899  ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLG 943


>gi|194246782|ref|YP_002004421.1| DNA-directed RNA polymerase subunit beta [Candidatus Phytoplasma
            mali]
 gi|254765298|sp|B3QZH0|RPOB_PHYMT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|193807139|emb|CAP18577.1| DNA-directed RNA polymerase, beta chain [Candidatus Phytoplasma mali]
          Length = 1273

 Score =  654 bits (1687), Expect = 0.0,   Method: Composition-based stats.
 Identities = 318/1402 (22%), Positives = 548/1402 (39%), Gaps = 155/1402 (11%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M    +  G    R+ + K    I++P+LIE+Q  S++ FL           EG++   K
Sbjct: 1    MEYRNIKYGTKTERRNYSKMNYDIELPNLIEIQTKSFELFL----------KEGIKKILK 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
             + PI + +G   L F  +  D PK+++++   RD+TY   L    RL            
Sbjct: 51   DISPIESNNGDLKLYFDDFYLDKPKYNIEEAKNRDITYYAQLFAKARL---------ENV 101

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              K+IKE +I + +LPL+T  GTF+I G +R+V+SQ+ RS GI+F           K+ Y
Sbjct: 102  LTKEIKESNILITELPLITPSGTFIINGTERVVISQIVRSSGIYFTKKFDS-----KIRY 156

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYS 239
              ++IP +G W++ E  +KD ++ ++DR +K+P+  F+  LG D++E I STF       
Sbjct: 157  LAQLIPTRGAWIEYEQSNKDFLYAKLDRSKKIPLNKFICCLGFDTKEKIESTFGYNKFLD 216

Query: 240  QRGDFWCFPLSAA-------DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
                                 L  G KV   +       ++  + K     LL   + K 
Sbjct: 217  LSLKKDQILNINEAIIELHSKLHRGEKVPVDVAREFIFSKLFYAKK---YDLLAVGRYKF 273

Query: 293  VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
             + L +    +   Y+A+D+++ ET EI++     ++E+ +E++ +        L     
Sbjct: 274  NQKLDVLK-RIKNTYLAKDLIDPETNEIFLSKKTFLNEEIIEKLKNKRNCFTFELVNADN 332

Query: 353  NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            N    I   ++T  N ++   L    +     ++      E +       +++     V 
Sbjct: 333  NLENEINEEILTYANYNKDKILELYIK----DNIINIKTGEILVEKDTLITEQ-----VM 383

Query: 413  RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
             +       +        +  +D+    K    + N    +  +DNLGN +         
Sbjct: 384  NIIRKNGQFIHDKVSKYFLCNKDLYQKHKERKGVFNEVLEVYILDNLGNPKPTIKV---- 439

Query: 473  NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                +G ++ E + +    S  I S+     +      +   +   + +L  + E     
Sbjct: 440  ----IGNIQSENNKQHITVSDIIASISYYLNLYEDIGKTDDIDHLGNRRLRLIGE----- 490

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
                  R    + +  +    +  +  ++                             ++
Sbjct: 491  LLTNQFRLGLIISEKNIKDKMSISKFNNITVNSLVNFTSLSAIIKTFFNSSRLSHFMDQI 550

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            N    +    R       T  +    A  E         + L    +     +    A  
Sbjct: 551  NPLAELTQKRRV--SALGTGGIDRDRAGIEIRDINNSHYAKLCPIETPEGPSI-GLIASL 607

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                  +K  FI     +V+          E+ D             +V  L ++  F  
Sbjct: 608  STYARVDKYCFIQTPYLKVIKNEQGQPKVSEHIDYLTADQEEKEVIASVTYLNSDNTFKE 667

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK---FQR 769
              + +     +G          +  +D     I SV     P     D  R +     QR
Sbjct: 668  KKIIARKNGETGL----HEIDKITYIDVSPKQIVSVATSSIPFLEHNDASRALMGANMQR 723

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                  + + P+V  G        I    + D G L L +N       +  Y     ++I
Sbjct: 724  QAVPLLIPESPIVGTG--------IEHRIAKDSGCLILAKN-----SGYVTYADAQKIVI 770

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG--------- 880
            +E+        +  I + E      K             +E  L N  +           
Sbjct: 771  TEKPKKTITINNEVIYKNEEEFNYEKAKILHKKNVFSCQTEYKLINFAKSNQDTLILQKP 830

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  VN  DI+        E  +     +  A    +  +  D  +     V   + 
Sbjct: 831  LVLDGDFVNKNDIITDGPATHKE-ELALGRNVTVAFMTWEGYNYEDAIIISEDLVKNDIY 889

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 +++ I   E       EQI     +   E +   +N+  R   I+ G     G  
Sbjct: 890  TSVHIDKYEIQTRELKKGAGVEQITREVPNVSAEAI---KNLDER-GIIIPGSEVKEGDI 945

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  + S  ++ +    +     + ++  +    SL+V       +   ++ +K    
Sbjct: 946  LV--GKITSQGMVEQTAYERLINVIIGEKSREHKDSSLRVPCGEGGIVQSVKYFSK---- 999

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            +  D +PP V   ++V++A KR I+ GDK+AGRHGNKG++S ILP ED+P++KDGT +DI
Sbjct: 1000 ENNDILPPEVNENIRVYIAKKRKIKEGDKIAGRHGNKGVISLILPKEDLPYMKDGTTIDI 1059

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG A   L  K+ + + D   N D+  +    +  +    
Sbjct: 1060 ILNPLGVPSRMNIGQILEMHLGIAAQKLNIKVATPVFDGVNNDDLRKIIKEAKLSLDGKM 1119

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                               G++      
Sbjct: 1120 TL-----------------------------------------------YDGRT------ 1126

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
             GEPFD  ++VG +YM+KL+HMV DK+++R+ G Y+L+ QQP+GG++  GGQR GEMEVW
Sbjct: 1127 -GEPFDSSISVGVMYMIKLSHMVEDKLHSRNIGPYTLMAQQPMGGRNQNGGQRFGEMEVW 1185

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             + AYGAA  LQE+LTIKSDD++GR + Y +I  G    +   PESF V  KE+QALGL 
Sbjct: 1186 SLYAYGAANSLQEILTIKSDDIIGRQKTYSAITNGLPLPKPSIPESFRVFAKELQALGLY 1245

Query: 1361 IDLENSRTKNSAKMEEIPDFNK 1382
            ++L NS+TK +  ++ + +  K
Sbjct: 1246 VELINSKTKENEILKSLVENQK 1267


>gi|145308246|gb|ABP57386.1| DNA-directed RNA polymerase beta subunit [Peanut witches'-broom
           phytoplasma]
          Length = 1214

 Score =  654 bits (1686), Expect = 0.0,   Method: Composition-based stats.
 Identities = 365/1031 (35%), Positives = 546/1031 (52%), Gaps = 103/1031 (9%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G    R+ + K    +D+P+LIE+Q  S+  FL          + G+QA+ KS+FPI
Sbjct: 7   VKYGTKVERRNYSKMKYDLDLPNLIEIQTKSFQEFL----------DYGIQASLKSIFPI 56

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            +++G   L F  +  + PKF+ +D   R  TY+  L + + L              K  
Sbjct: 57  ESYNGDLKLHFNDFFLEEPKFNAEDSKKRGFTYSAELFLNVTL---------ENVITKQT 107

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K+  I M DLPLMT  GTF+I G +R+VVSQ+ RS G +F       +   K  +  +II
Sbjct: 108 KKARILMTDLPLMTIAGTFIINGTERVVVSQIVRSAGAYFTSKLD--NKINKNRFTAQII 165

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTF------------ 232
           P +G W++ E ++KD ++ ++DR +K+P+T F+ ALG D+ EEI   F            
Sbjct: 166 PTRGAWIEFEQNNKDFLYAKLDRSKKIPLTKFIHALGFDTQEEIEKAFGINSLLDLSFKK 225

Query: 233 ------------------------------------YPKIVYSQRG---DFWCFPLSAAD 253
                                               + K  Y             L   +
Sbjct: 226 DNDSNCNDAIVELYSKLHQGERVPTNAAREFIRTRLFDKDKYDLSLVGRYKLNRKLDVLN 285

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
                 ++  + D+   + +  +G  L   ++K L     KF     +    L       
Sbjct: 286 RAENTFLAQDIKDLTNNKILFPAGTFLNYEIIKQLALHRDKFRVELVNSDFHLQNQNHDE 345

Query: 314 NGETGEIYIEAGDVIDEKSLEEIF--HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           N  T    I    +  ++ +         ++   +L  + +N         + DK     
Sbjct: 346 NIFTYRKSIHDNQIYIKEDIVHFQTGQVLVKADTLLDDNVLNTLLETHKYNIDDKIIKYF 405

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
                I +V+R                     + Y L           +  D  +D  +I
Sbjct: 406 ANKEYINKVVRDRQKV-----------FNESLEVYILDNKNNKSFIKIVGNDQSEDAENI 454

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
              DIIA I   ++L +  GTIDDID+LGNRR+R +GE+LKNQ R+GL R +++IK+R+S
Sbjct: 455 VLSDIIASISYYLNLYHNIGTIDDIDHLGNRRLRLIGELLKNQLRVGLNRTKKNIKDRMS 514

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
               +S+ P  L N   +  A+  FFCSS+LS   + +N L+ IT  RR+SALG GG+ R
Sbjct: 515 ISKFESITPGGLFNFSSLSMAIKTFFCSSRLSHFMDQINPLAIITQKRRISALGSGGIDR 574

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-- 609
            RAGVE+RDV+ ++YGR+CP ET EG +IGL+ SL ++A+V+ YGFIETP+ KV      
Sbjct: 575 DRAGVELRDVNDSYYGRLCPIETPEGPSIGLICSLATYAQVDKYGFIETPFFKVIRENGK 634

Query: 610 --VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             V+    YL++++EENR IA ++S L++D SF ++ V  R  GE  L   ++ID+ID S
Sbjct: 635 SVVSPKYEYLTSIQEENRIIATSSSCLNDDFSFKQQKVIARRNGEISLYNVDQIDYIDVS 694

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQ+VS+A + IPFLE++D++R LMG NMQRQA+PLL +EAP V TG+E  + K SG  +
Sbjct: 695 PKQIVSVATASIPFLEHNDASRALMGANMQRQALPLLISEAPIVATGIEHRIVKDSGCVV 754

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +A+ +G V  VDA +I+I++  G+         +Y L  F +SNQ+T + Q+P+VK  + 
Sbjct: 755 IAEDSGFVVYVDAKKIIIQNNHGEK-------KVYILSTFDKSNQDTLILQKPIVKFNEY 807

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V + DIIADG ST  G+LALG+N+ VAFM W GYN+ED++++SER+V ED+FTS+HI ++
Sbjct: 808 VNKGDIIADGSSTHQGELALGKNVTVAFMTWDGYNYEDAVILSERLVQEDIFTSVHISKY 867

Query: 848 EVMAR--DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT--PKGE 903
           E+  R      G EEITR+IPNVS E +KN+D  GII  G+EVN GD LVGKI   P+  
Sbjct: 868 EIQVRELKKGAGREEITREIPNVSAEAIKNLDSRGIIIPGSEVNEGDYLVGKIVIIPQSS 927

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN--RHGIDKNERSISVER 961
               P EKL++ I GEK+ D +D SL+VP G SG V  V+ F+  +           + +
Sbjct: 928 LENNPYEKLIQTIIGEKSRDYKDASLKVPCGESGIVQSVQYFSVKKGDFISTPGVNEIIK 987

Query: 962 EQIELLARDKD 972
             I    + ++
Sbjct: 988 VYIAKKRKIRE 998



 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 123/476 (25%), Positives = 206/476 (43%), Gaps = 64/476 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+     VN GD ++   +   +  +   + +  A       +  D  +     V   + 
Sbjct: 801  IVKFNEYVNKGD-IIADGSSTHQGELALGKNVTVAFMTWDGYNYEDAVILSERLVQEDIF 859

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 +++ I   E      RE+I     +   E +   +N+ SR   I+ G     G  
Sbjct: 860  TSVHISKYEIQVRELKKGAGREEITREIPNVSAEAI---KNLDSR-GIIIPGSEVNEGDY 915

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K  ++    +   P  +  Q  + ++       SLKV    S  +   ++      +
Sbjct: 916  LVGKIVIIPQSSLENNPYEKLIQTIIGEKSRDYKDASLKVPCGESGIVQSVQY----FSV 971

Query: 1061 QWGDDMP-PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            + GD +  PGV  ++KV++A KR I        R G+K                      
Sbjct: 972  KKGDFISTPGVNEIIKVYIAKKRKI--------REGDK---------------------- 1001

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                                         G K        K +       + ++ ++   
Sbjct: 1002 ------------------------IAGRHGNKGVISCIAAKVDMPYMSDGTPIDVILNPL 1037

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                +++      +       K  + V+TPV DGA+ E + ++++ A+L   G+  LYDG
Sbjct: 1038 GVPSRMNIGQILEMHLGMAAHKLNIKVATPVLDGANNEDLKNIMQEANLPFDGKMTLYDG 1097

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TGEP+D  ++VG +YMLKL+HMV DK++AR+ G+Y+L+ QQP  G++  GGQR+GEME 
Sbjct: 1098 RTGEPYDNSISVGILYMLKLSHMVEDKIHARNVGTYTLILQQPGSGRNFLGGQRIGEMET 1157

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            W + AYGAA+ LQE+LT+KSDD++GR ++Y +IV G    +   PESF V  KE +
Sbjct: 1158 WSLLAYGAAHTLQEILTLKSDDIIGRNQLYHAIVNGLRFPKPSIPESFRVFTKEFK 1213


>gi|39938746|ref|NP_950512.1| DNA-directed RNA polymerase subunit beta [Onion yellows phytoplasma
            OY-M]
 gi|81402498|sp|Q6YQW3|RPOB_ONYPE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|39721855|dbj|BAD04345.1| DNA-directed RNA polymerase beta subunit [Onion yellows phytoplasma
            OY-M]
          Length = 1273

 Score =  654 bits (1686), Expect = 0.0,   Method: Composition-based stats.
 Identities = 359/1052 (34%), Positives = 549/1052 (52%), Gaps = 105/1052 (9%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M    V  G    R+ + K    +D+P+LIE+Q  S+D FL            G++   +
Sbjct: 1    MGYHNVKYGKKAQRRNYSKTIYDVDLPNLIEIQNQSFDWFL----------KHGIKELLQ 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
               PI +++G   + F  Y   PPK+ +++   +D++Y   L +   L            
Sbjct: 51   DFCPIESYNGDLKIHFDDYFLAPPKYSIEETKIKDISYVAQLFVKTTL---------ENV 101

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               + K+ +I + +LPLMT  GTFVI G +R+VVSQ+ RS  ++F  +    S   +  Y
Sbjct: 102  LTGETKQSNILLTELPLMTPTGTFVINGTERVVVSQIVRSASVYFAGNFD--SKLNRTTY 159

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPK----- 235
            + ++IP +G W++ E  SK+I++ ++DR +K+P+++F+ ALG DS+E +   + K     
Sbjct: 160  SGQVIPSRGAWIEYEEGSKEILYAKLDRSKKIPLSNFIYALGFDSKEAIENVFGKSAIID 219

Query: 236  IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
             V+ +  D               +     VD            +    L K  + K  K 
Sbjct: 220  SVFDKETDMDSDNALVELYSKIRQGEKVPVDTARDFIRTRLFDQKKYDLAKVGRYKFNKK 279

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            L + +      Y+A D VN ET EI I   +++ ++ +  +  +    +  ++    N  
Sbjct: 280  LDVLT-RAENTYLACDFVNPETQEIIIAQDELLTKEKIAILKQNRHFLLQEIFDAKHNLE 338

Query: 356  AYIRNTLVTDKNKDRKDALL-----------------------DIYRVMRPGDVSTFSVA 392
                  ++  K   +K+ L                        DI   +R    +     
Sbjct: 339  NETDEEILAYKKDPQKNELFTKTNIINSRTGEVLVAKDTLVNDDIINHLRHNIHTLDEKV 398

Query: 393  ESMFNFLFFDSDKY----------------DLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
               F        K                    +         +  D  +  +HI   D+
Sbjct: 399  SKFFLGTKDIYQKEADRQGVFNEILEVYTSKDESGKLYHKVKLIGNDQRETKKHITLSDV 458

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            IA I   ++L    GT+DDID+LGNRR+R +GE+LKNQ+R+GL R E++IK+ IS+    
Sbjct: 459  IASINYYLNLYENVGTVDDIDHLGNRRLRLIGELLKNQFRIGLTRAEKNIKDMISTSKFS 518

Query: 497  SVM-PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
             V  P DL+N   ++S +  FF SS+LSQ  + +N L+ +T  RR+SALG GG+ R RAG
Sbjct: 519  EVNGPGDLVNFTFLMSVIKTFFTSSRLSQFMDQINPLAELTQKRRVSALGIGGINRDRAG 578

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---- 611
            +E+RDVH +HYGR+CP ET EG +IGL++SL+++A+VN YGFI+TP+ KV          
Sbjct: 579  IEVRDVHNSHYGRLCPIETPEGPSIGLITSLSTYAKVNKYGFIQTPFFKVLHQDGKTTLS 638

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
              + YL+A +E+   IA A   LD + +F ++ +  R  GE  +  R +I + D SPKQ+
Sbjct: 639  RHIDYLTADQEKEEIIASAGFVLDANNAFKDKKIIARSNGETGIFERSQITYADVSPKQI 698

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+A S IPFLE++D++R LMG NMQRQAVPLL  E+P VGTG+E   AK SG  I+A+ 
Sbjct: 699  VSVATSSIPFLEHNDASRALMGANMQRQAVPLLIPESPIVGTGVEYRAAKDSGCLIIARE 758

Query: 732  AGIVEQVDAIRIVIRSVEGDLDP-------------------------STSGVDIYRLMK 766
            +G V  VDA +I+I                                         Y L+ 
Sbjct: 759  SGFVTYVDAQKIIITKKPNQNVSLNGKTLYDTTQEFTYAQAKALYENNYKEHQAEYTLIN 818

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F +SNQ+T V Q+P+V +G+++   DI+  GPST  G+LALGRN+ VAFM W GYN+ED+
Sbjct: 819  FAKSNQDTLVLQKPIVVLGEQINEGDILVSGPSTSQGELALGRNVTVAFMTWEGYNYEDA 878

Query: 827  MLISERMVSEDVFTSIHIEEFEVMAR--DTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            +++SE +V  DV+TSIHI+++EV  R      G EEITR++PNV  + +KN+DE GII  
Sbjct: 879  IIMSEELVKHDVYTSIHIDKYEVQTRELKKGSGQEEITREVPNVGADAIKNLDERGIIIP 938

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G+EV  GDILVGKITP+G    +P EKL++ + GEKA + +D+SLRVP G  G V  V  
Sbjct: 939  GSEVKEGDILVGKITPQGNIEPSPSEKLIQIVIGEKAREYKDSSLRVPFGEGGIVQSVHY 998

Query: 945  FNRH-------GIDKNERSISVEREQIELLAR 969
            F+R        G+++N R    ++ +I    +
Sbjct: 999  FSRKNGDVLPAGVNENIRVFIAKKRKINEGDK 1030



 Score =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 167/511 (32%), Positives = 246/511 (48%), Gaps = 81/511 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR----VPSGVS 936
            I+ +G ++N GDILV   +   +  +     +  A    +  +  D  +     V   V 
Sbjct: 833  IVVLGEQINEGDILVSGPST-SQGELALGRNVTVAFMTWEGYNYEDAIIMSEELVKHDVY 891

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD---DEQVILDRNIYSRLMEILCGQ 993
             ++   +   +    K          ++  +  D     DE+ I+      +  +IL G+
Sbjct: 892  TSIHIDKYEVQTRELKKGSGQEEITREVPNVGADAIKNLDERGIIIPGSEVKEGDILVGK 951

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY-ETSKSILEDR 1052
                G              I   P  +  Q  + ++  +    SL+V + E         
Sbjct: 952  ITPQG-------------NIEPSPSEKLIQIVIGEKAREYKDSSLRVPFGEGGIVQSVHY 998

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F  K      GD +P GV   ++VF+A KR I  GDKMAGRHGNKG++SRILP ED+P++
Sbjct: 999  FSRK-----NGDVLPAGVNENIRVFIAKKRKINEGDKMAGRHGNKGVISRILPKEDLPYM 1053

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   + D+  +    
Sbjct: 1054 ADGTPIDIMLNPLGVPSRMNIGQILEIHLGMAAKKLGIKVATPVFDGVNDYDLKEIMKEA 1113

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                                       G
Sbjct: 1114 NLDPDGKMVL-----------------------------------------------YDG 1126

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            ++       GEP+D  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK   GGQ
Sbjct: 1127 RT-------GEPYDSRISVGVMYMVKLSHMVDDKLHARNVGPYTLVTQQPMGGKVQNGGQ 1179

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW + AYGAA+ LQE+LT+KSDD+VGR + Y +IV G    +   PESF V +K
Sbjct: 1180 RFGEMEVWALYAYGAAHTLQEILTVKSDDIVGRNKTYSAIVQGTPLPKPSIPESFRVFIK 1239

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            E+Q+LGL ++L  + TK +   + + D+ K 
Sbjct: 1240 ELQSLGLYVELIKTDTKENEVNKSLIDYKKE 1270


>gi|297179999|gb|ADI16224.1| hypothetical protein [uncultured bacterium HF0010_16H03]
          Length = 591

 Score =  653 bits (1685), Expect = 0.0,   Method: Composition-based stats.
 Identities = 277/596 (46%), Positives = 398/596 (66%), Gaps = 7/596 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG   +++D+P+LIE Q  SY  FL  ++APD R  +GL+  F+S+
Sbjct: 1   MSYSYTEKKRIRKNFGTFAKVMDLPNLIETQTKSYSEFLQADVAPDARKKQGLEDVFQSL 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + SG A LE+VSYE     +DV +CL + L+Y+ PL+I ++L+++D    +  K +
Sbjct: 61  FPIKSVSGNAALEYVSYELGKNTYDVQECLIQGLSYSAPLRIKVKLVLYDR--ESNFKEV 118

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKE  ++MG++PLMT D +FV+ G +R+VVSQLHRSPG+ +DHDKG+   SGK+LY+ 
Sbjct: 119 KDIKEGEVFMGEVPLMTSDASFVVNGTERVVVSQLHRSPGVFYDHDKGKTHSSGKVLYSA 178

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KDI+  RIDRRRK+P T  L AL M +EEILS FY + +++   
Sbjct: 179 RIIPYRGSWLDFEFDPKDILFSRIDRRRKIPATIMLRALDMGTEEILSEFYDEDLFTIDK 238

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           D     L    L  G  +   L      +  +E+GK++T+  +K L    V  + +  + 
Sbjct: 239 DTVKLALIPERL-RGETLPVDLKV--KSKVYVEAGKRITARHIKELSNAKVNEITLAEEF 295

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G  +++DI N ETGE+   A   IDE  L+ +  + + ++  L+++ ++   YI NTL
Sbjct: 296 LIGKVLSKDIFNKETGEVLFVANTEIDEVVLDSLKENNVNEVSCLFINELDKGPYISNTL 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   +R +AL++IYR+MRPG+  T   AE++F  LFF+ ++YDLS VGR+K N RL L
Sbjct: 356 RADPTSNRLEALVEIYRMMRPGEPPTKDSAETLFTNLFFNGERYDLSEVGRMKFNRRLKL 415

Query: 423 DTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
           D+  ++   + KEDII ++K +V++R+G   +DDID+LGNRRVRSVGEM  NQ+R+GL+R
Sbjct: 416 DSEKENPHILDKEDIIEVMKGIVNIRDGHDIVDDIDHLGNRRVRSVGEMTANQFRVGLIR 475

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER+++ER+S  + D + PQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 476 VERAVRERLSMAEADELGPQDLINAKPVTAAIKEFFGSSQLSQFMDQNNPLSEITHKRRV 535

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL-TSFARVNAYG 596
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+  L  +  ++N   
Sbjct: 536 SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIIPLPHTQEQINMDS 591


>gi|85057741|ref|YP_456657.1| DNA-directed RNA polymerase subunit beta [Aster yellows
            witches'-broom phytoplasma AYWB]
 gi|115305558|sp|Q2NJ15|RPOB_AYWBP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|84789846|gb|ABC65578.1| DNA-directed RNA polymerase beta chain [Aster yellows witches'-broom
            phytoplasma AYWB]
          Length = 1273

 Score =  652 bits (1683), Expect = 0.0,   Method: Composition-based stats.
 Identities = 356/1052 (33%), Positives = 548/1052 (52%), Gaps = 105/1052 (9%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            M    V  G    R+ + K    +D+P+LIE+Q  S+D FL            G++   +
Sbjct: 1    MGYHNVKYGKKAQRRNYSKTIYDVDLPNLIEIQNQSFDWFL----------KHGIKELLQ 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
               PI +++G   + F  Y   PPK+ +++   +D++Y   L +   L            
Sbjct: 51   DFCPIESYNGDLKIHFDDYFLTPPKYSIEETKIKDISYVAQLFVKTTL---------ENV 101

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               + K+ +I + +LPLMT  GTF+I G +R+VVSQ+ RS  ++F  +        + +Y
Sbjct: 102  LTGETKQSNILLTELPLMTSTGTFIINGTERVVVSQIVRSASVYFAGNFD--IKLNRTIY 159

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPK----- 235
            + ++IP +G W++ E  SK+I++ ++DR +K+P+++F+ ALG DS+E +   + K     
Sbjct: 160  SGQVIPSRGAWIEYEEGSKEILYAKLDRSKKIPLSNFIYALGFDSKEAIENVFGKSAILD 219

Query: 236  IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
             V+ +  D               +     VD            +    L K  + K  K 
Sbjct: 220  SVFDKETDMDSDNALVELYSKIRQGEKVPVDTARDFIRTRLFDQKKYDLAKVGRYKFNKK 279

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            L + +      Y+A D VN E  EI I   +++ ++ +  +  +    +  ++    N  
Sbjct: 280  LDVLT-RAENTYLACDFVNPENQEIMIAQDELLTKEKIAILKQNRHFLLQEIFDAKHNLE 338

Query: 356  AYIRNTLVTDKNKDRKDALL-----------------------DIYRVMRPGDVSTFSVA 392
                  ++  K   +K+ L                        DI   +R    +     
Sbjct: 339  NETDEEILAYKKYPQKNELFTKTNIINSRTGEVLVAKDTLVNDDIINHLRHNIHTLDEKV 398

Query: 393  ESMFNFLFFDSDKY----------------DLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
               F        K                    +         +  D  +  +HI   D+
Sbjct: 399  SKFFLGTKDIYQKEADRQGVFNEILEVYTSKDESGKLYNKVKLIGNDQRETKKHITLSDV 458

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI- 495
            IA I   ++L    GT+DDID+LGNRR+R +GE+LKNQ+R+GL R E++IK+ IS+    
Sbjct: 459  IASINYYLNLYENVGTVDDIDHLGNRRLRLIGELLKNQFRIGLTRAEKNIKDMISTSKFG 518

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            +   P DL+N   ++S +  FF +S+LSQ  + +N L+ +T  RR+SALG GG+ R RAG
Sbjct: 519  EVNGPGDLVNFTFLMSVIKTFFTNSRLSQFMDQINPLAELTQKRRVSALGIGGINRDRAG 578

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---- 611
            +E+RDVH +HYGR+CP ET EG +IGL++SL+++A+VN YGFI+TP+ KV          
Sbjct: 579  IEVRDVHNSHYGRLCPIETPEGPSIGLITSLSTYAKVNKYGFIQTPFFKVLQQDGKTTLS 638

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             D+ YL+A +E+   IA A   LD + SF ++ +  R  GE  +  R +I + D SPKQ+
Sbjct: 639  RDIDYLTADQEKEEIIASAGFVLDANNSFQDKKIIARSNGETGIFERNQITYADVSPKQI 698

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            VS+A S IPFLE++D++R LMG NMQRQAVPLL  E+P VGTG+E   AK SG  I+A+ 
Sbjct: 699  VSVATSSIPFLEHNDASRALMGANMQRQAVPLLIPESPIVGTGVEYRAAKDSGCLIIARE 758

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVD-------------------------IYRLMK 766
            +G V  VDA +I+I                                         Y L+ 
Sbjct: 759  SGFVTYVDAQKIIITKKPNQTVSLNGKTLYDTTQEFTYTQAKVLYENNHKEYQAEYTLIN 818

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F +SNQ+T V Q+P+V +G+ +   DI+  GPST  G+LALGRN+ VAFM W GYN+ED+
Sbjct: 819  FAKSNQDTLVLQKPIVVLGEHINEGDILVSGPSTSQGELALGRNVTVAFMTWEGYNYEDA 878

Query: 827  MLISERMVSEDVFTSIHIEEFEVMAR--DTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            +++SE +V  DV+TSIHI+++EV  R      G EEITR++PNV  + +KN+DE GII  
Sbjct: 879  IIMSEELVKHDVYTSIHIDKYEVQTRELKKGSGQEEITREVPNVGADAIKNLDERGIIIP 938

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G+EV  GDILVGKITP+G    +P EKL++ + GEKA + +D+SLRVP G  G V  V  
Sbjct: 939  GSEVKEGDILVGKITPQGNIEPSPSEKLIQIVIGEKAREYKDSSLRVPFGEGGIVQSVHY 998

Query: 945  FNRH-------GIDKNERSISVEREQIELLAR 969
            F+R        G+++N R    ++ +I    +
Sbjct: 999  FSRKNGDVLPAGVNENIRVFIAKKRKINEGDK 1030



 Score =  429 bits (1103), Expect = e-117,   Method: Composition-based stats.
 Identities = 169/511 (33%), Positives = 248/511 (48%), Gaps = 81/511 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR----VPSGVS 936
            I+ +G  +N GDILV   +   +  +     +  A    +  +  D  +     V   V 
Sbjct: 833  IVVLGEHINEGDILVSGPST-SQGELALGRNVTVAFMTWEGYNYEDAIIMSEELVKHDVY 891

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD---DEQVILDRNIYSRLMEILCGQ 993
             ++   +   +    K          ++  +  D     DE+ I+      +  +IL G+
Sbjct: 892  TSIHIDKYEVQTRELKKGSGQEEITREVPNVGADAIKNLDERGIIIPGSEVKEGDILVGK 951

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY-ETSKSILEDR 1052
                G              I   P  +  Q  + ++  +    SL+V + E         
Sbjct: 952  ITPQG-------------NIEPSPSEKLIQIVIGEKAREYKDSSLRVPFGEGGIVQSVHY 998

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            F  K      GD +P GV   ++VF+A KR I  GDKMAGRHGNKG++SRILP ED+P++
Sbjct: 999  FSRK-----NGDVLPAGVNENIRVFIAKKRKINEGDKMAGRHGNKGVISRILPKEDLPYM 1053

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   + D+  +    
Sbjct: 1054 ADGTPIDIMLNPLGVPSRMNIGQILEIHLGMAAKKLGIKVATPVFDGVNDYDLKEIMKEA 1113

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                       E     +L        G
Sbjct: 1114 NL-----------------------------------------EPDGKMVL------YDG 1126

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            ++       GEP+D  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK   GGQ
Sbjct: 1127 RT-------GEPYDSRISVGVMYMVKLSHMVDDKLHARNVGPYTLVTQQPMGGKVQNGGQ 1179

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW + AYGAA+ LQE+LT+KSDD+VGR + Y +IV G    +   PESF V +K
Sbjct: 1180 RFGEMEVWALYAYGAAHTLQEILTVKSDDIVGRNKTYSAIVQGTQLPKPSIPESFRVFIK 1239

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            E+Q+LGL ++L  + TK +   + + D+ K 
Sbjct: 1240 ELQSLGLYVELIKTDTKENEVNKSLIDYKKE 1270


>gi|99034581|ref|ZP_01314546.1| hypothetical protein Wendoof_01000639 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 708

 Score =  652 bits (1683), Expect = 0.0,   Method: Composition-based stats.
 Identities = 308/700 (44%), Positives = 461/700 (65%), Gaps = 22/700 (3%)

Query: 14  RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           R  + ++ ++ D + DL++VQK SYD F      P  + NE L+  F ++FPI      A
Sbjct: 16  RVSYSRSIDLKDSLLDLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLRRA 70

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTG 118
            +EF+S   D PK+D  +C+ R +T++  +  ++RL+V                 D    
Sbjct: 71  TIEFISCRVDDPKYDESECIKRGVTFSAQVIASIRLVVMQDGISLDEYKSIKESGDHSKL 130

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
           A  +K I+EQ ++   LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL
Sbjct: 131 ATVVKSIEEQKVHFCGLPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

Query: 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
           +Y+ RIIP  G W+DIEFD KD ++ R+DR+RK+P++  L ALG+ + +IL  FY KI Y
Sbjct: 191 IYSARIIPYMGSWLDIEFDVKDHLYFRVDRKRKLPISVLLKALGLSNNDILDRFYEKIKY 250

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D W  P    D   G ++   L+DI+ G  ++++  ++TS L K L +  +K   +
Sbjct: 251 VKHKDGWKVPFVP-DKFKGVRLPFDLMDIE-GNVLLKANVRITSRLAKKLYDNELKEYLV 308

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + +CGL++AED++   +    + AG+ I  + ++++    + +I +L + ++    YI
Sbjct: 309 PFNSICGLFLAEDLMGSASSTKILSAGESIKLEDIKKLELLSVNEISLLNIHNLFVGPYI 368

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            NTL  D+N   +DAL +IYRV+RPG++    + E  F  LFF  + YDLS +GR+K+N 
Sbjct: 369 LNTLFLDENMSYQDALYEIYRVLRPGELPVLQIVEEFFRNLFFSPEYYDLSNIGRLKLNS 428

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            L L+  +D+  +  EDII I+K +V LR+G+G++DDID+LGNRRVRSVGE ++NQ+R G
Sbjct: 429 YLGLNYDEDLTVLTHEDIIEIVKKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTG 488

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           LL++ER+I + +S+  +D V P D IN K + + + +FF SSQLSQ  +  N LS ITH 
Sbjct: 489 LLKLERAIVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL  +AR+N YGFI
Sbjct: 549 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFI 608

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYRKV +  VT+ + YLSA++E + +IA  +  LDE+  F +++++CR AG  ++V  
Sbjct: 609 ESPYRKVVNRVVTDQIEYLSAIDEGSHHIADTSVKLDENNCFVDDMLYCRYAGSFVMVSS 668

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           +++ ++D SPKQV+S+AASLIPFLENDD+NR LMG NMQR
Sbjct: 669 DQVSYMDVSPKQVISVAASLIPFLENDDANRALMGSNMQR 708


>gi|154250447|ref|YP_001411272.1| DNA-directed RNA polymerase subunit beta [Fervidobacterium nodosum
           Rt17-B1]
 gi|182676563|sp|A7HNY2|RPOB_FERNB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|154154383|gb|ABS61615.1| DNA-directed RNA polymerase, beta subunit [Fervidobacterium nodosum
           Rt17-B1]
          Length = 1182

 Score =  642 bits (1657), Expect = 0.0,   Method: Composition-based stats.
 Identities = 371/978 (37%), Positives = 580/978 (59%), Gaps = 115/978 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS- 69
            R R  FGK  EII +PDL+E+Q+ S++  L          N G+    K   PIT+   
Sbjct: 8   KRTRYSFGKVDEIIQVPDLVEIQRKSFEELL----------NHGILRILKKFSPITSAKV 57

Query: 70  -----GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                    LEFV++    P   V++C  R LTY  P   T+R+            S  +
Sbjct: 58  EGRREKGFNLEFVNFRVGAPLHSVEECKQRLLTYVAPFYATVRVT---------DVSTGE 108

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           ++E+ + +G+ P+MT++ TFVI G++R+VVSQL RSPG++F  +  +   + K +Y    
Sbjct: 109 MREEEVSLGNYPIMTENQTFVINGVERVVVSQLVRSPGVYFVEEPTKNIGA-KPIYLAHF 167

Query: 185 IPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           +P +G+W++I  +  D  ++ RIDRR+++ +   L  LG  ++ +ILS F     Y    
Sbjct: 168 LPVRGVWLEIMLNLNDETLYARIDRRKRLNLFLVLKTLGFQNDIDILSLF---PAYLDVE 224

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           D +    S   +++   VS       +GE + E G  LTS L++ L+E G++ + + ++ 
Sbjct: 225 DDYSLKQSEGIIILEKIVS------KSGEVIAEKGSVLTSTLVEILREHGIEKIKVVNNY 278

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           +   Y+              E   +  E+++ E+                          
Sbjct: 279 MFKTYMK-----------LKEKLKMPLEENISELR------------------------- 302

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-- 420
                     A ++IY+ +RPG+V  ++ A+S +N L+F+ ++++LS VGR KMN +L  
Sbjct: 303 ----------AFMEIYKELRPGEVFRYNAAKSYWNNLYFNEERFELSEVGRYKMNKKLTN 352

Query: 421 ------------------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
                              ++  +    +   DII +I++L++      T+D  D+L N+
Sbjct: 353 AYRKYLIEIEGRNPKSVERIEYEEKSNALTPIDIILVIRMLLETEKHPETLDTKDHLSNK 412

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RV++VGE++ +++     +    I+E+  +   +D +    LIN + V++++  FF ++ 
Sbjct: 413 RVKTVGELIGSEFERAFSKSIHQIQEKLATYTSLDKISIPSLINLRNVIASLNSFFATNP 472

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  + VN ++ +TH RRL+A+G GG+ R RA  E+RDVH +HYGR+CP ET EG NIG
Sbjct: 473 LSQFMDQVNPIAELTHKRRLTAVGPGGLKRERARFEVRDVHHSHYGRMCPIETPEGGNIG 532

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ +A ++ YGF+ TPYR++ +GK+ N+VVYL+A EEEN  IA    + D++G+  
Sbjct: 533 LITSLSVYATIDEYGFLVTPYRRITNGKLANEVVYLAADEEENYKIASVTIAFDKEGNII 592

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           +E V  R   + + V + ++D +D SPKQ+VS+  SLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 593 QERVPVRYLEKIVYVHKNEVDLVDISPKQIVSVTTSLIPFLEHDDANRALMGSNMQRQAV 652

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-----DLDPST 756
           P++K EAPFVGTGME   A  SG  ++AK  G+V++VD  +I+I  ++            
Sbjct: 653 PVIKPEAPFVGTGMEYAAAIYSGHVVLAKNDGVVKKVDGRKIIIHRIDENGQLMYDKKGN 712

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +D Y L+K+ RSNQ+T + Q+P+V VGD V++   IADGP+TD G+LALG+N+LVAF+
Sbjct: 713 PIIDEYTLLKYVRSNQDTSITQKPIVNVGDFVKKGSPIADGPATDNGELALGKNVLVAFL 772

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW GYNFED++L+SE ++ ED FTS+HIE +E  AR+T++GPEEIT +IPNVS+E ++N+
Sbjct: 773 PWEGYNFEDAILVSEELLEEDTFTSVHIEVYETTARETRVGPEEITSEIPNVSKENIRNL 832

Query: 877 DECGIICVGAEV------NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           DE GII +GA V         DILVGK+TPKGES  +PEEK++R++FGEK  DV+D+SLR
Sbjct: 833 DENGIIRIGAYVGKQKYFTSQDILVGKVTPKGESDASPEEKIMRSVFGEKGKDVKDSSLR 892

Query: 931 VPSGVSGTVVDVRIFNRH 948
           VP GV G V+ V +F++ 
Sbjct: 893 VPHGVEGRVIGVHVFHKE 910



 Score =  434 bits (1117), Expect = e-119,   Method: Composition-based stats.
 Identities = 162/500 (32%), Positives = 242/500 (48%), Gaps = 60/500 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG-VSGTV 939
            I+ VG  V  G  +           +   + +L A    +  +  D  L         T 
Sbjct: 737  IVNVGDFVKKGSPIADGPATDN-GELALGKNVLVAFLPWEGYNFEDAILVSEELLEEDTF 795

Query: 940  VDVRIFNRHGIDKNERSISVE-REQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
              V I       +  R    E   +I  ++++     DE  I+    Y    +    Q+ 
Sbjct: 796  TSVHIEVYETTARETRVGPEEITSEIPNVSKENIRNLDENGIIRIGAYVGKQKYFTSQDI 855

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            + G    K  +  S +   +  RS + +   + + V+ +   +    E     +    K 
Sbjct: 856  LVGKVTPKGESDASPE--EKIMRSVFGE---KGKDVKDSSLRVPHGVEGRVIGVHVFHKE 910

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++     GD + PGV  +V+V++A ++P++ GDK+AGRHGNKG+VS ILP EDMPFL DG
Sbjct: 911  EV-----GD-LGPGVNTLVRVYLATRKPLEVGDKLAGRHGNKGVVSMILPKEDMPFLPDG 964

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VL+PLGVPSRMN+GQ+ ET LGW      +   + + D     DI P    + + 
Sbjct: 965  TPVQVVLSPLGVPSRMNIGQVLETSLGWLAKLTNRYFATPVFDGAKEDDILPELYKVRET 1024

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +      +                                             + SG+  
Sbjct: 1025 LNLHHGDDPN-------------------------------------------NPSGKVT 1041

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TG+ FD PV VGY+Y++KL H+  DK++AR+TG YSL+ QQPLGGK+  GGQR G
Sbjct: 1042 LRDGRTGKEFDFPVLVGYMYIMKLIHIARDKIHARATGPYSLIHQQPLGGKAQFGGQRFG 1101

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+Y L EMLT+KSDD+ GRT VY++I+   +  E G PESF VLV+E++
Sbjct: 1102 EMEVWALEAYGASYTLNEMLTVKSDDIKGRTEVYKAIMKSKNLPEPGLPESFKVLVRELK 1161

Query: 1356 ALGLSIDLENSRTKNSAKME 1375
             L L + + +         +
Sbjct: 1162 GLALDVRVYDEHGNEIDIEK 1181


>gi|78043606|ref|YP_361127.1| DNA-directed RNA polymerase subunit beta [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|88909127|sp|Q3A9Q7|RPOB_CARHZ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|77995721|gb|ABB14620.1| DNA-directed RNA polymerase, beta subunit [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 1132

 Score =  641 bits (1653), Expect = 0.0,   Method: Composition-based stats.
 Identities = 346/950 (36%), Positives = 483/950 (50%), Gaps = 131/950 (13%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
           V  G   +R  + K PEI+++P LIE+QK SY  FL          +EGL+  F+ + PI
Sbjct: 4   VQVGKK-IRYSYAKFPEILELPYLIEIQKKSYQWFL----------DEGLREVFREISPI 52

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           T F+G   LEF+ Y    PK+ V++C  RD TY+ PL++ +RL+          K   +I
Sbjct: 53  TDFTGNLSLEFLDYYLGKPKYSVEECKERDFTYSAPLRVKVRLL---------NKETGEI 103

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           KEQ +++GD PLMT+ GTF+  G +R+V+SQ+ RSPG++F         +GK +Y   II
Sbjct: 104 KEQEVFLGDFPLMTEKGTFIFNGAERVVISQMVRSPGVYFSEQVD---PNGKKMYLATII 160

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDF 244
           P++G W++ E D  D I+VRIDR RK+PVT  L ALG +S+  I   F          + 
Sbjct: 161 PNRGAWLEFETDVNDHIYVRIDRTRKLPVTVLLKALGYESKGRIAELFDHDDKIIATLER 220

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                    L+   K       +  GE   +ES K L   +    K   +          
Sbjct: 221 DNTDSREEALIEIYK------KLRPGEPPTVESAKTLLDSMFFDPKRYDLGN-------- 266

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G Y     +N                               +LY     +     +  +
Sbjct: 267 VGRYKLFKKLNHG-----------------------------VLYRYLEEDGEKEYDKYL 297

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D    +++ + ++                             D+    R  + +     
Sbjct: 298 NDYVPVKREFIREL--------------------------TNEDIIYTIRYLLGLMRGQG 331

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
             DD+ H+    + ++ ++L +     G       +  R      + L  Q  +    + 
Sbjct: 332 KVDDIDHLGNRRLRSVGELLQNQFR-IGLARMERVVRERMTIQDADSLTPQVLINTRPIV 390

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE-EHVNSLSRITHTRRLS 542
            +IKE   S  +   M Q    A+              LS+            +H  R+ 
Sbjct: 391 AAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMC 450

Query: 543 AL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            +    G      G          +G I           G+V++   +   +        
Sbjct: 451 PIETPEGPNIGLIGNLTTYARVNEFGFIETPYRKVDKERGVVTNEIVYLTAD-------- 502

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                              EE    IAQAN  L  +G F +E+V  R   E + V   K+
Sbjct: 503 ------------------EEE-KYIIAQANVRLSPEGKFLDEMVNARHGSEILHVEPSKV 543

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           DF+D SPKQV S+A SLIPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTG+E   AK
Sbjct: 544 DFVDVSPKQVFSVATSLIPFLEHDDANRALMGANMQRQAVPLIRTEAPVVGTGIEYKAAK 603

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  ++AK  G+VE+V A  IVIR+ +G        +D Y+L+KFQRSNQ TC+NQ+P+
Sbjct: 604 DSGVVVLAKNPGVVERVTADEIVIRNDQGQ-------IDRYKLIKFQRSNQGTCINQKPI 656

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+ G+ V ++ IIADGPSTD G+LALG+N+LVA+MPW GYN+ED++LISE++V EDVFTS
Sbjct: 657 VRKGERVEKDQIIADGPSTDHGELALGKNVLVAYMPWEGYNYEDAILISEKLVKEDVFTS 716

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV PGDILVGK+TPK
Sbjct: 717 IHIEEYECDARDTKLGPEEITRDIPNVGEDALKDLDERGIIRIGAEVRPGDILVGKVTPK 776

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 777 GETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGKVVDVKVFSRENGD 826



 Score =  510 bits (1312), Expect = e-141,   Method: Composition-based stats.
 Identities = 192/538 (35%), Positives = 252/538 (46%), Gaps = 83/538 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  + I          I++  I+  G  V   D ++          +   + +
Sbjct: 628  RNDQGQIDRYKLIKFQRSNQGTCINQKPIVRKGERVE-KDQIIADGPSTDHGELALGKNV 686

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    +  +  D  L     V   V        +  + + R   +  E+I        
Sbjct: 687  LVAYMPWEGYNYEDAILISEKLVKEDVFTSIHIEEY--ECDARDTKLGPEEITRDIPNVG 744

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 745  EDALKDL-DERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 797

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   K+   + GD++ PGV  +V+V++A KR I
Sbjct: 798  -----------EVRDTSLRVPHGESGKVVDVKVFSRENGDELSPGVNMLVRVYIAQKRKI 846

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+V+RILP EDMPFL DGTPV+IVLNPLGVPSRMN+GQI E HLGWA
Sbjct: 847  SVGDKMAGRHGNKGVVARILPEEDMPFLPDGTPVEIVLNPLGVPSRMNIGQILECHLGWA 906

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + I +     DI                                   K+G+
Sbjct: 907  AKALGINVATPIFNGATEEDIFEALR------------------------------KAGL 936

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P                        E G+  + DG TGEPFD  VTVGY+YMLKL H+V 
Sbjct: 937  P------------------------EDGKIEVRDGRTGEPFDSRVTVGYVYMLKLAHLVD 972

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVG
Sbjct: 973  DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVG 1032

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            R + YE+IV G +  E G PESF VL+KE+Q+LGL + +     +     E   D  +
Sbjct: 1033 RVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVKVLTDNDEEVEIKEIDDDIGE 1090


>gi|254237130|ref|ZP_04930453.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Pseudomonas aeruginosa C3719]
 gi|126169061|gb|EAZ54572.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Pseudomonas aeruginosa C3719]
          Length = 544

 Score =  640 bits (1651), Expect = 0.0,   Method: Composition-based stats.
 Identities = 243/544 (44%), Positives = 355/544 (65%), Gaps = 4/544 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK F K P+++D+P L+ +Q  SY  FL      ++  + GL AAFKSV
Sbjct: 1   MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDIGLHAAFKSV 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG A LE+V Y    P FDV +C+ R +T+AVPL++ +RLI+FD    +  K+I
Sbjct: 61  FPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDR--ESSNKAI 118

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT++GTF+I G +R++VSQLHRSPG+ FDHD+G+   SGKLLY+ 
Sbjct: 119 KDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSA 178

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P +  L ALG  +EEIL+ FY   V+  +G
Sbjct: 179 RIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKG 238

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  + D  +G+ ++E G+++T+  +  L++ GV  L +  D 
Sbjct: 239 ETLNLELVPQRL-RGEVASIDIKDG-SGKVIVEQGRRITARHINQLEKAGVSQLEVPFDY 296

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G  +A+ IV+  TGEI  E    +    L ++  +++  I  LY + ++   +I +TL
Sbjct: 297 LIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTL 356

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   ++ +AL++IYR+MRPG+  T   AE++F  LFF +++YDLS VGR+K N R+  
Sbjct: 357 KIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGR 416

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
              +    + KEDII ++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+
Sbjct: 417 TEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRV 476

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQ+LINAKPV +A+ EFF S     +    N   R    RR+S
Sbjct: 477 ERAVKERLSMAESEGLMPQNLINAKPVAAAIKEFFGSKPAVAVHGQNNPGFRDHRQRRVS 536

Query: 543 ALGQ 546
           A+G 
Sbjct: 537 AVGP 540


>gi|10638379|emb|CAC10572.1| DNA-dependent RNA polymerase subunit beta [Weissella
           paramesenteroides]
          Length = 929

 Score =  639 bits (1649), Expect = 0.0,   Method: Composition-based stats.
 Identities = 374/831 (45%), Positives = 510/831 (61%), Gaps = 65/831 (7%)

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT  GTF+I G +R++VSQL RSPG++++ +  +   +G+  Y    IP +G W++ E
Sbjct: 1   PLMTPTGTFIINGAERVIVSQLVRSPGVYYNEELDK---NGRPNYGTTFIPSRGAWLEFE 57

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKIVYSQRGDFWCFPLSA 251
            D+K + +VRIDR RK+P+T  + ALG  S+ EIL      Y  I  +   D        
Sbjct: 58  TDAKGLSYVRIDRTRKLPITELVRALGYGSDSEILQMLGDQYDSISLTLDKDVHK---DI 114

Query: 252 ADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DC 302
               V   +      +  GE    +S + L +      K   +  +G             
Sbjct: 115 EHSRVEEALKDIYERLRPGEPKTADSARALLTARFFDPKRYDLAPVGRYKINKKLSLKSR 174

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L GL + E + +  TGEI  E G +ID+K +  +                      R   
Sbjct: 175 LMGLTLGETLADPYTGEIIAEKGTLIDKKVMSALSPYLD-----------------REDF 217

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                    DA++           +   V +++      D +K  L  +G  + +  +  
Sbjct: 218 KRTTFTPSDDAVV-----------TEPMVLQTILVENPEDPEK-TLPIIGNGQFDPAI-- 263

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 R ++  DIIA +   ++L  G GT DDID+LGNRR+R VGE+L+N +R+GL RM
Sbjct: 264 ------RTVKPADIIAGMNYFLNLPLGVGTTDDIDHLGNRRIRRVGELLQNTFRIGLSRM 317

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER+S  D D+V PQ LIN +PVV+AV EFF SSQLSQ  +  N L  +T+ RRLS
Sbjct: 318 ERVVRERMSIQDPDTVTPQQLINIRPVVAAVKEFFGSSQLSQFMDQTNPLGELTNKRRLS 377

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+ P ET EG NIGL++SL ++ RVN YGFIETPY
Sbjct: 378 ALGPGGLTRDRAGYEVRDVHYTHYGRMDPIETPEGPNIGLINSLATYGRVNKYGFIETPY 437

Query: 603 RKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R+V     KVT+ + YL+A EE+N  +AQ NS L+EDGSF  + V  R + E + VP ++
Sbjct: 438 RRVDWTTHKVTDRIDYLTADEEDNFVVAQGNSVLNEDGSFATDTVLARKSDENVEVPIDQ 497

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D SPKQ+V++A + IPFL NDDSNR LMG NM+RQAVPL+   AP +GTG+E   A
Sbjct: 498 VDYMDVSPKQIVAVATAAIPFLXNDDSNRALMGANMRRQAVPLIDPHAPLIGTGIEYKAA 557

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             +G AI+++  G+VE VD   I +R  +G LD        Y LMKF+RSN     NQRP
Sbjct: 558 HDAGVAIISQYPGVVEYVDGREIRVRREDGSLDK-------YALMKFRRSNAGKNYNQRP 610

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +VKVGD+V  ++++ADGPS + G+LALG+N L+AFM W GYNFED+++I+ER++ +DV+T
Sbjct: 611 IVKVGDKVDADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAIIINERLIRDDVYT 670

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEE TR+IPN  E+ LKN+DE GII +GAEV  GDILVGK+TP
Sbjct: 671 SIHIEEYESEARDTKLGPEEFTREIPNTGEDQLKNLDERGIIRIGAEVEDGDILVGKVTP 730

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G V DVRIF R   D
Sbjct: 731 KGVTELSAEERLLHAIFGEKAREVRDTSLKVPHGGGGFVQDVRIFTRENGD 781



 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 105/417 (25%), Positives = 170/417 (40%), Gaps = 73/417 (17%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +        KN ++  I+ VG +V+  ++L    +   +  +   +  
Sbjct: 583  RREDGSLDKYALMKFRRSNAGKNYNQRPIVKVGDKVDADEVLADGPS-MEQGELALGQNP 641

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE---REQIELLAR 969
            L A    +  +  D  +         + D    + H  +    +   +    E    +  
Sbjct: 642  LIAFMTWQGYNFEDAIIIN----ERLIRDDVYTSIHIEEYESEARDTKLGPEEFTREIPN 697

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +D+   LD     R+   +   + + G    K  T LS++       + + + A +  
Sbjct: 698  TGEDQLKNLDERGIIRIGAEVEDGDILVGKVTPKGVTELSAE--ERLLHAIFGEKAREVR 755

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 V      +             +I   + GD++ PGV  +V+V++A +R IQ GDK
Sbjct: 756  DTSLKVPHGGGGFVQ---------DVRIFTRENGDELSPGVNMMVRVYIAQRRKIQVGDK 806

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            M GRHGNKG VS I+P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG A   LG
Sbjct: 807  MXGRHGNKGTVSVIVPSEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLELHLGMAARELG 866

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + S + D   + DI                                   ++G+P    
Sbjct: 867  IHVASPVFDGARDTDIWDAIQ------------------------------EAGLP---- 892

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                       S+L        G        TGE FD+ V+VG ++ +KL HMV DK
Sbjct: 893  -------ADGKSIL------YDG-------RTGEAFDKRVSVGIMHYMKLAHMVDDK 929


>gi|293391584|ref|ZP_06635918.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
            actinomycetemcomitans D7S-1]
 gi|290952118|gb|EFE02237.1| DNA-directed RNA polymerase, beta subunit [Aggregatibacter
            actinomycetemcomitans D7S-1]
          Length = 440

 Score =  638 bits (1646), Expect = e-180,   Method: Composition-based stats.
 Identities = 234/456 (51%), Positives = 329/456 (72%), Gaps = 18/456 (3%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            +RAIFGEKA DV+D+SLRVP+ VSGTV+DV++F R G++K++R++ +E  Q++   +D  
Sbjct: 1    MRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLS 60

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +E  IL+  +++R+  +L                   +  + +  R++W +  + +E+ Q
Sbjct: 61   EEFEILEAGLFTRVRNLLLSGG-------------FDAKSLDKLDRTKWLEQTLDNEEKQ 107

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              +E L  Q+E  +   E + + +  KI  GDD+ PGVL+VVKV++A+KR IQ GDKMAG
Sbjct: 108  HQLEQLAEQHEELRKEFERKLEVQRNKIIQGDDLAPGVLKVVKVYLAVKRQIQPGDKMAG 167

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+GQI ETHLG A  G+G +I
Sbjct: 168  RHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNIGQILETHLGLAAKGIGDQI 227

Query: 1153 KSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             ++I   K    I+ LR +++K    G GS    +S + D+ V+R+A+  + G+PV+TPV
Sbjct: 228  NAMI---KQQQSIAKLREYMQKAYDLGGGSQKVDLSTFTDEEVMRLAQNLRKGLPVATPV 284

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FDGA E+ I  +L +  L  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+V DK++AR
Sbjct: 285  FDGAHEKEIKGLLELGGLPISGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHAR 344

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y+
Sbjct: 345  STGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYK 404

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +IV+GN   + GTPESFNV++KE+++LG++IDL+  
Sbjct: 405  NIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 440


>gi|12045200|ref|NP_073011.1| DNA-directed RNA polymerase subunit beta [Mycoplasma genitalium G37]
 gi|255660262|ref|ZP_05405671.1| DNA-directed RNA polymerase subunit beta [Mycoplasma genitalium G37]
 gi|1350845|sp|P47583|RPOB_MYCGE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|3844923|gb|AAC71566.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma genitalium G37]
 gi|166078792|gb|ABY79410.1| DNA-directed RNA polymerase, beta subunit [synthetic Mycoplasma
            genitalium JCVI-1.0]
          Length = 1390

 Score =  638 bits (1645), Expect = e-180,   Method: Composition-based stats.
 Identities = 314/1457 (21%), Positives = 560/1457 (38%), Gaps = 144/1457 (9%)

Query: 1    MAKGVVFNGLG----RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M++   F          R+++GK       P+L ++Q  SY  FL  +          L+
Sbjct: 1    MSQKSNFFQKRYSPTATRRYYGKIETNFIQPNLADIQIKSYQKFLDHD----------LE 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                S FPI + +    + F       P+ D      +  TY V +   L L+  D    
Sbjct: 51   KLIASYFPIKSPNDRYTINFRGLHRTEPERDEAQSRAQSKTYEVGIYADLELVDNDKGTV 110

Query: 117  TGAKSIKDIKEQS---IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRA 172
              A+  K     +   +++  +PL+T DG F+I GI++ V+SQ+ RSPGI+     + + 
Sbjct: 111  KKARKSKKNIASNTNGVFLASMPLITHDGVFIINGIEKFVISQITRSPGIYMLTKSQLKL 170

Query: 173  SLSGKLL---YACRIIPDQGLWMDIEFDSKDII---HVRI---DRRR---KV-PVTSFLM 219
            S S K +   Y C ++P  G  M I   +K  I    V+I   D  R   K+ P+T+ L 
Sbjct: 171  SNSRKRVQEGYVCEVLPANGSVMLIYISNKKKIEDAFVQILLRDAVREGAKIFPITTLLK 230

Query: 220  ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
            A G+++ EIL  F       +  +   +        V  ++ + L +   G+        
Sbjct: 231  AFGLNNREILKIFKNNEFIKRSLEAEIYNAKDFLSNVDPEIKNLLKEFRDGKT------- 283

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                    L+ KG+                    + +   +  E   +  + +  +    
Sbjct: 284  -------DLRRKGIAS------------------DQKLRSLVNEYVTLEKQYNALKQTSP 318

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                +  L ++  N    + + +     K   + L    R +   +        ++    
Sbjct: 319  NDSSLTALELEMENK---MDSVITERAAKHIVNELSISLRDIENTEECHEVSFHALLCAR 375

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            FF + +Y+LS  GR K++ +L L      + +  +  +   K+L+         ++ID +
Sbjct: 376  FFRNKRYNLSNAGRYKVSRKLRLTERIYQKTLACDLFLKDGKLLLKKGT-LLLKEEIDKI 434

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                  +    +         +     KE +    ID  +  D ++    V  +      
Sbjct: 435  KQAAKNNEISFVNKMQLTTDGKAVDLAKESLFYETIDVYITNDNLSVSVPVIGIHNENDL 494

Query: 520  SQLSQLEEHVNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            ++   L + + S+S + +             +   R  +    +           E    
Sbjct: 495  NKAMTLSDFIASISYVINLPYGIGKYDDIDHLGNKRVKLINELITAKLESGFTRMERFLK 554

Query: 578  HNIGLVSSLTSFARVNAYGFI----ETPYRKVCDGKVTNDV-----VYLSAMEEENRYIA 628
              + +   +    ++N  G +    E     +     +  +      + +  +       
Sbjct: 555  EKLTIADGVNRGQQINEEGQVIEQGEKKELTIKSLINSKPIQIVIKDFFNTHQLTQFLDH 614

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            Q   S   +      +     + E+  +    + +        +     +   L    ++
Sbjct: 615  QNPLSELSNKRRISAMGPGGISREDPNLDIRDVHYSQYGRICPIETPEGMNIGLIMSLAS 674

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
               +  N      P  K +A  +   +E + A      I+A+ + +V   +  +I+ + +
Sbjct: 675  FAKIDENGF-LMAPYRKIKAGVITDEVEYLTALREDEHIIAEISSLVNISNDNKILDKEI 733

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS--TDLGDLA 806
             G         D  ++     +          +V +G  +       D            
Sbjct: 734  IGRYRSMQGLYDPLKIDYIDVAPHQ-------VVSIGSSLIPFLENDDSARALMGTNMQR 786

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERM-VSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                ++  + P  G   E  +     + +S      +   +   +   +    +E    +
Sbjct: 787  QAYPLIKPYAPAVGTGQEHKIASDSGLTMSSPCSGVVSYVDNSKIIITSDSSKKETVNLV 846

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                       +   I+ +G  VN  +I+V       +S +   + +L A       +  
Sbjct: 847  KFERSNQNTCYNHKPIVEIGQRVNKDEIIVDGP-AVNKSELALGQNVLVAFTTWNGYNYE 905

Query: 926  DTSLRVPSGVSGTV-----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
            D  +     V   +     ++  +         +  I+ +   +    +   DE  I+  
Sbjct: 906  DAIVISERLVKEDILTSLTINEYVAQCLSTKNGDEQITRDIPNVSDANKRYLDENGIIMV 965

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                +  ++L G+ +  G         L   +  E  ++           V+ +   +  
Sbjct: 966  GAEVKEGDVLVGKVSPKGQVEVSPEEKLFKAIFPESVQN-----------VRDSSLKVSH 1014

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              +   S +      K   I  GD++  GV+ ++KV+V  KR IQ GDK+AGRHGNKG++
Sbjct: 1015 GGDGIVSAV------KRFSIANGDELNDGVIEMIKVYVVQKRKIQIGDKLAGRHGNKGVI 1068

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL------------ 1148
            S+++P EDMP L+DGTPVDI+LNPLGVPSRMN+GQIFETHLG+A   L            
Sbjct: 1069 SKVVPIEDMPHLEDGTPVDILLNPLGVPSRMNIGQIFETHLGYAAHKLAVRSLISSCFDQ 1128

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG----- 1203
             K  +  I   +    +  L   L+  I   +   +    +      ++   K       
Sbjct: 1129 NKAKEFAIEINQPQARVERLIKGLKNQINDRNIKSEKEALEKLDNSDISLVLKEIGMSFD 1188

Query: 1204 ---VPVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYML 1257
                 ++TP+F G +   +  +++ A LD     G+  L DG +G PF+RP+++G +YM+
Sbjct: 1189 DLIYKIATPIFQGVNFLDLQDVMQEAGLDPQKNQGKFKLIDGRSGMPFERPISLGIMYMM 1248

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KLNHMV DK++AR+ G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY LQE+LTI
Sbjct: 1249 KLNHMVDDKIHARAVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYNLQELLTI 1308

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM--- 1374
            KSDDV GR R Y +IV G    E G PESF +L KE+Q L LS+                
Sbjct: 1309 KSDDVQGRNRAYAAIVKGAAFPEPGIPESFKLLTKELQGLALSVSFIYDDNTQQDSNNVS 1368

Query: 1375 ------EEIPDFNKCEL 1385
                  E+   FN  E 
Sbjct: 1369 ILQSDGEQDEFFNDFEF 1385


>gi|294792784|ref|ZP_06757931.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. 6_1_27]
 gi|294456683|gb|EFG25046.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. 6_1_27]
          Length = 1268

 Score =  638 bits (1645), Expect = e-180,   Method: Composition-based stats.
 Identities = 379/842 (45%), Positives = 512/842 (60%), Gaps = 92/842 (10%)

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G W+++E D
Sbjct: 1   MTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGAWIELETD 57

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAAD 253
           + +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D
Sbjct: 58  ASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERIVRTLEKD 117

Query: 254 LMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DC 302
                   +      +  GE   +ES + L   L    +   +  +G             
Sbjct: 118 TTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQR 177

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI N  
Sbjct: 178 MLGQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYIVNND 231

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +      +  L                              YD  TV R         
Sbjct: 232 GVESKVICNNCNL-----------------------------PYDHRTVTR--------- 253

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                      ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RM
Sbjct: 254 -----------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRM 302

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 303 ERVVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 362

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PY
Sbjct: 363 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPY 422

Query: 603 RKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           RKV                 V++ VVY++A EEE   IAQANS LD +G FT E V CR 
Sbjct: 423 RKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTTEHVACRR 482

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP
Sbjct: 483 GHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAP 542

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y L KF R
Sbjct: 543 LVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYHLNKFLR 596

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+
Sbjct: 597 SNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILL 656

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+
Sbjct: 657 SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVH 716

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R  
Sbjct: 717 PGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTREN 776

Query: 950 ID 951
            D
Sbjct: 777 GD 778



 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 105/220 (47%), Positives = 143/220 (65%), Gaps = 5/220 (2%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        +I         D     + +   +G+ ++TPVFDGA
Sbjct: 983  EELEAISKVKNTLNNIHSAEEKRVEIRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1042

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1043 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1102

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV 
Sbjct: 1103 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKAYEKIVK 1162

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            G +  E G PESF VL+KE+Q++GL + + N   +     
Sbjct: 1163 GENIPEPGVPESFKVLLKELQSIGLDVKILNEDQEEVVMK 1202



 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 182/849 (21%), Positives = 306/849 (36%), Gaps = 68/849 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 76   VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 131

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 132  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 191

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 192  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 250

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQG--GVARARAG 555
                     +            L  L +       I H   RRL  +G+      R    
Sbjct: 251  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLT 300

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
               R V      R+   ET       L++     A       I+  +      +  +   
Sbjct: 301  RMERVVRE----RMTIQETESITPQALINIRPVVA------AIKEFFGSSQLSQFMDQTN 350

Query: 616  YLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             L+ +  + R  A     L  +   F    V     G    +   +   I          
Sbjct: 351  PLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYA 410

Query: 675  AASLIPFLE--NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
              +   F+E       +V        + V +  +++    T  E      + A       
Sbjct: 411  KVNEFGFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQAN---SPL 467

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
                      +  R     L+ +   VD   +              + +V +G       
Sbjct: 468  DAEGYFTTEHVACRRGHDVLEVTPDKVDYMDVSP------------KEVVSIGTAMIPFL 515

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 516  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 575

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  +       +        ++  I+  G  V  G +L       G   +  
Sbjct: 576  IHVLRDSDGRVDTYHLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 634

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-EL 966
               +L A    +  +  D  L           D+    +    + + R   +  E+I   
Sbjct: 635  GYNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRE 691

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            L    DD    LD +       I  G     G     K+T      +   P  +  +   
Sbjct: 692  LPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIF 744

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  
Sbjct: 745  GDKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHE 800

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  
Sbjct: 801  GDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQ 860

Query: 1147 GLGKKIKSL 1155
            GLG KIK+ 
Sbjct: 861  GLGMKIKAT 869


>gi|294794538|ref|ZP_06759674.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. 3_1_44]
 gi|294454868|gb|EFG23241.1| DNA-directed RNA polymerase, beta subunit [Veillonella sp. 3_1_44]
          Length = 1270

 Score =  637 bits (1643), Expect = e-180,   Method: Composition-based stats.
 Identities = 379/842 (45%), Positives = 512/842 (60%), Gaps = 92/842 (10%)

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G W+++E D
Sbjct: 1   MTDTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGAWIELETD 57

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAAD 253
           + +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D
Sbjct: 58  ASEVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERIVRTLEKD 117

Query: 254 LMV--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DC 302
                   +      +  GE   +ES + L   L    +   +  +G             
Sbjct: 118 TTQSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQR 177

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI N  
Sbjct: 178 MLGQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYIVNND 231

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +      +  L                              YD  TV R         
Sbjct: 232 GVESKVICNNCNL-----------------------------PYDHRTVTR--------- 253

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                      ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RM
Sbjct: 254 -----------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRM 302

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLS
Sbjct: 303 ERVVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 362

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PY
Sbjct: 363 ALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPY 422

Query: 603 RKVCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           RKV                 V++ VVY++A EEE   IAQANS LD +G FT E V CR 
Sbjct: 423 RKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTTEHVACRR 482

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP
Sbjct: 483 GHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAP 542

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  SG  ++A+ AG V +     I +         S   VD Y L KF R
Sbjct: 543 LVGTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYHLNKFLR 596

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+
Sbjct: 597 SNQSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILL 656

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+
Sbjct: 657 SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVH 716

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGDILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R  
Sbjct: 717 PGDILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTREN 776

Query: 950 ID 951
            D
Sbjct: 777 GD 778



 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 105/220 (47%), Positives = 143/220 (65%), Gaps = 5/220 (2%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        +I         D     + +   +G+ ++TPVFDGA
Sbjct: 983  EELEAISKVKNTLNNIHSAEEKRVEIRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1042

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1043 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1102

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE IV 
Sbjct: 1103 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVVGRVKAYEKIVK 1162

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            G +  E G PESF VL+KE+Q++GL + + N   +     
Sbjct: 1163 GENIPEPGVPESFKVLLKELQSIGLDVKILNEDQEEVIMK 1202



 Score =  230 bits (586), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 182/849 (21%), Positives = 306/849 (36%), Gaps = 68/849 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 76   VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 131

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 132  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 191

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 192  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 250

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQG--GVARARAG 555
                     +            L  L +       I H   RRL  +G+      R    
Sbjct: 251  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLT 300

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
               R V      R+   ET       L++     A       I+  +      +  +   
Sbjct: 301  RMERVVRE----RMTIQETESITPQALINIRPVVA------AIKEFFGSSQLSQFMDQTN 350

Query: 616  YLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             L+ +  + R  A     L  +   F    V     G    +   +   I          
Sbjct: 351  PLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYA 410

Query: 675  AASLIPFLE--NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
              +   F+E       +V        + V +  +++    T  E      + A       
Sbjct: 411  KVNEFGFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQAN---SPL 467

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
                      +  R     L+ +   VD   +              + +V +G       
Sbjct: 468  DAEGYFTTEHVACRRGHDVLEVTPDKVDYMDVSP------------KEVVSIGTAMIPFL 515

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 516  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 575

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  +       +        ++  I+  G  V  G +L       G   +  
Sbjct: 576  IHVLRDSDGRVDTYHLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 634

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-EL 966
               +L A    +  +  D  L           D+    +    + + R   +  E+I   
Sbjct: 635  GYNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRE 691

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            L    DD    LD +       I  G     G     K+T      +   P  +  +   
Sbjct: 692  LPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIF 744

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  
Sbjct: 745  GDKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHE 800

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  
Sbjct: 801  GDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQ 860

Query: 1147 GLGKKIKSL 1155
            GLG KIK+ 
Sbjct: 861  GLGMKIKAT 869


>gi|331703831|ref|YP_004400518.1| DNA directed RNA polymerase subunit beta [Mycoplasma mycoides
           subsp. capri LC str. 95010]
 gi|328802386|emb|CBW54541.1| DNA directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri LC str. 95010]
          Length = 1291

 Score =  633 bits (1632), Expect = e-179,   Method: Composition-based stats.
 Identities = 366/1024 (35%), Positives = 573/1024 (55%), Gaps = 143/1024 (13%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYA----VPLKI------------ 104
             FPI +F G+++L   ++ F  P+  V         Y       LK+            
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKEF 110

Query: 105 -------TLRLIVFDVDEFTGAKSIK--------------------------DIKEQ--- 128
                  TL+++   ++E T +K+I                           DI E    
Sbjct: 111 DGVVLDDTLKILTNWLEEKTVSKNITFKQQSQNSYFFELTIKKSDKPDLIQIDIIEDKKT 170

Query: 129 ------------SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                        +++GD PLMT+ GTF+I G Q+++VSQL RSPG +F+ +      +G
Sbjct: 171 SLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAYFNKEL--NRKTG 228

Query: 177 KLLYACRIIPDQGLWMDIEFDSK-------DIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           +++Y   IIP +G W++ E DSK       + ++V+ID+ RK   TS L+A G+  ++IL
Sbjct: 229 EMIYFADIIPSRGTWLEYETDSKKTGADAINPLYVKIDKSRKTTATSLLLAFGISKDDIL 288

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSL 288
           + F    V  +        +    +    +V      I  GE    E   K  + +L   
Sbjct: 289 NIFDNDEVLVETLQQDSI-IGDFKIDWSNQVQEIYKKIRQGETATSEGASKFINSILFDK 347

Query: 289 KEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           ++  +   G           + +    +AEDIV+     +  +    +++ ++++I    
Sbjct: 348 RKYDLTKAGRFKLKQKLSIKNRILNRVIAEDIVDANNNVLIAKD-TEVNKHNIKQISEIL 406

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            +D+  + ++ +++    R               +   +V +  ++ T +          
Sbjct: 407 DQDVMSVDLNYLSDIPGTRK--------------VQKIKVYKDSELKTDTT--------- 443

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                              + L +  +   I   DI++ +  L++L+   G IDDIDNLG
Sbjct: 444 -----------------CLIGLTSSSNEEFITVADILSTVSYLLNLKYNIGEIDDIDNLG 486

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP+ + + EFF  S
Sbjct: 487 NRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKPLTAIIGEFFNLS 546

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NI
Sbjct: 547 QLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNI 606

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G 
Sbjct: 607 GLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGK 666

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E++  R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQ
Sbjct: 667 ILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQ 726

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+
Sbjct: 727 AVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGI 778

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
             Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++
Sbjct: 779 RTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYN 838

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++++SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN+SE+  +++D  
Sbjct: 839 GYNFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAE 898

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V
Sbjct: 899 GIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIV 958

Query: 940 VDVR 943
             ++
Sbjct: 959 QSIK 962



 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 156/521 (29%), Positives = 236/521 (45%), Gaps = 81/521 (15%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 795  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 849

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 850  ERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 909

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 910  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 962

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 963  -----RFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPI 1017

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDM              P             E                   D   N    
Sbjct: 1018 EDM--------------PH-----------LE--------------DGTPVDIILNPQGV 1038

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P R  + +++                +       K    V TPVF+G +E+ +  ++  A
Sbjct: 1039 PSRMNIGQIL---------------EIHLGMAAKKLNQKVITPVFEGLNEKELEEIMAEA 1083

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +   G+  L DG TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK
Sbjct: 1084 GMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGK 1143

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PES
Sbjct: 1144 AQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGIPES 1203

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM-EEIPDFNKCELK 1386
            FNVL KE+  LG ++ + +   + S     +  DF+    +
Sbjct: 1204 FNVLSKEIMGLGFNMYMIDETGEKSVINAYDKKDFDADNYE 1244


>gi|121615263|gb|ABM63350.1| RNA polymerase B subunit [Veillonella parvula ATCC 17745]
          Length = 1125

 Score =  632 bits (1629), Expect = e-178,   Method: Composition-based stats.
 Identities = 380/865 (43%), Positives = 519/865 (60%), Gaps = 99/865 (11%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGAWIELETDAS 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLM 255
           +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D  
Sbjct: 58  EVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERIVRTLEKDTT 117

Query: 256 V--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
                 +      +  GE   +ES + L   L    +   +  +G             + 
Sbjct: 118 QSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRML 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI N    
Sbjct: 178 GQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYIVNNDGV 231

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           +      +  L                              YD  TV R           
Sbjct: 232 ESKVICNNCNL-----------------------------PYDHRTVTR----------- 251

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                    ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 252 ---------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 302

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 303 VVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSAL 362

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRK
Sbjct: 363 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRK 422

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 V++ VVY++A EEE   IAQANS LD +G FT E V CR   
Sbjct: 423 VEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTTEHVACRRGH 482

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 483 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 542

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+ AG V +     I +         S   VD Y L KF RSN
Sbjct: 543 GTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYHLNKFLRSN 596

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 597 QSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILLSE 656

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+PG
Sbjct: 657 ELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVHPG 716

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR---- 947
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R    
Sbjct: 717 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTRENGD 776

Query: 948 ---HGIDKNERSISVEREQIELLAR 969
               G++K  R    ++ +I    +
Sbjct: 777 ELQPGVNKLVRVYIAQKRKIHEGDK 801



 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 182/849 (21%), Positives = 306/849 (36%), Gaps = 68/849 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 74   VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 189

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 190  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 248

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQG--GVARARAG 555
                     +            L  L +       I H   RRL  +G+      R    
Sbjct: 249  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLT 298

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
               R V      R+   ET       L++     A       I+  +      +  +   
Sbjct: 299  RMERVVRE----RMTIQETESITPQALINIRPVVA------AIKEFFGSSQLSQFMDQTN 348

Query: 616  YLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             L+ +  + R  A     L  +   F    V     G    +   +   I          
Sbjct: 349  PLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYA 408

Query: 675  AASLIPFLE--NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
              +   F+E       +V        + V +  +++    T  E      + A       
Sbjct: 409  KVNEFGFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQAN---SPL 465

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
                      +  R     L+ +   VD   +              + +V +G       
Sbjct: 466  DAEGYFTTEHVACRRGHDVLEVTPDKVDYMDVSP------------KEVVSIGTAMIPFL 513

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 514  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 573

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  +       +        ++  I+  G  V  G +L       G   +  
Sbjct: 574  IHVLRDSDGRVDTYHLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 632

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-EL 966
               +L A    +  +  D  L           D+    +    + + R   +  E+I   
Sbjct: 633  GYNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRE 689

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            L    DD    LD +       I  G     G     K+T      +   P  +  +   
Sbjct: 690  LPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIF 742

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  
Sbjct: 743  GDKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHE 798

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  
Sbjct: 799  GDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQ 858

Query: 1147 GLGKKIKSL 1155
            GLG KIK+ 
Sbjct: 859  GLGMKIKAT 867



 Score =  223 bits (567), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 65/145 (44%), Positives = 91/145 (62%), Gaps = 5/145 (3%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        ++         D     + +   +G+ ++TPVFDGA
Sbjct: 981  EELEAISKVKNTLNNIHSAEEKRVELRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1040

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1041 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1100

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEV 1299
            YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1101 YSLVTQQPLGGKAQFGGQRFGEMEV 1125


>gi|256384358|gb|ACU78928.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|256385190|gb|ACU79759.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|296455347|gb|ADH21582.1| DNA-directed RNA polymerase, beta subunit [synthetic Mycoplasma
           mycoides JCVI-syn1.0]
          Length = 1291

 Score =  631 bits (1627), Expect = e-178,   Method: Composition-based stats.
 Identities = 366/1024 (35%), Positives = 572/1024 (55%), Gaps = 143/1024 (13%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYA----VPLKI------------ 104
             FPI +F G+++L   ++ F  P+  V         Y       LK+            
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKEF 110

Query: 105 -------TLRLIVFDVDEFTGAKSIK--------------------------DIKEQ--- 128
                  TL+++   ++E T +K+I                           DI E    
Sbjct: 111 DGVALDDTLKILTNWLEEKTVSKNITFKQQSQNSYFFELTIKKSDKPDLIQIDIIEDKKT 170

Query: 129 ------------SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                        +++GD PLMT+ GTF+I G Q+++VSQL RSPG +F+ +      +G
Sbjct: 171 SLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAYFNKEL--NRKTG 228

Query: 177 KLLYACRIIPDQGLWMDIEFDSK-------DIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           +++Y   IIP +G W++ E DSK       + ++V+ID+ RK   TS L+A G+  ++IL
Sbjct: 229 EMIYFADIIPSRGTWLEYETDSKKTGADAINPLYVKIDKSRKTTATSLLLAFGISKDDIL 288

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSL 288
             F    V  +        +    +    +V      I  GE    E   K  + +L   
Sbjct: 289 DIFDNDEVLVETLQQDSI-VGDFKIDWSNQVQEIYKKIRQGETATSEGASKFINSILFDK 347

Query: 289 KEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           ++  +   G           + +    +AEDIV+     + +     +++ ++++I    
Sbjct: 348 RKYDLTKAGRFKLKQKLSIKNRILNRVIAEDIVDANNN-VLVAKDTEVNKHNIKQISEIL 406

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            +D+  + ++ +++    R               +   +V +  ++ T +          
Sbjct: 407 DQDVMSVDLNYLSDILGTRK--------------VQKIKVYKDSELKTDTT--------- 443

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                              + L +  +   I   DI++ +  L++L+   G IDDIDNLG
Sbjct: 444 -----------------CLIGLTSSSNEEFITVADILSTVSYLLNLKYNIGEIDDIDNLG 486

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP+ + + EFF  S
Sbjct: 487 NRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKPLTAIIGEFFNLS 546

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NI
Sbjct: 547 QLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNI 606

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G 
Sbjct: 607 GLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGK 666

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E++  R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQ
Sbjct: 667 ILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQ 726

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+
Sbjct: 727 AVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGI 778

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
             Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++
Sbjct: 779 RTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYN 838

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++++SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN+SE+  +++D  
Sbjct: 839 GYNFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAE 898

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V
Sbjct: 899 GIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIV 958

Query: 940 VDVR 943
             ++
Sbjct: 959 QSIK 962



 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 156/521 (29%), Positives = 236/521 (45%), Gaps = 81/521 (15%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 795  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 849

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 850  ERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 909

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 910  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 962

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 963  -----RFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPI 1017

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDM              P             E                   D   N    
Sbjct: 1018 EDM--------------PH-----------LE--------------DGTPVDIILNPQGV 1038

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P R  + +++                +       K    V TPVF+G +E+ +  ++  A
Sbjct: 1039 PSRMNIGQIL---------------EIHLGMAAKKLNQKVITPVFEGLNEKELEEIMAEA 1083

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +   G+  L DG TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK
Sbjct: 1084 GMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGK 1143

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PES
Sbjct: 1144 AQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGIPES 1203

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM-EEIPDFNKCELK 1386
            FNVL KE+  LG ++ + +   + S     +  DF+    +
Sbjct: 1204 FNVLSKEIMGLGFNMYMIDETGEKSVINAYDKKDFDADNYE 1244


>gi|121615265|gb|ABM63351.1| RNA polymerase B subunit [Veillonella dispar]
          Length = 1125

 Score =  630 bits (1626), Expect = e-178,   Method: Composition-based stats.
 Identities = 378/840 (45%), Positives = 513/840 (61%), Gaps = 92/840 (10%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGAWIELETDAS 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLM 255
           +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D  
Sbjct: 58  EVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERIVRTLEKDTT 117

Query: 256 V--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
                 +      +  GE   +ES + L   L    +   +  +G             + 
Sbjct: 118 QSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRML 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI N    
Sbjct: 178 GQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYIVNNDGV 231

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           +      +  L                              YD  TV R           
Sbjct: 232 ESKVICNNCNL-----------------------------PYDHRTVTR----------- 251

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                    ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 252 ---------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 302

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 303 VVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSAL 362

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRK
Sbjct: 363 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRK 422

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 VT+ VVY++A EEE   IAQANS +D +G FT E V CR   
Sbjct: 423 VEKIYGTGADADKVVKVRVTDSVVYMTADEEEGMTIAQANSPIDAEGYFTNEHVACRRGH 482

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 483 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 542

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+ AG V +     I +         S   VD+YR+ KF RSN
Sbjct: 543 GTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDVYRMNKFLRSN 596

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 597 QSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILLSE 656

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+PG
Sbjct: 657 ELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEEGIICIGAEVHPG 716

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R   D
Sbjct: 717 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTRENGD 776



 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 175/847 (20%), Positives = 296/847 (34%), Gaps = 64/847 (7%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 74   VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 189

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 190  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 248

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQGGVARARAGVE 557
                     +            L  L +       I H   RRL  +G+           
Sbjct: 249  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGEL-------LQN 291

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
               +  T   R+      E   I  + S+T  A +N         R V          + 
Sbjct: 292  QFRIGLTRMERVV----RERMTIQEIESITPQALINI--------RPVVAAIK----EFF 335

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             + +           +          L     + E        +          +     
Sbjct: 336  GSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG 395

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV-----VAKSSGAAIVAKRA 732
              P +   +S       N         +      GTG ++          S   + A   
Sbjct: 396  --PNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGTGADADKVVKVRVTDSVVYMTADEE 453

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
              +    A   +        +          L           V+ + +V +G       
Sbjct: 454  EGMTIAQANSPIDAEGYFTNEHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIPFL 513

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 514  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 573

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  ++ R    +        ++  I+  G  V  G +L       G   +  
Sbjct: 574  IHVLRDSDGRVDVYRMNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 632

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
               +L A    +  +  D  L         +        +  D  +  +  E    EL  
Sbjct: 633  GYNVLVAFMPWEGYNYEDAILLSEELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPN 692

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
               D  + + +  I      I  G     G     K+T      +   P  +  +    D
Sbjct: 693  TGDDTLKNLDEEGI------ICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIFGD 744

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            ++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  GD
Sbjct: 745  KEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHEGD 800

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  GL
Sbjct: 801  KMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQGL 860

Query: 1149 GKKIKSL 1155
            G KIK+ 
Sbjct: 861  GMKIKAT 867



 Score =  221 bits (562), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/110 (56%), Positives = 81/110 (73%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E+ +   L +A   + G+++LYDG TGEP D  V
Sbjct: 1016 DYETYGMPKPDVAGIHIATPVFDGAHEKDVFETLGIAGRSDDGKTVLYDGRTGEPMDNRV 1075

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1076 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1125


>gi|197294699|ref|YP_001799240.1| DNA-directed RNA polymerase subunit beta [Candidatus Phytoplasma
            australiense]
 gi|226699427|sp|B1VAM6|RPOB_PHYAS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|171854026|emb|CAM11999.1| DNA-directed RNA polymerase beta chain [Candidatus Phytoplasma
            australiense]
          Length = 1240

 Score =  630 bits (1625), Expect = e-178,   Method: Composition-based stats.
 Identities = 306/1392 (21%), Positives = 543/1392 (39%), Gaps = 164/1392 (11%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA   V  G    R+ + K    +D+P+LIE+Q  S++ FL           +G++   +
Sbjct: 1    MAYRNVKYGKKVERRNYSKIIYDVDLPNLIEIQNKSFNWFL----------KDGIEELLQ 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
               PI +++G   + F       PK+ V++   +D +Y + L +   L            
Sbjct: 51   DFCPIESYNGDLKIYFGECYSTGPKYSVEESKTKDASYVIQLFVKATL---------ENT 101

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
               + K+ S+ + +LPL+T  GTF+I G +R+ VSQ+ RS  +++           K LY
Sbjct: 102  LTGETKKSSVLLTELPLITDTGTFIINGKERVAVSQIVRSSSVYYSSTFD--VKLNKNLY 159

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
            + ++IP +G W++ E  SK+I++V++DR +K+P+++F+ ALG ++ EI+   + K     
Sbjct: 160  SGQVIPARGAWIEYEEGSKEILYVKLDRSKKIPLSNFIYALGFNNREIIEKVFGKSPLLN 219

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                    +   D+  G  +      I  GE       K+     +    K +       
Sbjct: 220  SS-----FVKEEDMDTGNALIELYSKIRQGE-------KVPVDTARDFIRKRLFDQKKYD 267

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                G Y     ++     +   A        + +  + E ++I +     +  +     
Sbjct: 268  LTTVGRYKFNKKLD-----VLARAEKTY---LVHDFVNLETKEIILPKHTFLTKDKI--- 316

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             ++          L D    +           +              L+      +  + 
Sbjct: 317  EILRKNRHFLLQELFDAQHNLENETDEEILTYKKDPQSRELYIKTNILNFRTGEIIFPKD 376

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             L T + ++ +RK   +   K++      K            R     E+L+        
Sbjct: 377  TLVTDEVIKRLRKSIQLLDGKVIEFFLRSKDVYQKD----LERTGVFNEILEVYLS---K 429

Query: 481  RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
                +++ ++  V  +    +  I    +++++  +    +     + ++ L      RR
Sbjct: 430  DEHDNLQHKVQIVGNNQKETKKHITLSDIIASISYYLNLYEGIGNVDDIDHLG----NRR 485

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            L  +G+    + R G+   + H      +                L +F  +N  G I+T
Sbjct: 486  LRLIGELLKNQFRIGLTRAEKHIKDMISVSKFSEVG------PGELVNFGFLN--GVIKT 537

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             +      +  + +  L+ + ++ R  A     ++ D                 +     
Sbjct: 538  FFANSRLSQFMDQINPLAELTQKRRVSALGVGGINRD------------RAGVEVRDVHN 585

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
              +    P +     +  +       +     G          ++  A +V   +E + A
Sbjct: 586  SHYGRLCPIETPEGPSIGLIASLAIYAKVDDYGFIQTPFFKVFVQNGASYVSNQIEYLTA 645

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                  I+A  +G     DA        +  +      + IY     Q +  +    Q  
Sbjct: 646  DQEKEEIIA-SSGYELNSDATFQ----KDKVIARKNGEIGIYPKE--QVTYADISPKQIV 698

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVF 839
             +            +               +LV   P  G   E      S  ++     
Sbjct: 699  SIATASIPFLEHNDSSRALMGSNMQRQAVPLLVTESPIVGTGIEYRAAKDSGSLIIASQP 758

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              +   + + +    + G ++  +            I +  I+ +G  +  GDILV   +
Sbjct: 759  GIVTYVDAKKIVTSDQEGNKKEYQLTTFEKSNQDTLILQKPIVSLGDNIQKGDILVDGPS 818

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
               +  +     +L A    +  +  D  +     V   V      N++ +   E     
Sbjct: 819  T-NQGELALGRNILVAFMTWEGYNYEDAIIISEELVKNDVYTSVHINKYSVQTRELKKGS 877

Query: 960  EREQIELL-------ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             +E+I          A    DE+ I+      +  +IL G+    G              
Sbjct: 878  GKEEITREVPNVGADAIKNLDERGIIIPGSEVKEGDILVGKITPQG-------------N 924

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQY-ETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +   P+ +  Q  + ++  +    SL+V Y E         F  K      GD +PPGV 
Sbjct: 925  VDPTPQEKLIQIVIGEKAREYKDSSLRVPYGEGGIVQSVQYFSRK-----NGDILPPGVN 979

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++VF+A KR I  GDKMAGRHGNKG++SRILP ED+PF++DGT +D++LNPLGVPSRM
Sbjct: 980  ENIRVFIAKKRKISEGDKMAGRHGNKGVISRILPKEDLPFMEDGTTIDVMLNPLGVPSRM 1039

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQI E HLG +   L  K+ + + D   + D+  +                       
Sbjct: 1040 NIGQILEIHLGMSAKNLNIKVATPVFDGVNDQDLKEISQEAN------------------ 1081

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                           L +       + +LYDG TGEP++  ++V
Sbjct: 1082 -------------------------------LELDG-----KKVLYDGRTGEPYENRISV 1105

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YM+KL+HMV DK++AR+ G Y+LVTQQP+ GK   GGQR GEME W + A+GAAY L
Sbjct: 1106 GVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMRGKIREGGQRYGEMENWAVHAHGAAYTL 1165

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE LTIKSDD++GR + Y +IV G    +   PESF VL+KE+QALGL ++L  + TK +
Sbjct: 1166 QEFLTIKSDDIIGRNQTYSAIVQGKQLPKPNIPESFRVLIKELQALGLYVELIKTDTKEN 1225

Query: 1372 AKMEEIPDFNKC 1383
               + + D+ K 
Sbjct: 1226 EVNKSLIDYKKE 1237


>gi|1350848|sp|P47767|RPOB_SPICI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|886053|gb|AAC44217.1| DNA-dependent RNA polymerase beta subunit [Spiroplasma citri]
          Length = 1302

 Score =  630 bits (1625), Expect = e-178,   Method: Composition-based stats.
 Identities = 376/1079 (34%), Positives = 582/1079 (53%), Gaps = 140/1079 (12%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA      G    R  + K    +D+P+LIE+Q  +YD F             G+   F+
Sbjct: 1    MALKEKEFGHYAKRIDYTKVSGNLDLPNLIEIQTETYDWF----------KKTGISEVFR 50

Query: 61   SVFPITAFSGAAMLEFVSYE-----------------FDPPKFD------------VDDC 91
             VFPI    G  +LE + +E                 F+ P +             V+  
Sbjct: 51   EVFPIVGHEGNIVLEMLDWEFREPRRTISQAKDESKIFEAPIYSNLKLTINSKDVEVEKA 110

Query: 92   LWRD----------------LT----------Y---AVPLKITLRLIVFDVDEFTGAKSI 122
            + +                 +T          Y   +     T  + + +  +      I
Sbjct: 111  IVKGEPELIKAWIEERVGHMITILKKTTDVIYYDIHSGDEIATCTVTIKERLDDKLIVDI 170

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KE  ++ GD PLMT  GTF++ G +++VVSQL RSPG ++  D      +G+ +Y  
Sbjct: 171  TIEKEGEVFFGDFPLMTGKGTFIVNGSEKVVVSQLVRSPGAYYKIDL--NRKNGENVYYV 228

Query: 183  RIIPDQGLWMDIEFDSK-----------DIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
             +IP +G W++ E D K           ++ +V+ID+ RKV V +FL ALG+  E+ L  
Sbjct: 229  DLIPSRGTWLEFESDHKKIKVGKEEKFENVFYVKIDKSRKVSVANFLTALGIIKEDALDI 288

Query: 232  FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKE 290
            F    +     +   +            V      I +GE    +   K   GLL   ++
Sbjct: 289  FGDNKLVKSTYELDPYTGDIL-YDQSIAVQEIYKKIRSGETATPDGATKYLYGLLFDKRK 347

Query: 291  KGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
              +   G           + +    +AEDI +   G++    G ++D++++ ++      
Sbjct: 348  YDLTKAGRFKLIQKLSVENRIYNKILAEDIKDV-NGKVVFTEGTLMDKEAINKL------ 400

Query: 343  DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
                           ++      + K   +                      +       
Sbjct: 401  ------------KGILKAGACLQEVKFSDE----------------------IICSNKIQ 426

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              K  +    R ++   + +D      ++   D++A    L++L +G G +DDID+LGNR
Sbjct: 427  KIKVYVDNEVRSRVANIIGIDPNATDEYVTVPDVLATFSYLLNLTDGIGEVDDIDHLGNR 486

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVR++GE+L+NQ+R+GLLR+E+++KE++S+ ++  + P ++IN KP+ + + EFF  SQL
Sbjct: 487  RVRTIGELLQNQFRIGLLRIEKNVKEKMSTSNLFKMKPSNIINNKPLSAIIGEFFNLSQL 546

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL
Sbjct: 547  SQFMDQTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGL 606

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +++L ++A++N+YGFIETPYR+V   KVT +  YL+A EE+N  +AQAN  L + G   +
Sbjct: 607  INNLATYAKINSYGFIETPYRRVIGCKVTMENDYLTADEEKNYVVAQANIRLSDKGEILD 666

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+P
Sbjct: 667  EQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIP 726

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            L+   +P+VGTG+E   A+ SG AIV++  GIV+ VDA RIV+++ E        G+  Y
Sbjct: 727  LIAPNSPYVGTGVEYAAARDSGLAIVSQYDGIVDFVDATRIVLKTKE--------GLKNY 778

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L  F RSNQ T +   PLV+ G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN
Sbjct: 779  NLDTFVRSNQGTSLTHVPLVRQGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYN 838

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++
Sbjct: 839  YEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLV 898

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  +
Sbjct: 899  IIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAI 958

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            + F R   + +   + V +  I    + ++ +++         + +IL  ++      G
Sbjct: 959  KRFPREKYEVSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDG 1017



 Score =  455 bits (1171), Expect = e-125,   Method: Composition-based stats.
 Identities = 169/506 (33%), Positives = 250/506 (49%), Gaps = 69/506 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 797  LVRQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 855

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 856  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 909

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 910  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 967

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTPVDI
Sbjct: 968  -----VSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPVDI 1022

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +            
Sbjct: 1023 MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGMINEELIEIMD---------- 1072

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                    + ++        + +L DG 
Sbjct: 1073 ---------------------------------------KAGMKNFG-----KEVLIDGR 1088

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR GEMEVW
Sbjct: 1089 TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFGEMEVW 1148

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ L+E+LTIKSDD+ GRTR YESIV      E G PESFNVL +E+Q LG +
Sbjct: 1149 ALEAYGAAHTLREILTIKSDDIKGRTRAYESIVKDKKIPEPGIPESFNVLTREIQGLGFN 1208

Query: 1361 IDLENSRTK-NSAKMEEIPDFNKCEL 1385
            I + + +    + K  +  D+   +L
Sbjct: 1209 IHMIDEKGNIKNIKSYDEADYVDEDL 1234


>gi|121615259|gb|ABM63348.1| RNA polymerase B subunit [Veillonella parvula DSM 2008]
          Length = 1125

 Score =  630 bits (1625), Expect = e-178,   Method: Composition-based stats.
 Identities = 378/840 (45%), Positives = 511/840 (60%), Gaps = 92/840 (10%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG++++ +       G  LY   +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYNKEID---TMGNRLYDSTVIPNRGAWIELETDAS 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLM 255
           +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D  
Sbjct: 58  EVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGKTDEDGLPVYDERIVRTLEKDTT 117

Query: 256 V--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
                 +      +  GE   +ES + L   L    +   +  +G             + 
Sbjct: 118 QSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRML 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A+ IV+ ETGEI ++AG  + E+ L+ + +S       ++        YI N    
Sbjct: 178 GQTLAQPIVDPETGEIILDAGVQVGEEQLDIVANSH------VFDGEGFAEFYIVNNDGV 231

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           +      +  L                              YD  TV R           
Sbjct: 232 ESKVICNNCNL-----------------------------PYDHRTVTR----------- 251

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                    ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 252 ---------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 302

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  + +S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 303 VVRERMTIQETESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSAL 362

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRK
Sbjct: 363 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRK 422

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 V++ VVY++A EEE   IAQANS LD +G FT E V CR   
Sbjct: 423 VEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQANSPLDAEGYFTTEHVACRRGH 482

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 483 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 542

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+ AG V +     I +         S   VD YRL KF RSN
Sbjct: 543 GTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYRLNKFLRSN 596

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 597 QSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILLSE 656

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+PG
Sbjct: 657 ELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVHPG 716

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R   D
Sbjct: 717 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTRENGD 776



 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 183/849 (21%), Positives = 307/849 (36%), Gaps = 68/849 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 74   VLVRALGWDTNESILDLFWNGKTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLAQPIVDPE 189

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++  ++        GE     Y +    +E  +     ++  D   
Sbjct: 190  TGEII-LDAGVQVGEEQLDIVANSHVFDGEGFAEFYIVNNDGVESKVICNNCNLPYDHRT 248

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQG--GVARARAG 555
                     +            L  L +       I H   RRL  +G+      R    
Sbjct: 249  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLT 298

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
               R V      R+   ET       L++     A       I+  +      +  +   
Sbjct: 299  RMERVVRE----RMTIQETESITPQALINIRPVVA------AIKEFFGSSQLSQFMDQTN 348

Query: 616  YLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             L+ +  + R  A     L  +   F    V     G    +   +   I          
Sbjct: 349  PLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYA 408

Query: 675  AASLIPFLE--NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
              +   F+E       +V        + V +  +++    T  E      + A       
Sbjct: 409  KVNEFGFIEAPYRKVEKVYGKGKDADKVVKVRVSDSVVYMTADEEEGMTIAQAN---SPL 465

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRR 790
                      +  R     L+ +   VD   +              + +V +G       
Sbjct: 466  DAEGYFTTEHVACRRGHDVLEVTPDKVDYMDVSP------------KEVVSIGTAMIPFL 513

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFE 848
             +  A+              +L A  P  G   E   +      +++ +    +     E
Sbjct: 514  ENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRCWGNE 573

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +       G  +  R    +        ++  I+  G  V  G +L       G   +  
Sbjct: 574  IHVLRDSDGRVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-GELAL 632

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-EL 966
               +L A    +  +  D  L           D+    +    + + R   +  E+I   
Sbjct: 633  GYNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEEITRE 689

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            L    DD    LD +       I  G     G     K+T      +   P  +  +   
Sbjct: 690  LPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLLRAIF 742

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A KR I  
Sbjct: 743  GDKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKIHE 798

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA  
Sbjct: 799  GDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGWAVQ 858

Query: 1147 GLGKKIKSL 1155
            GLG KIK+ 
Sbjct: 859  GLGMKIKAT 867



 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 66/145 (45%), Positives = 91/145 (62%), Gaps = 5/145 (3%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    IS +++ L  +        +I         D     + +   +G+ ++TPVFDGA
Sbjct: 981  EELEAISKVKNTLNNIHSAEEKRVEIRKELESLGYDFDKYGMPKPDVAGIHIATPVFDGA 1040

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +A   + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1041 HEKDVFETLAIAGRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1100

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEV 1299
            YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1101 YSLVTQQPLGGKAQFGGQRFGEMEV 1125


>gi|110003980|emb|CAK98320.1| dna-directed rna polymerase beta chain protein [Spiroplasma citri]
          Length = 1301

 Score =  629 bits (1623), Expect = e-178,   Method: Composition-based stats.
 Identities = 376/1079 (34%), Positives = 582/1079 (53%), Gaps = 140/1079 (12%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA      G    R  + K    +D+P+LIE+Q  +YD F             G+   F+
Sbjct: 1    MALKEKEFGHYAKRIDYTKVSGNLDLPNLIEIQTETYDWF----------KKTGISEVFR 50

Query: 61   SVFPITAFSGAAMLEFVSYE-----------------FDPPKFD------------VDDC 91
             VFPI    G  +LE + +E                 F+ P +             V+  
Sbjct: 51   EVFPIVGHEGNIVLEMLDWEFREPRRTISQAKDESKIFEAPIYSNLKLTINSKDVEVEKA 110

Query: 92   LWRD----------------LT----------Y---AVPLKITLRLIVFDVDEFTGAKSI 122
            + +                 +T          Y   +     T  + + +  +      I
Sbjct: 111  IVKGEPELIKAWIEERVGHMITILKKTTDVIYYDIHSGDEIATCTVTIKERLDDKLIVDI 170

Query: 123  KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               KE  ++ GD PLMT  GTF++ G +++VVSQL RSPG ++  D      +G+ +Y  
Sbjct: 171  TIEKEGEVFFGDFPLMTGKGTFIVNGSEKVVVSQLVRSPGAYYKIDL--NRKNGENVYYV 228

Query: 183  RIIPDQGLWMDIEFDSK-----------DIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
             +IP +G W++ E D K           ++ +V+ID+ RKV V +FL ALG+  E+ L  
Sbjct: 229  DLIPSRGTWLEFESDHKKIKVGKEEKFENVFYVKIDKSRKVSVANFLTALGIIKEDALDI 288

Query: 232  FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKE 290
            F    +     +   +            V      I +GE    +   K   GLL   ++
Sbjct: 289  FGDNKLVKSTYELDPYTGDIL-YDQSIAVQEIYKKIRSGETATPDGATKYLYGLLFDKRK 347

Query: 291  KGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
              +   G           + +    +AEDI +   G++    G ++D++++ ++      
Sbjct: 348  YDLTKAGRFKLIQKLSVENRIYNKILAEDIKDV-NGKVVFTEGTLMDKEAINKL------ 400

Query: 343  DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
                           ++      + K   +                      +       
Sbjct: 401  ------------KGILKAGACLQEVKFSDE----------------------IICSNKIQ 426

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              K  +    R ++   + +D      ++   D++A    L++L +G G +DDID+LGNR
Sbjct: 427  KIKVYVDNEVRSRVANIIGIDPNATDEYVTVPDVLATFSYLLNLTDGIGEVDDIDHLGNR 486

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVR++GE+L+NQ+R+GLLR+E+++KE++S+ ++  + P ++IN KP+ + + EFF  SQL
Sbjct: 487  RVRTIGELLQNQFRIGLLRIEKNVKEKMSTSNLFKMKPSNIINNKPLSAIIGEFFNLSQL 546

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL
Sbjct: 547  SQFMDQTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGL 606

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +++L ++A++N+YGFIETPYR+V   KVT +  YL+A EE+N  +AQAN  L + G   +
Sbjct: 607  INNLATYAKINSYGFIETPYRRVIGCKVTMENDYLTADEEKNYVVAQANIRLSDKGEILD 666

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+P
Sbjct: 667  EQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIP 726

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            L+   +P+VGTG+E   A+ SG AIV++  GIV+ VDA RIV+++ E        G+  Y
Sbjct: 727  LIAPNSPYVGTGVEYAAARDSGLAIVSQYDGIVDFVDATRIVLKTKE--------GLKNY 778

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             L  F RSNQ T +   PLV+ G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN
Sbjct: 779  NLDTFVRSNQGTSLTHVPLVRQGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYN 838

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            +ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++
Sbjct: 839  YEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLV 898

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  +
Sbjct: 899  IIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAI 958

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            + F R   + +   + V +  I    + ++ +++         + +IL  ++      G
Sbjct: 959  KRFPREKYEVSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDG 1017



 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 170/506 (33%), Positives = 250/506 (49%), Gaps = 69/506 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 797  LVRQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 855

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 856  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 909

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 910  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 967

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTPVDI
Sbjct: 968  -----VSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPVDI 1022

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +            
Sbjct: 1023 MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGMINEELIEIMD---------- 1072

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                    + ++        + +L DG 
Sbjct: 1073 ---------------------------------------KAGMKNFG-----KEVLIDGR 1088

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR GEMEVW
Sbjct: 1089 TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFGEMEVW 1148

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ L+E+LTIKSDD+ GRTR YESIV      E G PESFNVL +E+Q LG +
Sbjct: 1149 ALEAYGAAHTLREILTIKSDDIKGRTRAYESIVKDKKIPEPGIPESFNVLTREIQGLGFN 1208

Query: 1361 IDLENSRTK-NSAKMEEIPDFNKCEL 1385
            I + + +    + K  +  D+   EL
Sbjct: 1209 IHMIDEKGNIKNIKSYDEADYVDEEL 1234


>gi|323149208|ref|YP_004222037.1| RNA polymerase beta chain [Coccomyxa sp. C-169]
 gi|317467264|gb|ADV29885.1| RNA polymerase beta chain [Coccomyxa sp. C-169]
          Length = 1449

 Score =  628 bits (1620), Expect = e-177,   Method: Composition-based stats.
 Identities = 341/1083 (31%), Positives = 496/1083 (45%), Gaps = 128/1083 (11%)

Query: 339  SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS-TFSVAESMFN 397
            + ++  P +     +    I      +     ++ALL+++  + P     +         
Sbjct: 420  ARLKKTPKVPFALFHEGMSICERKPNEWTIADREALLELHEEVNPTKKDLSPENGHQFLV 479

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              F +   YDL  VGR ++N R  L        +   D+ A  + + +L+N +  +DDID
Sbjct: 480  QKFKNPRTYDLGRVGRKRLNRRFGLSVLSHQ--LTSHDLYAAFEQIQELQNDQILVDDID 537

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            +L NRRVR+ GE+++ Q+  GL R+E++I  ++       + P+ L+N KP+  A+ EFF
Sbjct: 538  HLKNRRVRASGELVQGQFETGLYRLEKAILSKMRKP-PKELSPRTLLNTKPLNGALREFF 596

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             SS LSQ  +  N L+ IT  RR+S+LG GG++R  AG+ +R +HPTHYGRICP ET EG
Sbjct: 597  GSSPLSQYMDQTNPLAEITQKRRISSLGPGGISRETAGMAVRGIHPTHYGRICPIETPEG 656

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSA--MEEENRYIAQANSS 633
             N GLV+SLT++ RV   G +ETPY +V  G+V   +   Y SA   E     +A  +  
Sbjct: 657  KNAGLVNSLTTYTRVGDDGILETPYYRVVQGQVQTQMGFQYFSAGGEEHGEFRVAPGDVQ 716

Query: 634  LDEDGSFTEELVFCR----CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            L             R       +     RE ++++  SP Q++S+A SLIPFLE+DD+NR
Sbjct: 717  LSTCQLLPATSFPVREAGNREEDFRHADREDVNYMAISPIQMISVATSLIPFLEHDDANR 776

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             LMG NMQRQAVPLL+ E P VGTG+E+VV   SG A+ A+ +G V  V   R+ + S  
Sbjct: 777  ALMGSNMQRQAVPLLQPERPLVGTGLEAVVVAESGHALQAELSGYVSSVSGGRVSVYSCL 836

Query: 750  GDLDPSTSGVDIYRLMK---------------------------FQRSNQNTCVNQRPLV 782
                      +                                   R   N    Q    
Sbjct: 837  PSTRSKPPLTNTRLRWPSLTGAGLTGLTGLPGAGLTGLTGAGRSVGRVQPNDLALQASQA 896

Query: 783  KVGDEVRRNDIIADGPST---DLGDLALG--------RNMLVAFMPWHGYNFEDSMLISE 831
              G       +  DG        G L               VAF P  G +     ++  
Sbjct: 897  SQGQGPTPKGVPLDGFRVSLNKTGPLPPHWPGSDAQGHQARVAFQPLKGKSLSLKGVVDP 956

Query: 832  R---------MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                          D+ ++    ++  + R  +   E        VSE            
Sbjct: 957  SAGPTRQCPPNSQADLPSAAFSRDY-HLQRYHRSNQETCLTQTSAVSE------------ 1003

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
              G  V  GD+L    +      +   + +L A    +  +  D  +     +S  V   
Sbjct: 1004 --GDWVQSGDLLAD-CSASRFGELALGKNILIAYLPWEGYNFEDAVVISERLISDDVYTS 1060

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
                ++ I+  E    VE+     +    D E+  LD    +++     G     G    
Sbjct: 1061 IHVQKYDIETRETRFGVEKIT-RQIPGITDREKEHLDWRGIAKI-----GSWVKEGDILV 1114

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K +  SS  +S Y R  +    V+    +     +    E      +  F+     I+ 
Sbjct: 1115 GKVSPKSSQPLSPYERLAYDIANVEAATTEDTSLRVPKSVEGRVINCQ-FFEGPGVTIEK 1173

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                       V++++A KR +Q GDK+AGRHGNKGIVS +LP +DMP+L DGT VD+VL
Sbjct: 1174 QGPSTG----RVRIYLAEKRKLQVGDKVAGRHGNKGIVSTVLPRQDMPYLPDGTIVDMVL 1229

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLG+PSRMNVGQ+FE  LG A V LG++ K    D     + S    +L+         
Sbjct: 1230 NPLGIPSRMNVGQVFECLLGLAGVQLGQQFKITPFDEIYGAEASRSLVYLKLYQ------ 1283

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                           A        L  +     G++ L DG TG
Sbjct: 1284 -------------------------------ARLRTNQDWLFNSRFP--GKTPLLDGRTG 1310

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
              FD+ +TVGY YMLKL H+V +K++ARSTG YSLVT+QPLGG+S  GGQRLGEMEVW +
Sbjct: 1311 RLFDQWITVGYAYMLKLVHLVDEKIHARSTGPYSLVTKQPLGGRSKHGGQRLGEMEVWAL 1370

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIV-AGNDTFETGTPESFNVLVKEMQALGLSI 1361
            + +GAAY LQEMLT KSDDVVGR +V E+I+  G      G PE+F VLV+E+Q+L L +
Sbjct: 1371 EGFGAAYTLQEMLTSKSDDVVGREQVVEAILFKG--RMSLGNPEAFKVLVRELQSLCLDV 1428

Query: 1362 DLE 1364
             + 
Sbjct: 1429 GVY 1431



 Score =  115 bits (287), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 61/347 (17%), Positives = 120/347 (34%), Gaps = 37/347 (10%)

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +     + +G+LPLMTK G F++ G  R+V++QL RSPG++F           K      
Sbjct: 340 ETPLSWVLVGNLPLMTKRGHFIVNGSPRVVINQLVRSPGVYFHERTWGFGKRKKRTVYAD 399

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL---GMDSEEILSTFYPKIVYSQ 240
            +  +G W+ I+ D +     R+ +  KVP      AL   GM             +  +
Sbjct: 400 FVSRRGAWLRIQTDKEGNTWARLKKTPKVPF-----ALFHEGMS------------ICER 442

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           + + W      A L +  +V+ +  D+       E+G +      K+ +   +    +  
Sbjct: 443 KPNEWTIADREALLELHEEVNPTKKDLSP-----ENGHQFLVQKFKNPRTYDLGR--VGR 495

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             L   +    + +  T      A + I E   ++I    + DI  L    V  +  +  
Sbjct: 496 KRLNRRFGLSVLSHQLTSHDLYAAFEQIQELQNDQIL---VDDIDHLKNRRVRASGELVQ 552

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVS------TFSVAESMFNFLFFDSDKYDLSTVGRV 414
                     + A+L   R   P ++S      T  +  ++  F         +     +
Sbjct: 553 GQFETGLYRLEKAILSKMRK-PPKELSPRTLLNTKPLNGALREFFGSSPLSQYMDQTNPL 611

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +    +      I +E     ++ +     G+    +     N
Sbjct: 612 AEITQKRRISSLGPGGISRETAGMAVRGIHPTHYGRICPIETPEGKN 658



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 43/105 (40%), Gaps = 13/105 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           +PD +E+Q+ S+  FL           +G+   F  + PI +      L     SY    
Sbjct: 12  VPDFVEIQRRSFSRFL----------EKGIIEEFSKINPIRSDISKFELTLYPESYLIIA 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           P++ V + +    TY+  L +  +L   +       ++  + K+Q
Sbjct: 62  PEYTVTEAVLHGKTYSCKLYLPAKLS-SEHRSKRTNRNKANAKQQ 105


>gi|36333375|gb|AAP75745.1| RNA polymerase beta subunit [Bosea vestrisii]
          Length = 411

 Score =  627 bits (1618), Expect = e-177,   Method: Composition-based stats.
 Identities = 263/414 (63%), Positives = 328/414 (79%), Gaps = 3/414 (0%)

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            MTPEEKLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE+IE
Sbjct: 1    MTPEEKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIEREEIE 60

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             LA+D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW FA
Sbjct: 61   RLAKDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWWLFA 120

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR IQ
Sbjct: 121  TADDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKRKIQ 180

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA 
Sbjct: 181  PGDKMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAA 240

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
             GLGK+I   I+ Y+   D   LR+  + V       E I+  DD  ++ + +  + GVP
Sbjct: 241  AGLGKQIGKAIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDAELIEMGQNLRRGVP 297

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            ++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V D
Sbjct: 298  IATPVFNGAKESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHLVDD 357

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            K++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KS
Sbjct: 358  KIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 411


>gi|121615261|gb|ABM63349.1| RNA polymerase B subunit [Veillonella atypica]
          Length = 1125

 Score =  627 bits (1618), Expect = e-177,   Method: Composition-based stats.
 Identities = 371/840 (44%), Positives = 504/840 (60%), Gaps = 92/840 (10%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG+++  +       G  LY   +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYGKEID---TMGNRLYESTVIPNRGAWIELETDAS 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLM 255
           +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D  
Sbjct: 58  EVVAVRIDRNRKLPATVLVRALGWDTNESILDLFWNGQTDEDGLPVYDERIVRTLEKDTT 117

Query: 256 V--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
                 +      +  GE   +ES + L   L    +   +  +G             + 
Sbjct: 118 QSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRML 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A+ IV+ ETGEI ++AG  + E+ L+ +  S       ++        YI N+   
Sbjct: 178 GQTLAQPIVDTETGEIILDAGVQVGEEQLDIVAKSG------VFSGEGFAEFYITNSDGV 231

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                  +  L+                                                
Sbjct: 232 VSKIICNNCNLEFNHR-------------------------------------------- 247

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                 + +ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 248 -----TVTREDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 302

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 303 VVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSAL 362

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRK
Sbjct: 363 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRK 422

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 V+  V Y++A EEE   IAQANS LD DG F  + V CR   
Sbjct: 423 VEKIYGEGADADKVVKVRVSESVAYMTADEEEGMTIAQANSPLDADGCFANDHVACRRGH 482

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 483 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 542

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+ AG V +     I +         S   VD YRL KF RSN
Sbjct: 543 GTGMEYTAATDSGVCVLAREAGKVVRCWGNEIHVLRD------SDGRVDTYRLNKFLRSN 596

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 597 QSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGFNVLVAFMPWEGYNYEDAILLSE 656

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+DE GIIC+GAEV+PG
Sbjct: 657 ELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLKNLDEDGIICIGAEVHPG 716

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 717 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGECGKVVDVKVFTRENGD 776



 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 170/872 (19%), Positives = 296/872 (33%), Gaps = 76/872 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +   D   L V        I  TL  D  +   +AL++IY+
Sbjct: 74   VLVRALGWDTNESILDLFWNGQTDEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + +  + I+  
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTL-AQPIVDT 188

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                + L  G    ++  ++  +     GE     Y      +   I     +++ +   
Sbjct: 189  ETGEIILDAGVQVGEEQLDIVAKSGVFSGEGFAEFYITNSDGVVSKIICNNCNLEFNHRT 248

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
                   + +++ +         +   + ++ L       R          R       R
Sbjct: 249  VT----REDMIANISYLLNLMDGAGHTDDIDHLG--NRRLRCVGELLQNQFRIGLTRMER 302

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             V              E   I  + S+T  A +N         R V          +  +
Sbjct: 303  VVR-------------ERMTIQEIESITPQALINI--------RPVVAAIK----EFFGS 337

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             +           +          L     + E        +          +       
Sbjct: 338  SQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG-- 395

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P +   +S       N         +      G G        +   +  + +  V  + 
Sbjct: 396  PNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGEG------ADADKVVKVRVSESVAYMT 449

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN-----TCVNQRPLVKVGDEVRRNDII 794
            A      ++     P  +           R   +             V   + V     +
Sbjct: 450  ADEEEGMTIAQANSPLDADGCFANDHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGTAM 509

Query: 795  --------ADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHI 844
                    A+              +L A  P  G   E   +      +++ +    +  
Sbjct: 510  IPFLENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLAREAGKVVRC 569

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
               E+       G  +  R    +        ++  I+  G  V  G +L       G  
Sbjct: 570  WGNEIHVLRDSDGRVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG-G 628

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQ 963
             +     +L A    +  +  D  L           D+    +    + + R   +  E+
Sbjct: 629  ELALGFNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGAEE 685

Query: 964  I-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            I   L    DD    LD +       I  G     G     K+T      +   P  +  
Sbjct: 686  ITRELPNTGDDTLKNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEERLL 738

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D++ +    SL+V +     +++     K+   + GD++ PGV ++V+V++A KR
Sbjct: 739  RAIFGDKEREVRDTSLRVPHGECGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQKR 794

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLG
Sbjct: 795  KIHEGDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLG 854

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            WA  GLG KIK+     +     +       +
Sbjct: 855  WAVQGLGMKIKATDLHIQNVLKEARTDESYWE 886



 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/110 (57%), Positives = 81/110 (73%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E+ +   L +A   + G++ILYDG TGEP D  V
Sbjct: 1016 DYDTYGMPKPDVAGIHIATPVFDGAHEKDVFETLDIAGRPDDGKTILYDGRTGEPMDNRV 1075

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1076 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1125


>gi|121615267|gb|ABM63352.1| RNA polymerase B subunit [Veillonella denticariosi]
          Length = 1125

 Score =  627 bits (1617), Expect = e-177,   Method: Composition-based stats.
 Identities = 373/840 (44%), Positives = 509/840 (60%), Gaps = 92/840 (10%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG+++  +       G  LY   +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYGKEID---TMGNRLYESTVIPNRGAWIELETDAS 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRG---DFWCFPLSAADLM 255
           +++ VRIDR RK+P T  + ALG D+ E IL  F+            D         D  
Sbjct: 58  EVVSVRIDRNRKLPATVLVRALGWDTNESILDLFWNGETGEDGLPVYDERIVRTLEKDTT 117

Query: 256 V--GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
                 +      +  GE   +ES + L   L    +   +  +G             + 
Sbjct: 118 QSADEALVEIYKKLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRML 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  + + IV+ ETGEI ++AG  + E+ L  +  S       ++        YI+N+   
Sbjct: 178 GQTLVQPIVDTETGEIILDAGVQVSEEQLAVVAESH------VFDGEGFAEFYIQNSDGM 231

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                  +  L                              Y+  TV R           
Sbjct: 232 SSKVICNNCNL-----------------------------PYEHRTVTR----------- 251

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                    ED+IA I  L++L +G G  DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 252 ---------EDMIANISYLLNLMDGAGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 302

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  +I+S+ PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSAL
Sbjct: 303 VVRERMTIQEIESITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSAL 362

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYR+
Sbjct: 363 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRR 422

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 V++ VVY++A EEE   IAQANS +D DG F E+ V CR   
Sbjct: 423 VEKIYGKGKESDTVVKVRVSDSVVYMTADEEEGMTIAQANSPIDADGYFMEDHVACRRGH 482

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 483 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 542

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  ++A+ +G V +     I +         S   VD YRL KF RSN
Sbjct: 543 GTGMEYTAATDSGVCVLARESGKVVRCWGNEIHVLRD------SDGRVDTYRLNKFLRSN 596

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V +  ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 597 QSTCFNQKPIVNRGDHVVKGQVLADGPATDGGELALGYNVLVAFMPWEGYNYEDAILLSE 656

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ L+N+DE GIIC+GAEV+PG
Sbjct: 657 ELCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDTLRNLDEDGIICIGAEVHPG 716

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG VVDV++F R   D
Sbjct: 717 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKVVDVKVFTRENGD 776



 Score =  230 bits (586), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 176/855 (20%), Positives = 292/855 (34%), Gaps = 80/855 (9%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + + A      +S+ ++F +       L V        I  TL  D  +   +AL++IY+
Sbjct: 74   VLVRALGWDTNESILDLFWNGETGEDGLPVYDER----IVRTLEKDTTQSADEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD+ +YDL+ VGR K+N +L        + + +  +   
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDARRYDLARVGRYKLNKKLGWRQRMLGQTLVQPIVDTE 189

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++ L  G    ++   +        GE     Y      M   +     ++  +   
Sbjct: 190  TGEII-LDAGVQVSEEQLAVVAESHVFDGEGFAEFYIQNSDGMSSKVICNNCNLPYEHRT 248

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT--RRLSALGQGGVARARAGVE 557
                     +            L  L +       I H   RRL  +G+           
Sbjct: 249  VTREDMIANISY----------LLNLMDGAGHTDDIDHLGNRRLRCVGEL-------LQN 291

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
               +  T   R+      E   I  + S+T  A +N         R V          + 
Sbjct: 292  QFRIGLTRMERVV----RERMTIQEIESITPQALINI--------RPVVAAIK----EFF 335

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             + +           +          L     + E        +          +     
Sbjct: 336  GSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG 395

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
              P +   +S       N         +      G G E      S   +  + +  V  
Sbjct: 396  --PNIGLINSLSNYAKVNEFGFIEAPYRRVEKIYGKGKE------SDTVVKVRVSDSVVY 447

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN-----TCVNQRPLVKVGDEVRRND 792
            + A      ++     P  +           R   +             V   + V    
Sbjct: 448  MTADEEEGMTIAQANSPIDADGYFMEDHVACRRGHDVLEVTPDKVDYMDVSPKEVVSIGT 507

Query: 793  II--------ADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSI 842
             +        A+              +L A  P  G   E   +      +++ +    +
Sbjct: 508  AMIPFLENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCVLARESGKVV 567

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
                 E+       G  +  R    +        ++  I+  G  V  G +L       G
Sbjct: 568  RCWGNEIHVLRDSDGRVDTYRLNKFLRSNQSTCFNQKPIVNRGDHVVKGQVLADGPATDG 627

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVER 961
               +     +L A    +  +  D  L           D+    +    + + R   +  
Sbjct: 628  -GELALGYNVLVAFMPWEGYNYEDAILL---SEELCKEDIYTSIHIEEYECDARDTKLGA 683

Query: 962  EQI-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            E+I   L    DD    LD +       I  G     G     K+T      +   P  +
Sbjct: 684  EEITRELPNTGDDTLRNLDED-----GIICIGAEVHPGDILVGKATPKGETEL--TPEER 736

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              +    D++ +    SL+V +  S  +++     K+   + GD++ PGV ++V+V++A 
Sbjct: 737  LLRAIFGDKEREVRDTSLRVPHGESGKVVD----VKVFTRENGDELQPGVNKLVRVYIAQ 792

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR I  GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETH
Sbjct: 793  KRKIHEGDKMAGRHGNKGVVSRVMRKEDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETH 852

Query: 1141 LGWACVGLGKKIKSL 1155
            LGWA  GLG KIK  
Sbjct: 853  LGWAVQGLGMKIKET 867



 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 66/145 (45%), Positives = 92/145 (63%), Gaps = 5/145 (3%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYD-----DDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +    I  +++ L  +    +   +I         D     + +   +G+ ++TPVFDGA
Sbjct: 981  EELAAIDKVKNTLNDIESAEAKRVEIRKALEGLGYDYKKYGMPKPDVAGIHIATPVFDGA 1040

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E+ +   L +AD  + G+++LYDG TGEP D  VTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 1041 HEKDVFETLAIADRPDDGKTVLYDGRTGEPMDNRVTVGYVYMLKLHHLVDDKIHARSTGP 1100

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEV 1299
            YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1101 YSLVTQQPLGGKAQFGGQRFGEMEV 1125


>gi|10637859|emb|CAC10556.1| DNA-dependent RNA polymerase subunit beta [Leuconostoc
           mesenteroides]
          Length = 969

 Score =  627 bits (1616), Expect = e-177,   Method: Composition-based stats.
 Identities = 367/838 (43%), Positives = 512/838 (61%), Gaps = 68/838 (8%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R++VSQL RSPGI+++    +   +G+  +   +IP++G
Sbjct: 1   VFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGIYYNQTTDK---NGRPHFGTTVIPNRG 57

Query: 190 LWMDIEFDSKDII-HVRIDRRRKVPVTSFLMALGMDSE-EILSTF---YPKIVYSQRGDF 244
            W++ E D+K ++    I R   +  T  + ALG  S+ +I+  F   Y  +  +   D 
Sbjct: 58  AWLEYETDAKALLTSALIARVSAM--TELVRALGFGSDSDIIDIFSDQYDALNMTLEKDV 115

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGIT---- 299
                  +D  V   +      +  GE    +S + L        K   +  +G      
Sbjct: 116 HK---DMSDSRVEEALKDVYERLRPGEPKTADSSRALLVARFFDPKRYDLASVGRYKINK 172

Query: 300 ----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                  L    +AE + + ++GEI  E G ++D++ + ++        P L  +     
Sbjct: 173 KLSLKTRLLNQTLAETLADPDSGEIIAEKGTLVDKEVISKLT-------PYLDREDFKTT 225

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            Y  +           DA+L+        +  T    +              L+  G   
Sbjct: 226 TYTPSG----------DAVLE--------EPVTLQKIK--IESPENPEKTLLLTGNG--- 262

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                     +D R +R  DI+A +   ++L+ G G +DDID+LGNRR+RSVGE+L+NQ+
Sbjct: 263 -------HIDEDDRTVRPADILAGMNYFLNLQEGVGHVDDIDHLGNRRIRSVGELLQNQF 315

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL RMER ++ER+S  D ++V PQ LIN +PVV+AV EFF SSQLSQ  +  N L  +
Sbjct: 316 RIGLTRMERVVRERMSIQDANTVTPQQLINIRPVVAAVKEFFGSSQLSQFMDQTNPLGEM 375

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            H RRLSALG GG+ R RAGVE+RDVH THYGRI P ET EG NIGL++SL ++ R+N Y
Sbjct: 376 NHKRRLSALGPGGLTRDRAGVEVRDVHYTHYGRIDPIETPEGPNIGLINSLATYGRINKY 435

Query: 596 GFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GF+ETPYR+V     KVT+ + YL+A EE+N  +AQANS L+EDGSF    V  R   E 
Sbjct: 436 GFVETPYRRVDWTTHKVTDKIDYLTADEEDNYIVAQANSPLNEDGSFVHNTVMARFGEEN 495

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           I  P ++ID++D SPKQVVS+  + IPFLENDDSNR LMG NMQRQAVPLL   +P VGT
Sbjct: 496 IETPIDRIDYMDVSPKQVVSVGTAAIPFLENDDSNRALMGANMQRQAVPLLDPHSPLVGT 555

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+E   A  SG A++A+ +G VE VD  +I +R  +G LD        Y LMKF+RSN  
Sbjct: 556 GIEYKAAHDSGVAMIARASGEVEYVDGRQIRVRREDGQLD-------TYELMKFRRSNGG 608

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ+P+V VG+ +  ++++ADGPS + G+LALG+N L+AFM W GYNFED+++++ER+
Sbjct: 609 KNYNQKPIVHVGEHIEADEVLADGPSMEQGELALGQNPLIAFMTWQGYNFEDAIVLNERL 668

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V EDV+TSIHIEE++  ARDTKLGPEE+TR+IPN  E+ LK++D  GII VGAEV+ GDI
Sbjct: 669 VREDVYTSIHIEEYDSEARDTKLGPEEMTREIPNTGEDQLKDLDADGIIRVGAEVHDGDI 728

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + ++ EE++L AIFGEKA +VRDTSLRVP G  G V +VRI+     D
Sbjct: 729 LVGKVTPKGVTELSAEERVLHAIFGEKAREVRDTSLRVPHGGGGVVQNVRIYTPENGD 786



 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 135/449 (30%), Positives = 200/449 (44%), Gaps = 67/449 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +    +      G KN ++  I+ VG  +   ++L    +   +  +   +  
Sbjct: 588  RREDGQLDTYELMKFRRSNGGKNYNQKPIVHVGEHIEADEVLADGPS-MEQGELALGQNP 646

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     V   V        +  +  +  +  E    E +    +
Sbjct: 647  LIAFMTWQGYNFEDAIVLNERLVREDVYTSIHIEEYDSEARDTKLGPEEMTRE-IPNTGE 705

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+   LD +   R+     G     G     K T      +S   R     F  +  +V+
Sbjct: 706  DQLKDLDADGIIRV-----GAEVHDGDILVGKVTPKGVTELSAEERVLHAIFGEKAREVR 760

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      +I   + GD++ PGV  +V+V++A KR IQ GDKMAG
Sbjct: 761  DTSLRVPHGGGGVVQNV------RIYTPENGDELAPGVNMMVRVYIAQKRKIQVGDKMAG 814

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP++ DGTP+DI+L+P+GVPSRMN+GQ+ E HLG+A   LG  +
Sbjct: 815  RHGNKGTVSVVVPEEDMPYMPDGTPIDILLSPMGVPSRMNIGQVLELHLGFAAKKLGIHV 874

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S + D  ++ +I                         +  LR A   + G  V   V+D
Sbjct: 875  ASPVFDGASDDEI-------------------------EMALREAGLPQDGKSV---VYD 906

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G                           TGE FD+ V VG ++ +KL HMV DK++ARS 
Sbjct: 907  G--------------------------RTGEAFDKRVGVGVMHYMKLAHMVDDKIHARSI 940

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 941  GPYSLVTQQPLGGKAQFGGQRFGEMEVWA 969


>gi|330969828|gb|EGH69894.1| DNA-directed RNA polymerase subunit beta [Pseudomonas syringae pv.
            aceris str. M302273PT]
          Length = 401

 Score =  622 bits (1604), Expect = e-175,   Method: Composition-based stats.
 Identities = 210/405 (51%), Positives = 293/405 (72%), Gaps = 5/405 (1%)

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            Q++ + +D ++E  I++   + RL   L G+ A  G  G KK   ++++++      QW+
Sbjct: 1    QLDEIRKDLNEEFRIVEGATFERLRSALVGRIAEGG-AGLKKGQEITNEVLDGLEHGQWF 59

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  + ++ +   +E  +      + +L+D+F++K  K+Q GDD+ PGVL++VKV++A++R
Sbjct: 60   KLRMAEDALNEQLEKAQAYIVDRRRLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIRR 119

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             IQ GDKMAGRHGNKG+VS I+P EDMP   +GTPVDIVLNPLGVPSRMNVGQI ETHLG
Sbjct: 120  RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLG 179

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWK 1201
             A  GLG+KI  ++ + +    ++ LR FL ++    G   E + D  D+ +L +A+  +
Sbjct: 180  LAAKGLGEKINRMLEEQR---KVAELRKFLNEIYNEIGGRQESLEDLTDNEILDLAKNLR 236

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +GVP++TPVFDGA E  I +ML++AD+ ESGQ  L+DG TG  F+R VTVGY+YMLKLNH
Sbjct: 237  NGVPMATPVFDGAKESEIKAMLKLADMPESGQMQLFDGRTGNKFERAVTVGYMYMLKLNH 296

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD
Sbjct: 297  LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 356

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            V GRT++Y++IV G+   E G PESFNVL+KE+++LG+ IDLE  
Sbjct: 357  VNGRTKMYKNIVDGDHRMEPGMPESFNVLIKEIRSLGIDIDLETE 401


>gi|170288278|ref|YP_001738516.1| DNA-directed RNA polymerase, beta subunit [Thermotoga sp. RQ2]
 gi|226699456|sp|B1L935|RPOB_THESQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|170175781|gb|ACB08833.1| DNA-directed RNA polymerase, beta subunit [Thermotoga sp. RQ2]
          Length = 1263

 Score =  620 bits (1599), Expect = e-175,   Method: Composition-based stats.
 Identities = 378/1012 (37%), Positives = 564/1012 (55%), Gaps = 98/1012 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
            R R  FGK+ E + IPDL+E+QK SY  FL           EGL    K   PI +   
Sbjct: 8   RRTRVSFGKSREPLPIPDLVEIQKISYRRFL----------EEGLLEVLKKFSPIYSQAT 57

Query: 68  ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 58  RSDLKKSDRGFALEFVSTRIGEPVVDPLECKAKGLTYSVPIYATARLTDM---------K 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KE+ +++G +P MT  GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 109 SGEMKEEEVFLGYIPYMTDRGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 163

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 164 GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTYLDAD 222

Query: 241 RGDFWCF---PLSAADLMVGAK---VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
             D        +   D+  G +       ++  D  E+++         ++  + +   +
Sbjct: 223 DEDSLLLHVGSILLEDIYDGDRKIAEKWDILTKDLAERILMIDDINQIKIVHPIAQNTFE 282

Query: 295 FLG--ITSDCLCGLYVAEDIVNGETGEI-----YIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +   ++S    G    E        E+     Y+E    +  + L  I  ++     + 
Sbjct: 283 KMLELVSSSGEEGEEEEEKTKIYGLNEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLF 342

Query: 348 Y--------------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVS-- 387
           +              V+    NAYIR  +  +   D ++A   +Y     V++P D+   
Sbjct: 343 FNPERYDLSEVGRYKVNERLRNAYIRYLIEVEGE-DPEEARKKVYNETSLVLKPLDIVLA 401

Query: 388 --TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-------------MRLNLDTPDDVRHIR 432
                          F+ D Y+L  + R+                 +L      +     
Sbjct: 402 SRILFDYFERRYVNDFEIDSYELKNLIRIFKEEYLEKRKTAPYDLRKLVSVFRRNYGVTS 461

Query: 433 KEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
              + A I+ + ++     +I  D  D+LGN+RVR+VGE+++ ++     R +++I+ER+
Sbjct: 462 DLGVFAAIRYVSNINKELPSIPFDTKDHLGNKRVRTVGELVQREFERLFARAQKAIQERL 521

Query: 491 SSVDI-DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + ++    V  Q LIN K ++S V +FF  +QLSQ  + VN LS +TH RR+SA+G GG+
Sbjct: 522 TLINSLSKVSIQSLINIKSIISTVNQFFAMNQLSQFMDQVNPLSELTHKRRVSAVGPGGL 581

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R     E R+VH + YGR+CP ET EG NIG ++SL  +A+++ YGF+ TPYRKV +GK
Sbjct: 582 RRESKVFEARNVHYSQYGRLCPIETPEGANIGFITSLAIYAKIDEYGFLMTPYRKVVNGK 641

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT++VVYL A EEE   I  A + +DE+G+   E V  R   +  LVP+E++DF+D S K
Sbjct: 642 VTDEVVYLRANEEEEYKIIPATTPVDEEGNIIPERVVARMGEDIRLVPKEEVDFMDVSTK 701

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q  S++ASLIPFLE+DD++R LMG NMQRQAVPLLK EAP VGTGME   AK+SG  ++A
Sbjct: 702 QPFSVSASLIPFLEHDDASRALMGSNMQRQAVPLLKTEAPLVGTGMEWEAAKNSGYVVLA 761

Query: 730 KRAGIVEQVDAIRIVIRSVEG-----DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  GIV++VDA R+V+   +        D     VD YRL+KF RSNQ+T +NQ+P+V  
Sbjct: 762 EHDGIVKEVDAARVVVHRTDENGNLMYDDKGNPVVDEYRLLKFVRSNQDTMINQKPIVNE 821

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V++ D IADGP+TD+G+LALGRN+LVAFMPW GYN+ED++L+S+ ++ EDVFTSIHI
Sbjct: 822 GDFVKKGDPIADGPATDMGELALGRNILVAFMPWEGYNYEDAILVSQELLEEDVFTSIHI 881

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE------VNPGDILVGKI 898
           E +E  AR+T+LGPEEIT DIPNVS+E LKN+DE GII VGA       V    ILVGK+
Sbjct: 882 EVYETQARETRLGPEEITADIPNVSKELLKNLDENGIIRVGAYVVSDYGVGSQAILVGKV 941

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           TPKGE   TPEEK++R++FGE+  DV+DTSLR+P GV G V+ V +++++ I
Sbjct: 942 TPKGEGDTTPEEKIIRSVFGERGRDVKDTSLRLPHGVEGRVIRVDVYDQNDI 993



 Score =  439 bits (1129), Expect = e-120,   Method: Composition-based stats.
 Identities = 174/527 (33%), Positives = 245/527 (46%), Gaps = 72/527 (13%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  R +  V       I++  I+  G  V  GD +           +     +L A    
Sbjct: 797  DEYRLLKFVRSNQDTMINQKPIVNEGDFVKKGDPIADGP-ATDMGELALGRNILVAFMPW 855

Query: 920  KAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            +  +  D  L            S  +       R      E   +      + L ++ D+
Sbjct: 856  EGYNYEDAILVSQELLEEDVFTSIHIEVYETQARETRLGPEEITADIPNVSKELLKNLDE 915

Query: 974  EQVI-----LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +I     +  +       IL G+    G         +   +  E  R          
Sbjct: 916  NGIIRVGAYVVSDYGVGSQAILVGKVTPKGEGDTTPEEKIIRSVFGERGRD--------- 966

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              V+     L    E     ++   +N I       ++  GVL++V+V+VA ++ +  GD
Sbjct: 967  --VKDTSLRLPHGVEGRVIRVDVYDQNDIA------ELGAGVLKLVRVYVASRKTLDIGD 1018

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG+VS ILP EDMPFL DGTPV +VLNPLG+PSRMNVGQI ETHLGW     
Sbjct: 1019 KLAGRHGNKGVVSNILPKEDMPFLPDGTPVQMVLNPLGIPSRMNVGQILETHLGWLAKLT 1078

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK   + + +     +I                                E+ K G+ +  
Sbjct: 1079 GKWFATPVFEGAKEDEILRPL--------------------------YEERKKRGLHL-- 1110

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                G DE            + +G+ +L DG TGEPFD PV VGY+YMLKL H+  +K++
Sbjct: 1111 ----GDDEN-----------NPNGKVVLRDGRTGEPFDNPVVVGYMYMLKLIHIAKEKIH 1155

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSL+ QQPLGGKS+ GGQRLGEMEVW ++AYGAA+ L EMLTIKSDD+ GR   
Sbjct: 1156 ARSTGPYSLIHQQPLGGKSHFGGQRLGEMEVWALEAYGAAHTLAEMLTIKSDDIKGRNEA 1215

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            Y++I+   +  E G PESF VL+KE++ L L + L +         +
Sbjct: 1216 YKAILKNMNIPEPGVPESFRVLIKELRGLALDVRLYDENGNEIDIDK 1262


>gi|36333377|gb|AAP75746.1| RNA polymerase beta subunit [Bosea vestrisii]
          Length = 414

 Score =  620 bits (1598), Expect = e-175,   Method: Composition-based stats.
 Identities = 260/417 (62%), Positives = 325/417 (77%), Gaps = 3/417 (0%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G  P  P  KLLRAIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ER
Sbjct: 1    GREPDDPGRKLLRAIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIER 60

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQW
Sbjct: 61   EEIERLAKDRDDEQAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQW 120

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            W FA  D+ +   +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+K
Sbjct: 121  WLFATADDALMTEIEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVK 180

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHL
Sbjct: 181  RKIQPGDKMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHL 240

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWA  GLGK+I   I+ Y+   D   LR+  + V       E I+  DD  ++ + +  +
Sbjct: 241  GWAAAGLGKQIGKAIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDAELIEMGQNLR 297

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H
Sbjct: 298  RGVPIATPVFNGAKESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHH 357

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            +V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 358  LVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 414


>gi|15643224|ref|NP_228268.1| DNA-directed RNA polymerase subunit beta [Thermotoga maritima MSB8]
 gi|548824|sp|P29398|RPOB_THEMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|4980967|gb|AAD35543.1|AE001724_1 DNA-directed RNA polymerase, beta subunit [Thermotoga maritima
           MSB8]
 gi|425258|emb|CAA51246.1| RNA polymerase, beta subunit [Thermotoga maritima]
          Length = 1263

 Score =  619 bits (1597), Expect = e-175,   Method: Composition-based stats.
 Identities = 378/1012 (37%), Positives = 563/1012 (55%), Gaps = 98/1012 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
            R R  FGK+ E + IPDL+E+QK+SY  FL           EGL    K   PI +   
Sbjct: 8   RRTRVSFGKSREPLPIPDLVEIQKSSYRRFL----------EEGLLEVLKKFSPIYSQAT 57

Query: 68  ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 58  RSDLRKSDRGFALEFVSTRTGEPAIDPLECKAKGLTYSVPIYATARLTDM---------K 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KE+ +++G +P MT  GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 109 SGEMKEEEVFLGYIPYMTDRGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 163

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 164 GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTYLDAD 222

Query: 241 RGDFWCF---PLSAADLMVGAK---VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
             D        +   D+  G +       ++  D  E+++         ++  + +   +
Sbjct: 223 DEDSLLLHVGSILLEDIYDGGRKIAEKWDILTKDLAERILMIDDINQIKIVHPIAQNTFE 282

Query: 295 FLGITSDCLCGLYVAEDIVNGETG--EI-----YIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +             E+      G  E+     Y+E    +  + L  I  ++     + 
Sbjct: 283 KMLEVVSSSSEEGEEEEEKTKIYGLNEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLF 342

Query: 348 Y--------------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVS-- 387
           +              V+    NAYIR  +  +   D ++A   +Y     V++P D+   
Sbjct: 343 FNPERYDLSEVGRYKVNERLRNAYIRYLIEVEGE-DPEEARKKVYNETSLVLKPLDIVLA 401

Query: 388 --TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-------------MRLNLDTPDDVRHIR 432
                          F+ D Y+L  + R+                 +L      +     
Sbjct: 402 SRILFDYFERRYVNDFEIDSYELKNLIRIFKEEYLEKRKTAPYDLRKLVSVFRRNYGVTS 461

Query: 433 KEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
              + A I+ + ++     +I  D  D+LGN+RVR+VGE+++ ++     R +++I+ER+
Sbjct: 462 DLGVFAAIRYVSNINKELPSIPFDTKDHLGNKRVRTVGELVQREFERLFARAQKAIQERL 521

Query: 491 SSVDI-DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + ++    V  Q LIN K ++S V +FF  +QLSQ  + VN LS +TH RR+SA+G GG+
Sbjct: 522 TLINSLSKVSIQSLINIKSIISTVNQFFAMNQLSQFMDQVNPLSELTHKRRVSAVGPGGL 581

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R     E R+VH + YGR+CP ET EG NIG ++SL  +A+++ YGF+ TPYRKV +GK
Sbjct: 582 RRESKVFEARNVHYSQYGRLCPIETPEGANIGFITSLAIYAKIDEYGFLMTPYRKVVNGK 641

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT++VVYL A EEE   I  A + +DE+G+   E V  R   +  LVP+E++DF+D S K
Sbjct: 642 VTDEVVYLRANEEEEYKIIPATTPVDEEGNIIPERVVARMGEDIRLVPKEEVDFMDVSTK 701

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q  S++ASLIPFLE+DD++R LMG NMQRQAVPLLK EAP VGTGME   AK+SG  I+A
Sbjct: 702 QPFSVSASLIPFLEHDDASRALMGSNMQRQAVPLLKTEAPLVGTGMEWEAAKNSGYVILA 761

Query: 730 KRAGIVEQVDAIRIVIRSVEG-----DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  GIV++VDA R+V+   +        D     VD YRL+KF RSNQ+T +NQ+P+V  
Sbjct: 762 EHDGIVKEVDAARVVVHRTDENGNLMYDDKGNPVVDEYRLLKFVRSNQDTMINQKPIVNE 821

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V++ D IADGP+TD+G+LALGRN+LVAFMPW GYN+ED++L+S+ ++ EDVFTSIHI
Sbjct: 822 GDFVKKGDPIADGPATDMGELALGRNILVAFMPWEGYNYEDAILVSQELLEEDVFTSIHI 881

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE------VNPGDILVGKI 898
           E +E  AR+T+LGPEEIT DIPNVS+E LKN+DE GII VGA       V    ILVGK+
Sbjct: 882 EVYETQARETRLGPEEITADIPNVSKELLKNLDENGIIRVGAYVVSDYGVGSQAILVGKV 941

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           TPKGE   TPEEK++R++FGE+  DV+DTSLR+P GV G V+ V +++++ I
Sbjct: 942 TPKGEGDTTPEEKIIRSVFGERGRDVKDTSLRLPHGVEGRVIRVDVYDQNDI 993



 Score =  439 bits (1130), Expect = e-120,   Method: Composition-based stats.
 Identities = 174/527 (33%), Positives = 245/527 (46%), Gaps = 72/527 (13%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  R +  V       I++  I+  G  V  GD +           +     +L A    
Sbjct: 797  DEYRLLKFVRSNQDTMINQKPIVNEGDFVKKGDPIADGP-ATDMGELALGRNILVAFMPW 855

Query: 920  KAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            +  +  D  L            S  +       R      E   +      + L ++ D+
Sbjct: 856  EGYNYEDAILVSQELLEEDVFTSIHIEVYETQARETRLGPEEITADIPNVSKELLKNLDE 915

Query: 974  EQVI-----LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +I     +  +       IL G+    G         +   +  E  R          
Sbjct: 916  NGIIRVGAYVVSDYGVGSQAILVGKVTPKGEGDTTPEEKIIRSVFGERGRD--------- 966

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              V+     L    E     ++   +N I       ++  GVL++V+V+VA ++ +  GD
Sbjct: 967  --VKDTSLRLPHGVEGRVIRVDVYDQNDIA------ELGAGVLKLVRVYVASRKTLDIGD 1018

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG+VS ILP EDMPFL DGTPV +VLNPLG+PSRMNVGQI ETHLGW     
Sbjct: 1019 KLAGRHGNKGVVSNILPKEDMPFLPDGTPVQMVLNPLGIPSRMNVGQILETHLGWLAKLT 1078

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK   + + +     +I                                E+ K G+ +  
Sbjct: 1079 GKWFATPVFEGAKEDEILRPL--------------------------YEERKKRGLHL-- 1110

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                G DE            + +G+ +L DG TGEPFD PV VGY+YMLKL H+  +K++
Sbjct: 1111 ----GDDEN-----------NPNGKVVLRDGRTGEPFDNPVVVGYMYMLKLIHIAKEKIH 1155

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSL+ QQPLGGKS+ GGQRLGEMEVW ++AYGAA+ L EMLTIKSDD+ GR   
Sbjct: 1156 ARSTGPYSLIHQQPLGGKSHFGGQRLGEMEVWALEAYGAAHTLAEMLTIKSDDIKGRNEA 1215

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            Y++I+   +  E G PESF VL+KE++ L L + L +         +
Sbjct: 1216 YKAILKNMNIPEPGVPESFRVLIKELRGLALDVRLYDENGNEIDIDK 1262


>gi|148269602|ref|YP_001244062.1| DNA-directed RNA polymerase subunit beta [Thermotoga petrophila
           RKU-1]
 gi|182676578|sp|A5IJW3|RPOB_THEP1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|147735146|gb|ABQ46486.1| DNA-directed RNA polymerase, beta subunit [Thermotoga petrophila
           RKU-1]
          Length = 1263

 Score =  617 bits (1592), Expect = e-174,   Method: Composition-based stats.
 Identities = 381/1012 (37%), Positives = 565/1012 (55%), Gaps = 98/1012 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
            R R  FGK  E + IPDL+E+QK SY  FL           EGL    K   PI +   
Sbjct: 8   RRTRVSFGKTQEPLPIPDLVEIQKISYRRFL----------EEGLLEVLKKFSPIYSQAT 57

Query: 68  ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 58  RSDLKKSDRGFALEFVSTRIGEPVVDPLECKAKGLTYSVPIYATARLTDM---------K 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KE+ +++G +P MT  GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 109 SGEMKEEEVFLGYIPYMTDRGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 163

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 164 GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTYLDAD 222

Query: 241 RGDFWCF---PLSAADLMVGAK---VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
             D        +   D+  G +       ++  D  E+++         ++  + +   +
Sbjct: 223 DEDSLLLHVGSILLEDIYDGDRKIAEKWDILTKDLAERILMIDDINQIKIVHPIAQNTFE 282

Query: 295 FLG--ITSDCLCGLYVAEDIVNGETGEI-----YIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +   ++S    G    E        E+     Y+E    +  + L  I  ++     + 
Sbjct: 283 KMLELVSSSGEEGEEEEEKTKIYGLNEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLF 342

Query: 348 Y--------------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVS-- 387
           +              V+    NAYIR  +  +   D ++A   +Y     V++P D+   
Sbjct: 343 FNPERYDLSEVGRYKVNERLRNAYIRYLIEVEGE-DPEEARKKVYNENSLVLKPLDIVLA 401

Query: 388 --TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-------------MRLNLDTPDDVRHIR 432
                          F+ D Y+L  + R+                 +L      +     
Sbjct: 402 SRILFDYFERRYVNDFEIDSYELRNLIRIFKEEYLEKRKTASYDLRKLVSVFRRNYGVTS 461

Query: 433 KEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
              ++A I+ + ++     +I  D  D+LGN+RVR+VGE+++ ++     R +++I+ER+
Sbjct: 462 DLSVLAAIRYISNINKELPSIPFDTKDHLGNKRVRTVGELVQREFERLFARAQKAIQERL 521

Query: 491 SSVDI-DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + ++    V  Q LIN K ++S V +FF  +QLSQ  + VN LS +TH RR+SA+G GG+
Sbjct: 522 TLINSLSKVSIQSLINIKSIISTVNQFFAMNQLSQFMDQVNPLSELTHKRRVSAVGPGGL 581

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R     E R+VH + YGR+CP ET EG NIG ++SL  + +++ YGF+ TPYRKV +GK
Sbjct: 582 RRESKVFEARNVHYSQYGRLCPIETPEGANIGFITSLAIYTKIDEYGFLMTPYRKVVNGK 641

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT++VVYL A EEE+  I  A + +DE+G+   E V  R   +  LVPRE++DF+D S K
Sbjct: 642 VTDEVVYLRANEEEDFKIVPATTPVDEEGNIIPERVVARVGEDIRLVPREEVDFMDVSTK 701

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q  S++ASLIPFLE+DD++R LMG NMQRQAVPLLKAEAPFVGTGME   AK+SG   +A
Sbjct: 702 QPFSVSASLIPFLEHDDASRALMGSNMQRQAVPLLKAEAPFVGTGMEWEAAKNSGYVTLA 761

Query: 730 KRAGIVEQVDAIRIVIRSVEG-----DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  GIV++VDA RIV+   +        D     VD YRL+KF RSNQ+T +NQ+P+V  
Sbjct: 762 EHDGIVKEVDAARIVVHRTDENGNLMYDDKGNPVVDEYRLLKFVRSNQDTMINQKPIVNE 821

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V++ D IADGP+TD+G+LALGRN+LVAFMPW GYN+ED++L+S+ ++ EDVFTSIHI
Sbjct: 822 GDFVKKGDPIADGPATDMGELALGRNILVAFMPWEGYNYEDAILVSQELLEEDVFTSIHI 881

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE------VNPGDILVGKI 898
           E +E  AR+T+LGPEEIT DIPNVS+E LKN+DE GII VGA       V    ILVGK+
Sbjct: 882 EVYETQARETRLGPEEITADIPNVSKELLKNLDENGIIRVGAYVVSDYGVGSQAILVGKV 941

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           TPKGE   TPEEK++R++FGE+  DV+DTSLR+P GV G V+ V +++++ I
Sbjct: 942 TPKGEGDTTPEEKIIRSVFGERGRDVKDTSLRLPHGVEGRVIRVDVYDQNDI 993



 Score =  439 bits (1128), Expect = e-120,   Method: Composition-based stats.
 Identities = 174/527 (33%), Positives = 245/527 (46%), Gaps = 72/527 (13%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  R +  V       I++  I+  G  V  GD +           +     +L A    
Sbjct: 797  DEYRLLKFVRSNQDTMINQKPIVNEGDFVKKGDPIADGP-ATDMGELALGRNILVAFMPW 855

Query: 920  KAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            +  +  D  L            S  +       R      E   +      + L ++ D+
Sbjct: 856  EGYNYEDAILVSQELLEEDVFTSIHIEVYETQARETRLGPEEITADIPNVSKELLKNLDE 915

Query: 974  EQVI-----LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +I     +  +       IL G+    G         +   +  E  R          
Sbjct: 916  NGIIRVGAYVVSDYGVGSQAILVGKVTPKGEGDTTPEEKIIRSVFGERGRD--------- 966

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              V+     L    E     ++   +N I       ++  GVL++V+V+VA ++ +  GD
Sbjct: 967  --VKDTSLRLPHGVEGRVIRVDVYDQNDIA------ELGAGVLKLVRVYVASRKTLDIGD 1018

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG+VS ILP EDMPFL DGTPV +VLNPLG+PSRMNVGQI ETHLGW     
Sbjct: 1019 KLAGRHGNKGVVSNILPKEDMPFLPDGTPVQMVLNPLGIPSRMNVGQILETHLGWLAKLT 1078

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK   + + +     +I                                E+ K G+ +  
Sbjct: 1079 GKWFATPVFEGAKEDEILRPL--------------------------YEERKKRGLHL-- 1110

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                G DE            + +G+ +L DG TGEPFD PV VGY+YMLKL H+  +K++
Sbjct: 1111 ----GDDEN-----------NPNGKVVLRDGRTGEPFDNPVVVGYMYMLKLVHIAKEKIH 1155

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSL+ QQPLGGKS+ GGQRLGEMEVW ++AYGAA+ L EMLTIKSDD+ GR   
Sbjct: 1156 ARSTGPYSLIHQQPLGGKSHFGGQRLGEMEVWALEAYGAAHTLAEMLTIKSDDIKGRNEA 1215

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            Y++I+   +  E G PESF VL+KE++ L L + L +         +
Sbjct: 1216 YKAILKNMNIPEPGVPESFRVLIKELRGLALDVRLYDENGNEIDIDK 1262


>gi|281411680|ref|YP_003345759.1| DNA-directed RNA polymerase, beta subunit [Thermotoga naphthophila
           RKU-10]
 gi|281372783|gb|ADA66345.1| DNA-directed RNA polymerase, beta subunit [Thermotoga naphthophila
           RKU-10]
          Length = 1263

 Score =  617 bits (1592), Expect = e-174,   Method: Composition-based stats.
 Identities = 381/1012 (37%), Positives = 565/1012 (55%), Gaps = 98/1012 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
            R R  FGK  E + IPDL+E+QK SY  FL           EGL    K   PI +   
Sbjct: 8   RRTRVSFGKTQEPLPIPDLVEIQKISYRRFL----------EEGLLEVLKKFSPIYSQAT 57

Query: 68  ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 58  RSDLKKSDRGFALEFVSTRIGEPVVDPLECKAKGLTYSVPIYATARLTDM---------K 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KE+ +++G +P MT  GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 109 SGEMKEEEVFLGYIPYMTDRGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 163

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 164 GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTYLDAD 222

Query: 241 RGDFWCF---PLSAADLMVGAK---VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
             D        +   D+  G +       ++  D  E+++         ++  + +   +
Sbjct: 223 DEDSLLLHVGSILLEDIYDGDRKIAEKWDILTKDLAERILMIDDINQIKIVHPIAQNTFE 282

Query: 295 FLG--ITSDCLCGLYVAEDIVNGETGEI-----YIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +   ++S    G    E        E+     Y+E    +  + L  I  ++     + 
Sbjct: 283 KMLELVSSSGEEGEEEEEKTKIYGLNEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLF 342

Query: 348 Y--------------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVS-- 387
           +              V+    NAYIR  +  +   D ++A   +Y     V++P D+   
Sbjct: 343 FNPERYDLSEVGRYKVNERLRNAYIRYLIEVEGE-DPEEARKKVYNENSLVLKPLDIVLA 401

Query: 388 --TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-------------MRLNLDTPDDVRHIR 432
                          F+ D Y+L  + R+                 +L      +     
Sbjct: 402 SRILFDYFERRYVNDFEIDSYELRNLIRIFKEEYLEKRKTASYDLRKLVSVFRRNYGVTS 461

Query: 433 KEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
              ++A I+ + ++     +I  D  D+LGN+RVR+VGE+++ ++     R +++I+ER+
Sbjct: 462 DLSVLAAIRYISNINKELPSIPFDTKDHLGNKRVRTVGELVQREFERLFARAQKAIQERL 521

Query: 491 SSVDI-DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + ++    V  Q LIN K ++S V +FF  +QLSQ  + VN LS +TH RR+SA+G GG+
Sbjct: 522 TLINSLSKVSIQSLINIKSIISTVNQFFAMNQLSQFMDQVNPLSELTHKRRVSAVGPGGL 581

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R     E R+VH + YGR+CP ET EG NIG ++SL  + +++ YGF+ TPYRKV +GK
Sbjct: 582 RRESKVFEARNVHYSQYGRLCPIETPEGANIGFITSLAIYTKIDEYGFLMTPYRKVVNGK 641

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT++VVYL A EEE+  I  A + +DE+G+   E V  R   +  LVPRE++DF+D S K
Sbjct: 642 VTDEVVYLRANEEEDFKIVPATTPVDEEGNIIPERVVARVGEDIRLVPREEVDFMDVSTK 701

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q  S++ASLIPFLE+DD++R LMG NMQRQAVPLLKAEAPFVGTGME   AK+SG   +A
Sbjct: 702 QPFSVSASLIPFLEHDDASRALMGSNMQRQAVPLLKAEAPFVGTGMEWEAAKNSGYVTLA 761

Query: 730 KRAGIVEQVDAIRIVIRSVEG-----DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  GIV++VDA RIV+   +        D     VD YRL+KF RSNQ+T +NQ+P+V  
Sbjct: 762 EHDGIVKEVDAARIVVHRTDENGNLMYDDKGNPVVDEYRLLKFVRSNQDTMINQKPIVNE 821

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V++ D IADGP+TD+G+LALGRN+LVAFMPW GYN+ED++L+S+ ++ EDVFTSIHI
Sbjct: 822 GDFVKKGDPIADGPATDMGELALGRNILVAFMPWEGYNYEDAILVSQELLEEDVFTSIHI 881

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE------VNPGDILVGKI 898
           E +E  AR+T+LGPEEIT DIPNVS+E LKN+DE GII VGA       V    ILVGK+
Sbjct: 882 EVYETQARETRLGPEEITADIPNVSKELLKNLDENGIIRVGAYVVSDYGVGSQAILVGKV 941

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           TPKGE   TPEEK++R++FGE+  DV+DTSLR+P GV G V+ V +++++ I
Sbjct: 942 TPKGEGDTTPEEKIIRSVFGERGRDVKDTSLRLPHGVEGRVIRVDVYDQNDI 993



 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 174/527 (33%), Positives = 245/527 (46%), Gaps = 72/527 (13%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  R +  V       I++  I+  G  V  GD +           +     +L A    
Sbjct: 797  DEYRLLKFVRSNQDTMINQKPIVNEGDFVKKGDPIADGP-ATDMGELALGRNILVAFMPW 855

Query: 920  KAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            +  +  D  L            S  +       R      E   +      + L ++ D+
Sbjct: 856  EGYNYEDAILVSQELLEEDVFTSIHIEVYETQARETRLGPEEITADIPNVSKELLKNLDE 915

Query: 974  EQVI-----LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +I     +  +       IL G+    G         +   +  E  R          
Sbjct: 916  NGIIRVGAYVVSDYGVGSQAILVGKVTPKGEGDTTPEEKIIRSVFGERGRD--------- 966

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              V+     L    E     ++   +N I       ++  GVL++V+V+VA ++ +  GD
Sbjct: 967  --VKDTSLRLPHGVEGRVIRVDVYDQNDIA------ELGAGVLKLVRVYVASRKTLDIGD 1018

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG+VS ILP EDMPFL DGTPV +VLNPLG+PSRMNVGQI ETHLGW     
Sbjct: 1019 KLAGRHGNKGVVSNILPKEDMPFLPDGTPVQMVLNPLGIPSRMNVGQILETHLGWLAKLT 1078

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            GK   + + +     +I                                E+ K G+ +  
Sbjct: 1079 GKWFATPVFEGAKEDEILRPL--------------------------YEERKKRGLHL-- 1110

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                G DE            + +G+ +L DG TGEPFD PV VGY+YMLKL H+  +K++
Sbjct: 1111 ----GDDEN-----------NPNGKVVLRDGRTGEPFDNPVVVGYMYMLKLVHIAKEKIH 1155

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSL+ QQPLGGKS+ GGQRLGEMEVW ++AYGAA+ L EMLTIKSDD+ GR   
Sbjct: 1156 ARSTGPYSLIHQQPLGGKSHFGGQRLGEMEVWALEAYGAAHTLAEMLTIKSDDIKGRNEA 1215

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            Y++I+   +  E G PESF VL+KE++ L L + L +         +
Sbjct: 1216 YKAILKNMNIPEPGVPESFRVLIKELKGLALDVRLYDENGNEIDIDK 1262


>gi|36333379|gb|AAP75747.1| RNA polymerase beta subunit [Bosea eneae]
          Length = 414

 Score =  617 bits (1591), Expect = e-174,   Method: Composition-based stats.
 Identities = 253/404 (62%), Positives = 318/404 (78%), Gaps = 3/404 (0%)

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AIFGEKA DVRDTSLRVP GV GT+V+VR+FNRHG+DK+ER+ ++ERE+IE LA+D+DDE
Sbjct: 1    AIFGEKASDVRDTSLRVPPGVQGTIVEVRVFNRHGVDKDERAQAIEREEIERLAKDRDDE 60

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            Q ILDRN ++RL EIL G+  ++GPKGFKK TV++ +++SE+PRSQWW FA  D+ +   
Sbjct: 61   QAILDRNTFARLAEILTGKTGLAGPKGFKKDTVITREVMSEFPRSQWWLFATSDDALMTE 120

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR IQ GDKMAGRH
Sbjct: 121  IEAMRKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKRKIQPGDKMAGRH 180

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLGK+I  
Sbjct: 181  GNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGKQIGK 240

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             I+ Y+   D   LR+  + V       E I+  DD  ++ + +  + GVP++TPVF+GA
Sbjct: 241  AIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDAELIEMGQNLRRGVPIATPVFNGA 297

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             E  I  +L  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++ARS G 
Sbjct: 298  KESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIHARSIGP 357

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 358  YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 401


>gi|229915453|gb|ACQ90798.1| beta subunit of RNA polymerase [Oocystis solitaria]
          Length = 1115

 Score =  616 bits (1588), Expect = e-173,   Method: Composition-based stats.
 Identities = 320/1137 (28%), Positives = 522/1137 (45%), Gaps = 114/1137 (10%)

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                    +   +  +  K    +++      + +  +       +   +K  +      
Sbjct: 82   SKKIKTQWVLLTNFPLMTKRGHFIINGSPRIIINQIIRSPGIYYQEVFDKKKKRKYYADL 141

Query: 301  DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                G ++  +I   +             + S+     +      +++    +++    +
Sbjct: 142  ISFRGTWLRLEIDKKKA---IWARMKKTPKISILIFLQAMGLTNQLIFHSIEHSDFLKNS 198

Query: 361  TLVTDKNKDRKDALLDIYRVMRPGDVSTFS---VAESMFNFLFFDSDKYDLSTVGRVKMN 417
                +     ++AL  +Y  + P    T     + +      F +   YDLS +GR ++N
Sbjct: 199  FSDEENLTTTEEALKLLYSEINPKKEETSIKSSMGQKFLFRKFMNPRTYDLSELGRSRLN 258

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +L L        +   DI+  I  L+ L +G G IDDID+L NRRVR+ GE+L+NQ  L
Sbjct: 259  EKLGLSISKSKTTLTPHDILYAINYLIKLEHGFGKIDDIDHLKNRRVRASGEILQNQISL 318

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            GL+R+E+ I+E++   +  +++ Q+LI  K +  A+ EFF SSQLSQ  +  N L+ ITH
Sbjct: 319  GLIRLEKLIREKLKK-NRKNIILQNLITTKAINGALREFFGSSQLSQFMDQTNPLAEITH 377

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRL+++G  GV+R  AG+ +R +HPTHYGRICP ET EG N GLV+S+TS+A++N+ GF
Sbjct: 378  KRRLTSIGPNGVSRETAGMALRGIHPTHYGRICPIETPEGPNAGLVNSITSYAKINSKGF 437

Query: 598  IETPYRKVCDGKVTNDVVYL--SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            +ETP+ K   G++   +  L  SA EEE + +  ++ +  +     ++ +  R   E   
Sbjct: 438  LETPFYKTFKGQIQKKLKPLFFSAEEEETKILISSDLNSSKFYFLPKKKIPTRFGTETQQ 497

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              ++++++   S  Q++SIA SLIPFLE++D+NR LMG NMQRQAVPL+K E P VGTG+
Sbjct: 498  TKKDQVEYSAISQIQMISIATSLIPFLEHNDANRSLMGSNMQRQAVPLIKPERPVVGTGL 557

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E  +   S                         +  L    +G   Y   K         
Sbjct: 558  EGRIISDS-------------------------DHALQTQFTGYISYVSGK--------- 583

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
               + +V    + ++N  +    ST     +        F      N  + +  +  +  
Sbjct: 584  ---KIIVYT-IKKKKNLSLNLQKSTKNSFFSEYL-----FPKKLKKNSTNKIKKNPLIKR 634

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                 ++ IE  +   +  ++      R           +I E      G  +   D+L 
Sbjct: 635  ----NTLFIEIIKNSIKKNEILLHTFQRSNQETLLTHYASICE------GNWIQKNDLLA 684

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
                   +  +   + +L A    +  +  D  L     V   +       R  ++  + 
Sbjct: 685  DSSC-SLKGEIALGKNILIAYMPWEGYNFEDAVLINERLVYEDIYTSIHIERFELEIRDT 743

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
               +E+   +L          + +R I      +  G   +      KK +++  + +  
Sbjct: 744  KFGLEKITNKLPEVPFSQLLHLDERGIAKIGSWVEEGTILIGKITPIKKKSLIPHEKL-- 801

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                  +    +     R+      +  T + I  +  + K        +        V 
Sbjct: 802  -----LYDIIGKKTPTTRDSSLRAPKGLTGRIIHVEILETK----NLPPESLFEGPGRVH 852

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            +++A KR IQ GDK++GRHGNKGI+S+ILP +DMPFL DGTPVD+VLNPLGVPSRMNVGQ
Sbjct: 853  IYIAEKRKIQVGDKISGRHGNKGIISKILPRQDMPFLPDGTPVDMVLNPLGVPSRMNVGQ 912

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            I E  LG A + L ++ K    D K                G  +    +     ++ L+
Sbjct: 913  ILECLLGLAGIFLNQQYKITPFDEK---------------YGPEASRSLVFSKLYEARLK 957

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              ++W                        + + +  G+  L+DG  G+ FD+  T+G  Y
Sbjct: 958  TGQKW------------------------LFNPNFPGKIQLFDGRNGKCFDQHTTIGQAY 993

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKL H+V DK++ARSTG YSLVTQQPL G+S  GGQRLGEMEVW ++ +G+AY+LQE++
Sbjct: 994  ILKLVHLVDDKIHARSTGPYSLVTQQPLRGRSKHGGQRLGEMEVWALEGFGSAYILQELI 1053

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            TIKSDD  GR +V  +I+        GTPE+F VL+KE+Q+L L I +   +     
Sbjct: 1054 TIKSDDTKGRHQVINAILKNKSIS-LGTPEAFKVLIKELQSLCLDIIVYTRKASKLD 1109



 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 83/368 (22%), Positives = 151/368 (41%), Gaps = 34/368 (9%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEF 81
           + +PD IE+Q+ S++  L           +GL    K+  PIT       L F    Y+ 
Sbjct: 1   MYLPDFIEIQRNSFNALL----------KKGLIKEIKNRSPITNIKKNIELFFYPELYQL 50

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           +PP F     + +  TYA  L I ++L+           + K IK Q + + + PLMTK 
Sbjct: 51  NPPNFTNKTAILKAKTYACKLYIPVQLV---------NNTSKKIKTQWVLLTNFPLMTKR 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           G F+I G  RI+++Q+ RSPGI++     +     K  Y   +I  +G W+ +E D K  
Sbjct: 102 GHFIINGSPRIIINQIIRSPGIYYQEVFDKKK---KRKYYADLISFRGTWLRLEIDKKKA 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ +  K+ +  FL A+G+ ++ I   F+         + +    +        K+ 
Sbjct: 159 IWARMKKTPKISILIFLQAMGLTNQLI---FHSIEHSDFLKNSFSDEENLTTTEEALKLL 215

Query: 262 SSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYVAEDIVNGETG 318
            S ++    E  I+S  G+K       + +   +  LG +  +   GL +++        
Sbjct: 216 YSEINPKKEETSIKSSMGQKFLFRKFMNPRTYDLSELGRSRLNEKLGLSISKSKTTLTPH 275

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           +I      +I  +        +I DI  L    V  +  I    ++      +  + +  
Sbjct: 276 DILYAINYLIKLEH----GFGKIDDIDHLKNRRVRASGEILQNQISLGLIRLEKLIREKL 331

Query: 379 RVMRPGDV 386
           +  R   +
Sbjct: 332 KKNRKNII 339


>gi|160901839|ref|YP_001567420.1| DNA-directed RNA polymerase, beta subunit [Petrotoga mobilis SJ95]
 gi|182676570|sp|A9BF33|RPOB_PETMO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|160359483|gb|ABX31097.1| DNA-directed RNA polymerase, beta subunit [Petrotoga mobilis SJ95]
          Length = 1187

 Score =  615 bits (1587), Expect = e-173,   Method: Composition-based stats.
 Identities = 357/981 (36%), Positives = 562/981 (57%), Gaps = 114/981 (11%)

Query: 11  GRVRKFFGKNPEIIDI-PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF- 68
            R RKFFGK PE  +I  DL+++QK S+  FL          ++ +  + K   PI    
Sbjct: 10  RRERKFFGKVPEKTEIYEDLVKIQKDSFRDFL----------DKKIMESIKRYMPIKIPV 59

Query: 69  ------SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
                 +   +++FV  +F+   F  ++C  + LTYA    + +R+      E       
Sbjct: 60  KASGKKNKEFLIDFVDVKFEDSSFSENECRDKGLTYAGKAYLKVRITDSATGEM------ 113

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             I++  I++ ++P MT+ G F++ G +R++V+QL RSPG++F  ++     S K ++  
Sbjct: 114 --IEKDDIFLCNIPYMTERGIFIVNGAERVIVNQLVRSPGVYFIKEEE-TDTS-KEMFIA 169

Query: 183 RIIPDQGLWMDIEFDS---KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY 238
             +P +G W++I ++    K+++ VRIDR+RK     FL ALG +++ +IL  F  +I  
Sbjct: 170 HFLPIKGAWLEILYNPNPGKEVLQVRIDRKRKFNFFLFLRALGYENDLDILRLFPKEIDL 229

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                                              +E        +L  L  + +  +  
Sbjct: 230 DDE--------------------------------VELSNYNNCTVLSDLSFQELDDMDP 257

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                 G+ +                      + LE +   EI+ + + ++ +      +
Sbjct: 258 PRKSTYGMKLY---------------------EVLELLKKYEIKSVTVAHLVAEITLEKM 296

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           +     ++     +A  +I+  ++P ++     A+     ++F+ +K+D S +GR K+ +
Sbjct: 297 KKRYEKEERLTSLEAYKEIFSKLKPTEIPRAQKAKEEIEDMYFNPEKFDFSQIGRQKIQV 356

Query: 419 RLNL----------------DTPDDVRH------IRKEDIIAIIKILVDLRNGKGTIDDI 456
           +L                  D  D +++      + K DII   + L+ ++     +D  
Sbjct: 357 KLRKAYIDYLREVEKKDISEDMEDKIKYPIKTFAVDKLDIILSARYLLHVKENIEGLDTR 416

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCE 515
           D+LGN+RVRSVGE+++ ++     +M +   E+      I+ + PQ LIN++ +++A  +
Sbjct: 417 DHLGNKRVRSVGELMQIEFERAFSKMIQHAPEKLAGVQSINKISPQSLINSRSIMTAFHQ 476

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF SSQLSQ  + VN L+ +TH RRLSA+G GG+ R  A  E+RDVH +HYGR+CP ET 
Sbjct: 477 FFASSQLSQFLDQVNPLAELTHKRRLSAIGPGGLKREHAKFEVRDVHHSHYGRMCPIETP 536

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSL 634
           EG NIGL++S+   A+V+ YGF++TPY +V   KV  N++VYLSA EEE   IA A++ +
Sbjct: 537 EGANIGLITSMAILAKVDEYGFLKTPYYRVKHAKVDLNNIVYLSADEEELYRIAPASAEI 596

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            EDGS  EE +  R  G+  L  +++I++I  +PKQ+ S++A+LIPFLE+DD+NR LMG 
Sbjct: 597 GEDGSLVEEYIEARYLGKVSLFHKDEIEYISVTPKQIASVSAALIPFLEHDDANRALMGS 656

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD- 753
           NMQRQAVPLL+ +APFVGTG+E + A+ SG  I+AK  GIV+ VD  +IVI  ++ + + 
Sbjct: 657 NMQRQAVPLLRPQAPFVGTGVEWLAARDSGYLIMAKHKGIVDYVDGRKIVITRLDEENNV 716

Query: 754 ----PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                     D Y L+K+ RSNQ+ C+NQ P+V VGD V +   IADGPS D+G+LALGR
Sbjct: 717 LKDSNDEPLKDEYTLLKYVRSNQDMCINQVPIVNVGDVVTKGQAIADGPSMDMGELALGR 776

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+ + F+PW GYNFED++++S+ ++  D FTSIHIE FE  A DT+LGPEEIT DIPNV 
Sbjct: 777 NIFIGFLPWEGYNFEDAIVVSQELLENDAFTSIHIEVFETKAMDTQLGPEEITADIPNVK 836

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           +E L+N+DE GI+ +G+ V+ GDILVGK+TP+GES  TPEEKL++++FG+K  D++D+SL
Sbjct: 837 KELLRNLDEEGIVKIGSYVSSGDILVGKVTPRGESDTTPEEKLIKSVFGDKGRDIKDSSL 896

Query: 930 RVPSGVSGTVVDVRIFNRHGI 950
            VP G+ G V+DV+IF+R  I
Sbjct: 897 TVPHGIEGRVIDVQIFDRKDI 917



 Score =  427 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 170/554 (30%), Positives = 244/554 (44%), Gaps = 70/554 (12%)

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD----IPNVSEEGLKNIDECGIICVGA 886
            + +V       I I   +      K   +E  +D    +  V       I++  I+ VG 
Sbjct: 694  KGIVDYVDGRKIVITRLDEENNVLKDSNDEPLKDEYTLLKYVRSNQDMCINQVPIVNVGD 753

Query: 887  EVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVD----VRDTSLRVPSGVSGTVVD 941
             V  G  +  G     GE  +     +    +     +    V    L   +  S  +  
Sbjct: 754  VVTKGQAIADGPSMDMGELALGRNIFIGFLPWEGYNFEDAIVVSQELLENDAFTSIHIEV 813

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                        E   +      + L R+ D+E  I+    Y    +IL G+    G   
Sbjct: 814  FETKAMDTQLGPEEITADIPNVKKELLRNLDEE-GIVKIGSYVSSGDILVGKVTPRGESD 872

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                  L   +  +  R            ++ +  ++    E     ++  F  K     
Sbjct: 873  TTPEEKLIKSVFGDKGRD-----------IKDSSLTVPHGIEGRVIDVQ-IFDRK----- 915

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                +  GV + VKVF+A K+ +Q GDK+AGRHGNKG++S IL  EDMPFL DGTP+ ++
Sbjct: 916  DIPSLEIGVNKYVKVFIATKKTLQVGDKLAGRHGNKGVISTILNKEDMPFLPDGTPLQML 975

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            L+PLGVPSRMN+GQ+ E HLGW  +       + I D     +I    S + +       
Sbjct: 976  LSPLGVPSRMNIGQVLELHLGWLSMLTNDYYATPIFDGATESEIMDELSKVREEHELYLG 1035

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
             +                                               +G+ +L DG T
Sbjct: 1036 DDPD-------------------------------------------QPNGKIVLRDGRT 1052

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEPFD PV VG +YMLKL+H+  DK++ARSTG YSL+ QQPLGGK++ GGQR GEMEVW 
Sbjct: 1053 GEPFDFPVAVGSMYMLKLSHIAKDKIHARSTGPYSLIHQQPLGGKAHFGGQRFGEMEVWA 1112

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++A+GAA+ L EMLT KSDD+ GR  VY++I+ G +  E G PESF VL KE+Q L L I
Sbjct: 1113 LEAHGAAHTLNEMLTYKSDDIKGRNEVYKAILKGENLPEPGIPESFKVLTKELQGLMLDI 1172

Query: 1362 DLENSRTKNSAKME 1375
             L +          
Sbjct: 1173 KLYDEDGNELDVDR 1186


>gi|38195608|gb|AAR13471.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
          Length = 526

 Score =  614 bits (1583), Expect = e-173,   Method: Composition-based stats.
 Identities = 522/524 (99%), Positives = 522/524 (99%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKLLY
Sbjct: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
           ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ
Sbjct: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS
Sbjct: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN
Sbjct: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL
Sbjct: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           RMERSIKERISSVDIDSVMPQDLINAKPVVSAV EFFCSSQLSQ
Sbjct: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVYEFFCSSQLSQ 524


>gi|224533000|ref|ZP_03673607.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi
           WI91-23]
 gi|224512060|gb|EEF82454.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi
           WI91-23]
          Length = 763

 Score =  613 bits (1581), Expect = e-173,   Method: Composition-based stats.
 Identities = 319/814 (39%), Positives = 491/814 (60%), Gaps = 66/814 (8%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP--NEGLQAAFKSVFPITAFSGAAMLE 75
           G+  EI+D+P+LIE+Q  SY+ FL ++    ++P  NEGL++ F+++FPI + +G   LE
Sbjct: 10  GRADEILDLPNLIEIQLNSYEKFLQLDKLKSKKPLLNEGLESVFRNIFPIKSGNGDVALE 69

Query: 76  FVSYEFDPPK--FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           +  Y  +     F   +C  +  +Y   LK+ L L            +  +I+++ +YMG
Sbjct: 70  YERYYIENDALNFTEKECKRKGQSYEAVLKVRLNLQFL---------TTGEIRQKDVYMG 120

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            +PLMT+ GTF+I G +R+VVSQ+HRSPG+ F  +K         LY+ RIIP +G W++
Sbjct: 121 TIPLMTERGTFIINGAERVVVSQIHRSPGVVFYKEKD--------LYSARIIPYRGSWLE 172

Query: 194 IEFD-SKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D  KD ++V+IDR++++ +T FL ALG D+ E+I+ TFY         D     L  
Sbjct: 173 FEIDSKKDYLYVKIDRKKRILITLFLRALGFDTREKIIETFYNIKKIKVE-DGTKRDLPG 231

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L     +  ++           +G K+T   ++   + GV  + +         V  D
Sbjct: 232 QYLAKSINIRENM--------YYRAGDKITLQDVEDFLQNGVNEIEL---------VDFD 274

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +  +G+ ++ +                      + ++ +             K   ++
Sbjct: 275 GYDDISGKRFVSSN---------------------VILNCLEKEDAFFALKDGSKELPKE 313

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             +L +Y  + PG+  +   AE+    +FF   +YDL  VGR K++ +   D       +
Sbjct: 314 SVMLAVYSSLFPGEPISIDNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVL 372

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
             +DI+  I  L+ +  G   +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S
Sbjct: 373 TMDDIVNTISHLLRIYEGHDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMS 432

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + ++ ++ PQ+LI+ KP+VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R
Sbjct: 433 NKEVFNLKPQELISVKPIVSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSR 492

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVH THYGR+CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G VT
Sbjct: 493 DRAGFEVRDVHYTHYGRMCPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGVVT 552

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA++EE + IAQAN++ + +G + E+LV  R +G+        ID++D SP+Q+
Sbjct: 553 DQLEYLSAIDEEKKCIAQANAAFNSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQL 612

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           +S++++LIPFLE++D+NR LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR
Sbjct: 613 ISVSSALIPFLEHNDANRALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKR 672

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +G V    + +IV++  E     +   +D Y ++K++R+NQ+TC NQ  LVK G +V R 
Sbjct: 673 SGEVILATSSKIVVKPFE---ADNAKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERG 729

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +IIADGP+T  G+LALG N+L+  +PW+G+N+ED
Sbjct: 730 EIIADGPATRYGELALGNNLLLGVIPWNGFNYED 763


>gi|125950439|gb|ABN58744.1| RNA polymerase B subunit [Veillonella montpellierensis]
          Length = 1124

 Score =  613 bits (1580), Expect = e-173,   Method: Composition-based stats.
 Identities = 365/840 (43%), Positives = 497/840 (59%), Gaps = 93/840 (11%)

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG+++D +       G  LYA  +IP++G W+++E D+ 
Sbjct: 1   DTGTFIINGAERVIVSQLVRSPGVYYDKEID---TMGNRLYASTVIPNRGAWIELETDAN 57

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           +++ VRIDR RK+P T  + ALG D+ E IL  F+   V       +   L         
Sbjct: 58  EVVSVRIDRNRKIPATILVRALGWDTNESILELFWNGQVDEDGNPIYDERLLRTLEKDTT 117

Query: 259 KVSSS-----LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLC 304
           + S          +  GE   +ES + L   L    +      +G             + 
Sbjct: 118 ESSEEALVEIYKKLRPGEPPTVESARNLFDNLFFDPRRYDFARVGRYKVNKKLGWKQRMF 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +A+ I N ETGE+ ++AG  I E+ +E +  S +          ++ +         
Sbjct: 178 GQLLAQPIFNPETGEVILDAGTHIGEEEIEIVEKSGVFAGEGFAEFYIDIDGVHA----- 232

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                                         +         ++   T   +  N+   L+ 
Sbjct: 233 -----------------------------KVICNNCNLPYEFRTVTREDMIANISYLLNL 263

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
            D V H                       DDID+LGNRR+R VGE+L+NQ+R+GL RMER
Sbjct: 264 MDGVGH----------------------TDDIDHLGNRRLRCVGELLQNQFRIGLTRMER 301

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER++  + D + PQ LIN +PVV+AV EFF SSQLSQ  +  N L  +TH RRLSAL
Sbjct: 302 VVRERMTVQESDMITPQALINIRPVVAAVKEFFGSSQLSQFMDQTNPLGELTHKRRLSAL 361

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A+VN +GFIE PYRK
Sbjct: 362 GPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSNYAKVNEFGFIEAPYRK 421

Query: 605 VCDGK-------------VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V                 VT+ V Y++A EEE   IAQANS LDE+G F  + + CR   
Sbjct: 422 VEKIYGTGDEADKIVKVRVTDTVAYMTADEEEGMVIAQANSVLDEEGCFVSDHIACRSGH 481

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + + V  +K+D++D SPK+VVSI  ++IPFLENDD+NR LMG NMQRQAVPLL+A+AP V
Sbjct: 482 DVLEVTPDKVDYMDVSPKEVVSIGTAMIPFLENDDANRALMGANMQRQAVPLLRAQAPLV 541

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  SG  I+AK AG V +    +I +   +         VD+Y++ KF RSN
Sbjct: 542 GTGMEYTAATDSGVCILAKAAGTVVRCWGDQIHVMRDDNGR------VDVYKMNKFLRSN 595

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q+TC NQ+P+V  GD V    ++ADGP+TD G+LALG N+LVAFMPW GYN+ED++L+SE
Sbjct: 596 QSTCFNQKPIVHRGDHVVAGQVLADGPATDGGELALGFNILVAFMPWEGYNYEDAILLSE 655

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +  ED++TSIHIEE+E  ARDTKLG EEITR++PN  ++ LKN+D  GIIC+GAEV PG
Sbjct: 656 DLCKEDIYTSIHIEEYECDARDTKLGAEEITRELPNTGDDSLKNLDADGIICIGAEVKPG 715

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK TPKGE+ +TPEE+LLRAIFG+K  +VRDTSLRVP G SG +VDV++F R   D
Sbjct: 716 DILVGKATPKGETELTPEERLLRAIFGDKEREVRDTSLRVPHGESGKIVDVKVFTRENGD 775



 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 177/874 (20%), Positives = 308/874 (35%), Gaps = 73/874 (8%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            I + A      +S+ E+F +   D      + + +   +R TL  D  +  ++AL++IY+
Sbjct: 74   ILVRALGWDTNESILELFWNGQVDE---DGNPIYDERLLR-TLEKDTTESSEEALVEIYK 129

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +RPG+  T   A ++F+ LFFD  +YD + VGR K+N +L        + + +      
Sbjct: 130  KLRPGEPPTVESARNLFDNLFFDPRRYDFARVGRYKVNKKLGWKQRMFGQLLAQPIFNPE 189

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
               ++         ++I+ +    V +     +    +  +  +          +  +V 
Sbjct: 190  TGEVILDAGTHIGEEEIEIVEKSGVFAGEGFAEFYIDIDGVHAKVICNNCNLPYEFRTVT 249

Query: 500  PQDLI-NAKPVVSAVCEFFCSSQLSQLEEHVNSL--SRITHTRRLSALGQGGVARARAGV 556
             +D+I N   +++ +     +  +  L           + +  R+       V R R  V
Sbjct: 250  REDMIANISYLLNLMDGVGHTDDIDHLGNRRLRCVGELLQNQFRIGLTRMERVVRERMTV 309

Query: 557  EMRD-VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            +  D + P     I P   +     G         + N  G +    R            
Sbjct: 310  QESDMITPQALINIRPVVAAVKEFFGSSQLSQFMDQTNPLGELTHKRR------------ 357

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
             LSA                            R      +       +    P +     
Sbjct: 358  -LSA---------------------LGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEG- 394

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS---SGAAIVAKRA 732
                P +   +S       N         +      GTG E+        +         
Sbjct: 395  ----PNIGLINSLSNYAKVNEFGFIEAPYRKVEKIYGTGDEADKIVKVRVTDTVAYMTAD 450

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP--LVKVG--DEV 788
                 V A    +   EG              +     ++   ++  P  +V +G     
Sbjct: 451  EEEGMVIAQANSVLDEEGCFVSDHIACRSGHDVLEVTPDKVDYMDVSPKEVVSIGTAMIP 510

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEE 846
               +  A+              +L A  P  G   E   +      ++++   T +    
Sbjct: 511  FLENDDANRALMGANMQRQAVPLLRAQAPLVGTGMEYTAATDSGVCILAKAAGTVVRCWG 570

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
             ++       G  ++ +    +        ++  I+  G  V  G +L       G   +
Sbjct: 571  DQIHVMRDDNGRVDVYKMNKFLRSNQSTCFNQKPIVHRGDHVVAGQVLADGPATDG-GEL 629

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI- 964
                 +L A    +  +  D  L           D+    +    + + R   +  E+I 
Sbjct: 630  ALGFNILVAFMPWEGYNYEDAILL---SEDLCKEDIYTSIHIEEYECDARDTKLGAEEIT 686

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
              L    DD    LD +       I  G     G     K+T      +   P  +  + 
Sbjct: 687  RELPNTGDDSLKNLDAD-----GIICIGAEVKPGDILVGKATPKGETEL--TPEERLLRA 739

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D++ +    SL+V +  S  I++     K+   + GD++ PGV ++V+V++A KR I
Sbjct: 740  IFGDKEREVRDTSLRVPHGESGKIVD----VKVFTRENGDELQPGVNKLVRVYIAQKRKI 795

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSR++  EDMPFL DGTPV IVLNPLGVPSRMN+GQ+ ETHLG+A
Sbjct: 796  HEGDKMAGRHGNKGVVSRVMRREDMPFLPDGTPVQIVLNPLGVPSRMNIGQVLETHLGFA 855

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
              GLG KIK      K   + +   +     I  
Sbjct: 856  VQGLGMKIKDTDMQIKQVLERAKTDASYWDNIEE 889



 Score =  222 bits (565), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 63/110 (57%), Positives = 81/110 (73%)

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D     + +   +G+ ++TPVFDGA E  +   L++A   E G+++LYDG TGEP D  V
Sbjct: 1015 DYEQYGMPKPDVAGIHIATPVFDGASEVDVFEALQLAGKSEDGKTVLYDGRTGEPMDNRV 1074

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            TVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEV
Sbjct: 1075 TVGYVYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1124


>gi|23013725|ref|ZP_00053589.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Magnetospirillum magnetotacticum MS-1]
          Length = 357

 Score =  609 bits (1571), Expect = e-172,   Method: Composition-based stats.
 Identities = 210/356 (58%), Positives = 268/356 (75%), Gaps = 1/356 (0%)

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + E   S W   A+ D+ V  + E+LK  ++     L++RF+NK+EK+Q GD++PPGV++
Sbjct: 1    MDELHPSTWRNIAIDDDAVMADSEALKRAFDQQVDKLQERFENKVEKLQRGDELPPGVMK 60

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKVFVA+KR +Q GDKMAGRHGNKG++SRI+P EDMP+L+DG  VDIVLNPLGVPSRMN
Sbjct: 61   MVKVFVAVKRKLQPGDKMAGRHGNKGVISRIVPLEDMPYLEDGQQVDIVLNPLGVPSRMN 120

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYK-ANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            VGQI ETHLGWAC GLG++I  +++ YK     +  L+S L+ V G   + ++I+   D 
Sbjct: 121  VGQILETHLGWACAGLGQQIGGMLDKYKRNAATMIDLKSKLKDVYGDAIYEDEIAGLADH 180

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +  +A     GVP++TPVFDGA E  I  ML  A+   SGQ  L DG TGEPFDR VTV
Sbjct: 181  EITELAHNLTPGVPIATPVFDGARESDIVEMLTKANRSSSGQVTLVDGRTGEPFDRKVTV 240

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 241  GYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 300

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            QEMLT+KSDDV GRT+VYE+IV G+DTFE G PESFNVLVKE+++LGL+++L    
Sbjct: 301  QEMLTVKSDDVSGRTKVYEAIVRGDDTFEAGIPESFNVLVKELRSLGLNVELTQRN 356


>gi|148655415|ref|YP_001275620.1| DNA-directed RNA polymerase subunit beta [Roseiflexus sp. RS-1]
 gi|182676571|sp|A5USR7|RPOB_ROSS1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|148567525|gb|ABQ89670.1| DNA-directed RNA polymerase, beta subunit [Roseiflexus sp. RS-1]
          Length = 1229

 Score =  609 bits (1571), Expect = e-171,   Method: Composition-based stats.
 Identities = 327/979 (33%), Positives = 477/979 (48%), Gaps = 98/979 (10%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F +    I++P LIE Q  S++ F            EGL+  F+ + PIT F+G
Sbjct: 28  KIERYSFARISNAIELPKLIETQLNSFEWF----------RKEGLRELFEEISPITDFTG 77

Query: 71  -AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               L F+ Y F  P+++  +C  R +TY+ P+++ ++L +          S  ++KE  
Sbjct: 78  KNMELRFLDYHFGEPRYNEHECRERGITYSAPIRVNVQLRIL---------STGELKESE 128

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I++GD PLMT++GTFVI G +R+VVSQL RSPG++F  +K     SG+ L++ ++IP +G
Sbjct: 129 IFLGDFPLMTENGTFVINGAERVVVSQLIRSPGVYFKEEKDPT--SGRSLHSAKLIPSRG 186

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA-LGM--------------------DSEEI 228
            W++ E + +D+I V++DR+RK+PVT  L A LG                       EEI
Sbjct: 187 AWLEFETNKRDVISVKVDRKRKIPVTILLRAVLGWRANPDGSGQWAPDNELDQRGRDEEI 246

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKS 287
           L  F        +          A     A +      +  G+   +++ + L   LL +
Sbjct: 247 LELFAHLETGDHQYIKATLDKDPARHAKEA-LLELYKRLRPGDPPTLDNARNLIEALLFN 305

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +   +  +G          + +++   +T             +   +    ++R +   
Sbjct: 306 PRRYDLSRVGRYK-------LNKNLWEKDT-----------RPEVRRQAPDVKVRVLLPD 347

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
            +  +       N        D  D L    RV   G++        +        ++  
Sbjct: 348 DIFKIVERMIQLNNGTPGLRADDIDHL-GNRRVRTVGELIQQQFRVGLLRMERVIKERMS 406

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L        N  +N+        +           L    +    + ++ +         
Sbjct: 407 LQDPETATPNALVNIRP-----VVAAMREFFGGAQLSQFMDQTNPLAELTHKRRLSALGP 461

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           G + ++         E           I  V   +  N   + +       +        
Sbjct: 462 GGLSRD-----RAGFEVRDVHHSHYGRICPVETPEGPNIGLIGTMSTYARVNEMGFLETP 516

Query: 528 HVNSLSRITH----TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           +      + +     R+   L      R    + +R            A       I   
Sbjct: 517 YRKVYREVPNASEWERQGLLLRDVRDLRTGELIAVRGTRVDAAVARRIAVALLRGQILRE 576

Query: 584 SSLT-----SFARVNAYGFIETPYRKVC--------DGKVTNDVVYLSAMEEENRYIAQA 630
             +        A            R V            V+ +V YLSA EE+   I QA
Sbjct: 577 DVVDPTTGEVIAHAGQEVNRALAERIVETPLKIIKIRPVVSQEVDYLSADEEDRFVIVQA 636

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           N+ LDE   F E  V  R AG+   VP E++D++D SPKQVVS++ +LIPFLE+DD+NR 
Sbjct: 637 NAPLDEHNRFLEGTVSVRYAGDFDDVPIERVDYMDVSPKQVVSVSTALIPFLEHDDANRA 696

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ +AP VGTGME V A+ SG  +VAK  G+V    A  IVI   +G
Sbjct: 697 LMGSNMQRQAVPLLRPDAPIVGTGMEYVAARDSGQVVVAKADGVVLSATADEIVILEDDG 756

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          YRL KF RSNQ+TC+NQRP+V  G  VR+ DIIAD  STD G+LALG+N
Sbjct: 757 NERS-------YRLRKFMRSNQDTCINQRPIVSRGQRVRKGDIIADSSSTDNGELALGQN 809

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVAFMPW G NFED++L+SER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV +
Sbjct: 810 VLVAFMPWEGGNFEDAILVSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQ 869

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           + L+N+D+ GII +GAEV P DILVGKITPKGE+ +T EE+LLRAIFGEKA +V+D+SLR
Sbjct: 870 DSLRNLDDRGIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLR 929

Query: 931 VPSGVSGTVVDVRIFNRHG 949
           VP+GV G V+DV++F R  
Sbjct: 930 VPNGVRGKVIDVKVFTRDD 948



 Score =  593 bits (1529), Expect = e-167,   Method: Composition-based stats.
 Identities = 326/1055 (30%), Positives = 465/1055 (44%), Gaps = 103/1055 (9%)

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            +   + +       ++ YI+ TL  D  +  K+ALL++Y+ +RPGD  T   A ++   L
Sbjct: 243  DEEILELFAHLETGDHQYIKATLDKDPARHAKEALLELYKRLRPGDPPTLDNARNLIEAL 302

Query: 400  FFDSDKYDLSTVGRVKMNMRL----------NLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             F+  +YDLS VGR K+N  L                 VR +  +DI  I++ ++ L NG
Sbjct: 303  LFNPRRYDLSRVGRYKLNKNLWEKDTRPEVRRQAPDVKVRVLLPDDIFKIVERMIQLNNG 362

Query: 450  KGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
               +  DDID+LGNRRVR+VGE+++ Q+R+GLLRMER IKER+S  D ++  P  L+N +
Sbjct: 363  TPGLRADDIDHLGNRRVRTVGELIQQQFRVGLLRMERVIKERMSLQDPETATPNALVNIR 422

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            PVV+A+ EFF  +QLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +HYG
Sbjct: 423  PVVAAMREFFGGAQLSQFMDQTNPLAELTHKRRLSALGPGGLSRDRAGFEVRDVHHSHYG 482

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            RICP ET EG NIGL+ +++++ARVN  GF+ETPYRKV            +A E E + +
Sbjct: 483  RICPVETPEGPNIGLIGTMSTYARVNEMGFLETPYRKVYREVP-------NASEWERQGL 535

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +      G         R            +       + VV      +      + 
Sbjct: 536  LLRDVRDLRTGELIAVRGT-RVDAAVARRIAVALLRGQILREDVVDPTTGEVIAHAGQEV 594

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            NR L    ++     +             S   +     + A              V   
Sbjct: 595  NRALAERIVETPLKIIKIRPVVSQEVDYLSADEEDRFVIVQANAPLDEHNRFLEGTVSVR 654

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
              GD D        Y          +    Q   V            A+           
Sbjct: 655  YAGDFDDVPIERVDY---------MDVSPKQVVSVSTALIPFLEHDDANRALMGSNMQRQ 705

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTKLGPEEITR 863
               +L    P  G   E         V    ++ V  S   +E  ++  D   G E   R
Sbjct: 706  AVPLLRPDAPIVGTGMEYVAARDSGQVVVAKADGVVLSATADEIVILEDD---GNERSYR 762

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                +       I++  I+  G  V  GDI+    +      +   + +L A    +  +
Sbjct: 763  LRKFMRSNQDTCINQRPIVSRGQRVRKGDIIADSSSTDN-GELALGQNVLVAFMPWEGGN 821

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D  L     VS  +V   IF    I+K E      +   E + RD  +      RN+ 
Sbjct: 822  FEDAIL-----VSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQDSLRNLD 876

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             R   I  G           K T      ++   R     F  +  +V+ +   +     
Sbjct: 877  DR-GIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVR 935

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                 +      K+       ++P GV + V V +  KR I +GDKMAGRHGNK      
Sbjct: 936  GKVIDV------KVFTRDDDVELPVGVNQRVDVLLCQKRKISAGDKMAGRHGNK------ 983

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
                                  GV SR+                    I+ +        
Sbjct: 984  ----------------------GVVSRI------------------LPIEDMPFLPDGTP 1003

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                    ++ ++       +++              + G  V+TPVFDGA E  I   L
Sbjct: 1004 --------VDIILNPIGVPSRMNIGQILETHLGWAAARLGYRVATPVFDGATETEIKEWL 1055

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            + ADL   G+  LYDG TGE FDRPVTVGYIYM+KL H+V DK++ARSTG YSLVTQQPL
Sbjct: 1056 KRADLPPDGKITLYDGRTGEAFDRPVTVGYIYMMKLAHLVEDKIHARSTGPYSLVTQQPL 1115

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+IV G    E G 
Sbjct: 1116 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKTYEAIVKGEPIQEAGV 1175

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            PESF VL+KE+Q+LGLS+++ ++        ++  
Sbjct: 1176 PESFKVLIKELQSLGLSVEVLSADETPVELTDDAD 1210


>gi|298205320|gb|ADI61871.1| RNA polymerase beta subunit [Mesorhizobium sp. JS9]
          Length = 497

 Score =  608 bits (1567), Expect = e-171,   Method: Composition-based stats.
 Identities = 325/498 (65%), Positives = 397/498 (79%), Gaps = 1/498 (0%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVD 89
           IEVQKASYD FLM++     RP+EGLQA FKSVFPI+ FSGA+MLEFV YEF+ PKFDVD
Sbjct: 1   IEVQKASYDQFLMVDEPQGGRPDEGLQAVFKSVFPISDFSGASMLEFVKYEFEAPKFDVD 60

Query: 90  DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGI 149
           +C  RDLTYA PLK+TLRLIVFD+DE TG+KSIKDIKEQ +YMGD+PLMT +GTF+I G 
Sbjct: 61  ECRQRDLTYAAPLKVTLRLIVFDIDEDTGSKSIKDIKEQDVYMGDMPLMTLNGTFIINGT 120

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R++VSQ+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRR
Sbjct: 121 ERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRR 180

Query: 210 RKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           RK+P TS LMALGMD EEILSTFY KI Y Q GD W  P +      G K    LVD DT
Sbjct: 181 RKIPATSLLMALGMDGEEILSTFYNKIEYKQSGDHWRIPFTVE-RFRGLKAVDDLVDADT 239

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE V+E+GKK+T+   K L +KGVK +  T D L G Y+AED+V+  TGEI++EAGD ID
Sbjct: 240 GEIVVEAGKKITARQAKQLADKGVKAIKATQDDLYGSYLAEDVVDYSTGEIFLEAGDEID 299

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           EK+L+ +  +   +  +L +D +N   YIRNTL  DKN+ R+DAL DIYRVMRPG+  T 
Sbjct: 300 EKTLKVLLSTGAEEFTVLDIDHINVGGYIRNTLAIDKNESRQDALFDIYRVMRPGEPPTL 359

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             AE+MFN LFFD+D+YDLS VGRVKMNMRL+L   D VR +RKEDI+A++K LV+LR+G
Sbjct: 360 ETAEAMFNSLFFDADRYDLSAVGRVKMNMRLDLKAEDTVRVLRKEDILAVVKTLVELRDG 419

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
           KG IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP 
Sbjct: 420 KGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKPA 479

Query: 510 VSAVCEFFCSSQLSQLEE 527
            +AV EFF SSQLSQ  +
Sbjct: 480 AAAVREFFGSSQLSQFMD 497


>gi|156741580|ref|YP_001431709.1| DNA-directed RNA polymerase subunit beta [Roseiflexus castenholzii
           DSM 13941]
 gi|156232908|gb|ABU57691.1| DNA-directed RNA polymerase, beta subunit [Roseiflexus castenholzii
           DSM 13941]
          Length = 1245

 Score =  607 bits (1566), Expect = e-171,   Method: Composition-based stats.
 Identities = 329/989 (33%), Positives = 490/989 (49%), Gaps = 118/989 (11%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F +  + I++P LIE Q  S++ F            EGL+  F  + PIT F+G
Sbjct: 44  KIERYSFARISDAIELPKLIETQLKSFEWF----------RKEGLRELFDEISPITDFTG 93

Query: 71  -AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               L F+ Y F  P+++  +C  R +TY+ P+++ ++L +          S  ++KE  
Sbjct: 94  KNMELRFLDYHFGEPRYNEHECRERGITYSAPIRVNVQLRIL---------STGELKESE 144

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I++GD PLMT++GTFVI G +R+VVSQL RSPG++F  +K     SG+ L++ ++IP +G
Sbjct: 145 IFLGDFPLMTENGTFVINGAERVVVSQLIRSPGVYFKEEKDPT--SGRSLHSAKLIPSRG 202

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA-LGMD--------------------SEEI 228
            W++ E + +D+I V++DR+RK+PVT  L A LG                       E++
Sbjct: 203 AWLEFETNKRDVISVKVDRKRKIPVTILLRAVLGWKANPDGSGQWAPDTELDTRGRDEDV 262

Query: 229 LSTF-------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKK 279
           L  F       +  I  +   D       A   +           +D    +IE+     
Sbjct: 263 LELFTHVETGEHQYIRVTLDKDPARHAKEALLELYKRLRPGDPPTLDNARNLIEALLFNP 322

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAED----IVNGETGEIYIEAGDVIDEK---- 331
               L +  + K  K L      L     A D    ++  +     +E    ++ +    
Sbjct: 323 RRYDLSRVGRYKLNKNLWEKDTRLEVRSQAPDLKVRVLLPDDIFKIVERIIQLNNETPGL 382

Query: 332 ---SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT------DKNKDRKDALLDIYRVMR 382
               ++ + +  +R +  L              ++       D      +AL++I     
Sbjct: 383 RADDIDHLGNRRVRTVGELIQQQFRVGLLRMERVIKERMSLQDPETATPNALINI----- 437

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
                  +     F            + +  +    RL+   P     + ++     ++ 
Sbjct: 438 ---RPVVAAMREFFGGAQLSQFMDQTNPLAELTHKRRLSALGPGG---LSRDRAGFEVRD 491

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           +     G+    +                        + +  ++       ++  +    
Sbjct: 492 VHHSHYGRICPVETPEGP------------------NIGLIGTMSTYAQVNEMGFLETPY 533

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               + V +A         L   +        +   R            A + +  + + 
Sbjct: 534 RKVYREVPNASEWE--RQGLLLRDVRDLRTGELIAVRGTRVDAAVARRIAVSLLRGQILR 591

Query: 563 PTHYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVC-DGKVTNDVVYLSAM 620
                 I   +T E   + G   +     R+     +ETP R +     V+ +V YLSA 
Sbjct: 592 ED----IVDPKTGEVIASTGQEINRAIAERI-----VETPLRTIKIRPIVSQEVDYLSAD 642

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EE+   I QAN+ LDE   F E  V  R AG+   VP E++D++D SPKQVVS++ +LIP
Sbjct: 643 EEDRFVIVQANAPLDEHNRFLEGTVSVRYAGDFDDVPIERVDYMDVSPKQVVSVSTALIP 702

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE+DD+NR LMG NMQRQAVPLL+ +AP VGTGME V A+ SG  +VAK  G+V     
Sbjct: 703 FLEHDDANRALMGSNMQRQAVPLLRPDAPIVGTGMEYVAARDSGQVVVAKADGVVLSATG 762

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             I+I   +G+          YRL KF RSNQ+TC+NQRP V  G  VR+ DIIAD  ST
Sbjct: 763 DEIIILEDDGNERS-------YRLRKFMRSNQDTCINQRPSVSRGQRVRKGDIIADSSST 815

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           D G+LALG+N+LVAFMPW G NFED++L+SER+V ED+FTSIHIE++EV ARDTKLGPEE
Sbjct: 816 DNGELALGQNVLVAFMPWEGGNFEDAILVSERLVREDIFTSIHIEKYEVEARDTKLGPEE 875

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITRDIPNV +E L+N+D+ GII +GAEV P DILVGKITPKGE+ +T EE+LLRAIFGEK
Sbjct: 876 ITRDIPNVGQESLRNLDDRGIIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEK 935

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           A +V+D+SLRVP+GV G V+DV++F R+ 
Sbjct: 936 AREVKDSSLRVPNGVRGKVIDVKVFTRND 964



 Score =  590 bits (1521), Expect = e-166,   Method: Composition-based stats.
 Identities = 330/1051 (31%), Positives = 479/1051 (45%), Gaps = 123/1051 (11%)

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
             + YIR TL  D  +  K+ALL++Y+ +RPGD  T   A ++   L F+  +YDLS VGR
Sbjct: 273  EHQYIRVTLDKDPARHAKEALLELYKRLRPGDPPTLDNARNLIEALLFNPRRYDLSRVGR 332

Query: 414  VKMNMRL----------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGN 461
             K+N  L          +      VR +  +DI  I++ ++ L N    +  DDID+LGN
Sbjct: 333  YKLNKNLWEKDTRLEVRSQAPDLKVRVLLPDDIFKIVERIIQLNNETPGLRADDIDHLGN 392

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVR+VGE+++ Q+R+GLLRMER IKER+S  D ++  P  LIN +PVV+A+ EFF  +Q
Sbjct: 393  RRVRTVGELIQQQFRVGLLRMERVIKERMSLQDPETATPNALINIRPVVAAMREFFGGAQ 452

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIG
Sbjct: 453  LSQFMDQTNPLAELTHKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRICPVETPEGPNIG 512

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ +++++A+VN  GF+ETPYRKV            +A E E                  
Sbjct: 513  LIGTMSTYAQVNEMGFLETPYRKVYREVP-------NASEWER-------------QGLL 552

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
               V     GE I V   ++D    + +  VS+    I   +  D     +  +  ++  
Sbjct: 553  LRDVRDLRTGELIAVRGTRVDAA-VARRIAVSLLRGQILREDIVDPKTGEVIASTGQEIN 611

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
              +      V T + ++  +     IV++    +   +  R VI      LD     ++ 
Sbjct: 612  RAIA--ERIVETPLRTIKIR----PIVSQEVDYLSADEEDRFVIVQANAPLDEHNRFLEG 665

Query: 762  YRLMKFQRSNQNTCV----------NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
               +++     +  +           Q   V            A+              +
Sbjct: 666  TVSVRYAGDFDDVPIERVDYMDVSPKQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPL 725

Query: 812  LVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            L    P  G   E         V    ++ V  S   +E  ++  D   G E   R    
Sbjct: 726  LRPDAPIVGTGMEYVAARDSGQVVVAKADGVVLSATGDEIIILEDD---GNERSYRLRKF 782

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            +       I++   +  G  V  GDI+    +      +   + +L A    +  +  D 
Sbjct: 783  MRSNQDTCINQRPSVSRGQRVRKGDIIADSSSTDN-GELALGQNVLVAFMPWEGGNFEDA 841

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             L     VS  +V   IF    I+K E      +   E + RD  +      RN+  R  
Sbjct: 842  IL-----VSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQESLRNLDDR-G 895

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K T      ++   R     F  +  +V+ +   +         
Sbjct: 896  IIYIGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVRGKVI 955

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
             +      K+       ++P GV + V V +  KR I +GDKMAGRHGNK          
Sbjct: 956  DV------KVFTRNDDVELPVGVNQRVDVLLCQKRKISAGDKMAGRHGNK---------- 999

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
                              GV SR+                    I+ +            
Sbjct: 1000 ------------------GVVSRI------------------LPIEDMPFLPDGTP---- 1019

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                ++ ++       +++              + G  V+TPVFDGA E  I   L+ AD
Sbjct: 1020 ----VDIILNPIGVPSRMNIGQILETHLGWAAARLGYRVATPVFDGASETEIKEWLKRAD 1075

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            L   G+  LYDG TGEPFD PVTVGYIYM+KL H+V DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1076 LPPDGKITLYDGRTGEPFDHPVTVGYIYMMKLAHLVEDKIHARSTGPYSLVTQQPLGGKA 1135

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+IV G    E G PESF
Sbjct: 1136 QFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKTYEAIVKGEPIQEAGVPESF 1195

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             VL+KE+Q+LGLS+++ ++        +++ 
Sbjct: 1196 KVLIKELQSLGLSVEVLSADETPVELTDDVD 1226


>gi|23009165|ref|ZP_00050316.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Magnetospirillum magnetotacticum MS-1]
          Length = 348

 Score =  605 bits (1560), Expect = e-170,   Method: Composition-based stats.
 Identities = 211/347 (60%), Positives = 264/347 (76%), Gaps = 4/347 (1%)

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +E+++ QY+ SK  LE RF +K+EK+Q GD++PPGV+++VKVFVA+KR IQ GDKMA
Sbjct: 1    MTEIEAMQKQYDESKKRLEQRFLDKVEKLQRGDELPPGVMKMVKVFVAVKRKIQPGDKMA 60

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLG+K
Sbjct: 61   GRHGNKGVVSRIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGRK 120

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +   ++ Y    DI PL+  ++ +         +    D+ +       + GVP++TPVF
Sbjct: 121  VSKAVDAYLKTQDIGPLKEEMKAIYSPAE----LEGLSDEDLAEAGNNVRRGVPMATPVF 176

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            +GA E  I +ML MA LD S QS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++ARS
Sbjct: 177  NGAKEADIETMLEMAGLDRSAQSTLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIHARS 236

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT+VYE+
Sbjct: 237  IGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEA 296

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G+DTFE G PESFNVLVKEM++LGL+++L NS+ + +    E P
Sbjct: 297  IVRGDDTFEAGIPESFNVLVKEMRSLGLNVELTNSKQQAANDQLEPP 343


>gi|304372858|ref|YP_003856067.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyorhinis
           HUB-1]
 gi|304309049|gb|ADM21529.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyorhinis
           HUB-1]
          Length = 1236

 Score =  605 bits (1559), Expect = e-170,   Method: Composition-based stats.
 Identities = 337/994 (33%), Positives = 536/994 (53%), Gaps = 70/994 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +   G   +R+ + K    +  PD ++ QK S+  FL           EG++  F 
Sbjct: 1   MEFKLSKYGPTTLRRDYSKTKFSLPTPDFLDSQKQSFKWFL----------KEGIEETFN 50

Query: 61  SVFPITAFSGAAMLEF--VSYEFDPPK--FD-VDDCLWRDLTYAVPLKITLRLIVFDVDE 115
            ++PI + +G   + F   S   + P   +  + +   +  ++   +  TL         
Sbjct: 51  KIYPIISTNGKIEIRFKKGSVRVEDPDQDYTNIKELKRKGKSFVCKVFATL--------- 101

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                   ++++Q I  G++P MT+ GTF+I G ++++VSQL RSPG+ F  +  R   +
Sbjct: 102 EKLQVESGELEKQEILFGEIPYMTEGGTFIINGFEKVIVSQLIRSPGVCF-RENVRNRQA 160

Query: 176 GKLLYACRIIPDQGLWMDIEF----DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS- 230
             L     IIP  G W++I      ++ D + +RID+ + +P+ +FL A+G   ++I+  
Sbjct: 161 DDLFNKVEIIPQLGSWLEIFHRVTRNATDTVKLRIDKHKNIPLITFLKAIGFVDKDIIKK 220

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG-KKLTSGLLKSLK 289
            F       +      F            + S    I   +++   G K     LL + +
Sbjct: 221 YFGDSSELRESLKKDKFLRKDKVQEQLDSLESIYRTIRKDDRITTEGLKNFIPALLFNER 280

Query: 290 EKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
              +   G           D +   Y+AEDI + + G++    G  I  K   +I     
Sbjct: 281 RYNLSKTGRYMLNRKLNLLDRIIQTYLAEDIFDSK-GKLLYPLGTFITPKIANDIQSKFE 339

Query: 342 RDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             I P+  ++ ++ N Y R   +T                     ++T +   ++  +  
Sbjct: 340 NSILPLSEIEGIDENVYGRQLEITKNEN-----------------LNTRTKIITLRVWPN 382

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
             + + D +   + K  + +  D      H+   DI+AI+    +L    G  DD D+L 
Sbjct: 383 KRAMEQDANKEQQEKSVLVIGNDPTSTEMHLLISDIVAIVSYYFNLLANLGKNDDPDSLV 442

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCS 519
           N+RV +VGE+L+NQ+ + L ++E++ KERISS  D + +  +++ N KP+ +    FF S
Sbjct: 443 NKRVVNVGELLQNQFLIALSKLEKNTKERISSRGDSEKINIKNITNNKPIYNQFKNFFNS 502

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 503 SKLSQFMDQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQN 562

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDE 636
           IGL+ +   +A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE
Sbjct: 563 IGLILNFAVYAKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDE 622

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +    E  +  R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NM
Sbjct: 623 NNKIIEPEIIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNM 682

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+  EAP+V TG+E+ +AK S   I A   G V  VD+  I I++ +G      
Sbjct: 683 QRQAVPLITTEAPYVATGIEADIAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG------ 736

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +  Y L  F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF 
Sbjct: 737 -NIKTYHLRYFERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFS 795

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W+GYN+ED+++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++
Sbjct: 796 TWYGYNYEDAIIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHL 855

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ +G+EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  
Sbjct: 856 DENGIVRIGSEVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDG 915

Query: 937 GTVVDVRIFNRHGID-KNERSISVEREQIELLAR 969
           GTV+DV+I +R   D   +    + +  I    +
Sbjct: 916 GTVIDVQILSRTREDNLEDGVEKIIKVFIAQKRK 949



 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 235/1171 (20%), Positives = 421/1171 (35%), Gaps = 94/1171 (8%)

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
            ++ +EIL   + +I Y   G  +        ++     S  +   +              
Sbjct: 111  LEKQEIL---FGEIPYMTEGGTFIINGFEKVIVSQLIRSPGVCFRENVRNRQADDLFNKV 167

Query: 283  GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
             ++  L      F  +T +    + +  D         +++A   +D+  +++ F     
Sbjct: 168  EIIPQLGSWLEIFHRVTRNATDTVKLRIDKHKNIPLITFLKAIGFVDKDIIKKYFGDSSE 227

Query: 343  DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
                L  D           L  DK +++ D+L  IYR +R  D  T    ++    L F+
Sbjct: 228  LRESLKKD---------KFLRKDKVQEQLDSLESIYRTIRKDDRITTEGLKNFIPALLFN 278

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL--RNGKGTIDDIDNLG 460
              +Y+LS  GR  +N +LNL       ++ ++   +  K+L  L         +DI +  
Sbjct: 279  ERRYNLSKTGRYMLNRKLNLLDRIIQTYLAEDIFDSKGKLLYPLGTFITPKIANDIQSKF 338

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
               +  + E+      +   ++E   K    +     +  +   N + +     +     
Sbjct: 339  ENSILPLSEIEGIDENVYGRQLE-ITKNENLNTRTKIITLRVWPNKRAMEQDANKEQQEK 397

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +  +     S         + A+            +  D       R+        +  
Sbjct: 398  SVLVIGNDPTSTEMHLLISDIVAIVSYYFNLLANLGKNDDPDSLVNKRVVNVGELLQNQF 457

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR-YIAQANSSLDEDGS 639
             +  S                 +        N  +Y       N   ++Q    ++  G 
Sbjct: 458  LIALSKLEKNTKERISSRGDSEKINIKNITNNKPIYNQFKNFFNSSKLSQFMDQINPLGE 517

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
               +          +     + +  D        I     P  +N     +      +  
Sbjct: 518  MANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQNI-GLILNFAVYAKTN 576

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                ++     V  G+   V       +    A       A   ++      +      V
Sbjct: 577  PYGFIQTPYFPVENGV---VNYDPQNIVWLTAAEEFGYTFAQSSLLVDENNKIIEPEIIV 633

Query: 760  DIYRLMKFQRSNQNTCV----NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                     +  Q   +     Q   +         +  A+              ++   
Sbjct: 634  RKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNMQRQAVPLITTE 693

Query: 816  MPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             P+     E  +    S  + + +    + ++   +  ++ +   +         S +  
Sbjct: 694  APYVATGIEADIAKFSSTNIRASEDGEVVFVDSKSIQIKNEQGNIKTYHLRYFERSNQET 753

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              + +  I+ VG  V  GD++    +   +  +   + +L A       +  D  +    
Sbjct: 754  LIL-QRPIVEVGQFVKQGDLICDGPST-DQGELALGKNVLVAFSTWYGYNYEDAIIISEK 811

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V   V    I  +    +   S +   +    +       +  LD N   R+   +   
Sbjct: 812  LVKDDVF-TSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGSEVSAG 870

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
            + + G    K     + +   +   + W + A   +     V+           IL    
Sbjct: 871  DILVGRTSPKGEDNPTPE--EKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILSRTR 928

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            +         D++  GV +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMPFL+
Sbjct: 929  E---------DNLEDGVEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPFLE 979

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNP G+PSRMN+GQI E HLG     L  K    + D      +  L +   
Sbjct: 980  DGTPIDILLNPQGIPSRMNIGQILEMHLGMVAKKLDIKFVCPVFDGVKLDKMKELFN--- 1036

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       ++G+P                        ESG+
Sbjct: 1037 ---------------------------QAGIP------------------------ESGK 1045

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG+TG+PFD  V++GY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR
Sbjct: 1046 FTLYDGITGQPFDNDVSIGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQR 1105

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEME W ++++GA+ VL E+LT KSD++ GR  +Y ++V+G    + GTPESFNVL  E
Sbjct: 1106 FGEMETWALESFGASSVLLELLTYKSDNIQGRNALYNNLVSGGKIPKPGTPESFNVLAYE 1165

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            ++ LG+ +++     +         + +  E
Sbjct: 1166 LRGLGIKLEVHKKENQEEDPEANAENASNPE 1196


>gi|59896052|gb|AAX11386.1| RpoB [Streptococcus pneumoniae]
          Length = 659

 Score =  603 bits (1554), Expect = e-170,   Method: Composition-based stats.
 Identities = 286/714 (40%), Positives = 405/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKDFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVTTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG V+    +E         I       +N   YI N    D     +  +L  +
Sbjct: 278 EILVEAGTVMTRSVIE--------SIESHLDGDLNKIVYIPN----DAAVLTEPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNTNPDDKVRVVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGIGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|330723559|gb|AEC45929.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyorhinis
           MCLD]
          Length = 1236

 Score =  603 bits (1554), Expect = e-170,   Method: Composition-based stats.
 Identities = 338/994 (34%), Positives = 535/994 (53%), Gaps = 70/994 (7%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +   G   +R+ + K    +  PD ++ QK S+  FL           EG++  F 
Sbjct: 1   MEFKLSKYGPTTLRRDYSKTKFSLPTPDFLDSQKQSFKWFL----------KEGIEETFN 50

Query: 61  SVFPITAFSGAAMLEF--VSYEFDPPK--FD-VDDCLWRDLTYAVPLKITLRLIVFDVDE 115
            ++PI + +G   + F   S   + P   +  + +   +  ++   +  TL         
Sbjct: 51  KIYPIISTNGKIEIRFKKGSVRVEDPDQDYTNIKELKRKGKSFVCKVFATL--------- 101

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                   ++++Q I  G++P MT+ GTF+I G ++++VSQL RSPG+ F  +  R    
Sbjct: 102 EKLQVESGELEKQEILFGEIPYMTEGGTFIINGFEKVIVSQLIRSPGVCF-RENVRNRQV 160

Query: 176 GKLLYACRIIPDQGLWMDIEF----DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS- 230
             L     IIP  G W++I      ++ D + +RID+ + +P+ +FL A+G   ++I+  
Sbjct: 161 DDLFNKVEIIPQLGSWLEIFHRVTRNATDTVKLRIDKHKNIPLITFLKAIGFVDKDIIKK 220

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG-KKLTSGLLKSLK 289
            F       +      F            + S    I   +++   G K     LL + +
Sbjct: 221 YFGDSPELRESLKKDKFLRKDKVQEQLDSLESIYRTIRKDDRITTEGLKNFIPALLFNER 280

Query: 290 EKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
              +   G           D +   Y+AEDI + + G++    G  I  K   +I     
Sbjct: 281 RYNLSKTGRYMLNRKLNLLDRIIQTYLAEDIFDSK-GKLLYPLGTFITPKIANDIQSKFE 339

Query: 342 RDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             I P+  ++ ++ N Y R   +T                     ++T +   ++  +  
Sbjct: 340 NSILPLSEIEGIDENVYGRQLEITKNEN-----------------LNTRTKIITLRVWPN 382

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
             + + D +   + K  + +  D      H+   DI+AI+    +L    G  DD D+L 
Sbjct: 383 KHAMEQDANKEQQEKSVLVIGNDPTSIEMHLLISDIVAIVSYYFNLLANLGKNDDPDSLV 442

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCS 519
           N+RV +VGE+L+NQ+ + L ++E++ KERISS  D + +  +++ N KP+ +    FF S
Sbjct: 443 NKRVVNVGELLQNQFLIALSKLEKNTKERISSRGDSEKINIKNITNNKPIYNQFKNFFNS 502

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 503 SKLSQFMDQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQN 562

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDE 636
           IGL+ +   +A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE
Sbjct: 563 IGLILNFAVYAKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDE 622

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +    E  +  R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NM
Sbjct: 623 NNKIIEPEIIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNM 682

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+  EAP+V TG+E+ VAK S   I A   G V  VD+  I I++ +G      
Sbjct: 683 QRQAVPLITTEAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG------ 736

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +  Y L  F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF 
Sbjct: 737 -NIKTYHLRYFERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFS 795

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W+GYN+ED+++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++
Sbjct: 796 TWYGYNYEDAIIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHL 855

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ +G+EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  
Sbjct: 856 DENGIVRIGSEVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDG 915

Query: 937 GTVVDVRIFNRHGID-KNERSISVEREQIELLAR 969
           GTV+DV+I +R   D   +    + +  I    +
Sbjct: 916 GTVIDVQILSRTREDNLEDGVEKIIKVFIAQKRK 949



 Score =  446 bits (1148), Expect = e-122,   Method: Composition-based stats.
 Identities = 224/1073 (20%), Positives = 394/1073 (36%), Gaps = 91/1073 (8%)

Query: 321  YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            +++A   +D+  +++ F         L  D           L  DK +++ D+L  IYR 
Sbjct: 206  FLKAIGFVDKDIIKKYFGDSPELRESLKKD---------KFLRKDKVQEQLDSLESIYRT 256

Query: 381  MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
            +R  D  T    ++    L F+  +Y+LS  GR  +N +LNL       ++ ++   +  
Sbjct: 257  IRKDDRITTEGLKNFIPALLFNERRYNLSKTGRYMLNRKLNLLDRIIQTYLAEDIFDSKG 316

Query: 441  KILVDL--RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            K+L  L         +DI +     +  + E+      +   ++E   K    +     +
Sbjct: 317  KLLYPLGTFITPKIANDIQSKFENSILPLSEIEGIDENVYGRQLE-ITKNENLNTRTKII 375

Query: 499  MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
              +   N   +     +      +  +     S+        + A+            + 
Sbjct: 376  TLRVWPNKHAMEQDANKEQQEKSVLVIGNDPTSIEMHLLISDIVAIVSYYFNLLANLGKN 435

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             D       R+        +   +  S                 +        N  +Y  
Sbjct: 436  DDPDSLVNKRVVNVGELLQNQFLIALSKLEKNTKERISSRGDSEKINIKNITNNKPIYNQ 495

Query: 619  AMEEENR-YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
                 N   ++Q    ++  G    +          +     + +  D        I   
Sbjct: 496  FKNFFNSSKLSQFMDQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPV 555

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
              P  +N     +      +      ++     V  G+   V       +    A     
Sbjct: 556  ETPEGQNI-GLILNFAVYAKTNPYGFIQTPYFPVENGV---VNYDPQNIVWLTAAEEFGY 611

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV----NQRPLVKVGDEVRRNDI 793
              A   ++      +      V         +  Q   +     Q   +         + 
Sbjct: 612  TFAQSSLLVDENNKIIEPEIIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENN 671

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMA 851
             A+              ++    P+     E  +    S  + + +    + ++   +  
Sbjct: 672  DANRALMGSNMQRQAVPLITTEAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQI 731

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            ++ +   +         S +    + +  I+ VG  V  GD++    +   +  +   + 
Sbjct: 732  KNEQGNIKTYHLRYFERSNQETLIL-QRPIVEVGQFVKQGDLICDGPST-DQGELALGKN 789

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            +L A       +  D  +     V   V    I  +    +   S +   +    +    
Sbjct: 790  VLVAFSTWYGYNYEDAIIISEKLVKDDVF-TSIHIQEQTIQFRSSKAGNDDLTREIPNAS 848

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               +  LD N   R+   +   + + G    K     + +   +   + W + A   +  
Sbjct: 849  QRSKRHLDENGIVRIGSEVSAGDILVGRTSPKGEDNPTPE--EKLMNAIWGKKASSQKDT 906

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               V+           IL    +         D++  GV +++KVF+A KR I+ GDKMA
Sbjct: 907  SLKVKHGDGGTVIDVQILSRTRE---------DNLEDGVEKIIKVFIAQKRKIKVGDKMA 957

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++S +LP EDMPFL+DGTP+DI+LNP G+PSRMN+GQI E HLG     L  K
Sbjct: 958  GRHGNKGVISLVLPVEDMPFLEDGTPIDILLNPQGIPSRMNIGQILEMHLGMVAKKLDIK 1017

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                + D      +  L +                              ++G+P      
Sbjct: 1018 FVCPVFDGVKLDKMKELFN------------------------------QAGIP------ 1041

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                              ESG+  LYDG+TG+PFD  V++GY+YMLKL HMV DK++ARS
Sbjct: 1042 ------------------ESGKFTLYDGITGQPFDNDVSIGYMYMLKLQHMVDDKMHARS 1083

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G YSL TQQPLGGKS  GGQR GEME W ++++GA+ VL E+LT KSD++ GR  +Y +
Sbjct: 1084 VGPYSLTTQQPLGGKSQNGGQRFGEMETWALESFGASSVLLELLTYKSDNIQGRNALYNN 1143

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +V+G    + GTPESFNVL  E++ LG+ +++     +         + +  E
Sbjct: 1144 LVSGGKIPKPGTPESFNVLAYELRGLGIKLEVHKKENQEEDPEANAENASNPE 1196


>gi|59043129|gb|AAW83917.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 659

 Score =  602 bits (1553), Expect = e-169,   Method: Composition-based stats.
 Identities = 285/714 (39%), Positives = 405/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKDFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E         I       +N   YI N    D     +  +L  +
Sbjct: 278 EILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DAAVLTEPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNANPDDKVRVVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGIGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|294627835|ref|ZP_06706414.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans subsp.
            aurantifolii str. ICPB 11122]
 gi|292597749|gb|EFF41907.1| DNA-directed RNA polymerase beta subunit [Xanthomonas fuscans subsp.
            aurantifolii str. ICPB 11122]
          Length = 375

 Score =  601 bits (1549), Expect = e-169,   Method: Composition-based stats.
 Identities = 195/376 (51%), Positives = 258/376 (68%), Gaps = 7/376 (1%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    KK   ++   +    +  W+Q  ++DE     +E  + Q +  +   E RF
Sbjct: 3    KVANGGANLKKGDTVTDAYLDGLKKPDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARF 62

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K  KI  GDD+ PGVL++VKVF+A+KR IQ GDKMAGRHGNKG+VS ++P EDMP++ 
Sbjct: 63   ADKRGKITQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMA 122

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G  VDIVLNPLGVPSRMN+GQI E HLGWA  GLG+KI+ ++   +A   +S LR FL 
Sbjct: 123  TGESVDIVLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRML---EAQAAVSELRKFLN 179

Query: 1174 KVIGTGSHTE----KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
             +    +        +S + D+ +L + +    GVP++TPVFDGA E  I  ML +ADL 
Sbjct: 180  DIYNHDNAINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLP 239

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            +SGQ+ LYDG TGE FDR  TVGY++ LKLNH+V DK++ARSTG YSLVTQQPLGGK+  
Sbjct: 240  QSGQTQLYDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQF 299

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GR ++Y++IV G      G PESFNV
Sbjct: 300  GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNV 359

Query: 1350 LVKEMQALGLSIDLEN 1365
            LVKE+++L ++++LE 
Sbjct: 360  LVKEIRSLAINMELEE 375


>gi|159896777|ref|YP_001543024.1| DNA-directed RNA polymerase subunit beta [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|226699412|sp|A9B6J3|RPOB_HERA2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|159889816|gb|ABX02896.1| DNA-directed RNA polymerase, beta subunit [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 1217

 Score =  601 bits (1549), Expect = e-169,   Method: Composition-based stats.
 Identities = 328/961 (34%), Positives = 485/961 (50%), Gaps = 82/961 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AA 72
           R+ F +  + I++P LIE Q  S+  F            EGL+  F  + PI  F+G   
Sbjct: 31  RRSFARITDAIELPKLIETQIDSFRWF----------QREGLRELFDEINPIDDFTGKNL 80

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            L F  YEF  P+++  +C  RD+TYA PL++ +RL V         K+  +IKE  I++
Sbjct: 81  ELSFSDYEFGEPRYNEFECRERDMTYAAPLRVRVRLKV---------KTTGEIKESDIFL 131

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT +GTFVI G +R+VVSQL RSPG++F  +K     SG+ L++ ++IP++G W+
Sbjct: 132 GDFPLMTNNGTFVINGAERVVVSQLIRSPGVYFKEEKEPT--SGRSLHSAKLIPNRGAWL 189

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMA-LGM----------DSEEILSTFYPKIVYSQR 241
           + E + +D++ V++DR+RK+PVT  + A LG+           +E++++ F    V    
Sbjct: 190 EFETNKRDVLSVKVDRKRKLPVTILIRAVLGLFGDKPLDQCGLNEDVIALFANVDVNRDH 249

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
                             +      +  G+   +++ + L   LL + +   +  +G   
Sbjct: 250 QYIASTLDKDPSTNAKEAIMELYKRLRPGDPATVDNARSLLETLLFNARRYDLGKVGRYK 309

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                  + E     E  EI      V+ +  L +I               ++ N  I N
Sbjct: 310 ---LNRNLWEKSRLFEGQEIPSLTMRVLSKADLFKIVE-----------RLIDLNNGIGN 355

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
               D         L   RV   G++        +        ++  L        N  +
Sbjct: 356 PDDIDH--------LGNRRVRTVGELIQTQFRVGLLRMERVIKERMSLQEPEAATPNGLI 407

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           N+        +           L    +    + ++ +         G + +++    + 
Sbjct: 408 NIRP-----VVAAMREFFGGSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRDRAGFEVR 462

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF-----------CSSQLSQLEEHV 529
            +  S   RI  V+        LI      + V E                      E  
Sbjct: 463 DVHHSHYGRICPVETPEGPNIGLIGTMSTFARVNEMGFLETPYRRVYREVDNAPLWLERG 522

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +   + H      + + G        ++    V      R      + G  I    S  
Sbjct: 523 MTTRDVRHLSTGELIARAGARVDAELAKIIAIGVLNGQLLREDIVNPATGDLIAEAGSEI 582

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
             A       +     K+    VTN+  YL A EE+   IAQAN+ LDE   F +  V C
Sbjct: 583 DRALATKIADLPLRAIKIH-PVVTNETDYLPADEEDKFIIAQANALLDERFRFIDPTVSC 641

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R A + +  P   +D++D SPKQVVS++ +LIPFLE+DD+NR LMG NMQRQAVPLL+ +
Sbjct: 642 RHAEDFVQAPIASVDYMDVSPKQVVSVSTALIPFLEHDDANRALMGSNMQRQAVPLLRPD 701

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP +GTGME   A+ SG  +VA+   +V   ++ RI++R  +G           Y L+KF
Sbjct: 702 APIIGTGMEHKAARDSGQVVVARADAVVLSSNSERILVRENDGTE-------RTYPLLKF 754

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ+TC+NQRP V +GD++R  ++IAD  ST  G+LALG+N+LVA+MPW G NFED++
Sbjct: 755 LRSNQDTCINQRPSVFIGDKIRAGEVIADSSSTQNGELALGQNILVAYMPWEGGNFEDAI 814

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV ++ LKN+DE GII VGA+
Sbjct: 815 LVSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQDSLKNLDERGIIYVGAD 874

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V P DILVGKITPKGE+ +T EE+LLRAIFGEKA +V+D+SLRVP+GV G V+DV++F R
Sbjct: 875 VQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVKGKVIDVKVFTR 934

Query: 948 H 948
            
Sbjct: 935 D 935



 Score =  550 bits (1417), Expect = e-154,   Method: Composition-based stats.
 Identities = 312/1053 (29%), Positives = 464/1053 (44%), Gaps = 116/1053 (11%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             VD   ++ YI +TL  D + + K+A++++Y+ +RPGD +T   A S+   L F++ +YD
Sbjct: 242  NVDVNRDHQYIASTLDKDPSTNAKEAIMELYKRLRPGDPATVDNARSLLETLLFNARRYD 301

Query: 408  LSTVGRVKMNMRL---------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            L  VGR K+N  L                +R + K D+  I++ L+DL NG G  DDID+
Sbjct: 302  LGKVGRYKLNRNLWEKSRLFEGQEIPSLTMRVLSKADLFKIVERLIDLNNGIGNPDDIDH 361

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            LGNRRVR+VGE+++ Q+R+GLLRMER IKER+S  + ++  P  LIN +PVV+A+ EFF 
Sbjct: 362  LGNRRVRTVGELIQTQFRVGLLRMERVIKERMSLQEPEAATPNGLINIRPVVAAMREFFG 421

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG 
Sbjct: 422  GSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRICPVETPEGP 481

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKV-----------CDGKVTNDVVYLSAMEEENRYI 627
            NIGL+ ++++FARVN  GF+ETPYR+V             G  T DV +LS  E     I
Sbjct: 482  NIGLIGTMSTFARVNEMGFLETPYRRVYREVDNAPLWLERGMTTRDVRHLSTGE----LI 537

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A+A +               R   E   +    +       + +V+ A   +      + 
Sbjct: 538  ARAGA---------------RVDAELAKIIAIGVLNGQLLREDIVNPATGDLIAEAGSEI 582

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            +R L           +         T       +            I+ Q +A+      
Sbjct: 583  DRALATKIADLPLRAIKIHPVVTNETDYLPADEED---------KFIIAQANALLDERFR 633

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                        D  +         +    Q   V            A+           
Sbjct: 634  FIDPTVSCRHAEDFVQAPIASVDYMDVSPKQVVSVSTALIPFLEHDDANRALMGSNMQRQ 693

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-FEVMARDTKLGPEEITRDIP 866
               +L    P  G   E         V      ++ +    E +      G E     + 
Sbjct: 694  AVPLLRPDAPIIGTGMEHKAARDSGQVVVARADAVVLSSNSERILVRENDGTERTYPLLK 753

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             +       I++   + +G ++  G+++    + +    +   + +L A    +  +  D
Sbjct: 754  FLRSNQDTCINQRPSVFIGDKIRAGEVIADSSSTQN-GELALGQNILVAYMPWEGGNFED 812

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              L     VS  +V   IF    I+K E      +   E + RD  +      +N+  R 
Sbjct: 813  AIL-----VSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQDSLKNLDER- 866

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G +         K T      ++   R     F  +  +V+ +   +    +   
Sbjct: 867  GIIYVGADVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPNGVKGKV 926

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
              +      K+       +MP GV + V+V +  KR                   +I P 
Sbjct: 927  IDV------KVFTRDETTEMPVGVNQTVRVMLCQKR-------------------KISPG 961

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            + M                                       G K          +    
Sbjct: 962  DKM-----------------------------------AGRHGNKGVVSRVLPIEDMPFL 986

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P  + ++ V+   +   +++              + G  ++TPVFDGA +E I   L  +
Sbjct: 987  PDGTPVDIVLNPLAVPSRMNIGQILETHLGWAASRLGFRIATPVFDGARDEDIIKALAES 1046

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             L    +  LYDG TGE FD PVTVGY YMLKL H+V DK++ARSTG YSLVTQQPLGGK
Sbjct: 1047 GLPSDAKIDLYDGRTGEKFDNPVTVGYKYMLKLAHLVEDKIHARSTGPYSLVTQQPLGGK 1106

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY+LQEMLT+KSDDVVGR + YE+IV G+   E G PES
Sbjct: 1107 AQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVVGRVKTYEAIVKGDPINEAGVPES 1166

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+LGLS+D+  +  +     +   D
Sbjct: 1167 FKVLIKELQSLGLSVDVLTADERPVELTDSEAD 1199


>gi|59043091|gb|AAW83898.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  599 bits (1545), Expect = e-168,   Method: Composition-based stats.
 Identities = 284/714 (39%), Positives = 406/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKDFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     + +    +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKYI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLSVKTRLLNQTIAEPLVDSETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E         I       +N   YI N    D +      +L  +
Sbjct: 278 EILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DASVVTDPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +    I+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNANPDDKVRIVTPAYILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME  VA  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQVAHDSGAAVIAQ 653


>gi|59043089|gb|AAW83897.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043151|gb|AAW83928.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  599 bits (1545), Expect = e-168,   Method: Composition-based stats.
 Identities = 283/714 (39%), Positives = 404/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKAFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E         I       +N   YI N    D     +  +L  +
Sbjct: 278 EILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DAAVVTEPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNANPDDKVRIVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|59896050|gb|AAX11385.1| RpoB [Streptococcus pneumoniae]
          Length = 659

 Score =  598 bits (1542), Expect = e-168,   Method: Composition-based stats.
 Identities = 284/714 (39%), Positives = 405/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKAFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDITYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLSVKTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E         I       +N   YI N    D     +  +L  +
Sbjct: 278 EILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DAAVVTEPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 KVIAPTDPDRV--------------------------VTIIGNANPDDKVRTVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G + DID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGLGRVYDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSHLNEDGTFAEKVVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME  VA  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQVAHDSGAAVIAQ 653


>gi|59043109|gb|AAW83907.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  597 bits (1540), Expect = e-168,   Method: Composition-based stats.
 Identities = 284/714 (39%), Positives = 403/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKAFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDITYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E         I       +N   YI N    D     +  +L  +
Sbjct: 278 EILVEAGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DAAVLTEPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNANPDDKVRVVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGIGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ     N LS ++H RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMYQHNPLSELSHKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|59043071|gb|AAW83888.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  597 bits (1539), Expect = e-168,   Method: Composition-based stats.
 Identities = 284/714 (39%), Positives = 402/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKDFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKIYKKLSVNTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +EAG ++    +E I      D+        N   YI N    D        +L  +
Sbjct: 278 EILVEAGTLMTRSVIESIESYLDGDL--------NKIVYIPN----DAAVVTDPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           RV+ P D                              + +  N +  D VR +   DI+A
Sbjct: 326 RVVAPTDPDRV--------------------------VTIIGNANPDDKVRIVTPADILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G   I DID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMIYFLNLSEGLARIYDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQHIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPANVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|59043047|gb|AAW83876.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  597 bits (1538), Expect = e-168,   Method: Composition-based stats.
 Identities = 280/714 (39%), Positives = 401/714 (56%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          + GL+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKDFL----------DHGLKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKIDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLSVKTRLLNQTIAEPLVDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI +E G ++    +E         I       +N   YI N    D +      +L  +
Sbjct: 278 EILVETGTIMTRSVIE--------SIESHLDGDLNKIVYIPN----DASVVTDPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           +V+ P D                              + +  N +  D VR +    I+A
Sbjct: 326 KVVAPTDPDRV--------------------------VTIIGNANPDDKVRIVTPAYILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G + DID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + +
Sbjct: 360 EMSYFLNLAEGLGRVYDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPANVVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLINPKAPYVGTGMEYQAAHDSGAAVIAQ 653


>gi|224174626|emb|CAR92731.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 15245]
 gi|224174628|emb|CAR92732.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 15253]
          Length = 479

 Score =  594 bits (1531), Expect = e-167,   Method: Composition-based stats.
 Identities = 301/480 (62%), Positives = 378/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPAGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGAYIRNTLAADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174612|emb|CAR92724.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 15176]
 gi|224174614|emb|CAR92725.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 15181]
          Length = 479

 Score =  593 bits (1530), Expect = e-167,   Method: Composition-based stats.
 Identities = 303/480 (63%), Positives = 379/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPAGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G Y+AED+VN +TGEIY EAG+ I +KSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMADEELVGNYLAEDLVNPKTGEIYAEAGEEITDKSLKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFDS++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDSERYDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174584|emb|CAR92710.1| RNA polymerase, beta subunit [Bradyrhizobium elkanii]
          Length = 479

 Score =  593 bits (1530), Expect = e-167,   Method: Composition-based stats.
 Identities = 303/480 (63%), Positives = 380/480 (79%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPDGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174600|emb|CAR92718.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10677]
 gi|224174602|emb|CAR92719.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10691]
          Length = 479

 Score =  593 bits (1529), Expect = e-167,   Method: Composition-based stats.
 Identities = 302/480 (62%), Positives = 379/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVEEPAGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I +KSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITDKSLKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|47459116|ref|YP_015978.1| DNA-directed RNA polymerase subunit beta [Mycoplasma mobile 163K]
 gi|81614307|sp|Q6KI09|RPOB_MYCMO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|47458445|gb|AAT27767.1| DNA-directed RNA polymerase beta chain [Mycoplasma mobile 163K]
          Length = 1188

 Score =  592 bits (1527), Expect = e-166,   Method: Composition-based stats.
 Identities = 333/987 (33%), Positives = 537/987 (54%), Gaps = 77/987 (7%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R+ + +     +  D +E QK S+  F+          +EG+  A   ++PI + 
Sbjct: 10  GPVTERRDYSQTNRTWETFDFLETQKKSFKWFI----------DEGINQALNDIYPIHSN 59

Query: 69  SGAAMLEFVS------YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           +G  ++E+V+      Y+ D     + +   +  TY+  LK  L   + +          
Sbjct: 60  NGKVIIEYVNNSAKLEYKTDNEYKILAEARQKGTTYSGILKAKLTKTIVE---------T 110

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +I+   +  GD+P+MT  GTF+I G ++I+VSQL RSPG +F   K R   +  L    
Sbjct: 111 GEIETAEVLYGDVPIMTSGGTFLINGSEKIIVSQLIRSPGAYFGL-KVRNKQADDLFNKL 169

Query: 183 RIIPDQGLWMDIEF----DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
            IIP  G W++I      ++ D + V+ID+ + V + +FL A+GM  E I + F      
Sbjct: 170 EIIPKLGSWIEISHRVTGNTTDTVKVKIDKHKAVSLVTFLRAMGMKKETIQNLFGSHSTL 229

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDI---DTGEQVIESGKKLTSGLLKSLKEKGVKF 295
                     L+             L  +          ES   L S +L + +   +  
Sbjct: 230 EGENPILKETLNKEKFKTEDDALEYLYSVIWRGNNRITAESKSNLLSNILFNPRRYNLSK 289

Query: 296 LGITS--------DCLCGLYVAEDIVN---GETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            G           D + G Y+AED+ +    +  ++    G +I  +  E+I  S   +I
Sbjct: 290 TGRYMLNRKLSLVDRIIGTYLAEDLFSAKGTKNAKLVFAKGTLITREIAEKIQDSFKNNI 349

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             L               + D + D   A L+    +         ++ +++    +   
Sbjct: 350 FNL-------------IPIPDVSSDIYAAQLETNPKLA---ERIRVISLNIYPNKTWMEQ 393

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
                        + +  D      H+   D++AI+    +L +  G  DD D+L N+R+
Sbjct: 394 --------NTNPIIVIANDPNSTELHLLASDLVAIVSYYFNLVDRVGQDDDPDSLINKRI 445

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             VGE+L+NQ+++GL ++E++ KER+S+ +I+ + P+++ N+KPV +    FF SS+LSQ
Sbjct: 446 VGVGELLENQFKIGLSKLEKNAKERMSAKEIEKITPKNITNSKPVYNQFKTFFNSSKLSQ 505

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + VN L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 506 FMDQVNPLAEISNKRRVTSLGPGGLNRETAQFEVRDVHSTHYGRICPIETPEGPNIGLIL 565

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +  ++A+VN +GFI++PY KV DG +     ++L+A EE ++  AQ+  S+D+DG  T +
Sbjct: 566 NFATYAKVNDFGFIQSPYFKVNDGIIDYEKPIFLTAAEEIDKKFAQSTVSVDKDGKITTQ 625

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R   + ++V   ++D+ID S KQ+ SIAA+ IPFLEN+D+NR LMG NMQRQA+PL
Sbjct: 626 NITVRQNHDYLIVSPSEVDYIDISSKQMTSIAAAAIPFLENNDANRALMGSNMQRQAIPL 685

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           L+AEAP V TG+E+ +AK S + ++ K  G V  VD  +I ++S              Y 
Sbjct: 686 LEAEAPLVATGIEADIAKFSVSNLIVKEEGEVSYVDGTKIKVKSKNDKS-------KTYY 738

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F+ SNQ T ++Q+P+VK+GD+V   D++ D  S   G++ALG+N+++AF  W+GYN+
Sbjct: 739 LKNFEHSNQGTLLSQKPIVKLGDKVEIGDLLTDASSFKDGEMALGKNVMIAFSTWNGYNY 798

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISER+V +DVFTS+HIE+  +  R +K G +++TR+IPNVS    +N+DE GI+ 
Sbjct: 799 EDAIVISERLVKDDVFTSVHIEDQTIQFRTSKAGSDKLTREIPNVSNFSKRNLDEEGIVK 858

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV  GDILVG+++PKGE   +PEEKLL AIF +K    +DTSL+V  G +GTV+DV+
Sbjct: 859 VGSEVVAGDILVGRVSPKGEENPSPEEKLLAAIFQKKPSTDKDTSLKVKHGHAGTVLDVQ 918

Query: 944 IFNR-HGIDKNERSISVEREQIELLAR 969
           + +R  G    +    + +  I    +
Sbjct: 919 VLSRASGDVLEDSVEKIVKVSIAQKRK 945



 Score =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 232/1124 (20%), Positives = 409/1124 (36%), Gaps = 127/1124 (11%)

Query: 286  KSLKEKGVKFLGITS----DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K   +   K   I        +            +      +A  ++       +    I
Sbjct: 160  KQADDLFNKLEIIPKLGSWIEISHRVTGNTTDTVKVKIDKHKAVSLVTFLRAMGMKKETI 219

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLF 400
            +++   +      N  ++ TL  +K K   DAL  +Y V+ R  +  T     ++ + + 
Sbjct: 220  QNLFGSHSTLEGENPILKETLNKEKFKTEDDALEYLYSVIWRGNNRITAESKSNLLSNIL 279

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--- 457
            F+  +Y+LS  GR  +N +L+L       ++ ++   A       L   KGT+   +   
Sbjct: 280  FNPRRYNLSKTGRYMLNRKLSLVDRIIGTYLAEDLFSAKGTKNAKLVFAKGTLITREIAE 339

Query: 458  ----------NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
                                 ++   Q        ER     ++     + M Q+  N  
Sbjct: 340  KIQDSFKNNIFNLIPIPDVSSDIYAAQLETNPKLAERIRVISLNIYPNKTWMEQN-TNPI 398

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
             V++          L+     + S       R         +   R       +      
Sbjct: 399  IVIANDPNSTELHLLASDLVAIVSYYFNLVDRVGQDDDPDSLINKRIVGVGELLENQFKI 458

Query: 568  RICPAE-----TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             +   E           I  ++          Y   +T +      +  + V  L+  E 
Sbjct: 459  GLSKLEKNAKERMSAKEIEKITPKNITNSKPVYNQFKTFFNSSKLSQFMDQVNPLA--EI 516

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             N+    +      +    +  V    +     +       I+      + +  +   + 
Sbjct: 517  SNKRRVTSLGPGGLNRETAQFEVRDVHSTHYGRICP-----IETPEGPNIGLILNFATYA 571

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            + +D     +     +    ++  E P   T  E +  K + + +         ++    
Sbjct: 572  KVND--FGFIQSPYFKVNDGIIDYEKPIFLTAAEEIDKKFAQSTVS---VDKDGKITTQN 626

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            I +R     L  S S VD   +    +   +      P ++  D  R       G +   
Sbjct: 627  ITVRQNHDYLIVSPSEVDYIDIS--SKQMTSIAAAAIPFLENNDANRA----LMGSNMQR 680

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              + L              +     + +  +  E   + +   + +V +++ K       
Sbjct: 681  QAIPLLEAEAPLVATGIEADIAKFSVSNLIVKEEGEVSYVDGTKIKVKSKNDKS-KTYYL 739

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            ++  + ++  L  + +  I+ +G +V  GD+L    + K +  M   + ++ A       
Sbjct: 740  KNFEHSNQGTL--LSQKPIVKLGDKVEIGDLLTDASSFK-DGEMALGKNVMIAFSTWNGY 796

Query: 923  DVRDTSLRVPS------GVSGTVVDVRIFNRHGID-KNERSISVEREQIELLARDKDDEQ 975
            +  D  +            S  + D  I  R      ++ +  +    +   ++   DE+
Sbjct: 797  NYEDAIVISERLVKDDVFTSVHIEDQTIQFRTSKAGSDKLTREI--PNVSNFSKRNLDEE 854

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         +IL G+ +  G +       L + +  + P +                
Sbjct: 855  GIVKVGSEVVAGDILVGRVSPKGEENPSPEEKLLAAIFQKKPSTDKDT------------ 902

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
                   +            ++     GD +   V ++VKV +A KR I+ GDKMAGRHG
Sbjct: 903  -----SLKVKHGHAGTVLDVQVLSRASGDVLEDSVEKIVKVSIAQKRKIKVGDKMAGRHG 957

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S + P EDMP L+DGT +DI+LNP GVPSRMN+GQ+ E HLG A   L  K  S 
Sbjct: 958  NKGVISIVAPVEDMPHLEDGTVIDIILNPQGVPSRMNIGQVLELHLGMAAKTLSTKFVSP 1017

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D    G I  +    +                                          
Sbjct: 1018 GFDGLKFGTIQEILKEAK------------------------------------------ 1035

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   L         +  L D +TGE FD  V+VG +YMLKL+HMV DK++ARS G Y
Sbjct: 1036 -------LPENG-----KFTLIDPMTGEKFDNKVSVGIMYMLKLSHMVDDKMHARSIGPY 1083

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SL+TQQPLGGKS  GGQR GEME W ++A+GA+ +LQE+LT KSD++ GR  +Y S+  G
Sbjct: 1084 SLITQQPLGGKSQNGGQRFGEMETWALEAHGASNILQEILTYKSDNIEGRKGLYNSLATG 1143

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            N     GTPESFNVL  E++ L + ++   +  KN+  ++E+ D
Sbjct: 1144 NKIPAPGTPESFNVLSYELRGLSIKLE-SQAHFKNAQIVKEVMD 1186


>gi|224174622|emb|CAR92729.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10705]
 gi|224174624|emb|CAR92730.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10706]
          Length = 479

 Score =  592 bits (1527), Expect = e-166,   Method: Composition-based stats.
 Identities = 303/480 (63%), Positives = 380/480 (79%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPTGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKS++ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSMKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFDS++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDSERYDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|289546829|gb|ADD10122.1| DNA-directed RNA polymerase subunit beta [Candidatus Liberibacter
           solanacearum]
          Length = 514

 Score =  592 bits (1525), Expect = e-166,   Method: Composition-based stats.
 Identities = 439/514 (85%), Positives = 470/514 (91%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAK VVFNGLGR RKFFGK PEIIDIPDLIEVQ+ASYD FLMMN +P+ERPNEGLQAAFK
Sbjct: 1   MAKDVVFNGLGRARKFFGKIPEIIDIPDLIEVQRASYDQFLMMNSSPEERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEF SYEFD PKFDVDDCL RDLTYA PLKI LRLIVFD+DEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFESYEFDSPKFDVDDCLRRDLTYAAPLKIILRLIVFDIDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           SIKDIKEQSIYMGD+PLMTKDGTFVI G QRIVVSQLHRSPGI FDHDKGRASLSGKLLY
Sbjct: 121 SIKDIKEQSIYMGDVPLMTKDGTFVINGTQRIVVSQLHRSPGILFDHDKGRASLSGKLLY 180

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
           ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM+SE+ILSTFY KIVY +
Sbjct: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMNSEDILSTFYSKIVYVK 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           +G++WCFPLS ADL+VG+KVSSSL+D+DTGE+VIESGK+ T+ LLK+LKEKGV FLG+TS
Sbjct: 241 KGEYWCFPLSCADLIVGSKVSSSLIDVDTGERVIESGKRFTANLLKNLKEKGVGFLGVTS 300

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D L G YVAEDIVN  TGEIY+EAGD IDE +L  I    I DIP+L+VDS+++NAY+RN
Sbjct: 301 DYLYGSYVAEDIVNETTGEIYLEAGDAIDEPTLAAIVSCGIEDIPVLHVDSIDSNAYVRN 360

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           TLV DKNKD KDALLDIYRVMRPGDV T S AESMFNFLFFD DKYDLS VGRVKMNMRL
Sbjct: 361 TLVLDKNKDYKDALLDIYRVMRPGDVPTVSAAESMFNFLFFDPDKYDLSAVGRVKMNMRL 420

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           NLD PD VRH+RKED+IAIIKILVDLR+GKG IDDIDNLGNRRVRSVGEMLKNQYRLGLL
Sbjct: 421 NLDVPDTVRHVRKEDVIAIIKILVDLRDGKGKIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           RMERSIKERISSVDIDSVMPQDLINAKPVVSAV 
Sbjct: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVR 514


>gi|224174588|emb|CAR92712.1| RNA polymerase, beta subunit [Bradyrhizobium liaoningense]
          Length = 479

 Score =  589 bits (1519), Expect = e-165,   Method: Composition-based stats.
 Identities = 294/480 (61%), Positives = 378/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++  P  R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPPGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174606|emb|CAR92721.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 11955]
          Length = 477

 Score =  588 bits (1516), Expect = e-165,   Method: Composition-based stats.
 Identities = 291/478 (60%), Positives = 375/478 (78%), Gaps = 1/478 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +A 
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAC 477


>gi|59043075|gb|AAW83890.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 659

 Score =  588 bits (1516), Expect = e-165,   Method: Composition-based stats.
 Identities = 284/714 (39%), Positives = 397/714 (55%), Gaps = 73/714 (10%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LIE+Q  S+  FL          +  L+  F+ V PI+ F+    LEFV YE   PK+ +
Sbjct: 1   LIEIQTDSFKAFL----------DHALKEVFEDVLPISNFTDTMELEFVGYEIKEPKYTL 50

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++    D +Y+ P+ +T RLI          K   +IK Q ++ GD P+MT+ GTF+I G
Sbjct: 51  EEARIHDASYSAPIFVTFRLI---------NKETGEIKTQEVFFGDFPIMTEMGTFIING 101

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +RI+VSQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR
Sbjct: 102 GERIIVSQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDR 158

Query: 209 RRKVPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T+ + ALG    +EI   F    +     +      +  D      +      +
Sbjct: 159 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERL 217

Query: 268 DTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE    ES + L        +   +  +G             L    +AE +++ ETG
Sbjct: 218 RPGEPKTAESSRSLLVARFFDPRRYDLAGVGRYEINKKLNINTRLLNQTIAEPLIDPETG 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI  E G V+    +E         I  L    +N   Y  N    D        +L  +
Sbjct: 278 EILFEKGSVVTRDVIE--------SIESLLDGDLNKIVYTPN----DSCVLTDPVVLQKF 325

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
             + P D                              + +  + +  D VR I    I+A
Sbjct: 326 GGVAPTDPDRV--------------------------VTILGSANPDDKVRTISPAYILA 359

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +   ++L  G G IDDID+LGNRR+R+VGE+L NQ RL L RMERS++ER+S  D + +
Sbjct: 360 EVIYFLNLGEGIGRIDDIDHLGNRRIRAVGELLANQVRLALSRMERSVRERMSVQDNEVL 419

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 420 TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSEVSNKRRLSALGPGGLTRDRAGYEV 479

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV    GKVTN++V+
Sbjct: 480 RDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDRATGKVTNEIVW 539

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+ DG+F E++V  R  G     P   +D++D SPKQVV++A 
Sbjct: 540 LTADEEDEYTVAQANSKLNADGTFAEKVVMGRHQGVNQEYPASSVDYMDVSPKQVVAVAT 599

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           + IPFLENDDSNR LMG NMQRQAVPL+  +APFVGTGME   A  SGAAI+A+
Sbjct: 600 ACIPFLENDDSNRALMGANMQRQAVPLIDPKAPFVGTGMEYQAAHDSGAAIIAQ 653


>gi|224174590|emb|CAR92713.1| RNA polymerase, beta subunit [Bradyrhizobium liaoningense]
          Length = 479

 Score =  588 bits (1516), Expect = e-165,   Method: Composition-based stats.
 Identities = 293/480 (61%), Positives = 377/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++  P  R +EGLQA F+SVFPI+ FSG +MLEFV Y F+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPPGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYXFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174608|emb|CAR92722.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10300]
          Length = 479

 Score =  588 bits (1515), Expect = e-165,   Method: Composition-based stats.
 Identities = 296/480 (61%), Positives = 378/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPTGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY K++Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEQILSTFYKKLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTQRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174616|emb|CAR92726.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 11797]
 gi|224174618|emb|CAR92727.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 8300]
 gi|224174620|emb|CAR92728.1| RNA polymerase, beta subunit [Blastobacter denitrificans]
          Length = 479

 Score =  587 bits (1514), Expect = e-165,   Method: Composition-based stats.
 Identities = 296/480 (61%), Positives = 378/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPTGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY K++Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEQILSTFYKKLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + 
Sbjct: 240 AGKKLTVRTARQLQEKGLKALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTQRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174610|emb|CAR92723.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 11807]
          Length = 479

 Score =  587 bits (1514), Expect = e-165,   Method: Composition-based stats.
 Identities = 295/480 (61%), Positives = 378/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPTGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+IL+TFY K++Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEQILATFYKKLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +D+P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKDLPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLELDAPDTQRTLRKEDILAVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174592|emb|CAR92714.1| RNA polymerase, beta subunit [Bradyrhizobium yuanmingense]
 gi|224174594|emb|CAR92715.1| RNA polymerase, beta subunit [Bradyrhizobium yuanmingense]
 gi|224174596|emb|CAR92716.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 10727]
 gi|224174598|emb|CAR92717.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 15269]
          Length = 479

 Score =  587 bits (1514), Expect = e-165,   Method: Composition-based stats.
 Identities = 293/480 (61%), Positives = 377/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174604|emb|CAR92720.1| RNA polymerase, beta subunit [Bradyrhizobium sp. LMG 11950]
          Length = 476

 Score =  587 bits (1514), Expect = e-165,   Method: Composition-based stats.
 Identities = 290/476 (60%), Positives = 374/476 (78%), Gaps = 1/476 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ 
Sbjct: 240 AGKKLTVRAARQLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN   YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAA 475


>gi|319777035|ref|YP_004136686.1| DNA-directed RNA polymerase subunit beta [Mycoplasma fermentans
           M64]
 gi|318038110|gb|ADV34309.1| DNA-directed RNA polymerase subunit beta [Mycoplasma fermentans
           M64]
          Length = 1205

 Score =  587 bits (1513), Expect = e-165,   Method: Composition-based stats.
 Identities = 327/982 (33%), Positives = 538/982 (54%), Gaps = 53/982 (5%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
             G    R+ +       ++PD +   K S++ F             G++ + +  +PIT
Sbjct: 18  KYGPITERRDYSVTKITWNVPDFLVTSKESFEWF----------KKTGIEESLREHYPIT 67

Query: 67  AFSGAAMLEFV--SYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           A +    LE++  S + + P  +   + +   +   YA  L    R           A  
Sbjct: 68  ATNKKVSLEYIPNSADLEIPSKEYEAISEARVKGTNYAAKLYAKFR---------ATATE 118

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
              +K+  + +G++PLMT  G+F+I G ++++VSQL RSPG +F     R   S  L   
Sbjct: 119 TGIVKDDKVLLGEIPLMTSGGSFIINGSEKVIVSQLIRSPGAYFGRGV-RNKQSDDLFNK 177

Query: 182 CRIIPDQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
             I+P  G W++I       + D + ++ID+ + V + +FL +LG+D + I++ F    V
Sbjct: 178 VEILPRIGSWVEISHKVTTKTPDSVKIKIDKNKNVNLVTFLGSLGLDRQMIMNLFGKSDV 237

Query: 238 YS--QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVK 294
                + D    P    D ++          +  G+++  ES   L   LL   K   + 
Sbjct: 238 LKETIKKDKKVDPELDQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLS 297

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G        L + + I +   GE  +      DE+ +++      +   ++  +  + 
Sbjct: 298 ETGRYMLN-KKLNLVDRISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSG 356

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                               +   +++      +      +     + + K+    +  V
Sbjct: 357 KLPSVEIEGVRPE-------VAYAKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPV 409

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K+   +  D     +H+   DIIA +    +L +G G  DD D+L N+R+ +VGE+L++Q
Sbjct: 410 KV---IGNDPKSVEQHLLVSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQ 466

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             +GL+++E++ +ER+ + + D V P+++ N K + + +  FF SS+LSQ  + +N L+ 
Sbjct: 467 LNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAE 526

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++A+VN 
Sbjct: 527 ISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATYAQVNK 586

Query: 595 YGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+    ++ +  R     
Sbjct: 587 YGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNY 646

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL  EAPFV T
Sbjct: 647 IIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVAT 706

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+ES +AK S    VAK  G+VE VD  +I +R+ +G LD        Y L  FQRSNQ+
Sbjct: 707 GIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD-------TYYLKNFQRSNQD 759

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  + GYN+ED+++++ER+
Sbjct: 760 TVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYNYEDAVILNERL 819

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ +G+EV PGD+
Sbjct: 820 VKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDV 879

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GTV+ V + +R     +
Sbjct: 880 LVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG--D 937

Query: 954 ERSISVEREQIELLARDKDDEQ 975
                +E+     +A  +  + 
Sbjct: 938 ALEDGIEKIVKVSIAIKRKIKV 959



 Score =  427 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 229/1035 (22%), Positives = 384/1035 (37%), Gaps = 111/1035 (10%)

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D++   K+   +++RV+R GD  T     ++   L F   +Y LS  GR  +N +LNL  
Sbjct: 253  DQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLSETGRYMLNKKLNLVD 312

Query: 425  PDDVRHIRKE-----DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                  + ++           KI             I +  +       E+   +  +  
Sbjct: 313  RISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSGKLPSVEIEGVRPEVAY 372

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             ++    + +        ++ +     K +   +                +  S   H  
Sbjct: 373  AKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPVKVIGN--------DPKSVEQHLL 424

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
                +   G          +D  P            E     L   L    +        
Sbjct: 425  VSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQLNVGLVKLEKTTRERMGA 484

Query: 600  TPYRKVCDGKVTNDVVYLSAMEE--ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                KV    VTN+ +  + M+    +  ++Q    ++     + E          +   
Sbjct: 485  KEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAEISNERRITSLGPGGLNRD 544

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              + +  D        I     P    +    +      Q      L+     V  G+  
Sbjct: 545  TAQFEVRDVHATHYGRICPIETP-EGPNIGLILNFATYAQVNKYGFLQTPYYKVENGV-- 601

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV- 776
                          A  +    A  IV       L      +         +  +   + 
Sbjct: 602  ---VDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNYIIGKPKEVDYIE 658

Query: 777  ---NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               NQ   V  G      +  A+              +L+   P+     E  +   +  
Sbjct: 659  VAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYS 716

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVN 889
                V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+ 
Sbjct: 717  SGNFVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIK 775

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVR 943
             GD+LV   + K    +   + ++ A    K  +  D  +            S  + +  
Sbjct: 776  KGDLLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQT 834

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            I  R     ++  ++++   +   A    DE  I+         ++L G+ +  G     
Sbjct: 835  IQFRTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPS 893

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            +   L S ++                  QR +       +             +   + G
Sbjct: 894  QEEKLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG 936

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +  G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LN
Sbjct: 937  DALEDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLN 996

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P GVPSRMN+GQ+ E HLG A   LG K  +   D     +I  +               
Sbjct: 997  PQGVPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV--------------- 1041

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                             ++G+P+                        SG+  L D +TG 
Sbjct: 1042 ---------------TLEAGLPL------------------------SGKQWLIDPITGN 1062

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              D+PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W I+
Sbjct: 1063 KLDKPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETWAIE 1122

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +YGA  VLQE+LT KSDD+ GR ++Y ++ +G +  + G PESFNVL  E++ LG+ +DL
Sbjct: 1123 SYGATNVLQEILTYKSDDINGRNQLYAALASGRELPKPGVPESFNVLSYELKGLGMKLDL 1182

Query: 1364 ENSRTKNSAKMEEIP 1378
            +  +  ++   +   
Sbjct: 1183 KKVKQDDNDFQQHFD 1197


>gi|224174586|emb|CAR92711.1| RNA polymerase, beta subunit [Bradyrhizobium japonicum]
 gi|224174646|emb|CAR92741.1| RNA polymerase, beta subunit [Bradyrhizobium sp. RLA08]
 gi|224174652|emb|CAR92744.1| RNA polymerase, beta subunit [Bradyrhizobium sp. RLA11]
          Length = 479

 Score =  587 bits (1512), Expect = e-165,   Method: Composition-based stats.
 Identities = 293/480 (61%), Positives = 380/480 (79%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPAGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|308189820|ref|YP_003922751.1| DNA-directed RNA polymerase beta chain [Mycoplasma fermentans JER]
 gi|307624562|gb|ADN68867.1| DNA-directed RNA polymerase beta chain [Mycoplasma fermentans JER]
          Length = 1213

 Score =  586 bits (1511), Expect = e-165,   Method: Composition-based stats.
 Identities = 327/982 (33%), Positives = 538/982 (54%), Gaps = 53/982 (5%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
             G    R+ +       ++PD +   K S++ F             G++ + +  +PIT
Sbjct: 26  KYGPITERRDYSVTKITWNVPDFLVTSKESFEWF----------KKTGIEESLREHYPIT 75

Query: 67  AFSGAAMLEFV--SYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           A +    LE++  S + + P  +   + +   +   YA  L    R           A  
Sbjct: 76  ATNKKVSLEYIPNSADLEIPSKEYEAISEARVKGTNYAAKLYAKFR---------ATATE 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
              +K+  + +G++PLMT  G+F+I G ++++VSQL RSPG +F     R   S  L   
Sbjct: 127 TGIVKDDKVLLGEIPLMTSGGSFIINGSEKVIVSQLIRSPGAYFGRGV-RNKQSDDLFNK 185

Query: 182 CRIIPDQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
             I+P  G W++I       + D + ++ID+ + V + +FL +LG+D + I++ F    V
Sbjct: 186 VEILPRIGSWVEISHKVTTKTPDSVKIKIDKNKNVNLVTFLGSLGLDRQMIMNLFGKSDV 245

Query: 238 YS--QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVK 294
                + D    P    D ++          +  G+++  ES   L   LL   K   + 
Sbjct: 246 LKETIKKDKKVDPELDQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLS 305

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G        L + + I +   GE  +      DE+ +++      +   ++  +  + 
Sbjct: 306 ETGRYMLN-KKLNLVDRISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSG 364

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                               +   +++      +      +     + + K+    +  V
Sbjct: 365 KLPSVEIEGVRPE-------VAYAKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPV 417

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K+   +  D     +H+   DIIA +    +L +G G  DD D+L N+R+ +VGE+L++Q
Sbjct: 418 KV---IGNDPKSVEQHLLVSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQ 474

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             +GL+++E++ +ER+ + + D V P+++ N K + + +  FF SS+LSQ  + +N L+ 
Sbjct: 475 LNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAE 534

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++A+VN 
Sbjct: 535 ISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATYAQVNK 594

Query: 595 YGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+    ++ +  R     
Sbjct: 595 YGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNY 654

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL  EAPFV T
Sbjct: 655 IIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVAT 714

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+ES +AK S    VAK  G+VE VD  +I +R+ +G LD        Y L  FQRSNQ+
Sbjct: 715 GIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD-------TYYLKNFQRSNQD 767

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  + GYN+ED+++++ER+
Sbjct: 768 TVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYNYEDAVILNERL 827

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ +G+EV PGD+
Sbjct: 828 VKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDV 887

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GTV+ V + +R     +
Sbjct: 888 LVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG--D 945

Query: 954 ERSISVEREQIELLARDKDDEQ 975
                +E+     +A  +  + 
Sbjct: 946 ALEDGIEKIVKVSIAIKRKIKV 967



 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 229/1035 (22%), Positives = 384/1035 (37%), Gaps = 111/1035 (10%)

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D++   K+   +++RV+R GD  T     ++   L F   +Y LS  GR  +N +LNL  
Sbjct: 261  DQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLSETGRYMLNKKLNLVD 320

Query: 425  PDDVRHIRKE-----DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                  + ++           KI             I +  +       E+   +  +  
Sbjct: 321  RISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSGKLPSVEIEGVRPEVAY 380

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             ++    + +        ++ +     K +   +                +  S   H  
Sbjct: 381  AKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPVKVIGN--------DPKSVEQHLL 432

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
                +   G          +D  P            E     L   L    +        
Sbjct: 433  VSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQLNVGLVKLEKTTRERMGA 492

Query: 600  TPYRKVCDGKVTNDVVYLSAMEE--ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                KV    VTN+ +  + M+    +  ++Q    ++     + E          +   
Sbjct: 493  KEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAEISNERRITSLGPGGLNRD 552

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              + +  D        I     P    +    +      Q      L+     V  G+  
Sbjct: 553  TAQFEVRDVHATHYGRICPIETP-EGPNIGLILNFATYAQVNKYGFLQTPYYKVENGV-- 609

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV- 776
                          A  +    A  IV       L      +         +  +   + 
Sbjct: 610  ---VDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNYIIGKPKEVDYIE 666

Query: 777  ---NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               NQ   V  G      +  A+              +L+   P+     E  +   +  
Sbjct: 667  VAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYS 724

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVN 889
                V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+ 
Sbjct: 725  SGNFVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIK 783

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVR 943
             GD+LV   + K    +   + ++ A    K  +  D  +            S  + +  
Sbjct: 784  KGDLLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQT 842

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            I  R     ++  ++++   +   A    DE  I+         ++L G+ +  G     
Sbjct: 843  IQFRTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPS 901

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            +   L S ++                  QR +       +             +   + G
Sbjct: 902  QEEKLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG 944

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +  G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LN
Sbjct: 945  DALEDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLN 1004

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P GVPSRMN+GQ+ E HLG A   LG K  +   D     +I  +               
Sbjct: 1005 PQGVPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV--------------- 1049

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                             ++G+P+                        SG+  L D +TG 
Sbjct: 1050 ---------------TLEAGLPL------------------------SGKQWLIDPITGN 1070

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              D+PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W I+
Sbjct: 1071 KLDKPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETWAIE 1130

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +YGA  VLQE+LT KSDD+ GR ++Y ++ +G +  + G PESFNVL  E++ LG+ +DL
Sbjct: 1131 SYGATNVLQEILTYKSDDINGRNQLYAALASGRELPKPGVPESFNVLSYELKGLGMKLDL 1190

Query: 1364 ENSRTKNSAKMEEIP 1378
            +  +  ++   +   
Sbjct: 1191 KKVKQDDNDFQQHFD 1205


>gi|224174648|emb|CAR92742.1| RNA polymerase, beta subunit [Bradyrhizobium sp. RLA09]
 gi|224174650|emb|CAR92743.1| RNA polymerase, beta subunit [Bradyrhizobium sp. RLA10]
          Length = 479

 Score =  586 bits (1510), Expect = e-164,   Method: Composition-based stats.
 Identities = 293/480 (61%), Positives = 380/480 (79%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPVGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174576|emb|CAR92706.1| RNA polymerase, beta subunit [Bradyrhizobium betae]
 gi|224174578|emb|CAR92707.1| RNA polymerase, beta subunit [Bradyrhizobium betae]
          Length = 479

 Score =  585 bits (1508), Expect = e-164,   Method: Composition-based stats.
 Identities = 293/480 (61%), Positives = 380/480 (79%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPVGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEHGYKELPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174632|emb|CAR92734.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCLA12]
          Length = 479

 Score =  585 bits (1508), Expect = e-164,   Method: Composition-based stats.
 Identities = 295/480 (61%), Positives = 379/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRSDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++   L G Y+AED+VN +TGEIY EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDAELVGNYIAEDLVNPKTGEIYAEAGEEITDKSIKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEHGYKELPLLDIDHVNVGAYIRNTLAADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|224174580|emb|CAR92708.1| RNA polymerase, beta subunit [Bradyrhizobium canariense]
 gi|224174582|emb|CAR92709.1| RNA polymerase, beta subunit [Bradyrhizobium canariense]
 gi|224174630|emb|CAR92733.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCLA07]
 gi|224174634|emb|CAR92735.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCLA22]
 gi|224174638|emb|CAR92737.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCAH03]
 gi|224174640|emb|CAR92738.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCAH06]
 gi|224174642|emb|CAR92739.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCAH12]
 gi|224174644|emb|CAR92740.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCAH13]
 gi|224174656|emb|CAR92746.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCOC05]
 gi|224174658|emb|CAR92747.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCOC23]
 gi|224174660|emb|CAR92748.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCOC24]
          Length = 479

 Score =  584 bits (1505), Expect = e-164,   Method: Composition-based stats.
 Identities = 294/480 (61%), Positives = 379/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRSDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSMKA 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEQGYKELPLLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|206896263|ref|YP_002247341.1| putative DNA-directed RNA polymerase subunit beta [Coprothermobacter
            proteolyticus DSM 5265]
 gi|206738880|gb|ACI17958.1| putative DNA-directed RNA polymerase subunit beta [Coprothermobacter
            proteolyticus DSM 5265]
          Length = 1293

 Score =  584 bits (1505), Expect = e-164,   Method: Composition-based stats.
 Identities = 301/1384 (21%), Positives = 504/1384 (36%), Gaps = 185/1384 (13%)

Query: 24   IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF-- 81
            +  PD +E +K S++ F+           EGL+  F + FPI    G   ++ + Y F  
Sbjct: 22   VPYPDFLEAKKNSWNWFVT----------EGLRELFNTYFPIEDAKGRWRIDILDYYFEN 71

Query: 82   ------DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG-D 134
                    P    +D +    TYA  L + +R+               +I E+   +G  
Sbjct: 72   DVADETGNPINTPEDAIREHATYAKRLIVKVRVH---------NSETGEIVEKEHVLGKR 122

Query: 135  LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            +P MT  G F++ G +R+ ++QL RSPGI+ + D     +S        +IP +G W+DI
Sbjct: 123  IPWMTDSGDFIVNGSRRVTLNQLVRSPGIYLEADGSLRRIS--------LIPQRGTWIDI 174

Query: 195  EFDSKDIIHVRIDRR-RKVPVTSFLMALGM-DSEEI-----------LSTFYPKIVYSQR 241
            E+D K+ + + +DRR +K+ + ++L ALG    +EI           +  F     +  +
Sbjct: 175  EYDGKNPLSIVLDRRSKKLNLATYLRALGYMSDDEIRTRLKDSALKWIEFFLNDAGFDNK 234

Query: 242  GDFWCFPLSA---ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
              F    L +         +  + ++ +     + ++   +L   L +   E  +  +  
Sbjct: 235  KLFVSQNLVSYFNYLRSYYSSTAQTVSEFRNVLENLDVDDQLLERLEEYNVESVLDEIAE 294

Query: 299  TSDC----LCGLYVAEDIVNGETGEIYIEAGDVIDEKSL------EEIFHSEIRDIPILY 348
            +       L  L + + IV+     +  +  D     ++       +   + +R+  +L 
Sbjct: 295  SYASQYSGLEILNIFKTIVDENLKLLIDKTIDGDTSINIFTVSTVWDQIVAALRETELLE 354

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + + +         +D +         M         V   +   +         
Sbjct: 355  DVLDKDGSVVVRANSPMSTRDVETFFKSHVIPMVRSGKYDIKVKVPVRGQMKAYEGWVIA 414

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              V     ++      P+  + +RK      +++ +          +++        S  
Sbjct: 415  DDVEVDGESVEGRALDPELAKSLRKVSDFVTLQVPIKRFFQGSAFVELEKRRTGETLSER 474

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E  + ++R  L   +R+   R+ +  I+      +     +   +        L+     
Sbjct: 475  E-AERRFRQLLFDPKRNQIGRVGAYHIEHRYGIKVE--DSLTDEMLAELGGILLAYCIGS 531

Query: 529  VNSLS-RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                       RR+ A+G+              V    + R+      E  N      L 
Sbjct: 532  TMPDDIDHLSNRRVRAIGELYYE----------VFANAFERLVKTARDEMINQQKEPELK 581

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                +      +  +R V   +V   + Y + + E                   +  V  
Sbjct: 582  LHRVLAQNILTQYVWRFVNPSEVHQLLEYTNPLTEITH----------------KRRVTA 625

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               G         I+  D        +     P  +N      L       +   L+   
Sbjct: 626  MGRGGLSREHAS-IEVRDVHHTHYGRLCPIETPEGQNIGLILSLATYAKLNEHGFLITPY 684

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMK 766
               V   +           + A        V A   +                 +  + K
Sbjct: 685  RRVVNGEV-----TDEIVWMDALEEEKEYIVPADTPLNGRKINVDRVLARHRSQWVAVDK 739

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             Q +  +  V Q   +            A               ++ A  P      E  
Sbjct: 740  DQITLMDVSVTQPFSISASLVPFLESDDAIRALMGSNMQRQAVPLINAESPIVATGMEKH 799

Query: 827  MLIS-ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            ++ S + ++  +   ++   + + +    + G E+  +            +     +  G
Sbjct: 800  VVESLDYVIKANQDGTVSYVDGKQVKIKAEDGYEKTYQLKVFDRTNQDTVVHFRPKVKQG 859

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             +V  GD+L   IT      +     +L A    +  +  D  L     V   V      
Sbjct: 860  QKVKKGDVLAEAIT-SDNGELALGRNVLVAFMPWEGYNYEDAILISKRLVKDDVFTSVHI 918

Query: 946  NRHGIDKNE--RSISVE------REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
              + ++  E  R  S E          E   R  D E  I+      +  +IL G+    
Sbjct: 919  REYMVEVAELSRGRSEEITYDLPDSVSEQEKRYLDPETGIVMVGTEVKPGDILVGKVTPK 978

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
              +       + + L+S     +  +      +V      + V  +  ++          
Sbjct: 979  EEEDKS----IETKLLSAIFGEKLDKVKDTSLRVPPAEGGIVVDTQILRNS--------- 1025

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                       G ++ VKVFVA KR IQ GDKM+GRHGNKG+VSR+LP EDMPFL DG P
Sbjct: 1026 ---------ETGKIKAVKVFVAQKRKIQPGDKMSGRHGNKGVVSRVLPEEDMPFLPDGRP 1076

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ E HLG A   LG K++  I                     
Sbjct: 1077 VDIVLNPLGVPSRMNIGQLLELHLGLAAKVLGFKVEVPIFSNFGV--------------- 1121

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              +G  E     +LR A L E+G+ +L 
Sbjct: 1122 ----------------------------------EGVKE-----LLREAGLPENGKVVLR 1142

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            DG TGE F   +TVGY+YM+KL HMV DK +ARSTG Y+LVTQQPLGG+++ GGQRLGEM
Sbjct: 1143 DGRTGEEFLSDITVGYMYMMKLIHMVEDKWHARSTGDYALVTQQPLGGRAHFGGQRLGEM 1202

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++AYGA+YVLQEMLT+KSDDV GR + Y ++           PESF VL  E++AL
Sbjct: 1203 EVWALEAYGASYVLQEMLTVKSDDVEGRKKAYIALTRNQPLEPPQLPESFKVLELELKAL 1262

Query: 1358 GLSI 1361
            G  +
Sbjct: 1263 GFMV 1266


>gi|224174636|emb|CAR92736.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCLA23]
 gi|224174654|emb|CAR92745.1| RNA polymerase, beta subunit [Bradyrhizobium sp. MCOC04]
          Length = 479

 Score =  583 bits (1504), Expect = e-164,   Method: Composition-based stats.
 Identities = 294/480 (61%), Positives = 379/480 (78%), Gaps = 1/480 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPQGGRSDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSIKV 299

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +     +++P+L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++M
Sbjct: 300 LNEHGYKELPLLDIDHVNVGAYIRNTLAADKNMTREDALFDIYRVMRPGEPPTLDSAQAM 359

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  LFFD+++YDLS VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDD
Sbjct: 360 FQSLFFDAERYDLSAVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDD 419

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +AV E
Sbjct: 420 IDHLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAAAVRE 479


>gi|238809818|dbj|BAH69608.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 1214

 Score =  582 bits (1499), Expect = e-163,   Method: Composition-based stats.
 Identities = 326/982 (33%), Positives = 537/982 (54%), Gaps = 53/982 (5%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
             G    R+ +       ++PD +   K S++ F             G++ + +  +PIT
Sbjct: 27  KYGPITERRDYSVTKITWNVPDFLVTSKESFEWF----------KKTGIEESLREHYPIT 76

Query: 67  AFSGAAMLEFV--SYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           A +    LE++  S + + P  +   + +   +   YA  L    R           A  
Sbjct: 77  ATNKKVSLEYIPNSADLEIPSKEYEAISEARVKGTNYAAKLYAKFR---------ATATE 127

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
              +K+  + +G++PLMT   +F+I G ++++VSQL RSPG +F     R   S  L   
Sbjct: 128 TGIVKDDKVLLGEIPLMTSGWSFIINGSEKVIVSQLIRSPGAYFGRGV-RNKQSDDLFNK 186

Query: 182 CRIIPDQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
             I+P  G W++I       + D + ++ID+ + V + +FL +LG+D + I++ F    V
Sbjct: 187 VEILPRIGSWVEISHKVTTKTPDSVKIKIDKNKNVNLVTFLGSLGLDRQMIMNLFGKSDV 246

Query: 238 YS--QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVK 294
                + D    P    D ++          +  G+++  ES   L   LL   K   + 
Sbjct: 247 LKETIKKDKKVDPELDQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLS 306

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G        L + + I +   GE  +      DE+ +++      +   ++  +  + 
Sbjct: 307 ETGRYMLN-KKLNLVDRISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSG 365

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                               +   +++      +      +     + + K+    +  V
Sbjct: 366 KLPSVEIEGVRPE-------VAYAKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPV 418

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K+   +  D     +H+   DIIA +    +L +G G  DD D+L N+R+ +VGE+L++Q
Sbjct: 419 KV---IGNDPKSVEQHLLVSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQ 475

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
             +GL+++E++ +ER+ + + D V P+++ N K + + +  FF SS+LSQ  + +N L+ 
Sbjct: 476 LNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAE 535

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++A+VN 
Sbjct: 536 ISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATYAQVNK 595

Query: 595 YGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+    ++ +  R     
Sbjct: 596 YGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNY 655

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL  EAPFV T
Sbjct: 656 IIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVAT 715

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+ES +AK S    VAK  G+VE VD  +I +R+ +G LD        Y L  FQRSNQ+
Sbjct: 716 GIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD-------TYYLKNFQRSNQD 768

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  + GYN+ED+++++ER+
Sbjct: 769 TVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYNYEDAVILNERL 828

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ +G+EV PGD+
Sbjct: 829 VKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDV 888

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GTV+ V + +R     +
Sbjct: 889 LVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG--D 946

Query: 954 ERSISVEREQIELLARDKDDEQ 975
                +E+     +A  +  + 
Sbjct: 947 ALEDGIEKIVKVSIAIKRKIKV 968



 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 229/1035 (22%), Positives = 384/1035 (37%), Gaps = 111/1035 (10%)

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            D++   K+   +++RV+R GD  T     ++   L F   +Y LS  GR  +N +LNL  
Sbjct: 262  DQDTVIKNCQEELFRVLRRGDRITDESIANLIPSLLFHRKRYSLSETGRYMLNKKLNLVD 321

Query: 425  PDDVRHIRKE-----DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                  + ++           KI             I +  +       E+   +  +  
Sbjct: 322  RISDTFLGEDLVVINKNGDEEKIKKGTLITHKIALLIQSNFDSGKLPSVEIEGVRPEVAY 381

Query: 480  LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             ++    + +        ++ +     K +   +                +  S   H  
Sbjct: 382  AKLLSDAQNKSLKNRNKIIILKIYPTKKWMDKGLTPVKVIGN--------DPKSVEQHLL 433

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
                +   G          +D  P            E     L   L    +        
Sbjct: 434  VSDIIAAVGYYFNLLDGIGQDDDPDSLTNKRIVAVGELLQSQLNVGLVKLEKTTRERMGA 493

Query: 600  TPYRKVCDGKVTNDVVYLSAMEE--ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                KV    VTN+ +  + M+    +  ++Q    ++     + E          +   
Sbjct: 494  KEPDKVTPKNVTNNKLISTQMKTFFNSSKLSQFMDQINPLAEISNERRITSLGPGGLNRD 553

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              + +  D        I     P    +    +      Q      L+     V  G+  
Sbjct: 554  TAQFEVRDVHATHYGRICPIETP-EGPNIGLILNFATYAQVNKYGFLQTPYYKVENGV-- 610

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV- 776
                          A  +    A  IV       L      +         +  +   + 
Sbjct: 611  ---VDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMRHNYNYIIGKPKEVDYIE 667

Query: 777  ---NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               NQ   V  G      +  A+              +L+   P+     E  +   +  
Sbjct: 668  VAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYS 725

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVN 889
                V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+ 
Sbjct: 726  SGNFVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIK 784

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVR 943
             GD+LV   + K    +   + ++ A    K  +  D  +            S  + +  
Sbjct: 785  KGDLLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQT 843

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            I  R     ++  ++++   +   A    DE  I+         ++L G+ +  G     
Sbjct: 844  IQFRTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPS 902

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            +   L S ++                  QR +       +             +   + G
Sbjct: 903  QEEKLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENG 945

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +  G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LN
Sbjct: 946  DALEDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLN 1005

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P GVPSRMN+GQ+ E HLG A   LG K  +   D     +I  +               
Sbjct: 1006 PQGVPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV--------------- 1050

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                             ++G+P+                        SG+  L D +TG 
Sbjct: 1051 ---------------TLEAGLPL------------------------SGKQWLIDPITGN 1071

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              D+PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W I+
Sbjct: 1072 KLDKPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETWAIE 1131

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +YGA  VLQE+LT KSDD+ GR ++Y ++ +G +  + G PESFNVL  E++ LG+ +DL
Sbjct: 1132 SYGATNVLQEILTYKSDDINGRNQLYAALASGRELPKPGVPESFNVLSYELKGLGMKLDL 1191

Query: 1364 ENSRTKNSAKMEEIP 1378
            +  +  ++   +   
Sbjct: 1192 KKVKQDDNDFQQHFD 1206


>gi|313678761|ref|YP_004056501.1| DNA-directed RNA polymerase subunit beta [Mycoplasma bovis PG45]
 gi|312950668|gb|ADR25263.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma bovis PG45]
          Length = 1211

 Score =  582 bits (1499), Expect = e-163,   Method: Composition-based stats.
 Identities = 325/962 (33%), Positives = 522/962 (54%), Gaps = 71/962 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R+ +       ++PD + + K S++ F             G++   +  +PI + +  
Sbjct: 24  TERRDYSATKVTWEVPDFLNMSKESFEWF----------KKSGIEEILREHYPIVSSNKK 73

Query: 72  AMLEFV--SYEFDPP--KFD-VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
             LE++  S   + P  ++D + +   + + YA  L    ++                +K
Sbjct: 74  VSLEYILNSARLEVPPKEYDAIIEAKAKGINYAAKLFAKFKVTSDK----------GVVK 123

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  + +G++PLM   G+F+I G ++++VSQL RSP  +F     R   S  L     I+P
Sbjct: 124 DDEVLLGEIPLMNSGGSFIINGSEKVIVSQLIRSPSAYFGCGV-RNKQSDDLFNKLEILP 182

Query: 187 DQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQ 240
             G W++I       + D + ++ID+ + + +  FL ALG++ + I   F   P++  + 
Sbjct: 183 RLGSWVEISHKVTTKNPDSVKIKIDKNKNINLAVFLGALGLNEQNIHDLFGNSPELEETL 242

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEK-------- 291
             D           ++          I  G+ + E S   L   LL + K          
Sbjct: 243 LRDKSLKSSEDPMTVIQNCREILFRTIRRGDLMTETSAANLLPSLLFNKKRYSLGATGRY 302

Query: 292 GVKFLGITSDCLCGLYVAEDI-VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            +       D +   Y+ +D+ +  E GE          E  L  +  +   +  +   +
Sbjct: 303 KLNKKLSLIDRITETYLGQDLEIKDENGEQLFLEKGTFIEHKLALLIQNNFNNGTLKTTE 362

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N  I    +              Y  ++  +  T  +   +F              
Sbjct: 363 IEGINPEILYAKLYTDPA---------YPYLKKSNKVTKLL---VFANRKKMDKGLSTLV 410

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G          D   D +H+   DIIA I    +L  G G  DD D++ N+R+ SVGE+
Sbjct: 411 IGN---------DPKCDAQHLIASDIIAAINYYFNLLEGIGQDDDADSMINKRIVSVGEL 461

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ  +GL ++E++ +ER+S+ + + + P+++ N K V + +  FF SS+LSQ  + +N
Sbjct: 462 MQNQLNVGLSKLEKTTRERMSAKEPEKITPKNITNNKLVSNQMKTFFNSSKLSQFMDQIN 521

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           +L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A
Sbjct: 522 ALAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYA 581

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            VN YGF++TPY KV +  V  ++VVYL+A +E    IAQ+ +++D++    +E +  R 
Sbjct: 582 SVNEYGFLQTPYFKVENSVVDYDNVVYLTAADEFGYNIAQSTATVDDNNRLIDETLTIRK 641

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
               IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA 
Sbjct: 642 NYTYILGKPSDVDLIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEAA 701

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FV TG E+ +AK S A   A++ G VE VD  +I IR+ +G LD        Y L  FQR
Sbjct: 702 FVATGNEADIAKFSAANFRARQEGKVEYVDGAKIKIRNNKGTLD-------TYNLKNFQR 754

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ+T ++Q+P++KVG EV + D++ DG S   G+LALG+N+LVAF  + GYN+ED++++
Sbjct: 755 SNQDTVIHQKPIIKVGQEVAKGDLLVDGSSFKDGELALGKNLLVAFSTYKGYNYEDAIVL 814

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+  +DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV 
Sbjct: 815 NERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVI 874

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R  
Sbjct: 875 PGDVLVGRVSPKGDDNPSREEKLLAAILGQRQLNVKDTSLKVKNGHNGTVIGVEILSREN 934

Query: 950 ID 951
            D
Sbjct: 935 KD 936



 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 164/583 (28%), Positives = 240/583 (41%), Gaps = 80/583 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L           +  +       + R   E     +   + ++       
Sbjct: 685  GSNMQRQAVPLLETEAAFVATGNEADIAKFSAANFRARQEGKVEYVDGAKIKI---RNNK 741

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +               I +  II VG EV  GD+LV   + K +  +   + LL A 
Sbjct: 742  GTLDTYNLKNFQRSNQDTVIHQKPIIKVGQEVAKGDLLVDGSSFK-DGELALGKNLLVAF 800

Query: 917  FGEKAVDVRDTS-LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ----IELLARDK 971
               K  +  D   L         +  + I  +    +  ++ + E  +    +   A   
Sbjct: 801  STYKGYNYEDAIVLNERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRH 860

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+         ++L G+ +  G     +   L + ++                  
Sbjct: 861  LDEHGIVLVGSEVIPGDVLVGRVSPKGDDNPSREEKLLAAILG----------------- 903

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR +       +            +I   +  D +  G+  +VKV +A+KR I+ GDKM+
Sbjct: 904  QRQLNVKDTSLKVKNGHNGTVIGVEILSRENKDLLEDGIDMIVKVSIAVKRKIRVGDKMS 963

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VS ILP EDM              P             E          G  
Sbjct: 964  GRHGNKGVVSVILPEEDM--------------PH-----------LE---------DGTP 989

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I  ++                           +++      V         G    TPVF
Sbjct: 990  IDVML--------------------NPQGVPSRMNIGQVLEVHLGMAARSLGCKFVTPVF 1029

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG  +EAI  ++  A L  SG+  L D +TGE FD PV+VG +YM KLNHMV DK++ARS
Sbjct: 1030 DGVKKEAIQDVISEAGLPLSGKQTLIDPITGEKFDNPVSVGVMYMFKLNHMVDDKMHARS 1089

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G YSL+TQQPLGGKS  GGQR GEME W I++YGAA VLQE+LT KSDD+VGR ++Y S
Sbjct: 1090 VGPYSLITQQPLGGKSQNGGQRFGEMETWAIESYGAANVLQEILTYKSDDIVGRNQLYTS 1149

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            +V G D    G PESFNVL  E+  LG+ +D+  +  +   + 
Sbjct: 1150 LVTGKDLPTPGIPESFNVLNYELNGLGMKLDITTANNEEDDEE 1192


>gi|15829017|ref|NP_326377.1| DNA-directed RNA polymerase subunit beta [Mycoplasma pulmonis UAB
           CTIP]
 gi|41017784|sp|Q98Q23|RPOB_MYCPU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|14089961|emb|CAC13719.1| DNA-DIRECTED RNA POLYMERASE BETA CHAIN (TRANSCRIPTASE BETA CHAIN)
           (RNA POLYMERASE BETA SUBUNIT) [Mycoplasma pulmonis]
          Length = 1216

 Score =  581 bits (1497), Expect = e-163,   Method: Composition-based stats.
 Identities = 329/992 (33%), Positives = 536/992 (54%), Gaps = 69/992 (6%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R+ + K    + + D++ +QK S+D FL          N+ ++A  +  +PI + 
Sbjct: 13  GQYTKRRDYSKTRFSLPLTDVLAIQKESFDWFL----------NKAIEATLRKYYPIKSS 62

Query: 69  SGAAMLEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           +    +++V  S   + P       V +   + ++Y+  L + L+  + +          
Sbjct: 63  NNKVEIKYVLGSKRIEKPLVTEQKAVKEAKQKGISYSARLYVKLQKHITE---------T 113

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +I    + + D+PLMT  G+F+I G ++++VSQL RSPG +F   K R   S  L    
Sbjct: 114 GEISFDEVILCDIPLMTSSGSFIINGFEKVIVSQLIRSPGAYFAQ-KTRDKQSDDLFNKV 172

Query: 183 RIIPDQGLWMDIE---FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
            ++P  G W++I+     + D + ++ID+ +   +T+FL + G   E +   F       
Sbjct: 173 EVLPRIGSWIEIKHKVTSNLDSVKIKIDKHKSFLLTTFLSSFGFTEESMYKLFGNSETLK 232

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDI---DTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
                        D++   K +   +            E+ + L S LL + K   +   
Sbjct: 233 NTLSKDKILGKNKDIVEIRKEAQENIFRIVRRGDRITKEASQNLISNLLFNEKRYNLSKT 292

Query: 297 GIT--------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
           G           D +   Y+A+D        I ++  D   E  +     + I +   + 
Sbjct: 293 GRYMLNRKLSLFDRIITTYLAQD--------IVLKNVDPTMEAKILYPKGTYITNDIAIE 344

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           + +      I+N  + D           +Y  +   +        ++     F S K   
Sbjct: 345 IQNAFKEGLIKNIDLKDYGITSD-----VYGKLLDTNPK-LKNRMNIIGIYIFKSKKAME 398

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               +  +   +  D      H+   DI+AII    +L    G  DD D+L N+R+ SVG
Sbjct: 399 KDGEKHFV---IGNDPTSVENHLLISDIVAIINYYFNLNENIGRDDDPDSLINKRIVSVG 455

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L NQ  +GLL+ME++ +E++SS +I  + P+++ N K + + +  FF SS+LSQ  + 
Sbjct: 456 ELLLNQLNIGLLKMEKNTREKMSSKEISRITPKNITNNKMIQNQIKTFFNSSKLSQFMDQ 515

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS I+  R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L +
Sbjct: 516 TNPLSEISTKRKITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLAT 575

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A+V+ YGF++TPY KV +G V  +  VYL+A EE NR  AQ++ S+DE+G  T+E V  
Sbjct: 576 YAKVDEYGFLQTPYFKVTNGIVDFSQPVYLTAHEEINRTFAQSSISIDENGKITDEQVIV 635

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +   +  +V  +++D+ID S KQ+ S+AAS IPFLEN+D+NR LMG NMQRQAVPLL AE
Sbjct: 636 KSNFDYNVVSPKEVDYIDVSSKQMTSLAASSIPFLENNDANRALMGSNMQRQAVPLLFAE 695

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   + +   G V  VD  +I I+    D       +  Y+L  F
Sbjct: 696 APLVATGIEADIAKFSPNNLKSTVDGEVVFVDGSQIKIK----DSASEKGSIKTYQLKTF 751

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +++NQ T ++Q P+VK+GD+V + D+I+D  S   G++ALG+N+LV F  W+GYN+ED++
Sbjct: 752 EKTNQGTVISQSPIVKMGDKVLKGDLISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAI 811

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DVFTSIHIEE  +  R +K G +++T DIPN S +  +++DE GI+ +G+E
Sbjct: 812 IVSERLVKDDVFTSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSE 871

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG+++PKG+  ++P EKLL  IF +K  + +DTSL+V +G  GTV+DV I +R
Sbjct: 872 VVTGDILVGRVSPKGDENISPAEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSR 931

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQVILD 979
              +       V  E+I+++ +    ++  + 
Sbjct: 932 ENGN-------VLEEEIDMMIKVYVAQKRKIK 956



 Score =  412 bits (1059), Expect = e-112,   Method: Composition-based stats.
 Identities = 161/508 (31%), Positives = 238/508 (46%), Gaps = 69/508 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L+   +   +  M   + +L         +  D  +     V   V 
Sbjct: 765  IVKMGDKVLKGD-LISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 823

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  +S + + +    +       +  LD N   R+   +   + + G  
Sbjct: 824  -TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRV 882

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K    +S    +E   +  +   + +EK       +K  ++ +   +E      I   
Sbjct: 883  SPKGDENISP---AEKLLNGIFNQKISNEKDTSL--KVKNGHQGTVIDVE------ILSR 931

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + G+ +   +  ++KV+VA KR I+ GDKMAGRHGNKG++SR+LP EDMP+L+DGTP+DI
Sbjct: 932  ENGNVLEEEIDMMIKVYVAQKRKIKVGDKMAGRHGNKGVISRVLPVEDMPYLEDGTPLDI 991

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  S + D     DI       +       
Sbjct: 992  ILNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVSPVFDGVKKADIMDALEEAKLPRTGKM 1051

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VFD                            
Sbjct: 1052 K----------------------------VFDPT-------------------------- 1057

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D  ++VG +YM KL+HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1058 TGEKIDNEISVGVMYMFKLSHMVDDKMHSRSIGPYSLITQQPLGGKSQNGGQRFGEMETW 1117

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +++YGAA +LQE+LT KSDD+ GR  +Y ++ +G    + G PESF+VL  E++ LG+ 
Sbjct: 1118 ALESYGAANILQEILTYKSDDIQGRNNLYSALTSGTKLPKPGVPESFSVLAYELRGLGIK 1177

Query: 1361 IDL-ENSRTKNSAKMEEIPDFN-KCELK 1386
            + + E    K     +E    N   ELK
Sbjct: 1178 LQIHEKEEEKQELPSQEYESLNLDQELK 1205


>gi|298264640|gb|ADI72783.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05617]
          Length = 472

 Score =  581 bits (1497), Expect = e-163,   Method: Composition-based stats.
 Identities = 316/473 (66%), Positives = 391/473 (82%), Gaps = 1/473 (0%)

Query: 41  LMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAV 100
           LM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA 
Sbjct: 1   LMVDEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAA 60

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
           PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRS
Sbjct: 61  PLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRS 120

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
           PG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMA
Sbjct: 121 PGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMA 180

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           LGMD EEILSTFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKL
Sbjct: 181 LGMDGEEILSTFYTQSLYQRDGDGWRVPFQP-DALKGQKAIADMIDADTGEVVVEAGKKL 239

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           T  L++ L+EKG+K L  T D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  + 
Sbjct: 240 TPRLVRQLQEKGLKALKATDDDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLPVILSAG 299

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             +IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LF
Sbjct: 300 FDEIPVLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALF 359

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           FD+++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLG
Sbjct: 360 FDAERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLG 419

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           NRRVRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV
Sbjct: 420 NRRVRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAV 472


>gi|298264634|gb|ADI72780.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05631]
          Length = 473

 Score =  580 bits (1496), Expect = e-163,   Method: Composition-based stats.
 Identities = 313/474 (66%), Positives = 390/474 (82%), Gaps = 1/474 (0%)

Query: 41  LMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAV 100
           LM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA 
Sbjct: 1   LMVDEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAA 60

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
           PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRS
Sbjct: 61  PLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRS 120

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
           PG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS +MA
Sbjct: 121 PGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLMMA 180

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           LGMD EEIL TFY K +Y + GD W  P    D + G K  + ++D D+GE V+E+GKKL
Sbjct: 181 LGMDGEEILDTFYTKSLYQRDGDGWRVPFQP-DALKGQKALADMIDADSGEVVVEAGKKL 239

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           T  LL+ L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  + 
Sbjct: 240 TPRLLRQLQDKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILAAG 299

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             +IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LF
Sbjct: 300 FDEIPVLDIDHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALF 359

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           FD+++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLG
Sbjct: 360 FDAERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLG 419

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           NRRVRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV 
Sbjct: 420 NRRVRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVR 473


>gi|298264636|gb|ADI72781.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05672]
          Length = 472

 Score =  580 bits (1496), Expect = e-163,   Method: Composition-based stats.
 Identities = 312/472 (66%), Positives = 388/472 (82%), Gaps = 1/472 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK
Sbjct: 2   DEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLK 61

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 62  VTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 121

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGM
Sbjct: 122 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGM 181

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEIL TFY K +Y + GD W  P    D + G K  + ++D D+GE V+E+GKKLT  
Sbjct: 182 DGEEILDTFYTKSLYQRDGDGWRVPFQP-DALKGQKALADMIDADSGEVVVEAGKKLTPR 240

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           LL+ L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +
Sbjct: 241 LLRQLQDKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILAAGFDE 300

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+
Sbjct: 301 IPVLDIDHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDA 360

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRR
Sbjct: 361 ERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRR 420

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           VRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV +
Sbjct: 421 VRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVRD 472


>gi|313665004|ref|YP_004046875.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma leachii PG50]
 gi|312949953|gb|ADR24549.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma leachii PG50]
          Length = 1287

 Score =  580 bits (1495), Expect = e-163,   Method: Composition-based stats.
 Identities = 342/856 (39%), Positives = 523/856 (61%), Gaps = 72/856 (8%)

Query: 108 LIVFDVDEFTGAKSIKDI---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
           LI  D+ E      I ++   K   +++GD PLMT+ GTF+I G Q+++VSQL RSPG +
Sbjct: 159 LIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAY 218

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI-------IHVRIDRRRKVPVTSF 217
           F+ +      +G+++Y   IIP +G W++ E DSK I       ++V+ID+ RK   TS 
Sbjct: 219 FNKEL--NRKTGEMIYFADIIPSRGTWLEYETDSKKIGNDAINPLYVKIDKSRKTTATSL 276

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIES 276
           L+A G+  ++IL+ F    V  +        +    +    +V      I  GE    E 
Sbjct: 277 LLAFGISKDDILNIFDNDEVLVETLQQDSI-IGDFKIDWSNQVQEIYKKIRQGETATSEG 335

Query: 277 GKKLTSGLLKSLKEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             K  + +L + ++  +   G           + +    +AEDI++     +  + G  +
Sbjct: 336 ASKFINSILFNKRKYDLTKAGRFKLKQKLSIKNRILNRVIAEDILDANNNVLIAK-GTEV 394

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            + ++++I +   +DI  + +  +++    R               +   RV +  ++ T
Sbjct: 395 TKNNIQKISNILDQDIMSIDLKYLSDIPGTRK--------------VQKIRVYKDSELKT 440

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            +                             + L +  +   I   DI++ +  L++L+ 
Sbjct: 441 DTT--------------------------CLIGLTSSSNEEFITVADILSTVSYLLNLKY 474

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
             G IDDIDNLGNRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP
Sbjct: 475 NIGEIDDIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKP 534

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + + + EFF  SQLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGR
Sbjct: 535 LTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGR 594

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYI 627
           ICP ET EG NIGL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  I
Sbjct: 595 ICPIETPEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFII 654

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQ+N + DE+G   +E++  R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+
Sbjct: 655 AQSNVNQDENGKILDEIIVSRFNGDDYMARVEEIHYIDVSPKQIVSVATSGIPFLENDDA 714

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I    
Sbjct: 715 NRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI---- 770

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               +    SG+  Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+
Sbjct: 771 ----ITDGESGIRTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAI 826

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N++VAF  ++GYNFED++++SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN
Sbjct: 827 GQNVVVAFSTYNGYNFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPN 886

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +SE+  +++D  GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D 
Sbjct: 887 MSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDN 946

Query: 928 SLRVPSGVSGTVVDVR 943
           SLRVP+G  G V  ++
Sbjct: 947 SLRVPNGGEGIVQSIK 962



 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 154/520 (29%), Positives = 235/520 (45%), Gaps = 84/520 (16%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 795  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 849

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 850  ERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 909

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 910  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 962

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 963  -----RFKAKSASNLDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPV 1017

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDM              P             E                   D   N    
Sbjct: 1018 EDM--------------PH-----------LE--------------DGTPVDIILNPQGV 1038

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P R  + +++                +       K    V TPVF+G +E+ +  ++  A
Sbjct: 1039 PSRMNIGQIL---------------EIHLGMAAKKLNQKVITPVFEGLNEKELEEIMIEA 1083

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +   G+  L DG TGEPFD+P+ VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK
Sbjct: 1084 GMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHTRNVGPYSLITQQPLGGK 1143

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PES
Sbjct: 1144 AQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGIPES 1203

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            FNVL KE+  LG ++ + +   + S        ++K + +
Sbjct: 1204 FNVLSKEIMGLGFNMYMIDETGEKSVINA----YDKTDFE 1239



 Score = 98.6 bits (244), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 26/119 (21%), Positives = 48/119 (40%), Gaps = 10/119 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             FPI +F G+++L   ++ F  P+  V         Y  P+   L+L V   +E    
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKE 109


>gi|295984320|gb|ADG63628.1| RpoB [Sinorhizobium sp. CCBAU 05684]
          Length = 470

 Score =  580 bits (1494), Expect = e-163,   Method: Composition-based stats.
 Identities = 315/470 (67%), Positives = 387/470 (82%), Gaps = 1/470 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 1   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 60

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 61  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 120

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 121 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 180

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY K +Y + GD W  P    D + G K  S ++D +TGE V+E+GKKLT  LL
Sbjct: 181 EEILETFYTKSLYQRDGDGWRVPFQP-DALKGQKAVSEMIDAETGEVVVEAGKKLTPRLL 239

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 240 RQLQEKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILEAGFDEIP 299

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++
Sbjct: 300 VLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAER 359

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVR
Sbjct: 360 YDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVR 419

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           SVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV E
Sbjct: 420 SVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVRE 469


>gi|301321056|gb|ADK69699.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 1291

 Score =  580 bits (1494), Expect = e-163,   Method: Composition-based stats.
 Identities = 340/856 (39%), Positives = 522/856 (60%), Gaps = 72/856 (8%)

Query: 108 LIVFDVDEFTGAKSIKDI---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
           LI  D+ E      I ++   K   +++GD PLMT+ GTF+I G Q+++VSQL RSPG +
Sbjct: 159 LIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAY 218

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI-------IHVRIDRRRKVPVTSF 217
           F+ +      +G+++Y   IIP +G W++ E DSK I       ++V+ID+ RK   TS 
Sbjct: 219 FNKEL--NRKTGEMIYFADIIPSRGTWLEYETDSKKIGNDAINPLYVKIDKSRKTTATSL 276

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIES 276
           L+A G+  ++IL+ F    V  +        +    +    +V      I  GE    E 
Sbjct: 277 LLAFGISKDDILNIFDNDEVLVETLQQDSI-IGDFKIDWSNQVQEIYKKITQGETATSEG 335

Query: 277 GKKLTSGLLKSLKEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             K  + +L   ++  +   G           + +    +AEDIV+     +  +    +
Sbjct: 336 ASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNRILNRVIAEDIVDANNNVLIAKD-TEV 394

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           ++ ++++I     +D+  + ++ +++    R               +   +V +  ++ T
Sbjct: 395 NKHNIKQISEILDQDVMSIDLNYLSDIPGTRK--------------VQKIKVYKDSELKT 440

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            +                             + L +  +   I   DI++ +  L++L+ 
Sbjct: 441 DTT--------------------------CLIGLTSSSNEEFITVADILSTVSYLLNLKY 474

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
             G IDDIDNLGNRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP
Sbjct: 475 NIGEIDDIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKP 534

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + + + EFF  SQLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGR
Sbjct: 535 LTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGR 594

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYI 627
           ICP ET EG NIGL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  I
Sbjct: 595 ICPIETPEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFII 654

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQ+N + DE+G   +E++  R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+
Sbjct: 655 AQSNVNQDENGKILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDA 714

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I    
Sbjct: 715 NRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI---- 770

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               +    SG+  Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+
Sbjct: 771 ----ITDGESGIRTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAI 826

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N++VAF  ++GYNFED++++SER+V +D FTS HI+E+ +  R+TK G EE+TR+IPN
Sbjct: 827 GQNVVVAFSTYNGYNFEDAIVMSERIVIDDRFTSTHIDEYTLEVRNTKQGQEEVTREIPN 886

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +SE+  +++D  GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D 
Sbjct: 887 MSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDN 946

Query: 928 SLRVPSGVSGTVVDVR 943
           SLRVP+G  G V  ++
Sbjct: 947 SLRVPNGGEGIVQSIK 962



 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 154/508 (30%), Positives = 231/508 (45%), Gaps = 80/508 (15%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 795  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 849

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 850  ERIVIDDRFTSTHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 909

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 910  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 962

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 963  -----RFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPV 1017

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDM              P             E                   D   N    
Sbjct: 1018 EDM--------------PH-----------LE--------------DGTPVDIILNPQGV 1038

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P R  + +++                +       K    V TPVF+G +E+ +  ++  A
Sbjct: 1039 PSRMNIGQIL---------------EIHLGMAAKKLNQKVITPVFEGLNEKELEEIMAEA 1083

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +   G+  L DG TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK
Sbjct: 1084 GMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGK 1143

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PES
Sbjct: 1144 AQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKKIPEPGIPES 1203

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            FNVL KE+  LG ++ + +   + S   
Sbjct: 1204 FNVLSKEIMGLGFNMYMIDETGEKSVIN 1231



 Score = 97.8 bits (242), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 26/119 (21%), Positives = 48/119 (40%), Gaps = 10/119 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             FPI +F G+++L   ++ F  P+  V         Y  P+   L+L V   +E    
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAKEESKIYDAPIYANLKLSVNKTEEIQKE 109


>gi|295984318|gb|ADG63627.1| RpoB [Sinorhizobium sp. CCBAU 05640]
 gi|295984322|gb|ADG63629.1| RpoB [Sinorhizobium sp. CCBAU 05646]
 gi|295984324|gb|ADG63630.1| RpoB [Sinorhizobium sp. CCBAU 05606]
          Length = 470

 Score =  579 bits (1493), Expect = e-162,   Method: Composition-based stats.
 Identities = 314/471 (66%), Positives = 386/471 (81%), Gaps = 1/471 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK
Sbjct: 1   GEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEIL TFY K +Y + GD W  P    D + G K  S ++D +TGE V+E+GKKLT  
Sbjct: 181 DGEEILETFYTKSLYQRDGDGWRVPFQP-DALKGQKAVSEMIDAETGEVVVEAGKKLTPR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           LL+ L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +
Sbjct: 240 LLRQLQEKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILEAGFDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+
Sbjct: 300 IPVLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDA 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           VRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV 
Sbjct: 420 VRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVR 470


>gi|83319487|ref|YP_424065.1| DNA-directed RNA polymerase subunit beta [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
 gi|109904235|sp|Q2ST48|RPOB_MYCCT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|83283373|gb|ABC01305.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
          Length = 1287

 Score =  579 bits (1493), Expect = e-162,   Method: Composition-based stats.
 Identities = 341/856 (39%), Positives = 519/856 (60%), Gaps = 72/856 (8%)

Query: 108 LIVFDVDEFTGAKSIKDI---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
           LI  D+ E      I ++   K   +++GD PLMT+ GTF+I G Q+++VSQL RSPG +
Sbjct: 159 LIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAY 218

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI-------IHVRIDRRRKVPVTSF 217
           F+ +      +G+++Y   IIP +G W++ E DSK I       ++V+ID+ RK   TS 
Sbjct: 219 FNKEL--NRKTGEMIYFADIIPSRGTWLEYETDSKKIGSDAINPLYVKIDKSRKTTATSL 276

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIES 276
           L+A G+  ++IL+ F    V  +        +    +    +V      I  GE    E 
Sbjct: 277 LLAFGISKDDILNIFDNDEVLVETLQQDSI-IGDFKIDWSNQVQEIYKKIRQGETATSEG 335

Query: 277 GKKLTSGLLKSLKEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             K  + +L   ++  +   G           + +    +AEDI++     +  +    +
Sbjct: 336 ASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNRILNKVIAEDILDANNNVLIAKD-TEV 394

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            + +++EI     +D+  + +  +++    R               +   RV +  ++ T
Sbjct: 395 TKNNIQEISKILDQDVMSIDLKYLSDIPGNRK--------------VQKIRVYKDSELKT 440

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            +                             + L    +   I   DI++ +  L++L+ 
Sbjct: 441 DTT--------------------------CLIGLTNSSNEEFITVADILSTVSYLLNLKY 474

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
             G IDDIDNLGNRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP
Sbjct: 475 NIGEIDDIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKP 534

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + + + EFF  SQLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGR
Sbjct: 535 LTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGR 594

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYI 627
           ICP ET EG NIGL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  I
Sbjct: 595 ICPIETPEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFII 654

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQ+N + DE+G   +E++  R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+
Sbjct: 655 AQSNVNQDENGKILDEIIVSRFNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDA 714

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I    
Sbjct: 715 NRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI---- 770

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               +    SG+  Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+
Sbjct: 771 ----ITDGESGIRTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAI 826

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N++VAF  ++GYNFED++++SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN
Sbjct: 827 GQNVVVAFSTYNGYNFEDAIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPN 886

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +SE+  +++D  GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D 
Sbjct: 887 MSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDN 946

Query: 928 SLRVPSGVSGTVVDVR 943
           SLRVP+G  G V  ++
Sbjct: 947 SLRVPNGGEGIVQSIK 962



 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 240/1106 (21%), Positives = 404/1106 (36%), Gaps = 142/1106 (12%)

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              +  D +N    +I            L     S+   + I   D V      +++++ D
Sbjct: 251  KKIGSDAINPLYVKIDKSRKTTATS-LLLAFGISKDDILNIFDNDEVLVETLQQDSIIGD 309

Query: 366  KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
               D  + + +IY+ +R G+ +T   A    N + FD  KYDL+  GR K+  +L++   
Sbjct: 310  FKIDWSNQVQEIYKKIRQGETATSEGASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNR 369

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
               + I ++ + A   +L+         +  +         +   LK    +   R  + 
Sbjct: 370  ILNKVIAEDILDANNNVLIAKDTEVTKNNIQEISKILDQDVMSIDLKYLSDIPGNRKVQK 429

Query: 486  IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            I+    S           +        +      S +S L     ++  I          
Sbjct: 430  IRVYKDSELKTDTTCLIGLTNSSNEEFITVADILSTVSYLLNLKYNIGEID--------- 480

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                      +  R V     G +   +   G N    +     A  + Y        KV
Sbjct: 481  ------DIDNLGNRRVRT--VGELLQNQFRMGLNRIDKNVKEKLATSDLY--------KV 524

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEILVPREKID 662
                + N    L+A+  E   ++Q +  +D+       T +          +   R  ++
Sbjct: 525  KTSTIINA-KPLTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGPGGLSRDRAGLE 583

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
              D  P     I     P   N      L       +    +      V  G+       
Sbjct: 584  VRDVHPSHYGRICPIETPEGPNIGLINNLSTYARVNE-YGFITTPYRKVINGIIQNDQVE 642

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ---RSNQNTCVNQR 779
               A   K   I       +  +   E         V  +    +           V+ +
Sbjct: 643  YLTADQEKNFIIA------QSNVNQDENGKILDEIIVSRFNGDDYMAKVEEIHYIDVSPK 696

Query: 780  PLVKV---GDEVRRNDIIAD---GPSTDLGDLALGRNMLVAFMPWHGY----NFEDSMLI 829
             +V V   G     ND       G +     + L +           +    +  ++++ 
Sbjct: 697  QIVSVATSGIPFLENDDANRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVA 756

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
             E  + + V +   I + E   R   L   E + +  +        + +  I+ VG  V 
Sbjct: 757  KEDAIVKYVDSKTIITDGESGIRTYILSDYERSNNGTS--------LTQSPIVKVGDVVK 808

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             G+I+    +   +  +   + ++ A       +  D  +         V+D R  + H 
Sbjct: 809  KGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----SERIVIDDRFTSIHI 863

Query: 950  IDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
             +      + ++ Q E+           +   D + I+      ++ ++L G+    G  
Sbjct: 864  DEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQV 923

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                   L   +  E  R           +V    E +    +        RFK K    
Sbjct: 924  QLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--------RFKAKSALN 971

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP EDM           
Sbjct: 972  PDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPIEDM----------- 1020

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
               P             E                   D   N    P R  + +++    
Sbjct: 1021 ---PH-----------LE--------------DGTPVDIILNPQGVPSRMNIGQIL---- 1048

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                        +       K    V TPVF+G +E+ +  ++  A +   G+  L DG 
Sbjct: 1049 -----------EIHLGMAAKKLNQKVITPVFEGLNEKELEEIMAEAGMTNYGKVTLIDGQ 1097

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR GEMEVW
Sbjct: 1098 TGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGKAQNGGQRFGEMEVW 1157

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PESFNVL KE+  LG +
Sbjct: 1158 ALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKRIPEPGIPESFNVLSKEIMGLGFN 1217

Query: 1361 IDLENSRTKNSAKMEEIPDFNKCELK 1386
            + + +   + SA       ++K + +
Sbjct: 1218 MYMIDETGEKSAINA----YDKKDFE 1239



 Score = 98.6 bits (244), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 26/119 (21%), Positives = 48/119 (40%), Gaps = 10/119 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             FPI +F G+++L   ++ F  P+  V         Y  P+   L+L V   +E    
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKE 109


>gi|295984316|gb|ADG63626.1| RpoB [Sinorhizobium sp. CCBAU 05638]
          Length = 472

 Score =  579 bits (1493), Expect = e-162,   Method: Composition-based stats.
 Identities = 314/471 (66%), Positives = 386/471 (81%), Gaps = 1/471 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK
Sbjct: 3   GEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLK 62

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 63  VTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 122

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGM
Sbjct: 123 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGM 182

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEIL TFY K +Y + GD W  P    D + G K  S ++D +TGE V+E+GKKLT  
Sbjct: 183 DGEEILETFYTKSLYQRDGDGWRVPFQP-DALKGQKAVSEMIDAETGEVVVEAGKKLTPR 241

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           LL+ L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +
Sbjct: 242 LLRQLQEKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILEAGFDE 301

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+
Sbjct: 302 IPVLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDA 361

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRR
Sbjct: 362 ERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRR 421

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           VRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV 
Sbjct: 422 VRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVR 472


>gi|148377875|ref|YP_001256751.1| DNA-directed RNA polymerase subunit beta [Mycoplasma agalactiae
           PG2]
 gi|148291921|emb|CAL59312.1| DNA directed RNA polymerase beta chain [Mycoplasma agalactiae PG2]
          Length = 1211

 Score =  579 bits (1493), Expect = e-162,   Method: Composition-based stats.
 Identities = 328/962 (34%), Positives = 520/962 (54%), Gaps = 71/962 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R+ +       ++PD + + K S++ F             G++   +  +PI + +  
Sbjct: 24  TERRDYSATKVTWEVPDFLNMSKESFEWF----------KKSGIEEILREHYPIVSSNKK 73

Query: 72  AMLEFV--SYEFDPP--KFD-VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
             LE++  S   + P  ++D + +   + + YA  L    ++                +K
Sbjct: 74  VSLEYIHNSARLEVPPKEYDAIIEAKAKGINYAAKLFAKFKVTSDK----------GVVK 123

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  + +G++PLM   G+F+I G ++++VSQL RSP  +F     R   S  L     I+P
Sbjct: 124 DDEVLLGEVPLMNSGGSFIINGSEKVIVSQLIRSPSAYFGCGV-RNKQSDDLFNKLEILP 182

Query: 187 DQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQ 240
             G W++I       + D + ++ID+ + + +  FL ALG++ E I S F   P++  + 
Sbjct: 183 RLGSWVEISHKVTTKNPDSVKIKIDKNKNINLAVFLGALGLNEENIHSLFGNSPELEETL 242

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEK-------- 291
             D           ++          I  G+ + E S   L   LL + K          
Sbjct: 243 LRDKSLKSSEDPMTVIQNCREILFRTIRRGDLMTETSAANLLPSLLFNKKRYSLGATGRY 302

Query: 292 GVKFLGITSDCLCGLYVAEDI-VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            +       D +   Y+ +D+ +  E GE+         E  L  +      +  +   +
Sbjct: 303 KLNKKLSLIDRITETYLGQDLEIKDENGEVMFLEKGTFIEHKLALLIQENFNNGALKTTE 362

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N  I    +         A   + +  R   +        +F              
Sbjct: 363 IEGINPEILYAKL-----YNDPAYPYLKKSNRVAKLL-------VFANRKKMDKGLATLV 410

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G          D   D +H+   DIIA I    +L  G G  DD D++ N+R+ SVGE+
Sbjct: 411 IGN---------DPKCDAQHLIASDIIAAINYYFNLLEGIGQDDDADSMINKRIVSVGEL 461

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ  +GL ++E++ +ER+S+ + + + P+++ N K V + +  FF SS+LSQ  + +N
Sbjct: 462 MQNQLNVGLSKLEKTTRERMSAKEPEKITPKNITNNKLVSNQMKTFFNSSKLSQFMDQIN 521

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           +L+ I++ RR++ LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A
Sbjct: 522 ALAEISNERRITYLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYA 581

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            VN YGF++TPY KV +  V  +DVVYL+A +E    IAQ+ +++D+D    +E +  R 
Sbjct: 582 SVNEYGFLQTPYFKVNNSVVDYDDVVYLTAADEFGYNIAQSTATVDDDNRLVDETLTIRK 641

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
               IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA 
Sbjct: 642 NYTYILGKPGDVDLIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEAA 701

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FV TG E+ +AK S A   A+  G VE VD  +I IR+ +G LD        Y L  FQR
Sbjct: 702 FVATGNEADIAKFSAANFRARNEGKVEYVDGAKIKIRNNKGTLD-------TYSLKNFQR 754

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ+T ++Q+P++KVG +V + D++ DG S   G+LALG+N+LVAF  + GYN+ED++++
Sbjct: 755 SNQDTVIHQKPIIKVGQDVAKGDLLVDGSSFKDGELALGKNLLVAFSTYKGYNYEDAIVL 814

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+  +DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV 
Sbjct: 815 NERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVI 874

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R  
Sbjct: 875 PGDVLVGRVSPKGDDNPSREEKLLAAILGQRQLNVKDTSLKVKNGHNGTVIGVEILSREN 934

Query: 950 ID 951
            D
Sbjct: 935 KD 936



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 157/493 (31%), Positives = 221/493 (44%), Gaps = 77/493 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS-LRVPSGVSGTV 939
            II VG +V  GD+LV   + K +  +   + LL A    K  +  D   L         +
Sbjct: 766  IIKVGQDVAKGDLLVDGSSFK-DGELALGKNLLVAFSTYKGYNYEDAIVLNERLAKKDVL 824

Query: 940  VDVRIFNRHGIDKNERSISVEREQ----IELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
              + I  +    +  ++ + E  +    +   A    DE  I+         ++L G+ +
Sbjct: 825  TSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVIPGDVLVGRVS 884

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G     +   L + ++                  QR +       +            
Sbjct: 885  PKGDDNPSREEKLLAAILG-----------------QRQLNVKDTSLKVKNGHNGTVIGV 927

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +I   +  D +  G+  +VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM      
Sbjct: 928  EILSRENKDLLEDGIDMIVKVSIAVKRKIRVGDKMSGRHGNKGVVSVILPEEDM------ 981

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                    P             E          G  I  ++                   
Sbjct: 982  --------PH-----------LE---------DGTPIDVML------------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                    +++      V         G    TPVFDG  +EAI  ++  A L  SG+  
Sbjct: 995  -NPQGVPSRMNIGQVLEVHLGMAARSLGCKFVTPVFDGVKKEAIQDVISEAGLPLSGKQT 1053

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L D +TGE FD PV+VG +YM KLNHMV DK+YARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 1054 LIDPITGEKFDNPVSVGVMYMFKLNHMVDDKMYARSVGPYSLITQQPLGGKSQNGGQRFG 1113

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EME W I++YGA+ VLQE+LT KSDD+VGR ++Y S+V G D    G PESFNVL  E+ 
Sbjct: 1114 EMETWAIESYGASNVLQEILTYKSDDIVGRNQLYTSLVTGKDLPTPGIPESFNVLNYELN 1173

Query: 1356 ALGLSIDLENSRT 1368
             LG+ +D+  +  
Sbjct: 1174 GLGMKLDITTANN 1186


>gi|295984314|gb|ADG63625.1| RpoB [Ensifer mexicanus]
          Length = 475

 Score =  579 bits (1492), Expect = e-162,   Method: Composition-based stats.
 Identities = 314/475 (66%), Positives = 390/475 (82%), Gaps = 1/475 (0%)

Query: 41  LMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAV 100
           LM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA 
Sbjct: 1   LMVDEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAA 60

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
           PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRS
Sbjct: 61  PLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRS 120

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
           PG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMA
Sbjct: 121 PGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKLPVTSLLMA 180

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           LGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E+GKKL
Sbjct: 181 LGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITDMIDADTGEVVVEAGKKL 239

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           T  LL+ L+EKG+K L  T D L G Y+AED+VN  TGEIY+EAGD IDEK+L  I  + 
Sbjct: 240 TPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNYGTGEIYLEAGDEIDEKTLPVILSAG 299

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             +IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LF
Sbjct: 300 FDEIPVLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNTLF 359

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           FD+++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLG
Sbjct: 360 FDAERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLG 419

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           NRRVRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV +
Sbjct: 420 NRRVRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVRD 474


>gi|193216590|ref|YP_001999832.1| DNA-directed RNA polymerase subunit beta [Mycoplasma arthritidis
           158L3-1]
 gi|193001913|gb|ACF07128.1| DNA-directed RNA polymerase beta subunit [Mycoplasma arthritidis
           158L3-1]
          Length = 1197

 Score =  579 bits (1492), Expect = e-162,   Method: Composition-based stats.
 Identities = 326/1000 (32%), Positives = 525/1000 (52%), Gaps = 83/1000 (8%)

Query: 1   MAKGVVFNGLG----RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
           MA    +          R+ +  + +  + PD +E+Q+ S   FL          N G++
Sbjct: 1   MAMETKYELRKFGPITERRDYSLSQKKFETPDYLEMQRLSVVKFL----------NTGIE 50

Query: 57  AAFKSVFPITAFSGAAMLEFV--SYEFDPPKFDVDDC----LWRDLTYAVPLKITLRLIV 110
              + ++PI   +G   +E++  +  F+ PK    +C      +  +Y   LK  LR   
Sbjct: 51  EELREIYPIE-TAGKVRIEYILNTAHFEIPKKSEFECIKEAKQKGSSYVGKLKAKLRQT- 108

Query: 111 FDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
                        ++++  +   ++P+MT  G+F+I G ++++VSQL RS G +F     
Sbjct: 109 --------NIETGEVEDAEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGVGV- 159

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSE 226
           R   +  L     IIP  G W++I         D I V ID+ +   +T  L ALG    
Sbjct: 160 RNKQANDLFNKVEIIPQIGSWLEIYHKVTSNVVDPIKVHIDKNKSFYLTVLLKALGFSKN 219

Query: 227 EILSTFYPKIVYSQR-GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            I   F       +          +A D +  A+ +   +         +S + L   +L
Sbjct: 220 GIYEMFGQSKELEETFKKDKILGETAEDTIREAQETIYRLIRKGDRMTADSARNLIPSIL 279

Query: 286 KSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
            + K   +   G  +        + +   Y+AED++  +TGE+  E    I     ++I 
Sbjct: 280 FNAKRYNLSETGRFTLNRKLNVIERIANSYLAEDLL-TKTGEVKYEKDTFITWDIAKQIH 338

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                 I  ++     +     + +    N+  +  L      + P +            
Sbjct: 339 ADFEEGILAMWRLPDIDKEAYGSQIDNPGNESLETRLYAPRVWIYPTE------------ 386

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                                 L  D       +   D+IA I    +L +  G  DD D
Sbjct: 387 -----------KDKLNDHSVEVLGNDPTATETFLLIPDLIATISYYFNLIDKVGFDDDPD 435

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           +L N+R+ ++GE+L+NQ+R+GL+++E++ KERIS+ DID + P+++ N +P+ +    FF
Sbjct: 436 SLVNKRIVTIGELLQNQFRVGLIKLEKNTKERISAKDIDKITPKNVTNNRPIFNQFKSFF 495

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +S+LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG
Sbjct: 496 NTSKLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEG 555

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDE 636
            NIGL+ ++ SFA+++ +GFI++PY +V + K+  ++ +YL+A+EE     AQ+  ++ +
Sbjct: 556 QNIGLILNMASFAQIDKHGFIQSPYFRVKNRKIDFSEAIYLTAIEESGYTFAQSTINIKD 615

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           D    ++ V  R   E I V  E++DF+  + +Q+ SIAAS IPFLENDD+ R LMG NM
Sbjct: 616 D-YIVDDRVLVRYDNEYIEVNAEEVDFVGVNNRQITSIAASAIPFLENDDAYRALMGSNM 674

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVP++  EAP V TG+E+ +AK S     A + G+V  VDA  I +++        +
Sbjct: 675 QRQAVPIISPEAPLVATGVEADIAKYSSTNTRASKDGVVTYVDANVIKVQT------AGS 728

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           S V+ Y L  F+RSNQ T ++Q PLVKVG E++  D++ DGPS   G+LALG+N+LV F 
Sbjct: 729 SKVESYHLRTFERSNQGTLIHQVPLVKVGQEIKAGDLLVDGPSMKNGELALGKNILVGFT 788

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W GYN+ED+++ISER+V +DV+TSIHIEE  +  R +K G + +T DIPN S    + +
Sbjct: 789 TWKGYNYEDAVVISERLVKDDVYTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFL 848

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           +E GI+ +G+EV+ GDILVG+ +PKGE   TPEE+L+ AIFG+K    +DTSL+V  G +
Sbjct: 849 NEDGIVRIGSEVSAGDILVGRTSPKGEENPTPEERLMAAIFGQKTASRKDTSLKVKHGHN 908

Query: 937 GTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           GTVV V I +R        GI+K  +    ++ +I++  +
Sbjct: 909 GTVVAVEILSRELGDQLEDGIEKIVKVSIAQKRKIKVGDK 948



 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 157/499 (31%), Positives = 234/499 (46%), Gaps = 69/499 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   + K    +   + +L      K  +  D  +     V   V 
Sbjct: 753  LVKVGQEIKAGDLLVDGPSMKN-GELALGKNILVGFTTWKGYNYEDAVVISERLVKDDV- 810

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I     + +   S + E      +    +  +  L+ +   R+   +   + + G  
Sbjct: 811  YTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFLNEDGIVRIGSEVSAGDILVGRT 870

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +       + + Q     +     V+        +  IL           
Sbjct: 871  SPKGEENPTPE--ERLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEILSREL------- 921

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP E+MP+L+DGTP+D+
Sbjct: 922  --GDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPVEEMPYLEDGTPLDM 979

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG+A   L  K  + + D   +  I  +           +
Sbjct: 980  VLNPQGVPSRMNIGQVLELHLGFAARKLNTKFVTPVFDGITHNQIKEILEEANLDSSGKT 1039

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SGQ       
Sbjct: 1040 VV-----------------------------------------------YSGQ------- 1045

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1046 TGEKLDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1105

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             I++YGA  VLQE+LT KSD+++GR ++Y S+   +   + G PESFNVL  E++ LG  
Sbjct: 1106 AIESYGATNVLQELLTYKSDNIIGRNQLYNSLATNSRLPKAGMPESFNVLAYELRGLG-- 1163

Query: 1361 IDLENSRTKNSAKMEEIPD 1379
            I LE  +   S +++E+ +
Sbjct: 1164 IKLEVHKQNESGELDEVDN 1182


>gi|298264638|gb|ADI72782.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05600]
          Length = 466

 Score =  578 bits (1491), Expect = e-162,   Method: Composition-based stats.
 Identities = 310/466 (66%), Positives = 382/466 (81%), Gaps = 1/466 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 1   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 60

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 61  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 120

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 121 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 180

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY   +Y + GD W  P    D + G K  + ++D DTGE V+E GKKLT  LL
Sbjct: 181 EEILDTFYTSSLYQRDGDGWRVPFQP-DALKGQKAVTDMIDADTGEVVVEGGKKLTPRLL 239

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 240 RQLQDKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILEAGFDEIP 299

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++
Sbjct: 300 VLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAER 359

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVR
Sbjct: 360 YDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVR 419

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
           SVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +
Sbjct: 420 SVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAA 465


>gi|240047793|ref|YP_002961181.1| DNA-directed RNA polymerase subunit beta [Mycoplasma conjunctivae
           HRC/581]
 gi|239985365|emb|CAT05378.1| DNA-directed RNA polymerase subunit beta [Mycoplasma conjunctivae]
          Length = 1217

 Score =  578 bits (1490), Expect = e-162,   Method: Composition-based stats.
 Identities = 325/963 (33%), Positives = 518/963 (53%), Gaps = 76/963 (7%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G+   R+F+ K    ++ P+ ++ Q+ S+  FL           +G+  AF  +FP+ + 
Sbjct: 11  GISTQRRFYAKTKHTLETPNFLDSQRESFKWFL----------EQGITEAFNKIFPVFST 60

Query: 69  SGAAMLEF--VSYEFDPPKF---DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           +G   ++F   S E + P      + +   +  +Y   +  TL  +  +           
Sbjct: 61  NGKFEIQFQPGSIEIERPTNEYESIREAKQKGKSYVCKVYATLIKVHVED---------G 111

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +++   I +G++P MT  GTF+I G +++V+SQL RSPG+ F  +  R   +  L     
Sbjct: 112 EVETDRILLGEIPYMTHGGTFIINGFEKVVISQLIRSPGVCF-RENVRNRQADDLFNKVE 170

Query: 184 IIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYS 239
           IIP  GLW++I         D + +RI++ + +P+ +FL +LG  +E I   F       
Sbjct: 171 IIPQLGLWIEIFHKVTGHTVDTVKIRINKHKNIPLIAFLKSLGFTNETIRKYFGNSEELL 230

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG-KKLTSGLLKSLKEKGVKFLGI 298
           +         +  +L    ++      I   +++ E G K L   L+ S +   +   G 
Sbjct: 231 ESLKKHKLEKTEDNLEHIYRI------IRKDDRITEEGLKNLIPSLIFSERRYNLSATGR 284

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     D +   Y+AED+ + +   +Y +   +  E +L+     E    P+  V+
Sbjct: 285 YMLNTKLNLIDRIIQTYLAEDLYDQDGQLLYAQGTFINREMALDIQSKFEDGTFPMSQVE 344

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++ + Y                       ++       +   ++     + + +     
Sbjct: 345 GIDQSVYGN--------------------QLKISRNRDLAKRINIIQVKVWPNKRSM--- 381

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             +++  + +  D       +   D+IAI+    ++ +  G  DD D+L N+R+ SVGE+
Sbjct: 382 TQKLEPVLVIGNDPHSTETILLISDVIAIVSYYFNIIHNIGKNDDPDSLINKRIVSVGEL 441

Query: 471 LKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           L+NQ+ + L ++E++ KE+  S  + D +  + +IN KP+ +    FF SS+LSQ  E +
Sbjct: 442 LQNQFLIALSKIEKNTKEKISSKGESDKITVKTVINNKPIYNQFKNFFNSSKLSQFMEQI 501

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + + F
Sbjct: 502 NPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHATHYGRICPVETPEGQNIGLILNFSVF 561

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+ N YGFI TPY KV +  V  +   +L+A EE     AQ++ +++E      + V  R
Sbjct: 562 AKTNPYGFILTPYYKVTNKVVDYSKPHWLTAAEEFGLAFAQSSIAINEKNEIIADKVTVR 621

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++V   ++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPLLK+EA
Sbjct: 622 KNQTYLVVDASQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLLKSEA 681

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+ES VA  S   I ++  G+V  VDA +IVI   E            Y L  F+
Sbjct: 682 PLVATGIESDVALYSSTNIRSEVDGVVSFVDAKKIVITDYEDKQ-------HTYFLRYFE 734

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T + Q P+VKVG  + + D+I DGPSTD G+LALG+N+LVAF  W+GYN+ED+++
Sbjct: 735 KSNQETLIIQHPIVKVGQTINKGDLICDGPSTDNGELALGKNVLVAFSTWYGYNYEDAII 794

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DVFTSIHI+E  +  R +K G + +T D+PN S     ++D  GI+ +G+EV
Sbjct: 795 ISEKLVKDDVFTSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDANGIVRIGSEV 854

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           N GDILVG+ +PKGE   TPE+KL+ AI+G+K +  +DTSLRV  G  GTV+DV+I +R 
Sbjct: 855 NTGDILVGRTSPKGEDNPTPEDKLMSAIWGKKTLQQKDTSLRVKHGEGGTVIDVQIISRD 914

Query: 949 GID 951
             D
Sbjct: 915 LGD 917



 Score =  425 bits (1092), Expect = e-116,   Method: Composition-based stats.
 Identities = 169/516 (32%), Positives = 247/516 (47%), Gaps = 77/516 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +N GD++    +      +   + +L A       +  D  +     V   V 
Sbjct: 747  IVKVGQTINKGDLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 805

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    K   S +        L    +  +  LD N   R+   +   + + G  
Sbjct: 806  -TSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDANGIVRIGSEVNTGDILVGRT 864

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W +  +Q +     V+  +        I+           
Sbjct: 865  SPKGEDNPTPE--DKLMSAIWGKKTLQQKDTSLRVKHGEGGTVIDVQIISRDL------- 915

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++  GV  +VKV VA KR I+ GDKMAGRHGNKG+VS +LP EDMPFL+DGTPVDI
Sbjct: 916  --GDNLEDGVGMIVKVLVAQKRKIKVGDKMAGRHGNKGVVSIVLPVEDMPFLEDGTPVDI 973

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG+A   L  K  + + D      +  L            
Sbjct: 974  LLNPQGVPSRMNIGQVLELHLGFAAKKLNTKFVTPVFDGIKLETMQELFR---------- 1023

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 1024 --------------------EAGIP------------------------ESGKFTLYDGI 1039

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PFD  V+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR GEME W
Sbjct: 1040 TGQPFDNKVSVGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFGEMETW 1099

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++++GA+ VL E+LT KSD++ GR  +Y ++++G    + GTPESFNVL  E++ L + 
Sbjct: 1100 ALESFGASSVLSEILTYKSDNIQGRNNLYNNLISGGKIPKPGTPESFNVLAYELRGLLVK 1159

Query: 1361 IDLENSRTKNSAKME----------EIPDFNKCELK 1386
            +++   +     ++E          E  D+   +L+
Sbjct: 1160 LEVHKKQDAQEEELEIPNKIEYADIEEEDYPFEQLQ 1195


>gi|42561522|ref|NP_975973.1| DNA-directed RNA polymerase subunit beta [Mycoplasma mycoides
           subsp. mycoides SC str. PG1]
 gi|81400331|sp|Q6MRX6|RPOB_MYCMS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|42493021|emb|CAE77615.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           mycoides SC str. PG1]
          Length = 1291

 Score =  578 bits (1490), Expect = e-162,   Method: Composition-based stats.
 Identities = 339/856 (39%), Positives = 521/856 (60%), Gaps = 72/856 (8%)

Query: 108 LIVFDVDEFTGAKSIKDI---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
           LI  D+ E      I ++   K   +++GD PLMT+ GTF+I G Q+++VSQL RSPG +
Sbjct: 159 LIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAY 218

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI-------IHVRIDRRRKVPVTSF 217
           F+ +      +G+++Y   IIP +G W++ E DSK I       ++V+ID+ RK   TS 
Sbjct: 219 FNKEL--NRKTGEMIYFADIIPSRGTWLEYETDSKKIGNDAINPLYVKIDKSRKTTATSL 276

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIES 276
           L+A G+  ++IL+ F    V  +        +    +    +V      I  GE    E 
Sbjct: 277 LLAFGISKDDILNIFDNDEVLVETLQQDSI-IGDFKIDWSNQVQEIYKKITQGETATSEG 335

Query: 277 GKKLTSGLLKSLKEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             K  + +L   ++  +   G           + +    +AEDIV+     +  +    +
Sbjct: 336 ASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNRILNRVIAEDIVDANNNVLIAKD-TEV 394

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           ++ ++++I     +D+  + ++ +++    R               +   +V +  ++ T
Sbjct: 395 NKHNIKQISEILDQDVMSIDLNYLSDIPGTRK--------------VQKIKVYKDSELKT 440

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            +                             + L +  +   I   DI++ +  L++L+ 
Sbjct: 441 DTT--------------------------CLIGLTSSSNEEFITVADILSTVSYLLNLKY 474

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
             G IDDIDNLGNRRVR+VGE+L+NQ+R+GL R+++++KE++++ D+  V    +INAKP
Sbjct: 475 NIGEIDDIDNLGNRRVRTVGELLQNQFRMGLNRIDKNVKEKLATSDLYKVKTSTIINAKP 534

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + + + EFF  SQLSQ  + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGR
Sbjct: 535 LTAIIGEFFNLSQLSQFMDQINPLSELTNKRRLTALGSGGLSRDRAGLEVRDVHPSHYGR 594

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYI 627
           ICP ET EG NIGL+++L+++ARVN YGFI TPYRKV +     + V YL+A +E+N  I
Sbjct: 595 ICPIETPEGPNIGLINNLSTYARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFII 654

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQ+N + DE+G   +E++  R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+
Sbjct: 655 AQSNVNQDENGKILDEIIVSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDA 714

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL+K E+P V TG+E   A+ SG AIVAK   IV+ VD+  I    
Sbjct: 715 NRALMGANMQRQAVPLIKPESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI---- 770

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               +    SG+  Y L  ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+
Sbjct: 771 ----ITDGESGIRTYILSDYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAI 826

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N++VAF  ++GYNFED++++SER+V +D FTS HI+E+ +  R+TK G EE+ R+IPN
Sbjct: 827 GQNVVVAFSTYNGYNFEDAIVMSERIVIDDRFTSTHIDEYTLEVRNTKQGQEEVIREIPN 886

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +SE+  +++D  GI+ +G EV  GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D 
Sbjct: 887 MSEQAKRHLDAEGIVAIGTEVKVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDN 946

Query: 928 SLRVPSGVSGTVVDVR 943
           SLRVP+G  G V  ++
Sbjct: 947 SLRVPNGGEGIVQSIK 962



 Score =  392 bits (1006), Expect = e-106,   Method: Composition-based stats.
 Identities = 154/508 (30%), Positives = 231/508 (45%), Gaps = 80/508 (15%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 795  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 849

Query: 936  SGTVVDVRIFNRHGID---KNERSISVEREQIELL------ARDKDDEQVILDRNIYSRL 986
               V+D R  + H  +   +   +   + E I  +      A+   D + I+      ++
Sbjct: 850  ERIVIDDRFTSTHIDEYTLEVRNTKQGQEEVIREIPNMSEQAKRHLDAEGIVAIGTEVKV 909

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 910  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 962

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 963  -----RFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPV 1017

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDM              P             E                   D   N    
Sbjct: 1018 EDM--------------PH-----------LE--------------DGTPVDIILNPQGV 1038

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            P R  + +++                +       K    V TP F+G +E+ +  ++  A
Sbjct: 1039 PSRMNIGQIL---------------EIHLGMAAKKLNQKVITPAFEGLNEKELEEIMAEA 1083

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +   G+  L DG TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK
Sbjct: 1084 GMTNYGKVTLIDGQTGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGK 1143

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR++ YE+IV      E G PES
Sbjct: 1144 AQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDIKGRSKTYEAIVRSKKIPEPGIPES 1203

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            FNVL KE+  LG ++ + +   + S   
Sbjct: 1204 FNVLSKEIMGLGFNMYMIDETGEKSVIN 1231



 Score = 97.8 bits (242), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 26/119 (21%), Positives = 48/119 (40%), Gaps = 10/119 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +        R+ + K    + +P+LI +Q  +++ F            +G+Q    
Sbjct: 1   MAYKIRKINRNVERRDYTKVSMNLSLPNLIGIQTETFEWF----------KTKGIQEVLD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             FPI +F G+++L   ++ F  P+  V         Y  P+   L+L V   +E    
Sbjct: 51  EFFPILSFDGSSVLTLENWGFKEPRLSVRQAKEESKIYDAPIYANLKLSVNKTEEIQKE 109


>gi|197311414|gb|ACH61913.1| RNA polymerase beta subunit [Mycoplasma arthritidis]
          Length = 1133

 Score =  578 bits (1489), Expect = e-162,   Method: Composition-based stats.
 Identities = 324/984 (32%), Positives = 522/984 (53%), Gaps = 79/984 (8%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R+ +  + +  + PD +E+Q+ S   FL          N G++   + ++PI   +G  
Sbjct: 1   ERRDYSLSQKKFETPDYLEMQRLSVVKFL----------NTGIEEELREIYPIE-TAGKV 49

Query: 73  MLEFV--SYEFDPPKFDVDDC----LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            +E++  +  F+ PK    +C      +  +Y   LK  LR                +++
Sbjct: 50  RIEYILNTAHFEIPKKSEFECIKEAKQKGSSYVGKLKAKLRQT---------NIETGEVE 100

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  +   ++P+MT  G+F+I G ++++VSQL RS G +F     R   +  L     IIP
Sbjct: 101 DAEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGVGV-RNKQANDLFNKVEIIP 159

Query: 187 DQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
             G W++I         D I V ID+ +   +T  L ALG     I   F       +  
Sbjct: 160 QIGSWLEIYHKVTSNVVDPIKVHIDKNKSFYLTVLLKALGFSKNGIYEMFGQSKELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
                   +A D +  A+ +   +         +S + L   +L + K   +   G  + 
Sbjct: 220 KKDKILGETAEDTIREAQETIYRLIRKGDRMTADSARNLIPSILFNAKRYNLSETGRFTL 279

Query: 301 -------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                  + +   Y+AED++  +TGE+  E    I     ++I       I  ++     
Sbjct: 280 NRKLNVIERIANSYLAEDLL-TKTGEVKYEKDTFITWDIAKQIHADFEEGILAMWRLPDI 338

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +     + +    N+  +  L      + P +                            
Sbjct: 339 DKEAYGSQIDNPGNESLETRLYAPRVWIYPTE-----------------------KDKLN 375

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                 L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+N
Sbjct: 376 DHSVEVLGNDPTATETFLLIPDLIATISYYFNLIDKVGFDDDPDSLVNKRIVTIGELLQN 435

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL+++E++ KERIS+ DID + P+++ N +P+ +    FF +S+LSQ  +  N L+
Sbjct: 436 QFRVGLIKLEKNTKERISAKDIDKITPKNVTNNRPIFNQFKSFFNTSKLSQFMDQCNPLA 495

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ ++ SFA+++
Sbjct: 496 EISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNMASFAQID 555

Query: 594 AYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            +GFI++PY +V + K+  ++ +YL+A+EE     AQ+  ++ +D    ++ V  R   E
Sbjct: 556 KHGFIQSPYFRVKNRKIDFSEAIYLTAIEESGYTFAQSTINIKDD-YIVDDRVLVRYDNE 614

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V  E++DF+  + +Q+ SIAAS IPFLENDD+ R LMG NMQRQAVP++  EAP V 
Sbjct: 615 YIEVNAEEVDFVGVNNRQITSIAASAIPFLENDDAYRALMGSNMQRQAVPIISPEAPLVA 674

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E+ +AK S     A + G+V  VDA  I +++        +S V+ Y L  F+RSNQ
Sbjct: 675 TGVEADIAKYSSTNTRASKDGVVTYVDANVIKVQT------AGSSKVESYHLRTFERSNQ 728

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            T ++Q PLVKVG E++  D++ DGPS   G+LALG+N+LV F  W GYN+ED+++ISER
Sbjct: 729 GTLIHQVPLVKVGQEIKAGDLLVDGPSMKNGELALGKNILVGFTTWKGYNYEDAVVISER 788

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TSIHIEE  +  R +K G + +T DIPN S    + ++E GI+ +G+EV+ GD
Sbjct: 789 LVKDDVYTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFLNEDGIVRIGSEVSAGD 848

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR----- 947
           ILVG+ +PKGE   TPEE+L+ AIFG+K    +DTSL+V  G +GTVV V I +R     
Sbjct: 849 ILVGRTSPKGEENPTPEERLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEILSRELGDQ 908

Query: 948 --HGIDKNERSISVEREQIELLAR 969
              GI+K  +    ++ +I++  +
Sbjct: 909 LEDGIEKIVKVSIAQKRKIKVGDK 932



 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/464 (30%), Positives = 216/464 (46%), Gaps = 67/464 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   + K    +   + +L      K  +  D  +     V   V 
Sbjct: 737  LVKVGQEIKAGDLLVDGPSMKN-GELALGKNILVGFTTWKGYNYEDAVVISERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I     + +   S + E      +    +  +  L+ +   R+   +   + + G  
Sbjct: 795  YTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFLNEDGIVRIGSEVSAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +       + + Q     +     V+        +  IL           
Sbjct: 855  SPKGEENPTPE--ERLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEILSREL------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP E+MP+L+DGTP+D+
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPVEEMPYLEDGTPLDM 963

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG+A   L  K  + + D   +  I  +            
Sbjct: 964  VLNPQGVPSRMNIGQVLELHLGFAARKLNTKFVTPVFDGITHNQIKEILEEAN------- 1016

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      ++++Y G 
Sbjct: 1017 ------------------------------------------LDSSG-----KTVVYSGQ 1029

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1030 TGEKLDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1089

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
             I++YGA  VLQE+LT KSD+++GR ++Y S+   +   + G P
Sbjct: 1090 AIESYGATNVLQELLTYKSDNIIGRNQLYNSLATNSRLPKAGMP 1133


>gi|197311412|gb|ACH61912.1| RNA polymerase beta subunit [Mycoplasma arthritidis]
          Length = 1135

 Score =  578 bits (1489), Expect = e-162,   Method: Composition-based stats.
 Identities = 324/984 (32%), Positives = 522/984 (53%), Gaps = 79/984 (8%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R+ +  + +  + PD +E+Q+ S   FL          N G++   + ++PI   +G  
Sbjct: 1   ERRDYSLSQKKFETPDYLEMQRLSVVKFL----------NTGIEEELREIYPIE-TAGKV 49

Query: 73  MLEFV--SYEFDPPKFDVDDC----LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            +E++  +  F+ PK    +C      +  +Y   LK  LR                +++
Sbjct: 50  RIEYILNTAHFEIPKKSEFECIKEAKQKGSSYVGKLKAKLRQT---------NIETGEVE 100

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  +   ++P+MT  G+F+I G ++++VSQL RS G +F     R   +  L     IIP
Sbjct: 101 DAEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGVGV-RNKQANDLFNKVEIIP 159

Query: 187 DQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR- 241
             G W++I         D I V ID+ +   +T  L ALG     I   F       +  
Sbjct: 160 QIGSWLEIYHKVTSNVVDPIKVHIDKNKSFYLTVLLKALGFSKNGIYEMFGQSKELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
                   +A D +  A+ +   +         +S + L   +L + K   +   G  + 
Sbjct: 220 KKDKILGETAEDTIREAQETIYRLIRKGDRMTADSARNLIPSILFNAKRYNLSETGRFTL 279

Query: 301 -------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                  + +   Y+AED++  +TGE+  E    I     ++I       I  ++     
Sbjct: 280 NRKLNVIERIANSYLAEDLL-TKTGEVKYEKDTFITWDIAKQIHADFEEGILAMWRLPDI 338

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +     + +    N+  +  L      + P +                            
Sbjct: 339 DKEAYGSQIDNPGNESLETRLYAPRVWIYPTE-----------------------KDKLN 375

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                 L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+N
Sbjct: 376 DHSVEVLGNDPTATETFLLIPDLIATISYYFNLIDKVGFDDDPDSLVNKRIVTIGELLQN 435

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q+R+GL+++E++ KERIS+ DID + P+++ N +P+ +    FF +S+LSQ  +  N L+
Sbjct: 436 QFRVGLIKLEKNTKERISAKDIDKITPKNVTNNRPIFNQFKSFFNTSKLSQFMDQCNPLA 495

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ ++ SFA+++
Sbjct: 496 EISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNMASFAQID 555

Query: 594 AYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            +GFI++PY +V + K+  ++ +YL+A+EE     AQ+  ++ +D    ++ V  R   E
Sbjct: 556 KHGFIQSPYFRVKNRKIDFSEAIYLTAIEESGYTFAQSTINIKDD-YIVDDRVLVRYDNE 614

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I V  E++DF+  + +Q+ SIAAS IPFLENDD+ R LMG NMQRQAVP++  EAP V 
Sbjct: 615 YIEVNAEEVDFVGVNNRQITSIAASAIPFLENDDAYRALMGSNMQRQAVPIISPEAPLVA 674

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E+ +AK S     A + G+V  VDA  I +++        +S V+ Y L  F+RSNQ
Sbjct: 675 TGVEADIAKYSSTNTRASKDGVVTYVDANVIKVQT------AGSSKVESYHLRTFERSNQ 728

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            T ++Q PLVKVG E++  D++ DGPS   G+LALG+N+LV F  W GYN+ED+++ISER
Sbjct: 729 GTLIHQVPLVKVGQEIKAGDLLVDGPSMKNGELALGKNILVGFTTWKGYNYEDAVVISER 788

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DV+TSIHIEE  +  R +K G + +T DIPN S    + ++E GI+ +G+EV+ GD
Sbjct: 789 LVKDDVYTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFLNEDGIVRIGSEVSAGD 848

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR----- 947
           ILVG+ +PKGE   TPEE+L+ AIFG+K    +DTSL+V  G +GTVV V I +R     
Sbjct: 849 ILVGRTSPKGEENPTPEERLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEILSRELGDQ 908

Query: 948 --HGIDKNERSISVEREQIELLAR 969
              GI+K  +    ++ +I++  +
Sbjct: 909 LEDGIEKIVKVSIAQKRKIKVGDK 932



 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 145/466 (31%), Positives = 218/466 (46%), Gaps = 67/466 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   + K    +   + +L      K  +  D  +     V   V 
Sbjct: 737  LVKVGQEIKAGDLLVDGPSMKN-GELALGKNILVGFTTWKGYNYEDAVVISERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I     + +   S + E      +    +  +  L+ +   R+   +   + + G  
Sbjct: 795  YTSIHIEEQVIQFRHSKAGEDWLTSDIPNASNFSKRFLNEDGIVRIGSEVSAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +       + + Q     +     V+        +  IL           
Sbjct: 855  SPKGEENPTPE--ERLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEILSREL------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP E+MP+L+DGTP+D+
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPVEEMPYLEDGTPLDM 963

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG+A   L  K  + + D   +  I  +            
Sbjct: 964  VLNPQGVPSRMNIGQVLELHLGFAARKLNTKFVTPVFDGITHNQIKEILEEAN------- 1016

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      ++++Y G 
Sbjct: 1017 ------------------------------------------LDSSG-----KTVVYSGQ 1029

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1030 TGEKLDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1089

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
             I++YGA  VLQE+LT KSD+++GR ++Y S+   +   + G PES
Sbjct: 1090 AIESYGATNVLQELLTYKSDNIIGRNQLYNSLATNSRLPKAGMPES 1135


>gi|269128533|ref|YP_003301903.1| DNA-directed RNA polymerase subunit beta [Thermomonospora curvata
           DSM 43183]
 gi|268313491|gb|ACY99865.1| DNA-directed RNA polymerase, beta subunit [Thermomonospora curvata
           DSM 43183]
          Length = 1160

 Score =  577 bits (1486), Expect = e-162,   Method: Composition-based stats.
 Identities = 311/955 (32%), Positives = 442/955 (46%), Gaps = 143/955 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F +  E +++PDL+ +Q  S+D  L                        GL+  F+ 
Sbjct: 16  RVSFARIKEPLEVPDLLALQTDSFDWLLGNERWKARVEAALKAGVRDIPTQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+ +++C  +D+TY+ P+ +T   I           S
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSIEECRDKDMTYSAPMFVTAEFI---------NNS 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K +Y 
Sbjct: 127 TGEIKSQTVFMGDFPLMTPKGTFIINGTERVVVSQLVRSPGVYFDRSLDK--ASDKDIYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           CRIIP +G W++ E D +D + VRIDR+RK PVT  L ALG     I   F  Y  +  +
Sbjct: 185 CRIIPSRGAWLEFEIDKRDNVGVRIDRKRKQPVTVLLKALGWTEARIREHFGAYESMNIT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE    ES + L   L  + K   +  +G 
Sbjct: 245 LEKDHTSGQDDA--------LLDIYRKLRPGEPPTKESAQALLENLYFNPKRYDLAKVGR 296

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                         VN + G         + E  +       +R    L+          
Sbjct: 297 YK------------VNKKLGLRLDMNQGTLTEDDIVATIEYLVR----LHAGEEEAVLTA 340

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                     +  D      R +R            +         +  L+ + RV    
Sbjct: 341 AGPEGVSVPIEIDDIDHFGNRRLR--------TVGELIQNQV----RLGLARMERVVRER 388

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
               D       I  + +I I  ++  ++   GT      +      +     +    LG
Sbjct: 389 MTTQDVEA----ITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALG 444

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
              + R      +  ++  V P       P+ +                 VN    I   
Sbjct: 445 PGGLSRE----RAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSAYGRVNPFGFIETP 500

Query: 539 RRLSALGQ--GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            R    G+    +    A  E R +       + P  T                      
Sbjct: 501 YRKVVDGRVTDEIHYLTADEEDRYIKAQANSPLNPDGTFAE------------------- 541

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                  KV       ++ YL   E                                   
Sbjct: 542 ------EKVLVRTKGGEIEYLPPEE----------------------------------- 560

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               + ++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAP VGTGME
Sbjct: 561 ----VHYMDVSPRQMTSVATAMIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGME 616

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A  +G  I+A++ G+VE+V A  I + + +G           YR+ KF+RSNQ TC 
Sbjct: 617 YRAATDAGDVILAEKPGVVEEVSADYITVLNDDGTR-------TTYRVAKFKRSNQGTCF 669

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ+P+V  G  V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED++++S+R+V +
Sbjct: 670 NQKPIVDEGQRVEAGQVIADGPCTDQGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQD 729

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GA+V PGDILVG
Sbjct: 730 DVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGADVVPGDILVG 789

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ VR+F+R   D
Sbjct: 790 KVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEQGKVIGVRVFSREEGD 844



 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 193/508 (37%), Positives = 270/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL A    +  +  D  +     V   V+
Sbjct: 674  IVDEGQRVEAGQVIADGPCT-DQGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 732

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 733  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGADVVPGDILVGK 790

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +     ++  R    +  
Sbjct: 791  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGEQGKVIGVR----VFS 839

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPFL+DGTPVD
Sbjct: 840  REEGDELPPGVNELVRVYVAQKRKITDGDKLAGRHGNKGVIAKILPVEDMPFLEDGTPVD 899

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ ETHLGW     G KI+    D+K +                 
Sbjct: 900  IILNPLGVPGRMNVGQVLETHLGWVASQ-GWKIEGDDADWKRSLQAIG------------ 946

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A +       +TPVFDGA EE I  +L     +          
Sbjct: 947  -----------------ATEAGPWTKTATPVFDGAREEEITGLLSCTLPNRDGMRLIGPN 989

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ LYDG TGEPF  P+ VGYIY+LKL H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 990  GKAKLYDGRTGEPFKDPIAVGYIYILKLLHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1049

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1050 QRFGEMEVWALEAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLI 1109

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1110 KEMQSLCLNVEVLSSDGMSIEMRDSDED 1137


>gi|291320578|ref|YP_003515842.1| DNA directed RNA polymerase subunit beta [Mycoplasma agalactiae]
 gi|290752913|emb|CBH40888.1| DNA directed RNA polymerase beta chain [Mycoplasma agalactiae]
          Length = 1211

 Score =  576 bits (1485), Expect = e-162,   Method: Composition-based stats.
 Identities = 326/962 (33%), Positives = 520/962 (54%), Gaps = 71/962 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R+ +       ++PD + + K S++ F             G++   +  +PI + +  
Sbjct: 24  TERRDYSATKVTWEVPDFLNMSKESFEWF----------KKSGIEEILREHYPIVSSNKK 73

Query: 72  AMLEFV--SYEFDPP--KFD-VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
             LE++  S   + P  ++D + +   + + YA  L    ++                +K
Sbjct: 74  VSLEYIHNSARLEVPPKEYDAIIEAKAKGINYAAKLFAKFKVTSDK----------GVVK 123

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +  + +G++PLM   G+F+I G ++++VSQL  SP  +F     R   S  L     I+P
Sbjct: 124 DDEVLLGEVPLMNSGGSFIINGSEKVIVSQLICSPSAYFGCGV-RNKQSDDLFNKLEILP 182

Query: 187 DQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQ 240
             G W++I       + D + ++ID+ + + +  FL ALG++ E I S F   P++  + 
Sbjct: 183 RLGSWVEISHKVTTKNPDSVKIKIDKNKNINLAVFLGALGLNEENIHSLFGNSPELEETL 242

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEK-------- 291
             D           ++          I  G+ + E S   L   LL + K          
Sbjct: 243 LRDKSLKSSEDPMTVIQNCREILFRTIRRGDLMTETSAANLLPSLLFNKKRYSLGATGRY 302

Query: 292 GVKFLGITSDCLCGLYVAEDI-VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            +       D +   Y+ +D+ +  E GE+         E  L  +      +  +   +
Sbjct: 303 KLNKKLSLIDRITETYLGQDLEIKDENGEVMFLEKGTFIEHKLALLIQENFNNGALKTTE 362

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N  I    +         A   + +  R   +        +F              
Sbjct: 363 IEGINPEILYAKL-----YSDPAYPYLKKSNRVAKLL-------VFANRKKMDKGLATLV 410

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G          D   D +H+   DIIA I    +L  G G  DD D++ N+R+ SVGE+
Sbjct: 411 IGN---------DPKCDAQHLIASDIIAAINYYFNLLEGIGQDDDADSMINKRIVSVGEL 461

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ  +GL ++E++ +ER+S+ + + + P+++ N K V + +  FF SS+LSQ  + +N
Sbjct: 462 MQNQLNVGLSKLEKTTRERMSAKEPEKITPKNITNNKLVSNQMKTFFNSSKLSQFMDQIN 521

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           +L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A
Sbjct: 522 ALAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYA 581

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            VN YGF++TPY KV +  V  +DVVYL+A +E    IAQ+ +++D++    +E +  R 
Sbjct: 582 SVNEYGFLQTPYFKVNNSVVDYDDVVYLTAADEFGYNIAQSTATVDDENRLVDETLTIRK 641

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
               IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA 
Sbjct: 642 NYTYILGKPSDVDLIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEAA 701

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FV TG E+ +AK S A   A+  G VE VD  +I IR+ +G LD        Y L  FQR
Sbjct: 702 FVATGNEADIAKFSAANFRARNEGKVEYVDGAKIKIRNNKGTLD-------TYSLKNFQR 754

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ+T ++Q+P++KVG +V + D++ DG S   G+LALG+N+LVAF  + GYN+ED++++
Sbjct: 755 SNQDTVIHQKPIIKVGQDVAKGDLLVDGSSFKDGELALGKNLLVAFSTYKGYNYEDAIVL 814

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+  +DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV 
Sbjct: 815 NERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVI 874

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R  
Sbjct: 875 PGDVLVGRVSPKGDDNPSREEKLLAAILGQRQLNVKDTSLKVKNGHNGTVIGVEILSREN 934

Query: 950 ID 951
            D
Sbjct: 935 KD 936



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 156/493 (31%), Positives = 221/493 (44%), Gaps = 77/493 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS-LRVPSGVSGTV 939
            II VG +V  GD+LV   + K +  +   + LL A    K  +  D   L         +
Sbjct: 766  IIKVGQDVAKGDLLVDGSSFK-DGELALGKNLLVAFSTYKGYNYEDAIVLNERLAKKDVL 824

Query: 940  VDVRIFNRHGIDKNERSISVEREQ----IELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
              + I  +    +  ++ + E  +    +   A    DE  I+         ++L G+ +
Sbjct: 825  TSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVIPGDVLVGRVS 884

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G     +   L + ++                  QR +       +            
Sbjct: 885  PKGDDNPSREEKLLAAILG-----------------QRQLNVKDTSLKVKNGHNGTVIGV 927

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +I   +  D +  G+  +VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM      
Sbjct: 928  EILSRENKDLLEDGIDMIVKVSIAVKRKIRVGDKMSGRHGNKGVVSVILPEEDM------ 981

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                    P             E          G  I  ++                   
Sbjct: 982  --------PH-----------LE---------DGTPIDVML------------------- 994

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                    +++      V         G    TPVFDG  +EAI  ++  A L  SG+  
Sbjct: 995  -NPQGVPSRMNIGQVLEVHLGMAARSLGCKFVTPVFDGVKKEAIQDVISEAGLPLSGKQT 1053

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L D +TGE FD PV+VG +YM KLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 1054 LIDPITGEKFDNPVSVGVMYMFKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 1113

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EME W I++YGA+ VLQE+LT KSDD+VGR ++Y S+V G D    G PESFNVL  E+ 
Sbjct: 1114 EMETWAIESYGASNVLQEILTYKSDDIVGRNQLYTSLVTGKDLPTPGIPESFNVLNYELN 1173

Query: 1356 ALGLSIDLENSRT 1368
             LG+ +D+  +  
Sbjct: 1174 GLGMKLDITTANN 1186


>gi|321310989|ref|YP_004193318.1| DNA-directed RNA polymerase subunit beta [Mycoplasma haemofelis str.
            Langford 1]
 gi|319802833|emb|CBY93479.1| DNA-directed RNA polymerase beta subunit [Mycoplasma haemofelis str.
            Langford 1]
          Length = 1383

 Score =  576 bits (1484), Expect = e-161,   Method: Composition-based stats.
 Identities = 311/1422 (21%), Positives = 533/1422 (37%), Gaps = 133/1422 (9%)

Query: 14   RKFFGKNPEI-IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K        PDL  VQ  +Y  F+          N GL++  KS FPI + S + 
Sbjct: 17   RLDFSKVKSPNFVPPDLKGVQLGAYAKFV----------NGGLESLLKSFFPIYSHSKST 66

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             L        PP+    + L +  +Y   +++ ++L+         +K  +  K  ++++
Sbjct: 67   ALHLEEVVLVPPEISEHEALEKGKSYQYAVRLVMKLV------SQYSKDNEKSKTDNVFL 120

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLSGKLL---YACRIIPDQ 188
            G+LP +T    ++I GI++ ++SQ+ R+PG +     + + S S K +   + C ++P +
Sbjct: 121  GNLPALTARSNYIINGIEKFIISQIVRAPGAYMLSKSQIKLSSSKKRVQEGFICELLPLR 180

Query: 189  GLWMDIEFDSKDIIHVRIDRRRK---------VPVTSFLMALGMDSEEILSTF---YPKI 236
            G+ M   +  KD    RI    K          P+T+ L ALG   + IL  F      +
Sbjct: 181  GILMLFNY-QKD----RIKVTAKNNVGTDVIQFPLTTLLKALGFSEKNILDIFESAGHIV 235

Query: 237  VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE-KGVKF 295
                  D+    +  ++        +++V+    E+ +E  K+     L SL      K 
Sbjct: 236  NTLSDEDYRPKDMILSEGSFMKWFENTVVNQKDHEKWLEDSKESVFKTLNSLSYQYYDKH 295

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
               + + + G                  A      +  E    S  ++I   +       
Sbjct: 296  WRGSHENIIGK--------------LRMAAAANSTEDYEITKASLEKEIGKSHD------ 335

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
              +   +  +         + I   + P  VS+F     +    FF  + YD+   GR K
Sbjct: 336  --LLEAISVEWAAYHLVQDIGISPDISPYKVSSFQ---ELLWVYFFGKNYYDVGKSGRYK 390

Query: 416  MNMRLNLDTPDDVRHIRKEDI-----------IAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            ++ +L+L      + + ++ +             + +  V L +       +    +  +
Sbjct: 391  LDHKLSLSQRIFQKVLAQDVLSTDGEVVFPKGTYMTREKVFLFDDLSRQGKLKIRNSIDI 450

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF---CSSQ 521
              V +   N      + +E  +  +  + D   +          V + +         S 
Sbjct: 451  DYVPKTFPNYELHSKVEVESILIHQTQTTDSPVLRIVGTPRKISVDNNLFFSDFVAIVSY 510

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            ++ L   V     I H           +  AR  V           RI    T   +++ 
Sbjct: 511  ITNLGNQVGKYDDIDHLGNKRLKLVDQLLSARIQVA--------MARIVKFSTERMNSME 562

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +  +  R ++                +    + ++ +       Q   S   +    
Sbjct: 563  ARINYATL-RDSSDQDFTVKIMVNTRFFQSVIKEFFNSHQLTQFLDQQNPLSELTNKRKI 621

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              +       E+  +    + +        +     +   L    +    +         
Sbjct: 622  SAMGPGGIKREDPNLNIRDVHYSHYGKICPIETPEGMNIGLIMALAFFAQIDEYGF-FVT 680

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            P  K +   V   +E + A      I+++     ++   ++  I     D   S     +
Sbjct: 681  PYYKVKDGKVTDQVEWLSALKEEDFILSEAHVPRDEDGNLQGNITVRYKDSVESMDPKLV 740

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              +        +   +  P ++  D  R       G +     + L +           Y
Sbjct: 741  DYVDVACNQLVSISASLIPFLEHNDANRA----LMGSNMQRQAVPLLKPYSPVVGTGVEY 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
                   +S     +   TS+      V   D  LG EE++      S +     ++  +
Sbjct: 797  KIASDSGLSVLSKGDGQVTSVDGNSVSVKYDDPALGSEEVSLYKFERSNQNTCK-NQYPL 855

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V   D+L           +   + +L A       +  D  +            
Sbjct: 856  VKPGQRVKVKDVLANGP-AMQNGELALGQNVLVAFTTWFGYNYEDAII------------ 902

Query: 942  VRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              + +R   +    S+ ++   IE +  +  DDE      N        L     +    
Sbjct: 903  --LSSRLIEEDVYTSVHIQEHTIECMRTKIGDDEITRQIPNTNDHEKRYLDEDGIIMVGA 960

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEK 1059
              K+  +L   +       Q  +  +        V+S+K       +             
Sbjct: 961  EVKEGDILVGKVSPLANTEQTSEEKLLQAIFSEKVKSVKDSSLRVPTGGAGVVTRIMRLS 1020

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            I  GD +   V+ VVKVF+  KR IQ GDKMAGRHGNKGIVS+I   EDMP+L+DGTPVD
Sbjct: 1021 IYKGDKLDDDVIEVVKVFITQKRKIQVGDKMAGRHGNKGIVSKIALREDMPYLEDGTPVD 1080

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLG+A   L  K K L   +  + + +     L++     
Sbjct: 1081 IVLNPLGVPSRMNIGQVLETHLGYAARRLSFK-KLLEFKFNKDKESARSLFGLDENAVDK 1139

Query: 1180 SHTEKISDYDDDSVLRVAEQWKS-------------------GVPVSTPVFDGADEEAIN 1220
                      +  +    E                        + VSTP+F G + E + 
Sbjct: 1140 LFGVVEDYLSEKKISSYEEAKALKNIDFSIVLSKAGLKEDDLNIKVSTPIFCGVNNEDLV 1199

Query: 1221 SMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +++ AD+D S   G+  L DG TGE F +P+T G IYMLKL+HMV DK+YARS G YS 
Sbjct: 1200 KIMQDADIDPSLSNGKFTLIDGKTGEKFPKPITCGIIYMLKLDHMVDDKIYARSVGPYSK 1259

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPLGGK   GGQR GEMEVW ++AYGAAY L+E+LTIKSDD+  R+ ++ SI+    
Sbjct: 1260 ITQQPLGGKCQNGGQRFGEMEVWALEAYGAAYNLRELLTIKSDDIQSRSFIFSSIIKRQP 1319

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
                  PESF +LVK+++   L I+++           E  +
Sbjct: 1320 LPTPNIPESFKLLVKKLEGACLKINVQYGDENKFISCSEFIE 1361


>gi|298205318|gb|ADI61870.1| RNA polymerase beta subunit [Mesorhizobium sp. JS6]
          Length = 481

 Score =  576 bits (1484), Expect = e-161,   Method: Composition-based stats.
 Identities = 311/481 (64%), Positives = 382/481 (79%), Gaps = 1/481 (0%)

Query: 42  MMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVP 101
           M++     RP+EGLQA FKSVFPI+ FSGA+MLEFV YEF+ PKFDVD+C  RDLTYA P
Sbjct: 1   MVDEPQGGRPDEGLQAVFKSVFPISDFSGASMLEFVKYEFEAPKFDVDECRQRDLTYAAP 60

Query: 102 LKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSP 161
           LK+TLRLIVFD+DE TG+KSIKDIK Q +YMGD+PLMT +GTF+I G +R++VSQ+HRSP
Sbjct: 61  LKVTLRLIVFDIDEDTGSKSIKDIKGQDVYMGDMPLMTLNGTFIINGTERVIVSQMHRSP 120

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G+ FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+P TS LMAL
Sbjct: 121 GVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPATSLLMAL 180

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           GMD EEILSTFY KI Y Q GD W  P +      G K    LVD DTGE V+E+GKK+T
Sbjct: 181 GMDGEEILSTFYNKIEYKQSGDHWRIPFTVE-RFRGLKAVDDLVDADTGEIVVEAGKKIT 239

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           +   K L +KGVK +  T D L G Y+AED+V+  TGEI++EAGD IDEK+L+ +  +  
Sbjct: 240 ARQAKQLADKGVKAIKATQDDLYGSYLAEDVVDYSTGEIFLEAGDEIDEKTLKVLLSTGA 299

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
            +  +L +D +N   YIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFF
Sbjct: 300 EEFTVLDIDHINVGGYIRNTLAIDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFF 359

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           D+D+YDLS VGRVKMNMRL+L   D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGN
Sbjct: 360 DADRYDLSAVGRVKMNMRLDLKAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGN 419

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RRVRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQ
Sbjct: 420 RRVRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQ 479

Query: 522 L 522
           L
Sbjct: 480 L 480


>gi|211998842|gb|ACJ15333.1| RNA polymerase beta subunit [Mesorhizobium chacoense]
          Length = 466

 Score =  575 bits (1483), Expect = e-161,   Method: Composition-based stats.
 Identities = 306/465 (65%), Positives = 373/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFRSVFPISDFSGTSMLEFVKYEFEAPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDLDEDTGAKSIKDIKEQDVYMGDMPLMTSNGTFIINGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD D+GE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKKSGDHWRIPFNVE-RFRGLKAVGDLVDADSGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             K L EKG+K +  T D L G Y+AEDIVN  +GEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QAKQLAEKGLKAIKATEDDLFGSYLAEDIVNYASGEIFLEAGDEIDEKTLKVLLAAGEEE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I IL +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQILDIDHVNVGAYIRNTLAVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL LD  D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELDAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|222093435|gb|ACM43494.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  575 bits (1483), Expect = e-161,   Method: Composition-based stats.
 Identities = 340/984 (34%), Positives = 526/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++K+
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVKD 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|322510297|gb|ADX05534.1| RNA polymerase beta subunit [Ensifer numidicus]
          Length = 467

 Score =  575 bits (1482), Expect = e-161,   Method: Composition-based stats.
 Identities = 312/468 (66%), Positives = 385/468 (82%), Gaps = 1/468 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK
Sbjct: 1   DEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEIL TFY K +Y + G+ W  P    D++ G K    +VD DTGE V+E+GKKLT  
Sbjct: 181 DGEEILETFYTKSLYQRDGEGWRVPFQP-DVLKGQKAIVEMVDADTGEVVVEAGKKLTPR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           LL+ L++KG+K L  T D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  +   +
Sbjct: 240 LLRQLQDKGLKALKATDDDLYGNYLAEDIVNFETGEIYLEAGDEIDEKTLPVILSAGFDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           IP+L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+
Sbjct: 300 IPVLDIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNTLFFDA 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
           VRSVGE+++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP  +
Sbjct: 420 VRSVGELMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAA 467


>gi|211998826|gb|ACJ15325.1| RNA polymerase beta subunit [Mesorhizobium albiziae]
          Length = 466

 Score =  575 bits (1482), Expect = e-161,   Method: Composition-based stats.
 Identities = 307/465 (66%), Positives = 372/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG +MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGTSMLEFVKYEFEAPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF+I G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDLDEDTGAKSIKDIKEQDVYMGDMPLMTMNGTFIINGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y +  D W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRSKDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             K L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   D
Sbjct: 240 QAKQLAEKGLKAIKATEEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLMSAGEED 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I IL +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQILDIDHVNVGAYIRNTLAVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL LD  D VR +RKEDI+A+++ LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELDAEDTVRVLRKEDILAVVRTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|221327628|gb|ACM17481.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  573 bits (1478), Expect = e-161,   Method: Composition-based stats.
 Identities = 339/984 (34%), Positives = 527/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L +  L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIATTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIIDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|222093433|gb|ACM43493.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  573 bits (1478), Expect = e-161,   Method: Composition-based stats.
 Identities = 339/984 (34%), Positives = 526/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVIFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|221327624|gb|ACM17479.1| RNA polymerase beta subunit [Mycoplasma hominis]
 gi|221327630|gb|ACM17482.1| RNA polymerase beta subunit [Mycoplasma hominis]
 gi|222093431|gb|ACM43492.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  573 bits (1478), Expect = e-161,   Method: Composition-based stats.
 Identities = 339/984 (34%), Positives = 526/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|290889135|gb|ADD69917.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 462

 Score =  572 bits (1475), Expect = e-160,   Method: Composition-based stats.
 Identities = 312/459 (67%), Positives = 385/459 (83%), Gaps = 1/459 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 4   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 63

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 64  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 123

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 124 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 183

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL++L+
Sbjct: 184 STFYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRTLQ 242

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 243 EKGLKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDI 302

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 303 DHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLS 362

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 363 AVGRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 422

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 423 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKP 461


>gi|221327626|gb|ACM17480.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  572 bits (1475), Expect = e-160,   Method: Composition-based stats.
 Identities = 339/984 (34%), Positives = 526/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERVANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|221327622|gb|ACM17478.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  572 bits (1475), Expect = e-160,   Method: Composition-based stats.
 Identities = 339/984 (34%), Positives = 525/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  +  VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSKPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|72080945|ref|YP_288003.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           7448]
 gi|88909141|sp|Q4A7A9|RPOB_MYCH7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|71914069|gb|AAZ53980.1| DNA-directed RNA polymerase beta subunit [Mycoplasma hyopneumoniae
           7448]
          Length = 1220

 Score =  572 bits (1474), Expect = e-160,   Method: Composition-based stats.
 Identities = 328/968 (33%), Positives = 527/968 (54%), Gaps = 75/968 (7%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G+G  R+F+G   + ++ PD ++  + S+D FL +          G+  AF  +
Sbjct: 5   YKLKSYGIGTDRRFYGVANKTLETPDFLDPVRESFDWFLHV----------GIPEAFDRI 54

Query: 63  FPITAFSGAAMLEF--VSYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           FPI + +G   + F   S   + P+ +   + +   +  TY+  + +TL  +  +     
Sbjct: 55  FPIVSANGKLEISFRRGSLRVEKPENEYLAIREAKIKGKTYSARVYVTLVKVHSED---- 110

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 +++EQ I + + P MT+ GTF+I G +++VVSQL RSPG+ F  +  R   +  
Sbjct: 111 -----GEMEEQEILLAEFPFMTQGGTFIINGFEKVVVSQLIRSPGVCF-RENVRNQQADD 164

Query: 178 LLYACRIIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
           L     IIP  G WM+I         D +  RID+ + +P+ SFL A+G  +E +   F 
Sbjct: 165 LFNKVEIIPQLGSWMEIFHKVTGNQVDTVKFRIDKHKNIPLLSFLRAIGFTNETVRKYFG 224

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                 +            +L +  ++              E  K L   ++ + +   +
Sbjct: 225 NSPELLESIRRHKLESLEENLELIYRIVR-----KDDRITEEGLKNLIPSIIFNERRYNL 279

Query: 294 KFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
              G           + +   Y+AED+V+ +   ++ +   +  + +LE        +IP
Sbjct: 280 ASTGRFMLNAKLNLVERISQTYLAEDLVSKKNKILFKKGTYITRQLALEIQEKFNNEEIP 339

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +  ++ V++  Y R   +T      K   + I +V                         
Sbjct: 340 LSEIEGVDSTIYARQLEITRNENLWKRFYVAIVKVWPNKK-------------------- 379

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              S +   +    +  D   + + +   DIIAI+    +L +  G  DD D+L N+R+ 
Sbjct: 380 ---SMLQESEPVNVIATDPNLNEKTLVLSDIIAIVSYYFNLLSNLGKSDDPDSLVNKRIV 436

Query: 466 SVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           SVGE+L+NQ+ + L ++E++ KE+  +  D+  +  + +IN KP+ +    FF SS+LSQ
Sbjct: 437 SVGELLQNQFLIALTKIEKNSKEKISTKSDLSQLTVKSIINNKPIYNQFKNFFNSSKLSQ 496

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L  +   R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 497 FMDQINPLGEMASKRKVTSLGPGGLNRDTAQFEVRDVHTTHYGRICPVETPEGQNIGLIL 556

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           + + F+R+N YGFI TPY +V +  V  + V +L+A EE ++  AQ+   +D++     +
Sbjct: 557 NFSVFSRINQYGFIITPYYQVKNRIVDYSKVHWLAASEEFDKSFAQSGVEIDQNNRIIPD 616

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     +++  E++++ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL
Sbjct: 617 KLTVRKNQTYLVLDAEQVNYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPL 676

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +K+EAP V TG+E  VA+ S   + A  +G V  VDA +I+I              +I+ 
Sbjct: 677 IKSEAPLVATGIEEAVARFSATNLRASISGKVTYVDAKKIII--------DDGEKPEIHY 728

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F++SNQ T + Q+P VKVGD+V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 729 LRYFEKSNQETLILQKPTVKVGDKVKKGQLICDGPSTDNGELALGKNVLVAFSTWYGYNY 788

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R TK G + +T +IPN S +   ++D  GI+ 
Sbjct: 789 EDAIIISEKLVKDDVFTSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVI 848

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV+ GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+
Sbjct: 849 VGSEVDTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQ 908

Query: 944 IFNRHGID 951
           I +R   D
Sbjct: 909 ILSRDQGD 916



 Score =  421 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 161/504 (31%), Positives = 238/504 (47%), Gaps = 67/504 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG +V  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 747  VKVGDKVKKGQLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 804

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   + +        +       ++ LD N    +   +   + + G   
Sbjct: 805  TSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVIVGSEVDTGDILVGRTS 864

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 865  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 913

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  ++K+ +A KR I+ GDKMAGRHGNKG+VS ILP EDMPFL+DGTPVDIV
Sbjct: 914  QGDNLEEGVGMLIKILIAQKRKIKVGDKMAGRHGNKGVVSVILPVEDMPFLEDGTPVDIV 973

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG     L  K  + + D      I  L             
Sbjct: 974  LNPQGVPSRMNIGQVLELHLGMVAKKLKTKFVTPVFDGIKIETIKKL------------- 1020

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         FD             A++ ESG+  L+DG++
Sbjct: 1021 -----------------------------FD------------EANIPESGKFKLFDGIS 1039

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR GEME W 
Sbjct: 1040 GQAFENPVSVGYMYMLKLLHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRFGEMETWA 1099

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++++GA  VL E+LT KSD++ GR  +Y +I++G      GTPESFNVL  E++ L + +
Sbjct: 1100 LESFGATSVLSELLTYKSDNIQGRNLLYNNIISGGKIPSPGTPESFNVLAYELRGLLIKL 1159

Query: 1362 DLENSRTKNSAKMEEIPDFNKCEL 1385
            ++  +  +N    E        E+
Sbjct: 1160 EVHKNDQENQEVEEIKDPLELPEI 1183


>gi|312601560|gb|ADQ90815.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           168]
          Length = 1220

 Score =  572 bits (1474), Expect = e-160,   Method: Composition-based stats.
 Identities = 328/968 (33%), Positives = 527/968 (54%), Gaps = 75/968 (7%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G+G  R+F+G   + ++ PD ++  + S+D FL +          G+  AF  +
Sbjct: 5   YKLKSYGIGTDRRFYGVANKTLETPDFLDPVRESFDWFLHV----------GIPEAFDRI 54

Query: 63  FPITAFSGAAMLEF--VSYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           FPI + +G   + F   S   + P+ +   + +   +  TY+  + +TL  +  +     
Sbjct: 55  FPIVSANGKLEISFRRGSLRVEKPENEYLAIREAKIKGKTYSARVYVTLVKVHSED---- 110

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 +++EQ I + + P MT+ GTF+I G +++VVSQL RSPG+ F  +  R   +  
Sbjct: 111 -----GEMEEQEILLAEFPFMTQGGTFIINGFEKVVVSQLIRSPGVCF-RENVRNQQADD 164

Query: 178 LLYACRIIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
           L     IIP  G WM+I         D +  RID+ + +P+ SFL A+G  +E +   F 
Sbjct: 165 LFNKVEIIPQLGSWMEIFHKVTGNQVDTVKFRIDKHKNIPLLSFLRAIGFTNETVRKYFG 224

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                 +            +L +  ++              E  K L   ++ + +   +
Sbjct: 225 NSPELLESIRRHKLESLEENLELIYRIVR-----KDDRITEEGLKNLIPSIIFNERRYNL 279

Query: 294 KFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
              G           + +   Y+AED+V+ +   ++ +   +  + +LE        +IP
Sbjct: 280 ASTGRFMLNAKLNLVERISQTYLAEDLVSKKNKILFKKGTYITRQLALEIQEKFNNEEIP 339

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +  ++ V++  Y R   +T      K   + I +V                         
Sbjct: 340 LSEIEGVDSTIYARQLEITRNENLWKRFYVAIVKVWPNKK-------------------- 379

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              S +   +    +  D   + + +   DIIAI+    +L +  G  DD D+L N+R+ 
Sbjct: 380 ---SMLQESEPVNVIATDPNLNEKTLVLSDIIAIVSYYFNLLSNLGKSDDPDSLVNKRIV 436

Query: 466 SVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           SVGE+L+NQ+ + L ++E++ KE+  +  D+  +  + +IN KP+ +    FF SS+LSQ
Sbjct: 437 SVGELLQNQFLIALTKIEKNSKEKISTKSDLSQLTVKSIINNKPIYNQFKNFFNSSKLSQ 496

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L  +   R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 497 FMDQINPLGEMASKRKVTSLGPGGLNRDTAQFEVRDVHTTHYGRICPVETPEGQNIGLIL 556

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           + + F+R+N YGFI TPY +V +  V  + V +L+A EE ++  AQ+   +D++     +
Sbjct: 557 NFSVFSRINQYGFIITPYYQVKNRIVDYSKVHWLAASEEFDKSFAQSGVEIDQNNRIIPD 616

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     +++  E++++ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL
Sbjct: 617 KLTVRKNQTYLVLDAEQVNYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPL 676

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +K+EAP V TG+E  VA+ S   + A  +G V  VDA +I+I              +I+ 
Sbjct: 677 IKSEAPLVATGIEEAVARFSATNLRAAISGKVTYVDAKKIII--------DDGEKPEIHY 728

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F++SNQ T + Q+P VKVGD+V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 729 LRYFEKSNQETLILQKPTVKVGDKVKKGQLICDGPSTDNGELALGKNVLVAFSTWYGYNY 788

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R TK G + +T +IPN S +   ++D  GI+ 
Sbjct: 789 EDAIIISEKLVKDDVFTSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVI 848

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV+ GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+
Sbjct: 849 VGSEVDTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQ 908

Query: 944 IFNRHGID 951
           I +R   D
Sbjct: 909 ILSRDQGD 916



 Score =  421 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 161/504 (31%), Positives = 238/504 (47%), Gaps = 67/504 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG +V  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 747  VKVGDKVKKGQLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 804

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   + +        +       ++ LD N    +   +   + + G   
Sbjct: 805  TSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVIVGSEVDTGDILVGRTS 864

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 865  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 913

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  ++K+ +A KR I+ GDKMAGRHGNKG+VS ILP EDMPFL+DGTPVDIV
Sbjct: 914  QGDNLEEGVGMLIKILIAQKRKIKVGDKMAGRHGNKGVVSVILPVEDMPFLEDGTPVDIV 973

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG     L  K  + + D      I  L             
Sbjct: 974  LNPQGVPSRMNIGQVLELHLGMVAKKLKTKFVTPVFDGIKIETIKKL------------- 1020

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         FD             A++ ESG+  L+DG++
Sbjct: 1021 -----------------------------FD------------EANIPESGKFKLFDGIS 1039

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR GEME W 
Sbjct: 1040 GQAFENPVSVGYMYMLKLLHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRFGEMETWA 1099

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++++GA  VL E+LT KSD++ GR  +Y +I++G      GTPESFNVL  E++ L + +
Sbjct: 1100 LESFGATSVLSELLTYKSDNIQGRNLLYNNIISGGKIPSPGTPESFNVLAYELRGLLIKL 1159

Query: 1362 DLENSRTKNSAKMEEIPDFNKCEL 1385
            ++  +  +N    E        E+
Sbjct: 1160 EVHKNDQENQEVEEIKDPLELPEI 1183


>gi|54020629|ref|YP_116144.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           232]
 gi|81378457|sp|Q5ZZS1|RPOB_MYCH2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|53987802|gb|AAV28003.1| DNA-dependent RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           232]
          Length = 1220

 Score =  572 bits (1474), Expect = e-160,   Method: Composition-based stats.
 Identities = 328/968 (33%), Positives = 527/968 (54%), Gaps = 75/968 (7%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G+G  R+F+G   + ++ PD ++  + S+D FL +          G+  AF  +
Sbjct: 5   YKLKSYGIGTDRRFYGVANKTLETPDFLDPVRESFDWFLHV----------GIPEAFDRI 54

Query: 63  FPITAFSGAAMLEF--VSYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           FPI + +G   + F   S   + P+ +   + +   +  TY+  + +TL  +  +     
Sbjct: 55  FPIVSANGKLEISFRRGSLRVEKPENEYLAIREAKIKGKTYSARVYVTLVKVHSED---- 110

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 +++EQ I + + P MT+ GTF+I G +++VVSQL RSPG+ F  +  R   +  
Sbjct: 111 -----GEMEEQEILLAEFPFMTQGGTFIINGFEKVVVSQLIRSPGVCF-RENVRNQQADD 164

Query: 178 LLYACRIIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
           L     IIP  G WM+I         D +  RID+ + +P+ SFL A+G  +E +   F 
Sbjct: 165 LFNKVEIIPQLGSWMEIFHKVTGNQVDTVKFRIDKHKNIPLLSFLRAIGFTNETVRKYFG 224

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                 +            +L +  ++              E  K L   ++ + +   +
Sbjct: 225 NSPELLESIRRHKLESLEENLELIYRIVR-----KDDRITEEGLKNLIPSIIFNERRYNL 279

Query: 294 KFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
              G           + +   Y+AED+V+ +   ++ +   +  + +LE        +IP
Sbjct: 280 ASTGRFMLNAKLNLVERISQTYLAEDLVSKKNKILFKKGTYITRQLALEIQEKFNNEEIP 339

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +  ++ V++  Y R   +T      K   + I +V                         
Sbjct: 340 LSEIEGVDSTIYARQLEITRNENLWKRFYVAIVKVWPNKK-------------------- 379

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              S +   +    +  D   + + +   DIIAI+    +L +  G  DD D+L N+R+ 
Sbjct: 380 ---SMLQESEPVNVIATDPNLNEKTLVLSDIIAIVSYYFNLLSNLGKSDDPDSLVNKRIV 436

Query: 466 SVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           SVGE+L+NQ+ + L ++E++ KE+  +  D+  +  + +IN KP+ +    FF SS+LSQ
Sbjct: 437 SVGELLQNQFLIALTKIEKNSKEKISTKSDLSQLTVKSIINNKPIYNQFKNFFNSSKLSQ 496

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L  +   R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 497 FMDQINPLGEMASKRKVTSLGPGGLNRDTAQFEVRDVHTTHYGRICPVETPEGQNIGLIL 556

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           + + F+R+N YGFI TPY +V +  V  + V +L+A EE ++  AQ+   +D++     +
Sbjct: 557 NFSVFSRINQYGFIITPYYQVKNRIVDYSKVHWLAASEEFDKSFAQSGVEIDQNNRIIPD 616

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     +++  E++++ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL
Sbjct: 617 KLTVRKNQTYLVLDAEQVNYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPL 676

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +K+EAP V TG+E  VA+ S   + A  +G V  VDA +I+I              +I+ 
Sbjct: 677 IKSEAPLVATGIEEAVARFSATNLRAAISGKVTYVDAKKIII--------DDGEKPEIHY 728

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F++SNQ T + Q+P VKVGD+V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 729 LRYFEKSNQETLILQKPTVKVGDKVKKGQLICDGPSTDNGELALGKNVLVAFSTWYGYNY 788

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R TK G + +T +IPN S +   ++D  GI+ 
Sbjct: 789 EDAIIISEKLVKDDVFTSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVI 848

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV+ GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+
Sbjct: 849 VGSEVDTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQ 908

Query: 944 IFNRHGID 951
           I +R   D
Sbjct: 909 ILSRDQGD 916



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 161/504 (31%), Positives = 238/504 (47%), Gaps = 67/504 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG +V  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 747  VKVGDKVKKGQLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 804

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   + +        +       ++ LD N    +   +   + + G   
Sbjct: 805  TSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVIVGSEVDTGDILVGRTS 864

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 865  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 913

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  ++K+ +A KR I+ GDKMAGRHGNKG+VS ILP EDMPFL+DGTPVDIV
Sbjct: 914  QGDNLEEGVGMLIKILIAQKRKIKVGDKMAGRHGNKGVVSVILPVEDMPFLEDGTPVDIV 973

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG     L  K  + + D      I  L             
Sbjct: 974  LNPQGVPSRMNIGQVLELHLGMVAKKLKTKFVTPVFDGIKIETIKKL------------- 1020

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         FD             A++ ESG+  L+DG++
Sbjct: 1021 -----------------------------FD------------EANIPESGKFKLFDGIS 1039

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR GEME W 
Sbjct: 1040 GQAFENPVSVGYMYMLKLLHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRFGEMETWA 1099

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++++GA  VL E+LT KSD++ GR  +Y +I++G      GTPESFNVL  E++ L + +
Sbjct: 1100 LESFGATSVLSELLTYKSDNIQGRNLLYNNIISGGKIPSPGTPESFNVLAYELRGLLIKL 1159

Query: 1362 DLENSRTKNSAKMEEIPDFNKCEL 1385
            ++  +  +N    E        E+
Sbjct: 1160 EVHKNDQENQEGEEIKDPLELPEI 1183


>gi|71893967|ref|YP_279413.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           J]
 gi|88909142|sp|Q4A969|RPOB_MYCHJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|71852094|gb|AAZ44702.1| DNA-directed RNA polymerase subunit beta [Mycoplasma hyopneumoniae
           J]
          Length = 1220

 Score =  572 bits (1474), Expect = e-160,   Method: Composition-based stats.
 Identities = 328/968 (33%), Positives = 527/968 (54%), Gaps = 75/968 (7%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +   G+G  R+F+G   + ++ PD ++  + S+D FL +          G+  AF  +
Sbjct: 5   YKLKSYGIGTDRRFYGVANKTLETPDFLDPVRESFDWFLHV----------GIPEAFDRI 54

Query: 63  FPITAFSGAAMLEF--VSYEFDPPKFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           FPI + +G   + F   S   + P+ +   + +   +  TY+  + +TL  +  +     
Sbjct: 55  FPIVSANGKLEISFRRGSLRVEKPENEYLAIREAKIKGKTYSARVYVTLVKVHSED---- 110

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 +++EQ I + + P MT+ GTF+I G +++VVSQL RSPG+ F  +  R   +  
Sbjct: 111 -----GEMEEQEILLAEFPFMTQGGTFIINGFEKVVVSQLIRSPGVCF-RENVRNQQADD 164

Query: 178 LLYACRIIPDQGLWMDIEFDSK----DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
           L     IIP  G WM+I         D +  RID+ + +P+ SFL A+G  +E +   F 
Sbjct: 165 LFNKVEIIPQLGSWMEIFHKVTGNQVDTVKFRIDKHKNIPLLSFLRAIGFTNETVRKYFG 224

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                 +            +L +  ++              E  K L   ++ + +   +
Sbjct: 225 NSPELLESIRRHKLESLEENLELIYRIVR-----KDDRITEEGLKNLIPSIIFNERRYNL 279

Query: 294 KFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
              G           + +   Y+AED+V+ +   ++ +   +  + +LE        +IP
Sbjct: 280 ASTGRFMLNAKLNLVERISQTYLAEDLVSKKNKILFKKGTYITRQLALEIQEKFNNEEIP 339

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +  ++ V++  Y R   +T      K   + I +V                         
Sbjct: 340 LSEIEGVDSTIYARQLEITRNENLWKRFYVAIVKVWPNKK-------------------- 379

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              S +   +    +  D   + + +   DIIAI+    +L +  G  DD D+L N+R+ 
Sbjct: 380 ---SMLQESEPVNVIATDPNLNEKTLVLSDIIAIVSYYFNLLSNLGKSDDPDSLVNKRIV 436

Query: 466 SVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           SVGE+L+NQ+ + L ++E++ KE+  +  D+  +  + +IN KP+ +    FF SS+LSQ
Sbjct: 437 SVGELLQNQFLIALTKIEKNSKEKISTKSDLSQLTVKSIINNKPIYNQFKNFFNSSKLSQ 496

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L  +   R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 497 FMDQINPLGEMASKRKVTSLGPGGLNRDTAQFEVRDVHTTHYGRICPVETPEGQNIGLIL 556

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           + + F+R+N YGFI TPY +V +  V  + V +L+A EE ++  AQ+   +D++     +
Sbjct: 557 NFSVFSRINQYGFIITPYYQVKNRIVDYSKVHWLAASEEFDKSFAQSGVEIDQNNRIIPD 616

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     +++  E++++ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL
Sbjct: 617 KLTVRKNQTYLVLDAEQVNYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPL 676

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +K+EAP V TG+E  VA+ S   + A  +G V  VDA +I+I              +I+ 
Sbjct: 677 IKSEAPLVATGIEEAVARFSATNLRASISGKVTYVDAKKIII--------DDGEKPEIHY 728

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F++SNQ T + Q+P VKVGD+V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 729 LRYFEKSNQETLILQKPTVKVGDKVKKGQLICDGPSTDNGELALGKNVLVAFSTWYGYNY 788

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R TK G + +T +IPN S +   ++D  GI+ 
Sbjct: 789 EDAIIISEKLVKDDVFTSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVI 848

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV+ GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+
Sbjct: 849 VGSEVDTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQ 908

Query: 944 IFNRHGID 951
           I +R   D
Sbjct: 909 ILSRDQGD 916



 Score =  422 bits (1084), Expect = e-115,   Method: Composition-based stats.
 Identities = 162/504 (32%), Positives = 239/504 (47%), Gaps = 67/504 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG +V  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 747  VKVGDKVKKGQLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 804

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   + +        +       ++ LD N    +   +   + + G   
Sbjct: 805  TSIHIQEQTIKFRSTKAGNDILTAEIPNASAKSRLHLDANGIVIVGSEVDTGDILVGRTS 864

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 865  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 913

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  ++K+ +A KR I+ GDKMAGRHGNKG+VS ILP EDMPFL+DGTPVDIV
Sbjct: 914  QGDNLEEGVGMLIKILIAQKRKIKVGDKMAGRHGNKGVVSVILPVEDMPFLEDGTPVDIV 973

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG     L  K  + + D      I  L             
Sbjct: 974  LNPQGVPSRMNIGQVLELHLGMVAKKLKTKFVTPVFDGIKIETIKKL------------- 1020

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         FD             A++ ESG+  L+DG++
Sbjct: 1021 -----------------------------FD------------EANIPESGKFKLFDGIS 1039

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR GEME W 
Sbjct: 1040 GQPFENPVSVGYMYMLKLLHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRFGEMETWA 1099

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++++GA  VL E+LT KSD++ GR  +Y +I++G      GTPESFNVL  E++ L + +
Sbjct: 1100 LESFGATSVLSELLTYKSDNIQGRNLLYNNIISGGKIPSPGTPESFNVLAYELRGLLIKL 1159

Query: 1362 DLENSRTKNSAKMEEIPDFNKCEL 1385
            ++  +  +N    E        E+
Sbjct: 1160 EVHKNDQENQEVEEIKDPLELPEI 1183


>gi|309792540|ref|ZP_07687002.1| DNA-directed RNA polymerase, beta subunit [Oscillochloris
           trichoides DG6]
 gi|308225354|gb|EFO79120.1| DNA-directed RNA polymerase, beta subunit [Oscillochloris
           trichoides DG6]
          Length = 1220

 Score =  572 bits (1473), Expect = e-160,   Method: Composition-based stats.
 Identities = 314/974 (32%), Positives = 469/974 (48%), Gaps = 105/974 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLE 75
           F +  + ID+P LIE Q  S+D F            EGL+  F  + PIT F+G    L 
Sbjct: 26  FARIHDAIDVPRLIETQVNSFDWF----------KREGLRELFDEISPITDFTGKNLELH 75

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F  Y F  P+F   +C  RDLTYA PL++ + L V          +  +IKE  +++GD 
Sbjct: 76  FRDYVFGEPRFTEFECRERDLTYAAPLRVNVELRVL---------ATGEIKESELFLGDF 126

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           P+MT +GTF+  G +R+VVSQL RSPG++F  +K     SG+ L++ ++IP++G W++ E
Sbjct: 127 PVMTDNGTFIYNGAERVVVSQLIRSPGVYFKDEKEPT--SGRSLHSAKLIPNRGAWLEFE 184

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMAL-----------GMDSEEILSTFYPKIVY------ 238
            + +D+I V++DR+RK+PVT  + A+               +  L               
Sbjct: 185 TNKRDVISVKVDRKRKIPVTILIRAILAWQADETGEGHWVPDNELDQHGHNEHVIEVLKH 244

Query: 239 ------------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGL 284
                       +   D       A   +           ++    ++ES         L
Sbjct: 245 IDTVHEHPYTQATLDKDPARNSKEALMELYKRLRPGDPPTLENARSLLESLLFNPRRYDL 304

Query: 285 LKSLKEKGVKFLGITSDCLCG---------LYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            K  + K  K L        G           +    +     ++            ++ 
Sbjct: 305 AKVGRYKLNKNLWEREARRDGVSNAPSMSVRVLLPRDIIKIVEQLIQLNNGHGRPDDIDH 364

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVT--DKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
           + +  +R +  L              +V      +D   A  +    +RP        A 
Sbjct: 365 LGNRRVRTVGELIQQQFRVGLLRLERVVKERMSLQDPDSATPNGLINIRP-----VVAAM 419

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
             F      S   D +       N R    +      + ++     ++ +     G+  I
Sbjct: 420 REFFGGSQLSQFMDQTNPLAELTNKR--RLSALGPGGLSRDRAGFEVRDVHHSHYGR--I 475

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
             ++      +  +G M        +  +E   ++  + V+   V  +  I  + V    
Sbjct: 476 CPVETPEGPNIGLIGTMSTFSRVNEMGFLETPYRKVYNIVENAPVWLEKGILLRDVRDLR 535

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                ++           + +    R    L +G + R                 + P  
Sbjct: 536 TGDLIAA-------KGTRVDQAISKRIAIGLLRGQILRED--------------IVDPNS 574

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                      +     R+          R +    V+ +V YLSA EE+   + QAN+ 
Sbjct: 575 GETIAEAETEINRNLAERIVEMPIKTIKIRPI----VSQEVDYLSADEEDRFVVVQANAE 630

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +DE   F   +V CR   + +    +++D++D SPKQVVS++ +LIPFLE+DD+NR LMG
Sbjct: 631 IDEHNRFLSNMVACRFGEDFVSERIDRVDYMDVSPKQVVSVSTALIPFLEHDDANRALMG 690

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ +AP VGTGME   A+ SG  +VA++ G V      RI++   +G   
Sbjct: 691 SNMQRQAVPLLRPDAPIVGTGMEFRAARDSGQVVVARKPGTVLSATGDRIIVEEDDGTER 750

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y L KF RSNQ+TC+NQRP V  G  V+  ++IAD  STD G+LALG+N+LV
Sbjct: 751 E-------YPLRKFMRSNQDTCINQRPNVLRGQRVQAGEVIADSSSTDFGELALGQNILV 803

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+MPW G NFED++L+SER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV ++ L
Sbjct: 804 AYMPWEGGNFEDAILVSERLVREDIFTSIHIEKYEVEARDTKLGPEEITRDIPNVGQDSL 863

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +N+DE GII VGAEV P DILVGKITPKGE+ +T EE+LLRAIFGEKA +V+D+SLRVP+
Sbjct: 864 RNLDEHGIIYVGAEVQPNDILVGKITPKGETDLTAEERLLRAIFGEKAREVKDSSLRVPN 923

Query: 934 GVSGTVVDVRIFNR 947
           GV G V+DV++F+R
Sbjct: 924 GVRGKVIDVKVFSR 937



 Score =  558 bits (1439), Expect = e-156,   Method: Composition-based stats.
 Identities = 324/1143 (28%), Positives = 486/1143 (42%), Gaps = 124/1143 (10%)

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC-------LCGLYVAEDIVN 314
                +  +G  +  +      G     +      + +  D        +    +     +
Sbjct: 157  KDEKEPTSGRSLHSAKLIPNRGAWLEFETNKRDVISVKVDRKRKIPVTILIRAILAWQAD 216

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             ETGE     G  + +  L++  H+E     + ++D+V+ + Y + TL  D  ++ K+AL
Sbjct: 217  -ETGE-----GHWVPDNELDQHGHNEHVIEVLKHIDTVHEHPYTQATLDKDPARNSKEAL 270

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL----------NLDT 424
            +++Y+ +RPGD  T   A S+   L F+  +YDL+ VGR K+N  L          +   
Sbjct: 271  MELYKRLRPGDPPTLENARSLLESLLFNPRRYDLAKVGRYKLNKNLWEREARRDGVSNAP 330

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               VR +   DII I++ L+ L NG G  DDID+LGNRRVR+VGE+++ Q+R+GLLR+ER
Sbjct: 331  SMSVRVLLPRDIIKIVEQLIQLNNGHGRPDDIDHLGNRRVRTVGELIQQQFRVGLLRLER 390

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             +KER+S  D DS  P  LIN +PVV+A+ EFF  SQLSQ  +  N L+ +T+ RRLSAL
Sbjct: 391  VVKERMSLQDPDSATPNGLINIRPVVAAMREFFGGSQLSQFMDQTNPLAELTNKRRLSAL 450

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ ++++F+RVN  GF+ETPYRK
Sbjct: 451  GPGGLSRDRAGFEVRDVHHSHYGRICPVETPEGPNIGLIGTMSTFSRVNEMGFLETPYRK 510

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V                     I +      E G    + V     G+ I     ++D  
Sbjct: 511  V-------------------YNIVENAPVWLEKGILLRD-VRDLRTGDLIAAKGTRVD-Q 549

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE--APFVGTGMESVVAKS 722
              S +  + +    I   +  D N        + +    L        + T     +   
Sbjct: 550  AISKRIAIGLLRGQILREDIVDPNSGETIAEAETEINRNLAERIVEMPIKTIKIRPIVSQ 609

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSV--EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                + A        V A   +        ++     G D       +    +    Q  
Sbjct: 610  EVDYLSADEEDRFVVVQANAEIDEHNRFLSNMVACRFGEDFVSERIDRVDYMDVSPKQVV 669

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVF 839
             V            A+              +L    P  G   E      S ++V     
Sbjct: 670  SVSTALIPFLEHDDANRALMGSNMQRQAVPLLRPDAPIVGTGMEFRAARDSGQVVVARKP 729

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             ++     + +  +   G E        +       I++   +  G  V  G+++    +
Sbjct: 730  GTVLSATGDRIIVEEDDGTEREYPLRKFMRSNQDTCINQRPNVLRGQRVQAGEVIADSSS 789

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   + +L A    +  +  D  L     VS  +V   IF    I+K E     
Sbjct: 790  T-DFGELALGQNILVAYMPWEGGNFEDAIL-----VSERLVREDIFTSIHIEKYEVEARD 843

Query: 960  EREQIELLARDK----DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             +   E + RD      D    LD         I  G           K T      ++ 
Sbjct: 844  TKLGPEEITRDIPNVGQDSLRNLDE-----HGIIYVGAEVQPNDILVGKITPKGETDLTA 898

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R     F  +  +V+ +   +          +      K+     G ++P GV + V+
Sbjct: 899  EERLLRAIFGEKAREVKDSSLRVPNGVRGKVIDV------KVFSRSEGAELPVGVNQTVR 952

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +  KR                   +I P + M                          
Sbjct: 953  VLLCQKR-------------------KISPGDKM-------------------------- 967

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                         G K          +    P    ++ ++       +++         
Sbjct: 968  ---------AGRHGNKGVVSRVLPIEDMPFLPDGRPVDIILNPIGVPSRMNIGQILETHL 1018

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 + G  V+TPVFDGADE+ I  ML  + L   G+  LYDG TG PF  PVTVGY Y
Sbjct: 1019 GWAAARLGYRVATPVFDGADEKQIKQMLIDSGLPADGKVTLYDGRTGIPFHHPVTVGYAY 1078

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY+LQEML
Sbjct: 1079 MLKLAHLVEDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYILQEML 1138

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LGLS+++ +   K     +
Sbjct: 1139 TVKSDDVVGRVKTYEAIVKGEPIQEAGVPESFKVLIKELQSLGLSVEVLSEDEKPVELSD 1198

Query: 1376 EIP 1378
            ++ 
Sbjct: 1199 DVD 1201


>gi|171319358|ref|ZP_02908468.1| RNA polymerase Rpb2 domain 2 [Burkholderia ambifaria MEX-5]
 gi|171095429|gb|EDT40401.1| RNA polymerase Rpb2 domain 2 [Burkholderia ambifaria MEX-5]
          Length = 554

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 197/470 (41%), Positives = 293/470 (62%), Gaps = 3/470 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               F    R+RK F K P +  +P L+  Q  S+  FL  ++   +R  EGLQAAF SV
Sbjct: 1   MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPGTQRKPEGLQAAFTSV 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D  E      +
Sbjct: 61  FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVILDK-ESPNKPVV 119

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K++KEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 120 KEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 179

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KDI++ R+DRRRK+PVT  L A+G+  E+IL+ F+    ++   
Sbjct: 180 RIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMD 239

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +          L  G      + D   G+ +++  K++ +  ++ L+    KF+ +  D 
Sbjct: 240 EGAQLEFVPERL-RGEVARFDITD-RDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDY 297

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G  +A+++V+G+TGE+   A D + E  LE++  + I++I  LY + ++   YI +TL
Sbjct: 298 LLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKEIQTLYTNDLDQGPYISSTL 357

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D+  DR  A + IYR+MRPG+  T    E++FN LF+  + YDLS VGR+K N R++ 
Sbjct: 358 RVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKFNRRVSR 417

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           D       ++ +DI+A IKILV+LRNGKG +DDID+LGNRRVR VGE+ +
Sbjct: 418 DEITGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAE 467


>gi|290889117|gb|ADD69908.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
          Length = 457

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 287/456 (62%), Positives = 363/456 (79%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 2   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+IL
Sbjct: 122 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++
Sbjct: 182 STFYKKITYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRSARQMQ 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +D+P+L +
Sbjct: 241 EKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKVLNEQGYKDLPLLDI 300

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 301 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 360

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 361 AVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQDLIN
Sbjct: 421 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLIN 456


>gi|290889125|gb|ADD69912.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
          Length = 457

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 284/457 (62%), Positives = 360/457 (78%), Gaps = 1/457 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+T
Sbjct: 2   PAGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D 
Sbjct: 122 DHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           E+ILSTFY KI Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    
Sbjct: 182 EQILSTFYKKITYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRSA 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + ++EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +D+P
Sbjct: 241 RQMQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKVLNEQGYKDLP 300

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L +D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++
Sbjct: 301 LLDIDHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAER 360

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           YDLS VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVR
Sbjct: 361 YDLSAVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVR 420

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           SVGE+++NQYR+GLLRMER+IKER+SSVDID+VMPQD
Sbjct: 421 SVGELMENQYRIGLLRMERAIKERMSSVDIDTVMPQD 457


>gi|290889131|gb|ADD69915.1| RNA polymerase beta subunit [Rhizobium lusitanum]
          Length = 461

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 312/459 (67%), Positives = 385/459 (83%), Gaps = 1/459 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA F+SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFRSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY K +Y + GD W  P +A  L  GAK  + ++D DTGE V+E GKKLT  LL+ L+
Sbjct: 183 STFYTKSLYQRSGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVEGGKKLTPRLLRQLQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L  T + L GL++AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 DKGLKALKATDEELYGLFLAEDIVNLRTGEIYLEAGDEIDEKTLPVILKAGFEEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLSADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD  D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDVADTVRVLRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKP 460


>gi|269115042|ref|YP_003302805.1| DNA-dependent RNA polymerase subunit beta [Mycoplasma hominis]
 gi|268322667|emb|CAX37402.1| DNA-dependent RNA polymerase beta chain [Mycoplasma hominis ATCC
           23114]
          Length = 1199

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 338/986 (34%), Positives = 526/986 (53%), Gaps = 77/986 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            +R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G 
Sbjct: 16  TLRRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GK 64

Query: 72  AMLEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++
Sbjct: 65  VRIEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEV 115

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           ++  +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     II
Sbjct: 116 EDSEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEII 174

Query: 186 PDQGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           P  G W++I         D + + ID+ +   V +FL ALG     I   F   I   + 
Sbjct: 175 PQIGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEE 234

Query: 242 --GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI- 298
                    ++A ++   A+ +   +         +S + L    L + K   +   G  
Sbjct: 235 TFKRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRF 294

Query: 299 -------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVD 350
                    + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  + 
Sbjct: 295 TLNRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLP 353

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++ NAY     V                            +      ++    + D+  
Sbjct: 354 DIDENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLH 392

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+
Sbjct: 393 DQKVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGEL 449

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N
Sbjct: 450 LQNQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCN 509

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA
Sbjct: 510 PLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFA 569

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           +++ YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R 
Sbjct: 570 KIDKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRR 628

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP
Sbjct: 629 DNEYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAP 688

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            V TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+R
Sbjct: 689 LVATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFER 742

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ T ++Q  LVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++
Sbjct: 743 SNQGTLIHQVLLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVL 802

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV 
Sbjct: 803 SERLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVT 862

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R  
Sbjct: 863 AGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF 922

Query: 950 IDKNERSISVEREQIELLARDKDDEQ 975
              ++    +E+     +A+ +  + 
Sbjct: 923 G--DQLEDGIEKIVKVSIAQKRKIQV 946



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 165/497 (33%), Positives = 233/497 (46%), Gaps = 67/497 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 754  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 811

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 812  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 871

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 872  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 922

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 923  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 980

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D  ++  I  +       +   S
Sbjct: 981  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGISHNQIRDILEEANIDVTGKS 1040

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DGA                          
Sbjct: 1041 I----------------------------VYDGA-------------------------- 1046

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1047 TGEPFDHPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1106

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             I++YGA+ VLQE+LT KSDD+VGR ++Y S+       + GTPESFNVL  E++ LG+ 
Sbjct: 1107 AIESYGASNVLQELLTYKSDDIVGRNKLYNSLARDARLPKPGTPESFNVLAYELRGLGIK 1166

Query: 1361 IDLENSRTKNSAKMEEI 1377
            +++           EE 
Sbjct: 1167 LEVHQKSDNVVDDSEED 1183


>gi|211998810|gb|ACJ15317.1| RNA polymerase beta subunit [Mesorhizobium plurifarium]
          Length = 466

 Score =  570 bits (1470), Expect = e-160,   Method: Composition-based stats.
 Identities = 304/465 (65%), Positives = 373/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEAPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTSNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRSGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD ID+K+L+ +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDDKTLKVLLGTGEEE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I IL +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQILDIDHVNVGAYIRNTLAVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|222093427|gb|ACM43490.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 976

 Score =  569 bits (1467), Expect = e-159,   Method: Composition-based stats.
 Identities = 340/984 (34%), Positives = 526/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKCSSYQGKLKTHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T +NQ PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLINQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 112/253 (44%), Gaps = 13/253 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNV 1133
            VLNP GVPSRMN+
Sbjct: 964  VLNPQGVPSRMNI 976


>gi|222093429|gb|ACM43491.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 977

 Score =  569 bits (1467), Expect = e-159,   Method: Composition-based stats.
 Identities = 338/984 (34%), Positives = 525/984 (53%), Gaps = 77/984 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G   
Sbjct: 1   RRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GKVR 49

Query: 74  LEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++++
Sbjct: 50  IEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEVED 100

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
             +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     IIP 
Sbjct: 101 SEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEIIPQ 159

Query: 188 QGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR-- 241
            G W++I         D + + ID+ +   V +FL ALG     I   F   I   +   
Sbjct: 160 IGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEETF 219

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI--- 298
                  ++A ++   A+ +   +         +S + L    L + K   +   G    
Sbjct: 220 KRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRFTL 279

Query: 299 -----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVDSV 352
                  + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  +  +
Sbjct: 280 NRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLPDI 338

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
           + NAY     V                            +      ++    + D+    
Sbjct: 339 DENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLHDQ 377

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+L+
Sbjct: 378 KVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGELLQ 434

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GLL++E++ +ERIS+ DID +  +++ N KP+ +    FF +S+LSQ  +  N L
Sbjct: 435 NQFRIGLLKLEKNTRERISAKDIDKITAKNVTNNKPIFNQFKSFFNTSKLSQFMDQCNPL 494

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA++
Sbjct: 495 AEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFAKI 554

Query: 593 NAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R   
Sbjct: 555 DKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRRDN 613

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP V
Sbjct: 614 EYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAPLV 673

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+RSN
Sbjct: 674 ATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFERSN 727

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T ++Q  LVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++SE
Sbjct: 728 QGTLIHQVLLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVLSE 787

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV  G
Sbjct: 788 RLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAG 847

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R    
Sbjct: 848 DILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREFG- 906

Query: 952 KNERSISVEREQIELLARDKDDEQ 975
            ++    +E+     +A+ +  + 
Sbjct: 907 -DQLEDGIEKIVKVSIAQKRKIQV 929



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 73/254 (28%), Positives = 113/254 (44%), Gaps = 13/254 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 737  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 794

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 795  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 854

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 855  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 905

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 906  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 963

Query: 1121 VLNPLGVPSRMNVG 1134
            VLNP GVPSRMN+G
Sbjct: 964  VLNPQGVPSRMNIG 977


>gi|290889115|gb|ADD69907.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 457

 Score =  569 bits (1467), Expect = e-159,   Method: Composition-based stats.
 Identities = 310/457 (67%), Positives = 383/457 (83%), Gaps = 1/457 (0%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
           +EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLIVF
Sbjct: 2   DEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLIVF 61

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           D+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+
Sbjct: 62  DIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGK 121

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
           +  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEILST
Sbjct: 122 SHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILST 181

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL++L+EK
Sbjct: 182 FYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRTLQEK 240

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           G+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +D 
Sbjct: 241 GLKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDIDH 300

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS V
Sbjct: 301 INVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLSAV 360

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GRVKMNMRL+LD PD VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE++
Sbjct: 361 GRVKMNMRLDLDVPDTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELM 420

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 421 ENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKP 457


>gi|290889119|gb|ADD69909.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 457

 Score =  569 bits (1466), Expect = e-159,   Method: Composition-based stats.
 Identities = 281/456 (61%), Positives = 365/456 (80%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 3   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 123 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+
Sbjct: 183 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++P+L +
Sbjct: 242 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEQGYKELPLLDI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 302 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQDLIN
Sbjct: 422 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLIN 457


>gi|211998834|gb|ACJ15329.1| RNA polymerase beta subunit [Mesorhizobium sp. CCBAU 01550]
 gi|211998836|gb|ACJ15330.1| RNA polymerase beta subunit [Mesorhizobium sp. CCBAU 45265]
 gi|211998838|gb|ACJ15331.1| RNA polymerase beta subunit [Mesorhizobium sp. CCBAU 25300]
 gi|211998840|gb|ACJ15332.1| RNA polymerase beta subunit [Mesorhizobium sp. CCBAU 45272]
          Length = 466

 Score =  569 bits (1466), Expect = e-159,   Method: Composition-based stats.
 Identities = 305/465 (65%), Positives = 374/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTSNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +  D   G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNV-DRFRGLKAVGDLVDADTGEIVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD ID+K+L+ +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDDKTLKVLLGTGEDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I IL +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQILDIDHVNVGAYIRNTLAVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889099|gb|ADD69899.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 457

 Score =  568 bits (1465), Expect = e-159,   Method: Composition-based stats.
 Identities = 309/456 (67%), Positives = 381/456 (83%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 2   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 122 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL++L+
Sbjct: 182 STFYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRTLQ 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKGVK L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 241 EKGVKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDI 300

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 301 DHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLS 360

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 361 AVGRVKMNMRLDLDVADTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 421 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 456


>gi|290784132|gb|ADD62618.1| RNA polymerase beta subunit [Bradyrhizobium betae]
          Length = 462

 Score =  568 bits (1465), Expect = e-159,   Method: Composition-based stats.
 Identities = 284/459 (61%), Positives = 368/459 (80%), Gaps = 1/459 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 3   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 123 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++
Sbjct: 183 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +
Sbjct: 242 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEHGYKELPLLDI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 302 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP
Sbjct: 422 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKP 460


>gi|290889139|gb|ADD69919.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 461

 Score =  568 bits (1465), Expect = e-159,   Method: Composition-based stats.
 Identities = 284/459 (61%), Positives = 368/459 (80%), Gaps = 1/459 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 3   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 123 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++
Sbjct: 183 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +
Sbjct: 242 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 302 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP
Sbjct: 422 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKP 460


>gi|46202801|ref|ZP_00052575.2| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 496

 Score =  568 bits (1465), Expect = e-159,   Method: Composition-based stats.
 Identities = 256/477 (53%), Positives = 340/477 (71%), Gaps = 27/477 (5%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           +P+LIEVQK+SYDHFL M+ AP+ R N GLQ  FKSVFPI  FS    LEFV YE + PK
Sbjct: 1   MPNLIEVQKSSYDHFLQMDTAPEARGNVGLQEVFKSVFPIKDFSERGTLEFVRYELEQPK 60

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           +DV++C  R +T+A PLK+TLRL+V+D+DE TG++SI+DIKEQ +YMGD+PLMT +GTFV
Sbjct: 61  YDVEECQQRGMTFAAPLKVTLRLVVWDIDEDTGSRSIRDIKEQDVYMGDMPLMTSNGTFV 120

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+++VR
Sbjct: 121 INGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVR 180

Query: 206 IDRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQ 240
           IDRRRK+PVT+ L AL                         GM SEEILS FY K+VY++
Sbjct: 181 IDRRRKLPVTTLLYALDGLNTAQLRVARAAEGRGLEQSEIKGMTSEEILSYFYGKVVYTR 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
               W  P  A  L  G K+ S L+D  TGE+V ++G K+T  L K LKE G+  + I +
Sbjct: 241 GPKGWKTPFDAERL-KGVKLVSDLIDAKTGEKVADAGAKMTPRLGKKLKEAGLTDIQIFT 299

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + + G YVAEDI+N +TGEI+ EAGD +    + E+  + I ++P+L +D +N   Y+RN
Sbjct: 300 EDMVGQYVAEDIINEQTGEIFTEAGDELTAALVAELEKAGISELPVLAIDHINVGPYMRN 359

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           TL  DKN  R++AL+DIYRVMRPG+  T   AE++F  LFFDS++YDLS VGRVKMN RL
Sbjct: 360 TLAIDKNSSREEALIDIYRVMRPGEPPTLETAEALFQGLFFDSERYDLSAVGRVKMNSRL 419

Query: 421 N-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N  +  D VR +RKE I+ +IK+LV+L++GKG IDDID+LGNRRVRSVGE+++   R
Sbjct: 420 NTPEVADTVRVLRKEHILGVIKVLVELKDGKGEIDDIDHLGNRRVRSVGELMEISPR 476


>gi|290889111|gb|ADD69905.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 457

 Score =  568 bits (1464), Expect = e-159,   Method: Composition-based stats.
 Identities = 309/456 (67%), Positives = 381/456 (83%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL++L+
Sbjct: 183 STFYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRTLQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKGVK L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 EKGVKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDVADTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 457


>gi|290889101|gb|ADD69900.1| RNA polymerase beta subunit [Agrobacterium rhizogenes]
          Length = 457

 Score =  568 bits (1464), Expect = e-159,   Method: Composition-based stats.
 Identities = 308/456 (67%), Positives = 383/456 (83%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQSVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY K +Y + GD W  P +A  L  GAK  + ++D DTGE V+E GKKLT  LL+ L+
Sbjct: 183 STFYTKSLYERSGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVEGGKKLTPRLLRQLQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L  T + L GL++AEDIVN +TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 DKGLKALKATDEDLYGLFLAEDIVNFQTGEIYLEAGDEIDEKTLPVILKAGFDEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLSADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L+  D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLEVADTVRVLRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 457


>gi|290889097|gb|ADD69898.1| RNA polymerase beta subunit [Sinorhizobium fredii]
 gi|290889121|gb|ADD69910.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 457

 Score =  567 bits (1462), Expect = e-159,   Method: Composition-based stats.
 Identities = 306/453 (67%), Positives = 378/453 (83%), Gaps = 1/453 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 4   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 63

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 64  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 123

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 124 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 183

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  LL++L+
Sbjct: 184 STFYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVEAGKKLTPRLLRTLQ 242

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKGVK L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 243 EKGVKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIPVLDI 302

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 303 DHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNALFFDAERYDLS 362

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD  D VR +RKEDI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 363 AVGRVKMNMRLDLDVADTVRTLRKEDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 422

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQD
Sbjct: 423 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQD 455


>gi|211998830|gb|ACJ15327.1| RNA polymerase beta subunit [Mesorhizobium tarimense]
          Length = 466

 Score =  567 bits (1462), Expect = e-159,   Method: Composition-based stats.
 Identities = 302/465 (64%), Positives = 372/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI  FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPIQDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLSAGDDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLSVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889109|gb|ADD69904.1| RNA polymerase beta subunit [Bradyrhizobium yuanmingense]
          Length = 457

 Score =  567 bits (1461), Expect = e-159,   Method: Composition-based stats.
 Identities = 282/458 (61%), Positives = 363/458 (79%), Gaps = 1/458 (0%)

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+
Sbjct: 1   GLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDI 60

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+  
Sbjct: 61  DEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTH 120

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY
Sbjct: 121 SSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFY 180

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
            KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+
Sbjct: 181 KKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGL 239

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
           K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN
Sbjct: 240 KALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKELPLLDIDHVN 299

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
              YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGR
Sbjct: 300 VGPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAMFQSLFFDAERYDLSAVGR 359

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           VKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE+++N
Sbjct: 360 VKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGELMEN 419

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
           QYR+GLLRMER+IKER+SSVDID+VMPQDLINAKP  +
Sbjct: 420 QYRIGLLRMERAIKERMSSVDIDTVMPQDLINAKPAAA 457


>gi|211998812|gb|ACJ15318.1| RNA polymerase beta subunit [Mesorhizobium tianshanense]
          Length = 466

 Score =  567 bits (1461), Expect = e-159,   Method: Composition-based stats.
 Identities = 302/465 (64%), Positives = 372/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD ID+K+L+ +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDDKTLKVLLSAGDDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLSVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889105|gb|ADD69902.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 457

 Score =  567 bits (1460), Expect = e-159,   Method: Composition-based stats.
 Identities = 281/456 (61%), Positives = 365/456 (80%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 3   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 123 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++
Sbjct: 183 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +
Sbjct: 242 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 302 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQDLIN
Sbjct: 422 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQDLIN 457


>gi|211998832|gb|ACJ15328.1| RNA polymerase beta subunit [Mesorhizobium gobiense]
          Length = 466

 Score =  567 bits (1460), Expect = e-159,   Method: Composition-based stats.
 Identities = 303/465 (65%), Positives = 372/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLKVLLGAGDDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLSVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|323388478|gb|ADX60528.1| DNA-directed RNA polymerase [Geobacillus sp. NTU 03]
          Length = 549

 Score =  567 bits (1460), Expect = e-159,   Method: Composition-based stats.
 Identities = 225/614 (36%), Positives = 333/614 (54%), Gaps = 75/614 (12%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   MTGRLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFR 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FSG   LEF+ Y    PK+ V++   RD+TYA PL++ +RLI          K
Sbjct: 51  EISPIEDFSGNLSLEFIDYSLGEPKYTVEEAKERDVTYAAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KE  ++MGD PLMT+ GTF+I G +R++VSQL RSP +++     +   +GK  Y
Sbjct: 102 ETGEVKEHDVFMGDFPLMTETGTFIINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  +IP++G W++ E D+KD+++VRID  RK+PVT  L ALG  S+ EI+          
Sbjct: 159 SATVIPNRGAWLEYETDAKDVVYVRIDGTRKLPVTVLLRALGFSSDQEIIDLLGDNEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK------- 291
              +      +   L+           +  GE   +E+ K L +      K         
Sbjct: 219 NTLEKDNTDSTEKALI------EIYERLRPGEPPTLENAKNLLASRFFDPKRYDLASVGR 272

Query: 292 -GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE I++ ET E+  EAG +ID ++L  +     + + +    
Sbjct: 273 YKINKKLHIKNRLFNQRLAETIIDPETQEVIAEAGAMIDRRTLNRLLPYLEKGVGL---- 328

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                     T          D  L   ++  P D                         
Sbjct: 329 ---------QTYRPAGGVVDGDISLQTVQIYAPNDP------------------------ 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G    N+  N    +DV+HI   DIIA I    +L +G G  DDID+LGNRR+RSVGE+
Sbjct: 356 DGEKVTNVVGNGFIGEDVKHITPADIIASISYFFNLLHGVGDTDDIDHLGNRRLRSVGEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++A+ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIAAIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A
Sbjct: 476 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYA 535

Query: 591 RVNAYGFIETPYRK 604
           +VN +GFIETPYR+
Sbjct: 536 KVNKFGFIETPYRR 549


>gi|312874762|ref|ZP_07734781.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2053A-b]
 gi|311089507|gb|EFQ47932.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
           2053A-b]
          Length = 595

 Score =  566 bits (1459), Expect = e-159,   Method: Composition-based stats.
 Identities = 242/655 (36%), Positives = 359/655 (54%), Gaps = 72/655 (10%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           M    V  G  R R+ F +  E++ +P+L +VQ  SY  FL           EG++  F 
Sbjct: 1   MLGHAVNYGSHRTRRSFSRIKEVVKLPNLTDVQTESYKWFL----------KEGIREMFD 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI+ FSG   LEFV Y+   PK+ +++    D  Y+ PL +TLRL            
Sbjct: 51  DIMPISDFSGKLSLEFVDYKLLKPKYTLEEARDHDANYSAPLHVTLRLT---------NH 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD PLMT  GTFVI G +R++VSQL RSPG+++  D  +   +G+ +Y
Sbjct: 102 ETGEIKTQDVFFGDFPLMTDSGTFVINGAERVIVSQLVRSPGVYYHCDYDK---NGRPIY 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+K++ +VRIDR RK+P+T  + ALG++S+ +I   F      S
Sbjct: 159 GTTVIPNRGAWLEYETDAKNLAYVRIDRTRKLPMTVLVRALGLESDSDIQDFFGKSDSLS 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      + AD  V   +      +  GE    +S + L        K   +  +G 
Sbjct: 219 FTLEKD-MHKNPADTRVAESLKDIYERLRPGEPKTTDSSRSLLYARFFDPKRYDLAPVGR 277

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +AE + + +TGEI  + G V+  + ++++          L  D
Sbjct: 278 YKINKKLSLKNRLLRQTLAETLADPDTGEIIAKKGTVVTHELMDKLEKY-------LDRD 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                 Y  +          ++A+L         D  T    +           K D   
Sbjct: 331 DFKTVTYQPS----------EEAVL--------PDPITVQEIKVF--------SKVDPER 364

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           V ++  N  +     +DV+HI   D+++ I     L++G G+IDDID+LGNRR+R VGE+
Sbjct: 365 VVKLISNGHIG----EDVKHITPADVLSSINYFFALQDGLGSIDDIDHLGNRRIRRVGEL 420

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  DI +V PQ LIN +PVV++V EFF SSQLSQ  +  N
Sbjct: 421 LQNQFRIGLARMERVVRERMSIQDIATVTPQQLINIRPVVASVKEFFGSSQLSQFMDQNN 480

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L  +TH RR+SALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL++S+ ++A
Sbjct: 481 PLGELTHKRRMSALGPGGLSRDRAGYEVRDVHYTHYGRLCPIETPEGPNIGLINSMATYA 540

Query: 591 RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            VN YGFIETPYR++     KVT+ + YL+A  E+N  IA AN+ L+EDGSF E+
Sbjct: 541 VVNKYGFIETPYRRISWETHKVTDKIDYLTADVEDNYIIASANAPLNEDGSFKEK 595


>gi|26553531|ref|NP_757465.1| DNA-directed RNA polymerase subunit beta [Mycoplasma penetrans HF-2]
 gi|41017736|sp|Q8EWX1|RPOB_MYCPE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|26453537|dbj|BAC43869.1| DNA-directed RNA polymerase subunit beta [Mycoplasma penetrans HF-2]
          Length = 1375

 Score =  566 bits (1459), Expect = e-158,   Method: Composition-based stats.
 Identities = 346/1032 (33%), Positives = 530/1032 (51%), Gaps = 93/1032 (9%)

Query: 10   LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
               +R+ + K  +  + P+L+ +QK ++  F+          +  L+   KS+FPI +  
Sbjct: 13   KYVLRRDYSKIEKNFNEPNLLNLQKNAFHKFI----------DTELEGTIKSIFPIKSIG 62

Query: 70   GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK--- 126
            G   LE++  + + PK    +      TY  PL + L ++  +  E          K   
Sbjct: 63   GRYSLEYIGMKLEKPKRSEKEARNEGKTYDRPLYVDLAIVDNESGEVKKTTKSSKNKASN 122

Query: 127  EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF-DHDKGRASLSGKLL---YAC 182
               I+   +P++T+ GTF++ GI++ V+SQ+ RSPG +     + + S S K +   Y C
Sbjct: 123  TDGIFFASIPMITEKGTFIVNGIEKFVISQIVRSPGAYILTKSQIKLSNSRKRIQEGYIC 182

Query: 183  RIIPDQGLWMDIEFDS--KDIIHVRI-----DRRRKVPVTSFLMALGMDSEEILSTFYPK 235
             I+P +G  +   F +  KD I V       +    +P+T+FL ALG++ EEIL+ F   
Sbjct: 183  EILPAKGT-LFFIFMAENKDFIQVMFRDAIGESTHTIPITAFLKALGLNKEEILNIFANH 241

Query: 236  IVYSQRGDFWCFPL---------------------------SAADLMVGAKVSSSLVDID 268
                   D   +                                   +  K SS    ++
Sbjct: 242  KSIKNSLDNEIYNEKDVFETDELINLRKNLNSSDSNRSYGVDTKLRELFKKYSSLKSQLE 301

Query: 269  TGEQVIESGKKLTSGLLKSLKEKGVKFLGI----------TSDCLCGLYVAED--IVNGE 316
               +  E  K+L   +   + EK  K L I          +   L          I N  
Sbjct: 302  AEGKNAEKQKELNEVINNIISEKAAKDLVINLSISTKNIDSKFRLSNKETTYQSIIYNHF 361

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
                  +       K   ++  SE     +L  D  + N  +     T   K   D +  
Sbjct: 362  FSNKSFDLSKAGRFKMARKMRLSERLYQRVLAEDLKDINGKVVIKKNTLIQKHELDTIKQ 421

Query: 377  IYRVMRPGDVSTFSV---AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            + +  + G V   ++      M N + ++          + +    +  DT  D   +  
Sbjct: 422  LTKEGKLGIVHNVNLDERISKMANVVKYEKINVYQDNDSQDEFIPIIGTDTSLDKPTLSI 481

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             DI++I   +++L    G  DDID+LGN+R++ + E+LK + + GL+R+E+ I ++++  
Sbjct: 482  SDILSITSYVINLDYDIGFYDDIDHLGNKRLKLIDELLKTRAQAGLVRIEKFINDKLAIA 541

Query: 494  D--------------IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            D                S+  + +IN KP   +  EFF S QL+Q  +  N L+ +T+ R
Sbjct: 542  DGANKSQEQSEEQEPKKSLTVKSIINTKPFQISFKEFFNSHQLTQFLDQQNPLAELTNKR 601

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            R+SA+G GG++R    +++RDVH +HYG+ICP ET EG NIGL+ SL ++A  +  GF+ 
Sbjct: 602  RISAMGPGGISREDPNLDIRDVHYSHYGKICPIETPEGMNIGLIMSLATYASTDENGFLI 661

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            TPYR V +G +T+++ +L+A+ E+   IA +N ++ E   F E+ V CR          +
Sbjct: 662  TPYRIVKNGVITDEIRWLTALSEDEYIIACSNLNV-EKNKFKEDKVLCRYRSSWEFFDVK 720

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +DFID SPKQVVSIAAS IPFLENDD+NR LMG NMQRQA PL+   AP VGTG E  +
Sbjct: 721  DVDFIDISPKQVVSIAASSIPFLENDDANRALMGANMQRQATPLISPIAPIVGTGNEYKI 780

Query: 720  AKSSGA--AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            A  SG       ++ G V  VD   I I+        S S   +Y L KF +SNQNTC N
Sbjct: 781  AHDSGMAAVYDGEKDGTVSYVDGGTIKIK--------SGSEEKVYELTKFNKSNQNTCNN 832

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V VG++V +   IADGP+   G+LALG+N+LVAF  W GYN+ED++++S+R+  ED
Sbjct: 833  QVPIVSVGEKVTKGTTIADGPAMSNGELALGQNVLVAFTTWSGYNYEDAIILSKRLFMED 892

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +FTSIHI E+ V    TK G EEITRDIPNVSE   K +D+ GII VGAEV  GD+LVGK
Sbjct: 893  IFTSIHIVEYSVDCLKTKNGDEEITRDIPNVSESSKKYLDDEGIIMVGAEVKEGDVLVGK 952

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            I+PKG+  +T EEKLL+AIFG+K+ + ++TSL+VP G  GTV  V+ F +   D    + 
Sbjct: 953  ISPKGQVELTSEEKLLQAIFGDKSKNHKETSLKVPHGGEGTVAMVKRF-KVEDDYELNAD 1011

Query: 958  SVEREQIELLAR 969
             +E+ ++ ++ +
Sbjct: 1012 VIEQIKVYVVQK 1023



 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 176/619 (28%), Positives = 265/619 (42%), Gaps = 57/619 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM-ARDTKLGP 858
                       ++    P  G   E  +     M +           +        K G 
Sbjct: 753  MGANMQRQATPLISPIAPIVGTGNEYKIAHDSGMAAVYDGEKDGTVSYVDGGTIKIKSGS 812

Query: 859  EEITRD-IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EE   +             ++  I+ VG +V  G  +           +   + +L A  
Sbjct: 813  EEKVYELTKFNKSNQNTCNNQVPIVSVGEKVTKGTTIADGP-AMSNGELALGQNVLVAFT 871

Query: 918  GEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
                 +  D  +            S  +V+  +      + +E          E   +  
Sbjct: 872  TWSGYNYEDAIILSKRLFMEDIFTSIHIVEYSVDCLKTKNGDEEITRDIPNVSESSKKYL 931

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            DDE  I+      +  ++L G+ +  G         L   +  +  ++            
Sbjct: 932  DDE-GIIMVGAEVKEGDVLVGKISPKGQVELTSEEKLLQAIFGDKSKNHKETSLKVPHGG 990

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +  V  +                 K  K++   ++   V+  +KV+V  KR IQ GDKMA
Sbjct: 991  EGTVAMV-----------------KRFKVEDDYELNADVIEQIKVYVVQKRKIQIGDKMA 1033

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+S+I+P EDMP L+DGT +DI+LNPLGVPSRMN+GQI E HLG A   L   
Sbjct: 1034 GRHGNKGIISKIVPVEDMPHLEDGTTIDIMLNPLGVPSRMNIGQILELHLGLAMKKLTLS 1093

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV----- 1206
                +   K       L   + +              ++  +  + +  K          
Sbjct: 1094 KVLELYYDKKPASDFSLWFGIHEEASRNLIKNLEKILNEKQIKSLDQANKEFTDFDLSLA 1153

Query: 1207 ---------------STPVFDGADEEAINSMLRMADLDE---------SGQSILYDGLTG 1242
                           +TPVF+G +   +   +  A +D          SG+  L DG TG
Sbjct: 1154 LSRSGISREKLIYKTATPVFEGVNRTDLKEAMTEAGIDPINGKLGEGKSGKFNLIDGRTG 1213

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD  V+VG +YMLKL+HMV DK+++R+ G YS +TQQPLGGKS  GGQR GEMEVW +
Sbjct: 1214 EYFDGEVSVGIMYMLKLDHMVDDKIHSRAVGPYSKITQQPLGGKSQNGGQRFGEMEVWAL 1273

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +AYGAA+ L+E+LTIKSDDV GR   Y +I+ G    E+G PESF +L K++Q LGL + 
Sbjct: 1274 EAYGAAHNLRELLTIKSDDVKGRNNTYNAIIKGKPIPESGLPESFKLLTKQLQGLGLQVS 1333

Query: 1363 LENSRTK-NSAKMEEIPDF 1380
            +     K N+   ++I ++
Sbjct: 1334 ITKELGKANNNNFKDINEY 1352


>gi|290889127|gb|ADD69913.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 457

 Score =  566 bits (1458), Expect = e-158,   Method: Composition-based stats.
 Identities = 278/453 (61%), Positives = 362/453 (79%), Gaps = 1/453 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 4   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 63

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 64  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 123

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 124 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 183

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++
Sbjct: 184 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQ 242

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +
Sbjct: 243 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDI 302

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 303 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 362

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+LD PD  R +RKEDI+++IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 363 AVGRVKMNMRLDLDAPDTQRTLRKEDILSVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 422

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           +++NQYR+GLLRMER+IKER+SSVDID+VMPQD
Sbjct: 423 LMENQYRIGLLRMERAIKERMSSVDIDTVMPQD 455


>gi|293363690|ref|ZP_06610437.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma alligatoris
           A21JP2]
 gi|292552734|gb|EFF41497.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma alligatoris
           A21JP2]
          Length = 1202

 Score =  566 bits (1458), Expect = e-158,   Method: Composition-based stats.
 Identities = 325/1002 (32%), Positives = 534/1002 (53%), Gaps = 82/1002 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +   G    R+ +      + + D++   K SYD FL           EG++ A  
Sbjct: 4   LNYKLHKFGPKTYRRDYSVTKYSLPVFDILATNKESYDKFLS----------EGIEEALM 53

Query: 61  SVFPITAFSGAAMLEFV--SYEFDPP-KFDVDD------CLWRDLTYAVPLKITLRLIVF 111
             +PI A +    L+++  S   + P K    +      C  + + ++  +   L+    
Sbjct: 54  EHYPIEASNKQVKLDYIKKSLRIELPYKKGPSEGEEIRKCKAKGMNFSARIYAKLQ---- 109

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
                       +IK   + +G++P++T  G+F+I G ++++VSQL RSPG +F     R
Sbjct: 110 -----REITETGEIKSDEVLLGEVPMITSGGSFIINGSEKVIVSQLIRSPGAYFGRGV-R 163

Query: 172 ASLSGKLLYACRIIPDQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE 227
              S  L     ++P  G W++I       + D++ ++ID+ + V +++FL ALG++ + 
Sbjct: 164 NKQSDDLFNKVEVLPRLGSWLEISHKITTSNTDVVKIKIDKNKSVNLSTFLGALGLNVKT 223

Query: 228 ILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVSSSLVD--IDTGEQVIESGKKLTSG 283
           I   F        +   D +    +  D+ +       L            E+ K L  G
Sbjct: 224 IYKLFGNSKELVETINKDKFVNQENLTDIEITDACQEELFRGLRRGDRVSEEAKKTLLPG 283

Query: 284 LLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +L   K   +   G           D +   Y+AE +   + G++  E    ID K   E
Sbjct: 284 ILFDRKRYNLSVTGRYMLNKKLSLIDRITNTYLAEQL-KSKAGDVLFEKDIFIDYKVALE 342

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           I  +        + + +    YI N           +    + +  +   V  +   + M
Sbjct: 343 IQKA--------FDEGLIATVYIDNLRGEQVYYKLVEQNKSLSKRCKIATVKVYPNRKWM 394

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            N                    + +  D     +H+   DI+AI+    +L +G G  DD
Sbjct: 395 ENNPKNPV--------------LVIANDPKSVEQHLLISDIVAIVGYYFNLIDGVGQDDD 440

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            D++ N+R+ SVGE+L+NQ  + L ++E++ +ER+ + + D V  +++ N K + + +  
Sbjct: 441 PDSMTNKRIVSVGELLQNQLNVALAKLEKTTRERMGAKETDKVTSKNVTNNKLLTNQMKT 500

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF SS+L+Q  + +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET 
Sbjct: 501 FFNSSKLAQFMDQINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETP 560

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSL 634
           EG NIGL+ +  ++A+VN  GF++TPY KV +G +   D+ YL+A EE     AQ++  +
Sbjct: 561 EGPNIGLILNYATYAKVNELGFLQTPYFKVNEGVIDYEDLRYLTAAEETGLAFAQSSVRV 620

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           D+D    +E +  R     I+    +IDFI+ S KQ+VS+AA+ IPFLENDD+NR LMG 
Sbjct: 621 DQDNKIIDESLTIRKDYNYIIGKPTEIDFIEVSSKQMVSVAAAAIPFLENDDANRALMGA 680

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQ+VPLL+AEAP V TG+E  +A  S     AK  G V  VD+ +I I++ +     
Sbjct: 681 NMQRQSVPLLEAEAPLVATGIEKDIALYSAYNFRAKNDGEVTYVDSYKIHIKTND----- 735

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                D Y L  F+RSNQ T ++Q+ +VKVGD+V++ D++ DG S   G+LALG+N+LVA
Sbjct: 736 -KGTKDKYYLKNFERSNQGTIISQKAIVKVGDQVKKGDLLVDGSSFKDGELALGKNVLVA 794

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           F  ++GYN+ED+++++ER+V +DV+TS+HIEE  V+ R +K G + +T DIPN S+  L+
Sbjct: 795 FSTYNGYNYEDAVILNERLVKDDVYTSVHIEEQTVLFRSSKAGDDRLTADIPNTSKFSLR 854

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           N+DE GI+ VG+EV PGDILVG+++PKGE   + EEKLL A+  ++ ++ +DTSLRV +G
Sbjct: 855 NLDEMGIVRVGSEVVPGDILVGRVSPKGEENPSQEEKLLMAVLQQRPLNDKDTSLRVKNG 914

Query: 935 VSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
            +GTV+ + I +R        GIDK  +    ++ +I++  +
Sbjct: 915 HNGTVIGIEILSRQTGDILEDGIDKIVKVSIAQKRKIKVGDK 956



 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 192/1039 (18%), Positives = 361/1039 (34%), Gaps = 92/1039 (8%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            V+++N + ++    +TD          +++R +R GD  +    +++   + FD  +Y+L
Sbjct: 235  VETINKDKFVNQENLTDIEIT-DACQEELFRGLRRGDRVSEEAKKTLLPGILFDRKRYNL 293

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            S  GR  +N +L+L       ++ ++       +L +          ++       ++  
Sbjct: 294  SVTGRYMLNKKLSLIDRITNTYLAEQLKSKAGDVLFEKDIFIDYKVALE-----IQKAFD 348

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E L     +  LR E+   + +      S   +             E    + +  +   
Sbjct: 349  EGLIATVYIDNLRGEQVYYKLVEQNKSLSKRCKIATVKVYPNRKWMENNPKNPVLVIAND 408

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S   H      +   G          +D  P            E     L  +L  
Sbjct: 409  --PKSVEQHLLISDIVAIVGYYFNLIDGVGQDDDPDSMTNKRIVSVGELLQNQLNVALAK 466

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE---ENRYIAQANSSLDEDGSFTEELV 645
              +            KV    VTN+   L+   +    +  +AQ    ++     + +  
Sbjct: 467  LEKTTRERMGAKETDKVTSKNVTNN-KLLTNQMKTFFNSSKLAQFMDQINPLAEVSNKRR 525

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                    +     + +  D        I     P    +    +      +   +  L+
Sbjct: 526  VTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETP-EGPNIGLILNYATYAKVNELGFLQ 584

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                 V  G+  +  +       A+  G+     ++R+   +   D   +      Y + 
Sbjct: 585  TPYFKVNEGV--IDYEDLRYLTAAEETGLAFAQSSVRVDQDNKIIDESLTIRKDYNYIIG 642

Query: 766  KFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K    +       Q   V         +  A+              +L A  P      E
Sbjct: 643  KPTEIDFIEVSSKQMVSVAAAAIPFLENDDANRALMGANMQRQSVPLLEAEAPLVATGIE 702

Query: 825  DSMLI--SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
              + +  +    +++     +++ +++  +    G ++               I +  I+
Sbjct: 703  KDIALYSAYNFRAKNDGEVTYVDSYKIHIKTNDKGTKDKYYLKNFERSNQGTIISQKAIV 762

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             VG +V  GD+LV   + K +  +   + +L A       +  D  +     V   V   
Sbjct: 763  KVGDQVKKGDLLVDGSSFK-DGELALGKNVLVAFSTYNGYNYEDAVILNERLVKDDV-YT 820

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +           S + +      +          LD     R+   +   + + G    
Sbjct: 821  SVHIEEQTVLFRSSKAGDDRLTADIPNTSKFSLRNLDEMGIVRVGSEVVPGDILVGRVSP 880

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            K                         E+     E L +     + + +     +++    
Sbjct: 881  KG------------------------EENPSQEEKLLMAVLQQRPLNDKDTSLRVKNGHN 916

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G  +   +L             Q+GD                       L+DG   D ++
Sbjct: 917  GTVIGIEILSR-----------QTGD----------------------ILEDGI--DKIV 941

Query: 1123 NPLGVPSRMNVGQIFETHLG-WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
                   ++++ Q  +  +G       G K    I   + +       + ++ ++     
Sbjct: 942  -------KVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPVDIMLNPQGV 994

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
              +++      +       K      TP FDG  +  I  +L  A LD+SG++ L D +T
Sbjct: 995  PSRMNIGQILELHLGIAAKKLNTKFVTPSFDGVKKTDIEDVLEEAGLDKSGKAYLIDPIT 1054

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ FD PV+VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W 
Sbjct: 1055 GKKFDNPVSVGIMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETWA 1114

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            I++YGA  VLQE+LT KSDD+ GR  +Y ++  G +  + GTPESFNVL  E++ LG+ +
Sbjct: 1115 IESYGATNVLQEILTYKSDDITGRNSLYSALATGKELPKPGTPESFNVLSYELRGLGIKL 1174

Query: 1362 DLENSRTKNSAKMEEIPDF 1380
            +     T+ S  +E   D 
Sbjct: 1175 E-----TQESDILENDDDE 1188


>gi|211998820|gb|ACJ15322.1| RNA polymerase beta subunit [Mesorhizobium huakuii]
          Length = 466

 Score =  565 bits (1456), Expect = e-158,   Method: Composition-based stats.
 Identities = 304/465 (65%), Positives = 374/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYVRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +  ++
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLGTGEQE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RKEDI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKEDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|211998822|gb|ACJ15323.1| RNA polymerase beta subunit [Mesorhizobium mediterraneum]
          Length = 466

 Score =  565 bits (1456), Expect = e-158,   Method: Composition-based stats.
 Identities = 300/465 (64%), Positives = 372/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA F+SVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFRSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DT E V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTNEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLSAGDDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889133|gb|ADD69916.1| RNA polymerase beta subunit [Rhizobium alamii]
          Length = 461

 Score =  565 bits (1456), Expect = e-158,   Method: Composition-based stats.
 Identities = 310/459 (67%), Positives = 381/459 (83%), Gaps = 1/459 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL++L 
Sbjct: 183 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRTLS 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 DKGLKALKATDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILANHFDEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLSVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLINAKP 460


>gi|211998818|gb|ACJ15321.1| RNA polymerase beta subunit [Mesorhizobium ciceri]
          Length = 466

 Score =  565 bits (1455), Expect = e-158,   Method: Composition-based stats.
 Identities = 302/465 (64%), Positives = 373/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLGTGEDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|211998816|gb|ACJ15320.1| RNA polymerase beta subunit [Mesorhizobium temperatum]
          Length = 466

 Score =  565 bits (1455), Expect = e-158,   Method: Composition-based stats.
 Identities = 300/465 (64%), Positives = 371/465 (79%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEAPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PV+S LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVSSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    L+D DT E V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLIDADTNEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVLLSAGDDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|211998808|gb|ACJ15316.1| RNA polymerase beta subunit [Mesorhizobium loti]
          Length = 466

 Score =  564 bits (1454), Expect = e-158,   Method: Composition-based stats.
 Identities = 302/465 (64%), Positives = 373/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEVVVEAGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLKVLLGTGEDE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A+++ LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVRTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|294155590|ref|YP_003559974.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma crocodyli
           MP145]
 gi|291600297|gb|ADE19793.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma crocodyli
           MP145]
          Length = 1204

 Score =  564 bits (1454), Expect = e-158,   Method: Composition-based stats.
 Identities = 326/1005 (32%), Positives = 545/1005 (54%), Gaps = 88/1005 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +   G    R+ +      + + D++   K S+D FL           EG++ A  
Sbjct: 4   LNYRISKFGPKTSRRDYSVTKYSLPVFDILATNKESFDKFL----------KEGIEEALM 53

Query: 61  SVFPITAFSGAAMLEFV--SYEFDPP-KFDVDD------CLWRDLTYAVPLKITLRLIVF 111
             +PI A +    L+++  S   + P K    +      C  + + ++  +   L+    
Sbjct: 54  EHYPIEASNKQVKLDYIKKSLRIEYPYKKGPSEGEEIRKCKAKGMNFSARIYAELQ---- 109

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
                       +IK   + +G++P++T  G+F+I G ++++VSQL RSPG +F     R
Sbjct: 110 -----REITETGEIKRDEVLLGEIPMITSGGSFIINGSEKVIVSQLIRSPGAYFGRGV-R 163

Query: 172 ASLSGKLLYACRIIPDQGLWMDIE----FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE 227
              S  L     ++P  G W++I       + D++ ++ID+ + V + +FL ALG++++ 
Sbjct: 164 NKQSDDLFNKVEVLPRIGSWLEISHKITTSNIDVVKIKIDKNKNVNLATFLGALGLNTKM 223

Query: 228 ILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVSSSLVDI-DTGEQVIESGKK-LTSG 283
           +   F        +   D +    + +D  +       L      G+++ +  KK L   
Sbjct: 224 MYKYFGNSKELEETITKDKFVNQENLSDAEITDLCQEELFRWLRKGDRISDEAKKTLLPS 283

Query: 284 LLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +L   K   +   G           D +   Y+AEDI N +  E+    G  ID K   +
Sbjct: 284 ILFDKKRYNLSITGRYMLNNKLSLVDRITNTYLAEDIKN-KNNEVVFHNGTFIDYKLALD 342

Query: 336 IFHSEIR-DIPILYVDSVNNNAYIRNTLVTDKN--KDRKDALLDIYRVMRPGDVSTFSVA 392
           I  S    ++  +Y+D++         +  +K   K  K A++ +Y              
Sbjct: 343 IQKSFDEGEVATVYIDTLRGENVYYKLVDQNKALAKRCKIAIVKVYPN------------ 390

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
                    D+DK  +  +G          D     +H+   DI+A++    +L +G G 
Sbjct: 391 ----RKWMEDADKKPVIVIGN---------DPKSVEQHLLISDIVAVVGYYFNLIDGVGQ 437

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DD D++ N+R+ SVGE+L+NQ  + L ++E++ +ER+ + + + V  +++ N K + + 
Sbjct: 438 DDDPDSMVNKRIVSVGELLQNQLNVALAKLEKTTRERMGAKETEKVTSKNVTNNKLLTNQ 497

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           +  FF SS+LSQ  + +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP 
Sbjct: 498 MKTFFNSSKLSQFMDQINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPI 557

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQAN 631
           ET EG NIGL+ +  ++A+VN +GF++TPY KV +G +   D+ YL+A EE     AQ++
Sbjct: 558 ETPEGPNIGLILNYATYAKVNEHGFLQTPYFKVNNGVIDYEDLRYLTASEETGLAFAQSS 617

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +D+     E+ +  R     I+    +IDFI+ S KQ+VS+AA+ IPFLENDD+NR L
Sbjct: 618 VRVDDTNKIIEKTLTIRKDYNYIIGKPSEIDFIEVSSKQMVSVAAAAIPFLENDDANRAL 677

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           MG NMQRQ+VPL++AEAP V TG+E  +A  S     AK  G+V  VD+ +I +++ +  
Sbjct: 678 MGANMQRQSVPLIEAEAPLVATGIEKDIALYSAYNFRAKNDGVVSYVDSFKIYVKTHD-- 735

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                   D Y L  F+RSNQ T + Q+ +VKVGDEV++ D++ DG S   G+LALG+N+
Sbjct: 736 ----KGTQDKYYLKNFERSNQGTVICQKSIVKVGDEVKKGDLLVDGSSFKDGELALGKNV 791

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
           LVAF  ++GYN+ED+++++ER+V +DV+TSIHIEE  V+ R +K G +++T DIPN S+ 
Sbjct: 792 LVAFTTYNGYNYEDAVILNERLVKDDVYTSIHIEEQTVLFRSSKAGDDKLTADIPNTSKF 851

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             +N+DE GI+ VG+EV  GD+LVG+++PKGE   + EEKLL AI  ++ ++ +DTSLRV
Sbjct: 852 STRNLDEYGIVRVGSEVIAGDVLVGRVSPKGEENPSQEEKLLMAILQQRPLNDKDTSLRV 911

Query: 932 PSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
            +G +GTV+ + + +R        GIDK  +    ++ +I++  +
Sbjct: 912 KNGHNGTVIGIEVLSRETGDILEDGIDKIVKVSIAQKRKIKVGDK 956



 Score =  428 bits (1100), Expect = e-117,   Method: Composition-based stats.
 Identities = 220/1044 (21%), Positives = 390/1044 (37%), Gaps = 101/1044 (9%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +         N       +       +++R +R GD  +    +++   + FD  +Y+LS
Sbjct: 235  EETITKDKFVNQENLSDAEITDLCQEELFRWLRKGDRISDEAKKTLLPSILFDKKRYNLS 294

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
              GR  +N +L+L       ++ ++      +++            +D   +     V  
Sbjct: 295  ITGRYMLNNKLSLVDRITNTYLAEDIKNKNNEVVFHNGTFIDYKLALDIQKSFDEGEVAT 354

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +  +  R   +  +   + +  +      + +   N K +  A  +              
Sbjct: 355  VYIDTLRGENVYYKLVDQNKALAKRCKIAIVKVYPNRKWMEDADKKPVIVIG-------N 407

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            +  S   H      +   G          +D  P            E     L  +L   
Sbjct: 408  DPKSVEQHLLISDIVAVVGYYFNLIDGVGQDDDPDSMVNKRIVSVGELLQNQLNVALAKL 467

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE---ENRYIAQANSSLDEDGSFTEELVF 646
             +            KV    VTN+   L+   +    +  ++Q    ++     + +   
Sbjct: 468  EKTTRERMGAKETEKVTSKNVTNN-KLLTNQMKTFFNSSKLSQFMDQINPLAEVSNKRRV 526

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                   +     + +  D        I     P    +    +      +      L+ 
Sbjct: 527  TSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETP-EGPNIGLILNYATYAKVNEHGFLQT 585

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                V  G+  +  +       ++  G+     ++R+   +   +   +      Y + K
Sbjct: 586  PYFKVNNGV--IDYEDLRYLTASEETGLAFAQSSVRVDDTNKIIEKTLTIRKDYNYIIGK 643

Query: 767  FQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                +       Q   V         +  A+              ++ A  P      E 
Sbjct: 644  PSEIDFIEVSSKQMVSVAAAAIPFLENDDANRALMGANMQRQSVPLIEAEAPLVATGIEK 703

Query: 826  SMLI--SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
             + +  +    +++     +++ F++  +    G ++               I +  I+ 
Sbjct: 704  DIALYSAYNFRAKNDGVVSYVDSFKIYVKTHDKGTQDKYYLKNFERSNQGTVICQKSIVK 763

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSG 937
            VG EV  GD+LV   + K +  +   + +L A       +  D  +            S 
Sbjct: 764  VGDEVKKGDLLVDGSSFK-DGELALGKNVLVAFTTYNGYNYEDAVILNERLVKDDVYTSI 822

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             + +  +  R     +++  +      +   R+  DE  I+         ++L G+ +  
Sbjct: 823  HIEEQTVLFRSSKAGDDKLTADIPNTSKFSTRNL-DEYGIVRVGSEVIAGDVLVGRVSPK 881

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G +   +   L   ++ + P        + D+     V++          +L        
Sbjct: 882  GEENPSQEEKLLMAILQQRP--------LNDKDTSLRVKNGHNGTVIGIEVLSR------ 927

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP
Sbjct: 928  ---ETGDILEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISVVLPEEDMPYLEDGTP 984

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   L  K  +   D     DI  +         
Sbjct: 985  VDIMLNPQGVPSRMNIGQVLELHLGMAARKLNTKFVTPSFDGVKKSDIEDVLEEAG---- 1040

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                         L  +      ++ L 
Sbjct: 1041 ---------------------------------------------LDKSG-----KAYLI 1050

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            D +TG+  D+PV+VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR GEM
Sbjct: 1051 DPITGKKLDKPVSVGVMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEM 1110

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            E W I++YGA  VLQE+LT KSDD+ GR  +Y S+  G +  + G PESFNVL  E++ L
Sbjct: 1111 ETWAIESYGATNVLQEILTYKSDDIQGRNILYASLATGKELPKPGIPESFNVLSYELRGL 1170

Query: 1358 GLSIDLENSRTKNSAKMEEIPDFN 1381
            G+ ++     TK +  +E+  D +
Sbjct: 1171 GIKLE-----TKEAEILEDGDDTD 1189


>gi|290889143|gb|ADD69921.1| RNA polymerase beta subunit [Rhizobium mesosinicum]
          Length = 456

 Score =  564 bits (1453), Expect = e-158,   Method: Composition-based stats.
 Identities = 308/456 (67%), Positives = 377/456 (82%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 1   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 60

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 61  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 120

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 121 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 180

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 181 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 239

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 240 DKGLKALKATDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILANHFDEIPVLGI 299

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 300 DHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 359

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 360 AVGRVKMNMRLDLSVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 419

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 420 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 455


>gi|290889107|gb|ADD69903.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
          Length = 457

 Score =  563 bits (1452), Expect = e-158,   Method: Composition-based stats.
 Identities = 305/456 (66%), Positives = 375/456 (82%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 2   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 122 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 182 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 241 DKGLKALKAADDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPVLGI 300

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 301 DHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 360

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 361 AVGRVKMNMRLDLTVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGE 420

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 421 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 456


>gi|290889113|gb|ADD69906.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
          Length = 440

 Score =  563 bits (1451), Expect = e-158,   Method: Composition-based stats.
 Identities = 276/441 (62%), Positives = 349/441 (79%), Gaps = 1/441 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 1   RPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLI 60

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 61  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDK 120

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+IL
Sbjct: 121 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQIL 180

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+
Sbjct: 181 STFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRQARQLQ 239

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L ++ + L G Y+AED+VN +TGEIY EA + I EKSL+ +     +D+P+L +
Sbjct: 240 EKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEASEEITEKSLKVLNEQGYKDLPLLDI 299

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D VN  AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS
Sbjct: 300 DHVNVGAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLS 359

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL LD PD  R +RKEDI+A+IK LVDLR+GKG IDDID+LGNRRVRSVGE
Sbjct: 360 AVGRVKMNMRLELDAPDTHRTLRKEDILAVIKTLVDLRDGKGEIDDIDHLGNRRVRSVGE 419

Query: 470 MLKNQYRLGLLRMERSIKERI 490
           +++NQYR+GLLRMER+IKER+
Sbjct: 420 LMENQYRIGLLRMERAIKERM 440


>gi|211998814|gb|ACJ15319.1| RNA polymerase beta subunit [Mesorhizobium septentrionale]
          Length = 466

 Score =  563 bits (1451), Expect = e-158,   Method: Composition-based stats.
 Identities = 303/465 (65%), Positives = 371/465 (79%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEQGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L  +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLNVLLGTGEHE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889129|gb|ADD69914.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
 gi|290889137|gb|ADD69918.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
          Length = 457

 Score =  563 bits (1451), Expect = e-158,   Method: Composition-based stats.
 Identities = 305/456 (66%), Positives = 375/456 (82%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 183 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 DKGLKALKAADDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L   D VR +RK+DI+A++++LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLTVEDTVRILRKDDILAVVRMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 457


>gi|211998824|gb|ACJ15324.1| RNA polymerase beta subunit [Mesorhizobium amorphae]
          Length = 466

 Score =  563 bits (1450), Expect = e-158,   Method: Composition-based stats.
 Identities = 303/465 (65%), Positives = 373/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEQGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +   +
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLKVLLGTGEHE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 IQVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|211998828|gb|ACJ15326.1| RNA polymerase beta subunit [Mesorhizobium caraganae]
          Length = 466

 Score =  563 bits (1450), Expect = e-157,   Method: Composition-based stats.
 Identities = 302/465 (64%), Positives = 374/465 (80%), Gaps = 1/465 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEQGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +  +  ++
Sbjct: 240 QARALGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLKVLLGTGEQE 299

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L +D VN  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MFN LFFDS
Sbjct: 300 VKVLDIDHVNVGAYIRNTLNVDKNESRQDALFDIYRVMRPGEPPTLETAEAMFNSLFFDS 359

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++YDLS VGRVKMNMRL L   D VR +RK+DI+A++K LV+LR+GKG IDDIDNLGNRR
Sbjct: 360 ERYDLSAVGRVKMNMRLELKAEDTVRVLRKDDILAVVKTLVELRDGKGEIDDIDNLGNRR 419

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           VRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 VRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKP 464


>gi|290889123|gb|ADD69911.1| RNA polymerase beta subunit [Rhizobium sp. CCBAU 45133]
          Length = 457

 Score =  562 bits (1448), Expect = e-157,   Method: Composition-based stats.
 Identities = 306/456 (67%), Positives = 377/456 (82%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL++L 
Sbjct: 183 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRALS 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG+K L  T D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +
Sbjct: 242 DKGLKALKATDDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANHFDEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L   D VR +RK+DI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLTVEDTVRILRKDDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 457


>gi|290889103|gb|ADD69901.1| RNA polymerase beta subunit [Rhizobium sp. CCBAU 15278]
          Length = 457

 Score =  562 bits (1447), Expect = e-157,   Method: Composition-based stats.
 Identities = 307/456 (67%), Positives = 375/456 (82%), Gaps = 1/456 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQSVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY K  Y + G  W  P +   L  GAK    ++D DTGE V+E GKKLT  LL+ L 
Sbjct: 183 STFYTKSDYVRDGKGWRIPFTPETL-KGAKTIGDMIDADTGEIVVEGGKKLTPRLLRQLS 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L  T + L G ++AEDIVN  TGEIY+EAGD IDEKSL  I      +IP+L +
Sbjct: 242 EKGLKALQATDEDLYGNFLAEDIVNYSTGEIYLEAGDEIDEKSLAVILSHGFEEIPVLGI 301

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS
Sbjct: 302 DHINVGAYIRNTLNADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAERYDLS 361

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGRVKMNMRL+L+  D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE
Sbjct: 362 AVGRVKMNMRLDLEVEDTVRVLRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGE 421

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +++NQYRLGLLRMER+IKER+SS++ID+VMPQDLIN
Sbjct: 422 LMENQYRLGLLRMERAIKERMSSIEIDTVMPQDLIN 457


>gi|253795609|ref|YP_003038705.1| putative DNA-directed RNA polymerase, beta subunit [Candidatus
            Hodgkinia cicadicola Dsem]
 gi|253739917|gb|ACT34252.1| putative DNA-directed RNA polymerase, beta subunit [Candidatus
            Hodgkinia cicadicola Dsem]
          Length = 1267

 Score =  560 bits (1444), Expect = e-157,   Method: Composition-based stats.
 Identities = 301/889 (33%), Positives = 457/889 (51%), Gaps = 62/889 (6%)

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
             + +   V + F SS   Q  + VNSLS ++H  RL+ +G GGV    A    RDV   H
Sbjct: 411  QRKLQPVVSKLFRSSSACQYADQVNSLSELSHRLRLTCMGGGGVNARSADTRSRDVRKWH 470

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G++CP E+ EG +IGLV  L  +ARV A G I T + K   G ++N ++ L+   ++  
Sbjct: 471  FGKVCPIESPEGQSIGLVLQLAMYARVEASGHIATMFAKSRRGLISNQMLALNCFSQQAF 530

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             IA   +      S     V    A +  +     +D   A+  Q+ S A +LIPFLE++
Sbjct: 531  SIAIFGA------SPASARVMSFKACKPAMCAISAVDLWPATNAQLFSPAVNLIPFLEHN 584

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+ R LM  NM +QA+PL + +AP VGTG E  V  ++G  ++A +  +V + DA ++V+
Sbjct: 585  DATRALMASNMLKQALPLAEPQAPLVGTGEERAVMLAAGHNLLADQHCVVVRADAAQVVV 644

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                    P       Y + +  RSNQ  C   R +V+    ++  D++A+  S+D G++
Sbjct: 645  YC------PCADAYKAYLVPEPTRSNQGVCRRLRVVVEPNQVLKAGDVVAECQSSDNGEM 698

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            +LG N+LVAFM W+G+N+EDS+L+SE +++  +  S+H+ + +     T  G E +T ++
Sbjct: 699  SLGANLLVAFMCWNGFNYEDSILLSEAVIARGLLDSLHVLKLKAKVLRTAFGDELVTNEL 758

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK-------------- 911
            P V+E+   ++ E G++ VG  V   D+LVGK++P   +                     
Sbjct: 759  PMVAEKHKAHLSEQGVVSVGDTVCEHDVLVGKLSPVDYADSLDVATADAVATAGADDGGD 818

Query: 912  ------------LLRAIFGEKAVDVRDTSLRVPSGVS-GTVVDVRIFNRHGIDKNERSIS 958
                         L    GE    V+ TSLRVP+GV   +V+DV   +            
Sbjct: 819  DGDSGGDDGLSVTLVNDMGENIRYVKSTSLRVPTGVECASVIDVSFASC----------E 868

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             E    E        E  ++ R    RL ++     A  G  G        ++  S+   
Sbjct: 869  AEASLGESALDACVKELDLIQRRYARRLGKVAK--WAAVGFDG--------ANACSKPDH 918

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRVVKVF 1077
                +    + + Q+ +  L+  Y      L  R           D      VL  + V 
Sbjct: 919  GLVLEAKSSNAQAQQAISLLRQLYACEVDALFARASAAASARISCDGPNSASVLDEITVT 978

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            + +++ I++GDK++GRHGNKG++SR+ P EDMP L DGTP+DIVLNPL VPSRMN+GQI 
Sbjct: 979  LLVRKSIKAGDKVSGRHGNKGVISRVAPAEDMPHLADGTPIDIVLNPLSVPSRMNIGQIL 1038

Query: 1138 ETHLGWACVGLGKKIKSLIND-YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            E  LG   + LG + + +++    A+          +  I +   +  +       VL +
Sbjct: 1039 EARLGLVGLALGAEFERVVDACQVADASSERELEGAKSKISSLFPSLDLRRASASRVLAL 1098

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMAD-LDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            A +   GV +  P F    E  I ++ R A  LD SG+  L+DG+TG PFD+   VG IY
Sbjct: 1099 ARKLSRGVGLECPPFCHLSEACIKALCRRAGALDASGRLQLFDGVTGLPFDQQTAVGSIY 1158

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKLNH+V DK+YAR+TG YS+VTQQPL GK+N+GGQRLGEMEVW +Q+YG +Y+L+E L
Sbjct: 1159 VLKLNHLVDDKMYARATGPYSMVTQQPLKGKANKGGQRLGEMEVWALQSYGVSYMLKEAL 1218

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            T K DDV  R  +  SI       E+   ES  +LV+EM +L +    E
Sbjct: 1219 TAKCDDVAARHVMASSIAGCAPRVESSWGESLLLLVREMCSLCVDFRFE 1267


>gi|50365415|ref|YP_053840.1| DNA-directed RNA polymerase subunit beta [Mesoplasma florum L1]
 gi|81391714|sp|Q6F0L7|RPOB_MESFL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|50363971|gb|AAT75956.1| DNA-directed RNA polymerase beta subunit [Mesoplasma florum L1]
          Length = 1284

 Score =  560 bits (1443), Expect = e-157,   Method: Composition-based stats.
 Identities = 342/853 (40%), Positives = 498/853 (58%), Gaps = 66/853 (7%)

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
            ++ + +  E      +   K   ++ GD PLMT  GTFVI G Q+++VSQL RSPG +F
Sbjct: 160 FQITILEEKEDIIVAEVSVRKWGQVFFGDFPLMTDAGTFVINGSQKVIVSQLVRSPGSYF 219

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK------DIIHVRIDRRRKVPVTSFLM 219
             +    + +G+ LY   IIP +G W++ E D+K      + + V+ID+ RK   TSFL 
Sbjct: 220 KTEI--NNKTGESLYNGDIIPSRGTWLEFETDTKKTAETTNSLFVKIDKSRKTTATSFLK 277

Query: 220 ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGK 278
            LG+D + IL+  Y K                        V      I  GE    +   
Sbjct: 278 ILGLDRDTILNI-YDKDKVIVETLKNDNDTGDTYADWAQHVQEIYKKIRQGETATSDGAS 336

Query: 279 KLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           K  +GLL   ++  +   G           + L G  +AEDIV+  +G+I +     I +
Sbjct: 337 KYINGLLFDRRKYDLTKAGRFKLQQKLAVKNRLMGRILAEDIVDA-SGKILVAKNTEISK 395

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +++E+  +       L  D V  ++                            D+    
Sbjct: 396 ANIKEVSDA-------LSQDGVMVSSIEYRE-----------------------DIPGSR 425

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             + +  +   +S     + VG         +       HI   DI+A +  L+ L    
Sbjct: 426 QIQKVKVYQDNNSKDETFTIVG---------ITPNSKEEHITVVDIVATVSYLLGLEYNI 476

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           G  DDIDNL NRRVR+VGE+L+NQ+R+GL R+++++KE++S+ D+  V    +INAKP+ 
Sbjct: 477 GEYDDIDNLANRRVRTVGELLQNQFRMGLTRIDKNVKEKLSTSDLYKVKVSTIINAKPLT 536

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           + + EFF  SQLSQ  + +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRIC
Sbjct: 537 AVIGEFFNLSQLSQFMDQINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRIC 596

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL+++L+++A V+  GFI TPY KV DG + N+  YLSA EE+   I+Q+
Sbjct: 597 PIETPEGPNIGLINNLSTYAIVDELGFIRTPYLKVIDGVIQNEHEYLSADEEKEYIISQS 656

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           N + DE+G   +E V     G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR 
Sbjct: 657 NVTKDENGKILDETVVSHYKGDDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRA 716

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVP +  E+PFVGTG+E   A+ SG  IVA   GIV+ VDA +I +     
Sbjct: 717 LMGANMQRQAVPTIVPESPFVGTGIEFEAARDSGVCIVATENGIVKYVDAKQITV----- 771

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               S +G+  Y L  F+RSN  + + Q+P+VKVGD +    IIADGPS D G+LALG+N
Sbjct: 772 ---ESKAGIKTYTLANFERSNNGSSIVQKPIVKVGDSIEAGQIIADGPSVDNGELALGQN 828

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           ++VAF  ++GYNFED++++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+
Sbjct: 829 VVVAFTTYNGYNFEDAIVMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISD 888

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              K +D  GI+ +G EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+
Sbjct: 889 NAKKYLDNEGIVAIGTEVKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLK 948

Query: 931 VPSGVSGTVVDVR 943
           VP+G  G V  V+
Sbjct: 949 VPNGGEGIVQSVK 961



 Score =  477 bits (1228), Expect = e-132,   Method: Composition-based stats.
 Identities = 274/1436 (19%), Positives = 493/1436 (34%), Gaps = 254/1436 (17%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +     G  R+ + K    +++P+LIE+Q  +++ F            +G+     
Sbjct: 1    MAYKIKKVNRGVERRDYRKVSGNLELPNLIEIQTKTFEWF----------KTKGIDEVLN 50

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              F +++   +A L    +E    K        +   Y  P+ + L+L+         +K
Sbjct: 51   EFFAMSSNDASASLFLEGWEIKEAKISPSKAKEQSKIYDAPIYVDLQLMFTKT--EDISK 108

Query: 121  SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++                            +V           + D  +   +     
Sbjct: 109  EFEE----------------------------IV-----------EKDVKKVLSN----- 124

Query: 181  ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP-KIVYS 239
                      W+  + DSK++  V+                  +++ I   F+  K+  +
Sbjct: 125  ----------WIAEKTDSKNVSLVK------------------NTDNI--YFFDVKLKGT 154

Query: 240  QRGDFWCFPLSAAD----------LMVGAKVSSSLVDIDTGEQVIESG--KKLTSGLLKS 287
            ++ D +   +                 G         +      + +G  K + S L++S
Sbjct: 155  EKNDLFQITILEEKEDIIVAEVSVRKWGQVFFGDFPLMTDAGTFVINGSQKVIVSQLVRS 214

Query: 288  LKEKGVKFL------GITSDCLC---GLYVAEDIVNGETGE------IYIEAGDVIDEKS 332
                    +       + +  +    G ++  +    +T E      + I+        S
Sbjct: 215  PGSYFKTEINNKTGESLYNGDIIPSRGTWLEFETDTKKTAETTNSLFVKIDKSRKTTATS 274

Query: 333  LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT-DKNKDRKDALLDIYRVMRPGDVSTFSV 391
              +I   +   I  +Y         ++N   T D   D    + +IY+ +R G+ +T   
Sbjct: 275  FLKILGLDRDTILNIYDKDKVIVETLKNDNDTGDTYADWAQHVQEIYKKIRQGETATSDG 334

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL--VDLRNG 449
            A    N L FD  KYDL+  GR K+  +L +      R + ++ + A  KIL   +    
Sbjct: 335  ASKYINGLLFDRRKYDLTKAGRFKLQQKLAVKNRLMGRILAEDIVDASGKILVAKNTEIS 394

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM-----PQDLI 504
            K  I ++ +  ++    V  +   +   G  ++++    + ++   ++       P    
Sbjct: 395  KANIKEVSDALSQDGVMVSSIEYREDIPGSRQIQKVKVYQDNNSKDETFTIVGITPNSKE 454

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS------ALGQGGVARARAGVEM 558
                VV  V        L       + +  + + R  +         + G+ R    V+ 
Sbjct: 455  EHITVVDIVATVSYLLGLEYNIGEYDDIDNLANRRVRTVGELLQNQFRMGLTRIDKNVKE 514

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            +      Y        +      ++    + ++++ +                + +  L+
Sbjct: 515  KLSTSDLYKVKVSTIINAKPLTAVIGEFFNLSQLSQF---------------MDQINPLA 559

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             +  + R  A     L  D +  E                      D  P     I    
Sbjct: 560  ELTNKRRLTALGPGGLSRDRASLEVR--------------------DVHPSHYGRICPIE 599

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
             P   N      L    +  +   +       +  G+     +   A    +       V
Sbjct: 600  TPEGPNIGLINNLSTYAIVDELGFIRTPYLKVID-GVIQNEHEYLSADEEKEYIISQSNV 658

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                      E  +       D Y     +    +    Q   V         +  A+  
Sbjct: 659  TKDENGKILDETVVSHYKG--DDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRA 716

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDS--------MLISERMVSEDVFTSIHIEEFEVM 850
                         +V   P+ G   E          ++ +E  + + V       E +  
Sbjct: 717  LMGANMQRQAVPTIVPESPFVGTGIEFEAARDSGVCIVATENGIVKYVDAKQITVESKAG 776

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             +   L   E + +  ++ ++         I+ VG  +  G I+    +      +   +
Sbjct: 777  IKTYTLANFERSNNGSSIVQKP--------IVKVGDSIEAGQIIADGPS-VDNGELALGQ 827

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIE 965
             ++ A       +  D  +     +          + + ++        E        I 
Sbjct: 828  NVVVAFTTYNGYNFEDAIVMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNIS 887

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
              A+   D + I+      +  +IL G+    G         L   +  E  RS      
Sbjct: 888  DNAKKYLDNEGIVAIGTEVKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRS----VK 943

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                KV    E +    +        RFK K      G D+P  VL V+KV++  KR IQ
Sbjct: 944  DNSLKVPNGGEGIVQSVK--------RFKAKSAANPDGIDLPADVLEVIKVYIVQKRKIQ 995

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKM+GRHGNKGI+S++LP EDM              P             E       
Sbjct: 996  EGDKMSGRHGNKGIISKVLPVEDM--------------PH-----------LE------- 1023

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
                        D   N    P R  + +++                +       K GV 
Sbjct: 1024 -------DGTPVDILLNPQGIPSRMNIGQIL---------------EIHLGMAAKKLGVK 1061

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            ++TPVF+G +   ++ ++  A ++  G+  L DG TGE  D+P++VG +YMLKL+HMV D
Sbjct: 1062 IATPVFEGVNSNDLDEIMAEAGMENYGKVKLIDGQTGEAIDKPISVGVMYMLKLSHMVDD 1121

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARS G YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+ L+E+LTIKSDD+ GR
Sbjct: 1122 KLHARSVGPYSLITQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLREILTIKSDDLKGR 1181

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            T+ YE+IV   +    GTPESFNVL KE+  LG  I L +++   S       D +
Sbjct: 1182 TKTYEAIVRSKNIPTPGTPESFNVLSKEIMGLGFDIYLLDNKGNKSQINAYDDDND 1237


>gi|11467566|ref|NP_043712.1| RNA polymerase beta subunit [Odontella sinensis]
 gi|1350847|sp|P49466|RPOB_ODOSI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|1185261|emb|CAA91744.1| RNA polymerase beta-chain [Odontella sinensis]
          Length = 1379

 Score =  560 bits (1442), Expect = e-157,   Method: Composition-based stats.
 Identities = 295/1454 (20%), Positives = 495/1454 (34%), Gaps = 207/1454 (14%)

Query: 26   IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
            +PD IE+Q+ S+  F+           +GL         I  FS      L    Y    
Sbjct: 7    LPDFIEMQRVSFCWFIA----------QGLNDELTMFSRIHDFSYNTEYRLFGQEYSLVK 56

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG-----DLPLM 138
            P + +         Y+V L I L             K +  ++    Y G     +LPLM
Sbjct: 57   PVYTIVRAKKLAANYSVQLVIPL---------EVRNKKLNSVR----YFGQFTIINLPLM 103

Query: 139  TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR--------------- 183
            T   TFVI G +R++VSQ+ RSPGI+F  +K +     K  +  +               
Sbjct: 104  TTTATFVINGCERVIVSQIIRSPGIYF--EKNKNHRKRKQ-FKSQVLGHASKLGSFLPSG 160

Query: 184  ---IIPDQGLW---------------------MDIEF-DSKDI-IHVRIDRRRKVPVTS- 216
               IIP    W                     +D  F   K   I+ +I +    P+   
Sbjct: 161  VPWIIPYDQPWKPWIIGKKLGYSKYNSNKDTKLDFYFYSLKSFKIYQKISKITNSPIKVQ 220

Query: 217  ----FLMALGMDSEE--------------ILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                FL  L ++ +E              +L+ +     +  +  F           +  
Sbjct: 221  RIKLFLQWLKLNQKEFNFKNKLNLSELSFLLNYWNFIFKFIIKYQFLYKKNFEESYQIQE 280

Query: 259  KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE----DIVN 314
                ++      +  +     L    +  L     K +    + +   +         + 
Sbjct: 281  SEFKTIFKTWNNQPQLNDSFSL--KKIDQLTSNYEKKIQFYHNVIQQQFFDNLMLVPFIT 338

Query: 315  GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             E   + +E+     ++    +       I   +  S +     +      +        
Sbjct: 339  KEKKILNLESLANRQKQKKISLTLLTNESIKFAFYFSPSLKEVFKYRSPKKRKPKEAKIK 398

Query: 375  LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR-- 432
              I  +  P  +  F     + +       KYD         +       P+    IR  
Sbjct: 399  QPILYLRSPSKIVQFKDDHQVLDSY---KKKYDTK-------DFYTATLIPESGSWIRFG 448

Query: 433  --KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
              K   I   +  +  +  +  I          +  + EM    + +             
Sbjct: 449  FQKNTKINRYQYPIRHQEDEVIIQIDKITQKPILYLLKEMGLTDWEICSNLKHADFFYFT 508

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
                  S+  +  +    + S    +   S+ S + +            RL  +G+  + 
Sbjct: 509  KPFLTGSLTSKQPLPRFDLHSD--YYKNISEFSHIFDARYY--------RLGKIGRFQIN 558

Query: 551  RARAGVEMRDVHPTHYGRI-----CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                      ++   Y  I     C    S     G         RV + G +     +V
Sbjct: 559  NRLNLKLNNRIYTITYEDIFAILDCLVTLSISKTTGDDIDHLKNRRVRSVGELLQNLFRV 618

Query: 606  CDGKVTNDVVYLSAMEEEN----RYIA-------QANSSLDEDGSFTEELVFCRCAGEEI 654
               ++   +       E        I          +S L +    T  L          
Sbjct: 619  GFQRLVRKLGSQINKRESGQISSFNIIGATVREFFGSSQLSQYMDQTNPLSSLTHRRRIS 678

Query: 655  LV-----PREKIDF--IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
             +      R++I F   D  P     I     P   N      L  C    +   +    
Sbjct: 679  GLGPGGLDRDRISFAVRDIHPSHYGRICPIETPEGPNVGLIASLTTCARVNKLGFIETPF 738

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               +   +          A +     I    D        +  +L P     D   +  F
Sbjct: 739  WRVINGKVIKTGNPIYLTADIEDFYKIAP-ADISTNSKNYLTQNLIPVRYKQDFITVSPF 797

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            Q    +    Q   V            A+              ++++  P  G   E+ +
Sbjct: 798  QVDFISISPIQVVSVATSLIPFFEHDDANRALMGSNMQRQSVPLMLSQKPIVGTGLENQI 857

Query: 828  LISERMVSEDVFTSI-HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
             I   M        I H    + +      G +                I+   I+  G 
Sbjct: 858  AIDSGMTINAQGAGIVHSVTADYIIVKEYSGRKLKYILQKYQRSNQETCINHRPIVWKGE 917

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++  G IL         + +   + +L A    +  +  D  L              I  
Sbjct: 918  KIKSGQILTDGPGITN-NELALGQNVLVAYMPWQGYNFEDAIL--------------INE 962

Query: 947  RHGIDKNERSISVEREQIELLARD-KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            R   +    SI +ER  IE+   D   ++      N+    ++ L     V+     K  
Sbjct: 963  RLVYEDVFTSIHIERYDIEIEQDDDVSEQITKNIPNLSFSEIQNLNDDGIVALGTFVKPG 1022

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             +L   +I++    Q  +  +         + ++   +TS  + + ++   ++++ +   
Sbjct: 1023 DILVGKIIAKNDSEQLPEAKLLRAIFGAKAKGVR---DTSFRMPKGKYGRVVDRVTFNRK 1079

Query: 1066 MPPGV-LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                     ++VF+A  R I+ GDK+AGRHGNKGI+SRILP +DMPFL DGTPVDI+LNP
Sbjct: 1080 TKLAYKFEKIQVFIAQIRKIKVGDKIAGRHGNKGIISRILPRQDMPFLPDGTPVDIILNP 1139

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMNVGQ++E  LG A   L ++ K L  D               ++ G       
Sbjct: 1140 LGVPSRMNVGQLYECLLGIAGHKLNRRFKILPFD---------------EMYGPEVSRIL 1184

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            I+     + +   E W                        + +    G+ +L DG TG+ 
Sbjct: 1185 INKKLRQASIENDEAW------------------------LFNPYSPGKMVLIDGRTGKE 1220

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F+ P+TVG  YMLKL H+V DK++AR+TG YSL+TQQPLGGK+  GGQR GEMEVW ++ 
Sbjct: 1221 FENPITVGNAYMLKLIHLVDDKMHARATGPYSLITQQPLGGKAQHGGQRFGEMEVWALEG 1280

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +GAA+ L+E+LTIKSDD+ GR     +IV G    ++G PESF VL++E++++GL +   
Sbjct: 1281 FGAAFTLKELLTIKSDDMQGRNETLNAIVKGQLIPKSGVPESFKVLLQELRSIGLDMSTY 1340

Query: 1365 NSRTKNSAKMEEIP 1378
                 N  +  E+ 
Sbjct: 1341 KIENYNLNQHYELE 1354


>gi|213852735|ref|ZP_03382267.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica
           subsp. enterica serovar Typhi str. M223]
          Length = 445

 Score =  559 bits (1440), Expect = e-156,   Method: Composition-based stats.
 Identities = 186/454 (40%), Positives = 281/454 (61%), Gaps = 9/454 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235 NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292 IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352 RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           D  +    + K+DII ++K L+D+RNGKG +DDI
Sbjct: 412 DEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDI 445


>gi|224015730|ref|XP_002297513.1| hypothetical protein THAPSDRAFT_bd1267 [Thalassiosira pseudonana
            CCMP1335]
 gi|220967777|gb|EED86153.1| hypothetical protein THAPSDRAFT_bd1267 [Thalassiosira pseudonana
            CCMP1335]
          Length = 1358

 Score =  558 bits (1439), Expect = e-156,   Method: Composition-based stats.
 Identities = 295/1465 (20%), Positives = 529/1465 (36%), Gaps = 250/1465 (17%)

Query: 26   IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
            +PD IE+Q+ S+  F+           +GL     +   I  FS     +L    Y    
Sbjct: 7    LPDFIEMQRVSFCWFIA----------QGLNEELNTFSRIYDFSQNTEYVLFGQEYSLVK 56

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLPLMTKDG 142
            P +++         Y+  L I L             K    IK  S + + +LPLMT   
Sbjct: 57   PIYNIVRAKKYTANYSAQLVIPL---------EVRNKKTNIIKYHSKFPIINLPLMTSSA 107

Query: 143  TFVIKGIQRIVVSQLHRSPGIHFDHDKG--------RASLS--GKL-LYA--CRIIPDQG 189
            TFVI G +R++VSQ+ RSPG++F+ +K         +   S  GKL  +     I+P + 
Sbjct: 108  TFVINGCERVIVSQIIRSPGVYFEKNKHQKKNKKIRKLISSEIGKLKSFTPPSEILPTEK 167

Query: 190  LW---------------MDIEFD-----------SKDIIHVR-----IDR---------- 208
             W                D E D             D+  +R     I R          
Sbjct: 168  YWNWKGESLNIYSFKQIKDYEIDFSTSFVEHFKVYNDLFKIRHLSTKIKRIKIFLKWLAC 227

Query: 209  -------RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                    +K  +   + +  + S  I+       +   R +         D     KV 
Sbjct: 228  NNKFSLPNKKHLIFLLINSFNLLSRTIVKY----KILKTRNNENKNDFILNDYNQIKKVY 283

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKE---------KGVKFLGITSDCLCGLYVAEDI 312
              ++        +    ++ S +L+ L++           +         +    +   +
Sbjct: 284  DQVLQESETLLSLNINTQILSFILRDLEKFNQLNNFNFLKLNITPKIKVIIANDKIKSSL 343

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                + +  I+      +K  ++  +     I       +   + I         +D   
Sbjct: 344  YFTNSFKELIKFKYNFTKKEKDKKRNQSQATIFKNKTKYLKTKSKIIQYKDDHLIRDIYK 403

Query: 373  ALLDIYRVMRPGDVSTF--SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
               +   +     +  +   +          +  KY +      ++ ++L+  T   + H
Sbjct: 404  KKYEEKELYTATLIPEYGSWIRFGFQKNTKINISKYPIKN-QEDEIIIQLDKVTQKPIIH 462

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ--------------YR 476
            + KE  +  ++I  +L+N +    +   L N   +    +  N               + 
Sbjct: 463  LLKEMGVTDLEICQNLQNSEFFYFNKPILTNSIHQPNKLLRFNLNKNYYKNISEFSRIFD 522

Query: 477  LGLLRMERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
                R+ +  + ++++  DI+       I  + + + + +    S   Q+ + ++ L   
Sbjct: 523  PSYYRLGKIGRSKLNNRLDINLSKRITTITYEDIFAIIDKLITLSTAKQISDDIDHLK-- 580

Query: 536  THTRRLSALGQG--GVARARAGVEMRDVHP-------THYGRICPAETSEGHNIGLVSSL 586
               RR+ ++G+    + R      +R +         +          +     G     
Sbjct: 581  --NRRVRSVGELLQNLFRIGFQRLLRKLRSQTNKTYSSQLSSFNIVGATIKEFFGASQLS 638

Query: 587  TSFARVNAYGFIETPYRKVC---DGKVTNDVVYLSAMEEENRY--IAQANSSLDEDGSFT 641
                + N    +    R       G   + + +       + Y  I    +   ++    
Sbjct: 639  QYMDQTNPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVGLI 698

Query: 642  EELVFCRCAGEEILVP---REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN-MQ 697
              L  C    E   +       I+      +  + + A +  F +   ++      N + 
Sbjct: 699  ASLTTCARVNESGFLETPFWRVINGKVIKNRNPIYLTADIEDFYKIAPADISTNQENYLT 758

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSG---AAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            +  +P+   +     T  E      S     ++ A      E  DA R ++ S       
Sbjct: 759  KNLIPVRYKQDFLTVTPSEVDFIAVSPIQVVSVAASLIPFFEHDDANRALMGSN------ 812

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                         QR +    + Q+P+V  G        + +  + D G +   +     
Sbjct: 813  ------------MQRQSVPLLLPQKPIVGTG--------LENQIALDSGMVINAQRA--- 849

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
                      +S+  ++ ++ ED         ++   +  +   +E   +          
Sbjct: 850  -------GIVESVTANKIIILEDSGRH-----YKYDLQKYQRSNQETCINHRP------- 890

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  I+  G +V  G +L         S ++  + +L A    +  +  D  L     
Sbjct: 891  ------IVWEGEKVKSGQMLTDGPG-IISSELSLGQNVLVAYMPWQGYNFEDAILINERL 943

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V   +       R+ I+ +  +   E+    +      D Q + +  I +          
Sbjct: 944  VYEDIFTSIHIERYEIEIDRTAEMSEQTTNNIPNLSISDVQNLNEDGIVT--------IG 995

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                P       ++  D   + P S+  +               K   +TS  + E  + 
Sbjct: 996  TFVKPGDILVGKIIPKDDSEQLPESKLLRAIFG--------AKAKGVRDTSFRMPEGEYG 1047

Query: 1055 NKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              IE + +            +++F+A  R IQ GDK+AGRHGNKGI+SRILP +DMPFL 
Sbjct: 1048 RVIETLTFNRRTKLAYKFEKIQIFIAQIRKIQVGDKIAGRHGNKGIISRILPRQDMPFLP 1107

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDI+LNPLGVPSRMNVGQ++E  LG A   L ++ K L  D               
Sbjct: 1108 DGTPVDIILNPLGVPSRMNVGQLYECLLGLAGHKLNRRFKILPFD--------------- 1152

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
            ++ G       I+     + +   E W                        + +    G+
Sbjct: 1153 EMYGPEVSRILINKKLRQASIENDEAW------------------------LFNPYSPGK 1188

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             +L DG TG+ FD P+TVG  YMLKL H+V DK+++R+TG YSLVTQQPLGGK+  GGQR
Sbjct: 1189 MVLLDGRTGKEFDNPITVGNAYMLKLIHLVDDKMHSRATGPYSLVTQQPLGGKAQHGGQR 1248

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++ +GA++ L+E+LTIKSDD+ GR     SI+ G     +G PESF VLV+E
Sbjct: 1249 FGEMEVWALEGFGASFTLKELLTIKSDDMQGRNETLNSIIKGQPIPTSGVPESFKVLVQE 1308

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIP 1378
            ++++GL +        +S +  EI 
Sbjct: 1309 LRSIGLDLSTYRIDEFSSNQSYEIE 1333


>gi|269930923|gb|ACZ54196.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 602

 Score =  557 bits (1436), Expect = e-156,   Method: Composition-based stats.
 Identities = 441/603 (73%), Positives = 517/603 (85%), Gaps = 1/603 (0%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D IDEK L+ +       I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+
Sbjct: 1   DEIDEKVLKILLDVSADQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGE 60

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             T   AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+
Sbjct: 61  PPTIDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRVLRQEDILAVVKMLVE 120

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLIN
Sbjct: 121 LRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLIN 180

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
           AKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTH
Sbjct: 181 AKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 240

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           YGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   
Sbjct: 241 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAKH 300

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEND
Sbjct: 301 YVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEND 360

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ AKR+GIV+QVDA RIVI
Sbjct: 361 DANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVSAKRSGIVDQVDATRIVI 420

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD V + DIIADGPSTDLGDL
Sbjct: 421 RATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRVEKGDIIADGPSTDLGDL 479

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDI
Sbjct: 480 ALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDI 539

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV+EE L+N+DE GII +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVR
Sbjct: 540 PNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVR 599

Query: 926 DTS 928
           DTS
Sbjct: 600 DTS 602


>gi|290889141|gb|ADD69920.1| RNA polymerase beta subunit [Rhizobium alamii]
          Length = 453

 Score =  556 bits (1434), Expect = e-156,   Method: Composition-based stats.
 Identities = 307/454 (67%), Positives = 376/454 (82%), Gaps = 1/454 (0%)

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           LQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+D
Sbjct: 1   LQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDID 60

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
           E TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  
Sbjct: 61  EDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHS 120

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY 
Sbjct: 121 SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYT 180

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL++L +KG+K
Sbjct: 181 KSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRTLSDKGLK 239

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+L +D +N 
Sbjct: 240 ALKATDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILANHFDEIPVLGIDHINV 299

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD+++YDLS VGRV
Sbjct: 300 GAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRV 359

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           KMNMRL+L   D VR +RK+DI+A++K+LV+LR+GKG IDDIDNLGNRRVRSVGE+++NQ
Sbjct: 360 KMNMRLDLSVEDTVRILRKDDILAVVKMLVELRDGKGEIDDIDNLGNRRVRSVGELMENQ 419

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           YRLGLLRMER+IKER+SS++ID+VMPQDLINAKP
Sbjct: 420 YRLGLLRMERAIKERMSSIEIDTVMPQDLINAKP 453


>gi|151547|gb|AAA25986.1| RNA polymerase (rpoB) (EC 2.7.7.6) [Pseudomonas putida]
          Length = 322

 Score =  556 bits (1434), Expect = e-156,   Method: Composition-based stats.
 Identities = 193/324 (59%), Positives = 250/324 (77%), Gaps = 4/324 (1%)

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              + +L+D+F++K   +Q GDD+ PGVL++VKV++A++R IQ GDKMAGRHGNKG+VS I
Sbjct: 2    DRRRLLDDKFEDKKRNVQQGDDLAPGVLKIVKVYLAIRRRIQPGDKMAGRHGNKGVVSVI 61

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +P EDMP   +GTPVD+VLNPLGVPSRMNVGQI ETHLG A  GLG+KI  ++ + +   
Sbjct: 62   MPVEDMPHDANGTPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEKIDRMLEEQR--- 118

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              + LR FL +V    G   E + +++D+ VL +A   K GVP++TPVFDGA E  I +M
Sbjct: 119  KAAELRVFLTEVYNEIGGRQENLDEFNDEEVLALANNLKKGVPMATPVFDGAKEREIKAM 178

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++ADL ESGQ +L+DG T    +RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 179  LKLADLPESGQMVLFDGRTRNKSERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 238

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+   E G
Sbjct: 239  LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPG 298

Query: 1343 TPESFNVLVKEMQALGLSIDLENS 1366
              ESFNVL+KE+++LG+ IDLE  
Sbjct: 299  MAESFNVLIKEIRSLGIDIDLETE 322


>gi|297582232|ref|ZP_06944148.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Vibrio cholerae
           RC385]
 gi|297533533|gb|EFH72378.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Vibrio cholerae
           RC385]
          Length = 536

 Score =  555 bits (1430), Expect = e-155,   Method: Composition-based stats.
 Identities = 256/529 (48%), Positives = 366/529 (69%), Gaps = 4/529 (0%)

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           ++KDIK +S++ G +PLMT++GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY
Sbjct: 6   TVKDIKTRSLH-GRIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLY 64

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
             RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S EIL  F+ K+ +  
Sbjct: 65  NARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSAEILDIFFEKVNFEV 124

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           +       L    L  G   +  +     G+  +E G+++T+  ++ L++ GV F+ +  
Sbjct: 125 KDQTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPV 181

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           + + G   A+D VN  TGE+ I A   I  ++L  +  +  + + +L+ + +++  ++  
Sbjct: 182 EYIVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSE 241

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           TL  D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++YDLSTVGR+K N  +
Sbjct: 242 TLRVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSI 301

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             +  ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+
Sbjct: 302 GREDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLV 361

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 362 RVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 421

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ET
Sbjct: 422 ISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLET 481

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           PYR+V +G VT++V YLSA+EE    IAQAN+ L E+G F ++    R 
Sbjct: 482 PYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADDRTSKRR 530


>gi|315320481|ref|YP_004072537.1| DNA-directed RNA polymerase subunit beta [Thalassiosira oceanica
            CCMP1005]
 gi|283568954|gb|ADB27491.1| DNA-directed RNA polymerase subunit beta [Thalassiosira oceanica
            CCMP1005]
          Length = 1364

 Score =  555 bits (1430), Expect = e-155,   Method: Composition-based stats.
 Identities = 290/1430 (20%), Positives = 490/1430 (34%), Gaps = 175/1430 (12%)

Query: 26   IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
            +PD IE+Q+ S+  F+           +GL     +   I  FS     +L    Y    
Sbjct: 8    LPDFIEMQRVSFCWFIA----------QGLNEELSTFSRIYDFSQNTEYILFGQEYSLVK 57

Query: 84   PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLPLMTKDG 142
            P +++         Y+  L I L             K    IK  + + + +LPLMT   
Sbjct: 58   PVYNIVRAKKYTANYSAQLIIPL---------EVRNKKTNSIKYHNKFPIINLPLMTSAA 108

Query: 143  TFVIKGIQRIVVSQLHRSPGIHFDHDKG--RASLSGKLLYA-----------CRIIPDQG 189
            TFVI G +R++VSQ+ RSPG++F+ +K   +     K+L               I+P + 
Sbjct: 109  TFVINGCERVIVSQIIRSPGVYFEKNKHQKKNRKLKKILSNDIGKLKNFIPPSEILPTEK 168

Query: 190  L--WMDIEFDSKDIIHVR---IDR----RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
               ++    D KD ++ +   ID     +RK+        L       +S F     +  
Sbjct: 169  TLYFLKKVTDIKD-LNEKGEEIDELWKWKRKISTLYSFKNLKASEVNFISLF--IEYFKI 225

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT------SGLLKSLKEKGVK 294
                +     +            L           +  ++       + L+K L +   K
Sbjct: 226  YNSLFKITDLSEKTKRIKIFLKWLSTNKKSFISNNNKDRIFLLINYFNLLIKVLHKY--K 283

Query: 295  FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS---------LEEIFHSEIRDIP 345
             L         +    + +  E   I+ +A  + ++            +    ++I D  
Sbjct: 284  SLKNKKYNDSNISEHLEQIKKEHNNIFQKAKTLFEQNININLFNFVICDLSHFNQINDFS 343

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES----MFNFLFF 401
             L          I        N    D   ++ +  +     T  +        +     
Sbjct: 344  FLNSTISPKIRSILTKSNVQSNLYFTDGFKELIKYNKNDKNKTKYLKTKSQILEYKDEHS 403

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRH-IRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
              D Y      +      L  +    VR   +K     I K  +  +  +  I       
Sbjct: 404  IRDIYKKKYEEKELYTATLIPEYGSWVRFGFQKNTNTNISKYPIKNQEDEIIIQLDKVTQ 463

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV--CEFFC 518
               +  + EM  N   +                +   + P      K +   +    +  
Sbjct: 464  KPIIHLLKEMGVNDIEICQN----LQNSEFFYFNKPVLTPSIYAPRKLLRFTLSKNYYKN 519

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-------- 570
             S+ S++ +            +L+      +++    +  +D+       I         
Sbjct: 520  ISEFSRIFDPAYYRLGKIGRSKLNNRLNIQLSKRIVTITYQDIFAIIDKLITLSISKQIS 579

Query: 571  -PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV-----------VYLS 618
               +  +   +  V  L        +  +    R   +   ++ +            +  
Sbjct: 580  DDIDHLKNRRVRSVGELLQNLFRIGFQRLSRKLRSQTNKTYSSQLSSFNIVGATIREFFG 639

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID---FIDASPK-----Q 670
            A +           S          L       + I      I    +    P      Q
Sbjct: 640  ASQLSQYMDQTNPLSALTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQ 699

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             V + ASL      ++S  +            ++K   P   T       K + A I   
Sbjct: 700  NVGLIASLTTSARVNESGFLETPFWRVLNG-KVIKTGNPIYLTADIEDFYKIAPADIS-- 756

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                   +    I IR  +  L  + S VD   +             Q   V        
Sbjct: 757  -TNEDNYLTKELIPIRYKQDFLTVTPSEVDFIAVSPI----------QVVSVAASLIPFF 805

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                A+              +L+   P  G   E+ + +   MV       I        
Sbjct: 806  EHDDANRALMGSNMQRQSVPLLLPQKPIVGTGLENQIALDSGMVINAQRDGIVSSVTADK 865

Query: 851  ARDTKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                +    +   D+           I+   I+  G ++  G +L         S ++  
Sbjct: 866  IIILENSGRQCKYDLQKYQRSNQETCINYRPIVWEGEQIKSGQMLTDGPG-IISSELSLG 924

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + +L A    +  +  D  L     V   +       R+ I+ +  +   E+    +   
Sbjct: 925  QNVLVAYMPWQGYNFEDAILINERLVYEDIFTSIHIERYEIEIDRTAEISEQTTNNIPNL 984

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
               D + + +  I +              P       ++  D   + P S+  +      
Sbjct: 985  SISDVKNLNEDGIVT--------IGTFVKPGDILVGKIVPKDDSEQLPESKLLRAIFG-- 1034

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGD 1088
                     K   +TS  + E  +   IE + +            +++F+A  R IQ GD
Sbjct: 1035 ------AKAKGVRDTSFRMPEGEYGRVIETLTFNRRTKLAYKFEKIQIFIAQIRKIQVGD 1088

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKGI+SRIL  +DMPFL DGTP+DI+LNPLGVPSRMNVGQ++E  LG A   L
Sbjct: 1089 KIAGRHGNKGIISRILARQDMPFLPDGTPIDIILNPLGVPSRMNVGQLYECLLGLAGHKL 1148

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             ++ K L  D               ++ G       I+     + L   E W        
Sbjct: 1149 NRRFKILPFD---------------EMYGPEVSRILINKKLRQASLENDEAW-------- 1185

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                            + +    G+ +L DG TG+ FD P+TVG  YMLKL H+V DK++
Sbjct: 1186 ----------------LFNPYSPGKMVLLDGRTGKEFDNPITVGNAYMLKLIHLVDDKMH 1229

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +R+TG YSLVTQQPLGGK+  GGQR GEMEVW ++ +GA++ L+E+LTIKSDD+ GR   
Sbjct: 1230 SRATGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEGFGASFTLKEILTIKSDDMEGRNET 1289

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              SI+ G     +G PESF VLV+E++++GL +        +  +  EI 
Sbjct: 1290 LNSIIKGQTIPTSGIPESFKVLVQELRSIGLDLSTYRIDEFSGHQSYEIE 1339


>gi|221128023|ref|XP_002154919.1| PREDICTED: similar to DNA-directed RNA polymerase beta subunit [Hydra
            magnipapillata]
          Length = 1140

 Score =  555 bits (1430), Expect = e-155,   Method: Composition-based stats.
 Identities = 212/521 (40%), Positives = 294/521 (56%), Gaps = 35/521 (6%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF- 917
            +I   I         NI +  I+  G +++ GD++  G  T  GE  +     +    + 
Sbjct: 641  DIYNLIKYQRSNQNTNIHQRPIVKKGDKLSKGDVIADGASTDLGEIAIGQNMLVAFMPWN 700

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQ 975
            G    D    S RV +    T + +        D    +  + R+   +     ++ DE 
Sbjct: 701  GYNFEDSILISERVVAEDRYTSIHIEELVVMARDTKLGAEEITRDIPNLSEQQLNRLDES 760

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         + L G+    G         L   +  E            D+     V
Sbjct: 761  GIIYVGAEVLPGDTLVGKVTPKGETTLTPEEKLLRAIFGEKASDVKDTSLRVDQGSSGTV 820

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V                      GD++P GVL++VKV++A+KR +Q GDKMAGRHG
Sbjct: 821  IDVQVFTRE------------------GDELPAGVLKMVKVYIAVKRRLQPGDKMAGRHG 862

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS+I P EDMP+L DGTPVDIVLNPLGVPSRMN+GQ+ E HLGWA  GLG++I  +
Sbjct: 863  NKGVVSKITPVEDMPYLADGTPVDIVLNPLGVPSRMNIGQVLEVHLGWAGKGLGQRIGDM 922

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            +    A+ +I   R FLE+V  +    E ++   D  V  +A++  SGVP ++PVFDGA 
Sbjct: 923  LQREAASTEI---RGFLEQVYNSTGRKEDLAQLSDAEVQEMAKELTSGVPFASPVFDGAT 979

Query: 1216 EEAINSMLRMADLD----------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            E+ I  ML++A  D             Q+ LYDG +G+ F+R  TVGY++ LKL+H+V D
Sbjct: 980  EKEIGDMLQLAYPDDVAKAKGLTATRTQAQLYDGRSGDAFERTTTVGYMHYLKLHHLVDD 1039

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+YVLQEMLT+KSDDV GR
Sbjct: 1040 KMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVQGR 1099

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            T+VYE+IV G  + E G PESFNVLVKE+++LG+ I+L+ S
Sbjct: 1100 TKVYENIVKGEHSIEAGMPESFNVLVKEIRSLGIDIELDRS 1140



 Score =  541 bits (1394), Expect = e-151,   Method: Composition-based stats.
 Identities = 361/632 (57%), Positives = 467/632 (73%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +Y              +    + +  IL    ++  AYI  TL TD+  D   A + IYR
Sbjct: 201 LYFRVDRRRKMPVTILLKAIGLNNESILANFFLDQGAYISQTLRTDETVDEFAARVAIYR 260

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           +MRPG+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A+
Sbjct: 261 MMRPGEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKMGRSESTGPMVLTNEDILAV 320

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +KILVDLRNG+G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +M
Sbjct: 321 VKILVDLRNGRGDVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLM 380

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P DLIN+KP+ +A+ EFF +SQLSQ     N L+ ITH RR+SALG GG+ R RAG E+R
Sbjct: 381 PHDLINSKPISAALKEFFGASQLSQFMNQTNPLAEITHKRRVSALGPGGLTRERAGFEVR 440

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH THYGR+CP ET EG NIGL++SL  +AR+N YGFIETPYR+V D KVTN++ YLSA
Sbjct: 441 DVHVTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFIETPYRRVVDSKVTNEIDYLSA 500

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EE    IAQAN++LD++G+ T +LV  R  GE ILV  +++ ++D SP Q+VS+AASL+
Sbjct: 501 IEEGKYVIAQANAALDKEGTLTGDLVSAREKGESILVSADRVQYMDVSPAQIVSVAASLV 560

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NM RQAVP+L+ E P VGTG+E V A  SG  + A R GIV+ VD
Sbjct: 561 PFLEHDDANRALMGANMSRQAVPVLRPEKPMVGTGIERVAAVDSGTVVTATRGGIVDYVD 620

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A R+VIR  + +      GVDIY L+K+QRSNQNT ++QRP+VK GD++ + D+IADG S
Sbjct: 621 ATRVVIRVNDAEAQAGEVGVDIYNLIKYQRSNQNTNIHQRPIVKKGDKLSKGDVIADGAS 680

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TDLG++A+G+NMLVAFMPW+GYNFEDS+LISER+V+ED +TSIHIEE  VMARDTKLG E
Sbjct: 681 TDLGEIAIGQNMLVAFMPWNGYNFEDSILISERVVAEDRYTSIHIEELVVMARDTKLGAE 740

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPN+SE+ L  +DE GII VGAEV PGD LVGK+TPKGE+ +TPEEKLLRAIFGE
Sbjct: 741 EITRDIPNLSEQQLNRLDESGIIYVGAEVLPGDTLVGKVTPKGETTLTPEEKLLRAIFGE 800

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA DV+DTSLRV  G SGTV+DV++F R G +
Sbjct: 801 KASDVKDTSLRVDQGSSGTVIDVQVFTREGDE 832



 Score =  396 bits (1018), Expect = e-107,   Method: Composition-based stats.
 Identities = 107/232 (46%), Positives = 164/232 (70%), Gaps = 1/232 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG    +++IP L+++QK +Y  FL  ++ P +R NEGLQAAF++ 
Sbjct: 1   MAYTYTERKRIRKNFGSRDSVLEIPYLLQMQKDAYTAFLQADVGPKKRTNEGLQAAFEAA 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKS 121
           FPI + +G   ++++ Y    P FDV +C  R LTYA  ++  ++LI++D +  TG  K 
Sbjct: 61  FPIVSHNGFVEMKYLEYNLAKPAFDVRECQTRGLTYASAVRAKVQLIIYDRESSTGQNKV 120

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
           +K++KEQ +YMG++PLMT  G+F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++
Sbjct: 121 VKEVKEQEVYMGEVPLMTGKGSFIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFS 180

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            RIIP +G W+D EFD KD+++ R+DRRRK+PVT  L A+G+++E IL+ F+
Sbjct: 181 ARIIPYRGSWLDFEFDPKDLLYFRVDRRRKMPVTILLKAIGLNNESILANFF 232


>gi|7524891|ref|NP_045893.1| RNA polymerase beta'' chain [Chlorella vulgaris]
 gi|3024561|sp|P56299|RPOB_CHLVU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|2224485|dbj|BAA57969.1| RNA polymerase beta subunit [Chlorella vulgaris]
          Length = 1301

 Score =  554 bits (1428), Expect = e-155,   Method: Composition-based stats.
 Identities = 295/1092 (27%), Positives = 455/1092 (41%), Gaps = 108/1092 (9%)

Query: 333  LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV------ 386
            LE     +   +  L   S  ++  +    +      +++A   +Y   +          
Sbjct: 227  LEHSKILQNSFVAELGEGSARHDDVLERAGLYAHPATQEEAWQYLYSHFKEYSPYAHKNL 286

Query: 387  -STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             +    A   F    ++ DK  L  +GR +   ++    P +   + +ED++   + L+ 
Sbjct: 287  AAKEQTAREFFYSTLWNKDKLILGHIGRQQFREKIGSIEPLENTSLTREDLLEATQALLS 346

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS-------- 497
            L + K  +D+ID+L  +R+R   E L      G+   E   + +++ +            
Sbjct: 347  LMHKKRVVDEIDSLTQKRIRGCDEFLLEHLATGMKEFELFFRRKVTFLPATKSITGAENP 406

Query: 498  ----VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                      + +K V  +   FF S  L Q  +  NSL+  TH RRL+ LG GG++  +
Sbjct: 407  FRSLWRQNKAVFSKTVSKSWKRFFTSGTLGQFMDQTNSLAETTHKRRLTVLGPGGISGKQ 466

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG--FIETPYRKVCDGKVT 611
              +++R +HPT+YGR+CP ET EG N GLV+S T  + ++ YG   + TP+ +V  G+V 
Sbjct: 467  TTIQIRGIHPTYYGRLCPIETPEGKNAGLVNSFTVLSVLSKYGARTLTTPFYQVYKGQVQ 526

Query: 612  NDVVYL--SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
              +  L  S  +E     A A+  L       +  +  R           +I        
Sbjct: 527  KTLPPLRVSPRQEYKLIEAPADIQLTAWNVLPKTHLPVRKELNFHSDVATRITTQSVGIL 586

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS------- 722
            Q +S+A SLIPFLE++D+NR LMG NMQRQAVPLLK +AP VGTG+ES V          
Sbjct: 587  QNISVATSLIPFLEHNDANRALMGSNMQRQAVPLLKPQAPLVGTGLESRVIGDVNHSMQA 646

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN----- 777
            S    + K +    QV + R     V        S     +        Q+   N     
Sbjct: 647  SKTGFITKVSSTKIQVLSPRKTKAQVSVFSHVLFSLNKKKKKSLLNSEKQSFSKNGIFFI 706

Query: 778  ---QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY-NFEDSMLI---- 829
               Q+              +    S+          + +  M +    NF   +      
Sbjct: 707  KTLQQKSNLKNIFFSAQKALYQENSSFDLKFEAQNRLFIPKMTFSLAQNFSRKIPFLSFF 766

Query: 830  ------SERMVSEDVFTS------IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
                    R   +   +S       H +      R  K+        I            
Sbjct: 767  LKKKKERPRNPKKFFRSSDSFVNWKHKKLHSEDFRKNKVEITTTYSLIQYQRTNQSTCFS 826

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            E  I+     V  GD+L    +   +  ++  + +L A    +  +  D  L     V  
Sbjct: 827  ERPILPENEWVEKGDLLADGAS-SSQGKLSIGQNVLVAYLPWEGYNFEDAILISQRLVDQ 885

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +      + + I        +ER    +  +  D  + I           +  G     
Sbjct: 886  EIFTSLHMDHYDIAVQNTQYGLERITNLIPLKISDSTRDIYKMGNLDSRGLVEIGSWVEP 945

Query: 998  GPKGFKKSTVLSSDLIS-EYPRSQWWQFAVQDEKVQRNVESLK-----VQYETSKSILED 1051
            G     K + L       + P  + +   +Q EK      SL+       +     IL  
Sbjct: 946  GDYLVGKMSPLDPKSPPLQSPHEKLYNVILQREKTSFRNTSLRVPKGVQGFVLGVQILPS 1005

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            +  +     +  + +       V+V +  +R IQ GDKMAGRHGNKGIVS ILP +DMP+
Sbjct: 1006 QEPDVAALAEKDEIL------RVRVLLLQRRKIQVGDKMAGRHGNKGIVSLILPRQDMPY 1059

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTPVDIVLNPLGVPSRMNVGQI E  LG A   L ++  + + D +           
Sbjct: 1060 LPDGTPVDIVLNPLGVPSRMNVGQILECLLGLAGHFLHERYTTYLFDEQ----------- 1108

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                 G  +    +      + L+    W         VF+                   
Sbjct: 1109 ----YGAEASRSLVYSKLYQASLKTRNPW---------VFE---------------PHHP 1140

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  ++DG TG  FD+P+T GY Y+LKL H+V DK++AR TG YS +TQQP+ G++  GG
Sbjct: 1141 GKIRVFDGRTGLTFDQPITAGYAYILKLVHLVDDKIHARPTGPYSAITQQPVKGRARNGG 1200

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QRLGEMEVW +QAYGAA+ L E  T+KSDD+ GR +   +I A      TG PESF +++
Sbjct: 1201 QRLGEMEVWALQAYGAAHTLHEFFTVKSDDLDGRQQAVLNIYANKPV-TTGNPESFKLIL 1259

Query: 1352 KEMQALGLSIDL 1363
            +E+QAL  +  +
Sbjct: 1260 RELQALCFNFQV 1271



 Score =  140 bits (354), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 54/209 (25%), Positives = 96/209 (45%), Gaps = 29/209 (13%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEF 81
           ++IP+LI+VQ+ S+  F+            GL+ AF+     +       + F     +F
Sbjct: 40  MEIPNLIDVQRQSFYSFI----------EYGLKEAFQKPLRFSTTKHDLEIRFFPEGIQF 89

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P F     +     Y   + I + +          +K     + + +++G LP+MT+ 
Sbjct: 90  RKPDFTQKQAVVLGKIYGSAVYIPVGIH---------SKKSSTFRIEWLFVGILPIMTRQ 140

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           G FV+ G+ R+V+ Q+ R+PGI+            K+    RI+P++G W+ I  D K  
Sbjct: 141 GHFVVNGVSRVVLHQMVRNPGIY----TLPIHPRTKIG-TLRIVPEKGGWIHITVDKKHR 195

Query: 202 IHVRIDR--RRKVPVTSFLMALGMDSEEI 228
           +   + R  RRKV +  FL A+G+   +I
Sbjct: 196 VWF-LTRSLRRKVSLLIFLQAVGIPFHDI 223


>gi|269930925|gb|ACZ54197.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 599

 Score =  554 bits (1427), Expect = e-155,   Method: Composition-based stats.
 Identities = 438/600 (73%), Positives = 514/600 (85%), Gaps = 1/600 (0%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D IDEK L+ +       I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+
Sbjct: 1   DEIDEKVLKILLDVSADQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGE 60

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             T   AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+
Sbjct: 61  PPTIDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRVLRQEDILAVVKMLVE 120

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLIN
Sbjct: 121 LRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLIN 180

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
           AKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTH
Sbjct: 181 AKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 240

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           YGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   
Sbjct: 241 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAKH 300

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEND
Sbjct: 301 YVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEND 360

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ AKR+GIV+QVDA RIVI
Sbjct: 361 DANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVSAKRSGIVDQVDATRIVI 420

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD V + DIIADGPSTDLGDL
Sbjct: 421 RATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRVEKGDIIADGPSTDLGDL 479

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDI
Sbjct: 480 ALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDI 539

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV+EE L+N+DE GII +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DVR
Sbjct: 540 PNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVR 599


>gi|115443591|ref|YP_778610.1| RNA polymerase beta subunit [Bigelowiella natans]
 gi|122227441|sp|Q06J17|RPOB_BIGNA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|110810236|gb|ABG91442.1| RNA polymerase beta subunit [Bigelowiella natans]
          Length = 1099

 Score =  554 bits (1427), Expect = e-155,   Method: Composition-based stats.
 Identities = 304/1085 (28%), Positives = 514/1085 (47%), Gaps = 114/1085 (10%)

Query: 288  LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +           +D +        I   +   I+++   V    +L  +    +    ++
Sbjct: 122  IYYHKENENTYYADIIAERGNWLRIEIDKKNNIWMKVKKVPKVPALMFLQALGVTKSNLI 181

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDI--YRVMRPGDVST--FSVAESMFNFLFFDS 403
                +               K +K+AL  I  Y  +     S    +  +      F + 
Sbjct: 182  K---LLKYPIPNQNHNLGNFKSQKEALEKIELYSQLESSINSRNLKNQNKITIFDRFMNP 238

Query: 404  DKYDLSTVGRVKMNMRLN-LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              YDL T GR+++N + N ++       +  +D I  +  L+ ++      DDIDNL N+
Sbjct: 239  KYYDLGTRGRIQINKKFNNIEETIQHSTLTSKDFILAVHFLLKIKYKIEETDDIDNLKNK 298

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RV+  GE++++Q+ +G+LR+++ +K+++ ++   ++   ++ ++ P+ + + EFF  + L
Sbjct: 299  RVKIAGELIQSQFGIGILRLQKYVKDKLGNIKN-NLHLTNIFSSTPINTTLAEFFGVNPL 357

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  + VN L+ +TH RRLS+LG GGV R  A + +R +HPT YGRICP ET EG N GL
Sbjct: 358  SQFMDEVNPLATLTHKRRLSSLGIGGVNRDTATLTIRSIHPTLYGRICPIETPEGKNAGL 417

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSF 640
            V+S   FA +N+ G IETP+ +VC+G++  +  + YLSA +E+   I   +      G  
Sbjct: 418  VNSFALFAEINSEGLIETPFFRVCNGRILYEMGINYLSANQEDKSNIVPFDIKKSRIGFL 477

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            ++  +  R   +   V ++K+DFI  S  Q++S+A SLIPF+E++D+NRVLMG NMQRQA
Sbjct: 478  SKNKIAARIKQQFKEVSKKKVDFISISQLQMLSVATSLIPFMEHNDANRVLMGSNMQRQA 537

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPLLK E   VGTG+E+ +       + +   G +  +   +I I ++  +        +
Sbjct: 538  VPLLKTECCLVGTGLETKIFFDLQDNVKSPPNGFISYLSLKKITISNIRNEHKSFNFKSN 597

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +   +S        +                                         
Sbjct: 598  PLETITCIKSKSRNFNRLK----------------------------------------- 616

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN +D +  S+  +         I  +    R+ K+       +  N     +  +    
Sbjct: 617  YNLKDLLTNSKESLK--------ITNYMSYVREQKIQYYIKQYNSSNQGTCSVNRL---- 664

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +  G  +   + L+  ++    + +   + L       K  +  D  +     ++  +V
Sbjct: 665  TLNEGQFIIKKNPLISGLS-SCRNELALGKNLFVGYISWKGYNFEDAIV-----LNEQLV 718

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+    ++K E  I   +E  E++ RD  +    L++    +   I  G    S   
Sbjct: 719  INNIYTSTHLEKFETEIKKNKENSEIITRDIKN-ISFLNKKNLDKNGIIKIGSRVFSDDI 777

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K   + + ++S Y R   ++   +     RN      +Y+  +    D  K+K +  
Sbjct: 778  LVGKLLPIETRILSPY-RKLLYEILQKQNDHYRNTSLRVPKYKRGRITFVDYIKDKGKIK 836

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            +  + +    L+ +K+ +   R IQ GDK++GRHGNKG++S+IL  ++MP+L DG P+DI
Sbjct: 837  KKTEILKD--LKTIKIHLMQNRLIQIGDKISGRHGNKGVISKILKIQEMPYLNDGIPLDI 894

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E  LG +C  L ++ K +  D     ++S    +         
Sbjct: 895  LLNPLGVPSRMNIGQVLECLLGLSCFYLQRRFKVIPFDESFGFEVSRNFIYSNLYFS--- 951

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                K+G                N+ L        G++ ++D  
Sbjct: 952  ------------------NIKTG----------------NNWLLHPYYP--GKNRIFDSY 975

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +G PFD+P+T+G  Y+LKL H+V +KV+ARSTGSYSLVTQQPL GKS +GGQR+GEMEVW
Sbjct: 976  SGLPFDQPITIGKAYILKLIHLVEEKVHARSTGSYSLVTQQPLKGKSKKGGQRVGEMEVW 1035

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++ YGAAY L E+LT+KSDD+  R +V  SI+      + GT E+F VL++E+Q+L L+
Sbjct: 1036 ALEGYGAAYTLHEILTVKSDDIKSRQKVLTSILNSETI-KFGTTETFKVLIRELQSLCLN 1094

Query: 1361 IDLEN 1365
            I    
Sbjct: 1095 IQFFK 1099



 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 61/355 (17%), Positives = 132/355 (37%), Gaps = 37/355 (10%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           P+L+++Q+ S+  FL            G++   K +  IT      ++    ++ + P +
Sbjct: 9   PNLLKLQRKSFLTFL----------KYGIKKEIKKLD-ITKNKKKLLVYPNLFQLNLPTY 57

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVI 146
             ++C+    TY   L I +RLI +  +               I + ++P+MT    F+ 
Sbjct: 58  TCNECVITSKTYNCELVIPIRLISYKDEIE------------WITLTNIPIMTNKCNFIT 105

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G  R+++SQ+ R+PGI++  +           Y   II ++G W+ IE D K+ I +++
Sbjct: 106 NGSPRVIMSQITRAPGIYYHKENENT-------YYADIIAERGNWLRIEIDKKNNIWMKV 158

Query: 207 DRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
            +  KVP   FL ALG+    ++    YP    +     +     A + +       S +
Sbjct: 159 KKVPKVPALMFLQALGVTKSNLIKLLKYPIPNQNHNLGNFKSQKEALEKIELYSQLESSI 218

Query: 266 DIDTGE---QVIESGKKLTSGLLKSLKEKGV---KFLGITSDCLCGLYVAEDIVNGETGE 319
           +    +   ++    + +            +   K      + +    +           
Sbjct: 219 NSRNLKNQNKITIFDRFMNPKYYDLGTRGRIQINKKFNNIEETIQHSTLTSKDFILAVHF 278

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
           +      + +   ++ + +  ++    L               V DK  + K+ L
Sbjct: 279 LLKIKYKIEETDDIDNLKNKRVKIAGELIQSQFGIGILRLQKYVKDKLGNIKNNL 333


>gi|269930805|gb|ACZ54137.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 596

 Score =  553 bits (1425), Expect = e-155,   Method: Composition-based stats.
 Identities = 436/596 (73%), Positives = 512/596 (85%), Gaps = 1/596 (0%)

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           DEK L+ +F      I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T
Sbjct: 2   DEKILKILFDVNADQINILDIDHMNVGAYIRNTLKVDKNESRQDALFDIYRVMRPGEPPT 61

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
              AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+LR+
Sbjct: 62  MDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRTLRQEDILAVVKMLVELRD 121

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP
Sbjct: 122 GRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKP 181

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
             +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR
Sbjct: 182 AAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 241

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           ICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+A
Sbjct: 242 ICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIVDGKVTTEVIYLSAMEESKHYVA 301

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+N
Sbjct: 302 QANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDAN 361

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ 
Sbjct: 362 RALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVSAKRSGIVDQVDATRIVIRAT 421

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD + + DIIADGPSTDLGDLALG
Sbjct: 422 ED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRIEKGDIIADGPSTDLGDLALG 480

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           RN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDIPNV
Sbjct: 481 RNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDIPNV 540

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           +EE L+N+DE GII +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DV
Sbjct: 541 AEEALRNLDEAGIIYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDV 596


>gi|213163872|ref|ZP_03349582.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica
           subsp. enterica serovar Typhi str. E00-7866]
          Length = 436

 Score =  553 bits (1425), Expect = e-155,   Method: Composition-based stats.
 Identities = 179/445 (40%), Positives = 273/445 (61%), Gaps = 9/445 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235 NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  V++D V+  TGE+   A   +    L ++  S  + I  L+ + +++  YI  T+
Sbjct: 292 IAGKVVSKDYVDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETV 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AES+F  LFF  D+YDLS VGR+K N  L  
Sbjct: 352 RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLR 411

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLR 447
           D  +    + K+DII ++K L+D+R
Sbjct: 412 DEIEGSGILSKDDIIDVMKKLIDIR 436


>gi|298248452|ref|ZP_06972257.1| DNA-directed RNA polymerase, beta subunit [Ktedonobacter racemifer
           DSM 44963]
 gi|297551111|gb|EFH84977.1| DNA-directed RNA polymerase, beta subunit [Ktedonobacter racemifer
           DSM 44963]
          Length = 1163

 Score =  552 bits (1422), Expect = e-154,   Method: Composition-based stats.
 Identities = 310/978 (31%), Positives = 463/978 (47%), Gaps = 143/978 (14%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-A 71
            R  F + P+I  +P LI++Q  S++ F            EGL+  F  + PI  F+G  
Sbjct: 12  ERVSFARIPDIRPMPGLIQIQLDSFEWF----------KKEGLRELFAEISPIEDFTGKN 61

Query: 72  AMLEFV--SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             LEF+     F  PK+D D+C  RD TYA PL +  RLI          K   +I E+ 
Sbjct: 62  LSLEFIVPPEPFGKPKYDEDECRDRDATYAAPLNVKARLI---------NKETGEIIEKD 112

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMTK GTF+I G +R+VVSQL RSPG+++  D+     +GK L+A ++IP +G
Sbjct: 113 IFMGDFPLMTKAGTFIINGAERVVVSQLVRSPGVYYTVDEDAT--TGKKLFAAKLIPGRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA-------------LGMDSEE-ILSTFYPK 235
            W++ E  +K+++ V+IDR+RK+PVT+ L A             L + +++ IL  F   
Sbjct: 171 AWLEFETSNKNLLTVKIDRKRKLPVTTLLRAISRLAKEHWHVEDLDLSTDQGILDAFARV 230

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVK 294
                                   +      +  G+   +++ + L   L  + +   + 
Sbjct: 231 DNDPVIRYIQATLDRDPVKKEEEALLELYKKLRPGDPATLDNARSLVKNLFFNPRRYELG 290

Query: 295 FLGITS-DCLCG-------LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            +G    +             + +D +      +         +  ++ + +  +R +  
Sbjct: 291 NVGRYKLNRKLDLSIPQSQRILTQDDLVALIRRLVSLNNGRGRKDDIDHLGNRRVRCVGE 350

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRK------DALLDIYRVMRPGDVSTFSVAESMFNFLF 400
           L              +V ++   ++      +AL++I            +  +  F    
Sbjct: 351 LIQSQFRVGLLRMERVVKERMSIQEPGQATPNALINI--------RPVVAAIKEFFGGSQ 402

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                   + +  + +  RL+   P     + ++     ++ + +   G+  I  I+   
Sbjct: 403 LSQFMEQTNALAEIGVKRRLSALGPGG---LSRDRAGFDVRDVHESHYGR--ICPIETPE 457

Query: 461 NRRVRSVGEMLK-------NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
              +  +G +                 R+ + +      +    +          V    
Sbjct: 458 GPNIGLIGNLATYGQINPYGFIETPYRRVVKHLPATDMRLLGRELRGYYGRREDIVTEDG 517

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                 +   +++E +         ++LS LG   ++      +  D H           
Sbjct: 518 EVLLKCNNPVRVDEEL--------LKKLSFLGDTPLSVKPYVTDDVDYHTADN------- 562

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                                    E  Y              L+A+ E           
Sbjct: 563 -------------------------EENYYIAQANA------PLTAISE----------- 580

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                 F +  V  R  GE   VP + ID++D SP+Q VS+A +LIPFLE+DD NR LMG
Sbjct: 581 ------FADNRVLARYQGEFTEVPSDTIDYMDVSPRQTVSVATALIPFLEHDDVNRALMG 634

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ ++P  GTG+E  VA  SG  IVA+ +G V    A +I I        
Sbjct: 635 ANMQRQAVPLLRTQSPICGTGIERQVAVDSGQVIVAQASGEVVSSTARKIEIM------- 687

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +  +  + L KF RSN  TC+NQRP+VK GD V    +IADG ST+LG+LALG+N+LV
Sbjct: 688 DQSGELYTHTLRKFVRSNNGTCINQRPIVKKGDYVSAGQVIADGSSTELGELALGQNVLV 747

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFM W G NFED++LISER+V ED+FTSIHIE++EV ARDTKLGPEEITRDIPNV EEGL
Sbjct: 748 AFMSWEGGNFEDAILISERIVREDLFTSIHIEKYEVDARDTKLGPEEITRDIPNVGEEGL 807

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +N+DE GII VGAEV   DILVGKITPKGE+ +T EEKLLRAIFGEKA +V+DTSLR+P 
Sbjct: 808 RNLDERGIIYVGAEVGAQDILVGKITPKGETELTAEEKLLRAIFGEKAREVKDTSLRMPH 867

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G V++V++F+R   D
Sbjct: 868 GERGKVIEVKVFSREAGD 885



 Score =  435 bits (1119), Expect = e-119,   Method: Composition-based stats.
 Identities = 165/587 (28%), Positives = 258/587 (43%), Gaps = 68/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  + + S +++       +       +    + G 
Sbjct: 633  MGANMQRQAVPLLRTQSPICGTGIERQVAVDSGQVIVAQASGEVVSSTARKIEIMDQSGE 692

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                     V       I++  I+  G  V+ G ++    + +    +   + +L A   
Sbjct: 693  LYTHTLRKFVRSNNGTCINQRPIVKKGDYVSAGQVIADGSSTEL-GELALGQNVLVAFMS 751

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   +       ++  + + R   +  E+I        D   + 
Sbjct: 752  WEGGNFEDAILISERIVREDLFTSIHIEKY--EVDARDTKLGPEEITR------DIPNVG 803

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +  + +     +    A  G +      +            +  +    ++  +    SL
Sbjct: 804  EEGLRNLDERGIIYVGAEVGAQDILVGKITPKGETELTAEEKLLRAIFGEKAREVKDTSL 863

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            ++ +     ++    + K+   + GD++ PGV ++V+V +A KR I +GDKMAGRHGNK 
Sbjct: 864  RMPHGERGKVI----EVKVFSREAGDELSPGVNQLVRVSIAQKRKIGAGDKMAGRHGNK- 918

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                                       GV SR     +               I+ +   
Sbjct: 919  ---------------------------GVISR-----VL-------------PIEDMPFL 933

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                         ++ ++       +++                G  ++TPVFDGA EE 
Sbjct: 934  PDGTP--------VDIILNPLGVPHRMNIGQIMETHLGWAASVLGFKIATPVFDGATEED 985

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  MLR A L ESG+  LYDG TGEPFD PVTVGY YMLKL+H+V DKV+ARSTG YSL+
Sbjct: 986  IEEMLRRAGLPESGKVQLYDGRTGEPFDHPVTVGYTYMLKLHHLVEDKVHARSTGPYSLI 1045

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW ++AYGAA +LQE+LT+KSDDVVGR + YE+IV G + 
Sbjct: 1046 TQQPLGGKAQFGGQRFGEMEVWALEAYGAANILQEILTVKSDDVVGRVKTYEAIVKGENI 1105

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
             E G PESF VLVKE+Q+LG+++++ N   +    +E+  +    EL
Sbjct: 1106 MEPGVPESFKVLVKELQSLGINVEVLNEDEQKIQFVEDTSNDVMPEL 1152


>gi|269930941|gb|ACZ54205.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 597

 Score =  552 bits (1422), Expect = e-154,   Method: Composition-based stats.
 Identities = 432/598 (72%), Positives = 510/598 (85%), Gaps = 1/598 (0%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            IDEK+L+ +       I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+ 
Sbjct: 1   EIDEKTLKILSDVGADQINILDIDHMNVGAYIRNTLKMDKNESRQDALFDIYRVMRPGEP 60

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T + AE+MF  LFFD ++YDLS VGRVKMN+R+ LD PD VR +R+EDI+A++K+LV+L
Sbjct: 61  PTINTAEAMFRSLFFDPERYDLSAVGRVKMNLRMGLDCPDTVRVLRQEDILAVVKMLVEL 120

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
           R+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+S V+ID++MPQDLINA
Sbjct: 121 RDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSLVEIDTIMPQDLINA 180

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHY
Sbjct: 181 KPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHY 240

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y
Sbjct: 241 GRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEESKHY 300

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +AQANSSLD +G FTEE V CR AGE ++ PR++ID +D SPKQ+VS+AA+LIPFLENDD
Sbjct: 301 VAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDRIDLMDVSPKQLVSVAAALIPFLENDD 360

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGAAI AKR GIV+QVDA+RIVIR
Sbjct: 361 ANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGAAIGAKRGGIVDQVDAMRIVIR 420

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD + + DIIADG STDLGDLA
Sbjct: 421 ATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRIEKGDIIADGSSTDLGDLA 479

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDIP
Sbjct: 480 LGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDIP 539

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           NV+EE L+N+DE GI+ +GAEV+PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DV
Sbjct: 540 NVAEEALRNLDEAGIVYIGAEVHPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDV 597


>gi|269930803|gb|ACZ54136.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 598

 Score =  550 bits (1418), Expect = e-154,   Method: Composition-based stats.
 Identities = 437/599 (72%), Positives = 514/599 (85%), Gaps = 1/599 (0%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D IDEK L+ +F      I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+
Sbjct: 1   DEIDEKILKVLFEVNADRINILGIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGE 60

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             T   AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+
Sbjct: 61  PPTMDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRILRQEDILAVVKMLVE 120

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLIN
Sbjct: 121 LRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLIN 180

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
           AKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTH
Sbjct: 181 AKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 240

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           YGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   
Sbjct: 241 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIVDGKVTTEVIYLSAMEESKH 300

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEND
Sbjct: 301 YVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEND 360

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ AKR+G+V+QVDA RIVI
Sbjct: 361 DANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVSAKRSGVVDQVDATRIVI 420

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD + + DIIADGPSTDLGDL
Sbjct: 421 RATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDLIEKGDIIADGPSTDLGDL 479

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDI
Sbjct: 480 ALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDI 539

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           PNV+EE L+N+DE GII +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEKA DV
Sbjct: 540 PNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDV 598


>gi|296131828|ref|YP_003639075.1| DNA-directed RNA polymerase, beta subunit [Thermincola sp. JR]
 gi|296030406|gb|ADG81174.1| DNA-directed RNA polymerase, beta subunit [Thermincola potens JR]
          Length = 1116

 Score =  548 bits (1413), Expect = e-153,   Method: Composition-based stats.
 Identities = 368/753 (48%), Positives = 499/753 (66%), Gaps = 39/753 (5%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQV------------I 274
           +     + Y+     +                +V   L++ +TGE               
Sbjct: 59  NLILEFVDYTLGEPKYSVDECKERDVTYAAPLRVKVRLINKETGEVKEQEVFMGDFPLMT 118

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEK 331
           E G  + +G  + +  + V+  G+         G  +    +    G    E     ++ 
Sbjct: 119 EKGTFIINGAERVIVSQLVRSPGVYFSEQIDSTGKKLYNATIIPNRGAWL-ELETDANDN 177

Query: 332 SLEEIFHSEIRDIPILYV-----------DSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
               I  +    + +L             +   ++  IR TL  D     ++AL++IY+ 
Sbjct: 178 IFVRIDRTRKLPVTVLIRALGYGSNGKILELFQDDERIRATLERDNTDSEEEALVEIYKR 237

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPG+  T   A S+   LFFD  +YDL+ VGR K+N +L LD P +VR++ KEDI+A +
Sbjct: 238 LRPGEPPTVESARSLLETLFFDPKRYDLANVGRYKLNKKLKLDVPPEVRNLTKEDIVATV 297

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
              + L +G+G +DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER++  D+D + P
Sbjct: 298 AYTLKLMDGEGKVDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMTIQDVDVITP 357

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RD
Sbjct: 358 QVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRD 417

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLS 618
           VH +HYGR+CP ET EG NIGL+ SL+++AR+N +GFIETPYRKV    G VTN++ YL+
Sbjct: 418 VHHSHYGRMCPIETPEGPNIGLIGSLSTYARINEFGFIETPYRKVDKEKGIVTNEIEYLT 477

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+N  IAQAN+ LDE+G F  + V  R   E + VP +++D++D SPKQVVSIA +L
Sbjct: 478 ADEEDNFVIAQANAPLDEEGRFLTDKVNARHGHEILKVPVDRVDYMDVSPKQVVSIATAL 537

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDD+NR LMG NMQRQAVPLL+ +AP VGTGME   A  SG  ++AKR+G+V +V
Sbjct: 538 IPFLENDDANRALMGSNMQRQAVPLLRTDAPLVGTGMEYKAATDSGVVVLAKRSGVVTKV 597

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I++ +G+ D       +Y+L+KF RSNQ TC+NQ+P+V  G  V   ++IADGP
Sbjct: 598 TANEIRIKTDDGNED-------VYKLLKFTRSNQGTCMNQKPIVVKGARVEAGEVIADGP 650

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           STD G+LALGRN+LVAFMPW GYN+ED++L+S+++V ED FTSIHIEE+E  ARDTKLGP
Sbjct: 651 STDQGELALGRNVLVAFMPWEGYNYEDAILVSKKLVKEDYFTSIHIEEYECDARDTKLGP 710

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE LK++D+ GII +GAEV PGDILVGK+TPKGE+ +T EE+LLRAIFG
Sbjct: 711 EEITRDIPNVGEEVLKDLDDRGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 771 EKAREVRDTSLRVPHGESGKVVDVKVFSRENGD 803



 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 195/591 (32%), Positives = 273/591 (46%), Gaps = 80/591 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR-DTKLGP 858
                       +L    P  G   E        +V     + +  +      R  T  G 
Sbjct: 551  MGSNMQRQAVPLLRTDAPLVGTGMEYKAATDSGVVVLAKRSGVVTKVTANEIRIKTDDGN 610

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E++ + +          +++  I+  GA V  G+++    +   +  +     +L A   
Sbjct: 611  EDVYKLLKFTRSNQGTCMNQKPIVVKGARVEAGEVIADGPST-DQGELALGRNVLVAFMP 669

Query: 919  EKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
             +  +  D  L            S  + +     R      E          E + +D D
Sbjct: 670  WEGYNYEDAILVSKKLVKEDYFTSIHIEEYECDARDTKLGPEEITRDIPNVGEEVLKDLD 729

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D   I+      R  +IL G+    G         L   +  E  R              
Sbjct: 730  DR-GIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------------- 774

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E                   K+   + GD++ PGV ++V+V++A KR I  GDKMAG
Sbjct: 775  ---EVRDTSLRVPHGESGKVVDVKVFSRENGDELAPGVNQLVRVYIAQKRKISEGDKMAG 831

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+++RILP EDMPF+ DGTP++IVLNPLGVPSRMN+GQ+ ETHLGWA   +G  +
Sbjct: 832  RHGNKGVIARILPEEDMPFMPDGTPIEIVLNPLGVPSRMNLGQVLETHLGWAAKTMGIYM 891

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D                                             VF+
Sbjct: 892  ATPVFDGATEED---------------------------------------------VFE 906

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                      L+ A L  +G++ILYDG TGEPFD P+TVGY+YMLKL H+V DK++ARST
Sbjct: 907  ---------TLQKAGLPTTGKTILYDGRTGEPFDNPITVGYVYMLKLAHLVDDKIHARST 957

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I
Sbjct: 958  GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAI 1017

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            V G +  E G PESF VL+KE+Q+LGL + + +   +     E   D ++ 
Sbjct: 1018 VKGENVPEPGVPESFKVLIKELQSLGLDVKVLSEEDEEIEIKEVEDDVSET 1068



 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 125/472 (26%), Positives = 201/472 (42%), Gaps = 45/472 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R  + +  E++D+P+LIE+Q+ SYD FL           EGL+  F  + PI  F+G
Sbjct: 9   KRERWSYARIKEVLDMPNLIEIQQNSYDWFL----------KEGLREMFYDISPIQDFTG 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +LEFV Y    PK+ VD+C  RD+TYA PL++ +RLI          K   ++KEQ +
Sbjct: 59  NLILEFVDYTLGEPKYSVDECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R++VSQL RSPG++F         +GK LY   IIP++G 
Sbjct: 110 FMGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYFSEQID---STGKKLYNATIIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W+++E D+ D I VRIDR RK+PVT  + ALG  S  +IL  F          +      
Sbjct: 167 WLELETDANDNIFVRIDRTRKLPVTVLIRALGYGSNGKILELFQDDERIRATLERDNTDS 226

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               L+   K       +  GE   +ES + L   L    K   +  +G           
Sbjct: 227 EEEALVEIYK------RLRPGEPPTVESARSLLETLFFDPKRYDLANVGRYKLNKKLKLD 280

Query: 309 AEDIVNGETGEIYIE--------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
               V   T E  +                  ++ + +  +R +  L  +        R 
Sbjct: 281 VPPEVRNLTKEDIVATVAYTLKLMDGEGKVDDIDHLGNRRLRSVGELLQNQFRIG-LSRM 339

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             V  +    +D  +   +V+        ++    F            + +  +    RL
Sbjct: 340 ERVVRERMTIQDVDVITPQVLINIRPVVAAIK-EFFGSSQLSQFMDQTNPLAELTHKRRL 398

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +   P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 399 SALGPGG---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 445


>gi|10636182|emb|CAC10527.1| DNA-dependent RNA polymerase subunit beta [Clostridium
           argentinense]
          Length = 907

 Score =  547 bits (1410), Expect = e-153,   Method: Composition-based stats.
 Identities = 361/761 (47%), Positives = 482/761 (63%), Gaps = 32/761 (4%)

Query: 199 KDIIHVRIDRRRKVPVTSFLMAL-GMDSE-EILSTFYPKIVYS--QRGDFWCFPLSAADL 254
            DII+VRID+ RK+P+T  +  +    S+ EIL  F  +         D       A   
Sbjct: 2   NDIIYVRIDKTRKLPITVLVRVMMNYGSDAEILEFFGEEERLKATIEKDNTKDKNDALLE 61

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           +           +D+   +I+S         L +  + K  K L +    +     AE+I
Sbjct: 62  IYKRLRPGEPPTVDSAVSLIDSLFFDAKRYDLSRVGRYKFNKKLSVHL-RIANQIAAENI 120

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           VN  TGEI +E G+ ID ++ +EI    I  + I   D       I N  V        D
Sbjct: 121 VNPATGEIIVEKGEKIDRETAQEIQDLGINSVDIQVDDXKIR--VIGNNFVNISKHVNFD 178

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
                 R +              +  L    + Y+     + ++   +N   P   +HI 
Sbjct: 179 ISDLNIRELVH------------YPTLKEILENYNDEETIKEQIKSNINRLIP---KHII 223

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           K+DI A +   + L  G G IDDID+LGNRR+RSVGE+L+NQ+R+GL RMER +KER++ 
Sbjct: 224 KDDIYATVSYELGLTYGIGYIDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVKERMTI 283

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D D + PQ LIN +PVV+A+ EFF SSQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 284 QDQDIITPQALINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRE 343

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KV 610
           RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+VN YGF+ETPYR V     KV
Sbjct: 344 RAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLSSYAKVNEYGFMETPYRVVDKKTGKV 403

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ + Y++A EE+N  +AQAN  +DEDG F ++ V  R   E ++VP+E +D ID SP+Q
Sbjct: 404 TDTIRYMTADEEDNYLVAQANEPIDEDGMFVDKKVTVRAKHEIVIVPKEDVDLIDISPRQ 463

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +VS+A ++IPFLENDD++R LMG NMQRQAVPLLK + P VGTG+E   A  SG    AK
Sbjct: 464 IVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKTQTPIVGTGIEYKAAVDSGVLPKAK 523

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            AG V  V A  I ++  E       SG D Y+L+KF+RSNQ TC+NQRP+V  G++V  
Sbjct: 524 SAGTVSYVSANEIRVKRDE------DSGTDTYKLLKFKRSNQGTCINQRPIVSKGEKVEV 577

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
             ++ADGPSTDLG++ALG+N+ + F+ W GYN+ED+ML+SE +V +D+FTS+HIEE+E  
Sbjct: 578 GTVLADGPSTDLGEIALGKNIRIGFITWEGYNYEDAMLVSEELVKDDIFTSVHIEEYEAE 637

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           ARDTKLGPEEITRDIPNV EE LK+IDE GII +GAEV  GDILVGK+TPKGE+ +T EE
Sbjct: 638 ARDTKLGPEEITRDIPNVGEEALKDIDERGIIRIGAEVRSGDILVGKVTPKGETELTAEE 697

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +LLRAIFGEKA +VRDTSLRVP G +G +VDV++F +   D
Sbjct: 698 RLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTKENAD 738



 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 208/970 (21%), Positives = 337/970 (34%), Gaps = 129/970 (13%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +       ++ T+  D  KD+ DALL+IY+ +RPG+  T   A S+ + LFFD+ +YDLS
Sbjct: 35   EFFGEEERLKATIEKDNTKDKNDALLEIYKRLRPGEPPTVDSAVSLIDSLFFDAKRYDLS 94

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             VGR K N +L++       H+R  + IA    +V+   G+  ++  + +     + + +
Sbjct: 95   RVGRYKFNKKLSV-------HLRIANQIAAEN-IVNPATGEIIVEKGEKIDRETAQEIQD 146

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +  N   +      +    +I  +  + V     +N       + E      L ++ E+ 
Sbjct: 147  LGINSVDI------QVDDXKIRVIGNNFVNISKHVNFDISDLNIRELVHYPTLKEILENY 200

Query: 530  NSLSRITHTRRLSA--LGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVSS 585
            N    I    + +   L    + +      +       YG   I   +      +  V  
Sbjct: 201  NDEETIKEQIKSNINRLIPKHIIKDDIYATVSYELGLTYGIGYIDDIDHLGNRRLRSVGE 260

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L    +      +    R V +     D   ++         A  N              
Sbjct: 261  LL---QNQFRIGLSRMERVVKERMTIQDQDIITPQ-------ALINIRPVVAAIKEFFGS 310

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   +   P  ++              +      E  D +    G  M     P   
Sbjct: 311  SQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYG-RMCPIETPEGP 369

Query: 706  AEAPFVGTGMESVVAK--SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                       + V +                +  D IR +    E +   + +   I  
Sbjct: 370  NIGLINSLSSYAKVNEYGFMETPYRVVDKKTGKVTDTIRYMTADEEDNYLVAQANEPIDE 429

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDI-------------------IADGPSTDLGD 804
               F             ++   ++V   DI                    A         
Sbjct: 430  DGMFVDKKVTVRAKHEIVIVPKEDVDLIDISPRQIVSVATAMIPFLENDDASRALMGSNM 489

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF--EVMARDTKLGPEEIT 862
                  +L    P  G   E    +   ++ +             E+  +  +    +  
Sbjct: 490  QRQAVPLLKTQTPIVGTGIEYKAAVDSGVLPKAKSAGTVSYVSANEIRVKRDEDSGTDTY 549

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI-----F 917
            + +          I++  I+  G +V  G +L    +         +   +  I      
Sbjct: 550  KLLKFKRSNQGTCINQRPIVSKGEKVEVGTVLADGPSTDLGEIALGKNIRIGFITWEGYN 609

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
             E A+ V +  ++     S  + +     R      E          E   +D  DE+ I
Sbjct: 610  YEDAMLVSEELVKDDIFTSVHIEEYEAEARDTKLGPEEITRDIPNVGEEALKDI-DERGI 668

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            +      R  +IL G+    G         L   +  E  R                 E 
Sbjct: 669  IRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR-----------------EV 711

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                              K+   +  D++PPGV ++V+ ++A KR I  GDKMAGRHGNK
Sbjct: 712  RDTSLRVPHGEAGIIVDVKVFTKENADELPPGVNQLVRCYIAQKRKISVGDKMAGRHGNK 771

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++SR+LP EDMPFL DG P+ I LNPLGVPSRMN+GQ+ E HLGWA   LG  I + + 
Sbjct: 772  GVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAASELGWHIATPVF 831

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D   + +I                         +  L  A   + G              
Sbjct: 832  DGAXDTEI-------------------------EDCLEQAGYNRDG-------------- 852

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                           +++LYDG TGE FD  VTVGY+Y+LKL+H+V DK++ARSTG YSL
Sbjct: 853  ---------------KTVLYDGRTGEAFDNRVTVGYMYILKLHHLVDDKIHARSTGPYSL 897

Query: 1278 VTQQPLGGKS 1287
            VTQQPLGGK+
Sbjct: 898  VTQQPLGGKA 907


>gi|226328685|ref|ZP_03804203.1| hypothetical protein PROPEN_02580 [Proteus penneri ATCC 35198]
 gi|225201871|gb|EEG84225.1| hypothetical protein PROPEN_02580 [Proteus penneri ATCC 35198]
          Length = 297

 Score =  545 bits (1404), Expect = e-152,   Method: Composition-based stats.
 Identities = 176/297 (59%), Positives = 228/297 (76%)

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            +L++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVD+VLNPLGVPS
Sbjct: 1    MLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGNPVDLVLNPLGVPS 60

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQI ETHLG A  G+G KI +++   +    +         +         +  + 
Sbjct: 61   RMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQKAYDLGMAPRQKVDLDTFS 120

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D+ VLR+AE  K G+P +TPVFDGA+E  I  ML++ADL  SGQ  L+DG TGE F+RPV
Sbjct: 121  DEEVLRLAENLKKGMPTATPVFDGAEEMEIKEMLKLADLPTSGQITLFDGRTGEQFERPV 180

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 181  TVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 240

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             LQEMLT+KSDDV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 241  TLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 297


>gi|167629459|ref|YP_001679958.1| DNA-directed RNA polymerase, beta subunit [Heliobacterium
            modesticaldum Ice1]
 gi|226699411|sp|B0TC48|RPOB_HELMI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|167592199|gb|ABZ83947.1| DNA-directed RNA polymerase, beta subunit [Heliobacterium
            modesticaldum Ice1]
          Length = 1154

 Score =  543 bits (1400), Expect = e-152,   Method: Composition-based stats.
 Identities = 203/616 (32%), Positives = 277/616 (44%), Gaps = 94/616 (15%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       +L    P+ G   E        +            +  +E  +   D  
Sbjct: 552  MGANMQRQAVPLLRTDAPYVGTGMEFKAAYDSGVCAIARKAGYVERVTGDEILIRCDD-- 609

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  E  + +  +       I++  I   G  +  G I+    +   +  +     +L A
Sbjct: 610  -GTTEHHKLLKFLRSNQGTCINQKPICHKGQRIEAGQIIADGPST-DQGELALGRNVLVA 667

Query: 916  IFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                +  +  D  L      +     S  + +    +R      E          E + +
Sbjct: 668  FMTWEGYNYEDAILVNEKLVKEDYFTSIHIEEYECDSRDTKLGPEEITRDIPNVGEEVLK 727

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D DD   I+      R  +IL G+    G         L   +  E  R           
Sbjct: 728  DLDDR-GIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR----------- 775

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E                   K+   + GD++ PGV ++V+V++A KR I  GDK
Sbjct: 776  ------EVRDTSLRVPHGEAGKIVDVKVFSRENGDELAPGVNQLVRVYIAQKRKISEGDK 829

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG++SRI+P  DMP+L DGTPV+IVLNPLGVPSRMN+GQI ETHLGWA     
Sbjct: 830  MAGRHGNKGVISRIMPEADMPYLPDGTPVEIVLNPLGVPSRMNIGQILETHLGWASKH-- 887

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                                                   D   ++      + G+ V+TP
Sbjct: 888  --------------------------------------MDRGVLIEGKPSGEKGIRVATP 909

Query: 1210 VFDGADEEAINSMLRMADLDES----------------------GQSILYDGLTGEPFDR 1247
            VFDGA E+ I   L  A L ++                      G+SILYDG TGEPFD 
Sbjct: 910  VFDGATEDDIFEFLTKAGLPKANEIALTDTRTESLRESMAAVPLGKSILYDGRTGEPFDN 969

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P+TVGY+YMLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA
Sbjct: 970  PITVGYMYMLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1029

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL + + +  
Sbjct: 1030 AYTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVKILSED 1089

Query: 1368 TKNSAKMEEIPDFNKC 1383
             +     E   D  + 
Sbjct: 1090 EREIEIKEVEEDVAET 1105



 Score =  533 bits (1373), Expect = e-149,   Method: Composition-based stats.
 Identities = 359/753 (47%), Positives = 489/753 (64%), Gaps = 38/753 (5%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQV------------I 274
           +     I Y+     +                +V   L++ +TGE               
Sbjct: 59  NLILEFIDYALGEPKYSVEECKERDVTFAAPLRVKVRLINKETGEVKEQEVFMGDFPLMT 118

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLC----GLYVAEDIVNGETGEI---------- 320
           + G  + +G  + +  + V+  G+  +       G  +    +    G            
Sbjct: 119 DKGTFIINGAERVIVSQLVRSPGVYYNEAIDPPSGKKLFGATIIPNRGAWLEFETDINDN 178

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                D   +     +  +          +  + +  IR TL  D  ++ ++AL++IY+ 
Sbjct: 179 IFVRIDRTRKLPATVLIRALGYSNNAQVQELFDGDERIRITLERDNTENTEEALVEIYKR 238

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPG+  T   A S+   LFFD  +YDL+ VGR K+N RL +    +VRH+ K+DIIA I
Sbjct: 239 LRPGEPPTVDSARSLLETLFFDPKRYDLAKVGRYKINKRLGISVEREVRHLTKDDIIAAI 298

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           + L+ L  G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER++  D++ + P
Sbjct: 299 RELLKLMQGDGRADDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMTIQDVEVITP 358

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RD
Sbjct: 359 QVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRD 418

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLS 618
           VH +HYGR+CP ET EG NIGL+ SL++FAR+N YGFIETPYRKV   +  VT+ + YL+
Sbjct: 419 VHHSHYGRMCPIETPEGPNIGLIGSLSTFARINEYGFIETPYRKVDKERGVVTDQIDYLT 478

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+   +AQAN+ LDE+G F E+ V  R   + ++VP EK+D++D SPKQVVSIA +L
Sbjct: 479 ADEEDKYIVAQANAPLDEEGRFKEKRVNARHGHDILVVPVEKVDYMDVSPKQVVSIATAL 538

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPLL+ +AP+VGTGME   A  SG   +A++AG VE+V
Sbjct: 539 IPFLEHDDANRALMGANMQRQAVPLLRTDAPYVGTGMEFKAAYDSGVCAIARKAGYVERV 598

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               I+IR  +G  +        ++L+KF RSNQ TC+NQ+P+   G  +    IIADGP
Sbjct: 599 TGDEILIRCDDGTTE-------HHKLLKFLRSNQGTCINQKPICHKGQRIEAGQIIADGP 651

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           STD G+LALGRN+LVAFM W GYN+ED++L++E++V ED FTSIHIEE+E  +RDTKLGP
Sbjct: 652 STDQGELALGRNVLVAFMTWEGYNYEDAILVNEKLVKEDYFTSIHIEEYECDSRDTKLGP 711

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE LK++D+ GII VGAEV PGDILVGK+TPKGE+ +T EE+LLRAIFG
Sbjct: 712 EEITRDIPNVGEEVLKDLDDRGIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFG 771

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G +G +VDV++F+R   D
Sbjct: 772 EKAREVRDTSLRVPHGEAGKIVDVKVFSRENGD 804



 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 115/466 (24%), Positives = 204/466 (43%), Gaps = 34/466 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F +  E++D+P+LIE+Q+ SY  FL           EGL+  F+ + PI  F+G 
Sbjct: 10  RERWTFARIQEVMDMPNLIEIQQNSYRWFL----------EEGLREMFRDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK+ V++C  RD+T+A PL++ +RLI          K   ++KEQ ++
Sbjct: 60  LILEFIDYALGEPKYSVEECKERDVTFAAPLRVKVRLI---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG++++        SGK L+   IIP++G W
Sbjct: 111 MGDFPLMTDKGTFIINGAERVIVSQLVRSPGVYYNEAIDP--PSGKKLFGATIIPNRGAW 168

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY---PKIVYSQRGDFWCFP 248
           ++ E D  D I VRIDR RK+P T  + ALG  +   +   +    +I  +   D     
Sbjct: 169 LEFETDINDNIFVRIDRTRKLPATVLIRALGYSNNAQVQELFDGDERIRITLERDNTENT 228

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             A   +           +D+   ++E+         L K  + K  K LGI+ +     
Sbjct: 229 EEALVEIYKRLRPGEPPTVDSARSLLETLFFDPKRYDLAKVGRYKINKRLGISVEREV-R 287

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
           ++ +D +     E+            ++ + +  +R +  L  +           +V ++
Sbjct: 288 HLTKDDIIAAIRELLKLMQGDGRADDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRER 347

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
              +   +  I   +        +  +  F            + +  +    RL+   P 
Sbjct: 348 MTIQD--VEVITPQVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPG 405

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
               + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 406 G---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 446


>gi|23307628|gb|AAN17794.1|AF443616_3 DNA-dependent RNA polymerase beta chain [Mycoplasma hominis ATCC
           23114]
          Length = 997

 Score =  542 bits (1396), Expect = e-151,   Method: Composition-based stats.
 Identities = 325/986 (32%), Positives = 509/986 (51%), Gaps = 77/986 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
            +R+ +  + +  + PD +E+Q+ S + FL +          G++   ++++PI A  G 
Sbjct: 16  TLRRDYSISQKKFETPDFLEMQRESVEKFLTV----------GIEEELRNIYPIEAH-GK 64

Query: 72  AMLEFV--SYEFDPPKFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +E++  S  F+ PK      + +   +  +Y   LK  LR I              ++
Sbjct: 65  VRIEYIHNSAHFEYPKKTEYESIKEAKQKGSSYQGKLKAHLRQI---------NIETGEV 115

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           ++  +   ++P+MT  G+F+I G ++++VSQL RS G +F  +  R   +  L     II
Sbjct: 116 EDSEVVFAEIPIMTYGGSFIINGSEKVIVSQLIRSTGAYFGINV-RNKQANDLFNKVEII 174

Query: 186 PDQGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           P  G W++I         D + + ID+ +   V +FL ALG     I   F   I   + 
Sbjct: 175 PQIGSWVEIYHKVTSQNPDTVKIHIDKNKSFLVVTFLKALGFSESGIRRMFGENIPELEE 234

Query: 242 --GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI- 298
                    ++A ++   A+ +   +         +S + L    L + K   +   G  
Sbjct: 235 TFKRDKITGINAEEVTREAQEAIYRIIRKGDRMTADSARNLIPTTLFNEKRYSLTETGRF 294

Query: 299 -------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF-HSEIRDIPILYVD 350
                    + +   Y+AEDI + E GE+  E G  I      +I    +   IP+  + 
Sbjct: 295 TLNRKLNIIERIANSYLAEDIFSSE-GELLYEKGMFITWNIARKIHDEFKQGIIPMWKLP 353

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            ++ NAY     V                            +      ++    + D+  
Sbjct: 354 DIDENAYGSQLEVEGN---------------------EQLASRIFVTSIWIYPTENDMLH 392

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
             +V +   L  D       +   D+IA I    +L +  G  DD D+L N+R+ ++GE+
Sbjct: 393 DQKVLV---LGNDPTSTENFLLIPDLIATISYYFNLLSKVGVDDDPDSLVNKRIVTIGEL 449

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GLL++E++ +E      +  ++ + L      +  +           L    N
Sbjct: 450 LQNQFRIGLLKLEKNTREESQQKILIRLLLRTLQIINQYLINLNRSLTHQNFLNLWIQCN 509

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L SFA
Sbjct: 510 PLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASFA 569

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           +++ YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  R 
Sbjct: 570 KIDKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMVRR 628

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  EAP
Sbjct: 629 DNEYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPEAP 688

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            V TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F+R
Sbjct: 689 LVATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTFER 742

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ T ++Q  LVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++++
Sbjct: 743 SNQGTLIHQVLLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAVVL 802

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+EV 
Sbjct: 803 SERLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVT 862

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R  
Sbjct: 863 AGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF 922

Query: 950 IDKNERSISVEREQIELLARDKDDEQ 975
              ++    +E+     +A+ +  + 
Sbjct: 923 G--DQLEDGIEKIVKVSIAQKRKIQV 946



 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 74/257 (28%), Positives = 115/257 (44%), Gaps = 13/257 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 754  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 811

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 812  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 871

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 872  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 922

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 923  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 980

Query: 1121 VLNPLGVPSRMNVGQIF 1137
            VLNP GVPSRMN+GQ+ 
Sbjct: 981  VLNPQGVPSRMNIGQVL 997


>gi|148887420|sp|Q4A5S7|RPOB_MYCS5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|144575132|gb|AAZ43894.2| DNA-directed RNA polymerase beta subunit [Mycoplasma synoviae 53]
          Length = 1202

 Score =  541 bits (1395), Expect = e-151,   Method: Composition-based stats.
 Identities = 319/985 (32%), Positives = 520/985 (52%), Gaps = 74/985 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R+ +      + + D++   K SY  F+          N+ ++     ++PI A +  
Sbjct: 17  TERRDYSITKHSLPVGDILATSKKSYQDFI----------NKKIEELLNEIYPIEASNKE 66

Query: 72  AMLEF--VSYEFDPP-KFDVDD------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           A LE+   S +F+ P K    +      C  +   +++ + ITL+ +V            
Sbjct: 67  ASLEYEKKSVKFELPFKKAEHENLQIKTCKAKKTNFSMKVYITLKKVVS---------QT 117

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             +K++ I +G++P +T  G+F+I G ++++VSQL RSPG +F     R   S  L    
Sbjct: 118 GVVKKEKILLGEIPYITSSGSFIINGSEKVIVSQLIRSPGAYFGVSV-RNKQSEDLFNKL 176

Query: 183 RIIPDQGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP---- 234
            I+P  G W+++      +  D I ++ID+ + + + +FL + G+ +++I   F      
Sbjct: 177 EILPRIGSWIEVSHKVTSANLDAIKIKIDKNKNINIVTFLASFGLLADDIRYLFGKNEVL 236

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           +    +         S  ++M   +     +         ES + L SG+L   K   + 
Sbjct: 237 EETIRKNKTIDITEFSRQEIMDLCQEKIFRIIRKGDRISEESKRSLLSGMLFDKKRYNLS 296

Query: 295 FLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
             G           + +   Y+A+ +V+        + G  +  +  +EI  S       
Sbjct: 297 KTGRYMLNNKLSLVERITNTYLAQKVVSHLGNT--FDVGTYVTYEIAKEIQESFEAKAK- 353

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
               S  +   I N    D           + + +    +  +    +M           
Sbjct: 354 -DNKSNLHLEKIPNINPDDVYYKINKDNKSLNKRINIARIKIWPTKRAMDANETPSE--- 409

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
                        +  D      H+   DIIA I   ++L  G G  DD D+L N+R+ S
Sbjct: 410 ------------VIGNDPKATEEHLLLSDIIAAISYYLNLTVGIGQDDDPDSLMNKRIVS 457

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+L+ + R+ LL++E++ +ER+ + + D +  +++ N K + + +  FF +S+L+Q  
Sbjct: 458 VGELLEGELRIALLKLEKATRERMGAKEPDKITAKNVTNNKLITNQMKTFFNTSKLAQFM 517

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + 
Sbjct: 518 DQINPLAEISNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNY 577

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
             ++ VN  GF++TPY KV DG V  NDV YL++ EE     AQ++  +++     +E +
Sbjct: 578 AIYSTVNELGFLQTPYYKVNDGVVDYNDVRYLTSYEEIGYAFAQSSVHVNDKNEIIDEQI 637

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             +     I+   + IDF++ S KQ+VS+AA+ IPFLEN+D+NR LMG NMQRQAVPL++
Sbjct: 638 TIKKDYNYIIGSPKDIDFLEVSSKQIVSVAAAAIPFLENNDANRALMGSNMQRQAVPLIE 697

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           AEAP V TG+E+ +AK S   IVA   G V  VD  +I +R        +   +D Y L 
Sbjct: 698 AEAPLVATGIEADIAKFSSYNIVANNDGEVIYVDGTKIQVR--------TAKKIDTYNLK 749

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F++SNQ T + Q+P+VKVGD V+  D++ DG S   G++ALG+N+LV F  W+GYNFED
Sbjct: 750 NFEKSNQGTIIQQKPIVKVGDHVKEGDLLVDGSSFKDGEMALGKNLLVGFTTWNGYNFED 809

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++I+ER+V +DV TSI+IEE  +  R +K   + +TRDIPNVS+  ++N+DE GII VG
Sbjct: 810 AIIINERLVKDDVLTSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVG 869

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV  GD+LVG+I+PKGE   + EEKLL AIF ++  + +DTSL+V +G +GTV+ V + 
Sbjct: 870 SEVVAGDVLVGRISPKGEENPSQEEKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVL 929

Query: 946 NRHGIDKNERSI-SVEREQIELLAR 969
           +R   D  E  + S+ +  I    +
Sbjct: 930 SRENGDILEDGLDSIIKVYIAQKRK 954



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 159/501 (31%), Positives = 230/501 (45%), Gaps = 67/501 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V+
Sbjct: 765  IVKVGDHVKEGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVL 823

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+      +   S S E      +          LD     ++   +   + + G  
Sbjct: 824  -TSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRI 882

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V++          +L           
Sbjct: 883  SPKGEENPSQE--EKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVLSR--------- 931

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  ++KV++A KR I+ GDKMAGRHGNKG++S ILP EDMP L+DGTP+DI
Sbjct: 932  ENGDILEDGLDSIIKVYIAQKRKIKVGDKMAGRHGNKGVISIILPEEDMPHLEDGTPLDI 991

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D      I  L            
Sbjct: 992  MLNPQGVPSRMNIGQVLEMHLGMAAKKLGTKFVTPSFDGIKKETIEDLLQEAN------- 1044

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + ++ D +
Sbjct: 1045 ------------------------------------------LDKSG-----KQVVIDPI 1057

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD P++VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1058 TGEKFDNPISVGVIYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1117

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +++YGA+ +LQE+LT KSDD+  R  VY+++V  +     G PESFNVL  E++ L + 
Sbjct: 1118 ALESYGASNILQEILTYKSDDIYSRNLVYKALVNDSAIPNPGMPESFNVLSNELKGLLMK 1177

Query: 1361 IDLENSRTKNSAKMEEIPDFN 1381
            + +  + + +   ++      
Sbjct: 1178 LGITETESNSDELIQHFDHLG 1198


>gi|220930957|ref|YP_002507865.1| DNA-directed RNA polymerase, beta subunit [Halothermothrix orenii H
           168]
 gi|219992267|gb|ACL68870.1| DNA-directed RNA polymerase, beta subunit [Halothermothrix orenii H
           168]
          Length = 1090

 Score =  541 bits (1395), Expect = e-151,   Method: Composition-based stats.
 Identities = 340/605 (56%), Positives = 456/605 (75%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D    +  I +TL  D    +++AL+++Y+ +RPG+  T   A+++   LFFD  +YDL
Sbjct: 203 IDLFGEHEVIHDTLERDNTDSQEEALIELYKRLRPGEPPTVESAKNLLESLFFDPKRYDL 262

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRS 466
           + VGR K+N +L LD   D + + K DI+  ++ L+ + +   + +IDDID+LGNRR+++
Sbjct: 263 ALVGRYKINKKLGLDIDPDKKCLDKRDIVETVRYLLRIIDNDPEASIDDIDHLGNRRLKT 322

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+L+NQ+R+GL RMER +KER++  DID V PQ LIN +PVV+++ EFF SSQLSQ  
Sbjct: 323 VGELLQNQFRIGLSRMERVVKERMTIQDIDVVTPQALINTRPVVASIQEFFGSSQLSQFM 382

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RRLSALG GG++R RAG E+RDVH +HYGRICP ET EG NIGL+ S+
Sbjct: 383 DQTNPLSELTHKRRLSALGPGGLSRDRAGFEVRDVHHSHYGRICPIETPEGPNIGLIGSM 442

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +++AR N +GF+ETPYRKV +GK TN++ YL+A EE+   IAQAN   DEDG+F  +LV 
Sbjct: 443 STYARTNKFGFLETPYRKVVNGKATNEIEYLTADEEDKYTIAQANEPFDEDGNFLNDLVI 502

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+ + V  EK+D++D SPKQ+V ++AS+IPFLENDD+NR LMG NMQRQAVPL+K 
Sbjct: 503 ARHRGDILEVSPEKVDYMDVSPKQLVGVSASMIPFLENDDANRALMGANMQRQAVPLIKP 562

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +AP V TGME   AK SG  I+AK +G+V +V A  IVI++ +G        +D Y+++K
Sbjct: 563 DAPIVATGMEYRAAKDSGVVIIAKNSGVVTRVTADEIVIKTDDG-------KIDTYKILK 615

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ +C+NQRP+V+ G  V + D+IADGPSTD G++ALGRN L+AFMPW GYN+ED+
Sbjct: 616 FKRSNQGSCINQRPIVRKGQRVDKGDVIADGPSTDHGEMALGRNTLIAFMPWEGYNYEDA 675

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISE++V ED FTS+HIEE+E  ARDTKLGPEEITRDIPNV E  LKN+DE GII VGA
Sbjct: 676 ILISEKLVKEDAFTSVHIEEYEAEARDTKLGPEEITRDIPNVGENALKNLDERGIIRVGA 735

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ ++ EE+LLRAIFGEKA +VRDTSL+VP G  G +VDV++F+
Sbjct: 736 EVKEGDILVGKVTPKGETELSAEERLLRAIFGEKAREVRDTSLKVPHGEEGIIVDVKVFS 795

Query: 947 RHGID 951
           R   D
Sbjct: 796 RENGD 800



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/537 (35%), Positives = 258/537 (48%), Gaps = 79/537 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  + +          I++  I+  G  V+ GD++    +      M      
Sbjct: 602  KTDDGKIDTYKILKFKRSNQGSCINQRPIVRKGQRVDKGDVIADGPST-DHGEMALGRNT 660

Query: 913  LRAIFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L      +  +  S  + +     R      E          E 
Sbjct: 661  LIAFMPWEGYNYEDAILISEKLVKEDAFTSVHIEEYEAEARDTKLGPEEITRDIPNVGEN 720

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              ++  DE+ I+      +  +IL G+    G         L   +  E  R    +   
Sbjct: 721  ALKNL-DERGIIRVGAEVKEGDILVGKVTPKGETELSAEERLLRAIFGEKAR----EVRD 775

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
               KV    E + V               K+   + GD++ PGV ++V+V+VA KR I  
Sbjct: 776  TSLKVPHGEEGIIV-------------DVKVFSRENGDELKPGVNKLVRVYVATKRKISV 822

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL +G PV++VLNPLGVPSRMN+GQ+ ETHLG A  
Sbjct: 823  GDKMAGRHGNKGVISRILPEEDMPFLPNGEPVEVVLNPLGVPSRMNIGQVLETHLGLAAK 882

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  +++ + +     ++  L                                      
Sbjct: 883  ALGLYVETPVFNGALEEEVEDLLEKAG--------------------------------- 909

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                FD                   G+++LYDG TGEPFD  VTVGY+Y+LKL+H+V DK
Sbjct: 910  ----FD-----------------RDGKTVLYDGRTGEPFDNRVTVGYMYVLKLHHLVDDK 948

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLTIKSDDVVGR 
Sbjct: 949  IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYSLQEMLTIKSDDVVGRV 1008

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            + YE+IV G +  E G PESF VL+KEMQ+LGL   +     +     EE  +F   
Sbjct: 1009 KTYEAIVKGENVPEPGIPESFKVLIKEMQSLGLDAKIFTEDEEELQIAEEEEEFTDT 1065



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 120/464 (25%), Positives = 195/464 (42%), Gaps = 48/464 (10%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKG+      R R  F K  +  + P L+  Q +SY+ FL           EGL+  F+
Sbjct: 1   MAKGL-----RRERYSFAKIEDAHEAPYLLNTQISSYNWFL----------EEGLKEVFE 45

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  FS   +LEFV Y    PK++ ++C  RD TYA PL++ +RLI          K
Sbjct: 46  EISPIEDFSENLVLEFVDYHLGEPKYNEEECRDRDATYAAPLQVKVRLI---------NK 96

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++KEQ ++MGD PLMT  GTF+I G +R+VV+QL RS G++F  ++ +    G+ L 
Sbjct: 97  DTGEVKEQEVFMGDFPLMTDKGTFIINGAERVVVNQLIRSSGVYFGEERTKD---GRRLV 153

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +  IIP++G W++ E+D K I+ VR+DR RK+P T    ALG  ++ E++  F    V  
Sbjct: 154 SANIIPNRGAWIEFEYDKKRIVSVRVDRTRKMPSTVLFRALGYGTDAELIDLFGEHEVIH 213

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              +          L+           +  GE   +ES K L   L    K   +  +G 
Sbjct: 214 DTLERDNTDSQEEALI------ELYKRLRPGEPPTVESAKNLLESLFFDPKRYDLALVGR 267

Query: 299 TS-------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                    D        +     ET    +   D   E S+++I H   R +  +    
Sbjct: 268 YKINKKLGLDIDPDKKCLDKRDIVETVRYLLRIIDNDPEASIDDIDHLGNRRLKTVGELL 327

Query: 352 VNNNAY--IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            N       R   V  +    +D  +   + +        S+ +  F            +
Sbjct: 328 QNQFRIGLSRMERVVKERMTIQDIDVVTPQALINTRPVVASI-QEFFGSSQLSQFMDQTN 386

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +  +    RL+   P     + ++     ++ +     G+   
Sbjct: 387 PLSELTHKRRLSALGPGG---LSRDRAGFEVRDVHHSHYGRICP 427


>gi|71894497|ref|YP_278605.1| DNA-directed RNA polymerase subunit beta [Mycoplasma synoviae 53]
          Length = 1203

 Score =  541 bits (1394), Expect = e-151,   Method: Composition-based stats.
 Identities = 319/985 (32%), Positives = 520/985 (52%), Gaps = 74/985 (7%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
             R+ +      + + D++   K SY  F+          N+ ++     ++PI A +  
Sbjct: 18  TERRDYSITKHSLPVGDILATSKKSYQDFI----------NKKIEELLNEIYPIEASNKE 67

Query: 72  AMLEF--VSYEFDPP-KFDVDD------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           A LE+   S +F+ P K    +      C  +   +++ + ITL+ +V            
Sbjct: 68  ASLEYEKKSVKFELPFKKAEHENLQIKTCKAKKTNFSMKVYITLKKVVS---------QT 118

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
             +K++ I +G++P +T  G+F+I G ++++VSQL RSPG +F     R   S  L    
Sbjct: 119 GVVKKEKILLGEIPYITSSGSFIINGSEKVIVSQLIRSPGAYFGVSV-RNKQSEDLFNKL 177

Query: 183 RIIPDQGLWMDIE---FDSK-DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP---- 234
            I+P  G W+++      +  D I ++ID+ + + + +FL + G+ +++I   F      
Sbjct: 178 EILPRIGSWIEVSHKVTSANLDAIKIKIDKNKNINIVTFLASFGLLADDIRYLFGKNEVL 237

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           +    +         S  ++M   +     +         ES + L SG+L   K   + 
Sbjct: 238 EETIRKNKTIDITEFSRQEIMDLCQEKIFRIIRKGDRISEESKRSLLSGMLFDKKRYNLS 297

Query: 295 FLGITS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
             G           + +   Y+A+ +V+        + G  +  +  +EI  S       
Sbjct: 298 KTGRYMLNNKLSLVERITNTYLAQKVVSHLGNT--FDVGTYVTYEIAKEIQESFEAKAK- 354

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
               S  +   I N    D           + + +    +  +    +M           
Sbjct: 355 -DNKSNLHLEKIPNINPDDVYYKINKDNKSLNKRINIARIKIWPTKRAMDANETPSE--- 410

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
                        +  D      H+   DIIA I   ++L  G G  DD D+L N+R+ S
Sbjct: 411 ------------VIGNDPKATEEHLLLSDIIAAISYYLNLTVGIGQDDDPDSLMNKRIVS 458

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+L+ + R+ LL++E++ +ER+ + + D +  +++ N K + + +  FF +S+L+Q  
Sbjct: 459 VGELLEGELRIALLKLEKATRERMGAKEPDKITAKNVTNNKLITNQMKTFFNTSKLAQFM 518

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + 
Sbjct: 519 DQINPLAEISNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNY 578

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
             ++ VN  GF++TPY KV DG V  NDV YL++ EE     AQ++  +++     +E +
Sbjct: 579 AIYSTVNELGFLQTPYYKVNDGVVDYNDVRYLTSYEEIGYAFAQSSVHVNDKNEIIDEQI 638

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             +     I+   + IDF++ S KQ+VS+AA+ IPFLEN+D+NR LMG NMQRQAVPL++
Sbjct: 639 TIKKDYNYIIGSPKDIDFLEVSSKQIVSVAAAAIPFLENNDANRALMGSNMQRQAVPLIE 698

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           AEAP V TG+E+ +AK S   IVA   G V  VD  +I +R        +   +D Y L 
Sbjct: 699 AEAPLVATGIEADIAKFSSYNIVANNDGEVIYVDGTKIQVR--------TAKKIDTYNLK 750

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F++SNQ T + Q+P+VKVGD V+  D++ DG S   G++ALG+N+LV F  W+GYNFED
Sbjct: 751 NFEKSNQGTIIQQKPIVKVGDHVKEGDLLVDGSSFKDGEMALGKNLLVGFTTWNGYNFED 810

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++I+ER+V +DV TSI+IEE  +  R +K   + +TRDIPNVS+  ++N+DE GII VG
Sbjct: 811 AIIINERLVKDDVLTSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVG 870

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV  GD+LVG+I+PKGE   + EEKLL AIF ++  + +DTSL+V +G +GTV+ V + 
Sbjct: 871 SEVVAGDVLVGRISPKGEENPSQEEKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVL 930

Query: 946 NRHGIDKNERSI-SVEREQIELLAR 969
           +R   D  E  + S+ +  I    +
Sbjct: 931 SRENGDILEDGLDSIIKVYIAQKRK 955



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 159/501 (31%), Positives = 230/501 (45%), Gaps = 67/501 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V+
Sbjct: 766  IVKVGDHVKEGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVL 824

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+      +   S S E      +          LD     ++   +   + + G  
Sbjct: 825  -TSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRI 883

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V++          +L           
Sbjct: 884  SPKGEENPSQE--EKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVLSR--------- 932

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  ++KV++A KR I+ GDKMAGRHGNKG++S ILP EDMP L+DGTP+DI
Sbjct: 933  ENGDILEDGLDSIIKVYIAQKRKIKVGDKMAGRHGNKGVISIILPEEDMPHLEDGTPLDI 992

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D      I  L            
Sbjct: 993  MLNPQGVPSRMNIGQVLEMHLGMAAKKLGTKFVTPSFDGIKKETIEDLLQEAN------- 1045

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + ++ D +
Sbjct: 1046 ------------------------------------------LDKSG-----KQVVIDPI 1058

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD P++VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 1059 TGEKFDNPISVGVIYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 1118

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +++YGA+ +LQE+LT KSDD+  R  VY+++V  +     G PESFNVL  E++ L + 
Sbjct: 1119 ALESYGASNILQEILTYKSDDIYSRNLVYKALVNDSAIPNPGMPESFNVLSNELKGLLMK 1178

Query: 1361 IDLENSRTKNSAKMEEIPDFN 1381
            + +  + + +   ++      
Sbjct: 1179 LGITETESNSDELIQHFDHLG 1199


>gi|294668296|ref|ZP_06733400.1| hypothetical protein NEIELOOT_00209 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
 gi|291309750|gb|EFE50993.1| hypothetical protein NEIELOOT_00209 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
          Length = 321

 Score =  541 bits (1393), Expect = e-151,   Method: Composition-based stats.
 Identities = 176/320 (55%), Positives = 231/320 (72%), Gaps = 14/320 (4%)

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +  GD++ PGV ++VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVD
Sbjct: 1    MTQGDELQPGVQKMVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVD 60

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL--EKVIG 1177
            IVLNPLGVPSRMN+GQI E HLGWA  G+G++I  ++++ +   +I      +    + G
Sbjct: 61   IVLNPLGVPSRMNIGQILEVHLGWAAKGIGERIGRMLDEQRKTSEIRKFLDTMYNGDLGG 120

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
               H E +S   D+ +L +A+  ++G   ++PVFDGA E  I + L +A   +       
Sbjct: 121  PDMHKEDLSQLSDEEILVLAQNLRNGATFASPVFDGAHETEIKAFLDLAYPSDDPEVQKL 180

Query: 1232 G------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            G      Q  LYDG +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGG
Sbjct: 181  GFNDTKTQITLYDGRSGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGG 240

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PE
Sbjct: 241  KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPE 300

Query: 1346 SFNVLVKEMQALGLSIDLEN 1365
            SFNVLVKE+++LGL IDLE 
Sbjct: 301  SFNVLVKEIRSLGLDIDLER 320


>gi|157060634|gb|ABV03323.1| RpoB [Chlamydia trachomatis]
 gi|157060636|gb|ABV03324.1| RpoB [Chlamydia trachomatis]
 gi|157060638|gb|ABV03325.1| RpoB [Chlamydia trachomatis]
 gi|157060640|gb|ABV03326.1| RpoB [Chlamydia trachomatis]
 gi|157060642|gb|ABV03327.1| RpoB [Chlamydia trachomatis]
          Length = 686

 Score =  540 bits (1392), Expect = e-151,   Method: Composition-based stats.
 Identities = 338/750 (45%), Positives = 462/750 (61%), Gaps = 75/750 (10%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR---RRKV 212
           Q+HRSPGI+F+ +K      G +L++ RIIP +G W++  FD  D+I++ IDR   RRK+
Sbjct: 1   QVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWLEAVFDINDLIYIHIDRKKRRRKI 57

Query: 213 PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
              +F+ ALG  ++ +I+  F+     S                                
Sbjct: 58  LAMTFIRALGYSTDADIIEEFFSVEERSL------------------------------- 86

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
                           L++  V         L G  +A+++V+ ++  +Y +AG+ +   
Sbjct: 87  ---------------RLEKDFVA--------LVGKVLADNVVDADSSLVYGKAGEKLSTA 123

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ I  + ++ + I      + N  I   L  D     + AL D YR +RPG+ +T   
Sbjct: 124 MLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDSYEAALKDFYRRLRPGEPATLVN 181

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD---VRHIRKEDIIAIIKILVDLRN 448
           A S    LFFD+ +Y+L  VGR K+N +L     D+      +RKED+I  +K L+ LR 
Sbjct: 182 ARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETLSQVTLRKEDVIGALKYLIRLRM 241

Query: 449 G--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLI 504
           G  K +IDDID+L NRRVRSVGE+++N  R GL RME+ ++ER++  D   D++ P  +I
Sbjct: 242 GDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEKIVRERMNLFDFSSDTLTPGKII 301

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +AK +VS + +FF  SQLSQ  +  N +  +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 302 SAKGLVSVLKDFFSRSQLSQFMDQTNPVVELTHKRRLSALGPGGLNRERAGFEVRDVHAS 361

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL+SFA++N +GFIETPYR V DG VT+++ Y++A  EE 
Sbjct: 362 HYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPYRVVRDGIVTDEIEYMTADVEEE 421

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++ LDE   F   + + R  GE        +  +D SPKQ+VS+   LIPFLE+
Sbjct: 422 CVIAQASAELDEYNMFKTPVCWARYKGEAFEADTSTVTHMDVSPKQLVSVVTGLIPFLEH 481

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK SGA IVA+  G+VE VD+  IV
Sbjct: 482 DDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKDSGAIIVAQEDGVVEYVDSYEIV 541

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +              D Y+L KF RSN  TC+NQ PL  VGD V   D++ADGP+TD G+
Sbjct: 542 VAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLCSVGDVVTHGDVLADGPATDKGE 596

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI+IEEFE+ ARDTKLG EEITRD
Sbjct: 597 LALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSIYIEEFELTARDTKLGKEEITRD 656

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
           IPNVSEE L N+ E GI+ +GAEV PGDIL
Sbjct: 657 IPNVSEEVLANLGEDGIVRIGAEVKPGDIL 686


>gi|158564292|sp|Q250P0|RPOB_DESHY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1115

 Score =  540 bits (1392), Expect = e-151,   Method: Composition-based stats.
 Identities = 345/602 (57%), Positives = 457/602 (75%), Gaps = 7/602 (1%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +  ++N +IR TL  D  +  ++AL++IY+ +RPG+  T   A S+   LFFD  +YDL+
Sbjct: 207 ELFDDNEHIRITLERDNTESAEEALVEIYKRLRPGEPPTVDSARSLLEALFFDPKRYDLA 266

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +LNL  P DV H+ KEDI+A ++ ++ L +G+G  DDID+LGNRR+RSVGE
Sbjct: 267 KVGRYKLNKKLNLSVPTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGE 326

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER++  D+D + PQ LIN +PVV+A+ EFF SSQLSQ  +  
Sbjct: 327 LLQNQFRIGLSRMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFFGSSQLSQFMDQT 386

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++
Sbjct: 387 NPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTY 446

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+N YGFIE PYRKV +G+VT+ + YL+A EEE   +AQAN+ L +DG F EE +  R 
Sbjct: 447 GRINPYGFIEAPYRKVNNGQVTDQIDYLTADEEEKFVVAQANAPLTDDGHFIEEKIDGRH 506

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + +LV  E+ID++D SPKQ+VSIA +LIPFLE+DD+NR LMG NMQRQAVPLL+ +AP
Sbjct: 507 GPDFVLVAPERIDYMDVSPKQMVSIATALIPFLEHDDANRALMGANMQRQAVPLLRTDAP 566

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME   AK SG  ++A + G VE+  A  I+IR  +G L+        ++L+K+ R
Sbjct: 567 YVGTGMEYKAAKDSGVCVLASKDGTVERATAEDIIIRHDDGTLEK-------HKLLKYLR 619

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ TC+NQRP+V   + V    IIADGPSTD G+LALGRN+L+AFM W GYN+ED++LI
Sbjct: 620 SNQGTCINQRPIVMKNERVEAGQIIADGPSTDHGELALGRNVLIAFMTWEGYNYEDAILI 679

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE++V ED +TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV+
Sbjct: 680 SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITRDIPNVGEDVLKDLDERGIIRIGAEVS 739

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R  
Sbjct: 740 TGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFTREN 799

Query: 950 ID 951
            D
Sbjct: 800 GD 801



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/527 (35%), Positives = 256/527 (48%), Gaps = 85/527 (16%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +      G  E  + +  +       I++  I+     V  G I+    +      + 
Sbjct: 598  EDIIIRHDDGTLEKHKLLKYLRSNQGTCINQRPIVMKNERVEAGQIIADGPST-DHGELA 656

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-- 964
                +L A    +  +  D  L           D     +    + + R   +  E+I  
Sbjct: 657  LGRNVLIAFMTWEGYNYEDAILI---SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITR 713

Query: 965  ------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
                  E + +D  DE+ I+         +IL G+    G         L   +  E  R
Sbjct: 714  DIPNVGEDVLKDL-DERGIIRIGAEVSTGDILVGKVTPKGETELTAEERLLRAIFGEKAR 772

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                             E                   K+   + GD++ PGV  +V+V++
Sbjct: 773  -----------------EVRDTSLRVPHGEAGKIVDVKVFTRENGDELAPGVNELVRVYI 815

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKG++SRI+  EDMPFL DGTPV+IVLNPLGVPSRMN+GQ+ E
Sbjct: 816  AQKRKISVGDKMAGRHGNKGVISRIMKQEDMPFLPDGTPVEIVLNPLGVPSRMNIGQVME 875

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA   LG ++ + + D     D+                                 
Sbjct: 876  THLGWAAKALGLRLATPVFDGAQEEDV--------------------------------- 902

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +T              LR A L E+G+++LYDG TG+PFD  +TVGY+Y LK
Sbjct: 903  -------FAT--------------LRKAGLPETGKTVLYDGRTGDPFDNKITVGYMYFLK 941

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+K
Sbjct: 942  LHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVK 1001

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            SDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL + + +
Sbjct: 1002 SDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVRVLS 1048



 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 114/471 (24%), Positives = 201/471 (42%), Gaps = 45/471 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  E++D+P+LIE+Q+ SY  FL          +EGL+  F+ + PI  F+G 
Sbjct: 10  RERWSYSRIREVLDMPNLIEIQQNSYQWFL----------DEGLREMFRDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK++V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 60  LVLEFIDYSLGEPKYEVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG+++         SGK ++   +IP++G W
Sbjct: 111 MGDFPLMTTKGTFIINGAERVIVSQLVRSPGVYYSESID---PSGKKVFGATVIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D I VR+DR RK+P T  + ALG  +  +I   F          +      +
Sbjct: 168 LEFETDVNDNIFVRVDRTRKLPATVLIRALGYATNGQIAELFDDNEHIRITLERDNTESA 227

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              L+   K       +  GE   ++S + L   L    K   +  +G            
Sbjct: 228 EEALVEIYK------RLRPGEPPTVDSARSLLEALFFDPKRYDLAKVGRYKLNKKLNLSV 281

Query: 310 EDIVNGETGEIYIE--------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              V+  T E  +               +  ++ + +  +R +  L  +        R  
Sbjct: 282 PTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGELLQNQFRIG-LSRME 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            V  +    +D  +   +V+        ++    F            + +  +    RL+
Sbjct: 341 RVVRERMTIQDVDVITPQVLINIRPVVAAIK-EFFGSSQLSQFMDQTNPLAELTHKRRLS 399

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 400 ALGPGG---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 445


>gi|89893209|ref|YP_516696.1| DNA-directed RNA polymerase subunit beta [Desulfitobacterium
           hafniense Y51]
 gi|89332657|dbj|BAE82252.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 1121

 Score =  540 bits (1391), Expect = e-151,   Method: Composition-based stats.
 Identities = 345/602 (57%), Positives = 457/602 (75%), Gaps = 7/602 (1%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +  ++N +IR TL  D  +  ++AL++IY+ +RPG+  T   A S+   LFFD  +YDL+
Sbjct: 213 ELFDDNEHIRITLERDNTESAEEALVEIYKRLRPGEPPTVDSARSLLEALFFDPKRYDLA 272

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +LNL  P DV H+ KEDI+A ++ ++ L +G+G  DDID+LGNRR+RSVGE
Sbjct: 273 KVGRYKLNKKLNLSVPTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGE 332

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER++  D+D + PQ LIN +PVV+A+ EFF SSQLSQ  +  
Sbjct: 333 LLQNQFRIGLSRMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFFGSSQLSQFMDQT 392

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++
Sbjct: 393 NPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTY 452

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+N YGFIE PYRKV +G+VT+ + YL+A EEE   +AQAN+ L +DG F EE +  R 
Sbjct: 453 GRINPYGFIEAPYRKVNNGQVTDQIDYLTADEEEKFVVAQANAPLTDDGHFIEEKIDGRH 512

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + +LV  E+ID++D SPKQ+VSIA +LIPFLE+DD+NR LMG NMQRQAVPLL+ +AP
Sbjct: 513 GPDFVLVAPERIDYMDVSPKQMVSIATALIPFLEHDDANRALMGANMQRQAVPLLRTDAP 572

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME   AK SG  ++A + G VE+  A  I+IR  +G L+        ++L+K+ R
Sbjct: 573 YVGTGMEYKAAKDSGVCVLASKDGTVERATAEDIIIRHDDGTLEK-------HKLLKYLR 625

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ TC+NQRP+V   + V    IIADGPSTD G+LALGRN+L+AFM W GYN+ED++LI
Sbjct: 626 SNQGTCINQRPIVMKNERVEAGQIIADGPSTDHGELALGRNVLIAFMTWEGYNYEDAILI 685

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE++V ED +TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV+
Sbjct: 686 SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITRDIPNVGEDVLKDLDERGIIRIGAEVS 745

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R  
Sbjct: 746 TGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFTREN 805

Query: 950 ID 951
            D
Sbjct: 806 GD 807



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/527 (35%), Positives = 256/527 (48%), Gaps = 85/527 (16%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +      G  E  + +  +       I++  I+     V  G I+    +      + 
Sbjct: 604  EDIIIRHDDGTLEKHKLLKYLRSNQGTCINQRPIVMKNERVEAGQIIADGPST-DHGELA 662

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-- 964
                +L A    +  +  D  L           D     +    + + R   +  E+I  
Sbjct: 663  LGRNVLIAFMTWEGYNYEDAILI---SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITR 719

Query: 965  ------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
                  E + +D  DE+ I+         +IL G+    G         L   +  E  R
Sbjct: 720  DIPNVGEDVLKDL-DERGIIRIGAEVSTGDILVGKVTPKGETELTAEERLLRAIFGEKAR 778

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                             E                   K+   + GD++ PGV  +V+V++
Sbjct: 779  -----------------EVRDTSLRVPHGEAGKIVDVKVFTRENGDELAPGVNELVRVYI 821

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKG++SRI+  EDMPFL DGTPV+IVLNPLGVPSRMN+GQ+ E
Sbjct: 822  AQKRKISVGDKMAGRHGNKGVISRIMKQEDMPFLPDGTPVEIVLNPLGVPSRMNIGQVME 881

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA   LG ++ + + D     D+                                 
Sbjct: 882  THLGWAAKALGLRLATPVFDGAQEEDV--------------------------------- 908

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +T              LR A L E+G+++LYDG TG+PFD  +TVGY+Y LK
Sbjct: 909  -------FAT--------------LRKAGLPETGKTVLYDGRTGDPFDNKITVGYMYFLK 947

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+K
Sbjct: 948  LHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVK 1007

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            SDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL + + +
Sbjct: 1008 SDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVRVLS 1054



 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 114/471 (24%), Positives = 201/471 (42%), Gaps = 45/471 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  E++D+P+LIE+Q+ SY  FL          +EGL+  F+ + PI  F+G 
Sbjct: 16  RERWSYSRIREVLDMPNLIEIQQNSYQWFL----------DEGLREMFRDISPIQDFTGN 65

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK++V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 66  LVLEFIDYSLGEPKYEVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVF 116

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG+++         SGK ++   +IP++G W
Sbjct: 117 MGDFPLMTTKGTFIINGAERVIVSQLVRSPGVYYSESID---PSGKKVFGATVIPNRGAW 173

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D I VR+DR RK+P T  + ALG  +  +I   F          +      +
Sbjct: 174 LEFETDVNDNIFVRVDRTRKLPATVLIRALGYATNGQIAELFDDNEHIRITLERDNTESA 233

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              L+   K       +  GE   ++S + L   L    K   +  +G            
Sbjct: 234 EEALVEIYK------RLRPGEPPTVDSARSLLEALFFDPKRYDLAKVGRYKLNKKLNLSV 287

Query: 310 EDIVNGETGEIYIE--------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              V+  T E  +               +  ++ + +  +R +  L  +        R  
Sbjct: 288 PTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGELLQNQFRIG-LSRME 346

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            V  +    +D  +   +V+        ++    F            + +  +    RL+
Sbjct: 347 RVVRERMTIQDVDVITPQVLINIRPVVAAIK-EFFGSSQLSQFMDQTNPLAELTHKRRLS 405

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 406 ALGPGG---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 451


>gi|219666482|ref|YP_002456917.1| DNA-directed RNA polymerase subunit beta [Desulfitobacterium
           hafniense DCB-2]
 gi|254765286|sp|B8G1V8|RPOB_DESHD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|219536742|gb|ACL18481.1| DNA-directed RNA polymerase, beta subunit [Desulfitobacterium
           hafniense DCB-2]
          Length = 1115

 Score =  540 bits (1391), Expect = e-151,   Method: Composition-based stats.
 Identities = 344/602 (57%), Positives = 456/602 (75%), Gaps = 7/602 (1%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +  ++N +IR TL  D  +  ++AL++IY+ +RPG+  T   A S+   LFFD  +YDL+
Sbjct: 207 ELFDDNEHIRITLERDNTESAEEALVEIYKRLRPGEPPTVDSARSLLEALFFDPKRYDLA 266

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +L L  P DV H+ KEDI+A ++ ++ L +G+G  DDID+LGNRR+RSVGE
Sbjct: 267 KVGRYKLNKKLKLSVPTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGE 326

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ+R+GL RMER ++ER++  D+D + PQ LIN +PVV+A+ EFF SSQLSQ  +  
Sbjct: 327 LLQNQFRIGLSRMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFFGSSQLSQFMDQT 386

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++
Sbjct: 387 NPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTY 446

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+N YGFIE PYRKV +G+VT+ + YL+A EEE   +AQAN+ L +DG F EE +  R 
Sbjct: 447 GRINPYGFIEAPYRKVNNGQVTDQIDYLTADEEEKFVVAQANAPLTDDGHFIEEKIDGRH 506

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + +LV  E+ID++D SPKQ+VSIA +LIPFLE+DD+NR LMG NMQRQAVPLL+ +AP
Sbjct: 507 GPDFVLVAPERIDYMDVSPKQMVSIATALIPFLEHDDANRALMGANMQRQAVPLLRTDAP 566

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME   AK SG  ++A + G VE+  A  I+IR  +G L+        ++L+K+ R
Sbjct: 567 YVGTGMEYKAAKDSGVCVLASKDGTVERATAEDIIIRHDDGTLEK-------HKLLKYLR 619

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ TC+NQRP+V   + V    IIADGPSTD G+LALGRN+L+AFM W GYN+ED++LI
Sbjct: 620 SNQGTCINQRPIVMKNERVEAGQIIADGPSTDHGELALGRNVLIAFMTWEGYNYEDAILI 679

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE++V ED +TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAEV+
Sbjct: 680 SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITRDIPNVGEDVLKDLDERGIIRIGAEVS 739

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R  
Sbjct: 740 TGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFTREN 799

Query: 950 ID 951
            D
Sbjct: 800 GD 801



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/527 (35%), Positives = 256/527 (48%), Gaps = 85/527 (16%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +      G  E  + +  +       I++  I+     V  G I+    +      + 
Sbjct: 598  EDIIIRHDDGTLEKHKLLKYLRSNQGTCINQRPIVMKNERVEAGQIIADGPST-DHGELA 656

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI-- 964
                +L A    +  +  D  L           D     +    + + R   +  E+I  
Sbjct: 657  LGRNVLIAFMTWEGYNYEDAILI---SEKLVKEDYYTSIHIEEYEADARDTKLGPEEITR 713

Query: 965  ------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
                  E + +D  DE+ I+         +IL G+    G         L   +  E  R
Sbjct: 714  DIPNVGEDVLKDL-DERGIIRIGAEVSTGDILVGKVTPKGETELTAEERLLRAIFGEKAR 772

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                             E                   K+   + GD++ PGV  +V+V++
Sbjct: 773  -----------------EVRDTSLRVPHGEAGKIVDVKVFTRENGDELAPGVNELVRVYI 815

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A KR I  GDKMAGRHGNKG++SRI+  EDMPFL DGTPV+IVLNPLGVPSRMN+GQ+ E
Sbjct: 816  AQKRKISVGDKMAGRHGNKGVISRIMKQEDMPFLPDGTPVEIVLNPLGVPSRMNIGQVME 875

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA   LG ++ + + D     D+                                 
Sbjct: 876  THLGWAAKALGLRLATPVFDGAQEEDV--------------------------------- 902

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +T              LR A L E+G+++LYDG TG+PFD  +TVGY+Y LK
Sbjct: 903  -------FAT--------------LRKAGLPETGKTVLYDGRTGDPFDNKITVGYMYFLK 941

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+K
Sbjct: 942  LHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVK 1001

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            SDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL + + +
Sbjct: 1002 SDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVRVLS 1048



 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 114/471 (24%), Positives = 201/471 (42%), Gaps = 45/471 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  E++D+P+LIE+Q+ SY  FL          +EGL+  F+ + PI  F+G 
Sbjct: 10  RERWSYSRIREVLDMPNLIEIQQNSYQWFL----------DEGLREMFRDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK++V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 60  LVLEFIDYSLGEPKYEVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG+++         SGK ++   +IP++G W
Sbjct: 111 MGDFPLMTTKGTFIINGAERVIVSQLVRSPGVYYSESID---PSGKKVFGATVIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D I VR+DR RK+P T  + ALG  +  +I   F          +      +
Sbjct: 168 LEFETDVNDNIFVRVDRTRKLPATVLIRALGYATNGQIAELFDDNEHIRITLERDNTESA 227

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              L+   K       +  GE   ++S + L   L    K   +  +G            
Sbjct: 228 EEALVEIYK------RLRPGEPPTVDSARSLLEALFFDPKRYDLAKVGRYKLNKKLKLSV 281

Query: 310 EDIVNGETGEIYIE--------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              V+  T E  +               +  ++ + +  +R +  L  +        R  
Sbjct: 282 PTDVHHLTKEDIVASLRQMLTLMSGEGHKDDIDHLGNRRLRSVGELLQNQFRIG-LSRME 340

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            V  +    +D  +   +V+        ++    F            + +  +    RL+
Sbjct: 341 RVVRERMTIQDVDVITPQVLINIRPVVAAIK-EFFGSSQLSQFMDQTNPLAELTHKRRLS 399

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 400 ALGPGG---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 445


>gi|83591284|ref|YP_431293.1| DNA-directed RNA polymerase subunit beta [Moorella thermoacetica
           ATCC 39073]
 gi|109904224|sp|Q2RFN9|RPOB_MOOTA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|83574198|gb|ABC20750.1| DNA-directed RNA polymerase subunit beta [Moorella thermoacetica
           ATCC 39073]
          Length = 1141

 Score =  540 bits (1390), Expect = e-151,   Method: Composition-based stats.
 Identities = 350/612 (57%), Positives = 457/612 (74%), Gaps = 17/612 (2%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +  + +  I+NTL  D  +  ++AL++IY+ +RPG+  T   A ++   LFFD  +YDL 
Sbjct: 207 ELFDYDGRIQNTLEKDNTESEEEALVEIYKRLRPGEPPTVDSARNLLESLFFDPRRYDLG 266

Query: 410 TVGRVKMNMRLNLDT--------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            VGR K++ + N            + +R + KEDII  IK L+ L +G+   DDID+LGN
Sbjct: 267 NVGRYKLHKKFNHGILTREVDGREEYIRTLTKEDIIYTIKYLLRLMDGEVKPDDIDHLGN 326

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+RSVGE+L+NQ+R+GL RMER ++ER++  D+D + PQ LIN +PVV+A+ EFF SSQ
Sbjct: 327 RRLRSVGELLQNQFRIGLARMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFFGSSQ 386

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIG
Sbjct: 387 LSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIG 446

Query: 582 LVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L+ SL+++AR+N +GFIETPYR+V    G VTN V YL+A EE+  +IAQAN+ LDE+G 
Sbjct: 447 LIGSLSTYARINEFGFIETPYRRVDKEKGIVTNQVDYLTADEEDKYFIAQANAPLDEEGH 506

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F E+ V  R  GE ++VP  ++D++D SPKQ+VS+A +LIPFLE+DD+NR LMG NMQRQ
Sbjct: 507 FLEKRVNARHGGEILVVPASQVDYMDVSPKQMVSVATALIPFLEHDDANRALMGANMQRQ 566

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPLL+ EAP VGTGME   A+ SG  ++A+  G+VE+V A  IVIR+  G L+      
Sbjct: 567 AVPLLRTEAPIVGTGMEWRAARDSGTVVLARNNGVVERVTAREIVIRTDNGHLE------ 620

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
             YRL KF RSNQ TC+NQ+P+V+ G+ V     IADGPSTD G+LALGRN+LVAFM W 
Sbjct: 621 -TYRLQKFVRSNQGTCINQKPIVRKGERVSAGQTIADGPSTDQGELALGRNILVAFMTWE 679

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++LISE++V +D+FTSIHIEE+E  ARDTKLGPEEITRDIPNVSE+ LK++DE 
Sbjct: 680 GYNYEDAILISEKLVKDDIFTSIHIEEYECDARDTKLGPEEITRDIPNVSEDVLKDLDER 739

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV PGDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG V
Sbjct: 740 GIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIV 799

Query: 940 VDVRIFNRHGID 951
           VDV++F+R   D
Sbjct: 800 VDVKVFSRENGD 811



 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 195/538 (36%), Positives = 263/538 (48%), Gaps = 83/538 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  E  R    V       I++  I+  G  V+ G  +    +   +  +     +
Sbjct: 613  RTDNGHLETYRLQKFVRSNQGTCINQKPIVRKGERVSAGQTIADGPST-DQGELALGRNI 671

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    +  +  D  L     V   +        +  + + R   +  E+I        
Sbjct: 672  LVAFMTWEGYNYEDAILISEKLVKDDIFTSIHIEEY--ECDARDTKLGPEEITRDIPNVS 729

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E + +D  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 730  EDVLKDL-DERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 782

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   K+   + GD++ PGV  +V+V++A KR I
Sbjct: 783  -----------EVRDTSLRVPHGESGIVVDVKVFSRENGDELAPGVNELVRVYIAQKRKI 831

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG++SRILP EDMPFL DGTP++IVLNPLGVPSRMN+GQI ETHLG A
Sbjct: 832  SVGDKMAGRHGNKGVISRILPEEDMPFLPDGTPIEIVLNPLGVPSRMNLGQILETHLGRA 891

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D     +I                                   K+G+
Sbjct: 892  ARALGITVATPVFDGATEEEIKEAFR------------------------------KAGL 921

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            P                        E G++ILYDG TGEPFDRP+TVGY+YMLKL H+V 
Sbjct: 922  P------------------------EDGKTILYDGRTGEPFDRPITVGYMYMLKLAHLVD 957

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVG
Sbjct: 958  DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVG 1017

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            R + YE+IV G +  E G PESF VL+KE+Q+LGL + + +   +     E+  D ++
Sbjct: 1018 RVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGLDVKVLSEENEEIEIKEDDDDVSE 1075



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 111/481 (23%), Positives = 199/481 (41%), Gaps = 57/481 (11%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F K  E +++P+LIE+Q+ SY  F+          + GL+  F  + PI  F+G 
Sbjct: 10  RERWTFAKIKETLELPNLIEIQRNSYQWFI----------DTGLRELFHDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+FV Y    PK+  D+C  RD+TYA PL++ +RLI          +   ++KEQ ++
Sbjct: 60  LILQFVDYSLGEPKYSEDECKERDMTYAAPLRVKVRLI---------NRETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG ++         SG  +Y   +IP++G W
Sbjct: 111 MGDFPLMTDKGTFIINGAERVIVSQLVRSPGAYYAEGID---ASGTKVYGATVIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D+ + I+VRIDR RK+PVT  L ALG ++   IL  F          +       
Sbjct: 168 LEFETDNTESIYVRIDRTRKIPVTILLRALGYNTNARILELFDYDGRIQNTLEKDNTESE 227

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------- 300
              L+   K       +  GE   ++S + L   L    +   +  +G            
Sbjct: 228 EEALVEIYK------RLRPGEPPTVDSARNLLESLFFDPRRYDLGNVGRYKLHKKFNHGI 281

Query: 301 ---------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                    + +    + ++ +      +       +    ++ + +  +R +  L  + 
Sbjct: 282 LTREVDGREEYI--RTLTKEDIIYTIKYLLRLMDGEVKPDDIDHLGNRRLRSVGELLQNQ 339

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                  R   V  +    +D  +   +V+        ++    F            + +
Sbjct: 340 FRIG-LARMERVVRERMTIQDVDVITPQVLINIRPVVAAIK-EFFGSSQLSQFMDQTNPL 397

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
             +    RL+   P     + +E     ++ +     G+  +  I+      +  +G + 
Sbjct: 398 AELTHKRRLSALGPGG---LSRERAGFEVRDVHTSHYGR--MCPIETPEGPNIGLIGSLS 452

Query: 472 K 472
            
Sbjct: 453 T 453


>gi|84494796|ref|ZP_00993915.1| DNA-directed RNA polymerase beta subunit [Janibacter sp. HTCC2649]
 gi|84384289|gb|EAQ00169.1| DNA-directed RNA polymerase beta subunit [Janibacter sp. HTCC2649]
          Length = 1162

 Score =  539 bits (1388), Expect = e-150,   Method: Composition-based stats.
 Identities = 303/951 (31%), Positives = 448/951 (47%), Gaps = 135/951 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDER------------PNEGLQAAFKS 61
           R  FGK  E +++PDL+ +Q  S+D  L      +                 GL+  F+ 
Sbjct: 20  RLSFGKIREPMEVPDLLALQTESFDWLLGNERWQERVAQARAAGRDDVPERSGLEDIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+  K+ ++DC  RD TY+ PL +T   +           +
Sbjct: 80  ISPIEDFSGSMSLSFRDHRFEEVKYSIEDCKERDQTYSAPLFVTAEFM---------NNT 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K +Y 
Sbjct: 131 TGEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTPDKT--SDKDIYT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W++ E D +D++ VR+DR+RK  VT  L ALG+   +I   F         
Sbjct: 189 AKIIPSRGAWIEFEIDKRDMVGVRVDRKRKQSVTVLLKALGLTEAQIREEFAGYESIELT 248

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            D          L+   +       +  GE    E+ + L   L  + K   +  +G   
Sbjct: 249 LDKDNTEGQDDALLDIYR------KLRPGEPPTREAAQNLLDNLYFNGKRYDLAKVGRYK 302

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                       +N + G   IE+       ++ +I  +    + +   D        R 
Sbjct: 303 ------------INKKLG---IESELTDSTLNVNDIVATIKYIVALHNGD--ETLPGRRK 345

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                   +  D      R +R                L  +  +  LS + RV      
Sbjct: 346 GEDVAIRVETDDIDHFGNRRLRN------------VGELIQNQVRTGLSRMERVVRERMT 393

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             D       I  + +I I  ++  ++   GT      +      S     +    LG  
Sbjct: 394 TQDVEA----ITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPG 449

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            + R      + +D+  V P       P+ +                 +N+   I     
Sbjct: 450 GLSRD----RAGMDVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINAFGFI----- 500

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
                +    +   G    ++H             E     +  +  +          E 
Sbjct: 501 -----ETPYRKVTKGRVTDEIH--------YLSADEEDEHVIAQANAALDAAGERFTSER 547

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
              +V       +V Y+ A + +   +                                 
Sbjct: 548 VLVRVKG----GEVEYIPADDVDYIDV--------------------------------- 570

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
                 S +Q+VS A +LIPFLE+DD+NR LMG NMQRQAVPL+KAEAP VGTGME   A
Sbjct: 571 ------SARQMVSAATALIPFLEHDDANRALMGSNMQRQAVPLVKAEAPLVGTGMELRAA 624

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  ++A++AG+V +V A  + + + +G           YR+ KF RSNQ    NQR 
Sbjct: 625 VDSGDVVIAEKAGVVTEVSADLVTVAADDGTS-------RTYRIDKFTRSNQGNSYNQRV 677

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  GD V +  +IADGP+TD G++ALGRN+LVAFMPW G+N+ED++++S+R+V +DV +
Sbjct: 678 IVSEGDRVEKGGLIADGPATDGGEMALGRNLLVAFMPWEGHNYEDAIILSQRLVQDDVLS 737

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GAEV  GD+LVGK+TP
Sbjct: 738 SIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVRDGDLLVGKVTP 797

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ V++F++   D
Sbjct: 798 KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVKVFDKDEGD 848



 Score =  516 bits (1329), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/515 (37%), Positives = 263/515 (51%), Gaps = 69/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G  L+          M     LL A    +  +  D  +     V   V+
Sbjct: 678  IVSEGDRVEKG-GLIADGPATDGGEMALGRNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 736

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+      R  ++L G
Sbjct: 737  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVRDGDLLVG 793

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 794  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGTV 836

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+     GD++PPGV ++V+V VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 837  IGVKVFDKDEGDELPPGVNQLVRVHVANKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 896

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+VLNPLGVP RMN+GQI E HLGWA    G +I    +               
Sbjct: 897  EDGTPVDVVLNPLGVPGRMNIGQILELHLGWAAS-RGWEIVGNPDWA------------- 942

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM------- 1225
                              + +   A   + G  V++PVFDG  E+ I  +L         
Sbjct: 943  ------------------NLIPDDARSAEPGTRVASPVFDGVREDEIVGLLDSTRETRDG 984

Query: 1226 -ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +D SG++ L+DG +GEP+  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 985  VRLIDGSGKTPLFDGRSGEPYPEPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1044

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G++  E G P
Sbjct: 1045 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVNGRVKVYEAIVKGDNIPEPGIP 1104

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S  +     +   D
Sbjct: 1105 ESFKVLIKEMQSLCLNVEVLSSDGQAIEMHDAEED 1139


>gi|157060626|gb|ABV03319.1| RpoB [Chlamydia trachomatis]
 gi|157060628|gb|ABV03320.1| RpoB [Chlamydia trachomatis]
 gi|157060630|gb|ABV03321.1| RpoB [Chlamydia trachomatis]
 gi|157060632|gb|ABV03322.1| RpoB [Chlamydia trachomatis]
 gi|157060644|gb|ABV03328.1| RpoB [Chlamydia trachomatis]
 gi|157060646|gb|ABV03329.1| RpoB [Chlamydia trachomatis]
 gi|157060648|gb|ABV03330.1| RpoB [Chlamydia trachomatis]
 gi|157060650|gb|ABV03331.1| RpoB [Chlamydia trachomatis]
          Length = 686

 Score =  538 bits (1386), Expect = e-150,   Method: Composition-based stats.
 Identities = 337/750 (44%), Positives = 462/750 (61%), Gaps = 75/750 (10%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR---RRKV 212
           Q+HRSPGI+F+ +K      G +L++ RIIP +G W++  FD  D+I++ IDR   RRK+
Sbjct: 1   QVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWLEAVFDINDLIYIHIDRKKRRRKI 57

Query: 213 PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
              +F+ ALG  ++ +I+  F+     S                                
Sbjct: 58  LAMTFIRALGYSTDADIIEEFFSVEERSL------------------------------- 86

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
                           L++  V         L G  +A+++V+ ++  +Y +AG+ +   
Sbjct: 87  ---------------RLEKDFVA--------LVGKVLADNVVDADSSLVYGKAGEKLSTA 123

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ I  + ++ + I      + N  I   L  D     + AL D YR +RPG+ +T   
Sbjct: 124 MLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDSYEAALKDFYRRLRPGEPATLVN 181

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD---VRHIRKEDIIAIIKILVDLRN 448
           A S    LFFD+ +Y+L  VGR K+N +L     D+      +RKED+I  +K L+ LR 
Sbjct: 182 ARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETLSQVTLRKEDVIGALKYLIRLRM 241

Query: 449 G--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLI 504
           G  K +IDDID+L NRRVRSVGE+++N  R GL RME+ ++ER++  D   D++ P  +I
Sbjct: 242 GDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEKIVRERMNLFDFSSDTLTPGKII 301

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +AK +VS + +FF  SQLSQ  +  N +  +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 302 SAKGLVSVLKDFFSRSQLSQFMDQTNPVVELTHKRRLSALGPGGLNRERAGFEVRDVHAS 361

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL+SFA++N +GFIETPYR V DG VT+++ Y++A  EE 
Sbjct: 362 HYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPYRVVRDGIVTDEIEYMTADVEEE 421

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++ LDE   F   + + R  GE        +  +D SPKQ+VS+   LIPFLE+
Sbjct: 422 CVIAQASAELDEYDMFKTPVCWARYKGEAFEADTSTVTHMDVSPKQLVSVVTGLIPFLEH 481

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK SGA IVA+  G+VE VD+  IV
Sbjct: 482 DDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKDSGAIIVAQEDGVVEYVDSYEIV 541

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +              D Y+L KF RSN  TC+NQ PL  VGD V   D++ADGP+TD G+
Sbjct: 542 VAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLCSVGDVVTHGDVLADGPATDKGE 596

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI+IEEFE+ ARDTKLG EEITRD
Sbjct: 597 LALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSIYIEEFELTARDTKLGKEEITRD 656

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
           IPNVSEE L N+ E G++ +GAEV PGDIL
Sbjct: 657 IPNVSEEVLANLGEDGVVRIGAEVKPGDIL 686


>gi|156093703|ref|XP_001612890.1| DNA-directed RNA polymerase II 135 kDa polypeptide [Plasmodium vivax
            SaI-1]
 gi|148801764|gb|EDL43163.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative
            [Plasmodium vivax]
          Length = 1339

 Score =  538 bits (1386), Expect = e-150,   Method: Composition-based stats.
 Identities = 249/1483 (16%), Positives = 450/1483 (30%), Gaps = 337/1483 (22%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----------AFSGA--AMLE 75
            L+  Q  SY+ F+   +          Q        I              +      L+
Sbjct: 49   LVNQQIESYNDFIEYRM----------QEIIDEHPQIEIRPQPQYRSDRDDNKNVMYALK 98

Query: 76   FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            F     D P +D            +   R+LTY+  + I +    + VDE T ++ +K+ 
Sbjct: 99   FGQLSLDRPFYDERNLTNKNLWPQEARLRNLTYSSAIYIDIEQSTYVVDESTRSQILKEK 158

Query: 126  -KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
               + I +G +PLM K                         G F++ G ++++V+Q    
Sbjct: 159  FIYERINLGRIPLMLKSMFCWTKGLPESEIADMGECAFDQGGYFIVNGGEKVLVAQ---- 214

Query: 161  PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
                                              E  + + I+V    ++K P       
Sbjct: 215  ----------------------------------ERMAHNFIYVF---KKKQP------- 230

Query: 221  LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
                                    W   + +      A  + S+            G   
Sbjct: 231  --------------------SKFGWVAEIRSQMERSQATSAFSVKMKTKTGSRGSGGSAR 270

Query: 281  TSGLLKSLKEKGVKFLGI-TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            T G L +        + +       G     DI+     +   +       ++LEE    
Sbjct: 271  TGGQLVATLPYIRTEISVGILFRALGCTSDRDILQRIVYDFNDKMMINTLRETLEECIDY 330

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
              +DI + ++                    R+  +L    ++R   +        + +  
Sbjct: 331  PTQDICLDFI----------GKRGPTVGASREKRILYAKELLRKEVLPHMGTGPGVESK- 379

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                                            +   I  +I  L+    G+   DD D+ 
Sbjct: 380  --------------------------------KSYFIGYMINRLLLAELGRIKEDDRDHF 407

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL----INAKPVVSAVCE 515
            G +R+   G ++ + +     +M + +K R+    ID+  P D+     +   +   +  
Sbjct: 408  GKKRLDIAGPLMASSFSTYFRKMAKDVK-RVLQRQIDNNKPFDVAGAVRSCSQITQGMQY 466

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               ++Q+   +   S ++H RRL+      + R     + R +H
Sbjct: 467  QLATGNWGKDKDGKVIRTGVAQVLNRLTYSSCLSHLRRLNT----PLGREGKMAKPRQLH 522

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             TH+G ICP ET EG ++GLV +L+    ++        +  + +      +  +     
Sbjct: 523  NTHWGMICPFETPEGQSVGLVKNLSLMCDISVGTSTNNIFEFLLEW-GLESLDEVPPQLM 581

Query: 623  ENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            + +     N       +  + L+      R   +         D      K       ++
Sbjct: 582  KEKVKLFLNGKWVGCFNQIDNLIETLYELRRRCDISPEASIVRDVNSKEIKIFTDSGRAM 641

Query: 679  IPFLEN--------------------------------DDSNRVLMGCNMQRQAVPLLKA 706
             P                                     +     + C  +   +  +  
Sbjct: 642  RPLYVVKNVKGENKLKLTKEHVKNMMAYPETYNWDYLIQEGIIEYIDCEEEETTMISMFI 701

Query: 707  EAPFVGTGME--SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYR 763
            +    GTG        +   + I+   A I+   D  +    + +  +     G+     
Sbjct: 702  DDLKTGTGYHNNYTHCEIHPSLILGVCASIIPFSDHNQSPRNTYQSAMGKQAMGIYVTNF 761

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             ++           QRPLV                     DL  G N +VA M + GYN 
Sbjct: 762  NIRLDTLAHLLYYPQRPLV----------CTKVMEYLRFRDLPAGINAIVAIMCYTGYNQ 811

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDE 878
            EDS+++++  +   +F S+    +    +       E       R + N+       +D 
Sbjct: 812  EDSLIMNQSSIDRGLFRSVFYRTYTSEEKQQGSLIIESFEKPSIRCVKNLKRGDYTKLDN 871

Query: 879  CGIICVGAEVNPGDILVGKITPKGESP------------MTPEEKLLRAIFGEKAVDVRD 926
             G+I  G  V   DI++GK++P  E                          G        
Sbjct: 872  DGLIAPGIRVLGDDIIIGKVSPNIEDEDDIVIQKRVPNVQMSYPSGGSTSNGFITGKDSP 931

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD--KDDEQVILDRNIYS 984
            T   + +G +G+V          +       S+    +   A D    D          +
Sbjct: 932  TGGSMLNGSAGSVCGSGGSVCGSVSSPYSPSSIGGPNLIDSAPDSPMSDRYSSSGPVGTT 991

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
             +       +  S    F+    LSS     Y  +        + +V     S     + 
Sbjct: 992  TMAPPSVASSTPSNTTIFRSGNTLSSVSSPHYGTTIVSGSTKDELEVPTLTISTSNILKQ 1051

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPG--VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             K       +     +     +       +  KV V   R  Q GDK A RHG KG +  
Sbjct: 1052 YKKDCSLSLRENENGVIDTVMLSSNSRGNKFAKVKVRSVRVPQIGDKFASRHGQKGTIGI 1111

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  DGT  DI++NP  VPSRM +G + E   G      G             
Sbjct: 1112 TYRTEDMPFSSDGTFPDIIMNPHAVPSRMTIGHLVECLAGKVAAIEG------------- 1158

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                    G   +TP F     + I+  
Sbjct: 1159 ----------------------------------------GEGDATP-FSRITVQEISQR 1177

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L     ++ G  +LY+G  G+     + +G  Y  +L HMV DK++ARS G  +++T+QP
Sbjct: 1178 LHSLGYEKYGNDVLYNGHNGKMLKSKIFIGPTYYQRLKHMVEDKIHARSRGPLTMITRQP 1237

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------------DVVGRT 1326
              G+S  GG R GEME  C+ ++G+A +L+E L  +SD                D+    
Sbjct: 1238 TEGRSRDGGLRFGEMERDCMISHGSAKMLKERLFEESDAYRVHVCDNCGLCCIADIN--K 1295

Query: 1327 RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              YE  V     +  +   P +  +L +E+  + +   L    
Sbjct: 1296 NAYECTVCNSKTNISQIYIPYACKLLFQELMTMAIYPKLVLED 1338


>gi|169630948|ref|YP_001704597.1| DNA-directed RNA polymerase subunit beta [Mycobacterium abscessus
           ATCC 19977]
 gi|34391547|gb|AAN65351.1| RpoB [Mycobacterium abscessus]
 gi|169242915|emb|CAM63943.1| DNA-directed RNA polymerase beta chain [Mycobacterium abscessus]
          Length = 1171

 Score =  538 bits (1385), Expect = e-150,   Method: Composition-based stats.
 Identities = 306/949 (32%), Positives = 457/949 (48%), Gaps = 136/949 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNE----GLQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      +    R       GL+     + PI 
Sbjct: 32  RLSFAKLREPLAVPGLLDVQTESFEWLVGSPRWREVATARGEVNPTGGLEEILTELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 201 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 260

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
              P  A   +            ++ + ++E+   K+    L +  + K  K LG     
Sbjct: 261 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLG----- 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G   A+      T E  +        + L  +   +                 +    
Sbjct: 316 LGGTNPAQVTTTTLTEEDVVA-----TIEYLVRLHEGQTT---------------MTAPG 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +   D  D      R +R            +         +  LS + RV        
Sbjct: 356 GVEVPVDVDDIDHFGNRRLR--------TVGELIQN----QIRVGLSRMERVVRERMTTQ 403

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       I  + +I I  ++  ++   GT      +      S     +    LG   +
Sbjct: 404 DVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGL 459

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R      + +++  V P       P+ +             +   VN    I       
Sbjct: 460 TRD----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI------- 508

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              +    +   GV   D+H           T++  +  +V+   S    N     E   
Sbjct: 509 ---ETPYRKVSDGVVTDDIH---------YLTADEEDRHVVAQANSPVDANGRFTEE--- 553

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+   +   +V ++SA E                                       +D
Sbjct: 554 -KILVRRKGGEVEFVSATE---------------------------------------VD 573

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 574 YMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 633

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +G  +VA++AG++E+V A  + + + +G           YRL KF RSN  TC NQ+P+V
Sbjct: 634 AGDVVVAEKAGVIEEVSADYVTVMADDGTRQS-------YRLRKFARSNHGTCANQKPIV 686

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G  V    +IADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSI
Sbjct: 687 DEGQRVEAGQVIADGPCTENGEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVLTSI 746

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 747 HIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKG 806

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 807 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 855



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 264/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +        +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149


>gi|157060654|gb|ABV03333.1| RpoB [Chlamydia trachomatis]
          Length = 685

 Score =  538 bits (1385), Expect = e-150,   Method: Composition-based stats.
 Identities = 336/749 (44%), Positives = 461/749 (61%), Gaps = 75/749 (10%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR---RRKV 212
           Q+HRSPGI+F+ +K      G +L++ RIIP +G W++  FD  D+I++ IDR   RRK+
Sbjct: 1   QVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWLEAVFDINDLIYIHIDRKKRRRKI 57

Query: 213 PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
              +F+ ALG  ++ +I+  F+     S                                
Sbjct: 58  LAMTFIRALGYSTDADIIEEFFSVEERSL------------------------------- 86

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
                           L++  V         L G  +A+++V+ ++  +Y +AG+ +   
Sbjct: 87  ---------------RLEKDFVA--------LVGKVLADNVVDADSSLVYGKAGEKLSTA 123

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ I  + ++ + I      + N  I   L  D     + AL D YR +RPG+ +T   
Sbjct: 124 MLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDSYEAALKDFYRRLRPGEPATLVN 181

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD---VRHIRKEDIIAIIKILVDLRN 448
           A S    LFFD+ +Y+L  VGR K+N +L     D+      +RKED+I  +K L+ LR 
Sbjct: 182 ARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETLSQVTLRKEDVIGALKYLIRLRM 241

Query: 449 G--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLI 504
           G  K +IDDID+L NRRVRSVGE+++N  R GL RME+ ++ER++  D   D++ P  +I
Sbjct: 242 GDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEKIVRERMNLFDFSSDTLTPGKII 301

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +AK +VS + +FF  SQLSQ  +  N +  +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 302 SAKGLVSVLKDFFSRSQLSQFMDQTNPVVELTHKRRLSALGPGGLNRERAGFEVRDVHAS 361

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL+SFA++N +GFIETPYR V DG VT+++ Y++A  EE 
Sbjct: 362 HYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPYRVVRDGIVTDEIEYMTADVEEE 421

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++ LDE   F   + + R  GE        +  +D SPKQ+VS+   LIPFLE+
Sbjct: 422 CVIAQASAELDEYDMFKTPVCWARYKGEAFEADTSTVTHMDVSPKQLVSVVTGLIPFLEH 481

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK SGA IVA+  G+VE VD+  IV
Sbjct: 482 DDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKDSGAIIVAQEDGVVEYVDSYEIV 541

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +              D Y+L KF RSN  TC+NQ PL  VGD V   D++ADGP+TD G+
Sbjct: 542 VAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLCSVGDVVTHGDVLADGPATDKGE 596

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI+IEEFE+ ARDTKLG EEITRD
Sbjct: 597 LALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSIYIEEFELTARDTKLGKEEITRD 656

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           IPNVSEE L N+ E G++ +GAEV PGDI
Sbjct: 657 IPNVSEEVLANLGEDGVVRIGAEVKPGDI 685


>gi|209395053|gb|ACI45334.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395056|gb|ACI45336.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  537 bits (1383), Expect = e-150,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL   IAP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAGIAPLKRNVEGLQAAFDAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+  ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTARHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++   YI  TL TD+ +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQTLRTDETQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395125|gb|ACI45382.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  537 bits (1383), Expect = e-150,   Method: Composition-based stats.
 Identities = 205/488 (42%), Positives = 317/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQKDKAPQKRAVEGLQAAFNAAFPIVSHNGFVEMKFIEYSLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFDNDNFRLMDSGAQMEFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++   KF+ +  D L G  VA +IV+ +TGEI  +
Sbjct: 240 ITD-QSGKLIVAKDKRVTARHTRELEQSDSKFISVPEDFLIGRVVARNIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R +  +Y + ++  AYI NTL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRQLQCIYTNELDQGAYIANTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395059|gb|ACI45338.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  537 bits (1383), Expect = e-150,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 313/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL   IAP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAGIAPLKRNVEGLQAAFDAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAXMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+  ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTARHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L ++  + + D+  +Y + ++   YI  TL TD+ +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLRKLRGAGVPDVQCIYTNELDQGPYISQTLRTDETQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|34595755|gb|AAQ76600.1| RpoB [Mycobacterium abscessus]
          Length = 1171

 Score =  536 bits (1382), Expect = e-150,   Method: Composition-based stats.
 Identities = 305/949 (32%), Positives = 457/949 (48%), Gaps = 136/949 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNE----GLQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      +    R       GL+     + PI 
Sbjct: 32  RLSFAKLREPLAVPGLLDVQTESFEWLVGSPRWREVATARGEVNPTGGLEEILTELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 201 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 260

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
              P  A   +            ++ + ++E+   K+    L +  + K  K LG     
Sbjct: 261 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLG----- 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G   A+      T E  +        + L  +   +                 +    
Sbjct: 316 LGGTNPAQVTTTTLTEEDVVA-----TIEYLVRLHEGQTT---------------MTAPG 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +   D  D      R +R            +         +  LS + RV        
Sbjct: 356 GVEVPVDVDDIDHFGNRRLR--------TVGELIQN----QIRVGLSRMERVVRERMTTQ 403

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       I  + +I I  ++  ++   GT      +      S     +    LG   +
Sbjct: 404 DVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGL 459

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R      + +++  V P       P+ +             +   VN    I       
Sbjct: 460 TRD----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI------- 508

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              +    +   GV   ++H           T++  +  +V+   S    N     E   
Sbjct: 509 ---ETPYRKVSDGVVTDEIH---------YLTADEEDRHVVAQANSPVDANGRFTEE--- 553

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+   +   +V ++SA E                                       +D
Sbjct: 554 -KILVRRKGGEVEFVSATE---------------------------------------VD 573

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 574 YMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 633

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +G  +VA++AG++E+V A  + + + +G           YRL KF RSN  TC NQ+P+V
Sbjct: 634 AGDVVVAEKAGVIEEVSADYVTVMADDGTRQS-------YRLRKFARSNHGTCANQKPIV 686

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G  V    +IADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSI
Sbjct: 687 DEGQRVEAGQVIADGPCTENGEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVLTSI 746

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 747 HIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKG 806

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 807 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 855



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 264/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +        +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149


>gi|209395050|gb|ACI45332.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  536 bits (1381), Expect = e-150,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL   IAP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAGIAPLKRNVEGLQAAFDAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+  ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTARHIRELEQSGTTHVSVPEDFLVGRVVARGIVDTDTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++   YI  TL TD+ +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQTLRTDETQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKSNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   +++ +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAELEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395044|gb|ACI45328.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  536 bits (1380), Expect = e-149,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADTAPLKRSIEGLQAAFNAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTVRHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEVLLKKLRGAGVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A++KIL
Sbjct: 359 GEPPTEDAEQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR+GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRIGLARIEKAVKERLGQAEQEPLMPPDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|162286182|gb|AAT86005.2| RpoB [Mycobacterium massiliense]
          Length = 1171

 Score =  536 bits (1380), Expect = e-149,   Method: Composition-based stats.
 Identities = 304/949 (32%), Positives = 457/949 (48%), Gaps = 136/949 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNE----GLQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      +    R       GL+     + PI 
Sbjct: 32  RLSFAKLREPLAVPGLLDVQTESFEWLVGSPRWREVATARGEVNPTGGLEEILTELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 201 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 260

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
              P  A   +            ++ + ++E+   K+    L +  + K  K LG     
Sbjct: 261 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLG----- 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G   A+      T E  +        + L  +   +                 +    
Sbjct: 316 LGGTNPAQVTTTTLTEEDVVA-----TIEYLVRLHEGQTT---------------MTAPG 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +   D  D      R +R            +         +  LS + RV        
Sbjct: 356 GVEVPVDVDDIDHFGNRRLR--------TVGELIQN----QIRVGLSRMERVVRERMTTQ 403

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       I  + +I I  ++  ++   GT      +      S     +    LG   +
Sbjct: 404 DVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGL 459

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R      + +++  V P       P+ +             +   VN    I       
Sbjct: 460 TRD----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI------- 508

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              +    +   GV   ++H           T++  +  +V+   S    N     E   
Sbjct: 509 ---ETPYRKVSDGVVTDEIH---------YLTADEEDRHVVAQANSPVDANGRFTEE--- 553

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+   +   +V ++SA E                                       +D
Sbjct: 554 -KILVRRKGGEVEFVSATE---------------------------------------VD 573

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 574 YMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 633

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +G  +VA++AG++E+V A  + + + +G           YRL KF RSN  TC NQ+P+V
Sbjct: 634 AGDVVVAEKAGVIEEVSADYVTVMADDGTRQS-------YRLRKFARSNHGTCANQKPIV 686

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G  V    ++ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSI
Sbjct: 687 DEGQRVEAGQVVADGPCTENGEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVLTSI 746

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 747 HIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKG 806

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 807 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 855



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 266/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEAGQVVADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+      +                   
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +    +   +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149


>gi|157060656|gb|ABV03334.1| RpoB [Chlamydia trachomatis]
          Length = 683

 Score =  536 bits (1380), Expect = e-149,   Method: Composition-based stats.
 Identities = 334/747 (44%), Positives = 459/747 (61%), Gaps = 75/747 (10%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR---RRKV 212
           Q+HRSPGI+F+ +K      G +L++ RIIP +G W++  FD  D+I++ IDR   RRK+
Sbjct: 1   QVHRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWLEAVFDINDLIYIHIDRKKRRRKI 57

Query: 213 PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
              +F+ ALG  ++ +I+  F+     S                                
Sbjct: 58  LAMTFIRALGYSTDADIIEEFFSVEERSL------------------------------- 86

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
                           L++  V         L G  +A+++V+ ++  +Y +AG+ +   
Sbjct: 87  ---------------RLEKDFVA--------LVGKVLADNVVDADSSLVYGKAGEKLSTA 123

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ I  + ++ + I      + N  I   L  D     + AL D YR +RPG+ +T   
Sbjct: 124 MLKRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDSYEAALKDFYRRLRPGEPATLVN 181

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD---VRHIRKEDIIAIIKILVDLRN 448
           A S    LFFD+ +Y+L  VGR K+N +L     D+      +RKED+I  +K L+ LR 
Sbjct: 182 ARSTIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETLSQVTLRKEDVIGALKYLIRLRM 241

Query: 449 G--KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLI 504
           G  K +IDDID+L NRRVRSVGE+++N  R GL RME+ ++ER++  D   D++ P  +I
Sbjct: 242 GDEKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEKIVRERMNLFDFSSDTLTPGKII 301

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +AK +VS + +FF  SQLSQ  +  N +  +TH RRLSALG GG+ R RAG E+RDVH +
Sbjct: 302 SAKGLVSVLKDFFSRSQLSQFMDQTNPVVELTHKRRLSALGPGGLNRERAGFEVRDVHAS 361

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL+SFA++N +GFIETPYR V DG VT+++ Y++A  EE 
Sbjct: 362 HYGRICPIETPEGPNIGLITSLSSFAKINEFGFIETPYRVVRDGIVTDEIEYMTADVEEE 421

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++ LDE   F   + + R  GE        +  +D SPKQ+VS+   LIPFLE+
Sbjct: 422 CVIAQASAELDEYDMFKTPVCWARYKGEAFEADTSTVTHMDVSPKQLVSVVTGLIPFLEH 481

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK EA  VGTG+E   AK SGA IVA+  G+VE VD+  IV
Sbjct: 482 DDANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKDSGAIIVAQEDGVVEYVDSYEIV 541

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +              D Y+L KF RSN  TC+NQ PL  VGD V   D++ADGP+TD G+
Sbjct: 542 VAKKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLCSVGDVVTHGDVLADGPATDKGE 596

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI+IEEFE+ ARDTKLG EEITRD
Sbjct: 597 LALGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSIYIEEFELTARDTKLGKEEITRD 656

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPG 891
           IPNVSEE L N+ E G++ +GAEV PG
Sbjct: 657 IPNVSEEVLANLGEDGVVRIGAEVKPG 683


>gi|229544473|gb|ACQ76414.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  536 bits (1380), Expect = e-149,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 313/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL   IAP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAGIAPLKRNVEGLQAAFDAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+  ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTARHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y   ++   YI  TL TD+ +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTSELDQGPYISQTLRTDETQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGXAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|269962520|ref|ZP_06176868.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269832715|gb|EEZ86826.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 425

 Score =  535 bits (1379), Expect = e-149,   Method: Composition-based stats.
 Identities = 169/429 (39%), Positives = 263/429 (61%), Gaps = 9/429 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG  P+++DIP L+ +Q  S+D F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D   G  ++
Sbjct: 57  FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  SEEIL  F+ K+ +  + 
Sbjct: 175 RVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSEEILDIFFEKVNFEVKD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                 L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + 
Sbjct: 235 QTLLMELVP-DRLRGETASFDIE--ANGKTYVEQGRRVTARHIRQLEKDGVDHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G   ++D +N  TGEI + A   I  ++L  +  +  + +  L+ + +++  ++  TL
Sbjct: 292 IVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKSLETLFTNDLDHGPFMSETL 351

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  
Sbjct: 352 RIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGR 411

Query: 423 DTPDDVRHI 431
           +   +   +
Sbjct: 412 EDAQEQGTL 420


>gi|320160408|ref|YP_004173632.1| DNA-directed RNA polymerase beta chain [Anaerolinea thermophila
           UNI-1]
 gi|319994261|dbj|BAJ63032.1| DNA-directed RNA polymerase beta chain [Anaerolinea thermophila
           UNI-1]
          Length = 1314

 Score =  535 bits (1378), Expect = e-149,   Method: Composition-based stats.
 Identities = 312/968 (32%), Positives = 464/968 (47%), Gaps = 98/968 (10%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MA  +         K + + P + D+PDLI+VQ  S+               EGL   F 
Sbjct: 1   MASELTTT------KSYARIPVVFDLPDLIDVQVDSFKRL----------KQEGLIDLFD 44

Query: 61  SVFPITAFSGAAMLEF-----------VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
            + PI +++    L F           +   F  PK  +++C+ +DLTYA PL + + L 
Sbjct: 45  EISPIESYNKGMKLYFPGRSPEAQQFNLRIRFGEPKHSIEECVEKDLTYASPLYVGVLL- 103

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
                       + +   Q I++GD P MT  GTF+I G +R+VVSQL RSPG++FD   
Sbjct: 104 --------AGPEVPEPIRQEIFLGDFPEMTDKGTFIINGTERVVVSQLIRSPGVYFDAPV 155

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-----GMD 224
            R   +G+ L   ++IPD+G WM+ E    D + ++ +R+R VP+T FL AL     G+ 
Sbjct: 156 DR--ATGRRLAMAKLIPDRGAWMEFETRKNDYLILKFNRKRTVPITIFLRALAAVDDGLG 213

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
            E  +     + + +   D      +   L + + +    V   TG   I     L    
Sbjct: 214 GESPIKEGTDEELLALFQD---VDNNPERLFIVSTMRQEPVWDLTGGLTIAQAALL--EF 268

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            K ++      L      L      +   + E     +    +  +  L +      R I
Sbjct: 269 FKRMRPGDPATLENARQFLEEQLFDQRHYDLER----VGRYKLNQKLDLSDKIPVTHRTI 324

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
               + ++     + N    DK+       L   RV   G++    +   +        +
Sbjct: 325 TKWDILNLIRRMILINNEREDKD---DIDHLGNRRVKTVGELIQNKLRIGLRRMERVIKE 381

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL--GNR 462
           +  +                  D   +    ++ I  ++  LR   G+      +   N 
Sbjct: 382 RMSIR-----------------DQEQVTPMSLVNIRPVVAALREFFGSSQLSQFMDQTNP 424

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
                 +   +    G LR ER+        D+  V         P+ +           
Sbjct: 425 LAELRHKRTLSALGPGGLRRERA------GFDVRDVHHSHYGRICPIETPEGPNIGLIGR 478

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                 VN    I    R          +   G ++R+           A   E     +
Sbjct: 479 LATFSRVNEYGFIETPYRRVIKSLSSKDKRLVGRKLRETLTDPETGEVIAREGERVTAEM 538

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + ++    +   +              V+ DV YLSA  E+   IAQANS L+E   F +
Sbjct: 539 LPAIQKLNKTTIFVVP----------FVSEDVEYLSADAEDKFMIAQANSLLNEYNEFIQ 588

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           + + CR   +      + I+++D +P QVV I+A+LIPFLE+DD+NR LMG NMQ QAVP
Sbjct: 589 DRISCRYHSDFTEASPDSINYMDVAPNQVVGISAALIPFLEHDDANRALMGSNMQAQAVP 648

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L++ E P V TGME   A+ SG  +VA+  G V  V+  +I++R        ++SGV +Y
Sbjct: 649 LVRPEIPIVSTGMELYAARDSGQVLVAEEDGEVISVNGRQILLR--------TSSGVRVY 700

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +L K+QRSNQ+TC++QRP V  G  VR+ D++AD  ST  G+LALG+N++VAF+ W G N
Sbjct: 701 QLRKYQRSNQSTCIDQRPAVHKGQIVRKGDVLADSSSTVNGNLALGQNVVVAFLSWEGGN 760

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           FED++LISER+V +D FTS+HIE++EV ARDTKLGPEEITRDIPNV E+ +K++DE GII
Sbjct: 761 FEDAILISERLVQDDKFTSVHIEKYEVEARDTKLGPEEITRDIPNVGEDAIKDLDENGII 820

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +GAEV P DILVGKITPKGE  +TPEE+LLRAIFGEK+ DV+DTSLR+P G  G VVDV
Sbjct: 821 RIGAEVGPNDILVGKITPKGEKELTPEERLLRAIFGEKSRDVKDTSLRMPHGERGKVVDV 880

Query: 943 RIFNRHGI 950
           ++F R   
Sbjct: 881 KVFTRQDN 888



 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 260/983 (26%), Positives = 411/983 (41%), Gaps = 101/983 (10%)

Query: 263  SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC-------LCGLYVAEDIVNG 315
            + VD  TG ++  +      G     + +   +L +  +        +    +A  + +G
Sbjct: 153  APVDRATGRRLAMAKLIPDRGAWMEFETRKNDYLILKFNRKRTVPITIFLRALAA-VDDG 211

Query: 316  ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              GE  I+      ++ L  +F     +   L++ S      + +  +T      + ALL
Sbjct: 212  LGGESPIK---EGTDEELLALFQDVDNNPERLFIVSTMRQEPVWD--LTGGLTIAQAALL 266

Query: 376  DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL--DTPDDVRHIRK 433
            + ++ MRPGD +T   A        FD   YDL  VGR K+N +L+L    P   R I K
Sbjct: 267  EFFKRMRPGDPATLENARQFLEEQLFDQRHYDLERVGRYKLNQKLDLSDKIPVTHRTITK 326

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             DI+ +I+ ++ + N +   DDID+LGNRRV++VGE+++N+ R+GL RMER IKER+S  
Sbjct: 327  WDILNLIRRMILINNEREDKDDIDHLGNRRVKTVGELIQNKLRIGLRRMERVIKERMSIR 386

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            D + V P  L+N +PVV+A+ EFF SSQLSQ  +  N L+ + H R LSALG GG+ R R
Sbjct: 387  DQEQVTPMSLVNIRPVVAALREFFGSSQLSQFMDQTNPLAELRHKRTLSALGPGGLRRER 446

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            AG ++RDVH +HYGRICP ET EG NIGL+  L +F+RVN YGFIETPYR+V        
Sbjct: 447  AGFDVRDVHHSHYGRICPIETPEGPNIGLIGRLATFSRVNEYGFIETPYRRV-------- 498

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            +  LS+ ++               G    E +     GE I    E++        Q ++
Sbjct: 499  IKSLSSKDK------------RLVGRKLRETLTDPETGEVIAREGERVTAEMLPAIQKLN 546

Query: 674  IAASLIPFLENDDSNRVLMGCN---MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
                 +    ++D   +        M  QA  LL     F+   +               
Sbjct: 547  KTTIFVVPFVSEDVEYLSADAEDKFMIAQANSLLNEYNEFIQDRISCRYHSD-------- 598

Query: 731  RAGIVEQVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR-PLVKVGDEV 788
                    D+   + +   +     +     +      +    +    Q  PLV+    +
Sbjct: 599  --FTEASPDSINYMDVAPNQVVGISAALIPFLEHDDANRALMGSNMQAQAVPLVRPEIPI 656

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                      ST +   A   +  V      G    + + ++ R +     + + + +  
Sbjct: 657  ---------VSTGMELYAARDSGQVLVAEEDG----EVISVNGRQILLRTSSGVRVYQLR 703

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
               R  +                    ID+   +  G  V  GD+L    +      +  
Sbjct: 704  KYQRSNQST-----------------CIDQRPAVHKGQIVRKGDVLADSSSTVN-GNLAL 745

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             + ++ A    +  +  D  L         V D +  + H     E+     R+      
Sbjct: 746  GQNVVVAFLSWEGGNFEDAILI----SERLVQDDKFTSVHI----EKYEVEARDTKLGPE 797

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                D   + +  I       +    A  GP       +         P  +  +    +
Sbjct: 798  EITRDIPNVGEDAIKDLDENGIIRIGAEVGPNDILVGKITPKGEKELTPEERLLRAIFGE 857

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            +       SL++ +     +++     K+   Q   D+P GV  +V+V VA +R I +GD
Sbjct: 858  KSRDVKDTSLRMPHGERGKVVD----VKVFTRQDNTDLPAGVDMMVRVSVAQRRKITAGD 913

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR++P EDMPFL+DGTPVDI+LNPLGVP RMN+GQ+ ETHLGWA + L
Sbjct: 914  KMAGRHGNKGVVSRVVPVEDMPFLEDGTPVDIILNPLGVPGRMNIGQVLETHLGWAAMRL 973

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  + + D     +I    +    +      T   +           E ++       
Sbjct: 974  GFRAITPVFDGANETEIEAELARAYLIDLAWKETADAAWQWVKEQDVTPETFRDD----- 1028

Query: 1209 PVFDGADEEAINSMLRMADLDES 1231
               D      I   L     D  
Sbjct: 1029 ---DEVRALYIQQWLGERGYDMD 1048



 Score =  297 bits (761), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 81/147 (55%), Positives = 105/147 (71%)

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L DG TGE +D+PVTVG + M+KL+H+V DKV+ARSTG YSLVTQQPLGGK+  GG
Sbjct: 1139 GKQRLRDGKTGEFYDQPVTVGVMTMMKLHHLVEDKVHARSTGPYSLVTQQPLGGKAQFGG 1198

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAA+ LQEMLT+KSDDV GR   YE+IV      E   P +F VLV
Sbjct: 1199 QRFGEMEVWALEAYGAAHTLQEMLTVKSDDVQGRVATYEAIVKNEPIEEPSIPAAFRVLV 1258

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIP 1378
            KE+Q+LG++++      +     ++  
Sbjct: 1259 KELQSLGVAVEAIMENGEVVRFGKDEE 1285


>gi|157060652|gb|ABV03332.1| RpoB [Chlamydia trachomatis]
          Length = 684

 Score =  535 bits (1378), Expect = e-149,   Method: Composition-based stats.
 Identities = 335/747 (44%), Positives = 459/747 (61%), Gaps = 75/747 (10%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR---RRKVPV 214
           HRSPGI+F+ +K      G +L++ RIIP +G W++  FD  D+I++ IDR   RRK+  
Sbjct: 2   HRSPGINFEQEK---HSKGNVLFSFRIIPYRGSWLEAVFDINDLIYIHIDRKKRRRKILA 58

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            +F+ ALG  ++ +I+  F+     S                                  
Sbjct: 59  MTFIRALGYSTDADIIEEFFSVEERSL--------------------------------- 85

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
                         L++  V         L G  +A+++V+ ++  +Y +AG+ +    L
Sbjct: 86  -------------RLEKDFVA--------LVGKVLADNVVDADSSLVYGKAGEKLSTAML 124

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
           + I  + ++ + I      + N  I   L  D     + AL D YR +RPG+ +T   A 
Sbjct: 125 KRILDAGVQSLKIAV--GADENHPIIKMLAKDPTDSYEAALKDFYRRLRPGEPATLVNAR 182

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD---VRHIRKEDIIAIIKILVDLRNG- 449
           S    LFFD+ +Y+L  VGR K+N +L     D+      +RKED+I  +K L+ LR G 
Sbjct: 183 STIMRLFFDAKRYNLGRVGRYKLNKKLGFPLDDETLSQVTLRKEDVIGALKYLIRLRMGD 242

Query: 450 -KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINA 506
            K +IDDID+L NRRVRSVGE+++N  R GL RME+ ++ER++  D   D++ P  +I+A
Sbjct: 243 EKTSIDDIDHLANRRVRSVGELIQNHCRSGLARMEKIVRERMNLFDFSSDTLTPGKIISA 302

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           K +VS + +FF  SQLSQ  +  N +  +TH RRLSALG GG+ R RAG E+RDVH +HY
Sbjct: 303 KGLVSVLKDFFSRSQLSQFMDQTNPVVELTHKRRLSALGPGGLNRERAGFEVRDVHASHY 362

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GRICP ET EG NIGL++SL+SFA++N +GFIETPYR V DG VT+++ Y++A  EE   
Sbjct: 363 GRICPIETPEGPNIGLITSLSSFAKINEFGFIETPYRVVRDGIVTDEIEYMTADVEEECV 422

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++ LDE   F   + + R  GE        +  +D SPKQ+VS+   LIPFLE+DD
Sbjct: 423 IAQASAELDEYDMFKTPVCWARYKGEAFEADTSTVTHMDVSPKQLVSVVTGLIPFLEHDD 482

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVPLLK EA  VGTG+E   AK SGA IVA+  G+VE VD+  IV+ 
Sbjct: 483 ANRALMGSNMQRQAVPLLKTEAAIVGTGLEGRAAKDSGAIIVAQEDGVVEYVDSYEIVVA 542

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                        D Y+L KF RSN  TC+NQ PL  VGD V   D++ADGP+TD G+LA
Sbjct: 543 KKNNPTLK-----DRYQLKKFLRSNSGTCINQTPLCSVGDVVTHGDVLADGPATDKGELA 597

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW+GYNFED+++ISER++ +D +TSI+IEEFE+ ARDTKLG EEITRDIP
Sbjct: 598 LGKNVLVAFMPWYGYNFEDAIIISERLIKQDAYTSIYIEEFELTARDTKLGKEEITRDIP 657

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDI 893
           NVSEE L N+ E G++ +GAEV PGDI
Sbjct: 658 NVSEEVLANLGEDGVVRIGAEVKPGDI 684


>gi|209395062|gb|ACI45340.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  535 bits (1377), Expect = e-149,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 312/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL    AP +R  EGLQAAF + FPI + +G   + ++ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAEKAPQKRNVEGLQAAFDAAFPIVSHNGFVEMRYLEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  +++ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTVRHIRELEQSGTSHVSVPEDFLVGRVVARGVIDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEAPLKKLRGANVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|86605128|ref|YP_473891.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp.
           JA-3-3Ab]
 gi|109914402|sp|Q2JX64|RPOB_SYNJA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|86553670|gb|ABC98628.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp.
           JA-3-3Ab]
          Length = 1133

 Score =  535 bits (1377), Expect = e-149,   Method: Composition-based stats.
 Identities = 329/687 (47%), Positives = 461/687 (67%), Gaps = 10/687 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 125 INGAERVIVNQIVRSPGVYYKSELDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 184

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   DS+ +  + + T+  + +   ++AL+++YR +RPG+ 
Sbjct: 185 TRKLSAAVLLKALGLSDSEI--YDSLRHPEFFQKTMEKEGHYSEEEALMELYRKLRPGEP 242

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD  +YDL  VGR K+N +LNL+  ++VR +   DI+A+I  L++L
Sbjct: 243 PTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLNLNVAENVRVLTVTDILAVIDYLINL 302

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + +++ P  L+N 
Sbjct: 303 EYDIGHVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESENLTPASLVNP 362

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG  +RD+HP+HY
Sbjct: 363 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFAVRDIHPSHY 422

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGFIE+PY +V +G V  D+  VYL+A EE+ 
Sbjct: 423 GRICPIETPEGPNAGLIGSLATHARVNQYGFIESPYYRVENGVVRKDLGMVYLTADEEDE 482

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +  +D +G  T +LV  R   E       ++ ++  SP Q++S+A SLIPFLE+
Sbjct: 483 YRVAPGDVPVDAEGRITADLVPVRYRQEFTTAHPSEVHYVQVSPVQLISVATSLIPFLEH 542

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK + P+VGTG+E+  A+ SG  +V++ +G+V  V A  IV
Sbjct: 543 DDANRALMGANMQRQAVPLLKPDRPYVGTGLEAQAARDSGMVVVSRTSGVVTYVSADEIV 602

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  +G          +YRL K+QRSNQ+TC+NQRPLV  GD V    ++ADGP+T+ G+
Sbjct: 603 VRPDDG------GDPIVYRLQKYQRSNQDTCLNQRPLVYAGDRVVPGQVLADGPATEGGE 656

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DVFTS+HIE++E+ AR TKLGPEEITR+
Sbjct: 657 LALGQNVLVAYMPWEGYNYEDAILISERLVYDDVFTSVHIEKYEIEARQTKLGPEEITRE 716

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GI+ +GA V  GDILVGK+TPKGES   PEE+LLRAIFGEKA DV
Sbjct: 717 IPNVGEDALRNLDENGIVRIGAWVEAGDILVGKVTPKGESDQPPEERLLRAIFGEKARDV 776

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVRIF R   D
Sbjct: 777 RDNSLRVPNGERGRVVDVRIFTREQGD 803



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/586 (32%), Positives = 268/586 (45%), Gaps = 62/586 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P+ G   E        MV  S       ++   E++ R    G
Sbjct: 550  MGANMQRQAVPLLKPDRPYVGTGLEAQAARDSGMVVVSRTSGVVTYVSADEIVVRPDDGG 609

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
               + R            +++  ++  G  V PG +L      +G   +   + +L A  
Sbjct: 610  DPIVYRLQKYQRSNQDTCLNQRPLVYAGDRVVPGQVLADGPATEG-GELALGQNVLVAYM 668

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD--- 972
              +  +  D  L     V   V       ++ I+  +  +  E    +I  +  D     
Sbjct: 669  PWEGYNYEDAILISERLVYDDVFTSVHIEKYEIEARQTKLGPEEITREIPNVGEDALRNL 728

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 729  DENGIVRIGAWVEAGDILVGKVTPKGESDQPPEERLLRAIFGEKARDVRDN--------- 779

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                                   +I   + GD++PPG   VV+V++A+KR IQ GDK+AG
Sbjct: 780  --------SLRVPNGERGRVVDVRIFTREQGDELPPGANMVVRVYIALKRKIQVGDKIAG 831

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+SRILP EDMP+L DGTPVD+VLNPLGVPSRMNVGQ++E  LGWA   LG + 
Sbjct: 832  RHGNKGIISRILPIEDMPYLADGTPVDVVLNPLGVPSRMNVGQVYECLLGWAAEHLGVRF 891

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K +  D     + S L    +                                       
Sbjct: 892  KLMPFDEMHGLEASRLTVEAKLRE------------------------------------ 915

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
             A E+     +   +    G+  ++DG TGEPFD+PVTVG  YMLKL H+V DK++ARST
Sbjct: 916  -AREKTGKDWIFNPEGKYCGKIQVFDGRTGEPFDQPVTVGRAYMLKLVHLVDDKIHARST 974

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY+LQE+LT+KSDD+VGR     +I
Sbjct: 975  GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYILQELLTVKSDDMVGRNEALNAI 1034

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      GTPESF VLV+E+Q+L L + +      +  +  ++ 
Sbjct: 1035 VKGKPIPRPGTPESFKVLVRELQSLCLDVSVHKVEVDSDGQTRDVE 1080



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 97/465 (20%), Positives = 189/465 (40%), Gaps = 50/465 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV-------- 77
           +PDL+E+Q+ S+  FL           EG +    S  PI  ++G   L F+        
Sbjct: 14  LPDLVEIQRESFLWFLR----------EGFEEELLSFSPIVDYTGKLELHFLPEYRPGDP 63

Query: 78  --SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
              Y+ + P++D ++   RD TY   +++  RLI          K   +IK+  +++G+L
Sbjct: 64  SKGYKINKPRYDPEEAKRRDATYQAQIRVPTRLI---------NKETGEIKDMDVFIGEL 114

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT  GTF+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E
Sbjct: 115 PLMTDRGTFIINGAERVIVNQIVRSPGVYYKSELDK---NGRRTYSASLIPNRGAWLKFE 171

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLS 250
            D   ++ VRID+ RK+     L ALG+   EI        F+ K   +   +       
Sbjct: 172 TDKNGLVWVRIDKTRKLSAAVLLKALGLSDSEIYDSLRHPEFFQK---TMEKEGHYSEEE 228

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYV 308
           A   +           +  G+Q++ES         L +  + K  K L +       +  
Sbjct: 229 ALMELYRKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLNLNVAENVRVLT 288

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
             DI+      I +E  D+     ++ + +  +R +  L  + V         ++ ++  
Sbjct: 289 VTDILAVIDYLINLE-YDIGHVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMT 347

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             +   L    ++ P      +  +  F            + +  +    RL+   P   
Sbjct: 348 VSESENLTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG- 404

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             + +E     ++ +     G+  I  I+         +G +  +
Sbjct: 405 --LSRERAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 445


>gi|297250921|ref|ZP_06934376.1| DNA-directed RNA polymerase, beta subunit [Neisseria polysaccharea
            ATCC 43768]
 gi|296837682|gb|EFH21620.1| DNA-directed RNA polymerase, beta subunit [Neisseria polysaccharea
            ATCC 43768]
          Length = 303

 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 174/305 (57%), Positives = 219/305 (71%), Gaps = 15/305 (4%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDIVLNPLGVPSRMN
Sbjct: 1    MVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVPSRMN 60

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI E HLGWA  G+G++I  ++   K     S LR FL K+       E +    D+ 
Sbjct: 61   IGQILEVHLGWAAKGIGERIDRML---KEQRKASELREFLNKLYNGSGKKEDLDSLTDEE 117

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DLDES-GQSILYDGL 1240
            ++ +A   + G   ++PVFDGA E  I  ML +A             ++S  Q  LYDG 
Sbjct: 118  IIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGFNDSKTQITLYDGR 177

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 178  SGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 237

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESFNVLVKE+++LGL 
Sbjct: 238  ALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESFNVLVKEIRSLGLD 297

Query: 1361 IDLEN 1365
            IDLE 
Sbjct: 298  IDLER 302


>gi|209395116|gb|ACI45376.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  534 bits (1376), Expect = e-149,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 311/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRNTEGLQAAFDAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++L ++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLFIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPEAILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + +++ G   + +  D L G  VA  +V+ ETGEI  +
Sbjct: 240 VTD-KSGKVIVAKDKRVTARHTREIEQSGSTHISVPEDFLIGRVVARSVVDAETGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A + + E  L+++  + ++D+  +Y + ++  AYI  TL  D+  D   A + IYR+MRP
Sbjct: 299 ANEELTETLLKKLRSAAVQDLQCIYTNELDQGAYISQTLRIDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N  +          +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNATIGRSESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLR G G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRTGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|269215188|ref|ZP_06159098.1| DNA-directed RNA polymerase, beta subunit [Neisseria lactamica ATCC
            23970]
 gi|269208104|gb|EEZ74559.1| DNA-directed RNA polymerase, beta subunit [Neisseria lactamica ATCC
            23970]
          Length = 303

 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 173/305 (56%), Positives = 218/305 (71%), Gaps = 15/305 (4%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKVF+A+KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDIVLNPLGVPSRMN
Sbjct: 1    MVKVFIAIKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVPSRMN 60

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI E HLGWA  G+G++I  ++   K       LR FL K+       E +    D+ 
Sbjct: 61   IGQILEVHLGWAAKGIGERIDRML---KEQRKAGELREFLNKLYNGSGKKEDLDSLTDEE 117

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----------DLDES-GQSILYDGL 1240
            ++ +A   + G   ++PVFDGA E  I  ML +A             ++S  Q  LYDG 
Sbjct: 118  IIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGFNDSKTQITLYDGR 177

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +GEPFDR VTVG ++ LKL+H+V +K++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 178  SGEPFDRKVTVGVMHYLKLHHLVDEKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 237

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAAY LQEMLT+KSDDV GRT++YE+IV G    + G PESFNVLVKE+++LGL 
Sbjct: 238  ALEAYGAAYTLQEMLTVKSDDVNGRTKMYENIVKGEHKIDAGMPESFNVLVKEIRSLGLD 297

Query: 1361 IDLEN 1365
            IDLE 
Sbjct: 298  IDLER 302


>gi|289644515|ref|ZP_06476589.1| DNA-directed RNA polymerase, beta subunit [Frankia symbiont of
           Datisca glomerata]
 gi|289505677|gb|EFD26702.1| DNA-directed RNA polymerase, beta subunit [Frankia symbiont of
           Datisca glomerata]
          Length = 1168

 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 340/683 (49%), Positives = 477/683 (69%), Gaps = 17/683 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +  + +K +    +      G ++  ++   +T  + I+         
Sbjct: 183 LVRSPGVYFEKTIDKVSDKDLFSCKVIPSR--GAWLEFEVDKRDTVGVRIDRKRRQSVTV 240

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 241 L--LKALGWDEARIL--ERFGDFPSMRVTLEKDHTSSQDDALLDIYRKLRPGEPPTRESA 296

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
           +++   LFF+  +YDL+ VGR K+N +L +D P DV  + ++DI+  I+ +V L  G+  
Sbjct: 297 QTLLENLFFNPKRYDLAKVGRYKVNKKLEVDVPHDVGVLTEDDIVRTIEYVVQLHAGRDS 356

Query: 452 --TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +PV
Sbjct: 357 SYDVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRPV 416

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           V+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+HYGR+
Sbjct: 417 VASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRM 476

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ET EG NIGL+ SL++FARVN +GF+ETPYRKV  G+VT+ + YL+A EE+   IAQ
Sbjct: 477 CPIETPEGPNIGLIGSLSTFARVNPFGFVETPYRKVVAGRVTDQIDYLTADEEDRHVIAQ 536

Query: 630 ANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           AN+ L  DGSF E  V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+N
Sbjct: 537 ANAPLSSDGSFAEHRVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDAN 596

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  +V  +AG+VE + A  I +   
Sbjct: 597 RALMGSNMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVVVCAQAGVVEDLSADYITVMHD 656

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           +G           YR+ KF+RSNQ TC+NQ+P+V  GD V    +IADGP TD G++ALG
Sbjct: 657 DGTR-------RTYRMAKFRRSNQGTCINQKPIVDEGDRVEAGQVIADGPCTDNGEMALG 709

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNV
Sbjct: 710 KNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNV 769

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           +EE L ++DE GII +GAEV+PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS
Sbjct: 770 AEEVLADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTS 829

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           L+VP G SG V+ VR+F+R   D
Sbjct: 830 LKVPHGESGKVIGVRVFSREDGD 852



 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 194/533 (36%), Positives = 272/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  G  V  G ++           M   + LL A
Sbjct: 657  DGTRRTYRMAKFRRSNQGTCINQKPIVDEGDRVEAGQVIADGPCTDN-GEMALGKNLLVA 715

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 716  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 773

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 774  LADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 826

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 827  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 882

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL DGTPVD+VLNP GVP RMN+GQI ETHLGW     G ++  
Sbjct: 883  GNKGVIAKILPAEDMPFLSDGTPVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDG 941

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                +K                                    A+Q      V+TPVFDGA
Sbjct: 942  GAEGWKERLRGIR-----------------------------ADQAPPNTNVATPVFDGA 972

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ L+DG TGEP+  PV VGYIY+LKL H+V DK
Sbjct: 973  REEEITGLLASTLPNRDGVQLIGASGKAELFDGRTGEPYPYPVAVGYIYILKLLHLVDDK 1032

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR 
Sbjct: 1033 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVLGRV 1092

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1093 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVSIEMRDTDED 1145



 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 114/477 (23%), Positives = 203/477 (42%), Gaps = 36/477 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +  +   +                 GL+  F+ 
Sbjct: 37  RISFAKIIEPLEVPDLLALQTQSFDWLIGSDAWAERVQEAIDAGRDDVPVTSGLEEVFEE 96

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK+ V++C  +D+TY+ P+ +T               +
Sbjct: 97  ISPIEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTYSAPMFVTAEFT---------NNT 147

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K L++
Sbjct: 148 TGEIKSQTVFMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFEKTIDKV--SDKDLFS 205

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  +P +  +
Sbjct: 206 CKVIPSRGAWLEFEVDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGDFPSMRVT 265

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K L 
Sbjct: 266 LEKDHTSSQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLE 325

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDV--IDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           +      G+   +DIV      + + AG     D   ++   +  +R +  L  + V   
Sbjct: 326 VDVPHDVGVLTEDDIVRTIEYVVQLHAGRDSSYDVDDIDHFGNRRLRTVGELIQNQVRLG 385

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                 +V ++   +   +  I            +  +  F            + +  + 
Sbjct: 386 LARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLT 443

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              RL+   P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 444 HKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGSLST 495


>gi|209395089|gb|ACI45358.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  534 bits (1375), Expect = e-149,   Method: Composition-based stats.
 Identities = 204/488 (41%), Positives = 316/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQKDKAPQKRAVEGLQAAFNAAFPIVSHNGFVEMKFIEYSLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++L ++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLFIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++   KF+ +  D L G  VA +IV+ +TGEI  +
Sbjct: 240 ITD-QSGKLIVAKDKRVTARHTRELEQSDSKFISVPEDFLIGRVVARNIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R +  +Y + ++  AYI NTL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRQLQCIYTNELDQGAYIANTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|213418179|ref|ZP_03351245.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E01-6750]
          Length = 411

 Score =  533 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 219/423 (51%), Positives = 295/423 (69%), Gaps = 13/423 (3%)

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA D
Sbjct: 2    DIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASD 61

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q++   +D  +E  IL+  ++
Sbjct: 62   VKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLF 121

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
            SR+  +L                   ++ + + PR +W +  + DE+ Q  +E L  QY+
Sbjct: 122  SRIRAVLVSGGV-------------EAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYD 168

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              K   E + + K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I
Sbjct: 169  ELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKI 228

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
             P EDMP+ ++GTPVDIVLNPLGVPSRMN+GQI ETHLG A  G+G KI +++   +   
Sbjct: 229  NPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVA 288

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             +         +         +S + DD VLR+AE  + G+P++TPVFDGA E  I  +L
Sbjct: 289  KLREFIQRAYDLGADVRQKVDLSTFSDDEVLRLAENLRKGMPIATPVFDGAKEAEIKELL 348

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            ++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPL
Sbjct: 349  KLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 408

Query: 1284 GGK 1286
            GGK
Sbjct: 409  GGK 411


>gi|325288570|ref|YP_004264751.1| DNA-directed RNA polymerase subunit beta [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324963971|gb|ADY54750.1| DNA-directed RNA polymerase subunit beta [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 1130

 Score =  533 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 344/604 (56%), Positives = 457/604 (75%), Gaps = 8/604 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           V+    +  I+ TL  D  +  ++AL++IY+ +RPG+  T   A S+   LFFD  +YDL
Sbjct: 206 VEVFEEDENIKVTLERDNTESTEEALVEIYKRLRPGEPPTVDSARSLLESLFFDPKRYDL 265

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
           + VGR K+N +LN+D    VR++ K D+IA +  L+++  G+G  DDID+LGNRR+RSVG
Sbjct: 266 AKVGRYKLNKKLNMDVESHVRNLTKGDVIAAVARLLEIMKGEGHRDDIDHLGNRRLRSVG 325

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ+R+GL RMER ++ER++  D++ + PQ LIN +PVV+A+ EFF SSQLSQ  + 
Sbjct: 326 ELLQNQFRIGLSRMERVVRERMTIQDVEGITPQVLINIRPVVAAIKEFFGSSQLSQFMDQ 385

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++
Sbjct: 386 TNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLST 445

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED-GSFTEELVFC 647
           + R+N YGFIE PYRKV  G+VT+++ YL+A EEE   IAQAN+ ++E+ G F  + +  
Sbjct: 446 YGRINEYGFIEAPYRKVAGGRVTDEIHYLTADEEEKYIIAQANAPINEETGEFLTDKIEA 505

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + +LVP   + ++D SPKQ+VSIA +LIPFLE+DD+NR LMG NMQRQAVPLLK +
Sbjct: 506 RRGEDFVLVPATSLQYMDVSPKQMVSIATALIPFLEHDDANRALMGSNMQRQAVPLLKTD 565

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP++GTGME   A  SG  I+A+++G V +V A  ++IR+ EG LD        YRL+K+
Sbjct: 566 APYIGTGMEYKTAVDSGVCILARKSGTVSRVTADEVIIRNNEGTLDK-------YRLLKY 618

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ TC+NQRP+VK GD + +  +IADGPSTD G+LALGRN+LVAFMPW GYN+ED++
Sbjct: 619 LRSNQGTCINQRPIVKKGDVLEKGQVIADGPSTDNGELALGRNVLVAFMPWEGYNYEDAI 678

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE++V ED FTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII +GAE
Sbjct: 679 LISEKLVREDYFTSIHIEEYEADARDTKLGPEEITRDIPNVGEDVLKDLDERGIIRIGAE 738

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F R
Sbjct: 739 VRPGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFKR 798

Query: 948 HGID 951
              D
Sbjct: 799 ENGD 802



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 177/589 (30%), Positives = 254/589 (43%), Gaps = 82/589 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +           Y       +          + +  +E   +      
Sbjct: 551  GSNMQRQAVPLLKTDAPYIGTGMEYKTAVDSGVCILARKSGTVSRVTADE---VIIRNNE 607

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  +       I++  I+  G  +  G ++    +      +     +L A 
Sbjct: 608  GTLDKYRLLKYLRSNQGTCINQRPIVKKGDVLEKGQVIADGPSTDN-GELALGRNVLVAF 666

Query: 917  FGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +  D  L      R     S  + +     R      E          E + +D
Sbjct: 667  MPWEGYNYEDAILISEKLVREDYFTSIHIEEYEADARDTKLGPEEITRDIPNVGEDVLKD 726

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE+ I+      R  +IL G+    G         L   +  E  R            
Sbjct: 727  L-DERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------ 773

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 E                   K+ K + GD++ PGV ++V+V++A KR +  GDKM
Sbjct: 774  -----EVRDTSLRVPHGEAGKIVDVKVFKRENGDELAPGVNQLVRVYIAQKRKVSVGDKM 828

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SRI+  EDMPFL           P G P         E  L    V    
Sbjct: 829  AGRHGNKGVISRIMRQEDMPFL-----------PNGTP--------IEIVLNPLGVPSRM 869

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             I  ++  +      +                                    G+ ++TPV
Sbjct: 870  NIGQVLETHLGWAAKAL-----------------------------------GLHIATPV 894

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FDGA E+ +   L  A L +SG+S+LYDG TGEPFD  VTVGY+YMLKL+H+V DK++AR
Sbjct: 895  FDGAREDDVIETLVKAGLPDSGKSVLYDGRTGEPFDNEVTVGYMYMLKLHHLVDDKIHAR 954

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE
Sbjct: 955  STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYE 1014

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +IV G +  E G PESF VL+KE+Q+LGL + + +   +     +   D
Sbjct: 1015 AIVKGENIPEPGVPESFKVLIKELQSLGLDVSVLSEENEEIEIRDADED 1063



 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 114/471 (24%), Positives = 204/471 (43%), Gaps = 45/471 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  + +  E++D+P+LIE+Q+ SY  FL          +EGL+  F  + PI  F+G 
Sbjct: 10  RERWSYSRLREVLDMPNLIELQQNSYKWFL----------DEGLREMFHDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK++V++C  RD+T+A PL++ +RL+          K   ++KEQ ++
Sbjct: 60  LVLEFIDYSLGEPKYEVEECKERDVTFAAPLRVKVRLM---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG+++   K     SGK LY   IIP++G W
Sbjct: 111 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYYSETKD---ASGKTLYGATIIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D I VR+DR RK+P T  + ALG  +  +I+  F          +      +
Sbjct: 168 LEFESDINDNIFVRVDRTRKLPATVLIRALGYTTNSQIVEVFEEDENIKVTLERDNTEST 227

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYV 308
              L+   K       +  GE   ++S + L   L    K   +  +G    +    + V
Sbjct: 228 EEALVEIYK------RLRPGEPPTVDSARSLLESLFFDPKRYDLAKVGRYKLNKKLNMDV 281

Query: 309 AEDIVNGETGEIYIE-------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              + N   G++                   ++ + +  +R +  L  +           
Sbjct: 282 ESHVRNLTKGDVIAAVARLLEIMKGEGHRDDIDHLGNRRLRSVGELLQNQFRIGLSRMER 341

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +V ++   +   +  I   +        +  +  F            + +  +    RL+
Sbjct: 342 VVRERMTIQD--VEGITPQVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLS 399

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 400 ALGPGG---LSRERAGFEVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 445


>gi|186469897|gb|ACC85601.1| DNA-dependent RNA polymerase beta chain [Brucella abortus bv. 3]
          Length = 457

 Score =  533 bits (1374), Expect = e-149,   Method: Composition-based stats.
 Identities = 296/458 (64%), Positives = 364/458 (79%), Gaps = 1/458 (0%)

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           KEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+I
Sbjct: 1   KEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVI 60

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
           P +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W
Sbjct: 61  PYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNW 120

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
             P SA     G K+ S LVD DTGE V+E+GKKLT+   K L EKG+K +  T D L G
Sbjct: 121 RIPYSAE-RFKGMKIISDLVDADTGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFG 179

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
            Y+AED+VN  TGEIY+EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  D
Sbjct: 180 SYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVD 239

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           KN+ R++AL DIYRVMRPG+  T   AE+MF+ LFFDS++YDLS VGRVKMNMRL+LD  
Sbjct: 240 KNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDLDAE 299

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           D VR +RKEDI+A++K+LV+LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+
Sbjct: 300 DTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERA 359

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 360 IKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 419

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 420 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 457


>gi|209395065|gb|ACI45342.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  533 bits (1373), Expect = e-149,   Method: Composition-based stats.
 Identities = 202/488 (41%), Positives = 310/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +   FL  + AP +R  EGLQAAF + FPI + +G   + F  Y    P
Sbjct: 1   EVPYLLQMQKDACTAFLQADTAPLKRSVEGLQAAFDAAFPIVSHNGFVEMRFTEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTVRHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|27262300|gb|AAN87431.1| DNA-directed RNA polymerase beta chain [Heliobacillus mobilis]
          Length = 1150

 Score =  533 bits (1373), Expect = e-149,   Method: Composition-based stats.
 Identities = 361/753 (47%), Positives = 494/753 (65%), Gaps = 38/753 (5%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQV------------I 274
           +     I YS     +                +V   L++ +TGE               
Sbjct: 54  NLILEFIDYSLGEPKYSVEECKERDVTFAAPLRVKVRLINKETGEVKEQEVFMGDFPLMT 113

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLC----GLYVAEDIVNGETGEIY--------- 321
           E G  + +G  + +  + V+  G+  +       G  V    +    G            
Sbjct: 114 EKGTFIINGAERVIVSQLVRSPGVYFNETTDPTSGKKVYGATMIPNRGAWLEFESDANDN 173

Query: 322 -IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                D   +     +  +      +   +  + +  IR TL  D  ++ ++AL++IY+ 
Sbjct: 174 VYVRIDRTRKLPATVLIRALGYSNNVQVHELFDGDERIRITLERDNTENTEEALVEIYKR 233

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPG+  T   A S+ + LFFD  +YDL+ VGR K+N RL L    ++RH+ K+DIIA +
Sbjct: 234 LRPGEPPTVDSARSLLDTLFFDPKRYDLAKVGRYKINKRLGLQIEKEIRHLTKDDIIATV 293

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           + ++ L  G+G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER++  D++ + P
Sbjct: 294 REMLKLMQGEGHADDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMTIQDVEVITP 353

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RD
Sbjct: 354 QVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRD 413

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLS 618
           VH +HYGR+CP ET EG NIGL+ SL++FAR+N +GFIETPYRKV   +  VT  + YL+
Sbjct: 414 VHHSHYGRMCPIETPEGPNIGLIGSLSTFARINEFGFIETPYRKVDKERGAVTEQIDYLT 473

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+   +AQAN+ LDE+G F ++ V  R   + ++VP E +D++D SPKQVVSIA +L
Sbjct: 474 ADEEDKFIVAQANAPLDEEGRFIQKKVNARHGHDILVVPMEMVDYMDVSPKQVVSIATAL 533

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPLL+ +AP+VGTGME   AK SG   +AK+ G++E+V
Sbjct: 534 IPFLEHDDANRALMGANMQRQAVPLLRTDAPYVGTGMEYKAAKDSGVVAIAKKPGVIERV 593

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               I+IRS +G L+        ++L+KF RSNQ TC+NQ+P+   G  V   DIIADGP
Sbjct: 594 SGDEIIIRSDDGTLEQ-------HKLLKFLRSNQGTCINQKPICHKGQRVEAGDIIADGP 646

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           STD G+LALGRN+LVAFM W GYN+ED++L++E++V ED FTSIHIEE+E  +RDTKLGP
Sbjct: 647 STDQGELALGRNVLVAFMTWEGYNYEDAILVNEKLVREDYFTSIHIEEYECDSRDTKLGP 706

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE LK++D+ GII VGAEV PGDILVGK+TPKGE+ +T EE+LLRAIFG
Sbjct: 707 EEITRDIPNVGEEVLKDLDDRGIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFG 766

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G +G +VDV++F+R   D
Sbjct: 767 EKAREVRDTSLRVPHGEAGKIVDVKVFSRENGD 799



 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/559 (34%), Positives = 263/559 (47%), Gaps = 87/559 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             +  G  E  + +  +       I++  I   G  V  GDI+    +   +  +     +
Sbjct: 601  RSDDGTLEQHKLLKFLRSNQGTCINQKPICHKGQRVEAGDIIADGPST-DQGELALGRNV 659

Query: 913  LRAIFGEKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            L A    +  +  D  L      R     S  + +    +R      E          E 
Sbjct: 660  LVAFMTWEGYNYEDAILVNEKLVREDYFTSIHIEEYECDSRDTKLGPEEITRDIPNVGEE 719

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            + +D DD   I+      R  +IL G+    G         L   +  E  R        
Sbjct: 720  VLKDLDDR-GIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------- 770

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E                   K+   + GD++ PGV ++V+ ++A KR I  
Sbjct: 771  ---------EVRDTSLRVPHGEAGKIVDVKVFSRENGDELAPGVNQLVRCYIAQKRKISQ 821

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRI+   +MP+L DGTPV+IVLNPLGVPSRMN+GQ+ E HLGWA  
Sbjct: 822  GDKMAGRHGNKGVISRIMAEAEMPYLPDGTPVEIVLNPLGVPSRMNIGQVLECHLGWASK 881

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             + +                                          +       + G+ V
Sbjct: 882  NIDR----------------------------------------GLLADGEPSGERGIRV 901

Query: 1207 STPVFDGADEEAINSMLRMADLDE----------------------SGQSILYDGLTGEP 1244
            +TPVFDGA EE I   L  A L E                       G++IL+DG TGEP
Sbjct: 902  ATPVFDGATEEDIYEFLTQARLPELAETAMSDARTEHMREIFPSIPLGKTILFDGRTGEP 961

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            FD P+TVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 962  FDNPITVGYMYVLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1021

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE+Q+LGL + + 
Sbjct: 1022 YGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGVPESFKVLIKELQSLGLDVKIL 1081

Query: 1365 NSRTKNSAKMEEIPDFNKC 1383
            +   +     E   D  + 
Sbjct: 1082 SEDEREIEIKEVEEDVAET 1100



 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 102/454 (22%), Positives = 190/454 (41%), Gaps = 44/454 (9%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L+++   S   FL          +EGL+  F+ + PI  F+G  +LEF+ Y    PK+ V
Sbjct: 22  LVKIPTNSELWFL----------DEGLREMFRDISPIQDFTGNLILEFIDYSLGEPKYSV 71

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
           ++C  RD+T+A PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF+I G
Sbjct: 72  EECKERDVTFAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTEKGTFIING 122

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQL RSPG++F+        SGK +Y   +IP++G W++ E D+ D ++VRIDR
Sbjct: 123 AERVIVSQLVRSPGVYFNETTDPT--SGKKVYGATMIPNRGAWLEFESDANDNVYVRIDR 180

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            RK+P T  + ALG  +  ++   F          +      +   L+   K       +
Sbjct: 181 TRKLPATVLIRALGYSNNVQVHELFDGDERIRITLERDNTENTEEALVEIYK------RL 234

Query: 268 DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             GE   ++S + L   L    K   +  +G                 ++ +D +     
Sbjct: 235 RPGEPPTVDSARSLLDTLFFDPKRYDLAKVGRYKINKRLGLQIEKEIRHLTKDDIIATVR 294

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           E+            ++ + +  +R +  L  +           +V ++   +   +  I 
Sbjct: 295 EMLKLMQGEGHADDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMTIQD--VEVIT 352

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
             +        +  +  F            + +  +    RL+   P     + +E    
Sbjct: 353 PQVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LSRERAGF 409

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            ++ +     G+  +  I+      +  +G +  
Sbjct: 410 EVRDVHHSHYGR--MCPIETPEGPNIGLIGSLST 441


>gi|209395098|gb|ACI45364.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  533 bits (1372), Expect = e-148,   Method: Composition-based stats.
 Identities = 202/488 (41%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  +  P +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKEPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLARP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +               L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVPERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ ++GEI  +
Sbjct: 240 ITD-KSGKLIVAKDKRVTARHTRDLEQSGSTHISVPEDFLVGRVVARTIVDTDSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R++  +Y + ++  AYI +TL +D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRELQCIYTNELDQGAYISHTLRSDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N R+  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|207721918|ref|YP_002252356.1| dna-directed rna polymerase beta chain (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
 gi|206587088|emb|CAQ17672.1| probable dna-directed rna polymerase beta chain (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
          Length = 587

 Score =  533 bits (1372), Expect = e-148,   Method: Composition-based stats.
 Identities = 179/445 (40%), Positives = 268/445 (60%), Gaps = 5/445 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               F    R+RK F K   +  +P L+  Q  SY  FL  +++  +R  EGLQAAF ++
Sbjct: 1   MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHVSVAQRKTEGLQAAFNAI 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61  FPIVSHNGLARMEFVSYHLSHPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118 KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D +FD KDI++ R+DRRRK+PVT  L ++G+  E+IL+ F+    ++ + 
Sbjct: 178 RIIPYRGSWLDFQFDPKDILYFRVDRRRKMPVTILLKSIGLTPEQILAHFFVFDNFTLKS 237

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           D          L  G      + D   G+ VIE  K++ +  ++ L   G K + +  D 
Sbjct: 238 DGALMEFVPERL-RGEVARFDISD-KNGKVVIEKDKRINAKHIRDLDAAGTKLISVPEDY 295

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G  +A++IV+ +TGE+   A D + E  LE++  + ++DI  LY + ++   Y+  TL
Sbjct: 296 LLGRVLAKNIVDPDTGEVLANANDELTEGVLEKLRDAGVKDIQTLYTNDLDQGPYMSQTL 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            TD   D+  A + IYR+MRPG+  T    E++F  LF++ D YDLS VGR+K+N RLN 
Sbjct: 356 RTDDTVDQTAARIAIYRMMRPGEPPTEDAVEALFQRLFYNEDSYDLSRVGRMKVNSRLNR 415

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLR 447
                   +  +DI+  IK+LV+LR
Sbjct: 416 SEGTGPMVLTDDDILDTIKLLVNLR 440


>gi|209395020|gb|ACI45312.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  532 bits (1371), Expect = e-148,   Method: Composition-based stats.
 Identities = 200/488 (40%), Positives = 318/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|260893380|ref|YP_003239477.1| DNA-directed RNA polymerase, beta subunit [Ammonifex degensii KC4]
 gi|260865521|gb|ACX52627.1| DNA-directed RNA polymerase, beta subunit [Ammonifex degensii KC4]
          Length = 1126

 Score =  532 bits (1371), Expect = e-148,   Method: Composition-based stats.
 Identities = 355/628 (56%), Positives = 461/628 (73%), Gaps = 33/628 (5%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +  +++ +I+ TL  D + ++++ALL+IY+ +RPG+      A ++   LFFD  +YDL 
Sbjct: 208 ELFDHDKFIQETLSRDPSTNQEEALLEIYKRLRPGEPPAVDNARALLESLFFDPKRYDLG 267

Query: 410 TVGRVKMNMRLNLDT------------------------PDDVRHIRKEDIIAIIKILVD 445
            VGR K+  +L                             + +R +  EDI+A I+ L+ 
Sbjct: 268 NVGRYKLFKKLGHGILYRFKQENGPQEWDPYLKKMVPKDREFIRELLPEDIVATIRYLLK 327

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           +  G+G +DDID+LGNRRVRSVGE+L+NQ+R+GL RMER ++ER++  D++ V PQ LIN
Sbjct: 328 VMRGEGQVDDIDHLGNRRVRSVGELLQNQFRIGLARMERVVRERMTIQDVEVVTPQVLIN 387

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +PVV+A+ EF  SSQLSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH +H
Sbjct: 388 IRPVVAAIKEFLGSSQLSQFMDQTNPLSELTHKRRISALGPGGLSRERAGFEVRDVHHSH 447

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEE 623
           YGRICP ET EG NIGL+ SLT++ARVN +GFIETPYR+V   + +VT+++VYL+A EEE
Sbjct: 448 YGRICPIETPEGPNIGLIGSLTTYARVNEFGFIETPYRRVDKENRRVTDEIVYLTADEEE 507

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IAQAN +LDE+G F E+ V  R  GE ++VP E++D +D SPKQV S+ ASLIPFLE
Sbjct: 508 QYVIAQANVALDEEGRFLEDRVSARYKGEILVVPVEEVDLVDVSPKQVFSVGASLIPFLE 567

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           NDD+NR LMG NMQRQAVPL++ EAP VGTG+E  VA+ +GA +VA+R+G V +V A  I
Sbjct: 568 NDDANRALMGANMQRQAVPLIRTEAPLVGTGIEEKVARDAGAVVVARRSGTVTKVTANEI 627

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
           VI + +G+ D        Y L KFQRSNQ TC+NQRP+VK GD V    +IADGP TD G
Sbjct: 628 VITTDDGETD-------RYSLRKFQRSNQGTCINQRPIVKRGDRVEAGQVIADGPCTDHG 680

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L+LGRN+LVAFMPW GYN+ED++LISE++V ED FTSIHIEE+E  ARDTKLGPEEITR
Sbjct: 681 ELSLGRNVLVAFMPWEGYNYEDAILISEKLVKEDFFTSIHIEEYECEARDTKLGPEEITR 740

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNV E+ LK++DE GII +GAEV PGDILVGK+TPKGE+ +T EE+LLRAIFGEKA +
Sbjct: 741 DIPNVGEDALKDLDERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKARE 800

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G SGTVVDV+IF+R   D
Sbjct: 801 VRDTSLRVPHGESGTVVDVKIFSRDKGD 828



 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 202/592 (34%), Positives = 268/592 (45%), Gaps = 80/592 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E+ +      +V      ++       +   T  G 
Sbjct: 576  MGANMQRQAVPLIRTEAPLVGTGIEEKVARDAGAVVVARRSGTVTKVTANEIVITTDDGE 635

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +               I++  I+  G  V  G ++           ++    +L A   
Sbjct: 636  TDRYSLRKFQRSNQGTCINQRPIVKRGDRVEAGQVIADGPCT-DHGELSLGRNVLVAFMP 694

Query: 919  EKAVDVRDTSL------RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
             +  +  D  L      +     S  + +     R      E          E   +D  
Sbjct: 695  WEGYNYEDAILISEKLVKEDFFTSIHIEEYECEARDTKLGPEEITRDIPNVGEDALKDL- 753

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 754  DERGIIRIGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR-------------- 799

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E                   KI     GD++PPGV+++V+V+VA KR I  GDKMAG
Sbjct: 800  ---EVRDTSLRVPHGESGTVVDVKIFSRDKGDELPPGVIKLVRVYVAQKRKISVGDKMAG 856

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+V+RILP EDMPFL+DGTPV+IVLNPLGVPSRMN+GQ+ ETHLGWA   LG KI
Sbjct: 857  RHGNKGVVARILPEEDMPFLEDGTPVEIVLNPLGVPSRMNLGQVLETHLGWAAKKLGIKI 916

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S I       DI                                   ++G+P       
Sbjct: 917  SSPIFHGAKEEDIFETLE------------------------------RAGLP------- 939

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                              +G+  LYDG TGEPFD PVTVGYIYM+KL H+V DK++ARST
Sbjct: 940  -----------------RNGKVTLYDGRTGEPFDNPVTVGYIYMMKLAHLVDDKIHARST 982

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+I
Sbjct: 983  GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKTYEAI 1042

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            V G +  E G PESF VL+KE+Q+LGL + + +SR +     +   +    E
Sbjct: 1043 VKGENVPEPGVPESFKVLIKELQSLGLDVRVLSSRGEEVELKDTDSEGEPAE 1094



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 107/337 (31%), Positives = 165/337 (48%), Gaps = 34/337 (10%)

Query: 6   VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
            F      R  +GK  EI+ +PDL+E+Q+ SY  FL           +GL+ A   + PI
Sbjct: 5   SFKEGSGERVSYGKLQEILPLPDLLEIQRKSYRWFL----------EKGLREALADISPI 54

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             F+G  +LEF+ Y   PPK+   +C  RD+TYA PL++ +RLI          K   +I
Sbjct: 55  RDFTGNLILEFLDYTLGPPKYSEQECKDRDMTYAAPLRVKVRLI---------NKETGEI 105

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           KEQ ++MGDLPLMT+ GTF+I G +R+VVSQL RSPG+++          GK LY   II
Sbjct: 106 KEQEVFMGDLPLMTERGTFIINGAERVVVSQLVRSPGVYYGEQIDPT---GKKLYTATII 162

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDF 244
           P++G W++ E D+ D+I VR+DR RK+P T+ + ALG  +   IL  F     + Q    
Sbjct: 163 PNRGAWLEFETDASDVIWVRVDRTRKIPATTLVRALGYPTNAHILELF-DHDKFIQETLS 221

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
                +  + ++          +  GE   +++ + L   L    K   +  +G      
Sbjct: 222 RDPSTNQEEALLEI-----YKRLRPGEPPAVDNARALLESLFFDPKRYDLGNVGRYKLFK 276

Query: 304 CGLYVAEDIVNGETG----EIYIEAGDVIDEKSLEEI 336
              +        E G    + Y++     D + + E+
Sbjct: 277 KLGHGILYRFKQENGPQEWDPYLKKMVPKDREFIREL 313


>gi|229544491|gb|ACQ76426.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  532 bits (1370), Expect = e-148,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 316/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDL NG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER    + + +MP DL
Sbjct: 419 VDLHNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERXGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395017|gb|ACI45310.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  532 bits (1370), Expect = e-148,   Method: Composition-based stats.
 Identities = 202/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  +  P +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKEPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLARP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +               L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVPERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ ++GEI  +
Sbjct: 240 ITD-KSGKLIVAKDKRVTARHTRDLEQSGSTHISVPEDFLVGRVVARTIVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R++  +Y + ++  AYI +TL +D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRELQCIYTNELDQGAYISHTLRSDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N R+  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + +  MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPPMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395041|gb|ACI45326.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  532 bits (1370), Expect = e-148,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 311/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADTAPLKRSIEGLQAAFNAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D E D KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFESDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTVRHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEVLLKKLRGAGVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ + QYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAEKQYRTGLGRIEKAVKERLGHAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395071|gb|ACI45346.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  531 bits (1369), Expect = e-148,   Method: Composition-based stats.
 Identities = 200/488 (40%), Positives = 318/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|147676647|ref|YP_001210862.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Pelotomaculum thermopropionicum SI]
 gi|189043861|sp|A5D5I2|RPOB_PELTS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|146272744|dbj|BAF58493.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Pelotomaculum thermopropionicum SI]
          Length = 1224

 Score =  531 bits (1369), Expect = e-148,   Method: Composition-based stats.
 Identities = 187/576 (32%), Positives = 268/576 (46%), Gaps = 61/576 (10%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              +      G  +  + +          +++  I+  G  V  G ++    +      + 
Sbjct: 624  THIEIRNDRGYLDRYKLLKFTRSNQGTCVNQKPIVKKGERVEAGQVIADGPST-DYGELA 682

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--- 964
                +L A    +  +  D  L     V            +  + + R   +  E+I   
Sbjct: 683  LGRNVLVAFMPWEGYNYEDAILVSEKTVKEDYFTSIHIEEY--ECDARDTKLGPEEITRD 740

Query: 965  -----ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
                 E + +D DD   I+      R  +IL G+    G         L   +  E  R 
Sbjct: 741  IPNVGEEILKDLDDR-GIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR- 798

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                            E                   K+     GD++PPGV ++V+V++A
Sbjct: 799  ----------------EVRDTSLRVPHGESGKVVDVKVFSRDNGDELPPGVNQLVRVYIA 842

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDKMAGRHGNKG+++RILP EDMPFL DGTP++IVLNPLGVPSRMN+GQ+ E 
Sbjct: 843  QKRKISEGDKMAGRHGNKGVIARILPEEDMPFLPDGTPIEIVLNPLGVPSRMNIGQVLEA 902

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA   LG  + + + +  +   I                  + +  +++ ++   E 
Sbjct: 903  HLGWAAKVLGYYVSTPVFNGASEESIFEALKEAAFKESGLRSFMEKAGLNEEELIGAVET 962

Query: 1200 ----------WKSGVPVSTPVFD----------------------GADEEAINSMLRMAD 1227
                          V  +    +                      G  ++ I   ++   
Sbjct: 963  AEKRAGSREALIKEVEGAESSGETIMAAIERTGLTAGMVNRLEEAGMTKKEILGAMKKLL 1022

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
               SG+  LYDG TGEPFD P+TVGY+YMLKL H+V DK++ARSTG YSLVTQQPLGGK+
Sbjct: 1023 FARSGKMTLYDGRTGEPFDSPITVGYVYMLKLAHLVDDKIHARSTGPYSLVTQQPLGGKA 1082

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF
Sbjct: 1083 QFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESF 1142

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             VL+KE+Q+LGL + + +   +     E   D  + 
Sbjct: 1143 KVLIKELQSLGLDVKVLSEDDQEIEIREVEEDIGET 1178



 Score =  525 bits (1353), Expect = e-146,   Method: Composition-based stats.
 Identities = 369/777 (47%), Positives = 492/777 (63%), Gaps = 63/777 (8%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQV------------I 274
           +     + Y+     +                +V   L++ +TGE               
Sbjct: 59  NLVLEFLDYTLGEPKYTVEECKERDVTYAAPLRVKVRLINKETGEVKEQDVFMGDFPLMT 118

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEI----------Y 321
           E G  + +G  + +  + V+  G+  D      G  +    +    G             
Sbjct: 119 EKGTFIINGAERVIVSQLVRSPGVYFDETIDPSGKKLYTATIIPNRGAWLEFETDVNDHI 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
               D   +     +  +          +  N +  I  TL  D     ++AL++IY+ +
Sbjct: 179 FVRIDRTRKIPATVLVRALGYGTKAQVAELFNEDKNILETLARDNTDSEEEALVEIYKRL 238

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT----------------- 424
           RPG+  T   A S+   LFFD  +YDL+ VGR K+  +L                     
Sbjct: 239 RPGEPPTVDSARSLLTSLFFDPKRYDLANVGRYKIQKKLKHGVLYRYGPNPDGKTVFDPY 298

Query: 425 --------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                    + +R + KEDII  I+ L+ L NG+G +DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 299 LKKEVPQKREFIRELTKEDIIETIRYLLKLMNGEGQVDDIDHLGNRRLRSVGELLQNQFR 358

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER++  D+D + PQ LIN +PVV+A+ EFF SSQLSQ  +  N L+ +T
Sbjct: 359 IGLSRMERVVRERMTIQDVDVITPQVLINIRPVVAAIKEFFGSSQLSQFMDQTNPLAELT 418

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++AR+N +G
Sbjct: 419 HKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARINEFG 478

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           FIETPYRKV   + +VT+++VYL+A EEE   IAQAN+ LDE+G F E  V  R + E +
Sbjct: 479 FIETPYRKVDKENRRVTDEIVYLTADEEEGYVIAQANAPLDEEGRFIEPRVNAR-SPEIV 537

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +VP +++D++D SPKQV SIA +LIPFLE+DD+NR LMG NMQRQAVPLLKA+AP VGTG
Sbjct: 538 VVPADRVDYMDVSPKQVFSIATALIPFLEHDDANRALMGANMQRQAVPLLKAQAPLVGTG 597

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A+ SG  ++AK +G VE+V +  I IR+  G LD        Y+L+KF RSNQ T
Sbjct: 598 IEYKAARDSGVVVIAKESGTVEKVTSTHIEIRNDRGYLD-------RYKLLKFTRSNQGT 650

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           CVNQ+P+VK G+ V    +IADGPSTD G+LALGRN+LVAFMPW GYN+ED++L+SE+ V
Sbjct: 651 CVNQKPIVKKGERVEAGQVIADGPSTDYGELALGRNVLVAFMPWEGYNYEDAILVSEKTV 710

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED FTSIHIEE+E  ARDTKLGPEEITRDIPNV EE LK++D+ GII VGAEV PGDIL
Sbjct: 711 KEDYFTSIHIEEYECDARDTKLGPEEITRDIPNVGEEILKDLDDRGIIRVGAEVRPGDIL 770

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 771 VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGKVVDVKVFSRDNGD 827



 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 112/337 (33%), Positives = 166/337 (49%), Gaps = 32/337 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           RVR  FG+  E++D+P+LIEVQ+ SY  FL           EGL+  F+ + PI  F+G 
Sbjct: 10  RVRYNFGRLREVLDLPNLIEVQRNSYKWFL----------EEGLREVFQDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 60  LVLEFLDYTLGEPKYTVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++FD        SGK LY   IIP++G W
Sbjct: 111 MGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYFDETID---PSGKKLYTATIIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D  D I VRIDR RK+P T  + ALG  ++ ++   F       +          
Sbjct: 168 LEFETDVNDHIFVRIDRTRKIPATVLVRALGYGTKAQVAELFNEDKNILETLARDNTDSE 227

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS--DCLCGLY 307
              L+   K       +  GE   ++S + L + L    K   +  +G       L    
Sbjct: 228 EEALVEIYK------RLRPGEPPTVDSARSLLTSLFFDPKRYDLANVGRYKIQKKLKHGV 281

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +     N +   ++         +  E I      DI
Sbjct: 282 LYRYGPNPDGKTVFDPYLKKEVPQKREFIRELTKEDI 318


>gi|315079786|gb|EFT51762.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL078PA1]
          Length = 1185

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 100/353 (28%), Positives = 164/353 (46%), Gaps = 34/353 (9%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKSVFPI 65
            K  E +++P+L+++Q  S++  +   I              D     GL+  F+ + PI
Sbjct: 50  AKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEEISPI 109

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +S    L F  + F+ PK  VD+C  RD TYA PL +T   +             ++I
Sbjct: 110 EDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNETEEI 160

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ C++I
Sbjct: 161 KSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFTCKVI 218

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGD 243
           P +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +   D
Sbjct: 219 PSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQTLEKD 278

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
                   A L +  K+         GE    ++ ++L      + K   +  +G    +
Sbjct: 279 HGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGRYKIN 331

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 332 KKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 384


>gi|134298085|ref|YP_001111581.1| DNA-directed RNA polymerase subunit beta [Desulfotomaculum reducens
           MI-1]
 gi|172044214|sp|A4J103|RPOB_DESRM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|134050785|gb|ABO48756.1| DNA-directed RNA polymerase subunit beta [Desulfotomaculum reducens
           MI-1]
          Length = 1145

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 357/777 (45%), Positives = 491/777 (63%), Gaps = 62/777 (7%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQV------------I 274
           +     + Y+     +                +V   L++ +TGE               
Sbjct: 59  NLILEFLDYTLGEPKYSVEECKERDVTYAAPLRVKVRLINKETGEVKEQEVFMGDFPLMT 118

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEI----------Y 321
             G  + +G  + +  + V+  G+         G  +    +    G             
Sbjct: 119 SKGTFIINGAERVIVSQLVRSPGVYFADQIDPSGKRLFATTMIPNRGAWLEFETDVNDHI 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
               D   +     +  +       L ++   N+ +++ TL  D     ++AL++IY+ +
Sbjct: 179 FVRIDRTRKIPATVLIRALGYGSNALIMELFENDKFVQETLTRDNTDTEEEALVEIYKRL 238

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT----------------- 424
           RPG+  T   A S+ N LFFD  +YDL+ VGR K+  +L                     
Sbjct: 239 RPGEPPTVESARSLLNTLFFDPKRYDLAHVGRYKLQKKLKHGILYRYPNGEEGPKEWDRL 298

Query: 425 --------PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                    + +R + KEDIIA  + L++L  G+G +DDID+LGNRR+RSVGE+L+NQ+R
Sbjct: 299 LNKEVPVDREFIRELTKEDIIATFRYLLNLMQGEGIVDDIDHLGNRRLRSVGELLQNQFR 358

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL RMER ++ER++  D+D + PQ LIN +PVV+++ EFF SSQLSQ  +  N L+ +T
Sbjct: 359 IGLSRMERVVRERMTIQDVDVITPQVLINIRPVVASIKEFFGSSQLSQFMDQTNPLAELT 418

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL+++AR+N++G
Sbjct: 419 HKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARINSFG 478

Query: 597 FIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           F+E PYRKV   + +VT+++VYL+A EEE+  IAQAN+ LDE+G F EE V  R   + +
Sbjct: 479 FMEAPYRKVDKENKRVTDEIVYLTADEEEDHIIAQANAPLDENGYFVEERVNARRGHDTL 538

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           LVP ++++++D SPKQV S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTG
Sbjct: 539 LVPTDRVEYMDVSPKQVFSVATSLIPFLEHDDANRALMGANMQRQAVPLLRCQAPVVGTG 598

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   AK SG  IVA+R G V +V A  + +R+ EG  D        Y+L+KF RSNQ T
Sbjct: 599 IEHRAAKDSGVCIVAERGGEVVRVTATEVAVRTDEGRTD-------TYKLLKFTRSNQGT 651

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C+NQ+P+V  GD V    I+ADGP+T+ G+LALGRN+LVAFM W G N+ED++LISE+ V
Sbjct: 652 CINQKPIVNKGDRVEEGQILADGPATEQGELALGRNILVAFMTWEGNNYEDAILISEKAV 711

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED FTSIHIEE+E  ARDTKLGPEEITRDIPNV E+ LK++DE GII VGAEV PGDIL
Sbjct: 712 KEDFFTSIHIEEYECDARDTKLGPEEITRDIPNVGEDILKDLDERGIIRVGAEVRPGDIL 771

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G +G +VDV++F+R   D
Sbjct: 772 VGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGKIVDVKVFSRENGD 828



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 187/520 (35%), Positives = 247/520 (47%), Gaps = 83/520 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  + +          I++  I+  G  V  G IL      + +  +     +
Sbjct: 630  RTDEGRTDTYKLLKFTRSNQGTCINQKPIVNKGDRVEEGQILADGPATE-QGELALGRNI 688

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    +  +  D  L     V            +  + + R   +  E+I        
Sbjct: 689  LVAFMTWEGNNYEDAILISEKAVKEDFFTSIHIEEY--ECDARDTKLGPEEITRDIPNVG 746

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E + +D  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 747  EDILKDL-DERGIIRVGAEVRPGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 799

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   K+   + GD++PPGV  +V+ ++A KR I
Sbjct: 800  -----------EVRDTSLRVPHGEAGKIVDVKVFSRENGDELPPGVNHLVRCYIAQKRKI 848

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+V+RILP EDMPF+ DGTPV IVLNPLGVPSRMN+GQ+ ETHLGWA
Sbjct: 849  SEGDKMAGRHGNKGVVARILPEEDMPFMADGTPVQIVLNPLGVPSRMNIGQVLETHLGWA 908

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + +  +   I       E                               
Sbjct: 909  AKTLGFNVATPVFNGASEESIWETLRRAELPE---------------------------- 940

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                   DG                      LYDG TGEPFD  VTVGYIYM+KL+H+V 
Sbjct: 941  -------DGKTV-------------------LYDGRTGEPFDNRVTVGYIYMIKLHHLVD 974

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVG
Sbjct: 975  DKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVG 1034

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            R + YE+IV G +  E G PESF VL+KE+Q+LGL + + 
Sbjct: 1035 RVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGLDVKVL 1074



 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 117/364 (32%), Positives = 176/364 (48%), Gaps = 33/364 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           RVR  +GK  E++D+P+LIEVQ+ SY+ FL           EGL+  F  + PI  F+G 
Sbjct: 10  RVRWNYGKLREVLDLPNLIEVQRNSYEWFLQ----------EGLREVFHDISPIQDFTGN 59

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEF+ Y    PK+ V++C  RD+TYA PL++ +RLI          K   ++KEQ ++
Sbjct: 60  LILEFLDYTLGEPKYSVEECKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVF 110

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF+I G +R++VSQL RSPG++F     +   SGK L+A  +IP++G W
Sbjct: 111 MGDFPLMTSKGTFIINGAERVIVSQLVRSPGVYFA---DQIDPSGKRLFATTMIPNRGAW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           ++ E D  D I VRIDR RK+P T  + ALG  S  ++   +    + Q         + 
Sbjct: 168 LEFETDVNDHIFVRIDRTRKIPATVLIRALGYGSNALIMELFENDKFVQETLTRDNTDTE 227

Query: 252 ADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            + +V          +  GE   +ES + L + L    K   +  +G     L       
Sbjct: 228 EEALVEI-----YKRLRPGEPPTVESARSLLNTLFFDPKRYDLAHVGRYK--LQKKLKHG 280

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            +     GE   E     D    +E+         +   D +    Y+ N +  +   D 
Sbjct: 281 ILYRYPNGE---EGPKEWDRLLNKEVPVDREFIRELTKEDIIATFRYLLNLMQGEGIVDD 337

Query: 371 KDAL 374
            D L
Sbjct: 338 IDHL 341


>gi|229544488|gb|ACQ76424.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 318/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVAPFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELAEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN++P+ +
Sbjct: 479 INSQPISA 486


>gi|315104032|gb|EFT76008.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL050PA2]
          Length = 1185

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHLTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAT 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 110/494 (22%), Positives = 198/494 (40%), Gaps = 60/494 (12%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVI-------------------DEKSLEEIFH 338
              +   GL +  D       +I      V                    +   ++   +
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTATLPREGQDDIVVEPDDIDHFGN 387

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             +R +  L  + +         +V D+   +   +  I            +  +  F  
Sbjct: 388 RRLRTVGELIQNQLRTGLSRMERVVRDRMTTQD--IEAITPQTLINIRPVTAAIKEFFGT 445

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                     + +  +    RL+   P     + ++     ++ +     G+  +  I+ 
Sbjct: 446 SQLSQFMDQNNPLAEMTHKRRLSALGPGG---LSRDRAGMEVRDVHPSHYGR--MCPIET 500

Query: 459 LGNRRVRSVGEMLK 472
                +  +G +  
Sbjct: 501 PEGPNIGLIGSLAS 514


>gi|314924090|gb|EFS87921.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL001PA1]
 gi|314965012|gb|EFT09111.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL082PA2]
 gi|314983134|gb|EFT27226.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL110PA3]
 gi|315090631|gb|EFT62607.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL110PA4]
 gi|315093817|gb|EFT65793.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL060PA1]
 gi|327326454|gb|EGE68243.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL103PA1]
          Length = 1185

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDNA-ELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 338/692 (48%), Positives = 454/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAT 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD  +LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNAELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 110/494 (22%), Positives = 198/494 (40%), Gaps = 60/494 (12%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVI-------------------DEKSLEEIFH 338
              +   GL +  D       +I      V                    +   ++   +
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTATLPREGQDDIVVEPDDIDHFGN 387

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             +R +  L  + +         +V D+   +   +  I            +  +  F  
Sbjct: 388 RRLRTVGELIQNQLRTGLSRMERVVRDRMTTQD--IEAITPQTLINIRPVTAAIKEFFGT 445

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                     + +  +    RL+   P     + ++     ++ +     G+  +  I+ 
Sbjct: 446 SQLSQFMDQNNPLAEMTHKRRLSALGPGG---LSRDRAGMEVRDVHPSHYGR--MCPIET 500

Query: 459 LGNRRVRSVGEMLK 472
                +  +G +  
Sbjct: 501 PEGPNIGLIGSLAS 514


>gi|313763072|gb|EFS34436.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL013PA1]
 gi|313773034|gb|EFS39000.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL074PA1]
 gi|313794079|gb|EFS42101.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL110PA1]
 gi|313802429|gb|EFS43654.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL110PA2]
 gi|313812050|gb|EFS49764.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL083PA1]
 gi|313812124|gb|EFS49838.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL025PA1]
 gi|313816870|gb|EFS54584.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL059PA1]
 gi|313828441|gb|EFS66155.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL063PA2]
 gi|313831101|gb|EFS68815.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL007PA1]
 gi|313833495|gb|EFS71209.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL056PA1]
 gi|313838129|gb|EFS75843.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL086PA1]
 gi|314914569|gb|EFS78400.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL005PA4]
 gi|314919187|gb|EFS83018.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL050PA1]
 gi|314920621|gb|EFS84452.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL050PA3]
 gi|314931469|gb|EFS95300.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL067PA1]
 gi|314957029|gb|EFT01135.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL027PA1]
 gi|314957843|gb|EFT01946.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL002PA1]
 gi|314963360|gb|EFT07460.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL082PA1]
 gi|314974284|gb|EFT18380.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL053PA1]
 gi|314976946|gb|EFT21041.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL045PA1]
 gi|314985797|gb|EFT29889.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL005PA1]
 gi|315077094|gb|EFT49169.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL053PA2]
 gi|315096806|gb|EFT68782.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL038PA1]
 gi|315100108|gb|EFT72084.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL059PA2]
 gi|315100567|gb|EFT72543.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL046PA1]
 gi|315106008|gb|EFT77984.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL030PA1]
 gi|315109363|gb|EFT81339.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL030PA2]
 gi|327325652|gb|EGE67450.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL096PA2]
 gi|327445322|gb|EGE91976.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL043PA1]
 gi|327446963|gb|EGE93617.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL043PA2]
 gi|327451387|gb|EGE98041.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL092PA1]
 gi|327452614|gb|EGE99268.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL087PA3]
 gi|328751903|gb|EGF65519.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL087PA1]
 gi|328759036|gb|EGF72652.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL025PA2]
 gi|328762263|gb|EGF75755.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL099PA1]
          Length = 1185

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 166/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 384


>gi|209395122|gb|ACI45380.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  531 bits (1368), Expect = e-148,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 311/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL    AP +R  EGLQAAF + FPI + +G   + ++ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAEKAPQKRNVEGLQAAFDAAFPIVSHNGFVEMRYLEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRDDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  +++ +TGEI  +
Sbjct: 240 ITD-KSGKVILSKDKRVTVRHIRELEQSGTSHVSVPEDFLVGRVVARGVIDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGANVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPIPA 486


>gi|313836000|gb|EFS73714.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL037PA2]
 gi|314929676|gb|EFS93507.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL044PA1]
 gi|314970501|gb|EFT14599.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL037PA3]
          Length = 1177

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 195/533 (36%), Positives = 272/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +   +  +     +L A
Sbjct: 668  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPST-DKGELALGRNMLAA 726

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 727  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 784

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 785  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 842

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 843  VPHGEEGTVIGVRIFDT---------EDGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 893

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 894  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 952

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 953  AEGDWAERLREVGLIDVPEES-----------------------------RLATPVFDGA 983

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L            +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 984  TEEEITGLLEYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1043

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1044 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1103

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            RVYE+IV G +  E G PESF VLVKEM++L L++++ NS  +     +   D
Sbjct: 1104 RVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRDSEED 1156



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 336/692 (48%), Positives = 459/692 (66%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + ++      +++
Sbjct: 184 LVRSPGVYFEKTSDKTSDKDIFTCKVIPSR--GAWLEFEIDKRDTVGVRLDR---KRKQN 238

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           +     +       +  +  ++ +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 239 ITVFLKALGWTADRILEEFGDHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 298

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L LD P D + +  +D++A I  +  L  G   
Sbjct: 299 QQLLENYYFNPKRYDLAKVGRYKINKKLGLDLPFDQQVLTIDDLVAAIHFVCALHEGTEV 358

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 359 LPREGRDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLGRMERVVRDRMTTQDIEAITP 418

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 419 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 478

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 479 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 538

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD++G F  + V  R    E   VP   +D++D SP+Q+VS+A++LI
Sbjct: 539 EEDRHVIAQANAKLDDEGHFVNDRVLVRQRHGEADEVPSSDVDYMDVSPRQMVSVASALI 598

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 599 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 658

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 659 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 711

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 712 TDKGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 771

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 772 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 831

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 832 KAREVRDTSLKVPHGEEGTVIGVRIFDTEDGD 863



 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 110/487 (22%), Positives = 199/487 (40%), Gaps = 46/487 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 38  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSHVDAALAEGRTDINTKSGLEEIFEE 97

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 98  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 148

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 149 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTSDKT--SDKDIFT 206

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           C++IP +G W++ E D +D + VR+DR+RK  +T FL ALG  ++ IL  F       Q 
Sbjct: 207 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNITVFLKALGWTADRILEEFGDHESIRQT 266

Query: 242 GDFW---CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFL 296
            +          A   +            D  +Q++E+         L K  + K  K L
Sbjct: 267 LEKDHGVETQDQALLDIYKKLRPGEPPSRDAAQQLLENYYFNPKRYDLAKVGRYKINKKL 326

Query: 297 GITSDCLCGLYVAEDIVN--------GETGEIY---IEAGDVIDEKSLEEIFHSEIRDIP 345
           G+       +   +D+V          E  E+         V++   ++   +  +R + 
Sbjct: 327 GLDLPFDQQVLTIDDLVAAIHFVCALHEGTEVLPREGRDDIVVEPDDIDHFGNRRLRTVG 386

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
            L  + +         +V D+   +   +  I            +  +  F         
Sbjct: 387 ELIQNQLRTGLGRMERVVRDRMTTQD--IEAITPQTLINIRPVTAAIKEFFGTSQLSQFM 444

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              + +  +    RL+   P     + ++     ++ +     G+  +  I+      + 
Sbjct: 445 DQNNPLAEMTHKRRLSALGPGG---LSRDRAGMEVRDVHPSHYGR--MCPIETPEGPNIG 499

Query: 466 SVGEMLK 472
            +G +  
Sbjct: 500 LIGSLAS 506


>gi|313807838|gb|EFS46322.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL087PA2]
 gi|313819210|gb|EFS56924.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL046PA2]
 gi|313819751|gb|EFS57465.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL036PA1]
 gi|313823868|gb|EFS61582.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL036PA2]
 gi|313827229|gb|EFS64943.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL063PA1]
 gi|314925716|gb|EFS89547.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL036PA3]
 gi|314960684|gb|EFT04785.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL002PA2]
 gi|314979904|gb|EFT23998.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL072PA2]
 gi|314988419|gb|EFT32510.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL005PA2]
 gi|314988843|gb|EFT32934.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL005PA3]
 gi|315084906|gb|EFT56882.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL027PA2]
 gi|315087226|gb|EFT59202.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL002PA3]
 gi|315088959|gb|EFT60935.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL072PA1]
 gi|327327976|gb|EGE69746.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL096PA3]
 gi|327449041|gb|EGE95695.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL013PA2]
 gi|328756951|gb|EGF70567.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL020PA1]
          Length = 1185

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 167/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK+ VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKYSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 384


>gi|209395092|gb|ACI45360.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  +  P +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKEPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLARP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +               L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVPERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++     + +  D L G  VA  IV+ ++GEI  +
Sbjct: 240 ITD-KSGKLIVAKDKRVTARHTRDLEQSDSTHISVPEDFLVGRVVARTIVDTDSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R++  +Y + ++  AYI +TL +D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRELQCIYTNELDQGAYISHTLRSDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N R+  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPIFA 486


>gi|314969745|gb|EFT13843.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL037PA1]
          Length = 1185

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 166/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 384


>gi|328906254|gb|EGG26029.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium sp. P08]
          Length = 1159

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 195/533 (36%), Positives = 272/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +   +  +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPST-DKGELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------EDGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDVPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L            +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEEEITGLLEYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            RVYE+IV G +  E G PESF VLVKEM++L L++++ NS  +     +   D
Sbjct: 1086 RVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRDSEED 1138



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 336/692 (48%), Positives = 459/692 (66%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + ++      +++
Sbjct: 166 LVRSPGVYFEKTSDKTSDKDIFTCKVIPSR--GAWLEFEIDKRDTVGVRLDR---KRKQN 220

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           +     +       +  +  ++ +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 221 ITVFLKALGWTADRILEEFGDHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L LD P D + +  +D++A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLDLPFDQQVLTIDDLVAAIHFVCALHEGTEV 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGRDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLGRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD++G F  + V  R    E   VP   +D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDEGHFVNDRVLVRQRHGEADEVPSSDVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDKGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTEDGD 845



 Score =  327 bits (838), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 110/487 (22%), Positives = 199/487 (40%), Gaps = 46/487 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSHVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTSDKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           C++IP +G W++ E D +D + VR+DR+RK  +T FL ALG  ++ IL  F       Q 
Sbjct: 189 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNITVFLKALGWTADRILEEFGDHESIRQT 248

Query: 242 GDFW---CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFL 296
            +          A   +            D  +Q++E+         L K  + K  K L
Sbjct: 249 LEKDHGVETQDQALLDIYKKLRPGEPPSRDAAQQLLENYYFNPKRYDLAKVGRYKINKKL 308

Query: 297 GITSDCLCGLYVAEDIVN--------GETGEIY---IEAGDVIDEKSLEEIFHSEIRDIP 345
           G+       +   +D+V          E  E+         V++   ++   +  +R + 
Sbjct: 309 GLDLPFDQQVLTIDDLVAAIHFVCALHEGTEVLPREGRDDIVVEPDDIDHFGNRRLRTVG 368

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
            L  + +         +V D+   +   +  I            +  +  F         
Sbjct: 369 ELIQNQLRTGLGRMERVVRDRMTTQD--IEAITPQTLINIRPVTAAIKEFFGTSQLSQFM 426

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
              + +  +    RL+   P     + ++     ++ +     G+  +  I+      + 
Sbjct: 427 DQNNPLAEMTHKRRLSALGPGG---LSRDRAGMEVRDVHPSHYGR--MCPIETPEGPNIG 481

Query: 466 SVGEMLK 472
            +G +  
Sbjct: 482 LIGSLAS 488


>gi|86609871|ref|YP_478633.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|109914403|sp|Q2JJ19|RPOB_SYNJB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|86558413|gb|ABD03370.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 1139

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 327/687 (47%), Positives = 457/687 (66%), Gaps = 10/687 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 125 INGAERVIVNQIVRSPGVYYKSELDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 184

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   D++ +  + + T+  +     ++AL+++YR +RPG+ 
Sbjct: 185 TRKLSAAVLLKALGLSDSEI--YDNLRHPEFFQKTMEKEGPYTEEEALMELYRKLRPGEP 242

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD  +YDL  VGR K+N +LNL+  + VR +   DI+A+I  L++L
Sbjct: 243 PTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLNLNVAESVRVLTVTDILAVIDYLINL 302

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + +++ P  L+N 
Sbjct: 303 EYDIGHVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESENLTPASLVNP 362

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG  +RD+HP+HY
Sbjct: 363 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFAVRDIHPSHY 422

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGFIE+PY +V +G V  D+  VYL+A EE+ 
Sbjct: 423 GRICPIETPEGPNAGLIGSLATHARVNQYGFIESPYYRVENGVVRKDLGMVYLTADEEDE 482

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +  +D +G  T +LV  R   E       ++ ++  +P QV+S+A SLIPFLE+
Sbjct: 483 YRVAPGDVPVDAEGRITADLVPVRYRQEFTTAHPTEVHYVQVAPVQVISVATSLIPFLEH 542

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK + P+VGTG+E+  A+ SG  +V++  G+V  V A  IV
Sbjct: 543 DDANRALMGANMQRQAVPLLKPDRPYVGTGLEAQAARDSGMVVVSRTNGVVTYVSADEIV 602

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  +G          +YRL K+QRSNQ+TC+NQRPLV  GD V    ++ADGP+T+ G+
Sbjct: 603 VRPDDG------GDPIVYRLQKYQRSNQDTCLNQRPLVYTGDRVVAGQVLADGPATEGGE 656

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DVFTS+HIE+ E+ AR TKLGPEEITR+
Sbjct: 657 LALGQNVLVAYMPWEGYNYEDAILISERLVYDDVFTSVHIEKHEIEARQTKLGPEEITRE 716

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+++DE GI+ +GA V  GDILVGK+TPKGES   PEE+LLRAIFGEKA DV
Sbjct: 717 IPNVGEDALRDLDENGIVRIGAWVEAGDILVGKVTPKGESDQPPEERLLRAIFGEKARDV 776

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVRIF R   D
Sbjct: 777 RDNSLRVPNGERGRVVDVRIFTREQGD 803



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/586 (32%), Positives = 267/586 (45%), Gaps = 62/586 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P+ G   E        MV  S       ++   E++ R    G
Sbjct: 550  MGANMQRQAVPLLKPDRPYVGTGLEAQAARDSGMVVVSRTNGVVTYVSADEIVVRPDDGG 609

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
               + R            +++  ++  G  V  G +L      +G   +   + +L A  
Sbjct: 610  DPIVYRLQKYQRSNQDTCLNQRPLVYTGDRVVAGQVLADGPATEG-GELALGQNVLVAYM 668

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD--- 972
              +  +  D  L     V   V       +H I+  +  +  E    +I  +  D     
Sbjct: 669  PWEGYNYEDAILISERLVYDDVFTSVHIEKHEIEARQTKLGPEEITREIPNVGEDALRDL 728

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 729  DENGIVRIGAWVEAGDILVGKVTPKGESDQPPEERLLRAIFGEKARDVRDN--------- 779

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                                   +I   + GD++PPG   VV+V++A+KR IQ GDK+AG
Sbjct: 780  --------SLRVPNGERGRVVDVRIFTREQGDELPPGANMVVRVYIALKRKIQVGDKIAG 831

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+SRILP EDMP+L DGTPVD+VLNPLGVPSRMNVGQ++E  LGWA   LG + 
Sbjct: 832  RHGNKGIISRILPIEDMPYLADGTPVDVVLNPLGVPSRMNVGQVYECLLGWAAEHLGVRF 891

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K +  D     + S L    +                                       
Sbjct: 892  KLMPFDEMHGLEASRLTVEAKLRE------------------------------------ 915

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
             A E+     +   +    G+  ++DG TGEPFD+PVTVG  YMLKL H+V DK++ARST
Sbjct: 916  -AREKTGKDWIFNPEGKYCGKIQVFDGRTGEPFDQPVTVGRAYMLKLVHLVDDKIHARST 974

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY+LQE+LT+KSDD+VGR     +I
Sbjct: 975  GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYILQELLTVKSDDMVGRNEALNAI 1034

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      GTPESF VLV+E+Q+L L + +      +  +  ++ 
Sbjct: 1035 VKGKPIPRPGTPESFKVLVRELQSLCLDVSVHKVEVDSEGQTHDVE 1080



 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 97/464 (20%), Positives = 188/464 (40%), Gaps = 50/464 (10%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--------- 77
           PDL+E+Q+ S+  FL           EG +    S  PI  ++G   L F+         
Sbjct: 15  PDLVEIQRESFLWFLR----------EGFEEELLSFSPIIDYTGKLELHFLPEYRPGDPS 64

Query: 78  -SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
             Y+ + P++D ++   RD TY   +++  RLI          K   +IK+  +++G+LP
Sbjct: 65  KGYKINRPRYDPEEAKRRDATYQAQIRVPTRLI---------NKETGEIKDMDVFIGELP 115

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LMT  GTF+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E 
Sbjct: 116 LMTDRGTFIINGAERVIVNQIVRSPGVYYKSELDK---NGRRTYSASLIPNRGAWLKFET 172

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSA 251
           D   ++ VRID+ RK+     L ALG+   EI        F+ K   +   +       A
Sbjct: 173 DKNGLVWVRIDKTRKLSAAVLLKALGLSDSEIYDNLRHPEFFQK---TMEKEGPYTEEEA 229

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVA 309
              +           +  G+Q++ES         L +  + K  K L +       +   
Sbjct: 230 LMELYRKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLNLNVAESVRVLTV 289

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            DI+      I +E  D+     ++ + +  +R +  L  + V         ++ ++   
Sbjct: 290 TDILAVIDYLINLE-YDIGHVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTV 348

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            +   L    ++ P      +  +  F            + +  +    RL+   P    
Sbjct: 349 SESENLTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG-- 404

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            + +E     ++ +     G+  I  I+         +G +  +
Sbjct: 405 -LSRERAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 445


>gi|50843338|ref|YP_056565.1| DNA-directed RNA polymerase subunit beta [Propionibacterium acnes
            KPA171202]
 gi|81611188|sp|Q6A6K6|RPOB_PROAC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|50840940|gb|AAT83607.1| DNA-directed RNA polymerase beta chain [Propionibacterium acnes
            KPA171202]
          Length = 1159

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1086 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1138



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 454/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++   I   +T  + +       +  
Sbjct: 166 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFAIDKRDT--VGVRLDRKRKQNV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 222 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 845



 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 101/357 (28%), Positives = 165/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++   D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 189 CKVIPSRGAWLEFAIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 249 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 302 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 358


>gi|209395068|gb|ACI45344.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 310/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +   FL  + AP +R  EGLQAAF + FPI + +G   + F  Y    P
Sbjct: 1   EVPYLLQMQKDACTAFLQADTAPLKRSVEGLQAAFDAAFPIVSHNGFVEMRFTEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R++RRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVNRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTVRHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|327333170|gb|EGE74897.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL097PA1]
          Length = 1185

 Score =  531 bits (1367), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 676  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 734

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 735  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 792

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 793  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 850

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 851  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 901

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 902  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 960

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 961  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 991

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 992  SEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1051

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1052 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1111

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1112 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1164



 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 192 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 247

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 248 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 306

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 307 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 366

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 367 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 426

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 427 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 486

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 487 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 546

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 547 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 606

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 607 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 666

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 667 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 719

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 720 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 779

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 780 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 839

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 840 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 871



 Score =  329 bits (843), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 166/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 46  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 105

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 106 ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 156

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 157 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 214

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 215 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 274

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 275 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 327

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 328 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 384


>gi|297618392|ref|YP_003703551.1| DNA-directed RNA polymerase subunit beta [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146229|gb|ADI02986.1| DNA-directed RNA polymerase, beta subunit [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 1139

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 369/693 (53%), Positives = 482/693 (69%), Gaps = 24/693 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDC---LCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           + G  + +G  + +  + VK  G+  +    + G  +    +    G    E        
Sbjct: 119 DKGTFIINGAERVVVSQLVKSPGVYFNDRVDITGKTLYGATIIPNRGAW-FELEMDSSGA 177

Query: 332 SLEEIFHSEIRDIPIL-----------YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
               I  +    + +L            +   NN+  I  TL  D   +R++AL++ YR 
Sbjct: 178 VYTRIDKTRKIPVTVLLRALGYPTNEDILALFNNDETIVKTLEKDTTTNREEALIEFYRR 237

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPG+++T   AE + + LFFD  +YDL+ VGR K+N +LNLDTPDDVR ++  DIIA I
Sbjct: 238 LRPGELATVDGAEQLLHNLFFDPRRYDLAAVGRYKINKKLNLDTPDDVRCLQPRDIIATI 297

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
             L+ L  G+G  D ID+LGNRR+RSVGE+L+NQ+R GL+RMER +KER+S  D++++ P
Sbjct: 298 GYLLGLVRGEGKTDIIDHLGNRRLRSVGELLQNQFRTGLVRMERVVKERMSIHDVEALTP 357

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +P+ + V EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG ++RD
Sbjct: 358 QVLINIRPITAVVKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFQVRD 417

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLS 618
           VH +HYGRICP ET EG NIGL+ SL+++ARVN +GFIETPYRKV   + +VTN++ YLS
Sbjct: 418 VHHSHYGRICPIETPEGPNIGLIGSLSTYARVNRFGFIETPYRKVDKENRRVTNEIHYLS 477

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EEE   IAQANS +D DG F  + V  R   E I V  E++D++D SPKQV S+A SL
Sbjct: 478 ASEEEEYVIAQANSPVDADGYFLTDRVIARYGSEIIEVGVERVDYMDVSPKQVFSVATSL 537

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPL++ EAP VG G+E   AK SGA ++AK+ G+V++V
Sbjct: 538 IPFLEHDDANRALMGANMQRQAVPLIRTEAPIVGAGLEYRAAKDSGAVVIAKKGGVVKKV 597

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I + +G        +D Y L+KF RSN  TC+NQRP+V  G  V  ++IIADGP
Sbjct: 598 SANFIQILNDDG-------EIDTYHLLKFVRSNHGTCINQRPIVVAGQRVEADEIIADGP 650

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +TD G+LALGRN++VAFMPW GYNFED++LISE++V EDVFTSIHIEE+E  ARDTKLGP
Sbjct: 651 ATDQGELALGRNVMVAFMPWEGYNFEDAILISEKLVMEDVFTSIHIEEYECEARDTKLGP 710

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNVSE+ LKN+DE G+I VGAEV   DILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 711 EEITRDIPNVSEDMLKNLDERGVIRVGAEVRADDILVGKVTPKGETELTPEERLLRAIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRD+SLRVP G SG VVDV++F+R   D
Sbjct: 771 EKAREVRDSSLRVPHGESGKVVDVKVFSREAGD 803



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 174/536 (32%), Positives = 241/536 (44%), Gaps = 77/536 (14%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G  +    +  V       I++  I+  G  V   D ++       +  +     ++
Sbjct: 606  NDDGEIDTYHLLKFVRSNHGTCINQRPIVVAGQRVE-ADEIIADGPATDQGELALGRNVM 664

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  L     V   V        +  +  +  +  E     I  ++ D 
Sbjct: 665  VAFMPWEGYNFEDAILISEKLVMEDVFTSIHIEEYECEARDTKLGPEEITRDIPNVSEDM 724

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE+ ++      R  +IL G+    G         L   +  E  R          
Sbjct: 725  LKNLDERGVIRVGAEVRADDILVGKVTPKGETELTPEERLLRAIFGEKAR---------- 774

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E                   K+   + GD++ PGV ++V+V+VA KR I  GD
Sbjct: 775  -------EVRDSSLRVPHGESGKVVDVKVFSREAGDELAPGVNQLVRVYVAQKRKISEGD 827

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++SRILP EDMP+L DGTPV+IVLNPLGVPSRMN+GQ+ E HLG     L
Sbjct: 828  KMAGRHGNKGVISRILPVEDMPYLPDGTPVEIVLNPLGVPSRMNIGQVLECHLGLVAKTL 887

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  + S + D      I    +                                      
Sbjct: 888  GFNVASPVFDGATEELIFKKLAEAGLPPDGKIQL-------------------------- 921

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                   G++       GEPFD  VTVGY+YM+KL H+V DK++
Sbjct: 922  ---------------------YDGRT-------GEPFDNKVTVGYVYMMKLAHLVDDKIH 953

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + 
Sbjct: 954  ARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRLKT 1013

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            YESIV G +  E G PESF VL+KE+Q+L L + + +   +     E   + ++ E
Sbjct: 1014 YESIVKGENIPEPGVPESFKVLIKELQSLCLDVRILSEEDREIEIQESDHNLSEEE 1069



 Score =  358 bits (919), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 125/475 (26%), Positives = 204/475 (42%), Gaps = 38/475 (8%)

Query: 4   GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            VV  G  R R  +    E++++PDLIEVQK SY  FL            GL+ A + VF
Sbjct: 3   RVVKYGR-RERVSYSSIQEVMELPDLIEVQKKSYQWFL----------ETGLREALQEVF 51

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  F+G   L+F+ Y    PK++V +C  RD++Y  PLK+ +RL           K   
Sbjct: 52  PIEDFTGNLQLDFIDYTLGEPKYEVQECKERDVSYQAPLKLRVRLT---------DKENG 102

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +I+E  +YMGDLP+MT  GTF+I G +R+VVSQL +SPG++F+    R  ++GK LY   
Sbjct: 103 EIRESEVYMGDLPIMTDKGTFIINGAERVVVSQLVKSPGVYFN---DRVDITGKTLYGAT 159

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY--SQ 240
           IIP++G W ++E DS   ++ RID+ RK+PVT  L ALG   +E+IL+ F        + 
Sbjct: 160 IIPNRGAWFELEMDSSGAVYTRIDKTRKIPVTVLLRALGYPTNEDILALFNNDETIVKTL 219

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGI 298
             D       A            L  +D  EQ++ +         L    + K  K L +
Sbjct: 220 EKDTTTNREEALIEFYRRLRPGELATVDGAEQLLHNLFFDPRRYDLAAVGRYKINKKLNL 279

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            +       +    +    G +            ++ + +  +R +  L  +        
Sbjct: 280 DTPDDV-RCLQPRDIIATIGYLLGLVRGEGKTDIIDHLGNRRLRSVGELLQNQFRTGLVR 338

Query: 359 RNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
              +V ++      +AL    +V+      T  V    F            + +  +   
Sbjct: 339 MERVVKERMSIHDVEALTP--QVLINIRPITAVVK-EFFGSSQLSQFMDQTNPLAELTHK 395

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            RL+   P     + +E     ++ +     G+  I  I+      +  +G +  
Sbjct: 396 RRLSALGPGG---LTRERAGFQVRDVHHSHYGR--ICPIETPEGPNIGLIGSLST 445


>gi|229544482|gb|ACQ76420.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 319/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G    S 
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFLLMDSGAQMEFVAERL-RGEVARSD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSASVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREEFTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395038|gb|ACI45324.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 200/488 (40%), Positives = 318/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSASVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|327457656|gb|EGF04311.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            HL083PA2]
          Length = 1159

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1086 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1138



 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 166 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 222 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 845



 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 101/357 (28%), Positives = 165/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +                  D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNETWQSRVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 189 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 249 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 302 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 358


>gi|289424774|ref|ZP_06426556.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            SK187]
 gi|295131409|ref|YP_003582072.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            SK137]
 gi|289154737|gb|EFD03420.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            SK187]
 gi|291376158|gb|ADE00013.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            SK137]
          Length = 1159

 Score =  530 bits (1366), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1086 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1138



 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 166 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 222 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 845



 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 166/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 189 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 249 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 302 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 358


>gi|289427675|ref|ZP_06429387.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            J165]
 gi|289159166|gb|EFD07358.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            J165]
          Length = 1159

 Score =  530 bits (1365), Expect = e-148,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDN-GELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1086 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQEIDLRGSEED 1138



 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 339/692 (48%), Positives = 455/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 166 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 222 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAI 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G+LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDNGELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 845



 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 102/357 (28%), Positives = 167/357 (46%), Gaps = 34/357 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK+ VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKYSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 189 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 249 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +   GL +  D       +I      V        I   E +D  ++  D +++
Sbjct: 302 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAILPREGQDDIVVEPDDIDH 358


>gi|227549810|ref|ZP_03979859.1| DNA-directed RNA polymerase [Corynebacterium lipophiloflavum DSM
            44291]
 gi|227078065|gb|EEI16028.1| DNA-directed RNA polymerase [Corynebacterium lipophiloflavum DSM
            44291]
          Length = 1152

 Score =  530 bits (1365), Expect = e-148,   Method: Composition-based stats.
 Identities = 187/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K    M     LL A    +  +  D  +     V   ++
Sbjct: 664  IVSAGQRVEAGQVIADGPGTKN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 722

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 723  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 781

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 782  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 824

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 825  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 884

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 885  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYD 941

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L  +  +  G  
Sbjct: 942  VPPESLT-------------------------ATPVFDGASNEEITGLLANSKPNRDGDV 976

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 977  MVDGNGKTVLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1036

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1037 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1096

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++  +         +  DF++ 
Sbjct: 1097 FKVLLKELQSLCLNVEVLTADGTPMELSGDDDDFDQA 1133



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 317/661 (47%), Positives = 449/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I   +    +  +  TL +
Sbjct: 185 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTQQI--TERFGFSEIMMTTLES 240

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL+ VGR K+N +L L  
Sbjct: 241 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLGG 300

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 301 DHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEIIPINTDDIDHFGNRRLRTVGELI 360

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 361 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 420

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ +L S+AR
Sbjct: 421 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGALASYAR 480

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + +D++G+ T E +  R   
Sbjct: 481 VNAFGFIETPYQKVEDGKLTDQIDYLTADEEDRYAIAQAATPMDKEGNLTGERIEVRLKD 540

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQ+QAVPLL++EA +
Sbjct: 541 GDIGVVGASGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGANMQKQAVPLLRSEAAY 600

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TGME   A  +G  +++++AG++E V    I +   EG  D        Y L  F+R+
Sbjct: 601 VATGMEQRAAYDAGDTVISRKAGVIEDVTGDFITVMDDEGIRD-------TYLLRTFERT 653

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ P+V  G  V    +IADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 654 NQGTCYNQTPIVSAGQRVEAGQVIADGPGTKNGEMALGRNLLVAFMPWEGHNYEDAIILN 713

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +D+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GII +GA+V  
Sbjct: 714 QRVVEDDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIIRIGADVRD 773

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR F+R   
Sbjct: 774 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDD 833

Query: 951 D 951
           D
Sbjct: 834 D 834



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 96/389 (24%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP---------NEGLQAAFKSVF 63
            R  F K  E + +P L++VQ  S+   +      + +            GL+   + + 
Sbjct: 11  ERYSFAKISEPVSVPGLLDVQSESFAWLVGTQEWRERQRAERGDDAHIKSGLEDILEEIS 70

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 71  PIQDYSGNMSLSLSEPRFEEIKYSIDECKEKDINYSAPLYVTAEFINND---------TQ 121

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 122 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHAVK 179

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +++I   F     ++ +  
Sbjct: 180 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTQQITERFGFSEIMMTTLE 239

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 240 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 299

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGEI       I+   ++   +  +R
Sbjct: 300 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEII-----PINTDDIDHFGNRRLR 354

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 355 TVGELIQNQVRVGLSRMERVVRERMTTQD 383


>gi|209395095|gb|ACI45362.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  530 bits (1365), Expect = e-148,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  +  P +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKEPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLARP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI+R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGIERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +               L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVPERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ ++GEI  +
Sbjct: 240 ITD-KSGKLIVAKDKRVTARHTRDLEQSGSTHISVPEDFLVGRVVARTIVDTDSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R++  +Y + ++  AYI +TL +D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRELQCIYTNELDQGAYISHTLRSDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N R+  D       +  EDI A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNARIGRDESTGPMVLSNEDIPAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|295394358|ref|ZP_06804583.1| DNA-directed RNA polymerase subunit beta [Brevibacterium mcbrellneri
            ATCC 49030]
 gi|294972816|gb|EFG48666.1| DNA-directed RNA polymerase subunit beta [Brevibacterium mcbrellneri
            ATCC 49030]
          Length = 1217

 Score =  530 bits (1364), Expect = e-148,   Method: Composition-based stats.
 Identities = 184/517 (35%), Positives = 263/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L    + +    M   + LL A    +  +  D  +     V   V+
Sbjct: 732  IVDQGDRVEVGAVLADGPSTEN-GEMALGKNLLVAFMSWEGYNFEDAIILSQRMVQDDVL 790

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ D   + DE+ I+         +IL G+  
Sbjct: 791  SSIHIEEHEIDARDTKLGAEEITRDIPNISPDALAELDERGIIRIGAEVTDGDILVGKVT 850

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 851  PKGETELTPEERLLRAIFGEKSR-----------------EVRDTSLKVPHGETGTVIGV 893

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   +  D++ PGV ++V+V+VA +R I  GDKMAGRHGNKG++S+ILP EDMPF++DG
Sbjct: 894  KVFDREEDDELSPGVNQLVRVYVAQRRKITIGDKMAGRHGNKGVISQILPIEDMPFMEDG 953

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNP GVP RMN+GQ+FE HLGW     G  I+      K   D           
Sbjct: 954  TPVDVILNPHGVPRRMNIGQVFEIHLGWIA-NQGWHIEGNPEWAKELADG---------- 1002

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                               +     + G  V+TPVFDGA E  +  +L     +      
Sbjct: 1003 -------------------KFEFDAEPGTNVATPVFDGAHEHELRGLLDSTRPNRDGDRL 1043

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G++ L+DG +GEPF  P++VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1044 IDSTGKARLFDGRSGEPFPFPISVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1103

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDD+ GR +VYE+IV G++  + G PESF
Sbjct: 1104 QFGGQRFGEMEVWALEAYGAAYTLQELLTIKSDDIPGRVKVYEAIVKGDNLPDPGIPESF 1163

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
             VL+KEMQ+L L +++ +S  ++    ++   +   E
Sbjct: 1164 KVLIKEMQSLCLDVEVLSSDGQSVEMRDDDEVYRAAE 1200



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/634 (51%), Positives = 445/634 (70%), Gaps = 27/634 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       I++TL  D    R++ALLDIY+ +RP + +T   AE++
Sbjct: 278 LKALGWTESQIL--EEFGEFDSIKDTLAKDTVSTREEALLDIYKKLRPAEPATVDAAETL 335

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-- 453
              L+F+  +YDL+ VGR K+N +L +D       +  +DI+A I+ +V L  GK T+  
Sbjct: 336 LRNLYFNPKRYDLAKVGRYKINRKLGVDEALTESVLTVDDIVATIRYIVSLHAGKETMPG 395

Query: 454 -------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ P
Sbjct: 396 VRDGQKADIRVALDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEAITP 455

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+++RD
Sbjct: 456 QTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMDVRD 515

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL S+AR+N +GFIETPYRKV +G VT+   YL+A 
Sbjct: 516 VHPSHYGRMCPIETPEGPNIGLIGSLASYARINPFGFIETPYRKVENGVVTDKTQYLTAD 575

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSIAAS 677
           +E    IAQAN+ L ED  F EE V  R     GE  L+P ++IDF+D S +Q+VS+A +
Sbjct: 576 DELEFNIAQANAPLTEDQKFEEEFVLARPMGGGGEADLIPADEIDFMDVSARQMVSVATA 635

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPL++A+AP+VGTGME   A  +G  I A++AG+V +
Sbjct: 636 LIPFLEHDDANRALMGANMQRQAVPLVRAQAPYVGTGMEYRAAVDAGDVITAEKAGVVTE 695

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  + + + +G           Y+  KF+RSN  T  NQR +V  GD V    ++ADG
Sbjct: 696 VSADYVTVMNDDGT-------TTTYKAEKFRRSNHGTSYNQRIIVDQGDRVEVGAVLADG 748

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           PST+ G++ALG+N+LVAFM W GYNFED++++S+RMV +DV +SIHIEE E+ ARDTKLG
Sbjct: 749 PSTENGEMALGKNLLVAFMSWEGYNFEDAIILSQRMVQDDVLSSIHIEEHEIDARDTKLG 808

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPN+S + L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 809 AEEITRDIPNISPDALAELDERGIIRIGAEVTDGDILVGKVTPKGETELTPEERLLRAIF 868

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEK+ +VRDTSL+VP G +GTV+ V++F+R   D
Sbjct: 869 GEKSREVRDTSLKVPHGETGTVIGVKVFDREEDD 902



 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 90/300 (30%), Positives = 141/300 (47%), Gaps = 30/300 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++P+L+ +Q  S+D  +      D                 GL+  F+ 
Sbjct: 73  RVSFAKIHEPLEVPNLLGLQIDSFDWLIGNERWQDRVAEAIENGDDSVATTSGLEDIFEE 132

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + P+  FSGA  L F  + F+PPK+ +D+C  RD+TY+ PL +                +
Sbjct: 133 ISPVEDFSGAMSLSFSEHRFEPPKYSIDECKERDMTYSAPLFV---------IAEFMNNN 183

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG +F+    +   S + +Y 
Sbjct: 184 TGEIKSQTVFMGDFPLMTDKGTFIINGTERVVVSQLVRSPGAYFESVPDKT--SDRDIYT 241

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W++ E D +D + VR+DR+RK  VT  L ALG    +IL  F         
Sbjct: 242 AKIIPSRGAWLEFEVDKRDQVGVRLDRKRKQSVTVLLKALGWTESQILEEFGEFDSIKDT 301

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
                       L+   K       +   E   +++ + L   L  + K   +  +G   
Sbjct: 302 LAKDTVSTREEALLDIYK------KLRPAEPATVDAAETLLRNLYFNPKRYDLAKVGRYK 355


>gi|209395128|gb|ACI45384.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  530 bits (1364), Expect = e-147,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 311/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   + F  Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPLKRNIEGLQAAFDAAFPIVSHNGFVEMRFTEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDMLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + + + G+ V+   K++T+  ++ L++     + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITN-NAGKVVVAKDKRVTTRHIRELEQSATSHVSVPEDFLVGRVVARAIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVQDVQCIYTNELDQGPYISQTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGSMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDPLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPIFA 486


>gi|209395080|gb|ACI45352.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  530 bits (1364), Expect = e-147,   Method: Composition-based stats.
 Identities = 200/488 (40%), Positives = 312/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++L ++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLTIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTRSSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+                 +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNLRLMDSGAQMEFVSGRL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRIVARSIVDADTGEIIAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +  + ++  AYI  TL  D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGTGVLDVQCIXTNELDQGAYISQTLRIDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K+N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKLNAKIGRNESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395107|gb|ACI45370.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 312/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   + F  Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPLKRNIEGLQAAFDAAFPIVSHNGFVEMRFTEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDMLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + + + G+ V+   K++T+  ++ L++     + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITN-NAGKVVVAKDKRVTTRHIRELEQSATSHVSVPEDFLVGRVVARAIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  ++++D+  +Y + ++   YI  TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGADVQDVQCIYTNELDQGPYISQTLRTDETADEFAARVVIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGSMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E ++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEXAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|2668778|gb|AAB88812.1| DNA-dependent RNA polymerase beta subunit [Rickettsia typhi]
          Length = 335

 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 189/335 (56%), Positives = 245/335 (73%), Gaps = 3/335 (0%)

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             V   +E +K+ Y+  K  L+ RF  K+EK+Q GDD+P G L+VVKVF+A K  +Q GDK
Sbjct: 3    NVMNEIEQIKIHYDEKKHALDKRFATKVEKLQSGDDLPQGALKVVKVFIATKHKLQPGDK 62

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG++SRI+P EDMPFL+DGT VDIVLNPLG+PSRMN+GQI ETHLGWA + L 
Sbjct: 63   MAGRHGNKGVISRIVPEEDMPFLEDGTVVDIVLNPLGLPSRMNIGQILETHLGWASINLA 122

Query: 1150 KKIKSLINDYKANG-DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            KKI +L+ +YK N  DI  ++ FL ++ G       I +  ++ ++    +   GV  +T
Sbjct: 123  KKISTLVKEYKDNNIDIEQIKKFLLELYGKDI--NYILEGSEEGIISFCNKVSKGVYFAT 180

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            PVFDGA  + +  ML++AD D SGQ  L DG TGE FDR VTVG+ Y+LKL H+V +K++
Sbjct: 181  PVFDGAKVQDVKDMLKLADQDLSGQVKLIDGRTGEYFDRLVTVGHKYLLKLPHLVDNKIH 240

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RS G YSLVTQQPLG KS+ GGQR GEME W +QAYGAAY LQEMLT+KSDDV GR + 
Sbjct: 241  SRSIGPYSLVTQQPLGSKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDVNGRIKT 300

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            Y+SIV G + FE+G PESFNV++KE ++L L++ L
Sbjct: 301  YDSIVRGENNFESGIPESFNVMIKEFRSLCLNVKL 335


>gi|229544485|gb|ACQ76422.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  529 bits (1363), Expect = e-147,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 317/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D  FD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFXFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQTEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395023|gb|ACI45314.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  529 bits (1362), Expect = e-147,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 318/488 (65%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDRGKTHGSGKLLFSARIIPHRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCVYTNELDQGAYISHTLRTDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|282855228|ref|ZP_06264560.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            J139]
 gi|282581816|gb|EFB87201.1| DNA-directed RNA polymerase, beta subunit [Propionibacterium acnes
            J139]
          Length = 1159

 Score =  529 bits (1362), Expect = e-147,   Method: Composition-based stats.
 Identities = 193/533 (36%), Positives = 271/533 (50%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  +            I++  ++ VG  V  G  L    +      +     +L A
Sbjct: 650  DGTYQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPSTDNA-ELALGRNMLAA 708

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-LARDKDDE 974
                + ++  D  +     VS  V+       H  + + R   +  E+I   +    +D 
Sbjct: 709  FMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDM 766

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD N   R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 767  LANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        I +          + GD++ PGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 825  VPHGEEGTVIGVRIFDT---------ENGDELAPGVNQMVRVYVAQKRKISIGDKLAGRH 875

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL DGTPVDI+LNPLGVPSRMNVGQ+ E HLGW     G  I  
Sbjct: 876  GNKGVISKILPVEDMPFLPDGTPVDIILNPLGVPSRMNVGQVLEMHLGWIA-HSGWDITQ 934

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+        L    E+                               ++TPVFDGA
Sbjct: 935  AEGDWAERLREVGLIDIPEES-----------------------------RLATPVFDGA 965

Query: 1215 DEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I  +L+           +D  G++ L+DG TGEPF   V VGY+YMLKL+H+V DK
Sbjct: 966  TEQEITGLLQYGHPTRDGEMLVDTDGKATLFDGRTGEPFPSKVGVGYMYMLKLHHLVDDK 1025

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDV GR 
Sbjct: 1026 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAWALQELLTIKSDDVPGRV 1085

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEM++L L++++ NS  +         D
Sbjct: 1086 KVYEAIVKGENIPEPGIPESFKVLVKEMKSLCLNVEVLNSEGQGIDLRGSEED 1138



 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 338/692 (48%), Positives = 454/692 (65%), Gaps = 25/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + +       +  
Sbjct: 166 LVRSPGVYFEKTADKTSDKDIFTCKVIPSR--GAWLEFEIDKRDT--VGVRLDRKRKQNV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +   + +  +        + +  ALLDIY+ +RPG+  +   A
Sbjct: 222 TVFLKALGWTADRIL-EEFGTHESIRQTLEKDHGVETQDQALLDIYKKLRPGEPPSRDAA 280

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--- 449
           + +    +F+  +YDL+ VGR K+N +L L  P D + +  +DI+A I  +  L  G   
Sbjct: 281 QQLLENYYFNPKRYDLAKVGRYKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTAT 340

Query: 450 ---------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                        DDID+ GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ P
Sbjct: 341 LPREGQDDIVVEPDDIDHFGNRRLRTVGELIQNQLRTGLSRMERVVRDRMTTQDIEAITP 400

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 401 QTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLAEMTHKRRLSALGPGGLSRDRAGMEVRD 460

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV DG VT++VVYL+A 
Sbjct: 461 VHPSHYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVVDGHVTDEVVYLTAD 520

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   IAQAN+ LD+DG F  + V  R    E   VP  ++D++D SP+Q+VS+A++LI
Sbjct: 521 EEDRHVIAQANAKLDDDGHFANDRVLVRQRHGEADEVPSSEVDYMDVSPRQMVSVASALI 580

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD++R LMG NMQRQAVPL++ EAPFVGTGME   A   G   +A++AG V  V 
Sbjct: 581 PFLEHDDASRALMGANMQRQAVPLVRTEAPFVGTGMEYRCAVDVGDVTLAEKAGSVLSVS 640

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I I   +G           Y+L KF+RSN  TC+NQRPLVKVG  V     +ADGPS
Sbjct: 641 ADLIDIACDDGT-------YQTYKLEKFRRSNAGTCINQRPLVKVGQRVEVGTPLADGPS 693

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD  +LALGRNML AFMPW G N+ED++++S+R+VS+DV TSIHIEE EV ARDTKLG E
Sbjct: 694 TDNAELALGRNMLAAFMPWQGLNYEDAIILSQRIVSDDVLTSIHIEEHEVDARDTKLGAE 753

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSE+ L N+DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 754 EITRDIPNVSEDMLANLDENGIVRIGAEVGTGDILVGKVTPKGETELTPEERLLRAIFGE 813

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  GTV+ VRIF+    D
Sbjct: 814 KAREVRDTSLKVPHGEEGTVIGVRIFDTENGD 845



 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 110/494 (22%), Positives = 198/494 (40%), Gaps = 60/494 (12%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+++Q  S++  +   I              D     GL+  F+ 
Sbjct: 20  RISFAKIHEPLEVPNLLDLQVESFNWLVGNEIWQSRVDAALAEGRTDINTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  +S    L F  + F+ PK  VD+C  RD TYA PL +T   +            
Sbjct: 80  ISPIEDYSQTMSLSFRDHRFEDPKHSVDECKDRDTTYAAPLFVTAEFM---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
            ++IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 131 TEEIKSQTVFIGDFPLMTSKGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDKDIFT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT FL ALG  ++ IL  F     I  +
Sbjct: 189 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVFLKALGWTADRILEEFGTHESIRQT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K+         GE    ++ ++L      + K   +  +G 
Sbjct: 249 LEKDHGVETQDQALLDIYKKL-------RPGEPPSRDAAQQLLENYYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVI-------------------DEKSLEEIFH 338
              +   GL +  D       +I      V                    +   ++   +
Sbjct: 302 YKINKKLGLSLPFDQQVLTVDDIVAAIHFVCALHEGTATLPREGQDDIVVEPDDIDHFGN 361

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             +R +  L  + +         +V D+   +   +  I            +  +  F  
Sbjct: 362 RRLRTVGELIQNQLRTGLSRMERVVRDRMTTQD--IEAITPQTLINIRPVTAAIKEFFGT 419

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                     + +  +    RL+   P     + ++     ++ +     G+  +  I+ 
Sbjct: 420 SQLSQFMDQNNPLAEMTHKRRLSALGPGG---LSRDRAGMEVRDVHPSHYGR--MCPIET 474

Query: 459 LGNRRVRSVGEMLK 472
                +  +G +  
Sbjct: 475 PEGPNIGLIGSLAS 488


>gi|225376346|ref|ZP_03753567.1| hypothetical protein ROSEINA2194_01987 [Roseburia inulinivorans DSM
            16841]
 gi|225211722|gb|EEG94076.1| hypothetical protein ROSEINA2194_01987 [Roseburia inulinivorans DSM
            16841]
          Length = 381

 Score =  529 bits (1362), Expect = e-147,   Method: Composition-based stats.
 Identities = 152/333 (45%), Positives = 206/333 (61%), Gaps = 15/333 (4%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
             + K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL
Sbjct: 1    MEAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFL 60

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI       
Sbjct: 61   PNGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGAKEIDIQDTLELA 120

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
               +       +    D      +   W +                  ++ +   +   G
Sbjct: 121  NDYVNFEWEDFEAKYKDVLGEEVMKYLWDN--------------RDHRALWKGVPISRDG 166

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L DG TGEPFD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 167  KVQLRDGRTGEPFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQ 226

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+I+ G++  E G PESF VL+K
Sbjct: 227  RFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIIKGDNIPEPGIPESFKVLLK 286

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            E+Q+LGL + + +        ME   ++   +L
Sbjct: 287  ELQSLGLDVTVLDDEGNEVELMET-SEYGNTDL 318


>gi|62720646|gb|AAX93859.1| RNA polymerase subunit B [Mycobacterium bolletii]
          Length = 1171

 Score =  528 bits (1361), Expect = e-147,   Method: Composition-based stats.
 Identities = 303/949 (31%), Positives = 454/949 (47%), Gaps = 136/949 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNE----GLQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      +    R       GL+     + PI 
Sbjct: 32  RLSFAKLREPLAVPGLLDVQTESFEWLVGSPRWREVATARGEVNPTGGLEEILTELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 201 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 260

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
              P  A   +            ++ + ++E+   K+    L +  + K  K LG     
Sbjct: 261 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLG----- 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G   A+      T E  +        + L  +   +                 +    
Sbjct: 316 LGGTNPAQVTTTTLTEEDVVA-----TIEYLVRLHEGQTT---------------MTAPG 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +   D  D      R +R            +         +  LS + RV        
Sbjct: 356 GVEVPVDVDDIDHFGNRRLR--------TVGELIQN----QIRVGLSRMERVVRERMTTQ 403

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       I  + +I I  ++  ++   GT      +      S     +    LG   +
Sbjct: 404 DVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGL 459

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R      + +++  V P       P+ +             +   VN    I       
Sbjct: 460 TRD----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI------- 508

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              +    +   GV   ++H           T++  +  +V+   S    N     E   
Sbjct: 509 ---ETPYRKVSDGVVTDEIH---------YLTADEEDRHVVAQANSPVDANGRFTEE--- 553

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+   +   +V ++SA E +   +                                   
Sbjct: 554 -KILVRRKGGEVEFVSATEVDYMDV----------------------------------- 577

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
               SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 578 ----SPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 633

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +G  +VA++AG++E+V A  + + + +G           YRL KF RSN  TC NQ+P+V
Sbjct: 634 AGDVVVAEKAGVIEEVSADYVTVMADDGTRQS-------YRLRKFARSNHGTCANQKPIV 686

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G  V    +IADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSI
Sbjct: 687 DEGQRVEAGQVIADGPCTENGEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVLTSI 746

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 747 HIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKG 806

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 807 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 855



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 266/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+      +                   
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +    +   +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149


>gi|256825894|ref|YP_003149854.1| DNA-directed RNA polymerase subunit beta [Kytococcus sedentarius DSM
            20547]
 gi|256689287|gb|ACV07089.1| DNA-directed RNA polymerase subunit beta [Kytococcus sedentarius DSM
            20547]
          Length = 1161

 Score =  528 bits (1361), Expect = e-147,   Method: Composition-based stats.
 Identities = 192/540 (35%), Positives = 269/540 (49%), Gaps = 63/540 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  R             ++  ++  G  V  G ++    +      M   + L
Sbjct: 649  QNDDGTYQSYRIDKFSRSNQGTCYNQRVVVAAGDHVEKGQLIADGPSTDN-GEMALGKNL 707

Query: 913  LRAIF---GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            L A     G    D    S R+    + + + +        D       + R+   +   
Sbjct: 708  LVAFMPWEGYNYEDAIILSQRLVQDDTLSSIHIEEHEIDARDTKLGPEEITRDIPNVSDE 767

Query: 970  DKDD--EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               D  E+ I+      R  ++L G+    G         L   +  E  R         
Sbjct: 768  VLADLDERGIIRIGAEVRDGDLLVGKVTPKGETELTPEERLLRAIFGEKAR--------- 818

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E      +            K+   + GD++PPGV ++V+V+VA KR I  G
Sbjct: 819  --------EVRDTSMKVPHGETGTVIGVKVFDREEGDELPPGVNQMVRVYVANKRKITDG 870

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK+AGRHGNKG++S+ILP EDMPFL DGTPVD+VLNPLGVPSRMNVGQ+ E HLGWA   
Sbjct: 871  DKLAGRHGNKGVISKILPVEDMPFLPDGTPVDVVLNPLGVPSRMNVGQVLELHLGWAAAN 930

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G KI+                                     +++     +      V+
Sbjct: 931  -GWKIEGSPEWA-------------------------------ENLAEEHREAGPWTRVA 958

Query: 1208 TPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDGA EE I  +L            +D SG++ L+DG TGEP+  PV+VGY+Y+LKL
Sbjct: 959  TPVFDGAREEEITGLLDSTIPSRDGQRLIDGSGKAQLFDGRTGEPYPEPVSVGYMYILKL 1018

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKS
Sbjct: 1019 HHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKS 1078

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV GR +VYESIV G +  E G PESF VL+KEMQ+L L++++ ++  +N    E+  +
Sbjct: 1079 DDVTGRVKVYESIVKGENVPEPGIPESFKVLIKEMQSLCLNVEVLSTDGQNIDLREQDQE 1138



 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 332/695 (47%), Positives = 468/695 (67%), Gaps = 29/695 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K V    +      G ++  ++   +   + ++         
Sbjct: 166 IVRSPGVYFERSIDRATDKEVYSAKVIPSR--GAWLEFEVDKKDMVGVRVDRKRKQSVTV 223

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       IR TL  D   ++ +ALLDIYR +RPG+  T   A
Sbjct: 224 L--LKALGWTEAQIL--EEFGQYESIRATLEKDHTANQDEALLDIYRKLRPGEPPTVEAA 279

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++ + L+F+  +YDL+ VGR K+N +L LD P     +  +D++  IK +V L  G+ T
Sbjct: 280 QNLLDNLYFNGKRYDLAKVGRYKINKKLGLDAPLTDSTLSVDDVVRTIKYIVALHAGETT 339

Query: 453 I---------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           +               DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 340 MEGVRHGEAVDLRVETDDIDHFGNRRLRTVGELIQNQVRTGLSRMERVVRERMTTQDVEA 399

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 400 ITPQTLINIRPVVAAIREFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 459

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ +L S+ R+N +GF+ETPYRKV  G VT+DV YL
Sbjct: 460 VRDVHPSHYGRMCPIETPEGPNIGLIGALASYGRINPFGFVETPYRKVKGGFVTDDVEYL 519

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAA 676
           +A EE++  IAQAN+ L EDG F  E V  R   GE   VPR+++ ++D SP+Q+VS A 
Sbjct: 520 TADEEDDFVIAQANAPLTEDGQFAGERVLVRSKGGEVEFVPRDEVHYMDVSPRQMVSAAT 579

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           ++IPFLE+DD+NR LMG NMQRQ VPL+KAEAP VGTG+E   A  +G  + A++AG+++
Sbjct: 580 AMIPFLEHDDANRALMGANMQRQGVPLVKAEAPLVGTGIEYRAALDTGDVVRAEKAGVIQ 639

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            V A  +  ++ +G           YR+ KF RSNQ TC NQR +V  GD V +  +IAD
Sbjct: 640 SVSADLVTAQNDDGTYQS-------YRIDKFSRSNQGTCYNQRVVVAAGDHVEKGQLIAD 692

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GPSTD G++ALG+N+LVAFMPW GYN+ED++++S+R+V +D  +SIHIEE E+ ARDTKL
Sbjct: 693 GPSTDNGEMALGKNLLVAFMPWEGYNYEDAIILSQRLVQDDTLSSIHIEEHEIDARDTKL 752

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITRDIPNVS+E L ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 753 GPEEITRDIPNVSDEVLADLDERGIIRIGAEVRDGDLLVGKVTPKGETELTPEERLLRAI 812

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA +VRDTS++VP G +GTV+ V++F+R   D
Sbjct: 813 FGEKAREVRDTSMKVPHGETGTVIGVKVFDREEGD 847



 Score =  336 bits (862), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 92/302 (30%), Positives = 146/302 (48%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F +  E +++PDL+ +Q  S+D  L      +                 GL+  F+ 
Sbjct: 20  RLSFSRIHEPLEVPDLLALQTESFDWLLGNEAWQERVAEASAAGRNDTSTTSGLEDIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FS    L F  + F+  K+  ++C+ RD+TY+ PL +T   +            
Sbjct: 80  ISPIEDFSETMSLSFSEHRFEEIKYTEEECIERDMTYSAPLFVTAEFM---------NGE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMTK GTF+I G +R+VVSQ+ RSPG++F+    R   + K +Y+
Sbjct: 131 TGEIKSQTVFMGDFPLMTKRGTFIINGTERVVVSQIVRSPGVYFERSIDR--ATDKEVYS 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D KD++ VR+DR+RK  VT  L ALG    +IL  F  Y  I  +
Sbjct: 189 AKVIPSRGAWLEFEVDKKDMVGVRVDRKRKQSVTVLLKALGWTEAQILEEFGQYESIRAT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   L  + K   +  +G 
Sbjct: 249 LEKDHTANQDEA--------LLDIYRKLRPGEPPTVEAAQNLLDNLYFNGKRYDLAKVGR 300

Query: 299 TS 300
             
Sbjct: 301 YK 302


>gi|34595751|gb|AAQ76598.1| RpoB [Mycobacterium immunogenum]
          Length = 1171

 Score =  528 bits (1361), Expect = e-147,   Method: Composition-based stats.
 Identities = 302/949 (31%), Positives = 455/949 (47%), Gaps = 136/949 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNE----GLQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      +    R       GL+     + PI 
Sbjct: 32  RLSFAKLREPLAVPGLLDVQTDSFEWLVGSPRWREVATARGEVNPTGGLEEILTELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD +  +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDENIDK--STEKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 201 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 260

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
              P  A   +            ++ + ++E+   K+    L +  + K  K LG     
Sbjct: 261 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLG----- 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G   A+      T E  +        + L  +   +                 +    
Sbjct: 316 LGGTNPAQVTTTTLTEEDVVA-----TIEYLVRLHEGQTT---------------MTAPG 355

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             +   D  D      R +R            +         +  LS + RV        
Sbjct: 356 GVEVPVDVDDIDHFGNRRLR--------TVGELIQN----QIRVGLSRMERVVRERMTTQ 403

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D       I  + +I I  ++  ++   GT      +      S     +    LG   +
Sbjct: 404 DVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGL 459

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R      + +++  V P       P+ +             +   VN    I       
Sbjct: 460 TRD----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI------- 508

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              +    +   GV   ++H           T++  +  +V+   S    N     E   
Sbjct: 509 ---ETPYRKVSDGVVTDEIH---------YLTADEEDRHVVAQANSPVDANGRFTEE--- 553

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+   +   +V ++SA E +   +                                   
Sbjct: 554 -KILVRRKGGEVEFVSATEVDYMDV----------------------------------- 577

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
               SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 578 ----SPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 633

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +G  +VA++AG++E+V A  + + + +G           YRL KF RSN  TC NQ+P+V
Sbjct: 634 AGDVVVAEKAGVIEEVSADYVTVMADDGTRQS-------YRLRKFARSNHGTCANQKPIV 686

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G  V    ++ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSI
Sbjct: 687 DEGQRVEVGQVLADGPCTENGEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVLTSI 746

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 747 HIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKG 806

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 807 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 855



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 266/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEVGQVLADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+      +                   
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +    +   +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149


>gi|209395047|gb|ACI45330.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  528 bits (1360), Expect = e-147,   Method: Composition-based stats.
 Identities = 197/488 (40%), Positives = 310/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL    AP +R  EGLQAAF + FPI + +G   + ++ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAEKAPQKRNVEGLQAAFDAAFPIVSHNGLVEMRYLEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++K Q +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKGQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKDHSSGKLLFSARIIPYRGSWLDFEFDPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  +++ +TGEI  +
Sbjct: 240 ITD-KSGKVILAKDKRVTVRHIRELEQSGTSHVSVPEDFLVGRVVARGVIDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGANVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRR R VGE+ +NQYR GL R+E+++KER+  V+ + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRARCVGELAENQYRTGLARIEKAVKERLGHVEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           I +KP+ +
Sbjct: 479 IYSKPISA 486


>gi|300779860|ref|ZP_07089716.1| DNA-directed RNA polymerase subunit beta [Corynebacterium genitalium
            ATCC 33030]
 gi|300533970|gb|EFK55029.1| DNA-directed RNA polymerase subunit beta [Corynebacterium genitalium
            ATCC 33030]
          Length = 1165

 Score =  528 bits (1360), Expect = e-147,   Method: Composition-based stats.
 Identities = 193/577 (33%), Positives = 277/577 (48%), Gaps = 68/577 (11%)

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            Y+  D ++ +   V EDV         +V+      G  E                ++  
Sbjct: 624  YDAGDIVIANNAGVVEDVTG-------DVITIMDDEGQRESYLLRTFERTNQGTCYNQTP 676

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   V+
Sbjct: 677  IVSAGDRVEAGQVIADGPGTK-DGEMALGTNLLVAFMPWEGHNYEDAIILNQRVVEQDVL 735

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 736  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 794

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 795  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 837

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 838  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPEEDMPFMAD 897

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 898  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEQLYD 954

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L     +  G  
Sbjct: 955  VPPESLT-------------------------ATPVFDGATNDEIAGLLANTKPNRDGDV 989

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 990  MVDGDGKTVLFDGRSGEPFKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1050 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  ++++ 
Sbjct: 1110 FKVLLKELQSLCLNVEVLSTDGTPMELSGDDDEYDQA 1146



 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 326/760 (42%), Positives = 467/760 (61%), Gaps = 48/760 (6%)

Query: 230 STFYPKIVYSQR--GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKL 280
             ++  I Y+     D      SA   +    +++   +I +    I       + G  +
Sbjct: 98  DPYFEDIKYTIDECKDKDIN-YSAPLYVTAEFINNDTQEIKSQTVFIGDFPLMTDKGTFI 156

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIY-----------IEAG 325
            +G  + +  + V+  G+  D          +    V    G              +   
Sbjct: 157 VNGTERVIVSQLVRSPGVYFDETIDKSTERPLHSVKVIPSRGAWLEFDVDKRDTVGVRID 216

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
               +     +         I   +    +  +  TL  D   +  +ALL+IYR  RPG+
Sbjct: 217 RKRRQPVTVLLKALGWTTEQI--KERFGFSEIMMTTLENDGVANTDEALLEIYRKQRPGE 274

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILV 444
             T  +A+S+    FF + +YDL+ VGR K+N +L L    D    + +EDI   ++ LV
Sbjct: 275 QPTRDLAQSLLENAFFRAKRYDLARVGRYKVNRKLGLGGDHDGEMTLTEEDIATTLEYLV 334

Query: 445 DLRNGKG------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            L  G+               DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++
Sbjct: 335 RLHAGEREMTSPEGVVIPINTDDIDHFGNRRLRTVGELVQNQVRVGLSRMERVVRERMTT 394

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R 
Sbjct: 395 QDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRE 454

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ +L S+ARVN +GFIETPY+KV DG++T+
Sbjct: 455 RAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGALASYARVNPFGFIETPYQKVVDGQITD 514

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   IA+A ++ D D + T + +  R   G+  +V  + +D++D SP+Q+
Sbjct: 515 EIDYLTADEEDRFAIAEAATAHDADRNITADRIEVRLKDGDIGVVGPKDVDYVDISPRQM 574

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+A ++IPFLE+DD+NR LMG NMQ+QAVPLL++EA +V TG E   A  +G  ++A  
Sbjct: 575 VSVATAMIPFLEHDDANRALMGANMQKQAVPLLRSEAAYVATGTEMRAAYDAGDIVIANN 634

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG+VE V    I I   EG  +        Y L  F+R+NQ TC NQ P+V  GD V   
Sbjct: 635 AGVVEDVTGDVITIMDDEGQRES-------YLLRTFERTNQGTCYNQTPIVSAGDRVEAG 687

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            +IADGP T  G++ALG N+LVAFMPW G+N+ED++++++R+V +DV TS+HIEE E+ A
Sbjct: 688 QVIADGPGTKDGEMALGTNLLVAFMPWEGHNYEDAIILNQRVVEQDVLTSVHIEEHEIDA 747

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLG EEITR+IPNVSE+ LK++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+
Sbjct: 748 RDTKLGAEEITREIPNVSEDVLKDLDERGIIRIGADVRDGDILVGKVTPKGETELTPEER 807

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LLRAIFGEKA +VRDTSL+VP G +G V+ VR F+R   D
Sbjct: 808 LLRAIFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDDD 847



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 94/389 (24%), Positives = 171/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +      + +  E         GL+   + + 
Sbjct: 24  ERYSFAKIAEPIALPGLLDVQSESFAWLVGTPEWRERQAEERGSDARITSGLEDILEEIS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 84  PIQDYSGNMSLSLSDPYFEDIKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ +
Sbjct: 135 EIKSQTVFIGDFPLMTDKGTFIVNGTERVIVSQLVRSPGVYFDETIDK--STERPLHSVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIKERFGFSEIMMTTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 253 NDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRAKRYDLARVGRYKVNRKLGLG 312

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G +       I+   ++   +  +R
Sbjct: 313 GDHDGEMTLTEEDIATTLEYLVRLHAGEREMTSPEGVVI-----PINTDDIDHFGNRRLR 367

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 368 TVGELVQNQVRVGLSRMERVVRERMTTQD 396


>gi|209395113|gb|ACI45374.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  528 bits (1359), Expect = e-147,   Method: Composition-based stats.
 Identities = 201/488 (41%), Positives = 313/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRNIEGLQAAFDAAFPIVSHNGFVGMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R L +A  ++  ++L ++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLAFASAVRAKVQLFIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFDSKDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDSKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPEAILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + +++ G   + +  D L G  VA  +V+ ETGEI  +
Sbjct: 240 VTD-KSGKVIVAKDKRVTARHTREIEQSGSTHISVPEDFLIGRVVARSVVDAETGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A + + E  L+++  + ++D+  +Y + ++  AYI  TL  D+  D   A + IYR+MRP
Sbjct: 299 ANEELTETLLKKLRSAAVQDLQCIYTNELDQGAYISQTLRIDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI+A+IKIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRSESTGPMVLSNEDILAVIKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|152964649|ref|YP_001360433.1| DNA-directed RNA polymerase subunit beta [Kineococcus radiotolerans
            SRS30216]
 gi|182676583|sp|A6W5T0|RPOB_KINRD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|151359166|gb|ABS02169.1| DNA-directed RNA polymerase, beta subunit [Kineococcus radiotolerans
            SRS30216]
          Length = 1171

 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 192/515 (37%), Positives = 263/515 (51%), Gaps = 69/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +I  G  V  G +L    +  G   M     L+ A    +  +  D  +     V   V+
Sbjct: 687  VINEGDRVEVGTVLADGPSTDG-GEMALGRNLMVAFMPWEGHNYEDAIILSQRLVQDDVL 745

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+      R  ++L G
Sbjct: 746  SSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEVLADL-DERGIIRIGAEVRDGDLLVG 802

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 803  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGTV 845

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+     GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 846  IGVKVFDRDEGDELPPGVNQLVRVYVANKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 905

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD++LNPLGVPSRMNVGQ+ E HLGW     G KI+   +  K            
Sbjct: 906  EDGTPVDVILNPLGVPSRMNVGQVLELHLGWIAS-RGWKIEGQPDWAK------------ 952

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE-- 1230
                                +     +  +G  ++TPVFDGA EE I  +L         
Sbjct: 953  -------------------LIPEEIREAPAGSRIATPVFDGAREEEITGLLSSTIPTRDG 993

Query: 1231 ------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 994  DRLVGGDGKARLFDGRSGEPFPDPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1053

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G P
Sbjct: 1054 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIP 1113

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S        +   D
Sbjct: 1114 ESFKVLIKEMQSLCLNVEVLSSDGMAIEMRDSDED 1148



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/663 (49%), Positives = 455/663 (68%), Gaps = 27/663 (4%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  +I   +T  + ++         L +        I   + D  +    + +TL  
Sbjct: 206 GAWLEFEIDKRDTVGVRVDRKRKQSVTVLMKALGWSESQIREEFADYES----MISTLEK 261

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D     +DALLDIYR +RPG+  T   A ++ + L+F+  +YDL+ VGR K+N +L  + 
Sbjct: 262 DHTSGVEDALLDIYRKLRPGEPPTQEAARNLLDNLYFNPKRYDLAKVGRYKVNKKLGTEE 321

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGE 469
           P     +  +DI+  IK LV L  G+                 +DDID+ GNRR+RSVGE
Sbjct: 322 PLSDSVLSVDDIVRTIKYLVKLHAGEVTMPGVKNGQPVDVRVEVDDIDHFGNRRLRSVGE 381

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQLSQ  +  
Sbjct: 382 LIQNQVRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQT 441

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+
Sbjct: 442 NPLAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSY 501

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR- 648
            R+N +GFIETPYRK+ DG V+++V YL+A EE+   IAQAN+ LD D  F E  V  R 
Sbjct: 502 GRINPFGFIETPYRKIVDGVVSDEVEYLTADEEDAFVIAQANAPLDADSRFAEARVLVRA 561

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE   VPR+++D++D + +Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+K+EA
Sbjct: 562 KGGETEFVPRDEVDYMDVAARQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVKSEA 621

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTGME   A  +G  +VA +AG+   V A  I   + +G           Y++ KF+
Sbjct: 622 PLIGTGMEFRAAVDAGDVVVATKAGVATDVSADMITTSNDDGTS-------TTYKVAKFR 674

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T  NQ+ ++  GD V    ++ADGPSTD G++ALGRN++VAFMPW G+N+ED+++
Sbjct: 675 RSNHGTAYNQQVVINEGDRVEVGTVLADGPSTDGGEMALGRNLMVAFMPWEGHNYEDAII 734

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNV+EE L ++DE GII +GAEV
Sbjct: 735 LSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVAEEVLADLDERGIIRIGAEV 794

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ V++F+R 
Sbjct: 795 RDGDLLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVKVFDRD 854

Query: 949 GID 951
             D
Sbjct: 855 EGD 857



 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 97/299 (32%), Positives = 144/299 (48%), Gaps = 29/299 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKSV 62
           R  FGK  E +++PDL+ +Q  S+D  L      D                GL+  F+ +
Sbjct: 31  RYSFGKIHEPLEVPDLLALQTDSFDWLLGNKRWQDRVEASTNGGLAVPTTSGLEEIFEEI 90

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG+  L F  + F+PPK+ +DDC  RDLTY+ PL +T   I           + 
Sbjct: 91  SPIEDFSGSMSLSFRDHRFEPPKYSLDDCKERDLTYSAPLFVTAEFI---------NGNT 141

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPGI+F+    +   S +  +  
Sbjct: 142 GEIKSQTVFMGDFPLMTDRGTFVINGTERVVVSQLVRSPGIYFERVPDKT--SDRDTWTA 199

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           +IIP +G W++ E D +D + VR+DR+RK  VT  + ALG    +I   F          
Sbjct: 200 KIIPSRGAWLEFEIDKRDTVGVRVDRKRKQSVTVLMKALGWSESQIREEFADYESMISTL 259

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           +          L+   +       +  GE    E+ + L   L  + K   +  +G   
Sbjct: 260 EKDHTSGVEDALLDIYR------KLRPGEPPTQEAARNLLDNLYFNPKRYDLAKVGRYK 312


>gi|158317799|ref|YP_001510307.1| DNA-directed RNA polymerase subunit beta [Frankia sp. EAN1pec]
 gi|226699407|sp|A8LC64|RPOB_FRASN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158113204|gb|ABW15401.1| DNA-directed RNA polymerase, beta subunit [Frankia sp. EAN1pec]
          Length = 1141

 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 337/684 (49%), Positives = 476/684 (69%), Gaps = 18/684 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K +    +      G ++  +I   +T  + I+         
Sbjct: 155 LVRSPGVYFEKAIDKASDKDLFSCKVIPSR--GAWLEFEIDKRDTVGVRIDRKRRQSVTV 212

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 213 L--LKALGWDEARIL--ERFGDFPSMRVTLEKDHTSSQDDALLDIYRKLRPGEPPTRESA 268

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   LFF+  +YDL+ VGR K+N +L L+   DV  + ++D++  I+ +V L  G+  
Sbjct: 269 QTLLENLFFNPKRYDLAKVGRYKVNKKLTLEVAHDVGVLTEDDVVRTIEYIVKLHAGQDP 328

Query: 453 ----IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +P
Sbjct: 329 DNYEVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRP 388

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           VV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+HYGR
Sbjct: 389 VVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGR 448

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL+ SL++FARVN +GF+ETPYRKV +G+VT  + YL+A EE+    A
Sbjct: 449 MCPIETPEGPNIGLIGSLSTFARVNPFGFVETPYRKVENGRVTGQIDYLTADEEDRHVKA 508

Query: 629 QANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           QAN+ L+ DG+F E+ V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+
Sbjct: 509 QANTPLNADGTFAEDRVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDA 568

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  +V  ++G+VE + A  I +  
Sbjct: 569 NRALMGSNMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVVVCAQSGVVEDLSADYITVMH 628

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G           YRL KF+RSNQ TC+NQ+P+V  GD V    +IADGP TD G++AL
Sbjct: 629 DDGTR-------RTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDNGEMAL 681

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPN
Sbjct: 682 GKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPN 741

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V+EE L ++DE GII +GAEV+PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDT
Sbjct: 742 VAEEVLADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDT 801

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SL+VP G SG V+ VR+F+R   D
Sbjct: 802 SLKVPHGESGKVIGVRVFSREDGD 825



 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 196/533 (36%), Positives = 272/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  G  V  G ++           M   + LL A
Sbjct: 630  DGTRRTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDN-GEMALGKNLLVA 688

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 689  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 746

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 747  LADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 799

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 800  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 855

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL DGT VD+VLNP GVP RMN+GQI ETHLGW     G ++ S
Sbjct: 856  GNKGVIAKILPVEDMPFLPDGTAVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDS 914

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                +K                                    A+    G  V+TPVFDGA
Sbjct: 915  GAEGWKERLRGIG-----------------------------ADAAPPGTNVATPVFDGA 945

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ LYDG TGEP+  PV VGYIY+LKL H+V DK
Sbjct: 946  REEEITGLLDATLPNRDGQQMIGSSGKAELYDGRTGEPYPYPVAVGYIYILKLLHLVDDK 1005

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1006 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1065

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1066 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVSIEMRDTDED 1118



 Score =  340 bits (873), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 105/350 (30%), Positives = 171/350 (48%), Gaps = 27/350 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +  +I  +                 GL+  F+ 
Sbjct: 9   RISFAKIIEPLEVPDLLALQTQSFDWLIGNDIWAERVQEAIDADRNDVPITSGLEEVFEE 68

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK+ V++C  +D+TY+ PL +T               +
Sbjct: 69  ISPIEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTYSAPLFVTAEFT---------NNT 119

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K L++
Sbjct: 120 TGEIKSQTVFMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFEKAIDK--ASDKDLFS 177

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  +P +  +
Sbjct: 178 CKVIPSRGAWLEFEIDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGDFPSMRVT 237

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K L 
Sbjct: 238 LEKDHTSSQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLT 297

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +      G+   +D+V      + + AG   D   +++I H   R +  +
Sbjct: 298 LEVAHDVGVLTEDDVVRTIEYIVKLHAGQDPDNYEVDDIDHFGNRRLRTV 347


>gi|209395029|gb|ACI45318.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395119|gb|ACI45378.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  527 bits (1358), Expect = e-147,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 317/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI   +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVPHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL T++  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTNETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|329938251|ref|ZP_08287702.1| DNA-directed RNA polymerase subunit beta [Streptomyces
            griseoaurantiacus M045]
 gi|329302740|gb|EGG46630.1| DNA-directed RNA polymerase subunit beta [Streptomyces
            griseoaurantiacus M045]
          Length = 1161

 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 188/508 (37%), Positives = 274/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVNEGDRVIAGQVLADGPATQN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVVAGDILVGK 791

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +     ++  R  ++   
Sbjct: 792  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGEIGKVIGVRLFDR--- 841

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 842  -EEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 900

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L  ++                    
Sbjct: 901  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEEWAQRLQGIG------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                             A+  + G  V+TPVFDGA E+ +  +L+           +  +
Sbjct: 948  -----------------ADNVQPGTNVATPVFDGAREDELAGLLQHTIPNRDGERMVQPT 990

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 991  GKARLFDGRSGEPFPAPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1050

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1051 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1110

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1111 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 341/670 (50%), Positives = 456/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  EDII+ IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADAPLDAGILTVEDIISTIKYLVQLHAGETETVGDNGQPVVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG+VT+DV YL+A EE+   IAQAN++L +D  F E
Sbjct: 483 IGSLASYGRVNAFGFVETPYRKVVDGQVTDDVDYLTADEEDRFVIAQANATLTDDLRFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 TRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTTNDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD V    ++ADGP+T  G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLAKFSRSNQGTSVNQKVIVNEGDRVIAGQVLADGPATQNGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRLFDREEGD 845



 Score =  340 bits (872), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 203/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVESALESGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   EDI++     + + AG+                 ++   +  +R +  
Sbjct: 310 ADAPLDAGILTVEDIISTIKYLVQLHAGETETVGDNGQPVVVETDDIDHFGNRRLRSVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|288917220|ref|ZP_06411589.1| DNA-directed RNA polymerase, beta subunit [Frankia sp. EUN1f]
 gi|288351411|gb|EFC85619.1| DNA-directed RNA polymerase, beta subunit [Frankia sp. EUN1f]
          Length = 1141

 Score =  527 bits (1357), Expect = e-147,   Method: Composition-based stats.
 Identities = 340/684 (49%), Positives = 475/684 (69%), Gaps = 18/684 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K +    I      G ++  +I   +T  + I+         
Sbjct: 155 LVRSPGVYFEKAIDKASDKDLFSCKIIPSR--GAWLEFEIDKRDTVGVRIDRKRRQSVTV 212

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 213 L--LKALGWDEARIL--ERFGEFPSMRVTLEKDHTSSQDDALLDIYRKLRPGEPPTRESA 268

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   LFF+  +YDL+ VGR K+N +L L+   DV  + ++D++  I+ +V L  G+  
Sbjct: 269 QTLLENLFFNPKRYDLAKVGRYKVNKKLELEVAYDVGVLTEDDVVRTIEYIVKLHAGQEP 328

Query: 453 ----IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +P
Sbjct: 329 DTYEVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRP 388

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           VV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+HYGR
Sbjct: 389 VVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGR 448

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL+ SL++FARVN +GF+ETPYRKV +G+VT  + YL+A EE+    A
Sbjct: 449 MCPIETPEGPNIGLIGSLSTFARVNPFGFVETPYRKVENGRVTGQIDYLTADEEDRHVKA 508

Query: 629 QANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           QAN+ L+ DGSF EE V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+
Sbjct: 509 QANTPLNADGSFAEERVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDA 568

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  +V  ++G+VE + A  I +  
Sbjct: 569 NRALMGSNMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVVVCAQSGVVEDLSADYITVMH 628

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G           YRL KF+RSNQ TC+NQ+P+V  GD V    +IADGP TD G++AL
Sbjct: 629 DDGTR-------RTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDNGEMAL 681

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPN
Sbjct: 682 GKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPN 741

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V+EE L ++DE GII +GAEV+PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDT
Sbjct: 742 VAEEVLADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDT 801

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SL+VP G SG V+ VR+F+R   D
Sbjct: 802 SLKVPHGESGKVIGVRVFSREDGD 825



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 197/533 (36%), Positives = 273/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  G  V  G ++           M   + LL A
Sbjct: 630  DGTRRTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDN-GEMALGKNLLVA 688

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 689  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 746

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 747  LADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 799

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 800  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 855

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL DGT VD+VLNP GVP RMN+GQI ETHLGW     G ++ S
Sbjct: 856  GNKGVIAKILPVEDMPFLSDGTAVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDS 914

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+K                                    A+    G  V+TPVFDGA
Sbjct: 915  GSEDWKERLRGIG-----------------------------ADAAPPGTNVATPVFDGA 945

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ LYDG TGEP+  PV VGYIY+LKL H+V DK
Sbjct: 946  REEEITGLLDATLPNRDGTQLIGSSGKAELYDGRTGEPYPYPVAVGYIYILKLLHLVDDK 1005

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1006 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1065

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1066 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVSIEMRDTDED 1118



 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 104/350 (29%), Positives = 170/350 (48%), Gaps = 27/350 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE------------GLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +  +   +                 GL+  F+ 
Sbjct: 9   RISFAKIIEPLEVPDLLALQTQSFDWLIGNDAWAERVQESIDAGRDDVPITSGLEEVFEE 68

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK+ V++C  +D+T++ PL +T               +
Sbjct: 69  ISPIEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTFSAPLFVTAEFT---------NNT 119

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K L++
Sbjct: 120 TGEIKSQTVFMGDFPLMTTKGTFVINGTERVVVSQLVRSPGVYFEKAIDK--ASDKDLFS 177

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C+IIP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  +P +  +
Sbjct: 178 CKIIPSRGAWLEFEIDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGEFPSMRVT 237

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K L 
Sbjct: 238 LEKDHTSSQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLE 297

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +      G+   +D+V      + + AG   D   +++I H   R +  +
Sbjct: 298 LEVAYDVGVLTEDDVVRTIEYIVKLHAGQEPDTYEVDDIDHFGNRRLRTV 347


>gi|284034014|ref|YP_003383945.1| DNA-directed RNA polymerase subunit beta [Kribbella flavida DSM
            17836]
 gi|283813307|gb|ADB35146.1| DNA-directed RNA polymerase, beta subunit [Kribbella flavida DSM
            17836]
          Length = 1160

 Score =  526 bits (1356), Expect = e-147,   Method: Composition-based stats.
 Identities = 192/533 (36%), Positives = 267/533 (50%), Gaps = 52/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R            I++  ++  G  V  G  L        E  M     LL A
Sbjct: 648  DGTYQTYRLAKFRRSNQGTCINQRPLVDAGQRVEVGSPLADGPCT-DEGEMALGRNLLVA 706

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   ++       H  + + R   +  E+I     +  DE 
Sbjct: 707  FMPWEGHNYEDAIILSQRVVQQDLLTSIHIEEH--EVDARDTKLGPEEITRDIPNVSDEM 764

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +      R+ + + A +       
Sbjct: 765  LADLDERGIIRIGAEVTTGDILVGKVTPKGETELTPE--ERLLRAIFGEKAREVRDTSLK 822

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            V   +        + +            GD++PPGV ++V+V+VA KR I  GDK+AGRH
Sbjct: 823  VPHGENGTVIGVRVFDRD---------NGDELPPGVNQLVRVYVAQKRKISVGDKLAGRH 873

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPF++DGT VDI+LNPLGVP RMNVGQ+ ETHLGW     G K+  
Sbjct: 874  GNKGVISKILPVEDMPFMEDGTQVDIILNPLGVPGRMNVGQVLETHLGWVAS-RGWKVDE 932

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               +  A   I         +                              V+TPVFDGA
Sbjct: 933  TNTEEWAQRLIKIGAGEAPPMTN----------------------------VATPVFDGA 964

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE +  +L     +          G++ L+DG +GEPF  PV VGY+YMLKL+H+V DK
Sbjct: 965  KEEEVIGLLGSTLPNRDGDRMVDQTGKARLFDGRSGEPFPEPVGVGYMYMLKLHHLVDDK 1024

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR 
Sbjct: 1025 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFALQELLTIKSDDVVGRV 1084

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VLVKEMQ+L L++++ +S        +   D
Sbjct: 1085 KVYEAIVKGENIPEPGIPESFKVLVKEMQSLCLNVEVLSSDGSRVEMRDSEED 1137



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 334/628 (53%), Positives = 447/628 (71%), Gaps = 21/628 (3%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      D  IL  +       IR TL  D    + DALLDIYR +RPG+  T   A+++
Sbjct: 225 LKALGWTDAQIL--EEFGEYESIRLTLEKDHTSGQDDALLDIYRKLRPGEPPTREAAQAL 282

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-- 453
            +  +F+  +YDL+ VGR K+N +L  D   D   +   DI+A IK LV L  GK  +  
Sbjct: 283 LDNYYFNGKRYDLAKVGRYKINKKLGRDEMHDTAVLTINDIVATIKYLVALHEGKTELAA 342

Query: 454 ---------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
                    DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LI
Sbjct: 343 PTGEIVVEEDDIDHFGNRRLRTVGELIQNQLRTGLARMERVVRERMTTQDVEAITPQTLI 402

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+A+ EFF +SQLSQ  +  N ++ +TH RRLSALG GG++R RAG E+RDVHP+
Sbjct: 403 NIRPVVAALKEFFGTSQLSQFMDQTNPIAGLTHKRRLSALGPGGLSRERAGFEVRDVHPS 462

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL ++ RVN +GF+ETPYRKV DG+VT+ V YL+A EE+ 
Sbjct: 463 HYGRMCPIETPEGPNIGLIGSLATYGRVNPFGFVETPYRKVVDGQVTDAVDYLTADEEDR 522

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             IAQAN++L +D  F E+ V  R    E  LV  E +D++D SP+Q+VS+A ++IPFLE
Sbjct: 523 FVIAQANAALTDDNRFAEDRVLVRRRHGEVELVLVEDVDYMDVSPRQMVSVATAMIPFLE 582

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPL+ A+AP VGTGME   A  +G  +V+++AG++++V A  I
Sbjct: 583 HDDANRALMGSNMQRQAVPLITADAPLVGTGMEFRGAVDAGDVLVSEKAGVIKEVSADLI 642

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            + + +G           YRL KF+RSNQ TC+NQRPLV  G  V     +ADGP TD G
Sbjct: 643 EVAADDGT-------YQTYRLAKFRRSNQGTCINQRPLVDAGQRVEVGSPLADGPCTDEG 695

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           ++ALGRN+LVAFMPW G+N+ED++++S+R+V +D+ TSIHIEE EV ARDTKLGPEEITR
Sbjct: 696 EMALGRNLLVAFMPWEGHNYEDAIILSQRVVQQDLLTSIHIEEHEVDARDTKLGPEEITR 755

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNVS+E L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +
Sbjct: 756 DIPNVSDEMLADLDERGIIRIGAEVTTGDILVGKVTPKGETELTPEERLLRAIFGEKARE 815

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSL+VP G +GTV+ VR+F+R   D
Sbjct: 816 VRDTSLKVPHGENGTVIGVRVFDRDNGD 843



 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 117/503 (23%), Positives = 202/503 (40%), Gaps = 57/503 (11%)

Query: 3   KGVVFNGLGRVRK-FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DE 49
           +   F  +   R+  F K    I++PDL+ +Q  S+D  +                  + 
Sbjct: 8   QSDSFTDVSTSRRISFAKISSPIEVPDLLALQVDSFDWLVGNETWQARVAAAEAEGRTEL 67

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
               GL+  F+ + PI  FSG   L F  + F+PPK  VD+C  RD+TY+ PL +T   +
Sbjct: 68  SGPSGLEEIFEEISPIEDFSGTMSLSFRDHRFEPPKNTVDECKERDVTYSAPLFVTAEFM 127

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
                         +IK Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG++F+   
Sbjct: 128 ---------NNETGEIKSQTVFMGDFPLMTRKGTFVINGTERVVVSQLVRSPGVYFERTP 178

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
            +   S K ++  +IIP +G W++ E D +D++ VR+DR+RK  VT  L ALG    +IL
Sbjct: 179 DKT--SDKDIFTAKIIPSRGAWLEFEVDKRDMVGVRLDRKRKQNVTVLLKALGWTDAQIL 236

Query: 230 STF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LL 285
             F  Y  I  +   D       A   +            +  + ++++         L 
Sbjct: 237 EEFGEYESIRLTLEKDHTSGQDDALLDIYRKLRPGEPPTREAAQALLDNYYFNGKRYDLA 296

Query: 286 KSLKEKGVKFLGITS----------------DCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           K  + K  K LG                     L  L+  +  +   TGEI +E      
Sbjct: 297 KVGRYKINKKLGRDEMHDTAVLTINDIVATIKYLVALHEGKTELAAPTGEIVVE------ 350

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E  ++   +  +R +  L  + +         +V ++   +   +  I            
Sbjct: 351 EDDIDHFGNRRLRTVGELIQNQLRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVV 408

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           +  +  F            + +  +    RL+   P     + +E     ++ +     G
Sbjct: 409 AALKEFFGTSQLSQFMDQTNPIAGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYG 465

Query: 450 KGTIDDIDNLGNRRVRSVGEMLK 472
           +  +  I+      +  +G +  
Sbjct: 466 R--MCPIETPEGPNIGLIGSLAT 486


>gi|111220537|ref|YP_711331.1| DNA-directed RNA polymerase subunit beta [Frankia alni ACN14a]
 gi|122954583|sp|Q0RRT0|RPOB_FRAAA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|111148069|emb|CAJ59737.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase beta subunit)
            [Frankia alni ACN14a]
          Length = 1141

 Score =  526 bits (1356), Expect = e-147,   Method: Composition-based stats.
 Identities = 197/533 (36%), Positives = 274/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  G  V  G ++           M   + LL A
Sbjct: 630  DGTRRTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDN-GEMALGKNLLVA 688

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 689  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 746

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 747  LADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 799

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 800  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 855

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL+DGTPVDIVLNP GVP RMN+GQI ETHLGW     G ++ +
Sbjct: 856  GNKGVIAKILPQEDMPFLEDGTPVDIVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDA 914

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+K                                    A+    G  V+TPVFDGA
Sbjct: 915  GTEDWKERLRGIG-----------------------------ADSSTPGTNVATPVFDGA 945

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ L+DG TGEP+  PV VGYIY+LKL H+V DK
Sbjct: 946  REEEITGLLDSTLPNRDGVQLIGSSGKATLFDGRTGEPYPYPVAVGYIYILKLLHLVDDK 1005

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1006 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1065

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S        +   D
Sbjct: 1066 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVQIEMRDTDED 1118



 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 340/684 (49%), Positives = 475/684 (69%), Gaps = 18/684 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        L    +K +    +      G ++  +I   +T  + I+         
Sbjct: 155 LVRSPGVYFERSLDKASDKDLYSCKVIPSR--GAWLEFEIDKRDTVGVRIDRKRRQSVTV 212

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 213 L--LKALGWDEARIL--ERFGDFPSMRITLEKDHTASQDDALLDIYRKLRPGEPPTRESA 268

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   LFF+  +YDL+ VGR K+N +L L+   DV  + ++DI+  I+ +V L  G   
Sbjct: 269 QTLLENLFFNPKRYDLAKVGRYKVNKKLTLEIAHDVGVLTEDDIVRTIEYVVKLHAGADP 328

Query: 453 ----IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +P
Sbjct: 329 AEYEVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRP 388

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           VV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+HYGR
Sbjct: 389 VVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGR 448

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL+ SL++FARVN +GF+ETPYRKV +G+VT+ + YL+A EE+    A
Sbjct: 449 MCPIETPEGPNIGLIGSLSTFARVNPFGFVETPYRKVVNGRVTDQIDYLTADEEDRHVKA 508

Query: 629 QANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           QAN+ L  DG+F E+ V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+
Sbjct: 509 QANTPLSPDGTFAEDRVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDA 568

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  +V  +AG+VE + A  I +  
Sbjct: 569 NRALMGSNMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVVVCVQAGVVEDLSADYITVMH 628

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G           YRL KF+RSNQ TC+NQ+P+V  GD V    +IADGP TD G++AL
Sbjct: 629 DDGTR-------RTYRLAKFRRSNQGTCINQKPIVFEGDRVEAGQVIADGPCTDNGEMAL 681

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPN
Sbjct: 682 GKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPN 741

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V+EE L ++DE GII +GAEV+PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDT
Sbjct: 742 VAEEVLADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDT 801

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SL+VP G SG V+ VR+F+R   D
Sbjct: 802 SLKVPHGESGKVIGVRVFSREDGD 825



 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 104/347 (29%), Positives = 169/347 (48%), Gaps = 27/347 (7%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKSVFP 64
           F K  E +++PDL+ +Q  S+D  +  +   +                 GL+  F+ + P
Sbjct: 12  FAKIIEPLEVPDLLALQTQSFDWLIGSDAWAERVQEAIDSGRDDVPITSGLEEVFEEISP 71

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG+  L F  + F+PPK+ V++C  +D+T++ PL +T               +  +
Sbjct: 72  IEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTFSAPLFVTAEFT---------NNTTGE 122

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K LY+C++
Sbjct: 123 IKSQTVFMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFERSLDK--ASDKDLYSCKV 180

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRG 242
           IP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  +P +  +   
Sbjct: 181 IPSRGAWLEFEIDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGDFPSMRITLEK 240

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D       A   +            ++ + ++E+         L K  + K  K L +  
Sbjct: 241 DHTASQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLTLEI 300

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
               G+   +DIV      + + AG    E  +++I H   R +  +
Sbjct: 301 AHDVGVLTEDDIVRTIEYVVKLHAGADPAEYEVDDIDHFGNRRLRTV 347


>gi|117927508|ref|YP_872059.1| DNA-directed RNA polymerase subunit beta [Acidothermus
           cellulolyticus 11B]
 gi|158512360|sp|A0LRL3|RPOB_ACIC1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|117647971|gb|ABK52073.1| DNA-directed RNA polymerase subunit beta [Acidothermus
           cellulolyticus 11B]
          Length = 1169

 Score =  526 bits (1356), Expect = e-147,   Method: Composition-based stats.
 Identities = 354/704 (50%), Positives = 469/704 (66%), Gaps = 36/704 (5%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI----VNGETGEIY--------- 321
           E G  + +G  + +  + V+  G+  D         DI    +    G            
Sbjct: 158 EKGTFIINGTERVVVSQLVRSPGVYFDRTVDKTSDRDIYGCKIIPSRGAWLELEIDKRDN 217

Query: 322 --IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
             +       +     +      D  IL  +       IR TL  D    +++ALLDIYR
Sbjct: 218 VGVRIDRKRKQSVTVLLKALGWDDARIL--ERFGEFEAIRATLEKDHVHTQEEALLDIYR 275

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  T+  A+++ N L+F+  +YDL+ VGR K+N +L LD P     + +EDI+A 
Sbjct: 276 KLRPGEPPTYEAAQTLLNNLYFNPKRYDLAKVGRYKVNKKLGLDLPYTQNTLTEEDIVAT 335

Query: 440 IKILVDLRNGK-----------GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           I  LV L  G+              DDID+ GNRR+R+VGE+++NQ RLGL RMER ++E
Sbjct: 336 IDYLVRLHAGQTETTRNGRTVIIETDDIDHFGNRRLRTVGELIQNQIRLGLARMERVVRE 395

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+++ DI ++ PQ LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRL+ALG GG
Sbjct: 396 RMTTQDIVAITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLNALGPGG 455

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL +  RVNA+GF+ETPYRKV +G
Sbjct: 456 LSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATHGRVNAFGFVETPYRKVING 515

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDAS 667
           +VT+ V YL+A EE+   IAQAN+ L+EDGSF EE V  R   GE   V    +D++D S
Sbjct: 516 RVTDQVDYLTADEEDRHVIAQANAPLNEDGSFAEERVLVRRRGGEVDYVHPSTVDYMDVS 575

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL+AEAP VGTGME   A  +G  +
Sbjct: 576 PRQMVSVATALIPFLEHDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEFRAAVDAGDVV 635

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +A +AG+VE+V A  I I + +G           YRL KF+RSNQ TC+NQ+P+V  G  
Sbjct: 636 IASKAGVVEEVSADAITIAADDGTRQ-------TYRLAKFRRSNQGTCINQKPIVDEGQR 688

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V     IADGP T  G+LALGRN+LVAFM W G+N+ED+++ISER+V ED+ +SIHIEE 
Sbjct: 689 VEAGQPIADGPCTQGGELALGRNLLVAFMSWEGHNYEDAIIISERLVKEDILSSIHIEEH 748

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
           EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GA+V PGDILVGK+TPKGE+ +T
Sbjct: 749 EVDARDTKLGPEEITRDIPNVSEEILADLDERGIIRIGADVVPGDILVGKVTPKGETELT 808

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+DV++F R   +
Sbjct: 809 PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIDVKVFTRDDAE 852



 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 195/534 (36%), Positives = 280/534 (52%), Gaps = 54/534 (10%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R            I++  I+  G  V  G  +      +G   +     LL A
Sbjct: 657  DGTRQTYRLAKFRRSNQGTCINQKPIVDEGQRVEAGQPIADGPCTQG-GELALGRNLLVA 715

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   ++       H  + + R   +  E+I     +  +E 
Sbjct: 716  FMSWEGHNYEDAIIISERLVKEDILSSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEI 773

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 774  LADLDERGIIRIGADVVPGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 826

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              SLKV +  S  +++      ++     D ++PPGV  +V+V+VA KR I  GDK+AGR
Sbjct: 827  DTSLKVPHGESGKVID------VKVFTRDDAELPPGVNELVRVYVAQKRKITDGDKLAGR 880

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++++ILP EDMPFL+DGTPVDI+LNPLGVP RMNVGQ+ ETHLGWA    G K++
Sbjct: 881  HGNKGVIAKILPEEDMPFLEDGTPVDIILNPLGVPGRMNVGQVLETHLGWAAKS-GWKVE 939

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                    NG     R  L  +    +    +                    V+TPVFDG
Sbjct: 940  L-------NGQPEGWRKRLADIGALDAPPNTL--------------------VATPVFDG 972

Query: 1214 ADEEAINSMLRMADLD--------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A E+ I  +L  A  +          G++ L+DG TGEP+  P++VGYIY++KL+H+V D
Sbjct: 973  AKEDEIRGLLENALPNSDGLRMVGPDGKARLFDGRTGEPYPEPISVGYIYIMKLHHLVDD 1032

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR
Sbjct: 1033 KLHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVLGR 1092

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             +VYE+IV G +  E G PESF VLVKEMQAL L++++ +S        E   +
Sbjct: 1093 VKVYEAIVKGENIPEPGIPESFKVLVKEMQALCLNVEVLSSDGMTVEMRETDDE 1146



 Score =  337 bits (864), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 96/300 (32%), Positives = 146/300 (48%), Gaps = 30/300 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +  +               D   + GL+  F+ 
Sbjct: 29  RVSFAKIHEPLDLPNLLALQIESFDWLVGNDAWKARVEAALAAGRTDVNTSSGLEEIFEE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI   SG   L F  + F+PPK   D+C  RD TY+ PL +T   +           +
Sbjct: 89  ISPIEDISGTMSLSFRDHRFEPPKNTPDECRERDFTYSAPLFVTAEFV---------NNT 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++FD    +   S + +Y 
Sbjct: 140 TGEIKSQTVFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFDRTVDKT--SDRDIYG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
           C+IIP +G W+++E D +D + VRIDR+RK  VT  L ALG D   IL  F         
Sbjct: 198 CKIIPSRGAWLELEIDKRDNVGVRIDRKRKQSVTVLLKALGWDDARILERFGEFEAIRAT 257

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +       +  GE    E+ + L + L  + K   +  +G   
Sbjct: 258 LEKDHVHTQEEALLDIYR------KLRPGEPPTYEAAQTLLNNLYFNPKRYDLAKVGRYK 311


>gi|209395104|gb|ACI45368.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  526 bits (1355), Expect = e-147,   Method: Composition-based stats.
 Identities = 197/488 (40%), Positives = 310/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK ++  FL    AP +R  EGLQAAF + FPI + +G   + ++ Y    P
Sbjct: 1   EVPYLLQMQKDAHTAFLQAEKAPQKRNVEGLQAAFDAAFPIVSHNGFVEMRYLEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG  F+HDKG+   SGKLL++ RIIP +G W+D EF+ KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGAFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFNPKDLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDSFRLMDSGALMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T   ++ L++ G   + +  D L G  VA  +++ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTVRHIRELEQSGTSHVSVPEDFLVGRVVARGVIDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD  +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGANVQDVQCIYTNELDQGPYISQTLRTDDTQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN KP+ +
Sbjct: 479 INTKPISA 486


>gi|209395077|gb|ACI45350.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  526 bits (1355), Expect = e-146,   Method: Composition-based stats.
 Identities = 202/488 (41%), Positives = 311/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G  +D EFD KDI+H
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSRLDFEFDPKDILH 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRIVARSIVDADTGEIIAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L++   + + D+  +Y + ++  AYI  TL  D+  D   A + IYR MRP
Sbjct: 299 ANDELTEALLKKPRGTGVLDVQCIYTNELDQGAYISQTLRIDETVDEFAARVAIYRTMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRNESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|209395032|gb|ACI45320.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  526 bits (1355), Expect = e-146,   Method: Composition-based stats.
 Identities = 199/488 (40%), Positives = 316/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +   EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKGTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G 
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGP 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGDGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|311744824|ref|ZP_07718620.1| DNA-directed RNA polymerase subunit beta [Aeromicrobium marinum DSM
            15272]
 gi|311311941|gb|EFQ81862.1| DNA-directed RNA polymerase subunit beta [Aeromicrobium marinum DSM
            15272]
          Length = 1156

 Score =  526 bits (1355), Expect = e-146,   Method: Composition-based stats.
 Identities = 185/509 (36%), Positives = 267/509 (52%), Gaps = 53/509 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  L        E  M     L+ A    + ++  D  +     V    +
Sbjct: 670  LVAAGQRVEVGTPLADGPCT-DEGEMALGTNLMVAFMPWQGLNYEDAIILSQRLVQDDTL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLANLDERGIIRIGAEVGNGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +        + +         
Sbjct: 787  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGESGTVIGVRVFDS-------- 836

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++ PGV ++V+V+VA KR I  GDK+AGRHGNKG++SRILP EDMPFL+DGTPVD
Sbjct: 837  -ESGDELSPGVNQLVRVYVAQKRKISVGDKLAGRHGNKGVISRILPIEDMPFLEDGTPVD 895

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ E HLGW     G K+                  + +++   G
Sbjct: 896  ILLNPLGVPGRMNVGQVLELHLGWIAK-TGWKVD------------EKTAEWAKRLASIG 942

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
            +    +                    V+TPVFDGA E+ I+ +L     +          
Sbjct: 943  ASEAPVDSL-----------------VATPVFDGAREDEISGLLASTLPNRDGNRMVNPQ 985

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 986  GKAVLFDGRSGEPFPDPVSVGYMYVLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1045

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VYE+IV G +  E G PESF VLV
Sbjct: 1046 QRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVYEAIVKGENVPEPGIPESFKVLV 1105

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            KEMQ+L L++++ +S        +   D 
Sbjct: 1106 KEMQSLCLNVEVLSSDGTAVEMRDAEEDL 1134



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 340/685 (49%), Positives = 456/685 (66%), Gaps = 25/685 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +   + ++         
Sbjct: 163 LVRSPGVYFERTADKTSDKDIFTARVIPSR--GAWLEFEIDKRDMVGVRLDRKRKQSVTV 220

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       IR TL  D    + DALLDIYR +RPG+  +   A
Sbjct: 221 L--LKALGWSEAQIL--EEFGQYESIRLTLEKDNTVGQDDALLDIYRKLRPGEPPSREAA 276

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++    +F+  +YD + VGR K+N +L +D   D + +  +DI+A IK +V L  G+ T
Sbjct: 277 QTLLENYYFNPKRYDTAKVGRYKINKKLGVDEAFDQQTLTVDDIVATIKYIVALHAGEET 336

Query: 453 I-----------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
           +           DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ
Sbjct: 337 LASPAGDTIVEADDIDHFGNRRMRTVGELIQNQLRTGLARMERVVRERMTTQDVEAITPQ 396

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDV
Sbjct: 397 TLINIRPVVAALKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGYEVRDV 456

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           HP+HYGR+CP ET EG NIGL+ SL SF R+N++GF+ETPYRKV DG VT+ + YL+A E
Sbjct: 457 HPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFVETPYRKVVDGVVTDQIDYLTATE 516

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+   IAQANS L E  +F E+ V  R   GE  L P   +D++D SP+Q+VS+A +LIP
Sbjct: 517 EDRYIIAQANSILTEQSTFAEDAVLVRQRGGEADLRPAGDVDYMDVSPRQMVSVATALIP 576

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE+DD+NR LMG NMQRQAVPL++++APFVGTGME   A  +G   VAK+ G+V++V A
Sbjct: 577 FLEHDDANRALMGSNMQRQAVPLIRSDAPFVGTGMEFRAAVDAGDVTVAKKPGVVKEVSA 636

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             + I   EG           YRL KF RSNQ TC NQRPLV  G  V     +ADGP T
Sbjct: 637 DAVEIAEDEGT-------YTTYRLSKFHRSNQGTCTNQRPLVAAGQRVEVGTPLADGPCT 689

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           D G++ALG N++VAFMPW G N+ED++++S+R+V +D  TSIHIEE EV ARDTKLGPEE
Sbjct: 690 DEGEMALGTNLMVAFMPWQGLNYEDAIILSQRLVQDDTLTSIHIEEHEVDARDTKLGPEE 749

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITRDIPNVSEE L N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK
Sbjct: 750 ITRDIPNVSEEMLANLDERGIIRIGAEVGNGDILVGKVTPKGETELTPEERLLRAIFGEK 809

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIF 945
           A +VRDTSL+VP G SGTV+ VR+F
Sbjct: 810 AREVRDTSLKVPHGESGTVIGVRVF 834



 Score =  339 bits (869), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 110/485 (22%), Positives = 196/485 (40%), Gaps = 44/485 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++P+L+ +Q  S+   +  +               D     GL+  F+ 
Sbjct: 17  RISFAKIAEPLEVPELLALQTDSFSWLIGDDTWRAGVDAALEAGRTDVSTKSGLEEIFEE 76

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FS    L F  + F+PPK+ VDDC  RD+TYA PL +T   +            
Sbjct: 77  ISPIEDFSETMSLSFRDHRFEPPKYSVDDCKLRDVTYAAPLFVTAEFM---------NNE 127

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 128 TGEIKSQTVFMGDFPLMTDAGTFIVNGTERVVVSQLVRSPGVYFERTADKT--SDKDIFT 185

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            R+IP +G W++ E D +D++ VR+DR+RK  VT  L ALG    +IL  F  Y  I  +
Sbjct: 186 ARVIPSRGAWLEFEIDKRDMVGVRLDRKRKQSVTVLLKALGWSEAQILEEFGQYESIRLT 245

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLG 297
              D       A   +            +  + ++E+           K  + K  K LG
Sbjct: 246 LEKDNTVGQDDALLDIYRKLRPGEPPSREAAQTLLENYYFNPKRYDTAKVGRYKINKKLG 305

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEA----------GDVIDEKSLEEIFHSEIRDIPIL 347
           +           +DIV      + + A            +++   ++   +  +R +  L
Sbjct: 306 VDEAFDQQTLTVDDIVATIKYIVALHAGEETLASPAGDTIVEADDIDHFGNRRMRTVGEL 365

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + +         +V ++   +   +  I            +  +  F           
Sbjct: 366 IQNQLRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVAALKEFFGTSQLSQFMDQ 423

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  +
Sbjct: 424 NNPLAGLTHKRRLSALGPGG---LSRERAGYEVRDVHPSHYGR--MCPIETPEGPNIGLI 478

Query: 468 GEMLK 472
           G +  
Sbjct: 479 GSLAS 483


>gi|302523969|ref|ZP_07276311.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. AA4]
 gi|302432864|gb|EFL04680.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. AA4]
          Length = 1167

 Score =  526 bits (1354), Expect = e-146,   Method: Composition-based stats.
 Identities = 183/513 (35%), Positives = 256/513 (49%), Gaps = 65/513 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++    + +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 680  IVNEGDRVEQGQVIADGPSTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSERLVQDDVL 738

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E +  D  DE+ I+      R  +IL G+ 
Sbjct: 739  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADL-DERGIIRIGAEVRDGDILVGKV 797

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 798  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 840

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF++D
Sbjct: 841  IRVFSREDDDELPPGVNELVRVYVAQKRKIQPGDKLAGRHGNKGVIGKILPVEDMPFMED 900

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI E HLGW     G  I+   +  K              
Sbjct: 901  GTPVDIILNTHGVPRRMNIGQILELHLGWLASQ-GWTIEGNPDWAKN------------- 946

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES--- 1231
                              +         G   +TPVFDGA EE +  +L     +     
Sbjct: 947  ------------------LSPELYDVAPGTNTATPVFDGAKEEELTGLLGATKPNRDGER 988

Query: 1232 -----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEP+  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 989  MVKENGKATLFDGRSGEPYPYPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1048

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1049 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1108

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ +S        +   +
Sbjct: 1109 FKVLLKELQSLCLNVEVLSSDGAAIEMRDSDDE 1141



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 327/602 (54%), Positives = 439/602 (72%), Gaps = 20/602 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 256 EKDHTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKPKRYDLAKVGRYKVNKKLGL 315

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
           DTP +   + +EDI++ I+ LV L  G+  +            DDID+ GNRR+R+VGE+
Sbjct: 316 DTPYETGTLTEEDIVSAIEYLVRLHAGEDKMTSSAGVEVPVETDDIDHFGNRRLRTVGEL 375

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL R ER ++ER+++ D++++ PQ LIN +P+ +A+ EFF +SQLSQ  +  N
Sbjct: 376 IQNQIRVGLSRTERVVRERMTTQDVEAITPQTLINIRPIGAAIKEFFGTSQLSQFMDQNN 435

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 436 PLSGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLCSYA 495

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV +G+VT+ V YL+A EE+    AQAN+ L +DG F EE V  R  
Sbjct: 496 RVNPFGFIETPYRKVVEGQVTDQVDYLTADEEDRYVKAQANAPLTDDGHFVEEKVLGRRK 555

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE  L+   +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+ +AP
Sbjct: 556 GGEVELIDPLEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRNQAP 615

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTG+E   A  +G  +VA++AG+VE++ A  I I   +G           Y L KF+R
Sbjct: 616 YVGTGVELRAAVDAGDVLVAEQAGVVEELSADIITIMHDDGTRKS-------YGLYKFRR 668

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC N RP+V  GD V +  +IADGPST+ G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 669 SNHGTCFNHRPIVNEGDRVEQGQVIADGPSTENGEMALGKNLLVAVMPWEGHNYEDAIIL 728

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVSEE L ++DE GII +GAEV 
Sbjct: 729 SERLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADLDERGIIRIGAEVR 788

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ +R+F+R  
Sbjct: 789 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGIRVFSRED 848

Query: 950 ID 951
            D
Sbjct: 849 DD 850



 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 111/481 (23%), Positives = 202/481 (41%), Gaps = 40/481 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +  P+L++VQ  S+  F       + R NEG       L+     + PI 
Sbjct: 31  RVSFAKIREPLSTPNLLDVQIQSFQWFTGNEAWFERRVNEGEENPVGGLEEVLNEISPIE 90

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F +  FD  K  +++C  +D+TYA PL +T   +           +  +IK
Sbjct: 91  DFSGSMSLSFSAPRFDEVKASIEECKDKDMTYAAPLFVTAEFV---------NNNTGEIK 141

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K +++ R+IP
Sbjct: 142 SQTVFLGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDSSVDKT--TDKDVFSVRVIP 199

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I    +F   ++ +   D 
Sbjct: 200 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEAIRERFSFSETLLATLEKDH 259

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K     L K  + K  K LG+ +  
Sbjct: 260 TAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKPKRYDLAKVGRYKVNKKLGLDTPY 319

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPILYVDS 351
             G    EDIV+     + + AG+                 ++   +  +R +  L  + 
Sbjct: 320 ETGTLTEEDIVSAIEYLVRLHAGEDKMTSSAGVEVPVETDDIDHFGNRRLRTVGELIQNQ 379

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +         +V ++   +   +  I            +  +  F            + +
Sbjct: 380 IRVGLSRTERVVRERMTTQD--VEAITPQTLINIRPIGAAIKEFFGTSQLSQFMDQNNPL 437

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
             +    RL+   P     + +E     ++ +     G+  +  I+      +  +G + 
Sbjct: 438 SGLTHKRRLSALGPGG---LSRERAGMEVRDVHPSHYGR--MCPIETPEGPNIGLIGSLC 492

Query: 472 K 472
            
Sbjct: 493 S 493


>gi|114567849|ref|YP_755003.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|122317278|sp|Q0AUH2|RPOB_SYNWW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|114338784|gb|ABI69632.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 1107

 Score =  526 bits (1354), Expect = e-146,   Method: Composition-based stats.
 Identities = 356/719 (49%), Positives = 484/719 (67%), Gaps = 10/719 (1%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+  + + +            +          I+  E+V+ S    + G+  + +     
Sbjct: 93  KVRLTDKENGEIKESEVYMGDLPLMTEKGTFIINGAERVVVSQLVKSPGVYFNERMDVAG 152

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                +  +       ++     G +Y              +         ++ +D  + 
Sbjct: 153 HPLFGATIIPNRGAWFELEMDSAGLVYTRIDKTRKIPVTVLLRALGYESNEVI-LDMYDG 211

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  I  TL  D + ++K+AL++ YR +RPG+++T   AE +   LFFD  +YD++ VGR 
Sbjct: 212 DETIARTLEKDTSTNKKEALIEFYRRLRPGELATEDAAEQLLKNLFFDPRRYDMAAVGRY 271

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K+N +L L+ P + RH+  EDI A I  L+ L  G+G  D ID+LGNRR+RS+GE+L+NQ
Sbjct: 272 KVNKKLGLNIPPENRHLTLEDITATIGYLLKLIKGEGKTDVIDHLGNRRLRSIGELLQNQ 331

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R GL+RMER ++ER+S  D++++ PQ LIN +P+ +AV EFF SSQLSQ  +  N L+ 
Sbjct: 332 FRTGLVRMERVVRERMSIHDVETLTPQVLINIRPITAAVKEFFGSSQLSQFMDQTNPLAE 391

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RRLSALG GG+ R RAG ++RDVH +HYGRICP ET EG NIGL+  L +F +VN 
Sbjct: 392 LTHKRRLSALGPGGLTRERAGFQVRDVHHSHYGRICPIETPEGPNIGLIGYLATFGQVND 451

Query: 595 YGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           +GFIETPYRKV     +V N++VYLSA EE+  Y+AQAN+ LDE+G F EE V  R   E
Sbjct: 452 FGFIETPYRKVDKKLGRVLNEIVYLSADEEDEYYVAQANAPLDENGYFIEEKVEARYFEE 511

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +P+ ++D++D SPKQV S+A +LIPFLENDD+NR LMG NMQRQAVPL+K EAP VG
Sbjct: 512 ILEIPKNRVDYMDVSPKQVFSVATALIPFLENDDANRALMGANMQRQAVPLVKTEAPIVG 571

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A+ SGA ++AK+AG V++  A RI I   +G        +D Y L+KF RSNQ
Sbjct: 572 TGLEHKAARDSGAVVIAKKAGTVKKASASRISIEKDDGT-------IDNYELLKFMRSNQ 624

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            TC NQRP+VKVG+ V  N++IADGPST+ G+LALGRN++VAFMPW GYN+ED++LISE+
Sbjct: 625 GTCYNQRPIVKVGERVEANEVIADGPSTEQGELALGRNVMVAFMPWEGYNYEDAILISEK 684

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V +DVFTSIHIEE+E  ARDTKLG EEITRDIPNVSE+ LKN+D+ G+I VGAEV P D
Sbjct: 685 LVKDDVFTSIHIEEYECEARDTKLGSEEITRDIPNVSEDMLKNLDDQGVIRVGAEVRPDD 744

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRD+SLRVP G +G VV V+ F+R   D
Sbjct: 745 ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDSSLRVPHGEAGKVVAVKRFSREKGD 803



 Score =  501 bits (1290), Expect = e-139,   Method: Composition-based stats.
 Identities = 181/538 (33%), Positives = 252/538 (46%), Gaps = 79/538 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +   G  +    +  +        ++  I+ VG  V   +++    + + +  +     +
Sbjct: 605  EKDDGTIDNYELLKFMRSNQGTCYNQRPIVKVGERVEANEVIADGPSTE-QGELALGRNV 663

Query: 913  LRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            + A    +  +  D  L            S  + +     R     +E          E 
Sbjct: 664  MVAFMPWEGYNYEDAILISEKLVKDDVFTSIHIEEYECEARDTKLGSEEITRDIPNVSED 723

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            + ++ DD+  ++      R  +IL G+    G         L   +  E  R        
Sbjct: 724  MLKNLDDQ-GVIRVGAEVRPDDILVGKVTPKGETELTPEERLLRAIFGEKAR-------- 774

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E                   K    + GD++PPGV ++V+V++A KR I  
Sbjct: 775  ---------EVRDSSLRVPHGEAGKVVAVKRFSREKGDELPPGVNQLVRVYIAQKRKISE 825

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG++SRILP EDMPFL+DGTPV+IVLNPLGVPSRMN+GQI E H+GWA  
Sbjct: 826  GDKMAGRHGNKGVISRILPEEDMPFLEDGTPVEIVLNPLGVPSRMNIGQILECHMGWAAR 885

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  I + + D     DI                                         
Sbjct: 886  ALGLNIATPVFDGANEEDI----------------------------------------- 904

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                F    E         A L ESG++IL+DG TGE F   +TVGY+YMLKL H+V DK
Sbjct: 905  ----FTKLRE---------ASLLESGKTILFDGRTGEKFKHEITVGYVYMLKLAHLVDDK 951

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYG++Y LQE+LT+KSDDV GR 
Sbjct: 952  IHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGSSYTLQEILTVKSDDVAGRL 1011

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            + YESIV G +  E G PE F VL+KE+Q+L L + +           +   + N+ E
Sbjct: 1012 KTYESIVKGENIPEPGVPEGFKVLIKELQSLALDVRILAGDDHEILIKDNDNEGNEKE 1069



 Score =  342 bits (876), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 116/469 (24%), Positives = 202/469 (43%), Gaps = 45/469 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  + +  E +++P+LI++QK SYD FL            GL+ A + VFPI+ F+G   
Sbjct: 12  RLSYSRIKEPVELPNLIQIQKNSYDWFL----------EHGLREALQEVFPISDFTGNLE 61

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           L F+ Y    PK+ +++C  RD++Y  PLK+ +RL           K   +IKE  +YMG
Sbjct: 62  LGFLDYSMGEPKYSINECKERDVSYQAPLKLKVRLT---------DKENGEIKESEVYMG 112

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           DLPLMT+ GTF+I G +R+VVSQL +SPG++F+    R  ++G  L+   IIP++G W +
Sbjct: 113 DLPLMTEKGTFIINGAERVVVSQLVKSPGVYFNE---RMDVAGHPLFGATIIPNRGAWFE 169

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAA 252
           +E DS  +++ RID+ RK+PVT  L ALG +S E IL  +      ++  +         
Sbjct: 170 LEMDSAGLVYTRIDKTRKIPVTVLLRALGYESNEVILDMYDGDETIARTLEKDTSTNKKE 229

Query: 253 DLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLLKSLKEKGVKFLGITSDCL-------- 303
            L+           +  GE   E + ++L   L    +   +  +G              
Sbjct: 230 ALI------EFYRRLRPGELATEDAAEQLLKNLFFDPRRYDMAAVGRYKVNKKLGLNIPP 283

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
              ++  + +    G +            ++ + +  +R I  L  +       +R   V
Sbjct: 284 ENRHLTLEDITATIGYLLKLIKGEGKTDVIDHLGNRRLRSIGELLQNQFRTG-LVRMERV 342

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +     D      +V+      T +V    F            + +  +    RL+  
Sbjct: 343 VRERMSIHDVETLTPQVLINIRPITAAVK-EFFGSSQLSQFMDQTNPLAELTHKRRLSAL 401

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  I  I+      +  +G +  
Sbjct: 402 GPGG---LTRERAGFQVRDVHHSHYGR--ICPIETPEGPNIGLIGYLAT 445


>gi|229544494|gb|ACQ76428.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  526 bits (1354), Expect = e-146,   Method: Composition-based stats.
 Identities = 197/488 (40%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R   GLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKGGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            F V +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFGVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   +  ++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTREHEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|308178144|ref|YP_003917550.1| DNA-directed RNA polymerase subunit beta [Arthrobacter arilaitensis
           Re117]
 gi|307745607|emb|CBT76579.1| DNA-directed RNA polymerase beta chain [Arthrobacter arilaitensis
           Re117]
          Length = 1168

 Score =  525 bits (1353), Expect = e-146,   Method: Composition-based stats.
 Identities = 301/953 (31%), Positives = 436/953 (45%), Gaps = 135/953 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++P+L+ +Q  S+D  +      +                 GL   F+ 
Sbjct: 23  RLSFAKIHEPLEVPNLLALQTESFDRLVGNQNWVERLAKAEAAGDFSVPNTSGLAEIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F   EF  PK+ + +C  RD TYA PL +    +            
Sbjct: 83  ISPIEDFQDTMSLSFSEPEFADPKYSIAECKDRDATYAAPLYVKAEFM---------NNE 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLM++ GTF+I G +R+VVSQL RSPG +F+    +   S K +Y+
Sbjct: 134 TGEIKQQTVFMGDFPLMSEKGTFIINGTERVVVSQLVRSPGAYFESAPDKT--SDKTIYS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            RIIP +G W ++E D +D I VR+DR+RK  VT  L ALG   E+ILS F  Y  +  +
Sbjct: 192 ARIIPSRGAWFELEIDKRDQIGVRLDRKRKQSVTVLLKALGWSEEQILSEFGQYDSMRAT 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D                +      +  GE   +E+ + L   +    K   +  +G 
Sbjct: 252 LEKDSIK--------DQNEALLDIYRKLRPGEPPTVEAAQALLKNMYFEPKRYDLAKVGR 303

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               +      E  VN E   +           SL+++       + +   +        
Sbjct: 304 YK--INRKLGVETPVNAENASVL----------SLDDLVAMIRYLVALHAGEKSVKGT-- 349

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           R   + D   +  D      R +R                L  +  +  LS + RV    
Sbjct: 350 RKGEIVDVPVNVDDIDHFGNRRIRA------------VGELIENQVRTGLSRMERVVRER 397

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
               D       I  + +I I  ++  ++   GT      +      +     +    LG
Sbjct: 398 MTTQDVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALG 453

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
              + R      + +++  V P       P+ +                 +NS   I   
Sbjct: 454 PGGLSRD----RAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRINSFGFIETP 509

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
            R  A G                            T++      ++   +    N     
Sbjct: 510 YRRVANGVVSNE-------------------VDYLTADDELQHYIAQANAPLDENGRFVE 550

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           ET                                 + E G   E ++        + V  
Sbjct: 551 ET-------------------------------VLVREKGGGGEPVIVDSAEVTFMDVSP 579

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            +          +VS+A +LIPFLE+DD+NR LMG NMQRQAVPLLK+E P VGTGME  
Sbjct: 580 RQ----------MVSVATALIPFLEHDDANRALMGANMQRQAVPLLKSERPLVGTGMEKF 629

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  +G ++VA + G+V +V A  +V+ + +G           Y +MKF RSNQ    NQ
Sbjct: 630 AAVDAGDSVVASKPGVVTEVSADLVVVMNDDGTESM-------YPIMKFARSNQGNAYNQ 682

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           R  V  GD +    IIADGPSTD G+L+LG+N+LVAFM W GYN+ED++++S+RM+ +DV
Sbjct: 683 RVRVSEGDRLEYQSIIADGPSTDSGELSLGKNLLVAFMSWEGYNYEDAIILSQRMIFDDV 742

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            TSIHIEE EV ARDTKLG EEITRDIPNVSE+ L  +D+ GI+ +GAEV  GD+LVG++
Sbjct: 743 LTSIHIEEHEVDARDTKLGAEEITRDIPNVSEDILSQLDDRGIVYIGAEVEAGDVLVGRV 802

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D
Sbjct: 803 TPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRDNDD 855



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 156/332 (46%), Positives = 209/332 (62%), Gaps = 41/332 (12%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +I      DD+ PGV ++V+V+VA KR I  GDK+AGRHGNKG++SRI+P EDMPFL+DG
Sbjct: 847  RIFDRDNDDDLSPGVNQLVRVYVAQKRKISIGDKLAGRHGNKGVISRIMPLEDMPFLEDG 906

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNPLGVP RMNVGQ+ E HLGWA    G  I+      +   ++          
Sbjct: 907  TPLDVILNPLGVPGRMNVGQVMEIHLGWAAKQ-GWTIEGEPEWVRDLPNLPRE------- 958

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                                          V+TPVFDGA EE I  +L   +        
Sbjct: 959  -------------------------SGSTTVATPVFDGASEEEIRGILDATNKTRDGVRL 993

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +  SG++ L+DG +G+P   PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 994  IGNSGKAKLFDGRSGDPLPDPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1053

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDD+ GR +VYE+IV G +  E G PESF
Sbjct: 1054 QFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDIHGRVKVYEAIVKGENVPEPGVPESF 1113

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++  +        E   +
Sbjct: 1114 KVLIKEMQSLCLNVEVLGTDGNTIEMRESDEE 1145


>gi|229544479|gb|ACQ76418.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 200/488 (40%), Positives = 317/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  +RLI++D +  T  +K +K++KEQ ++MG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVRLIIYDRESSTSQSKVVKEVKEQEVHMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTRGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFLLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+     L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTHELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSASVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREEFTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|29831457|ref|NP_826091.1| DNA-directed RNA polymerase subunit beta [Streptomyces avermitilis
            MA-4680]
          Length = 1181

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 190/515 (36%), Positives = 267/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 695  VVDEGARVIAGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 753

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 754  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 810

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 811  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 853

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 854  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 913

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +D+             
Sbjct: 914  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADDWAQRLQAIE----- 967

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 968  ------------------------ADQVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 1003

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 1004 ERMVLPTGKAPLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1063

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1064 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1123

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1124 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1158



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 335/670 (50%), Positives = 455/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 221 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 265

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 266 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 322

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  + P D   +  EDII+ IK LV L  G+               DDID+ GNR
Sbjct: 323 KVNKKLGGEAPLDAGILTVEDIISSIKYLVKLHAGETETVGDNGTSIVVETDDIDHFGNR 382

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 383 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 442

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 443 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 502

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L +D  F E
Sbjct: 503 IGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANAPLGDDFRFEE 562

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 563 TRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 622

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + +++ G+V++V A  +   + +G           
Sbjct: 623 PLIKSEAPLVGTGMEYRCAVDAGDVLKSEKDGVVQEVSADYVTTANDDGT-------YTT 675

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  G  V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 676 YRLHKFSRSNQGTSVNQKVVVDEGARVIAGQVLADGPATENGEMALGKNLLVAFMPWEGH 735

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 736 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 795

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 796 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 855

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 856 VRVFDREEGD 865



 Score =  341 bits (874), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 41  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEAALDSGQDVPTKSGLEEIFEE 100

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 101 ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 151

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 152 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 209

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 210 AKVIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 269

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 270 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 329

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   EDI++     + + AG+                 ++   +  +R++  
Sbjct: 330 GEAPLDAGILTVEDIISSIKYLVKLHAGETETVGDNGTSIVVETDDIDHFGNRRLRNVGE 389

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 390 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 447

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 448 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 502

Query: 467 VGEMLK 472
           +G +  
Sbjct: 503 IGSLAS 508


>gi|296268531|ref|YP_003651163.1| DNA-directed RNA polymerase subunit beta [Thermobispora bispora DSM
           43833]
 gi|296091318|gb|ADG87270.1| DNA-directed RNA polymerase, beta subunit [Thermobispora bispora
           DSM 43833]
          Length = 1155

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 338/692 (48%), Positives = 476/692 (68%), Gaps = 26/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K V    I      G ++  +I   ++  + I+         
Sbjct: 161 LVRSPGVYFDRTVDKTSDKDVYSCKIIPSR--GAWLEFEIDKRDSVGVRIDRKRKQPVTV 218

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       +R TL  D    ++DAL+DIYR +RPG+  T   A
Sbjct: 219 L--LKALGWTNDRIL--ERFGQYESMRATLEKDHTTGQEDALIDIYRKLRPGEPPTKESA 274

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   L+F+  +YDL+ VGR K+N +L +D       + ++DI+A I+ LV L  G+ T
Sbjct: 275 QALLENLYFNPKRYDLAKVGRYKLNKKLGVDADITQGTLTEDDIVATIEYLVRLHAGEET 334

Query: 453 I------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           +            DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ P
Sbjct: 335 MIGANGREVIVETDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITP 394

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PV +++ EFF +SQLSQ  +  N L+ +TH RRL+ALG GG++R RAG E+RD
Sbjct: 395 QTLINVRPVTASIREFFGTSQLSQFMDQTNPLAGLTHKRRLNALGPGGLSRERAGFEVRD 454

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL ++ARVNA+GF+ETPYRKV DG+VT+ + YL+A 
Sbjct: 455 VHPSHYGRMCPIETPEGPNIGLIGSLATYARVNAFGFVETPYRKVVDGRVTDQIEYLTAD 514

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   +AQAN+ ++ DG+F E+ V  R   GE   V   ++D++D SP+Q+VS+A ++I
Sbjct: 515 EEDRYVVAQANTVVNPDGTFAEKRVLARRKGGEFEAVDPSEVDYMDVSPRQMVSVATAMI 574

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NMQRQAVPLL++EAP VGTGME   A  +G  I+A+++G+VE+V 
Sbjct: 575 PFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEYRAATDAGDVIIAEKSGVVEEVS 634

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I + + +G           YR++KF+RSNQ TC NQ+P+V+ GD V +  +IADGP 
Sbjct: 635 ADYITVLNDDGTR-------TTYRVVKFKRSNQGTCYNQKPIVEEGDRVEQGQVIADGPC 687

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T+ G++ALG+N+LVAFMPW G+N+ED++++S+R+V +DV TSIHIEE EV ARDTKLGPE
Sbjct: 688 TENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEVDARDTKLGPE 747

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSEE L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 748 EITRDIPNVSEEVLADLDERGIIRIGAEVTTGDILVGKVTPKGETELTPEERLLRAIFGE 807

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G SG V+ VR+F R   D
Sbjct: 808 KAREVRDTSLKVPHGESGKVIGVRVFRREDGD 839



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 192/534 (35%), Positives = 275/534 (51%), Gaps = 51/534 (9%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G     R +           ++  I+  G  V  G ++      +    M   + LL
Sbjct: 642  NDDGTRTTYRVVKFKRSNQGTCYNQKPIVEEGDRVEQGQVIADGPCTEN-GEMALGKNLL 700

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  +     +S  +V   +     I+++E      +   E + RD  +
Sbjct: 701  VAFMPWEGHNYEDAII-----LSQRLVQDDVLTSIHIEEHEVDARDTKLGPEEITRDIPN 755

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +  ++  R   I  G    +G     K T      ++   R     F  +  +V+ 
Sbjct: 756  VSEEVLADLDER-GIIRIGAEVTTGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRD 814

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +          +      ++ + + GD++PPGV  +V+V+VA KR I  GDK+AGR
Sbjct: 815  TSLKVPHGESGKVIGV------RVFRREDGDELPPGVNELVRVYVAQKRKITDGDKLAGR 868

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++++ILP EDMPFL+DGTPVDI+LNPLGVP RMN+GQ+ ETHLGWA    G  I 
Sbjct: 869  HGNKGVIAKILPVEDMPFLEDGTPVDIILNPLGVPGRMNLGQVLETHLGWAAKQ-GWDIS 927

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  ++        +                             E+      V+TPVFDG
Sbjct: 928  GVEEEWAKRLREKGM-----------------------------EKVGPDTKVATPVFDG 958

Query: 1214 ADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A EE I  +L+    +          G++ILYDG +GEPF  PV+VGYIY+LKL H+V D
Sbjct: 959  AREEEIVGLLQHTLPNRDGQRLVGPNGKAILYDGRSGEPFPYPVSVGYIYILKLAHLVDD 1018

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR
Sbjct: 1019 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGR 1078

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    E   D
Sbjct: 1079 VKVYEAIVKGENIPEAGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMREAEED 1132



 Score =  343 bits (881), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 103/316 (32%), Positives = 158/316 (50%), Gaps = 27/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE--------RPN----EGLQAAFKS 61
           R  F +  E +++PDL+ VQ  S+D  +                R +     GL+  F+ 
Sbjct: 15  RLSFARIQEPLEVPDLLAVQIESFDWLIGNERWKARVEAARKAGRKDIPMQSGLEEVFEE 74

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK  +++C  +D+TY+  L +T   I           +
Sbjct: 75  ISPIEDFSGTMSLSFRDHRFEPPKHTIEECRDKDMTYSASLFVTAEFI---------NNT 125

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K +Y+
Sbjct: 126 TGEIKSQTVFMGDFPLMTPKGTFIINGTERVVVSQLVRSPGVYFDRTVDKT--SDKDVYS 183

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C+IIP +G W++ E D +D + VRIDR+RK PVT  L ALG  ++ IL  F  Y  +  +
Sbjct: 184 CKIIPSRGAWLEFEIDKRDSVGVRIDRKRKQPVTVLLKALGWTNDRILERFGQYESMRAT 243

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 244 LEKDHTTGQEDALIDIYRKLRPGEPPTKESAQALLENLYFNPKRYDLAKVGRYKLNKKLG 303

Query: 298 ITSDCLCGLYVAEDIV 313
           + +D   G    +DIV
Sbjct: 304 VDADITQGTLTEDDIV 319


>gi|22298184|ref|NP_681431.1| DNA-directed RNA polymerase subunit beta [Thermosynechococcus
           elongatus BP-1]
 gi|41018025|sp|Q8DL55|RPOB_THEEB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|22294363|dbj|BAC08193.1| RNA polymerase beta subunit [Thermosynechococcus elongatus BP-1]
          Length = 1108

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 326/618 (52%), Positives = 439/618 (71%), Gaps = 11/618 (1%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +    + D  IL  + + +  Y + T+  +     ++AL+++Y+ +RPG+  T S  + +
Sbjct: 186 LKALGLTDSEIL--ERLRHPEYYQKTVEKEGKFSEEEALIELYKKLRPGEPPTVSGGQQL 243

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
               FFD  +YDL  VGR K+N +L L+ PD VR +  EDI+A I  L++L    GTIDD
Sbjct: 244 LESRFFDPKRYDLGRVGRYKLNRKLQLNIPDSVRILTPEDILAAIDYLINLEFDLGTIDD 303

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D DS+ P  L+N KP+V+A+ E
Sbjct: 304 IDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDTDSLTPTSLVNPKPLVAAIKE 363

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET 
Sbjct: 364 FFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETP 423

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSS 633
           EG N GL+ SL + ARVN YGFIETP+  V DG+V  D   +Y++A EE+++ +A  +  
Sbjct: 424 EGPNAGLIGSLATHARVNEYGFIETPFYPVKDGRVLKDQPPIYMTADEEDDKRVAPGDVP 483

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            DE+G    ++V  R   +      +++D++  SP Q++S+A SLIPFLE+DD+NR LMG
Sbjct: 484 TDENGYILGDVVPVRYRQDFTTTTPDQVDYVAVSPVQIISVATSLIPFLEHDDANRALMG 543

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ + P VGTG+E+  A+ SG  I+++  G+V  VDA +I +++  G   
Sbjct: 544 SNMQRQAVPLLRPQRPLVGTGLEAQAARDSGMVILSQTNGVVSYVDANQIRVKTDNGPEI 603

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y L K+QRSNQ+TC+NQRP+V VGD V+   +IADG +T+ G+LALG+N+LV
Sbjct: 604 -------TYTLQKYQRSNQDTCLNQRPIVFVGDRVQAGQVIADGSATEGGELALGQNILV 656

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+MPW GYN+ED++LISER+V EDV+TSIHIE++E+ AR TKLGPEEITR++PNVSEE L
Sbjct: 657 AYMPWEGYNYEDAILISERLVQEDVYTSIHIEKYEIEARQTKLGPEEITREVPNVSEEAL 716

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           + +DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+
Sbjct: 717 RQLDENGIIRIGAFVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPN 776

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G VVDVR+F R   D
Sbjct: 777 GEKGRVVDVRVFTREQGD 794



 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 198/593 (33%), Positives = 273/593 (46%), Gaps = 65/593 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR-DTKLGP 858
                       +L    P  G   E        MV       +         R  T  GP
Sbjct: 542  MGSNMQRQAVPLLRPQRPLVGTGLEAQAARDSGMVILSQTNGVVSYVDANQIRVKTDNGP 601

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ VG  V  G ++      +G   +   + +L A   
Sbjct: 602  EITYTLQKYQRSNQDTCLNQRPIVFVGDRVQAGQVIADGSATEG-GELALGQNILVAYMP 660

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE-----LLARDKDD 973
             +  +  D  L     V   V       ++ I+  +  +  E    E       A  + D
Sbjct: 661  WEGYNYEDAILISERLVQEDVYTSIHIEKYEIEARQTKLGPEEITREVPNVSEEALRQLD 720

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 721  ENGIIRIGAFVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD-------------- 766

Query: 1034 NVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMAG
Sbjct: 767  ----VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAG 822

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+SRILP EDMPFL DG PVDIVLNPLGVPSRMNVGQ++E  LGWA   LG++ 
Sbjct: 823  RHGNKGIISRILPVEDMPFLPDGRPVDIVLNPLGVPSRMNVGQVYECLLGWAGACLGRRF 882

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K    D               ++ G     E +     ++     + W         VF 
Sbjct: 883  KITPFD---------------EMHGKEKSRETVHAKLQEARDVTGQDW---------VF- 917

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                          + +  G+ ++YDG TGEPFDRPVTVG  YMLKL H+V DK++ARST
Sbjct: 918  --------------NPENPGKMVVYDGRTGEPFDRPVTVGMAYMLKLVHLVDDKIHARST 963

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY+LQE+LT+KSDD+ GR     +I
Sbjct: 964  GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYILQELLTVKSDDMQGRNEALNAI 1023

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            V G      GTPESF VL++E+Q+L L I +  +   +     E+    + +L
Sbjct: 1024 VKGQSIPRPGTPESFKVLMRELQSLCLDISVRKASIPSFDDDGEMKPDPEVDL 1076



 Score =  301 bits (772), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 98/459 (21%), Positives = 180/459 (39%), Gaps = 46/459 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDL+E+Q+AS+  FL   +  +            S  PIT ++G   L F+   Y    
Sbjct: 14  LPDLVEIQRASFRWFLEEGLIEELE----------SFSPITDYTGKIELHFLAKDYRLKE 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+   RD TY++ + +  RLI          K   +I +Q +++GDLPLMT  GT
Sbjct: 64  PKYSVDEAKRRDATYSMQMYVPTRLI---------NKENGNIIDQDVFIGDLPLMTDRGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y   +IP++G W+  E D  D++ 
Sbjct: 115 FIINGAERVIVNQIVRSPGVYYKSETDK---NGRRTYNASLIPNRGAWLKFETDKNDLLW 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+   EIL              +               +   
Sbjct: 172 VRIDKTRKLSAHVLLKALGLTDSEILE------RLRHPEYYQKTVEKEGKFSEEEALIEL 225

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G             D V   T E  +
Sbjct: 226 YKKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNRKLQLNIPDSVRILTPEDIL 285

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++        
Sbjct: 286 AAIDYLINLEFDLGTIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDTDS 345

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 346 LTPTSLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 400

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 401 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 437


>gi|300857737|ref|YP_003782720.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudotuberculosis FRC41]
 gi|300685191|gb|ADK28113.1| DNA-directed RNA polymerase beta subunit [Corynebacterium
            pseudotuberculosis FRC41]
          Length = 1178

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 184/514 (35%), Positives = 259/514 (50%), Gaps = 61/514 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M+    LL A    +  +  D  +     V   ++
Sbjct: 689  LVNLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 747

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 748  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 806

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 807  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 849

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 850  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPD 909

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L++  E 
Sbjct: 910  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPED 963

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 964  LYDVP----------------------AGSLTATPVFDGATNEEVAGLLANSRPNRDGDV 1001

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 1002 MVDANGKAQLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1061

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1062 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1121

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VL+KE+Q+L L++++ ++            D 
Sbjct: 1122 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDDE 1155



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 441/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 250 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDL 309

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + ++DI   ++ LV L  G+ T+            DD
Sbjct: 310 AKVGRYKVNRKLGLGGDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVIPVDTDD 369

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 370 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 429

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 430 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 489

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN++GFIETPYRKV +G +T+ + YL+A EE+   + QA+  +D
Sbjct: 490 EGPNIGLIGSLASYARVNSFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQAHVEVD 549

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             G  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 550 AQGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 609

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AG VE V A  I + + +G  + 
Sbjct: 610 NMQRQAVPLVRSEAPFVGTGMERRAAYDAGDLIINKKAGAVENVSADFITVMADDGTRE- 668

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 669 ------TYMLRKFERTNQGTCYNQIPLVNLGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 722

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 723 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 782

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 783 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 842

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 843 ETGKVIGVRRFSREDDD 859



 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 170/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 36  ERFSFAKITEPIEVPGLLDIQLDSFAWLIGTPEWRARQQEELGESVRITSGLEEILEELS 95

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 96  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 146

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 147 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 204

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 205 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 264

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 265 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLG 324

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G++       +D   ++   +  +R
Sbjct: 325 GDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVI-----PVDTDDIDHFGNRRLR 379

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 380 TVGELIQNQVRVGLSRMERVVRERMTTQD 408


>gi|121728872|ref|ZP_01681881.1| DNA-directed RNA polymerase, beta subunit, putative [Vibrio cholerae
            V52]
 gi|121628840|gb|EAX61300.1| DNA-directed RNA polymerase, beta subunit, putative [Vibrio cholerae
            V52]
          Length = 302

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 176/284 (61%), Positives = 221/284 (77%), Gaps = 5/284 (1%)

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E H
Sbjct: 2    KRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVH 61

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAE 1198
            LG A  G+G KI  +I   K   +++ LR FL+KV   G       IS+  D+ V  +A 
Sbjct: 62   LGLAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAH 118

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLK
Sbjct: 119  NLRAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLK 178

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            LNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+K
Sbjct: 179  LNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 238

Query: 1319 SDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            SDDV GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+
Sbjct: 239  SDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIE 282


>gi|311896602|dbj|BAJ29010.1| putative DNA-directed RNA polymerase subunit beta [Kitasatospora
            setae KM-6054]
          Length = 1157

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 190/508 (37%), Positives = 277/508 (54%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V    +L        E  M   + LL A    +  +  D  +     V   V+
Sbjct: 671  LVDEGQRVEVNQVLADGPCT-DEGEMALGKNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 729

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 730  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGADVVTGDILVGK 787

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 788  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFD 836

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I +GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 837  REEGDELPPGVNQLVRVYVAQKRKITNGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 896

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++                    
Sbjct: 897  IILNPLGVPSRMNPGQVLEIHLGWLA-MQGWDVSGLADEWAQRLQAIG------------ 943

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL--------DES 1231
                             A+  + G  ++TPVFDGA E+ I  +L    L        + +
Sbjct: 944  -----------------ADTVEGGTNLATPVFDGAREDEITGLLDNTTLTRDGERLVNST 986

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 987  GKARLFDGRSGEPFPMPVSVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1046

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1047 QRFGEMEVWALEAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLI 1106

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S  ++    +   D
Sbjct: 1107 KEMQSLCLNVEVLSSDGQSIEMRDSDED 1134



 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 336/670 (50%), Positives = 449/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E  LEE    E              
Sbjct: 197 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEMILEEFGEYES------------- 241

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 242 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 298

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNR 462
           K+N +L      D   + + DII  IK LV L  G+              +DDID+ GNR
Sbjct: 299 KVNRKLGNAESLDSGVLTEPDIINTIKYLVKLHAGETEWRDDEGRDIVIEVDDIDHFGNR 358

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 359 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 418

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 419 SQFMDQTNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 478

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG VT  V YL+A EE+   IAQAN+ L  + +F E
Sbjct: 479 IGSLASYGRVNAFGFIETPYRKVVDGVVTESVDYLTADEEDRYVIAQANAPLTAELTFAE 538

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   +P  +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 539 PRVLVRRRGGEIDYIPGTEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSNMMRQAV 598

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PLL++EAP VGTGME   A  +   I A +AG+V++V A  + + + +G         + 
Sbjct: 599 PLLRSEAPLVGTGMEYRCAVDAADVITADKAGVVQEVSADYVTVANDDGT-------YNT 651

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR  KF RSNQ T  NQ+ LV  G  V  N ++ADGP TD G++ALG+N+LVAFM W G+
Sbjct: 652 YRAAKFTRSNQGTAFNQKVLVDEGQRVEVNQVLADGPCTDEGEMALGKNLLVAFMSWEGH 711

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 712 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 771

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ 
Sbjct: 772 IRIGADVVTGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIG 831

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 832 VRVFDREEGD 841



 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 107/368 (29%), Positives = 167/368 (45%), Gaps = 27/368 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 17  LRVSFAKIKEPLEVPNLLALQTESFDWLLGNAAWKSRVEAALESGQDVPTKSGLEEIFEE 76

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 77  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTFAAPLFVTAEFT---------NNE 127

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 128 TGEIKSQTVFMGDFPLMTNKGTFIINGTERVVVSQLVRSPGVYFDSTLDKV--SDKDIFS 185

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E IL  F  Y  +  +
Sbjct: 186 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEMILEEFGEYESMRAT 245

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  + LG
Sbjct: 246 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNRKLG 305

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEA-GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
                  G+    DI+N     + + A      +    +I                N   
Sbjct: 306 NAESLDSGVLTEPDIINTIKYLVKLHAGETEWRDDEGRDIVIEVDDIDHFGNRRLRNVGE 365

Query: 357 YIRNTLVT 364
            I+N + T
Sbjct: 366 LIQNQVRT 373


>gi|312200028|ref|YP_004020089.1| DNA-directed RNA polymerase, subunit beta [Frankia sp. EuI1c]
 gi|311231364|gb|ADP84219.1| DNA-directed RNA polymerase, beta subunit [Frankia sp. EuI1c]
          Length = 1140

 Score =  525 bits (1352), Expect = e-146,   Method: Composition-based stats.
 Identities = 338/683 (49%), Positives = 473/683 (69%), Gaps = 17/683 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        L    +K +    +      G ++  +I   +T  + I+         
Sbjct: 155 LVRSPGVYFEKSLDKTSDKDLFSCKVIPSR--GAWLEFEIDKRDTVGVRIDRKRRQSVTV 212

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 213 L--LKALGWDEARIL--ERFGDYPSMRVTLEKDHTSGQDDALLDIYRKLRPGEPPTRESA 268

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   LFF+  +YDL+ VGR K+N +L L        + ++DI+  I+ +V L  G   
Sbjct: 269 QTLLENLFFNPKRYDLAKVGRYKVNKKLELHVEGATGVLTEDDIVRTIEYVVKLHEGTDP 328

Query: 453 ---IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +PV
Sbjct: 329 AYEVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRPV 388

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           V+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+
Sbjct: 389 VASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRM 448

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ET EG NIGL+ SL++FARVN +GF+ETPYRKV  G+VT+ + YL+A EE+   +AQ
Sbjct: 449 CPIETPEGPNIGLIGSLSTFARVNPFGFVETPYRKVVAGRVTDQIDYLTADEEDRHVVAQ 508

Query: 630 ANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           AN+ L  DGSF E+ V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+N
Sbjct: 509 ANAPLTADGSFAEDRVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDAN 568

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQ+VPLL++E+P VGTGME+  AK +G  +V ++AG+VE + A  I +   
Sbjct: 569 RALMGSNMQRQSVPLLRSESPLVGTGMEARAAKDAGDVVVCQQAGVVEDLSADYITVMHD 628

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           +G           YRL KF+RSNQ TC+NQ+P+V  G  V    +IADGP TD G++ALG
Sbjct: 629 DGTR-------RTYRLAKFRRSNQGTCINQKPIVDEGARVEAGQVIADGPCTDNGEMALG 681

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNV
Sbjct: 682 KNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNV 741

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           +EE L ++DE GII +GAEVNPGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS
Sbjct: 742 AEEVLADLDERGIIRIGAEVNPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTS 801

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           L+VP G SG V+ VR+F+R   D
Sbjct: 802 LKVPHGESGKVIGVRVFSREDGD 824



 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 194/533 (36%), Positives = 273/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  GA V  G ++           M   + LL A
Sbjct: 629  DGTRRTYRLAKFRRSNQGTCINQKPIVDEGARVEAGQVIADGPCTDN-GEMALGKNLLVA 687

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 688  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 745

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 746  LADLDERGIIRIGAEVNPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 798

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 799  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 854

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++I+P EDMPFL+DGTPVD+VLNP GVP RMN+GQI ETHLGW     G ++ S
Sbjct: 855  GNKGVIAKIMPQEDMPFLEDGTPVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDS 913

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               ++K       + S                                G  V+TPVFDGA
Sbjct: 914  GDEEWKERLRSIGVDSAAP-----------------------------GTNVATPVFDGA 944

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ L+DG TGE +  PV VGYIY+LKL H+V DK
Sbjct: 945  REEEITGLLDATLPNRDGVQLIGSSGKAKLFDGRTGEQYPYPVAVGYIYILKLLHLVDDK 1004

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR 
Sbjct: 1005 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVHGRV 1064

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S        +   D
Sbjct: 1065 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVQIEMRDTDED 1117



 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 114/479 (23%), Positives = 206/479 (43%), Gaps = 40/479 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE------------GLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +  +   +   +             GL+  F+ 
Sbjct: 9   RISFAKIVEPLEVPDLLALQTQSFDWLIGSDAWQERVQDSVDAGRDDVPLTSGLEEVFEE 68

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK+ V++C  +D+T++ P+ +T               +
Sbjct: 69  ISPIEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTFSAPMFVTAEFT---------NNT 119

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K L++
Sbjct: 120 TGEIKSQTVFMGDFPLMTTKGTFVINGTERVVVSQLVRSPGVYFEKSLDKT--SDKDLFS 177

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  YP +  +
Sbjct: 178 CKVIPSRGAWLEFEIDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGDYPSMRVT 237

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K L 
Sbjct: 238 LEKDHTSGQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLE 297

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE----KSLEEIFHSEIRDIPILYVDSVN 353
           +  +   G+   +DIV   T E  ++  +  D       ++   +  +R +  L  + V 
Sbjct: 298 LHVEGATGVLTEDDIV--RTIEYVVKLHEGTDPAYEVDDIDHFGNRRLRTVGELIQNQVR 355

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                   +V ++   +   +  I            +  +  F            + +  
Sbjct: 356 LGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAG 413

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           +    RL+   P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 414 LTHKRRLSALGPGG---LSRERAGMEVRDVHPSHYGR--MCPIETPEGPNIGLIGSLST 467


>gi|302205477|gb|ADL09819.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudotuberculosis C231]
 gi|308275713|gb|ADO25612.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudotuberculosis I19]
          Length = 1178

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 184/514 (35%), Positives = 259/514 (50%), Gaps = 61/514 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M+    LL A    +  +  D  +     V   ++
Sbjct: 689  LVNLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 747

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 748  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 806

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 807  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 849

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 850  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPD 909

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L++  E 
Sbjct: 910  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPED 963

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 964  LYDVP----------------------AGSLTATPVFDGATNEEVAGLLTNSRPNRDGDV 1001

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 1002 MVDANGKAQLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1061

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1062 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1121

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VL+KE+Q+L L++++ ++            D 
Sbjct: 1122 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDDE 1155



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 441/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 250 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDL 309

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + ++DI   ++ LV L  G+ T+            DD
Sbjct: 310 AKVGRYKVNRKLGLGGDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVIPVDTDD 369

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 370 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 429

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 430 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 489

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN++GFIETPYRKV +G +T+ + YL+A EE+   + QA+  +D
Sbjct: 490 EGPNIGLIGSLASYARVNSFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQAHVEVD 549

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             G  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 550 AQGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 609

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AG VE V A  I + + +G  + 
Sbjct: 610 NMQRQAVPLVRSEAPFVGTGMERRAAYDAGDLIINKKAGAVENVSADFITVMADDGTRE- 668

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 669 ------TYMLRKFERTNQGTCYNQIPLVNLGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 722

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 723 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 782

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 783 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 842

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 843 ETGKVIGVRRFSREDDD 859



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 170/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 36  ERFSFAKITEPIEVPGLLDIQLDSFAWLIGTPEWRARQQEELGESVRITSGLEEILEELS 95

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 96  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 146

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 147 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 204

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 205 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 264

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 265 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLG 324

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G++       +D   ++   +  +R
Sbjct: 325 GDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVI-----PVDTDDIDHFGNRRLR 379

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 380 TVGELIQNQVRVGLSRMERVVRERMTTQD 408


>gi|226322723|ref|ZP_03798241.1| hypothetical protein COPCOM_00495 [Coprococcus comes ATCC 27758]
 gi|225208884|gb|EEG91238.1| hypothetical protein COPCOM_00495 [Coprococcus comes ATCC 27758]
          Length = 406

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 150/332 (45%), Positives = 206/332 (62%), Gaps = 15/332 (4%)

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++ PGV + V++++A KR I  GDKMAGRHGNKG+VSR+LP EDMPFL 
Sbjct: 28   DAKVFTRENGDELSPGVNQAVRIYIAQKRKISVGDKMAGRHGNKGVVSRVLPVEDMPFLP 87

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G P+DIVLNPLGVPSRMN+GQ+ E HL  A   LG  I + + D     DI        
Sbjct: 88   NGRPLDIVLNPLGVPSRMNIGQVLEIHLSLAAKALGFNIATPVFDGANEVDIMDTLDLAN 147

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
              +       +    ++     +   +++                  ++ +   L   G+
Sbjct: 148  DYVNLSWEEFEARHKEELLPEVMDYLYEN--------------RDHRALWKGVPLSRDGK 193

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L DG TGE FD PVT+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 194  VRLRDGRTGEYFDSPVTIGHMHYLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQR 253

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE+I+ G +  E G PESF VL+KE
Sbjct: 254  FGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYEAIIKGENIPEPGIPESFKVLLKE 313

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            +Q+LGL + + +   +    ME + D+    L
Sbjct: 314  LQSLGLDVRVLDENNEEVQIMESV-DYGDTNL 344


>gi|154507874|ref|ZP_02043516.1| hypothetical protein ACTODO_00356 [Actinomyces odontolyticus ATCC
            17982]
 gi|153797508|gb|EDN79928.1| hypothetical protein ACTODO_00356 [Actinomyces odontolyticus ATCC
            17982]
          Length = 1158

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 186/513 (36%), Positives = 264/513 (51%), Gaps = 52/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+L           +   + LL A    + ++  D  +     V   ++
Sbjct: 670  IVDEGDRVEAGDVLADGPATSN-GEVALGKNLLVAYMSWEGLNYEDAIILSRRVVEEDIL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEY--EVDARETKLGEEEITRDIPNVSEESLADLDERGIIRIGAEVTAGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+S+      R+ + + A +       V   +           D        
Sbjct: 787  VTPKGETELTSE--ERLLRAIFGEKAREVRDTSLRVPHGEEGIVIGVREFNDD------- 837

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+ PGV + V+V+VA +R I  GDKMAGRHGNKG+VS+ILP EDMPFL DGTPVD
Sbjct: 838  ---EDDLNPGVRQTVRVYVAQRRKITIGDKMAGRHGNKGVVSKILPVEDMPFLADGTPVD 894

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ E HLGW     G    + +   +                   
Sbjct: 895  IILNPLGVPGRMNVGQVLEYHLGWLAHQ-GWDASAAVEAGEEWAA--------------- 938

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                         +     + + G PV+TPVFDG + + +  +LR  + +          
Sbjct: 939  ------------HLPADGIKTEPGTPVATPVFDGLEADELAGLLRNVNPNRDGDVLTNYE 986

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 987  GKARLFDGRSGEPFPYPISVGYTYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1046

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDD  GR +VYE+IV G D  E G PESF VL+
Sbjct: 1047 QRFGEMEVWALEAYGAAYALQELLTIKSDDTTGRVKVYEAIVKGEDIPEPGIPESFRVLI 1106

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +EM++L L+++  ++        E+  DFN  E
Sbjct: 1107 QEMRSLCLNVEALDAAGNVIDLREQDEDFNARE 1139



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 330/636 (51%), Positives = 443/636 (69%), Gaps = 23/636 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           ++      +  TL  D    +++ALLDIYR +RPG+ +    A+++ N  +FDS +YDL+
Sbjct: 230 ETFAAYPVLLETLEKDTVATQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLA 289

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K+N +L ++       +  EDI+A +K L+ L  G               +  +D
Sbjct: 290 KVGRYKINKKLAIEADPKASTLSLEDIVATVKYLLALHQGDKTFAGTRNGEPVEVRVEVD 349

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN  NRR+R+VGE+++ Q R GL RMER+++ER+++ + DS+ PQ LIN +PVV+A+ 
Sbjct: 350 DIDNFANRRIRAVGELIQGQVRTGLARMERTVRERMTTQETDSITPQTLINIRPVVAAIK 409

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP E+
Sbjct: 410 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPIES 469

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +FAR+N +GFIETPYR V DGKVT+++ YL+A +E+  YIAQA+S L
Sbjct: 470 PEGPNIGLIGSLATFARINPFGFIETPYRVVKDGKVTDEIRYLTADDEKGHYIAQASSPL 529

Query: 635 DEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + DGSF E  V CR    +  L+ R+++D++D S +Q+VS+AA+ IPFLE+DD+NR LMG
Sbjct: 530 EADGSFAEHDVLCRVAGDDPTLIARDRVDYMDVSARQMVSVAAAFIPFLEHDDANRALMG 589

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL  EAP VGTGME   A  SG  I+A  +G+V +V A  IV+ + EG   
Sbjct: 590 ANMQRQAVPLLTTEAPLVGTGMEMRAAHDSGEMILAAHSGVVSEVSADLIVVSTDEG--- 646

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               G D YRL KF+RSN   C NQR +V  GD V   D++ADGP+T  G++ALG+N+LV
Sbjct: 647 ----GRDSYRLEKFERSNPGNCTNQRVIVDEGDRVEAGDVLADGPATSNGEVALGKNLLV 702

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+M W G N+ED++++S R+V ED+ TSIHIEE+EV AR+TKLG EEITRDIPNVSEE L
Sbjct: 703 AYMSWEGLNYEDAIILSRRVVEEDILTSIHIEEYEVDARETKLGEEEITRDIPNVSEESL 762

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP 
Sbjct: 763 ADLDERGIIRIGAEVTAGDILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPH 822

Query: 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           G  G V+ VR FN    D N       R  +    +
Sbjct: 823 GEEGIVIGVREFNDDEDDLNPGVRQTVRVYVAQRRK 858



 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 92/308 (29%), Positives = 148/308 (48%), Gaps = 29/308 (9%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFL------------MMNIAPDERPNEGLQA 57
             R+   F K  E +  P+L+ +Q  S+D  L              +   D     GL+ 
Sbjct: 11  KHRI--SFAKLREPLQAPNLLGLQVESFDWLLGNDAWKARVEAAQASGHGDVPDVSGLEE 68

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F  + PI   +G   L F  +  + PK+ +++   +D TY+ P+ +T   + ++     
Sbjct: 69  IFHEISPIEDVAGTMSLSFHDHRLESPKYSMEEAKAKDYTYSAPMYVTAEFMNYE----- 123

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                 +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F  +K     S K
Sbjct: 124 ----TGEIKSQTVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYF--EKLSDRSSDK 177

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPK 235
             +  ++IP +G W++ E D +D + VRIDR+RK  VT FL A+GM   EI  TF  YP 
Sbjct: 178 ETFGAKVIPSRGAWLEFEIDKRDAVGVRIDRKRKQSVTHFLKAVGMTESEIRETFAAYPV 237

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGV 293
           ++ +   D       A   +          ++D  + ++ +    +    L K  + K  
Sbjct: 238 LLETLEKDTVATQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLAKVGRYKIN 297

Query: 294 KFLGITSD 301
           K L I +D
Sbjct: 298 KKLAIEAD 305


>gi|302330031|gb|ADL20225.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudotuberculosis 1002]
          Length = 1166

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 184/514 (35%), Positives = 259/514 (50%), Gaps = 61/514 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M+    LL A    +  +  D  +     V   ++
Sbjct: 677  LVNLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 735

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 736  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 794

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 795  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 837

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 838  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPD 897

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L++  E 
Sbjct: 898  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPED 951

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 952  LYDVP----------------------AGSLTATPVFDGATNEEVAGLLANSRPNRDGDV 989

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 990  MVDANGKAQLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1050 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VL+KE+Q+L L++++ ++            D 
Sbjct: 1110 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDDE 1143



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 441/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 238 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDL 297

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + ++DI   ++ LV L  G+ T+            DD
Sbjct: 298 AKVGRYKVNRKLGLGGDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVIPVDTDD 357

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 358 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 417

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 418 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 477

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN++GFIETPYRKV +G +T+ + YL+A EE+   + QA+  +D
Sbjct: 478 EGPNIGLIGSLASYARVNSFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQAHVEVD 537

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             G  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 538 AQGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 597

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AG VE V A  I + + +G  + 
Sbjct: 598 NMQRQAVPLVRSEAPFVGTGMERRAAYDAGDLIINKKAGAVENVSADFITVMADDGTRE- 656

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 657 ------TYMLRKFERTNQGTCYNQIPLVNLGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 710

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 711 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 770

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 771 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 830

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 831 ETGKVIGVRRFSREDDD 847



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 170/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 24  ERFSFAKITEPIEVPGLLDIQLDSFAWLIGTPEWRARQQEELGESVRITSGLEEILEELS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 84  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 135 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 253 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLG 312

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G++       +D   ++   +  +R
Sbjct: 313 GDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVI-----PVDTDDIDHFGNRRLR 367

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 368 TVGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|209395101|gb|ACI45366.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 195/488 (39%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILADFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCIYTNELDQGAYISHTLRTDETVDEFTARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNR VR VGE+ + QYR GL R+E+++KER+   + + + P +L
Sbjct: 419 VDLRNGNGEVDDIDHLGNRPVRCVGELAEKQYRTGLARIEKAVKERLGLAEQEPLKPHEL 478

Query: 504 INAKPVVS 511
           IN++P+ +
Sbjct: 479 INSQPISA 486


>gi|46360936|gb|AAS89201.1| RpoB [Corynebacterium pseudotuberculosis]
          Length = 1148

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 184/514 (35%), Positives = 259/514 (50%), Gaps = 61/514 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M+    LL A    +  +  D  +     V   ++
Sbjct: 668  LVNLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L++  E 
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPED 942

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 943  LYDVP----------------------AGSLTATPVFDGATNEEVAGLLTNSRPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDANGKAQLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VL+KE+Q+L L++++ ++            D 
Sbjct: 1101 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDDE 1134



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 441/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + ++DI   ++ LV L  G+ T+            DD
Sbjct: 289 AKVGRYKVNRKLGLGGDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVIPVDTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN++GFIETPYRKV +G +T+ + YL+A EE+   + QA+  +D
Sbjct: 469 EGPNIGLIGSLASYARVNSFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQAHVEVD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             G  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 AQGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AG VE V A  I + + +G  + 
Sbjct: 589 NMQRQAVPLVRSEAPFVGTGMERRAAYDAGDLIINKKAGAVENVSADFITVMADDGTRE- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 648 ------TYMLRKFERTNQGTCYNQIPLVNLGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 762 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIGVRRFSREDDD 838



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 170/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 15  ERFSFAKITEPIEVPGLLDIQLDSFAWLIGTPEWRARQQEELGESVRITSGLEEILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 75  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G++       +D   ++   +  +R
Sbjct: 304 GDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVI-----PVDTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|315605890|ref|ZP_07880921.1| DNA-directed RNA polymerase subunit beta [Actinomyces sp. oral taxon
            180 str. F0310]
 gi|315312172|gb|EFU60258.1| DNA-directed RNA polymerase subunit beta [Actinomyces sp. oral taxon
            180 str. F0310]
          Length = 1158

 Score =  525 bits (1351), Expect = e-146,   Method: Composition-based stats.
 Identities = 187/513 (36%), Positives = 264/513 (51%), Gaps = 52/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+L    +      +   + LL A    + ++  D  +     V   ++
Sbjct: 670  IVDEGDRVEVGDVLADGPSTSN-GEVALGKNLLVAYMSWEGLNYEDAIILSRRVVEEDIL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEY--EVDARETKLGEEEITRDIPNVSEESLADLDERGIIRIGAEVTAGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+S+      R+ + + A +       V   +           D        
Sbjct: 787  VTPKGETELTSE--ERLLRAIFGEKAREVRDTSLRVPHGEEGIVIGVREFNDD------- 837

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+ PGV + V+V+VA +R I  GDKMAGRHGNKG+VS+ILP EDMPFL DGTPVD
Sbjct: 838  ---EDDLNPGVRQTVRVYVAQRRKITIGDKMAGRHGNKGVVSKILPVEDMPFLADGTPVD 894

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ E HLGW     G    + +   +      P      +     
Sbjct: 895  IILNPLGVPGRMNVGQVLEYHLGWLAHQ-GWDASAAVEAGEEWATHLPADGVTTE----- 948

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                                   G PV+TPVFDG + + +  +LR  + +          
Sbjct: 949  ----------------------PGTPVATPVFDGLEADELAGLLRNVNPNRDGDVLTNYE 986

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 987  GKARLFDGRSGEPFPYPISVGYTYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1046

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDD  GR +VYE+IV G D  E G PESF VL+
Sbjct: 1047 QRFGEMEVWALEAYGAAYALQELLTIKSDDTTGRVKVYEAIVKGEDIPEPGIPESFRVLI 1106

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +EM++L L+++  ++        E+  DFN  E
Sbjct: 1107 QEMRSLCLNVEALDAAGNVIDLREQDEDFNARE 1139



 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 331/636 (52%), Positives = 442/636 (69%), Gaps = 23/636 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      +  TL  D    +++ALLDIYR +RPG+ +    A+++ N  +FDS +YDL+
Sbjct: 230 DTFAAYPVLLETLEKDTVSTQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLA 289

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K+N +L ++       +  EDI+A +K L+ L  G               +  +D
Sbjct: 290 KVGRYKINKKLAIEADPKASTLSLEDIVATVKYLLALHQGDKAFAGTRGGEPVEVRVEVD 349

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN  NRR+R+VGE+++ Q R GL RMER+++ER+++ + DS+ PQ LIN +PVV+A+ 
Sbjct: 350 DIDNFANRRIRAVGELIQGQVRTGLARMERTVRERMTTQETDSITPQTLINIRPVVAAIK 409

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP E+
Sbjct: 410 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPIES 469

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +FAR+N +GFIETPYR V  GKVT+++ YL+A +E+  +IAQA+S L
Sbjct: 470 PEGPNIGLIGSLATFARINPFGFIETPYRVVEAGKVTDEIRYLTADDEKGHFIAQASSPL 529

Query: 635 DEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + DGSF E  V CR    +  L+ RE++D++D S +Q+VS+AA+ IPFLE+DD+NR LMG
Sbjct: 530 NADGSFAERDVLCRVAGEDPTLIARERVDYMDVSARQMVSVAAAFIPFLEHDDANRALMG 589

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL  EAP VGTGME   A  SG  I+A  +G+V +V A  IV+ + EG   
Sbjct: 590 ANMQRQAVPLLTTEAPLVGTGMEMRAAHDSGEMILAAHSGVVSEVSADLIVVSTDEG--- 646

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               G D YRL KF+RSN   C NQR +V  GD V   D++ADGPST  G++ALG+N+LV
Sbjct: 647 ----GRDSYRLEKFERSNPGNCTNQRVIVDEGDRVEVGDVLADGPSTSNGEVALGKNLLV 702

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+M W G N+ED++++S R+V ED+ TSIHIEE+EV AR+TKLG EEITRDIPNVSEE L
Sbjct: 703 AYMSWEGLNYEDAIILSRRVVEEDILTSIHIEEYEVDARETKLGEEEITRDIPNVSEESL 762

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP 
Sbjct: 763 ADLDERGIIRIGAEVTAGDILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPH 822

Query: 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           G  G V+ VR FN    D N       R  +    +
Sbjct: 823 GEEGIVIGVREFNDDEDDLNPGVRQTVRVYVAQRRK 858



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 92/306 (30%), Positives = 148/306 (48%), Gaps = 27/306 (8%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFL------------MMNIAPDERPNEGLQAAF 59
           R R  F K  E +  P+L+ +Q  S+D  L              +   D     GL+  F
Sbjct: 11  RHRISFAKLHEPLQAPNLLGLQVESFDWLLGNDAWKARVEAAQASGRSDVPDVSGLEEIF 70

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             + PI   +G   L F  +  + PK+ +++   +D TY+ P+ +T   + ++       
Sbjct: 71  HEISPIEDVAGTMSLSFHDHRLESPKYSMEEAKAKDYTYSAPMYVTAEFMNYE------- 123

Query: 120 KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
               +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F+    R   + K  
Sbjct: 124 --TGEIKSQTVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFEKLSDRT--TDKET 179

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIV 237
           +  ++IP +G W++ E D +D + VRIDR+RK  VT FL A+GM   EI  TF  YP ++
Sbjct: 180 FGAKVIPSRGAWLEFEIDKRDAVGVRIDRKRKQSVTHFLKAIGMTESEIRDTFAAYPVLL 239

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF 295
            +   D       A   +          ++D  + ++ +    +    L K  + K  K 
Sbjct: 240 ETLEKDTVSTQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLAKVGRYKINKK 299

Query: 296 LGITSD 301
           L I +D
Sbjct: 300 LAIEAD 305


>gi|209395110|gb|ACI45372.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 198/488 (40%), Positives = 309/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL ++ AP +R  EGLQAAF + FPI + +G   + F  Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQVDKAPLKRNIEGLQAAFDAAFPIVSHNGFVEMRFTEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT-GAKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTAQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F HDKG+   SGKLL++ RIIP +G W+D EFD KD+++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFGHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKDMLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+  +    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANLFVNDSFRLMDSGALMEFVAQRL-RGEIARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + + + G+ V+   K++T+  ++ L++     + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITN-NAGKVVVAKDKRVTTRHIRELEQSATSHVSVPEDLLVGRVVARAIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++D+  +Y + ++   YI  TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLHGAGVQDVQCIYTNELDQGLYISQTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGSMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E ++KER+   + + +MP DL
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEXAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
            ++KP+ +
Sbjct: 479 XHSKPISA 486


>gi|86739286|ref|YP_479686.1| DNA-directed RNA polymerase subunit beta [Frankia sp. CcI3]
 gi|108884786|sp|Q2JFI5|RPOB_FRASC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|86566148|gb|ABD09957.1| DNA-directed RNA polymerase subunit beta [Frankia sp. CcI3]
          Length = 1141

 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 340/684 (49%), Positives = 473/684 (69%), Gaps = 18/684 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        L    +K +    +      G ++  +I   +T  + I+         
Sbjct: 155 LVRSPGVYFERSLDKASDKDLYSCKVIPSR--GAWLEFEIDKRDTVGVRIDRKRRQSVTV 212

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 213 L--LKALGWDEARIL--ERFGDFPSMRITLEKDHTAGQDDALLDIYRKLRPGEPPTRESA 268

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   LFF+  +YDL+ VGR K+N +L+L    DV  + + DI+  I+ +V L  G   
Sbjct: 269 QTLLENLFFNPKRYDLAKVGRYKVNKKLSLGVAHDVGVLTENDIVRTIEYVVKLHAGADP 328

Query: 453 ----IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN +P
Sbjct: 329 AEYEVDDIDHFGNRRIRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLINIRP 388

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           VV+++ EFF +SQLSQ  +  N L+ +TH RRL+ALG GG++R RAG E+RDVHP+HYGR
Sbjct: 389 VVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGR 448

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL+ SL++FARVN +GFIETPYRKV +G+VT  + +L+A EE+    A
Sbjct: 449 MCPIETPEGPNIGLIGSLSTFARVNPFGFIETPYRKVENGRVTGQIDWLTADEEDRHVKA 508

Query: 629 QANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           QAN+ L  DGSF E+ V  R   GE   +P +++D++D SP+Q+VS+A ++IPFLE+DD+
Sbjct: 509 QANTPLRPDGSFAEDRVLVRRKGGEVEFIPPDEVDYMDVSPRQMVSVATAMIPFLEHDDA 568

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  +V  +AG+VE + A  I +  
Sbjct: 569 NRALMGSNMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVVVCAQAGVVEDLSADYITVMH 628

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G           YRL KF+RSNQ TC+NQ+P+V  GD V    +IADGP TD G++AL
Sbjct: 629 DDGTR-------RTYRLAKFRRSNQGTCINQKPIVNEGDRVGAGQVIADGPCTDNGEMAL 681

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPN
Sbjct: 682 GKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPN 741

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V+EE L ++DE GII +GAEV+PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDT
Sbjct: 742 VAEEVLADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDT 801

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SL+VP G SG V+ VR+F+R   D
Sbjct: 802 SLKVPHGESGKVIGVRVFSREDGD 825



 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 197/533 (36%), Positives = 275/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G     R            I++  I+  G  V  G ++           M   + LL A
Sbjct: 630  DGTRRTYRLAKFRRSNQGTCINQKPIVNEGDRVGAGQVIADGPCTDN-GEMALGKNLLVA 688

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 689  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVAEEV 746

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 747  LADLDERGIIRIGAEVSPGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 799

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 800  DTSLKVPHGESGKVIGVR----VFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 855

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL+DGTPVD+VLNP GVP RMN+GQI ETHLGW     G ++ S
Sbjct: 856  GNKGVIAKILPAEDMPFLEDGTPVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDS 914

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               D+K                                    A+   +G  V+TPVFDGA
Sbjct: 915  GTEDWKERLRGIG-----------------------------ADAASAGTNVATPVFDGA 945

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE I  +L     +          G++ L+DG TGEP+  PV VGYIY+LKL H+V DK
Sbjct: 946  REEEITGLLDSTLPNRDGIQLIGSSGKAKLFDGRTGEPYPYPVAVGYIYILKLLHLVDDK 1005

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1006 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1065

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S        +   D
Sbjct: 1066 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGVQIEMRDTDED 1118



 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 106/347 (30%), Positives = 168/347 (48%), Gaps = 27/347 (7%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKSVFP 64
           F K  E +++PDL+ +Q  S+D  +  +   +                 GL+  FK + P
Sbjct: 12  FAKIIEPLEVPDLLALQTQSFDWLIGSDAWAERVQEAIDSGRDDVPITSGLEEVFKEISP 71

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG+  L F  + F+PPK+ V++C  +D+T++ PL +T               +  +
Sbjct: 72  IEDFSGSMSLSFRDHRFEPPKYSVEECKDKDMTFSAPLFVTAEFT---------NNNTGE 122

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K LY+C++
Sbjct: 123 IKSQTVFMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFERSLDK--ASDKDLYSCKV 180

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRG 242
           IP +G W++ E D +D + VRIDR+R+  VT  L ALG D   IL  F  +P +  +   
Sbjct: 181 IPSRGAWLEFEIDKRDTVGVRIDRKRRQSVTVLLKALGWDEARILERFGDFPSMRITLEK 240

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D       A   +            ++ + ++E+         L K  + K  K L +  
Sbjct: 241 DHTAGQDDALLDIYRKLRPGEPPTRESAQTLLENLFFNPKRYDLAKVGRYKVNKKLSLGV 300

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
               G+    DIV      + + AG    E  +++I H   R I  +
Sbjct: 301 AHDVGVLTENDIVRTIEYVVKLHAGADPAEYEVDDIDHFGNRRIRTV 347


>gi|260905737|ref|ZP_05914059.1| DNA-directed RNA polymerase, beta subunit [Brevibacterium linens BL2]
          Length = 1159

 Score =  524 bits (1350), Expect = e-146,   Method: Composition-based stats.
 Identities = 185/518 (35%), Positives = 262/518 (50%), Gaps = 64/518 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L    + +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVDEGDRVEAGTVLADGPSTQN-GEMALGKNLLVAFMSWEGYNFEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H +D  +  +  E     I  ++ D     D++ I+         +IL G+  
Sbjct: 734  SSIHIEEHEVDARDTKLGAEEITRDIPNISPDALADLDDRGIIRIGAEVTDGDILVGKVT 793

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E            +      
Sbjct: 794  PKGETELTPEERLLRAIFGEKSR-----------------EVRDTSLRVPHGEIGTVIGV 836

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++ PGV ++V+V+VA +R I  GDKMAGRHGNKG++S ILP EDMPFL DG
Sbjct: 837  RVFDREEDDELSPGVNQMVRVYVAQRRKITIGDKMAGRHGNKGVISTILPVEDMPFLADG 896

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVP RMN+GQ+FE HLGW     G KI+                      
Sbjct: 897  TPVDIILNPHGVPRRMNIGQVFEVHLGWISKQ-GWKIEGNPEWAA--------------- 940

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +   A + ++G  ++TPVFDGA E+ +  +L            
Sbjct: 941  ----------------ELPEAAREAEAGTNLATPVFDGAHEQELRGLLDSTTPNRDGDRL 984

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D SG++ L+DG +GEPF  P+ VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 985  IDSSGKAQLFDGRSGEPFPYPIAVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1044

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDD+ GR +VYE+IV G +  + G PESF
Sbjct: 1045 QFGGQRFGEMEVWALEAYGAAYTLQELLTIKSDDIPGRVKVYEAIVKGENLPDPGIPESF 1104

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
             VL+KEMQ+L L++++ +S        + E   +   E
Sbjct: 1105 KVLIKEMQSLCLNVEVLSSDGAEVEMRDGEDEVYRAAE 1142



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 322/634 (50%), Positives = 436/634 (68%), Gaps = 27/634 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       IR T+  D    + +ALLDIY+ +RP + +T   A ++
Sbjct: 221 LKALGWSEAKIL--EEFGEFESIRETMAKDTVNTQDEALLDIYKKLRPAEPATAEAARNL 278

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---- 451
            N L+F+  +YDL+ VGR K+N +L +D P     +  +D++A I+ LV L  G      
Sbjct: 279 LNNLYFNPKRYDLAKVGRYKVNRKLGVDAPLSDSVLSTDDVVATIRYLVSLHAGVDTSKG 338

Query: 452 -----------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                       +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ P
Sbjct: 339 VRDGEDIELSVKLDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEAITP 398

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E+RD
Sbjct: 399 QTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAAMEVRD 458

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL S+AR+N +GFIETPYRKV DG VT+D  YL+A 
Sbjct: 459 VHPSHYGRMCPIETPEGPNIGLIGSLASYARINPFGFIETPYRKVVDGVVTDDTEYLTAD 518

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSIAAS 677
           +E    IAQAN+ L E+  F E  V  R     GE  LV  + IDF+D S +Q+VS+A++
Sbjct: 519 DELEFNIAQANAPLTEEQRFAEVEVLARPKGGGGEAELVQYDTIDFMDVSARQMVSVASA 578

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPL+ +E+P VGTGME   A  +G  I A R G++ +
Sbjct: 579 LIPFLEHDDANRALMGANMQRQAVPLVMSESPVVGTGMEYRAAVDAGDVITADRPGVITE 638

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  + + + +G        +  YR  KF+RSN  T  NQR +V  GD V    ++ADG
Sbjct: 639 VSADFVTVLADDGT-------MQTYRAAKFKRSNHGTSYNQRIIVDEGDRVEAGTVLADG 691

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           PST  G++ALG+N+LVAFM W GYNFED++++S+R+V +DV +SIHIEE EV ARDTKLG
Sbjct: 692 PSTQNGEMALGKNLLVAFMSWEGYNFEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLG 751

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPN+S + L ++D+ GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 752 AEEITRDIPNISPDALADLDDRGIIRIGAEVTDGDILVGKVTPKGETELTPEERLLRAIF 811

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEK+ +VRDTSLRVP G  GTV+ VR+F+R   D
Sbjct: 812 GEKSREVRDTSLRVPHGEIGTVIGVRVFDREEDD 845



 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 143/322 (44%), Gaps = 29/322 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +      D                 GL+  F+ 
Sbjct: 16  RISFAKIREPLEVPDLLGLQTDSFDWLIGSEAWQDRVAEAIEIGDDSVATTSGLEDIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G+  L F  + F+  K+ +D+C  RD+TY+ PL +T   +           +
Sbjct: 76  ISPIEDFGGSMSLSFREHRFEAAKYSIDECKERDMTYSAPLYVTAEFM---------NNN 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF++ G +R+VVSQL RSPG +F+    +   + K ++ 
Sbjct: 127 TGEIKSQTVFMGDFPLMTDKGTFIVNGTERVVVSQLVRSPGAYFESSVDKT--TDKDIFT 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W++ E D +D + VR+DR+RK  VT  L ALG    +IL  F       + 
Sbjct: 185 AKIIPSRGAWLEFEVDKRDQVGVRLDRKRKQSVTVLLKALGWSEAKILEEFGEFESIRET 244

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
                       L+   K                  + L + L  + K   +  +G    
Sbjct: 245 MAKDTVNTQDEALLDIYKKLRPAEPATAEAA-----RNLLNNLYFNPKRYDLAKVGRYKV 299

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   G+          T ++  
Sbjct: 300 NRKLGVDAPLSDSVLSTDDVVA 321


>gi|16329957|ref|NP_440685.1| DNA-directed RNA polymerase subunit beta [Synechocystis sp. PCC
           6803]
 gi|2500610|sp|P77965|RPOB_SYNY3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|1652443|dbj|BAA17365.1| RNA polymerase beta subunit [Synechocystis sp. PCC 6803]
          Length = 1102

 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 331/687 (48%), Positives = 457/687 (66%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +Y+    
Sbjct: 112 INGAERVIVNQIVRSPGVYYKKELDKNGRRTYSASLIPNRGAWLKFETDKNGLVYVRIDK 171

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  DS+++  + + TL  + N   ++AL+++Y+ +RPG+ 
Sbjct: 172 TRKLSAQVLLKAIGLSDNEIL--DSLSHPEFYQKTLDKEGNPTEEEALVELYKKLRPGEP 229

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD  +YDL  VGR K+N +L L+  D  R +  +DI+A I  L++L
Sbjct: 230 PTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLNEADTTRVLTPQDILAAINYLINL 289

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               GT DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + D++ P  L+N 
Sbjct: 290 EFDVGTTDDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMTVSESDALTPASLVNP 349

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 350 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 409

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGFIETPY +V  G+V  D+  VYL+A EE++
Sbjct: 410 GRICPVETPEGPNAGLIGSLATCARVNDYGFIETPYFRVESGRVRKDLDPVYLTADEEDD 469

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +   DE+G+   E V  R   E      E++D++  SP Q++S+A S+IPFLE+
Sbjct: 470 MRVAPGDIPTDEEGNIIGESVPIRYRQEFSTTSPEQVDYVAVSPVQIISVATSMIPFLEH 529

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV  VDA  I 
Sbjct: 530 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTHGIVTYVDATEIR 589

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++    D         +Y + K+QRSNQ+TC+NQRPLV  G++V    ++ADG +T+ G+
Sbjct: 590 VQPHSPDNPAEKGEEIVYPIQKYQRSNQDTCLNQRPLVYAGEDVVPGQVLADGSATEGGE 649

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+
Sbjct: 650 LALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITRE 709

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V  GDILVGK+TPKGE+   PEEKLLRAIFGEKA DV
Sbjct: 710 IPNVGEDALRNLDEHGIIRIGAWVESGDILVGKVTPKGEADQPPEEKLLRAIFGEKARDV 769

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 770 RDNSLRVPNGEKGRVVDVRVFTREKGD 796



 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 194/615 (31%), Positives = 273/615 (44%), Gaps = 72/615 (11%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V            A+              +L    P  G   E        MV   
Sbjct: 515  QIISVATSMIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVS 574

Query: 838  VFTSIHIEEFEVMARDTKL--------GPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
                I         R            G E +              +++  ++  G +V 
Sbjct: 575  RTHGIVTYVDATEIRVQPHSPDNPAEKGEEIVYPIQKYQRSNQDTCLNQRPLVYAGEDVV 634

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PG +L      +G   +   + +L A    +  +  D  L     V   V       +  
Sbjct: 635  PGQVLADGSATEG-GELALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFE 693

Query: 950  IDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            I+  +  +  E    +I  +  D     DE  I+    +    +IL G+    G      
Sbjct: 694  IEARQTKLGPEEITREIPNVGEDALRNLDEHGIIRIGAWVESGDILVGKVTPKGEADQPP 753

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWG 1063
               L   +  E  R                   ++       +  + R  + ++   + G
Sbjct: 754  EEKLLRAIFGEKARD------------------VRDNSLRVPNGEKGRVVDVRVFTREKG 795

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++PPG   VV+++VA KR IQ GDKMAGRHGNKGI+SRILP EDMP+L DG P+DI LN
Sbjct: 796  DELPPGANMVVRIYVAQKRKIQVGDKMAGRHGNKGIISRILPIEDMPYLPDGRPIDIALN 855

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PLGVPSRMNVGQ+FE  LGWA   LG + K    D               ++ G  +  +
Sbjct: 856  PLGVPSRMNVGQVFECLLGWAGENLGVRFKITPFD---------------EMYGEEASRD 900

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
             +    +++  R  + W         VF+                +  G+  ++DG TGE
Sbjct: 901  TVHGLLEEASQRPNKDW---------VFNE---------------NHPGKIQVFDGRTGE 936

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            PFDRP+TVG  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++
Sbjct: 937  PFDRPITVGQAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALE 996

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY+LQE+LT+KSDD+ GR     +IV G      GTPESF VL++E+Q+LGL I  
Sbjct: 997  AYGAAYILQELLTVKSDDMQGRNEALNAIVKGKSIPRPGTPESFKVLMRELQSLGLDIAA 1056

Query: 1364 ENSRTKNSAKMEEIP 1378
               +     +  +  
Sbjct: 1057 HKVQLSEDGESADAE 1071



 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 103/495 (20%), Positives = 198/495 (40%), Gaps = 54/495 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLIE+Q AS+  FL           EGL     S  PI+ ++G   L F+   Y+   
Sbjct: 9   LPDLIEIQHASFHWFL----------EEGLIEELNSFSPISDYTGKLELHFLGKDYKLKQ 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD +Y+V + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 59  PKYDVDESKRRDASYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTERGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   +++
Sbjct: 110 FIINGAERVIVNQIVRSPGVYYKKELDK---NGRRTYSASLIPNRGAWLKFETDKNGLVY 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL +      Y +  D    P     L+        
Sbjct: 167 VRIDKTRKLSAQVLLKAIGLSDNEILDSLSHPEFYQKTLDKEGNPTEEEALV------EL 220

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVN 314
              +  GE   +  G++L        K           +      ++      +    + 
Sbjct: 221 YKKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLNEADTTRVLTPQDIL 280

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +     DV     ++ + +  +R +  L  + +         ++ ++    +   
Sbjct: 281 AAINYLINLEFDVGTTDDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMTVSESDA 340

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    R++   P     + +E
Sbjct: 341 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRE 395

Query: 435 DIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMER 484
                ++ +    +G+    +                 RV   G +    +R+   R+ +
Sbjct: 396 RAGFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATCARVNDYGFIETPYFRVESGRVRK 455

Query: 485 SIKERISSVDIDSVM 499
            +     + D +  M
Sbjct: 456 DLDPVYLTADEEDDM 470


>gi|158518631|sp|Q82DQ5|RPOB_STRAW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|148878564|dbj|BAC72626.2| RNA polymerase beta subunit [Streptomyces avermitilis MA-4680]
          Length = 1161

 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 190/515 (36%), Positives = 267/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  VVDEGARVIAGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +D+             
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADDWAQRLQAIE----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 948  ------------------------ADQVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 983

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  ERMVLPTGKAPLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  508 bits (1307), Expect = e-141,   Method: Composition-based stats.
 Identities = 335/670 (50%), Positives = 455/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  + P D   +  EDII+ IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGGEAPLDAGILTVEDIISSIKYLVKLHAGETETVGDNGTSIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L +D  F E
Sbjct: 483 IGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANAPLGDDFRFEE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 TRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + +++ G+V++V A  +   + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCAVDAGDVLKSEKDGVVQEVSADYVTTANDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  G  V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLHKFSRSNQGTSVNQKVVVDEGARVIAGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKVIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   EDI++     + + AG+                 ++   +  +R++  
Sbjct: 310 GEAPLDAGILTVEDIISSIKYLVKLHAGETETVGDNGTSIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|297159573|gb|ADI09285.1| DNA-directed RNA polymerase subunit beta [Streptomyces
            bingchenggensis BCW-1]
          Length = 1160

 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L    + + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 675  VVDEGARVIAGQVLADGPSTE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G K++      +    I       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWKVEGSEEWMQRLQAIG------ 946

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++   G  V+TPVFDGA E+ I+ +      +   
Sbjct: 947  ------------------------ADEVAPGTNVATPVFDGAREDEISGLFDSTIPNRDG 982

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ ++DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  DRLVQSSGKARMFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 455/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSIT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L    P D   +  ED+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGAAAPLDAGVLTVEDVIASIKYLVKLHAGETETTGENGQMIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQTNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG VT+DV YL+A EE+   IAQAN+ L +D  F E
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGVVTDDVDYLTADEEDRFVIAQANAPLTDDLHFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 NRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSNMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PLLKAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G         + 
Sbjct: 603 PLLKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGT-------YNT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T  NQ+ +V  G  V    ++ADGPST+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRVAKFSRSNQGTSFNQKVVVDEGARVIAGQVLADGPSTEDGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 205/486 (42%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W+++E D +D++ VRIDR+RK  +T  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 VKVIPSRGAWLEMEIDKRDMVGVRIDRKRKQSITVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   ED++      + + AG+                 ++   +  IR++  
Sbjct: 310 AAAPLDAGVLTVEDVIASIKYLVKLHAGETETTGENGQMIVVETDDIDHFGNRRIRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QTNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|297201712|ref|ZP_06919109.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sviceus ATCC
            29083]
 gi|197710915|gb|EDY54949.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sviceus ATCC
            29083]
          Length = 1161

 Score =  524 bits (1349), Expect = e-146,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 266/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVNEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L  D+     +       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEDWAQRLQVIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                                    A+    G  V+TPVFDGA E+ +  +L+        
Sbjct: 948  ------------------------ADAVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 983

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  +G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  ERMVQPTGKARLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 339/670 (50%), Positives = 458/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  EDII+ IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADAPLDAGILTVEDIISTIKYLVKLHAGETETTGDSGTSIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV  G VT++V YL+A EE+   IAQAN++L++D  F E
Sbjct: 483 IGSLASYGRVNAFGFVETPYRKVTGGVVTDEVDYLTADEEDRFVIAQANATLNDDMRFEE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 SRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 603 PLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLAKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  343 bits (879), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALESGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   EDI++     + + AG+                 ++   +  +R +  
Sbjct: 310 ADAPLDAGILTVEDIISTIKYLVKLHAGETETTGDSGTSIVVETDDIDHFGNRRLRSVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|293190271|ref|ZP_06608767.1| DNA-directed RNA polymerase, beta subunit [Actinomyces odontolyticus
            F0309]
 gi|292821087|gb|EFF80040.1| DNA-directed RNA polymerase, beta subunit [Actinomyces odontolyticus
            F0309]
          Length = 1158

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 186/513 (36%), Positives = 264/513 (51%), Gaps = 52/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+L           +   + LL A    + ++  D  +     V   ++
Sbjct: 670  IVDEGDRVEVGDVLADGPATSN-GEVALGKNLLVAYMSWEGLNYEDAIILSRRVVEEDIL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEY--EVDARETKLGEEEITRDIPNVSEESLADLDERGIIRIGAEVTAGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+S+      R+ + + A +       V   +           D        
Sbjct: 787  VTPKGETELTSE--ERLLRAIFGEKAREVRDTSLRVPHGEEGIVIGVREFNDD------- 837

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+ PGV + V+V+VA +R I  GDKMAGRHGNKG+VS+ILP EDMPFL DGTPVD
Sbjct: 838  ---QDDLNPGVRQTVRVYVAQRRKITIGDKMAGRHGNKGVVSKILPVEDMPFLADGTPVD 894

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ E HLGW     G    + +   +                   
Sbjct: 895  IILNPLGVPGRMNVGQVLEYHLGWLAHQ-GWDASAAVEAGEEWAA--------------- 938

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                         +     + + G PV+TPVFDG + + +  +LR  + +          
Sbjct: 939  ------------HLPADGIKTEPGTPVATPVFDGLEADELAGLLRNVNPNRDGDVLTNYE 986

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 987  GKARLFDGRSGEPFPYPISVGYTYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1046

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDD  GR +VYE+IV G D  E G PESF VL+
Sbjct: 1047 QRFGEMEVWALEAYGAAYALQELLTIKSDDTTGRVKVYEAIVKGEDIPEPGIPESFRVLI 1106

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +EM++L L+++  ++        E+  DFN  E
Sbjct: 1107 QEMRSLCLNVEALDAAGNVIDLREQDEDFNARE 1139



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 330/636 (51%), Positives = 443/636 (69%), Gaps = 23/636 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           ++      +  TL  D    +++ALLDIYR +RPG+ +    A+++ N  +FDS +YDL+
Sbjct: 230 ETFAAYPVLLETLEKDTVATQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLA 289

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K+N +L ++       +  EDI+A +K L+ L  G               +  +D
Sbjct: 290 KVGRYKINKKLAIEADPKASTLSLEDIVATVKYLLALHQGDKTFAGTRNGEAVEVRVEVD 349

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN  NRR+R+VGE+++ Q R GL RMER+++ER+++ + DS+ PQ LIN +PVV+A+ 
Sbjct: 350 DIDNFANRRIRAVGELIQGQVRTGLARMERTVRERMTTQETDSITPQTLINIRPVVAAIK 409

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP E+
Sbjct: 410 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPIES 469

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +FAR+N +GFIETPYR V DGKVT+++ YL+A +E+  YIAQA+S L
Sbjct: 470 PEGPNIGLIGSLATFARINPFGFIETPYRVVKDGKVTDEIRYLTADDEKGHYIAQASSPL 529

Query: 635 DEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + DGSF E  V CR    +  L+ R+++D++D S +Q+VS+AA+ IPFLE+DD+NR LMG
Sbjct: 530 EADGSFAEHDVLCRVAGDDPTLIARDRVDYMDVSARQMVSVAAAFIPFLEHDDANRALMG 589

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL  EAP VGTGME   A  SG  I+A  +G+V +V A  IV+ + EG   
Sbjct: 590 ANMQRQAVPLLTTEAPLVGTGMEMRAAHDSGEMILAAHSGVVSEVSADLIVVSTDEG--- 646

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               G D YRL KF+RSN   C NQR +V  GD V   D++ADGP+T  G++ALG+N+LV
Sbjct: 647 ----GRDSYRLEKFERSNPGNCTNQRVIVDEGDRVEVGDVLADGPATSNGEVALGKNLLV 702

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+M W G N+ED++++S R+V ED+ TSIHIEE+EV AR+TKLG EEITRDIPNVSEE L
Sbjct: 703 AYMSWEGLNYEDAIILSRRVVEEDILTSIHIEEYEVDARETKLGEEEITRDIPNVSEESL 762

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP 
Sbjct: 763 ADLDERGIIRIGAEVTAGDILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPH 822

Query: 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           G  G V+ VR FN    D N       R  +    +
Sbjct: 823 GEEGIVIGVREFNDDQDDLNPGVRQTVRVYVAQRRK 858


>gi|88854711|ref|ZP_01129377.1| DNA-directed RNA polymerase beta subunit [marine actinobacterium
            PHSC20C1]
 gi|88815872|gb|EAR25728.1| DNA-directed RNA polymerase beta subunit [marine actinobacterium
            PHSC20C1]
          Length = 1174

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 184/515 (35%), Positives = 261/515 (50%), Gaps = 69/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    +   + LL A    +  +  D  +   + V   V+
Sbjct: 689  IVSAGERVEVGQVIADGPATEN-GELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   +  + + R   + +E+I          L  D  DE+ I+      R  +IL G
Sbjct: 748  SSIHIEEY--EVDARDTKLGKEEITRDLPNVSPELLADL-DERGIIRIGAEVRPGDILVG 804

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   + +E  R                 E      +         
Sbjct: 805  KVTPKGETELSAEERLLRAIFNEKSR-----------------EVRDTSLKVPHGEQGTI 847

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K       D++  GV + V V++A KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 848  IAVKEFSADNDDELGSGVNQRVVVYIAQKRKITEGDKLAGRHGNKGVISKILPVEDMPFL 907

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLG+P RMN GQ+ ETHLGW     G +++      K            
Sbjct: 908  ADGTPVDIILNPLGIPGRMNFGQVLETHLGWVAKQ-GWEVEGNPEWAKN----------- 955

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM------- 1225
                                +   A + + G  V+TPVFDGA EE I  +L         
Sbjct: 956  --------------------LPAEAYKAEPGTKVATPVFDGAYEEEIAGLLDSTTPTRDG 995

Query: 1226 -ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +D SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 996  VRLIDSSGKTPLFDGRSGEPFPAPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1055

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VYE+IV G +  E G P
Sbjct: 1056 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVYEAIVKGENIQEPGIP 1115

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ ++        +   +
Sbjct: 1116 ESFKVLIKEMQSLCLNVEVLSADGSTVNLRDTDDE 1150



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 333/711 (46%), Positives = 461/711 (64%), Gaps = 41/711 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    + + +    I S  +    G ++  +I   +   + +     
Sbjct: 160 ERVVVSQLVRSPGVYFDRQPEKLSDKDIYSARIIPSRGAWLEFEI--DKRDHVGVRIDRK 217

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +     +    +    IL  D       I  TL  D    +++AL DIYR +RPG+  
Sbjct: 218 RKQSVTVFLKALGLTSEEIL--DEFKGFPSIEATLEKDNILTKEEALKDIYRKLRPGEQV 275

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+S +YDL+ VGR K+N +L LDT      +  EDIIA IK +V L 
Sbjct: 276 AAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGLDTDIKESVLTVEDIIATIKYMVSLH 335

Query: 448 NGKGT--------------------------IDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
           +                              IDDID+ GNRR+R+VGE+++NQ R GL R
Sbjct: 336 DNSAPSVSVSDSGVASVKGVRDGKKVNVRLDIDDIDHFGNRRIRAVGELIQNQVRTGLSR 395

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRL
Sbjct: 396 MERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRL 455

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+NA+GFIETP
Sbjct: 456 SALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINAFGFIETP 515

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREK 660
           YR++ +G V+  + YL+A +E++  +AQAN+ L +D  F E  V  R   GE  LVP E 
Sbjct: 516 YRRLINGTVSTTIDYLTASDEDDYIVAQANAPLTKDMKFAEPRVLARKKGGEVDLVPVED 575

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           I ++D SP+Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTGME+  A
Sbjct: 576 IAYMDVSPRQMVSVATSIIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTGMEAFAA 635

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG  + A +AG+V +V A  +V++  EG           Y L KF RSNQ T  N R 
Sbjct: 636 IDSGDVVTALKAGVVSEVSADMVVVQLDEGGTQD-------YFLRKFNRSNQGTSYNHRV 688

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V  G+ V    +IADGP+T+ G+LALG+N+LVAFMPW G+NFED++++S+ +V +DV +
Sbjct: 689 IVSAGERVEVGQVIADGPATENGELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDVLS 748

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+EV ARDTKLG EEITRD+PNVS E L ++DE GII +GAEV PGDILVGK+TP
Sbjct: 749 SIHIEEYEVDARDTKLGKEEITRDLPNVSPELLADLDERGIIRIGAEVRPGDILVGKVTP 808

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ ++ EE+LLRAIF EK+ +VRDTSL+VP G  GT++ V+ F+    D
Sbjct: 809 KGETELSAEERLLRAIFNEKSREVRDTSLKVPHGEQGTIIAVKEFSADNDD 859



 Score =  337 bits (864), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 99/311 (31%), Positives = 149/311 (47%), Gaps = 27/311 (8%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EG 54
            NG    R  F K  + + +PDL+ +Q  S+D  +  +I      +             G
Sbjct: 14  KNGRSASRLSFAKITDTLTVPDLLALQTESFDWLVGNDIWKQRVTDGVAAGRTDLPTRSG 73

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           L   F+ + PI        L F   E + PK+ +D+C  R  T+A PL +    +     
Sbjct: 74  LDEIFEEISPIEDLGETMQLSFTEPELEEPKYSIDECKERGKTFAAPLYVNAEFM----- 128

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                    +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   
Sbjct: 129 ----NHLTGEIKTQTVFMGDFPLMTARGTFIINGTERVVVSQLVRSPGVYFDRQPEKL-- 182

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-- 232
           S K +Y+ RIIP +G W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  
Sbjct: 183 SDKDIYSARIIPSRGAWLEFEIDKRDHVGVRIDRKRKQSVTVFLKALGLTSEEILDEFKG 242

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKE 290
           +P I  +   D       A   +         V  +    ++++    +    L K  + 
Sbjct: 243 FPSIEATLEKDNILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRY 302

Query: 291 KGVKFLGITSD 301
           K  + LG+ +D
Sbjct: 303 KINRKLGLDTD 313


>gi|307328018|ref|ZP_07607199.1| DNA-directed RNA polymerase, beta subunit [Streptomyces
            violaceusniger Tu 4113]
 gi|306886323|gb|EFN17328.1| DNA-directed RNA polymerase, beta subunit [Streptomyces
            violaceusniger Tu 4113]
          Length = 1160

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 269/515 (52%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L    + + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 675  VVDEGARVIAGQVLADGPSTE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G K++   +  +    I       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWKVEGSEDWMQRLQAIG------ 946

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ I  +      +   
Sbjct: 947  ------------------------ADEVQPGTNVATPVFDGAREDEIAGLFDSTIPNRDG 982

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  DRLVQSSGKAHLFDGRSGEPFPEPISIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 337/670 (50%), Positives = 454/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L    P D   +  ED+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGSAAPLDAGVLTVEDVIASIKYLVKLHAGETETVGDNGQSVVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQTNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG VT+DV YL+A EE+   IAQAN+ L +D  F E
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGVVTDDVDYLTADEEDRFVIAQANAPLADDLRFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 NRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSNMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G           
Sbjct: 603 PLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T  NQ+ +V  G  V    ++ADGPST+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRVAKFSRSNQGTSFNQKVVVDEGARVIAGQVLADGPSTEDGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  335 bits (860), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIREPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF I G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTDKGTFCINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 VKVIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   ED++      + + AG+                 ++   +  IR++  
Sbjct: 310 SAAPLDAGVLTVEDVIASIKYLVKLHAGETETVGDNGQSVVVETDDIDHFGNRRIRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QTNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|269955428|ref|YP_003325217.1| DNA-directed RNA polymerase subunit beta [Xylanimonas cellulosilytica
            DSM 15894]
 gi|269304109|gb|ACZ29659.1| DNA-directed RNA polymerase, beta subunit [Xylanimonas
            cellulosilytica DSM 15894]
          Length = 1165

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 185/508 (36%), Positives = 265/508 (52%), Gaps = 52/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V PG +L        E  +     LL A    +  +  D  +     +   V+
Sbjct: 676  IVDEGQRVEPGSVLADGP-ATDEGELALGRNLLVAFMSWEGHNYEDAIILSQRLIEDDVL 734

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL-LARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I   +    +D    LD     R+   +   + + G 
Sbjct: 735  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEDVLADLDERGIIRIGAEVGAGDVLVGK 792

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 793  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGESGTVIGVREFNR-------- 842

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++P GV ++V+V++A +R I  GDK+AGRHGNKG++S+ILP EDMPFL DGTPVD
Sbjct: 843  -EDGDELPAGVNQLVRVYIAQRRKITVGDKLAGRHGNKGVISKILPQEDMPFLPDGTPVD 901

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +VLNPLGVP RMNVGQ+ ETHLGW     G  +++   D     D+  + +  E      
Sbjct: 902  VVLNPLGVPGRMNVGQVLETHLGWVAS-RGWDVEAAEGDTAWTADVPDIAAKAEPF---- 956

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                     PV+TPVFDG  E A+  +L     +          
Sbjct: 957  ------------------------TPVATPVFDGLAENALQGLLTTTLPNRDGDRMVGGD 992

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 993  GKARLFDGRSGEPFPDPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1052

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G PESF VL+
Sbjct: 1053 QRFGEMEVWALEAYGAAYTLQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIPESFKVLL 1112

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    E   +
Sbjct: 1113 KEMQSLCLNVEVLSSDGSSIEMKESDDE 1140



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 317/618 (51%), Positives = 431/618 (69%), Gaps = 23/618 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +       + +TL  D      +AL+D+YR +RPG+  T     ++    +F+  +YDL+
Sbjct: 236 EEFAQFPAVLDTLEKDHVHTEDEALVDLYRKIRPGEPPTVEAGRALLENFYFNPKRYDLA 295

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---------------NGKGTID 454
            VGR K++ +L +D P     + + DI+A IK L  L                  +   D
Sbjct: 296 KVGRYKVSKKLGIDAPLTDSTLTRADIVATIKYLAALHADVATLNGTRNGEPVEVRVETD 355

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ 
Sbjct: 356 DIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVASIR 415

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET
Sbjct: 416 EFFGTSQLSQFMDQNNPLAGLTHKRRLNALGPGGLSRDRAGMEVRDVHPSHYGRMCPIET 475

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL SF R+N +GFIETPYRKV  G VT+ + YL+A +E+   IAQAN+ L
Sbjct: 476 PEGPNIGLIGSLASFGRINPFGFIETPYRKVEGGLVTDRIDYLTADDEDRYVIAQANTPL 535

Query: 635 DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            EDG F E+ V  R   GE   VP  ++D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG
Sbjct: 536 TEDGHFQEQRVLVRVKGGETSDVPVSEVDYIDVSPRQMVSVATALIPFLEHDDANRALMG 595

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTGME   A  +G  +VA + G+V +V A  +++ + +    
Sbjct: 596 ANMQRQAVPLVRSEMPLVGTGMERRAAIDAGDVVVATKPGVVTEVSADLVLVANDDATTS 655

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   YR+ KF RSNQ T  NQR +V  G  V    ++ADGP+TD G+LALGRN+LV
Sbjct: 656 S-------YRISKFVRSNQGTSYNQRVIVDEGQRVEPGSVLADGPATDEGELALGRNLLV 708

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFM W G+N+ED++++S+R++ +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSE+ L
Sbjct: 709 AFMSWEGHNYEDAIILSQRLIEDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEDVL 768

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP 
Sbjct: 769 ADLDERGIIRIGAEVGAGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPH 828

Query: 934 GVSGTVVDVRIFNRHGID 951
           G SGTV+ VR FNR   D
Sbjct: 829 GESGTVIGVREFNREDGD 846



 Score =  334 bits (857), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 94/298 (31%), Positives = 148/298 (49%), Gaps = 30/298 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMN--------IAPDERPNEGLQAAFKSVFPI 65
           R  F K  E +++PDL+ +Q  S+D  L            +       GL+  F+ + PI
Sbjct: 23  RLSFAKIYEPLEVPDLLGLQTESFDWLLGNEAWQARVAAASSAVPATSGLEEIFEEISPI 82

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             F  +  L F ++ F+PPK+  ++C  +D TYA PL +T   + +         +  +I
Sbjct: 83  EDFGQSMSLSFSNHRFEPPKYTAEECKEKDFTYAAPLFVTAEFVNY---------TTGEI 133

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++  +II
Sbjct: 134 KSQTVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFERTPDKT--SDKDIFTSKII 191

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGD 243
           P +G W++ E D +D + VR+DR+RK  VT  L ALGM   EI   F  +P ++ +   D
Sbjct: 192 PSRGAWLEFEIDKRDAVGVRVDRKRKQSVTVLLKALGMTESEIREEFAQFPAVLDTLEKD 251

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                  A        +      I  GE   +E+G+ L      + K   +  +G   
Sbjct: 252 HVHTEDEA--------LVDLYRKIRPGEPPTVEAGRALLENFYFNPKRYDLAKVGRYK 301


>gi|119960861|ref|YP_948666.1| DNA-directed RNA polymerase subunit beta [Arthrobacter aurescens TC1]
 gi|158512968|sp|A1R8V4|RPOB_ARTAT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119947720|gb|ABM06631.1| DNA-directed RNA polymerase, beta subunit [Arthrobacter aurescens
            TC1]
          Length = 1173

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 189/544 (34%), Positives = 267/544 (49%), Gaps = 64/544 (11%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E++      G E   R             +   ++  G  +  G  ++       +  + 
Sbjct: 657  ELVVMINDDGTETNYRINKFARSNQGNCYNHRVLVNEGQRLEVG-GIIADGPATDQGELA 715

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIE 965
              + LL A    +  +  D  +     V+  V+       H ID  +  +  E     I 
Sbjct: 716  LGKNLLVAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDTKLGAEEITRDIP 775

Query: 966  LLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             ++ +     DE+ I+         +IL G+    G         L   +  E  R    
Sbjct: 776  NVSEEVLAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSR---- 831

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                         E      +            ++      D++PPGV ++V+V+VA KR
Sbjct: 832  -------------EVRDTSLKVPHGESGTVIGVRVFDRDNDDELPPGVNQLVRVYVAAKR 878

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I  GDK+AGRHGNKG++S+ILP EDMPFL DGTPVDIVLNPLGVP RMNVGQ+ ETHLG
Sbjct: 879  KITDGDKLAGRHGNKGVISKILPIEDMPFLADGTPVDIVLNPLGVPGRMNVGQVLETHLG 938

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            W     G KI+      K   ++                                     
Sbjct: 939  WVAK-TGWKIEGEPEWVKNLPNLPRE--------------------------------TG 965

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYI 1254
               V+TPVFDGA EE I  +L   +        +D SG++ L+DG +GEPF  P++VGY+
Sbjct: 966  QTTVATPVFDGAREEEITGLLDSTNVTRDGDRLIDSSGKTRLFDGRSGEPFPDPISVGYM 1025

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+
Sbjct: 1026 YILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEL 1085

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LTIKSDD+ GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ ++        
Sbjct: 1086 LTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSTDGTTIEMR 1145

Query: 1375 EEIP 1378
            +   
Sbjct: 1146 DSDD 1149



 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 337/637 (52%), Positives = 451/637 (70%), Gaps = 30/637 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       +R TL  D  + R+DALLDIYR +RPG+  T   A+S+
Sbjct: 233 LKALGWTEGQIL--EEFGQYDSMRATLEKDATETREDALLDIYRKLRPGEPPTVEAAQSL 290

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNGKG- 451
            + L+F++ +YDL+ VGR K+N +L +D     +    +  EDI+A+IK LV L  G+  
Sbjct: 291 LDNLYFNAKRYDLAKVGRYKINRKLGIDRSLGDKEASVLHVEDIVAMIKFLVALHAGEKT 350

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 351 LMGKRDGEDHELRVDVDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEA 410

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E
Sbjct: 411 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRDRAGME 470

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GFIETPYR V +G V+++V YL
Sbjct: 471 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPYRLVSEGVVSDEVQYL 530

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSI 674
           +A +E    IAQAN+ LD D  F+EE V  R     GE +LVP   + F+D SP+Q+VS+
Sbjct: 531 TADDEAEVLIAQANAPLDADKKFSEETVLVRARGGGGEPVLVPAADVQFMDVSPRQMVSV 590

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAPFVGTGME   A  +G  ++AK+AG+
Sbjct: 591 ATALIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAVDAGDVVIAKKAGV 650

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +V+ + +G           YR+ KF RSNQ  C N R LV  G  +    II
Sbjct: 651 VTEVSAELVVMINDDGTE-------TNYRINKFARSNQGNCYNHRVLVNEGQRLEVGGII 703

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+TD G+LALG+N+LVAFM W G+NFED++++S+R+V+EDV +SIHIEE E+ ARDT
Sbjct: 704 ADGPATDQGELALGKNLLVAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDT 763

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 764 KLGAEEITRDIPNVSEEVLAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 823

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D
Sbjct: 824 AIFGEKSREVRDTSLKVPHGESGTVIGVRVFDRDNDD 860



 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 94/314 (29%), Positives = 144/314 (45%), Gaps = 35/314 (11%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN--------- 52
           A     +G  R R  F K  E +D+P+L+ +Q  S+D  +                    
Sbjct: 17  ANTASTDGATR-RLSFAKIHEPLDVPNLLALQTDSFDWLVGNERWQARVAKAVEEGDLSV 75

Query: 53  ---EGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
               GL   F+ + PI  F G   L F   EF  PK+ + +C  RD TY+ PL +    +
Sbjct: 76  ATTSGLADIFEEISPIEDFQGTMSLSFSEPEFADPKYTMAECKDRDATYSAPLYVKAEFM 135

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
                      +  +IK+Q+++MGD PLMT+ GTFV+ G +R+VVSQL RSPG +F+   
Sbjct: 136 ---------NNNTGEIKQQTVFMGDFPLMTEKGTFVVNGTERVVVSQLVRSPGAYFERTA 186

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
            +   S K ++  +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL
Sbjct: 187 DKT--SDKDIFTAKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEGQIL 244

Query: 230 STF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLK 286
             F  Y  +  +   D       A        +      +  GE   +E+ + L   L  
Sbjct: 245 EEFGQYDSMRATLEKDATETREDA--------LLDIYRKLRPGEPPTVEAAQSLLDNLYF 296

Query: 287 SLKEKGVKFLGITS 300
           + K   +  +G   
Sbjct: 297 NAKRYDLAKVGRYK 310


>gi|294630866|ref|ZP_06709426.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. e14]
 gi|292834199|gb|EFF92548.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. e14]
          Length = 1171

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 265/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 685  IVNEGDHVVAGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGADVVAGDILVG 800

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 801  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 844  IGVRLFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 903

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L  ++             
Sbjct: 904  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEEWAQRLQAIG----- 957

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 958  ------------------------ADQVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 993

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 994  ERMVLPTGKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1053

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1054 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1113

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1114 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1148



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 342/670 (51%), Positives = 460/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A    +E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTNEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++ + L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLDNLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  EDII+ IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADAPLDAGILTVEDIISTIKYLVKLHAGETETAGDNGGTIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG+VT+DV YL+A EE+   IAQAN++L +D  F E
Sbjct: 493 IGSLASYGRVNAFGFVETPYRKVVDGQVTDDVDYLTADEEDRFVIAQANATLGDDMRFAE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 ARVLVRRRGGEVDYVSPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 613 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDGT-------YIT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRLAKFARSNQGTSVNQKVIVNEGDHVVAGQVLADGPATENGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 786 IRIGADVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRLFDREEGD 855



 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 203/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEAALESGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTNEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++++         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLDNLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE-----------KSLEEIFHSEIRDIPI 346
             +    G+   EDI++     + + AG+                 ++   +  +R +  
Sbjct: 320 ADAPLDAGILTVEDIISTIKYLVKLHAGETETAGDNGGTIVVETDDIDHFGNRRLRSVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAS 498


>gi|229821635|ref|YP_002883161.1| DNA-directed RNA polymerase, beta subunit [Beutenbergia cavernae DSM
            12333]
 gi|229567548|gb|ACQ81399.1| DNA-directed RNA polymerase, beta subunit [Beutenbergia cavernae DSM
            12333]
          Length = 1169

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 187/508 (36%), Positives = 266/508 (52%), Gaps = 48/508 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L        E  +     LL      +  +  D  +     V+  V+
Sbjct: 677  LVSEGARVEVGSVLADGP-ATDEGELALGRNLLVGFMSWEGHNYEDAIILSQRLVAEDVL 735

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 736  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVGAGDVLVGK 793

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 794  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGESGTVIGVREFNR-------- 843

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA +R I  GDK+AGRHGNKG++S+ILP EDMPFL DGTP+D
Sbjct: 844  -EDGDELPPGVNQLVRVYVAQRRKITDGDKLAGRHGNKGVISKILPIEDMPFLSDGTPLD 902

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVP RMNVGQ+ ETHLGW                                 G  
Sbjct: 903  IVLNPLGVPGRMNVGQVLETHLGWVAKQ-------------------------GWDAGIE 937

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
               +         + R A Q + G PV+TPVFDG  E+ +  +L            +D S
Sbjct: 938  DAKKGKLPSWAQHLDRGALQGEPGTPVATPVFDGVREDELAGLLDSTLVTRDGERLVDSS 997

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  P+ VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKALLFDGRSGEPFPEPIAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1058 QRFGEMEVWALEAYGAAYALQELLTIKSDDVPGRVKVYEAIVKGENIPEPGIPESFKVLI 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   +
Sbjct: 1118 KEMQSLCLNVEVLSSDGTSIEMRDTDEE 1145



 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 327/618 (52%), Positives = 437/618 (70%), Gaps = 23/618 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +   +   +  TL  D    R++ALLDIYR +RPG+  T     ++    +F+  +YDL+
Sbjct: 237 EQFADYPVVIETLEKDTVNTREEALLDIYRKIRPGEPPTVEAGAALLENFYFNPKRYDLA 296

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K++ +L LD P     ++  D++A IK L  L  G               +   D
Sbjct: 297 KVGRYKIDKKLGLDAPLTDSVMQVADVVATIKYLAALHKGVTELTGTRSGEEVALRVETD 356

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ 
Sbjct: 357 DIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVASIK 416

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E+RDVHP+HYGR+CP ET
Sbjct: 417 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRASMEVRDVHPSHYGRMCPIET 476

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL ++AR+N +GF+ETPYRKV  GKVT+DVVYL+A +E+   IAQAN+ L
Sbjct: 477 PEGPNIGLIGSLATYARINPFGFVETPYRKVVKGKVTDDVVYLTADDEDRHVIAQANAPL 536

Query: 635 DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            E  +F E  V  R   GE  LVP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG
Sbjct: 537 SEKSTFVEATVLVRTRGGEAELVPAAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMG 596

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++EAP VGTGME   A  +G  IVA + G+V +V A  IV+   +G   
Sbjct: 597 ANMQRQAVPLVRSEAPLVGTGMERRAAVDAGDVIVAAKPGVVAEVSADAIVVAQDDGT-- 654

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y++ KF RSNQ T  NQR LV  G  V    ++ADGP+TD G+LALGRN+LV
Sbjct: 655 -----TFTYKVAKFHRSNQGTSYNQRVLVSEGARVEVGSVLADGPATDEGELALGRNLLV 709

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            FM W G+N+ED++++S+R+V+EDV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L
Sbjct: 710 GFMSWEGHNYEDAIILSQRLVAEDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVL 769

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP 
Sbjct: 770 ADLDERGIIRIGAEVGAGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPH 829

Query: 934 GVSGTVVDVRIFNRHGID 951
           G SGTV+ VR FNR   D
Sbjct: 830 GESGTVIGVREFNREDGD 847



 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 93/301 (30%), Positives = 145/301 (48%), Gaps = 33/301 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMN-----------IAPDERPNEGLQAAFKSV 62
           R  F K  E +  PDL+ +Q  S+D  L                     + GL+  F  +
Sbjct: 21  RVSFAKITEPLQAPDLLSLQTNSFDWLLGNERWRARVDAAASKNVSVPSSSGLEEIFSEI 80

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  F G+  L F  + F+P K+  ++C  +D TY+ PL +T   + +         + 
Sbjct: 81  SPIEDFGGSMSLSFRDHRFEPAKYTPEECKEKDFTYSAPLFVTAEFVNY---------TT 131

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K ++  
Sbjct: 132 GEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTPDKT--SDKDVFTA 189

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQ 240
           +IIP +G W++ E D +D + VR+DR+RK  +T FL ALG+   EI   F  YP ++ + 
Sbjct: 190 KIIPSRGAWLEFEIDKRDAVGVRVDRKRKQSITVFLKALGLSEAEIREQFADYPVVIETL 249

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGIT 299
             D       A        +      I  GE   +E+G  L      + K   +  +G  
Sbjct: 250 EKDTVNTREEA--------LLDIYRKIRPGEPPTVEAGAALLENFYFNPKRYDLAKVGRY 301

Query: 300 S 300
            
Sbjct: 302 K 302


>gi|42824|emb|CAA23629.1| unnamed protein product [Escherichia coli]
          Length = 390

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 155/392 (39%), Positives = 236/392 (60%), Gaps = 10/392 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+++         ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYG---EAPEGTV 113

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 114 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 173

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 174 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 233

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 234 NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 290

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  VA+D ++  TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL
Sbjct: 291 IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL 350

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
             D   DR  AL++IYR+MRPG+  T   AES
Sbjct: 351 RVDPTNDRLSALVEIYRMMRPGEPPTREAAES 382


>gi|259508465|ref|ZP_05751365.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium efficiens
            YS-314]
 gi|259163929|gb|EEW48483.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium efficiens
            YS-314]
          Length = 1199

 Score =  523 bits (1348), Expect = e-146,   Method: Composition-based stats.
 Identities = 185/517 (35%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M+    LL A    +  +  D  +   + V   ++
Sbjct: 711  LVNQGDRVEAGQVIADGPGTFN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQNIVEQDIL 769

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E + +D  DE+ I+      R  +IL G+ 
Sbjct: 770  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDL-DERGIVRIGADVRDGDILVGKV 828

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 829  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 871

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 872  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 931

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +     D K    I  L   L  
Sbjct: 932  GTPVDIILNTHGVPRRMNIGQVLETHLGWLAAA-GWSVD--PEDPKNAELIKTLPKELYD 988

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 989  V-------------------------PAGSLTATPVFDGASNEELAGLLANSRPNRDGDV 1023

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEP+  PV++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 1024 MVNADGKATLIDGRSGEPYPYPVSIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1083

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1084 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1143

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  DF++ 
Sbjct: 1144 FKVLLKELQSLCLNVEVLSADGTPMELAGDDDDFDQA 1180



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/617 (52%), Positives = 440/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 272 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFKAKRYDL 331

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 332 AKVGRYKINRKLGLGGDNDGLMTLTEEDIATAIEYLVRLHAGERVMTSPTGEEIPVETDD 391

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 392 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 451

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 452 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 511

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR+V DGK+T+ + YL+A EE+   +AQAN+  D
Sbjct: 512 EGPNIGLIGSLASYARVNPFGFIETPYRRVIDGKLTDQIDYLTADEEDRFVVAQANTHYD 571

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           EDG  T+E V  R   G+  +V R  +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 572 EDGVITDESVTVRLKDGDIAMVSRTDVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 631

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++  +AG+VE V A  + I   EG  D 
Sbjct: 632 NMQKQAVPLVRAEAPFVGTGMELRAAYDAGDLVITPKAGVVENVTADIVTIMDDEGKRD- 690

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV  GD V    +IADGP T  G+++LGRN+LVA
Sbjct: 691 ------TYVLRKFQRTNQGTSYNQKPLVNQGDRVEAGQVIADGPGTFNGEMSLGRNLLVA 744

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TSIHIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 745 FMPWEGHNYEDAIILNQNIVEQDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 804

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 805 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 864

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 865 ETGKVIGVRRFSREDDD 881



 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 145/326 (44%), Gaps = 30/326 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L+++Q  S+   +                 R   GL+   + + P
Sbjct: 59  RYSFAKVSAPIEVPGLLDLQLDSFAWLIGTPEWRARQQEEFGEGARITSGLENILEELSP 118

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  +D+   +D+ YA PL +T   +           +  +
Sbjct: 119 IQDYSGNMSLSLSEPRFEPVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTGE 169

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 170 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVKV 227

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   
Sbjct: 228 IPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLES 287

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +           +   +  + L        K   +  +G    +
Sbjct: 288 DGVANTDEALLEIYRKQRPGE-------QPTRDLAQSLLDNSFFKAKRYDLAKVGRYKIN 340

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDV 327
              GL    D +   T E    A + 
Sbjct: 341 RKLGLGGDNDGLMTLTEEDIATAIEY 366


>gi|238626068|gb|ACR48347.1| Nos5 [Streptomyces actuosus]
          Length = 1181

 Score =  523 bits (1347), Expect = e-146,   Method: Composition-based stats.
 Identities = 188/508 (37%), Positives = 275/508 (54%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 695  IVNEGDRVITGQVLADGPATQN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 753

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 754  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 811

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 812  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 860

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 861  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 920

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++                    
Sbjct: 921  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADEWAQRLQAIG------------ 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A++ + G  V+TPVFDGA E+ +  +L+    +          
Sbjct: 968  -----------------ADKVEPGTNVATPVFDGAREDELAGLLQHTIPNRDGERMVLPS 1010

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1011 GKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1070

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1071 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1130

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1131 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1158



 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 342/670 (51%), Positives = 456/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 221 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 265

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 266 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 322

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  DTP D   +  EDIIA IK LV L  G+               DDID+ GNR
Sbjct: 323 KVNKKLGTDTPLDAGILTVEDIIATIKYLVKLHAGETETVGDNGQPVVVETDDIDHFGNR 382

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 383 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 442

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 443 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 502

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL ++ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L  D  F E
Sbjct: 503 IGSLATYGRVNAFGFVETPYRKVVDGQVTDEVNYLTADEEDRFVIAQANAPLTADMRFEE 562

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 563 ARVLVRRRGGEVDYVAPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 622

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 623 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTANDDGT-------YIT 675

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD V    ++ADGP+T  G++ALG+N+LVAFMPW G+
Sbjct: 676 YRLAKFSRSNQGTSVNQKVIVNEGDRVITGQVLADGPATQNGEMALGKNLLVAFMPWEGH 735

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 736 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 795

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 796 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 855

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 856 VRVFDREEGD 865



 Score =  342 bits (876), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 201/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 41  LRISFAKIKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALENGQDVPTKSGLEEIFEE 100

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 101 ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 151

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 152 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 209

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 210 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 269

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 270 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 329

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   EDI+      + + AG+                 ++   +  +R +  
Sbjct: 330 TDTPLDAGILTVEDIIATIKYLVKLHAGETETVGDNGQPVVVETDDIDHFGNRRLRSVGE 389

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 390 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 447

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 448 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 502

Query: 467 VGEMLK 472
           +G +  
Sbjct: 503 IGSLAT 508


>gi|239918208|ref|YP_002957766.1| DNA-directed RNA polymerase, beta subunit [Micrococcus luteus NCTC
           2665]
 gi|239839415|gb|ACS31212.1| DNA-directed RNA polymerase, beta subunit [Micrococcus luteus NCTC
           2665]
          Length = 1168

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 305/954 (31%), Positives = 436/954 (45%), Gaps = 137/954 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F K  E +D+PDL+ +Q  S+D  +                        GL   F+ 
Sbjct: 23  RVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVDAALAADDHSVPVTSGLTDIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF   K   ++C  RD T++ PL +    +           +
Sbjct: 83  ISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFSAPLYVKAEFM---------NNT 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT++GTF+I G +R+VVSQL RSPG +F+    +   S K +++
Sbjct: 134 TGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERTPDKT--SDKEIFS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK PVT  L A+G     IL  F  Y  I  +
Sbjct: 192 AKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILEEFGHYDSIRAT 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +++ + L + L  + K   +  +G 
Sbjct: 252 LEKDGTADQDEA--------LLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAKVGR 303

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              +   G       V+   G+         D   +     +                  
Sbjct: 304 YKLNRKLG-------VDVHLGDPNASVLTEDDIVQMVHFIAALH--------AGETAING 348

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            R+    D   +  D      R +R                L  +  +  LS + RV   
Sbjct: 349 TRDGEPVDVRVEVDDIDHFGNRRIRA------------VGELIENQIRTGLSRMERVVRE 396

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                D       I  + +I I  ++  ++   GT      +      +     +    L
Sbjct: 397 RMTTQDVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 452

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G   + R      + +++  V P       P+ +                 +NS   I  
Sbjct: 453 GPGGLSRD----RAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATFGRINSFGFIE- 507

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
                                R V            T++      ++     A V+  G 
Sbjct: 508 ------------------TPYRRVVDGRVTDTVDYLTADDELAFQIAQAN--APVDEDGR 547

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            E             + V  +  E +                                  
Sbjct: 548 FEEELVLCRQRGGDGEPVLSTVDEID---------------------------------- 573

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                ++D SP+Q+VS A +LIPFLE+DD+NR LMG NMQRQAVPLL++EAP+VGTGME 
Sbjct: 574 -----YMDVSPRQMVSAATALIPFLEHDDANRALMGANMQRQAVPLLRSEAPYVGTGMEK 628

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  +G ++ A + G+V +V A  + + + +G           Y +MKF RSNQ    N
Sbjct: 629 YVAVDAGDSVTATQGGVVTEVAADLVTVMNDDGT-------TTHYPIMKFARSNQGNAYN 681

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QR  V  G+ V    IIADGP+TD G+LALG+N+LVAFMPW G N+ED++++S+RMVSED
Sbjct: 682 QRVRVSEGERVEPLSIIADGPATDHGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSED 741

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TSIHIEE EV ARDTKLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVG+
Sbjct: 742 VLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGR 801

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D
Sbjct: 802 VTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRDEDD 855



 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/511 (36%), Positives = 260/511 (50%), Gaps = 64/511 (12%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V P   ++          +   + LL A    + ++  D  +     VS  V+ 
Sbjct: 686  VSEGERVEP-LSIIADGPATDHGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSEDVLT 744

Query: 942  VRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNAV 996
                  H +D  +  +  E     I  ++ +   + DE+ I+         +IL G+   
Sbjct: 745  SIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGRVTP 804

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R                 E      +            +
Sbjct: 805  KGETELTPEERLLRAIFGEKSR-----------------EVRDTSLKVPHGESGTVIGVR 847

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I      DD+PPGV ++V+V+VA KR I  GDKMAGRHGNKG++S+ILP EDMPFL DGT
Sbjct: 848  IFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPIEDMPFLADGT 907

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDIVLNPLGVP RMN+GQ+ E HLGWA    G  I+      K   +            
Sbjct: 908  PVDIVLNPLGVPGRMNLGQVMELHLGWAAS-RGWDIQGEPEWIKDLPNFPRQ-------- 958

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------L 1228
                                       V V+TPVFDGA+   I  +L   +        +
Sbjct: 959  ------------------------SGPVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLM 994

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             +SG++ L+DG TGEPF  PV+VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+ 
Sbjct: 995  SDSGKAQLFDGRTGEPFPDPVSVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQ 1054

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQE+LTIKSDD+ GR +VYE+IV G +  E G PESF 
Sbjct: 1055 FGGQRFGEMEVWALEAYGAAFTLQELLTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFK 1114

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            VL+KEMQ+L L++++ ++  +     +   +
Sbjct: 1115 VLIKEMQSLCLNVEVLSADGQAIEMRDAEDE 1145


>gi|302543374|ref|ZP_07295716.1| DNA-directed RNA polymerase, beta subunit [Streptomyces hygroscopicus
            ATCC 53653]
 gi|302460992|gb|EFL24085.1| DNA-directed RNA polymerase, beta subunit [Streptomyces
            himastatinicus ATCC 53653]
          Length = 1170

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L    + + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 685  VVDEGARVITGQVLADGPSTE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 800

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 801  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 844  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 903

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G K++      +    I       
Sbjct: 904  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWKVEGSEEWMQRLQAIG------ 956

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ I  +      +   
Sbjct: 957  ------------------------ADEVQPGTNVATPVFDGAREDEIAGLFESTIPNRDG 992

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VG++Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 993  DRLVQPSGKARLFDGRSGEPFPDPISVGFMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1052

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1053 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1112

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1113 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1147



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 335/670 (50%), Positives = 455/670 (67%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADAPLDAGVLTTDDVIATIKYLVKLHAGETETVGEAGDMIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQTNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV +G VT+ V +L+A EE+   IAQAN+ L ED ++ E
Sbjct: 493 IGSLASYGRVNAFGFVETPYRKVHEGVVTDKVDFLTADEEDRFVIAQANAPLAEDNTYAE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 NRVLVRRRGGEVDYVPGSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSNMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G           
Sbjct: 613 PLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGT-------YTT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T  NQ+ +V  G  V    ++ADGPST+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRIAKFSRSNQGTSFNQKVVVDEGARVITGQVLADGPSTEDGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 786 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  340 bits (873), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 110/368 (29%), Positives = 173/368 (47%), Gaps = 27/368 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF I G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 142 TGEIKSQTVFMGDFPLMTPKGTFCINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNA 356
             +    G+   +D++      + + AG+        ++   E  DI         N   
Sbjct: 320 ADAPLDAGVLTTDDVIATIKYLVKLHAGETETVGEAGDMIVVETDDIDHFGNRRLRNVGE 379

Query: 357 YIRNTLVT 364
            I+N + T
Sbjct: 380 LIQNQVRT 387


>gi|254391405|ref|ZP_05006608.1| DNA-directed RNA polymerase subunit beta [Streptomyces clavuligerus
            ATCC 27064]
 gi|294814459|ref|ZP_06773102.1| DNA-directed RNA polymerase subunit beta [Streptomyces clavuligerus
            ATCC 27064]
 gi|197705095|gb|EDY50907.1| DNA-directed RNA polymerase subunit beta [Streptomyces clavuligerus
            ATCC 27064]
 gi|294327058|gb|EFG08701.1| DNA-directed RNA polymerase subunit beta [Streptomyces clavuligerus
            ATCC 27064]
          Length = 1170

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 265/515 (51%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V    +L      + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 685  IVSEGDRVIESQVLADGPATE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 800

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 801  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 844  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 903

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G K++      +    I       
Sbjct: 904  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLASQ-GWKVEGNEEWMERLKSIG------ 956

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ I  +      +   
Sbjct: 957  ------------------------ADEVQPGTNVATPVFDGAREDEIAGLFENTIPNRDG 992

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ ++DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 993  DRMVLPSGKARMFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1052

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1053 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1112

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1113 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1147



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 460/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGSQIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L+++  FTE
Sbjct: 493 IGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAALNDELQFTE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 ARVLVRRRGGEVDYVLPAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+ AEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G           
Sbjct: 613 PLITAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDGT-------FTT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD V  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRVAKFSRSNQGTSVNQKVIVSEGDRVIESQVLADGPATEDGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 786 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALESGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +Y 
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIYT 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 320 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGSQIVVETDDIDHFGNRRLRNVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAS 498


>gi|325124255|gb|ADY83778.1| RNA polymerase subunit B [Acinetobacter calcoaceticus PHEA-2]
          Length = 485

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 215/498 (43%), Positives = 322/498 (64%), Gaps = 22/498 (4%)

Query: 42  MMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVP 101
                P  R + GLQAAF+SVFPI ++SG A LEFV Y    P+FDV +C+ R  TYA P
Sbjct: 2   QDGKTPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAP 61

Query: 102 LKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSP 161
           +++ +RLI+ D +     KSIKD++EQ +YMG++PLMT++GTFVI G +R++VSQLHRSP
Sbjct: 62  MRVKIRLIIKDRE----TKSIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSP 117

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G+ FDHDKG+   SGK+LY+ RIIP +G W+D EFD+KD+++VR      +  T  L AL
Sbjct: 118 GVFFDHDKGKTHSSGKVLYSARIIPYRGSWLDFEFDAKDLVYVR------LLATVVLRAL 171

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G ++E+IL+ FY K+        +   L    L  G      + D D G+ ++E GK++ 
Sbjct: 172 GYNNEQILNLFYEKVPVYLDMGSYQIDLVPERL-RGEMAQFDIADND-GKVIVEQGKRIN 229

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           +  ++ ++  G+  L +  + L     AE+I   + GE+   A  ++  + + ++    +
Sbjct: 230 ARHVRQMEAAGLTKLSVPDEYLYERITAENITLRD-GEVIA-ANTLLSHEVMVKLAEGGV 287

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           +   IL+ + ++  +++ +TL  D    R++AL++IY+VMRPG+  T   AE++FN LFF
Sbjct: 288 KQFNILFTNDIDRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFF 347

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTP--------DDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            S++YDLS VGR+K N RL             +    +  EDII +++ LV++RNGKG +
Sbjct: 348 SSERYDLSPVGRMKFNRRLGRPYEVGTDQKSREVEGILSHEDIIDVLRTLVEIRNGKGEV 407

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRRVRSVGEM +NQ+R+GL+R+ER++KER+S  + D++ PQDLINAKPV +A+
Sbjct: 408 DDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAETDNLSPQDLINAKPVAAAI 467

Query: 514 CEFFCSSQLSQLEEHVNS 531
            EFF SSQLSQ  +  N 
Sbjct: 468 KEFFGSSQLSQFMDQNNP 485


>gi|281415601|ref|ZP_06247343.1| DNA-directed RNA polymerase subunit beta [Micrococcus luteus NCTC
           2665]
          Length = 1173

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 305/954 (31%), Positives = 436/954 (45%), Gaps = 137/954 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F K  E +D+PDL+ +Q  S+D  +                        GL   F+ 
Sbjct: 28  RVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVDAALAADDHSVPVTSGLTDIFEE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF   K   ++C  RD T++ PL +    +           +
Sbjct: 88  ISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFSAPLYVKAEFM---------NNT 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT++GTF+I G +R+VVSQL RSPG +F+    +   S K +++
Sbjct: 139 TGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERTPDKT--SDKEIFS 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK PVT  L A+G     IL  F  Y  I  +
Sbjct: 197 AKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILEEFGHYDSIRAT 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +++ + L + L  + K   +  +G 
Sbjct: 257 LEKDGTADQDEA--------LLDIYRKLRPGEPAAVDAAQTLLNNLYFTPKRYDLAKVGR 308

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              +   G       V+   G+         D   +     +                  
Sbjct: 309 YKLNRKLG-------VDVHLGDPNASVLTEDDIVQMVHFIAALH--------AGETAING 353

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            R+    D   +  D      R +R                L  +  +  LS + RV   
Sbjct: 354 TRDGEPVDVRVEVDDIDHFGNRRIRA------------VGELIENQIRTGLSRMERVVRE 401

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                D       I  + +I I  ++  ++   GT      +      +     +    L
Sbjct: 402 RMTTQDVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 457

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G   + R      + +++  V P       P+ +                 +NS   I  
Sbjct: 458 GPGGLSRD----RAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATFGRINSFGFIE- 512

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
                                R V            T++      ++     A V+  G 
Sbjct: 513 ------------------TPYRRVVDGRVTDTVDYLTADDELAFQIAQAN--APVDEDGR 552

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            E             + V  +  E +                                  
Sbjct: 553 FEEELVLCRQRGGDGEPVLSTVDEID---------------------------------- 578

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                ++D SP+Q+VS A +LIPFLE+DD+NR LMG NMQRQAVPLL++EAP+VGTGME 
Sbjct: 579 -----YMDVSPRQMVSAATALIPFLEHDDANRALMGANMQRQAVPLLRSEAPYVGTGMEK 633

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  +G ++ A + G+V +V A  + + + +G           Y +MKF RSNQ    N
Sbjct: 634 YVAVDAGDSVTATQGGVVTEVAADLVTVMNDDGT-------TTHYPIMKFARSNQGNAYN 686

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QR  V  G+ V    IIADGP+TD G+LALG+N+LVAFMPW G N+ED++++S+RMVSED
Sbjct: 687 QRVRVSEGERVEPLSIIADGPATDHGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSED 746

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TSIHIEE EV ARDTKLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVG+
Sbjct: 747 VLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGR 806

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D
Sbjct: 807 VTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRDEDD 860



 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/511 (36%), Positives = 260/511 (50%), Gaps = 64/511 (12%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V P   ++          +   + LL A    + ++  D  +     VS  V+ 
Sbjct: 691  VSEGERVEP-LSIIADGPATDHGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSEDVLT 749

Query: 942  VRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNAV 996
                  H +D  +  +  E     I  ++ +   + DE+ I+         +IL G+   
Sbjct: 750  SIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGRVTP 809

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R                 E      +            +
Sbjct: 810  KGETELTPEERLLRAIFGEKSR-----------------EVRDTSLKVPHGESGTVIGVR 852

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I      DD+PPGV ++V+V+VA KR I  GDKMAGRHGNKG++S+ILP EDMPFL DGT
Sbjct: 853  IFDRDEDDDLPPGVNQLVRVYVAQKRKIIDGDKMAGRHGNKGVISKILPIEDMPFLADGT 912

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDIVLNPLGVP RMN+GQ+ E HLGWA    G  I+      K   +            
Sbjct: 913  PVDIVLNPLGVPGRMNLGQVMELHLGWAAS-RGWDIQGEPEWIKDLPNFPRQ-------- 963

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------L 1228
                                       V V+TPVFDGA+   I  +L   +        +
Sbjct: 964  ------------------------SGPVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLM 999

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             +SG++ L+DG TGEPF  PV+VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+ 
Sbjct: 1000 SDSGKAQLFDGRTGEPFPDPVSVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQ 1059

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQE+LTIKSDD+ GR +VYE+IV G +  E G PESF 
Sbjct: 1060 FGGQRFGEMEVWALEAYGAAFTLQELLTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFK 1119

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            VL+KEMQ+L L++++ ++  +     +   +
Sbjct: 1120 VLIKEMQSLCLNVEVLSADGQAIEMRDAEDE 1150


>gi|297192714|ref|ZP_06910112.1| DNA-directed RNA polymerase subunit beta [Streptomyces
            pristinaespiralis ATCC 25486]
 gi|197721631|gb|EDY65539.1| DNA-directed RNA polymerase subunit beta [Streptomyces
            pristinaespiralis ATCC 25486]
          Length = 1171

 Score =  523 bits (1346), Expect = e-145,   Method: Composition-based stats.
 Identities = 189/508 (37%), Positives = 272/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 685  IVSEGDRVIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVVAGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 851  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +D+                    
Sbjct: 911  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADDWAQRLQAIG------------ 957

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A+Q   G  V+TPVFDGA E+ I  +      +          
Sbjct: 958  -----------------ADQVAPGTNVATPVFDGAREDEIAGLFDATIPNRDGDRLVQSS 1000

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1001 GKANLFDGRSGEPFPDPISIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1060

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1061 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1120

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1121 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1148



 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 461/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGTQIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L ++  FTE
Sbjct: 493 IGSLASYGRVNAFGFVETPYRKVTDGQVTDEVDYLTADEEDRFVIAQANATLSDELRFTE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 ARVLVRRRGGEVDYVPPTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+KAEAP VGTGME   A  +G  I A++ G++++V A  + + + +G           
Sbjct: 613 PLIKAEAPLVGTGMEYRCATDAGDVIKAEKDGVIQEVSADYVTVANDDGT-------YTT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRIAKFSRSNQGTSVNQKVIVSEGDRVIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 786 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 203/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALESGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD +  +   S K ++ 
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSNIDKT--SDKDIFT 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 320 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGTQIVVETDDIDHFGNRRLRNVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAS 498


>gi|320094589|ref|ZP_08026355.1| DNA-directed RNA polymerase subunit beta [Actinomyces sp. oral taxon
            178 str. F0338]
 gi|319978504|gb|EFW10081.1| DNA-directed RNA polymerase subunit beta [Actinomyces sp. oral taxon
            178 str. F0338]
          Length = 1158

 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 185/513 (36%), Positives = 261/513 (50%), Gaps = 52/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+L           +   + LL A    + ++  D  +     V   V+
Sbjct: 670  IVDEGDRVEAGDVLADGPATSN-GEVALGKNLLVAYMSWEGLNYEDAIILSRRVVEEDVL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEY--EVDARETKLGEEEITRDIPNVSEESLADLDERGIIRIGAEVTAGDVLVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+S+      R+ + + A +       V   +           D        
Sbjct: 787  VTPKGETELTSE--ERLLRAIFGEKAREVRDTSLRVPHGEEGIVIGVREFNDD------- 837

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+ PGV + V+V+VA +R I  GDKMAGRHGNKG+VS+ILP EDMPFL+DGTPVD
Sbjct: 838  ---EDDLNPGVRQTVRVYVAQRRKITIGDKMAGRHGNKGVVSKILPVEDMPFLEDGTPVD 894

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ E HLGW     G      +   +                   
Sbjct: 895  IILNPLGVPGRMNVGQVLEYHLGWLAHQ-GWDASGAVEAGEEWTR--------------- 938

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                         +         G  V+TPVFDG + + +  +LR  + +          
Sbjct: 939  ------------QLPSDGIATAPGTRVATPVFDGLEADELAGLLRNVNPNRDGDVLTNPD 986

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 987  GKARLFDGRSGEPFPYPISVGYTYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1046

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDD  GR +VYE+IV G D  E G PESF VL+
Sbjct: 1047 QRFGEMEVWALEAYGAAYALQELLTIKSDDTTGRVKVYEAIVKGEDIPEPGIPESFRVLI 1106

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            +EM++L L+++  ++        ++  DFN  E
Sbjct: 1107 QEMRSLCLNVEALDAAGNVIDLRDQDEDFNARE 1139



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 328/636 (51%), Positives = 440/636 (69%), Gaps = 23/636 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           DS  +   +  TL  D    +++ALLDIYR +RPG+ +    A+++ N  +FDS +YDL+
Sbjct: 230 DSFADYPVLLETLEKDTVNTQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLA 289

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L ++       +  EDI+A +K L+ L  G+                  D
Sbjct: 290 KVGRYKINKKLAIEADPRASTLSLEDIVATVKYLLALHQGEASFAGTRGGEAVQVRVETD 349

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN  NRR+R+VGE+++ Q R GL RMER+++ER+++ + DS+ PQ LIN +PVV+A+ 
Sbjct: 350 DIDNFANRRIRAVGELIQGQVRTGLARMERTVRERMTTQETDSITPQSLINIRPVVAAIK 409

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E+RDVHP+HYGR+CP E+
Sbjct: 410 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRASMEVRDVHPSHYGRMCPIES 469

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +FAR+N +GFIETPYR V DGKVT+++ Y++A +E+  +IAQA+S L
Sbjct: 470 PEGPNIGLIGSLATFARINPFGFIETPYRIVRDGKVTDEIRYMTADDEKAHFIAQASSPL 529

Query: 635 DEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            EDG+F E  V CR    E  L+ RE++D++D S +Q+VS+AA+ IPFLE+DD+NR LMG
Sbjct: 530 TEDGTFAERDVLCRVAGEEPTLIARERVDYMDVSARQMVSVAAAFIPFLEHDDANRALMG 589

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL  EAP VGTGME   A  SG  ++A  +G+V +V A  IV+ +      
Sbjct: 590 ANMQRQAVPLLTTEAPLVGTGMEERAAHDSGEMVLAAHSGVVSEVSADLIVVSTD----- 644

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               G D YRL KF+RSN   C NQR +V  GD V   D++ADGP+T  G++ALG+N+LV
Sbjct: 645 --AGGRDSYRLEKFERSNPGNCTNQRVIVDEGDRVEAGDVLADGPATSNGEVALGKNLLV 702

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+M W G N+ED++++S R+V EDV TSIHIEE+EV AR+TKLG EEITRDIPNVSEE L
Sbjct: 703 AYMSWEGLNYEDAIILSRRVVEEDVLTSIHIEEYEVDARETKLGEEEITRDIPNVSEESL 762

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV  GD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP 
Sbjct: 763 ADLDERGIIRIGAEVTAGDVLVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPH 822

Query: 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           G  G V+ VR FN    D N       R  +    +
Sbjct: 823 GEEGIVIGVREFNDDEDDLNPGVRQTVRVYVAQRRK 858



 Score =  317 bits (812), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 90/309 (29%), Positives = 149/309 (48%), Gaps = 27/309 (8%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI--------APDERPN----EGLQ 56
                R  F K  E +  P+L+ +Q  S+D  L  +           + R +     GL+
Sbjct: 8   KQHTPRVSFAKLREPLQAPNLLGLQVESFDWLLGNDAWKARVEAAKENGRTDVPDVSGLE 67

Query: 57  AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
             F  + PI   +G   L F  +  + PK+ +++   +D TY+ P+ +T   + ++    
Sbjct: 68  EIFHEISPIEDVAGTMSLSFRDHRLESPKYSMEEAKTKDYTYSAPMYVTAEFMNYE---- 123

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                  +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F  +K     + 
Sbjct: 124 -----TGEIKSQTVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYF--EKLSDRSTD 176

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YP 234
           K  +  ++IP +G W++ E D +D + VRIDR+RK  VT FL A+GM   EI  +F  YP
Sbjct: 177 KDTFGAKVIPSRGAWLEFEIDKRDAVGVRIDRKRKQSVTHFLKAIGMTESEIRDSFADYP 236

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
            ++ +   D       A   +          ++D  + ++ +    +    L K  + K 
Sbjct: 237 VLLETLEKDTVNTQEEALLDIYRKLRPGEPANVDAAQTLLNNFYFDSRRYDLAKVGRYKI 296

Query: 293 VKFLGITSD 301
            K L I +D
Sbjct: 297 NKKLAIEAD 305


>gi|326442848|ref|ZP_08217582.1| DNA-directed RNA polymerase subunit beta [Streptomyces clavuligerus
            ATCC 27064]
          Length = 1160

 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 265/515 (51%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V    +L      + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVSEGDRVIESQVLADGPATE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G K++      +    I       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLASQ-GWKVEGNEEWMERLKSIG------ 946

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ I  +      +   
Sbjct: 947  ------------------------ADEVQPGTNVATPVFDGAREDEIAGLFENTIPNRDG 982

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ ++DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  DRMVLPSGKARMFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 460/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGSQIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L+++  FTE
Sbjct: 483 IGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAALNDELQFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 ARVLVRRRGGEVDYVLPAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+ AEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G           
Sbjct: 603 PLITAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDGT-------FTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD V  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRVAKFSRSNQGTSVNQKVIVSEGDRVIESQVLADGPATEDGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALESGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +Y 
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIYT 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGSQIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|116671530|ref|YP_832463.1| DNA-directed RNA polymerase subunit beta [Arthrobacter sp. FB24]
 gi|158512272|sp|A0JZ93|RPOB_ARTS2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|116611639|gb|ABK04363.1| DNA-directed RNA polymerase subunit beta [Arthrobacter sp. FB24]
          Length = 1171

 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/538 (34%), Positives = 264/538 (49%), Gaps = 64/538 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   R             +   ++  G  +  G  ++       +  +   + LL
Sbjct: 661  NDDGTETNYRINKFARSNQGNCYNHRVLVSEGQRLEVG-GIIADGPATDQGELALGKNLL 719

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  +     V+  V+       H ID  +  +  E     I  ++ + 
Sbjct: 720  VAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDTKLGAEEITRDIPNVSEEV 779

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE+ I+         +IL G+    G         L   +  E  R          
Sbjct: 780  LAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSR---------- 829

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E      +            ++      D++PPGV ++V+V+VA KR I  GD
Sbjct: 830  -------EVRDTSLKVPHGESGTVIGVRVFDRDNDDELPPGVNQLVRVYVAAKRKITDGD 882

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG++S+ILP EDMPFL DGTPVDIVLNPLGVP RMNVGQ+ ETHLGW     
Sbjct: 883  KLAGRHGNKGVISKILPIEDMPFLADGTPVDIVLNPLGVPGRMNVGQVLETHLGWVAK-T 941

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G KI+      K   ++                                        V+T
Sbjct: 942  GWKIEGEPEWVKQLPNLPRE--------------------------------SGSTTVAT 969

Query: 1209 PVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            PVFDGA EE I  +L   +        ++ SG++ L+DG +GEPF  P++VGY+Y+LKL+
Sbjct: 970  PVFDGAREEEITGLLDSTNVTRDGDRLINSSGKTRLFDGRSGEPFPDPISVGYMYILKLH 1029

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSD
Sbjct: 1030 HLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTIKSD 1089

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            D+ GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ ++        +   
Sbjct: 1090 DIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSTDGTTIEMRDSDD 1147



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 338/637 (53%), Positives = 452/637 (70%), Gaps = 30/637 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       +R TL  D  + R+DALLDIYR +RPG+  T   A+S+
Sbjct: 231 LKALGWTEGQIL--EEFGQYDSMRATLEKDATETREDALLDIYRKLRPGEPPTVEAAQSL 288

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNGKG- 451
            + L+F+S +YDL+ VGR K+N +L +D     +    +  EDI+A+IK LV L  G+  
Sbjct: 289 LDNLYFNSKRYDLAKVGRYKINRKLGIDRSLGDKEASVLHVEDIVAMIKFLVALHAGEKT 348

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 349 LTGKRDGQDHELRVEIDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEA 408

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E
Sbjct: 409 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRDRAGME 468

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GFIETPYR V +G V+++V YL
Sbjct: 469 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPYRLVSEGVVSDEVQYL 528

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSI 674
           +A +E    IAQAN+ LDE+  F EE V  R     GE +LVP   ++F+D SP+Q+VS+
Sbjct: 529 TADDEAEVLIAQANAPLDENKKFAEETVLVRARGGGGEPVLVPAADVEFMDVSPRQMVSV 588

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAPFVGTGME   A  +G  ++AK+AG+
Sbjct: 589 ATALIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAVDAGDVVIAKKAGV 648

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++ + +G           YR+ KF RSNQ  C N R LV  G  +    II
Sbjct: 649 VTEVSAELVIMLNDDGTE-------TNYRINKFARSNQGNCYNHRVLVSEGQRLEVGGII 701

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+TD G+LALG+N+LVAFM W G+NFED++++S+R+V+EDV +SIHIEE E+ ARDT
Sbjct: 702 ADGPATDQGELALGKNLLVAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDT 761

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 762 KLGAEEITRDIPNVSEEVLAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 821

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D
Sbjct: 822 AIFGEKSREVRDTSLKVPHGESGTVIGVRVFDRDNDD 858



 Score =  321 bits (822), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 91/302 (30%), Positives = 140/302 (46%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +                        GL   F+ 
Sbjct: 26  RLSFAKIHEPLDVPNLLALQTDSFDWLVGNERWQARVAKAVEEGDLSVATSSGLSDIFEE 85

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF  PK+ + +C  RD TY+ PL +    +           +
Sbjct: 86  ISPIEDFQGTMSLSFSDPEFADPKYTMAECKDRDATYSAPLYVKAEFM---------NNN 136

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT+ GTFV+ G +R+VVSQL RSPG +F+    +   S K ++ 
Sbjct: 137 TGEIKQQTVFMGDFPLMTEKGTFVVNGTERVVVSQLVRSPGAYFERTADKT--SDKDIFT 194

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL  F  Y  +  +
Sbjct: 195 AKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEGQILEEFGQYDSMRAT 254

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   L  + K   +  +G 
Sbjct: 255 LEKDATETREDA--------LLDIYRKLRPGEPPTVEAAQSLLDNLYFNSKRYDLAKVGR 306

Query: 299 TS 300
             
Sbjct: 307 YK 308


>gi|25027053|ref|NP_737107.1| DNA-directed RNA polymerase subunit beta [Corynebacterium efficiens
            YS-314]
 gi|41017740|sp|Q8FS97|RPOB_COREF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|23492333|dbj|BAC17307.1| putative DNA-directed RNA polymerase beta chain [Corynebacterium
            efficiens YS-314]
          Length = 1171

 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 185/517 (35%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M+    LL A    +  +  D  +   + V   ++
Sbjct: 683  LVNQGDRVEAGQVIADGPGTFN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQNIVEQDIL 741

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E + +D  DE+ I+      R  +IL G+ 
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDL-DERGIVRIGADVRDGDILVGKV 800

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 801  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 843

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 844  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 903

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +     D K    I  L   L  
Sbjct: 904  GTPVDIILNTHGVPRRMNIGQVLETHLGWLAAA-GWSVD--PEDPKNAELIKTLPKELYD 960

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 961  V-------------------------PAGSLTATPVFDGASNEELAGLLANSRPNRDGDV 995

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEP+  PV++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 996  MVNADGKATLIDGRSGEPYPYPVSIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1055

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1056 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1115

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  DF++ 
Sbjct: 1116 FKVLLKELQSLCLNVEVLSADGTPMELAGDDDDFDQA 1152



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/617 (52%), Positives = 440/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 244 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFKAKRYDL 303

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 304 AKVGRYKINRKLGLGGDNDGLMTLTEEDIATAIEYLVRLHAGERVMTSPTGEEIPVETDD 363

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 364 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 423

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 424 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 483

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR+V DGK+T+ + YL+A EE+   +AQAN+  D
Sbjct: 484 EGPNIGLIGSLASYARVNPFGFIETPYRRVIDGKLTDQIDYLTADEEDRFVVAQANTHYD 543

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           EDG  T+E V  R   G+  +V R  +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 544 EDGVITDESVTVRLKDGDIAMVSRTDVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 603

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++  +AG+VE V A  + I   EG  D 
Sbjct: 604 NMQKQAVPLVRAEAPFVGTGMELRAAYDAGDLVITPKAGVVENVTADIVTIMDDEGKRD- 662

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV  GD V    +IADGP T  G+++LGRN+LVA
Sbjct: 663 ------TYVLRKFQRTNQGTSYNQKPLVNQGDRVEAGQVIADGPGTFNGEMSLGRNLLVA 716

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TSIHIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 717 FMPWEGHNYEDAIILNQNIVEQDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 776

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 777 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 836

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 837 ETGKVIGVRRFSREDDD 853



 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 145/326 (44%), Gaps = 30/326 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L+++Q  S+   +                 R   GL+   + + P
Sbjct: 31  RYSFAKVSAPIEVPGLLDLQLDSFAWLIGTPEWRARQQEEFGEGARITSGLENILEELSP 90

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  +D+   +D+ YA PL +T   +           +  +
Sbjct: 91  IQDYSGNMSLSLSEPRFEPVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTGE 141

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 142 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVKV 199

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   
Sbjct: 200 IPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLES 259

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +           +   +  + L        K   +  +G    +
Sbjct: 260 DGVANTDEALLEIYRKQRPGE-------QPTRDLAQSLLDNSFFKAKRYDLAKVGRYKIN 312

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDV 327
              GL    D +   T E    A + 
Sbjct: 313 RKLGLGGDNDGLMTLTEEDIATAIEY 338


>gi|282860798|ref|ZP_06269864.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. ACTE]
 gi|282564534|gb|EFB70070.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. ACTE]
          Length = 1161

 Score =  522 bits (1345), Expect = e-145,   Method: Composition-based stats.
 Identities = 192/516 (37%), Positives = 267/516 (51%), Gaps = 69/516 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  VVSEGDRVVEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++             
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQAIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD--- 1229
                                    A+Q   G  V+TPVFDGA E+ I+  L  A +    
Sbjct: 948  ------------------------ADQVAPGTNVATPVFDGAREDEISG-LFGATIPNRD 982

Query: 1230 ------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                   SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 983  GDRLVQPSGKAQLFDGRSGEPFPDPVSVGYMYILKLHHLVDDKLHARSTGPYSMITQQPL 1042

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
            GGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G 
Sbjct: 1043 GGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGI 1102

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 PESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 339/670 (50%), Positives = 459/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +DIIA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTSDDIIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L ++  FTE
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRFVIAQANATLSDELRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 PRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRIAKFSRSNQGTSVNQKVVVSEGDRVVEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 205/486 (42%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+  ++DI+      + + AG+                 ++   +  +R++  
Sbjct: 310 ADEPLDAGVLTSDDIIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|72163053|ref|YP_290710.1| DNA-directed RNA polymerase subunit beta [Thermobifida fusca YX]
 gi|88909644|sp|Q47LI5|RPOB_THEFY RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|71916785|gb|AAZ56687.1| DNA-directed RNA polymerase, beta subunit [Thermobifida fusca YX]
          Length = 1155

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 194/533 (36%), Positives = 276/533 (51%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L    + +    M   + LL A
Sbjct: 644  DGTRKTYRVHKFRRTNQGTCFNQRPIVEEGQRVEEGQVLADGPSTE-AGEMALGKNLLVA 702

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   ++       H  + + R   +  E+I     +  +E 
Sbjct: 703  YMSWEGHNYEDAIVLSQRLVEEDILSSIHIEEH--EVDARETKLGPEEITREIPNVSEEV 760

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 761  LADLDERGIIRIGAEVVDGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 813

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 814  DTSLKVPHGESGKVIGVR----VFSREEGDELPPGVNELVRVYVAQKRKITDGDKLAGRH 869

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL+DGTPVDIVLNPLGVP RMN+GQI E HLGW     G K+  
Sbjct: 870  GNKGVIAKILPKEDMPFLEDGTPVDIVLNPLGVPGRMNIGQIMEMHLGWLAKH-GWKV-- 926

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                    GD +  +  L  +    +                         V+TPVFDGA
Sbjct: 927  -------EGDDAEWKRRLRDIGAHEAPPNS--------------------KVATPVFDGA 959

Query: 1215 DEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             E+ I+ +L     D+         G++ LYDG TGEPF  PV VGY Y LKL+H+V DK
Sbjct: 960  REDEISGLLSCVLPDQDGDILVNKFGKAKLYDGRTGEPFKEPVAVGYAYFLKLHHLVDDK 1019

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD+ GR 
Sbjct: 1020 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDINGRV 1079

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +    +    +   D
Sbjct: 1080 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSRDGMSIEMRDSEED 1132



 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 330/628 (52%), Positives = 451/628 (71%), Gaps = 21/628 (3%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +         IL  +       IR TL  D      DALLDIYR +RPG+  T   A+++
Sbjct: 221 LKALGWTTDQIL--ERFGEYESIRATLEKDPTAGTDDALLDIYRKLRPGEPPTKEAAQAL 278

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK----- 450
              L+F+  +YDL+ VGR K+N +L L+       + +EDI+A +  LV L  G+     
Sbjct: 279 LENLYFNPKRYDLAKVGRYKINKKLGLEIDITQGTLTEEDIVATVDYLVRLHAGEKELVR 338

Query: 451 ------GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
                   +DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LI
Sbjct: 339 PHGTFPIEVDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLI 398

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+
Sbjct: 399 NIRPVVASIREFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPS 458

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL ++ARVN++GFIETPYRKV DG++T++VVYL+A EE+ 
Sbjct: 459 HYGRMCPIETPEGPNIGLIGSLAAYARVNSFGFIETPYRKVVDGRITDEVVYLTADEEDR 518

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             IAQAN+ ++ DG+F E  V  R   GE   V  E++ ++D SP+Q+VS+A ++IPFLE
Sbjct: 519 YVIAQANTPVNPDGTFAESQVLARRKGGEFESVAAEEVHYMDISPRQMVSVATAMIPFLE 578

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPLL+AEAP VGTGME   A  +G  I+A+++G+VE V A  I
Sbjct: 579 HDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEYRAATDAGDVILAEKSGVVEDVTADYI 638

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            + + +G           YR+ KF+R+NQ TC NQRP+V+ G  V    ++ADGPST+ G
Sbjct: 639 TVLADDGTR-------KTYRVHKFRRTNQGTCFNQRPIVEEGQRVEEGQVLADGPSTEAG 691

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           ++ALG+N+LVA+M W G+N+ED++++S+R+V ED+ +SIHIEE EV AR+TKLGPEEITR
Sbjct: 692 EMALGKNLLVAYMSWEGHNYEDAIVLSQRLVEEDILSSIHIEEHEVDARETKLGPEEITR 751

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNVSEE L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +
Sbjct: 752 EIPNVSEEVLADLDERGIIRIGAEVVDGDILVGKVTPKGETELTPEERLLRAIFGEKARE 811

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 812 VRDTSLKVPHGESGKVIGVRVFSREEGD 839



 Score =  345 bits (884), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 105/316 (33%), Positives = 155/316 (49%), Gaps = 27/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA------------PDERPNEGLQAAFKS 61
           R  F +  E +++P+L+ +Q  S+D  L                  D     GL+  F+ 
Sbjct: 16  RVSFARIKEPLEVPNLLALQTESFDWLLGNERWRARVEAARKAGRKDIPEQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+  ++C  +D+TY+ P+ +T   I  D         
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSEEECKDKDMTYSAPMFVTAEFINND--------- 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K LY 
Sbjct: 127 TGEIKSQTVFMGDFPLMTAKGTFIINGTERVVVSQLVRSPGVYFDSQMDK--SSDKELYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C+IIP +G W++ E D +D + VRIDR+RK  VT  L ALG  +++IL  F  Y  I  +
Sbjct: 185 CKIIPSRGAWLEFEIDKRDFVGVRIDRKRKQAVTILLKALGWTTDQILERFGEYESIRAT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 245 LEKDPTAGTDDALLDIYRKLRPGEPPTKEAAQALLENLYFNPKRYDLAKVGRYKINKKLG 304

Query: 298 ITSDCLCGLYVAEDIV 313
           +  D   G    EDIV
Sbjct: 305 LEIDITQGTLTEEDIV 320


>gi|297625770|ref|YP_003687533.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase subunit beta)
            [Propionibacterium freudenreichii subsp. shermanii
            CIRM-BIA1]
 gi|296921535|emb|CBL56089.1| DNA-directed RNA polymerase beta chain (RNAP beta subunit)
            (Transcriptase beta chain) (RNA polymerase subunit beta)
            [Propionibacterium freudenreichii subsp. shermanii
            CIRM-BIA1]
          Length = 1158

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 184/514 (35%), Positives = 260/514 (50%), Gaps = 55/514 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G  L        +  +     LL A    + ++  D  +     VS  ++
Sbjct: 669  IVTPGQHVEAGTPLADGPCT-DQGELALGRNLLCAFMPWRGLNYEDAIIISQRVVSEDIL 727

Query: 941  DVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I   +    DD    LD     R+   +   + + G 
Sbjct: 728  TSIHIEEY--EVDARDTKLGPEEITHDIPNVSDDMIASLDDRGIVRIGAEVRPGDILVGK 785

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +        I +         
Sbjct: 786  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSMKVPHGEEGTVIGVRIFDR-------- 835

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++PPGV ++V+V+VA KR +Q GDK+AGRHGNKG++SRILP EDMPF+ DGTPVD
Sbjct: 836  -EENDELPPGVNQMVRVYVAQKRKVQVGDKLAGRHGNKGVISRILPIEDMPFMADGTPVD 894

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN+GQ+ E HLGW          +     +   ++              
Sbjct: 895  IMLNPLGVPSRMNLGQVLEMHLGWIAHSGWDLGDATDPWAEHLREVGL------------ 942

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD---------E 1230
                              E     V ++TPVFDGA+E  I  +L    L           
Sbjct: 943  ------------------EHVDGDVRLATPVFDGAEEHEITGLL-AHGLPNRDGDHIVDS 983

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G++ L+DG TGE F   V VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  G
Sbjct: 984  DGKTTLFDGRTGEEFPEEVGVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFG 1043

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAA+ LQEMLTIKSDDV GR +VYE+IV G +  E G PE F VL
Sbjct: 1044 GQRFGEMEVWALEAYGAAWALQEMLTIKSDDVAGRVKVYEAIVKGENIPEPGIPEGFKVL 1103

Query: 1351 VKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            V+EM++L L++++  S        E   D+   +
Sbjct: 1104 VQEMKSLCLNVEVLGSDGAVIDLRETEDDYRTVD 1137



 Score =  506 bits (1302), Expect = e-140,   Method: Composition-based stats.
 Identities = 330/688 (47%), Positives = 457/688 (66%), Gaps = 22/688 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    +      G ++  +I   +T  + ++     +   
Sbjct: 165 LVRSPGVYFEQTPDKTSDKDIFTCKVIPSR--GAWLEFEIDKRDTVGVRLDRKRKQNVTV 222

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       IR T+  D    + +ALLDIYR +RPG+      A
Sbjct: 223 L--LKALGWTEERIL--EEFGEYESIRMTMEKDHVTTQDEALLDIYRKLRPGEPPARDAA 278

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++ +  +F+  +YD + VGR K+N +L L  P D + +  +DI+A I  +  L  GK  
Sbjct: 279 QTLLDNFYFNPKRYDTAKVGRYKINKKLGLSLPYDQQVLTMDDIVAAIHYICALHEGKTE 338

Query: 453 --------IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
                    DDID+ GNRRVR+VGE+++NQ R GL RMER +++R+++ DI+++ PQ LI
Sbjct: 339 LADGLPVEPDDIDHFGNRRVRTVGELIQNQLRTGLGRMERVVRDRMTTQDIEAITPQTLI 398

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF +SQLSQ  +  N L+ +TH RRLSA+G GG++R RAG+E+RDVHP+
Sbjct: 399 NVRPVTAALKEFFGTSQLSQFMDQNNPLAELTHKRRLSAVGPGGLSRDRAGMEVRDVHPS 458

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL SFARVNA+GFIETPYRKV  G VT+ + YL+A EE+ 
Sbjct: 459 HYGRMCPIETPEGPNIGLIGSLASFARVNAFGFIETPYRKVDKGLVTDHIDYLTADEEDR 518

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             IAQAN+++++ G  TE+ V  R +  +  LVP +++D+ID S +Q+VS+ ++LIPFLE
Sbjct: 519 FVIAQANATMNDKGELTEDRVLVRVSHGDVDLVPADEVDYIDVSARQMVSVGSALIPFLE 578

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DDS+R LMG NMQRQAVPL++ E+P+VGTGME   A   G   +A + G V  V    I
Sbjct: 579 HDDSSRALMGANMQRQAVPLVRNESPYVGTGMEYRAAVDVGEVTLASKPGTVTGVTGDLI 638

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            I   +G           ++L KFQRSN  TCVNQRP+V  G  V     +ADGP TD G
Sbjct: 639 DIACDDGT-------YQTFKLEKFQRSNAGTCVNQRPIVTPGQHVEAGTPLADGPCTDQG 691

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +LALGRN+L AFMPW G N+ED+++IS+R+VSED+ TSIHIEE+EV ARDTKLGPEEIT 
Sbjct: 692 ELALGRNLLCAFMPWRGLNYEDAIIISQRVVSEDILTSIHIEEYEVDARDTKLGPEEITH 751

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNVS++ + ++D+ GI+ +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +
Sbjct: 752 DIPNVSDDMIASLDDRGIVRIGAEVRPGDILVGKVTPKGETELTPEERLLRAIFGEKARE 811

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTS++VP G  GTV+ VRIF+R   D
Sbjct: 812 VRDTSMKVPHGEEGTVIGVRIFDREEND 839



 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 102/381 (26%), Positives = 171/381 (44%), Gaps = 34/381 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE------------RPNEGLQAAFKS 61
           R  F K  E + IP+L+++Q  S++  +      +E                GL+  F+ 
Sbjct: 19  RISFAKIREPLGIPNLLDLQVKSFNWLVGNENWQNEVDQALSEGRTDVNTKSGLEEIFEE 78

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FS    L F  + F+ PK+ +++C  RD TYA PL +T   +  D         
Sbjct: 79  ISPIEDFSQTMSLSFRDHRFEEPKYTIEECKDRDATYAAPLFVTAEFMNND--------- 129

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q++++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K ++ 
Sbjct: 130 TGEIKSQTVFIGDFPLMTDKGTFIITGTERVVVSQLVRSPGVYFEQTPDKT--SDKDIFT 187

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VR+DR+RK  VT  L ALG   E IL  F  Y  I  +
Sbjct: 188 CKVIPSRGAWLEFEIDKRDTVGVRLDRKRKQNVTVLLKALGWTEERILEEFGEYESIRMT 247

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLG 297
              D       A   +            D  + ++++           K  + K  K LG
Sbjct: 248 MEKDHVTTQDEALLDIYRKLRPGEPPARDAAQTLLDNFYFNPKRYDTAKVGRYKINKKLG 307

Query: 298 ITSDCLCGLYVAEDIVNG-------ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
           ++      +   +DIV           G+  +  G  ++   ++   +  +R +  L  +
Sbjct: 308 LSLPYDQQVLTMDDIVAAIHYICALHEGKTELADGLPVEPDDIDHFGNRRVRTVGELIQN 367

Query: 351 SVNNNAYIRNTLVTDKNKDRK 371
            +         +V D+   + 
Sbjct: 368 QLRTGLGRMERVVRDRMTTQD 388


>gi|297564030|ref|YP_003683003.1| DNA-directed RNA polymerase, beta subunit [Nocardiopsis dassonvillei
            subsp. dassonvillei DSM 43111]
 gi|296848479|gb|ADH70497.1| DNA-directed RNA polymerase, beta subunit [Nocardiopsis dassonvillei
            subsp. dassonvillei DSM 43111]
          Length = 1155

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/533 (34%), Positives = 279/533 (52%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V    +L    +   +  M+  + LL A
Sbjct: 644  DGTRKTYRMGKFQRSNQGTCFNQRPIVAEGQRVEERQVLADGPST-DQGEMSLGKNLLVA 702

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 703  YMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITREIPNVSEEV 760

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 761  LADLDDRGIIRIGAEVVDGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 813

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  +  ++  R    +   + GD++ PGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 814  DTSLKVPHGETGKVIGVR----VFSREDGDELAPGVNEMVRVYVAQKRKITDGDKLAGRH 869

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMPFL+DGTPVDI+LNPLGVP RMNVGQ+ E HLGW     G  ++ 
Sbjct: 870  GNKGVISKILPQEDMPFLEDGTPVDIILNPLGVPGRMNVGQVLEVHLGWLAKN-GWLVEG 928

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +  +++ + +                                A        V+TPVFDG 
Sbjct: 929  VEEEWQKSLEAIG-----------------------------ATDVPPDSRVATPVFDGL 959

Query: 1215 DEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
              + ++ +++           ++E G++ L+DG TGEPF  P++VGY Y+LKL+H+V DK
Sbjct: 960  RGDELSGLIKSVRPNADGNRLINEDGKARLFDGRTGEPFAEPISVGYKYILKLHHLVDDK 1019

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1020 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1079

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1080 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDSDED 1132



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 331/628 (52%), Positives = 447/628 (71%), Gaps = 21/628 (3%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +         IL  +       IRNTL  D      DALLDIYR +RPG+  T   A+++
Sbjct: 221 LKALGWTTDQIL--ERFGQYESIRNTLEKDPTAGTDDALLDIYRKLRPGEPPTKESAQAL 278

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK----- 450
              L+F+  +YDL+ VGR K+N +L LDT      + +EDI+A I  LV L  G+     
Sbjct: 279 LENLYFNPKRYDLAKVGRYKINKKLGLDTDYRQGTLTEEDIVATIDYLVRLHAGETEKET 338

Query: 451 ------GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
                    DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LI
Sbjct: 339 VNGPRPIETDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLI 398

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+++ EFF +SQLSQ     N L  +TH RRLSALG GG++R RAG E+RDVHP+
Sbjct: 399 NIRPVVASIKEFFGTSQLSQFMGQTNPLEGLTHKRRLSALGPGGLSRERAGFEVRDVHPS 458

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL ++ RVN++GF+ETPYR++ DGKV++ V YL+A EE+ 
Sbjct: 459 HYGRMCPIETPEGPNIGLIGSLAAYGRVNSFGFVETPYRRIIDGKVSDQVDYLTADEEDL 518

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             IAQAN+ ++ DGSF E  V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE
Sbjct: 519 HVIAQANTPMNPDGSFAEAGVLVRRKGGEFEQVSTDEVDYMDVSPRQMVSVATAMIPFLE 578

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPLL AE+PFVGTGME   A  +G  ++A++AG+VE V A  +
Sbjct: 579 HDDANRALMGSNMQRQAVPLLMAESPFVGTGMEYRAATDAGEVVLAQKAGVVEDVTADYV 638

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            + + +G           YR+ KFQRSNQ TC NQRP+V  G  V    ++ADGPSTD G
Sbjct: 639 TVMADDGTR-------KTYRMGKFQRSNQGTCFNQRPIVAEGQRVEERQVLADGPSTDQG 691

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +++LG+N+LVA+M W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITR
Sbjct: 692 EMSLGKNLLVAYMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITR 751

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNVSEE L ++D+ GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +
Sbjct: 752 EIPNVSEEVLADLDDRGIIRIGAEVVDGDILVGKVTPKGETELTPEERLLRAIFGEKARE 811

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSL+VP G +G V+ VR+F+R   D
Sbjct: 812 VRDTSLKVPHGETGKVIGVRVFSREDGD 839



 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 106/316 (33%), Positives = 159/316 (50%), Gaps = 27/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F +  E +++P+L+ +Q  S+D  L  +               D     GL+  F+ 
Sbjct: 16  RVSFARIQEPLEVPNLLALQTESFDWLLGNDRWKTRVETARNAGRKDVPEQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+  D+C  RD+TY+ P+ +T   I  D         
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSEDECKDRDMTYSAPMFVTAEFINND--------- 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++FD    +   S K LY 
Sbjct: 127 TGEIKSQTVFMGDFPLMTETGTFIINGTERVVVSQLVRSPGVYFDKSVDKT--SDKDLYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+RK  VT  L ALG  +++IL  F  Y  I  +
Sbjct: 185 CKVIPSRGAWLEFEVDKRDFVGVRIDRKRKQGVTVLLKALGWTTDQILERFGQYESIRNT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 245 LEKDPTAGTDDALLDIYRKLRPGEPPTKESAQALLENLYFNPKRYDLAKVGRYKINKKLG 304

Query: 298 ITSDCLCGLYVAEDIV 313
           + +D   G    EDIV
Sbjct: 305 LDTDYRQGTLTEEDIV 320


>gi|284106476|ref|ZP_06386262.1| DNA-directed RNA polymerase, beta subunit [Candidatus Poribacteria
           sp. WGA-A3]
 gi|283830072|gb|EFC34343.1| DNA-directed RNA polymerase, beta subunit [Candidatus Poribacteria
           sp. WGA-A3]
          Length = 486

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 203/475 (42%), Positives = 299/475 (62%), Gaps = 2/475 (0%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F K    IDIPDL+EVQK SY+ FL      + R  +GLQAA  SVFPI  F+ +A+
Sbjct: 12  RTDFSKIQSTIDIPDLVEVQKRSYEGFLQKETDSERRAEKGLQAALMSVFPIADFNSSAI 71

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF-TGAKSIKDIKEQSIYM 132
           LEF SY    PK+D+ +CL + +T+A PLK+ +RL+VFD  E       + D++EQ +Y+
Sbjct: 72  LEFSSYSLGTPKYDMRECLEQGMTFAAPLKLRIRLVVFDPQEKGVKNSKVLDVREQEVYV 131

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G+LPLMT  GTF+I G +R+VVSQLHRSPG  F HDKGR   SGK+L++ RIIP +G W+
Sbjct: 132 GELPLMTDRGTFIINGTERVVVSQLHRSPGASFSHDKGRTHSSGKVLFSARIIPYRGSWL 191

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
           D EFD++DI++VRIDRRRK+P T  L A G+ ++++L  +YP        D         
Sbjct: 192 DFEFDARDILYVRIDRRRKMPATILLKAFGLSTDDVLKMYYPIEEIRVS-DGQLMRKLDP 250

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           DL  G + S  + +    + ++  G +L   L+  ++  GVK + +  + L G  V  +I
Sbjct: 251 DLHTGLRSSVEVFEKGVKDPIVREGTRLNKSLMAKVRAAGVKEIPVKPEELVGRAVLTEI 310

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            + E GE+ +E    +    LE +   +     ++Y+DSV     I +TL  ++   +K+
Sbjct: 311 RDSEKGEVLVEKNQRLTLPMLERLLELKPSSFKVIYLDSVVATPIILDTLEAERTTSQKE 370

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           A ++IY+ +RPG++ +   A+ +F  LF +  +YDLS VGR+KMN R +LD     R + 
Sbjct: 371 AWVEIYKRLRPGEMPSVDSAKLLFENLFVNPKRYDLSPVGRLKMNNRFSLDLALTQRVLT 430

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            +D++ +++ LV+L+ GKG +DDID+LGNRRVR+VGE+L+NQ RLGL RMERSIK
Sbjct: 431 AQDVVEVVRCLVELKMGKGDVDDIDHLGNRRVRTVGELLENQIRLGLARMERSIK 485


>gi|302553515|ref|ZP_07305857.1| DNA-directed RNA polymerase, beta subunit [Streptomyces
            viridochromogenes DSM 40736]
 gi|302471133|gb|EFL34226.1| DNA-directed RNA polymerase, beta subunit [Streptomyces
            viridochromogenes DSM 40736]
          Length = 1181

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/508 (36%), Positives = 275/508 (54%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 695  IVSEGDRIIEGQVLADGPATQ-QGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 753

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 754  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 811

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 812  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 860

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 861  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 920

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L  ++                    
Sbjct: 921  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLSEEWAQRLQAIE------------ 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                             A+Q   G  V+TPVFDGA E+ +  +L+           +  +
Sbjct: 968  -----------------ADQVAPGTNVATPVFDGAREDELAGLLQHTIPNRDGERMVQPT 1010

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1011 GKARLFDGRSGEPFPDPISIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1070

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1071 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1130

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1131 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1158



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 456/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 221 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 265

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 266 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 322

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  ED+I+ IK LV L  G+               DDID+ GNR
Sbjct: 323 KVNKKLGADAPLDAGILTVEDVISTIKYLVKLHAGETETVGDSGTSIVVETDDIDHFGNR 382

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 383 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 442

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 443 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 502

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN+ L +D  F E
Sbjct: 503 IGSLASYGRVNAFGFVETPYRKVFEGQVTDEVDYLTADEEDRFVIAQANAQLTDDLRFAE 562

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 563 ARVLVRRKGGEVDYVTGEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 622

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 623 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKPGVVQEVSADYITTANDDGT-------YIT 675

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++ALG+N+LVAFMPW G+
Sbjct: 676 YRLAKFARSNQGTSVNQKVIVSEGDRIIEGQVLADGPATQQGEMALGKNLLVAFMPWEGH 735

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 736 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 795

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 796 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 855

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 856 VRVFDREEGD 865



 Score =  343 bits (879), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 41  LRISFAKIKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALDNGQDVPTKSGLEEIFEE 100

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 101 ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 151

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 152 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 209

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 210 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 269

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 270 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 329

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   ED+++     + + AG+                 ++   +  +R +  
Sbjct: 330 ADAPLDAGILTVEDVISTIKYLVKLHAGETETVGDSGTSIVVETDDIDHFGNRRLRSVGE 389

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 390 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 447

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 448 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 502

Query: 467 VGEMLK 472
           +G +  
Sbjct: 503 IGSLAS 508


>gi|325964174|ref|YP_004242080.1| DNA-directed RNA polymerase subunit beta [Arthrobacter
            phenanthrenivorans Sphe3]
 gi|323470261|gb|ADX73946.1| DNA-directed RNA polymerase subunit beta [Arthrobacter
            phenanthrenivorans Sphe3]
          Length = 1169

 Score =  522 bits (1344), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/538 (34%), Positives = 264/538 (49%), Gaps = 64/538 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   R             +   ++  G  +  G  ++       +  +   + LL
Sbjct: 659  NDDGTETNYRINKFARSNQGNCYNHRVLVNEGQRLEVG-GIIADGPATDQGELALGKNLL 717

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  +     V+  V+       H ID  +  +  E     I  ++ + 
Sbjct: 718  VAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDTKLGAEEITRDIPNVSEEV 777

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE+ I+         +IL G+    G         L   +  E  R          
Sbjct: 778  LAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSR---------- 827

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E      +            ++      D++PPGV ++V+V+VA KR I  GD
Sbjct: 828  -------EVRDTSLKVPHGESGTVIGVRVFDRDNDDELPPGVNQLVRVYVAAKRKITDGD 880

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG++S+ILP EDMPFL DGTPVDIVLNPLGVP RMNVGQ+ ETHLGW     
Sbjct: 881  KLAGRHGNKGVISKILPVEDMPFLADGTPVDIVLNPLGVPGRMNVGQVLETHLGWVAK-T 939

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G KI+      K   ++                                        V+T
Sbjct: 940  GWKIEGEPEWVKQLPNLPRE--------------------------------SGQTTVAT 967

Query: 1209 PVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            PVFDGA EE I  +L   +        ++ SG++ L+DG +GEPF  P++VGY+Y+LKL+
Sbjct: 968  PVFDGAREEEITGLLDSTNPTRDGERLINSSGKTRLFDGRSGEPFPDPISVGYMYILKLH 1027

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSD
Sbjct: 1028 HLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTIKSD 1087

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            D+ GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ ++        +   
Sbjct: 1088 DIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSTDGTTIEMRDSDD 1145



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 340/637 (53%), Positives = 453/637 (71%), Gaps = 30/637 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       +R TL  D  + R+DALLDIYR +RPG+  T   A+S+
Sbjct: 229 LKALGWTEGQIL--EEFGQYDSMRATLEKDATETREDALLDIYRKLRPGEPPTVEAAQSL 286

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNGKG- 451
            + L+F+S +YDL+ VGR K+N +L +D     +    +  EDI+A+IK LV L  G+  
Sbjct: 287 LDNLYFNSKRYDLAKVGRYKINRKLGIDRSLGDKEASVLHVEDIVAMIKFLVALHAGEKT 346

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 347 IKGTRDGQEVDLRVEIDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEA 406

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E
Sbjct: 407 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRDRAGME 466

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GFIETPYR V +G V++DV YL
Sbjct: 467 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPYRLVKNGVVSDDVQYL 526

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSI 674
           +A +E    IAQAN+ LDE+  F EE V  R     GE +LVP E ++F+D SP+Q+VS+
Sbjct: 527 TADDEAEVLIAQANAPLDENKKFAEETVLVRARGGGGEPVLVPAEDVEFMDVSPRQMVSV 586

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAPFVGTGME   A  +G  ++AK+AG+
Sbjct: 587 ATALIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAVDAGDVVIAKKAGV 646

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++ + +G           YR+ KF RSNQ  C N R LV  G  +    II
Sbjct: 647 VTEVSAELVIMLNDDGTE-------TNYRINKFARSNQGNCYNHRVLVNEGQRLEVGGII 699

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+TD G+LALG+N+LVAFM W G+NFED++++S+R+V+EDV +SIHIEE E+ ARDT
Sbjct: 700 ADGPATDQGELALGKNLLVAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDT 759

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 760 KLGAEEITRDIPNVSEEVLAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 819

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D
Sbjct: 820 AIFGEKSREVRDTSLKVPHGESGTVIGVRVFDRDNDD 856



 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 93/302 (30%), Positives = 143/302 (47%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPN-------EGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +        +A     N        GL   F+ 
Sbjct: 24  RLSFAKIHEPLDVPNLLALQTDSFDWLVGNERWQARVAKAVEENDLSVATTSGLSDIFEE 83

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF  PK+ + +C  RD TY+ PL +    +           +
Sbjct: 84  ISPIEDFQGTMSLSFSDPEFADPKYTMAECKDRDATYSAPLYVKAEFM---------NNN 134

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT+ GTFV+ G +R+VVSQL RSPG +F+    +   S K ++ 
Sbjct: 135 TGEIKQQTVFMGDFPLMTEKGTFVVNGTERVVVSQLVRSPGAYFERAADKT--SDKDIFT 192

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL  F  Y  +  +
Sbjct: 193 AKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEGQILEEFGQYDSMRAT 252

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   L  + K   +  +G 
Sbjct: 253 LEKDATETREDA--------LLDIYRKLRPGEPPTVEAAQSLLDNLYFNSKRYDLAKVGR 304

Query: 299 TS 300
             
Sbjct: 305 YK 306


>gi|309387046|gb|ADO67767.1| Tpa5 [Nocardiopsis sp. TFS65-07]
          Length = 1155

 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 184/533 (34%), Positives = 278/533 (52%), Gaps = 53/533 (9%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V    +L    +   +  M+  + LL A
Sbjct: 644  DGTRKTYRMGKFQRSNQGTCFNQRPIVHEGQRVEVKQVLADGPST-DQGEMSLGKNLLVA 702

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  +     V   V+       H  + + R   +  E+I     +  +E 
Sbjct: 703  YMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITREIPNVSEEV 760

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 761  LADLDDRGIIRIGAEVVDGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 813

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  +  ++  R    +   + GD++ PGV  +V+V+VA KR I  GDK+AGRH
Sbjct: 814  DTSLKVPHGETGKVIGVR----VFSREEGDELAPGVNEMVRVYVAQKRKITDGDKLAGRH 869

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++++ILP EDMPFL+DGTPVDI+LNPLGVP RMNVGQ+ E HLGW     G  ++ 
Sbjct: 870  GNKGVIAKILPQEDMPFLEDGTPVDIILNPLGVPGRMNVGQVLEVHLGWLAKN-GWVVEG 928

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
               +++ +                                  A   +    V+TPVFDG 
Sbjct: 929  TEEEWQKSLHAIG-----------------------------ASDVEPNSRVATPVFDGL 959

Query: 1215 DEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
              + ++ +++           +++ G++ L+DG TGEPF  P++VGY Y+LKL+H+V DK
Sbjct: 960  HGDELSGLIKSVRPNKDGNRLINDDGKARLFDGRTGEPFAEPISVGYKYILKLHHLVDDK 1019

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1020 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGRV 1079

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1080 KVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDSDED 1132



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 333/628 (53%), Positives = 449/628 (71%), Gaps = 21/628 (3%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +         IL  +       IRNTL  D      DALLDIYR +RPG+  T   A+++
Sbjct: 221 LKALGWTTDQIL--ERFGQYESIRNTLEKDPTAGTDDALLDIYRKLRPGEPPTKESAQAL 278

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK----- 450
              L+F+  +YDL+ VGR K+N +L LDT      + +EDI+A I  LV L  G+     
Sbjct: 279 LENLYFNPKRYDLAKVGRYKINKKLGLDTDYTQGTLTEEDIVATIDYLVRLHAGEVEKET 338

Query: 451 ------GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
                    DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ LI
Sbjct: 339 VFGLRPIETDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQTLI 398

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+
Sbjct: 399 NIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPS 458

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL ++ RVN++GF+ETPYRKV DG++++ + YL+A EE+ 
Sbjct: 459 HYGRMCPIETPEGPNIGLIGSLAAYGRVNSFGFVETPYRKVIDGRISDQIDYLTADEEDL 518

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             IAQAN+ L+ DGSF E  V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE
Sbjct: 519 YVIAQANTPLNADGSFAESGVLVRRKGGEFEQVDTSEVDYMDVSPRQMVSVATAMIPFLE 578

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPLL+AEAPFVGTGME   A  +G  I+A++AG+VE V A  +
Sbjct: 579 HDDANRALMGSNMQRQAVPLLRAEAPFVGTGMEYRAATDAGEVILAEKAGVVEDVTADYV 638

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            + + +G           YR+ KFQRSNQ TC NQRP+V  G  V    ++ADGPSTD G
Sbjct: 639 TVMADDGTR-------KTYRMGKFQRSNQGTCFNQRPIVHEGQRVEVKQVLADGPSTDQG 691

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +++LG+N+LVA+M W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITR
Sbjct: 692 EMSLGKNLLVAYMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITR 751

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNVSEE L ++D+ GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +
Sbjct: 752 EIPNVSEEVLADLDDRGIIRIGAEVVDGDILVGKVTPKGETELTPEERLLRAIFGEKARE 811

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSL+VP G +G V+ VR+F+R   D
Sbjct: 812 VRDTSLKVPHGETGKVIGVRVFSREEGD 839



 Score =  342 bits (877), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 102/316 (32%), Positives = 157/316 (49%), Gaps = 27/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F +  E + +P+L+ +Q  S+D  L  +               D     GL+  F+ 
Sbjct: 16  RVSFARIQEPLAVPNLLALQTESFDWLLGNDTWKTRVETARNAGRKDVPEQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+  ++C  +D+T++ P+ +T   I  D         
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSEEECKDKDMTFSAPMFVTAEFINND--------- 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K L+ 
Sbjct: 127 TGEIKSQTVFMGDFPLMTAKGTFIINGTERVVVSQLVRSPGVYFDKSVDKT--SDKDLFG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+RK  VT  L ALG  +++IL  F  Y  I  +
Sbjct: 185 CKVIPSRGAWLEFEVDKRDFVGVRIDRKRKQGVTVLLKALGWTTDQILERFGQYESIRNT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 245 LEKDPTAGTDDALLDIYRKLRPGEPPTKESAQALLENLYFNPKRYDLAKVGRYKINKKLG 304

Query: 298 ITSDCLCGLYVAEDIV 313
           + +D   G    EDIV
Sbjct: 305 LDTDYTQGTLTEEDIV 320


>gi|326333393|ref|ZP_08199639.1| DNA-directed RNA polymerase, beta subunit [Nocardioidaceae bacterium
            Broad-1]
 gi|325948789|gb|EGD40883.1| DNA-directed RNA polymerase, beta subunit [Nocardioidaceae bacterium
            Broad-1]
          Length = 1156

 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 182/508 (35%), Positives = 264/508 (51%), Gaps = 49/508 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G  L      +G   M     LL A    +  +  D  +     V    +
Sbjct: 666  LVDEGARVEVGSPLADGPATQGA-EMALGANLLVAFQSWQGHNYEDAIILSQRLVQQDYL 724

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 725  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVTTGDILVGK 782

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +        + +         
Sbjct: 783  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSMKVPHGEEGTVIGVRVFDR-------- 832

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPF++DGTPVD
Sbjct: 833  -EEGDELPPGVNQLVRVYVAQKRKISVGDKLAGRHGNKGVIAKILPVEDMPFMEDGTPVD 891

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            ++LNPLGVP RMN+GQ+ E HLGW     G  +    +   +      ++   +K     
Sbjct: 892  VLLNPLGVPRRMNIGQVLELHLGWLAKQ-GWDLNLSDDPDDSAWKQRLIKIHADKA---- 946

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                   G  V+TPVFDGA E+ I  +L     +          
Sbjct: 947  ---------------------DPGTKVATPVFDGAREDEITGLLASTLPNRDGQRVVGTD 985

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 986  GKARLFDGRSGEPFPEPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1045

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G PESF VLV
Sbjct: 1046 QRFGEMEVWAMEAYGAAYALQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIPESFKVLV 1105

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +         +   D
Sbjct: 1106 KEMQSLCLNVEVLSQDGSAIELRDAEED 1133



 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/669 (48%), Positives = 451/669 (67%), Gaps = 37/669 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I    L G+ +        T  + ++A    +E+  EE    E   + +        
Sbjct: 193 EFEIDKRDLVGVRLDRKRKQNVT--VLLKALGWTNEQIREEFGEYESMMLTL-------- 242

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                     D    + DALLDIYR +RPG+  T   A+++ N  +F+  +YD + VGR 
Sbjct: 243 --------EKDSTTAQDDALLDIYRKLRPGEPPTREAAQTLLNNYYFNPKRYDTAKVGRY 294

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-----------DDIDNLGNRR 463
           K+N +L L    D + +  +DI+A IK +V L +G+  +           DDID+ GNRR
Sbjct: 295 KVNKKLGLTEAFDQQTLTVDDIVATIKYVVALHDGRTQLETPQGTIDIAADDIDHFGNRR 354

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLS
Sbjct: 355 MRTVGELIQNQLRTGLARMERVVRERMTTQDVEAITPQSLINIRPVVAALKEFFGTSQLS 414

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+
Sbjct: 415 QFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPIETPEGPNIGLI 474

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL SF R+N +GF+ETPYRKV +G VT+ + YL+A +E+   IAQAN+++DE+  F  E
Sbjct: 475 GSLASFGRINPFGFVETPYRKVVNGVVTDQIDYLTADDEDKYVIAQANAAVDENMKFATE 534

Query: 644 LVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            V  R    E   +  +++D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 535 RVLVRQRDGEVSELLADEVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVP 594

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L+++++P VGTG+E   A  +G  +VAK+AG+V++V A  I   + +G           Y
Sbjct: 595 LVRSDSPLVGTGIEYRAAVDAGDVLVAKKAGVVKEVSADVIETLNDDGT-------YTTY 647

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +L KF+RSNQ  CVNQ+PLV  G  V     +ADGP+T   ++ALG N+LVAF  W G+N
Sbjct: 648 KLAKFERSNQGNCVNQQPLVDEGARVEVGSPLADGPATQGAEMALGANLLVAFQSWQGHN 707

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++++S+R+V +D  TSIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII
Sbjct: 708 YEDAIILSQRLVQQDYLTSIHIEEHEVDARDTKLGPEEITRDIPNVSEEMLADLDERGII 767

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G  GTV+ V
Sbjct: 768 RIGAEVTTGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGEEGTVIGV 827

Query: 943 RIFNRHGID 951
           R+F+R   D
Sbjct: 828 RVFDREEGD 836



 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 106/384 (27%), Positives = 166/384 (43%), Gaps = 34/384 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-----------RPNEGLQAAFKSV 62
           R  F K  E +++P L+ +Q  S+D  +      ++               GLQ  F+ +
Sbjct: 14  RISFAKISEPLELPQLLALQTESFDWLIGNERWQEQVAAREAAGEDVSHKSGLQEIFEEI 73

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FS    L F S  F  PK+ V++C  +D TY+ PL ++      D          
Sbjct: 74  SPIEDFSETMSLSFESPVFYDPKYTVEECKEKDFTYSAPLYVSAEFTNND---------T 124

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K +Y  
Sbjct: 125 GEIKGQTVFMGDFPLMTDQGTFVINGTERVVVSQLVRSPGVYFERTADKT--SDKDIYTA 182

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQ 240
           ++IP +G W++ E D +D++ VR+DR+RK  VT  L ALG  +E+I   F  Y  ++ + 
Sbjct: 183 KLIPSRGAWLEFEIDKRDLVGVRLDRKRKQNVTVLLKALGWTNEQIREEFGEYESMMLTL 242

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGIT 299
             D       A        +      +  GE    E+ + L +    + K      +G  
Sbjct: 243 EKDSTTAQDDA--------LLDIYRKLRPGEPPTREAAQTLLNNYYFNPKRYDTAKVGRY 294

Query: 300 S-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             +   GL  A D       +I      V+          +    I I   D  +     
Sbjct: 295 KVNKKLGLTEAFDQQTLTVDDIVATIKYVVALHDGRTQLETPQGTIDIAADDIDHFGNRR 354

Query: 359 RNTLVTDKNKDRKDALLDIYRVMR 382
             T+        +  L  + RV+R
Sbjct: 355 MRTVGELIQNQLRTGLARMERVVR 378


>gi|220913442|ref|YP_002488751.1| DNA-directed RNA polymerase subunit beta [Arthrobacter
            chlorophenolicus A6]
 gi|219860320|gb|ACL40662.1| DNA-directed RNA polymerase, beta subunit [Arthrobacter
            chlorophenolicus A6]
          Length = 1169

 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/538 (34%), Positives = 264/538 (49%), Gaps = 64/538 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   R             +   ++  G  +  G  ++       +  +   + LL
Sbjct: 659  NDDGTETNYRINKFARSNQGNCYNNRVLVNEGQRLEVG-GIIADGPATDQGELALGKNLL 717

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  +     V+  V+       H ID  +  +  E     I  ++ + 
Sbjct: 718  VAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDTKLGAEEITRDIPNVSEEV 777

Query: 972  D---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE+ I+         +IL G+    G         L   +  E  R          
Sbjct: 778  LAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSR---------- 827

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E      +            ++      D++PPGV ++V+V+VA KR I  GD
Sbjct: 828  -------EVRDTSLKVPHGESGTVIGVRVFDRDNDDELPPGVNQLVRVYVAAKRKITDGD 880

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKG++S+ILP EDMPFL DGTPVDIVLNPLGVP RMNVGQ+ ETHLGW     
Sbjct: 881  KLAGRHGNKGVISKILPIEDMPFLADGTPVDIVLNPLGVPGRMNVGQVLETHLGWVAK-T 939

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G KI+      K   ++                                        V+T
Sbjct: 940  GWKIEGEPEWVKQLPNLPRE--------------------------------SGPTTVAT 967

Query: 1209 PVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            PVFDGA EE I  +L   +        ++ SG++ L+DG +GEPF  P++VGY+Y+LKL+
Sbjct: 968  PVFDGAREEEITGLLDSTNVTRDGDRLINSSGKTRLFDGRSGEPFPDPISVGYMYILKLH 1027

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSD
Sbjct: 1028 HLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTIKSD 1087

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            D+ GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ ++        +   
Sbjct: 1088 DIHGRVKVYEAIVKGENIPEPGVPESFKVLIKEMQSLCLNVEVLSTDGTTIEMRDSDD 1145



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 340/637 (53%), Positives = 451/637 (70%), Gaps = 30/637 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       +R TL  D  + R+DALLDIYR +RPG+  T   A+S+
Sbjct: 229 LKALGWTEGQIL--EEFGQYDSMRATLEKDATETREDALLDIYRKLRPGEPPTVEAAQSL 286

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNGKG- 451
            + L+F+S +YDL+ VGR K+N +L +D     +    +  EDI+A+IK LV L  G+  
Sbjct: 287 LDNLYFNSKRYDLAKVGRYKINRKLGIDRSLGDKEASVLHVEDIVAMIKFLVALHAGEKT 346

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 347 IKGTRDGQEVDLRVEIDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEA 406

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E
Sbjct: 407 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRDRAGME 466

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GFIETPYR V DG V++DV YL
Sbjct: 467 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPYRLVKDGVVSDDVQYL 526

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSI 674
           +A +E    IAQAN+ LDE+  F EE V  R     GE +LVP   ++F+D SP+Q+VS+
Sbjct: 527 TADDEAEVLIAQANAPLDENKRFAEETVLVRARGGGGEPVLVPAADVEFMDVSPRQMVSV 586

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAPFVGTGME   A  +G   +AK+AG+
Sbjct: 587 ATALIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAVDAGDVTIAKKAGV 646

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++ + +G           YR+ KF RSNQ  C N R LV  G  +    II
Sbjct: 647 VTEVSAELVIMLNDDGTE-------TNYRINKFARSNQGNCYNNRVLVNEGQRLEVGGII 699

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+TD G+LALG+N+LVAFM W G+NFED++++S+R+V+EDV +SIHIEE E+ ARDT
Sbjct: 700 ADGPATDQGELALGKNLLVAFMSWEGHNFEDAIILSQRIVAEDVLSSIHIEEHEIDARDT 759

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 760 KLGAEEITRDIPNVSEEVLAGLDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 819

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D
Sbjct: 820 AIFGEKSREVRDTSLKVPHGESGTVIGVRVFDRDNDD 856



 Score =  321 bits (823), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 93/302 (30%), Positives = 143/302 (47%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPN-------EGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +        +A     N        GL   F+ 
Sbjct: 24  RLSFAKIHEPLDVPNLLALQTDSFDWLVGNERWQARVAKAVEENDLSVATTSGLSDIFEE 83

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF  PK+ + +C  RD TY+ PL +    +           +
Sbjct: 84  ISPIEDFQGTMSLSFSDPEFADPKYTMAECKDRDATYSAPLYVKAEFM---------NNN 134

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT+ GTFV+ G +R+VVSQL RSPG +F+    +   S K ++ 
Sbjct: 135 TGEIKQQTVFMGDFPLMTEKGTFVVNGTERVVVSQLVRSPGAYFERAADKT--SDKDIFT 192

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL  F  Y  +  +
Sbjct: 193 AKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEGQILEEFGQYDSMRAT 252

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   L  + K   +  +G 
Sbjct: 253 LEKDATETREDA--------LLDIYRKLRPGEPPTVEAAQSLLDNLYFNSKRYDLAKVGR 304

Query: 299 TS 300
             
Sbjct: 305 YK 306


>gi|46360926|gb|AAS89196.1| RpoB [Corynebacterium auris]
          Length = 1118

 Score =  521 bits (1343), Expect = e-145,   Method: Composition-based stats.
 Identities = 185/498 (37%), Positives = 253/498 (50%), Gaps = 61/498 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K    M+    LL A    +  +  D  +     V   ++
Sbjct: 668  IVSQGERVEAGQVIADGPGTKN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF++D
Sbjct: 829  VRRFSREDDDDLNPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMED 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAELLETLPEHLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L     +  G  
Sbjct: 946  VPAESLT-------------------------ATPVFDGATNEEIAGLLANTKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVNGDGKARLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F VL+KE+Q+L L++++ 
Sbjct: 1101 FKVLLKELQSLCLNVEVL 1118



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 310/617 (50%), Positives = 434/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K+N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 289 ARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPNGAVVRINTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L S+ARVNA+GFIETPY+KV DG++T+ + YL+A EE+   IAQA + ++
Sbjct: 469 EGPNIGLIGALASYARVNAFGFIETPYQKVEDGRLTDQIDYLTADEEDRYAIAQAATPMN 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +     E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 AERELIAERIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL++EAP+V TGME   A  +G  ++ +++G V  V    I I   EG  D 
Sbjct: 589 NMQKQAVPLLRSEAPYVATGMEQRAAYDAGDTVITRKSGAVTNVTGDFITIMDDEGIQD- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L  F+R+NQ TC NQ P+V  G+ V    +IADGP T  G+++LGRN+LVA
Sbjct: 648 ------TYMLRTFERTNQGTCYNQVPIVSQGERVEAGQVIADGPGTKNGEMSLGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 762 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIAVRRFSREDDD 838



 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 95/385 (24%), Positives = 167/385 (43%), Gaps = 38/385 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ+ S+   +                 R   GL+   + + 
Sbjct: 15  QRYSFAKISEPITVPGLLDVQRESFAWLVGTPEWREREQAARGEGVRVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIQDYSGNMSLSLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTAEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGIT 299
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRAKRYDLARVGRYKVNRKLGLG 303

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDE-------------KSLEEIFHSEIRDIPI 346
            D   GL    +     T E  +       E               ++   +  +R +  
Sbjct: 304 GDHD-GLMTLTEEDIATTLEYLVRLHAGETEMTSPNGAVVRINTDDIDHFGNRRLRTVGE 362

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRK 371
           L  + V         +V ++   + 
Sbjct: 363 LIQNQVRVGLSRMERVVRERMTTQD 387


>gi|209395086|gb|ACI45356.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 203/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQKDKAPQKRAVEGLQAAFNAAFPIVSHNGFVEMKFIEYSLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTLGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+  +    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANSFVNDNFRLMDSGAQMGFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T    + L++   KF+ +  D L G  VA +IV+ +TGEI  +
Sbjct: 240 ITD-QSGKLIVAKDKRVTVRHTRELEQSDSKFISVPEDFLIGRVVARNIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R +  +Y + ++  AYI NTL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRQLQCIYTNELDQGAYIANTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDL  VGR+K N ++  D       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLPRVGRMKFNAKIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRRVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|296395086|ref|YP_003659970.1| DNA-directed RNA polymerase subunit beta [Segniliparus rotundus DSM
            44985]
 gi|296182233|gb|ADG99139.1| DNA-directed RNA polymerase, beta subunit [Segniliparus rotundus DSM
            44985]
          Length = 1175

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 184/509 (36%), Positives = 265/509 (52%), Gaps = 50/509 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 683  IVDEGQRVETGQVLADGHCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 742  TSIHIEEY--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIIRIGAEVRDGDVLVGK 799

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 800  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 848

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 849  REDDDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPIEDMPFMPDGTPVD 908

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI E HLGW     G K+++           +     LE    + 
Sbjct: 909  IILNSHGVPRRMNIGQILEAHLGWVAK-TGWKVEADKKGELPEWAQNLPEDALEAPPNSR 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
            +                          +TPVFDGA EE +  +L     +  G       
Sbjct: 968  A--------------------------ATPVFDGAREEELQGILASTLPNRDGEVLVGPD 1001

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1002 GKATLFDGRSGEPFPHPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1061

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1062 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1121

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            KE+Q+L L++++ +         +   D 
Sbjct: 1122 KELQSLCLNVEVLSKDGAAIEMRDTDDDE 1150



 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 330/666 (49%), Positives = 452/666 (67%), Gaps = 30/666 (4%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + ++         L +        I    V+    +  +  TL  
Sbjct: 199 GAWLEFDVDKRDTIGVRVDRKRRQPVTVLLKALGWTNEQI----VERFGFSEIVMTTLEK 254

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD- 423
           D      +ALLDI+R +RPG+  T   A+++ + L F   +YDL+ VGR K+  +L L  
Sbjct: 255 DNIAGTDEALLDIFRKLRPGEPPTREGAQALLDNLLFQEKRYDLARVGRYKLGKKLGLSE 314

Query: 424 -TPDDVRHIRKEDIIAIIKILVDLRNG----------------KGTIDDIDNLGNRRVRS 466
             P  V  +  EDI A I+ LV L                      +DDID+ GNRR+R+
Sbjct: 315 VVPSHVTTLTVEDIAATIEYLVRLHEATPGIPETMTPPGGTEVPVEVDDIDHFGNRRLRT 374

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  
Sbjct: 375 VGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFM 434

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL
Sbjct: 435 DQNNPLSGLTHKRRISALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSL 494

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + FARVN +GFIETPYRKV  GKVT+D+ YL+A EE+   +AQANS LDE+G F EE V 
Sbjct: 495 SVFARVNPFGFIETPYRKVVGGKVTDDIHYLTADEEDRYVVAQANSPLDENGKFLEERVL 554

Query: 647 CRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            R   GE   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL++
Sbjct: 555 VRRKGGEVEYIGSDQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLIR 614

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           +E+PFVGTGME   A  +G  IV  + G+VE+V A  I + + +G           +RL 
Sbjct: 615 SESPFVGTGMELRAAIDAGDVIVTDKTGVVEEVSADYITVLADDGSR-------KTHRLR 667

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN  TC NQRP+V  G  V    ++ADG  T+ G++ALG+N+LVA MPW G+N+ED
Sbjct: 668 KFARSNHGTCANQRPIVDEGQRVETGQVLADGHCTENGEMALGKNLLVAVMPWEGHNYED 727

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++S+R+V EDV TSIHIEE+E+ ARDTKLG EEITRDIPNVS+E L ++DE GII +G
Sbjct: 728 AIILSQRLVEEDVLTSIHIEEYEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIIRIG 787

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F
Sbjct: 788 AEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVF 847

Query: 946 NRHGID 951
           +R   D
Sbjct: 848 SREDDD 853


>gi|145294640|ref|YP_001137461.1| DNA-directed RNA polymerase subunit beta [Corynebacterium glutamicum
            R]
 gi|158513582|sp|A4QBG2|RPOB_CORGB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|140844560|dbj|BAF53559.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 1165

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 182/517 (35%), Positives = 262/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M+    LL A    +  +  D  +   + V   ++
Sbjct: 677  LVNLGERVEAGQVIADGPGTFN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQNIVEQDIL 735

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E + +D DD   I+      R  +IL G+ 
Sbjct: 736  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDLDDR-GIVRIGADVRDGDILVGKV 794

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  ++               
Sbjct: 795  TPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRH-------------- 840

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++++VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 841  ---FSREDDDDLAPGVNEMIRIYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 897

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +     D +    +  L + L +
Sbjct: 898  GTPVDIILNTHGVPRRMNIGQVLETHLGWLASA-GWSVD--PEDPENAELVKTLPADLLE 954

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E ++ +L  +  +  G  
Sbjct: 955  V-------------------------PAGSLTATPVFDGASNEELSGLLANSRPNRDGDV 989

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEP+  PV++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 990  MVNADGKATLIDGRSGEPYPYPVSIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1050 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  DF++ 
Sbjct: 1110 FKVLLKELQSLCLNVEVLSADGTPMELAGDDDDFDQA 1146



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 319/617 (51%), Positives = 442/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 238 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 297

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 298 ARVGRYKINRKLGLGGDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEIPVETDD 357

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 358 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 417

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 418 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 477

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR++ DGK+T+ + YL+A EE+   +AQAN+  D
Sbjct: 478 EGPNIGLIGSLASYARVNPFGFIETPYRRIIDGKLTDQIDYLTADEEDRFVVAQANTHYD 537

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G+ T+E V  R   G+  +V R  +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 538 EEGNITDETVTVRLKDGDIAMVGRNAVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 597

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++   AG+VE V A  I I + +G  + 
Sbjct: 598 NMQKQAVPLIRAEAPFVGTGMEQRAAYDAGDLVITPVAGVVENVSADFITIMADDGKRE- 656

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV +G+ V    +IADGP T  G+++LGRN+LVA
Sbjct: 657 ------TYLLRKFQRTNQGTSYNQKPLVNLGERVEAGQVIADGPGTFNGEMSLGRNLLVA 710

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TSIHIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 711 FMPWEGHNYEDAIILNQNIVEQDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 770

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++D+ GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 771 DLDDRGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 830

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 831 ETGKVIGVRHFSREDDD 847



 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 168/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVF 63
            R  F K    I++P L+++Q  SY   +        +  E         GL+   + + 
Sbjct: 24  QRYSFAKVSAPIEVPGLLDLQLDSYSWLIGTPEWRARQKEEFGEGARVTSGLENILEELS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+   +D+ YA PL +T   +           +  
Sbjct: 84  PIQDYSGNMSLSLSEPRFEDVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTG 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 135 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L +  + K  + LG+ 
Sbjct: 253 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKINRKLGLG 312

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E ++    GE        ++   ++   +  +R
Sbjct: 313 GDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEI-----PVETDDIDHFGNRRLR 367

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 368 TVGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|111018959|ref|YP_701931.1| DNA-directed RNA polymerase subunit beta [Rhodococcus jostii RHA1]
 gi|123340762|sp|Q0SFB3|RPOB_RHOSR RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|110818489|gb|ABG93773.1| DNA-directed RNA polymerase beta subunit [Rhodococcus jostii RHA1]
          Length = 1168

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 188/545 (34%), Positives = 265/545 (48%), Gaps = 64/545 (11%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGSRKTYRMRKFARSNQGTCANQRPIVDEGQRVEFGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          + +  
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  ++L G+    G         L   +  E  R           
Sbjct: 770  DL-DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAR----------- 817

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++      DD+PPGV  +V+V+VA KR IQ GDK
Sbjct: 818  ------EVRDTSLKVPHGETGKVIGIRVFSRDDDDDLPPGVNELVRVYVAQKRKIQDGDK 871

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQI ETHLGW     G
Sbjct: 872  LAGRHGNKGVIGKILPQEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIGK-TG 930

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              ++   +  + +         L     +                           ++TP
Sbjct: 931  WNVQIAGDGSRPDWAEQLPEEMLSAPADSN--------------------------IATP 964

Query: 1210 VFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA E+ +  +L     +  G        ++ L+DG +GEPF  PV+VGY+Y++KL+H
Sbjct: 965  VFDGAKEDELTGLLGSTLPNRDGEVMVASDGKATLFDGRSGEPFPYPVSVGYMYIIKLHH 1024

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD
Sbjct: 1025 LVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDD 1084

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S     A      D +
Sbjct: 1085 VVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIAMA----DGD 1140

Query: 1382 KCELK 1386
              +L+
Sbjct: 1141 DEDLE 1145



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 457/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG +    +   + G     +    +   + +       +     +         I   
Sbjct: 179 DKGTEKDLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQI--T 236

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 237 ERFGFSEILMATLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 296

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+   P     + +EDI+A I+ LV L  G               +DD
Sbjct: 297 RVGRYKINKKLGLNLGQPIVASTLTEEDIVATIEYLVRLHAGDTEMTAPGGSAVPVEVDD 356

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 357 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 416

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 417 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 476

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G+VT+ V YL+A EE+   +AQANS+LD
Sbjct: 477 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGQVTDQVDYLTADEEDRHVVAQANSALD 536

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FT++ +  R   GE   V   +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 537 ANGHFTDDRILVRRKGGEVEFVSSAEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 596

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V A  + + + +G    
Sbjct: 597 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSADYVTVMADDGSR-- 654

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 655 -----KTYRMRKFARSNQGTCANQRPIVDEGQRVEFGQVLADGPCTENGEMALGKNLLVA 709

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 710 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 770 DLDERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 829

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ +R+F+R   D
Sbjct: 830 ETGKVIGIRVFSRDDDD 846



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 97/315 (30%), Positives = 153/315 (48%), Gaps = 26/315 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +    R +     GL+     + PI 
Sbjct: 25  RVSFAKIREPLEVPGLLDVQTDSFEWLIGAQSWRERAAARGDSAISGGLEDILAELSPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K   D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFDEVKASTDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FDH   +   + K L++ ++IP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDHSVDK--GTEKDLHSVKVIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 194 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEILMATLEKDN 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLC 304
              +   L+   +       +  GE    ES + L   L    K   +  +G    +   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYKINKKL 307

Query: 305 GLYVAEDIVNGETGE 319
           GL + + IV     E
Sbjct: 308 GLNLGQPIVASTLTE 322


>gi|163840927|ref|YP_001625332.1| DNA-directed RNA polymerase subunit beta [Renibacterium salmoninarum
            ATCC 33209]
 gi|189043864|sp|A9WSY0|RPOB_RENSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|162954403|gb|ABY23918.1| DNA-directed RNA polymerase beta chain [Renibacterium salmoninarum
            ATCC 33209]
          Length = 1175

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 190/534 (35%), Positives = 279/534 (52%), Gaps = 53/534 (9%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   R             ++  ++  GA +  G  ++       +  +   + LL
Sbjct: 664  NDDGTETNYRIAKYNRSNQGTAYNQRVLVSEGARLEVG-GIIADGPATDQGELALGKNLL 722

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  +     VS  V+       H ID  +  +  E      + RD  +
Sbjct: 723  VAFMSWEGHNFEDAIILSQRLVSEDVLSSIHIEEHEIDARDTKLGAEE-----ITRDIPN 777

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +   +  R   I  G    +G     K T      +   P  +  +    D+  + 
Sbjct: 778  VSEEILAGLDER-GIIHIGAEVDAGDILVGKVTPKGETEL--TPEERLLRAIFGDKSGEV 834

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               SLKV +  S +++  RF ++    +  DD+ PGV ++V+++VA KR I +GDK+AGR
Sbjct: 835  RDTSLKVPHGESGTVIGVRFFDR----ENDDDLAPGVNQLVRIYVAAKRKITNGDKLAGR 890

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+ILP EDMPFL DGTPVDIVLNPLGVP RMNVGQ+ E HLGW     G KI 
Sbjct: 891  HGNKGVISKILPIEDMPFLADGTPVDIVLNPLGVPGRMNVGQVLELHLGWIAK-TGWKID 949

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
               +  K                                +  +  +      ++TPVFDG
Sbjct: 950  GEPDWVKN-------------------------------LPNLPRETGRDQILATPVFDG 978

Query: 1214 ADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A EE I+ +L   +        ++ SG++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 979  AREEEISGLLDSTNVTRDGDLLINRSGKTRLFDGRSGEPFPDPISVGYMYILKLHHLVDD 1038

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD+ GR
Sbjct: 1039 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELLTIKSDDIHGR 1098

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             +VYE+IV G +  E G PESF VL+KEM++L L++++ ++        +   +
Sbjct: 1099 VKVYEAIVKGENIPEPGIPESFKVLIKEMRSLCLNVEVLSTEGSTIEMRDSDEE 1152



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 334/637 (52%), Positives = 447/637 (70%), Gaps = 30/637 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       IR TL  D    R+DALLDIYR +RPG+  T   A+++
Sbjct: 234 LKALGWTESQIL--EEFGEFDSIRATLEKDGTSTREDALLDIYRKLRPGEPPTVEAAQTL 291

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---DVRHIRKEDIIAIIKILVDLRNG--- 449
            + L+F+  +YDL+ VGR K+N +L +D      D   +   DI+AIIK LV L  G   
Sbjct: 292 LDNLYFNPKRYDLAKVGRYKINRKLGIDKSLASPDASVLDINDIVAIIKFLVTLHAGGKS 351

Query: 450 ------------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                       +  +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 352 LTAKRDGKDFELRVDVDDIDHFGNRRIRAVGELIENQVRTGLSRMERVVRERMTTQDVEA 411

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E
Sbjct: 412 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGYE 471

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N  GFIETPYRKV  G V+++V YL
Sbjct: 472 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPLGFIETPYRKVSKGHVSDEVDYL 531

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCA---GEEILVPREKIDFIDASPKQVVSI 674
           +A +E N  IAQAN+ LD   SF E+ V  R     GE +LV  + ++++D SP+Q+VS+
Sbjct: 532 TADDELNYIIAQANAPLDSKSSFVEDQVLVRQRGGGGEPVLVAADDVEYMDVSPRQMVSV 591

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  ++AK+AG+
Sbjct: 592 ATALIPFLEHDDANRALMGANMQRQAVPLVRSEAPVVGTGMERAAAVDAGDVVIAKKAGV 651

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++ + +G           YR+ K+ RSNQ T  NQR LV  G  +    II
Sbjct: 652 VTEVSADLVIMLNDDGTE-------TNYRIAKYNRSNQGTAYNQRVLVSEGARLEVGGII 704

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+TD G+LALG+N+LVAFM W G+NFED++++S+R+VSEDV +SIHIEE E+ ARDT
Sbjct: 705 ADGPATDQGELALGKNLLVAFMSWEGHNFEDAIILSQRLVSEDVLSSIHIEEHEIDARDT 764

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV+ GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 765 KLGAEEITRDIPNVSEEILAGLDERGIIHIGAEVDAGDILVGKVTPKGETELTPEERLLR 824

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFG+K+ +VRDTSL+VP G SGTV+ VR F+R   D
Sbjct: 825 AIFGDKSGEVRDTSLKVPHGESGTVIGVRFFDRENDD 861



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 92/302 (30%), Positives = 141/302 (46%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +      D                 GL   F+ 
Sbjct: 29  RISFAKIHEPLDVPNLLALQTESFDWLVGNGRWQDRMQKAVDAGDESVATTSGLSDIFEE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF  PK+ + +C  RD T++ PL +    +           +
Sbjct: 89  ISPIEDFQGTMSLSFSEPEFADPKYTMAECKDRDATFSAPLYVKAEFM---------NNN 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG +F+    +   S K ++ 
Sbjct: 140 TGEIKQQTVFMGDFPLMTEKGTFVINGTERVVVSQLVRSPGAYFERTADKT--SDKDIFT 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL  F  +  I  +
Sbjct: 198 AKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTESQILEEFGEFDSIRAT 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   L  + K   +  +G 
Sbjct: 258 LEKDGTSTREDA--------LLDIYRKLRPGEPPTVEAAQTLLDNLYFNPKRYDLAKVGR 309

Query: 299 TS 300
             
Sbjct: 310 YK 311


>gi|302536241|ref|ZP_07288583.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. C]
 gi|302445136|gb|EFL16952.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. C]
          Length = 1160

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 266/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +    +L      + E  M   + LL A    +  +  D  +     V   V+
Sbjct: 674  IVNEGDRIIEAQVLADGPATE-EGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 732

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 733  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGADVVAGDILVG 789

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 790  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 832

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 833  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 892

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++             
Sbjct: 893  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADEWAQRLQAIG----- 946

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 947  ------------------------ADQVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 982

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  ERMVLPTGKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 337/670 (50%), Positives = 459/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + +    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 200 EMEVDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 244

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 245 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 301

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 302 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGRSIVVETDDIDHFGNR 361

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 362 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 421

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 422 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 481

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN+ LD++  FTE
Sbjct: 482 IGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANARLDDELRFTE 541

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 542 NRVLVRKRGGEVDYVEPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 601

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+KAEAP VGTGME   A  +G +I A++ G+V++V A  I + + +G           
Sbjct: 602 PLIKAEAPLVGTGMEYRCAVDAGDSIKAEKDGVVQEVSADYITVANDDGT-------YTT 654

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 655 YRVAKFSRSNQGTSVNQKVIVNEGDRIIEAQVLADGPATEEGEMALGKNLLVAFMPWEGH 714

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 715 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 774

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 775 IRIGADVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 834

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 835 VRVFDREEGD 844



 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 20  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKSRVESALESGQDVPTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+P K  VD+C  RD TYA PL +T                
Sbjct: 80  ISPIEDFSGSMSLTFRDHRFEPAKNSVDECKERDFTYAAPLFVTAEFT---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 131 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 189 AKIIPSRGAWLEMEVDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 249 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 308

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 309 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGRSIVVETDDIDHFGNRRLRNVGE 368

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 369 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 426

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 427 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 481

Query: 467 VGEMLK 472
           +G +  
Sbjct: 482 IGSLAS 487


>gi|166368191|ref|YP_001660464.1| DNA-directed RNA polymerase subunit beta [Microcystis aeruginosa
           NIES-843]
 gi|166090564|dbj|BAG05272.1| RNA polymerase beta subunit [Microcystis aeruginosa NIES-843]
          Length = 1111

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 330/687 (48%), Positives = 456/687 (66%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 120 INGAERVIVNQIVRSPGVYYKAEIDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 179

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   DS+ +  + + TL  + N   ++ALLD+YR +RPG+ 
Sbjct: 180 TRKLSAQVLLKAIGLSDNEI--FDSLRHPEFYQKTLDKEGNPSEEEALLDLYRKLRPGEP 237

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T +  + +    FFD+ +YDL  VGR K+N +L L+ PD+ R +   DI+A I  L++L
Sbjct: 238 PTVTGGQQLLESRFFDNKRYDLGRVGRYKLNKKLRLNVPDNQRVLTTTDILAAIDYLINL 297

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G  DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  +  ++ P  L+N 
Sbjct: 298 EFDIGNTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESQNLTPASLVNP 357

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 358 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 417

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETP   V +G+V  D  V YL+A EE++
Sbjct: 418 GRICPVETPEGPNAGLIGSLATYARVNDYGFIETPCYVVENGRVRYDLPVKYLTADEEDD 477

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + + DE+G    E +  R   E      E++D++  SP Q+VS+A SLIPFLE+
Sbjct: 478 LRVAPGDVATDENGYILGETIPVRYRQEFSTTSPEQVDYVCVSPVQIVSVATSLIPFLEH 537

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  VDA RI 
Sbjct: 538 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSYVDANRIR 597

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  + D +        Y + K+QRSNQ+TC+NQRPLV  G++V    I+ADG +T+ G+
Sbjct: 598 IKVADEDKEIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEGGE 657

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           +ALG+N+LVA+MPW GYN+ED++LISER+V++DV+TSIHIE++E+ AR TKLGPEEITR+
Sbjct: 658 IALGQNILVAYMPWEGYNYEDAILISERLVAQDVYTSIHIEKYEIEARQTKLGPEEITRE 717

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V   DILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 718 IPNVGEDALRNLDERGIIRIGAWVEASDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 777

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 778 RDNSLRVPNGEKGRVVDVRVFTREQGD 804



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 199/593 (33%), Positives = 273/593 (46%), Gaps = 72/593 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-------IEEFEVMAR 852
                       +L    P  G   E        MV       +        I        
Sbjct: 545  MGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSYVDANRIRIKVADED 604

Query: 853  DTKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                G  EI  +I           +++  ++  G +V PG IL      +G   +   + 
Sbjct: 605  KEIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEG-GEIALGQN 663

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLAR 969
            +L A    +  +  D  L     V+  V       ++ I+  +  +  E    +I  +  
Sbjct: 664  ILVAYMPWEGYNYEDAILISERLVAQDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGE 723

Query: 970  DKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            D     DE+ I+    +    +IL G+    G         L   +  E  R        
Sbjct: 724  DALRNLDERGIIRIGAWVEASDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------- 776

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                       ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ
Sbjct: 777  -----------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQ 825

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKGI+SRILP EDMP+L DG PVDIVLNPLGVPSRMNVGQ+FE  LGWA 
Sbjct: 826  VGDKMAGRHGNKGIISRILPLEDMPYLPDGRPVDIVLNPLGVPSRMNVGQVFECLLGWAG 885

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG + K    D               ++ G  +    +    +++  +    W     
Sbjct: 886  ENLGVRFKITPFD---------------EMYGEEASRLTVHGLLENASKKPNRDW----- 925

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                VF    EE             +G+  +YDG TGEPFDRPVTVG  YMLKL H+V D
Sbjct: 926  ----VF---KEE------------HAGKVTVYDGRTGEPFDRPVTVGMAYMLKLVHLVDD 966

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR
Sbjct: 967  KIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGR 1026

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                 +IV G      GTPESF VL++E+Q+LGL I +            ++ 
Sbjct: 1027 NEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVENAPDGTSRDVE 1079



 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 92/433 (21%), Positives = 179/433 (41%), Gaps = 32/433 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLIE+Q +S+  FL           EGL     S  PI+ ++G   L F+   Y    
Sbjct: 17  LPDLIEIQHSSFRWFL----------EEGLIEELNSFSPISDYTGKLELHFLGQDYRLKE 66

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK++VD+   RD TY+V + +  RLI          K   +  EQ +++GDLPLMT+ GT
Sbjct: 67  PKYNVDEAKRRDSTYSVQMYVPTRLI---------NKETGENIEQEVFIGDLPLMTERGT 117

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 118 FIINGAERVIVNQIVRSPGVYYKAEIDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 174

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK--VS 261
           VRID+ RK+     L A+G+   EI  +      Y +  D    P     L+   +    
Sbjct: 175 VRIDKTRKLSAQVLLKAIGLSDNEIFDSLRHPEFYQKTLDKEGNPSEEEALLDLYRKLRP 234

Query: 262 SSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
                +  G+Q++ES         L  +    +      +       +    +      +
Sbjct: 235 GEPPTVTGGQQLLESRFFDNKRYDLGRVGRYKLNKKLRLNVPDNQRVLTTTDILAAIDYL 294

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                D+ +   ++ + +  +R +  L  + V         ++ ++    +   L    +
Sbjct: 295 INLEFDIGNTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESQNLTPASL 354

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           + P      +  +  F            + +  +    R++   P     + +E     +
Sbjct: 355 VNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRERAGFAV 409

Query: 441 KILVDLRNGKGTI 453
           + +    +G+   
Sbjct: 410 RDIHPSHHGRICP 422


>gi|311111983|ref|YP_003983205.1| DNA-directed RNA polymerase subunit beta [Rothia dentocariosa ATCC
            17931]
 gi|310943477|gb|ADP39771.1| DNA-directed RNA polymerase subunit beta [Rothia dentocariosa ATCC
            17931]
          Length = 1192

 Score =  521 bits (1342), Expect = e-145,   Method: Composition-based stats.
 Identities = 178/508 (35%), Positives = 265/508 (52%), Gaps = 54/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D++    +  G   +   + LL A    + ++  D  +     VS  V+
Sbjct: 707  VVKAGQRVEERDVIADGPSTDG-GELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVL 765

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD      +   +   + + G 
Sbjct: 766  TSIHIEEH--EIDARDTKLGPEEITRDIPNVSEEVLSALDDRGIIHIGAEVEAGDILVGK 823

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + + +       V   +        I +    ++   
Sbjct: 824  VTPKGETELTPE--ERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRESDDE--- 878

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 879  ----DDLPPGVNKLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 934

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            ++LNPLGVP RMN+GQ+ E H GW     G KI+      K   +               
Sbjct: 935  VILNPLGVPGRMNIGQVLEVHTGWLAKQ-GWKIEGDPAWLKNMPNFPKE----------- 982

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                                      ++TPVFDGA E+ +  ++  A+ +          
Sbjct: 983  ---------------------SGPTRLATPVFDGAHEDELFDLMDHANPNRDGDRLITRS 1021

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L DG +GEPF  P++VGY Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1022 GKARLIDGRSGEPFPDPISVGYQYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1081

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LT+KSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1082 QRFGEMEVWALEAYGAAYTLQEILTVKSDDVAGRVKVYEAIVKGENIPEPGIPESFKVLI 1141

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ ++  K     +   +
Sbjct: 1142 KEMQSLCLNVEVLSTDGKTIEMSDSEEE 1169



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 338/640 (52%), Positives = 453/640 (70%), Gaps = 30/640 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL      N   IR TL  D    R +ALLDIYR +RPG+  T   A+++
Sbjct: 250 LKALGWTEAKIL--AEFGNYDSIRATLEKDSVSTRDEALLDIYRKLRPGEPPTVEAAQAL 307

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV---RHIRKEDIIAIIKILVDLR----- 447
            + ++F   +YDL+ VGR K+N +L +D P D      + ++DI  +I  L  L      
Sbjct: 308 LDNMYFTPRRYDLAKVGRYKVNRKLGVDVPLDSPEASVLSQDDIAQMIHYLCALHAQESS 367

Query: 448 ----------NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                     + K  IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+DS
Sbjct: 368 IPGKRDGKEISVKIDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVDS 427

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ L+N +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 428 ITPQSLVNIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 487

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL ++ R+N+YGFIETPYR V DGKVT+ V YL
Sbjct: 488 VRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRINSYGFIETPYRVVEDGKVTDKVRYL 547

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG---EEILVPREKIDFIDASPKQVVSI 674
           +A +E++  IAQAN+ L  + +F E+ V CR      E +LV    + ++D SP+Q+VS+
Sbjct: 548 TADDEKSVIIAQANAPLTNERTFAEDEVLCRAGDGSGEAVLVAPGAVQYMDVSPRQMVSV 607

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIP+LE+DD+NR LMG NMQRQAVPLL++EAP VGTGME   A  SG +++AK+AG+
Sbjct: 608 ATALIPYLEHDDANRALMGANMQRQAVPLLESEAPVVGTGMEKYAALDSGDSVLAKKAGV 667

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++R+ +G           Y +MKF RSN   C NQR +VK G  V   D+I
Sbjct: 668 VSEVSADLVLVRNDDGTTSS-------YPIMKFSRSNPGNCYNQRVVVKAGQRVEERDVI 720

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD G+LALG+N+LVA+MPW G N+ED++++S+RMVSEDV TSIHIEE E+ ARDT
Sbjct: 721 ADGPSTDGGELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEIDARDT 780

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSEE L  +D+ GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 781 KLGPEEITRDIPNVSEEVLSALDDRGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 840

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           AIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D+++
Sbjct: 841 AIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRESDDEDD 880



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 101/410 (24%), Positives = 165/410 (40%), Gaps = 44/410 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL------------MMNIAPDERPNEGLQAAFKS 61
           R  F K  E + +P+L+ +Q  S+D  +                        GL   F+ 
Sbjct: 45  RISFAKISEPLKVPNLLAIQTDSFDRLVGNERWAKRLENAQATGDTSVPEKSGLAEIFEE 104

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F   EF  PK+ +++C  RD TYA PL +    +           +
Sbjct: 105 ISPIRDFQETMQLSFSDPEFSDPKYTMEECKDRDATYAAPLYVKAEFM---------NLT 155

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG +F+    R   S K +Y+
Sbjct: 156 TGEVKQQTLFMGDFPLMTESGTFVINGTERVVVSQLVRSPGAYFEKAPDRT--SDKDIYS 213

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            R+IP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL+ F  Y  I  +
Sbjct: 214 ARVIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEAKILAEFGNYDSIRAT 273

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   +  + +   +  +G 
Sbjct: 274 LEKDSVSTRDEA--------LLDIYRKLRPGEPPTVEAAQALLDNMYFTPRRYDLAKVGR 325

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              +   G+ V  D           EA  +  +   + I +          +    +   
Sbjct: 326 YKVNRKLGVDVPLDSP---------EASVLSQDDIAQMIHYLCALHAQESSIPGKRDGKE 376

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           I   +  D      +  +     +    + T              +   D
Sbjct: 377 ISVKIDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVD 426


>gi|300742065|ref|ZP_07072086.1| DNA-directed RNA polymerase, beta subunit [Rothia dentocariosa M567]
 gi|300381250|gb|EFJ77812.1| DNA-directed RNA polymerase, beta subunit [Rothia dentocariosa M567]
          Length = 1169

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 178/508 (35%), Positives = 265/508 (52%), Gaps = 54/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D++    +  G   +   + LL A    + ++  D  +     VS  V+
Sbjct: 684  VVKAGQRVEERDVIADGPSTDG-GELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVL 742

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD      +   +   + + G 
Sbjct: 743  TSIHIEEH--EIDARDTKLGPEEITRDIPNVSEEVLSALDDRGIIHIGAEVEAGDILVGK 800

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + + +       V   +        I +    ++   
Sbjct: 801  VTPKGETELTPE--ERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRESDDE--- 855

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 856  ----DDLPPGVNKLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 911

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            ++LNPLGVP RMN+GQ+ E H GW     G KI+      K   +               
Sbjct: 912  VILNPLGVPGRMNIGQVLEVHTGWLAKQ-GWKIEGDPAWLKNMPNFPKE----------- 959

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                                      ++TPVFDGA E+ +  ++  A+ +          
Sbjct: 960  ---------------------SGPTRLATPVFDGAHEDELFDLMDHANPNRDGDRLITRS 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L DG +GEPF  P++VGY Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLIDGRSGEPFPDPISVGYQYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LT+KSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMEVWALEAYGAAYTLQEILTVKSDDVAGRVKVYEAIVKGENIPEPGIPESFKVLI 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ ++  K     +   +
Sbjct: 1119 KEMQSLCLNVEVLSTDGKTIEMSDSEEE 1146



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 338/640 (52%), Positives = 453/640 (70%), Gaps = 30/640 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL      N   IR TL  D    R +ALLDIYR +RPG+  T   A+++
Sbjct: 227 LKALGWTEAKIL--AEFGNYDSIRATLEKDSVSTRDEALLDIYRKLRPGEPPTVEAAQAL 284

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV---RHIRKEDIIAIIKILVDLR----- 447
            + ++F   +YDL+ VGR K+N +L +D P D      + ++DI  +I  L  L      
Sbjct: 285 LDNMYFTPRRYDLAKVGRYKVNRKLGVDVPLDSPEASVLSQDDIAQMIHYLCALHAQESS 344

Query: 448 ----------NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                     + K  IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+DS
Sbjct: 345 IPGKRDGKEISVKIDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVDS 404

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ L+N +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 405 ITPQSLVNIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 464

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL ++ R+N+YGFIETPYR V DGKVT+ V YL
Sbjct: 465 VRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRINSYGFIETPYRVVEDGKVTDKVRYL 524

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG---EEILVPREKIDFIDASPKQVVSI 674
           +A +E++  IAQAN+ L  + +F E+ V CR      E +LV    + ++D SP+Q+VS+
Sbjct: 525 TADDEKSVIIAQANAPLTNERTFAEDEVLCRAGDGSGEAVLVAPGAVQYMDVSPRQMVSV 584

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIP+LE+DD+NR LMG NMQRQAVPLL++EAP VGTGME   A  SG +++AK+AG+
Sbjct: 585 ATALIPYLEHDDANRALMGANMQRQAVPLLESEAPVVGTGMEKYAALDSGDSVLAKKAGV 644

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V +V A  +++R+ +G           Y +MKF RSN   C NQR +VK G  V   D+I
Sbjct: 645 VSEVSADLVLVRNDDGTTSS-------YPIMKFSRSNPGNCYNQRVVVKAGQRVEERDVI 697

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD G+LALG+N+LVA+MPW G N+ED++++S+RMVSEDV TSIHIEE E+ ARDT
Sbjct: 698 ADGPSTDGGELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEIDARDT 757

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSEE L  +D+ GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 758 KLGPEEITRDIPNVSEEVLSALDDRGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 817

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           AIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D+++
Sbjct: 818 AIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRESDDEDD 857



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 102/410 (24%), Positives = 166/410 (40%), Gaps = 44/410 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E + +P+L+ +Q  S+D  +          N             GL   F+ 
Sbjct: 22  RISFAKISEPLKVPNLLAIQTDSFDRLVGNERWAKRLENAQAAGDTSVPEKSGLAEIFEE 81

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F   EF  PK+ +++C  RD TYA PL +    +           +
Sbjct: 82  ISPIRDFQETMQLSFSDPEFSDPKYTMEECKDRDATYAAPLYVKAEFM---------NLT 132

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG +F+    R   S K +Y+
Sbjct: 133 TGEVKQQTLFMGDFPLMTESGTFVINGTERVVVSQLVRSPGAYFEKAPDRT--SDKDIYS 190

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            R+IP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL+ F  Y  I  +
Sbjct: 191 ARVIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTEAKILAEFGNYDSIRAT 250

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +E+ + L   +  + +   +  +G 
Sbjct: 251 LEKDSVSTRDEA--------LLDIYRKLRPGEPPTVEAAQALLDNMYFTPRRYDLAKVGR 302

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              +   G+ V  D           EA  +  +   + I +          +    +   
Sbjct: 303 YKVNRKLGVDVPLDSP---------EASVLSQDDIAQMIHYLCALHAQESSIPGKRDGKE 353

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           I   +  D      +  +     +    + T              +   D
Sbjct: 354 ISVKIDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVD 403


>gi|328884392|emb|CCA57631.1| DNA-directed RNA polymerase beta subunit [Streptomyces venezuelae
            ATCC 10712]
          Length = 1178

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 266/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L      + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 692  VVDEGDRVIEGQVLADGPATE-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 750

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 751  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 807

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 808  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKI 850

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 851  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 910

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++             
Sbjct: 911  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLADEWAQRLQAIG----- 964

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++   G  V+TPVFDGA E+ +  +L     +   
Sbjct: 965  ------------------------ADKVAPGTNVATPVFDGAREDELAGLLNHTIPNRDG 1000

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 1001 ERMVLPTGKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1060

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1061 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1120

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1121 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1155



 Score =  510 bits (1312), Expect = e-141,   Method: Composition-based stats.
 Identities = 337/670 (50%), Positives = 459/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    L G+ +        T  + ++A     E+ L+E    E              
Sbjct: 218 EMEIDKRDLVGVRIDRKRKQSVT--VLLKALGWTTEQILQEFGEYES------------- 262

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 263 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 319

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 320 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGNEIVVETDDIDHFGNR 379

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 380 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 439

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 440 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 499

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++LDE+  F+E
Sbjct: 500 IGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANAALDEELRFSE 559

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 560 NRVLVRKRGGEVDYVEPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 619

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V+++ A  I + + +G           
Sbjct: 620 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQELSADYITVANDDGT-------YIT 672

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD V    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 673 YRLHKFSRSNQGTSVNQKVVVDEGDRVIEGQVLADGPATEDGEMALGKNLLVAFMPWEGH 732

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 733 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 792

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G ++ 
Sbjct: 793 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKIIG 852

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 853 VRVFDREEGD 862



 Score =  336 bits (862), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 116/486 (23%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 38  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALESGQDVPTKSGLEEIFEE 97

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TY  PL +T                
Sbjct: 98  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYGAPLFVTAEFT---------NNE 148

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 149 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 206

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 207 AKIIPSRGAWLEMEIDKRDLVGVRIDRKRKQSVTVLLKALGWTTEQILQEFGEYESMRAT 266

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 267 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 326

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 327 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGNEIVVETDDIDHFGNRRLRNVGE 386

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 387 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 444

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 445 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 499

Query: 467 VGEMLK 472
           +G +  
Sbjct: 500 IGSLAS 505


>gi|62389386|ref|YP_224788.1| DNA-directed RNA polymerase subunit beta [Corynebacterium glutamicum
            ATCC 13032]
 gi|41017761|sp|Q8NT26|RPOB_CORGL RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21323253|dbj|BAB97881.1| DNA-directed RNA polymerase beta subunit/140 kD subunit (split gene
            in Mjan, Mthe, Aful) [Corynebacterium glutamicum ATCC
            13032]
 gi|41324720|emb|CAF19202.1| DNA-DIRECTED RNA POLYMERASE BETA CHAIN [Corynebacterium glutamicum
            ATCC 13032]
          Length = 1165

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 182/517 (35%), Positives = 261/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M+    LL A    +  +  D  +   + V   ++
Sbjct: 677  LVNLGERVEAGQVIADGPGTFN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQNIVEQDIL 735

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E + +D DD   I+      R  +IL G+ 
Sbjct: 736  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDLDDR-GIVRIGADVRDGDILVGKV 794

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  ++               
Sbjct: 795  TPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRH-------------- 840

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++++VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 841  ---FSREDDDDLAPGVNEMIRIYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 897

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +     D +    +  L + L +
Sbjct: 898  GTPVDIILNTHGVPRRMNIGQVLETHLGWLASA-GWSVD--PEDPENAELVKTLPADLLE 954

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 955  V-------------------------PAGSLTATPVFDGASNEELAGLLANSRPNRDGDV 989

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEP+  PV++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 990  MVNADGKATLIDGRSGEPYPYPVSIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1050 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  DF++ 
Sbjct: 1110 FKVLLKELQSLCLNVEVLSADGTPMELAGDDDDFDQA 1146



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 319/617 (51%), Positives = 442/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 238 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 297

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 298 ARVGRYKINRKLGLGGDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEIPVETDD 357

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 358 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 417

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 418 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 477

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR++ DGK+T+ + YL+A EE+   +AQAN+  D
Sbjct: 478 EGPNIGLIGSLASYARVNPFGFIETPYRRIIDGKLTDQIDYLTADEEDRFVVAQANTHYD 537

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G+ T+E V  R   G+  +V R  +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 538 EEGNITDETVTVRLKDGDIAMVGRNAVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 597

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++   AG+VE V A  I I + +G  + 
Sbjct: 598 NMQKQAVPLIRAEAPFVGTGMEQRAAYDAGDLVITPVAGVVENVSADFITIMADDGKRE- 656

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV +G+ V    +IADGP T  G+++LGRN+LVA
Sbjct: 657 ------TYLLRKFQRTNQGTSYNQKPLVNLGERVEAGQVIADGPGTFNGEMSLGRNLLVA 710

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TSIHIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 711 FMPWEGHNYEDAIILNQNIVEQDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 770

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++D+ GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 771 DLDDRGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 830

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 831 ETGKVIGVRHFSREDDD 847



 Score =  295 bits (755), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 168/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVF 63
            R  F K    I++P L+++Q  SY   +        +  E         GL+   + + 
Sbjct: 24  QRYSFAKVSAPIEVPGLLDLQLDSYSWLIGTPEWRARQKEEFGEGARVTSGLENILEELS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+   +D+ YA PL +T   +           +  
Sbjct: 84  PIQDYSGNMSLSLSEPRFEDVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTG 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 135 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L +  + K  + LG+ 
Sbjct: 253 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKINRKLGLG 312

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E ++    GE        ++   ++   +  +R
Sbjct: 313 GDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEI-----PVETDDIDHFGNRRLR 367

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 368 TVGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|290958175|ref|YP_003489357.1| DNA-directed RNA polymerase subunit beta [Streptomyces scabiei 87.22]
 gi|260647701|emb|CBG70806.1| DNA-directed RNA polymerase beta chain [Streptomyces scabiei 87.22]
          Length = 1161

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 267/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVNEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +D+     +       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDDWAKRLQVIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                                    A+    G  V+TPVFDGA E+ +  +L+        
Sbjct: 948  ------------------------ADSVAPGTNVATPVFDGAREDELAGLLQHTIPNRDG 983

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  +G++ ++DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  ERMVQPTGKARMFDGRSGEPFPDPISIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 340/670 (50%), Positives = 460/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  + P D   +  ED+I+ IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGAEAPLDAGVLTVEDVISTIKYLVKLHAGETETAADNGTTIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN++LD+D  FTE
Sbjct: 483 IGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANATLDDDMRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 NRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTTNDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLAKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALENGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTHKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE-----------KSLEEIFHSEIRDIPI 346
             +    G+   ED+++     + + AG+                 ++   +  +R +  
Sbjct: 310 AEAPLDAGVLTVEDVISTIKYLVKLHAGETETAADNGTTIVVETDDIDHFGNRRLRSVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|226305222|ref|YP_002765180.1| DNA-directed RNA polymerase beta chain [Rhodococcus erythropolis PR4]
 gi|259494190|sp|C0ZVQ6|RPOB_RHOE4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226184337|dbj|BAH32441.1| DNA-directed RNA polymerase beta chain [Rhodococcus erythropolis PR4]
          Length = 1168

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 189/546 (34%), Positives = 267/546 (48%), Gaps = 66/546 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGSRKTYRMRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          + +  
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  ++L G+    G         L   +  E  R           
Sbjct: 770  DL-DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAR----------- 817

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++      DD+PPGV  +V+V+VA KR IQ GDK
Sbjct: 818  ------EVRDTSLKVPHGETGKVIGIRVFSRDEDDDLPPGVNELVRVYVAQKRKIQDGDK 871

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQ+ ETHLGW     G
Sbjct: 872  LAGRHGNKGVIGKILPQEDMPFLSDGTPVDIILNTHGVPRRMNIGQVLETHLGWIGK-TG 930

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I+   +  + +   +     L     +                           ++TP
Sbjct: 931  WNIQIASDGTRPDWAATLPEEMLSAPADSN--------------------------IATP 964

Query: 1210 VFDGADEEAINSMLRMADLD---------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            VFDGA E+ +  +L  A L            G++ L+DG +GEPF  PV+VGY+Y++KL+
Sbjct: 965  VFDGAKEDELTGLL-GATLPNRDGEQMVGPDGKATLFDGRSGEPFPYPVSVGYMYIIKLH 1023

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSD
Sbjct: 1024 HLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSD 1083

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S          + D 
Sbjct: 1084 DVVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAI----TMADG 1139

Query: 1381 NKCELK 1386
            +  +L+
Sbjct: 1140 DDEDLE 1145



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 329/735 (44%), Positives = 469/735 (63%), Gaps = 25/735 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK-EK 291
           +    +           +                I+  E+V+ S    + G+   +  +K
Sbjct: 121 FVTAEFINNNTGEIKSQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDMSVDK 180

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
             +    +   + G     +    +   + +       +     +         I   + 
Sbjct: 181 STEKDLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQI--TER 238

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
              +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ V
Sbjct: 239 FGFSEILMATLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARV 298

Query: 412 GRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDDID 457
           GR K+N +L L+   P     + +EDI+A ++ LV L  G               +DDID
Sbjct: 299 GRYKINKKLGLNAGQPIVASTLTEEDIVATVEYLVRLHAGDTSMTAPGGVEVPVEVDDID 358

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF
Sbjct: 359 HFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIREFF 418

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG
Sbjct: 419 GTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEG 478

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL+ +ARVN +GFIETPYR+V DG+VT++V YL+A EE+   +AQANS++D +
Sbjct: 479 PNIGLIGSLSVYARVNPFGFIETPYRRVVDGQVTDEVDYLTADEEDRHVVAQANSAIDRE 538

Query: 638 GSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G FT+  +  R   GE   V    ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM
Sbjct: 539 GRFTDSKILVRRKGGEVEFVASSDIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANM 598

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++EAP VGTGME   A  +G  I+ ++ G+VE++ A  + + + +G      
Sbjct: 599 QRQAVPLVRSEAPLVGTGMELRAAVDAGDVIITEKTGVVEEISADYVTVMADDGSR---- 654

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                YR+ KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA M
Sbjct: 655 ---KTYRMRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVAIM 711

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L ++
Sbjct: 712 PWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL 771

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +
Sbjct: 772 DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGET 831

Query: 937 GTVVDVRIFNRHGID 951
           G V+ +R+F+R   D
Sbjct: 832 GKVIGIRVFSRDEDD 846



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 89/295 (30%), Positives = 142/295 (48%), Gaps = 25/295 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-------NEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +          + GL+     + PI 
Sbjct: 25  RVSFAKVREPLEVPGLLDVQTDSFEWLIGAQSWRERAAALGDNAVSGGLEDILAELSPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K   D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 85  DFNGTMSLSFSDPRFDEVKASTDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDMSVDK--STEKDLHSVKVIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 194 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEILMATLEKDN 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +   L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYK 302


>gi|19551731|ref|NP_599733.1| DNA-directed RNA polymerase subunit beta [Corynebacterium glutamicum
            ATCC 13032]
          Length = 1159

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 182/517 (35%), Positives = 261/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M+    LL A    +  +  D  +   + V   ++
Sbjct: 671  LVNLGERVEAGQVIADGPGTFN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQNIVEQDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E + +D DD   I+      R  +IL G+ 
Sbjct: 730  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDLDDR-GIVRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  ++               
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRH-------------- 834

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++++VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 835  ---FSREDDDDLAPGVNEMIRIYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +     D +    +  L + L +
Sbjct: 892  GTPVDIILNTHGVPRRMNIGQVLETHLGWLASA-GWSVD--PEDPENAELVKTLPADLLE 948

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 949  V-------------------------PAGSLTATPVFDGASNEELAGLLANSRPNRDGDV 983

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEP+  PV++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 984  MVNADGKATLIDGRSGEPYPYPVSIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1044 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1103

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            F VL+KE+Q+L L++++ ++         +  DF++ 
Sbjct: 1104 FKVLLKELQSLCLNVEVLSADGTPMELAGDDDDFDQA 1140



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 319/617 (51%), Positives = 442/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 232 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 291

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 292 ARVGRYKINRKLGLGGDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEIPVETDD 351

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 352 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 411

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 412 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 471

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR++ DGK+T+ + YL+A EE+   +AQAN+  D
Sbjct: 472 EGPNIGLIGSLASYARVNPFGFIETPYRRIIDGKLTDQIDYLTADEEDRFVVAQANTHYD 531

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G+ T+E V  R   G+  +V R  +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 532 EEGNITDETVTVRLKDGDIAMVGRNAVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 591

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++   AG+VE V A  I I + +G  + 
Sbjct: 592 NMQKQAVPLIRAEAPFVGTGMEQRAAYDAGDLVITPVAGVVENVSADFITIMADDGKRE- 650

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV +G+ V    +IADGP T  G+++LGRN+LVA
Sbjct: 651 ------TYLLRKFQRTNQGTSYNQKPLVNLGERVEAGQVIADGPGTFNGEMSLGRNLLVA 704

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TSIHIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 705 FMPWEGHNYEDAIILNQNIVEQDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 764

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++D+ GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 765 DLDDRGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 824

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 825 ETGKVIGVRHFSREDDD 841



 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 168/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVF 63
            R  F K    I++P L+++Q  SY   +        +  E         GL+   + + 
Sbjct: 18  QRYSFAKVSAPIEVPGLLDLQLDSYSWLIGTPEWRARQKEEFGEGARVTSGLENILEELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+   +D+ YA PL +T   +           +  
Sbjct: 78  PIQDYSGNMSLSLSEPRFEDVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTG 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 129 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 187 VIPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L +  + K  + LG+ 
Sbjct: 247 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKINRKLGLG 306

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E ++    GE        ++   ++   +  +R
Sbjct: 307 GDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPNGEEI-----PVETDDIDHFGNRRLR 361

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 362 TVGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|229490735|ref|ZP_04384573.1| DNA-directed RNA polymerase, beta subunit [Rhodococcus erythropolis
            SK121]
 gi|229322555|gb|EEN88338.1| DNA-directed RNA polymerase, beta subunit [Rhodococcus erythropolis
            SK121]
          Length = 1168

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 188/546 (34%), Positives = 267/546 (48%), Gaps = 66/546 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGSRKTYRMRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          + +  
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  ++L G+    G         L   +  E  R           
Sbjct: 770  DL-DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAR----------- 817

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++      DD+PPGV  +V+V+VA KR IQ GDK
Sbjct: 818  ------EVRDTSLKVPHGETGKVIGIRVFSRDEDDDLPPGVNELVRVYVAQKRKIQDGDK 871

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQ+ ETHLGW     G
Sbjct: 872  LAGRHGNKGVIGKILPQEDMPFLSDGTPVDIILNTHGVPRRMNIGQVLETHLGWIGK-TG 930

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              ++   +  + +   +     L     +                           ++TP
Sbjct: 931  WNVQIASDGSRPDWAATLPEEMLSAPADSN--------------------------IATP 964

Query: 1210 VFDGADEEAINSMLRMADLD---------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            VFDGA E+ +  +L  A L            G++ L+DG +GEPF  PV+VGY+Y++KL+
Sbjct: 965  VFDGAKEDELTGLL-GATLPNRDGEQMVGPDGKATLFDGRSGEPFPYPVSVGYMYIIKLH 1023

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSD
Sbjct: 1024 HLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSD 1083

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DVVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S          + D 
Sbjct: 1084 DVVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAI----TMADG 1139

Query: 1381 NKCELK 1386
            +  +L+
Sbjct: 1140 DDEDLE 1145



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 329/735 (44%), Positives = 469/735 (63%), Gaps = 25/735 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK-EK 291
           +    +           +                I+  E+V+ S    + G+   +  +K
Sbjct: 121 FVTAEFINNNTGEIKSQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDMSVDK 180

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
             +    +   + G     +    +   + +       +     +         I   + 
Sbjct: 181 STEKDLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQI--TER 238

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
              +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ V
Sbjct: 239 FGFSEILMATLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARV 298

Query: 412 GRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDDID 457
           GR K+N +L L+   P     + +EDI+A ++ LV L  G               +DDID
Sbjct: 299 GRYKINKKLGLNAGQPIVASTLTEEDIVATVEYLVRLHAGDTSMTAPGGVEVPVEVDDID 358

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF
Sbjct: 359 HFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIREFF 418

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG
Sbjct: 419 GTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEG 478

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL+ +ARVN +GFIETPYR+V DG+VT++V YL+A EE+   +AQANS++D +
Sbjct: 479 PNIGLIGSLSVYARVNPFGFIETPYRRVVDGQVTDEVDYLTADEEDRHVVAQANSAIDRE 538

Query: 638 GSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G FT+  +  R   GE   V    ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM
Sbjct: 539 GRFTDSKILVRRKGGEVEFVASSDIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANM 598

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++EAP VGTGME   A  +G  I+ ++ G+VE++ A  + + + +G      
Sbjct: 599 QRQAVPLVRSEAPLVGTGMELRAAVDAGDVIITEKTGVVEEISADYVTVMADDGSR---- 654

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                YR+ KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA M
Sbjct: 655 ---KTYRMRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVAIM 711

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L ++
Sbjct: 712 PWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL 771

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +
Sbjct: 772 DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGET 831

Query: 937 GTVVDVRIFNRHGID 951
           G V+ +R+F+R   D
Sbjct: 832 GKVIGIRVFSRDEDD 846



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 89/295 (30%), Positives = 142/295 (48%), Gaps = 25/295 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-------NEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +          + GL+     + PI 
Sbjct: 25  RVSFAKVREPLEVPGLLDVQTDSFEWLIGAQSWRERAAALGDNAVSGGLEDILAELSPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K   D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 85  DFNGTMSLSFSDPRFDEVKASTDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDMSVDK--STEKDLHSVKVIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 194 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEILMATLEKDN 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +   L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYK 302


>gi|46360952|gb|AAS89209.1| RpoB [Corynebacterium capitovis]
          Length = 1116

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 184/496 (37%), Positives = 251/496 (50%), Gaps = 61/496 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K    M     LL A    +  +  D  +     V   ++
Sbjct: 668  IVAQGDRVEAGQVIADGPGTKN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAELLETLPEQLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA    I  +L  +  +  G  
Sbjct: 946  VPPESLT-------------------------ATPVFDGATNAEIAGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDANGKTMLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGLSID 1362
            F VL+KE+Q+L L+++
Sbjct: 1101 FKVLLKELQSLCLNVE 1116



 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 318/611 (52%), Positives = 434/611 (71%), Gaps = 21/611 (3%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  +  TL +D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL+ VGR 
Sbjct: 235 SEIMMATLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRAKRYDLARVGRY 294

Query: 415 KMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGN 461
           K+N +L L    D +  + +EDI   ++ LV L  G+  +            DDID+ GN
Sbjct: 295 KVNRKLGLGGDHDGLMTLTEEDIATALEYLVRLHAGEAEMTSPTGTVVPISTDDIDHFGN 354

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQ
Sbjct: 355 RRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQ 414

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIG
Sbjct: 415 LSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIG 474

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ +L S+ARVNA+GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + +D DG+ T
Sbjct: 475 LIGALASYARVNAFGFIETPYQKVVDGKLTDQIDYLTADEEDRYAIAQAATPMDADGTLT 534

Query: 642 EELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            + +  R   G+  +V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQ+QA
Sbjct: 535 ADRIEVRLKDGDIGVVGPHGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGANMQKQA 594

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPLL+AEAP+V TGME   A  +G  + + +AG V  V    I I   EG  D       
Sbjct: 595 VPLLRAEAPYVATGMEQRAAYDAGDVVTSAKAGAVTNVTGDFITIMDDEGIQD------- 647

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y L  F+R+NQ TC NQ P+V  GD V    +IADGP T  G++ALGRN+LVAFMPW G
Sbjct: 648 TYMLRTFERTNQGTCYNQSPIVAQGDRVEAGQVIADGPGTKNGEMALGRNLLVAFMPWEG 707

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           +N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE G
Sbjct: 708 HNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERG 767

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+
Sbjct: 768 IIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVI 827

Query: 941 DVRIFNRHGID 951
            VR F+R   D
Sbjct: 828 AVRRFSREDDD 838



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 90/324 (27%), Positives = 150/324 (46%), Gaps = 30/324 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +               D R   GL+   + + 
Sbjct: 15  QRYSFAKISEPITVPGLLDVQLESFAWLVGTPEWREREQAARGDDARVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG+  L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIQDYSGSMSLSLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITKRFGFSEIMMATLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D  + ++E+            K   +  +G    
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENA-------FFRAKRYDLARVGRYKV 296

Query: 301 DCLCGLYVAEDIVNGETGEIYIEA 324
           +   GL    D +   T E    A
Sbjct: 297 NRKLGLGGDHDGLMTLTEEDIATA 320


>gi|225593148|gb|ACN96066.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Fischerella sp. MV11]
          Length = 1138

 Score =  521 bits (1341), Expect = e-145,   Method: Composition-based stats.
 Identities = 321/607 (52%), Positives = 434/607 (71%), Gaps = 4/607 (0%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 227 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 286

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  P+ +R +  +DI+A +  L++L    G+IDDID+LGNRRVRSVG
Sbjct: 287 GRVGRYKLNKKLRLQVPETMRVLTPQDILAAVDYLINLEYDIGSIDDIDHLGNRRVRSVG 346

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 347 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 406

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 407 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 466

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +G+V  D+  VY++A EE++  +A  ++ +DE+G      V 
Sbjct: 467 HARVNQYGFLETPFRPVENGRVRYDLPPVYMTADEEDDFRVAAGDAPIDENGHLIGPEVP 526

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E      E++D+I  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 527 VRYRQEFSTTTPEQVDYIAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 586

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS--VEGDLDPSTSGVDIYRL 764
           E P VGTG+E+  A+ SG  IV++  G V  VDA +I +R     G+ +        Y L
Sbjct: 587 ERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATKIRVRPRVRPGEENAKPPAEIEYIL 646

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N++VA+MPW GYN+E
Sbjct: 647 SKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNIIVAYMPWEGYNYE 706

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++LISER+V +DV+TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+N+DE GII +
Sbjct: 707 DAILISERLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRNLDEQGIIRI 766

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVRI
Sbjct: 767 GAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRI 826

Query: 945 FNRHGID 951
           F R   D
Sbjct: 827 FTREQGD 833



 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 185/526 (35%), Positives = 262/526 (49%), Gaps = 64/526 (12%)

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  ++ +G  V  G +L    + +G   +   + ++ A   
Sbjct: 641  EIEYILSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEG-GELALGQNIIVAYMP 699

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  L     V   V       ++ I+  +  +  E    +I  +  D     D
Sbjct: 700  WEGYNYEDAILISERLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRNLD 759

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            EQ I+    +    +IL G+    G         L   +  E  R               
Sbjct: 760  EQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD-------------- 805

Query: 1034 NVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                ++       +  + R  + +I   + GD++PPG   VV+V+VA KR IQ GDKMAG
Sbjct: 806  ----VRDNSLRVPNGEKGRVVDVRIFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAG 861

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+S+ILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   +G + 
Sbjct: 862  RHGNKGIISKILPIEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGHVMGVRF 921

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K    D               ++ G  +    +     ++     + W         VF 
Sbjct: 922  KITPFD---------------EMYGEEASRSIVHGKLQEARDETGKNW---------VF- 956

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                          + D+ G+ ++YDG TGEPFDRPVTVG  YMLKL H+V DK++ARST
Sbjct: 957  --------------NPDDPGKIMVYDGRTGEPFDRPVTVGVAYMLKLVHLVDDKIHARST 1002

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +I
Sbjct: 1003 GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNAI 1062

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1063 VKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQTDGSTVDVE 1108



 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 108/481 (22%), Positives = 200/481 (41%), Gaps = 36/481 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 44  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGQNYKLKE 93

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TYAV + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 94  PKYDVDEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTERGT 144

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 145 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 201

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 202 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 261

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L +       +   +DI+      
Sbjct: 262 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLQVPETMRVLTPQDILAAVDYL 321

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 322 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 380

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 381 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 435

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +     G+  I  I+         +G +  +        +E   +   +      + 
Sbjct: 436 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNQYGFLETPFRPVENGRVRYDLP 493

Query: 500 P 500
           P
Sbjct: 494 P 494


>gi|38233060|ref|NP_938827.1| DNA-directed RNA polymerase subunit beta [Corynebacterium diphtheriae
            NCTC 13129]
 gi|41017599|sp|P60280|RPOB_CORDI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|38199319|emb|CAE48951.1| DNA-directed RNA polymerase beta chain [Corynebacterium diphtheriae]
          Length = 1175

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 192/618 (31%), Positives = 281/618 (45%), Gaps = 62/618 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E +       ++  
Sbjct: 582  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAYDAGDLIIN 641

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  E                ++  ++ +G  V  G +L  
Sbjct: 642  KKGGVVENVSADIITVMADDGTRETYILRKFERTNQGTCYNQTPLVNIGDRVEAGQVLAD 701

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 702  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTK 760

Query: 957  ISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +  E    +I    E + +D  DE+ I+      R  +IL G+    G         L  
Sbjct: 761  LGPEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLR 819

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +  E  R                 E      +            +       DD+ PGV
Sbjct: 820  AIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRRFSRDDDDDLAPGV 862

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVDI+LN  GVP R
Sbjct: 863  NEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPDGTPVDIILNTHGVPRR 922

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLGW     G KI +     +   +   L++  E +               
Sbjct: 923  MNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP----------- 965

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTG 1242
                       +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +G
Sbjct: 966  -----------AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSG 1014

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +
Sbjct: 1015 EPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAM 1074

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L+++
Sbjct: 1075 QAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLNVE 1134

Query: 1363 LENSRTKNSAKMEEIPDF 1380
            + ++            D 
Sbjct: 1135 VLSADGTPMELSGSDDDE 1152



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 319/613 (52%), Positives = 442/613 (72%), Gaps = 21/613 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 247 TERFGFSEIMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 306

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + +EDI   ++ LV L  G+ T+            DD
Sbjct: 307 AKVGRYKVNRKLGLGGDNEGLMTLTEEDIATTLEYLVRLHAGETTMTSPTGEVIPVETDD 366

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 367 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 426

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 427 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 486

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVNA+GFIETPYRKV +G +T+ + YL+A EE+   +AQAN   D
Sbjct: 487 EGPNIGLIGSLASYARVNAFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVAQANVEHD 546

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 547 ADGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 606

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+ G+VE V A  I + + +G  + 
Sbjct: 607 NMQRQAVPLVRSEAPFVGTGMERAAAYDAGDLIINKKGGVVENVSADIITVMADDGTRE- 665

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 666 ------TYILRKFERTNQGTCYNQTPLVNIGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 719

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVSE+ LK
Sbjct: 720 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSEDVLK 779

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 780 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 839

Query: 935 VSGTVVDVRIFNR 947
            +G V+ VR F+R
Sbjct: 840 ETGKVIGVRRFSR 852



 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/389 (24%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 33  ERKSFAKITEPIEVPGLLDIQLNSFAWLIGTPEWRARQQEELGDSVRVTSGLEDILEELS 92

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 93  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 143

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 144 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 201

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 202 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 261

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 262 SDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLG 321

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGE+       ++   ++   +  +R
Sbjct: 322 GDNEGLMTLTEEDIATTLEYLVRLHAGETTMTSPTGEVI-----PVETDDIDHFGNRRLR 376

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 377 TVGELIQNQVRVGLSRMERVVRERMTTQD 405


>gi|226361054|ref|YP_002778832.1| DNA-directed RNA polymerase subunit beta [Rhodococcus opacus B4]
 gi|254765300|sp|C1AYV9|RPOB_RHOOB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|226239539|dbj|BAH49887.1| DNA-directed RNA polymerase beta subunit [Rhodococcus opacus B4]
          Length = 1168

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/545 (34%), Positives = 265/545 (48%), Gaps = 64/545 (11%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGSRKTYRMRKFARSNQGTCANQRPIVDEGQRVESGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          + +  
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  ++L G+    G         L   +  E  R           
Sbjct: 770  DL-DERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAR----------- 817

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++      DD+PPGV  +V+V+VA KR IQ GDK
Sbjct: 818  ------EVRDTSLKVPHGETGKVIGIRVFSRDDDDDLPPGVNELVRVYVAQKRKIQDGDK 871

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL DGTP+DI+LN  GVP RMN+GQI ETHLGW     G
Sbjct: 872  LAGRHGNKGVIGKILPQEDMPFLPDGTPIDIILNTHGVPRRMNIGQILETHLGWIGK-TG 930

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              ++   +  + +         L     +                           ++TP
Sbjct: 931  WNVQIAGDGSRPDWAEQLPEEMLSAPSDSN--------------------------IATP 964

Query: 1210 VFDGADEEAINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA E+ +  +L     +          G++ L+DG +GEPF  PV+VGY+Y++KL+H
Sbjct: 965  VFDGAKEDELTGLLGSTLPNRDGEVMVASDGKATLFDGRSGEPFPYPVSVGYMYIIKLHH 1024

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD
Sbjct: 1025 LVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDD 1084

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S     A      D +
Sbjct: 1085 VVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIAMA----DGD 1140

Query: 1382 KCELK 1386
              +L+
Sbjct: 1141 DEDLE 1145



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 457/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +KG +    +   + G     +    +   + +       +     +         I   
Sbjct: 179 DKGTEKDLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQI--A 236

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 237 ERFGFSEILMATLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 296

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+T  P     + +EDI+A I+ LV L  G               +DD
Sbjct: 297 RVGRYKINKKLGLNTGQPIVASTLTEEDIVATIEYLVRLHAGDTEMTAPGGVAVPVEVDD 356

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 357 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 416

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 417 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 476

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV  G+VT+ V YL+A EE+   +AQANS++D
Sbjct: 477 EGPNIGLIGSLSVYARVNPFGFIETPYRKVEGGQVTDQVDYLTADEEDRHVVAQANSAVD 536

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FT++ +  R   GE   V   +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 537 ANGHFTDDRILVRRKGGEVEFVSSAEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 596

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V A  + + + +G    
Sbjct: 597 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSADYVTVMADDGSR-- 654

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 655 -----KTYRMRKFARSNQGTCANQRPIVDEGQRVESGQVLADGPCTENGEMALGKNLLVA 709

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 710 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 769

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 770 DLDERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 829

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ +R+F+R   D
Sbjct: 830 ETGKVIGIRVFSRDDDD 846



 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 91/295 (30%), Positives = 145/295 (49%), Gaps = 25/295 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S++  +      +    R +     GL+     + PI 
Sbjct: 25  RVSFAKIREPLEVPGLLDLQTDSFEWLIGAQSWRERAAARGDSAISGGLEDILAELSPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K   D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFDEVKASTDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FDH   +   + K L++ ++IP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDHSVDK--GTEKDLHSVKVIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 194 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIAERFGFSEILMATLEKDN 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +   L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYK 302


>gi|325675363|ref|ZP_08155047.1| DNA-directed RNA polymerase subunit beta [Rhodococcus equi ATCC
            33707]
 gi|325553334|gb|EGD23012.1| DNA-directed RNA polymerase subunit beta [Rhodococcus equi ATCC
            33707]
          Length = 1162

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 272/515 (52%), Gaps = 54/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 670  IVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 787  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 835

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 836  REDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 895

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQ+ ETHLGW     G  ++   +  + +   +     L     + 
Sbjct: 896  IILNTHGVPRRMNIGQVLETHLGWIGK-TGWNVQIAGDGSRPDWAATLPEEMLSAPADSN 954

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
                                      ++TPVFDGA E+ +  +L     +  G       
Sbjct: 955  --------------------------IATPVFDGAKEDELTGLLGSTLPNRDGERMVGPD 988

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 989  GKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1048

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1049 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1108

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S     A      D +  +L+
Sbjct: 1109 KELQSLCLNVEVLSSDGAAIAMA----DGDDEDLE 1139



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 459/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +    + D  I   
Sbjct: 173 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEI--R 230

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D  K+  +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 231 ERFGFSEIMMATLEKDPAKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 290

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKGT------------IDD 455
            VGR K+N +L L+T  P +   + ++DI+  I+ LV L  G               +DD
Sbjct: 291 RVGRYKINKKLGLNTGLPIEASTLTEDDIVTTIEYLVRLHAGDTMMTAPGGVEVPVEVDD 350

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 351 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 410

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 411 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 470

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G++T+ V YL+A EE+   +AQANS +D
Sbjct: 471 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGQLTDQVDYLTADEEDRHVVAQANSPVD 530

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 531 ANGRFTEDRVLVRRKGGEVEFVSSSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 590

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V +  + + + +G    
Sbjct: 591 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSSDYVTVMADDGSR-- 648

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 649 -----TTYRLRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVA 703

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 704 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 763

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 764 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 823

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 824 ESGKVIGIRVFSREDDD 840



 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 148/296 (50%), Gaps = 22/296 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-------GLQAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S++  +      +            GL+     + PI 
Sbjct: 19  RVSFAKIREPLEVPGLLDLQTDSFEWLVGSPSWRERAAARRDGAVTGGLEEILAELSPIE 78

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 79  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 129

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 130 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 187

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT+ L ALGM  EEI   F     ++ +   D 
Sbjct: 188 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEIRERFGFSEIMMATLEKDP 247

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGI 298
                 A   +            ++ + ++E+   K     L +  + K  K LG+
Sbjct: 248 AKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYKINKKLGL 303


>gi|46360918|gb|AAS89192.1| RpoB [Corynebacterium diphtheriae]
          Length = 1158

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 192/618 (31%), Positives = 282/618 (45%), Gaps = 62/618 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E +       ++  
Sbjct: 565  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERAAAYDAGDLIIN 624

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  E                ++  ++ +G  V  G +L  
Sbjct: 625  KKGGVVENVSADIITVMADDGTRETYILRKFERTNQGTCYNQTPLVNIGDRVEAGQVLAD 684

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 685  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTK 743

Query: 957  ISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +  E    +I    E + +D  DE+ I+      R  +IL G+    G         L  
Sbjct: 744  LGPEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLR 802

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +  E  R                 E      +            +       DD+ PGV
Sbjct: 803  AIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRRFSRDDDDDLAPGV 845

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVDI+LN  GVP R
Sbjct: 846  NEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPDGTPVDIILNTHGVPRR 905

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ E HLGW     G KI +     +   +   L++  E +               
Sbjct: 906  MNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYD------------- 946

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTG 1242
                     + +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +G
Sbjct: 947  ---------FPAGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSG 997

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +
Sbjct: 998  EPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAM 1057

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L+++
Sbjct: 1058 QAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLNVE 1117

Query: 1363 LENSRTKNSAKMEEIPDF 1380
            + ++            D 
Sbjct: 1118 VLSADGTPMELSGSDDDE 1135



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 319/613 (52%), Positives = 442/613 (72%), Gaps = 21/613 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 230 TERFGFSEIMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 289

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + +EDI   ++ LV L  G+ T+            DD
Sbjct: 290 AKVGRYKVNRKLGLGGDNEGLMTLTEEDIATTLEYLVRLHAGETTMTSPTGEVIPVETDD 349

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 350 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 409

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 410 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 469

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVNA+GFIETPYRKV +G +T+ + YL+A EE+   +AQAN   D
Sbjct: 470 EGPNIGLIGSLASYARVNAFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVAQANVEHD 529

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 530 ADGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 589

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+ G+VE V A  I + + +G  + 
Sbjct: 590 NMQRQAVPLVRSEAPFVGTGMERAAAYDAGDLIINKKGGVVENVSADIITVMADDGTRE- 648

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 649 ------TYILRKFERTNQGTCYNQTPLVNIGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 702

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVSE+ LK
Sbjct: 703 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSEDVLK 762

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 763 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 822

Query: 935 VSGTVVDVRIFNR 947
            +G V+ VR F+R
Sbjct: 823 ETGKVIGVRRFSR 835



 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/389 (24%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K  E I++P L+++Q  S+   +            +    R   GL+   + + 
Sbjct: 16  ERKSFAKITEPIEVPGLLDIQLNSFAWLIGTPEWRARQQEELGDSVRVTSGLEDILEELS 75

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 76  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 126

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 127 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 184

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 185 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 244

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 245 SDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLG 304

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGE+       ++   ++   +  +R
Sbjct: 305 GDNEGLMTLTEEDIATTLEYLVRLHAGETTMTSPTGEVI-----PVETDDIDHFGNRRLR 359

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 360 TVGELIQNQVRVGLSRMERVVRERMTTQD 388


>gi|330470182|ref|YP_004407925.1| DNA-directed RNA polymerase subunit beta [Verrucosispora maris
            AB-18-032]
 gi|328813153|gb|AEB47325.1| DNA-directed RNA polymerase subunit beta [Verrucosispora maris
            AB-18-032]
          Length = 1143

 Score =  520 bits (1340), Expect = e-145,   Method: Composition-based stats.
 Identities = 190/508 (37%), Positives = 265/508 (52%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++        E  M     LL A    +  +  D  +     V   V+
Sbjct: 657  VVFEGDRVEAGQVIADGPCT-DEGEMALGRNLLVAFMCWEGHNYEDAIILSQRLVQQDVL 715

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 716  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDILVGK 773

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 774  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSR-------- 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 824  -EDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 882

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                   
Sbjct: 883  IVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLQSIG------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A+  +    V+TPVFDGA EE I+ +L     +          
Sbjct: 930  -----------------ADSSEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIGAT 972

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP   P+ VGYIY+LKLNH+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 973  GKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1032

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1033 QRFGEMECWAMQAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLL 1092

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        E   +
Sbjct: 1093 KELQSLCLNVEVLSSDGVALEMRETDDE 1120



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/600 (54%), Positives = 440/600 (73%), Gaps = 10/600 (1%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  +  TL  D    + +ALLDIYR +RPG+  T   A+++ + LFF+  +YD++ VGR 
Sbjct: 235 SELMMTTLEKDHIAGQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRY 294

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLK 472
           K N +L LD P     + ++DI+A ++ L  L  G+     DDID+ GNRR+R+VGE+++
Sbjct: 295 KFNKKLELDVPITTGTLTEDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQ 354

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 355 NQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQTNPL 414

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ +L++FARV
Sbjct: 415 AGLTHRRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGALSTFARV 474

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-G 651
           N +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ L  DG+F E+ V  R   G
Sbjct: 475 NPFGFIETPYRKVVDGRVTDQIDYLTADEEDRFVKAQANAPLRADGTFAEDRVLVRRKGG 534

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E   VP   +D++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPL+KAE+P V
Sbjct: 535 ETEDVPPAAVDYMDVSPRQMTSVATAMIPFLEHDDANRALMGANMQRQAVPLVKAESPLV 594

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  +VA+  G+VE + A  I +   +G           Y L KF+RSN
Sbjct: 595 GTGMEYRAAVDAGDVVVAEVGGVVEDLCADYITVHQDDGHR-------RTYLLHKFRRSN 647

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +CVNQ+P+V  GD V    +IADGP TD G++ALGRN+LVAFM W G+N+ED++++S+
Sbjct: 648 AGSCVNQKPVVFEGDRVEAGQVIADGPCTDEGEMALGRNLLVAFMCWEGHNYEDAIILSQ 707

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV TSIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GAEV PG
Sbjct: 708 RLVQQDVLTSIHIEEHEVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPG 767

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ VR F+R   D
Sbjct: 768 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSREDGD 827



 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 103/469 (21%), Positives = 187/469 (39%), Gaps = 28/469 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNEGLQAAFKSVFPITAF 68
           R  FG+  E +++P+L+ +Q  S+D  +         A D     GL      + PI  F
Sbjct: 20  RVSFGRITEHLEVPNLLAIQNESFDWLVGNEAWQGRSADDPHARSGLAEILDEISPIEDF 79

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           SG   L F +  FD  K  +++C  +DLTY  PL +T               +  +IK Q
Sbjct: 80  SGTMSLSFSAPRFDEVKASIEECKEKDLTYCAPLFVTAEFT---------NNTTGEIKSQ 130

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   S + L + ++IP +
Sbjct: 131 TVFMGDFPMMTPKGTFIINGTERVVVSQLVRSPGVYFDKQPDKT--SDRDLSSVKVIPSR 188

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWC 246
           G W++ + D +D + VRIDR+R+  VT  L A+G  +E I   F    +   +   D   
Sbjct: 189 GAWLEFDIDKRDTVGVRIDRKRRQAVTVLLKAIGWSAERIREKFGWSELMMTTLEKDHIA 248

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +            +  + ++++         + K  + K  K L +      
Sbjct: 249 GQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLELDVPITT 308

Query: 305 GLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G    +DIV   E         +  +   ++   +  +R +  L  + V         +V
Sbjct: 309 GTLTEDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVV 368

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            ++   +   +  I            +     F            + +  +    RL+  
Sbjct: 369 RERMTTQD--VEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQTNPLAGLTHRRRLSAL 426

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 427 GPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGALST 470


>gi|269930927|gb|ACZ54198.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 565

 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 405/566 (71%), Positives = 481/566 (84%), Gaps = 1/566 (0%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D IDEK L+ +       I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+
Sbjct: 1   DEIDEKVLKILLDVSADQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGE 60

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             T   AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+
Sbjct: 61  PPTIDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRVLRQEDILAVVKMLVE 120

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           LR+G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLIN
Sbjct: 121 LRDGRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLIN 180

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
           AKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTH
Sbjct: 181 AKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 240

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           YGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   
Sbjct: 241 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAKH 300

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEND
Sbjct: 301 YVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEND 360

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ AKR+GIV+QVDA RIVI
Sbjct: 361 DANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVSAKRSGIVDQVDATRIVI 420

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD V + DIIADGPSTDLGDL
Sbjct: 421 RATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRVEKGDIIADGPSTDLGDL 479

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDI
Sbjct: 480 ALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDI 539

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPG 891
           PNV+EE L+N+DE GII +GAEV PG
Sbjct: 540 PNVAEEALRNLDEAGIIYIGAEVQPG 565


>gi|256785866|ref|ZP_05524297.1| DNA-directed RNA polymerase subunit beta [Streptomyces lividans TK24]
 gi|289769758|ref|ZP_06529136.1| DNA-directed RNA polymerase, beta subunit [Streptomyces lividans
            TK24]
 gi|289699957|gb|EFD67386.1| DNA-directed RNA polymerase, beta subunit [Streptomyces lividans
            TK24]
          Length = 1161

 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 266/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVAEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+I P EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKINPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L  ++     +       
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEEWAQRLQVIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 948  ------------------------ADKVEPGTNVATPVFDGAREDELAGLLQHTIPNRDG 983

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  ERMVLPSGKARLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 336/670 (50%), Positives = 458/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ R+N +GFIETPYRKV +G+VT+DV YL+A EE+   IAQAN++L +D  F E
Sbjct: 483 IGSLASYGRINPFGFIETPYRKVVEGQVTDDVDYLTADEEDRFVIAQANAALGDDMRFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 ARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 603 PLIKSESPLVGTGMEYRSAADAGDVVKAEKAGVVQEVSADYITTTNDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLAKFSRSNQGTSVNQKVIVAEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVESALESGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  IR++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGREIVVETDDIDHFGNRRIRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|62720652|gb|AAX93862.1| RNA polymerase subunit B [Mycobacterium conceptionense]
          Length = 1170

 Score =  520 bits (1339), Expect = e-145,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 959

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 960  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVDSD 997

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1058 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1118 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1148



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 302 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS +D
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPID 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 ADGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++AG+VE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKAGVVEEVSADYITVMADDGSR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 30  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAVDRGETDPKGGLEEVLEELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 342


>gi|34595747|gb|AAQ76596.1| RpoB [Mycobacterium porcinum]
          Length = 1169

 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 959  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVDSD 996

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1147



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 327/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ + YL+A EE+   +AQANS +D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVIDGVVSDQIDYLTADEEDRHVVAQANSPID 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 NDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++AG+VE+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKAGVVEEVSADYITVMADDGSR-- 658

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 659 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAVDRGETDPKGGLEEVLEELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 341


>gi|34391563|gb|AAN65359.1| RpoB [Mycobacterium fortuitum]
          Length = 1208

 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 719  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 777

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 778  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 835

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 836  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 884

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 885  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 944

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 945  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASRLPE------QLYSAP 997

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
              +                       VSTPVFDGA EE +  +L     +          
Sbjct: 998  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 1035

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1036 GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1095

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1096 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1155

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1156 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1186



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 222 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 279

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 280 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 339

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 340 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 399

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 400 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 459

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 460 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 519

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ + YL+A EE+   +AQANS +D
Sbjct: 520 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDQIDYLTADEEDRHVVAQANSPID 579

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 580 ADGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 639

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AG+VE+V A  I + + +G    
Sbjct: 640 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGVVEEVSADYITVMADDGSR-- 697

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 698 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 752

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 753 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 812

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 813 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 872

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 873 ESGKVIGIRVFSREDDD 889



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 68  RVSFAKLREPLEVPGLLDVQTDSFDWLVGADGWRQKAVDRGETDPKGGLEEVLEELSPIE 127

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 128 DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 178

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 179 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 236

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 237 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 296

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 297 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 347

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 348 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 380


>gi|317125882|ref|YP_004099994.1| DNA-directed RNA polymerase subunit beta [Intrasporangium calvum DSM
            43043]
 gi|315589970|gb|ADU49267.1| DNA-directed RNA polymerase subunit beta [Intrasporangium calvum DSM
            43043]
          Length = 1150

 Score =  520 bits (1338), Expect = e-145,   Method: Composition-based stats.
 Identities = 191/512 (37%), Positives = 262/512 (51%), Gaps = 63/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++       G   M     LL A    +  +  D  +     V   V+
Sbjct: 666  VVNEGDRVETGGVIADGPATDG-GEMALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 724

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H +D  +  +  E     I  ++ D     DE+ I+      R  ++L G+  
Sbjct: 725  SSIHIEEHEVDARDTKLGPEEITRDIPNVSEDVLADLDERGIIRVGAEVRDGDLLVGKVT 784

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 785  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGTVIGV 827

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  +   GDD+PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DG
Sbjct: 828  KEFRADLGDDLPPGVNQLVRVYVANKRKITDGDKLAGRHGNKGVISKILPVEDMPFLEDG 887

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNP GVP RMN+GQI E HLGWA    G KI+      K               
Sbjct: 888  TPVDVILNPHGVPRRMNLGQILELHLGWAA-NRGWKIEGNPEWAK--------------- 931

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM--------AD 1227
                             +   A +   G  V+TPVFDGA E+ +  +L            
Sbjct: 932  ----------------QIPADAHEAPPGSRVATPVFDGASEDVVTGLLDSTLKTRDGVRL 975

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D +G++ L+DG +GEPF  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 976  IDGTGKTRLFDGRSGEPFPEPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1035

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G PESF
Sbjct: 1036 QFGGQRFGEMEVWALEAYGAAYTLQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIPESF 1095

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++ NS        E   +
Sbjct: 1096 KVLLKEMQSLCLNVEVLNSEGTTIEMKESDEE 1127



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 334/686 (48%), Positives = 464/686 (67%), Gaps = 28/686 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    I      G ++  +I   +   + ++         
Sbjct: 156 LVRSPGVYFERTPDKTSDKDIYTTKIIPSR--GAWLEFEIDKRDMVGVRVDRKRKQSVTV 213

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +   +   +R TL  D  + + DALLDIYR +RPG+  T   A
Sbjct: 214 L--LKALGWTEAQIL--EEFGDFESMRLTLEKDHTQGQDDALLDIYRKLRPGEPPTKEAA 269

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
           +++ + L+F+  +YDL+ VGR K+N +L LD   +   +  +DI+A IK LV L +G+  
Sbjct: 270 QTLLDNLYFNPKRYDLAKVGRYKINKKLGLDGSINDSTLAIDDIVATIKFLVTLHDGRDS 329

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDID+ GNRR+RSVGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 330 MQGVKNGEPIDVRVEVDDIDHFGNRRLRSVGELIQNQVRTGLSRMERVVRERMTTQDVEA 389

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E
Sbjct: 390 ITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGISRDRAQME 449

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVH +HYGR+CP ET EG NIGL+ SL S+ R+NA+GFIETPYRKV +G V+++V YL
Sbjct: 450 VRDVHHSHYGRMCPIETPEGPNIGLIGSLASYGRINAFGFIETPYRKVNEGVVSDEVHYL 509

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA EE+   +AQAN+ +DEDG F E+ V  R  GE  L+P E +D++D SP+Q+VS A +
Sbjct: 510 SADEEDKYVVAQANARVDEDGRFAEDRVLVRRKGEVELIPGEDVDYMDVSPRQMVSAATA 569

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+K+EAP VGTGME   A  SG  + A++AG+V++
Sbjct: 570 MIPFLEHDDANRALMGANMQRQAVPLVKSEAPLVGTGMEFRAALDSGDVVRAEKAGVVQE 629

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  + + + +G           YR+ KF RSNQ T  NQ  +V  GD V    +IADG
Sbjct: 630 VSADLVTVANDDGT-------YQTYRIAKFARSNQGTSYNQVVVVNEGDRVETGGVIADG 682

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+TD G++ALGRN+LVAFM W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLG
Sbjct: 683 PATDGGEMALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLG 742

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEITRDIPNVSE+ L ++DE GII VGAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 743 PEEITRDIPNVSEDVLADLDERGIIRVGAEVRDGDLLVGKVTPKGETELTPEERLLRAIF 802

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVR 943
           GEKA +VRDTSL+VP G +GTV+ V+
Sbjct: 803 GEKAREVRDTSLKVPHGETGTVIGVK 828



 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 105/412 (25%), Positives = 179/412 (43%), Gaps = 48/412 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMN--------IAPDERPN----EGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  L              + R +     GL+  F+ 
Sbjct: 10  RLSFAKIREPLEVPDLLALQTESFDWLLGNERWQARVAAAKAEGRTDVPDRSGLEEIFEE 69

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+  +  ++ C  RD TY  PL +T   +            
Sbjct: 70  ISPIEDFSGSMSLSFRDHRFEETRKTIEACKERDQTYDAPLFVTAEFM---------NAQ 120

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K +Y 
Sbjct: 121 TGEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTPDKT--SDKDIYT 178

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W++ E D +D++ VR+DR+RK  VT  L ALG    +IL  F         
Sbjct: 179 TKIIPSRGAWLEFEIDKRDMVGVRVDRKRKQSVTVLLKALGWTEAQILEEFGDFESMRLT 238

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +       +  GE    E+ + L   L  + K   +  +G   
Sbjct: 239 LEKDHTQGQDDALLDIYR------KLRPGEPPTKEAAQTLLDNLYFNPKRYDLAKVGRYK 292

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                       +N + G   ++        ++++I  + I+ +  L+ D  ++   ++N
Sbjct: 293 ------------INKKLG---LDGSINDSTLAIDDIV-ATIKFLVTLH-DGRDSMQGVKN 335

Query: 361 TLVTDKNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
               D   +  D      R +R  G++    V   +        ++     V
Sbjct: 336 GEPIDVRVEVDDIDHFGNRRLRSVGELIQNQVRTGLSRMERVVRERMTTQDV 387


>gi|145596444|ref|YP_001160741.1| DNA-directed RNA polymerase subunit beta [Salinispora tropica
           CNB-440]
 gi|145305781|gb|ABP56363.1| DNA-directed RNA polymerase, beta subunit [Salinispora tropica
           CNB-440]
          Length = 1143

 Score =  520 bits (1338), Expect = e-144,   Method: Composition-based stats.
 Identities = 331/600 (55%), Positives = 440/600 (73%), Gaps = 10/600 (1%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  +  TL  D    + +ALLDIYR +RPG+  T   A+++ + LFF+  +YD++ VGR 
Sbjct: 235 SELMMTTLEKDHIASQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRY 294

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLK 472
           K N +L LD   D   + ++DI+A ++ L  L  G+     DDID+ GNRR+R+VGE+++
Sbjct: 295 KFNKKLELDLSIDTGVLTQDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQ 354

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 355 NQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPL 414

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ +L++FARV
Sbjct: 415 AGLTHRRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGALSTFARV 474

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-G 651
           N +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ L  DGSF EE V  R   G
Sbjct: 475 NPFGFIETPYRKVVDGRVTDQIDYLTADEEDRFVKAQANAPLRADGSFAEERVLVRRKGG 534

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E   VP   +D++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPL+KAEAP V
Sbjct: 535 ETEDVPPAAVDYMDVSPRQMTSVATAMIPFLEHDDANRALMGANMQRQAVPLVKAEAPLV 594

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  +VA+  G+VE + A  I +   +G           Y L KF+RSN
Sbjct: 595 GTGMEYRAAVDAGDVVVAEFGGVVEDLCADYITVHQDDGHR-------RTYLLHKFRRSN 647

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +CVNQ+P+V  GD V    +IADGP TD G++ALGRN+LVAFM W G+N+ED++++S+
Sbjct: 648 AGSCVNQKPVVFEGDRVEAGQVIADGPCTDDGEMALGRNLLVAFMTWEGHNYEDAIILSQ 707

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV TSIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GAEV PG
Sbjct: 708 RLVQQDVLTSIHIEEHEVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPG 767

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           D+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ VR F+R   D
Sbjct: 768 DVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSREDGD 827



 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/508 (37%), Positives = 269/508 (52%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++        +  M     LL A    +  +  D  +     V   V+
Sbjct: 657  VVFEGDRVEAGQVIADGPCT-DDGEMALGRNLLVAFMTWEGHNYEDAIILSQRLVQQDVL 715

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 716  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDVLVGK 773

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 774  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSR-------- 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 824  -EDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 882

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                   
Sbjct: 883  IVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLQAIS------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--RMAD------LDES 1231
                             A++ +    V+TPVFDGA EE I+ +L    A+      +  S
Sbjct: 930  -----------------ADESEPDSNVATPVFDGAREEEISGLLASTRANRDGKQLIGSS 972

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP   P+ VGYIY+LKLNH+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 973  GKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1032

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1033 QRFGEMECWAMQAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLL 1092

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        E   +
Sbjct: 1093 KELQSLCLNVEVLSSDGVALEMRETDDE 1120



 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 102/469 (21%), Positives = 190/469 (40%), Gaps = 28/469 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNEGLQAAFKSVFPITAF 68
           R  FG+  E +++P+L+ +Q  S+D  +         A D     GL      + PI  F
Sbjct: 20  RVSFGRITEHLEVPNLLAIQTESFDWLVGNEAWQGRSADDPHARSGLAEILDEISPIEDF 79

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           SG   L F +  FD  K  +++C  +DLTY  PL +T               +  +IK Q
Sbjct: 80  SGTMSLSFSAPRFDEVKASIEECKEKDLTYCAPLFVTAEFT---------NNTTGEIKSQ 130

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   S + L + ++IP +
Sbjct: 131 TVFMGDFPMMTPKGTFIINGTERVVVSQLVRSPGVYFDKQPDKT--SDRDLSSVKVIPSR 188

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWC 246
           G W++ + D ++ + VRIDR+R+  VT  L A+G  +E+I   F    +   +   D   
Sbjct: 189 GAWLEFDIDKRETVGVRIDRKRRQAVTVLLKAIGWTAEQIRERFGWSELMMTTLEKDHIA 248

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +            +  + ++++         + K  + K  K L +      
Sbjct: 249 SQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLELDLSIDT 308

Query: 305 GLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G+   +DIV   E         +  +   ++   +  +R +  L  + V         +V
Sbjct: 309 GVLTQDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVV 368

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            ++   +   +  I            +  +  F            + +  +    RL+  
Sbjct: 369 RERMTTQD--VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHRRRLSAL 426

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 427 GPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGALST 470


>gi|295094083|emb|CBK83174.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Coprococcus
            sp. ART55/1]
          Length = 725

 Score =  520 bits (1338), Expect = e-144,   Method: Composition-based stats.
 Identities = 190/569 (33%), Positives = 275/569 (48%), Gaps = 47/569 (8%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            ++   A+   M  + +   G   + ++     +V++      +    EV  R  + G ++
Sbjct: 132  NMQRQAVPLMMTESAVVGTGMEAKAAVDSGVCVVAKRDGVVEYSNSTEVCVRADEDGTKD 191

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            +   I          +++  I+  G  V  G+++    +  G   +   +  L      +
Sbjct: 192  VYHIIKFARSNQGNCMNQRPIVFKGDHVKAGEVIADGPSTSG-GEIALGKNPLIGFMTWE 250

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD-------- 972
              +  D  L     +S  +V   ++    I+K E      +   E + RD          
Sbjct: 251  GYNYEDAVL-----LSERLVQDDVYTSIHIEKYECEARDTKLGKEEITRDLAGLSNDVLK 305

Query: 973  --DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      R  +IL G+    G         L   +  E  R            
Sbjct: 306  DLDENGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAR------------ 353

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 E      +            K+     GDD+P GV + V+V++A KR IQ GDKM
Sbjct: 354  -----EVRDTSLKVPHGAFGIVIDAKVFTRADGDDLPAGVDKKVRVYIAQKRKIQVGDKM 408

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG+VSR+LP EDMPFL +G P+DIVLNPLGVPSRMN+GQ+ E HLG A   LG 
Sbjct: 409  AGRHGNKGVVSRVLPVEDMPFLPNGRPLDIVLNPLGVPSRMNIGQVLEIHLGLASQVLGF 468

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            K+ + + +     DI             G+  +  + Y D     V +            
Sbjct: 469  KVSTPVFNGATEFDIMDTLEMAND-YANGTWEDFEAKYKDTVKPEVMDYLY--------- 518

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                      +  +   ++ +G+  L DG TGE FD PVT+GY++ LKL+H+V DK++AR
Sbjct: 519  ----TNRDHRAEWKGVPINRTGKVQLRDGRTGENFDAPVTIGYMHYLKLHHLVDDKIHAR 574

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE+LT+KSDDVVGR + YE
Sbjct: 575  STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEILTVKSDDVVGRVKTYE 634

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            +I+ G++    G PESF VL+KE QALGL
Sbjct: 635  AIIKGDNIPAPGVPESFKVLLKEFQALGL 663



 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 213/413 (51%), Positives = 291/413 (70%), Gaps = 18/413 (4%)

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEE 623
           +CP ET EG NIGL++SL ++AR+N YGF+E PYRK+      +  VT++VVYL+A EE+
Sbjct: 1   MCPIETPEGPNIGLINSLATYARINEYGFVEAPYRKLDKTDPSNPVVTDEVVYLTADEED 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              + QAN  +DE+G F +  V  R   +    P+ K+D +D SPK V S+A S+IPFL+
Sbjct: 61  RYRVVQANEPIDENGHFVKNNVSGRFRADTTEFPKSKVDLMDVSPKMVFSVATSMIPFLQ 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           NDD+NR LMG NMQRQAVPL+  E+  VGTGME+  A  SG  +VAKR G+VE  ++  +
Sbjct: 121 NDDANRALMGSNMQRQAVPLMMTESAVVGTGMEAKAAVDSGVCVVAKRDGVVEYSNSTEV 180

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            +R+ E          D+Y ++KF RSNQ  C+NQRP+V  GD V+  ++IADGPST  G
Sbjct: 181 CVRADE------DGTKDVYHIIKFARSNQGNCMNQRPIVFKGDHVKAGEVIADGPSTSGG 234

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           ++ALG+N L+ FM W GYN+ED++L+SER+V +DV+TSIHIE++E  ARDTKLG EEITR
Sbjct: 235 EIALGKNPLIGFMTWEGYNYEDAVLLSERLVQDDVYTSIHIEKYECEARDTKLGKEEITR 294

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           D+  +S + LK++DE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +
Sbjct: 295 DLAGLSNDVLKDLDENGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKARE 354

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           VRDTSL+VP G  G V+D ++F R        G+DK  R    ++ +I++  +
Sbjct: 355 VRDTSLKVPHGAFGIVIDAKVFTRADGDDLPAGVDKKVRVYIAQKRKIQVGDK 407


>gi|238061130|ref|ZP_04605839.1| DNA-directed RNA polymerase, beta subunit [Micromonospora sp. ATCC
            39149]
 gi|237882941|gb|EEP71769.1| DNA-directed RNA polymerase, beta subunit [Micromonospora sp. ATCC
            39149]
          Length = 1143

 Score =  520 bits (1338), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/508 (37%), Positives = 263/508 (51%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++        E  M     LL A    +  +  D  +     V   V+
Sbjct: 657  VVFEGDRVEAGQVIADGPCT-DEGEMALGRNLLVAFMCWEGHNYEDAIILSQRLVQQDVL 715

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 716  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDILVGK 773

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 774  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSR-------- 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 824  -EDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 882

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                   
Sbjct: 883  IVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A + +    V+TPVFDGA EE I+ +L     +          
Sbjct: 930  -----------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIGSS 972

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP   P+ VGYIY+LKLNH+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 973  GKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1032

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1033 QRFGEMECWAMQAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLL 1092

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        E   +
Sbjct: 1093 KELQSLCLNVEVLSSDGVALEMRETDDE 1120



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 325/592 (54%), Positives = 434/592 (73%), Gaps = 10/592 (1%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    + +ALLDIYR +RPG+  T   A+++ + LFF+  +YD++ VGR K N +L L
Sbjct: 243 EKDHIAGQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLEL 302

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             P     + ++DI+A ++ L  L  G+     DDID+ GNRR+R+VGE+++NQ R+GL 
Sbjct: 303 SVPITTGTLTEDDIVATVEYLCRLHAGEDGYEADDIDHFGNRRLRTVGELIQNQVRVGLS 362

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RR
Sbjct: 363 RMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHRRR 422

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ +L++FARVN +GFIET
Sbjct: 423 LSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGALSTFARVNPFGFIET 482

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPRE 659
           PYRKV DG+VT+ + YL+A EE+    AQAN+ L  DG+F E+ V  R   GE   V   
Sbjct: 483 PYRKVVDGRVTDQIDYLTADEEDRFVKAQANAPLKADGTFVEDRVLVRRKGGETEDVAPG 542

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +D++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPL+KAE+P VGTGME   
Sbjct: 543 AVDYMDVSPRQMTSVATAMIPFLEHDDANRALMGANMQRQAVPLVKAESPLVGTGMEYRA 602

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  +G  +VA+  G++E + A  I I   +G           Y L KF+RSN  +CVNQ+
Sbjct: 603 AVDAGDVVVAEVGGVIEDLCADYITIHQDDGHR-------RTYLLHKFRRSNAGSCVNQK 655

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V  GD V    +IADGP TD G++ALGRN+LVAFM W G+N+ED++++S+R+V +DV 
Sbjct: 656 PVVFEGDRVEAGQVIADGPCTDEGEMALGRNLLVAFMCWEGHNYEDAIILSQRLVQQDVL 715

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GAEV PGDILVGK+T
Sbjct: 716 TSIHIEEHEVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDILVGKVT 775

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ VR F+R   D
Sbjct: 776 PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSREDGD 827



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 104/469 (22%), Positives = 189/469 (40%), Gaps = 28/469 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNEGLQAAFKSVFPITAF 68
           R  FG+  E +++P+L+ +Q  S+D  +         A D     GL      + PI  F
Sbjct: 20  RVSFGRITEHLEVPNLLAIQNESFDWLVGNEAWQGRSADDPHARSGLAEILDEISPIEDF 79

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           SG   L F +  FD  K  +++C  +DLTY  PL +T               +  +IK Q
Sbjct: 80  SGTMSLSFSAPRFDEVKASIEECKEKDLTYCAPLFVTAEFT---------NNTTGEIKSQ 130

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   S + L + ++IP +
Sbjct: 131 TVFMGDFPMMTPKGTFIINGTERVVVSQLVRSPGVYFDKQPDKT--SDRDLSSVKVIPSR 188

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWC 246
           G W++ + D +D + VRIDR+R+  VT  L A+G  +E I   F    +   +   D   
Sbjct: 189 GAWLEFDIDKRDTVGVRIDRKRRQAVTVLLKAIGWSAERIREKFGWSELLMTTLEKDHIA 248

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +            +  + ++++         + K  + K  K L ++     
Sbjct: 249 GQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLELSVPITT 308

Query: 305 GLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G    +DIV   E         D  +   ++   +  +R +  L  + V         +V
Sbjct: 309 GTLTEDDIVATVEYLCRLHAGEDGYEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVV 368

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            ++   +   +  I            +  +  F            + +  +    RL+  
Sbjct: 369 RERMTTQD--VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHRRRLSAL 426

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 427 GPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGALST 470


>gi|297571943|ref|YP_003697717.1| DNA-directed RNA polymerase subunit beta [Arcanobacterium
            haemolyticum DSM 20595]
 gi|296932290|gb|ADH93098.1| DNA-directed RNA polymerase, beta subunit [Arcanobacterium
            haemolyticum DSM 20595]
          Length = 1154

 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 194/600 (32%), Positives = 280/600 (46%), Gaps = 72/600 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS---------ERMVSEDVFTSIHIEEFEVM 850
                       ++    P+ G   E    +            +V+E     +H+EE    
Sbjct: 584  MGANMQRQAVPLIRPVAPYVGTGIESRAAVDAGEVIVAKAPGVVTEVSADIVHVEEDNGT 643

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV--GAEVNPGDILVGKITPKGESPMTP 908
             R  KL   E +                  I+ V  G  V  G ++       G   +  
Sbjct: 644  HRVYKLLKFERSNPGNCT----------NQIVRVSEGDRVEKGSLIADGPATDG-GELAL 692

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL-L 967
             + LL A       +  D  +      S  ++       H  + + R   +  E+I   +
Sbjct: 693  GQNLLVAFMAWNGYNYEDAIILSQRCQSEDLLTSIHIEEH--EVDARDTKLGPEEITRDI 750

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                +D    LD     R+   +   + + G    K  T L+S+      R+ + + A +
Sbjct: 751  PNVGEDMLAHLDDRGIIRIGAEVSAGDILVGKITPKGETELTSE--ERLLRAIFGEKAKE 808

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                   V   +                     +  D++   V + V+V +A +R I  G
Sbjct: 809  VRDTSLRVPHGESGIVIGVKEFSS---------ENHDELAADVRQTVRVHIAQRRKITIG 859

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++SRILP EDMPF+ DGTPVDIVLNPLGVPSRMN+GQ+FE HLGW    
Sbjct: 860  DKMAGRHGNKGVISRILPLEDMPFMADGTPVDIVLNPLGVPSRMNLGQVFELHLGWVAS- 918

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
                            D +  R   E+                  +   A   K+   V+
Sbjct: 919  -------------QGWDATTAREAGEEWA--------------VRLPENAVVGKAQGRVA 951

Query: 1208 TPVFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG +   +  +L    ++          G++ L+DG TG+PF  PV+VGY+YMLKL
Sbjct: 952  TPVFDGVESNELRGLLENTTVNRDGDRLIGASGKAQLFDGRTGDPFPEPVSVGYMYMLKL 1011

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS+VTQQPLGGK+  GGQR GEMEVW ++AYGA++ LQEMLTIKS
Sbjct: 1012 HHLVDDKIHARSTGPYSMVTQQPLGGKAQFGGQRFGEMEVWALEAYGASHTLQEMLTIKS 1071

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DD VGR +VYE+IV G++  E G PESF VLV+EM++L L+++  ++        +   D
Sbjct: 1072 DDTVGRVKVYEAIVKGDNVPEPGIPESFKVLVQEMRSLCLNVEALDAAGNPINLQDSDDD 1131



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 316/693 (45%), Positives = 456/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S       +     +K +    +      G ++  +I   +T  + ++         
Sbjct: 157 LVRSPGVYFERMADKTSDKYIYSTKVIPSR--GAWLEFEIDKRDTVGVRVDRKRKQSATV 214

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +    + +  I   +   +   + +TL  D  K ++DAL D+YR +RPG+  T    
Sbjct: 215 F--LKALGMSEAEI--REEFKDFPILLDTLDKDTVKTQEDALQDLYRKLRPGEPPTAEAG 270

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++ N  + +  +YD++ VGR K+N +L  +   D R ++ +D+ A ++ L+ L   + T
Sbjct: 271 RALINNFYHNPKRYDMAKVGRYKINKKLGTEIEMDKRQLQLQDVTATLRYLLALHANETT 330

Query: 453 I-------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I             DDID+ GNRR+R+VGE+++NQ R GL R++R ++ER+++ + +++ 
Sbjct: 331 IATVEGGREVPVETDDIDHFGNRRIRAVGELIQNQVRTGLARLDRMVRERMTTQEAEAIT 390

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +P+V+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E+R
Sbjct: 391 PSSLINIRPIVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRASMEVR 450

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVHP+HYGR+CP ET EG NIGL+ SL ++ RVNAYGFIETPYRKV DG+VT+ + YL A
Sbjct: 451 DVHPSHYGRMCPIETPEGPNIGLIGSLATYGRVNAYGFIETPYRKVVDGRVTDQIDYLDA 510

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAASL 678
            +E+   +AQA++SLD++G F ++ V  R   GE  LVP +++ ++D S +Q+VS+  + 
Sbjct: 511 ADEDRYNVAQASASLDDNGHFVDDEVLVRLPGGEPALVPADEVGYMDVSARQMVSVGTAA 570

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPL++  AP+VGTG+ES  A  +G  IVAK  G+V +V
Sbjct: 571 IPFLEHDDANRALMGANMQRQAVPLIRPVAPYVGTGIESRAAVDAGEVIVAKAPGVVTEV 630

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  + +    G          +Y+L+KF+RSN   C NQ   V  GD V +  +IADGP
Sbjct: 631 SADIVHVEEDNGT-------HRVYKLLKFERSNPGNCTNQIVRVSEGDRVEKGSLIADGP 683

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +TD G+LALG+N+LVAFM W+GYN+ED++++S+R  SED+ TSIHIEE EV ARDTKLGP
Sbjct: 684 ATDGGELALGQNLLVAFMAWNGYNYEDAIILSQRCQSEDLLTSIHIEEHEVDARDTKLGP 743

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV E+ L ++D+ GII +GAEV+ GDILVGKITPKGE+ +T EE+LLRAIFG
Sbjct: 744 EEITRDIPNVGEDMLAHLDDRGIIRIGAEVSAGDILVGKITPKGETELTSEERLLRAIFG 803

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G SG V+ V+ F+    D
Sbjct: 804 EKAKEVRDTSLRVPHGESGIVIGVKEFSSENHD 836



 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 88/293 (30%), Positives = 140/293 (47%), Gaps = 25/293 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD---ERPNEGLQAAFKSVFPITAFSG 70
           R  F K  E + +PDL+ +Q +SY   +  +   +   E    GL+  F  V PI   +G
Sbjct: 20  RVSFAKIHEPLSVPDLLGLQTSSYGWLIGSDEWRESAAEGEKSGLEEIFDEVSPIENTAG 79

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L       +  K  + +C  +DLTY+  L +T     ++           +IK Q+ 
Sbjct: 80  TMGLVLSQPHLEEEKASMAECKEKDLTYSAALYVTAEFQNYE---------TGEIKSQTT 130

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           ++GD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K +Y+ ++IP +G 
Sbjct: 131 FIGDFPLMTPQGTFIINGTERVVVSQLVRSPGVYFERMADKT--SDKYIYSTKVIPSRGA 188

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VR+DR+RK   T FL ALGM   EI   F  +P ++ +   D     
Sbjct: 189 WLEFEIDKRDTVGVRVDRKRKQSATVFLKALGMSEAEIREEFKDFPILLDTLDKDTVKTQ 248

Query: 249 LSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             A        +      +  GE    E+G+ L +    + K   +  +G   
Sbjct: 249 EDA--------LQDLYRKLRPGEPPTAEAGRALINNFYHNPKRYDMAKVGRYK 293


>gi|295837040|ref|ZP_06823973.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. SPB74]
 gi|295826331|gb|EDY45891.2| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. SPB74]
          Length = 1172

 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 263/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+     V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 686  IVNENDRVIVGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 744

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 745  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVIAGDILVG 801

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 802  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 844

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 845  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFL 904

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  +  D+             
Sbjct: 905  EDGTPVDIILNPLGVPSRMNPGQVMEIHLGWLASQ-GWDVSQVPEDWAQRLQAIS----- 958

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q +    V+TPVFDGA E+ +  +L     +   
Sbjct: 959  ------------------------ADQVEPRTNVATPVFDGAREDELAGLLEHTIPNRDG 994

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 995  DRMVQPTGKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1054

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1055 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1114

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1115 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1149



 Score =  507 bits (1305), Expect = e-141,   Method: Composition-based stats.
 Identities = 337/671 (50%), Positives = 454/671 (67%), Gaps = 39/671 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGQYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT-------------IDDIDNLGN 461
           K+N +L  + P D   +  +DI+A IK LV L  G+                DDID+ GN
Sbjct: 313 KVNKKLGSEAPLDAGVLTTDDILATIKYLVQLHAGETEASVGDEGKTIVVETDDIDHFGN 372

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQ
Sbjct: 373 RRLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQ 432

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIG
Sbjct: 433 LSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 492

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN+ L +D  F 
Sbjct: 493 LIGSLASYGRVNAFGFVETPYRKVIEGVVTDDVDYLTADEEDRFVIAQANAPLTDDLHFE 552

Query: 642 EELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQA
Sbjct: 553 EARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQA 612

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL+K+EAP VGTGME   A  +G  + A + G+V++V A  I   + +G          
Sbjct: 613 VPLIKSEAPIVGTGMEYRSATDAGDVLKADKDGVVQEVSADYITTANDDGT-------YT 665

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            YRL KF RSNQ T VNQ+ +V   D V    ++ADGP+T+ G++ALG+N+LVAFMPW G
Sbjct: 666 TYRLAKFSRSNQGTSVNQKVIVNENDRVIVGQVLADGPATENGEMALGKNLLVAFMPWEG 725

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           +N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE G
Sbjct: 726 HNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERG 785

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+
Sbjct: 786 IIRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVI 845

Query: 941 DVRIFNRHGID 951
            VR+F+R   D
Sbjct: 846 GVRVFDREEGD 856



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 104/325 (32%), Positives = 155/325 (47%), Gaps = 34/325 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 31  LRISFAKIREPLEVPNLLALQTESFDWLLGNDAWKSRVEAALAGGMSVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +Y+
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIYS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGQYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE    E+ + L   L  + K   +  +G 
Sbjct: 260 LEKDHTQGQDDA--------LLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGR 311

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYI 322
              +   G     D     T +I  
Sbjct: 312 YKVNKKLGSEAPLDAGVLTTDDILA 336


>gi|159039844|ref|YP_001539097.1| DNA-directed RNA polymerase subunit beta [Salinispora arenicola
           CNS-205]
 gi|157918679|gb|ABW00107.1| DNA-directed RNA polymerase, beta subunit [Salinispora arenicola
           CNS-205]
          Length = 1143

 Score =  519 bits (1337), Expect = e-144,   Method: Composition-based stats.
 Identities = 337/682 (49%), Positives = 464/682 (68%), Gaps = 16/682 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             ++ +  + +      G ++  DI   +T  + I+         
Sbjct: 159 LVRSSGVYFDKQPDKTSDRDLSSVKVIPSR--GAWLEFDIDKRDTVGVRIDRKRRQAVTV 216

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  +  TL  D    + +ALLDIYR +RPG+  T   A
Sbjct: 217 LLKAIGWSAEQI----REKFGWSELMMTTLEKDHIAGQDEALLDIYRKLRPGEPPTRENA 272

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++ + LFF+  +YD++ VGR K N +L+LD P D   + ++DI+A ++ L  L  G+  
Sbjct: 273 QTLLDNLFFNPKRYDVAKVGRYKFNKKLDLDLPIDTGVLTQDDIVATVEYLCRLHAGEEG 332

Query: 453 I--DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
              DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV
Sbjct: 333 YEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVV 392

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +A+ EFF +SQLSQ  +  N L+ +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+C
Sbjct: 393 AAIKEFFGTSQLSQFMDQTNPLAGLTHRRRLNALGPGGLSRERAGFEVRDVHPSHYGRMC 452

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL+ +L++FARVN +GFIETPYRKV DG+VT+ V YL+A +E+    AQA
Sbjct: 453 PIETPEGPNIGLIGNLSTFARVNPFGFIETPYRKVVDGRVTDQVDYLTADDEDRFVKAQA 512

Query: 631 NSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           N+ L+ DGSF E+ V  R   GE   V    +D++D SP+Q+VS+  ++IPFLE+DD+NR
Sbjct: 513 NAPLNADGSFAEDRVLVRRKGGETEDVAPSAVDYMDISPRQMVSVGTAMIPFLEHDDANR 572

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL+KAEAP VGTGME   A  +G  +VA+  G++E + A  + I   +
Sbjct: 573 ALMGANMQRQAVPLVKAEAPLVGTGMEYRAAVDAGDVVVAEVGGVIEDLCADYVTIHQDD 632

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G           Y L KF+RSN  +CVNQ+P+V  GD V    +IADGP TD G++ALGR
Sbjct: 633 GHR-------RTYLLHKFRRSNSGSCVNQKPVVFEGDRVEAGQVIADGPCTDEGEMALGR 685

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVAFM W GYN+ED++++S+R+V +DV TSIHIEE EV ARDTKLGPEEITRDIPNVS
Sbjct: 686 NLLVAFMTWEGYNYEDAIILSQRLVQQDVLTSIHIEEHEVDARDTKLGPEEITRDIPNVS 745

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE L ++DE GII +GAEV PGD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL
Sbjct: 746 EEMLADLDERGIIRIGAEVVPGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSL 805

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           +VP G +GTV+ VR F+R   D
Sbjct: 806 KVPHGETGTVIGVRTFSREDGD 827



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/508 (37%), Positives = 267/508 (52%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++        E  M     LL A    +  +  D  +     V   V+
Sbjct: 657  VVFEGDRVEAGQVIADGPCT-DEGEMALGRNLLVAFMTWEGYNYEDAIILSQRLVQQDVL 715

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 716  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDVLVGK 773

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 774  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSR-------- 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 824  -EDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 882

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                   
Sbjct: 883  IVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLQAIG------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                             A++ +    V+TPVFDGA EE I+ +L            +  S
Sbjct: 930  -----------------ADESEPDSNVATPVFDGAREEEISGLLASTRSNRDGKQLIGSS 972

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP   P+ VGYIY+LKLNH+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 973  GKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1032

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1033 QRFGEMECWAMQAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLL 1092

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        E   +
Sbjct: 1093 KELQSLCLNVEVLSSDGVALEMRETDDE 1120



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 102/469 (21%), Positives = 188/469 (40%), Gaps = 28/469 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNEGLQAAFKSVFPITAF 68
           R  FG+  E +++P+L+ +Q  S+D  +         A D     GL      + PI  F
Sbjct: 20  RVSFGRITEHLEVPNLLAIQTESFDWLVGNEAWQGRSADDPHARSGLAEILDEISPIEDF 79

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           SG   L F +  FD  K  +++C  +DLTY  PL +T               +  +IK Q
Sbjct: 80  SGTMSLSFSAPRFDEVKASIEECKEKDLTYCAPLFVTAEFT---------NNTTGEIKSQ 130

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +++MGD P+MT  GTF+I G +R+V SQL RS G++FD    +   S + L + ++IP +
Sbjct: 131 TVFMGDFPMMTPKGTFIINGTERVVTSQLVRSSGVYFDKQPDKT--SDRDLSSVKVIPSR 188

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWC 246
           G W++ + D +D + VRIDR+R+  VT  L A+G  +E+I   F    +   +   D   
Sbjct: 189 GAWLEFDIDKRDTVGVRIDRKRRQAVTVLLKAIGWSAEQIREKFGWSELMMTTLEKDHIA 248

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +            +  + ++++         + K  + K  K L +      
Sbjct: 249 GQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLDLDLPIDT 308

Query: 305 GLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G+   +DIV   E         +  +   ++   +  +R +  L  + V         +V
Sbjct: 309 GVLTQDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVV 368

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            ++   +   +  I            +  +  F            + +  +    RLN  
Sbjct: 369 RERMTTQD--VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHRRRLNAL 426

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 427 GPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGNLST 470


>gi|240167668|ref|ZP_04746327.1| DNA-directed RNA polymerase subunit beta [Mycobacterium kansasii
           ATCC 12478]
          Length = 1173

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 456/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL  
Sbjct: 207 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSERI----TERFGFSEIMMSTLEK 262

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L+T
Sbjct: 263 DNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLNT 322

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 323 NHPITTTTLTEEDVVATIEYLVRLHEGQATMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 382

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 383 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 442

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 443 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 502

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG VT+++ YL+A EE+   +AQANS +D +G F E  V  R  
Sbjct: 503 RVNPFGFIETPYRKVIDGLVTDEIHYLTADEEDRHVVAQANSPIDAEGRFVEPRVLVRRK 562

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 563 AGEVEYVASSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 622

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+++G++E+V A  I + + +G           YR+ KF R
Sbjct: 623 LVGTGMELRAAIDAGDVVVAEKSGVIEEVSADYITVMADDGTR-------HTYRMRKFAR 675

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  G+ V    +IADGP T  G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 676 SNHGTCANQSPIVDAGERVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIIL 735

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V ED+ TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV 
Sbjct: 736 SNRLVEEDILTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVR 795

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 796 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 855

Query: 950 ID 951
            D
Sbjct: 856 DD 857



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 185/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   ++
Sbjct: 687  IVDAGERVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDIL 745

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 746  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 803

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 804  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 852

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DGTPVD
Sbjct: 853  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDGTPVD 912

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +      
Sbjct: 913  IILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI----- 966

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                      VSTPVFDGA E  +  +L     +          
Sbjct: 967  --------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVLVDGD 1000

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1001 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1060

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1061 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1120

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1121 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1153



 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 98/337 (29%), Positives = 153/337 (45%), Gaps = 32/337 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE--------GLQAAFKSV 62
           R  F K  E +++P L++VQ  S++  +      D    R           GL+     +
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSQRWRDSAIARGEAAGGINPIGGLEEVLDEL 91

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           + 
Sbjct: 92  SPIEDFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNT 142

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ 
Sbjct: 143 GEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSV 200

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           ++IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE I   F    +     
Sbjct: 201 KVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSERITERFGFSEIMMSTL 260

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
           +      +   L+   +       +  GE    ES + L   L    K   +  +G    
Sbjct: 261 EKDNTAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK- 313

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
                 +  +  +  T     E   V   + L  +  
Sbjct: 314 --VNKKLGLNTNHPITTTTLTEEDVVATIEYLVRLHE 348


>gi|309812270|ref|ZP_07706025.1| DNA-directed RNA polymerase, beta subunit [Dermacoccus sp. Ellin185]
 gi|308433575|gb|EFP57452.1| DNA-directed RNA polymerase, beta subunit [Dermacoccus sp. Ellin185]
          Length = 1161

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 184/512 (35%), Positives = 260/512 (50%), Gaps = 63/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF---GEKAVDVRDTSLRVPSGVSG 937
            ++  G  +  G ++       G   M+  + LL A     G    D    S R+    + 
Sbjct: 677  VVNEGERLEEGAVIADGPATDG-GEMSLGKNLLVAFMPWEGYNYEDAIILSQRLVQDDTL 735

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD--EQVILDRNIYSRLMEILCGQNA 995
            + + +        D       + R+   +      D  E+ I+      R  ++L G+  
Sbjct: 736  SSIHIEEHEIDARDTKLGPEEITRDIPNVSDEVLADLDERGIIRVGAEVRDGDLLVGKVT 795

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 796  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGTVIGV 838

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+     GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DG
Sbjct: 839  KVFDRDEGDELPPGVNQLVRVYVANKRKITDGDKLAGRHGNKGVISKILPVEDMPFLEDG 898

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+VLNPLGVPSRMN GQ+ E H+GWA    G KI+                      
Sbjct: 899  TPVDVVLNPLGVPSRMNPGQVLELHMGWAAS-RGWKIEGDPEWAAK-------------- 943

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                             +   A +      ++TPVFDGA E  I  +L   +        
Sbjct: 944  -----------------IPADARETGPNTRIATPVFDGARETEIRGLLESTNTTRDGVRL 986

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            + +SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 987  IGDSGKAQLFDGRSGEPFPEPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1046

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF
Sbjct: 1047 QFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESF 1106

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++ +S        +   +
Sbjct: 1107 KVLIKEMQSLCLNVEVLSSDGTAIDLRDSEQE 1138



 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 329/695 (47%), Positives = 463/695 (66%), Gaps = 29/695 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K +    +      G ++  +I   +   + ++         
Sbjct: 166 LVRSPGVYFERSIDKTSDKEIYTAKVIPSR--GAWLEFEIDKRDMVGVRVDRKRKQSVTV 223

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       +R TL  D   D+  ALL+IYR +RPG+  T   A
Sbjct: 224 L--LKALGWTEAQIL--EEFGQYESMRATLEKDHTADQDAALLEIYRKLRPGEPPTREAA 279

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
           + + + L+F+  +YDL+ VGR K+N +L +D   +   +  +DI+A IK +V L  G+  
Sbjct: 280 QQLLDNLYFNGKRYDLAKVGRYKVNKKLGVDGGLEDSTLGIDDIVATIKYIVALHAGEET 339

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 340 MKGTRHGEEIDVRVEIDDIDHFGNRRLRNVGELIQNQVRTGLSRMERVVRERMTTQDVEA 399

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 400 ITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 459

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N +GF+ETPYRKV DG+VT+DV YL
Sbjct: 460 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINPFGFVETPYRKVVDGQVTDDVDYL 519

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAA 676
           SA EE+   IAQAN+ L  D  F E+ V  R   GE   V  E +D++D S +Q+VS A 
Sbjct: 520 SADEEDTFVIAQANAPLTPDNHFAEDRVMARTKGGEASDVAIEDVDYMDVSARQMVSAAT 579

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           +LIPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTG+E   A  SG  + A +AG+V+
Sbjct: 580 ALIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGIEYRAALDSGDVVRATKAGVVQ 639

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +V A  + + + +       +    YR+ KF RSNQ TC NQR +V  G+ +    +IAD
Sbjct: 640 EVSADLVTVANDD-------ATYSTYRIAKFTRSNQGTCYNQRVVVNEGERLEEGAVIAD 692

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GP+TD G+++LG+N+LVAFMPW GYN+ED++++S+R+V +D  +SIHIEE E+ ARDTKL
Sbjct: 693 GPATDGGEMSLGKNLLVAFMPWEGYNYEDAIILSQRLVQDDTLSSIHIEEHEIDARDTKL 752

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITRDIPNVS+E L ++DE GII VGAEV  GD+LVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 753 GPEEITRDIPNVSDEVLADLDERGIIRVGAEVRDGDLLVGKVTPKGETELTPEERLLRAI 812

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA +VRDTS++VP G +GTV+ V++F+R   D
Sbjct: 813 FGEKAREVRDTSMKVPHGETGTVIGVKVFDRDEGD 847



 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 99/302 (32%), Positives = 151/302 (50%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI--------APDERPN----EGLQAAFKS 61
           R  F K  E ++IPDL+ +Q  S+D  L              + R +     GL+  F+ 
Sbjct: 20  RLTFAKIREPLEIPDLLALQTESFDWLLGNEKWQARVAAAKSEGRVDVPERSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+  K+ +++C  RD+TYA PL +T   +            
Sbjct: 80  ISPIEDFSGSMSLSFRDHRFEDVKYSIEECKERDMTYAAPLFVTAEFM---------NAE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K +Y 
Sbjct: 131 TGEIKSQTVFMGDFPLMTDRGTFVINGTERVVVSQLVRSPGVYFERSIDKT--SDKEIYT 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D +D++ VR+DR+RK  VT  L ALG    +IL  F  Y  +  +
Sbjct: 189 AKVIPSRGAWLEFEIDKRDMVGVRVDRKRKQSVTVLLKALGWTEAQILEEFGQYESMRAT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       AA L +  K+         GE    E+ ++L   L  + K   +  +G 
Sbjct: 249 LEKD-HTADQDAALLEIYRKL-------RPGEPPTREAAQQLLDNLYFNGKRYDLAKVGR 300

Query: 299 TS 300
             
Sbjct: 301 YK 302


>gi|54027073|ref|YP_121315.1| DNA-directed RNA polymerase subunit beta [Nocardia farcinica IFM
            10152]
 gi|81373140|sp|Q5YPE0|RPOB2_NOCFA RecName: Full=DNA-directed RNA polymerase subunit beta 2; Short=RNAP
            subunit beta 2; AltName: Full=RNA polymerase subunit beta
            2; AltName: Full=Transcriptase subunit beta 2
 gi|54018581|dbj|BAD59951.1| putative RNA polymerase beta subunit [Nocardia farcinica IFM 10152]
          Length = 1163

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 193/538 (35%), Positives = 274/538 (50%), Gaps = 56/538 (10%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGTRKSYRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
            I   +  +  D  +     V   V+       H  + + R   +  E+I     +  DE 
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEV 767

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 768  LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 820

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++      ++   +  DD+PPGV  +V+V+VA KR IQ GDK+AGRH
Sbjct: 821  DTSLKVPHGESGKVI----GIRVFSREDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRH 876

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQI ETHLGW     G K++ 
Sbjct: 877  GNKGVIGKILPTEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIGKA-GWKVEG 935

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                 K                                +     +  +   ++TPVFDGA
Sbjct: 936  NPEWAK-------------------------------DLPEEMWEAPADSNIATPVFDGA 964

Query: 1215 DEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE +  +L     +  G        +++L+DG +GEPF  PV VGY+Y+LKL+H+V DK
Sbjct: 965  REEELTGLLGSTLPNRDGERMVDDNGKAVLFDGRSGEPFPYPVAVGYMYILKLHHLVDDK 1024

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1025 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRV 1084

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1085 KVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1142



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 335/694 (48%), Positives = 465/694 (67%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 166 LVRSPGVYFDHSIDKGTEKDLHSVRVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 223

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +       +I     +    +  + +TL  D    + +ALLDIYR +RPG+  T   A
Sbjct: 224 LLKALGWTTEEIA----ERFGFSEIMMSTLEKDNTAGQDEALLDIYRKLRPGEPPTKESA 279

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG- 449
           +++   LFF   +YDL+ VGR K+N +L +    P     + KEDI+  I+ LV L  G 
Sbjct: 280 QTLLENLFFKEKRYDLARVGRYKINKKLGIHVGEPVTGSVLTKEDIVTTIEYLVRLHAGD 339

Query: 450 -----------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
                         +DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++
Sbjct: 340 KTMTAPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAI 399

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 400 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 459

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG+VT++VVYL+
Sbjct: 460 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGRVTDEVVYLT 519

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+    AQANS +  DG F E+ V CR    E   V   ++DF+D SP+Q+VS+A +
Sbjct: 520 ADEEDRHVRAQANSPVGPDGRFLEDRVLCRRGNEEMEYVAATEVDFMDVSPRQMVSVATA 579

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +V ++AG+VE+
Sbjct: 580 MIPFLEHDDANRALMGANMQRQAVPLIRSEAPIVGTGMELRAAVDAGDVVVNEKAGVVEE 639

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  + + + +G           YR+ KF RSNQ TC NQRP+V  G  V    ++ADG
Sbjct: 640 VSADYVTVMADDGTRKS-------YRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADG 692

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG
Sbjct: 693 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLG 752

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 753 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 812

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 813 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 846



 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 96/332 (28%), Positives = 155/332 (46%), Gaps = 28/332 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNEGL----QAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S+   +      +    R + GL    +   + + PI 
Sbjct: 25  RVSFAKIREPLEVPGLLDLQTESFAWLIGSPEWRERAAARGDVGLVGGLEEVLEELSPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    F+  K  +D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFEEVKASIDECKEKDMTYAAPLFVTAEFI---------NNNTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FDH   +   + K L++ R+IP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDHSIDK--GTEKDLHSVRVIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +EEI   F    +     +   
Sbjct: 194 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEEIAERFGFSEIMMSTLEKDN 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 254 TAGQDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---IN 304

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             +   +    TG +  +   V   + L  + 
Sbjct: 305 KKLGIHVGEPVTGSVLTKEDIVTTIEYLVRLH 336


>gi|21223036|ref|NP_628815.1| DNA-directed RNA polymerase subunit beta [Streptomyces coelicolor
            A3(2)]
 gi|41018149|sp|Q9L0L0|RPOB_STRCO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|7248348|emb|CAB77428.1| DNA-directed RNA polymerase beta chain [Streptomyces coelicolor
            A3(2)]
          Length = 1161

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 185/515 (35%), Positives = 265/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVAEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+I P EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKINPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPL VPSRMN GQ+ E HLGW     G  +  L  ++     +       
Sbjct: 894  EDGTPVDIILNPLAVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEEWAQRLQVIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 948  ------------------------ADKVEPGTNVATPVFDGAREDELAGLLQHTIPNRDG 983

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  ERMVLPSGKARLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 336/670 (50%), Positives = 458/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ R+N +GFIETPYRKV +G+VT+DV YL+A EE+   IAQAN++L +D  F E
Sbjct: 483 IGSLASYGRINPFGFIETPYRKVVEGQVTDDVDYLTADEEDRFVIAQANAALGDDMRFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 ARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 603 PLIKSESPLVGTGMEYRSAADAGDVVKAEKAGVVQEVSADYITTTNDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLAKFSRSNQGTSVNQKVIVAEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVESALESGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  IR++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGREIVVETDDIDHFGNRRIRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|41410228|ref|NP_963064.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium subsp.
            paratuberculosis K-10]
 gi|41399062|gb|AAS06680.1| RpoB [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 1198

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 712  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 770

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 771  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 828

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 829  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 877

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 878  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 937

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I                           
Sbjct: 938  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN------------------ 978

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA EE +  ML            +D  
Sbjct: 979  -------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVMVDGD 1025

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1026 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1085

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1086 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1145

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1146 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1178



 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 334/694 (48%), Positives = 466/694 (67%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 202 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 259

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  + +TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 260 LLKALGWTNEQI----TERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESA 315

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +ED++A I+ LV L  G+
Sbjct: 316 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHEGQ 375

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 376 PTMTVPGGIEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 435

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 436 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 495

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+
Sbjct: 496 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLT 555

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+VS+A +
Sbjct: 556 ADEEDRHVVAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATA 615

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G++E+
Sbjct: 616 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKSGVIEE 675

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF+RSN  TC NQ P+V  GD V    +IADG
Sbjct: 676 VSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAGDRVEAGQVIADG 728

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 729 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 788

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 789 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 848

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 849 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 882



 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-------RPNEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +         P  GL+     + PI 
Sbjct: 61  RVSFAKLREPLEVPGLLDVQIDSFEWLIGAPRWREAAIARGDAEPKGGLEEVLDELSPIE 120

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 121 DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 171

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 172 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 229

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 230 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 289

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 290 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 340

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 341 KKLGLHAGEPITSSTLTEEDVVATIEYLVRLHE 373


>gi|291437855|ref|ZP_06577245.1| DNA-directed RNA polymerase subunit beta [Streptomyces ghanaensis
            ATCC 14672]
 gi|291340750|gb|EFE67706.1| DNA-directed RNA polymerase subunit beta [Streptomyces ghanaensis
            ATCC 14672]
          Length = 1171

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/508 (36%), Positives = 273/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 685  IVNEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 851  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++                    
Sbjct: 911  IILNPLGVPSRMNPGQVLEIHLGWLASQ-GWDVSGLADEWAQRLQDIS------------ 957

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A++ +    V+TPVFDGA E+ +  +L     +          
Sbjct: 958  -----------------ADRVEPRTNVATPVFDGAREDELTGLLEHTIPNRDGDRMVLPS 1000

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1001 GKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1060

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1061 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1120

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1121 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1148



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 339/670 (50%), Positives = 457/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  ED+I+ IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADAPLDAGVLTVEDVISTIKYLVKLHAGEIETVGDSGQTIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL ++ RVNA+GF+ETPYRKV DG+VT+ V YL+A EE+   IAQAN+ L +D  F E
Sbjct: 493 IGSLATYGRVNAFGFVETPYRKVNDGQVTDTVDYLTADEEDRFVIAQANAPLTDDLRFAE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 ARVLVRRKGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 613 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDGT-------YIT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRLHKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 786 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  343 bits (881), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEEALENGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   ED+++     + + AG++                ++   +  +R +  
Sbjct: 320 ADAPLDAGVLTVEDVISTIKYLVKLHAGEIETVGDSGQTIVVETDDIDHFGNRRLRSVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAT 498


>gi|254383181|ref|ZP_04998535.1| DNA-directed RNA polymerase subunit beta [Streptomyces sp. Mg1]
 gi|194342080|gb|EDX23046.1| DNA-directed RNA polymerase subunit beta [Streptomyces sp. Mg1]
          Length = 1160

 Score =  519 bits (1336), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 265/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +    +L      + E  M   + LL A    +  +  D  +     V   V+
Sbjct: 674  IVNEGDRIVEAQVLADGPATE-EGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 732

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 733  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGADVVAGDILVG 789

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 790  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 832

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 833  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 892

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L  D+     +       
Sbjct: 893  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEDWAERLKVIG----- 946

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A++ + G  V+TPVFDGA E+ +  +      +   
Sbjct: 947  ------------------------ADRVEPGTNVATPVFDGAREDELAGLFEHTIPNRDG 982

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  DRLVLPSGKARLFDGRSGEPFPDPISIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  506 bits (1303), Expect = e-140,   Method: Composition-based stats.
 Identities = 339/670 (50%), Positives = 458/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 200 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 244

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 245 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 301

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +DIIA IK LV L  G+               DDID+ GNR
Sbjct: 302 KVNKKLGADEPLDAGVLTTDDIIATIKYLVRLHAGETETIGESGRSIVVETDDIDHFGNR 361

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 362 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 421

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 422 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 481

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV DG VT+DV YL+A EE+   IAQAN+ L ED  FTE
Sbjct: 482 IGSLASYGRVNAFGFVETPYRKVIDGVVTDDVDYLTADEEDRFVIAQANAGLSEDMRFTE 541

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 542 NRVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 601

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+KAEAP VGTGME   A  +G +I A++ G+V++V A  + + + +G           
Sbjct: 602 PLIKAEAPLVGTGMEYRCAVDAGDSIRAEKDGVVQEVSADYVTVANDDGT-------YTT 654

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 655 YRVAKFSRSNQGTSVNQKVIVNEGDRIVEAQVLADGPATEEGEMALGKNLLVAFMPWEGH 714

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 715 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 774

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 775 IRIGADVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 834

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 835 VRVFDREEGD 844



 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 202/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            +    D     GL+  F+ 
Sbjct: 20  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKSRVESALESGQDVPTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+P K  VD+C  RD TYA PL +T                
Sbjct: 80  ISPIEDFSGSMSLTFRDHRFEPAKNSVDECKERDFTYAAPLFVTAEFT---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 131 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 189 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 248

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 249 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 308

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +DI+      + + AG+                 ++   +  +R++  
Sbjct: 309 ADEPLDAGVLTTDDIIATIKYLVRLHAGETETIGESGRSIVVETDDIDHFGNRRLRNVGE 368

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 369 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 426

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 427 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 481

Query: 467 VGEMLK 472
           +G +  
Sbjct: 482 IGSLAS 487


>gi|62720654|gb|AAX93863.1| RNA polymerase subunit B [Mycobacterium barrassiae]
          Length = 1167

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/515 (37%), Positives = 269/515 (52%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGWA    G KI    +                      
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWAAKA-GWKIDGSPDWAAN------------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
                       + +L V         VSTPVFDGA E  +  +L     +  G       
Sbjct: 948  ---------LPEEMLEVEPN----TIVSTPVFDGAREAELQGLLSATLPNRDGDTLVDGD 994

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 995  GKAQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1054

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1055 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1114

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1115 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1145



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 331/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMGTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G               +DD
Sbjct: 302 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHQGDQTMTAPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+D+ YL+A EE+   +AQANS  D
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVKDGVVTDDIEYLTADEEDRHVVAQANSPTD 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E G F EE V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 EKGRFLEERVLVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +VA +AG++E+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKAGVIEEVSADYITVMADDGTR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  GD V    +IADGP T+ G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGDRVEAGQVIADGPCTENGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 95/334 (28%), Positives = 154/334 (46%), Gaps = 29/334 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG--------LQAAFKSVFPI 65
           R  F K  E +++P L++VQ  S++  +  +   +     G        L+     + PI
Sbjct: 29  RISFAKLREPLEVPGLLDVQTESFEWLIGSDRWRENAKLRGDAIEPVGGLEEVLTELSPI 88

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +I
Sbjct: 89  EDFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEI 139

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++I
Sbjct: 140 KSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVI 197

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +  
Sbjct: 198 PGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKD 257

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
               +   L+   +       +  GE    ES + L   L    K   +  +G       
Sbjct: 258 NTAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---V 308

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
              +  +     T     E   V   + L  +  
Sbjct: 309 NKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHQ 342


>gi|312141000|ref|YP_004008336.1| DNA-directed RNA polymerase beta subunit rpob [Rhodococcus equi 103S]
 gi|311890339|emb|CBH49657.1| DNA-directed RNA polymerase beta subunit RpoB [Rhodococcus equi 103S]
          Length = 1118

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 272/515 (52%), Gaps = 54/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 626  IVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 684

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 685  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 742

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 743  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 791

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 792  REDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 851

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQ+ ETHLGW     G  ++   +  + +   +     L     + 
Sbjct: 852  IILNTHGVPRRMNIGQVLETHLGWIGK-TGWNVQIAGDGSRPDWAATLPEEMLSAPADSN 910

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
                                      ++TPVFDGA E+ +  +L     +  G       
Sbjct: 911  --------------------------IATPVFDGAKEDELTGLLGSTLPNRDGERMVGPD 944

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 945  GKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1004

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1005 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1064

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S     A      D +  +L+
Sbjct: 1065 KELQSLCLNVEVLSSDGAAIAMA----DGDDEDLE 1095



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 459/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +    + D  I   
Sbjct: 129 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEI--R 186

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D  K+  +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 187 ERFGFSEIMMATLEKDPAKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 246

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKGT------------IDD 455
            VGR K+N +L L+T  P +   + ++DI+  I+ LV L  G               +DD
Sbjct: 247 RVGRYKINKKLGLNTGLPIEASTLTEDDIVTTIEYLVRLHAGDTMMTAPGGVEVPVEVDD 306

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 307 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 366

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 367 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 426

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G++T+ V YL+A EE+   +AQANS +D
Sbjct: 427 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGQLTDQVDYLTADEEDRHVVAQANSPVD 486

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 487 ANGRFTEDRVLVRRKGGEVEFVSSSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 546

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V +  + + + +G    
Sbjct: 547 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSSDYVTVMADDGSR-- 604

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 605 -----TTYRLRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVA 659

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 660 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 719

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 720 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 779

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 780 ESGKVIGIRVFSREDDD 796



 Score =  281 bits (719), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 130/249 (52%), Gaps = 15/249 (6%)

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL+     + PI  FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I    
Sbjct: 22  GLEEILAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---- 77

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                  +  +IK Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +  
Sbjct: 78  -----NNNTGEIKSQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESIDK-- 130

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            + K L++ ++IP +G W++ + D +D + VRIDR+R+ PVT+ L ALGM  EEI   F 
Sbjct: 131 STEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEIRERFG 190

Query: 234 --PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLK 289
               ++ +   D       A   +            ++ + ++E+   K     L +  +
Sbjct: 191 FSEIMMATLEKDPAKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARVGR 250

Query: 290 EKGVKFLGI 298
            K  K LG+
Sbjct: 251 YKINKKLGL 259


>gi|41017808|sp|Q9L637|RPOB_AMYMD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|7331268|gb|AAF60349.1|AF242549_1 DNA-dependent RNA polymerase beta subunit [Amycolatopsis mediterranei
            S699]
 gi|41581816|gb|AAS07760.1| RpoB [Amycolatopsis mediterranei S699]
          Length = 1167

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 184/520 (35%), Positives = 260/520 (50%), Gaps = 69/520 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G ++    + +    +   + LL A+   +  +  D  +     V   V+
Sbjct: 680  IVNEGDRIEAGQVIADGPSTEN-GEVALGKNLLVAVMPWEGHNYEDAIILSERLVQDDVL 738

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E +  D  DE+ I+      R  +IL G+ 
Sbjct: 739  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADL-DERGIIRIGAEVRDGDILVGKV 797

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 798  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 840

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF++D
Sbjct: 841  IRVFSREDDDELPPGVNELVRVYVAQKRKIQPGDKLAGRHGNKGVIGKILPVEDMPFMED 900

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI E HLGW     G  I+   +  K              
Sbjct: 901  GTPVDIILNTHGVPRRMNIGQILELHLGWLASQ-GWTIEGDPDWAKN------------- 946

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES--- 1231
                              +         G   +TPVFDGA EE +  +L     +     
Sbjct: 947  ------------------LSAELRDVAPGTNTATPVFDGAKEEELTGLLSATKPNRDGER 988

Query: 1232 -----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEP+  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 989  MVKENGKANLFDGRSGEPYPYPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1048

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1049 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1108

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+L L++++ +S   +     E+ D    +L+
Sbjct: 1109 FKVLLKELQSLCLNVEVLSSDGSSI----EMRDSGDEDLE 1144



 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 320/602 (53%), Positives = 438/602 (72%), Gaps = 20/602 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D      +ALLDIYR +RPG+  T   A+++   LFF + +YDL+ VGR K+N +L L
Sbjct: 256 EKDHTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKAKRYDLAKVGRYKVNKKLGL 315

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
            TP +   + +EDI+ II+ LV L  G+  +            DDID+ GNRR+R+VGE+
Sbjct: 316 STPIENGTLTEEDIVTIIEYLVRLHAGEDKMTAANNTEIPVETDDIDHFGNRRIRTVGEL 375

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL R ER ++ER+++ D++++ PQ LIN +P+ +A+ EFF +SQLSQ  +  N
Sbjct: 376 IQNQIRVGLSRTERVVRERMTTQDVEAITPQTLINIRPIGAAIKEFFGTSQLSQFMQQTN 435

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +  +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 436 PIDGLTHKRRLNALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLCSYA 495

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV +G+VT+ + YL+A EE+    AQAN+ + +DG+F E+ V  R  
Sbjct: 496 RVNPFGFIETPYRKVVEGRVTDQIDYLTADEEDRFVKAQANAPISDDGTFIEDRVMARRK 555

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE  L+    ID++D SP+Q+VSIA ++IPFLE+DD+NR LMG NMQRQAVPLL+++AP
Sbjct: 556 GGEVELIDPLDIDYMDVSPRQMVSIATAMIPFLEHDDANRALMGANMQRQAVPLLRSQAP 615

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTG+E   A  SG  +VA+++G+VE++ A  I +   +G           Y L KF+R
Sbjct: 616 YVGTGVELRAAIDSGDMLVAEQSGVVEELSADLITVMHDDGTRKS-------YSLYKFRR 668

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC N RP+V  GD +    +IADGPST+ G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 669 SNHGTCFNHRPIVNEGDRIEAGQVIADGPSTENGEVALGKNLLVAVMPWEGHNYEDAIIL 728

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVSEE L ++DE GII +GAEV 
Sbjct: 729 SERLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADLDERGIIRIGAEVR 788

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ +R+F+R  
Sbjct: 789 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGIRVFSRED 848

Query: 950 ID 951
            D
Sbjct: 849 DD 850



 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 113/481 (23%), Positives = 201/481 (41%), Gaps = 40/481 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E ++ P+L++VQ  S+  F         R  EG       L+     + PI 
Sbjct: 31  RVSFAKIREPLNTPNLLDVQIQSFQWFTGDEAWFQRRVEEGEENPVGGLEEVLNEISPIE 90

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F +  FD  K  +++C  +D+TYA PL +T   +           +  +IK
Sbjct: 91  DFSGSMSLSFSAPRFDEVKASIEECKDKDMTYAAPLFVTAEFV---------NNNTGEIK 141

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q++++GD P+MT  GTFVI G +R+VVSQL RSPG+++  D  +   S K +++ R+IP
Sbjct: 142 SQTVFLGDFPVMTDKGTFVINGTERVVVSQLVRSPGVYYSKDIDKT--SDKDVFSVRVIP 199

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I    +F   ++ +   D 
Sbjct: 200 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEAIRERFSFSETLLATLEKDH 259

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K     L K  + K  K LG+++  
Sbjct: 260 TAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKAKRYDLAKVGRYKVNKKLGLSTPI 319

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPILYVDS 351
             G    EDIV      + + AG+                 ++   +  IR +  L  + 
Sbjct: 320 ENGTLTEEDIVTIIEYLVRLHAGEDKMTAANNTEIPVETDDIDHFGNRRIRTVGELIQNQ 379

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +         +V ++   +   +  I            +  +  F            + +
Sbjct: 380 IRVGLSRTERVVRERMTTQD--VEAITPQTLINIRPIGAAIKEFFGTSQLSQFMQQTNPI 437

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
             +    RLN   P     + +E     ++ +     G+  +  I+      +  +G + 
Sbjct: 438 DGLTHKRRLNALGPGG---LSRERAGMEVRDVHPSHYGR--MCPIETPEGPNIGLIGSLC 492

Query: 472 K 472
            
Sbjct: 493 S 493


>gi|289705071|ref|ZP_06501482.1| DNA-directed RNA polymerase, beta subunit [Micrococcus luteus SK58]
 gi|289558234|gb|EFD51514.1| DNA-directed RNA polymerase, beta subunit [Micrococcus luteus SK58]
          Length = 1168

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/511 (36%), Positives = 260/511 (50%), Gaps = 64/511 (12%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V P   ++          +   + LL A    + ++  D  +     VS  V+ 
Sbjct: 686  VSEGERVEP-LSIIADGPATDNGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSEDVLT 744

Query: 942  VRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNAV 996
                  H +D  +  +  E     I  ++ +   + DE+ I+         +IL G+   
Sbjct: 745  SIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGRVTP 804

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             G         L   +  E  R                 E      +            +
Sbjct: 805  KGETELTPEERLLRAIFGEKSR-----------------EVRDTSLKVPHGESGTVIGVR 847

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I      DD+PPGV ++V+V+VA KR I  GDKMAGRHGNKG++S+ILP EDMPFL DGT
Sbjct: 848  IFDRDEDDDLPPGVNQLVRVYVAQKRKITDGDKMAGRHGNKGVISKILPLEDMPFLADGT 907

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDIVLNPLGVP RMN+GQ+ E HLGWA    G  I+      K   +            
Sbjct: 908  PVDIVLNPLGVPGRMNLGQVMELHLGWAAS-RGWDIQGEPEWIKDLPNFPRQ-------- 958

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------L 1228
                                       V V+TPVFDGA+   I  +L   +        +
Sbjct: 959  ------------------------SGPVNVATPVFDGAEAYEITGLLGHVNVTRDGDRLM 994

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             +SG++ L+DG TGEPF  PV+VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+ 
Sbjct: 995  SDSGKAQLFDGRTGEPFPDPVSVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQ 1054

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQE+LTIKSDD+ GR +VYE+IV G +  E G PESF 
Sbjct: 1055 FGGQRFGEMEVWALEAYGAAFTLQELLTIKSDDIHGRVKVYEAIVKGENIPEPGVPESFK 1114

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            VL+KEMQ+L L++++ ++  +     +   +
Sbjct: 1115 VLIKEMQSLCLNVEVLSADGQAIEMRDAEDE 1145



 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 303/954 (31%), Positives = 433/954 (45%), Gaps = 137/954 (14%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F K  E +D+PDL+ +Q  S+D  +                        GL   F+ 
Sbjct: 23  RVSFAKISEPLDVPDLLALQTESFDRLIGNERWAARVDAALAADDHSVPVTSGLTDIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF   K   ++C  RD T++ PL +    +           +
Sbjct: 83  ISPIEDFQGTMSLSFAEPEFADAKMTEEECKDRDATFSAPLYVKAEFM---------NNT 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT++GTF+I G +R+VVSQL RSPG +F+    +   S K +++
Sbjct: 134 TGEIKQQTVFMGDFPLMTRNGTFIINGTERVVVSQLVRSPGAYFERTPDKT--SDKEIFS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W ++E D +D + VR+DR+RK PVT  L A+G     IL  F  Y  I  +
Sbjct: 192 AKIIPSRGAWFELEVDKRDQVGVRLDRKRKQPVTVLLKAMGWTESRILEEFGHYDSIRAT 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE   +++ + L + L  + K   +  +G 
Sbjct: 252 LEKDGTADQDEA--------LLDIYRKLRPGEPAAVDAAQSLLNNLYFTPKRYDLAKVGR 303

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              +   G       V+   G+         D   +     +                  
Sbjct: 304 YKLNRKLG-------VDVHLGDPNASVLTEDDIVQMVHFIAALH--------AGETAIKG 348

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            R+    D   +  D      R +R                L  +  +  LS + RV   
Sbjct: 349 TRDGEPVDVRVEIDDIDHFGNRRIRA------------VGELIENQIRTGLSRMERVVRE 396

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                D       I  + +I I  ++  ++   GT      +      +     +    L
Sbjct: 397 RMTTQDVEA----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 452

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           G   + R      + +++  V P       P+ +                 +NS   I  
Sbjct: 453 GPGGLSRD----RAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATFGRINSFGFIE- 507

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
                                R V            T++      ++     A V+  G 
Sbjct: 508 ------------------TPYRRVVDGRVTDTVDYLTADDELAFQIAQAN--APVDEDGR 547

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                          + V  +  E +   +                              
Sbjct: 548 FVEELVLCRQRGGDGEPVLSTVDEIDYMDV------------------------------ 577

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                    SP+Q+VS A +LIPFLE+DD+NR LMG NMQRQAVPLL++EAP+VGTGME 
Sbjct: 578 ---------SPRQMVSAATALIPFLEHDDANRALMGANMQRQAVPLLRSEAPYVGTGMEK 628

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  +G ++ A + G+V +V A  + + + +G           Y +MKF RSNQ    N
Sbjct: 629 YVAVDAGDSVTATQGGVVTEVAADLVTVMNDDGT-------TTHYPIMKFARSNQGNAYN 681

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QR  V  G+ V    IIADGP+TD G+LALG+N+LVAFMPW G N+ED++++S+RMVSED
Sbjct: 682 QRVRVSEGERVEPLSIIADGPATDNGELALGKNLLVAFMPWEGLNYEDAIILSQRMVSED 741

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           V TSIHIEE EV ARDTKLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVG+
Sbjct: 742 VLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEEVLSQLDERGIIHIGAEVEAGDILVGR 801

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL+VP G SGTV+ VRIF+R   D
Sbjct: 802 VTPKGETELTPEERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRIFDRDEDD 855


>gi|145225673|ref|YP_001136351.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gilvum
            PYR-GCK]
 gi|315446024|ref|YP_004078903.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. Spyr1]
 gi|189043860|sp|A4T1P4|RPOB_MYCGI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|145218159|gb|ABP47563.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gilvum
            PYR-GCK]
 gi|315264327|gb|ADU01069.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. Spyr1]
          Length = 1174

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/520 (35%), Positives = 264/520 (50%), Gaps = 59/520 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 678  IVDAGQRVETGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 736

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 737  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIIRIGAEVRDGDILVGKV 795

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 796  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIG 838

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 839  IRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPD 898

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +    + ++    + L +
Sbjct: 899  GTPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIRLASDGADGSTEVPAWAAKLPE 957

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MA 1226
             + +                           V+TPVFDGA E  +  +L           
Sbjct: 958  HMLSAPADSI---------------------VATPVFDGAQEGELQGLLGATLPNRDGET 996

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             ++  G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 997  MVNSDGKAVLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1056

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PES
Sbjct: 1057 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPES 1116

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 FKVLLKELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1152



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 453/677 (66%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 181 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 238

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 239 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 298

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G               +DD
Sbjct: 299 RVGRYKVNKKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQGDQTMTAPGGSEVPVEVDD 358

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 359 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 418

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 419 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 478

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ + YL+A EE+   +AQANS LD
Sbjct: 479 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDQIDYLTADEEDRHVVAQANSPLD 538

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F EE V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 539 GDGRFEEERVLVRRKGGEVEFVSASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 598

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V  +AG+VE+V A  I + + +G    
Sbjct: 599 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVTDKAGVVEEVSADYITVMADDGTR-- 656

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 657 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVETGQVLADGPCTENGEMALGKNLLVA 711

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 712 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 771

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 772 DLDERGIIRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 831

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 832 ESGKVIGIRVFSREDDD 848



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 155/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +          + G       LQ   + + PI 
Sbjct: 27  RISFAKLREPLEVPGLLDVQTESFEWLIGAEDWFQRAVDRGDVDPKGGLQEVLEELSPIE 86

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 87  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 137

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 138 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 195

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 196 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMSTLEKDN 255

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 256 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 306

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  ++    T     E   V   + L  +  
Sbjct: 307 KKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQ 339


>gi|239929529|ref|ZP_04686482.1| DNA-directed RNA polymerase subunit beta [Streptomyces ghanaensis
            ATCC 14672]
          Length = 1161

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/508 (36%), Positives = 273/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  IVNEGDRIIEGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 791

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 792  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 840

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 841  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 900

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++                    
Sbjct: 901  IILNPLGVPSRMNPGQVLEIHLGWLASQ-GWDVSGLADEWAQRLQDIS------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A++ +    V+TPVFDGA E+ +  +L     +          
Sbjct: 948  -----------------ADRVEPRTNVATPVFDGAREDELTGLLEHTIPNRDGDRMVLPS 990

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 991  GKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1050

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1051 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1110

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1111 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 339/670 (50%), Positives = 457/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  ED+I+ IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADAPLDAGVLTVEDVISTIKYLVKLHAGEIETVGDSGQTIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL ++ RVNA+GF+ETPYRKV DG+VT+ V YL+A EE+   IAQAN+ L +D  F E
Sbjct: 483 IGSLATYGRVNAFGFVETPYRKVNDGQVTDTVDYLTADEEDRFVIAQANAPLTDDLRFAE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 ARVLVRRKGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDGT-------YIT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRLHKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 776 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 117/486 (24%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEEALENGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
             +    G+   ED+++     + + AG++                ++   +  +R +  
Sbjct: 310 ADAPLDAGVLTVEDVISTIKYLVKLHAGEIETVGDSGQTIVVETDDIDHFGNRRLRSVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAT 488


>gi|258651304|ref|YP_003200460.1| DNA-directed RNA polymerase subunit beta [Nakamurella multipartita
            DSM 44233]
 gi|258554529|gb|ACV77471.1| DNA-directed RNA polymerase, beta subunit [Nakamurella multipartita
            DSM 44233]
          Length = 1149

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/535 (34%), Positives = 262/535 (48%), Gaps = 52/535 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     R           + ++  I+  GA V  GD++       G   M   + L
Sbjct: 633  MNDDGTHRTYRLNKFRRSNQGTSFNQKPIVDEGARVEAGDVIADGPCTDG-GEMALGKNL 691

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     +S  +V   +     I+++E      +   E + RD  
Sbjct: 692  LVAFMPWEGHNYEDAII-----LSQRIVQDDVLTSIHIEEHEIDARDTKLGPEEITRDIP 746

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +    +  ++  R   +  G     G     K T      ++   R     F  +  +V+
Sbjct: 747  NVSEEVLADLDER-GIVRVGAEVQDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVR 805

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +         +   G ++PPGV  +V+V+VA KR IQ GDK+AG
Sbjct: 806  DTSLKVPHGETGKVIGI-----RVFNRDDDGAELPPGVNELVRVYVAQKRKIQDGDKLAG 860

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++ +ILP EDMPFL DGTPVDIVLNP GVP RMN+GQI ETHLGW     G ++
Sbjct: 861  RHGNKGVIGKILPVEDMPFLPDGTPVDIVLNPHGVPRRMNIGQILETHLGWVASQ-GWQV 919

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            +      K                                +     +       +TPVF 
Sbjct: 920  EGEPGWAKN-------------------------------LSEQTREAGPWTKTATPVFS 948

Query: 1213 GADEEAINSML--------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            GA E+ I  +L            +   G++ L+DG TGEPF  PV VGY+Y++KL H+V 
Sbjct: 949  GASEDEIMGLLGSTTPTRDGERLVHTDGKATLFDGRTGEPFPYPVAVGYMYIIKLLHLVD 1008

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD+VG
Sbjct: 1009 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDIVG 1068

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R +VYE+IV G +  E G PESF VL+KE+QAL L++++ +S        +   D
Sbjct: 1069 RVKVYEAIVKGENIPEPGIPESFKVLLKELQALCLNVEVLSSDGVAIEMRDSDDD 1123



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 334/690 (48%), Positives = 469/690 (67%), Gaps = 26/690 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        L     K V    +      G ++  D+   +T  + I+         
Sbjct: 153 LVRSPGVYFDKSLDKTAGKDVFSCKVIPSR--GAWLEFDVDKRDTIGVRIDRKRRQPVSV 210

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +    +   I     +  + +  +  TL  D    + +ALLDIYR +RPG+  T   A
Sbjct: 211 LLKALGWDTERI----REHFSWSPVLLATLEKDHIAGQDEALLDIYRKLRPGEPPTKESA 266

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++ + LFF   +YDL+ VGR KMN +L ++ P  V  + ++D+++I++ L+ L  G   
Sbjct: 267 QALLDNLFFKDKRYDLAKVGRYKMNKKLGVNQPTSVGTLTEDDLLSIVEYLLRLHQGDAE 326

Query: 453 -----------IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
                       DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ
Sbjct: 327 WTKNGRVYPVETDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQ 386

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RA +E+RDV
Sbjct: 387 TLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRDRASLEVRDV 446

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           HP+HYGR+CP ET EG NIGL+ SL++FARVN +GFIETPYRKV DG  T+ + YL+A E
Sbjct: 447 HPSHYGRMCPIETPEGPNIGLIGSLSTFARVNPFGFIETPYRKVIDGVATDQIEYLTADE 506

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLI 679
           E+   IAQA++ LD DG FTE  V  R    GE   VP  +++++D SP+Q VS+A ++I
Sbjct: 507 EDRFIIAQASAKLDNDGRFTENRVLVRRKGSGEVDQVPPAEVEYMDVSPRQTVSVATAMI 566

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+D++NR LMG NMQRQ+VPLL++EAP VGTGME+  AK +G  ++A+++G+VE+  
Sbjct: 567 PFLEHDEANRALMGANMQRQSVPLLRSEAPLVGTGMEARAAKDAGDVLIAEKSGVVEEAT 626

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I + + +G           YRL KF+RSNQ T  NQ+P+V  G  V   D+IADGP 
Sbjct: 627 ADYISVMNDDGT-------HRTYRLNKFRRSNQGTSFNQKPIVDEGARVEAGDVIADGPC 679

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G++ALG+N+LVAFMPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLGPE
Sbjct: 680 TDGGEMALGKNLLVAFMPWEGHNYEDAIILSQRIVQDDVLTSIHIEEHEIDARDTKLGPE 739

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSEE L ++DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 740 EITRDIPNVSEEVLADLDERGIVRVGAEVQDGDILVGKVTPKGETELTPEERLLRAIFGE 799

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           KA +VRDTSL+VP G +G V+ +R+FNR  
Sbjct: 800 KAREVRDTSLKVPHGETGKVIGIRVFNRDD 829



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 92/292 (31%), Positives = 144/292 (49%), Gaps = 23/292 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE----GLQAAFKSVFPITAFS 69
           R  F K  E +++P+L+ +Q  S+   L+       R +E    GL    + + PI  FS
Sbjct: 16  RVSFAKLREPLEVPNLLALQTDSFAW-LVGGADWRARQDEPTPSGLDEILEEISPIEDFS 74

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           G   L F    FD  K + ++C  +D+TY+ PL +T   +              +IK Q+
Sbjct: 75  GNLSLSFSDPRFDEVKANEEECRDKDMTYSAPLFVTAEFM---------NGETGEIKSQT 125

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   +GK +++C++IP +G
Sbjct: 126 VFMGDFPMMTSKGTFIINGTERVVVSQLVRSPGVYFDKSLDKT--AGKDVFSCKVIPSRG 183

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPL 249
            W++ + D +D I VRIDR+R+ PV+  L ALG D+E I   F    V     +      
Sbjct: 184 AWLEFDVDKRDTIGVRIDRKRRQPVSVLLKALGWDTERIREHFSWSPVLLATLEKDHIAG 243

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
               L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 244 QDEALLDIYR------KLRPGEPPTKESAQALLDNLFFKDKRYDLAKVGRYK 289


>gi|302559014|ref|ZP_07311356.1| DNA-directed RNA polymerase, beta subunit [Streptomyces griseoflavus
            Tu4000]
 gi|302476632|gb|EFL39725.1| DNA-directed RNA polymerase, beta subunit [Streptomyces griseoflavus
            Tu4000]
          Length = 1171

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/508 (36%), Positives = 274/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 685  IVNEGDRIITGQVLADGPATQN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 744  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+I P EDMPFL+DGTPVD
Sbjct: 851  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKINPIEDMPFLEDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L  ++     +              
Sbjct: 911  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLAEEWAERLQVIG------------ 957

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A++ + G  V+TPVFDGA E+ +  +L+    +          
Sbjct: 958  -----------------ADKVEPGTNVATPVFDGAREDELAGLLQHTIPNRDGERMVLPS 1000

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ LYDG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1001 GKARLYDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1060

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1061 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1120

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1121 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1148



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 334/670 (49%), Positives = 458/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +DIIA IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGGDEPLDAGVLTTDDIIATIKYLVQLHAGETETVGGSGRSIIVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ R+N +GFIETPYRKV DG+VT++V YL+A EE+   IAQAN+ L+++  F E
Sbjct: 493 IGSLASYGRINPFGFIETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAPLNDEMRFVE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             +  R   GE   VP +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 NRILVRRRGGEVDYVPGDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+E+P VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 613 PLIKSESPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTANDDGT-------YIT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++ALG+N+LVAFMPW G+
Sbjct: 666 YRLAKFSRSNQGTSVNQKVIVNEGDRIITGQVLADGPATQNGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 786 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 119/486 (24%), Positives = 201/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALESGHDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +DI+      + + AG+                 ++   +  IR++  
Sbjct: 320 GDEPLDAGVLTTDDIIATIKYLVQLHAGETETVGGSGRSIIVETDDIDHFGNRRIRNVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAS 498


>gi|302869981|ref|YP_003838618.1| DNA-directed RNA polymerase subunit beta [Micromonospora aurantiaca
            ATCC 27029]
 gi|315501442|ref|YP_004080329.1| DNA-directed RNA polymerase, beta subunit [Micromonospora sp. L5]
 gi|302572840|gb|ADL49042.1| DNA-directed RNA polymerase, beta subunit [Micromonospora aurantiaca
            ATCC 27029]
 gi|315408061|gb|ADU06178.1| DNA-directed RNA polymerase, beta subunit [Micromonospora sp. L5]
          Length = 1143

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/508 (37%), Positives = 263/508 (51%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++        E  M     LL A    +  +  D  +     V   V+
Sbjct: 657  VVFEGDRVEAGQVIADGPCT-DEGEMALGRNLLVAFMCWEGHNYEDAIILSQRLVQQDVL 715

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 716  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPGDILVGK 773

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V   +                    
Sbjct: 774  VTPKGETELTPE--ERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSR-------- 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 824  -EDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 882

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                   
Sbjct: 883  IVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIN------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A + +    V+TPVFDGA EE I+ +L     +          
Sbjct: 930  -----------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIGGS 972

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP   P+ VGY+Y+LKLNH+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 973  GKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1032

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+
Sbjct: 1033 QRFGEMECWAMQAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLL 1092

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        E   +
Sbjct: 1093 KELQSLCLNVEVLSSDGVALEMRETDDE 1120



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 329/600 (54%), Positives = 439/600 (73%), Gaps = 10/600 (1%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  +  TL  D    + +ALLDIYR +RPG+  T   A+++ + LFF+  +YD++ VGR 
Sbjct: 235 SELMMTTLEKDHIAGQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRY 294

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLK 472
           K N +L LD P     + ++DI+A ++ L  L  G+     DDID+ GNRR+R+VGE+++
Sbjct: 295 KFNKKLELDVPITTGTLTEDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQ 354

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 355 NQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPL 414

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ +L++FARV
Sbjct: 415 AGLTHRRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGALSTFARV 474

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-G 651
           N +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ L  DG+F E+ V  R   G
Sbjct: 475 NPFGFIETPYRKVIDGRVTDQIDYLTADEEDRFVKAQANAPLKSDGTFAEDRVLVRRKGG 534

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E   V    +D++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPL+KAEAP V
Sbjct: 535 ETEDVAPGAVDYMDVSPRQMTSVATAMIPFLEHDDANRALMGANMQRQAVPLVKAEAPLV 594

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  +VA+  G+VE + A  I +   +G           Y L KF+RSN
Sbjct: 595 GTGMEYRAAVDAGDVVVAEVGGVVEDLCADYITVHQDDGHR-------RTYLLHKFRRSN 647

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             +CVNQ+P+V  GD V    +IADGP TD G++ALGRN+LVAFM W G+N+ED++++S+
Sbjct: 648 AGSCVNQKPVVFEGDRVEAGQVIADGPCTDEGEMALGRNLLVAFMCWEGHNYEDAIILSQ 707

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV TSIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GII +GAEV PG
Sbjct: 708 RLVQQDVLTSIHIEEHEVDARDTKLGPEEITRDIPNVSEEMLADLDERGIIRIGAEVVPG 767

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +GTV+ VR F+R   D
Sbjct: 768 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGTVIGVRTFSREDGD 827



 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 103/469 (21%), Positives = 188/469 (40%), Gaps = 28/469 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNEGLQAAFKSVFPITAF 68
           R  FG+  E +++P+L+ +Q  S+D  +         A D     GL      + PI  F
Sbjct: 20  RVSFGRITEHLEVPNLLAIQNESFDWLVGNEAWQGRSADDPHARSGLAEILDEISPIEDF 79

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           SG   L F +  FD  K  +++C  +DLTY  PL +T               +  +IK Q
Sbjct: 80  SGTMSLSFSAPRFDEVKASIEECKEKDLTYCAPLFVTAEFT---------NNTTGEIKSQ 130

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   S + L + ++IP +
Sbjct: 131 TVFMGDFPMMTPKGTFIINGTERVVVSQLVRSPGVYFDKQPDKT--SDRDLSSVKVIPSR 188

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWC 246
           G W++ + D +D + VRIDR+R+  VT  L A+G  +E I   F    +   +   D   
Sbjct: 189 GAWLEFDIDKRDTVGVRIDRKRRQAVTVLLKAIGWSAERIREKFGWSELMMTTLEKDHIA 248

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLC 304
               A   +            +  + ++++         + K  + K  K L +      
Sbjct: 249 GQDEALLDIYRKLRPGEPPTRENAQTLLDNLFFNPKRYDVAKVGRYKFNKKLELDVPITT 308

Query: 305 GLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G    +DIV   E         +  +   ++   +  +R +  L  + V         +V
Sbjct: 309 GTLTEDDIVATVEYLCRLHAGEEGYEADDIDHFGNRRLRTVGELIQNQVRVGLSRMERVV 368

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            ++   +   +  I            +  +  F            + +  +    RL+  
Sbjct: 369 RERMTTQD--VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHRRRLSAL 426

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 427 GPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLIGALST 470


>gi|320009114|gb|ADW03964.1| DNA-directed RNA polymerase, beta subunit [Streptomyces flavogriseus
            ATCC 33331]
          Length = 1161

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 264/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V    +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 675  VVSEGDRVIESQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 734  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVG 790

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 791  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 833

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 834  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 893

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++             
Sbjct: 894  EDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQAIG----- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ I  + +    +   
Sbjct: 948  ------------------------ADQVAPGTNVATPVFDGAREDEITGLFQATIPNRDG 983

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  PV++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  DRLVLPSGKANLFDGRSGEPFPDPVSIGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 460/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +DIIA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTSDDIIATIKYLVKLHAGETETVGESGRSIMVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ R+N +GFIETPYRKV +G VT+DV YL+A EE+   IAQAN++L +D  FTE
Sbjct: 483 IGSLASYGRINPFGFIETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANATLSDDMRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 ARVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I + + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKAGVVQEVSADYITVTNDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD V  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRIAKFSRSNQGTSVNQKVVVSEGDRVIESQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 119/486 (24%), Positives = 205/486 (42%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+  ++DI+      + + AG+                 ++   +  IR++  
Sbjct: 310 ADEPLDAGVLTSDDIIATIKYLVKLHAGETETVGESGRSIMVETDDIDHFGNRRIRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|302521308|ref|ZP_07273650.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. SPB78]
 gi|302430203|gb|EFL02019.1| DNA-directed RNA polymerase, beta subunit [Streptomyces sp. SPB78]
          Length = 1172

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 264/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+     V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 686  IVNENDRVIVGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 744

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 745  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVIAGDILVG 801

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 802  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 844

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 845  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 904

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  +  D+             
Sbjct: 905  EDGTPVDIILNPLGVPSRMNPGQVMEIHLGWLASQ-GWDVSQVPEDWAQRLQAIS----- 958

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 959  ------------------------ADQVAPGTNVATPVFDGAREDELTGLLQHTIPNRDG 994

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 995  DRMVLPSGKARLFDGRSGEPFPDPISLGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1054

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1055 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1114

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1115 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1149



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 338/671 (50%), Positives = 454/671 (67%), Gaps = 39/671 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGQYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT-------------IDDIDNLGN 461
           K+N +L  + P D   +  +DI+A IK LV L  G+                DDID+ GN
Sbjct: 313 KVNKKLGSEAPLDAGVLTTDDILATIKYLVQLHAGETEATVGDEGKTIVVETDDIDHFGN 372

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQ
Sbjct: 373 RRLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQ 432

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIG
Sbjct: 433 LSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 492

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL S+ RVNA+GF+ETPYRKV DG VT+DV YL+A EE+   IAQAN+ L +D  F 
Sbjct: 493 LIGSLASYGRVNAFGFVETPYRKVVDGVVTDDVDYLTADEEDRFVIAQANAPLTDDLHFE 552

Query: 642 EELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQA
Sbjct: 553 EARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQA 612

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL+K+EAP VGTGME   A  +G  + A + G+V++V A  I   + +G          
Sbjct: 613 VPLIKSEAPIVGTGMEYRSATDAGDVLKADKDGVVQEVSADYITTANDDGT-------YT 665

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            YRL KF RSNQ T VNQ+ +V   D V    ++ADGP+T+ G++ALG+N+LVAFMPW G
Sbjct: 666 TYRLAKFSRSNQGTSVNQKVIVNENDRVIVGQVLADGPATENGEMALGKNLLVAFMPWEG 725

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           +N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE G
Sbjct: 726 HNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERG 785

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+
Sbjct: 786 IIRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVI 845

Query: 941 DVRIFNRHGID 951
            VR+F+R   D
Sbjct: 846 GVRVFDREEGD 856



 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 104/325 (32%), Positives = 155/325 (47%), Gaps = 34/325 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 31  LRISFAKIREPLEVPNLLALQTESFDWLLGNDAWKSRVEAALAGGMSVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +Y+
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIYS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGQYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE    E+ + L   L  + K   +  +G 
Sbjct: 260 LEKDHTQGQDDA--------LLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGR 311

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYI 322
              +   G     D     T +I  
Sbjct: 312 YKVNKKLGSEAPLDAGVLTTDDILA 336


>gi|296130503|ref|YP_003637753.1| DNA-directed RNA polymerase, beta subunit [Cellulomonas flavigena DSM
            20109]
 gi|296022318|gb|ADG75554.1| DNA-directed RNA polymerase, beta subunit [Cellulomonas flavigena DSM
            20109]
          Length = 1168

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/515 (37%), Positives = 264/515 (51%), Gaps = 66/515 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V PG +L        E  +     LL A    +  +  D  +     V   V+
Sbjct: 680  LVEHGARVEPGSVLADGP-ATDEGELALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 739  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLGDL-DERGIIRIGAEVAAGDILVG 795

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 796  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGTV 838

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
             + +      GD++P GV  +V+V++A +R I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 839  IEVRTFSRDDGDELPAGVNELVRVYIAQRRKITDGDKLAGRHGNKGVISKILPVEDMPFL 898

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVD+VLNPLGVP RMNVGQ+ ETHLGW     G  I+    +              
Sbjct: 899  EDGTPVDVVLNPLGVPGRMNVGQVLETHLGWVAKQ-GWDIELAEGEATWR---------- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                              D V  VA +   G PV+TPVFDG  EE +  +L     +  G
Sbjct: 948  ------------------DGVPAVAARSTPGNPVATPVFDGVPEETLTGLLSTTLPNRDG 989

Query: 1233 --------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                    ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 990  ERTVKGDGKARLFDGRSGEPFPEPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1049

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G P
Sbjct: 1050 GKAQFGGQRFGEMEVWALEAYGAAYTLQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIP 1109

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    E   +
Sbjct: 1110 ESFKVLLKEMQSLCLNVEVLSSDGVSIDMKENDDE 1144



 Score =  499 bits (1286), Expect = e-139,   Method: Composition-based stats.
 Identities = 331/695 (47%), Positives = 462/695 (66%), Gaps = 29/695 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K V    +      G ++  +I   +   + ++     +   
Sbjct: 169 LVRSPGVYFERTADKTSDKDVLTAKVIPSR--GAWLEFEIDKRDNVGVRVDRKRKQNATV 226

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +    + +  I   +       + +TL  D  + + +ALLD+YR +RPG+  T    
Sbjct: 227 L--LKALGMTESEI--REEFAEYPAVIDTLEKDHVQTQDEALLDLYRKIRPGEPPTVEAG 282

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR----- 447
            ++    +F+  +YDL+ VGR K+N +L  D P     +   D++A IK L  L      
Sbjct: 283 RALLENFYFNPKRYDLAKVGRYKLNKKLGQDAPLSDSVLALSDVVATIKYLAALHIDKPT 342

Query: 448 ----------NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                       +   DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 343 LPGTRGGQAVEIRVEPDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDVEA 402

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 403 ITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 462

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVH +HYGR+CP ET EG NIGL+ SL ++ R+N +GF+ETPYR+V DGKVT++V YL
Sbjct: 463 VRDVHTSHYGRMCPIETPEGPNIGLIGSLATYGRINPFGFVETPYRRVVDGKVTDEVDYL 522

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAA 676
           +A +E+   IAQAN+ L+ DGSFTE  V  R   GE  LVP   +D++D SP+Q+VS+A 
Sbjct: 523 TADDEDRHVIAQANAPLNADGSFTESTVLVRTKGGEPDLVPGANVDYMDVSPRQMVSVAT 582

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           +LIPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA +AG+V 
Sbjct: 583 ALIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMERRAAVDAGDVVVATKAGVVT 642

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +V A  + + + +       +    YR+ KF+RSNQ TC NQR LV+ G  V    ++AD
Sbjct: 643 EVSADLVTVANDD-------ATTSTYRIAKFRRSNQGTCYNQRVLVEHGARVEPGSVLAD 695

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GP+TD G+LALGRN+LVAFM W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKL
Sbjct: 696 GPATDEGELALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKL 755

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITRDIPNVSEE L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 756 GPEEITRDIPNVSEEVLGDLDERGIIRIGAEVAAGDILVGKVTPKGETELTPEERLLRAI 815

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA +VRDTSL+VP G SGTV++VR F+R   D
Sbjct: 816 FGEKAREVRDTSLKVPHGESGTVIEVRTFSRDDGD 850



 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 94/302 (31%), Positives = 146/302 (48%), Gaps = 34/302 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAP------------DERPNEGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  L                  D     GL+  F+ 
Sbjct: 23  RISFAKIHEPLEVPDLLGLQTESFDWLLGNERWQARVAAALEVGRNDVPETAGLEEIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F  + F+PPK+  ++C  +D T+A PL +T   + +         +
Sbjct: 83  ISPIEDFGGTMSLSFREHRFEPPKYTAEECKEKDFTFAAPLFVTAEFVNY---------T 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K +  
Sbjct: 134 TGEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTADKT--SDKDVLT 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D +D + VR+DR+RK   T  L ALGM   EI   F  YP ++ +
Sbjct: 192 AKVIPSRGAWLEFEIDKRDNVGVRVDRKRKQNATVLLKALGMTESEIREEFAEYPAVIDT 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      I  GE   +E+G+ L      + K   +  +G 
Sbjct: 252 LEKDHVQTQDEA--------LLDLYRKIRPGEPPTVEAGRALLENFYFNPKRYDLAKVGR 303

Query: 299 TS 300
             
Sbjct: 304 YK 305


>gi|319443079|ref|ZP_07992235.1| DNA-directed RNA polymerase subunit beta [Corynebacterium variabile
            DSM 44702]
          Length = 1163

 Score =  518 bits (1335), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/516 (36%), Positives = 259/516 (50%), Gaps = 63/516 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  +      +    M+    LL A    +  +  D  +     V   ++
Sbjct: 670  LVDQGQRVEAGQAIADGPGTRN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDLL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D DD   I+      R  +IL G
Sbjct: 729  TSIHIEEH--EIDARDTKLGPEEITRDIPNVGEDVLADLDDR-GIVRIGADVRDGDILVG 785

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 786  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKV 828

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   +  DD+ PGV ++V+V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPFL
Sbjct: 829  IGVRVFSREDDDDLAPGVNQMVRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFL 888

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD +LN  GVP RMN+GQ+ ETHLGW     G  + +   D K    ++ L   L
Sbjct: 889  PDGTPVDFILNTHGVPRRMNIGQVLETHLGWLAKY-GWTVDTQSEDPKVQAMLNTLPEDL 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
             +V                              V+TPVFDGA+ E I+ +LR  + +  G
Sbjct: 948  YEVPPESL-------------------------VATPVFDGAENEEISGLLRSINPNADG 982

Query: 1233 --------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                    +++L DG +GEPF  PV+VGY YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 983  MKLTDEFGKAVLIDGRSGEPFPYPVSVGYKYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G P
Sbjct: 1043 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            ESF VL+KE+Q+L L++++  +            D 
Sbjct: 1103 ESFKVLLKELQSLCLNVEVLAADGTPMELSSTDDDE 1138



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 321/660 (48%), Positives = 448/660 (67%), Gaps = 24/660 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +       +I     +    +  +  TL  
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEI----TERFGFSEIMMTTLEK 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L LD 
Sbjct: 248 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 307

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLK 472
                 + ++DI+  I+ LV L  G+ ++            DDID+ GNRR+R+VGE+++
Sbjct: 308 DTGAMTLTEQDILTTIEYLVRLHAGEKSMTSPDGTEIPLGTDDIDHFGNRRLRTVGELIQ 367

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSL
Sbjct: 368 NQIRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSL 427

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ +L ++ARV
Sbjct: 428 SGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETPEGPNIGLIGNLATYARV 487

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N +GFIETPYR+V +G +T+ V YL+A EE+   IAQA + +D +G F +E +  R  AG
Sbjct: 488 NPFGFIETPYRRVDNGVITDQVDYLTADEEDRHIIAQAKTPVDAEGRFVDEQIEVRLRAG 547

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           +  +VP  ++D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPLL+ EAP+V
Sbjct: 548 DVEVVPATEVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLLRGEAPYV 607

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  IV  +AG VE V A  I I   +G  D        Y L KF+R+N
Sbjct: 608 GTGMELRAAYDAGDVIVTPKAGAVEYVSADYITIMDDDGVRD-------TYMLRKFERTN 660

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC NQ PLV  G  V     IADGP T  G+++LGRN+LVAFMPW G+N+ED++++++
Sbjct: 661 QGTCYNQIPLVDQGQRVEAGQAIADGPGTRNGEMSLGRNLLVAFMPWEGHNYEDAIILNQ 720

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED+ TSIHIEE E+ ARDTKLGPEEITRDIPNV E+ L ++D+ GI+ +GA+V  G
Sbjct: 721 RVVEEDLLTSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDDRGIVRIGADVRDG 780

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   D
Sbjct: 781 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDDD 840



 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 142/301 (47%), Gaps = 24/301 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L++VQ+ S+   +                 R   GL+     + P
Sbjct: 19  RYSFAKIDAPIEVPGLLDVQRESFAWLVGTPEWRARRQAQAEEGTRVTSGLEDILDELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +  +S    L      FD  K  +D+C  +D+ Y+ PL +T                  +
Sbjct: 79  VEDYSENMSLTLSEPRFDDVKNTIDECKDKDINYSAPLYVTAEFT---------NALSGE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+A ++
Sbjct: 130 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESID--ASTERPLHAVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +EEI   F     ++ +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEITERFGFSEIMMTTLEK 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D       A   +   +        D+ + ++E+         L K  + K  + LG+  
Sbjct: 248 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 307

Query: 301 D 301
           D
Sbjct: 308 D 308


>gi|190149256|gb|ABW91171.2| RNA polymerase beta subunit [Mycobacterium lepromatosis]
          Length = 1178

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/508 (36%), Positives = 264/508 (51%), Gaps = 52/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 805

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 806  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 854

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 855  HEDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVD 914

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G KI           ++              
Sbjct: 915  IILNTHGVPRRMNIGQILETHLGWVAKS-GWKIDVAAGMPDWAVNLPEELLHA------- 966

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                 K    VSTPVFDGA EE +  +L     +          
Sbjct: 967  ---------------------KPNQIVSTPVFDGAKEEELQGLLSSTLPNRDGDVMVDGD 1005

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1006 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1065

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1066 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1125

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S   +    E   +
Sbjct: 1126 KELQSLCLNVEVLSSDGASIELRESEDE 1153



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/689 (47%), Positives = 463/689 (67%), Gaps = 28/689 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + +       +  
Sbjct: 179 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 234

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         I   +    +  +R+TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 235 TVLLKALGWTSEQI--TERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESA 292

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L   +      + +ED++A I+ LV L  G+
Sbjct: 293 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEQITSSTLTEEDVVATIEYLVRLHEGQ 352

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 353 STMTVLGGVELPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 412

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 413 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 472

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++++ YL+
Sbjct: 473 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIEYLT 532

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D+DG F E  V  R   GE   V   ++D++D SP+Q+VS+A +
Sbjct: 533 ADEEDRHVVAQANSPIDKDGCFLEPRVLVRRKAGEVEYVASSEVDYMDVSPRQMVSVATA 592

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  ++A+++G++E+
Sbjct: 593 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGHVVIAEKSGVIEE 652

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF RSN  TC NQ P+V  GD V    +IADG
Sbjct: 653 VSADYITVMADDGTR-------RTYRMRKFARSNHGTCANQSPIVDAGDRVEAGQVIADG 705

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 706 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 765

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 766 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 825

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           GEKA +VRDTSL+VP G SG V+ +R+F+
Sbjct: 826 GEKAREVRDTSLKVPHGESGKVIGIRVFS 854



 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 97/333 (29%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMM---NIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +       A   R +     GL+     + PI 
Sbjct: 38  RISFAKLHEPLEVPGLLDVQTDSFEWLIGSPLWRAAATSRGDLKPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+V+SQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVISQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 318 KKLGLHAGEQITSSTLTEEDVVATIEYLVRLHE 350


>gi|182436662|ref|YP_001824381.1| DNA-directed RNA polymerase subunit beta [Streptomyces griseus subsp.
            griseus NBRC 13350]
 gi|178465178|dbj|BAG19698.1| RNA polymerase beta subunit [Streptomyces griseus subsp. griseus NBRC
            13350]
          Length = 1171

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/514 (37%), Positives = 265/514 (51%), Gaps = 73/514 (14%)

Query: 888  VNPGDILVGKIT-----PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            V+ GD +V               M   + LL A    +  +  D  +     V   V+  
Sbjct: 686  VSEGDRIVADQVLADGPATENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSS 745

Query: 943  RIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                 H  + + R   +  E+I        E +  D  DE+ I+         +IL G+ 
Sbjct: 746  IHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVGKV 802

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +     +     
Sbjct: 803  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKVIG 845

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+D
Sbjct: 846  VRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLED 905

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++               
Sbjct: 906  GTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQAIG------- 957

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----- 1229
                                  A+Q   G  V+TPVFDGA E+ I+  L  A +      
Sbjct: 958  ----------------------ADQVAPGTNVATPVFDGAREDEISG-LFEATIPNRDGD 994

Query: 1230 ----ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 SG++ L+DG +GEPF  PV+VG++Y+LKL+H+V DK++ARSTG YS++TQQPLGG
Sbjct: 995  RLVQPSGKAQLFDGRSGEPFPDPVSVGFMYILKLHHLVDDKLHARSTGPYSMITQQPLGG 1054

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PE
Sbjct: 1055 KAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPE 1114

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            SF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1115 SFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1148



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 461/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 211 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 255

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 256 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 312

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 313 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNR 372

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 373 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 432

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 433 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 492

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L+++  FTE
Sbjct: 493 IGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLNDELRFTE 552

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 553 PRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 612

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G           
Sbjct: 613 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDGT-------YTT 665

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 666 YRIAKFMRSNQGTSVNQKVVVSEGDRIVADQVLADGPATENGEMALGKNLLVAFMPWEGH 725

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 726 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 785

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 786 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 845

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 846 VRVFDREEGD 855



 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 116/486 (23%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 31  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 90

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 91  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 141

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 142 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 199

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 200 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 259

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 260 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 319

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 320 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNRRLRNVGE 379

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 380 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 437

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 438 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 492

Query: 467 VGEMLK 472
           +G +  
Sbjct: 493 IGSLAS 498


>gi|288558676|dbj|BAI68380.1| RNA polymerase beta-subunit [Streptomyces incarnatus]
          Length = 1181

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/508 (36%), Positives = 273/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 695  IVNEGDRIITGQVLADGPATQN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 753

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 754  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVIAGDILVGK 811

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 812  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFD 860

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 861  REEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVD 920

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++                    
Sbjct: 921  IILNPLGVPSRMNPGQVLEIHLGWLAS-RGWXVSGLADEWAQRLQAIG------------ 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                             A+Q      V+TPVFDGA E+ +  +L+    +          
Sbjct: 968  -----------------ADQVAPRTNVATPVFDGAREDELAGLLQHTIPNRDGERMVLPS 1010

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1011 GKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1070

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1071 QRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLI 1130

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1131 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1158



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 337/670 (50%), Positives = 457/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 221 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 265

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 266 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 322

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 323 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETVAESGRTIMVETDDIDHFGNR 382

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 383 RIRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 442

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRL+ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 443 SQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 502

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV +G+VT++V YL+A EE+   IAQAN+ L+++  F E
Sbjct: 503 IGSLASYGRVNAFGFIETPYRKVVEGQVTDEVDYLTADEEDRFVIAQANAPLNDEMRFAE 562

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 563 ARVLVRRRGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 622

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 623 PLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTANDDGT-------YIT 675

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++ALG+N+LVAFMPW G+
Sbjct: 676 YRLAKFSRSNQGTSVNQKVIVNEGDRIITGQVLADGPATQNGEMALGKNLLVAFMPWEGH 735

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 736 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 795

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 796 IRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 855

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 856 VRVFDREEGD 865



 Score =  337 bits (865), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 118/486 (24%), Positives = 200/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-----------EGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L                       GL+  F+ 
Sbjct: 41  LRFSFAKFKEPLEVPNLLALQTESFDWLLGNTAWQSRVEEALENGQDVPTKSGLEEIFEE 100

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 101 ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTYAAPLFVTAEFT---------NNE 151

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 152 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSTIDKT--SDKDIFS 209

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 210 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 269

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 270 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 329

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  IR +  
Sbjct: 330 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETVAESGRTIMVETDDIDHFGNRRIRSVGE 389

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 390 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 447

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RLN   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 448 QNNPLSGLTHKRRLNALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 502

Query: 467 VGEMLK 472
           +G +  
Sbjct: 503 IGSLAS 508


>gi|239990019|ref|ZP_04710683.1| DNA-directed RNA polymerase subunit beta [Streptomyces roseosporus
            NRRL 11379]
          Length = 1161

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 190/514 (36%), Positives = 265/514 (51%), Gaps = 73/514 (14%)

Query: 888  VNPGDILVGKIT-----PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            V+ GD ++               M   + LL A    +  +  D  +     V   V+  
Sbjct: 676  VSEGDRIIADQVLADGPATENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSS 735

Query: 943  RIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                 H  + + R   +  E+I        E +  D  DE+ I+         +IL G+ 
Sbjct: 736  IHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVGKV 792

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +     +     
Sbjct: 793  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKVIG 835

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+D
Sbjct: 836  VRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLED 895

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++               
Sbjct: 896  GTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQAIG------- 947

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----- 1229
                                  A+Q   G  V+TPVFDGA E+ I+  L  A +      
Sbjct: 948  ----------------------ADQVAPGTNVATPVFDGAREDEISG-LFEATIPNRDGD 984

Query: 1230 ----ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 SG++ L+DG +GEPF  PV+VG++Y+LKL+H+V DK++ARSTG YS++TQQPLGG
Sbjct: 985  RLVQPSGKAQLFDGRSGEPFPDPVSVGFMYILKLHHLVDDKLHARSTGPYSMITQQPLGG 1044

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PE
Sbjct: 1045 KAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPE 1104

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            SF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1105 SFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 462/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L+++  FTE
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLNDELRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 PRVLVRRRGGEVDYVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRIAKFMRSNQGTSVNQKVVVSEGDRIIADQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 116/486 (23%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|62720650|gb|AAX93861.1| RNA polymerase subunit B [Mycobacterium aubagnense]
          Length = 1172

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 185/508 (36%), Positives = 262/508 (51%), Gaps = 50/508 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 681  IVDSGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEQDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 847  REDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I++  N                      
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEADANGAYPEWAA-------------- 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                        ++            V+TPVFDGA E  +  +L     +          
Sbjct: 952  ------------NLPDGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVMVDAE 999

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1000 GKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1059

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1060 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1119

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        +   +
Sbjct: 1120 KELQSLCLNVEVLSSDGAAIEMRDSDDE 1147



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 326/679 (48%), Positives = 452/679 (66%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +         I   
Sbjct: 182 DKATEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQI--R 239

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 240 ERFGFSEIMMGTLEKDPTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 299

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNG------------KGTI 453
            VGR K+N +L L   +        + +EDI+A I+ LV L +G               +
Sbjct: 300 RVGRYKVNKKLGLHDGNPAQVTATTLTEEDIVATIEYLVRLHDGDTKMTAPGGVEVPVEV 359

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 360 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 419

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP E
Sbjct: 420 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIE 479

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS 
Sbjct: 480 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSP 539

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           LD+ G FTE+ +  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 540 LDDGGHFTEDKILVRRKGGEVEFVSANDVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 599

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA ++G++E+V A  + + + +G  
Sbjct: 600 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKSGVIEEVSADYVTVMADDGSR 659

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 660 -------HTYRMRKFNRSNHGTCANQRPIVDSGQRVEAGQVIADGPCTENGEMALGKNLL 712

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 713 VAVMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 772

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 773 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 832

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ VR+F+R   D
Sbjct: 833 HGESGKVIGVRVFSREDDD 851



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/298 (30%), Positives = 150/298 (50%), Gaps = 22/298 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    +  + G       L+     + PI 
Sbjct: 28  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSDRWRAKAVDRGDINPVGGLEEVLAELSPIE 87

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K  VD+C  +D TYA PL +T   I           +  +IK
Sbjct: 88  DFAGTLSLSFSDPRFDEVKAPVDECKEKDQTYAAPLFVTAEFI---------NNTTGEIK 138

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 139 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--ATEKTLHSVKVIP 196

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F     ++ +   D 
Sbjct: 197 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIRERFGFSEIMMGTLEKDP 256

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
              P  A   +            ++ + ++E+   K+    L +  + K  K LG+  
Sbjct: 257 TAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHD 314


>gi|239943566|ref|ZP_04695503.1| DNA-directed RNA polymerase subunit beta [Streptomyces roseosporus
            NRRL 15998]
 gi|291447033|ref|ZP_06586423.1| DNA-directed RNA polymerase subunit beta [Streptomyces roseosporus
            NRRL 15998]
 gi|291349980|gb|EFE76884.1| DNA-directed RNA polymerase subunit beta [Streptomyces roseosporus
            NRRL 15998]
          Length = 1161

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 190/514 (36%), Positives = 266/514 (51%), Gaps = 73/514 (14%)

Query: 888  VNPGDILVGKIT-----PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            V+ GD ++               M   + LL A    +  +  D  +     V   V+  
Sbjct: 676  VSEGDRIIADQVLADGPATENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSS 735

Query: 943  RIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                 H  + + R   +  E+I        E +  D  DE+ I+         +IL G+ 
Sbjct: 736  IHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVGKV 792

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +     +     
Sbjct: 793  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKVIG 835

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+D
Sbjct: 836  VRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLED 895

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++     +         
Sbjct: 896  GTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQVIG------- 947

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----- 1229
                                  A+Q   G  V+TPVFDGA E+ I+  L  A +      
Sbjct: 948  ----------------------ADQVAPGTNVATPVFDGAREDEISG-LFEATIPNRDGD 984

Query: 1230 ----ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 SG++ L+DG +GEPF  PV+VG++Y+LKL+H+V DK++ARSTG YS++TQQPLGG
Sbjct: 985  RLVQPSGKAQLFDGRSGEPFPDPVSVGFMYILKLHHLVDDKLHARSTGPYSMITQQPLGG 1044

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PE
Sbjct: 1045 KAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPE 1104

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            SF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1105 SFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  510 bits (1312), Expect = e-142,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 462/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L+++  FTE
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLNDELRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 PRVLVRRRGGEVDYVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRIAKFMRSNQGTSVNQKVVVSEGDRIIADQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 116/486 (23%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|255326833|ref|ZP_05367909.1| DNA-directed RNA polymerase, beta subunit [Rothia mucilaginosa ATCC
            25296]
 gi|255296050|gb|EET75391.1| DNA-directed RNA polymerase, beta subunit [Rothia mucilaginosa ATCC
            25296]
          Length = 1168

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 182/512 (35%), Positives = 263/512 (51%), Gaps = 62/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D++    +  G   +   + LL A    + ++  D  +     VS  V+
Sbjct: 683  VVKEGQRVEYRDVIADGPSTDG-GELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ D     DE+ I+         +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGPEEITRDIPNVSEDVLSALDERGIIHIGAEVEAGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                V   +        I +    +
Sbjct: 802  PKGETELTPEERLLRAIFGEKSREV--------RDTSLKVPHGESGTVIGIRIFDRENND 853

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +       DD+PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DG
Sbjct: 854  E-------DDLPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDG 906

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVP RMN+GQ+ E H GW     G KI+      K   +           
Sbjct: 907  TPVDVILNPLGVPGRMNIGQVLEVHTGWLAKQ-GWKIEGEPEWLKHMPNFPKE------- 958

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                                          ++TPVFDGA E+ +  ++  ++        
Sbjct: 959  -------------------------SGPTRLATPVFDGAHEDELFDLMDHSNPNRDGDRL 993

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++ SG++ L DG +GEPF  P++VGY Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 994  INRSGKARLIDGRSGEPFPDPISVGYQYILKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1053

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR +VYE+IV G +  E G PESF
Sbjct: 1054 QFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVAGRVKVYEAIVKGENIPEPGIPESF 1113

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++ ++  K     +   +
Sbjct: 1114 KVLIKEMQSLCLNVEVLSTDGKIIEMSDSEEE 1145



 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 338/640 (52%), Positives = 456/640 (71%), Gaps = 30/640 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL          IR TL  D  KDR +ALLDIYR +RPG+  T   A+++
Sbjct: 226 LKALGWTESKIL--AEFGQYDSIRATLEKDSVKDRDEALLDIYRKLRPGEPPTVEAAQAL 283

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV---RHIRKEDIIAIIKILVDLRNG--- 449
            + ++F   +YDL+ VGR K+N +L +D P D      + ++DI  +I+ L  L  G   
Sbjct: 284 LDNMYFTPRRYDLAKVGRYKLNRKLGVDVPMDSPEASVLSQDDIAQMIRYLCALHAGETS 343

Query: 450 ------------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                       K  IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+D+
Sbjct: 344 IPGVRDGEEIPLKIDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVDA 403

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ L+N +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 404 ITPQSLVNIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 463

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL ++ R+N++GFIETPYR V DG+VT++V YL
Sbjct: 464 VRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRINSFGFIETPYRVVTDGRVTDEVRYL 523

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG---EEILVPREKIDFIDASPKQVVSI 674
           +A +E++  IAQAN+ L+ D +F E  V CR      E +LV    + ++D SP+Q+VS+
Sbjct: 524 TADDEKSVVIAQANAPLNADRTFAENEVLCRAGDGSGEAVLVAPGAVQYMDVSPRQMVSV 583

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIP+LE+DD+NR LMG NMQRQAVPLL++EAP VGTGME   A  SG +++AK+ G+
Sbjct: 584 ATALIPYLEHDDANRALMGANMQRQAVPLLESEAPVVGTGMEKYAALDSGDSVLAKKPGV 643

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V  VDA  +++R+ +G        V  Y +MKF RSN   C NQR +VK G  V   D+I
Sbjct: 644 VSSVDAKTVIVRNDDGS-------VSTYPIMKFSRSNPGNCYNQRVVVKEGQRVEYRDVI 696

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD G+LALG+N+LVA+MPW G N+ED++++S+RMVSEDV TSIHIEE E+ ARDT
Sbjct: 697 ADGPSTDGGELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEIDARDT 756

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSE+ L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 757 KLGPEEITRDIPNVSEDVLSALDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 816

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           AIFGEK+ +VRDTSL+VP G SGTV+ +RIF+R   D+++
Sbjct: 817 AIFGEKSREVRDTSLKVPHGESGTVIGIRIFDRENNDEDD 856



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/314 (29%), Positives = 146/314 (46%), Gaps = 35/314 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E + +P+L+ +Q  S+D  +      +                 GL   F+ 
Sbjct: 21  RISFAKINEPLKVPNLLAIQTDSFDRLVGNERWAERLEKAQAAGDTSVPAQSGLAEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F   EF  PK+ V++C  RD TY+ PL I    +           +
Sbjct: 81  ISPIRDFQETMQLSFSEPEFADPKYSVEECKDRDATYSAPLYIKAEFM---------NLA 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG +F+    R   S K +Y+
Sbjct: 132 TGEVKQQTLFMGDFPLMTEAGTFVINGTERVVVSQLVRSPGAYFEKAPDRT--SDKDIYS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            R+IP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL+ F  Y  I  +
Sbjct: 190 ARVIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTESKILAEFGQYDSIRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D                +      +  GE   +E+ + L   +  + +   +  +G 
Sbjct: 250 LEKDSVK--------DRDEALLDIYRKLRPGEPPTVEAAQALLDNMYFTPRRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAED 311
              +   G+ V  D
Sbjct: 302 YKLNRKLGVDVPMD 315


>gi|254822773|ref|ZP_05227774.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            intracellulare ATCC 13950]
 gi|226511029|gb|ABD96035.2| RpoB [Mycobacterium indicus pranii]
          Length = 1148

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 190/513 (37%), Positives = 266/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 662  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 720

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 721  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 778

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 779  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 827

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 828  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 887

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+   +                      
Sbjct: 888  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN------------------ 928

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA EE +  ML            +D  
Sbjct: 929  -------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVMVDGD 975

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 976  GKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1035

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1036 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1095

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1096 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1128



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 335/694 (48%), Positives = 464/694 (66%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 152 LVRSPGVYFDETIDKSTEKLLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 209

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  + +TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 210 LLKALGWTNEQI----TERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESA 265

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +ED++A I+ LV L  G+
Sbjct: 266 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHEGQ 325

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 326 PTMTVPGGIEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 385

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 386 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 445

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+
Sbjct: 446 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLT 505

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+VS+A +
Sbjct: 506 ADEEDRHVVAQANSPIDAKGRFEESRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATA 565

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA +AG++E+
Sbjct: 566 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKAGVIEE 625

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF+RSN  TC NQ P+V  GD V    +IADG
Sbjct: 626 VSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAGDRVEAGQVIADG 678

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 679 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 738

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 739 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 798

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 799 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 832



 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 98/337 (29%), Positives = 154/337 (45%), Gaps = 32/337 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL-----------MMNIAPDERPNEGLQAAFKSV 62
           R  F K  E +++P L++VQ  S++  +             +  P   P  GL+     +
Sbjct: 7   RVSFAKLREPLEVPGLLDVQIDSFEWLIGAPRWREAAAARGDGKPGVTPVGGLEEVLLEL 66

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           + 
Sbjct: 67  SPIEDFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNT 117

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + KLL++ 
Sbjct: 118 GEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKLLHSV 175

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           ++IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     
Sbjct: 176 KVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTL 235

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
           +      +   L+   +       +  GE    ES + L   L    K   +  +G    
Sbjct: 236 EKDNTAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK- 288

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
                 +        T     E   V   + L  +  
Sbjct: 289 --VNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHE 323


>gi|283457532|ref|YP_003362115.1| DNA-directed RNA polymerase subunit beta [Rothia mucilaginosa DY-18]
 gi|283133530|dbj|BAI64295.1| DNA-directed RNA polymerase, beta subunit [Rothia mucilaginosa DY-18]
          Length = 1168

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 182/512 (35%), Positives = 263/512 (51%), Gaps = 62/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V   D++    +  G   +   + LL A    + ++  D  +     VS  V+
Sbjct: 683  VVKEGQRVEYRDVIADGPSTDG-GELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ D     DE+ I+         +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGPEEITRDIPNVSEDVLSALDERGIIHIGAEVEAGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                V   +        I +    +
Sbjct: 802  PKGETELTPEERLLRAIFGEKSREV--------RDTSLKVPHGESGTVIGIRIFDRENND 853

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +       DD+PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DG
Sbjct: 854  E-------DDLPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDG 906

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVP RMN+GQ+ E H GW     G KI+      K   +           
Sbjct: 907  TPVDVILNPLGVPGRMNIGQVLEVHTGWLAKQ-GWKIEGEPEWLKHMPNFPKE------- 958

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                                          ++TPVFDGA E+ +  ++  ++        
Sbjct: 959  -------------------------SGPTRLATPVFDGAHEDELFDLMDHSNPNRDGDRL 993

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++ SG++ L DG +GEPF  P++VGY Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 994  INRSGKARLIDGRSGEPFPDPISVGYQYILKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1053

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR +VYE+IV G +  E G PESF
Sbjct: 1054 QFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVAGRVKVYEAIVKGENIPEPGIPESF 1113

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++ ++  K     +   +
Sbjct: 1114 KVLIKEMQSLCLNVEVLSTDGKIIEMSDSEEE 1145



 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 338/640 (52%), Positives = 455/640 (71%), Gaps = 30/640 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL          IR TL  D  KDR +ALLDIYR +RPG+  T   A+ +
Sbjct: 226 LKALGWTESKIL--AEFGQYDSIRATLEKDSVKDRDEALLDIYRKLRPGEPPTVEAAQGL 283

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV---RHIRKEDIIAIIKILVDLRNG--- 449
            + ++F   +YDL+ VGR K+N +L +D P D      + ++DI  +I+ L  L  G   
Sbjct: 284 LDNMYFTPRRYDLAKVGRYKLNRKLGVDVPMDSPEASVLSQDDIAQMIRYLCALHAGETT 343

Query: 450 ------------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                       K  IDDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+D+
Sbjct: 344 IPGVRDGEEISLKVDIDDIDHFGNRRIRTVGELIENQIRTGLSRMERVVRERMTTQDVDA 403

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ L+N +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 404 ITPQSLVNIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 463

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL ++ R+N++GFIETPYR V DG+VT++V YL
Sbjct: 464 VRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRINSFGFIETPYRVVTDGRVTDEVRYL 523

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG---EEILVPREKIDFIDASPKQVVSI 674
           +A +E++  IAQAN+ L+ D +F E  V CR      E +LV    + ++D SP+Q+VS+
Sbjct: 524 TADDEKSVVIAQANAPLNADRTFAENEVLCRAGDGSGEAVLVAPGAVQYMDVSPRQMVSV 583

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIP+LE+DD+NR LMG NMQRQAVPLL++EAP VGTGME   A  SG +++AK+ G+
Sbjct: 584 ATALIPYLEHDDANRALMGANMQRQAVPLLESEAPVVGTGMEKYAALDSGDSVLAKKPGV 643

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V  VDA  +++R+ +G        V  Y +MKF RSN   C NQR +VK G  V   D+I
Sbjct: 644 VSSVDAKTVIVRNDDGS-------VSTYPIMKFSRSNPGNCYNQRVVVKEGQRVEYRDVI 696

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD G+LALG+N+LVA+MPW G N+ED++++S+RMVSEDV TSIHIEE E+ ARDT
Sbjct: 697 ADGPSTDGGELALGKNLLVAYMPWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEIDARDT 756

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPNVSE+ L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 757 KLGPEEITRDIPNVSEDVLSALDERGIIHIGAEVEAGDILVGKVTPKGETELTPEERLLR 816

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           AIFGEK+ +VRDTSL+VP G SGTV+ +RIF+R   D+++
Sbjct: 817 AIFGEKSREVRDTSLKVPHGESGTVIGIRIFDRENNDEDD 856



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 94/314 (29%), Positives = 146/314 (46%), Gaps = 35/314 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E + +P+L+ +Q  S+D  +      +                 GL   F+ 
Sbjct: 21  RISFAKINEPLKVPNLLAIQTDSFDRLVGNERWAERLEKAQAAGDNSVPAQSGLAEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F   EF  PK+ V++C  RD TY+ PL I    +           +
Sbjct: 81  ISPIRDFQETMQLSFSEPEFADPKYSVEECKDRDATYSAPLYIKAEFM---------NLA 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q+++MGD PLMT+ GTFVI G +R+VVSQL RSPG +F+    R   S K +Y+
Sbjct: 132 TGEVKQQTLFMGDFPLMTEAGTFVINGTERVVVSQLVRSPGAYFEKAPDRT--SDKDIYS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            R+IP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL+ F  Y  I  +
Sbjct: 190 ARVIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWTESKILAEFGQYDSIRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D                +      +  GE   +E+ + L   +  + +   +  +G 
Sbjct: 250 LEKDSVK--------DRDEALLDIYRKLRPGEPPTVEAAQGLLDNMYFTPRRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAED 311
              +   G+ V  D
Sbjct: 302 YKLNRKLGVDVPMD 315


>gi|318056672|ref|ZP_07975395.1| DNA-directed RNA polymerase subunit beta [Streptomyces sp. SA3_actG]
          Length = 1162

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 264/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+     V  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 676  IVNENDRVIVGQVLADGPATEN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 734

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 735  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVIAGDILVG 791

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +     +   
Sbjct: 792  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKV 834

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 835  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 894

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  +  D+             
Sbjct: 895  EDGTPVDIILNPLGVPSRMNPGQVMEIHLGWLASQ-GWDVSQVPEDWAQRLQAIS----- 948

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES- 1231
                                    A+Q   G  V+TPVFDGA E+ +  +L+    +   
Sbjct: 949  ------------------------ADQVAPGTNVATPVFDGAREDELTGLLQHTIPNRDG 984

Query: 1232 -------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GEPF  P+++GY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 985  DRMVLPSGKARLFDGRSGEPFPDPISLGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1044

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1045 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1104

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1105 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1139



 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 338/671 (50%), Positives = 454/671 (67%), Gaps = 39/671 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGQYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT-------------IDDIDNLGN 461
           K+N +L  + P D   +  +DI+A IK LV L  G+                DDID+ GN
Sbjct: 303 KVNKKLGSEAPLDAGVLTTDDILATIKYLVQLHAGETEATVGDEGKTIVVETDDIDHFGN 362

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQ
Sbjct: 363 RRLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQ 422

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIG
Sbjct: 423 LSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 482

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL S+ RVNA+GF+ETPYRKV DG VT+DV YL+A EE+   IAQAN+ L +D  F 
Sbjct: 483 LIGSLASYGRVNAFGFVETPYRKVVDGVVTDDVDYLTADEEDRFVIAQANAPLTDDLHFE 542

Query: 642 EELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQA
Sbjct: 543 EARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQA 602

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL+K+EAP VGTGME   A  +G  + A + G+V++V A  I   + +G          
Sbjct: 603 VPLIKSEAPIVGTGMEYRSATDAGDVLKADKDGVVQEVSADYITTANDDGT-------YT 655

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            YRL KF RSNQ T VNQ+ +V   D V    ++ADGP+T+ G++ALG+N+LVAFMPW G
Sbjct: 656 TYRLAKFSRSNQGTSVNQKVIVNENDRVIVGQVLADGPATENGEMALGKNLLVAFMPWEG 715

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           +N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE G
Sbjct: 716 HNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERG 775

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+
Sbjct: 776 IIRIGAEVIAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVI 835

Query: 941 DVRIFNRHGID 951
            VR+F+R   D
Sbjct: 836 GVRVFDREEGD 846



 Score =  340 bits (871), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 104/325 (32%), Positives = 155/325 (47%), Gaps = 34/325 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 21  LRISFAKIREPLEVPNLLALQTESFDWLLGNDAWKSRVEAALAGGMSVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD TYA PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +Y+
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIYS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGQYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      +  GE    E+ + L   L  + K   +  +G 
Sbjct: 250 LEKDHTQGQDDA--------LLDIYRKLRPGEPPTREAAQNLLENLYFNPKRYDLAKVGR 301

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYI 322
              +   G     D     T +I  
Sbjct: 302 YKVNKKLGSEAPLDAGVLTTDDILA 326


>gi|15840070|ref|NP_335107.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis CDC1551]
 gi|215429504|ref|ZP_03427423.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis EAS054]
 gi|254363617|ref|ZP_04979663.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis str. Haarlem]
 gi|289744390|ref|ZP_06503768.1| DNA-directed RNA polymerase beta subunit rpoB [Mycobacterium
           tuberculosis 02_1987]
 gi|308231612|ref|ZP_07413113.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu001]
 gi|308369985|ref|ZP_07419828.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu002]
 gi|308370471|ref|ZP_07421638.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu003]
 gi|308371732|ref|ZP_07426008.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu004]
 gi|308373544|ref|ZP_07432754.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu005]
 gi|308374070|ref|ZP_07434722.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu006]
 gi|308375224|ref|ZP_07443157.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu007]
 gi|308376470|ref|ZP_07438947.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu008]
 gi|308377489|ref|ZP_07479348.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu009]
 gi|308378694|ref|ZP_07483541.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu010]
 gi|308379838|ref|ZP_07487778.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu011]
 gi|308396371|ref|ZP_07492284.2| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu012]
 gi|61234284|sp|P0A680|RPOB_MYCTU RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|61234288|sp|P0A681|RPOB_MYCBO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|158513177|sp|A1KGE7|RPOB_MYCBP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|13880218|gb|AAK44921.1| DNA-directed RNA polymerase, beta subunit [Mycobacterium
           tuberculosis CDC1551]
 gi|134149131|gb|EBA41176.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis str. Haarlem]
 gi|289684918|gb|EFD52406.1| DNA-directed RNA polymerase beta subunit rpoB [Mycobacterium
           tuberculosis 02_1987]
 gi|308216669|gb|EFO76068.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu001]
 gi|308325788|gb|EFP14639.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu002]
 gi|308331812|gb|EFP20663.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu003]
 gi|308335598|gb|EFP24449.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu004]
 gi|308337215|gb|EFP26066.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu005]
 gi|308343081|gb|EFP31932.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu006]
 gi|308346965|gb|EFP35816.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu007]
 gi|308350945|gb|EFP39796.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu008]
 gi|308355541|gb|EFP44392.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu009]
 gi|308359500|gb|EFP48351.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu010]
 gi|308363404|gb|EFP52255.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu011]
 gi|308367132|gb|EFP55983.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis SUMu012]
 gi|323720889|gb|EGB29955.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis CDC1551A]
 gi|328457389|gb|AEB02812.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis KZN 4207]
          Length = 1178

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 455/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 209 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 264

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 265 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 324

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 325 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 384

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 385 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 444

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 445 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 504

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 505 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 564

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 565 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 624

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 625 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 677

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 678 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 737

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 738 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 797

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 798 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 857

Query: 950 ID 951
            D
Sbjct: 858 ED 859



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 748  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 807

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 808  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 850

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 851  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 910

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 911  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 960

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 961  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 1001

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1002 VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1061

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1062 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1121

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1122 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1158



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 318 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 350


>gi|15828010|ref|NP_302273.1| DNA-directed RNA polymerase subunit beta [Mycobacterium leprae TN]
 gi|221230487|ref|YP_002503903.1| DNA-directed RNA polymerase subunit beta [Mycobacterium leprae
            Br4923]
 gi|13432231|sp|P30760|RPOB_MYCLE RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|254765297|sp|B8ZSC7|RPOB_MYCLB RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|13093563|emb|CAC30845.1| [beta] subunit of RNA polymerase [Mycobacterium leprae]
 gi|219933594|emb|CAR71987.1| [beta] subunit of RNA polymerase [Mycobacterium leprae Br4923]
          Length = 1178

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/513 (37%), Positives = 268/513 (52%), Gaps = 53/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 805

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 806  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 854

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 855  HEDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVD 914

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMNVGQI ETHLGW     G KI           ++              
Sbjct: 915  IILNTHGVPRRMNVGQILETHLGWVAKS-GWKIDVAGGIPDWAVNLP------------- 960

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                       + +L  A        VSTPVFDGA EE +  +L     +          
Sbjct: 961  -----------EELLHAAPNQI----VSTPVFDGAKEEELQGLLSSTLPNRDGDVMVGGD 1005

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1006 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1065

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1066 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1125

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1126 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1158



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/689 (47%), Positives = 462/689 (67%), Gaps = 28/689 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + +       +  
Sbjct: 179 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 234

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         I   +    +  +R+TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 235 TVLLKALGWTSEQI--TERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESA 292

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L   +      + +ED++A I+ LV L  G+
Sbjct: 293 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGELITSSTLTEEDVVATIEYLVRLHEGQ 352

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 353 STMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 412

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 413 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 472

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++++ YL+
Sbjct: 473 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIEYLT 532

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +DE G F E  V  R   GE   V   ++D++D SP+Q+VS+A +
Sbjct: 533 ADEEDRHVVAQANSPIDEAGRFLEPRVLVRRKAGEVEYVASSEVDYMDVSPRQMVSVATA 592

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G++E+
Sbjct: 593 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGHVVVAEKSGVIEE 652

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF RSN  TC NQ P+V  GD V    +IADG
Sbjct: 653 VSADYITVMADDGTR-------RTYRMRKFARSNHGTCANQSPIVDAGDRVEAGQVIADG 705

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 706 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 765

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 766 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 825

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           GEKA +VRDTSL+VP G SG V+ +R+F+
Sbjct: 826 GEKAREVRDTSLKVPHGESGKVIGIRVFS 854



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 99/370 (26%), Positives = 168/370 (45%), Gaps = 25/370 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMM---NIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +       A   R +     GL+     + PI 
Sbjct: 38  RISFAKLREPLEVPGLLDVQTDSFEWLIGSPCWRAAAASRGDLKPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVEECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F     +  +   D 
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMRSTLEKDN 266

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+ +  
Sbjct: 267 TVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGE 326

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV---DSVNNNAYIR 359
           L       +     T E  +   +     ++       +    I +            I+
Sbjct: 327 LITSSTLTEEDVVATIEYLVRLHEGQSTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQ 386

Query: 360 NTLVTDKNKD 369
           N +    ++ 
Sbjct: 387 NQIRVGMSRM 396


>gi|126433605|ref|YP_001069296.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. JLS]
 gi|158513447|sp|A3PV78|RPOB_MYCSJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|126233405|gb|ABN96805.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. JLS]
          Length = 1172

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 270/515 (52%), Gaps = 54/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I     D   +                 
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAGADGVPDWA--------------- 950

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                       + +        S   V+TPVFDGA E  ++ +L            ++E 
Sbjct: 951  -----------EKLPEELYSAPSDSIVATPVFDGARENELSGLLASTLPNRDGDVMVNED 999

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1000 GKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1059

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1060 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1119

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1120 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1150



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 456/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNL--DTPDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L  D P     + +ED++A I+ LV L  G+              +DD
Sbjct: 302 RVGRYKVNKKLGLNTDKPITSSTLTEEDVVATIEYLVRLHEGQATMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS LD
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPLD 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           ++G FTE+ V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 DEGHFTEDRVLVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++AG+VE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKAGVVEEVSADYITVMADDGTR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T  G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTQNGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  313 bits (803), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 97/333 (29%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +        R +     GL+     + PI 
Sbjct: 30  RISFAKLREPLEVPGLLDVQTESFDWLIGADSWRQRATARGDVNPTGGLEEVLTELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNTDKPITSSTLTEEDVVATIEYLVRLHE 342


>gi|34391553|gb|AAN65354.1| RpoB [Mycobacterium septicum]
          Length = 1185

 Score =  518 bits (1334), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 265/515 (51%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 696  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 754

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 755  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 812

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 813  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 861

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 862  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDGTPVD 921

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +              
Sbjct: 922  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP------ 974

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                      VSTPVFDGA EE +  +L     +          
Sbjct: 975  ----------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 1012

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1013 GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1072

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1073 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1132

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1133 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1163



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 456/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 199 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 256

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 257 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 316

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 317 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 376

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 377 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 436

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 437 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 496

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ + YL+A EE+   +AQANS +D
Sbjct: 497 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDQIDYLTADEEDRHVVAQANSPID 556

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DGSFTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 557 ADGSFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 616

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AG+VE+V A  I + + +G    
Sbjct: 617 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGVVEEVSADYITVMADDGSR-- 674

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 675 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 729

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 730 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 789

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 790 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 849

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 850 ESGKVIGIRVFSREDDD 866



 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 155/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 45  RVSFAKLREPLEVPGLLDVQTDSFDWLVGADGWRQKAVDRGETNPKGGLEEVLEELSPIE 104

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 105 DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 155

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 156 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDDSIDK--STEKTLHSVKVIP 213

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 214 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDS 273

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 274 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 324

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 325 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 357


>gi|118468129|ref|YP_885753.1| DNA-directed RNA polymerase subunit beta [Mycobacterium smegmatis
            str. MC2 155]
 gi|41017600|sp|P60281|RPOB_MYCS2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|38174793|emb|CAE53837.1| RNA polymerase, beta subunit [Mycobacterium smegmatis]
 gi|118169416|gb|ABK70312.1| DNA-directed RNA polymerase, beta subunit [Mycobacterium smegmatis
            str. MC2 155]
          Length = 1169

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +        ++    
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGVPDWASKLPE------ELYSAP 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
            + +                       V+TPVFDGA E  +  +L            +D  
Sbjct: 959  ADST----------------------VATPVFDGAQEGELAGLLGSTLPNRDGEVMVDAD 996

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1147



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 455/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGKPITSSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS  D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTD 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G FTE+ V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 ENGRFTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +VA + G++E+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGVIEEVSADYITVMADDGTRQS 660

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSN  TC NQRP+V  G  V    +IADGP T  G++ALG+N+LVA
Sbjct: 661 -------YRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 98/333 (29%), Positives = 157/333 (47%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI---APDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    A  +R  E    GL+     + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEENPVGGLEEVLAELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDT 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TSGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGKPITSSTLTEEDVVATIEYLVRLHE 341


>gi|326777284|ref|ZP_08236549.1| DNA-directed RNA polymerase subunit beta [Streptomyces cf. griseus
            XylebKG-1]
 gi|326657617|gb|EGE42463.1| DNA-directed RNA polymerase subunit beta [Streptomyces cf. griseus
            XylebKG-1]
          Length = 1161

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 191/514 (37%), Positives = 265/514 (51%), Gaps = 73/514 (14%)

Query: 888  VNPGDILVGKIT-----PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            V+ GD +V               M   + LL A    +  +  D  +     V   V+  
Sbjct: 676  VSEGDRIVADQVLADGPATENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSS 735

Query: 943  RIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                 H  + + R   +  E+I        E +  D  DE+ I+         +IL G+ 
Sbjct: 736  IHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVVAGDILVGKV 792

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +     +     
Sbjct: 793  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEIGKVIG 835

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+D
Sbjct: 836  VRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLED 895

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  +  L +++               
Sbjct: 896  GTPVDIILNPLGVPSRMNPGQVLEIHLGWLAS-RGWDVSGLGDEWAQRLQAIG------- 947

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----- 1229
                                  A+Q   G  V+TPVFDGA E+ I+  L  A +      
Sbjct: 948  ----------------------ADQVAPGTNVATPVFDGAREDEISG-LFEATIPNRDGD 984

Query: 1230 ----ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 SG++ L+DG +GEPF  PV+VG++Y+LKL+H+V DK++ARSTG YS++TQQPLGG
Sbjct: 985  RLVQPSGKAQLFDGRSGEPFPDPVSVGFMYILKLHHLVDDKLHARSTGPYSMITQQPLGG 1044

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PE
Sbjct: 1045 KAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPE 1104

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            SF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1105 SFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1138



 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 461/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 201 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 245

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 246 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 302

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 303 KVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNR 362

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 363 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 422

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 423 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 482

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L+++  FTE
Sbjct: 483 IGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLNDELRFTE 542

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             V  R   GE   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 543 PRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 602

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G           
Sbjct: 603 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDGT-------YTT 655

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++ALG+N+LVAFMPW G+
Sbjct: 656 YRIAKFMRSNQGTSVNQKVVVSEGDRIVADQVLADGPATENGEMALGKNLLVAFMPWEGH 715

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 716 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 775

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ 
Sbjct: 776 IRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIG 835

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 836 VRVFDREEGD 845



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 116/486 (23%), Positives = 204/486 (41%), Gaps = 44/486 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 189

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F  Y  +  +
Sbjct: 190 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 249

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            +  + ++E+         L K  + K  K LG
Sbjct: 250 LEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 309

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPI 346
                  G+   +D++      + + AG+                 ++   +  +R++  
Sbjct: 310 ADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGESGREIVVETDDIDHFGNRRLRNVGE 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  + V         +V ++   +   +  I            +  +  F          
Sbjct: 370 LIQNQVRTGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMD 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
             + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  
Sbjct: 428 QNNPLSGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGL 482

Query: 467 VGEMLK 472
           +G +  
Sbjct: 483 IGSLAS 488


>gi|269219017|ref|ZP_06162871.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            848 str. F0332]
 gi|269212128|gb|EEZ78468.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            848 str. F0332]
          Length = 1153

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 172/510 (33%), Positives = 258/510 (50%), Gaps = 55/510 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G ++      +G   +   + LL A       +  D  +     V   ++
Sbjct: 665  VVGPGDRLEAGTLIADGPATEG-GELALGQNLLVAFMTWNGFNYEDAIILSERCVKDDLL 723

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD +   R+   +   + + G 
Sbjct: 724  TSIHIEEH--EVDARDTKLGPEEITRDIPNVSDEMLSHLDEHGVIRIGAEVQAGDILVGK 781

Query: 1000 KGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
               K  T L+S+  L+      +  +      +V      + +                 
Sbjct: 782  ITPKGETELTSEERLLRAIFGEKAKEVRDTSLRVPHGESGIVIGVRQFTKD--------- 832

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                  D++   V   V+V++A +R I  GDKMAGRHGNKG++SRILP EDMPF++DGTP
Sbjct: 833  ----NNDELASDVNETVRVYIAQRRKITIGDKMAGRHGNKGVISRILPVEDMPFMEDGTP 888

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNPLGVP RMN+GQ++E HLGW                                  
Sbjct: 889  VDIILNPLGVPGRMNLGQVYELHLGWIASQ----------------------------GW 920

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
              S   +  +   + +     + K G  V+TPVFDG   + +  +L     +        
Sbjct: 921  DASAAREAGEAWAERLPEATVKGKPGQHVATPVFDGVRGDELAGLLGSTLPNRDGEVLVN 980

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G++ L+DG +GEPF  P++VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  
Sbjct: 981  AEGKARLFDGRSGEPFPEPISVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQF 1040

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGA++ LQEMLTIKSDD VGR +VYE+IV G++  E G PESF V
Sbjct: 1041 GGQRFGEMEVWALEAYGASHTLQEMLTIKSDDTVGRVKVYEAIVKGDNVPEAGIPESFKV 1100

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            L++EM++L L+++  ++  +     +   D
Sbjct: 1101 LIQEMRSLCLNVEALDAAGQAINLQDTEED 1130



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 323/706 (45%), Positives = 454/706 (64%), Gaps = 38/706 (5%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGEIY--------- 321
           E G  + +G  + +  + V+  G+  + L      +D+ N       G            
Sbjct: 139 ERGTFIINGTERVVVSQLVRSPGVYYERLADKTSDKDVFNVKIIPSRGAWLEFEIDKRDA 198

Query: 322 --IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
             +       +     +    + +  I   +   +   +  TL  D    +++AL D+YR
Sbjct: 199 VGVRVDRKRKQSVTVFLKALGMSESEI--REIFGDFPALIETLEKDTVHTQEEALTDLYR 256

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  T     ++ N  +F++ +YD + VGR K+N +L LD  ++ R +   DI A+
Sbjct: 257 KLRPGEPPTAEAGRALLNNFYFNTKRYDTAKVGRFKLNKKLGLDPANESRQLGISDITAV 316

Query: 440 IKILVDLRNGKGTI-------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           ++ L+ L  G   +             DDID+ GNRR+R+VGE+++NQ R GL R++R +
Sbjct: 317 LRYLLALHAGHEKVVCGEGGAEVEIETDDIDHFGNRRIRAVGELIQNQVRTGLSRLDRMV 376

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+++ + +++ P  LIN +P+V+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG 
Sbjct: 377 RERMTTQEAEAITPSSLINIRPIVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGP 436

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL SFAR+N +GFIETPYR V 
Sbjct: 437 GGLSRDRAGMEVRDVHSSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFIETPYRVVN 496

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGEEILVPREKIDFID 665
           +G VT+++VYL A +E+   IAQA   LDE+  F +E V CR   GE  LVP ++IDF+D
Sbjct: 497 NGVVTDEIVYLQADDEDRAVIAQAEVPLDENNRFVDEEVLCRMPGGEPALVPVDEIDFMD 556

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +Q+ S+  ++IPFLE+DD+NR LMG NMQRQAVPL++  AP+VGTGME   A  +G 
Sbjct: 557 VSARQMCSVGTAMIPFLEHDDANRALMGANMQRQAVPLIRPSAPYVGTGMEMRSAVDAGD 616

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAK  G+V +VDA  +V+    G           Y+L KF RSN   C NQ+ +V  G
Sbjct: 617 VTVAKEPGVVLEVDADSVVVEQDNGRHV-------TYKLTKFDRSNPGNCTNQQVVVGPG 669

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D +    +IADGP+T+ G+LALG+N+LVAFM W+G+N+ED++++SER V +D+ TSIHIE
Sbjct: 670 DRLEAGTLIADGPATEGGELALGQNLLVAFMTWNGFNYEDAIILSERCVKDDLLTSIHIE 729

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           E EV ARDTKLGPEEITRDIPNVS+E L ++DE G+I +GAEV  GDILVGKITPKGE+ 
Sbjct: 730 EHEVDARDTKLGPEEITRDIPNVSDEMLSHLDEHGVIRIGAEVQAGDILVGKITPKGETE 789

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +T EE+LLRAIFGEKA +VRDTSLRVP G SG V+ VR F +   D
Sbjct: 790 LTSEERLLRAIFGEKAKEVRDTSLRVPHGESGIVIGVRQFTKDNND 835



 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 88/292 (30%), Positives = 141/292 (48%), Gaps = 17/292 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMN--IAPDERPNEGLQAAFKSVFPITAFSGA 71
           R  F K  E +  P+L+ +Q  S+   +      + +     GL+  F+ + PI   +  
Sbjct: 20  RVSFAKIHEPLQPPNLLGLQTDSFGWLVGSEQWTSRNPGSQSGLEEIFEEISPIENAAQT 79

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L   S   + PK+ + +C  RDLTYA PL +T     ++           +IK Q+ +
Sbjct: 80  MGLVLSSPHLEDPKYSIAECRERDLTYAAPLYVTAEFQNYE---------TGEIKSQTTF 130

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +GD PLMT+ GTF+I G +R+VVSQL RSPG++++    +   S K ++  +IIP +G W
Sbjct: 131 IGDFPLMTERGTFIINGTERVVVSQLVRSPGVYYERLADKT--SDKDVFNVKIIPSRGAW 188

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VR+DR+RK  VT FL ALGM   EI   F  +P ++ +   D      
Sbjct: 189 LEFEIDKRDAVGVRVDRKRKQSVTVFLKALGMSESEIREIFGDFPALIETLEKDTVHTQE 248

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLGIT 299
            A   +            + G  ++ +    T      K  + K  K LG+ 
Sbjct: 249 EALTDLYRKLRPGEPPTAEAGRALLNNFYFNTKRYDTAKVGRFKLNKKLGLD 300


>gi|158513701|sp|A5U052|RPOB_MYCTA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1177

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 455/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 208 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 263

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 264 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 323

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 324 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 383

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 384 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 443

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 444 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 503

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 504 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 563

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 564 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 623

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 624 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 676

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 677 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 736

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 737 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 796

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 797 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 856

Query: 950 ID 951
            D
Sbjct: 857 ED 858



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 688  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 746

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 747  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 806

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 807  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 849

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 850  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 909

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 910  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 959

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 960  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 1000

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1001 VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1060

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1061 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1120

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1121 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1157



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 37  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 96

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 97  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 147

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 148 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 205

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 206 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 265

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 266 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 316

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 317 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 349


>gi|300782587|ref|YP_003762878.1| DNA-directed RNA polymerase subunit beta [Amycolatopsis mediterranei
            U32]
 gi|299792101|gb|ADJ42476.1| DNA-directed RNA polymerase subunit beta [Amycolatopsis mediterranei
            U32]
          Length = 1167

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 182/513 (35%), Positives = 257/513 (50%), Gaps = 65/513 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G ++    + +    +   + LL A+   +  +  D  +     V   V+
Sbjct: 680  IVNEGDRIEAGQVIADGPSTEN-GEVALGKNLLVAVMPWEGHNYEDAIILSERLVQDDVL 738

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          E +  D  DE+ I+      R  +IL G+ 
Sbjct: 739  TSIHIEEHEIDARDTKLGAEEITWDIPNVSEEVLADL-DERGIIRIGAEVRDGDILVGKV 797

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 798  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 840

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++PPGV  +V+V+VA KR IQSGDK+AGRHGNKG++ +ILP EDMPF++D
Sbjct: 841  IRVFSREDDDELPPGVNELVRVYVAQKRKIQSGDKLAGRHGNKGVIGKILPVEDMPFMED 900

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI E HLGW     G  I+   +  K              
Sbjct: 901  GTPVDIILNTHGVPRRMNIGQILELHLGWLASQ-GWTIEGDPDWAKN------------- 946

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES--- 1231
                              +         G   +TPVFDGA EE +  +L     +     
Sbjct: 947  ------------------LSAELRDVAPGTNTATPVFDGAKEEELTGLLSATKPNRDGER 988

Query: 1232 -----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEP+  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 989  MVKENGKANLFDGRSGEPYPYPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1048

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1049 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1108

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ +S   +    +   +
Sbjct: 1109 FKVLLKELQSLCLNVEVLSSDGSSIEMRDSDDE 1141



 Score =  506 bits (1302), Expect = e-140,   Method: Composition-based stats.
 Identities = 319/602 (52%), Positives = 437/602 (72%), Gaps = 20/602 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D      +ALLDIYR +RPG+  T   A+++   LFF + +YDL+ VGR K+N +L L
Sbjct: 256 EKDHTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKAKRYDLAKVGRYKVNKKLGL 315

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
            TP +   + +EDI+ II+ LV L  G+  +            DDID+ GNRR+R+VGE+
Sbjct: 316 STPIENGTLTEEDIVTIIEYLVRLHAGEDKMTAANNTEIPVETDDIDHFGNRRIRTVGEL 375

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL R ER ++ER+++ D++++ PQ LIN +P+ +A+ EFF +SQLSQ  +  N
Sbjct: 376 IQNQIRVGLSRTERVVRERMTTQDVEAITPQTLINIRPIGAAIKEFFGTSQLSQFMQQTN 435

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +  +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 436 PIDGLTHKRRLNALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLCSYA 495

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV +G+VT+ + YL+A EE+    AQAN+ + +DG+F E+ V  R  
Sbjct: 496 RVNPFGFIETPYRKVVEGRVTDQIDYLTADEEDRFVKAQANAPISDDGTFIEDRVMARRK 555

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE  L+    ID++D SP+Q+VSIA ++IPFLE+DD+NR LMG NMQRQAVPLL+++AP
Sbjct: 556 GGEVELIDPLDIDYMDVSPRQMVSIATAMIPFLEHDDANRALMGANMQRQAVPLLRSQAP 615

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTG+E   A  SG  +VA+++G+VE++ A  I +   +G           Y L KF+R
Sbjct: 616 YVGTGVELRAAIDSGDMLVAEQSGVVEELSADLITVMHDDGTRKS-------YSLYKFRR 668

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC N RP+V  GD +    +IADGPST+ G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 669 SNHGTCFNHRPIVNEGDRIEAGQVIADGPSTENGEVALGKNLLVAVMPWEGHNYEDAIIL 728

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV TSIHIEE E+ ARDTKLG EEIT DIPNVSEE L ++DE GII +GAEV 
Sbjct: 729 SERLVQDDVLTSIHIEEHEIDARDTKLGAEEITWDIPNVSEEVLADLDERGIIRIGAEVR 788

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ +R+F+R  
Sbjct: 789 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGIRVFSRED 848

Query: 950 ID 951
            D
Sbjct: 849 DD 850



 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 113/481 (23%), Positives = 201/481 (41%), Gaps = 40/481 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E ++ P+L++VQ  S+  F         R  EG       L+     + PI 
Sbjct: 31  RVSFAKIREPLNTPNLLDVQIQSFQWFTGDEAWFQRRVEEGEENPVGGLEEVLNEISPIE 90

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F +  FD  K  +++C  +D+TYA PL +T   +           +  +IK
Sbjct: 91  DFSGSMSLSFSAPRFDEVKASIEECKDKDMTYAAPLFVTAEFV---------NNNTGEIK 141

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q++++GD P+MT  GTFVI G +R+VVSQL RSPG+++  D  +   S K +++ R+IP
Sbjct: 142 SQTVFLGDFPVMTDKGTFVINGTERVVVSQLVRSPGVYYSKDIDKT--SDKDVFSVRVIP 199

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I    +F   ++ +   D 
Sbjct: 200 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEAIRERFSFSETLLATLEKDH 259

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K     L K  + K  K LG+++  
Sbjct: 260 TAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKAKRYDLAKVGRYKVNKKLGLSTPI 319

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVID-----------EKSLEEIFHSEIRDIPILYVDS 351
             G    EDIV      + + AG+                 ++   +  IR +  L  + 
Sbjct: 320 ENGTLTEEDIVTIIEYLVRLHAGEDKMTAANNTEIPVETDDIDHFGNRRIRTVGELIQNQ 379

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +         +V ++   +   +  I            +  +  F            + +
Sbjct: 380 IRVGLSRTERVVRERMTTQD--VEAITPQTLINIRPIGAAIKEFFGTSQLSQFMQQTNPI 437

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
             +    RLN   P     + +E     ++ +     G+  +  I+      +  +G + 
Sbjct: 438 DGLTHKRRLNALGPGG---LSRERAGMEVRDVHPSHYGR--MCPIETPEGPNIGLIGSLC 492

Query: 472 K 472
            
Sbjct: 493 S 493


>gi|169830427|ref|YP_001716409.1| DNA-directed RNA polymerase subunit beta [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637271|gb|ACA58777.1| DNA-directed RNA polymerase, beta subunit [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 1183

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 343/629 (54%), Positives = 450/629 (71%), Gaps = 34/629 (5%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D  + +  I+ TL  D     +DAL++IY+ +RPG+  T   A S+   LFFD  +YDL+
Sbjct: 204 DLFDQHKSIQETLNKDNTDSEEDALIEIYKRLRPGEPPTADSARSLLETLFFDPKRYDLA 263

Query: 410 TVGRVKMNMRLNLDT-------------------------PDDVRHIRKEDIIAIIKILV 444
            VGR K+  +L                              + +R + +EDI+A ++ L+
Sbjct: 264 AVGRYKLFKKLKHGVLYRFDKEQSGRTEFDPYLKQEVPVEREFIRELTREDILATVRYLI 323

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L  G+G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER++  D++ + PQ LI
Sbjct: 324 RLMQGEGRADDIDHLGNRRLRSVGELLQNQFRIGLARMERVVRERMTIQDVEVITPQALI 383

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVH +
Sbjct: 384 NIRPVVASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHS 443

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+ SLT++ARVN +GFIETPY+KV     +VT ++VYL+A EE
Sbjct: 444 HYGRVCPIETPEGPNIGLIGSLTTYARVNEFGFIETPYQKVDKEKRRVTEEIVYLTADEE 503

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   IAQAN  LDE+G F E  V CR  GE ++V   ++D++D SPKQV S+A SLIPFL
Sbjct: 504 EEYVIAQANVELDENGHFVENRVDCRYRGEIMVVDAGRVDYVDVSPKQVFSVATSLIPFL 563

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+DD+NR LMG NMQRQAVPLL +EAPF+GTG+E+  A  SG  ++A+R G+ E+V A  
Sbjct: 564 EHDDANRALMGANMQRQAVPLLISEAPFIGTGIEAKAAYDSGVLVIAERGGVAERVTATE 623

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           I IR+       S+  VD YRL KF RSNQ TC NQRP++  GD +    +IADGP TD 
Sbjct: 624 IKIRT-------SSGAVDHYRLTKFGRSNQGTCFNQRPIISRGDRIAAGQVIADGPCTDH 676

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
           G+LALGRN+L AFMPW GYN+ED++L+SE++V ED++TSIHIEE+E  ARDTKLGPEEIT
Sbjct: 677 GELALGRNVLTAFMPWEGYNYEDAILVSEKLVKEDLYTSIHIEEYECDARDTKLGPEEIT 736

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV +E LK++D+ G+I +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA 
Sbjct: 737 RDIPNVGDEALKDLDDRGVIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR 796

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G SG VVDV++F+R   D
Sbjct: 797 EVRDTSLRVPHGESGKVVDVKVFSRENGD 825



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 184/589 (31%), Positives = 261/589 (44%), Gaps = 76/589 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       +L++  P+ G   E        ++       V   +   E ++    T 
Sbjct: 573  MGANMQRQAVPLLISEAPFIGTGIEAKAAYDSGVLVIAERGGVAERVTATEIKI---RTS 629

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  II  G  +  G ++           +     +L A
Sbjct: 630  SGAVDHYRLTKFGRSNQGTCFNQRPIISRGDRIAAGQVIADGPCT-DHGELALGRNVLTA 688

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
                +  +  D  L     V   +      +    + + R   +  E+I     +  DE 
Sbjct: 689  FMPWEGYNYEDAILVSEKLVKEDL--YTSIHIEEYECDARDTKLGPEEITRDIPNVGDEA 746

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+     G    SG     K T      ++   R     F  +  +V+  
Sbjct: 747  LKDLDDRGVIRI-----GAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDT 801

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +          +      K+   + GD++PPGV R+V+V+VA KR +  GDKMAGRH
Sbjct: 802  SLRVPHGESGKVVDV------KVFSRENGDELPPGVNRLVRVYVAQKRKLSEGDKMAGRH 855

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+++RI+P EDMPF+ DGTP+++VLNPLGVPSRMN+GQ+FE+HLGWA   LG  I +
Sbjct: 856  GNKGVIARIMPEEDMPFMPDGTPIEVVLNPLGVPSRMNIGQVFESHLGWAAKILGYNIAT 915

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             +    +  +I                                                 
Sbjct: 916  PVFSGASEAEIIRTLEESGLPTDGKVRL-------------------------------- 943

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G++       G+ FD PVTVGY+YMLKL H+V DK++ARSTG 
Sbjct: 944  ---------------RDGRT-------GKEFDNPVTVGYLYMLKLAHLVDDKIHARSTGP 981

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV 
Sbjct: 982  YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVK 1041

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            G +  E G PESF VLVKE+Q+LGL + +           E   D  + 
Sbjct: 1042 GENVPEPGVPESFKVLVKELQSLGLDVKVLTEENTEIEIKELDEDVTET 1090



 Score =  367 bits (942), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 160/309 (51%), Gaps = 30/309 (9%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R R+ FGK  E++D+PDL+EVQK SYD FL          ++GL+  F  + PI  F+
Sbjct: 5   KPRERRLFGKLREVLDLPDLVEVQKRSYDWFL----------DKGLREVFHDISPIQDFT 54

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           G  +LEF+ Y+   PK+ V +C  RD+T+A P++I +RLI          +   ++KEQ 
Sbjct: 55  GNLVLEFLDYQLGEPKYTVQECKDRDVTFAAPMRIKVRLI---------NRETGEVKEQD 105

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R++VSQL RSPG++FD        SGK +Y+  +IP++G
Sbjct: 106 VFMGDFPLMTEKGTFIINGAERVIVSQLVRSPGVYFDIQPD---PSGKQIYSATVIPNRG 162

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFP 248
            W++ E D +D I VR+DR RK+P T  + ALG  ++  IL  F       +  +     
Sbjct: 163 AWLEFETDVQDQIWVRVDRTRKIPATVLIKALGFGNKARILDLFDQHKSIQETLNKDNTD 222

Query: 249 LSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
                L+   K       +  GE    +S + L   L    K   +  +G         +
Sbjct: 223 SEEDALIEIYK------RLRPGEPPTADSARSLLETLFFDPKRYDLAAVGRYKLFKKLKH 276

Query: 308 VAEDIVNGE 316
                 + E
Sbjct: 277 GVLYRFDKE 285


>gi|119867039|ref|YP_936991.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. KMS]
 gi|158513056|sp|A1UBJ3|RPOB_MYCSK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158564121|sp|Q1BDF0|RPOB_MYCSS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119693128|gb|ABL90201.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. KMS]
          Length = 1172

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 270/515 (52%), Gaps = 54/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I     D   +                 
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAGADGVPDWA--------------- 950

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                       + +        S   V+TPVFDGA E  ++ +L            ++E 
Sbjct: 951  -----------EKLPEELYSAPSDSIVATPVFDGARENELSGLLASTLPNRDGDVMVNED 999

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1000 GKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1059

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1060 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1119

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1120 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1150



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 455/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNL--DTPDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L  D P     + +ED++A I+ LV L  G               +DD
Sbjct: 302 RVGRYKVNKKLGLNTDKPITSSTLTEEDVVATIEYLVRLHQGDTVMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS LD
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPLD 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           ++G FTE+ V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 DEGHFTEDRVLVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++AG+VE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKAGVVEEVSADYITVMADDGTR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T  G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTQNGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 97/333 (29%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +        R +     GL+     + PI 
Sbjct: 30  RISFAKLREPLEVPGLLDVQTESFDWLIGADSWRQRATARGDVNPTGGLEEVLTELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNTDKPITSSTLTEEDVVATIEYLVRLHQ 342


>gi|15607807|ref|NP_215181.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis H37Rv]
 gi|31791851|ref|NP_854344.1| DNA-directed RNA polymerase subunit beta [Mycobacterium bovis
           AF2122/97]
 gi|121636588|ref|YP_976811.1| DNA-directed RNA polymerase subunit beta [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|148660441|ref|YP_001281964.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis H37Ra]
 gi|224989060|ref|YP_002643747.1| DNA-directed RNA polymerase subunit beta [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|260185548|ref|ZP_05763022.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis CPHL_A]
 gi|260199674|ref|ZP_05767165.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis T46]
 gi|289442064|ref|ZP_06431808.1| DNA-directed RNA polymerase, beta subunit [Mycobacterium
           tuberculosis T46]
 gi|289446225|ref|ZP_06435969.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis CPHL_A]
 gi|289568606|ref|ZP_06448833.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis T17]
 gi|289752713|ref|ZP_06512091.1| RNA polymerase subunit beta [Mycobacterium tuberculosis EAS054]
 gi|289756754|ref|ZP_06516132.1| RNA polymerase subunit beta [Mycobacterium tuberculosis T85]
 gi|289760792|ref|ZP_06520170.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis GM 1503]
 gi|294992935|ref|ZP_06798626.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis 210]
 gi|297633165|ref|ZP_06950945.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis KZN 4207]
 gi|298524158|ref|ZP_07011567.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|2143293|emb|CAB09390.1| DNA-DIRECTED RNA POLYMERASE (BETA CHAIN) RPOB (TRANSCRIPTASE BETA
           CHAIN) (RNA POLYMERASE BETA SUBUNIT) [Mycobacterium
           tuberculosis H37Rv]
 gi|31617438|emb|CAD93548.1| DNA-DIRECTED RNA POLYMERASE (BETA CHAIN) RPOB (TRANSCRIPTASE BETA
           CHAIN) (RNA POLYMERASE BETA SUBUNIT) [Mycobacterium
           bovis AF2122/97]
 gi|121492235|emb|CAL70702.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|148504593|gb|ABQ72402.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis H37Ra]
 gi|224772173|dbj|BAH24979.1| DNA-directed RNA polymerase subunit beta [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|289414983|gb|EFD12223.1| DNA-directed RNA polymerase, beta subunit [Mycobacterium
           tuberculosis T46]
 gi|289419183|gb|EFD16384.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis CPHL_A]
 gi|289542360|gb|EFD46008.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis T17]
 gi|289693300|gb|EFD60729.1| RNA polymerase subunit beta [Mycobacterium tuberculosis EAS054]
 gi|289708298|gb|EFD72314.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis GM 1503]
 gi|289712318|gb|EFD76330.1| RNA polymerase subunit beta [Mycobacterium tuberculosis T85]
 gi|298493952|gb|EFI29246.1| DNA-directed RNA polymerase (beta chain) rpoB [Mycobacterium
           tuberculosis 94_M4241A]
          Length = 1172

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 455/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|254776938|ref|ZP_05218454.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium subsp.
            avium ATCC 25291]
          Length = 1148

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 662  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 720

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 721  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 778

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 779  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 827

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 828  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 887

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I                           
Sbjct: 888  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN------------------ 928

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA EE +  ML            +D  
Sbjct: 929  -------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVMVDGD 975

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 976  GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1035

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1036 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1095

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1096 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1128



 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 334/694 (48%), Positives = 465/694 (67%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 152 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 209

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  + +TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 210 LLKALGWTNEQI----TERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESA 265

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +ED++A I+ LV L  G+
Sbjct: 266 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHEGQ 325

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 326 PTMTVPGGIEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 385

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 386 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 445

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+
Sbjct: 446 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLT 505

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+VS+A +
Sbjct: 506 ADEEDRHVVAQANSPIDGKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATA 565

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G++E+
Sbjct: 566 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKSGVIEE 625

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF+RSN  TC NQ P+V  GD V    +IADG
Sbjct: 626 VSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAGDRVEAGQVIADG 678

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 679 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 738

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 739 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 798

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 799 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 832



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-------RPNEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +         P  GL+     + PI 
Sbjct: 11  RVSFAKLREPLEVPGLLDVQIDSFEWLIGAPRWREAAIARGDAEPKGGLEEVLDELSPIE 70

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 71  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 121

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 122 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 179

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 180 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 239

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 240 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 290

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 291 KKLGLHAGEPITSSTLTEEDVVATIEYLVRLHE 323


>gi|108797943|ref|YP_638140.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. MCS]
 gi|108768362|gb|ABG07084.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. MCS]
          Length = 1166

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/515 (36%), Positives = 270/515 (52%), Gaps = 54/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 675  IVDAGQRVEAGQVVADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 733

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 734  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 791

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 792  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 840

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 841  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 900

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I     D   +                 
Sbjct: 901  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAGADGVPDWA--------------- 944

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                       + +        S   V+TPVFDGA E  ++ +L            ++E 
Sbjct: 945  -----------EKLPEELYSAPSDSIVATPVFDGARENELSGLLASTLPNRDGDVMVNED 993

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 994  GKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1053

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1054 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1113

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1114 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1144



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 455/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 178 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 235

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 236 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 295

Query: 410 TVGRVKMNMRLNL--DTPDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L  D P     + +ED++A I+ LV L  G               +DD
Sbjct: 296 RVGRYKVNKKLGLNTDKPITSSTLTEEDVVATIEYLVRLHQGDTVMTVPGGVEVPVEVDD 355

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 356 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 415

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 416 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 475

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS LD
Sbjct: 476 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPLD 535

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           ++G FTE+ V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 536 DEGHFTEDRVLVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 595

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++AG+VE+V A  I + + +G    
Sbjct: 596 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKAGVVEEVSADYITVMADDGTR-- 653

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T  G++ALG+N+LVA
Sbjct: 654 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTQNGEMALGKNLLVA 708

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 709 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 768

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 769 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 828

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 829 ESGKVIGIRVFSREDDD 845



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 97/333 (29%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---RPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +        R +     GL+     + PI 
Sbjct: 24  RISFAKLREPLEVPGLLDVQTESFDWLIGADSWRQRATARGDVNPTGGLEEVLTELSPIE 83

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 84  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 134

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 135 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 192

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 193 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 252

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 253 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 303

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 304 KKLGLNTDKPITSSTLTEEDVVATIEYLVRLHQ 336


>gi|34595743|gb|AAQ76594.1| RpoB [Mycobacterium smegmatis]
          Length = 1169

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +        ++    
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGVPDWASKLPE------ELYSAP 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
            + +                       V+TPVFDGA E  +  +L            ++  
Sbjct: 959  ADST----------------------VATPVFDGAQEGELAGLLGSTLPNRDGEVMVNAD 996

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1147



 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 455/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGKPITSSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS  D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTD 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G FTE+ V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 ENGRFTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +VA + G++E+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGVIEEVSADYITVMADDGTRQS 660

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSN  TC NQRP+V  G  V    +IADGP T  G++ALG+N+LVA
Sbjct: 661 -------YRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 98/333 (29%), Positives = 157/333 (47%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI---APDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    A  +R  E    GL+     + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEENPVGGLEEVLAELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDT 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TSGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGKPITSSTLTEEDVVATIEYLVRLHE 341


>gi|88909143|sp|Q73SE4|RPOB_MYCPA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|158512716|sp|A0QL49|RPOB_MYCA1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1175

 Score =  518 bits (1333), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 805

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 806  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 854

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 855  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 914

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I                           
Sbjct: 915  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN------------------ 955

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA EE +  ML            +D  
Sbjct: 956  -------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVMVDGD 1002

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1003 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1062

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1063 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1122

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1123 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1155



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 334/694 (48%), Positives = 466/694 (67%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 179 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 236

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  + +TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 237 LLKALGWTNEQI----TERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESA 292

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +ED++A I+ LV L  G+
Sbjct: 293 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHEGQ 352

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 353 PTMTVPGGIEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 412

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 413 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 472

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+
Sbjct: 473 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLT 532

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+VS+A +
Sbjct: 533 ADEEDRHVVAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATA 592

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G++E+
Sbjct: 593 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKSGVIEE 652

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF+RSN  TC NQ P+V  GD V    +IADG
Sbjct: 653 VSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAGDRVEAGQVIADG 705

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 706 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 765

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 766 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 825

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 826 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 859



 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-------RPNEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +         P  GL+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQIDSFEWLIGAPRWREAAIARGDAEPKGGLEEVLDELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 318 KKLGLHAGEPITSSTLTEEDVVATIEYLVRLHE 350


>gi|256371208|ref|YP_003109032.1| DNA-directed RNA polymerase, beta subunit [Acidimicrobium
            ferrooxidans DSM 10331]
 gi|256007792|gb|ACU53359.1| DNA-directed RNA polymerase, beta subunit [Acidimicrobium
            ferrooxidans DSM 10331]
          Length = 1181

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 183/540 (33%), Positives = 269/540 (49%), Gaps = 68/540 (12%)

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                        ++   +  G  V  GD+L           +   + LL A    +  + 
Sbjct: 664  TKFQRSNQNTCWNQRPTVATGDRVELGDVLADGPATMH-GELALGKNLLVAFMPWEGYNF 722

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIY 983
             D  +     V   V+          + + R   +  E+I     +  +E    LD    
Sbjct: 723  EDAIIISERLVRDDVLSSLHIEEF--ETDARDTKLGAEEITRDIPNLSEEALADLDERGI 780

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             R+   +   + + G    K  T L+ +        +  +    ++  +    SL+V + 
Sbjct: 781  VRIGAEVGPGDILVGKVTPKGETELTPE-------ERLLRAIFGEKSREVRDTSLRVPHG 833

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                +++     K+   +   ++PPGV  +V+V+VA  R IQ GDK+AGRHGNKG++SRI
Sbjct: 834  EYGKVID----VKVFTREDATELPPGVNELVRVYVAQHRKIQVGDKLAGRHGNKGVISRI 889

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMP L+DGTPVDI+LNPLGVPSRMN+GQ+ E HLG+A     + I     +++   
Sbjct: 890  LPIEDMPRLEDGTPVDIILNPLGVPSRMNIGQVLEAHLGYAARWGWEPIGEGAREHRKTR 949

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA----- 1218
             ++    +                                  V++P FDGA  +      
Sbjct: 950  PVTVPARW----------------------------------VASPAFDGAHWDESEEAG 975

Query: 1219 ----INSMLRMADL---------DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                I  +L   +             G+++LY+G TGE +D PV VGY+YMLKL HMV D
Sbjct: 976  DLPTIKELLERLNPQSRDGERLVQPDGKAVLYNGRTGERYDNPVMVGYVYMLKLAHMVDD 1035

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR
Sbjct: 1036 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVVGR 1095

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKCE 1384
             +VYE+IV G++  E G PESF VL+KEMQ+L L++++     +     E E   ++  E
Sbjct: 1096 VKVYEAIVKGDNIPEPGIPESFKVLIKEMQSLCLNVEVLAPNGERVQLREFEDEAYSAAE 1155



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 338/756 (44%), Positives = 462/756 (61%), Gaps = 44/756 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F  +  Y  +               G         I+  E+V+ S    + G+L      
Sbjct: 99  FLNRQTYEIKQQIVFMGDFPLMTDRGT------FIINGTERVVVSQLVRSPGVLFQPGRD 152

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS--LEEIFHSEIRDIPILYV 349
               +  T +   G ++  D+      +I          +      +  + + D   L  
Sbjct: 153 QHTVVTATINPYRGEWLEFDVEARPGRDINAGGRVARKRRLSLFTVLRAAGLDDPADLER 212

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
              + +         D ++ R DAL++++R +RPG+      A   F   FF S +YDL+
Sbjct: 213 LVAHFDFLEPQWAKEDHSQTRDDALMEVFRRVRPGEPINVEAARLYFETAFFQSRRYDLT 272

Query: 410 TVGRVKMNMRLNLDTP--------------DDVRHIRKEDIIAIIKILVDLRNGKG--TI 453
            VGR K++ RL+ +                +    + + DIIA    ++ L  G+     
Sbjct: 273 RVGRYKIDKRLSAEIERVEEILGHPLDRTSESPLVLSRADIIATASYMLHLVAGEPGYRF 332

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DD D+  NRRVRSVGE+++NQ ++GL R+ER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 333 DDQDHFSNRRVRSVGELIQNQLKIGLSRLERLVRERMTTQDVEAITPQSLINIRPVVAAI 392

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS + H RRLSALG GG++R RAG E+RDVH +HYGR+CP E
Sbjct: 393 KEFFSTSQLSQFMDQNNPLSGLAHKRRLSALGPGGLSRERAGFEVRDVHSSHYGRMCPIE 452

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ +L S+AR+N YGFIETPYR+V DGKVT++VVYL+A EEE+  IAQAN+ 
Sbjct: 453 TPEGPNIGLIGALASYARLNRYGFIETPYRRVVDGKVTDEVVYLTADEEEDYVIAQANAK 512

Query: 634 LDEDGSFTEELVFCRCAG------------------EEILVPREKIDFIDASPKQVVSIA 675
           LD +G F E  V  R                     E  L   +++D +D SP QVVS++
Sbjct: 513 LDAEGRFVEPKVLVRRGPQGAVVRVGAMAVSYGATSEVELATPDEVDLMDVSPAQVVSVS 572

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPF+E+DD+NR LMG NMQ+QAVPLL  EAPFVGTG+E+     +G  +VA+  G+V
Sbjct: 573 TSLIPFVEHDDANRALMGANMQKQAVPLLVPEAPFVGTGVEARAGLDAGDVLVAEGPGVV 632

Query: 736 EQVDAIRIVIRSVEGDLDPST--SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +V    I +   +   D +    G   Y L KFQRSNQNTC NQRP V  GD V   D+
Sbjct: 633 SEVTGASIAVTYDDSVTDDAGRPLGTRRYWLTKFQRSNQNTCWNQRPTVATGDRVELGDV 692

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGP+T  G+LALG+N+LVAFMPW GYNFED+++ISER+V +DV +S+HIEEFE  ARD
Sbjct: 693 LADGPATMHGELALGKNLLVAFMPWEGYNFEDAIIISERLVRDDVLSSLHIEEFETDARD 752

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           TKLG EEITRDIPN+SEE L ++DE GI+ +GAEV PGDILVGK+TPKGE+ +TPEE+LL
Sbjct: 753 TKLGAEEITRDIPNLSEEALADLDERGIVRIGAEVGPGDILVGKVTPKGETELTPEERLL 812

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           RAIFGEK+ +VRDTSLRVP G  G V+DV++F R  
Sbjct: 813 RAIFGEKSREVRDTSLRVPHGEYGKVIDVKVFTRED 848



 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 82/306 (26%), Positives = 135/306 (44%), Gaps = 46/306 (15%)

Query: 10  LGR--VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
             R   R  F     ++ +PDLI VQ+ S+  FL          NEGL  AF+ + PI  
Sbjct: 4   RHRPPERFSFASARNVLPLPDLIAVQRDSFRWFL----------NEGLAEAFRDISPIED 53

Query: 68  FSGAAMLEFV----SYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           +SG   LE        +  P PKF  ++C  +D+TYA P+ +  R +          +  
Sbjct: 54  YSGQLALELEYDPSDPDLAPVPKFSAEECREKDMTYAGPIFVRARFL---------NRQT 104

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK+Q ++MGD PLMT  GTF+I G +R+VVSQL RSPG+ F   + +       +   
Sbjct: 105 YEIKQQIVFMGDFPLMTDRGTFIINGTERVVVSQLVRSPGVLFQPGRDQ-----HTVVTA 159

Query: 183 RIIPDQGLWMDIEFDS---KDIIHV--RIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
            I P +G W++ + ++   +D I+   R+ R+R++ + + L A G+D    L        
Sbjct: 160 TINPYRGEWLEFDVEARPGRD-INAGGRVARKRRLSLFTVLRAAGLDDPADLE------R 212

Query: 238 YSQRGDFWCFPLSAAD--LMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVK 294
                DF     +  D        +      +  GE + +E+ +          +   + 
Sbjct: 213 LVAHFDFLEPQWAKEDHSQTRDDALMEVFRRVRPGEPINVEAARLYFETAFFQSRRYDLT 272

Query: 295 FLGITS 300
            +G   
Sbjct: 273 RVGRYK 278


>gi|34595749|gb|AAQ76597.1| RpoB [Mycobacterium senegalense]
          Length = 1170

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 959

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 960  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 997

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1058 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1118 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1148



 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 302 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS +D
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPID 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 TDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AG+VE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGVVEEVSADYITVMADDGSR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 30  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAVDRGETDPKGGLEEVLEELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 342


>gi|34391559|gb|AAN65357.1| RpoB [Mycobacterium mucogenicum]
          Length = 1167

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 184/508 (36%), Positives = 259/508 (50%), Gaps = 55/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 681  IVDSGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEQDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 847  REDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN------------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                         +            V+TPVFDGA E  +  +L     +          
Sbjct: 948  -------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVMVDAD 994

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 995  GKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1054

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1055 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1114

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        +   +
Sbjct: 1115 KELQSLCLNVEVLSSDGAAIEMRDSDDE 1142



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 327/679 (48%), Positives = 453/679 (66%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 182 DKATEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--R 239

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 240 ERFGFSEIMMGTLEKDPTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 299

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNG------------KGTI 453
            VGR K+N +L L   +        + +EDI+A I+ LV L +G               +
Sbjct: 300 RVGRYKVNKKLGLHDGNPAQVTATTLTEEDIVATIEYLVRLHDGDTKMTAPGGVEVPVEV 359

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 360 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 419

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP E
Sbjct: 420 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIE 479

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS 
Sbjct: 480 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGIVTDQIDYLTADEEDRHVVAQANSP 539

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           LD +G FTEE +  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 540 LDANGHFTEEKILVRRKGGEVEFVSANDVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 599

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA ++G++E+V A  + + + +G  
Sbjct: 600 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKSGVIEEVSADYVTVMADDGSR 659

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 660 -------HTYRMRKFNRSNHGTCANQRPIVDSGQRVEAGQVIADGPCTENGEMALGKNLL 712

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 713 VAVMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 772

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 773 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 832

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ VR+F+R   D
Sbjct: 833 HGESGKVIGVRVFSREDDD 851



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 91/298 (30%), Positives = 150/298 (50%), Gaps = 22/298 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    +  + G       L+     + PI 
Sbjct: 28  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSDRWRSKAVDRGDINPVGGLEEVLAELSPIE 87

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K  VD+C  +D TYA PL +T   I           +  +IK
Sbjct: 88  DFAGTLSLSFSDPRFDEVKAPVDECKEKDQTYAAPLFVTAEFI---------NNTTGEIK 138

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 139 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--ATEKTLHSVKVIP 196

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   D 
Sbjct: 197 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIRERFGFSEIMMGTLEKDP 256

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
              P  A   +            ++ + ++E+   K+    L +  + K  K LG+  
Sbjct: 257 TAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHD 314


>gi|34391549|gb|AAN65352.1| RpoB [Mycobacterium fortuitum]
          Length = 1170

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 959

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 960  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 997

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1058 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1118 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1148



 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 330/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 302 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS +D
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPID 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 PDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AGIVE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGIVEEVSADYITVMADDGSR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  314 bits (805), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 30  RVSFAKLREPLEVPGLLDVQTDSFDWLVGADEWRQKAVDRGETDPKGGLEEVLEELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 342


>gi|34391561|gb|AAN65358.1| RpoB [Mycobacterium mucogenicum]
          Length = 1167

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 185/508 (36%), Positives = 260/508 (51%), Gaps = 55/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 681  IVDSGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEQDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 847  REDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN------------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMADLDES 1231
                         +            V+TPVFDGA E  +  +L            +D  
Sbjct: 948  -------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGEVMVDAD 994

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 995  GKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1054

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1055 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1114

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        +   +
Sbjct: 1115 KELQSLCLNVEVLSSDGAAIEMRDSDDE 1142



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 327/679 (48%), Positives = 453/679 (66%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 182 DKATEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--R 239

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 240 ERFGFSEIMMGTLEKDPTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 299

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNG------------KGTI 453
            VGR K+N +L L   +        + +EDI+A I+ LV L +G               +
Sbjct: 300 RVGRYKVNKKLGLHDGNPAQVTATTLTEEDIVATIEYLVRLHDGDKTMTAPGGVEVPVEV 359

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 360 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 419

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP E
Sbjct: 420 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIE 479

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS 
Sbjct: 480 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGIVTDQIDYLTADEEDRHVVAQANSP 539

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           LD +G FTEE +  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 540 LDANGHFTEEKILVRRKGGEVEFVSANDVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 599

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA ++G++E+V A  + + + +G  
Sbjct: 600 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKSGVIEEVSADYVTVMADDGSR 659

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 660 -------HTYRMRKFNRSNHGTCANQRPIVDSGQRVEAGQVIADGPCTENGEMALGKNLL 712

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 713 VAVMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 772

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 773 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 832

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ VR+F+R   D
Sbjct: 833 HGESGKVIGVRVFSREDDD 851



 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 91/298 (30%), Positives = 150/298 (50%), Gaps = 22/298 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    +  + G       L+     + PI 
Sbjct: 28  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSDRWRSKAVDRGDINPVGGLEEVLAELSPIE 87

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K  VD+C  +D TYA PL +T   I           +  +IK
Sbjct: 88  DFAGTLSLSFSDPRFDEVKAPVDECKEKDQTYAAPLFVTAEFI---------NNNTGEIK 138

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 139 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--ATEKTLHSVKVIP 196

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   D 
Sbjct: 197 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIRERFGFSEIMMGTLEKDP 256

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
              P  A   +            ++ + ++E+   K+    L +  + K  K LG+  
Sbjct: 257 TAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHD 314


>gi|34595757|gb|AAQ76601.1| RpoB [Mycobacterium farcinogenes]
          Length = 1170

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 681  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 847  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 959

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 960  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 997

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1058 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1118 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1148



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 184 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 241

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 242 ERFGFSEIMMVTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 301

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 302 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 361

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 362 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 421

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 422 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 481

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQAN+ +D
Sbjct: 482 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANTPID 541

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 542 TDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 601

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AG+VE+V A  I + + +G    
Sbjct: 602 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGVVEEVSADYITVMADDGSR-- 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 660 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 714

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 715 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 774

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 775 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 834

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 835 ESGKVIGIRVFSREDDD 851



 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 30  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAVDRGETDPKGGLEEVLEELSPIE 89

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 90  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 140

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 141 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 198

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 199 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMVTLEKDS 258

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 259 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 309

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 310 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 342


>gi|118465939|ref|YP_883637.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium 104]
 gi|118167226|gb|ABK68123.1| DNA-directed RNA polymerase, beta subunit [Mycobacterium avium 104]
          Length = 1144

 Score =  517 bits (1332), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 658  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 716

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 717  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 774

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 775  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 823

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 824  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 883

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I                           
Sbjct: 884  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN------------------ 924

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA EE +  ML            +D  
Sbjct: 925  -------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVMVDGD 971

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 972  GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1031

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1032 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1091

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1092 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1124



 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 334/694 (48%), Positives = 466/694 (67%), Gaps = 28/694 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 148 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 205

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +    +  + +TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 206 LLKALGWTNEQI----TERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESA 261

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +ED++A I+ LV L  G+
Sbjct: 262 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEDVVATIEYLVRLHEGQ 321

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 322 PTMTVPGGIEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 381

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 382 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 441

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+
Sbjct: 442 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLT 501

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+VS+A +
Sbjct: 502 ADEEDRHVVAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATA 561

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G++E+
Sbjct: 562 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKSGVIEE 621

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF+RSN  TC NQ P+V  GD V    +IADG
Sbjct: 622 VSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAGDRVEAGQVIADG 674

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG
Sbjct: 675 PCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLG 734

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIF
Sbjct: 735 AEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIF 794

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 795 GEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 828



 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-------RPNEGLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +         P  GL+     + PI 
Sbjct: 7   RVSFAKLREPLEVPGLLDVQIDSFEWLIGAPRWREAAIARGDAEPKGGLEEVLDELSPIE 66

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 67  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 117

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 118 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 175

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 176 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMSTLEKDN 235

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 236 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 286

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 287 KKLGLHAGEPITSSTLTEEDVVATIEYLVRLHE 319


>gi|172039980|ref|YP_001799694.1| DNA-directed RNA polymerase subunit beta [Corynebacterium urealyticum
            DSM 7109]
 gi|226699391|sp|B1VES1|RPOB_CORU7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|171851284|emb|CAQ04260.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            urealyticum DSM 7109]
          Length = 1170

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 199/620 (32%), Positives = 283/620 (45%), Gaps = 64/620 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V            A+              +L A  P+ G   E         +   
Sbjct: 573  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPYVGTGIEQRAAYDAGDLI-- 630

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDI 893
            +     + E+ V A    +  +E  RD   + +    N     ++  ++  G  V  G +
Sbjct: 631  IAPKAGVVEY-VSADYITIMDDEGIRDTFMLRKFERTNQGTSYNQKPLVNQGDRVEAGQV 689

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +           M   + LL A    +  +  D  +     V   V+       + ID  
Sbjct: 690  IADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRMVEEDVLTSIHIEEYEIDAR 748

Query: 954  ERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            +  +  E     I  +  D     DE+ I+      R  +IL G+    G         L
Sbjct: 749  DTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERL 808

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               +  E  R                 E      +            ++   +  DD+  
Sbjct: 809  LRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAA 851

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTPVDI+LN  GVP
Sbjct: 852  GVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPVDIILNTHGVP 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
             RMN+GQ+ E HLGW     G ++ +  +D K    +  L   L  V             
Sbjct: 912  RRMNIGQVLEVHLGWLAKA-GWQVDTNSDDPKIKAMLETLPEDLYDVPADSLT------- 963

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGL 1240
                              STPVFDGA    ++ +LR +  D  G        ++ L DG 
Sbjct: 964  ------------------STPVFDGASNAELSGLLRSSRPDRDGIRLVDDFGKAQLIDGR 1005

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP++ P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 1006 TGEPYEHPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1065

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L+
Sbjct: 1066 AMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLN 1125

Query: 1361 IDLENSRTKNSAKMEEIPDF 1380
            +++  +         +  D 
Sbjct: 1126 VEVLAADGTPMELSSDDDDE 1145



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 458/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 198 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSEIMMSTLEK 253

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D  ++  +ALL+IYR  RPG+  T   A+++    FF   +YDL+ VGR K+N +L L  
Sbjct: 254 DGVENTDEALLEIYRKQRPGESPTRDSAQALLENSFFRPKRYDLAKVGRYKVNRKLGLGG 313

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D    + +EDI+  I+ LV L  G+              +DDID+ GNRR+R+VGE++
Sbjct: 314 DTDGTMTLTEEDILTTIEYLVRLHAGERTMTSPEGVEIPIEVDDIDHFGNRRLRTVGELI 373

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 374 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 433

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 434 LSGLTHKRRLNALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 493

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V DG++T++V Y +A EE+   IAQAN+  D D  FTE+ +  R   
Sbjct: 494 VNPFGFIETPYRRVVDGQITDEVEYFTADEEDRHVIAQANTPFDADMKFTEDQIEVRLRG 553

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+AEAP+
Sbjct: 554 GDVEVVPASQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPY 613

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  +G  I+A +AG+VE V A  I I   EG  D          L KF+R+
Sbjct: 614 VGTGIEQRAAYDAGDLIIAPKAGVVEYVSADYITIMDDEGIRDTFM-------LRKFERT 666

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED++++S
Sbjct: 667 NQGTSYNQKPLVNQGDRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILS 726

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++DE GI+ +GA+V  
Sbjct: 727 QRMVEEDVLTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRD 786

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 787 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 846

Query: 951 D 951
           D
Sbjct: 847 D 847



 Score =  291 bits (746), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 143/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 24  TRYSFAKIDAPIEVPGLLDLQRESFAWLVGAPEWRARMQAEAGEGVRVTSGLEDILEELS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 84  PIEDYSENMSLTLSEPRFDDMKTSIDEAKEKDINYAAPLYVTAEFT---------NAQSG 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+  +
Sbjct: 135 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESID--TSTERPLHGVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSEIMMSTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 253 KDGVENTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFRPKRYDLAKVGRYKV 305

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D     T E  +
Sbjct: 306 NRKLGLGGDTDGTMTLTEEDIL 327


>gi|158513166|sp|A1T4J2|RPOB_MYCVP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1167

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/520 (35%), Positives = 255/520 (49%), Gaps = 66/520 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 678  IVDAGQRVESGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 736

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 737  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIIRIGAEVRDGDILVGKV 795

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 796  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIG 838

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 839  IRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPD 898

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +         
Sbjct: 899  GTPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWAAKLPEQMLSAP- 956

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE---- 1230
                                       +   V+TPVFDGA E  +  +L     +     
Sbjct: 957  ---------------------------ADSIVATPVFDGAQEGELQGLLGSTLPNRDGET 989

Query: 1231 ----SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 990  MVNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PES
Sbjct: 1050 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1110 FKVLLKELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1145



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 181 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 238

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 239 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 298

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G               +DD
Sbjct: 299 RVGRYKVNKKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQGDQTMTAPGGSEVPVEVDD 358

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 359 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 418

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 419 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 478

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS LD
Sbjct: 479 EGPNIGLIGSLSVYARVNPFGFIETPYRKVTDGVVTDQIDYLTADEEDRHVVAQANSPLD 538

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F EE V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 539 GDGHFEEERVLVRRKGGEVEFVSAAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 598

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V ++AG+VE+V A  I + + +G    
Sbjct: 599 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVTEKAGVVEEVSADYITVMADDGTR-- 656

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 657 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVESGQVLADGPCTENGEMALGKNLLVA 711

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 712 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 771

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 772 DLDERGIIRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 831

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 832 ESGKVIGIRVFSREDDD 848



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 155/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +          + G       LQ   + + PI 
Sbjct: 27  RISFAKLREPLEVPGLLDVQTESFEWLIGAEDWFQRAADRGDVDPKGGLQEVLEELSPIE 86

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 87  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 137

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 138 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 195

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 196 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMSTLEKDN 255

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 256 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 306

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  ++    T     E   V   + L  +  
Sbjct: 307 KKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQ 339


>gi|34391551|gb|AAN65353.1| RpoB [Mycobacterium peregrinum]
          Length = 1169

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 185/513 (36%), Positives = 263/513 (51%), Gaps = 53/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +              
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP------ 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                      VSTPVFDGA EE +  +L     +          
Sbjct: 959  ----------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 996

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        + +  D ++ 
Sbjct: 1117 KELQSLCLNVEVLSSDGAAIEMRDGDDEDLDRA 1149



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/677 (48%), Positives = 453/677 (66%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +         I   
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQI--T 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ + YL+A EE+   +AQANS +D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDQIDYLTADEEDRHVVAQANSPID 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 TDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AG+VE+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGVVEEVSADYITVMADDGSR-- 658

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 659 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 97/333 (29%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFDWLVGADGWRQKAVDRGETDPKGGLEEVLEELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMMGTLEKDS 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 341


>gi|284042791|ref|YP_003393131.1| DNA-directed RNA polymerase subunit beta [Conexibacter woesei DSM
            14684]
 gi|283947012|gb|ADB49756.1| DNA-directed RNA polymerase, beta subunit [Conexibacter woesei DSM
            14684]
          Length = 1192

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 196/601 (32%), Positives = 285/601 (47%), Gaps = 69/601 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E    +    +V      +I   + + +  +T+ G 
Sbjct: 578  MGSNMQRQAVPLLRTDAPLVGTGMEYRAAVDSGDVVIAKRAGTIAYIDADQIVIETEDGG 637

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            ++       +       I    ++  G  V  G +L    +   +  M   + L  A   
Sbjct: 638  KDEYVLQKFMRSNQGTLIHHKPLVRNGQAVVEGTVLADGSST-DQGEMALGKNLRVAFMS 696

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVI 977
             +  +  D  +     V     ++   +    + + R+  +  E+I     ++ +E    
Sbjct: 697  WEGYNFEDAIILSKRLVKD--DELTSIHIEEYEIDARTTKLGDEEITRDIPNRSEESLRN 754

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD     R+   +   + + G    K  T L+++   +  R+ + + A +       V  
Sbjct: 755  LDDRGIVRIGAEVGSGDLLVGKVTPKGETELTAE--EKLIRAIFKEKAREVRDTSLKVPH 812

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             +                K      GDD+PPGV  +V+VFVA KR I  GDK+AGRHGNK
Sbjct: 813  GEGGV---------VIDVKTFSRDAGDDLPPGVNDLVRVFVAKKRKIAEGDKLAGRHGNK 863

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+I+  +DMPFL+DG+PVD++LNPLGVPSRMN+GQI ETHLGWA             
Sbjct: 864  GVISKIVDEQDMPFLEDGSPVDVILNPLGVPSRMNIGQILETHLGWAAA----------- 912

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                         D  +   +  +   +  V VSTPVFDGA  E
Sbjct: 913  ------------------------EGWYDDGSEAYKIAHSNGDRPRVYVSTPVFDGATVE 948

Query: 1218 AINSML------------------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             +++ L                    A    SG+  L++G TGEPF+  VTVGY+Y+LKL
Sbjct: 949  DVDTALLKWQQEHRGRIRMKTAPDDRAGTKASGKFTLFNGRTGEPFETQVTVGYMYILKL 1008

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLTIKS
Sbjct: 1009 HHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTIKS 1068

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DD VGR + YE+IV G +  E   PESF VL+KEMQ+L L +++ +     +   EE  D
Sbjct: 1069 DDTVGRVKAYEAIVKGENIAEPSIPESFKVLLKEMQSLALDVNVVSEEGTRAEMREEDDD 1128

Query: 1380 F 1380
             
Sbjct: 1129 L 1129



 Score =  480 bits (1235), Expect = e-133,   Method: Composition-based stats.
 Identities = 318/649 (48%), Positives = 442/649 (68%), Gaps = 40/649 (6%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD--KNKDRKDALLDIYRVMRPGDVSTF 389
            L  + ++   +I  L+ DS+    YIRNTL +D    K  + AL+++++  RPG+  + 
Sbjct: 193 LLRAMGYASDEEIASLFDDSL----YIRNTLESDTEVTKTEEGALIELFKKQRPGEPPSV 248

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             A ++ + LFFD  +YDL+ VGR K+N RL LD   + R +  +DIIA+IK LV L   
Sbjct: 249 DAARALLHQLFFDPKRYDLTRVGRYKLNSRLRLDIDLETRTLTHDDIIALIKELVTLPKL 308

Query: 450 KGTIDDID--------------------------NLGNRRVRSVGEMLKNQYRLGLLRME 483
            G  +  D                          + GNRR+R+VGE+++  +R+GL RME
Sbjct: 309 LGMPEQPDVEIRDYAAEAVTYPREPVADHLDEYEHFGNRRLRTVGELIQEAFRIGLYRME 368

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+++ D D++ PQ ++N +PVV+A+ EFF SSQLSQ  +  NSLS +TH RRLSA
Sbjct: 369 RVVRERLTTEDADTITPQTIVNIRPVVAALKEFFGSSQLSQFMDQNNSLSGLTHRRRLSA 428

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVHPTHYGR+CP ET EG NIGL+ SL+S+A+++ YGF+ TPYR
Sbjct: 429 LGAGGLTRERAPIEVRDVHPTHYGRMCPIETPEGPNIGLLGSLSSYAQISEYGFVTTPYR 488

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKID 662
            V DGKVT+++V+L A +EE   IAQA++ +++ G      + CR  AG  +      +D
Sbjct: 489 VVKDGKVTDEIVHLDATQEEEAKIAQADTPINDAGELVGTDIVCRTQAGSYVRAEPGDVD 548

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SP+Q+ S++ ++IPFLE+DD+NR LMG NMQRQAVPLL+ +AP VGTGME   A  
Sbjct: 549 LMDVSPEQIWSVSTAMIPFLEHDDANRALMGSNMQRQAVPLLRTDAPLVGTGMEYRAAVD 608

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  ++AKRAG +  +DA +IVI + +G       G D Y L KF RSNQ T ++ +PLV
Sbjct: 609 SGDVVIAKRAGTIAYIDADQIVIETEDG-------GKDEYVLQKFMRSNQGTLIHHKPLV 661

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + G  V    ++ADG STD G++ALG+N+ VAFM W GYNFED++++S+R+V +D  TSI
Sbjct: 662 RNGQAVVEGTVLADGSSTDQGEMALGKNLRVAFMSWEGYNFEDAIILSKRLVKDDELTSI 721

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+E+ AR TKLG EEITRDIPN SEE L+N+D+ GI+ +GAEV  GD+LVGK+TPKG
Sbjct: 722 HIEEYEIDARTTKLGDEEITRDIPNRSEESLRNLDDRGIVRIGAEVGSGDLLVGKVTPKG 781

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +T EEKL+RAIF EKA +VRDTSL+VP G  G V+DV+ F+R   D
Sbjct: 782 ETELTAEEKLIRAIFKEKAREVRDTSLKVPHGEGGVVIDVKTFSRDAGD 830



 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 83/290 (28%), Positives = 147/290 (50%), Gaps = 24/290 (8%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ F +  + +++P+LI++QK S+                GL+     + PI  ++G 
Sbjct: 8   RTRRTFARLSKALEVPNLIDIQKKSFAWLTDAESG-------GLRETIDDISPIEDYTGN 60

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             ++F  + FD P   +D+C  +DLTYA PL +T+  +          +   +I+EQS++
Sbjct: 61  LAVQFGEFTFDEPVASLDECREKDLTYARPLTVTVAFV---------NRETGEIREQSVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD P MT+ GTF+I G +R+VV+QL RSPG +    K R     K ++   ++P +G W
Sbjct: 112 MGDFPWMTERGTFIINGTERVVVTQLVRSPGAYLMEAKDRE----KQVFIANLMPARGSW 167

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +++E D K  ++VRIDR+RK+PVT  L A+G  S+E +++ +   +Y +        ++ 
Sbjct: 168 LELEIDKKGKVYVRIDRKRKLPVTVLLRAMGYASDEEIASLFDDSLYIRNTLESDTEVTK 227

Query: 252 ADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      +         GE   +++ + L   L    K   +  +G   
Sbjct: 228 TE---EGALIELFKKQRPGEPPSVDAARALLHQLFFDPKRYDLTRVGRYK 274


>gi|34391565|gb|AAN65360.1| RpoB [Mycobacterium fortuitum]
          Length = 1177

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 688  IVDAGQRVEAGQVVADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 746

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 747  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 804

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 805  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 853

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 854  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 913

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++    
Sbjct: 914  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QLYSAP 966

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
              +                       VSTPVFDGA EE +  +L     +  G       
Sbjct: 967  VDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVMVNAD 1004

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1005 GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1064

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1065 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1124

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1125 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1155



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 191 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--T 248

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 249 ERFGFSEIMMGTLEKDSTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 308

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 309 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 368

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           +D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 369 MDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 428

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 429 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 488

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS +D
Sbjct: 489 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPID 548

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 549 PDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 608

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV+++AGIVE+V A  I + + +G    
Sbjct: 609 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVIVSEKAGIVEEVSADYITVMADDGSR-- 666

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 667 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVVADGPCTENGEMALGKNLLVA 721

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 722 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 781

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 782 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 841

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 842 ESGKVIGIRVFSREDDD 858



 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 37  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAVDRGETDPKGGLEEVLEELSPIE 96

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 97  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 147

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 148 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 205

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 206 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQITERFGFSEIMMGTLEKDS 265

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 266 TAGPDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 316

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 317 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 349


>gi|120402269|ref|YP_952098.1| DNA-directed RNA polymerase subunit beta [Mycobacterium vanbaalenii
            PYR-1]
 gi|119955087|gb|ABM12092.1| DNA-directed RNA polymerase subunit beta [Mycobacterium vanbaalenii
            PYR-1]
          Length = 1161

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/520 (35%), Positives = 255/520 (49%), Gaps = 66/520 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 672  IVDAGQRVESGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 730

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 731  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIIRIGAEVRDGDILVGKV 789

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 790  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIG 832

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 833  IRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPD 892

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +         
Sbjct: 893  GTPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWAAKLPEQMLSAP- 950

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE---- 1230
                                       +   V+TPVFDGA E  +  +L     +     
Sbjct: 951  ---------------------------ADSIVATPVFDGAQEGELQGLLGSTLPNRDGET 983

Query: 1231 ----SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 984  MVNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PES
Sbjct: 1044 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPES 1103

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1104 FKVLLKELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1139



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 175 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 232

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 233 ERFGFSEIMMSTLEKDNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 292

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G               +DD
Sbjct: 293 RVGRYKVNKKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQGDQTMTAPGGSEVPVEVDD 352

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 353 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 412

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 413 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 472

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS LD
Sbjct: 473 EGPNIGLIGSLSVYARVNPFGFIETPYRKVTDGVVTDQIDYLTADEEDRHVVAQANSPLD 532

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F EE V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 533 GDGHFEEERVLVRRKGGEVEFVSAAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 592

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V ++AG+VE+V A  I + + +G    
Sbjct: 593 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVTEKAGVVEEVSADYITVMADDGTR-- 650

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 651 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVESGQVLADGPCTENGEMALGKNLLVA 705

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 706 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 765

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 766 DLDERGIIRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 825

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 826 ESGKVIGIRVFSREDDD 842



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 155/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +          + G       LQ   + + PI 
Sbjct: 21  RISFAKLREPLEVPGLLDVQTESFEWLIGAEDWFQRAADRGDVDPKGGLQEVLEELSPIE 80

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 81  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 131

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 132 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 189

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 190 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMSTLEKDN 249

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 250 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 300

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  ++    T     E   V   + L  +  
Sbjct: 301 KKLGLNVGQPITSSTLTEEDVVATIEYLVRLHQ 333


>gi|34595753|gb|AAQ76599.1| RpoB [Mycobacterium chelonae]
          Length = 1171

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 266/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEVGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+      +                   
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +    +   +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 326/679 (48%), Positives = 456/679 (67%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 186 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 243

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 244 ERFGFSEIMMGTLEKDNIAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLA 303

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNGKG------------TI 453
            VGR K+N +L L   +        + +ED++A I+ LV L  G+              +
Sbjct: 304 RVGRYKVNKKLGLGGANPALVTATTLTEEDVVATIEYLVRLHEGQTTMTAPGGLEVPVEV 363

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 364 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 423

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP E
Sbjct: 424 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPSHYGRMCPIE 483

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A EE+   +AQANS 
Sbjct: 484 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTADEEDRHVVAQANSP 543

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 544 VDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 603

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA++AG++E+V A  + + + +G  
Sbjct: 604 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKAGVIEEVSADYVTVMADDGTR 663

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YRL KF RSN  TC NQ+P+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 664 QS-------YRLRKFARSNHGTCANQKPIVDEGQRVEVGQVIADGPCTENGEMALGKNLL 716

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 717 VAVMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 776

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 777 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 836

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ +R+F+R   D
Sbjct: 837 HGESGKVIGIRVFSRDDDD 855


>gi|34391545|gb|AAN65350.1| RpoB [Mycobacterium chelonae]
          Length = 1171

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/515 (36%), Positives = 266/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 685  IVDEGQRVEVGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSNRLVEEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 744  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 801

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 802  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 850

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 851  RDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 910

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+      +                   
Sbjct: 911  IILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN------------------ 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +    +   +    +TPVFDGA EE +  +L            +D  
Sbjct: 952  -------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVMVDGD 998

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 999  GKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1058

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1059 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1118

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +          E+ D +  +L+
Sbjct: 1119 KELQSLCLNVEVLSKDGAAI----EMRDGDDEDLE 1149



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 326/679 (48%), Positives = 456/679 (67%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 186 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 243

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 244 ERFGFSEIMMGTLEKDNIAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLA 303

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNGKG------------TI 453
            VGR K+N +L L   +        + +ED++A I+ LV L  G+              +
Sbjct: 304 RVGRYKVNKKLGLGGANPALVTATTLTEEDVVATIEYLVRLHEGQTTMTAPGGLEVPVEV 363

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 364 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 423

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP E
Sbjct: 424 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPSHYGRMCPIE 483

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A EE+   +AQANS 
Sbjct: 484 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTADEEDRHVVAQANSP 543

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 544 VDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 603

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA++AG++E+V A  + + + +G  
Sbjct: 604 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKAGVIEEVSADYVTVMADDGTR 663

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YRL KF RSN  TC NQ+P+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 664 QS-------YRLRKFARSNHGTCANQKPIVDEGQRVEVGQVIADGPCTENGEMALGKNLL 716

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 717 VAVMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 776

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 777 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 836

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ +R+F+R   D
Sbjct: 837 HGESGKVIGIRVFSRDDDD 855


>gi|116488418|gb|AAQ76602.2| RpoB [Mycobacterium wolinskyi]
          Length = 1169

 Score =  517 bits (1331), Expect = e-144,   Method: Composition-based stats.
 Identities = 327/677 (48%), Positives = 453/677 (66%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDSTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS +D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPID 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 ADGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+++ G+VE+V A  + + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSEKTGVVEEVSADYVTVMADDGTR-- 658

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    +IADGP T  G++ALG+N+LVA
Sbjct: 659 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVESGQVIADGPCTQNGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVESGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +        ++    
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPDWASKLPE------QLYSAP 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
            + +                       VSTPVFDGA E  +  +L            +D  
Sbjct: 959  ADSI----------------------VSTPVFDGAQEGELQGLLGSTLPNRDGEVMVDAD 996

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 KELQSLCLNVEVLSSDGAAI----EMRDGDDADLE 1147



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 156/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S+D  +  +    +  + G       L+   + + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFDWLVGSDEWRQKAIDRGETDPKGGLEEVLEELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDS 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 341


>gi|159029167|emb|CAO87527.1| rpoB [Microcystis aeruginosa PCC 7806]
          Length = 1103

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/687 (47%), Positives = 456/687 (66%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 112 INGAERVIVNQIVRSPGVYYKAEIDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 171

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   DS+ +  + + TL  + N   ++ALLD+YR +RPG+ 
Sbjct: 172 TRKLSAQVLLKAIGLSDNEI--FDSLRHPEFYQKTLDKEGNPSEEEALLDLYRKLRPGEP 229

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T +  + +    FFD+ +YDL  VGR K+N +L L+ PD+ R +   DI++ I  L++L
Sbjct: 230 PTVTGGQQLLESRFFDNKRYDLGRVGRYKLNKKLRLNVPDNQRVLTTTDILSAIDYLINL 289

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G  DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  +  ++ P  L+N 
Sbjct: 290 EFDIGNTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESQNLTPASLVNP 349

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 350 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 409

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETP   V +G+V  D  V YL+A EE++
Sbjct: 410 GRICPVETPEGPNAGLIGSLATYARVNDYGFIETPCYGVENGRVRYDLPVKYLTADEEDD 469

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + + DE+G    E +  R   E      E++D++  SP Q+VS+A SLIPFLE+
Sbjct: 470 LRVAPGDVATDENGYILGETIPVRYRQEFSTTSPEQVDYVCVSPVQIVSVATSLIPFLEH 529

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  VDA RI 
Sbjct: 530 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSHVDANRIR 589

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  + D +        Y + K+QRSNQ+TC+NQRPLV  G++V    I+ADG +T+ G+
Sbjct: 590 IKVADQDKEIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEGGE 649

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           +ALG+N+LVA+MPW GYN+ED++LISER+V++DV+TSIHIE++E+ AR TKLGPEEITR+
Sbjct: 650 IALGQNILVAYMPWEGYNYEDAILISERLVAQDVYTSIHIEKYEIEARQTKLGPEEITRE 709

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V   DILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 710 IPNVGEDALRNLDERGIIRIGAWVEASDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 769

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 770 RDNSLRVPNGEKGRVVDVRVFTREQGD 796



 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 199/593 (33%), Positives = 273/593 (46%), Gaps = 72/593 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-------IEEFEVMAR 852
                       +L    P  G   E        MV       +        I        
Sbjct: 537  MGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSHVDANRIRIKVADQD 596

Query: 853  DTKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                G  EI  +I           +++  ++  G +V PG IL      +G   +   + 
Sbjct: 597  KEIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEG-GEIALGQN 655

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLAR 969
            +L A    +  +  D  L     V+  V       ++ I+  +  +  E    +I  +  
Sbjct: 656  ILVAYMPWEGYNYEDAILISERLVAQDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGE 715

Query: 970  DKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            D     DE+ I+    +    +IL G+    G         L   +  E  R        
Sbjct: 716  DALRNLDERGIIRIGAWVEASDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------- 768

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                       ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ
Sbjct: 769  -----------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQ 817

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKGI+SRILP EDMP+L DG PVDIVLNPLGVPSRMNVGQ+FE  LGWA 
Sbjct: 818  VGDKMAGRHGNKGIISRILPLEDMPYLPDGRPVDIVLNPLGVPSRMNVGQVFECLLGWAG 877

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG + K    D               ++ G  +    +    +++  +    W     
Sbjct: 878  ENLGVRFKITPFD---------------EMYGEEASRLTVHGLLENASKKPNRDW----- 917

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                VF    EE             +G+  +YDG TGEPFDRPVTVG  YMLKL H+V D
Sbjct: 918  ----VF---KEE------------HAGKVTVYDGRTGEPFDRPVTVGMAYMLKLVHLVDD 958

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR
Sbjct: 959  KIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGR 1018

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                 +IV G      GTPESF VL++E+Q+LGL I +            ++ 
Sbjct: 1019 NEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVENAPDGTSRDVE 1071



 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 97/487 (19%), Positives = 193/487 (39%), Gaps = 42/487 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLIE+Q +S+  FL           EGL     S  PI+ ++G   L F+   Y    
Sbjct: 9   LPDLIEIQHSSFRWFL----------EEGLIEELNSFSPISDYTGKLELHFLGQDYRLKE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK++VD+   RD +Y+V + +  RLI          K   +  EQ +++GDLPLMT+ GT
Sbjct: 59  PKYNVDEAKRRDSSYSVQMYVPTRLI---------NKETGENIEQEVFIGDLPLMTERGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 110 FIINGAERVIVNQIVRSPGVYYKAEIDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK--VS 261
           VRID+ RK+     L A+G+   EI  +      Y +  D    P     L+   +    
Sbjct: 167 VRIDKTRKLSAQVLLKAIGLSDNEIFDSLRHPEFYQKTLDKEGNPSEEEALLDLYRKLRP 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
                +  G+Q++ES         L  +    +      +       +    +      +
Sbjct: 227 GEPPTVTGGQQLLESRFFDNKRYDLGRVGRYKLNKKLRLNVPDNQRVLTTTDILSAIDYL 286

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                D+ +   ++ + +  +R +  L  + V         ++ ++    +   L    +
Sbjct: 287 INLEFDIGNTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESQNLTPASL 346

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           + P      +  +  F            + +  +    R++   P     + +E     +
Sbjct: 347 VNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRERAGFAV 401

Query: 441 KILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           + +    +G+    +                 RV   G +    Y +   R+   +  + 
Sbjct: 402 RDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNDYGFIETPCYGVENGRVRYDLPVKY 461

Query: 491 SSVDIDS 497
            + D + 
Sbjct: 462 LTADEED 468


>gi|34595745|gb|AAQ76595.1| RpoB [Mycobacterium goodii]
          Length = 1169

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 268/515 (52%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 680  IVDAGQRVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 739  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 846  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +        ++    
Sbjct: 906  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGVPDWASKLPE------ELYTAP 958

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
            S +                       V+TPVFDGA E  +  +L            ++  
Sbjct: 959  SDSI----------------------VATPVFDGAQEGELAGLLGSTLPNRDGEVMVNAD 996

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 997  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1056

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1057 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1116

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1117 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1147



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 331/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 301 RVGRYKVNKKLGLNAGKPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS  D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQIDYLTADEEDRHVVAQANSPTD 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G FTEE V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 ENGRFTEERVMVRKKGGEVEFVSAGQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +VA + G++E+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGVIEEVSADYITVMADDGTRQS 660

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSN  TC NQRP+V  G  V    +IADGP T  G++ALG+N+LVA
Sbjct: 661 -------YRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVA 713

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 714 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 773

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 774 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 833

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 834 ESGKVIGIRVFSREDDD 850



 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 98/333 (29%), Positives = 157/333 (47%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI---APDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    A  +R  E    GL+     + PI 
Sbjct: 29  RVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGEENPVGGLEEVLAELSPIE 88

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 89  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 139

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 140 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 197

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +   
Sbjct: 198 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDT 257

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 258 TSGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 308

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 309 KKLGLNAGKPITSSTLTEEDVVATIEYLVRLHE 341


>gi|581334|emb|CAA78668.1| RNA polymerase beta subunit [Mycobacterium leprae]
          Length = 1179

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 268/513 (52%), Gaps = 52/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI         + ++ + + +    V
Sbjct: 689  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAINAVGGSTTNEDAIILSNRLVEEDV 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
               I      + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  LTSIHI-EEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 806

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 807  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 855

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 856  HEDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVD 915

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMNVGQI ETHLGW     G KI           ++              
Sbjct: 916  IILNTHGVPRRMNVGQILETHLGWVAKS-GWKIDVAGGIPDWAVNLP------------- 961

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                       + +L  A        VSTPVFDGA EE +  +L     +          
Sbjct: 962  -----------EELLHAAPNQI----VSTPVFDGAKEEELQGLLSSTLPNRDGDVMVGGD 1006

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1007 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1066

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1067 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1126

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1127 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1159



 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 321/690 (46%), Positives = 454/690 (65%), Gaps = 29/690 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + +       +  
Sbjct: 179 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 234

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         I   +    +  +R+TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 235 TVLLKALGWTSEQI--TERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESA 292

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L   +      + +ED++A I+ LV L  G+
Sbjct: 293 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGELITSSTLTEEDVVATIEYLVRLHEGQ 352

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 353 STMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 412

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 413 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 472

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++++ YL+
Sbjct: 473 RDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIEYLT 532

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAAS 677
           A EE+   +AQANS +DE G  +    + R   GE   V   ++D++D SP+Q+VS+A +
Sbjct: 533 ADEEDRHVVAQANSPIDEAGRSSSRACWVRRKAGEVEYVASSEVDYMDVSPRQMVSVATA 592

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPFLE+DD+NR LMG NMQRQAVPL+++E P VGTGME   A  +G  +VA+++G++E+
Sbjct: 593 MIPFLEHDDANRALMGANMQRQAVPLVRSERPLVGTGMELRAAIDAGHVVVAEKSGVIEE 652

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V A  I + + +G           YR+ KF RSN  TC NQ P+V  GD V    +IADG
Sbjct: 653 VSADYITVMADDGTR-------RTYRMRKFARSNHGTCANQSPIVDAGDRVEAGQVIADG 705

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNF-EDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           P T+ G++ALG+N+LVA     G    ED++++S R+V EDV TSIHIEE E+ ARDTKL
Sbjct: 706 PCTENGEMALGKNLLVAINAVGGSTTNEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKL 765

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           G EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 766 GAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAI 825

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           FGEKA +VRDTSL+VP G SG V+ +R+F+
Sbjct: 826 FGEKAREVRDTSLKVPHGESGKVIGIRVFS 855



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 99/370 (26%), Positives = 168/370 (45%), Gaps = 25/370 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMM---NIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +       A   R +     GL+     + PI 
Sbjct: 38  RISFAKLREPLEVPGLLDVQTDSFEWLIGSPCWRAAAASRGDLKPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVEECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F     +  +   D 
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMRSTLEKDN 266

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+ +  
Sbjct: 267 TVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGE 326

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV---DSVNNNAYIR 359
           L       +     T E  +   +     ++       +    I +            I+
Sbjct: 327 LITSSTLTEEDVVATIEYLVRLHEGQSTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQ 386

Query: 360 NTLVTDKNKD 369
           N +    ++ 
Sbjct: 387 NQIRVGMSRM 396


>gi|75910405|ref|YP_324701.1| DNA-directed RNA polymerase subunit beta [Anabaena variabilis ATCC
           29413]
 gi|115305557|sp|Q3M5D0|RPOB_ANAVT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|75704130|gb|ABA23806.1| DNA-directed RNA polymerase subunit beta [Anabaena variabilis ATCC
           29413]
          Length = 1117

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 319/617 (51%), Positives = 429/617 (69%), Gaps = 14/617 (2%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 196 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD VR +   DI+A +  L++L    G+IDDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLSVPDTVRVLTSGDILAAVDYLINLEYDIGSIDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +G+V  D   VY++A EE++  +A  +  +DE+G      V 
Sbjct: 436 HARVNQYGFLETPFRPVENGRVRFDQPAVYMTADEEDDLRVAPGDIPVDENGHIIGPQVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 496 VRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR------------SVEGDLDP 754
           E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R            +  G L  
Sbjct: 556 ERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDATEIRVRVSGQLPAASGKSTDNGQLTS 615

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y + K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N++VA
Sbjct: 616 QKGQEIRYTVSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNIVVA 675

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           +MPW GYN+ED++LISER+V +D++TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+
Sbjct: 676 YMPWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALR 735

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G
Sbjct: 736 QLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNG 795

Query: 935 VSGTVVDVRIFNRHGID 951
             G VVDVR+F R   D
Sbjct: 796 EKGRVVDVRLFTREQGD 812



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 183/528 (34%), Positives = 262/528 (49%), Gaps = 64/528 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G E                +++  ++ +G  V  G +L    + +G   +   + ++ A 
Sbjct: 618  GQEIRYTVSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEG-GELALGQNIVVAY 676

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---K 971
               +  +  D  L     V   +       ++ I+  +  +  E    +I  +  D   +
Sbjct: 677  MPWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQ 736

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DEQ I+    +    +IL G+    G         L   +  E  R             
Sbjct: 737  LDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------ 784

Query: 1032 QRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                  ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKM
Sbjct: 785  ------VRDNSLRVPNGEKGRVVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKM 838

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGI+SRILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG 
Sbjct: 839  AGRHGNKGIISRILPIEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGHTLGV 898

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K    D               ++ G  S    +     ++     + W          
Sbjct: 899  RFKITPFD---------------EMYGEESSRRIVHGKLQEARDETGKDWVY-------- 935

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                            + D+ G+ +++DG TGEPFDRPVT+G  YMLKL H+V DK++AR
Sbjct: 936  ----------------NPDDPGKIMVFDGRTGEPFDRPVTIGVAYMLKLVHLVDDKIHAR 979

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     
Sbjct: 980  STGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALN 1039

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            +IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1040 AIVKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQADGSSLDVE 1087



 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 104/454 (22%), Positives = 193/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 13  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGHNYKLKE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TYAV + +  RL+          K   DIKEQ +++GDLPLMT  GT
Sbjct: 63  PKYSVEEAKRRDSTYAVQMYVPTRLL---------NKETGDIKEQEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L ++      +  + DI+      
Sbjct: 231 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLSVPDTVRVLTSGDILAAVDYL 290

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 291 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +     G+  I  I+         +G +  +
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|209395026|gb|ACI45316.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 196/488 (40%), Positives = 313/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  F   + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFQQADKAPRKRTKEGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PL+T  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLVTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDK +   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKSKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + ++++   Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSANVQELQCNYTNELDQGAYISHTLRTDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G   T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GGPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+ +++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIGKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|260203836|ref|ZP_05771327.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis K85]
 gi|289573272|ref|ZP_06453499.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis K85]
 gi|289537703|gb|EFD42281.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis K85]
          Length = 1172

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 332/662 (50%), Positives = 455/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+LRMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 379 IQNQIRVGMLRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA  +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVADESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|62720648|gb|AAX93860.1| RNA polymerase subunit B [Mycobacterium phocaicum]
          Length = 1167

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 183/508 (36%), Positives = 259/508 (50%), Gaps = 55/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 681  IVDSGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEQDVL 739

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 740  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 797

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 798  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFS 846

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 847  REDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDGTPVD 906

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 907  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN------------------ 947

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                         +            V+TPVFDGA E  +  +L     +          
Sbjct: 948  -------------LPEGMHSAPRDSIVATPVFDGARENELQGLLGSTLPNRDGDVMVDAD 994

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 995  GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1054

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1055 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1114

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        +   +
Sbjct: 1115 KELQSLCLNVEVLSSDGAAIEMRDSDDE 1142



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 326/679 (48%), Positives = 454/679 (66%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 182 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 239

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 240 ERFGFSEIMMGTLEKDNIAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLA 299

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNGKG------------TI 453
            VGR K+N +L L   +        + +ED++A I+ LV L  G+              +
Sbjct: 300 RVGRYKVNKKLGLGGANPALVTATTLTEEDVVATIEYLVRLHEGQTTMTAPGGLEVPVEV 359

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 360 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 419

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP E
Sbjct: 420 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIE 479

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS 
Sbjct: 480 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGIVTDQIDYLTADEEDRHVVAQANSP 539

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           LD +G FTEE +  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 540 LDANGHFTEEKILVRRKGGEVEFVSANDVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 599

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA ++G++E+V A  + + + +G  
Sbjct: 600 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKSGVIEEVSADYVTVMADDGSR 659

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 660 -------HTYRMRKFNRSNHGTCANQRPIVDSGQRVEAGQVIADGPCTENGEMALGKNLL 712

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 713 VAVMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 772

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 773 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 832

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ VR+F+R   D
Sbjct: 833 HGESGKVIGVRVFSREDDD 851



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 91/296 (30%), Positives = 151/296 (51%), Gaps = 22/296 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +    +  + G       L+     + PI 
Sbjct: 28  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSDRWRSKAVDRGDINPVGGLEEVLAELSPIE 87

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K  VD+C  +D TYA PL +T   I           +  +IK
Sbjct: 88  DFAGTLSLSFSDPRFDEVKAPVDECKEKDQTYAAPLFVTAEFI---------NNNTGEIK 138

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD +  +   + K L++ ++IP
Sbjct: 139 SQTVFMGDFPMMTDMGTFIINGTERVVVSQLVRSPGVYFDENIDK--STEKTLHSVKVIP 196

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +   D 
Sbjct: 197 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDN 256

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGI 298
              P  A   +            ++ + ++E+   K+    L +  + K  K LG+
Sbjct: 257 IAGPDEALLDIYRKLRPGEPPTKESAQALLENLFFKEKRYDLARVGRYKVNKKLGL 312


>gi|325067671|ref|ZP_08126344.1| DNA-directed RNA polymerase subunit beta [Actinomyces oris K20]
          Length = 1173

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 186/598 (31%), Positives = 275/598 (45%), Gaps = 59/598 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGP 858
                       ++    P  G   E    +    V       +  E      R     G 
Sbjct: 598  MGANMQRQAVPLIRPDAPLVGTGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGT 657

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF- 917
            E + +             ++  +   G  V  G +L        E  +   + LL A   
Sbjct: 658  EIVYKVAKFRRSNQGNCYNQRVVATEGERVEVGTVLADGP-ATNEGDLALGQNLLVAFMT 716

Query: 918  --GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--D 973
              G    D    S RV +    T + +        D    +  + R+   +        D
Sbjct: 717  WEGLNYEDAIIISQRVVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLD 776

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R      +++    + 
Sbjct: 777  ERGIIRIGAEVRSGDILVGKVTPKGETELTSEERLLRAIFGEKARE-VRDTSLRVPHGEY 835

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             + +   + + +    E               +P GV R+V+V++A +R I  GDK++GR
Sbjct: 836  GIVTGVREIDAASDDAE---------------LPAGVNRMVRVYIAQRRKITVGDKLSGR 880

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+ILP EDMPFL DGTPVD++LNPLGVPSRMNVGQ+ E HLGW      +   
Sbjct: 881  HGNKGVISKILPVEDMPFLADGTPVDVILNPLGVPSRMNVGQVLELHLGWVAS---RGWD 937

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +           + L                              + +   PV+TPVFDG
Sbjct: 938  ATAAREAGEAWTANL-------------------------PENGIKAEPRTPVATPVFDG 972

Query: 1214 ADEEAINSMLRMA-----DLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              +  +  +L         L     +G++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 973  VRDNELMGLLGSTLPTSDGLQLVEPNGKARLFDGRSGEPFPYPISVGYMYILKLHHLVDD 1032

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1033 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAHALQELLTVKSDDVNGR 1092

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             +VYE+IV G D  E G PESF VL+KEMQ+L L+++  ++     A  +   D ++ 
Sbjct: 1093 VKVYEAIVKGEDIPEPGIPESFKVLMKEMQSLCLNVEALDAEGVAIALDDTDDDGSRA 1150



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 330/771 (42%), Positives = 469/771 (60%), Gaps = 61/771 (7%)

Query: 226 EEI--LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS--------SLVDIDTGEQV-- 273
           +EI  +  F   +  S     +  P   A+      ++            +  TGE    
Sbjct: 80  DEISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYVVADFENFSTGEIKSQ 139

Query: 274 ----------IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGE 319
                      + G  + +G  + +  + V+  G+  +        + + N       G 
Sbjct: 140 TVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEKATDKYVYNVKFIPSRGA 199

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-----------KNK 368
              E      ++    I     +D+ +  +    + + IR                 K  
Sbjct: 200 WL-EFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSALDEDRKIT 258

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            + +ALLDIY+ +RPG+  +     ++    +F+  +YDL+ VGR K+N +L L +    
Sbjct: 259 TQDEALLDIYKKIRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYKINKKLGLASDLTE 318

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI---------------DDIDNLGNRRVRSVGEMLKN 473
             +R EDI+A ++ L+ L +G  T+               DDID+LGNRR+R+VGE+++ 
Sbjct: 319 STLRIEDIVAALRYLLALHSGAETVEGVRDGEITEIAVEYDDIDHLGNRRIRAVGELIQA 378

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R G+ RMER ++ER+++ D++++ P  LIN +PV +A+ EFF +SQLSQ  +  N L+
Sbjct: 379 QVRTGMSRMERQVRERMTTQDVEAITPNTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLA 438

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG++R RA +E+RDVH +HYGR+CP E+ EG NIGL+ SL +F R+N
Sbjct: 439 GLTHKRRLSALGPGGLSRERASMEVRDVHTSHYGRMCPIESPEGPNIGLIGSLATFGRIN 498

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGE 652
            +GF+ETPYR V DG+VT++  YL+A +E+   IAQAN +L EDG F E+ V CR   GE
Sbjct: 499 PFGFVETPYRVVVDGQVTDETHYLTADDEDRHVIAQANVALTEDGHFAEDHVLCRVTGGE 558

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             LVP  ++D +D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPL++ +AP VG
Sbjct: 559 PALVPSSQVDLMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLIRPDAPLVG 618

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  +G  +VA +AG+V +V A  + + + +G          +Y++ KF+RSNQ
Sbjct: 619 TGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGTEI-------VYKVAKFRRSNQ 671

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             C NQR +   G+ V    ++ADGP+T+ GDLALG+N+LVAFM W G N+ED+++IS+R
Sbjct: 672 GNCYNQRVVATEGERVEVGTVLADGPATNEGDLALGQNLLVAFMTWEGLNYEDAIIISQR 731

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V+ED+ TSIHIEE EV ARDTKLG EEITRDIPNVSEE L N+DE GII +GAEV  GD
Sbjct: 732 VVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLDERGIIRIGAEVRSGD 791

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V  VR
Sbjct: 792 ILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPHGEYGIVTGVR 842



 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 94/302 (31%), Positives = 142/302 (47%), Gaps = 33/302 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDER------------PNEGLQAAFKS 61
           R  F K  E +  P+L+ +Q  S+D  +      +                 GL+  F  
Sbjct: 22  RINFAKIAEPMQAPNLLALQTESFDWLVGNERWRERMTAANKAHPGSLPETSGLEEIFDE 81

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F  + F+ PK+  ++C  +DLTY+ PL +                S
Sbjct: 82  ISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYV---------VADFENFS 132

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   + K +Y 
Sbjct: 133 TGEIKSQTVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEK--ATDKYVYN 190

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            + IP +G W++ E D  D + VRIDR+RK  VT FL+ALGMD  EI   F  +P +  +
Sbjct: 191 VKFIPSRGAWLEFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSA 250

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K       I  GE   +E+G+ L      + K   +  +G 
Sbjct: 251 LDEDRKITTQDEALLDIYKK-------IRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGR 303

Query: 299 TS 300
             
Sbjct: 304 YK 305


>gi|209395074|gb|ACI45348.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 198/488 (40%), Positives = 310/488 (63%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQADKAPRKRTIEGLQAAFDAAFPIVSHNGFVEMKFIEYNLARP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+A  ++  ++LI++D +  T  +K +K++KEQ +YMG++P  T  G+
Sbjct: 61  AFDVRECQTRGLTFASAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPPRTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD K I++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKGILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT    A+G++ E IL+ F+    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILPKAIGLNPESILAXFFVNDNFRLMDSGAQMEFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRIVARSIVDADTGEIIAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++  AYI  TL  D+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGTGVLDVQCIYTNELDQGAYISQTLRIDETVDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRNESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|118616532|ref|YP_904864.1| DNA-directed RNA polymerase subunit beta [Mycobacterium ulcerans
           Agy99]
 gi|158512376|sp|A0PM24|RPOB_MYCUA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|118568642|gb|ABL03393.1| DNA-directed RNA polymerase, beta subunit, RpoB [Mycobacterium
           ulcerans Agy99]
          Length = 1176

 Score =  516 bits (1330), Expect = e-144,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 451/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  +  TL  
Sbjct: 207 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSNEQIH----ERFGFSEIMMGTLEK 262

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L+ 
Sbjct: 263 DNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLNA 322

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+               DDID+ GNRR+R+VGE+
Sbjct: 323 GQPITSSTLTEEDVVATIEYLVRLHEGQTAMTAPGGVEVPVETDDIDHFGNRRLRTVGEL 382

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 383 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 442

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 443 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 502

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++ YL+A EE+   +AQANS +D  G F E  V  R  
Sbjct: 503 RVNPFGFIETPYRKVVDGVVSDEIHYLTADEEDRHVVAQANSPIDAQGRFVEPRVLVRRK 562

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 563 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 622

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA +AG++E+V A  I + + +G           YR+ KF R
Sbjct: 623 LVGTGMELRAAIDAGDVVVADKAGVIEEVSADYITVMADDGTR-------HTYRMRKFAR 675

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  G+ V    +IADGP T  G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 676 SNHGTCANQSPIVDAGERVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIIL 735

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV 
Sbjct: 736 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVR 795

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 796 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 855

Query: 950 ID 951
            D
Sbjct: 856 DD 857



 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/518 (35%), Positives = 253/518 (48%), Gaps = 63/518 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 687  IVDAGERVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 745

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 746  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIVRIGAEVRDGDILVGKV 804

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 805  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIG 847

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 848  IRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPD 907

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +  G +       + 
Sbjct: 908  GTPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDVANGVPEWAGKLPENLLSAQ- 965

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE---- 1230
                                           VSTPVFDGA E  +  +L     +     
Sbjct: 966  ---------------------------PDSIVSTPVFDGAQEAELQGLLSATLPNRDGEV 998

Query: 1231 ----SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 999  LVDGDGKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGK 1058

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PES
Sbjct: 1059 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPES 1118

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            F VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1119 FKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1156



 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 95/333 (28%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 36  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSQRWRESAAQRGDATPVGGLEEVLYELSPIE 95

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 96  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 146

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MG  P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + KLL++ ++IP
Sbjct: 147 SQTVFMGGFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKLLHSVKVIP 204

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 205 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSNEQIHERFGFSEIMMGTLEKDN 264

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 265 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 315

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 316 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 348


>gi|183981015|ref|YP_001849306.1| DNA-directed RNA polymerase, beta subunit, RpoB [Mycobacterium
           marinum M]
 gi|226699424|sp|B2HSJ3|RPOB_MYCMM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|183174341|gb|ACC39451.1| DNA-directed RNA polymerase, beta subunit, RpoB [Mycobacterium
           marinum M]
          Length = 1176

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 451/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  +  TL  
Sbjct: 207 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSNEQIH----ERFGFSEIMMGTLEK 262

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L+ 
Sbjct: 263 DNTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLNA 322

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+               DDID+ GNRR+R+VGE+
Sbjct: 323 GQPITSSTLTEEDVVATIEYLVRLHEGQTAMTAPGGVEVPVETDDIDHFGNRRLRTVGEL 382

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 383 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 442

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 443 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 502

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++ YL+A EE+   +AQANS +D  G F E  V  R  
Sbjct: 503 RVNPFGFIETPYRKVVDGVVSDEIHYLTADEEDRHVVAQANSPIDAQGRFVEPRVLVRRK 562

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 563 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 622

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA +AG++E+V A  I + + +G           YR+ KF R
Sbjct: 623 LVGTGMELRAAIDAGDVVVADKAGVIEEVSADYITVMADDGTR-------HTYRMRKFAR 675

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  G+ V    +IADGP T  G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 676 SNHGTCANQSPIVDAGERVEAGQVIADGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIIL 735

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV 
Sbjct: 736 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVR 795

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 796 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 855

Query: 950 ID 951
            D
Sbjct: 856 DD 857



 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 187/513 (36%), Positives = 263/513 (51%), Gaps = 53/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 687  IVDAGERVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 745

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 746  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 803

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 804  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 852

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 853  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVD 912

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       +  G +       +      
Sbjct: 913  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDVANGVPEWAGKLPENLLSAQ------ 965

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                      VSTPVFDGA E  +  +L     +          
Sbjct: 966  ----------------------PDSIVSTPVFDGAQEAELQGLLSATLPNRDGEVLVDGD 1003

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1004 GKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1063

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1064 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1123

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1124 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1156



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 36  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSQRWRESAAQRGDATPVGGLEEVLYELSPIE 95

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 96  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 146

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + KLL++ ++IP
Sbjct: 147 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKLLHSVKVIP 204

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 205 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSNEQIHERFGFSEIMMGTLEKDN 264

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 265 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 315

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 316 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 348


>gi|323357423|ref|YP_004223819.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Microbacterium testaceum StLB037]
 gi|323273794|dbj|BAJ73939.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Microbacterium testaceum StLB037]
          Length = 1164

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 180/515 (34%), Positives = 260/515 (50%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G+++      +    +   + LL A    +  +  D  +     V    +
Sbjct: 678  VVSAGERIEAGEVIADGPATEN-GELALGKNLLVAFMTWEGHNFEDAIILSQDLVKDDTL 736

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL--------LARDKDDEQVILDRNIYSRLMEILCG 992
                   +  + + R   + +E+I          L +D  DE+ I+      R  +IL G
Sbjct: 737  SSIHIEEY--EVDARDTKLGKEEITRDLPNVSPDLLKDL-DERGIVRIGAEVRPGDILVG 793

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   + +E  R                V   +     +       
Sbjct: 794  KVTPKGETELSAEERLLRAIFNEKSREV--------RDTSLKVPHGEQGTIIAVKEFNAE 845

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +        D++  GV R V V++A KR I  GDK+AGRHGNKG++++ILP EDMPFL
Sbjct: 846  DGD--------DELGSGVNRRVVVYIAQKRKITEGDKLAGRHGNKGVIAKILPIEDMPFL 897

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD+VLNPLG+P RMN GQ+ E HLGW     G K++                   
Sbjct: 898  ADGTPVDVVLNPLGIPGRMNFGQVLELHLGWIAQQ-GWKVEGTPEWAAH----------- 945

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                                +  VA +   G  V+TPVFDGA E+ I  +L         
Sbjct: 946  --------------------LPEVAREAAPGTKVATPVFDGAFEDEIAGLLDSTIPNRDG 985

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +D SG++IL+DG  GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 986  DRLIDSSGKTILFDGRYGEPFPAPISVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1045

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VYE+IV G +  E G P
Sbjct: 1046 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVYEAIVKGENIQEPGIP 1105

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ ++        +   D
Sbjct: 1106 ESFKVLMKEMQSLCLNVEVLSADGTAVNLRDTDDD 1140



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 318/613 (51%), Positives = 432/613 (70%), Gaps = 24/613 (3%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 243 DSIEETLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 302

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L LD P     +  +DI+A IK LV L  G                   DDIDN G
Sbjct: 303 INQKLGLDKPLSDSVLTVDDIVATIKYLVRLHRGDVSFDGVRGGKPAEIRLDTDDIDNFG 362

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 363 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 422

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 423 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 482

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL+ SL SFAR+NA+GFIETPYR+V DG+VT+ + YL+A EE +  +AQA  +L  DG F
Sbjct: 483 GLIGSLASFARINAFGFIETPYRRVVDGRVTDTIDYLTASEESDHIVAQAGVALKADGHF 542

Query: 641 TEELVFCRCAG--EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            E+ +  R     E  L P E+I ++D SP+Q+VS+A SLIPFLE+DD+NR LMG NMQR
Sbjct: 543 VEDRILARRGQGGEVDLFPVEEIGYMDVSPRQMVSVATSLIPFLEHDDANRALMGANMQR 602

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+++E+P VGTGME   A  +G  + A+++G+V +V A  + ++  EG        
Sbjct: 603 QAVPLVRSESPVVGTGMEGFAAIDAGDVVTAEKSGVVLEVSADVVTVQLDEGGTQD---- 658

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y L KF RSNQ T  NQR +V  G+ +   ++IADGP+T+ G+LALG+N+LVAFM W
Sbjct: 659 ---YFLRKFDRSNQGTSYNQRVVVSAGERIEAGEVIADGPATENGELALGKNLLVAFMTW 715

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            G+NFED++++S+ +V +D  +SIHIEE+EV ARDTKLG EEITRD+PNVS + LK++DE
Sbjct: 716 EGHNFEDAIILSQDLVKDDTLSSIHIEEYEVDARDTKLGKEEITRDLPNVSPDLLKDLDE 775

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+ +VRDTSL+VP G  GT
Sbjct: 776 RGIVRIGAEVRPGDILVGKVTPKGETELSAEERLLRAIFNEKSREVRDTSLKVPHGEQGT 835

Query: 939 VVDVRIFNRHGID 951
           ++ V+ FN    D
Sbjct: 836 IIAVKEFNAEDGD 848



 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 93/310 (30%), Positives = 145/310 (46%), Gaps = 27/310 (8%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFL------------MMNIAPDERPNEG 54
            +G G  R  F K  + + +PDL+ +Q  S+D  +                  D     G
Sbjct: 13  KSGRGASRLSFAKISDKLTVPDLLALQTESFDWLVGNDAWKARVAEAQAEGRTDVPEISG 72

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           L+  F+ + PI   S    L F +   +P K+ +++C  R  TYA PL +         +
Sbjct: 73  LEEIFEEISPIEDLSETMQLSFTNPYLEPEKYSIEECKERGKTYAAPLYV---------E 123

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                    +IK Q+++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   
Sbjct: 124 AEFMNHQTGEIKTQTVFMGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT-- 181

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-- 232
           S K + + R+IP +G W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  
Sbjct: 182 SDKDIVSARVIPSRGAWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDILAEFAG 241

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKE 290
           +  I  +   D       A   +         V  +    ++++         L K  + 
Sbjct: 242 FDSIEETLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRY 301

Query: 291 KGVKFLGITS 300
           K  + LG+  
Sbjct: 302 KINQKLGLDK 311


>gi|296168513|ref|ZP_06850329.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295896691|gb|EFG76328.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 1149

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 292/946 (30%), Positives = 437/946 (46%), Gaps = 127/946 (13%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMM---NIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +       A   R +     GL+     + PI 
Sbjct: 7   RVSFAKLREPLEVPGLLDVQIDSFEWLIGSPRWREAAAARGDVKPVGGLEEVLDELSPIE 66

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 67  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 117

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + KLL++ ++IP
Sbjct: 118 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKLLHSVKVIP 175

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +     +   
Sbjct: 176 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIHERFGFSEIMMGTLEKDN 235

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 236 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 286

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +        T     E   V   + L  + H+              + A +      +
Sbjct: 287 KKLGLHAGEPITSSTLTEEDVVATIEYLVRLHHARTD----------GHPAVMTVPGGIE 336

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
              +  D      R +R            +         +  +S + RV        D  
Sbjct: 337 VPVETDDIDHFGNRRLR--------TVGELIQN----QIRVGMSRMERVVRERMTTQDVE 384

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                I  + +I I  ++  ++   GT      +      S     +    LG   + R 
Sbjct: 385 A----ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 440

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
                + +++  V P       P+ +             +   VN    I          
Sbjct: 441 ----RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFI---------- 486

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
           +    +   GV   ++H           T++  +  +V+     + ++A G  E     V
Sbjct: 487 ETPYRKVVDGVVTDEIH---------YLTADEEDRHVVAQAN--SPIDASGRFEESRVLV 535

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                  +V Y+ + E +                     V  R            ++  D
Sbjct: 536 RRKA--GEVEYVPSSEVDYMD------------------VSPRQMVSVATAMIPFLEHDD 575

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
                                +NR LMG NMQRQAVPL+++EAP VGTGME   A  +G 
Sbjct: 576 ---------------------ANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGD 614

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +VA +AG++E+V A  I + + +G           YR+ KF+RSN  TC NQ P+V  G
Sbjct: 615 VVVADKAGVIEEVSADYITVMADDGTR-------HTYRMRKFERSNHGTCANQSPIVDAG 667

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D V    +IADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIE
Sbjct: 668 DRVEAGQVIADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIE 727

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           E E+ ARDTKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ 
Sbjct: 728 EHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETE 787

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 788 LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 833



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/513 (36%), Positives = 264/513 (51%), Gaps = 56/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 663  IVDAGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 721

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 722  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 779

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 780  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 828

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DGTPVD
Sbjct: 829  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDGTPVD 888

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+   +                      
Sbjct: 889  IILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAAN------------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDES 1231
                         +       +    VSTPVFDGA E  +  +L            +D  
Sbjct: 930  -------------LPEDLLHAQPNAIVSTPVFDGAREAELQGLLSCTLPNRDNEVMVDGD 976

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 977  GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1036

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1037 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1096

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1097 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1129


>gi|256390126|ref|YP_003111690.1| DNA-directed RNA polymerase subunit beta [Catenulispora acidiphila
            DSM 44928]
 gi|256356352|gb|ACU69849.1| DNA-directed RNA polymerase, beta subunit [Catenulispora acidiphila
            DSM 44928]
          Length = 1158

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 188/508 (37%), Positives = 270/508 (53%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L      + +  M   + LL A    +  +  D  +     V   V+
Sbjct: 672  VVAEGERVEVGSVLADGPCTQ-DGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 730

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 731  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGADVVPGDILVGK 788

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +     I+  R    I  
Sbjct: 789  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGEQGKIIGVR----IFD 837

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
               GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPFL+DGTPVD
Sbjct: 838  RDSGDELPPGVNQLVRVYVAQKRKITHGDKLAGRHGNKGVIAKILPVEDMPFLEDGTPVD 897

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN GQ+ ETHLGW         +      +    I              
Sbjct: 898  IVLNPLGVPSRMNPGQVLETHLGWIAATGWDVGEGNAEWQERLRSIG------------- 944

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM--------ADLDES 1231
                             A+       V+TPVFDGA E+ I  +L            +D +
Sbjct: 945  -----------------ADSAAPKTKVATPVFDGAREDEITGLLGNTLKTRDGVRLVDST 987

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ ++DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 988  GKARMFDGRSGEPFPYPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGG 1047

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV+GR +VYE+IV G++  E G PESF VL+
Sbjct: 1048 QRFGEMEVWALEAYGAAYALQELLTIKSDDVLGRVKVYEAIVKGDNIPEPGIPESFKVLI 1107

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +         +   D
Sbjct: 1108 KEMQSLCLNVEVLSKDGTMIELRDTDED 1135



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 318/631 (50%), Positives = 446/631 (70%), Gaps = 24/631 (3%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      D  IL  +       +R TL  D    + +ALLDIYR +RPG+  T   A+++
Sbjct: 221 LKALGWDDARIL--EEFGEYESMRQTLEKDHTAGQDEALLDIYRKLRPGEPPTREAAQTL 278

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            + L+F+  +YDL+ VGR K++ +L   +  D   + ++DI+  IK LV L  G+  +D 
Sbjct: 279 LDNLYFNPKRYDLAKVGRYKIDKKLGQASGIDNTVLTEDDIVNAIKFLVKLHAGETEMDP 338

Query: 456 --------------IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
                         ID+ GNRR+RSVGE+++NQ R GL RMER ++ER+++ D++++ PQ
Sbjct: 339 QAEGMPMVVVEEDDIDHFGNRRLRSVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQ 398

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            LIN +PVV+++ EFF +SQLSQ  +  N LS +TH RRL+ALG GG++R RAG E+RDV
Sbjct: 399 TLINIRPVVASIKEFFGTSQLSQFMDQTNPLSGLTHKRRLNALGPGGLSRERAGFEVRDV 458

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           HP+HYGR+CP ET EG NIGL+ SL S+ R+NA+GFIETPYRKV DG+VT+ + YL+A E
Sbjct: 459 HPSHYGRMCPIETPEGPNIGLIGSLASYGRINAFGFIETPYRKVEDGRVTDHIDYLTADE 518

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+   +AQAN+ + +DGS+T+E V CR   GE  ++    ID++D SP+Q+VS+A ++IP
Sbjct: 519 EDRYVVAQANAPVRDDGSYTDERVLCRRKGGEIEMMAPADIDYMDVSPRQMVSVATAMIP 578

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE+DD+NR LMG NM RQAVPLL++++P+VGTGME   A  +   + A + G+V +V A
Sbjct: 579 FLEHDDANRALMGANMMRQAVPLLQSDSPYVGTGMEYRCAVDAADVVTADKGGVVTEVSA 638

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             + + + +       +   +YR+ KF+RSNQ T  NQ+ +V  G+ V    ++ADGP T
Sbjct: 639 DLVTVANDD-------ATTSVYRIAKFRRSNQGTSFNQKVVVAEGERVEVGSVLADGPCT 691

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G++ALG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEE
Sbjct: 692 QDGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEE 751

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITRDIPNVSEE L ++DE GII +GA+V PGDILVGK+TPKGE+ +TPEE+LLRAIFGEK
Sbjct: 752 ITRDIPNVSEEVLADLDERGIIRIGADVVPGDILVGKVTPKGETELTPEERLLRAIFGEK 811

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           A +VRDTSL+VP G  G ++ VRIF+R   D
Sbjct: 812 AREVRDTSLKVPHGEQGKIIGVRIFDRDSGD 842



 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 94/311 (30%), Positives = 146/311 (46%), Gaps = 31/311 (9%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-------- 53
           A+ +  N   R+   F K  E +++P+L+ +Q  S+D  +           +        
Sbjct: 7   AQNITKNAARRI--SFAKIKEPLEVPNLLALQTESFDWLVGNATWKGRVSEQQAAGLDVP 64

Query: 54  ---GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIV 110
              GL+  F+ + PI  F G   L F  + F+P K+ +D+C  RD TYA PL +T     
Sbjct: 65  TTSGLEEIFEEISPIEDFQGTMSLTFRDHRFEPAKYSIDECKDRDFTYAAPLFVTAEFT- 123

Query: 111 FDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
                        +IK Q+++MGD PLMT  GTF+I G +R+VV+QL RSPG++F  D  
Sbjct: 124 --------NNETGEIKSQTVFMGDFPLMTNKGTFIINGTERVVVTQLVRSPGLYFSQDID 175

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS 230
           +   S K ++  +IIP +G W++ E D +D++ VR+DR+RK  VT  L ALG D   IL 
Sbjct: 176 KT--SDKDVFNAKIIPSRGAWLEFEIDKRDMVGVRVDRKRKQHVTVLLKALGWDDARILE 233

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK 289
            F       Q  +          L+   +       +  GE    E+ + L   L  + K
Sbjct: 234 EFGEYESMRQTLEKDHTAGQDEALLDIYR------KLRPGEPPTREAAQTLLDNLYFNPK 287

Query: 290 EKGVKFLGITS 300
              +  +G   
Sbjct: 288 RYDLAKVGRYK 298


>gi|186685076|ref|YP_001868272.1| DNA-directed RNA polymerase subunit beta [Nostoc punctiforme PCC
           73102]
 gi|186467528|gb|ACC83329.1| DNA-directed RNA polymerase, beta subunit RpoB [Nostoc punctiforme
           PCC 73102]
          Length = 1099

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 318/605 (52%), Positives = 426/605 (70%), Gaps = 8/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 196 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD +R +   DI+A +  L++L    G IDDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLSVPDTMRVLTAGDILAAVDYLINLEYDIGNIDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +G+V  D+   Y++A EE++  +A  +  +DE G     LV 
Sbjct: 436 HARVNLYGFLETPFRPVENGRVRFDLPPAYMTADEEDDLRVAPGDIPVDETGHIIGPLVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 496 VRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R      +        Y L K
Sbjct: 556 ERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNTPE------IKYTLSK 609

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N++VA+MPW GYN+ED+
Sbjct: 610 YQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNIVVAYMPWEGYNYEDA 669

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V +DV+TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+ +DE GII +GA
Sbjct: 670 ILISERLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQLDEQGIIRIGA 729

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 730 WVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRLFT 789

Query: 947 RHGID 951
           R   D
Sbjct: 790 REQGD 794



 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 191/587 (32%), Positives = 273/587 (46%), Gaps = 66/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E        MV          +++  E+  R     
Sbjct: 541  MGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNT 600

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            PE                +++  ++ +G  V  G +L    + +G   +   + ++ A  
Sbjct: 601  PEIKYTLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEG-GELALGQNIVVAYM 659

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   V       ++ I+  +  +  E    +I  +  D   + 
Sbjct: 660  PWEGYNYEDAILISERLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQL 719

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DEQ I+    +    +IL G+    G         L   +  E  R              
Sbjct: 720  DEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 766

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMA
Sbjct: 767  -----VRDNSLRVPNGEKGRVVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMA 821

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG +
Sbjct: 822  GRHGNKGIISRILPAEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGQTLGVR 881

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  S    +     ++     + W           
Sbjct: 882  FKITPFD---------------EMYGEESSRRIVHGKLQEARDETGKDWVY--------- 917

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                           + D  G+ ++YDG TGEPFDR +T+G  YMLKL H+V DK++ARS
Sbjct: 918  ---------------NPDNPGKIMVYDGRTGEPFDRAITIGVAYMLKLVHLVDDKIHARS 962

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +
Sbjct: 963  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNA 1022

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1023 IVKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQADGSSLDVE 1069



 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 107/481 (22%), Positives = 200/481 (41%), Gaps = 36/481 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 13  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGHNYKLKE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TYAV + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 63  PKYSVEEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L ++      +  A DI+      
Sbjct: 231 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLSVPDTMRVLTAGDILAAVDYL 290

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+ +   ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 291 INLE-YDIGNIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +     G+  I  I+         +G +  +        +E   +   +      + 
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNLYGFLETPFRPVENGRVRFDLP 462

Query: 500 P 500
           P
Sbjct: 463 P 463


>gi|329944330|ref|ZP_08292589.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            170 str. F0386]
 gi|328531060|gb|EGF57916.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            170 str. F0386]
          Length = 1142

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 185/598 (30%), Positives = 276/598 (46%), Gaps = 59/598 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGP 858
                       ++    P  G   E    +    V       +  E      R     G 
Sbjct: 567  MGANMQRQAVPLIRPDAPLVGTGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGT 626

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF- 917
            E + +             ++  +   G  V  G +L        E  +   + LL A   
Sbjct: 627  ENVYKVAKFRRSNQGNCYNQRVVATEGERVEVGSVLADGP-ATNEGDLALGQNLLVAFMT 685

Query: 918  --GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--D 973
              G    D    S RV +    T + +        D    +  + R+   +        D
Sbjct: 686  WEGLNYEDAIIVSQRVVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLD 745

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R      +++    + 
Sbjct: 746  ERGIIRIGAEVRSGDILVGKVTPKGETELTSEERLLRAIFGEKARE-VRDTSLRVPHGEY 804

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             + +   + + +    E               +P GV R+V+V++A +R I  GDK++GR
Sbjct: 805  GIVTGVREIDAASDDAE---------------LPAGVNRMVRVYIAQRRKITVGDKLSGR 849

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+ILP EDMPFL DGTPVD++LNPLGVPSRMNVGQ+ E HLGW          
Sbjct: 850  HGNKGVISKILPVEDMPFLADGTPVDVILNPLGVPSRMNVGQVLELHLGWVASR------ 903

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                      +   +  +    ++     + +   PV+TPVFDG
Sbjct: 904  ----------------------GWDATAAHEAGEAWTANLPENGIKAEPRTPVATPVFDG 941

Query: 1214 ADEEAINSMLRMA-----DLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              +  +  +L         L     +G++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 942  VRDNELMGLLDSTLPTSDGLQLVEPNGKARLFDGRSGEPFPYPISVGYMYILKLHHLVDD 1001

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1002 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAHALQELLTVKSDDVNGR 1061

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             +VYE+IV G D  E G PESF VL+KEMQ+L L+++  ++     A  +   D ++ 
Sbjct: 1062 VKVYEAIVKGEDIPEPGIPESFKVLMKEMQSLCLNVEALDAEGSAIALDDTDDDGSRA 1119



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 329/771 (42%), Positives = 469/771 (60%), Gaps = 61/771 (7%)

Query: 226 EEI--LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS--------SLVDIDTGEQV-- 273
           +EI  +  F   +  S     +  P   A+      ++            +  TGE    
Sbjct: 49  DEISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYVVADFENFSTGEIKSQ 108

Query: 274 ----------IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGE 319
                      + G  + +G  + +  + V+  G+  +        + + N       G 
Sbjct: 109 TVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEKATDKYVYNVKFIPSRGA 168

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-----------KNK 368
              E      ++    I     +D+ +  +    + + IR                 K  
Sbjct: 169 WL-EFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSALDEDRKIT 227

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            + +ALLDIY+ +RPG+  +     ++    +F+  +YDL+ VGR K+N +L L +    
Sbjct: 228 TQDEALLDIYKKIRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYKINKKLGLASDLTE 287

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI---------------DDIDNLGNRRVRSVGEMLKN 473
             +R EDI+A ++ L+ L  G  T+               DDID+LGNRR+R+VGE+++ 
Sbjct: 288 STLRIEDIVAALRYLLALHAGAETVEGVRDGEITEIAVEYDDIDHLGNRRIRAVGELIQA 347

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R G+ RMER ++ER+++ D++++ P  LIN +PV +A+ EFF +SQLSQ  +  N L+
Sbjct: 348 QVRTGMSRMERQVRERMTTQDVEAITPNTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLA 407

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG++R RA +E+RDVH +HYGR+CP E+ EG NIGL+ SL +F R+N
Sbjct: 408 GLTHKRRLSALGPGGLSRERASMEVRDVHTSHYGRMCPIESPEGPNIGLIGSLATFGRIN 467

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGE 652
            +GF+ETPYR V DG+VT++  YL+A +E+   IAQAN +L EDG F E+ V CR   GE
Sbjct: 468 PFGFVETPYRVVVDGQVTDETHYLTADDEDRHVIAQANVTLTEDGHFAEDHVLCRVTGGE 527

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             LVP  ++D +D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPL++ +AP VG
Sbjct: 528 PALVPSSQVDLMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLIRPDAPLVG 587

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  +G  +VA +AG+V +V A  + + + +G         ++Y++ KF+RSNQ
Sbjct: 588 TGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGTE-------NVYKVAKFRRSNQ 640

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             C NQR +   G+ V    ++ADGP+T+ GDLALG+N+LVAFM W G N+ED++++S+R
Sbjct: 641 GNCYNQRVVATEGERVEVGSVLADGPATNEGDLALGQNLLVAFMTWEGLNYEDAIIVSQR 700

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V+ED+ TSIHIEE EV ARDTKLG EEITRDIPNVSEE L N+DE GII +GAEV  GD
Sbjct: 701 VVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLDERGIIRIGAEVRSGD 760

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V  VR
Sbjct: 761 ILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPHGEYGIVTGVR 811



 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/292 (30%), Positives = 138/292 (47%), Gaps = 33/292 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDER------------PNEGLQAAFKSVFPITAFSGA 71
           +  P+L+ +Q  S+D  +      +                 GL+  F  + PI  F   
Sbjct: 1   MQAPNLLALQTESFDWLVGNERWRERMTAANRAHPGSLPETSGLEEIFDEISPIEDFGET 60

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F  + F+ PK+  ++C  +DLTY+ PL +                S  +IK Q+++
Sbjct: 61  MALSFHDHRFEEPKYTAEECQEKDLTYSAPLYV---------VADFENFSTGEIKSQTVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   + K +Y  + IP +G W
Sbjct: 112 MGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEK--ATDKYVYNVKFIPSRGAW 169

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D  D + VRIDR+RK  VT FL+ALGMD  EI   F  +P +  +   D      
Sbjct: 170 LEFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSALDEDRKITTQ 229

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             A L +  K       I  GE   +E+G+ L      + K   +  +G   
Sbjct: 230 DEALLDIYKK-------IRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYK 274


>gi|294786445|ref|ZP_06751699.1| DNA-directed RNA polymerase, beta subunit [Parascardovia denticolens
            F0305]
 gi|315226015|ref|ZP_07867803.1| DNA-directed RNA polymerase subunit beta [Parascardovia denticolens
            DSM 10105]
 gi|294485278|gb|EFG32912.1| DNA-directed RNA polymerase, beta subunit [Parascardovia denticolens
            F0305]
 gi|315120147|gb|EFT83279.1| DNA-directed RNA polymerase subunit beta [Parascardovia denticolens
            DSM 10105]
          Length = 1192

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 190/535 (35%), Positives = 268/535 (50%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +         +   ++  ++  G  V  G +L      + E  M   + L
Sbjct: 658  MNDDGSSNSYKLTKFQRSNQMTCYNQVPVVKKGERVETGSVLADGPATE-EGEMALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     V    +         ID  E  +  E E    L    D
Sbjct: 717  LVAFMPWNGYNYEDAVIISQRLVRDDTLSSIHIEEFEIDARETKLGAE-EITRDLPNVSD 775

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D    LD N   R+     G    +G     K T      ++   R     F  +  +V+
Sbjct: 776  DAVANLDENGIIRV-----GAEVEAGDILVGKVTPKGETELTPEERLLRAIFGAKSREVR 830

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   ++   K + E    GD++P GV +V++V++A  R I  GDK++G
Sbjct: 831  DTSLRVPHGERGTVISIKSMTKEQAE--DEGDELPTGVNQVIRVYIAQHRKITQGDKLSG 888

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 889  RHGNKGVISRILPEEDMPFLADGTPIDIMLNPLGVPSRMNLGQVLELHLGWIA-HSGWDI 947

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                            +       +   AE+ ++G  V+TPVFD
Sbjct: 948  SIDP---------------------------DLEAEWKKHIPAGAEKGEAGSHVATPVFD 980

Query: 1213 GADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G   +A++ +L     D  G        ++ L+DG TGEPF +P++VGY+YMLKL+H+V 
Sbjct: 981  GVRTDAMHGLLHTTLPDRDGNYLVGDDGKAQLFDGRTGEPFPKPISVGYMYMLKLHHLVD 1040

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+TIKSDDV G
Sbjct: 1041 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTIKSDDVDG 1100

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R R Y +IV G++    G PESF VL+KEMQ+L L++++ N+  +     EE  D
Sbjct: 1101 RVRAYGAIVKGDNLPPAGIPESFKVLLKEMQSLALNVEVLNAEGQAIDMKEEDDD 1155



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 304/618 (49%), Positives = 427/618 (69%), Gaps = 23/618 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +   +   +   L  +    +  AL+++YR +RPGD +T     ++    +F++ +YDL+
Sbjct: 246 NEFKDYPLVMEALNKEPEISQDQALIELYRRIRPGDTATPEAGRNLLESFYFNTKRYDLA 305

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L LDT    R + +EDI++ +K LV L +GK                  D
Sbjct: 306 RVGRYKINRKLGLDTDYQNRSLTREDILSTMKYLVTLHDGKTSFKGQRDGQEVDLPVDTD 365

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN GNRR+R VGE+++ Q R GL RMER  +ER+++ D +++ PQ L+N +PV + + 
Sbjct: 366 DIDNFGNRRIRQVGELIQTQLRTGLSRMERVARERMTTQDPEAITPQSLLNIRPVAATIK 425

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 426 EFFGTSQLSQFLDQNNPLASVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 485

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+  L++FAR+N +GFIETPYRKV + +VTNDVVY++A +E    IAQAN  L
Sbjct: 486 PEGPNIGLIGCLSTFARINPFGFIETPYRKVVEDQVTNDVVYMTADQEHGHVIAQANQEL 545

Query: 635 DEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D +G F  +    R    E   VP   +D++D SP+Q+VSI +SLIPFLE+D+ +R LMG
Sbjct: 546 DAEGHFLTKSALVRDDEAEAEDVPVADVDYMDVSPRQMVSIGSSLIPFLEHDEGHRALMG 605

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  ++A++ G+V  V A  I   + +G  +
Sbjct: 606 ANMQRQAVPLIRSERPLVGTGGEWAAAVDSGDVVLAEKDGVVTYVSADLIRTMNDDGSSN 665

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ P+VK G+ V    ++ADGP+T+ G++ALG+N+LV
Sbjct: 666 S-------YKLTKFQRSNQMTCYNQVPVVKKGERVETGSVLADGPATEEGEMALGKNLLV 718

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEEFE+ AR+TKLG EEITRD+PNVS++ +
Sbjct: 719 AFMPWNGYNYEDAVIISQRLVRDDTLSSIHIEEFEIDARETKLGAEEITRDLPNVSDDAV 778

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII VGAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFG K+ +VRDTSLRVP 
Sbjct: 779 ANLDENGIIRVGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGAKSREVRDTSLRVPH 838

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  GTV+ ++   +   +
Sbjct: 839 GERGTVISIKSMTKEQAE 856



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/305 (31%), Positives = 145/305 (47%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E I +PDL+ VQ  S+D  +  +                     GLQ  F  
Sbjct: 29  RINFGSIREPISVPDLLGVQTNSFDWLIGNDRWAQRVAEDEKNGAYTVDHTSGLQEVFDE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+  +  V +C  +D TY+ PL +      +D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEESRHTVQECRDKDQTYSAPLYVNAEFTNYD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMTK GTF+I G +R++VSQL RSPG++F     R   S K +Y 
Sbjct: 140 TGEIKSQTVFMGDFPLMTKHGTFIIGGTERVIVSQLVRSPGVYFGRTSDRT--SDKDVYD 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W+++E D +D++ VRIDR+RK     FL A+GM  EEI + F  YP ++ +
Sbjct: 198 AKIIPSRGAWLELEIDKRDVLGVRIDRKRKQSAIVFLQAIGMSREEIANEFKDYPLVMEA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +            + G  ++ES    T    L +  + K  + LG
Sbjct: 258 LNKEPEISQDQALIELYRRIRPGDTATPEAGRNLLESFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 LDTDY 322


>gi|209395035|gb|ACI45322.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 198/488 (40%), Positives = 315/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++ K +Y  FL  + AP +R  EGLQAAF++ FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMLKDAYTAFLQADKAPRKRTREGLQAAFEAAFPIVSHNGFVEMKFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVKEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP  G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYCGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+   + L++ G   + +  D L G  VA ++V+ ++GEI  +
Sbjct: 240 VTD-KSGKLIVAKDKRVTARHTRELEQSGTTHVSVPEDFLIGRVVARNVVDADSGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D + E  L+++  + ++++  +Y + ++  AYI +TL TD+  D   A + IYR+MRP
Sbjct: 299 VNDGLTEALLKKLRSASVQELQCIYTNELDQGAYISHTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++  +       +  EDI+A++KIL
Sbjct: 359 GESPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGREESTGSMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|54026619|ref|YP_120861.1| DNA-directed RNA polymerase subunit beta [Nocardia farcinica IFM
            10152]
 gi|81373434|sp|Q5YQP4|RPOB1_NOCFA RecName: Full=DNA-directed RNA polymerase subunit beta 1; Short=RNAP
            subunit beta 1; AltName: Full=RNA polymerase subunit beta
            1; AltName: Full=Transcriptase subunit beta 1
 gi|54018127|dbj|BAD59497.1| RNA polymerase beta subunit [Nocardia farcinica IFM 10152]
          Length = 1162

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 190/520 (36%), Positives = 271/520 (52%), Gaps = 55/520 (10%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 651  DGTRKSYRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVA 709

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE- 974
            I   +  +  D  +     V   V+       H  + + R   +  E+I     +  DE 
Sbjct: 710  IMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEV 767

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
               LD     R+   +   + + G    K  T L+ +        +  +    ++  +  
Sbjct: 768  LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAREVR 820

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              SLKV +  S  ++      ++   +  DD+PPGV  +V+V+VA KR IQ GDK+AGRH
Sbjct: 821  DTSLKVPHGESGKVI----GIRVFSREDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRH 876

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQI ETHLGW     G K++ 
Sbjct: 877  GNKGVIGKILPTEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIGKA-GWKVEG 935

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                 K                                +     +  +   ++TPVFDGA
Sbjct: 936  NPEWAK-------------------------------DLPEEMWEAPADSNIATPVFDGA 964

Query: 1215 DEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             EE +  +L     +  G        +++L+DG +GEPF  PV VGY+Y+LKL+H+V DK
Sbjct: 965  REEELTGLLGSTLPNRDGERMVDDNGKAVLFDGRSGEPFPYPVAVGYMYILKLHHLVDDK 1024

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR 
Sbjct: 1025 IHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRV 1084

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +VYE+IV G++  E G PESF VL+KE+QAL L++++ ++
Sbjct: 1085 KVYEAIVKGDNIPEPGVPESFKVLLKELQALCLNVEVLSA 1124



 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 326/697 (46%), Positives = 460/697 (65%), Gaps = 27/697 (3%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+             + S  +    G ++  D+   +T  + I+    
Sbjct: 161 ERVVVSQLVRSPGVYFDHAIDKGSEKDVHSARVIPSRGAWLEFDVDKRDTLGVRIDRKRR 220

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                L +        I     +       I  +L  D      DALL+I+R +RPG+  
Sbjct: 221 QPVTVLLKALGWSAERIA----ERFGFAPLIMASLAKDNVAGTDDALLEIHRKLRPGEPP 276

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A+++   LFF   +YDL+ VGR K++ +L L  P   R + ++DI A I+ LV L 
Sbjct: 277 TKESAQNLLANLFFTEKRYDLARVGRYKIDKKLGLRAPGAPRVLTEDDIAATIEYLVRLH 336

Query: 448 NGKG------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            G+              +DDID+ GNRRVR+VGE+++NQ R+GL RMER ++ER+++ D+
Sbjct: 337 AGERTMIAPGGVEVPVEVDDIDHFGNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDV 396

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           +++ PQ L+N +PVV+A+ EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RAG
Sbjct: 397 EAITPQSLMNIRPVVAAMKEFFGTSQLSQFMDQRNPLASLTNKRRLSALGPGGLSRERAG 456

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
           +E+RDVH +HYGR+CP ET EG NIGL+  L+ +ARVN +GF+ETPYR+V DG+VT++V 
Sbjct: 457 LEVRDVHYSHYGRMCPIETPEGPNIGLMGYLSVYARVNPFGFVETPYRRVVDGRVTDEVD 516

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSI 674
           YL+A EE+   +AQAN  LD +G F    +  R    E  LV    +D++D SP+Q+VS+
Sbjct: 517 YLTADEEDRHVVAQANEPLDAEGRFLAARIPVRRKNSEVELVDSAAVDYMDVSPRQMVSV 576

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +V ++AG+
Sbjct: 577 ATAMIPFLEHDDANRALMGANMQRQAVPLIRSEAPIVGTGMELRAAVDAGDVVVNEKAGV 636

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           VE+V A  + + + +G           YR+ KF RSNQ TC NQRP+V  G  V    ++
Sbjct: 637 VEEVSADYVTVMADDGTRKS-------YRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVL 689

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDT
Sbjct: 690 ADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDT 749

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 750 KLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLR 809

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 810 AIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 846



 Score =  293 bits (750), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 88/294 (29%), Positives = 139/294 (47%), Gaps = 24/294 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA---PDERPNE---GLQAAFKSVFPITA 67
           R  F +  E + +P L+++Q  S+   +           R  E   GL      + PI  
Sbjct: 28  RLSFARIREPLAVPGLLDIQTESFGWLIGAPDWCARAAARGTEPVAGLAEVLAEISPIED 87

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   L      F+  K  V++C  +DLTYA P  +T   +           +  +IK 
Sbjct: 88  FAGTMSLTLSDPRFEEVKASVEECKDKDLTYAAPWFVTAEFV---------NNNTGEIKS 138

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q+++MGD P+MT  GTFV+ G +R+VVSQL RSPG++FDH   +   S K +++ R+IP 
Sbjct: 139 QTVFMGDFPMMTAHGTFVVNGTERVVVSQLVRSPGVYFDHAIDK--GSEKDVHSARVIPS 196

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
           +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I   F    +          
Sbjct: 197 RGAWLEFDVDKRDTLGVRIDRKRRQPVTVLLKALGWSAERIAERFGFAPLIMASLAKDNV 256

Query: 248 PLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             +   L+   +       +  GE    ES + L + L  + K   +  +G   
Sbjct: 257 AGTDDALLEIHR------KLRPGEPPTKESAQNLLANLFFTEKRYDLARVGRYK 304


>gi|34391567|gb|AAN65361.1| RpoB [Mycobacterium mucogenicum]
          Length = 1184

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 184/508 (36%), Positives = 259/508 (50%), Gaps = 55/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 698  IVDSGQRVEAGQVIADGPCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEQDVL 756

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 757  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 814

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++  R    +  
Sbjct: 815  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVR----VFS 863

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 864  REDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDGTPVD 923

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I+                          
Sbjct: 924  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN------------------ 964

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                         +            V+TPVFDGA E  +  +L     +          
Sbjct: 965  -------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVMVDAD 1011

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1012 GKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1071

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1072 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1131

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+L L++++ +S        +   +
Sbjct: 1132 KELQSLCLNVEVLSSDGAAIEMRDSDDE 1159



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 327/679 (48%), Positives = 453/679 (66%), Gaps = 26/679 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I   
Sbjct: 199 DKATEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI--R 256

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 257 ERFGFSEIMMGTLEKDPTAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 316

Query: 410 TVGRVKMNMRLNLDTPD----DVRHIRKEDIIAIIKILVDLRNG------------KGTI 453
            VGR K+N +L L   +        + +EDI+A I+ LV L +G               +
Sbjct: 317 RVGRYKVNKKLGLHDGNPAQVTATTLTEEDIVATIEYLVRLHDGDTKMTAPGGVEVPVEV 376

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+
Sbjct: 377 DDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAI 436

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP E
Sbjct: 437 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHSSHYGRMCPIE 496

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ + YL+A EE+   +AQANS 
Sbjct: 497 TPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGIVTDQIDYLTADEEDRHVVAQANSP 556

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           LD +G FTEE +  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LM
Sbjct: 557 LDANGHFTEEKILVRRKGGEVEFVSANDVDYMDVSPRQMVSVATAMIPFLEHDDANRALM 616

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPL+++EAP VGTGME   A  +G  +VA ++G++E+V A  + + + +G  
Sbjct: 617 GANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKSGVIEEVSADYVTVMADDGSR 676

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+L
Sbjct: 677 -------HTYRMRKFNRSNHGTCANQRPIVDSGQRVEAGQVIADGPCTENGEMALGKNLL 729

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E 
Sbjct: 730 VAVMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEV 789

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 790 LADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVP 849

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G SG V+ VR+F+R   D
Sbjct: 850 HGESGKVIGVRVFSREDDD 868



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/298 (30%), Positives = 150/298 (50%), Gaps = 22/298 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L+EVQ  S++  +  +    +  + G       L+     + PI 
Sbjct: 45  RVSFAKLREPLEVPGLLEVQTDSFEWLIGSDRWRSKAVDRGDINPVGGLEEVLAELSPIE 104

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   L F    FD  K  VD+C  +D TYA PL +T   I           +  +IK
Sbjct: 105 DFAGTLSLSFSDPRFDEVKAPVDECKEKDQTYAAPLFVTAEFI---------NNTTGEIK 155

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 156 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDESIDK--ATEKTLHSVKVIP 213

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   D 
Sbjct: 214 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIRERFGFSEIMMGTLEKDP 273

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
              P  A   +            ++ + ++E+   K+    L +  + K  K LG+  
Sbjct: 274 TAGPDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHD 331


>gi|148821872|ref|YP_001286626.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis F11]
 gi|148720399|gb|ABR05024.1| DNA-directed RNA polymerase beta subunit rpoB [Mycobacterium
           tuberculosis F11]
          Length = 1178

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 454/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 209 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 264

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 265 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 324

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 325 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 384

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 385 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 444

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 445 PLSGLTHKRRLLALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 504

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 505 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 564

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 565 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 624

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 625 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 677

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 678 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 737

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 738 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 797

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 798 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 857

Query: 950 ID 951
            D
Sbjct: 858 ED 859



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 748  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 807

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 808  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 850

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 851  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 910

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 911  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 960

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 961  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 1001

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1002 VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1061

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1062 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1121

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1122 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1158



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 318 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 350


>gi|37521852|ref|NP_925229.1| DNA-directed RNA polymerase subunit beta [Gloeobacter violaceus PCC
           7421]
 gi|41017641|sp|Q7NIA0|RPOB_GLOVI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|35212851|dbj|BAC90224.1| RNA polymerase beta subunit [Gloeobacter violaceus PCC 7421]
          Length = 1112

 Score =  516 bits (1329), Expect = e-143,   Method: Composition-based stats.
 Identities = 324/632 (51%), Positives = 438/632 (69%), Gaps = 9/632 (1%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +++         ++  +    + D  IL  D+  +  Y + T+  + N   ++ALL++YR
Sbjct: 181 VWVRIDKTRKLSAVVLLKALGLSDNEIL--DAFRHPEYFQKTIEKEGNYSEEEALLELYR 238

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  T S  + +    FFD  +YDL  VGR K+N +L L  P+  R +  +DI+A 
Sbjct: 239 KLRPGEPPTVSGGQQLLETRFFDPKRYDLGRVGRYKLNKKLRLSVPETTRILTPQDILAS 298

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I  L++L    G+ DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + +++ 
Sbjct: 299 IDYLINLEFDIGSPDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEAETLT 358

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  L+N KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +R
Sbjct: 359 PASLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVR 418

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           D+HP+HYGRICP ET EG N GL+ SL + ARVN+YGFIETPY+ V DG+++ ++ YL+A
Sbjct: 419 DIHPSHYGRICPIETPEGPNAGLIGSLATHARVNSYGFIETPYKVVKDGRLSGEIKYLTA 478

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            EE+   +A  + ++DE G+     V  R   E  L    ++D++  SP Q+VS+A SLI
Sbjct: 479 DEEDEFRVAAGDVAVDEGGNILANPVTIRYRQEFGLASPAEVDYVAVSPIQIVSVATSLI 538

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NMQRQAVPLL+ E P VGTG+E   A+ SG  IV+   G +  V 
Sbjct: 539 PFLEHDDANRALMGANMQRQAVPLLRPERPLVGTGLEGQAARDSGMVIVSDIDGAITYVS 598

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
             +I +R   G           Y L K+QRSNQ+TC++QRP+V VGD+VR   I+ADG +
Sbjct: 599 GEQIRVRGENGQEFA-------YPLQKYQRSNQDTCLSQRPIVNVGDQVRNGQILADGSA 651

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T+ G+LALG+N+LVAFMPW GYN+ED++LISER+V +DVFTSIH+E+FE+ AR TKLGPE
Sbjct: 652 TEGGELALGQNILVAFMPWEGYNYEDAILISERLVYDDVFTSIHVEKFEIEARQTKLGPE 711

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITR+IPNV E+ L+N+DE GI+ +GA +  GDILVGK+TPKGES   PEEKLLRAIFGE
Sbjct: 712 EITREIPNVGEDSLRNLDERGIVRIGAWMEAGDILVGKVTPKGESDQPPEEKLLRAIFGE 771

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 772 KARDVRDNSLRVPNGEKGRVVDVRVFTREQGD 803



 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 195/586 (33%), Positives = 270/586 (46%), Gaps = 63/586 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E        MV   D+  +I     E +    + G 
Sbjct: 551  MGANMQRQAVPLLRPERPLVGTGLEGQAARDSGMVIVSDIDGAITYVSGEQIRVRGENGQ 610

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                + +  I+ VG +V  G IL      +G   +   + +L A   
Sbjct: 611  EFAYPLQKYQRSNQDTCLSQRPIVNVGDQVRNGQILADGSATEG-GELALGQNILVAFMP 669

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   V       +  I+  +  +  E    +I  +  D     D
Sbjct: 670  WEGYNYEDAILISERLVYDDVFTSIHVEKFEIEARQTKLGPEEITREIPNVGEDSLRNLD 729

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+    +    +IL G+    G         L   +  E  R               
Sbjct: 730  ERGIVRIGAWMEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD-------------- 775

Query: 1034 NVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                ++       +  + R  + ++   + GD++PPG   VV+V++A KR +Q GDK+AG
Sbjct: 776  ----VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYLAQKRKVQVGDKVAG 831

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+S+ILP EDMP+L DG PVDIVLNPLGVPSRMNVGQ+FET LGWA   L  + 
Sbjct: 832  RHGNKGIISKILPKEDMPYLPDGRPVDIVLNPLGVPSRMNVGQVFETLLGWAGACLNVRF 891

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K    D     + S      EK++     T     Y D            G  +      
Sbjct: 892  KVTPFDEMYIKEASRYLVH-EKLMEAREVTGDPWVYSDT-----------GKHI------ 933

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G+  +YDG TGE FDRPVTVG IYM+KL H+V DK++ARST
Sbjct: 934  -------------------GKIQVYDGRTGEAFDRPVTVGQIYMMKLVHLVDDKIHARST 974

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +I
Sbjct: 975  GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMTGRNEALNAI 1034

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      G PESF VLV+E+Q+LGL + +    T++     ++ 
Sbjct: 1035 VKGKAIPRPGIPESFKVLVRELQSLGLDVSVHKIETQHDGSSRDVE 1080



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 98/453 (21%), Positives = 193/453 (42%), Gaps = 35/453 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV-SYEFDPP 84
           +PDL+E+Q+ S+  FL   +  +            S  PIT ++G   L F+  Y+   P
Sbjct: 26  LPDLVEIQRESFRWFLEEGLIEELL----------SFSPITDYTGKMELHFLQDYKLKEP 75

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD TY+V + ++ RL+          K   +IKEQ +++G+LPLMT  GTF
Sbjct: 76  KYSVEEAKRRDSTYSVQMYVSTRLV---------NKETGEIKEQQVFIGELPLMTDRGTF 126

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           +I G +R++V+Q+ RSPG+++  +      +G+  +   +IP++G W+  E D+ D++ V
Sbjct: 127 IINGAERVIVNQIVRSPGVYYKQELD---TNGRKTFNASLIPNRGAWLKFETDANDLVWV 183

Query: 205 RIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVSS 262
           RID+ RK+     L ALG+   EIL  F     +  +   +       A   +       
Sbjct: 184 RIDKTRKLSAVVLLKALGLSDNEILDAFRHPEYFQKTIEKEGNYSEEEALLELYRKLRPG 243

Query: 263 SLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
               +  G+Q++E+         L +  + K  K L ++      +   +DI+      I
Sbjct: 244 EPPTVSGGQQLLETRFFDPKRYDLGRVGRYKLNKKLRLSVPETTRILTPQDILASIDYLI 303

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            +E  D+     ++ + +  +R +  L  + V         ++ ++    +   L    +
Sbjct: 304 NLE-FDIGSPDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEAETLTPASL 362

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           + P      +  +  F            + +  +    RL+   P     + +E     +
Sbjct: 363 VNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFAV 417

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           + +     G+  I  I+         +G +  +
Sbjct: 418 RDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 448


>gi|309389940|gb|ADO77820.1| DNA-directed RNA polymerase subunit beta [Halanaerobium praevalens
           DSM 2228]
          Length = 1084

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/605 (54%), Positives = 450/605 (74%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D   ++  + +TL  D    +++AL+++Y+ +RPG+  T   A ++ + LFFD  +YD+
Sbjct: 201 TDEFGDSEVLHDTLERDNTDSKEEALIELYKRLRPGEPPTVESATNLLDSLFFDHKRYDM 260

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL--RNGKGTIDDIDNLGNRRVRS 466
           + VGR K+N +L +D   D +++  +DI A +K ++ L   + +  IDDID+LGNRR+++
Sbjct: 261 AAVGRYKLNKKLEVDVDKDRKYLHIDDIAATVKYMIKLIYNDPEAYIDDIDHLGNRRLKT 320

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+L+NQ+R+GL RMER ++ER++  DID V PQ LIN +PVV+++ EFF SSQLSQ  
Sbjct: 321 VGELLQNQFRIGLSRMERVVRERMTIQDIDVVTPQALINTRPVVASIQEFFGSSQLSQFM 380

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N +S +TH RRLSALG GG++R RAG ++RDVH +HYGRICP ET EG NIGL+ ++
Sbjct: 381 DQTNPMSELTHKRRLSALGPGGLSRERAGFDVRDVHHSHYGRICPIETPEGPNIGLIGTM 440

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A+ N +GFI TPYR+V D +VT+D+ YL+A EE+   IAQAN+ +DEDG+FT E V 
Sbjct: 441 GTYAKTNEFGFIMTPYRRVVDCRVTSDIDYLTADEEDKHIIAQANAEIDEDGNFTSEFVI 500

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+ + V  E +D++D S KQ+V ++A++IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 501 ARKRGDILEVHPEDLDYMDVSTKQMVGVSAAMIPFLENDDANRALMGANMQRQAVPLMIT 560

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +AP V TGME   AK SGA IVA++ G +  V + +I++++ EG +D        Y LMK
Sbjct: 561 DAPMVATGMEYKAAKDSGAVIVAEKGGEIVSVSSNKIMVKNDEGLIDS-------YHLMK 613

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           ++RSNQ +C+NQ+P+V  GD + + DIIADGPST+ G++ALGRN L+AFMPW GYN+ED+
Sbjct: 614 YKRSNQGSCMNQKPIVAKGDTIEKGDIIADGPSTEKGEMALGRNSLIAFMPWEGYNYEDA 673

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISE +V ED FT+IHIEE E  ARDTKLGPEEITRDIPNV E  LKN+DE GII VGA
Sbjct: 674 ILISENLVKEDAFTTIHIEEHEAEARDTKLGPEEITRDIPNVGESSLKNLDERGIIRVGA 733

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ ++ EE+LLRAIFGEKA +VRDTSL+VP G  G VVDV++F+
Sbjct: 734 EVEEGDILVGKVTPKGETELSAEERLLRAIFGEKAREVRDTSLKVPHGEVGIVVDVKVFS 793

Query: 947 RHGID 951
           R   D
Sbjct: 794 REQGD 798



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 180/533 (33%), Positives = 251/533 (47%), Gaps = 79/533 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +    +          +++  I+  G  +  GDI+    + + +  M      
Sbjct: 600  KNDEGLIDSYHLMKYKRSNQGSCMNQKPIVAKGDTIEKGDIIADGPSTE-KGEMALGRNS 658

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIEL 966
            L A    +  +  D  L   + V            H  +  +  +  E          E 
Sbjct: 659  LIAFMPWEGYNYEDAILISENLVKEDAFTTIHIEEHEAEARDTKLGPEEITRDIPNVGES 718

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              ++  DE+ I+         +IL G+    G         L   +  E  R        
Sbjct: 719  SLKNL-DERGIIRVGAEVEEGDILVGKVTPKGETELSAEERLLRAIFGEKAR-------- 769

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E      +     +      K+   + GDD+ PGV R+V+V+VA KR I  
Sbjct: 770  ---------EVRDTSLKVPHGEVGIVVDVKVFSREQGDDLKPGVNRLVRVYVATKRKISV 820

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK+AGRHGNKG++SRILP EDMPFL +G PV++VLNPLGVPSRMN+GQ+ ETHLG A  
Sbjct: 821  GDKLAGRHGNKGVISRILPEEDMPFLPNGEPVEVVLNPLGVPSRMNIGQVLETHLGMAAR 880

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG   ++ + +     ++                         + +L  A   + G   
Sbjct: 881  ALGIYTETPVFNGATEIEV-------------------------EDILEEAGLSRDG--- 912

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                      +++LYDG TGE F+  VTVG +Y+LKL+H+V DK
Sbjct: 913  --------------------------KTVLYDGRTGERFEERVTVGVMYILKLHHLVDDK 946

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLTIKSDDVVGR 
Sbjct: 947  LHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTIKSDDVVGRV 1006

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            + YE+IV G +  + G PESF VL+KEMQ+LGL   +  S  +     E   +
Sbjct: 1007 KAYEAIVKGENVPDPGIPESFKVLIKEMQSLGLDARIFTSDEEELQVAENEDE 1059



 Score =  348 bits (892), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 103/339 (30%), Positives = 159/339 (46%), Gaps = 34/339 (10%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F K  + +D+PDLI  Q  SY  FL           EGL   F  + PI  FS  
Sbjct: 5   RKRYSFSKIDDAMDLPDLIYTQLNSYQWFL----------EEGLHEVFNEISPIEDFSEN 54

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEFV Y  + P++ V +C  RD TY+  L++ +RLI          K   ++KEQ ++
Sbjct: 55  LVLEFVDYYLEDPEYTVQECRDRDATYSASLQVKVRLI---------NKETGEVKEQEVF 105

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+  TF+I G +R+VV+QL RS G++F  ++ +    G+ L    IIP++G W
Sbjct: 106 MGDFPLMTEKATFIINGAERVVVNQLVRSSGVYFSDERTKD---GRRLITGSIIPNRGAW 162

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E+D K I+ VR+DR RK+P T  L ALG  ++ EI   F    V     +       
Sbjct: 163 IEFEYDKKRIVSVRVDRTRKLPSTVLLRALGFGTDAEITDEFGDSEVLHDTLERDNTDSK 222

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
              L+           +  GE   +ES   L   L    K   +  +G          + 
Sbjct: 223 EEALI------ELYKRLRPGEPPTVESATNLLDSLFFDHKRYDMAAVGRYK---LNKKLE 273

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            D V+ +   ++I+      +  ++ I++     I  + 
Sbjct: 274 VD-VDKDRKYLHIDDIAATVKYMIKLIYNDPEAYIDDID 311


>gi|188532108|gb|ACD63067.1| RNA polymerase beta-subunit [Actinosynnema pretiosum subsp.
           auranticum]
          Length = 1160

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 320/601 (53%), Positives = 439/601 (73%), Gaps = 19/601 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 250 EKDHTAGTDEALLDIYRKLRPGEPPTKESAQALLETLFFKEKRYDLAKVGRYKVNKKLGL 309

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKG-----------TIDDIDNLGNRRVRSVGEML 471
           DTP     + ++DI+  I+ LV L  G+             +DDID+ GNRR+R+VGE++
Sbjct: 310 DTPISTGVLTEDDIVTTIEYLVRLHAGETSMQPGETEVPVEVDDIDHFGNRRLRTVGELI 369

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N 
Sbjct: 370 QNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNP 429

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+ R
Sbjct: 430 LAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYGR 489

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           VN +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ +D +G+F E  V  R  G
Sbjct: 490 VNPFGFIETPYRKVVDGRVTDQIDYLTADEEDRYVKAQANARIDGEGNFLEGKVLVRKKG 549

Query: 652 -EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E  ++    +D++D SP+Q+VS A ++IPFLE+DD+NR LMG NMQRQAVPLL++E+P 
Sbjct: 550 GEVEMIDPRDVDYMDVSPRQMVSAATAMIPFLEHDDANRALMGANMQRQAVPLLRSESPL 609

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +VAK+ G+VE++ A  + + + +G           Y + KF+RS
Sbjct: 610 VGTGMELRAAVDAGDVVVAKKTGVVEEISADYVTVMADDGSRQ-------TYGMHKFRRS 662

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC+NQ+P+V  GD V+   ++ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S
Sbjct: 663 NQGTCINQKPIVNEGDRVQVGQVLADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILS 722

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVSEE L ++DE GII +GAEV P
Sbjct: 723 QRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADLDERGIIRIGAEVQP 782

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ +R+F+R   
Sbjct: 783 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEYGKVIGIRVFSREDD 842

Query: 951 D 951
           D
Sbjct: 843 D 843



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 191/545 (35%), Positives = 266/545 (48%), Gaps = 69/545 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +               I++  I+  G  V  G +L      +    M   + LL A
Sbjct: 648  DGSRQTYGMHKFRRSNQGTCINQKPIVNEGDRVQVGQVLADGPCTEN-GEMALGKNLLVA 706

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          E +  
Sbjct: 707  IMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLA 766

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      +  +IL G+    G         L   +  E  R           
Sbjct: 767  DL-DERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 814

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++   +  D++PPGV  +V+V+VA KR IQ GDK
Sbjct: 815  ------EVRDTSLKVPHGEYGKVIGIRVFSREDDDELPPGVNELVRVYVAQKRKIQDGDK 868

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL+DGTPVDIVLN  GVP RMN+GQ+ ETHLGW     G
Sbjct: 869  LAGRHGNKGVIGKILPVEDMPFLEDGTPVDIVLNTHGVPRRMNIGQVLETHLGWIAKQ-G 927

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I    +  K                                +     + + G   +TP
Sbjct: 928  WSINGDPDWAKN-------------------------------LPADLYEVEPGTKTATP 956

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA EE I  +L     +          G++ L+DG +GEP+  PV+VGY+Y+LKL H
Sbjct: 957  VFDGAREEEITGLLGSTVPNRDGERMVKENGKAQLFDGRSGEPYPFPVSVGYMYILKLLH 1016

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD
Sbjct: 1017 LVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDD 1076

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            V+GR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S         E+ D +
Sbjct: 1077 VLGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAI----EMRDGD 1132

Query: 1382 KCELK 1386
              +L+
Sbjct: 1133 DEDLE 1137



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 88/295 (29%), Positives = 140/295 (47%), Gaps = 25/295 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +  P+L+++Q  S++           R +EG       L+     + PI 
Sbjct: 25  RVSFAKIHEPLQTPNLLDLQIQSFEWLTGDEAWFQRRVDEGDEAPTGGLEEVLNEISPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K   ++C  +D+TYA PL +T               +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFDEVKASTEECKDKDMTYAAPLFVTAEFT---------NHTTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG+++D    +   + K +++ +IIP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYYDTAIDKT--TDKDVFSVKIIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F          +   
Sbjct: 194 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSTEQIRERFSFSETLLTTLEKDH 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +   L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQALLETLFFKEKRYDLAKVGRYK 302


>gi|271962625|ref|YP_003336821.1| DNA-directed RNA polymerase [Streptosporangium roseum DSM 43021]
 gi|270505800|gb|ACZ84078.1| DNA-directed RNA polymerase [Streptosporangium roseum DSM 43021]
          Length = 1155

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 190/536 (35%), Positives = 275/536 (51%), Gaps = 53/536 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     R             ++  I+  G  +    ++        +  M   + L
Sbjct: 641  MNDDGTRTTYRVAKFKRSNQGTCFNQKPIVKEGDRIEVNQVVADGPCT-DDGEMALGKNL 699

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  +     V   V+       H  + + R   +  E+I     +  
Sbjct: 700  LVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLGPEEITRDIPNVS 757

Query: 973  DE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            +E    LD     R+   +   + + G    K  T L+ +        +  +    ++  
Sbjct: 758  EEVLADLDERGIIRIGAEVVPGDILVGKVTPKGETELTPE-------ERLLRAIFGEKAR 810

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +    SLKV +     ++  R    +   + GD++PPGV  +V+V+VA KR I  GDK+A
Sbjct: 811  EVRDTSLKVPHGEQGKVIGVR----VFSREEGDELPPGVNELVRVYVAQKRKITDGDKLA 866

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++S+ILP EDMPFL+DGTPVDI+LNPLGVP RMNVGQ+ ETHLGW        
Sbjct: 867  GRHGNKGVISKILPVEDMPFLEDGTPVDIILNPLGVPGRMNVGQVLETHLGWIAA----- 921

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                        DIS +     + +      E     +                ++TPVF
Sbjct: 922  ---------RGWDISGIEEAWAERLRDKGFAEVDPRTN----------------MATPVF 956

Query: 1212 DGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            DGA+EE I  +L    ++          G++ L+DG +GEPF  P++VGYIY+LKL H+V
Sbjct: 957  DGANEEEIVGLLDNTLVNRDGGRMVGANGKAQLFDGRSGEPFPHPISVGYIYILKLLHLV 1016

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV+
Sbjct: 1017 DDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVL 1076

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1077 GRVKVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1132



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 338/691 (48%), Positives = 472/691 (68%), Gaps = 25/691 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K +    +      G ++  +I   ++  + I+         
Sbjct: 162 LVRSPGVYFDRSVDKTSDKDLYGCKVIPSR--GAWLEFEIDKRDSVGVRIDRKRKQAVTV 219

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +      +  IL  +       +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 220 L--LKALGWTNDQIL--ERFGQYESMRATLEKDHTAGQDDALLDIYRKLRPGEPPTKESA 275

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +++   L+F+  +YDL+ VGR K+N +L +D+      + +EDI+A I+ +V L  G+ +
Sbjct: 276 QTLLENLYFNHKRYDLAKVGRYKINKKLGVDSEITQGTLTEEDIVATIEYIVKLHAGETS 335

Query: 453 I-----------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
           +           DDID+ GNRR+R+VGE+++NQ RLGL RMER ++ER+++ D++++ PQ
Sbjct: 336 MAGANGEIVVETDDIDHFGNRRLRTVGELIQNQVRLGLARMERVVRERMTTQDVEAITPQ 395

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDV
Sbjct: 396 TLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRDV 455

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           HP+HYGR+CP ET EG NIGL+ SL SF RVN++GF+ETPYRKV DG+VT+ V YL+A E
Sbjct: 456 HPSHYGRMCPIETPEGPNIGLIGSLASFGRVNSFGFVETPYRKVLDGRVTDTVEYLTADE 515

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+   IAQAN+ +  DG+F E+ V  R   GE   +   ++D++D S +Q+VS+A ++IP
Sbjct: 516 EDRYVIAQANTPIGSDGTFLEDRVLVRRKGGEFESLRANEVDYMDVSARQMVSVATAMIP 575

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE+DD+NR LMG NMQRQ+VPLLK+EAP VGTGME   A  +G  I A +AG+VE+V A
Sbjct: 576 FLEHDDANRALMGSNMQRQSVPLLKSEAPLVGTGMEYRAATDAGDVITADKAGVVEEVSA 635

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             + + + +G           YR+ KF+RSNQ TC NQ+P+VK GD +  N ++ADGP T
Sbjct: 636 DYVTVMNDDGTR-------TTYRVAKFKRSNQGTCFNQKPIVKEGDRIEVNQVVADGPCT 688

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           D G++ALG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEE
Sbjct: 689 DDGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEE 748

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITRDIPNVSEE L ++DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEK
Sbjct: 749 ITRDIPNVSEEVLADLDERGIIRIGAEVVPGDILVGKVTPKGETELTPEERLLRAIFGEK 808

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           A +VRDTSL+VP G  G V+ VR+F+R   D
Sbjct: 809 AREVRDTSLKVPHGEQGKVIGVRVFSREEGD 839



 Score =  343 bits (879), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 120/485 (24%), Positives = 205/485 (42%), Gaps = 44/485 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE--------RPN----EGLQAAFKS 61
           R  F +  E +++PDL+ +Q  S+D  L                R +     GL+  F+ 
Sbjct: 16  RVSFARIQEPLEVPDLLALQTESFDWLLGNEKWKGRVEAARQAGRKDVPAQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+ VD+C  +D+TY+ P+ +T   I           +
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSVDECKDKDMTYSAPMFVTAEFI---------NNT 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++FD    +   S K LY 
Sbjct: 127 TGEIKSQTVFMGDFPLMTGKGTFIINGTERVVVSQLVRSPGVYFDRSVDKT--SDKDLYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+RK  VT  L ALG  +++IL  F  Y  +  +
Sbjct: 185 CKVIPSRGAWLEFEIDKRDSVGVRIDRKRKQAVTVLLKALGWTNDQILERFGQYESMRAT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 245 LEKDHTAGQDDALLDIYRKLRPGEPPTKESAQTLLENLYFNHKRYDLAKVGRYKINKKLG 304

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE----------KSLEEIFHSEIRDIPIL 347
           + S+   G    EDIV      + + AG+                ++   +  +R +  L
Sbjct: 305 VDSEITQGTLTEEDIVATIEYIVKLHAGETSMAGANGEIVVETDDIDHFGNRRLRTVGEL 364

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + V         +V ++   +   +  I            +  +  F           
Sbjct: 365 IQNQVRLGLARMERVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQ 422

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            + +  +    RL+   P     + +E     ++ +     G+  +  I+      +  +
Sbjct: 423 TNPLAGLTHKRRLSALGPGG---LSRERAGFEVRDVHPSHYGR--MCPIETPEGPNIGLI 477

Query: 468 GEMLK 472
           G +  
Sbjct: 478 GSLAS 482


>gi|254549627|ref|ZP_05140074.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis '98-R604 INH-RIF-EM']
          Length = 1172

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 454/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ     N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMVQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|326905112|gb|EGE52045.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis W-148]
          Length = 1172

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 454/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLLALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|172038401|ref|YP_001804902.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. ATCC
           51142]
 gi|171699855|gb|ACB52836.1| RNA polymerase beta subunit [Cyanothece sp. ATCC 51142]
          Length = 1104

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 338/687 (49%), Positives = 463/687 (67%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 115 INGAERVIVNQIVRSPGVYYKAETDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 174

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  DS+ +  + + TL  + N   +DALL++YR +RPG+ 
Sbjct: 175 TRKLSAQVLLKAIGLSDNEIL--DSLRHPEFYQRTLDKEGNPSEEDALLELYRKLRPGEP 232

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFDS +YDL  VGR K+N +L L+ PD +R +R EDI++ I  L++L
Sbjct: 233 PTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLNAPDTIRVLRPEDILSAIDYLINL 292

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               GT+DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + DS+ P  L+N 
Sbjct: 293 EFDVGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDSLTPASLVNP 352

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 353 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 412

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY +V DG+V  D+  VYL+A EE++
Sbjct: 413 GRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVQDGRVRRDLDPVYLTADEEDD 472

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + S DE+G+     V  R   E  +   +++D++  SP Q++S+A S+IPFLE+
Sbjct: 473 LRVAPGDISTDEEGNILGNAVPTRYRQEFFITSPDQVDYVAVSPVQIISVATSMIPFLEH 532

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV   DA  I 
Sbjct: 533 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTEGIVTYADANEIR 592

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R    +          Y L K+QRSNQ+TC+NQRPLV VG++V    ++ADG +T+ G+
Sbjct: 593 VRVTGPEGHEKVGQEIQYILQKYQRSNQDTCLNQRPLVFVGEDVVPGQVLADGSATEGGE 652

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIH+E+FE+ AR TKLGPEEITR+
Sbjct: 653 LALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKFEIEARQTKLGPEEITRE 712

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 713 IPNVGEDSLRNLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 772

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 773 RDNSLRVPNGEKGRVVDVRVFTREQGD 799



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 205/654 (31%), Positives = 280/654 (42%), Gaps = 77/654 (11%)

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN-----QRPLVKVGDEVRRNDIIADGP 798
             I + E       +    YR   F  S            Q   V            A+  
Sbjct: 479  DISTDEEGNILGNAVPTRYRQEFFITSPDQVDYVAVSPVQIISVATSMIPFLEHDDANRA 538

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR------ 852
                        +L    P  G   E        MV       I         R      
Sbjct: 539  LMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTEGIVTYADANEIRVRVTGP 598

Query: 853  --DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                K+G E                +++  ++ VG +V PG +L      +G   +   +
Sbjct: 599  EGHEKVGQEIQYILQKYQRSNQDTCLNQRPLVFVGEDVVPGQVLADGSATEG-GELALGQ 657

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLA 968
             +L A    +  +  D  L     V   V       +  I+  +  +  E    +I  + 
Sbjct: 658  NILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKFEIEARQTKLGPEEITREIPNVG 717

Query: 969  RD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             D     DEQ I+    +    +IL G+    G         L   +  E  R       
Sbjct: 718  EDSLRNLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------ 771

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                        ++       +  + R  + ++   + GD++PPG   VV+V+VA KR I
Sbjct: 772  ------------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKI 819

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKGI+SRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQ+FE  LGWA
Sbjct: 820  QVGDKMAGRHGNKGIISRILPIEDMPYLPDGRPIDIVLNPLGVPSRMNVGQVFECLLGWA 879

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG + K    D               ++ G  S  + +    + +  +  + W    
Sbjct: 880  GENLGVRFKITPFD---------------EMYGEESSRKTVHGLLEKAAKKPRKDWVYNT 924

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                    D  G+  +YDG TGE FDR VTVG  YMLKL H+V 
Sbjct: 925  ------------------------DHPGKIDVYDGRTGEKFDRAVTVGQAYMLKLVHLVD 960

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ G
Sbjct: 961  DKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQG 1020

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            R     +IV G      GTPESF VL++E+Q+LGL I +    T +     ++ 
Sbjct: 1021 RNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVETADDGTSRDVE 1074



 Score =  322 bits (824), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 109/493 (22%), Positives = 198/493 (40%), Gaps = 54/493 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q +S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 12  LPDLIEIQHSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGENYKLKE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD +Y+V + +  RL+          K   +IKEQ +++GDLPLMT  GT
Sbjct: 62  PKYDVDEAKRRDASYSVQMYVPTRLM---------NKETGEIKEQEVFIGDLPLMTDRGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 113 FIINGAERVIVNQIVRSPGVYYKAETDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL +      Y +  D    P     L+        
Sbjct: 170 VRIDKTRKLSAQVLLKAIGLSDNEILDSLRHPEFYQRTLDKEGNPSEEDALL------EL 223

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G           A D +     E  +
Sbjct: 224 YRKLRPGEPPTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLNAPDTIRVLRPEDIL 283

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         DV     ++ + +  +R +  L  + V         ++ ++    +   
Sbjct: 284 SAIDYLINLEFDVGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDS 343

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    R++   P     + +E
Sbjct: 344 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRE 398

Query: 435 DIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMER 484
                ++ +    +G+    +                 RV   G +    YR+   R+ R
Sbjct: 399 RAGFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVQDGRVRR 458

Query: 485 SIKERISSVDIDS 497
            +     + D + 
Sbjct: 459 DLDPVYLTADEED 471


>gi|256380610|ref|YP_003104270.1| DNA-directed RNA polymerase subunit beta [Actinosynnema mirum DSM
           43827]
 gi|255924913|gb|ACU40424.1| DNA-directed RNA polymerase, beta subunit [Actinosynnema mirum DSM
           43827]
          Length = 1160

 Score =  516 bits (1328), Expect = e-143,   Method: Composition-based stats.
 Identities = 320/601 (53%), Positives = 440/601 (73%), Gaps = 19/601 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 250 EKDHTAGTDEALLDIYRKLRPGEPPTKESAQALLETLFFKEKRYDLAKVGRYKVNKKLGL 309

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKG-----------TIDDIDNLGNRRVRSVGEML 471
           DTP     + ++DI+  I+ LV L  G+             +DDID+ GNRR+R+VGE++
Sbjct: 310 DTPISTGVLTEDDIVTTIEYLVRLHAGETSMQPGETEVPVEVDDIDHFGNRRLRTVGELI 369

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N 
Sbjct: 370 QNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNP 429

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+ R
Sbjct: 430 LAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYGR 489

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           VN +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ +D +G+F E  V  R  G
Sbjct: 490 VNPFGFIETPYRKVVDGRVTDQIDYLTADEEDRYVKAQANARIDGEGNFLEGKVLVRKKG 549

Query: 652 -EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E  ++    +D++D SP+Q+VS A ++IPFLE+DD+NR LMG NMQRQAVPLL++E+P 
Sbjct: 550 GEVEMIDPRDVDYMDVSPRQMVSAATAMIPFLEHDDANRALMGANMQRQAVPLLRSESPL 609

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +VAK+ G+VE++ A  + + + +G           Y + KF+RS
Sbjct: 610 VGTGMELRAAVDAGDVVVAKKTGVVEEISADYVTVMADDGSRQ-------TYGMHKFRRS 662

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC+NQ+P+V  GD+V+   ++ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S
Sbjct: 663 NQGTCINQKPIVNEGDQVKVGQVLADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILS 722

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVSEE L ++DE GII +GAEV P
Sbjct: 723 QRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADLDERGIIRIGAEVQP 782

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G  G V+ +R+F+R   
Sbjct: 783 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEYGKVIGIRVFSREDD 842

Query: 951 D 951
           D
Sbjct: 843 D 843



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 191/545 (35%), Positives = 266/545 (48%), Gaps = 69/545 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +               I++  I+  G +V  G +L      +    M   + LL A
Sbjct: 648  DGSRQTYGMHKFRRSNQGTCINQKPIVNEGDQVKVGQVLADGPCTEN-GEMALGKNLLVA 706

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          E +  
Sbjct: 707  IMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLA 766

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      +  +IL G+    G         L   +  E  R           
Sbjct: 767  DL-DERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 814

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +            ++   +  D++PPGV  +V+V+VA KR IQ GDK
Sbjct: 815  ------EVRDTSLKVPHGEYGKVIGIRVFSREDDDELPPGVNELVRVYVAQKRKIQDGDK 868

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL+DGTPVDIVLN  GVP RMN+GQ+ ETHLGW     G
Sbjct: 869  LAGRHGNKGVIGKILPVEDMPFLEDGTPVDIVLNTHGVPRRMNIGQVLETHLGWIAKQ-G 927

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I    +  K                                +     +   G   +TP
Sbjct: 928  WSINGDPDWAKN-------------------------------LPADLYEVDPGTKTATP 956

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA EE I  +L     +          G++ L+DG +GEP+  PV+VGY+Y+LKL H
Sbjct: 957  VFDGAREEEITGLLGSTVPNRDGERMVKENGKAQLFDGRSGEPYPFPVSVGYMYILKLLH 1016

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD
Sbjct: 1017 LVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDD 1076

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            V+GR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S         E+ D +
Sbjct: 1077 VLGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAI----EMRDGD 1132

Query: 1382 KCELK 1386
              +L+
Sbjct: 1133 DEDLE 1137



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 88/295 (29%), Positives = 140/295 (47%), Gaps = 25/295 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +  P+L+++Q  S++           R +EG       L+     + PI 
Sbjct: 25  RVSFAKIHEPLQTPNLLDLQIQSFEWLTGDEAWFQRRVDEGDEAPTGGLEEVLNEISPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K   ++C  +D+TYA PL +T               +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFDEVKASTEECKDKDMTYAAPLFVTAEFT---------NHTTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG+++D    +   + K +++ +IIP
Sbjct: 136 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYYDTAIDKT--TDKDVFSVKIIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F          +   
Sbjct: 194 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSTEQIRERFSFSETLLTTLEKDH 253

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
              +   L+   +       +  GE    ES + L   L    K   +  +G   
Sbjct: 254 TAGTDEALLDIYR------KLRPGEPPTKESAQALLETLFFKEKRYDLAKVGRYK 302


>gi|326772037|ref|ZP_08231322.1| DNA-directed RNA polymerase, beta subunit [Actinomyces viscosus C505]
 gi|326638170|gb|EGE39071.1| DNA-directed RNA polymerase, beta subunit [Actinomyces viscosus C505]
          Length = 1173

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/598 (31%), Positives = 275/598 (45%), Gaps = 59/598 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGP 858
                       ++    P  G   E    +    V       +  E      R     G 
Sbjct: 598  MGANMQRQAVPLIRPDAPLVGTGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGT 657

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF- 917
            E + +             ++  +   G  V  G +L        E  +   + LL A   
Sbjct: 658  ENVYKVAKFRRSNQGNCYNQRVVATEGERVEVGTVLADGP-ATNEGDLALGQNLLVAFMT 716

Query: 918  --GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--D 973
              G    D    S RV +    T + +        D    +  + R+   +        D
Sbjct: 717  WEGLNYEDAIIISQRVVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLD 776

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R      +++    + 
Sbjct: 777  ERGIIRIGAEVRSGDILVGKVTPKGETELTSEERLLRAIFGEKARE-VRDTSLRVPHGEY 835

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             + +   + + +    E               +P GV R+V+V++A +R I  GDK++GR
Sbjct: 836  GIVTGVREIDAASDDAE---------------LPAGVNRMVRVYIAQRRKITVGDKLSGR 880

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+ILP EDMPFL DGTPVD++LNPLGVPSRMNVGQ+ E HLGW      +   
Sbjct: 881  HGNKGVISKILPVEDMPFLADGTPVDVILNPLGVPSRMNVGQVLELHLGWVAS---RGWD 937

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +           + L                              + +   PV+TPVFDG
Sbjct: 938  ATAAREAGEAWTANL-------------------------PENGIKAEPRTPVATPVFDG 972

Query: 1214 ADEEAINSMLRMA-----DLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              +  +  +L         L     +G++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 973  VRDNELMGLLGSTLPTSDGLQLVEPNGKARLFDGRSGEPFPYPISVGYMYILKLHHLVDD 1032

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1033 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAHALQELLTVKSDDVNGR 1092

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             +VYE+IV G D  E G PESF VL+KEMQ+L L+++  ++     A  +   D ++ 
Sbjct: 1093 VKVYEAIVKGEDIPEPGIPESFKVLMKEMQSLCLNVEALDAEGVAIALDDTDDDGSRA 1150



 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 330/771 (42%), Positives = 470/771 (60%), Gaps = 61/771 (7%)

Query: 226 EEI--LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS--------SLVDIDTGEQV-- 273
           +EI  +  F   +  S     +  P   A+      ++            +  TGE    
Sbjct: 80  DEISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYVVADFENFSTGEIKSQ 139

Query: 274 ----------IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGE 319
                      + G  + +G  + +  + V+  G+  +        + + N       G 
Sbjct: 140 TVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEKATDKYVYNVKFIPSRGA 199

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-----------KNK 368
              E      ++    I     +D+ +  +    + + IR                 K  
Sbjct: 200 WL-EFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADYPALTSALDEDRKIT 258

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            + +ALLDIY+ +RPG+  +     ++    +F+  +YDL+ VGR K+N +L L +    
Sbjct: 259 TQDEALLDIYKKIRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYKINKKLGLASDLTE 318

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI---------------DDIDNLGNRRVRSVGEMLKN 473
             +R EDI+A ++ L+ L +G  T+               DDID+LGNRR+R+VGE+++ 
Sbjct: 319 STLRIEDIVAALRYLLALHSGAETVEGVRDGEITEIAVEYDDIDHLGNRRIRAVGELIQA 378

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R G+ RMER ++ER+++ D++++ P  LIN +PV +A+ EFF +SQLSQ  +  N L+
Sbjct: 379 QVRTGMSRMERQVRERMTTQDVEAITPNTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLA 438

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG++R RA +E+RDVH +HYGR+CP E+ EG NIGL+ SL +F R+N
Sbjct: 439 GLTHKRRLSALGPGGLSRERASMEVRDVHTSHYGRMCPIESPEGPNIGLIGSLATFGRIN 498

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGE 652
            +GF+ETPYR V DG+VT++  YL+A +E+   IAQAN +L EDG F E+ V CR   GE
Sbjct: 499 PFGFVETPYRVVVDGRVTDETHYLTADDEDRHVIAQANVALTEDGHFAEDHVLCRVTGGE 558

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             LVP  ++D +D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPL++ +AP VG
Sbjct: 559 PALVPSSQVDLMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLIRPDAPLVG 618

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  +G  +VA +AG+V +V A  + + + +G         ++Y++ KF+RSNQ
Sbjct: 619 TGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGTE-------NVYKVAKFRRSNQ 671

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             C NQR +   G+ V    ++ADGP+T+ GDLALG+N+LVAFM W G N+ED+++IS+R
Sbjct: 672 GNCYNQRVVATEGERVEVGTVLADGPATNEGDLALGQNLLVAFMTWEGLNYEDAIIISQR 731

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V+ED+ TSIHIEE EV ARDTKLG EEITRDIPNVSEE L N+DE GII +GAEV  GD
Sbjct: 732 VVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLDERGIIRIGAEVRSGD 791

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V  VR
Sbjct: 792 ILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPHGEYGIVTGVR 842



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 95/302 (31%), Positives = 142/302 (47%), Gaps = 33/302 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDER------------PNEGLQAAFKS 61
           R  F K  E +  P+L+ +Q  S+D  +      +                 GL+  F  
Sbjct: 22  RINFAKIAEPMQAPNLLALQTESFDWLVGNERWRERMTAANKAHPGSLPETSGLEEIFDE 81

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F  + F+ PK+  ++C  +DLTY+ PL +                S
Sbjct: 82  ISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYV---------VADFENFS 132

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   + K +Y 
Sbjct: 133 TGEIKSQTVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEK--ATDKYVYN 190

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            + IP +G W++ E D  D + VRIDR+RK  VT FL+ALGMD  EI   F  YP +  +
Sbjct: 191 VKFIPSRGAWLEFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADYPALTSA 250

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A L +  K       I  GE   +E+G+ L      + K   +  +G 
Sbjct: 251 LDEDRKITTQDEALLDIYKK-------IRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGR 303

Query: 299 TS 300
             
Sbjct: 304 YK 305


>gi|253740489|gb|ACT34878.1| RNA polymerase sigma factor [Mycobacterium haemophilum]
          Length = 1182

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 189/513 (36%), Positives = 259/513 (50%), Gaps = 53/513 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 693  IVDSGDRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 751

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 752  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 809

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +      R+ + + A +       V              E     ++  
Sbjct: 810  VTPKGETELTPE--ERLLRAIFGEKAPEVRDTSLKVAHG---------ESEKVIAIRVFS 858

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD P GV  +V V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 859  REDEDDFPAGVNELVGVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVD 918

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G KI       +   ++       E      
Sbjct: 919  IILNTHGVPRRMNIGQILETHLGWVAKS-GWKIDVAGGMPEWAANLPAELLHAE------ 971

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                                      VSTPVFDGA EE +  +L     +          
Sbjct: 972  ----------------------PNQIVSTPVFDGAKEEELQGLLSSTLPNRDGDVMVDGD 1009

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1010 GKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1069

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1070 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1129

Query: 1352 KEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1130 KELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1162



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 325/698 (46%), Positives = 460/698 (65%), Gaps = 32/698 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + +       +  
Sbjct: 179 LVRSPGVYFDETIDKSTEKTLHSVKVIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 234

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         I+  +    +  +R+TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 235 TVLLKALGWTSEQII--ERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESA 292

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +++   LFF   +YDL+ VGR K+N +L L    P     + +E+++A I+ LV L  G+
Sbjct: 293 QTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGEPITSSTLTEEEVVATIEYLVRLHEGQ 352

Query: 451 GTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            T+            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++
Sbjct: 353 STMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAI 412

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+
Sbjct: 413 TPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEV 472

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHP+HYGR+CP ET EG  IGL+ S + +ARVN +GFIETPYRKV DG VT+D+ YL+
Sbjct: 473 RDVHPSHYGRMCPIETPEGPKIGLIGSWSVYARVNPFGFIETPYRKVVDGVVTDDIEYLT 532

Query: 619 AMEEENRYIAQANSSLDEDG-----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           A EE+   +AQANS   ++G          ++  R AGE   V   ++D++D SP+Q+VS
Sbjct: 533 ADEEDRHVVAQANSPTKDNGAGAQVFAEPRVLVRRKAGEVEYVASSEVDYMDVSPRQMVS 592

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  +VA+++G
Sbjct: 593 VATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEKSG 652

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           ++E+V A  I + + +G           YR+ KF RSN  TC NQ P+V  GD V    +
Sbjct: 653 VIEEVSADYITVMADDGTR-------RTYRMRKFARSNHGTCANQSPIVDSGDRVEAGQV 705

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           IADGP T+ G++ALG+N+LVA MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARD
Sbjct: 706 IADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARD 765

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           TKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LL
Sbjct: 766 TKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLL 825

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RAIFGEKA +VRDTSL+V  G S  V+ +R+F+R   D
Sbjct: 826 RAIFGEKAPEVRDTSLKVAHGESEKVIAIRVFSREDED 863



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 98/333 (29%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMM---NIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +       A   R +     GL+     + PI 
Sbjct: 38  RISFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRAAAASRGDLKPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIIERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +        T     E   V   + L  +  
Sbjct: 318 KKLGLHAGEPITSSTLTEEEVVATIEYLVRLHE 350


>gi|46361030|gb|AAS89248.1| RpoB [Rhodococcus equi]
          Length = 1107

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 459/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +    + D  I   
Sbjct: 173 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEI--R 230

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D  K+  +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 231 ERFGFSEIMMATLEKDPAKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 290

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKGT------------IDD 455
            VGR K+N +L L+T  P +   + ++DI+  I+ LV L  G               +DD
Sbjct: 291 RVGRYKINKKLGLNTGLPIEASTLTEDDIVTTIEYLVRLHAGDTMMTAPGGVEVPVEVDD 350

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 351 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 410

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 411 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 470

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G++T+ V YL+A EE+   +AQANS +D
Sbjct: 471 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGQLTDQVDYLTADEEDRHVVAQANSPVD 530

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 531 ANGRFTEDRVLVRRKGGEVEFVSSSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 590

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V +  + + + +G    
Sbjct: 591 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSSDYVTVMADDGSR-- 648

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 649 -----TTYRLRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVA 703

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 704 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 763

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 764 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 823

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 824 ESGKVIGIRVFSREDDD 840



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 178/479 (37%), Positives = 252/479 (52%), Gaps = 50/479 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 670  IVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 728

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 729  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 786

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 787  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 835

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 836  REDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 895

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQ+ ETHLGW     G  ++   +  + +   +     L     + 
Sbjct: 896  IILNTHGVPRRMNIGQVLETHLGWIGK-TGWNVQIAGDGSRPDWAATLPEEMLSAPADSN 954

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
                                      ++TPVFDGA E+ +  +L     +  G       
Sbjct: 955  --------------------------IATPVFDGAKEDELTGLLGSTLPNRDGERMVGPD 988

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 989  GKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1048

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL
Sbjct: 1049 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVL 1107



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 148/296 (50%), Gaps = 22/296 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-------GLQAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S++  +      +            GL+     + PI 
Sbjct: 19  RVSFAKIREPLEVPGLLDLQTDSFEWLVGSPSWRERAAARRDGAVTGGLEEILAELSPIE 78

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 79  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 129

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 130 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 187

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT+ L ALGM  EEI   F     ++ +   D 
Sbjct: 188 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEIRERFGFSEIMMATLEKDP 247

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGI 298
                 A   +            ++ + ++E+   K     L +  + K  K LG+
Sbjct: 248 AKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYKINKKLGL 303


>gi|307155095|ref|YP_003890479.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. PCC 7822]
 gi|306985323|gb|ADN17204.1| DNA-directed RNA polymerase, beta subunit [Cyanothece sp. PCC 7822]
          Length = 1095

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 335/687 (48%), Positives = 462/687 (67%), Gaps = 10/687 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 112 INGAERVIVNQIVRSPGVYYKCEYDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 171

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  D++ +  + + TL  + N   ++ALL++YR +RPG+ 
Sbjct: 172 TRKLSAQVLLKAIGLSDNEIL--DALRHPDFYQKTLDKEGNPSEEEALLELYRKLRPGEP 229

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD+ +YDL  VGR K+N +L L+  D +R +R+EDI+A I  L++L
Sbjct: 230 PTVSGGQLLLESRFFDNKRYDLGRVGRYKLNKKLRLNVADTIRVLRQEDILAAIDYLINL 289

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+ DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + DS+ P  L+N 
Sbjct: 290 EFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADSLTPASLVNP 349

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+H+
Sbjct: 350 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHH 409

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY +V +G+V  ++  VYL+A EE++
Sbjct: 410 GRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRVRRELAPVYLTADEEDD 469

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + + DE G    E V  R   E      E++D++  SP Q+VS+A SLIPFLE+
Sbjct: 470 FRVAPGDVATDEAGVIVGESVPVRYRQEFSTTEPEQVDYVAVSPVQIVSVATSLIPFLEH 529

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  VDA  I 
Sbjct: 530 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQTARDSGMVIVSRSHGVVTHVDATTIR 589

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++        S   V  Y L K+QRSNQ+TC+NQRPLV +G+EV    ++ADG +T+ G+
Sbjct: 590 VK------VKSEERVIEYELQKYQRSNQDTCLNQRPLVYMGEEVVPGQVLADGSATEGGE 643

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           +ALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIH+E++E+ AR TKLGPEEITR+
Sbjct: 644 IALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITRE 703

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 704 IPNVGEDALRNLDERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 763

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 764 RDNSLRVPNGEKGRVVDVRVFTREQGD 790



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 197/587 (33%), Positives = 273/587 (46%), Gaps = 66/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E        MV          H++   +  +     
Sbjct: 537  MGSNMQRQAVPLLRPERPLVGTGLEAQTARDSGMVIVSRSHGVVTHVDATTIRVKVKSEE 596

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                              +++  ++ +G EV PG +L      +G   +   + +L A  
Sbjct: 597  RVIEYELQKYQRSNQDTCLNQRPLVYMGEEVVPGQVLADGSATEG-GEIALGQNILVAYM 655

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD--- 972
              +  +  D  L     V   V       ++ I+  +  +  E    +I  +  D     
Sbjct: 656  PWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITREIPNVGEDALRNL 715

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+    +    +IL G+    G         L   +  E  R              
Sbjct: 716  DERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 762

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMA
Sbjct: 763  -----VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMA 817

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DG PVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG +
Sbjct: 818  GRHGNKGIISRILPIEDMPYLPDGRPVDIVLNPLGVPSRMNVGQVFECLLGWAGENLGVR 877

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  +  E +    + +  R  ++W         VF
Sbjct: 878  FKITPFD---------------EMYGEEASRETVHGLLNQASNRPGKEW---------VF 913

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                             D  G+ ++YDG TGEPFDRPVTVG  YMLKL H+V DK++ARS
Sbjct: 914  SQ---------------DHPGKIMVYDGRTGEPFDRPVTVGQAYMLKLVHLVDDKIHARS 958

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +
Sbjct: 959  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNA 1018

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +    T       ++ 
Sbjct: 1019 IVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVETLTDGTSRDVE 1065



 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 108/493 (21%), Positives = 195/493 (39%), Gaps = 54/493 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLI +Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 9   LPDLISIQRSSFRWFL----------EEGLIEELDSFSPITDYTGKLELHFLGQDYKLKE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 59  PKYAVDEAKRRDSTYSVQMYVPTRLI---------NKETGNIKEQEVFIGDLPLMTERGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 110 FIINGAERVIVNQIVRSPGVYYKCEYDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL        Y +  D    P     L+        
Sbjct: 167 VRIDKTRKLSAQVLLKAIGLSDNEILDALRHPDFYQKTLDKEGNPSEEEALL------EL 220

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G+ L        K   +  +G             D +     E  +
Sbjct: 221 YRKLRPGEPPTVSGGQLLLESRFFDNKRYDLGRVGRYKLNKKLRLNVADTIRVLRQEDIL 280

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++    +   
Sbjct: 281 AAIDYLINLEFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADS 340

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 341 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 395

Query: 435 DIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMER 484
                ++ +    +G+    +                 RV   G +    YR+   R+ R
Sbjct: 396 RAGFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRVRR 455

Query: 485 SIKERISSVDIDS 497
            +     + D + 
Sbjct: 456 ELAPVYLTADEED 468


>gi|262201131|ref|YP_003272339.1| DNA-directed RNA polymerase subunit beta [Gordonia bronchialis DSM
            43247]
 gi|262084478|gb|ACY20446.1| DNA-directed RNA polymerase, beta subunit [Gordonia bronchialis DSM
            43247]
          Length = 1168

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 185/513 (36%), Positives = 250/513 (48%), Gaps = 62/513 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI      +  D  +     V   V+
Sbjct: 678  IVDEGQRVESGQVLADGPCTEN-GEMALGKNLLVAIMPWDGHNYEDAIILSQRLVEEDVL 736

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 737  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIVRIGAEVRDGDILVGKV 795

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 796  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 838

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++      DD+ PGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 839  VRVFSRDDDDDLAPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPAEDMPFLPD 898

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +         
Sbjct: 899  GTPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVANGVPDWASKLPE------D 951

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +      T                        +TPVFDGA EE +  +L     +  G  
Sbjct: 952  MYSAEPDTNT----------------------ATPVFDGAREEELTGLLSSTLPNRDGEV 989

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 990  MVNGDGKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGK 1049

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1050 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1109

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ +S        +   +
Sbjct: 1110 FKVLLKELQSLCLNVEVLSSDGAAIQMHDTDDE 1142



 Score =  506 bits (1302), Expect = e-140,   Method: Composition-based stats.
 Identities = 326/698 (46%), Positives = 462/698 (66%), Gaps = 32/698 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + I+         
Sbjct: 164 LVRSPGVYFDAAIDKATEKTLHTVKVIPGR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 221

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +       +I     +    +  + +TL  D   ++ +ALL++YR +RPG+  T   A
Sbjct: 222 LLKALGLTTEEI----TERFGFSEIMMSTLEKDNTANQDEALLEVYRKLRPGEPPTKESA 277

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNL--DTPDDVRHIRKEDIIAIIKILVDLRNGK 450
           E++   LFF   +YDL+ VGR K+N +L L  +       + +EDI+A ++ LV L    
Sbjct: 278 ENLLENLFFKDKRYDLARVGRYKVNKKLGLTDNPMVGESTLTREDIVATVEYLVRLHEAD 337

Query: 451 GT----------------IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                             +DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D
Sbjct: 338 PHTTTYMTVPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQD 397

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           ++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RA
Sbjct: 398 VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERA 457

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+ +
Sbjct: 458 GLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDQI 517

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVS 673
            Y++A EE+   I QAN++ D DG+ T+E V  R    E   V   +++++D SP+Q+VS
Sbjct: 518 EYMTADEEDRYLIGQANTTYDTDGNITDERVLVRKKGSEVEFVDAAQVEYLDVSPRQMVS 577

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +A ++IPFLE+DD+NR LMG NMQRQAVPL++ E+P VGTGME   A  +G  +V+ + G
Sbjct: 578 VATAMIPFLEHDDANRALMGANMQRQAVPLVRNESPLVGTGMELRAAVDAGDVVVSDKTG 637

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +VE+V A  I + + +G  D        YR+ KF RSN  TC NQRP+V  G  V    +
Sbjct: 638 VVEEVSADYITVMADDGTRD-------TYRMRKFARSNHGTCANQRPIVDEGQRVESGQV 690

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGP T+ G++ALG+N+LVA MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARD
Sbjct: 691 LADGPCTENGEMALGKNLLVAIMPWDGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARD 750

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           TKLG EEITRDIPNVS+E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LL
Sbjct: 751 TKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLL 810

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RAIFGEKA +VRDTSL+VP G +G V+ VR+F+R   D
Sbjct: 811 RAIFGEKAREVRDTSLKVPHGETGKVIGVRVFSRDDDD 848



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 97/324 (29%), Positives = 157/324 (48%), Gaps = 22/324 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---MMNIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++PDL+++Q  S++  +           R  E    GL+     + PI 
Sbjct: 23  RASFAKISEPLEVPDLLDLQLDSFEWLVGSPEWRAKAIARGEENPTGGLEDILHELSPIE 82

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T   I           +  +IK
Sbjct: 83  DFSGSMSLSFSDPHFDEVKASVEECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 133

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  G+F+I G +R+VVSQL RSPG++FD    +   + K L+  ++IP
Sbjct: 134 SQTVFMGDFPIMTDKGSFIINGTERVVVSQLVRSPGVYFDAAIDK--ATEKTLHTVKVIP 191

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +EEI   F     ++ +   D 
Sbjct: 192 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEITERFGFSEIMMSTLEKDN 251

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ E ++E+   K     L +  + K  K LG+T + 
Sbjct: 252 TANQDEALLEVYRKLRPGEPPTKESAENLLENLFFKDKRYDLARVGRYKVNKKLGLTDNP 311

Query: 303 LCGLYVAEDIVNGETGEIYIEAGD 326
           + G           T E  +   +
Sbjct: 312 MVGESTLTREDIVATVEYLVRLHE 335


>gi|331699183|ref|YP_004335422.1| DNA-directed RNA polymerase subunit beta [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953872|gb|AEA27569.1| DNA-directed RNA polymerase subunit beta [Pseudonocardia
           dioxanivorans CB1190]
          Length = 1175

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 343/742 (46%), Positives = 477/742 (64%), Gaps = 34/742 (4%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +    ++          +                I+  E+V+ S    + G+        
Sbjct: 125 FVTAEFTNNTTGEIKSQTVFMGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDHAIDK 184

Query: 293 VKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                + S  +    G ++  D+   +T  + I+         L +        I     
Sbjct: 185 TTEKDVYSVKIIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQI----S 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  I  TL  D    + +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSETIMATLEKDHTAGQDEALLDIYRKLRPGEPPTRESAQTLLENLFFKDKRYDLA 300

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI---------------- 453
            VGR K N +L L   + V  + +EDI   I+ LV L  G+ ++                
Sbjct: 301 KVGRYKANKKLGLAIDNSVGTLTEEDIATTIEYLVRLHAGETSMAGGGNGTAGIPGEVVP 360

Query: 454 ---DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
              DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV
Sbjct: 361 VETDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVV 420

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RDVHP+HYGR+C
Sbjct: 421 AAIKEFFGTSQLSQFMDQHNPLAGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMC 480

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL+ SL++FA+VN +GFI+TPYRKV DG VT  + YL+A EE+   IAQA
Sbjct: 481 PIETPEGPNIGLIGSLSTFAQVNPFGFIQTPYRKVVDGVVTEQIDYLTADEEDRFVIAQA 540

Query: 631 NSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           N+ L++DGSFTE+ V  R   GE  L+P   +++ID SP+Q+VS+A +LIPFLE+DD+NR
Sbjct: 541 NAPLNDDGSFTEDRVLVRRKGGEVDLIPPTGVEYIDVSPRQMVSVATALIPFLEHDDANR 600

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQ+VPLL++EAP VGTGME   A  +G  +VA++AG+VE++ A  I + + E
Sbjct: 601 ALMGANMQRQSVPLLRSEAPLVGTGMELRAAVDAGDVLVAEKAGVVEELCADYITVMADE 660

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G           YRL KF+RSNQ TC NQ+P+V  G  V    ++ADGP T+ G++ALG+
Sbjct: 661 GTRQ-------TYRLNKFRRSNQGTCNNQKPIVDEGQRVEVGQVLADGPCTENGEMALGK 713

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVA MPW G+N+ED++++S+R+V +DV TSIHIEE E+ ARDTKLG EEITRDIPNVS
Sbjct: 714 NLLVAIMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVS 773

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE L ++DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL
Sbjct: 774 EEVLADLDERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSL 833

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           +VP G +G V+ +R+F+R   D
Sbjct: 834 KVPHGENGKVIGIRVFSRDDED 855



 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/538 (34%), Positives = 258/538 (47%), Gaps = 65/538 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  I+  G  V  G +L      +    M   + LL A
Sbjct: 660  EGTRQTYRLNKFRRSNQGTCNNQKPIVDEGQRVEVGQVLADGPCTEN-GEMALGKNLLVA 718

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLAR 969
            I   +  +  D  +     V   V+       H ID  +  +  E          E +  
Sbjct: 719  IMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLA 778

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      +  +IL G+    G         L   +  E  R           
Sbjct: 779  DL-DERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPH 837

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 V  +                 ++      D++ PGV  +V+V+VA KR IQ GDK
Sbjct: 838  GENGKVIGI-----------------RVFSRDDEDELAPGVNELVRVYVAQKRKIQDGDK 880

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQ+ ETHLGW     G
Sbjct: 881  LAGRHGNKGVIGKILPAEDMPFLPDGTPVDIILNTHGVPRRMNIGQVLETHLGWIAKS-G 939

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +I+                              + +    + +  VA         +TP
Sbjct: 940  WEIEGTP---------------------------EWASKMPEELYSVAPN----TNTATP 968

Query: 1210 VFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA E  I  +L     +  G        ++ L+DG +GEP+  PV VGY+Y+LKL H
Sbjct: 969  VFDGAKEHEITGLLASTRPNRDGDRMVGPDGKAQLFDGRSGEPYPFPVAVGYMYILKLAH 1028

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD
Sbjct: 1029 LVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDD 1088

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            VVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S        +   +
Sbjct: 1089 VVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIEMRDSDDE 1146



 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 153/311 (49%), Gaps = 22/311 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPI 65
            R  F K  E +++PDL+++Q  S++  +        R + G       L+     + PI
Sbjct: 28  TRVSFAKIREPLEVPDLLDLQIQSFEWLVGSEAWFQRRIDAGDDNPVGGLEEILAEISPI 87

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             FSG+  L F    FD  K  V++C  +D+TY  PL +T               +  +I
Sbjct: 88  EDFSGSMSLSFSDPRFDEVKASVEECRDKDMTYGAPLFVTAEFT---------NNTTGEI 138

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FDH   +   + K +Y+ +II
Sbjct: 139 KSQTVFMGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDHAIDKT--TEKDVYSVKII 196

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     I+ +   D
Sbjct: 197 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQISERFGFSETIMATLEKD 256

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSD 301
                  A   +            ++ + ++E+   K     L K  + K  K LG+  D
Sbjct: 257 HTAGQDEALLDIYRKLRPGEPPTRESAQTLLENLFFKDKRYDLAKVGRYKANKKLGLAID 316

Query: 302 CLCGLYVAEDI 312
              G    EDI
Sbjct: 317 NSVGTLTEEDI 327


>gi|167967486|ref|ZP_02549763.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis H37Ra]
 gi|215402448|ref|ZP_03414629.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis 02_1987]
 gi|215410219|ref|ZP_03419027.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis 94_M4241A]
 gi|215444789|ref|ZP_03431541.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis T85]
 gi|218752317|ref|ZP_03531113.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis GM 1503]
 gi|219556511|ref|ZP_03535587.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis T17]
          Length = 1096

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 455/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 127 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 182

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 183 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 242

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 243 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 302

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 303 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 362

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 363 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 422

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 423 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 482

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 483 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 542

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 543 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 595

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 596 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 655

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 656 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 715

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 716 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 775

Query: 950 ID 951
            D
Sbjct: 776 ED 777



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 607  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 665

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 666  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 725

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 726  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 768

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 769  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 828

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 829  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 878

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 879  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 919

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 920  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 979

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 980  QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1039

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1040 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1076



 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/286 (30%), Positives = 135/286 (47%), Gaps = 21/286 (7%)

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL+     + PI  FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I    
Sbjct: 3   GLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---- 58

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                  +  +IK Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +  
Sbjct: 59  -----NNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK-- 111

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            + K L++ ++IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F 
Sbjct: 112 STDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFG 171

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
              +     +      +   L+   +       +  GE    ES + L   L    K   
Sbjct: 172 FSEIMRSTLEKDNTVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYD 225

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           +  +G          +   +    T     E   V   + L  +  
Sbjct: 226 LARVGRYK---VNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 268


>gi|46361028|gb|AAS89247.1| RpoB [Rhodococcus equi]
          Length = 1118

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/677 (48%), Positives = 459/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +    + D  I   
Sbjct: 170 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEI--R 227

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D  K+  +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 228 ERFGFSEIMMATLEKDPAKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 287

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKGT------------IDD 455
            VGR K+N +L L+T  P +   + ++DI+  I+ LV L  G               +DD
Sbjct: 288 RVGRYKINKKLGLNTGLPIEASTLTEDDIVTTIEYLVRLHAGDTMMTAPGGVEVPVEVDD 347

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 348 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 407

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 408 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 467

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G++T+ V YL+A EE+   +AQANS +D
Sbjct: 468 EGPNIGLIGSLSVYARVNPFGFIETPYRKVENGQLTDQVDYLTADEEDRHVVAQANSPVD 527

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G FTE+ V  R   GE   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 528 ANGRFTEDRVLVRRKGGEVEFVSSSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 587

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  IV ++ G+VE+V +  + + + +G    
Sbjct: 588 NMQRQAVPLVRSEAPLVGTGMELRAAVDAGDVIVTEKTGVVEEVSSDYVTVMADDGSR-- 645

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSNQ TC NQRP+V  G  V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 646 -----TTYRLRKFARSNQGTCANQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVA 700

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 701 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 760

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 761 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 820

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 821 ESGKVIGIRVFSREDDD 837



 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 183/493 (37%), Positives = 264/493 (53%), Gaps = 50/493 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 667  IVDEGQRVEAGQVLADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 725

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 726  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 783

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 784  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 832

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  DD+PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 833  REDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPQEDMPFLPDGTPVD 892

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQ+ ETHLGW     G  ++   +  + +   +     L     + 
Sbjct: 893  IILNTHGVPRRMNIGQVLETHLGWIGK-TGWNVQIAGDGSRPDWAATLPEEMLSAPADSN 951

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
                                      ++TPVFDGA E+ +  +L     +  G       
Sbjct: 952  --------------------------IATPVFDGAKEDELTGLLGSTLPNRDGERMVGPD 985

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 986  GKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1045

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1046 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1105

Query: 1352 KEMQALGLSIDLE 1364
            KE+Q+L L++++ 
Sbjct: 1106 KELQSLCLNVEVL 1118



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 148/296 (50%), Gaps = 22/296 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE-------GLQAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S++  +      +            GL+     + PI 
Sbjct: 16  RVSFAKIREPLEVPGLLDLQTDSFEWLVGSPSWRERAAARRDGAVTGGLEEILAELSPIE 75

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 76  DFSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 126

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 127 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESIDK--STEKTLHSVKVIP 184

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT+ L ALGM  EEI   F     ++ +   D 
Sbjct: 185 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTTLLKALGMTDEEIRERFGFSEIMMATLEKDP 244

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGI 298
                 A   +            ++ + ++E+   K     L +  + K  K LG+
Sbjct: 245 AKNTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYKINKKLGL 300


>gi|50955586|ref|YP_062874.1| DNA-directed RNA polymerase subunit beta [Leifsonia xyli subsp. xyli
            str. CTCB07]
 gi|81390570|sp|Q6ACX5|RPOB_LEIXX RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|50952068|gb|AAT89769.1| DNA-directed RNA polymerase, beta subunit [Leifsonia xyli subsp. xyli
            str. CTCB07]
          Length = 1165

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 188/605 (31%), Positives = 279/605 (46%), Gaps = 85/605 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +L +  P  G   E    I            + I E   +  +      
Sbjct: 597  MGANMQRQAVPLLRSESPVVGTGMEGYAAIDAG--------DVVIAEKSGIVSEVSADAV 648

Query: 860  EITRDIPNVSEEGLKNID---------ECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             +  D   V    L+  D            ++  G  +  G+++      +    +   +
Sbjct: 649  TVQADDGTVKTYYLRKFDRSNQGTSYNHRVVVDEGDRIEAGEVVADGPATEN-GELALGK 707

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL---- 966
             LL A    +  +  D  +   + V    +       +  + + R   + +E+I      
Sbjct: 708  NLLVAFMPWEGHNFEDAIILSQNLVKDDTLSSIHIEEY--EVDARDTKLGKEEITRDLPN 765

Query: 967  ----LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
                L  D  DE+ I+      R  +IL G+    G         L   + +E  R    
Sbjct: 766  VSPDLLADL-DERGIIRIGAEVRPGDILVGKVTPKGETELSAEERLLRAIFNEKSREV-- 822

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                        V   +        + + +  +        D++  GV + V V++A KR
Sbjct: 823  ------RDTSLKVPHGEEGTIIGVKVFDAQDGD--------DELGSGVNQRVVVYIAQKR 868

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I +GDK+AGRHGNKG++S+ILP EDMPFL DGTPVD++LNPLGVP RMN GQ+ E HLG
Sbjct: 869  KITAGDKLAGRHGNKGVISKILPVEDMPFLADGTPVDVILNPLGVPGRMNFGQVLEIHLG 928

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            W     G +IK                                       +   A     
Sbjct: 929  WIAKN-GWEIKGKPKWAA-------------------------------ELPETAFSAAP 956

Query: 1203 GVPVSTPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
               V+TPVFDGA EE I  +L            +  SG++ L+DG +GEP+  PV+VGY+
Sbjct: 957  NTKVATPVFDGAKEEEIAGLLDVTLPTRDGDRLIGSSGKTQLFDGRSGEPYPDPVSVGYM 1016

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+
Sbjct: 1017 YILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQEL 1076

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LTIKSDD++GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ ++  +  +  
Sbjct: 1077 LTIKSDDILGRVKVYEAIVKGENIQEPGIPESFKVLIKEMQSLCLNVEVLSADGQAVSLR 1136

Query: 1375 EEIPD 1379
            +   +
Sbjct: 1137 DADDE 1141



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 319/605 (52%), Positives = 436/605 (72%), Gaps = 23/605 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    +++AL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L L
Sbjct: 252 EKDAILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGL 311

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGK---------------GTIDDIDNLGNRRVRSV 467
           + P     +  +DIIA IK LV L +G+                 IDDID+ GNRR+R+V
Sbjct: 312 EAPLTDSVLTVQDIIATIKYLVSLHDGQTSFTGLRSGVETDIRLDIDDIDHFGNRRIRAV 371

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 372 GELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMD 431

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL 
Sbjct: 432 QNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA 491

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           SFAR+N++GFIETPYRKV DG VT+ + YL+A EE++  +AQAN+ LD  G F EE V  
Sbjct: 492 SFARINSFGFIETPYRKVVDGLVTDQIDYLTASEEDDFVVAQANAPLDARGHFVEERVLA 551

Query: 648 RCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R   GE  LVP E+I ++D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPLL++
Sbjct: 552 RQKGGEVDLVPAEEIGYMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLLRS 611

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTGME   A  +G  ++A+++GIV +V A  + +++ +G        V  Y L K
Sbjct: 612 ESPVVGTGMEGYAAIDAGDVVIAEKSGIVSEVSADAVTVQADDGT-------VKTYYLRK 664

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ T  N R +V  GD +   +++ADGP+T+ G+LALG+N+LVAFMPW G+NFED+
Sbjct: 665 FDRSNQGTSYNHRVVVDEGDRIEAGEVVADGPATENGELALGKNLLVAFMPWEGHNFEDA 724

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++S+ +V +D  +SIHIEE+EV ARDTKLG EEITRD+PNVS + L ++DE GII +GA
Sbjct: 725 IILSQNLVKDDTLSSIHIEEYEVDARDTKLGKEEITRDLPNVSPDLLADLDERGIIRIGA 784

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+ +VRDTSL+VP G  GT++ V++F+
Sbjct: 785 EVRPGDILVGKVTPKGETELSAEERLLRAIFNEKSREVRDTSLKVPHGEEGTIIGVKVFD 844

Query: 947 RHGID 951
               D
Sbjct: 845 AQDGD 849



 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 95/309 (30%), Positives = 147/309 (47%), Gaps = 34/309 (11%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI--------APDERPN----EG 54
            NG    R  F K  + + +PDL+ +Q  S+D  +  +             R +     G
Sbjct: 15  KNGRDVSRLSFAKITDTLTVPDLLALQTESFDWLVGNDAWQARVAAAEAQGRQDLPAATG 74

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           L+  F+ + PI        L F +   +  K+ +D+C  +  TYA PL +         +
Sbjct: 75  LEEIFEEISPIEDLGETMQLSFTNPFLEEKKYSIDECKEKGRTYAAPLYV---------E 125

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                    +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   
Sbjct: 126 AEFMNHLTGEIKTQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFEAAADKT-- 183

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-- 232
           S K +Y+ R+IP +G W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL+ F  
Sbjct: 184 SDKDIYSARVIPSRGSWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILAEFAG 243

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEK 291
           +  I  +   D       A   +           +  GEQV  E+ + L      + K  
Sbjct: 244 FQSIELTLEKDAILTKEEALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRY 295

Query: 292 GVKFLGITS 300
            +  +G   
Sbjct: 296 DLAKVGRYK 304


>gi|282895797|ref|ZP_06303884.1| DNA-directed RNA polymerase, beta subunit [Raphidiopsis brookii D9]
 gi|281199297|gb|EFA74163.1| DNA-directed RNA polymerase, beta subunit [Raphidiopsis brookii D9]
          Length = 1133

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 329/695 (47%), Positives = 450/695 (64%), Gaps = 12/695 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +                +++    
Sbjct: 136 INGAERVIVNQIVRSPGVYYKSEIDKNGRRTYSASLIPNRGAWLKFETDRNDLVWVRIDK 195

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                    +    + D  IL  D++ +  Y + T+  +     ++ALL++YR +RPG+ 
Sbjct: 196 TRKLSIQVLLKALGLSDNEIL--DALRHPEYFQKTIEKEGQFSEEEALLELYRKLRPGEP 253

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T    + +    FFD  +YDL  VGR K+N +L L  PD  R +   DI++ +  L++L
Sbjct: 254 PTVMGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLSVPDTTRVLTPGDILSAVDYLINL 313

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+IDDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D + + P  L+N 
Sbjct: 314 EYDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNP 373

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HY
Sbjct: 374 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHY 433

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGF+ETP+R V +G+V  +   VY++A EE++
Sbjct: 434 GRICPIETPEGPNAGLIGSLATHARVNQYGFLETPFRPVENGRVCYEKPAVYMTADEEDD 493

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +  +D++G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+
Sbjct: 494 LRVAPGDIPVDDNGQILGIQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEH 553

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I 
Sbjct: 554 DDANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDATEIR 613

Query: 745 IRSVEG--------DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +R  E         +  P       Y L K+QRSNQ+TC+NQ+PLV++G++V    ++AD
Sbjct: 614 VRVKEKAALTNRESETIPHKPQEVKYVLSKYQRSNQDTCLNQKPLVRIGEKVIAGQVLAD 673

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G ST+ G+LALG+N++VA+MPW GYN+ED++LISER+V EDV+TSIHIE+FE+ AR TKL
Sbjct: 674 GSSTEGGELALGQNVIVAYMPWEGYNYEDAILISERLVQEDVYTSIHIEKFEIEARQTKL 733

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITR+IPNV E+ L+ +DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAI
Sbjct: 734 GPEEITREIPNVGEDALRQLDEQGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAI 793

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 794 FGEKARDVRDNSLRVPNGEKGRVVDVRLFTREQGD 828



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 184/527 (34%), Positives = 259/527 (49%), Gaps = 64/527 (12%)

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E                +++  ++ +G +V  G +L    + +G   +   + ++ A  
Sbjct: 635  QEVKYVLSKYQRSNQDTCLNQKPLVRIGEKVIAGQVLADGSSTEG-GELALGQNVIVAYM 693

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   V       +  I+  +  +  E    +I  +  D   + 
Sbjct: 694  PWEGYNYEDAILISERLVQEDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDALRQL 753

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DEQ I+    +    +IL G+    G         L   +  E  R              
Sbjct: 754  DEQGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 800

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMA
Sbjct: 801  -----VRDNSLRVPNGEKGRVVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMA 855

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG +
Sbjct: 856  GRHGNKGIISRILPLEDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFECLLGWAGHNLGVR 915

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  S    +     ++    +  W           
Sbjct: 916  FKITPFD---------------EMYGEESSRRIVHGKLWEAREETSRDWVY--------- 951

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                           + +  G+ ++YDG TGEPFDR VTVG  YMLKL H+V DK++ARS
Sbjct: 952  ---------------NPENPGKIMVYDGRTGEPFDRAVTVGIAYMLKLVHLVDDKIHARS 996

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +
Sbjct: 997  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNA 1056

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1057 IVKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQTDGSSLDVE 1103



 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 105/454 (23%), Positives = 194/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 33  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGHNYKLKE 82

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TY V + +  RL+          K   DIKEQ +++GDLPLMT  GT
Sbjct: 83  PKYSVEESKRRDSTYGVQMYVPTRLL---------NKETGDIKEQEVFIGDLPLMTDRGT 133

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 134 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 190

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+ +   L ALG+   EIL        +  +   +       A   +      
Sbjct: 191 VRIDKTRKLSIQVLLKALGLSDNEILDALRHPEYFQKTIEKEGQFSEEEALLELYRKLRP 250

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q++ES         L +  + K  K L ++      +    DI++     
Sbjct: 251 GEPPTVMGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLSVPDTTRVLTPGDILSAVDYL 310

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 311 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 369

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 370 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 424

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +     G+  I  I+         +G +  +
Sbjct: 425 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 456


>gi|289552922|ref|ZP_06442132.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis KZN 605]
 gi|289437554|gb|EFD20047.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis KZN 605]
          Length = 1177

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 453/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 208 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 263

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 264 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 323

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 324 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 383

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ     N
Sbjct: 384 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMGQNN 443

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSA G GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 444 PLSGLTHKRRLSAPGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 503

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 504 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 563

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 564 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 623

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 624 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 676

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 677 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 736

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 737 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 796

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 797 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 856

Query: 950 ID 951
            D
Sbjct: 857 ED 858



 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 190/517 (36%), Positives = 260/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 688  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 746

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 747  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 806

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 807  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 849

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 850  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 909

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 910  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 959

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 960  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 1000

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1001 VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1060

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +T E G PESF
Sbjct: 1061 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENTPEPGIPESF 1120

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1121 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1157



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 37  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 96

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 97  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 147

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 148 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 205

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 206 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 265

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 266 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 316

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 317 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 349


>gi|289749170|ref|ZP_06508548.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis T92]
 gi|289689757|gb|EFD57186.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis T92]
          Length = 1172

 Score =  515 bits (1327), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 453/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++   +++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQGREAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|259559669|gb|ACW83033.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp. DSM 3803]
          Length = 1178

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 265/515 (51%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGQRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 805

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 806  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 854

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 855  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 914

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +              
Sbjct: 915  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVADGTPDWASKLPEGLLSAP------ 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMADLDES 1231
                                  +   VSTPVFDGA E  +  +L            +D  
Sbjct: 968  ----------------------ADSIVSTPVFDGAQEGELAGLLGSTLPNRDGEVMVDGD 1005

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1006 GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1065

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1066 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1125

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1126 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1156



 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 325/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +         I+  
Sbjct: 192 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIV-- 249

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 250 ERFGFSEIMMGTLEKDSTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 309

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 310 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 369

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 370 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 429

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 430 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETP 489

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS  D
Sbjct: 490 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVEGVVTDQIDYLTADEEDRHVVAQANSPTD 549

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F+E+ V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 550 ADGRFSEDRVMVRKKGGEVEFVAADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 609

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+ +AG++E+V A  + + + +G    
Sbjct: 610 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSDKAGVIEEVSADYVTVMADDGTR-- 667

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+LVA
Sbjct: 668 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTENGEMALGKNLLVA 722

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 723 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 782

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 783 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 842

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 843 ESGKVIGIRVFSREDDD 859



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +  +       + G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQNAVDRGEENPVGGLEEVLAELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMMGTLEKDS 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 318 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 350


>gi|134103282|ref|YP_001108943.1| DNA-directed RNA polymerase subunit beta [Saccharopolyspora erythraea
            NRRL 2338]
 gi|158513556|sp|A4FPP3|RPOB_SACEN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|133915905|emb|CAM06018.1| DNA-directed RNA polymerase, beta subunit [Saccharopolyspora
            erythraea NRRL 2338]
          Length = 1164

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 267/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + L  AI   +  +  D  +     V   V+
Sbjct: 677  IVNEGDRVEAGQVIADGPCTQN-GEMALGKNLRVAIMPWEGHNYEDAIILSQRLVQDDVL 735

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL-LARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I   +    +D    LD     R+   + G + + G 
Sbjct: 736  TSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDVLADLDERGIIRIGAEVQGGDILVGK 793

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 794  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFN 842

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF +DGTPVD
Sbjct: 843  REDDDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPAEDMPFTEDGTPVD 902

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       K                   
Sbjct: 903  IILNTHGVPRRMNIGQILETHLGWIASQ-GWSIDGDPEWAKR------------------ 943

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                         +         G   ++PVFDGA EE I  +L     +          
Sbjct: 944  -------------LPEELYDVDPGTNTASPVFDGAREEEITGLLASTKPNRDGERMVKAN 990

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP+  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 991  GKAQLFDGRSGEPYPYPVAVGYMYILKLSHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1050

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1051 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1110

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1111 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1141



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 323/605 (53%), Positives = 437/605 (72%), Gaps = 23/605 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    + +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 250 EKDHTAGQDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGL 309

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNLGNRRVRSV 467
           D P +   + +EDI+  I+ LV L  G+                 +DDID+ GNRR+R+V
Sbjct: 310 DLPFESGVLTEEDIVTTIEYLVRLHAGEAEMPDRGQGGDATIPVEVDDIDHFGNRRLRTV 369

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 370 GELIQNQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 429

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N ++ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL 
Sbjct: 430 QTNPIAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA 489

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +FARVN +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ +D++G+F  + V  
Sbjct: 490 TFARVNPFGFIETPYRKVVDGRVTDQIDYLTADEEDRFVKAQANTPIDDEGNFLADRVLG 549

Query: 648 RCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R   GE  L+   +ID++D SP+Q+VS A ++IPFLE+DD+NR LMG NMQRQAVPLL++
Sbjct: 550 RRKGGEVELLAPTEIDYMDVSPRQMVSAATAMIPFLEHDDANRALMGANMQRQAVPLLRS 609

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP VGTGME   A  +G  + A++AG++E++ A  I + + +G           YRL K
Sbjct: 610 EAPLVGTGMELRAAVDAGDVVTAEKAGVIEELCADYITVMADDGTR-------RTYRLQK 662

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  TC NQ+P+V  GD V    +IADGP T  G++ALG+N+ VA MPW G+N+ED+
Sbjct: 663 FSRSNHGTCTNQKPIVNEGDRVEAGQVIADGPCTQNGEMALGKNLRVAIMPWEGHNYEDA 722

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++S+R+V +DV TSIHIEE EV ARDTKLG EEITRDIPNVSE+ L ++DE GII +GA
Sbjct: 723 IILSQRLVQDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEDVLADLDERGIIRIGA 782

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR+FN
Sbjct: 783 EVQGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVRVFN 842

Query: 947 RHGID 951
           R   D
Sbjct: 843 REDDD 847



 Score =  320 bits (821), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 97/329 (29%), Positives = 158/329 (48%), Gaps = 22/329 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F    E +++PDL+++Q  S++  +        R + G       L+     + PI 
Sbjct: 25  RVSFANIREPLEVPDLLDLQVQSFEWLVGDETWFQRRVDAGDENPVGGLEEVLSEISPIE 84

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T               +  +IK
Sbjct: 85  DFSGSMSLSFSDPRFDEVKASVEECKDKDMTYAAPLFVTAEFT---------NHTTGEIK 135

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K +Y+ +IIP
Sbjct: 136 SQTVFMGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDQSVDKT--TDKDVYSVKIIP 193

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I   F     ++ +   D 
Sbjct: 194 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTAEAIRERFGFSETLMATLEKDH 253

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+    
Sbjct: 254 TAGQDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLDLPF 313

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
             G+   EDIV      + + AG+     
Sbjct: 314 ESGVLTEEDIVTTIEYLVRLHAGEAEMPD 342


>gi|119511559|ref|ZP_01630667.1| DNA-directed RNA polymerase beta subunit [Nodularia spumigena
           CCY9414]
 gi|119463794|gb|EAW44723.1| DNA-directed RNA polymerase beta subunit [Nodularia spumigena
           CCY9414]
          Length = 1099

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 318/605 (52%), Positives = 430/605 (71%), Gaps = 8/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 196 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD +R +   DI+A +  L++L    G IDDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLSVPDTMRVLTPGDILAAVDYLINLEYDIGNIDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +G+V  D+  VY++A EE++   A  +  LDE+G      V 
Sbjct: 436 HARVNLYGFLETPFRPVENGRVRFDLPPVYMTADEEDDLRTATGDIPLDENGYIKGPQVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 496 VRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R  +G+ +        YRL K
Sbjct: 556 ERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKDGNSE------IRYRLSK 609

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N+++A+MPW GYN+ED+
Sbjct: 610 YQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNIVIAYMPWEGYNYEDA 669

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISE++V +DV+TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+ +DE GII +GA
Sbjct: 670 ILISEKLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQLDEQGIIRIGA 729

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 730 WVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRLFT 789

Query: 947 RHGID 951
           R   D
Sbjct: 790 REQGD 794



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 189/587 (32%), Positives = 273/587 (46%), Gaps = 66/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E        MV          +++  E+  R     
Sbjct: 541  MGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKDGN 600

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E   R            +++  ++ +G  V  G +L    + +G   +   + ++ A  
Sbjct: 601  SEIRYRLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEG-GELALGQNIVIAYM 659

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   V       ++ I+  +  +  E    +I  +  D   + 
Sbjct: 660  PWEGYNYEDAILISEKLVQDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQL 719

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DEQ I+    +    +IL G+    G         L   +  E  R              
Sbjct: 720  DEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 766

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMA
Sbjct: 767  -----VRDNSLRVPNGEKGRVVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMA 821

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DG+ VDIVLNPLGVPSRMNVGQ+FE  LGWA   LG +
Sbjct: 822  GRHGNKGIISRILPVEDMPYLADGSTVDIVLNPLGVPSRMNVGQVFECMLGWAAHTLGVR 881

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  +    +     ++     + W           
Sbjct: 882  FKITPFD---------------EMYGEETSRSIVHGKLQEARDETGKDWVY--------- 917

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                           + D  G+ +++DG TGEPFDRP+TVG  Y+LKL H+V DK++ARS
Sbjct: 918  ---------------NPDNPGKIMVFDGRTGEPFDRPITVGVAYILKLVHLVDDKIHARS 962

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +
Sbjct: 963  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNA 1022

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1023 IVKGKSIPRPGTPESFKVLMRELQSLGLDIAVHKVETQTDGSSLDVE 1069



 Score =  324 bits (830), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 106/481 (22%), Positives = 199/481 (41%), Gaps = 36/481 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 13  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGNNYKLKE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TYAV + +  RL+          K   DIKEQ +++GDLPLMT  GT
Sbjct: 63  PKYSVEESKRRDSTYAVQMYVPTRLL---------NKETGDIKEQEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L ++      +    DI+      
Sbjct: 231 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLSVPDTMRVLTPGDILAAVDYL 290

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+ +   ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 291 INLE-YDIGNIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +     G+  I  I+         +G +  +        +E   +   +      + 
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNLYGFLETPFRPVENGRVRFDLP 462

Query: 500 P 500
           P
Sbjct: 463 P 463


>gi|297730145|ref|ZP_06959263.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis KZN R506]
          Length = 1172

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 453/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ     N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMGQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSA G GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSAPGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1315), Expect = e-142,   Method: Composition-based stats.
 Identities = 190/517 (36%), Positives = 260/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +T E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENTPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|320532562|ref|ZP_08033369.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            171 str. F0337]
 gi|320135233|gb|EFW27374.1| DNA-directed RNA polymerase, beta subunit [Actinomyces sp. oral taxon
            171 str. F0337]
          Length = 1142

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 185/598 (30%), Positives = 276/598 (46%), Gaps = 59/598 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGP 858
                       ++    P  G   E    +    V       +  E      R     G 
Sbjct: 567  MGANMQRQAVPLIRPDAPLVGTGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGT 626

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF- 917
            E + +             ++  +   G  V  G +L        E  +   + LL A   
Sbjct: 627  ENVYKVAKFRRSNQGNCYNQRVVAAEGERVEVGSVLADGP-ATNEGDLALGQNLLVAFMT 685

Query: 918  --GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD--D 973
              G    D    S RV +    T + +        D    +  + R+   +        D
Sbjct: 686  WEGLNYEDAIIISQRVVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLD 745

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R      +++    + 
Sbjct: 746  ERGIIRIGAEVRSGDILVGKVTPKGETELTSEERLLRAIFGEKARE-VRDTSLRVPHGEY 804

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             + +   + + +    E               +P GV R+V+V++A +R I  GDK++GR
Sbjct: 805  GIVTGVREIDAASDDAE---------------LPAGVNRMVRVYIAQRRKITVGDKLSGR 849

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+ILP EDMPFL DGTPVD++LNPLGVPSRMNVGQ+ E HLGW          
Sbjct: 850  HGNKGVISKILPVEDMPFLADGTPVDVILNPLGVPSRMNVGQVLELHLGWVASR------ 903

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                      +   +  +    ++     + +   PV+TPVFDG
Sbjct: 904  ----------------------GWDATAAHEAGEAWTANLPENGIKAEPRTPVATPVFDG 941

Query: 1214 ADEEAINSMLRMA-----DLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              +  +  +L         L     +G++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 942  VRDNELMGLLNSTLPTSDGLQLVEPNGKARLFDGRSGEPFPYPISVGYMYILKLHHLVDD 1001

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1002 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAHALQELLTVKSDDVNGR 1061

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             +VYE+IV G D  E G PESF VL+KEMQ+L L+++  ++     A  +   D ++ 
Sbjct: 1062 VKVYEAIVKGEDIPEPGIPESFKVLMKEMQSLCLNVEALDAEGVAIALDDTDDDGSRA 1119



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 330/771 (42%), Positives = 469/771 (60%), Gaps = 61/771 (7%)

Query: 226 EEI--LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS--------SLVDIDTGEQV-- 273
           +EI  +  F   +  S     +  P   A+      ++            +  TGE    
Sbjct: 49  DEISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYVVADFENFSTGEIKSQ 108

Query: 274 ----------IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGE 319
                      + G  + +G  + +  + V+  G+  +        + + N       G 
Sbjct: 109 TVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEKATDKYVYNVKFIPSRGA 168

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-----------KNK 368
              E      ++    I     +D+ +  +    + + IR                 K  
Sbjct: 169 WL-EFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSALDEDRKIT 227

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            + +ALLDIY+ +RPG+  +     ++    +F+  +YDL+ VGR K+N +L L +    
Sbjct: 228 TQDEALLDIYKKIRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYKINKKLGLASDLTE 287

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI---------------DDIDNLGNRRVRSVGEMLKN 473
             +R EDI+A ++ L+ L  G  T+               DDID+LGNRR+R+VGE+++ 
Sbjct: 288 STLRIEDIVAALRYLLALHAGAETVEGVRDGEITEIAVEYDDIDHLGNRRIRAVGELIQA 347

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R G+ RMER ++ER+++ D++++ P  LIN +PV +A+ EFF +SQLSQ  +  N L+
Sbjct: 348 QVRTGMSRMERQVRERMTTQDVEAITPNTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLA 407

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG++R RA +E+RDVH +HYGR+CP E+ EG NIGL+ SL +F R+N
Sbjct: 408 GLTHKRRLSALGPGGLSRERASMEVRDVHTSHYGRMCPIESPEGPNIGLIGSLATFGRIN 467

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGE 652
            +GF+ETPYR V DG+VT++  YL+A +E+   IAQAN +L EDG F E+ V CR   GE
Sbjct: 468 PFGFVETPYRVVVDGRVTDETHYLTADDEDRHVIAQANVTLTEDGHFAEDHVLCRVTGGE 527

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             LVP  ++D +D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPL++ +AP VG
Sbjct: 528 PALVPSSQVDLMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLIRPDAPLVG 587

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  +G  +VA +AG+V +V A  + + + +G         ++Y++ KF+RSNQ
Sbjct: 588 TGMERRTAVDAGDVLVADKAGVVTEVCADFVRVANDDGTE-------NVYKVAKFRRSNQ 640

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             C NQR +   G+ V    ++ADGP+T+ GDLALG+N+LVAFM W G N+ED+++IS+R
Sbjct: 641 GNCYNQRVVAAEGERVEVGSVLADGPATNEGDLALGQNLLVAFMTWEGLNYEDAIIISQR 700

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V+ED+ TSIHIEE EV ARDTKLG EEITRDIPNVSEE L N+DE GII +GAEV  GD
Sbjct: 701 VVAEDMLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLDERGIIRIGAEVRSGD 760

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V  VR
Sbjct: 761 ILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPHGEYGIVTGVR 811



 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 90/292 (30%), Positives = 138/292 (47%), Gaps = 33/292 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDER------------PNEGLQAAFKSVFPITAFSGA 71
           +  P+L+ +Q  S+D  +      +                 GL+  F  + PI  F   
Sbjct: 1   MQAPNLLALQTESFDWLVGNERWRERMTAANKAHPGSLPETSGLEEIFDEISPIEDFGET 60

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F  + F+ PK+  ++C  +DLTY+ PL +                S  +IK Q+++
Sbjct: 61  MALSFHDHRFEEPKYTAEECQEKDLTYSAPLYV---------VADFENFSTGEIKSQTVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   + K +Y  + IP +G W
Sbjct: 112 MGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEK--ATDKYVYNVKFIPSRGAW 169

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D  D + VRIDR+RK  VT FL+ALGMD  EI   F  +P +  +   D      
Sbjct: 170 LEFEIDKSDRVAVRIDRKRKQDVTVFLLALGMDESEIRKEFADFPALTSALDEDRKITTQ 229

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             A L +  K       I  GE   +E+G+ L      + K   +  +G   
Sbjct: 230 DEALLDIYKK-------IRPGEPPSVEAGRTLLENFYFNPKRYDLAKVGRYK 274


>gi|34391555|gb|AAN65355.1| RpoB [Mycobacterium mageritense]
 gi|34391557|gb|AAN65356.1| RpoB [Mycobacterium mageritense]
          Length = 1178

 Score =  515 bits (1326), Expect = e-143,   Method: Composition-based stats.
 Identities = 188/515 (36%), Positives = 265/515 (51%), Gaps = 56/515 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGQRVEAGQVIADGPCTEN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 748  TSIHIEEH--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGK 805

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 806  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 854

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVD
Sbjct: 855  REDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVD 914

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I            +              
Sbjct: 915  IILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVADGTPDWASKLPEGLLSAP------ 967

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMADLDES 1231
                                  +   VSTPVFDGA E  +  +L            +D  
Sbjct: 968  ----------------------ADSIVSTPVFDGAQEGELAGLLGSTLPNRDGEVMVDGD 1005

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 1006 GKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1065

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+
Sbjct: 1066 QRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLL 1125

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1126 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1156



 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 325/677 (48%), Positives = 454/677 (67%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +         I+  
Sbjct: 192 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIV-- 249

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 250 ERFGFSEIMMGTLEKDSTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 309

Query: 410 TVGRVKMNMRLNLDT--PDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+              +DD
Sbjct: 310 RVGRYKVNKKLGLNAGQPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVEVDD 369

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 370 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 429

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 430 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETP 489

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS  D
Sbjct: 490 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVEGVVTDQIDYLTADEEDRHVVAQANSPTD 549

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F+E+ V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 550 ADGRFSEDRVMVRKKGGEVEFVAADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 609

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  +V+ +AG++E+V A  + + + +G    
Sbjct: 610 NMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVSDKAGVIEEVSADYVTVMADDGTR-- 667

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YR+ KF RSN  TC NQRP+V  G  V    +IADGP T+ G++ALG+N+LVA
Sbjct: 668 -----HTYRMRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTENGEMALGKNLLVA 722

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 723 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 782

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 783 DLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 842

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 843 ESGKVIGIRVFSREDDD 859



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 95/333 (28%), Positives = 154/333 (46%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  + K  E +++P L++VQ  S++  +  +       + G       L+     + PI 
Sbjct: 38  RVSYAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQNAVDRGEENPVGGLEEVLAELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDEVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMMGTLEKDS 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TAGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +  +     T     E   V   + L  +  
Sbjct: 318 KKLGLNAGQPITSSTLTEEDVVATIEYLVRLHE 350


>gi|227497159|ref|ZP_03927407.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
 gi|226833416|gb|EEH65799.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
          Length = 1142

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 183/594 (30%), Positives = 275/594 (46%), Gaps = 59/594 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGP 858
                       ++    P  G   E    +    V       +  E      R     G 
Sbjct: 567  MGANMQRQAVPLIRPDAPLVGTGMERRTAVDAGDVLVASKPGVVTEVCADFVRVANDDGS 626

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E + +             ++  +   G  V  G +L      +G   +   + LL A   
Sbjct: 627  ETVYKVAKFRRSNQGNCYNQRVVATEGEHVEAGSVLADGPATEG-GDLALGQNLLVAFMT 685

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             + ++  D  +     VS  ++       H +D  +  +  E     I  ++ +     D
Sbjct: 686  WEGLNYEDAIIVSQRVVSEDLLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLD 745

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R      +++    + 
Sbjct: 746  ERGIIRIGAEVRSGDILVGKVTPKGETELTSEERLLRAIFGEKARE-VRDTSLRVPHGEY 804

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             + +   +++ S    E               +P GV  +V+V++A +R I  GDK++GR
Sbjct: 805  GIVTGVREFDASNEDAE---------------LPAGVNHMVRVYIAQRRKITVGDKLSGR 849

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+I P EDMPFL DGTPVD++LNPLGVPSRMNVGQ+ E HLGW      +   
Sbjct: 850  HGNKGVISKINPIEDMPFLADGTPVDVILNPLGVPSRMNVGQVLELHLGWVAS---RGWD 906

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +             L +   K                              PV+TPVFDG
Sbjct: 907  ATAARKAGEEWAVRLPANGVKAEPR-------------------------TPVATPVFDG 941

Query: 1214 ADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              ++ +  +L     +  G        ++ L+DG +GEPF  P++VGY+Y+LKL+H+V D
Sbjct: 942  VRDDELMGLLSSTLPNRDGMQLIAPNGKARLFDGRSGEPFPYPISVGYMYILKLHHLVDD 1001

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDDV GR
Sbjct: 1002 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAHALQELLTVKSDDVNGR 1061

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             +VYE+IV G D  E G PESF VL+KEMQ+L L+++  ++        +   D
Sbjct: 1062 VKVYEAIVKGEDIPEPGIPESFKVLMKEMQSLCLNVEALDAEGNVIGLDDTDED 1115



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 335/779 (43%), Positives = 470/779 (60%), Gaps = 61/779 (7%)

Query: 226 EEI--LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS--------SLVDIDTGEQV-- 273
           EEI  +  F   +  S     +  P   A+      ++            +  TGE    
Sbjct: 49  EEISPIEDFGETMALSFHDHRFEEPKYTAEECQEKDLTYSAPLYVVADFENFQTGEIKSQ 108

Query: 274 ----------IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGE 319
                      + G  + +G  + +  + V+  G+  +        + + N       G 
Sbjct: 109 TVFMGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEKASDKYVYNVKFIPSRGA 168

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-----------KNK 368
              E     ++     I     +DI +  +    + + IR                 K  
Sbjct: 169 WL-EFEVDKNDHVAVRIDRKRKQDITVFLLALGMDESEIREEFKAYPALTSALDEDRKVT 227

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           ++ +ALLDIY+ +RPG+  +     ++    +F++ +YDL+ VGR K+N +L L      
Sbjct: 228 NQDEALLDIYKKIRPGEPPSVEAGRTLLENFYFNAKRYDLAKVGRYKINKKLGLAADLAD 287

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI---------------DDIDNLGNRRVRSVGEMLKN 473
             +R EDI+A IK L+ L  G  T+               DDID+LGNRR+R+VGE++++
Sbjct: 288 SVLRIEDIVAAIKYLLALHAGAETVEGVKDGEIVDIAVEFDDIDHLGNRRIRAVGELIQS 347

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R G+ RMER ++ER+++ D++++ P  LIN +PV +A+ EFF +SQLSQ  +  N L+
Sbjct: 348 QVRTGMSRMERQVRERMTTQDVEAITPNTLINIRPVTAAIKEFFGTSQLSQFMDQNNPLA 407

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RRLSALG GG++R RA +E+RDVH +HYGR+CP E+ EG NIGL+ SL +FAR+N
Sbjct: 408 GLTHKRRLSALGPGGLSRERASMEVRDVHTSHYGRMCPIESPEGPNIGLIGSLATFARIN 467

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGE 652
            +GF+ETPYR V +G+VT++  YL+A +E+   IAQAN  L EDG F E  V CR   GE
Sbjct: 468 PFGFVETPYRVVKNGQVTDETHYLTADDEDRHIIAQANVELTEDGHFAESHVLCRVTGGE 527

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             LVP   +D +D SP+Q+VS+  SLIPFLE+DD+NR LMG NMQRQAVPL++ +AP VG
Sbjct: 528 PALVPAGDVDLMDVSPRQMVSVGTSLIPFLEHDDANRALMGANMQRQAVPLIRPDAPLVG 587

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME   A  +G  +VA + G+V +V A  + + + +G          +Y++ KF+RSNQ
Sbjct: 588 TGMERRTAVDAGDVLVASKPGVVTEVCADFVRVANDDGSE-------TVYKVAKFRRSNQ 640

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             C NQR +   G+ V    ++ADGP+T+ GDLALG+N+LVAFM W G N+ED++++S+R
Sbjct: 641 GNCYNQRVVATEGEHVEAGSVLADGPATEGGDLALGQNLLVAFMTWEGLNYEDAIIVSQR 700

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +VSED+ TSIHIEE EV ARDTKLG EEITRDIPNVSEE L N+DE GII +GAEV  GD
Sbjct: 701 VVSEDLLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEETLANLDERGIIRIGAEVRSGD 760

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G  G V  VR F+    D
Sbjct: 761 ILVGKVTPKGETELTSEERLLRAIFGEKAREVRDTSLRVPHGEYGIVTGVREFDASNED 819



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 90/292 (30%), Positives = 137/292 (46%), Gaps = 33/292 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNI------------APDERPNEGLQAAFKSVFPITAFSGA 71
           +  P+L+ +Q  S+D  +                        GL+  F+ + PI  F   
Sbjct: 1   MQAPNLLALQTESFDWLVGNEKWRARVDAANSARPGSLPETSGLEEIFEEISPIEDFGET 60

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F  + F+ PK+  ++C  +DLTY+ PL +                   +IK Q+++
Sbjct: 61  MALSFHDHRFEEPKYTAEECQEKDLTYSAPLYV---------VADFENFQTGEIKSQTVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF++ G +R+VVSQL RSPG++F+    +   S K +Y  + IP +G W
Sbjct: 112 MGDFPLMTDKGTFIVNGSERVVVSQLVRSPGVYFERTTEK--ASDKYVYNVKFIPSRGAW 169

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D  D + VRIDR+RK  +T FL+ALGMD  EI   F  YP +  +   D      
Sbjct: 170 LEFEVDKNDHVAVRIDRKRKQDITVFLLALGMDESEIREEFKAYPALTSALDEDRKVTNQ 229

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             A L +  K       I  GE   +E+G+ L      + K   +  +G   
Sbjct: 230 DEALLDIYKK-------IRPGEPPSVEAGRTLLENFYFNAKRYDLAKVGRYK 274


>gi|325000500|ref|ZP_08121612.1| DNA-directed RNA polymerase subunit beta [Pseudonocardia sp. P1]
          Length = 1169

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 337/738 (45%), Positives = 473/738 (64%), Gaps = 30/738 (4%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +    ++          +                I+  E+V+ S    + G+        
Sbjct: 123 FVTAEFTNNTTGEIKSQTVFMGEFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDHSIDK 182

Query: 293 VKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                + S  +    G ++  D+   +T  + I+         L +        I     
Sbjct: 183 TTEKDVYSVKIIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTAEQIG---- 238

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  I  TL  D    + +ALLDIYR +RPG+  T   A+++   LFF   +YD++
Sbjct: 239 ERFGFSETIMTTLEKDNTAGQDEALLDIYRKLRPGEPPTRESAQALLENLFFKDKRYDMA 298

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI---------------D 454
            VGR K N +L LD  + V  + +ED+   I+ LV L  G+ T+               D
Sbjct: 299 KVGRYKANKKLGLDIENSVGTLTEEDVATTIEYLVRLHAGETTMSVGSGDSAREIPVETD 358

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R+VGE+++NQ R+GL R ER ++ER+++ D++++ PQ LIN +P+ +A+ 
Sbjct: 359 DIDHFGNRRLRTVGELIQNQVRVGLSRTERVVRERMTTQDVEAITPQTLINTRPITAAIR 418

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET
Sbjct: 419 EFFGTSQLSQFMDQHNPLAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIET 478

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL S+ARVN +GFIETPYRKV +G VT  + YL+A EE+   +AQAN+ L
Sbjct: 479 PEGPNIGLIGSLASYARVNPFGFIETPYRKVTEGVVTEQIDYLTADEEDRFVVAQANARL 538

Query: 635 DEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +EDGSF E+ V  R   GE  L+    +++ID SP+Q+VS+A ++IPFLE+DD+NR LMG
Sbjct: 539 NEDGSFAEDRVLVRRKGGEVDLISPTGVEYIDVSPRQMVSVATAMIPFLEHDDANRALMG 598

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQ+VPLL++E+P VGTGME   A  +G  +VA++AG+VE++ A  I +   EG   
Sbjct: 599 ANMQRQSVPLLRSESPLVGTGMELRAAVDAGDVVVAEQAGVVEELCADYITVMDDEGQRQ 658

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   YRL KF+RSNQ TC NQ+P+V  G  V    ++ADGP T+ G++ALG+N+LV
Sbjct: 659 -------TYRLNKFRRSNQGTCNNQKPIVDEGMRVEVGQVLADGPCTENGEMALGKNLLV 711

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A MPW G+N+ED++++S+R+V +DV TSIHIEE EV ARDTKLG EEITRDIPNVSE+ L
Sbjct: 712 AIMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEDVL 771

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP 
Sbjct: 772 ADLDERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPH 831

Query: 934 GVSGTVVDVRIFNRHGID 951
           G +G V+ +R+F+R   D
Sbjct: 832 GENGKVIGIRVFSRDDDD 849



 Score =  506 bits (1302), Expect = e-140,   Method: Composition-based stats.
 Identities = 183/540 (33%), Positives = 253/540 (46%), Gaps = 63/540 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  R             ++  I+  G  V  G +L      +    M   + L
Sbjct: 651  MDDEGQRQTYRLNKFRRSNQGTCNNQKPIVDEGMRVEVGQVLADGPCTEN-GEMALGKNL 709

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L AI   +  +  D  +     V   V+       H +D  +  +  E     I  ++ D
Sbjct: 710  LVAIMPWEGHNYEDAIILSQRLVQDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSED 769

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+      +  +IL G+    G         L   +  E  R         
Sbjct: 770  VLADLDERGIIRIGAEVQPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKV 829

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                   V  +                 ++      D++ PGV  +V+V+VA KR I  G
Sbjct: 830  PHGENGKVIGI-----------------RVFSRDDDDELAPGVNELVRVYVAQKRKISDG 872

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK+AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQI ETHLGW    
Sbjct: 873  DKLAGRHGNKGVIGKILPAEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK- 931

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +I+                                       +        +    +
Sbjct: 932  TGWEIEGQPEWASR-------------------------------MPEELYSVPADTKTA 960

Query: 1208 TPVFDGADEEAINSML--------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDGA E  I  +L            +   G++ L DG +GEP+  PV VGY+Y+LKL
Sbjct: 961  TPVFDGAREHEITGLLGSTLPNRDGERMVQPDGKAQLLDGRSGEPYPFPVAVGYMYILKL 1020

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKS
Sbjct: 1021 AHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKS 1080

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDVVGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S        +   +
Sbjct: 1081 DDVVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIEMRDADDE 1140



 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 99/353 (28%), Positives = 160/353 (45%), Gaps = 24/353 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN-------EGLQAAFKSVFPI 65
            R  F K  E +++PDL+++Q  SY+  +        R          GL+     + PI
Sbjct: 26  TRVTFAKISEPLEVPDLLDLQIQSYEWLVGSEAWFQRRIEAGDDLPVSGLEEILTEISPI 85

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             FSG+  L F    FD  K  V++C  +D+TY  PL +T               +  +I
Sbjct: 86  EDFSGSMSLSFSDPRFDEVKASVEECRDKDMTYGAPLFVTAEFT---------NNTTGEI 136

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MG+ P+MT  GTF+I G +R+VVSQL RSPG++FDH   +   + K +Y+ +II
Sbjct: 137 KSQTVFMGEFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDHSIDKT--TEKDVYSVKII 194

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F        +   D
Sbjct: 195 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTAEQIGERFGFSETIMTTLEKD 254

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSD 301
                  A   +            ++ + ++E+   K     + K  + K  K LG+  +
Sbjct: 255 NTAGQDEALLDIYRKLRPGEPPTRESAQALLENLFFKDKRYDMAKVGRYKANKKLGLDIE 314

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              G    ED+    T E  +         S+     +    +    +D   N
Sbjct: 315 NSVGTLTEEDV--ATTIEYLVRLHAGETTMSVGSGDSAREIPVETDDIDHFGN 365


>gi|300932744|ref|ZP_07148000.1| DNA-directed RNA polymerase subunit beta [Corynebacterium resistens
            DSM 45100]
          Length = 1170

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 187/513 (36%), Positives = 257/513 (50%), Gaps = 57/513 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L        +  M   + LL A    +  +  D  +     V   V+
Sbjct: 677  LVDEGDRVEAGQVLADGPGT-ADGEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVL 735

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  +  D     DE+ I+      R  +IL G+  
Sbjct: 736  TSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIIRIGADVRDGDILVGKVT 795

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 796  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 838

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+ PGV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DG
Sbjct: 839  RVFSREDDDDLAPGVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPAEDMPFLPDG 898

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LN  GVP RMN+GQ+ E HLGW     G K+ +   D K    +  L S L  V
Sbjct: 899  TPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWKVDTDSQDPKIQKMLETLPSELYDV 957

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                                           +TPVFDGA    ++ +LR +  +  G   
Sbjct: 958  PADSLT-------------------------ATPVFDGASNAELSGLLRSSRPNRDGIRL 992

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 993  VDDFGKAQLMDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1052

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF
Sbjct: 1053 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESF 1112

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
             VL+KE+Q+L L++++  +         +  D 
Sbjct: 1113 KVLLKELQSLCLNVEVLAADGTPMELSSDDDDE 1145



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 331/661 (50%), Positives = 457/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 198 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSEIMMSTLEK 253

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF   +YDL+ VGR K+N +L L  
Sbjct: 254 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKPKRYDLAKVGRYKVNRKLGLGA 313

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             +    + +EDI+  I+ LV L  G+ T+            DDID+ GNRR+R+VGE++
Sbjct: 314 DNEGTMTLTEEDILTTIEYLVRLHAGEKTMTSPEGVEIPIGTDDIDHFGNRRLRTVGELI 373

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 374 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 433

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 434 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 493

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V DG++T++V Y +A EE+   IAQAN+  DE+  FTE+ +  R   
Sbjct: 494 VNPFGFIETPYRRVVDGQITDEVHYFTADEEDRHVIAQANTPFDENHRFTEDAIEVRLRG 553

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 554 GDVEVVPVAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 613

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   +G  D          L KF+R+
Sbjct: 614 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDDGIRDTFM-------LRKFERT 666

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    ++ADGP T  G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 667 NQGTSYNQKPLVDEGDRVEAGQVLADGPGTADGEMALGKNLLVAFMPWEGHNYEDAIILN 726

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE E+ ARDTKLGPEEITRDIPNV E+ L ++DE GII +GA+V  
Sbjct: 727 QRMVEEDVLTSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIIRIGADVRD 786

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 787 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 846

Query: 951 D 951
           D
Sbjct: 847 D 847



 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 143/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 24  QRYSFAKIDAPIEVPGLLDLQRESFAWLIGSPEWRARAQAEAGEGARVTSGLEDILEELS 83

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      F+  K  +D+   +D+ YA PL +T                  
Sbjct: 84  PIEDYSENMSLTLSEPRFEDVKSTIDEAKDKDINYAAPLYVTAEFT---------NAMSG 134

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+  +
Sbjct: 135 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHGVK 192

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +  
Sbjct: 193 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSEIMMSTLE 252

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 253 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKPKRYDLAKVGRYKV 305

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    +     T E  +
Sbjct: 306 NRKLGLGADNEGTMTLTEEDIL 327


>gi|68536938|ref|YP_251643.1| DNA-directed RNA polymerase subunit beta [Corynebacterium jeikeium
            K411]
 gi|88909131|sp|Q4JT32|RPOB_CORJK RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|68264537|emb|CAI38025.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium jeikeium
            K411]
          Length = 1164

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 193/617 (31%), Positives = 272/617 (44%), Gaps = 58/617 (9%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              +L +  P+ G   E         M+  
Sbjct: 567  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPFVGTGMELRAAYDAGDMIIA 626

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     + +      G  +                ++  ++  G  V  G +L  
Sbjct: 627  PKAGVVEYVSADYITVMDDEGVRDTFMLRKFERTNQGTCYNQTPLVDEGDRVEAGQVLAD 686

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M   + LL A    +  +  D  +     V   V+       + ID  +  
Sbjct: 687  GPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVLTSIHIEEYEIDARDTK 745

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E     I  +  D     DE+ I+      R  +IL G+    G         L   
Sbjct: 746  LGPEEITRDIPNVGEDVLADLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRA 805

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E      +            ++   +  DD+  GV 
Sbjct: 806  IFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAAGVN 848

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTP+DI+LN  GVP RM
Sbjct: 849  EMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPIDIILNTHGVPRRM 908

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+     D K    +  L   L ++                
Sbjct: 909  NIGQVLEVHLGWLAKA-GWKVDPDSQDPKIQKMLETLPEELYEIPADSLT---------- 957

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA    ++ +LR +  +  G        +S L DG +GE
Sbjct: 958  ---------------ATPVFDGASNAELSGLLRSSLPNRDGERQVDDFGKSNLIDGRSGE 1002

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            PF  PV VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 1003 PFPYPVAVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1062

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L++++
Sbjct: 1063 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLNVEV 1122

Query: 1364 ENSRTKNSAKMEEIPDF 1380
              +         +  D 
Sbjct: 1123 LAADGTPMELSSDDDDE 1139



 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 336/661 (50%), Positives = 459/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSELMMSTLEK 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D V  + +EDI+  I+ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DTDGVMTLTEEDILTTIEYLVRLHAGEKSMTSPDGTEIPIDTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DG++T++V Y +A EE+   IAQAN+  DE+  FTEE +  R   
Sbjct: 488 VNPFGFIETPYRKVVDGQITDEVYYFTADEEDRHVIAQANTPFDENHRFTEERIEVRLRG 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 548 GDVEVVPYTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   EG  D          L KF+R+
Sbjct: 608 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDEGVRDTFM-------LRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ PLV  GD V    ++ADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 661 NQGTCYNQTPLVDEGDRVEAGQVLADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++DE GI+ +GA+V  
Sbjct: 721 QRMVEEDVLTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRD 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 86/322 (26%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +               D R   GL+   + + 
Sbjct: 18  QRHSFAKIDAPIEVPGLLDLQRESFAWLVGTPEWRARAQAEAGEDVRIMSGLEEILEELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 78  PIEDYSENMSLTLSEPRFDDVKSTIDEAKDKDINYAAPLYVTAEFT---------NSMSG 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L++ +
Sbjct: 129 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F    +   +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSELMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 247 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKAKRYDLAKVGRYKV 299

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D V   T E  +
Sbjct: 300 NRKLGLGGDTDGVMTLTEEDIL 321


>gi|269796264|ref|YP_003315719.1| DNA-directed RNA polymerase subunit beta [Sanguibacter keddieii DSM
            10542]
 gi|269098449|gb|ACZ22885.1| DNA-directed RNA polymerase subunit beta [Sanguibacter keddieii DSM
            10542]
          Length = 1170

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 189/508 (37%), Positives = 272/508 (53%), Gaps = 51/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  GA V  G +L        E  +     LL A    +  +  D  +     V   V+
Sbjct: 680  LVDEGARVEVGSVLADGP-ATDEGELALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 738

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL-LARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I   +    +D    LD     R+   +   + + G 
Sbjct: 739  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEDVLADLDERGIIRIGAEVSSGDVLVGK 796

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S +++E R       
Sbjct: 797  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGTVIEVR----TFN 845

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GD++P GV  +V+V++A +R I +GDK+AGRHGNKG++S ILP EDMPFL+DGTPVD
Sbjct: 846  REDGDELPAGVNELVRVYIAQRRKITAGDKLAGRHGNKGVISTILPVEDMPFLEDGTPVD 905

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNP+GVP RMNVGQ+ E HLGW     G  +        +                  
Sbjct: 906  IVLNPMGVPGRMNVGQVLEVHLGWIAAQ-GWDVDLATEGDLSWK---------------- 948

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                       ++V  VA   K   PV+TPVFDG  E A++ +L+    +          
Sbjct: 949  -----------ENVPAVASTSKPRNPVATPVFDGLQENALSGLLQSTLPNRDGARMVQPD 997

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF   V VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 998  GKARLFDGRSGEPFPEAVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1057

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G PESF VL+
Sbjct: 1058 QRFGEMEVWALEAYGAAYTLQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIPESFKVLL 1117

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    E   D
Sbjct: 1118 KEMQSLCLNVEVLSSDGVSIEMRESDDD 1145



 Score =  499 bits (1286), Expect = e-138,   Method: Composition-based stats.
 Identities = 337/695 (48%), Positives = 459/695 (66%), Gaps = 29/695 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S             +K +    I      G ++  +I   +   + ++         
Sbjct: 169 LVRSPGVYFERAADKTSDKDIFSAKIIPQR--GAWLEFEIDKRDAVGVRVDRKRKQSVTV 226

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +       +I     +       I +TL  D     ++AL+D+YR +RPG+  T    
Sbjct: 227 LLKALGLTESEI----REEFAAFPAILDTLEKDNVTTEEEALVDLYRKIRPGEPPTVEAG 282

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR----- 447
            S+    +F+S +YDL+ VGR K+N +L +D P     +   DI+  IK L  L      
Sbjct: 283 RSLLENFYFNSKRYDLAKVGRYKVNKKLGIDAPLADSVLTVTDIVKTIKYLAALHADVTA 342

Query: 448 ----------NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                       +   DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 343 LDGVKNGEAVEVRVETDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDVEA 402

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 403 IAPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 462

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N +GFIETPYRKV +GKV++DVVYL
Sbjct: 463 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINPFGFIETPYRKVENGKVSDDVVYL 522

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAA 676
           +A +E+   IAQAN+ L+EDGSF +E V  R   GE   V    +D++D SP+Q+VS+A 
Sbjct: 523 TADDEDRYVIAQANTELNEDGSFRQERVLVRTKGGETDDVLGSNVDYMDVSPRQMVSVAT 582

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           +LIPFLE+DD+NR LMG NMQRQAVPL+++EAPFVGTGME   A  +G  IVA + G+V 
Sbjct: 583 ALIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMERRAAIDAGDVIVATKPGVVT 642

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +V A  IV+ + +            YR  KF+RSNQ T  NQR LV  G  V    ++AD
Sbjct: 643 EVSADLIVVANDDATTTS-------YRAAKFRRSNQGTSYNQRVLVDEGARVEVGSVLAD 695

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GP+TD G+LALGRN+LVAFM W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKL
Sbjct: 696 GPATDEGELALGRNLLVAFMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKL 755

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITRDIPNVSE+ L ++DE GII +GAEV+ GD+LVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 756 GPEEITRDIPNVSEDVLADLDERGIIRIGAEVSSGDVLVGKVTPKGETELTPEERLLRAI 815

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA +VRDTSL+VP G SGTV++VR FNR   D
Sbjct: 816 FGEKAREVRDTSLKVPHGESGTVIEVRTFNREDGD 850



 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 96/302 (31%), Positives = 150/302 (49%), Gaps = 27/302 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA------------PDERPNEGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  L                  D     GL+  F+ 
Sbjct: 23  RVSFAKIFEPLEVPDLLGLQTDSFDWLLGNEKWRARVAAAMKLGTQDVPETSGLEEIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F  +  L F ++ F+PPK   ++C  +D TYA PL +T     ++         
Sbjct: 83  ISPIEDFGSSMSLSFSNHRFEPPKHTAEECKEKDFTYAAPLFVTAEFFNYN--------- 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K +++
Sbjct: 134 TGEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERAADKT--SDKDIFS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D + VR+DR+RK  VT  L ALG+   EI   F  +P I+ +
Sbjct: 192 AKIIPQRGAWLEFEIDKRDAVGVRVDRKRKQSVTVLLKALGLTESEIREEFAAFPAILDT 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              D       A   +           ++ G  ++E+    +    L K  + K  K LG
Sbjct: 252 LEKDNVTTEEEALVDLYRKIRPGEPPTVEAGRSLLENFYFNSKRYDLAKVGRYKVNKKLG 311

Query: 298 IT 299
           I 
Sbjct: 312 ID 313


>gi|17229086|ref|NP_485634.1| DNA-directed RNA polymerase subunit beta [Nostoc sp. PCC 7120]
 gi|20141699|sp|P22703|RPOB_ANASP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|17135414|dbj|BAB77960.1| RNA polymerase beta subunit [Nostoc sp. PCC 7120]
          Length = 1131

 Score =  515 bits (1325), Expect = e-143,   Method: Composition-based stats.
 Identities = 318/617 (51%), Positives = 428/617 (69%), Gaps = 14/617 (2%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 210 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 269

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD VR +   DI+A +  L++L    G+IDDID+LGNRRVRSVG
Sbjct: 270 GRVGRYKLNKKLRLSVPDTVRVLTSGDILAAVDYLINLEYDIGSIDDIDHLGNRRVRSVG 329

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 330 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 389

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 390 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 449

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +G+V  D    Y++A EE++  +A  +  +DE+G      V 
Sbjct: 450 HARVNQYGFLETPFRPVENGRVRFDQPAAYMTADEEDDLRVAPGDIPVDENGYIIGPQVP 509

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 510 VRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 569

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR------------SVEGDLDP 754
           E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R            +  G L  
Sbjct: 570 ERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDATEIRVRVSGQLPTASGKSTDNGQLTS 629

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y + K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N++VA
Sbjct: 630 QKGQEIRYTVSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNIVVA 689

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           +MPW GYN+ED++LISER+V +D++TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+
Sbjct: 690 YMPWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALR 749

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G
Sbjct: 750 QLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNG 809

Query: 935 VSGTVVDVRIFNRHGID 951
             G VVDVR+F R   D
Sbjct: 810 EKGRVVDVRLFTREQGD 826



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 183/528 (34%), Positives = 261/528 (49%), Gaps = 64/528 (12%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G E                +++  ++ +G  V  G +L    + +G   +   + ++ A 
Sbjct: 632  GQEIRYTVSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEG-GELALGQNIVVAY 690

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---K 971
               +  +  D  L     V   +       ++ I+  +  +  E    +I  +  D   +
Sbjct: 691  MPWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQ 750

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DEQ I+    +    +IL G+    G         L   +  E  R             
Sbjct: 751  LDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------ 798

Query: 1032 QRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                  ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKM
Sbjct: 799  ------VRDNSLRVPNGEKGRVVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKM 852

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGI+SRILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG 
Sbjct: 853  AGRHGNKGIISRILPIEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGHTLGV 912

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K    D               ++ G  S    +     ++     + W          
Sbjct: 913  RFKITPFD---------------EMYGEESSRRIVHGKLQEARDETGKDWVY-------- 949

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                            + D+ G+ ++YDG TGE FDRPVT+G  YMLKL H+V DK++AR
Sbjct: 950  ----------------NPDDPGKIMVYDGRTGEAFDRPVTIGVAYMLKLVHLVDDKIHAR 993

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     
Sbjct: 994  STGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALN 1053

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            +IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1054 AIVKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQADGSSLDVE 1101



 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 104/454 (22%), Positives = 193/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 27  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGHNYKLKE 76

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TYAV + +  RL+          K   DIKEQ +++GDLPLMT  GT
Sbjct: 77  PKYSVEEAKRRDSTYAVQMYVPTRLL---------NKETGDIKEQEVFIGDLPLMTDRGT 127

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 128 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 184

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 185 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 244

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L ++      +  + DI+      
Sbjct: 245 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLSVPDTVRVLTSGDILAAVDYL 304

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 305 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 363

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 364 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 418

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +     G+  I  I+         +G +  +
Sbjct: 419 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 450


>gi|282900416|ref|ZP_06308366.1| DNA-directed RNA polymerase, beta subunit [Cylindrospermopsis
           raciborskii CS-505]
 gi|281194729|gb|EFA69676.1| DNA-directed RNA polymerase, beta subunit [Cylindrospermopsis
           raciborskii CS-505]
          Length = 1113

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 328/695 (47%), Positives = 450/695 (64%), Gaps = 12/695 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +                +++    
Sbjct: 116 INGAERVIVNQIVRSPGVYYKSEIDKNGRRTYSASLIPNRGAWLKFETDRNDLVWVRIDK 175

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                    +    + D  IL  D++ +  Y + T+  +     ++ALL++YR +RPG+ 
Sbjct: 176 TRKLSIQVLLKALGLLDNEIL--DALRHPEYFQKTIEKEGQFSEEEALLELYRKLRPGEP 233

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T    + +    FFD  +YDL  VGR K+N +L L  PD  R +   DI++ +  L++L
Sbjct: 234 PTVMGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLSVPDTTRVLTPGDILSAVDYLINL 293

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+IDDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D + + P  L+N 
Sbjct: 294 EYDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNP 353

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HY
Sbjct: 354 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHY 413

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGF+ETP+R V +G+V  +   VY++A EE++
Sbjct: 414 GRICPIETPEGPNAGLIGSLATHARVNQYGFLETPFRPVENGRVCYEKPAVYMTADEEDD 473

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +  +D++G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+
Sbjct: 474 LRVAPGDIPVDDNGQILGIQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEH 533

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I 
Sbjct: 534 DDANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDATEIR 593

Query: 745 IRSVEG--------DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +R  E         +  P       Y L K+QRSNQ+TC+NQ+PLV++G++V    ++AD
Sbjct: 594 VRVKEKAALTNRESESIPHKPQEIKYVLSKYQRSNQDTCLNQKPLVRIGEKVIAGQVLAD 653

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G ST+ G+LALG+N++VA+MPW GYN+ED++LISER+V EDV+TSIHIE+FE+ AR TKL
Sbjct: 654 GSSTEGGELALGQNVIVAYMPWEGYNYEDAILISERLVQEDVYTSIHIEKFEIEARQTKL 713

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITR+IPNV E+ L+ +DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAI
Sbjct: 714 GPEEITREIPNVGEDALRQLDEQGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAI 773

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEKA DVRD SLRVP+G  G +VDVR+F R   D
Sbjct: 774 FGEKARDVRDNSLRVPNGEKGRIVDVRLFTREQGD 808



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 184/527 (34%), Positives = 260/527 (49%), Gaps = 64/527 (12%)

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E                +++  ++ +G +V  G +L    + +G   +   + ++ A  
Sbjct: 615  QEIKYVLSKYQRSNQDTCLNQKPLVRIGEKVIAGQVLADGSSTEG-GELALGQNVIVAYM 673

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   V       +  I+  +  +  E    +I  +  D   + 
Sbjct: 674  PWEGYNYEDAILISERLVQEDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDALRQL 733

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DEQ I+    +    +IL G+    G         L   +  E  R              
Sbjct: 734  DEQGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 780

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMA
Sbjct: 781  -----VRDNSLRVPNGEKGRIVDVRLFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMA 835

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG +
Sbjct: 836  GRHGNKGIISRILPLEDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFECLLGWAGHNLGVR 895

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  S    +     ++    ++ W           
Sbjct: 896  FKITPFD---------------EMYGEESSRRIVHGKLWEAREETSKDWVY--------- 931

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                           + +  G+ ++YDG TGEPFDR VTVG  YMLKL H+V DK++ARS
Sbjct: 932  ---------------NPENPGKIMVYDGRTGEPFDRAVTVGIAYMLKLVHLVDDKIHARS 976

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +
Sbjct: 977  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNA 1036

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1037 IVKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQTDGSSLDVE 1083



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 105/454 (23%), Positives = 194/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 13  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGHNYKLKE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TY V + +  RL+          K   DIKEQ +++GDLPLMT  GT
Sbjct: 63  PKYSVEESKRRDSTYGVQMYVPTRLL---------NKETGDIKEQEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+ +   L ALG+   EIL        +  +   +       A   +      
Sbjct: 171 VRIDKTRKLSIQVLLKALGLLDNEILDALRHPEYFQKTIEKEGQFSEEEALLELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q++ES         L +  + K  K L ++      +    DI++     
Sbjct: 231 GEPPTVMGGQQLLESRFFDPKRYDLGRVGRYKLNKKLRLSVPDTTRVLTPGDILSAVDYL 290

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 291 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +     G+  I  I+         +G +  +
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|148273815|ref|YP_001223376.1| DNA-directed RNA polymerase subunit beta [Clavibacter michiganensis
            subsp. michiganensis NCPPB 382]
 gi|182676558|sp|A5CUC7|RPOB_CLAM3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|147831745|emb|CAN02714.1| DNA-directed RNA polymerase beta chain [Clavibacter michiganensis
            subsp. michiganensis NCPPB 382]
          Length = 1162

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 179/515 (34%), Positives = 265/515 (51%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G+++      +    +   + LL A    +  +  D  +   + V    +
Sbjct: 676  LVSAGDRIEAGEVIADGPATEN-GELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDTL 734

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   +  + + R   + +E+I          L  D  DE+ I+      R  +IL G
Sbjct: 735  SSIHIEEY--EVDARDTKLGKEEITRDLPNVSPELLADL-DERGIIRIGAEVRPGDILVG 791

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   + +E  R                V   +        + + +
Sbjct: 792  KVTPKGETELSAEERLLRAIFNEKSREV--------RDTSLKVPHGEQGTIIGVKVFDSQ 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +        D++  GV + V VF+A KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 844  DGD--------DELGSGVNQRVVVFIAQKRKITEGDKLAGRHGNKGVISKILPVEDMPFL 895

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD++LNPLG+P RMN GQ+ ETHLGW     G +++                   
Sbjct: 896  ADGTPVDVILNPLGIPGRMNFGQVLETHLGWIAKQ-GWEVEGKPKWA------------- 941

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                              + +   A Q  +G  V+TPVFDGA EE I  +L         
Sbjct: 942  ------------------ERLPDHARQAPAGTKVATPVFDGALEEEIAGLLDSTTVTRDG 983

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  DRLIGSSGKTRLFDGRSGEPFPEPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVYEAIVKGENIQEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ ++  +  +  +   +
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSADGQAVSLRDTDDE 1138



 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 337/765 (44%), Positives = 478/765 (62%), Gaps = 43/765 (5%)

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA---KVSSSLVDIDTGEQVIESG 277
           LG  +  +    Y      +RG  +  PL      +     ++ +  V +     + E G
Sbjct: 91  LGFTNPYLEEQKYSIDECKERGKTYSAPLYVEAEFMNHLTGEIKTQTVFMGDFPLMTEKG 150

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGEIYI 322
             + +G  + +  + V+  G+  +        +DI +                +  ++ +
Sbjct: 151 TFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQVGV 210

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
                  +     +    +    IL  +     A I  TL  D    +++AL DIYR +R
Sbjct: 211 RIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYRKLR 268

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
           PG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A IK 
Sbjct: 269 PGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILATIKY 328

Query: 443 LVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++
Sbjct: 329 LVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVR 388

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG G
Sbjct: 389 ERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPG 448

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N++GFIETPYR+V D
Sbjct: 449 GLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINSFGFIETPYRRVVD 508

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDA 666
           G VT+ + YL+A EE+   +AQAN+ L +D  F E+ V  R   GE  LV +E + ++D 
Sbjct: 509 GVVTDTIDYLTASEEDEFLVAQANAPLTKDFRFAEDRVLVRPKGGEVELVAKENVHYMDV 568

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SP+Q+VS+A SLIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTGME   A  +G  
Sbjct: 569 SPRQMVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTGMEGYAAIDAGDV 628

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           + A  +G+V++V A  + I+  EG       G   Y L KF RSNQ T  N R LV  GD
Sbjct: 629 LTADASGVVQEVSAEVVTIQLDEG-------GTQTYYLRKFDRSNQGTSYNHRVLVSAGD 681

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            +   ++IADGP+T+ G+LALG+N+LVAFMPW G+NFED++++S+ +V +D  +SIHIEE
Sbjct: 682 RIEAGEVIADGPATENGELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDTLSSIHIEE 741

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +EV ARDTKLG EEITRD+PNVS E L ++DE GII +GAEV PGDILVGK+TPKGE+ +
Sbjct: 742 YEVDARDTKLGKEEITRDLPNVSPELLADLDERGIIRIGAEVRPGDILVGKVTPKGETEL 801

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + EE+LLRAIF EK+ +VRDTSL+VP G  GT++ V++F+    D
Sbjct: 802 SAEERLLRAIFNEKSREVRDTSLKVPHGEQGTIIGVKVFDSQDGD 846



 Score =  331 bits (849), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 93/310 (30%), Positives = 145/310 (46%), Gaps = 27/310 (8%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEG 54
            NG    R  F K  + + +PDL+ +Q  S+D  +  +                   N G
Sbjct: 12  QNGRDASRLSFAKITDTLTVPDLLALQTESFDWLVGSDAWKRRVEEGTAQGRTDLALNSG 71

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           L+  F+ + PI        L F +   +  K+ +D+C  R  TY+ PL +         +
Sbjct: 72  LEEIFEEISPIEDLGETMQLGFTNPYLEEQKYSIDECKERGKTYSAPLYV---------E 122

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                    +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   
Sbjct: 123 AEFMNHLTGEIKTQTVFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT-- 180

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-- 232
           S K +Y+ R+IP +G W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F  
Sbjct: 181 SDKDIYSARVIPSRGAWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKG 240

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKE 290
              I  +   D       A   +         V  +    ++++         L K  + 
Sbjct: 241 VASIELTLEKDSILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRY 300

Query: 291 KGVKFLGITS 300
           K  + LGI  
Sbjct: 301 KINRKLGIDK 310


>gi|170078649|ref|YP_001735287.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. PCC
           7002]
 gi|169886318|gb|ACB00032.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp. PCC
           7002]
          Length = 1103

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/634 (52%), Positives = 441/634 (69%), Gaps = 20/634 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A  + D + L+ + H+                 + + TL  + N   ++ALL++YR
Sbjct: 179 VLLKAMGLSDSEILDALRHA----------------DFYQKTLEKEGNPSEEEALLELYR 222

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  T S  + +    FFD+ +YDL  VGR K+N +L L+ PD VR +   DI++ 
Sbjct: 223 KLRPGEPPTVSGGQQLLESRFFDNKRYDLGKVGRYKINKKLRLNIPDTVRVLTPTDILSA 282

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I  L++L    G IDDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + D++ 
Sbjct: 283 IDYLINLEFDTGNIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADTLT 342

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  L+N KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +R
Sbjct: 343 PASLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVR 402

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYL 617
           D+HPT YGRICP ET EG N GL+ SL ++ARVN YGFIETPY KV +GK+  D   VYL
Sbjct: 403 DIHPTQYGRICPVETPEGPNAGLIGSLATYARVNEYGFIETPYYKVENGKILFDQGSVYL 462

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE++  +A  +   DEDG+   E V  R   E      E++D++  SP Q+VS+A S
Sbjct: 463 TAGEEDDLRVAPGDVPRDEDGNILGETVPVRYRREFSTTTPEQVDYVAVSPLQIVSVATS 522

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  
Sbjct: 523 LIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRCDGVVTF 582

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA   VIR          +   +Y L K+QRSNQ+TC+NQRPLV +G++V    ++ADG
Sbjct: 583 VDAT--VIRVQPTGEGTEDAAEIVYPLQKYQRSNQDTCLNQRPLVDIGEDVVAGQVLADG 640

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            +T+ G++ALG+N+ +A+MPW GYN+ED++LISER+V +DV+TSIHIE+FE+ AR TKLG
Sbjct: 641 SATEGGEIALGQNVTIAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLG 700

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEITR+IPNV E+ L+++DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIF
Sbjct: 701 PEEITREIPNVGEDALRHLDEQGIIRIGAWVESGDILVGKVTPKGESDQPPEEKLLRAIF 760

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 761 GEKARDVRDNSLRVPNGEKGRVVDVRVFTREQGD 794



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 191/591 (32%), Positives = 263/591 (44%), Gaps = 70/591 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP- 858
                       +L    P  G   E        MV       +       + R    G  
Sbjct: 537  MGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRCDGVVTFVDATVIRVQPTGEG 596

Query: 859  -----EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                 E +              +++  ++ +G +V  G +L      +G   +   + + 
Sbjct: 597  TEDAAEIVYPLQKYQRSNQDTCLNQRPLVDIGEDVVAGQVLADGSATEG-GEIALGQNVT 655

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD- 970
             A    +  +  D  L     V   V       +  I+  +  +  E    +I  +  D 
Sbjct: 656  IAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDA 715

Query: 971  --KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DEQ I+    +    +IL G+    G         L   +  E  R          
Sbjct: 716  LRHLDEQGIIRIGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD--------- 766

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                     ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ G
Sbjct: 767  ---------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVG 817

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKGI+SRILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   
Sbjct: 818  DKMAGRHGNKGIISRILPIEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGEH 877

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L  + K +  D     + S      +         +                        
Sbjct: 878  LNARFKMMPFDEMHGAEASRETVHGKIREAAKKPNKDW---------------------- 915

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              VF+                DE G+  +YDG TGE FDR VTVG  YMLKL H+V DK+
Sbjct: 916  --VFNE---------------DEPGKIQVYDGRTGESFDRAVTVGKAYMLKLVHLVDDKI 958

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR  
Sbjct: 959  HARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNE 1018

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
               +IV G      GTPESF VL++E+Q+LGL I +      +     ++ 
Sbjct: 1019 ALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVEAADDGTSRDVE 1069



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 102/437 (23%), Positives = 185/437 (42%), Gaps = 40/437 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLI++Q++S+  FL           +GL     S  PIT ++G   L F+   Y    
Sbjct: 9   LPDLIDIQRSSFRWFL----------EKGLIEELNSFSPITDYTGKLELHFIGEKYRLKE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ + +   RD TY V + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 59  PKYSMSEAKSRDSTYGVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +    G+  Y+  +IP++G W+  E D  +I+ 
Sbjct: 110 FIINGAERVIVNQIVRSPGVYYKSEVDKH---GRRTYSASLIPNRGAWLKFETDKNNIVW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILST-----FYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VRID+ RK+     L A+G+   EIL       FY K   +   +       A   +   
Sbjct: 167 VRIDKTRKLSAQVLLKAMGLSDSEILDALRHADFYQK---TLEKEGNPSEEEALLELYRK 223

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ES         L K  + K  K L +       +    DI++  
Sbjct: 224 LRPGEPPTVSGGQQLLESRFFDNKRYDLGKVGRYKINKKLRLNIPDTVRVLTPTDILSAI 283

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              I +E  D  +   ++ + +  +R +  L  + V         ++ ++    +   L 
Sbjct: 284 DYLINLE-FDTGNIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADTLT 342

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
              ++ P      +  +  F            + +  +    RL+   P     + +E  
Sbjct: 343 PASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERA 397

Query: 437 IAIIKILVDLRNGKGTI 453
              ++ +   + G+   
Sbjct: 398 GFAVRDIHPTQYGRICP 414


>gi|284992886|ref|YP_003411440.1| DNA-directed RNA polymerase subunit beta [Geodermatophilus obscurus
           DSM 43160]
 gi|284066131|gb|ADB77069.1| DNA-directed RNA polymerase, beta subunit [Geodermatophilus
           obscurus DSM 43160]
          Length = 1169

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/660 (50%), Positives = 455/660 (68%), Gaps = 28/660 (4%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +      G+ +        T  + ++A     E  + E F      +  L       
Sbjct: 221 EFDVDKRDTVGVRIDRKRRQPVT--VLLKALG-WTEDRIREHFQWSPTVLATL------- 270

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                     D    + +ALLDIYR +RPG+  T   A+++   LFF+  +YDL+ VGR 
Sbjct: 271 --------EKDHIAGQDEALLDIYRKLRPGEPPTRESAQALLENLFFNGKRYDLAKVGRY 322

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT--IDDIDNLGNRRVRSVGEMLK 472
           K+N +L +D P     + ++DI+A I+ +V L  G+    +DDID+ GNRR+R+VGE+++
Sbjct: 323 KVNKKLGVDVPQATLTLTEDDIVATIEYVVRLHAGEPDHGVDDIDHFGNRRLRTVGELIQ 382

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQLSQ  +  N L
Sbjct: 383 NQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPL 442

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+++ RV
Sbjct: 443 AGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSAYGRV 502

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           NA+GFIETPYR+V +G VT+ + YL+A EE+   +AQANS LD  G F E+ V  R   G
Sbjct: 503 NAFGFIETPYRRVQNGVVTDTIDYLTADEEDRFVVAQANSPLDAQGRFAEDRVLVRTKGG 562

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E   +  E +D++D SP+Q+ S+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAP V
Sbjct: 563 EVDYLVPENVDYMDVSPRQMTSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPLV 622

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  +VA++AG+VE   A  + + + +G           YRL+KF+RSN
Sbjct: 623 GTGMELRAAVDAGDVVVAEKAGVVEDSTADYVTVMADDGTRQ-------TYRLLKFRRSN 675

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q T +NQ P+V  G  V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED++++S+
Sbjct: 676 QGTSINQTPVVDEGQRVEVGQVIADGPCTDEGEMALGKNLLVAFMPWEGHNYEDAIILSQ 735

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV +SIHIEEFEV ARDTKLG EEITRDIPNVSEE L ++DE GII +GAEV PG
Sbjct: 736 RLVQDDVLSSIHIEEFEVDARDTKLGAEEITRDIPNVSEEVLADLDERGIIRIGAEVVPG 795

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+V  G SG V+ VR+F+R   D
Sbjct: 796 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVKHGESGKVIGVRVFSREDGD 855



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 182/540 (33%), Positives = 262/540 (48%), Gaps = 69/540 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R +         +I++  ++  G  V  G ++        E  M   + LL A
Sbjct: 660  DGTRQTYRLLKFRRSNQGTSINQTPVVDEGQRVEVGQVIADGPCT-DEGEMALGKNLLVA 718

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI--------ELL 967
                +  +  D  +     V   V+          + + R   +  E+I        E +
Sbjct: 719  FMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEF--EVDARDTKLGAEEITRDIPNVSEEV 776

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
              D  DE+ I+         +IL G+    G         L   +  E  R         
Sbjct: 777  LADL-DERGIIRIGAEVVPGDILVGKVTPKGETELTPEERLLRAIFGEKAR--------- 826

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    E      +            ++   + GD++P GV  +++V+VA  R I  G
Sbjct: 827  --------EVRDTSLKVKHGESGKVIGVRVFSREDGDELPAGVNELIRVYVAQMRKISDG 878

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK+AGRHGNKG++++ILP EDMPFL+DGTPVDIVLNPLGVP RMNVGQ+ ETHLGW    
Sbjct: 879  DKLAGRHGNKGVIAKILPQEDMPFLEDGTPVDIVLNPLGVPGRMNVGQVLETHLGWVAKS 938

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +++                                       +   A     G   +
Sbjct: 939  -GWQVEGTPEWAVN-------------------------------LPDPARAAGPGTRTA 966

Query: 1208 TPVFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDGA EE I  +L     +          G++ L+DG +GEPF   ++VGY+Y+LKL
Sbjct: 967  TPVFDGAREEEIVGLLGSTIPNRDGNRMVQPTGKARLFDGRSGEPFPEAISVGYVYILKL 1026

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKS
Sbjct: 1027 LHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYALQELLTIKS 1086

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DD++GR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +   +     +   +
Sbjct: 1087 DDILGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSGDGQAIELRDTDDE 1146



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 109/470 (23%), Positives = 204/470 (43%), Gaps = 30/470 (6%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL-----MMNIAPDERPNE--GLQAAFKSVFPI 65
           +R  F K  E +++PDL+ +Q AS+D  +        ++P+E+ +   GL    + + PI
Sbjct: 45  LRVSFAKISEPLEVPDLLALQTASFDWLIGSPTWRATLSPEEQADAVGGLAEILEEISPI 104

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             FSG+  L F +  F+  K  +++C  +D+TYA PL +T   +           +  +I
Sbjct: 105 EDFSGSMSLSFSNPRFEDVKASLEECKDKDMTYAAPLFVTAEFM---------NNTTGEI 155

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MGD P+MT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++ ++I
Sbjct: 156 KSQTVFMGDFPIMTNKGTFVINGTERVVVSQLVRSPGVYFDKTLDKT--SDKDVFSAKVI 213

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG   + I   F   P ++ +   D
Sbjct: 214 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEDRIREHFQWSPTVLATLEKD 273

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSD 301
                  A   +            ++ + ++E+         L K  + K  K LG+   
Sbjct: 274 HIAGQDEALLDIYRKLRPGEPPTRESAQALLENLFFNGKRYDLAKVGRYKVNKKLGVDVP 333

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVID-EKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                   +DIV      + + AG+       ++   +  +R +  L  + +        
Sbjct: 334 QATLTLTEDDIVATIEYVVRLHAGEPDHGVDDIDHFGNRRLRTVGELIQNQIRVGLSRME 393

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +V ++   +   +  I            +  +  F            + +  +    RL
Sbjct: 394 RVVRERMTTQD--VEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRL 451

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +   P     + +E     ++ +     G+  +  I+      +  +G +
Sbjct: 452 SALGPGG---LSRERAGMEVRDVHPSHYGR--MCPIETPEGPNIGLIGSL 496


>gi|313657472|ref|ZP_07814352.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis KZN V2475]
          Length = 1172

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 331/662 (50%), Positives = 454/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 203 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 259 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 318

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 319 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 378

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ     N
Sbjct: 379 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMYQNN 438

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 439 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 498

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 499 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 558

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 559 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 618

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 619 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 671

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 672 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 731

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 732 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 791

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 792 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 851

Query: 950 ID 951
            D
Sbjct: 852 ED 853



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 905  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 954

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 955  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 995

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 996  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1055

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1056 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1115

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1116 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1152



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 32  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 91

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 92  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 142

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 143 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 200

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 201 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 260

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 261 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 311

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 312 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 344


>gi|184200247|ref|YP_001854454.1| DNA-directed RNA polymerase subunit beta [Kocuria rhizophila DC2201]
 gi|183580477|dbj|BAG28948.1| DNA-directed RNA polymerase beta subunit [Kocuria rhizophila DC2201]
          Length = 1169

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 181/512 (35%), Positives = 259/512 (50%), Gaps = 63/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V P  ++    +      +   + LL A    + ++  D  +     VS  V+
Sbjct: 685  IVSEGQRVEPRTVIADGPST-DHGELALGKNLLIAYMSWEGLNYEDAIILSQRMVSEDVL 743

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      +  +IL G+  
Sbjct: 744  TSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLSALDERGIIHIGAEVQAGDILVGKVT 803

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                V   +        + +   ++
Sbjct: 804  PKGETELTPEERLLRAIFGEKSREV--------RDTSLKVPHGESGTVIGVRVFDREDED 855

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                    DD+P GV +VV+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPF++DG
Sbjct: 856  --------DDLPAGVNQVVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFMEDG 907

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVP RMN+GQ+ E H GW     G  I+      K   +           
Sbjct: 908  TPVDVILNPLGVPGRMNLGQVLEVHTGWLAKQ-GWNIEGDPEWLKGLSNFPKS------- 959

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                                          V+TPVFDGA E+ I  +L   +        
Sbjct: 960  -------------------------TGPTNVATPVFDGAREDEIFDLLDHTNPTRDGQRL 994

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +  SG++ L+DG +G+PF  PV+VGY Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 995  IGRSGKAKLFDGRSGQPFPDPVSVGYQYILKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1054

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR +VYE+IV G +  E G PESF
Sbjct: 1055 QFGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDVHGRVKVYEAIVKGENIPEPGVPESF 1114

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KEMQ+L L++++ ++        +   D
Sbjct: 1115 KVLIKEMQSLCLNVEVLSADGNAVEMRDSDDD 1146



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 336/639 (52%), Positives = 451/639 (70%), Gaps = 30/639 (4%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +      +  IL  +       IR TL  D  + R++ALLDIYR +RPG+  T   A+S+
Sbjct: 228 LKALGWSESKIL--EEFGEFDSIRATLEKDATETREEALLDIYRKLRPGEPPTVDAAQSL 285

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTP---DDVRHIRKEDIIAIIKILVDLRNG--- 449
            + ++F+  +YDL+ VGR K+N +L LD P    D   +  +DI+A+I+ LV L +G   
Sbjct: 286 LDNMYFNPKRYDLAKVGRYKLNRKLGLDKPFTDPDASVLSLDDIVAMIRYLVTLHDGGST 345

Query: 450 ------------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D+++
Sbjct: 346 MPGTRDGESREIHVDVDDIDHFGNRRIRAVGELIENQIRTGLSRMERVVRERMTTQDVEA 405

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E
Sbjct: 406 ITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGME 465

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHP+HYGR+CP ET EG NIGL+ SL ++AR+N +GFIETPYRKV DG VT+DVVYL
Sbjct: 466 VRDVHPSHYGRMCPIETPEGSNIGLIGSLATYARINPFGFIETPYRKVVDGTVTDDVVYL 525

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG---EEILVPREKIDFIDASPKQVVSI 674
           +A +E    IAQAN+ L EDG F E+ V  R +    E +LV  E I+F+D SP+Q+VS+
Sbjct: 526 TADDERGLTIAQANAPLTEDGHFAEDAVLSRASDGSGEAVLVAPEDIEFMDVSPRQMVSV 585

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A +LIP+LE+DD+NR LMG NMQRQAVPLL +EAP VGTGME   A  +G +++A + G+
Sbjct: 586 ATALIPYLEHDDANRALMGANMQRQAVPLLTSEAPLVGTGMERYSALDAGDSVLATKPGV 645

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           VE+V A  + + + +G          +Y + KF RSN     NQR +V  G  V    +I
Sbjct: 646 VEEVSADLVTVLNDDGT-------TKLYPINKFVRSNPGNTYNQRVIVSEGQRVEPRTVI 698

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD G+LALG+N+L+A+M W G N+ED++++S+RMVSEDV TSIHIEE E+ ARDT
Sbjct: 699 ADGPSTDHGELALGKNLLIAYMSWEGLNYEDAIILSQRMVSEDVLTSIHIEEHEIDARDT 758

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLG EEITRDIPNVSEE L  +DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLR
Sbjct: 759 KLGAEEITRDIPNVSEEVLSALDERGIIHIGAEVQAGDILVGKVTPKGETELTPEERLLR 818

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           AIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D +
Sbjct: 819 AIFGEKSREVRDTSLKVPHGESGTVIGVRVFDREDEDDD 857



 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 93/315 (29%), Positives = 144/315 (45%), Gaps = 31/315 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL------------MMNIAPDERPNEGLQAAFKS 61
           R  F K  E +D+P+L+ +Q  S+D  +                        GL   F+ 
Sbjct: 23  RVSFAKIHEPLDVPNLLALQTDSFDRLVGNERWQARVVEAQETGDTSVSTTSGLSDIFEE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F G   L F   EF  PK+ +D+C  RD TY+ PL +    +           +
Sbjct: 83  ISPIEDFQGTMSLSFSEPEFYDPKYTMDECKDRDATYSAPLYVKAEFM---------NNN 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK+Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG +F+  + R   S K +Y+
Sbjct: 134 TGEIKQQTVFMGDFPLMTDKGTFVINGSERVVVSQLVRSPGAYFEKGQDRT--SDKDIYS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W ++E D +D + VR+DR+RK  VT  L ALG    +IL  F         
Sbjct: 192 AKIIPSRGAWFELEIDKRDQVGVRLDRKRKQSVTVLLKALGWSESKILEEFGEFDSIRAT 251

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +       +  GE   +++ + L   +  + K   +  +G   
Sbjct: 252 LEKDATETREEALLDIYR------KLRPGEPPTVDAAQSLLDNMYFNPKRYDLAKVGRYK 305

Query: 301 -DCLCGLYVAEDIVN 314
            +   GL       +
Sbjct: 306 LNRKLGLDKPFTDPD 320


>gi|225020322|ref|ZP_03709514.1| hypothetical protein CORMATOL_00329 [Corynebacterium matruchotii ATCC
            33806]
 gi|224946711|gb|EEG27920.1| hypothetical protein CORMATOL_00329 [Corynebacterium matruchotii ATCC
            33806]
          Length = 1187

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 179/512 (34%), Positives = 255/512 (49%), Gaps = 59/512 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M     LL A    +  +  D  +     V   ++
Sbjct: 698  LVDEGDRVEEGQVVADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 756

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKD-----DEQVILDRNIYSRLMEILCGQNA 995
                  +H ID  +  +  E    E+L   +D     DE+ I+      R  +IL G+  
Sbjct: 757  TSIHIEQHEIDARDTKLGAEEITREILNVSEDVLKDLDERGIVRIGADVRDGDILVGKVT 816

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 817  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 859

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DG
Sbjct: 860  RRFSREDEDDLGPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDG 919

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQ+ E HLGW     G K+                       
Sbjct: 920  TPVDVILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKVDV--------------------- 957

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                   +  +    +++        +G   +TPVFDGA  + I  +L  +  +  G   
Sbjct: 958  ------NDPANAKLLETLPEDLYDVPAGSLTATPVFDGATNDEIAGLLANSLPNRDGDVM 1011

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 1012 VNADGKAQLFDGRSGEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1071

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF
Sbjct: 1072 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESF 1131

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KE+Q+L L++++ ++            D
Sbjct: 1132 KVLLKELQSLCLNVEVLSADGTPMELSGSDDD 1163



 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 327/661 (49%), Positives = 453/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  + +TL  
Sbjct: 219 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTEQIV--ERFGFSEIMMSTLEN 274

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF   +YDL+ VGR K N +L L  
Sbjct: 275 DGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLGG 334

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             D +  + +EDI   I+ LV L  G+ ++            DDID+ GNRR+R+VGE++
Sbjct: 335 DHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEIIPVETDDIDHFGNRRLRTVGELI 394

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF SSQLSQ  +  NS
Sbjct: 395 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGSSQLSQFMDLNNS 454

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 455 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 514

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN++GFIETPYRKV DG VT++V YL+A EE+   +AQAN+  DE+G  TE+ V  R   
Sbjct: 515 VNSFGFIETPYRKVVDGVVTDEVDYLTADEEDRYVVAQANTKFDENGVITEDRVTVRLKK 574

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V  + I+++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP 
Sbjct: 575 GDIQVVDGKDINYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPL 634

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I++K+AG+VE V A  I I   +G  D        Y L KF+R+
Sbjct: 635 VGTGMELRAAYDAGDLIISKKAGVVETVCADYITIMGDDGVRD-------TYMLRKFERT 687

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    ++ADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 688 NQGTSYNQKPLVDEGDRVEEGQVVADGPGTHNGEMALGRNLLVAFMPWEGHNYEDAIILN 747

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIE+ E+ ARDTKLG EEITR+I NVSE+ LK++DE GI+ +GA+V  
Sbjct: 748 QRLVEEDILTSIHIEQHEIDARDTKLGAEEITREILNVSEDVLKDLDERGIVRIGADVRD 807

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR F+R   
Sbjct: 808 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRRFSREDE 867

Query: 951 D 951
           D
Sbjct: 868 D 868



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 97/389 (24%), Positives = 174/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K    I++P L+++Q  S+   +            +  D R   GL+   + + 
Sbjct: 45  ERKSFAKIQSPIEVPGLLDIQLESFAWLIGSPEWRARRQAELGEDVRVTSGLEDILEELS 104

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 105 PIQDYSGNMSLSLSEPRFEEMKNSIDECKDKDINYSAPLYVTAEFI---------NNETQ 155

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 156 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 213

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +  
Sbjct: 214 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIVERFGFSEIMMSTLE 273

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L K  + K  + LG+ 
Sbjct: 274 NDGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLG 333

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+V E  +   TGEI       ++   ++   +  +R
Sbjct: 334 GDHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEII-----PVETDDIDHFGNRRLR 388

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 389 TVGELIQNQVRVGLSRMERVVRERMTTQD 417


>gi|294790442|ref|ZP_06755600.1| DNA-directed RNA polymerase, beta subunit [Scardovia inopinata F0304]
 gi|294458339|gb|EFG26692.1| DNA-directed RNA polymerase, beta subunit [Scardovia inopinata F0304]
          Length = 1189

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 182/527 (34%), Positives = 268/527 (50%), Gaps = 45/527 (8%)

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                    +   ++  ++  G  V  G +L        +  +   + LL A       + 
Sbjct: 670  TKFQRSNQMTCYNQVPLVSQGERVEEGSVLADGP-ATDQGEIALGKNLLVAFMPWNGYNY 728

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +     +S  +V     +   I++ E      +   E + RD  +       N+  
Sbjct: 729  EDAVI-----ISQRLVRDDTLSSIHIEEFEIDARETKLGSEEITRDLPNVSEDAVANLDD 783

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R   +  G    +G     K T      ++   R     F  +  +V+     +      
Sbjct: 784  R-GIVRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGERG 842

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            +   +++  K + E  + GD++P GV ++++V++A  R I  GDK++GRHGNKG++SRIL
Sbjct: 843  TVISIKEITKEEAE--EAGDELPTGVNQMIRVYIAQHRKITQGDKLSGRHGNKGVISRIL 900

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLGW     G  I            
Sbjct: 901  PEEDMPFLADGTPIDIMLNPLGVPSRMNLGQVLELHLGWIA-HSGWDISIDP-------- 951

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                +       +   AE+   G  V+TPVFDG   +A++ +L 
Sbjct: 952  -------------------DLEAEWKKHIPAGAEKGDPGSHVATPVFDGVRTDAMHGLLH 992

Query: 1225 MADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                D  G        ++ L+DG TGEPF +P++VGY+YMLKL+H+V DK++ARSTG YS
Sbjct: 993  TTRPDRDGNYLVGDDGKAQLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHARSTGPYS 1052

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            ++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+TIKSDDV GR R Y +IV G+
Sbjct: 1053 MITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTIKSDDVDGRVRAYGAIVKGD 1112

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            +    G PESF VL+KEMQ+L L++++ N+  +     EE  D    
Sbjct: 1113 NLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGQAIDMKEEDDDPQSA 1159



 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 301/618 (48%), Positives = 429/618 (69%), Gaps = 23/618 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           ++  +   + + L  +    +  AL ++YR +RPGD +T     ++    +F++ +YDL+
Sbjct: 246 EAFTDYPLVMDALSKEPEISQDQALTELYRRIRPGDTATPEAGRNLLESFYFNNKRYDLA 305

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L LDT    R + ++DI+A +K LV L +GK                  D
Sbjct: 306 RVGRYKINRKLGLDTDYQNRSLTRDDIVATMKYLVTLHDGKDTFPGKREGKDIELPVDTD 365

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN GNRR+R VGE+++ Q R GL RMER  +ER+++ + +++ PQ L+N +PV + + 
Sbjct: 366 DIDNFGNRRIRQVGELIQTQLRTGLSRMERVARERMTTQEPEAITPQSLLNIRPVAATIK 425

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 426 EFFGTSQLSQFLDQNNPLASVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 485

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+  L++FAR+N +GFIETPYRKV +G VTNDVVY++A +E    IAQAN  L
Sbjct: 486 PEGPNIGLIGCLSTFARINPFGFIETPYRKVENGHVTNDVVYMTADQEHGHVIAQANQEL 545

Query: 635 DEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D +G+F  +    R    E   VP +++D++D S +Q+VS+ +SLIPFLE+D+ +R LMG
Sbjct: 546 DSEGNFLTKSALVRDDEAEAEDVPVDQVDYMDVSARQMVSVGSSLIPFLEHDEGHRALMG 605

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  +++++ G+V  V A  I + + +    
Sbjct: 606 ANMQRQAVPLVKSERPLVGTGGEWSAAVDSGDVVLSEKNGVVTYVSADLIRVMNDDDTTS 665

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PLV  G+ V    ++ADGP+TD G++ALG+N+LV
Sbjct: 666 S-------YKLTKFQRSNQMTCYNQVPLVSQGERVEEGSVLADGPATDQGEIALGKNLLV 718

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEEFE+ AR+TKLG EEITRD+PNVSE+ +
Sbjct: 719 AFMPWNGYNYEDAVIISQRLVRDDTLSSIHIEEFEIDARETKLGSEEITRDLPNVSEDAV 778

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+D+ GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 779 ANLDDRGIVRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 838

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  GTV+ ++   +   +
Sbjct: 839 GERGTVISIKEITKEEAE 856



 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E I +PDL+ VQ  S+D  +                        GLQ  F  
Sbjct: 29  RINFGSIREPISVPDLLGVQTNSFDWLVGNERWRKRVEEDEKNGTYTVGHTSGLQEVFDE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +      +D         
Sbjct: 89  ISPIENFAQTMSLTFTDPYFEEPRHTVQECREKDQTYSAPLYVNAEFTNYD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMTK GTF+I G +R++VSQL RSPG++F     R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLMTKHGTFIIGGTERVIVSQLVRSPGVYFGRTPDRT--SDKDVFD 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VRIDR+RK     FL A+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKRDVLGVRIDRKRKQSAIIFLQAIGMTRSEIAEAFTDYPLVMDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +            + G  ++ES         L +  + K  + LG
Sbjct: 258 LSKEPEISQDQALTELYRRIRPGDTATPEAGRNLLESFYFNNKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 LDTDY 322


>gi|291004501|ref|ZP_06562474.1| DNA-directed RNA polymerase subunit beta [Saccharopolyspora erythraea
            NRRL 2338]
          Length = 1150

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 187/515 (36%), Positives = 267/515 (51%), Gaps = 59/515 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + L  AI   +  +  D  +     V   V+
Sbjct: 663  IVNEGDRVEAGQVIADGPCTQN-GEMALGKNLRVAIMPWEGHNYEDAIILSQRLVQDDVL 721

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL-LARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I   +    +D    LD     R+   + G + + G 
Sbjct: 722  TSIHIEEH--EVDARDTKLGAEEITRDIPNVSEDVLADLDERGIIRIGAEVQGGDILVGK 779

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  +  ++  R    +  
Sbjct: 780  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVR----VFN 828

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF +DGTPVD
Sbjct: 829  REDDDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPAEDMPFTEDGTPVD 888

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI ETHLGW     G  I       K                   
Sbjct: 889  IILNTHGVPRRMNIGQILETHLGWIASQ-GWSIDGDPEWAKR------------------ 929

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES-------- 1231
                         +         G   ++PVFDGA EE I  +L     +          
Sbjct: 930  -------------LPEELYDVDPGTNTASPVFDGAREEEITGLLASTKPNRDGERMVKAN 976

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEP+  PV VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 977  GKAQLFDGRSGEPYPYPVAVGYMYILKLSHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1036

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1037 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1096

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1097 KELQSLCLNVEVLSSDGAAI----EMRDGDDEDLE 1127



 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 323/605 (53%), Positives = 437/605 (72%), Gaps = 23/605 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    + +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 236 EKDHTAGQDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGL 295

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNLGNRRVRSV 467
           D P +   + +EDI+  I+ LV L  G+                 +DDID+ GNRR+R+V
Sbjct: 296 DLPFESGVLTEEDIVTTIEYLVRLHAGEAEMPDRGQGGDATIPVEVDDIDHFGNRRLRTV 355

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 356 GELIQNQVRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 415

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N ++ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL 
Sbjct: 416 QTNPIAGLTHKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA 475

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +FARVN +GFIETPYRKV DG+VT+ + YL+A EE+    AQAN+ +D++G+F  + V  
Sbjct: 476 TFARVNPFGFIETPYRKVVDGRVTDQIDYLTADEEDRFVKAQANTPIDDEGNFLADRVLG 535

Query: 648 RCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R   GE  L+   +ID++D SP+Q+VS A ++IPFLE+DD+NR LMG NMQRQAVPLL++
Sbjct: 536 RRKGGEVELLAPTEIDYMDVSPRQMVSAATAMIPFLEHDDANRALMGANMQRQAVPLLRS 595

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP VGTGME   A  +G  + A++AG++E++ A  I + + +G           YRL K
Sbjct: 596 EAPLVGTGMELRAAVDAGDVVTAEKAGVIEELCADYITVMADDGTR-------RTYRLQK 648

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  TC NQ+P+V  GD V    +IADGP T  G++ALG+N+ VA MPW G+N+ED+
Sbjct: 649 FSRSNHGTCTNQKPIVNEGDRVEAGQVIADGPCTQNGEMALGKNLRVAIMPWEGHNYEDA 708

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++S+R+V +DV TSIHIEE EV ARDTKLG EEITRDIPNVSE+ L ++DE GII +GA
Sbjct: 709 IILSQRLVQDDVLTSIHIEEHEVDARDTKLGAEEITRDIPNVSEDVLADLDERGIIRIGA 768

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR+FN
Sbjct: 769 EVQGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVRVFN 828

Query: 947 RHGID 951
           R   D
Sbjct: 829 REDDD 833



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 97/329 (29%), Positives = 158/329 (48%), Gaps = 22/329 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F    E +++PDL+++Q  S++  +        R + G       L+     + PI 
Sbjct: 11  RVSFANIREPLEVPDLLDLQVQSFEWLVGDETWFQRRVDAGDENPVGGLEEVLSEISPIE 70

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T               +  +IK
Sbjct: 71  DFSGSMSLSFSDPRFDEVKASVEECKDKDMTYAAPLFVTAEFT---------NHTTGEIK 121

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K +Y+ +IIP
Sbjct: 122 SQTVFMGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDQSVDKT--TDKDVYSVKIIP 179

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E I   F     ++ +   D 
Sbjct: 180 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTAEAIRERFGFSETLMATLEKDH 239

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+    
Sbjct: 240 TAGQDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLDLPF 299

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
             G+   EDIV      + + AG+     
Sbjct: 300 ESGVLTEEDIVTTIEYLVRLHAGEAEMPD 328


>gi|46360960|gb|AAS89213.1| RpoB [Corynebacterium cystitidis]
          Length = 1113

 Score =  514 bits (1324), Expect = e-143,   Method: Composition-based stats.
 Identities = 183/493 (37%), Positives = 250/493 (50%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++      K    M+    LL A    +  +  D  +     V   ++
Sbjct: 668  LVNIGDRVEAGQVIADGPGTKN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEEVLKDL-DERGIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAALLETLPEALHD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L     +  G  
Sbjct: 946  VPADSLT-------------------------ATPVFDGATNEEIAGLLVNTKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDGDGKTVLFDGRSGEPFKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1101 FKVLLKELQSLCL 1113



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 320/661 (48%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   +    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEAQI--KERFGFSEIMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF   +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKPKRYDLAKVGRYKINRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D +  + +ED+   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLLTLTEEDLATSLEYLVRLHAGEKEMTSPTGEVIPINTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ +L S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGALASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPY+KV +GK+T+ + YL+A EE+   IAQA   +D DG+  EE +  R   
Sbjct: 485 VNAFGFIETPYQKVENGKLTDHIDYLTADEEDRYAIAQAAIEMDADGTIIEERIEVRIKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +   + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQ+QAVPLL+AEAPF
Sbjct: 545 GDIAVTDAQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGANMQKQAVPLLRAEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TGME   A  +G  +++++AG+VE V    I I   EG  D        Y L  ++R+
Sbjct: 605 VATGMEQRAAYDAGDMVISEKAGVVENVSGDIITIMDDEGQRD-------TYLLRTYERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ PLV +GD V    +IADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQLPLVNIGDRVEAGQVIADGPGTKNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +D+ TS+HIEE E+ ARDTKLG EEITR+IPNVSEE LK++DE GI+ +GA+V  
Sbjct: 718 QRVVEDDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEEVLKDLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 100/388 (25%), Positives = 172/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E + +P L++VQ  S+   +              PD R   GL+   + + P
Sbjct: 16  RYSFAKISEPLAVPGLLDVQSESFSWLVGTPEWRERQQELRGPDARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      FD  K+ VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFDSVKYTVDECKDKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG    +I   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEAQIKERFGFSEIMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG--KKLTSGLLKSLKEKGVKFLGI-- 298
           D       A   +   +        D  + ++E+   K     L K  + K  + LG+  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKPKRYDLAKVGRYKINRKLGLGG 304

Query: 299 ---------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                          + + L  L+  E  +   TGE+       I+   ++   +  +R 
Sbjct: 305 DHDGLLTLTEEDLATSLEYLVRLHAGEKEMTSPTGEVI-----PINTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|257054452|ref|YP_003132284.1| DNA-directed RNA polymerase subunit beta [Saccharomonospora viridis
            DSM 43017]
 gi|256584324|gb|ACU95457.1| DNA-directed RNA polymerase subunit beta [Saccharomonospora viridis
            DSM 43017]
          Length = 1170

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 185/512 (36%), Positives = 255/512 (49%), Gaps = 63/512 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++    +   +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 683  IVNEGDRVERGQVIADGPST-DKGEMALGKNLLVAIMPWEGHNYEDAIVISQRLVQDDVL 741

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   + ID  +  +  E     I  ++ D     DE+ I+      R  +IL G+  
Sbjct: 742  TSIHIEEYEIDARDTKLGAEEITRDIPNVSEDVLADLDERGIVRIGAEVRDGDILVGKVT 801

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 802  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIGV 844

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++PPGV  +V+V+VA K  IQ GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 845  RVFSREEDDELPPGVNELVRVYVAKKSKIQDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 904

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+VLN  GVP RMN+GQI E HLGW     G K++      K               
Sbjct: 905  TPVDVVLNTHGVPRRMNIGQIMELHLGWLASQ-GWKVEGNPEWAKN-------------- 949

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +       + G   +TPVFDGA EE I  +L     +      
Sbjct: 950  -----------------LTEELRDVEPGTNTATPVFDGAREEEITGLLGCTKPNRDGQRL 992

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G++ L+DG TGEPF  PV VGY+Y+LKL+HMV +K++ARSTG YS++TQQPLGGK+
Sbjct: 993  VGPDGKATLFDGRTGEPFPYPVAVGYMYILKLHHMVDEKIHARSTGPYSMITQQPLGGKA 1052

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +    G PESF
Sbjct: 1053 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENMPSPGIPESF 1112

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KE+Q+L L++++ +S   +    +   +
Sbjct: 1113 KVLLKELQSLCLNVEVLSSDGASIEMRDSDDE 1144



 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/601 (54%), Positives = 442/601 (73%), Gaps = 19/601 (3%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    + +ALLDI+R +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L
Sbjct: 260 EKDPTTTQDEALLDIHRKLRPGEPPTKESAQALVENLFFKEKRYDLAKVGRYKVNKKLGL 319

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKG-----------TIDDIDNLGNRRVRSVGEML 471
           + P DV  + +EDI+A I+ LV L  G+             +DDID+ GNRRVR+VGE++
Sbjct: 320 NIPYDVGTLTEEDIVATIEYLVRLHAGEETMKVGDVEVPVEVDDIDHFGNRRVRTVGELI 379

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N 
Sbjct: 380 QNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQNNP 439

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRL+ALG GG++R RAG+++RDVHP+HYGR+CP ET EG NIGL+ SL S AR
Sbjct: 440 LSGLTHKRRLNALGPGGLSRERAGMDVRDVHPSHYGRMCPIETPEGPNIGLIGSLASHAR 499

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA- 650
           VN +GFIETPYRKV +G+VT++V YL+A EE+    AQAN+ L EDG F EE V  R   
Sbjct: 500 VNPFGFIETPYRKVVNGRVTDEVHYLTADEEDRFVKAQANAPLTEDGYFAEEKVLGRRKG 559

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           GE  L+   +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAP 
Sbjct: 560 GEVELLDPMEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPL 619

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  +G  +VA+ +G+VE++ A  I I   +G           Y L KF+R+
Sbjct: 620 VGTGVELPAAVDAGDVVVAEESGVVEELSADMITIMQDDGTRRS-------YGLYKFRRT 672

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N  TC N RP+V  GD V R  +IADGPSTD G++ALG+N+LVA MPW G+N+ED+++IS
Sbjct: 673 NAGTCFNHRPIVNEGDRVERGQVIADGPSTDKGEMALGKNLLVAIMPWEGHNYEDAIVIS 732

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +DV TSIHIEE+E+ ARDTKLG EEITRDIPNVSE+ L ++DE GI+ +GAEV  
Sbjct: 733 QRLVQDDVLTSIHIEEYEIDARDTKLGAEEITRDIPNVSEDVLADLDERGIVRIGAEVRD 792

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR+F+R   
Sbjct: 793 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVRVFSREED 852

Query: 951 D 951
           D
Sbjct: 853 D 853



 Score =  334 bits (856), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 114/481 (23%), Positives = 204/481 (42%), Gaps = 39/481 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  FG+  E + IP+L++VQ  S++ F       +   NEG       L+     + PI 
Sbjct: 35  RVSFGEIREPLGIPNLLDVQIQSFEWFTGSEAWYERAVNEGEENPVGGLEEVLNEISPIE 94

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  V++C  +D+TYA PL +T   +           +  +IK
Sbjct: 95  DFSGSMSLSFSDPRFDEVKASVEECKDKDMTYAAPLFVTAEFV---------NHNTGEIK 145

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K +++ +IIP
Sbjct: 146 SQTVFMGDFPVMTDKGTFIINGTERVVVSQLVRSPGVYFDQSIDK--STDKDVFSVKIIP 203

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I    +F   ++ +   D 
Sbjct: 204 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIRERFSFSETLLATLEKDP 263

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L K  + K  K LG+    
Sbjct: 264 TTTQDEALLDIHRKLRPGEPPTKESAQALVENLFFKEKRYDLAKVGRYKVNKKLGLNIPY 323

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDE----------KSLEEIFHSEIRDIPILYVDSV 352
             G    EDIV      + + AG+   +            ++   +  +R +  L  + +
Sbjct: 324 DVGTLTEEDIVATIEYLVRLHAGEETMKVGDVEVPVEVDDIDHFGNRRVRTVGELIQNQI 383

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                    +V ++   +   +  I            +     F            + + 
Sbjct: 384 RVGLSRMERVVRERMTTQD--VEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQNNPLS 441

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
            +    RLN   P     + +E     ++ +     G+  +  I+      +  +G +  
Sbjct: 442 GLTHKRRLNALGPGG---LSRERAGMDVRDVHPSHYGR--MCPIETPEGPNIGLIGSLAS 496

Query: 473 N 473
           +
Sbjct: 497 H 497


>gi|170780719|ref|YP_001709051.1| DNA-directed RNA polymerase subunit beta [Clavibacter michiganensis
            subsp. sepedonicus]
 gi|189043851|sp|B0RB25|RPOB_CLAMS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|169155287|emb|CAQ00390.1| DNA-directed RNA polymerase beta chain [Clavibacter michiganensis
            subsp. sepedonicus]
          Length = 1162

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 179/515 (34%), Positives = 266/515 (51%), Gaps = 68/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G+++      +    +   + LL A    +  +  D  +   + V    +
Sbjct: 676  LVSAGDRIEAGEVIADGPATEN-GELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDTL 734

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   +  + + R   + +E+I          L  D  DE+ I+      R  +IL G
Sbjct: 735  SSIHIEEY--EVDARDTKLGKEEITRDLPNVSPELLADL-DERGIIRIGAEVRPGDILVG 791

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   + +E  R                V   +        + + +
Sbjct: 792  KVTPKGETELSAEERLLRAIFNEKSREV--------RDTSLKVPHGEQGTIIGVKVFDSQ 843

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +        D++  GV + V VF+A KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 844  DGD--------DELGSGVNQRVVVFIAQKRKITEGDKLAGRHGNKGVISKILPVEDMPFL 895

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD++LNPLG+P RMN GQ+ ETHLGW+    G +++                   
Sbjct: 896  ADGTPVDVILNPLGIPGRMNFGQVLETHLGWSAKQ-GWEVEGKPKWA------------- 941

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                              + +   A Q  +G  V+TPVFDGA EE I  +L         
Sbjct: 942  ------------------ERLPDHARQAPAGTKVATPVFDGALEEEIAGLLDSTTVTRDG 983

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 984  DRLIGSSGKTRLFDGRSGEPFPEPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 1043

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VYE+IV G +  E G P
Sbjct: 1044 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVYEAIVKGENIQEPGIP 1103

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ ++  +  +  +   +
Sbjct: 1104 ESFKVLIKEMQSLCLNVEVLSADGQAVSLRDTDDE 1138



 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 337/765 (44%), Positives = 477/765 (62%), Gaps = 43/765 (5%)

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA---KVSSSLVDIDTGEQVIESG 277
           LG  +  +    Y      +RG  +  PL      +     ++ +  V +     + E G
Sbjct: 91  LGFTNPYLEEQKYSIDECKERGKTYSAPLYVEAEFMNHLTGEIKTQTVFMGDFPLMTEKG 150

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGEIYI 322
             + +G  + +  + V+  G+  +        +DI +                +  ++ +
Sbjct: 151 TFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQVGV 210

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
                  +     +    +    IL  +     A I  TL  D    +++AL DIYR +R
Sbjct: 211 RIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYRKLR 268

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
           PG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A IK 
Sbjct: 269 PGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILATIKY 328

Query: 443 LVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++
Sbjct: 329 LVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVR 388

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG G
Sbjct: 389 ERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPG 448

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N++GFIETPYR+V D
Sbjct: 449 GLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINSFGFIETPYRRVVD 508

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDA 666
           G VT+ + YL+A EE+   +AQAN+ L +D  F E+ V  R   GE  LV +E + ++D 
Sbjct: 509 GVVTDQIDYLTASEEDEFLVAQANAPLTKDFRFAEDRVLVRPKGGEVELVAKENVHYMDV 568

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SP+Q+VS+A SLIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTGME   A  +G  
Sbjct: 569 SPRQMVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTGMEGYAAIDAGDV 628

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           + A  +G+V +V A  + I+  EG       G   Y L KF RSNQ T  N R LV  GD
Sbjct: 629 LTADASGVVAEVSAEVVTIQLDEG-------GTQTYYLRKFDRSNQGTSYNHRVLVSAGD 681

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            +   ++IADGP+T+ G+LALG+N+LVAFMPW G+NFED++++S+ +V +D  +SIHIEE
Sbjct: 682 RIEAGEVIADGPATENGELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDTLSSIHIEE 741

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +EV ARDTKLG EEITRD+PNVS E L ++DE GII +GAEV PGDILVGK+TPKGE+ +
Sbjct: 742 YEVDARDTKLGKEEITRDLPNVSPELLADLDERGIIRIGAEVRPGDILVGKVTPKGETEL 801

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + EE+LLRAIF EK+ +VRDTSL+VP G  GT++ V++F+    D
Sbjct: 802 SAEERLLRAIFNEKSREVRDTSLKVPHGEQGTIIGVKVFDSQDGD 846



 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 93/310 (30%), Positives = 145/310 (46%), Gaps = 27/310 (8%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEG 54
            NG    R  F K  + + +PDL+ +Q  S+D  +  +                   N G
Sbjct: 12  QNGRDASRLSFAKITDTLTVPDLLALQTESFDWLVGSDAWKRRVEEGTKQGRTDLALNSG 71

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           L+  F+ + PI        L F +   +  K+ +D+C  R  TY+ PL +         +
Sbjct: 72  LEEIFEEISPIEDLGETMQLGFTNPYLEEQKYSIDECKERGKTYSAPLYV---------E 122

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                    +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   
Sbjct: 123 AEFMNHLTGEIKTQTVFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT-- 180

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-- 232
           S K +Y+ R+IP +G W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F  
Sbjct: 181 SDKDIYSARVIPSRGAWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKG 240

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKE 290
              I  +   D       A   +         V  +    ++++         L K  + 
Sbjct: 241 VASIELTLEKDSILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRY 300

Query: 291 KGVKFLGITS 300
           K  + LGI  
Sbjct: 301 KINRKLGIDK 310


>gi|312144255|ref|YP_003995701.1| DNA-directed RNA polymerase, beta subunit [Halanaerobium sp.
           'sapolanicus']
 gi|311904906|gb|ADQ15347.1| DNA-directed RNA polymerase, beta subunit [Halanaerobium sp.
           'sapolanicus']
          Length = 1084

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 326/605 (53%), Positives = 452/605 (74%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D   ++  I +TL  D  + +++AL+++Y+ +RPG+  T   A ++ + LFFD  +YD+
Sbjct: 201 IDEFGDSEVIHDTLERDSTESKEEALIELYKRLRPGEPPTVESATNLLDSLFFDHKRYDM 260

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL--RNGKGTIDDIDNLGNRRVRS 466
           + VGR K+N +L+L+   D +++  +DI+  ++ +V+L   N    IDDID+LGNRR+++
Sbjct: 261 AAVGRYKLNKKLDLEVDKDRKYLHIDDIVETVRYMVNLIYHNDDAYIDDIDHLGNRRLKT 320

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+L+NQ+R+GL RMER ++ER++  D+D V PQ LIN +PVV+++ EFF SSQLSQ  
Sbjct: 321 VGELLQNQFRIGLSRMERVVRERMTIQDVDVVTPQALINTRPVVASIQEFFGSSQLSQFM 380

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N +S +TH RRLSALG GG++R RAG ++RDVH +HYGRICP ET EG NIGL+ ++
Sbjct: 381 DQTNPMSELTHKRRLSALGPGGLSRERAGFDVRDVHHSHYGRICPIETPEGPNIGLIGTM 440

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A+ N +GF+ TPYR+V D +VT ++ YL+A EE+   IAQANS LDE+  F  E V 
Sbjct: 441 GTYAKTNEFGFLMTPYRRVVDNQVTENIDYLTADEEDKYIIAQANSELDEENKFVSEFVV 500

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+ + V  + ID++D S KQ+V ++A++IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 501 ARKRGDILEVHPDDIDYMDVSTKQLVGVSAAMIPFLENDDANRALMGANMQRQAVPLMIT 560

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +AP V TGME   AK SGA ++A++ G V  V + +I+I++ EG +D        Y+LMK
Sbjct: 561 DAPIVATGMEYKAAKDSGAVVIAEKGGEVVNVTSNKIMIKNDEGLIDS-------YKLMK 613

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           ++RSNQ +C+NQ+P+V+ GD V +NDIIADGPST+ G++ALGRN L+AFMPW GYN+ED+
Sbjct: 614 YKRSNQGSCMNQKPIVEKGDIVDKNDIIADGPSTEKGEMALGRNTLIAFMPWEGYNYEDA 673

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISE +V ED FT+IHIEE E  ARDTKLGPEEITRDIPNV E  LKN+D+ GII VGA
Sbjct: 674 ILISENLVKEDSFTTIHIEEHEAEARDTKLGPEEITRDIPNVGENALKNLDDRGIIRVGA 733

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE+ ++ EE+LLRAIFGEKA +VRDTSL+VP G  G VVDV++F+
Sbjct: 734 EVEEGDILVGKVTPKGETELSAEERLLRAIFGEKAREVRDTSLKVPHGEEGKVVDVKVFS 793

Query: 947 RHGID 951
           R   D
Sbjct: 794 REQGD 798



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 187/527 (35%), Positives = 260/527 (49%), Gaps = 67/527 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  + +          +++  I+  G  V+  DI+    + + +  M      
Sbjct: 600  KNDEGLIDSYKLMKYKRSNQGSCMNQKPIVEKGDIVDKNDIIADGPSTE-KGEMALGRNT 658

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L     +S  +V    F    I+++E      +   E + RD  
Sbjct: 659  LIAFMPWEGYNYEDAIL-----ISENLVKEDSFTTIHIEEHEAEARDTKLGPEEITRDIP 713

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +      +N+  R   I  G     G     K T      +S   R     F  +  +V+
Sbjct: 714  NVGENALKNLDDR-GIIRVGAEVEEGDILVGKVTPKGETELSAEERLLRAIFGEKAREVR 772

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    E     +      K+   + GDD+ PGV R+V+V+VA KR I  GDK+AG
Sbjct: 773  DTSLKVPHGEEGKVVDV------KVFSREQGDDLKPGVNRLVRVYVATKRKISVGDKLAG 826

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL +G PV+IVLNPLGVPSRMN+GQ+ ETHLG A   LG   
Sbjct: 827  RHGNKGVISRILPEEDMPFLPNGEPVEIVLNPLGVPSRMNIGQVLETHLGMAAKELGIYT 886

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            ++ + +     ++                         + VL  A   + G         
Sbjct: 887  ETPVFNGATEIEV-------------------------EDVLEEAGLARDG--------- 912

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                                +++LYDG TGE F+  VTVG +Y+LKL+H+V DK++ARST
Sbjct: 913  --------------------KTVLYDGRTGERFEGRVTVGLMYILKLHHLVDDKLHARST 952

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDVVGR + YE+I
Sbjct: 953  GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRVKAYEAI 1012

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            V G +  E G PESF VL+KEMQ+LGL   +  S  +     E   +
Sbjct: 1013 VKGENVPEPGIPESFKVLIKEMQSLGLDARIFTSDEEELQVAENEDE 1059



 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 116/453 (25%), Positives = 186/453 (41%), Gaps = 43/453 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ F K  + +D+PDLI  Q  SY  FL           EGL+  F  + PI  FS  
Sbjct: 5   RERRSFSKIEDAMDLPDLIYTQLNSYQWFL----------EEGLKEVFAEISPIEDFSEN 54

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +LEFV Y  + P++ V +C  RD TY+  L++ +RLI          K   ++KEQ ++
Sbjct: 55  LVLEFVDYYLEDPEYTVQECRDRDDTYSASLQVKVRLI---------NKETGEVKEQEVF 105

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT   TF+I G +R+VV+QL RS G++F  ++ +    G+ L    IIP++G W
Sbjct: 106 MGDFPLMTDKATFIINGAERVVVNQLVRSSGVYFSDERTKD---GRRLITGSIIPNRGAW 162

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E+D K II VR+DR RK+P T  L ALG  ++ EI+  F    V     +       
Sbjct: 163 IEFEYDKKRIISVRVDRTRKLPSTVLLRALGYGTDSEIIDEFGDSEVIHDTLERDSTESK 222

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-------DC 302
              L+           +  GE   +ES   L   L    K   +  +G          + 
Sbjct: 223 EEALI------ELYKRLRPGEPPTVESATNLLDSLFFDHKRYDMAAVGRYKLNKKLDLEV 276

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY--IRN 360
                        ET    +      D+  +++I H   R +  +     N       R 
Sbjct: 277 DKDRKYLHIDDIVETVRYMVNLIYHNDDAYIDDIDHLGNRRLKTVGELLQNQFRIGLSRM 336

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             V  +    +D  +   + +        S+ +  F            + +  +    RL
Sbjct: 337 ERVVRERMTIQDVDVVTPQALINTRPVVASI-QEFFGSSQLSQFMDQTNPMSELTHKRRL 395

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           +   P     + +E     ++ +     G+   
Sbjct: 396 SALGPGG---LSRERAGFDVRDVHHSHYGRICP 425


>gi|46360920|gb|AAS89193.1| RpoB [Corynebacterium jeikeium]
          Length = 1154

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 193/620 (31%), Positives = 274/620 (44%), Gaps = 64/620 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              +L +  P+ G   E         M+  
Sbjct: 567  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPYVGTGMELRAAYDAGDMIIA 626

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     + +      G  +                ++  ++  G  V  G +L  
Sbjct: 627  PKAGVVEYVSADYITVMDDEGVRDTFMLRKFERTNQGTCYNQKPLVDEGDRVEAGQVLAD 686

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M   + LL A    +  +  D  +     V   ++       +  + + R 
Sbjct: 687  GPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDILTSIHIEEY--EIDARD 743

Query: 957  ISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              +  E+I        E +  D DD   I+      R  +IL G+    G         L
Sbjct: 744  TKLGPEEITRDIPNVGEDVLADLDDR-GIVRIGADVRDGDILVGKVTPKGETELTPEERL 802

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               +  E  R                 E      +            ++   +  DD+  
Sbjct: 803  LRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAA 845

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTP+DI+LN  GVP
Sbjct: 846  GVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPIDIILNTHGVP 905

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
             RMN+GQ+ E HLGW     G K+ +   D K    +  L   L +V             
Sbjct: 906  RRMNIGQVLEVHLGWLAKA-GWKVDTDSQDPKIQKMLETLPEELYEVPADSLT------- 957

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGL 1240
                              +TPVFDGA    ++ +LR +  +  G        +S L DG 
Sbjct: 958  ------------------ATPVFDGASNAELSGLLRSSLPNRDGERQVDDFGKSNLIDGR 999

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +GEPF  PV VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 1000 SGEPFPYPVAVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1059

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L+
Sbjct: 1060 AMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLN 1119

Query: 1361 IDLENSRTKNSAKMEEIPDF 1380
            +++  +         +  D 
Sbjct: 1120 VEVLAADGTPMELSSDDDDE 1139



 Score =  505 bits (1300), Expect = e-140,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 460/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSELMMSTLEK 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D V  + +EDI+  I+ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DTDGVMTLTEEDILTTIEYLVRLHAGEKSMTSPDGTEIPIDTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DG++T++V Y +A EE+   IAQAN+  DE+  FTEE +  R   
Sbjct: 488 VNPFGFIETPYRKVVDGQITDEVYYFTADEEDRHVIAQANTPFDENHRFTEERIEVRLRG 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAP+
Sbjct: 548 GDVEVVPYTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPY 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   EG  D          L KF+R+
Sbjct: 608 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDEGVRDTFM-------LRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV  GD V    ++ADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 661 NQGTCYNQKPLVDEGDRVEAGQVLADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV ED+ TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++D+ GI+ +GA+V  
Sbjct: 721 QRMVEEDILTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDDRGIVRIGADVRD 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 85/322 (26%), Positives = 144/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 18  QRHSFAKIDAPIEVPGLLDLQRESFAWLVGTPEWRARAQAEAGEGVRIMSGLEEILEELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 78  PIEDYSENMSLTLSEPRFDDVKSTIDEAKDKDINYAAPLYVTAEFT---------NSMSG 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L++ +
Sbjct: 129 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F    +   +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSELMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 247 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKAKRYDLAKVGRYKV 299

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D V   T E  +
Sbjct: 300 NRKLGLGGDTDGVMTLTEEDIL 321


>gi|227832198|ref|YP_002833905.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            aurimucosum ATCC 700975]
 gi|262183949|ref|ZP_06043370.1| DNA-directed RNA polymerase subunit beta [Corynebacterium aurimucosum
            ATCC 700975]
 gi|227453214|gb|ACP31967.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            aurimucosum ATCC 700975]
          Length = 1159

 Score =  514 bits (1323), Expect = e-143,   Method: Composition-based stats.
 Identities = 194/610 (31%), Positives = 287/610 (47%), Gaps = 60/610 (9%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 567  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMEQRAAYDAGDLIIT 626

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 627  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQNTNYNQTPLVSLGERVEAGQVLAD 686

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 687  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 745

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 746  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 805

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                        ET K I   RF  + +     DD+ PGV 
Sbjct: 806  IFGEKAREVRDT------------SMKVPHGETGKVIGVSRFSREDD-----DDLAPGVN 848

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RM
Sbjct: 849  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRM 908

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G KI +     +   +   L++  E++      +         
Sbjct: 909  NIGQVLEVHLGWLAHA-GWKIDT-----EDPANAELLKTLPEELYDVPPESLT------- 955

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +GE
Sbjct: 956  ---------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGE 1000

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 1001 PYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE+Q+L L++++
Sbjct: 1061 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEV 1120

Query: 1364 ENSRTKNSAK 1373
             ++       
Sbjct: 1121 LSTDGTPMEL 1130



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 324/661 (49%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIK----ERFGFSELMMSTLES 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+++ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMISIHTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+ T + +  R   
Sbjct: 488 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDRFAIAQAEVEKDADGTLTGDRIEVRLKD 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 548 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNT  NQ PLV +G+ V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 661 NQNTNYNQTPLVSLGERVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 721 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVSRFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  SY   +               D R   GL+   + + P
Sbjct: 19  RYSFAKISEPIAVPGLLDLQLDSYAWLIGTPEWREREQAERGEDARVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 79  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT+ GTF++ G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 130 IKSQTVFIGDFPMMTEKGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHSVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIKERFGFSELMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        D  + ++++         L K  + K  +      
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+  E  +    GE+       I    ++   +  +R 
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMI-----SIHTDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|305679975|ref|ZP_07402785.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            matruchotii ATCC 14266]
 gi|305660595|gb|EFM50092.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            matruchotii ATCC 14266]
          Length = 1187

 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 179/513 (34%), Positives = 256/513 (49%), Gaps = 61/513 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M     LL A    +  +  D  +     V   ++
Sbjct: 698  LVDEGDRVEEGQVVADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 756

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                  +H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 757  TSIHIEQHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 815

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 816  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 858

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 859  VRRFSREDEDDLGPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 918

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD++LN  GVP RMN+GQ+ E HLGW     G K+                      
Sbjct: 919  GTPVDVILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKVDV-------------------- 957

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
                    +  +    +++        +G   +TPVFDGA  + I  +L  +  +  G  
Sbjct: 958  -------NDPANAKLLETLPEDLYDVPAGSLTATPVFDGATNDEIAGLLANSLPNRDGDV 1010

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 1011 MVNADGKAQLFDGRSGEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGK 1070

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1071 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1130

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ ++            D
Sbjct: 1131 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDD 1163



 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 328/661 (49%), Positives = 454/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  + +TL  
Sbjct: 219 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTEQIV--ERFGFSEIMMSTLEN 274

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF   +YDL+ VGR K N +L L  
Sbjct: 275 DGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLGG 334

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             D +  + +EDI   I+ LV L  G+ ++            DDID+ GNRR+R+VGE++
Sbjct: 335 DHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEIIPVETDDIDHFGNRRLRTVGELI 394

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF SSQLSQ  +  NS
Sbjct: 395 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGSSQLSQFMDLNNS 454

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 455 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 514

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN++GFIETPYRKV DG VT++V YL+A EE+   +AQAN+  DE+G  TE+ V  R   
Sbjct: 515 VNSFGFIETPYRKVVDGVVTDEVDYLTADEEDRYVVAQANTKFDENGVITEDRVTVRLKK 574

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V  + I+++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP 
Sbjct: 575 GDIQVVDGKDINYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPL 634

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I++K+AG+VE V A  I I   +G  D        Y L KF+R+
Sbjct: 635 VGTGMELRAAYDAGDLIISKKAGVVETVCADYITIMGDDGVRD-------TYMLRKFERT 687

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    ++ADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 688 NQGTSYNQKPLVDEGDRVEEGQVVADGPGTHNGEMALGRNLLVAFMPWEGHNYEDAIILN 747

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIE+ E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V  
Sbjct: 748 QRLVEEDILTSIHIEQHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVRD 807

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR F+R   
Sbjct: 808 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRRFSREDE 867

Query: 951 D 951
           D
Sbjct: 868 D 868



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 97/389 (24%), Positives = 174/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K    I++P L+++Q  S+   +            +  D R   GL+   + + 
Sbjct: 45  ERKSFAKIQSPIEVPGLLDIQLESFAWLIGSPEWRARRQAELGEDVRVTSGLEDILEELS 104

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 105 PIQDYSGNMSLSLSEPRFEEMKNSIDECKDKDINYSAPLYVTAEFI---------NNETQ 155

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 156 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 213

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +  
Sbjct: 214 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIVERFGFSEIMMSTLE 273

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L K  + K  + LG+ 
Sbjct: 274 NDGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLG 333

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+V E  +   TGEI       ++   ++   +  +R
Sbjct: 334 GDHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEII-----PVETDDIDHFGNRRLR 388

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 389 TVGELIQNQVRVGLSRMERVVRERMTTQD 417


>gi|253797608|ref|YP_003030609.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis KZN 1435]
 gi|253319111|gb|ACT23714.1| DNA-directed RNA polymerase subunit beta rpoB [Mycobacterium
           tuberculosis KZN 1435]
          Length = 1178

 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 454/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 209 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 264

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 265 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 324

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 325 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 384

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ     N
Sbjct: 385 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMYQNN 444

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG +IGL+ SL+ +A
Sbjct: 445 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPSIGLIGSLSVYA 504

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 505 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 564

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 565 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 624

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 625 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 677

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 678 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 737

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 738 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 797

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 798 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 857

Query: 950 ID 951
            D
Sbjct: 858 ED 859



 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 689  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 747

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 748  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 807

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 808  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 850

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 851  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 910

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 911  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 960

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 961  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 1001

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 1002 VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 1061

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 1062 QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1121

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1122 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1158



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 107/481 (22%), Positives = 196/481 (40%), Gaps = 42/481 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F     +  +   D 
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 266

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+    
Sbjct: 267 TVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGE 326

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVID-------------EKSLEEIFHSEIRDIPILYV 349
                   +     T E  +   +                   ++   +  +R +  L  
Sbjct: 327 PITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQ 386

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           + +         +V ++   +   +  I            +  +  F         Y  +
Sbjct: 387 NQIRVGMSRMERVVRERMTTQD--VEAITPQTLINIRPVVAAIKEFFGTSQLSQFMYQNN 444

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            +  +    RL+   P     + +E     ++ +     G+  +  I+      +  +G 
Sbjct: 445 PLSGLTHKRRLSALGPGG---LSRERAGLEVRDVHPSHYGR--MCPIETPEGPSIGLIGS 499

Query: 470 M 470
           +
Sbjct: 500 L 500


>gi|260579283|ref|ZP_05847166.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium jeikeium
            ATCC 43734]
 gi|258602582|gb|EEW15876.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium jeikeium
            ATCC 43734]
          Length = 1175

 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 193/620 (31%), Positives = 274/620 (44%), Gaps = 64/620 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              +L +  P+ G   E         M+  
Sbjct: 578  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPYVGTGMELRAAYDAGDMIIA 637

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     + +      G  +                ++  ++  G  V  G +L  
Sbjct: 638  PKAGVVEYVSADYITVMDDEGVRDTFMLRKFERTNQGTCYNQKPLVDEGDRVEAGQVLAD 697

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M   + LL A    +  +  D  +     V   ++       +  + + R 
Sbjct: 698  GPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDILTSIHIEEY--EIDARD 754

Query: 957  ISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              +  E+I        E +  D DD   I+      R  +IL G+    G         L
Sbjct: 755  TKLGPEEITRDIPNVGEDVLADLDDR-GIVRIGADVRDGDILVGKVTPKGETELTPEERL 813

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               +  E  R                 E      +            ++   +  DD+  
Sbjct: 814  LRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAA 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTP+DI+LN  GVP
Sbjct: 857  GVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPIDIILNTHGVP 916

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
             RMN+GQ+ E HLGW     G K+ +   D K    +  L   L +V             
Sbjct: 917  RRMNIGQVLEVHLGWLAKA-GWKVDTDSQDPKIQKMLETLPEELYEVPADSLT------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGL 1240
                              +TPVFDGA    ++ +LR +  +  G        +S L DG 
Sbjct: 969  ------------------ATPVFDGASNAELSGLLRSSLPNRDGERQVDDFGKSNLIDGR 1010

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +GEPF  PV VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 1011 SGEPFPYPVAVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1070

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PESF VL+KE+Q+L L+
Sbjct: 1071 AMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCLN 1130

Query: 1361 IDLENSRTKNSAKMEEIPDF 1380
            +++  +         +  D 
Sbjct: 1131 VEVLAADGTPMELSSDDDDE 1150



 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 460/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 203 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSELMMSTLEK 258

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L L  
Sbjct: 259 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLGG 318

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D V  + +EDI+  I+ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 319 DTDGVMTLTEEDILTTIEYLVRLHAGEKSMTSPDGTEIPIDTDDIDHFGNRRLRTVGELI 378

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 379 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 438

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 439 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 498

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DG++T++V Y +A EE+   IAQAN+  DE+  FTEE +  R   
Sbjct: 499 VNPFGFIETPYRKVVDGQITDEVYYFTADEEDRHVIAQANTPFDENHRFTEERIEVRLRG 558

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAP+
Sbjct: 559 GDVEVVPYTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPY 618

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   EG  D          L KF+R+
Sbjct: 619 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDEGVRDTFM-------LRKFERT 671

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV  GD V    ++ADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 672 NQGTCYNQKPLVDEGDRVEAGQVLADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 731

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV ED+ TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++D+ GI+ +GA+V  
Sbjct: 732 QRMVEEDILTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDDRGIVRIGADVRD 791

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 792 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 851

Query: 951 D 951
           D
Sbjct: 852 D 852



 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 85/322 (26%), Positives = 144/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 29  QRHSFAKIDAPIEVPGLLDLQRESFAWLVGTPEWRARAQAEAGEGVRIMSGLEEILEELS 88

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 89  PIEDYSENMSLTLSEPRFDDVKSTIDEAKDKDINYAAPLYVTAEFT---------NSMSG 139

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L++ +
Sbjct: 140 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHSVK 197

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F    +   +  
Sbjct: 198 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSELMMSTLE 257

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 258 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKAKRYDLAKVGRYKV 310

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D V   T E  +
Sbjct: 311 NRKLGLGGDTDGVMTLTEEDIL 332


>gi|468334|gb|AAA21416.1| RNA polymerase beta-subunit [Mycobacterium tuberculosis]
          Length = 1177

 Score =  513 bits (1322), Expect = e-143,   Method: Composition-based stats.
 Identities = 201/620 (32%), Positives = 281/620 (45%), Gaps = 61/620 (9%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V            A+              ++ +  P  G   E    I     S  
Sbjct: 585  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAATSSSQ 644

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                I     + +      G     R             ++C I+  G  V  G ++   
Sbjct: 645  ESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADG 704

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                 +  M   + LL AI   +  +  D  +     V   V+       H ID  +  +
Sbjct: 705  PCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKL 763

Query: 958  SVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              E     I  ++ +     DE+ I+      R  +IL G+    G         L   +
Sbjct: 764  GAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAI 823

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              E  R                 E      +            ++   +  D++P GV  
Sbjct: 824  FGEKAR-----------------EVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNE 866

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN
Sbjct: 867  LVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMN 926

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI ETHLGW C   G K+ +                            +  +   D+ 
Sbjct: 927  IGQILETHLGW-CAHSGWKVDAA-----------------------KGVPDWAARLPDEL 962

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEP 1244
            +   A        VSTPVFDGA E  +  +L            +D  G+++L+DG +GEP
Sbjct: 963  LEAHANAI-----VSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEP 1017

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QA
Sbjct: 1018 FPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQA 1077

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            YGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ 
Sbjct: 1078 YGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVL 1137

Query: 1365 NSRTKNSAKME-EIPDFNKC 1383
            +S        E E  D  + 
Sbjct: 1138 SSDGAAIELREGEDEDLERA 1157



 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 453/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 209 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 264

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 265 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 324

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 325 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 384

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 385 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 444

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 445 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 504

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 505 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 564

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 565 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 624

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  + A   ++ +G++E+V A  I +    G           YR+ KF R
Sbjct: 625 LVGTGMELRAAIDA-ATSSSQESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 676

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 677 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 736

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 737 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 796

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 797 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 856

Query: 950 ID 951
            D
Sbjct: 857 ED 858



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 318 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 350


>gi|218246583|ref|YP_002371954.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. PCC 8801]
 gi|257059625|ref|YP_003137513.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. PCC 8802]
 gi|218167061|gb|ACK65798.1| DNA-directed RNA polymerase, beta subunit [Cyanothece sp. PCC 8801]
 gi|256589791|gb|ACV00678.1| DNA-directed RNA polymerase, beta subunit [Cyanothece sp. PCC 8802]
          Length = 1103

 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 330/687 (48%), Positives = 457/687 (66%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 114 INGAERVIVNQIVRSPGVYYKAEIDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 173

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  D + +  + + TL  + N   ++ALL++YR +RPG+ 
Sbjct: 174 TRKLSAQVLLKAIGLSDAEIL--DGLRHPDFYQRTLDKEGNPSEEEALLELYRKLRPGEP 231

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T +  + + +  FFDS +YDL  VGR K+N +L L+ PD +R +R  DI+A I  L++L
Sbjct: 232 PTVTGGQQLLDSRFFDSKRYDLGRVGRYKLNKKLRLNAPDTIRVLRPADIMAAIDYLINL 291

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+ DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + D + P  L+N 
Sbjct: 292 EFDVGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDGLTPASLVNP 351

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 352 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 411

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY K  +G+V  D+  VYL+A EE++
Sbjct: 412 GRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYKAENGRVRRDLDPVYLTADEEDD 471

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +   +++ D +G+   E V  R   E      E++D++  SP Q+VS+A S+IPFLE+
Sbjct: 472 LRVCPGDAATDAEGNILGESVPIRYRQEFSTTSPEQVDYVAVSPVQIVSVATSMIPFLEH 531

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV  VDA  I 
Sbjct: 532 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTYGIVTYVDASEIR 591

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++    +          Y L K+QRSNQ+TC+NQRPLV V +EV    ++ADG +T+ G+
Sbjct: 592 VQVTGPENHDKLGTEITYLLQKYQRSNQDTCLNQRPLVYVNEEVVPGQVLADGSATEGGE 651

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIH+E++E+ AR TKLGPEEITR+
Sbjct: 652 LALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITRE 711

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA    GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 712 IPNVGEDSLRNLDEQGIIRIGAWTEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 771

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 772 RDNSLRVPNGEKGRVVDVRVFTREQGD 798



 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 196/593 (33%), Positives = 270/593 (45%), Gaps = 72/593 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR------- 852
                       +L    P  G   E        MV       I         R       
Sbjct: 539  MGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTYGIVTYVDASEIRVQVTGPE 598

Query: 853  -DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
               KLG E                +++  ++ V  EV PG +L      +G   +   + 
Sbjct: 599  NHDKLGTEITYLLQKYQRSNQDTCLNQRPLVYVNEEVVPGQVLADGSATEG-GELALGQN 657

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLAR 969
            +L A    +  +  D  L     V   V       ++ I+  +  +  E    +I  +  
Sbjct: 658  ILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITREIPNVGE 717

Query: 970  D---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            D     DEQ I+    ++   +IL G+    G         L   +  E  R        
Sbjct: 718  DSLRNLDEQGIIRIGAWTEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------- 770

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                       ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ
Sbjct: 771  -----------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQ 819

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKMAGRHGNKGI+SRILP EDMP+L DG PVDIVLNPLGVPSRMNVGQ+FE  LGWA 
Sbjct: 820  VGDKMAGRHGNKGIISRILPIEDMPYLPDGRPVDIVLNPLGVPSRMNVGQVFECLLGWAG 879

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG + K    D               ++ G  +  + +     ++  +  + W     
Sbjct: 880  ENLGVRFKVTPFD---------------EMYGEETSRKTVHGKLQEASHKRGKSWIYQE- 923

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                   +  G+  ++DG TGEPFDRPVTVG  YMLKL H+V D
Sbjct: 924  -----------------------ENPGKIQVFDGRTGEPFDRPVTVGQAYMLKLVHLVDD 960

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR
Sbjct: 961  KIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGR 1020

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                 +IV G    + GTPESF VL++E+Q+LGL I +            ++ 
Sbjct: 1021 NEALNAIVKGKPIPQPGTPESFKVLMRELQSLGLDIAVHKVENAEDGTSRDVE 1073



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 101/439 (23%), Positives = 183/439 (41%), Gaps = 44/439 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PI+ ++G   L F+   Y+   
Sbjct: 11  LPDLIEIQRSSFRWFL----------EEGLIEELDSFSPISDYTGKLELHFLGENYKLKQ 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 61  PKYDVDEAKRRDSTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTERGT 111

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 112 FIINGAERVIVNQIVRSPGVYYKAEIDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL        Y +  D    P     L+        
Sbjct: 169 VRIDKTRKLSAQVLLKAIGLSDAEILDGLRHPDFYQRTLDKEGNPSEEEALL------EL 222

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G           A D +        +
Sbjct: 223 YRKLRPGEPPTVTGGQQLLDSRFFDSKRYDLGRVGRYKLNKKLRLNAPDTIRVLRPADIM 282

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         DV     ++ + +  +R +  L  + V         ++ ++    +   
Sbjct: 283 AAIDYLINLEFDVGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDG 342

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    R++   P     + +E
Sbjct: 343 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRE 397

Query: 435 DIIAIIKILVDLRNGKGTI 453
                ++ +    +G+   
Sbjct: 398 RAGFAVRDIHPSHHGRICP 416


>gi|46360930|gb|AAS89198.1| RpoB [Corynebacterium bovis DSM 20582]
          Length = 1149

 Score =  513 bits (1321), Expect = e-143,   Method: Composition-based stats.
 Identities = 186/520 (35%), Positives = 256/520 (49%), Gaps = 63/520 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  +           M   + LL A    +  +  D  +     V   V+
Sbjct: 668  LVDEGDRVEAGQAIADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVL 726

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D DD   I+      R  +IL G
Sbjct: 727  TSIHIEEH--EIDARDTKLGPEEITRDIPNVGEDVLADLDDR-GIVRIGADVRDGDILVG 783

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                V  +              
Sbjct: 784  KVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGESGKVIGV-------------- 829

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   ++ DD+ PGV  +V+V+VA KR IQ GDK+AGRHGNKG+V RILP EDMPFL
Sbjct: 830  ---RVFSREYDDDLAPGVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGRILPAEDMPFL 886

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G  + +  +D K    +  L   L
Sbjct: 887  PDGTPVDIILNTHGVPRRMNIGQVLEIHLGWLAKA-GWSVDTNSDDPKIKAMLEQLPEEL 945

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
              V                               +TPVFDGA  E ++ +LR +  +  G
Sbjct: 946  YDVPADSLT-------------------------ATPVFDGASNEELSGLLRSSRPNRDG 980

Query: 1233 --------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                    ++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 981  IRLVDDYGKAELIDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1040

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G P
Sbjct: 1041 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIP 1100

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            ESF VL+KE+Q+L L++++  +            + +   
Sbjct: 1101 ESFKVLLKELQSLCLNVEVLAADGTPMELSSTDDELDHAN 1140



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 331/661 (50%), Positives = 458/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     +    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TERFGFSEIMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++     F   +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSLFRPKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGT------------IDDIDNLGNRRVRSVGEML 471
             +    + +EDI+  I+ LV L  G+ T            +DDID+ GNRR+R+VGE++
Sbjct: 305 DTEGTMTLTEEDILTTIEYLVRLHAGEKTMTSPEGVEIAIGVDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V +G++T+ V YL+A EE+   +AQAN+  DED  FTE+ +  R   
Sbjct: 485 VNPFGFIETPYRRVENGQITDVVDYLTADEEDRHVVAQANTPFDEDKRFTEDRIEVRLKG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 545 GDVEVVPVDQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I +   +G  D        Y L KF+R+
Sbjct: 605 VGTGMELRAAYDAGDVIITPKAGVVEFVSADYITVMDDDGVRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV  GD V     IADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQKPLVDEGDRVEAGQAIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE E+ ARDTKLGPEEITRDIPNV E+ L ++D+ GI+ +GA+V  
Sbjct: 718 QRMVEEDVLTSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDDRGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G SG V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGESGKVIGVRVFSREYD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 84/298 (28%), Positives = 145/298 (48%), Gaps = 24/298 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L+++Q+ S+   +            +    R   GL+   + + P
Sbjct: 16  RYSFAKINAPIEVPGLLDLQRESFAWLVGTPEWRARRQAEVGDGVRVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L F    FD  K  +D+C  +D+ Y+ PL +T                  +
Sbjct: 76  IEDYSENMSLTFSEPRFDEVKNTIDECKDKDINYSAPLYVTAEFT---------NSMSGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      S + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESID--SSTERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITERFGFSEIMMSTLEK 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG--KKLTSGLLKSLKEKGVKFLGI 298
           D       A   +   +        D+ + ++E+   +     L K  + K  + LG+
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSLFRPKRYDLAKVGRYKVNRKLGL 302


>gi|215425904|ref|ZP_03423823.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
           tuberculosis T92]
          Length = 1096

 Score =  513 bits (1321), Expect = e-142,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 453/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 127 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 182

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 183 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 242

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 243 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 302

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++   +++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 303 IQNQIRVGMSRMERVVRERMTTQGREAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 362

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 363 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 422

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 423 RVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 482

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 483 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 542

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  +G  +VA+ +G++E+V A  I +    G           YR+ KF R
Sbjct: 543 LVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 595

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 596 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 655

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 656 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 715

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 716 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 775

Query: 950 ID 951
            D
Sbjct: 776 ED 777



 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 189/517 (36%), Positives = 259/517 (50%), Gaps = 61/517 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 607  IVDAGDRVEAGQVIADGPCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 665

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 666  TSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVT 725

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 726  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIGI 768

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 769  RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 828

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 829  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 878

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 879  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 919

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 920  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 979

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF
Sbjct: 980  QFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESF 1039

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
             VL+KE+Q+L L++++ +S        E E  D  + 
Sbjct: 1040 KVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERA 1076



 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/286 (30%), Positives = 135/286 (47%), Gaps = 21/286 (7%)

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL+     + PI  FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I    
Sbjct: 3   GLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---- 58

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                  +  +IK Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +  
Sbjct: 59  -----NNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK-- 111

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            + K L++ ++IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F 
Sbjct: 112 STDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFG 171

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
              +     +      +   L+   +       +  GE    ES + L   L    K   
Sbjct: 172 FSEIMRSTLEKDNTVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYD 225

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           +  +G          +   +    T     E   V   + L  +  
Sbjct: 226 LARVGRYK---VNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 268


>gi|220905930|ref|YP_002481241.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. PCC 7425]
 gi|219862541|gb|ACL42880.1| DNA-directed RNA polymerase, beta subunit [Cyanothece sp. PCC 7425]
          Length = 1099

 Score =  513 bits (1321), Expect = e-142,   Method: Composition-based stats.
 Identities = 319/605 (52%), Positives = 426/605 (70%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D + +  Y + T+  +   + +DAL+++YR +RPG+  T S  + + +  FFD  +YDL
Sbjct: 196 FDRLRHPEYYQKTIDKEGQFNEEDALMELYRKLRPGEPPTVSGGQQLLDSRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L+ P+  R +  EDI+A I  L++L    G IDDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLNVPETTRVLTSEDILAAIDYLINLEYDIGMIDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D D++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDTDALTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGFIETP+  V DG+V  D   VY++A EE+++ +A  + S D DG    E+V 
Sbjct: 436 HARVNEYGFIETPFYPVKDGRVLKDQAPVYMTADEEDDKRVAPGDVSTDADGHILGEVVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      +++DF+  SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 496 VRYRRDFTTTTPDQVDFVAVSPVQIISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
             P VGTG+E+  A+ SG  +  +  G V  V A  I +R+ +G           Y L K
Sbjct: 556 HRPLVGTGLEAQAARDSGMVVTTRSDGEVSYVSADVIRVRATQGHEIE-------YPLQK 608

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRP+V  GD+V    +IADG +T+ G+LALG+N+L+A+MPW GYN+ED+
Sbjct: 609 YQRSNQDTCLNQRPIVFAGDKVTAGQVIADGSATEGGELALGQNVLIAYMPWEGYNYEDA 668

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V +DV+TSIH+E++E+ AR TKLGPEEITR+IPNV E+ L+ ++E GII  GA
Sbjct: 669 ILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITREIPNVGEDALRQLNENGIIRTGA 728

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 729 WVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 788

Query: 947 RHGID 951
           R   D
Sbjct: 789 REQGD 793



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 197/583 (33%), Positives = 271/583 (46%), Gaps = 59/583 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR-DTKLGP 858
                       +L    P  G   E        MV               + R     G 
Sbjct: 541  MGSNMQRQAVPLLRPHRPLVGTGLEAQAARDSGMVVTTRSDGEVSYVSADVIRVRATQGH 600

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+  G +V  G ++      +G   +   + +L A   
Sbjct: 601  EIEYPLQKYQRSNQDTCLNQRPIVFAGDKVTAGQVIADGSATEG-GELALGQNVLIAYMP 659

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     +S  +V   ++    ++K E    +E  Q +L   +   E   +
Sbjct: 660  WEGYNYEDAIL-----ISERLVYDDVYTSIHVEKYE----IEARQTKLGPEEITREIPNV 710

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              +   +L E   I  G    +G     K T        + P  +  +    ++      
Sbjct: 711  GEDALRQLNENGIIRTGAWVEAGDILVGKVTPKGES--DQPPEEKLLRAIFGEKARDVRD 768

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V       +++ R    +   + GD++PPG   VV+V+VA KR IQ GDKMAGRHG
Sbjct: 769  NSLRVPNGEKGRVVDVR----VFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHG 824

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+SRILP EDMP+L DGTPVD+VLNPLGVPSRMNVGQ+FE  LGWA   LG + K  
Sbjct: 825  NKGIISRILPQEDMPYLPDGTPVDVVLNPLGVPSRMNVGQVFECLLGWAGYHLGARFKIT 884

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D     + S L                +    D++       W         VFD   
Sbjct: 885  PFDEMHGAEASRL---------------TVHGKLDEAKELTGRDW---------VFD--- 917

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                         D  G++ ++DG TGE FDRPVTVG  YMLKL H+V DK++ARSTG Y
Sbjct: 918  ------------PDNPGKTQIFDGRTGEAFDRPVTVGKAYMLKLVHLVDDKIHARSTGPY 965

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV G
Sbjct: 966  SLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKG 1025

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                  GTPESF VL++E+Q+L L I +            ++ 
Sbjct: 1026 QAIPRPGTPESFKVLMRELQSLCLDIGVHKVEATEDGSNRDVE 1068



 Score =  304 bits (778), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 101/459 (22%), Positives = 181/459 (39%), Gaps = 46/459 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDL+E+Q+ S+  FL   +  +            S  PIT ++G   L  +   Y+   
Sbjct: 13  LPDLVEIQRESFRWFLEEGLIEELE----------SFSPITDYTGKIELHILAKDYKLKR 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+   RD TYAV + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 63  PKYSVDEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEQDVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y   +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEVDK---NGRRTYNASLIPNRGAWLKFETDKNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+   EI         Y +  D          LM        
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDAEIFDRLRHPEYYQKTIDKEGQFNEEDALM------EL 224

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G             +     T E  +
Sbjct: 225 YRKLRPGEPPTVSGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLNVPETTRVLTSEDIL 284

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++        
Sbjct: 285 AAIDYLINLEYDIGMIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDTDA 344

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 345 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 399

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 400 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|46360924|gb|AAS89195.1| RpoB [Corynebacterium xerosis]
          Length = 1149

 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 183/514 (35%), Positives = 255/514 (49%), Gaps = 65/514 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M   + LL A    +  +  D  +     V   ++
Sbjct: 671  LVDEGDRVEAGQVIADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEDDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D DD   I+      R  +IL G+ 
Sbjct: 730  TSIHIEEHEIDARDTKLGPEEITREIPNVGEDMLKDLDDR-GIVRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  +                
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAREVRDTSMRVPHGESGKVIGV---------------- 832

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG++ +ILP EDMPFL D
Sbjct: 833  -RVFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVIGKILPQEDMPFLPD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I+   +  K              
Sbjct: 892  GTPVDILLNTHGVPRRMNIGQVLEVHLGWLAKA-GWTIEGDPDWAKR------------- 937

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE---- 1230
                              +        +   V+TPVFDGA+ E +  +L  +  D     
Sbjct: 938  ------------------LPAELHDVPADSLVATPVFDGAENEELAGLLASSRPDRDGDV 979

Query: 1231 ----SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 980  LVNADGKAQLIDGRSGEPFPFPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1039

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1040 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1099

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            F VL+KE+Q+L L++++ ++            D 
Sbjct: 1100 FKVLLKELQSLCLNVEVLSADGVPVELSSTDDDE 1133



 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 329/661 (49%), Positives = 453/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L + F     +I     +    +  +  TL  
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIK----ERFGFSEIMMATLEK 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A ++    FF   +YDL+ VGR K+N +L L  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEPPTRESAMALLENNFFKPKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 PD-DVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
                  + ++DI   I+ LV L +G+              +DDID+ GNRR+R+VGE++
Sbjct: 308 DGVGEMVLTEQDIATTIEYLVRLHDGEKTMTSPDGREVPVEVDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDVESIQPTTLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA- 650
           VN +GFIETPYR+V DGK+T +V YL+A EE+   +AQAN+ +DE+G F  E +  R   
Sbjct: 488 VNPFGFIETPYRRVVDGKLTTEVDYLTADEEDRFVVAQANTPVDENGQFVNETLPVRKKG 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+AEAPF
Sbjct: 548 GDVEVVRATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPF 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  ++A  AG+VE V A  I I   EG           + L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDLVIAPCAGVVETVSADFITIMDDEGQR-------HTFILRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 661 NQGTSYNQKPLVDEGDRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV +D+ TSIHIEE E+ ARDTKLGPEEITR+IPNV E+ LK++D+ GI+ +GA+V  
Sbjct: 721 QRMVEDDILTSIHIEEHEIDARDTKLGPEEITREIPNVGEDMLKDLDDRGIVRIGADVRD 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS+RVP G SG V+ VR+F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMRVPHGESGKVIGVRVFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 82/298 (27%), Positives = 133/298 (44%), Gaps = 29/298 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q+ S+   +        R  E         GL+     + P
Sbjct: 19  RYSFAKISEPIPVPGLLDLQRESFAWLIGTPEWRARRQEELGDGAQVTSGLEDILDELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      FD  K  VD+C  +D+ Y+ PL +T              +   +
Sbjct: 79  IEDYSQKMSLTLSDPWFDSVKNTVDECKDKDINYSAPLYVTAEFT---------NRETGE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+M+  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +I
Sbjct: 130 IKSQTVFIGDFPMMSDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKI 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L A G  +EEI   F     ++ +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIKERFGFSEIMMATLEK 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +               ES   L        K   +  +G   
Sbjct: 248 DGVANTDEALLEIYRKQRPGEP-------PTRESAMALLENNFFKPKRYDLAKVGRYK 298


>gi|326382974|ref|ZP_08204663.1| DNA-directed RNA polymerase subunit beta [Gordonia neofelifaecis NRRL
            B-59395]
 gi|326198110|gb|EGD55295.1| DNA-directed RNA polymerase subunit beta [Gordonia neofelifaecis NRRL
            B-59395]
          Length = 1172

 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/520 (35%), Positives = 257/520 (49%), Gaps = 66/520 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L        +  M   + LL AI   +  +  D  +     V   V+
Sbjct: 682  IVDEGQRVESGQVLADGPCT-DQGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 740

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 741  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIVRIGAEVRDGDILVGKV 799

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 800  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 842

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +       DD+ PGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 843  VRTFSRDEDDDLAPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPAEDMPFLPD 902

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  I +   + +    +         
Sbjct: 903  GTPVDIILNTHGVPRRMNIGQILETHLGWVSKA-GWNIDTEKLEEEWAKRLPEAMHSAPP 961

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
               T                            +TPVFDGA ++ +  +L     +  G  
Sbjct: 962  NTNT----------------------------ATPVFDGAKDDELAGLLGSTLPNRDGEV 993

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 994  MVGPDGKATLFDGRSGEPFPYPVSVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGK 1053

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1054 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1113

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
            F VL+KE+Q+L L++++ +S         E+ D +  +L+
Sbjct: 1114 FKVLLKELQSLCLNVEVLSSEGTAI----EMSDTDDEDLE 1149



 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 452/681 (66%), Gaps = 28/681 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +    + +  I   
Sbjct: 181 DKTTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTILLKALGMTNEAI--T 238

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D   ++ +ALL++YR +RPG+  T   AES+   LFF   +YDL+
Sbjct: 239 ERFGFSEIMMSTLEKDSTSNQDEALLEVYRKLRPGEPPTKESAESLLENLFFKEKRYDLA 298

Query: 410 TVGRVKMNMRLNL--DTPDDVRHIRKEDIIAIIKILVDLRNGKGT--------------- 452
            VGR K+N +L L  +       +  EDIIA ++ LV L                     
Sbjct: 299 RVGRYKINKKLGLTANPMVGESTLTTEDIIATVEYLVRLHESDPNITSMMTVPGGVEVPV 358

Query: 453 -IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +++ PQ LIN +PVV+
Sbjct: 359 EVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDAEAITPQTLINIRPVVA 418

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
           A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP
Sbjct: 419 AIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCP 478

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ Y++A EE+   I QAN
Sbjct: 479 IETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIAYMTADEEDRYLIGQAN 538

Query: 632 SSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           ++ D DG+ T+E V  R    E   VP + ++ +D SP+Q+VS+A ++IPFLE+DD+NR 
Sbjct: 539 TNYDADGTITDERVLVRIKGAEVEFVPAKSVELLDVSPRQMVSVATAMIPFLEHDDANRA 598

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPL+++E+P VGTGME   A  +G  IV  + G+VE+V A  I + + +G
Sbjct: 599 LMGANMQRQAVPLVRSESPLVGTGMELRAAVDAGDVIVTGKTGVVEEVSADFITVMADDG 658

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
             D        YRL KF+RSN  TC NQ P+V  G  V    ++ADGP TD G++ALG+N
Sbjct: 659 TRDS-------YRLRKFERSNHGTCANQVPIVDEGQRVESGQVLADGPCTDQGEMALGKN 711

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVA MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+
Sbjct: 712 LLVAIMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSD 771

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L ++DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+
Sbjct: 772 EVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLK 831

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP G +G V+ VR F+R   D
Sbjct: 832 VPHGETGKVIGVRTFSRDEDD 852



 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 95/324 (29%), Positives = 158/324 (48%), Gaps = 22/324 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---MMNIAPDERPNE----GLQAAFKSVFPIT 66
           R  F K  E +++P L+++Q  S++  +           R  E    GL+   + + PI 
Sbjct: 27  RASFAKIDEPLEVPGLLDLQLDSFEWLVGTPEWRAKAITRGEENPVGGLEEVLRELSPIE 86

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FS +  L F    FD  K  +D+C  +D+TYA PL +T   I           +  +IK
Sbjct: 87  DFSSSMSLSFSDPHFDEVKASIDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 137

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  G+F+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 138 SQTVFMGDFPIMTDKGSFIINGTERVVVSQLVRSPGVYFDSTIDKT--TEKTLHSVKVIP 195

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALGM +E I   F     ++ +   D 
Sbjct: 196 GRGAWLEFDVDKRDTVGVRIDRKRRQPVTILLKALGMTNEAITERFGFSEIMMSTLEKDS 255

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ E ++E+   K+    L +  + K  K LG+T++ 
Sbjct: 256 TSNQDEALLEVYRKLRPGEPPTKESAESLLENLFFKEKRYDLARVGRYKINKKLGLTANP 315

Query: 303 LCGLYVAEDIVNGETGEIYIEAGD 326
           + G           T E  +   +
Sbjct: 316 MVGESTLTTEDIIATVEYLVRLHE 339


>gi|218437736|ref|YP_002376065.1| DNA-directed RNA polymerase subunit beta [Cyanothece sp. PCC 7424]
 gi|218170464|gb|ACK69197.1| DNA-directed RNA polymerase, beta subunit [Cyanothece sp. PCC 7424]
          Length = 1096

 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 332/687 (48%), Positives = 455/687 (66%), Gaps = 10/687 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 112 INGAERVIVNQIVRSPGVYYKCEYDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 171

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  D++ +  + + TL  + N   ++ALL++YR +RPG+ 
Sbjct: 172 TRKLSAQVLLKAIGLSDNEIL--DALRHPDFYQKTLDKEGNPSEEEALLELYRKLRPGEP 229

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD+ +YDL  VGR K+N +L L+  D  R +  EDI++ I  L++L
Sbjct: 230 PTVSGGQLLLESRFFDNKRYDLGRVGRYKLNKKLRLNVTDTTRVLTSEDILSAIDYLINL 289

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+ DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + DS+ P  L+N 
Sbjct: 290 EFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADSLTPASLVNP 349

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+H+
Sbjct: 350 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHH 409

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN--DVVYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY +V +G+     + VYL+A EE+ 
Sbjct: 410 GRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRARRDLEPVYLTADEEDE 469

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + + DE+G    E V  R   E      +++D+I  SP Q+VS+A SLIPFLE+
Sbjct: 470 FRVAPGDVATDEEGHIIGESVPVRYRHEFSTTEPQQVDYIAVSPVQIVSVATSLIPFLEH 529

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV  VDA  I 
Sbjct: 530 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQTARDSGMVIVSRTHGIVTHVDATTIR 589

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++            V  Y L K+QRSNQ+TC+NQRPLV  G+EV    ++ADG +T+ G+
Sbjct: 590 VQ------VKGEERVIEYELQKYQRSNQDTCLNQRPLVYTGEEVVPGQVLADGSATEGGE 643

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           +ALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIH+E++E+ AR TKLGPEEITR+
Sbjct: 644 IALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEARQTKLGPEEITRE 703

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 704 IPNVGEDALRNLDERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 763

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 764 RDNSLRVPNGEKGRVVDVRVFTREQGD 790



 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 211/671 (31%), Positives = 287/671 (42%), Gaps = 79/671 (11%)

Query: 729  AKRAGIVEQVDAIRIV--------IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN--- 777
            A+R      + A            + + E       S    YR        Q        
Sbjct: 453  ARRDLEPVYLTADEEDEFRVAPGDVATDEEGHIIGESVPVRYRHEFSTTEPQQVDYIAVS 512

Query: 778  --QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              Q   V            A+              +L    P  G   E        MV 
Sbjct: 513  PVQIVSVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQTARDSGMVI 572

Query: 836  EDVFTSIHIEEFEVMARDTKLGPE--EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
                  I         R    G E                  +++  ++  G EV PG +
Sbjct: 573  VSRTHGIVTHVDATTIRVQVKGEERVIEYELQKYQRSNQDTCLNQRPLVYTGEEVVPGQV 632

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L      +G   +   + +L A    +  +  D  L     V   V       ++ I+  
Sbjct: 633  LADGSATEG-GEIALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKYEIEAR 691

Query: 954  ERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            +  +  E    +I  +  D     DE+ I+    +    +IL G+    G         L
Sbjct: 692  QTKLGPEEITREIPNVGEDALRNLDERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKL 751

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMP 1067
               +  E  R                   ++       +  + R  + ++   + GD++P
Sbjct: 752  LRAIFGEKARD------------------VRDNSLRVPNGEKGRVVDVRVFTREQGDELP 793

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PG   VV+V+VA KR IQ GDKMAGRHGNKGI+SRILP EDMP+L DG PVDIVLNPLGV
Sbjct: 794  PGANMVVRVYVAQKRKIQVGDKMAGRHGNKGIISRILPIEDMPYLPDGRPVDIVLNPLGV 853

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMNVGQ+FE  LGWA   LG + K    D               ++ G  +  E +  
Sbjct: 854  PSRMNVGQVFECLLGWAGENLGVRFKITPFD---------------EMYGEEASRETVHG 898

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              + +  R  + W         VFD  +                G+ ++YDG TGEPFDR
Sbjct: 899  LLEQASHRPGKDW---------VFDTEN---------------PGKIMVYDGRTGEPFDR 934

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            PVTVG  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGA
Sbjct: 935  PVTVGQAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGA 994

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            AY LQE+LT+KSDD+ GR     +IV G      GTPESF VL++E+Q+LGL I +    
Sbjct: 995  AYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVE 1054

Query: 1368 TKNSAKMEEIP 1378
            T       ++ 
Sbjct: 1055 TLTDGTSRDVE 1065



 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 109/493 (22%), Positives = 195/493 (39%), Gaps = 54/493 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLI +Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 9   LPDLISIQRSSFRWFLQ----------EGLIEELDSFSPITDYTGKLELHFLGQDYKLKE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 59  PKYTVDEAKRRDSTYSVQMYVPTRLI---------NKETGNIKEQEVFIGDLPLMTERGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 110 FIINGAERVIVNQIVRSPGVYYKCEYDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL        Y +  D    P     L+        
Sbjct: 167 VRIDKTRKLSAQVLLKAIGLSDNEILDALRHPDFYQKTLDKEGNPSEEEALL------EL 220

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G+ L        K   +  +G             D     T E  +
Sbjct: 221 YRKLRPGEPPTVSGGQLLLESRFFDNKRYDLGRVGRYKLNKKLRLNVTDTTRVLTSEDIL 280

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++    +   
Sbjct: 281 SAIDYLINLEFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSEADS 340

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 341 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 395

Query: 435 DIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMER 484
                ++ +    +G+    +                 RV   G +    YR+   R  R
Sbjct: 396 RAGFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRARR 455

Query: 485 SIKERISSVDIDS 497
            ++    + D + 
Sbjct: 456 DLEPVYLTADEED 468


>gi|291451927|ref|ZP_06591317.1| DNA-directed RNA polymerase subunit beta [Streptomyces albus J1074]
 gi|291354876|gb|EFE81778.1| DNA-directed RNA polymerase subunit beta [Streptomyces albus J1074]
          Length = 1170

 Score =  513 bits (1320), Expect = e-142,   Method: Composition-based stats.
 Identities = 185/515 (35%), Positives = 264/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 684  VVDEGDRIIEGQVLADGPATEL-GEMALGKNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 742

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 743  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVDAGDILVG 799

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 800  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKV 842

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 843  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 902

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  I  +  ++        +    
Sbjct: 903  EDGTPVDIILNPLGVPSRMNPGQVMEIHLGWLASQ-GWDISGVDTEWAQRLQSIGI---- 957

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                                     ++ + G  V+TPVFDG  E+ +  ++         
Sbjct: 958  -------------------------DRVEPGTNVATPVFDGTREDELAGLIDHTIPNRDG 992

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 993  ERMVQSSGKARLFDGRSGEPFPDPVSVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1052

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1053 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1112

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1113 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1147



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 459/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 210 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 254

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 255 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 311

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 312 KVNKKLGGDAPLDAGVLTTDDVIATIKYLVKLHAGETETTGENGTQIVVETDDIDHFGNR 371

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 372 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 431

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 432 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 491

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L ED  F E
Sbjct: 492 IGSLASYGRVNAFGFVETPYRRVTDGIVTDEVDYLTADEEDRFVIAQANAGLTEDLHFAE 551

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           + V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 552 DRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 611

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 612 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITTTNDDGT-------YTT 664

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+LG++ALG+N+LVAFM W G+
Sbjct: 665 YRLAKFSRSNQGTSVNQKVVVDEGDRIIEGQVLADGPATELGEMALGKNLLVAFMSWEGH 724

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 725 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 784

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV+ GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 785 IRIGAEVDAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 844

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 845 VRVFDREEGD 854



 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 99/323 (30%), Positives = 153/323 (47%), Gaps = 30/323 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 30  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEAALDSGQDVPTKSGLEEIFEE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 90  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 141 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F         
Sbjct: 199 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 258

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +       +  GE    E+ + L   L  + K   +  +G   
Sbjct: 259 LEKDHTQGQDDALLDIYR------KLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYK 312

Query: 301 -DCLCGLYVAEDIVNGETGEIYI 322
            +   G     D     T ++  
Sbjct: 313 VNKKLGGDAPLDAGVLTTDDVIA 335


>gi|255324713|ref|ZP_05365827.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            tuberculostearicum SK141]
 gi|255298188|gb|EET77491.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            tuberculostearicum SK141]
          Length = 1164

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/588 (31%), Positives = 276/588 (46%), Gaps = 60/588 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E         +V       +     +V+      G 
Sbjct: 595  MGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENVTADVITIMDDEGQ 654

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +              N ++  ++ +G  V  G +L           M+    LL A   
Sbjct: 655  RDTYILRKFERTNQGTNYNQTPLVSMGERVEAGQVLADGPGT-HNGEMSLGRNLLVAFMP 713

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  +     V   ++       H ID  +  +  E    +I  ++ D     D
Sbjct: 714  WEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLSDLD 773

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 774  ERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAR--------------- 818

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +     +              DD+ PGV  +++V+VA KR IQ GDKMAGR
Sbjct: 819  --EVRDTSMKVPHGEVGKVIGVARFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGR 876

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+ 
Sbjct: 877  HGNKGVVGKILPPEDMPFMEDGTPVDILLNTHGVPRRMNIGQVLEVHLGWLAHA-GWKVD 935

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +     +   +   L++  E++    + +                        +TPVFDG
Sbjct: 936  T-----EDPKNAELLKTLPEELYDVPADSLT----------------------ATPVFDG 968

Query: 1214 ADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A    I  +L  +  +  G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +
Sbjct: 969  ATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDE 1028

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR
Sbjct: 1029 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGR 1088

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
             +VYE+IV G++  + G PESF VL+KE+Q+L L++++ ++       
Sbjct: 1089 VKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSTDGTPMEL 1136



 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 324/693 (46%), Positives = 455/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + +      G ++  D+   +T  + I+         
Sbjct: 168 LVRSPGVYFDRSIDKSTERPLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 225

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     D    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 226 LLKALGWSEEQI----RDRFGFSELMMSTLESDGVANTDEALLEIYRKQRPGEQPTRELA 281

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  G+ 
Sbjct: 282 QSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGGDHDGLMTLTEEDIAVTLEYLVRLHVGER 341

Query: 452 ------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                         DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 342 EMKAPNGEMIALHTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 401

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQLSQ  +H NSLS +TH RRLSALG GG++R RAG+E+R
Sbjct: 402 PTSLINVRPVSAAIREFFGTSQLSQFMDHNNSLSGLTHKRRLSALGPGGLSRERAGIEVR 461

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGR+CP ET EG NIGL+ +L S+ARVNA+GFIETPYRKV DGK+T+ V YL+A
Sbjct: 462 DVHASHYGRMCPIETPEGPNIGLIGALASYARVNAFGFIETPYRKVVDGKITDQVEYLTA 521

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   IAQA    D +G+ T E +  R   G+  L     +D++D SP+Q+VS+  ++
Sbjct: 522 DEEDRFAIAQAEVEQDAEGNLTGERIEVRLKDGDIGLTDAAGVDYVDVSPRQMVSVGTAM 581

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQ+QAVPL+++EAP VGTGME   A  +G  ++  +AG+VE V
Sbjct: 582 IPFLEHDDANRALMGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENV 641

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I   EG  D        Y L KF+R+NQ T  NQ PLV +G+ V    ++ADGP
Sbjct: 642 TADVITIMDDEGQRD-------TYILRKFERTNQGTNYNQTPLVSMGERVEAGQVLADGP 694

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T  G+++LGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG 
Sbjct: 695 GTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGA 754

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ L ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 755 EEITREIPNVSEDVLSDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFG 814

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G  G V+ V  F+R   D
Sbjct: 815 EKAREVRDTSMKVPHGEVGKVIGVARFSRDDDD 847



 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 96/388 (24%), Positives = 169/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+D  +               D R   GL+   + + P
Sbjct: 25  RYSFAKISEPIALPGLLDVQLDSFDWLVGAPEWREREQAERGDDARVTSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 85  IEDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 136 IKSQTVFIGDFPIMTDMGTFIVNGTERVVVSQLVRSPGVYFDRSIDK--STERPLHSVKV 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 194 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIRDRFGFSELMMSTLES 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 254 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 313

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE+       +    ++   +  +R 
Sbjct: 314 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMKAPNGEMIA-----LHTDDIDHFGNRRLRT 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 369 VGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|46360954|gb|AAS89210.1| RpoB [Corynebacterium confusum]
          Length = 1118

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 182/503 (36%), Positives = 259/503 (51%), Gaps = 59/503 (11%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 662  NYNQTPLVSMGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRI 720

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEI 989
            V   ++       H ID  +  +  E    +I  +A D     DE+ I+      R  +I
Sbjct: 721  VEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVAEDVLSDLDERGIIRIGADVRPGDI 780

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                 E      +     +
Sbjct: 781  LVGKVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGEV 823

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                       +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDM
Sbjct: 824  GKVIGVARFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPPEDM 883

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+                 
Sbjct: 884  PFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWKVDV--------------- 927

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                      ++ E +    ++     A+        +TPVFDGA  E I+ +L  +  +
Sbjct: 928  -------DDPANAELLQTLPEELYDVPADSLT-----ATPVFDGATNEEISRLLASSRPN 975

Query: 1230 ESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQ
Sbjct: 976  RDGDVLVDGEGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQ 1035

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + 
Sbjct: 1036 PLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDP 1095

Query: 1342 GTPESFNVLVKEMQALGLSIDLE 1364
            G PESF VL+KE+Q+L L++++ 
Sbjct: 1096 GIPESFKVLLKELQSLCLNVEVL 1118



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 323/661 (48%), Positives = 448/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQI----RERFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVASTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+G              DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIAVALEYLVRLHVGEGEMKAPNGEMISINTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPVETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           VN++GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D +G+   + +  R   
Sbjct: 485 VNSFGFIETPYRKVVDGKVTDQVEYLTADEEDRFSIAQAEVEQDAEGNIVGDRIEVRQRD 544

Query: 652 -EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            +  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 545 GDIAVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  ++  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLVITPKAGVVEDVTADLITIMDDEGQRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTNYNQTPLVSMGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNV+E+ L ++DE GII +GA+V P
Sbjct: 718 QRIVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVAEDVLSDLDERGIIRIGADVRP 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G  G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGEVGKVIGVARFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 93/388 (23%), Positives = 167/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +                 R   GL+   + + P
Sbjct: 16  RYSFAKISEPIAVPGLLDLQLDSFAWLIGTPEWRERQQAERGDGARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IEDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIRERFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVASTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +  + L  L+V E  +    GE+       I+   ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVALEYLVRLHVGEGEMKAPNGEMI-----SINTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|311739231|ref|ZP_07713068.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudogenitalium ATCC 33035]
 gi|311305657|gb|EFQ81723.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            pseudogenitalium ATCC 33035]
          Length = 1164

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/588 (31%), Positives = 276/588 (46%), Gaps = 60/588 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E         +V       +     +V+      G 
Sbjct: 595  MGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENVTADVITIMDDEGQ 654

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +              N ++  ++ +G  V  G +L           M+    LL A   
Sbjct: 655  RDTYILRKFERTNQGTNYNQTPLVSMGERVEAGQVLADGPGT-HNGEMSLGRNLLVAFMP 713

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  +     V   ++       H ID  +  +  E    +I  ++ D     D
Sbjct: 714  WEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLSDLD 773

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 774  ERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAR--------------- 818

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +     +              DD+ PGV  +++V+VA KR IQ GDKMAGR
Sbjct: 819  --EVRDTSMKVPHGEVGKVIGVARFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGR 876

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+ 
Sbjct: 877  HGNKGVVGKILPPEDMPFMEDGTPVDILLNTHGVPRRMNIGQVLEVHLGWLAHA-GWKVD 935

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +     +   +   L++  E++    + +                        +TPVFDG
Sbjct: 936  T-----EDPKNAELLKTLPEELYDVPADSLT----------------------ATPVFDG 968

Query: 1214 ADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A    I  +L  +  +  G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +
Sbjct: 969  ATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDE 1028

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR
Sbjct: 1029 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGR 1088

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
             +VYE+IV G++  + G PESF VL+KE+Q+L L++++ ++       
Sbjct: 1089 VKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSTDGTPMEL 1136



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 324/693 (46%), Positives = 455/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + +      G ++  D+   +T  + I+         
Sbjct: 168 LVRSPGVYFDRSIDKSTERPLHSVKVIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 225

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     D    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 226 LLKALGWSEEQIK----DRFGFSELMMSTLESDGVANTDEALLEIYRKQRPGEQPTRELA 281

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  G+ 
Sbjct: 282 QSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGGDHDGLMTLTEEDIAVTLEYLVRLHVGER 341

Query: 452 ------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                         DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 342 EMKAPNGEMIALHTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 401

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQLSQ  +H NSLS +TH RRLSALG GG++R RAG+E+R
Sbjct: 402 PTSLINVRPVSAAIREFFGTSQLSQFMDHNNSLSGLTHKRRLSALGPGGLSRERAGIEVR 461

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGR+CP ET EG NIGL+ +L S+ARVNA+GFIETPYRKV DGK+T+ V YL+A
Sbjct: 462 DVHASHYGRMCPIETPEGPNIGLIGALASYARVNAFGFIETPYRKVVDGKITDQVEYLTA 521

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   IAQA    D +G+ T E +  R   G+  L     +D++D SP+Q+VS+  ++
Sbjct: 522 DEEDRFAIAQAEVEQDAEGNLTGERIEVRLKDGDIGLTDAAGVDYVDVSPRQMVSVGTAM 581

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQ+QAVPL+++EAP VGTGME   A  +G  ++  +AG+VE V
Sbjct: 582 IPFLEHDDANRALMGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENV 641

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I   EG  D        Y L KF+R+NQ T  NQ PLV +G+ V    ++ADGP
Sbjct: 642 TADVITIMDDEGQRD-------TYILRKFERTNQGTNYNQTPLVSMGERVEAGQVLADGP 694

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T  G+++LGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG 
Sbjct: 695 GTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGA 754

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ L ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 755 EEITREIPNVSEDVLSDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFG 814

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G  G V+ V  F+R   D
Sbjct: 815 EKAREVRDTSMKVPHGEVGKVIGVARFSRDDDD 847



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 96/388 (24%), Positives = 169/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+D  +               D R   GL+   + + P
Sbjct: 25  RYSFAKISEPIALPGLLDVQLDSFDWLVGAPEWREREQAERGDDARVTSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 85  IEDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 136 IKSQTVFIGDFPIMTDMGTFIVNGTERVVVSQLVRSPGVYFDRSIDK--STERPLHSVKV 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 194 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIKDRFGFSELMMSTLES 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 254 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 313

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE+       +    ++   +  +R 
Sbjct: 314 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMKAPNGEMIA-----LHTDDIDHFGNRRLRT 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 369 VGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|239980073|ref|ZP_04702597.1| DNA-directed RNA polymerase subunit beta [Streptomyces albus J1074]
          Length = 1160

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 185/515 (35%), Positives = 264/515 (51%), Gaps = 67/515 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G +L      +    M   + LL A    +  +  D  +     V   V+
Sbjct: 674  VVDEGDRIIEGQVLADGPATEL-GEMALGKNLLVAFMSWEGHNYEDAIILSQRLVQDDVL 732

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D  DE+ I+         +IL G
Sbjct: 733  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADL-DERGIIRIGAEVDAGDILVG 789

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 790  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKV 832

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   + GD++PPGV ++V+V+VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 833  IGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFL 892

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +DGTPVDI+LNPLGVPSRMN GQ+ E HLGW     G  I  +  ++        +    
Sbjct: 893  EDGTPVDIILNPLGVPSRMNPGQVMEIHLGWLASQ-GWDISGVDTEWAQRLQSIGI---- 947

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-------- 1224
                                     ++ + G  V+TPVFDG  E+ +  ++         
Sbjct: 948  -------------------------DRVEPGTNVATPVFDGTREDELAGLIDHTIPNRDG 982

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +  SG++ L+DG +GEPF  PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 983  ERMVQSSGKARLFDGRSGEPFPDPVSVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLG 1042

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G P
Sbjct: 1043 GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIP 1102

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KEMQ+L L++++ +S   +    +   D
Sbjct: 1103 ESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDED 1137



 Score =  507 bits (1305), Expect = e-141,   Method: Composition-based stats.
 Identities = 338/670 (50%), Positives = 459/670 (68%), Gaps = 38/670 (5%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            + I    + G+ +        T  + ++A     E+ LEE    E              
Sbjct: 200 EMEIDKRDMVGVRIDRKRKQSVT--VLLKALGWTTEQILEEFGEYES------------- 244

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +R TL  D  + + DALLDIYR +RPG+  T   A+++   L+F+  +YDL+ VGR 
Sbjct: 245 ---MRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRY 301

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNR 462
           K+N +L  D P D   +  +D+IA IK LV L  G+               DDID+ GNR
Sbjct: 302 KVNKKLGGDAPLDAGVLTTDDVIATIKYLVKLHAGETETTGENGTQIVVETDDIDHFGNR 361

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 362 RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 421

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 422 SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 481

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L ED  F E
Sbjct: 482 IGSLASYGRVNAFGFVETPYRRVTDGIVTDEVDYLTADEEDRFVIAQANAGLTEDLHFAE 541

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           + V  R   GE   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAV
Sbjct: 542 DRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAV 601

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G           
Sbjct: 602 PLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITTTNDDGT-------YTT 654

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+LG++ALG+N+LVAFM W G+
Sbjct: 655 YRLAKFSRSNQGTSVNQKVVVDEGDRIIEGQVLADGPATELGEMALGKNLLVAFMSWEGH 714

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIPNVSEE L ++DE GI
Sbjct: 715 NYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGI 774

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I +GAEV+ GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ 
Sbjct: 775 IRIGAEVDAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG 834

Query: 942 VRIFNRHGID 951
           VR+F+R   D
Sbjct: 835 VRVFDREEGD 844



 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 99/323 (30%), Positives = 153/323 (47%), Gaps = 30/323 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP-----------NEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L  +                    GL+  F+ 
Sbjct: 20  LRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVEAALDSGQDVPTKSGLEEIFEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 80  ISPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD    +   S K +++
Sbjct: 131 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKT--SDKDIFS 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            +IIP +G W+++E D +D++ VRIDR+RK  VT  L ALG  +E+IL  F         
Sbjct: 189 AKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRAT 248

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +       +  GE    E+ + L   L  + K   +  +G   
Sbjct: 249 LEKDHTQGQDDALLDIYR------KLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYK 302

Query: 301 -DCLCGLYVAEDIVNGETGEIYI 322
            +   G     D     T ++  
Sbjct: 303 VNKKLGGDAPLDAGVLTTDDVIA 325


>gi|46360940|gb|AAS89203.1| RpoB [Corynebacterium amycolatum]
          Length = 1144

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 180/516 (34%), Positives = 255/516 (49%), Gaps = 69/516 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M   + LL A    +  +  D  +     V   ++
Sbjct: 668  LVDEGQRVEAGQVIADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E + +D  DE+ I+      R  +IL  
Sbjct: 727  TSIHIEEH--EIDARDTKLGPEEITRDIPNASEEMLKDL-DERGIVRIGADVRDGDILVA 783

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                V  +              
Sbjct: 784  KTTPKGETELTPEERLLRAIFGEKSREVRDTSMRVPHGESGKVIGV-------------- 829

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   +  DD+ PGV  +V+V+VA KR IQ GDKMAGRHGNKG++ +ILP EDMPFL
Sbjct: 830  ---RVFSREDDDDLAPGVNEMVRVYVAQKRKIQDGDKMAGRHGNKGVIGKILPQEDMPFL 886

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I+   +  K            
Sbjct: 887  PDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWSIEGDPDWAKR----------- 934

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE-- 1230
                                +        S   V+TPVFDGA+ E +  +L  +  +   
Sbjct: 935  --------------------LPADLHDVPSDSLVATPVFDGAENEELAGLLASSRPNRDG 974

Query: 1231 ------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GE F  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 975  EVLVNADGKATLFDGRSGEKFPFPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1034

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G P
Sbjct: 1035 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIP 1094

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            ESF VL+KE+Q+L L++++ ++            + 
Sbjct: 1095 ESFKVLLKELQSLCLNVEVLSADGVPVELGSSDDEE 1130



 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L + F     +I     +    +  +  TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIK----ERFGFSEIMMATLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A ++    FF   +YDL+ VGR K+N +L L T
Sbjct: 245 DGVANTDEALLEIYRKQRPGEPPTRESALALLENNFFKPKRYDLAKVGRYKVNRKLGLGT 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
                  + ++DI   I+ LV L +G+               DDID+ GNRR+R+VGE++
Sbjct: 305 EVSGEMVLTEQDIATTIEYLVRLHDGENVMTSPEGVEIPVETDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDVESIQPTTLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +AR
Sbjct: 425 LSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSCYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA- 650
           VN +GFIETPYR+V DG +T++V YL+A EE+   +AQAN+ +DE+G F +E +  R   
Sbjct: 485 VNPFGFIETPYRRVRDGVITDEVDYLTADEEDRYVVAQANTPIDENGHFVQETLSVRKKG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 545 GDVESVRADEVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  IVA  AG+VE V A  I I   EG           Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDVIVASAAGVVETVSADFITIMDDEGQR-------HTYLLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV  G  V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQKPLVDEGQRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV ED+ TSIHIEE E+ ARDTKLGPEEITRDIPN SEE LK++DE GI+ +GA+V  
Sbjct: 718 QRMVEEDILTSIHIEEHEIDARDTKLGPEEITRDIPNASEEMLKDLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILV K TPKGE+ +TPEE+LLRAIFGEK+ +VRDTS+RVP G SG V+ VR+F+R   
Sbjct: 778 GDILVAKTTPKGETELTPEERLLRAIFGEKSREVRDTSMRVPHGESGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 91/349 (26%), Positives = 158/349 (45%), Gaps = 25/349 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q+ S+   +            +  D R   GL+   + + P
Sbjct: 16  RYSFAKIQEPIAVPGLLDLQRESFAWLIGTPEWRARRQEELGEDARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      FD  K  VD+   +D+ Y+ PL +T              +   +
Sbjct: 76  IEDYSQKMSLTLSDPWFDSVKNTVDESKDKDINYSAPLYVTAEFT---------NRETGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +I
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKI 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L A G  +EEI   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIKERFGFSEIMMATLEK 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +        ++   ++E+   K     L K  + K  + LG+ +
Sbjct: 245 DGVANTDEALLEIYRKQRPGEPPTRESALALLENNFFKPKRYDLAKVGRYKVNRKLGLGT 304

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           + + G  V  +     T E  +   D  +  +  E     +    I + 
Sbjct: 305 E-VSGEMVLTEQDIATTIEYLVRLHDGENVMTSPEGVEIPVETDDIDHF 352


>gi|213964975|ref|ZP_03393174.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium amycolatum
            SK46]
 gi|213952511|gb|EEB63894.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium amycolatum
            SK46]
          Length = 1156

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 180/516 (34%), Positives = 255/516 (49%), Gaps = 69/516 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M   + LL A    +  +  D  +     V   ++
Sbjct: 671  LVDEGQRVEAGQVIADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDIL 729

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E + +D  DE+ I+      R  +IL  
Sbjct: 730  TSIHIEEH--EIDARDTKLGPEEITRDIPNASEEMLKDL-DERGIVRIGADVRDGDILVA 786

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                V  +              
Sbjct: 787  KTTPKGETELTPEERLLRAIFGEKSREVRDTSMRVPHGESGKVIGV-------------- 832

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   +  DD+ PGV  +V+V+VA KR IQ GDKMAGRHGNKG++ +ILP EDMPFL
Sbjct: 833  ---RVFSREDDDDLAPGVNEMVRVYVAQKRKIQDGDKMAGRHGNKGVIGKILPQEDMPFL 889

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I+   +  K            
Sbjct: 890  PDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWSIEGDPDWAKR----------- 937

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE-- 1230
                                +        S   V+TPVFDGA+ E +  +L  +  +   
Sbjct: 938  --------------------LPADLHDVPSDSLVATPVFDGAENEELAGLLASSRPNRDG 977

Query: 1231 ------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G++ L+DG +GE F  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 978  EVLVNADGKATLFDGRSGEKFPFPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1037

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G P
Sbjct: 1038 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIP 1097

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            ESF VL+KE+Q+L L++++ ++            + 
Sbjct: 1098 ESFKVLLKELQSLCLNVEVLSADGVPVELGSSDDEE 1133



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 332/661 (50%), Positives = 450/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L + F     +I     +    +  +  TL  
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIK----ERFGFSEIMMATLEK 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A ++    FF   +YDL+ VGR K+N +L L T
Sbjct: 248 DGVANTDEALLEIYRKQRPGEPPTRESALALLENNFFKPKRYDLAKVGRYKVNRKLGLGT 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
                  + ++DI   I+ LV L +G+               DDID+ GNRR+R+VGE++
Sbjct: 308 EVSGEMVLTEQDIATTIEYLVRLHDGENVMTSPEGVEIPVETDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDVESIQPTTLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG+ R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +AR
Sbjct: 428 LSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSCYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA- 650
           VN +GFIETPYR+V DG +T++V YL+A EE+   +AQAN+ +DE+G F +E +  R   
Sbjct: 488 VNPFGFIETPYRRVRDGVITDEVDYLTADEEDRYVVAQANTPIDENGRFVQETLSVRKKG 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 548 GDVESVRADEVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  IVA   G+VE V A  I I   EG           Y L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDVIVASATGVVETVSADFITIMDDEGQR-------HTYLLRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV  G  V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 661 NQGTCYNQKPLVDEGQRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV ED+ TSIHIEE E+ ARDTKLGPEEITRDIPN SEE LK++DE GI+ +GA+V  
Sbjct: 721 QRMVEEDILTSIHIEEHEIDARDTKLGPEEITRDIPNASEEMLKDLDERGIVRIGADVRD 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILV K TPKGE+ +TPEE+LLRAIFGEK+ +VRDTS+RVP G SG V+ VR+F+R   
Sbjct: 781 GDILVAKTTPKGETELTPEERLLRAIFGEKSREVRDTSMRVPHGESGKVIGVRVFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 91/349 (26%), Positives = 158/349 (45%), Gaps = 25/349 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q+ S+   +            +  D R   GL+   + + P
Sbjct: 19  RYSFAKIQEPIAVPGLLDLQRESFAWLIGTPEWRARRQEELGEDARVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      FD  K  VD+   +D+ Y+ PL +T              +   +
Sbjct: 79  IEDYSQKMSLTLSDPWFDSVKNTVDESKDKDINYSAPLYVTAEFT---------NRETGE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +I
Sbjct: 130 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKI 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L A G  +EEI   F     ++ +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIKERFGFSEIMMATLEK 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +        ++   ++E+   K     L K  + K  + LG+ +
Sbjct: 248 DGVANTDEALLEIYRKQRPGEPPTRESALALLENNFFKPKRYDLAKVGRYKVNRKLGLGT 307

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           + + G  V  +     T E  +   D  +  +  E     +    I + 
Sbjct: 308 E-VSGEMVLTEQDIATTIEYLVRLHDGENVMTSPEGVEIPVETDDIDHF 355


>gi|317509032|ref|ZP_07966663.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
 gi|316252687|gb|EFV12126.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
          Length = 1167

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 181/503 (35%), Positives = 260/503 (51%), Gaps = 52/503 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L      +    M   + LL A+   +  +  D  +     V   V+
Sbjct: 677  IVDEGQRVEKGQVLADGHCTEN-GEMALGKNLLVAVMPWEGHNYEDAIILSQRLVEEDVL 735

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   +  + + R   +  E+I     +  DE    LD     R+   +   + + G 
Sbjct: 736  TSIHIEEY--EIDARDTKLGAEEITRDIPNVSDEVLADLDERGIIRIGAEVRDGDVLVGK 793

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 794  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGKVI----GIRVFS 842

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             +  D++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVD
Sbjct: 843  REDDDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPIEDMPFMPDGTPVD 902

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LN  GVP RMN+GQI E HLGW     G K+       +   +               
Sbjct: 903  IILNSHGVPRRMNIGQILEAHLGWIAK-TGWKVDDENGLPEWAQN--------------- 946

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------S 1231
                         +   A         +TPVFDGA EE +  +L     +          
Sbjct: 947  -------------LPEDALSAPPNSRAATPVFDGAREEELQGLLSSTIPNRDGEVLVGPD 993

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  PV +GY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 994  GKATLFDGRSGEPFPHPVAIGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1053

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PESF VL+
Sbjct: 1054 QRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPESFKVLL 1113

Query: 1352 KEMQALGLSIDLENSRTKNSAKM 1374
            KE+Q+L L++++ +         
Sbjct: 1114 KELQSLCLNVEVLSKDGAAIEMR 1136



 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 331/666 (49%), Positives = 453/666 (68%), Gaps = 30/666 (4%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + ++         L +        I    V+    +  +  TL  
Sbjct: 193 GAWLEFDVDKRDTVGVRVDRKRRQPVTVLLKALGWTNEQI----VERFGFSEIVMTTLEK 248

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD- 423
           D      +ALLDI+R +RPG+  T   A+++ + L F   +YDL+ VGR K+N +L L+ 
Sbjct: 249 DNIAGTDEALLDIFRKLRPGEPPTREGAQALLDNLLFQEKRYDLARVGRYKLNKKLGLND 308

Query: 424 -TPDDVRHIRKEDIIAIIKILVDLRNG----------------KGTIDDIDNLGNRRVRS 466
                V  +  EDI A I+ LV L                      +DDID+ GNRR+R+
Sbjct: 309 VVASHVTTLTVEDIAATIEYLVRLHEATPGIPETMTPPGGSEVPVEVDDIDHFGNRRLRT 368

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  
Sbjct: 369 VGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFM 428

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL
Sbjct: 429 DQNNPLSGLTHKRRISALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSL 488

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + FARVN +GFIETPYRKV DGKVT+++ YL+A EE+   +AQANS LDE G F EE V 
Sbjct: 489 SVFARVNPFGFIETPYRKVVDGKVTDEIHYLTADEEDRYVVAQANSPLDEQGKFLEERVL 548

Query: 647 CRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL++
Sbjct: 549 VRRKGGEVEFVSSAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLIR 608

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           +E+PFVGTGME   A  +G  IV  + G+VE+V A  I + + +G           +RL 
Sbjct: 609 SESPFVGTGMELRAAIDAGDVIVTDKTGVVEEVSADYITVMADDGSR-------KTHRLR 661

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSN  TC NQRP+V  G  V +  ++ADG  T+ G++ALG+N+LVA MPW G+N+ED
Sbjct: 662 KFARSNHGTCANQRPIVDEGQRVEKGQVLADGHCTENGEMALGKNLLVAVMPWEGHNYED 721

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++S+R+V EDV TSIHIEE+E+ ARDTKLG EEITRDIPNVS+E L ++DE GII +G
Sbjct: 722 AIILSQRLVEEDVLTSIHIEEYEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIIRIG 781

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F
Sbjct: 782 AEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVF 841

Query: 946 NRHGID 951
           +R   D
Sbjct: 842 SREDDD 847



 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 87/300 (29%), Positives = 142/300 (47%), Gaps = 30/300 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  E +++P L++VQ  S+   +      +                 GL+     
Sbjct: 17  RVSFAKIREPLEVPGLLDVQTDSFAWLIGAPWWRERSLERGEHLNGQGKPTSGLEDVLNE 76

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F    FD  K    +C  +D+TYA PL +T   I           +
Sbjct: 77  ISPIEDFSGSMSLSFSEPRFDEVKASEAECKDKDMTYAAPLFVTAEFI---------NNN 127

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD P+MT+ GTF+I G +R+VVSQ+ RSPG++FD    +   + K L++
Sbjct: 128 TGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQVVRSPGVYFDDTIDK--STEKTLHS 185

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            ++IP +G W++ + D +D + VR+DR+R+ PVT  L ALG  +E+I+  F    +    
Sbjct: 186 VKVIPSRGAWLEFDVDKRDTVGVRVDRKRRQPVTVLLKALGWTNEQIVERFGFSEIVMTT 245

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +      +   L+   +       +  GE    E  + L   LL   K   +  +G   
Sbjct: 246 LEKDNIAGTDEALLDIFR------KLRPGEPPTREGAQALLDNLLFQEKRYDLARVGRYK 299


>gi|284929148|ref|YP_003421670.1| DNA-directed RNA polymerase subunit beta [cyanobacterium UCYN-A]
 gi|284809607|gb|ADB95312.1| DNA-directed RNA polymerase subunit beta [cyanobacterium UCYN-A]
          Length = 1103

 Score =  512 bits (1319), Expect = e-142,   Method: Composition-based stats.
 Identities = 335/687 (48%), Positives = 464/687 (67%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 114 INGAERVIVNQIVRSPGVYYKAETDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 173

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   DS+ +  + + TL  + N   +DALL++YR +RPG+ 
Sbjct: 174 TRKLSAQVLLKAIGLNDNEI--FDSLRHPEFYQRTLEKEGNPTEEDALLELYRKLRPGEP 231

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFDS +YDL  VGR K+N +L L  PD +R +R++DI++ I  L++L
Sbjct: 232 PTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLTAPDTMRVLRQQDILSAIDYLINL 291

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               GT+DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + DS+ P  L+N 
Sbjct: 292 EFDIGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDSLTPASLVNP 351

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+AR RAG  +RD+HP+H+
Sbjct: 352 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLARERAGFAVRDIHPSHH 411

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY +V +G+V  D+   YL+A EE++
Sbjct: 412 GRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRVRRDLDPTYLTADEEDD 471

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + S D DG+    +V  R   E  +   +++DF+  SP Q++S+A S+IPFLE+
Sbjct: 472 LRVAPGDISTDTDGNIIGSVVPTRYRQEFFITSPDQVDFVAVSPVQIISVATSMIPFLEH 531

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV  VDA +I 
Sbjct: 532 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTEGIVSYVDANKIR 591

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++    +          Y L K+QRSNQ+TC+NQRPLV VG++V    ++ADG +T+ G+
Sbjct: 592 VKVTGPENHDKVGQEIQYILQKYQRSNQDTCLNQRPLVYVGEDVVPGQVLADGSATEGGE 651

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +D++TSIH+E+FE+ AR TKLGPEEITR+
Sbjct: 652 LALGQNILVAYMPWEGYNYEDAILISERLVFDDIYTSIHVEKFEIEARQTKLGPEEITRE 711

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPN+ E+ LKN+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 712 IPNIGEDSLKNLDEQGIIHIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 771

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 772 RDNSLRVPNGEKGRVVDVRVFTREQGD 798



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 186/535 (34%), Positives = 259/535 (48%), Gaps = 64/535 (11%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                 K+G E                +++  ++ VG +V PG +L      +G   +   
Sbjct: 597  PENHDKVGQEIQYILQKYQRSNQDTCLNQRPLVYVGEDVVPGQVLADGSATEG-GELALG 655

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELL 967
            + +L A    +  +  D  L     V   +       +  I+  +  +  E    +I  +
Sbjct: 656  QNILVAYMPWEGYNYEDAILISERLVFDDIYTSIHVEKFEIEARQTKLGPEEITREIPNI 715

Query: 968  ARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
              D     DEQ I+    +    +IL G+    G         L   +  E  R      
Sbjct: 716  GEDSLKNLDEQGIIHIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD----- 770

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                         ++       +  + R  + ++   + GD++PPG   VV+V+VA KR 
Sbjct: 771  -------------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANIVVRVYVAQKRK 817

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            IQ GDKMAGRHGNKGI+SRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQ+FE  LGW
Sbjct: 818  IQVGDKMAGRHGNKGIISRILPIEDMPYLPDGRPMDIVLNPLGVPSRMNVGQVFECLLGW 877

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG + K    D               ++ G  S  + +      +  +  + W   
Sbjct: 878  AGENLGVRFKITPFD---------------EMYGEESSRKTVHGLLAKAAEKPRKNWVYE 922

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                     +  G+  +YDG TGE FDRP+TVG  YMLKL H+V
Sbjct: 923  N------------------------NHPGKIAVYDGRTGEKFDRPITVGQAYMLKLVHLV 958

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ 
Sbjct: 959  DDKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDME 1018

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            GR     +IV G      GTPESF VL++E+Q+LGL I +    T +     ++ 
Sbjct: 1019 GRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVETADDGTSRDVE 1073



 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 111/491 (22%), Positives = 204/491 (41%), Gaps = 50/491 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q  S+  FL           EGL     S  PIT + G   L F+   Y+   
Sbjct: 11  LPDLIEIQHLSFRWFL----------EEGLIEELNSFSPITDYVGKLELHFLGNNYKLKE 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK DVD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 61  PKHDVDEAKRRDSTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 111

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 112 FIINGAERVIVNQIVRSPGVYYKAETDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VRID+ RK+     L A+G++  EI        FY +   +   +       A   +   
Sbjct: 169 VRIDKTRKLSAQVLLKAIGLNDNEIFDSLRHPEFYQR---TLEKEGNPTEEDALLELYRK 225

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ES    +    L +  + K  K L +T+     +   +DI++  
Sbjct: 226 LRPGEPPTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLTAPDTMRVLRQQDILSAI 285

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              I +E  D+     ++ + +  +R +  L  + V         ++ ++    +   L 
Sbjct: 286 DYLINLE-FDIGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDSLT 344

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
              ++ P      +  +  F            + +  +    R++   P     + +E  
Sbjct: 345 PASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LARERA 399

Query: 437 IAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERSI 486
              ++ +    +G+    +                 RV   G +    YR+   R+ R +
Sbjct: 400 GFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNQYGFIETPYYRVENGRVRRDL 459

Query: 487 KERISSVDIDS 497
                + D + 
Sbjct: 460 DPTYLTADEED 470


>gi|227502630|ref|ZP_03932679.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|306835195|ref|ZP_07468230.1| DNA-directed RNA polymerase subunit beta [Corynebacterium accolens
            ATCC 49726]
 gi|227076670|gb|EEI14633.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|304568916|gb|EFM44446.1| DNA-directed RNA polymerase subunit beta [Corynebacterium accolens
            ATCC 49726]
          Length = 1164

 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/588 (31%), Positives = 276/588 (46%), Gaps = 60/588 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E         +V       +     +V+      G 
Sbjct: 595  MGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENVTADVITIMDDEGQ 654

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +              N ++  ++ +G  V  G +L           M+    LL A   
Sbjct: 655  RDTYILRKFERTNQGTNYNQTPLVSMGQRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMP 713

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  +     V   ++       H ID  +  +  E    +I  ++ D     D
Sbjct: 714  WEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLSDLD 773

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 774  ERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAR--------------- 818

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +     +              DD+ PGV  +++V+VA KR IQ GDKMAGR
Sbjct: 819  --EVRDTSMKVPHGEVGKVIGVARFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGR 876

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+ 
Sbjct: 877  HGNKGVVGKILPPEDMPFMEDGTPVDILLNTHGVPRRMNIGQVLELHLGWLAHA-GWKVD 935

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +     +   +   L++  E++    + +                        +TPVFDG
Sbjct: 936  T-----EDPANAELLKTLPEELYDVPADSLT----------------------ATPVFDG 968

Query: 1214 ADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A    I  +L  +  +  G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +
Sbjct: 969  ATNHEIERLLASSRPNRDGDVLVNEHGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDE 1028

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR
Sbjct: 1029 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGR 1088

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
             +VYE+IV G++  + G PESF VL+KE+Q+L L++++ ++       
Sbjct: 1089 VKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSTDGTPMEL 1136



 Score =  477 bits (1228), Expect = e-132,   Method: Composition-based stats.
 Identities = 321/693 (46%), Positives = 452/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + I      G ++  D+   +T  + +       +  
Sbjct: 168 LVRSPGVYFDRSIDKSTERPLHSVKIIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 223

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +      +  I   +  + +  + +TL +D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 224 TVLLKALGWTEEQI--RERFSFSELMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRELA 281

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K N +L L    D +  + +EDI   ++ LV L  G+ 
Sbjct: 282 QSLLDNSFFRAKRYDLAKVGRYKANRKLGLGGDHDGLMTLTEEDIAVTLEYLVRLHVGER 341

Query: 452 ------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                         DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 342 EMKAPNGEMISLNTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 401

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQLSQ  +H NSLS +TH RRLSALG GG++R RAG+E+R
Sbjct: 402 PTSLINVRPVSAAIREFFGTSQLSQFMDHNNSLSGLTHKRRLSALGPGGLSRERAGIEVR 461

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGR+CP ET EG NIGL+ +L S+ARVN +GFIETPYRKV DGKVT+ V YL+A
Sbjct: 462 DVHASHYGRMCPIETPEGPNIGLIGALASYARVNPFGFIETPYRKVVDGKVTDQVEYLTA 521

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   IAQA    DE+G    E +  R   G+  +     +D++D SP+Q+VS+  ++
Sbjct: 522 DEEDRFAIAQAEVEQDEEGRLIGERIEVRLKEGDIGVTDASGVDYVDVSPRQMVSVGTAM 581

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQ+QAVPL+++EAP VGTGME   A  +G  ++  +AG+VE V
Sbjct: 582 IPFLEHDDANRALMGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENV 641

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I   EG  D        Y L KF+R+NQ T  NQ PLV +G  V    ++ADGP
Sbjct: 642 TADVITIMDDEGQRD-------TYILRKFERTNQGTNYNQTPLVSMGQRVEAGQVLADGP 694

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T  G+++LGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG 
Sbjct: 695 GTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGA 754

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ L ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 755 EEITREIPNVSEDVLSDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFG 814

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G  G V+ V  F+R   D
Sbjct: 815 EKAREVRDTSMKVPHGEVGKVIGVARFSRDDDD 847



 Score =  304 bits (778), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 94/388 (24%), Positives = 171/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+   +               + R   GL+   + + P
Sbjct: 25  RYSFAKISEPIALPGLLDVQLDSFAWLVGSPEWREREQAERGDNARVTSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 85  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ +I
Sbjct: 136 IKSQTVFIGDFPIMTDMGTFIVNGTERVIVSQLVRSPGVYFDRSIDK--STERPLHSVKI 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I    +F   ++ +   
Sbjct: 194 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFSFSELMMSTLES 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 254 DGVSNTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKANRKLGLGG 313

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE+       ++   ++   +  +R 
Sbjct: 314 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMKAPNGEMI-----SLNTDDIDHFGNRRLRT 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 369 VGELIQNQVRVGLSRMERVVRERMTTQD 396


>gi|319950501|ref|ZP_08024414.1| DNA-directed RNA polymerase subunit beta [Dietzia cinnamea P4]
 gi|319435860|gb|EFV91067.1| DNA-directed RNA polymerase subunit beta [Dietzia cinnamea P4]
          Length = 1162

 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 332/737 (45%), Positives = 467/737 (63%), Gaps = 29/737 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +    +           +                I+  E+V+ S    + G+        
Sbjct: 115 FVTAEFENTETGEIKSQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDRSRDK 174

Query: 293 VKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                + S  +    G ++  D+   +T  + I+         L +       +I     
Sbjct: 175 STERDVHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQSVTVLLKALGWTTTEIK---- 230

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D  +D   ALL+IYR +RPG+  T   AE++   LFF   +YDL+
Sbjct: 231 ERYGFSEIMMSTLEKDTVEDTDQALLEIYRKLRPGEPPTRESAEALLENLFFKEKRYDLA 290

Query: 410 TVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L  P+      + +EDI A I+ LV L  G+              +DD
Sbjct: 291 RVGRYKVNRKLGLPDPEGDATTTLTREDIAATIEYLVRLHAGEESMQVAGGREVPVEVDD 350

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +++ PQ LIN +P+ +A+ E
Sbjct: 351 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDSEAITPQSLINIRPITAALKE 410

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQ+SQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 411 FFGTSQMSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETP 470

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYR+V +G VT+ V YL+A EE+   +AQANS +D
Sbjct: 471 EGPNIGLIGSLSVYARVNPFGFIETPYRRVYEGVVTDQVDYLTADEEDRYVVAQANSEID 530

Query: 636 EDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            DG F E+ +  R    +  +V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 531 ADGRFVEDRILVRKKHGDVEMVEPGDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 590

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQ+VPL+++EAP VGTGME   A  +G  +V    G+VE+V A  I +   +G    
Sbjct: 591 NMQRQSVPLVRSEAPLVGTGMELRAAVDAGDVVVNTAPGMVEEVSADFITVMDDDG---- 646

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              G   YRL KF RSNQ TC NQRP+V  GD V    ++ADGP T+ G++ALG+N+LVA
Sbjct: 647 ---GRQTYRLSKFARSNQGTCSNQRPIVDEGDRVEVGQVLADGPCTENGEMALGKNLLVA 703

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPNVS+E L 
Sbjct: 704 IMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLA 763

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++D+ GI+ +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 764 DLDDRGIVRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 823

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ VR+F+R   D
Sbjct: 824 ESGKVIGVRVFSRDDDD 840



 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/532 (35%), Positives = 269/532 (50%), Gaps = 50/532 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +  R             ++  I+  G  V  G +L      +    M   + L
Sbjct: 642  MDDDGGRQTYRLSKFARSNQGTCSNQRPIVDEGDRVEVGQVLADGPCTEN-GEMALGKNL 700

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L AI   +  +  D  +     V   V+       H  + + R   +  E+I     +  
Sbjct: 701  LVAIMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEH--EIDARDTKLGAEEITRDIPNVS 758

Query: 973  DE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            DE    LD     R+   +   + + G    K  T L+ +        +  +    ++  
Sbjct: 759  DEVLADLDDRGIVRIGAEVRDGDVLVGKVTPKGETELTPE-------ERLLRAIFGEKAR 811

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +    SLKV +  S  ++  R    +      DD+PPGV  +V+V+VA KR IQ GDK+A
Sbjct: 812  EVRDTSLKVPHGESGKVIGVR----VFSRDDDDDLPPGVNELVRVYVAQKRKIQDGDKLA 867

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG++ +ILP EDMPF+ DGTPVDI+LN  GVP RMN+GQI ETHLGW     G +
Sbjct: 868  GRHGNKGVIGKILPAEDMPFMPDGTPVDIILNTHGVPRRMNIGQIMETHLGWLAKA-GWE 926

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +    +    +                              +       + G   +TPVF
Sbjct: 927  VPREADGSLPDWATK--------------------------LPEEIHHVEPGTNTATPVF 960

Query: 1212 DGADEEAINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            DGA +  I  +L     +          G++ L+DG +GEPF  PV VGY+Y+LKL+H+V
Sbjct: 961  DGAADTEITGLLGCTLPNRDGERMVKADGKATLFDGRSGEPFPYPVAVGYMYILKLHHLV 1020

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDDVV
Sbjct: 1021 DDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVV 1080

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            GR +VYE+IV G +  E G PESF VL+KE+Q+L L++++ +S  +  +  E
Sbjct: 1081 GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGQAVSLGE 1132



 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 86/298 (28%), Positives = 145/298 (48%), Gaps = 22/298 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE-------RPNEGLQAAFKSVFPIT 66
           R  F K  E + +P L+++Q  S++ F+       E           GL++  K + PI 
Sbjct: 19  RVSFAKLSEPLPVPGLLDLQTESFEWFIGSEEWQKEAASRGVTNLEGGLESILKEISPIE 78

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    F+  K  ++DC  +D TY  PL +T                  +IK
Sbjct: 79  DFSGSMSLSFSEPYFEEVKASLEDCREKDRTYEAPLFVTA---------EFENTETGEIK 129

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD  + +   + + +++ ++IP
Sbjct: 130 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDRSRDK--STERDVHSVKVIP 187

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+  VT  L ALG  + EI     F   ++ +   D 
Sbjct: 188 SRGAWLEFDVDKRDTVGVRIDRKRRQSVTVLLKALGWTTTEIKERYGFSEIMMSTLEKDT 247

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITS 300
                 A   +            ++ E ++E+   K+    L +  + K  + LG+  
Sbjct: 248 VEDTDQALLEIYRKLRPGEPPTRESAEALLENLFFKEKRYDLARVGRYKVNRKLGLPD 305


>gi|67922541|ref|ZP_00516049.1| DNA-directed RNA polymerase, beta subunit [Crocosphaera watsonii WH
           8501]
 gi|67855625|gb|EAM50876.1| DNA-directed RNA polymerase, beta subunit [Crocosphaera watsonii WH
           8501]
          Length = 1104

 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 336/687 (48%), Positives = 461/687 (67%), Gaps = 4/687 (0%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +         ++  +            + G +++    
Sbjct: 115 INGAERVIVNQIVRSPGVYYKAETDKNGRRTYSASLIPNRGAWLKFETDKNGLVWVRIDK 174

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  DS+ +  + + TL  + N   +DALL++YR +RPG+ 
Sbjct: 175 TRKLSAQVLLKAIGLSDNEIL--DSLRHPEFYQRTLDKEGNPTEEDALLELYRKLRPGEP 232

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFDS +YDL  VGR K+N +L L+ PD +R +R EDI++ I  L+ L
Sbjct: 233 PTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLNAPDVMRTLRSEDILSAIDYLISL 292

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               GT+DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  + DS+ P  L+N 
Sbjct: 293 EFDIGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDSLTPASLVNP 352

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+
Sbjct: 353 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHH 412

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEEN 624
           GRICP ET EG N GL+ SL ++ARVN YGFIETPY +V +G+V  D+  VYL+A EE++
Sbjct: 413 GRICPVETPEGPNAGLIGSLATYARVNNYGFIETPYYRVENGRVRRDLDPVYLTADEEDD 472

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  + S DE+G+     V  R   E  +    ++D++  SP Q++S+A S+IPFLE+
Sbjct: 473 LRVAPGDISTDEEGNILGNAVPTRYRQEFFITGPAQVDYVAVSPVQIISVATSMIPFLEH 532

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  GIV   DA  I 
Sbjct: 533 DDANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTEGIVTYADANEIR 592

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           ++    +          Y L K+QRSNQ+TC+NQRPLV VG++V    ++ADG +T+ G+
Sbjct: 593 VKVTGPEGHEKVGQEIQYILQKYQRSNQDTCLNQRPLVYVGEDVVPGQVLADGSATEGGE 652

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIH+E+FE+ AR TKLGPEEITR+
Sbjct: 653 LALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKFEIEARQTKLGPEEITRE 712

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DV
Sbjct: 713 IPNVGEDSLRNLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDV 772

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RD SLRVP+G  G VVDVR+F R   D
Sbjct: 773 RDNSLRVPNGEKGRVVDVRVFTREQGD 799



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 205/654 (31%), Positives = 281/654 (42%), Gaps = 77/654 (11%)

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN-----QRPLVKVGDEVRRNDIIADGP 798
             I + E       +    YR   F               Q   V            A+  
Sbjct: 479  DISTDEEGNILGNAVPTRYRQEFFITGPAQVDYVAVSPVQIISVATSMIPFLEHDDANRA 538

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT---- 854
                        +L    P  G   E        MV       I         R      
Sbjct: 539  LMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTEGIVTYADANEIRVKVTGP 598

Query: 855  ----KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                K+G E                +++  ++ VG +V PG +L      +G   +   +
Sbjct: 599  EGHEKVGQEIQYILQKYQRSNQDTCLNQRPLVYVGEDVVPGQVLADGSATEG-GELALGQ 657

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLA 968
             +L A    +  +  D  L     V   V       +  I+  +  +  E    +I  + 
Sbjct: 658  NILVAYMPWEGYNYEDAILISERLVYDDVYTSIHVEKFEIEARQTKLGPEEITREIPNVG 717

Query: 969  RD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             D     DEQ I+    +    +IL G+    G         L   +  E  R       
Sbjct: 718  EDSLRNLDEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------ 771

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                        ++       +  + R  + ++   + GD++PPG   VV+ +VA KR I
Sbjct: 772  ------------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRAYVAQKRKI 819

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKGI+SRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQ+FE  LGWA
Sbjct: 820  QVGDKMAGRHGNKGIISRILPIEDMPYLPDGRPMDIVLNPLGVPSRMNVGQVFECLLGWA 879

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG + K    D               ++ G  S  + +    + +  +  + W    
Sbjct: 880  GENLGVRFKITPFD---------------EMYGEESSRKTVHGLLEKASNKPRKDWVY-- 922

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                      +EE              G+  +YDG TGE FDRPVTVG  YMLKL H+V 
Sbjct: 923  ----------NEE------------HPGKIDVYDGRTGEKFDRPVTVGEAYMLKLVHLVD 960

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ G
Sbjct: 961  DKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYTLQELLTVKSDDMQG 1020

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            R     +IV G      GTPESF VL++E+Q+LGL I +    T +     ++ 
Sbjct: 1021 RNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVHKVETADDGTSRDVE 1074



 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 108/493 (21%), Positives = 200/493 (40%), Gaps = 54/493 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDLIE+Q AS+  FL           +GL     S  PI+ ++G   L F+   Y+   
Sbjct: 12  LPDLIEIQHASFRWFL----------EQGLIEELNSFSPISDYTGKLELHFLGENYKLKE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD +Y+V + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 62  PKYDVDEAKRRDASYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D   ++ 
Sbjct: 113 FIINGAERVIVNQIVRSPGVYYKAETDK---NGRRTYSASLIPNRGAWLKFETDKNGLVW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L A+G+   EIL +      Y +  D    P     L+        
Sbjct: 170 VRIDKTRKLSAQVLLKAIGLSDNEILDSLRHPEFYQRTLDKEGNPTEEDALL------EL 223

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G           A D++     E  +
Sbjct: 224 YRKLRPGEPPTVSGGQQLLESRFFDSKRYDLGRVGRYKLNKKLRLNAPDVMRTLRSEDIL 283

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++    +   
Sbjct: 284 SAIDYLISLEFDIGTVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSESDS 343

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    R++   P     + +E
Sbjct: 344 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRE 398

Query: 435 DIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMER 484
                ++ +    +G+    +                 RV + G +    YR+   R+ R
Sbjct: 399 RAGFAVRDIHPSHHGRICPVETPEGPNAGLIGSLATYARVNNYGFIETPYYRVENGRVRR 458

Query: 485 SIKERISSVDIDS 497
            +     + D + 
Sbjct: 459 DLDPVYLTADEED 471


>gi|291298701|ref|YP_003509979.1| DNA-directed RNA polymerase subunit beta [Stackebrandtia nassauensis
            DSM 44728]
 gi|290567921|gb|ADD40886.1| DNA-directed RNA polymerase, beta subunit [Stackebrandtia nassauensis
            DSM 44728]
          Length = 1142

 Score =  512 bits (1318), Expect = e-142,   Method: Composition-based stats.
 Identities = 179/512 (34%), Positives = 258/512 (50%), Gaps = 61/512 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +I  G  V  G ++        +  M   + LL A    +  +  D  +     V   V+
Sbjct: 654  VINEGDRVEAGQVMADGPCT-DKGEMALGKNLLVAFMPWEGQNYEDAIILSSRLVQEDVL 712

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                 + H +D  +  +  E    +I  ++ +     DE+ I+      R  +IL G+  
Sbjct: 713  TSIHIDEHEVDARDTKLGPEEITREIPNVSEEMLSDLDERGIIRIGAEVRDGDILVGKVT 772

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 773  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGTVIGV 815

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +      GD++ PGV  +V+V++A KR I  GDK+AGRHGNKG++S+I+P EDMPFL DG
Sbjct: 816  RTFSRDDGDELSPGVNELVRVYIAQKRKISDGDKLAGRHGNKGVISKIVPAEDMPFLPDG 875

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+VLNPLGVP RMN+GQ+ E HLGW     G ++      ++ +             
Sbjct: 876  TPVDVVLNPLGVPGRMNIGQVLELHLGWIAKS-GWQLAGDAEGWQKSLKAIG-------- 926

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                 AE+      V+TPVFDG   E I  +L  A  +      
Sbjct: 927  ---------------------AEEAPPDSTVATPVFDGVHLEEITGLLESARPNRDGDRM 965

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G++ L+DG TGEPF  P++VGY+Y+LKLNH+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 966  VGTDGKAKLFDGRTGEPFPGPISVGYMYILKLNHLVDDKIHARSTGPYSMITQQPLGGKA 1025

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEME W +QAYGA+Y LQE+LTIKSDD++GR +VYE++V G +  E G PESF
Sbjct: 1026 QFGGQRFGEMECWAMQAYGASYALQELLTIKSDDILGRVKVYEAVVKGENIPEPGIPESF 1085

Query: 1348 NVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             VL+KE+Q+L L++++ +S        +   +
Sbjct: 1086 KVLLKELQSLCLNVEVLSSDGTAVELRDSDDE 1117



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 331/650 (50%), Positives = 455/650 (70%), Gaps = 14/650 (2%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  DI   ET  + I+         L +        I     +    +  +  TL  
Sbjct: 186 GAWLEFDIDKRETAGVRIDRKRRQAVTVLLKAIGWTNDQI----RERFGWSEIMMATLEK 241

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D    + +ALLDIYR +RPG+  T   AE++ + LFF+  +YDL+ VGR ++N +  L T
Sbjct: 242 DHVGSQDEALLDIYRKLRPGEPPTKENAETLLDNLFFNPKRYDLAKVGRYQVNKKFGLST 301

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDD--IDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           P     + + D+++II+ L  L+NG+   D   ID+ GNRR+R+VGE+++NQ R+GL RM
Sbjct: 302 PISTGVLTEADLVSIIEYLCRLQNGEDGYDRDDIDHFGNRRIRTVGELIQNQVRVGLSRM 361

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  + VN ++ +TH RRL+
Sbjct: 362 ERVVRERMTTQDVEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQVNPIAGLTHRRRLN 421

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RA +E+RDVHP+HYGR+CP ET EG NIGL+ +L +FARVN +GFIETPY
Sbjct: 422 ALGPGGLSRDRAAMEVRDVHPSHYGRMCPIETPEGPNIGLIGALAAFARVNPFGFIETPY 481

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKI 661
           R++ +G+VT+DV YL+A EE+   IAQAN+ L++DG+F EE +  R   GE  LV  + +
Sbjct: 482 RRIDNGRVTDDVKYLTADEEDRCVIAQANTKLNDDGTFAEERILVRRKGGEMELVGHDAV 541

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D SP+Q+ S+A +++PFLE+DD+NR LMG NMQRQAVPL+K ++PFVGTGME   A 
Sbjct: 542 DYMDVSPRQMTSVATAMVPFLEHDDANRALMGANMQRQAVPLIKTQSPFVGTGMEYRAAV 601

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            +G  +V + AG+ E V A  I +   +G           Y L KF RSN  TCVNQ P+
Sbjct: 602 DAGDVVVNEVAGVAEDVCADYITVHQDDGFR-------RTYLLHKFHRSNAGTCVNQIPV 654

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           +  GD V    ++ADGP TD G++ALG+N+LVAFMPW G N+ED++++S R+V EDV TS
Sbjct: 655 INEGDRVEAGQVMADGPCTDKGEMALGKNLLVAFMPWEGQNYEDAIILSSRLVQEDVLTS 714

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHI+E EV ARDTKLGPEEITR+IPNVSEE L ++DE GII +GAEV  GDILVGK+TPK
Sbjct: 715 IHIDEHEVDARDTKLGPEEITREIPNVSEEMLSDLDERGIIRIGAEVRDGDILVGKVTPK 774

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SGTV+ VR F+R   D
Sbjct: 775 GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGTVIGVRTFSRDDGD 824



 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 103/465 (22%), Positives = 194/465 (41%), Gaps = 26/465 (5%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNI---APDERPNEGLQAAFKSVFPITAFSG 70
           R  FG+  E +++P+L+ +Q  S+D  +  +      +     GL    + + PI  FSG
Sbjct: 19  RISFGRITEHLEVPNLLALQTDSFDWLVGNDAYRARTEAGATCGLDDILEEISPIEDFSG 78

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F +  FD  K  +++C  +DLTY  PL +T   I           +  +IK Q++
Sbjct: 79  TMSLSFSNPRFDEVKAPIEECKEKDLTYCAPLFVTAEFI---------NHNTGEIKSQTV 129

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   S + L + ++IP +G 
Sbjct: 130 FMGDFPMMTPKGTFIINGTERVVVSQLVRSPGVYFDKQPDKT--SDRDLSSVKVIPGRGA 187

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDFWCFP 248
           W++ + D ++   VRIDR+R+  VT  L A+G  +++I   F     ++ +   D     
Sbjct: 188 WLEFDIDKRETAGVRIDRKRRQAVTVLLKAIGWTNDQIRERFGWSEIMMATLEKDHVGSQ 247

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGL 306
             A   +            +  E ++++         L K  + +  K  G+++    G+
Sbjct: 248 DEALLDIYRKLRPGEPPTKENAETLLDNLFFNPKRYDLAKVGRYQVNKKFGLSTPISTGV 307

Query: 307 YVAEDIVN-GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
               D+V+  E         D  D   ++   +  IR +  L  + V         +V +
Sbjct: 308 LTEADLVSIIEYLCRLQNGEDGYDRDDIDHFGNRRIRTVGELIQNQVRVGLSRMERVVRE 367

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +   +   +  I            +     F           ++ +  +    RLN   P
Sbjct: 368 RMTTQD--VEAITPQTLINIRPVVAAIREFFGTSQLSQFMDQVNPIAGLTHRRRLNALGP 425

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
                + ++     ++ +     G+  +  I+      +  +G +
Sbjct: 426 GG---LSRDRAAMEVRDVHPSHYGR--MCPIETPEGPNIGLIGAL 465


>gi|46360938|gb|AAS89202.1| RpoB [Corynebacterium renale]
          Length = 1146

 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 183/513 (35%), Positives = 253/513 (49%), Gaps = 61/513 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  L           M     LL A    +  +  D  +     V   ++
Sbjct: 668  LVNTGDRVEAGQPLADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRIVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVEREQIE------LLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    E       +  D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSIHIEEHEIDARDTKLGAEEITREIPNVGDEVLADL-DERGIVRIGADVRAGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +       DD+P GV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++D
Sbjct: 829  VQRFSRDDDDDLPAGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMED 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G ++                      
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLETHLGWLASA-GWQLDE-------------------- 927

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
                  + E +    ++     A         +TPVFDGA  E I  +LR +  +  G  
Sbjct: 928  --NDERNAELLKTLPEELHSVPAGSLT-----ATPVFDGATNEEIAGLLRSSRPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDEDGKAMLLDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ ++            D
Sbjct: 1101 FKVLLKELQSLCLNVEVLSADGTPMELSGSDDD 1133



 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 322/661 (48%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  D    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTQQIV--DRFGFSEIMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D  +    ALL IYR  RPG+  T  +A+S+ N  FF S +YDL+ VGR K+N +L L  
Sbjct: 245 DGVESTDQALLVIYRKQRPGEQPTRELAQSLLNNSFFSSKRYDLARVGRYKINRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             D ++ + +EDI   ++ LV L  G+ T+            DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLQTLTEEDIATTLEYLVRLHAGERTMTSPDGVEIPVETDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+++AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN++GFIETPYRKV +G VT+ V YL+A EE+   IA+A + ++ DG   +E +  R   
Sbjct: 485 VNSFGFIETPYRKVDNGHVTDIVEYLTADEEDRYAIAEATTEVNADGDIIQERIEVRVKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +   + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+ E+P+
Sbjct: 545 GDIQVTGPQGVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRPESPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +++K+AG+VE + A  I I    G  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLVISKKAGVVEDMSADYITIMDDNGQRD-------TYLLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ PLV  GD V     +ADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQTPLVNTGDRVEAGQPLADGPGTHNGEMALGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNV +E L ++DE GI+ +GA+V  
Sbjct: 718 QRIVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVGDEVLADLDERGIVRIGADVRA 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ V+ F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVQRFSRDDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 90/320 (28%), Positives = 151/320 (47%), Gaps = 28/320 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I+IP L++VQ+ S+   +               D R   GL+   + + P
Sbjct: 16  RYSFAKYQEPIEIPGLLDVQRDSFSWLIGAPEWRAEQQELRGEDARVVSGLEEILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  +++   +D+ Y+ PL +T   I             ++
Sbjct: 76  IEDYSGNMSLSLSEPRFEPVKNTIEEAKEKDINYSAPLYVTAEFI---------NNETQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT+ GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 127 IKSQTVFIGDFPMMTEKGTFIVNGTERVVVSQLVRSPGVYFDQSIDK--STERPLHAVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +++I+  F    +     + 
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTQQIVDRFGFSEIMMSTLES 244

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DC 302
                +   L+V  +          GE    E  + L +    S K   +  +G    + 
Sbjct: 245 DGVESTDQALLVIYR------KQRPGEQPTRELAQSLLNNSFFSSKRYDLARVGRYKINR 298

Query: 303 LCGLYVAEDIVNGETGEIYI 322
             GL    D +   T E   
Sbjct: 299 KLGLGGDHDGLQTLTEEDIA 318


>gi|46360978|gb|AAS89222.1| RpoB [Corynebacterium lipophiloflavum]
          Length = 1113

 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 185/493 (37%), Positives = 249/493 (50%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K    M     LL A    +  +  D  +     V   ++
Sbjct: 668  IVSAGQRVEAGQVIADGPGTKN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L  +  +  G  
Sbjct: 946  VPPESLT-------------------------ATPVFDGASNEEITGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDGNGKTVLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1101 FKVLLKELQSLCL 1113



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 317/661 (47%), Positives = 449/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I   +    +  +  TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTQQI--TERFGFSEIMMTTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEIIPINTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ +L S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGALASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + +D++G+ T E +  R   
Sbjct: 485 VNAFGFIETPYQKVEDGKLTDQIDYLTADEEDRYAIAQAATPMDKEGNLTGERIEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQ+QAVPLL++EA +
Sbjct: 545 GDIGVVGASGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGANMQKQAVPLLRSEAAY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TGME   A  +G  +++++AG++E V    I +   EG  D        Y L  F+R+
Sbjct: 605 VATGMEQRAAYDAGDTVISRKAGVIEDVTGDFITVMDDEGIRD-------TYLLRTFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ P+V  G  V    +IADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQTPIVSAGQRVEAGQVIADGPGTKNGEMALGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +D+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GII +GA+V  
Sbjct: 718 QRVVEDDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIIRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 96/389 (24%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP---------NEGLQAAFKSVF 63
            R  F K  E + +P L++VQ  S+   +      + +            GL+   + + 
Sbjct: 15  ERYSFAKISEPVSVPGLLDVQSESFAWLVGTQEWRERQRAERGDDAHIKSGLEDILEEIS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIQDYSGNMSLSLSEPRFEEIKYSIDECKEKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHAVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +++I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTQQITERFGFSEIMMTTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGEI       I+   ++   +  +R
Sbjct: 304 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEII-----PINTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|119714958|ref|YP_921923.1| DNA-directed RNA polymerase subunit beta [Nocardioides sp. JS614]
 gi|158513097|sp|A1SEK1|RPOB_NOCSJ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|119535619|gb|ABL80236.1| DNA-directed RNA polymerase subunit beta [Nocardioides sp. JS614]
          Length = 1166

 Score =  511 bits (1317), Expect = e-142,   Method: Composition-based stats.
 Identities = 186/540 (34%), Positives = 273/540 (50%), Gaps = 49/540 (9%)

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V+      G     R            I++  ++  G  +  G  +        E+ M  
Sbjct: 644  VIETMNDDGTYSTYRLAKFKRSNQGTCINQRPLVSEGDRLEIGTPIADGPCT-DEAEMAL 702

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
               LL A    +  +  D  +     V   ++       H  + + R   +  E+I    
Sbjct: 703  GTNLLVAFMPWQGHNYEDAIILSQRLVQEDILTSIHIEEH--EVDARDTKLGPEEITRDI 760

Query: 969  RDKDDE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             +  +E    LD     R+   +   + + G    K  T L+ +      R+ + + A +
Sbjct: 761  PNVSEEMLADLDERGIIRIGAEVTTGDVLVGKVTPKGETELTPE--ERLLRAIFGEKARE 818

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                   V   +        + +          + GD++PPGV ++V+V+VA KR I  G
Sbjct: 819  VRDTSMKVPHGESGTVIGVRVFDR---------EDGDELPPGVNQLVRVYVAQKRKISVG 869

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK+AGRHGNKG++++ILP EDMPF++DGTPVD+VLNPLGVP RMN+GQI E HLGW    
Sbjct: 870  DKLAGRHGNKGVIAKILPIEDMPFMEDGTPVDVVLNPLGVPRRMNIGQILELHLGWLAKQ 929

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  +    +   A+     ++   +K                          + G  V+
Sbjct: 930  -GWDLNLNDDKSGADWKQRLIKIHADKA-------------------------EPGTKVA 963

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDGA E+ I  +L     +  G        ++ L+DG +GEPF  PV VGY+Y+LKL
Sbjct: 964  TPVFDGAREDEITGLLGSTIPNRDGVRMIDNTGKASLFDGRSGEPFPEPVAVGYMYILKL 1023

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKS
Sbjct: 1024 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAYALQELLTIKS 1083

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV GR +VYE+IV G +  ++G PESF VLVKEMQ+L L++++ +         +   D
Sbjct: 1084 DDVPGRVKVYEAIVKGENIPDSGIPESFKVLVKEMQSLCLNVEVLSQDGTAIEMRDAEED 1143



 Score =  498 bits (1283), Expect = e-138,   Method: Composition-based stats.
 Identities = 342/752 (45%), Positives = 477/752 (63%), Gaps = 39/752 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           FY             F  SA   +     ++   +I      +       + G  + +G 
Sbjct: 102 FYDPKYTVDECKEKDFTYSAPLYVSAEFTNNDTGEIKGQTVFMGDFPLMTDKGTFIINGT 161

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVN----GETGEIYIEAGDVIDEKSLEEIFHSE 340
            + +  + V+  G+  +        +DI         G       D  D   +      +
Sbjct: 162 ERVVVSQLVRSPGVYFERTADKTSDKDIYTAKLIPSRGAWLEFEIDKRDMVGVRLDRKRK 221

Query: 341 IRDIPILY---------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
                +L           +       +  TL  D  + + DALLDIYR +RPG+  T   
Sbjct: 222 QNVTVLLKALGWTNEQIREEFGEYESMMLTLEKDHTQGQDDALLDIYRKLRPGEPPTREA 281

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           A+++ N  +F+  +YDL+ VGR K+N +L L    D + +  +D++A IK +V L +G+ 
Sbjct: 282 AQTLLNNYYFNPKRYDLAKVGRYKINKKLGLLEAFDQQTLTIDDVVAAIKYIVALHDGRE 341

Query: 452 TI-----------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
            I           DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ P
Sbjct: 342 QIEAPQGTLDISADDIDHFGNRRMRTVGELIQNQLRTGLARMERVVRERMTTQDVEAITP 401

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF +SQLSQ  +  N ++ +TH RRLSALG GG++R RAG+E+RD
Sbjct: 402 QSLINIRPVVAALKEFFGTSQLSQFMDQTNPIAGLTHKRRLSALGPGGLSRDRAGMEVRD 461

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GF+ETPYRKV  GKVT+ + YL+A 
Sbjct: 462 VHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFVETPYRKVTKGKVTDQIDYLTAD 521

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLI 679
           +E+   IAQAN++LD+   F EE V  R    E   V  +++D++D SP+Q+VS+A +LI
Sbjct: 522 DEDRYVIAQANAALDDKSRFVEERVLVRQRDGEVSEVLADEVDYMDVSPRQMVSVATALI 581

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NMQRQAVPL+K+++P VGTG+E   A  +G  +VA  AG+V++V 
Sbjct: 582 PFLEHDDANRALMGANMQRQAVPLIKSDSPLVGTGIEYRAAVDAGDVVVATAAGVVKEVS 641

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  I   + +G           YRL KF+RSNQ TC+NQRPLV  GD +     IADGP 
Sbjct: 642 ADVIETMNDDGT-------YSTYRLAKFKRSNQGTCINQRPLVSEGDRLEIGTPIADGPC 694

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD  ++ALG N+LVAFMPW G+N+ED++++S+R+V ED+ TSIHIEE EV ARDTKLGPE
Sbjct: 695 TDEAEMALGTNLLVAFMPWQGHNYEDAIILSQRLVQEDILTSIHIEEHEVDARDTKLGPE 754

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSEE L ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 755 EITRDIPNVSEEMLADLDERGIIRIGAEVTTGDVLVGKVTPKGETELTPEERLLRAIFGE 814

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTS++VP G SGTV+ VR+F+R   D
Sbjct: 815 KAREVRDTSMKVPHGESGTVIGVRVFDREDGD 846



 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 102/382 (26%), Positives = 165/382 (43%), Gaps = 30/382 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIA-----------PDERPNEGLQAAFKSV 62
           R  F K  E +++P L+ +Q  S+D  +  +              D     GLQ  F+ +
Sbjct: 24  RISFAKITEPLEVPQLLSLQTDSFDWLVGNDKWNAAVERRRSEGEDVSSKSGLQEIFEEI 83

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  FS    L F +  F  PK+ VD+C  +D TY+ PL ++      D          
Sbjct: 84  SPIEDFSETMSLSFENPVFYDPKYTVDECKEKDFTYSAPLYVSAEFTNND---------T 134

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K +Y  
Sbjct: 135 GEIKGQTVFMGDFPLMTDKGTFIINGTERVVVSQLVRSPGVYFERTADKT--SDKDIYTA 192

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           ++IP +G W++ E D +D++ VR+DR+RK  VT  L ALG  +E+I   F          
Sbjct: 193 KLIPSRGAWLEFEIDKRDMVGVRLDRKRKQNVTVLLKALGWTNEQIREEFGEYESMMLTL 252

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
           +          L+   +       +  GE    E+ + L +    + K   +  +G    
Sbjct: 253 EKDHTQGQDDALLDIYR------KLRPGEPPTREAAQTLLNNYYFNPKRYDLAKVGRYKI 306

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           +   GL  A D       ++      ++      E   +    + I   D  +       
Sbjct: 307 NKKLGLLEAFDQQTLTIDDVVAAIKYIVALHDGREQIEAPQGTLDISADDIDHFGNRRMR 366

Query: 361 TLVTDKNKDRKDALLDIYRVMR 382
           T+        +  L  + RV+R
Sbjct: 367 TVGELIQNQLRTGLARMERVVR 388


>gi|81300331|ref|YP_400539.1| DNA-directed RNA polymerase subunit beta [Synechococcus elongatus
           PCC 7942]
 gi|109914404|sp|Q31N17|RPOB_SYNE7 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|81169212|gb|ABB57552.1| DNA-directed RNA polymerase, beta subunit [Synechococcus elongatus
           PCC 7942]
          Length = 1100

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 329/689 (47%), Positives = 448/689 (65%), Gaps = 13/689 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +      L   +  +            + G +++    
Sbjct: 117 INGAERVIVNQIVRSPGVYYKSERDKNGRLTHNASLIPNRGAWLKFETDKNGLVWVRIDK 176

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   D + +  Y + T+  +      +AL+++YR +RPG+ 
Sbjct: 177 TRKLSAQVLLKALGLSDNEI--YDKLRHPEYYQKTIDKEGQFSEDEALMELYRKLRPGEP 234

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD  +YDL  VGR K+N +L L+  D VR +  EDI+A I  L++L
Sbjct: 235 PTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLGLNVADTVRTLTSEDILAAIDYLINL 294

Query: 447 RN--GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
               G   +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D DS+ P  L+
Sbjct: 295 ELDLGGCEVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDSDSLSPASLV 354

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+
Sbjct: 355 NPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPS 414

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEE 622
           HYGRICP ET EG N GL+ SL + ARVN YGFIETP+ +V +G+V  D+  VY++A +E
Sbjct: 415 HYGRICPIETPEGPNAGLIGSLATHARVNDYGFIETPFWRVEEGRVRKDLAPVYMTADQE 474

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           ++  +A  + + D+ G      +  R   +      E++D++  SP Q++S+A SLIPFL
Sbjct: 475 DDLRVAPGDVATDDAGYILGTTIPVRYRQDFTTTTPERVDYVALSPVQIISVATSLIPFL 534

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+DD+NR LMG NMQRQAVPLL+ E P VGTG+E   A+ SG  I +   G +  VDA  
Sbjct: 535 EHDDANRALMGSNMQRQAVPLLRPERPLVGTGLEPQAARDSGMVITSPVDGTISYVDATH 594

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           I + +  G+          Y L K+QRSNQ+TC+NQRP+V  GD V+R  +IADG +T+ 
Sbjct: 595 IEVTADTGEKYG-------YALQKYQRSNQDTCLNQRPIVFEGDRVQRGQVIADGSATEK 647

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
           G+LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIHIE+FE+ AR TKLGPEEIT
Sbjct: 648 GELALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEIT 707

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+ +DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA 
Sbjct: 708 REIPNVGEDALRQLDENGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKAR 767

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 768 DVRDNSLRVPNGEKGRVVDVRLFTREQGD 796



 Score =  501 bits (1289), Expect = e-139,   Method: Composition-based stats.
 Identities = 200/583 (34%), Positives = 282/583 (48%), Gaps = 59/583 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E        MV    V  +I   +   +      G 
Sbjct: 544  MGSNMQRQAVPLLRPERPLVGTGLEPQAARDSGMVITSPVDGTISYVDATHIEVTADTGE 603

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G  ++   +   +  +   + +L A   
Sbjct: 604  KYGYALQKYQRSNQDTCLNQRPIVFEGDRVQRGQ-VIADGSATEKGELALGQNILVAYMP 662

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     +S  +V   ++    I+K E    +E  Q +L   +   E   +
Sbjct: 663  WEGYNYEDAIL-----ISERLVYDDVYTSIHIEKFE----IEARQTKLGPEEITREIPNV 713

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              +   +L E   I  G    SG     K T        + P  +  +    ++      
Sbjct: 714  GEDALRQLDENGIIRVGAWVESGDILVGKVTPKGES--DQPPEEKLLRAIFGEKARDVRD 771

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V       +++ R        + GD++PPG   VV+V+VA KR IQ GDKMAGRHG
Sbjct: 772  NSLRVPNGEKGRVVDVRL----FTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHG 827

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+SRILPCEDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE  LGWA   L  + K  
Sbjct: 828  NKGIISRILPCEDMPYLPDGTPLDIVLNPLGVPSRMNVGQVFECMLGWAGQLLDARFKVT 887

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D               ++ G  +    ++    ++  +  + W         VF    
Sbjct: 888  PFD---------------EMYGAEASRLTVNAKLSEAREQTGQPW---------VFSD-- 921

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                         DE G+  +YDG TGEPFDRPVTVG  YMLKL H+V DK++ARSTG Y
Sbjct: 922  -------------DEPGKIQVYDGRTGEPFDRPVTVGRAYMLKLVHLVDDKIHARSTGPY 968

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY+LQE+LT+KSDD+ GR     +IV G
Sbjct: 969  SLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYILQELLTVKSDDMQGRNEALNAIVKG 1028

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                  GTPESF VL++E+Q+L L I +  + T++  + +E+ 
Sbjct: 1029 KAIPRPGTPESFKVLMRELQSLCLDIAVYKASTEDYEEDKEVD 1071



 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 109/496 (21%), Positives = 198/496 (39%), Gaps = 58/496 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+ +Q+ S+  FL   +  +            S  PIT ++G   L F+   Y+   
Sbjct: 14  LPDLVAIQRNSFRWFLEEGLIEELE----------SFSPITDYTGKLELHFLGKQYKLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 64  PKYDVDEAKRRDGTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  ++ +   +G+L +   +IP++G W+  E D   ++ 
Sbjct: 115 FIINGAERVIVNQIVRSPGVYYKSERDK---NGRLTHNASLIPNRGAWLKFETDKNGLVW 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+   EI         Y +  D          LM        
Sbjct: 172 VRIDKTRKLSAQVLLKALGLSDNEIYDKLRHPEYYQKTIDKEGQFSEDEALM------EL 225

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYVAEDIVNGETGEIY 321
              +  GE   +  G++L        K   +  +G    +   GL VA D V   T E  
Sbjct: 226 YRKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLGLNVA-DTVRTLTSEDI 284

Query: 322 IEAGDV----------IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           + A D            +   ++ + +  +R +  L  + V         ++ ++     
Sbjct: 285 LAAIDYLINLELDLGGCEVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSD 344

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              L    ++ P      +  +  F            + +  +    RL+   P     +
Sbjct: 345 SDSLSPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---L 399

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLR 481
            +E     ++ +     G+    +               + RV   G +    +R+   R
Sbjct: 400 TRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLATHARVNDYGFIETPFWRVEEGR 459

Query: 482 MERSIKERISSVDIDS 497
           + + +     + D + 
Sbjct: 460 VRKDLAPVYMTADQED 475


>gi|13508255|ref|NP_110204.1| DNA-directed RNA polymerase subunit beta [Mycoplasma pneumoniae M129]
 gi|2500606|sp|P78013|RPOB_MYCPN RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|1674000|gb|AAB95974.1| RNA polymerase beta subunit [Mycoplasma pneumoniae M129]
          Length = 1391

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 333/1045 (31%), Positives = 517/1045 (49%), Gaps = 116/1045 (11%)

Query: 1    MAKGVVFNGLG----RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M++   F          R+++GK       P+L ++Q  SY  FL  +          L+
Sbjct: 1    MSQKPSFFQKKYSPTATRRYYGKIATDFVQPNLADIQIRSYQTFLDHD----------LE 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                + FPI + +    + F       P+ +         TY + +   L LI       
Sbjct: 51   NLIAAYFPIKSPNDRYTINFKGLRRTAPERNEAQSRSESKTYEIGIYADLELIDSATGTI 110

Query: 117  TGAKSIKDIKE----QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGR 171
               +  K          +++ +LPL+T+DG F++ GI++ V++Q+ RSPGI+     + +
Sbjct: 111  KKPRKSKKNSATSSVDGVFLTNLPLITRDGVFIVNGIEKFVIAQITRSPGIYMLTKSQLK 170

Query: 172  ASLSGKLL---YACRIIPDQGLWMDIEFDSKDII---HVRI---DRRR---KV-PVTSFL 218
             S S K +   Y C ++P  G  M I   +K  I    V+I   D  R   K+ P+T+ L
Sbjct: 171  LSSSRKRVQEGYVCEVLPANGSVMLIYISNKKKIEDAFVQILLRDAVREGAKIFPITTLL 230

Query: 219  MALGMDSEEILSTF--------------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
             A GM  +EIL  F              Y    +    D     L          +    
Sbjct: 231  KAFGMSGKEILKVFKNNEFITRSLEAEVYNAKDFLNNVDPEIKNLLREFRDGKTDLRRKG 290

Query: 265  VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI-----TSDCLCGLYVAEDIVNGETGE 319
            +  D   + + S   L     K+L E       +       D L    + E        E
Sbjct: 291  IASDQKIRSLVSDYVLLEKEHKALSEAKPNDPKVGQLEADMDELMDKIITERAAKHIVHE 350

Query: 320  IYI-----EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            + I     E  D   E S   +  S         + +       R   +T++   +  A 
Sbjct: 351  LSISLRGLENTDECPENSYHALLCSRFFRQRRYNLSAAGRYKVSRKLRITERIYQKTLAC 410

Query: 375  LDIYR----VMRPGDVSTFSVAESMFNFLFFDS--------------------------- 403
                +    +++ G +      + +      +                            
Sbjct: 411  DLHLKNGELLLKKGTLLVKEEIDKIKQAAQNNQIDFVQKIKLTTDGSAVNLSPESLLYES 470

Query: 404  -DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             D Y  +    V + +    +  D  + I   D IA I  ++++ +  G  DDID+LGN+
Sbjct: 471  LDVYVNNDNFDVSVPVVGIHNDNDLNKAITLSDFIASISYVINIPSAIGKYDDIDHLGNK 530

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVD-------------------IDSVMPQDL 503
            RV+ + E++ ++   G+ RMER +KE+++  D                      +  + L
Sbjct: 531  RVKLINELISSRLESGITRMERFLKEKLTIADGVNRGQQINEEGQVIEQAEKKELTIKSL 590

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            IN+KP+   + +FF + QL+Q  +H N LS +++ RR+SA+G GG++R    +++RDVH 
Sbjct: 591  INSKPIQIVIRDFFNTHQLTQFLDHQNPLSELSNKRRISAMGPGGISREDPNLDIRDVHY 650

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            + YGRICP ET EG NIGL+ SL SFA+++  GF+  PYRK+ +G +T++V YL+A+ E+
Sbjct: 651  SQYGRICPIETPEGMNIGLIMSLASFAKIDENGFLMAPYRKIKNGVITDEVEYLTALRED 710

Query: 624  NRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
               IA+ +   ++DE+    ++ +  R    + L    KID+ID +P QVVSI +SLIPF
Sbjct: 711  EHIIAEISSLVNIDENNKILDKEIIGRYRSMQGLYDPSKIDYIDVAPHQVVSIGSSLIPF 770

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LENDDS R LMG NMQRQA PL+K  AP VGTG E  +A+ SG  ++A  +G V+ VD  
Sbjct: 771  LENDDSARALMGTNMQRQAYPLIKPYAPVVGTGQEYKIARDSGLTMLAPCSGTVKYVDNS 830

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            +I I S  G+            L+KF+RSNQNTC N  PLV+ G  V ++++IADGP+ +
Sbjct: 831  KITIESDSGEQHTLD-------LIKFERSNQNTCYNHVPLVEKGQRVTKDEVIADGPAVN 883

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
              +L+LG+N+LVAF  W+GYN+ED+++ISER+V +DV TS+ I E+      TK G E+I
Sbjct: 884  KSELSLGQNVLVAFTTWNGYNYEDAIVISERLVKDDVLTSLTINEYVAQCLSTKNGDEQI 943

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            TRDIPNVS+   + +DE GII VGAEV  GD+LVGK++PKG+  ++PEEKL +AIF E  
Sbjct: 944  TRDIPNVSDANKRYLDENGIIMVGAEVKEGDVLVGKVSPKGQVEVSPEEKLFKAIFPESV 1003

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFN 946
             +VRD+SL++P G  G V  V+ F+
Sbjct: 1004 QNVRDSSLKLPHGGDGIVSCVKRFS 1028



 Score =  474 bits (1219), Expect = e-131,   Method: Composition-based stats.
 Identities = 179/624 (28%), Positives = 282/624 (45%), Gaps = 56/624 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGP 858
                       ++  + P  G   E  +     +        ++   +   +  ++  G 
Sbjct: 781  MGTNMQRQAYPLIKPYAPVVGTGQEYKIARDSGLTMLAPCSGTVKYVDNSKITIESDSGE 840

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +     I           +   ++  G  V   D ++       +S ++  + +L A   
Sbjct: 841  QHTLDLIKFERSNQNTCYNHVPLVEKGQRV-TKDEVIADGPAVNKSELSLGQNVLVAFTT 899

Query: 919  EKAVDVRDTSLRVPSGVSGTV-----VDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                +  D  +     V   V     ++  +         +  I+ +   +    +   D
Sbjct: 900  WNGYNYEDAIVISERLVKDDVLTSLTINEYVAQCLSTKNGDEQITRDIPNVSDANKRYLD 959

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+      +  ++L G+ +  G         L   +  E  ++           V+ 
Sbjct: 960  ENGIIMVGAEVKEGDVLVGKVSPKGQVEVSPEEKLFKAIFPESVQN-----------VRD 1008

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            +   L    +   S +      K   I  G+++  GV+ ++KV+V  KR IQ GDK+AGR
Sbjct: 1009 SSLKLPHGGDGIVSCV------KRFSIANGNELNDGVIEMIKVYVVQKRKIQIGDKLAGR 1062

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+++P  DMP L+DGTPVDI+LNPLGVPSRMN+GQIFE HLG+A   L K++ 
Sbjct: 1063 HGNKGVISKVVPVADMPHLEDGTPVDILLNPLGVPSRMNIGQIFEMHLGYAAHNLAKRML 1122

Query: 1154 SLI------------NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                              +    +  L + L+  I      ++ +     +   +A   K
Sbjct: 1123 ISACFDDKKAQALSTEINQPQYKLDRLITGLKAQITNRGLKDEQAALAQLNNGDIALVLK 1182

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADL---DESGQSILYDGLTGEPFDRPVT 1250
                        V+TP+F G + + +  ++  A L   +  G+  L DG TG PF++P++
Sbjct: 1183 EIGMSFDDLHFKVATPIFQGVNFQDLQDIMDEAGLKPAETHGKFKLIDGRTGLPFEKPIS 1242

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +Y++KLNHMV DK++AR+ G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1243 LGIMYIMKLNHMVDDKIHARAVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1302

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LTIKSDDV GR + Y +IV G    E G PESF +L KE+Q L LS+         
Sbjct: 1303 LQELLTIKSDDVQGRNKAYAAIVKGAAFPEPGIPESFKLLTKELQGLALSVSFIYDDNTQ 1362

Query: 1371 SAKM---------EEIPDFNKCEL 1385
                         E+   FN  E 
Sbjct: 1363 QDSNNVSILQADGEQDDLFNDFEF 1386


>gi|301633290|gb|ADK86844.1| DNA-directed RNA polymerase, beta subunit [Mycoplasma pneumoniae FH]
          Length = 1391

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 333/1045 (31%), Positives = 517/1045 (49%), Gaps = 116/1045 (11%)

Query: 1    MAKGVVFNGLG----RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQ 56
            M++   F          R+++GK       P+L ++Q  SY  FL  +          L+
Sbjct: 1    MSQKPSFFQKKYSPTATRRYYGKIATDFVQPNLADIQIRSYQTFLDHD----------LE 50

Query: 57   AAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                + FPI + +    + F       P+ +         TY + +   L LI       
Sbjct: 51   NLIAAYFPIKSPNDRYTINFKGLRRTAPERNEAQSRSESKTYEIGIYADLELIDSATGTI 110

Query: 117  TGAKSIKDIKE----QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGR 171
               +  K          +++ +LPL+T+DG F++ GI++ V++Q+ RSPGI+     + +
Sbjct: 111  KKPRKSKKNSATSSVDGVFLTNLPLITRDGVFIVNGIEKFVIAQITRSPGIYMLTKSQLK 170

Query: 172  ASLSGKLL---YACRIIPDQGLWMDIEFDSKDII---HVRI---DRRR---KV-PVTSFL 218
             S S K +   Y C ++P  G  M I   +K  I    V+I   D  R   K+ P+T+ L
Sbjct: 171  LSSSRKRVQEGYVCEVLPANGSVMLIYISNKKKIEDAFVQILLRDAVREGAKIFPITTLL 230

Query: 219  MALGMDSEEILSTF--------------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
             A GM  +EIL  F              Y    +    D     L          +    
Sbjct: 231  KAFGMSGKEILKVFKNNEFITRSLEAEVYNAKDFLNNVDPEIKNLLREFRDGKTDLRRKG 290

Query: 265  VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI-----TSDCLCGLYVAEDIVNGETGE 319
            +  D   + + S   L     K+L E       +       D L    + E        E
Sbjct: 291  IASDQKIRSLVSDYVLLEKEHKALSEAKPNDPKVGQLEADMDELMDKIITERAAKHIVHE 350

Query: 320  IYI-----EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            + I     E  D   E S   +  S         + +       R   +T++   +  A 
Sbjct: 351  LSISLRGLENTDECPENSYHALLCSRFFRQRRYNLSAAGRYKVSRKLRITERIYQKTLAC 410

Query: 375  LDIYR----VMRPGDVSTFSVAESMFNFLFFDS--------------------------- 403
                +    +++ G +      + +      +                            
Sbjct: 411  DLHLKNGELLLKKGTLLVKEEIDKIKQAAQNNQIDFVQKIKLTTDGSAVNLSPESLLYES 470

Query: 404  -DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             D Y  +    V + +    +  D  + I   D IA I  ++++ +  G  DDID+LGN+
Sbjct: 471  LDVYVNNDNFDVSVPVVGIHNDNDLNKAITLSDFIASISYVINIPSAIGKYDDIDHLGNK 530

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVD-------------------IDSVMPQDL 503
            RV+ + E++ ++   G+ RMER +KE+++  D                      +  + L
Sbjct: 531  RVKLINELISSRLESGITRMERFLKEKLTIADGVNRGQQINEEGQVIEQAEKKELTIKSL 590

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            IN+KP+   + +FF + QL+Q  +H N LS +++ RR+SA+G GG++R    +++RDVH 
Sbjct: 591  INSKPIQIVIRDFFNTHQLTQFLDHQNPLSELSNKRRISAMGPGGISREDPNLDIRDVHY 650

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            + YGRICP ET EG NIGL+ SL SFA+++  GF+  PYRK+ +G +T++V YL+A+ E+
Sbjct: 651  SQYGRICPIETPEGMNIGLIMSLASFAKIDENGFLMAPYRKIKNGVITDEVEYLTALRED 710

Query: 624  NRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
               IA+ +   ++DE+    ++ +  R    + L    KID+ID +P QVVSI +SLIPF
Sbjct: 711  EHIIAEISSLVNIDENNKILDKEIIGRYRSMQGLYDPSKIDYIDVAPHQVVSIGSSLIPF 770

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            LENDDS R LMG NMQRQA PL+K  AP VGTG E  +A+ SG  ++A  +G V+ VD  
Sbjct: 771  LENDDSARALMGTNMQRQAYPLIKPYAPVVGTGQEYKIARDSGLTMLAPCSGTVKYVDNS 830

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            +I I S  G+            L+KF+RSNQNTC N  PLV+ G  V ++++IADGP+ +
Sbjct: 831  KITIESDSGEQHTLD-------LIKFERSNQNTCYNHVPLVEKGQRVTKDEVIADGPAVN 883

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
              +L+LG+N+LVAF  W+GYN+ED+++ISER+V +DV TS+ I E+      TK G E+I
Sbjct: 884  KSELSLGQNVLVAFTTWNGYNYEDAIVISERLVKDDVLTSLTINEYVAQCLSTKNGDEQI 943

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            TRDIPNVS+   + +DE GII VGAEV  GD+LVGK++PKG+  ++PEEKL +AIF E  
Sbjct: 944  TRDIPNVSDANKRYLDENGIIMVGAEVKEGDVLVGKVSPKGQVEVSPEEKLFKAIFPESV 1003

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFN 946
             +VRD+SL++P G  G V  V+ F+
Sbjct: 1004 QNVRDSSLKLPHGGDGIVSCVKRFS 1028



 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 180/624 (28%), Positives = 282/624 (45%), Gaps = 56/624 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGP 858
                       ++  + P  G   E  +     +        ++   +   +  ++  G 
Sbjct: 781  MGTNMQRQAYPLIKPYAPVVGTGQEYKIARDSGLTMLAPCSGTVKYVDNSKITIESDSGE 840

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +     I           +   ++  G  V   D ++       +S ++  + +L A   
Sbjct: 841  QHTLDLIKFERSNQNTCYNHVPLVEKGQRV-TKDEVIADGPAVNKSELSLGQNVLVAFTT 899

Query: 919  EKAVDVRDTSLRVPSGVSGTV-----VDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                +  D  +     V   V     ++  +         +  I+ +   +    +   D
Sbjct: 900  WNGYNYEDAIVISERLVKDDVLTSLTINEYVAQCLSTKNGDEQITRDIPNVSDANKRYLD 959

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+      +  ++L G+ +  G         L   +  E  ++           V+ 
Sbjct: 960  ENGIIMVGAEVKEGDVLVGKVSPKGQVEVSPEEKLFKAIFPESVQN-----------VRD 1008

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            +   L    +   S +      K   I  G+++  GV+ ++KV+V  KR IQ GDK+AGR
Sbjct: 1009 SSLKLPHGGDGIVSCV------KRFSIANGNELNDGVIEMIKVYVVQKRKIQIGDKLAGR 1062

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG++S+++P  DMP L+DGTPVDI+LNPLGVPSRMN+GQIFE HLG+A   L K++ 
Sbjct: 1063 HGNKGVISKVVPVADMPHLEDGTPVDILLNPLGVPSRMNIGQIFEMHLGYAAHNLAKRML 1122

Query: 1154 SLI------------NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                              +    +  L + L+  I      ++ +     +   +A   K
Sbjct: 1123 ISACFDDKKAQALSTEINQPQYKLDRLITGLKAQITNRGLKDEQAALAQLNNGDIALVLK 1182

Query: 1202 S--------GVPVSTPVFDGADEEAINSMLRMADL---DESGQSILYDGLTGEPFDRPVT 1250
                        V+TP+F G + + +  ++  A L   +  G+  L DG TG PF++P++
Sbjct: 1183 EIGMSFDDLHFKVATPIFQGVNFQDLQDIMDEAGLKPAETHGKFKLIDGRTGLPFEKPIS 1242

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +YM+KLNHMV DK++AR+ G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY 
Sbjct: 1243 LGIMYMMKLNHMVDDKIHARAVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYN 1302

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            LQE+LTIKSDDV GR + Y +IV G    E G PESF +L KE+Q L LS+         
Sbjct: 1303 LQELLTIKSDDVQGRNKAYAAIVKGAAFPEPGIPESFKLLTKELQGLALSVSFIYDDNTQ 1362

Query: 1371 SAKM---------EEIPDFNKCEL 1385
                         E+   FN  E 
Sbjct: 1363 QDSNNVSILQADGEQDDLFNDFEF 1386


>gi|46360994|gb|AAS89230.1| RpoB [Corynebacterium sundsvallense]
          Length = 1120

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 185/493 (37%), Positives = 250/493 (50%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M+    LL A    +  +  D  +     V   ++
Sbjct: 675  IVNTGDRVEAGQVIADGPGTK-DGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 733

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 734  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 792

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 793  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 835

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V RILP EDMPF+ D
Sbjct: 836  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGRILPQEDMPFMAD 895

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D K    +  L   L  
Sbjct: 896  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYD 952

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               STPVFDGA  + I  +L  +  +  G  
Sbjct: 953  VPADSLT-------------------------STPVFDGATNDEIAGLLANSKPNRDGDV 987

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEP+  P+ VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 988  MVDENGKTTLFDGRSGEPYKYPIAVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1047

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1048 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1107

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1108 FKVLLKELQSLCL 1120



 Score =  479 bits (1232), Expect = e-132,   Method: Composition-based stats.
 Identities = 328/756 (43%), Positives = 470/756 (62%), Gaps = 46/756 (6%)

Query: 233 YPKIVYSQRGDFWC-FPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           +  + YS           SA   +    +++   +I +    I       + G  + +G 
Sbjct: 99  FEDVKYSIEEAKDKDINYSAPLYVTAEFINNDTQEIKSQTVFIGDFPLMTDKGTFIVNGT 158

Query: 285 LKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    V    G              +       
Sbjct: 159 ERVVVSQLVRSPGVYFDETIDKSTERPLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRR 218

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +         I        +  +  TL +D   +  +ALL+IYR  RPG+  T 
Sbjct: 219 QPVTVLLKALGWTTEQI--TQRFGFSEIMMTTLESDGVANTDEALLEIYRKQRPGEQPTR 276

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRN 448
            +A+S+    FF + +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  
Sbjct: 277 DLAQSLLENAFFRAKRYDLARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHA 336

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+  +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 337 GETEMTAPNGETIPISTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAE 396

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+
Sbjct: 397 SITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGI 456

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ +L S+AR NA+GFIETPY+KV +G +TN + Y
Sbjct: 457 EVRDVHPSHYGRMCPIETPEGPNIGLIGALASYARANAFGFIETPYQKVENGVLTNQIDY 516

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIA 675
           L+A EE+   IAQA + +D+DG+ T + +  R   G+  +V  + +D++D SP+Q+VS+A
Sbjct: 517 LTADEEDRYAIAQAATPMDKDGTLTGDRIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVA 576

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQ+QAVPLL+AEAP+V TGME   A  +G  ++  +AG+V
Sbjct: 577 TAMIPFLEHDDANRALMGANMQKQAVPLLRAEAPYVATGMEQRAAYDAGDTVINAKAGVV 636

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V    I +   EG  D        Y L  F+R+NQ TC NQ P+V  GD V    +IA
Sbjct: 637 ETVTGDYITVMDDEGVRD-------TYMLRTFERTNQGTCYNQTPIVNTGDRVEAGQVIA 689

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G+++LGRN+LVAFMPW G+N+ED++++++R+V +D+ TS+HIEE E+ ARDTK
Sbjct: 690 DGPGTKDGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEDDILTSVHIEEHEIDARDTK 749

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNVSE+ LK++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 750 LGAEEITREIPNVSEDVLKDLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRA 809

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTSL+VP G +G V+ VR F+R   D
Sbjct: 810 IFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDDD 845



 Score =  300 bits (769), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 92/367 (25%), Positives = 158/367 (43%), Gaps = 26/367 (7%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +                 R   GL+   + + 
Sbjct: 22  ERYSFAKIAEPITVPGLLDVQLESFAWLVGTSEWREREQQLRGESARVTSGLEDILEEIS 81

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L   +  F+  K+ +++   +D+ Y+ PL +T   I  D          +
Sbjct: 82  PIQDYSGNMSLTLSAPRFEDVKYSIEEAKDKDINYSAPLYVTAEFINND---------TQ 132

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 133 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 190

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 191 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITQRFGFSEIMMTTLE 250

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 251 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRAKRYDLARVGRYKVNRKLGLG 310

Query: 299 -TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
              D L  L   +     E           +   + E I  S                  
Sbjct: 311 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTAPNGETIPISTDDIDHFGNRRLRTVGEL 370

Query: 358 IRNTLVT 364
           I+N +  
Sbjct: 371 IQNQVRV 377


>gi|46360922|gb|AAS89194.1| RpoB [Corynebacterium pseudodiphtheriticum]
          Length = 1158

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 197/661 (29%), Positives = 297/661 (44%), Gaps = 69/661 (10%)

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            + + RI +R  +GD+  +T+    Y  +  +         Q   V            A+ 
Sbjct: 536  ITSDRIEVRQKDGDIAVTTADGVDYVDVSPR---------QMVSVATAMIPFLEHDDANR 586

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKL 856
                         ++ +  P+ G   E         +V       +     +++      
Sbjct: 587  ALMGANMQRQAVPLVRSEAPYVGTGMELRAAYDAGDVVITPKAGVVENVSADLITIMDDD 646

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +              N ++  ++ +G  V  G +L           M+    +L A 
Sbjct: 647  GIRDTYMLRKFERTNQGTNYNQTPLVNIGDRVEAGQVLADGPGT-HNGEMSLGRNMLVAF 705

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
               +  +  D  +   S V    +       H ID  +  +  E    +I  ++ D    
Sbjct: 706  MPWEGHNYEDAIILNQSIVEDDSLTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLRD 765

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      R  +IL G+    G         L   +  E  R             
Sbjct: 766  LDERGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGE 825

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               V  +                      +  DD+ PGV  +++V+VA KR IQ GDK+A
Sbjct: 826  TGKVIGVA-----------------RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKLA 868

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+V +ILP EDMPF++DGTPVD++LN  GVP RMN+GQ+ E HLGW     G K
Sbjct: 869  GRHGNKGVVGKILPPEDMPFMEDGTPVDVILNTHGVPRRMNIGQVLEIHLGWLAHA-GWK 927

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +    ND +    I  L   L  V                               +TPVF
Sbjct: 928  VD--PNDPQNEELIKTLPKELYDVPAHSLT-------------------------ATPVF 960

Query: 1212 DGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            DGA  E ++ +L  +  +  G        ++ L+DG +GEPF+ P++VGY+Y+LKL+H++
Sbjct: 961  DGASNEEVSGLLANSRPNRDGNVMVDRHGKARLFDGRSGEPFEHPISVGYMYILKLHHLI 1020

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             +K++ARSTG YS++TQQPLGGK+  GG+R GEMEVW +QAYGAAY LQE+LTIKSDDVV
Sbjct: 1021 DEKIHARSTGPYSMITQQPLGGKAQFGGERFGEMEVWAMQAYGAAYTLQELLTIKSDDVV 1080

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            GR +VYE+IV G++  + G PESF VL+KE+Q+L L++++ +S            D    
Sbjct: 1081 GRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSSDGTPMELSGSDEDDEAG 1140

Query: 1384 E 1384
             
Sbjct: 1141 P 1141



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 330/756 (43%), Positives = 469/756 (62%), Gaps = 45/756 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           F P               SA   +    ++S   +I +    I       E G  + +G 
Sbjct: 95  FEPVKNTVDEAKEKDINYSAPLYVTAEFINSDTQEIKSQTVFIGDFPMMTEKGTFIVNGT 154

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDI----VNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    V    G              +       
Sbjct: 155 ERVIVSQLVRSPGVYFDRSIDKSTERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRR 214

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +      +  I   D    +  + +TL  D   +  +ALL+IYR  RPG+  T 
Sbjct: 215 QPVTVLLKALGWTEEKI--RDRFGFSELMMSTLEADGVANTDEALLEIYRKQRPGEQPTR 272

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRN 448
            +A+S+ +  FF+  +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  
Sbjct: 273 DLAQSLLDNSFFNPKRYDLARVGRYKINRKLGLGGDHDGLSTLTEEDIATTLEYLVRLHT 332

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+  +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 333 GEREMQSPEGQHLMLDTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAE 392

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +++ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+
Sbjct: 393 SITPTSLINVRPVSASIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGI 452

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ SL S+ARVN++GFIETPYRKV DG+VT++V Y
Sbjct: 453 EVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNSFGFIETPYRKVVDGRVTDEVEY 512

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIA 675
           L+A  E+   IAQA     EDG+ T + +  R    +  +   + +D++D SP+Q+VS+A
Sbjct: 513 LAADAEDRYSIAQAEVPTAEDGTITSDRIEVRQKDGDIAVTTADGVDYVDVSPRQMVSVA 572

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+VGTGME   A  +G  ++  +AG+V
Sbjct: 573 TAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMELRAAYDAGDVVITPKAGVV 632

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V A  I I   +G  D        Y L KF+R+NQ T  NQ PLV +GD V    ++A
Sbjct: 633 ENVSADLITIMDDDGIRD-------TYMLRKFERTNQGTNYNQTPLVNIGDRVEAGQVLA 685

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G+++LGRNMLVAFMPW G+N+ED++++++ +V +D  TS+HIEE E+ ARDTK
Sbjct: 686 DGPGTHNGEMSLGRNMLVAFMPWEGHNYEDAIILNQSIVEDDSLTSVHIEEHEIDARDTK 745

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNVSE+ L+++DE GII +GA+V PGDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 746 LGAEEITREIPNVSEDVLRDLDERGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRA 805

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTS++VP G +G V+ V  F+R   D
Sbjct: 806 IFGEKAREVRDTSMKVPHGETGKVIGVARFSREDDD 841



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 147/322 (45%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L+++Q+ SYD  +               D +   GL+     + 
Sbjct: 18  QRYSFAKINEPIAVPGLLDLQRDSYDWLIGTPEWREREQERRGADAQITSGLEDILNELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+P K  VD+   +D+ Y+ PL +T   I  D          +
Sbjct: 78  PIEDYSGNMSLSLSEPRFEPVKNTVDEAKEKDINYSAPLYVTAEFINSD---------TQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT+ GTF++ G +R++VSQL RSPG++FD    +   + + L+A +
Sbjct: 129 EIKSQTVFIGDFPMMTEKGTFIVNGTERVIVSQLVRSPGVYFDRSIDK--STERPLHAVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEKIRDRFGFSELMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +           +   +  + L      + K   +  +G    
Sbjct: 247 ADGVANTDEALLEIYRKQRPGE-------QPTRDLAQSLLDNSFFNPKRYDLARVGRYKI 299

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D ++  T E   
Sbjct: 300 NRKLGLGGDHDGLSTLTEEDIA 321


>gi|254410869|ref|ZP_05024647.1| DNA-directed RNA polymerase, beta subunit [Microcoleus
           chthonoplastes PCC 7420]
 gi|196182224|gb|EDX77210.1| DNA-directed RNA polymerase, beta subunit [Microcoleus
           chthonoplastes PCC 7420]
          Length = 1116

 Score =  511 bits (1316), Expect = e-142,   Method: Composition-based stats.
 Identities = 324/615 (52%), Positives = 435/615 (70%), Gaps = 12/615 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D++ +  Y + TL  + N   ++AL+++YR +RPG+  T S  + + +  FFD+ +YDL
Sbjct: 196 IDALRHPDYYQKTLDKEGNPSEEEALMELYRKLRPGEPPTVSGGQQLLDSRFFDAKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L+  D +R +  +DI+  I  L++L    G+ DDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKINRKLRLNVADTIRVLTPQDIMGAIDYLINLEFDIGSTDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D D++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDSDTLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVNAYGFIETP   V +G+V  D   +Y++A EE++  +A  +  +DE+G    E V 
Sbjct: 436 HARVNAYGFIETPSYPVENGRVIKDKAPLYMTADEEDDLRVAPGDIPMDENGYIMGESVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E      +++DF+  SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 496 VRYRQEFTTTTPDQVDFVAVSPVQIISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS----------VEGDLDPST 756
           E P VGTG+E+  A+ SG  +VA++AG V  VDA +I +++                 S 
Sbjct: 556 ERPLVGTGLEAQAARDSGMVVVARKAGEVVYVDATKIRVQTAPSTPALPGDSTETAQTSE 615

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +  Y + K+QRSNQ+TC+NQRPLV  GD+V    I+ADG +T+ G+LALG+N+LVA+M
Sbjct: 616 PEIIEYEIQKYQRSNQDTCLNQRPLVFYGDDVEAGQILADGSATEGGELALGQNILVAYM 675

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW GYN+ED++LISER+V +DV+TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+ +
Sbjct: 676 PWEGYNYEDAILISERLVLDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDSLRQL 735

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  
Sbjct: 736 DEQGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEK 795

Query: 937 GTVVDVRIFNRHGID 951
           G VVDVRIF R   D
Sbjct: 796 GRVVDVRIFTREQGD 810



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 183/510 (35%), Positives = 258/510 (50%), Gaps = 64/510 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++  ++  G +V  G IL      +G   +   + +L A    +  +  D  L     
Sbjct: 634  CLNQRPLVFYGDDVEAGQILADGSATEG-GELALGQNILVAYMPWEGYNYEDAILISERL 692

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEI 989
            V   V       ++ I+  +  +  E    +I  +  D   + DEQ I+    +    +I
Sbjct: 693  VLDDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDSLRQLDEQGIIRIGAWVEAGDI 752

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                   ++       +  
Sbjct: 753  LVGKVTPKGESDQPPEEKLLRAIFGEKARD------------------VRDNSLRVPNGE 794

Query: 1050 EDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            + R  + +I   + GD++PPG   VV+V+VA KR IQ GDKMAGRHGNKGI+SRILP ED
Sbjct: 795  KGRVVDVRIFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHGNKGIISRILPMED 854

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTP+DI+LNPLGVPSRMNVGQ+FE  LGWA   L  + K +  D          
Sbjct: 855  MPYLPDGTPLDIILNPLGVPSRMNVGQVFECLLGWAGENLDLRFKMIPFD---------- 904

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                 ++ G  +    +    + +     + W         VFD  +             
Sbjct: 905  -----EMYGEEASRLTVHGKLEQAREETQQDW---------VFDPEN------------- 937

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G+  ++DG TGE FDRPVT+G  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 938  --PGKIQVFDGRTGEAFDRPVTIGIAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQ 995

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
            +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +IV G      GTPESF 
Sbjct: 996  QGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNAIVKGKAIPRPGTPESFK 1055

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            VL++E+Q+LGL I +    T +     ++ 
Sbjct: 1056 VLMRELQSLGLDIAVHKVETDDDGSSRDLE 1085



 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 107/459 (23%), Positives = 188/459 (40%), Gaps = 46/459 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDL+E+Q+AS+  FL            GL     S  PI+ ++G   L FV   Y+   
Sbjct: 13  LPDLVEIQRASFRWFL----------EAGLIEELDSFSPISDYTGKLELHFVGKDYKLKR 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TYAV + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 63  PKYDVDEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NGRRTYSASLIPNRGAWLKFETDKNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+   EI+        Y +  D    P     LM        
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDNEIIDALRHPDYYQKTLDKEGNPSEEEALM------EL 224

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L        K   +  +G             D +   T +  +
Sbjct: 225 YRKLRPGEPPTVSGGQQLLDSRFFDAKRYDLGRVGRYKINRKLRLNVADTIRVLTPQDIM 284

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+     ++ + +  +R +  L  + V         ++ ++        
Sbjct: 285 GAIDYLINLEFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDSDT 344

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 345 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 399

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 400 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|158336724|ref|YP_001517898.1| DNA-directed RNA polymerase subunit beta [Acaryochloris marina
           MBIC11017]
 gi|158306965|gb|ABW28582.1| DNA-directed RNA polymerase, beta subunit [Acaryochloris marina
           MBIC11017]
          Length = 1099

 Score =  511 bits (1315), Expect = e-142,   Method: Composition-based stats.
 Identities = 322/605 (53%), Positives = 430/605 (71%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D + +  Y + T+  +     ++ALL++YR +RPG+  T S    +    FFD  +YDL
Sbjct: 196 FDRLRHPEYYQKTIDKEGQFGEEEALLELYRKLRPGEPPTVSGGTQLLESRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L+TP+  R +  +DI+A I  L++L    G++DDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLNTPEPTRVLTPDDILAAIDYLINLEFDIGSVDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER IKER++  D++S+ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIKERMTVSDVESLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGFIETP+  V  G+V  +    Y++A EE++  +A  +  +D +G    E+V 
Sbjct: 436 HARVNPYGFIETPFYPVEHGRVLKEQAPQYMTADEEDDLRVAPGDIPMDAEGYIQGEIVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      E++D++  SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 496 VRYRQDFTTTSPEEVDYVAVSPVQIISVATSLIPFLEHDDANRALMGSNMQRQAVPLLQP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E P VGTG+E+  A+ SG  I+++  G V  V A  I IR +EG+ +        Y + K
Sbjct: 556 ERPLVGTGLEAQAARDSGMVIISQTDGEVTYVSADSIHIRDLEGNENE-------YLIQK 608

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRP+V VGD+VR   IIADG +T+ G+LALG+N+LV +MPW GYN+ED+
Sbjct: 609 YQRSNQDTCLNQRPIVFVGDQVREGQIIADGSATEGGELALGQNILVVYMPWEGYNYEDA 668

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+ L+ +DE GII +GA
Sbjct: 669 ILVSERLVRDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDSLRQLDENGIIRIGA 728

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 729 WVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 788

Query: 947 RHGID 951
           R   D
Sbjct: 789 REQGD 793



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 189/587 (32%), Positives = 275/587 (46%), Gaps = 67/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E        MV   +      ++    +  RD +  
Sbjct: 541  MGSNMQRQAVPLLQPERPLVGTGLEAQAARDSGMVIISQTDGEVTYVSADSIHIRDLEGN 600

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              E        S +    +++  I+ VG +V  G I+      +G   +   + +L    
Sbjct: 601  ENEYLIQKYQRSNQD-TCLNQRPIVFVGDQVREGQIIADGSATEG-GELALGQNILVVYM 658

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   V       +  I+  +  +  E    +I  +  D   + 
Sbjct: 659  PWEGYNYEDAILVSERLVRDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDSLRQL 718

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 719  DENGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 765

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +  + R  + ++   + GD++PPG   VV+V+VA KR +Q GDKMA
Sbjct: 766  -----VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKLQVGDKMA 820

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DGTPVD+VLNPLGVPSRMNVGQ+FE  LGWA   L  +
Sbjct: 821  GRHGNKGIISRILPIEDMPYLADGTPVDLVLNPLGVPSRMNVGQVFECLLGWAGQNLNTR 880

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             K    D               ++ G  +    +    +++  +  + W           
Sbjct: 881  FKLTPFD---------------EMHGEEASRSTVHGKLEEAQQKTGKDW----------- 914

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                         + D ++ G+  ++DG TGEPFD+PVTVG  YMLKL H+V DK++ARS
Sbjct: 915  -------------LYDPEKPGKLQVFDGRTGEPFDQPVTVGKAYMLKLVHLVDDKIHARS 961

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +
Sbjct: 962  TGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNA 1021

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+L L I +    T++     ++ 
Sbjct: 1022 IVKGQAIPRPGTPESFKVLMRELQSLCLDIAVHKIETEDDGGSRDME 1068



 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 104/484 (21%), Positives = 193/484 (39%), Gaps = 36/484 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDL+E+Q+ S+  FL           EGL    +S  PI+ ++G   L F+  +Y+   
Sbjct: 13  LPDLVEIQRESFRSFL----------KEGLIEELESFSPISDYTGKIELHFLAKNYKLKR 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TY V + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 63  PKYDVDEAKRRDSTYGVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTERGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y   +IP++G W+  E D   ++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSETDK---NGRRTYNASLIPNRGAWLKFETDKNSLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         Y  +   +       A   +      
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDGEIFDRLRHPEYYQKTIDKEGQFGEEEALLELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G Q++ES         L +  + K  K L + +       +  D +      
Sbjct: 231 GEPPTVSGGTQLLESRFFDPKRYDLGRVGRYKLNKKLRLNTPE-PTRVLTPDDILAAIDY 289

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +     D+     ++ + +  +R +  L  + V         ++ ++        L    
Sbjct: 290 LINLEFDIGSVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVSDVESLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +     G+  I  I+         +G +  +        +E           +    
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNPYGFIETPFYPVEHGRVLKEQA 462

Query: 500 PQDL 503
           PQ +
Sbjct: 463 PQYM 466


>gi|227505180|ref|ZP_03935229.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
 gi|227198229|gb|EEI78277.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
          Length = 1164

 Score =  511 bits (1315), Expect = e-142,   Method: Composition-based stats.
 Identities = 188/610 (30%), Positives = 279/610 (45%), Gaps = 60/610 (9%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 573  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIIT 632

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 633  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQGTNYNQTPLVELGQRVEAGQVLAD 692

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 693  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 751

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 752  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 811

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                V  +                      +  DD+ PGV 
Sbjct: 812  IFGEKAREVRDTSMKVPHGENGKVIGVA-----------------RFSREDDDDLAPGVN 854

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVD++LN  GVP RM
Sbjct: 855  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMADGTPVDVILNTHGVPRRM 914

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+           +   L++  E++                
Sbjct: 915  NIGQVLEVHLGWLAHA-GWKVDV-----DDPANAELLKTLPEELYDVP------------ 956

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                      +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GE
Sbjct: 957  ----------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGE 1006

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 1007 PYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1066

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE+Q+L L++++
Sbjct: 1067 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEV 1126

Query: 1364 ENSRTKNSAK 1373
             ++       
Sbjct: 1127 LSTDGTPMEL 1136



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 325/661 (49%), Positives = 450/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 198 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWSEQQI--KDRFGFSELMMSTLES 253

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 254 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 313

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 314 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMIAPNGETIAIHTDDIDHFGNRRLRTVGELI 373

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H NS
Sbjct: 374 QNQIRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNNS 433

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 434 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 493

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+   E +  R   
Sbjct: 494 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDKFAIAQAELEKDADGTIIGERIEVRLKD 553

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAPF
Sbjct: 554 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPF 613

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 614 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 666

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV++G  V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 667 NQGTNYNQTPLVELGQRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 726

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 727 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 786

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 787 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGVARFSREDD 846

Query: 951 D 951
           D
Sbjct: 847 D 847



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 93/388 (23%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +              P+ R   GL+   + + P
Sbjct: 25  RYSFAKISEPIAVPGLLDLQLDSFAWLIGTPEWREREQAERGPEARVTSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 85  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 136 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   
Sbjct: 194 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEQQIKDRFGFSELMMSTLES 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 254 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 313

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE        I    ++   +  +R 
Sbjct: 314 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMIAPNGETIA-----IHTDDIDHFGNRRLRT 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + +         +V ++   + 
Sbjct: 369 VGELIQNQIRVGLSRMERVVRERMTTQD 396


>gi|257069520|ref|YP_003155775.1| DNA-directed RNA polymerase subunit beta [Brachybacterium faecium DSM
            4810]
 gi|256560338|gb|ACU86185.1| DNA-directed RNA polymerase subunit beta [Brachybacterium faecium DSM
            4810]
          Length = 1162

 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 181/504 (35%), Positives = 260/504 (51%), Gaps = 54/504 (10%)

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            G  V  G IL    +   +  +   + LL A    +  +  D  +     V   V+    
Sbjct: 678  GDRVEAGSILADGPST-DQGELAIGKNLLVAFMSWEGHNYEDGIILSSRMVQDDVLTSIH 736

Query: 945  FNRHGIDKNERSISVEREQIEL-LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               H  + + R   + +E+I   +    DD    LD     R+   +   + + G    K
Sbjct: 737  IEEH--EVDARDTKLGKEEITRDIPNVGDDVLADLDERGIIRIGAEVEPGDILVGKVTPK 794

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
              T L+ +      R+ + + A +       V   +        +  D         + G
Sbjct: 795  GETELTPE--ERLLRAIFGEKAREVRDTSLRVPHGESGTVIGVQVFNDD--------EDG 844

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +P GV  +V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPFL+DGTP+DI+LN
Sbjct: 845  DILPTGVNEMVRVYVAQKRKITDGDKLAGRHGNKGVIAKILPVEDMPFLEDGTPIDIILN 904

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P+GVP RMN+GQ+ ETHLGW                                        
Sbjct: 905  PMGVPGRMNIGQVMETHLGWVAK--------------------------------AGWDL 932

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------SGQSI 1235
              SD     +   A   + G PV+ PVFDG   + ++ ++     +          G++ 
Sbjct: 933  DPSDATAADLPEPALHGEPGTPVAVPVFDGLTADEVSGLIANHRPNRDGERMIKEDGKAR 992

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L+DG +GEPF  PV+VGY+YMLKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 993  LFDGRSGEPFPDPVSVGYMYMLKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGGQRFG 1052

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LTIKSDD+ GR +VYE+IV G +  E G PESF VL+KEMQ
Sbjct: 1053 EMEVWALEAYGAAYALQELLTIKSDDIAGRVKVYEAIVKGENIPEPGIPESFRVLLKEMQ 1112

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPD 1379
            +L L++++ +S        E   +
Sbjct: 1113 SLCLNVEVLSSDGTAHEVQESDEE 1136



 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 335/731 (45%), Positives = 464/731 (63%), Gaps = 27/731 (3%)

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           ++ F        +               G       +   T   V+    +      +  
Sbjct: 123 IAEFMNNETGEIKTQTVFMGEFPLMTDKGT-----FIINGTERVVVSQLVRSPGVYFEES 177

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            +K       ++  +       +    +  ++ +       +     +    +    IL 
Sbjct: 178 IDKTSDKHIFSAKVIPSRGAWLEFEVDKRDQVGVRIDRKRKQSVTTLLQALGMSHSDIL- 236

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +       +R+TL  D+   + +AL+DIYR  RPG+  T    E+M N L+F++ +YDL
Sbjct: 237 -EEFGEFESMRSTLEKDRITSQDEALIDIYRKQRPGEPPTRDAGEAMLNNLYFNAKRYDL 295

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDDI 456
           + VGR K+  +L L+       +R +D++A IK +V L +G            +   DDI
Sbjct: 296 AKVGRYKIGKKLGLEGTLSESTLRLQDVVAAIKYIVALHDGVSEYTSVDGKPVRVETDDI 355

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ P  LIN +PV +A+ EF
Sbjct: 356 DHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDVEAITPLTLINIRPVTAAIKEF 415

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 416 FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPIETPE 475

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL +FAR+N +GFIETPYRKV DG VT++VVYL+A +E+   IAQAN+ +DE
Sbjct: 476 GPNIGLIGSLATFARINPFGFIETPYRKVVDGHVTDEVVYLTADDEDRHIIAQANAKIDE 535

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +G F EE V  R   GE  LV  E +D++D S +Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 536 EGRFLEEEVLVRLAGGEPDLVAVEDVDYMDVSARQMVSVATAMIPFLEHDDANRALMGSN 595

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL++E P VGTGME   A  +G  IVA++ G++E++ A  IV+ + +G     
Sbjct: 596 MQRQAVPLLRSEMPLVGTGMERRAAVDAGDVIVAEKGGVIEELSADLIVVMADDGSRQ-- 653

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KFQRSN     NQR L   GD V    I+ADGPSTD G+LA+G+N+LVAF
Sbjct: 654 -----TYPIGKFQRSNAGNSYNQRVLFDEGDRVEAGSILADGPSTDQGELAIGKNLLVAF 708

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M W G+N+ED +++S RMV +DV TSIHIEE EV ARDTKLG EEITRDIPNV ++ L +
Sbjct: 709 MSWEGHNYEDGIILSSRMVQDDVLTSIHIEEHEVDARDTKLGKEEITRDIPNVGDDVLAD 768

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSLRVP G 
Sbjct: 769 LDERGIIRIGAEVEPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGE 828

Query: 936 SGTVVDVRIFN 946
           SGTV+ V++FN
Sbjct: 829 SGTVIGVQVFN 839



 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 91/300 (30%), Positives = 142/300 (47%), Gaps = 30/300 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F K  + I++PDL+ +Q  S+D  L      +                 GL    + 
Sbjct: 20  RVTFAKLGDPIEVPDLLSLQTTSFDWLLGNERWQERAAEASAAGREDVPQTSGLADILEE 79

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   L F  + FD PK+ VD+C  +DLTYA PL +                 
Sbjct: 80  ISPIEDFAGNMSLSFRDHTFDDPKYTVDECKEKDLTYAAPLYV---------IAEFMNNE 130

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MG+ PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S K +++
Sbjct: 131 TGEIKTQTVFMGEFPLMTDKGTFIINGTERVVVSQLVRSPGVYFEESIDKT--SDKHIFS 188

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            ++IP +G W++ E D +D + VRIDR+RK  VT+ L ALGM   +IL  F         
Sbjct: 189 AKVIPSRGAWLEFEVDKRDQVGVRIDRKRKQSVTTLLQALGMSHSDILEEFGEFESMRST 248

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
            +          L+   +          GE    ++G+ + + L  + K   +  +G   
Sbjct: 249 LEKDRITSQDEALIDIYR------KQRPGEPPTRDAGEAMLNNLYFNAKRYDLAKVGRYK 302


>gi|317183726|gb|ADV15557.1| RNA polymerase beta subunit [Lactobacillus ruminis]
          Length = 526

 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 210/586 (35%), Positives = 320/586 (54%), Gaps = 70/586 (11%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           + + +  E++++P+LIE+Q  SY  FL          +EGL+  F+ + PI  F+G   L
Sbjct: 1   RSYSRIKEVLELPNLIEIQTDSYKWFL----------DEGLREMFEEIMPIEDFAGKLSL 50

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFV+Y+   PK+ VD+    D  Y+ PL +TLRLI          K   +IK Q ++ GD
Sbjct: 51  EFVNYQLLEPKYTVDEAREHDANYSAPLHVTLRLI---------NKETGEIKSQDVFFGD 101

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            PLMTK GTF+I G +R++VSQL RSPG++F+ +  +   +G+  Y   +IP++G W++ 
Sbjct: 102 FPLMTKQGTFIINGAERVIVSQLVRSPGVYFNSEMDK---NGRETYGTTVIPNRGAWLEY 158

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAAD 253
           E D+K+I +VRIDR RK+P+T  + ALG  ++ EI+             +      +  D
Sbjct: 159 ETDAKNISYVRIDRTRKIPLTELVRALGYGTDSEIIEILGQNDCLMNTLEKD-VHKNTED 217

Query: 254 LMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLC 304
             V   +      +  GE    +S + L +      K   +  +G             L 
Sbjct: 218 SRVEESLKDIYERLRPGEPKTADSSRSLLTARFFDPKRYDLAAVGRYKINKKLDLKTRLL 277

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +AE + + ETGEI +E+G+V+ +  +E++     RD   ++    +    ++  +  
Sbjct: 278 GARLAETLADPETGEIIVESGEVVTKPIMEKLAPYLKRDDFKMFTFHPSEEGVVQEPMT- 336

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                     L I +V    +                              +N+  N + 
Sbjct: 337 ----------LQIIKVYSETNP--------------------------EEVINLIGNGNV 360

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           P + +HI   DI+A +    +L+ G G+ DDID+LGNRR+RSVGE+L+NQ+R+GL RMER
Sbjct: 361 PLEYKHITPSDILASMNYFFNLQEGLGSTDDIDHLGNRRIRSVGELLQNQFRIGLTRMER 420

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+S  DI +V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSAL
Sbjct: 421 VVRERMSIQDIATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSAL 480

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           G GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+++A
Sbjct: 481 GPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSTYA 526


>gi|311063839|ref|YP_003970564.1| DNA-directed RNA polymerase subunit beta RpoB [Bifidobacterium
            bifidum PRL2010]
 gi|310866158|gb|ADP35527.1| RpoB DNA-directed RNA polymerase beta chain [Bifidobacterium bifidum
            PRL2010]
          Length = 1210

 Score =  510 bits (1314), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/591 (31%), Positives = 280/591 (47%), Gaps = 46/591 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E  +      ++  D    +     +++      G 
Sbjct: 628  MGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDDGT 687

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                +             ++  II  G  V  G +L        +  +   + LL A   
Sbjct: 688  TSSYKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGP-AIQKGDLALGKNLLIAFMP 746

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     +S  +V     +   I++ E      +   E + RD  +     
Sbjct: 747  WNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDA 801

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              N+  R   I  G    +G     K T      ++   R     F  +  +V+     +
Sbjct: 802  VANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRV 860

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                  +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++GRHGNKG
Sbjct: 861  PHGETGTVIAVKEITREDAE--EDGDELPNGVNQMIRVYIAQHRKITVGDKLSGRHGNKG 918

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I    + 
Sbjct: 919  CISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-HSGWDISLDPDL 977

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                              V + AE+     PV+TPVFDG   + 
Sbjct: 978  EAEWKKY---------------------------VPKGAEKGAPNTPVATPVFDGVRPDV 1010

Query: 1219 INSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            I  +L+    +          G++ L+DG TGEPF +P++VGY+YMLKL+H+V DK++AR
Sbjct: 1011 IKGLLKSTLPNRDGDQMVGEDGKARLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHAR 1070

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV GR RVY 
Sbjct: 1071 STGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDGRVRVYG 1130

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +IV G +    G PESF VL+KEMQ+L L++++ N+        +E  D +
Sbjct: 1131 AIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEDDDPS 1181



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 311/684 (45%), Positives = 447/684 (65%), Gaps = 32/684 (4%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY------ 348
           +   + D   G  +    +    G       D  D   +      +   I  L       
Sbjct: 206 YFDRSRDRATGKEIFGAKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTK 265

Query: 349 ---VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
               D+    + + + L  +  + + +AL D+YR +RP D +T     ++ +  +F++ +
Sbjct: 266 PEIRDAFEGYSLVLDALEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKR 325

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------K 450
           YDL+ VGR K++ +L L+   + R + ++DIIA +K LV L +G                
Sbjct: 326 YDLARVGRYKIDRKLGLEHEINDRSLSRDDIIATLKYLVTLHDGGKTFPGKRNGEDVDLH 385

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +DDID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV 
Sbjct: 386 VDVDDIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVN 445

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           + + EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVH +H+GR+C
Sbjct: 446 ATIKEFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHASHFGRMC 505

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P E+ EG NIGL+ SL +F RVN +GFIETPYRKV DG++T++VV+++A +E    IAQ 
Sbjct: 506 PIESPEGPNIGLIGSLATFGRVNPFGFIETPYRKVVDGQITDEVVHMTADQEVGHVIAQV 565

Query: 631 NSSLDEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           N  +DE+G F       R   EE + VP  ++D +D SP+Q+VSI +SLIPFLE+D+ +R
Sbjct: 566 NQEIDENGRFVNSQALARKDEEEAVDVPVSEVDLMDVSPRQMVSIGSSLIPFLEHDEGHR 625

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL+++E P VGTG E  VA  SG  I+A + G+V  V A  I + + +
Sbjct: 626 ALMGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDD 685

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G           Y+L KFQRSNQ TC NQRP++K G+ V    ++ADGP+   GDLALG+
Sbjct: 686 GTTSS-------YKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGPAIQKGDLALGK 738

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+L+AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV 
Sbjct: 739 NLLIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVG 798

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ + N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL
Sbjct: 799 EDAVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSL 858

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKN 953
           RVP G +GTV+ V+   R   +++
Sbjct: 859 RVPHGETGTVIAVKEITREDAEED 882



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 91/316 (28%), Positives = 145/316 (45%), Gaps = 28/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E I +P L+ VQ  S+D  +                        GL   F  
Sbjct: 53  RVNFGSIREPIPVPYLLGVQTDSFDWLIGNERWKKRVEEDEANGTDTVPHMSGLDEVFNE 112

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 113 ISPIENFAQTMSLTFSEPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 163

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   +GK ++ 
Sbjct: 164 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSRDR--ATGKEIFG 221

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM   EI   F  Y  ++ +
Sbjct: 222 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKPEIRDAFEGYSLVLDA 281

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      S     + G  +++S    T    L +  + K  + LG
Sbjct: 282 LEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKRYDLARVGRYKIDRKLG 341

Query: 298 ITSDCLCGLYVAEDIV 313
           +  + +    ++ D +
Sbjct: 342 LEHE-INDRSLSRDDI 356


>gi|46360998|gb|AAS89232.1| RpoB [Corynebacterium thomssenii]
          Length = 1117

 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 184/493 (37%), Positives = 250/493 (50%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 672  IVSQGDRVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 730

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 731  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 789

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 790  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 832

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V RILP EDMPF+ D
Sbjct: 833  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGRILPQEDMPFMAD 892

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D K    +  L   L  
Sbjct: 893  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYD 949

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 950  VPADSLT-------------------------ATPVFDGATNDEIAGLLANSKPNRDGDV 984

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 985  MVDENGKTKLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1044

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1045 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1104

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1105 FKVLLKELQSLCL 1117



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 327/756 (43%), Positives = 470/756 (62%), Gaps = 46/756 (6%)

Query: 233 YPKIVYSQRGDFWC-FPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           +  + YS           SA   +    +++   +I +    I       + G  + +G 
Sbjct: 96  FEDVKYSIEEAKDKDINYSAPLYVTAEFINNDTQEIKSQTVFIGDFPLMTDKGTFIVNGT 155

Query: 285 LKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    V    G              +       
Sbjct: 156 ERVVVSQLVRSPGVYFDETIDKSTERPLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRR 215

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +         I   +    +  +  TL +D   +  +ALL+IYR  RPG+  T 
Sbjct: 216 QPVTVLLKALGWTTEQI--TERFGFSEIMMTTLESDGVANTDEALLEIYRKQRPGEQPTR 273

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRN 448
            +A+S+    FF   +YDL+ VGR K+N +L L    + +  + +EDI   ++ LV L  
Sbjct: 274 DLAQSLLENAFFRPKRYDLARVGRYKVNRKLGLGGDHEGLMILTEEDIATTLEYLVRLHA 333

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+  +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 334 GEAEMTSPNGETIPVSTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAE 393

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+
Sbjct: 394 SITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGI 453

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ +L S+ARVNA+GFIETPY+KV +G +T+ + Y
Sbjct: 454 EVRDVHPSHYGRMCPIETPEGPNIGLIGALASYARVNAFGFIETPYQKVDNGVLTDQIDY 513

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIA 675
           L+A EE+   IAQA + LD+DG+ T + +  R   G+  +V  + +D++D SP+Q+VS+A
Sbjct: 514 LTADEEDRYAIAQAATPLDKDGALTGDRIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVA 573

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQ+QAVPLL++EA +V TGME   A  +G  ++  +AG+V
Sbjct: 574 TAMIPFLEHDDANRALMGANMQKQAVPLLRSEAAYVATGMEQRAAYDAGDTVINAKAGVV 633

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V    I +   EG  D        Y L  F+R+NQ TC NQ P+V  GD V    +IA
Sbjct: 634 ETVTGDYITVMDDEGVRD-------TYMLRTFERTNQGTCYNQTPIVSQGDRVEAGQVIA 686

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G++ALGRN+LVAFMPW G+N+ED++++++R+V +D+ TS+HIEE E+ ARDTK
Sbjct: 687 DGPGTKDGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEDDILTSVHIEEHEIDARDTK 746

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNVSE+ LK++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 747 LGAEEITREIPNVSEDVLKDLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRA 806

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTSL+VP G +G V+ VR F+R   D
Sbjct: 807 IFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDDD 842



 Score =  301 bits (770), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 93/389 (23%), Positives = 167/389 (42%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +                 R   GL+   + + 
Sbjct: 19  ERYSFAKIAEPITVPGLLDVQLESFAWLVGTPEWREREQQLRGDSARVTSGLEDILEEIS 78

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +++   +D+ Y+ PL +T   I  D          +
Sbjct: 79  PIQDYSGNMSLTLSEPRFEDVKYSIEEAKDKDINYSAPLYVTAEFINND---------TQ 129

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 130 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 187

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 188 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMTTLE 247

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 248 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENAFFRPKRYDLARVGRYKVNRKLGLG 307

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    GE        +    ++   +  +R
Sbjct: 308 GDHEGLMILTEEDIATTLEYLVRLHAGEAEMTSPNGETI-----PVSTDDIDHFGNRRLR 362

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 363 TVGELIQNQVRVGLSRMERVVRERMTTQD 391


>gi|296138486|ref|YP_003645729.1| DNA-directed RNA polymerase subunit beta [Tsukamurella paurometabola
            DSM 20162]
 gi|296026620|gb|ADG77390.1| DNA-directed RNA polymerase, beta subunit [Tsukamurella paurometabola
            DSM 20162]
          Length = 1170

 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 182/513 (35%), Positives = 254/513 (49%), Gaps = 61/513 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G +L           M   + LL AI   +  +  D  +     V   V+
Sbjct: 679  IVSAGQRVEIGQVLADGPCTDN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVL 737

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E          + +  D  DE+ I+      R  +IL G+ 
Sbjct: 738  TSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADL-DERGIIRIGAEVRDGDILVGKV 796

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 797  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 839

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  D++ PGV  +V+V+VA KR +Q GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 840  VRVFSREDDDELAPGVNELVRVYVAQKRKVQDGDKLAGRHGNKGVIGKILPAEDMPFLPD 899

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQI ETHLGW     G  ++      +            E+
Sbjct: 900  GTPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWDVRD-----EKGNIPEWASQLPEQ 953

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +    S T                        +TPVFDGA +E +  +L     +  G  
Sbjct: 954  MYAQPSDTNT----------------------ATPVFDGARDEELAGLLGSTLPNRDGDV 991

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV +GY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 992  MVGADGKATLFDGRSGEPFPYPVAIGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGK 1051

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 1052 AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 1111

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            F VL+KE+Q+L L++++ +S        +   +
Sbjct: 1112 FKVLLKELQSLCLNVEVLSSDGAAIEMADSDDE 1144



 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 329/699 (47%), Positives = 464/699 (66%), Gaps = 33/699 (4%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    EK +  + +      G ++  D+   +T  + +       +  
Sbjct: 164 LVRSPGVYFDETIDKSTEKPLHSVKVIPAR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 219

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         IL  +    +  +R+TL  D      +ALLDIYR +RPG+  T   A
Sbjct: 220 TVLLKALGWTSEQIL--ERFGFSEIMRSTLEKDATAGTDEALLDIYRKLRPGEPPTKESA 277

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNG 449
           +++   LFF   +YDL+ VGR K+N +L L    D      + ++DI+AI++ LV L + 
Sbjct: 278 QTLLENLFFKEKRYDLARVGRYKLNKKLGLPANADGTQSYVLNEDDIVAIVEYLVRLHDA 337

Query: 450 KGT----------------IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                              +DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ 
Sbjct: 338 PSEQLTYMTVPGGVEVPVEVDDIDHFGNRRIRTVGELIQNQLRVGLSRMERVVRERMTTQ 397

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D++++ PQ LIN +PV +A+ EFF +SQLSQ  +  N LS +TH RRL+ALG GG++R R
Sbjct: 398 DVEAITPQTLINIRPVSAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLNALGPGGLSRER 457

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG  T++
Sbjct: 458 AGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVTDGVATDE 517

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVV 672
           +VY++A EE+  YIAQAN++ D+ G  T++ V  R    E   V   +++++D SP+Q+V
Sbjct: 518 IVYMTADEEDRFYIAQANAATDDKGRLTDDRVLVRKRGSEVEFVSTAQVEYMDISPRQMV 577

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           S+A ++IPFLE+DD+NR LMG NMQRQAVPL+++E+P VGTGME   A  +G  I+ ++A
Sbjct: 578 SVATAMIPFLEHDDANRALMGANMQRQAVPLVRSESPLVGTGMELRAAVDAGDVIITEKA 637

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           G VE+V A  I + + +G           +RL KF RSNQ TC NQRP+V  G  V    
Sbjct: 638 GAVEEVSADFITVMADDGTR-------KTHRLRKFARSNQGTCANQRPIVSAGQRVEIGQ 690

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           ++ADGP TD G++ALG+N+LVA MPW G+N+ED++++S+R+V EDV TSIHIEE E+ AR
Sbjct: 691 VLADGPCTDNGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEEDVLTSIHIEEHEIDAR 750

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           DTKLG EEITRDIPNVS+E L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+L
Sbjct: 751 DTKLGAEEITRDIPNVSDEVLADLDERGIIRIGAEVRDGDILVGKVTPKGETELTPEERL 810

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LRAIFGEKA +VRDTSL+VP G +G V+ VR+F+R   D
Sbjct: 811 LRAIFGEKAREVRDTSLKVPHGETGKVIGVRVFSREDDD 849



 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 95/353 (26%), Positives = 164/353 (46%), Gaps = 22/353 (6%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E + +P L++VQ  S++  +      ++  + G       L+     + PI 
Sbjct: 23  RVSFAKLSEPLPVPGLLDVQTDSFEWLVGSPEWREKAASRGEANPTGGLEDILAELSPIE 82

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  +++C  +D+TYA PL +T   I           +  +IK
Sbjct: 83  DFSGSMSLSFSDPRFDEVKASIEECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 133

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 134 SQTVFMGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKPLHSVKVIP 191

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRGDF 244
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+IL  F     +  +   D 
Sbjct: 192 ARGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQILERFGFSEIMRSTLEKDA 251

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDC 302
                 A   +            ++ + ++E+   K+    L +  + K  K LG+ ++ 
Sbjct: 252 TAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKLNKKLGLPANA 311

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                   +  +      Y+        + L  +      ++P+   D  +  
Sbjct: 312 DGTQSYVLNEDDIVAIVEYLVRLHDAPSEQLTYMTVPGGVEVPVEVDDIDHFG 364


>gi|291557507|emb|CBL34624.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Eubacterium
            siraeum V10Sc8a]
          Length = 671

 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 184/530 (34%), Positives = 261/530 (49%), Gaps = 47/530 (8%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E   + I          +++   +  G E+  GD+L        +  ++  +  L
Sbjct: 131  DDNGVEHSYKLIKFKRSNQGTCVNQRPAVTKGMEIKVGDVLADGP-ATSQGEISLGKNAL 189

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                  +  +  D  L     V   V        + ++  +  +  E    E +    +D
Sbjct: 190  IGFMTWEGYNYEDAVLINEKLVYNDVYTSIHIEEYELECRDTKLGPEEITRE-IPNVSED 248

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD     R+   +   + + G    K  T L+++        +  +    D+  + 
Sbjct: 249  ALKDLDERGIIRIGAEVHSGDIMVGKVTPKGETELTAE-------ERLLRAIFGDKAREV 301

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               SL+V +  S  I++     K+   Q  D++ PGV  VV+ ++A KR I  GDKMAGR
Sbjct: 302  RDNSLRVPHGESGIIVD----VKVFTRQNCDELSPGVNMVVRCYIAQKRKISVGDKMAGR 357

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRIL  EDMPFL DGTP+DIVLNPLGVPSRMN+GQ+ E HLG+AC  L  +I 
Sbjct: 358  HGNKGVVSRILKQEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYACKALDWQIM 417

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     DI       E                                      D 
Sbjct: 418  TPVFDGAHEADIRACFEKAEAERENYKDK-----------------------------DS 448

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A  +          +    ++ L DG TGE FD PVTVGY+Y LKL+H+V DK++ARSTG
Sbjct: 449  AKID-----FSKIPMRPDCKTQLTDGRTGEKFDSPVTVGYMYYLKLHHLVDDKIHARSTG 503

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+VGR + YE+IV
Sbjct: 504  PYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDIVGRVKTYEAIV 563

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
             G+   + G PESF VL KE+Q+LGL I + ++        +   + ++ 
Sbjct: 564  KGDPVPKAGVPESFKVLFKELQSLGLDIKVLDADKNEIDLRQTYEEDDEY 613



 Score =  293 bits (750), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 188/335 (56%), Positives = 247/335 (73%), Gaps = 7/335 (2%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           ++A  E+N  +AQAN  LDE G F  + V  R   E + V R+++D++D SPK VVS+A 
Sbjct: 1   MTADMEDNYVVAQANEPLDEQGKFARKRVNARFREEILEVDRDRVDYMDVSPKMVVSVAT 60

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           ++IPFLENDD+NR LMG NMQRQAVPL+  + P VGTGME   A  SGA +VAK  G+V 
Sbjct: 61  AMIPFLENDDANRALMGANMQRQAVPLMVTQNPIVGTGMEYKAAVDSGAVVVAKEDGVVT 120

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +  A  IV+    G           Y+L+KF+RSNQ TCVNQRP V  G E++  D++AD
Sbjct: 121 KCSADEIVVTDDNGVEHS-------YKLIKFKRSNQGTCVNQRPAVTKGMEIKVGDVLAD 173

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GP+T  G+++LG+N L+ FM W GYN+ED++LI+E++V  DV+TSIHIEE+E+  RDTKL
Sbjct: 174 GPATSQGEISLGKNALIGFMTWEGYNYEDAVLINEKLVYNDVYTSIHIEEYELECRDTKL 233

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITR+IPNVSE+ LK++DE GII +GAEV+ GDI+VGK+TPKGE+ +T EE+LLRAI
Sbjct: 234 GPEEITREIPNVSEDALKDLDERGIIRIGAEVHSGDIMVGKVTPKGETELTAEERLLRAI 293

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FG+KA +VRD SLRVP G SG +VDV++F R   D
Sbjct: 294 FGDKAREVRDNSLRVPHGESGIIVDVKVFTRQNCD 328


>gi|281486598|gb|ADA70801.1| DNA-directed RNA polymerase subunit B [Acinetobacter sp. G16(2009)]
          Length = 273

 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 172/276 (62%), Positives = 214/276 (77%), Gaps = 4/276 (1%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I
Sbjct: 1    RHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQI 60

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              ++   K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVF
Sbjct: 61   DKML---KQQREIAELREFLDKIYNKVGGEQEDLDSLTDDEILVLAGNLRAGVPLATPVF 117

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGAEEGQIKELLELAELPRSGQTVLYDGRTGEKFDRPVTVGYMYMLKLNHLVDDKMHARS 177

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+Y++
Sbjct: 178  TGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKN 237

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            IV GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 238  IVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 273


>gi|237786414|ref|YP_002907119.1| DNA-directed RNA polymerase subunit beta [Corynebacterium
            kroppenstedtii DSM 44385]
 gi|259494177|sp|C4LL71|RPOB_CORK4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|237759326|gb|ACR18576.1| DNA-directed RNA polymerase, beta chain [Corynebacterium
            kroppenstedtii DSM 44385]
          Length = 1168

 Score =  510 bits (1313), Expect = e-142,   Method: Composition-based stats.
 Identities = 181/501 (36%), Positives = 254/501 (50%), Gaps = 57/501 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G  L      +    M     LL A    +  +  D  +     V   V+
Sbjct: 678  LVEAGDRIEEGQALADGPGTEN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRIVEEDVL 736

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKD-----DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E    ++    +D     DE+ I+      R  +IL G+  
Sbjct: 737  TSIHIEEHEIDARDTKLGPEEITRDIPNASEDILADLDERGIVRIGADVRDGDILVGKVT 796

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 797  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 839

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+ PGV ++V+V+VA KR IQ GDK++GRHGNKG+V +ILP EDMPFL DG
Sbjct: 840  RVFSREDDDDLAPGVNQMVRVYVAQKRKIQDGDKLSGRHGNKGVVGKILPAEDMPFLPDG 899

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQ+ E HLG      G K+     D      +  L   L  V
Sbjct: 900  TPVDVILNTHGVPRRMNIGQVLELHLGMLAKS-GWKVDPESQDPAIKAMLETLPEDLYDV 958

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                                          V+TPVFDG   E ++ ++R +  +  G   
Sbjct: 959  PADSR-------------------------VATPVFDGTTNEELSGLMRSSRPNRDGDQM 993

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 +S L DG TGEPF +P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 994  VNEFGKSTLIDGRTGEPFQQPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1053

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF
Sbjct: 1054 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESF 1113

Query: 1348 NVLVKEMQALGLSIDLENSRT 1368
             VL+KE+Q+L L++++ ++  
Sbjct: 1114 KVLLKELQSLCLNVEVLSADG 1134



 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 328/662 (49%), Positives = 456/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  DI   +T  + I+         L +      +DI     D    +  + +TL  
Sbjct: 198 GAWLEFDIDKRDTVGVRIDRKRRQPVTVLLKALGLSTQDI----TDRFGFSELMMSTLEH 253

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++ +  FF+  +YDL+ VGR K+N +L L  
Sbjct: 254 DGVANTDEALLEIYRKQRPGESPTRDSAQALLDNSFFNPKRYDLAKVGRYKVNRKLGLGG 313

Query: 425 PDD--VRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
                   + +EDI+  I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 314 GSTTGEHTLTEEDILTTIEYLVRLHAGERTMESPDGTELMIATDDIDHFGNRRLRTVGEL 373

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 374 VQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 433

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+++RDVH +HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 434 SLSGLTHKRRLSALGPGGLSRERAGLDVRDVHASHYGRMCPIETPEGPNIGLIGSLASYA 493

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPYR+V +G+ T+ V YL+A EE+   +AQAN+ +D +G F E+ V  R  
Sbjct: 494 RVNPFGFIETPYRRVENGQATDVVDYLTADEEDRHIVAQANTKMDSEGRFVEDTVEVRMK 553

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+ EAP
Sbjct: 554 GGNVEVVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRNEAP 613

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FVGTGME   A  +G  ++A+R+G+VE V A  I     +G  D        + L KF+R
Sbjct: 614 FVGTGMELRAAHDAGDVVIARRSGVVETVCADFITTLGDDGQRD-------TFLLRKFER 666

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQ TC NQ+PLV+ GD +     +ADGP T+ G++ALGRN+LVAFMPW G+N+ED++++
Sbjct: 667 TNQGTCYNQKPLVEAGDRIEEGQALADGPGTENGEMALGRNLLVAFMPWEGHNYEDAIIL 726

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V EDV TSIHIEE E+ ARDTKLGPEEITRDIPN SE+ L ++DE GI+ +GA+V 
Sbjct: 727 NQRIVEEDVLTSIHIEEHEIDARDTKLGPEEITRDIPNASEDILADLDERGIVRIGADVR 786

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R  
Sbjct: 787 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSRED 846

Query: 950 ID 951
            D
Sbjct: 847 DD 848



 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 139/298 (46%), Gaps = 29/298 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I++P L+++Q+ S+   +                 R   GL+   + + P
Sbjct: 25  RYSFAKIKEPIEVPGLLDLQRDSFAWLIGAPEWRAKKQAESEEGARITSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      FD  K  +D+   +D+ Y+ PL +T                  +
Sbjct: 85  IEDYSGNMSLTLSEPRFDDVKNTIDEAKDKDINYSAPLYVTAEFT---------NAMSGE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 136 IKSQTVFIGDFPMMTDKGTFIINGTERVIVSQLVRSPGVYFDESIDK--STERPLHSVKV 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +++I   F    +   +   
Sbjct: 194 IPSRGAWLEFDIDKRDTVGVRIDRKRRQPVTVLLKALGLSTQDITDRFGFSELMMSTLEH 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +        D+ + ++++          + K   +  +G   
Sbjct: 254 DGVANTDEALLEIYRKQRPGESPTRDSAQALLDNS-------FFNPKRYDLAKVGRYK 304


>gi|310286963|ref|YP_003938221.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium bifidum
            S17]
 gi|309250899|gb|ADO52647.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium bifidum
            S17]
          Length = 1210

 Score =  510 bits (1312), Expect = e-142,   Method: Composition-based stats.
 Identities = 189/591 (31%), Positives = 280/591 (47%), Gaps = 46/591 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E  +      ++  D    +     +++      G 
Sbjct: 628  MGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDDGT 687

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                +             ++  II  G  V  G +L        +  +   + LL A   
Sbjct: 688  ISSYKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGP-AIQKGDLALGKNLLIAFMP 746

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     +S  +V     +   I++ E      +   E + RD  +     
Sbjct: 747  WNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDA 801

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              N+  R   I  G    +G     K T      ++   R     F  +  +V+     +
Sbjct: 802  VANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRV 860

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                  +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++GRHGNKG
Sbjct: 861  PHGETGTVIAVKEITREDAE--EDGDELPNGVNQMIRVYIAQHRKITVGDKLSGRHGNKG 918

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I    + 
Sbjct: 919  CISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-HSGWDISLDPDL 977

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                              V + AE+     PV+TPVFDG   + 
Sbjct: 978  EAEWKKY---------------------------VPKGAEKGAPNTPVATPVFDGVRPDV 1010

Query: 1219 INSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            I  +L+    +          G++ L+DG TGEPF +P++VGY+YMLKL+H+V DK++AR
Sbjct: 1011 IKGLLKSTLPNRDGDQMVGEDGKARLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHAR 1070

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV GR RVY 
Sbjct: 1071 STGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDGRVRVYG 1130

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +IV G +    G PESF VL+KEMQ+L L++++ N+        +E  D +
Sbjct: 1131 AIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEDDDPS 1181



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 311/684 (45%), Positives = 448/684 (65%), Gaps = 32/684 (4%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY------ 348
           +   + D   G  +    +    G       D  D   +      +   I  L       
Sbjct: 206 YFDRSRDRATGKEIFGAKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTK 265

Query: 349 ---VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
               D+    + + + L  +  + + +AL D+YR +RP D +T     ++ +  +F++ +
Sbjct: 266 PEIRDAFEGYSLVLDALEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKR 325

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------K 450
           YDL+ VGR K++ +L L+   + R + ++DIIA +K LV L +G                
Sbjct: 326 YDLARVGRYKIDRKLGLEHEINDRSLSRDDIIATLKYLVTLHDGGKTFPGKRNGEDVDLH 385

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +DDID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV 
Sbjct: 386 VDVDDIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVN 445

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           + + EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVH +H+GR+C
Sbjct: 446 ATIKEFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHASHFGRMC 505

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P E+ EG NIGL+ SL +F RVN +GFIETPYRKV DG++T++VV+++A +E    IAQ 
Sbjct: 506 PIESPEGPNIGLIGSLATFGRVNPFGFIETPYRKVVDGQITDEVVHMTADQEVGHVIAQV 565

Query: 631 NSSLDEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           N  +DE+G F       R   EE + VP  ++D +D SP+Q+VSI +SLIPFLE+D+ +R
Sbjct: 566 NQEIDENGRFVNSQALARKDEEEAVDVPVSEVDLMDVSPRQMVSIGSSLIPFLEHDEGHR 625

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL+++E P VGTG E  VA  SG  I+A + G+V  V A  I + + +
Sbjct: 626 ALMGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDD 685

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G        +  Y+L KFQRSNQ TC NQRP++K G+ V    ++ADGP+   GDLALG+
Sbjct: 686 GT-------ISSYKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGPAIQKGDLALGK 738

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+L+AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV 
Sbjct: 739 NLLIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVG 798

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ + N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL
Sbjct: 799 EDAVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSL 858

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKN 953
           RVP G +GTV+ V+   R   +++
Sbjct: 859 RVPHGETGTVIAVKEITREDAEED 882



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 91/316 (28%), Positives = 145/316 (45%), Gaps = 28/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E I +P L+ VQ  S+D  +                        GL   F  
Sbjct: 53  RVNFGSIREPIPVPYLLGVQTDSFDWLIGNERWKKRVEEDEANGTDTVPHMSGLDEVFNE 112

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 113 ISPIENFAQTMSLTFSEPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 163

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   +GK ++ 
Sbjct: 164 TGEIKSQTVFMGDFPLQTPHGTFIISGTERVIVSQLVRSPGVYFDRSRDR--ATGKEIFG 221

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM   EI   F  Y  ++ +
Sbjct: 222 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKPEIRDAFEGYSLVLDA 281

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      S     + G  +++S    T    L +  + K  + LG
Sbjct: 282 LEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKRYDLARVGRYKIDRKLG 341

Query: 298 ITSDCLCGLYVAEDIV 313
           +  + +    ++ D +
Sbjct: 342 LEHE-INDRSLSRDDI 356


>gi|224282501|ref|ZP_03645823.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium bifidum
            NCIMB 41171]
 gi|313139653|ref|ZP_07801846.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium bifidum
            NCIMB 41171]
 gi|313132163|gb|EFR49780.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium bifidum
            NCIMB 41171]
          Length = 1187

 Score =  510 bits (1312), Expect = e-141,   Method: Composition-based stats.
 Identities = 189/591 (31%), Positives = 280/591 (47%), Gaps = 46/591 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E  +      ++  D    +     +++      G 
Sbjct: 605  MGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDDGT 664

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                +             ++  II  G  V  G +L        +  +   + LL A   
Sbjct: 665  TSSYKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGP-AIQKGDLALGKNLLIAFMP 723

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     +S  +V     +   I++ E      +   E + RD  +     
Sbjct: 724  WNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDA 778

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              N+  R   I  G    +G     K T      ++   R     F  +  +V+     +
Sbjct: 779  VANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRV 837

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                  +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++GRHGNKG
Sbjct: 838  PHGETGTVIAVKEITREDAE--EDGDELPNGVNQMIRVYIAQHRKITVGDKLSGRHGNKG 895

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I    + 
Sbjct: 896  CISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-HSGWDISLDPDL 954

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                              V + AE+     PV+TPVFDG   + 
Sbjct: 955  EAEWKKY---------------------------VPKGAEKGAPNTPVATPVFDGVRPDV 987

Query: 1219 INSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            I  +L+    +          G++ L+DG TGEPF +P++VGY+YMLKL+H+V DK++AR
Sbjct: 988  IKGLLKSTLPNRDGDQMVGEDGKARLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHAR 1047

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV GR RVY 
Sbjct: 1048 STGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDGRVRVYG 1107

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +IV G +    G PESF VL+KEMQ+L L++++ N+        +E  D +
Sbjct: 1108 AIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEDDDPS 1158



 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 311/684 (45%), Positives = 447/684 (65%), Gaps = 32/684 (4%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY------ 348
           +   + D   G  +    +    G       D  D   +      +   I  L       
Sbjct: 183 YFDRSRDRATGKEIFGAKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTK 242

Query: 349 ---VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
               D+    + + + L  +  + + +AL D+YR +RP D +T     ++ +  +F++ +
Sbjct: 243 PEIRDAFEGYSLVLDALEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKR 302

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------K 450
           YDL+ VGR K++ +L L+   + R + ++DIIA +K LV L +G                
Sbjct: 303 YDLARVGRYKIDRKLGLEHEINDRSLSRDDIIATLKYLVTLHDGGKTFPGKRNGEDVDLH 362

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +DDID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV 
Sbjct: 363 VDVDDIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVN 422

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           + + EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVH +H+GR+C
Sbjct: 423 ATIKEFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHASHFGRMC 482

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P E+ EG NIGL+ SL +F RVN +GFIETPYRKV DG++T++VV+++A +E    IAQ 
Sbjct: 483 PIESPEGPNIGLIGSLATFGRVNPFGFIETPYRKVVDGQITDEVVHMTADQEVGHVIAQV 542

Query: 631 NSSLDEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           N  +DE+G F       R   EE + VP  ++D +D SP+Q+VSI +SLIPFLE+D+ +R
Sbjct: 543 NQEIDENGRFVNSQALARKDEEEAVDVPVSEVDLMDVSPRQMVSIGSSLIPFLEHDEGHR 602

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL+++E P VGTG E  VA  SG  I+A + G+V  V A  I + + +
Sbjct: 603 ALMGTNMQRQAVPLIESERPLVGTGSEWRVAYDSGDVIIADKPGVVTYVSADIIRVMNDD 662

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G           Y+L KFQRSNQ TC NQRP++K G+ V    ++ADGP+   GDLALG+
Sbjct: 663 GTTSS-------YKLSKFQRSNQTTCYNQRPIIKDGERVEAGTVLADGPAIQKGDLALGK 715

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+L+AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV 
Sbjct: 716 NLLIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVG 775

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ + N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSL
Sbjct: 776 EDAVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSL 835

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKN 953
           RVP G +GTV+ V+   R   +++
Sbjct: 836 RVPHGETGTVIAVKEITREDAEED 859



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 91/316 (28%), Positives = 145/316 (45%), Gaps = 28/316 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E I +P L+ VQ  S+D  +                        GL   F  
Sbjct: 30  RVNFGSIREPIPVPYLLGVQTDSFDWLIGNERWKKRVEEDEANGTDTVPHMSGLDEVFNE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 90  ISPIENFAQTMSLTFSEPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   +GK ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSRDR--ATGKEIFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM   EI   F  Y  ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKPEIRDAFEGYSLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      S     + G  +++S    T    L +  + K  + LG
Sbjct: 259 LEKETIETQDEALTDLYRKIRPSDTATPEAGRNLLDSFYFNTKRYDLARVGRYKIDRKLG 318

Query: 298 ITSDCLCGLYVAEDIV 313
           +  + +    ++ D +
Sbjct: 319 LEHE-INDRSLSRDDI 333


>gi|209395083|gb|ACI45354.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 487

 Score =  509 bits (1311), Expect = e-141,   Method: Composition-based stats.
 Identities = 204/488 (41%), Positives = 314/488 (64%), Gaps = 3/488 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL  + AP +R  EGLQAAF + FPI + +G   ++F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQKDKAPQKRAVEGLQAAFNAAFPIVSHNGFVEMKFIEYSLTKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LT+   ++  ++LI++D +  T  +K ++++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTFGSAVRAKVQLIIYDRESSTSQSKVVEEVKEQEVYMGEVPLMTDKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD KDI++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKTHGSGKLLFSARIIPYRGSWLDFEFDPKDILY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL+ F+    +            +  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILANFFVNDNFRLMDSGAQMEFVSERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T    + L++   KF+ +  D L G  VA +IV+ +TGEI  +
Sbjct: 240 ITD-QSGKLIVAKDKRVTVRHTRELEQSDSKFISVPEDFLIGRVVARNIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + +R +   Y + ++  AYI NTL TD+  D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRSAAVRQLQCTYTNELDQGAYIANTLRTDETADEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G   T    +++F  LF++ D YDLS VGR+K N ++  D       +  EDI+A++KIL
Sbjct: 359 GGPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRDESTGPMVLSNEDILAVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R+E+++KER+   + + +MP DL
Sbjct: 419 VDLRNGNGEVDDIDHLGNRRVRCVGELAENQYRTGLARIEKAVKERLGQAEQEPLMPHDL 478

Query: 504 INAKPVVS 511
           IN+KP+ +
Sbjct: 479 INSKPISA 486


>gi|119026337|ref|YP_910182.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium
            adolescentis ATCC 15703]
 gi|118765921|dbj|BAF40100.1| DNA-directed RNA polymerase beta chain [Bifidobacterium adolescentis
            ATCC 15703]
          Length = 1165

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 190/539 (35%), Positives = 264/539 (48%), Gaps = 59/539 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 636  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 694

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 695  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 754

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 755  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 808

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 809  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 861

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 862  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 921

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +   A                               V + AE+   G PV+
Sbjct: 922  -GWDISLDPDAEAAWKKY---------------------------VPQGAEKGAPGTPVA 953

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG   E I  +L          ++      G++ L+DG TGEPF +P++VGY+YML
Sbjct: 954  TPVFDGVRPETIKGLLSCTLPDRDGNKLVG--PDGKATLFDGRTGEPFPKPISVGYMYML 1011

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1012 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1071

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            KSDDV GR RVY +IV G +    G PESF VL+KEMQ+L L++++ N+        EE
Sbjct: 1072 KSDDVDGRVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNADGVAIDMKEE 1130



 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 301/620 (48%), Positives = 429/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +  + + +AL D+YR +RP D  T    +++ +  +F++ +YDL+
Sbjct: 224 DAFKDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLA 283

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDIIA IK LV L  G+                   
Sbjct: 284 RVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGETKFPGKRDGQDVDLRVDVD 343

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 344 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 403

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 404 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 463

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 464 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 523

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 524 DENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 583

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I   + +G   
Sbjct: 584 TNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTS 643

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 644 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 696

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 697 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 756

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 757 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 816

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 817 GETGTVIAVKEITREDAEED 836



 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 144/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 7   RVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVQEDLENGTNTVPHTSGLDEVFQE 66

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 67  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 117

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 118 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEVFG 175

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 176 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDA 235

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 236 LAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 295

Query: 298 ITSD 301
           +  D
Sbjct: 296 LEKD 299


>gi|256831820|ref|YP_003160547.1| DNA-directed RNA polymerase, beta subunit [Jonesia denitrificans DSM
            20603]
 gi|256685351|gb|ACV08244.1| DNA-directed RNA polymerase, beta subunit [Jonesia denitrificans DSM
            20603]
          Length = 1170

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 174/441 (39%), Positives = 247/441 (56%), Gaps = 52/441 (11%)

Query: 956  SISVEREQI---------ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            SI +E  +I         E + RD  +    +  ++  R   I  G    SG     K T
Sbjct: 740  SIHIEEHEIDARDTKLGPEEITRDIPNVSEDVLADLDER-GIIRIGAEVTSGDILVGKVT 798

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  ++   R     F  +  +V+     +      +   +           + GD++
Sbjct: 799  PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGTVIAIRT------FNREDGDEL 852

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            P GV  +V+V++A +R I +GDK+AGRHGNKG++S ILP EDMPFL+DGT VD++LNP+G
Sbjct: 853  PAGVNELVRVYIAQRRKITAGDKLAGRHGNKGVISTILPVEDMPFLEDGTAVDVILNPMG 912

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VP RMNVGQ+ E HLGW                              +   T   TE   
Sbjct: 913  VPGRMNVGQVLEVHLGWIAS---------------------------RGWDTSLVTEGNL 945

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------SGQSILYD 1238
            D+ D  +   A +   G PV+TPVFDG +EEA+  +L+               G++ L+D
Sbjct: 946  DWKDT-LPEFAHKVAPGTPVATPVFDGLEEEALVGLLKSTLPSRDGDQLVQADGKARLFD 1004

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 1005 GRSGEPFPEPISVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 1064

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  ++G PESF VL+KEMQ+L 
Sbjct: 1065 VWALEAYGAAYTLQELLTIKSDDVPGRVKVYEAIVKGENIPDSGIPESFKVLLKEMQSLC 1124

Query: 1359 LSIDLENSRTKNSAKMEEIPD 1379
            L++++ +S   +    E   +
Sbjct: 1125 LNVEVLSSDGVSIEMKENDDE 1145



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 335/740 (45%), Positives = 468/740 (63%), Gaps = 36/740 (4%)

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
            F+       +               G         I+  E+V+ S    + G+      
Sbjct: 128 EFFNYNTGEIKSQTVFMGDFPLMTERGT------FIINGTERVVVSQLVRSPGVYFERTP 181

Query: 291 KGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                  I S  +    G ++  +I   +   + ++         L +       +I   
Sbjct: 182 DKTSDKDILSAKIIPSRGAWLEFEIDKRDAVGVRVDRKRKQSVTVLLKALGMSESEI--- 238

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             ++      + + L  D     ++AL+D+YR +RPG+  T     ++    +F   +YD
Sbjct: 239 -RETFAEFPVVLDVLEKDSVHTEEEALVDLYRKIRPGEPPTVEAGRNLLENFYFKPKRYD 297

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---------------NGKGT 452
           L+ VGR K+N ++ +D   D   +  +DIIA IK L  L                + +  
Sbjct: 298 LAKVGRYKLNKKIGVDAAIDQAVLSLDDIIATIKYLAALHADKNSMSVDIDGQATDIRVE 357

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 358 TDDIDHFGNRRIRAVGELIQNQIRTGLSRMERVVRERMTTQDVEAIAPQTLINIRPVVAA 417

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 418 IKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPI 477

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL+ SL SF R+N +GFIETPYRKV +G+VT ++VYL+A +E+   IAQAN+
Sbjct: 478 ETPEGPNIGLIGSLASFGRINPFGFIETPYRKVENGRVTEELVYLTADDEDRYVIAQANT 537

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            L+EDGSF ++ V  R   GE   V    +D++D SP+Q+VS+A +LIPFLE+DD+NR L
Sbjct: 538 PLNEDGSFAQDRVLVRTKGGETDDVLAAAVDYMDVSPRQMVSVATALIPFLEHDDANRAL 597

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           MG NMQRQAVPL+++EAP+VGTGME   A  +G  IVA + G+V +V A  IV+ + +G 
Sbjct: 598 MGANMQRQAVPLVRSEAPYVGTGMEWRAAVDAGDVIVATKPGVVTEVSADLIVVANDDGT 657

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                     YR+ KF+RSNQ T  NQR +    + V    ++ADGP+TD G+LALGRN+
Sbjct: 658 TTS-------YRVSKFRRSNQGTSYNQRVVAVQDERVEVGTVLADGPATDGGELALGRNL 710

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
           LVAFM W G+NFED++++S+R+V +DV +SIHIEE E+ ARDTKLGPEEITRDIPNVSE+
Sbjct: 711 LVAFMSWEGHNFEDAIILSQRLVQDDVLSSIHIEEHEIDARDTKLGPEEITRDIPNVSED 770

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L ++DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+V
Sbjct: 771 VLADLDERGIIRIGAEVTSGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKV 830

Query: 932 PSGVSGTVVDVRIFNRHGID 951
           P G SGTV+ +R FNR   D
Sbjct: 831 PHGESGTVIAIRTFNREDGD 850



 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 101/325 (31%), Positives = 154/325 (47%), Gaps = 35/325 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMN--------IAPDERPN----EGLQAAFKS 61
           R  F K  E +++PDL+ +Q  S+D  +  +             R +     GL+  F+ 
Sbjct: 23  RVSFAKIYEPLEVPDLLGLQVDSFDWLIGHDRWRARVDAAKAAGRKDVPETSGLEEVFQE 82

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F     L F +Y F+PPK   D+C  +D TYA PL +T     ++         
Sbjct: 83  ISPIEDFGQTMSLSFSNYRFEPPKHTADECKDKDFTYAAPLFVTAEFFNYN--------- 133

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K + +
Sbjct: 134 TGEIKSQTVFMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTPDKT--SDKDILS 191

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D + VR+DR+RK  VT  L ALGM   EI  TF  +P ++  
Sbjct: 192 AKIIPSRGAWLEFEIDKRDAVGVRVDRKRKQSVTVLLKALGMSESEIRETFAEFPVVLDV 251

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D       A        +      I  GE   +E+G+ L        K   +  +G 
Sbjct: 252 LEKDSVHTEEEA--------LVDLYRKIRPGEPPTVEAGRNLLENFYFKPKRYDLAKVGR 303

Query: 299 TS-DCLCGLYVAEDIVNGETGEIYI 322
              +   G+  A D       +I  
Sbjct: 304 YKLNKKIGVDAAIDQAVLSLDDIIA 328


>gi|209527607|ref|ZP_03276107.1| DNA-directed RNA polymerase, beta subunit [Arthrospira maxima CS-328]
 gi|209491956|gb|EDZ92311.1| DNA-directed RNA polymerase, beta subunit [Arthrospira maxima CS-328]
          Length = 1621

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 320/605 (52%), Positives = 421/605 (69%), Gaps = 9/605 (1%)

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
             D++ +  Y + T+  +     +DAL+++YR +RPG+  T +  E +    FFD  +YDL
Sbjct: 715  FDALRHPDYFQKTIEKEGEFSEEDALMELYRKLRPGEPPTITGGEQLLQNRFFDPKRYDL 774

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              VGR K+N +L L  PD  R +   DI++ I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 775  GRVGRHKLNRKLRLSVPDSTRVLTPTDILSAIDYLINLEYDIGETDDIDHLGNRRVRSVG 834

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            E+L+NQ R+GL R+ER I+ER++  D +++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 835  ELLQNQIRVGLNRLERIIRERMTVGDAETLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 894

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 895  TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 954

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             ARVN YGFIETPY  V +G+V  D+  VY++A EE++  +A  + S D +G    +LV 
Sbjct: 955  HARVNPYGFIETPYYPVENGRVRRDLSPVYMTADEEDDLRVAPGDISYDSEGYILGDLVP 1014

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R   +      +++D++  SP Q+VS+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 1015 VRYRQDFTKTSPDQVDYVAVSPVQIVSVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 1074

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E PFVGTG+E+  A+ SG  IV++  G V  VD  +I +                Y L K
Sbjct: 1075 ERPFVGTGLEAQAARDSGMVIVSRTDGEVSYVDGAKIRV-------IDPEGWEIEYELQK 1127

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            +QRSNQ+TC+NQRPLV  GD+V    ++ADG ST+  +LALG N+LVA+MPW GYN+ED+
Sbjct: 1128 YQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGAELALGHNVLVAYMPWEGYNYEDA 1187

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +LISER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+ L+ +D  GII +GA
Sbjct: 1188 ILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDSLRQLDASGIIRIGA 1247

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 1248 WVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 1307

Query: 947  RHGID 951
            R   D
Sbjct: 1308 REQGD 1312



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 180/534 (33%), Positives = 253/534 (47%), Gaps = 64/534 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E                +++  ++  G +V  G +L    + +G   +     +L
Sbjct: 1115 DPEGWEIEYELQKYQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGA-ELALGHNVL 1173

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  L     V   V       +  I+  +  +  E    +I  +  D 
Sbjct: 1174 VAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDS 1233

Query: 972  DDEQV---ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +     I+    +    +IL G+    G         L   +  E  R          
Sbjct: 1234 LRQLDASGIIRIGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD--------- 1284

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                     ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ G
Sbjct: 1285 ---------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVG 1335

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKGIVSRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQIFE  +GWA   
Sbjct: 1336 DKMAGRHGNKGIVSRILPIEDMPYLPDGRPMDIVLNPLGVPSRMNVGQIFECLMGWAGEN 1395

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L ++ K +  D     ++S      +                                  
Sbjct: 1396 LKRRFKVIPFDEMFGQEMSRETVHSKLKE------------------------------- 1424

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                  A E+     L   +    G++I+YDG TGE FD+PVTVG  Y+LKL H+V DK+
Sbjct: 1425 ------AREKLKKDWLFSEEYP--GKTIVYDGRTGEAFDQPVTVGIAYILKLVHLVDDKI 1476

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR  
Sbjct: 1477 HARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMAGRNE 1536

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
               +IV G      GTPESF VL++E+Q+L L I +    T       +  + +
Sbjct: 1537 ALNAIVKGKAIPRPGTPESFKVLMRELQSLCLDIAVHKVETNKKDGASKDVEVD 1590



 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 102/465 (21%), Positives = 195/465 (41%), Gaps = 37/465 (7%)

Query: 16  FFGKN-PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
            F +      ++PDLIE+Q++S+  FL            GL    +S  PI+ ++G   L
Sbjct: 521 DFSEIQRSRFELPDLIEIQRSSFRWFL----------ETGLIEELESFSPISDYTGKLEL 570

Query: 75  EFV--SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            F+   Y+   PK+DVDD   RD TY+V + +  RLI          K   +IKEQ +++
Sbjct: 571 HFLARYYKLKQPKYDVDDAKRRDSTYSVQMYVPTRLI---------NKETGEIKEQEVFI 621

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GDLPLMT+ GTF+I G +R++V+Q+ RSPG+++  +  +   + +  Y+  +IP++G W+
Sbjct: 622 GDLPLMTERGTFIINGAERVIVNQIVRSPGVYYKSEIDK---NQRRTYSASLIPNRGAWL 678

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLS 250
             E D  D++ VRID+ RK+     L ALG+ + EI         +  +   +       
Sbjct: 679 KFETDKNDLVWVRIDKTRKLSAQILLKALGLTNNEIFDALRHPDYFQKTIEKEGEFSEED 738

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYV 308
           A   +           I  GEQ++++         L +  + K  + L ++      +  
Sbjct: 739 ALMELYRKLRPGEPPTITGGEQLLQNRFFDPKRYDLGRVGRHKLNRKLRLSVPDSTRVLT 798

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
             DI++     I +E         ++ + +  +R +  L  + +         ++ ++  
Sbjct: 799 PTDILSAIDYLINLEYDIGET-DDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMT 857

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                 L    ++ P      +  +  F            + +  +    RL+   P   
Sbjct: 858 VGDAETLTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG- 914

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             + +E     ++ +     G+  I  I+         +G +  +
Sbjct: 915 --LTRERAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 955


>gi|158512701|sp|A1A317|RPOB_BIFAA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1186

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 190/539 (35%), Positives = 264/539 (48%), Gaps = 59/539 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 657  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 715

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 716  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 775

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 776  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 829

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 830  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 882

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 883  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +   A                               V + AE+   G PV+
Sbjct: 943  -GWDISLDPDAEAAWKKY---------------------------VPQGAEKGAPGTPVA 974

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG   E I  +L          ++      G++ L+DG TGEPF +P++VGY+YML
Sbjct: 975  TPVFDGVRPETIKGLLSCTLPDRDGNKLVG--PDGKATLFDGRTGEPFPKPISVGYMYML 1032

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1033 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1092

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            KSDDV GR RVY +IV G +    G PESF VL+KEMQ+L L++++ N+        EE
Sbjct: 1093 KSDDVDGRVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNADGVAIDMKEE 1151



 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 301/620 (48%), Positives = 429/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +  + + +AL D+YR +RP D  T    +++ +  +F++ +YDL+
Sbjct: 245 DAFKDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLA 304

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDIIA IK LV L  G+                   
Sbjct: 305 RVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGETKFPGKRDGQDVDLRVDVD 364

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 365 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 424

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 425 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 484

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 485 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 544

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 545 DENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 604

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I   + +G   
Sbjct: 605 TNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTS 664

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 665 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 717

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 718 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 777

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 778 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 837

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 838 GETGTVIAVKEITREDAEED 857



 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 144/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 28  RVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVQEDLENGTNTVPHTSGLDEVFQE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 88  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 139 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEVFG 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 197 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDA 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 257 LAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 316

Query: 298 ITSD 301
           +  D
Sbjct: 317 LEKD 320


>gi|270284107|ref|ZP_05965549.2| DNA-directed RNA polymerase, beta subunit [Bifidobacterium gallicum
            DSM 20093]
 gi|270277104|gb|EFA22958.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium gallicum
            DSM 20093]
          Length = 1200

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 189/540 (35%), Positives = 266/540 (49%), Gaps = 55/540 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 671  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIKDGERVEKGTVLADGPATE-KGEMALGKNL 729

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 730  LVAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 789

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 790  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 843

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 844  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPSGVNQMIRVYIAQHRKITQG 896

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 897  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWVAHQ 956

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +                                   V + AE+ + G PV+
Sbjct: 957  -GWDISLDPDLEAEWKQY---------------------------VPKGAEKAEPGTPVA 988

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG  +E +  +L     D  G        ++ L+DG TGEPF +P++VGY+YMLKL
Sbjct: 989  TPVFDGVKQETLKGLLSTTLADRDGNKLVGDNGKATLFDGRTGEPFPKPISVGYMYMLKL 1048

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1049 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1108

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1109 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEDDD 1168



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 308/620 (49%), Positives = 439/620 (70%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           ++      + + L  +  + + +AL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 259 EAFEGYPLVLDALENETIETQDEALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 318

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K+N +L L+   + R + +EDI+A IK LV L  G               +  +D
Sbjct: 319 RVGRYKINRKLGLEKDYNDRSLSQEDIVATIKYLVTLHAGGATFAGKRDGEDVELRVDVD 378

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 379 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 438

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 439 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 498

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++VVY++A  + +  IAQAN  L
Sbjct: 499 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVVYMTADRDMDHVIAQANQKL 558

Query: 635 DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D++G F E+    R  AGE   VP + +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 559 DKNGDFVEKDALVRDAAGEAEDVPVDMVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 618

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 619 TNMQRQAVPLIKSERPLVGTGAEWRSAVDSGDVILAEKPGVVVYVSADIIRVMNDDGTTS 678

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+K G+ V +  ++ADGP+T+ G++ALG+N+LV
Sbjct: 679 S-------YKLAKFQRSNQTTCYNQVPLIKDGERVEKGTVLADGPATEKGEMALGKNLLV 731

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 732 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 791

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 792 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 851

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 852 GETGTVIAVKEITREDAEED 871



 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 91/305 (29%), Positives = 139/305 (45%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 42  RVNFGSIKEPIDVPYLLGVQTDSFDWLVGNERWAKRVEEDEKNGTNTVAHISGLDEVFQE 101

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 102 ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNA---------EFENGE 152

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD    R   S K ++ 
Sbjct: 153 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRTPDR--SSDKEVFG 210

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D + VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 211 AKIIPSRGAWLEFEIDKRDFLGVRVDRKRKQSAIVFLMAIGMTKPEIREAFEGYPLVLDA 270

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 271 LENETIETQDEALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 330

Query: 298 ITSDC 302
           +  D 
Sbjct: 331 LEKDY 335


>gi|54303713|gb|AAV33243.1| rifampicin-resistant RNA polymerase beta chain [Nonomuraea sp. ATCC
            39727]
          Length = 1149

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 188/508 (37%), Positives = 264/508 (51%), Gaps = 53/508 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V    ++        +  M   + LL A    +  +  D  +     V   V+
Sbjct: 663  IVAEGDRVEVNQVIADGPCT-DQGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVL 721

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGP 999
                   H  + + R   +  E+I     +  +E    LD     R+   +   + + G 
Sbjct: 722  SSIHIEEH--EVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVVPGDILVGK 779

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+ +        +  +    ++  +    SLKV +  S  ++      ++  
Sbjct: 780  VTPKGETELTPE-------ERLLRAIFGEKAREVRDTSLKVPHGESGRVIHT----QVFS 828

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
               GD++PPGV  +V+V VA KR I  GDK+AGRHGNKG++S+ILP EDMPFL+DGTPVD
Sbjct: 829  RDEGDELPPGVNVLVRVLVAQKRKITDGDKLAGRHGNKGVISKILPVEDMPFLEDGTPVD 888

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+LNPLGVP RMNVGQ+ ETHLGW     G  I  +   +              +     
Sbjct: 889  IILNPLGVPGRMNVGQVLETHLGWIAA-RGWDISGIQEAWAERLRDKGFEQVAPR----- 942

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMADLDES 1231
                                      ++TPVFDGA EE I  +L            +  S
Sbjct: 943  ------------------------TNMATPVFDGAHEEEIIGLLGNTVPTRDGDRLVQSS 978

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G++ L+DG +GEPF  P+ VGYIY+LKL H+V DK++ARSTG YS++TQQPLGGK+  GG
Sbjct: 979  GKARLFDGRSGEPFPYPIAVGYIYILKLLHLVDDKIHARSTGPYSMITQQPLGGKAQFGG 1038

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDV GR +VYE+IV G +  E G PESF VL+
Sbjct: 1039 QRFGEMEVWAMEAYGAAYALQELLTIKSDDVQGRVKVYEAIVKGENIPEPGIPESFKVLI 1098

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KEMQ+L L++++ +S   +    +   D
Sbjct: 1099 KEMQSLCLNVEVLSSDGMSIEMRDTDED 1126



 Score =  508 bits (1308), Expect = e-141,   Method: Composition-based stats.
 Identities = 339/686 (49%), Positives = 467/686 (68%), Gaps = 21/686 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           +I S        +    +K +    +      G ++  +I   ++  + I+         
Sbjct: 162 LIRSPGVYFERTVDKTSDKDLYGCKVIPSR--GAWLEFEIDKRDSVGVRIDRKRKQPVTV 219

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +         IL  +       +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 220 L--LKALGWTSERIL--ERFGRFESMRATLEKDHTAGQDDALLDIYRKLRPGEPPTKESA 275

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
           +++   L+F+  +YDL+ VGR K+N +L LD   DV  + ++DI+A I+ LV L  G+  
Sbjct: 276 QTLLENLYFNPKRYDLAKVGRYKVNKKLGLDLDIDVTVLTEDDIVATIEYLVRLHAGEES 335

Query: 452 -----TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
                 +DDID+ GNRRVRSVGE+++NQ RLGL RMER ++ER+++ D++++ PQ LIN 
Sbjct: 336 TGLPLEVDDIDHFGNRRVRSVGELIQNQVRLGLSRMERVVRERMTTQDVEAITPQSLINI 395

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           +PVV+++ EF+ +SQLSQ  +  N L+ +T+ RRL+ALG GG++R RAG+E+RDVHP+HY
Sbjct: 396 RPVVASIREFYGTSQLSQFMDQTNPLAGLTNKRRLNALGPGGLSRERAGMEVRDVHPSHY 455

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL+  L  F R+NA+GFIETPYRKV DG+VT+ + YL+A EE+   
Sbjct: 456 GRMCPIETPEGPNIGLIGYLACFGRLNAFGFIETPYRKVVDGRVTDQIDYLTADEEDQFV 515

Query: 627 IAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           IAQANS L  DG+F +  V  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE+D
Sbjct: 516 IAQANSPLTADGAFADHRVLVRTKGGEFEYVRSGEVDYMDVSPRQMVSVATAMIPFLEHD 575

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR   G NMQRQ+VPLLK+EAP VGTGME   A  +G  I A++AG+VE+V A  + +
Sbjct: 576 DANRPD-GANMQRQSVPLLKSEAPLVGTGMEYRAATDTGDVISAEKAGVVEEVSADYVTV 634

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            + +G           YR+ KF+RSNQ T  NQ+P+V  GD V  N +IADGP TD G++
Sbjct: 635 MNDDGTR-------TTYRVAKFKRSNQGTSFNQKPIVAEGDRVEVNQVIADGPCTDQGEM 687

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDI
Sbjct: 688 ALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDI 747

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNVSEE L ++DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VR
Sbjct: 748 PNVSEEVLADLDERGIIRIGAEVVPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVR 807

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSL+VP G SG V+  ++F+R   D
Sbjct: 808 DTSLKVPHGESGRVIHTQVFSRDEGD 833



 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 105/379 (27%), Positives = 176/379 (46%), Gaps = 32/379 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F +  E +++PDL+ +Q  S+D  L  +                     GLQ  F+ 
Sbjct: 16  RVSFARIQEPLEVPDLLALQTESFDWLLGNDRWKARVEAARQAGRRNVPSQSGLQEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK+ V++C  +D+T++ P+ +T   I           +
Sbjct: 76  ISPIEDFSGSMSLSFRDHRFEPPKYSVEECKEKDMTFSAPMFVTAEFI---------NNT 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  G+F++ G +R+V SQL RSPG++F+    +   S K LY 
Sbjct: 127 TGEIKSQTVFMGDFPLMTPKGSFIVNGTERVVTSQLIRSPGVYFERTVDKT--SDKDLYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+RK PVT  L ALG  SE IL  F  +  +  +
Sbjct: 185 CKVIPSRGAWLEFEIDKRDSVGVRIDRKRKQPVTVLLKALGWTSERILERFGRFESMRAT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 245 LEKDHTAGQDDALLDIYRKLRPGEPPTKESAQTLLENLYFNPKRYDLAKVGRYKVNKKLG 304

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-----EKSLEEIFHSEIRDIPILYVDSV 352
           +  D    +   +DIV      + + AG+           ++   +  +R +  L  + V
Sbjct: 305 LDLDIDVTVLTEDDIVATIEYLVRLHAGEESTGLPLEVDDIDHFGNRRVRSVGELIQNQV 364

Query: 353 NNNAYIRNTLVTDKNKDRK 371
                    +V ++   + 
Sbjct: 365 RLGLSRMERVVRERMTTQD 383


>gi|254423389|ref|ZP_05037107.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp. PCC
           7335]
 gi|196190878|gb|EDX85842.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp. PCC
           7335]
          Length = 1150

 Score =  509 bits (1310), Expect = e-141,   Method: Composition-based stats.
 Identities = 311/605 (51%), Positives = 425/605 (70%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            DS+ +  Y + T+  +     ++ALL++YR +RPG+  T +  + +    FFD  +YDL
Sbjct: 217 FDSLRHPEYFQKTIEKEGQFSEEEALLELYRKLRPGEPPTVNGGQQLLESRFFDPKRYDL 276

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L+ P+  R +  +DI++ I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 277 GKVGRHKLNRKLRLNIPESTRVLTPQDIVSAIDYLINLEFDIGNPDDIDHLGNRRVRSVG 336

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D DS+ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 337 ELLQNQVRVGLNRLERIIRERMTVSDADSLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 396

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RR+SALG GG+ R RAG  +RD+HP+H+GRICP ET EG N GL+ SL +
Sbjct: 397 TNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHHGRICPIETPEGPNAGLIGSLAT 456

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN +GFIETP+  V +G++  D   VY++A EE++  +A  +  +D D +   E V 
Sbjct: 457 HARVNDFGFIETPFFPVVNGQIVKDKPAVYMTADEEDDLRVAPGDVPIDSDNNILGESVP 516

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +  +   +++D++  SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 517 VRYRQDFTVTSPKEVDYVAVSPVQIISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 576

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E   VGTG+E+  A+ SG   +++  G+V  VDA  I +  +EG        V  Y L K
Sbjct: 577 ERALVGTGLEAQAARDSGMVTISRTDGVVSYVDANWIKVTDLEGQ-------VHSYELQK 629

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRP V  G +V    ++ADG +T+ G++ALG+N+L+ +MPW GYN+ED+
Sbjct: 630 YQRSNQDTCLNQRPFVFEGTKVVAGQVMADGSATEGGEIALGQNVLITYMPWEGYNYEDA 689

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V EDV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+ L+ +DE GII VGA
Sbjct: 690 ILLSERLVYEDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDALRQLDETGIIRVGA 749

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+ GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 750 WVSSGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 809

Query: 947 RHGID 951
           R   D
Sbjct: 810 REQGD 814



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 182/529 (34%), Positives = 253/529 (47%), Gaps = 64/529 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G                  +++   +  G +V  G ++      +G   +   + +L  
Sbjct: 619  EGQVHSYELQKYQRSNQDTCLNQRPFVFEGTKVVAGQVMADGSATEG-GEIALGQNVLIT 677

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD--- 970
                +  +  D  L     V   V       +  I+  +  +  E    +I  +  D   
Sbjct: 678  YMPWEGYNYEDAILLSERLVYEDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDALR 737

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + DE  I+    +    +IL G+    G         L   +  E  R            
Sbjct: 738  QLDETGIIRVGAWVSSGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD----------- 786

Query: 1031 VQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                   ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDK
Sbjct: 787  -------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVGDK 839

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGI+SRILP EDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE  LGWA   L 
Sbjct: 840  MAGRHGNKGIISRILPVEDMPYLPDGTPIDIVLNPLGVPSRMNVGQVFEALLGWAGQNLD 899

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             + K    D               ++ G  +  E       ++  +  + W         
Sbjct: 900  ARFKVTPFD---------------EMYGEEASLETTHGKLQEARNQTGKDW--------- 935

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF               + D  G+  LYDG TGEPFD+ VTVG  YMLKL H+V DK++A
Sbjct: 936  VF---------------NPDNPGKIQLYDGRTGEPFDQEVTVGQSYMLKLVHLVDDKIHA 980

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR    
Sbjct: 981  RSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEAL 1040

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             +IV G      GTPESF VL++E+Q+L L I +    T+      +  
Sbjct: 1041 NAIVKGKAIPRPGTPESFKVLMRELQSLCLDIAVHKLETQEDGTSRDSE 1089



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 106/454 (23%), Positives = 194/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDL+E+Q+AS+  FL           EGL    +S  PIT ++G   L F+   Y    
Sbjct: 34  LPDLVEIQRASFRWFLG----------EGLVEELESFSPITDYTGKLELHFLGKDYRLKA 83

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+   RD TY+V + +  RLI          K   DIKEQ +++GDLPLMT  GT
Sbjct: 84  PKYMVDEAKRRDSTYSVQMYVPTRLI---------NKETGDIKEQEVFIGDLPLMTDRGT 134

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +    G+  Y   +IP++G W+  E D  D++ 
Sbjct: 135 FIINGAERVIVNQIVRSPGVYYKAETDKH---GRRTYTANLIPNRGAWLKFETDKNDLVW 191

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI  +      +  +   +       A   +      
Sbjct: 192 VRIDKTRKLSAQVLLKALGLSDGEIFDSLRHPEYFQKTIEKEGQFSEEEALLELYRKLRP 251

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                ++ G+Q++ES         L K  + K  + L +       +   +DIV+     
Sbjct: 252 GEPPTVNGGQQLLESRFFDPKRYDLGKVGRHKLNRKLRLNIPESTRVLTPQDIVSAIDYL 311

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+ +   ++ + +  +R +  L  + V         ++ ++        L    
Sbjct: 312 INLE-FDIGNPDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDADSLTPAS 370

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    R++   P     + +E     
Sbjct: 371 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRERAGFA 425

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +    +G+  I  I+         +G +  +
Sbjct: 426 VRDIHPSHHGR--ICPIETPEGPNAGLIGSLATH 457


>gi|46360928|gb|AAS89197.1| RpoB [Corynebacterium minutissimum]
          Length = 1118

 Score =  508 bits (1309), Expect = e-141,   Method: Composition-based stats.
 Identities = 201/638 (31%), Positives = 297/638 (46%), Gaps = 69/638 (10%)

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
             A RI +R  +GD+  + +    Y  +  +         Q   V            A+  
Sbjct: 534  TADRIEVRLKDGDIGVTDASGVDYVDVSPR---------QMVSVATAMIPFLEHDDANRA 584

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLG 857
                        ++ +  P+ G   E         ++       +     +++      G
Sbjct: 585  LMGANMQRQAVPLVRSEAPYVGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEG 644

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +              N ++  ++ +G  V  G +L           M+    LL A  
Sbjct: 645  QRDTYMLRKFERTNQNTNYNQTPLVSLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFM 703

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD--- 972
              +  +  D  +     V   ++       H ID  +  +  E    +I  ++ D     
Sbjct: 704  PWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDL 763

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 764  DERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDT--------- 814

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                      ET K I   RF  + +     DD+ PGV  +++V+VA KR IQ GDK+AG
Sbjct: 815  ---SMKVPHGETGKVIGVSRFSREDD-----DDLAPGVNEMIRVYVAQKRKIQDGDKLAG 866

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI
Sbjct: 867  RHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWKI 925

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +     +   +   L+   E++      +                        +TPVFD
Sbjct: 926  DT-----EDPANADLLKKLPEELYDVPPESLT----------------------ATPVFD 958

Query: 1213 GADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            GA  E I+ +L  +  +  G        ++ L+DG +GEP+  PV+VGY+YMLKL+H+V 
Sbjct: 959  GATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGEPYMYPVSVGYMYMLKLHHLVD 1018

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVG
Sbjct: 1019 EKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVG 1078

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            R +VYE+IV G++  + G PESF VL+KE+Q+L L+++
Sbjct: 1079 RVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVE 1116



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 325/661 (49%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIK----ERFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+++ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMISIHTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+ T + +  R   
Sbjct: 485 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDRYAIAQAEVEKDADGTLTADRIEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 545 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNT  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQNTNYNQTPLVSLGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 718 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVSRFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 167/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  SY   +               D R   GL+   + + P
Sbjct: 16  RYSFAKISEPIAVPGLLDLQLDSYAWLIGTPEWREREQAERGDDARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIKERFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        D  + ++++         L K  + K  +      
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+  E  +    GE+       I    ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMI-----SIHTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|221632985|ref|YP_002522208.1| DNA-directed RNA polymerase subunit beta [Thermomicrobium roseum DSM
            5159]
 gi|221157073|gb|ACM06200.1| DNA-directed RNA polymerase, beta subunit [Thermomicrobium roseum DSM
            5159]
          Length = 1162

 Score =  508 bits (1307), Expect = e-141,   Method: Composition-based stats.
 Identities = 195/525 (37%), Positives = 267/525 (50%), Gaps = 73/525 (13%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G E +      V       I++  I+  G  +  GD++    + +    +   + +L A
Sbjct: 683  DGNERVYELRKFVRSNQDTCINQRPIVQKGQRIEAGDVIADSSSTEN-GELALGQNVLVA 741

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK---- 971
                +  +  D  L     +S  +V   ++    I+K E      +   E + RD     
Sbjct: 742  FMSWEGGNFEDAVL-----ISERLVREDVYTSIHIEKYECEARDTKLGPEEITRDIPNVG 796

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            +D    LD +   R+   +   + + G    +  T LS++      R+ + + A   +  
Sbjct: 797  EDSLRNLDADGIIRIGAQVGPNDILVGKVTPRGETELSAE--ERLLRAIFGERARDVKDT 854

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               V                  ++       G ++P GV  +V+VF+A KR I  GDKMA
Sbjct: 855  SLRVPHGVHGIVIDVKRFRRDDES-------GVELPAGVNEMVRVFIAQKRKISEGDKMA 907

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSRI+P EDMP+L DGTPVDI+LNP+GVPSRMN+GQI ETHLGWA   LG K
Sbjct: 908  GRHGNKGVVSRIVPIEDMPYLPDGTPVDIILNPIGVPSRMNLGQILETHLGWAAHTLGIK 967

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            + S + D     +I  L                                K+G+P      
Sbjct: 968  VASPVFDGAKEEEIRELLR------------------------------KAGLP------ 991

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                              E G+  LYDG TGE FDRPVTVG IYM+KL H+V DK++ARS
Sbjct: 992  ------------------EDGKVELYDGRTGEKFDRPVTVGIIYMMKLVHLVEDKIHARS 1033

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDDVVGR + YE+
Sbjct: 1034 TGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTVKSDDVVGRVKTYEA 1093

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            IV G    E G PESF VLVKE+++LGLS+++ N   +     E+
Sbjct: 1094 IVKGEPIVEAGVPESFKVLVKELRSLGLSVEVLNEDEEPIEFGED 1138



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 254/689 (36%), Positives = 359/689 (52%), Gaps = 74/689 (10%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A     ++ L E+F           VD+  ++ YI  T+  D+ K R++A ++IY+
Sbjct: 207 VLLRAVGYGRDEELFELFA---------DVDTDPDHRYIAATIERDRTKSREEAQMEIYK 257

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKY----------------------------DLSTV 411
            +RPGD  T   A ++   LFF+   Y                            DL+ +
Sbjct: 258 TLRPGDPPTRENAAALIERLFFNPRTYDLGKVGRYKLNKRLGLETPADVRVLTREDLAAL 317

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            R  + +   LD PDD+ H+     +  +  L+ +    G       +  R      +  
Sbjct: 318 VRTMILVNRGLDRPDDIDHL-GNRRVRTVGELIQMHLRTGLQRLERGIRERMTIVDIDTA 376

Query: 472 KNQYRLGLLR-MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE-EHV 529
                +   R +  +I+E  +   +   M Q    A+              L++      
Sbjct: 377 TPASLISSTRPLRAAIREFFAGSQLSQFMDQTNPLAELTHKRRVSALGPGGLNRERAGFE 436

Query: 530 NSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLT 587
                 +H  R+  +    G                 YG I  P      H      +  
Sbjct: 437 VRDVHDSHYGRICPIETPEGPNIGLITSLATYAKVNEYGFITAPYRRVYRHIELPSQADL 496

Query: 588 SFARV--NAYGFIETPY-----------------------RKVCDGKVTNDVVYLSAMEE 622
              +V        ET                         R      V+++V YL+A +E
Sbjct: 497 LIGQVLRTDVVDPETGELLAGRGTTVDRGLCDRLIAAGVTRVDVLPFVSDEVDYLTADQE 556

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E+  IAQAN+ LDE   F    +  R AG+ +L   EK+D++D SPKQVVS++A+LIPFL
Sbjct: 557 EHFTIAQANTPLDEGMRFVASRIEARRAGKFVLEVPEKVDYMDVSPKQVVSVSAALIPFL 616

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+DD+NR LMG NMQRQAVPLL+  AP VGTG+E   A+ SG  +VA++ GIV+ V A R
Sbjct: 617 EHDDANRALMGANMQRQAVPLLRPRAPIVGTGVEYQAARDSGQVVVAQKGGIVKSVTARR 676

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           IV+   +G+         +Y L KF RSNQ+TC+NQRP+V+ G  +   D+IAD  ST+ 
Sbjct: 677 IVVLEDDGNE-------RVYELRKFVRSNQDTCINQRPIVQKGQRIEAGDVIADSSSTEN 729

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
           G+LALG+N+LVAFM W G NFED++LISER+V EDV+TSIHIE++E  ARDTKLGPEEIT
Sbjct: 730 GELALGQNVLVAFMSWEGGNFEDAVLISERLVREDVYTSIHIEKYECEARDTKLGPEEIT 789

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D  GII +GA+V P DILVGK+TP+GE+ ++ EE+LLRAIFGE+A 
Sbjct: 790 RDIPNVGEDSLRNLDADGIIRIGAQVGPNDILVGKVTPRGETELSAEERLLRAIFGERAR 849

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DV+DTSLRVP GV G V+DV+ F R    
Sbjct: 850 DVKDTSLRVPHGVHGIVIDVKRFRRDDES 878



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 139/289 (48%), Gaps = 23/289 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R  F + P ++++P+LIE+Q  S++ F            EGL+   +   PI  ++    
Sbjct: 26  RVSFARIPTVLEMPNLIELQLKSFEWF----------KTEGLRELLEEFSPIIDYNQKLE 75

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           + F+ + F+ P++  + C  RD+TYA PL   +RL++ D           ++KE  IY+ 
Sbjct: 76  VHFLRHWFEKPRYTPEICRERDMTYAAPLYFRVRLVIRD---------TGEVKESDIYID 126

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D P+MT+ GTFVI G +R+VVSQL RSPG +F+ +      +G+ L   ++IP +G W++
Sbjct: 127 DFPMMTETGTFVINGAERVVVSQLVRSPGAYFELEPDP--ATGRQLCMAKLIPTRGAWLE 184

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDFWCFPLSAA 252
            E  ++D++ V+IDR+RK+PVT  L A+G   +E L   F                    
Sbjct: 185 FETSNRDVLSVKIDRKRKIPVTVLLRAVGYGRDEELFELFADVDTDPDHRYIAATIERDR 244

Query: 253 DLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                         +  G+    E+   L   L  + +   +  +G   
Sbjct: 245 TKSREEAQMEIYKTLRPGDPPTRENAAALIERLFFNPRTYDLGKVGRYK 293


>gi|56752516|ref|YP_173217.1| DNA-directed RNA polymerase subunit beta [Synechococcus elongatus
           PCC 6301]
 gi|81561186|sp|Q5MZ23|RPOB_SYNP6 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|56687475|dbj|BAD80697.1| RNA polymerase beta subunit [Synechococcus elongatus PCC 6301]
          Length = 1100

 Score =  507 bits (1306), Expect = e-141,   Method: Composition-based stats.
 Identities = 327/689 (47%), Positives = 446/689 (64%), Gaps = 13/689 (1%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +      L   +  +            + G +++    
Sbjct: 117 INGAERVIVNQIVRSPGVYYKSERDKNGRLTHNASLIPNRGAWLKFETDKNGLVWVRIDK 176

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  I   D + +  Y + T+  +      +AL+++YR +RPG+ 
Sbjct: 177 TRKLSAQVLLKALGLSDNEI--YDKLRHPEYYQKTIDKEGQFSEDEALMELYRKLRPGEP 234

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T S  + +    FFD  +YDL  VGR K+N +L L+  D VR +  EDI+A I  L++L
Sbjct: 235 PTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLGLNVADTVRTLTSEDILAAIDYLINL 294

Query: 447 RN--GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
               G   +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D DS+ P  L+
Sbjct: 295 ELDLGGCEVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDSDSLSPASLV 354

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+
Sbjct: 355 NPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPS 414

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEE 622
           HYGRICP ET EG N GL+ SL + ARVN YGFIETP+ +V +G+V  D+  VY++A +E
Sbjct: 415 HYGRICPIETPEGPNAGLIGSLATHARVNDYGFIETPFWRVEEGRVRKDLAPVYMTADQE 474

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           ++  +A  + + D+ G      +  R   +      E++D++  SP Q++S+A SLIPFL
Sbjct: 475 DDLRVAPGDVATDDAGYILGTTIPVRYRQDFTTTTPERVDYVALSPVQIISVATSLIPFL 534

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+DD+NR LM  NMQRQAVPLL+ E P VGTG+E   A+ SG  I +   G +  VDA  
Sbjct: 535 EHDDANRALMSSNMQRQAVPLLRPERPLVGTGLEPQAARDSGMVITSPVDGTISYVDATH 594

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           I + +  G+          Y L K+QRSNQ+TC+NQRP+V  GD  +R  +IADG +T+ 
Sbjct: 595 IEVTADTGEKYG-------YALQKYQRSNQDTCLNQRPIVFEGDRGQRGQVIADGSATEK 647

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
           G+LALG+N+LVA+MPW GYN+ED++LISER+V +DV+TSIHIE+FE+ AR TKLGPEEIT
Sbjct: 648 GELALGQNILVAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEIT 707

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+ +DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA 
Sbjct: 708 REIPNVGEDALRQLDENGIIRVGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKAR 767

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 768 DVRDNSLRVPNGEKGRVVDVRLFTREQGD 796



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 199/583 (34%), Positives = 281/583 (48%), Gaps = 59/583 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS-EDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E        MV    V  +I   +   +      G 
Sbjct: 544  MSSNMQRQAVPLLRPERPLVGTGLEPQAARDSGMVITSPVDGTISYVDATHIEVTADTGE 603

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G     G  ++   +   +  +   + +L A   
Sbjct: 604  KYGYALQKYQRSNQDTCLNQRPIVFEGDRGQRGQ-VIADGSATEKGELALGQNILVAYMP 662

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     +S  +V   ++    I+K E    +E  Q +L   +   E   +
Sbjct: 663  WEGYNYEDAIL-----ISERLVYDDVYTSIHIEKFE----IEARQTKLGPEEITREIPNV 713

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              +   +L E   I  G    SG     K T        + P  +  +    ++      
Sbjct: 714  GEDALRQLDENGIIRVGAWVESGDILVGKVTPKGES--DQPPEEKLLRAIFGEKARDVRD 771

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SL+V       +++ R        + GD++PPG   VV+V+VA KR IQ GDKMAGRHG
Sbjct: 772  NSLRVPNGEKGRVVDVRL----FTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHG 827

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+SRILPCEDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE  LGWA   L  + K  
Sbjct: 828  NKGIISRILPCEDMPYLPDGTPLDIVLNPLGVPSRMNVGQVFECMLGWAGQLLDARFKVT 887

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D               ++ G  +    ++    ++  +  + W         VF    
Sbjct: 888  PFD---------------EMYGAEASRLTVNAKLSEAREQTGQPW---------VFSD-- 921

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                         DE G+  +YDG TGEPFDRPVTVG  YMLKL H+V DK++ARSTG Y
Sbjct: 922  -------------DEPGKIQVYDGRTGEPFDRPVTVGRAYMLKLVHLVDDKIHARSTGPY 968

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+ +GGQR GEMEVW ++AYGAAY+LQE+LT+KSDD+ GR     +IV G
Sbjct: 969  SLVTQQPLGGKAQQGGQRFGEMEVWALEAYGAAYILQELLTVKSDDMQGRNEALNAIVKG 1028

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                  GTPESF VL++E+Q+L L I +  + T++  + +E+ 
Sbjct: 1029 KAIPRPGTPESFKVLMRELQSLCLDIAVYKASTEDYEEDKEVD 1071



 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 109/496 (21%), Positives = 198/496 (39%), Gaps = 58/496 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+ +Q+ S+  FL   +  +            S  PIT ++G   L F+   Y+   
Sbjct: 14  LPDLVAIQRNSFRWFLEEGLIEELE----------SFSPITDYTGKLELHFLGKQYKLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TY+V + +  RLI          K   +IKEQ +++GDLPLMT  GT
Sbjct: 64  PKYDVDEAKRRDGTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTDRGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  ++ +   +G+L +   +IP++G W+  E D   ++ 
Sbjct: 115 FIINGAERVIVNQIVRSPGVYYKSERDK---NGRLTHNASLIPNRGAWLKFETDKNGLVW 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+   EI         Y +  D          LM        
Sbjct: 172 VRIDKTRKLSAQVLLKALGLSDNEIYDKLRHPEYYQKTIDKEGQFSEDEALM------EL 225

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYVAEDIVNGETGEIY 321
              +  GE   +  G++L        K   +  +G    +   GL VA D V   T E  
Sbjct: 226 YRKLRPGEPPTVSGGQQLLESRFFDPKRYDLGRVGRYKLNKKLGLNVA-DTVRTLTSEDI 284

Query: 322 IEAGDV----------IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           + A D            +   ++ + +  +R +  L  + V         ++ ++     
Sbjct: 285 LAAIDYLINLELDLGGCEVDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSD 344

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              L    ++ P      +  +  F            + +  +    RL+   P     +
Sbjct: 345 SDSLSPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---L 399

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLR 481
            +E     ++ +     G+    +               + RV   G +    +R+   R
Sbjct: 400 TRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLATHARVNDYGFIETPFWRVEEGR 459

Query: 482 MERSIKERISSVDIDS 497
           + + +     + D + 
Sbjct: 460 VRKDLAPVYMTADQED 475


>gi|311115093|ref|YP_003986314.1| DNA-directed RNA polymerase subunit beta [Gardnerella vaginalis ATCC
            14019]
 gi|310946587|gb|ADP39291.1| DNA-directed RNA polymerase subunit beta [Gardnerella vaginalis ATCC
            14019]
          Length = 1188

 Score =  507 bits (1305), Expect = e-141,   Method: Composition-based stats.
 Identities = 185/537 (34%), Positives = 266/537 (49%), Gaps = 49/537 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +   +             ++  +I  G  V  G +L        +  +   + L
Sbjct: 659  MNDDGTQSSYKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGP-ATDKGELALGKNL 717

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 718  LVAFMPWNGYNYEDAII-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLP 772

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 773  NVGEDAIANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 831

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E    GD++P GV ++++V++A  R I  GDK++G
Sbjct: 832  DTSLRVPHGETGTVIAVKEITREDAE--DDGDELPNGVNQMIRVYIAQHRKITQGDKLSG 889

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 890  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA-GWDI 948

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                +   A                               V   AE      PV+TPVFD
Sbjct: 949  NLDPDLEAAWKKY---------------------------VPEGAEHGDPCTPVATPVFD 981

Query: 1213 GADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G   E +  +L          ++      G++ L+DG TGEPF +P++VGY+Y+LKL+H+
Sbjct: 982  GVRPETLKGLLSTTLADRDGNKLVG--SDGKATLFDGRTGEPFPKPISVGYMYILKLHHL 1039

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV
Sbjct: 1040 VDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDV 1099

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             GR RVY +IV G++    G PESF VL+KEMQ+L L++++ NS        +E  D
Sbjct: 1100 DGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNSEGVAIDMKDEDDD 1156



 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 311/615 (50%), Positives = 430/615 (69%), Gaps = 23/615 (3%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + + L  +    + DAL D+YR +RP D +T     ++    +F++ +YDL+ VGR 
Sbjct: 252 YPLVLDALEKEPIDTQNDALTDLYRKIRPADTATPDAGRNLLESFYFNTKRYDLARVGRY 311

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L L+   + R + +EDIIA IK LV L +G+                 +DDID+ 
Sbjct: 312 KINRKLGLEADYNDRSLNREDIIATIKYLVTLHSGEKTFPGKRDGEDVQLRVDVDDIDHF 371

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF +
Sbjct: 372 GNRRIRQVGELVQNQIRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFFGT 431

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG N
Sbjct: 432 SQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEGPN 491

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL+ SL +F R+N +GFIETPYRKV +G VTN+V Y++A  E    IAQAN  LDE+G+
Sbjct: 492 IGLIGSLATFGRINPFGFIETPYRKVVNGHVTNEVEYMTADREAEHVIAQANQELDENGN 551

Query: 640 FTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           F       R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NMQR
Sbjct: 552 FVGTQALARVDEEEAVDVPVSTVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNMQR 611

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+K+E P VGTG E   A  SG  I++++ G+V  V A  I + + +G        
Sbjct: 612 QAVPLIKSERPLVGTGSEWRAAVDSGDVILSEKPGVVTYVSADIIRVMNDDGTQSS---- 667

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y+L KFQRSNQ TC NQ PL+K G+ V    ++ADGP+TD G+LALG+N+LVAFMPW
Sbjct: 668 ---YKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGPATDKGELALGKNLLVAFMPW 724

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+DE
Sbjct: 725 NGYNYEDAIIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAIANLDE 784

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +GT
Sbjct: 785 RGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGETGT 844

Query: 939 VVDVRIFNRHGIDKN 953
           V+ V+   R   + +
Sbjct: 845 VIAVKEITREDAEDD 859



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 92/305 (30%), Positives = 142/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL+  F+ 
Sbjct: 30  RVNFGSICEPIDVPYLLGVQTDSFDWLIGSERWKKRVEEDEANGTHTVPHVSGLEEVFQE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 90  ISPIENFAETMSLTFSDPYFEEPRHTVLECKEKDYTYSAPLYVNA---------EFENGE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRTQDRT--SDKDVFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+R      FLMA+GM   EI   F  YP ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRTQSAIVFLMAIGMTKPEIAEAFQGYPLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     D G  ++ES    T    L +  + K  + LG
Sbjct: 259 LEKEPIDTQNDALTDLYRKIRPADTATPDAGRNLLESFYFNTKRYDLARVGRYKINRKLG 318

Query: 298 ITSDC 302
           + +D 
Sbjct: 319 LEADY 323


>gi|73913595|gb|AAZ91715.1| DNA-directed RNA polymerase beta chain [Corynebacterium stationis]
          Length = 1164

 Score =  507 bits (1305), Expect = e-141,   Method: Composition-based stats.
 Identities = 181/519 (34%), Positives = 266/519 (51%), Gaps = 61/519 (11%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 670  NYNQTPLVNMGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILSQRI 728

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLME 988
            V   ++       H ID  +  +  E    +I    E + RD DD   I+      R  +
Sbjct: 729  VEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIIRVGADVRPGD 787

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                V  +          
Sbjct: 788  ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA--------- 838

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                           DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V ++LP ED
Sbjct: 839  --------RFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKVLPPED 890

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF+ DGTPVD++LN  GVP RMN+GQ+ E HLGW     G K+ +     +   +   L
Sbjct: 891  MPFMADGTPVDVLLNTHGVPRRMNIGQVLELHLGWLA-HTGWKVDT-----EDPKNAELL 944

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD- 1227
            ++  +++    + +                        +TPVFDGA  E I+ +L  +  
Sbjct: 945  KTLPQELYDVPADSLT----------------------ATPVFDGATNEEISRLLASSKP 982

Query: 1228 -------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                   +DE G+++L+DG +GEP+  P++VGY+YMLKL+H++ +K++ARSTG YS++TQ
Sbjct: 983  NRDGDVMIDEDGKTVLFDGRSGEPYQYPISVGYMYMLKLHHLIDEKIHARSTGPYSMITQ 1042

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  +
Sbjct: 1043 QPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPD 1102

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             G PESF VL+KE+Q+L L++++ ++            D
Sbjct: 1103 PGIPESFKVLLKELQSLCLNVEVLSADGTPMELSGSDDD 1141



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 321/661 (48%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   +    +  + +TL +
Sbjct: 197 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEEQI--RERFGFSELMMSTLES 252

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 253 DGIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGG 312

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             + +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 313 DHEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGDIIPINTDDIDHFGNRRLRTVGELI 372

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 373 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 432

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 433 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 492

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV +G+VT++V YL+A EE+   I QA    D DG+  ++ +  R   
Sbjct: 493 VNAFGFIETPYRKVENGRVTDEVYYLTADEEDRYAIGQAEVEQDADGNIIDDRIEVRLKD 552

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +DF+D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPL++AEAP+
Sbjct: 553 GDIGVTDANGVDFVDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLVRAEAPY 612

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  ++  +AG+VE V+A  I I   EG  D        Y L KF+R+
Sbjct: 613 VGTGMELRAAYDAGDMVITPKAGVVENVNADLITIMDDEGIRD-------TYMLRKFERT 665

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED++++S
Sbjct: 666 NQGTNYNQTPLVNMGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILS 725

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++D+ GII VGA+V P
Sbjct: 726 QRIVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRVGADVRP 785

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 786 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDED 845

Query: 951 D 951
           D
Sbjct: 846 D 846



 Score =  296 bits (757), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 108/543 (19%), Positives = 210/543 (38%), Gaps = 58/543 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE--------GLQAAFKSVFPI 65
           R  F K  E I +P L+++Q  S+   +      + +  E        GL+     + PI
Sbjct: 25  RYSFAKISEPIAVPGLLDLQLESFAWLIGTPEWRERQQEERGQDHVSSGLEDILAELSPI 84

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++I
Sbjct: 85  QDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQEI 135

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q++++GD P+MT +GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++I
Sbjct: 136 KSQTVFIGDFPMMTDEGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVKVI 193

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   D
Sbjct: 194 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFGFSELMMSTLESD 253

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF------ 295
                  A   +   +        D  + ++++         L +  + K  +       
Sbjct: 254 GIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGGD 313

Query: 296 -----------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
                      + +T + L  L+  E  +    G+I       I+   ++   +  +R +
Sbjct: 314 HEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGDII-----PINTDDIDHFGNRRLRTV 368

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             L  + V      R   V  +    +DA       +      + ++    F        
Sbjct: 369 GELIQNQVRVG-LSRMERVVRERMTTQDAESITPTSLINVRPVSAAI-REFFGTSQLSQF 426

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
               +++  +    RL+   P     + +E     ++ +     G+  +  I+      +
Sbjct: 427 MDQNNSLSGLTHKRRLSALGPGG---LSRERAGIEVRDVHPSHYGR--MCPIETPEGPNI 481

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             +G +          R+            +++    D +               +++ Q
Sbjct: 482 GLIGSLA------SYARVNAFGFIETPYRKVENGRVTDEVYYLTADEEDRYAIGQAEVEQ 535

Query: 525 LEE 527
             +
Sbjct: 536 DAD 538


>gi|113476515|ref|YP_722576.1| DNA-directed RNA polymerase subunit beta [Trichodesmium erythraeum
           IMS101]
 gi|123160622|sp|Q110H1|RPOB_TRIEI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|110167563|gb|ABG52103.1| DNA-directed RNA polymerase, beta subunit [Trichodesmium erythraeum
           IMS101]
          Length = 1102

 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 320/605 (52%), Positives = 428/605 (70%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            DS+ +  Y + T+  +     ++ALL++YR +RPG+  T +  E + +  FFD  +YDL
Sbjct: 202 FDSLRHPDYFQKTIEKEGQYGEEEALLELYRKLRPGEPPTIAGGEQLLHSRFFDQKRYDL 261

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L+ P+ VR + KEDI+A I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 262 GQVGRYKLNNKLRLNLPNTVRVLTKEDILASIDYLINLEYDIGQTDDIDHLGNRRVRSVG 321

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  + +++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 322 ELLQNQIRVGLNRLERIIRERMTVSESETLTPTSLVNPKPLVAAIKEFFGSSQLSQFMDQ 381

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 382 TNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAN 441

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            A+VN+YGFIETPY  V +G+V  D   +Y++A  E++  +A  +   D +G    ++V 
Sbjct: 442 HAKVNSYGFIETPYYPVENGRVLRDRTPIYMTADAEDDLRVAPGDIMTDAEGKILGDVVP 501

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      +++D++  SP QVVS+A SLIPFLE+DD+NR LMG NMQRQAVPLL  
Sbjct: 502 VRYRQDFTTTNPQQVDYVAVSPVQVVSVATSLIPFLEHDDANRALMGSNMQRQAVPLLNP 561

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E   A+ SG  +V +  G V  VD+ +I +   EG+          Y L K
Sbjct: 562 DRPLVGTGLEPQAARDSGMVVVTRTDGEVSYVDSTKISVIDKEGNQAD-------YPLCK 614

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRPLV  GD+V    ++ADG ST+  +LALG+N+LVA+MPW GYN+ED+
Sbjct: 615 YQRSNQDTCLNQRPLVFEGDQVVAGQVLADGSSTEGAELALGQNVLVAYMPWEGYNYEDA 674

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+GL+N+DE GII VGA
Sbjct: 675 ILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDGLRNLDEQGIIRVGA 734

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G +VDVR+F 
Sbjct: 735 WVQSGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRIVDVRVFT 794

Query: 947 RHGID 951
           R   D
Sbjct: 795 REKGD 799



 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 184/538 (34%), Positives = 258/538 (47%), Gaps = 64/538 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             K G +                +++  ++  G +V  G +L    + +G   +   + +L
Sbjct: 602  DKEGNQADYPLCKYQRSNQDTCLNQRPLVFEGDQVVAGQVLADGSSTEGA-ELALGQNVL 660

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD- 970
             A    +  +  D  L     V   V       +  I+  +  +  E    +I  +  D 
Sbjct: 661  VAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDG 720

Query: 971  --KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DEQ I+    + +  +IL G+    G         L   +  E  R          
Sbjct: 721  LRNLDEQGIIRVGAWVQSGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD--------- 771

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                     ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ G
Sbjct: 772  ---------VRDNSLRVPNGEKGRIVDVRVFTREKGDELPPGANMVVRVYVAQKRKIQVG 822

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK+AGRHGNKGI+SRILP EDMP+L DGTP+D+VLNPLGVPSRMNVGQIFE  LGWA   
Sbjct: 823  DKVAGRHGNKGIISRILPIEDMPYLPDGTPIDVVLNPLGVPSRMNVGQIFECLLGWAGEI 882

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L  + K +  D     + S     L   +   +  +                        
Sbjct: 883  LSVRFKCVPFDEMHGPEKSRETVHLMLKLARDNSGKDW---------------------- 920

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              VFD                   G+  ++DG TGE FDRPVTVG  YMLKL H+V DK+
Sbjct: 921  --VFDE---------------KHPGKIWVFDGRTGERFDRPVTVGIAYMLKLVHLVDDKI 963

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR  
Sbjct: 964  HARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNE 1023

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
               +IV G      GTPESF VL++E+Q+L L I      T +    +++      +L
Sbjct: 1024 ALNAIVKGKAIPRPGTPESFKVLMRELQSLCLDIAAHKVETVDDGTTQDVEVDLMADL 1081



 Score =  317 bits (812), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 98/457 (21%), Positives = 188/457 (41%), Gaps = 34/457 (7%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SY 79
           +I ++PDLIE+Q+AS+  FL            GL     S  PIT ++G   L F+  +Y
Sbjct: 15  QIFNMPDLIEIQRASFRWFL----------EYGLIEELDSYSPITDYTGKLELHFIAKNY 64

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
           +   PK+ V++   RD +YAV + +  RLI          K   +IKEQ +++GDLPLMT
Sbjct: 65  KLKQPKYSVEESKRRDSSYAVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMT 115

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++V+Q+ RSPG+++  +  +   SG+  Y   +IP++G W+  E D  
Sbjct: 116 DRGTFIINGAERVIVNQIVRSPGVYYKSETDK---SGRRTYNASLIPNRGAWLKFETDKN 172

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVG 257
           D++ VRID+ RK+     L ALG+   EI  +      +  +   +       A   +  
Sbjct: 173 DLVWVRIDKTRKLSAQVLLKALGLGDSEIFDSLRHPDYFQKTIEKEGQYGEEEALLELYR 232

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                    I  GEQ++ S         L  +    +      +       + ++ +   
Sbjct: 233 KLRPGEPPTIAGGEQLLHSRFFDQKRYDLGQVGRYKLNNKLRLNLPNTVRVLTKEDILAS 292

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              +     D+     ++ + +  +R +  L  + +         ++ ++    +   L 
Sbjct: 293 IDYLINLEYDIGQTDDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMTVSESETLT 352

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
              ++ P      +  +  F            + +  +    R++   P     + +E  
Sbjct: 353 PTSLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRERA 407

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
              ++ +     G+  I  I+         +G +  +
Sbjct: 408 GFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLANH 442


>gi|229544476|gb|ACQ76416.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 456

 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 188/458 (41%), Positives = 285/458 (62%), Gaps = 3/458 (0%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+++QK +Y  FL    AP +R  EGLQAAF + FPI + +G   + F+ Y    P
Sbjct: 1   EVPYLLQMQKDAYTAFLQAGTAPLKRNIEGLQAAFDAAFPIVSHNGFVEMRFIEYNLAKP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKDIKEQSIYMGDLPLMTKDGT 143
            FDV +C  R LTYA  ++  ++LI++D +  T  +K +K++KEQ +YMG++PLMT  G+
Sbjct: 61  AFDVRECQTRGLTYASAVRAKVQLIIYDRESSTTQSKVVKEVKEQEVYMGEVPLMTNKGS 120

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ RIIP +G W+D EFD K +++
Sbjct: 121 FIINGTERVIVSQLHRSPGVFFEHDKGKGHSSGKLLFSARIIPYRGSWLDFEFDPKXLLY 180

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+DRRRK+PVT  L A+G++ E IL                     A  L  G      
Sbjct: 181 FRVDRRRKMPVTILLKAIGLNPESILXXXXXXXXXRLMDSGAQMEFVAERL-RGEVARFD 239

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D  +G+ ++   K++T+  ++ L++ G   + +  D L G  VA  IV+ +TGEI  +
Sbjct: 240 ITD-KSGKVIVVKDKRVTARHIRELEQSGTTHVSVPEDFLVGRVVARGIVDADTGEILAK 298

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A D + E  L+++  + + D+  +Y + ++   YI  TL TD+ +D   A + IYR+MRP
Sbjct: 299 ANDELTEALLKKLRGAGVPDVQCIYTNELDQGPYISQTLRTDETQDEFAARVAIYRMMRP 358

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T    +++F  LF++ D YDLS VGR+K N ++          +  EDI++++KIL
Sbjct: 359 GEPPTEDAVQALFQRLFYNPDTYDLSRVGRMKFNAKIGRAESTGAMVLSNEDILSVVKIL 418

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
           VDLRNG G +DDID+LGNRRVR VGE+ +NQYR GL R
Sbjct: 419 VDLRNGHGEVDDIDHLGNRRVRCVGELAENQYRTGLAR 456


>gi|54303711|gb|AAV33242.1| rifampicin-sensitive RNA polymerase beta chain [Nonomuraea sp. ATCC
            39727]
          Length = 1155

 Score =  506 bits (1304), Expect = e-141,   Method: Composition-based stats.
 Identities = 184/488 (37%), Positives = 262/488 (53%), Gaps = 52/488 (10%)

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
              +  M   + LL A    +  +  D  +     V   V+       H  + + R   + 
Sbjct: 688  TDQGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEH--EVDARDTKLG 745

Query: 961  REQIELLARDKDDE-QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             E+I     +  +E    LD     R+   +   + + G    K  T L+ +        
Sbjct: 746  PEEITRDIPNVSEEVLADLDERGIIRIGAEVVPGDILVGKVTPKGETELTPE-------E 798

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +  +    ++  +    SLKV +     ++  R    +   + GD++PPGV  +V+V+VA
Sbjct: 799  RLLRAIFGEKAREVRDTSLKVPHGEQGKVIAVR----VNSREEGDELPPGVNELVRVYVA 854

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
             KR I  GDK+AGRHGNKG++S+ILP EDMPF +DGTPVDI+LNPLGVP RMNVGQ+ ET
Sbjct: 855  QKRKITDGDKLAGRHGNKGVISKILPVEDMPFPEDGTPVDIILNPLGVPGRMNVGQVLET 914

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGW     G  I  +   +              +                         
Sbjct: 915  HLGWIAA-RGWDISGIQEAWAERLRDKGFEQVAPR------------------------- 948

Query: 1200 WKSGVPVSTPVFDGADEEAINSML--RMAD------LDESGQSILYDGLTGEPFDRPVTV 1251
                  ++TPVFDGA EE I  +L   +A+      +  +G++ L+DG +GEPF  P+ V
Sbjct: 949  ----TNMATPVFDGAHEEEIVGLLGNTIANRDGDRMVQPTGKARLFDGRSGEPFPYPIAV 1004

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GYIY+LKL H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1005 GYIYILKLLHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYAL 1064

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LTIKSDDV+GR +VYE+IV G +  E G PESF VL+KEMQ+L L++++ +S   + 
Sbjct: 1065 QELLTIKSDDVLGRVKVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSI 1124

Query: 1372 AKMEEIPD 1379
               +   D
Sbjct: 1125 EMRDTDED 1132



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 336/692 (48%), Positives = 466/692 (67%), Gaps = 27/692 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    +K +    +      G ++  +I   ++  + I+         
Sbjct: 162 LVRSPGVYFERNVDKTSDKDLYGCKVIPSR--GAWLEFEIDKRDSVGVRIDRKRKQAVTV 219

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L  +         IL  +       +R TL  D    + DALLDIYR +RPG+  T   A
Sbjct: 220 L--LKALGWTSDQIL--ERFGQYESMRATLEKDHTAGQDDALLDIYRKLRPGEPPTKESA 275

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
           +++   L+F+  +YDL+ VGR K+N +L +D+      + +EDI+A I+ +V L  G+  
Sbjct: 276 QTLLENLYFNPKRYDLAKVGRYKINKKLGVDSEITQGTLTEEDIVATIEYIVRLHAGEES 335

Query: 452 -----------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                       +DDID+ GNRR+RSVGE+++NQ RLGL RMER ++ER+++ D++++ P
Sbjct: 336 MPGANDREVIVEVDDIDHFGNRRLRSVGELIQNQVRLGLARMERVVRERMTTQDVEAITP 395

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+++ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG E+RD
Sbjct: 396 QTLINIRPVVASIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGGLSRERAGFEVRD 455

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL S+ R+NA+GF+ETPYRKV DGKVT+ + YL+A 
Sbjct: 456 VHPSHYGRMCPIETPEGPNIGLIGSLASYGRINAFGFVETPYRKVVDGKVTDQIDYLTAD 515

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+    AQAN+ L+ DGSF E  V  R   GE  L+  +++D+ID SP+Q+VS+A ++I
Sbjct: 516 EEDRYVKAQANTVLNADGSFAEARVLVRTKGGETELMRADEVDYIDVSPRQMVSVATAMI 575

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           P LE+DD+NR  MG NMQRQ+ PLLK+EAP VGTGM+   A  +G  I A++AG+VE+V 
Sbjct: 576 PSLEHDDANRP-MGSNMQRQSAPLLKSEAPLVGTGMDYRAATDAGDVISAEKAGVVEEVS 634

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A  + + + +G           YR+ KF+RSNQ T  NQ+P+V   D V  N +IADGP 
Sbjct: 635 ADYVTVMNDDGTR-------RRYRVAKFKRSNQGTSFNQKPIVADPDRVEVNQVIADGPC 687

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD G++ALG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPE
Sbjct: 688 TDQGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPE 747

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNVSEE L ++DE GII +GAEV PGDILVGK+TPKGE+ +TPEE+LLRAIFGE
Sbjct: 748 EITRDIPNVSEEVLADLDERGIIRIGAEVVPGDILVGKVTPKGETELTPEERLLRAIFGE 807

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSL+VP G  G V+ VR+ +R   D
Sbjct: 808 KAREVRDTSLKVPHGEQGKVIAVRVNSREEGD 839



 Score =  343 bits (881), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 110/367 (29%), Positives = 174/367 (47%), Gaps = 28/367 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP------------NEGLQAAFKS 61
           R  F +  E +++PDL+ +Q  S+D  L                        GL+  F+ 
Sbjct: 16  RVSFARIQEPLEVPDLLALQTESFDWLLGNEKWKARVEAARQAGRRDVPTQSGLEEIFEE 75

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG   L F  + F+PPK+ VD+C  +D+T++ P+ +T   I           +
Sbjct: 76  ISPIEDFSGTMSLSFRDHRFEPPKYSVDECKEKDMTFSAPMFVTAEFI---------NNT 126

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PLMT  GTF+I G +R+VVSQL RSPG++F+ +  +   S K LY 
Sbjct: 127 TGEIKSQTVFMGDFPLMTPKGTFIINGTERVVVSQLVRSPGVYFERNVDKT--SDKDLYG 184

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
           C++IP +G W++ E D +D + VRIDR+RK  VT  L ALG  S++IL  F  Y  +  +
Sbjct: 185 CKVIPSRGAWLEFEIDKRDSVGVRIDRKRKQAVTVLLKALGWTSDQILERFGQYESMRAT 244

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLG 297
              D       A   +            ++ + ++E+         L K  + K  K LG
Sbjct: 245 LEKDHTAGQDDALLDIYRKLRPGEPPTKESAQTLLENLYFNPKRYDLAKVGRYKINKKLG 304

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNA 356
           + S+   G    EDIV      + + AG+     + +     E+ DI         +   
Sbjct: 305 VDSEITQGTLTEEDIVATIEYIVRLHAGEESMPGANDREVIVEVDDIDHFGNRRLRSVGE 364

Query: 357 YIRNTLV 363
            I+N + 
Sbjct: 365 LIQNQVR 371


>gi|7144499|gb|AAA20242.2| RNA-polymerase beta subunit [Mycobacterium tuberculosis H37Rv]
          Length = 1092

 Score =  506 bits (1303), Expect = e-140,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 452/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  +R+TL  
Sbjct: 209 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTSEQIV--ERFGFSEIMRSTLEK 264

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 265 DNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 324

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 325 GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 384

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 385 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 444

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +A
Sbjct: 445 PLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYA 504

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN +GFIETPYRKV DG V++ +VYL+A EE+   +AQANS +D DG F E  V  R  
Sbjct: 505 RVNPFGFIETPYRKVVDGVVSDGIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRK 564

Query: 651 -GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 565 AGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 624

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  + A   ++ +G++E+V A  I +    G           YR+ KF R
Sbjct: 625 LVGTGMELRAAIDA-ATSSSQESGVIEEVSADYITVMHDNGTR-------RTYRMRKFAR 676

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN  TC NQ P+V  GD V    +IADGP TD G++ALG+N+LVA MPW G+N+ED++++
Sbjct: 677 SNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIIL 736

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           S R+V EDV TSIHIEE E+ ARDTKLG EEITRDIPN+S+E L ++DE GI+ +GAEV 
Sbjct: 737 SNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVR 796

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R  
Sbjct: 797 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRED 856

Query: 950 ID 951
            D
Sbjct: 857 ED 858



 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 173/555 (31%), Positives = 239/555 (43%), Gaps = 60/555 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V            A+              ++ +  P  G   E    I     S  
Sbjct: 585  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAATSSSQ 644

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                I     + +      G     R             ++C I+  G  V  G ++   
Sbjct: 645  ESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADG 704

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                 +  M   + LL AI   +  +  D  +     V   V+       H ID  +  +
Sbjct: 705  PCT-DDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKL 763

Query: 958  SVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              E     I  ++ +     DE+ I+      R  +IL G+    G         L   +
Sbjct: 764  GAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAI 823

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              E  R                 E      +            ++   +  D++P GV  
Sbjct: 824  FGEKAR-----------------EVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNE 866

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGTPVDI+LN  GVP RMN
Sbjct: 867  LVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMN 926

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI ETHLGW C   G K+ +          +                         D 
Sbjct: 927  IGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP------------------------DE 961

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEP 1244
            +L           VSTPVFDGA E  +  +L            +D  G+++L+DG +GEP
Sbjct: 962  LLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEP 1017

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEME W +QA
Sbjct: 1018 FPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQA 1077

Query: 1305 YGAAYVLQEMLTIKS 1319
            YGAAY LQE+LTIKS
Sbjct: 1078 YGAAYTLQELLTIKS 1092



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/333 (28%), Positives = 153/333 (45%), Gaps = 28/333 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E +++P L++VQ  S++  +      +     G       L+     + PI 
Sbjct: 38  RVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIE 97

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK
Sbjct: 98  DFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIK 148

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP
Sbjct: 149 SQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STDKTLHSVKVIP 206

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I+  F    +     +   
Sbjct: 207 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDN 266

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +   L+   +       +  GE    ES + L   L    K   +  +G        
Sbjct: 267 TVGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VN 317

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             +   +    T     E   V   + L  +  
Sbjct: 318 KKLGLHVGEPITSSTLTEEDVVATIEYLVRLHE 350


>gi|298490329|ref|YP_003720506.1| DNA-directed RNA polymerase subunit beta ['Nostoc azollae' 0708]
 gi|298232247|gb|ADI63383.1| DNA-directed RNA polymerase, beta subunit ['Nostoc azollae' 0708]
          Length = 1122

 Score =  506 bits (1303), Expect = e-140,   Method: Composition-based stats.
 Identities = 317/622 (50%), Positives = 428/622 (68%), Gaps = 19/622 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     ++AL+++YR +RPG+  T    + + +  FFD  +YDL
Sbjct: 196 FDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRPGEPPTVLGGQQLLDSRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD +R +   DI+A +  L++L    G+IDDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNKKLRLSVPDTMRILTPGDILAAVDYLINLEYDIGSIDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D + + P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDAEVLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGF+ETP+R V +GKV  DV  +Y++A EE++   A  +  +DE+G      V 
Sbjct: 436 HARVNQYGFLETPFRPVENGKVRFDVQPIYMTADEEDDLRTATGDIPVDENGYIKGPQVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG NMQRQAVPLLK 
Sbjct: 496 VRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGSNMQRQAVPLLKP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-----------------SVE 749
           E P VGTG+E+  A+ SG  IV++  G V  VDA +I +R                    
Sbjct: 556 ERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDAAQIRVRVRGDLSGVTGNLIGGKQQTN 615

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                 T     Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+LALG+
Sbjct: 616 EQGQQVTDKEIRYVLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGELALGQ 675

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N++VA+MPW GYN+ED++LISER+V +D++TSIHIE++E+ AR TKLGPEEITR+IPNV 
Sbjct: 676 NIVVAYMPWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVG 735

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ L+ +DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SL
Sbjct: 736 EDALRQLDERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSL 795

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           RVP+G  G VV VR+F R   D
Sbjct: 796 RVPNGEKGRVVYVRLFTREQGD 817



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 185/526 (35%), Positives = 262/526 (49%), Gaps = 62/526 (11%)

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E                +++  ++ +G +V  G +L    + +G   +   + ++ A  
Sbjct: 624  KEIRYVLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEG-GELALGQNIVVAYM 682

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   +       ++ I+  +  +  E    +I  +  D   + 
Sbjct: 683  PWEGYNYEDAILISERLVQDDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDALRQL 742

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+    +    +IL G+    G         L   +  E  R       V+D  ++
Sbjct: 743  DERGIIRIGAWVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------VRDNSLR 796

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                      E  + +    F       + GD++PPG   VV+V+VA KR IQ GDKMAG
Sbjct: 797  ------VPNGEKGRVVYVRLFTR-----EQGDELPPGANMVVRVYVAQKRKIQVGDKMAG 845

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+SRILP EDMP+L DG+PVDIVLNPLGVPSRMNVGQ+FE  LGWA   LG + 
Sbjct: 846  RHGNKGIISRILPAEDMPYLPDGSPVDIVLNPLGVPSRMNVGQVFECLLGWAGHNLGVRF 905

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K    D               ++ G  S    +     ++     + W            
Sbjct: 906  KITPFD---------------EMYGEESSRRIVHGKLQEARDETGKNWVY---------- 940

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                          +  + G+ ++YDG TGEPFDRPVTVG  YMLKL H+V DK++ARST
Sbjct: 941  --------------NPHDPGKIMVYDGRTGEPFDRPVTVGVAYMLKLVHLVDDKIHARST 986

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +I
Sbjct: 987  GPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNAI 1046

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      GTPESF VL++E+Q+LGL I +    T+      ++ 
Sbjct: 1047 VKGKAIPRPGTPESFKVLMRELQSLGLDIAVHKVETQADGSSLDVE 1092



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 106/481 (22%), Positives = 197/481 (40%), Gaps = 36/481 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLIE+Q++S+  FL           EGL     S  PIT ++G   L F+   Y+   
Sbjct: 13  LPDLIEIQRSSFRWFL----------EEGLIEELNSFSPITDYTGKLELHFLGDKYKLKE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ V++   RD TYAV + +  RL+          K   DIKE  +++GDLPLMT  GT
Sbjct: 63  PKYSVEESKRRDSTYAVQMYVPTRLL---------NKETGDIKELEVFIGDLPLMTDRGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSELDK---NGRRTYSASLIPNRGAWLKFETDRNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EI         +  +   +       A   +      
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSDNEIFDALRHPEYFQKTIEKEGQFSEEEALMELYRKLRP 230

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  G+Q+++S         L +  + K  K L ++      +    DI+      
Sbjct: 231 GEPPTVLGGQQLLDSRFFDPKRYDLGRVGRYKLNKKLRLSVPDTMRILTPGDILAAVDYL 290

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++       +L    
Sbjct: 291 INLE-YDIGSIDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAEVLTPAS 349

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 350 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 404

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +     G+  I  I+         +G +  +        +E   +   +      V 
Sbjct: 405 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNQYGFLETPFRPVENGKVRFDVQ 462

Query: 500 P 500
           P
Sbjct: 463 P 463


>gi|229818123|ref|ZP_04448405.1| hypothetical protein BIFANG_03415 [Bifidobacterium angulatum DSM
            20098]
 gi|229784727|gb|EEP20841.1| hypothetical protein BIFANG_03415 [Bifidobacterium angulatum DSM
            20098]
          Length = 1188

 Score =  505 bits (1301), Expect = e-140,   Method: Composition-based stats.
 Identities = 185/535 (34%), Positives = 266/535 (49%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L        +  +   + L
Sbjct: 659  MNDDGTTSSYKLAKFQRSNQTTCYNQRPLIHDGERVEAGSVLADGP-AIQKGELALGKNL 717

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 718  LIAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLP 772

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 773  NVGEDAVANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 831

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++G
Sbjct: 832  DTSLRVPHGETGTVIGIKEITREDAE--EDGDELPNGVNQMIRVYIAQHRKITVGDKLSG 889

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 890  RHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHC-GWDI 948

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                N       +                           + + AE+ +   PV+TPVFD
Sbjct: 949  SLDPNMEAEWKKL---------------------------IPQGAEKAEPNTPVATPVFD 981

Query: 1213 GADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G   + +  +L     +  G        ++ LYDG TGEPF RP++VGY+YMLKL+H+V 
Sbjct: 982  GVKPDVLKGLLSTTLPNRDGDRLVGPDGKATLYDGRTGEPFFRPISVGYMYMLKLHHLVD 1041

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV G
Sbjct: 1042 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDG 1101

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R RVY +IV G +    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1102 RVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNADGVAIDMKDEDDD 1156



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 316/740 (42%), Positives = 464/740 (62%), Gaps = 30/740 (4%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           Y    +           +        +       I   E+VI S    + G+    ++  
Sbjct: 131 YVNAEFENGETGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDR 190

Query: 293 VKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                +    +    G ++  +I   +  ++ ++         +  +    +    I   
Sbjct: 191 NSDKEVFGAKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSA--IVFLMAIGMTKQEI--R 246

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           ++  +   + + L   K + + +AL D+Y  +RP D +T    +++ +  +F++ +YDL+
Sbjct: 247 EAFQDYPLVLDALDNTKLQTQDEALKDMYSKIRPADTATPEAGKNLLDSFYFNTKRYDLA 306

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L L+T  + R + +EDIIA IK LV L +GK                 +D
Sbjct: 307 RVGRYKINRKLGLETDMNDRSLSREDIIATIKYLVTLHDGKATFPGKRNGEDVELRVDVD 366

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 367 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 426

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 427 EFFGTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 486

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  L
Sbjct: 487 PEGPNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQEL 546

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+ +F       R   EE + VP  ++D++D SP+Q+ S+ ASLIPFLE+D+ +R LMG
Sbjct: 547 DENNNFVHSDALARVGEEEAVDVPVSQVDYMDVSPRQMTSLGASLIPFLEHDEGHRALMG 606

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I A + G+V  V A  I + + +G   
Sbjct: 607 TNMQRQAVPLIESERPLVGTGSEWRAANDSGDVIKADKDGVVTYVSADMIRVMNDDGTTS 666

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQRPL+  G+ V    ++ADGP+   G+LALG+N+L+
Sbjct: 667 S-------YKLAKFQRSNQTTCYNQRPLIHDGERVEAGSVLADGPAIQKGELALGKNLLI 719

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 720 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 779

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 780 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 839

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ ++   R   +++
Sbjct: 840 GETGTVIGIKEITREDAEED 859



 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 93/304 (30%), Positives = 141/304 (46%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +  +                     GL   F  
Sbjct: 30  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGADRWKKRVEEDEKNGTITTPHVSGLDEVFNE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 90  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNA---------EFENGE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRN--SDKEVFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKQEIREAFQDYPLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
                      A   M      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 259 LDNTKLQTQDEALKDMYSKIRPADTATPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 318

Query: 298 ITSD 301
           + +D
Sbjct: 319 LETD 322


>gi|46360932|gb|AAS89199.1| RpoB [Corynebacterium freneyi]
          Length = 1114

 Score =  505 bits (1301), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/498 (36%), Positives = 253/498 (50%), Gaps = 65/498 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M   + LL A    +  +  D  +     V   ++
Sbjct: 668  LVDEGDRVEAGQVIADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D DD   I+      R  +IL G+ 
Sbjct: 727  TSIHIEEHEIDARDTKLGPEEITREIPNVGEDMLKDLDDR-GIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  +                
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAREVRDTSMRVPHGESGKVIGV---------------- 829

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++   +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG++ +ILP EDMPFL D
Sbjct: 830  -RVFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVIGKILPQEDMPFLPD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I+               +   ++
Sbjct: 889  GTPVDILLNTHGVPRRMNIGQVLEVHLGWLAKA-GWTIEGDPEWA---------KRLPKE 938

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE---- 1230
            +    + +                       V+TPVFDGA+ E +  +L  +  D     
Sbjct: 939  LYDVPADSL----------------------VATPVFDGAENEELAGLLASSRPDRDGDV 976

Query: 1231 ----SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 977  LVNADGKAQLIDGRSGEPFPFPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1036

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1037 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1096

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F VL+KE+Q+L L++++ 
Sbjct: 1097 FKVLLKELQSLCLNVEVL 1114



 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 329/661 (49%), Positives = 452/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L + F     +I     +    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIK----ERFGFSEIMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A ++    FF   +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEPPTRESALALLENNFFKPKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 PD-DVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
                  + ++DI   I+ LV L +G+              +DDID+ GNRR+R+VGE++
Sbjct: 305 DGVGEMVLTEQDIATTIEYLVRLHDGEKTMTSPDGREVPVEVDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDVESIQPTTLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA- 650
           VN +GFIETPYR+V DGK+T DV YL+A EE+   +AQAN+ +D DG F  + +  R   
Sbjct: 485 VNPFGFIETPYRRVVDGKLTTDVDYLTADEEDRYVVAQANTPVDADGQFVNDTLPVRKRG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+AEAPF
Sbjct: 545 GDVEVVRATEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A   G+VE V A  I +   EG           + L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLIIAPCDGVVETVSADFITVMDDEGQR-------HTFILRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTSYNQKPLVDEGDRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNV E+ LK++D+ GI+ +GA+V  
Sbjct: 718 QRMVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVGEDMLKDLDDRGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS+RVP G SG V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMRVPHGESGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 80/298 (26%), Positives = 136/298 (45%), Gaps = 29/298 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q+ S+   +        R  E         GL+     + P
Sbjct: 16  RYSFAKISEPIPVPGLLDLQRESFAWLIGTPEWRARRQEELGEGAQVTSGLEDILDELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      FD  K  VD+C  +D+ Y+ PL +T              +   +
Sbjct: 76  IEDYSQKMSLTLSDPWFDSVKNTVDECKDKDINYSAPLYVTAEFT---------NRETGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+M+  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +I
Sbjct: 127 IKSQTVFIGDFPMMSDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKI 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L A G  +EEI   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKAFGWTTEEIKERFGFSEIMMSTLEK 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +        ++   ++E+            K   +  +G   
Sbjct: 245 DGVANTDEALLEIYRKQRPGEPPTRESALALLENN-------FFKPKRYDLAKVGRYK 295


>gi|46360988|gb|AAS89227.1| RpoB [Corynebacterium afermentans subsp. afermentans]
          Length = 1116

 Score =  505 bits (1301), Expect = e-140,   Method: Composition-based stats.
 Identities = 186/493 (37%), Positives = 252/493 (51%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 671  IVSAGDRVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 730  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +     ++  R  
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAREVRDT-------------SLKVPHGEQGKVIAVR-- 833

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 834  --RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GT VDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 892  GTQVDIILNTHGVPRRMNIGQVLEIHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYD 948

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L     +  G  
Sbjct: 949  VPADSLT-------------------------ATPVFDGATNEEIAGLLANTKPNRDGDV 983

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 984  MVDGEGKTTLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1044 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1103

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1104 FKVLLKELQSLCL 1116



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 437/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 232 TERFGFSEIMMSTLENDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 291

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 292 ARVGRYKTNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPAGEIIPINTDD 351

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 352 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 411

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 412 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPVETP 471

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L+++ARVNA+GFIETPY+KV DGK+T  + YL+A EE+   IA+A + +D
Sbjct: 472 EGPNIGLIGALSTYARVNAFGFIETPYQKVNDGKLTGQIDYLTADEEDRYAIAEAATPMD 531

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +D + T E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 532 KDNNLTGERIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 591

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL+AE+ +V TGME   A  +G  +++K+AG++E V    I +   EG    
Sbjct: 592 NMQKQAVPLLRAESAYVATGMEQRAAYDAGDTVISKKAGVIENVTGDFITVMDDEG---- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              G D Y L  F+R+NQ TC NQ P+V  GD V    +IADGP T  G++ALGRN+LVA
Sbjct: 648 ---GRDTYMLRTFERTNQGTCYNQTPIVSAGDRVEAGQVIADGPGTKDGEMALGRNLLVA 704

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 705 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 764

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 765 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 824

Query: 935 VSGTVVDVRIFNRHGID 951
             G V+ VR F+R   D
Sbjct: 825 EQGKVIAVRRFSREDDD 841



 Score =  308 bits (788), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 99/389 (25%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +           N   D R   GL+   + + 
Sbjct: 18  ERYSFAKINEPITVPGLLDVQLESFAWLVGTQEWREREQANRGDDTRITSGLEDILEELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 78  PIEDYSGNMSLTLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 129 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 247 NDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKTNRKLGLG 306

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    GEI       I+   ++   +  +R
Sbjct: 307 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPAGEII-----PINTDDIDHFGNRRLR 361

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 362 TVGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|209522760|ref|ZP_03271318.1| DNA-directed RNA polymerase, beta subunit [Arthrospira maxima
           CS-328]
 gi|209496809|gb|EDZ97106.1| DNA-directed RNA polymerase, beta subunit [Arthrospira maxima
           CS-328]
          Length = 1102

 Score =  505 bits (1301), Expect = e-140,   Method: Composition-based stats.
 Identities = 320/605 (52%), Positives = 421/605 (69%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     +DAL+++YR +RPG+  T +  E +    FFD  +YDL
Sbjct: 196 FDALRHPDYFQKTIEKEGEFSEEDALMELYRKLRPGEPPTITGGEQLLQNRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD  R +   DI++ I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 256 GRVGRHKLNRKLRLSVPDSTRVLTPTDILSAIDYLINLEYDIGETDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D +++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQIRVGLNRLERIIRERMTVGDAETLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGFIETPY  V +G+V  D+  VY++A EE++  +A  + S D +G    +LV 
Sbjct: 436 HARVNPYGFIETPYYPVENGRVRRDLSPVYMTADEEDDLRVAPGDISYDSEGYILGDLVP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      +++D++  SP Q+VS+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 496 VRYRQDFTKTSPDQVDYVAVSPVQIVSVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E PFVGTG+E+  A+ SG  IV++  G V  VD  +I +                Y L K
Sbjct: 556 ERPFVGTGLEAQAARDSGMVIVSRTDGEVSYVDGAKIRV-------IDPEGWEIEYELQK 608

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRPLV  GD+V    ++ADG ST+  +LALG N+LVA+MPW GYN+ED+
Sbjct: 609 YQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGAELALGHNVLVAYMPWEGYNYEDA 668

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+ L+ +D  GII +GA
Sbjct: 669 ILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDSLRQLDASGIIRIGA 728

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 729 WVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 788

Query: 947 RHGID 951
           R   D
Sbjct: 789 REQGD 793



 Score =  480 bits (1236), Expect = e-133,   Method: Composition-based stats.
 Identities = 186/522 (35%), Positives = 257/522 (49%), Gaps = 58/522 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E                +++  ++  G +V  G +L    + +G   +     +L
Sbjct: 596  DPEGWEIEYELQKYQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGA-ELALGHNVL 654

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  L     +S  +V   ++    I+K E    +E  Q +L   +   
Sbjct: 655  VAYMPWEGYNYEDAIL-----ISERLVYDDVYTSIHIEKFE----IEARQTKLGPEEITR 705

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            E   +  +   +L     I  G    SG     K T        + P  +  +    ++ 
Sbjct: 706  EIPNVGEDSLRQLDASGIIRIGAWVESGDILVGKVTPKGES--DQPPEEKLLRAIFGEKA 763

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                  SL+V       +++ R    +   + GD++PPG   VV+V+VA KR IQ GDKM
Sbjct: 764  RDVRDNSLRVPNGEKGRVVDVR----VFTREQGDELPPGANMVVRVYVAQKRKIQVGDKM 819

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGIVSRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQIFE  +GWA   L +
Sbjct: 820  AGRHGNKGIVSRILPIEDMPYLPDGRPMDIVLNPLGVPSRMNVGQIFECLMGWAGENLKR 879

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K +  D     ++S      +                                     
Sbjct: 880  RFKVIPFDEMFGQEMSRETVHSKLKE---------------------------------- 905

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
               A E+     L   +    G++I+YDG TGE FD+PVTVG  Y+LKL H+V DK++AR
Sbjct: 906  ---AREKLKKDWLFSEEYP--GKTIVYDGRTGEAFDQPVTVGIAYILKLVHLVDDKIHAR 960

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     
Sbjct: 961  STGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMAGRNEALN 1020

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            +IV G      GTPESF VL++E+Q+L L I      T    
Sbjct: 1021 AIVKGKAIPRPGTPESFKVLMRELQSLCLDIAAHKVETNKKD 1062



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 101/459 (22%), Positives = 193/459 (42%), Gaps = 36/459 (7%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--S 78
               ++PDLIE+Q++S+  FL            GL    +S  PI+ ++G   L F+   
Sbjct: 8   ESAFELPDLIEIQRSSFRWFL----------ETGLIEELESFSPISDYTGKLELHFLARD 57

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   PK+DVDD   RD TY+V + +  RLI          K   +IKEQ +++GDLPLM
Sbjct: 58  YKLKQPKYDVDDAKRRDSTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLM 108

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++V+Q+ RSPG+++  +  +   + +  Y+  +IP++G W+  E D 
Sbjct: 109 TERGTFIINGAERVIVNQIVRSPGVYYKSEIDK---NQRRTYSASLIPNRGAWLKFETDK 165

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMV 256
            D++ VRID+ RK+     L ALG+ + EI         +  +   +       A   + 
Sbjct: 166 NDLVWVRIDKTRKLSAQILLKALGLTNNEIFDALRHPDYFQKTIEKEGEFSEEDALMELY 225

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                     I  GEQ++++         L +  + K  + L ++      +    DI++
Sbjct: 226 RKLRPGEPPTITGGEQLLQNRFFDPKRYDLGRVGRHKLNRKLRLSVPDSTRVLTPTDILS 285

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                I +E         ++ + +  +R +  L  + +         ++ ++        
Sbjct: 286 AIDYLINLEYDIGET-DDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMTVGDAET 344

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 345 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 399

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 400 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|154488235|ref|ZP_02029352.1| hypothetical protein BIFADO_01809 [Bifidobacterium adolescentis
            L2-32]
 gi|154083386|gb|EDN82431.1| hypothetical protein BIFADO_01809 [Bifidobacterium adolescentis
            L2-32]
          Length = 1186

 Score =  505 bits (1301), Expect = e-140,   Method: Composition-based stats.
 Identities = 188/537 (35%), Positives = 262/537 (48%), Gaps = 59/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 657  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 715

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 716  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 775

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 776  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 829

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 830  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 882

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 883  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +   A                               V + AE+   G PV+
Sbjct: 943  -GWDISLDPDAEAAWKKY---------------------------VPQGAEKGAPGTPVA 974

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG   E I  +L          ++      G++ L+DG TGEPF +P++VGY+YML
Sbjct: 975  TPVFDGVRPETIKGLLSCTLPDRDGNKLVG--PDGKATLFDGRTGEPFPKPISVGYMYML 1032

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1033 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1092

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            KSDDV GR RVY +IV G +    G PESF VL+KEMQ+L L++++ N+        
Sbjct: 1093 KSDDVDGRVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMK 1149



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 301/620 (48%), Positives = 429/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +  + + +AL D+YR +RP D  T    +++ +  +F++ +YDL+
Sbjct: 245 DAFKDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLA 304

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDIIA IK LV L  G+                   
Sbjct: 305 RVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGETKFPGKRDGQDVDLRVDVD 364

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 365 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 424

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 425 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 484

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 485 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 544

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 545 DENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 604

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I   + +G   
Sbjct: 605 TNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTS 664

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 665 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 717

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 718 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 777

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 778 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 837

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 838 GETGTVIAVKEITREDAEED 857



 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 144/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 28  RVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVQEDLENGTNTVPHTSGLDEVFQE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 88  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 139 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEVFG 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 197 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDA 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 257 LAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 316

Query: 298 ITSD 301
           +  D
Sbjct: 317 LEKD 320


>gi|298252930|ref|ZP_06976724.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis 5-1]
 gi|297533294|gb|EFH72178.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis 5-1]
          Length = 1141

 Score =  505 bits (1300), Expect = e-140,   Method: Composition-based stats.
 Identities = 186/535 (34%), Positives = 270/535 (50%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +   +             ++  +I  G  V  G +L      + +  +   + L
Sbjct: 612  MNDDGTQSSYKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGPATE-KGELALGKNL 670

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 671  LVAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLP 725

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 726  NVGEDAIANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 784

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E    GD++P GV ++++V++A  R I  GDK++G
Sbjct: 785  DTSLRVPHGETGTVIAVKEITREDAE--DDGDELPNGVNQMIRVYIAQHRKITQGDKLSG 842

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 843  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA-GWDI 901

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                +   A                               V + AE      PV+TPVFD
Sbjct: 902  NLDPDLEAAWKKY---------------------------VPQGAEHGDPCTPVATPVFD 934

Query: 1213 GADEEAINSMLR--MADLD------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G   E +  +L   +A+ D        G++ L+DG TGEPF +P++VGY+Y+LKL+H+V 
Sbjct: 935  GVRPETLKGLLSTTLANRDGDKLVGSDGKATLFDGRTGEPFPKPISVGYMYILKLHHLVD 994

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV G
Sbjct: 995  DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDG 1054

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1055 RVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEEDD 1109



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 311/620 (50%), Positives = 433/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      + + L  +  + + DAL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 200 DAFQGYPLVLDALAKEPIETQDDALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 259

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L ++     R + +EDIIA IK LV L +G+                 +D
Sbjct: 260 RVGRYKINRKLGIEADYSDRSLNREDIIATIKYLVTLHSGEKTFPGKRDGQDVQLRVDVD 319

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 320 DIDHFGNRRIRQVGELVQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 379

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 380 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 439

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VTN+V Y++A  E    IAQAN  L
Sbjct: 440 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTNEVEYMTADREAEHVIAQANQEL 499

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F       R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 500 DENGNFVGTQALARVDEEEAVDVPVSTVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMG 559

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 560 TNMQRQAVPLIKSERPLVGTGSEWRAAVDSGDVILAEKPGVVTYVSADIIRVMNDDGTQS 619

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+K G+ V    ++ADGP+T+ G+LALG+N+LV
Sbjct: 620 S-------YKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGPATEKGELALGKNLLV 672

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 673 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLPNVGEDAI 732

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 733 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 792

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   + +
Sbjct: 793 GETGTVIAVKEITREDAEDD 812



 Score =  283 bits (725), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 133/287 (46%), Gaps = 27/287 (9%)

Query: 32  VQKASYDHFLMMNIAPDERPN------------EGLQAAFKSVFPITAFSGAAMLEFVSY 79
           +Q  S+D  +                        GL   F+ + PI  F+    L F   
Sbjct: 1   MQTDSFDWLIGSERWKKRVAEDEANGTHTVPHVSGLDEVFQEISPIENFAETMSLTFSDP 60

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
            F+ P+  V +C  +D TY+ PL +                   +IK Q+++MGD PL T
Sbjct: 61  YFEEPRHTVLECKEKDYTYSAPLYVNA---------EFENGETGEIKSQTVFMGDFPLQT 111

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSPG++FD  + R   S K ++  +IIP +G W++ E D +
Sbjct: 112 PHGTFIIGGTERVIVSQLVRSPGVYFDRTQDRT--SDKDVFGAKIIPSRGAWLEFEIDKR 169

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAADLMVG 257
           D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +   +       A   +  
Sbjct: 170 DVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFQGYPLVLDALAKEPIETQDDALTDLYR 229

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDC 302
               +     + G  +++S    T    L +  + K  + LGI +D 
Sbjct: 230 KIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLGIEADY 276


>gi|297243867|ref|ZP_06927797.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis AMD]
 gi|296888288|gb|EFH27030.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis AMD]
          Length = 1188

 Score =  505 bits (1300), Expect = e-140,   Method: Composition-based stats.
 Identities = 186/535 (34%), Positives = 270/535 (50%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +   +             ++  +I  G  V  G +L      + +  +   + L
Sbjct: 659  MNDDGTQSSYKLSKFQRSNQTTCYNQVPLIKDGERVETGTVLADGPATE-KGELALGKNL 717

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 718  LVAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLP 772

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 773  NVGEDAIANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 831

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E    GD++P GV ++++V++A  R I  GDK++G
Sbjct: 832  DTSLRVPHGETGTVIAVKEITREDAE--DDGDELPNGVNQMIRVYIAQHRKITQGDKLSG 889

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 890  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA-GWDI 948

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                +   A                               V + AE      PV+TPVFD
Sbjct: 949  NLDPDLEAAWKKY---------------------------VPQGAEHGDPCTPVATPVFD 981

Query: 1213 GADEEAINSMLR--MADLD------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G   E +  +L   +A+ D        G++ L+DG TGEPF +P++VGY+Y+LKL+H+V 
Sbjct: 982  GVRPETLKGLLSTTLANRDGDKLVGSDGKATLFDGRTGEPFPKPISVGYMYILKLHHLVD 1041

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV G
Sbjct: 1042 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDG 1101

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1102 RVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEEDD 1156



 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 311/620 (50%), Positives = 433/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      + + L  +  + + DAL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 247 DAFQGYPLVLDALAKEPIETQDDALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 306

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L ++     R + +EDIIA IK LV L +G+                 +D
Sbjct: 307 RVGRYKINRKLGIEADYSDRSLNREDIIATIKYLVTLHSGEKTFPGKRDGQDVQLRVDVD 366

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 367 DIDHFGNRRIRQVGELVQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 426

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 427 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 486

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VTN+V Y++A  E    IAQAN  L
Sbjct: 487 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTNEVEYMTADREAEHVIAQANQEL 546

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F       R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 547 DENGNFVGTQALARVDEEEAVDVPVSTVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMG 606

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 607 TNMQRQAVPLIKSERPLVGTGSEWRAAVDSGDVILAEKPGVVTYVSADIIRVMNDDGTQS 666

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+K G+ V    ++ADGP+T+ G+LALG+N+LV
Sbjct: 667 S-------YKLSKFQRSNQTTCYNQVPLIKDGERVETGTVLADGPATEKGELALGKNLLV 719

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 720 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLPNVGEDAI 779

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 780 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 839

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   + +
Sbjct: 840 GETGTVIAVKEITREDAEDD 859



 Score =  308 bits (789), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 92/305 (30%), Positives = 143/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 30  RVNFGSICEPIDVPYLLGVQTDSFDWLIGSERWKKRVAEDEANGTHTVPHVSGLDEVFQE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 90  ISPIENFAETMSLTFSDPYFEEPRHTVLECKEKDYTYSAPLYVNA---------EFENGE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRTQDRT--SDKDVFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFQGYPLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 259 LAKEPIETQDDALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 318

Query: 298 ITSDC 302
           I +D 
Sbjct: 319 IEADY 323


>gi|302390951|ref|YP_003826771.1| DNA-directed RNA polymerase subunit beta [Acetohalobium arabaticum
           DSM 5501]
 gi|302203028|gb|ADL11706.1| DNA-directed RNA polymerase subunit beta [Acetohalobium arabaticum
           DSM 5501]
          Length = 1083

 Score =  505 bits (1300), Expect = e-140,   Method: Composition-based stats.
 Identities = 333/639 (52%), Positives = 447/639 (69%), Gaps = 9/639 (1%)

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            +   I     D   +     +F +         +D + ++  + +T+  D  ++R++AL
Sbjct: 172 YDKKRIIAVRVDRARKMPSTVLFRALGYSTDSELIDLLGDHEIVHDTIDRDNTENREEAL 231

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           +++Y+ +RPG+  T   AE++   LFFD  +YDL+ VGR K+N +L LDT  D R ++KE
Sbjct: 232 IELYKKLRPGEPPTVESAENLIESLFFDPKRYDLAEVGRYKLNNKLGLDTDLDQRTLQKE 291

Query: 435 DIIAIIKILVDLRNGKGTIDDID--NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           DI+  +K L+ L +        D  +LGNRR+++VGE+L+NQ+R+GL RMER I+ER++ 
Sbjct: 292 DIVETVKYLIKLIHDDDDAYIDDIDHLGNRRLKTVGELLQNQFRIGLSRMERVIRERMTI 351

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DID + PQ LIN +PVV+A+ EFF S QLSQ  +  N LS +TH RR+SALG GG++R 
Sbjct: 352 QDIDVITPQALINTRPVVAAIKEFFGSGQLSQFMDQTNPLSELTHKRRMSALGPGGLSRE 411

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG ++RDVH THYGRICP ET EG NIGL+ SL  + + N YGFI TPYRKV DG+VT 
Sbjct: 412 RAGFDVRDVHHTHYGRICPIETPEGPNIGLIGSLCLYGKTNKYGFIMTPYRKVEDGQVTG 471

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + YL+A +EE   I Q N SLD++G+  +E    R   + + V R+KID++D SP Q+V
Sbjct: 472 KIEYLTANDEEGNVITQGNVSLDDEGNILDERPRARYREDILEVTRDKIDYVDVSPGQIV 531

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           S++A+LIPFLENDD+NR LMG NMQRQ VPLLK +AP+VGTG+E   AK SG A+VAK +
Sbjct: 532 SVSAALIPFLENDDANRALMGANMQRQGVPLLKTDAPYVGTGIEYKAAKDSGVAVVAKNS 591

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           G V +V A +I++++ +G        VD Y L KF RSNQ T    +P+V+ GD V   D
Sbjct: 592 GEVMRVTAKKILVKTDDG-------DVDKYELDKFVRSNQGTSFTHKPIVRKGDRVEAGD 644

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           +I DGP+ D G+LALGRN LVAFM W GYN+ED++LISE++V +D  TS+HIEE E  AR
Sbjct: 645 VIGDGPAMDQGELALGRNCLVAFMTWEGYNYEDAILISEKLVKDDSLTSVHIEEHEAEAR 704

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           DTKLGPEEIT+DIPNVSEE LK++DE GII  GAEV PGDILVGK+TPKGE+ ++ EE+L
Sbjct: 705 DTKLGPEEITKDIPNVSEEALKDLDERGIIRPGAEVRPGDILVGKVTPKGETELSAEERL 764

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LRAIFGEKA +VRDTSL+VP G  G V+DV++F R   D
Sbjct: 765 LRAIFGEKAREVRDTSLKVPHGEKGIVIDVKVFTRDDGD 803



 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 170/492 (34%), Positives = 232/492 (47%), Gaps = 79/492 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD ++G      +  +      L A    +  +  D  L     V    +
Sbjct: 633  IVRKGDRVEAGD-VIGDGPAMDQGELALGRNCLVAFMTWEGYNYEDAILISEKLVKDDSL 691

Query: 941  DVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H  +  +  +  E          E   +D  DE+ I+      R  +IL G+ 
Sbjct: 692  TSVHIEEHEAEARDTKLGPEEITKDIPNVSEEALKDL-DERGIIRPGAEVRPGDILVGKV 750

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 751  TPKGETELSAEERLLRAIFGEKAR-----------------EVRDTSLKVPHGEKGIVID 793

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+     GDD+ PGV ++V+V++A K  I+ GDK+AGRHGNKG++SR+LP EDMP+L +
Sbjct: 794  VKVFTRDDGDDLKPGVNKLVRVYIARKGKIEVGDKLAGRHGNKGVISRVLPEEDMPYLPN 853

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G PV+IVLNPLGVPSRMN+GQ+ ETHLGWA   LG  +++ + +     D+  +      
Sbjct: 854  GEPVEIVLNPLGVPSRMNLGQVLETHLGWAAEELGIHVETPVFNGATEDDVMDMLEEAGL 913

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                     G++
Sbjct: 914  PRDGKVQL-----------------------------------------------YDGRT 926

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   GE F   VTVGY+Y+LKL+H+  DK++ARSTG YSLVTQQPLGGK+  GGQRL
Sbjct: 927  -------GEEFKERVTVGYMYILKLHHLADDKIHARSTGPYSLVTQQPLGGKAQFGGQRL 979

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGAA+ LQEMLT+KSDDVVGR   YESIV G +  E+G PESF VL+KEM
Sbjct: 980  GEMEVWALEAYGAAHCLQEMLTVKSDDVVGRVEAYESIVKGENIPESGIPESFKVLIKEM 1039

Query: 1355 QALGLSIDLENS 1366
            Q++GL   + + 
Sbjct: 1040 QSIGLDAKVYSD 1051



 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 97/358 (27%), Positives = 160/358 (44%), Gaps = 34/358 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
            R R+ F K  + +++P L+E QK+SY  F           + G+   F  + PI  FS 
Sbjct: 9   RRKRRSFAKVEDGMEVPYLLETQKSSYQWFF----------DNGILEMFDEISPIQDFSE 58

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             +LEF+ Y    PK+D  +   RD+TY  PL++ +RLI          +   ++KEQ +
Sbjct: 59  NLVLEFLDYSLGEPKYDEVESKHRDVTYDAPLEVKVRLI---------NQETGEVKEQEV 109

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGDLPLMT  GTF+I G +R++V+QL RS G++F  ++ +    G+ L    IIP++G 
Sbjct: 110 FMGDLPLMTDKGTFIINGAERVIVNQLIRSAGVYFGEERTKD---GRQLIDGSIIPNRGA 166

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E+D K II VR+DR RK+P T    ALG  ++ E++       +     D      
Sbjct: 167 WIEFEYDKKRIIAVRVDRARKMPSTVLFRALGYSTDSELIDLLGDHEIVHDTIDRDNTEN 226

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               L+           +  GE   +ES + L   L    K   +  +G     L     
Sbjct: 227 REEALI------ELYKKLRPGEPPTVESAENLIESLFFDPKRYDLAEVGRYK--LNNKLG 278

Query: 309 AEDIVNGET--GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
            +  ++  T   E  +E    + +   ++          +           ++N    
Sbjct: 279 LDTDLDQRTLQKEDIVETVKYLIKLIHDDDDAYIDDIDHLGNRRLKTVGELLQNQFRI 336


>gi|227487140|ref|ZP_03917456.1| DNA-directed RNA polymerase [Corynebacterium glucuronolyticum ATCC
            51867]
 gi|227092798|gb|EEI28110.1| DNA-directed RNA polymerase [Corynebacterium glucuronolyticum ATCC
            51867]
          Length = 1155

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 182/539 (33%), Positives = 256/539 (47%), Gaps = 65/539 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  ++ +G  V  G ++        +  M+    LL A
Sbjct: 646  EGKRDTYRLRKFERTNQNTCYNQKPLVDIGDRVEKGQVMADGPGT-HDGEMSLGVNLLVA 704

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLAR 969
                +  +  D  +     V   ++       H ID  +  +  E    +I    E + +
Sbjct: 705  FMPWQGHNYEDAIILNQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 764

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  +IL G+    G         L   +  E  R           
Sbjct: 765  DL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 812

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +                   GD++P GV  ++++ VA KR IQ GDK
Sbjct: 813  ------EVRDTSLKVPHGETGKVIGVSRFSRDEGDELPAGVNEMIRIHVAQKRKIQDGDK 866

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG+V +ILP EDMPF++DGTP+DI+LN  GVP RMN+GQ+ E HLGW     G
Sbjct: 867  LAGRHGNKGVVGKILPQEDMPFMEDGTPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-G 925

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I+   +  K                                +        +   V+TP
Sbjct: 926  WAIEGDPDWAKR-------------------------------IPEELRNVPADSLVATP 954

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA  E I  +L     D          G++ L+DG +GEPF  PV VG  YMLKL+H
Sbjct: 955  VFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLKLHH 1014

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDD
Sbjct: 1015 LVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDD 1074

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            V GR RVYE+IV G++  + G PESF VL+KE+Q+L L++++ ++            D 
Sbjct: 1075 VNGRVRVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSADGTPVELSGADDDE 1133



 Score =  483 bits (1243), Expect = e-134,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 456/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G ++  D+   +T G              L+ +  SE +       +    +  + +TL 
Sbjct: 192 GAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEK-----IRERFGFSEIMMSTLE 246

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D      +ALL+IYR  RPG+  T  +A+++    FF   +YDL+ VGR K+N +L L 
Sbjct: 247 NDGAASEDEALLEIYRKQRPGEQPTRDLAQALLENSFFKPKRYDLAKVGRYKVNRKLGLG 306

Query: 424 TP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
              D V+ + +EDI   I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 307 GDHDGVKTLTEEDIATTIEYLVRLHAGERTMTSPDGVEIPLETDDIDHFGNRRLRTVGEL 366

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 367 IQNQVRVGLARMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 426

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 427 SLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYA 486

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPY+KV +GK+ + V YL+A EE+   I QA++  DE+G  T+E    R  
Sbjct: 487 RVNPFGFIETPYQKVENGKIIDQVDYLTADEEDRFVIGQADTEHDENGVITQERNEVRLK 546

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +V  E I++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++++P
Sbjct: 547 DGAIEVVGPEAIEYIDVSPRQIVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSQSP 606

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME+  A  +G  ++ K AG+VE V A  I + S EG  D        YRL KF+R
Sbjct: 607 YVGTGMEAPAAYDAGDLVINKHAGVVENVCADFITVMSDEGKRD-------TYRLRKFER 659

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQNTC NQ+PLV +GD V +  ++ADGP T  G+++LG N+LVAFMPW G+N+ED++++
Sbjct: 660 TNQNTCYNQKPLVDIGDRVEKGQVMADGPGTHDGEMSLGVNLLVAFMPWQGHNYEDAIIL 719

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V 
Sbjct: 720 NQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVR 779

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ V  F+R  
Sbjct: 780 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVSRFSRDE 839

Query: 950 ID 951
            D
Sbjct: 840 GD 841



 Score =  293 bits (750), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 147/321 (45%), Gaps = 30/321 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +      +++  E         GL+   + + P
Sbjct: 19  RYSFAKIKEPIGLPGLLDLQLNSFAWLVGTPEWREQQKAEKGEDYKVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG   L      F+  K  VD+C  +D+ Y+ PL +T              K   +
Sbjct: 79  IQDFSGNMSLSLSEPYFEQVKASVDECKEKDINYSAPLYVTA---------EFENKDTGE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 130 IKSQTVFIGDFPMMTPKGTFIVNGTERVVVSQLVRSPGVYFDETLDK--STERPLHAVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++I+ D KD + VRIDR+R+ PVT  L ALG   E+I   F     ++ +   
Sbjct: 188 IPSRGAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEKIRERFGFSEIMMSTLEN 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +        D  + ++E+            K   +  +G    +
Sbjct: 248 DGAASEDEALLEIYRKQRPGEQPTRDLAQALLENS-------FFKPKRYDLAKVGRYKVN 300

Query: 302 CLCGLYVAEDIVNGETGEIYI 322
              GL    D V   T E   
Sbjct: 301 RKLGLGGDHDGVKTLTEEDIA 321


>gi|108804981|ref|YP_644918.1| DNA-directed RNA polymerase subunit beta [Rubrobacter xylanophilus
           DSM 9941]
 gi|122381569|sp|Q1AU22|RPOB_RUBXD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|108766224|gb|ABG05106.1| DNA-directed RNA polymerase, beta subunit [Rubrobacter xylanophilus
           DSM 9941]
          Length = 1141

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 339/611 (55%), Positives = 446/611 (72%), Gaps = 24/611 (3%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           IRNTL  D    R+DALL+++R  RPG+      A+++ + LFFD  +YDLS VGR K+N
Sbjct: 229 IRNTLERDDTTSREDALLEVFRRQRPGEPVNLENAQNLVDGLFFDPKRYDLSEVGRYKVN 288

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLGNR 462
            +L LD P DV  +  EDI  +++ L+ +                     +D+ ++ GNR
Sbjct: 289 KKLRLDVPRDVHTLTIEDIEGLLRRLLGIAEEVAEEEEFGRINYERIRHKLDEYEHFGNR 348

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++  +R+G+ RMER ++ER+++ D +S+ PQ ++N KPV SA+ EFF SSQL
Sbjct: 349 RLRTVGELVQEAFRIGMYRMERVVRERMTTQDEESITPQTVVNTKPVASAIKEFFGSSQL 408

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N+L+ ++H RRL+A+G GG++R RA +E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 409 SQFMDQTNTLAGLSHRRRLNAMGAGGLSRERAPIEVRDVHPTHYGRMCPIETPEGPNIGL 468

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD-EDGSFT 641
           +  L++FARVN YGF++TPYRKV DG+VT++V YLSA EEE   IAQAN+ +D E G  T
Sbjct: 469 IGQLSTFARVNEYGFVQTPYRKVEDGRVTDEVEYLSADEEEEYTIAQANTPVDLETGRIT 528

Query: 642 EELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            E V  R   G+   V  E++D++D SP Q VS+A SLIPFLE+DD+NR LMG NMQRQA
Sbjct: 529 AETVLARSRGGDVTTVSPEEVDYMDVSPVQTVSVATSLIPFLEHDDANRALMGANMQRQA 588

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPLL++EAP+VGTGME   A  +G  ++A+ AG VE+V A RIV+R  +G       G+D
Sbjct: 589 VPLLRSEAPYVGTGMEFRAATDTGDVLLARNAGTVERVTASRIVVRREDG-------GLD 641

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y L KF RSNQ TCVNQRPLVK G+EV    ++ADG STD G+LALG+N+LVAFMPW G
Sbjct: 642 EYALRKFARSNQGTCVNQRPLVKEGEEVEAGTVLADGSSTDQGELALGKNLLVAFMPWEG 701

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED+++ISER+V EDV TSIHIEE+EV ARDTKLGPEEITRDIP+ S++ L N+D  G
Sbjct: 702 YNFEDAIIISERLVKEDVLTSIHIEEYEVQARDTKLGPEEITRDIPHASDDVLMNLDADG 761

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           II +GAEV+ GD+LVGK+TPKGES  TPEEKLLRAIFGEKA +V+D+SL+VP G  G V+
Sbjct: 762 IIRIGAEVSSGDVLVGKVTPKGESEPTPEEKLLRAIFGEKAREVKDSSLKVPHGEGGVVI 821

Query: 941 DVRIFNRHGID 951
           DV+ F+R   D
Sbjct: 822 DVKRFSREAGD 832



 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 184/511 (36%), Positives = 256/511 (50%), Gaps = 68/511 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G EV  G +L    +   +  +   + LL A    +  +  D  +     V   V+
Sbjct: 662  LVKEGEEVEAGTVLADGSST-DQGELALGKNLLVAFMPWEGYNFEDAIIISERLVKEDVL 720

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   +     E    +    DD  + LD +   R+   +   + + G  
Sbjct: 721  -TSIHIEEYEVQARDTKLGPEEITRDIPHASDDVLMNLDADGIIRIGAEVSSGDVLVGKV 779

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K  +  + +   +  R+ + + A + +     V   +                K    
Sbjct: 780  TPKGESEPTPE--EKLLRAIFGEKAREVKDSSLKVPHGEGGV---------VIDVKRFSR 828

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GDD+PPGV  +V+VFVA KR I  GDK+AGRHGNKG++S+I+P EDMPF++DGTPVD+
Sbjct: 829  EAGDDLPPGVNEMVRVFVATKRKIAEGDKLAGRHGNKGVISKIVPEEDMPFMEDGTPVDV 888

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +L+PLGVPSRMN+GQI ETHLGWA                                    
Sbjct: 889  ILSPLGVPSRMNIGQILETHLGWAASK--------------------------------- 915

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDESG 1232
                           + E     V VSTPVF GA    IN  +            +   G
Sbjct: 916  --------------GLGENGGEPVFVSTPVFSGATVADINEAIDKVRRNGAAEVGMSGGG 961

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  LYDG TGEPF+  +TVGY+Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 962  KVTLYDGRTGEPFENKITVGYMYILKLLHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQ 1021

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAA+ LQE+LTIKSDD VGR + YE+IV G +      P SF VL+K
Sbjct: 1022 RFGEMEVWALEAYGAAHTLQELLTIKSDDRVGRVKSYEAIVKGENIPSPSVPASFKVLLK 1081

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            EMQ+LGLS+         S + +E  D+++ 
Sbjct: 1082 EMQSLGLSVKPIYDVEAVSEEDQERRDWDEA 1112



 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 104/484 (21%), Positives = 200/484 (41%), Gaps = 54/484 (11%)

Query: 11  GRVRKFFGKNPE-IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
            R R  + +       +P+LI++Q +S+  F+          +EG++   + + PI  +S
Sbjct: 23  RRKRHSYARLQSADAQLPNLIQIQLSSFQKFM----------DEGIRRTLEDISPIEDYS 72

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           G+  +EF  + F+ P   +++C+ +D TYA PL + +R ++         K   +++EQ 
Sbjct: 73  GSYAVEFGEHRFEEPPVSIEECMSKDKTYAAPLFVRVRFVI---------KETGEVREQD 123

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTF+I G +R+VV+QL RSPG +    K       K +    ++P +G
Sbjct: 124 VFMGDFPLMTDWGTFIINGTERVVVTQLVRSPGAYVMEPKDPT----KQVLTASLMPHRG 179

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPK--IVYSQRGDFWC 246
            W++ E ++K  + VRIDR+RK+PVT  L ALG    EEIL+ F     I  +   D   
Sbjct: 180 SWLEFEVETKGYVSVRIDRKRKLPVTVLLKALGFGGPEEILARFGNSWLIRNTLERDDTT 239

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVI------------------ESGKKLTSGLLKSL 288
               A   +   +     V+++  + ++                  +  KKL   + + +
Sbjct: 240 SREDALLEVFRRQRPGEPVNLENAQNLVDGLFFDPKRYDLSEVGRYKVNKKLRLDVPRDV 299

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
               ++ +      L G    E     E G I  E      ++  E   +  +R +  L 
Sbjct: 300 HTLTIEDIEGLLRRLLG-IAEEVAEEEEFGRINYERIRHKLDE-YEHFGNRRLRTVGELV 357

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            ++     Y    +V ++   + +  +    V+      T  VA ++  F         +
Sbjct: 358 QEAFRIGMYRMERVVRERMTTQDEESITPQTVVN-----TKPVASAIKEFFGSSQLSQFM 412

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
                +                + +E     ++ +     G+  +  I+      +  +G
Sbjct: 413 DQTNTLAGLSHRRRLNAMGAGGLSRERAPIEVRDVHPTHYGR--MCPIETPEGPNIGLIG 470

Query: 469 EMLK 472
           ++  
Sbjct: 471 QLST 474


>gi|283783613|ref|YP_003374367.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis
            409-05]
 gi|283441313|gb|ADB13779.1| DNA-directed RNA polymerase, beta subunit [Gardnerella vaginalis
            409-05]
          Length = 1188

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 185/535 (34%), Positives = 269/535 (50%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G +   +             ++  +I  G  V  G +L      + +  +   + L
Sbjct: 659  MNDDGTQSSYKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGPATE-KGELALGKNL 717

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 718  LVAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLP 772

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 773  NVGEDAIANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 831

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E    GD++P GV ++++V++A  R I  GDK++G
Sbjct: 832  DTSLRVPHGETGTVIAVKEITREDAE--DDGDELPNGVNQMIRVYIAQHRKITQGDKLSG 889

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 890  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA-GWDI 948

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                            +       V + AE      PV+TPVFD
Sbjct: 949  N---------------------------LDSDLEAAWKKYVPQGAEHGDPCTPVATPVFD 981

Query: 1213 GADEEAINSMLR--MADLD------ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G   E +  +L   +A+ D        G++ L+DG TGEPF +P++VGY+Y+LKL+H+V 
Sbjct: 982  GVRPETLKGLLSTTLANRDGDKLVGSDGKATLFDGRTGEPFPKPISVGYMYILKLHHLVD 1041

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV G
Sbjct: 1042 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDG 1101

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1102 RVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEEDD 1156



 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 311/620 (50%), Positives = 433/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      + + L  +  + + DAL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 247 DAFQGYPLVLDALAKEPIETQDDALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 306

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L ++     R + +EDIIA IK LV L +G+                 +D
Sbjct: 307 RVGRYKINRKLGIEADYSDRSLNREDIIATIKYLVTLHSGEKTFPGKRDGQDVQLRVDVD 366

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 367 DIDHFGNRRIRQVGELVQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 426

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 427 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 486

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VTN+V Y++A  E    IAQAN  L
Sbjct: 487 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTNEVEYMTADREAEHVIAQANQEL 546

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F       R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 547 DENGNFVGTQALARVDEEEAVDVPVSTVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMG 606

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 607 TNMQRQAVPLIKSERPLVGTGSEWRAAVDSGDVILAEKPGVVTYVSADIIRVMNDDGTQS 666

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+K G+ V    ++ADGP+T+ G+LALG+N+LV
Sbjct: 667 S-------YKLSKFQRSNQTTCYNQVPLIKDGERVEAGTVLADGPATEKGELALGKNLLV 719

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 720 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGSEEITRDLPNVGEDAI 779

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 780 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 839

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   + +
Sbjct: 840 GETGTVIAVKEITREDAEDD 859



 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 92/305 (30%), Positives = 143/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 30  RVNFGSICEPIDVPYLLGVQTDSFDWLIGSERWKKRVAEDEANGTHTVPHVSGLDEVFQE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 90  ISPIENFAETMSLTFSDPYFEEPRHTVLECKEKDYTYSAPLYVNA---------EFENGE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRTQDRT--SDKDVFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFQGYPLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 259 LAKEPIETQDDALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 318

Query: 298 ITSDC 302
           I +D 
Sbjct: 319 IEADY 323


>gi|283456629|ref|YP_003361193.1| DNA-directed RNA polymerase subunit beta RpoB [Bifidobacterium
            dentium Bd1]
 gi|283103263|gb|ADB10369.1| DNA-directed RNA polymerase subunit beta RpoB [Bifidobacterium
            dentium Bd1]
          Length = 1186

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 184/532 (34%), Positives = 268/532 (50%), Gaps = 49/532 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 657  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 715

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 716  LIAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLP 770

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 771  NVGEDAVANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 829

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++G
Sbjct: 830  DTSLRVPHGETGTVIAVKEITREDAE--EAGDELPNGVNQMIRVYIAQHRKITQGDKLSG 887

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 888  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA-GWDI 946

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                +   A                               V + AE+   G PV+TPVFD
Sbjct: 947  SLDPDAEAAWKKF---------------------------VPQGAEKGAPGTPVATPVFD 979

Query: 1213 GADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G  ++ +  +L          ++      G++ L+DG TGEPF +P++VGY+YMLKL+H+
Sbjct: 980  GVRQDTLKGLLSCTLPDRDGNKLVG--PDGKATLFDGRTGEPFPKPISVGYMYMLKLHHL 1037

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV
Sbjct: 1038 VDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDV 1097

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        
Sbjct: 1098 DGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMK 1149



 Score =  486 bits (1252), Expect = e-134,   Method: Composition-based stats.
 Identities = 301/618 (48%), Positives = 425/618 (68%), Gaps = 23/618 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +    ++ AL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 245 DAFKDYPLVMDALAKETVDTQEAALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 304

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDIIA IK LV L  G+                   
Sbjct: 305 RVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGEAKFPGKRDGQDVDLRVDVD 364

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 365 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 424

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 425 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 484

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 485 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 544

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F +     R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 545 DENGNFVKSQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 604

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I   + +G   
Sbjct: 605 TNMQRQAVPLIQSERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTS 664

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 665 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 717

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 718 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 777

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 778 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 837

Query: 934 GVSGTVVDVRIFNRHGID 951
           G +GTV+ V+   R   +
Sbjct: 838 GETGTVIAVKEITREDAE 855



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 144/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 28  RVNFGSIREPIDVPYLLGVQTDSFDWLIGSERWKQRVEEDLENGTNTVPHTSGLDEVFQE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 88  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 139 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEIFG 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 197 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKQEIADAFKDYPLVMDA 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +      +A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 257 LAKETVDTQEAALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 316

Query: 298 ITSD 301
           +  D
Sbjct: 317 LEKD 320


>gi|171742261|ref|ZP_02918068.1| hypothetical protein BIFDEN_01367 [Bifidobacterium dentium ATCC
            27678]
 gi|306822203|ref|ZP_07455585.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium dentium
            ATCC 27679]
 gi|309802221|ref|ZP_07696329.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium dentium
            JCVIHMP022]
 gi|171277875|gb|EDT45536.1| hypothetical protein BIFDEN_01367 [Bifidobacterium dentium ATCC
            27678]
 gi|304554585|gb|EFM42490.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium dentium
            ATCC 27679]
 gi|308221104|gb|EFO77408.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium dentium
            JCVIHMP022]
          Length = 1186

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 186/537 (34%), Positives = 264/537 (49%), Gaps = 59/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 657  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 715

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 716  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 775

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 776  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 829

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 830  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 882

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 883  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +   A                               V + AE+   G PV+
Sbjct: 943  -GWDISLDPDAEAAWKKF---------------------------VPQGAEKGAPGTPVA 974

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG  ++ +  +L          ++      G++ L+DG TGEPF +P++VGY+YML
Sbjct: 975  TPVFDGVRQDTLKGLLSCTLPDRDGNKLVG--PDGKATLFDGRTGEPFPKPISVGYMYML 1032

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1033 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1092

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            KSDDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        
Sbjct: 1093 KSDDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMK 1149



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 301/620 (48%), Positives = 427/620 (68%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +    ++ AL D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 245 DAFKDYPLVMDALAKETVDTQEAALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLA 304

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDIIA IK LV L  G+                   
Sbjct: 305 RVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGEAKFPGKRDGQDVDLRVDVD 364

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 365 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 424

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 425 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 484

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 485 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 544

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F +     R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 545 DENGNFVKSQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 604

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I   + +G   
Sbjct: 605 TNMQRQAVPLIQSERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTS 664

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 665 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 717

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 718 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 777

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 778 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 837

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 838 GETGTVIAVKEITREDAEED 857



 Score =  311 bits (797), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 144/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 28  RVNFGSIREPIDVPYLLGVQTDSFDWLIGSERWKQRVEEDLENGTNTVPHTSGLDEVFQE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 88  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 139 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEIFG 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 197 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKQEIADAFKDYPLVMDA 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +      +A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 257 LAKETVDTQEAALTDLYRKIRPADTATPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 316

Query: 298 ITSD 301
           +  D
Sbjct: 317 LEKD 320


>gi|46360992|gb|AAS89229.1| RpoB [Corynebacterium striatum]
          Length = 1115

 Score =  504 bits (1299), Expect = e-140,   Method: Composition-based stats.
 Identities = 188/598 (31%), Positives = 275/598 (45%), Gaps = 60/598 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 564  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIIT 623

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 624  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQGTNYNQTPLVELGQRVEAGQVLAD 683

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 684  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 742

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 743  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 802

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                V  +                      +  DD+ PGV 
Sbjct: 803  IFGEKAREVRDTSMKVPHGENGKVIGVA-----------------RFSREDDDDLAPGVN 845

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVD++LN  GVP RM
Sbjct: 846  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMADGTPVDVILNTHGVPRRM 905

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+           +   L++  E++                
Sbjct: 906  NIGQVLEVHLGWLAHA-GWKVDV-----DDPANAELLKTLPEELYDVP------------ 947

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                      +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GE
Sbjct: 948  ----------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGE 997

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 998  PYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1057

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE+Q+L L++
Sbjct: 1058 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNV 1115



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 325/661 (49%), Positives = 450/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWSEQQI--KDRFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMIAPNGETIAIHTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H NS
Sbjct: 365 QNQIRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+   E +  R   
Sbjct: 485 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDKFAIAQAELEKDADGTIIGERIEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAPF
Sbjct: 545 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV++G  V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTNYNQTPLVELGQRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 718 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGVARFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 93/388 (23%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +              P+ R   GL+   + + P
Sbjct: 16  RYSFAKISEPIAVPGLLDLQLDSFAWLIGTPEWREREQAERGPEARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEQQIKDRFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE        I    ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMIAPNGETIA-----IHTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + +         +V ++   + 
Sbjct: 360 VGELIQNQIRVGLSRMERVVRERMTTQD 387


>gi|183602128|ref|ZP_02963496.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis HN019]
 gi|219683040|ref|YP_002469423.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis AD011]
 gi|241191360|ref|YP_002968754.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis Bl-04]
 gi|241196766|ref|YP_002970321.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis DSM 10140]
 gi|183218621|gb|EDT89264.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis HN019]
 gi|219620690|gb|ACL28847.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium animalis
            subsp. lactis AD011]
 gi|240249752|gb|ACS46692.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis Bl-04]
 gi|240251320|gb|ACS48259.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis DSM 10140]
 gi|289177486|gb|ADC84732.1| DNA-directed RNA polymerase beta chain [Bifidobacterium animalis
            subsp. lactis BB-12]
 gi|295794353|gb|ADG33888.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium animalis
            subsp. lactis V9]
          Length = 1186

 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 185/535 (34%), Positives = 271/535 (50%), Gaps = 45/535 (8%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 657  MNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEKGTVLADGPATE-KGEMALGKNL 715

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A       +  D  +     +S  +V     +   I++ E      +   E + RD  
Sbjct: 716  LVAFMPWNGYNYEDAVI-----ISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLP 770

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       N+  R   I  G    +G     K T      ++   R     F  +  +V+
Sbjct: 771  NVGEDAVANLDER-GIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVR 829

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +      +   +++  +   E  + GD++P GV ++++V++A  R I  GDK++G
Sbjct: 830  DTSLRVPHGETGTVIAVKEITREDAE--EDGDELPNGVNQMIRVYIAQHRKITQGDKLSG 887

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW     G  I
Sbjct: 888  RHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWVAHA-GWDI 946

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                +       +                           V + AE+ + G PV+TPVFD
Sbjct: 947  SLDPDMEAEWKKM---------------------------VPKGAEKGEPGTPVATPVFD 979

Query: 1213 GADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            G  ++ +  +L     D          G++ L+DG TGEP+ +P++VGY+YMLKL+H+V 
Sbjct: 980  GVRQDVLKGLLSTTLTDRDGNKLVGDNGKATLFDGRTGEPYPKPISVGYMYMLKLHHLVD 1039

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KSDDV G
Sbjct: 1040 DKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDG 1099

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            R RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1100 RVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEDDD 1154



 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 312/620 (50%), Positives = 437/620 (70%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +       AL+D+YR +RP D +T     ++ +  +F++ +YDL+
Sbjct: 245 DAFKDYPLVLDALEKETIDSEDAALVDLYRKIRPADAATPEAGRTLLDSFYFNTKRYDLA 304

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTID 454
            VGR K+N +L L+   + R + +EDIIA IK LV L  G               +  +D
Sbjct: 305 RVGRYKINRKLGLEKDYNDRSLSREDIIATIKYLVTLHAGDATFPGKRDGEDVELRVDVD 364

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DID+ GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 365 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIK 424

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 425 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 484

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++VVY++A  E    IAQAN  L
Sbjct: 485 PEGPNIGLIGSLATFGRINPFGFIETPYRKVENGHVTDEVVYMTADREVEHVIAQANQKL 544

Query: 635 DEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F E+    R  AGE   VP E +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 545 DENGNFVEKEALVRDAAGEAEDVPVEMVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 604

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+K+E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 605 TNMQRQAVPLIKSERPLVGTGAEWRAAVDSGDVILAEKPGVVIYVSADIIRVMNDDGTTS 664

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KFQRSNQ TC NQ PL+  G+ V +  ++ADGP+T+ G++ALG+N+LV
Sbjct: 665 S-------YKLAKFQRSNQTTCYNQVPLIHDGERVEKGTVLADGPATEKGEMALGKNLLV 717

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 718 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 777

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 778 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 837

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 838 GETGTVIAVKEITREDAEED 857



 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 91/305 (29%), Positives = 139/305 (45%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 28  RVNFGSIKEPIDVPYLLGVQTDSFDWLVGNERWKKRVEEDEANGTNTVPHVSGLDEVFHE 87

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 88  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNA---------EFENGE 138

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD    R   S K ++ 
Sbjct: 139 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQPDRT--SDKEIFG 196

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D + VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 197 AKIIPSRGAWLEFEIDKRDFLGVRVDRKRKQSAIVFLMAIGMTRSEIRDAFKDYPLVLDA 256

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +      +A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 257 LEKETIDSEDAALVDLYRKIRPADAATPEAGRTLLDSFYFNTKRYDLARVGRYKINRKLG 316

Query: 298 ITSDC 302
           +  D 
Sbjct: 317 LEKDY 321


>gi|46361002|gb|AAS89234.1| RpoB [Corynebacterium variabile]
          Length = 1114

 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 187/495 (37%), Positives = 253/495 (51%), Gaps = 63/495 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  +      +    M+    LL A    +  +  D  +     V   ++
Sbjct: 667  LVDQGQRVEAGQAIADGPGTRN-GEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDLL 725

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        E +  D DD   I+      R  +IL G
Sbjct: 726  TSIHIEEH--EIDARDTKLGPEEITRDIPNVGEDVLADLDDR-GIVRIGADVRDGDILVG 782

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 783  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKV 825

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   +  DD+ PGV ++V+V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPFL
Sbjct: 826  IGVRVFSREDDDDLAPGVNQMVRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFL 885

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD +LN  GVP RMN+GQ+ ETHLGW     G  + +   D K    ++ L   L
Sbjct: 886  PDGTPVDFILNTHGVPRRMNIGQVLETHLGWLAKY-GWTVDTHSEDPKVQAMLNTLPEDL 944

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
             +V                              V+TPVFDGA+ E I+ +LR  + +  G
Sbjct: 945  YEVPPESL-------------------------VATPVFDGAENEEISGLLRSINPNADG 979

Query: 1233 --------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                    +++L DG +GEPF  PV+VGY YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 980  MKLTDEFGKAVLIDGRSGEPFPYPVSVGYKYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1039

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G P
Sbjct: 1040 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIP 1099

Query: 1345 ESFNVLVKEMQALGL 1359
            ESF VL+KE+Q+L L
Sbjct: 1100 ESFKVLLKELQSLCL 1114



 Score =  499 bits (1286), Expect = e-138,   Method: Composition-based stats.
 Identities = 321/660 (48%), Positives = 448/660 (67%), Gaps = 24/660 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +       +I     +    +  +  TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEI----TERFGFSEIMMTTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L LD 
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 304

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLK 472
                 + ++DI+  I+ LV L  G+ ++            DDID+ GNRR+R+VGE+++
Sbjct: 305 DTGAMTLTEQDILTTIEYLVRLHAGERSMTSPDGTEIPLGTDDIDHFGNRRLRTVGELIQ 364

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSL
Sbjct: 365 NQIRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSL 424

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ +L ++ARV
Sbjct: 425 SGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETPEGPNIGLIGNLATYARV 484

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N +GFIETPYR+V +G +T+ V YL+A EE+   IAQA + +D +G F +E +  R  AG
Sbjct: 485 NPFGFIETPYRRVDNGVITDQVDYLTADEEDRHIIAQAKTPVDAEGRFVDEQIEVRLRAG 544

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           +  +VP  ++D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPLL+ EAP+V
Sbjct: 545 DVEVVPATEVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLLRGEAPYV 604

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  IV  +AG VE V A  I I   +G  D        Y L KF+R+N
Sbjct: 605 GTGMELRAAYDAGDVIVTPKAGTVEYVSADYITIMDDDGVRD-------TYMLRKFERTN 657

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC NQ PLV  G  V     IADGP T  G+++LGRN+LVAFMPW G+N+ED++++++
Sbjct: 658 QGTCYNQIPLVDQGQRVEAGQAIADGPGTRNGEMSLGRNLLVAFMPWEGHNYEDAIILNQ 717

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED+ TSIHIEE E+ ARDTKLGPEEITRDIPNV E+ L ++D+ GI+ +GA+V  G
Sbjct: 718 RVVEEDLLTSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDDRGIVRIGADVRDG 777

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   D
Sbjct: 778 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDDD 837



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 142/301 (47%), Gaps = 24/301 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L++VQ+ S+   +                 R   GL+     + P
Sbjct: 16  RYSFAKIDAPIEVPGLLDVQRESFAWLVGTPEWRARRQAQAEEGTRVTSGLEDILDELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +  +S    L      FD  K  +D+C  +D+ Y+ PL +T                  +
Sbjct: 76  VEDYSENMSLTLSEPRFDDVKNTIDECKDKDINYSAPLYVTAEFT---------NALSGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+A ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESID--ASTERPLHAVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +EEI   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEITERFGFSEIMMTTLEK 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D       A   +   +        D+ + ++E+         L K  + K  + LG+  
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 304

Query: 301 D 301
           D
Sbjct: 305 D 305


>gi|296119189|ref|ZP_06837759.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            ammoniagenes DSM 20306]
 gi|295967815|gb|EFG81070.1| DNA-directed RNA polymerase, beta subunit [Corynebacterium
            ammoniagenes DSM 20306]
          Length = 1164

 Score =  504 bits (1298), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/519 (34%), Positives = 260/519 (50%), Gaps = 61/519 (11%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 670  NYNQTPLVNMGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILSQRI 728

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLME 988
            V   V+       H ID  +  +  E    +I    E + RD DD   I+      R  +
Sbjct: 729  VEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIIRIGADVRAGD 787

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                V  +          
Sbjct: 788  ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA--------- 838

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                        +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V ++LP ED
Sbjct: 839  --------RFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKVLPPED 890

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF+ DGTPVD++LN  GVP RMN+GQ+ E HLGW     G  + +   D K    +  L
Sbjct: 891  MPFMADGTPVDVILNTHGVPRRMNIGQVLELHLGWLA-HTGWTVDT--EDPKNEELLKTL 947

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
               L  V                               +TPVFDGA  E I+ +L  +  
Sbjct: 948  PEELYDVPADSLT-------------------------ATPVFDGATNEEISRLLASSKP 982

Query: 1229 DESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +  G        +++L+DG +GEP+  P++VG++Y+LKL+H++ +K++ARSTG YS++TQ
Sbjct: 983  NRDGDVMVDEDGKTVLFDGRSGEPYQYPISVGFMYILKLHHLIDEKIHARSTGPYSMITQ 1042

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  +
Sbjct: 1043 QPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPD 1102

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             G PESF VL+KE+Q+L L++++ ++            D
Sbjct: 1103 PGIPESFKVLLKELQSLCLNVEVLSADGTPMELSGSDDD 1141



 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 320/661 (48%), Positives = 450/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 197 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEQQI--RDRFGFSELMMSTLES 252

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 253 DGIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGG 312

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             + +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 313 DHEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGEMIPVNTDDIDHFGNRRLRTVGELI 372

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 373 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 432

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 433 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 492

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV +G+VT++V YL+A EE+   IAQA    D DG+   + +  R   
Sbjct: 493 VNAFGFIETPYRKVENGRVTDEVRYLTADEEDRYSIAQAEVEQDADGNIVGDRIEVRLKD 552

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPL++ EAP+
Sbjct: 553 GDIGVTDANGVDYVDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLVRGEAPY 612

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +++ +AG+VE V+A  I I   EG  D        Y L KF+R+
Sbjct: 613 VGTGMELRAAYDAGDMVISPKAGVVENVNADLITIMDDEGVRD-------TYMLRKFERT 665

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED++++S
Sbjct: 666 NQGTNYNQTPLVNMGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILS 725

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V EDV TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++D+ GII +GA+V  
Sbjct: 726 QRIVEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRA 785

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 786 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSREDD 845

Query: 951 D 951
           D
Sbjct: 846 D 846



 Score =  294 bits (752), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 90/387 (23%), Positives = 169/387 (43%), Gaps = 45/387 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN--------EGLQAAFKSVFPI 65
           R  F K  E I +P L+++Q  S+   +  +   + +           GL+     + PI
Sbjct: 25  RYSFAKISEPIAVPGLLDLQLESFAWLIGTSEWRERQQEERGEEHVSSGLEDILAELSPI 84

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++I
Sbjct: 85  QDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQEI 135

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q++++GD P+MT +GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++I
Sbjct: 136 KSQTVFIGDFPMMTDEGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKVI 193

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   D
Sbjct: 194 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEQQIRDRFGFSELMMSTLESD 253

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF------ 295
                  A   +   +        D  + ++++         L +  + K  +       
Sbjct: 254 GIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGGD 313

Query: 296 -----------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
                      + +T + L  L+  E  +    GE+       ++   ++   +  +R +
Sbjct: 314 HEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGEMI-----PVNTDDIDHFGNRRLRTV 368

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRK 371
             L  + V         +V ++   + 
Sbjct: 369 GELIQNQVRVGLSRMERVVRERMTTQD 395


>gi|46360976|gb|AAS89221.1| RpoB [Corynebacterium imitans]
          Length = 1110

 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/490 (36%), Positives = 249/490 (50%), Gaps = 61/490 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M+    LL A    +  +  D  +     V   ++
Sbjct: 668  IVSAGQRVEAGQVIADGPGTK-DGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF++D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPTEDMPFMED 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAALLETLPEKLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 946  VPPESLT-------------------------ATPVFDGASNDEIAGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ LYDG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDAQGKTTLYDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQA 1356
            F VL+KE+Q+
Sbjct: 1101 FKVLLKELQS 1110



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 309/617 (50%), Positives = 433/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 229 TERFGFSELMMSTLENDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K+N +L L    + +  + +EDI   ++ LV L  G+               DD
Sbjct: 289 ARVGRYKVNRKLGLGGDHEGLMTLTEEDIATTLEYLVRLHAGETEMTSPSGEIIPINTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L+S+ARVN +GFIETPYRKV +G++T+ + YL+A EE+   IAQA + + 
Sbjct: 469 EGPNIGLIGALSSYARVNPFGFIETPYRKVDNGQLTDQIDYLTADEEDRYAIAQAATPMT 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +DG  T E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 KDGELTGERIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NM +QAVPLL+AEAP+V TGME   A  +G  +++  +G+VE V    I +   +G  D 
Sbjct: 589 NMHKQAVPLLRAEAPYVATGMEQRAAYDAGDTVISPLSGVVETVTGDYITVLGDDGTRD- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                   +L  F R+NQ TC NQ P+V  G  V    +IADGP T  G+++LGRN+LVA
Sbjct: 648 ------TQQLRTFHRTNQGTCYNQTPIVSAGQRVEAGQVIADGPGTKDGEMSLGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 762 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIAVRRFSREDDD 838



 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 96/389 (24%), Positives = 169/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +               + R   GL+     + 
Sbjct: 15  ERYSFAKIEEPITVPGLLDVQLESFAWLVGTSEWREREQELRGDEARVKSGLEDILDEIS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +++   +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIQDYSGNMSLTLSEPRFEDAKYTIEEAKDKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHAVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +   +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSELMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 NDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   +GEI       I+   ++   +  +R
Sbjct: 304 GDHEGLMTLTEEDIATTLEYLVRLHAGETEMTSPSGEII-----PINTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|149072056|ref|YP_001293553.1| RNA polymerase beta' chain [Rhodomonas salina]
 gi|158513797|sp|A6MVX4|RPOB_RHDSA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|134303007|gb|ABO70811.1| RNA polymerase beta' chain [Rhodomonas salina]
          Length = 1097

 Score =  504 bits (1297), Expect = e-140,   Method: Composition-based stats.
 Identities = 306/604 (50%), Positives = 428/604 (70%), Gaps = 9/604 (1%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           + + +  Y++ +   + N   ++AL+ +Y  +RPG+ +T +  + +    FFD  +YDL 
Sbjct: 195 NGLRHPEYLKKSFRVEGNYTTEEALIQMYTKLRPGEPATVNGGQQILYSRFFDPKRYDLG 254

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +L L  P++++ +  +D ++ I  L++L+   G  DDID+LGNRRVRSVGE
Sbjct: 255 KVGRYKINKKLALSIPENIKVLTPQDTLSAIDYLINLKFNIGETDDIDHLGNRRVRSVGE 314

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ R+GL R+ER I+ER++  D +S+ P  L+N KP+++A+ EFF SSQLSQ  +  
Sbjct: 315 LLQNQVRVGLNRLERIIRERMTICDSESLAPNTLVNPKPIIAAIREFFGSSQLSQFMDQT 374

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+  L + 
Sbjct: 375 NPLAELTHKRRISALGPGGLNRDRAGFAVRDIHPSHYGRICPIETPEGPNAGLIGVLATH 434

Query: 590 ARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+N+YGFIETP+ +V +GKV +D   VYL+A +E+N  IA  + ++DE+ +   ++V  
Sbjct: 435 ARINSYGFIETPFYQVINGKVVSDGNPVYLTADQEDNFRIAPGDIAIDENNAINNDIVPV 494

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E  +   E+ID+I  SP QV+SIA SLIPFLE+DD+NR LMG NMQRQAVPLL  E
Sbjct: 495 RYRQEFTITKPEQIDYIQVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPE 554

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P +GTG+E+  A+ SG  +V+ + G V  V A +I I   EG          +Y L K+
Sbjct: 555 SPLIGTGIEAQAARDSGMVVVSYQDGRVTYVSANKICITDDEGKEV-------VYYLQKY 607

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSNQ+TC+NQRP V +G++V    +IADG +T+ G+LALG+N+L+A++PW GYN+ED+ 
Sbjct: 608 QRSNQDTCINQRPSVWLGEKVVAGQVIADGAATEGGELALGQNILIAYLPWEGYNYEDAF 667

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISER+V  DV+TS+HIE++E+ AR TKLG EEITR++PN+ E  L+ +D+ GII +G+ 
Sbjct: 668 LISERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNIGEYSLRKLDDNGIIVIGSW 727

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKGES   PE KLLRAIFGEKA DVRDTSLRVP+G  G V+DVRIF R
Sbjct: 728 VEVGDILVGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRVLDVRIFTR 787

Query: 948 HGID 951
              D
Sbjct: 788 EKGD 791



 Score =  475 bits (1223), Expect = e-131,   Method: Composition-based stats.
 Identities = 185/528 (35%), Positives = 258/528 (48%), Gaps = 58/528 (10%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E +              I++   + +G +V  G ++      +G   +   + +L
Sbjct: 594  DDEGKEVVYYLQKYQRSNQDTCINQRPSVWLGEKVVAGQVIADGAATEG-GELALGQNIL 652

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  L     +S  +V   ++    I+K E    +E  Q +L + +   
Sbjct: 653  IAYLPWEGYNYEDAFL-----ISERLVYNDVYTSVHIEKYE----IEARQTKLGSEEITR 703

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            E   +      +L +   I+ G     G     K T        + P  +  +    ++ 
Sbjct: 704  ELPNIGEYSLRKLDDNGIIVIGSWVEVGDILVGKVTPKGES--DQPPEGKLLRAIFGEKA 761

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                  SL+V       +L+ R    I   + GD++P G   V++V+VA  R IQ GDKM
Sbjct: 762  RDVRDTSLRVPNGGRGRVLDVR----IFTREKGDELPTGANIVIRVYVAQTRKIQVGDKM 817

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGI+SRILP +DMP+L DGTPVD+VLNPLGVPSRMNVGQIFE  LG A   L K
Sbjct: 818  AGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLDK 877

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K +  D     + S +    + +       +                          +
Sbjct: 878  RFKIIPFDEMNGAEASRVLVNEKLMEARTLTEKDW------------------------I 913

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FD               L   G++ L+DG TGE FD PVTVG  YMLKL H+V DK++AR
Sbjct: 914  FD---------------LRHPGKTQLFDGRTGEAFDNPVTVGISYMLKLVHLVDDKIHAR 958

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+  GGQRLGEMEVW ++A+GA+Y LQE+LT+KSDD+ GR     
Sbjct: 959  STGPYSLVTQQPLGGKAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLN 1018

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            +IV G      GTPESF VL++E+Q+LGL I           +   I 
Sbjct: 1019 AIVKGKPIPRPGTPESFKVLMRELQSLGLDIGAYKIENLPDGQTRGIE 1066



 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 102/456 (22%), Positives = 192/456 (42%), Gaps = 40/456 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+E+Q+AS+  FL           EGL    KS  PIT ++G   L F    ++   
Sbjct: 11  LPDLVEIQRASFCWFL----------EEGLAEEIKSFSPITDYTGNLELHFFGDQFKLKC 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+++ +   RD TY+V + +  RLI          +    IKEQ +++GDLPLMT  GT
Sbjct: 61  PKYNLLESKRRDATYSVQVYVPARLI---------NRDTGIIKEQEVFIGDLPLMTDRGT 111

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPGI++  +  R    G+  Y+  +I ++G W+  E D  D++ 
Sbjct: 112 FIINGAERVIVNQIVRSPGIYYKSETDRQ---GRRTYSGSLISNRGAWVKFETDRNDLVW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF----YPKIVYSQRGDFWCFPLSAADLMVGAK 259
           VRID+ RK+P   FL A+G+   +I +      Y K  +   G++      A   M    
Sbjct: 169 VRIDKTRKIPAHVFLKAMGLSDSDIYNGLRHPEYLKKSFRVEGNY--TTEEALIQMYTKL 226

Query: 260 VSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
                  ++ G+Q++ S         L K  + K  K L ++      +   +D ++   
Sbjct: 227 RPGEPATVNGGQQILYSRFFDPKRYDLGKVGRYKINKKLALSIPENIKVLTPQDTLSAID 286

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I ++         ++ + +  +R +  L  + V         ++ ++        L  
Sbjct: 287 YLINLKFNIGET-DDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTICDSESLAP 345

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             ++ P      +     F            + +  +    R++   P     + ++   
Sbjct: 346 NTLVNPK--PIIAAIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LNRDRAG 400

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             ++ +     G+  I  I+         +G +  +
Sbjct: 401 FAVRDIHPSHYGR--ICPIETPEGPNAGLIGVLATH 434


>gi|269977640|ref|ZP_06184607.1| DNA-directed RNA polymerase, beta subunit [Mobiluncus mulieris 28-1]
 gi|306817848|ref|ZP_07451587.1| DNA-directed RNA polymerase subunit beta [Mobiluncus mulieris ATCC
            35239]
 gi|307701272|ref|ZP_07638293.1| DNA-directed RNA polymerase, beta subunit [Mobiluncus mulieris
            FB024-16]
 gi|269934243|gb|EEZ90810.1| DNA-directed RNA polymerase, beta subunit [Mobiluncus mulieris 28-1]
 gi|304649327|gb|EFM46613.1| DNA-directed RNA polymerase subunit beta [Mobiluncus mulieris ATCC
            35239]
 gi|307613433|gb|EFN92681.1| DNA-directed RNA polymerase, beta subunit [Mobiluncus mulieris
            FB024-16]
          Length = 1165

 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/546 (33%), Positives = 269/546 (49%), Gaps = 67/546 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  +             ++  ++  G  +  GD++        +  M   + L
Sbjct: 644  QTDAGRVDNYKLEKFQRSNQGNCYNQQVLVDEGQRLEVGDVIADGP-ATDQGEMALGKNL 702

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    + ++  D  +     VS  ++       H  + + R   +  E+I        
Sbjct: 703  LVAYMSWEGLNYEDAIILSQRVVSEDLLTSIHIEEH--EIDARDTKLGPEEITRDIPNVS 760

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D DD   I+         +IL G+    G         L   ++ E  +      
Sbjct: 761  EAARKDLDDR-GIIRVGAEVHAGDILVGKITPKGETELTSEERLLRAILGEKAKEA---- 815

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                      V   +     +     D  ++         ++ PGV  +V+V+VA +R I
Sbjct: 816  ----RDTSLRVPHGESGIVIAVKEFTDEDED--------SELAPGVNHMVRVYVAQRRKI 863

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKM+GRHGNKG +S+ILP EDMPFL+DGTPVDI+LNP+GVP RMN+GQ+ E HLGW 
Sbjct: 864  TVGDKMSGRHGNKGCISKILPVEDMPFLEDGTPVDIILNPMGVPGRMNIGQVLEFHLGWI 923

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G  I   +   +      PL +                              + G 
Sbjct: 924  AHE-GWDITKALESGEQWAKHVPLPTA-----------------------------EPGQ 953

Query: 1205 PVSTPVFDGADEEAINSMLRMAD---------LDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             V+TPVFDGA+ + I  ML+            +DE+G++ L+DG +GEPF   + VGY Y
Sbjct: 954  HVATPVFDGAEADVITGMLQSTRVRDKFDHQLIDENGKAQLFDGRSGEPFPYRIAVGYKY 1013

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+L
Sbjct: 1014 MLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQEIL 1073

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDV GR +VYE+IV G D  + G PESF VL++EM++L L++++ +         +
Sbjct: 1074 TVKSDDVQGRVKVYEAIVRGEDLPQPGIPESFRVLMQEMRSLCLNVEVLDFDGHPLDMRD 1133

Query: 1376 EIPDFN 1381
            +  + +
Sbjct: 1134 DADEAS 1139



 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 320/676 (47%), Positives = 446/676 (65%), Gaps = 41/676 (6%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I      G+ +        T  I+++A  +   +  E      +  +  L  D    
Sbjct: 193 EFEIDKRDSVGVRIDRKRKQSAT--IFLKAMGMSTAEIREAFADFPM-MLETLEKDGPIE 249

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                          ++ AL DIYR +RPG+  +     ++ +  + +  +YDL+ VGR 
Sbjct: 250 --------------TQEQALEDIYRKIRPGEPPSAEAGRALLHNFYTNPKRYDLAEVGRY 295

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDN 458
           K+N +L +    D R +   D++A  + L+ LR G   +                DDID+
Sbjct: 296 KINKKLGVAHEMDQRTLSLTDMVAAFRYLLALREGMDVVSIKGAAGEALDVKVKTDDIDH 355

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            GNRRVR+VGE+++ Q+R G+ RMER ++ER+S+ D+++++P+ LIN +PVV+A+ EFF 
Sbjct: 356 FGNRRVRAVGELIQLQFRTGMSRMERVVRERMSTQDMEAIVPKSLINIRPVVAAIKEFFG 415

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG 
Sbjct: 416 TSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPVETPEGP 475

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL+ SL +FAR+N +GF+ETPYR V DG VT+++ Y++A +EE   IAQA+++L +D 
Sbjct: 476 NIGLIGSLATFARINPFGFVETPYRVVRDGVVTDEIHYITADDEEGLNIAQASATLTDDN 535

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            F E+ V CR   G+ +LV  E++D +D S +Q+VS+A ++IPFLE+DD+NR LMG NMQ
Sbjct: 536 HFVEKEVLCRSTGGDPVLVSPEEVDLMDVSARQMVSVATAMIPFLEHDDANRALMGANMQ 595

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPLL+ EAP VGTG+E   A  +G  +VAK AG+V +V A  + I++  G       
Sbjct: 596 RQAVPLLRTEAPLVGTGIEKRAAVDAGDVVVAKNAGVVTEVSADLVKIQTDAGR------ 649

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            VD Y+L KFQRSNQ  C NQ+ LV  G  +   D+IADGP+TD G++ALG+N+LVA+M 
Sbjct: 650 -VDNYKLEKFQRSNQGNCYNQQVLVDEGQRLEVGDVIADGPATDQGEMALGKNLLVAYMS 708

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W G N+ED++++S+R+VSED+ TSIHIEE E+ ARDTKLGPEEITRDIPNVSE   K++D
Sbjct: 709 WEGLNYEDAIILSQRVVSEDLLTSIHIEEHEIDARDTKLGPEEITRDIPNVSEAARKDLD 768

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII VGAEV+ GDILVGKITPKGE+ +T EE+LLRAI GEKA + RDTSLRVP G SG
Sbjct: 769 DRGIIRVGAEVHAGDILVGKITPKGETELTSEERLLRAILGEKAKEARDTSLRVPHGESG 828

Query: 938 TVVDVRIFNRHGIDKN 953
            V+ V+ F     D  
Sbjct: 829 IVIAVKEFTDEDEDSE 844



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 88/302 (29%), Positives = 139/302 (46%), Gaps = 33/302 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F +  E +  P+L+ +Q  S+D FL  +                     GLQ     
Sbjct: 13  RVSFAQIKEPMTAPNLLALQTESFDWFLGNDAWKQRVEAAASGEGKHVPTVSGLQEVLNE 72

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI    G   L F SY  +   + +D+C  +DLTY  PL +    I+ +         
Sbjct: 73  MSPIEDAGGTMSLSFNSYTLEDAPYTIDECRDKDLTYDAPLCVEAEFIMNE--------- 123

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q++++G+ PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S + +Y 
Sbjct: 124 TGEIKNQTVFLGNFPLMTPRGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDRDIYL 181

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D +D + VRIDR+RK   T FL A+GM + EI   F  +P ++ +
Sbjct: 182 GKVIPSRGAWLEFEIDKRDSVGVRIDRKRKQSATIFLKAMGMSTAEIREAFADFPMMLET 241

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D                +      I  GE    E+G+ L      + K   +  +G 
Sbjct: 242 LEKDGPIET-------QEQALEDIYRKIRPGEPPSAEAGRALLHNFYTNPKRYDLAEVGR 294

Query: 299 TS 300
             
Sbjct: 295 YK 296


>gi|227541693|ref|ZP_03971742.1| DNA-directed RNA polymerase [Corynebacterium glucuronolyticum ATCC
            51866]
 gi|227182508|gb|EEI63480.1| DNA-directed RNA polymerase [Corynebacterium glucuronolyticum ATCC
            51866]
          Length = 1161

 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 182/539 (33%), Positives = 255/539 (47%), Gaps = 65/539 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  ++  G  V  G ++        +  M+    LL A
Sbjct: 652  EGKRDTYRLRKFERTNQNTCYNQKPLVDSGDRVEKGQVMADGPGT-HDGEMSLGVNLLVA 710

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLAR 969
                +  +  D  +     V   ++       H ID  +  +  E    +I    E + +
Sbjct: 711  FMPWQGHNYEDAIILNQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 770

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  +IL G+    G         L   +  E  R           
Sbjct: 771  DL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 818

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +                   GD++P GV  ++++ VA KR IQ GDK
Sbjct: 819  ------EVRDTSLKVPHGETGKVIGVSRFSRDEGDELPAGVNEMIRIHVAQKRKIQDGDK 872

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG+V +ILP EDMPF++DGTP+DI+LN  GVP RMN+GQ+ E HLGW     G
Sbjct: 873  LAGRHGNKGVVGKILPQEDMPFMEDGTPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-G 931

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I+   +  K                                +        +   V+TP
Sbjct: 932  WAIEGDPDWAKR-------------------------------IPEELRNVPADSLVATP 960

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA  E I  +L     D          G++ L+DG +GEPF  PV VG  YMLKL+H
Sbjct: 961  VFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLKLHH 1020

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDD
Sbjct: 1021 LVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDD 1080

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            V GR RVYE+IV G++  + G PESF VL+KE+Q+L L++++ ++            D 
Sbjct: 1081 VNGRVRVYEAIVKGDNIPDPGIPESFKVLLKELQSLCLNVEVLSADGTPVELSGADDDE 1139



 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 329/662 (49%), Positives = 455/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G ++  D+   +T G              L+ +  SE +       +    +  + +TL 
Sbjct: 198 GAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEK-----IRERFGFSEIMMSTLE 252

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D      +ALL+IYR  RPG+  T  +A+++    FF   +YDL+ VGR K+N +L L 
Sbjct: 253 NDGAASEDEALLEIYRKQRPGEQPTRDLAQALLENSFFKPKRYDLAKVGRYKVNRKLGLG 312

Query: 424 TP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
              D V+ + +EDI   I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 313 GDHDGVKTLTEEDIATTIEYLVRLHAGERTMTSPDGVEIPLETDDIDHFGNRRLRTVGEL 372

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 373 IQNQVRVGLARMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 432

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 433 SLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYA 492

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPY+KV +GK+ + V YL+A EE+   I QA++  DE+G  T+E    R  
Sbjct: 493 RVNPFGFIETPYQKVENGKIIDQVDYLTADEEDRFVIGQADTEHDENGVITQERNEVRLK 552

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +V  E I++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++++P
Sbjct: 553 DGAIEVVGPEAIEYIDVSPRQIVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSQSP 612

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME+  A  +G  ++ K AG+VE V A  I + S EG  D        YRL KF+R
Sbjct: 613 YVGTGMEAPAAYDAGDLVINKHAGVVENVCADFITVMSDEGKRD-------TYRLRKFER 665

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQNTC NQ+PLV  GD V +  ++ADGP T  G+++LG N+LVAFMPW G+N+ED++++
Sbjct: 666 TNQNTCYNQKPLVDSGDRVEKGQVMADGPGTHDGEMSLGVNLLVAFMPWQGHNYEDAIIL 725

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V 
Sbjct: 726 NQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVR 785

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ V  F+R  
Sbjct: 786 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVSRFSRDE 845

Query: 950 ID 951
            D
Sbjct: 846 GD 847



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 147/321 (45%), Gaps = 30/321 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +      +++  E         GL+   + + P
Sbjct: 25  RYSFAKIKEPIGLPGLLDLQLNSFAWLVGTPEWREQQKAEKGEDYKVTSGLEDILEELSP 84

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG   L      F+  K  VD+C  +D+ Y+ PL +T              K   +
Sbjct: 85  IQDFSGNMSLSLSEPYFEQVKASVDECKEKDINYSAPLYVTA---------EFENKDTGE 135

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 136 IKSQTVFIGDFPMMTPKGTFIVNGTERVVVSQLVRSPGVYFDETLDK--STERPLHAVKV 193

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++I+ D KD + VRIDR+R+ PVT  L ALG   E+I   F     ++ +   
Sbjct: 194 IPSRGAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEKIRERFGFSEIMMSTLEN 253

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +        D  + ++E+            K   +  +G    +
Sbjct: 254 DGAASEDEALLEIYRKQRPGEQPTRDLAQALLENS-------FFKPKRYDLAKVGRYKVN 306

Query: 302 CLCGLYVAEDIVNGETGEIYI 322
              GL    D V   T E   
Sbjct: 307 RKLGLGGDHDGVKTLTEEDIA 327


>gi|284050631|ref|ZP_06380841.1| DNA-directed RNA polymerase subunit beta [Arthrospira platensis
           str. Paraca]
 gi|291568317|dbj|BAI90589.1| RNA polymerase beta subunit [Arthrospira platensis NIES-39]
          Length = 1127

 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 319/605 (52%), Positives = 421/605 (69%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     +DAL+++YR +RPG+  T +  E + +  FFD  +YDL
Sbjct: 221 FDALRHPDYFQKTIEKEGEFSEEDALMELYRKLRPGEPPTITGGEQLLHNRFFDPKRYDL 280

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD  R +   DI++ I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 281 GRVGRHKLNRKLRLSVPDSTRVLTPTDILSAIDYLINLEYDIGETDDIDHLGNRRVRSVG 340

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D +++ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 341 ELLQNQIRVGLNRLERIIRERMTVGDAETLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 400

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 401 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 460

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGFIETPY  V +G+V  D+  VY++A EE++  +A  + S D +G    +LV 
Sbjct: 461 HARVNPYGFIETPYYPVENGRVRRDLSPVYMTADEEDDLRVAPGDISYDSEGHILGDLVP 520

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      +++D++  SP Q+VS+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 521 VRYRQDFTKTSPDQVDYVAVSPVQIVSVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 580

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E PFVGTG+E+  A+ SG  IV++  G V  VD  +I +                Y L K
Sbjct: 581 ERPFVGTGLEAQAARDSGMVIVSRTDGEVSYVDGAKIRV-------IDPEGWEIEYELQK 633

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSNQ+TC+NQRPLV  GD+V    ++ADG ST+  +LALG N+LVA+MPW GYN+ED+
Sbjct: 634 YQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGAELALGHNILVAYMPWEGYNYEDA 693

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V +DV+TSIHIE+FE+ AR TKLGPEEITR+IPNV E+ L+ +   GII +GA
Sbjct: 694 ILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDSLRQLTADGIIRIGA 753

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 754 WVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 813

Query: 947 RHGID 951
           R   D
Sbjct: 814 REQGD 818



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 181/525 (34%), Positives = 251/525 (47%), Gaps = 64/525 (12%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E                +++  ++  G +V  G +L    + +G   +     +L
Sbjct: 621  DPEGWEIEYELQKYQRSNQDTCLNQRPLVYEGDQVVAGQVLADGSSTEGA-ELALGHNIL 679

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDK 971
             A    +  +  D  L     V   V       +  I+  +  +  E    +I  +  D 
Sbjct: 680  VAYMPWEGYNYEDAILISERLVYDDVYTSIHIEKFEIEARQTKLGPEEITREIPNVGEDS 739

Query: 972  DDEQ---VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              +     I+    +    +IL G+    G         L   +  E  R          
Sbjct: 740  LRQLTADGIIRIGAWVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD--------- 790

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                     ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ G
Sbjct: 791  ---------VRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVG 841

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKGIVSRILP EDMP+L DG P+DIVLNPLGVPSRMNVGQIFE  +GWA   
Sbjct: 842  DKMAGRHGNKGIVSRILPIEDMPYLPDGRPMDIVLNPLGVPSRMNVGQIFECLMGWAGEN 901

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L ++ K +  D     ++S      +                                  
Sbjct: 902  LKRRFKVIPFDEMFGQEMSRETVHSKLKE------------------------------- 930

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                  A E+     L   +    G++I+YDG TGEPFD+PVTVG  Y+LKL H+V DK+
Sbjct: 931  ------AREKLKKDWLFSEEYP--GKTIVYDGRTGEPFDQPVTVGIAYILKLVHLVDDKI 982

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR  
Sbjct: 983  HARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMAGRNE 1042

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
               +IV G      GTPESF VL++E+Q+L L I +    T    
Sbjct: 1043 ALNAIVKGKAIPRPGTPESFKVLMRELQSLCLDIAVHKVETNKKD 1087



 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 101/459 (22%), Positives = 192/459 (41%), Gaps = 36/459 (7%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--S 78
               ++PDLIE+Q++S+  FL            GL    +S  PI+ ++G   L F+   
Sbjct: 33  ESAFELPDLIEIQRSSFRWFL----------ETGLIEELESFSPISDYTGKLELHFLARD 82

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   PK+DVDD   RD TY+V + +  RLI          K   +IKEQ +++GDLPLM
Sbjct: 83  YKLKQPKYDVDDAKRRDSTYSVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLM 133

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++V+Q+ RSPG+++  +  +   + +  Y+  +IP++G W+  E D 
Sbjct: 134 TERGTFIINGAERVIVNQIVRSPGVYYKSEIDK---NQRRTYSASLIPNRGAWLKFETDK 190

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMV 256
            D++ VRID+ RK+     L ALG+ + EI         +  +   +       A   + 
Sbjct: 191 NDLVWVRIDKTRKLSAQILLKALGLTNNEIFDALRHPDYFQKTIEKEGEFSEEDALMELY 250

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
                     I  GEQ++ +         L +  + K  + L ++      +    DI++
Sbjct: 251 RKLRPGEPPTITGGEQLLHNRFFDPKRYDLGRVGRHKLNRKLRLSVPDSTRVLTPTDILS 310

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                I +E         ++ + +  +R +  L  + +         ++ ++        
Sbjct: 311 AIDYLINLEYDIGET-DDIDHLGNRRVRSVGELLQNQIRVGLNRLERIIRERMTVGDAET 369

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 370 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 424

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 425 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 461


>gi|227874562|ref|ZP_03992725.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
 gi|227844771|gb|EEJ54917.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
          Length = 1143

 Score =  503 bits (1296), Expect = e-140,   Method: Composition-based stats.
 Identities = 181/546 (33%), Positives = 269/546 (49%), Gaps = 67/546 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T  G  +  +             ++  ++  G  +  GD++        +  M   + L
Sbjct: 622  QTDAGRVDNYKLEKFQRSNQGNCYNQQVLVDEGQRLEVGDVIADGP-ATDQGEMALGKNL 680

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-------- 964
            L A    + ++  D  +     VS  ++       H  + + R   +  E+I        
Sbjct: 681  LVAYMSWEGLNYEDAIILSQRVVSEDLLTSIHIEEH--EIDARDTKLGPEEITRDIPNVS 738

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D DD   I+         +IL G+    G         L   ++ E  +      
Sbjct: 739  EAARKDLDDR-GIIRVGAEVHAGDILVGKITPKGETELTSEERLLRAILGEKAKEA---- 793

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                      V   +     +     D  ++         ++ PGV  +V+V+VA +R I
Sbjct: 794  ----RDTSLRVPHGESGIVIAVKEFTDEDED--------SELAPGVNHMVRVYVAQRRKI 841

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKM+GRHGNKG +S+ILP EDMPFL+DGTPVDI+LNP+GVP RMN+GQ+ E HLGW 
Sbjct: 842  TVGDKMSGRHGNKGCISKILPVEDMPFLEDGTPVDIILNPMGVPGRMNIGQVLEFHLGWI 901

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G  I   +   +      PL +                              + G 
Sbjct: 902  AHE-GWDITKALESGEQWAKHVPLPTA-----------------------------EPGQ 931

Query: 1205 PVSTPVFDGADEEAINSMLRMAD---------LDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             V+TPVFDGA+ + I  ML+            +DE+G++ L+DG +GEPF   + VGY Y
Sbjct: 932  HVATPVFDGAEADVITGMLQSTRVRDKFDHQLIDENGKAQLFDGRSGEPFPYRIAVGYKY 991

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            MLKL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+L
Sbjct: 992  MLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQEIL 1051

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDDV GR +VYE+IV G D  + G PESF VL++EM++L L++++ +         +
Sbjct: 1052 TVKSDDVQGRVKVYEAIVRGEDLPQPGIPESFRVLMQEMRSLCLNVEVLDFDGHPLDMRD 1111

Query: 1376 EIPDFN 1381
            +  + +
Sbjct: 1112 DADEAS 1117



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 320/676 (47%), Positives = 446/676 (65%), Gaps = 41/676 (6%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I      G+ +        T  I+++A  +   +  E      +  +  L  D    
Sbjct: 171 EFEIDKRDSVGVRIDRKRKQSAT--IFLKAMGMSTAEIREAFADFPM-MLETLEKDGPIE 227

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                          ++ AL DIYR +RPG+  +     ++ +  + +  +YDL+ VGR 
Sbjct: 228 --------------TQEQALEDIYRKIRPGEPPSAEAGRALLHNFYTNPKRYDLAEVGRY 273

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDN 458
           K+N +L +    D R +   D++A  + L+ LR G   +                DDID+
Sbjct: 274 KINKKLGVAHEMDQRTLSLTDMVAAFRYLLALREGMDVVSIKGAAGEALDVKVKTDDIDH 333

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            GNRRVR+VGE+++ Q+R G+ RMER ++ER+S+ D+++++P+ LIN +PVV+A+ EFF 
Sbjct: 334 FGNRRVRAVGELIQLQFRTGMSRMERVVRERMSTQDMEAIVPKSLINIRPVVAAIKEFFG 393

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG 
Sbjct: 394 TSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPVETPEGP 453

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL+ SL +FAR+N +GF+ETPYR V DG VT+++ Y++A +EE   IAQA+++L +D 
Sbjct: 454 NIGLIGSLATFARINPFGFVETPYRVVRDGVVTDEIHYITADDEEGLNIAQASATLTDDN 513

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            F E+ V CR   G+ +LV  E++D +D S +Q+VS+A ++IPFLE+DD+NR LMG NMQ
Sbjct: 514 HFVEKEVLCRSTGGDPVLVSPEEVDLMDVSARQMVSVATAMIPFLEHDDANRALMGANMQ 573

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPLL+ EAP VGTG+E   A  +G  +VAK AG+V +V A  + I++  G       
Sbjct: 574 RQAVPLLRTEAPLVGTGIEKRAAVDAGDVVVAKNAGVVTEVSADLVKIQTDAGR------ 627

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            VD Y+L KFQRSNQ  C NQ+ LV  G  +   D+IADGP+TD G++ALG+N+LVA+M 
Sbjct: 628 -VDNYKLEKFQRSNQGNCYNQQVLVDEGQRLEVGDVIADGPATDQGEMALGKNLLVAYMS 686

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W G N+ED++++S+R+VSED+ TSIHIEE E+ ARDTKLGPEEITRDIPNVSE   K++D
Sbjct: 687 WEGLNYEDAIILSQRVVSEDLLTSIHIEEHEIDARDTKLGPEEITRDIPNVSEAARKDLD 746

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII VGAEV+ GDILVGKITPKGE+ +T EE+LLRAI GEKA + RDTSLRVP G SG
Sbjct: 747 DRGIIRVGAEVHAGDILVGKITPKGETELTSEERLLRAILGEKAKEARDTSLRVPHGESG 806

Query: 938 TVVDVRIFNRHGIDKN 953
            V+ V+ F     D  
Sbjct: 807 IVIAVKEFTDEDEDSE 822



 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 85/289 (29%), Positives = 134/289 (46%), Gaps = 33/289 (11%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKSVFPITAFSGAAML 74
           P+L+ +Q  S+D FL  +                     GLQ     + PI    G   L
Sbjct: 4   PNLLALQTESFDWFLGNDAWKQRVEAAASGEGKHVPTVSGLQEVLNEMSPIEDAGGTMSL 63

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            F SY  +   + +D+C  +DLTY  PL +    I+ +           +IK Q++++G+
Sbjct: 64  SFNSYTLEDAPYTIDECRDKDLTYDAPLCVEAEFIMNE---------TGEIKNQTVFLGN 114

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            PLMT  GTF+I G +R+VVSQL RSPG++F+    +   S + +Y  ++IP +G W++ 
Sbjct: 115 FPLMTPRGTFIINGTERVVVSQLVRSPGVYFEKTADKT--SDRDIYLGKVIPSRGAWLEF 172

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAA 252
           E D +D + VRIDR+RK   T FL A+GM + EI   F  +P ++ +   D         
Sbjct: 173 EIDKRDSVGVRIDRKRKQSATIFLKAMGMSTAEIREAFADFPMMLETLEKDGPIET---- 228

Query: 253 DLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                  +      I  GE    E+G+ L      + K   +  +G   
Sbjct: 229 ---QEQALEDIYRKIRPGEPPSAEAGRALLHNFYTNPKRYDLAEVGRYK 274


>gi|212716241|ref|ZP_03324369.1| hypothetical protein BIFCAT_01157 [Bifidobacterium catenulatum DSM
            16992]
 gi|212660753|gb|EEB21328.1| hypothetical protein BIFCAT_01157 [Bifidobacterium catenulatum DSM
            16992]
          Length = 1209

 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 186/537 (34%), Positives = 267/537 (49%), Gaps = 59/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  +I  G  V  G +L      + +  M   + L
Sbjct: 680  MNDDGTTSSYKLAKFRRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 738

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 739  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 798

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 799  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 852

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++          +  +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 853  DTSLRVPHGETGTVIDVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 905

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 906  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 965

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I                                I      ++ + AE+ + G PV+
Sbjct: 966  -GWDISLDP---------------------------DIEAAWKKNIPQGAEKGEPGTPVA 997

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG   E I  +L          ++    + G+++L+DG TGEP+ +P++VGY+YML
Sbjct: 998  TPVFDGVRPETIKGLLSCTLPDRDGNKLVG--DDGKAVLFDGRTGEPYPKPISVGYMYML 1055

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1056 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1115

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            KSDDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        
Sbjct: 1116 KSDDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMK 1172



 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 299/620 (48%), Positives = 429/620 (69%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +  + + +AL D+YR +RP D  T     ++ +  +F++ +YDL+
Sbjct: 268 DAFKDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGRNLLDSFYFNTKRYDLA 327

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDII+ IK LV L  G                    
Sbjct: 328 RVGRYKINRKLGLEKDINDRSLSREDIISTIKYLVTLHAGDTKFPGKRDGQDVDLRVDVD 387

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 388 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 447

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 448 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 507

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 508 PEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQEL 567

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D++G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 568 DDNGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 627

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 628 TNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRVMNDDGTTS 687

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KF+RSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 688 S-------YKLAKFRRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 740

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 741 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 800

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 801 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 860

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+DV+   R   +++
Sbjct: 861 GETGTVIDVKEITREDAEED 880



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 143/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 51  RVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVEKDLENGTNTVSHTSGLDEVFQE 110

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 111 ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 161

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 162 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEVFG 219

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 220 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDA 279

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 280 LAKETVQTQDEALTDLYRKIRPADTPTPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 339

Query: 298 ITSD 301
           +  D
Sbjct: 340 LEKD 343


>gi|186660361|gb|ACC86063.1| beta-subunit RNA polymerase [Corynebacterium genitalium ATCC 33030]
          Length = 1056

 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 336/661 (50%), Positives = 461/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSELMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             D V  + +EDI+  I+ LV L  G+ ++            DDID+ GNRR+R+VGE++
Sbjct: 305 DTDGVMTLTEEDILTTIEYLVRLHAGERSMTSPDGTEIPIDTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DG++T++V Y +A EE+   IAQAN+  DE+  FTEE +  R   
Sbjct: 485 VNPFGFIETPYRKVVDGQITDEVYYFTADEEDRHVIAQANTPFDENHRFTEERIEVRLRG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 545 GDVEVVPYTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   EG  D          L KF+R+
Sbjct: 605 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDEGVRDTFM-------LRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ PLV  GD V    ++ADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQTPLVDEGDRVEAGQVLADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++DE GI+ +GA+V  
Sbjct: 718 QRMVEEDVLTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 153/537 (28%), Positives = 217/537 (40%), Gaps = 58/537 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              +L +  P+ G   E         M+  
Sbjct: 564  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPFVGTGMELRAAYDAGDMIIA 623

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     + +      G  +                ++  ++  G  V  G +L  
Sbjct: 624  PKAGVVEYVSADYITVMDDEGVRDTFMLRKFERTNQGTCYNQTPLVDEGDRVEAGQVLAD 683

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M   + LL A    +  +  D  +     V   V+       + ID  +  
Sbjct: 684  GPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVLTSIHIEEYEIDARDTK 742

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E     I  +  D     DE+ I+      R  +IL G+    G         L   
Sbjct: 743  LGPEEITRDIPNVGEDVLADLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRA 802

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E      +            ++   +  DD+  GV 
Sbjct: 803  IFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAAGVN 845

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTP+DI+LN  GVP RM
Sbjct: 846  EMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPIDIILNTHGVPRRM 905

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+     D K    +  L   L ++                
Sbjct: 906  NIGQVLEVHLGWLAKA-GWKVDPDSQDPKIQKMLETLPEELYEIPADSLT---------- 954

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA    ++ +LR +  +  G        +S L DG +GE
Sbjct: 955  ---------------ATPVFDGASNAELSGLLRSSLPNRDGERQVDDFGKSNLIDGRSGE 999

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            PF  PV VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 1000 PFPYPVAVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1056



 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 86/322 (26%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +               D R   GL+   + + 
Sbjct: 15  QRHSFAKIDAPIEVPGLLDLQRESFAWLVGTPEWRARAQAEAGEDVRIMSGLEEILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 75  PIEDYSENMSLTLSEPRFDDVKSTIDEAKDKDINYAAPLYVTAEFT---------NSMSG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L++ +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F    +   +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSELMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 244 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKAKRYDLAKVGRYKV 296

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D V   T E  +
Sbjct: 297 NRKLGLGGDTDGVMTLTEEDIL 318


>gi|46361008|gb|AAS89237.1| RpoB [Corynebacterium urealyticum DSM 7109]
          Length = 1057

 Score =  503 bits (1295), Expect = e-140,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 458/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSEIMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D  ++  +ALL+IYR  RPG+  T   A+++    FF   +YDL+ VGR K+N +L L  
Sbjct: 245 DGVENTDEALLEIYRKQRPGESPTRDSAQALLENSFFRPKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D    + +EDI+  I+ LV L  G+              +DDID+ GNRR+R+VGE++
Sbjct: 305 DTDGTMTLTEEDILTTIEYLVRLHAGERTMTSPEGVEIPIEVDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 425 LSGLTHKRRLNALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V DG++T++V Y +A EE+   IAQAN+  D D  FTE+ +  R   
Sbjct: 485 VNPFGFIETPYRRVVDGQITDEVEYFTADEEDRHVIAQANTPFDADMKFTEDQIEVRLRG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+AEAP+
Sbjct: 545 GDVEVVPASQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  +G  I+A +AG+VE V A  I I   EG  D          L KF+R+
Sbjct: 605 VGTGIEQRAAYDAGDLIIAPKAGVVEYVSADYITIMDDEGIRDTFM-------LRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    +IADGP TD G++ALG+N+LVAFMPW G+N+ED++++S
Sbjct: 658 NQGTSYNQKPLVNQGDRVEAGQVIADGPGTDNGEMALGKNLLVAFMPWEGHNYEDAIILS 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE+E+ ARDTKLGPEEITRDIPNV E+ L ++DE GI+ +GA+V  
Sbjct: 718 QRMVEEDVLTSIHIEEYEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 159/541 (29%), Positives = 228/541 (42%), Gaps = 64/541 (11%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V            A+              +L A  P+ G   E         +   
Sbjct: 564  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRAEAPYVGTGIEQRAAYDAGDLI-- 621

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDI 893
            +     + E+ V A    +  +E  RD   + +    N     ++  ++  G  V  G +
Sbjct: 622  IAPKAGVVEY-VSADYITIMDDEGIRDTFMLRKFERTNQGTSYNQKPLVNQGDRVEAGQV 680

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +           M   + LL A    +  +  D  +     V   V+       + ID  
Sbjct: 681  IADGPGTDN-GEMALGKNLLVAFMPWEGHNYEDAIILSQRMVEEDVLTSIHIEEYEIDAR 739

Query: 954  ERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            +  +  E     I  +  D     DE+ I+      R  +IL G+    G         L
Sbjct: 740  DTKLGPEEITRDIPNVGEDVLADLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERL 799

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               +  E  R                 E      +            ++   +  DD+  
Sbjct: 800  LRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGVRVFSREDDDDLAA 842

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DGTPVDI+LN  GVP
Sbjct: 843  GVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDGTPVDIILNTHGVP 902

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
             RMN+GQ+ E HLGW     G ++ +  +D K    +  L   L  V             
Sbjct: 903  RRMNIGQVLEVHLGWLAKA-GWQVDTNSDDPKIKAMLETLPEDLYDVPADSLT------- 954

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGL 1240
                              STPVFDGA    ++ +LR +  D  G        ++ L DG 
Sbjct: 955  ------------------STPVFDGASNAELSGLLRSSRPDRDGIRLVDDFGKAQLIDGR 996

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP++ P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 997  TGEPYEHPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1056

Query: 1301 C 1301
             
Sbjct: 1057 A 1057



 Score =  291 bits (744), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 143/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 15  TRYSFAKIDAPIEVPGLLDLQRESFAWLVGAPEWRARMQAEAGEGVRVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 75  PIEDYSENMSLTLSEPRFDDMKTSIDEAKEKDINYAAPLYVTAEFT---------NAQSG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+  +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESID--TSTERPLHGVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 244 KDGVENTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFRPKRYDLAKVGRYKV 296

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    D     T E  +
Sbjct: 297 NRKLGLGGDTDGTMTLTEEDIL 318


>gi|225351759|ref|ZP_03742782.1| hypothetical protein BIFPSEUDO_03356 [Bifidobacterium
            pseudocatenulatum DSM 20438]
 gi|225158103|gb|EEG71386.1| hypothetical protein BIFPSEUDO_03356 [Bifidobacterium
            pseudocatenulatum DSM 20438]
          Length = 1209

 Score =  503 bits (1295), Expect = e-139,   Method: Composition-based stats.
 Identities = 186/537 (34%), Positives = 267/537 (49%), Gaps = 59/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +    +        ++  +I  G  V  G +L      + +  M   + L
Sbjct: 680  MNDDGTTSSYKLAKFLRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQ-KGEMALGKNL 738

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 739  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 798

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 799  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 852

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 853  DTSLRVPHGETGTVIAVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITQG 905

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 906  DKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHA 965

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    +   A                               + + AE+ + G PV+
Sbjct: 966  -GWDISLDPDTEAAWKKY---------------------------IPQGAEKGEPGTPVA 997

Query: 1208 TPVFDGADEEAINSML----------RMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
            TPVFDG   E I  +L          ++    + G+++L+DG TGEP+ +P++VGY+YML
Sbjct: 998  TPVFDGVRPETIKGLLSCTLPDRDGNKLVG--DDGKAVLFDGRTGEPYPKPISVGYMYML 1055

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL+H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T 
Sbjct: 1056 KLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTT 1115

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            KSDDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        
Sbjct: 1116 KSDDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMK 1172



 Score =  489 bits (1258), Expect = e-135,   Method: Composition-based stats.
 Identities = 299/620 (48%), Positives = 427/620 (68%), Gaps = 23/620 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+  +   + + L  +  + + +AL D+YR +RP D  T     ++ +  +F++ +YDL+
Sbjct: 268 DAFRDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGRNLLDSFYFNTKRYDLA 327

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID------------ 457
            VGR K+N +L L+   + R + +EDII+ IK LV L  G                    
Sbjct: 328 RVGRYKINRKLGLEKDVNDRSLSREDIISTIKYLVTLHAGDTKFPGKRDGQDVDLRVDVD 387

Query: 458 ---NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + 
Sbjct: 388 DIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIK 447

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+
Sbjct: 448 EFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIES 507

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL+ SL +F R+N +GFIETPYRKV +G VT++V Y++A  +    IAQAN  L
Sbjct: 508 PEGPNIGLIGSLATFGRINPFGFIETPYRKVINGHVTDEVEYMTADRDAEHVIAQANQEL 567

Query: 635 DEDGSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           DE+G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG
Sbjct: 568 DENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMG 627

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL+++E P VGTG E   A  SG  I+A++ G+V  V A  I + + +G   
Sbjct: 628 TNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRVMNDDGTTS 687

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+L KF RSNQ TC NQ PL+  G+ V    ++ADGP+T  G++ALG+N+L+
Sbjct: 688 S-------YKLAKFLRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLI 740

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMPW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ +
Sbjct: 741 AFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAV 800

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            N+DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP 
Sbjct: 801 ANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPH 860

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G +GTV+ V+   R   +++
Sbjct: 861 GETGTVIAVKEITREDAEED 880



 Score =  311 bits (797), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 143/304 (47%), Gaps = 27/304 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F+ 
Sbjct: 51  RVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVEEDLANGTNTVPHTSGLDEVFQE 110

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 111 ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 161

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 162 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRT--SDKEVFG 219

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+RK     FLMA+GM  +EI   F  YP ++ +
Sbjct: 220 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFRDYPLVMDA 279

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G  +++S    T    L +  + K  + LG
Sbjct: 280 LAKETVQTQDEALTDLYRKIRPADTPTPEAGRNLLDSFYFNTKRYDLARVGRYKINRKLG 339

Query: 298 ITSD 301
           +  D
Sbjct: 340 LEKD 343


>gi|46360964|gb|AAS89215.1| RpoB [Corynebacterium falsenii]
          Length = 1109

 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 330/661 (49%), Positives = 460/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSEIMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF   +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKPKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             +    + +EDI+  I+ LV L  G+ T+            DDID+ GNRR+R+VGE++
Sbjct: 305 DNEGTMTLTEEDILTTIEYLVRLHAGERTMTSPAGVEIPIATDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V DG++T++V Y +A EE+   IAQAN+  DE+  FTE+ +  R   
Sbjct: 485 VNPFGFIETPYRRVVDGQITDEVHYFTADEEDRHVIAQANTPFDENHRFTEDRIEVRLRG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP +++DF+D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 545 GDVEVVPFDQVDFMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   +G  D          L KF+R+
Sbjct: 605 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDDGVRDTFM-------LRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  G+ V    ++ADGP TD G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTSYNQKPLVDEGERVEAGQVLADGPGTDQGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE+E+ ARDTKLGPEEITRDIPNV ++ L ++DE GI+ +GA+V  
Sbjct: 718 QRMVEEDVLTSIHIEEYEIDARDTKLGPEEITRDIPNVGDDVLADLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 180/486 (37%), Positives = 243/486 (50%), Gaps = 57/486 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L        +  M   + LL A    +  +  D  +     V   V+
Sbjct: 668  LVDEGERVEAGQVLADGPGT-DQGEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   + ID  +  +  E     I  +  D     DE+ I+      R  +IL G+  
Sbjct: 727  TSIHIEEYEIDARDTKLGPEEITRDIPNVGDDVLADLDERGIVRIGADVRDGDILVGKVT 786

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 787  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 829

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+  GV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DG
Sbjct: 830  RVFSREDDDDLAAGVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPDG 889

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LN  GVP RMN+GQ+ E HLGW     G K+ +   D K    +  L   L  V
Sbjct: 890  TPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWKVDTNSEDPKIQKMLETLPEDLYDV 948

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                                           +TPVFDGA    ++ +LR +  +  G   
Sbjct: 949  PADSLT-------------------------ATPVFDGASNSELSGLLRSSRPNRDGIRL 983

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 984  VDDFGKAQLMDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1043

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF
Sbjct: 1044 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGXPESF 1103

Query: 1348 NVLVKE 1353
             VL+KE
Sbjct: 1104 KVLLKE 1109



 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 83/322 (25%), Positives = 144/322 (44%), Gaps = 30/322 (9%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +                 R   GL+   + + 
Sbjct: 15  QRYSFAKIDSPIEVPGLLDLQRESFAWLVGSADWRARAQAEAGEGVRVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      FD  K  +D+   +D+ YA PL +T                  
Sbjct: 75  PIEDYSENMSLTLSEPRFDEVKSTIDEAKDKDINYAAPLYVTAEFT---------NAMSG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L++ +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESMD--ASTERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS- 300
            D       A   +   +        D+ + ++E+            K   +  +G    
Sbjct: 244 KDGVANTDEALLEIYRKQRPGESPTRDSAQALLENS-------FFKPKRYDLAKVGRYKV 296

Query: 301 DCLCGLYVAEDIVNGETGEIYI 322
           +   GL    +     T E  +
Sbjct: 297 NRKLGLGGDNEGTMTLTEEDIL 318


>gi|328478127|gb|EGF47985.1| DNA-directed RNA polymerase subunit beta [Lactobacillus rhamnosus
            MTCC 5462]
          Length = 831

 Score =  502 bits (1293), Expect = e-139,   Method: Composition-based stats.
 Identities = 171/522 (32%), Positives = 243/522 (46%), Gaps = 67/522 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G  +  + +        KN ++  I+ +G  V   D ++          +   +  
Sbjct: 329  RREDGALDTYKLMKFKRSNAGKNYNQRPIVTIGDHV-DVDEIIADGPAMQNGELALGQNP 387

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + A       +  D  +         V D    + H  +    +   +    E+     +
Sbjct: 388  IIAFMTWNMYNYEDAIVL----SERLVKDDVYTSIHIEEYESEARDTKLGPEEVTREIPN 443

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              +  L          +  G     G     K T      +S   R     F  +  +V+
Sbjct: 444  VGEEALKD--LDEFGVVRVGAEVRDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVR 501

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI   + GD++ PGV  +V+V++  KR IQ GDKMAG
Sbjct: 502  DTSLRVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKRKIQVGDKMAG 555

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG VS ++P EDMP+L DGTPVDI L+P+GVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 556  RHGNKGTVSVVVPEEDMPYLPDGTPVDICLSPMGVPSRMNIGQVLELHLGMAARNLGIHV 615

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D+                                               
Sbjct: 616  ATPVFDGANDKDLW---------------------------------------------- 629

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
             A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL+HMV DK++ARS 
Sbjct: 630  -ATVKE-------AGMPSDGKSVLYDGRTGEPFENRVSVGVMYYMKLSHMVDDKIHARSI 681

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+I
Sbjct: 682  GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKTYEAI 741

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            V G+   + G PESF VLVKE+QALGL + +  +  +     
Sbjct: 742  VKGDPIPKPGVPESFRVLVKELQALGLDMKVLGADKQEIELR 783



 Score =  477 bits (1228), Expect = e-132,   Method: Composition-based stats.
 Identities = 305/531 (57%), Positives = 394/531 (74%), Gaps = 9/531 (1%)

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                V+HI   D++A +   ++L+ G GT+DDID+LGNRR+RSVGE+L+NQ+R+GL RM
Sbjct: 4   HIGKKVKHILPADVLASMNYFLNLQEGLGTVDDIDHLGNRRIRSVGELLQNQFRIGLSRM 63

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLS
Sbjct: 64  ERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLS 123

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A VN YGFIETPY
Sbjct: 124 ALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYAVVNPYGFIETPY 183

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           R+V     KVT+ + YL+A EE+N  +AQANS L++DGSF ++ V  R     I +  +K
Sbjct: 184 RRVSWDTHKVTDKIDYLTADEEDNYIVAQANSPLNDDGSFVDDTVLARHKDNNIEISPDK 243

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP VGTGME   A
Sbjct: 244 VDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPHAPLVGTGMEYKAA 303

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG A++A  AG VE VDA +I +R  +G LD        Y+LMKF+RSN     NQRP
Sbjct: 304 HDSGTAVLANNAGTVEYVDAKQIRVRREDGALD-------TYKLMKFKRSNAGKNYNQRP 356

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V +GD V  ++IIADGP+   G+LALG+N ++AFM W+ YN+ED++++SER+V +DV+T
Sbjct: 357 IVTIGDHVDVDEIIADGPAMQNGELALGQNPIIAFMTWNMYNYEDAIVLSERLVKDDVYT 416

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEE+E  ARDTKLGPEE+TR+IPNV EE LK++DE G++ VGAEV  GDILVGK+TP
Sbjct: 417 SIHIEEYESEARDTKLGPEEVTREIPNVGEEALKDLDEFGVVRVGAEVRDGDILVGKVTP 476

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R   D
Sbjct: 477 KGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVKIFTREAGD 527


>gi|46360982|gb|AAS89224.1| RpoB [Corynebacterium mycetoides]
          Length = 1110

 Score =  502 bits (1292), Expect = e-139,   Method: Composition-based stats.
 Identities = 183/490 (37%), Positives = 247/490 (50%), Gaps = 61/490 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K    M     LL A    +  +  D  +     V   ++
Sbjct: 668  IVNAGDRVEAGQVIADGPGTKN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWTVN--PDDPANAELLQTLPEHLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L  +  +  G  
Sbjct: 946  VPPESLT-------------------------ATPVFDGASNEEIAGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDGNGKTMLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQA 1356
            F VL+KE+Q+
Sbjct: 1101 FKVLLKELQS 1110



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 313/617 (50%), Positives = 436/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K+N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 289 ARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEIIPINTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L S+ARVNA+GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + LD
Sbjct: 469 EGPNIGLIGALASYARVNAFGFIETPYQKVVDGKLTDQIDYLTADEEDRYAIAQAATPLD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            + +   E +  R   G+  +V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 GERNLVGERIEVRLKDGDIGVVGAHGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL++EA +V TGME   A  +G  +++++AG++E V    I +   +G  D 
Sbjct: 589 NMQKQAVPLLRSEAAYVATGMEQRAAYDAGDTVISRKAGVIEDVTGDYITVMDDDGIRD- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L  F+R+NQ TC NQ P+V  GD V    +IADGP T  G++ALGRN+LVA
Sbjct: 648 ------TYMLRTFERTNQGTCYNQTPIVNAGDRVEAGQVIADGPGTKNGEMALGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 762 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIAVRRFSREDDD 838



 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 98/389 (25%), Positives = 171/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDE---------RPNEGLQAAFKSVF 63
            R  F K  E + +P L++VQ  S+   +      +          R   GL+     + 
Sbjct: 15  ERYSFAKISEPVTVPGLLDVQSESFAWLVGTEEWRERQRAERGDDARITSGLEDILDEIS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIQDYSGNMSLSLSEPRFEEIKYSIDECKEKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHAVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 SDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGEI       I+   ++   +  +R
Sbjct: 304 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPTGEII-----PINTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|46360966|gb|AAS89216.1| RpoB [Corynebacterium felinum]
          Length = 1111

 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 183/493 (37%), Positives = 252/493 (51%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M     LL A    +  +  D  +     V   ++
Sbjct: 666  LVDLGERVEEGQVLADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 724

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 725  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 783

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 784  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 826

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 827  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 886

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI +     +   +   L++  E 
Sbjct: 887  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAEILKTLPED 940

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                           G   +TPVFDGA  + +  +LR +  +  G  
Sbjct: 941  LYDVE----------------------PGSLTATPVFDGATNDELAGLLRSSRPNRDGDV 978

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 979  MVDENGKAQLFDGRSGEPFPFPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGK 1038

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1039 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1098

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1099 FKVLLKELQSLCL 1111



 Score =  489 bits (1258), Expect = e-135,   Method: Composition-based stats.
 Identities = 328/616 (53%), Positives = 444/616 (72%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+
Sbjct: 228 ERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLA 287

Query: 410 TVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDI 456
            VGR K+N +L L    + +  +  EDI   I+ LV L  G+ T+            DDI
Sbjct: 288 KVGRYKVNRKLGLGGDNEGLMTLTDEDIATTIEYLVRLHAGETTMTSPTGEVIPVETDDI 347

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EF
Sbjct: 348 DHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREF 407

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET E
Sbjct: 408 FGTSQLSQFMDLNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPE 467

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ARVN +GFIETPYRKV DG VT+ V YL+A EE+   +AQAN+  DE
Sbjct: 468 GPNIGLIGSLASYARVNTFGFIETPYRKVVDGVVTDHVDYLTADEEDRYVVAQANTEYDE 527

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +G  TE+ V  R   G+  +V  + ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 528 NGVITEDRVTVRLKKGDIQVVSGKDIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 587

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AGIVE V A  I I S EG  D  
Sbjct: 588 MQRQAVPLVRSEAPFVGTGMELRAAYDAGDLIINKKAGIVESVSADYITIMSDEGIRD-- 645

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y L KF+R+NQ T  NQ+PLV +G+ V    ++ADGP T  G++ALGRN+LVAF
Sbjct: 646 -----TYMLRKFERTNQGTSYNQKPLVDLGERVEEGQVLADGPGTHNGEMALGRNLLVAF 700

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK+
Sbjct: 701 MPWEGHNYEDAIILNQRLVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKD 760

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G 
Sbjct: 761 LDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGE 820

Query: 936 SGTVVDVRIFNRHGID 951
           +G V+ VR F+R   D
Sbjct: 821 TGKVIGVRRFSREDDD 836



 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 93/389 (23%), Positives = 171/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K  E I++P L+++Q  S+   +            +    +   GL+     + 
Sbjct: 13  ERKSFAKITEPIEVPGLLDIQLESFAWLIGSPEWRARRQAELGEGVKVTSGLEDILAELS 72

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I  D           
Sbjct: 73  PIVDYSGNMSLSLSEPRFEEKKNSIDECKDKDINYSAPLYVTAEFINTD---------TG 123

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++ D P+MT+ GTF++ G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 124 EIKSQTVFICDFPMMTEKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVK 181

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 182 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIQERFGFSEIMMSTLE 241

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        +  + ++++         L K  + K  + LG+ 
Sbjct: 242 SDGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLG 301

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TGE+       ++   ++   +  +R
Sbjct: 302 GDNEGLMTLTDEDIATTIEYLVRLHAGETTMTSPTGEVI-----PVETDDIDHFGNRRLR 356

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 357 TVGELIQNQVRVGLSRMERVVRERMTTQD 385


>gi|291456192|ref|ZP_06595582.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium breve DSM
            20213]
 gi|291381469|gb|EFE88987.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium breve DSM
            20213]
          Length = 1187

 Score =  501 bits (1291), Expect = e-139,   Method: Composition-based stats.
 Identities = 185/540 (34%), Positives = 261/540 (48%), Gaps = 55/540 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  II  G  V  G +L        +  +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGP-AIQKGDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNLEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ + ++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLRGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKQISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E  D
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDEEDD 1155



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 306/617 (49%), Positives = 433/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELVQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F  +    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVSKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I A + G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKADKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP++  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGPAIQKGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGNERWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEVDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAKAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|46360934|gb|AAS89200.1| RpoB [Corynebacterium matruchotii]
          Length = 1112

 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 178/494 (36%), Positives = 250/494 (50%), Gaps = 61/494 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G ++           M     LL A    +  +  D  +     V   ++
Sbjct: 666  LVDEGDRVEEGQVVADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 724

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                  +H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 725  TSIHIEQHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 783

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 784  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 826

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 827  VRRFSREDEDDLGPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 886

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD++LN  GVP RMN+GQ+ E HLGW     G K+                      
Sbjct: 887  GTPVDVILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKVDV-------------------- 925

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
                    +  +    +++        +G   +TPVFDGA  + I  +L  +  +  G  
Sbjct: 926  -------NDPANAKLLETLPEDLYDVPAGSLTATPVFDGATNDEIAGLLANSLPNRDGDV 978

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 979  MVNADGKAQLFDGRSGEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGK 1038

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1039 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1098

Query: 1347 FNVLVKEMQALGLS 1360
            F VL+KE+Q+L L+
Sbjct: 1099 FKVLLKELQSLCLN 1112



 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 328/661 (49%), Positives = 454/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  + +TL  
Sbjct: 187 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTEQIV--ERFGFSEIMMSTLEN 242

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF   +YDL+ VGR K N +L L  
Sbjct: 243 DGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLGG 302

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             D +  + +EDI   I+ LV L  G+ ++            DDID+ GNRR+R+VGE++
Sbjct: 303 DHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEIIPVETDDIDHFGNRRLRTVGELI 362

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF SSQLSQ  +  NS
Sbjct: 363 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGSSQLSQFMDLNNS 422

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 423 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 482

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN++GFIETPYRKV DG VT++V YL+A EE+   +AQAN+  DE+G  TE+ V  R   
Sbjct: 483 VNSFGFIETPYRKVVDGVVTDEVDYLTADEEDRYVVAQANTKFDENGVITEDRVTVRLKK 542

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V  + I+++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP 
Sbjct: 543 GDIQVVDGKDINYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPL 602

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I++K+AG+VE V A  I I   +G  D        Y L KF+R+
Sbjct: 603 VGTGMELRAAYDAGDLIISKKAGVVETVCADYITIMGDDGVRD-------TYMLRKFERT 655

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    ++ADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 656 NQGTSYNQKPLVDEGDRVEEGQVVADGPGTHNGEMALGRNLLVAFMPWEGHNYEDAIILN 715

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIE+ E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V  
Sbjct: 716 QRLVEEDILTSIHIEQHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVRD 775

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR F+R   
Sbjct: 776 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRRFSREDE 835

Query: 951 D 951
           D
Sbjct: 836 D 836



 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 97/389 (24%), Positives = 174/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            RK F K    I++P L+++Q  S+   +            +  D R   GL+   + + 
Sbjct: 13  ERKSFAKIQSPIEVPGLLDIQLESFAWLIGSPEWRARRQAELGEDVRVTSGLEDILEELS 72

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 73  PIQDYSGNMSLSLSEPRFEEMKNSIDECKDKDINYSAPLYVTAEFI---------NNETQ 123

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 124 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 181

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ +  
Sbjct: 182 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIVERFGFSEIMMSTLE 241

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L K  + K  + LG+ 
Sbjct: 242 NDGVANMDEALLEIYRKQRPGEQPTRDLAQSLLENSFFRPKRYDLAKVGRYKFNRKLGLG 301

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+V E  +   TGEI       ++   ++   +  +R
Sbjct: 302 GDHDGLMTLTEEDIATTIEYLVRLHVGETSMTSPTGEII-----PVETDDIDHFGNRRLR 356

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 357 TVGELIQNQVRVGLSRMERVVRERMTTQD 385


>gi|55139438|gb|AAV41383.1| RpoB [Corynebacterium aurimucosum ATCC 700975]
          Length = 1113

 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 193/595 (32%), Positives = 280/595 (47%), Gaps = 60/595 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 565  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMEQRAAYDAGDLIIT 624

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 625  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQNTNYNQTPLVSLGERVEAGQVLAD 684

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 685  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 743

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 744  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 803

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                        ET K I   RF  + +     DD+ PGV 
Sbjct: 804  IFGEKAREVRDT------------SMKVPHGETGKVIGVSRFSREDD-----DDLAPGVN 846

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RM
Sbjct: 847  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRM 906

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G KI +     +   +   L++  E++      +         
Sbjct: 907  NIGQVLEVHLGWLAHA-GWKIDT-----EDPANAELLKTLPEELYDVPPESLT------- 953

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +GE
Sbjct: 954  ---------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGE 998

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 999  PYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1058

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE+Q+L 
Sbjct: 1059 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLC 1113



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 324/661 (49%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 190 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIK----ERFGFSELMMSTLES 245

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+++ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 246 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 305

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 306 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMISIHTDDIDHFGNRRLRTVGELI 365

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 366 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 425

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 426 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 485

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+ T + +  R   
Sbjct: 486 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDRFAIAQAEVEKDADGTLTGDRIEVRLKD 545

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 546 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 605

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 606 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 658

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNT  NQ PLV +G+ V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 659 NQNTNYNQTPLVSLGERVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 718

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 719 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 778

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 779 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVSRFSREDD 838

Query: 951 D 951
           D
Sbjct: 839 D 839



 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  SY   +               D R   GL+   + + P
Sbjct: 17  RYSFAKISEPIAVPGLLDLQLDSYAWLIGTPEWREREQAERGEDARVTSGLEDILEELSP 76

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 77  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 127

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT+ GTF++ G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 128 IKSQTVFIGDFPMMTEKGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHSVKV 185

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 186 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIKERFGFSELMMSTLES 245

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        D  + ++++         L K  + K  +      
Sbjct: 246 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 305

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+  E  +    GE+       I    ++   +  +R 
Sbjct: 306 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMI-----SIHTDDIDHFGNRRLRT 360

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 361 VGELIQNQVRVGLSRMERVVRERMTTQD 388


>gi|257064682|ref|YP_003144354.1| DNA-directed RNA polymerase subunit beta [Slackia heliotrinireducens
            DSM 20476]
 gi|256792335|gb|ACV23005.1| DNA-directed RNA polymerase subunit beta [Slackia heliotrinireducens
            DSM 20476]
          Length = 1185

 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 199/678 (29%), Positives = 306/678 (45%), Gaps = 85/678 (12%)

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            R      V + +++ R+ +             +++ F     +    Q   V        
Sbjct: 511  RTVDGVFVPSTKVLCRTTDAKGVFGEPDEVDPQMVDFM----DVSPRQMTSVATSLIPFL 566

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFE 848
                A+              +L    P+ G   E  + +   E +++++     +++   
Sbjct: 567  EHDDANRALMGSNMQRQAVPLLNPHAPYVGTGIEHRIAVDSGEMLIAQNPGVVDYVDGST 626

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            ++ R      +E        S +    I+   I+  G EV+ GD+L    +    + +  
Sbjct: 627  IIIRTDDGDFDEYLIPKFQRSNQS-GCINHKPIVRKGDEVHSGDVLADGPS-CDHAELAL 684

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             + LL A    +  +  D  +     V+  ++     + + ID  +  +  E    E + 
Sbjct: 685  GQNLLIAYMTWEGYNYEDAIIISERVVAEDLLTSVHISEYEIDARDTKLGPEEITRE-IP 743

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
               +D    LD +   R+     G     G     K T      ++   R     F  + 
Sbjct: 744  NISEDMISDLDADGIIRI-----GAEVFPGDVLVGKVTPKGETELTAEERLLRAIFGEKA 798

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
             +V+     +          +           + GDD+ PGV  +V+V++A KR +Q GD
Sbjct: 799  REVRDTSLKVPHGAGGRIVGIN------RFSRENGDDLAPGVNELVRVYIAQKRKVQQGD 852

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K++GRHGNKG++SR+LP EDMP+L DGTP+D++LNPLGVPSRMNVGQ+ E HLGWA    
Sbjct: 853  KLSGRHGNKGVISRVLPVEDMPYLADGTPIDVMLNPLGVPSRMNVGQLLECHLGWAAK-- 910

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
                                                 ++  D+ V       +  + V+T
Sbjct: 911  ----------------------------------WGWNEESDEPV-------EGPMFVAT 929

Query: 1209 PVFDGADEEAINSMLRMAD----------------------LDESGQSILYDGLTGEPFD 1246
            PVFDGA EE I  +++ A+                      L+  G++ LYDG TGEPF 
Sbjct: 930  PVFDGATEEEIADVIQKANRNLINVHHAKYGDKAREELVPQLNAFGKTTLYDGRTGEPFR 989

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
             P+TVGY Y+LKL HMV DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW + AYG
Sbjct: 990  EPITVGYPYILKLGHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALYAYG 1049

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            A+ VLQE+LT+KSDD  GR + YE+IV G +      PESF VL+KEM++LGL++++   
Sbjct: 1050 ASNVLQEILTVKSDDTAGRVKAYEAIVKGENIPPAEVPESFKVLLKEMKSLGLNVEMVGE 1109

Query: 1367 RTKNSAKMEEIPDFNKCE 1384
                     E  +    E
Sbjct: 1110 DKATIDLDAEYDEKPNAE 1127



 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 329/738 (44%), Positives = 465/738 (63%), Gaps = 29/738 (3%)

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
           I +  R                         I+  E+V+ S    + G+  S +      
Sbjct: 98  IRFVNRETGEIKEQDVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFSAERDKTSN 157

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIY-IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             I    +     A      +  +I  +       + +   +    I +     +D + +
Sbjct: 158 KTIYGAKVIPSRGAWLEFETDKRDILSVRIDRKRKQPATLLLRALGIAETREEIIDVLGS 217

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           +  +  TL  D    R++AL+++Y+  RPG+  T   A ++   LFF+  +YDL+ VGR 
Sbjct: 218 SEMVLRTLDRDPATTREEALIELYKRFRPGEPPTLDSASTLLEGLFFNPQRYDLARVGRY 277

Query: 415 KMNMRLNLDTP---DDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGE 469
           K N +L  D      D   + ++DI+A ++ +V L  G+   T DDID+ GNRR+R+VGE
Sbjct: 278 KANKKLGFDPEGEGADSSTLTEQDIVATMRYVVALHEGEEGFTTDDIDHFGNRRIRTVGE 337

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ+R+GL RMER ++ER+S  + D + PQ L+N +P+V+A+ EFF SSQLSQ  +  
Sbjct: 338 LIQNQFRIGLSRMERVVRERMSMQEADEITPQSLVNIRPIVAAIKEFFGSSQLSQFMDQS 397

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N  + ITH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL ++
Sbjct: 398 NPAAGITHKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLATY 457

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN+YGFIETPYR+V DGKVT++VVY++A EEE   IAQAN   D++       V    
Sbjct: 458 ARVNSYGFIETPYRRVVDGKVTDEVVYMTADEEEKHTIAQANDYFDQETREFGRTVDGVF 517

Query: 650 ----------------AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                            GE   V  + +DF+D SP+Q+ S+A SLIPFLE+DD+NR LMG
Sbjct: 518 VPSTKVLCRTTDAKGVFGEPDEVDPQMVDFMDVSPRQMTSVATSLIPFLEHDDANRALMG 577

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL   AP+VGTG+E  +A  SG  ++A+  G+V+ VD   I+IR+ +GD D
Sbjct: 578 SNMQRQAVPLLNPHAPYVGTGIEHRIAVDSGEMLIAQNPGVVDYVDGSTIIIRTDDGDFD 637

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y + KFQRSNQ+ C+N +P+V+ GDEV   D++ADGPS D  +LALG+N+L+
Sbjct: 638 E-------YLIPKFQRSNQSGCINHKPIVRKGDEVHSGDVLADGPSCDHAELALGQNLLI 690

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+M W GYN+ED+++ISER+V+ED+ TS+HI E+E+ ARDTKLGPEEITR+IPN+SE+ +
Sbjct: 691 AYMTWEGYNYEDAIIISERVVAEDLLTSVHISEYEIDARDTKLGPEEITREIPNISEDMI 750

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++D  GII +GAEV PGD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP 
Sbjct: 751 SDLDADGIIRIGAEVFPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVPH 810

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G +V +  F+R   D
Sbjct: 811 GAGGRIVGINRFSRENGD 828



 Score =  340 bits (873), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 100/296 (33%), Positives = 151/296 (51%), Gaps = 30/296 (10%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G+ R R+ F K P+++D+P+LI +Q  S+  F+          NEG+  AF SV PI +
Sbjct: 10  TGVYRERRSFAKIPDVMDVPNLIAIQTESFKWFM----------NEGITDAFNSVCPIES 59

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            S    +EF  +EF  PK  VD+C  +D +Y  PL   +R +          +   +IKE
Sbjct: 60  SSKDMYVEFGDHEFGEPKQSVDECKEKDASYQAPLTAQIRFV---------NRETGEIKE 110

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++MGD PLMT  GTF+I G +R+VVSQL RSPG++F  ++ +   S K +Y  ++IP 
Sbjct: 111 QDVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFSAERDKT--SNKTIYGAKVIPS 168

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFW 245
           +G W++ E D +DI+ VRIDR+RK P T  L ALG+    EEI+       +  +  D  
Sbjct: 169 RGAWLEFETDKRDILSVRIDRKRKQPATLLLRALGIAETREEIIDVLGSSEMVLRTLDRD 228

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                   L+              GE   ++S   L  GL  + +   +  +G   
Sbjct: 229 PATTREEALI------ELYKRFRPGEPPTLDSASTLLEGLFFNPQRYDLARVGRYK 278


>gi|46360946|gb|AAS89206.1| RpoB [Corynebacterium auriscanis]
          Length = 1115

 Score =  500 bits (1288), Expect = e-139,   Method: Composition-based stats.
 Identities = 187/492 (38%), Positives = 250/492 (50%), Gaps = 57/492 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G +L        E  M   + LL A    +  +  D  +     V   V+
Sbjct: 668  LVNEGDRVEAGQVLADGPGT-AEGEMALGKNLLVAFMPWEGHNYEDAIILNQRMVEEDVL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E     I  +  D     DE+ I+      R  +IL G+  
Sbjct: 727  TSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIIRIGADVRDGDILVGKVT 786

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 787  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 829

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+ PGV  +V+V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL DG
Sbjct: 830  RVFSREDDDDLAPGVNEMVRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPAEDMPFLPDG 889

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LN  GVP RMN+GQ+ E HLGW     G K+ +   D K    +  L S L  V
Sbjct: 890  TPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWKVDTDSQDPKIQKMLETLPSELYDV 948

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                                           +TPVFDGA    ++ +LR +  +  G   
Sbjct: 949  PSDSLT-------------------------ATPVFDGASNAELSGLLRSSRPNRDGIRL 983

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 984  VDDFGKAQLMDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1043

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF
Sbjct: 1044 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESF 1103

Query: 1348 NVLVKEMQALGL 1359
             VL+KE+Q+L L
Sbjct: 1104 KVLLKELQSLCL 1115



 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 333/661 (50%), Positives = 458/661 (69%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +      ++I     D    +  + +TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEI----TDRFGFSEIMMSTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEML 471
             +    + +EDI+  I+ LV L  G+ T+            DDID+ GNRR+R+VGE++
Sbjct: 305 DNEGNMTLTEEDILTTIEYLVRLHAGEKTMTSPEGVEIPIGTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFLDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYR+V DG++T++V Y +A EE+   IAQAN+  DE+  FTEE +  R   
Sbjct: 485 VNPFGFIETPYRRVIDGQITDEVHYFTADEEDRHVIAQANTPFDENHRFTEETIEVRLRG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL++EAPF
Sbjct: 545 GDVEVVPVAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+A +AG+VE V A  I +   EG  D          L KF+R+
Sbjct: 605 VGTGMELRAAYDAGDMIIAPKAGVVEYVSADYITVMDDEGIRDTFM-------LRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ+PLV  GD V    ++ADGP T  G++ALG+N+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTSYNQKPLVNEGDRVEAGQVLADGPGTAEGEMALGKNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +RMV EDV TSIHIEE E+ ARDTKLGPEEITRDIPNV E+ L ++DE GII +GA+V  
Sbjct: 718 QRMVEEDVLTSIHIEEHEIDARDTKLGPEEITRDIPNVGEDVLADLDERGIIRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 82/299 (27%), Positives = 141/299 (47%), Gaps = 24/299 (8%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K    I++P L+++Q+ S+   +               D R   GL+   + + 
Sbjct: 15  QRYSFAKIDSPIEVPGLLDLQRESFAWLIGSPEWRARAQAEAGEDVRITSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +S    L      F+  K  +D+   +D+ YA PL +T                  
Sbjct: 75  PIEDYSENMSLTLSEPRFEDVKSTIDEAKDKDINYAAPLYVTAEFT---------NAMSG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD      + + + L+  +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDASID--ASTERPLHGVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ ++EI   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTQEITDRFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI 298
            D       A   +   +        D+ + ++E+         L K  + K  + LG+
Sbjct: 244 KDGVDNTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGL 302


>gi|46360948|gb|AAS89207.1| RpoB [Corynebacterium callunae]
          Length = 1113

 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 190/575 (33%), Positives = 269/575 (46%), Gaps = 62/575 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ A  P+ G   E         +V   V   +     +++      G 
Sbjct: 586  MGANMQKQAVPLVRAEAPFVGTGMEQRAAYDAGDLVITPVAGVVENVSADIITIMADDGK 645

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             E              + ++  ++ +G  V  G ++           M+    LL A   
Sbjct: 646  RETYMLRKFQRTNQGTSYNQKPLVNLGDRVEAGQVIADGPGTFN-GEMSLGRNLLVAFMP 704

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER------EQIELLARDKD 972
             +  +  D  +   + V   ++       H ID  +  +  E          E + +D  
Sbjct: 705  WEGHNYEDAIILNQNIVEQDILTSVHIEEHEIDARDTKLGAEEITRDIPNVSEEVLKDL- 763

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R              
Sbjct: 764  DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGET 823

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              V  ++                     +  DD+ PGV  +++++VA KR IQ GDK+AG
Sbjct: 824  GKVIGVRH-----------------FSREDDDDLAPGVNEMIRIYVAQKRKIQDGDKLAG 866

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+V +ILP EDMPFL DGTPVDI+LN  GVP RMN+GQ+ ETHLGW     G  +
Sbjct: 867  RHGNKGVVGKILPQEDMPFLPDGTPVDIILNTHGVPRRMNIGQVLETHLGWLASA-GWSV 925

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                 D K    I  L   L +V                          +G   +TPVFD
Sbjct: 926  D--PEDPKNAELIKTLPKELYEV-------------------------PAGSLTATPVFD 958

Query: 1213 GADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            GA  E +  +L  +  +  G        ++ L DG +GEP+  PV++GY+YMLKL+H+V 
Sbjct: 959  GASNEELVGLLANSRPNRDGDVMVNKDGKATLMDGRSGEPYPYPVSIGYMYMLKLHHLVD 1018

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVG
Sbjct: 1019 EKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVG 1078

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            R +VYE+IV G +  + G PESF VL+KE+Q+L L
Sbjct: 1079 RVKVYEAIVKGENIPDPGIPESFKVLLKELQSLCL 1113



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 321/617 (52%), Positives = 445/617 (72%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
           + VGR K+N +L L    D +  + +EDI   I+ LV L  G+               DD
Sbjct: 289 ARVGRYKINRKLGLGGDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPRGEEIPVETDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN +GFIETPYR++ +GK+T+ + YL+A EE+   +AQAN++ D
Sbjct: 469 EGPNIGLIGSLASYARVNPFGFIETPYRRIVEGKLTDQIDYLTADEEDRYVVAQANTNYD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           EDG+ T+E V  R   G+  +V RE++D++D SP+Q+VS+  ++IPFLE+DD+NR LMG 
Sbjct: 529 EDGNITDETVTVRLKDGDIAMVNREEVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPL++AEAPFVGTGME   A  +G  ++   AG+VE V A  I I + +G  + 
Sbjct: 589 NMQKQAVPLVRAEAPFVGTGMEQRAAYDAGDLVITPVAGVVENVSADIITIMADDGKRE- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KFQR+NQ T  NQ+PLV +GD V    +IADGP T  G+++LGRN+LVA
Sbjct: 648 ------TYMLRKFQRTNQGTSYNQKPLVNLGDRVEAGQVIADGPGTFNGEMSLGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++ +V +D+ TS+HIEE E+ ARDTKLG EEITRDIPNVSEE LK
Sbjct: 702 FMPWEGHNYEDAIILNQNIVEQDILTSVHIEEHEIDARDTKLGAEEITRDIPNVSEEVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 762 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIGVRHFSREDDD 838



 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 168/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVF 63
            R  F K    I++P L+++Q  SY   +        +  E         GL+   + + 
Sbjct: 15  QRYSFAKVSAPIEVPGLLDLQLDSYSWLIGTPEWRARQKEEFGEGARVTSGLENILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+   +D+ YA PL +T   +           +  
Sbjct: 75  PIQDYSGNMSLSLSEPRFEDVKNTIDEAKEKDINYAAPLYVTAEFV---------NNTTG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + + L+A +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDQTIDK--STERPLHAVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDSVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L +  + K  + LG+ 
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKINRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E ++    GE        ++   ++   +  +R
Sbjct: 304 GDHDGLMTLTEEDIATTIEYLVRLHAGERVMTSPRGEEI-----PVETDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|281486601|gb|ADA70803.1| DNA-directed RNA polymerase subunit B [Acinetobacter sp. MO]
          Length = 270

 Score =  500 bits (1287), Expect = e-139,   Method: Composition-based stats.
 Identities = 169/273 (61%), Positives = 211/273 (77%), Gaps = 4/273 (1%)

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 1    NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKM 60

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA
Sbjct: 61   L---KQQREIAELREFLDKIYNKVGGEQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGA 117

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V DK++ARSTGS
Sbjct: 118  EEGQIKELLELAELPRSGQTVLYDGRTGEKFDRPVTVGYMYMLKLNHLVDDKMHARSTGS 177

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV 
Sbjct: 178  YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVD 237

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            GN   + G PESFNVL KE+++LG++I+L+N  
Sbjct: 238  GNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 270


>gi|256826828|ref|YP_003150787.1| DNA-directed RNA polymerase subunit beta [Cryptobacterium curtum DSM
            15641]
 gi|256582971|gb|ACU94105.1| DNA-directed RNA polymerase subunit beta [Cryptobacterium curtum DSM
            15641]
          Length = 1178

 Score =  499 bits (1286), Expect = e-138,   Method: Composition-based stats.
 Identities = 198/615 (32%), Positives = 289/615 (46%), Gaps = 81/615 (13%)

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMAR 852
            A               +L    P+ G   E  + +   E +++++     +++   +   
Sbjct: 569  AHRALMGSNMQRQAVPLLRPHAPFVGTGIEHRIAVDSGEILIAQNSGLVDYVDGEVINIL 628

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                  +E        S +G   ++   ++  G  V  GD+L    +    + ++  + L
Sbjct: 629  TDDGEYDEYLIPKFQRSNQGY-CVNHKPLVRKGDRVEVGDVLADGQS-CDHAELSLGQNL 686

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDK 971
            L A    +  +  D  +     V+  ++     + +  + + R   +  E+I   +    
Sbjct: 687  LVAYMPWEGYNYEDAIVISERVVAEDLLTSIHISEY--EADARDTKLGPEEITREIPNIS 744

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            +D    LD +   R+     G     G     K T      ++   R     F  +  +V
Sbjct: 745  EDMIADLDGDGIIRI-----GAEVNPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREV 799

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +          +             GD++ PGV   V+V+VA KR IQ GDKM+
Sbjct: 800  RDTSLKVPHGAGGRVIGIH------RFSRASGDELAPGVNEQVRVYVAQKRKIQQGDKMS 853

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VSR+LP EDMP+L DGTPVDI+LNPLGVPSRMNVGQ+ E HLGWA       
Sbjct: 854  GRHGNKGVVSRVLPVEDMPYLADGTPVDIMLNPLGVPSRMNVGQLLECHLGWAAK----- 908

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                + DD     A   +  + VSTPVF
Sbjct: 909  ----------------------------------WGWSDDENSDEA--VEGPIYVSTPVF 932

Query: 1212 DGADEEAINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPV 1249
            D A EE I  ++  ++                      L+E G++ LYDG TGEPF  P+
Sbjct: 933  DSATEEEIRDVIEKSNRNLVNLNREKYGDAMREEFVPQLNEFGKTTLYDGRTGEPFREPI 992

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGY YMLKL HMV DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW + AYGA+ 
Sbjct: 993  TVGYPYMLKLGHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALYAYGASN 1052

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            VLQE+LT+KSDD VGR + YE+IV G +  +   PESF VL+KEM++L L+++LE    +
Sbjct: 1053 VLQEILTVKSDDTVGRVKTYEAIVKGENMPDAEVPESFKVLIKEMRSLCLNVELEGHNRE 1112

Query: 1370 NSAKMEEIPDFNKCE 1384
                +E  P+    +
Sbjct: 1113 VLDVIESHPERTNDD 1127



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 319/739 (43%), Positives = 464/739 (62%), Gaps = 27/739 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           + ++ ++                           ++  E+V+ S    + G+    +   
Sbjct: 95  FAEVRFTNLETGEIKEQDVFMGDFPLMTPRGTFIVNGTERVVVSQLVRSPGVYFGAERDK 154

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIY-IEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                I +  +     A      +  +I  +       + +   +    + +     +++
Sbjct: 155 TSNKTIYNAKVIPSRGAWLEFETDKRDILSVRIDRKRKQPATLLLRALGLAETREEIIEA 214

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + ++  +  T+  D    R ++L+++Y+  RPG+  T   A ++ + LFF+  +Y+L+ V
Sbjct: 215 LGDSEMVLRTIDRDPATTRDESLIELYKRFRPGEPPTIDSARTLLDGLFFNPQRYNLAKV 274

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGE 469
           GR K+N +L  D   D   +  +DIIA ++ +V L NG+     DDID+ GNRR+R+VGE
Sbjct: 275 GRYKINKKLGFDAEGDSSTLTNDDIIATMRYIVALHNGEEGYVTDDIDHFGNRRIRTVGE 334

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ+R+GL RMER ++ER+S  + D + PQ LIN +P+V+++ EFF SSQLSQ  +  
Sbjct: 335 LIQNQFRIGLSRMERVVRERMSMQEPDEITPQSLINIRPIVASIKEFFGSSQLSQFMDQA 394

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N ++ +TH RRLSALG GG++R RAG E+RDVH +HY R+CP ET EG NIGL+ SL ++
Sbjct: 395 NPVAGVTHKRRLSALGPGGLSRERAGFEVRDVHNSHYSRMCPIETPEGPNIGLIGSLATY 454

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS---------- 639
           ARVN YGFIE PYR+V +GKVTNDV YL+A EEE+  IAQAN   D              
Sbjct: 455 ARVNNYGFIEAPYRRVVEGKVTNDVDYLTADEEEHHTIAQANEPYDTKTGILGTTDESGT 514

Query: 640 -FTEELVFCRCAG------EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
               E +  R         +   V   ++D++D SP+Q+VS+A SLIPFLE+DD++R LM
Sbjct: 515 FHPTERLLARTRNSHGEFGDPAEVSVSQVDYMDISPRQMVSVATSLIPFLEHDDAHRALM 574

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPLL+  APFVGTG+E  +A  SG  ++A+ +G+V+ VD   I I + +G+ 
Sbjct: 575 GSNMQRQAVPLLRPHAPFVGTGIEHRIAVDSGEILIAQNSGLVDYVDGEVINILTDDGEY 634

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           D        Y + KFQRSNQ  CVN +PLV+ GD V   D++ADG S D  +L+LG+N+L
Sbjct: 635 DE-------YLIPKFQRSNQGYCVNHKPLVRKGDRVEVGDVLADGQSCDHAELSLGQNLL 687

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA+MPW GYN+ED+++ISER+V+ED+ TSIHI E+E  ARDTKLGPEEITR+IPN+SE+ 
Sbjct: 688 VAYMPWEGYNYEDAIVISERVVAEDLLTSIHISEYEADARDTKLGPEEITREIPNISEDM 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           + ++D  GII +GAEVNPGD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 748 IADLDGDGIIRIGAEVNPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVP 807

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G  G V+ +  F+R   D
Sbjct: 808 HGAGGRVIGIHRFSRASGD 826



 Score =  337 bits (865), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 107/373 (28%), Positives = 167/373 (44%), Gaps = 40/373 (10%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ F K P +IDIP+LI +Q  S+D F            EGL  AF+ + PI + +  
Sbjct: 14  RSRRSFAKIPPVIDIPNLIAIQTESFDWF----------KGEGLDQAFQDICPIESNTKN 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +E   +EF  PK+ VD+C  +DLTY  PL   +R                +IKEQ ++
Sbjct: 64  MRVEIGKHEFGDPKYPVDECKVKDLTYQAPLFAEVRFT---------NLETGEIKEQDVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTF++ G +R+VVSQL RSPG++F  ++ +   S K +Y  ++IP +G W
Sbjct: 115 MGDFPLMTPRGTFIVNGTERVVVSQLVRSPGVYFGAERDKT--SNKTIYNAKVIPSRGAW 172

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPL 249
           ++ E D +DI+ VRIDR+RK P T  L ALG+    EEI+       +  +  D      
Sbjct: 173 LEFETDKRDILSVRIDRKRKQPATLLLRALGLAETREEIIEALGDSEMVLRTIDRDPATT 232

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLY 307
               L+              GE   I+S + L  GL  + +   +  +G    +   G  
Sbjct: 233 RDESLI------ELYKRFRPGEPPTIDSARTLLDGLFFNPQRYNLAKVGRYKINKKLGFD 286

Query: 308 VAEDIVNGETGEIYIEAGDV---------IDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
              D       +I      +              ++   +  IR +  L  +        
Sbjct: 287 AEGDSSTLTNDDIIATMRYIVALHNGEEGYVTDDIDHFGNRRIRTVGELIQNQFRIGLSR 346

Query: 359 RNTLVTDKNKDRK 371
              +V ++   ++
Sbjct: 347 MERVVRERMSMQE 359


>gi|46360950|gb|AAS89208.1| RpoB [Corynebacterium camporealensis]
          Length = 1113

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/596 (31%), Positives = 273/596 (45%), Gaps = 60/596 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         +V  
Sbjct: 564  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLVIT 623

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 624  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQGTNYNQTPLVSIGDRVEAGQVLAD 683

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 684  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTK 742

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 743  LGPEEITREIPNVSEDVLSDLDERGIVRIGADVRPGDILVGKVTPKGETELTPEERLLRA 802

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                 E      +     +           +  DD+ PGV 
Sbjct: 803  IFGEKAR-----------------EVRDTSMKVPHGEVGKVIGVARFSREEDDDLAPGVN 845

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RM
Sbjct: 846  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRM 905

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+   ++D      +  L   L  V                
Sbjct: 906  NIGQVLEVHLGWLAHA-GWKVD--VDDPANEELLKTLPEELYDVPADSLT---------- 952

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GE
Sbjct: 953  ---------------ATPVFDGASNEEVGRLLASSRPNRDGDVLVDGDGKAKLFDGRSGE 997

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 998  PYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1057

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE+Q+L L
Sbjct: 1058 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKELQSLCL 1113



 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 325/662 (49%), Positives = 449/662 (67%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G ++  D+   +T G              L+ +  SE +       +    +  + +TL 
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEK-----IRERFGFSELMMSTLE 243

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
           +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L 
Sbjct: 244 SDGVSNTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLG 303

Query: 424 TP-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEM 470
              D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE+
Sbjct: 304 GDHDGLMTLTEEDIAVTLEYLVRLHVGEREMQAPNGETISINTDDIDHFGNRRLRTVGEL 363

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H N
Sbjct: 364 IQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNN 423

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 424 SLSGLTHKRRLSALGPGGLTRDRAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYA 483

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN++GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D +G+   + +  R  
Sbjct: 484 RVNSFGFIETPYRKVVDGKVTDQVEYLTADEEDRFAIAQAEVEQDAEGNIIGDRIEVRLK 543

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP
Sbjct: 544 DGDIGVTEASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAP 603

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FVGTGME   A  +G  ++  +AG+VE V A  I I   EG  D        Y L KF+R
Sbjct: 604 FVGTGMEQRAAYDAGDLVITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFER 656

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED++++
Sbjct: 657 TNQGTNYNQTPLVSIGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIIL 716

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V ED+ TS+HIEE E+ ARDTKLGPEEITR+IPNVSE+ L ++DE GI+ +GA+V 
Sbjct: 717 NQRIVEEDILTSVHIEEHEIDARDTKLGPEEITREIPNVSEDVLSDLDERGIVRIGADVR 776

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           PGDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G  G V+ V  F+R  
Sbjct: 777 PGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGEVGKVIGVARFSREE 836

Query: 950 ID 951
            D
Sbjct: 837 DD 838



 Score =  302 bits (774), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 97/388 (25%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +               D R   GL+   + + P
Sbjct: 16  RYSFAKISEPIALPGLLDLQLDSFSWLVGTPEWREKQQAERGEDARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          K+
Sbjct: 76  IQDYSGNMSLSLSEPRFEPTKNTVDECKEKDINYSAPLYVTAEFINND---------TKE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEKIRERFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVSNTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE        I+   ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMQAPNGETI-----SINTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|46191128|ref|ZP_00120579.2| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
            [Bifidobacterium longum DJO10A]
 gi|189439828|ref|YP_001954909.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            DJO10A]
 gi|226699371|sp|B3DTE2|RPOB_BIFLD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|189428263|gb|ACD98411.1| DNA-directed RNA polymerase beta subunit [Bifidobacterium longum
            DJO10A]
          Length = 1187

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 183/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  I+  G  V  G ++      +    +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQN-GDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNLEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 306/617 (49%), Positives = 434/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +    + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLGTQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVQKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP+V  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQNGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGNERWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLGTQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|239622389|ref|ZP_04665420.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. infantis CCUG 52486]
 gi|239514386|gb|EEQ54253.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. infantis CCUG 52486]
          Length = 1187

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 183/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  I+  G  V  G ++      +    +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQN-GDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNLEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 306/617 (49%), Positives = 435/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVQKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP+V  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQNGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 142/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +  +                     GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGSDRWKKRVEEDEANGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|46361006|gb|AAS89236.1| RpoB [Corynebacterium kroppenstedtii DSM 44385]
          Length = 1116

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 181/492 (36%), Positives = 248/492 (50%), Gaps = 57/492 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  G  L      +    M     LL A    +  +  D  +     V   V+
Sbjct: 669  LVEAGDRIEEGQALADGPGTEN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRIVEEDVL 727

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKD-----DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E    ++    +D     DE+ I+      R  +IL G+  
Sbjct: 728  TSIHIEEHEIDARDTKLGPEEITRDIPNASEDILADLDERGIVRIGADVRDGDILVGKVT 787

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 788  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIGV 830

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+ PGV ++V+V+VA KR IQ GDK++GRHGNKG+V +ILP EDMPFL DG
Sbjct: 831  RVFSREDDDDLAPGVNQMVRVYVAQKRKIQDGDKLSGRHGNKGVVGKILPAEDMPFLPDG 890

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQ+ E HLG      G K+     D      +  L   L  V
Sbjct: 891  TPVDVILNTHGVPRRMNIGQVLELHLGMLAKS-GWKVDPESQDPAIKAMLETLPEDLYDV 949

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                                          V+TPVFDG   E ++ ++R +  +  G   
Sbjct: 950  PADSR-------------------------VATPVFDGTTNEELSGLMRSSRPNRDGDQM 984

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 +S L DG TGEPF +P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 985  VNEFGKSTLIDGRTGEPFQQPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1044

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF
Sbjct: 1045 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESF 1104

Query: 1348 NVLVKEMQALGL 1359
             VL+KE+Q+L L
Sbjct: 1105 KVLLKELQSLCL 1116



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 328/662 (49%), Positives = 456/662 (68%), Gaps = 26/662 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  DI   +T  + I+         L +      +DI     D    +  + +TL  
Sbjct: 189 GAWLEFDIDKRDTVGVRIDRKRRQPVTVLLKALGLSTQDI----TDRFGFSELMMSTLEH 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++ +  FF+  +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLDNSFFNPKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 PDD--VRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
                   + +EDI+  I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 305 GSTTGEHTLTEEDILTTIEYLVRLHAGERTMESPDGTELMIATDDIDHFGNRRLRTVGEL 364

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 365 VQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 424

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+++RDVH +HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 425 SLSGLTHKRRLSALGPGGLSRERAGLDVRDVHASHYGRMCPIETPEGPNIGLIGSLASYA 484

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPYR+V +G+ T+ V YL+A EE+   +AQAN+ +D +G F E+ V  R  
Sbjct: 485 RVNPFGFIETPYRRVENGQATDVVDYLTADEEDRHIVAQANTKMDSEGRFVEDTVEVRMK 544

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLL+ EAP
Sbjct: 545 GGNVEVVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLRNEAP 604

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           FVGTGME   A  +G  ++A+R+G+VE V A  I     +G  D        + L KF+R
Sbjct: 605 FVGTGMELRAAHDAGDVVIARRSGVVETVCADFITTLGDDGQRD-------TFLLRKFER 657

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQ TC NQ+PLV+ GD +     +ADGP T+ G++ALGRN+LVAFMPW G+N+ED++++
Sbjct: 658 TNQGTCYNQKPLVEAGDRIEEGQALADGPGTENGEMALGRNLLVAFMPWEGHNYEDAIIL 717

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V EDV TSIHIEE E+ ARDTKLGPEEITRDIPN SE+ L ++DE GI+ +GA+V 
Sbjct: 718 NQRIVEEDVLTSIHIEEHEIDARDTKLGPEEITRDIPNASEDILADLDERGIVRIGADVR 777

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R  
Sbjct: 778 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSRED 837

Query: 950 ID 951
            D
Sbjct: 838 DD 839



 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 139/298 (46%), Gaps = 29/298 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I++P L+++Q+ S+   +                 R   GL+   + + P
Sbjct: 16  RYSFAKIKEPIEVPGLLDLQRDSFAWLIGAPEWRAKKQAESEEGARITSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      FD  K  +D+   +D+ Y+ PL +T                  +
Sbjct: 76  IEDYSGNMSLTLSEPRFDDVKNTIDEAKDKDINYSAPLYVTAEFT---------NAMSGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIINGTERVIVSQLVRSPGVYFDESIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +++I   F    +   +   
Sbjct: 185 IPSRGAWLEFDIDKRDTVGVRIDRKRRQPVTVLLKALGLSTQDITDRFGFSELMMSTLEH 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
           D       A   +   +        D+ + ++++          + K   +  +G   
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLDNS-------FFNPKRYDLAKVGRYK 295


>gi|213692905|ref|YP_002323491.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium longum
            subsp. infantis ATCC 15697]
 gi|254765273|sp|B7GUG7|RPOB_BIFLI RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|213524366|gb|ACJ53113.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium longum
            subsp. infantis ATCC 15697]
 gi|320459083|dbj|BAJ69704.1| DNA-directed RNA polymerase beta subunit [Bifidobacterium longum
            subsp. infantis ATCC 15697]
          Length = 1187

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 186/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  II  G  V  G +L        +  +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGP-AIQKGDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           V   AE+ +   PV+
Sbjct: 943  SGWDISLDPNMEAEWKKL---------------------------VPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 305/617 (49%), Positives = 434/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F  +    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVSKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP++  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGPAIQKGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 142/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +  +                     GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGSDRWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|296453630|ref|YP_003660773.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. longum JDM301]
 gi|296183061|gb|ADG99942.1| DNA-directed RNA polymerase, beta subunit [Bifidobacterium longum
            subsp. longum JDM301]
          Length = 1187

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 185/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  II  G  V  G +L        +  +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGP-AIQKGDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNMEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 305/617 (49%), Positives = 434/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F  +    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVSKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP++  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGPAIQKGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 142/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +  +                     GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGSDRWKKRVEEDEANGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|23465772|ref|NP_696375.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            NCC2705]
 gi|227546386|ref|ZP_03976435.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. infantis ATCC 55813]
 gi|312133233|ref|YP_004000572.1| rpob [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482581|ref|ZP_07941596.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
 gi|41017742|sp|Q8G514|RPOB_BIFLO RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|23326461|gb|AAN25011.1| RpoB [Bifidobacterium longum NCC2705]
 gi|227213367|gb|EEI81239.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. infantis ATCC 55813]
 gi|311772435|gb|ADQ01923.1| RpoB [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916003|gb|EFV37410.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
          Length = 1187

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 183/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  I+  G  V  G ++      +    +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQN-GDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNLEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 306/617 (49%), Positives = 435/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVQKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP+V  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQNGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGNERWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|46360956|gb|AAS89211.1| RpoB [Corynebacterium argentoratense]
          Length = 1116

 Score =  499 bits (1285), Expect = e-138,   Method: Composition-based stats.
 Identities = 181/493 (36%), Positives = 247/493 (50%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M     LL A    +  +  D  +     V   ++
Sbjct: 671  LVDMGQRVEAGQVIADGPGTDN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 730  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIS 831

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 832  VRRFSREEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPAEDMPFLPD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I +   + K   +I         
Sbjct: 892  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWNIDTNNPENKELMEI--------- 941

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
                              +        +G   +TPVFDGA    +  +L  +  +  G  
Sbjct: 942  ------------------LPEELYDVPAGSLTATPVFDGASNAELAGLLANSRPNRDGDV 983

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 984  MVDGDGKAQLIDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1044 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1103

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1104 FKVLLKELQSLCL 1116



 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 325/693 (46%), Positives = 463/693 (66%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + +      G ++  D+   +T  + +       +  
Sbjct: 162 LVRSPGVYFDRTIDKSTERPLHSVKVIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 217

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +         I   +    +  +  TL  D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 218 TVLLKALGWTTEQI--TERFGFSEIMMTTLENDGVANTDEALLEIYRKQRPGEQPTRDLA 275

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K+N +L L    + +  + +EDI   ++ LV L  G+ 
Sbjct: 276 QSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGGDHEGLMTLTEEDIATTLEYLVRLHAGET 335

Query: 452 TI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
            +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 336 QMTSPNGTVIPVETDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 395

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQ+SQ  +  NSLS +T+ RRLSALG GG++R RAG+E+R
Sbjct: 396 PTSLINVRPVSAAIREFFGTSQMSQFMDQNNSLSGLTNKRRLSALGPGGLSRERAGIEVR 455

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN++GFIETPYRK+ DG +T++V YL+A
Sbjct: 456 DVHPSHYGRMCPIETPEGPNIGLIGSLSCYARVNSFGFIETPYRKIVDGHITDEVHYLTA 515

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   +AQAN+  D+DG  TEE +  R   G   +V  E I+++D SP+Q+VS+A ++
Sbjct: 516 DEEDRYVVAQANTPHDKDGKITEERIVVRTKGGNIEVVGPEAIEYMDVSPRQMVSVATAM 575

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  +G  I+  + G+VE V
Sbjct: 576 IPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAYDAGDMIINAKGGVVENV 635

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I + + +G  D        Y L KFQR+NQ TC NQ+PLV +G  V    +IADGP
Sbjct: 636 CADYITVMADDGTRD-------TYMLRKFQRTNQGTCYNQKPLVDMGQRVEAGQVIADGP 688

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            TD G++ALGRN+LVAFMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG 
Sbjct: 689 GTDNGEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDILTSIHIEEHEIDARDTKLGA 748

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ LK++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 749 EEITREIPNVSEDVLKDLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFG 808

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G +G V+ VR F+R   D
Sbjct: 809 EKAREVRDTSMKVPHGETGKVISVRRFSREEDD 841



 Score =  298 bits (763), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 104/490 (21%), Positives = 197/490 (40%), Gaps = 53/490 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            I    R   GL+   + + 
Sbjct: 18  ERYSFAKITEPIEVPGLLDLQLDSFAWLVGTPEWRERTQAEIGEGNRVTSGLEDILEELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 78  PIQDYSGTMSLSLSEPRFEEVKNSIDECKDKDINYSAPLYVTAEFI---------NNETQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 129 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDRTIDK--STERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMTTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 247 NDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLG 306

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G +       ++   ++   +  +R
Sbjct: 307 GDHEGLMTLTEEDIATTLEYLVRLHAGETQMTSPNGTVI-----PVETDDIDHFGNRRLR 361

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            +  L  + V         +V ++   +    +    ++    V   S A   F      
Sbjct: 362 TVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLIN---VRPVSAAIREFFGTSQM 418

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           S   D +       N R    +      + +E     ++ +     G+  +  I+     
Sbjct: 419 SQFMDQNNSLSGLTNKR--RLSALGPGGLSRERAGIEVRDVHPSHYGR--MCPIETPEGP 474

Query: 463 RVRSVGEMLK 472
            +  +G +  
Sbjct: 475 NIGLIGSLSC 484


>gi|322688610|ref|YP_004208344.1| DNA-directed RNA polymerase subunit beta [Bifidobacterium longum
            subsp. infantis 157F]
 gi|320459946|dbj|BAJ70566.1| DNA-directed RNA polymerase beta subunit [Bifidobacterium longum
            subsp. infantis 157F]
          Length = 1187

 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 186/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  II  G  V  G +L        +  +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGP-AIQKGDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           V   AE+ +   PV+
Sbjct: 943  SGWDISLDPNMEAEWKKL---------------------------VPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 305/617 (49%), Positives = 434/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F  +    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVSKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP++  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIIHDGERVEAGSVLADGPAIQKGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGNERWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|257790477|ref|YP_003181083.1| DNA-directed RNA polymerase, beta subunit [Eggerthella lenta DSM
           2243]
 gi|317490023|ref|ZP_07948514.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325829932|ref|ZP_08163390.1| DNA-directed RNA polymerase, beta subunit [Eggerthella sp. HGA1]
 gi|257474374|gb|ACV54694.1| DNA-directed RNA polymerase, beta subunit [Eggerthella lenta DSM
           2243]
 gi|316910864|gb|EFV32482.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325488099|gb|EGC90536.1| DNA-directed RNA polymerase, beta subunit [Eggerthella sp. HGA1]
          Length = 1178

 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 315/622 (50%), Positives = 439/622 (70%), Gaps = 26/622 (4%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           ++ + N+  +  TL  D    ++++L+++Y+  RPG+  T   A ++   LFF+  +YDL
Sbjct: 212 IELLGNDEMVLRTLDRDPATTKEESLIELYKRFRPGEPPTIDSARTLLEGLFFNPQRYDL 271

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRS 466
           + VGR K+N +L  D   +   +  +DI+  ++ +V L  G   +  DDID+ GNRR+R+
Sbjct: 272 AKVGRYKINKKLGFDPDYEASTLTDDDIVRTMQYIVALHAGDEGVQTDDIDHFGNRRIRT 331

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+++NQ+R+GL RMER ++ER+S  + D + PQ L+N +P+V+A+ EFF SSQLSQ  
Sbjct: 332 VGELIQNQFRIGLSRMERVVRERMSMQEPDEITPQSLVNIRPIVAAIKEFFGSSQLSQFM 391

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N  + ITH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL
Sbjct: 392 DQTNPAAGITHKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSL 451

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL---------DED 637
            ++AR+N YGFIETPYR+V DGKVT++V YL+A EEEN  IAQAN             +D
Sbjct: 452 ATYARINPYGFIETPYRRVVDGKVTDEVDYLTADEEENYTIAQANDLFDPETRKFGTFDD 511

Query: 638 GSFTEELVFCRCAG--------EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                E V   C          E   V  E ++++D SP+Q+VS+A SLIPFLE+DD+NR
Sbjct: 512 QGVFHEAVRVLCRTKDAAGVFGEPDEVAPELVNYMDVSPRQMVSVATSLIPFLEHDDANR 571

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPLL+ +AP VGTG+E  +A  SG  +VA+  G+V+ VD   I++ + +
Sbjct: 572 ALMGSNMQRQAVPLLRPDAPLVGTGIEHRIAVDSGEILVAQNPGVVDYVDGQTIIVLNND 631

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           G+ D        Y + KFQRSNQ+ C+N RP+V+ GDEV+  D++ADGPS D G+LALG+
Sbjct: 632 GEYDE-------YLVPKFQRSNQSGCINHRPIVRKGDEVQAGDVLADGPSCDGGELALGQ 684

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N++VA+MPW GYN+ED++++SER+V+ED+ TSIHI E+EV ARDTKLGPEEITR+IPN+S
Sbjct: 685 NLMVAYMPWEGYNYEDAIIVSERVVAEDLLTSIHISEYEVDARDTKLGPEEITREIPNIS 744

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           ++ + ++D  GII VGAEV PGD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL
Sbjct: 745 DDMISDLDADGIIRVGAEVFPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSL 804

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           +VP G  G V+ +  F+R   D
Sbjct: 805 KVPHGSGGRVIGMSRFSRDAGD 826



 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 189/610 (30%), Positives = 286/610 (46%), Gaps = 81/610 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E  + +   E +V+++     +++   ++  +    
Sbjct: 574  MGSNMQRQAVPLLRPDAPLVGTGIEHRIAVDSGEILVAQNPGVVDYVDGQTIIVLNNDGE 633

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +E        S +    I+   I+  G EV  GD+L    +  G   +   + L+ A  
Sbjct: 634  YDEYLVPKFQRSNQS-GCINHRPIVRKGDEVQAGDVLADGPSCDG-GELALGQNLMVAYM 691

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQV 976
              +  +  D  +     V+  ++     + +  + + R   +  E+I   +    DD   
Sbjct: 692  PWEGYNYEDAIIVSERVVAEDLLTSIHISEY--EVDARDTKLGPEEITREIPNISDDMIS 749

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+   +   + + G    K  T L+++               +  +  R+  
Sbjct: 750  DLDADGIIRVGAEVFPGDVLVGKVTPKGETELTAEE------RLLRAIFGEKAREVRDTS 803

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                     + I   RF         GD++ PGV  +V+++VA KR +Q GDK++GRHGN
Sbjct: 804  LKVPHGSGGRVIGMSRFSR-----DAGDELAPGVNELVRIYVAQKRKVQQGDKLSGRHGN 858

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++SR+LP EDMP+L DGTP+D++LNPLGVPSRMNVGQ+ E HLGWA            
Sbjct: 859  KGVISRVLPVEDMPYLADGTPIDVILNPLGVPSRMNVGQLLENHLGWAAK---------- 908

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                           +  D         +  + V+TPVFDGA E
Sbjct: 909  -------------------------------WGWDDAEETDAVVEGPMHVATPVFDGATE 937

Query: 1217 EAINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYI 1254
            + I+  +  A+                      L  +G++ LYDG TGE F  P+TVG  
Sbjct: 938  KEISDAIEKANRNLINKNHATYGDLARDEFVPQLSRTGKTWLYDGRTGEKFREPITVGQS 997

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL HMV DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW + AYGA+ VLQE+
Sbjct: 998  YILKLGHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQEI 1057

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDD  GR + YE+IV G +      PESF VLVKEM++L L+++LE    +     
Sbjct: 1058 LTVKSDDTAGRVKSYEAIVKGENIPAPEVPESFKVLVKEMKSLCLNVELEGHDHRTIDVT 1117

Query: 1375 EEIPDFNKCE 1384
            ++I      +
Sbjct: 1118 QDIDGQEDGD 1127



 Score =  346 bits (888), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 124/550 (22%), Positives = 223/550 (40%), Gaps = 36/550 (6%)

Query: 1   MAK--GVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAA 58
           MA+        L R R+ F K P+++D+P+LI +Q  S++ F            EGL  A
Sbjct: 1   MAQGKTTDQTSLYRDRRSFAKIPDVMDVPNLIAIQTDSFEFF----------KGEGLAQA 50

Query: 59  FKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           F+ + PI   +    +EF  +EF  PK+ VD+C  +D++Y  PL + +R I         
Sbjct: 51  FQDISPIENNTKDMCVEFGRHEFGEPKYTVDECKEKDVSYQAPLFVEIRFI--------- 101

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            +   +IKEQ ++MGD PLMT  GTF+I G +R+VVSQL RSPG++F  ++ +   S K 
Sbjct: 102 NRETGEIKEQDVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFASERDK--ASDKT 159

Query: 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKI 236
           L+  ++IP +G W++ E D +DI+ VRIDR+RK P T  + ALG+    EEI+       
Sbjct: 160 LFNAKVIPSRGAWLEFETDKRDILSVRIDRKRKQPATLLVRALGLAETREEIIELLGNDE 219

Query: 237 VY--SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKG 292
           +   +   D       +   +           ID+   ++E          L K  + K 
Sbjct: 220 MVLRTLDRDPATTKEESLIELYKRFRPGEPPTIDSARTLLEGLFFNPQRYDLAKVGRYKI 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE-KSLEEIFHSEIRDIPILYVDS 351
            K LG   D        +DIV      + + AGD   +   ++   +  IR +  L  + 
Sbjct: 280 NKKLGFDPDYEASTLTDDDIVRTMQYIVALHAGDEGVQTDDIDHFGNRRIRTVGELIQNQ 339

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                     +V ++   ++    +I            +  +  F            +  
Sbjct: 340 FRIGLSRMERVVRERMSMQEP--DEITPQSLVNIRPIVAAIKEFFGSSQLSQFMDQTNPA 397

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNRRVRSVGEM 470
             +    RL+   P     + +E     ++ +     G+   I+  +      + S+   
Sbjct: 398 AGITHKRRLSALGPGG---LSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLATY 454

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            +      +    R + +   + ++D +   +  N     +       + +    ++   
Sbjct: 455 ARINPYGFIETPYRRVVDGKVTDEVDYLTADEEENYTIAQANDLFDPETRKFGTFDDQGV 514

Query: 531 SLSRITHTRR 540
               +    R
Sbjct: 515 FHEAVRVLCR 524


>gi|322690596|ref|YP_004220166.1| DNA-directed RNA polymerase beta subunit [Bifidobacterium longum
            subsp. longum JCM 1217]
 gi|320455452|dbj|BAJ66074.1| DNA-directed RNA polymerase beta subunit [Bifidobacterium longum
            subsp. longum JCM 1217]
          Length = 1187

 Score =  499 bits (1284), Expect = e-138,   Method: Composition-based stats.
 Identities = 183/537 (34%), Positives = 261/537 (48%), Gaps = 55/537 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G     +             ++  I+  G  V  G ++      +    +   + L
Sbjct: 658  MNDDGTTSSYKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQN-GDLALGKNL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A       +  D  +     V    +       + ID  E  +  E     +  +  D
Sbjct: 717  LIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGED 776

Query: 971  KD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         +IL G+    G         L   +  E  R       V+
Sbjct: 777  AVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSRE------VR 830

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  ++             +   ED  ++       GD++P GV ++++V++A  R I  G
Sbjct: 831  DTSLRVPHGETGTVIGVKEITREDAEED-------GDELPNGVNQMIRVYIAQHRKITVG 883

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK++GRHGNKG +SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLGW    
Sbjct: 884  DKLSGRHGNKGCISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIA-H 942

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  I    N       +                           +   AE+ +   PV+
Sbjct: 943  SGWDISLDPNMEAEWKKL---------------------------IPSGAEKAEPNTPVA 975

Query: 1208 TPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            TPVFDG   E +  +L     +  G        ++ L+DG TGEP+ +P++VGY+YMLKL
Sbjct: 976  TPVFDGVKPEVLKGLLSTTLPNRDGDRLVGPDGKATLFDGRTGEPYTKPISVGYMYMLKL 1035

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
            +H+V DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY L EM+T KS
Sbjct: 1036 HHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKS 1095

Query: 1320 DDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            DDV GR RVY +IV G++    G PESF VL+KEMQ+L L++++ N+        +E
Sbjct: 1096 DDVDGRVRVYGAIVKGDNLPPAGIPESFKVLLKEMQSLSLNVEVLNAEGVAIDMKDE 1152



 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 306/617 (49%), Positives = 435/617 (70%), Gaps = 23/617 (3%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 249 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 308

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 309 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 368

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 369 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 428

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 429 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 488

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 489 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 548

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 549 GNFVQKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 608

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPL+++E P VGTG E   A  SG  I +++ G+V  V A  I + + +G      
Sbjct: 609 QRQAVPLIESERPLVGTGSEWRAANDSGDVIKSEKDGVVTYVSADLIRVMNDDGTTSS-- 666

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y+L KFQRSNQ TC NQRP+V  G+ V    ++ADGP+   GDLALG+N+L+AFM
Sbjct: 667 -----YKLAKFQRSNQTTCYNQRPIVHDGERVEAGSVMADGPAIQNGDLALGKNLLIAFM 721

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW+GYN+ED+++IS+R+V +D  +SIHIEE+E+ AR+TKLG EEITRD+PNV E+ + N+
Sbjct: 722 PWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANL 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE+ +TPEE+LLRAIFGEK+ +VRDTSLRVP G +
Sbjct: 782 DERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGET 841

Query: 937 GTVVDVRIFNRHGIDKN 953
           GTV+ V+   R   +++
Sbjct: 842 GTVIGVKEITREDAEED 858



 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 141/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL   F  
Sbjct: 29  RVNFGSIKEPIDVPYLLGVQTDSFDWLIGNERWKARVEEDEKNGTNTVAHTSGLDEVFNE 88

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +       D         
Sbjct: 89  ISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGD--------- 139

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 140 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFG 197

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +
Sbjct: 198 AKIIPSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDA 257

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     + G+ +++S    T    L +  + K  + LG
Sbjct: 258 LEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLG 317

Query: 298 ITSDC 302
           + +D 
Sbjct: 318 VEADF 322


>gi|123969221|ref|YP_001010079.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. AS9601]
 gi|158512723|sp|A2BT61|RPOB_PROMS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|123199331|gb|ABM70972.1| RNA polymerase beta subunit [Prochlorococcus marinus str. AS9601]
          Length = 1097

 Score =  498 bits (1283), Expect = e-138,   Method: Composition-based stats.
 Identities = 326/686 (47%), Positives = 458/686 (66%), Gaps = 27/686 (3%)

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +++ ++G++  +  +   +   +KF    ++ L         +N     + + A  + D
Sbjct: 138 KDELDKNGRRTYNANVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSD 194

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              ++++ H E     I             ++   +       ALL++Y+ +RPG+  + 
Sbjct: 195 NDVVDKLRHPEFYQNSI-------------DSANDEGINSEDQALLELYKKLRPGEPPSV 241

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           S  + + N  FFD  +YDL  VGR K+N +L L  PDDVR +  ED+++ I  L++L   
Sbjct: 242 SGGQQLLNSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTIDYLINLELD 301

Query: 450 KG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N K
Sbjct: 302 IGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPK 361

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYG
Sbjct: 362 PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYG 421

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENR 625
           R+CP ET EG N GL++SL + ARVN YGFIETP+ +V +GKV  +   VYLSA  E+  
Sbjct: 422 RLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVKNGKVNKEGNPVYLSADLEDEC 481

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + D+DG+   +L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+D
Sbjct: 482 RVAPGDVATDKDGNIIADLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHD 541

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  G V  VDA  IV+
Sbjct: 542 DANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVV 601

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +   G+          + L K+QRSNQ+TC+NQRP+VK+GD+V    ++ADG + + G++
Sbjct: 602 KDDHGNE-------HFHYLQKYQRSNQDTCLNQRPIVKIGDKVISGQVLADGSACEGGEI 654

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+I
Sbjct: 655 ALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREI 714

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PN+SEE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVR
Sbjct: 715 PNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVR 774

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           D SLRVP    G V+DVRI+ R   D
Sbjct: 775 DNSLRVPKTEKGRVLDVRIYTREQGD 800



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/584 (32%), Positives = 273/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVVKDDHGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ +G +V  G +L      +G   +   + +L A   
Sbjct: 608  EHFHYLQKYQRSNQDTCLNQRPIVKIGDKVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAAANLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQPGKAWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + ++ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPEDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M++I
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDI 1074



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 188/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PI+ ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELQNFSPISDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDELDK---NGRRTYNANVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY   + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQNSIDSANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLNSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|116073733|ref|ZP_01470995.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. RS9916]
 gi|116069038|gb|EAU74790.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. RS9916]
          Length = 1097

 Score =  498 bits (1283), Expect = e-138,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 449/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSI-------------EAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGVVLKQGDPLYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDADGRILADLIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+R  EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 VD-------HTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 188/584 (32%), Positives = 270/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDI LNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDICLNPLGVPSRMNVGQVFELLMGWAASNLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  +  ++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSQQTVEAFLKEAASQPGKDWIY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D  G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDSPGKLLLTDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVFTDEGKEVDLMQDV 1074



 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 96/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|295106722|emb|CBL04265.1| DNA-directed RNA polymerase subunit beta [Gordonibacter pamelaeae
           7-10-1-b]
          Length = 1154

 Score =  498 bits (1283), Expect = e-138,   Method: Composition-based stats.
 Identities = 327/739 (44%), Positives = 470/739 (63%), Gaps = 27/739 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           + +I +  R                         I+  E+V+ S    + G+  + +   
Sbjct: 70  FVEIRFINRETGEIKEQDVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGVYFAAERDK 129

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS-EIRDIPILYVDS 351
                I +  +     A      +  +I     D   ++    +  +  + +     ++ 
Sbjct: 130 TSDKTIYNAKVIPSRGAWLEFETDKRDILSVRIDRKRKQPATLLVRALGLAETREEIIEL 189

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           + ++  +  TL  D    ++++L+++Y+  RPG+  T   A ++   LFF+  +YDL+ V
Sbjct: 190 LGSDEMVLRTLDRDPATTKEESLIELYKRFRPGEPPTIDSARTLLEGLFFNPQRYDLAKV 249

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG--KGTIDDIDNLGNRRVRSVGE 469
           GR K+N +L  D   +   +  +DI+  ++ +V L  G      DDID+ GNRR+R+VGE
Sbjct: 250 GRYKINKKLGFDPDYEASTLTDDDIVRTMQYIVGLHAGAEDFQTDDIDHFGNRRIRTVGE 309

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ+R+GL RMER ++ER+S  + D + PQ L+N +P+V+A+ EFF SSQLSQ  +  
Sbjct: 310 LIQNQFRIGLSRMERVVRERMSMQEPDEITPQSLVNIRPIVAAIKEFFGSSQLSQFMDQT 369

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N  + ITH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL ++
Sbjct: 370 NPAAGITHKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLATY 429

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS---------- 639
           AR+N YGFIETPYR+V DGKVT+DV YL+A EEEN  IAQAN   D +            
Sbjct: 430 ARINPYGFIETPYRRVVDGKVTDDVDYLTADEEENYVIAQANDLFDPETRQFGTFDENGE 489

Query: 640 -FTEELVFCRCAG------EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                 V CR         E   +P  ++D++D SP+Q+VS+A SLIPFLE+DD+NR LM
Sbjct: 490 FHVAARVLCRTKDANGVFGEPDELPPSQVDYMDVSPRQMVSVATSLIPFLEHDDANRALM 549

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPLL+  AP VGTG+E  +A  SG  +VA+  G+V+ VD   I+I + +G+ 
Sbjct: 550 GSNMQRQAVPLLRPNAPLVGTGIEHRIAVDSGEILVAQNPGVVDYVDGQTIIILNDDGEY 609

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           D        Y + KFQRSNQ+ C+N RP+V+ GDEV++ D++ADGPS D G+LALG+N++
Sbjct: 610 DE-------YLVPKFQRSNQSGCINHRPIVRKGDEVQKGDVLADGPSCDGGELALGQNLM 662

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA+MPW GYN+ED++++SER+VSED+ TSIHI E+E+ ARDTKLGPEEITR+IPN+S++ 
Sbjct: 663 VAYMPWEGYNYEDAIIVSERVVSEDLLTSIHISEYEIDARDTKLGPEEITREIPNISDDM 722

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           + ++D  GII VGAEV PGD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+VP
Sbjct: 723 ISDLDADGIIRVGAEVFPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLKVP 782

Query: 933 SGVSGTVVDVRIFNRHGID 951
            G  G V+ +  F+R   D
Sbjct: 783 HGSGGRVIGMARFSRAAGD 801



 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 192/609 (31%), Positives = 282/609 (46%), Gaps = 79/609 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E  + +   E +V+++     +++   ++  +    
Sbjct: 549  MGSNMQRQAVPLLRPNAPLVGTGIEHRIAVDSGEILVAQNPGVVDYVDGQTIIILNDDGE 608

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +E        S +    I+   I+  G EV  GD+L    +  G   +   + L+ A  
Sbjct: 609  YDEYLVPKFQRSNQS-GCINHRPIVRKGDEVQKGDVLADGPSCDG-GELALGQNLMVAYM 666

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     VS  ++     + + ID  +  +  E    E +    DD    
Sbjct: 667  PWEGYNYEDAIIVSERVVSEDLLTSIHISEYEIDARDTKLGPEEITRE-IPNISDDMISD 725

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +   R+   +   + + G    K  T L+++               +  +  R+   
Sbjct: 726  LDADGIIRVGAEVFPGDVLVGKVTPKGETELTAEE------RLLRAIFGEKAREVRDTSL 779

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                    + I   RF         GD++ PGV  +V+++VA KR +Q GDK++GRHGNK
Sbjct: 780  KVPHGSGGRVIGMARFSR-----AAGDELAPGVNELVRIYVAQKRKVQQGDKLSGRHGNK 834

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++SR+LP EDMP+L DGTP+D++LNPLGVPSRMNVGQ+ E HLGWA             
Sbjct: 835  GVISRVLPLEDMPYLADGTPIDVILNPLGVPSRMNVGQLLENHLGWAAK----------- 883

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                          +  D         +  + V+TPVFDGA E 
Sbjct: 884  ------------------------------WGWDDAEETDAVVEGPMHVATPVFDGATER 913

Query: 1218 AINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             I+  +  A+                      L  +G++ LYDG TGE F  P+TVG  Y
Sbjct: 914  EISDAIEKANRNLININHAKYGDKARDEFVPQLSRTGKTWLYDGRTGEKFREPITVGQSY 973

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKL HMV DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW + AYGA+ VLQE+L
Sbjct: 974  ILKLGHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQEIL 1033

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            T+KSDD  GR + YESIV G +      PESF VLVKEM++L L+++LE    +      
Sbjct: 1034 TVKSDDTAGRVKSYESIVKGENIPAAEVPESFKVLVKEMKSLCLNVELEGHDHQTIDVTV 1093

Query: 1376 EIPDFNKCE 1384
            E       +
Sbjct: 1094 ESEGQEDGD 1102



 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 101/355 (28%), Positives = 164/355 (46%), Gaps = 28/355 (7%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P+LI +Q  S++ F            EGL  AF  + PI   +    +EF  +EF  
Sbjct: 1   MDVPNLIAIQTDSFEFF----------KGEGLAQAFHDISPIENSTKDMCVEFGKHEFGE 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+C  +D++Y  PL + +R I          +   +IKEQ ++MGD PLMT  GT
Sbjct: 51  PKYTVDECKEKDVSYQAPLFVEIRFI---------NRETGEIKEQDVFMGDFPLMTPRGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R+VVSQL RSPG++F  ++ +   S K +Y  ++IP +G W++ E D +DI+ 
Sbjct: 102 FIINGTERVVVSQLVRSPGVYFAAERDKT--SDKTIYNAKVIPSRGAWLEFETDKRDILS 159

Query: 204 VRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAK 259
           VRIDR+RK P T  + ALG+    EEI+       +   +   D       +   +    
Sbjct: 160 VRIDRKRKQPATLLVRALGLAETREEIIELLGSDEMVLRTLDRDPATTKEESLIELYKRF 219

Query: 260 VSSSLVDIDTGEQVIES--GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
                  ID+   ++E          L K  + K  K LG   D        +DIV    
Sbjct: 220 RPGEPPTIDSARTLLEGLFFNPQRYDLAKVGRYKINKKLGFDPDYEASTLTDDDIVRTMQ 279

Query: 318 GEIYIEA-GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             + + A  +      ++   +  IR +  L  +           +V ++   ++
Sbjct: 280 YIVGLHAGAEDFQTDDIDHFGNRRIRTVGELIQNQFRIGLSRMERVVRERMSMQE 334


>gi|151337018|gb|ABS00954.1| RNA polymerase beta subunit [Thermus aquaticus]
          Length = 1119

 Score =  498 bits (1283), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/509 (37%), Positives = 254/509 (49%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 638  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 696

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 697  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 755

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 756  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 796

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 797  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 856

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  
Sbjct: 857  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKE 916

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +    
Sbjct: 917  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFVQ- 969

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 970  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1024

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   YE+I+ G D  E   PES
Sbjct: 1025 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYEAIIKGEDVPEPSVPES 1084

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1085 FRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L         + L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVE-------HPLRRYARSNQGTAFDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 810



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|46360980|gb|AAS89223.1| RpoB [Corynebacterium mucifaciens]
          Length = 1109

 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 185/489 (37%), Positives = 252/489 (51%), Gaps = 61/489 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 668  IVSAGERVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +     ++  R  
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAREVRDT-------------SLKVPHGEQGKVIAVR-- 830

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 831  --RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D K    +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEIHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 946  VPADSLT-------------------------ATPVFDGATNDEIAGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDENGKTTLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVLVKEMQ 1355
            F VL+KE+Q
Sbjct: 1101 FKVLLKELQ 1109



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 316/617 (51%), Positives = 438/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLENDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K+N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 289 ARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPEGEIIPINTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L S+ARVN +GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + +D
Sbjct: 469 EGPNIGLIGALASYARVNPFGFIETPYQKVDDGKLTDQIDYLTADEEDRYAIAQAATPMD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +DG+ T E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 KDGNLTGERIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL++EA +V TGME   A  +G  +++K+AG++E V    I +   EG    
Sbjct: 589 NMQKQAVPLLRSEAAYVATGMEQRAAYDAGDTVISKKAGVIENVTGDFITVMDDEG---- 644

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              G D Y L  F+R+NQ TC NQ P+V  G+ V    +IADGP T  G++ALGRN+LVA
Sbjct: 645 ---GRDTYMLRTFERTNQGTCYNQTPIVSAGERVEAGQVIADGPGTKDGEMALGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 762 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
             G V+ VR F+R   D
Sbjct: 822 EQGKVIAVRRFSREDDD 838



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 99/389 (25%), Positives = 171/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +           N   D R   GL+     + 
Sbjct: 15  ERYSFAKINEPITVPGLLDVQLESFAWLVGTPEWREREQANRGSDARITSGLEDILDEIS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIEDYSGNMSLTLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 NDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    GEI       I+   ++   +  +R
Sbjct: 304 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPEGEII-----PINTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|119485960|ref|ZP_01620022.1| DNA-directed RNA polymerase beta subunit [Lyngbya sp. PCC 8106]
 gi|119456735|gb|EAW37863.1| DNA-directed RNA polymerase beta subunit [Lyngbya sp. PCC 8106]
          Length = 1099

 Score =  498 bits (1282), Expect = e-138,   Method: Composition-based stats.
 Identities = 319/605 (52%), Positives = 420/605 (69%), Gaps = 9/605 (1%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D++ +  Y + T+  +     +DAL+++YR +RPG+  T +  E + N  FFD  +YDL
Sbjct: 196 FDALRHPDYFQKTIDREGEFSEEDALMELYRKLRPGEPPTVAGGEQLLNNRFFDPKRYDL 255

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR K+N +L L  PD  R +   DI+A I  L++L    G  DDID+LGNRRVRSVG
Sbjct: 256 GRVGRYKLNRKLRLTIPDITRVLTPTDILAAIDYLINLEYDIGETDDIDHLGNRRVRSVG 315

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L+NQ R+GL R+ER I+ER++  D DS+ P  L+N KP+V+A+ EFF SSQLSQ  + 
Sbjct: 316 ELLQNQVRVGLNRLERIIRERMTVSDSDSLTPASLVNPKPLVAAIKEFFGSSQLSQFMDQ 375

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL +
Sbjct: 376 TNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAT 435

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ARVN YGFI TPY    +G+V  D   VY++A EE++  +A  + S D +G+   E++ 
Sbjct: 436 HARVNPYGFIATPYYPAENGRVRRDGPPVYMTADEEDDLRVAPGDVSTDAEGNILGEVIP 495

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +      +++D++  SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ 
Sbjct: 496 VRYRQDFTETTPDQVDYVAVSPVQIISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRP 555

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E+  A+ SG  IV++  G V  VD  RI + S EG           Y L K
Sbjct: 556 QRPLVGTGLEAQAARDSGMVIVSQIDGEVSYVDGARIRVTSPEGQEVE-------YELQK 608

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           + RSNQ+TC+NQRPLV  GD+V    ++ADG ST+  +LALG N++V +MPW GYN+ED+
Sbjct: 609 YNRSNQDTCLNQRPLVYEGDQVVVGQVLADGSSTEGAELALGHNVVVTYMPWEGYNYEDA 668

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V ED++TSIHIE++E+ AR TKLGPEEITR+IPNV E+ L+ +D  GII VGA
Sbjct: 669 ILISERLVYEDIYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDSLRQLDANGIIRVGA 728

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F 
Sbjct: 729 WVEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFT 788

Query: 947 RHGID 951
           R   D
Sbjct: 789 REQGD 793



 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 189/583 (32%), Positives = 260/583 (44%), Gaps = 59/583 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT-KLGP 858
                       +L    P  G   E        MV                 R T   G 
Sbjct: 541  MGSNMQRQAVPLLRPQRPLVGTGLEAQAARDSGMVIVSQIDGEVSYVDGARIRVTSPEGQ 600

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  ++  G +V  G +L    + +G   +     ++     
Sbjct: 601  EVEYELQKYNRSNQDTCLNQRPLVYEGDQVVVGQVLADGSSTEGA-ELALGHNVVVTYMP 659

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK--DDEQV 976
             +  +  D  L              I  R   +    SI +E+ +IE        ++   
Sbjct: 660  WEGYNYEDAIL--------------ISERLVYEDIYTSIHIEKYEIEARQTKLGPEEITR 705

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             +       L ++        G    +   +L   +  +    Q  +  +          
Sbjct: 706  EIPNVGEDSLRQLDANGIIRVGAW-VEAGDILVGKVTPKGESDQPPEEKLLRAIFGEKAR 764

Query: 1037 SLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             ++       +  + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMAGRHG
Sbjct: 765  DVRDNSLRVPNGEKGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHG 824

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGIVSRILP EDMP+L DG  VDIVLNPLGVPSRMNVGQIFE  LGWA   L  + K +
Sbjct: 825  NKGIVSRILPVEDMPYLPDGRAVDIVLNPLGVPSRMNVGQIFECLLGWAGENLKTRYKVI 884

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D     ++S      E  +                                     A 
Sbjct: 885  PFDEMHGEEMSRETVHGELQL-------------------------------------AR 907

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E+     L  A  D  G+ +LYDG TGEPFD+PVTVG  YMLKL H+V DK++ARSTG Y
Sbjct: 908  EKNKKDWLFNA--DNPGKVLLYDGRTGEPFDQPVTVGVAYMLKLVHLVDDKIHARSTGPY 965

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SLVTQQPLGGK+ +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +IV G
Sbjct: 966  SLVTQQPLGGKAQQGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNAIVKG 1025

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
                  GTPESF VL++E+Q+L L I +    T       ++ 
Sbjct: 1026 KAIPRPGTPESFKVLMRELQSLCLDIAVHKVETGEDGVGRDLE 1068



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 102/459 (22%), Positives = 189/459 (41%), Gaps = 46/459 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLI++Q++S+  FL            GL    +S  PIT ++G   L F+  +Y    
Sbjct: 13  LPDLIDIQRSSFRWFL----------ESGLIEELESFSPITDYTGKLELHFLAQNYRLKQ 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TYAV + +  RLI          K   +IKEQ +++GDLPLMT+ GT
Sbjct: 63  PKYDVDEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEQEVFIGDLPLMTERGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   + +  Y+  +IP++G W+  E D  D++ 
Sbjct: 114 FIINGAERVIVNQIVRSPGVYYKSEIDK---NQRRTYSASLIPNRGAWLKFETDKNDLVW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           VRID+ RK+     L ALG+ + EI         + +  D         +      +   
Sbjct: 171 VRIDKTRKLSAQVLLKALGLSNNEIFDALRHPDYFQKTID------REGEFSEEDALMEL 224

Query: 264 LVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +  GE   +  G++L +      K   +  +G             DI    T    +
Sbjct: 225 YRKLRPGEPPTVAGGEQLLNNRFFDPKRYDLGRVGRYKLNRKLRLTIPDITRVLTPTDIL 284

Query: 323 EA--------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            A         D+ +   ++ + +  +R +  L  + V         ++ ++        
Sbjct: 285 AAIDYLINLEYDIGETDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDSDS 344

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L    ++ P      +  +  F            + +  +    RL+   P     + +E
Sbjct: 345 LTPASLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRE 399

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                ++ +     G+  I  I+         +G +  +
Sbjct: 400 RAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 436


>gi|328949973|ref|YP_004367308.1| DNA-directed RNA polymerase subunit beta [Marinithermus
            hydrothermalis DSM 14884]
 gi|328450297|gb|AEB11198.1| DNA-directed RNA polymerase subunit beta [Marinithermus
            hydrothermalis DSM 14884]
          Length = 1121

 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 193/577 (33%), Positives = 276/577 (47%), Gaps = 24/577 (4%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGP 858
                  A    ++ A  P  G   ED ++      V  DV   +   + E +  + + G 
Sbjct: 562  MGSNMQAQAVPLIRADAPVVGTGIEDRVVRDSLTSVYADVDGVVRYVDGERIVIEQENGN 621

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                     V       +D+   + VG  V  GD+L    +      +   + +L AI  
Sbjct: 622  VREYVLSRFVRSNQGTTLDQRPRVNVGQRVKRGDLLADGPSA-DHGRLALGQNVLVAIMP 680

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     +           R+ I+  +  +  E+   + +    +     L
Sbjct: 681  FDGYNFEDAIIISEDLLRRDYYTSIHIERYEIEARDTKLGPEKITRD-IPNLSEAALRDL 739

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D +   R+   +   + + G   FK  T  S +      RS + + A   +     V   
Sbjct: 740  DEDGIVRVGAEVKAGDILVGRTSFKGETEPSPE--ERLLRSIFGEKARDVKDTSLRVPPG 797

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +         L+        +   G ++ PGV  VV+V+VA KR +Q GDK+A RHGNKG
Sbjct: 798  EGGIVVRTVRLK--------RGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKG 849

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VS+ILP EDMP L DGTPVDIV NPLGVPSRMN+GQI ETHLG A   LG    + I D
Sbjct: 850  VVSKILPPEDMPHLPDGTPVDIVFNPLGVPSRMNLGQILETHLGLAARELGFTFVTPIFD 909

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                 +I  L      +         +   D      +    K G+  +    D  + E 
Sbjct: 910  GATEAEIKALLDEAFTLRWAQREQSNL-GIDVREREVLKRAAKQGLVPA----DLPEVEQ 964

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +  + +       G+ +LYDG TGEP + P+ VG +Y++KL HMV DK++ARSTG YSL+
Sbjct: 965  LRELFKQ------GKVVLYDGRTGEPIEGPIVVGLMYVMKLYHMVEDKMHARSTGPYSLI 1018

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD+ GR   YE++V G D 
Sbjct: 1019 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAVVKGGDV 1078

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             E   PESF VLVKE+QALGL ++  +   +     E
Sbjct: 1079 PEPSVPESFRVLVKELQALGLDVETYDENDRPIDIFE 1115



 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 300/592 (50%), Positives = 401/592 (67%), Gaps = 15/592 (2%)

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                ++ALL ++ V+RPGD      A S    L  D  +YDL   GR K+  +L ++ P
Sbjct: 228 FEMSPQEALLRLFTVLRPGDPPKRDKAVSYLYSLLADPRRYDLGEAGRYKVQHKLGVEMP 287

Query: 426 D------DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRL 477
           D           + E ++A +K L+ L+ G      DDID+LGNRR+R+VGE+L +Q+R+
Sbjct: 288 DRTLLSFKDGEFKDEALLATLKYLLGLQAGLEGYEPDDIDHLGNRRIRTVGELLADQFRV 347

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RM R ++ER+     ++  P  LIN +P+ +A+ EFF  SQLSQ ++  N LS + H
Sbjct: 348 GLGRMARGVRERMLMGSPEAATPAKLINNRPLAAAIREFFGRSQLSQFKDQTNPLSELRH 407

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL ++  +N  GF
Sbjct: 408 KRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLAAYGTINELGF 467

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           I TPYR+V DG+VT++V Y++A EE+   IAQAN+ LD++G    E V  R  GE ++VP
Sbjct: 468 IMTPYRRVVDGRVTDEVHYMTADEEDRYTIAQANTPLDDEGRIATEKVVARRKGEPVIVP 527

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP VGTG+E 
Sbjct: 528 ASEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQAQAVPLIRADAPVVGTGIED 587

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V + S  ++ A   G+V  VD  RIVI    G        V  Y L +F RSNQ T ++
Sbjct: 588 RVVRDSLTSVYADVDGVVRYVDGERIVIEQENG-------NVREYVLSRFVRSNQGTTLD 640

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           QRP V VG  V+R D++ADGPS D G LALG+N+LVA MP+ GYNFED+++ISE ++  D
Sbjct: 641 QRPRVNVGQRVKRGDLLADGPSADHGRLALGQNVLVAIMPFDGYNFEDAIIISEDLLRRD 700

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +TSIHIE +E+ ARDTKLGPE+ITRDIPN+SE  L+++DE GI+ VGAEV  GDILVG+
Sbjct: 701 YYTSIHIERYEIEARDTKLGPEKITRDIPNLSEAALRDLDEDGIVRVGAEVKAGDILVGR 760

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            + KGE+  +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 TSFKGETEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLKRGD 812



 Score =  256 bits (653), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 83/213 (38%), Positives = 122/213 (57%), Gaps = 20/213 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF---SGA 71
           K FG+  E+I +P L ++Q  S+   L +++ P +R N G+QAAF+ VFPI       G 
Sbjct: 5   KRFGQIQEVIPLPPLTQIQVESFRKALQLDVPPHQRENIGIQAAFREVFPIEEGERGRGG 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 65  LVLDFLEYRLGDPPFSPDECREKDLTYQAPLYARLQLIHKDSGL---------IKEDEVF 115

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +GDLPLMT DG+F+I G  R++VSQ+HRSPG++F  D      +    Y   IIP   +G
Sbjct: 116 LGDLPLMTPDGSFIINGADRVIVSQIHRSPGVYFTMD-----PNRPGRYVASIIPLPKRG 170

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
            W+D+EFDS   + ++++ ++K PV   L  LG
Sbjct: 171 PWIDLEFDSSGALLMKVN-KKKFPVVLLLRVLG 202


>gi|290490552|dbj|BAI79263.1| RNA polymerase subunit B [Tomitella biformata]
 gi|290490554|dbj|BAI79264.1| RNA polymerase subunit B [Tomitella biformata]
          Length = 964

 Score =  498 bits (1281), Expect = e-138,   Method: Composition-based stats.
 Identities = 325/677 (48%), Positives = 450/677 (66%), Gaps = 24/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +         I   
Sbjct: 36  DKTTEKELHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEMI--Q 93

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 94  ERFGFSEIMMTTLEKDSTAGVDEALLDIYRKLRPGEPPTKESAQTLLENLFFKDKRYDLA 153

Query: 410 TVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKG------------TIDD 455
            VGR K+N +L L   T DD   + + DI+  ++ LV L  G               +DD
Sbjct: 154 RVGRYKINKKLGLTSATTDDPLVLTESDIVTTVEYLVRLHEGHKSMVSPDGVEVPVEVDD 213

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PV +A+ E
Sbjct: 214 IDHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVSAAIKE 273

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 274 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 333

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+DV YL+A EE+   +AQANS+ D
Sbjct: 334 EGPNIGLIGSLSVYARVNPFGFIETPYRKVIDGVVTDDVDYLTADEEDRHIVAQANSASD 393

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G  T+E V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 394 ANGVLTDERVLVRKKGGEVEYVPPVEVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGA 453

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++E+P VGTGME   A  +G  +   +AG++E+V A  I + + +G    
Sbjct: 454 NMQRQAVPLVRSESPLVGTGMELRAAVDAGDCVTTDKAGVIEEVSADFITVMADDGTRQ- 512

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  + L KF+RSNQ T  NQ P++  GD V    ++ADGP T  G++ALG+N+LVA
Sbjct: 513 ------THLLRKFERSNQGTSANQTPIINDGDRVEAGQVLADGPCTQNGEMALGKNLLVA 566

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S+R+V EDV TSIHIEE+E+ ARDTKLG EEITRDIPNVSEE L 
Sbjct: 567 IMPWEGHNYEDAIILSQRIVEEDVLTSIHIEEYEIDARDTKLGAEEITRDIPNVSEEVLA 626

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GAEV  GD+LVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 627 DLDERGIIRIGAEVRDGDVLVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 686

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ VR+ +R   D
Sbjct: 687 ESGKVIGVRMVSRDDDD 703



 Score =  470 bits (1209), Expect = e-130,   Method: Composition-based stats.
 Identities = 179/483 (37%), Positives = 241/483 (49%), Gaps = 65/483 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            II  G  V  G +L      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 533  IINDGDRVEAGQVLADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSQRIVEEDVL 591

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ID  +  +  E          E +  D  DE+ I+      R  ++L G+ 
Sbjct: 592  TSIHIEEYEIDARDTKLGAEEITRDIPNVSEEVLADL-DERGIIRIGAEVRDGDVLVGKV 650

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 651  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVIG 693

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             ++      D++ PGV  +V+V+VA KR IQ GDK+AGRHGNKG++ +ILP EDMPFL D
Sbjct: 694  VRMVSRDDDDELAPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPQEDMPFLPD 753

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LN  GVP RMN+GQI ETHLGW     G K++      K   +          
Sbjct: 754  GTPIDIILNTHGVPRRMNIGQIMETHLGWIAK-TGWKVEGDPEWAKRLPE---------- 802

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MA 1226
                    E +    D +              +TPVFDGA+ + I  ML           
Sbjct: 803  --------EMLEAPADSNT-------------ATPVFDGAEPDEIEGMLACTLKNRDGER 841

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
             +D +G+++L+DG +GEPF  PV VGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK
Sbjct: 842  MVDGTGKAVLFDGRSGEPFPYPVAVGYMYIIKLHHLVDDKIHARSTGPYSMITQQPLGGK 901

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEME W +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  E G PES
Sbjct: 902  AQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPEPGIPES 961

Query: 1347 FNV 1349
            F V
Sbjct: 962  FKV 964



 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 57/211 (27%), Positives = 92/211 (43%), Gaps = 12/211 (5%)

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            P+MT  GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP +G W++ 
Sbjct: 1   FPMMTPKGTFIINGTERVVVSQLVRSPGVYFDETIDKT--TEKELHSVKVIPGRGAWLEF 58

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
           + D +D + VRIDR+R+ PVT  L ALG  SE I   F    +     +          L
Sbjct: 59  DVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEMIQERFGFSEIMMTTLEKDSTAGVDEAL 118

Query: 255 MVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           +   +       +  GE    ES + L   L    K   +  +G          +     
Sbjct: 119 LDIYR------KLRPGEPPTKESAQTLLENLFFKDKRYDLARVGRYK---INKKLGLTSA 169

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
             +   +  E+  V   + L  +       +
Sbjct: 170 TTDDPLVLTESDIVTTVEYLVRLHEGHKSMV 200


>gi|254430308|ref|ZP_05044011.1| DNA-directed RNA polymerase, beta subunit [Cyanobium sp. PCC 7001]
 gi|197624761|gb|EDY37320.1| DNA-directed RNA polymerase, beta subunit [Cyanobium sp. PCC 7001]
          Length = 1096

 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 331/726 (45%), Positives = 455/726 (62%), Gaps = 14/726 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
            Y       +              +          I+  E+VI +    + G+    ++ 
Sbjct: 82  MYVTCRLVNKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD 141

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS-EIRDIPILYVD 350
                   +  +     A      +  ++     D   + +   +  +  + D  +L   
Sbjct: 142 KNGRKTFNASLIPNRG-AWLKFETDKNDLLHVRVDKTRKINAHVLMRAIGLTDNDVLDKL 200

Query: 351 SVNNNAYIRNTLVTDKNKDRKD-ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
                         D+    +D ALL++Y+ +RPG+  + S  +S+ +  FFD  +YDL 
Sbjct: 201 RHPEYYQKSIESANDEGISSEDQALLELYKKLRPGEPPSVSGGQSLLHSRFFDPKRYDLG 260

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSV 467
            VGR K+N +L L  PD VR +  ED+++ I  L++L    G  ++DDID+LGNRRVRSV
Sbjct: 261 RVGRYKINKKLRLTIPDAVRTLTPEDVLSTIDYLINLELDVGGASLDDIDHLGNRRVRSV 320

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ R+GL R+ER IKER++  + +S+ P  L+N KP+V+A+ EFF SSQLSQ  +
Sbjct: 321 GELLQNQVRVGLNRLERIIKERMTVGETESLTPAQLVNPKPLVAAIKEFFGSSQLSQFMD 380

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL 
Sbjct: 381 QTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLA 440

Query: 588 SFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           + ARVN YGFIETP+ KV +G V    D +YLSA  E+   +A  +   D DG  T +LV
Sbjct: 441 THARVNEYGFIETPFWKVEEGIVLKQGDPIYLSADLEDECRVAPGDVPTDADGRITADLV 500

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +   VP E++DF+  SP QV+S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+
Sbjct: 501 PVRYRQDFEKVPPEQVDFVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLR 560

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E P VGTG+E+ VA+ SG   + +  G V  VDA  IVIR  +G           + L 
Sbjct: 561 PERPLVGTGLETQVARDSGMVPITRVNGTVTYVDATAIVIRDEDGVD-------HTHYLQ 613

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+QRSNQ+TC+NQRP+V+ GD+V    ++A+G + + G++ALG+N+L+A+MPW GYN+ED
Sbjct: 614 KYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEGGEIALGQNVLIAYMPWEGYNYED 673

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+EE L N+DE GII VG
Sbjct: 674 AILVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLDEMGIIRVG 733

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           A V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVPS   G VVDVRI+
Sbjct: 734 AFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPSTERGRVVDVRIY 793

Query: 946 NRHGID 951
            R   D
Sbjct: 794 TREQGD 799



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 188/584 (32%), Positives = 275/584 (47%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGTVTYVDATAIVIRDEDGV 606

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G +V  G +L      +G   +   + +L A   
Sbjct: 607  DHTHYLQKYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEG-GEIALGQNVLIAYMP 665

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 666  WEGYNYEDAILVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 725

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 726  EMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 775

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +  IQ GDKMAGR
Sbjct: 776  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAKRLKIQVGDKMAGR 828

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE  +GWA   LG ++K
Sbjct: 829  HGNKGIISRILPREDMPYLPDGTPIDIVLNPLGVPSRMNVGQVFECLMGWASSHLGCRVK 888

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++     + W         V+D 
Sbjct: 889  VVPFD---------------EMHGAEKSKQTVQAFLEEAASLPGKDW---------VYDP 924

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             +                G+  L DG TGEPFD+PVTVG+ ++LKL H+V DK++ARSTG
Sbjct: 925  EN---------------PGKIQLIDGRTGEPFDQPVTVGFAHILKLVHLVDDKIHARSTG 969

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 970  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1029

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     +    M+++
Sbjct: 1030 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDAGEEVDLMQDV 1073



 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 99/458 (21%), Positives = 196/458 (42%), Gaps = 39/458 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L F+   Y    
Sbjct: 14  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFIGSEYRLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 64  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  +   +IP++G W+  E D  D++H
Sbjct: 115 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRKTFNASLIPNRGAWLKFETDKNDLLH 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       +Y K + S   +       A   +   
Sbjct: 172 VRVDKTRKINAHVLMRAIGLTDNDVLDKLRHPEYYQKSIESANDEGISSEDQALLELYKK 231

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+ ++ S         L +  + K  K L +T          ED+++  
Sbjct: 232 LRPGEPPSVSGGQSLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDAVRTLTPEDVLSTI 291

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 292 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETESL 351

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 352 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 406

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
               ++ +     G+  I  I+         +G +  +
Sbjct: 407 AGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|126697014|ref|YP_001091900.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9301]
 gi|158513423|sp|A3PEX4|RPOB_PROM0 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|126544057|gb|ABO18299.1| RNA polymerase beta subunit [Prochlorococcus marinus str. MIT 9301]
          Length = 1097

 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 324/686 (47%), Positives = 456/686 (66%), Gaps = 27/686 (3%)

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +++ ++G++  +  +   +   +KF    ++ L         +N     + + A  + D
Sbjct: 138 KDELDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSD 194

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              ++++ H E     I              +   +       ALL++Y+ +RPG+  + 
Sbjct: 195 NDVVDKLRHPEFYQSSI-------------ESANDEGINSEDQALLELYKKLRPGEPPSV 241

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           S  + + +  FFD  +YDL  VGR K+N +L L  PD+VR +  ED+++ I  L++L   
Sbjct: 242 SGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDNVRTLTHEDVLSTIDYLINLELD 301

Query: 450 KG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N K
Sbjct: 302 IGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPK 361

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYG
Sbjct: 362 PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYG 421

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENR 625
           R+CP ET EG N GL++SL + ARVN YGFIETP+ +V +GKV  +   VYLSA  E+  
Sbjct: 422 RLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVKNGKVDKEGNPVYLSADLEDEC 481

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + D+DG+    L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+D
Sbjct: 482 RVAPGDVATDKDGNIIANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHD 541

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  G V  VDA  IV+
Sbjct: 542 DANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVV 601

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +  +G+          + L K+QRSNQ+TC+NQRP+VK+GD V    ++ADG + + G++
Sbjct: 602 KDEDGNE-------HFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEGGEI 654

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+I
Sbjct: 655 ALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREI 714

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PN+SEE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVR
Sbjct: 715 PNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVR 774

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           D SLRVP    G V+DVRI+ R   D
Sbjct: 775 DNSLRVPKTEKGRVLDVRIYTREQGD 800



 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/584 (32%), Positives = 273/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVVKDEDGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ +G  V  G +L      +G   +   + +L A   
Sbjct: 608  EHFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAAANLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQPGKAWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M++I
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDI 1074



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 188/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PI+ ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELQNFSPISDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDELDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY   + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIESANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDNVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|21466005|pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
            Resolution
 gi|21466011|pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
            Resolution
 gi|21466018|pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
            Promoter Dna Complex At 6.5 A Resolution
          Length = 1118

 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/509 (37%), Positives = 255/509 (50%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 637  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 695

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 696  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 754

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 755  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 795

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 796  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 855

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  
Sbjct: 856  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKE 915

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +  + 
Sbjct: 916  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFDL- 968

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 969  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1023

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y++I+ G D  E   PES
Sbjct: 1024 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPES 1083

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1084 FRVLVKELQALALDVQTLDEKDNPVDIFE 1112



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 400/590 (67%), Gaps = 17/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L        ++ L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRL--------VHPLRRYARSNQGTAFDQR 639

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 640 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 699

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 700 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 759

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 760 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 809



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|20139789|sp|Q9KWU7|RPOB_THEAQ RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|62738682|pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
 gi|62738688|pdb|1YNN|C Chain C, Taq Rna Polymerase-Rifampicin Complex
 gi|109157856|pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For Structural
            Studies
 gi|7573273|emb|CAB65465.2| RNA polymerase, beta subunit [Thermus aquaticus]
          Length = 1119

 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/509 (37%), Positives = 255/509 (50%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 638  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 696

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 697  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 755

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 756  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 796

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 797  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 856

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  
Sbjct: 857  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKE 916

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +  + 
Sbjct: 917  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFDL- 969

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 970  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1024

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y++I+ G D  E   PES
Sbjct: 1025 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPES 1084

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1085 FRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L         + L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVE-------HPLRRYARSNQGTAFDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 810



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|13096178|pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
            Includes Complete Structure With Side-Chains (Except For
            Disordered Regions)-Further Refined From Original
            Deposition-Contains Additional Sequence Information
          Length = 1119

 Score =  497 bits (1280), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/509 (37%), Positives = 255/509 (50%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 638  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 696

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 697  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 755

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 756  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 796

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 797  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 856

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  
Sbjct: 857  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKE 916

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +  + 
Sbjct: 917  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFDL- 969

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 970  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1024

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y++I+ G D  E   PES
Sbjct: 1025 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPES 1084

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1085 FRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L         + L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVE-------HPLRRYARSNQGTAFDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 810



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|148240398|ref|YP_001225785.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. WH
           7803]
 gi|158513320|sp|A5GNH3|RPOB_SYNPW RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|147848937|emb|CAK24488.1| DNA-directed RNA polymerase beta chain [Synechococcus sp. WH 7803]
          Length = 1097

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 451/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSI-------------EAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G+V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGRVLKQGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG+   +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDSDGAILADLIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+R  EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 VDHS-------HYLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 188/584 (32%), Positives = 272/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHSHYLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAAANLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  +  ++  +  ++W             
Sbjct: 890  VVPFD---------------EMYGAEKSQQTVETFLKEAAKQPGKEWIY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+  L DG +GEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLQLIDGRSGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVFTDEGKEVDLMQDV 1074



 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 96/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|87301294|ref|ZP_01084135.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. WH
           5701]
 gi|87284262|gb|EAQ76215.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. WH
           5701]
          Length = 1096

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 329/726 (45%), Positives = 454/726 (62%), Gaps = 14/726 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
            Y       +              +          I+  E+VI +    + G+    ++ 
Sbjct: 82  MYVTCRLVNKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD 141

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS-EIRDIPILYVD 350
                   +  +     A      +  ++     D   + +   +  +  + D  +L   
Sbjct: 142 KNGRKTFNASLIPNRG-AWLKFETDKNDLLHVRVDKTRKINAHVLMRAIGLSDNDVLDKL 200

Query: 351 SVNNNAYIRNTLVTDKNKDRKD-ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
                         D+    +D ALL++Y+ +RPG+  + S  + + +  FFD  +YDL 
Sbjct: 201 RHPEYYKKSIEAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLG 260

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSV 467
            VGR K+N +L L  PD VR +  ED+++ I  L++L    G  ++DDID+LGNRRVRSV
Sbjct: 261 RVGRYKINKKLRLTIPDAVRTLTAEDVLSTIDYLINLELDVGGASLDDIDHLGNRRVRSV 320

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ R+GL R+ER IKER++  + +S+ P  L+N KP+V+A+ EFF SSQLSQ  +
Sbjct: 321 GELLQNQVRVGLNRLERIIKERMTVGETESLTPAQLVNPKPLVAAIKEFFGSSQLSQFMD 380

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL 
Sbjct: 381 QTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLA 440

Query: 588 SFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           + ARVN YGFIETP+ KV +G V    D +YLSA  E+   +A  + + D DG    EL+
Sbjct: 441 THARVNEYGFIETPFWKVENGFVHKQGDPIYLSADLEDECRVAPGDVATDADGRILAELI 500

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+
Sbjct: 501 PVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLR 560

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E P VGTG+E+ VA+ SG   + +  GIV  VDA  IVIR  +G          I+ L 
Sbjct: 561 PERPLVGTGLETQVARDSGMVPITRVNGIVTFVDATAIVIRDEQGTD-------HIHHLQ 613

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+QRSNQ+TC+NQRP+V  GD+V    ++A+G + + G++ALG+N+L+A+MPW GYN+ED
Sbjct: 614 KYQRSNQDTCLNQRPIVSQGDQVIAGQVLANGSACEGGEIALGQNVLIAYMPWEGYNYED 673

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+EE L N+DE GII +G
Sbjct: 674 AILVSERLVQDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLDEMGIIRIG 733

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           A V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVPS   G VVDVRI+
Sbjct: 734 AYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPSTERGRVVDVRIY 793

Query: 946 NRHGID 951
            R   D
Sbjct: 794 TREQGD 799



 Score =  493 bits (1269), Expect = e-137,   Method: Composition-based stats.
 Identities = 191/584 (32%), Positives = 272/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-FEVMARDTKLGP 858
                       +L    P  G   E  +     MV       I        +    + G 
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGIVTFVDATAIVIRDEQGT 606

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            + I              +++  I+  G +V  G +L      +G   +   + +L A   
Sbjct: 607  DHIHHLQKYQRSNQDTCLNQRPIVSQGDQVIAGQVLANGSACEG-GEIALGQNVLIAYMP 665

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 666  WEGYNYEDAILVSERLVQDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 725

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    Y    +IL G+    G         L   +  E  R               
Sbjct: 726  EMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 775

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 776  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 828

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DG+P+DIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 829  HGNKGIISRILPREDMPYLPDGSPIDIVLNPLGVPSRMNVGQVFECLMGWAASHLNCRVK 888

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G  +    +  Y +++     ++W         V+D 
Sbjct: 889  VVPFD---------------EMHGNETSKNTVQKYLEEAASEPGKEW---------VYDP 924

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             +                G+  L DG TGEPFD+PVTVGY ++LKL H+V DK++ARSTG
Sbjct: 925  EN---------------PGKIQLVDGRTGEPFDQPVTVGYAHILKLVHLVDDKIHARSTG 969

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 970  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1029

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +          M+++
Sbjct: 1030 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGVEVDLMQDV 1073



 Score =  317 bits (812), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 101/463 (21%), Positives = 198/463 (42%), Gaps = 39/463 (8%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS-- 78
             +  +PDL+EVQ+AS+  FL           +GL     S  PIT ++G   L FV   
Sbjct: 9   KTVTYLPDLVEVQRASFKWFL----------EKGLIEELDSFSPITDYTGKLELHFVGTE 58

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLM
Sbjct: 59  YRLKRPRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLM 109

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++V+Q+ RSPG++F  ++ +   +G+  +   +IP++G W+  E D 
Sbjct: 110 TERGTFIINGAERVIVNQIVRSPGVYFKDEQDK---NGRKTFNASLIPNRGAWLKFETDK 166

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAAD 253
            D++HVR+D+ RK+     + A+G+   ++L       +Y K + +   +       A  
Sbjct: 167 NDLLHVRVDKTRKINAHVLMRAIGLSDNDVLDKLRHPEYYKKSIEAANDEGISSEDQALL 226

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +           +  G+Q++ S         L +  + K  K L +T         AED
Sbjct: 227 ELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDAVRTLTAED 286

Query: 312 IVNGETGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           +++     I +E          ++ + +  +R +  L  + V         ++ ++    
Sbjct: 287 VLSTIDYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVG 346

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           +   L   +++ P      +  +  F            + +  +    R++   P     
Sbjct: 347 ETESLTPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG--- 401

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           + +E     ++ +     G+  I  I+         +G +  +
Sbjct: 402 LTRERAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|113953748|ref|YP_731555.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. CC9311]
 gi|123327615|sp|Q0I7L7|RPOB_SYNS3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|113881099|gb|ABI46057.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp.
           CC9311]
          Length = 1097

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 449/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVVD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSI-------------EAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ +V +G V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWRVENGVVQKSGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    EL+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDADGQILAELIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+R  EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 YD-------HTHFLQKYQRSNQDTCLNQRPIVRQGDPVIIGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 188/584 (32%), Positives = 271/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEGY 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHFLQKYQRSNQDTCLNQRPIVRQGDPVIIGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDI LNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDICLNPLGVPSRMNVGQVFELLMGWAAANLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  Y  ++  +  + W             
Sbjct: 890  IVPFD---------------EMYGPEKSQQTVQAYLKEAASQPGKDWIY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + ++ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPEDPGKLLLRDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVFTDEGKEVDLMQDV 1074



 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 96/440 (21%), Positives = 193/440 (43%), Gaps = 37/440 (8%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS-- 78
             +  +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L FV   
Sbjct: 10  KTVTYLPDLVEVQRASFKWFL----------DKGLIEELESFSPITDYTGKLELHFVGSE 59

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLM
Sbjct: 60  YRLKRPRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLM 110

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D 
Sbjct: 111 TERGTFIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDK 167

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAAD 253
            D++HVR+D+ RK+     + A+G+   +++       +Y K + +   +       A  
Sbjct: 168 NDLLHVRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEYYKKSIEAANDEGISSEDQALL 227

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +           +  G+Q++++         L +  + K  K L +T          ED
Sbjct: 228 ELYKKLRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHED 287

Query: 312 IVNGETGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           +++     I +E          ++ + +  +R +  L  + V         ++ ++    
Sbjct: 288 VLSTLDYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVG 347

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           +   L   +++ P      +  +  F            + +  +    R++   P     
Sbjct: 348 ETDSLTPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG--- 402

Query: 431 IRKEDIIAIIKILVDLRNGK 450
           + +E     ++ +     G+
Sbjct: 403 LTRERAGFAVRDIHPSHYGR 422


>gi|41017622|sp|Q50388|RPOB_MYCSM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|7144498|gb|AAA91426.2| DNA polymerase [Mycobacterium smegmatis]
          Length = 1169

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 319/677 (47%), Positives = 448/677 (66%), Gaps = 25/677 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +K  +    +   + G     +    +   + +       +     +      +  I+  
Sbjct: 183 DKSTEKTLHSVKVIPGRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIV-- 240

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  +  TL  D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+
Sbjct: 241 ERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLA 300

Query: 410 TVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
            VGR K+N +L L+   P     + +ED++A I+ LV L  G+ ++             D
Sbjct: 301 RVGRYKVNKKLGLNAGKPITSSTLTEEDVVATIEYLVRLHEGQTSMTVPGGVEFAVESHD 360

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+ L RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 361 IDHFGNRRLRTVGELIQNQIRVRLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 420

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 421 FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 480

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+ + YL+A EE+   +AQANS  D
Sbjct: 481 EGPNIGLIGSLSVYARVNPFGFIETPYRKVVEGVVTDQIDYLTADEEDRHVVAQANSPTD 540

Query: 636 EDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+G FTE+ V  R   GE   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 541 ENGRFTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 600

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +     + + G++E+V A  I + + +G    
Sbjct: 601 NMQRQAVPLVRSEAPLVGTGMELRAAIDA-VTWSSHKTGVIEEVSADYITVMADDGTRQS 659

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  YRL KF RSN  TC NQRP+V  G  V    +IADGP T  G++ALG+N+LVA
Sbjct: 660 -------YRLRKFARSNHGTCANQRPIVDAGQRVEAGQVIADGPCTQNGEMALGKNLLVA 712

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            MPW G+N+ED++++S R+V EDV TSIHIEE E+ ARDTKLG EEITR IP +S+E L 
Sbjct: 713 IMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRVIPKLSDEVLA 772

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE  I+ +GAEV  G+ILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 773 DLDEPRIVRIGAEVRDGEILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 832

Query: 935 VSGTVVDVRIFNRHGID 951
            SG V+ +R+F+R   D
Sbjct: 833 ESGKVIGIRVFSREDDD 849



 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 182/524 (34%), Positives = 256/524 (48%), Gaps = 73/524 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      +    M   + LL AI   +  +  D  +     V   V+
Sbjct: 679  IVDAGQRVEAGQVIADGPCTQN-GEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVL 737

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ-------VILDRNIYSRLMEILCGQ 993
                   H  + + R   +  E+I  +     DE         I+      R  EIL G+
Sbjct: 738  TSIHIEEH--EIDARDTKLGAEEITRVIPKLSDEVLADLDEPRIVRIGAEVRDGEILVGK 795

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G         L   +  E  R                 E      +          
Sbjct: 796  VTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGESGKVI 838

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              ++   +  D++P GV  +V+V+VA KR I  GDK+A RHGNKG++ +ILP EDMPFL 
Sbjct: 839  GIRVFSREDDDELPVGVNELVRVYVAQKRKISDGDKLARRHGNKGVIGKILPVEDMPFLP 898

Query: 1114 DGTPVDIVLNPLGVPSR--MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            DGTPVDI+LN  G   R  +N+GQI ETHLGW     G  I  L         +      
Sbjct: 899  DGTPVDIILNTHGC--RVVLNIGQILETHLGWGAKA-GWNIDVLAGVPDWASKLPE---- 951

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR------- 1224
              ++    + +                       V+TPVFDGA E  +  +L        
Sbjct: 952  --ELYSAPADST----------------------VATPVFDGAQEGELAGLLGSTLPNRD 987

Query: 1225 -MADLDESGQSILYDGLT-GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                ++  G++ L+DG + GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQP
Sbjct: 988  GEVMVNADGKATLFDGRSSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQP 1047

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            LGGK+  GGQR GEME W +QAYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G
Sbjct: 1048 LGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPG 1107

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCELK 1386
             PESF VL+KE+Q+L L++++ +S  +      E+ D +  +L+
Sbjct: 1108 IPESFKVLLKELQSLCLNVEVLSSDGRAI----EMRDGDDEDLE 1147



 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 96/332 (28%), Positives = 155/332 (46%), Gaps = 28/332 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFL---MMNIAPDERPNE----GLQAAFKSVFPITA 67
             F K  E +++  L++VQ  S++  +    +  A  +R  E    GL+     + PI  
Sbjct: 30  VSFAKLREPLEVRGLLDVQTDSFEWLVGSRRVRQAAIDRGEENPVGGLEEVLAELSPIED 89

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG+  L F    FD  K  VD+C  +D+TYA PL +T   I           +  +IK 
Sbjct: 90  FSGSMSLSFSDPRFDEVKASVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIKS 140

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q+++MGD P+MT+ GTF+I G +R+VVSQL RSPG++FD    +   + K L++ ++IP 
Sbjct: 141 QTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKTLHSVKVIPG 198

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
           +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F    +     +    
Sbjct: 199 RGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTNEQIVERFGFSEIMMGTLEKDTT 258

Query: 248 PLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             +   L+   +       +  GE    ES + L   L    K   +  +G         
Sbjct: 259 SGTDEALLDIYR------KLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYK---VNK 309

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            +  +     T     E   V   + L  +  
Sbjct: 310 KLGLNAGKPITSSTLTEEDVVATIEYLVRLHE 341


>gi|157414087|ref|YP_001484953.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
            str. MIT 9215]
 gi|166991526|sp|A8G6Y6|RPOB_PROM2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|157388662|gb|ABV51367.1| RNA polymerase beta subunit [Prochlorococcus marinus str. MIT 9215]
          Length = 1097

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/584 (32%), Positives = 270/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV       I    +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDDHGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ +G  V  G +L      +G   +   + +L A   
Sbjct: 608  EHFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQPGKAWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M++I
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDI 1074



 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/686 (47%), Positives = 456/686 (66%), Gaps = 27/686 (3%)

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +++ ++G++  +  +   +   +KF    ++ L         +N     + + A  + D
Sbjct: 138 KDELDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSD 194

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              ++++ H E     I              +   +       ALL++Y+ +RPG+  + 
Sbjct: 195 NDVVDKLRHPEFYQSSI-------------ESANDEGINSEDQALLELYKKLRPGEPPSV 241

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           S  + + +  FFD  +YDL  VGR K+N +L L  PDDVR +  ED+++ I  L++L   
Sbjct: 242 SGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTIDYLINLELD 301

Query: 450 KG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N K
Sbjct: 302 IGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPK 361

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYG
Sbjct: 362 PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYG 421

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENR 625
           R+CP ET EG N GL++SL + ARVN YGFIETP+ +V +GKV  +   VYLSA  E+  
Sbjct: 422 RLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGKVDKEGNPVYLSADLEDEC 481

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + D++G+    L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+D
Sbjct: 482 RVAPGDVATDKEGNIIANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHD 541

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  GIV  VDA  IV+
Sbjct: 542 DANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVV 601

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +   G+          + L K+QRSNQ+TC+NQRP+VK+GD V    ++ADG + + G++
Sbjct: 602 KDDHGNE-------HFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEGGEI 654

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+I
Sbjct: 655 ALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREI 714

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PN+SEE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVR
Sbjct: 715 PNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVR 774

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           D SLRVP    G V+DVRI+ R   D
Sbjct: 775 DNSLRVPKTEKGRVLDVRIYTREQGD 800



 Score =  314 bits (804), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 188/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PI+ ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EQGLIEELQNFSPISDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDELDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY   + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIESANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|14278483|pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 1118

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 190/509 (37%), Positives = 255/509 (50%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 637  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 695

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 696  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 754

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 755  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 795

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 796  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 855

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  
Sbjct: 856  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKE 915

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +  + 
Sbjct: 916  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFDL- 968

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 969  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1023

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y++I+ G D  E   PES
Sbjct: 1024 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPSVPES 1083

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1084 FRVLVKELQALALDVQTLDEKDNPVDVFE 1112



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 400/590 (67%), Gaps = 17/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L        ++ L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRL--------VHPLRRYARSNQGTAFDQR 639

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 640 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 699

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 700 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 759

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 760 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 809



 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|331123716|gb|AEC53646.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123718|gb|AEC53647.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123720|gb|AEC53648.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123722|gb|AEC53649.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123724|gb|AEC53650.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123726|gb|AEC53651.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123734|gb|AEC53655.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123736|gb|AEC53656.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123744|gb|AEC53660.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123748|gb|AEC53662.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123770|gb|AEC53673.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123772|gb|AEC53674.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123784|gb|AEC53680.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123786|gb|AEC53681.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123788|gb|AEC53682.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123790|gb|AEC53683.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123792|gb|AEC53684.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123796|gb|AEC53686.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123800|gb|AEC53688.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123804|gb|AEC53690.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123824|gb|AEC53700.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123828|gb|AEC53702.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123832|gb|AEC53704.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123870|gb|AEC53723.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123872|gb|AEC53724.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123890|gb|AEC53733.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123908|gb|AEC53742.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123914|gb|AEC53745.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123916|gb|AEC53746.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123922|gb|AEC53749.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123924|gb|AEC53750.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123930|gb|AEC53753.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123938|gb|AEC53757.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123940|gb|AEC53758.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123942|gb|AEC53759.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123944|gb|AEC53760.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123946|gb|AEC53761.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123952|gb|AEC53764.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123956|gb|AEC53766.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123958|gb|AEC53767.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123962|gb|AEC53769.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123964|gb|AEC53770.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123966|gb|AEC53771.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123968|gb|AEC53772.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123970|gb|AEC53773.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123972|gb|AEC53774.1| RNA polymerase subunit B [Vibrio harveyi]
 gi|331123974|gb|AEC53775.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123976|gb|AEC53776.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123980|gb|AEC53778.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123982|gb|AEC53779.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123984|gb|AEC53780.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123986|gb|AEC53781.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123988|gb|AEC53782.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123990|gb|AEC53783.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 523

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 257/526 (48%), Positives = 363/526 (69%), Gaps = 3/526 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 523


>gi|46360996|gb|AAS89231.1| RpoB [Corynebacterium terpenotabidum]
          Length = 1094

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 319/660 (48%), Positives = 448/660 (67%), Gaps = 24/660 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +       +I          +  +  TL  
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEI----TQRFGFSEIMMTTLEK 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T   A+++    FF + +YDL+ VGR K+N +L LD 
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 304

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGT------------IDDIDNLGNRRVRSVGEMLK 472
                 + ++DI+  I+ LV L  G+ +            +DDID+ GNRR+R+VGE+++
Sbjct: 305 DSGAMTLTEQDILTTIEYLVRLHAGEKSMTSPDGQDIPLGVDDIDHFGNRRLRTVGELIQ 364

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSL
Sbjct: 365 NQIRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSL 424

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ +L ++ARV
Sbjct: 425 SGLTHKRRLSALGPGGLSRERAGLEVRDVHASHYGRMCPIETPEGPNIGLIGNLATYARV 484

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N +GFIETPYR+V +G +T+ V YL+A EE+   IAQA + +D DG F +  +  R   G
Sbjct: 485 NPFGFIETPYRRVSEGVITDQVDYLTADEEDRHIIAQAKTLVDADGRFVDAEIEVRLRGG 544

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           +  +VP  ++D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPLL++EAP+V
Sbjct: 545 DVEVVPATQVDYMDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLLRSEAPYV 604

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME   A  +G  IV  +AG VE V A  I I   +G  D        Y L KF+R+N
Sbjct: 605 GTGMELRSAYDAGDVIVTPKAGAVEYVSADYITIMDDDGVRD-------TYMLRKFERTN 657

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC NQ+PLV+ G  V     IADGP T  G+++LGRN+LVAFMPW G+N+ED++++++
Sbjct: 658 QGTCYNQKPLVEQGQRVEAGQAIADGPGTHHGEMSLGRNLLVAFMPWEGHNYEDAIILNQ 717

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           RMV +D+ TSIHIEE E+ ARDTKLGPEEITRDIPNV ++ L ++D+ GI+ +GA+V  G
Sbjct: 718 RMVEDDLLTSIHIEEHEIDARDTKLGPEEITRDIPNVGDDVLADLDDRGIVRIGADVRDG 777

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR+F+R   D
Sbjct: 778 DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRVFSREDDD 837



 Score =  452 bits (1164), Expect = e-124,   Method: Composition-based stats.
 Identities = 175/475 (36%), Positives = 235/475 (49%), Gaps = 63/475 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  G  +           M+    LL A    +  +  D  +     V   ++
Sbjct: 667  LVEQGQRVEAGQAIADGPGT-HHGEMSLGRNLLVAFMPWEGHNYEDAIILNQRMVEDDLL 725

Query: 941  DVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRLMEILCG 992
                   H  + + R   +  E+I        + +  D DD   I+      R  +IL G
Sbjct: 726  TSIHIEEH--EIDARDTKLGPEEITRDIPNVGDDVLADLDDR-GIVRIGADVRDGDILVG 782

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   +  E  R                 E      +         
Sbjct: 783  KVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKV 825

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               ++   +  DD+ PGV ++V+V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPFL
Sbjct: 826  IGVRVFSREDDDDLAPGVNQMVRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPAEDMPFL 885

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LN  GVP RMN+GQ+ ETHLGW     G K+     D K    +  L   L
Sbjct: 886  PDGTPVDIILNTHGVPRRMNIGQVLETHLGWLAKN-GWKVDPESPDPKIQEMLKTLPEDL 944

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA-----D 1227
              V                              VSTPVFDGA+   ++ +LR        
Sbjct: 945  YDVPPESL-------------------------VSTPVFDGAENAELSGLLRSVRPNADG 979

Query: 1228 LD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
            L    E G+++L DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLG
Sbjct: 980  LPLTDEFGKAVLIDGRSGEPYPYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLG 1039

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            GK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  
Sbjct: 1040 GKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIP 1094



 Score =  294 bits (752), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 142/301 (47%), Gaps = 24/301 (7%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L++VQ+ S+   +                +R   GL+     + P
Sbjct: 16  RYSFAKIHAPIEVPGLLDVQRESFAWLVGTPEWRARRQAQAEEGDRVTSGLEDILDELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +  +S    L      FD  K  +D+C  +D+ Y+ PL +T                  +
Sbjct: 76  VEDYSENMSLTLSEPRFDDVKNTIDECKDKDINYSAPLYVTAEFT---------NALSGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF+I G +R+VVSQL RSPG++FD        + + L+A ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIINGTERVVVSQLVRSPGVYFDESIDP--STERPLHAVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG+ +EEI   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGLTTEEITQRFGFSEIMMTTLEK 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           D       A   +   +        D+ + ++E+         L K  + K  + LG+  
Sbjct: 245 DGVANTDEALLEIYRKQRPGESPTRDSAQALLENSFFKAKRYDLAKVGRYKVNRKLGLDG 304

Query: 301 D 301
           D
Sbjct: 305 D 305


>gi|254526732|ref|ZP_05138784.1| DNA-directed RNA polymerase, beta subunit [Prochlorococcus marinus
            str. MIT 9202]
 gi|221538156|gb|EEE40609.1| DNA-directed RNA polymerase, beta subunit [Prochlorococcus marinus
            str. MIT 9202]
          Length = 1097

 Score =  497 bits (1279), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/584 (32%), Positives = 270/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV       I    +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDDHGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ +G  V  G +L      +G   +   + +L A   
Sbjct: 608  EHFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQPGKAWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M++I
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDI 1074



 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/686 (47%), Positives = 456/686 (66%), Gaps = 27/686 (3%)

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +++ ++G++  +  +   +   +KF    ++ L         +N     + + A  + D
Sbjct: 138 KDELDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSD 194

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              ++++ H E     I              +   +       ALL++Y+ +RPG+  + 
Sbjct: 195 NDVVDKLRHPEFYQNSI-------------ESANDEGINSEDQALLELYKKLRPGEPPSV 241

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           S  + + +  FFD  +YDL  VGR K+N +L L  PDDVR +  ED+++ I  L++L   
Sbjct: 242 SGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTIDYLINLELD 301

Query: 450 KG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N K
Sbjct: 302 IGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPK 361

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYG
Sbjct: 362 PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYG 421

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENR 625
           R+CP ET EG N GL++SL + ARVN YGFIETP+ +V +GKV  +   VYLSA  E+  
Sbjct: 422 RLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVKNGKVDKEGNPVYLSADLEDEC 481

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + D++G+    L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+D
Sbjct: 482 RVAPGDVATDKEGNIIANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHD 541

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  GIV  VDA  IV+
Sbjct: 542 DANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVV 601

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +   G+          + L K+QRSNQ+TC+NQRP+VK+GD V    ++ADG + + G++
Sbjct: 602 KDDHGNE-------HFHYLQKYQRSNQDTCLNQRPIVKIGDRVISGQVLADGSACEGGEI 654

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+I
Sbjct: 655 ALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREI 714

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PN+SEE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVR
Sbjct: 715 PNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVR 774

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           D SLRVP    G V+DVRI+ R   D
Sbjct: 775 DNSLRVPKTEKGRVLDVRIYTREQGD 800



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 188/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PI+ ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EQGLIEELQNFSPISDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDELDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY   + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQNSIESANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|46360962|gb|AAS89214.1| RpoB [Corynebacterium durum]
          Length = 1113

 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 181/493 (36%), Positives = 245/493 (49%), Gaps = 61/493 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M     LL A    +  +  D  +     V   ++
Sbjct: 668  LVDIGDRVEAGQVIADGPGTDN-GEMALGRNLLVAFMPWEGHNYEDAIILNQRLVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D DD   I+      R  +IL G+ 
Sbjct: 727  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDDR-GIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +       DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 829  VRRFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFLPD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  I +   D K              
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWSIDTNNPDNKD------------- 934

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
                            + +        +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 935  --------------LMEMLPEELYDVPAGSLTATPVFDGASNEELAGLLANSRPNRDGDI 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  LVDGNGKAQLIDGRSGEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1100

Query: 1347 FNVLVKEMQALGL 1359
            F VL+KE+Q+L L
Sbjct: 1101 FKVLLKELQSLCL 1113



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 329/657 (50%), Positives = 460/657 (70%), Gaps = 25/657 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I    V+    +  +  TL +
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTHEQI----VERFGFSEIMMTTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDSSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D    + +EDI   ++ LV L  G+              +DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGTMVLTEEDIATTLEYLVRLHAGETTMTSPTGAVIPVEVDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+S+A+
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSYAQ 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DGK+T+ + YL+A EE+   +AQAN+  D+DG+ TEE V  R   
Sbjct: 485 VNPFGFIETPYRKVVDGKLTDQIDYLTADEEDRHVVAQANTPFDKDGNITEERVVVRMKG 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V    ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 545 GDIEVVNATDIDYMDISPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +++K++G+VE + A  I +   +G  D        Y L KFQR+
Sbjct: 605 VGTGMELRAAYDAGDLVISKKSGVVENLSADFITVMGDDGIRD-------TYILRKFQRT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ+PLV +GD V    +IADGP TD G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQKPLVDIGDRVEAGQVIADGPGTDNGEMALGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK++D+ GI+ +GA+V  
Sbjct: 718 QRLVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDDRGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR F+R
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRRFSR 834



 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 93/389 (23%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            ++   R   GL+   + + 
Sbjct: 15  ERYSFAKITEPIEVPGLLDLQLESFAWLIGTPEWRARMQEKVSEGTRVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   +  D           
Sbjct: 75  PIQDYSGNMSLSLSEPRFEEVKYSIDECKEKDINYSAPLYVTAEFVNND---------TG 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERALHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I+  F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTHEQIVERFGFSEIMMTTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + +++S         L K  + K  + LG+ 
Sbjct: 244 SDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLDSSFFRAKRYDLAKVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   TG +       ++   ++   +  +R
Sbjct: 304 GDHDGTMVLTEEDIATTLEYLVRLHAGETTMTSPTGAVI-----PVEVDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|124022146|ref|YP_001016453.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9303]
 gi|158512749|sp|A2C6S8|RPOB_PROM3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|123962432|gb|ABM77188.1| RNA polymerase beta subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 1097

 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 324/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSIEAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 VKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G++  +   +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNQYGFIETPFWKVENGRLIKEGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    EL+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDADGQILAELIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G+V  VDA  I++R  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGMVTFVDATAIIVRDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 VD-------HTHYLQKYQRSNQDTCLNQRPIVCQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVA+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLVAYMPWEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 268/584 (45%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-FEVMARDTKLGP 858
                       +L    P  G   E  +     MV       +        +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGMVTFVDATAIIVRDEDGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+C G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHYLQKYQRSNQDTCLNQRPIVCQGDPVIVGQVLADGSACEG-GEIALGQNVLVAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   V +V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVARVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMPFL DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPFLPDGTPVDIVLNPLGVPSRMNVGQVFECLMGWAAANLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  Y  ++  +  ++W             
Sbjct: 890  VVPFD---------------EMYGAEKSQQTVEAYLKEAAKQPGKEWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + +  G+  L DG +GEPFD+PVTVGY  +LKL H+V DK++ARSTG
Sbjct: 924  -------------NPENPGKLQLIDGRSGEPFDQPVTVGYAQILKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGKEVDLMQDV 1074



 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 103/492 (20%), Positives = 207/492 (42%), Gaps = 47/492 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          +EGL     S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DEGLIEELDSFSPITDYTGKLELHFVGNEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAANEEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAVKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERS 485
               ++ +     G+    +               + RV   G +    +++   R+ + 
Sbjct: 408 AGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNQYGFIETPFWKVENGRLIKE 467

Query: 486 IKERISSVDIDS 497
                 S D++ 
Sbjct: 468 GDPIYLSADLED 479


>gi|253757163|gb|ACT35180.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    ++E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFVNEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|221194783|ref|ZP_03567840.1| DNA-directed RNA polymerase, beta subunit [Atopobium rimae ATCC
            49626]
 gi|221185687|gb|EEE18077.1| DNA-directed RNA polymerase, beta subunit [Atopobium rimae ATCC
            49626]
          Length = 1183

 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 191/618 (30%), Positives = 281/618 (45%), Gaps = 88/618 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI-------HIEEFEVMAR 852
                       ++ +  P+ G   E    +    +               H+  +     
Sbjct: 588  MGANMQRQAVPLIRSHAPYVGTGMEARAALDSGELICAKHAGEITEADAAHVTVYSDE-- 645

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G E         S +    I+   I+ VG  V  G  L    +    S +     L
Sbjct: 646  ---YGSETYDLPKYERSNQS-TCINHRPIVKVGDLVEKGQPLADGPS-VDHSELALGANL 700

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK- 971
              A    +  +  D  +     +   ++     +RH  + + R   +  E+I     +  
Sbjct: 701  TVAYMPWEGYNYEDGIIVSERVMQEDLLTSVNISRH--EIDARDTKIGSEEITREIPNVG 758

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            +D    LD +   R+        A  GP       V      SE   ++  +    ++  
Sbjct: 759  EDMLANLDEDGIIRIG-------AEVGPGDILVGKVTPKGETSETAEAKLLRAIFGNKSN 811

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEK--IQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 SL+V + +   +++    ++ +K   + G+++PPGV  +V+V++A +R IQ GDK
Sbjct: 812  DVRDTSLRVPHGSYGRVVDVVRFDRKDKGSDEKGNELPPGVNTLVRVYIAQRRKIQQGDK 871

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG++ ++LP EDMP++ DGTP+D++L+PLGVPSRMNVGQ+ E HLGW      
Sbjct: 872  IAGRHGNKGVICKVLPVEDMPYMADGTPIDVILDPLGVPSRMNVGQLLECHLGWGAAH-- 929

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                                                    DD            +PVSTP
Sbjct: 930  --------------------------------------GWDDDDADSKRYVPGPIPVSTP 951

Query: 1210 VFDGADEEAINS--------MLRMA--------------DLDESGQSILYDGLTGEPFDR 1247
            +FDGA +E +          ML  A               L+  G++ LYDG TGE F  
Sbjct: 952  LFDGATDEDVAEIVRRTNINMLNKAQQEYGEHMREEFIPQLNGRGKTTLYDGRTGEAFKS 1011

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P+TVG  Y+LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA
Sbjct: 1012 PITVGCSYILKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGA 1071

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            A VLQE+LT+KSDD  GR + YESI+ G +    G PESF VLVKE+++L L I+  + R
Sbjct: 1072 ANVLQEILTVKSDDTNGRVKTYESIIKGENIPTAGIPESFKVLVKEIRSLALDIEPISYR 1131

Query: 1368 TKNSAKMEEIPDFNKCEL 1385
             +N    +   D ++   
Sbjct: 1132 KRNEQTHKSTEDSSEKTF 1149



 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 313/667 (46%), Positives = 428/667 (64%), Gaps = 34/667 (5%)

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
           + G + +         +   +    I       +  + ++  +RNT+  D    ++DALL
Sbjct: 185 KRGHLVVSIDRKRRMSATIFLRALGIAVTDDEILSLLGDSDVVRNTIERDTATTKEDALL 244

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           +++R  RPG+  T   A ++ N L+F   +YDL+ VGR K+N +L L+   D R +  ED
Sbjct: 245 EVFRRQRPGEPPTVDSARTLINNLYFHHQRYDLARVGRYKINKKLGLEIAADQRILTDED 304

Query: 436 IIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
           I+A ++ L+ +  G     +DDID+ GNRRVR+VGE+++NQ+R+G+ RMER ++ER++S 
Sbjct: 305 IVAALQFLLAVHAGDETKHLDDIDHFGNRRVRTVGELVQNQFRIGMSRMERVVRERMASQ 364

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV---- 549
           D D + P  LIN +P+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+    
Sbjct: 365 DPDDIAPDTLINIRPIVAAIKEFFGSSQLSQFMDQSNPLAGLTHKRRLSALGPGGLAGHK 424

Query: 550 ----ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                R      +RDVH +HY R+CP ET EG NIGL+ SL  +A VN YGFIE PYRKV
Sbjct: 425 SGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGPNIGLIGSLALYAHVNEYGFIEAPYRKV 484

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE-----------LVFCRCAGE-- 652
             GK TN++V+++A EEEN  IA AN+ +D       E            V  R      
Sbjct: 485 AGGKATNEIVWMTADEEENHIIAPANTPIDPKTGRFVEIDHSGKVVNADRVIARTRDFDG 544

Query: 653 ----EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                  V  E +D +D SP+Q++S+AA+LIPFLE+DD+ R LMG NMQRQAVPL+++ A
Sbjct: 545 SFGAPAQVSVEDVDRMDVSPRQLLSVAANLIPFLEHDDAKRTLMGANMQRQAVPLIRSHA 604

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTGME+  A  SG  I AK AG + + DA  + + S E        G + Y L K++
Sbjct: 605 PYVGTGMEARAALDSGELICAKHAGEITEADAAHVTVYSDE-------YGSETYDLPKYE 657

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+TC+N RP+VKVGD V +   +ADGPS D  +LALG N+ VA+MPW GYN+ED ++
Sbjct: 658 RSNQSTCINHRPIVKVGDLVEKGQPLADGPSVDHSELALGANLTVAYMPWEGYNYEDGII 717

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER++ ED+ TS++I   E+ ARDTK+G EEITR+IPNV E+ L N+DE GII +GAEV
Sbjct: 718 VSERVMQEDLLTSVNISRHEIDARDTKIGSEEITREIPNVGEDMLANLDEDGIIRIGAEV 777

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVGK+TPKGE+  T E KLLRAIFG K+ DVRDTSLRVP G  G VVDV  F+R 
Sbjct: 778 GPGDILVGKVTPKGETSETAEAKLLRAIFGNKSNDVRDTSLRVPHGSYGRVVDVVRFDRK 837

Query: 949 GIDKNER 955
               +E+
Sbjct: 838 DKGSDEK 844



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 100/372 (26%), Positives = 167/372 (44%), Gaps = 44/372 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ F K PE + +P+LIEVQ+ S++ F+           EGLQ +F    PI + +G   
Sbjct: 24  RRTFSKIPEAMPLPNLIEVQRESFERFMG----------EGLQESFSEFSPIESNNGTME 73

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           + F  ++F  P   + +C  +D+TY  PL + +  +          K   + KEQ IYMG
Sbjct: 74  VVFGDHQFGDPISSIAECRAKDMTYQAPLMVDITFL---------NKETGEKKEQLIYMG 124

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D PLMT+ GTF+I G +R+VVSQL RSPG++F  +      +G L++  + IP +G W++
Sbjct: 125 DFPLMTERGTFIINGTERVVVSQLVRSPGVYFSAEMD----NGILVHHAQFIPARGAWLE 180

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D +  + V IDR+R++  T FL ALG+    +EILS      V     +        
Sbjct: 181 FEIDKRGHLVVSIDRKRRMSATIFLRALGIAVTDDEILSLLGDSDVVRNTIERDTATTKE 240

Query: 252 ADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYVA 309
             L+   +          GE   ++S + L + L    +   +  +G    +   GL +A
Sbjct: 241 DALLEVFRRQ------RPGEPPTVDSARTLINNLYFHHQRYDLARVGRYKINKKLGLEIA 294

Query: 310 EDIVNGETGEIYIEA----------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
            D     T E  + A           +      ++   +  +R +  L  +         
Sbjct: 295 ADQR-ILTDEDIVAALQFLLAVHAGDETKHLDDIDHFGNRRVRTVGELVQNQFRIGMSRM 353

Query: 360 NTLVTDKNKDRK 371
             +V ++   + 
Sbjct: 354 ERVVRERMASQD 365


>gi|318042319|ref|ZP_07974275.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. CB0101]
          Length = 1096

 Score =  496 bits (1278), Expect = e-138,   Method: Composition-based stats.
 Identities = 331/681 (48%), Positives = 447/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G+K  +  L   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 142 KNGRKTFNASLIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAIGLSDNDVLD 198

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  ++
Sbjct: 199 KLRHPEYYQKSI-------------EAANDEGIASEDQALLELYKKLRPGEPPSVSGGQT 245

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR K+N +L L  PD  R +  ED+++ I  L++L    G  T
Sbjct: 246 LLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDATRTLTPEDVLSTIDYLINLELDVGGAT 305

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + +S+ P  L+N KP+V+A
Sbjct: 306 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETESLTPAQLVNPKPLVAA 365

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP 
Sbjct: 366 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRICPI 425

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL+ SL + ARVN YGFIETP+ KV +G V    D +YLSA  E+   +A  
Sbjct: 426 ETPEGPNAGLIGSLATHARVNEYGFIETPFWKVENGIVLKQGDPLYLSADLEDECRVAPG 485

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    +LV  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 486 DVATDADGRIKADLVPVRYRQDFETVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 545

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +    G V  VDA  IVIR  EG
Sbjct: 546 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITTVNGTVAYVDATAIVIRDEEG 605

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+N RP+VK+GD V    ++A+G + + G++ALG+N
Sbjct: 606 ND-------HTHYLQKYQRSNQDTCLNHRPIVKLGDPVIAGQVLANGSACEGGEIALGQN 658

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 659 VLIAYMPWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 718

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 719 ESLGNLDEMGIIRVGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 778

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 779 VPSTERGRVVDVRIYTREQGD 799



 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 190/584 (32%), Positives = 272/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITTVNGTVAYVDATAIVIRDEEGN 606

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                ++   I+ +G  V  G +L      +G   +   + +L A   
Sbjct: 607  DHTHYLQKYQRSNQDTCLNHRPIVKLGDPVIAGQVLANGSACEG-GEIALGQNVLIAYMP 665

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 666  WEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 725

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    Y    +IL G+    G         L   +  E  R               
Sbjct: 726  EMGIIRVGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 775

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 776  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 828

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DG+P+DIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 829  HGNKGIISRILPLEDMPYLPDGSPIDIVLNPLGVPSRMNVGQVFECLMGWAASHLDCRVK 888

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G  +    +  Y + +  +  + W         V+D 
Sbjct: 889  VVPFD---------------EMHGPETSKNTVQAYLEAAKSQPGKDW---------VYDP 924

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             +                G+  L DG TGE FD+PVTVGY ++LKL H+V DK++ARSTG
Sbjct: 925  EN---------------PGKIQLIDGRTGEAFDQPVTVGYAHILKLVHLVDDKIHARSTG 969

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 970  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1029

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     +    M++I
Sbjct: 1030 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDAGEEVDLMQDI 1073



 Score =  313 bits (803), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 98/458 (21%), Positives = 196/458 (42%), Gaps = 39/458 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L F+   Y    
Sbjct: 14  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFIGSEYRLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 64  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  +   +IP++G W+  E D  D++H
Sbjct: 115 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRKTFNASLIPNRGAWLKFETDKNDLLH 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       +Y K + +   +       A   +   
Sbjct: 172 VRVDKTRKINAHVLMRAIGLSDNDVLDKLRHPEYYQKSIEAANDEGIASEDQALLELYKK 231

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+ ++ S         L +  + K  K L +T          ED+++  
Sbjct: 232 LRPGEPPSVSGGQTLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDATRTLTPEDVLSTI 291

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 292 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETESL 351

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 352 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 406

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
               ++ +     G+  I  I+         +G +  +
Sbjct: 407 AGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|253757199|gb|ACT35198.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757137|gb|ACT35167.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
 gi|253757181|gb|ACT35189.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|87125367|ref|ZP_01081213.1| RNA polymerases beta subunit [Synechococcus sp. RS9917]
 gi|86167136|gb|EAQ68397.1| RNA polymerases beta subunit [Synechococcus sp. RS9917]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVVD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYRKSI-------------EAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G+V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVDNGRVLKQGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D +G    +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDAEGQILADLIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+R  EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 VD-------HTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V+ED++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVNEDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 272/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEEGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVNEDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  +  ++  +  + W             
Sbjct: 890  VVPFD---------------EMYGDEKSQQTVEAFLKEAASQPGKDWIY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLLLRDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVFTDEGKEVDLMQDV 1074



 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 96/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEYYRKSIEAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|116071172|ref|ZP_01468441.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. BL107]
 gi|116066577|gb|EAU72334.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. BL107]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 321/681 (47%), Positives = 449/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVLD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             +    +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSI-------------DAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD+ +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDAKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G V  + D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGVVIKSGDPIYLSADREDEVRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + +++G    +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATEDNGEIKADLIPVRYRQDFEKVPPEQVDYVALSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E   VGTG+E+ VA+ SG   +++  G V  VDA  IV+   +G
Sbjct: 547 LMGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTVVYVDANAIVVLDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG +   G++ALG+N
Sbjct: 607 QE-------HTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACQGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G VVDVRI+ R   D
Sbjct: 780 VPGTERGRVVDVRIYTREQGD 800



 Score =  487 bits (1253), Expect = e-135,   Method: Composition-based stats.
 Identities = 182/529 (34%), Positives = 257/529 (48%), Gaps = 62/529 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             + G E                +++  I+  G  V  G +L      +G   +   + +L
Sbjct: 603  DEDGQEHTHFLQKYQRSNQDTCLNQRPIVRQGDPVIVGQVLADGSACQG-GEIALGQNVL 661

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD- 970
             A    +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A + 
Sbjct: 662  IAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEES 721

Query: 971  --KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE  I+    +    +IL G+    G         L   +  E  R          
Sbjct: 722  LGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN----- 776

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                              +        +I   + GD++PPG   VV+V+VA +R IQ GD
Sbjct: 777  ------------SLRVPGTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGD 824

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L
Sbjct: 825  KMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNL 884

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
              ++K +  D               ++ G     + ++ +  ++     + W        
Sbjct: 885  DCRVKIVPFD---------------EMHGAEKSQQTVTTFLTEAAKLSGKDWVY------ 923

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                              + D  G+ +L DG TG PFD+PV VGY + LKL H+V DK++
Sbjct: 924  ------------------NPDNPGKLVLRDGRTGLPFDQPVAVGYSHFLKLVHLVDDKIH 965

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR   
Sbjct: 966  ARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEA 1025

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
              +IV G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1026 LNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVYTEEGKEVDLMQDV 1074



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 97/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DKGLIEELESFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVLDKLRHPEFYKKSIDAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDAKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|260435164|ref|ZP_05789134.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp. WH
           8109]
 gi|260413038|gb|EEX06334.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp. WH
           8109]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 322/676 (47%), Positives = 449/676 (66%), Gaps = 27/676 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVLD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             +    +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSI-------------DAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGVVLKDGDPIYLSADREDEVRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D+DG  + +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDDDGRISADLIPVRYRQDFEKVPPEQVDYVALSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E   VGTG+E+ VA+ SG   +++  G V  VDA  IV++  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTVTYVDANAIVVQDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 ND-------HTHFLQKYQRSNQDTCLNQRPIVRCGDPVIVGQVMADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V+ED++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDALLVSERLVTEDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFN 946
           VP    G VVDVRI+ 
Sbjct: 780 VPGTERGRVVDVRIYT 795



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 180/530 (33%), Positives = 259/530 (48%), Gaps = 62/530 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G +                +++  I+  G  V  G ++      +G   +   + +
Sbjct: 602  QDEDGNDHTHFLQKYQRSNQDTCLNQRPIVRCGDPVIVGQVMADGSACEG-GEIALGQNV 660

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A    +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +
Sbjct: 661  LIAYMPWEGYNYEDALLVSERLVTEDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEE 720

Query: 971  ---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE  I+    +    +IL G+    G         L   +  E  R         
Sbjct: 721  SLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---- 776

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                               +        +I   + GD++PPG   VV+V+VA +R IQ G
Sbjct: 777  -------------SLRVPGTERGRVVDVRIYTGEQGDELPPGANMVVRVYVAQRRKIQVG 823

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   
Sbjct: 824  DKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASN 883

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L  +++ +  D               ++ G     + +  +  ++  +  + W       
Sbjct: 884  LDCRVRIVPFD---------------EMHGAEKSQQTVETFLKEAAKQPGKGW------- 921

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              V+D                ++ G+  L DG TG PFD+PV VGY + LKL H+V DK+
Sbjct: 922  --VYD---------------PEDPGKLQLRDGRTGLPFDQPVAVGYSHFLKLVHLVDDKI 964

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR  
Sbjct: 965  HARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNE 1024

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
               +IV G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1025 ALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGKEVDLMQDV 1074



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 97/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DQGLIEELESFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVLDKLRHPEFYKKSIDAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|331123730|gb|AEC53653.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123742|gb|AEC53659.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123758|gb|AEC53667.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123764|gb|AEC53670.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123766|gb|AEC53671.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123768|gb|AEC53672.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123774|gb|AEC53675.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123810|gb|AEC53693.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123812|gb|AEC53694.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123814|gb|AEC53695.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123862|gb|AEC53719.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123918|gb|AEC53747.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|331123994|gb|AEC53785.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 523

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 258/526 (49%), Positives = 363/526 (69%), Gaps = 3/526 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 523


>gi|291296088|ref|YP_003507486.1| DNA-directed RNA polymerase subunit beta [Meiothermus ruber DSM 1279]
 gi|290471047|gb|ADD28466.1| DNA-directed RNA polymerase, beta subunit [Meiothermus ruber DSM
            1279]
          Length = 1124

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 204/626 (32%), Positives = 288/626 (46%), Gaps = 61/626 (9%)

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI--------- 829
             P+V   +EV   D+      +   +L        A     G N +   +          
Sbjct: 525  EPMVMRPEEVEYMDVSPKQIFSVNTNLIPFLEHDDANRALMGSNMQAQAVPLLRAQSPVV 584

Query: 830  ---SERMVSEDVFTSIH-----IEEFEVMARDTKLGPEEITRDI---PNVSEEGLKNIDE 878
                E  V  D  TS++     + E+   ++    G ++   +      V       +D+
Sbjct: 585  MTGVEERVVRDSLTSLYSPVDGVVEYVDGSKILVRGEDKGLYEFNLRRFVRSNQGTALDQ 644

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LRVP 932
               +  G +V  GD+L        E  +   + +L AI      +  D        LR  
Sbjct: 645  RPRVSKGQKVRKGDLLADGP-ASEEGYLALGQNILLAIMPFDGYNYEDAIVISEDLLRRD 703

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
               S  +    I  R      ER         E   RD  DE  ++      +  +IL G
Sbjct: 704  FYTSVHIERYEIEARDTKLGPERITRDIPNLSEAALRDL-DEDGVVRIGAEVKAGDILVG 762

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            + +  G         L   +  E  R                               E  
Sbjct: 763  RTSFKGETEPTPEERLLRSIFGEKARD-------------------VKDTSLRVPPGEGG 803

Query: 1053 FKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
               +  +++ GD    + PGV  VV+V+VA KR +Q GDK+A RHGNKG+VS+ILP EDM
Sbjct: 804  IVVRTLRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVSKILPPEDM 863

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P + DGTPVDIVLNPLGVPSRMN+GQI ETHLG A   LG K  + + D     +I  L 
Sbjct: 864  PHMPDGTPVDIVLNPLGVPSRMNLGQILETHLGLAGYELGLKFITPVFDGITEEEIKQLL 923

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                               D+     +A   K G+  +    + ++ E +  + +     
Sbjct: 924  GKAFDKKWEARTQAGF-GLDNREREVLARAAKLGLVSA----EASEVEQLREVFQQ---- 974

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G+S+LYDG TGEP + P+ VG +Y++KL HMV DK++ARSTG YSL+TQQPLGGK+  
Sbjct: 975  --GKSVLYDGRTGEPIEAPIVVGVMYIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQF 1032

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ LQE+LTIKSDD+ GR   YE++V G D  E   PESF V
Sbjct: 1033 GGQRFGEMEVWALEAYGAAHTLQEILTIKSDDIEGRNAAYEAVVKGEDVPEASVPESFRV 1092

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKME 1375
            LVKE+Q+LGL ++  +  ++N    E
Sbjct: 1093 LVKELQSLGLDVETYDENSRNLDIFE 1118



 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 281/587 (47%), Positives = 400/587 (68%), Gaps = 15/587 (2%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---- 426
            +ALL ++  +RPGD      A +  + L  D  +YDL   G+ K   +L +        
Sbjct: 236 DEALLKLFTELRPGDPPKRDKAITYLHSLLSDPRRYDLGEAGKYKAQQKLGIQLSGRMLI 295

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +    + E ++ ++K L  L++G+     DDID+LGNRR+R+VGE+L +Q+R+GL R+
Sbjct: 296 RFENGEFKDEALLPVLKYLFALQSGEPGYEADDIDHLGNRRIRTVGELLADQFRVGLSRL 355

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R ++ER+     +S  P  L+N +P+V+A+ EFF  SQLSQ ++  N LS + H RR+S
Sbjct: 356 ARGVRERMLLGSPESATPAKLVNNRPLVAAIREFFGRSQLSQFKDQTNPLSELRHKRRIS 415

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL SF R+N  GFI TPY
Sbjct: 416 ALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLASFGRINDLGFILTPY 475

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RKV +G+VT+ V +++A EE+   IAQAN+ L  DG F  + V  R  GE +++  E+++
Sbjct: 476 RKVINGRVTDQVDFMTATEEDRYAIAQANTPLKPDGHFDTQQVVVRKKGEPMVMRPEEVE 535

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQ+ S+  +LIPFLE+DD+NR LMG NMQ QAVPLL+A++P V TG+E  V + 
Sbjct: 536 YMDVSPKQIFSVNTNLIPFLEHDDANRALMGSNMQAQAVPLLRAQSPVVMTGVEERVVRD 595

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           S  ++ +   G+VE VD  +I++R  +        G+  + L +F RSNQ T ++QRP V
Sbjct: 596 SLTSLYSPVDGVVEYVDGSKILVRGEDK-------GLYEFNLRRFVRSNQGTALDQRPRV 648

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G +VR+ D++ADGP+++ G LALG+N+L+A MP+ GYN+ED+++ISE ++  D +TS+
Sbjct: 649 SKGQKVRKGDLLADGPASEEGYLALGQNILLAIMPFDGYNYEDAIVISEDLLRRDFYTSV 708

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIE +E+ ARDTKLGPE ITRDIPN+SE  L+++DE G++ +GAEV  GDILVG+ + KG
Sbjct: 709 HIERYEIEARDTKLGPERITRDIPNLSEAALRDLDEDGVVRIGAEVKAGDILVGRTSFKG 768

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           E+  TPEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 769 ETEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTLRLRRGD 815



 Score =  228 bits (581), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 81/214 (37%), Positives = 120/214 (56%), Gaps = 19/214 (8%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSGA-AML 74
           +GK  E+I +P L E+Q  S+   L  N+ P +R N GLQAAFK  FPI     G   +L
Sbjct: 6   YGKINEVIPLPPLTEIQVDSFTKALQANVPPSKRENIGLQAAFKETFPIEEGEKGRGLVL 65

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           +F+ Y    P FD D+C  +DLTY  PL   L L+  D            +KE  +++GD
Sbjct: 66  DFLEYRLGEPPFDQDECREKDLTYQAPLYAKLLLVHKD---------TGLLKEDEVFLGD 116

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QGLWM 192
           LPLMT+DG+F++ G  R++VSQ+HRSPG++F  D+ R        +   +IP   +G W+
Sbjct: 117 LPLMTQDGSFIVNGADRVIVSQIHRSPGVYFTADQTRPGR-----FVASVIPLPKRGPWI 171

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           D+EF+   ++ V    ++K P+   L  LG  +E
Sbjct: 172 DLEFEQSGVV-VMKVNKKKFPLALLLRVLGFTAE 204


>gi|227494537|ref|ZP_03924853.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
 gi|226832271|gb|EEH64654.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
          Length = 1191

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 176/535 (32%), Positives = 261/535 (48%), Gaps = 54/535 (10%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T  G  +  R             ++  ++  G  V  GD++           +   + LL
Sbjct: 675  TDAGSYDSYRLEKFQRSNSGNCTNQRVVVVEGDRVEAGDLIADGPATDL-GELALGKNLL 733

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    + ++  D  +     V   ++   I        +  +   + E    L    +D
Sbjct: 734  VAYMSWEGLNYEDAIILSRRVVEEDLL-TSIHIEEYEVASRETKLGDEEITRDLPNVSED 792

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKV 1031
                LD     R+   +   + + G    K  T L+++  L+      +  +      +V
Sbjct: 793  ALADLDERGIIRIGAEVESGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRV 852

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                  + +    + +                DD+ PGV+R V+V+VA +R I  GDK+A
Sbjct: 853  PHGESGIVIGVREANND--------------DDDLQPGVIRKVRVYVAQRRKITIGDKLA 898

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VS++LP EDMPFL+DGTPVDI+LNPLGVP RMNVGQ+ E HLGW    +G  
Sbjct: 899  GRHGNKGVVSKVLPIEDMPFLEDGTPVDIILNPLGVPGRMNVGQVLEYHLGWIAA-MGWD 957

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            ++  + + +                                +        +   V+TPVF
Sbjct: 958  VREAVKNGENWAKY---------------------------IPEEGLSAPARTNVATPVF 990

Query: 1212 DGADEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            DG +++ +  +LR        M  ++E G++ L+DG +GEPF  P+ VGY YMLKL+H+V
Sbjct: 991  DGVEQDTLMGLLRNTLPNRDGMRLINEDGKAQLFDGRSGEPFPYPIAVGYTYMLKLHHLV 1050

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDD+ 
Sbjct: 1051 DDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTVKSDDMK 1110

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            GR  V  SIV G D  E G PESF VL+ EM++L L ++  +             
Sbjct: 1111 GRVSVVNSIVKGEDIPEAGIPESFRVLMYEMRSLCLDVEALDKEGNAIDLTTSRD 1165



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 324/623 (52%), Positives = 436/623 (69%), Gaps = 32/623 (5%)

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +   +  TL  D  K  ++AL DIYR +RPG+  +   A ++    +F+  +YDL+ VGR
Sbjct: 257 DFPVLLETLEKDTAKTEEEALTDIYRKIRPGEQVSAEAARNLLENFYFNGKRYDLAKVGR 316

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-------------------RNGKG--- 451
            K+N +L LDTP     +R EDI+  +K L+ L                   RNG+    
Sbjct: 317 YKLNKKLGLDTPLTESVLRIEDIVTTVKYLLSLHKRGLATGRDRDGMKFAGVRNGEPVEL 376

Query: 452 --TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
               DDID+ GNRR+R+VGE+++ Q R G+ RMER+I+ER+++ D +++ P  LIN +PV
Sbjct: 377 PLETDDIDHFGNRRIRAVGELIQAQVRTGMARMERTIRERMTTQDAEAITPTSLINIRPV 436

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+
Sbjct: 437 TAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRM 496

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ET EG NIGL+ SL +FAR+N +GF+ETP+R V +G+VTN++ YL+A EE+   IAQ
Sbjct: 497 CPIETPEGPNIGLIGSLATFARINPFGFVETPFRVVRNGQVTNELHYLTADEEDGHPIAQ 556

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEIL-VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           A++ L  DG F E+ V CR +GE+   VP E+ID +D S +Q+VS+A ++IPFLE+DD+N
Sbjct: 557 ASAELTADGHFVEDQVLCRISGEDPALVPVEEIDLMDVSARQMVSVATAMIPFLEHDDAN 616

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPLL+ EAP VGTG+E   A  +G  I+A+ AG+V +V A  + + + 
Sbjct: 617 RALMGANMQRQAVPLLRTEAPLVGTGIERRAASDAGEMILARNAGVVTEVSADLVTVATD 676

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            G  D        YRL KFQRSN   C NQR +V  GD V   D+IADGP+TDLG+LALG
Sbjct: 677 AGSYDS-------YRLEKFQRSNSGNCTNQRVVVVEGDRVEAGDLIADGPATDLGELALG 729

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +N+LVA+M W G N+ED++++S R+V ED+ TSIHIEE+EV +R+TKLG EEITRD+PNV
Sbjct: 730 KNLLVAYMSWEGLNYEDAIILSRRVVEEDLLTSIHIEEYEVASRETKLGDEEITRDLPNV 789

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           SE+ L ++DE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTS
Sbjct: 790 SEDALADLDERGIIRIGAEVESGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTS 849

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           LRVP G SG V+ VR  N    D
Sbjct: 850 LRVPHGESGIVIGVREANNDDDD 872



 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 91/314 (28%), Positives = 145/314 (46%), Gaps = 27/314 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERP---------- 51
           A+        + R  F K  E +  P+L+ +Q  S++  L                    
Sbjct: 24  AQSNSAAKHTKERISFAKLREPMQAPNLLSLQTESFEWLLGTEEWRKRVEAANASGNNLL 83

Query: 52  --NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
               GL+  F  + PI        L F  + F+PPK+ V++C  +D TY  PL +     
Sbjct: 84  PTTSGLEDIFAEISPIEDMGQTMSLVFRDFHFEPPKYSVEECREKDKTYEAPLYV----- 138

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
                      +  +IK Q++++GD PLMT+ GTF+I G +R+VVSQL RSPG++F+   
Sbjct: 139 ----QADFMNHTTGEIKGQTVFLGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFEATS 194

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
            +   S + +Y+ +IIP +G W++ E D +D + VRIDR+RK PVT FL ALGM   ++ 
Sbjct: 195 DKT--SDRTIYSAKIIPSRGAWLEFEIDKRDSVGVRIDRKRKQPVTHFLKALGMSEADLR 252

Query: 230 STF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LL 285
             F  +P ++ +   D       A   +         V  +    ++E+         L 
Sbjct: 253 KEFADFPVLLETLEKDTAKTEEEALTDIYRKIRPGEQVSAEAARNLLENFYFNGKRYDLA 312

Query: 286 KSLKEKGVKFLGIT 299
           K  + K  K LG+ 
Sbjct: 313 KVGRYKLNKKLGLD 326


>gi|78779962|ref|YP_398074.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9312]
 gi|109904738|sp|Q318Q7|RPOB_PROM9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|78713461|gb|ABB50638.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9312]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/681 (47%), Positives = 453/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    ++ L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSDNDVVD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I              +   +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYQNSI-------------ESANDEGINSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PDDVR +  ED+++ I  L++L    G  +
Sbjct: 247 LLFSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTIDYLINLELDIGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +GKV    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVNNGKVNKDGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D+DG+    L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDKDGNILANLIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  G V  VDA  IV++  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVVKGEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+NQRP+V +GD+V    ++ADG + + G++ALG+N
Sbjct: 607 NE-------HFHYLQKYQRSNQDTCLNQRPIVNIGDQVISGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+IPN+SE
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           + L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 DSLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G V+DVRI+ R   D
Sbjct: 780 VPKTEKGRVLDVRIYTREQGD 800



 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 191/584 (32%), Positives = 276/584 (47%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGTVSYVDANEIVVKGEDGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+ +G +V  G +L      +G   +   + +L A   
Sbjct: 608  EHFHYLQKYQRSNQDTCLNQRPIVNIGDQVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  ++ D     D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEDSLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQPGKAWIY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + ++ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPEDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M++I
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDI 1074



 Score =  314 bits (804), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 189/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PI+ ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELQNFSPISDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY   + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQNSIESANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLFSRFFDPKRYDLGRVGRYKINKKLRLTVPDDVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|331123998|gb|AEC53787.1| RNA polymerase subunit B [Vibrio sp. SO185]
 gi|331124044|gb|AEC53810.1| RNA polymerase subunit B [Vibrio sp. SO180]
          Length = 522

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 260/525 (49%), Positives = 363/525 (69%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ KI 
Sbjct: 1   VLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKIN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L    L  G   S  +     G+  +E G+++T+  ++ L++  V F+ 
Sbjct: 61  FEVKDQTLMMELVPERL-RGETASFDIE--ADGKVYVEKGRRVTARHIRQLEKDDVSFIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  +SL  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVSSKDYINEATGEIIVAANQEISLESLANLSQAGYKKLEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D + DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSSNDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +     ++   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIERADAEEQGTLDETDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE ++++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHVNYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|33863774|ref|NP_895334.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9313]
 gi|41017659|sp|Q7V5P1|RPOB_PROMM RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|33635357|emb|CAE21682.1| RNA polymerases beta subunit [Prochlorococcus marinus str. MIT
           9313]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSIEAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 VKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G++  +   +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNQYGFIETPFWKVENGRLIKEGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    EL+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDADGQILAELIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G+V  VDA  I++R  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGMVTFVDATAIIVRDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 VD-------HTHYLQKYQRSNQDTCLNQRPIVCQGDAVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVA+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLVAYMPWEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 190/584 (32%), Positives = 268/584 (45%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-FEVMARDTKLGP 858
                       +L    P  G   E  +     MV       +        +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGMVTFVDATAIIVRDEDGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+C G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHYLQKYQRSNQDTCLNQRPIVCQGDAVIVGQVLADGSACEG-GEIALGQNVLVAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   V +V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVARVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMPFL DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPFLPDGTPVDIVLNPLGVPSRMNVGQVFECLMGWAAANLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  Y  ++  +  ++W             
Sbjct: 890  VVPFD---------------EMYGAEKSQQTVEAYLKEAAKQPGKEWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D  G+  L DG +GEPFD+PVTVGY  +LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDNPGKLQLIDGRSGEPFDQPVTVGYAQILKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGKEVDLMQDV 1074



 Score =  317 bits (812), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 103/492 (20%), Positives = 207/492 (42%), Gaps = 47/492 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          +EGL     S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DEGLIEELDSFSPITDYTGKLELHFVGNEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAANEEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAVKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERS 485
               ++ +     G+    +               + RV   G +    +++   R+ + 
Sbjct: 408 AGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNQYGFIETPFWKVENGRLIKE 467

Query: 486 IKERISSVDIDS 497
                 S D++ 
Sbjct: 468 GDPIYLSADLED 479


>gi|253757201|gb|ACT35199.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 457/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   +V     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           + ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 RYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-VTNDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G  + +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVAIVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331123728|gb|AEC53652.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123732|gb|AEC53654.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123738|gb|AEC53657.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123740|gb|AEC53658.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123746|gb|AEC53661.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123750|gb|AEC53663.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123752|gb|AEC53664.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123754|gb|AEC53665.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123756|gb|AEC53666.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123762|gb|AEC53669.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123776|gb|AEC53676.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123778|gb|AEC53677.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123780|gb|AEC53678.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123782|gb|AEC53679.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123794|gb|AEC53685.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123798|gb|AEC53687.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123802|gb|AEC53689.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123806|gb|AEC53691.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123808|gb|AEC53692.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123816|gb|AEC53696.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123818|gb|AEC53697.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123820|gb|AEC53698.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123822|gb|AEC53699.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123826|gb|AEC53701.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123830|gb|AEC53703.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123834|gb|AEC53705.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123836|gb|AEC53706.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123838|gb|AEC53707.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123840|gb|AEC53708.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123842|gb|AEC53709.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123844|gb|AEC53710.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123846|gb|AEC53711.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123848|gb|AEC53712.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123850|gb|AEC53713.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123852|gb|AEC53714.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123854|gb|AEC53715.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123856|gb|AEC53716.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123858|gb|AEC53717.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123860|gb|AEC53718.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123864|gb|AEC53720.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123866|gb|AEC53721.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123868|gb|AEC53722.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123874|gb|AEC53725.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123876|gb|AEC53726.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123878|gb|AEC53727.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123880|gb|AEC53728.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123882|gb|AEC53729.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123884|gb|AEC53730.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123886|gb|AEC53731.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123888|gb|AEC53732.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123892|gb|AEC53734.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123894|gb|AEC53735.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123896|gb|AEC53736.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123898|gb|AEC53737.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123900|gb|AEC53738.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123902|gb|AEC53739.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123904|gb|AEC53740.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123906|gb|AEC53741.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123910|gb|AEC53743.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123912|gb|AEC53744.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123920|gb|AEC53748.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123926|gb|AEC53751.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123928|gb|AEC53752.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123932|gb|AEC53754.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123934|gb|AEC53755.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123936|gb|AEC53756.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123948|gb|AEC53762.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123950|gb|AEC53763.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123954|gb|AEC53765.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123960|gb|AEC53768.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123978|gb|AEC53777.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331123992|gb|AEC53784.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 523

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 257/526 (48%), Positives = 363/526 (69%), Gaps = 3/526 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 523


>gi|331124012|gb|AEC53794.1| RNA polymerase subunit B [Vibrio sp. SO96]
 gi|331124014|gb|AEC53795.1| RNA polymerase subunit B [Vibrio sp. SO97]
          Length = 522

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 258/525 (49%), Positives = 361/525 (68%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  RIIP +G W+D EFD KD ++VRIDRRRK+P T  L ALG  + EIL  F+ K+ 
Sbjct: 1   VLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPSTIILRALGKTTAEILDMFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L    L  G   S  +     G   +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLMMELVPERL-RGETASFDIE--ANGNVYVEKGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVSSKDYINEATGEIIVAANQEISLEALANLSQAGHKSLQVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   D   + + DI+ ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDALDQGTLDETDIVEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVIDGIVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|78213583|ref|YP_382362.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. CC9605]
 gi|109914406|sp|Q3AHX5|RPOB_SYNSC RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|78198042|gb|ABB35807.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp.
           CC9605]
          Length = 1097

 Score =  496 bits (1277), Expect = e-137,   Method: Composition-based stats.
 Identities = 322/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVLD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             +    +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSI-------------DAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV  G V    D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVEYGVVLKDGDPIYLSADREDEVRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + ++DG  + +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATEDDGRISADLIPVRYRQDFEKVPPEQVDYVALSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E   VGTG+E+ VA+ SG   +++  G V  VDA  IV++  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTVTYVDANAIVVQDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+NQRP+V+ GD V    ++ADG + + G++ALG+N
Sbjct: 607 ND-------HTHFLQKYQRSNQDTCLNQRPIVRCGDPVIVGQVMADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G VVDVRI+ R   D
Sbjct: 780 VPGTERGRVVDVRIYTREQGD 800



 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 180/530 (33%), Positives = 259/530 (48%), Gaps = 62/530 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              + G +                +++  I+  G  V  G ++      +G   +   + +
Sbjct: 602  QDEDGNDHTHFLQKYQRSNQDTCLNQRPIVRCGDPVIVGQVMADGSACEG-GEIALGQNV 660

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD 970
            L A    +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +
Sbjct: 661  LIAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEE 720

Query: 971  ---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE  I+    +    +IL G+    G         L   +  E  R         
Sbjct: 721  SLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---- 776

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                               +        +I   + GD++PPG   VV+V+VA +R IQ G
Sbjct: 777  -------------SLRVPGTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVG 823

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   
Sbjct: 824  DKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASN 883

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            L  +++ +  D               ++ G     + +  +  ++  +  + W       
Sbjct: 884  LDCRVRIVPFD---------------EMHGAEKSQQTVETFLKEAAKQPGKGW------- 921

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              V+D                ++ G+  L DG TG PFD+PV VGY + LKL H+V DK+
Sbjct: 922  --VYD---------------PEDPGKLQLRDGRTGLPFDQPVAVGYSHFLKLVHLVDDKI 964

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            +ARSTG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR  
Sbjct: 965  HARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNE 1024

Query: 1328 VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
               +IV G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1025 ALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGKEVDLMQDV 1074



 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 97/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DQGLIEELESFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVLDKLRHPEFYKKSIDAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|11467690|ref|NP_050742.1| RNA polymerase beta subunit [Guillardia theta]
 gi|6094123|sp|O78485|RPOB_GUITH RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|3603015|gb|AAC35676.1| RNA polymerase b-chain [Guillardia theta]
          Length = 1096

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 307/604 (50%), Positives = 419/604 (69%), Gaps = 9/604 (1%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           + + +  Y++ T   + N   + AL+ +Y  +RPG+ +T +  + +    FFD  +YDL 
Sbjct: 195 NGLRHPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFFDPKRYDLG 254

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +LNL  P++VR +  +D +A I  L++L+   G  DDID+LGNRRVRSVGE
Sbjct: 255 KVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGE 314

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +L+NQ R+GL R+ER I+ER++  DI S+ P  L+N KP+++++ EFF SSQLSQ  +  
Sbjct: 315 LLQNQVRIGLNRLERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQT 374

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+  L + 
Sbjct: 375 NPLAELTHKRRISALGPGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATH 434

Query: 590 ARVNAYGFIETPYRKVCDGKVTN--DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+N YGFIE P+ KV DG+V N    +YL+A +E+   IA  + +LDE      ++V  
Sbjct: 435 ARINTYGFIEAPFFKVQDGQVYNHSQPIYLTADQEDKYRIAPGDITLDETNRIATKIVPI 494

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +   E       ++DFI  SP QV+SIA SLIPFLE+DD+NR LMG NMQRQAVPLL  E
Sbjct: 495 KYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPE 554

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E+  A+ SG  +V+   G V  V   +I + + +GD          Y L K+
Sbjct: 555 SPLVGTGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNKKGDEIA-------YYLQKY 607

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSNQ+TC+NQRP V +G++V    +IADG +T+ G+LALG+N+LVA++PW GYN+ED+ 
Sbjct: 608 QRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELALGQNILVAYLPWEGYNYEDAF 667

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LI+ER+V  DV+TS+HIE++E+ AR TKLG EEITR++PNV E  L+ +DE GII +G+ 
Sbjct: 668 LINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGSW 727

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDIL+GK+TPKGES   PE KLLRAIFGEKA DVRDTSLRVP+G  G ++DVRIF R
Sbjct: 728 VEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR 787

Query: 948 HGID 951
              D
Sbjct: 788 EKGD 791



 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 182/528 (34%), Positives = 256/528 (48%), Gaps = 58/528 (10%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             K G E                I++   + +G +V  G ++      +G   +   + +L
Sbjct: 594  NKKGDEIAYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEG-GELALGQNIL 652

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  L     ++  +V   ++    I+K E    +E  Q +L + +   
Sbjct: 653  VAYLPWEGYNYEDAFL-----INERLVYNDVYTSVHIEKYE----IEARQTKLGSEEITR 703

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            E   +      +L E   I+ G    +G     K T           +     F  +   
Sbjct: 704  ELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARD 763

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +                 +I   + GD++P G   V++V++A  R IQ GDKM
Sbjct: 764  VRDTSLRVPNGGRGRI------LDVRIFTREKGDELPTGANIVIRVYIAQSRKIQVGDKM 817

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKGI+SRILP +DMP+L DGTPVD+VLNPLGVPSRMNVGQIFE  LG A   L K
Sbjct: 818  AGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNK 877

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K    D     + S +                +++  +++ ++  E W          
Sbjct: 878  RFKITPFDEMHGAEASRVL---------------VNEKLNEAKIKTGENWL--------- 913

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FD               L   G+  LYDG TGE FD PVT+G  YMLKL H+V DK++AR
Sbjct: 914  FD---------------LRHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHAR 958

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGG++  GGQRLGEMEVW ++A+GA+Y LQE+LT+KSDD+ GR     
Sbjct: 959  STGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLN 1018

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            +IV G      GTPESF VL++E+Q+LGL I           +   I 
Sbjct: 1019 AIVKGKPIPRPGTPESFKVLMRELQSLGLDIGAYKIENLPDGQTRGIE 1066



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 101/456 (22%), Positives = 194/456 (42%), Gaps = 40/456 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +PDL+E+Q+AS+  FL          NEGL    +S  PI  ++G   L  F   Y    
Sbjct: 11  LPDLVEIQRASFCWFL----------NEGLAEEIQSFSPIVNYTGNLELHLFGDQYTLRY 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK ++++C  RD TY+V + +  +LI          +    IKEQ +++GDLPLMT  GT
Sbjct: 61  PKHNINECKRRDTTYSVQIYVPAQLI---------NRETGVIKEQEVFIGDLPLMTDRGT 111

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPGI++  +  +    G+  Y+  +I ++G W+  E D  D++ 
Sbjct: 112 FIINGAERVIVNQIVRSPGIYYKSELDKQ---GRRTYSSSLISNRGAWVKFETDRNDLVW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF----YPKIVYSQRGDFWCFPLSAADLMVGAK 259
           VRID+ RK+P   FL A+G+   +I +      Y K  +   G++     +A   M    
Sbjct: 169 VRIDKTRKIPAHVFLKAMGLSDTDIYNGLRHPEYLKKTFRFEGNY--TTETALIQMYNKL 226

Query: 260 VSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
                  +  G+Q++ S         L K  + K  K L ++      +   +D +    
Sbjct: 227 RPGEPATVTGGQQLLYSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAID 286

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I ++  ++ +   ++ + +  +R +  L  + V         ++ ++        L  
Sbjct: 287 YLINLK-FEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTICDITSLTP 345

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             ++ P      +     F            + +  +    R++   P     + ++   
Sbjct: 346 NTLVNPK--PIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LNRDRAG 400

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
             ++ +     G+  I  I+         +G +  +
Sbjct: 401 FGVRDIHPSHYGR--ICPIETPEGPNAGLIGVLATH 434


>gi|452610|emb|CAA54509.1| RNA polymerase, beta subunit [Campylobacter jejuni]
          Length = 694

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/689 (47%), Positives = 451/689 (65%), Gaps = 10/689 (1%)

Query: 343  DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              PI+   + +           + + +   A + IY+VMRPG+      A++  N LFF+
Sbjct: 8    MQPIINSFAQDGETLKLLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFFN 67

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             ++YDL+ VGR+KMN +L L+ P+ V  +  EDII   K L+ ++NGKG IDD D+LGNR
Sbjct: 68   PERYDLTKVGRMKMNHKLGLEVPEYVTVLTNEDIIKTAKYLIKVKNGKGHIDDRDHLGNR 127

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+RS+GE+L N+  LGL +M+++I+++ +  + D+D VMP DLIN K + + + EFF   
Sbjct: 128  RIRSIGELLANELHLGLAKMQKAIRDKFTSLNADLDKVMPYDLINPKMITTTIIEFFTGG 187

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            QLSQ  +  N LS +TH RRLSALG+GG+ + R G E+RDVH THYGRICP ET EG NI
Sbjct: 188  QLSQFMDQTNPLSEVTHKRRLSALGEGGLVKERRGFEVRDVHATHYGRICPVETPEGQNI 247

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL+++L+++A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+ 
Sbjct: 248  GLINTLSTYAKVNELGFVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNI 307

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             EE V  R  GE IL  RE++  ID S   VV +AASLIPFLE+DD NR LMG NMQRQA
Sbjct: 308  VEEFVEARQDGETILARREEVQLIDLSSGMVVGVAASLIPFLEHDDRNRALMGSNMQRQA 367

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPLL A AP VGTGME ++A+ +  A+ AKR G+VE+VD   I I   +         +D
Sbjct: 368  VPLLTASAPIVGTGMEQIIARDAWEAVKAKRGGVVEKVDNKSIFILGEDDK----GPFID 423

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             Y + K  R+NQNT   Q P+VK GD V+   IIADGPS D G+LA+G+N L+AFMPW+G
Sbjct: 424  HYTMEKNLRTNQNTNYIQHPIVKKGDIVKAGQIIADGPSMDQGELAIGKNALIAFMPWNG 483

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN+ED++++SER++ ED FTS+HI E E+ AR+ K G EEIT+DIPNV EE + ++DE G
Sbjct: 484  YNYEDAIVVSERIIREDTFTSVHIYEKEIEARELKDGIEEITKDIPNVKEEDVAHLDESG 543

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I  +G  + PG ILVGK++PKGE   TPEE+LLRAIFGEKA  V + SL   + + G VV
Sbjct: 544  IAKIGTHIKPGMILVGKVSPKGEVKPTPEERLLRAIFGEKAGHVVNKSLYATASLEGVVV 603

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAV 996
            DV+IF + G +K++R+I    ++   L ++  D  +++DR    R+  +L       +  
Sbjct: 604  DVKIFTKKGYEKDDRAIKSYDKEKMALEKEHHDRLLMMDREEMLRVCALLSKASLNSDQK 663

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             G K +KK        + +  R       
Sbjct: 664  IGDKNYKKGQTADISELEKINRFTLTTLI 692


>gi|78184182|ref|YP_376617.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. CC9902]
 gi|109914405|sp|Q3AZA4|RPOB_SYNS9 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|78168476|gb|ABB25573.1| DNA-directed RNA polymerase, beta subunit [Synechococcus sp.
           CC9902]
          Length = 1097

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 321/681 (47%), Positives = 449/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVLD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             +    +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSI-------------DAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD+ +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDAKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G V  + D +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGVVIKSGDPIYLSADREDEVRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + +++G    +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATEDNGEIKADLIPVRYRQDFEKVPPEQVDYVALSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E   VGTG+E+ VA+ SG   +++  G V  VDA  IV+   +G
Sbjct: 547 LMGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTVVYVDANAIVVLDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 QE-------HTHFLQKYQRSNQDTCLNQRPIVHQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 660 VLIAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G VVDVRI+ R   D
Sbjct: 780 VPGTERGRVVDVRIYTREQGD 800



 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 181/529 (34%), Positives = 257/529 (48%), Gaps = 62/529 (11%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             + G E                +++  I+  G  V  G +L      +G   +   + +L
Sbjct: 603  DEDGQEHTHFLQKYQRSNQDTCLNQRPIVHQGDPVIVGQVLADGSACEG-GEIALGQNVL 661

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD- 970
             A    +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A + 
Sbjct: 662  IAYMPWEGYNYEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEES 721

Query: 971  --KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE  I+    +    +IL G+    G         L   +  E  R          
Sbjct: 722  LGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN----- 776

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                              +        +I   + GD++PPG   VV+V+VA +R IQ GD
Sbjct: 777  ------------SLRVPGTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGD 824

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L
Sbjct: 825  KMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNL 884

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
              ++K +  D               ++ G     + ++ +  ++     + W        
Sbjct: 885  DCRVKIIPFD---------------EMHGAEKSQQTVTTFLTEAAKLSGKDWVY------ 923

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                              + +  G+ +L DG TG PFD+PV VGY + LKL H+V DK++
Sbjct: 924  ------------------NPENPGKLVLRDGRTGLPFDQPVAVGYSHFLKLVHLVDDKIH 965

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR   
Sbjct: 966  ARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEA 1025

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
              +IV G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1026 LNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVYTEEGKEVDLMQDV 1074



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 97/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          ++GL    +S  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DKGLIEELESFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVLDKLRHPEFYKKSIDAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDAKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|331124002|gb|AEC53789.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 522

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 258/525 (49%), Positives = 363/525 (69%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|46360944|gb|AAS89205.1| RpoB [Corynebacterium ammoniagenes]
          Length = 1116

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 180/503 (35%), Positives = 257/503 (51%), Gaps = 61/503 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 661  NYNQTPLVNMGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILSQRI 719

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLME 988
            V   V+       H ID  +  +  E    +I    E + RD DD   I+      R  +
Sbjct: 720  VEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIIRIGADVRAGD 778

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                V  +          
Sbjct: 779  ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA--------- 829

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                        +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V ++LP ED
Sbjct: 830  --------RFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKVLPPED 881

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF+ DGTPVD++LN  GVP RMN+GQ+ E HLGW     G  + +   D K    +  L
Sbjct: 882  MPFMADGTPVDVILNTHGVPRRMNIGQVLELHLGWLA-HTGWTVDT--EDPKNEELLKTL 938

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
               L  V                               +TPVFDGA  E I+ +L  +  
Sbjct: 939  PEELYDVPADSLT-------------------------ATPVFDGATNEEISRLLASSKP 973

Query: 1229 DESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +  G        +++L+DG +GEP+  P++VG++Y+LKL+H++ +K++ARSTG YS++TQ
Sbjct: 974  NRDGDVMVDEDGKTVLFDGRSGEPYQYPISVGFMYILKLHHLIDEKIHARSTGPYSMITQ 1033

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  +
Sbjct: 1034 QPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPD 1093

Query: 1341 TGTPESFNVLVKEMQALGLSIDL 1363
             G PESF VL+KE+Q+L L++++
Sbjct: 1094 PGIPESFKVLLKELQSLCLNVEV 1116



 Score =  487 bits (1253), Expect = e-135,   Method: Composition-based stats.
 Identities = 320/661 (48%), Positives = 450/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 188 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEQQI--RDRFGFSELMMSTLES 243

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 244 DGIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGG 303

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             + +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 304 DHEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGEMIPVNTDDIDHFGNRRLRTVGELI 363

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 364 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 423

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 424 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 483

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV +G+VT++V YL+A EE+   IAQA    D DG+   + +  R   
Sbjct: 484 VNAFGFIETPYRKVENGRVTDEVRYLTADEEDRYSIAQAEVEQDADGNIVGDRIEVRLKD 543

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPL++ EAP+
Sbjct: 544 GDIGVTDANGVDYVDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLVRGEAPY 603

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +++ +AG+VE V+A  I I   EG  D        Y L KF+R+
Sbjct: 604 VGTGMELRAAYDAGDMVISPKAGVVENVNADLITIMDDEGVRD-------TYMLRKFERT 656

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED++++S
Sbjct: 657 NQGTNYNQTPLVNMGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILS 716

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V EDV TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++D+ GII +GA+V  
Sbjct: 717 QRIVEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRA 776

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 777 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSREDD 836

Query: 951 D 951
           D
Sbjct: 837 D 837



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 90/387 (23%), Positives = 169/387 (43%), Gaps = 45/387 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN--------EGLQAAFKSVFPI 65
           R  F K  E I +P L+++Q  S+   +  +   + +           GL+     + PI
Sbjct: 16  RYSFAKISEPIAVPGLLDLQLESFAWLIGTSEWRERQQEERGEEHVSSGLEDILAELSPI 75

Query: 66  TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
             +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++I
Sbjct: 76  QDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQEI 126

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q++++GD P+MT +GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++I
Sbjct: 127 KSQTVFIGDFPMMTDEGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKVI 184

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRGD 243
           P +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   D
Sbjct: 185 PSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEQQIRDRFGFSELMMSTLESD 244

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF------ 295
                  A   +   +        D  + ++++         L +  + K  +       
Sbjct: 245 GIANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGGD 304

Query: 296 -----------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
                      + +T + L  L+  E  +    GE+       ++   ++   +  +R +
Sbjct: 305 HEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGEMI-----PVNTDDIDHFGNRRLRTV 359

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRK 371
             L  + V         +V ++   + 
Sbjct: 360 GELIQNQVRVGLSRMERVVRERMTTQD 386


>gi|253757175|gb|ACT35186.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             EA   I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEAEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +         RL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTCRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTCRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYD  TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDERTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757195|gb|ACT35196.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757153|gb|ACT35175.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL L+ P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLNVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD++R LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDASRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A               +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDASRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757171|gb|ACT35184.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 454/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++      LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LRGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDL+LGRN+L+ FMPW GYN+ED +LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKQGDLSLGRNILMGFMPWEGYNYEDVILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    DV   S R+       S  + +  I  R    
Sbjct: 470  GPATKQGDLSLGRNILMGFMPWEGYNYEDVILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757159|gb|ACT35178.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 328/659 (49%), Positives = 454/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I+E+ +  +  ++I  I   +V   N    + NTL+ D      +A++++++ 
Sbjct: 1   IAETETLINEEVINNLIENKIESISYWFVGPENK--LVANTLMADTTSTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD+     + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKKNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       +        YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIVIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNSVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|153805704|gb|ABS52576.1| RNA polymerase beta subunit [Bartonella tamiae]
          Length = 523

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 395/521 (75%), Positives = 459/521 (88%), Gaps = 1/521 (0%)

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
           FFD ++YDLS VGRVKMNMR++LD PD VR +RKEDI+A++K+LV+LR+G+G IDDIDNL
Sbjct: 3   FFDPERYDLSAVGRVKMNMRMDLDCPDTVRILRKEDILAVVKMLVELRDGRGEIDDIDNL 62

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRRVRSVGE+++NQYR+GLLRMER+IKER+SS++ID+VMPQDLINAKP  +AV EFF S
Sbjct: 63  GNRRVRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGS 122

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 123 SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 182

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL +FARVN YGFIE+PYRK+ DGKVT DVVYLSAMEE   Y+AQANSSLD    
Sbjct: 183 IGLINSLATFARVNKYGFIESPYRKIVDGKVTTDVVYLSAMEESKHYVAQANSSLDAQAR 242

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQ
Sbjct: 243 FTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQ 302

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL++AEAPFVGTGMESVVA+ SGAAI A+RAGIV+QVDA RIVI + E  LDP+ SGV
Sbjct: 303 AVPLVRAEAPFVGTGMESVVARDSGAAIGARRAGIVDQVDATRIVIHATED-LDPTKSGV 361

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           DIYRL KFQRSNQ+TC+NQRPLV+VGD + + DIIADGPSTDLGDLALGRN+LVAFMPW+
Sbjct: 362 DIYRLQKFQRSNQSTCINQRPLVRVGDRIEKGDIIADGPSTDLGDLALGRNVLVAFMPWN 421

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEITRDIPNVSEE LKN+DE 
Sbjct: 422 GYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEA 481

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           GI+ +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFG+K
Sbjct: 482 GIVYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGKK 522


>gi|253757193|gb|ACT35195.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  496 bits (1276), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   +V     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +   + ++V YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVAIVDNVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|15705366|gb|AAL05611.1| RpoB [bacterium DR-2001]
          Length = 1216

 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/587 (32%), Positives = 286/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 655  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 713

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 714  KHRDYHVGKFVRSNQGNCYNQXVVVRSGDRVEKGTVLAHGPCT-DKGELSLGRNLLVAFM 772

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 773  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 827

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 828  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 884

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 885  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 941

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 942  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 1000

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 1001 WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 1027

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 1028 EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1087

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1088 RSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1147

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1148 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1194



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 308/616 (50%), Positives = 429/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 299 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 358

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 359 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 418

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 419 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 478

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 479 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 538

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 539 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 598

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 599 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 658

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 659 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 717

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQ  +V+ GD V +  ++A GP TD G+L+LGRN+LVAF
Sbjct: 718 ------YHVGKFVRSNQGNCYNQXVVVRSGDRVEKGTVLAHGPCTDKGELSLGRNLLVAF 771

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 772 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 831

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 832 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 891

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 892 QGTVIDVKLFDAVDGE 907



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 89/312 (28%), Positives = 140/312 (44%), Gaps = 32/312 (10%)

Query: 11  GRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNIAPDERPNE 53
            RV    R   GK  + +++P+L+++Q  S+D  +                         
Sbjct: 74  KRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRVALDAYRKNPSGAPIAEKS 133

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL +    +  D 
Sbjct: 134 GLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVEAEFMNHD- 192

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                     +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +  
Sbjct: 193 --------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYFERTPEKN- 243

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF- 232
            S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  +EI   F 
Sbjct: 244 -SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTDDEIRDAFG 302

Query: 233 -YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLK 289
            +  I      +       A   +            + G  ++E+    +    L +  +
Sbjct: 303 EFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLARVGR 362

Query: 290 EKGVKFLGITSD 301
            K  + LG+  D
Sbjct: 363 YKVNRKLGVDVD 374


>gi|253757169|gb|ACT35183.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 457/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL ++ + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKVNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E+LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEDLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG                                                 
Sbjct: 692  NIGQVLEVHLGM------------------------------------------------ 703

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 704  ----TMRTLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331124010|gb|AEC53793.1| RNA polymerase subunit B [Vibrio sp. SO92]
          Length = 522

 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 257/525 (48%), Positives = 362/525 (68%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  RIIP +G W+D EFD KD ++VRIDRRRK+P T  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPSTIILRALGKTTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L    L  G   S  +     G   +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLMMELVPERL-RGETASFDIE--ANGNVYVEKGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVSSKDYINEATGEIIVAANQEISLEALANLSQAGHKSLQVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DI+ ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIVEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S+++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSMSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVIDGIVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|317968941|ref|ZP_07970331.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. CB0205]
          Length = 1096

 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 332/681 (48%), Positives = 448/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G+K  +  L   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 142 KNGRKTFNASLIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAIGLSDNDVLD 198

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  ++
Sbjct: 199 KLRHPEYYQKSI-------------EAANDEGIASEDQALLELYKKLRPGEPPSVSGGQT 245

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR K+N +L L  PD  R +  ED+++ I  L++L    G  T
Sbjct: 246 LLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDATRTLTPEDVLSTIDYLINLELDVGGAT 305

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + +S+ P  L+N KP+V+A
Sbjct: 306 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETESLTPAQLVNPKPLVAA 365

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP 
Sbjct: 366 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRICPI 425

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL+ SL + ARVN YGFIETP+ KV DG V    D +YLSA  E+   +A  
Sbjct: 426 ETPEGPNAGLIGSLATHARVNEYGFIETPFWKVEDGIVLKQGDPLYLSADLEDECRVAPG 485

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG    ELV  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 486 DVATDADGRIKAELVPVRYRQDFETVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 545

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +    G V  VDA  IVIR  EG
Sbjct: 546 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITTVNGTVSFVDATAIVIRDEEG 605

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+N RP+VK+GD+V    ++A+G + + G++ALG+N
Sbjct: 606 ND-------HTHYLQKYQRSNQDTCLNHRPIVKLGDQVIAGQVLANGSACEGGEIALGQN 658

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+E
Sbjct: 659 VLIAYMPWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAE 718

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 719 ESLGNLDEMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 778

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 779 VPSTERGRVVDVRIYTREQGD 799



 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 271/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITTVNGTVSFVDATAIVIRDEEGN 606

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                ++   I+ +G +V  G +L      +G   +   + +L A   
Sbjct: 607  DHTHYLQKYQRSNQDTCLNHRPIVKLGDQVIAGQVLANGSACEG-GEIALGQNVLIAYMP 665

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 666  WEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 725

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    Y    +IL G+    G         L   +  E  R               
Sbjct: 726  EMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 775

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 776  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 828

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 829  HGNKGIISRILPLEDMPYLPDGTPIDIVLNPLGVPSRMNVGQVFECLMGWAASHLDCRVK 888

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G  +    +  Y + +  +  + W             
Sbjct: 889  VVPFD---------------EMHGPETSKNTVQAYLEAAKSQPGKDWVY----------- 922

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D  G+  L DG TGE FD+PVTVGY ++LKL H+V DK++ARSTG
Sbjct: 923  -------------NPDNPGKIQLIDGRTGEAFDQPVTVGYAHILKLVHLVDDKIHARSTG 969

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 970  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1029

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     +    M+++
Sbjct: 1030 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDAGEEVDLMQDV 1073



 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 98/458 (21%), Positives = 196/458 (42%), Gaps = 39/458 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L F+   Y    
Sbjct: 14  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFIGSEYRLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 64  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  +   +IP++G W+  E D  D++H
Sbjct: 115 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRKTFNASLIPNRGAWLKFETDKNDLLH 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       +Y K + +   +       A   +   
Sbjct: 172 VRVDKTRKINAHVLMRAIGLSDNDVLDKLRHPEYYQKSIEAANDEGIASEDQALLELYKK 231

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+ ++ S         L +  + K  K L +T          ED+++  
Sbjct: 232 LRPGEPPSVSGGQTLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPDATRTLTPEDVLSTI 291

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 292 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETESL 351

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 352 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 406

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
               ++ +     G+  I  I+         +G +  +
Sbjct: 407 AGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|218294705|ref|ZP_03495559.1| DNA-directed RNA polymerase, beta subunit [Thermus aquaticus Y51MC23]
 gi|218244613|gb|EED11137.1| DNA-directed RNA polymerase, beta subunit [Thermus aquaticus Y51MC23]
          Length = 1119

 Score =  495 bits (1275), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/509 (37%), Positives = 253/509 (49%), Gaps = 43/509 (8%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------LR 930
            D+   + VG  V  GD+L        E  +   + +L AI      +  D        L+
Sbjct: 638  DQRPRVRVGQRVKKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLK 696

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                 S  +    I  R      ER         E   RD D+E  I+      +  +IL
Sbjct: 697  RDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GIVRIGAEVKPGDIL 755

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G +       L   +  E  R                               E
Sbjct: 756  VGRTSFKGEQEPSPEERLLRSIFGEKARD-------------------VKDTSLRVPPGE 796

Query: 1051 DRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                    +++ GD    + PGV  VV+VFVA KR +Q GDK+A RHGNKG+V++ILP E
Sbjct: 797  GGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANRHGNKGVVAKILPVE 856

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   L ++  S + D     +I  
Sbjct: 857  DMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLSQRYISPVFDGATEPEIKE 916

Query: 1168 LRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
            L +    +       E    D  +  VL  AE+     P  +P      EE +  +    
Sbjct: 917  LLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP------EEQLKELFVQ- 969

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 G+ +LYDG TGEPF+ P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK
Sbjct: 970  -----GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK 1024

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   YE+I+ G D  E   PES
Sbjct: 1025 AQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYEAIIKGEDVPEPSVPES 1084

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            F VLVKE+QAL L +   + +       E
Sbjct: 1085 FRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 284/590 (48%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++A++ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+A GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT +VVY++A EE+   IAQAN+ L+ D     + V  R  GE ++V  E
Sbjct: 469 TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGD-RIATDRVVARRRGEPVIVAPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RI +R  +G L         + L ++ RSNQ T  +QR
Sbjct: 588 VRDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVE-------HPLRRYARSNQGTAFDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+VG  V++ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVRVGQRVKKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE GI+ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGD 810



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 84/217 (38%), Positives = 123/217 (56%), Gaps = 20/217 (9%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G LPLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHLPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
            W+D+E ++  ++ ++++ +RK P+   L  LG D E
Sbjct: 170 PWIDLEVEASGVVTMKVN-KRKFPLVLLLRVLGYDQE 205


>gi|253757157|gb|ACT35177.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 459/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             EA   I+E+ + ++  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAEAEAFINEEVINKLIENKVDKISYWYVRP--ESKLVANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE G+I +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGVIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 222/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGVIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|302122445|gb|ADK92893.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122447|gb|ADK92894.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122473|gb|ADK92907.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122481|gb|ADK92911.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122485|gb|ADK92913.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122501|gb|ADK92921.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122505|gb|ADK92923.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122515|gb|ADK92928.1| RNA polymerase subunit B [Vibrio sp. SO11]
 gi|302122517|gb|ADK92929.1| RNA polymerase subunit B [Vibrio sp. SO12]
          Length = 521

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 256/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|254994317|ref|ZP_05276507.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J2-064]
          Length = 680

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 350/707 (49%), Positives = 457/707 (64%), Gaps = 51/707 (7%)

Query: 257 GAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEK--------GVKFLGITSDCLCGLY 307
              +      +  GE   +++ + L        K           +       + L    
Sbjct: 5   EKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRYKINKKLHLKNRLFNQT 64

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           +AE +V+ ETGEI    GD++D ++L++I            + ++ N    R    TD  
Sbjct: 65  LAETLVDPETGEIIASKGDILDRRNLDQI------------IPNLENGVGFRTLRPTDGV 112

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +    L+   ++  P D                             ++N+  N    ++
Sbjct: 113 ME-DSVLVQSIKIYAPND--------------------------EEKEINIIGNAYIEEN 145

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           V+HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++
Sbjct: 146 VKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR 205

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ER+S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG G
Sbjct: 206 ERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPG 265

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV-- 605
           G+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V  
Sbjct: 266 GLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDP 325

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
              +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R   E + V +E+ID++D
Sbjct: 326 ETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERIDYMD 385

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK SGA
Sbjct: 386 VSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGA 445

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           A+ AK  GIVE V+A  I +R V   D    T G+D Y L KF RSNQ TC NQRP V  
Sbjct: 446 AVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAE 505

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+TSIHI
Sbjct: 506 GDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHI 565

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TPKG +
Sbjct: 566 EEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVT 625

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R   D
Sbjct: 626 ELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGD 672


>gi|88807332|ref|ZP_01122844.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. WH
           7805]
 gi|88788546|gb|EAR19701.1| DNA-directed RNA polymerase beta subunit [Synechococcus sp. WH
           7805]
          Length = 1097

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 321/681 (47%), Positives = 449/681 (65%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I                  +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEYYKKSI-------------EAANDEGISSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ +  L++L    G  +
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTLDYLINLELDVGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G V    + +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGHVLKQGNPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D +G+   +L+  R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDSEGAILADLIPVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+R  +G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                      + L K+QRSNQ+TC+NQRP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 VDHS-------HYLQKYQRSNQDTCLNQRPIVHQGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V++D++TS+HIE++E+ AR TKLGPEEITR++PNV+E
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITRELPNVAE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 191/589 (32%), Positives = 273/589 (46%), Gaps = 73/589 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISRVNGTVTFVDATAIVVRDEDGV 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHSHYLQKYQRSNQDTCLNQRPIVHQGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD------ 972
             +  +  D  L     VS  +V+  ++    I+K E      +   E + R+        
Sbjct: 667  WEGYNYEDAIL-----VSERLVNDDLYTSVHIEKYEIEARQTKLGPEEITRELPNVAEES 721

Query: 973  ----DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                DE  I+    +    +IL G+    G         L   +  E  R          
Sbjct: 722  LGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN----- 776

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                              +        +I   + GD++PPG   VV+V+VA +R IQ GD
Sbjct: 777  ------------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGD 824

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L
Sbjct: 825  KMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAAANL 884

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
              ++K +  D               ++ G     + +  +  ++  +  ++W        
Sbjct: 885  DCRVKVVPFD---------------EMYGAEKSQQTVETFLKEAAKQPGKEWIY------ 923

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                              + D+ G+  L DG +GEPFD+PV VGY + LKL H+V DK++
Sbjct: 924  ------------------NPDDPGKLQLIDGRSGEPFDQPVAVGYSHFLKLVHLVDDKIH 965

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            ARSTG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR   
Sbjct: 966  ARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEA 1025

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
              +IV G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1026 LNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVFTDEGKEVDLMQDV 1074



 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 96/435 (22%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    +S  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|124026591|ref|YP_001015706.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. NATL1A]
 gi|158512746|sp|A2C4N2|RPOB_PROM1 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|123961659|gb|ABM76442.1| RNA polymerase beta subunit [Prochlorococcus marinus str. NATL1A]
          Length = 1095

 Score =  495 bits (1274), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSIDAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD++R +  ED+++ +  L++L    G  T
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDNLRTLTNEDVLSTLDYLINLELDVGGAT 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G++  +   +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGRLIKEGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + +E+G    ELV  R   +   V  E++D++  SP QV+S+AASLIPFLE+DD+NR 
Sbjct: 487 DVATNEEGKIMAELVPVRYRQDFETVSPEQVDYVQLSPVQVISVAASLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   ++K  G V  VDA  IV+   EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISKVNGTVSYVDANAIVVTDDEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+N RP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 ND-------HTHYLQKYQRSNQDTCLNHRPIVFNGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNVSE
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVSE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ENLGNLDEMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 267/584 (45%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISKVNGTVSYVDANAIVVTDDEGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                ++   I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHYLQKYQRSNQDTCLNHRPIVFNGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  ++ +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVSEENLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    Y    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDI LNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDICLNPLGVPSRMNVGQVFELLMGWAASNLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  Y  ++  +  + W             
Sbjct: 890  IVPFD---------------EMYGPEMSNQTVQAYLKEAAKQPGKSWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         +  + G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPKDPGKLLLKDGRTGEPFDQPVAVGYAHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     SIV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNSIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDDGKEVDLMQDV 1074



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 192/435 (44%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ++S+  FL          ++GL     +  PIT ++G   L F+   Y+   
Sbjct: 15  LPDLVEVQRSSFKWFL----------DKGLIEELDNFSPITDYTGKLELHFIGAEYKLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEFYKKSIDAANEEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDNLRTLTNEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|253757187|gb|ACT35192.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 325/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   +V     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           + ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 RYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG G ++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGSLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-VTNDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G  + +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVAIVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757151|gb|ACT35174.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 457/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEEVINKLIENKVAKISYWYVGP--ESKLVANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757145|gb|ACT35171.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. animalis ATCC 51191]
          Length = 805

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++ +I   +V     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEELINNLIENKVENISYWHVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTPDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +   + +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVAIVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C+ Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLQQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  357 bits (915), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLQQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331123996|gb|AEC53786.1| RNA polymerase subunit B [Vibrio harveyi]
          Length = 522

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 256/525 (48%), Positives = 361/525 (68%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  SEEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTSEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKTYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + +  L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKSLETLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGGFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|159904148|ref|YP_001551492.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. MIT 9211]
 gi|226699430|sp|A9BCH6|RPOB_PROM4 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|159889324|gb|ABX09538.1| RNA polymerase beta subunit [Prochlorococcus marinus str. MIT 9211]
          Length = 1096

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 323/726 (44%), Positives = 451/726 (62%), Gaps = 14/726 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
            Y       +              +          I+  E+VI +    + G+    ++ 
Sbjct: 83  MYVTCRLINKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD 142

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                   +  +     A      +  ++     D   + +   +  +       +    
Sbjct: 143 KNGRRTYNASVIPNRG-AWLKFETDKNDLLHVRVDKTRKINAHVLMRAMGLSDNDVIDKL 201

Query: 352 VNNNAYIRNTLVTDKN--KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +   Y ++    D+        ALL++Y+ +RPG+  + S  + +    FFD  +YDL 
Sbjct: 202 RHPEYYKKSIEAADEEGISSEDQALLELYKKLRPGEPPSVSGGQQLLQSRFFDPKRYDLG 261

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSV 467
            VGR K+N +L L  PD VR +  ED+++ I  L++L    G  T+DDID+LGNRRVRSV
Sbjct: 262 RVGRYKINKKLRLTIPDSVRTLTHEDVLSTIDYLINLELDVGGATLDDIDHLGNRRVRSV 321

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+AV EFF SSQLSQ  +
Sbjct: 322 GELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAAVKEFFGSSQLSQFMD 381

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP ET EG N GL++SL 
Sbjct: 382 QTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLA 441

Query: 588 SFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           + ARVN YGFIETP+ KV  G+V  +   +YLSA  E+   +A  + + D++G    +L+
Sbjct: 442 THARVNDYGFIETPFWKVDKGRVIKEGKPIYLSADLEDECRVAPGDVATDKEGMIVADLI 501

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +   VP E++D++  SP QV+S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+
Sbjct: 502 PVRYRQDFEKVPPEQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLR 561

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+   EG           + L 
Sbjct: 562 PERPLVGTGLETQVARDSGMVPISQVNGTVTYVDANIIVVTDEEGSE-------HHHSLQ 614

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+QRSNQ+TC+NQRP+V  GD V    ++ADG + + G++ALG+N+L+A+MPW GYN+ED
Sbjct: 615 KYQRSNQDTCLNQRPIVHNGDPVIIGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYED 674

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPN++EE L N+DE GII +G
Sbjct: 675 AILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNIAEESLGNLDEMGIIRIG 734

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           A V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVPS   G VVDVRI+
Sbjct: 735 AFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPSTERGRVVDVRIY 794

Query: 946 NRHGID 951
            R   D
Sbjct: 795 TREQGD 800



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 190/584 (32%), Positives = 273/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +  ++    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISQVNGTVTYVDANIIVVTDEEGS 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                +++  I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  EHHHSLQKYQRSNQDTCLNQRPIVHNGDPVIIGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNIAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + ++ Y  ++     ++W             
Sbjct: 890  VVPFD---------------EMYGAEKSYQTVTAYLKEAASLPGKEWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + ++ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPEDPGKLLLRDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDV 1074



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 103/492 (20%), Positives = 208/492 (42%), Gaps = 47/492 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELENFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKKRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIEAADEEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q+++S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQSRFFDPKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAVKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERS 485
               ++ +     G+    +               + RV   G +    +++   R+ + 
Sbjct: 408 AGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNDYGFIETPFWKVDKGRVIKE 467

Query: 486 IKERISSVDIDS 497
            K    S D++ 
Sbjct: 468 GKPIYLSADLED 479


>gi|302122453|gb|ADK92897.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122465|gb|ADK92903.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122483|gb|ADK92912.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122487|gb|ADK92914.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122489|gb|ADK92915.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122491|gb|ADK92916.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122507|gb|ADK92924.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|302122509|gb|ADK92925.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 521

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 257/524 (49%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757139|gb|ACT35168.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
 gi|253757189|gb|ACT35193.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
 gi|253757191|gb|ACT35194.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 459/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             EA   I+E+ + ++  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAEAEAFINEEVINKLIENKVDKISYWYVGP--ESKLVANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE G+I +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGVIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 222/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGVIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331123760|gb|AEC53668.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 523

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 257/526 (48%), Positives = 362/526 (68%), Gaps = 3/526 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN  L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANDKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 523


>gi|302122437|gb|ADK92889.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122441|gb|ADK92891.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122455|gb|ADK92898.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122457|gb|ADK92899.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122459|gb|ADK92900.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122461|gb|ADK92901.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122463|gb|ADK92902.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122467|gb|ADK92904.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122469|gb|ADK92905.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122471|gb|ADK92906.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122475|gb|ADK92908.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122479|gb|ADK92910.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 256/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757209|gb|ACT35203.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
 gi|253757211|gb|ACT35204.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  494 bits (1273), Expect = e-137,   Method: Composition-based stats.
 Identities = 329/659 (49%), Positives = 450/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEATITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  DD   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCISTPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757207|gb|ACT35202.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 328/659 (49%), Positives = 451/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  +D   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVAEDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (928), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|33241089|ref|NP_876031.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|41017662|sp|Q7VA29|RPOB_PROMA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|33238618|gb|AAQ00684.1| DNA-directed RNA polymerase beta subunit/140 kD subunit
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 1096

 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/726 (44%), Positives = 456/726 (62%), Gaps = 14/726 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
            Y       +              +          I+  E+VI +    + G+    ++ 
Sbjct: 83  MYVTCRLVNKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD 142

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                   +  +     A      +  ++     D   + +   +  +       +    
Sbjct: 143 KNGRRTYNASVIPNRG-AWLKFETDKNDLLHVRVDKTRKINAHVLMRAMGLSDNDVIDKL 201

Query: 352 VNNNAYIRNTLVTDKN--KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            +   Y ++    D         ALL++Y+ +RPG+  + S  + +    FFD+ +YDL 
Sbjct: 202 RHPEYYKKSIQAADDEGISSEDQALLELYKKLRPGEPPSVSGGQQLLQSRFFDAKRYDLG 261

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSV 467
            VGR K+N +L L  PD VR +  ED+++ I  L++L    G  T+DDID+LGNRRVRSV
Sbjct: 262 RVGRYKINKKLRLTIPDSVRTLTHEDVLSTIDYLINLELDVGGATLDDIDHLGNRRVRSV 321

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A+ EFF SSQLSQ  +
Sbjct: 322 GELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMD 381

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP ET EG N GL++SL 
Sbjct: 382 QTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLA 441

Query: 588 SFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           + ARVN+YGFIETP+ KV +G+V    D +YLSA  E+   +A  + + D+DG    +L+
Sbjct: 442 THARVNSYGFIETPFWKVEEGRVIKVGDPIYLSADLEDECRVAPGDVATDKDGMILADLI 501

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   +   VP  ++D++  SP QV+S+A SLIPF+E+DD+NR LMG NMQRQAVPLL+
Sbjct: 502 PVRYRQDFEKVPPAQVDYVQLSPVQVISVATSLIPFVEHDDANRALMGSNMQRQAVPLLR 561

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E P VGTG+E+ VA+ SG   +++  G V  VDA  IV+   EG       G  ++ L 
Sbjct: 562 PERPLVGTGLETQVARDSGMVPISQVNGTVTYVDANSIVVTDDEG-------GEHLHELQ 614

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+QRSNQ+TC+NQRP+V+ GD+V    ++ADG + + G++ALG+N+L+A+MPW GYN+ED
Sbjct: 615 KYQRSNQDTCLNQRPIVRNGDKVIIGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYED 674

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPN++EE L N+DE GII VG
Sbjct: 675 AILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNIAEESLGNLDEMGIIRVG 734

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           A V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLRVPS   G VVDVRI+
Sbjct: 735 AFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPSTEKGRVVDVRIY 794

Query: 946 NRHGID 951
            R   D
Sbjct: 795 TREQGD 800



 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 195/585 (33%), Positives = 279/585 (47%), Gaps = 65/585 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V  ++   +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISQVNGTVTYVDANSIVVTDDEGG 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E +              +++  I+  G +V  G +L      +G   +   + +L A   
Sbjct: 608  EHLHELQKYQRSNQDTCLNQRPIVRNGDKVIIGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNIAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD-------------- 772

Query: 1034 NVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                ++       S  + R  + +I   + GD++PPG   VV+V+VA +R IQ GDKMAG
Sbjct: 773  ----VRDNSLRVPSTEKGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAG 828

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++
Sbjct: 829  RHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAAANLDCRV 888

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K +  D               ++ G     E +  Y  ++  +  ++W         VF 
Sbjct: 889  KVVPFD---------------EMYGAEKSYETVQLYLKEAAKQPGKEW---------VF- 923

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                          + D+ G+ +L DG TGE FD+PV VGY + LKL H+V DK++ARST
Sbjct: 924  --------------NPDDPGKLLLRDGRTGEAFDQPVAVGYSHFLKLVHLVDDKIHARST 969

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +I
Sbjct: 970  GPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAI 1029

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            V G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1030 VKGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDV 1074



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 95/435 (21%), Positives = 191/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    ++  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELENFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       +Y K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEYYKKSIQAADDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q+++S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQSRFFDAKRYDLGRVGRYKINKKLRLTIPDSVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|72382854|ref|YP_292209.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. NATL2A]
 gi|88909627|sp|Q46J22|RPOB_PROMT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|72002704|gb|AAZ58506.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           str. NATL2A]
          Length = 1095

 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 324/681 (47%), Positives = 450/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    +D L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VLMRAMGLSDNDVID 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKKSIDAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           +    FFD  +YDL  VGR K+N +L L  PD++R +  ED+++ +  L++L    G  T
Sbjct: 247 LLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDNLRTLTNEDVLSTLDYLINLELDVGGAT 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ KV +G++  +   +YLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGRLIKEGDPIYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + +E+G    ELV  R   +   V  E++D++  SP QV+S+AASLIPFLE+DD+NR 
Sbjct: 487 DVATNEEGKIMAELVPVRYRQDFETVSPEQVDYVQLSPVQVISVAASLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   ++K  G V  VDA  IV+   EG
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISKVNGKVTYVDANAIVVTDDEG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +          + L K+QRSNQ+TC+N RP+V  GD V    ++ADG + + G++ALG+N
Sbjct: 607 ND-------HTHYLQKYQRSNQDTCLNHRPIVFNGDPVIVGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNVSE
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVSE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ENLGNLDEMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VPS   G VVDVRI+ R   D
Sbjct: 780 VPSTERGRVVDVRIYTREQGD 800



 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 265/584 (45%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV-SEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV    V   +   +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPISKVNGKVTYVDANAIVVTDDEGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +                ++   I+  G  V  G +L      +G   +   + +L A   
Sbjct: 608  DHTHYLQKYQRSNQDTCLNHRPIVFNGDPVIVGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  L     V   +       ++ I+  +  +  E    +I  ++ +     D
Sbjct: 667  WEGYNYEDAILVSERLVKDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVSEENLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    Y    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRIGAYVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPSTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDI LNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDICLNPLGVPSRMNVGQVFELLMGWAASNLDCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  Y   +  +  + W             
Sbjct: 890  IVPFD---------------EMYGPEMSNQTVQAYLKKAAKQPGKSWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         +  + G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPKDPGKLLLKDGRTGEPFDQPVAVGYAHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     SIV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNSIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDDGKEVDLMQDV 1074



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/435 (21%), Positives = 192/435 (44%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ++S+  FL          ++GL     +  PIT ++G   L F+   Y+   
Sbjct: 15  LPDLVEVQRSSFKWFL----------DKGLIEELDNFSPITDYTGKLELHFIGAEYKLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASVIPNRGAWLKFETDKNDLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVIDKLRHPEFYKKSIDAANEEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDNLRTLTNEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGATLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|253757205|gb|ACT35201.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  494 bits (1272), Expect = e-137,   Method: Composition-based stats.
 Identities = 329/659 (49%), Positives = 449/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEATITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  DD   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRTRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757185|gb|ACT35191.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL L+ P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLNVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGSGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGIALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757217|gb|ACT35207.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
 gi|253757221|gb|ACT35209.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 451/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  +D   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVAEDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      Y+L+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  360 bits (925), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 152/526 (28%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   + +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|194476580|ref|YP_002048759.1| DNA-directed RNA polymerase beta subunit [Paulinella chromatophora]
 gi|171191587|gb|ACB42549.1| DNA-directed RNA polymerase beta subunit [Paulinella chromatophora]
          Length = 1102

 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 314/636 (49%), Positives = 428/636 (67%), Gaps = 24/636 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  + D   L+++ H E     I   D    +                 ALL++Y+
Sbjct: 184 VLMRAIGLSDNDVLDKLRHPEYYRKSIDEADEEGIS-------------SEDQALLELYK 230

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  + +  + + +  FFD  +YDL  VGR K+N +L L  P  VR +  ED+++ 
Sbjct: 231 KLRPGEPPSVTGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPSSVRILTAEDVLST 290

Query: 440 IKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           +  L++L    G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS
Sbjct: 291 LDYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDS 350

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + P  L+N KP+V+++ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  
Sbjct: 351 LTPAQLVNPKPLVASIKEFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGGLTRERAGFA 410

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VV 615
           +RD+HP+HYGRICP ET EG N GL+ SL + ARVN YGFIETP+ +V DG V  +   +
Sbjct: 411 VRDIHPSHYGRICPIETPEGPNAGLIGSLATHARVNDYGFIETPFWRVIDGSVCKEGDPI 470

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y SA  E++  +A  +   D +     + V  R       VP E++D+I  SP Q++S+A
Sbjct: 471 YFSADVEDDYRVAPGDVGTDVNDRIKIDFVPVRYRQNFESVPPEQVDYIHLSPVQIISVA 530

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE+DD+NR LMG NMQRQAVPLL+ E P VGTG+E  VA+ SG   + K  G V
Sbjct: 531 TSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLEPQVARDSGMVPITKVDGTV 590

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             VDA  I++R  +        G  I+ L K+QRSNQ+TC+NQRP+VK GD+V    ++A
Sbjct: 591 TFVDATAIIVRDEKD-------GDHIHLLQKYQRSNQDTCLNQRPIVKQGDKVVAGQVLA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG + + G++ALG+N+L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TK
Sbjct: 644 DGSACEGGEIALGQNVLIAYMPWEGYNYEDAILVSERLVEDDLYTSVHIEKYEIEARQTK 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LGPEE+TR+IPNVSEE L ++DE GII +GA V  GDILVGK+TPKGES   PEEKLLRA
Sbjct: 704 LGPEEVTREIPNVSEESLAHLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRA 763

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA DVRD SLRVP+   G VVDVRI+ R   D
Sbjct: 764 IFGEKARDVRDNSLRVPNTERGRVVDVRIYTREQGD 799



 Score =  487 bits (1253), Expect = e-135,   Method: Composition-based stats.
 Identities = 194/587 (33%), Positives = 278/587 (47%), Gaps = 67/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E  +     MV   +   T   ++   ++ RD K G
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLEPQVARDSGMVPITKVDGTVTFVDATAIIVRDEKDG 606

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                              +++  I+  G +V  G +L      +G   +   + +L A  
Sbjct: 607  DHI-HLLQKYQRSNQDTCLNQRPIVKQGDKVVAGQVLADGSACEG-GEIALGQNVLIAYM 664

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   +       ++ I+  +  +  E    +I  ++ +     
Sbjct: 665  PWEGYNYEDAILVSERLVEDDLYTSVHIEKYEIEARQTKLGPEEVTREIPNVSEESLAHL 724

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 725  DEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 771

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +    R  + +I   + GD++PPG   VV+V+VA +R IQ GDKMA
Sbjct: 772  -----VRDNSLRVPNTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMA 826

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ++E  LGWA   L  +
Sbjct: 827  GRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVYECLLGWAAANLDNR 886

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +K +  D               ++ G    TE +  +   +  +  + W           
Sbjct: 887  MKVVPFD---------------EMHGLEKSTETMKAFLRAAAKQPGKDWVYNHK------ 925

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                              + G+  L DG TGEPFD+PVTVGY ++LKL H+V DK++ARS
Sbjct: 926  ------------------DPGKLQLIDGRTGEPFDKPVTVGYAHILKLVHLVDDKIHARS 967

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +
Sbjct: 968  TGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNA 1027

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            IV G      GTPESF VL++E+Q+LGL I +     K++   +E+ 
Sbjct: 1028 IVKGKPIPRPGTPESFKVLMRELQSLGLDISVYLQSLKDNEPDKEVD 1074



 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 97/463 (20%), Positives = 194/463 (41%), Gaps = 39/463 (8%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--S 78
             +  +PDL+EVQ+ S+  FL           +GL     S  PIT ++G   L F+   
Sbjct: 9   QTVAYLPDLVEVQRTSFKWFL----------EKGLIEELDSFSPITDYTGKLELHFIGSD 58

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    P+ +V++   RD T+A  + +T RLI          K   + +EQ +++G+LPLM
Sbjct: 59  YRLKRPRHNVEEAKRRDATFASQMYVTCRLI---------NKETSETREQEVFIGELPLM 109

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++V+Q+ RSPG++F  D  +   +G+  +   +IP++G W+  E D 
Sbjct: 110 TERGTFIINGAERVIVNQIVRSPGVYFKDDHDK---NGRKTFNASMIPNRGAWLKFETDK 166

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAAD 253
             ++HVR+D+ RK+     + A+G+   ++L       +Y K +     +       A  
Sbjct: 167 NSLLHVRVDKTRKINAHVLMRAIGLSDNDVLDKLRHPEYYRKSIDEADEEGISSEDQALL 226

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAED 311
            +           +  G+Q++ S         L +  + K  K L +T      +  AED
Sbjct: 227 ELYKKLRPGEPPSVTGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTIPSSVRILTAED 286

Query: 312 IVNGETGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           +++     I +E          ++ + +  +R +  L  + V         ++ ++    
Sbjct: 287 VLSTLDYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVG 346

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           +   L   +++ P      +  +  F            + +  +    R++   P     
Sbjct: 347 ETDSLTPAQLVNPK--PLVASIKEFFGSSQLSQFMDQTNPLAELTHKRRVSALGPGG--- 401

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           + +E     ++ +     G+  I  I+         +G +  +
Sbjct: 402 LTRERAGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|33865147|ref|NP_896706.1| DNA-directed RNA polymerase subunit beta [Synechococcus sp. WH
           8102]
 gi|41017924|sp|Q7U8K4|RPOB_SYNPX RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|33638831|emb|CAE07128.1| DNA-directed RNA polymerase beta chain [Synechococcus sp. WH 8102]
          Length = 1097

 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 317/636 (49%), Positives = 433/636 (68%), Gaps = 24/636 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  + D   L+++ H E     I             +    +       ALL++Y+
Sbjct: 185 VLMRAMGLSDNDVLDKLRHPEFYKKSI-------------DAANDEGISSEDQALLELYK 231

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+  + S  + +    FFD  +YDL  VGR K+N +L L  PD VR +  ED+++ 
Sbjct: 232 KLRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLST 291

Query: 440 IKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           +  L++L    G  ++DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS
Sbjct: 292 LDYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDS 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + P  L+N KP+V+A+ EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  
Sbjct: 352 LTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFA 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVV 615
           +RD+HP+HYGR+CP ET EG N GL++SL + ARVN YGFIETP+ KV +G V    D +
Sbjct: 412 VRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWKVENGVVIKDGDPI 471

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLSA  E+   +A  + + + DG    +L+  R   +   VP E++D++  SP QV+S+A
Sbjct: 472 YLSADREDEVRVAPGDVATESDGRIKADLIPVRYRQDFEKVPPEQVDYVALSPVQVISVA 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVPLL+ E   VGTG+E+ VA+ SG   +++  G V
Sbjct: 532 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTV 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             VDA  IV++  +G           + L K+QRSNQ+TC+N RP+V+ GD+V    ++A
Sbjct: 592 IFVDATAIVVQDEDGQE-------HTHYLQKYQRSNQDTCLNHRPIVRCGDQVIVGQVMA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG + + G++ALG+N+L+A+MPW GYNFED++L+SER+V++D++TS+HIE++E+ AR TK
Sbjct: 645 DGSACEGGEIALGQNVLIAYMPWEGYNFEDALLVSERLVTDDLYTSVHIEKYEIEARQTK 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LGPEEITR+IPNV+EE L N+DE GII VGA V  GDILVGK+TPKGES   PEEKLLRA
Sbjct: 705 LGPEEITREIPNVAEESLGNLDEMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRA 764

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA DVRD SLRVP    G VVDVRI+ R   D
Sbjct: 765 IFGEKARDVRDNSLRVPGTERGRVVDVRIYTREQGD 800



 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 186/584 (31%), Positives = 266/584 (45%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-FEVMARDTKLGP 858
                       +L       G   E  +     MV         I      +    + G 
Sbjct: 548  MGSNMQRQAVPLLRPERALVGTGLETQVARDSGMVPISRVNGTVIFVDATAIVVQDEDGQ 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E                ++   I+  G +V  G ++      +G   +   + +L A   
Sbjct: 608  EHTHYLQKYQRSNQDTCLNHRPIVRCGDQVIVGQVMADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E    +I  +A +     D
Sbjct: 667  WEGYNFEDALLVSERLVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRVGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                         +        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPGTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDI LNPLGVPSRMNVGQ+FE  +GWA   L  +++
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDICLNPLGVPSRMNVGQVFELLMGWAASNLDSRVR 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     E    +  ++  +  + W             
Sbjct: 890  IVPFD---------------EMHGAEMSQETCEAFLKEAAKQPGKAWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + D+ G+ +L DG TG+PFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPDDPGKLVLRDGRTGQPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGKEVDLMQDV 1074



 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 96/435 (22%), Positives = 189/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL          + GL    +S  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------DLGLIEELESFSPITDYTGKLELHFIGSEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D   ++H
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNSLLH 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       FY K + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVLDKLRHPEFYKKSIDAANDEGISSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++++         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLQTRFFDPKRYDLGRVGRYKINKKLRLTIPDTVRTLTHEDVLSTL 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDVGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|253757177|gb|ACT35187.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  494 bits (1271), Expect = e-137,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 455/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++  RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSSERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|257784972|ref|YP_003180189.1| DNA-directed RNA polymerase, beta subunit [Atopobium parvulum DSM
            20469]
 gi|257473479|gb|ACV51598.1| DNA-directed RNA polymerase, beta subunit [Atopobium parvulum DSM
            20469]
          Length = 1171

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 188/529 (35%), Positives = 267/529 (50%), Gaps = 78/529 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  G  +    +    S +     L  A    +  +  D  +     V   ++
Sbjct: 664  IVTMGQKVEKGQPIADGPS-VDHSELALGANLTVAYMPWEGYNYEDGIIVSERVVQEDLL 722

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGP 999
                 +RH  + + R   +  E+I     +  +D    LD +   R+   +   + + G 
Sbjct: 723  TSVNISRH--EIDARDTKLGAEEITREIPNLGEDMLANLDDDGIIRIGAEVGPGDILVGK 780

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K  T L+++              V+D     +++     Y     ++          
Sbjct: 781  VTPKGETALTAEERLLRAIFGAKAHDVRD----TSLKMPHGSYGRVVDVV-------RFS 829

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             + GDD+PPGV  +V+VFVA +R IQ GDK+AGRHGNKG++ ++LP EDMP++ DGTPVD
Sbjct: 830  REAGDDLPPGVNDLVRVFVAQRRKIQQGDKIAGRHGNKGVICKVLPVEDMPYMADGTPVD 889

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            ++L+PLGVPSRMNVGQ+ E HLGW                                    
Sbjct: 890  VILDPLGVPSRMNVGQLLECHLGWGAAH-------------------------------- 917

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA------------INSMLRMAD 1227
                      DD         +  +PV+TP+FDGA +E+            IN  L+   
Sbjct: 918  --------GWDDDDADSKRYVEGPIPVATPLFDGATDESVAEIVRRANINMINKALKEYG 969

Query: 1228 ----------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                      L+E G++ LYDG TGE F  P+TVG  Y+LKL HMV DK++ARSTG YSL
Sbjct: 970  ENMREEFVPQLNERGKTTLYDGRTGEAFKSPITVGVSYILKLGHMVDDKIHARSTGPYSL 1029

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGGK+  GGQR GEMEVW + AYGAA VLQE+LT+KSDD  GR + YESIV G +
Sbjct: 1030 VTQQPLGGKAQFGGQRFGEMEVWALYAYGAANVLQEILTVKSDDTNGRVKTYESIVKGEN 1089

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTK-NSAKMEEIPDFNKCEL 1385
                G PESF VLVKE+++L L I+  + R + N+AK+ +  + N  E+
Sbjct: 1090 IPTAGIPESFKVLVKEIRSLALDIEPISYRKRANTAKVTDPEEKNAVEI 1138



 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 320/663 (48%), Positives = 437/663 (65%), Gaps = 34/663 (5%)

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
           + G + +       + +   +    I       +  + ++  +RNTL  D    R+DAL+
Sbjct: 179 KRGHLVVSIDRKRRQSATVFLRALGIAVTDDEILSLLGDSDVVRNTLERDVATTREDALI 238

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           +IYR  RPG+  T   A S+ + LFF+  +YDL+ VGR K+N +L  + P DVR + KED
Sbjct: 239 EIYRRQRPGEPPTVDSARSLLDGLFFNEQRYDLARVGRYKINKKLEEEIPADVRVLTKED 298

Query: 436 IIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
           I+A ++ L+ +  G     +DDID+ GNRRVR+VGE+++NQ+R+G+ RMER ++ER++S 
Sbjct: 299 IVAALQYLLAVHAGDESKHLDDIDHFGNRRVRTVGELVQNQFRIGMSRMERVVRERMASQ 358

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV---- 549
           D D + PQ LIN +P+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+    
Sbjct: 359 DADDITPQSLINIRPIVAAIKEFFGSSQLSQFMDQANPLAGLTHKRRLSALGPGGLAGHK 418

Query: 550 ----ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                R      +RDVH +HY R+CP ET EG NIGL+ SL  +A VN YGFIE PYRKV
Sbjct: 419 SGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGPNIGLIGSLALYAHVNEYGFIEAPYRKV 478

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLD----------EDGSFTEELVFCRCAGEEI- 654
             G V++D+V+++A EEEN  IA AN+ +D          +DG   +         +   
Sbjct: 479 TGGVVSDDIVWMTADEEENHIIAPANTPIDPKTKKFVEVDKDGKIVDADRVIARTRDFDG 538

Query: 655 ------LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                  VP E +D++D SP+Q++S+AA+LIPFLE+DD+ R LMG NMQRQAVPL+++ A
Sbjct: 539 SFGAPAQVPVEDVDYMDVSPRQLLSVAANLIPFLEHDDAKRTLMGANMQRQAVPLIQSHA 598

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTGME   A+ SG  I A+ AG V +VDA  +VI S E        G   Y L K++
Sbjct: 599 PFVGTGMEGRAAQDSGELICAEFAGEVTEVDAAHVVIYSDE-------HGSQRYDLPKYE 651

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+TC+N RP+V +G +V +   IADGPS D  +LALG N+ VA+MPW GYN+ED ++
Sbjct: 652 RSNQSTCINHRPIVTMGQKVEKGQPIADGPSVDHSELALGANLTVAYMPWEGYNYEDGII 711

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V ED+ TS++I   E+ ARDTKLG EEITR+IPN+ E+ L N+D+ GII +GAEV
Sbjct: 712 VSERVVQEDLLTSVNISRHEIDARDTKLGAEEITREIPNLGEDMLANLDDDGIIRIGAEV 771

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVGK+TPKGE+ +T EE+LLRAIFG KA DVRDTSL++P G  G VVDV  F+R 
Sbjct: 772 GPGDILVGKVTPKGETALTAEERLLRAIFGAKAHDVRDTSLKMPHGSYGRVVDVVRFSRE 831

Query: 949 GID 951
             D
Sbjct: 832 AGD 834



 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 96/374 (25%), Positives = 165/374 (44%), Gaps = 48/374 (12%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ F K P  +++P+LI VQK S++ F+           EGL  +F    PI   +G   
Sbjct: 18  RRTFSKIPAAMELPNLITVQKESFERFMG----------EGLAESFAEFSPIENSAGTMQ 67

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           + F  ++F  P   + +C  +D++Y  PL + +R +          K   ++KEQ ++MG
Sbjct: 68  VTFGDHQFGDPANSMAECRAKDISYQAPLFVDVRFV---------NKETGEMKEQLVFMG 118

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D PLMT+ GTF+I G +R+VVSQL RSPG++F  +      +G L++  + IP +G W++
Sbjct: 119 DFPLMTERGTFIINGSERVVVSQLVRSPGVYFSSEMD----NGVLVHKSQFIPARGAWLE 174

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            E D +  + V IDR+R+   T FL ALG+    +EILS      V     +        
Sbjct: 175 FEVDKRGHLVVSIDRKRRQSATVFLRALGIAVTDDEILSLLGDSDVVRNTLERDVATTRE 234

Query: 252 ADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             L+   +          GE   ++S + L  GL  + +   +  +G          + E
Sbjct: 235 DALIEIYRRQ------RPGEPPTVDSARSLLDGLFFNEQRYDLARVGRYK---INKKLEE 285

Query: 311 DI---VNGETGEIYIEA----------GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +I   V   T E  + A           +      ++   +  +R +  L  +       
Sbjct: 286 EIPADVRVLTKEDIVAALQYLLAVHAGDESKHLDDIDHFGNRRVRTVGELVQNQFRIGMS 345

Query: 358 IRNTLVTDKNKDRK 371
               +V ++   + 
Sbjct: 346 RMERVVRERMASQD 359


>gi|253757155|gb|ACT35176.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 329/659 (49%), Positives = 455/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I+E+ +  +  ++I  I   +V   N    + NTL+TD      +A++++++ 
Sbjct: 1   IAETEALINEEVINNLIENKIESISYWFVGPENK--LVANTLMTDTTSTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD+     + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKKNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       +        YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDKDKKEHAYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIVIEDKDKKEHAYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNSVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|302122493|gb|ADK92917.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 256/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEAPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|304390147|ref|ZP_07372101.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii subsp.
            curtisii ATCC 35241]
 gi|315657406|ref|ZP_07910288.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii subsp.
            holmesii ATCC 35242]
 gi|304326629|gb|EFL93873.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii subsp.
            curtisii ATCC 35241]
 gi|315491878|gb|EFU81487.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii subsp.
            holmesii ATCC 35242]
          Length = 1168

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 185/527 (35%), Positives = 263/527 (49%), Gaps = 67/527 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+  G  V  GD+L       G   M   + LL A    + ++  D  +     
Sbjct: 667  CYNQQAIVDEGDRVEAGDVLADGPATDG-GEMALGKNLLVAYMSWEGLNYEDAIILSQRV 725

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRL 986
            VS  ++       H  + + R   +  E+I        E   +D  DE+ I+        
Sbjct: 726  VSEDLLTSIHIEEH--EIDARDTKLGEEEITRDIPNVSEAARKDL-DERGIIRVGAEVNA 782

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   ++ E  R                V   +       
Sbjct: 783  GDILVGKVTPKGETELTSEERLLRAILGEKAREA--------RDTSLRVPHGESGIVIGV 834

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                D   +          + PGV  +V+VF+A +R +  GDKMAGRHGNKG VS+ILP 
Sbjct: 835  KEFTDEDDDA--------ALGPGVKHMVRVFIAQRRKMTVGDKMAGRHGNKGCVSKILPV 886

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPFL+DGTPVDI+LNP+GVP RMN+GQ+ E HLGW                       
Sbjct: 887  EDMPFLEDGTPVDIILNPMGVPGRMNLGQVLEFHLGWLA--------------------- 925

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-- 1224
                           +E     ++ +     E  + G  V+TPVFDGA+ + I  +LR  
Sbjct: 926  ---------HEGWDVSEARKAGEEWAQRVPLEVCEPGQHVATPVFDGAEADEITGLLRNT 976

Query: 1225 -------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                      +DE G++ L+DG +GEPF  P+ +GY YMLKL+H+V DK++ARSTG YS+
Sbjct: 977  RVREDFDRPLIDEMGKAKLFDGRSGEPFPYPIAIGYKYMLKLHHLVDDKIHARSTGPYSM 1036

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR RVYESIV G D
Sbjct: 1037 ITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAYALQELLTVKSDDVQGRVRVYESIVRGED 1096

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
              + G PESF VL++EM++L L+++  ++        ++  + ++  
Sbjct: 1097 LPQPGIPESFRVLMQEMRSLCLNVEALDAAGNAIDLRDDEDEASRGP 1143



 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 313/600 (52%), Positives = 424/600 (70%), Gaps = 24/600 (4%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            +  AL DIYR +RPG+  +     ++ +  + +  +YDL+ VGR K+N +L ++     
Sbjct: 251 TQDQALEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGRYKINKKLGVEREMGE 310

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVGEMLK 472
           R +   DI+A  + L+ LR G  T+                DDID+ GNRRVR VGE+++
Sbjct: 311 RTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHIKTDDIDHFGNRRVRPVGELIQ 370

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            Q R G+ RMER++KER+S+ D++++ P  LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 371 MQVRTGMSRMERTVKERMSTQDVEAITPNSLINIRPVVAAIKEFFGTSQLSQFMDQNNPL 430

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL +FAR+
Sbjct: 431 AGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPVETPEGPNIGLIGSLATFARI 490

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYR V DG VTN++ Y++A +EE + IAQA++ L +DG F E  V CR   G
Sbjct: 491 NPYGFVETPYRVVKDGVVTNEIHYITADDEEGKNIAQASAQLTKDGHFVESTVLCRSTGG 550

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + +LV  E++D +D S +Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLLK EAP V
Sbjct: 551 DPVLVSPEEVDLMDVSARQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLKTEAPLV 610

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  +G  +VAK+ G+V +V A  + ++  +G          +Y L KF+RSN
Sbjct: 611 GTGIEKRAAIDAGDVVVAKKGGVVTEVSADLVRLQEDDG-------ETRLYTLEKFKRSN 663

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q  C NQ+ +V  GD V   D++ADGP+TD G++ALG+N+LVA+M W G N+ED++++S+
Sbjct: 664 QGNCYNQQAIVDEGDRVEAGDVLADGPATDGGEMALGKNLLVAYMSWEGLNYEDAIILSQ 723

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+VSED+ TSIHIEE E+ ARDTKLG EEITRDIPNVSE   K++DE GII VGAEVN G
Sbjct: 724 RVVSEDLLTSIHIEEHEIDARDTKLGEEEITRDIPNVSEAARKDLDERGIIRVGAEVNAG 783

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAI GEKA + RDTSLRVP G SG V+ V+ F     D
Sbjct: 784 DILVGKVTPKGETELTSEERLLRAILGEKAREARDTSLRVPHGESGIVIGVKEFTDEDDD 843



 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 105/425 (24%), Positives = 174/425 (40%), Gaps = 50/425 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F +  E +  P+L+ +Q  S+D FL      +                 GLQ     
Sbjct: 14  RVSFAQIDEPMAPPNLLALQTESFDWFLGNEAWQERVKEADKTGDKHVPRTSGLQEILNE 73

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI    G   L F  Y  + P + +D+C  +DLTY  P+ +T   I ++         
Sbjct: 74  MSPIEDNGGTMCLSFKDYTLESPHYTIDECKDKDLTYNAPMYVTAEFITYE--------- 124

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q++++G+ PLMT  GTF++ G +R+VVSQL RSPG++F+    +   S + +Y 
Sbjct: 125 TGEIKTQTVFLGEFPLMTPRGTFIVNGTERVVVSQLVRSPGVYFEKTADKT--SDRDIYL 182

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D KD + VRIDR+RK   T FL ALGM   EI   F  +P ++ +
Sbjct: 183 GKVIPSRGAWLEFEIDKKDTVGVRIDRKRKQSATIFLKALGMSVGEIREAFHDFPLMLET 242

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A       +      I  GE    E+G+ L      + K   +  +G 
Sbjct: 243 LEKDGAIETQDQA-------LEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGR 295

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                    +    V  E GE  ++  D++          +    + +          +I
Sbjct: 296 YK---INKKLG---VEREMGERTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHI 349

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +   +               R +RP G++    V   M        ++     V  +  N
Sbjct: 350 KTDDIDHFGN----------RRVRPVGELIQMQVRTGMSRMERTVKERMSTQDVEAITPN 399

Query: 418 MRLNL 422
             +N+
Sbjct: 400 SLINI 404


>gi|28493038|ref|NP_787199.1| DNA-directed RNA polymerase subunit beta [Tropheryma whipplei str.
            Twist]
 gi|28476078|gb|AAO44168.1| DNA-directed RNA polymerase beta chain [Tropheryma whipplei str.
            Twist]
          Length = 1188

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 190/587 (32%), Positives = 286/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 627  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 685

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 686  KHRDYHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCT-DKGELSLGRNLLVAFM 744

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 745  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 799

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 800  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 856

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 857  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 913

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 914  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 972

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 973  WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 999

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 1000 EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1059

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1060 RSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1119

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1120 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1166



 Score =  483 bits (1243), Expect = e-134,   Method: Composition-based stats.
 Identities = 310/616 (50%), Positives = 431/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 271 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 330

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 331 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 390

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 391 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 450

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 451 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 510

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 511 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 570

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 571 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 630

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 631 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 689

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQR +V+ GD V +  ++ADGP TD G+L+LGRN+LVAF
Sbjct: 690 ------YHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCTDKGELSLGRNLLVAF 743

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 744 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 803

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 804 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 863

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 864 QGTVIDVKLFDAVDGE 879



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 89/312 (28%), Positives = 140/312 (44%), Gaps = 32/312 (10%)

Query: 11  GRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNIAPDERPNE 53
            RV    R   GK  + +++P+L+++Q  S+D  +                         
Sbjct: 46  KRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRVALDAYRKNPSGAPIAEKS 105

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL +    +  D 
Sbjct: 106 GLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVEAEFMNHD- 164

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                     +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +  
Sbjct: 165 --------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYFERTPEKN- 215

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF- 232
            S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  +EI   F 
Sbjct: 216 -SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTDDEIRDAFG 274

Query: 233 -YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLK 289
            +  I      +       A   +            + G  ++E+    +    L +  +
Sbjct: 275 EFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLARVGR 334

Query: 290 EKGVKFLGITSD 301
            K  + LG+  D
Sbjct: 335 YKVNRKLGVDVD 346


>gi|298346094|ref|YP_003718781.1| DNA-directed RNA polymerase [Mobiluncus curtisii ATCC 43063]
 gi|298236155|gb|ADI67287.1| DNA-directed RNA polymerase [Mobiluncus curtisii ATCC 43063]
          Length = 1145

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 185/527 (35%), Positives = 263/527 (49%), Gaps = 67/527 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+  G  V  GD+L       G   M   + LL A    + ++  D  +     
Sbjct: 644  CYNQQAIVDEGDRVEAGDVLADGPATDG-GEMALGKNLLVAYMSWEGLNYEDAIILSQRV 702

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRL 986
            VS  ++       H  + + R   +  E+I        E   +D  DE+ I+        
Sbjct: 703  VSEDLLTSIHIEEH--EIDARDTKLGEEEITRDIPNVSEAARKDL-DERGIIRVGAEVNA 759

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   ++ E  R                V   +       
Sbjct: 760  GDILVGKVTPKGETELTSEERLLRAILGEKAREA--------RDTSLRVPHGESGIVIGV 811

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                D   +          + PGV  +V+VF+A +R +  GDKMAGRHGNKG VS+ILP 
Sbjct: 812  KEFTDEDDDA--------ALGPGVKHMVRVFIAQRRKMTVGDKMAGRHGNKGCVSKILPV 863

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPFL+DGTPVDI+LNP+GVP RMN+GQ+ E HLGW                       
Sbjct: 864  EDMPFLEDGTPVDIILNPMGVPGRMNLGQVLEFHLGWLA--------------------- 902

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-- 1224
                           +E     ++ +     E  + G  V+TPVFDGA+ + I  +LR  
Sbjct: 903  ---------HEGWDVSEARKAGEEWAQRVPLEVCEPGQHVATPVFDGAEADEITGLLRNT 953

Query: 1225 -------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                      +DE G++ L+DG +GEPF  P+ +GY YMLKL+H+V DK++ARSTG YS+
Sbjct: 954  RVREDFDRPLIDEMGKAKLFDGRSGEPFPYPIAIGYKYMLKLHHLVDDKIHARSTGPYSM 1013

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR RVYESIV G D
Sbjct: 1014 ITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAYALQELLTVKSDDVQGRVRVYESIVRGED 1073

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
              + G PESF VL++EM++L L+++  ++        ++  + ++  
Sbjct: 1074 LPQPGIPESFRVLMQEMRSLCLNVEALDAAGNAIDLRDDEDEASRGP 1120



 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 313/600 (52%), Positives = 424/600 (70%), Gaps = 24/600 (4%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            +  AL DIYR +RPG+  +     ++ +  + +  +YDL+ VGR K+N +L ++     
Sbjct: 228 TQDQALEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGRYKINKKLGVEREMGE 287

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVGEMLK 472
           R +   DI+A  + L+ LR G  T+                DDID+ GNRRVR VGE+++
Sbjct: 288 RTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHIKTDDIDHFGNRRVRPVGELIQ 347

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            Q R G+ RMER++KER+S+ D++++ P  LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 348 MQVRTGMSRMERTVKERMSTQDVEAITPNSLINIRPVVAAIKEFFGTSQLSQFMDQNNPL 407

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL +FAR+
Sbjct: 408 AGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPVETPEGPNIGLIGSLATFARI 467

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYR V DG VTN++ Y++A +EE + IAQA++ L +DG F E  V CR   G
Sbjct: 468 NPYGFVETPYRVVKDGVVTNEIHYITADDEEGKNIAQASAQLTKDGHFVESTVLCRSTGG 527

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + +LV  E++D +D S +Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLLK EAP V
Sbjct: 528 DPVLVSPEEVDLMDVSARQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLKTEAPLV 587

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  +G  +VAK+ G+V +V A  + ++  +G          +Y L KF+RSN
Sbjct: 588 GTGIEKRAAIDAGDVVVAKKGGVVTEVSADLVRLQEDDG-------ETRLYTLEKFKRSN 640

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q  C NQ+ +V  GD V   D++ADGP+TD G++ALG+N+LVA+M W G N+ED++++S+
Sbjct: 641 QGNCYNQQAIVDEGDRVEAGDVLADGPATDGGEMALGKNLLVAYMSWEGLNYEDAIILSQ 700

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+VSED+ TSIHIEE E+ ARDTKLG EEITRDIPNVSE   K++DE GII VGAEVN G
Sbjct: 701 RVVSEDLLTSIHIEEHEIDARDTKLGEEEITRDIPNVSEAARKDLDERGIIRVGAEVNAG 760

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAI GEKA + RDTSLRVP G SG V+ V+ F     D
Sbjct: 761 DILVGKVTPKGETELTSEERLLRAILGEKAREARDTSLRVPHGESGIVIGVKEFTDEDDD 820



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 102/415 (24%), Positives = 170/415 (40%), Gaps = 50/415 (12%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKSVFPITAFSGA 71
           +  P+L+ +Q  S+D FL      +                 GLQ     + PI    G 
Sbjct: 1   MAPPNLLALQTESFDWFLGNEAWQERVKEADKTGDKHVPRTSGLQEILNEMSPIEDNGGT 60

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L F  Y  + P + +D+C  +DLTY  P+ +T   I ++           +IK Q+++
Sbjct: 61  MCLSFKDYTLESPHYTIDECKDKDLTYNAPMYVTAEFITYE---------TGEIKTQTVF 111

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +G+ PLMT  GTF++ G +R+VVSQL RSPG++F+    +   S + +Y  ++IP +G W
Sbjct: 112 LGEFPLMTPRGTFIVNGTERVVVSQLVRSPGVYFEKTADKT--SDRDIYLGKVIPSRGAW 169

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D KD + VRIDR+RK   T FL ALGM   EI   F  +P ++ +   D      
Sbjct: 170 LEFEIDKKDTVGVRIDRKRKQSATIFLKALGMSVGEIREAFHDFPLMLETLEKDGAIETQ 229

Query: 250 SAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             A       +      I  GE    E+G+ L      + K   +  +G          +
Sbjct: 230 DQA-------LEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGRYK---INKKL 279

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               V  E GE  ++  D++          +    + +          +I+   +     
Sbjct: 280 G---VEREMGERTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHIKTDDIDHFGN 336

Query: 369 DRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                     R +RP G++    V   M        ++     V  +  N  +N+
Sbjct: 337 ----------RRVRPVGELIQMQVRTGMSRMERTVKERMSTQDVEAITPNSLINI 381


>gi|302122503|gb|ADK92922.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 255/524 (48%), Positives = 361/524 (68%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +   VVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNXVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|33862041|ref|NP_893602.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
           subsp. pastoris str. CCMP1986]
 gi|41017655|sp|Q7V006|RPOB_PROMP RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|33634259|emb|CAE19944.1| RNA polymerase beta subunit [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
          Length = 1097

 Score =  493 bits (1270), Expect = e-137,   Method: Composition-based stats.
 Identities = 323/681 (47%), Positives = 455/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    ++ L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSDNDVVD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             ++   +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKQSI-------------DSANDEGINSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR K+N +L L  P++VR +  ED+++ I  L++L    G  +
Sbjct: 247 LLHSRFFDPKRYDLGRVGRYKINKKLRLTVPNEVRTLTHEDVLSTIDYLINLELDIGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ +V  G+V  +   VYLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWEVEKGRVMKEGNPVYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D+ G+   +L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDKSGNILADLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  GIV  VDA  IV++ V+G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDVDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +         ++ L K+QRSNQ+TC+NQRP+VK GD+V    ++ADG + + G++ALG+N
Sbjct: 607 NE-------HVHFLQKYQRSNQDTCLNQRPIVKNGDQVISGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+IPN+SE
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII  GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLNNLDEMGIIRTGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G V+DVRI+ R   D
Sbjct: 780 VPKTEKGRVLDVRIYTREQGD 800



 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 270/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV       I    +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDVDGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E +              +++  I+  G +V  G +L      +G   +   + +L A   
Sbjct: 608  EHVHFLQKYQRSNQDTCLNQRPIVKNGDQVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRTGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  + +++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLEEASKQDGKDWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         +  + G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPKDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDV 1074



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 98/435 (22%), Positives = 189/435 (43%), Gaps = 37/435 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    KS  PIT ++G   L FV   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELKSFSPITDYTGKLELHFVGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY + + S   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYKQSIDSANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPNEVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGK 450
               ++ +     G+
Sbjct: 408 AGFAVRDIHPSHYGR 422


>gi|253757213|gb|ACT35205.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  493 bits (1269), Expect = e-137,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 451/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETESIITEELINVLIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  +D   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVAEDQISLTKEDVLGSM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      Y+L+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 151/526 (28%), Positives = 217/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   + +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHG KG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGTKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|315654676|ref|ZP_07907582.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii ATCC
            51333]
 gi|315491140|gb|EFU80759.1| DNA-directed RNA polymerase subunit beta [Mobiluncus curtisii ATCC
            51333]
          Length = 1168

 Score =  493 bits (1269), Expect = e-137,   Method: Composition-based stats.
 Identities = 185/527 (35%), Positives = 263/527 (49%), Gaps = 67/527 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              ++  I+  G  V  GD+L       G   M   + LL A    + ++  D  +     
Sbjct: 667  CYNQQAIVDEGDRVEAGDVLADGPATDG-GEMALGKNLLVAYMSWEGLNYEDAIILSQRV 725

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQI--------ELLARDKDDEQVILDRNIYSRL 986
            VS  ++       H  + + R   +  E+I        E   +D  DE+ I+        
Sbjct: 726  VSEDLLTSIHIEEH--EIDARDTKLGEEEITRDIPNVSEAARKDL-DERGIIRVGAEVNA 782

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             +IL G+    G         L   ++ E  R                V   +       
Sbjct: 783  GDILVGKVTPKGETELTSEERLLRAILGEKAREA--------RDTSLRVPHGESGIVIGV 834

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                D   +          + PGV  +V+VF+A +R +  GDKMAGRHGNKG VS+ILP 
Sbjct: 835  KEFTDEDDDA--------ALGPGVKHMVRVFIAQRRKMTVGDKMAGRHGNKGCVSKILPV 886

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPFL+DGTPVDI+LNP+GVP RMN+GQ+ E HLGW                       
Sbjct: 887  EDMPFLEDGTPVDIILNPMGVPGRMNLGQVLEFHLGWLA--------------------- 925

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR-- 1224
                           +E     ++ +     E  + G  V+TPVFDGA+ + I  +LR  
Sbjct: 926  ---------HEGWDVSEARKAGEEWAQRVPLEICEPGQHVATPVFDGAEADEITGLLRNT 976

Query: 1225 -------MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                      +DE G++ L+DG +GEPF  P+ +GY YMLKL+H+V DK++ARSTG YS+
Sbjct: 977  RVREDFDRPLIDEMGKAKLFDGRSGEPFPYPIAIGYKYMLKLHHLVDDKIHARSTGPYSM 1036

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV GR RVYESIV G D
Sbjct: 1037 ITQQPLGGKAQFGGQRFGEMEVWAMEAYGAAYALQELLTVKSDDVQGRVRVYESIVRGED 1096

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
              + G PESF VL++EM++L L+++  ++        ++  + ++  
Sbjct: 1097 LPQPGIPESFRVLMQEMRSLCLNVEALDAAGNAIDLRDDEDEASRGP 1143



 Score =  475 bits (1223), Expect = e-131,   Method: Composition-based stats.
 Identities = 313/600 (52%), Positives = 424/600 (70%), Gaps = 24/600 (4%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            +  AL DIYR +RPG+  +     ++ +  + +  +YDL+ VGR K+N +L ++     
Sbjct: 251 TQDQALEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGRYKINKKLGVEREMGE 310

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVGEMLK 472
           R +   DI+A  + L+ LR G  T+                DDID+ GNRRVR VGE+++
Sbjct: 311 RTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHIKTDDIDHFGNRRVRPVGELIQ 370

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            Q R G+ RMER++KER+S+ D++++ P  LIN +PVV+A+ EFF +SQLSQ  +  N L
Sbjct: 371 MQVRTGMSRMERTVKERMSTQDVEAITPNSLINIRPVVAAIKEFFGTSQLSQFMDQNNPL 430

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL +FAR+
Sbjct: 431 AGLTHKRRLSALGPGGLSRDRAGMEVRDVHPSHYGRMCPVETPEGPNIGLIGSLATFARI 490

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYR V DG VTN++ Y++A +EE + IAQA++ L +DG F E  V CR   G
Sbjct: 491 NPYGFVETPYRVVKDGVVTNEIHYITADDEEGKNIAQASAQLTKDGHFVESSVLCRSTGG 550

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           + +LV  E++D +D S +Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPLLK EAP V
Sbjct: 551 DPVLVSPEEVDLMDVSARQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLLKTEAPLV 610

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  +G  +VAK+ G+V +V A  + ++  +G          +Y L KF+RSN
Sbjct: 611 GTGIEKRAAIDAGDVVVAKKGGVVTEVSADLVRLQEDDG-------ETHLYTLEKFKRSN 663

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q  C NQ+ +V  GD V   D++ADGP+TD G++ALG+N+LVA+M W G N+ED++++S+
Sbjct: 664 QGNCYNQQAIVDEGDRVEAGDVLADGPATDGGEMALGKNLLVAYMSWEGLNYEDAIILSQ 723

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+VSED+ TSIHIEE E+ ARDTKLG EEITRDIPNVSE   K++DE GII VGAEVN G
Sbjct: 724 RVVSEDLLTSIHIEEHEIDARDTKLGEEEITRDIPNVSEAARKDLDERGIIRVGAEVNAG 783

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKGE+ +T EE+LLRAI GEKA + RDTSLRVP G SG V+ V+ F     D
Sbjct: 784 DILVGKVTPKGETELTSEERLLRAILGEKAREARDTSLRVPHGESGIVIGVKEFTDEDDD 843



 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 105/425 (24%), Positives = 174/425 (40%), Gaps = 50/425 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  F +  E +  P+L+ +Q  S+D FL      +                 GLQ     
Sbjct: 14  RVSFAQIDEPMAPPNLLALQTESFDWFLGNEAWQERVKEADKTGDKHVPRTSGLQEILNE 73

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI    G   L F  Y  + P + +D+C  +DLTY  P+ +T   I ++         
Sbjct: 74  MSPIEDNGGTMCLSFKDYTLESPHYTIDECKDKDLTYNAPMYVTAEFITYE--------- 124

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q++++G+ PLMT  GTF++ G +R+VVSQL RSPG++F+    +   S + +Y 
Sbjct: 125 TGEIKTQTVFLGEFPLMTPRGTFIVNGTERVVVSQLVRSPGVYFEKTADKT--SDRDIYL 182

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            ++IP +G W++ E D KD + VRIDR+RK   T FL ALGM   EI   F  +P ++ +
Sbjct: 183 GKVIPSRGAWLEFEIDKKDTVGVRIDRKRKQSATIFLKALGMSVGEIREAFHDFPLMLET 242

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGI 298
              D        A       +      I  GE    E+G+ L      + K   +  +G 
Sbjct: 243 LEKDGAIETQDQA-------LEDIYRKIRPGEPPSAEAGRNLLHNFYTNPKRYDLAEVGR 295

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                    +    V  E GE  ++  D++          +    + +          +I
Sbjct: 296 YK---INKKLG---VEREMGERTLDLTDIVAAFRYLLALRAGDDTVAVKDAAGQETELHI 349

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +   +               R +RP G++    V   M        ++     V  +  N
Sbjct: 350 KTDDIDHFGN----------RRVRPVGELIQMQVRTGMSRMERTVKERMSTQDVEAITPN 399

Query: 418 MRLNL 422
             +N+
Sbjct: 400 SLINI 404


>gi|302122495|gb|ADK92918.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 257/524 (49%), Positives = 363/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ LK+ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ADGKVYVEQGRRVTARHIRQLKKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L ++  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQGISLEALSKLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEAPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757215|gb|ACT35206.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 451/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  +D   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVAEDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      Y+L+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYKLLNYERSNQSMCLHQTPLVGLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 152/526 (28%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   + +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYKLLNYERSNQSMCLHQTPLVGLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757219|gb|ACT35208.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 450/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I E+ +  +  ++I  I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEAIITEELINILIENKIETISYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +F +  +YDL  VGR KMN RL LD  +D   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFLNPQRYDLEPVGRYKMNKRLKLDVAEDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 KYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+ EAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTTKVAGKVIY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      Y+L+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 152/526 (28%), Positives = 218/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L    P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   + +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVIYVDGKKIVIEDADKKEHTYKLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|46361024|gb|AAS89245.1| RpoB [Corynebacterium spheniscorum]
          Length = 1094

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 322/616 (52%), Positives = 446/616 (72%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL +D  +    ALL+IYR  RPG+  T  +A+S+ +  FF   +YDL+
Sbjct: 233 ERFGFSELMMSTLESDGVESTDAALLEIYRKQRPGEQPTRDLAQSLLDNSFFRPKRYDLA 292

Query: 410 TVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDI 456
            VGR K+N +L L    D +  + +EDI   ++ LV L  G+ T+            DDI
Sbjct: 293 KVGRYKINRKLGLGGDHDGLMILTEEDIATTLEYLVRLHAGERTMTSPTGEVIPVETDDI 352

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EF
Sbjct: 353 DHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREF 412

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 413 FGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPE 472

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL+S+ARVN +GFIETPYRKV +GK+T+ + YL+A EE+   +AQAN+ +D+
Sbjct: 473 GPNIGLIGSLSSYARVNPFGFIETPYRKVENGKLTDQIDYLTADEEDRYAVAQANTEIDK 532

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           DG+  EE V  R   G+  +V  ++ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 533 DGNIAEERVVVRVKNGDIQVVNGDEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 592

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL++AE P VGTGME   A  +G  ++ + AG+VE V A  I +   EG  +  
Sbjct: 593 MQRQAVPLVRAEPPLVGTGMEQRAAYDAGDLLINRNAGVVENVCADFITVMDDEGRRE-- 650

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y L KFQR+NQ TC NQ+PLV++GD V    ++ADGP T  G+++LGRN+LVAF
Sbjct: 651 -----TYMLRKFQRTNQGTCYNQKPLVEIGDRVEAGQVLADGPGTCNGEMSLGRNLLVAF 705

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK+
Sbjct: 706 MPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKD 765

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G 
Sbjct: 766 LDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGE 825

Query: 936 SGTVVDVRIFNRHGID 951
           +G V+ VR F+R   D
Sbjct: 826 TGKVIGVRRFSREDDD 841



 Score =  452 bits (1162), Expect = e-124,   Method: Composition-based stats.
 Identities = 172/499 (34%), Positives = 242/499 (48%), Gaps = 61/499 (12%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  E                ++  ++ +G  V  G +L           M+    L
Sbjct: 643  MDDEGRRETYMLRKFQRTNQGTCYNQKPLVEIGDRVEAGQVLADGPGT-CNGEMSLGRNL 701

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----EL 966
            L A    +  +  D  +     V   ++       H ID  +  +  E    +I    E 
Sbjct: 702  LVAFMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSED 761

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
            + +D  DE+ I+      R  +IL G+    G         L   +  E  R        
Sbjct: 762  VLKDL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAR-------- 812

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E      +            +    +  DD+ PGV  +++V+VA KR IQ 
Sbjct: 813  ---------EVRDTSMKVPHGETGKVIGVRRFSREDDDDLAPGVNEMIRVYVAQKRKIQD 863

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVDI+LN  GVP RMN+GQ+ E HLGW   
Sbjct: 864  GDKLAGRHGNKGVVGKILPPEDMPFMADGTPVDIILNTHGVPRRMNIGQVLEIHLGWLAA 923

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G K+       +   +   L++  E++                          +G   
Sbjct: 924  A-GWKVD-----PEDPKNAELLKTLPEELYDVP----------------------AGSLT 955

Query: 1207 STPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  PV+VGY+YMLK
Sbjct: 956  ATPVFDGASNEELAGLLANSRPNRDGDVLVDENGKAKLFDGRSGEPFQFPVSVGYMYMLK 1015

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIK
Sbjct: 1016 LHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIK 1075

Query: 1319 SDDVVGRTRVYESIVAGND 1337
            SDDVVGR +VYE+IV G++
Sbjct: 1076 SDDVVGRVKVYEAIVKGDN 1094



 Score =  297 bits (761), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 176/388 (45%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I++P L+++Q+ S+   +            +  D R   GL+   + + P
Sbjct: 19  RFSFAKITEPIEVPGLLDLQRESFAWLVGTTEWRERQREELGEDARITSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 79  IQDYSGNMSLSLSQPRFEDVKNTIDECKDKDINYSAPLYVTAEFINND---------TQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT+ GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 130 IKSQTVFIGDFPMMTEKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R++PVT  L ALG  +E+I   F    +   +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRLPVTVLLKALGWTAEQIKERFGFSELMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI-- 298
           D      +A   +   +        D  + ++++         L K  + K  + LG+  
Sbjct: 248 DGVESTDAALLEIYRKQRPGEQPTRDLAQSLLDNSFFRPKRYDLAKVGRYKINRKLGLGG 307

Query: 299 ---------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                          T + L  L+  E  +   TGE+       ++   ++   +  +R 
Sbjct: 308 DHDGLMILTEEDIATTLEYLVRLHAGERTMTSPTGEVI-----PVETDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|253757161|gb|ACT35179.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 328/659 (49%), Positives = 455/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I+E+ +  +  ++I  I   +V   N    + NTL+TD      +A++++++ 
Sbjct: 1   IAETEALINEEVINNLIENKIESISYWFVGPENK--LVANTLMTDTTSTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLS+  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSRFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD+     + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKKNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       +        YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIVIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNSVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757183|gb|ACT35190.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 459/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             EA   I+E+ + ++  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAEAEAFINEEVINKLIENKVDKISYWYVGP--ESKLVANTLMNDTTLTEGEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG+  +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGEQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE G+I +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGVIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 222/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGVIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331124030|gb|AEC53803.1| RNA polymerase subunit B [Vibrio sp. SO136]
          Length = 519

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 259/522 (49%), Positives = 360/522 (68%), Gaps = 3/522 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ KI +  +
Sbjct: 1   ARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKINFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L    L  G   S  +     G+  +E G+++T+  ++ L++ GV F+ +  +
Sbjct: 61  DQTLMMELVPERL-RGETASFDIE--ADGKLYVEKGRRVTARHIRQLEKDGVTFIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  +SL  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVSSKDYINEATGEIIVAANQEISLESLANLSQAGYKKLEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRVDSTTDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIE 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
               ++   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 RADAEEQGTLDETDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE +
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHV 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 NYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 519


>gi|253757167|gb|ACT35182.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 454/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I+E+ +  +  ++I  I   +V   N    + NTL+ D      +A++++++ 
Sbjct: 1   IAETEALINEEVINNLIENKIESISYWFVGPENK--LVANTLMADTTSTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  ++DL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRHDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD+     + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKKNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       +        YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIVIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNSVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|139438555|ref|ZP_01772071.1| Hypothetical protein COLAER_01069 [Collinsella aerofaciens ATCC
            25986]
 gi|133776094|gb|EBA39914.1| Hypothetical protein COLAER_01069 [Collinsella aerofaciens ATCC
            25986]
          Length = 1142

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 186/612 (30%), Positives = 261/612 (42%), Gaps = 85/612 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++    P+ G   E    +    V+        I            G  
Sbjct: 555  MGANMQRQAVPLVHPAAPYVGTGMERRAALDSGEVTLAKNAGEVIFADAAKIIVKHAGGM 614

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +               I+   ++ VG  V  G+ L    +      +   + L  A    
Sbjct: 615  DEYHLAKYQRSNQSTCINHRPLVRVGDTVEQGEPLADGPST-DHGELALGQNLTVAYMPW 673

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DE 974
            +  +  D  +     V+  ++      RH ID  +  +  E    +I  L+ D     DE
Sbjct: 674  EGFNYEDGIVVSERLVAEDLLTTINITRHEIDARDTKLGPEEITREIPNLSEDMLANLDE 733

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I+         +IL G+    G         L   +                      
Sbjct: 734  DGIIRIGAEVGPGDILVGKVTPKGESALTAEERLLRAIFGAKAHDVRDT----------- 782

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                    +                 + GDD+ PGV   V+V+VA +R IQ GDK+AGRH
Sbjct: 783  ------SLKMPHGAYGRVIDVVRFSRENGDDLAPGVNEQVRVYVAQRRKIQQGDKIAGRH 836

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++  +LP EDMP++ DGTP+D++LNPLGVPSRMNVGQ+ E HLGWA          
Sbjct: 837  GNKGVICNVLPVEDMPYMADGTPIDVILNPLGVPSRMNVGQLLECHLGWAAAC------- 889

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                               D       +        +TPVFDGA
Sbjct: 890  ---------------------------------GWDTEQADSDKYVPGPFFTATPVFDGA 916

Query: 1215 DEEAINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVG 1252
             E+ I  ++R A+                      LDE G++ L+DG TGE F  P+TVG
Sbjct: 917  KEDEIAEVIRRANKNMLNKATAAFGDHMRPEFVTQLDERGKTRLFDGRTGEEFREPITVG 976

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA+ VLQ
Sbjct: 977  TSYILKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQ 1036

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LT+KSDD VGR + YESIV G +    G PESF VLVKE+++L L I+  +   ++++
Sbjct: 1037 EILTVKSDDTVGRVKTYESIVKGENVPVPGIPESFKVLVKEIRSLALDIEPMHDADEDAS 1096

Query: 1373 KMEEIPDFNKCE 1384
                  + +  +
Sbjct: 1097 APVTAEETSALD 1108



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 315/630 (50%), Positives = 429/630 (68%), Gaps = 35/630 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           ++ + N+  I+ TL  D    R+DAL++IYR +RPG+  T   + S+   L F+  +YDL
Sbjct: 185 IELLGNSDVIKRTLERDTALTREDALIEIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDL 244

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRS 466
           + VGR K+N +LNL T ++V  +  EDI+A ++ L+ L  G+    +DDID+ GNRR+R+
Sbjct: 245 ARVGRYKVNKKLNLTTEEEVTVLTDEDIVATLRYLLSLAAGEQGFKVDDIDHFGNRRIRT 304

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE++ NQ+R+G+ RMER ++ER+SS DID + PQ LIN +P+V+++ EFF SSQLSQ  
Sbjct: 305 VGELVANQFRIGMSRMERVVRERMSSQDIDEITPQSLINIRPIVASIKEFFGSSQLSQFM 364

Query: 527 EHVNSLSRITHTRRLSALGQGGV--------ARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  N L+ +TH RRLSALG GG+         R      +RDVH +HY R+CP ET EG 
Sbjct: 365 DQANPLTGLTHKRRLSALGPGGLAGHKSGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGP 424

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED- 637
           NIGL+ SL  +ARVN YGFIE P+R+V +G  T+ + +++A EEE   IA AN+ LD   
Sbjct: 425 NIGLIGSLALYARVNEYGFIEAPFRRVENGVATDQIDWMTADEEEKHVIAPANTPLDPKT 484

Query: 638 ---------GSFTEELVFCRCAGEEI-------LVPREKIDFIDASPKQVVSIAASLIPF 681
                    G             +          VP E +D++D SP+Q++S+AA+LIPF
Sbjct: 485 NEFITTDAEGKIVRPHTVIARTRDFDGSFGAPADVPVEDVDYMDVSPRQMLSVAATLIPF 544

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE+DD+ R LMG NMQRQAVPL+   AP+VGTGME   A  SG   +AK AG V   DA 
Sbjct: 545 LEHDDAKRTLMGANMQRQAVPLVHPAAPYVGTGMERRAALDSGEVTLAKNAGEVIFADAA 604

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I+++           G+D Y L K+QRSNQ+TC+N RPLV+VGD V + + +ADGPSTD
Sbjct: 605 KIIVKH--------AGGMDEYHLAKYQRSNQSTCINHRPLVRVGDTVEQGEPLADGPSTD 656

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+ VA+MPW G+N+ED +++SER+V+ED+ T+I+I   E+ ARDTKLGPEEI
Sbjct: 657 HGELALGQNLTVAYMPWEGFNYEDGIVVSERLVAEDLLTTINITRHEIDARDTKLGPEEI 716

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TR+IPN+SE+ L N+DE GII +GAEV PGDILVGK+TPKGES +T EE+LLRAIFG KA
Sbjct: 717 TREIPNLSEDMLANLDEDGIIRIGAEVGPGDILVGKVTPKGESALTAEERLLRAIFGAKA 776

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DVRDTSL++P G  G V+DV  F+R   D
Sbjct: 777 HDVRDTSLKMPHGAYGRVIDVVRFSRENGD 806



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 100/361 (27%), Positives = 169/361 (46%), Gaps = 42/361 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +++P+LI VQ+ S++ F           +EGL+ AFK   PI + +    + F  ++F  
Sbjct: 1   MELPNLISVQRESFERF----------KDEGLREAFKESSPIQSQNHVLEVTFGEHQFGD 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P   V++C  +D+TY  PL   +RL           K   +IKEQ ++MGD P+MT  GT
Sbjct: 51  PAHTVEECREKDMTYQAPLLTDVRLT---------NKETGEIKEQLVFMGDFPMMTDQGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +RIVVSQL RSPG+++  +      SGK +Y  +IIP +G W++ E D +D + 
Sbjct: 102 FIINGTERIVVSQLVRSPGVYYSSEMD----SGKQIYKAQIIPSRGAWLEFEVDKRDQLM 157

Query: 204 VRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           V IDR+RK   T FL ALG+   +++I+       V  +  +          L     + 
Sbjct: 158 VSIDRKRKQSATMFLRALGIAVTNDDIIELLGNSDVIKRTLERDTA------LTREDALI 211

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV---------KFLGITSDCLCGLYVAED 311
                +  GE   +++ + L  GLL + +   +         K L +T++    +   ED
Sbjct: 212 EIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDLARVGRYKVNKKLNLTTEEEVTVLTDED 271

Query: 312 IVNGETGEIYIEAGDV-IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           IV      + + AG+       ++   +  IR +  L  +           +V ++   +
Sbjct: 272 IVATLRYLLSLAAGEQGFKVDDIDHFGNRRIRTVGELVANQFRIGMSRMERVVRERMSSQ 331

Query: 371 K 371
            
Sbjct: 332 D 332


>gi|302122435|gb|ADK92888.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 256/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPGEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDGTADRISALVEIYRMMRPGEAPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757165|gb|ACT35181.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 325/659 (49%), Positives = 455/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  ++AQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFVAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA D RDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDARDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R             +    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------ARDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPTEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331124000|gb|AEC53788.1| RNA polymerase subunit B [Vibrio harveyi]
          Length = 522

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 257/525 (48%), Positives = 362/525 (68%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVK 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L    L  G   S  +     G   +E G+++T+  ++ L++  V F+ 
Sbjct: 61  FEVKDQTLLMELVPERL-RGETASFDIE--ANGTVYVEKGRRVTARHIRQLEKDNVDFIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D VN  TGE+ + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYVNEATGEVIVSANQEISLEALANLSQAGYKKLEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AES+F  LFF  ++YDLSTVGR+K N
Sbjct: 178 VSETLRIDSTVDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   ++  + + DII ++K L+ +RNG G +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIEREDAGELGTLDETDIIEVMKKLIAIRNGIGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA++E    IAQAN+ L E+G+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANAILTEEGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|302122439|gb|ADK92890.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 256/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISALVEIYRMMRPGEAPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757149|gb|ACT35173.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++ +++ 
Sbjct: 1   IAEVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVKVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD +T   A+S+   +FF+  +YDL  VGR KMN RL LD P+D   + KED++  I
Sbjct: 59  LRPGDQATVDSAKSLIKQMFFNPQRYDLKPVGRYKMNKRLKLDVPEDQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    E LV CR   E + +  E+ +++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERENYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHPVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757197|gb|ACT35197.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 324/659 (49%), Positives = 454/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   +V     +  I NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEELINNLIENKVESISYWHVGP--ESKLIANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           + ++DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E +++ DI++V
Sbjct: 119 RYVIDLNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREEMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-GKVTNDVVYL 617
           RDVH +HYGRICP ET E  NIGL+ SL ++A++N YGFIETPY KV +   + +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEEPNIGLIGSLATYAKINKYGFIETPYVKVENGVAIVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       + +      YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDLALGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVDV   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDVLELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDADKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                +          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATRLGDLALGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDVLELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  +STPVFDGA EE I   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTYISTPVFDGATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|55981782|ref|YP_145079.1| DNA-directed RNA polymerase subunit beta [Thermus thermophilus HB8]
 gi|41018085|sp|Q8RQE9|RPOB_THET8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|21730339|pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
            Thermus Thermophilus At 2.6a Resolution
 gi|21730345|pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
            Thermus Thermophilus At 2.6a Resolution
 gi|49259057|pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
            Ppgpp
 gi|49259063|pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
            Ppgpp
 gi|78101159|pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
            In Complex With The Antibiotic Streptolydigin
 gi|78101165|pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
            In Complex With The Antibiotic Streptolydigin
 gi|78101221|pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101227|pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101233|pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101239|pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101245|pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme
 gi|78101251|pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme
 gi|78101257|pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101263|pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101759|pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
            Holoenzyme At 3.3 Angstroms Resolution
 gi|78101765|pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
            Holoenzyme At 3.3 Angstroms Resolution
 gi|83754374|pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754380|pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|151567771|pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Elongation Complex
 gi|151567776|pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Elongation Complex
 gi|151567787|pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
            Elongation Complex With The Ntp Substrate Analog
 gi|151567792|pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
            Elongation Complex With The Ntp Substrate Analog
 gi|152149353|pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
            Elongation Complex With The Ntp Substrate Analog And
            Antibiotic Streptolydigin
 gi|152149358|pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
            Elongation Complex With The Ntp Substrate Analog And
            Antibiotic Streptolydigin
 gi|209447475|pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
            Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447481|pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
            Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|210061066|pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061072|pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
            Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|313754165|pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754170|pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754175|pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754185|pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754190|pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754195|pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|20160390|dbj|BAB89400.1| DNA-directed RNA polymerase beta chain [Thermus thermophilus]
 gi|55773195|dbj|BAD71636.1| DNA-directed RNA polymerase beta chain (RpoB) [Thermus thermophilus
            HB8]
          Length = 1119

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 190/510 (37%), Positives = 256/510 (50%), Gaps = 43/510 (8%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------L 929
            +D+   + VG  V  GD+L      +    +   + +L AI      +  D        L
Sbjct: 637  LDQRPRVVVGQRVRKGDLLADGPASEN-GFLALGQNVLVAIMPFDGYNFEDAIVISEELL 695

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
            +     S  +    I  R      ER         E   RD D+E  ++      +  +I
Sbjct: 696  KRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GVVRIGAEVKPGDI 754

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+ +  G         L   +  E  R                               
Sbjct: 755  LVGRTSFKGESEPTPEERLLRSIFGEKARD-------------------VKDTSLRVPPG 795

Query: 1050 EDRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            E     +  +++ GD    + PGV  VV+V+VA KR +Q GDK+A RHGNKG+V++ILP 
Sbjct: 796  EGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPV 855

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S I D     +I 
Sbjct: 856  EDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIK 915

Query: 1167 PLRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
             L +   +V       E    D  +  VLR AE+     P  TP      EE +  +   
Sbjct: 916  ELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTP------EEQLKELFLQ 969

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G+ +LYDG TGEP + P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGG
Sbjct: 970  ------GKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGG 1023

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD+ GR   YE+I+ G D  E   PE
Sbjct: 1024 KAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPE 1083

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            SF VLVKE+QAL L +   + +       E
Sbjct: 1084 SFRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1138), Expect = e-121,   Method: Composition-based stats.
 Identities = 291/590 (49%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++AL+ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     DS+ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+  GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V  G VT++VVY++A EE+   IAQAN+ L E      E V  R  GE ++V  E
Sbjct: 469 TPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPL-EGNRIAAERVVARRKGEPVIVSPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RIV+R  +G L         Y L +F RSNQ T ++QR
Sbjct: 588 VRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVE-------YPLRRFYRSNQGTALDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V VG  VR+ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE G++ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGES  TPEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGD 810



 Score =  262 bits (669), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 106/457 (23%), Positives = 186/457 (40%), Gaps = 38/457 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAF+  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G +PLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W+D+E +   ++ ++++ +RK P+   L  LG D E +      Y ++V     +    
Sbjct: 170 PWIDLEVEPNGVVSMKVN-KRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFA 228

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-KFLGITSDCLCGL 306
                 L+    +          + V      +       L E G  K        L G 
Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGR 288

Query: 307 YVAEDIVNGETGEIYIEAGDVI----------DEKSLEEIFHSEIRDIPILYVDSVNNNA 356
            +A         E+++     +          +   ++ + +  IR +  L  D      
Sbjct: 289 TLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGL 348

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 V ++     +  L   +++        +     F+       K + + +  ++ 
Sbjct: 349 ARLARGVRERMLMGSEDSLTPAKLVNS--RPLEAAIREFFSRSQLSQFKDETNPLSSLRH 406

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
             R++   P     + +E     ++ +     G+   
Sbjct: 407 KRRISALGPGG---LTRERAGFDVRDVHRTHYGRICP 440


>gi|253757173|gb|ACT35185.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 453/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E   +I+E+ +  +  ++I  I   +V   N    + NTL+ D      +A++++++ 
Sbjct: 1   IAETETLINEEVINNLIENKIESISYWFVGPENK--LVANTLMADTTSTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R +AG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSREKAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFI TPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIVTPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD+     + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKKNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVSGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       +        YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 155/526 (29%), Positives = 220/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVSGKVVYVDGKKIVIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNSVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|253757179|gb|ACT35188.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 803

 Score =  493 bits (1268), Expect = e-136,   Method: Composition-based stats.
 Identities = 325/657 (49%), Positives = 455/657 (69%), Gaps = 20/657 (3%)

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           E    I+E+ + ++  +++  I   YV     +  I NTL+ D      +A++++++ +R
Sbjct: 1   EVEAFINEEVINKLIENKVDKISYWYVGP--ESKLIANTLMNDTTLTEDEAVVEVFKKLR 58

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
           PGD  T   A ++   +FF+  +YDL  VGR KMN RL L+ P+D   + KED++  IK 
Sbjct: 59  PGDQVTVDSARNLIRQMFFNPQRYDLEPVGRYKMNKRLKLNVPEDQISLTKEDVLGTIKY 118

Query: 443 LVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V P
Sbjct: 119 VIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETVTP 178

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+RD
Sbjct: 179 QSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEVRD 238

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSA 619
           VH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL+A
Sbjct: 239 VHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYLAA 298

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            EE+  +IAQA++ LD++    E LV CR   E + +  E+++++D SPKQVVS++A LI
Sbjct: 299 DEEDGLFIAQADTKLDKNNK-LEGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAGLI 357

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NMQRQAVPLL++EAPF+GTG+E  VA  SGA +  K +G V  VD
Sbjct: 358 PFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTTKVSGKVVYVD 417

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
             +I+I       +        YRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADGP+
Sbjct: 418 GKKIII-------EDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADGPA 470

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG E
Sbjct: 471 TKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLGDE 530

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIFGE
Sbjct: 531 EITREIPNVSESALRNLDENGIIMIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIFGE 590

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           KA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E  +I +  +
Sbjct: 591 KARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEERKITVGDK 647



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 153/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 348  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPFIGTGLERKVAVDSGAVVTT 407

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E   R +          + +  ++ +G +V  GDI+  
Sbjct: 408  KVSGKVVYVDGKKIIIEDKDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 467

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 468  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 527

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 528  GDEEITREIPNVSESALRNLDENGIIMIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 586

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 587  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 629

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA +R I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 630  KSIRVLVAEERKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 689

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 690  NIGQVLEVHLGMAMRT-------------------------------------------- 705

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 706  --------LNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 757

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 758  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 803


>gi|123966898|ref|YP_001011979.1| DNA-directed RNA polymerase subunit beta [Prochlorococcus marinus
            str. MIT 9515]
 gi|158512735|sp|A2BYL1|RPOB_PROM5 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|123201264|gb|ABM72872.1| RNA polymerase beta subunit [Prochlorococcus marinus str. MIT 9515]
          Length = 1097

 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 189/584 (32%), Positives = 270/584 (46%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGP 858
                       +L    P  G   E  +     MV       I    +   +      G 
Sbjct: 548  MGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDVDGN 607

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E +              +++  I+  G +V  G +L      +G   +   + +L A   
Sbjct: 608  EHVHYLQKYQRSNQDTCLNQRPIVKNGDQVISGQVLADGSACEG-GEIALGQNVLIAYMP 666

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER-----EQIELLARDKDD 973
             +  +  D  L     V+  +       ++ I+  +  +  E        I   + +  D
Sbjct: 667  WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLD 726

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  I+    +    +IL G+    G         L   +  E  R               
Sbjct: 727  EMGIIRTGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDN---------- 776

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                        K+        +I   + GD++PPG   VV+V+VA +R IQ GDKMAGR
Sbjct: 777  -------SLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGR 829

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+SRILP EDMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  +GWA   L  ++K
Sbjct: 830  HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVK 889

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D               ++ G     + +  +  ++  +  + W             
Sbjct: 890  VVPFD---------------EMYGAEKSHQTVQAFLKEASKQNGKDWVY----------- 923

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                         + ++ G+ +L DG TGEPFD+PV VGY + LKL H+V DK++ARSTG
Sbjct: 924  -------------NPEDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTG 970

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV
Sbjct: 971  PYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV 1030

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             G      GTPESF VL++E+Q+LGL I +     K    M+++
Sbjct: 1031 KGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKEVDLMQDV 1074



 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 324/681 (47%), Positives = 453/681 (66%), Gaps = 27/681 (3%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  +   +   +KF    ++ L         +N     + + A  + D   ++
Sbjct: 143 KNGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAH---VLMRAMGLSDNDVVD 199

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I             +    +       ALL++Y+ +RPG+  + S  + 
Sbjct: 200 KLRHPEFYKQSI-------------DAANDEGINSEDQALLELYKKLRPGEPPSVSGGQQ 246

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR K+N +L L  PD+VR +  ED+++ I  L++L    G  +
Sbjct: 247 LLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDNVRTLTHEDVLSTIDYLINLELDIGGAS 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 307 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 366

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGR+CP 
Sbjct: 367 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPI 426

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQA 630
           ET EG N GL++SL + ARVN YGFIETP+ +V  G+V  +   VYLSA  E+   +A  
Sbjct: 427 ETPEGPNAGLINSLATHARVNEYGFIETPFWEVEKGRVIKEGKPVYLSADLEDECRVAPG 486

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D+ G+    L+  R   +   VP  ++D++  SP QV+S+A SLIPFLE+DD+NR 
Sbjct: 487 DVATDKSGNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRA 546

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+ES VA+ SG   + K  GIV  VDA  IV++ V+G
Sbjct: 547 LMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDVDG 606

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +         ++ L K+QRSNQ+TC+NQRP+VK GD+V    ++ADG + + G++ALG+N
Sbjct: 607 NE-------HVHYLQKYQRSNQDTCLNQRPIVKNGDQVISGQVLADGSACEGGEIALGQN 659

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +L+A+MPW GYN+ED++L+SERMV++D++TS+HIE++E+ AR TKLGPEEITR+IPN+SE
Sbjct: 660 VLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISE 719

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           E L N+DE GII  GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SLR
Sbjct: 720 ESLNNLDEMGIIRTGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLR 779

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP    G V+DVRI+ R   D
Sbjct: 780 VPKTEKGRVLDVRIYTREQGD 800



 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 103/492 (20%), Positives = 205/492 (41%), Gaps = 47/492 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+AS+  FL           +GL    KS  PIT ++G   L F+   Y    
Sbjct: 15  LPDLVEVQRASFKWFL----------EKGLIEELKSFSPITDYTGKLELHFIGEEYRLKR 64

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RLI          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 65  PRHDVEEAKRRDATFASQMYVTCRLI---------NKETGEIKEQEVFIGELPLMTERGT 115

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  +  +   +G+  Y   +IP++G W+  E D  ++++
Sbjct: 116 FIINGAERVIVNQIVRSPGVYFKDEMDK---NGRRTYNASVIPNRGAWLKFETDKNNLLY 172

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   +++       FY + + +   +       A   +   
Sbjct: 173 VRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYKQSIDAANDEGINSEDQALLELYKK 232

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 233 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDNVRTLTHEDVLSTI 292

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 293 DYLINLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++   P     + +E 
Sbjct: 353 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG---LTRER 407

Query: 436 IIAIIKILVDLRNGKGTIDDIDN----------LGNRRVRSVGEMLKNQYRLGLLRMERS 485
               ++ +     G+    +               + RV   G +    + +   R+ + 
Sbjct: 408 AGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVEKGRVIKE 467

Query: 486 IKERISSVDIDS 497
            K    S D++ 
Sbjct: 468 GKPVYLSADLED 479


>gi|331124004|gb|AEC53790.1| RNA polymerase subunit B [Vibrio sp. SO201]
 gi|331124006|gb|AEC53791.1| RNA polymerase subunit B [Vibrio sp. SO203]
 gi|331124008|gb|AEC53792.1| RNA polymerase subunit B [Vibrio sp. SO204]
          Length = 522

 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 255/525 (48%), Positives = 360/525 (68%), Gaps = 3/525 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +E++L  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEQVLDIFFDKVK 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L    L  G   +  +     G+  +E G+++T+  ++ L++  V F+ 
Sbjct: 61  FEVKDQTLMMELVPERL-RGETATFDIES--NGKVYVEKGRRVTARHIRQLEKDEVSFIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  D + G   A+D +N  TGE+ + A   +  + L  +  +  + + +L+ + ++N  +
Sbjct: 118 VPVDYIVGKISAKDYINEATGEVILAANQEVTLEVLANLSQAGYKKLEVLFTNDLDNGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRVDSTSDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSPERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +     ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIERTDAEEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L +D  F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAKLTDDSRFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           RE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP
Sbjct: 478 REHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVP 522


>gi|253757203|gb|ACT35200.1| DNA-directed RNA polymerase beta chain [Fusobacterium
           periodonticum]
          Length = 805

 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 329/659 (49%), Positives = 452/659 (68%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I E+ +  +  ++I +I   +V   +    + NTL  D+    + A++++++ 
Sbjct: 1   IAETEATITEELINILIENKIENITYWFVGPEDK--LLANTLANDETLTEEQAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD  DD   + KED++  +
Sbjct: 59  LRPGDQVTIDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVADDQISLTKEDVLGTM 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           + + DL NG   +   DIDNL NRR+R VGE+L  Q + GL +M + +KE++++ DI++V
Sbjct: 119 RYVTDLYNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVKEKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 SPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVRYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ L + G+  + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLGK-GNKLQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLL+AEAPF+GTG+E  VA  SGA +  K AG V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTTKVAGKVVY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +IVI       + +      YRL+ ++RSNQ+ C++Q PLV +GD V+  DIIADG
Sbjct: 418 VDGKKIVI-------EDTDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T  GDLALGRN+L+ FMPW GYN+ED++LIS+R+  EDVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE GII +G+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGIIIIGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 154/526 (29%), Positives = 219/526 (41%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L A  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLRAEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  +     E   R +          + +  ++ +G  V  GDI+  
Sbjct: 410  KVAGKVVYVDGKKIVIEDTDKKEHTYRLLNYERSNQSMCLHQTPLVDLGDVVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKSGDLALGRNILMGFMPWEGYNYEDAILISDRLRKEDVFTSIHIEEYEIDARATKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  +I+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGIIIIGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMRT-------------------------------------------- 707

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 708  --------LNGGTCIATPVFDGATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|269216201|ref|ZP_06160055.1| DNA-directed RNA polymerase, beta subunit [Slackia exigua ATCC
            700122]
 gi|269130460|gb|EEZ61538.1| DNA-directed RNA polymerase, beta subunit [Slackia exigua ATCC
            700122]
          Length = 1164

 Score =  492 bits (1267), Expect = e-136,   Method: Composition-based stats.
 Identities = 187/609 (30%), Positives = 284/609 (46%), Gaps = 79/609 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L    P+ G   E  + +    +V+      +   +   +      G 
Sbjct: 551  MGSNMQRQAVPLLKTAAPYVGTGIEHRIAVDSGEVVAAQNPGVVDYVDGSTVIIRNDEGE 610

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +               ++   ++  G EV  GD+L    +    + +   + LL A   
Sbjct: 611  FDEYLVPKFQRSNQSGCVNHKPLVRKGDEVFAGDVLTDGPS-CDMAELALGKNLLVAYTT 669

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVI 977
             +  +  D  +     V+  ++     + +  + + R   +  E+I   +    +D    
Sbjct: 670  WEGYNYEDAIVISERVVAEDLLTSIHISEY--EVDARDTKLGPEEITREIPNISEDMIAD 727

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +   R+   +   + + G    K  T L+++               +  +  R+   
Sbjct: 728  LDADGIIRVGAEVEPGDVLVGKVTPKGETELTAEE------RLLRAIFGEKAREVRDTSL 781

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                    + +   RF  + +     D++ PGV  +V+VF+A KR +Q GDK++GRHGNK
Sbjct: 782  KVPHGAGGRVVGISRFSRESD-----DELAPGVNELVRVFIAQKRKVQQGDKLSGRHGNK 836

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+VSR+LP EDMP+L DGTPVD++LNPLGVPSRMNVGQ+ E HLGWA             
Sbjct: 837  GVVSRVLPVEDMPYLADGTPVDVMLNPLGVPSRMNVGQLLECHLGWAAK----------- 885

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                          + D      +E     + V+TPVFDGA E+
Sbjct: 886  ----------------------------WGWSDAE--ETSESVDGPIYVATPVFDGATEQ 915

Query: 1218 AINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             I  +++ A+                      LD  G++ L+DG TGEPF  P+TVGY Y
Sbjct: 916  EIADVIQKANRNLINRNHEKFGDLARDEFVPQLDSFGKTTLFDGRTGEPFREPITVGYPY 975

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKL HMV DK++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW + AYGA+ VLQE+L
Sbjct: 976  ILKLGHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQEIL 1035

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            TIKSDD  GR + YE+IV G +      PESF VL+KEM++LGL++++  S  +     +
Sbjct: 1036 TIKSDDTAGRVKAYEAIVKGENIPPAEVPESFKVLLKEMKSLGLNVEMIGSDDQAIDLDD 1095

Query: 1376 EIPDFNKCE 1384
               +    +
Sbjct: 1096 MDSEERSAD 1104



 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 328/741 (44%), Positives = 463/741 (62%), Gaps = 29/741 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           + ++ +  R                         I+  E+V+ S    + G+  S +   
Sbjct: 70  FAEVRFVNRETGEIKEQQVFMGDFPLMTPRGTFIINGTERVVVSQLVRSPGIYFSAERDK 129

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIY-IEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                I    +     A      +  +I  +       + +   +    I +     ++ 
Sbjct: 130 TSDKTIYGAKVIPSRGAWLEFETDKRDILSVRIDRKRKQPATLLLRALGIAETREEIIEV 189

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +  +  +  TL  D    +++AL+++Y+  RPG+  T   A ++ + LFF+  +YDL+ V
Sbjct: 190 LGGSEMVLRTLDRDPATTKEEALIELYKRFRPGEPPTLDSASTLLDGLFFNPQRYDLAKV 249

Query: 412 GRVKMNMRLNLDTPDDVR---HIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRS 466
           GR K N +L  D  D++     + + DII+ ++ +V L  G+    +DDID+ GNRR+R+
Sbjct: 250 GRYKANKKLGFDPDDELGASSTLTERDIISTMRYVVALHGGEEGFQVDDIDHFGNRRIRT 309

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE+++NQ+R+GL RMER ++ER+   + D + PQ L+N +P+V+A+ EFF SSQLSQ  
Sbjct: 310 VGELIQNQFRIGLSRMERVVRERMGMQESDEITPQSLVNIRPIVAAIKEFFGSSQLSQFM 369

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N  + ITH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL
Sbjct: 370 DQSNPAAGITHKRRLSALGPGGLSRERAGFEVRDVHNSHYGRMCPIETPEGPNIGLIGSL 429

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN--------------- 631
            ++ARVN YGFIETPYR+V DGKVT+ V YL+A EEE   IAQAN               
Sbjct: 430 ATYARVNPYGFIETPYRRVIDGKVTDKVDYLTADEEEKHTIAQANDFFDQETRVFGRTVD 489

Query: 632 -SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            + +  D             GE   VP  ++D++D SP+Q+ S+A SLIPFLE+DD+NR 
Sbjct: 490 GAFVPSDRVLCRTRDSKGVFGEPSEVPVGQVDYMDVSPRQMTSVATSLIPFLEHDDANRA 549

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLLK  AP+VGTG+E  +A  SG  + A+  G+V+ VD   ++IR+ EG
Sbjct: 550 LMGSNMQRQAVPLLKTAAPYVGTGIEHRIAVDSGEVVAAQNPGVVDYVDGSTVIIRNDEG 609

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           + D        Y + KFQRSNQ+ CVN +PLV+ GDEV   D++ DGPS D+ +LALG+N
Sbjct: 610 EFDE-------YLVPKFQRSNQSGCVNHKPLVRKGDEVFAGDVLTDGPSCDMAELALGKN 662

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVA+  W GYN+ED+++ISER+V+ED+ TSIHI E+EV ARDTKLGPEEITR+IPN+SE
Sbjct: 663 LLVAYTTWEGYNYEDAIVISERVVAEDLLTSIHISEYEVDARDTKLGPEEITREIPNISE 722

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           + + ++D  GII VGAEV PGD+LVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSL+
Sbjct: 723 DMIADLDADGIIRVGAEVEPGDVLVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLK 782

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP G  G VV +  F+R   D
Sbjct: 783 VPHGAGGRVVGISRFSRESDD 803



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 94/280 (33%), Positives = 143/280 (51%), Gaps = 30/280 (10%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +D+P+LI VQ  S+  F+           EG+  AF +V PI + S    +EF ++EF  
Sbjct: 1   MDVPNLISVQTDSFTWFMT----------EGITEAFNAVCPIESSSKDMFVEFGAHEFGD 50

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+ VD+C  +D++Y  PL   +R +          +   +IKEQ ++MGD PLMT  GT
Sbjct: 51  PKYTVDECKEKDVSYQAPLFAEVRFV---------NRETGEIKEQQVFMGDFPLMTPRGT 101

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R+VVSQL RSPGI+F  ++ +   S K +Y  ++IP +G W++ E D +DI+ 
Sbjct: 102 FIINGTERVVVSQLVRSPGIYFSAERDKT--SDKTIYGAKVIPSRGAWLEFETDKRDILS 159

Query: 204 VRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           VRIDR+RK P T  L ALG+    EEI+       +  +  D          L+      
Sbjct: 160 VRIDRKRKQPATLLLRALGIAETREEIIEVLGGSEMVLRTLDRDPATTKEEALI------ 213

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                   GE   ++S   L  GL  + +   +  +G   
Sbjct: 214 ELYKRFRPGEPPTLDSASTLLDGLFFNPQRYDLAKVGRYK 253


>gi|253757147|gb|ACT35172.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum]
          Length = 805

 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 327/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTGDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL VP G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTVPHGSKGVVVDILGLSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 221/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     +    +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTVPHGSKGVVVDILGLSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|300866789|ref|ZP_07111469.1| DNA-directed RNA polymerase subunit beta [Oscillatoria sp. PCC
           6506]
 gi|300335198|emb|CBN56629.1| DNA-directed RNA polymerase subunit beta [Oscillatoria sp. PCC
           6506]
          Length = 1129

 Score =  492 bits (1266), Expect = e-136,   Method: Composition-based stats.
 Identities = 324/710 (45%), Positives = 444/710 (62%), Gaps = 27/710 (3%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  E+VI +    + G+    +          +  +            +   +++    
Sbjct: 117 INGAERVIVNQIVRSPGVYYKSETDKNGRRSYNASLIPNRGAWLKFETDKNDLVWVRIDK 176

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                +   +    + D  IL  D++ +  Y + T+  +     ++AL+++YR +RPG+ 
Sbjct: 177 TRKLSAQVLLKALGLSDGEIL--DALRHPEYFQKTIEKEGQFGEEEALMELYRKLRPGEP 234

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T +  E + N  FFD  +YDL  VGR K+N +L L  PD +R +  +DI++ +  L++L
Sbjct: 235 PTVAGGEQLLNSRFFDPKRYDLGKVGRYKLNKKLRLSVPDTMRVLTPQDILSCVDYLINL 294

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G+ DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER++  D +S+ P  L+N 
Sbjct: 295 EFDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAESLTPASLVNP 354

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KP+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RAG  +RD+HP+HY
Sbjct: 355 KPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFAVRDIHPSHY 414

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEEN 624
           GRICP ET EG N GL+ SL + ARVN YGF+ETP+  V  G++  D    Y++A EE++
Sbjct: 415 GRICPIETPEGPNAGLIGSLATHARVNPYGFLETPFYPVEKGRILRDRAPAYMTADEEDD 474

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  +   D +G+   + V  R   E       ++D++  SP Q+VS+A SLIPFLE+
Sbjct: 475 LRVAPGDIRTDAEGNIQGDSVPVRYRQEFTTTTPMQVDYVAVSPVQIVSVATSLIPFLEH 534

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLL  E P VGTG+E+  A+ SG  +V+K  G V  +DA RI+
Sbjct: 535 DDANRALMGSNMQRQAVPLLLPERPLVGTGLEAQAARDSGMVVVSKFDGEVVYIDATRII 594

Query: 745 IRS-----------------------VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
           ++S                                +G   Y L K+QRSNQ+TC+NQRPL
Sbjct: 595 VKSIKPGVVEEEVHFSIRDYSDLRSKNPHAFKAKYAGFIEYELQKYQRSNQDTCLNQRPL 654

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           +  GD V    ++ADG ST+  +LALG N+LV +MPW GYN+ED+MLISER+V EDV+TS
Sbjct: 655 IYEGDFVVAGQVLADGSSTEGAELALGHNILVVYMPWEGYNYEDAMLISERLVYEDVYTS 714

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIE++E+ AR TKLGPEEITR+IPNV E+ L+ +DE GII  GA V   DILVGK+TPK
Sbjct: 715 IHIEKYEIEARQTKLGPEEITREIPNVGEDSLRQLDEQGIIRKGAWVEASDILVGKVTPK 774

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GES   PEEKLLRAIFGEKA DVRD SLRVP+G  G VVDVR+F R   D
Sbjct: 775 GESDQPPEEKLLRAIFGEKARDVRDNSLRVPNGEKGRVVDVRVFTREQGD 824



 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 185/510 (36%), Positives = 256/510 (50%), Gaps = 64/510 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++  +I  G  V  G +L    + +G   +     +L      +  +  D  L     
Sbjct: 648  CLNQRPLIYEGDFVVAGQVLADGSSTEGA-ELALGHNILVVYMPWEGYNYEDAMLISERL 706

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KDDEQVILDRNIYSRLMEI 989
            V   V       ++ I+  +  +  E    +I  +  D   + DEQ I+ +  +    +I
Sbjct: 707  VYEDVYTSIHIEKYEIEARQTKLGPEEITREIPNVGEDSLRQLDEQGIIRKGAWVEASDI 766

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                   ++       +  
Sbjct: 767  LVGKVTPKGESDQPPEEKLLRAIFGEKARD------------------VRDNSLRVPNGE 808

Query: 1050 EDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            + R  + ++   + GD++PPG   VV+V+VA KR IQ GDKMAGRHGNKGIVSRILP ED
Sbjct: 809  KGRVVDVRVFTREQGDELPPGANMVVRVYVAQKRKIQVGDKMAGRHGNKGIVSRILPKED 868

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DG PVDIVLNPLGVPSRMNVGQIFE  LGWA   LG + K +  D          
Sbjct: 869  MPYLPDGRPVDIVLNPLGVPSRMNVGQIFECLLGWAGENLGLRFKIVPFD---------- 918

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                 ++ G     E +     ++  +  + W         +FD                
Sbjct: 919  -----EMHGAEKSRESVHGKLREAREKTGKGW---------IFDE--------------- 949

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
            +  G+S ++DG TGE FDRP+TVG  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+ 
Sbjct: 950  NHPGKSTVFDGRTGEAFDRPITVGVAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQ 1009

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
            +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR     +IV G      GTPESF 
Sbjct: 1010 QGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNEALNAIVKGKAIPRPGTPESFK 1069

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            VL++E+Q+L L I +    T       +  
Sbjct: 1070 VLMRELQSLCLDIAVHKVETAEDGSSRDAE 1099



 Score =  318 bits (816), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 107/454 (23%), Positives = 192/454 (42%), Gaps = 36/454 (7%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PDLIE+Q+AS+  FL            GL     S  PIT ++G   L F+   ++   
Sbjct: 14  LPDLIEIQRASFRWFL----------ESGLIEELDSFSPITDYTGKLELHFLGKDFKLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PK+DVD+   RD TYAV + +  RLI          K   +IKE  +++GDLPLMT+ GT
Sbjct: 64  PKYDVDEAKRRDSTYAVQMYVPTRLI---------NKETGEIKEMEVFIGDLPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG+++  +  +   +G+  Y   +IP++G W+  E D  D++ 
Sbjct: 115 FIINGAERVIVNQIVRSPGVYYKSETDK---NGRRSYNASLIPNRGAWLKFETDKNDLVW 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVS 261
           VRID+ RK+     L ALG+   EIL        +  +   +       A   +      
Sbjct: 172 VRIDKTRKLSAQVLLKALGLSDGEILDALRHPEYFQKTIEKEGQFGEEEALMELYRKLRP 231

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +  GEQ++ S         L K  + K  K L ++      +   +DI++     
Sbjct: 232 GEPPTVAGGEQLLNSRFFDPKRYDLGKVGRYKLNKKLRLSVPDTMRVLTPQDILSCVDYL 291

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I +E  D+     ++ + +  +R +  L  + V         ++ ++        L    
Sbjct: 292 INLE-FDIGSTDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIRERMTVSDAESLTPAS 350

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           ++ P      +  +  F            + +  +    RL+   P     + +E     
Sbjct: 351 LVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG---LTRERAGFA 405

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ +     G+  I  I+         +G +  +
Sbjct: 406 VRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 437


>gi|302122477|gb|ADK92909.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 521

 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 255/524 (48%), Positives = 362/524 (69%), Gaps = 3/524 (0%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           +LY  R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ 
Sbjct: 1   VLYNARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVN 60

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +  +       L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + 
Sbjct: 61  FEVKDQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIE 117

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           +  + + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  +
Sbjct: 118 VPVEYIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPF 177

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  TL  D   DR  A+++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N
Sbjct: 178 MSETLRIDSTVDRISAVVEIYRMMRPGEAPTKEAAEALFESLFFSEERYDLSTVGRMKFN 237

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+
Sbjct: 238 SSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 297

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH
Sbjct: 298 GLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTH 357

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF
Sbjct: 358 KRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGF 417

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L P
Sbjct: 418 LETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHP 477

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           RE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 REHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 521


>gi|253757141|gb|ACT35169.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
          Length = 805

 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 326/659 (49%), Positives = 456/659 (69%), Gaps = 20/659 (3%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             E    I+E+ +  +  +++  I   YV     +  + NTL+ D      +A++++++ 
Sbjct: 1   IAETEAFINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTTLTEDEAVVEVFKK 58

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +RPGD  T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  I
Sbjct: 59  LRPGDQVTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTI 118

Query: 441 KILVDLRNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K +++L NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V
Sbjct: 119 KYVIELNNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETV 178

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ L+N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+
Sbjct: 179 TPQSLLNTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEV 238

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH +HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL
Sbjct: 239 RDVHDSHYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYL 298

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A EE+  +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A 
Sbjct: 299 AADEEDGLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAG 357

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  
Sbjct: 358 LIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTY 417

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I+I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADG
Sbjct: 418 VDGKKIII-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADG 470

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           P+T LGDL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG
Sbjct: 471 PATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLG 530

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+    EEKLLRAIF
Sbjct: 531 DEEITREIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIF 590

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           GEKA DVRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 591 GEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 649



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 222/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 350  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 409

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 410  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 469

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 470  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 529

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 530  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 588

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 589  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 631

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 632  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 691

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 692  NIGQVLEVHLGMAMR--------------------------------------------- 706

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 707  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 759

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 760  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 805


>gi|331124016|gb|AEC53796.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 519

 Score =  491 bits (1265), Expect = e-136,   Method: Composition-based stats.
 Identities = 255/522 (48%), Positives = 360/522 (68%), Gaps = 3/522 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 519


>gi|148243058|ref|YP_001228215.1| DNA-directed RNA polymerase beta chain [Synechococcus sp. RCC307]
 gi|147851368|emb|CAK28862.1| DNA-directed RNA polymerase beta chain [Synechococcus sp. RCC307]
          Length = 932

 Score =  491 bits (1264), Expect = e-136,   Method: Composition-based stats.
 Identities = 329/682 (48%), Positives = 451/682 (66%), Gaps = 29/682 (4%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  L   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 142 KNGRRTYNASLIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VMMRAIGLSDNDVLD 198

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 199 KLRHPEYYKKSIDAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 245

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR KMN +L L  PD VR +  ED+++ +  L++L    G   
Sbjct: 246 LLHSRFFDPKRYDLGRVGRYKMNKKLRLTIPDAVRTLTPEDVLSTLDYLINLELDVGGAC 305

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 306 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 365

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG G + R RAG  +RD+HP+HYGRICP 
Sbjct: 366 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGVLTRERAGFAVRDIHPSHYGRICPI 425

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
           ET EG N GL+ SL + ARVN YGFIETP+ KV DG V  + D +YLSA  E+   +A  
Sbjct: 426 ETPEGPNAGLIGSLATHARVNEYGFIETPFWKVTDGVVDKSGDPIYLSADLEDECRVAPG 485

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG  T EL+  R   +   VP  ++D++  SP QV+S+AASLIPFLE+DD+NR 
Sbjct: 486 DVATDADGRITAELIPVRYRLDFETVPPNQVDYVQLSPVQVISVAASLIPFLEHDDANRA 545

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   + +  G V  VD+ +I++R  + 
Sbjct: 546 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGEVVFVDSTQIIVRDDQ- 604

Query: 751 DLDPSTSGVDIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                  GVD Y L  K+QRSNQ+TC+NQRP+V+ GD+V    ++A+G + + G++ALG+
Sbjct: 605 -------GVDHYHLLQKYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEGGEIALGQ 657

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+
Sbjct: 658 NCLIAYMPWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVA 717

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SL
Sbjct: 718 EESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSL 777

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           RVP+   G VVDVRI+ R   D
Sbjct: 778 RVPNTERGRVVDVRIYTREQGD 799



 Score =  314 bits (804), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 99/458 (21%), Positives = 195/458 (42%), Gaps = 39/458 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+ S+  FL           +GL    +S  PIT ++G   L FV   Y    
Sbjct: 14  LPDLVEVQRGSFKWFL----------EKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 64  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 115 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASLIPNRGAWLKFETDKNDLLH 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       +Y K + +   +       A   +   
Sbjct: 172 VRVDKTRKINAHVMMRAIGLSDNDVLDKLRHPEYYKKSIDAANEEGISSEDQALLELYKK 231

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 232 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKMNKKLRLTIPDAVRTLTPEDVLSTL 291

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 292 DYLINLELDVGGACLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 351

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++         + +E 
Sbjct: 352 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISA---LGPGVLTRER 406

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
               ++ +     G+  I  I+         +G +  +
Sbjct: 407 AGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 95/348 (27%), Positives = 144/348 (41%), Gaps = 28/348 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E  +     MV         + ++  +++ RD   G
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGEVVFVDSTQIIVRDD-QG 605

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +                +++  I+  G +V  G +L      +G   +   +  L A  
Sbjct: 606  VDHYHLLQKYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEG-GEIALGQNCLIAYM 664

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     
Sbjct: 665  PWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNL 724

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 725  DEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 771

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +    R  + +I   + GD++PPG   VV+V+VA +R IQ GDKMA
Sbjct: 772  -----VRDNSLRVPNTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMA 826

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            GRHGNKGI+SRILP EDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE 
Sbjct: 827  GRHGNKGIISRILPLEDMPYLPDGTPIDIVLNPLGVPSRMNVGQVFEC 874


>gi|30173235|sp|P59642|RPOB_TROW8 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1157

 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 190/587 (32%), Positives = 286/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 596  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 654

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 655  KHRDYHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCT-DKGELSLGRNLLVAFM 713

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 714  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 768

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 769  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 825

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 826  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 882

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 883  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 941

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 942  WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 968

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 969  EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1028

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1029 RSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1088

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1089 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1135



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 310/616 (50%), Positives = 431/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 240 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 299

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 300 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 359

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 360 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 419

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 420 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 479

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 480 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 539

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 540 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 599

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 600 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 658

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQR +V+ GD V +  ++ADGP TD G+L+LGRN+LVAF
Sbjct: 659 ------YHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCTDKGELSLGRNLLVAF 712

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 713 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 772

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 773 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 832

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 833 QGTVIDVKLFDAVDGE 848



 Score =  305 bits (782), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 90/320 (28%), Positives = 142/320 (44%), Gaps = 32/320 (10%)

Query: 3   KGVVFNGLGRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNI 45
             + F    RV    R   GK  + +++P+L+++Q  S+D  +                 
Sbjct: 7   GFLAFAKGKRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRAALDAYRKNPS 66

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
                   GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL + 
Sbjct: 67  GAPIAEKSGLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVE 126

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
              +  D           +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F
Sbjct: 127 AEFMNHD---------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYF 177

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           +    +   S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  
Sbjct: 178 ERTPEKN--SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTD 235

Query: 226 EEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           +EI   F  +  I      +       A   +            + G  ++E+    +  
Sbjct: 236 DEIRDAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRR 295

Query: 284 --LLKSLKEKGVKFLGITSD 301
             L +  + K  + LG+  D
Sbjct: 296 FDLARVGRYKVNRKLGVDVD 315


>gi|30179895|sp|Q93GF2|RPOB_TROWT RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1157

 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 190/587 (32%), Positives = 286/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 596  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 654

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 655  KHRDYHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCT-DKGELSLGRNLLVAFM 713

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 714  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 768

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 769  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 825

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 826  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 882

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 883  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 941

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 942  WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 968

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 969  EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1028

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1029 RSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1088

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1089 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1135



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 310/616 (50%), Positives = 431/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 240 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 299

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 300 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 359

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 360 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 419

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 420 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 479

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 480 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 539

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 540 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 599

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 600 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 658

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQR +V+ GD V +  ++ADGP TD G+L+LGRN+LVAF
Sbjct: 659 ------YHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCTDKGELSLGRNLLVAF 712

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 713 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 772

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 773 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 832

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 833 QGTVIDVKLFDAVDGE 848



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 89/312 (28%), Positives = 140/312 (44%), Gaps = 32/312 (10%)

Query: 11  GRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNIAPDERPNE 53
            RV    R   GK  + +++P+L+++Q  S+D  +                         
Sbjct: 15  KRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRVALDAYRKNPSGAPIAEKS 74

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL +    +  D 
Sbjct: 75  GLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVEAEFMNHD- 133

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
                     +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +  
Sbjct: 134 --------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYFERTPEKN- 184

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF- 232
            S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  +EI   F 
Sbjct: 185 -SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTDDEIRDAFG 243

Query: 233 -YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLK 289
            +  I      +       A   +            + G  ++E+    +    L +  +
Sbjct: 244 EFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLARVGR 303

Query: 290 EKGVKFLGITSD 301
            K  + LG+  D
Sbjct: 304 YKVNRKLGVDVD 315


>gi|28572249|ref|NP_789029.1| DNA-directed RNA polymerase subunit beta [Tropheryma whipplei
            TW08/27]
 gi|28410380|emb|CAD66766.1| DNA-directed RNA polymerase beta chain [Tropheryma whipplei TW08/27]
          Length = 1155

 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 190/587 (32%), Positives = 286/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 594  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 652

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 653  KHRDYHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCT-DKGELSLGRNLLVAFM 711

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 712  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 766

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 767  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 823

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 824  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 880

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 881  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 939

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 940  WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 966

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 967  EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1026

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1027 RSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1086

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1087 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1133



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 310/616 (50%), Positives = 431/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 238 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 297

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 298 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 357

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 358 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 417

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 418 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 477

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 478 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 537

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 538 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 597

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 598 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 656

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQR +V+ GD V +  ++ADGP TD G+L+LGRN+LVAF
Sbjct: 657 ------YHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCTDKGELSLGRNLLVAF 710

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 711 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 770

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 771 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 830

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 831 QGTVIDVKLFDAVDGE 846



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 90/320 (28%), Positives = 142/320 (44%), Gaps = 32/320 (10%)

Query: 3   KGVVFNGLGRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNI 45
             + F    RV    R   GK  + +++P+L+++Q  S+D  +                 
Sbjct: 5   GFLAFAKGKRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRAALDAYRKNPS 64

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
                   GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL + 
Sbjct: 65  GAPIAEKSGLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVE 124

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
              +  D           +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F
Sbjct: 125 AEFMNHD---------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYF 175

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           +    +   S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  
Sbjct: 176 ERTPEKN--SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTD 233

Query: 226 EEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           +EI   F  +  I      +       A   +            + G  ++E+    +  
Sbjct: 234 DEIRDAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRR 293

Query: 284 --LLKSLKEKGVKFLGITSD 301
             L +  + K  + LG+  D
Sbjct: 294 FDLARVGRYKVNRKLGVDVD 313


>gi|269930921|gb|ACZ54195.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 546

 Score =  491 bits (1263), Expect = e-136,   Method: Composition-based stats.
 Identities = 387/546 (70%), Positives = 461/546 (84%), Gaps = 1/546 (0%)

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           DEK L+ +       I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T
Sbjct: 2   DEKVLKILLDVSADQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGEPPT 61

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
              AE+MF+ LFFD ++YDLS VGRVKMN+R++LD PD VR +R+EDI+A++K+LV+LR+
Sbjct: 62  IDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLDCPDTVRVLRQEDILAVVKMLVELRD 121

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP
Sbjct: 122 GRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKP 181

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
             +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR
Sbjct: 182 AAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 241

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           ICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+A
Sbjct: 242 ICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVA 301

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+N
Sbjct: 302 QANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDAN 361

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ 
Sbjct: 362 RALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVSAKRSGIVDQVDATRIVIRAT 421

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD V + DIIADGPSTDLGDLALG
Sbjct: 422 ED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDRVEKGDIIADGPSTDLGDLALG 480

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           RN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEEIT DI  V
Sbjct: 481 RNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEEITLDIAKV 540

Query: 869 SEEGLK 874
           ++E L 
Sbjct: 541 ADEALM 546


>gi|331124018|gb|AEC53797.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331124020|gb|AEC53798.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331124022|gb|AEC53799.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331124024|gb|AEC53800.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331124026|gb|AEC53801.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|331124028|gb|AEC53802.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 519

 Score =  490 bits (1262), Expect = e-136,   Method: Composition-based stats.
 Identities = 255/522 (48%), Positives = 360/522 (68%), Gaps = 3/522 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 519


>gi|46360970|gb|AAS89218.1| RpoB [Corynebacterium glucuronolyticum]
          Length = 1109

 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 181/518 (34%), Positives = 249/518 (48%), Gaps = 65/518 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  ++ +G  V  G ++        +  M+    LL A
Sbjct: 643  EGKRDTYRLRKFERTNQNTCYNQKPLVDIGDRVEKGQVMADGPGT-HDGEMSLGVNLLVA 701

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLAR 969
                +  +  D  +     V   ++       H ID  +  +  E    +I    E + +
Sbjct: 702  FMPWQGHNYEDAIILNQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  +IL G+    G         L   +  E  R           
Sbjct: 762  DL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 809

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +                   GD++P GV  ++++ VA KR IQ GDK
Sbjct: 810  ------EVRDTSLKVPHGETGKVIGVSRFSRDEGDELPAGVNEMIRIHVAQKRKIQDGDK 863

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG+V +ILP EDMPF++DGTP+DI+LN  GVP RMN+GQ+ E HLGW     G
Sbjct: 864  LAGRHGNKGVVGKILPQEDMPFMEDGTPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-G 922

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I+   +  K                                +        +   V+TP
Sbjct: 923  WAIEGDPDWAKR-------------------------------IPEELRNVPADSLVATP 951

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA  E I  +L     D          G++ L+DG +GEPF  PV VG  YMLKL+H
Sbjct: 952  VFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLKLHH 1011

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDD
Sbjct: 1012 LVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDD 1071

Query: 1322 VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            V GR RVYE+IV G++  + G PESF VL+KE+Q+L L
Sbjct: 1072 VNGRVRVYEAIVKGDNIPDPGIPESFKVLLKELQSLCL 1109



 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 330/662 (49%), Positives = 456/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G ++  D+   +T G              L+ +  SE +       +    +  + +TL 
Sbjct: 189 GAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEK-----IRERFGFSEIMMSTLE 243

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D      +ALL+IYR  RPG+  T  +A+++    FF   +YDL+ VGR K+N +L L 
Sbjct: 244 NDGAASEDEALLEIYRKQRPGEQPTRDLAQALLENSFFKPKRYDLAKVGRYKVNRKLGLG 303

Query: 424 TP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
              D V+ + +EDI   I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 304 GDHDGVKTLTEEDIATTIEYLVRLHAGERTMTSPDGVEIPLETDDIDHFGNRRLRTVGEL 363

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 364 IQNQVRVGLARMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 423

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 424 SLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYA 483

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPY+KV DGK+ + V YL+A EE+   I QA++  DE+G  T+E    R  
Sbjct: 484 RVNPFGFIETPYQKVEDGKIIDQVDYLTADEEDRFVIGQADTEHDENGVITQERNEVRLK 543

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +V  E I++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++++P
Sbjct: 544 DGAIEVVGPEAIEYIDVSPRQIVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSQSP 603

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME+  A  +G  ++ K AG+VE V A  I + S EG  D        YRL KF+R
Sbjct: 604 YVGTGMEAPAAYDAGDLVINKHAGVVENVCADFITVMSDEGKRD-------TYRLRKFER 656

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQNTC NQ+PLV +GD V +  ++ADGP T  G+++LG N+LVAFMPW G+N+ED++++
Sbjct: 657 TNQNTCYNQKPLVDIGDRVEKGQVMADGPGTHDGEMSLGVNLLVAFMPWQGHNYEDAIIL 716

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V 
Sbjct: 717 NQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVR 776

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ V  F+R  
Sbjct: 777 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVSRFSRDE 836

Query: 950 ID 951
            D
Sbjct: 837 GD 838



 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 147/321 (45%), Gaps = 30/321 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +      +++  E         GL+   + + P
Sbjct: 16  RYSFAKIKEPIGLPGLLDLQLNSFAWLVGTPEWREQQKAEKGEDYKVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG   L      F+  K  VD+C  +D+ Y+ PL +T              K   +
Sbjct: 76  IQDFSGNMSLSLSEPYFEQVKASVDECKEKDINYSAPLYVTA---------EFENKDTGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 127 IKSQTVFIGDFPMMTPKGTFIVNGTERVVVSQLVRSPGVYFDETLDK--STERPLHAVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++I+ D KD + VRIDR+R+ PVT  L ALG   E+I   F     ++ +   
Sbjct: 185 IPSRGAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEKIRERFGFSEIMMSTLEN 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +        D  + ++E+            K   +  +G    +
Sbjct: 245 DGAASEDEALLEIYRKQRPGEQPTRDLAQALLENS-------FFKPKRYDLAKVGRYKVN 297

Query: 302 CLCGLYVAEDIVNGETGEIYI 322
              GL    D V   T E   
Sbjct: 298 RKLGLGGDHDGVKTLTEEDIA 318


>gi|182676588|sp|A5GVF3|RPOB_SYNR3 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 1097

 Score =  490 bits (1261), Expect = e-136,   Method: Composition-based stats.
 Identities = 329/682 (48%), Positives = 451/682 (66%), Gaps = 29/682 (4%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           ++G++  +  L   +   +KF    +D L         +N     + + A  + D   L+
Sbjct: 142 KNGRRTYNASLIPNRGAWLKFETDKNDLLHVRVDKTRKINAH---VMMRAIGLSDNDVLD 198

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           ++ H E     I   +    +                 ALL++Y+ +RPG+  + S  + 
Sbjct: 199 KLRHPEYYKKSIDAANEEGIS-------------SEDQALLELYKKLRPGEPPSVSGGQQ 245

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--T 452
           + +  FFD  +YDL  VGR KMN +L L  PD VR +  ED+++ +  L++L    G   
Sbjct: 246 LLHSRFFDPKRYDLGRVGRYKMNKKLRLTIPDAVRTLTPEDVLSTLDYLINLELDVGGAC 305

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVRSVGE+L+NQ R+GL R+ER IKER++  + DS+ P  L+N KP+V+A
Sbjct: 306 LDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAA 365

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF SSQLSQ  +  N L+ +TH RR+SALG G + R RAG  +RD+HP+HYGRICP 
Sbjct: 366 IKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGVLTRERAGFAVRDIHPSHYGRICPI 425

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
           ET EG N GL+ SL + ARVN YGFIETP+ KV DG V  + D +YLSA  E+   +A  
Sbjct: 426 ETPEGPNAGLIGSLATHARVNEYGFIETPFWKVTDGVVDKSGDPIYLSADLEDECRVAPG 485

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + + D DG  T EL+  R   +   VP  ++D++  SP QV+S+AASLIPFLE+DD+NR 
Sbjct: 486 DVATDADGRITAELIPVRYRLDFETVPPNQVDYVQLSPVQVISVAASLIPFLEHDDANRA 545

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLL+ E P VGTG+E+ VA+ SG   + +  G V  VD+ +I++R  + 
Sbjct: 546 LMGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGEVVFVDSTQIIVRDDQ- 604

Query: 751 DLDPSTSGVDIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                  GVD Y L  K+QRSNQ+TC+NQRP+V+ GD+V    ++A+G + + G++ALG+
Sbjct: 605 -------GVDHYHLLQKYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEGGEIALGQ 657

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N L+A+MPW GYN+ED++L+SER+V +D++TS+HIE++E+ AR TKLGPEEITR+IPNV+
Sbjct: 658 NCLIAYMPWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVA 717

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE L N+DE GII +GA V  GDILVGK+TPKGES   PEEKLLRAIFGEKA DVRD SL
Sbjct: 718 EESLGNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSL 777

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           RVP+   G VVDVRI+ R   D
Sbjct: 778 RVPNTERGRVVDVRIYTREQGD 799



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 192/587 (32%), Positives = 276/587 (47%), Gaps = 68/587 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS--EDVFTSIHIEEFEVMARDTKLG 857
                       +L    P  G   E  +     MV         + ++  +++ RD   G
Sbjct: 547  MGSNMQRQAVPLLRPERPLVGTGLETQVARDSGMVPITRVNGEVVFVDSTQIIVRDD-QG 605

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +                +++  I+  G +V  G +L      +G   +   +  L A  
Sbjct: 606  VDHYHLLQKYQRSNQDTCLNQRPIVQQGDQVIAGQVLANGSACEG-GEIALGQNCLIAYM 664

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARD---KD 972
              +  +  D  L     V   +       ++ I+  +  +  E    +I  +A +     
Sbjct: 665  PWEGYNYEDAILVSERLVRDDLYTSVHIEKYEIEARQTKLGPEEITREIPNVAEESLGNL 724

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+    +    +IL G+    G         L   +  E  R              
Sbjct: 725  DEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARD------------- 771

Query: 1033 RNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                 ++       +    R  + +I   + GD++PPG   VV+V+VA +R IQ GDKMA
Sbjct: 772  -----VRDNSLRVPNTERGRVVDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMA 826

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET-HLGWACVGLGK 1150
            GRHGNKGI+SRILP EDMP+L DGTP+DIVLNPLGVPSRMNVGQ+FE   +GWA   L  
Sbjct: 827  GRHGNKGIISRILPLEDMPYLPDGTPIDIVLNPLGVPSRMNVGQVFECALMGWAADNLDS 886

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K +  D               ++ G     E +  Y  ++  +   +W         V
Sbjct: 887  RFKIVPFD---------------EMHGAEKSRETVEGYLKEAAKQPGREW---------V 922

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +D  +                G+  L DG +GEPFD+PVTVG  Y+LKL H+V DK++AR
Sbjct: 923  YDPEN---------------PGKIQLIDGRSGEPFDQPVTVGRAYILKLVHLVDDKIHAR 967

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSLVTQQPLGGK+ +GGQRLGEMEVW ++AYGAAY LQE+LT+KSDD+ GR     
Sbjct: 968  STGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALN 1027

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            +IV G      GTPESF VL++E+Q+LGL I +          M+++
Sbjct: 1028 AIVKGKPIPRPGTPESFKVLMRELQSLGLDIAVYTDEGAEVDLMQDV 1074



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 99/458 (21%), Positives = 195/458 (42%), Gaps = 39/458 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PDL+EVQ+ S+  FL           +GL    +S  PIT ++G   L FV   Y    
Sbjct: 14  LPDLVEVQRGSFKWFL----------EKGLIEELESFSPITDYTGKLELHFVGSEYRLKR 63

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ DV++   RD T+A  + +T RL+          K   +IKEQ +++G+LPLMT+ GT
Sbjct: 64  PRHDVEEAKRRDATFASQMYVTCRLV---------NKETGEIKEQEVFIGELPLMTERGT 114

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++V+Q+ RSPG++F  ++ +   +G+  Y   +IP++G W+  E D  D++H
Sbjct: 115 FIINGAERVIVNQIVRSPGVYFKDEQDK---NGRRTYNASLIPNRGAWLKFETDKNDLLH 171

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           VR+D+ RK+     + A+G+   ++L       +Y K + +   +       A   +   
Sbjct: 172 VRVDKTRKINAHVMMRAIGLSDNDVLDKLRHPEYYKKSIDAANEEGISSEDQALLELYKK 231

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   +  G+Q++ S         L +  + K  K L +T          ED+++  
Sbjct: 232 LRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKMNKKLRLTIPDAVRTLTPEDVLSTL 291

Query: 317 TGEIYIE-AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              I +E          ++ + +  +R +  L  + V         ++ ++    +   L
Sbjct: 292 DYLINLELDVGGACLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSL 351

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              +++ P      +  +  F            + +  +    R++         + +E 
Sbjct: 352 TPAQLVNPK--PLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISA---LGPGVLTRER 406

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
               ++ +     G+  I  I+         +G +  +
Sbjct: 407 AGFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATH 442


>gi|253757143|gb|ACT35170.1| DNA-directed RNA polymerase beta chain [Fusobacterium nucleatum
           subsp. fusiforme]
          Length = 800

 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 325/653 (49%), Positives = 455/653 (69%), Gaps = 20/653 (3%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            I+E+ +  +  +++  I   YV     +  + NTL+ D      +A++++++ +RPGD 
Sbjct: 2   FINEEVINNLIENKVDKISYWYVGP--ESKLVANTLMNDTTLTEDEAVVEVFKKLRPGDQ 59

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T   A S+   +FF+  +YDL  VGR KMN RL LD P++   + KED++  IK +++L
Sbjct: 60  VTVDSARSLIRQMFFNPQRYDLEPVGRYKMNKRLKLDVPEEQISLTKEDVLGTIKYVIEL 119

Query: 447 RNGKGTID--DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            NG   +   DIDNL NRR+R VGE+L  Q + GL +M + ++E++++ DI++V PQ L+
Sbjct: 120 NNGDQNVHTDDIDNLSNRRIRGVGELLLMQIKTGLAKMNKMVREKMTTQDIETVTPQSLL 179

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +P+ + + +FF S QLSQ  +  N L+ +TH RR+SALG GG++R RAG E+RDVH +
Sbjct: 180 NTRPLNALIQDFFGSGQLSQFMDQSNPLAELTHKRRISALGPGGLSRERAGFEVRDVHDS 239

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEE 623
           HYGRICP ET EG NIGL+ SL ++A++N YGFIETPY KV +G    +DV YL+A EE+
Sbjct: 240 HYGRICPIETPEGPNIGLIGSLATYAKINKYGFIETPYVKVENGVALVDDVHYLAADEED 299

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             +IAQA++ LD++    + LV CR   E + +  E+++++D SPKQVVS++A LIPFLE
Sbjct: 300 GLFIAQADTKLDKNNK-LQGLVVCRYGHEIVEIEPERVNYMDVSPKQVVSVSAGLIPFLE 358

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPLLK+EAPF+GTG+E  VA  SGA +  K +G V  VD  +I
Sbjct: 359 HDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTTKVSGKVTYVDGKKI 418

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
           +I       +       IYRL+ ++RSNQ+ C++Q PLV +GD+V+  DIIADGP+T LG
Sbjct: 419 II-------EDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIADGPATKLG 471

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           DL+LGRN+L+ FMPW GYN+ED++LIS+R+  +DVFTSIHIEE+E+ AR TKLG EEITR
Sbjct: 472 DLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLGDEEITR 531

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNVSE  L+N+DE G+I VG+EV PGDILVGK  PKGE+    EEKLLRAIFGEKA D
Sbjct: 532 EIPNVSESALRNLDENGVIMVGSEVGPGDILVGKTAPKGETEPPAEEKLLRAIFGEKARD 591

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIELLAR 969
           VRDTSL +P G  G VVD+   +R        G++K+ R +  E+ +I +  +
Sbjct: 592 VRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 644



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 156/526 (29%), Positives = 222/526 (42%), Gaps = 76/526 (14%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSE 836
            Q   V  G         A+              +L +  P+ G   E  + + S  +V+ 
Sbjct: 345  QVVSVSAGLIPFLEHDDANRALMGSNMQRQAVPLLKSEAPFIGTGLERKVAVDSGAVVTT 404

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V   +   + + +  + K   E I R +          + +  ++ +G +V  GDI+  
Sbjct: 405  KVSGKVTYVDGKKIIIEDKDKKEHIYRLLNYERSNQSMCLHQTPLVDLGDKVKAGDIIAD 464

Query: 897  KITPKGESPMTPEEKLLRAIF--GEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGID 951
                K          L+  +   G    D    S R+       S  + +  I  R    
Sbjct: 465  GPATKLGDLSLGRNILMGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKL 524

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             +E          E   R+ D+  VI+  +      +IL G+ A  G         L   
Sbjct: 525  GDEEITREIPNVSESALRNLDENGVIMVGSEVG-PGDILVGKTAPKGETEPPAEEKLLRA 583

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R            V+    ++    +     + +  +        GD++  GV 
Sbjct: 584  IFGEKARD-----------VRDTSLTMPHGSKGVVVDILELSRE------NGDELKAGVN 626

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + ++V VA KR I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRM
Sbjct: 627  KSIRVLVAEKRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRM 686

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A                                               
Sbjct: 687  NIGQVLEVHLGMAMR--------------------------------------------- 701

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                       G  ++TPVFDGA EE +   L       +G+  LYDG TGE FD  VTV
Sbjct: 702  -------SLNGGTCIATPVFDGATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTV 754

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            G +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEM
Sbjct: 755  GIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEM 800


>gi|323155521|gb|EFZ41699.1| DNA-directed RNA polymerase subunit beta domain protein
           [Escherichia coli EPECa14]
          Length = 387

 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 141/366 (38%), Positives = 221/366 (60%), Gaps = 9/366 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
            G++     R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 31  YGLLLYREKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 86

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 87  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 144

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 145 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 204

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 205 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 264

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 265 NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 321

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G  VA+D ++  TGE+   A   +    L ++  S  + I   + + +++  YI  TL
Sbjct: 322 IAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETPFTNDLDHGPYISETL 381

Query: 363 VTDKNK 368
             D   
Sbjct: 382 RVDPTN 387


>gi|46199763|ref|YP_005430.1| DNA-directed RNA polymerase subunit beta [Thermus thermophilus HB27]
 gi|81405493|sp|Q72HM5|RPOB_THET2 RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|46197390|gb|AAS81803.1| DNA-directed RNA polymerase beta chain [Thermus thermophilus HB27]
          Length = 1119

 Score =  489 bits (1260), Expect = e-135,   Method: Composition-based stats.
 Identities = 189/510 (37%), Positives = 255/510 (50%), Gaps = 43/510 (8%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------L 929
            +D+   + VG  V  GD+L      +    +   + +L AI      +  D        L
Sbjct: 637  LDQRPRVVVGQRVRKGDLLADGPASEN-GFLALGQNVLVAIMPFDGYNFEDAIVISEELL 695

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
            +     S  +    I  R      ER         E   RD D+E  ++      +  +I
Sbjct: 696  KRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GVVRIGAEVKPGDI 754

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+ +  G         L   +  E  R                               
Sbjct: 755  LVGRTSFKGESEPTPEERLLRSIFGEKARD-------------------VKDTSLRVPPG 795

Query: 1050 EDRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            E     +  +++ GD    + PGV  VV+V+VA KR +Q GDK+A RHGNKG+V++ILP 
Sbjct: 796  EGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPV 855

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP L DGTPVD++LNPLGVPSRMN+GQI ETHLG A   LG++  S I D     +I 
Sbjct: 856  EDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIK 915

Query: 1167 PLRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
             L +   +V       E    D  +  VLR AE+     P   P      EE +  +   
Sbjct: 916  ELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKPP------EEQLKELFLQ 969

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G+ +LYDG TGEP + P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGG
Sbjct: 970  ------GKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGG 1023

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD+ GR   YE+I+ G D  E   PE
Sbjct: 1024 KAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPE 1083

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            SF VLVKE+QAL L +   + +       E
Sbjct: 1084 SFRVLVKELQALALDVQTLDEKDNPVDIFE 1113



 Score =  442 bits (1138), Expect = e-121,   Method: Composition-based stats.
 Identities = 291/590 (49%), Positives = 399/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++AL+ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     DS+ P  L+N++P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 ARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+  GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V  G VT++VVY++A EE+   IAQAN+ L E      E V  R  GE ++V  E
Sbjct: 469 TPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPL-EGNRIAAERVVARRKGEPVIVSPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V +VD  RIV+R  +G L         Y L +F RSNQ T ++QR
Sbjct: 588 VRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVE-------YPLRRFYRSNQGTALDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V VG  VR+ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE G++ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGES  TPEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGD 810



 Score =  262 bits (669), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 106/457 (23%), Positives = 186/457 (40%), Gaps = 38/457 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ P++R N G+QAAF+  FPI       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  LVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G +PLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        Y   IIP   +G
Sbjct: 115 LGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----YIASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W+D+E +   ++ ++++ +RK P+   L  LG D E +      Y ++V     +    
Sbjct: 170 PWIDLEVEPNGVVSMKVN-KRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFA 228

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-KFLGITSDCLCGL 306
                 L+    +          + V      +       L E G  K        L G 
Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGR 288

Query: 307 YVAEDIVNGETGEIYIEAGDVI----------DEKSLEEIFHSEIRDIPILYVDSVNNNA 356
            +A         E+++     +          +   ++ + +  IR +  L  D      
Sbjct: 289 TLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGL 348

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 V ++     +  L   +++        +     F+       K + + +  ++ 
Sbjct: 349 ARLARGVRERMLMGSEDSLTPAKLVNS--RPLEAAIREFFSRSQLSQFKDETNPLSSLRH 406

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
             R++   P     + +E     ++ +     G+   
Sbjct: 407 KRRISALGPGG---LTRERAGFDVRDVHRTHYGRICP 440


>gi|302122499|gb|ADK92920.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 517

 Score =  489 bits (1259), Expect = e-135,   Method: Composition-based stats.
 Identities = 255/520 (49%), Positives = 359/520 (69%), Gaps = 3/520 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAV
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAV 517


>gi|84872489|gb|ABC67290.1| RNA polymerase beta subunit [Fusobacterium necrophorum subsp.
            necrophorum]
          Length = 299

 Score =  489 bits (1258), Expect = e-135,   Method: Composition-based stats.
 Identities = 149/315 (47%), Positives = 188/315 (59%), Gaps = 52/315 (16%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            GV + ++V VA  R I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVP
Sbjct: 2    GVNKAIRVLVAENRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVP 61

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMN+GQ+ E HLG A                                            
Sbjct: 62   SRMNIGQVLEVHLGMAMR------------------------------------------ 79

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                          G  ++TPVFDGA EE I   L       SG+  LYDG TG+ FD  
Sbjct: 80   ----------SLNGGTHIATPVFDGATEEQIKDYLENQGHPRSGKVTLYDGRTGDKFDNK 129

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +TVG +YMLKL+H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+
Sbjct: 130  ITVGIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVWALEAYGAS 189

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             +LQEMLT+KSDDV GRT+ YE+I+ G +  ++  PESF VL+KE QAL L ++L +   
Sbjct: 190  NILQEMLTVKSDDVTGRTKTYEAIIKGEEMPDSDLPESFKVLLKEFQALALDVELCDEND 249

Query: 1369 KNSAKMEEIPDFNKC 1383
                  EE+      
Sbjct: 250  NVINVDEELNKEETT 264


>gi|291557506|emb|CBL34623.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Eubacterium siraeum V10Sc8a]
          Length = 563

 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 197/575 (34%), Positives = 300/575 (52%), Gaps = 46/575 (8%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F K  E+  +P+LIE+QK SY  FL          +EG++  FK +  IT  +G
Sbjct: 11  RNTRMSFSKIDEVQKMPNLIEIQKDSYKWFL----------DEGIKEVFKDISSITDANG 60

Query: 71  AAMLEFVSYEFDP-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             +L FV Y  D  PK+ +++C  RD TYA PL++  +L               ++ E  
Sbjct: 61  KLVLSFVDYRLDENPKYSIEECKERDTTYAAPLRVKAQL---------RNNETGEVVENE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT+ GTFVI G +R++VSQL RSPG+++  D  +    GK L+   +IP++G
Sbjct: 112 IFMGDFPLMTESGTFVINGAERVIVSQLVRSPGVYYSFDYDKT---GKKLFKSTVIPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVY---SQRGDFW 245
            W++ E DS DI +VRID+ RK+P T+F+ ALG+ S ++++  F          Q  D  
Sbjct: 169 AWLEYEMDSNDIFYVRIDKNRKIPATTFIRALGISSDDDLIDLFGEDPRIVQTIQEKDAT 228

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +           +D+    I +         L +  + K  K LG+ +  +
Sbjct: 229 KNTEEALLEVYRKLRPGEPPTVDSANTHINNLFFDAKRYDLARFGRYKYNKKLGV-ASRI 287

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G   A+ I++  TGEI ++  + I+ +  + +  + +++  I   + +          +
Sbjct: 288 AGHKAAQPIIDPTTGEILVDENEFINAEKAQAVEQAGVKECVIFSEEKIAKVLGNGMVDI 347

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                +  DA       +   +   FSV   + +    D +        RV         
Sbjct: 348 AGYIPESIDA-----ESLGINEKVCFSVLREILDKCGDDVEALTAELSNRV--------- 393

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                +HI  +DI A +   ++L  G G +DDID+LGNRR+RSVGE+L+NQ+R+G  RME
Sbjct: 394 EDLIPKHITLDDIFATVSYFINLCEGVGEVDDIDHLGNRRIRSVGELLQNQFRIGFARME 453

Query: 484 RSIKERI--SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           R I+ER+   S + D V P  LIN +PVV+A+ EFF SS LSQ  +  N L+ +TH RRL
Sbjct: 454 RVIRERMGLQSQEGDKVTPNALINIRPVVAAIKEFFGSSPLSQFMDQNNPLAELTHKRRL 513

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           SALG GG++R RA  E+RDVH +HYGR+CP ET +
Sbjct: 514 SALGPGGLSRDRASFEVRDVHYSHYGRMCPIETPK 548


>gi|46361000|gb|AAS89233.1| RpoB [Corynebacterium ulcerans]
          Length = 1058

 Score =  488 bits (1257), Expect = e-135,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 442/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    + +  + ++DI   ++ LV L  G+ T+            DD
Sbjct: 289 AKVGRYKVNRKLGLGGDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVIPVDTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ SL S+ARVN++GFIETPYRKV +G +T+ + YL+A EE+   + QA+  +D
Sbjct: 469 EGPNIGLIGSLASYARVNSFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQAHVEVD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G  T + V  R   G+  +V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 ANGKITADSVTVRVKNGDIQVVAPESVDYLDVSPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAPFVGTGME   A  +G  I+ K+AG VE V A  I + + +G  + 
Sbjct: 589 NMQRQAVPLVRSEAPFVGTGMERRAAYDAGDLIINKKAGAVENVSADFITVMADDGTRE- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 648 ------TYMLRKFERTNQGTCYNQIPLVNLGDRVEAGQVLADGPGTHNGEMSLGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 762 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 822 ETGKVIGVRRFSREDDD 838



 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 146/438 (33%), Positives = 208/438 (47%), Gaps = 61/438 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L           M+    LL A    +  +  D  +     V   ++
Sbjct: 668  LVNLGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDMPFMPD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L++  E+
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEE 942

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  +  +  G  
Sbjct: 943  LYDVP----------------------AGSLTATPVFDGATNEEVAGLLANSRPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDENGKAQLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQA 1304
            +  GGQR GEMEVW +QA
Sbjct: 1041 AQFGGQRFGEMEVWALQA 1058



 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 92/389 (23%), Positives = 171/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I++P L+++Q  S+   +            +  + R   GL+   + + 
Sbjct: 15  ERFSFAKITEPIEVPGLLDIQLDSFAWLIGTPEWRARQQEELGENVRVTSGLEDILEELS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K  +D+C  +D+ Y+ PL +T   I             +
Sbjct: 75  PIQDYSGNMSLSLSEPRFEDMKNTIDECKDKDINYSAPLYVTAEFI---------NNETQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPMMTNKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++++         L K  + K  + LG+ 
Sbjct: 244 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    G++       +D   ++   +  +R
Sbjct: 304 GDNEGLMTLTEQDIATTLEYLVRLHAGESTMVAPNGDVI-----PVDTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|320449513|ref|YP_004201609.1| DNA-directed RNA polymerase subunit beta [Thermus scotoductus SA-01]
 gi|320149682|gb|ADW21060.1| DNA-directed RNA polymerase, subunit beta [Thermus scotoductus SA-01]
          Length = 1119

 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 185/507 (36%), Positives = 258/507 (50%), Gaps = 37/507 (7%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------L 929
            +D+   + VG  V  GD+L        E  +   + +L AI      +  D        L
Sbjct: 637  LDQRPRVTVGQRVRKGDLLADGP-ASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELL 695

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
            +     S  +    I  R      ER         E   RD D+E  ++      +  +I
Sbjct: 696  KRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEE-GVVRIGAEVKPGDI 754

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+ +  G +       L   +  +  R      +++    +  +    ++        
Sbjct: 755  LVGRTSFKGEQEPSPEERLLRSIFGDKAR-DVKDTSLRVPPGEGGIVVGTLRLR------ 807

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                     +   G ++ PGV  VV+V+VA KR +Q GDK+A RHGNKG+V++ILP EDM
Sbjct: 808  ---------RGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDM 858

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P L DGTPVDI+LNPLGVPSRMN+GQI ETHLG A   LG++  S + D     +I  L 
Sbjct: 859  PHLPDGTPVDIILNPLGVPSRMNLGQILETHLGLAGFFLGQRYISPVFDGATEPEIKALL 918

Query: 1170 SFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
            +    +       E    D  +  VL  AE+     P  +P      EE +  +      
Sbjct: 919  AEAFDLYFGKRKEEGFGVDKRELEVLARAEKLGLVSPGKSP------EEQLRELFTQ--- 969

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G+ +LYDG +GEP + P+ VG ++++KL HMV DK++ARSTG YSL+TQQPLGGK+ 
Sbjct: 970  ---GKVVLYDGRSGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQ 1026

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD+ GR   YE+I+ G D  E   PESF 
Sbjct: 1027 FGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFR 1086

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKME 1375
            VLVKE+QAL L +   + R       E
Sbjct: 1087 VLVKELQALALDVQTLDERDNPVDIFE 1113



 Score =  440 bits (1132), Expect = e-121,   Method: Composition-based stats.
 Identities = 285/590 (48%), Positives = 396/590 (67%), Gaps = 16/590 (2%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD- 426
              ++AL+ ++ ++RPGD      A +    L  D  +YDL   GR K   +L +     
Sbjct: 229 MRPEEALVRLFTLLRPGDPPKKDKALAYLFGLLADPRRYDLGEAGRYKAEEKLGVRLSGR 288

Query: 427 -----DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                +    + E  +  ++ L  L  G     +DDID+LGNRR+R+VGE++ +Q+R+GL
Sbjct: 289 TLARFEDGEFKDEIFLPTLRYLFALMAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
            R+ R ++ER+     D++ P  L+N +P+ +A+ EFF  SQLSQ ++  N LS + H R
Sbjct: 349 SRLARGVRERMVMGSADTLTPAKLVNNRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKR 408

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++ARV+  GFI 
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDGLGFIR 468

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYR+V +G VT++VVY++A EE+   IAQAN+ L E      + V  R  GE ++V  E
Sbjct: 469 TPYRRVRNGVVTDEVVYMTATEEDRYTIAQANTPL-EGNRIATDRVVARRRGEPVIVGPE 527

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A+AP V TG+E  V
Sbjct: 528 EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERV 587

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            + S AA+ A+  G V  VD  RI +R  +G L         Y L +F RSNQ T ++QR
Sbjct: 588 VRDSLAAVYAEEDGEVVAVDGRRIAVRYEDGRLVE-------YTLRRFVRSNQGTALDQR 640

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V VG  VR+ D++ADGP+++ G LALG+N+LVA MP+ GYNFED+++ISE ++  D +
Sbjct: 641 PRVTVGQRVRKGDLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFY 700

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +E+ ARDTKLGPE ITRDIP++SE  L+++DE G++ +GAEV PGDILVG+ +
Sbjct: 701 TSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTS 760

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            KGE   +PEE+LLR+IFG+KA DV+DTSLRVP G  G VV      R  
Sbjct: 761 FKGEQEPSPEERLLRSIFGDKARDVKDTSLRVPPGEGGIVVGTLRLRRGD 810



 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 108/457 (23%), Positives = 186/457 (40%), Gaps = 38/457 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GA 71
           K FG+  E+I +P L E+Q  SY   L  ++ PD+R + G+QAAFK  FP+       G 
Sbjct: 4   KRFGRIREVIPLPPLTEIQVDSYKRALQADVPPDKREDVGIQAAFKETFPVEEGDKGKGG 63

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+F+ Y    P F  D+C  +DLTY  PL   L+LI  D            IKE  ++
Sbjct: 64  MVLDFLEYRIGEPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVF 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +G +PLMT+DG+F+I G  R++VSQ+HRSPG++F  D  R        +   IIP   +G
Sbjct: 115 LGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR-----FVASIIPLPKRG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W+D+E +    + ++++ +RK P+   L  LG D+E +      Y +++     +    
Sbjct: 170 PWIDLEVEQNGTVSMKVN-KRKFPLILLLRVLGYDAETLNRELGAYGELLGGLLDEAVLV 228

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-KFLGITSDCLCGL 306
                 L+    +          + +      L       L E G  K        L G 
Sbjct: 229 MRPEEALVRLFTLLRPGDPPKKDKALAYLFGLLADPRRYDLGEAGRYKAEEKLGVRLSGR 288

Query: 307 YVAEDIVNGETGEIY---------IEAGDVIDE-KSLEEIFHSEIRDIPILYVDSVNNNA 356
            +A         EI+         + AG    E   ++ + +  IR +  L  D      
Sbjct: 289 TLARFEDGEFKDEIFLPTLRYLFALMAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL 348

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 V ++        L   +++        +     F+       K + + +  ++ 
Sbjct: 349 SRLARGVRERMVMGSADTLTPAKLVNN--RPLEAAIREFFSRSQLSQFKDETNPLSSLRH 406

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
             R++   P     + +E     ++ +     G+   
Sbjct: 407 KRRISALGPGG---LTRERAGFDVRDVHRTHYGRICP 440


>gi|46361022|gb|AAS89244.1| RpoB [Corynebacterium aurimucosum]
          Length = 1110

 Score =  488 bits (1256), Expect = e-135,   Method: Composition-based stats.
 Identities = 191/590 (32%), Positives = 276/590 (46%), Gaps = 60/590 (10%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 567  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMEQRAAYDAGDLIIT 626

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 627  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQNTNYNQTPLVSLGDRVEAGQVLAD 686

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 687  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 745

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 746  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 805

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                        ET K I   RF  + +     DD+ PGV 
Sbjct: 806  IFGEKAREVRDT------------SMKVPHGETGKVIGVSRFSREDD-----DDLAPGVN 848

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RM
Sbjct: 849  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRM 908

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G KI +     +   +   L++  E++      +         
Sbjct: 909  NIGQVLEVHLGWLAHA-GWKIDT-----EDPANAELLKTLPEELYDVPPESLT------- 955

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +GE
Sbjct: 956  ---------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGE 1000

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 1001 PYLYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
            AYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PESF VL+KE
Sbjct: 1061 AYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPESFKVLLKE 1110



 Score =  483 bits (1243), Expect = e-133,   Method: Composition-based stats.
 Identities = 325/661 (49%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIK----ERFGFSELMMSTLES 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+++ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMISIHTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+ T + +  R   
Sbjct: 488 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDRFAIAQAEVEKDADGTLTGDRIEVRLKD 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 548 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNT  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 661 NQNTNYNQTPLVSLGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 721 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVSRFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 167/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  SY   +               D R   GL+   + + P
Sbjct: 19  RYSFAKISEPIAVPGLLDLQLDSYAWLIGTPEWREREQAERGEDARVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 79  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 130 IKSQTVFIGDFPMMTDKGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHSVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIKERFGFSELMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        D  + ++++         L K  + K  +      
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+  E  +    GE+       I    ++   +  +R 
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGEMI-----SIHTDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|229815795|ref|ZP_04446120.1| hypothetical protein COLINT_02844 [Collinsella intestinalis DSM
            13280]
 gi|229808711|gb|EEP44488.1| hypothetical protein COLINT_02844 [Collinsella intestinalis DSM
            13280]
          Length = 1162

 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 191/611 (31%), Positives = 276/611 (45%), Gaps = 82/611 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       ++    P+ G   E    I   E  +++     I  +  ++  + T  G
Sbjct: 581  MGANMQRQAVPLVHPVAPYVGTGMEKRAAIDSGEVTLAKRAGEVIFADAAKITVK-TAEG 639

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             +         S +    I+   ++ VG +V  G  L    +      +   + L  A  
Sbjct: 640  LDTYKMPKYQRSNQS-TCINHRPLVRVGDQVTQGQPLADGPST-DHGELALGQNLTVAYM 697

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQV 976
              +  +  D  +     VS  ++     +R+  + + R   +  E+I     +  +D   
Sbjct: 698  PWEGFNYEDGIIVSERLVSEDLLTTINISRY--ELDARDTKLGPEEITREIPNLSEDMLA 755

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+     G    +G     K +      ++   R     F  +   V+    
Sbjct: 756  NLDEDGIIRI-----GAEVKAGDILVGKVSPKGESALTAEERLLRAIFGTKAHDVRDTSL 810

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +    E     +           + GDD+ PGV   V+V+VA +R IQ GDK+AGRHGN
Sbjct: 811  KMPHGAEGRVIDVV------RFSRENGDDLAPGVNEQVRVYVAQRRKIQQGDKIAGRHGN 864

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++  +LP EDMP++ DGTPVD++LNPLGVPSRMNVGQ+ E HLGWA            
Sbjct: 865  KGVICEVLPVEDMPYMSDGTPVDVILNPLGVPSRMNVGQLLECHLGWAAAC--------- 915

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                             D       +        +TPVFDGA E
Sbjct: 916  -------------------------------GWDTESADSDKYIPGPFFTATPVFDGAHE 944

Query: 1217 EAINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYI 1254
            + I  ++R A+                      LDE G+++LYDG +GE F  P+T+G  
Sbjct: 945  DEIAEVIRRANRNMVNLATERFGEHMNPAFVTQLDERGKTVLYDGRSGEQFREPITIGTS 1004

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGAA VLQE+
Sbjct: 1005 YILKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGAANVLQEI 1064

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDD VGR + YE+I  G +    G PESF VLVKE+++L L I+         A  
Sbjct: 1065 LTVKSDDTVGRVKTYEAITKGENVPMAGIPESFKVLVKEIRSLALDIEPIRDAEPAPAPA 1124

Query: 1375 EEIPDFNKCEL 1385
                D ++ +L
Sbjct: 1125 PAAED-SELDL 1134



 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 314/630 (49%), Positives = 433/630 (68%), Gaps = 35/630 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + ++  ++ T+  D    R+DAL++IYR +RPG+  T   + S+   L F+  +YDL
Sbjct: 211 FELLGDSDVVKRTIERDTALTREDALIEIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRS 466
           + VGR K+N +LNL T +DV  +  EDIIA ++ L+ L  G+    +DDID+ GNRR+R+
Sbjct: 271 ARVGRYKVNKKLNLTTEEDVTVLTDEDIIATLRYLLSLAAGEHGFKVDDIDHFGNRRIRT 330

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE++ NQ+R+G+ RMER ++ER+SS D+D + PQ LIN +P+V+++ EFF SSQLSQ  
Sbjct: 331 VGELVANQFRIGMSRMERVVRERMSSQDVDEITPQSLINIRPIVASIKEFFGSSQLSQFM 390

Query: 527 EHVNSLSRITHTRRLSALGQGGV--------ARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  N L+ +TH RRLSALG GG+         R      +RDVH +HY R+CP ET EG 
Sbjct: 391 DQANPLTGLTHKRRLSALGPGGLAGHKSGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGP 450

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-- 636
           NIGL+ SL  +ARVN YGFIE PYRK+ +G  T+ + +++A EEE   IA AN+ +D   
Sbjct: 451 NIGLIGSLALYARVNEYGFIEAPYRKIENGVATDQIDWMTADEEELHIIAPANTPIDPET 510

Query: 637 --------DGSFTEELVFCRCAGEEI-------LVPREKIDFIDASPKQVVSIAASLIPF 681
                   DG+            +          VP E +D++D SP+Q++S+AA+LIPF
Sbjct: 511 NELVTVDADGNLVRPHTVVARTRDFDGSFGAPADVPVEDVDYMDVSPRQMLSVAATLIPF 570

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE+DD+ R LMG NMQRQAVPL+   AP+VGTGME   A  SG   +AKRAG V   DA 
Sbjct: 571 LEHDDAKRTLMGANMQRQAVPLVHPVAPYVGTGMEKRAAIDSGEVTLAKRAGEVIFADAA 630

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I +++ E        G+D Y++ K+QRSNQ+TC+N RPLV+VGD+V +   +ADGPSTD
Sbjct: 631 KITVKTAE--------GLDTYKMPKYQRSNQSTCINHRPLVRVGDQVTQGQPLADGPSTD 682

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+ VA+MPW G+N+ED +++SER+VSED+ T+I+I  +E+ ARDTKLGPEEI
Sbjct: 683 HGELALGQNLTVAYMPWEGFNYEDGIIVSERLVSEDLLTTINISRYELDARDTKLGPEEI 742

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TR+IPN+SE+ L N+DE GII +GAEV  GDILVGK++PKGES +T EE+LLRAIFG KA
Sbjct: 743 TREIPNLSEDMLANLDEDGIIRIGAEVKAGDILVGKVSPKGESALTAEERLLRAIFGTKA 802

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DVRDTSL++P G  G V+DV  F+R   D
Sbjct: 803 HDVRDTSLKMPHGAEGRVIDVVRFSRENGD 832



 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 105/377 (27%), Positives = 168/377 (44%), Gaps = 32/377 (8%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
            + V      R R  FGK PE +++P+LI VQK S++ F+          +EGL+ AFK 
Sbjct: 7   TQTVTATE--RTRVNFGKIPETMELPNLISVQKESFERFM----------DEGLRDAFKE 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
             PI + +    + F  ++F  P   VD+C  +D+TY  PL   +RL             
Sbjct: 55  SSPIQSQNHQLEVTFGHHQFGDPSHTVDECREKDMTYQAPLLTEVRLT---------NLE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IKEQ ++MGD P+MT  GTF+I G +RIVVSQL RSPG+++  +       GK +Y 
Sbjct: 106 TGEIKEQLVFMGDFPMMTDQGTFIINGTERIVVSQLVRSPGVYYGSEMD----GGKQVYK 161

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYS 239
            ++IP +G W++ E D +D + V IDR+RK   T FL ALG+   ++EI        V  
Sbjct: 162 AQVIPARGAWLEFEVDKRDQLVVSIDRKRKQSATMFLRALGIAVTNDEIFELLGDSDVVK 221

Query: 240 --QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE--SGKKLTSGLLKSLKEKGVKF 295
                D       A   +           +D    ++E          L +  + K  K 
Sbjct: 222 RTIERDTALTREDALIEIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDLARVGRYKVNKK 281

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEA-GDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
           L +T++    +   EDI+      + + A         ++   +  IR +  L  +    
Sbjct: 282 LNLTTEEDVTVLTDEDIIATLRYLLSLAAGEHGFKVDDIDHFGNRRIRTVGELVANQFRI 341

Query: 355 NAYIRNTLVTDKNKDRK 371
                  +V ++   + 
Sbjct: 342 GMSRMERVVRERMSSQD 358


>gi|210630990|ref|ZP_03296715.1| hypothetical protein COLSTE_00600 [Collinsella stercoris DSM 13279]
 gi|210160206|gb|EEA91177.1| hypothetical protein COLSTE_00600 [Collinsella stercoris DSM 13279]
          Length = 1166

 Score =  488 bits (1255), Expect = e-135,   Method: Composition-based stats.
 Identities = 186/586 (31%), Positives = 262/586 (44%), Gaps = 77/586 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++    P+ G   E    I    V+        I               
Sbjct: 581  MGANMQRQAVPLVHPVAPYIGTGMESRAAIDSGEVTLAKHAGEVIFADAAKITVKTAESM 640

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  +            I+   ++ VG +V  G  L    +      +   + L  A    
Sbjct: 641  DTYKLPKYQRSNQSTCINHRPLVRVGDQVVVGQPLADGPST-DHGELALGQNLTVAYMPW 699

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  +     VS  ++     +R+  + + R   +  E+I     +  +D    L
Sbjct: 700  EGFNYEDGIIVSERLVSEDLLTTINISRY--ELDARDTKLGPEEITREIPNLSEDMLANL 757

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D +   R+     G    +G     K +      ++   R     F  +   V+     +
Sbjct: 758  DEDGIIRI-----GAEVKAGDILVGKVSPKGESALTAEERLLRAIFGTKAHDVRDTSLKM 812

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     +           + GDD+ PGV   V+V+VA +R IQ GDK+AGRHGNKG
Sbjct: 813  PHGAEGRVIDVV------RFSRENGDDLAPGVNEQVRVYVAQRRKIQQGDKIAGRHGNKG 866

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  +LP EDMP++ DGTPVD++LNPLGVPSRMNVGQ+ E HLGWA              
Sbjct: 867  VICEVLPVEDMPYMADGTPVDVILNPLGVPSRMNVGQLLECHLGWAAAC----------- 915

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                           D       +       VSTPVFDGA E+ 
Sbjct: 916  -----------------------------GWDTESADSDKYVPGPFFVSTPVFDGAHEDE 946

Query: 1219 INSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            I  ++R A+                      LDE G+++LYDG +GE F  P+TVG  Y+
Sbjct: 947  IAEVIRRANKNMLNLASERFGEHMNPSFVTQLDERGKTVLYDGRSGEQFREPITVGTSYI 1006

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA+ VLQE+LT
Sbjct: 1007 LKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQEILT 1066

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +KSDD +GR + YE+I  G +    G PESF VLVKE+++L L I+
Sbjct: 1067 VKSDDTIGRVKTYEAITKGENVPMAGIPESFKVLVKEIRSLALDIE 1112



 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 315/630 (50%), Positives = 431/630 (68%), Gaps = 35/630 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + ++  I+ T+  D    R+DAL++IYR +RPG+  T   + S+   L F+  +YDL
Sbjct: 211 FELLGDSDVIKRTIERDTALTREDALIEIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRS 466
           + VGR K+N +L L T ++V  +  EDIIA ++ L+ L  G+    IDDID+ GNRR+R+
Sbjct: 271 ARVGRYKVNKKLGLTTEEEVAVLTDEDIIATLRYLLSLAAGEPGFKIDDIDHFGNRRIRT 330

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE++ NQ+R+G+ RMER ++ER+SS DID + PQ LIN +P+V+++ EFF SSQLSQ  
Sbjct: 331 VGELVANQFRIGMSRMERVVRERMSSQDIDEITPQSLINIRPIVASIKEFFGSSQLSQFM 390

Query: 527 EHVNSLSRITHTRRLSALGQGGV--------ARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  N L+ +TH RRLSALG GG+         R      +RDVH +HY R+CP ET EG 
Sbjct: 391 DQANPLTGLTHKRRLSALGPGGLAGHKSGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGP 450

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-- 636
           NIGL+ SL  +ARVN YGFIE PYRK+ +G  T+ + +++A EEEN  IA AN+ +D   
Sbjct: 451 NIGLIGSLALYARVNQYGFIEAPYRKIENGVATDQIDWMTADEEENHIIAPANTPIDPKT 510

Query: 637 --------DGSFTEELVFCRCAGEEI-------LVPREKIDFIDASPKQVVSIAASLIPF 681
                   DG+            +          VP E +D++D SP+Q++S+AA+LIPF
Sbjct: 511 GELVTIDADGNLVRPHTVVARTRDFDGSFGAPADVPVEDVDYMDVSPRQMLSVAATLIPF 570

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE+DD+ R LMG NMQRQAVPL+   AP++GTGMES  A  SG   +AK AG V   DA 
Sbjct: 571 LEHDDAKRTLMGANMQRQAVPLVHPVAPYIGTGMESRAAIDSGEVTLAKHAGEVIFADAA 630

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I +++ E         +D Y+L K+QRSNQ+TC+N RPLV+VGD+V     +ADGPSTD
Sbjct: 631 KITVKTAES--------MDTYKLPKYQRSNQSTCINHRPLVRVGDQVVVGQPLADGPSTD 682

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+ VA+MPW G+N+ED +++SER+VSED+ T+I+I  +E+ ARDTKLGPEEI
Sbjct: 683 HGELALGQNLTVAYMPWEGFNYEDGIIVSERLVSEDLLTTINISRYELDARDTKLGPEEI 742

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TR+IPN+SE+ L N+DE GII +GAEV  GDILVGK++PKGES +T EE+LLRAIFG KA
Sbjct: 743 TREIPNLSEDMLANLDEDGIIRIGAEVKAGDILVGKVSPKGESALTAEERLLRAIFGTKA 802

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DVRDTSL++P G  G V+DV  F+R   D
Sbjct: 803 HDVRDTSLKMPHGAEGRVIDVVRFSRENGD 832



 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 95/296 (32%), Positives = 148/296 (50%), Gaps = 32/296 (10%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
               R R  FGK PE +++P+LI VQK S++ F+          +EGL+ AF+   PI +
Sbjct: 11  TATERTRVNFGKIPETMELPNLISVQKESFERFM----------DEGLRDAFRESSPIQS 60

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            +    + F  ++F  P   VD+C  +D+TY  PL   +RL           K   +IKE
Sbjct: 61  QNHQLEVTFGHHQFGDPSHTVDECREKDMTYQAPLLTEVRLT---------NKETGEIKE 111

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++MGD P+MT  GTF+I G +RIVVSQL RSPG+++  +       GK +Y  +IIP 
Sbjct: 112 QLVFMGDFPMMTDQGTFIINGTERIVVSQLVRSPGVYYSSEMD----GGKQVYKAQIIPA 167

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFW 245
           +G W++ E D +D + V IDR+RK   T FL ALG+   +++I        V  +  +  
Sbjct: 168 RGAWLEFEVDKRDQLVVSIDRKRKQSATMFLRALGIAVTNDDIFELLGDSDVIKRTIERD 227

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                   L     +      +  GE   +++ + L  GLL + +   +  +G   
Sbjct: 228 TA------LTREDALIEIYRRLRPGEPPTVDASRSLLEGLLFNPQRYDLARVGRYK 277


>gi|331124034|gb|AEC53805.1| RNA polymerase subunit B [Vibrio sp. SO205]
 gi|331124036|gb|AEC53806.1| RNA polymerase subunit B [Vibrio sp. SO232]
          Length = 519

 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 253/522 (48%), Positives = 357/522 (68%), Gaps = 3/522 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +E++L  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEQVLDIFFDKVKFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L    L  G   +  +     G+  +E G+++T+  ++ L++  V F+ +  D
Sbjct: 61  DQTLMMELVPERL-RGETATFDIES--NGKVYVEKGRRVTARHIRQLEKDEVSFIEVPVD 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   A+D +N  TGE+ + A   +  + L  +  +  + + +L+ + ++N  ++  T
Sbjct: 118 YIVGKISAKDYINEATGEVILAANQEVTLEVLANLSQAGYKKLEVLFTNDLDNGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRVDSTSDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSPERYDLSTVGRMKFNSSIE 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
               ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 RTDAEEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L +D  F +EL+  R  GE  L PRE +
Sbjct: 418 YRRVVDGIVTDEVDYLSAIEEGQFVIAQANAKLTDDSRFADELITARQKGESGLHPREHV 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 478 DYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 519


>gi|46360972|gb|AAS89219.1| RpoB [Corynebacterium kutscheri]
          Length = 1055

 Score =  487 bits (1254), Expect = e-135,   Method: Composition-based stats.
 Identities = 320/661 (48%), Positives = 449/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +         I+  +    +  + +TL  
Sbjct: 187 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTTEQIV--ERFGFSEIMMSTLEA 242

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 243 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 302

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   I+ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 303 DNDGLMTLTEEDIATTIEYLVRLHAGEHSMTSPQGVTIPVETDDIDHFGNRRLRTVGELI 362

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 363 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 422

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 423 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 482

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV +G +T+ + YL+A EE+   + QAN  +D  G  T E V  R   
Sbjct: 483 VNDFGFIETPYRKVENGVLTDQIDYLTADEEDRFVVGQANVEVDGQGRITAERVTVRVKN 542

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +V  E ++++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAPF
Sbjct: 543 GDIQVVSPEAVEYLDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPF 602

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  +++K++G+VE + A  I I    G  D        Y L KF+R+
Sbjct: 603 VGTGMELRAAYDAGDMVISKKSGVVENLSADFITIMDDTGIRD-------TYLLRKFERT 655

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ    NQ+PLV +GD V    +IADGP T  G++ALGRN+LVAFMPW G+N+ED+++++
Sbjct: 656 NQGNNYNQKPLVDIGDRVEAGQVIADGPGTHNGEMALGRNLLVAFMPWEGHNYEDAIILN 715

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++DE GI+ +GA+V  
Sbjct: 716 QRLVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDERGIVRIGADVRD 775

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ VR F+R   
Sbjct: 776 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVRRFSREDD 835

Query: 951 D 951
           D
Sbjct: 836 D 836



 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 140/441 (31%), Positives = 205/441 (46%), Gaps = 59/441 (13%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G ++           M     LL A    +  +  D  +     
Sbjct: 660  NYNQKPLVDIGDRVEAGQVIADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRL 718

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEI 989
            V   ++       H ID  +  +  E    +I  ++ D     DE+ I+      R  +I
Sbjct: 719  VEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDERGIVRIGADVRDGDI 778

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                 E      +      
Sbjct: 779  LVGKVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGET 821

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                  +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDM
Sbjct: 822  GKVIGVRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPQEDM 881

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF+ DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI +     +   +   ++
Sbjct: 882  PFMPDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAELMK 935

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
               E +                          +G   +TPVFDGA  + +  +L     +
Sbjct: 936  MLPEDLYEVP----------------------AGTLTATPVFDGASNDELKGLLGNTRPN 973

Query: 1230 ESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              G        ++ L+DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQ
Sbjct: 974  RDGDVMVDSDGKAQLFDGRSGEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQ 1033

Query: 1282 PLGGKSNRGGQRLGEMEVWCI 1302
            PLGGK+  GGQR GEMEVW +
Sbjct: 1034 PLGGKAQFGGQRFGEMEVWAL 1054



 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 86/323 (26%), Positives = 147/323 (45%), Gaps = 30/323 (9%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSV 62
             RK F K  E I++P L++VQ  S+   +            +    R   GL+   + +
Sbjct: 12  TERKSFAKITEPIEVPGLLDVQLNSFAWLIGSPEWRARKQEELGEGVRVTSGLEDILEEL 71

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  +SG   L   +  F+  K  VD+   +D+ Y+ PL +T   I             
Sbjct: 72  SPIQDYSGNMSLSLSAPRFEDMKNTVDEAKDKDINYSAPLYVTAEFI---------NNET 122

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           ++IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ 
Sbjct: 123 QEIKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQSIDK--STERPLHSV 180

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQ 240
           ++IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I+  F     ++ + 
Sbjct: 181 KVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIVERFGFSEIMMSTL 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             D       A   +   +           +   +  + L        K   +  +G   
Sbjct: 241 EADGVANTDEALLEIYRKQRPGE-------QPTRDLAQSLLDNSFFRAKRYDLAKVGRYK 293

Query: 301 -DCLCGLYVAEDIVNGETGEIYI 322
            +   GL    D +   T E   
Sbjct: 294 VNRKLGLGGDNDGLMTLTEEDIA 316


>gi|46360958|gb|AAS89212.1| RpoB [Corynebacterium coyleae]
          Length = 1104

 Score =  486 bits (1252), Expect = e-135,   Method: Composition-based stats.
 Identities = 181/484 (37%), Positives = 247/484 (51%), Gaps = 61/484 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 668  IVSAGDRVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +     ++  R  
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAREVRDT-------------SLKVPHGEQGKVIAVR-- 830

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 831  --RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 946  VPPESLT-------------------------ATPVFDGATNDEIAGLLANSKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDGDGKTVLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  + G PES
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPDPGIPES 1100

Query: 1347 FNVL 1350
            F VL
Sbjct: 1101 FKVL 1104



 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 317/617 (51%), Positives = 439/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 229 TERFGFSEIMMSTLENDGVNNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 288

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K+N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 289 ARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGESEMTSPSGEIIPINTDD 348

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 349 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 408

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 409 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 468

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L+S+ARVN +GFIETPY+KV DGK+T+ + YL+A EE+   IAQA + +D
Sbjct: 469 EGPNIGLIGALSSYARVNPFGFIETPYQKVEDGKLTDQIDYLTADEEDRYAIAQAATPMD 528

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +DG+ T E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 529 KDGNLTGERIEVRLKDGDIGVVGPKGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 588

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL+AE+ +V TGME   A  +G  +++K+AG++E V    I +   EG    
Sbjct: 589 NMQKQAVPLLRAESAYVATGMEQRAAYDAGDTVISKKAGVIENVTGDYITVMDDEG---- 644

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              G D Y L  F+R+NQ TC NQ P+V  GD V    +IADGP T  G++ALGRN+LVA
Sbjct: 645 ---GRDTYMLRTFERTNQGTCYNQTPIVSAGDRVEAGQVIADGPGTKDGEMALGRNLLVA 701

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 702 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 762 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 821

Query: 935 VSGTVVDVRIFNRHGID 951
             G V+ VR F+R   D
Sbjct: 822 EQGKVIAVRRFSREDDD 838



 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 98/389 (25%), Positives = 173/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +           +   D R   GL+   + + 
Sbjct: 15  ERYSFAKINEPITVPGLLDVQLESFAWLVGTSEWRENEQASRGDDARVTSGLEDILEEIS 74

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 75  PIEDYSGNMSLTLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 125

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 126 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDESIDK--STERPLHSVK 183

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 184 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 243

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 244 NDGVNNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 303

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   +GEI       I+   ++   +  +R
Sbjct: 304 GDHDGLMTLTEEDIATTLEYLVRLHAGESEMTSPSGEII-----PINTDDIDHFGNRRLR 358

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 359 TVGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|196051507|gb|ACG68887.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|196051509|gb|ACG68888.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|196051511|gb|ACG68889.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|196051517|gb|ACG68892.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
 gi|196051519|gb|ACG68893.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 513

 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 251/516 (48%), Positives = 355/516 (68%), Gaps = 3/516 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQ
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQ 513


>gi|328955920|ref|YP_004373253.1| DNA-directed RNA polymerase subunit beta [Coriobacterium glomerans
            PW2]
 gi|328456244|gb|AEB07438.1| DNA-directed RNA polymerase subunit beta [Coriobacterium glomerans
            PW2]
          Length = 1169

 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 190/609 (31%), Positives = 275/609 (45%), Gaps = 82/609 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--ERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       ++    P+ G   E    +   E  ++ +    +  +  ++  + T+ G
Sbjct: 581  MGANMQRQAVPLVHPSAPFVGTGMERRAALDSGEVTLAREAGEVVFADASKITVK-TETG 639

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             ++        S +    I+   ++ VG EV  G  L    +      +   + L  A  
Sbjct: 640  MDDYVLPKYQRSNQS-TCINHRPLVRVGDEVALGQPLADGPST-DHGELALGQNLTVAYM 697

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQV 976
              +  +  D  +     V+  ++     +RH  + + R   +  E+I     +  +D   
Sbjct: 698  SWEGYNYEDAIVVSERVVADDLLTTINISRH--EIDARDTKLGPEEITREVPNLSEDMLA 755

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             LD +   R+   +   + + G    K  +  +++              V+D        
Sbjct: 756  NLDEDGIIRIGAEVGPGDILVGKVTPKGESTQTAEERLLKAIFGAKAHDVRD-------- 807

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                  +                   GDD+ PGV   V+V+VA +R IQ GDK+AGRHGN
Sbjct: 808  ---TSLKMPHGAYGRVIDVVRFSRDAGDDLAPGVNEQVRVYVAQRRKIQQGDKIAGRHGN 864

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S ILP EDMPF+ DGTPVD++LNPLGVPSRMNVGQ+ E HLGWA            
Sbjct: 865  KGVISEILPIEDMPFMADGTPVDVILNPLGVPSRMNVGQLLECHLGWAAA---------- 914

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                             D               VS+PVFDGA E
Sbjct: 915  ------------------------------SGWDPDDADSERYVPGPFFVSSPVFDGAHE 944

Query: 1217 EAINSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYI 1254
            + I  ++R A+                      LD  G++ L DG +GE F  P+TVG  
Sbjct: 945  DEIAEVIRRANKNKINFASMRYGKHMRPEFVTQLDARGKTKLTDGRSGEEFREPITVGTS 1004

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA+ VLQE+
Sbjct: 1005 YILKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLQEI 1064

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            LT+KSDD VGR + YESIV G +    G PESF VLVKE+++L L I+  +   + +A  
Sbjct: 1065 LTVKSDDTVGRVKTYESIVKGENIPIPGIPESFKVLVKEIRSLALDIEPLH-DAQPAATA 1123

Query: 1375 EEIPDFNKC 1383
            +E     + 
Sbjct: 1124 DEAEQEGEA 1132



 Score =  481 bits (1239), Expect = e-133,   Method: Composition-based stats.
 Identities = 313/630 (49%), Positives = 426/630 (67%), Gaps = 35/630 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           ++ + ++  ++ ++  D    R+DAL++IYR +RPG+  T   + S+   L F+  +YDL
Sbjct: 211 IELLGDSEIVKRSIERDVALTREDALIEIYRRLRPGEPPTVESSRSLLEGLLFNPQRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRS 466
           + VGR KMN +L L T ++V  +  EDI+A ++ L+ L  G+     DDID+ GNRRVR+
Sbjct: 271 ARVGRYKMNKKLGLTTDEEVTTLTDEDIVATLRYLLALAAGEPGFKTDDIDHFGNRRVRT 330

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           VGE++ NQ+R+G+ RMER ++ER+SS DID + PQ LIN +P+V+++ EFF SSQLSQ  
Sbjct: 331 VGELVANQFRIGMSRMERVVRERMSSQDIDEITPQSLINIRPIVASIKEFFGSSQLSQFM 390

Query: 527 EHVNSLSRITHTRRLSALGQGGV--------ARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  N L+ +TH RRLSALG GG+         R      +RDVH +HY R+CP ET EG 
Sbjct: 391 DQANPLTGLTHKRRLSALGPGGLAGHKSGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGP 450

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED- 637
           NIGL+ SL  +ARVN YGFIE PYR+V DG+VT+ + +++A EEEN  IA AN+ LD   
Sbjct: 451 NIGLIGSLALYARVNEYGFIEAPYRRVQDGRVTDQIDWMTADEEENHIIAPANTPLDPKT 510

Query: 638 ---------GSFTEELVFCRCAGEEI-------LVPREKIDFIDASPKQVVSIAASLIPF 681
                    G             +          VP   +D++D SP+Q++S+AA+LIPF
Sbjct: 511 GEFVVADASGELKRPHSVVARTRDFDGSFGAPADVPVASVDYMDVSPRQMISVAATLIPF 570

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE+DD+ R LMG NMQRQAVPL+   APFVGTGME   A  SG   +A+ AG V   DA 
Sbjct: 571 LEHDDAKRTLMGANMQRQAVPLVHPSAPFVGTGMERRAALDSGEVTLAREAGEVVFADAS 630

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I +++  G  D        Y L K+QRSNQ+TC+N RPLV+VGDEV     +ADGPSTD
Sbjct: 631 KITVKTETGMDD--------YVLPKYQRSNQSTCINHRPLVRVGDEVALGQPLADGPSTD 682

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+ VA+M W GYN+ED++++SER+V++D+ T+I+I   E+ ARDTKLGPEEI
Sbjct: 683 HGELALGQNLTVAYMSWEGYNYEDAIVVSERVVADDLLTTINISRHEIDARDTKLGPEEI 742

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           TR++PN+SE+ L N+DE GII +GAEV PGDILVGK+TPKGES  T EE+LL+AIFG KA
Sbjct: 743 TREVPNLSEDMLANLDEDGIIRIGAEVGPGDILVGKVTPKGESTQTAEERLLKAIFGAKA 802

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DVRDTSL++P G  G V+DV  F+R   D
Sbjct: 803 HDVRDTSLKMPHGAYGRVIDVVRFSRDAGD 832



 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 145/296 (48%), Gaps = 32/296 (10%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
               R R  FGK P  +++P+LI VQK S+D F+           EGLQ AF+   PI +
Sbjct: 11  TATERERLNFGKIPVAMELPNLISVQKQSFDRFMA----------EGLQEAFRESSPIQS 60

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            +    + F +++F  P   V++C  +D+TY   L   +R            K   +IKE
Sbjct: 61  SNHTLEVSFGTHQFSDPVHSVEECREKDMTYQASLLTEVRFT---------NKETGEIKE 111

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++MGD P+MT+ GTF+I G +RIVVSQL RSPG+++  +       G  +Y  + IP 
Sbjct: 112 QLVFMGDFPMMTEQGTFIINGTERIVVSQLVRSPGVYYSSELD----GGHRVYKAQSIPA 167

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYSQRGDFW 245
           +G W++ E D +D + V IDR+RK   T FL ALG+   +++I+       +  +  +  
Sbjct: 168 RGAWLEFEVDKRDQLVVSIDRKRKQSATMFLRALGIAVTNDDIIELLGDSEIVKRSIERD 227

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                   L     +      +  GE   +ES + L  GLL + +   +  +G   
Sbjct: 228 VA------LTREDALIEIYRRLRPGEPPTVESSRSLLEGLLFNPQRYDLARVGRYK 277


>gi|30248018|sp|P59643|RPOB_TROWH RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|29422141|gb|AAO84493.1|AF483653_1 DNA-directed RNA polymerase beta chain [Tropheryma whipplei]
          Length = 1157

 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 189/587 (32%), Positives = 285/587 (48%), Gaps = 57/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLG 857
                       +LV   P  G   E  + I     +++ED      +    V  +    G
Sbjct: 596  MGSNMQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQD-DG 654

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V        ++  ++  G  V  G +L        +  ++    LL A  
Sbjct: 655  KHRDYHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCT-DKGELSLGRNLLVAFM 713

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     +S  +V     +   I+++E S    +   E + RD  +  + 
Sbjct: 714  PWEGYNFEDAII-----ISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMD 768

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              +++  R   I  G     G     K T      +S     +  +    ++ ++    S
Sbjct: 769  YIKDLDER-GIIRIGAEVGPGDILVGKVTPKGETELS--AEERLLRAIFNEKSMEVRDTS 825

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LKV +    ++++ +  + ++     D +  G+ + V V++A KR I  GDK+AGRHGNK
Sbjct: 826  LKVPHGQQGTVIDVKLFDAVD---GEDKLGAGINQRVVVYIAHKRKITEGDKLAGRHGNK 882

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G++S+ILP EDMPF+ DGTPVDI+LNPLGVP+RMN GQ+ ETHLGW     G KI+   +
Sbjct: 883  GVISKILPVEDMPFMADGTPVDIILNPLGVPARMNFGQVLETHLGWISKQ-GWKIEGDPD 941

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K                                      + +    VS+PVFDG  E 
Sbjct: 942  WAKDIR---------------------------------VREAQPDSRVSSPVFDGISEG 968

Query: 1218 AINSMLRMADLDE--------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             I  +      +          G++ILYDG TGEPF  P++VGY+Y+LKL+H+V DK++A
Sbjct: 969  EITGLFSSVFPNRDGERAVGSDGKAILYDGRTGEPFPEPISVGYMYVLKLHHLVDDKIHA 1028

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YS++ QQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LTIKSDDVVGR +VY
Sbjct: 1029 RSTGPYSMIIQQPLGGKAQFGGQRFGEMEVWALEAYGAAHALQELLTIKSDDVVGRVKVY 1088

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ++IV G      G PESF V+VKEMQ+L ++I++ +    + +   E
Sbjct: 1089 DAIVKGYPIPTPGVPESFKVIVKEMQSLCINIEVVSDGEDDVSADAE 1135



 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 310/616 (50%), Positives = 431/616 (69%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D+      I      +    R DAL +IYR +RPG+ ++     ++    +F S ++DL+
Sbjct: 240 DAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRRFDLA 299

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-------------DDI 456
            VGR K+N +L +D       + + DIIA I+ L  L  G   +             DDI
Sbjct: 300 RVGRYKVNRKLGVDVDPTRMVLTRSDIIATIRYLAALHLGFSEVAVLNSNKSVPISTDDI 359

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+LGNRR+R VGE+++NQ R GL RMER ++ER+++ DI++++PQ LIN  P+V+A+ EF
Sbjct: 360 DHLGNRRIRPVGELVQNQLRAGLARMERVVRERMTTQDIEAIIPQTLINVMPIVAALKEF 419

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           + +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDV+P+HYGR+CP ET E
Sbjct: 420 YGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVNPSHYGRMCPIETPE 479

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL  ++RVN++GFIETPYR+V +GKVT+D+ Y++A +E+   IAQA++ L  
Sbjct: 480 GPNIGLIGSLACYSRVNSFGFIETPYRRVVNGKVTDDIEYMTATQEDEHAIAQASTPLRP 539

Query: 637 DGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D SF +E V  R   GE  +VP +++D++D S +Q+VS+A SLIPFLE++D+NR LMG N
Sbjct: 540 DNSFVDERVLVRRKGGEVEVVPADQVDYMDVSGRQMVSVATSLIPFLEHNDANRALMGSN 599

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  E+P VGTGME  VA  +G  ++A+  GIV  V A  + ++  +G     
Sbjct: 600 MQRQAVPLLVTESPLVGTGMERYVAIDAGDVLIAEDPGIVGDVSADVVTVKQDDGKHRD- 658

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                 Y + KF RSNQ  C NQR +V+ GD V +  ++ADGP TD G+L+LGRN+LVAF
Sbjct: 659 ------YHVGKFVRSNQGNCYNQRVVVRSGDRVEKGTVLADGPCTDKGELSLGRNLLVAF 712

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+++IS+ +V +D  +SIHIEE EV  RDTKLG EEITRD+PNVS + +K+
Sbjct: 713 MPWEGYNFEDAIIISQNLVKDDTLSSIHIEEHEVSTRDTKLGSEEITRDLPNVSMDYIKD 772

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+LLRAIF EK+++VRDTSL+VP G 
Sbjct: 773 LDERGIIRIGAEVGPGDILVGKVTPKGETELSAEERLLRAIFNEKSMEVRDTSLKVPHGQ 832

Query: 936 SGTVVDVRIFNRHGID 951
            GTV+DV++F+    +
Sbjct: 833 QGTVIDVKLFDAVDGE 848



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 90/320 (28%), Positives = 142/320 (44%), Gaps = 32/320 (10%)

Query: 3   KGVVFNGLGRV----RKFFGKNPEIIDIPDLIEVQKASYDHFL-------------MMNI 45
             + F    RV    R   GK  + +++P+L+++Q  S+D  +                 
Sbjct: 7   GFLAFAKGKRVCAIGRSSLGKISDPLEVPNLLDLQLDSFDWLIGGPRWRAALDAYRKNPS 66

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
                   GL   F  + PI   +G   L F     +  +  V +C  R  TY+ PL + 
Sbjct: 67  GAPIAEKSGLDEVFDEISPIEDSAGNMQLNFSKPVLEAEELSVRECRVRGRTYSAPLYVE 126

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
              +  D           +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++F
Sbjct: 127 AEFMNHD---------TGEIKTQTVFMGDFPLMTDKGTFVINGTERVVVSQLVRSPGVYF 177

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           +    +   S K L++ RIIP +G W++ E D  D + VR+DR+R+ PV  FL A+GM  
Sbjct: 178 ERTPEKN--SEKDLFSGRIIPARGAWLEFEVDRHDQLGVRVDRKRRQPVIFFLRAIGMTD 235

Query: 226 EEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           +EI   F  +  I      +       A   +            + G  ++E+    +  
Sbjct: 236 DEIRDAFGEFESISVQHEKNIGLSRDDALREIYRRVRPGEQASAEAGRALLENFYFTSRR 295

Query: 284 --LLKSLKEKGVKFLGITSD 301
             L +  + K  + LG+  D
Sbjct: 296 FDLARVGRYKVNRKLGVDVD 315


>gi|46361020|gb|AAS89243.1| RpoB [Corynebacterium mastitidis]
          Length = 1058

 Score =  486 bits (1251), Expect = e-134,   Method: Composition-based stats.
 Identities = 319/616 (51%), Positives = 443/616 (71%), Gaps = 21/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL  D  ++   ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+
Sbjct: 231 ERFGFSEIMMSTLENDGVENTDQALLEIYRKQRPGEQPTRELAQSLLDNAFFRAKRYDLA 290

Query: 410 TVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDI 456
            VGR K+N +L L    D +  + +EDI   ++ LV L  G+ T+            DDI
Sbjct: 291 KVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGERTMTSPTGEVIPVETDDI 350

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EF
Sbjct: 351 DHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREF 410

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 411 FGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPE 470

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL ++ARVN +GFIETPYRKV DGKVT++V YL+A EE+   +A+A++ +D 
Sbjct: 471 GPNIGLIGSLATYARVNPFGFIETPYRKVVDGKVTDEVEYLTADEEDRFAVAEASTEVDA 530

Query: 637 DGSFTEELVFCRCAGEEILVPREK-IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +G+ T+  +  R    +I V   + +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG N
Sbjct: 531 EGNITQGRIEVRVKDGDIQVSTAQGVDYLDVSPRQMVSVGTAMIPFLEHDDANRALMGAN 590

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQ+QAVPLL++EAP VGTGME   A  +G  ++A RAG+VE V A  I I   EG  D  
Sbjct: 591 MQKQAVPLLRSEAPLVGTGMEYRAAYDAGDLVIAPRAGVVENVSADFITIMDDEGQRDTF 650

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L KF+R+NQ TC NQ PLVK+G  V   +++ADGP T  G++ALGRN+LVAF
Sbjct: 651 M-------LRKFERTNQGTCYNQTPLVKIGQRVEAGEVLADGPGTHNGEMALGRNLLVAF 703

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L++
Sbjct: 704 MPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRD 763

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G 
Sbjct: 764 LDDRGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGE 823

Query: 936 SGTVVDVRIFNRHGID 951
           +G V+ VR F+R   D
Sbjct: 824 TGKVIGVRRFSREDDD 839



 Score =  367 bits (942), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 142/437 (32%), Positives = 205/437 (46%), Gaps = 61/437 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G++L           M     LL A    +  +  D  +     V   ++
Sbjct: 669  LVKIGQRVEAGEVLADGPGT-HNGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 727

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + RD DD   I+      R  +IL G+ 
Sbjct: 728  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIVRIGADVRAGDILVGKV 786

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 787  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIG 829

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+  GV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 830  VRRFSREDDDDLAAGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMAD 889

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ ETHLGW     G ++       +   +   L++  ++
Sbjct: 890  GTPVDIILNTHGVPRRMNIGQVLETHLGWLAAA-GWQVD-----PEDEKNAELLKTLPKE 943

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA    +  +L  +  +  G  
Sbjct: 944  LYDVP----------------------AGSLTATPVFDGATNTEVAGLLANSRPNRDGDV 981

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 982  MVDGNGKTMLLDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1041

Query: 1287 SNRGGQRLGEMEVWCIQ 1303
            +  GGQR GEMEVW +Q
Sbjct: 1042 AQFGGQRFGEMEVWAMQ 1058



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 173/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I+IP L++VQ+ S+D  +              P+ R   GL+     + P
Sbjct: 17  RYSFAKYTEPIEIPGLLDVQRDSFDWLVGTPQWRARQQEERGPEARITSGLEDILDELSP 76

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+  K  +++   +D+ Y+ PL +T   I  D          ++
Sbjct: 77  IQDYSGNMSLSLSEPRFEEVKNSIEESKDKDINYSAPLYVTAEFINND---------TQE 127

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 128 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 185

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   
Sbjct: 186 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIRERFGFSEIMMSTLEN 245

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI-- 298
           D       A   +   +        +  + ++++         L K  + K  + LG+  
Sbjct: 246 DGVENTDQALLEIYRKQRPGEQPTRELAQSLLDNAFFRAKRYDLAKVGRYKVNRKLGLGG 305

Query: 299 ---------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                          T + L  L+  E  +   TGE+       ++   ++   +  +R 
Sbjct: 306 DHDGLMTLTEEDIATTLEYLVRLHAGERTMTSPTGEVI-----PVETDDIDHFGNRRLRT 360

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 361 VGELIQNQVRVGLSRMERVVRERMTTQD 388


>gi|331124032|gb|AEC53804.1| RNA polymerase subunit B [Vibrio sp. SO200]
          Length = 519

 Score =  486 bits (1250), Expect = e-134,   Method: Composition-based stats.
 Identities = 252/522 (48%), Positives = 356/522 (68%), Gaps = 3/522 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +E++L  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEQVLDIFFDKVKFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L    L  G   +  +     G+  +E G+++T+  ++ L++  V F+ +  D
Sbjct: 61  DQTLMMELVPERL-RGETATFDIES--NGKVYVEKGRRVTARHIRQLEKDEVSFIEVPVD 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   A+D +N  TGE+ + A   +  + L  +  +  + + +L+ + ++N  ++  T
Sbjct: 118 YIVGKISAKDYINEATGEVILAANQEVTLEVLANLSQAGYKKLEVLFTNDLDNGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRVDSTSDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSPERYDLSTVGRMKFNSSIE 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
               ++   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 RTDAEEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L +D  F +EL+  R  GE  L PRE +
Sbjct: 418 YRRVVDGIVTDEVDYLSAIEEGQFVIAQANAKLTDDSRFADELITARQKGESGLHPREHV 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           D++D +  QVVSIAASLIP LE+DD+NR LMG NMQRQAVP 
Sbjct: 478 DYMDVATNQVVSIAASLIPLLEHDDANRALMGANMQRQAVPT 519


>gi|206900188|ref|YP_002250694.1| DNA-directed RNA polymerase, beta subunit [Dictyoglomus thermophilum
            H-6-12]
 gi|206739291|gb|ACI18349.1| DNA-directed RNA polymerase, beta subunit [Dictyoglomus thermophilum
            H-6-12]
          Length = 1070

 Score =  485 bits (1249), Expect = e-134,   Method: Composition-based stats.
 Identities = 190/583 (32%), Positives = 261/583 (44%), Gaps = 65/583 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E+++  +   MV  DV   +       +  +T    
Sbjct: 552  MGANMQRQAVPLINTEPPLVGTGIEETVARNTGVMVISDVDGIVKKVSSSEIVIETDNKE 611

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E+  + I           ++  I+ VG  V  GD+L           +     +L A   
Sbjct: 612  EKRYQLIKYRRTNQGTCWNQKPIVEVGQRVKKGDVLADGPATSN-GKLALGRNVLVAFMP 670

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     V   +    I       K   +     E    +    +D    L
Sbjct: 671  WGGYNYEDAIIISERLVKEDIF-TSIHIEEYEIKARDTKLGPEEITRDIPNISEDAIRYL 729

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D++       I+ G           K T      ++   R     F  +  + +     +
Sbjct: 730  DKD-----GIIMIGAEVGPNDILVGKVTPKGETELTPEERLLRAIFGEKSRETKDTSLRM 784

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                      +      K+   +  D++PPGV ++VKV VA  R I  GDK+AGRHGNKG
Sbjct: 785  PHGEWGKVIDV------KVLSRENDDELPPGVNKIVKVRVAQIRKISVGDKLAGRHGNKG 838

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +++ ILP EDMPFL+DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LG        D
Sbjct: 839  VIATILPEEDMPFLEDGTPVDIILNPLGVPSRMNVGQILETHLGWAAKELGLYAIVPPFD 898

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                 + S                                                    
Sbjct: 899  EVLGENRSANL------------------------------------------------- 909

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +  MLR A L E G+ +LYDG TGEPF++ VTVGY+Y+LKL H+  DK++ARS G YSLV
Sbjct: 910  VKEMLRKAGLPEDGRVVLYDGRTGEPFNQKVTVGYMYILKLIHLADDKIHARSVGPYSLV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGG++  GGQR GEMEVW ++AYGAA+ L+EMLT KSDDV GRT  Y +IV+GN  
Sbjct: 970  TQQPLGGRAQFGGQRFGEMEVWALEAYGAAHTLEEMLTYKSDDVAGRTEAYSAIVSGNLI 1029

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
             E G PESF VLV+E+Q LG+ +            + +I D +
Sbjct: 1030 KEPGIPESFKVLVRELQGLGIKVSAY--IGNRLVNLYKIEDES 1070



 Score =  473 bits (1217), Expect = e-130,   Method: Composition-based stats.
 Identities = 304/637 (47%), Positives = 432/637 (67%), Gaps = 8/637 (1%)

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
             G IYI    +        +            +       Y+  T   D   DR  A+ 
Sbjct: 175 SNGIIYIHPNGMKKFPVSLLLRALGYDLDYFSEILGPEELNYLEMTYAKDNVNDRSQAIF 234

Query: 376 DIYRVMRPGDVST-FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           +    +RPGDV +    A  +   +FFD  +Y+L  VGR K+N RL L+ P D   + ++
Sbjct: 235 EACAKLRPGDVPSREEDALRVIKQMFFDVRRYNLGKVGRYKLNQRLGLNIPLDNYALTED 294

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           D+I IIK L  ++ GK   DDID+LGNRR+RSVGE+L+ Q+R GL R+E+ I+E+++  D
Sbjct: 295 DLIEIIKRLTMVKTGKDETDDIDHLGNRRIRSVGELLQMQFRAGLARVEKLIREKMALTD 354

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +   P  L++ +P+++AV EFF  + LSQ  +  N LS + H RR+SALG GG+ R RA
Sbjct: 355 PEQASPIALVSTRPLMAAVKEFFNRNPLSQFMDQTNPLSELAHKRRISALGPGGLTRERA 414

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             E+RD+HP+HYGR+CP ET EG N GL++ L++ A V+ YGF+ TPY +V DGK+T+++
Sbjct: 415 TFEVRDIHPSHYGRVCPIETPEGPNAGLINYLSTLAIVDEYGFLRTPYYRVKDGKITDEI 474

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           VYLSA EE+   IA  +  ++E+    +EL+  R  G+ +L   +++DF+  SP Q VSI
Sbjct: 475 VYLSATEEDKYTIASFDVHINENREIVDELIHARRKGKFVLCSPKEVDFVGVSPYQTVSI 534

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           + +LIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTG+E  VA+++G  +++   GI
Sbjct: 535 STALIPFLEHDDANRALMGANMQRQAVPLINTEPPLVGTGIEETVARNTGVMVISDVDGI 594

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V++V +  IVI +              Y+L+K++R+NQ TC NQ+P+V+VG  V++ D++
Sbjct: 595 VKKVSSSEIVIETD-------NKEEKRYQLIKYRRTNQGTCWNQKPIVEVGQRVKKGDVL 647

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP+T  G LALGRN+LVAFMPW GYN+ED+++ISER+V ED+FTSIHIEE+E+ ARDT
Sbjct: 648 ADGPATSNGKLALGRNVLVAFMPWGGYNYEDAIIISERLVKEDIFTSIHIEEYEIKARDT 707

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           KLGPEEITRDIPN+SE+ ++ +D+ GII +GAEV P DILVGK+TPKGE+ +TPEE+LLR
Sbjct: 708 KLGPEEITRDIPNISEDAIRYLDKDGIIMIGAEVGPNDILVGKVTPKGETELTPEERLLR 767

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIFGEK+ + +DTSLR+P G  G V+DV++ +R   D
Sbjct: 768 AIFGEKSRETKDTSLRMPHGEWGKVIDVKVLSRENDD 804



 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 99/534 (18%), Positives = 189/534 (35%), Gaps = 55/534 (10%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYE 80
           +IPDL+++Q  S++ FL           +GL+     + PI +      LEFV      +
Sbjct: 21  NIPDLLKIQYDSFNWFLT----------QGLREVLDEINPIESVRQGLSLEFVTTEDGIK 70

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
            DPP    D+CL + LTY   + +  RL   D       ++IKDIKEQ +++G++P MT 
Sbjct: 71  IDPPTKTPDECLEKGLTYESSIYVKTRLYFKD-----ENRNIKDIKEQMVFLGNIPQMTN 125

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
             TF++ G ++++V+Q+ RSPG+ F  +               +IP +G W++ E DS  
Sbjct: 126 RATFIVNGTEKVIVNQITRSPGVFFQEEGHSII--------ATLIPTRGGWIEFELDSNG 177

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           II++  +  +K PV+  L ALG D    L  F   +   +                   +
Sbjct: 178 IIYIHPNGMKKFPVSLLLRALGYD----LDYFSEILGPEELNYLEMTYAKDNVNDRSQAI 233

Query: 261 SSSLVDIDTGEQ--VIESGKKLTSGLLKSLKEKGVKFLGITSDC--------LCGLYVAE 310
             +   +  G+     E   ++   +   ++   +  +G             L    + E
Sbjct: 234 FEACAKLRPGDVPSREEDALRVIKQMFFDVRRYNLGKVGRYKLNQRLGLNIPLDNYALTE 293

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           D +      + +      +   ++ + +  IR +  L                 +K    
Sbjct: 294 DDLIEIIKRLTMVKTGKDETDDIDHLGNRRIRSVGELLQMQFRAG-----LARVEKLIRE 348

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           K AL D  +      VST  +  ++  F   +     +     +         +      
Sbjct: 349 KMALTDPEQASPIALVSTRPLMAAVKEFFNRNPLSQFMDQTNPLSELAHKRRISALGPGG 408

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           + +E     ++ +     G+    +     N  + +    L      G LR      +  
Sbjct: 409 LTRERATFEVRDIHPSHYGRVCPIETPEGPNAGLINYLSTLAIVDEYGFLRTPYYRVKDG 468

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
              D    +     +   + S             + E+   +  + H RR    
Sbjct: 469 KITDEIVYLSATEEDKYTIASFD---------VHINENREIVDELIHARRKGKF 513


>gi|195537261|dbj|BAG68219.1| RNA polymerase subunit B [Glaciibacter superstes]
 gi|195537263|dbj|BAG68220.1| RNA polymerase subunit B [Glaciibacter superstes]
          Length = 946

 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 325/700 (46%), Positives = 461/700 (65%), Gaps = 30/700 (4%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++      I S  +    G ++  +I   +  ++ +     
Sbjct: 16  ERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEI--DKRDQVGVRIDRK 73

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +     +    +    IL  +     + I  TL  D    +++AL DIYR +RPG+  
Sbjct: 74  RKQSVTVFLKALGLTSEEIL--EEFKGYSSIELTLEKDAILTKEEALKDIYRKLRPGEQV 131

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+S +YDL+ VGR K+N +L +D P     +  +DI+  IK LV L 
Sbjct: 132 AAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIDAPLADSVLTLKDILGTIKYLVALH 191

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           + +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 192 DNQTTLPGVRDGKKIDLRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 251

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 252 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRD 311

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N++GFIETPYR+V +G VT 
Sbjct: 312 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINSFGFIETPYRRVVNGVVTT 371

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           D+ YL+A EE+   +AQAN+ L +D  F E+ V  R   GE  L P ++I ++D SP+Q+
Sbjct: 372 DIDYLTASEEDEYIVAQANAPLTKDAHFAEDRVLARKKGGEVDLFPHDEIGYMDVSPRQM 431

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+  SLIPFLE+DD+NR LMG NMQRQAVPLL++++P VGTGME   A  +G  I A  
Sbjct: 432 VSVGTSLIPFLEHDDANRALMGANMQRQAVPLLRSDSPLVGTGMEGYAAIDAGDVITALG 491

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           AG+V +V A  + ++           G   Y L KF R+NQ T  N R +V  GD +   
Sbjct: 492 AGVVSEVAADAVTVQLD-------AGGTQEYFLRKFDRANQGTSYNNRVIVNAGDRIEVG 544

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           ++IADGP+TD G+LALG+N+LVAFMPW G+NFED++++S+ +V +DV +SIHIEE+EV A
Sbjct: 545 EVIADGPATDNGELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDVLSSIHIEEYEVDA 604

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           RDTKLG EEITRD+PNVS + L ++DE GII +GAEV PGDILVGK+TPKGE+ ++ EE+
Sbjct: 605 RDTKLGKEEITRDLPNVSPDLLADLDERGIIRIGAEVRPGDILVGKVTPKGETELSAEER 664

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LLRAIF EK+ +VRDTSL+VP G  GT++ V++F+    D
Sbjct: 665 LLRAIFNEKSREVRDTSLKVPHGEQGTIIGVKVFDAQDGD 704



 Score =  436 bits (1120), Expect = e-119,   Method: Composition-based stats.
 Identities = 163/465 (35%), Positives = 234/465 (50%), Gaps = 68/465 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  +  G+++           +   + LL A    +  +  D  +   + V   V+
Sbjct: 534  IVNAGDRIEVGEVIADGPATDN-GELALGKNLLVAFMPWEGHNFEDAIILSQNLVKDDVL 592

Query: 941  DVRIFNRHGIDKNERSISVEREQIEL--------LARDKDDEQVILDRNIYSRLMEILCG 992
                   +  + + R   + +E+I          L  D  DE+ I+      R  +IL G
Sbjct: 593  SSIHIEEY--EVDARDTKLGKEEITRDLPNVSPDLLADL-DERGIIRIGAEVRPGDILVG 649

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +    G         L   + +E  R                V   +        + + +
Sbjct: 650  KVTPKGETELSAEERLLRAIFNEKSREV--------RDTSLKVPHGEQGTIIGVKVFDAQ 701

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +        D++  GV + V VF+A KR I  GDK+AGRHGNKG++S+ILP EDMPFL
Sbjct: 702  DGD--------DELGSGVNQRVVVFIAQKRKITEGDKLAGRHGNKGVISKILPAEDMPFL 753

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLG+P RMN GQ+ ETHLGW     G K++                   
Sbjct: 754  ADGTPVDIILNPLGIPGRMNFGQVLETHLGWIAKQ-GWKVEGKPKWASR----------- 801

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD----- 1227
                                +   A     G  V+TPVFDGA E+ I  +L   +     
Sbjct: 802  --------------------LPEEAHSAAPGTKVATPVFDGALEQEIEGLLDSTNPTRDG 841

Query: 1228 ---LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
               +D +G+++L+DG +GEPF +PV+VGY+Y+LKL+H+V DK++ARSTG YS++TQQPLG
Sbjct: 842  DRLIDSTGKTLLFDGRSGEPFPQPVSVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLG 901

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDD++GR +VY
Sbjct: 902  GKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDILGRVKVY 946



 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 63/169 (37%), Positives = 90/169 (53%), Gaps = 6/169 (3%)

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            PLMT  GTFVI G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W++ 
Sbjct: 1   FPLMTPKGTFVINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAWLEF 58

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAA 252
           E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D       A 
Sbjct: 59  EIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEEFKGYSSIELTLEKDAILTKEEAL 118

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGIT 299
             +         V  +    ++++    +    L K  + K  + LGI 
Sbjct: 119 KDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGID 167


>gi|196051515|gb|ACG68891.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 513

 Score =  485 bits (1248), Expect = e-134,   Method: Composition-based stats.
 Identities = 252/516 (48%), Positives = 356/516 (68%), Gaps = 3/516 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+G ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTAGHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQ
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQ 513


>gi|196051505|gb|ACG68886.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 513

 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 250/516 (48%), Positives = 355/516 (68%), Gaps = 3/516 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGLNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQ
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQ 513


>gi|94984743|ref|YP_604107.1| DNA-directed RNA polymerase subunit beta [Deinococcus geothermalis
            DSM 11300]
 gi|158564160|sp|Q1J0P6|RPOB_DEIGD RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
 gi|94555024|gb|ABF44938.1| DNA-directed RNA polymerase subunit beta [Deinococcus geothermalis
            DSM 11300]
          Length = 1152

 Score =  484 bits (1247), Expect = e-134,   Method: Composition-based stats.
 Identities = 186/505 (36%), Positives = 269/505 (53%), Gaps = 30/505 (5%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+D+  I+ VG EV PG ++        +  +   + +  AI      +  D        
Sbjct: 668  NLDQHPIVSVGDEVVPGQVIADGP-ASDQGRLALGQNITIAIMPFDGFNFEDAIC----- 721

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDEQVILDRNIYSRLMEIL 990
            +S  +V    +    I+K+E      +   E + RD     +     LD +   R+   +
Sbjct: 722  ISEGLVRKDFYTSVHIEKDEIEARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGAEV 781

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
               + + G   FK  +  + +      RS + + A + +     V+S +           
Sbjct: 782  KPGDILVGKTSFKGESEPTPE--ERLLRSIFGEKAREVKDTSLRVQSGQGGIVVKTVRFR 839

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                    +   G D+ PGV  +V+V+VA KR +Q GDK+A RHGNKG+VS+ILP EDMP
Sbjct: 840  --------RGDEGVDLKPGVREMVRVYVAQKRQLQVGDKVANRHGNKGVVSKILPPEDMP 891

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L+DGTPVD+V NPLGVPSRMN+GQI ETHLG      G+K  + + D      I  +  
Sbjct: 892  YLEDGTPVDLVFNPLGVPSRMNLGQILETHLGEVARLTGQKFVTPVFDSATEEAIKEMLE 951

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
             +          ++  + D      +    K GV +S P  D A      + +++A    
Sbjct: 952  -VAAAERLQRRKDEGFELDKREQEVLDRAGKLGV-ISPPNGDYA-----AAQMQLA---R 1001

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
            +G+S+LYDG TGEP   PV VG +Y++KL HMV DK++ARSTG YSL+TQQPLGGK+  G
Sbjct: 1002 TGKSVLYDGRTGEPISGPVVVGTMYVMKLYHMVEDKLHARSTGPYSLITQQPLGGKAQFG 1061

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y+SIV G +   +  PESF VL
Sbjct: 1062 GQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIDGRDAAYQSIVKGEEVSGSTIPESFKVL 1121

Query: 1351 VKEMQALGLSIDLENSRTKNSAKME 1375
            VKE+ +LGL +++ ++  K     E
Sbjct: 1122 VKELHSLGLDVEVLDNNDKPVDIFE 1146



 Score =  444 bits (1141), Expect = e-122,   Method: Composition-based stats.
 Identities = 316/713 (44%), Positives = 435/713 (61%), Gaps = 29/713 (4%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+  ++V+ S    + G+  +   KG+K +   +  +  +      +  E     +E   
Sbjct: 137 INGADRVVISQIHRSPGVYFTSSYKGIKKM--YTAAIIPMPKRGPWIELEFNGGVLEMKV 194

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
              +  +  +      D   L       +             +  +ALL ++ V+RPGD 
Sbjct: 195 NKRKFPVSLLLRVLGYDDAQLKALFTEFDPAAELPEDKSAGMNPDEALLRLFTVLRPGDP 254

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED-------IIAI 439
                A      L  D  +YDL   GR KMN +L      D   +  ED       ++  
Sbjct: 255 PKRDKAIQYLYGLLADPKRYDLGEPGRFKMNTKLGTRR-QDRTLLTFEDGRFGDAGLVDT 313

Query: 440 IKILVDLRNGKGTI-----------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           I+ L+ L+ G  T+                 DDID+LGNRRVR+VGE+L +Q R+G+ RM
Sbjct: 314 IRYLMALQQGLETVTMGADEDGVAIEVPVTEDDIDHLGNRRVRTVGELLADQLRVGMGRM 373

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLSQ ++  N LS + H RR+S
Sbjct: 374 ARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLSQFKDQTNPLSDLRHKRRIS 433

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL+S+A+VN  GFIE PY
Sbjct: 434 ALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLSSYAKVNDLGFIEAPY 493

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R+V DG+VT+DVVY++A  E+   IAQANS L+ DG+F EE V  R  G+ +L    ++D
Sbjct: 494 RRVVDGRVTDDVVYMTADIEDRYVIAQANSPLNPDGTFAEERVLARKKGDPMLYAPTEVD 553

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           F+D SPKQ+VSI  SLIPFLE+DD+NR LMG NMQ QAVPL++A++P VGTG+E  V   
Sbjct: 554 FMDVSPKQIVSINTSLIPFLEHDDANRALMGSNMQSQAVPLVRADSPAVGTGVEERVVTD 613

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS--TSGVDIYRLMKFQRSNQNTCVNQRP 780
           SG ++++   G V  VDA  I +   E           V  + L++F RSNQ T ++Q P
Sbjct: 614 SGTSVISDVTGRVTYVDARAIQVTLTEDAPQIGLVKGNVRTFELVRFTRSNQGTNLDQHP 673

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V VGDEV    +IADGP++D G LALG+N+ +A MP+ G+NFED++ ISE +V +D +T
Sbjct: 674 IVSVGDEVVPGQVIADGPASDQGRLALGQNITIAIMPFDGFNFEDAICISEGLVRKDFYT 733

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           S+HIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI+ VGAEV PGDILVGK + 
Sbjct: 734 SVHIEKDEIEARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGAEVKPGDILVGKTSF 793

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           KGES  TPEE+LLR+IFGEKA +V+DTSLRV SG  G VV    F R     +
Sbjct: 794 KGESEPTPEERLLRSIFGEKAREVKDTSLRVQSGQGGIVVKTVRFRRGDEGVD 846



 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/238 (36%), Positives = 133/238 (55%), Gaps = 25/238 (10%)

Query: 5   VVFNGLG-RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
           +       R+ + FG+  E+I +P+L EVQ  S+  FL  + APDER + GLQ+AF+ VF
Sbjct: 1   MSLTDQKPRIER-FGEITEVIPLPNLTEVQVNSFKAFLQADKAPDERDDTGLQSAFREVF 59

Query: 64  PITAFSGA-----AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           PI   +        +L+F+ Y    P +  ++C  +DLTY  PL   L+LI  D      
Sbjct: 60  PI-DETEKGRSTGLVLDFLEYRLGEPPYTPEECREKDLTYQAPLYAKLQLIHKDSGL--- 115

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                 IKE  +++GDLPLMT DG+FVI G  R+V+SQ+HRSPG++F           K 
Sbjct: 116 ------IKEDQVFLGDLPLMTDDGSFVINGADRVVISQIHRSPGVYFTSS----YKGIKK 165

Query: 179 LYACRIIPD--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           +Y   IIP   +G W+++EF+   ++ ++++ +RK PV+  L  LG D  ++ + F  
Sbjct: 166 MYTAAIIPMPKRGPWIELEFNG-GVLEMKVN-KRKFPVSLLLRVLGYDDAQLKALFTE 221


>gi|302336391|ref|YP_003801598.1| DNA-directed RNA polymerase subunit beta [Olsenella uli DSM 7084]
 gi|301320231|gb|ADK68718.1| DNA-directed RNA polymerase subunit beta [Olsenella uli DSM 7084]
          Length = 1171

 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 190/610 (31%), Positives = 276/610 (45%), Gaps = 77/610 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ A  P+ G   E +       +         +E              
Sbjct: 581  MGANMQRQAVPLIKAHAPYVGTGLEYAAAQDSGELICAAHAGTVVEVDAAHIVVDGERGP 640

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            E               I+   ++ VG +V  GD L    +  G   +     L  A    
Sbjct: 641  ERYDLPKYERSNQSTCINHRPVVHVGQKVEAGDPLTDGTSVDG-GELALGANLNVAYMPW 699

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE-QVIL 978
            +  +  D  +     V   ++     +RH  + + R   +  E+I     ++ +E    L
Sbjct: 700  EGYNYEDGIIVSERVVRDDLLTSVNISRH--EIDARDTKLGPEEITREVPNQSEEMLADL 757

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D +   R+   +   + + G    K  T L+++              V+D     +++  
Sbjct: 758  DDDGIIRIGAEVGPGDILVGKVTPKGETALTAEERLLRAIFGAKAHDVRD----TSLKMP 813

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
               Y     ++           + GDD+PPGV  +V+VFVA +R IQ GDK+AGRHGNKG
Sbjct: 814  HGAYGRVVDVV-------RFSREAGDDLPPGVNELVRVFVAQRRKIQQGDKIAGRHGNKG 866

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +V  +LP EDMP++ DGTPVD++L+PLGVPSRMNVGQ+ E HLGWA    G  I S  +D
Sbjct: 867  VVCNVLPVEDMPYMVDGTPVDVLLDPLGVPSRMNVGQLLECHLGWAASH-GYDIDSAESD 925

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
               +G                                        + VSTPV DGA +  
Sbjct: 926  EIVDGP---------------------------------------MYVSTPVLDGATDTE 946

Query: 1219 INSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            +   LR  +                      L++ G++ LYDG TGE F  P+TVG  Y+
Sbjct: 947  VAEALRRTNVNLMNKALRTYGRHMRQEFVPQLNDKGKTTLYDGRTGEAFKSPITVGTSYI 1006

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA+ VL E++T
Sbjct: 1007 LKLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLHEIMT 1066

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            +KSDD  GR + YE+IV G +  E G PESF VLVKE+++L L I     + +   + + 
Sbjct: 1067 VKSDDTNGRVKTYEAIVKGENVPEPGIPESFKVLVKEIRSLALDIAPIAYKPEEPVERDS 1126

Query: 1377 IPDFNKCELK 1386
                +   ++
Sbjct: 1127 DEAADASAVE 1136



 Score =  475 bits (1223), Expect = e-131,   Method: Composition-based stats.
 Identities = 313/661 (47%), Positives = 432/661 (65%), Gaps = 35/661 (5%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G + +       + +   +    I +     +  + ++  +R TL  D    R+DAL++I
Sbjct: 180 GHLVVSIDRKRRQSATLLLRALGIAESDDEIMSLLGDSDVVRATLERDIATTREDALIEI 239

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           YR  RPG+  T   A S+ + L+F+S +YDL+ VGR K+N +L L+     + +  EDI+
Sbjct: 240 YRRQRPGEPPTVDSARSLLDGLYFNSQRYDLARVGRYKINKKLGLELEATQKVLTDEDIV 299

Query: 438 AIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           + ++ L+ L  G     +DDID+ GNRRVR+VGE+++NQ+R+G+ RMER I+ER++S D+
Sbjct: 300 SALRYLLALHGGDQAKKLDDIDHFGNRRVRTVGELVQNQFRIGMSRMERVIRERMASQDV 359

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV------ 549
           D + PQ LIN +P+V+A+ EF+ SSQLSQ  +  N L+ +TH RRLSALG GG+      
Sbjct: 360 DDITPQSLINIRPIVAAIKEFYGSSQLSQFMDQSNPLAGLTHKRRLSALGPGGLAGHKSG 419

Query: 550 --ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
              R      +RDVH +HYGR+CP ET EG NIGL+ SL  +A VN YGFIE+PYR+V D
Sbjct: 420 SSRRTNVPTAVRDVHNSHYGRMCPIETPEGPNIGLIGSLALYAHVNEYGFIESPYRRVVD 479

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS------------FTEELVFCRCAGE--- 652
           G VT+DV +++A EEEN  IA AN  +D                  + +V      +   
Sbjct: 480 GVVTSDVDWMTADEEENHVIAPANVPVDPKTGRFVAVDSHGNIYNPDAIVARTRNYDGSF 539

Query: 653 --EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                V  E +D++D SP+Q++S+AA+LIPFLE+DD+ R LMG NMQRQAVPL+KA AP+
Sbjct: 540 GAPAEVAVETVDYMDVSPRQLLSVAANLIPFLEHDDAKRTLMGANMQRQAVPLIKAHAPY 599

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A+ SG  I A  AG V +VDA  IV+            G + Y L K++RS
Sbjct: 600 VGTGLEYAAAQDSGELICAAHAGTVVEVDAAHIVV--------DGERGPERYDLPKYERS 651

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC+N RP+V VG +V   D + DG S D G+LALG N+ VA+MPW GYN+ED +++S
Sbjct: 652 NQSTCINHRPVVHVGQKVEAGDPLTDGTSVDGGELALGANLNVAYMPWEGYNYEDGIIVS 711

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +D+ TS++I   E+ ARDTKLGPEEITR++PN SEE L ++D+ GII +GAEV P
Sbjct: 712 ERVVRDDLLTSVNISRHEIDARDTKLGPEEITREVPNQSEEMLADLDDDGIIRIGAEVGP 771

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +T EE+LLRAIFG KA DVRDTSL++P G  G VVDV  F+R   
Sbjct: 772 GDILVGKVTPKGETALTAEERLLRAIFGAKAHDVRDTSLKMPHGAYGRVVDVVRFSREAG 831

Query: 951 D 951
           D
Sbjct: 832 D 832



 Score =  298 bits (762), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 91/367 (24%), Positives = 161/367 (43%), Gaps = 30/367 (8%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R  F K    +++P+LI VQK S++ F+            GL  +F    PI   +G 
Sbjct: 15  RTRVSFSKISAAMELPNLISVQKESFERFMTD----------GLAESFAEFSPIENSAGT 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             + F  ++F      + +C  +D++Y  PL + +R +          K   +IKEQ ++
Sbjct: 65  MEVSFGEHQFGDAPSTIAECRAKDISYQAPLFVDVRFV---------NKETGEIKEQLVF 115

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F  +      +G   +  + IP +G W
Sbjct: 116 MGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFSEEMD----NGVQTHHAQFIPARGAW 171

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVY--SQRGDFWCF 247
           ++ E D    + V IDR+R+   T  L ALG+    +EI+S      V   +   D    
Sbjct: 172 LEFEVDKHGHLVVSIDRKRRQSATLLLRALGIAESDDEIMSLLGDSDVVRATLERDIATT 231

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIE--SGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              A   +   +       +D+   +++          L +  + K  K LG+  +    
Sbjct: 232 REDALIEIYRRQRPGEPPTVDSARSLLDGLYFNSQRYDLARVGRYKINKKLGLELEATQK 291

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDE-KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           +   EDIV+     + +  GD   +   ++   +  +R +  L  +           ++ 
Sbjct: 292 VLTDEDIVSALRYLLALHGGDQAKKLDDIDHFGNRRVRTVGELVQNQFRIGMSRMERVIR 351

Query: 365 DKNKDRK 371
           ++   + 
Sbjct: 352 ERMASQD 358


>gi|218678198|ref|ZP_03526095.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli CIAT 894]
          Length = 310

 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 205/310 (66%), Positives = 249/310 (80%), Gaps = 1/310 (0%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           KFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FKSVFPIT FSGA+ML
Sbjct: 1   KFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFKSVFPITDFSGASML 60

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD
Sbjct: 61  EFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGD 120

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SG+LL+A R+IP +G W+DI
Sbjct: 121 MPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGQLLFAARVIPYRGSWLDI 180

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
           EFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL TFY K +Y + G+ W  P     L
Sbjct: 181 EFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYKRDGEGWRIPFKPETL 240

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
             GAK  + +VD DTGE V+E+GKKLT  LL+ L +KG+K L    D L G Y+AEDIVN
Sbjct: 241 -KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLSDKGLKALKAGDDDLYGNYLAEDIVN 299

Query: 315 GETGEIYIEA 324
             TGEIY+EA
Sbjct: 300 YSTGEIYLEA 309


>gi|226731985|gb|ACO82063.1| RNA polymerase beta subunit [Aeromonas media]
          Length = 484

 Score =  484 bits (1246), Expect = e-134,   Method: Composition-based stats.
 Identities = 296/483 (61%), Positives = 379/483 (78%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG
Sbjct: 2   DTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAG 61

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V 
Sbjct: 62  FEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVD 121

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+A
Sbjct: 122 YLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVA 181

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           A+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  +VAKR G++
Sbjct: 182 AALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVDSGVTVVAKRGGMI 241

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V +G+ V   D++A
Sbjct: 242 DYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCVMLGEPVMAGDVLA 301

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTDLG+LALG+N+ VAFMPW+GYNFEDS+L++ER+V ED  T+IHI+E   ++RDTK
Sbjct: 302 DGPSTDLGELALGQNLRVAFMPWNGYNFEDSILVNERVVQEDRLTTIHIQELACISRDTK 361

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LGPEEIT DIPNV E  L  +DE GI+ VGAEV  GDILVGK+TPKGE+ +TPEEKLLRA
Sbjct: 362 LGPEEITADIPNVGEAALSKLDESGIVYVGAEVKGGDILVGKVTPKGETQLTPEEKLLRA 421

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
           IFGEKA DV+D+SLRVP+GV GTVVDV++F R G++K++R+  +E  Q++   +D  +E 
Sbjct: 422 IFGEKASDVKDSSLRVPNGVYGTVVDVQVFTRDGVEKDKRAKEIEEMQLKEAKKDLTEEF 481

Query: 976 VIL 978
            IL
Sbjct: 482 KIL 484


>gi|75762690|ref|ZP_00742528.1| DNA-directed RNA polymerase beta chain [Bacillus thuringiensis
            serovar israelensis ATCC 35646]
 gi|74489824|gb|EAO53202.1| DNA-directed RNA polymerase beta chain [Bacillus thuringiensis
            serovar israelensis ATCC 35646]
          Length = 665

 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 182/568 (32%), Positives = 262/568 (46%), Gaps = 69/568 (12%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 149  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 208

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 209  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 263

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 264  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 321

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 322  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 375

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 376  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYLP 435

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+        
Sbjct: 436  DGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEAG 495

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 496  MANDAK----------------------------TILYDG-------------------- 507

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR
Sbjct: 508  ------RTGEPFDNRVSVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQR 561

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
             GEMEVW ++AYGAAY LQE+LT+KSDDVVGR + YE+IV G +  E G PESF VL+KE
Sbjct: 562  FGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGVPESFKVLIKE 621

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            +Q+LG+ + + +S        +   D +
Sbjct: 622  LQSLGMDVKMMSSDDTEIEMRDTEDDDD 649



 Score =  347 bits (889), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 236/386 (61%), Positives = 296/386 (76%), Gaps = 3/386 (0%)

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRY 626
           +CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  
Sbjct: 1   MCPIETPEGPNIGLINSLSSFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYV 60

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +AQAN  L ++G F  E +  R  GE I+  RE+ID++D SPKQVVS A + IPFLENDD
Sbjct: 61  VAQANMKLSDEGEFLSEDIVARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDD 120

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           SNR LMG NMQRQAVPL+  E+P VGTGME V AK SGAA++ K  G+VE+V+A  + +R
Sbjct: 121 SNRALMGANMQRQAVPLMNPESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVR 180

Query: 747 -SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             VE D       +D Y++ KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+L
Sbjct: 181 RYVEVDGQTVKGDLDRYKMQKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGEL 240

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALGRN+LV FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDI
Sbjct: 241 ALGRNVLVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDI 300

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VR
Sbjct: 301 PNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVR 360

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G ++DV++FNR   D
Sbjct: 361 DTSLRVPHGGGGIILDVKVFNREDGD 386


>gi|46361016|gb|AAS89241.1| RpoB [Corynebacterium propinquum]
          Length = 1059

 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 329/756 (43%), Positives = 467/756 (61%), Gaps = 45/756 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           F P               SA   +    ++S   +I +    I       E G  + +G 
Sbjct: 95  FEPVKNTVDEAKEKDINYSAPLYVTAEFINSDTQEIKSQTVFIGDFPMMTEKGTFIVNGT 154

Query: 285 LKSLKEKGVKFLGITSDCLCG----LYVAEDIVNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    V    G              +       
Sbjct: 155 ERVIVSQLVRSPGVYFDRSIDKSTERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRR 214

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +      +  I   +    +  + +TL  D   +  +ALL+IYR  RPG+  T 
Sbjct: 215 QPVTVLLKALGWTEEKI--RERFGFSELMMSTLEADGVANTDEALLEIYRKQRPGEQPTR 272

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRN 448
            +A+S+ +  FF+  +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  
Sbjct: 273 DLAQSLLDNSFFNPKRYDLARVGRYKINRKLGLGGDHDGLSTLTEEDIATTLEYLVRLHT 332

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+  +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 333 GEREMESPDGQHLMLDTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAE 392

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +++ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+
Sbjct: 393 SITPTSLINVRPVSASIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGI 452

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ SL S+ RVN++GFIETPYRKV DGKVTN+V Y
Sbjct: 453 EVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRVNSFGFIETPYRKVVDGKVTNEVEY 512

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIA 675
           L+A  E+   IAQA     EDG+   + +  R    +  +   + +D++D SP+Q+VS+A
Sbjct: 513 LAADAEDRYSIAQAEVPTAEDGTILSDRIEVRQKDGDIAVTTADGVDYVDVSPRQMVSVA 572

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+VGTGME   A  +G  ++  +AG+V
Sbjct: 573 TAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMELRAAYDAGDVVITPKAGVV 632

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V A  I I   +G  D        Y L KF+R+NQ T  NQ PLV +GD V    ++A
Sbjct: 633 ENVSADLITIMDDDGIRD-------TYMLRKFERTNQGTNYNQTPLVNIGDRVEAGQVLA 685

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G+++LGRNMLVAFMPW G+N+ED++++++ +V +D  TS+HIEE E+ ARDTK
Sbjct: 686 DGPGTHNGEMSLGRNMLVAFMPWEGHNYEDAIILNQSIVEDDSLTSVHIEEHEIDARDTK 745

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNVSE+ L+++DE GII +GA+V PGDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 746 LGAEEITREIPNVSEDVLRDLDERGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRA 805

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTS++VP G +G V+ V  F+R   D
Sbjct: 806 IFGEKAREVRDTSMKVPHGETGKVIGVARFSREDDD 841



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 142/440 (32%), Positives = 206/440 (46%), Gaps = 59/440 (13%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    +L A    +  +  D  +   S 
Sbjct: 665  NYNQTPLVNIGDRVEAGQVLADGPGT-HNGEMSLGRNMLVAFMPWEGHNYEDAIILNQSI 723

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEI 989
            V    +       H ID  +  +  E    +I  ++ D     DE+ I+      R  +I
Sbjct: 724  VEDDSLTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDERGIIRIGADVRPGDI 783

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                V  +           
Sbjct: 784  LVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA---------- 833

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                       +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDM
Sbjct: 834  -------RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDM 886

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF++DGTPVD++LN  GVP RMN+GQ+ E HLGW     G K+    ND +    I  L 
Sbjct: 887  PFMEDGTPVDVILNTHGVPRRMNIGQVLEIHLGWLAHA-GWKVD--PNDPQNEELIKTLP 943

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L  V                               +TPVFDGA  E ++ +L  +  +
Sbjct: 944  KELYDVPANSLT-------------------------ATPVFDGASNEEVSGLLANSRPN 978

Query: 1230 ESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              G        ++ L+DG +GEPF+ P++VGY+Y+LKL+H++ +K++ARSTG YS++TQQ
Sbjct: 979  RDGNVMVDRHGKARLFDGRSGEPFEHPISVGYMYILKLHHLIDEKIHARSTGPYSMITQQ 1038

Query: 1282 PLGGKSNRGGQRLGEMEVWC 1301
            PLGGK+  GGQR GEMEVW 
Sbjct: 1039 PLGGKAQFGGQRFGEMEVWA 1058



 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 98/386 (25%), Positives = 174/386 (45%), Gaps = 40/386 (10%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L+++Q+ SYD  +               D +   GL+     + 
Sbjct: 18  QRYSFAKIDEPIAVPGLLDLQRDSYDWLIGTPEWREREQERRGADAQITSGLEDILNELS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+P K  VD+   +D+ Y+ PL +T   I  D          +
Sbjct: 78  PIEDYSGNMSLSLSEPRFEPVKNTVDEAKEKDINYSAPLYVTAEFINSD---------TQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD P+MT+ GTF++ G +R++VSQL RSPG++FD    +   + + L+A +
Sbjct: 129 EIKSQTVFIGDFPMMTEKGTFIVNGTERVIVSQLVRSPGVYFDRSIDK--STERPLHAVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEKIRERFGFSELMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG-- 297
            D       A   +   +        D  + ++++         L +  + K  + LG  
Sbjct: 247 ADGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFNPKRYDLARVGRYKINRKLGLG 306

Query: 298 --------ITSDCLCGLYVAEDIVNGETGEIYIEAGD----VIDEKSLEEIFHSEIRDIP 345
                   +T + +      E +V   TGE  +E+ D    ++D   ++   +  +R + 
Sbjct: 307 GDHDGLSTLTEEDIA--TTLEYLVRLHTGEREMESPDGQHLMLDTDDIDHFGNRRLRTVG 364

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRK 371
            L  + V         +V ++   + 
Sbjct: 365 ELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|217967362|ref|YP_002352868.1| DNA-directed RNA polymerase, beta subunit [Dictyoglomus turgidum DSM
            6724]
 gi|217336461|gb|ACK42254.1| DNA-directed RNA polymerase, beta subunit [Dictyoglomus turgidum DSM
            6724]
          Length = 1070

 Score =  484 bits (1245), Expect = e-134,   Method: Composition-based stats.
 Identities = 189/580 (32%), Positives = 258/580 (44%), Gaps = 63/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E+++  +   MV  DV   +       +  +T    
Sbjct: 552  MGANMQRQAVPLINTEPPLVGTGIEETVARNTGVMVISDVDGVVKKVSSSEIVIETDNKE 611

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E+  + I           ++  I+ VG  V  GD+L           +     +L A   
Sbjct: 612  EKRYQLIKYRRTNQGTCWNQKPIVEVGQRVKKGDVLADGPATSN-GKLALGRNVLVAFMP 670

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D  +     V   +    I       K   +     E    +    +D    L
Sbjct: 671  WGGYNYEDAIIISERLVKEDIF-TSIHIEEYEIKARDTKLGPEEITRDIPNISEDAIRYL 729

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D++       I+ G           K T      ++   R     F  +  + +     +
Sbjct: 730  DKD-----GIIMIGAEVGPNDILVGKVTPKGETELTPEERLLRAIFGEKSRETKDTSLRM 784

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                      +      K+   +  D++PPGV ++VKV VA  R I  GDK+AGRHGNKG
Sbjct: 785  PHGEWGKVIDV------KVLTRENDDELPPGVNKIVKVRVAQIRKISVGDKLAGRHGNKG 838

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +++ ILP EDMPFL+DGTPVDI+LNPLGVPSRMNVGQI ETHLGWA   LG        D
Sbjct: 839  VIATILPEEDMPFLEDGTPVDIILNPLGVPSRMNVGQILETHLGWAAKELGIYAIVPPFD 898

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                 + S                                                    
Sbjct: 899  EVLGENRSANL------------------------------------------------- 909

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +  MLR A L E G+ +LYDG TGEPF++ VTVGY+Y+LKL H+  DK++ARS G YSLV
Sbjct: 910  VKEMLRKAGLPEDGRVVLYDGRTGEPFNQKVTVGYMYILKLIHLADDKIHARSVGPYSLV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGG++  GGQR GEMEVW ++AYGAA+ L+EMLT KSDDV GRT  Y +IV+GN  
Sbjct: 970  TQQPLGGRAQFGGQRFGEMEVWALEAYGAAHTLEEMLTYKSDDVAGRTEAYSAIVSGNLI 1029

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             E G PESF VLV+E+Q LG+ +         +    E  
Sbjct: 1030 KEPGIPESFKVLVRELQGLGIKVSAYIGNRLVNLSKIEDE 1069



 Score =  470 bits (1209), Expect = e-130,   Method: Composition-based stats.
 Identities = 305/635 (48%), Positives = 430/635 (67%), Gaps = 8/635 (1%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G IYI    +        +            +      +Y+  T   D   DR  A+ + 
Sbjct: 177 GIIYIHPNGIKKFPVSLILRALGYDLDYFKEILGPEELSYLEITYAKDNVSDRTQAIFEA 236

Query: 378 YRVMRPGDVST-FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
              +RPGDV +    A  +   +FFD  +Y+L  VGR K+N RL L    D   + ++D+
Sbjct: 237 CGRLRPGDVPSREEDALRVIRQMFFDVRRYNLGKVGRYKLNQRLGLSISLDNYALTEDDL 296

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           I IIK L  ++ GK   DDID+LGNRR+RSVGE+L+ Q+R GL R+E+ I+E+++  D +
Sbjct: 297 IEIIKRLTMIKTGKDETDDIDHLGNRRIRSVGELLQMQFRAGLARVEKLIREKMALTDPE 356

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
              P  L++ +P+++AV EFF  + LSQ  +  N LS + H RR+SALG GG+ R RA  
Sbjct: 357 QASPIALVSTRPLMAAVKEFFNRNPLSQFMDQTNPLSELAHKRRISALGPGGLTRERATF 416

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RD+HP+HYGR+CP ET EG N GL++ L++ A V+ YGF+ TPY +V DGK+T+++VY
Sbjct: 417 EVRDIHPSHYGRVCPIETPEGPNAGLINYLSTLAIVDEYGFLRTPYYRVKDGKITDEIVY 476

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA EE+   IA  +  ++E+    +ELV  R  G+ IL   ++IDF+  SP Q VSI+ 
Sbjct: 477 LSATEEDKYTIASFDVHINENREIIDELVHARRKGKFILCSPKEIDFVGVSPYQTVSIST 536

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           +LIPFLE+DD+NR LMG NMQRQAVPL+  E P VGTG+E  VA+++G  +++   G+V+
Sbjct: 537 ALIPFLEHDDANRALMGANMQRQAVPLINTEPPLVGTGIEETVARNTGVMVISDVDGVVK 596

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +V +  IVI +              Y+L+K++R+NQ TC NQ+P+V+VG  V++ D++AD
Sbjct: 597 KVSSSEIVIETD-------NKEEKRYQLIKYRRTNQGTCWNQKPIVEVGQRVKKGDVLAD 649

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GP+T  G LALGRN+LVAFMPW GYN+ED+++ISER+V ED+FTSIHIEE+E+ ARDTKL
Sbjct: 650 GPATSNGKLALGRNVLVAFMPWGGYNYEDAIIISERLVKEDIFTSIHIEEYEIKARDTKL 709

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPEEITRDIPN+SE+ ++ +D+ GII +GAEV P DILVGK+TPKGE+ +TPEE+LLRAI
Sbjct: 710 GPEEITRDIPNISEDAIRYLDKDGIIMIGAEVGPNDILVGKVTPKGETELTPEERLLRAI 769

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           FGEK+ + +DTSLR+P G  G V+DV++  R   D
Sbjct: 770 FGEKSRETKDTSLRMPHGEWGKVIDVKVLTRENDD 804



 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 104/541 (19%), Positives = 194/541 (35%), Gaps = 63/541 (11%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYE 80
           +IPDL+++Q  S++ FL           +GL+     + PI +      LEFV      +
Sbjct: 21  NIPDLLKIQYDSFNWFL----------KQGLREVLDEINPIESIRQGLSLEFVTTEDGIK 70

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
            +PP    D+CL + LTY   + +  RL   D       ++IKDIKEQ +++G++P MT 
Sbjct: 71  IEPPTKTPDECLEKGLTYESSIYVKTRLYFKD-----ENRNIKDIKEQMVFLGNIPQMTD 125

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
             TF++ G ++++V+Q+ RSPG+ F  +  R            +IP +G W++ E D   
Sbjct: 126 RATFIVNGTEKVIVNQITRSPGVFFQEEGNRII--------ATLIPTRGGWIEFELDGGG 177

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE---EIL---STFYPKIVYSQRGDFWCFPLSAADL 254
           II++  +  +K PV+  L ALG D +   EIL      Y +I Y+   D       A   
Sbjct: 178 IIYIHPNGIKKFPVSLILRALGYDLDYFKEILGPEELSYLEITYA--KDNVSDRTQAIFE 235

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGL 306
             G      +   +      E   ++   +   ++   +  +G             L   
Sbjct: 236 ACGRLRPGDVPSRE------EDALRVIRQMFFDVRRYNLGKVGRYKLNQRLGLSISLDNY 289

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            + ED +      + +      +   ++ + +  IR +  L                 +K
Sbjct: 290 ALTEDDLIEIIKRLTMIKTGKDETDDIDHLGNRRIRSVGELLQMQFRAG-----LARVEK 344

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
               K AL D  +      VST  +  ++  F   +     +     +         +  
Sbjct: 345 LIREKMALTDPEQASPIALVSTRPLMAAVKEFFNRNPLSQFMDQTNPLSELAHKRRISAL 404

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
               + +E     ++ +     G+    +     N  + +    L      G LR     
Sbjct: 405 GPGGLTRERATFEVRDIHPSHYGRVCPIETPEGPNAGLINYLSTLAIVDEYGFLRTPYYR 464

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            +     D    +     +   + S             + E+   +  + H RR      
Sbjct: 465 VKDGKITDEIVYLSATEEDKYTIASFD---------VHINENREIIDELVHARRKGKFIL 515

Query: 547 G 547
            
Sbjct: 516 C 516


>gi|46361004|gb|AAS89235.1| RpoB [Corynebacterium vitaeruminis]
          Length = 1098

 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 313/617 (50%), Positives = 444/617 (71%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL
Sbjct: 227 TERFGFSELMMSTLEADGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDL 286

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DD 455
           + VGR K+N +L L    D +  + +EDI   ++ LV L  G+ ++            DD
Sbjct: 287 AKVGRYKVNRKLGLGGDNDGLMTLTEEDIATTLEYLVRLHAGETSMTSPSGTVIPVETDD 346

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 347 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 406

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQ+SQ  +  NSLS +T+ RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET 
Sbjct: 407 FFGTSQMSQFMDQNNSLSGLTNKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETP 466

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L S+ARVN +GFIETPYRKV +GK+T+ + YL+A EE+   +AQA +++D
Sbjct: 467 EGPNIGLIGALASYARVNPFGFIETPYRKVENGKLTDQIDYLTADEEDRFRVAQAKTAVD 526

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +G+  ++ V  R   G+  +V  ++ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 527 AEGNIIDDRVTVRMKNGDIAVVSGDEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGA 586

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL+++EAP VGTGME   A  +G  I+ K AG+VE V A  I +   +G  + 
Sbjct: 587 NMQRQAVPLVRSEAPLVGTGMELRAAYDAGDLIINKAAGVVENVCADYITVMQDDGLRE- 645

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ TC NQ+PLV +GD V    ++ADGP T  G+++LGRN+LVA
Sbjct: 646 ------TYLLRKFERTNQGTCYNQKPLVNIGDRVEDGQVLADGPGTKDGEMSLGRNLLVA 699

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 700 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 759

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 760 DLDERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 819

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F+R   D
Sbjct: 820 ETGKVIGVRRFSREDDD 836



 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 174/479 (36%), Positives = 240/479 (50%), Gaps = 61/479 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G +L      K +  M+    LL A    +  +  D  +     V   ++
Sbjct: 666  LVNIGDRVEDGQVLADGPGTK-DGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 724

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 725  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIVRIGADVRDGDILVGKV 783

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 784  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGETGKVIG 826

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPFL D
Sbjct: 827  VRRFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPAEDMPFLPD 886

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +           +   L+   E 
Sbjct: 887  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAAA-GWHVD-----PADPKNAELLKVLPED 940

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            +                          +G   +TPVFDGA  E +  +L  ++ +  G  
Sbjct: 941  LYDVP----------------------AGTLTATPVFDGASNEELAGLLANSNPNRDGDV 978

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 979  MVDENGKATLFDGRSGEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1038

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PE
Sbjct: 1039 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPE 1097



 Score =  301 bits (771), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 145/321 (45%), Gaps = 30/321 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           RK F K  E I++P L+++Q  S+   +            +    R   GL+   + + P
Sbjct: 14  RKSFAKITEPIEVPGLLDIQLDSFAWLVGTPEWRARKQEELGEGARVTSGLEDILEELSP 73

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+  K  +++   +D+ Y+ PL +T   I  D          ++
Sbjct: 74  IQDYSGNMSLSLSEPRFEDMKNTIEEAKDKDINYSAPLYVTAEFINND---------TQE 124

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 125 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 182

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F    +   +   
Sbjct: 183 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSELMMSTLEA 242

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +           +   +  + L        K   +  +G    +
Sbjct: 243 DGVANTDEALLEIYRKQRPGE-------QPTRDLAQSLLDNSFFRAKRYDLAKVGRYKVN 295

Query: 302 CLCGLYVAEDIVNGETGEIYI 322
              GL    D +   T E   
Sbjct: 296 RKLGLGGDNDGLMTLTEEDIA 316


>gi|313679517|ref|YP_004057256.1| DNA-directed RNA polymerase subunit beta [Oceanithermus profundus DSM
            14977]
 gi|313152232|gb|ADR36083.1| DNA-directed RNA polymerase subunit beta [Oceanithermus profundus DSM
            14977]
          Length = 1124

 Score =  483 bits (1244), Expect = e-134,   Method: Composition-based stats.
 Identities = 196/586 (33%), Positives = 272/586 (46%), Gaps = 42/586 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE-RMVSEDVFTSIHIEEFEVMARDTKLGP 858
                  A    ++ A  P  G   ED ++      V  DV   +   + + +  + K   
Sbjct: 565  MGSNMQAQAVPVIRAEAPAVGTGIEDRVIRDSLTSVYSDVDGVVKYVDGDTIVIEQKNKN 624

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                +    V       ID+   + VG ++  GD+L           +   + +L AI  
Sbjct: 625  LREYKLRRFVRSNQGTTIDQRPRVNVGDKIKKGDLLADGPAA-DHGRLALGQNVLVAIMP 683

Query: 919  EKAVDVRD------TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
                +  D        LR     S  +    I  R      E+         E   RD  
Sbjct: 684  FDGYNFEDAIIISENLLRRDHYTSIHIERYEIEARDTKLGPEKITRDIPNLGEAALRDL- 742

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+ +  G         L   +  E  R              
Sbjct: 743  DEDGIVRVGAEVKAGDILVGRTSFKGETEPSPEERLLRSIFGEKARD------------- 789

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDK 1089
                             E     +  +++ GD    + PGV  VV+V+VA KR +Q GDK
Sbjct: 790  ------VKDTSLRVPPGEGGIVVRTLRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDK 843

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +A RHGNKG+VS+ILP EDMP L DGTPVDIVLNPLGVPSRMN+GQI E HLG A   LG
Sbjct: 844  LANRHGNKGVVSKILPPEDMPHLPDGTPVDIVLNPLGVPSRMNLGQILEIHLGLAAYELG 903

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  + + D  +  +I  L     +          +   D   +  +A   K GV     
Sbjct: 904  MEFITPVFDGASEEEIKELLDQAFEQRWAEREKHGV-GLDRRELEVMARAAKMGVVPE-- 960

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
              D    E + ++ +       G+++LYDG TG+P + P+ +G  Y++KL HMV DK++A
Sbjct: 961  --DLEPREQLKALFKQ------GKAVLYDGRTGQPIEGPIVIGIQYIMKLYHMVEDKMHA 1012

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLT+KSDD+ GR   Y
Sbjct: 1013 RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAFTLQEMLTLKSDDIEGRNAAY 1072

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            E+IV G D      PESF VLVKE+QALGL ++  +   +     E
Sbjct: 1073 EAIVKGQDVPTPSVPESFRVLVKELQALGLDVETLDENERVIDIFE 1118



 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 287/594 (48%), Positives = 396/594 (66%), Gaps = 18/594 (3%)

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                +ALL ++ ++RPGD      A S    L  D  +YDL   GR K+  +L +  P 
Sbjct: 229 EMSPSEALLRLFTILRPGDPPKKDKATSYLVSLLADPRRYDLGEPGRYKVEEKLGIKLPS 288

Query: 427 ------DVRHIRKEDIIAIIKILVDLRNGKGTI--DDIDNLGNRRVRSVGEMLKNQYRLG 478
                 +    +   ++A IK L+ L +G+     DDID+LGNRR+R+VGE+L +Q+R+G
Sbjct: 289 RTILGFEDGEFKDYALLATIKYLLALSSGEEGYEADDIDHLGNRRIRTVGELLADQFRIG 348

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           L RM R ++ER+   + ++  P  LIN +P+ +A+ EFF  SQLSQ +   N L  + H 
Sbjct: 349 LGRMARGVRERMIMGNPEAATPAKLINNRPLAAAIREFFGRSQLSQFKGQTNPLDEMRHK 408

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL ++  +N  GF+
Sbjct: 409 RRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLINSLAAYGLINDLGFV 468

Query: 599 ETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            TPYRKV  G V+    DVVY++A EE+   IAQAN+ +DE+G    + V  R  GE  +
Sbjct: 469 MTPYRKVKKGVVSMNPKDVVYMTATEEDKYTIAQANTPVDENGRIATDRVVARRKGEPEI 528

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V   +++F+D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVP+++AEAP VGTG+
Sbjct: 529 VDASEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQAQAVPVIRAEAPAVGTGI 588

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E  V + S  ++ +   G+V+ VD   IVI       +     +  Y+L +F RSNQ T 
Sbjct: 589 EDRVIRDSLTSVYSDVDGVVKYVDGDTIVI-------EQKNKNLREYKLRRFVRSNQGTT 641

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           ++QRP V VGD++++ D++ADGP+ D G LALG+N+LVA MP+ GYNFED+++ISE ++ 
Sbjct: 642 IDQRPRVNVGDKIKKGDLLADGPAADHGRLALGQNVLVAIMPFDGYNFEDAIIISENLLR 701

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            D +TSIHIE +E+ ARDTKLGPE+ITRDIPN+ E  L+++DE GI+ VGAEV  GDILV
Sbjct: 702 RDHYTSIHIERYEIEARDTKLGPEKITRDIPNLGEAALRDLDEDGIVRVGAEVKAGDILV 761

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           G+ + KGE+  +PEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 762 GRTSFKGETEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTLRLRRGD 815



 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 150/321 (46%), Gaps = 35/321 (10%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF- 68
               R  FG   E+I +P L ++Q  S+   L + +AP +R N GLQAAFK VFP+    
Sbjct: 2   RKTKR--FGSIKEVIPLPPLTQIQVDSFRKALQLEVAPSKRENFGLQAAFKEVFPVEESE 59

Query: 69  --SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
              G  +L+F+ Y    PKF  DDC  +DLTY  PL   L+LI  D            IK
Sbjct: 60  KGRGGLVLDFLEYRLGEPKFGPDDCREKDLTYQAPLYARLQLIHRDSGL---------IK 110

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           E  +++GDLPLMT DG+F+I G  R++VSQ+HRSPG++F  D  RA       +   +IP
Sbjct: 111 EDEVFLGDLPLMTDDGSFIINGADRVIVSQIHRSPGVYFTPDPNRADR-----FVAAVIP 165

Query: 187 D--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG---MDSEEILSTFYPKIVYSQR 241
              +G W+D+EFDS   + +R++ +RK PV   L  LG   +  ++ L  F   +     
Sbjct: 166 LPKRGPWIDLEFDSSGALLMRVN-KRKFPVILLLRVLGHDAVSLKKELGAFPELLTGVLD 224

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                   S A L +   +         G+    +        LL   +   +   G   
Sbjct: 225 ESILEMSPSEALLRLFTIL-------RPGDPPKKDKATSYLVSLLADPRRYDLGEPGRYK 277

Query: 301 --DCLCGLYVAEDIVNGETGE 319
             + L     +  I+  E GE
Sbjct: 278 VEEKLGIKLPSRTILGFEDGE 298


>gi|186660359|gb|ACC86062.1| beta-subunit RNA polymerase [Corynebacterium casei]
          Length = 1054

 Score =  483 bits (1243), Expect = e-134,   Method: Composition-based stats.
 Identities = 318/661 (48%), Positives = 449/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEQQI--RDRFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             + +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGDTIPVNTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV +G+VT++V YL+A EE+   IAQA    D +G+   + +  R   
Sbjct: 485 VNAFGFIETPYRKVENGRVTDEVRYLTADEEDRYSIAQAEVEQDAEGNIIGDRIEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPL++ EAP 
Sbjct: 545 GDIGVTDANGVDYVDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLVRGEAPC 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  ++  +AG+VE V+A  I I   EG  D        Y L KF+R+
Sbjct: 605 VGTGMELRAAYDAGDMVITPKAGVVENVNADLITIMDDEGIRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTNYNQTPLVNMGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++D+ GII +GA+V P
Sbjct: 718 QRIVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRP 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  353 bits (905), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 137/440 (31%), Positives = 205/440 (46%), Gaps = 61/440 (13%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 662  NYNQTPLVNMGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRI 720

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLME 988
            V   ++       H ID  +  +  E    +I    E + RD DD   I+      R  +
Sbjct: 721  VEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIIRIGADVRPGD 779

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                V  +          
Sbjct: 780  ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA--------- 830

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                        +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V ++LP ED
Sbjct: 831  --------RFSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKVLPPED 882

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF+ DGTPVD++LN  GVP RMN+GQ+ E HLGW     G  + +     +   +   L
Sbjct: 883  MPFMADGTPVDVILNTHGVPRRMNIGQVLELHLGWLAK-TGWTVDT-----EDPNNEELL 936

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
            ++   ++    + +                        +TPVFDGA  E +  +L  +  
Sbjct: 937  KTLPPELYDVPADSLT----------------------ATPVFDGATNEELTRLLASSKP 974

Query: 1229 DESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +  G        ++ L+DG +GEP+  P++VGY+YMLKL+H++ +K++ARSTG YS++TQ
Sbjct: 975  NRDGDVMVNENGKAQLFDGRSGEPYMYPISVGYMYMLKLHHLIDEKIHARSTGPYSMITQ 1034

Query: 1281 QPLGGKSNRGGQRLGEMEVW 1300
            QPLGGK+  GGQR GEMEVW
Sbjct: 1035 QPLGGKAQFGGQRFGEMEVW 1054



 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 95/383 (24%), Positives = 171/383 (44%), Gaps = 36/383 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +               + R + GL+     + P
Sbjct: 16  RYSFAKISEPIAVPGLLDLQLESFSWLIGTPEWRERQQEERGAEARISSGLEDILDELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT +GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDEGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEQQIRDRFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI-- 298
           D       A   +   +        D  + ++++         L +  + K  + LG+  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLDNSFFRAKRYDLARVGRYKVNRKLGLGG 304

Query: 299 TSDCLCGLY------VAEDIVNGETGEIYIEAGDVID----EKSLEEIFHSEIRDIPILY 348
             + L  L         E +V   TGE  ++A +          ++   +  +R +  L 
Sbjct: 305 DHEGLMTLTEEDIAVTLEYLVRLHTGEREMKAPNGDTIPVNTDDIDHFGNRRLRTVGELI 364

Query: 349 VDSVNNNAYIRNTLVTDKNKDRK 371
            + V         +V ++   + 
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQD 387


>gi|196051513|gb|ACG68890.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 513

 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 250/516 (48%), Positives = 354/516 (68%), Gaps = 3/516 (0%)

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
            R+IP +G W D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +
Sbjct: 1   ARVIPYRGSWFDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVK 60

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  +
Sbjct: 61  DQTLLMELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVE 117

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  T
Sbjct: 118 YIVGKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSET 177

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  + 
Sbjct: 178 LRIDSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIG 237

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R
Sbjct: 238 REDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR 297

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+
Sbjct: 298 VERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRI 357

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETP
Sbjct: 358 SALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETP 417

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL+  R  GE  L PRE  
Sbjct: 418 YRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADELITARQKGESGLHPREHA 477

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQ
Sbjct: 478 QYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQ 513


>gi|46361014|gb|AAS89240.1| RpoB [Corynebacterium riegelii]
          Length = 1060

 Score =  483 bits (1242), Expect = e-133,   Method: Composition-based stats.
 Identities = 333/756 (44%), Positives = 471/756 (62%), Gaps = 46/756 (6%)

Query: 233 YPKIVYSQRGDFWC-FPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           +  + Y+           SA   +    +++   +I +    I       E G  + +G 
Sbjct: 95  FEDVKYTIEEAKDKDINYSAPLYVTAEFINNDTQEIKSQTVFIGDFPLMTEKGTFIVNGT 154

Query: 285 LKSLKEKGVKFLGITSDCLCG----LYVAEDIVNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    V    G              +       
Sbjct: 155 ERVVVSQLVRSPGVYFDETIDKSTERPLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRR 214

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +         I   +    +  +  TL +D   +  +ALL+IYR  RPG+  T 
Sbjct: 215 QPVTVLLKALGWTTEQI--TERFGFSEIMMATLESDGVANTDEALLEIYRKQRPGEQPTR 272

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRN 448
            +A+S+    FF + +YDL+ VGR K+N +L L    D +  + +EDI   ++ LV L  
Sbjct: 273 DLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHA 332

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+  +            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 333 GESEMTSPSGEIIPISTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAE 392

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +A+ EFF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+
Sbjct: 393 SITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGI 452

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ +L S+ARVN +GFIETPY+KV DGK+T+ V Y
Sbjct: 453 EVRDVHPSHYGRMCPIETPEGPNIGLIGALASYARVNPFGFIETPYQKVNDGKLTDQVDY 512

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIA 675
           L+A EE+   IAQA + +D+DG+ T E +  R   G+  +V  + +D++D SP+Q+VS+A
Sbjct: 513 LTADEEDRYAIAQAATPMDKDGNLTGERIEVRLKDGDIGVVGPKGVDYLDISPRQMVSVA 572

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQ+QAVPLL+AEA +V TGME   A  +G  +++ +AG+V
Sbjct: 573 TAMIPFLEHDDANRALMGANMQKQAVPLLRAEAAYVATGMEQRAAYDAGDTVISPKAGVV 632

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V    I +   EG       G D Y L  F+R+NQ TC NQ P+V  GD V    +IA
Sbjct: 633 ETVTGDYITVMDDEG-------GRDTYMLRTFERTNQGTCYNQTPIVSQGDRVEAGQVIA 685

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G++ALGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTK
Sbjct: 686 DGPGTKDGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTK 745

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNVSE+ LK++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 746 LGAEEITREIPNVSEDVLKDLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRA 805

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTSL+VP G  G V+ VR F R   D
Sbjct: 806 IFGEKAREVRDTSLKVPHGEQGKVIAVRRFAREDDD 841



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 149/437 (34%), Positives = 209/437 (47%), Gaps = 61/437 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 671  IVSQGDRVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 730  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +     ++  R  
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAREVRDT-------------SLKVPHGEQGKVIAVR-- 833

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 834  --RFAREDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D K    +  L   L  
Sbjct: 892  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYD 948

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 949  VPANSLT-------------------------ATPVFDGATNDEIAGLLANSKPNRDGDV 983

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 984  MVDENGKTMLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCIQ 1303
            +  GGQR GEMEVW +Q
Sbjct: 1044 AQFGGQRFGEMEVWAMQ 1060



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 95/389 (24%), Positives = 170/389 (43%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +                 R   GL+   + + 
Sbjct: 18  ERYSFAKINEPITVPGLLDVQLESFAWLVGTSEWREREQQLRGETARVTSGLEDILEEIS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +++   +D+ Y+ PL +T   I  D          +
Sbjct: 78  PIQDYSGNMSLSLSEPRFEDVKYTIEEAKDKDINYSAPLYVTAEFINND---------TQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT+ GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 129 EIKSQTVFIGDFPLMTEKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMATLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 247 SDGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKVNRKLGLG 306

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +   +GEI       I    ++   +  +R
Sbjct: 307 GDHDGLMTLTEEDIATTLEYLVRLHAGESEMTSPSGEII-----PISTDDIDHFGNRRLR 361

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 362 TVGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|15805937|ref|NP_294636.1| DNA-directed RNA polymerase subunit beta [Deinococcus radiodurans R1]
 gi|6458635|gb|AAF10490.1|AE001944_1 DNA-directed RNA polymerase, beta subunit [Deinococcus radiodurans
            R1]
          Length = 1179

 Score =  482 bits (1241), Expect = e-133,   Method: Composition-based stats.
 Identities = 190/590 (32%), Positives = 283/590 (47%), Gaps = 40/590 (6%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSML----------ISERMVSEDVFTSIHIEEFEV 849
                  +    ++ A  P  G   E  ++          ++ R+   D          + 
Sbjct: 610  MGSNMQSQAVPLVRADSPAVGTGVERRVVTDSGTSVVSDVNGRVSYVDARAIQVTLSEDH 669

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               +   G       I         N+D+  I+ VG EV  G ++      +    +   
Sbjct: 670  RELNMNAGNVRTFELIRFTRSNQGTNLDQHPIVSVGDEVKVGQVIADGPASER-GRLALG 728

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + +  AI      +  D        ++  +V    +    I+K+E      +   E + R
Sbjct: 729  QNITIAIMPFDGFNFEDAIC-----INEDLVRQDFYTSVHIEKDEIEARDTKLGPEKITR 783

Query: 970  DK----DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            D     +     LD +   R+   +   + + G   FK  +  + +      RS + + A
Sbjct: 784  DIPGLSEAALRDLDEDGIVRVGAEVKPGDILVGKTSFKGESEPTPE--ERLLRSIFGEKA 841

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             + +     V+S +                   +   G D+ PGV  +V+V+VA KR +Q
Sbjct: 842  REVKDTSLRVQSGQGGIVVKTVRFR--------RGDEGVDLKPGVREMVRVYVAQKRQLQ 893

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK+A RHGNKG+VS+I+  EDMP+L+DGTPVDIV NPLGVPSRMN+GQI ETHLG   
Sbjct: 894  VGDKVANRHGNKGVVSKIVRPEDMPYLEDGTPVDIVFNPLGVPSRMNLGQILETHLGEVA 953

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G+K ++ + D      I  +   +       +  +   + D      +    K G  
Sbjct: 954  RLTGQKFETPVFDSVTEATIKEMLE-VAAAERLQARKDDGFELDKREQEVLDRAGKLG-- 1010

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                V D   ++     +++A    +G+SILYDG TGEP   PV VG +Y++KL HMV D
Sbjct: 1011 ----VIDAPGDDYEKGQMQLA---RTGKSILYDGRTGEPISGPVVVGIMYVMKLYHMVED 1063

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+VLQEMLTIKSDD+ GR
Sbjct: 1064 KLHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHVLQEMLTIKSDDIDGR 1123

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
               Y+SIV G +   +  PESF VLVKE+ +LGL +++ +   K     E
Sbjct: 1124 DAAYQSIVKGEEVSGSTIPESFKVLVKELHSLGLDVEVLDHGDKAVDIFE 1173



 Score =  440 bits (1131), Expect = e-120,   Method: Composition-based stats.
 Identities = 299/607 (49%), Positives = 408/607 (67%), Gaps = 24/607 (3%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---- 426
            +ALL ++ V+RPGD      A      L  D  +YDL   GR KMN +L +   +    
Sbjct: 267 DEALLRLFTVLRPGDPPKRDKAIQYLFGLLADPRRYDLGEPGRFKMNTKLGVQRQERTLL 326

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVG 468
             +        ++  I+ L+ L+ G  T+                DDID+LGNRRVR+VG
Sbjct: 327 KFEDGKFSDAGLVDTIRYLMALQQGLETVPMVDEDGVVTDVPVAEDDIDHLGNRRVRTVG 386

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L +Q R+G+ RM R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLSQ ++ 
Sbjct: 387 ELLADQLRVGMGRMARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLSQFKDQ 446

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS + H RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL+S
Sbjct: 447 TNPLSDLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLSS 506

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +A+VN  GFI  PYRKV DGKVTN V Y++A  E+   IAQANS L+ED +F +E V  R
Sbjct: 507 YAKVNDLGFIMAPYRKVEDGKVTNQVEYMTADIEDRYTIAQANSPLNEDNTFADERVLAR 566

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ +L   +++D++D SPKQ+VSI  SLIPFLE+DD+NR LMG NMQ QAVPL++A++
Sbjct: 567 RKGDPLLYTPDEVDYMDVSPKQIVSINTSLIPFLEHDDANRALMGSNMQSQAVPLVRADS 626

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVD--AIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           P VGTG+E  V   SG ++V+   G V  VD  AI++ +     +L+ +   V  + L++
Sbjct: 627 PAVGTGVERRVVTDSGTSVVSDVNGRVSYVDARAIQVTLSEDHRELNMNAGNVRTFELIR 686

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ T ++Q P+V VGDEV+   +IADGP+++ G LALG+N+ +A MP+ G+NFED+
Sbjct: 687 FTRSNQGTNLDQHPIVSVGDEVKVGQVIADGPASERGRLALGQNITIAIMPFDGFNFEDA 746

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           + I+E +V +D +TS+HIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI+ VGA
Sbjct: 747 ICINEDLVRQDFYTSVHIEKDEIEARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGA 806

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVGK + KGES  TPEE+LLR+IFGEKA +V+DTSLRV SG  G VV    F 
Sbjct: 807 EVKPGDILVGKTSFKGESEPTPEERLLRSIFGEKAREVKDTSLRVQSGQGGIVVKTVRFR 866

Query: 947 RHGIDKN 953
           R     +
Sbjct: 867 RGDEGVD 873



 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/238 (36%), Positives = 132/238 (55%), Gaps = 15/238 (6%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +        R  FG   E+I +P+L EVQ  S+  FL  + APD+R + GLQ+AF+ V
Sbjct: 21  MTLSKTPPRIER--FGDITEVIPLPNLTEVQVNSFKAFLQDDKAPDQREDVGLQSAFREV 78

Query: 63  FPI-TAFSGA---AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           FPI  +  G     +L+F+ Y    P++  ++C  +DLTY  PL + L LI  D     G
Sbjct: 79  FPIDESEKGRSTGMVLDFIEYRLGEPEYSPEECREKDLTYEAPLYVKLELIHKDTGVIKG 138

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            K      E  +++G+LPLMT DG+F+I G  R+V+SQ+HRSPG++F           K 
Sbjct: 139 FK-PDSPPESWVFLGNLPLMTFDGSFIINGADRVVISQIHRSPGVYFTSS----YKGIKK 193

Query: 179 LYACRIIPD--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
            Y   IIP   +G W+++EF + D++ ++++ +RK PV+  L  LGMD   I + F  
Sbjct: 194 QYTAAIIPMPKRGPWIELEF-AGDVLEMKVN-KRKFPVSLLLRVLGMDDASIRALFTE 249


>gi|46361018|gb|AAS89242.1| RpoB [Corynebacterium singulare]
          Length = 1060

 Score =  482 bits (1240), Expect = e-133,   Method: Composition-based stats.
 Identities = 324/661 (49%), Positives = 451/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 192 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIK----ERFGFSELMMSTLES 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+++ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             + +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DHEGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGETISIHTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT+ V YL+A EE+   IAQA    D DG+ T + +  R   
Sbjct: 488 VNAFGFIETPYRKVVDGKVTDQVEYLTADEEDRFAIAQAEVEKDADGTLTGDRIEVRLKD 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP+
Sbjct: 548 GDIGVTDAAGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPY 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AG+VE V A  I I   EG  D        Y L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDLIITPKAGVVENVTADLITIMDDEGQRD-------TYMLRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNT  NQ PLV +GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 661 NQNTNYNQTPLVSLGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V ED+ TSIHIEE E+ ARDTKLGPEEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 721 QRIVEEDILTSIHIEEHEIDARDTKLGPEEITREIPNVSDDVLRDLDERGIVRIGADVRA 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVSRFSREDD 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 156/540 (28%), Positives = 233/540 (43%), Gaps = 60/540 (11%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 567  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPYVGTGMEQRAAYDAGDLIIT 626

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 627  PKAGVVENVTADLITIMDDEGQRDTYMLRKFERTNQNTNYNQTPLVSLGDRVEAGQVLAD 686

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   ++       H ID  +  
Sbjct: 687  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSIHIEEHEIDARDTK 745

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 746  LGPEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 805

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                        ET K I   RF  + +     DD+ PGV 
Sbjct: 806  IFGEKAREVRDT------------SMKVPHGETGKVIGVSRFSREDD-----DDLAPGVN 848

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RM
Sbjct: 849  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRM 908

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G KI +     +   +   L+   E++      +         
Sbjct: 909  NIGQVLEVHLGWLAHA-GWKIDT-----EDPANADLLKKLPEELYDVPPESLT------- 955

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                           +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +GE
Sbjct: 956  ---------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGE 1000

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 1001 PYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060



 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 166/388 (42%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  SY   +               D R   GL+   + + P
Sbjct: 19  RYSFAKISEPIAVPGLLDLQLDSYAWLIGTPEWREREQAERGDDARVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 79  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ ++
Sbjct: 130 IKSQTVFIGDFPMMTDKGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHSVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIKERFGFSELMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        D  + ++++         L K  + K  +      
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLAQALLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+  E  +    GE        I    ++   +  +R 
Sbjct: 308 DHEGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGETI-----SIHTDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|46360986|gb|AAS89226.1| RpoB [Corynebacterium simulans]
          Length = 1058

 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 325/661 (49%), Positives = 449/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + I+         L +        I     +    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQI----RERFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMTAPNGETIAIHTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DGKVT++V YL+A EE+   IAQA    + DG+     +  R   
Sbjct: 485 VNAFGFIETPYRKVVDGKVTDEVEYLTADEEDKYAIAQAEIEKEADGTIVGTRIEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAPF
Sbjct: 545 GDIGVTDASGVDYVDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPF 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  +AGIVE V A  I I   EG  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLIITPKAGIVENVTADLITIMDDEGQRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV++G  V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTNYNQTPLVELGQRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +DV TSIHIEE E+ ARDTKLG EEITR+IPNVS++ L+++DE GII +GA+V  
Sbjct: 718 QRIVEDDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSDDVLRDLDERGIIRIGADVRA 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGVARFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 152/541 (28%), Positives = 227/541 (41%), Gaps = 60/541 (11%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSE 836
            Q   V            A+              ++ +  P+ G   E         ++  
Sbjct: 564  QMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIIT 623

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +     +++      G  +              N ++  ++ +G  V  G +L  
Sbjct: 624  PKAGIVENVTADLITIMDDEGQRDTYMLRKFERTNQGTNYNQTPLVELGQRVEAGQVLAD 683

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                     M+    LL A    +  +  D  +     V   V+       H ID  +  
Sbjct: 684  GPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEDDVLTSIHIEEHEIDARDTK 742

Query: 957  ISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  E    +I  ++ D     DE+ I+      R  +IL G+    G         L   
Sbjct: 743  LGAEEITREIPNVSDDVLRDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRA 802

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +  E  R                V  +                      +  DD+ PGV 
Sbjct: 803  IFGEKAREVRDTSMKVPHGENGKVIGVA-----------------RFSREDDDDLAPGVN 845

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ DGTPVD++LN  GVP RM
Sbjct: 846  EMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMADGTPVDVILNTHGVPRRM 905

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLGW     G K+           +   L++  E++                
Sbjct: 906  NIGQVLEVHLGWLAHA-GWKVDV-----DDPANAELLKTLPEELYDVP------------ 947

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGE 1243
                      +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GE
Sbjct: 948  ----------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGE 997

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +Q
Sbjct: 998  PYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALQ 1057

Query: 1304 A 1304
            A
Sbjct: 1058 A 1058



 Score =  305 bits (780), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 168/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +              P+ R   GL+   + + P
Sbjct: 16  RYSFAKINEPIAVPGLLDLQLDSFAWLIGSPEWREREQAERGPEARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPMMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWSEEQIRERFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE        I    ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMTAPNGETIA-----IHTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|261825394|gb|ACX94446.1| RNA polymerase beta subunit [Bacillus sp. fiply 3A]
          Length = 481

 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 175/546 (32%), Positives = 276/546 (50%), Gaps = 75/546 (13%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +   +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+
Sbjct: 1   LTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQ 50

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K
Sbjct: 51  DISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NK 101

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +
Sbjct: 102 ETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGF 158

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
              +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EIL          
Sbjct: 159 TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLR 218

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK--------E 290
              D      S   L+           +  GE   +E+ K L        K         
Sbjct: 219 NTLDKDNTENSDKALL------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGR 272

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L    +AE +V+ ETGEI  E G ++D ++L++             V 
Sbjct: 273 YKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDK-------------VL 319

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
               N      L  +      + +L   ++  P D                         
Sbjct: 320 PYLENGIGFRKLYPNGGVVEDEVMLQSIKIYAPTD------------------------A 355

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            G   +N+  N    + +++I   DII+ I    +L +G G  DDID+LGNRR+RSV E+
Sbjct: 356 EGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVCEL 415

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PV++++ EFF SSQLSQ  +  N
Sbjct: 416 LQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTN 475

Query: 531 SLSRIT 536
            L+ +T
Sbjct: 476 PLAELT 481


>gi|11465718|ref|NP_053862.1| RNA polymerase beta subunit [Porphyra purpurea]
 gi|1710671|sp|P51252|RPOB_PORPU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|1276718|gb|AAC08138.1| DNA-directed RNA polymerase beta chain [Porphyra purpurea]
          Length = 1143

 Score =  481 bits (1238), Expect = e-133,   Method: Composition-based stats.
 Identities = 316/683 (46%), Positives = 447/683 (65%), Gaps = 17/683 (2%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           + ++GK++ S  L S +   +KF       +   ++  D  +     I++ A  +   + 
Sbjct: 169 IDKNGKQIYSASLISNRGSWLKFEIDPKGEI---WIRIDKTHKVNAYIFLRAIGLNKNEI 225

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN-KDRKDALLDIYRVMRPGDVSTFSV 391
            + +         I    S +     +     D      ++ALL +Y  +RP + +T  V
Sbjct: 226 QKGLSKY---AFLISASQSYSVKELAKEIGKNDIEEVTDEEALLIVYSKLRPNEPATVPV 282

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK- 450
           A+ M    FFD  +YDL  VGR K+N +L L+ P   R +  +DI++ I  L+++++   
Sbjct: 283 AKQMLYSRFFDPKRYDLGEVGRYKINKKLGLNIPKTFRVLSPQDILSSIDYLINIKDKNS 342

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           G +DDID+LGNRRVRSVGE+L+NQ+R+GL R+ER I+ER+   DIDS+   +LIN KP++
Sbjct: 343 GNLDDIDHLGNRRVRSVGELLQNQFRVGLNRLERIIRERMMICDIDSLSLSNLINPKPLI 402

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           ++V EFF SSQLSQ  +  N ++ +TH RR+SALG GG  + RAG  +RD+HP+HYGRIC
Sbjct: 403 ASVREFFGSSQLSQFMDQTNPVAELTHKRRISALGPGGFNKDRAGFAVRDLHPSHYGRIC 462

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIA 628
           P ET EG N GL+ SL + ARVN +GFIETP+  V +G+V  +N+ +YL+A EE++  +A
Sbjct: 463 PIETPEGPNAGLIGSLATCARVNIFGFIETPFYPVHNGQVDYSNNPIYLTADEEDDFRVA 522

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
             +  ++       +++  R   E +     ++D+I  SP QV+S A SLIPFLE+DD+N
Sbjct: 523 PGDVKVNVQNYIEGDIIPVRYRQEFVTTIPNQVDYIAISPIQVISAATSLIPFLEHDDAN 582

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPLL  E P +GTG+E+ +A+ SG  ++++ +G V  V A +I I+  
Sbjct: 583 RALMGSNMQRQAVPLLYPEKPIIGTGLETKIARDSGMVVISRTSGCVNYVSANKIGIQDN 642

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            G          +YRL K+ RSNQ+TC+NQRP+V VG+++     +ADG STD G++ALG
Sbjct: 643 NGRTV-------LYRLKKYYRSNQDTCINQRPIVWVGEKIVVGQTLADGASTDCGEIALG 695

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           RN+LVA+MPW GYN+ED+ LISER+V EDV+TSIHIE++EV  R TKLGPEEITR+IPNV
Sbjct: 696 RNILVAYMPWEGYNYEDAFLISERLVYEDVYTSIHIEKYEVECRQTKLGPEEITREIPNV 755

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           S+  LK++D  GI+  G+ V  GDILVGKITPKGE+   PE KLLRAIFGEKA DVRDTS
Sbjct: 756 SDHSLKDLDRNGIVVCGSWVEAGDILVGKITPKGEADQLPEGKLLRAIFGEKARDVRDTS 815

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           LR+P+   G VV+VR+F R   D
Sbjct: 816 LRLPNAAKGRVVNVRVFTRQKGD 838



 Score =  470 bits (1210), Expect = e-130,   Method: Composition-based stats.
 Identities = 162/458 (35%), Positives = 240/458 (52%), Gaps = 44/458 (9%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIELLARDK--DDEQVILDRN 981
            R+  +           D  + +   + ++  + I +E+ ++E        ++    +   
Sbjct: 696  RNILVAYMPWEGYNYEDAFLISERLVYEDVYTSIHIEKYEVECRQTKLGPEEITREIPNV 755

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                L ++      V G    +   +L   +  +    Q  +  +           ++  
Sbjct: 756  SDHSLKDLDRNGIVVCGSW-VEAGDILVGKITPKGEADQLPEGKLLRAIFGEKARDVRDT 814

Query: 1042 YETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                 +  + R  N ++   Q GD++PPG   +++V+VA KR IQ GDKMAGRHGNKGI+
Sbjct: 815  SLRLPNAAKGRVVNVRVFTRQKGDELPPGTNAMIRVYVAQKRKIQVGDKMAGRHGNKGII 874

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            SRILP +DMP+L DGTPVDIVLNPLGVPSRMNVGQ+FE  LG A   L K+ K +  D  
Sbjct: 875  SRILPKQDMPYLCDGTPVDIVLNPLGVPSRMNVGQVFECLLGLAGGYLDKRFKIIPFD-- 932

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                         ++ G  +    ++    ++ +    +W         +F+        
Sbjct: 933  -------------EMYGAEASRALVNRKLQEASILTKNKW---------IFND------- 963

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+  ++DG TGEPFD PVT+G  YMLKL H+V DK++ARSTG YSLVTQ
Sbjct: 964  --------QHPGKMQVFDGRTGEPFDNPVTIGRAYMLKLVHLVDDKIHARSTGPYSLVTQ 1015

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QPLGG++  GGQRLGEMEVW ++A+GAAY LQE+LT+KSDD+  R     +IV G    +
Sbjct: 1016 QPLGGRAQHGGQRLGEMEVWALEAFGAAYTLQELLTVKSDDMQARNEALNAIVKGKPIPK 1075

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
             GTPESF VL++E+Q+LGL I +   +   + +   + 
Sbjct: 1076 PGTPESFKVLMRELQSLGLDIAVHKLKLFENGQRRTVE 1113



 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 93/492 (18%), Positives = 184/492 (37%), Gaps = 66/492 (13%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEF--VSYEFD 82
           +PDL+E+Q+ S+  FL+          EGL       FP I+  +    L+     Y+  
Sbjct: 12  LPDLVEIQRDSFKWFLL----------EGLTEVL-EFFPNISDPTSRLELQLFGKEYKIK 60

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS------------- 129
            P++ V     RD TY+  + +  +L   D+D  +  ++ K IK                
Sbjct: 61  FPRYSVRQAKSRDRTYSAQIYVPAKLTRKDIDLPSKDQN-KTIKSLDLSSNHLQFSAEKQ 119

Query: 130 ----------IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
                     +++GDLP+MT  GTF++ G +R++++Q+ RSPGI++  D  +   +GK +
Sbjct: 120 IKNKKYKKRLVFIGDLPIMTNRGTFIVSGTERVIINQIIRSPGIYYKQDIDK---NGKQI 176

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-------TF 232
           Y+  +I ++G W+  E D K  I +RID+  KV    FL A+G++  EI           
Sbjct: 177 YSASLISNRGSWLKFEIDPKGEIWIRIDKTHKVNAYIFLRAIGLNKNEIQKGLSKYAFLI 236

Query: 233 YPKIVYS-QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKE 290
                YS +            ++     +      +   E   +   K++        K 
Sbjct: 237 SASQSYSVKELAKEIGKNDIEEVTDEEALLIVYSKLRPNEPATVPVAKQMLYSRFFDPKR 296

Query: 291 KGVKFLGITS-DCLCGLYVAE--------DIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             +  +G    +   GL + +        DI++     I I+  +  +   ++ + +  +
Sbjct: 297 YDLGEVGRYKINKKLGLNIPKTFRVLSPQDILSSIDYLINIKDKNSGNLDDIDHLGNRRV 356

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R +  L  +           ++ ++        L +  ++ P      +     F     
Sbjct: 357 RSVGELLQNQFRVGLNRLERIIRERMMICDIDSLSLSNLINPK--PLIASVREFFGSSQL 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                  + V  +    R++   P       K+     ++ L     G+  I  I+    
Sbjct: 415 SQFMDQTNPVAELTHKRRISALGPGGF---NKDRAGFAVRDLHPSHYGR--ICPIETPEG 469

Query: 462 RRVRSVGEMLKN 473
                +G +   
Sbjct: 470 PNAGLIGSLATC 481


>gi|46360968|gb|AAS89217.1| RpoB [Corynebacterium flavescens]
          Length = 1100

 Score =  481 bits (1237), Expect = e-133,   Method: Composition-based stats.
 Identities = 318/661 (48%), Positives = 446/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   D    +  + +TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEQQI--KDRFGFSELMMSTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+ +  FF + +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMTAPNGEQIAIHTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +H NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDHNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHASHYGRMCPIETPEGPNIGLIGSLASYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPYRKV DG VT+ V YL+A EE+   IAQA    D +G+ T + V  R   
Sbjct: 485 VNAFGFIETPYRKVIDGCVTDQVDYLTADEEDRFAIAQAEIEKDAEGNITADRVEVRLKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +     +D++D SP+Q+VS+  ++IPFLE+DD+NR LMG NMQ+QAVPL+++EAP 
Sbjct: 545 GDIGVTAAANVDYVDVSPRQMVSVGTAMIPFLEHDDANRALMGANMQKQAVPLVRSEAPL 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  ++  ++G+VE V A  I +   EG  D        Y L KF+R+
Sbjct: 605 VGTGMEQRAAYDAGDLVITPKSGVVENVSADLITVMDDEGQRD-------TYMLRKFERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV +G  V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTNYNQTPLVSLGQRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V EDV TSIHIEE E+ ARDTKLG EEITR+IPNVS++ L+++DE GI+ +GA+V  
Sbjct: 718 QRIVEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSDDVLRDLDERGIVRIGADVRA 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGVAHFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 175/485 (36%), Positives = 243/485 (50%), Gaps = 59/485 (12%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 662  NYNQTPLVSLGQRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRI 720

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEI 989
            V   V+       H ID  +  +  E    +I  ++ D     DE+ I+      R  +I
Sbjct: 721  VEEDVLTSIHIEEHEIDARDTKLGAEEITREIPNVSDDVLRDLDERGIVRIGADVRAGDI 780

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                V  +           
Sbjct: 781  LVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGVAH--------- 831

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                       +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDM
Sbjct: 832  --------FSREDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPPEDM 883

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF+ DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+       +   +   L+
Sbjct: 884  PFMADGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHA-GWKVDV-----EDPANADLLK 937

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
            +  E++    + +                        +TPVFDGA  E I  +L  +  +
Sbjct: 938  TLPEELYEVPADSLT----------------------ATPVFDGASNEEIARLLASSKPN 975

Query: 1230 ESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              G        ++ L+DG +GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQ
Sbjct: 976  RDGDVLVDEHGKAQLFDGRSGEPYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQ 1035

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + 
Sbjct: 1036 PLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDP 1095

Query: 1342 GTPES 1346
            G PES
Sbjct: 1096 GIPES 1100



 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 94/388 (24%), Positives = 166/388 (42%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+   +               D R   GL+   + + P
Sbjct: 16  RYSFAKISEPIAVPGLLDVQLDSFAWLVGTPEWRERQQAERGEDARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I             ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFI---------NNETQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPIMTDKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   ++I   F    +   +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEQQIKDRFGFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE        I    ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMTAPNGEQIA-----IHTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|158523290|sp|Q9RVV9|RPOB_DEIRA RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
            subunit beta; AltName: Full=RNA polymerase subunit beta;
            AltName: Full=Transcriptase subunit beta
          Length = 1159

 Score =  480 bits (1236), Expect = e-133,   Method: Composition-based stats.
 Identities = 190/590 (32%), Positives = 283/590 (47%), Gaps = 40/590 (6%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSML----------ISERMVSEDVFTSIHIEEFEV 849
                  +    ++ A  P  G   E  ++          ++ R+   D          + 
Sbjct: 590  MGSNMQSQAVPLVRADSPAVGTGVERRVVTDSGTSVVSDVNGRVSYVDARAIQVTLSEDH 649

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               +   G       I         N+D+  I+ VG EV  G ++      +    +   
Sbjct: 650  RELNMNAGNVRTFELIRFTRSNQGTNLDQHPIVSVGDEVKVGQVIADGPASER-GRLALG 708

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + +  AI      +  D        ++  +V    +    I+K+E      +   E + R
Sbjct: 709  QNITIAIMPFDGFNFEDAIC-----INEDLVRQDFYTSVHIEKDEIEARDTKLGPEKITR 763

Query: 970  DK----DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            D     +     LD +   R+   +   + + G   FK  +  + +      RS + + A
Sbjct: 764  DIPGLSEAALRDLDEDGIVRVGAEVKPGDILVGKTSFKGESEPTPE--ERLLRSIFGEKA 821

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             + +     V+S +                   +   G D+ PGV  +V+V+VA KR +Q
Sbjct: 822  REVKDTSLRVQSGQGGIVVKTVRFR--------RGDEGVDLKPGVREMVRVYVAQKRQLQ 873

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK+A RHGNKG+VS+I+  EDMP+L+DGTPVDIV NPLGVPSRMN+GQI ETHLG   
Sbjct: 874  VGDKVANRHGNKGVVSKIVRPEDMPYLEDGTPVDIVFNPLGVPSRMNLGQILETHLGEVA 933

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G+K ++ + D      I  +   +       +  +   + D      +    K G  
Sbjct: 934  RLTGQKFETPVFDSVTEATIKEMLE-VAAAERLQARKDDGFELDKREQEVLDRAGKLG-- 990

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                V D   ++     +++A    +G+SILYDG TGEP   PV VG +Y++KL HMV D
Sbjct: 991  ----VIDAPGDDYEKGQMQLA---RTGKSILYDGRTGEPISGPVVVGIMYVMKLYHMVED 1043

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+VLQEMLTIKSDD+ GR
Sbjct: 1044 KLHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHVLQEMLTIKSDDIDGR 1103

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
               Y+SIV G +   +  PESF VLVKE+ +LGL +++ +   K     E
Sbjct: 1104 DAAYQSIVKGEEVSGSTIPESFKVLVKELHSLGLDVEVLDHGDKAVDIFE 1153



 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 299/607 (49%), Positives = 408/607 (67%), Gaps = 24/607 (3%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---- 426
            +ALL ++ V+RPGD      A      L  D  +YDL   GR KMN +L +   +    
Sbjct: 247 DEALLRLFTVLRPGDPPKRDKAIQYLFGLLADPRRYDLGEPGRFKMNTKLGVQRQERTLL 306

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVG 468
             +        ++  I+ L+ L+ G  T+                DDID+LGNRRVR+VG
Sbjct: 307 KFEDGKFSDAGLVDTIRYLMALQQGLETVPMVDEDGVVTDVPVAEDDIDHLGNRRVRTVG 366

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L +Q R+G+ RM R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLSQ ++ 
Sbjct: 367 ELLADQLRVGMGRMARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLSQFKDQ 426

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS + H RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL+S
Sbjct: 427 TNPLSDLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLSS 486

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +A+VN  GFI  PYRKV DGKVTN V Y++A  E+   IAQANS L+ED +F +E V  R
Sbjct: 487 YAKVNDLGFIMAPYRKVEDGKVTNQVEYMTADIEDRYTIAQANSPLNEDNTFADERVLAR 546

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ +L   +++D++D SPKQ+VSI  SLIPFLE+DD+NR LMG NMQ QAVPL++A++
Sbjct: 547 RKGDPLLYTPDEVDYMDVSPKQIVSINTSLIPFLEHDDANRALMGSNMQSQAVPLVRADS 606

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVD--AIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           P VGTG+E  V   SG ++V+   G V  VD  AI++ +     +L+ +   V  + L++
Sbjct: 607 PAVGTGVERRVVTDSGTSVVSDVNGRVSYVDARAIQVTLSEDHRELNMNAGNVRTFELIR 666

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ T ++Q P+V VGDEV+   +IADGP+++ G LALG+N+ +A MP+ G+NFED+
Sbjct: 667 FTRSNQGTNLDQHPIVSVGDEVKVGQVIADGPASERGRLALGQNITIAIMPFDGFNFEDA 726

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           + I+E +V +D +TS+HIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI+ VGA
Sbjct: 727 ICINEDLVRQDFYTSVHIEKDEIEARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGA 786

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVGK + KGES  TPEE+LLR+IFGEKA +V+DTSLRV SG  G VV    F 
Sbjct: 787 EVKPGDILVGKTSFKGESEPTPEERLLRSIFGEKAREVKDTSLRVQSGQGGIVVKTVRFR 846

Query: 947 RHGIDKN 953
           R     +
Sbjct: 847 RGDEGVD 853



 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/238 (36%), Positives = 132/238 (55%), Gaps = 15/238 (6%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +        R  FG   E+I +P+L EVQ  S+  FL  + APD+R + GLQ+AF+ V
Sbjct: 1   MTLSKTPPRIER--FGDITEVIPLPNLTEVQVNSFKAFLQDDKAPDQREDVGLQSAFREV 58

Query: 63  FPI-TAFSGA---AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           FPI  +  G     +L+F+ Y    P++  ++C  +DLTY  PL + L LI  D     G
Sbjct: 59  FPIDESEKGRSTGMVLDFIEYRLGEPEYSPEECREKDLTYEAPLYVKLELIHKDTGVIKG 118

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            K      E  +++G+LPLMT DG+F+I G  R+V+SQ+HRSPG++F           K 
Sbjct: 119 FK-PDSPPESWVFLGNLPLMTFDGSFIINGADRVVISQIHRSPGVYFTSS----YKGIKK 173

Query: 179 LYACRIIPD--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
            Y   IIP   +G W+++EF + D++ ++++ +RK PV+  L  LGMD   I + F  
Sbjct: 174 QYTAAIIPMPKRGPWIELEF-AGDVLEMKVN-KRKFPVSLLLRVLGMDDASIRALFTE 229


>gi|182684896|ref|YP_001836643.1| hypothetical protein SPCG_1925 [Streptococcus pneumoniae CGSP14]
 gi|182630230|gb|ACB91178.1| hypothetical protein SPCG_1925 [Streptococcus pneumoniae CGSP14]
          Length = 824

 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 167/507 (32%), Positives = 238/507 (46%), Gaps = 77/507 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD +    +      M   +  + A    +  +  D  +     V   V 
Sbjct: 346  LVKVGDVVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVY 404

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  +IL G+  
Sbjct: 405  TSVHLEEYESETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVT 464

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G K       L   +  +  R           +V+     +    +     +      
Sbjct: 465  PKGEKDLSAEERLLHAIFGDKSR-----------EVRDTSLRVPHGADGVVRDV------ 507

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 508  KIFTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 567

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 568  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWSTVKEAGM- 626

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    +    ++L        G   
Sbjct: 627  ----------------------------------------DSDAKTIL------YDG--- 637

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL+HMV DK++ARS G YS VTQQPLGGK+  GGQR G
Sbjct: 638  ----RTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSTVTQQPLGGKAQFGGQRFG 693

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA+ VLQE+LT KSDD+ GR + YE+I  G    + G PESF VLVKE+Q
Sbjct: 694  EMEVWALEAYGASNVLQEILTYKSDDINGRLKAYEAITKGKPIPKPGVPESFRVLVKELQ 753

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            +LGL + + +   +     +     ++
Sbjct: 754  SLGLDMRVLDEDDQEVELRDLDEGMDE 780



 Score =  456 bits (1174), Expect = e-125,   Method: Composition-based stats.
 Identities = 295/523 (56%), Positives = 387/523 (73%), Gaps = 9/523 (1%)

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+
Sbjct: 1   MTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERM 60

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ 
Sbjct: 61  SVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLT 120

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK- 609
           R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV     
Sbjct: 121 RDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETG 180

Query: 610 -VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  G     P   +D++D SP
Sbjct: 181 VVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSP 240

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++
Sbjct: 241 KQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVI 300

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+  G V   DA ++ +R  +G LD       +Y + KF+RSN  T  NQR LVKVGD V
Sbjct: 301 AQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRSNSGTAYNQRTLVKVGDVV 353

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            + D IADGPS + G++ALG+N +VA+M W GYNFED++++SER+V +DV+TS+H+EE+E
Sbjct: 354 EKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAVIMSERLVKDDVYTSVHLEEYE 413

Query: 849 VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              RDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ 
Sbjct: 414 SETRDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSA 473

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 474 EERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRVNGD 516


>gi|289432490|ref|YP_003462363.1| DNA-directed RNA polymerase subunit beta [Dehalococcoides sp. GT]
 gi|288946210|gb|ADC73907.1| DNA-directed RNA polymerase, beta subunit [Dehalococcoides sp. GT]
          Length = 1273

 Score =  479 bits (1234), Expect = e-132,   Method: Composition-based stats.
 Identities = 195/573 (34%), Positives = 283/573 (49%), Gaps = 53/573 (9%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +   T  G  +       V       I++  II  G ++  G +L      +    + 
Sbjct: 665  EKIIIRTAEGGHDEYLLKKFVRTNQGTCINQHAIINKGQKIAAGQVLADSSATEN-GELA 723

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
              +  + A    +  +  D  +     +S  +V    F    I K+E      +  +E +
Sbjct: 724  LGQNCVVAFMSWQGFNYEDAII-----LSERLVREDAFTSIHITKHELEARDTKLGVEEI 778

Query: 968  ARDK----DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             RD     ++    LD +   R+   +   + + G    K  T LS++   +  R+ + +
Sbjct: 779  TRDIPNVGEESLRELDEDGIIRIGAEVGPDDILVGKITPKGETELSAE--EKLLRAIFGE 836

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
             A + +                          +I     GDD+P  V + V+V+VA KR 
Sbjct: 837  KAREVKDT---------SLRMPHGEWGKVINVRIFSRDSGDDLPARVNKWVQVWVAQKRK 887

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +  GDK+AGRHGNKG++S I P EDMP+L DGTPVD+VLNP+GVPSRMN+GQI ETHLGW
Sbjct: 888  VSVGDKLAGRHGNKGVISIIAPVEDMPYLPDGTPVDVVLNPIGVPSRMNLGQILETHLGW 947

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   LG ++ + + D   +  I    +        G+      +    +    A +W   
Sbjct: 948  AGHLLGFRVATPVFDGADDTVIEDALARSWLSAKAGAIDMSPENKRPSADAHKAIEWIKQ 1007

Query: 1204 VPV-STPVFDG-----ADEEAINSMLRMADLDES-------------------------G 1232
                   +FD      A E ++   L+   +D S                         G
Sbjct: 1008 QGFDGKKIFDEKHPGLAKEVSLKLWLKDMGVDASALSGAELEKKAYDVSSQSRLPSPIVG 1067

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +S+L DG TGE FD+PVTVG +Y+LKL H+V DKV+AR+TG YSL++QQPLGGK+  GGQ
Sbjct: 1068 KSVLRDGRTGETFDQPVTVGNMYILKLIHLVEDKVHARATGPYSLISQQPLGGKAQFGGQ 1127

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW + AYG A+ LQEMLTIKSDD+ GR + YESIV G D  + G PESF VLVK
Sbjct: 1128 RFGEMEVWAMYAYGTAHNLQEMLTIKSDDIAGRAKAYESIVKGEDVLQPGVPESFKVLVK 1187

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            E+Q+LGL++++ N   K  A  E++   N+  L
Sbjct: 1188 ELQSLGLAVEVINEEVK-IAPSEKVSSLNEGNL 1219



 Score =  472 bits (1214), Expect = e-130,   Method: Composition-based stats.
 Identities = 331/676 (48%), Positives = 446/676 (65%), Gaps = 63/676 (9%)

Query: 332 SLEEIFHSEIRDIPILY--VDSVNNNAYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVST 388
            L  I +S+  DI  L+  +D+     YI++++  D   KD   AL+DIY  +RPGD   
Sbjct: 200 LLRAIGYSDDLDILNLFEVIDNDPERHYIQSSIDRDPLIKDEISALIDIYSRLRPGDPPN 259

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDL 446
              A  + N +FFD   YDL  VGR K+N RL L + +  + R + +EDI+AII+ ++ +
Sbjct: 260 ADNARKLINEMFFDPQHYDLGKVGRYKVNRRLELPSREVGENRALTREDIVAIIQRIIMV 319

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            NG+   DDID+LGNRR+R+VGE+++NQ+R+GL+R+ER  +ER+S V+++ V P  L+N 
Sbjct: 320 NNGQDNPDDIDHLGNRRIRTVGELVQNQFRIGLVRLERVARERMSIVNLEMVTPSALVNI 379

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           +PVVSAV EFF  SQLSQ  +  N L+ IT+ RRLSA+G GG++R RAG ++RDVH +HY
Sbjct: 380 RPVVSAVKEFFGGSQLSQFMDQTNPLAEITNKRRLSAMGPGGLSRERAGFDVRDVHYSHY 439

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--------------------- 605
           GRICP ET EG NIGL+ SL +++R+N YGF+ETPYRKV                     
Sbjct: 440 GRICPIETPEGPNIGLIGSLATYSRINRYGFVETPYRKVYSKLKNNDKKLVGLKLKTEIS 499

Query: 606 ------------------------------CDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                                             V+ +V Y+ A EE+   IAQAN+ LD
Sbjct: 500 EKGKVLAAAGSTISEDSFKIISKLPECDILVMPFVSAEVKYMPADEEDRYIIAQANTRLD 559

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E G F ++ +  R A   ++ P +KID++D SPKQ+ S+AASLIPFLE+DD+NR LMG N
Sbjct: 560 EKGYFLDDRIEARLAERYVVEPPDKIDYMDVSPKQIFSVAASLIPFLEHDDANRALMGAN 619

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL+AEAP V TGME   A+ SG  I AK AG+   V + +I+IR+ EG     
Sbjct: 620 MQRQAVPLLRAEAPMVATGMEREAARYSGQVIFAKHAGVASSVTSEKIIIRTAEG----- 674

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             G D Y L KF R+NQ TC+NQ  ++  G ++    ++AD  +T+ G+LALG+N +VAF
Sbjct: 675 --GHDEYLLKKFVRTNQGTCINQHAIINKGQKIAAGQVLADSSATENGELALGQNCVVAF 732

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M W G+N+ED++++SER+V ED FTSIHI + E+ ARDTKLG EEITRDIPNV EE L+ 
Sbjct: 733 MSWQGFNYEDAIILSERLVREDAFTSIHITKHELEARDTKLGVEEITRDIPNVGEESLRE 792

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV P DILVGKITPKGE+ ++ EEKLLRAIFGEKA +V+DTSLR+P G 
Sbjct: 793 LDEDGIIRIGAEVGPDDILVGKITPKGETELSAEEKLLRAIFGEKAREVKDTSLRMPHGE 852

Query: 936 SGTVVDVRIFNRHGID 951
            G V++VRIF+R   D
Sbjct: 853 WGKVINVRIFSRDSGD 868



 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 99/361 (27%), Positives = 169/361 (46%), Gaps = 42/361 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA- 71
           +RK + + PE++++P+LIE+Q  S+  F            EGL+   + + PI  F G  
Sbjct: 15  IRKSYAQLPEVVNVPNLIEMQLQSFVWF----------QEEGLRELIEEISPIKDFVGNR 64

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SI 130
             LEF+ YEF  P+    +C  RD TY+VPL +  RLIV         K+  +IKE   +
Sbjct: 65  LELEFIGYEFREPRLSEYECTQRDQTYSVPLYVKARLIV---------KTTGEIKEPFDL 115

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           + GD+PLMT  GTF+  G +R+VVSQL RSPG++F         +G+ L    +IP +G 
Sbjct: 116 FFGDIPLMTALGTFITSGTERVVVSQLLRSPGVYFTISDDP--ATGRPLCHTNLIPSRGA 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           W++ E  ++D+I V+ID RRK+PV++ L A+G   + +IL+ F    V     +      
Sbjct: 174 WLEFETSNRDVISVKIDGRRKIPVSTLLRAIGYSDDLDILNLF---EVIDNDPERHYIQS 230

Query: 250 SAADLMVGAKVSSSLVDI----DTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS---- 300
           S     +     S+L+DI      G+    ++ +KL + +    +   +  +G       
Sbjct: 231 SIDRDPLIKDEISALIDIYSRLRPGDPPNADNARKLINEMFFDPQHYDLGKVGRYKVNRR 290

Query: 301 ------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                 +      +  + +      I +      +   ++ + +  IR +  L  +    
Sbjct: 291 LELPSREVGENRALTREDIVAIIQRIIMVNNGQDNPDDIDHLGNRRIRTVGELVQNQFRI 350

Query: 355 N 355
            
Sbjct: 351 G 351


>gi|46360990|gb|AAS89228.1| RpoB [Corynebacterium afermentans subsp. lipophilum]
          Length = 1059

 Score =  479 bits (1233), Expect = e-132,   Method: Composition-based stats.
 Identities = 315/617 (51%), Positives = 437/617 (70%), Gaps = 21/617 (3%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    +  + +TL  D   +  +ALL+IYR  RPG+  T  +A+S+    FF + +YDL
Sbjct: 232 TERFGFSEIMMSTLENDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDL 291

Query: 409 STVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGK------------GTIDD 455
           + VGR K N +L L    D +  + +EDI   ++ LV L  G+               DD
Sbjct: 292 ARVGRYKTNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPAGEIIPINTDD 351

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ E
Sbjct: 352 IDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIRE 411

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 412 FFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETP 471

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL+ +L+++ARVNA+GFIETPY+KV DGK+T  + YL+A EE+   IA+A + +D
Sbjct: 472 EGPNIGLIGALSTYARVNAFGFIETPYQKVNDGKLTGQIDYLTADEEDRYAIAEAATPMD 531

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +D + T E +  R   G+  +V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 532 KDNNLTGERIEVRLKDGDIGVVGPQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGA 591

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQ+QAVPLL+AE+ +V TGME   A  +G  +++K+AG++E V    I +   EG    
Sbjct: 592 NMQKQAVPLLRAESAYVATGMEQRAAYDAGDTVISKKAGVIENVTGDFITVMDDEG---- 647

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              G D Y L  F+R+NQ TC NQ P+V  GD V    +IADGP T  G++ALGRN+LVA
Sbjct: 648 ---GRDTYMLRTFERTNQGTCYNQTPIVSAGDRVEAGQVIADGPGTKDGEMALGRNLLVA 704

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG EEITR+IPNVSE+ LK
Sbjct: 705 FMPWEGHNYEDAIILNQRVVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 764

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G
Sbjct: 765 DLDERGIIRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHG 824

Query: 935 VSGTVVDVRIFNRHGID 951
             G V+ VR F+R   D
Sbjct: 825 EQGKVIAVRRFSREDDD 841



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/436 (33%), Positives = 206/436 (47%), Gaps = 61/436 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G ++      K +  M     LL A    +  +  D  +     V   ++
Sbjct: 671  IVSAGDRVEAGQVIADGPGTK-DGEMALGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 729

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 730  TSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDL-DERGIIRIGADVRDGDILVGKV 788

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +     ++  R  
Sbjct: 789  TPKGETELTPEERLLRAIFGEKAREVRDT-------------SLKVPHGEQGKVIAVR-- 833

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 834  --RFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 891

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 892  GTPVDIILNTHGVPRRMNIGQVLEIHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYD 948

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  + I  +L  +  +  G  
Sbjct: 949  VPADSLT-------------------------ATPVFDGATNDEIAGLLANSKPNRDGDV 983

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 984  MVDGEGKTTLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1043

Query: 1287 SNRGGQRLGEMEVWCI 1302
            +  GGQR GEMEVW +
Sbjct: 1044 AQFGGQRFGEMEVWAM 1059



 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 99/389 (25%), Positives = 172/389 (44%), Gaps = 46/389 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVF 63
            R  F K  E I +P L++VQ  S+   +           N   D R   GL+   + + 
Sbjct: 18  ERYSFAKINEPITVPGLLDVQLESFAWLVGTQEWREREQANRGDDARITSGLEDILEEIS 77

Query: 64  PITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           PI  +SG   L      F+  K+ +D+C  +D+ Y+ PL +T   I  D          +
Sbjct: 78  PIEDYSGNMSLTLSEPRFEDVKYTIDECKDKDINYSAPLYVTAEFINND---------TQ 128

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           +IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ +
Sbjct: 129 EIKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVK 186

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQR 241
           +IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +  
Sbjct: 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQITERFGFSEIMMSTLE 246

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI- 298
            D       A   +   +        D  + ++E+         L +  + K  + LG+ 
Sbjct: 247 NDGVSNTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFKAKRYDLARVGRYKTNRKLGLG 306

Query: 299 ----------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                           T + L  L+  E  +    GEI       I+   ++   +  +R
Sbjct: 307 GDHDGLMTLTEEDIATTLEYLVRLHAGETEMTSPAGEII-----PINTDDIDHFGNRRLR 361

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  L  + V         +V ++   + 
Sbjct: 362 TVGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|11467373|ref|NP_043230.1| RNA polymerase beta subunit [Cyanophora paradoxa]
 gi|1350843|sp|P48119|RPOB_CYAPA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|1016174|gb|AAA81261.1| beta subunit of RNA polymerase [Cyanophora paradoxa]
          Length = 1103

 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 180/551 (32%), Positives = 259/551 (47%), Gaps = 63/551 (11%)

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SE +V       I I         T  G E     I          I +  I+  G  V 
Sbjct: 582  SEGLVKRVTGDHICI--------QTDTGKEINYTLIKYQRSNQDTCITQRPIVFEGERVK 633

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             G IL    T   +  +   + LL A    +  +  D  L     V   V       ++ 
Sbjct: 634  KGQILADD-TATDKGELALGQNLLVAYMPWEGYNYEDAILINERLVYEDVYTSIHIEKYE 692

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             +  +  + +E    E+   ++   + + ++ I S       G     G        V  
Sbjct: 693  TETRQTKLGIEEITREIPNVNEYSLRNLDEKGIVS------VGSWIKGGDILV--GKVAP 744

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
                 + P  +  +    ++       SL++       I++ R    I   ++G+ + PG
Sbjct: 745  KAESDQPPEGKLLKAIFGEKNRDVRDTSLRMPSGEKGRIVDVR----IFIREFGEMLYPG 800

Query: 1070 VLR---VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  +V++++A KR IQ GDKMAGRHGNKGI+S+ILP +DMP+L DGTP+DI+LNPLG
Sbjct: 801  ANTANTIVRIYIAQKRKIQVGDKMAGRHGNKGIISKILPRQDMPYLPDGTPIDIILNPLG 860

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMNVGQ++E  LGWA   LG + K +  D +     S      +             
Sbjct: 861  VPSRMNVGQVYECLLGWAAEHLGVRFKLIPFDERFGKQASRTFIHEKLKE---------- 910

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                       A E    + L  +  +  G+  L+DG TGE FD
Sbjct: 911  ---------------------------AKELTNKNWLFNS--NHPGKIQLFDGRTGESFD 941

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
             P+ VG  YMLKL H+V DK++ARSTG YSL+TQQPLGGK+ +GGQR GEMEVW ++A+G
Sbjct: 942  NPIMVGKAYMLKLVHLVDDKIHARSTGPYSLITQQPLGGKAQQGGQRFGEMEVWALEAFG 1001

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            AAY LQE+LTIKSDD++GR    ++IV G      G PESF VL++E+QAL L +     
Sbjct: 1002 AAYTLQEILTIKSDDMLGRNEALKAIVKGKAIPRPGIPESFKVLMRELQALCLDVVAYKI 1061

Query: 1367 RTKNSAKMEEI 1377
            +  +  + E +
Sbjct: 1062 QNGDQDECEAL 1072



 Score =  471 bits (1211), Expect = e-130,   Method: Composition-based stats.
 Identities = 305/663 (46%), Positives = 427/663 (64%), Gaps = 31/663 (4%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              +  D L   ++  D  +     I+++A ++ + + L  +                 +
Sbjct: 158 KFEVDKDDLI--WMRIDKTHRLPCHIFLKALNLSESEILSAL----------------TH 199

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             +++ T+    +   ++AL++ +R +RPG+         +    FFD  +YDL  VGR 
Sbjct: 200 PEFLQKTIYEHGDCTEEEALIEFHRQLRPGEPPNSIQGRYLLYSRFFDPKRYDLGFVGRY 259

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K+N +LNL+   ++R +  +DI+ I+  L++L+ G G IDDID+LGNRRV++VGE+L++Q
Sbjct: 260 KLNKKLNLNVSPNIRILTTQDILEILNYLINLQFGMGQIDDIDHLGNRRVKAVGELLQSQ 319

Query: 475 YRLGLLRMERSIKERISSVDIDSVM----PQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
            R+GL R+ER I +R+S +   S         LINAKP+   + EFF SSQLSQ  +  N
Sbjct: 320 LRIGLNRLERLIHDRLSMLTTKSFKKRKKLTTLINAKPINECLKEFFGSSQLSQFMDQTN 379

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ + H RRL+ LG GG++R RAG  +RD+HP+HYGRICP ET EG N GLV SLT+ A
Sbjct: 380 PLAELIHKRRLTILGPGGLSRDRAGCAVRDIHPSHYGRICPIETPEGQNAGLVGSLTTHA 439

Query: 591 RVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +N YGFIETP+ KV  G +  +  ++YL+A EE+   IA A+  ++E      E +  R
Sbjct: 440 HLNQYGFIETPFYKVEKGYIQKELGIIYLTADEEDQYRIAAADVLINETNKIIGEDISVR 499

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E I    ++IDFI  SP Q  S++ SLIPFLE+DD+NR LMG NMQRQAVPLL AE 
Sbjct: 500 YRQEFITTKIDQIDFIAISPLQTFSVSTSLIPFLEHDDANRALMGSNMQRQAVPLLHAEK 559

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  VAK S   ++ K  G+V++V    I I++  G           Y L+K+Q
Sbjct: 560 PLVGTGLEFQVAKDSRRVLINKSEGLVKRVTGDHICIQTDTGKEI-------NYTLIKYQ 612

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+TC+ QRP+V  G+ V++  I+AD  +TD G+LALG+N+LVA+MPW GYN+ED++L
Sbjct: 613 RSNQDTCITQRPIVFEGERVKKGQILADDTATDKGELALGQNLLVAYMPWEGYNYEDAIL 672

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V EDV+TSIHIE++E   R TKLG EEITR+IPNV+E  L+N+DE GI+ VG+ +
Sbjct: 673 INERLVYEDVYTSIHIEKYETETRQTKLGIEEITREIPNVNEYSLRNLDEKGIVSVGSWI 732

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+ PK ES   PE KLL+AIFGEK  DVRDTSLR+PSG  G +VDVRIF R 
Sbjct: 733 KGGDILVGKVAPKAESDQPPEGKLLKAIFGEKNRDVRDTSLRMPSGEKGRIVDVRIFIRE 792

Query: 949 GID 951
             +
Sbjct: 793 FGE 795



 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 123/279 (44%), Gaps = 32/279 (11%)

Query: 26  IP-DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFD 82
           IP DL+E+QKAS+  F            EGL    ++  P+    G   + F   +YE +
Sbjct: 10  IPFDLLEIQKASFKWFF----------EEGLIEEIENFSPVIDLRGNFEVHFYLKNYELE 59

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            P F +++   RDLTYA  L I + L   +            +K+  I+ G++PLMT   
Sbjct: 60  APTFTLEEAKQRDLTYAAQLYIPVELRDLE---------TGIVKQDRIFFGEIPLMTDRC 110

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G++R++++Q+ RSPGI++  +       G   Y   II ++G W+  E D  D+I
Sbjct: 111 TFLINGVERVIINQIIRSPGIYYSVN---TDEQGTRTYDVTIISNRGAWLKFEVDKDDLI 167

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            +RID+  ++P   FL AL +   EILS         +             L+   +   
Sbjct: 168 WMRIDKTHRLPCHIFLKALNLSESEILSALTHPEFLQKTIYEHGDCTEEEALIEFHRQ-- 225

Query: 263 SLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
               +  GE      G+ L        K   + F+G   
Sbjct: 226 ----LRPGEPPNSIQGRYLLYSRFFDPKRYDLGFVGRYK 260


>gi|90994443|ref|YP_536933.1| RNA polymerase beta subunit [Porphyra yezoensis]
 gi|109904721|sp|Q1XDN5|RPOB_PORYE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|90819007|dbj|BAE92376.1| DNA-directed RNA polymerase beta chain [Porphyra yezoensis]
          Length = 1143

 Score =  478 bits (1231), Expect = e-132,   Method: Composition-based stats.
 Identities = 314/685 (45%), Positives = 443/685 (64%), Gaps = 15/685 (2%)

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +++ ++GK++ S  L S +   +KF       +   ++  D  +     I++ A  +  
Sbjct: 166 KQEIDKNGKQIYSASLISNRGSWLKFEIDPKGEI---WIRIDKTHKVNAYIFLRAIGLNK 222

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           ++  + +                     I    +       ++ALL +Y  +RP + +T 
Sbjct: 223 DEIEKGLSKYAFLISASQIYSVKELAKEIGKNNIE--EVTDEEALLIVYSKLRPNEPATV 280

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           +VA+ M    FFD  +YDL  VGR K+N +L L+ P   R +  +DI++ I  L+++++ 
Sbjct: 281 AVAKQMLYSRFFDPKRYDLGEVGRYKINKKLGLNIPKTFRVLSPQDILSSIDYLINIKDK 340

Query: 450 K-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
             G +DDID+LGNRRVRSVGE+L+NQ+R+GL R+ER I+ER+   DIDS+   +LIN KP
Sbjct: 341 NSGNLDDIDHLGNRRVRSVGELLQNQFRVGLNRLERIIRERMMICDIDSLSLSNLINPKP 400

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           ++++V EFF SSQLSQ  +  N ++ +TH RR+SALG GG  + RAG  +RD+HP+HYGR
Sbjct: 401 LIASVREFFGSSQLSQFMDQTNPVAELTHKRRISALGPGGFNKDRAGFAVRDLHPSHYGR 460

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRY 626
           ICP ET EG N GL+ SL + ARVN +GFIETP+  V  G+V   N  VYL+A EE++  
Sbjct: 461 ICPIETPEGPNAGLIGSLATCARVNVFGFIETPFYPVNQGQVIYHNSPVYLTADEEDDFR 520

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +A  +  + +      +++  R   E I     ++D+I  SP QV+S A SLIPFLE+DD
Sbjct: 521 VAPGDVKVSKQHYIEGDIIPVRYRQEFITTTPTQVDYIAISPIQVISAATSLIPFLEHDD 580

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVPLL  E P +GTG+E+ +A+ SG  ++++ +G V  V A +I I+
Sbjct: 581 ANRALMGSNMQRQAVPLLYPEKPIIGTGLETKIARDSGMVVISRTSGHVNYVSANKIGIQ 640

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              G           YRL K+ RSNQ+TC+NQRP+V VG+++     +ADG STD G++A
Sbjct: 641 DNSGRTV-------HYRLKKYYRSNQDTCINQRPIVWVGEKIVVGQTLADGASTDGGEIA 693

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LGRN+LVA+MPW GYN+ED+ LISER+V +D++TSIHIE++EV  R TKLGPEEITR+IP
Sbjct: 694 LGRNILVAYMPWEGYNYEDAFLISERLVYDDLYTSIHIEKYEVECRQTKLGPEEITREIP 753

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           NVS+  LK++D  GI+  G+ V  GDILVGKITPKGE+   PE KLLRAIFGEKA DVRD
Sbjct: 754 NVSDNSLKDLDRNGIVVGGSWVEAGDILVGKITPKGEADQLPEGKLLRAIFGEKARDVRD 813

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGID 951
           TSLR+P+   G VV VR+F R   D
Sbjct: 814 TSLRLPNAAKGRVVKVRVFTRQKGD 838



 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 165/425 (38%), Positives = 232/425 (54%), Gaps = 41/425 (9%)

Query: 956  SISVEREQIELLARDKD-DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            SI +E+ ++E        +E      N+    ++ L     V G    +   +L   +  
Sbjct: 728  SIHIEKYEVECRQTKLGPEEITREIPNVSDNSLKDLDRNGIVVGGSWVEAGDILVGKITP 787

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF-KNKIEKIQWGDDMPPGVLRV 1073
            +    Q  +  +           ++       +  + R  K ++   Q GD++PPG   +
Sbjct: 788  KGEADQLPEGKLLRAIFGEKARDVRDTSLRLPNAAKGRVVKVRVFTRQKGDELPPGTNAM 847

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            ++V+VA KR IQ GDKMAGRHGNKGI+SRILP +DMP+L DGTPVDIVLNPLGVPSRMNV
Sbjct: 848  IRVYVAQKRKIQVGDKMAGRHGNKGIISRILPKQDMPYLSDGTPVDIVLNPLGVPSRMNV 907

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+FE  LG A   LGK+ K +  D               ++ G  +    ++    ++ 
Sbjct: 908  GQVFECLLGLAGGYLGKRFKIIPFD---------------EMYGAEASRALVNRKLKEAS 952

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            L  + +W                        + +    G+  ++DG TGEPFD PVTVG 
Sbjct: 953  LITSNKW------------------------LFNDQHPGKMQVFDGRTGEPFDNPVTVGR 988

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             YMLKL H+V DK++ARSTG YSLVTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQE
Sbjct: 989  AYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGAAYTLQE 1048

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +LT+KSDD+  R     +IV G    + GTPESF VL++E+Q+LGL I +   +     +
Sbjct: 1049 LLTVKSDDMQARNEALNAIVKGKPIPKPGTPESFKVLMRELQSLGLDIAVHKLKLFEDGQ 1108

Query: 1374 MEEIP 1378
               + 
Sbjct: 1109 RRTVE 1113



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 94/492 (19%), Positives = 191/492 (38%), Gaps = 66/492 (13%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLE-FVS-YEFD 82
           +PDL+E+Q+AS+  FL+          EGL      +FP I+  +    L+ F + Y+  
Sbjct: 12  LPDLVEIQRASFKWFLL----------EGLTEVL-EIFPKISDPTSRLELQLFGNEYKIK 60

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS------------- 129
            P++ V     RD TY+  + +  +L   D+D  +  +  K+IK                
Sbjct: 61  FPRYSVRQAKNRDKTYSAQIYVPAKLTRKDIDLPSKNQE-KNIKSLDLSSTHLQLSAEKQ 119

Query: 130 ----------IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
                     +++GDLP+MT  GTF++ G +R++++Q+ RSPGI++  +  +   +GK +
Sbjct: 120 IKNKKYKKRLVFIGDLPIMTNRGTFIVSGTERVIINQIIRSPGIYYKQEIDK---NGKQI 176

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-------TF 232
           Y+  +I ++G W+  E D K  I +RID+  KV    FL A+G++ +EI           
Sbjct: 177 YSASLISNRGSWLKFEIDPKGEIWIRIDKTHKVNAYIFLRAIGLNKDEIEKGLSKYAFLI 236

Query: 233 YPKIVYS-QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKE 290
               +YS +         +  ++     +      +   E   +   K++        K 
Sbjct: 237 SASQIYSVKELAKEIGKNNIEEVTDEEALLIVYSKLRPNEPATVAVAKQMLYSRFFDPKR 296

Query: 291 KGVKFLGITS-DCLCGLYVAE--------DIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             +  +G    +   GL + +        DI++     I I+  +  +   ++ + +  +
Sbjct: 297 YDLGEVGRYKINKKLGLNIPKTFRVLSPQDILSSIDYLINIKDKNSGNLDDIDHLGNRRV 356

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R +  L  +           ++ ++        L +  ++ P      +     F     
Sbjct: 357 RSVGELLQNQFRVGLNRLERIIRERMMICDIDSLSLSNLINPK--PLIASVREFFGSSQL 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                  + V  +    R++   P       K+     ++ L     G+  I  I+    
Sbjct: 415 SQFMDQTNPVAELTHKRRISALGPGGF---NKDRAGFAVRDLHPSHYGR--ICPIETPEG 469

Query: 462 RRVRSVGEMLKN 473
                +G +   
Sbjct: 470 PNAGLIGSLATC 481


>gi|255520551|ref|ZP_05387788.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes FSL
            J1-175]
          Length = 695

 Score =  478 bits (1230), Expect = e-132,   Method: Composition-based stats.
 Identities = 165/434 (38%), Positives = 228/434 (52%), Gaps = 62/434 (14%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V  +D
Sbjct: 295  KDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGA--EVKDND 352

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           KI   + GD+
Sbjct: 353  LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGDE 412

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPL
Sbjct: 413  LPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPL 472

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E HLG A   LG  + + + D     D+                    
Sbjct: 473  GVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARDAK------ 526

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           +GE F
Sbjct: 527  ----------------------TILYDG--------------------------RSGEAF 538

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 539  DNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 598

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            GAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + + +
Sbjct: 599  GAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLS 658

Query: 1366 SRTKNSAKMEEIPD 1379
            +  +     +   D
Sbjct: 659  ADEEEIEMRDMDDD 672



 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 259/411 (63%), Positives = 315/411 (76%), Gaps = 3/411 (0%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR
Sbjct: 1   LGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYR 60

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           +V     +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R   E + V +E+I
Sbjct: 61  RVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERI 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D SPKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK
Sbjct: 121 DYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAK 180

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            SGAA+ AK  GIVE V+A  I +R V   D    T G+D Y L KF RSNQ TC NQRP
Sbjct: 181 DSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRP 240

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            V  GD V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+T
Sbjct: 241 NVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYT 300

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           SIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TP
Sbjct: 301 SIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTP 360

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF R   D
Sbjct: 361 KGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGD 411


>gi|313620903|gb|EFR92084.1| DNA-directed RNA polymerase, beta subunit [Listeria innocua FSL
            S4-378]
          Length = 796

 Score =  478 bits (1229), Expect = e-132,   Method: Composition-based stats.
 Identities = 165/434 (38%), Positives = 228/434 (52%), Gaps = 62/434 (14%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V  +D
Sbjct: 396  KDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGA--EVKDND 453

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           KI   + GD+
Sbjct: 454  LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGDE 513

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPL
Sbjct: 514  LPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPL 573

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E HLG A   LG  + + + D     D+                    
Sbjct: 574  GVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARDAK------ 627

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           +GE F
Sbjct: 628  ----------------------TVLYDG--------------------------RSGEAF 639

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 640  DNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 699

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            GAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + + +
Sbjct: 700  GAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLS 759

Query: 1366 SRTKNSAKMEEIPD 1379
            +  +     +   D
Sbjct: 760  ADEEEIEMRDMDDD 773



 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 316/512 (61%), Positives = 392/512 (76%), Gaps = 3/512 (0%)

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
             +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D+ ++ PQ 
Sbjct: 1   FFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDMTTITPQQ 60

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH
Sbjct: 61  LINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRERAGYEVRDVH 120

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAM 620
            +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V     +VT+ + YL+A 
Sbjct: 121 YSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPETNRVTDKIDYLTAD 180

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EE+N  +AQANS LDE G+FTEE V  R   E + V +E+ID++D SPKQVVS+A + IP
Sbjct: 181 EEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERIDYMDVSPKQVVSVATACIP 240

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK SGAA+ AK  GIVE V+A
Sbjct: 241 FLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGAAVTAKHDGIVEHVEA 300

Query: 741 IRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
             I +R V   D    T G+D Y L KF RSNQ TC NQRP V  GD V + +I+ +GPS
Sbjct: 301 REIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAEGDRVVKGEILGNGPS 360

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
            D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+TSIHIEEFE  ARDTKLGPE
Sbjct: 361 MDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEFESEARDTKLGPE 420

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           E+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TPKG + +T EE+LL AIFGE
Sbjct: 421 EMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTELTAEERLLHAIFGE 480

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSLRVP G  G V+DV+IF R   D
Sbjct: 481 KAREVRDTSLRVPHGGGGIVLDVKIFTREAGD 512


>gi|320333430|ref|YP_004170141.1| DNA-directed RNA polymerase subunit beta [Deinococcus maricopensis
            DSM 21211]
 gi|319754719|gb|ADV66476.1| DNA-directed RNA polymerase subunit beta [Deinococcus maricopensis
            DSM 21211]
          Length = 1147

 Score =  477 bits (1228), Expect = e-132,   Method: Composition-based stats.
 Identities = 182/524 (34%), Positives = 262/524 (50%), Gaps = 32/524 (6%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G       I         N+D+  I+ +G  V  G+++           +   + +  AI
Sbjct: 645  GNVRTFELIRFTRSNQGTNLDQHPIVNIGDTVKRGEVIADGP-ASDYGRLALGQNITIAI 703

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----D 972
                  +  D        +S ++V    +    I+K+E      +   E + RD     +
Sbjct: 704  MPFDGFNFEDAIC-----ISESLVRKDFYTSVHIEKDEIDARDTKLGPEKITRDIPGLSE 758

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                 LD +   R+   +   + + G   FK  +  + +      RS + + A + +   
Sbjct: 759  AALRDLDEDGIVRVGAEVKPGDILVGKTSFKGESEPTPE--ERLLRSIFGEKAREVKDTS 816

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              V S +                   +   G D+ PGV  +V+V+VA KR +Q GDK+A 
Sbjct: 817  LRVRSGEGGIVVKTVRFR--------RGDEGVDLKPGVREMVRVYVAQKRRLQVGDKVAN 868

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VS+ILP EDMP+L DGTPVD+V NPLGVPSRMN+GQI ETHLG     +G K 
Sbjct: 869  RHGNKGVVSKILPPEDMPYLPDGTPVDLVFNPLGVPSRMNLGQILETHLGEVARLVGAKF 928

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVF 1211
             + + D      I  +              E    D  +  VL  A +          V 
Sbjct: 929  VTPVFDSATEAAIKDMLEVAAAERLQKRRDEGFETDVREAEVLDRAGKLG--------VI 980

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            D    E   + ++   L  +G+S+L+DG TGE    PV VG +Y++KL HMV DK++ARS
Sbjct: 981  DHPGGEYDKAQMQ---LSRTGKSVLFDGRTGEAVSGPVVVGTMYVMKLYHMVEDKLHARS 1037

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y++
Sbjct: 1038 TGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRDAAYQA 1097

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            IV G++   +  PESF VLVKE+ +LGL +++ +   K     E
Sbjct: 1098 IVKGDEVAASTIPESFKVLVKELHSLGLDVEVLDQGDKAVDIFE 1141



 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 296/630 (46%), Positives = 413/630 (65%), Gaps = 27/630 (4%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +  +ALL ++ V+RPGD      A      L  D  +YDL   GR KMN +L  +  + 
Sbjct: 231 MNADEALLRLFTVLRPGDPPKRDKAVQYLYGLLADPKRYDLGDPGRFKMNRKLGTNRDER 290

Query: 428 VRHIRKED-------IIAIIKILVDLRNGKGTI-----------------DDIDNLGNRR 463
              +  E+       +I  I+ L+ L+ G   +                 DDID+LGNRR
Sbjct: 291 -TLLTFENGKFADAGLIDTIRYLLALQTGLEEMTVGADEDGVAITVPVGEDDIDHLGNRR 349

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           VR+VGE+L +Q R+GL RM R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLS
Sbjct: 350 VRTVGELLADQLRVGLGRMARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLS 409

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q ++  N L+ + H RR+SALG GG+ R RAG ++RDVH THYGR+CP ET EG NIGL+
Sbjct: 410 QFKDQTNPLAELRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRVCPIETPEGANIGLI 469

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           SSL SF++VN  GF+E PYRKV DG+VT++V+Y++A  E+   IAQANS L+ DGSF E+
Sbjct: 470 SSLASFSKVNDLGFMEAPYRKVVDGRVTDNVMYMTADVEDLYAIAQANSPLNPDGSFAED 529

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            V  R  G+        + ++D SPKQ+VS++ +LIPFLE+DD+NR LMG NMQ QAVPL
Sbjct: 530 RVLARKKGDPSFYEPADVQYMDVSPKQIVSVSTALIPFLEHDDANRALMGSNMQSQAVPL 589

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDPSTSGVDI 761
           ++AE+P VGTG+E  V   SG ++V+   G V  VDA  I++ +      +      V  
Sbjct: 590 VRAESPAVGTGVEERVVIDSGTSVVSDVDGTVTYVDARVIQVTLGEDAPHVGMVKGNVRT 649

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + L++F RSNQ T ++Q P+V +GD V+R ++IADGP++D G LALG+N+ +A MP+ G+
Sbjct: 650 FELIRFTRSNQGTNLDQHPIVNIGDTVKRGEVIADGPASDYGRLALGQNITIAIMPFDGF 709

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++ ISE +V +D +TS+HIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI
Sbjct: 710 NFEDAICISESLVRKDFYTSVHIEKDEIDARDTKLGPEKITRDIPGLSEAALRDLDEDGI 769

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + VGAEV PGDILVGK + KGES  TPEE+LLR+IFGEKA +V+DTSLRV SG  G VV 
Sbjct: 770 VRVGAEVKPGDILVGKTSFKGESEPTPEERLLRSIFGEKAREVKDTSLRVRSGEGGIVVK 829

Query: 942 VRIFNRHGIDKNERSISVEREQIELLARDK 971
              F R     + +    E  ++ +  + +
Sbjct: 830 TVRFRRGDEGVDLKPGVREMVRVYVAQKRR 859



 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 93/271 (34%), Positives = 138/271 (50%), Gaps = 27/271 (9%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+ + FG+  E+I +PDL EVQ  S++ FL   +A D R N GLQ+AFK VFPI   +
Sbjct: 2   RPRIER-FGEITEVIPLPDLTEVQVRSFNQFLQTGVAADRRENAGLQSAFKEVFPI-DET 59

Query: 70  GA-----AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                   +L+F+ Y+     +  ++C  +DLTY  PL   L+LI  D            
Sbjct: 60  EKGRSSGLVLDFLEYKLGDAPYTPEECREKDLTYQAPLYAKLQLIHKDSGL--------- 110

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IKE  +++GDLPLMT DG+FVI G  R+V+SQ+HRSPG++F           K  Y   I
Sbjct: 111 IKEDQVFLGDLPLMTIDGSFVINGADRVVISQIHRSPGVYFTSS----YKGIKKTYTGAI 166

Query: 185 IPD--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI---LSTFYPKIVYS 239
           IP   +G W+++EF+S  ++ ++++ +RK PV+  L  LGMD  +I   L+ F P     
Sbjct: 167 IPMPKRGPWIELEFNS-GVLEMKVN-KRKFPVSMLLRVLGMDDAQIKTLLTEFDPNGEVP 224

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +          A   +            D  
Sbjct: 225 EDKSAGMNADEALLRLFTVLRPGDPPKRDKA 255


>gi|46361026|gb|AAS89246.1| RpoB [Corynebacterium testudinoris]
          Length = 1107

 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 319/617 (51%), Positives = 437/617 (70%), Gaps = 22/617 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +    +  + +TL +D   +  +ALL+IYR  RPG+  T  +A S+ +  FF + +YDL+
Sbjct: 233 ERFGFSEIMMSTLESDGVANTDEALLEIYRKQRPGEQPTRDLARSLLDNSFFRAKRYDLA 292

Query: 410 TVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDI 456
            VGR K+N +L L    D +  + +EDI   ++ LV L  G+ ++            DDI
Sbjct: 293 KVGRYKVNRKLGLGGDHDGLMTLTEEDIATTLEYLVRLHVGERSMTSPTGEIIPVETDDI 352

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EF
Sbjct: 353 DHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREF 412

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  NSLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 413 FGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPE 472

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ARVNA+GFIETPY KV +G+VT+ V YL+A EE+   IAQA+   D 
Sbjct: 473 GPNIGLIGSLASYARVNAFGFIETPYLKVVEGRVTDIVEYLTADEEDRYAIAQASIERDA 532

Query: 637 DGSFTEELVFCRCAGEEILVPRE--KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DG  T + +  R     I V  +   +D+ID SP+Q+VS+A ++IPFLE+DD+NR LMG 
Sbjct: 533 DGVITADRIEVRLKDGAIGVVTDGYGVDYIDVSPRQMVSVATAMIPFLEHDDANRALMGA 592

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPL++AEAP+VGTGME   A  +G  ++  +AG+VE V A  I I   EG  D 
Sbjct: 593 NMQRQAVPLVRAEAPYVGTGMEKRAAYDAGDMVITPKAGVVENVSADVITIMDDEGIRD- 651

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L KF+R+NQ T  NQ PLV +G+ V    +IADGP T  G+++LGRN+LVA
Sbjct: 652 ------TYLLRKFERTNQGTSYNQTPLVNMGERVEAGQVIADGPGTHNGEMSLGRNLLVA 705

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+
Sbjct: 706 FMPWEGHNYEDAIILNQRVVEEDILTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLR 765

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           ++D+ GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G
Sbjct: 766 DLDDRGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHG 825

Query: 935 VSGTVVDVRIFNRHGID 951
            +G V+ VR F R   D
Sbjct: 826 ENGKVIGVRRFAREDDD 842



 Score =  473 bits (1218), Expect = e-131,   Method: Composition-based stats.
 Identities = 178/483 (36%), Positives = 241/483 (49%), Gaps = 61/483 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++           M+    LL A    +  +  D  +     V   ++
Sbjct: 672  LVNMGERVEAGQVIADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEEDIL 730

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + RD DD   I+      R  +IL G+ 
Sbjct: 731  TSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIVRIGADVRAGDILVGKV 789

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                V  +                
Sbjct: 790  TPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGENGKVIGV---------------- 833

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP EDMPF+ D
Sbjct: 834  -RRFAREDDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMAD 892

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +     D K    I  L   L  
Sbjct: 893  GTPVDIILNTHGVPRRMNIGQVLEIHLGWLAAA-GWSVD--PEDPKNAELIKTLPEELYD 949

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                          +G   +TPVFDGA  E ++ +L  +  +  G  
Sbjct: 950  V-------------------------PAGSLTATPVFDGATNEELSGLLANSRPNRDGDV 984

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L DG +GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 985  MVDETGKTMLLDGRSGEPFPYPVSVGYMYLLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1044

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G +  + G PES
Sbjct: 1045 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGENIPDPGIPES 1104

Query: 1347 FNV 1349
            F V
Sbjct: 1105 FKV 1107



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 95/388 (24%), Positives = 171/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K    I++P L+++Q+ S+   +              P+ R   GL+     + P
Sbjct: 19  RYSFAKISAPIEVPGLLDLQRESFAWLIGTPEWRARHQEERGPEARVTSGLEDILDELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      F+P K  +D+C  +D+ Y+ PL +T   I             ++
Sbjct: 79  IQDYSENMSLSLSEPRFEPVKNSIDECKDKDINYSAPLYVTAEFI---------NNETQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 130 IKSQTVFIGDFPMMTPKGTFIVNGTERVVVSQLVRSPGVYFDQTIDK--STERPLHSVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG  +E+I   F     ++ +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEQIQERFGFSEIMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI-- 298
           D       A   +   +        D    ++++         L K  + K  + LG+  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLARSLLDNSFFRAKRYDLAKVGRYKVNRKLGLGG 307

Query: 299 ---------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                          T + L  L+V E  +   TGEI       ++   ++   +  +R 
Sbjct: 308 DHDGLMTLTEEDIATTLEYLVRLHVGERSMTSPTGEII-----PVETDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|46360974|gb|AAS89220.1| RpoB [Corynebacterium pilosum]
          Length = 1098

 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 317/661 (47%), Positives = 454/661 (68%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   +    +  +  TL +
Sbjct: 189 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEAQI--KERFGFSEIMMTTLES 244

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A+S+    FF++ +YDL+ VGR K+N +L L  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFNAKRYDLAKVGRYKINRKLGLGG 304

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +ED+   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 305 DHDGLLTLTEEDLATSLEYLVRLHAGEREMTSPTGEVIPINTDDIDHFGNRRLRTVGELI 364

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 365 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 424

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ +L+S+AR
Sbjct: 425 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGALSSYAR 484

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VNA+GFIETPY+KV +GK+T+ + YL+A EE+   IAQA + +D++G+ TEE +  R   
Sbjct: 485 VNAFGFIETPYQKVENGKLTDQIDYLTADEEDRFAIAQAATEMDDEGNITEERIEVRIKD 544

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +   + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQ+QAVPLL+AEAP+
Sbjct: 545 GDIAVTDAQGVDYLDISPRQMVSVATAMIPFLEHDDANRALMGANMQKQAVPLLRAEAPY 604

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TGME   A  +G  +++ +AG+VE V    I I   EG  D        Y L  ++R+
Sbjct: 605 VATGMEQRAAYDAGDMVISAKAGVVENVSGDMITIMDDEGQRD-------TYLLRTYERT 657

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ TC NQ PLV +GD V    +IADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 658 NQGTCYNQLPLVNIGDRVEAGQVIADGPGTKDGEMSLGRNLLVAFMPWEGHNYEDAIILN 717

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +R+V +D+ TS+HIEE E+ ARDTKLG EEITR+IPNV E+ LK++DE GI+ +GA+V  
Sbjct: 718 QRVVEDDILTSVHIEEHEIDARDTKLGAEEITREIPNVGEDVLKDLDERGIVRIGADVRD 777

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ VR F+R   
Sbjct: 778 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIAVRRFSREDD 837

Query: 951 D 951
           D
Sbjct: 838 D 838



 Score =  468 bits (1203), Expect = e-129,   Method: Composition-based stats.
 Identities = 172/473 (36%), Positives = 236/473 (49%), Gaps = 61/473 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  G ++      K +  M+    LL A    +  +  D  +     V   ++
Sbjct: 668  LVNIGDRVEAGQVIADGPGTK-DGEMSLGRNLLVAFMPWEGHNYEDAIILNQRVVEDDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   H ID  +  +  E    +I    E + +D  DE+ I+      R  +IL G+ 
Sbjct: 727  TSVHIEEHEIDARDTKLGAEEITREIPNVGEDVLKDL-DERGIVRIGADVRDGDILVGKV 785

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                 E      +           
Sbjct: 786  TPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIA 828

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +    +  DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ D
Sbjct: 829  VRRFSREDDDDLSPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPQEDMPFMAD 888

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LN  GVP RMN+GQ+ E HLGW     G  +    +D      +  L   L  
Sbjct: 889  GTPVDIILNTHGVPRRMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEALYD 945

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG-- 1232
            V                               +TPVFDGA  E I  +L     +  G  
Sbjct: 946  VPADSLT-------------------------ATPVFDGATNEEIAGLLANTKPNRDGDV 980

Query: 1233 ------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                  +++L+DG +GEPFD P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK
Sbjct: 981  MVDGDGKTVLFDGRSGEPFDYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGK 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            +  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +VYE+IV G++  
Sbjct: 1041 AQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIP 1093



 Score =  304 bits (778), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 100/388 (25%), Positives = 170/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+   +              PD R   GL+     + P
Sbjct: 16  RYSFAKISEPIPVPGLLDVQSESFSWLVGTPEWRERQQELRGPDARVTSGLEDILDELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      FD  K+ VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFDSVKYTVDECKDKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD PLMT  GTF++ G +R+VVSQL RSPG++FD    +   + + L++ ++
Sbjct: 127 IKSQTVFIGDFPLMTDKGTFIVNGTERVVVSQLVRSPGVYFDETIDK--STERPLHSVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG    +I   F     ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEAQIKERFGFSEIMMTTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGI-- 298
           D       A   +   +        D  + ++E+         L K  + K  + LG+  
Sbjct: 245 DGVANTDEALLEIYRKQRPGEQPTRDLAQSLLENSFFNAKRYDLAKVGRYKINRKLGLGG 304

Query: 299 ---------------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                          + + L  L+  E  +   TGE+       I+   ++   +  +R 
Sbjct: 305 DHDGLLTLTEEDLATSLEYLVRLHAGEREMTSPTGEVI-----PINTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|46361032|gb|AAS89249.1| RpoB [Turicella otitidis]
          Length = 1083

 Score =  477 bits (1227), Expect = e-132,   Method: Composition-based stats.
 Identities = 329/756 (43%), Positives = 466/756 (61%), Gaps = 45/756 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-------ESGKKLTSGL 284
           F       +         SA   +    +++   +I +    I       + G  + +G 
Sbjct: 92  FEDVKTTIEEAKEKDINYSAPLYVTAEFINNDTQEIKSQTVFIGDFPMMTDKGTFIINGT 151

Query: 285 LKSLKEKGVKFLGITSDCLCG----LYVAEDIVNGETGEIY-----------IEAGDVID 329
            + +  + V+  G+  D          +    +    G              +       
Sbjct: 152 ERVIVSQLVRSPGVYFDETIDKSTERPLHSVKIIPSRGAWLEFDVDKRDTVGVRIDRKRR 211

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           +     +         I   D    +  + +TL  D   +   ALL+IYR  RPG+  T 
Sbjct: 212 QPVTVLLKALGWTSEQI--RDRFGFSELMMSTLENDAVDNTDQALLEIYRKQRPGEQPTR 269

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-DVRHIRKEDIIAIIKILVDLRN 448
            +A+S+ +  FF+  +Y L+ VGR K + +L L+  D  +  + +EDI   ++ LV L  
Sbjct: 270 ELAQSLLDNSFFEPKRYSLAKVGRYKASRKLGLNRDDNGLMTLTEEDIATTLEYLVRLHA 329

Query: 449 GKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           G+ T+            DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +
Sbjct: 330 GERTMTSPDGVELSIETDDIDHFGNRRLRTVGELVQNQVRVGLARMERVVRERMTTQDAE 389

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ P  LIN +PV +A+ EFF +SQLSQ  +  N+LS +TH RRLSALG GG++R RAG+
Sbjct: 390 SITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNALSGLTHKRRLSALGPGGLSRERAGI 449

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHP+HYGR+CP ET EG NIGL+ SL ++ RVNA+GFIETPYRKV DGKVT++V Y
Sbjct: 450 EVRDVHPSHYGRMCPIETPEGPNIGLIGSLATYGRVNAFGFIETPYRKVVDGKVTDEVEY 509

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIA 675
           L A EE+   IA+A + +D +G+ T+  +  R   G+  +   + +D++D SP+Q+VS+A
Sbjct: 510 LPADEEDRFAIAEAKTEVDAEGNITQGRIEVRVKDGDIQVTDAKGVDYLDVSPRQMVSVA 569

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ++IPFLE+DD+NR LMG NMQRQAVPLL+ E+P VGTGME   A  SG  + AKRAG+V
Sbjct: 570 TAMIPFLEHDDANRALMGANMQRQAVPLLRPESPLVGTGMEKYAAYDSGDLVTAKRAGVV 629

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E V A  I +   EG             L KF+R+NQ TC NQ PLV VGD V    ++A
Sbjct: 630 EDVTADYITVMDDEGKR-------YTELLRKFERTNQGTCYNQTPLVSVGDRVEEGHVLA 682

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGP T  G+L+LGRN+LV FMPW G+N+ED++++++R+V ED+ TSIHIEE E+ ARDTK
Sbjct: 683 DGPGTHDGELSLGRNLLVGFMPWEGHNYEDAVILNQRIVEEDILTSIHIEEHEIDARDTK 742

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           LG EEITR+IPNV+E+ L ++DE GI+ +GA+V  GDILVGK+TPKGE+ +TPEE+LLRA
Sbjct: 743 LGAEEITREIPNVAEDVLADLDEHGIVRIGADVRAGDILVGKVTPKGETELTPEERLLRA 802

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFGEKA +VRDTSL+VP G +G V+ V  F+R   D
Sbjct: 803 IFGEKAREVRDTSLKVPHGETGKVIGVERFSREDDD 838



 Score =  424 bits (1091), Expect = e-116,   Method: Composition-based stats.
 Identities = 163/460 (35%), Positives = 228/460 (49%), Gaps = 59/460 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  G +L        +  ++    LL      +  +  D  +     V   ++
Sbjct: 668  LVSVGDRVEEGHVLADGPGT-HDGELSLGRNLLVGFMPWEGHNYEDAVILNQRIVEEDIL 726

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   H ID  +  +  E    +I  +A D     DE  I+      R  +IL G+  
Sbjct: 727  TSIHIEEHEIDARDTKLGAEEITREIPNVAEDVLADLDEHGIVRIGADVRAGDILVGKVT 786

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E      +            
Sbjct: 787  PKGETELTPEERLLRAIFGEKAR-----------------EVRDTSLKVPHGETGKVIGV 829

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +    +  DD+  GV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDMPF+ DG
Sbjct: 830  ERFSREDDDDLSAGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPPEDMPFMADG 889

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LN  GVP RMN+GQ+ ETHLGW     G K+           +   L++  E++
Sbjct: 890  TPMDILLNTHGVPRRMNIGQVLETHLGWLASA-GWKVD-----PDDERNAELLKTLPEEL 943

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                +++                        +TPVFDGA    IN +L  +  +  G   
Sbjct: 944  YDVPANSLT----------------------ATPVFDGALNSEINGLLANSRPNRDGDVM 981

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 982  VDDQGKAVLFDGRSGEPFPFPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 1041

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
              GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR +
Sbjct: 1042 QFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGRVK 1081



 Score =  296 bits (757), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 87/318 (27%), Positives = 147/318 (46%), Gaps = 26/318 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG-------LQAAFKSVFPIT 66
           R  F K  E I+IP L+++Q+ S+   +      D +  +G       L+   + + PI 
Sbjct: 18  RYSFAKYSEPIEIPGLLDLQRQSFSWLIGTPEWRDRQREQGVESPRSGLEEILEELSPIQ 77

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            +SG   L      F+  K  +++   +D+ Y+ PL +T   I  D          ++IK
Sbjct: 78  DYSGTMSLSLSEPRFEDVKTTIEEAKEKDINYSAPLYVTAEFINND---------TQEIK 128

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
            Q++++GD P+MT  GTF+I G +R++VSQL RSPG++FD    +   + + L++ +IIP
Sbjct: 129 SQTVFIGDFPMMTDKGTFIINGTERVIVSQLVRSPGVYFDETIDK--STERPLHSVKIIP 186

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W++ + D +D + VRIDR+R+ PVT  L ALG  SE+I   F    +     +   
Sbjct: 187 SRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIRDRFGFSELMMSTLENDA 246

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLC 304
              +   L+   +          GE    E  + L        K   +  +G        
Sbjct: 247 VDNTDQALLEIYR------KQRPGEQPTRELAQSLLDNSFFEPKRYSLAKVGRYKASRKL 300

Query: 305 GLYVAEDIVNGETGEIYI 322
           GL   ++ +   T E   
Sbjct: 301 GLNRDDNGLMTLTEEDIA 318


>gi|297565270|ref|YP_003684242.1| DNA-directed RNA polymerase subunit beta [Meiothermus silvanus DSM
            9946]
 gi|296849719|gb|ADH62734.1| DNA-directed RNA polymerase, beta subunit [Meiothermus silvanus DSM
            9946]
          Length = 1125

 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 185/510 (36%), Positives = 256/510 (50%), Gaps = 43/510 (8%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS------L 929
            +D+   + VG  V  GD+L        E  +   + +L AI      +  D        L
Sbjct: 643  LDQRPRVEVGQRVKKGDLLADGP-ASDEGRLALGQNVLIAIMPFDGYNYEDAIVISEDLL 701

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
            R     S  +    I  R      ER         E   RD  DE  ++      +  +I
Sbjct: 702  RKDFYTSVHIERYEIEARDTKLGPERITRDIPNLSEAALRDL-DEDGVVRTGAEVKPGDI 760

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+ +  G         L   +  E  R                               
Sbjct: 761  LVGRTSFKGETEPTPEERLLRSIFGEKARD-------------------VKDTSLRVPPG 801

Query: 1050 EDRFKNKIEKIQWGDD---MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            E     +  +++ GD    + PGV  VV+V+VA KR +Q GDK+A RHGNKG+VS+ILP 
Sbjct: 802  EGGVVVRSLRLKRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVSKILPP 861

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG-KKIKSLINDYKANGDI 1165
            EDMP L DGTPVDIVLNPLGVPSRMN+GQI ETHLG A + LG + I  + +        
Sbjct: 862  EDMPHLPDGTPVDIVLNPLGVPSRMNLGQILETHLGIAGLDLGIRFITPVFDGATEEEIK 921

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            + L    ++            D  +  VL  A +             G  +E +++  ++
Sbjct: 922  NLLGEAFDQKWAQRKAEGFGLDRREQEVLARAAKL------------GIVDEKLDAEGQL 969

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
              + + G+SILYDG +GEP + P+ VG +Y++KL HMV DK++ARSTG YSL+TQQPLGG
Sbjct: 970  RQVAQQGKSILYDGRSGEPIEAPIVVGVMYIMKLYHMVEDKMHARSTGPYSLITQQPLGG 1029

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++AYGA++ LQE+LT+KSDD+ GR   YE++V G D      PE
Sbjct: 1030 KAQFGGQRFGEMEVWALEAYGASHTLQEILTLKSDDIEGRNAAYEAVVKGEDVPTASVPE 1089

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
            SF VLVKE+Q+LGL ++  +   +N    E
Sbjct: 1090 SFRVLVKELQSLGLDVETYDENDRNLDIFE 1119



 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 281/587 (47%), Positives = 405/587 (68%), Gaps = 15/587 (2%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---- 426
           +++LL ++  +RPGD      A +  + L  D  +YDL   GR K N +L ++       
Sbjct: 237 EESLLKLFTELRPGDPPKRDKAITYLHSLLSDPRRYDLGEAGRYKANTKLGMELSGRTLI 296

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             +    + E ++ ++  L  L++G+     DDID+LGNRR+R+VGE+L +Q+R+GL R+
Sbjct: 297 KFENGEFKDEGLLRVLLYLFGLQSGREGFESDDIDHLGNRRIRTVGELLADQFRVGLSRL 356

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R ++ER+     +S  P  L+N +P+V+A+ EFF  SQLSQ ++  N LS + H RR+S
Sbjct: 357 ARGVRERMLLGTPESATPAKLVNNRPLVAAIREFFGRSQLSQFKDQTNPLSELRHKRRIS 416

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL ++ R+N  GFI TPY
Sbjct: 417 ALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLAAYGRINELGFILTPY 476

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RKV +G+VT +VV+++A EE+   IAQAN+ +DE+G F  + +  R  G+ ++V  E ++
Sbjct: 477 RKVENGRVTQEVVFMTASEEDRYLIAQANTPIDENGKFATDRIVTRRKGDPVIVRPEDVE 536

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQV S+  +LIPFLE+DD+NR LMG NMQ QAVPL++A++P V TG+E  V + 
Sbjct: 537 YMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQAQAVPLIRAQSPIVMTGVEERVVRD 596

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           S  ++ ++  G+V+ V   +IVI+  +        G   Y L +F RSNQ T ++QRP V
Sbjct: 597 SLTSVYSEVDGVVKSVSGDKIVIKGDDK-------GEYEYYLRRFVRSNQGTALDQRPRV 649

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           +VG  V++ D++ADGP++D G LALG+N+L+A MP+ GYN+ED+++ISE ++ +D +TS+
Sbjct: 650 EVGQRVKKGDLLADGPASDEGRLALGQNVLIAIMPFDGYNYEDAIVISEDLLRKDFYTSV 709

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIE +E+ ARDTKLGPE ITRDIPN+SE  L+++DE G++  GAEV PGDILVG+ + KG
Sbjct: 710 HIERYEIEARDTKLGPERITRDIPNLSEAALRDLDEDGVVRTGAEVKPGDILVGRTSFKG 769

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           E+  TPEE+LLR+IFGEKA DV+DTSLRVP G  G VV      R  
Sbjct: 770 ETEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGVVVRSLRLKRGD 816



 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 85/215 (39%), Positives = 123/215 (57%), Gaps = 20/215 (9%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF---SGAAM 73
           FG+  E+I +P L E+Q  S+   L +N  P +R N GLQAAFK  FPI       G  +
Sbjct: 6   FGRIEEVIPLPTLTEIQVDSFRKALQLNTPPHQRQNLGLQAAFKETFPIEEGEKGRGGLV 65

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           L+F+ Y    P FD D+C  +DLTY  PL   L+LI  D            IKE  +++G
Sbjct: 66  LDFLEYRLAEPPFDQDECREKDLTYQAPLYAKLQLIHKD---------TGLIKEDEVFLG 116

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QGLW 191
           DLPLMT+DG+F++ G  R++VSQ+HRSPG++F  D+ R    GK  +   +IP   +G W
Sbjct: 117 DLPLMTEDGSFIVNGADRVIVSQIHRSPGVYFTPDQAR---PGK--FVASVIPLPKRGPW 171

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           +D+EF+   ++ V    ++K P+   L  LG  +E
Sbjct: 172 IDLEFEQSGVV-VMKVNKKKFPLALLLRVLGYTAE 205


>gi|46361010|gb|AAS89238.1| RpoB [Corynebacterium macginleyi]
          Length = 1058

 Score =  476 bits (1226), Expect = e-132,   Method: Composition-based stats.
 Identities = 324/693 (46%), Positives = 452/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + I      G ++  D+   +T  + I+         
Sbjct: 162 LVRSPGVYFDRSIDKSTERPLHSVKIIPSR--GAWLEFDVDKRDTVGVRIDRKRRQPVTV 219

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L +        I     +  + +  + +TL +D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 220 LLKALGWTEEQIK----ERFSFSELMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRELA 275

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K N +L L    D    + +EDI   ++ LV L  G+ 
Sbjct: 276 QSLLDNSFFRAKRYDLAKVGRYKANRKLGLGGDHDGPMTLTEEDIAVTLEYLVRLHVGER 335

Query: 452 ------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                         DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 336 EMKAPNGEMISLNTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 395

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQLSQ  +H NSLS +TH RRLSALG GG++R RAG+E+R
Sbjct: 396 PTSLINVRPVSAAIREFFGTSQLSQFMDHNNSLSGLTHKRRLSALGPGGLSRERAGIEVR 455

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGR+CP ET EG NIGL+ +L S+ARVNA+GFIETPYRKV DGKVT+ V YL+A
Sbjct: 456 DVHASHYGRMCPIETPEGPNIGLIGALASYARVNAFGFIETPYRKVVDGKVTDQVEYLTA 515

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   IAQA    DE+G    E +  R   G+  +     +D++D SP+Q+VS+  ++
Sbjct: 516 DEEDRFAIAQAEVEQDEEGRLIGERIEVRLKEGDIGVTDASGVDYVDVSPRQMVSVGTAM 575

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQ+QAVPL+++EAP VGTGME   A  +G  ++  +AG+VE V
Sbjct: 576 IPFLEHDDANRALMGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENV 635

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I   EG  D        Y L KF+R+NQ T  NQ PLV +G  V    ++ADGP
Sbjct: 636 TADVITIMDDEGQRDS-------YVLRKFERTNQGTNYNQTPLVSMGQRVEAGQVLADGP 688

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T  G+++LGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG 
Sbjct: 689 GTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGA 748

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ L ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 749 EEITREIPNVSEDVLSDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFG 808

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G  G V+ V  F+R   D
Sbjct: 809 EKAREVRDTSMKVPHGEVGKVIGVARFSRDDDD 841



 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 141/440 (32%), Positives = 207/440 (47%), Gaps = 59/440 (13%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++ +G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 665  NYNQTPLVSMGQRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRI 723

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEI 989
            V   ++       H ID  +  +  E    +I  ++ D     DE+ I+      R  +I
Sbjct: 724  VEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLSDLDERGIIRIGADVRAGDI 783

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L G+    G         L   +  E  R                 E      +     +
Sbjct: 784  LVGKVTPKGETELTPEERLLRAIFGEKAR-----------------EVRDTSMKVPHGEV 826

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                          DD+ PGV  +++V+VA KR IQ GDKMAGRHGNKG+V +ILP EDM
Sbjct: 827  GKVIGVARFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGRHGNKGVVGKILPPEDM 886

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+ +     +   +   L+
Sbjct: 887  PFMEDGTPVDILLNTHGVPRRMNIGQVLELHLGWLAHA-GWKVDT-----EDPANAELLK 940

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
            +  E++    + +                        +TPVFDGA    I  +L  +  +
Sbjct: 941  TLPEELYDVPADSLT----------------------ATPVFDGATNHEIERLLASSRPN 978

Query: 1230 ESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQ
Sbjct: 979  RDGDVLVDEHGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQ 1038

Query: 1282 PLGGKSNRGGQRLGEMEVWC 1301
            PLGGK+  GGQR GEMEVW 
Sbjct: 1039 PLGGKAQFGGQRFGEMEVWA 1058



 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 94/388 (24%), Positives = 171/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+   +               + R   GL+   + + P
Sbjct: 19  RYSFAKISEPIALPGLLDVQLDSFAWLVGSPEWREREQAERGDNARVTSGLEDILEELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 79  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ +I
Sbjct: 130 IKSQTVFIGDFPIMTDMGTFIVNGTERVIVSQLVRSPGVYFDRSIDK--STERPLHSVKI 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I    +F   ++ +   
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIKERFSFSELMMSTLES 247

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 248 DGVSNTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKANRKLGLGG 307

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE+       ++   ++   +  +R 
Sbjct: 308 DHDGPMTLTEEDIAVTLEYLVRLHVGEREMKAPNGEMI-----SLNTDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|46360942|gb|AAS89204.1| RpoB [Corynebacterium accolens]
          Length = 1093

 Score =  476 bits (1225), Expect = e-131,   Method: Composition-based stats.
 Identities = 321/693 (46%), Positives = 452/693 (65%), Gaps = 27/693 (3%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S        +    E+ +  + I      G ++  D+   +T  + +       +  
Sbjct: 159 LVRSPGVYFDRSIDKSTERPLHSVKIIPSR--GAWLEFDVDKRDT--VGVRIDRKRRQPV 214

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +      +  I   +  + +  + +TL +D   +  +ALL+IYR  RPG+  T  +A
Sbjct: 215 TVLLKALGWTEEQI--RERFSFSELMMSTLESDGVSNTDEALLEIYRKQRPGEQPTRELA 272

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKG 451
           +S+ +  FF + +YDL+ VGR K N +L L    D +  + +EDI   ++ LV L  G+ 
Sbjct: 273 QSLLDNSFFRAKRYDLAKVGRYKANRKLGLGGDHDGLMTLTEEDIAVTLEYLVRLHVGER 332

Query: 452 ------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                         DDID+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D +S+ 
Sbjct: 333 EMKAPNGEMISLNTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESIT 392

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           P  LIN +PV +A+ EFF +SQLSQ  +H NSLS +TH RRLSALG GG++R RAG+E+R
Sbjct: 393 PTSLINVRPVSAAIREFFGTSQLSQFMDHNNSLSGLTHKRRLSALGPGGLSRERAGIEVR 452

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGR+CP ET EG NIGL+ +L S+ARVN +GFIETPYRKV DGKVT+ V YL+A
Sbjct: 453 DVHASHYGRMCPIETPEGPNIGLIGALASYARVNPFGFIETPYRKVVDGKVTDQVEYLTA 512

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASL 678
            EE+   IAQA    DE+G    E +  R   G+  +     +D++D SP+Q+VS+  ++
Sbjct: 513 DEEDRFAIAQAEVEQDEEGRLIGERIEVRLKEGDIGVTDASGVDYVDVSPRQMVSVGTAM 572

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQ+QAVPL+++EAP VGTGME   A  +G  ++  +AG+VE V
Sbjct: 573 IPFLEHDDANRALMGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENV 632

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A  I I   EG  D        Y L KF+R+NQ T  NQ PLV +G  V    ++ADGP
Sbjct: 633 TADVITIMDDEGQRD-------TYILRKFERTNQGTNYNQTPLVSMGQRVEAGQVLADGP 685

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T  G+++LGRN+LVAFMPW G+N+ED++++++R+V ED+ TS+HIEE E+ ARDTKLG 
Sbjct: 686 GTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGA 745

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNVSE+ L ++DE GII +GA+V  GDILVGK+TPKGE+ +TPEE+LLRAIFG
Sbjct: 746 EEITREIPNVSEDVLSDLDERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFG 805

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTS++VP G  G V+ V  F+R   D
Sbjct: 806 EKAREVRDTSMKVPHGEVGKVIGVARFSRDDDD 838



 Score =  453 bits (1165), Expect = e-124,   Method: Composition-based stats.
 Identities = 174/554 (31%), Positives = 254/554 (45%), Gaps = 60/554 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER-MVSEDVFTSIHIEEFEVMARDTKLGP 858
                       ++ +  P  G   E         +V       +     +V+      G 
Sbjct: 586  MGANMQKQAVPLVRSEAPLVGTGMEQRAAYDAGDVVITPKAGVVENVTADVITIMDDEGQ 645

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +              N ++  ++ +G  V  G +L           M+    LL A   
Sbjct: 646  RDTYILRKFERTNQGTNYNQTPLVSMGQRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMP 704

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---D 973
             +  +  D  +     V   ++       H ID  +  +  E    +I  ++ D     D
Sbjct: 705  WEGHNYEDAIILNQRIVEEDILTSVHIEEHEIDARDTKLGAEEITREIPNVSEDVLSDLD 764

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E+ I+      R  +IL G+    G         L   +  E  R               
Sbjct: 765  ERGIIRIGADVRAGDILVGKVTPKGETELTPEERLLRAIFGEKAR--------------- 809

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E      +     +              DD+ PGV  +++V+VA KR IQ GDKMAGR
Sbjct: 810  --EVRDTSMKVPHGEVGKVIGVARFSRDDDDDLAPGVNEMIRVYVAQKRKIQDGDKMAGR 867

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+V +ILP EDMPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G K+ 
Sbjct: 868  HGNKGVVGKILPPEDMPFMEDGTPVDILLNTHGVPRRMNIGQVLELHLGWLAHA-GWKVD 926

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +     +   +   L++  E++    + +                        +TPVFDG
Sbjct: 927  T-----EDPANAELLKTLPEELYDVPADSLT----------------------ATPVFDG 959

Query: 1214 ADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            A    I  +L  +  +  G        ++ L+DG +GEP+  P++VGY+YMLKL+H+V +
Sbjct: 960  ATNHEIERLLASSRPNRDGDVLVNEHGKATLFDGRSGEPYKYPISVGYMYMLKLHHLVDE 1019

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW +QAYGAAY LQE+LTIKSDDVVGR
Sbjct: 1020 KIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQAYGAAYTLQELLTIKSDDVVGR 1079

Query: 1326 TRVYESIVAGNDTF 1339
             +VYE+IV G++  
Sbjct: 1080 VKVYEAIVKGDNMP 1093



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 94/388 (24%), Positives = 171/388 (44%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  S+   +               + R   GL+   + + P
Sbjct: 16  RYSFAKISEPIALPGLLDVQLDSFAWLVGSPEWREREQAERGDNARVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +SG   L      F+P K  VD+C  +D+ Y+ PL +T   I  D          ++
Sbjct: 76  IQDYSGNMSLSLSEPRFEPVKNTVDECKEKDINYSAPLYVTAEFINND---------TQE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L++ +I
Sbjct: 127 IKSQTVFIGDFPIMTDMGTFIVNGTERVIVSQLVRSPGVYFDRSIDK--STERPLHSVKI 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS--TFYPKIVYSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I    +F   ++ +   
Sbjct: 185 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFSFSELMMSTLES 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKF----- 295
           D       A   +   +        +  + ++++         L K  + K  +      
Sbjct: 245 DGVSNTDEALLEIYRKQRPGEQPTRELAQSLLDNSFFRAKRYDLAKVGRYKANRKLGLGG 304

Query: 296 ------------LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                       + +T + L  L+V E  +    GE+       ++   ++   +  +R 
Sbjct: 305 DHDGLMTLTEEDIAVTLEYLVRLHVGEREMKAPNGEMI-----SLNTDDIDHFGNRRLRT 359

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 360 VGELIQNQVRVGLSRMERVVRERMTTQD 387


>gi|11465577|ref|NP_045031.1| RNA polymerase beta subunit [Cyanidium caldarium]
 gi|14195191|sp|Q9TM35|RPOB_CYACA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|6466433|gb|AAF13014.1|AF022186_187 unknown [Cyanidium caldarium]
          Length = 1081

 Score =  476 bits (1224), Expect = e-131,   Method: Composition-based stats.
 Identities = 312/726 (42%), Positives = 451/726 (62%), Gaps = 15/726 (2%)

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I++  + K     +               G  V      I+  E+VI +    + G+  +
Sbjct: 82  IVTQLFNKNSGDVKEQEILLGEIPLMTQKGTFV------INGAERVIVNQIVRSPGIYFN 135

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +             +            +   I+I                  I    + 
Sbjct: 136 SEMDKNNLKTFNFLIIPNRGAWLKCEIDKNDLIWIRIDKNKKINLSIFFKALGIDHDDLR 195

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             ++     +I   L  D+N  +++AL ++++ + PG+ +T   +  +  F FF+  KYD
Sbjct: 196 IKNAFRQPEFIYKNLNKDENYTQQEALEELHKKLFPGEPATSEASTKILYFKFFNPKKYD 255

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           L  VGR K+N +L+L++P+++R +  +DI++ I  L++L+ G G IDDID+L NRR++SV
Sbjct: 256 LGIVGRKKINKKLDLNSPENIRILTIQDILSGINYLINLKFGFGNIDDIDHLANRRLKSV 315

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+L++Q  +GL+R+ER IKER++  +  S++P  LIN KP+ +A+ EFF SSQLSQ  +
Sbjct: 316 GELLQSQISIGLIRLERLIKERMTICEQSSLVPSALINPKPIFAAIKEFFNSSQLSQFMD 375

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            VN L+ +TH RR+S+LG GG+++ RAG  +RD+HP+HYGRICP ET EG N GL+ SL 
Sbjct: 376 QVNPLAELTHKRRVSSLGPGGLSKERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLA 435

Query: 588 SFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            +AR+N  GFIE P+ KV  G+V  +  ++YL A +E+   IA  +  ++E     E  V
Sbjct: 436 IYARINPDGFIEAPFYKVNQGQVLKNKGIIYLDAEQEDEFKIAPGDIRINETNFIKEINV 495

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E    P E+IDFI  SP QV+S A SLIPFLE++D+NR LMG NMQRQAVPL+ 
Sbjct: 496 PVRYRQEFTQCPAEEIDFIAVSPIQVISAATSLIPFLEHNDANRALMGSNMQRQAVPLIF 555

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E P VGTG+E+ +AK SG   +++  GIV+   A +I++         S++    Y L 
Sbjct: 556 PERPLVGTGLEAQIAKDSGIMAISRSNGIVKFTSAEKIIV-------TDSSNNQITYNLQ 608

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+Q+SNQ TC+N RP+V  G+ +++  I+ADG +TD G+LALGR++LVA+MPW GYN+ED
Sbjct: 609 KYQKSNQETCINHRPIVWPGERIKKGQILADGSATDTGELALGRDVLVAYMPWEGYNYED 668

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           + LIS+R+V ED++TSIHIE++E+ AR TKLGPEEITR+IPNV E  LK +DE GI+ V 
Sbjct: 669 AFLISDRLVYEDLYTSIHIEKYEIEARQTKLGPEEITRNIPNVGENSLKQLDENGIVVVS 728

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           + V  G ILVGK+TPKGES   PE KLL+AIFGEK  DV+DTSLR+P+G  G VVDVRIF
Sbjct: 729 SFVESGSILVGKVTPKGESDQPPESKLLQAIFGEKNKDVKDTSLRLPNGTRGRVVDVRIF 788

Query: 946 NRHGID 951
           +R   D
Sbjct: 789 SREKGD 794



 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 177/584 (30%), Positives = 264/584 (45%), Gaps = 61/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       ++    P  G   E  +     +++  +  S  I +F    +       
Sbjct: 542  MGSNMQRQAVPLIFPERPLVGTGLEAQIAKDSGIMA--ISRSNGIVKFTSAEKIIVTDSS 599

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
              +                I+   I+  G  +  G IL    +      +     +L A 
Sbjct: 600  NNQITYNLQKYQKSNQETCINHRPIVWPGERIKKGQILAD-GSATDTGELALGRDVLVAY 658

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD-DEQ 975
               +  +  D                 I +R   +    SI +E+ +IE        +E 
Sbjct: 659  MPWEGYNYEDA--------------FLISDRLVYEDLYTSIHIEKYEIEARQTKLGPEEI 704

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 N+    ++ L     V      +  ++L   +  +    Q  +  +         
Sbjct: 705  TRNIPNVGENSLKQLDENGIVVVSSFVESGSILVGKVTPKGESDQPPESKLLQAIFGEKN 764

Query: 1036 ESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            + +K       +    R  + +I   + GD++  G+  +V+++VA KR IQ GDKMAGRH
Sbjct: 765  KDVKDTSLRLPNGTRGRVVDVRIFSREKGDELAVGINYIVRIYVAQKRKIQIGDKMAGRH 824

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKGI+S+ILP +DMP+L +GTPVDI+LNPLGVPSRMNVGQIFE  LG +   L K+ + 
Sbjct: 825  GNKGIISKILPRQDMPYLPNGTPVDIILNPLGVPSRMNVGQIFECILGISAFNLKKRFRI 884

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            L  D     D S  R  + + +        +    +++ L                    
Sbjct: 885  LPFDEMYESDSS--RILINQKLKEAQTLTNLDYLFNENHL-------------------- 922

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G+  L+DG +GE FD PV VG IYM+KL H+V DK+++RSTG 
Sbjct: 923  -----------------GKVALFDGRSGEKFDNPVLVGKIYMMKLVHLVDDKIHSRSTGP 965

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+ +GGQRLGEMEVW  +A+GAAY LQE+LTIKSDD+ GR     +IV 
Sbjct: 966  YSLVTQQPLGGKAQQGGQRLGEMEVWAFEAFGAAYALQELLTIKSDDIQGRNEALTAIVR 1025

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            G    + GTPES  VL++E+Q+LGL I        +  +++ I 
Sbjct: 1026 GKTIPKPGTPESLKVLMREIQSLGLDIAAYRLPNLHHGEIKSIE 1069



 Score =  248 bits (632), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 93/440 (21%), Positives = 183/440 (41%), Gaps = 48/440 (10%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDPPK 85
           DL+ VQ+ S+  FL           EGL     +  PI  ++G   L  V        PK
Sbjct: 14  DLLSVQRESFYSFLT----------EGLAKELNNFSPIIDYTGKLELHLVTNQLVIKKPK 63

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           F  ++   RD +Y + + I  +L           K+  D+KEQ I +G++PLMT+ GTFV
Sbjct: 64  FSFEEAKRRDCSYTISINIVTQL---------FNKNSGDVKEQEILLGEIPLMTQKGTFV 114

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           I G +R++V+Q+ RSPGI+F+ +  + +L     +   IIP++G W+  E D  D+I +R
Sbjct: 115 INGAERVIVNQIVRSPGIYFNSEMDKNNL---KTFNFLIIPNRGAWLKCEIDKNDLIWIR 171

Query: 206 IDRRRKVPVTSFLMALGMDSEE--ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           ID+ +K+ ++ F  ALG+D ++  I + F       +  +         +      +   
Sbjct: 172 IDKNKKINLSIFFKALGIDHDDLRIKNAFRQPEFIYKNLNKD------ENYTQQEALEEL 225

Query: 264 LVDIDTGEQ-VIESGKKLTSGLLKSLKEKGV---------KFLGITSDCLCGLYVAEDIV 313
              +  GE    E+  K+      + K+  +         K L + S     +   +DI+
Sbjct: 226 HKKLFPGEPATSEASTKILYFKFFNPKKYDLGIVGRKKINKKLDLNSPENIRILTIQDIL 285

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           +G    I ++     +   ++ + +  ++ +  L    ++        L+ ++    + +
Sbjct: 286 SGINYLINLK-FGFGNIDDIDHLANRRLKSVGELLQSQISIGLIRLERLIKERMTICEQS 344

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L    ++ P     F+  +  FN          ++ +  +    R++         + K
Sbjct: 345 SLVPSALINPK--PIFAAIKEFFNSSQLSQFMDQVNPLAELTHKRRVS---SLGPGGLSK 399

Query: 434 EDIIAIIKILVDLRNGKGTI 453
           E     ++ +     G+   
Sbjct: 400 ERAGFAVRDIHPSHYGRICP 419


>gi|71482616|gb|AAZ32300.1| RpoB [Bosea sp. CRIB-07]
          Length = 245

 Score =  475 bits (1222), Expect = e-131,   Method: Composition-based stats.
 Identities = 158/248 (63%), Positives = 188/248 (75%), Gaps = 3/248 (1%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRM
Sbjct: 1    KMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRIVPAEDMPFLEDGTHADIVLNPLGVPSRM 60

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI ETHLGWA  GLGK+I   I+ Y+   D   LR+  + V       E I+  DD 
Sbjct: 61   NVGQILETHLGWAAAGLGKQIGKAIDAYRKAHDSKALRASFDAVYEDN---EIIASMDDA 117

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             ++ + +  + GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VT+
Sbjct: 118  ELIEMGQNLRRGVPIATPVFNGAKESDIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTM 177

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            GYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 178  GYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 237

Query: 1312 QEMLTIKS 1319
            QEMLT+ S
Sbjct: 238  QEMLTVSS 245


>gi|312874763|ref|ZP_07734782.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
            2053A-b]
 gi|311089508|gb|EFQ47933.1| DNA-directed RNA polymerase, beta subunit [Lactobacillus iners LEAF
            2053A-b]
          Length = 614

 Score =  474 bits (1221), Expect = e-131,   Method: Composition-based stats.
 Identities = 166/523 (31%), Positives = 234/523 (44%), Gaps = 79/523 (15%)

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    KN ++   +  G +V  G+++           +   +  + A       +  
Sbjct: 96   KYRRSNATKNYNQTPNVHCGEKVVEGEVIADGP-AMENGELALGQNPIIAFATWNMYNYE 154

Query: 926  DTSLRVPSGVSG------TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            D  +     V         + D    +R      E          E   +D  DE  I+ 
Sbjct: 155  DAVMISERMVKDDVYTSIHIEDYESESRDTKLGPEEITREIPNVGEDALKDL-DEDGIVR 213

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +  +IL G+    G         L   +  E  R    +      +V      + 
Sbjct: 214  VGAEVQDGDILVGKVTPKGVTDLSAEEKLLHAIFGEKAR----EVRDTSLRVPHGGGGII 269

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                             +   + GD++ PGV ++V+V++  KR IQ GDKM+GRHGNKG 
Sbjct: 270  QNVR-------------VFSREAGDELAPGVNKMVRVYIVQKRKIQVGDKMSGRHGNKGT 316

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P EDMP+L DG PVDI LNP+GVPSRMN+GQ+ E HLG A   LG  + + + D 
Sbjct: 317  IALVCPEEDMPYLPDGRPVDICLNPMGVPSRMNIGQVLEMHLGIASKHLGVHVATPVFDG 376

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                          ++ +  +  +   G    T ++DG      
Sbjct: 377  A----------------------------SEEDMWNMVREAGLGKDGKTVLYDG------ 402

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                 TGEPF   V+VG +Y LKL HMV DK++ARS G YSLVT
Sbjct: 403  --------------------RTGEPFHNRVSVGVMYYLKLTHMVDDKLHARSIGPYSLVT 442

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSDDVVGR + YE+IV G    
Sbjct: 443  QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDVVGRVKAYEAIVKGEKIP 502

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            + G PESF VLVKE+Q+LGL I + +S        +   D ++
Sbjct: 503  KPGVPESFRVLVKELQSLGLDIKVLDSDKNEIELRDMDDDSDE 545



 Score =  244 bits (624), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 170/313 (54%), Positives = 224/313 (71%), Gaps = 14/313 (4%)

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D  PKQVVS+ ++ IPFLENDDSNR LMG N QRQAVPL+   +P VGTGME   A  S
Sbjct: 1   MDVIPKQVVSVTSACIPFLENDDSNRALMGANHQRQAVPLINPHSPLVGTGMEYRAAHDS 60

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G AI+AK AG+VE VDA  I +R  +  LD        Y L K++RSN     NQ P V 
Sbjct: 61  GDAILAKAAGVVEYVDANVIKVRRDDKTLDE-------YVLEKYRRSNATKNYNQTPNVH 113

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            G++V   ++IADGP+ + G+LALG+N ++AF  W+ YN+ED+++ISERMV +DV+TSIH
Sbjct: 114 CGEKVVEGEVIADGPAMENGELALGQNPIIAFATWNMYNYEDAVMISERMVKDDVYTSIH 173

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IE++E  +RDTKLGPEEITR+IPNV E+ LK++DE GI+ VGAEV  GDILVGK+TPKG 
Sbjct: 174 IEDYESESRDTKLGPEEITREIPNVGEDALKDLDEDGIVRVGAEVQDGDILVGKVTPKGV 233

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERS 956
           + ++ EEKLL AIFGEKA +VRDTSLRVP G  G + +VR+F+R        G++K  R 
Sbjct: 234 TDLSAEEKLLHAIFGEKAREVRDTSLRVPHGGGGIIQNVRVFSREAGDELAPGVNKMVRV 293

Query: 957 ISVEREQIELLAR 969
             V++ +I++  +
Sbjct: 294 YIVQKRKIQVGDK 306


>gi|21702604|gb|AAM76000.1|AF481103_10 RNA polymerase beta-subunit [Candidatus Tremblaya princeps]
          Length = 1290

 Score =  474 bits (1220), Expect = e-131,   Method: Composition-based stats.
 Identities = 267/946 (28%), Positives = 443/946 (46%), Gaps = 24/946 (2%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
             PDL+ VQ+++++     +  P  R   GLQ    S+FP+ +  GAA++E V Y    P
Sbjct: 20  PYPDLLGVQRSAFNRLTQHSTHPSARNPYGLQRLLFSMFPMMSHDGAALIELVKYTIGKP 79

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
                +CL   LTY+ PL +TL+ I        G   ++  +   +Y+GD+P+MT+ G+F
Sbjct: 80  CSTDAECLRSGLTYSAPLSLTLK-ITSRTPSNDGTWHVRYSRSHQVYLGDMPMMTRKGSF 138

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           +++G +R ++   +R+ G+ F      +      + + RI+P +G W+++      ++  
Sbjct: 139 IVRGTERTLLVLQNRAYGLGFVPYLTYSMYDTPTVCSLRIVPHRGTWLELSIQDGAVLF- 197

Query: 205 RIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
           R +    +P T  L   G  ++ I     P+   +         +  +D      ++  +
Sbjct: 198 RFNAGVFMPATILLKGFGASTDAIAGMLTPRAGIAISPGGASIAIDLSD------IAFDV 251

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
              DT         +LT  L KS      + L I    +   +  E   +   G   + +
Sbjct: 252 QHFDTRLGHA----RLTRRLAKSRGSLEGRPLHIEDADVVNKF--ELASDASLGGRTVGS 305

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNN-AYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           G ++ ++ +          + ++          YI  TL  D+  D  DA   I   +  
Sbjct: 306 GTLLSQRVISMARADRESYLAVVNRCHHGAYLRYIARTLRMDRTVDPHDARACIAGHIGI 365

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                 + A S+F  +  ++  Y L+  GR ++N R+          +   DI   +K+L
Sbjct: 366 MRHLDPASAHSLFQGIMENARAYCLTPCGRSQLNARIGRHFSQGGDTLDARDIALSLKLL 425

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           ++        DD+D++ NR+ R   + L +  R   L ++R ++   ++          L
Sbjct: 426 INATRRNVRPDDVDDMSNRKARDACDALCDALRPAFLGLKRRLRSH-TANSRPGEAIAIL 484

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           +    V     +   +S+L+Q  +  N L+ +TH RR++ +        RA +  RDVH 
Sbjct: 485 LGLHAVTHQAYDELTNSRLAQPLDQTNPLAEVTHKRRVAIIAGSDSGPRRAPLGARDVHA 544

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL + AR++A G I  PY             Y+S  EE 
Sbjct: 545 THYGRLCPVETPEGQNIGLIASLAARARIDAQGTILAPYVVTRRNATRAAARYISPQEEV 604

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
               A +              +  R      +V   ++  +D + +  +S A + IPFLE
Sbjct: 605 GAMSAPSAIVPHSRRRT----IMARIGHGVAMVHPSEVILVDGANEMALSAATATIPFLE 660

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++D+ R LMG NMQRQAVP      P V TGME  VA+ +  AI A+ AG V  VD + I
Sbjct: 661 HNDACRALMGSNMQRQAVPCCYPRKPRVHTGMEQAVAQHAMVAIRARYAGRVAYVDPLHI 720

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            I  +      +      YRL +  R+NQ T  + RP V  G  V+  D+IADGP+++ G
Sbjct: 721 AIVPICE----NQGHACTYRLARNVRTNQGTQADHRPTVIPGSYVQAGDVIADGPASEGG 776

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            LALGR++LVAFMPW GYN+EDS+ +SE ++    +TS+H++E  V           ++R
Sbjct: 777 VLALGRDVLVAFMPWEGYNYEDSVAVSEALLRNGAYTSVHLDEVSVDMDGDDGCGTVLSR 836

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            +P +++     +DE GI+ VG+ V PGDI+VG+I+P+          LLR         
Sbjct: 837 CVPGITQSQRDRLDERGIVRVGSMVYPGDIIVGRISPRHAGIAPKGNSLLRTALATSEQA 896

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            RD+S+R   G++GTVV  RI   +  D ++        +  LL R
Sbjct: 897 NRDSSIRATQGMTGTVVYSRIEPCNQPDVHDDLPGQCAGEQSLLRR 942



 Score =  406 bits (1044), Expect = e-110,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 191/305 (62%), Gaps = 17/305 (5%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R +KV +A +  +Q GDK++GRHGNKG+VS+++P EDMP++K+G  VD+++NPLGVPSRM
Sbjct: 993  RTLKVAIASRIDLQPGDKVSGRHGNKGVVSKVVPIEDMPYMKNGRSVDVIVNPLGVPSRM 1052

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQ+ ETH+G A + L  +  +  +   ++     +   L    G        +     
Sbjct: 1053 NVGQLLETHIGLASIALEARSNTAEHLLCSSAYHDAMCHGLMACDGRCYPACSAAGGSPG 1112

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA---------DLDESGQSILYDGLTG 1242
              + +            P FDG  E  I SM R A          L    Q+ILYDG TG
Sbjct: 1113 HRVTLCTL--------CPAFDGPSEAEIRSMARAAATQGVRFKHGLHRRHQAILYDGRTG 1164

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
              +DRPVTVG++Y LKLNH+  +KV++RSTG YSLVT+QPLGGK+  GGQR+GEMEVW +
Sbjct: 1165 TQYDRPVTVGFMYYLKLNHLARNKVHSRSTGPYSLVTEQPLGGKARSGGQRVGEMEVWAL 1224

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            +A+GAA+ LQEMLTIKSDDV GR RV++ I         GTPES  +LV+E+++L + + 
Sbjct: 1225 EAHGAAFTLQEMLTIKSDDVGGRRRVHDHIAQDVRPLSYGTPESIGLLVRELRSLCVDVV 1284

Query: 1363 LENSR 1367
             E ++
Sbjct: 1285 AEQAQ 1289


>gi|313625345|gb|EFR95142.1| DNA-directed RNA polymerase, beta subunit [Listeria innocua FSL
            J1-023]
          Length = 419

 Score =  474 bits (1219), Expect = e-131,   Method: Composition-based stats.
 Identities = 148/327 (45%), Positives = 191/327 (58%), Gaps = 54/327 (16%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 124  LDVKIFTREAGDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFM 183

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 184  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEA 243

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 244  GMARDAK----------------------------TVLYDG------------------- 256

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 257  -------RSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 309

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            R GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+K
Sbjct: 310  RFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIK 369

Query: 1353 EMQALGLSIDLENSRTKNSAKMEEIPD 1379
            E+Q+LG+ + + ++  +     +   D
Sbjct: 370  ELQSLGMDVKMLSADEEEIEMRDMDDD 396



 Score =  132 bits (333), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 89/135 (65%), Positives = 110/135 (81%)

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W GYN+ED++++SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV E+ L+++
Sbjct: 1   TWDGYNYEDAIIMSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDL 60

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII VGAEV   D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  
Sbjct: 61  DERGIIRVGAEVKDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGG 120

Query: 937 GTVVDVRIFNRHGID 951
           G V+DV+IF R   D
Sbjct: 121 GIVLDVKIFTREAGD 135


>gi|51209978|ref|YP_063642.1| RNA polymerase beta subunit [Gracilaria tenuistipitata var. liui]
 gi|68053109|sp|Q6B8R8|RPOB_GRATL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|50657732|gb|AAT79717.1| RNA polymerase beta subunit [Gracilaria tenuistipitata var. liui]
          Length = 1120

 Score =  474 bits (1219), Expect = e-131,   Method: Composition-based stats.
 Identities = 338/803 (42%), Positives = 473/803 (58%), Gaps = 49/803 (6%)

Query: 165 FDHDKGRASLSGKLLYACRI-IPDQGLWMDIEFDS------KDIIHVR----IDRR-RKV 212
           F     R + S    Y+ +I IP +    DIE         KD+ +      I+++ RK 
Sbjct: 64  FPRYSVRKAKSRDKTYSAQIYIPAKLTRRDIEVIKENISTSKDLSYFFNSQDINKKYRKR 123

Query: 213 PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
           PV              L     +  +   G          + +V +       ++D   +
Sbjct: 124 PVFI----------GDLPLMTNRGTFVISG----TERIIINQIVRSPGVYYKKELDKNNK 169

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
            I S   +++       E   K              A          I++ +  + +E  
Sbjct: 170 QIYSCSIISNRGSWLKFEIDSKAQIWAKIDKNHKVSAY---------IFLRSIGLNNEDI 220

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK-DRKDALLDIYRVMRPGDVSTFSV 391
            + +          L   +     + ++    D  K   ++AL+ +Y  +RP + +T +V
Sbjct: 221 RKRLTKYNYLINSSL---TYYKKEFSKDVNNVDIEKITEEEALVIVYSKLRPNEPATLAV 277

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN-GK 450
           A+ M    FFD  +YDL  VGR K+N +LNL  P   R +  EDI+  +  L++++    
Sbjct: 278 AKQMLYTRFFDPKRYDLGAVGRHKINQKLNLKVPTHFRVLSPEDILVSLDYLLNIKEQNI 337

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           GT DDID+LGNRRVRSVGE+L+NQ R+GL R+ER I+ER+   D+DS+   +L+N KP++
Sbjct: 338 GTFDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMIICDLDSLSLSNLVNPKPLM 397

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           ++V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ + RAG  +RD+HP+HYGRIC
Sbjct: 398 ASVREFFSSSQLSQFMDQTNPLSELTHKRRISALGPGGLNKDRAGFAVRDLHPSHYGRIC 457

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIA 628
           P ET EG N GL+ SL+ +A+VN YGFIETP  KV DG+V   + + Y++A +E+   IA
Sbjct: 458 PIETPEGPNAGLIGSLSIYAKVNRYGFIETPCYKVTDGQVLKKDKLYYITADQEDYLRIA 517

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            A+ SLD +    ++++  R   E I     ++D++  SP Q +S A SLIPFLE+DD+N
Sbjct: 518 PADISLDVNDFIQDKIIAVRYKQEFITATISQVDYMAVSPIQFISAATSLIPFLEHDDAN 577

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPLL  E   VGTG+E+ +AK SG  I+++  G V  V   +I I++ 
Sbjct: 578 RALMGSNMQRQAVPLLFPEKSIVGTGLEAKIAKDSGMTIISRTNGTVSYVSGTKIGIQNK 637

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           EG           YRL K+ RSNQ+TC+NQRP+V  G+ +R    IADG STD G++ALG
Sbjct: 638 EGYTI-------HYRLKKYYRSNQDTCINQRPIVWPGENIRIGQTIADGASTDGGEIALG 690

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           RN++VA+MPW GYN+ED+ LISER+V ED++TSIHIE +E+  R TKLG EEITRDIPNV
Sbjct: 691 RNIIVAYMPWEGYNYEDAFLISERLVYEDLYTSIHIERYELECRQTKLGSEEITRDIPNV 750

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           SE  +  +D+ GII +G+ V+ GDILVGK+TPKGES   PE KLLRAIFGEKA DVRDTS
Sbjct: 751 SEASIGLLDKNGIISIGSWVDAGDILVGKVTPKGESDQLPEGKLLRAIFGEKARDVRDTS 810

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           LR+P+   G VV+V+IF R   D
Sbjct: 811 LRLPNATKGRVVNVKIFKRQKGD 833



 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 183/537 (34%), Positives = 260/537 (48%), Gaps = 63/537 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              K G     R            I++  I+  G  +  G  +    +  G       E  
Sbjct: 635  QNKEGYTIHYRLKKYYRSNQDTCINQRPIVWPGENIRIGQTIADGASTDG------GEIA 688

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIELLARDK 971
            L           R+  +           D  + +   + ++  + I +ER ++E      
Sbjct: 689  LG----------RNIIVAYMPWEGYNYEDAFLISERLVYEDLYTSIHIERYELECRQTKL 738

Query: 972  DDEQVILDR-NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              E++  D  N+    + +L     +S         +L   +  +    Q  +  +    
Sbjct: 739  GSEEITRDIPNVSEASIGLLDKNGIISIGSWVDAGDILVGKVTPKGESDQLPEGKLLRAI 798

Query: 1031 VQRNVESLKVQYETSKSILEDRFKN-KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                   ++       +  + R  N KI K Q GD++PPG   +++V+VA KR IQ GDK
Sbjct: 799  FGEKARDVRDTSLRLPNATKGRVVNVKIFKRQKGDELPPGTNEIIRVYVAQKRKIQVGDK 858

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGI+SRIL  +DMPFL DGTPVDI+LNPLGVPSRMNVGQ+FE  LG A     
Sbjct: 859  MAGRHGNKGIISRILSLQDMPFLPDGTPVDIILNPLGVPSRMNVGQLFECLLGLAGEYSS 918

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            K+ K +  D     + S    +        +  ++ S  +D S L  A            
Sbjct: 919  KRFKIIPFDEMYGSEASRALVY--------NKLKQASSMNDKSWLFNAL----------- 959

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                  G+ +L DG TGE FD PVTVG  Y+LKL H+V DK++A
Sbjct: 960  --------------------HPGKVMLVDGRTGEFFDNPVTVGKAYILKLVHLVDDKIHA 999

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGG++  GGQRLGEMEVW ++A+GAAY LQE+LT+KSDD+ GR    
Sbjct: 1000 RSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGAAYTLQELLTVKSDDMQGRNDAL 1059

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSI-----DLENSRTKNSAKMEEIPDFN 1381
             +IV G    + GTPESF VL++E+Q+L L I     +L ++  K S +++ + D  
Sbjct: 1060 NAIVKGKPIPKPGTPESFKVLMRELQSLALDIAVHKLELLDNGNKASIEIDLMSDEQ 1116



 Score =  247 bits (631), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 89/461 (19%), Positives = 175/461 (37%), Gaps = 52/461 (11%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPP 84
           PDL  +QK S+  FL+          EGL     S   I   +G   L+F    Y+   P
Sbjct: 16  PDLAAIQKESFKSFLL----------EGLSEVLDSFPIIVDPTGKLELQFFGKDYKLKFP 65

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI--------------KDIKEQSI 130
           ++ V     RD TY+  + I  +L   D++      S               K  +++ +
Sbjct: 66  RYSVRKAKSRDKTYSAQIYIPAKLTRRDIEVIKENISTSKDLSYFFNSQDINKKYRKRPV 125

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           ++GDLPLMT  GTFVI G +RI+++Q+ RSPG+++  +  +   + K +Y+C II ++G 
Sbjct: 126 FIGDLPLMTNRGTFVISGTERIIINQIVRSPGVYYKKELDK---NNKQIYSCSIISNRGS 182

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI--------VYSQRG 242
           W+  E DSK  I  +ID+  KV    FL ++G+++E+I                 Y +  
Sbjct: 183 WLKFEIDSKAQIWAKIDKNHKVSAYIFLRSIGLNNEDIRKRLTKYNYLINSSLTYYKKEF 242

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGV-------- 293
                 +    +     +      +   E   +   K++        K   +        
Sbjct: 243 SKDVNNVDIEKITEEEALVIVYSKLRPNEPATLAVAKQMLYTRFFDPKRYDLGAVGRHKI 302

Query: 294 -KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            + L +       +   EDI+      + I+  ++     ++ + +  +R +  L  + V
Sbjct: 303 NQKLNLKVPTHFRVLSPEDILVSLDYLLNIKEQNIGTFDDIDHLGNRRVRSVGELLQNQV 362

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                    ++ ++        L +  ++ P      +     F+           + + 
Sbjct: 363 RIGLNRLERIIRERMIICDLDSLSLSNLVNPK--PLMASVREFFSSSQLSQFMDQTNPLS 420

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +    R++   P     + K+     ++ L     G+   
Sbjct: 421 ELTHKRRISALGPGG---LNKDRAGFAVRDLHPSHYGRICP 458


>gi|46361012|gb|AAS89239.1| RpoB [Corynebacterium phocae]
          Length = 1060

 Score =  473 bits (1218), Expect = e-131,   Method: Composition-based stats.
 Identities = 321/661 (48%), Positives = 445/661 (67%), Gaps = 25/661 (3%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++  D+   +T  + +       +     +      +  I   +    +  + +TL  
Sbjct: 192 GAWLEFDVDKRDT--VGVRIDRKRRQPVTVLLKALGWTEEQI--RERFGFSELMMSTLEG 247

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   +  +ALL+IYR  RPG+  T  +A +M    FF + +YDL+ VGR K+N +L L  
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGG 307

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKG------------TIDDIDNLGNRRVRSVGEML 471
             D +  + +EDI   ++ LV L  G+               DDID+ GNRR+R+VGE++
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGQMIPLNTDDIDHFGNRRLRTVGELI 367

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  NS
Sbjct: 368 QNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNS 427

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+AR
Sbjct: 428 LSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 487

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CA 650
           VN +GFIETPYRKV DG++T++VVY++A EE+   IAQA    DE G  T+  +  R   
Sbjct: 488 VNPFGFIETPYRKVEDGRITDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKE 547

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G+  +   + +DFID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAPF
Sbjct: 548 GDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPF 607

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  +G  I+  + G+VE V A  I I    G  D        Y L KF+R+
Sbjct: 608 VGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIMDDSGQRD-------TYLLRKFERT 660

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ T  NQ PLV  GD V    ++ADGP T  G+++LGRN+LVAFMPW G+N+ED+++++
Sbjct: 661 NQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILN 720

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +++V +D  TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ L+++D+ GII +GA+V P
Sbjct: 721 QQIVEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRP 780

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTS++VP G +G V+ V  F+R   
Sbjct: 781 GDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDED 840

Query: 951 D 951
           D
Sbjct: 841 D 841



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 146/443 (32%), Positives = 207/443 (46%), Gaps = 61/443 (13%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N ++  ++  G  V  G +L           M+    LL A    +  +  D  +     
Sbjct: 665  NYNQTPLVSAGDRVEAGQVLADGPGT-HNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQI 723

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLME 988
            V    +       H ID  +  +  E    +I    E + RD DD   I+      R  +
Sbjct: 724  VEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDR-GIIRIGADVRPGD 782

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            IL G+    G         L   +  E  R                V  +          
Sbjct: 783  ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVA--------- 833

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                           DD+ PGV  +++V+VA KR IQ GDK+AGRHGNKG+V +ILP ED
Sbjct: 834  --------RFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPED 885

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF++DGTPVDI+LN  GVP RMN+GQ+ E HLGW     G KI       +   +   L
Sbjct: 886  MPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLA-HSGWKIDV-----EDPKNAEIL 939

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
            ++  E++    + +                        +TPVFDGA  E I+ +L  +  
Sbjct: 940  KTLPEELYDVPADSLT----------------------ATPVFDGATNEEISRLLASSRP 977

Query: 1229 DESG--------QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +  G        ++ L+DG +GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQ
Sbjct: 978  NRDGDVLVDEHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQ 1037

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQ 1303
            QPLGGK+  GGQR GEMEVW +Q
Sbjct: 1038 QPLGGKAQFGGQRFGEMEVWAMQ 1060



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 92/388 (23%), Positives = 169/388 (43%), Gaps = 46/388 (11%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFL---------MMNIAPDERPNEGLQAAFKSVFP 64
           R  F K  E I +P L++VQ  SY   +              PD R   GL+     + P
Sbjct: 19  RYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREREQELRGPDARVTSGLEDILNELSP 78

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  +S    L      F+P K+ VD+   +D+ Y+ PL +T   +          K  ++
Sbjct: 79  IEDYSERMSLSLSEPRFEPVKYTVDESKEKDINYSAPLYVTAEFV---------NKDTQE 129

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R++VSQL RSPG++FD    +   + + L+A ++
Sbjct: 130 IKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQTIDK--STERPLHAVKV 187

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV--YSQRG 242
           IP +G W++ + D +D + VRIDR+R+ PVT  L ALG   E+I   F    +   +  G
Sbjct: 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFGFSELMMSTLEG 247

Query: 243 DFWCFPLSAADLMV-----GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV---- 293
           D       A   +      G + +  L          ++ +   + + +    + +    
Sbjct: 248 DGVANTDEALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGG 307

Query: 294 ----------KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                     + + +T + L  L+  E  +    G++       ++   ++   +  +R 
Sbjct: 308 DHDGLMTLTEEDIAVTLEYLVRLHAGEREMKAPNGQMI-----PLNTDDIDHFGNRRLRT 362

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +  L  + V         +V ++   + 
Sbjct: 363 VGELIQNQVRVGLSRMERVVRERMTTQD 390


>gi|108773319|ref|YP_635874.1| beta subunit of RNA polymerase [Oltmannsiellopsis viridis]
 gi|109904551|sp|Q20EX1|RPOB_OLTVI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|82541901|gb|ABB81942.1| beta subunit of RNA polymerase [Oltmannsiellopsis viridis]
          Length = 1416

 Score =  473 bits (1217), Expect = e-130,   Method: Composition-based stats.
 Identities = 256/759 (33%), Positives = 384/759 (50%), Gaps = 84/759 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           +PD I VQ+ S+  FL            GL        PIT  +    L F    Y+  P
Sbjct: 12  VPDFIAVQRNSFSQFL----------ESGLIQEISKRNPITNSTKELELCFYPQYYKLSP 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P+ +    + ++ TY+  L I ++L           K  K +K Q + +G+LPLMTK G 
Sbjct: 62  PELNAKQSILKNKTYSCRLYIPVKLT---------NKRTKTLKLQWVVLGNLPLMTKRGH 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G  R++++Q+ RSPG++F   K  +    KL Y   +I  +G W+ IE D K  I 
Sbjct: 113 FIINGSPRVIINQMVRSPGVYF---KEVSHADQKLTYYADLIAYRGAWLRIELDKKADIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ +  K+P+   L ALG++   IL +  YPK   +   D                   
Sbjct: 170 ARMKKTPKLPMLILLQALGLNLPTILKSLNYPKFFENLGHDGNFMKQ------------- 216

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                      ++ G+  +    + L         ++                       
Sbjct: 217 -----------LKKGRVSSRSSSQELSGSFNLSEDVSL-------------------RLD 246

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY---R 379
           ++   +  ++++     +      L+ D   ++ Y          K +++AL  +Y    
Sbjct: 247 DSSKNMGAENVQRAPLQKSTKKATLFGDFSRSSVY---------CKTQEEALWALYALTH 297

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            ++  D  T ++ +S     F +S  YDLS +GR+++N +LNL   +++  I  +D++ I
Sbjct: 298 PLKNPDEVTANLGKSFLYRKFMNSRVYDLSPLGRLRLNQKLNLSVNENITTITAQDLLFI 357

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
              L++L  G G +DDIDNL NRR+R+ GE+++NQ+ +GLLR+E+ I+E++       + 
Sbjct: 358 TNTLINLNYGVGKVDDIDNLKNRRIRTAGELVQNQFGIGLLRLEKIIREKLKQQQT-KLS 416

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
              LIN KP+  A+ EFF SS LSQ  +  N L+ ITH RRLS+LG GGV R  AG+ +R
Sbjct: 417 IGSLINTKPINGALREFFGSSPLSQFMDQTNPLAEITHKRRLSSLGPGGVNRETAGMAIR 476

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN--DVVYL 617
            +HPTHYGRICP ET EG N GLV+SLT ++RVN YGFIETP+ KV  G+V N    ++ 
Sbjct: 477 GIHPTHYGRICPIETPEGQNAGLVNSLTIYSRVNPYGFIETPFYKVVKGQVQNSTRPIFF 536

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA +EE + +A  +   ++     +  +  R   E     REKID+I  SP Q++SIA S
Sbjct: 537 SAYQEEKKLLAPGDIYANKLKYLPKSELPIRKLAEFTRTTREKIDYISVSPLQMISIATS 596

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPL+ AEAP VGTG+E  VA  SG  + AK++G V  
Sbjct: 597 LIPFLEHDDANRALMGSNMQRQAVPLMTAEAPVVGTGLECRVASDSGHVLQAKKSGFVTY 656

Query: 738 VDAIRIVI-RSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
             A +I I   V+                 F  S   +C
Sbjct: 657 SSAEKITILSPVDSTPAVPKLSKGNNSPQHFHESVGGSC 695



 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 170/491 (34%), Positives = 237/491 (48%), Gaps = 60/491 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  VN GD+L    T  G   ++  + LL A    +  +  D  L     VS    
Sbjct: 970  VVREGEWVNRGDLLADNSTTVG-GELSLGKNLLLAYMPWEGYNFEDAILISERLVSDDAY 1028

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLAR-DKDDEQVILDRNIYSRLMEILCGQNAVS 997
                  R+ ++  E    +E+   QI    +    D   I     +    +IL G+ A  
Sbjct: 1029 TSLHIERYEVEIRETKFGLEQITSQIPDEGKLSHLDHFGIAKPGTWVEEGDILIGKVAPM 1088

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
              K   +   L    + +    +         +V R V    +  E   +          
Sbjct: 1089 PQKNLSRYEKL----LYDVVGKKISTTRDTSLRVPRGVSGRVIHVEILNAE--------- 1135

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                   +        V +++A KR I  GDKMAGRHGNKGI+S ILP +DMP+L DGTP
Sbjct: 1136 ---NLPPEFVFEGPSRVNLYIAEKRKIHVGDKMAGRHGNKGIISNILPRQDMPYLPDGTP 1192

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            +D+VLNPLGVPSRMNVGQI+E  LG A   LG+K K    D               ++ G
Sbjct: 1193 LDMVLNPLGVPSRMNVGQIYECLLGLAGRYLGQKFKVRPFD---------------EIYG 1237

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
              +    +     ++ LR  ++W                        + +    G++ L+
Sbjct: 1238 PQTSRSLVYSKLYEARLRTGQRW------------------------LFNPASPGKTRLF 1273

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            DG TGE F +PVTVG  YMLKL H+V +K++ARS G YSLVTQQPL G+S  GGQRLGEM
Sbjct: 1274 DGRTGECFSQPVTVGQAYMLKLIHLVDEKIHARSIGPYSLVTQQPLRGRSKHGGQRLGEM 1333

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQAL 1357
            EVW ++ +GAAY LQE+LT+KSDD+ GR +V ESI         GTPESF VL++E+Q+L
Sbjct: 1334 EVWALEGFGAAYTLQELLTVKSDDIKGREQVMESIQKNKTIS-LGTPESFKVLIRELQSL 1392

Query: 1358 GLSIDLENSRT 1368
             L + +     
Sbjct: 1393 CLDVGVYAVDG 1403



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 94/198 (47%), Positives = 128/198 (64%), Gaps = 2/198 (1%)

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                  +      Y L K  RSNQ+T +  RP+V+ G+ V R D++AD  +T  G+L+LG
Sbjct: 938  MDFSTKTQLKPITYELQKLFRSNQDTSIMHRPVVREGEWVNRGDLLADNSTTVGGELSLG 997

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +N+L+A+MPW GYNFED++LISER+VS+D +TS+HIE +EV  R+TK G E+IT  IP  
Sbjct: 998  KNLLLAYMPWEGYNFEDAILISERLVSDDAYTSLHIERYEVEIRETKFGLEQITSQIP-- 1055

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
             E  L ++D  GI   G  V  GDIL+GK+ P  +  ++  EKLL  + G+K    RDTS
Sbjct: 1056 DEGKLSHLDHFGIAKPGTWVEEGDILIGKVAPMPQKNLSRYEKLLYDVVGKKISTTRDTS 1115

Query: 929  LRVPSGVSGTVVDVRIFN 946
            LRVP GVSG V+ V I N
Sbjct: 1116 LRVPRGVSGRVIHVEILN 1133


>gi|208751317|gb|ACI31271.1| beta subunit of RNA polymerase [Volvox carteri]
 gi|261888211|gb|ACY06066.1| beta subunit of RNA polymerase [Volvox carteri f. nagariensis]
          Length = 652

 Score =  473 bits (1217), Expect = e-130,   Method: Composition-based stats.
 Identities = 217/639 (33%), Positives = 306/639 (47%), Gaps = 108/639 (16%)

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            + ++   +    PS      Y L  ++RSNQ+TC+ Q+P VK GD +   D++AD  S+ 
Sbjct: 98   KKLLSYPKNYSTPSRKLFLKYNLETYRRSNQDTCLIQKPAVKEGDWIETGDLLADSASSV 157

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             G+LA+G N++VA+MPW GYN+ED++LI+ER+V ED++TS+HIE +              
Sbjct: 158  GGELAIGHNIIVAYMPWEGYNYEDAILINERLVYEDLYTSVHIERY-------------- 203

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                                     EV   D  +G      E P T E         E +
Sbjct: 204  -------------------------EVLTTDTKLGSEQITREIPDTNE--------NEIS 230

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
               ++   ++ S V    + V       I            Q +LL +  + +      +
Sbjct: 231  HLDKNGIAKIGSWVEEGDILVGKVTPFNIKT-------LTPQQKLLYKIFNKQLSATKDS 283

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                         A  G K    +  +      E       +  +  +     +    + 
Sbjct: 284  ----------SLRAPKGIKANVINVNILKKQKIELNNKDKKKIVITKKAKINLLTQQTIS 333

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             + +++   +    +  K +  +   P     V +++A KR IQ GDKMAGRHGNKGI+S
Sbjct: 334  VQNNQNQNTNNTNGRRRKREISNTYAPS---YVHIYLAEKRKIQVGDKMAGRHGNKGIIS 390

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            RILP +DMPFL DGT VDIVLNPLGVPSRMNVGQI+E  LG A   LG+  K    D   
Sbjct: 391  RILPRQDMPFLPDGTSVDIVLNPLGVPSRMNVGQIYECLLGLAGRYLGEHYKIPPFD--- 447

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                        ++ G  +    +     D+  +    W          FD         
Sbjct: 448  ------------EMYGADASRSFVLSKLYDARKKTGLNWL---------FD--------- 477

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+  L+DG   E FD+ VTVG  Y+LKL HMV DK++ARSTG YSLVTQQ
Sbjct: 478  ------PNHPGKIRLFDGRNSECFDQTVTVGIAYVLKLVHMVDDKLHARSTGPYSLVTQQ 531

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G+S +GGQRLGEMEVW I+ YGAA+VL EMLTIKSDD+ GR  ++++++  ND    
Sbjct: 532  PLRGRSKQGGQRLGEMEVWAIEGYGAAFVLSEMLTIKSDDMTGRQNLWKNLIENNDIS-L 590

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT-KNSAKMEEIPD 1379
            G+PESF VLV E+QAL L I L      K    +  + D
Sbjct: 591  GSPESFKVLVCELQALCLDIGLFRKNGIKQDINLINLED 629


>gi|297624693|ref|YP_003706127.1| DNA-directed RNA polymerase subunit beta [Truepera radiovictrix DSM
            17093]
 gi|297165873|gb|ADI15584.1| DNA-directed RNA polymerase, beta subunit [Truepera radiovictrix DSM
            17093]
          Length = 1133

 Score =  473 bits (1216), Expect = e-130,   Method: Composition-based stats.
 Identities = 180/509 (35%), Positives = 256/509 (50%), Gaps = 33/509 (6%)

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                      N+D+  ++ VG  V  G I+      +    +   + +L AI      + 
Sbjct: 641  TRFQRSNQNTNLDQRPLVDVGDRVEAGQIIADGPASQN-GRLALGQNVLIAIMPFDGYNF 699

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDEQVILDR 980
             D  +     +S  +V    +    I+K E+     +   E + RD     +     LD 
Sbjct: 700  EDAIV-----LSERLVRSDAYTSVHIEKYEKEARDTKLGPEKITRDIPGLSEAALRDLDE 754

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +   R+   +   + + G   FK  T  + +      RS + + A + +     V     
Sbjct: 755  DGVVRIGAEVKQGDILVGHTSFKGETEPTPE--ERLLRSIFGEKAREVKDTSLRVPPGDG 812

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                              +   G ++ PGV  +V+V+VA KR +  GDK+A RHGNKG+V
Sbjct: 813  GIVLRTVRFR--------RGDPGVELKPGVQEMVRVYVAQKRRLIEGDKLANRHGNKGVV 864

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            ++ILP EDMP+L DGTPVD+V NPLGVPSRMN+GQI ETHLG A    G    + + D  
Sbjct: 865  AKILPPEDMPYLPDGTPVDLVFNPLGVPSRMNLGQILETHLGLAAFKNGVSYVTPVFDSA 924

Query: 1161 ANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
               +I  L   + +           + D  +  V+R A +             G     +
Sbjct: 925  REEEIKDLLEAVTERELAEEREAGFVPDRREQQVMRRAAKL------------GIIGRDL 972

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +       L  +G+S+LYDG TGE  D P+ VG +Y++KL HMV DK++ARSTG YSL+T
Sbjct: 973  SYEEARLALARTGKSVLYDGQTGEAIDAPIVVGVMYVMKLYHMVEDKMHARSTGPYSLIT 1032

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPLGGK+  GGQRLGEME W +QA+GAA+ LQEMLTIKSDD+ GR   YE+IV GND  
Sbjct: 1033 QQPLGGKAQFGGQRLGEMECWALQAHGAAHTLQEMLTIKSDDIDGRNASYEAIVKGNDVL 1092

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            E   PESF VLVKE+ +LGL + + +   
Sbjct: 1093 EPTIPESFKVLVKELHSLGLDVQVMDGER 1121



 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 308/638 (48%), Positives = 418/638 (65%), Gaps = 25/638 (3%)

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                ++ALL ++ V+RPGD      A S    L  D  +YDL   GR KMN +L L   
Sbjct: 231 MGATVEEALLRLFTVLRPGDPPKVDKAISYLYSLLADPRRYDLGEAGRYKMNSKLGLTYQ 290

Query: 426 D------DVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
                  +        ++  I+ LV L+ G+  +            DDID+LGNRR+R+V
Sbjct: 291 QSTLMGFEEGRFVDYGLVPTIQYLVKLQAGETEMTSPAGETVAVEEDDIDHLGNRRIRTV 350

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE++ +Q R+GL RM R ++ER+   + D+  PQ L+N +P+V+A+ EFF  SQLSQ ++
Sbjct: 351 GELVADQIRVGLGRMARGVRERMLLGNPDAATPQKLVNNRPIVAALREFFGRSQLSQFKD 410

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            VN LS + H RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL++SL 
Sbjct: 411 QVNPLSELRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLITSLA 470

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           S++RVN  GFIE PYR+V +G+VT+DV Y++A EE+   IAQAN+ L +D  F EE V  
Sbjct: 471 SYSRVNPLGFIEAPYRRVENGRVTSDVQYMTAHEEDRYVIAQANTPLTDDNRFAEESVLT 530

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G+   VP E ++F+D SPKQ+VS+  SLIPFLE+DD+NR LMG NMQ QAVPL+K +
Sbjct: 531 RRLGDPYYVPPEAVEFMDVSPKQIVSVPTSLIPFLEHDDANRALMGSNMQSQAVPLIKPD 590

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP+VGTG+E  V++ SG  ++A+ AG V  VDA RIVI +              Y L +F
Sbjct: 591 APYVGTGVEERVSRDSGTVVIAQEAGTVTFVDASRIVIEND-------RQVAREYVLTRF 643

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSNQNT ++QRPLV VGD V    IIADGP++  G LALG+N+L+A MP+ GYNFED++
Sbjct: 644 QRSNQNTNLDQRPLVDVGDRVEAGQIIADGPASQNGRLALGQNVLIAIMPFDGYNFEDAI 703

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V  D +TS+HIE++E  ARDTKLGPE+ITRDIP +SE  L+++DE G++ +GAE
Sbjct: 704 VLSERLVRSDAYTSVHIEKYEKEARDTKLGPEKITRDIPGLSEAALRDLDEDGVVRIGAE 763

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG  + KGE+  TPEE+LLR+IFGEKA +V+DTSLRVP G  G V+    F R
Sbjct: 764 VKQGDILVGHTSFKGETEPTPEERLLRSIFGEKAREVKDTSLRVPPGDGGIVLRTVRFRR 823

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
                  +    E  ++ +  + +  E   L     ++
Sbjct: 824 GDPGVELKPGVQEMVRVYVAQKRRLIEGDKLANRHGNK 861



 Score =  276 bits (705), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 97/295 (32%), Positives = 149/295 (50%), Gaps = 32/295 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGA---A 72
           FG   E+I++P+L ++Q  SY+ FL +  AP ER N GLQ+AF+ VFPI     G     
Sbjct: 7   FGSIEEVIELPNLTDIQIKSYNTFLQLGRAPAERENIGLQSAFREVFPIDETERGRQTGL 66

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           +L+F+ Y   PP+F  ++C  +DLTY   L   L+L+  D            IKE  +++
Sbjct: 67  VLDFLEYTLHPPEFSPEECREKDLTYQAGLFAKLQLVHKD---------TGLIKEDQVFL 117

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QGL 190
           GDLPLMT+DG+FVI G  R++VSQ+HRSPG +F    G    +G+  Y   IIP   +G 
Sbjct: 118 GDLPLMTEDGSFVINGADRVIVSQIHRSPGAYFT---GAPKGTGRT-YMASIIPMPKRGP 173

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
           W+++EFD+ D++ ++++ ++K P T  L  LG    EI   F                  
Sbjct: 174 WIELEFDNADVLWMKVN-KKKFPFTLLLRVLGFGDAEIRGLFSGNETL-------IEATF 225

Query: 251 AADLMVGAKVSSSLVD----IDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             D  +GA V  +L+     +  G+   ++        LL   +   +   G   
Sbjct: 226 EEDAAMGATVEEALLRLFTVLRPGDPPKVDKAISYLYSLLADPRRYDLGEAGRYK 280


>gi|255023018|ref|ZP_05295004.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J1-208]
          Length = 600

 Score =  471 bits (1213), Expect = e-130,   Method: Composition-based stats.
 Identities = 342/639 (53%), Positives = 440/639 (68%), Gaps = 42/639 (6%)

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
           E +V+ ETGEI    GD++D ++L++I            + ++ N    R    TD   +
Sbjct: 1   ETLVDPETGEIIASKGDILDRRNLDQI------------IPNLENGVGFRTLRPTDGVME 48

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
               L+   ++  P D                             ++N+  N    ++V+
Sbjct: 49  -DSVLVQSIKIYAPND--------------------------EEKEINIIGNAYIEENVK 81

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
           HI   DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER
Sbjct: 82  HITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRER 141

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +S  D+ ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+
Sbjct: 142 MSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGL 201

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CD 607
            R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V    
Sbjct: 202 TRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPET 261

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            +VT+ + YL+A EE+N  +AQANS LDE G+FTEE V  R   E + V +E+ID++D S
Sbjct: 262 NRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERIDYMDVS 321

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQVVS+A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V AK SGAA+
Sbjct: 322 PKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGAAV 381

Query: 728 VAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            AK  GIVE V+A  I +R V   D    T G+D Y L KF RSNQ TC NQRP V  GD
Sbjct: 382 TAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAEGD 441

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V + +I+ +GPS D G+LALGRN+LVAFM W GYN+ED++++SER+V +DV+TSIHIEE
Sbjct: 442 RVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEE 501

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           FE  ARDTKLGPEE+TRDIPNV E+ L+++DE GII VGAEV   D+LVGK+TPKG + +
Sbjct: 502 FESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTEL 561

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV+IF
Sbjct: 562 TAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIF 600


>gi|124112108|ref|YP_001019104.1| beta subunit of RNA polymerase [Chlorokybus atmophyticus]
 gi|158564117|sp|Q19V98|RPOB_CHLAT RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|124012217|gb|ABD62240.2| beta subunit of RNA polymerase [Chlorokybus atmophyticus]
          Length = 1088

 Score =  471 bits (1211), Expect = e-130,   Method: Composition-based stats.
 Identities = 179/497 (36%), Positives = 258/497 (51%), Gaps = 55/497 (11%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  +  GDIL       G   +T  + +L A    +  +  D  L     +S  +V
Sbjct: 643  VVHQGEFIKKGDILADGAATVG-GQLTLGKNVLVAYMPWEGYNFEDAIL-----ISQRLV 696

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+    I+K E      +   E + R+  +    + RN+      ++ G    +G  
Sbjct: 697  YDDIYTSIHIEKYEIEARKTKLGPEKITREVPNLGDYVLRNLDEN-GIVIPGAWVEAGDI 755

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T    + + ++P  +  +    ++       SL       +     R +    + 
Sbjct: 756  LVGKVTP--KEDLDQHPEGKLLRAIFSEKARDVRDTSL-------RVPNGVRGRVVDVRR 806

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G ++P GV  VV +F++ KR IQ GDKMAGRHGNKGI+SRILP +DMP+L+DGTPVD+
Sbjct: 807  LKGSELPSGVNMVVHIFISQKRKIQVGDKMAGRHGNKGIISRILPRQDMPYLQDGTPVDM 866

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQ++E  LG A   LG++ K +  D               ++ G  +
Sbjct: 867  VLNPLGVPSRMNVGQVYECLLGLAGHFLGEEYKLIPFD---------------EMYGKEA 911

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                +     ++  +    W          FD A+                G+S L+DG 
Sbjct: 912  SRGFVYSKLYEARKKTGYPWL---------FDIAN---------------PGKSQLFDGR 947

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEPFD+PVTVG  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQRLGEMEVW
Sbjct: 948  TGEPFDQPVTVGRAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAKHGGQRLGEMEVW 1007

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++ +GAAY LQE+LT+KSDD+ GR     +I+ G    + GTPESF VL++E+Q+L L 
Sbjct: 1008 ALEGFGAAYTLQELLTVKSDDMKGRNEAQHAIIKGRPIPKPGTPESFKVLIRELQSLCLD 1067

Query: 1361 IDLENSRTKNSAKMEEI 1377
            I +         +  ++
Sbjct: 1068 IGIYKIDKTKKGQEIDL 1084



 Score =  456 bits (1173), Expect = e-125,   Method: Composition-based stats.
 Identities = 292/654 (44%), Positives = 415/654 (63%), Gaps = 14/654 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           ++G+K    ++  +C       +   + G ++   G V        +    +    IL  
Sbjct: 146 KEGIKTY--SASIICNRGAWLRLETDKNGFVWARIGKVRKVSGFILLRAMGLTKSKIL-- 201

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +S+ +  + + T+         DAL+D++  + P   ST   A  +    FFD   YDL 
Sbjct: 202 NSLRHPEFFQKTIEEGDPYSENDALIDLHSQLYPERPSTLFAARELLKSKFFDPKYYDLG 261

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            VGR K+N +L L  P+D+R +  +DI+  I  L++L    GT+DDID+L NRRVRSVGE
Sbjct: 262 KVGRYKINKKLQLSIPEDIRVLTPQDILTAIDYLINLEFNIGTLDDIDHLKNRRVRSVGE 321

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ R+GL R+ER   +R++    D++ P  LIN KP+V  + EFF SSQLSQ  +  
Sbjct: 322 LIENQVRVGLSRLERMTYKRMAESHPDALTPASLINPKPLVGVLREFFGSSQLSQFMDQT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RR+S LG GG+++ RAG+ +RD+HP+HYGRICP ET EG N GL+ SL + 
Sbjct: 382 NPLSEMTHKRRISCLGPGGLSKERAGLAVRDIHPSHYGRICPIETPEGPNAGLIGSLATH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ARVN YGF+E+P+    + KV      +YLS  +E+   ++  +  L   G    + V  
Sbjct: 442 ARVNPYGFLESPFYPTKNRKVFKKTLPIYLSPDQEDELRVSPGDLLLSSSGKLEGKTVPI 501

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   +      +++D++  SP Q +SIA SLIPFLE+DD+NR LMG NMQRQAVP+++ E
Sbjct: 502 RYKQDFSTSRSDQVDYVGISPIQAISIATSLIPFLEHDDANRALMGSNMQRQAVPVIRPE 561

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP--------STSGV 759
            P VGTG+E+  A  SG  IVA+  GIV  VD+ +I++RS  G                +
Sbjct: 562 RPVVGTGLEAQAALDSGTVIVARHDGIVSLVDSNKIILRSSCGSNQTKVDSVGLNFDYQI 621

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L K+ RSNQ+TC+NQRP+V  G+ +++ DI+ADG +T  G L LG+N+LVA+MPW 
Sbjct: 622 DRYHLQKYNRSNQDTCINQRPVVHQGEFIKKGDILADGAATVGGQLTLGKNVLVAYMPWE 681

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++LIS+R+V +D++TSIHIE++E+ AR TKLGPE+ITR++PN+ +  L+N+DE 
Sbjct: 682 GYNFEDAILISQRLVYDDIYTSIHIEKYEIEARKTKLGPEKITREVPNLGDYVLRNLDEN 741

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           GI+  GA V  GDILVGK+TPK +    PE KLLRAIF EKA DVRDTSLRVP+
Sbjct: 742 GIVIPGAWVEAGDILVGKVTPKEDLDQHPEGKLLRAIFSEKARDVRDTSLRVPN 795



 Score =  251 bits (641), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 96/492 (19%), Positives = 182/492 (36%), Gaps = 39/492 (7%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K+   I +PDL+ +Q  S+  FL           +GL    +    IT  +    L  
Sbjct: 8   FKKDAFDILLPDLVGIQLESFSTFL----------KKGLIEQLRDFSVITDPTNNLELRL 57

Query: 77  V--SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           +   Y+   P+++   C+ R  TYA  L I  +LI          K    ++EQ +++G+
Sbjct: 58  LVEQYKLKRPRYNEKKCIRRACTYASQLYIPAQLI---------NKKTGKVQEQDVFLGE 108

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +P+MT  G F+I G  R++V+Q+ RSPGI++  +       G   Y+  II ++G W+ +
Sbjct: 109 MPIMTSRGNFIINGSARVIVNQIVRSPGIYYKREIDPKE--GIKTYSASIICNRGAWLRL 166

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS-----TFYPKIVYSQRGDFWCFPL 249
           E D    +  RI + RKV     L A+G+   +IL+      F+ K +  + GD +    
Sbjct: 167 ETDKNGFVWARIGKVRKVSGFILLRAMGLTKSKILNSLRHPEFFQKTI--EEGDPYSEND 224

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIES-GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           +  DL                E +           L K  + K  K L ++      +  
Sbjct: 225 ALIDLHSQLYPERPSTLFAARELLKSKFFDPKYYDLGKVGRYKINKKLQLSIPEDIRVLT 284

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            +DI+      I +E  ++     ++ + +  +R +  L  + V         +   +  
Sbjct: 285 PQDILTAIDYLINLE-FNIGTLDDIDHLKNRRVRSVGELIENQVRVGLSRLERMTYKRMA 343

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           +     L    ++ P       V    F            + +  +    R++   P   
Sbjct: 344 ESHPDALTPASLINPK--PLVGVLREFFGSSQLSQFMDQTNPLSEMTHKRRISCLGPGG- 400

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             + KE     ++ +     G+  I  I+         +G +  +        +E     
Sbjct: 401 --LSKERAGLAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHARVNPYGFLESPFYP 456

Query: 489 RISSVDIDSVMP 500
             +       +P
Sbjct: 457 TKNRKVFKKTLP 468


>gi|71482618|gb|AAZ32301.1| RpoB [Afipia birgiae]
          Length = 248

 Score =  470 bits (1210), Expect = e-130,   Method: Composition-based stats.
 Identities = 161/251 (64%), Positives = 196/251 (78%), Gaps = 5/251 (1%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRM
Sbjct: 1    KMVKVFVAVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRM 60

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANG--DISPLRSFLEKVIGTGSHTEKISDYD 1189
            NVGQI ETHLGWAC GLGK+I   ++ Y  +G  DI PL+  L+KV G     E I   +
Sbjct: 61   NVGQILETHLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKETLKKVYGDD---EVIKTLN 117

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D  ++ +    ++GVP++TPVFDGA E  I  ML +A +++SGQS +YDG TG+ FDR V
Sbjct: 118  DTELMELGRNLRAGVPIATPVFDGAKEADIEQMLELAGMNKSGQSTVYDGRTGDQFDRNV 177

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 178  TVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 237

Query: 1310 VLQEMLTIKSD 1320
             LQEMLT+ SD
Sbjct: 238  TLQEMLTVSSD 248


>gi|46360984|gb|AAS89225.1| RpoB [Corynebacterium glucuronolyticum]
          Length = 1050

 Score =  470 bits (1210), Expect = e-130,   Method: Composition-based stats.
 Identities = 327/662 (49%), Positives = 454/662 (68%), Gaps = 27/662 (4%)

Query: 305 GLYVAEDIVNGET-GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           G ++  D+   +T G              L+ +  SE +       +    +  + +TL 
Sbjct: 189 GAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEK-----IRERFGFSEIMMSTLE 243

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            D      +ALL+IYR  RPG+  T  +A+++    FF   +YDL+ VGR K+N +L L 
Sbjct: 244 NDGAASEDEALLEIYRKQRPGEQPTRDLAQALLENSFFKPKRYDLAKVGRYKVNRKLGLG 303

Query: 424 TP-DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
              D V+ + +EDI   I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 304 GDHDGVKTLTEEDIATTIEYLVRLHAGERTMTSPDGVEIPLETDDIDHFGNRRLRTVGEL 363

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+GL R  R ++ER+++ D +S+ P  LIN +PV +A+ EFF +SQLSQ  +  N
Sbjct: 364 IQNQVRVGLARXXRVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNN 423

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           SLS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL S+A
Sbjct: 424 SLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYA 483

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           RVN +GFIETPY+KV +GK+ + V YL+A EE+   I QA++  DE+G  T+E    R  
Sbjct: 484 RVNPFGFIETPYQKVENGKIIDQVDYLTADEEDRFVIGQADTEHDENGVITQERNEVRLK 543

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G   +V  E I++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++++P
Sbjct: 544 DGAIEVVGPEAIEYIDVSPRQIVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSQSP 603

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +VGTGME+  A  +G  ++ K AG+VE V A  I + S EG  D        YRL KF+R
Sbjct: 604 YVGTGMEAPAAYDAGDLVINKHAGVVENVCADFITVMSDEGKRD-------TYRLRKFER 656

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +NQNTC NQ+PLV +GD V +  ++ADGP T  G+++LG N+LVAFMPW G+N+ED++++
Sbjct: 657 TNQNTCYNQKPLVDIGDRVEKGQVMADGPGTHDGEMSLGVNLLVAFMPWQGHNYEDAIIL 716

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ++R+V ED+ TSIHIEE E+ ARDTKLG EEITR+IPNVSE+ LK++DE GI+ +GA+V 
Sbjct: 717 NQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLKDLDERGIVRIGADVR 776

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G +G V+ V  F+R  
Sbjct: 777 DGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIGVSRFSRDE 836

Query: 950 ID 951
            D
Sbjct: 837 GD 838



 Score =  355 bits (912), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 142/459 (30%), Positives = 201/459 (43%), Gaps = 65/459 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  R             ++  ++ +G  V  G ++        +  M+    LL A
Sbjct: 643  EGKRDTYRLRKFERTNQNTCYNQKPLVDIGDRVEKGQVMADGPGT-HDGEMSLGVNLLVA 701

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQI----ELLAR 969
                +  +  D  +     V   ++       H ID  +  +  E    +I    E + +
Sbjct: 702  FMPWQGHNYEDAIILNQRVVEEDLLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLK 761

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  DE+ I+      R  +IL G+    G         L   +  E  R           
Sbjct: 762  DL-DERGIVRIGADVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAR----------- 809

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                  E      +                   GD++P GV  ++++ VA KR IQ GDK
Sbjct: 810  ------EVRDTSLKVPHGETGKVIGVSRFSRDEGDELPAGVNEMIRIHVAQKRKIQDGDK 863

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKG+V +ILP EDMPF++DGTP+DI+LN  GVP RMN+GQ+ E HLGW     G
Sbjct: 864  LAGRHGNKGVVGKILPQEDMPFMEDGTPIDIILNTHGVPRRMNIGQVLEVHLGWLAKA-G 922

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              I+   +  K                                +        +   V+TP
Sbjct: 923  WAIEGDPDWAKR-------------------------------IPEELRNVPADSLVATP 951

Query: 1210 VFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VFDGA  E I  +L     D          G++ L+DG +GEPF  PV VG  YMLKL+H
Sbjct: 952  VFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLKLHH 1011

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +V +K++ARSTG YS++TQQPLGGK+  GGQR GEMEVW
Sbjct: 1012 LVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVW 1050



 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 147/321 (45%), Gaps = 30/321 (9%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNE---------GLQAAFKSVFP 64
           R  F K  E I +P L+++Q  S+   +      +++  E         GL+   + + P
Sbjct: 16  RYSFAKIKEPIGLPGLLDLQLNSFAWLVGTPEWREQQKAEKGEDYKVTSGLEDILEELSP 75

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           I  FSG   L      F+  K  VD+C  +D+ Y+ PL +T              K   +
Sbjct: 76  IQDFSGNMSLSLSEPYFEQVKASVDECKEKDINYSAPLYVTA---------EFENKDTGE 126

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           IK Q++++GD P+MT  GTF++ G +R+VVSQL RSPG++FD    +   + + L+A ++
Sbjct: 127 IKSQTVFIGDFPMMTPKGTFIVNGTERVVVSQLVRSPGVYFDETLDK--STERPLHAVKV 184

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY--PKIVYSQRG 242
           IP +G W++I+ D KD + VRIDR+R+ PVT  L ALG   E+I   F     ++ +   
Sbjct: 185 IPSRGAWLEIDVDKKDTVGVRIDRKRRQPVTLLLKALGWSEEKIRERFGFSEIMMSTLEN 244

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-D 301
           D       A   +   +        D  + ++E+            K   +  +G    +
Sbjct: 245 DGAASEDEALLEIYRKQRPGEQPTRDLAQALLENS-------FFKPKRYDLAKVGRYKVN 297

Query: 302 CLCGLYVAEDIVNGETGEIYI 322
              GL    D V   T E   
Sbjct: 298 RKLGLGGDHDGVKTLTEEDIA 318


>gi|133918621|emb|CAL29515.1| RNA polymerase beta subunit [Sinorhizobium saheli]
 gi|133918623|emb|CAL29516.1| RNA polymerase beta subunit [Sinorhizobium saheli]
 gi|133918627|emb|CAL29518.1| RNA polymerase beta subunit [Sinorhizobium saheli]
          Length = 318

 Score =  469 bits (1208), Expect = e-129,   Method: Composition-based stats.
 Identities = 202/319 (63%), Positives = 251/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + GD W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILETFYTKSLYQRDGDGWRVPFQP-DALKGQKAVAEMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|289810154|ref|ZP_06540783.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 317

 Score =  469 bits (1207), Expect = e-129,   Method: Composition-based stats.
 Identities = 132/323 (40%), Positives = 202/323 (62%), Gaps = 9/323 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+V+  R 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  +K + +  + 
Sbjct: 235 NKLQMELIPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEY 291

Query: 303 LCGLYVAEDIVNGETGEIYIEAG 325
           + G  V++D V+  TGE+   A 
Sbjct: 292 IAGKVVSKDYVDESTGELICAAN 314


>gi|133918619|emb|CAL29514.1| RNA polymerase beta subunit [Sinorhizobium americanum]
          Length = 318

 Score =  469 bits (1207), Expect = e-129,   Method: Composition-based stats.
 Identities = 202/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + GD W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGDGWRVPFQP-DALKGQKTLADMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNLGTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|313898216|ref|ZP_07831754.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. HGF2]
 gi|312956980|gb|EFR38610.1| DNA-directed RNA polymerase, beta subunit [Clostridium sp. HGF2]
          Length = 1403

 Score =  469 bits (1206), Expect = e-129,   Method: Composition-based stats.
 Identities = 178/531 (33%), Positives = 245/531 (46%), Gaps = 67/531 (12%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
              G     R           NI++  II  G  +  GDIL    +      +   + +  
Sbjct: 878  NDGNRREYRLRKFQRSNNGTNINQSPIISKGERIEKGDILADGPS-MERGELALGQNVTI 936

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            A       +  D  +         V D    + H  + +       +   E + RD  + 
Sbjct: 937  AYMTWYGYNYEDAIIM----SERLVRDDVYTSIHIEEYDIDCRET-KLGPEEITRDIPNV 991

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                 RN+ SR   I+ G   + G     K T      IS   +     F  +  +V+ N
Sbjct: 992  SENACRNLDSR-GIIMVGAEVMEGDILVGKVTPKGQSEISPEEKLLLAIFGEKSREVRDN 1050

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +          +      ++ K   G D+PPGV   VKV++  KR I  GDKMAGRH
Sbjct: 1051 SLKVPHGGAGIVHSI------RVFKRSEGHDLPPGVNETVKVYIVQKRKISEGDKMAGRH 1104

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMP++ DGTPVDI+LNP GVPSRMN+GQ+ E HLG+A   LG K  +
Sbjct: 1105 GNKGVISKILPVEDMPYMPDGTPVDIMLNPFGVPSRMNIGQVLEIHLGYAAKKLGVKFST 1164

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D   N ++S +    E  +                                      
Sbjct: 1165 PVFDGINNTELSDIMKEAEMTVDGKQVL-------------------------------- 1192

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G        TGEPFD  ++VG +YM+KL HMV DK++AR+TG 
Sbjct: 1193 ---------------YDG-------RTGEPFDERISVGVMYMIKLAHMVDDKLHARATGP 1230

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAA+ LQE+LT+KSDD+VGRT+ YE+I+ 
Sbjct: 1231 YSLVTQQPLGGKAQNGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDIVGRTKTYEAIIK 1290

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCEL 1385
            G D  E G PESF VL  E+QAL + + + +         +E        L
Sbjct: 1291 GKDIPEPGIPESFRVLKHELQALAIDVKMLDEDGNEVDISKEDNSEAAATL 1341



 Score =  429 bits (1102), Expect = e-117,   Method: Composition-based stats.
 Identities = 285/554 (51%), Positives = 391/554 (70%), Gaps = 10/554 (1%)

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            ++ +L   + +  L       +   +  D   D   I   D+ A     ++   G G  D
Sbjct: 526  LYAWLVGAAIQEILIRDHDGAVVKVMGNDPYADKHTITISDMYAFYAYNLNNMEGVGDTD 585

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
            DID LGNRR+RSVGE+++NQ+R+GL RMER +KER+S  DI ++ P+ L N +P+ +A+ 
Sbjct: 586  DIDMLGNRRIRSVGELIQNQFRIGLSRMERVVKERMSIADIATLTPKKLTNIRPLTAAIK 645

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            EFF SSQLSQ  +  N L+ +T+ RR+SALG GG+ R RA  E+RDVH +HYGRICP ET
Sbjct: 646  EFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGITRDRASYEVRDVHSSHYGRICPIET 705

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVC-DGKVTNDVVYLSAMEEENRYIAQANSS 633
             EG NIGL+S+LT++ ++N YGFI+TPYR V  DG V  + +YLSA EE +  IAQAN  
Sbjct: 706  PEGPNIGLISNLTTYGKINEYGFIQTPYRIVNADGTVQEEALYLSADEEADYVIAQANEV 765

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G    E V  R AG+ I+  RE+++  D SPKQ+VS+A + +PFLENDD++R LMG
Sbjct: 766  V--EGRLINEHVVARKAGDTIIARREEVELTDVSPKQIVSVATACVPFLENDDASRALMG 823

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             NMQRQAVPLL+  +P+VGTG+E  +AK SG  IVA+  G+VE VD+ RI++   +G+  
Sbjct: 824  ANMQRQAVPLLQPHSPYVGTGVEFKIAKDSGVGIVARENGVVEYVDSQRIIVSENDGNRR 883

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                    YRL KFQRSN  T +NQ P++  G+ + + DI+ADGPS + G+LALG+N+ +
Sbjct: 884  E-------YRLRKFQRSNNGTNINQSPIISKGERIEKGDILADGPSMERGELALGQNVTI 936

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A+M W+GYN+ED++++SER+V +DV+TSIHIEE+++  R+TKLGPEEITRDIPNVSE   
Sbjct: 937  AYMTWYGYNYEDAIIMSERLVRDDVYTSIHIEEYDIDCRETKLGPEEITRDIPNVSENAC 996

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +N+D  GII VGAEV  GDILVGK+TPKG+S ++PEEKLL AIFGEK+ +VRD SL+VP 
Sbjct: 997  RNLDSRGIIMVGAEVMEGDILVGKVTPKGQSEISPEEKLLLAIFGEKSREVRDNSLKVPH 1056

Query: 934  GVSGTVVDVRIFNR 947
            G +G V  +R+F R
Sbjct: 1057 GGAGIVHSIRVFKR 1070



 Score =  281 bits (719), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 86/398 (21%), Positives = 173/398 (43%), Gaps = 75/398 (18%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V +G    R+ + K    +++P+L+E+Q  S++ F           NEG+   F  +
Sbjct: 7   YRIVASGKKAERRDYSKVSGHLELPNLVEIQTDSFEWF----------KNEGIGEVFNEI 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           +PI  + G   L+F  YEF  PKF+ ++ ++R+  +A PLK  + L + D        + 
Sbjct: 57  YPIQNYGGNIKLKFAGYEFGEPKFNAEESMYRECNFAAPLKARMELEITDN-------TT 109

Query: 123 KDI--KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
            ++  K + +++GD PLMT+ GTF+I G +R++VSQ+ RSPG +F    G    +GK  +
Sbjct: 110 GEVINKWEDVFLGDFPLMTETGTFIINGAERVIVSQIVRSPGAYF--STGYEEKTGKESF 167

Query: 181 ACRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMDSE--------- 226
           AC +IP +G W++   + K      ++++ IDR+RK+  +    A+GM  +         
Sbjct: 168 ACELIPSRGTWLEFLTEVKKASTGRVLNMSIDRKRKMLSSILFKAIGMSVDLDRSEDAHD 227

Query: 227 -------------EILSTF-----------------------YPKIVYSQRGDFWCFPLS 250
                        +I+                          Y +I  +   D       
Sbjct: 228 TMQIKTFLKAMGRDIVENVAIDDEDREFMNLYLTLYASFFGKYEEIENTLMADKVKTTQE 287

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLGITSDCLCGLYV 308
           A   +   + S  +  +D G   + + K        L       ++      + +   ++
Sbjct: 288 ALLSIYENQRSDEIPTLD-GSITLMNAKFFDPRRYDLTKAGRYKLRKKLNAINRVDKHHL 346

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           A+DI++ + G +++ +G +++      +     + + +
Sbjct: 347 AQDILDAD-GSVFMPSGTMVNRDERNALRKELEKGMHV 383



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 84/245 (34%), Gaps = 11/245 (4%)

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
            F          + +   L  +       ++  +    TG  +  S  +    L   L +
Sbjct: 153 YFSTGYEEKTGKESFACELIPSRGTWLEFLT-EVKKASTGRVLNMSIDRKRKMLSSILFK 211

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                + +         +         G   +E   + DE          +     LY  
Sbjct: 212 AIGMSVDLDRSEDAHDTMQIKTFLKAMGRDIVENVAIDDEDR------EFMNLYLTLYAS 265

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  I NTL+ DK K  ++ALL IY   R  ++ T   + ++ N  FFD  +YDL+ 
Sbjct: 266 FFGKYEEIENTLMADKVKTTQEALLSIYENQRSDEIPTLDGSITLMNAKFFDPRRYDLTK 325

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            GR K+  +LN     D  H+ ++ + A   + +      GT+ + D     R      M
Sbjct: 326 AGRYKLRKKLNAINRVDKHHLAQDILDADGSVFMP----SGTMVNRDERNALRKELEKGM 381

Query: 471 LKNQY 475
             N +
Sbjct: 382 HVNAF 386


>gi|332179228|gb|AEE14917.1| DNA-directed RNA polymerase subunit beta [Thermodesulfobium narugense
            DSM 14796]
          Length = 1100

 Score =  469 bits (1206), Expect = e-129,   Method: Composition-based stats.
 Identities = 194/587 (33%), Positives = 263/587 (44%), Gaps = 55/587 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       ++V   PW G   E    I   MV     +    S    +  +   D  
Sbjct: 553  MGCNMQRQAVPLVVEEAPWVGTGMEMVAAIDSGMVHVAEKDGTVRSAAGGKIIIDFDD-- 610

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G  +  + +  V        ++  ++  G  V  G +L           +     +L A
Sbjct: 611  -GTSKEYKLMKFVRTNNATCFNQKALVRAGDRVKKGQVLTS-GCATDSGELALGRNVLVA 668

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                   +  D  L     V   V           +   RS  +  E+I     +  +E 
Sbjct: 669  FMPFGGYNFEDAILISNRLVREDVFTSIHI--ESYEVEARSTKLGDEEITREIPNVSEEA 726

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                         ++ G    +G     K T      +      +  +    D+      
Sbjct: 727  R----RHLDEQGIVVVGTEVEAGDYLVGKLTPKGD--VEPPSEERLLRAIFGDKLKDMRD 780

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLK+ +     +++     K+     GDD+PPGV+  V+V VA  R I  GDKM GRHG
Sbjct: 781  TSLKLPHGEKGKVID----VKVFSRNNGDDLPPGVITKVRVTVAQLRKISVGDKMTGRHG 836

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S+ILP  DMP+L DGTPVD+VLNPLGVPSRMNVGQIFE  LG A   L    K  
Sbjct: 837  NKGVISKILPEADMPYLPDGTPVDVVLNPLGVPSRMNVGQIFEVLLGLAAGVLNNFGKDK 896

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              +YK                   S  E+ S+   +  L  A + K         F G  
Sbjct: 897  NVEYKFEATPF-----------DESFGERASERFVEEYLEKAREIKP--------FIG-- 935

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                          ++G+  LYDG TG+PF  PVTVGY+Y+LKL H+V DK++ARSTG Y
Sbjct: 936  --------------KNGKVTLYDGKTGDPFLSPVTVGYMYLLKLVHLVDDKIHARSTGPY 981

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            SL+TQQPLGGK+  GGQR GEMEVW ++AYGAA VLQE+LTIKSDD+ GRT+  E+I+ G
Sbjct: 982  SLITQQPLGGKAQFGGQRFGEMEVWALEAYGAANVLQEILTIKSDDITGRTKAMEAIIKG 1041

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
             +    G PESF VLV+E+Q L L I L +             D N 
Sbjct: 1042 KNLGTPGLPESFKVLVRELQGLALDITLIHQDGSQIDLEHIDEDDNN 1088



 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 314/738 (42%), Positives = 453/738 (61%), Gaps = 21/738 (2%)

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           SEE +           +         + +++    +   +  +      I +G +    +
Sbjct: 78  SEEEVRIKDKTYEAQIKVKLRLLDKQSQEVVESEVLLGEIPIMTKRATFIVNGSE--RVI 135

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-EKSLEEIFHSEIRD 343
           +  L      +     D +        ++  +   I  EA         +E+     +  
Sbjct: 136 VNQLTRSPGVYFKEDKDLMDRKTFVGTVIPVKGNWINFEAPSNGTVWIRIEKSRKLPVST 195

Query: 344 IPILY-------VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                        +++ ++ + + T   D  ++R++AL + Y+ +RPG+      A+ + 
Sbjct: 196 FLKACGIEQSRIEEALVDDKFRKATFAQDNTQNREEALQEFYKKIRPGEAPNPEAAKGII 255

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLD--TPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
           N  FFD  ++DL  VGR+K+N +L L+   P D   + +ED++AI+K LV+L  G GT+D
Sbjct: 256 NNRFFDKKRFDLGEVGRLKINEKLGLNGIVPLDCLVLHREDMLAIVKYLVNLHYGDGTLD 315

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD-IDSVMPQDLINAKPVVSAV 513
           DID+L NRRVR VGE+++ ++R GL RME  I ER+S       +   ++IN+ P+  A+
Sbjct: 316 DIDHLENRRVRLVGELVRQKFREGLYRMEHVIHERMSLYKGTTKLKISNIINSGPLTVAL 375

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFFC+ QLSQ  +  N L+ +TH RR+S LG GG+ R RAG E+RD+HP++YGR CP E
Sbjct: 376 REFFCTGQLSQYMDQTNPLAELTHKRRISVLGPGGLTRERAGFEVRDIHPSYYGRFCPIE 435

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG N+GL+SS T +A VN YGF+ETPYRKV +GK+T+ +   +A +E N YIA A+  
Sbjct: 436 TPEGPNVGLISSPTIYAVVNDYGFLETPYRKVKNGKLTDIIESFTASKERNVYIASADVK 495

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + E+     + V  R  GE   VP +KID+I  SPKQ++S+++SLIPF+E++D+NR LMG
Sbjct: 496 V-ENKKIVGDTVVARYNGEFQQVPPDKIDYIGVSPKQMLSLSSSLIPFVEHNDANRALMG 554

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           CNMQRQAVPL+  EAP+VGTGME V A  SG   VA++ G V      +I+I   +G   
Sbjct: 555 CNMQRQAVPLVVEEAPWVGTGMEMVAAIDSGMVHVAEKDGTVRSAAGGKIIIDFDDGTS- 613

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y+LMKF R+N  TC NQ+ LV+ GD V++  ++  G +TD G+LALGRN+LV
Sbjct: 614 ------KEYKLMKFVRTNNATCFNQKALVRAGDRVKKGQVLTSGCATDSGELALGRNVLV 667

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFMP+ GYNFED++LIS R+V EDVFTSIHIE +EV AR TKLG EEITR+IPNVSEE  
Sbjct: 668 AFMPFGGYNFEDAILISNRLVREDVFTSIHIESYEVEARSTKLGDEEITREIPNVSEEAR 727

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +++DE GI+ VG EV  GD LVGK+TPKG+     EE+LLRAIFG+K  D+RDTSL++P 
Sbjct: 728 RHLDEQGIVVVGTEVEAGDYLVGKLTPKGDVEPPSEERLLRAIFGDKLKDMRDTSLKLPH 787

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G V+DV++F+R+  D
Sbjct: 788 GEKGKVIDVKVFSRNNGD 805



 Score =  251 bits (640), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 100/509 (19%), Positives = 190/509 (37%), Gaps = 48/509 (9%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           K      IP+L+++QK SY+ FL           +G+     S FPI        L FVS
Sbjct: 20  KQKIEAPIPNLLDLQKKSYEKFLY----------QGIGEELSSYFPIVDAGDRFELSFVS 69

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y  + PK   ++   +D TY   +K+ LRL+          K  +++ E  + +G++P+M
Sbjct: 70  YRLEEPKLSEEEVRIKDKTYEAQIKVKLRLL---------DKQSQEVVESEVLLGEIPIM 120

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           TK  TF++ G +R++V+QL RSPG++F  DK    L  +  +   +IP +G W++ E  S
Sbjct: 121 TKRATFIVNGSERVIVNQLTRSPGVYFKEDKD---LMDRKTFVGTVIPVKGNWINFEAPS 177

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD--LMV 256
              + +RI++ RK+PV++FL A G++          +I  +   D +     A D     
Sbjct: 178 NGTVWIRIEKSRKLPVSTFLKACGIEQ--------SRIEEALVDDKFRKATFAQDNTQNR 229

Query: 257 GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSDC----------LCG 305
              +      I  GE    E+ K + +      K   +  +G               L  
Sbjct: 230 EEALQEFYKKIRPGEAPNPEAAKGIINNRFFDKKRFDLGEVGRLKINEKLGLNGIVPLDC 289

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
           L +  + +      +            ++ + +  +R +  L         Y    ++ +
Sbjct: 290 LVLHREDMLAIVKYLVNLHYGDGTLDDIDHLENRRVRLVGELVRQKFREGLYRMEHVIHE 349

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +    K         +      T ++    F            + +  +    R+++  P
Sbjct: 350 RMSLYKGTTKLKISNIINSGPLTVAL-REFFCTGQLSQYMDQTNPLAELTHKRRISVLGP 408

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME-R 484
                + +E     ++ +     G+    +     N  + S   +       G L    R
Sbjct: 409 GG---LTRERAGFEVRDIHPSYYGRFCPIETPEGPNVGLISSPTIYAVVNDYGFLETPYR 465

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAV 513
            +K    +  I+S       N     + V
Sbjct: 466 KVKNGKLTDIIESFTASKERNVYIASADV 494


>gi|226355458|ref|YP_002785198.1| DNA-directed RNA polymerase subunit beta [Deinococcus deserti VCD115]
 gi|226317448|gb|ACO45444.1| putative DNA-directed RNA polymerase subunit beta [Deinococcus
            deserti VCD115]
          Length = 1151

 Score =  469 bits (1206), Expect = e-129,   Method: Composition-based stats.
 Identities = 180/506 (35%), Positives = 262/506 (51%), Gaps = 32/506 (6%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+D+  I+ VG EV  G ++           +   + +  AI      +  D        
Sbjct: 667  NLDQAPIVNVGDEVVAGQVIADGP-ASDLGRLALGQNITIAIMPFDGFNFEDAIC----- 720

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK----DDEQVILDRNIYSRLMEIL 990
            +S  +V    +    I+K+E      +   E + RD     +     LD +   R+   +
Sbjct: 721  ISEGLVQKDFYTSVHIEKDEIDARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGAEV 780

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
               + + G   FK  +  + +      RS + + A + +     V S +           
Sbjct: 781  KPGDILVGKTSFKGESEPTPE--ERLLRSIFGEKAREVKDTSLRVMSGQGGIVVKTVRFR 838

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                    +   G D+ PGV  +V+V+VA KR +Q GDK+A RHGNKG+VS+I+  EDMP
Sbjct: 839  --------RGDEGVDLKPGVREMVRVYVAQKRQLQVGDKVANRHGNKGVVSKIMRPEDMP 890

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L+DGTPVD+V NPLGVPSRMN+GQI ETHLG      G+K ++ + D      I  +  
Sbjct: 891  YLEDGTPVDLVFNPLGVPSRMNLGQILETHLGEVARLTGQKFETPVFDSVTEATIKEMLE 950

Query: 1171 FLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                        E    D  +  VL  A +          V D    +   + +++A   
Sbjct: 951  VAAAERLQARKDEGFELDKREQEVLDRAGKLG--------VIDAPGSDYERAQMQLA--- 999

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
             +G+SILYDG +GEP   PV VG +Y++KL HMV DK++ARSTG YSL+TQQPLGGK+  
Sbjct: 1000 RTGKSILYDGRSGEPISGPVVVGTMYVMKLYHMVEDKLHARSTGPYSLITQQPLGGKAQN 1059

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ LQEMLTIKSDD+ GR   Y+SIV G +   +  PESF V
Sbjct: 1060 GGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIDGRDAAYQSIVKGEEVSGSTIPESFKV 1119

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKME 1375
            L+KE+ +LGL +++ ++  +     E
Sbjct: 1120 LLKELHSLGLDVEVLDAGDRPVDIFE 1145



 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 302/607 (49%), Positives = 408/607 (67%), Gaps = 24/607 (3%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD---- 426
            +ALL ++ V+RPGD      A      L  D  +YDL   GR KMN +L ++ P+    
Sbjct: 239 DEALLRLFTVLRPGDPPKRDKATQYLYGLLADPRRYDLGEPGRFKMNTKLGVNRPERTLL 298

Query: 427 --DVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGNRRVRSVG 468
             +        ++  I+ L+ L+ G  T+                DDID+LGNRRVR+VG
Sbjct: 299 KFEDGKFSDAGLVDTIRYLMALQQGLETVKMVDEDGVVTDVPVGEDDIDHLGNRRVRTVG 358

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           E+L +Q R+G+ RM R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLSQ ++ 
Sbjct: 359 ELLADQLRVGMGRMARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLSQFKDQ 418

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS + H RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+SSL+S
Sbjct: 419 TNPLSDLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLISSLSS 478

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +++VN  GFIE PYR+V +G+VT+DVVY++A  E+   IAQANS L++D +F +E V  R
Sbjct: 479 YSKVNDLGFIEAPYRRVENGRVTDDVVYMTADIEDRYTIAQANSPLNDDNTFADERVLAR 538

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ +    E++DF+D SPKQ+VSI  SLIPFLE+DD+NR LMG NMQ QAVPL++A++
Sbjct: 539 RKGDPLWYTPEEVDFMDVSPKQIVSINTSLIPFLEHDDANRALMGSNMQSQAVPLVRADS 598

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS--TSGVDIYRLMK 766
           P VGTG+E  V   SG ++V+   G V  VDA  I I   E   +       V  + L++
Sbjct: 599 PAVGTGVERRVVTDSGTSVVSDVTGRVTYVDARAIQITLSEDSAEAGMVKGNVRTFELVR 658

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ T ++Q P+V VGDEV    +IADGP++DLG LALG+N+ +A MP+ G+NFED+
Sbjct: 659 FTRSNQGTNLDQAPIVNVGDEVVAGQVIADGPASDLGRLALGQNITIAIMPFDGFNFEDA 718

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           + ISE +V +D +TS+HIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI+ VGA
Sbjct: 719 ICISEGLVQKDFYTSVHIEKDEIDARDTKLGPEKITRDIPGLSEAALRDLDEDGIVRVGA 778

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVGK + KGES  TPEE+LLR+IFGEKA +V+DTSLRV SG  G VV    F 
Sbjct: 779 EVKPGDILVGKTSFKGESEPTPEERLLRSIFGEKAREVKDTSLRVMSGQGGIVVKTVRFR 838

Query: 947 RHGIDKN 953
           R     +
Sbjct: 839 RGDEGVD 845



 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 87/240 (36%), Positives = 135/240 (56%), Gaps = 25/240 (10%)

Query: 5   VVFNGLG-RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
           + FNG+  R+ + FG   E+I +P+L EVQ  S+  FL  + APD R + GLQ+AFK VF
Sbjct: 1   MSFNGIEPRIER-FGDIKEVIPLPNLTEVQVNSFRAFLQADRAPDRREDAGLQSAFKEVF 59

Query: 64  PITAFSGA-----AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
           PI   +        +L+++ Y    P +  ++C  +DLTY  P+   L+LI  D      
Sbjct: 60  PI-DETEKGRSTGLVLDYLEYRLGDPPYSPEECREKDLTYQAPMYAKLQLIHKDSGL--- 115

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                 IKE  +++GDLPLMT+DG+FVI G  R+V+SQ+HRSPG++F           K 
Sbjct: 116 ------IKEDQVFLGDLPLMTEDGSFVINGADRVVISQIHRSPGVYFTSS----YKGIKK 165

Query: 179 LYACRIIPD--QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKI 236
           +Y   IIP   +G W+++EF +  ++ ++++ +RK PV   L  LG D  ++ + F    
Sbjct: 166 MYTGAIIPMPKRGPWIELEF-AGGVLEMKVN-KRKFPVALLLRVLGYDDAQLRALFTEFE 223


>gi|306996355|gb|ADN21397.1| DNA-directed RNA polymerase beta subunit [Rhizobium endophyticum CCGE
            2052]
          Length = 241

 Score =  468 bits (1204), Expect = e-129,   Method: Composition-based stats.
 Identities = 171/241 (70%), Positives = 200/241 (82%)

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KVFVA+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVG
Sbjct: 1    KVFVAVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVG 60

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            QI ETHLGWAC G+G++I  ++  YKA+G+I PLR  +  V+G G   E++ D+DDDSVL
Sbjct: 61   QILETHLGWACAGMGRQIGDMLEAYKASGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVL 120

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            R+A+QWK GV ++TPVFDGA E  +N ML +A L ESGQS LYDG TGE FDR VTVGYI
Sbjct: 121  RLADQWKRGVSIATPVFDGAHEGDVNEMLALAGLKESGQSTLYDGRTGEQFDRQVTVGYI 180

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            YMLKLNH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEM
Sbjct: 181  YMLKLNHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 240

Query: 1315 L 1315
            L
Sbjct: 241  L 241


>gi|318066553|emb|CBY88845.1| rna polymerase, beta subunit [Rhizobium sp. LMG 26191]
 gi|318066555|emb|CBY88847.1| rna polymerase, beta subunit [Rhizobium sp. LMG 26192]
 gi|318066559|emb|CBY88849.1| RNA polymerase, beta subunit [Rhizobium sp. LMG 26193]
          Length = 319

 Score =  468 bits (1204), Expect = e-129,   Method: Composition-based stats.
 Identities = 202/320 (63%), Positives = 254/320 (79%), Gaps = 1/320 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGL A F+SVFPIT FSGA+MLEFVSYEF+PPKFD ++C  RD
Sbjct: 1   SYDQFLMVKEPEGGRPDEGLNAVFRSVFPITDFSGASMLEFVSYEFEPPKFDTEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKS+KDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSVKDIKEQSVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KD+++ RIDRRRK+P T
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDVVYARIDRRRKLPAT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + GD W FP    D++ GAK  + LVD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKANYLRDGDGWRFPFQP-DVLKGAKAITELVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  L++ L +KG+KF+  +++ L G Y+AEDIVN ETGEIY+EAGD IDEK+L+ 
Sbjct: 240 AGKKLTPRLIRQLSDKGLKFIKASNEDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLKL 299

Query: 336 IFHSEIRDIPILYVDSVNNN 355
           I  S   +IPIL +D +N  
Sbjct: 300 IDESGFNEIPILNIDHINVG 319


>gi|148806659|gb|ABR13264.1| RNA polymerase B' subunit [Candidatus Liberibacter asiaticus]
 gi|148806663|gb|ABR13266.1| RNA polymerase B' subunit [Candidatus Liberibacter asiaticus]
 gi|148806665|gb|ABR13267.1| RNA polymerase B' subunit [Candidatus Liberibacter asiaticus]
          Length = 478

 Score =  468 bits (1204), Expect = e-129,   Method: Composition-based stats.
 Identities = 478/478 (100%), Positives = 478/478 (100%)

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK
Sbjct: 1    GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 60

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI
Sbjct: 61   VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 120

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG
Sbjct: 121  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 180

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV
Sbjct: 181  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 240

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI
Sbjct: 241  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 300

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES
Sbjct: 301  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 360

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI
Sbjct: 361  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 420

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW
Sbjct: 421  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 478


>gi|133918669|emb|CAL29539.1| RNA polymerase beta subunit [Sinorhizobium medicae]
 gi|133918671|emb|CAL29540.1| RNA polymerase beta subunit [Sinorhizobium medicae]
          Length = 318

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 201/318 (63%), Positives = 250/318 (78%), Gaps = 1/318 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + L+D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKALADLIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQDKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVN 353
           I  +   +IP+L +D +N
Sbjct: 300 ILSAGFDEIPVLDIDHIN 317


>gi|133918633|emb|CAL29521.1| RNA polymerase beta subunit [Sinorhizobium kostiense]
 gi|133918635|emb|CAL29522.1| RNA polymerase beta subunit [Sinorhizobium kostiense]
 gi|133918637|emb|CAL29523.1| RNA polymerase beta subunit [Sinorhizobium kostiense]
          Length = 318

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 204/319 (63%), Positives = 249/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPEGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + GD W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSIYQRDGDGWRVPFQP-DALKGQKAVADMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L+EKG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEKSL  
Sbjct: 240 GGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDIVNVATGEIYLEAGDEIDEKSLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILEAGFDEIPVLDIDHINV 318


>gi|303232379|ref|ZP_07319071.1| DNA-directed RNA polymerase, beta subunit [Atopobium vaginae
           PB189-T1-4]
 gi|302481463|gb|EFL44531.1| DNA-directed RNA polymerase, beta subunit [Atopobium vaginae
           PB189-T1-4]
          Length = 1175

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 318/762 (41%), Positives = 439/762 (57%), Gaps = 44/762 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F  K     +               G       +   T   V+    +          + 
Sbjct: 101 FINKETGEIKEQLVFMGDFPLMTDRGT-----FIINGTERVVVSQLVRSPGVYFSQEVDN 155

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           GV+   +      G ++  ++       + I+     +   L         D  IL    
Sbjct: 156 GVQTHHVQFIPARGAWLEFEVDKHGHLVVSIDRKRRQNATLLLRAMGIAESDEEIL--SL 213

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +NN  ++ TL  D    R+DAL++IYR  RPG+      A ++   L+F++ +YDL+ V
Sbjct: 214 FDNNEIVKATLERDVATTREDALIEIYRRQRPGEPPAVDSARTLIEGLYFNNQRYDLARV 273

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGE 469
           GR K+N +L L    +V+ + KEDI+A ++ L+ L +G     +DDID+ GNRRVR+VGE
Sbjct: 274 GRYKVNKKLGLTCDANVKTLTKEDIVAALRYLLALHDGDTTKHVDDIDHFGNRRVRTVGE 333

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +++NQ+R+GL RMER ++ER+++ + D + PQ LIN +P+V+A+ EFF SSQLSQ  +  
Sbjct: 334 LVQNQFRIGLSRMERVVRERMATQNPDEISPQSLINIRPIVAAIKEFFGSSQLSQFMDQS 393

Query: 530 NSLSRITHTRRLSALGQGGV--------ARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           N L+ +TH RRLSALG GG+         R      +RDVH +HY R+CP ET EG NIG
Sbjct: 394 NPLAGLTHKRRLSALGPGGLAGHKSGSSRRTNVPTAVRDVHNSHYSRMCPIETPEGPNIG 453

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS-- 639
           L+ SL  FA VN YGFIE PYR+V DGKVTN++ +L A EEEN  I  AN+++D      
Sbjct: 454 LIGSLALFAHVNEYGFIEAPYRRVVDGKVTNEIDWLIADEEENHVIVPANAAVDPKTGKF 513

Query: 640 ----------FTEELVFCRCAGE-----EILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                     + + +V      +        V    +D++D SP Q++S AA+LIPFLE+
Sbjct: 514 VATKSNGEVYYPDSVVARTRNFDGSFGAPAEVYVTDVDYMDVSPSQMLSAAANLIPFLEH 573

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+ R LMG NMQRQAVPL++  APFVGTG+E   A  SG ++ A  AG V +VDA   V
Sbjct: 574 DDAKRTLMGANMQRQAVPLIRPHAPFVGTGLERAAAFDSGESVCATAAGEVVEVDAAHAV 633

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +++ +        G   Y   K+QRSNQ+TC+N RP+V VG  V     + DG S D G+
Sbjct: 634 VQTND--------GPIRYDFPKYQRSNQSTCINHRPVVHVGQHVDEGQPLTDGTSIDKGE 685

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITR 863
           LALG N+ VA+MPW GYN+ED +++SER+V  D+ TSI+I   EV ARD      EEITR
Sbjct: 686 LALGVNLTVAYMPWEGYNYEDGIVVSERLVQNDLLTSINISRHEVDARDISAKHAEEITR 745

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPN SEE L N+DE GI+ +GAEV PGDILVGK+TPKGE   TPE++L+ AIFG +A D
Sbjct: 746 EIPNQSEEALANLDEDGIVRIGAEVGPGDILVGKVTPKGEPAPTPEQRLIAAIFGNRAQD 805

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRH-GIDKNERSISVEREQI 964
           VRDTSLR+P G  G VVDV  F R     K+       +E I
Sbjct: 806 VRDTSLRMPHGAYGRVVDVMRFVRPEDKSKDNELPPGVKELI 847



 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 171/520 (32%), Positives = 246/520 (47%), Gaps = 70/520 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V+ G  L    +   +  +     L  A    +  +  D  +     V   ++
Sbjct: 662  VVHVGQHVDEGQPLTDGTS-IDKGELALGVNLTVAYMPWEGYNYEDGIVVSERLVQNDLL 720

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 +RH +D  + S     E    +    ++    LD +   R+   +   + + G  
Sbjct: 721  TSINISRHEVDARDISAKHAEEITREIPNQSEEALANLDEDGIVRIGAEVGPGDILVGKV 780

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +              V+D     ++      Y     ++         K 
Sbjct: 781  TPKGEPAPTPEQRLIAAIFGNRAQDVRD----TSLRMPHGAYGRVVDVMRFVRPEDKSKD 836

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +PPGV  +++VFVA +R IQ GDK++GRHGNKG++  +LP EDMP++ DGTP+D+
Sbjct: 837  NE---LPPGVKELIRVFVAQRRKIQQGDKISGRHGNKGVICNVLPIEDMPYMADGTPIDV 893

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +L+PLGVPSRMNVGQ+ E HLGWA                                    
Sbjct: 894  LLDPLGVPSRMNVGQLLECHLGWAAAH--------------------------------- 920

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD------------- 1227
                     D       E     + VSTP+FDGA +  +   +R ++             
Sbjct: 921  -------GYDVESPNSKEIVDGPMYVSTPIFDGATDVEVADAIRRSNINMINKAMRTYGK 973

Query: 1228 ---------LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                     L+E G++ LYDG TGE F+ P+TVG  Y+LKL HMV DK++ARSTG YSLV
Sbjct: 974  KMNTSFVPQLNEKGKTTLYDGRTGEAFESPITVGTSYILKLGHMVDDKIHARSTGPYSLV 1033

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW + AYGA+ VL E++T+KSDD  GR + YESIV G + 
Sbjct: 1034 TQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLHELMTVKSDDTNGRVKTYESIVKGENV 1093

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
               G PESF VLVKE+++L L I+    +       E+ P
Sbjct: 1094 PTPGIPESFKVLVKEIRSLALDIEPIVYKQNKKDTPEQQP 1133



 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 98/344 (28%), Positives = 153/344 (44%), Gaps = 31/344 (9%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R R  F K   ++++P+LI VQK S+  F+            GL  +F    PI   +
Sbjct: 13  KQRTRVSFNKIAPVMELPNLISVQKESFARFMTD----------GLAESFVEFSPIENAA 62

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               + F  ++F  P   + +C  +D++Y  PL + +R I          K   +IKEQ 
Sbjct: 63  KTMEVTFGEHQFSDPPHTIAECRAKDISYQAPLLVNVRFI---------NKETGEIKEQL 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTF+I G +R+VVSQL RSPG++F  +      +G   +  + IP +G
Sbjct: 114 VFMGDFPLMTDRGTFIINGTERVVVSQLVRSPGVYFSQEVD----NGVQTHHVQFIPARG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTF--YPKIVYSQRGDFW 245
            W++ E D    + V IDR+R+   T  L A+G+    EEILS F     +  +   D  
Sbjct: 170 AWLEFEVDKHGHLVVSIDRKRRQNATLLLRAMGIAESDEEILSLFDNNEIVKATLERDVA 229

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +   +       +D+   +IE          L +  + K  K LG+T D  
Sbjct: 230 TTREDALIEIYRRQRPGEPPAVDSARTLIEGLYFNNQRYDLARVGRYKVNKKLGLTCDAN 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                 EDIV        +   D    K +++I H   R +  +
Sbjct: 290 VKTLTKEDIVAALRY--LLALHDGDTTKHVDDIDHFGNRRVRTV 331


>gi|133918639|emb|CAL29524.1| RNA polymerase beta subunit [Ensifer adhaerens]
 gi|133918641|emb|CAL29525.1| RNA polymerase beta subunit [Ensifer adhaerens]
 gi|133918643|emb|CAL29526.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 318

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 201/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNFATGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|133918667|emb|CAL29538.1| RNA polymerase beta subunit [Sinorhizobium medicae]
          Length = 318

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 201/318 (63%), Positives = 250/318 (78%), Gaps = 1/318 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + L+D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKALADLIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQDKGLKALKATDDDLYGNYLAEDVVNLETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVN 353
           I  +   +IP+L +D +N
Sbjct: 300 ILSAGFDEIPVLDIDHIN 317


>gi|27375110|gb|AAO12762.1| RNA polymerase beta subunit [Fusobacterium necrophorum subsp.
            necrophorum]
          Length = 382

 Score =  467 bits (1201), Expect = e-129,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 189/323 (58%), Gaps = 53/323 (16%)

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD++  GV + ++V VA  R I  GDKM+GRHGNKG+VSR+LP EDMPFL+DGT +D+
Sbjct: 77   ENGDELKAGVNKAIRVLVAENRKITVGDKMSGRHGNKGVVSRVLPAEDMPFLEDGTHLDV 136

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VL  +G PSRMN+GQ+ E HLG A                                    
Sbjct: 137  VL-IIGRPSRMNIGQVLEVHLGMAMR---------------------------------- 161

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                  G  ++TPVFDGA EE I   L       SG+  LYDG 
Sbjct: 162  ------------------SLNGGTHIATPVFDGATEEQIKDYLENQGHPRSGKVTLYDGR 203

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+ +D  +TVG +YMLK +H+V DK++AR+ G YSLVTQQPLGGK+  GGQRLGEMEVW
Sbjct: 204  TGDKYDNKITVGIMYMLKFHHLVEDKMHARAIGPYSLVTQQPLGGKAQFGGQRLGEMEVW 263

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGA+ +LQEMLT+KSDDV GRT+ YE+I+ G +  ++  PESF VL+KE QAL L 
Sbjct: 264  ALEAYGASNILQEMLTVKSDDVTGRTKTYEAIIKGEEMPDSDLPESFKVLLKEFQALALD 323

Query: 1361 IDLENSRTKNSAKMEEIPDFNKC 1383
            ++L +         EE+      
Sbjct: 324  VELCDENDNVINVDEELNKEETT 346



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 45/80 (56%), Positives = 58/80 (72%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L+N+D  G+I +G+EV PGDILVGK +PKGE+    EEKLL + FGEKA DVRD+SLR+
Sbjct: 1   ALRNLDANGVIMIGSEVEPGDILVGKTSPKGETEPPAEEKLLASYFGEKARDVRDSSLRM 60

Query: 932 PSGVSGTVVDVRIFNRHGID 951
           P G  GTVV++   +R   D
Sbjct: 61  PHGSKGTVVEILELSRENGD 80


>gi|224533239|ref|ZP_03673839.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi
            WI91-23]
 gi|224511966|gb|EEF82367.1| DNA-directed RNA polymerase subunit beta [Borrelia burgdorferi
            WI91-23]
          Length = 302

 Score =  466 bits (1200), Expect = e-129,   Method: Composition-based stats.
 Identities = 151/357 (42%), Positives = 209/357 (58%), Gaps = 60/357 (16%)

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
            F  + ++ + N   +    E +   ++   K  +       ++ PGV  ++KV+VA KR 
Sbjct: 2    FWRKSKRCKNNSLKVPHGTEGTVIDVQRITKEDVG------NLSPGVEEILKVYVAKKRK 55

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            ++ GDKMAGRHGNKG+V++ILP EDMP+L DGTP+DI LNPLGVPSRMN+GQ+ E+ LG 
Sbjct: 56   LKEGDKMAGRHGNKGVVAKILPVEDMPYLADGTPLDICLNPLGVPSRMNIGQLMESQLGL 115

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A                          +L +                             
Sbjct: 116  AG------------------------KYLGESYNV------------------------- 126

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                 PVF+ A  E I+  L+ A  + + + ILYDG TGEPF+  V VG IYMLKL+H+V
Sbjct: 127  -----PVFESATNEQIHEKLKKAGFNPTSKEILYDGYTGEPFENEVMVGVIYMLKLHHLV 181

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTG YSLV+QQPLGGK+  GGQRLGEMEVW ++AYGAA+ LQE+LT+KSDD+ 
Sbjct: 182  DDKMHARSTGPYSLVSQQPLGGKAQFGGQRLGEMEVWALEAYGAAHTLQELLTVKSDDMS 241

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            GR ++YE+IV G  T  +G PESFNVL++E++ LGL + + +         E+  + 
Sbjct: 242  GRVKIYENIVKGVPTNVSGIPESFNVLMQELRGLGLDLSIYDDAGNQVPLTEKEEEL 298


>gi|133918661|emb|CAL29535.1| RNA polymerase beta subunit [Sinorhizobium meliloti]
 gi|133918663|emb|CAL29536.1| RNA polymerase beta subunit [Sinorhizobium meliloti]
 gi|133918665|emb|CAL29537.1| RNA polymerase beta subunit [Sinorhizobium meliloti]
          Length = 318

 Score =  466 bits (1200), Expect = e-128,   Method: Composition-based stats.
 Identities = 202/318 (63%), Positives = 251/318 (78%), Gaps = 1/318 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKTLADMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           SGKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 SGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVN 353
           I  +   +IP+L +D +N
Sbjct: 300 ILSAGFDEIPVLDIDHIN 317


>gi|133918673|emb|CAL29541.1| RNA polymerase beta subunit [Rhizobium giardinii]
          Length = 318

 Score =  466 bits (1199), Expect = e-128,   Method: Composition-based stats.
 Identities = 200/319 (62%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQSVFKSVFPITDFSGASMLEFVSYEFEQPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KD++H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDVVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K  Y + G  W  P    D + G K  S L+D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILETFYTKSFYQRDGKGWRIPFQP-DTLKGQKALSDLIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           SGKKLT  LLK+LKEKG+K +  + D L G ++AED+VN  TGEI++EAGD IDEK+L  
Sbjct: 240 SGKKLTPRLLKTLKEKGLKAIKASDDDLYGNFLAEDLVNMSTGEIFLEAGDEIDEKTLGV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILGAGFDEIPVLDIDHINV 318


>gi|133918659|emb|CAL29534.1| RNA polymerase beta subunit [Sinorhizobium arboris]
          Length = 318

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 201/318 (63%), Positives = 250/318 (78%), Gaps = 1/318 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKALADMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVN 353
           I  +   +IP+L +D +N
Sbjct: 300 ILSAGFDEIPVLDIDHIN 317


>gi|133918603|emb|CAL29506.1| RNA polymerase beta subunit [Agrobacterium rhizogenes]
          Length = 318

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 205/319 (64%), Positives = 255/319 (79%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQSVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K +Y + GD W  P +A  L  GAK  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKSLYERSGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L++KG+K L  T + L GL++AEDIVN +TGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQDKGLKALKATDEDLYGLFLAEDIVNFQTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILKAGFDEIPVLGIDHINV 318


>gi|133918625|emb|CAL29517.1| RNA polymerase beta subunit [Sinorhizobium terangae]
 gi|133918629|emb|CAL29519.1| RNA polymerase beta subunit [Sinorhizobium terangae]
 gi|133918631|emb|CAL29520.1| RNA polymerase beta subunit [Sinorhizobium terangae]
          Length = 318

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 201/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L+EKG+K L  T D L G Y+AED+VN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQEKGLKALKATDDDLYGNYLAEDVVNYGTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|73697649|gb|AAZ81441.1| RNA polymerase beta subunit [Acholeplasma axanthum]
          Length = 636

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 261/779 (33%), Positives = 375/779 (48%), Gaps = 159/779 (20%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +T  RR+SALG GG+AR RAGVE+RDVH THYGRICP ET EG +IGL+SSL ++
Sbjct: 2    NPLSELTQKRRVSALGTGGLARDRAGVEVRDVHNTHYGRICPIETPEGPSIGLISSLATY 61

Query: 590  ARVNAYGFIETPYRKVCD----------GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             +V+ YGFI+TPY K+             KV  + VYL+A EE+   IA A + LDE+G 
Sbjct: 62   GKVDEYGFIQTPYLKLNRDTLDENGLVIPKVEKEYVYLTADEEQEEIIASAATLLDENGY 121

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              E+ V  R  GE  +  R++I F+D SPKQ+VS+A + IPFLE+DD+ R LMG NMQRQ
Sbjct: 122  IVEDRVIGRSRGETNMYTRDEITFMDVSPKQIVSVATATIPFLEHDDATRALMGANMQRQ 181

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVPL+  ++P VGTG+E   AK SG+ +VA+  GIV  VDA ++VI     +        
Sbjct: 182  AVPLINPDSPIVGTGIEYRAAKDSGSVVVAQNPGIVSYVDANKVVITKQPDE-------- 233

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                                 +VKVG                           + + P  
Sbjct: 234  ---------------------IVKVG-------------------------GTILYDPKV 247

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            G+N E + L+                      R+  +   +    I          I + 
Sbjct: 248  GFNVESANLL----------------------RNYGMDESDTYELIKFNRSNQDTCILQK 285

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             ++  G  +  GDI+    +   +  +     +  A       +  D  +     +S  +
Sbjct: 286  PLVEAGETIEKGDIIADGPST-AKGELALGRNVTVAFMTWDGYNYEDAII-----MSEEL 339

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            V   ++    ID+ E    +E   I+    +  +E      N  +  ++ L     +   
Sbjct: 340  VKNDVYTSIHIDQYE----IETRDIKAAGSNYQEEITREVPNAGADALKSLDEDGIIIVG 395

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K+  +L                   +  +Q  +     +Y  +   +       +EK
Sbjct: 396  SEVKEGDILVGK----ITPKGVNDPTPSERLIQSILGDKSREYRDTSLRVPHGGGGVVEK 451

Query: 1060 IQ-----WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +Q      GD +P GV +V+KVF+A KR I+ GDKMAGRHGNKG++S+ILP EDMP++ D
Sbjct: 452  VQCYSKENGDVLPSGVNKVIKVFIAKKRKIREGDKMAGRHGNKGVISKILPREDMPYMAD 511

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG KI + + D  ++ D+  +      
Sbjct: 512  GTPVDIMLNPLGVPSRMNIGQVLEIHLGMAARKLGLKIATPVFDGVSDDDLKAIM----- 566

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     E  I+           G++
Sbjct: 567  ----------------------------------------KEAGIDE---------DGKT 577

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +LYDG TGEPFD  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 578  VLYDGRTGEPFDNRISVGVMYMIKLSHMVDDKLHARAVGPYTLVTQQPMGGKAQNGGQR 636


>gi|285307446|emb|CAX16732.1| DNA-directed RNA polymerase subunit beta [Candidatus Erwinia
           dacicola]
          Length = 330

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 138/339 (40%), Positives = 210/339 (61%), Gaps = 9/339 (2%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R+RK FGK P+++DIP L+ +Q  S+  F+  +         GL+AAF+SVFPI ++SG 
Sbjct: 1   RIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSVFPIQSYSGN 56

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
           + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++KDIKEQ +Y
Sbjct: 57  SELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVIYEREAPEG--TVKDIKEQEVY 114

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MG++PLMT +GTFVI G +R++VSQLH SPG+ FD DKG+   SGK+LY  RIIP +G W
Sbjct: 115 MGEIPLMTDNGTFVINGTERVIVSQLHGSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSW 174

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+VY  R +     L  
Sbjct: 175 LDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVYEIRDNKLQMELVP 234

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L  G   S  +     G   +E G+++T+  ++ L++  ++ + +  + + G  VA+D
Sbjct: 235 ERL-RGETASFDIES--NGTVYVEKGRRITARHIRQLEKDNIQHIEVPVEYIAGKVVAKD 291

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            ++  TGE+ I A   +    L E+  S  + I  L+ +
Sbjct: 292 YIDESTGEMLITANMELSLDLLAELSQSGHKRIETLFTN 330


>gi|78714181|gb|ABB51073.1| RNA polymerase beta subunit [Acholeplasma axanthum]
 gi|78714183|gb|ABB51074.1| RNA polymerase beta subunit [Acholeplasma axanthum]
 gi|80978869|gb|ABB54683.1| RNA polymerase beta subunit [Acholeplasma axanthum]
          Length = 636

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 262/779 (33%), Positives = 375/779 (48%), Gaps = 159/779 (20%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N LS +T  RR+SALG GG+AR RAGVE+RDVH THYGRICP ET EG +IGL+SSL ++
Sbjct: 2    NPLSELTQKRRVSALGTGGLARDRAGVEVRDVHNTHYGRICPIETPEGPSIGLISSLATY 61

Query: 590  ARVNAYGFIETPYRKVCD----------GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             +V+ YGFI+TPY K+             KV  + VYL+A EE+   IA A + LDE+G 
Sbjct: 62   GKVDEYGFIQTPYLKLNRDTLDENGLVIPKVEKEYVYLTADEEQEEIIASAATLLDENGY 121

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              E+ V  R  GE  +  R++I F+D SPKQ+VS+A + IPFLE+DD+ R LMG NMQRQ
Sbjct: 122  IVEDRVIGRSRGETNMYTRDEITFMDVSPKQIVSVATATIPFLEHDDATRALMGANMQRQ 181

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVPL+  ++P VGTG+E   AK SG+ +VA+  GIV  VDA ++VI     +        
Sbjct: 182  AVPLINPDSPIVGTGIEYRAAKDSGSVVVAQNPGIVSYVDANKVVITKQPDE-------- 233

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                                 +VKVG                           + + P  
Sbjct: 234  ---------------------IVKVG-------------------------GTILYDPKV 247

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            G+N E + L+                      R+  +   +    I          I + 
Sbjct: 248  GFNVESANLL----------------------RNYGMDESDTYELIKFNRSNQDTCILQK 285

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             ++  G  +  GDI+    +   +  +     +  A       +  D  +     +S  +
Sbjct: 286  PLVETGETIEKGDIIADGPST-AKGELALGRNVTVAFMTWDGYNYEDAII-----MSEEL 339

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
            V   ++    ID+ E    +E   I+    +  +E      N  +  ++ L     +   
Sbjct: 340  VKNDVYTSIHIDQYE----IETRDIKAAGSNYQEEITREVPNAGADALKSLDEDGIIIVG 395

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
               K+  +L                   +  +Q  +     +Y  +   +       +EK
Sbjct: 396  SEVKEGDILVGK----ITPKGVNDPTPSERLIQSILGDKSREYRDTSLRVPHGGGGVVEK 451

Query: 1060 IQ-----WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +Q      GD +P GV +V+KVFVA KR I+ GDKMAGRHGNKG++S+ILP EDMP++ D
Sbjct: 452  VQCYSKENGDVLPSGVNKVIKVFVAKKRKIREGDKMAGRHGNKGVISKILPREDMPYMAD 511

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG KI + + D  ++ D+  +      
Sbjct: 512  GTPVDIMLNPLGVPSRMNIGQVLEIHLGMAARKLGLKIATPVFDGVSDDDLKAIM----- 566

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                     E  I+           G++
Sbjct: 567  ----------------------------------------KEAGIDE---------DGKT 577

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +LYDG TGEPFD  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 578  VLYDGRTGEPFDNRISVGVMYMIKLSHMVDDKLHARAVGPYTLVTQQPMGGKAQNGGQR 636


>gi|133918645|emb|CAL29527.1| RNA polymerase beta subunit [Ensifer adhaerens]
 gi|133918647|emb|CAL29528.1| RNA polymerase beta subunit [Ensifer adhaerens]
 gi|133918649|emb|CAL29529.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 318

 Score =  466 bits (1198), Expect = e-128,   Method: Composition-based stats.
 Identities = 202/319 (63%), Positives = 251/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L+EKG+K L  T+D L G Y+AED+VN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQEKGLKALKATNDDLYGNYLAEDVVNYSTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|133918607|emb|CAL29508.1| RNA polymerase beta subunit [Sinorhizobium xinjiangense]
 gi|133918609|emb|CAL29509.1| RNA polymerase beta subunit [Sinorhizobium xinjiangense]
 gi|133918611|emb|CAL29510.1| RNA polymerase beta subunit [Sinorhizobium fredii]
 gi|133918613|emb|CAL29511.1| RNA polymerase beta subunit [Sinorhizobium fredii]
 gi|133918615|emb|CAL29512.1| RNA polymerase beta subunit [Sinorhizobium fredii]
 gi|133918617|emb|CAL29513.1| RNA polymerase beta subunit [Sinorhizobium fredii]
          Length = 318

 Score =  465 bits (1197), Expect = e-128,   Method: Composition-based stats.
 Identities = 204/319 (63%), Positives = 253/319 (79%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY + +Y + GD W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTQSLYQRDGDGWRVPFQP-DALKGQKAIAEMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL++L+EKGVK L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRTLQEKGVKALKSTDDELYGNYLAEDVVNYETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|133918655|emb|CAL29532.1| RNA polymerase beta subunit [Sinorhizobium arboris]
 gi|133918657|emb|CAL29533.1| RNA polymerase beta subunit [Sinorhizobium arboris LMG 14919]
          Length = 318

 Score =  465 bits (1197), Expect = e-128,   Method: Composition-based stats.
 Identities = 200/318 (62%), Positives = 250/318 (78%), Gaps = 1/318 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPQGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKALADMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQDKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVN 353
           I  +   +IP+L +D +N
Sbjct: 300 ILSAGFDEIPVLDIDHIN 317


>gi|228481107|gb|ACQ42252.1| RNA polymerase beta subunit [Mycoplasma sp. LR5794]
          Length = 952

 Score =  465 bits (1197), Expect = e-128,   Method: Composition-based stats.
 Identities = 308/837 (36%), Positives = 472/837 (56%), Gaps = 58/837 (6%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF----DSKDIIHVRIDRR 209
           VSQL RS G +F  +  R   +  L     I+P  G W++I      ++ D + +RID+ 
Sbjct: 1   VSQLIRSAGAYFGRNV-RNKQADDLFNKVEILPQLGSWIEIFHRVTGNTIDTVKIRIDKH 59

Query: 210 RKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           + + + SFL ALG+  E I   F    V  +         S  +L    +     +    
Sbjct: 60  KNISLISFLNALGLQKETISQLFGTSEVLLESLKKEKNYNSKENLESIYR-----IIRKG 114

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEIY 321
                E+   L    L + +   +   G           + +   Y+A+D+V  + GE+ 
Sbjct: 115 DRITDEAVANLIPTTLFNERRYNLSRTGRYMLNRKLNLVERILETYLAQDLV-TKQGEVL 173

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
              G ++  K   EI     + I P + +  ++   Y R   V                 
Sbjct: 174 YAKGTLVTPKLAAEIQKQYDKGILPTVEIPEIDKEVYGRQLEVN---------------- 217

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
                    +    +     + S K   +     +  + +  D      H+   D+IA I
Sbjct: 218 ------PELAKRTKVIMVRVWSSKKAMET---EKEPTLVIANDPTSKEMHLLISDLIATI 268

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
               +L +  G  DD D+L N+R+  VGE+L+NQ+ +GL ++E+  KE++SS +ID + P
Sbjct: 269 SYYFNLIDNLGKEDDPDSLVNKRIVGVGELLQNQFIIGLTKLEKHAKEKLSSKEIDKITP 328

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           + + N KP+ +    FF SS+LSQ  + +N L+ I + RR+++LG GG+ R  A  E+RD
Sbjct: 329 KSITNNKPIYNQFKTFFNSSKLSQFMDQINPLAEIANKRRITSLGPGGLNRDTAQFEVRD 388

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSA 619
           VH THYGRICP ET EG NIGL+ +L S+++V+ YGFI+TPY  V +G V  + + +L+A
Sbjct: 389 VHATHYGRICPIETPEGQNIGLILNLASYSKVDDYGFIQTPYYAVENGVVNYDKIEWLTA 448

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           ++E     AQ++ ++DE+     + +  R   +  LV  E +D++D + KQ+ SIAAS I
Sbjct: 449 VQEYGYTFAQSSITVDENNRILGDTITVRKDHQYQLVKPEAVDYVDVASKQMTSIAASAI 508

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLENDD+NR LMG NMQRQAVPL+++EAPFVGTG+E  VAK +   + A++ G V  VD
Sbjct: 509 PFLENDDANRALMGANMQRQAVPLVQSEAPFVGTGVEHDVAKYAATNLRARKDGEVIFVD 568

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           + +I I+S E   +     +  Y L  F+RSNQ T + Q+P+V+VG +V+  D+I DGPS
Sbjct: 569 STKIQIKSNEPKEE-----ILTYTLRIFERSNQGTIITQKPIVQVGQKVKAGDLICDGPS 623

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+LALG+N+LVAF  W+G+NFED+++I+ER+V +DVFTSIHIEE  +  R +K+G +
Sbjct: 624 TKDGELALGKNVLVAFSTWNGFNFEDAIIINERLVKDDVFTSIHIEEQTIQFRVSKVGDD 683

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +T DIPN S +  +++DE GI+ VG+EV+ GD LVG+ +PKGE   TPEEKLL AIFG 
Sbjct: 684 ILTADIPNASLKAKRHLDENGIVRVGSEVSAGDYLVGRTSPKGEENPTPEEKLLNAIFGA 743

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           KA + +DTSL+V  G +GTV+DV+I +R        GIDK  +    ++ +I++  +
Sbjct: 744 KASNQKDTSLKVKHGDAGTVIDVQILSRANGDSLEDGIDKIVKVFIAQKRKIKVGDK 800



 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 126/415 (30%), Positives = 180/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  GD++    + K +  +   + +L A       +  D  +     V   V 
Sbjct: 605  IVQVGQKVKAGDLICDGPSTK-DGELALGKNVLVAFSTWNGFNFEDAIIINERLVKDDVF 663

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S   +      +       +  LD N   R+   +   + + G  
Sbjct: 664  -TSIHIEEQTIQFRVSKVGDDILTADIPNASLKAKRHLDENGIVRVGSEVSAGDYLVGRT 722

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +        +        +   +   SLKV++  + ++++     +I   
Sbjct: 723  SPKGEENPTPE-------EKLLNAIFGAKASNQKDTSLKVKHGDAGTVID----VQILSR 771

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKVF+A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTPVDI
Sbjct: 772  ANGDSLEDGIDKIVKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPYLEDGTPVDI 831

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  S + D   N +I  L    +       
Sbjct: 832  LLNPQGVPSRMNIGQVLELHLGMAAKKLNVKFVSPVFDGVKNNEIKSLLKDAQLPETGKF 891

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                          +DG              L            
Sbjct: 892  KL----------------------------YDGIT-----------GLP----------- 901

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                FD  V+VG +YMLKL HMV DK+ ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 902  ----FDNEVSVGIMYMLKLQHMVDDKMNARSVGPYSLITQQPLGGKSQNGGQRFG 952


>gi|133918605|emb|CAL29507.1| RNA polymerase beta subunit [Rhizobium tropici]
          Length = 318

 Score =  465 bits (1196), Expect = e-128,   Method: Composition-based stats.
 Identities = 207/319 (64%), Positives = 254/319 (79%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K +Y + GD W  P  A  L  GAK  + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKSLYERSGDGWRIPFKAETL-KGAKTVTDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  LL+ L++KG+K L  T + L GL++AEDIVN +TGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLLRQLQDKGLKALKATDEELYGLFLAEDIVNFQTGEIYLEAGDEIDEKTLPI 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IPIL +D +N 
Sbjct: 300 ILKAGFDEIPILGIDHINV 318


>gi|242620025|ref|YP_003002029.1| DNA-directed RNA polymerase beta chain [Aureococcus anophagefferens]
 gi|239997270|gb|ACS36793.1| DNA-directed RNA polymerase beta chain [Aureococcus anophagefferens]
          Length = 1080

 Score =  465 bits (1196), Expect = e-128,   Method: Composition-based stats.
 Identities = 181/526 (34%), Positives = 251/526 (47%), Gaps = 52/526 (9%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             T        +    V       +++  I+    +V  G ++       G   +   + L
Sbjct: 586  RTNENDVINYKLQKYVRSNQDTCVNQRPIVWPSEKVESGQVIADGPGTNG-GELALGQNL 644

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L A    +  +  D  L     V+  +V   +F    I+K +  +      +E + RD  
Sbjct: 645  LVAYMPWEGYNYEDAIL-----VNERLVQEDLFTSIHIEKFDMEVRQTSFGVEKITRDLP 699

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +    +  N+  R   I  G    SG     K T    D   + P  +  +    ++   
Sbjct: 700  NITDDIISNL-DRNGIICKGTFVKSGDILIGKVTP--KDETDQLPEGRLLRAIFGEKSKN 756

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             +           K         ++ +   G D+  G + +V++F+A  R IQ GDK+AG
Sbjct: 757  VS----DTSLRVPKGTSGRVINVRVFRRTKGYDLADGSISLVRIFIAQIRKIQVGDKIAG 812

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGIVSRILP +DMPFL +G PVDI+LNPLGVPSRMNVGQIFE  LG A   L ++ 
Sbjct: 813  RHGNKGIVSRILPQQDMPFLPNGVPVDILLNPLGVPSRMNVGQIFECLLGLAGSKLNRRF 872

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
            K +  D               ++ G  +    ++ Y + +  +  E W         VF 
Sbjct: 873  KVMPFD---------------EMYGVETSRNLVNRYLNMAAAKSQEPW---------VF- 907

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                   NS L        G+  L DG TG+ FD PV VG  YMLKL H V DK++ARST
Sbjct: 908  -------NSYL-------PGRVALRDGRTGQLFDNPVLVGKTYMLKLIHQVDDKMHARST 953

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G YSL+TQQPLGGKS  GGQR GEMEVW +QA+G AY LQE+LT+KSDD+ GR  V  +I
Sbjct: 954  GPYSLITQQPLGGKSRHGGQRFGEMEVWALQAFGCAYTLQELLTLKSDDMEGRNEVLNAI 1013

Query: 1333 VAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            V G      G PESF VL++E+ +LGL I L      +  +  E  
Sbjct: 1014 VKGLPIPRPGIPESFKVLIRELHSLGLDISLYKMDKASRGQTNETE 1059



 Score =  432 bits (1111), Expect = e-118,   Method: Composition-based stats.
 Identities = 286/575 (49%), Positives = 393/575 (68%), Gaps = 11/575 (1%)

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             F+   Y L  +GR K+N +L L   D V  +  ED+IAI   LV+L    G +DDIDN
Sbjct: 236 QIFNEKIYSLGKIGRKKLNSKLGLSISDSVTRVTIEDVIAISNYLVNLHGNNGELDDIDN 295

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L NRRVRS+GE+L+ Q+ +GL R+ERSI ER+   +  +  P  +IN KP+++++ EFF 
Sbjct: 296 LRNRRVRSIGELLQIQFGIGLSRLERSINERLVIANPQTFKPATIINPKPIIASIKEFFG 355

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           SSQLSQ  +  N ++ +TH RR+S+LG GG+ R R  + +RD+HP+HYGRICP ET EG 
Sbjct: 356 SSQLSQFMDQTNPIASLTHKRRISSLGPGGLNRDRLSLAVRDIHPSHYGRICPIETPEGQ 415

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDE 636
           N G+++SL+ +AR+N  GF+ETP+ KV +GKV ND    YL+  EEE    A A+  L+E
Sbjct: 416 NAGIIASLSCYARINESGFLETPFFKVKNGKVQNDELPTYLTTEEEELILTAPADRVLNE 475

Query: 637 DG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  SF ++LV  R   E  LVP  ++  +  SP Q  SIA +LIPFLE+DD+NR LMG N
Sbjct: 476 NSTSFKQQLVPVRYKNEFSLVPINQVKLVSVSPLQNFSIATALIPFLEHDDANRALMGSN 535

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQ+VPLL    P VGTG+E  +A  SGA +++K AG V+ V +  I IR+ E      
Sbjct: 536 MQRQSVPLLYPHKPIVGTGLEHQLAADSGAVVISKFAGDVKYVSSRLISIRTNEN----- 590

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              V  Y+L K+ RSNQ+TCVNQRP+V   ++V    +IADGP T+ G+LALG+N+LVA+
Sbjct: 591 --DVINYKLQKYVRSNQDTCVNQRPIVWPSEKVESGQVIADGPGTNGGELALGQNLLVAY 648

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYN+ED++L++ER+V ED+FTSIHIE+F++  R T  G E+ITRD+PN++++ + N
Sbjct: 649 MPWEGYNYEDAILVNERLVQEDLFTSIHIEKFDMEVRQTSFGVEKITRDLPNITDDIISN 708

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  GIIC G  V  GDIL+GK+TPK E+   PE +LLRAIFGEK+ +V DTSLRVP G 
Sbjct: 709 LDRNGIICKGTFVKSGDILIGKVTPKDETDQLPEGRLLRAIFGEKSKNVSDTSLRVPKGT 768

Query: 936 SGTVVDVRIFNR-HGIDKNERSISVEREQIELLAR 969
           SG V++VR+F R  G D  + SIS+ R  I  + +
Sbjct: 769 SGRVINVRVFRRTKGYDLADGSISLVRIFIAQIRK 803



 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 49/193 (25%), Positives = 89/193 (46%), Gaps = 36/193 (18%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML-----EFV 77
           +  IP   E    S+  FL            GL    ++       +    +     EF+
Sbjct: 7   VTTIPHFAEANLNSFCWFL----------ESGLSDELRNFSSALNLNQKLNIKIYSDEFI 56

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                 PK+    C   DLTYA+ L + + LI  D            + E   + G++PL
Sbjct: 57  ---LKRPKYSAVQCKRYDLTYAIRLYVPIELIEED-----------SVNECLAFFGEIPL 102

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHD-KGRASLSGKLLYACRIIPDQGLWMDIEF 196
           MT++GTF+I G +R++++Q+ RSPGI++  + + +      L Y+  +I D+G W+  EF
Sbjct: 103 MTEEGTFIINGCERVIINQIIRSPGIYYRREAQEKT-----LQYSATLISDRGSWLKFEF 157

Query: 197 DSKDIIHVRIDRR 209
           ++   + +R+++ 
Sbjct: 158 ET-GTVQIRLNKT 169


>gi|133918593|emb|CAL29501.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
          Length = 318

 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 186/319 (58%), Positives = 243/319 (76%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQA F+SVFPI+ FSG +MLEFV YEF+PPK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPEGGRPDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEPPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           +     +D+P+L +D VN 
Sbjct: 300 LNEQGYKDLPLLDIDHVNV 318


>gi|11466382|ref|NP_038385.1| RNA polymerase beta subunit [Mesostigma viride]
 gi|13878753|sp|Q9MUS5|RPOB_MESVI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|7259525|gb|AAF43826.1|AF166114_38 beta subunit of RNA polymerase [Mesostigma viride]
          Length = 1080

 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 180/588 (30%), Positives = 267/588 (45%), Gaps = 66/588 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI-----EEFEVMARDT 854
                       +L    P  G  FE+ + +    V       I I            R  
Sbjct: 545  MGSNMQRQAVPLLKPNRPIVGTGFEEQVALDSGTVVICRHKGIVISVDSKTILVRSLRMN 604

Query: 855  KLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              G +    D   + +    N D    +  ++  G  V  GDIL    +      +T  +
Sbjct: 605  AKGIQHSHIDRYYLQKYNRSNQDTCINQKPVVSQGEWVQKGDILAD-GSATVNGELTLGQ 663

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
             +L A    +  +  D  L           D+             SI +E+ +++     
Sbjct: 664  NILVAYMPWEGYNFEDAILI---SEKLVYEDIYT-----------SIHIEKYEVDARKTK 709

Query: 971  KDDEQVILDR-NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
               E++  +  N+   L+  L     V      +   +L   +  +    Q  +  +   
Sbjct: 710  LGPEKITREIPNVNDHLLRNLDDNGIVIPGARVESGDILVGKVTPKEDLDQHPEGKLLRA 769

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                    ++       + +     N       G ++P GV+ +V V ++ KR IQ GDK
Sbjct: 770  IFGEKARDVRDSSLRVPNGVSGTVVNVRR--LTGKELPSGVIMMVHVSISQKRKIQVGDK 827

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGI+S+ILP +DMP+L+DGTPVD+VLNPLGVPSRMNVGQ+FE  LG A   L 
Sbjct: 828  MAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQVFECLLGLAGEYLS 887

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +  K +  D               ++ G  +    +     ++  +    W         
Sbjct: 888  ENYKLMPFD---------------EMYGKETSRGLVYSKLYEARQKTGYPW--------- 923

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                           + ++   G+S L+DG TGE FD+PVT+G  YMLKL H+V DK++A
Sbjct: 924  ---------------LFNIQSPGKSKLFDGRTGESFDQPVTIGKAYMLKLVHLVDDKIHA 968

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG YSLVTQQPLGG++  GGQRLGEMEVW ++ +GAAY LQE+LTIKSDD+ GR    
Sbjct: 969  RSTGPYSLVTQQPLGGRAKHGGQRLGEMEVWALEGFGAAYTLQELLTIKSDDMKGRNDAL 1028

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
             +I+ G    + GTPESF VL++E+Q+L L I +      N  +  ++
Sbjct: 1029 NAIIKGRPIPKPGTPESFKVLIRELQSLCLDIGVYKVHKSNKNQEIDL 1076



 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 298/630 (47%), Positives = 407/630 (64%), Gaps = 21/630 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I  +A  +   +  + +     +    L       + Y+ N +  D + + +        
Sbjct: 189 IVFKAMGLTKNEIFDAL-----KYPQFLKKTIQETDPYLENDIQHDDDFENES------- 236

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                  ST      +    FF S  YDL  VGR K+N +L L+ P+++R +  +DI+A 
Sbjct: 237 ------TSTLLSTREILESRFFQSKYYDLGKVGRYKINKKLQLNIPENIRVLTVQDILAA 290

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +  L++L    GT+DDID+L NRRVRSVGE+++NQ R+GL R+ER I +R+     DS+ 
Sbjct: 291 VDYLINLEFNIGTLDDIDHLKNRRVRSVGELIQNQVRVGLGRLERMIYKRMGESSPDSLT 350

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
              L+N KP+V A+ EFF SSQLSQ  +  N LS ITH RRLS LG GG++R RAG+ +R
Sbjct: 351 LTSLVNPKPLVGAIREFFGSSQLSQFMDQTNPLSEITHKRRLSCLGPGGLSRERAGLAVR 410

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYL 617
           D+HP+HYGRICP ET EG N GL+ SL + +RVN YGF+E+P+    + KV  +   +YL
Sbjct: 411 DIHPSHYGRICPIETPEGPNAGLIGSLATHSRVNEYGFLESPFYITKNRKVIKSELPIYL 470

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +  +E+   +A  +  L    S     V  R   E      E++D++  SP Q +SIA S
Sbjct: 471 APDQEDQFKVAPGDLLLSCYSSIENNYVPVRYKQEFTTSKAEEVDYVGISPTQAISIATS 530

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVPLLK   P VGTG E  VA  SG  ++ +  GIV  
Sbjct: 531 LIPFLEHDDANRALMGSNMQRQAVPLLKPNRPIVGTGFEEQVALDSGTVVICRHKGIVIS 590

Query: 738 VDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           VD+  I++RS+         S +D Y L K+ RSNQ+TC+NQ+P+V  G+ V++ DI+AD
Sbjct: 591 VDSKTILVRSLRMNAKGIQHSHIDRYYLQKYNRSNQDTCINQKPVVSQGEWVQKGDILAD 650

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L LG+N+LVA+MPW GYNFED++LISE++V ED++TSIHIE++EV AR TKL
Sbjct: 651 GSATVNGELTLGQNILVAYMPWEGYNFEDAILISEKLVYEDIYTSIHIEKYEVDARKTKL 710

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           GPE+ITR+IPNV++  L+N+D+ GI+  GA V  GDILVGK+TPK +    PE KLLRAI
Sbjct: 711 GPEKITREIPNVNDHLLRNLDDNGIVIPGARVESGDILVGKVTPKEDLDQHPEGKLLRAI 770

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           FGEKA DVRD+SLRVP+GVSGTVV+VR   
Sbjct: 771 FGEKARDVRDSSLRVPNGVSGTVVNVRRLT 800



 Score =  251 bits (642), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 96/483 (19%), Positives = 180/483 (37%), Gaps = 38/483 (7%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEF 81
             IPDLIE+Q +S+  FL           +GL    K    I+       L F    Y+ 
Sbjct: 17  FKIPDLIEMQLSSFRIFL----------KKGLIEELKDFSVISNSKKNLELRFFPEKYKL 66

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK++    + R  TY   L +  +L           K   +I+EQ +++G++PLMT  
Sbjct: 67  KRPKYNERTSIRRASTYTCQLYVPAKLT---------NKRTGEIQEQDVFLGEIPLMTGR 117

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           G+F+I G  R++V+Q+ RSPGI++  +  +    G+  ++  II ++G W+ IE D   +
Sbjct: 118 GSFIINGSSRVIVNQIVRSPGIYYKREIDKK---GRKTHSATIISNRGAWLRIETDKNGL 174

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF----YPKIVYSQRGDFWCFPLSAADLMVG 257
           I  RI + RKV +     A+G+   EI        + K    +   +    +   D    
Sbjct: 175 IWARIGKIRKVSIMIVFKAMGLTKNEIFDALKYPQFLKKTIQETDPYLENDIQHDDDFEN 234

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
              S+ L   +  E      K     L K  + K  K L +       +   +DI+    
Sbjct: 235 ESTSTLLSTREILESRFFQSK--YYDLGKVGRYKINKKLQLNIPENIRVLTVQDILAAVD 292

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I +E  ++     ++ + +  +R +  L  + V         ++  +  +     L +
Sbjct: 293 YLINLE-FNIGTLDDIDHLKNRRVRSVGELIQNQVRVGLGRLERMIYKRMGESSPDSLTL 351

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             ++ P            F            + +  +    RL+   P     + +E   
Sbjct: 352 TSLVNPK--PLVGAIREFFGSSQLSQFMDQTNPLSEITHKRRLSCLGPGG---LSRERAG 406

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             ++ +     G+  I  I+         +G +  +        +E       +   I S
Sbjct: 407 LAVRDIHPSHYGR--ICPIETPEGPNAGLIGSLATHSRVNEYGFLESPFYITKNRKVIKS 464

Query: 498 VMP 500
            +P
Sbjct: 465 ELP 467


>gi|133918677|emb|CAL29543.1| RNA polymerase beta subunit [Rhizobium huautlense]
          Length = 318

 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 204/319 (63%), Positives = 253/319 (79%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGL A FKSVFPIT FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPKGGRPDEGLNAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TG+KSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGSKSIKDIKEQSVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD E+ILSTFY K  Y + GD W  P     L  GAK  S ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEDILSTFYSKSNYERDGDGWRIPFQPETL-KGAKTLSDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           SGKKLT  LL+ L +KG+K L  T+D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  
Sbjct: 240 SGKKLTPRLLRQLSDKGLKALKATNDDLYGNYLAEDIVNMETGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I ++   +IP+L +D +N 
Sbjct: 300 ILNAGFDEIPVLGIDHINV 318


>gi|68619793|gb|AAY00157.1| RNA polymerase beta subunit [Afipia lausannensis]
          Length = 248

 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 160/249 (64%), Positives = 196/249 (78%), Gaps = 5/249 (2%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKVFVA+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRM
Sbjct: 1    KMVKVFVAVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRM 60

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANG--DISPLRSFLEKVIGTGSHTEKISDYD 1189
            NVGQI ETHLGWAC GLGK+I   ++ Y  +G  DI PL+  L+KV G     E I   +
Sbjct: 61   NVGQILETHLGWACAGLGKRIGQAVDAYYGHGKSDIKPLKETLKKVYGDD---EVIKTLN 117

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            D  ++ +    ++GVP++TPVFDGA E+ I  ML +A +++SGQS +YDG TG+ FDR V
Sbjct: 118  DTELMELGRNLRAGVPIATPVFDGAKEKDIEDMLDLAGMNKSGQSTVYDGRTGDQFDRNV 177

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            TVGYIYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY
Sbjct: 178  TVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAY 237

Query: 1310 VLQEMLTIK 1318
             LQEMLT+K
Sbjct: 238  TLQEMLTVK 246


>gi|108773403|ref|YP_635922.1| PEP RNA polymerase beta subunit [Helicosporidium sp. ex Simulium
            jonesii]
 gi|122197339|sp|Q2EEX2|RPOB_HELSJ RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|87242978|gb|ABD33970.1| RNA polymerase beta chain [Helicosporidium sp. ex Simulium jonesi]
          Length = 1247

 Score =  464 bits (1195), Expect = e-128,   Method: Composition-based stats.
 Identities = 265/1029 (25%), Positives = 451/1029 (43%), Gaps = 91/1029 (8%)

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +S+ + F+  I +  ++     N NA I+     D      D L  + +  +  ++    
Sbjct: 219  ESIFQFFNYNINNFKLIPNKYDNTNALIK--ARNDIFILYSDLLPLLNKTKKNFEIKYII 276

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK-ILVDLRNG 449
                 F    ++S+        R+ +  ++      +   + + D I I K  +  L N 
Sbjct: 277  NHY--FFSYIWNSNTRYCGEATRLHLYNKVGSPLSLNSLFLEEIDFIYITKIFIYRLINN 334

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP- 508
                ++ DNL N R R+ G+ +  Q R GL   E  +   + +++ +S       N K  
Sbjct: 335  NFKDENNDNLKNMRFRNGGDYIYLQTRQGLFDFESFLNINLHNIENNSFFCNITTNKKKE 394

Query: 509  -------------------------VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
                                     ++ +   FF S  LSQ  E++N LS ITH RR ++
Sbjct: 395  DIYSIKKKKNIKNFNLSKISFLKHILLKSWKSFFLSGTLSQFAENLNPLSYITHARRFTS 454

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            LG G + +A A +E+R ++P++ GR+CP ET EG N GLV S + ++     G +  P+ 
Sbjct: 455  LGPGSLKKAEASIEVRSINPSYNGRVCPIETPEGFNAGLVHSFSLYSFKGVNGELLLPFY 514

Query: 604  KVCDGKVTNDV---VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             +      +     ++ +  EE N+ I   +   ++   F  + +  R           K
Sbjct: 515  FIYKNIKQSYYLPPIFFNIEEESNQSIITGDLIHEKWNDFLNKKLSLRNNFHLDKNDISK 574

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I F   SP  ++S+A SLIPFLE++D+NR LMG NMQRQ VP+L A    V TG+++   
Sbjct: 575  ISFQSLSPYHMISLATSLIPFLEHNDANRALMGSNMQRQTVPVLGAHNFIVRTGLDTKFF 634

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                +  +++  G   + +        ++  +   T     Y  +K  ++N N+      
Sbjct: 635  SDISSIPISQINGFNFESNNNYCYFYKIDNLI---TLNNISYNYIK--KTNHNSLYINES 689

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            + K     ++ D + +    + G LALG N+L+A++PWHGYN+ED+++I+ER VS+ + T
Sbjct: 690  IKKKNPWHQQGDFLINNSVIENGKLALGPNLLLAYLPWHGYNYEDAVIINERCVSQKILT 749

Query: 841  SIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            S+HI                 +E   ++P   E                     +     
Sbjct: 750  SLHIITLTNSLELAYREINKKKEFFYEVPVKLEILFSFFAP--FYYNLKYYKNQEF---- 803

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
             +   +   +     +      K  D   +  R+    S  +          + +   + 
Sbjct: 804  -SQFEKKNPSYYTNNINIGTFLKKGDCIFSKCRIRFSFSRELRLQYKELFILLREAFPTF 862

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
               +    + A DK  +++   +   +  ++        +     K       +  +   
Sbjct: 863  EDFKNFANIFAYDKYKQKLDRKKQKKNTRLKTDNFIFNKNSTLFKKHKLKALINYYNIED 922

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQY-ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             + + Q   +   + ++++ + + Y   +   LE+    K  K +   ++     + + +
Sbjct: 923  STIYAQKNQEGLIISKHLKKVPMTYTSITPFDLEEFLSTKESKKKEYYNLFFT--KSINI 980

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R IQ GDK AGRHGNKGI+S+I P  +MP L DGTP+DI+LNPLG+PSRMNVGQI
Sbjct: 981  EILQLRDIQLGDKCAGRHGNKGIISKICPINEMPLLPDGTPIDIILNPLGIPSRMNVGQI 1040

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE+ LG A   L +     I D +   + S     L K+      + K   +   +    
Sbjct: 1041 FESLLGLAGFYLNETYTINIFDEQFGLEASRSF-VLSKLYKASILSNKPWLFLKKNA--- 1096

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                                               G++ + DGLTG+ F +P+T+GY  +
Sbjct: 1097 -----------------------------------GKTNIIDGLTGKYFQQPITIGYSSI 1121

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            LKL HMV+DK++ RS G YS +T QP  GKS  GGQR+GEME+W +Q YGA++ LQE+ T
Sbjct: 1122 LKLIHMVTDKLHGRSIGGYSTLTLQPTKGKSLLGGQRVGEMELWALQGYGASWALQELYT 1181

Query: 1317 IKSDDVVGR 1325
            +KSD V  R
Sbjct: 1182 LKSDLVEAR 1190



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 72/367 (19%), Positives = 137/367 (37%), Gaps = 43/367 (11%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF- 86
           +L+  Q+ ++  FL+           GL+ AFK        +   +++ V   F   KF 
Sbjct: 30  NLLINQRENWRFFLI----------NGLKLAFKEFEHFKIKNNNFIIDIV---FQE-KFL 75

Query: 87  ---DVDDCLWRDL-TYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
               +     + + T+   + I + +    +++            + + +G LP ++   
Sbjct: 76  FFKQIRQAYLKKVETFGYNIFIPIIITQKILNKKNNLNLT---FFKWLDLGILPSLSPKT 132

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC--RIIPDQGLWMDIEFDSKD 200
           +F I GI R V +Q  +SPG+ FD D  + S   K       +II  +G W  I +    
Sbjct: 133 SFYIDGISRAVSTQKKKSPGLMFDFDLTKKSSLEKREGEAFLKIIAPRGSWFKISYSEDH 192

Query: 201 IIHVRIDRRR--KVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVG 257
           II + I R    K+P+ +FL ALG   E I   F Y    +    + +    +       
Sbjct: 193 IIFIEI-RNIAYKIPIFTFLCALGFSLESIFQFFNYNINNFKLIPNKYDNTNAL------ 245

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            K  + +  + +    + +  K    +   +      ++  ++   CG      + N   
Sbjct: 246 IKARNDIFILYSDLLPLLNKTKKNFEIKYIINHYFFSYIWNSNTRYCGEATRLHLYNK-- 303

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
               + +   ++   LEEI    I  I   ++  + NN +        KN   ++    I
Sbjct: 304 ----VGSPLSLNSLFLEEIDFIYITKI---FIYRLINNNFKDENNDNLKNMRFRNGGDYI 356

Query: 378 YRVMRPG 384
           Y   R G
Sbjct: 357 YLQTRQG 363


>gi|133918675|emb|CAL29542.1| RNA polymerase beta subunit [Rhizobium galegae]
          Length = 318

 Score =  464 bits (1194), Expect = e-128,   Method: Composition-based stats.
 Identities = 202/319 (63%), Positives = 251/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGL A F+SVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPKGGRPDEGLNAVFRSVFPITDFSGASMLEFVSYEFELPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + GD W  P     L  GAK  S ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKSSYQRDGDGWRIPFQPETL-KGAKTLSDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           SGKKLT  LL+ L +KG+K L  T+D + G Y+AEDIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 SGKKLTPRLLRQLTDKGLKALKATNDDIYGNYLAEDIVNAATGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I ++   ++P+L +D +N 
Sbjct: 300 ILNAGFDEVPVLGIDHINV 318


>gi|226320546|ref|ZP_03796107.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
            29805]
 gi|226234044|gb|EEH32764.1| DNA-directed RNA polymerase, beta subunit [Borrelia burgdorferi
            29805]
          Length = 949

 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 175/505 (34%), Positives = 250/505 (49%), Gaps = 77/505 (15%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIFGEKAVDV----RDTSLRVPSGV 935
            ++  G +V  G+I+  G  T  GE  +     L    +     +      D  ++     
Sbjct: 513  LVKEGQKVERGEIIADGPATRYGELALGNNLLLGVIPWNGFNYEDAILISDRIVKEDLYT 572

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  + +  I  R      E+         E +     DE  I+    Y +  +IL G+  
Sbjct: 573  SIHIKEFSIEVRETKLGPEKVTGDIPNVSEKILNKL-DENGIIRIGTYVKPGDILVGKVT 631

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L + +  E  +            V+ N   +    E +   ++   K 
Sbjct: 632  PKSEGDITPEFRLLTSIFGEKAKD-----------VKNNSLKVPHGTEGTVIDVQRITKE 680

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +       ++ PGV  ++KV+VA KR ++ GDKMAGRHGNKG+V++ILP EDMP+L DG
Sbjct: 681  DVG------NLSPGVEEILKVYVAKKRKLKEGDKMAGRHGNKGVVAKILPVEDMPYLADG 734

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNPLGVPSRMN+GQ+ E+ LG A                          +L + 
Sbjct: 735  TPLDICLNPLGVPSRMNIGQLMESQLGLAG------------------------KYLGES 770

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PVF+ A  E I   L+ A  + + + I
Sbjct: 771  YNV------------------------------PVFESATNEQIQEKLKTAGFNPTSKEI 800

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG TGEPF+  V VG IYMLKL+H+V DK++ARSTG YSLV+QQPLGGK+  GGQRLG
Sbjct: 801  LYDGYTGEPFENEVMVGVIYMLKLHHLVDDKMHARSTGPYSLVSQQPLGGKAQFGGQRLG 860

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAA+ LQE+LT+KSDD+ GR ++YE+IV G  T  +G PESFNVL++E++
Sbjct: 861  EMEVWALEAYGAAHTLQELLTVKSDDMSGRVKIYENIVKGVPTNVSGIPESFNVLMQELR 920

Query: 1356 ALGLSIDLENSRTKNSAKMEEIPDF 1380
             LGL + + +         E+  + 
Sbjct: 921  GLGLDLSIYDDAGNQVPLTEKEEEL 945



 Score =  463 bits (1190), Expect = e-127,   Method: Composition-based stats.
 Identities = 313/681 (45%), Positives = 457/681 (67%), Gaps = 27/681 (3%)

Query: 291 KGVKFLGI---TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
             +K + +   T   L G Y+A+ I   E   +Y  AGD I  + +E+   + + +I ++
Sbjct: 8   YNIKKIKVEDGTKRDLPGQYLAKSINIREN--MYYRAGDKITLQDVEDFLQNGVNEIELV 65

Query: 348 YVDSVNN--------NAYIRNTLVTDKNKD----------RKDALLDIYRVMRPGDVSTF 389
             D  ++        +  I N L  +              ++  +L +Y  + PG+  + 
Sbjct: 66  DFDGYDDISGKRFVSSNVILNCLEKEDAFFALKDGSKELPKESVMLAVYGSLFPGEPISI 125

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             AE+    +FF   +YDL  VGR K++ +   D       +  +DI+  I  L+ +  G
Sbjct: 126 DNAENDLKTIFFSERRYDLGRVGRYKLSKKFGFD-DLTTSVLTMDDIVNTISHLLRIYEG 184

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +DDID+LGNRRVRSVGE+L N Y+  + R+E+  K+R+S+ ++ ++ PQ+LI+ KP+
Sbjct: 185 HDILDDIDHLGNRRVRSVGELLTNIYKGAMSRVEKIAKDRMSNKEVFNLKPQELISVKPI 244

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           VSAV EFF +SQLSQ  + VN L+ +TH RRL+ALG GG++R RAG E+RDVH THYGR+
Sbjct: 245 VSAVKEFFATSQLSQFMDQVNPLAELTHKRRLNALGPGGLSRDRAGFEVRDVHYTHYGRM 304

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ET EG NIGL+ SL +++RVN YGF+ETPYRKV +G+VT+ + YLSA++EE + IAQ
Sbjct: 305 CPIETPEGPNIGLIVSLATYSRVNDYGFLETPYRKVVNGEVTDQLEYLSAIDEEKKCIAQ 364

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           AN++ D +G + E+LV  R +G+        ID++D SP+Q++S++++LIPFLE++D+NR
Sbjct: 365 ANAAFDSNGKYLEDLVSVRISGDYTTTSPTNIDYMDVSPRQLISVSSALIPFLEHNDANR 424

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPLL  + P VGTGMESVVAK SG  + AKR+G V    + +IV++  E
Sbjct: 425 ALMGSNMQRQAVPLLFPKPPIVGTGMESVVAKDSGVVVKAKRSGEVILATSSKIVVKPFE 484

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                ++  +D Y ++K++R+NQ+TC NQ  LVK G +V R +IIADGP+T  G+LALG 
Sbjct: 485 ---AENSKDLDEYHIVKYERTNQDTCFNQSVLVKEGQKVERGEIIADGPATRYGELALGN 541

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+L+  +PW+G+N+ED++LIS+R+V ED++TSIHI+EF +  R+TKLGPE++T DIPNVS
Sbjct: 542 NLLLGVIPWNGFNYEDAILISDRIVKEDLYTSIHIKEFSIEVRETKLGPEKVTGDIPNVS 601

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ L  +DE GII +G  V PGDILVGK+TPK E  +TPE +LL +IFGEKA DV++ SL
Sbjct: 602 EKILNKLDENGIIRIGTYVKPGDILVGKVTPKSEGDITPEFRLLTSIFGEKAKDVKNNSL 661

Query: 930 RVPSGVSGTVVDVRIFNRHGI 950
           +VP G  GTV+DV+   +  +
Sbjct: 662 KVPHGTEGTVIDVQRITKEDV 682


>gi|133918591|emb|CAL29500.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 318

 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 200/319 (62%), Positives = 251/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P    D + G K  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L++KG+K L  T+D L G Y+AED+VN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQDKGLKALKATNDDLYGNYLAEDVVNFATGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|331124040|gb|AEC53808.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 499

 Score =  463 bits (1192), Expect = e-128,   Method: Composition-based stats.
 Identities = 240/502 (47%), Positives = 344/502 (68%), Gaps = 3/502 (0%)

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +     
Sbjct: 1   YRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDLFFEKVNFEVKDQTLL 60

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + + G 
Sbjct: 61  MELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEYIVGK 117

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL  D 
Sbjct: 118 VASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETLRIDS 177

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  +   
Sbjct: 178 TVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQ 237

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++
Sbjct: 238 EQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAV 297

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 298 KERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGP 357

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V 
Sbjct: 358 GGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVV 417

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   ++D 
Sbjct: 418 DGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQYMDV 477

Query: 667 SPKQVVSIAASLIPFLENDDSN 688
           +  QVVSIAASLIPFLE+DD+N
Sbjct: 478 ATNQVVSIAASLIPFLEHDDAN 499


>gi|133918685|emb|CAL29547.1| RNA polymerase beta subunit [Agrobacterium rubi]
          Length = 318

 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 201/319 (63%), Positives = 255/319 (79%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGL A F+SVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPEGGRPDEGLNAVFRSVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KD+++ RIDRRRK+P T
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDVVYARIDRRRKLPAT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + G+ W +P    D++ GAK  + LVD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKANYVRDGEGWRYPYQP-DVLKGAKAITELVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  L++ + +KG+KFL  +++ L G Y+AEDIVN ETGEIY+EAGD IDEK+L+ 
Sbjct: 240 AGKKLTPRLIRQMSDKGLKFLKASNEDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLKL 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  S   +IPIL +D +N 
Sbjct: 300 ILDSGFDEIPILNIDHINV 318


>gi|331124038|gb|AEC53807.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 499

 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 241/502 (48%), Positives = 344/502 (68%), Gaps = 3/502 (0%)

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +     
Sbjct: 1   YRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKDQTLL 60

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + + G 
Sbjct: 61  MELVP-DRLRGETASFDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEYIVGK 117

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL  D 
Sbjct: 118 VASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETLRIDS 177

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  +   
Sbjct: 178 TVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQ 237

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++
Sbjct: 238 EQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAV 297

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 298 KERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGP 357

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V 
Sbjct: 358 GGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVV 417

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   ++D 
Sbjct: 418 DGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQYMDV 477

Query: 667 SPKQVVSIAASLIPFLENDDSN 688
           +  QVVSIAASLIPFLE+DD+N
Sbjct: 478 ATNQVVSIAASLIPFLEHDDAN 499


>gi|331124042|gb|AEC53809.1| RNA polymerase subunit B [Vibrio sp. SO183]
          Length = 499

 Score =  463 bits (1191), Expect = e-127,   Method: Composition-based stats.
 Identities = 242/502 (48%), Positives = 344/502 (68%), Gaps = 3/502 (0%)

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
            +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ KI +  +     
Sbjct: 1   YRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTTEEILDIFFEKINFEVKDQTLM 60

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             L    L  G   S  +     G+  +E G+++T+  ++ L++  V F+ +  + + G 
Sbjct: 61  MELVPERL-RGETASFDIE--ADGKVYVEKGRRVTARHIRQLEKDDVSFIEVPVEYIVGK 117

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             ++D +N  TGEI + A   I  +SL  +  +  + + +L+ + +++  ++  TL  D 
Sbjct: 118 VSSKDYINEATGEIIVAANQEISLESLANLSQAGYKKLEVLFTNDLDHGPFMSETLRIDS 177

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
           + DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +     +
Sbjct: 178 SNDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIERADAE 237

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   + + DI+ ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++
Sbjct: 238 EQGTLDETDIVEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAV 297

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 298 KERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGP 357

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V 
Sbjct: 358 GGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVV 417

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT++V YLSA+EE    IAQAN+ L E+G F +ELV  R  GE  L PRE ++++D 
Sbjct: 418 DGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVNYMDV 477

Query: 667 SPKQVVSIAASLIPFLENDDSN 688
           +  QVVSIAASLIPFLE+DD+N
Sbjct: 478 ATNQVVSIAASLIPFLEHDDAN 499


>gi|133918683|emb|CAL29546.1| RNA polymerase beta subunit [Agrobacterium tumefaciens]
          Length = 318

 Score =  463 bits (1190), Expect = e-127,   Method: Composition-based stats.
 Identities = 203/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGL A FKSVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPKGGRPDEGLNAVFKSVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + GD W  P    D +  AKV + ++D DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKATYERAGDGWRIPFQP-DALKNAKVITDMIDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            GKKLT  L++ L +KG+K L  T + L G ++AEDIVN ETGEIY+EAGD IDEK+L  
Sbjct: 240 GGKKLTPRLIRQLVDKGLKALKATDEDLYGNFLAEDIVNYETGEIYLEAGDEIDEKTLGL 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  S   +IP+L +D VN 
Sbjct: 300 ILQSGFDEIPVLNIDHVNV 318


>gi|133918601|emb|CAL29505.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
          Length = 318

 Score =  462 bits (1189), Expect = e-127,   Method: Composition-based stats.
 Identities = 203/319 (63%), Positives = 248/319 (77%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLSDKGLKALKAADDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILANGFDEIPVLGIDHINV 318


>gi|269925824|ref|YP_003322447.1| DNA-directed RNA polymerase, beta subunit [Thermobaculum terrenum
           ATCC BAA-798]
 gi|269789484|gb|ACZ41625.1| DNA-directed RNA polymerase, beta subunit [Thermobaculum terrenum
           ATCC BAA-798]
          Length = 1203

 Score =  462 bits (1189), Expect = e-127,   Method: Composition-based stats.
 Identities = 347/724 (47%), Positives = 449/724 (62%), Gaps = 99/724 (13%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPI------LYVDSVNNNAY--IRNTLVTDKNKDRK 371
           + + A   ID + +E                  LY     +  Y  +  T+  D  K+ +
Sbjct: 209 VLLRAVAAIDSEVVEAEGDMGPTTPGTDEWLWALYGKVSRDGRYQNLAATIERDPTKNSQ 268

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP------ 425
           +AL+++YR +RPGD      A ++   L FD  +YDL+ VGR K+  +            
Sbjct: 269 EALVELYRRLRPGDPPNPENARTLLRQLLFDPRRYDLARVGRYKLTRKWEQLREVVARSN 328

Query: 426 --------------DDVRHIRKEDIIAIIKILVDLRN----GKGTIDDIDNLGNRRVRSV 467
                         + +R I   D+I I+  L+ L N     +   DDID+LGNRRVR+V
Sbjct: 329 GPTFDFEIDSRVYGERLRTITGRDLINIVGNLIRLNNLPPGSEEEGDDIDHLGNRRVRAV 388

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ+R+GLLRMER IKER+S  D +S  P +LIN +PVV+A+ EFF  SQLSQ  +
Sbjct: 389 GELIQNQFRVGLLRMERVIKERMSIQDAESATPNNLINIRPVVAAMREFFGGSQLSQFMD 448

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            VN+LS I H RRLSALG GG++R RAG+++RDVHP+HYGRICP ET EG NIGL+  L 
Sbjct: 449 QVNALSEINHKRRLSALGPGGLSRDRAGLDVRDVHPSHYGRICPIETPEGPNIGLIGQLA 508

Query: 588 SFARVNAYGFIETPYRKVCD---------------------------------------- 607
           ++AR+N YGFIETPYRKV                                          
Sbjct: 509 TYARINEYGFIETPYRKVVKSVPGDSIDAMVGHITREPIMDSNGQEVVPVGTEITREVAE 568

Query: 608 -------------GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----- 649
                         +V N+V YLSA  E+   +AQANS LDE G F E+ V  R      
Sbjct: 569 KIVALGLDEIKVKPRVLNEVEYLSADREDLFTVAQANSPLDERGYFLEDRVEARASIRLR 628

Query: 650 --AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E ++VP +++D++DASPKQVVS+A+SLIPFLE+DD+NR LMG NMQRQAVPLL  +
Sbjct: 629 RGGTEFMIVPVDEVDYVDASPKQVVSVASSLIPFLEHDDANRALMGANMQRQAVPLLVPD 688

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E+ VA+ SG  ++AK  GIV  V A RIV+   +G        +  Y L KF
Sbjct: 689 SPVVGTGVEAQVARDSGQVVIAKADGIVRSVTAERIVVEEDDG-------NLRTYELEKF 741

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            R+NQ+T +NQRP+V  GD +    IIAD  ST  G++ALG+N+LVAFMPW G NFED++
Sbjct: 742 VRTNQDTLLNQRPIVNKGDRIYAGQIIADSASTSNGEIALGQNVLVAFMPWEGGNFEDAV 801

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISER+V +DV+TSIHIE++EV ARDTKLGPEEITRDIPNV EE L N+DE GI+ VGAE
Sbjct: 802 LISERLVRDDVYTSIHIEKYEVEARDTKLGPEEITRDIPNVGEEALANLDERGIVYVGAE 861

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V P DILVGK+TPKGE+ MT EE+LLRAIF EKA DVRDTSLRVP+GV G V+DV++F R
Sbjct: 862 VKPNDILVGKVTPKGETEMTAEERLLRAIFSEKARDVRDTSLRVPNGVHGQVIDVKVFTR 921

Query: 948 HGID 951
              D
Sbjct: 922 VEND 925



 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 170/581 (29%), Positives = 241/581 (41%), Gaps = 92/581 (15%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV---SEDVFTSIHIEEFEVMARDTKL 856
                       +LV   P  G   E  +      V     D        E  V+  D   
Sbjct: 673  MGANMQRQAVPLLVPDSPVVGTGVEAQVARDSGQVVIAKADGIVRSVTAERIVVEEDDGN 732

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                        +++ L  +++  I+  G  +  G I+    +      +   + +L A 
Sbjct: 733  LRTYELEKFVRTNQDTL--LNQRPIVNKGDRIYAGQIIADSASTSN-GEIALGQNVLVAF 789

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD---- 972
               +  +  D  L     +S  +V   ++    I+K E      +   E + RD      
Sbjct: 790  MPWEGGNFEDAVL-----ISERLVRDDVYTSIHIEKYEVEARDTKLGPEEITRDIPNVGE 844

Query: 973  ------DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  DE+ I+      +  +IL G+    G         L   + SE  R        
Sbjct: 845  EALANLDERGIVYVGAEVKPNDILVGKVTPKGETEMTAEERLLRAIFSEKARD------- 897

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                V+     +          +      K+      DD+P GV ++V+V +A KR I  
Sbjct: 898  ----VRDTSLRVPNGVHGQVIDV------KVFTRVENDDLPAGVNQMVRVMIAQKRKISE 947

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK+AGRHGNK                            GV SR+               
Sbjct: 948  GDKVAGRHGNK----------------------------GVISRI--------------- 964

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
                 I+ +                ++ ++       +++                G  V
Sbjct: 965  ---LPIEDMPFLPDGRP--------VDVILNPIGVPSRMNLGQILECHLGWAASTLGFKV 1013

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            + PVFDGA EE I   LR A L E G+  LYDG TGE FD+PV VG +Y++KL H+V DK
Sbjct: 1014 ACPVFDGASEEMIKEELRRAGLPEDGKIELYDGRTGEKFDQPVAVGVMYIMKLAHLVEDK 1073

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDD VGR 
Sbjct: 1074 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDTVGRV 1133

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            R YE+IV G      G PESF VL+KE+Q+LGLS+++ N  
Sbjct: 1134 RTYEAIVKGEPISGAGVPESFKVLMKELQSLGLSVEVLNED 1174


>gi|318066547|emb|CBY88842.1| RNA polymerase, beta subunit [Agrobacterium larrymoorei]
          Length = 319

 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 202/320 (63%), Positives = 248/320 (77%), Gaps = 1/320 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGL A FKSVFPIT FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVDEPKGGRPDEGLNAVFKSVFPITDFSGASMLEFVSYEFEAPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + GD W  P     L   AKV + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYTKATYVREGDGWRIPFQPETL-KNAKVVTEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L +KG+K L  + + L G Y+AEDIVN ETGEIY+EAGD ID+K+L  
Sbjct: 240 AGKKLTPRLLRQLTDKGLKALKASDEDLYGNYLAEDIVNYETGEIYLEAGDEIDDKTLTV 299

Query: 336 IFHSEIRDIPILYVDSVNNN 355
           I      +IP+L +D +N  
Sbjct: 300 ILGHGFDEIPVLNIDHINVG 319


>gi|295094084|emb|CBK83175.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Coprococcus sp. ART55/1]
          Length = 537

 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 195/573 (34%), Positives = 297/573 (51%), Gaps = 56/573 (9%)

Query: 9   GLGRV---------RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAF 59
              R+         R  + K  +++++P+ IEVQK SY+ FL            GL+ AF
Sbjct: 2   EKNRISPVKSGKGYRMSYAKQKDVLEMPNFIEVQKNSYNWFLTD----------GLKEAF 51

Query: 60  KSVFPITAFSGAAMLEFVSYEF--DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           + + PIT +SG   LEFV ++F  D  K+ +++C  RD TYA PL++ +RL V D     
Sbjct: 52  RDISPITDYSGQYSLEFVDFQFCKDDLKYSIEECKERDATYAAPLRVKVRLRVGDA---- 107

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                K++ +  I+MGDLPLMT+ GTFVI G +R++VSQL RSPGI++D    +    GK
Sbjct: 108 -----KEMSDHEIFMGDLPLMTETGTFVINGAERVIVSQLVRSPGIYYDITHDKV---GK 159

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP-- 234
            LYAC +IP++G W++ E DS D+ +VR+DR RKVPVT  + ALG+ ++ EI+  F    
Sbjct: 160 KLYACTVIPNRGAWLEYETDSNDVFYVRVDRTRKVPVTVLIRALGLGTDQEIIDLFGEEP 219

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKG 292
           KI+ S   D           +           ++  E +I +         L K  + K 
Sbjct: 220 KIMESLNKDPAKSYSEGVVELYKKIRPDEPSVVENAESLINAMFFDARRYDLAKVGRYKF 279

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            K L +    + G  +AED ++  TGE+  EAG V+ E+  + I  +    +P + + + 
Sbjct: 280 NKKLAL-KARIAGHVLAEDAIDPSTGEVIAEAGTVVSEELADTIQDA---AVPYVMIQTE 335

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             N  + + ++ +                   D +   + E ++  +     +       
Sbjct: 336 ERNVKVLSNMMVNIANYVD------------FDPAELGIVERVYYPVLEGLLEEYGDDTE 383

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           ++K  +     +    +HI KEDI A I   + L  G G  DDID+LGNRR+R+VGE+L+
Sbjct: 384 KLKAAVE-RDMSDLVPKHITKEDIFASINYNIHLEYGIGFDDDIDHLGNRRIRAVGELLQ 442

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQYR+GL R+ER ++ER+++ D +S+ PQ LIN KPV +AV EFF SSQLSQ  +  N L
Sbjct: 443 NQYRIGLSRLERVVRERMTTQDAESITPQSLINIKPVTAAVKEFFGSSQLSQFMDQNNPL 502

Query: 533 SRITHTRRLSALGQ-GGVARARAGVEMRDVHPT 564
           S +TH RRL +        R       R    T
Sbjct: 503 SELTHKRRLFSPWPWWTFTRQSRIRGPRCTLYT 535


>gi|30468229|ref|NP_849116.1| RNA polymerase beta subunit [Cyanidioschyzon merolae strain 10D]
 gi|41017710|sp|Q85FR7|RPOB_CYAME RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|30409329|dbj|BAC76278.1| DNA-directed RNA polymerase beta chain [Cyanidioschyzon merolae
           strain 10D]
          Length = 1036

 Score =  462 bits (1188), Expect = e-127,   Method: Composition-based stats.
 Identities = 291/601 (48%), Positives = 394/601 (65%), Gaps = 14/601 (2%)

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            + N      +       + + AL++ Y+ MRPG+ +T   A+ +    FFD  KYDLS 
Sbjct: 186 HLTNREVFERSWENHAVNNTEAALVEFYKKMRPGEPATVHSAKQLLYARFFDPKKYDLSE 245

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           VGR K+N +L+LD P  V  +   D++A +  L+ L   +  +DDID+L NRR++ VGE+
Sbjct: 246 VGRYKLNQKLHLDIPLSVHILTTSDLLAGLDYLIQLCLDRARVDDIDHLANRRLKCVGEL 305

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L+NQ R+GL R+E+ ++E+++  +   + P  L+N KP+ SA+ EFF SSQLSQ  + +N
Sbjct: 306 LQNQVRIGLSRLEKLLREKMTIGE--KLQPSSLLNPKPLTSAIREFFASSQLSQFMDQIN 363

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ +TH RR+SALG GG+ R RAG  +RD+HP+HYGRICP ET EG N GL+ SL  FA
Sbjct: 364 PLAELTHKRRISALGAGGLTRERAGFAVRDIHPSHYGRICPIETPEGPNAGLIGSLAIFA 423

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           RVN YGFIETPY  V  G+V   +VYL+A  E+N  +A A+   D +G     +V  R  
Sbjct: 424 RVNRYGFIETPYYPVKKGQVQKSIVYLTADVEDNYRLAPADVKYDREGQICSPIVAVRYR 483

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E        +D++  SP Q +S A  LIPFLE+DD+NR LMG NMQRQAVPL++A  P+
Sbjct: 484 QEWTTCDASHVDYMAISPIQFISAATCLIPFLEHDDANRALMGSNMQRQAVPLIRASKPY 543

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V TG E  + +     + +K  GIV  V A  I I+   G +D        Y L+K+Q+S
Sbjct: 544 VSTGQEKWMVQ----GVFSKADGIVRSVQATSIRIQHARGPVD--------YALLKYQKS 591

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC++ RPLV VG+ V +  +IA   + D G+LALG+N+L+A+MPW GYNFED+ +IS
Sbjct: 592 NQDTCIDYRPLVWVGEHVVKGQLIAQSAAMDSGELALGQNVLIAYMPWEGYNFEDAFVIS 651

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V EDV+TSIHIE++E  AR TKLG E+ITR IPNV E  L+ +DE GII VG+ V  
Sbjct: 652 ERLVYEDVYTSIHIEKYETDARQTKLGAEQITRQIPNVGEHALRQLDEHGIISVGSWVEA 711

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           G ILVGKITPKGES   PE KLLRAIFGEK   V+D+SLR+P+G  G V+ VRI +R   
Sbjct: 712 GSILVGKITPKGESDQPPEGKLLRAIFGEKNQHVKDSSLRMPNGSRGRVIHVRILSRDQG 771

Query: 951 D 951
           D
Sbjct: 772 D 772



 Score =  449 bits (1156), Expect = e-123,   Method: Composition-based stats.
 Identities = 155/318 (48%), Positives = 196/318 (61%), Gaps = 51/318 (16%)

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++P GV   V+V VA+KR IQ GDKMAGRHGNKGIV+RILP  DMP+L DGTPVD++
Sbjct: 770  QGDELPAGVNISVRVSVAVKRVIQVGDKMAGRHGNKGIVARILPRCDMPYLPDGTPVDVI 829

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQ+FE  LG A   L K+IK +  D   + +                 
Sbjct: 830  LNPLGVPSRMNVGQLFEALLGLAAHRLRKRIKIVPFDEMYHKE----------------- 872

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     ++ +F       ++  L+ A L  S Q+ILYDG +
Sbjct: 873  -------------------------ASRIF-------VHQQLKRAAL--SAQTILYDGRS 898

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GE FD  VTVG  YMLKL H+V +K++ARSTG YSLVTQQPLGG++  GGQRLGEMEVW 
Sbjct: 899  GEKFDNAVTVGMAYMLKLVHLVDEKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWA 958

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++AYGAAY LQE+LT+KSDD+ GRT    +IV        GTPESF VL++E+QALGL +
Sbjct: 959  LEAYGAAYTLQELLTLKSDDMEGRTATLNAIVKAQPIPRGGTPESFKVLMRELQALGLDV 1018

Query: 1362 DLENSRTKNSAKMEEIPD 1379
             +    ++    M+   D
Sbjct: 1019 TVLQLESQALCVMQSKLD 1036



 Score =  249 bits (635), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 91/454 (20%), Positives = 180/454 (39%), Gaps = 48/454 (10%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDPPK 85
           DLI VQ+ SY  FL  +          L+  F  + PI  ++G   L  +    E  PPK
Sbjct: 3   DLIAVQRNSYYTFLTKS----------LKEEFDKISPIVDYTGQLELHLITSKMELKPPK 52

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
                   +D+TY+V + + ++L               D+++Q IY G++PLMT+D TF+
Sbjct: 53  ITPVQAKRQDITYSVGMYMPVQL---------WNHQTGDVRQQMIYFGEIPLMTEDATFI 103

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           I G +R+VV+Q+ RSPG++F     +  +     +    + ++G W+  E D + ++ VR
Sbjct: 104 INGAERVVVNQIVRSPGVYFQALWDKQHV---RTFEATFMANRGAWIKYELDKQKLLWVR 160

Query: 206 IDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           +D+ RK+P+  FL ALG++ +EI      + V+ +  +      + A L+          
Sbjct: 161 LDKNRKMPLVIFLQALGLNLQEIKPHLTNREVFERSWENHAVNNTEAALV------EFYK 214

Query: 266 DIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCGLYVAEDIVNGETGEIYIE 323
            +  GE   + S K+L        K+  +  +G    +    L +   +    T ++   
Sbjct: 215 KMRPGEPATVHSAKQLLYARFFDPKKYDLSEVGRYKLNQKLHLDIPLSVHILTTSDLLAG 274

Query: 324 -------AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
                    D      ++ + +  ++ +  L  + V         L+ +K    +   L 
Sbjct: 275 LDYLIQLCLDRARVDDIDHLANRRLKCVGELLQNQVRIGLSRLEKLLREKMTIGE--KLQ 332

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
              ++ P      S     F           ++ +  +    R++         + +E  
Sbjct: 333 PSSLLNPK--PLTSAIREFFASSQLSQFMDQINPLAELTHKRRISA---LGAGGLTRERA 387

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
              ++ +     G+  I  I+         +G +
Sbjct: 388 GFAVRDIHPSHYGR--ICPIETPEGPNAGLIGSL 419


>gi|133918599|emb|CAL29504.1| RNA polymerase beta subunit [Rhizobium gallicum]
          Length = 318

 Score =  461 bits (1187), Expect = e-127,   Method: Composition-based stats.
 Identities = 204/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYKRDGEGWRIPFQPEAL-KGAKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L +KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLSDKGLKALKATDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILANGFDEIPVLGIDHINV 318


>gi|133918681|emb|CAL29545.1| RNA polymerase beta subunit [Agrobacterium vitis]
          Length = 318

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 203/319 (63%), Positives = 250/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP+EGLQ  FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVDEPEGGRPDEGLQTVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGA+SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGARSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY K  Y + G  W  P  A  L  G+K    +VD D+GE V+E
Sbjct: 181 SLLMALGMDGEEILSTFYSKSDYKRDGKGWRVPFQAETL-KGSKTLVDMVDADSGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L++KG+K L  T + L G Y+AEDIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQDKGLKALKATDEDLYGNYLAEDIVNFATGEIYLEAGDEIDEKTLPI 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILEAGFDEIPVLGIDHINV 318


>gi|133918651|emb|CAL29530.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 318

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 200/319 (62%), Positives = 248/319 (77%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEQPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G  W  P    D + G K  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGAGWRVPFQP-DALKGQKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L++KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQDKGLKALKATDDDLYGNYLAEDIVNFATGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|133918653|emb|CAL29531.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 318

 Score =  461 bits (1186), Expect = e-127,   Method: Composition-based stats.
 Identities = 200/319 (62%), Positives = 248/319 (77%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEQPKFDVEECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEIL TFY K +Y + G  W  P    D + G K  + +VD DTGE V+E
Sbjct: 181 SLLMALGMDGEEILDTFYTKSLYQRDGAGWRVPFQP-DALKGQKAITEMVDADTGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L++KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  
Sbjct: 240 AGKKLTPRLLRQLQDKGLKALKATDDDLYGNYLAEDIVNFSTGEIYLEAGDEIDEKTLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D +N 
Sbjct: 300 ILSAGFDEIPVLDIDHINV 318


>gi|156101694|ref|XP_001616540.1| DNA-directed RNA polymerase III subunit [Plasmodium vivax SaI-1]
 gi|148805414|gb|EDL46813.1| DNA-directed RNA polymerase III subunit, putative [Plasmodium vivax]
          Length = 1427

 Score =  461 bits (1185), Expect = e-127,   Method: Composition-based stats.
 Identities = 218/1423 (15%), Positives = 419/1423 (29%), Gaps = 332/1423 (23%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L++    SY++F+   I              KS            +EF+      P    
Sbjct: 232  LVKQHIESYNYFIKQEIKTIMNATT--NKILKS-----DIDEHFYVEFLDIFVGKPSVEE 284

Query: 86   ------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                       C  RDLTY+ P+ + +  +          K    I++ ++ +G LP+M 
Sbjct: 285  NMIETNLTPQICRQRDLTYSAPIYVDVEYV----------KGSNIIRKNNVEIGRLPVML 334

Query: 140  ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                      G F++KG +R+++ Q   S               
Sbjct: 335  RSDICILNNKSEEELMKLGECPYDPGGYFIVKGTERVLLMQEQLSKN------------- 381

Query: 176  GKLLYACRIIPDQGLWMDIEFDSKDIIHVRID--------------RRRKVP-------- 213
                   RII        +E D K  I   I               +  K+         
Sbjct: 382  -------RII--------VEMDIKHNICATITSTTAESKSRCAIVYKNNKLYLKHNSFIE 426

Query: 214  ---VTSFLMALGMDSEE---------------ILSTFYP--KIVYSQRGDFWCF---PLS 250
               V   L A+G +S++               IL + Y           D   +    + 
Sbjct: 427  DIGVCIILRAMGYESDQEIFQMIGSHRNYLNGILLSLYELYSENIKTNLDALLYIGKKIR 486

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
               L  G   S     +   + +IE G    S +L S  ++  K+          L +  
Sbjct: 487  PRLLAKGFFSSMKEKQVKNEKDIIEEGLDFLSRVLLSHIQQKNKYDFRNKARCICLMI-R 545

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +++G   +  ++  D    K LE            LY           +  ++   +  
Sbjct: 546  RVLDGANNKNELDDKDYYGNKRLELAGQLISLLFEDLYKRFYFTLKKQIDQTLSKYMQSN 605

Query: 371  KDALLDIYRVMRPGDVSTFSVAES-MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
              + L     +       F      +       +       + R KM           + 
Sbjct: 606  YTSKLKYSGNVNDTYPDVFRSLPKDIITRGMQAAISTGNWNIKRFKMEKSGVSQVLSRLS 665

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             I    ++  +    +          +       +             GL++    +   
Sbjct: 666  FIACIGMMTRLNSQFEKGRKVSGPRALQPSQWGVLCPCDTPEGESC--GLVKNLALMTHV 723

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG- 548
             +  + +  + + L       S         +        N +    H +    + +   
Sbjct: 724  TNDNENNEHLIEILYTLGVEDSDSLTGEEMYKQGIFFVIFNGILLGVHKKPRIFMRRIRC 783

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKV 605
            + R     +   ++           T  G     +  + +            +E      
Sbjct: 784  LRRYGKIGQFVSIYDNFLHNAIYISTDGGRLCRPLIIVENGKSKLSQEHILSLEKGIINF 843

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             D   ++ + ++   E+ N  IA   S +  +                          ++
Sbjct: 844  FDLLKSSVIEWIDVNEQNNLLIALNESDISVN-----------------------TTHLE 880

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
              P  ++ + A LIP+  ++ S R    C M +QA+                        
Sbjct: 881  IDPLTILGVVAGLIPYPNHNQSPRNTYQCAMGKQAIG----------------------- 917

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                               I   +     +   + +Y               Q+PLVK  
Sbjct: 918  ------------------AIGYNQFVRCDTLLYLLVYP--------------QKPLVKS- 944

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                           +   L  G+N +VA M + GY+ ED++++++  +       + + 
Sbjct: 945  ---------KTIEFINFEKLPAGQNAIVAVMSFCGYDIEDAIVMNKSSIDRGFGRCMSLR 995

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +  V  +    G  ++    P                          + + K+  + E  
Sbjct: 996  KHAVELKKYFNGSNDLVLPSP--------------------------LAISKLQQRQERQ 1029

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
               +         ++  + ++    +         + ++       K ER          
Sbjct: 1030 RREKRDRREKREKQEMREKQEAQETLEK--QPQAQEDQLAPPRQHAKEERDHEENGADSN 1087

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            +    +   + I   +       +  G     G     K +  +             +  
Sbjct: 1088 VEEPKRFQNKEIKKYHALDVDGVVSIGYLLREGQVYINKYSPKNVKD----HVKDISKID 1143

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            + D K                   +  + + ++KI +        L++ K+ +   R  +
Sbjct: 1144 LNDLKSNE-------------VKYKSVYPSYVDKIIF--TENAEGLKIYKIIMRQTRLPE 1188

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK + RHG KG+V  ++  EDMPF + G   D+++NP G PSRM VG++ E     + 
Sbjct: 1189 LGDKFSSRHGQKGVVGLLVNQEDMPFTESGICPDLIMNPHGFPSRMTVGKLLELVASKSA 1248

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
            V  G+     I       +                                         
Sbjct: 1249 VLDGEFKYGSIFSGTPFEE----------------------------------------- 1267

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++ +F                 + S + +LY GLTGEP +  + +G IY  KL HMV D
Sbjct: 1268 MASILF-------------KYGFNCSCKELLYSGLTGEPLETYIFMGPIYYQKLKHMVQD 1314

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DV- 1322
            K++AR+ G   L+T+QP  G+S  GG RLGEME  C+ AYG + +L E L + SD  DV 
Sbjct: 1315 KIHARARGPRQLLTRQPTEGRSKEGGLRLGEMERDCLIAYGVSNLLLERLMLSSDVCDVY 1374

Query: 1323 ----VGRTRVYESI----VAGNDTFETGTPESFNVLVKEMQAL 1357
                 G    Y++        +       P +  +L +E+Q +
Sbjct: 1375 ICEDCG-MMGYDTYCTFCQKCDKNALVKMPYACKLLFQELQTM 1416


>gi|308233482|ref|ZP_07664219.1| DNA-directed RNA polymerase, beta subunit [Atopobium vaginae DSM
            15829]
 gi|328943546|ref|ZP_08241011.1| DNA-directed RNA polymerase subunit beta [Atopobium vaginae DSM
            15829]
 gi|327491515|gb|EGF23289.1| DNA-directed RNA polymerase subunit beta [Atopobium vaginae DSM
            15829]
          Length = 1175

 Score =  461 bits (1185), Expect = e-127,   Method: Composition-based stats.
 Identities = 179/606 (29%), Positives = 261/606 (43%), Gaps = 70/606 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++    P+ G   E +                 +E     A        
Sbjct: 581  MGANMQRQAVPLIKPHAPYVGTGLERAAAYDSGESVMATHAGQVVEVDASHAVVQTEDGF 640

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            E               I+   ++ VG +V  G  L    +   +  +     L  A    
Sbjct: 641  ERYDFPKYQRSNQSTCINHRPVVKVGQKVEQGQPLTDGTS-IDKGELALGVNLTVAYMPW 699

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  +     V   ++     +RH +D  + S     E    +    ++    LD
Sbjct: 700  EGYNYEDGIVVSERLVQDDLLTSVNISRHEVDARDISAKHAEEITREIPNQSEEALANLD 759

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +   R+   +   + + G    K     + +              V+D     ++    
Sbjct: 760  EDGIVRIGAEVGPGDILVGKVTPKGEPAPTPEQRLIAAIFGNRAQDVRD----TSLRMPH 815

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
              Y     ++         K      +PPGV  +++VFVA +R IQ GDK++GRHGNKG+
Sbjct: 816  GAYGRVVDVVRFVRPEDKSKENE---LPPGVKELIRVFVAQRRKIQQGDKISGRHGNKGV 872

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  +LP EDMP++ DGTP+D++L+PLGVPSRMNVGQ+ E HLGWA               
Sbjct: 873  ICNVLPVEDMPYMADGTPIDVLLDPLGVPSRMNVGQLLECHLGWAASH------------ 920

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                          D       +  +  + VSTP+FDGA +  +
Sbjct: 921  ----------------------------GYDVDSEDSDKVVEGPMFVSTPIFDGATDVEV 952

Query: 1220 NSMLRMAD----------------------LDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
               +R  +                      L+E G++ LYDG TGE F  P+TVG  Y+L
Sbjct: 953  ADAIRRTNINMINKAMRTYGKRMNKAFVPQLNEQGKTTLYDGRTGEAFKSPITVGTSYIL 1012

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW + AYGA+ VL E++T+
Sbjct: 1013 KLGHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALYAYGASNVLHELMTV 1072

Query: 1318 KSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEI 1377
            KSDD  GR + YESIV G +    G PESF VLVKE+++L L+I+    +    AK  E 
Sbjct: 1073 KSDDTNGRVKTYESIVKGENAPRPGIPESFKVLVKEIRSLALNIEPIVYKENVPAKPVEQ 1132

Query: 1378 PDFNKC 1383
             D  + 
Sbjct: 1133 EDKPEA 1138



 Score =  458 bits (1177), Expect = e-126,   Method: Composition-based stats.
 Identities = 295/645 (45%), Positives = 412/645 (63%), Gaps = 36/645 (5%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G + +       + +   +    I +     +  + ++  ++ TL  D    R+DAL++I
Sbjct: 180 GHLVVSIDRKRRQNATLLLRALGIAESDEEIIKLLGDSEIVKATLQRDVATTREDALIEI 239

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           YR  RPG+      A S+   L+F++ +YDL+ VGR K+N +L L+    V+ + KEDI+
Sbjct: 240 YRRQRPGEPPAVDSARSLIEGLYFNNQRYDLARVGRYKVNKKLALEIDPSVKILTKEDIV 299

Query: 438 AIIKILVDLRNGK--GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           A ++ L+ L  G      DDID+ GNRRVR+VGE+++NQ+R+GL RMER I+ER+++ D 
Sbjct: 300 AALRYLLALHAGDTTKKTDDIDHFGNRRVRTVGELVQNQFRIGLSRMERVIRERMATQDP 359

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV------ 549
           D + PQ LIN +P+V+A+ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+      
Sbjct: 360 DDISPQSLINIRPIVAAIKEFFGSSQLSQFMDQSNPLAGLTHKRRLSALGPGGLAGHKSG 419

Query: 550 --ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
              R      +RDVH +HY R+CP ET EG NIGL+ SL  FA VN YGFIE PYRK+ D
Sbjct: 420 SSRRTNVPTAVRDVHNSHYSRMCPIETPEGPNIGLIGSLALFAHVNEYGFIEAPYRKIVD 479

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGS------------FTEELVFCRCAGE--- 652
           GKVT+++ ++ A EEE+  I  A+  +D                + E +V      +   
Sbjct: 480 GKVTDEIDWMIADEEEHHVIVPADVPVDPKTGRFVATDAHGKIYYPETVVARTRNFDGTF 539

Query: 653 --EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                V   ++D++D SP Q++S AA+LIPFLE+DD+ R LMG NMQRQAVPL+K  AP+
Sbjct: 540 GAPSEVDVNEVDYMDVSPSQMLSAAANLIPFLEHDDAKRTLMGANMQRQAVPLIKPHAPY 599

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SG +++A  AG V +VDA   V+++ +        G + Y   K+QRS
Sbjct: 600 VGTGLERAAAYDSGESVMATHAGQVVEVDASHAVVQTED--------GFERYDFPKYQRS 651

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC+N RP+VKVG +V +   + DG S D G+LALG N+ VA+MPW GYN+ED +++S
Sbjct: 652 NQSTCINHRPVVKVGQKVEQGQPLTDGTSIDKGELALGVNLTVAYMPWEGYNYEDGIVVS 711

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           ER+V +D+ TS++I   EV ARD      EEITR+IPN SEE L N+DE GI+ +GAEV 
Sbjct: 712 ERLVQDDLLTSVNISRHEVDARDISAKHAEEITREIPNQSEEALANLDEDGIVRIGAEVG 771

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           PGDILVGK+TPKGE   TPE++L+ AIFG +A DVRDTSLR+P G
Sbjct: 772 PGDILVGKVTPKGEPAPTPEQRLIAAIFGNRAQDVRDTSLRMPHG 816



 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 94/369 (25%), Positives = 158/369 (42%), Gaps = 30/369 (8%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R R  F K    +++P+LI VQK S+  F+            GL  +F    PI   +
Sbjct: 13  KQRDRVSFSKIAPTMELPNLISVQKESFARFMTD----------GLAESFMEFSPIENST 62

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               + F +++F  P   + +C  +D++Y  PL + +R I          K   ++KEQ 
Sbjct: 63  QTMEVTFGAHQFSDPPHTIAECRAKDISYQAPLLVNVRFI---------NKETGEMKEQL 113

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R+VVSQL RSPG++F  +      +G   +  + IP +G
Sbjct: 114 VFMGDFPLMTDRGTFVINGTERVVVSQLVRSPGVYFSEEMD----NGVQTHHVQFIPARG 169

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTFYPKIVYS--QRGDFW 245
            W++ E D    + V IDR+R+   T  L ALG+    EEI+       +     + D  
Sbjct: 170 AWLEFEVDKHGHLVVSIDRKRRQNATLLLRALGIAESDEEIIKLLGDSEIVKATLQRDVA 229

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCL 303
                A   +   +       +D+   +IE          L +  + K  K L +  D  
Sbjct: 230 TTREDALIEIYRRQRPGEPPAVDSARSLIEGLYFNNQRYDLARVGRYKVNKKLALEIDPS 289

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDE-KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
             +   EDIV      + + AGD   +   ++   +  +R +  L  +           +
Sbjct: 290 VKILTKEDIVAALRYLLALHAGDTTKKTDDIDHFGNRRVRTVGELVQNQFRIGLSRMERV 349

Query: 363 VTDKNKDRK 371
           + ++   + 
Sbjct: 350 IRERMATQD 358


>gi|299780660|gb|ADJ40006.1| RNA polymerase beta subunit [Ureaplasma gallorale]
          Length = 838

 Score =  460 bits (1183), Expect = e-127,   Method: Composition-based stats.
 Identities = 191/532 (35%), Positives = 277/532 (52%), Gaps = 31/532 (5%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +   G  +  + I           ++  I+    +++ G+ +           +     +
Sbjct: 319  ENDKGKLDTYKLIKYRKSNQDTCNNQTPIVNKNQQISKGETIADGP-AMQNGELALGRNI 377

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L      +  +  D  +     +S  +VD  +F    ID++       +   E + RD  
Sbjct: 378  LVGYTTWRGYNFEDAII-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITRDMP 432

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +      R        IL G     G     K T   +  ++   R     F  + + V+
Sbjct: 433  N-VSDHARRFLDNEGVILVGAEVHEGDVLVGKITPRGNVEVAPEDRLLQTIFGDKSKSVR 491

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             +   +K   E   + ++     +I+    G D+P  VL ++KV++  KR IQ GDKMAG
Sbjct: 492  DSSLKVKHGQEGIVASVK-----RIKATDEGADLPDDVLEIIKVYIVQKRKIQVGDKMAG 546

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGIVS+I+P +DMPFL DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   +GKK 
Sbjct: 547  RHGNKGIVSKIVPIQDMPFLADGTPLDIMLNPLGVPSRMNIGQIFELHLGYAAAEIGKKQ 606

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD--------DDSVLRVAEQWKS-- 1202
               I   K   +       L + +    + + ++  D        D +++ V    +S  
Sbjct: 607  LVQIAINKEGFEKYVHLFGLNEHVAKNLYAKMLNLVDQKQAQTPKDVNLIDVTIVLRSLG 666

Query: 1203 ------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVTVGY 1253
                  G+ V+TPVF+GA+   I  ++  A++D     G+  L DG+TGE FD  V+VG 
Sbjct: 667  LTYDDIGIKVATPVFNGANHNDIVDIMNEANIDIEYNKGKQTLIDGITGEAFDGLVSVGL 726

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYGAAY L E
Sbjct: 727  TYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYGAAYNLLE 786

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +LTIKSDDV GR + Y +I+ G D    GTPESF +L K+MQ LGL I +E 
Sbjct: 787  ILTIKSDDVHGRNQTYNNIIKGQDVVANGTPESFKLLTKQMQGLGLCISVET 838



 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 223/478 (46%), Positives = 311/478 (65%), Gaps = 9/478 (1%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  + +IN K   + V +FF S QL Q  +  N L+ +T+ RR+SA+G GG++R  
Sbjct: 67  KKRIISVKSIINTKNFQTRVKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISRED 126

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             +++RDVH +HY RICP ET EG NIGL+ SL S A+V+  GFI +PY  V DG VT++
Sbjct: 127 PNLDIRDVHHSHYSRICPIETPEGMNIGLIMSLASLAKVDENGFIVSPYYVVRDGVVTDE 186

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
             YL+A E++N  I++++ +LDE+     E V  R  G   L    ++DFID  PKQVVS
Sbjct: 187 YKYLTAHEDDNYIISESSITLDENKKILNEHVVARYRGSTGLYTPAEVDFIDILPKQVVS 246

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           IAAS IPF+ENDD  R LMG NMQRQA PL+K  AP VGTG E  +A  SG A+ AK +G
Sbjct: 247 IAASAIPFIENDDGARALMGSNMQRQATPLIKPYAPIVGTGTEFKIAHDSGMAVTAKNSG 306

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +V+ VD   IV+ + +G LD        Y+L+K+++SNQ+TC NQ P+V    ++ + + 
Sbjct: 307 VVKSVDGHSIVVENDKGKLD-------TYKLIKYRKSNQDTCNNQTPIVNKNQQISKGET 359

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           IADGP+   G+LALGRN+LV +  W GYNFED+++ISER+V +DVFTSIHI+E  +    
Sbjct: 360 IADGPAMQNGELALGRNILVGYTTWRGYNFEDAIIISERLVDQDVFTSIHIDEHTIQCMK 419

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           TK G EEITRD+PNVS+   + +D  G+I VGAEV+ GD+LVGKITP+G   + PE++LL
Sbjct: 420 TKNGDEEITRDMPNVSDHARRFLDNEGVILVGAEVHEGDVLVGKITPRGNVEVAPEDRLL 479

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF--NRHGIDKNERSISVEREQIELLAR 969
           + IFG+K+  VRD+SL+V  G  G V  V+       G D  +  + + +  I    +
Sbjct: 480 QTIFGDKSKSVRDSSLKVKHGQEGIVASVKRIKATDEGADLPDDVLEIIKVYIVQKRK 537


>gi|325973547|ref|YP_004250611.1| DNA-directed RNA polymerase, beta' subunit [Mycoplasma suis str.
            Illinois]
 gi|323652149|gb|ADX98231.1| DNA-directed RNA polymerase, beta' subunit [Mycoplasma suis str.
            Illinois]
          Length = 2643

 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 314/1016 (30%), Positives = 499/1016 (49%), Gaps = 103/1016 (10%)

Query: 14   RKFFGKNPE-IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K P     +P+L  +Q  SY  FL            G+Q      FPIT+ SG  
Sbjct: 14   RIDFSKYPTADWSLPNLRGIQIDSYKKFL----------ESGIQELISKYFPITSASGNT 63

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             +     E        ++ +    +Y   + + LRL+    +  +   + +      I+ 
Sbjct: 64   QVFLDGIEITEVDVTEEEAVNSSKSYQRSIYLKLRLVSKYSEGKSKLSTSR------IFF 117

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLSGKLL---YACRIIPDQ 188
            G++P+ +    F+I GI++ V+ Q+ RSPG++  +  + R S S K       C ++P +
Sbjct: 118  GNMPIFSSSSNFIINGIEKFVICQIVRSPGLYVLNKAQIRLSNSRKRTQEGIVCELLPVK 177

Query: 189  GLWMDIEF----DSKD--------IIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFY 233
            G+ +        D KD         +  R          PVT FL ALG+ ++ I S F 
Sbjct: 178  GVLLLFHLPNPSDKKDGGEESTSIKLIARNTSGNNAYSFPVTVFLKALGISTKTITSLFE 237

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                      F     + +  +  + V S L +I + +   +  + L+ G ++       
Sbjct: 238  KNPE--LMRAFSQESFNPSGALNDSLVVSILSEISSAK-GAQKMRDLSKGWIRETLYSLC 294

Query: 294  KFLGITSDCLCGLYVAEDIVNGETGEI----YIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                          V EDI+     E+     I +  +  E +  EI   +       Y 
Sbjct: 295  MRYTEAEREGASRAVKEDILEKIAIELAAKQLISSFSINTEIARREIHSYQELLWSYFYD 354

Query: 350  DSVNN----NAYIRNTLVTDKNKDRKDALLDIYRVM---------------RPGDVSTFS 390
             +  +      Y  N  ++   + R   L      +               +  +    +
Sbjct: 355  KNYYHILPAGRYKLNYKLSVWERMRNKYLAQDICDLSGSVVFAKDTFMDFEKLSEFKEAA 414

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--------------------PDDVRH 430
            +A+ +     FD  +      GR +    +  +                      +D + 
Sbjct: 415  IAKKLNIRHKFDITRTFDDIEGRYRDFDVIEYEKVSIYSGGLDSEVITLLGTPYLEDEKP 474

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +   D +AII  ++ L+   G  DDIDNLGN+R++ + E+LK++  + L R+++   +R+
Sbjct: 475  LNPSDALAIISYMLHLKKKVGEYDDIDNLGNKRLKLIDELLKDRIAIALTRIQKFSVDRM 534

Query: 491  SSVDI-------------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +S++              D      ++N KP    + EFF S QL Q  +  N LS IT+
Sbjct: 535  NSLESKLSYFSLQDGELEDYFSLSSIMNTKPFQIVIKEFFNSHQLVQFLDQQNVLSEITN 594

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             R++SA+G GG+ R    + +RDVH ++YGR+CP ET EG NIGL+ +L S +RV+ YGF
Sbjct: 595  KRKISAMGPGGIKREDPNLSIRDVHYSYYGRVCPIETPEGMNIGLIMALASLSRVDKYGF 654

Query: 598  IETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            + TPY +V +     +  V+L++++E +  IA+A +  DE+G      V  R   E   V
Sbjct: 655  LNTPYYRVKNGVIQKDQKVWLNSIQERSFCIAEATTERDENGRLIGP-VTVRRDEEVESV 713

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              E++ +ID    Q+ SI+ SLIPFLE+DD+NR LMG NMQRQAVPL+  ++P V TG+E
Sbjct: 714  DPEEVSYIDVDCTQITSISTSLIPFLEHDDANRALMGANMQRQAVPLISPKSPIVATGVE 773

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            S +A+ SG  I A+  GI+  +D+ +I ++           G   Y L KF ++NQNTC 
Sbjct: 774  SRIARDSGVVIQAEDDGIITYMDSSQIRVKY------RGELGEKTYSLQKFIKTNQNTCK 827

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ  + +   EV++ DI+ DG +   G+LALG+N+LVAF  W+GYN+ED++++S R+V E
Sbjct: 828  NQLVVPRNSREVKKGDILVDGHAIQNGELALGQNILVAFTSWYGYNYEDAIILSSRLVQE 887

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            +V+TS+HI+E+ V    TK+G EEITR IP  + E  K +DE G+I VGA V  GDILVG
Sbjct: 888  NVYTSLHIQEYTVNCMRTKIGDEEITRFIPGCTAEEKKYLDEDGVILVGAAVKEGDILVG 947

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K +PK    +TPEEKLL+AIF EKA  V+D+SLR+PSG  G V  +  ++    D+
Sbjct: 948  KTSPKAMGEVTPEEKLLQAIFSEKAKSVKDSSLRLPSGSEGIVTKILRYSAAKGDR 1003



 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 172/593 (29%), Positives = 270/593 (45%), Gaps = 47/593 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLG 857
                       ++    P      E  +     +V +  D     +++  ++  +     
Sbjct: 749  MGANMQRQAVPLISPKSPIVATGVESRIARDSGVVIQAEDDGIITYMDSSQIRVKYRGEL 808

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E+       +        ++  +     EV  GDILV     +    +   + +L A  
Sbjct: 809  GEKTYSLQKFIKTNQNTCKNQLVVPRNSREVKKGDILVDGHAIQN-GELALGQNILVAFT 867

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D  + + S +    V   +  +       R+   + E    +     +E+  
Sbjct: 868  SWYGYNYEDAII-LSSRLVQENVYTSLHIQEYTVNCMRTKIGDEEITRFIPGCTAEEKKY 926

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +       IL G     G     K+                 +   +++ +Q     
Sbjct: 927  LDED-----GVILVGAAVKEGDILVGKT-----------SPKAMGEVTPEEKLLQAIFSE 970

Query: 1038 LKVQYETSKSILEDRFKNKIEKI-----QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 + S   L    +  + KI       GD +   VL  +K+FV  KR IQ GDKM G
Sbjct: 971  KAKSVKDSSLRLPSGSEGIVTKILRYSAAKGDRLGDDVLETIKIFVTSKRNIQIGDKMVG 1030

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGIVS+++P EDMP+L+DGT VDI+LNPLGVPSRMN+GQI E++L ++   L  K 
Sbjct: 1031 RHGNKGIVSKVVPVEDMPYLEDGTAVDILLNPLGVPSRMNIGQILESYLAFSARKLVFKK 1090

Query: 1153 KSLIND-----------YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                              ++  ++  L   ++  + + +   +       + L  +    
Sbjct: 1091 ILEAFFDSSLESCDTLFSRSKVELESLGKVIKSYLESKNIKSREEALSKLTQLDFSIILS 1150

Query: 1202 SG--------VPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                      + V TP+F G     + +++  A +D    +G+  LYDG TGE F  P++
Sbjct: 1151 HAGIKYDELEIKVLTPIFAGCKNSDLINIMADAGVDFKHHNGRFTLYDGRTGEKFKDPIS 1210

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG IYMLKL+HMV DK+YARS G YS +TQQPLGGK   GGQR GEMEVW ++AYGAA+ 
Sbjct: 1211 VGIIYMLKLDHMVDDKIYARSVGPYSKITQQPLGGKCQNGGQRFGEMEVWALEAYGAAHN 1270

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            L+E+L++KSDD+  R  +Y SI+ G    +    ESF +LVK++QALGL +++
Sbjct: 1271 LRELLSLKSDDIQARNLIYYSIIKGQALPKPTISESFKLLVKKLQALGLRVNI 1323


>gi|133918597|emb|CAL29503.1| RNA polymerase beta subunit [Mesorhizobium mediterraneum]
          Length = 318

 Score =  459 bits (1182), Expect = e-126,   Method: Composition-based stats.
 Identities = 195/319 (61%), Positives = 245/319 (76%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM+      RP+EGLQA F+SVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RD
Sbjct: 1   SYDQFLMVEEPKGGRPDEGLQAVFRSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD EEILSTFY KI Y + GD W  P +      G K    LVD DT E V+E
Sbjct: 181 SLLMALGMDGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTNEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKK+T+   ++L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ 
Sbjct: 240 AGKKITARQARALGEKGLKAIKATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           +  +   +I +L +D VN 
Sbjct: 300 LLSAGDDEIKVLDIDHVNV 318


>gi|133918679|emb|CAL29544.1| RNA polymerase beta subunit [Rhizobium undicola]
          Length = 318

 Score =  459 bits (1180), Expect = e-126,   Method: Composition-based stats.
 Identities = 205/319 (64%), Positives = 249/319 (78%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     RP EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RD
Sbjct: 1   SYDQFLMVDEPKGGRPEEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRD 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           LTYA PLK+TLRLIVFD+DE TGA+SIKDIKEQS+YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  LTYAAPLKVTLRLIVFDIDEDTGARSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PV+
Sbjct: 121 QMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVS 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S LMALGMD E+ILSTFY K VY + G  W  P     L  G+K    +VD D+GE V+E
Sbjct: 181 SLLMALGMDGEDILSTFYSKAVYQRDGKGWRVPFQPETL-KGSKTIVDMVDADSGEVVVE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT  LL+ L EKG+K L  T + L G Y+AEDIVN  TGEIY+EAGD IDEKSL  
Sbjct: 240 AGKKLTPRLLRQLTEKGLKALKATDEDLYGNYLAEDIVNFRTGEIYMEAGDEIDEKSLPV 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           I  +   +IP+L +D VN 
Sbjct: 300 ILEAGFEEIPVLGIDHVNV 318


>gi|221053005|ref|XP_002257877.1| DNA-directed RNA polymerase II second largest subunit [Plasmodium
            knowlesi strain H]
 gi|193807709|emb|CAQ38413.1| DNA-directed RNA polymerase II second largest subunit, putative
            [Plasmodium knowlesi strain H]
          Length = 1371

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 185/1024 (18%), Positives = 335/1024 (32%), Gaps = 160/1024 (15%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   I  +I  L+    G+   DD D+ G +R+   G ++ + +     +M + +K R+ 
Sbjct: 419  KSYFIGYMINRLLLAELGRIKEDDRDHFGKKRLDIAGPLMASSFSTYFRKMAKDVK-RVL 477

Query: 492  SVDIDSVMPQDL----INAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSR 534
               ID+  P D+     +   +   +     +               ++Q+   +   S 
Sbjct: 478  QRQIDNNKPFDVAGAVRSCSQITQGMQYQLATGNWGKDKDGKVIRTGVAQVLNRLTYSSC 537

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ++H RRL+      + R     + R +H TH+G ICP ET EG ++GLV +L+    ++ 
Sbjct: 538  LSHLRRLNT----PLGREGKMAKPRQLHNTHWGMICPFETPEGQSVGLVKNLSLMCDISV 593

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCA 650
                   +  + +      +  +     + +     N       +  + L+      R  
Sbjct: 594  GTSTNNIFEFLLEW-GLESLDEVPPQLMKEKVKLFLNGKWVGCFNQIDNLIETLYELRRR 652

Query: 651  GEEILVPREKIDFIDASPKQVVSIAASLIPFLEN-------------------------- 684
             +         D      K       ++ P                              
Sbjct: 653  CDISPEASIVRDVNSKEIKIFTDSGRAMRPLYVVKNVKGENKLKLTKEHVKNMMAYPETY 712

Query: 685  ------DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME--SVVAKSSGAAIVAKRAGIVE 736
                   +     + C  +   +  +  +    GTG        +   + I+   A I+ 
Sbjct: 713  NWDYLIQEGIIEYIDCEEEETTMISMFIDDLKTGTGYHNNYTHCEIHPSLILGVCASIIP 772

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D  +    + +  +     G+      ++           QRPLV             
Sbjct: 773  FSDHNQSPRNTYQSAMGKQAMGIYVTNFNIRLDTLAHLLYYPQRPLV----------CTK 822

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    +L  G N +VA M + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 823  VMEYLRFRELPAGINAIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSVFYRTYTSEEKQQG 882

Query: 856  LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP----- 905
                E       R + N+       +D  G+I  G  V   DI++GK++P  E       
Sbjct: 883  SLIIESFEKPSIRYVKNLKRGDYTKLDNDGLIAPGIRVLGDDIIIGKVSPNIEDEDDIVI 942

Query: 906  --MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              M   +    +        +          V          +      +  ++      
Sbjct: 943  QRMPNIQMGYNSGASTSNGFMIGKESSAGGSVLNGSASSVCGSVSSSPYSPSTMGGSNMM 1002

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
              +      D          + +       +  S    F+    +SS    +Y  +    
Sbjct: 1003 DSMPDSPVSDRYSSSGPVGSATVGPASVSSSTPSNTTIFRSGNTISSVNSPQYGTTIVSG 1062

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG--VLRVVKVFVAMK 1081
                D ++     S     +  K       +     +     +       +  KV V   
Sbjct: 1063 STKDDLEIPTLTISTSNILKQYKKDCSLSLRENENGVIDTVMLSSNSRGNKFAKVKVRSV 1122

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK A RHG KG +      EDMPF  DGT  DI++NP  VPSRM +G + E   
Sbjct: 1123 RIPQIGDKFASRHGQKGTIGITYRTEDMPFSSDGTFPDIIMNPHAVPSRMTIGHLVECLA 1182

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G                                                    
Sbjct: 1183 GKVAAIEG---------------------------------------------------- 1190

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G   +TP F     + I+  L     ++ G  +LY+G  G+     + +G  Y  +L H
Sbjct: 1191 -GEGDATP-FSKITVQEISQRLHNLGYEKYGNDVLYNGHNGKMLKSKIFIGPTYYQRLKH 1248

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK++ARS G  +++T+QP  G+S  GG R GEME  C+ ++G+A +L+E L  +SD 
Sbjct: 1249 MVEDKIHARSRGPLTMITRQPTEGRSRDGGLRFGEMERDCMISHGSAKMLKERLFEESDA 1308

Query: 1321 ---------------DVVGRTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                           D+      YE  V     +  +   P +  +L +E+  + +   L
Sbjct: 1309 YRVHVCDNCGLCCIADIN--KNAYECTVCNSKTNISQIYIPYACKLLFQELMTMAIYPKL 1366

Query: 1364 ENSR 1367
                
Sbjct: 1367 VLED 1370



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 118/869 (13%), Positives = 241/869 (27%), Gaps = 159/869 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----------AFSGA--AMLE 75
           L+  Q  SY+ F+   +          Q        +                     L+
Sbjct: 90  LVNQQIESYNDFIEYRM----------QEIIDEHPALEIRPQAQYRSEGDEQKNVMYALK 139

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F     D P +D            +   R+LTY+  + I +    + VDE +G++ +KD 
Sbjct: 140 FGQLSLDRPFYDERNLTNKNLWPQEARLRNLTYSSAIYIDIEQSTYVVDESSGSQILKDK 199

Query: 126 -KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + I +G +PLM K                         G F++ G ++++V+Q   +
Sbjct: 200 FIYERINLGRIPLMLKSMFCWTKGLPESEIADMGECAFDQGGYFIVNGGEKVLVAQERMA 259

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIP--------------------DQGLWMDIEFDSKD 200
               +     +     K  +   I                       +G  +     +  
Sbjct: 260 HNFIY---VFKKKQPSKFGWVAEIRSQMERSQATSAFSVKMKTKTGSRGSSVR----TGG 312

Query: 201 II-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +     ++R +    + V     ALG  S+ +IL     +IVY          L     
Sbjct: 313 QLVATLPYIRTE----ISVGILFRALGCTSDRDILQ----RIVYDFNDKMMINTLRETLE 364

Query: 255 MVGAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKGV-------KFLGITSDCLCG 305
                 +  +     G+    + + ++      K L  K V         +        G
Sbjct: 365 ECIDYPTQDICLDFIGKRGPTVGASREKRILYAKELLRKEVLPHMGTGPGVESKKSYFIG 424

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +   ++  E G I  +  D   +K L+             +     +   +    + +
Sbjct: 425 YMINRLLL-AELGRIKEDDRDHFGKKRLDIAGPLMASSFSTYFRKMAKDVKRVLQRQIDN 483

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                     D+   +R     T  +   +    +       +   G  ++  RL   + 
Sbjct: 484 NKP------FDVAGAVRSCSQITQGMQYQLATGNWGKDKDGKVIRTGVAQVLNRLTYSSC 537

Query: 426 DDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                R          +     L N    +         +   + + L     + +    
Sbjct: 538 LSHLRRLNTPLGREGKMAKPRQLHNTHWGMICPFETPEGQSVGLVKNLSLMCDISVGTST 597

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            +I E +       +   D +  + +   V  F     +    +  N +  +   RR   
Sbjct: 598 NNIFEFLL---EWGLESLDEVPPQLMKEKVKLFLNGKWVGCFNQIDNLIETLYELRRRCD 654

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           +            +   +       + P    +         LT     N   + ET   
Sbjct: 655 ISPEASIVRDVNSKEIKIFTDSGRAMRPLYVVKNVKGENKLKLTKEHVKNMMAYPET--Y 712

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                     + Y+   EEE   I+     L     +                       
Sbjct: 713 NWDYLIQEGIIEYIDCEEEETTMISMFIDDLKTGTGYHNNY-----------------TH 755

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAE 707
            +  P  ++ + AS+IPF +++ S R      M +QA+                 L   +
Sbjct: 756 CEIHPSLILGVCASIIPFSDHNQSPRNTYQSAMGKQAMGIYVTNFNIRLDTLAHLLYYPQ 815

Query: 708 APFVGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            P V T  ME +  +   A I A  A +          +   +  +D        YR   
Sbjct: 816 RPLVCTKVMEYLRFRELPAGINAIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSVFYRTYT 875

Query: 767 FQRSNQNTCVN---QRPLVKVGDEVRRND 792
            +   Q + +    ++P ++    ++R D
Sbjct: 876 SEEKQQGSLIIESFEKPSIRYVKNLKRGD 904


>gi|325990002|ref|YP_004249701.1| DNA-directed RNA polymerase subunit beta [Mycoplasma suis KI3806]
 gi|323575087|emb|CBZ40748.1| DNA-directed RNA polymerase subunit beta [Mycoplasma suis]
          Length = 2643

 Score =  458 bits (1179), Expect = e-126,   Method: Composition-based stats.
 Identities = 314/1016 (30%), Positives = 499/1016 (49%), Gaps = 103/1016 (10%)

Query: 14   RKFFGKNPE-IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F K P     +P+L  +Q  SY  FL            G+Q      FPIT+ SG  
Sbjct: 14   RIDFSKYPTADWSLPNLRGIQIDSYKKFL----------ESGIQELISRYFPITSASGNT 63

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
             +     E        ++ +    +Y   + + LRL+    +  +   + +      I+ 
Sbjct: 64   QVFLDGIEITEVDVTEEEAVNSSKSYQRSIYLKLRLVSKYSEGKSKLSTSR------IFF 117

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH-FDHDKGRASLSGKLL---YACRIIPDQ 188
            G++P+ +    F+I GI++ V+ Q+ RSPG++  +  + R S S K       C ++P +
Sbjct: 118  GNMPIFSSSSNFIINGIEKFVICQIVRSPGLYVLNKAQIRLSNSRKRTQEGIVCELLPVK 177

Query: 189  GLWMDIEF----DSKD--------IIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFY 233
            G+ +        D KD         +  R          PVT FL ALG+ ++ I S F 
Sbjct: 178  GVLLLFHLPNPSDKKDGGEESTSIKLIARNTSGNNAYSFPVTVFLKALGISTKTITSLFE 237

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                      F     + +  +  + V S L +I + +   +  + L+ G ++       
Sbjct: 238  KNPE--LMRAFSQESFNPSGALNDSLVVSILSEISSAK-GAQKMRDLSKGWIRETLYSLC 294

Query: 294  KFLGITSDCLCGLYVAEDIVNGETGEI----YIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                          V EDI+     E+     I +  +  E +  EI   +       Y 
Sbjct: 295  MRYTEAEREGASRAVKEDILEKIAIELAAKQLISSFSINTEIARREIHSYQELLWSYFYD 354

Query: 350  DSVNN----NAYIRNTLVTDKNKDRKDALLDIYRVM---------------RPGDVSTFS 390
             +  +      Y  N  ++   + R   L      +               +  +    +
Sbjct: 355  KNYYHILPAGRYKLNYKLSVWERMRNKYLAQDICDLSGNVVFAKDTFMDFEKLSEFKEAA 414

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--------------------PDDVRH 430
            +A+ +     FD  +      GR +    +  +                      +D + 
Sbjct: 415  IAKKLNIRHKFDITRTFDDIEGRYRDFDVIEYEKVSIYSVGLDSEVITLLGTPYLEDEKP 474

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            +   D +AII  ++ L+   G  DDIDNLGN+R++ + E+LK++  + L R+++   +R+
Sbjct: 475  LNPSDALAIISYMLHLKKKVGEYDDIDNLGNKRLKLIDELLKDRIAIALTRIQKFSVDRM 534

Query: 491  SSVDI-------------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +S++              D      ++N KP    + EFF S QL Q  +  N LS IT+
Sbjct: 535  NSLESKLSYFSLQDGELEDYFSLSSIMNTKPFQIVIKEFFNSHQLVQFLDQQNVLSEITN 594

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             R++SA+G GG+ R    + +RDVH ++YGR+CP ET EG NIGL+ +L S +RV+ YGF
Sbjct: 595  KRKISAMGPGGIKREDPNLSIRDVHYSYYGRVCPIETPEGMNIGLIMALASLSRVDKYGF 654

Query: 598  IETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            + TPY +V +     +  V+L++++E +  IA+A +  DE+G      V  R   E   V
Sbjct: 655  LNTPYYRVKNGVIQKDQKVWLNSIQERSFCIAEATTERDENGRLIGP-VTVRRDEEVESV 713

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              E++ +ID    Q+ SI+ SLIPFLE+DD+NR LMG NMQRQAVPL+  ++P V TG+E
Sbjct: 714  DPEEVSYIDVDCTQITSISTSLIPFLEHDDANRALMGANMQRQAVPLISPKSPIVATGVE 773

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            S +A+ SG  I A+  GI+  +D+ +I ++           G   Y L KF ++NQNTC 
Sbjct: 774  SRIARDSGVVIQAEDDGIITYMDSSQIRVKY------RGELGEKTYSLQKFIKTNQNTCK 827

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ  + +   EV++ DI+ DG +   G+LALG+N+LVAF  W+GYN+ED++++S R+V E
Sbjct: 828  NQLVVPRNSREVKKGDILVDGHAIQNGELALGQNILVAFTSWYGYNYEDAIILSSRLVQE 887

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            +V+TS+HI+E+ V    TK+G EEITR IP  + E  K +DE G+I VGA V  GDILVG
Sbjct: 888  NVYTSLHIQEYTVNCMRTKIGDEEITRFIPGCTAEEKKYLDEDGVILVGAAVKEGDILVG 947

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K +PK    +TPEEKLL+AIF EKA  V+D+SLR+PSG  G V  +  ++    D+
Sbjct: 948  KTSPKAMGEVTPEEKLLQAIFSEKAKSVKDSSLRLPSGSEGIVTKILRYSAAKGDR 1003



 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 172/593 (29%), Positives = 270/593 (45%), Gaps = 47/593 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLG 857
                       ++    P      E  +     +V +  D     +++  ++  +     
Sbjct: 749  MGANMQRQAVPLISPKSPIVATGVESRIARDSGVVIQAEDDGIITYMDSSQIRVKYRGEL 808

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E+       +        ++  +     EV  GDILV     +    +   + +L A  
Sbjct: 809  GEKTYSLQKFIKTNQNTCKNQLVVPRNSREVKKGDILVDGHAIQN-GELALGQNILVAFT 867

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D  + + S +    V   +  +       R+   + E    +     +E+  
Sbjct: 868  SWYGYNYEDAII-LSSRLVQENVYTSLHIQEYTVNCMRTKIGDEEITRFIPGCTAEEKKY 926

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +       IL G     G     K+                 +   +++ +Q     
Sbjct: 927  LDED-----GVILVGAAVKEGDILVGKT-----------SPKAMGEVTPEEKLLQAIFSE 970

Query: 1038 LKVQYETSKSILEDRFKNKIEKI-----QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 + S   L    +  + KI       GD +   VL  +K+FV  KR IQ GDKM G
Sbjct: 971  KAKSVKDSSLRLPSGSEGIVTKILRYSAAKGDRLGDDVLETIKIFVTSKRNIQIGDKMVG 1030

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKGIVS+++P EDMP+L+DGT VDI+LNPLGVPSRMN+GQI E++L ++   L  K 
Sbjct: 1031 RHGNKGIVSKVVPVEDMPYLEDGTAVDILLNPLGVPSRMNIGQILESYLAFSARKLVFKK 1090

Query: 1153 KSLIND-----------YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                              ++  ++  L   ++  + + +   +       + L  +    
Sbjct: 1091 ILEAFFDSSLESCDTLFSRSKVELESLGKVIKSYLESKNIKSREEALSKLTQLDFSIILS 1150

Query: 1202 SG--------VPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVT 1250
                      + V TP+F G     + +++  A +D    +G+  LYDG TGE F  P++
Sbjct: 1151 HAGIKYDELEIKVLTPIFAGCKNSDLINIMADAGVDFKHHNGRFTLYDGRTGEKFKDPIS 1210

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG IYMLKL+HMV DK+YARS G YS +TQQPLGGK   GGQR GEMEVW ++AYGAA+ 
Sbjct: 1211 VGIIYMLKLDHMVDDKIYARSVGPYSKITQQPLGGKCQNGGQRFGEMEVWALEAYGAAHN 1270

Query: 1311 LQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            L+E+L++KSDD+  R  +Y SI+ G    +    ESF +LVK++QALGL +++
Sbjct: 1271 LRELLSLKSDDIQARNLIYYSIIKGQALPKPTISESFKLLVKKLQALGLRVNI 1323


>gi|133918595|emb|CAL29502.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
          Length = 318

 Score =  458 bits (1178), Expect = e-126,   Method: Composition-based stats.
 Identities = 177/319 (55%), Positives = 242/319 (75%), Gaps = 1/319 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPAGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + ++EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ 
Sbjct: 240 AGKKLTVRGARQMQEKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKA 299

Query: 336 IFHSEIRDIPILYVDSVNN 354
           +     +++P+L +D VN 
Sbjct: 300 LNEQGYKELPLLDIDHVNV 318


>gi|71842272|ref|YP_277360.1| RNA polymerase beta subunit [Emiliania huxleyi]
 gi|88909137|sp|Q4G3A7|RPOB_EMIHU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|60101515|gb|AAX13859.1| RNA polymerase beta subunit [Emiliania huxleyi]
          Length = 1093

 Score =  457 bits (1175), Expect = e-126,   Method: Composition-based stats.
 Identities = 171/474 (36%), Positives = 237/474 (50%), Gaps = 59/474 (12%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIELLARDKDDEQ--VILDRN 981
            ++  +           D  + N   +  +  + I +E+ +IE        E+    L   
Sbjct: 651  QNILIAYMPWEGYNYEDAFVVNERLLYDDLHTSIHIEKFEIESRQTKLGAEEITRDLPNV 710

Query: 982  IYSRLMEILCGQNAVSG----PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
                L ++        G    P       +         P  +  +    ++       S
Sbjct: 711  NEKSLSKLDENGIIHIGSWVEPGDILVGKLTPKGESDYLPEGKLLRAIFGEKSRDVRNTS 770

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LK+ +  +  +L+     KI      DD+ PG   V+KV++A  R IQ GDK+AGRHGNK
Sbjct: 771  LKLHHGVNGRVLD----VKIFSRANQDDLSPGTNEVIKVYIAQIRKIQIGDKVAGRHGNK 826

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+S+ILP +DMP+L DGTPVDI+LNPLGVPSRMNVGQIFE  LG A   L  + K +  
Sbjct: 827  GIISKILPRQDMPYLPDGTPVDILLNPLGVPSRMNVGQIFECLLGLAAEHLNARFKVIPF 886

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D     + S                     + +++++  AE  K     ST         
Sbjct: 887  DEMNGVEASR-------------------GFVNNTLMEAAE--KQPWVFST--------- 916

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                          G+ +L DG TGE FD P+TVG  Y+LKL H+V DK++ARSTG YSL
Sbjct: 917  -----------QHPGKMMLTDGQTGEMFDNPITVGRAYVLKLVHLVDDKIHARSTGPYSL 965

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGG++ +GGQRLGEMEVW ++A+GAAY LQE+LTIKSDD+ GR     +IV G  
Sbjct: 966  VTQQPLGGRAQQGGQRLGEMEVWALEAFGAAYTLQELLTIKSDDMQGRNETLNAIVKGYP 1025

Query: 1338 TFETGTPESFNVLVKEMQALGLSI---DLEN----SRTKNSAKMEEIPDFNKCE 1384
                GTPESF VL++E+QAL L I    +E+    +  K    M E+      +
Sbjct: 1026 IPRPGTPESFKVLLRELQALCLDIAAYKIEDTTLLTEDKEINLMSELNSSRDDQ 1079



 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 300/653 (45%), Positives = 429/653 (65%), Gaps = 12/653 (1%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +YI+            +    + +  I   +S+ N  Y R T  TD+    +  LL+++ 
Sbjct: 169 VYIKIDKAKKFSIFVFLKALGLDNQEI--FNSIENINYFRKTSNTDEQLTTEQCLLEVHS 226

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            ++P + +T    + +    FFDS KYDL  VGR K+N  L LD   DVR +   D+I I
Sbjct: 227 HLKPEEPATAKGCQKLLYAKFFDSKKYDLGYVGRHKLNQALMLDIDSDVRILTSLDLIGI 286

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I  L+  R      DDID+LGNRR+RSVGE++ NQ R+GL R+ER ++ER++  +   + 
Sbjct: 287 INQLIRFRFMPIVSDDIDHLGNRRIRSVGELMANQIRIGLNRLERVVRERMAICEHSYLR 346

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
              L+N KP+ +++ EFF S+ LSQ  +  N L+ +TH RR+S LG GG+AR RAG  +R
Sbjct: 347 VNTLVNPKPLAASIREFFGSNPLSQFMDQTNPLAELTHKRRISVLGPGGIARDRAGFVVR 406

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYL 617
           D+HP+ YGRICP ET EG N GL+ SL+++ ++NAYGFIETP+ KV  GKV  D+  +YL
Sbjct: 407 DIHPSQYGRICPVETPEGPNAGLIGSLSTYGKINAYGFIETPFYKVKQGKVLKDLPPIYL 466

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            A+ EE   +A  + + DE G   +  V  R     + V + ++D+I  SP QVVS+A S
Sbjct: 467 DAIAEEQYKLAAGDVATDEHGVLKQPDVPVRYQQNIVTVSKNEVDYIAVSPIQVVSLATS 526

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQ+VPLL A+AP VGTG+ES  A+ SG AI++   G V  
Sbjct: 527 LIPFLEHDDANRALMGSNMQRQSVPLLYADAPLVGTGLESQTARDSGMAILSSNCGKVVT 586

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           +   +IV++              IY L K++RSNQ+TC+NQ+P V + ++VR   ++ADG
Sbjct: 587 LSDEQIVVQ-------DKNGNQLIYNLTKYKRSNQDTCINQKPCVSLYEKVRVGQLLADG 639

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            ST+ G+LA+G+N+L+A+MPW GYN+ED+ +++ER++ +D+ TSIHIE+FE+ +R TKLG
Sbjct: 640 TSTETGELAVGQNILIAYMPWEGYNYEDAFVVNERLLYDDLHTSIHIEKFEIESRQTKLG 699

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRD+PNV+E+ L  +DE GII +G+ V PGDILVGK+TPKGES   PE KLLRAIF
Sbjct: 700 AEEITRDLPNVNEKSLSKLDENGIIHIGSWVEPGDILVGKLTPKGESDYLPEGKLLRAIF 759

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI-DKNERSISVEREQIELLAR 969
           GEK+ DVR+TSL++  GV+G V+DV+IF+R    D +  +  V +  I  + +
Sbjct: 760 GEKSRDVRNTSLKLHHGVNGRVLDVKIFSRANQDDLSPGTNEVIKVYIAQIRK 812



 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 84/442 (19%), Positives = 182/442 (41%), Gaps = 50/442 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           +P+L++VQ+ASY  FL           +G     ++   I  + G   L F    Y  +P
Sbjct: 13  LPNLLDVQRASYCWFL----------EKGFVQELRTFSVIRDYLGDLELNFATKFYTINP 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P++ +++   +D TY+V + I  +L   +           D +E+ +++GD+PLMT  GT
Sbjct: 63  PRYTLEEAKRKDATYSVRIFIRAQLNYLEG---------ADPQEKQVFLGDIPLMTDSGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI+RI+++Q+ RSPGI++  +  +    G  +Y   +I ++G W+  E D  D+++
Sbjct: 114 FLVNGIERIIINQIVRSPGIYYKSEADKQ---GVRIYTASLISNRGTWVKFEIDKDDLVY 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           ++ID+ +K  +  FL ALG+D++EI ++      +           +   L     +   
Sbjct: 171 IKIDKAKKFSIFVFLKALGLDNQEIFNSIENINYFR------KTSNTDEQLTTEQCLLEV 224

Query: 264 LVDIDTGEQVIESG-KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET----- 317
              +   E     G +KL        K+  + ++G          +  DI +        
Sbjct: 225 HSHLKPEEPATAKGCQKLLYAKFFDSKKYDLGYVGRHK---LNQALMLDIDSDVRILTSL 281

Query: 318 ------GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
                  ++       I    ++ + +  IR +  L  + +         +V ++    +
Sbjct: 282 DLIGIINQLIRFRFMPIVSDDIDHLGNRRIRSVGELMANQIRIGLNRLERVVRERMAICE 341

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + L +  ++ P      +     F            + +  +    R+++  P     I
Sbjct: 342 HSYLRVNTLVNPK--PLAASIREFFGSNPLSQFMDQTNPLAELTHKRRISVLGPGG---I 396

Query: 432 RKEDIIAIIKILVDLRNGKGTI 453
            ++    +++ +   + G+   
Sbjct: 397 ARDRAGFVVRDIHPSQYGRICP 418


>gi|289190500|gb|ADC93355.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-27]
 gi|289190502|gb|ADC93356.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-27]
          Length = 235

 Score =  456 bits (1173), Expect = e-125,   Method: Composition-based stats.
 Identities = 164/235 (69%), Positives = 195/235 (82%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G++I  ++  Y+A+G+I PLR  +  V+G G   E++ D+DDDSVLR+A+
Sbjct: 61   THLGWACAGMGRQIGDMLEAYRASGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVLRLAD 120

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            QWK GV ++TPVFDGA E  +N+ML +A L ESGQS LYDG TGE FDR VTVGYIYMLK
Sbjct: 121  QWKRGVSIATPVFDGAHEGDVNAMLALAGLKESGQSTLYDGRTGEQFDRQVTVGYIYMLK 180

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            LNH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 181  LNHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 235


>gi|289190492|gb|ADC93351.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-25]
 gi|289190494|gb|ADC93352.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-25]
          Length = 235

 Score =  456 bits (1173), Expect = e-125,   Method: Composition-based stats.
 Identities = 165/235 (70%), Positives = 195/235 (82%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G++I  ++  YKA+G+I PLR  +  V+G G   E++ D+DDDSVLR+A+
Sbjct: 61   THLGWACAGMGRQIGDMLEAYKASGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVLRLAD 120

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            QWK GV ++TPVFDGA E  +N+ML +A L ESGQS LYDG TGE FDR VTVGYIYMLK
Sbjct: 121  QWKRGVSIATPVFDGAHEGDVNAMLALAGLKESGQSTLYDGRTGEQFDRQVTVGYIYMLK 180

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            LNH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 181  LNHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 235


>gi|218282082|ref|ZP_03488381.1| hypothetical protein EUBIFOR_00956 [Eubacterium biforme DSM 3989]
 gi|218216937|gb|EEC90475.1| hypothetical protein EUBIFOR_00956 [Eubacterium biforme DSM 3989]
          Length = 529

 Score =  456 bits (1173), Expect = e-125,   Method: Composition-based stats.
 Identities = 172/493 (34%), Positives = 233/493 (47%), Gaps = 67/493 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  GDIL    +      +   + ++ A       +  D  +     VS  V 
Sbjct: 66   IVEVGEKVEKGDILADGPS-MQNGELALGQNVVIAYTTWHGYNYEDAIIMSERMVSDDVY 124

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + ID  E  +  E E    +    +     LD N       I+ G     G  
Sbjct: 125  TSIHVEEYDIDCRETKLGPE-EITRDIPNVSEAAVRKLDSN-----GIIMVGAEVKEGDI 178

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  +  +V+ N   +          +      ++ K 
Sbjct: 179  LVGKVTPKGQSEVSPEEKLLLAIFGEKSREVRDNSLKVPHGGAGIVHSI------RVFKR 232

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G D+PPGV   VKV++  KR I  GDKM+GRHGNKG++S+ILP EDMPF+ DG PVDI
Sbjct: 233  GDGSDLPPGVNMRVKVYIVQKRKISEGDKMSGRHGNKGVISKILPIEDMPFMADGHPVDI 292

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG+A   LG K  + + D  +N D+  +       +    
Sbjct: 293  LLNPFGVPSRMNIGQILEIHLGYAARKLGVKFSTSVFDGLSNEDLQDVMREASMTVDGKQ 352

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                               GQ       
Sbjct: 353  VL-----------------------------------------------YDGQ------- 358

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PFD  ++VG +YM+KL HMV DK++AR+TG YSLVTQQPLGGK+  GGQR GEMEVW
Sbjct: 359  TGQPFDERISVGVMYMIKLAHMVDDKLHARATGPYSLVTQQPLGGKAQNGGQRFGEMEVW 418

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++AYGAA+ LQE+LTIKSDD+ GR + YE+I+ G D  E G PESF VL+ E+Q L + 
Sbjct: 419  ALEAYGAAHTLQEILTIKSDDIQGRIKTYEAIIKGKDIPEPGVPESFRVLMHELQGLAID 478

Query: 1361 IDLENSRTKNSAK 1373
            I L +        
Sbjct: 479  IRLLDENNNEVDI 491



 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 139/241 (57%), Positives = 189/241 (78%), Gaps = 7/241 (2%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+VGTG+E  +AK SG  IVAK+ G++E VD +RIV++  EG+          Y+L KF 
Sbjct: 1   PYVGTGIEYKIAKDSGVGIVAKQDGVIEYVDGLRIVVKDNEGEN-------HTYQLRKFA 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +TC+NQRP+V+VG++V + DI+ADGPS   G+LALG+N+++A+  WHGYN+ED+++
Sbjct: 54  RSNASTCINQRPIVEVGEKVEKGDILADGPSMQNGELALGQNVVIAYTTWHGYNYEDAII 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SERMVS+DV+TSIH+EE+++  R+TKLGPEEITRDIPNVSE  ++ +D  GII VGAEV
Sbjct: 114 MSERMVSDDVYTSIHVEEYDIDCRETKLGPEEITRDIPNVSEAAVRKLDSNGIIMVGAEV 173

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKG+S ++PEEKLL AIFGEK+ +VRD SL+VP G +G V  +R+F R 
Sbjct: 174 KEGDILVGKVTPKGQSEVSPEEKLLLAIFGEKSREVRDNSLKVPHGGAGIVHSIRVFKRG 233

Query: 949 G 949
            
Sbjct: 234 D 234


>gi|299780662|gb|ADJ40007.1| RNA polymerase beta subunit [Ureaplasma felinum]
          Length = 845

 Score =  456 bits (1173), Expect = e-125,   Method: Composition-based stats.
 Identities = 194/596 (32%), Positives = 285/596 (47%), Gaps = 48/596 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       ++  + P  G   E  +     M     ++ + T +   E  V  +D K
Sbjct: 265  MGSNMQRQATPLIKPYAPVVGTGTEFKIAHDSGMAVVAKNDGIITKVDGREIVVETKDNK 324

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                ++ + I           ++  I+ +G EV   +  +G         +     +L A
Sbjct: 325  K---DVYKLIKYRKSNQDTCNNQTPIVSLGQEVKASET-IGDGPAMKNGELALGRNILAA 380

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  +     +S  +VD  +F    ID++       +   E + RD  +  
Sbjct: 381  YTTWRGYNFEDAII-----ISERLVDEDVFTSIHIDEHTIQCMKTKNGDEEITRDTPN-V 434

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                R        I  G     G     K+T      +   P  +  Q    D+      
Sbjct: 435  SDYARRFLDADGIITVGSEVSEGDVLVGKTTP--RANVDTIPEDRLIQTIFGDKAKTVKD 492

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLK                +I     G+++P  VL ++K+++  KR IQ GDKMAGRHG
Sbjct: 493  SSLK---VKHGQEGIVAAVRRITSTDEGNELPDDVLEIIKIYIVQKRKIQVGDKMAGRHG 549

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK--IK 1153
            NKGIVS+++P +DMP+L DGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +GKK  ++
Sbjct: 550  NKGIVSKVVPIQDMPYLADGTPIDIMLNPLGVPSRMNIGQILELHLGYAASEIGKKQVVQ 609

Query: 1154 SLINDYKANGDISPLRSF----------------LEKVIGTGSHTEKISDYDDDSVLRVA 1197
             +++D        P+  +                L + I      + I    +   + + 
Sbjct: 610  IVLDDISNEQQNKPVLGYQRYVDLFGIEHENARLLYQKITQLIKDKNIKHSKEVDQVDMK 669

Query: 1198 EQWKS--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFD 1246
               KS         + V+TPVF GA++  I   +    +D   + G+  LYDG TGEPFD
Sbjct: 670  IILKSIGLSYDDIAIKVATPVFSGANKNDIIEAMNEVGIDIENKKGKQTLYDGKTGEPFD 729

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              ++VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR GEMEVW ++AYG
Sbjct: 730  GLISVGVSYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFGEMEVWALEAYG 789

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
            AAY L E+LTIKSDDV GR R Y SI+ G +    G PESF +L K++Q L LS++
Sbjct: 790  AAYNLLEILTIKSDDVHGRNRAYNSIIKGKEISIDGMPESFKLLTKQIQGLALSME 845



 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 229/543 (42%), Positives = 328/543 (60%), Gaps = 40/543 (7%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI--------------- 504
           GN+R++ + E+L+ +  + + R+E+ I E+++  D  S    +                 
Sbjct: 2   GNKRLKLIHELLRQRIGISMARIEKFISEKLAIADGSSNNITNQNDRDIDPELDEKIDAI 61

Query: 505 ----------------NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
                           N K   S V EFF S QL Q  +  N L+ +T+ RR+SA+G GG
Sbjct: 62  EDEEEKKKAISVKSVINTKQFQSLVKEFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGG 121

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R    +++RDVH +HY RICP ET EG NIGL+ SL S A+++  GFI  PY  V DG
Sbjct: 122 ISREDPNLDIRDVHSSHYSRICPIETPEGMNIGLIMSLASLAKIDDNGFITAPYYVVKDG 181

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT++V YL+A E+++  I+++N  LDE+     + V  R  G        ++++ID  P
Sbjct: 182 IVTDEVRYLTAHEDDDCVISESNVELDENNRILNDKVIARYNGHTNEFKPSQVEYIDIVP 241

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVSIAAS IPF+ENDD  R LMG NMQRQA PL+K  AP VGTG E  +A  SG A+V
Sbjct: 242 RQVVSIAASSIPFIENDDGARALMGSNMQRQATPLIKPYAPVVGTGTEFKIAHDSGMAVV 301

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AK  GI+ +VD   IV+ + +   D       +Y+L+K+++SNQ+TC NQ P+V +G EV
Sbjct: 302 AKNDGIITKVDGREIVVETKDNKKD-------VYKLIKYRKSNQDTCNNQTPIVSLGQEV 354

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           + ++ I DGP+   G+LALGRN+L A+  W GYNFED+++ISER+V EDVFTSIHI+E  
Sbjct: 355 KASETIGDGPAMKNGELALGRNILAAYTTWRGYNFEDAIIISERLVDEDVFTSIHIDEHT 414

Query: 849 VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
           +    TK G EEITRD PNVS+   + +D  GII VG+EV+ GD+LVGK TP+      P
Sbjct: 415 IQCMKTKNGDEEITRDTPNVSDYARRFLDADGIITVGSEVSEGDVLVGKTTPRANVDTIP 474

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR--IFNRHGIDKNERSISVEREQIEL 966
           E++L++ IFG+KA  V+D+SL+V  G  G V  VR       G +  +  + + +  I  
Sbjct: 475 EDRLIQTIFGDKAKTVKDSSLKVKHGQEGIVAAVRRITSTDEGNELPDDVLEIIKIYIVQ 534

Query: 967 LAR 969
             +
Sbjct: 535 KRK 537


>gi|289190496|gb|ADC93353.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-24]
          Length = 235

 Score =  456 bits (1172), Expect = e-125,   Method: Composition-based stats.
 Identities = 165/235 (70%), Positives = 194/235 (82%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G++I  ++  YKA+G+I PLR  +  V+G G   E++ D+DDDSVLR+A+
Sbjct: 61   THLGWACAGMGRQIGDMLEAYKASGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVLRLAD 120

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            QWK GV ++TPVFDGA E  +N ML +A L ESGQS LYDG TGE FDR VTVGYIYMLK
Sbjct: 121  QWKRGVSIATPVFDGAHEGDVNEMLALAGLKESGQSTLYDGRTGEQFDRQVTVGYIYMLK 180

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            LNH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 181  LNHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 235


>gi|331029421|gb|AEC49860.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 656]
          Length = 319

 Score =  456 bits (1172), Expect = e-125,   Method: Composition-based stats.
 Identities = 172/304 (56%), Positives = 232/304 (76%), Gaps = 1/304 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++  P  R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 2   SYDQFLMVDEPPGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 61

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VS
Sbjct: 62  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVS 121

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVT
Sbjct: 122 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVT 181

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E
Sbjct: 182 SLMFALGLDGEAILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 240

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN  TGEI+ EA + ID+++++ 
Sbjct: 241 AGKKLTVRAARQLQEKGLKALRLSDEELVGNYLAEDLVNPNTGEIHAEAVEEIDDQNMKA 300

Query: 336 IFHS 339
           +   
Sbjct: 301 LNEQ 304


>gi|51469306|emb|CAH04382.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 488

 Score =  455 bits (1171), Expect = e-125,   Method: Composition-based stats.
 Identities = 234/491 (47%), Positives = 331/491 (67%), Gaps = 3/491 (0%)

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   V+  +G+     L  
Sbjct: 1   LDFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNVFHVKGEALSLELVP 60

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L  G   S  + D + G+ ++E G+++T+  +  L + G+K L +  D + G   A+ 
Sbjct: 61  QRL-RGEIASFDITD-ENGKVIVEQGRRITARHINQLDKSGIKSLDMPMDYVLGRTTAKA 118

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IV+  TGEI  E    +  + L ++  +++     LY + ++   +I +TL  D   ++ 
Sbjct: 119 IVHPATGEIIAECNTELTVEVLAKLVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQL 178

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +AL++IYR+MRPG+  T   AE++FN LFF S++YDLS VGR+K N R+     +    +
Sbjct: 179 EALVEIYRMMRPGEPPTKDAAETLFNNLFFASERYDLSAVGRMKFNRRIGRTEIEGSGVL 238

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S
Sbjct: 239 SREDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLS 298

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 299 MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 358

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT
Sbjct: 359 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVNEGEVT 418

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 419 DEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHQNEFTVKAPEDVTLMDVSPKQV 477

Query: 672 VSIAASLIPFL 682
           VS+AASLIPFL
Sbjct: 478 VSVAASLIPFL 488


>gi|50344532|emb|CAH04381.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 488

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 234/491 (47%), Positives = 331/491 (67%), Gaps = 3/491 (0%)

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   V+  +G+     L  
Sbjct: 1   LDFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNVFHVKGEALSLELVP 60

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L  G   S  + D + G+ ++E G+++T+  +  L + G+K L +  D + G   A+ 
Sbjct: 61  QRL-RGEIASFDITD-ENGKVIVEQGRRITARHINQLDKSGIKSLDMPMDYVLGRTTAKA 118

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IV+  TGEI  E    +  + L ++  +++     LY + ++   +I +TL  D   ++ 
Sbjct: 119 IVHPATGEIIAECNTELTVEVLAKLVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQL 178

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +AL++IYR+MRPG+  T   AE++FN LFF S++YDLS VGR+K N R+     +    +
Sbjct: 179 EALVEIYRMMRPGEPPTKDAAETLFNNLFFASERYDLSAVGRMKFNRRIGRTEIEGSGVL 238

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S
Sbjct: 239 SREDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLS 298

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 299 MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 358

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT
Sbjct: 359 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVNEGEVT 418

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 419 DEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHQNEFTVKAPEDVTLMDVSPKQV 477

Query: 672 VSIAASLIPFL 682
           VS+AASLIPFL
Sbjct: 478 VSLAASLIPFL 488


>gi|323182084|gb|EFZ67494.1| DNA-directed RNA polymerase subunit beta domain protein
           [Escherichia coli 1357]
          Length = 302

 Score =  455 bits (1170), Expect = e-125,   Method: Composition-based stats.
 Identities = 127/308 (41%), Positives = 194/308 (62%), Gaps = 9/308 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R 
Sbjct: 175 RIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRD 234

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           +     L    L  G   S  +     G+  +E G+++T+  ++ L++  VK + +  + 
Sbjct: 235 NKLQMELVPERL-RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEY 291

Query: 303 LCGLYVAE 310
           + G  VA+
Sbjct: 292 VAGKVVAK 299


>gi|331029437|gb|AEC49868.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6148]
          Length = 314

 Score =  454 bits (1169), Expect = e-125,   Method: Composition-based stats.
 Identities = 176/303 (58%), Positives = 230/303 (75%), Gaps = 1/303 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +EGLQ  F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPAGGRLDEGLQPVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI + +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITFKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ 
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKV 299

Query: 336 IFH 338
           +  
Sbjct: 300 LNE 302


>gi|50344556|emb|CAH03847.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|50344558|emb|CAH03848.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|50344560|emb|CAH03849.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|50344564|emb|CAH03851.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|50344566|emb|CAH03852.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 488

 Score =  454 bits (1168), Expect = e-125,   Method: Composition-based stats.
 Identities = 235/491 (47%), Positives = 333/491 (67%), Gaps = 3/491 (0%)

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   ++  +G+     L  
Sbjct: 1   LDFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNIFHVKGESLALELVP 60

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L  G   +  + D ++G+ ++E G+++T+  +  L + G+K L +  D + G  VA+ 
Sbjct: 61  QRL-RGEIATFDIKD-ESGKVIVEQGRRITARHINQLDKSGIKELEMPMDYVLGRTVAKA 118

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IV+  TGEI  E    +   +L +I  +++     LY + ++   +I +TL  D   ++ 
Sbjct: 119 IVHPATGEIIAECNTELTVDALAKIVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQL 178

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +AL++IYR+MRPG+  T   AE++FN LFF S++YDLS VGR+K N R+     +    +
Sbjct: 179 EALVEIYRMMRPGEPPTKDAAETLFNNLFFASERYDLSAVGRMKFNRRIGRTEIEGSGVL 238

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S
Sbjct: 239 SREDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLS 298

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 299 MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 358

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT
Sbjct: 359 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVT 418

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 419 DEIVFLSAIEEADHVIAQASAKL-EGLKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 477

Query: 672 VSIAASLIPFL 682
           VS+AASLIPFL
Sbjct: 478 VSVAASLIPFL 488


>gi|50344562|emb|CAH03850.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 488

 Score =  453 bits (1166), Expect = e-125,   Method: Composition-based stats.
 Identities = 234/491 (47%), Positives = 331/491 (67%), Gaps = 3/491 (0%)

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           +D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   ++  +G+     L  
Sbjct: 1   LDFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNIFHVKGESLALELVP 60

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
             L  G   S  + D + G+ ++E G+++T+  +  L + G+K L +  D + G  VA+ 
Sbjct: 61  QRL-RGEIASFDIKD-ENGKVIVEQGRRITARHINQLDKSGIKELEMPMDYVLGRTVAKA 118

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IV+  TGEI  E    +    + +I  +++     LY + ++   +I +TL  D   ++ 
Sbjct: 119 IVHPATGEIIAECNTELTVDVMAKIVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQL 178

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +AL++IYR+MRPG+  T   AE++FN LFF S++YDLS VGR+K N R+     +    +
Sbjct: 179 EALVEIYRMMRPGEPPTKDAAETLFNNLFFASERYDLSAVGRMKFNRRIGRTEIEGSGVL 238

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S
Sbjct: 239 SREDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLS 298

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 299 MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 358

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT
Sbjct: 359 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVT 418

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 419 DEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 477

Query: 672 VSIAASLIPFL 682
           VS+AASLIPFL
Sbjct: 478 VSVAASLIPFL 488


>gi|289190498|gb|ADC93354.1| RNA polymerase beta subunit [Rhizobium genosp. TUXTLAS-26]
          Length = 235

 Score =  453 bits (1165), Expect = e-124,   Method: Composition-based stats.
 Identities = 165/235 (70%), Positives = 194/235 (82%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTSVDVVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC G+G++I  +I  YKA+GDI PLR  +E+++G+G   E + DYDD S+LR+AE
Sbjct: 61   THLGWACAGMGRQIGEMIEAYKASGDIKPLRLTMEELMGSGPKAEPVKDYDDQSLLRLAE 120

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            Q K GV ++TPVFDGA E  IN +L  A + E+GQS LYDG TGE FDRPVTVGYIYMLK
Sbjct: 121  QSKKGVSIATPVFDGAHEADINKLLAKAGVSETGQSTLYDGRTGEAFDRPVTVGYIYMLK 180

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            LNH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 181  LNHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 235


>gi|160331027|ref|XP_001712221.1| rpb2 [Hemiselmis andersenii]
 gi|159765668|gb|ABW97896.1| rpb2 [Hemiselmis andersenii]
          Length = 1222

 Score =  453 bits (1165), Expect = e-124,   Method: Composition-based stats.
 Identities = 240/1424 (16%), Positives = 449/1424 (31%), Gaps = 319/1424 (22%)

Query: 28   DLIEVQKASYDHFLMMNIAPDERPNEGL--QAAFKSVFPITAFSGA---AMLEFVSYEFD 82
            +L+  Q  S++ F+   +         +  +  F      ++ +      +L F      
Sbjct: 27   NLVRQQLDSFNEFIQNTMQDIIDDIPPIVIKTEFDKFK--SSETKKSLKLILRFGQLHLS 84

Query: 83   PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE----- 127
             P F            ++   R+LTY+ PL   +  I  ++ E        +IKE     
Sbjct: 85   KPTFIEENGTTHTLLPNEARLRNLTYSSPLYCDISTITLNITEEL----TGEIKENFLKD 140

Query: 128  --QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
              Q I +G +P+M K                         G F+I G ++++V Q   + 
Sbjct: 141  DHQKILLGRIPIMVKSRFCVLDKLLPMDLIRIGECPIDPGGYFIINGSEKVIVGQEQLAW 200

Query: 162  G-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
              ++    K     S KL                 +  K++++                 
Sbjct: 201  NYVYIFSKKETTKNSSKL---------------YFYTKKNLLY----------------- 228

Query: 221  LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
                        + +         W   L    + +        V     +   +S    
Sbjct: 229  ------------FAECRSVAEFGRWSPSLLTVKVCIT-------VFPKKNKINKQSSSST 269

Query: 281  TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
             S L           L +    +   ++ + +      EI        +++ L E     
Sbjct: 270  NSALHFYGGLYLRAILPLFKKDIPVTWIFKALGFENETEILRHICYNDEDEELIESIRYS 329

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            + D  ++  ++ +N + I          D++ AL  I + +  G               +
Sbjct: 330  LEDDKLMASETFSNISSIL---------DQETALAAIGQHISRG------AQSLRIKHAY 374

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                K  L  VG                   +      II  L+  + GK   DD D+ G
Sbjct: 375  ETLQKEFLPHVG-----------IGQGFELRKGFFFGYIINKLMATQIGKRATDDRDHYG 423

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIK---ERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            ++R+   G +L   +R  L ++ + ++   +R S++  +     D I    + + +    
Sbjct: 424  HKRLDVAGPLLSVLFRQLLGKVIKDLRTSLQRKSNLGKNFNQISDFIKPSFLTTGIQYAL 483

Query: 518  CSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
             +             +SQ+   ++  S ++H RRL++       +     + R +H +H+
Sbjct: 484  ATGNWGTDKQASRTGVSQVLNRLSFSSTLSHLRRLNS----PSGKDGNLTKPRQLHNSHW 539

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN-- 624
            G ICPAET EGH+ GLV +L   A V            + +      +  LS ++ E   
Sbjct: 540  GLICPAETPEGHSCGLVRNLALSAFVTIGSSTLPIMEFLEEF----KIENLSDVKLEKLK 595

Query: 625  --RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS---LI 679
                I      +         +   R       +  E     D   K++     S     
Sbjct: 596  FSYKIFVNGCWIGIHDKPLNLVKNLRKGRRLGFLREEISISFDIKEKEIRISTDSGRICR 655

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P +  ++           +  +PLLK       + +  +    S +     + GIVE +D
Sbjct: 656  PLIVLNEKLSKNTNGTEIKTFLPLLK------KSHLSKIKNDPSFSFHDLLKEGIVEFID 709

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A    I  +   L  +           FQ+  ++  +                     PS
Sbjct: 710  AEEEEICLISMFLKET-----------FQKKFRSLNI-------------EYTHCEIHPS 745

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  +F+P+  +N          M  +    +I I       R   +   
Sbjct: 746  LILG-------VCGSFIPFSDHNQSPRNTYQAAMGKQ----AIGINSLNFQFRMDTMAHI 794

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                  P V                         +   +              + AI   
Sbjct: 795  LYYPQTPLV-------------------------VTRAMKFMNYKNFPNGINSIVAIACY 829

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +     +   +     +                        ++  +   L 
Sbjct: 830  GGYNQEDSIIMSQDAIDRGLFRSVFYRC-------------------YRDEEKTKFGGLK 870

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                    E   G    S  K      V     +S               K++ ++  L+
Sbjct: 871  EIFEIPKFEDCIGCKTGSYQKLDLDGLVSEGTRVSGDDIIIGKTVPYDFSKIKSSLAPLE 930

Query: 1040 VQYETSKSI---LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
               +  K             ++K+  G        ++VK+ +   R  Q GDK A RHG 
Sbjct: 931  KTLKFKKDASTAARSFESGVVDKVMIG--TSDLGTKLVKIRIRSVRIPQIGDKFASRHGQ 988

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KGIV  +    D+PF KDG   DI++NP  +PSRM +G + E  L               
Sbjct: 989  KGIVGMLYKQVDLPFTKDGIIPDIIMNPHAIPSRMTIGHLLEGLLSK------------- 1035

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                V  +      G P     F     
Sbjct: 1036 ------------------------------------VSALGGMEGDGSP-----FCNITV 1054

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            E I+  L   + +++G  I+ +G TG   +  + +G  Y  +L HMV DK+++R+ G   
Sbjct: 1055 EKISKKLESLNFEKNGWEIMRNGETGNNLNAMIFIGPTYYQRLKHMVDDKIHSRARGPVQ 1114

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG----- 1324
            ++T+QP+ G+S  GG R GEME  C+ ++GA+  L++ L  +SD       D+ G     
Sbjct: 1115 ILTRQPVEGRSRDGGLRFGEMERDCMMSHGASIFLKDRLMDQSDAFSIFLCDLCGLIAIA 1174

Query: 1325 --RTRVYE--SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              + R++E  S +  N       P +  +L +E+ A+ ++  + 
Sbjct: 1175 NPKKRIFECRSCLNRNSISLVKIPYACKLLFQELMAMAIAPRMI 1218


>gi|50344568|emb|CAH03853.2| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 488

 Score =  453 bits (1165), Expect = e-124,   Method: Composition-based stats.
 Identities = 238/490 (48%), Positives = 332/490 (67%), Gaps = 3/490 (0%)

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
           D EFD KD + VRIDRRRK+P +  L AL   +EEIL  FY   V+  +G+     L   
Sbjct: 2   DFEFDPKDAVFVRIDRRRKLPASVLLRALNYSTEEILDAFYDTNVFHVKGEMLALELVPQ 61

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            L  G   S  + D  +G+ ++E G+++T+  +  L + GVK L +  D + G  VA+ I
Sbjct: 62  RL-RGEIASFDITDG-SGKLIVEQGRRITARHINQLDKSGVKELEMPMDYVLGRTVAKAI 119

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           V+  TGEI  E    +  + L +I  +++     LY + ++   +I +TL  D   ++ +
Sbjct: 120 VHPATGEIIAECNTELTVEVLAKIVKAQVVRFETLYTNDIDCGPFISDTLKIDSTTNQLE 179

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           AL++IYR+MRPG+  T   AE++FN LFF S++YDLS VGR+K N R+  +  +    + 
Sbjct: 180 ALVEIYRMMRPGEPPTKDAAETLFNNLFFASERYDLSAVGRMKFNRRIGREEIEGPGVLS 239

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           +EDI+A++K LVD+RNGKG +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S 
Sbjct: 240 REDIVAVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSM 299

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R 
Sbjct: 300 AESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRE 359

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+
Sbjct: 360 RAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTD 419

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVV
Sbjct: 420 EIVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVV 478

Query: 673 SIAASLIPFL 682
           S+AASLIPFL
Sbjct: 479 SVAASLIPFL 488


>gi|148806661|gb|ABR13265.1| RNA polymerase B' subunit [Candidatus Liberibacter africanus]
          Length = 478

 Score =  452 bits (1164), Expect = e-124,   Method: Composition-based stats.
 Identities = 449/478 (93%), Positives = 466/478 (97%)

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK
Sbjct: 1    GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 60

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            VC+GKVT++VVYLSAMEEENRYI+QA++SLDE+G+FTE+LVFCRCAGEEILVP+EKIDFI
Sbjct: 61   VCNGKVTDEVVYLSAMEEENRYISQASASLDENGAFTEDLVFCRCAGEEILVPKEKIDFI 120

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG
Sbjct: 121  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 180

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            AAIVAKRAGIVEQVDAIRIVIR VE DLDPS SGVDIYRLMKFQRSNQNTCVNQRPLVKV
Sbjct: 181  AAIVAKRAGIVEQVDAIRIVIRVVEDDLDPSASGVDIYRLMKFQRSNQNTCVNQRPLVKV 240

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GDEV RNDIIADGPSTDLGDLALGRNMLVAF+PWHGYNFEDSMLISERMVSEDVFTSIHI
Sbjct: 241  GDEVGRNDIIADGPSTDLGDLALGRNMLVAFVPWHGYNFEDSMLISERMVSEDVFTSIHI 300

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES
Sbjct: 301  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 360

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV+VRIFNRHG+DKNERSISVEREQI
Sbjct: 361  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVEVRIFNRHGVDKNERSISVEREQI 420

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            +LL RDKDDEQ ILDRN+YSRL EILCGQ A+SGPK FKK +VLSSDLIS Y RSQWW
Sbjct: 421  DLLIRDKDDEQAILDRNVYSRLKEILCGQTAISGPKDFKKLSVLSSDLISRYQRSQWW 478


>gi|227809522|gb|ACP40980.1| RNA polymerase beta subunit [Mycoplasma bovigenitalium]
          Length = 973

 Score =  451 bits (1160), Expect = e-124,   Method: Composition-based stats.
 Identities = 286/814 (35%), Positives = 445/814 (54%), Gaps = 47/814 (5%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE---FDSK-DIIHVRIDRRRK 211
           QL RSPG +F     R   S  L     I+P  G W++I         D + +RID+ + 
Sbjct: 1   QLIRSPGAYFGRGV-RNKQSDDLFNKVEILPRVGSWVEISHKVTSKNPDSVKIRIDKNKN 59

Query: 212 VPVTSFLMALGMDSEEILSTFYPKIVYSQR---GDFWCFPLSAADLMVGAKVSSSLVDID 268
           V + +FL ALG+  ++I   F    V  +            +  +++   +         
Sbjct: 60  VNIVTFLGALGIMHDDIFELFGRSDVILESIKRDKKATTEFTPEEVIKNCQDELFRTIRK 119

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIV--NGETG 318
                 ES   L   +L   K   +   G           D + G  + +D+V  +    
Sbjct: 120 GDRVSDESIANLIPSMLFHKKHYNLSATGRYMLNIKLNLVDRISGTILGQDLVIKDKNGE 179

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI ++ G  I  K    I  +                  +   L+ D           I 
Sbjct: 180 EISLKIGTPITHKLAVLIQWNFNNGKLSSEKLKCIKTDVVYAKLLNDPANSSLKRRDKII 239

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            +              +F    +     D   V        +  D   +  H+   D+IA
Sbjct: 240 SI-------------KVFPNKKWMEKGLDPVRV--------IGTDPKANETHLVVSDLIA 278

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I    ++ +G G  DD D L N+R+ ++GE+++N  ++GL ++E++ +ER+ + + D V
Sbjct: 279 AINYYFNMLDGIGQDDDPDALTNKRIVAIGELIQNNLKVGLAKLEKTTRERMGAKEPDKV 338

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            P++  N K + + +  FF SS+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+
Sbjct: 339 SPKNATNNKLISNQMKTFFNSSKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEV 398

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH THYGRICP ET EG NIGL+ +  ++A VN +GF++TPY +V +  V  ++ VYL
Sbjct: 399 RDVHATHYGRICPIETPEGPNIGLILNYATYASVNEFGFLQTPYYRVENCVVNYSEPVYL 458

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A +E    IAQ+   +DE+    +  +  R      +   ++IDFI+ SP Q+VS+AA 
Sbjct: 459 TAADEMGYKIAQSTVKVDENNRIIDTNITIRHNYTYQIASADEIDFIEVSPNQMVSVAAG 518

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            IPFLENDD+NR LMG NMQRQAVPLL+AEAPFV TG+E+ +AK S    VA+  G+VE 
Sbjct: 519 CIPFLENDDANRALMGANMQRQAVPLLEAEAPFVATGIEADIAKYSSGNFVARNDGLVEY 578

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I IR+       + + +D Y L  FQRSNQ+T V+Q+PLVK G EV++ D++ DG
Sbjct: 579 VDGKKIKIRN-------AKNALDTYYLKNFQRSNQDTVVHQKPLVKEGQEVKKGDLLVDG 631

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            S   G+L+LG+N++VAF  + GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G
Sbjct: 632 ASFKDGELSLGKNVVVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSKAG 691

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            +E+T D+PNVS+   +++DE GI+ +G++V PGD+LVG+++PKG+   + EEKLL A+ 
Sbjct: 692 DDELTADLPNVSKFATRHLDEFGIVRIGSDVTPGDVLVGRVSPKGDDNPSQEEKLLLAVL 751

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++   V+DTSL+V +G  GTV+ V + +R   D
Sbjct: 752 QQRQQPVKDTSLKVKNGHGGTVIAVEVLSRENKD 785



 Score =  281 bits (718), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 175/991 (17%), Positives = 315/991 (31%), Gaps = 113/991 (11%)

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL----DIYRVMRPGDVSTFSVAESM 395
               DI  L+  S      I+           ++ +     +++R +R GD  +     ++
Sbjct: 72   MHDDIFELFGRSDVILESIKRDKKATTEFTPEEVIKNCQDELFRTIRKGDRVSDESIANL 131

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-----RKEDIIAIIKILVDLRNGK 450
               + F    Y+LS  GR  +N++LNL        +      K+     I + +      
Sbjct: 132  IPSMLFHKKHYNLSATGRYMLNIKLNLVDRISGTILGQDLVIKDKNGEEISLKIGTPITH 191

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                 I    N    S  ++   +  +   ++               +  +   N K   
Sbjct: 192  KLAVLIQWNFNNGKLSSEKLKCIKTDVVYAKLLNDPANSSLKRRDKIISIKVFPNKK--- 248

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +  +     +         L A             +  D       RI 
Sbjct: 249  ---WMEKGLDPVRVIGTDPKANETHLVVSDLIAAINYYFNMLDGIGQDDDPDALTNKRIV 305

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV-----VYLSAMEEENR 625
                   +N+ +  +          G  E       +      +      + ++ +    
Sbjct: 306  AIGELIQNNLKVGLAKLEKTTRERMGAKEPDKVSPKNATNNKLISNQMKTFFNSSKLSQF 365

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                   +   +      L       +        +          +         L  +
Sbjct: 366  MDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILN 425

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             +    +      Q             +    + A      +  K A    +VD    +I
Sbjct: 426  YATYASVNEFGFLQTPYYRVENCVVNYSEPVYLTAADE---MGYKIAQSTVKVDENNRII 482

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             +        T  +     + F         NQ   V  G      +  A+         
Sbjct: 483  DTNITIRHNYTYQIASADEIDFIE----VSPNQMVSVAAGCIPFLENDDANRALMGANMQ 538

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +L A  P+     E  +   +      V  +  + E+ V  +  K+   +   D 
Sbjct: 539  RQAVPLLEAEAPFVATGIEADIA--KYSSGNFVARNDGLVEY-VDGKKIKIRNAKNALDT 595

Query: 866  PNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              +      N D    +  ++  G EV  GD+LV   + K +  ++  + ++ A    K 
Sbjct: 596  YYLKNFQRSNQDTVVHQKPLVKEGQEVKKGDLLVDGASFK-DGELSLGKNVVVAFSTYKG 654

Query: 922  VDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
             +  D  +            S  + +  I  R     ++  ++ +   +   A    DE 
Sbjct: 655  YNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDE-LTADLPNVSKFATRHLDEF 713

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         ++L G+ +  G     +   L   ++ +  +          +     V
Sbjct: 714  GIVRIGSDVTPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQQPV--------KDTSLKV 765

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            ++       +  +L    K         D +  G+ ++VKV +A+KR I+ GDKM+GRHG
Sbjct: 766  KNGHGGTVIAVEVLSRENK---------DQLEDGITKIVKVSIAVKRKIKVGDKMSGRHG 816

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS +LP EDM              P                     +  G  +  +
Sbjct: 817  NKGVVSIVLPEEDM--------------PH--------------------LLDGTPVDVM 842

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            +                           +++      +              T  FDG  
Sbjct: 843  L--------------------NPQGVPSRMNIGQVLEIHLGMAARTLQTKFVTRPFDGIK 882

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            +E I  ++  A+L  +G+ IL D +TGE FD PV+VG +YMLKLNHMV DK++ARS G Y
Sbjct: 883  KEEIYDVIEEANLPTTGKQILIDPITGEKFDNPVSVGVMYMLKLNHMVDDKMHARSVGPY 942

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            SL+TQQPLGGKS  GGQR GEME W I++YG
Sbjct: 943  SLITQQPLGGKSQNGGQRFGEMETWAIESYG 973


>gi|317183724|gb|ADV15556.1| RNA polymerase beta subunit [Lactobacillus sakei]
          Length = 662

 Score =  451 bits (1159), Expect = e-124,   Method: Composition-based stats.
 Identities = 291/494 (58%), Positives = 368/494 (74%), Gaps = 9/494 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF S
Sbjct: 1   GNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGS 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL++SL S+A VN YGFIETPYR+V      VT+ + YL+A EE+N  IAQANS L++D
Sbjct: 121 IGLINSLASYAVVNRYGFIETPYRRVSWDTHDVTDKIDYLTADEEDNYVIAQANSPLNDD 180

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           GSF +  V  R   + I    +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQ
Sbjct: 181 GSFVDNTVLARYKDDNIETSIDKLDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQ 240

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL+   AP VGTGME   A  SG A++A+ AG VE VDA  I +R  +       S
Sbjct: 241 RQAVPLVNPHAPLVGTGMEYKAAHDSGIALLAQHAGTVEYVDAKVIRVRRED-------S 293

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y LMKF+RSN     NQRP+V  GD V  ++IIADGP+ + G+LALG+N L+AFM 
Sbjct: 294 SLDTYELMKFRRSNAGKNYNQRPIVAKGDHVDVDEIIADGPAMEKGELALGQNPLIAFMT 353

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W+ YN+ED++++SER+V ED++TSIHIEE+E  ARDTKLGPEEITR+IPNV E+ LK++D
Sbjct: 354 WNMYNYEDAIVLSERLVKEDLYTSIHIEEYESEARDTKLGPEEITREIPNVGEDSLKDLD 413

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GI+ VGAEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSL+VP G  G
Sbjct: 414 EFGIVRVGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLKVPHGGGG 473

Query: 938 TVVDVRIFNRHGID 951
            + DV+IF R   D
Sbjct: 474 IIQDVKIFTREAGD 487



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 135/449 (30%), Positives = 192/449 (42%), Gaps = 84/449 (18%)

Query: 846  EFEVM-ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +E+M  R +  G     R I    +    ++D   II  G  +  G++ +G        
Sbjct: 297  TYELMKFRRSNAGKNYNQRPIVAKGD----HVDVDEIIADGPAMEKGELALG-------Q 345

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
                          E A+ + +  ++     S  + +     R      E          
Sbjct: 346  NPLIAFMTWNMYNYEDAIVLSERLVKEDLYTSIHIEEYESEARDTKLGPEEITREIPNVG 405

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G         L   +  E  R      
Sbjct: 406  EDSLKDL-DEFGIVRVGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR------ 458

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 459  -----EVRDTSLKVPHGGGGIIQDV------KIFTREAGDELSPGVNMMVRVYITQKRKI 507

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG VS ++P EDMP++ DGTPVDI+L+P+GVPSRMN+GQ+ E HLG A
Sbjct: 508  QVGDKMAGRHGNKGTVSIVVPEEDMPYMPDGTPVDILLSPMGVPSRMNIGQVLELHLGMA 567

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D   + D+                                       
Sbjct: 568  ARNLGIHVATPVFDGAQDKDLW-------------------------------------- 589

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                   D   E          ++   G+SILYDG TGEPFD  V+VG +Y +KL HMV 
Sbjct: 590  -------DAVREA---------NMPSDGKSILYDGRTGEPFDTRVSVGVMYYMKLAHMVD 633

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            DK++ARS G YSLVTQQPLGGK+  GGQR
Sbjct: 634  DKLHARSIGPYSLVTQQPLGGKAQFGGQR 662


>gi|229915534|gb|ACQ90878.1| beta subunit of RNA polymerase [Pedinomonas minor]
          Length = 1157

 Score =  451 bits (1159), Expect = e-124,   Method: Composition-based stats.
 Identities = 169/500 (33%), Positives = 251/500 (50%), Gaps = 49/500 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GDIL    +   +  +     LL A    +  +  D  L     +S  +V
Sbjct: 707  IVSEGDWVEAGDILAD-GSASEKGELALGHNLLVAYIPWEGFNFEDAIL-----ISERLV 760

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               ++    I+K E  I   +  +E +     D     D         +  G     G  
Sbjct: 761  TQDLYTSLHIEKYEMEIRETKFGLEKITNKLPD-VRKKDLKNLDAQGIVKPGTWVQEGDI 819

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T +    +S + R  +      +  V+ +   +    +     ++  + ++  K+
Sbjct: 820  LVGKVTPIRKKPLSPHERLLYDIVGKINPTVRDSSLRVPRGTQARVLDIQIIYSDEKTKL 879

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G++    V   V++ +A +R IQ GDKMAGRHGNKGI+SRILP +DMP+L DGTP+DI
Sbjct: 880  --GEEFVGKVPLKVQILLAQRRRIQVGDKMAGRHGNKGIISRILPIQDMPYLPDGTPLDI 937

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNPLGVPSRMNVGQ++E  L  A   LG+  + +  D      IS   ++ +    +  
Sbjct: 938  VLNPLGVPSRMNVGQVYECLLSLAGRYLGENYRVVPFDELFGPHISRSLTYSKLYESSLK 997

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
            + +                                         + + +  G++ ++DG 
Sbjct: 998  NKQHW---------------------------------------LFNPNCPGKTKIFDGR 1018

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD+PVTVG  Y+LKL H+V DK++ARSTG YSLVTQQPL G+S  GGQRLGEMEVW
Sbjct: 1019 TGECFDQPVTVGEAYVLKLVHLVDDKIHARSTGPYSLVTQQPLRGRSKHGGQRLGEMEVW 1078

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
             ++ +GAAY+LQE+LT+KSDDV GR ++  SI+ G +    GTPE F VLVKE+Q+L L 
Sbjct: 1079 ALEGFGAAYILQELLTVKSDDVKGRHKIMYSILTGKN-MTMGTPECFKVLVKELQSLCLD 1137

Query: 1361 IDLENSRTKNSAKMEEIPDF 1380
            + + +  T    ++ +  D 
Sbjct: 1138 VGVYSIDTFGKRELRDFIDL 1157



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 242/629 (38%), Positives = 362/629 (57%), Gaps = 53/629 (8%)

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           I    +   +    + +      F +   YDL  +GR+++N R  L      R +  EDI
Sbjct: 250 IQARTKKEILVNSEMGKKFLMKKFRNPRSYDLGFIGRLRLNKRFGLSIATSYRQLTAEDI 309

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              + +L+ +  G  ++DDID+L NRRVRS+GE+L+ Q  L LLR+E+ I++R S +  +
Sbjct: 310 FHSVNLLISVSQGVASLDDIDHLENRRVRSIGELLQIQLGLALLRLEKMIRDRSSFLLEN 369

Query: 497 SVM-----PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           +V       +  I+ K +  A+ EFF SS LSQ  +  N L+ +TH RRL++LG  GV+R
Sbjct: 370 NVSSVAKDIRSFISTKALNGAMREFFGSSPLSQFLDQTNPLAELTHKRRLTSLGPSGVSR 429

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
             AG+ +R +HP+HYGRICP ET EG N GLV+SLT ++RV+  GFI++P+  + +G++ 
Sbjct: 430 ETAGMAVRGIHPSHYGRICPIETPEGQNAGLVNSLTVYSRVDQNGFIQSPFYLLNNGQIQ 489

Query: 612 ND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            +  + +LSA +E ++ I   +   +  G    + +  R   E +   R  ID I  SP 
Sbjct: 490 KEANLTFLSAKDEMSKTIIPGDIHFNSLGFIENDSLPSRKNQEFVRQQRGNIDLIATSPL 549

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q++S+A SLIPFLE+DD+NR LMG NMQRQAVP L AE P VGTG+ES +    G  +  
Sbjct: 550 QMISVATSLIPFLEHDDANRALMGSNMQRQAVPTLYAERPRVGTGLESKIVTDIGHIVQT 609

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPS---------------------------------- 755
           + +G V  VD+ +I+I+S     +                                    
Sbjct: 610 RWSGYVSYVDSQKIIIQSFVKHSETFLPTQSIRFLETVSTSKKYSSSLKTDSIEKVFLKS 669

Query: 756 ------------TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                             Y L  +  SNQ+T   Q+P+V  GD V   DI+ADG +++ G
Sbjct: 670 KPGELKTKLEEYEFKTVEYLLENYSGSNQSTFFVQKPIVSEGDWVEAGDILADGSASEKG 729

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +LALG N+LVA++PW G+NFED++LISER+V++D++TS+HIE++E+  R+TK G E+IT 
Sbjct: 730 ELALGHNLLVAYIPWEGFNFEDAILISERLVTQDLYTSLHIEKYEMEIRETKFGLEKITN 789

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            +P+V ++ LKN+D  GI+  G  V  GDILVGK+TP  + P++P E+LL  I G+    
Sbjct: 790 KLPDVRKKDLKNLDAQGIVKPGTWVQEGDILVGKVTPIRKKPLSPHERLLYDIVGKINPT 849

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VRD+SLRVP G    V+D++I       K
Sbjct: 850 VRDSSLRVPRGTQARVLDIQIIYSDEKTK 878



 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 89/480 (18%), Positives = 179/480 (37%), Gaps = 56/480 (11%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F    +++  PD +E+Q+ S+  FL            G+    K   PIT+ +    +
Sbjct: 1   MSFNNISKLL-TPDFLEIQRVSFVKFL----------ESGIINEIKRRNPITSSAKEYQI 49

Query: 75  EF--VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            F   +Y+ + P+F   D L    +YA  L + ++L           +   +IK Q + +
Sbjct: 50  FFYPEAYQLEAPEFSPKDALLYGKSYASRLFLPVQLT---------NQVTGEIKFQWVLL 100

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G LPL+TK G F++ G  R+V++QL RSPG+++     R     + ++    I ++G W+
Sbjct: 101 GTLPLLTKRGHFILNGCPRVVINQLIRSPGVYYQK---RLDSQKRDIFYADFICERGAWL 157

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS------------TFYPKIVYSQ 240
            IE D+   I  R+ R  K+PV   L ++GM  + I S              Y +   ++
Sbjct: 158 RIEMDTSQRIWARMKRTPKIPVLILLQSMGMSLQTIFSSTSQRTILAKSLLPYEQKGKTK 217

Query: 241 RGDFWCFPLSAADLMV--------GAKVSSSLVDIDTGEQVI---ESGKKLTSGLLKSLK 289
                    +   L+           KV S+L+   T ++++   E GKK      ++ +
Sbjct: 218 TLPKLVKAQNPLLLVRRHPVSQDTALKVLSALIQARTKKEILVNSEMGKKFLMKKFRNPR 277

Query: 290 EKGVKFLGITS-DCLCG-------LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
              + F+G    +   G         +  + +      +   +  V     ++ + +  +
Sbjct: 278 SYDLGFIGRLRLNKRFGLSIATSYRQLTAEDIFHSVNLLISVSQGVASLDDIDHLENRRV 337

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R I  L    +         ++ D++    +  +          +ST ++  +M  F   
Sbjct: 338 RSIGELLQIQLGLALLRLEKMIRDRSSFLLENNVSSVAKDIRSFISTKALNGAMREFFGS 397

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L     +         T      + +E     ++ +     G+    +     N
Sbjct: 398 SPLSQFLDQTNPLAELTHKRRLTSLGPSGVSRETAGMAVRGIHPSHYGRICPIETPEGQN 457


>gi|269856494|gb|ACZ51474.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 307

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 194/306 (63%), Positives = 242/306 (79%), Gaps = 1/306 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 3   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 62

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 63  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 122

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 123 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 182

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P    D + G K  + +VD DTGE V+E+GKKLT  LL+ L+
Sbjct: 183 DTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITEMVDADTGEVVVEAGKKLTPRLLRQLQ 241

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           EKG+K L  T+D L G Y+AED+VN  TGEIY+EAGD IDE+    I  +   +IP+L +
Sbjct: 242 EKGLKALKATNDDLYGNYLAEDVVNYSTGEIYLEAGDEIDERPFPVILSAGFDEIPVLDI 301

Query: 350 DSVNNN 355
           D +N  
Sbjct: 302 DHINVG 307


>gi|226968681|ref|YP_002808641.1| RNA polymerase beta chain [Micromonas sp. RCC299]
 gi|226431159|gb|ACO55565.1| RNA polymerase beta chain [Micromonas sp. RCC299]
          Length = 1076

 Score =  450 bits (1158), Expect = e-124,   Method: Composition-based stats.
 Identities = 170/482 (35%), Positives = 230/482 (47%), Gaps = 54/482 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +     V+ G+ L    +      +   + LL A    +  +  D  L     V   V  
Sbjct: 643  VVPNTWVHAGECLADTASTV-AGELALGKNLLVAYMPWEGYNFEDAVLVSERLVFDDVFT 701

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I  +      E    ++      DE  ++    +    +IL G+ +      
Sbjct: 702  SVHIERYDISTSRTRDGQEYITSKVEKNTHLDEFGVIKVGTWVEPGDILVGKVSPQQESE 761

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                  L   +     R       V    V   V   +  +E +K   E      +    
Sbjct: 762  NTPEGRLLRAIFGGATRDVKDTPLVVPSGVTGRVLECRTLFEKTKYNEELDSYESVG--- 818

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        V +F+  KR +Q GDK+AGRHGNKGI+S ILP +DMPFL++GTPVD+V
Sbjct: 819  -----------SVHIFLVQKRKVQVGDKIAGRHGNKGIISNILPRQDMPFLQNGTPVDMV 867

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE  LG A   L +  K L  D     ++S    + +++      
Sbjct: 868  LNPLGVPSRMNVGQIFECLLGLAAHTLEQNYKVLPFDEMHGDEVSRGFVY-QQLYKARCA 926

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T +   +  +                                        G+SIL+DG T
Sbjct: 927  TNQKWVFRPE--------------------------------------SPGKSILFDGRT 948

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G PFD+PVTVGY Y+LKL H+V DK++ARSTG YSLVTQQPLGG+S  GGQRLGEMEVW 
Sbjct: 949  GYPFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKHGGQRLGEMEVWA 1008

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            ++ +GAAY LQE+LTIKSDD+ GR   + SI+ GN   + G PESF VLV E++ L L I
Sbjct: 1009 LEGFGAAYTLQELLTIKSDDMRGRNLAFMSIIRGNLLPKPGVPESFKVLVCELRGLCLDI 1068

Query: 1362 DL 1363
             L
Sbjct: 1069 SL 1070



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 253/591 (42%), Positives = 356/591 (60%), Gaps = 23/591 (3%)

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           K +  +DA++ +  +M P    +   A+      FF + +Y LS VGR ++N +L +   
Sbjct: 221 KPQSCEDAMVMMTALMFPHRAGSVLKAKKFLFTHFFHARRYSLSEVGRKRINRKLRMRHN 280

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGT-IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
                +  ED++A +  L+ + NG+   +DDID+L NRR R  GE+++ Q+RLGL R+ER
Sbjct: 281 LPSLTLMPEDVLAGVDYLLRVSNGETQFLDDIDHLKNRRARLAGELIQTQFRLGLNRLER 340

Query: 485 SIKERIS-----SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           S+  RIS           V    LI  + V S   EFF S+QLSQ  +  N L+ ITH R
Sbjct: 341 SVHTRISDETLLRQKRLGVALPSLIRTQIVGSVFKEFFGSNQLSQFMDQTNPLAEITHKR 400

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLS+LG GG+ R RAG+ +R +HP++YGRICP ET EG N GLV S+ ++ARVN+ GF+E
Sbjct: 401 RLSSLGPGGLHRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATYARVNSDGFLE 460

Query: 600 TPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +PY  +        +    L+A  E+   +A A++        T   V  R   E I   
Sbjct: 461 SPYILMESEKSNQDDGFFLLNASYEDKVIVAAADT------QMTAARVPARTRREFIETD 514

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             +I F+   P Q +SIA +LIPFLE+DD+NR LMG NMQRQAV LL  +  FVGTG+E+
Sbjct: 515 PNEITFLGLCPIQFMSIATALIPFLEHDDANRALMGSNMQRQAVSLLTPQRAFVGTGLEA 574

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE----GDLDPSTSGVDIYRLMKFQRSNQN 773
            V   SGA    +++G V   DA RI + + +      ++  T   +   L  +QRSNQ+
Sbjct: 575 RVTHDSGAVARIRKSGYVLYADAQRIDVLTEKSSVSQFVNEPTFKRETISLTTYQRSNQD 634

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC++QRP V     V   + +AD  ST  G+LALG+N+LVA+MPW GYNFED++L+SER+
Sbjct: 635 TCMHQRPSVVPNTWVHAGECLADTASTVAGELALGKNLLVAYMPWEGYNFEDAVLVSERL 694

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DVFTS+HIE +++    T+ G E IT  +     E   ++DE G+I VG  V PGDI
Sbjct: 695 VFDDVFTSVHIERYDISTSRTRDGQEYITSKV-----EKNTHLDEFGVIKVGTWVEPGDI 749

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           LVGK++P+ ES  TPE +LLRAIFG    DV+DT L VPSGV+G V++ R 
Sbjct: 750 LVGKVSPQQESENTPEGRLLRAIFGGATRDVKDTPLVVPSGVTGRVLECRT 800



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 74/463 (15%), Positives = 150/463 (32%), Gaps = 49/463 (10%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI----------TAFSG 70
            + + IPD ++ Q+ S+  FL            G++   + V PI             + 
Sbjct: 5   RQKVAIPDFLDAQRKSFRLFL----------ETGIRRELEFVSPIIGNSLGTSIRQPTNR 54

Query: 71  AAMLEFV--SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              + F+   +    P +   + +    TY+  L + + +    +D              
Sbjct: 55  YISVSFLAQDFYLKAPSYTPQEAIHNMETYSSQLVVPVHISSQSLDVSCVLP-------- 106

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            +   DLPLMT+ GTF+I G  R++V Q+ R PG++    K +     +  +    +   
Sbjct: 107 -VTFCDLPLMTEHGTFIINGSPRVIVHQIVRCPGVYI---KAQFDQKNRRSHLVSFLSSY 162

Query: 189 GLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
           G W+ +E   ++  ++  ID  RK+PVT  L ALG + +++ +            +    
Sbjct: 163 GSWLRLETVPRNPEVYACIDNLRKLPVTLLLAALGFNFKQVCAVVSDPNALVFT-ESLLK 221

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
           P S  D MV            +    +   KK         +   +  +G          
Sbjct: 222 PQSCEDAMVMMTALMFPHRAGS----VLKAKKFLFTHFFHARRYSLSEVGRKRINRKLRM 277

Query: 308 ------VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
                 +     +   G  Y+      + + L++I H + R   +             N 
Sbjct: 278 RHNLPSLTLMPEDVLAGVDYLLRVSNGETQFLDDIDHLKNRRARLAGELIQTQFRLGLNR 337

Query: 362 LVTDKNKDRKDALLDIYRVM---RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           L    +    D  L   + +    P  + T  V      F   +     +     +    
Sbjct: 338 LERSVHTRISDETLLRQKRLGVALPSLIRTQIVGSVFKEFFGSNQLSQFMDQTNPLAEIT 397

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                +      + ++    I++ +     G+    +     N
Sbjct: 398 HKRRLSSLGPGGLHRDRAGLIVRGIHPSYYGRICPIETPEGKN 440


>gi|35396499|gb|AAQ84769.1| RpoB [Bradyrhizobium liaoningense]
          Length = 231

 Score =  450 bits (1157), Expect = e-124,   Method: Composition-based stats.
 Identities = 152/233 (65%), Positives = 181/233 (77%), Gaps = 3/233 (1%)

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETH
Sbjct: 2    KRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 61

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            LGWAC GLGK+I   ++ Y +  DI PL+  L+KV G     E I   +D+ ++ + +  
Sbjct: 62   LGWACAGLGKRIGQTVDAYLSKQDIKPLKETLKKVYGED---ETIKSLNDNELIELGQNL 118

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+PFDR VTVGYIYMLKL+
Sbjct: 119  SRGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDPFDRKVTVGYIYMLKLH 178

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 179  HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 231


>gi|227809524|gb|ACP40981.1| RNA polymerase beta subunit [Mycoplasma bovigenitalium]
          Length = 966

 Score =  450 bits (1157), Expect = e-123,   Method: Composition-based stats.
 Identities = 284/814 (34%), Positives = 444/814 (54%), Gaps = 47/814 (5%)

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE---FDSK-DIIHVRIDRRRK 211
           QL RSPG +F     R   S  L     I+P  G W++I         D + +RID+ + 
Sbjct: 1   QLIRSPGAYFGRGV-RNKQSDDLFNKVEILPRVGSWVEISHKVTSKNPDSVKIRIDKNKN 59

Query: 212 VPVTSFLMALGMDSEEILSTFYPKIVYSQR---GDFWCFPLSAADLMVGAKVSSSLVDID 268
           V + +FL ALG+  ++I   F    V  +            +  +++   +         
Sbjct: 60  VNIVTFLGALGIMHDDIFELFGRSDVILESIKRDKKATTEFTPEEVIKNCQDELFRTIRK 119

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIV--NGETG 318
                 ES   L   +L   K   +   G           D + G  + +D+V  +    
Sbjct: 120 GDRVSDESIANLIPSMLFHKKHYNLSATGRYMLNIKLNLVDRISGTILGQDLVIKDKNGE 179

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EI ++ G  I  K    I  +                  +   L+ D           I 
Sbjct: 180 EISLKIGTPITHKLAVLIQWNFNNGKLSSEKLKCIKTDVVYAKLLNDPANSSLKRRDKII 239

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            +              +F    +     D   V        +  D   +  H+   D++A
Sbjct: 240 SI-------------KVFPNKKWMEKGLDPVRV--------IGTDPKANETHLVVSDLVA 278

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I    ++ +G G  DD D L N+R+ ++GE+++N  ++GL ++E++ +ER+ + + D V
Sbjct: 279 AINYYFNMLDGIGQDDDPDALTNKRIVAIGELIQNNLKVGLAKLEKTTRERMGAKEPDKV 338

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            P++  N K + + +  FF SS+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+
Sbjct: 339 SPKNATNNKLISNQMKTFFNSSKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEV 398

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYL 617
           RDVH THYGRICP ET EG NIGL+ +  ++A VN +GF++TPY +V +  V  ++ VYL
Sbjct: 399 RDVHATHYGRICPIETPEGPNIGLILNYATYASVNEFGFLQTPYYRVENCVVNYSEPVYL 458

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           +A +E    IAQ+   +DE+    +  +  R      +    +IDFI+ SP Q+VS+AA 
Sbjct: 459 TAADEMGYKIAQSTVKVDENNRIIDTNITIRHNYTYQIASAYEIDFIEVSPNQMVSVAAG 518

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            IPFLENDD+NR LMG NMQRQAVPLL+AEAPFV TG+E+ +AK S    VA+  G+VE 
Sbjct: 519 CIPFLENDDANRALMGANMQRQAVPLLEAEAPFVATGIEADIAKYSSGNFVARNDGLVEY 578

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VD  +I IR+       + + +D Y L  FQRSNQ+T V+Q+PLVK G +V++ D++ DG
Sbjct: 579 VDGKKIKIRN-------AKNALDTYYLKNFQRSNQDTVVHQKPLVKEGQQVKKGDLLVDG 631

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            S   G+L+LG+N++VAF  + GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G
Sbjct: 632 ASFKDGELSLGKNVVVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSKAG 691

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            +E+T D+PNVS+   +++DE GI+ +G++V PGD+LVG+++PKG+   + EEKLL A+ 
Sbjct: 692 DDELTADLPNVSKFATRHLDEFGIVRIGSDVTPGDVLVGRVSPKGDDNPSQEEKLLLAVL 751

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++   V+DTSL+V +G  GTV+ V + +R   D
Sbjct: 752 QQRQQPVKDTSLKVKNGHGGTVIAVEVLSRENKD 785



 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 171/983 (17%), Positives = 309/983 (31%), Gaps = 113/983 (11%)

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL----DIYRVMRPGDVSTFSVAESM 395
               DI  L+  S      I+           ++ +     +++R +R GD  +     ++
Sbjct: 72   MHDDIFELFGRSDVILESIKRDKKATTEFTPEEVIKNCQDELFRTIRKGDRVSDESIANL 131

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-----RKEDIIAIIKILVDLRNGK 450
               + F    Y+LS  GR  +N++LNL        +      K+     I + +      
Sbjct: 132  IPSMLFHKKHYNLSATGRYMLNIKLNLVDRISGTILGQDLVIKDKNGEEISLKIGTPITH 191

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                 I    N    S  ++   +  +   ++               +  +   N K   
Sbjct: 192  KLAVLIQWNFNNGKLSSEKLKCIKTDVVYAKLLNDPANSSLKRRDKIISIKVFPNKK--- 248

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +  +     +         L A             +  D       RI 
Sbjct: 249  ---WMEKGLDPVRVIGTDPKANETHLVVSDLVAAINYYFNMLDGIGQDDDPDALTNKRIV 305

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV-----VYLSAMEEENR 625
                   +N+ +  +          G  E       +      +      + ++ +    
Sbjct: 306  AIGELIQNNLKVGLAKLEKTTRERMGAKEPDKVSPKNATNNKLISNQMKTFFNSSKLSQF 365

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                   +   +      L       +        +          +         L  +
Sbjct: 366  MDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILN 425

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             +    +      Q             +    + A      +  K A    +VD    +I
Sbjct: 426  YATYASVNEFGFLQTPYYRVENCVVNYSEPVYLTAADE---MGYKIAQSTVKVDENNRII 482

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             +        T  +     + F         NQ   V  G      +  A+         
Sbjct: 483  DTNITIRHNYTYQIASAYEIDFIE----VSPNQMVSVAAGCIPFLENDDANRALMGANMQ 538

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +L A  P+     E  +   +      V  +  + E+ V  +  K+   +   D 
Sbjct: 539  RQAVPLLEAEAPFVATGIEADIA--KYSSGNFVARNDGLVEY-VDGKKIKIRNAKNALDT 595

Query: 866  PNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              +      N D    +  ++  G +V  GD+LV   + K +  ++  + ++ A    K 
Sbjct: 596  YYLKNFQRSNQDTVVHQKPLVKEGQQVKKGDLLVDGASFK-DGELSLGKNVVVAFSTYKG 654

Query: 922  VDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
             +  D  +            S  + +  I  R     ++  ++ +   +   A    DE 
Sbjct: 655  YNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDE-LTADLPNVSKFATRHLDEF 713

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I+         ++L G+ +  G     +   L   ++ +  +          +     V
Sbjct: 714  GIVRIGSDVTPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQQPV--------KDTSLKV 765

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            ++       +  +L    K         D +  G+ ++VKV +A+KR IQ GDKM+GRHG
Sbjct: 766  KNGHGGTVIAVEVLSRENK---------DQLEDGITKIVKVSIAVKRKIQVGDKMSGRHG 816

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS +LP EDM              P                     +  G  +  +
Sbjct: 817  NKGVVSIVLPEEDM--------------PH--------------------LLDGTPVDVM 842

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            +                           +++      +              T  FDG  
Sbjct: 843  L--------------------NPQGVPSRMNIGQVLEIHLGMAARTLQTKFVTRPFDGIK 882

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            +E I  ++  A+L  +G+ IL D +TGE FD PV+VG +YMLKLNHMV DK++ARS G Y
Sbjct: 883  KEEIYDVIEEANLPTTGKQILIDPITGEKFDNPVSVGVMYMLKLNHMVDDKMHARSVGPY 942

Query: 1276 SLVTQQPLGGKSNRGGQRLGEME 1298
            SL+TQQPLGGKS  GGQR GEME
Sbjct: 943  SLITQQPLGGKSQNGGQRFGEME 965


>gi|35396501|gb|AAQ84770.1| RpoB [Afipia broomeae]
          Length = 232

 Score =  450 bits (1157), Expect = e-123,   Method: Composition-based stats.
 Identities = 152/235 (64%), Positives = 182/235 (77%), Gaps = 3/235 (1%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I      Y +  D+ PL+  L+KV G     E I   +D  +L +A 
Sbjct: 61   THLGWACAGLGKRIGQAAEAYWSKQDLKPLKETLKKVYGDD---ETIKSLNDSELLELAR 117

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K GVP++TPVFDGA E+ I  ML +A +++SGQS++YDG TG+ FDR VTVGYIYMLK
Sbjct: 118  NLKPGVPIATPVFDGAKEKDIEDMLDLAGMNKSGQSVVYDGRTGDQFDRNVTVGYIYMLK 177

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE
Sbjct: 178  LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 232


>gi|322510309|gb|ADX05540.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05696]
          Length = 300

 Score =  449 bits (1156), Expect = e-123,   Method: Composition-based stats.
 Identities = 191/299 (63%), Positives = 237/299 (79%), Gaps = 1/299 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 2   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY K +Y + GD W  P    D + G K  + ++D D+GE V+E+GKKLT  LL
Sbjct: 182 EEILDTFYTKSLYQRDGDGWRVPFQP-DALKGQKALADMIDADSGEVVVEAGKKLTPRLL 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           + L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +I
Sbjct: 241 RQLQDKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILAAGFDEI 299


>gi|331029441|gb|AEC49870.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6160]
          Length = 316

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 176/304 (57%), Positives = 228/304 (75%), Gaps = 1/304 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           S D FLM++     R +EGLQ  F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SXDQFLMVDEPTGGRLDEGLQPVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL  
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLXV 299

Query: 336 IFHS 339
           +   
Sbjct: 300 LNEQ 303


>gi|315360837|gb|ADU05392.1| RNA polymerase beta subunit [Ensifer garamanticus]
          Length = 304

 Score =  448 bits (1153), Expect = e-123,   Method: Composition-based stats.
 Identities = 192/304 (63%), Positives = 241/304 (79%), Gaps = 1/304 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 2   PKGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+E+GKKLT  LL
Sbjct: 182 EEILDTFYTKSLYQRDGEGWRVPFQP-DALKGQKAITEMIDADTGEVVVEAGKKLTPRLL 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + L++KG+K L  T+D L G Y+AED+VN  TGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 241 RQLQDKGLKALKATNDDLYGNYLAEDVVNYGTGEIYLEAGDEIDEKTLPVILSAGFDEIP 300

Query: 346 ILYV 349
           +L +
Sbjct: 301 VLDI 304


>gi|242624339|ref|YP_003002257.1| DNA-directed RNA polymerase beta chain [Aureoumbra lagunensis]
 gi|239997447|gb|ACS36969.1| DNA-directed RNA polymerase beta chain [Aureoumbra lagunensis]
          Length = 1091

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 168/589 (28%), Positives = 259/589 (43%), Gaps = 57/589 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH-IEEFEVMARDTKLGP 858
                       +L +  P  G   E+ +         + F  I       +++ +TK G 
Sbjct: 543  MGSNMQRQSVPLLYSQKPIVGTGLENQLTTDSGGAIVNKFDGIVKYVSARIISIETKNGE 602

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                     +       I++  I+    +V  G ++        E  +   + LL A   
Sbjct: 603  IVTYNLQKFMRSNQDTCINQRPIVWPYEKVFSGQVIADGPGT-NEGELALGKNLLVAYMP 661

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   +       +  ++  E ++ +E+                L
Sbjct: 662  WEGYNYEDAILVNERLVEEDLFTSAHIEKFDLEIRETTVGIEKIT------------RDL 709

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                   +  +        G        +L   +  +    Q  +  +        V+++
Sbjct: 710  PNTTNESIQNLDSNGIVYPGTFVMP-GDILVGKVTPKVEPDQLPEGRLLRAIFGEKVKNV 768

Query: 1039 KVQYETSKSILEDR-FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                      +  R    ++ +     +     + +V++F+A +R I+ GDK+AGRHGNK
Sbjct: 769  YDSSLRVPKGISGRVINVRVFRNGIDYEFEEKAVSLVRIFIAQRRKIKVGDKIAGRHGNK 828

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+S+ILP +DMPFL +G P+DI+LNPLGVPSRMNVGQIFE  LG A   L ++ K    
Sbjct: 829  GIISKILPKQDMPFLPNGVPIDILLNPLGVPSRMNVGQIFECLLGLAGSKLNRRFKVRPF 888

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D               ++ G+ +  + ++ Y   +  +  E W     V           
Sbjct: 889  D---------------EMYGSETSRKLVNHYLQKAAQKTQEPWLYNSWV----------- 922

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                          G+  L DG TG  FD PV VG  Y+LKL H V DK++AR+TG YSL
Sbjct: 923  -------------PGRITLRDGRTGTLFDNPVLVGQTYILKLIHQVDDKMHARATGPYSL 969

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPLGGK+  GGQR GEMEVW +QA+G AY LQE+LT+KSDD+ GR  V  +IV G  
Sbjct: 970  ITQQPLGGKARHGGQRFGEMEVWALQAFGCAYTLQELLTLKSDDMEGRNEVLNAIVKGLP 1029

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRT--KNSAKMEEIPDFNKCE 1384
              + G PESF VL++E+ +LGL I L   +   +N +  +EI    + E
Sbjct: 1030 IPKAGIPESFKVLIRELHSLGLDISLYKMQKASRNVSNEQEIDLLQEYE 1078



 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 304/775 (39%), Positives = 453/775 (58%), Gaps = 29/775 (3%)

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE------------KGVKFL 296
                +L+ G  ++ +L+       + +SG  + +G  + +              +G+K L
Sbjct: 81   FLPIELIDGNVITEALIFFGEIPLMTDSGTFIINGCERVIINQIIRSPGIYFQWEGLKKL 140

Query: 297  GITSDCLCGL--YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              ++  +     ++  +     T  + I             +   E +++       +  
Sbjct: 141  QYSATLISNRGSWLKFECC-PRTKNVLIRLNKTTVIDFYRLLEICETQELITNQYFCITP 199

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF---DSDKYDLSTV 411
             + +  T      K  +     + + +  G ++           +FF   +   Y L T+
Sbjct: 200  ESEVVKTQQELNFKSSEFLDRTVNQSLDIGTITQTKKNYGSIENIFFQIFNEKVYSLGTI 259

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR K+N +LNL TP+ V  +  EDI AI   L+ L N  G IDDIDNL NRRVRSVGE+L
Sbjct: 260  GRRKLNKKLNLATPEHVIRLTIEDISAIANYLIQLHNNIGEIDDIDNLKNRRVRSVGELL 319

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            + Q+ +GL R+ERSI+ER + ++  ++    +IN+KPV++ + EFF SSQLSQ  +  N 
Sbjct: 320  QLQFGIGLNRLERSIRERFTILNSANLKASTIINSKPVIAVIKEFFGSSQLSQFMDQTNP 379

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            ++ +TH RR+S+LG GG+ R R  + +RD+HP+ YGRICP ET EG N GL+ SL S+AR
Sbjct: 380  IASLTHKRRISSLGPGGLNRDRLSLAVRDIHPSQYGRICPIETPEGQNAGLLVSLASYAR 439

Query: 592  VNAYGFIETPYRKVCDGKVTN--DVVYLSAMEEENRYIAQANSSLDE-DGSFTEELVFCR 648
            VN  GF+ETP+ K+ DG++ N    +YL+  EEE   +A A+  +D  D +  ++L+  R
Sbjct: 440  VNESGFLETPFFKLKDGRILNSQIPIYLTTEEEEKNTVAAADCVIDNMDTAQRKQLIPIR 499

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E  LV   ++  +  SP Q  SIA SLIPFLE+DD+NR LMG NMQRQ+VPLL ++ 
Sbjct: 500  QNNEFNLVALNQVKLVSVSPIQNFSIATSLIPFLEHDDANRALMGSNMQRQSVPLLYSQK 559

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTG+E+ +   SG AIV K  GIV+ V A  I I +  G        +  Y L KF 
Sbjct: 560  PIVGTGLENQLTTDSGGAIVNKFDGIVKYVSARIISIETKNG-------EIVTYNLQKFM 612

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQ+TC+NQRP+V   ++V    +IADGP T+ G+LALG+N+LVA+MPW GYN+ED++L
Sbjct: 613  RSNQDTCINQRPIVWPYEKVFSGQVIADGPGTNEGELALGKNLLVAYMPWEGYNYEDAIL 672

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ++ER+V ED+FTS HIE+F++  R+T +G E+ITRD+PN + E ++N+D  GI+  G  V
Sbjct: 673  VNERLVEEDLFTSAHIEKFDLEIRETTVGIEKITRDLPNTTNESIQNLDSNGIVYPGTFV 732

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             PGDILVGK+TPK E    PE +LLRAIFGEK  +V D+SLRVP G+SG V++VR+F   
Sbjct: 733  MPGDILVGKVTPKVEPDQLPEGRLLRAIFGEKVKNVYDSSLRVPKGISGRVINVRVFRNG 792

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
               +  E+++S+ R  I    + K  +++         + +IL  Q+    P G 
Sbjct: 793  IDYEFEEKAVSLVRIFIAQRRKIKVGDKIAGRHGNKGIISKILPKQDMPFLPNGV 847



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 72/338 (21%), Positives = 132/338 (39%), Gaps = 47/338 (13%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF------PITAFSGAAMLEFVSY 79
           IP+  E    S+  FL   +  + +        F S        PI         EF+  
Sbjct: 10  IPNFSETTINSFCWFLENGLPIELKK-------FASSLDTYDTLPIK--IRIYSDEFI-- 58

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               P      C   DL+Y++ + + + LI  +V           I E  I+ G++PLMT
Sbjct: 59  -LQKPLCSPLHCKKYDLSYSIRIFLPIELIDGNV-----------ITEALIFFGEIPLMT 106

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS- 198
             GTF+I G +R++++Q+ RSPGI+F  +  +     KL Y+  +I ++G W+  E    
Sbjct: 107 DSGTFIINGCERVIINQIIRSPGIYFQWEGLK-----KLQYSATLISNRGSWLKFECCPR 161

Query: 199 -KDIIHVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            K+++ +R+++     V  F   L + +++E+++  Y  I            L+      
Sbjct: 162 TKNVL-IRLNKTT---VIDFYRLLEICETQELITNQYFCITPESEVVKTQQELNFKSSEF 217

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             +  +  +DI T  Q  ++   +   +   +  + V  LG       G       +N  
Sbjct: 218 LDRTVNQSLDIGTITQTKKNYGSI-ENIFFQIFNEKVYSLGT-----IGRRKLNKKLNLA 271

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
           T E  I             +         I  +D++ N
Sbjct: 272 TPEHVIRLTIEDISAIANYLIQLHNNIGEIDDIDNLKN 309


>gi|322510305|gb|ADX05538.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05643]
          Length = 300

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 194/300 (64%), Positives = 239/300 (79%), Gaps = 1/300 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 2   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEILSTFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  L+
Sbjct: 182 EEILSTFYTQSLYQRDGDGWRVPFQP-DALKGQKAIADMIDADTGEVVVEAGKKLTPRLV 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + L+EKG+K L  T D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 241 RQLQEKGLKALKATDDDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLPVILSAGFDEIP 300


>gi|260748898|gb|ACX48757.1| RNA polymerase beta subunit [Mesorhizobium septentrionale]
          Length = 313

 Score =  448 bits (1152), Expect = e-123,   Method: Composition-based stats.
 Identities = 193/314 (61%), Positives = 239/314 (76%), Gaps = 1/314 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
           +     RP+EGLQA FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK
Sbjct: 1   DEPKGGRPDEGLQAVFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQDVYMGDMPLMTLNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY KI Y + GD W  P +      G K    LVD DTGE V+E GKK+T+ 
Sbjct: 181 DGEEILSTFYNKITYKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEQGKKITAR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L EKG+K +  T + L G Y+AEDIVN  TGEI++EAGD IDEK+L  +  +   +
Sbjct: 240 QARQLGEKGLKAIKATDEDLLGNYLAEDIVNYGTGEIFLEAGDEIDEKTLNVLLGTGEHE 299

Query: 344 IPILYVDSVNNNAY 357
           I +L +D VN  AY
Sbjct: 300 IKVLDIDHVNVGAY 313


>gi|283769320|ref|ZP_06342220.1| DNA-directed RNA polymerase, beta subunit [Bulleidia extructa W1219]
 gi|283104096|gb|EFC05479.1| DNA-directed RNA polymerase, beta subunit [Bulleidia extructa W1219]
          Length = 1378

 Score =  447 bits (1150), Expect = e-123,   Method: Composition-based stats.
 Identities = 315/781 (40%), Positives = 461/781 (59%), Gaps = 88/781 (11%)

Query: 232  FYPKIVYSQRG---DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
            F+    Y             L+  D ++G  ++ +L+  + G+ +++ G  +   L   L
Sbjct: 315  FFDHKAYDLTKAGRYKVRRKLNILDRIIGHSLTENLIGAE-GKVLVKKGTVIERSLKNEL 373

Query: 289  KEKGVKFLGIT--------------------SDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
            +E+  K + ++                       L G  +A+D+    TG+  +E G V+
Sbjct: 374  REEINKGIAMSAVPFVHAFSHPDVVSVKTAWKKSLVGRILAQDV----TGDYELERGTVL 429

Query: 329  DEKSLEEIFHSE--------------------------------------IRDIPILYVD 350
             E  +++I                                          + +  ++  D
Sbjct: 430  TETDVKKISKQYESVLIYAGIYANEVKVTNDNVNAVLNLGDRLFQIGRITVNEKDLVNSD 489

Query: 351  SV-NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
             V   N Y+ N   ++     ++A   I + +  G+  T  +  +    +  + D   + 
Sbjct: 490  GVAYVNGYVPNVRRSNMTVRNQEA---IVKAVMAGEEVTIWLVGAAVQTVEINVDGNPVK 546

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +G         +D  ++   I   DI A+    + + +G G+ DDID L NRR+R++GE
Sbjct: 547  IIG---------IDPLNEKETITISDIYALYNYQLTMLDGVGSQDDIDMLSNRRIRTMGE 597

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +L+NQYRLGL R ER+IK+R+S  D  ++ P+ L+N +P+ + V EFF +SQLSQ  +  
Sbjct: 598  LLQNQYRLGLSRAERTIKDRMSISDTSALTPKTLVNIRPLTTPVKEFFSASQLSQFMDQE 657

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L+ +++ RR+SALG GG+ R RAG E+RD+H +HYGRICP ET EG NIGL+S LT++
Sbjct: 658  NPLAELSNKRRISALGPGGLTRERAGFEVRDIHNSHYGRICPIETPEGPNIGLISYLTTY 717

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            A+VN YGFIETPYRKV  G VT++VVY+ A EE    IAQ+N+   +D     + V  R 
Sbjct: 718  AKVNEYGFIETPYRKVKKGVVTDEVVYMDAEEENEHVIAQSNA--IKDRKLIADKVVARV 775

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            AGE ++   E +DF D SP+Q+VS+A + +PFLENDD  R LMG NMQRQAVPLL   +P
Sbjct: 776  AGETVMAEAETVDFADVSPRQIVSVATACVPFLENDDCTRALMGANMQRQAVPLLNPHSP 835

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            FVGTGME ++A+ SG A VA   G+V  VDA R+++   +G        +  Y L K+ R
Sbjct: 836  FVGTGMEHMIARYSGEACVATAPGVVTYVDASRVIVAQDDGQ-------LKEYELAKYSR 888

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN +TC+NQ+P+V  G+ V R DI+ADGPS   G+LALG+N+ +AFM W GYN+ED++++
Sbjct: 889  SNASTCINQKPIVLKGEHVERGDILADGPSMQNGELALGQNVTIAFMTWKGYNYEDAIIM 948

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SE+M +ED +TS+HIEE+ +  R TKLG EEIT DIPNV+E   KN+D  GII +GA+V 
Sbjct: 949  SEKMQAEDYYTSVHIEEYSLECRATKLGDEEITYDIPNVAEAAKKNLDPRGIIMIGADVK 1008

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK+TPKG++ ++PEEKLL AIFGEK+ +VRD SL+VP G +GTV+DVRIF+RH 
Sbjct: 1009 EGDILVGKVTPKGQTDVSPEEKLLLAIFGEKSREVRDNSLKVPHGGAGTVLDVRIFHRHD 1068

Query: 950  I 950
             
Sbjct: 1069 K 1069



 Score =  397 bits (1020), Expect = e-108,   Method: Composition-based stats.
 Identities = 149/510 (29%), Positives = 224/510 (43%), Gaps = 79/510 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG------ 934
            I+  G  V  GDIL    +      +   + +  A    K  +  D  +           
Sbjct: 900  IVLKGEHVERGDILADGPS-MQNGELALGQNVTIAFMTWKGYNYEDAIIMSEKMQAEDYY 958

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  +  R     +E          E   ++  D + I+      +  +IL G+ 
Sbjct: 959  TSVHIEEYSLECRATKLGDEEITYDIPNVAEAAKKNL-DPRGIIMIGADVKEGDILVGKV 1017

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   +  E  R                  SLKV +  + ++L+ R  
Sbjct: 1018 TPKGQTDVSPEEKLLLAIFGEKSREVRDN-------------SLKVPHGGAGTVLDVRIF 1064

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            ++ +K   G ++  GV  +VKVF+  KR I  GDKMAGRHGNK                 
Sbjct: 1065 HRHDK---GVELKNGVKSMVKVFIVQKRKISEGDKMAGRHGNK----------------- 1104

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
                       GV SR+N                             +       + ++ 
Sbjct: 1105 -----------GVISRIN--------------------------PVEDMPYMADGTPIDV 1127

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            ++       +++      V       + GV  +TPVFDG   E + ++++ A     G+ 
Sbjct: 1128 MLNPFGVPSRMNIGQVLEVHLGLAAKRLGVKFATPVFDGVSNEDLANIMKEAGSSPDGKY 1187

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LYDG+TGE +D  ++VG +YM+KL HMV DK++AR+TG YSLVTQQPLGGK+  GGQR 
Sbjct: 1188 VLYDGMTGEAYDERISVGVMYMIKLAHMVDDKLHARATGPYSLVTQQPLGGKAQNGGQRF 1247

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++AYGA+  LQE+LT+KSDD+ GRT+ YE+IV G D    G PESF VLV E+
Sbjct: 1248 GEMEVWALEAYGASNTLQEILTVKSDDITGRTKTYEAIVKGKDMPTPGIPESFRVLVHEL 1307

Query: 1355 QALGLSIDLENSRTKNSAKME-EIPDFNKC 1383
            Q+L + + + +         E E  D  + 
Sbjct: 1308 QSLAIDVRMLDGDGHEMDLKEMEQQDLKEE 1337



 Score =  277 bits (709), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 97/394 (24%), Positives = 165/394 (41%), Gaps = 69/394 (17%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           A  VV  G    R+ + K    +D+PDL+E+Q  S++ FL           EG+Q  F  
Sbjct: 6   AYHVVKYGNKATRRDYSKVSSGLDLPDLVEIQTESFNWFLR----------EGIQEVFDG 55

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           +FPIT  S +  L+F+ Y  D P   V +C  + + Y   +   + L +  VD+ TG   
Sbjct: 56  IFPITNHSESIRLKFLGYRLDEPVLSVSECKHKQVNYCAKMYGDMELEM--VDQETGEVL 113

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
               K + +Y+G+LPLMT  GTF+I G +R++VSQ+ RSPG +F         +G+  Y 
Sbjct: 114 T---KREDVYLGELPLMTPGGTFIINGAERVIVSQIVRSPGAYFG--IVSEERTGRDTYT 168

Query: 182 CRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMD------------ 224
             +IP +G W++   D K      ++   +DRRRK+  T FL A+G+             
Sbjct: 169 SELIPARGTWLEFLTDEKKANLGRVVMASVDRRRKILSTVFLKAIGLSLNREKNGGIVSV 228

Query: 225 -----------------------SEEILSTF----------YPKIVYSQRGDFWCFPLSA 251
                                  + E+L+ +          Y ++  S   D       A
Sbjct: 229 SEMQKFLKALKLPIYKDVVVPKETTELLNEYSLLYTSIFGNYEELRNSLAADKLPTTNDA 288

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAE 310
              +   +    +  +D    +++S         L       V+      D + G  + E
Sbjct: 289 LYTIYQNQRQDEIATVDGAMNLMDSRFFDHKAYDLTKAGRYKVRRKLNILDRIIGHSLTE 348

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +++  E G++ ++ G VI+     E+     + I
Sbjct: 349 NLIGAE-GKVLVKKGTVIERSLKNELREEINKGI 381



 Score = 49.7 bits (117), Expect = 0.003,   Method: Composition-based stats.
 Identities = 44/215 (20%), Positives = 79/215 (36%), Gaps = 7/215 (3%)

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
            F          D +   L  A       ++      + G  V+ S         K L  
Sbjct: 153 YFGIVSEERTGRDTYTSELIPARGTWLEFLT-DEKKANLGRVVMASVD----RRRKILST 207

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +K +G++ +           V+     +      +  +  + +     + +  +LY  
Sbjct: 208 VFLKAIGLSLNR--EKNGGIVSVSEMQKFLKALKLPIYKDVVVPKETTELLNEYSLLYTS 265

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
              N   +RN+L  DK     DAL  IY+  R  +++T   A ++ +  FFD   YDL+ 
Sbjct: 266 IFGNYEELRNSLAADKLPTTNDALYTIYQNQRQDEIATVDGAMNLMDSRFFDHKAYDLTK 325

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
            GR K+  +LN+        + +  I A  K+LV 
Sbjct: 326 AGRYKVRRKLNILDRIIGHSLTENLIGAEGKVLVK 360


>gi|322510307|gb|ADX05539.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05593]
          Length = 303

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 193/301 (64%), Positives = 238/301 (79%), Gaps = 1/301 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK
Sbjct: 1   GEPAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  
Sbjct: 181 DGEEILSTFYTQSLYQRDGDGWRVPFQP-DALKGQKAIADMIDADTGEVVVEAGKKLTPR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           L++ L+EKG+K L  T D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  +   +
Sbjct: 240 LVRQLQEKGLKALKATDDDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLPVILSAGFDE 299

Query: 344 I 344
           I
Sbjct: 300 I 300


>gi|330850816|ref|YP_004376566.1| DNA-directed RNA polymerase beta chain [Fistulifera sp. JPCC DA0580]
 gi|328835636|dbj|BAK18932.1| DNA-directed RNA polymerase beta chain [Fistulifera sp. JPCC DA0580]
          Length = 1397

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 169/581 (29%), Positives = 257/581 (44%), Gaps = 58/581 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE-DVFTSIHIEEFEVMARDTKLGP 858
                       ++    P  G   E+ + I   +     +  +I       +   ++ G 
Sbjct: 848  MGSNMQRQSVPLIFPQKPIVGTGLENQISIDSGLTLNAQLAGTITSVTANKIVVTSESGK 907

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +   R    +       I++  I+  G  V  G IL           ++  + +L     
Sbjct: 908  KLTYRLQKYLRSNQQTCINQRPIVWKGETVQSGQILTDGP-AITSGELSLGQNVLVGYMP 966

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   V       R+ I+ +  S + ER   + +     +E   L
Sbjct: 967  WQGYNFEDAILVSERLVYDDVFTSIHIERYKIEIDRNSETSERTT-KNIPNLTSNELNHL 1025

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            + +   ++   +        P       V+SS+   + P S+  +     +         
Sbjct: 1026 NEDGIVKVGTFVK-------PGDILVGKVVSSNTSEQLPESKLLRAIFGAKAKGVK---- 1074

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL-RVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                + S  + +  +   IE + +            + +F+A  R IQ GDK+AGRHGNK
Sbjct: 1075 ----DNSYKMPDGDYGRVIETVTFNRRTKVTYQFEKIYIFIAQIRKIQVGDKIAGRHGNK 1130

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+SRILP +DMPFL DGTPVDI+LNPLGVPSRMNVGQ++E  LG A   L  + K L  
Sbjct: 1131 GIISRILPRQDMPFLPDGTPVDILLNPLGVPSRMNVGQLYECLLGLAGDKLNCRFKILPF 1190

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D     ++S +    +    + S  E                                  
Sbjct: 1191 DEMYGLEVSRILINKKLRQASISKNESW-------------------------------- 1218

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                   + +    G+ +L DG TG  F+ PVTVG  YMLKL H+V DK++AR+TG YSL
Sbjct: 1219 -------LFNPYAPGKIVLIDGRTGIEFENPVTVGNAYMLKLIHLVDDKMHARATGPYSL 1271

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPL GK+  GGQR GEMEVW ++ +GAA+ L+E+LTIKSDD+ GR     +IV G  
Sbjct: 1272 ITQQPLRGKAQHGGQRFGEMEVWALEGFGAAFTLKELLTIKSDDMQGRNETLNAIVKGQQ 1331

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              + G PESF VL+ E++++GL +        +S K  E+ 
Sbjct: 1332 IPKFGIPESFKVLLHELRSIGLDMSTYKIEKFSSDKKYEVE 1372



 Score =  409 bits (1051), Expect = e-111,   Method: Composition-based stats.
 Identities = 279/729 (38%), Positives = 410/729 (56%), Gaps = 36/729 (4%)

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
            P I +S         +   + +         +   T   +     ++ +   K   EK +
Sbjct: 391  PTIYFSVSLKEHLKYIFGKNKLAYKPDRHKYLKTKTQFLLYRKDHEIKTNYNKKYDEKDL 450

Query: 294  KFLGITSDCLCGLYV------------AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
                +  +   G ++             +  +  +  EI I+   V  +  L  +    +
Sbjct: 451  YTATLIPEY--GSWIRFSFQKNTKINSYKYPLKNQEDEIIIQLDKVNQKPILHLLKEMGL 508

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             D+ I Y +  ++  +  N  +   +K     L       R    ST+    S F    F
Sbjct: 509  TDLEI-YQNLEHSEFFYFNKPLLFNSKYSNQPL------SRFNLNSTYFNNISEF-SKIF 560

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            D   Y L  VGR+K+N RLN+   +  + I  EDI AII  L++L   K   DDID+L N
Sbjct: 561  DPSYYRLGRVGRLKLNNRLNVQINERFQTITYEDIFAIIDKLINLTITKTVQDDIDHLKN 620

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            RRVRSVGE+L+N  ++G  R+ R ++ + + +D   ++  +++N     + V EFF SSQ
Sbjct: 621  RRVRSVGELLQNLLQIGFQRLIRKLRNQTNKMDAGQLLSFNIVN-----ATVREFFGSSQ 675

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ  +  N LS +TH RR+S LG GG  R R    +RD+HP+HYGRICP ET EG N+G
Sbjct: 676  LSQYLDQTNPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVG 735

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            L++SLT+ ARVN  GF+ETP+ +V +GKV  T   +YL+A  E+   IA A+ +++++  
Sbjct: 736  LIASLTTCARVNKSGFLETPFWRVINGKVIKTGSPIYLTADIEDFYKIAPADIAVNKENY 795

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              + L+  R   + + V   ++DFI  SP QVVS+AASLIPF E+DD+NR LMG NMQRQ
Sbjct: 796  LIKNLIPVRYKQDFVNVTPSEVDFIAISPVQVVSVAASLIPFFEHDDANRALMGSNMQRQ 855

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            +VPL+  + P VGTG+E+ ++  SG  + A+ AG +  V A +IV+ S  G         
Sbjct: 856  SVPLIFPQKPIVGTGLENQISIDSGLTLNAQLAGTITSVTANKIVVTSESGKK------- 908

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              YRL K+ RSNQ TC+NQRP+V  G+ V+   I+ DGP+   G+L+LG+N+LV +MPW 
Sbjct: 909  LTYRLQKYLRSNQQTCINQRPIVWKGETVQSGQILTDGPAITSGELSLGQNVLVGYMPWQ 968

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFED++L+SER+V +DVFTSIHIE +++         E  T++IPN++   L +++E 
Sbjct: 969  GYNFEDAILVSERLVYDDVFTSIHIERYKIEIDRNSETSERTTKNIPNLTSNELNHLNED 1028

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ VG  V PGDILVGK+     S   PE KLLRAIFG KA  V+D S ++P G  G V
Sbjct: 1029 GIVKVGTFVKPGDILVGKVVSSNTSEQLPESKLLRAIFGAKAKGVKDNSYKMPDGDYGRV 1088

Query: 940  VDVRIFNRH 948
            ++   FNR 
Sbjct: 1089 IETVTFNRR 1097



 Score =  135 bits (340), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 41/169 (24%), Positives = 68/169 (40%), Gaps = 27/169 (15%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYEF 81
           +PD + +Q+ S+  F+           EGL         I  FS     E++     Y  
Sbjct: 11  LPDFLAMQRISFCWFIT----------EGLNEELSLFSRIQDFSQNT--EYIMFGEEYRL 58

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLPLMTK 140
             P +++         Y   L I +             K    +K Q  + +   PLMT 
Sbjct: 59  IKPSYNLLIARKYSGNYRAQLVIPI---------EVRNKIANSVKYQKQFPVITFPLMTT 109

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKG-RASLSGKLLYACRIIPDQ 188
           D TF+I G +R++VSQ+ RSPG++F+ +K  +     K   +  I   +
Sbjct: 110 DATFIINGCERVIVSQIIRSPGVYFEKNKNQKTRNQFKRKLSTDINKLR 158



 Score = 48.5 bits (114), Expect = 0.008,   Method: Composition-based stats.
 Identities = 44/337 (13%), Positives = 103/337 (30%), Gaps = 19/337 (5%)

Query: 177 KLLYACRIIPDQGLWMDIEFDSK--------------DIIHVRIDRRRKVPVTSFLMALG 222
           K LY   +IP+ G W+   F                 D I +++D+  + P+   L  +G
Sbjct: 448 KDLYTATLIPEYGSWIRFSFQKNTKINSYKYPLKNQEDEIIIQLDKVNQKPILHLLKEMG 507

Query: 223 MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
           +   EI         +            +   +    ++S+  +     +  +       
Sbjct: 508 LTDLEIYQNLEHSEFFYFNKPLLFNSKYSNQPLSRFNLNSTYFN--NISEFSKIFDPSYY 565

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
            L +  + K    L +  +        EDI       I +       +  ++ + +  +R
Sbjct: 566 RLGRVGRLKLNNRLNVQINERFQTITYEDIFAIIDKLINL-TITKTVQDDIDHLKNRRVR 624

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            +  L  + +    + R         ++ DA   +   +    V  F  +  +  +L   
Sbjct: 625 SVGELLQNLLQIG-FQRLIRKLRNQTNKMDAGQLLSFNIVNATVREFFGSSQLSQYLDQT 683

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL-VDLRNGKGTIDDIDNLGN 461
           +    L+   R+        D       +R        +I  ++   G+           
Sbjct: 684 NPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVGLIASLTTC 743

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            RV   G +    +R+   ++ ++      + DI+  
Sbjct: 744 ARVNKSGFLETPFWRVINGKVIKTGSPIYLTADIEDF 780


>gi|331029439|gb|AEC49869.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6154]
          Length = 303

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 175/301 (58%), Positives = 226/301 (75%), Gaps = 1/301 (0%)

Query: 38  DHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLT 97
           D FLM++     R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T
Sbjct: 1   DQFLMVDEPAGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMT 60

Query: 98  YAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQL 157
           +A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VSQ+
Sbjct: 61  FAAPLKVTLRLIVFDIDEETGAKSVKDIKEQEVYMGDIPLMTMNGTFVVNGTERVIVSQM 120

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
           HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS 
Sbjct: 121 HRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSL 180

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           + ALG+D E+ILSTFY KI Y +  D W  P  A +   G      LVD DTG+ V+E+G
Sbjct: 181 MYALGLDGEQILSTFYKKITYKRTKDGWRVPFEA-NRFRGYSTVXDLVDADTGKVVLEAG 239

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           KKLT    + L+EKG+K L ++ + L G Y+AED+VN +TG IY  AG+ I EKSL+ + 
Sbjct: 240 KKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGXIYAXAGEEITEKSLKVLN 299

Query: 338 H 338
            
Sbjct: 300 E 300


>gi|322510301|gb|ADX05536.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05591]
          Length = 301

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 190/299 (63%), Positives = 237/299 (79%), Gaps = 1/299 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 3   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 62

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 63  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 122

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS +MALGMD 
Sbjct: 123 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLMMALGMDG 182

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY K +Y + GD W  P    D + G K  + ++D D+GE V+E+GKKLT  LL
Sbjct: 183 EEILDTFYTKSLYQRDGDGWRVPFQP-DALKGQKALADMIDADSGEVVVEAGKKLTPRLL 241

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           + L++KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +I
Sbjct: 242 RQLQDKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILAAGFDEI 300


>gi|322510299|gb|ADX05535.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05637]
          Length = 297

 Score =  447 bits (1149), Expect = e-123,   Method: Composition-based stats.
 Identities = 190/295 (64%), Positives = 237/295 (80%), Gaps = 1/295 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 4   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 63

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 64  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 123

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS +MALGMD EEIL
Sbjct: 124 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLMMALGMDGEEIL 183

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + GD W  P    D + G K  + ++D D+GE V+E+GKKLT  LL+ L+
Sbjct: 184 DTFYTKSLYQRDGDGWRVPFQP-DALKGQKALADMIDADSGEVVVEAGKKLTPRLLRQLQ 242

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +KG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +I
Sbjct: 243 DKGLKALKATDDDLYGNYLAEDVVNVETGEIYLEAGDEIDEKTLPVILAAGFDEI 297


>gi|226968546|ref|YP_002808499.1| RNA polymerase beta chain [Micromonas pusilla CCMP1545]
 gi|226348841|gb|ACO50744.1| RNA polymerase beta chain [Micromonas pusilla CCMP1545]
          Length = 1079

 Score =  446 bits (1148), Expect = e-122,   Method: Composition-based stats.
 Identities = 171/507 (33%), Positives = 238/507 (46%), Gaps = 56/507 (11%)

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              E               I +   +     V+ G+ L    +      +   + +L A  
Sbjct: 622  KHETVWLTTYQRSNQDTCIHQRPSVVPHTWVHAGECLADTSSTV-AGELALGKNILVAYM 680

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD-DEQV 976
              +  +  D  L     V   V       R+ I    R+   +      + ++   D   
Sbjct: 681  PWEGYNFEDAVLVSERLVFDDVFTSVHIERYDIST-ARTREGQEYITAKVEKNVHLDSFG 739

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            ++    +    +IL G+              L   +     R       V    V   V 
Sbjct: 740  VVHVGTWVEPGDILVGKIVPQQESENTPEGRLLRAIFGGAARDVKDMPLVVPSGVTGRVL 799

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
              +  ++T K      +  ++E  +            V VF+  KR +Q GDK+AGRHGN
Sbjct: 800  EARTNFDTQK------YNEEVEAFES--------AGSVYVFLVQKRKVQVGDKIAGRHGN 845

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KGI+S ILP +DMPFL++G PVD+VLNPLGVPSRMNVGQIFE  LG A   L +  K L 
Sbjct: 846  KGIISNILPRQDMPFLQNGVPVDMVLNPLGVPSRMNVGQIFECLLGLAAHTLEENFKVLP 905

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     ++S    + +++      T++   +                  ++P       
Sbjct: 906  FDEMHGDEVSRGFVY-QQLYKARLATKQDWLFRP----------------ASP------- 941

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G+SIL+DG TG PFD+PVTVGY Y+LKL H+V DK++ARSTG YS
Sbjct: 942  ---------------GKSILFDGRTGYPFDQPVTVGYPYILKLVHLVDDKIHARSTGPYS 986

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            LVTQQPLGG+S  GGQRLGEMEVW ++ +GAAY LQE+LTIKSDD+ GR   + SI+ GN
Sbjct: 987  LVTQQPLGGRSKHGGQRLGEMEVWALEGFGAAYTLQELLTIKSDDMRGRNLAFMSIIRGN 1046

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDL 1363
               + G PESF VLV E++ L L I L
Sbjct: 1047 LLPKPGVPESFKVLVCELRGLCLDISL 1073



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 255/682 (37%), Positives = 380/682 (55%), Gaps = 27/682 (3%)

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
              +K  +   ++     G ++  +      GE++    ++        +          
Sbjct: 145 QFDQKNRRSHMVSFLSSYGSWLRLETSPTYFGELHACIDNLRKLPLTIFLHALGFDLD-- 202

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L   +++++A +  T +  +    + A++ +  ++ P    +   A+      FF++ +Y
Sbjct: 203 LVAMTISDSAVVWPTHMWVQTTSVEHAMIIMTALIFPHRAGSVYKAKKFLFNHFFNAQRY 262

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG-TIDDIDNLGNRRVR 465
            LS+VGR ++N +L +        +  ED++A    L+ + NG    +DDID+L NRR R
Sbjct: 263 SLSSVGRKRVNRKLQMRPGIHRLTLTPEDVLAGADYLMRVENGDTQYLDDIDHLKNRRAR 322

Query: 466 SVGEMLKNQYRLGLLRMERSIKERIS-----SVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             GE+++ Q+RLGL R+ERS++ R+S           V    LI  + V S   EFF S+
Sbjct: 323 LAGELIQTQFRLGLNRLERSVRTRLSDENLVRHKRLPVALPSLIRTQIVGSVFREFFGSN 382

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ ITH RRLS+LG GG+ R RAG+ +R +HP++YGRICP ET EG N 
Sbjct: 383 QLSQFMDQTNPLAEITHKRRLSSLGPGGLHRDRAGIVVRGIHPSYYGRICPIETPEGKNA 442

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV---YLSAMEEENRYIAQANSSLDED 637
           GLV S+ ++ARVNA GF+++PY  V   +  +D      L+A  E+   +A A++ +   
Sbjct: 443 GLVGSIATYARVNADGFLQSPYTLVTSAQEPDDTHGFFLLNAAYEDTVVVASADTPMSA- 501

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                  +  R   E I    + ++F+   P Q +SIA +LIPFLE+DD+NR LMG NMQ
Sbjct: 502 -----TRIPARVGSEFIETRPKTVNFLGLCPIQFMSIATALIPFLEHDDANRALMGSNMQ 556

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAV LL  +  FVGTG+E+ V   SGA    + +G V   DA RI + +        T+
Sbjct: 557 RQAVSLLTPQRAFVGTGLEARVPHDSGAVARLRHSGYVLYADAQRIDVLTQPVPTGRPTA 616

Query: 758 -----GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                  +   L  +QRSNQ+TC++QRP V     V   + +AD  ST  G+LALG+N+L
Sbjct: 617 QEPPCKHETVWLTTYQRSNQDTCIHQRPSVVPHTWVHAGECLADTSSTVAGELALGKNIL 676

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA+MPW GYNFED++L+SER+V +DVFTS+HIE +++    T+ G E IT  +     E 
Sbjct: 677 VAYMPWEGYNFEDAVLVSERLVFDDVFTSVHIERYDISTARTREGQEYITAKV-----EK 731

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             ++D  G++ VG  V PGDILVGKI P+ ES  TPE +LLRAIFG  A DV+D  L VP
Sbjct: 732 NVHLDSFGVVHVGTWVEPGDILVGKIVPQQESENTPEGRLLRAIFGGAARDVKDMPLVVP 791

Query: 933 SGVSGTVVDVRIFNRHGIDKNE 954
           SGV+G V++ R          E
Sbjct: 792 SGVTGRVLEARTNFDTQKYNEE 813



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 80/460 (17%), Positives = 152/460 (33%), Gaps = 52/460 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGA---------AMLE 75
           IPD ++ Q+ S+  FL            G++   + V PI    SG            + 
Sbjct: 10  IPDFLDSQRKSFRLFL----------ETGIRRELEFVSPIKGDPSGTSVSQPTTRSISVS 59

Query: 76  FV--SYEFDPPKFDVDDCLWRDL-TYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           F+   + F  P    ++ + R + TY   L + + ++   +D               +  
Sbjct: 60  FLAQDFYFKRPTHTPEEAI-RSMETYTSALVVPVHIVSKCLDLSRILP---------VTF 109

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            DLPLMT+ GTF+I G  R++V Q+ R PG++    K +     +  +    +   G W+
Sbjct: 110 CDLPLMTQHGTFIINGSPRVIVHQIVRCPGVYI---KAQFDQKNRRSHMVSFLSSYGSWL 166

Query: 193 DIEFDSK--DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            +E        +H  ID  RK+P+T FL ALG D + +  T     V       W    S
Sbjct: 167 RLETSPTYFGELHACIDNLRKLPLTIFLHALGFDLDLVAMTISDSAVVWPT-HMWVQTTS 225

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS-DCLCG---- 305
               M+            +    +   KK       + +   +  +G    +        
Sbjct: 226 VEHAMIIMTALIFPHRAGS----VYKAKKFLFNHFFNAQRYSLSSVGRKRVNRKLQMRPG 281

Query: 306 -LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
              +     +   G  Y+   +  D + L++I H + R   +             N L  
Sbjct: 282 IHRLTLTPEDVLAGADYLMRVENGDTQYLDDIDHLKNRRARLAGELIQTQFRLGLNRLER 341

Query: 365 DKNKDRKDALLDIYRVM---RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                  D  L  ++ +    P  + T  V      F   +     +     +       
Sbjct: 342 SVRTRLSDENLVRHKRLPVALPSLIRTQIVGSVFREFFGSNQLSQFMDQTNPLAEITHKR 401

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             +      + ++    +++ +     G+    +     N
Sbjct: 402 RLSSLGPGGLHRDRAGIVVRGIHPSYYGRICPIETPEGKN 441


>gi|322510303|gb|ADX05537.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05583]
          Length = 300

 Score =  446 bits (1148), Expect = e-122,   Method: Composition-based stats.
 Identities = 193/299 (64%), Positives = 238/299 (79%), Gaps = 1/299 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+T
Sbjct: 2   PAGGRPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEILSTFY + +Y + GD W  P    D + G K  + ++D DTGE V+E+GKKLT  L+
Sbjct: 182 EEILSTFYTQSLYQRDGDGWRVPFQP-DALKGQKAIADMIDADTGEVVVEAGKKLTPRLV 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           + L+EKG+K L  T D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  +   +I
Sbjct: 241 RQLQEKGLKALKATDDDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLPVILSAGFDEI 299


>gi|283794883|ref|YP_003359236.1| RNA polymerase beta subunit [Cryptomonas paramecium]
 gi|253981855|gb|ACT46772.1| RNA polymerase beta subunit [Cryptomonas paramecium]
          Length = 1071

 Score =  446 bits (1148), Expect = e-122,   Method: Composition-based stats.
 Identities = 178/556 (32%), Positives = 265/556 (47%), Gaps = 53/556 (9%)

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARD 853
            A+              +L    P  G  FE  +   S+ +V+     ++     + +  +
Sbjct: 534  ANRSLMGSNMQRQAVPLLFPEKPLVGTGFEAQIARDSKTVVTSLTKGNVTYVSSKKVCIE 593

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               G E                I++  ++  G  +  G ++   +  +G   +   + +L
Sbjct: 594  NTRGIEICYHLQKYERTNQDTCINQKPLVWYGDSIIKGQVIADGLATEG-GELALGQNVL 652

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  L     VS  ++   ++    I+K E      +   E + +   +
Sbjct: 653  VAYMPWEGYNYEDAIL-----VSDRLIYDNVYTSVHIEKYEIEARRTKLGHEEITKKVPN 707

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                L RN+  +   I  G     G     K   ++    +E P       A+  EK++ 
Sbjct: 708  TSSHLLRNL-DKNGIIARGSWVEGGDVLVGK---ITPKKDAEQPLLSKLMKAILVEKIRE 763

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              ++     + +   +      ++   +  D++  G   +V+++VA  R ++ GDKMAGR
Sbjct: 764  VKDTSLRMPDNNAGRI---LDVRVLTKKSSDEISTGANIMVRIYVAQTRKLKVGDKMAGR 820

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGIVS+ILP +DMP+L DGTP+DIVLNPLGVPSRMNVGQIFE  LG A   LGK+ +
Sbjct: 821  HGNKGIVSKILPRQDMPYLPDGTPIDIVLNPLGVPSRMNVGQIFECLLGLAAEHLGKRFR 880

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             L  D     + S +                I++   D+ L+  + W             
Sbjct: 881  ILPFDEMQGREASRVL---------------INNSLLDAKLKTGKNW------------- 912

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                       +  LD  G+ ILYDG TGEPF  P+TVG  Y+LKL H+V DK++ARSTG
Sbjct: 913  -----------LFSLDHPGKMILYDGRTGEPFKNPITVGVSYILKLAHLVDDKMHARSTG 961

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             YSLVTQQPLGGK+  GGQRLGEMEVW ++AYGA+Y LQE LTIKSDD+ GR     +++
Sbjct: 962  PYSLVTQQPLGGKAQHGGQRLGEMEVWALEAYGASYTLQEFLTIKSDDMEGRNEALRAMI 1021

Query: 1334 AGNDTFETGTPESFNV 1349
             G    +  TPESF V
Sbjct: 1022 KGTPMPKPRTPESFKV 1037



 Score =  422 bits (1085), Expect = e-115,   Method: Composition-based stats.
 Identities = 264/630 (41%), Positives = 391/630 (62%), Gaps = 9/630 (1%)

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A      + L  IF   +    +     V N   ++ T     N   + A +++      
Sbjct: 169 ARIDKSRRVLIHIFLKALGLTDLDIYHGVKNPNLLKKTFCLKGNSMPEAAFIELSSKFIA 228

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
            D  + +  + +    FFD  +YDL  VGR K+N +L L  P  +  +  +DI+A I  L
Sbjct: 229 TDEESLAEGQEIIYSRFFDPKRYDLGKVGRYKLNKKLQLSVPRSITVLTPQDILACIDYL 288

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           ++L+      D+ID+L NRRVRSVGE+L+NQ R+GL R+E+  +E++ S   D+     L
Sbjct: 289 INLKLSLNEPDNIDHLSNRRVRSVGELLQNQIRIGLQRLEKFTREQMISCAKDTTDANSL 348

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           +N KP+ +++ EFF SSQLSQ  +  N L+ ITH RR+SALG GG+ R R G  +RD+HP
Sbjct: 349 LNPKPIQASIREFFGSSQLSQFMDQTNPLAEITHKRRISALGLGGLHRDRIGSSVRDIHP 408

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAME 621
           +HYGRICP ET EG N GL+  L+ +ARVN YGF+ETP+ K+ +      N   YL+A +
Sbjct: 409 SHYGRICPIETPEGQNAGLIGVLSIYARVNTYGFLETPFNKIVNSREIQNNSPTYLTADQ 468

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E+  YIA A++  +  G   +  +  +   E I +   K ++   SP Q +SIA SLIPF
Sbjct: 469 EDLLYIAPADTITNLKGQIQKHTLTAKHQQEFIQILTTKTNWKPVSPIQTISIATSLIPF 528

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE++D+NR LMG NMQRQAVPLL  E P VGTG E+ +A+ S   + +   G V  V + 
Sbjct: 529 LEHNDANRSLMGSNMQRQAVPLLFPEKPLVGTGFEAQIARDSKTVVTSLTKGNVTYVSSK 588

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           ++ I       + +      Y L K++R+NQ+TC+NQ+PLV  GD + +  +IADG +T+
Sbjct: 589 KVCI-------ENTRGIEICYHLQKYERTNQDTCINQKPLVWYGDSIIKGQVIADGLATE 641

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+LVA+MPW GYN+ED++L+S+R++ ++V+TS+HIE++E+ AR TKLG EEI
Sbjct: 642 GGELALGQNVLVAYMPWEGYNYEDAILVSDRLIYDNVYTSVHIEKYEIEARRTKLGHEEI 701

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           T+ +PN S   L+N+D+ GII  G+ V  GD+LVGKITPK ++      KL++AI  EK 
Sbjct: 702 TKKVPNTSSHLLRNLDKNGIIARGSWVEGGDVLVGKITPKKDAEQPLLSKLMKAILVEKI 761

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +V+DTSLR+P   +G ++DVR+  +   D
Sbjct: 762 REVKDTSLRMPDNNAGRILDVRVLTKKSSD 791



 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 89/487 (18%), Positives = 193/487 (39%), Gaps = 36/487 (7%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS-- 78
           P  + +P+L E+Q++S+   L           EGL    ++  PI+       +  +S  
Sbjct: 6   PYHLRLPNLTELQRSSFCWLLQ----------EGLAEVIRNFSPISNSEENLEIHILSDK 55

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   PK +  + + ++ TY   + I + ++          K  K  KEQ I  G+LPLM
Sbjct: 56  YKLKYPKNNPSEAIRKNSTYCTEIHIPVIIV---------NKEKKVTKEQEICFGELPLM 106

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T+ GTF+I G +R++++Q+ RSPGI++       +      Y+  +I ++G W+  E D 
Sbjct: 107 TERGTFIINGTERVIINQIIRSPGIYYT---IHTNSQKDKTYSGNLISNRGAWIKFELDK 163

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR--GDFWCFPLSAADLMV 256
             +I  RID+ R+V +  FL ALG+   +I        +  +         P +A   + 
Sbjct: 164 HGLIWARIDKSRRVLIHIFLKALGLTDLDIYHGVKNPNLLKKTFCLKGNSMPEAAFIELS 223

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
              +++    +  G+++I S         L K  + K  K L ++      +   +DI+ 
Sbjct: 224 SKFIATDEESLAEGQEIIYSRFFDPKRYDLGKVGRYKLNKKLQLSVPRSITVLTPQDILA 283

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                I ++   + +  +++ + +  +R +  L  + +            ++        
Sbjct: 284 CIDYLINLK-LSLNEPDNIDHLSNRRVRSVGELLQNQIRIGLQRLEKFTREQMISCAKDT 342

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            D   ++ P      +     F            + +  +    R++      +  + ++
Sbjct: 343 TDANSLLNPK--PIQASIREFFGSSQLSQFMDQTNPLAEITHKRRISA---LGLGGLHRD 397

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            I + ++ +     G+  I  I+    +    +G +           +E    + ++S +
Sbjct: 398 RIGSSVRDIHPSHYGR--ICPIETPEGQNAGLIGVLSIYARVNTYGFLETPFNKIVNSRE 455

Query: 495 IDSVMPQ 501
           I +  P 
Sbjct: 456 IQNNSPT 462


>gi|315360833|gb|ADU05390.1| RNA polymerase beta subunit [Sinorhizobium kummerowiae]
          Length = 296

 Score =  446 bits (1147), Expect = e-122,   Method: Composition-based stats.
 Identities = 193/296 (65%), Positives = 237/296 (80%), Gaps = 1/296 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+ PKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 2   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEAPKFDVEECRQRDLTYAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 122 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P    D + G K  + ++D DTGE V+ESGKKLT  LL+ L+
Sbjct: 182 DTFYTKSLYQRDGEGWRVPFQP-DALKGQKTLADMIDADTGEVVVESGKKLTPRLLRQLQ 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 241 EKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILSAGFDEIP 296


>gi|317183722|gb|ADV15555.1| RNA polymerase beta subunit [Lactobacillus sp. SL1108]
          Length = 652

 Score =  446 bits (1146), Expect = e-122,   Method: Composition-based stats.
 Identities = 283/482 (58%), Positives = 359/482 (74%), Gaps = 9/482 (1%)

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF SSQLSQ  +  N 
Sbjct: 3   ANQFRIGLSRMERVVRERMSIQDTSTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNP 62

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL S+A 
Sbjct: 63  LGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLASYAV 122

Query: 592 VNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++DGSF EE V  R 
Sbjct: 123 VNPYGFIETPYRRVDWDTNKVTDKIDYLTADEEDNYVVAQANSPLNDDGSFVEETVLARK 182

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             + I    +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP
Sbjct: 183 KDDNIETTPDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLVDPKAP 242

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTGME   A  SG AI+A   G VE VDA +I +R  +G LD        Y LMKF+R
Sbjct: 243 LVGTGMEYKAAHDSGTAILAAHPGTVEYVDAKQIRVRREDGALDK-------YSLMKFRR 295

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN     NQRP+V++GD+V  N+IIADGP+ + G+LALG+N ++AFM W+ YN+ED++++
Sbjct: 296 SNAGKNYNQRPIVRLGDKVDANEIIADGPAMENGELALGQNPVIAFMTWNMYNYEDAIVM 355

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE++V ED +TSIHIEE+E  ARDTKLGPEE+TR++PNV E+ LK++DE GI+ VGAEV 
Sbjct: 356 SEKLVREDKYTSIHIEEYESEARDTKLGPEEVTRELPNVGEDALKDLDEFGIVRVGAEVK 415

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G + DVRIF R  
Sbjct: 416 DGDILVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIQDVRIFTREA 475

Query: 950 ID 951
            D
Sbjct: 476 GD 477



 Score =  325 bits (832), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 133/443 (30%), Positives = 186/443 (41%), Gaps = 83/443 (18%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R +  G     R I  + +     +D   II  G  +  G++ +G              
Sbjct: 293  FRRSNAGKNYNQRPIVRLGD----KVDANEIIADGPAMENGELALG-------QNPVIAF 341

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
                    E A+ + +  +R     S  + +     R      E          E   +D
Sbjct: 342  MTWNMYNYEDAIVMSEKLVREDKYTSIHIEEYESEARDTKLGPEEVTRELPNVGEDALKD 401

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      +  +IL G+    G         L   +  E  R           +
Sbjct: 402  L-DEFGIVRVGAEVKDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR-----------E 449

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V+     +          +      +I   + GD++ PGV  +V+V++  KR IQ GDKM
Sbjct: 450  VRDTSLRVPHGGGGIIQDV------RIFTREAGDELSPGVNMMVRVYITQKRKIQVGDKM 503

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPFL DGTPVDI L+P+GVPSRMN+GQ+ E HLG A   LG 
Sbjct: 504  AGRHGNKGTVSVVVPEEDMPFLPDGTPVDICLSPMGVPSRMNIGQVLELHLGMAARNLGI 563

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + + + D     D+                                             
Sbjct: 564  HVATPVFDGANEKDLW-------------------------------------------- 579

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
               A  +        A +   G+S+LYDG TGEPF+  V+VG +Y +KL HMV DK++AR
Sbjct: 580  ---ATVKE-------AGMASDGKSVLYDGRTGEPFENRVSVGVMYYMKLAHMVDDKLHAR 629

Query: 1271 STGSYSLVTQQPLGGKSNRGGQR 1293
            S G YSLVTQQPLGGK+  GGQR
Sbjct: 630  SIGPYSLVTQQPLGGKAQFGGQR 652


>gi|269101092|ref|YP_003289240.1| Plastid-encoded DNA-directed RNA polymerase subunit beta
           [Ectocarpus siliculosus]
 gi|266631600|emb|CAV31271.1| Plastid-encoded DNA-directed RNA polymerase subunit beta
           [Ectocarpus siliculosus]
 gi|270118730|emb|CAT18810.1| Plastid-encoded DNA-directed RNA polymerase subunit beta
           [Ectocarpus siliculosus]
          Length = 1139

 Score =  446 bits (1146), Expect = e-122,   Method: Composition-based stats.
 Identities = 298/942 (31%), Positives = 468/942 (49%), Gaps = 107/942 (11%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV- 77
           K    I +PDL EVQ+ S+  FL           EGL     +   I   +  + +E + 
Sbjct: 9   KQKSPIILPDLSEVQRISFCWFLT----------EGLPEELTNCPSI--LNQNSGIELII 56

Query: 78  ---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
               Y+   P F + + L +   Y + + + + L   ++ +    +     +++ ++ G+
Sbjct: 57  YGQEYKIYYPGFALLNALTKKGNYNLRIYVLMSLKKNEIIKKGIVQPEDFSRKERVFFGE 116

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDH-DKGRASLSGKLLYACRIIPDQGLWMD 193
           +PL+T+ GTF+  G +R+++SQ+ RSPG+++    K +     K+ Y   II   G W+ 
Sbjct: 117 IPLLTEKGTFIFNGCERVIISQIIRSPGVYYKQIIKEK-----KIFYEGTIISKYGSWLT 171

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            E +   +I V+ D++ K+P+  FL  +G+  EE  S  Y  +   Q  +F    LSA  
Sbjct: 172 FELEYN-LIWVKFDKQYKIPINWFL--VGLSLEE--SEVYQTV---QNFNFLIKSLSAIR 223

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           L +  K++S            E  K +     ++     +  +    + +    + + + 
Sbjct: 224 LAIFDKMTS----------KSEKNKVVDKENHEAYNRNILLTVFRVQELINQRLLDKGVY 273

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           +   GE+               +    +  + IL V     +    N  + D +      
Sbjct: 274 D--LGEV-GRIKLNKKLDIGLPLSRRTLTSLDILKVIDKLIHISFHNEKLDDIDN----- 325

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L+  RV   G++    V  ++                GR+K  +  +     ++  I+K
Sbjct: 326 -LENRRVRSVGELLQLQVRVAL----------------GRIKKKINTDEKLTAEMFRIKK 368

Query: 434 EDIIAIIK--ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
               A +K       ++ K           +      E+L ++    ++R          
Sbjct: 369 NKKRAGMKNSTPKKNKSTKKNQLGRKKKPQKETLMPNELLNSKVLTSVIR---------- 418

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
                                  EFF  S LSQ  + VN+L+++TH RR+S+LG GG+  
Sbjct: 419 -----------------------EFFGLSPLSQYFDEVNALAQLTHKRRISSLGPGGLNS 455

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                  RD+HPT YGR+CP ET EG   GL++SL + AR+N YGFI TP+ +V  GKV 
Sbjct: 456 EHVSFAARDIHPTQYGRLCPIETPEGQKAGLIASLATHARINNYGFITTPFFRVYKGKVL 515

Query: 612 NDV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            ++  VYL+A +E    +A  +  L  D  F  ++V  R   E I V    ++F+  SP 
Sbjct: 516 YELGPVYLTAEQEATYNVASGDVLLTRDNFFRTKIVPVRSFNEFITVDAINVNFLAVSPI 575

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q++++ ASLIPFLE+DD+NR LMG NMQRQAVPLL  + P +GTG+E  +A  S   ++ 
Sbjct: 576 QILAVGASLIPFLEHDDANRALMGSNMQRQAVPLLYPKKPIIGTGIEHQIAADSQVVLIN 635

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
              GI++ V + RI I               +Y L K++RSNQ T +NQ+PL+  G+ V 
Sbjct: 636 LLDGIIDSVCSDRITIIDN-----KYLGSSKMYFLDKYRRSNQETIINQKPLIWNGEIVE 690

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
              IIADGP T+ G+LALG+N+ VA+MPW GYNFED++L+S+R+V +D+FTSIHIE++E+
Sbjct: 691 PGQIIADGPGTEGGELALGQNLTVAYMPWDGYNFEDAILVSDRLVQDDLFTSIHIEKYEL 750

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
              D     EEIT  IPN+ EE + N+D  GII  G  VN GDILVGKITP  E    PE
Sbjct: 751 QLMDESDTIEEITTSIPNIEEEEIINLDMNGIIKKGTFVNGGDILVGKITPILEEDELPE 810

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            KLLRAIF  ++ +  D+SLRVP+GVSG V++++  +R   D
Sbjct: 811 SKLLRAIFNIESPEPEDSSLRVPNGVSGRVIEIQTASREKGD 852



 Score =  428 bits (1100), Expect = e-117,   Method: Composition-based stats.
 Identities = 174/580 (30%), Positives = 264/580 (45%), Gaps = 59/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI---HIEEFEVMARDTKL 856
                       +L    P  G   E  +    ++V  ++   I      +   +  +  L
Sbjct: 598  MGSNMQRQAVPLLYPKKPIIGTGIEHQIAADSQVVLINLLDGIIDSVCSDRITIIDNKYL 657

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  ++              I++  +I  G  V PG I+      +G   +   + L  A 
Sbjct: 658  GSSKMYFLDKYRRSNQETIINQKPLIWNGEIVEPGQIIADGPGTEG-GELALGQNLTVAY 716

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  L     VS  +V   +F    I+K E  +  E + IE +     + + 
Sbjct: 717  MPWDGYNFEDAIL-----VSDRLVQDDLFTSIHIEKYELQLMDESDTIEEITTSIPNIEE 771

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                N+      I  G     G     K T +  +      +     F ++  + + +  
Sbjct: 772  EEIINL-DMNGIIKKGTFVNGGDILVGKITPILEEDELPESKLLRAIFNIESPEPEDSSL 830

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +          ++   + K      GD++  G+   V + +A  + I+ GDK++GRHGN
Sbjct: 831  RVPNGVSGRVIEIQTASREK------GDNLGSGIYEWVCISIAQIKKIRIGDKLSGRHGN 884

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S+I+P +DMPFL DGT VD++LNPLGVPSRMNVGQIFE  LG+A   L ++ K + 
Sbjct: 885  KGVISKIIPTDDMPFLPDGTIVDVILNPLGVPSRMNVGQIFECLLGFAGDYLNRRFKVIP 944

Query: 1157 NDYKANGDISPLR--SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             D     + S +     L+K           + +                          
Sbjct: 945  FDEMYKPNASRILINKALKKAAKETDKCWLFNKFS------------------------- 979

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             G+ +L DG TG+ FD  V VG  Y+LKL H+V  K++ARSTGS
Sbjct: 980  ----------------PGKVLLTDGRTGDVFDNSVLVGKPYILKLIHLVDKKMHARSTGS 1023

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGKS  GGQR GEMEVW ++A+G AY LQE+LTIKSDD+ GR  V+ +I+ 
Sbjct: 1024 YSLVTQQPLGGKSKHGGQRFGEMEVWALEAFGVAYTLQELLTIKSDDINGRHEVFTAIIK 1083

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
            G++  E G PESFNVL++E+ ALGL +        N++++
Sbjct: 1084 GHNIPEPGIPESFNVLLRELNALGLDMTTHEIGKLNNSEI 1123


>gi|118411017|ref|YP_874412.1| DNA-directed RNA polymerase beta chain [Phaeodactylum tricornutum]
 gi|125987643|sp|A0T0D7|RPOB_PHATC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|116739764|gb|ABK20635.1| DNA-directed RNA polymerase beta chain [Phaeodactylum tricornutum]
          Length = 1389

 Score =  446 bits (1146), Expect = e-122,   Method: Composition-based stats.
 Identities = 172/581 (29%), Positives = 254/581 (43%), Gaps = 58/581 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI-EEFEVMARDTKLGP 858
                       +L+   P  G   E+ + I   M        +        +  + K G 
Sbjct: 840  MGSNMQRQSVPLLLPQKPIVGTGLENQIAIDSGMTLNSYSNGVVSSVTANKIVVNDKTGK 899

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                +    +       I+   I+  G +V  G IL         S ++  + +L     
Sbjct: 900  RLTYKLQKYLRSNQQTCINHRPIVWKGEQVKSGQILTDGP-AITSSELSLGQNVLIGYMP 958

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   V       R+ I+ +  S ++ER    +            
Sbjct: 959  WQGYNFEDAILINERLVYDDVFTSIHIERYKIEIDRNSDTLERTTKNIP----------- 1007

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              N+  R +  L     V+     +   +L   +IS     Q  +  +         + +
Sbjct: 1008 --NLNPREIRHLNDDGIVTVGTFVRPGDILVGKVISNNTSEQLPESKLLRAIFGAKAKGV 1065

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            K     S  + +  +   IE + +            + VF+A  R IQ GDK+AGRHGNK
Sbjct: 1066 KDN---SYRMSDGEYGRVIETVTFNRRTKLTYKFEKIYVFIAQIRKIQVGDKIAGRHGNK 1122

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+SRIL  +DMPFL DGTP+DI+LNPLGVPSRMNVGQ++E  LG A   L  + K L  
Sbjct: 1123 GIISRILSRQDMPFLPDGTPLDILLNPLGVPSRMNVGQLYECLLGLAGDKLNARFKILPF 1182

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D     +IS +    +    + +  E                                  
Sbjct: 1183 DEMYGLEISRILINKKLRQASIAKNESW-------------------------------- 1210

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                   + +    G+ +L DG TG+ F+ PVTVG  YMLKL H+V DK++AR+TG YSL
Sbjct: 1211 -------LFNPYAPGKMVLIDGRTGKEFENPVTVGNAYMLKLIHLVDDKMHARATGPYSL 1263

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPL GK+  GGQR GEMEVW ++ +GAA+ L+E+LTIKSDD+ GR     +IV G  
Sbjct: 1264 ITQQPLRGKAQHGGQRFGEMEVWALEGFGAAFTLKELLTIKSDDMQGRNETLNAIVKGQQ 1323

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              + G PESF VL+ E++++GL +        NS K  E+ 
Sbjct: 1324 IPKFGIPESFKVLLHELRSIGLDMSTYKINRFNSTKRYEVE 1364



 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 273/728 (37%), Positives = 409/728 (56%), Gaps = 24/728 (3%)

Query: 229  LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
            L    P I +S         +   + +         +   T   +     ++ +   K  
Sbjct: 378  LQNLKPAIYFSISLKEQLKYVFGKNKLTYKSDRHKYLKTKTQFLLYRKDHEIKTNYNKKY 437

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIV-NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
             EK +    +  +   G ++      N +            DE  ++    ++   + +L
Sbjct: 438  DEKDLYTATVIPEY--GSWIRIGFQRNTKINSYKYPLKSQEDEVIIQLDKINQKPVLYLL 495

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF-----LFFD 402
                + +    +N    D     K  L++  R+  P  +S F++  S F         FD
Sbjct: 496  KEMGLTDLEIYQNLEYADFFYFNKPLLINSKRLSEP--LSRFNLGLSYFKNISEFSRIFD 553

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
               Y L  VGR+K+N RLNL   + ++ I  EDI AI   L++L   K   DDID+L NR
Sbjct: 554  PTYYRLGRVGRLKINSRLNLKMSERLQTITYEDIFAITDKLINLTISKTVQDDIDHLKNR 613

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            RVRSVGE+L+N +R+G  R+ R ++ + + +D   ++  +++N     +++ EFF SSQL
Sbjct: 614  RVRSVGELLQNLFRIGFQRLGRKLRNQTNKIDSGQLLSFNIVN-----ASIREFFGSSQL 668

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ  +  N LS +TH RR+S LG GG  R R    +RD+HP+HYGRICP ET EG N+GL
Sbjct: 669  SQYLDQTNPLSSLTHRRRVSGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVGL 728

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            ++SLT+ ARVN  GF+ETP+ +V +GKV  T   VYL+A  E+   IA A+ + ++D   
Sbjct: 729  IASLTTCARVNKSGFLETPFWRVINGKVVKTGQPVYLTADIEDFYKIAPADIATNKDNYL 788

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            T+ ++  R   + + V   ++DFI  S  QVVS+AASLIPF E+DD+NR LMG NMQRQ+
Sbjct: 789  TKNVIPVRYKQDFVNVTPSEVDFIAISTIQVVSVAASLIPFFEHDDANRALMGSNMQRQS 848

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPLL  + P VGTG+E+ +A  SG  + +   G+V  V A +IV+       +  T    
Sbjct: 849  VPLLLPQKPIVGTGLENQIAIDSGMTLNSYSNGVVSSVTANKIVV-------NDKTGKRL 901

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             Y+L K+ RSNQ TC+N RP+V  G++V+   I+ DGP+    +L+LG+N+L+ +MPW G
Sbjct: 902  TYKLQKYLRSNQQTCINHRPIVWKGEQVKSGQILTDGPAITSSELSLGQNVLIGYMPWQG 961

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFED++LI+ER+V +DVFTSIHIE +++         E  T++IPN++   ++++++ G
Sbjct: 962  YNFEDAILINERLVYDDVFTSIHIERYKIEIDRNSDTLERTTKNIPNLNPREIRHLNDDG 1021

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V PGDILVGK+     S   PE KLLRAIFG KA  V+D S R+  G  G V+
Sbjct: 1022 IVTVGTFVRPGDILVGKVISNNTSEQLPESKLLRAIFGAKAKGVKDNSYRMSDGEYGRVI 1081

Query: 941  DVRIFNRH 948
            +   FNR 
Sbjct: 1082 ETVTFNRR 1089



 Score =  134 bits (337), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 41/169 (24%), Positives = 69/169 (40%), Gaps = 27/169 (15%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYEF 81
           +PD + +Q+ S+  F+           +GL         I  FS     E+V     Y  
Sbjct: 7   LPDFLAMQRISFCWFIT----------QGLTEELALFSRIQDFSQNT--EYVMFGEEYSL 54

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLPLMTK 140
             P + +         Y   L I +             K +  I+  + + +  LPLMT 
Sbjct: 55  IKPSYSLLIARKYSGNYRAQLVIPI---------EVRNKVVNSIRYHNQFPIITLPLMTT 105

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKG-RASLSGKLLYACRIIPDQ 188
           D TF+I G +R++VSQ+ RSPG++F+ +K  +     K   +  I   +
Sbjct: 106 DATFIINGCERVIVSQIIRSPGVYFEKNKNQKTRNQFKKKLSTDINKLR 154


>gi|306569703|gb|ADN03346.1| RNA polymerase beta subunit [Bradyrhizobium liaoningense]
          Length = 307

 Score =  446 bits (1146), Expect = e-122,   Method: Composition-based stats.
 Identities = 173/308 (56%), Positives = 233/308 (75%), Gaps = 1/308 (0%)

Query: 47  PDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITL 106
           P  R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TL
Sbjct: 1   PGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTL 60

Query: 107 RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           RLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FD
Sbjct: 61  RLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFD 120

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E
Sbjct: 121 HDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGE 180

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
            ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    +
Sbjct: 181 AILSTFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAAR 239

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L+EKG+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+
Sbjct: 240 QLQEKGLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKELPL 299

Query: 347 LYVDSVNN 354
           L +D VN 
Sbjct: 300 LDIDHVNV 307


>gi|313799158|gb|ADR82159.1| RNA polymerase beta subunit [Lactobacillus equi]
          Length = 662

 Score =  446 bits (1146), Expect = e-122,   Method: Composition-based stats.
 Identities = 294/494 (59%), Positives = 373/494 (75%), Gaps = 9/494 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF S
Sbjct: 1   GNRRIRSVGELLQNQFRIGLTRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGS 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL+SSL+S+ RVN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++D
Sbjct: 121 IGLISSLSSYGRVNRYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYVVAQANSPLNDD 180

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           GSF  ++V  R   E I V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQ
Sbjct: 181 GSFVNDVVMARAEEENIEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQ 240

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL++  AP VGTG+E   A  +G A++A  AG+VE VDA  I +R  +  LD    
Sbjct: 241 RQAVPLIQPHAPLVGTGIEYKAAHDAGDAVIADHAGVVEYVDAREIRVRREDATLDK--- 297

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               Y+LMKF+RSN     NQ P+V+VGD V  ++I+ADGP+ + G+LALG+N L+AFM 
Sbjct: 298 ----YKLMKFRRSNAGKNYNQTPIVRVGDRVDADEILADGPAMEGGELALGQNPLIAFMT 353

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYNFED++ I+ER+V +DV+TSIHIEE +  ARDTKLGPEEITR+IPNV E+ LKN+D
Sbjct: 354 WDGYNFEDAIAINERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALKNLD 413

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GII +GAEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 414 EFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGG 473

Query: 938 TVVDVRIFNRHGID 951
            V +V+I+ R G D
Sbjct: 474 IVQNVKIYTREGGD 487



 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 123/443 (27%), Positives = 180/443 (40%), Gaps = 85/443 (19%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  + +        KN ++  I+ VG  V   D ++          +   +  L A    
Sbjct: 296  DKYKLMKFRRSNAGKNYNQTPIVRVGDRV-DADEILADGPAMEGGELALGQNPLIAFMTW 354

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI------SVEREQIELLARDKD- 972
               +  D            V D    + H  + +  +            +I  +  D   
Sbjct: 355  DGYNFEDAIAIN----ERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALK 410

Query: 973  --DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      +  +IL G+    G         L   +  E  R    +      +
Sbjct: 411  NLDEFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAR----EVRDTSLR 466

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V      +                 KI   + GD++ PGV ++V+V++A KR +Q GDKM
Sbjct: 467  VPHGGGGIVQNV-------------KIYTREGGDELAPGVNQMVRVYIAQKRKLQVGDKM 513

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ + HLG A   LG 
Sbjct: 514  AGRHGNKGTVSIVIPEEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLDLHLGMAARELGI 573

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + S + D   + DI                                          T +
Sbjct: 574  HVASPVFDGARDDDIWDALKEAGLPSDGK----------------------------TIL 605

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +DG                           TGE FD  + VG +Y +KL+HMV DK+++R
Sbjct: 606  YDG--------------------------RTGEAFDNRIAVGVMYYMKLSHMVDDKIHSR 639

Query: 1271 STGSYSLVTQQPLGGKSNRGGQR 1293
            S G YSLVTQQPLGGK+  GGQR
Sbjct: 640  SIGPYSLVTQQPLGGKAQFGGQR 662


>gi|313799164|gb|ADR82161.1| RNA polymerase beta subunit [Lactobacillus equi]
          Length = 658

 Score =  445 bits (1145), Expect = e-122,   Method: Composition-based stats.
 Identities = 294/494 (59%), Positives = 373/494 (75%), Gaps = 9/494 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF S
Sbjct: 1   GNRRIRSVGELLQNQFRIGLTRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGS 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL+SSL+S+ RVN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++D
Sbjct: 121 IGLISSLSSYGRVNRYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYVVAQANSPLNDD 180

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           GSF  ++V  R   E I V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQ
Sbjct: 181 GSFVNDVVMARAEEENIEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQ 240

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL++  AP VGTG+E   A  +G A++A  AG+VE VDA  I +R  +  LD    
Sbjct: 241 RQAVPLIQPHAPLVGTGIEYKAAHDAGDAVIADHAGVVEYVDAREIRVRREDATLDK--- 297

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               Y+LMKF+RSN     NQ P+V+VGD V  ++I+ADGP+ + G+LALG+N L+AFM 
Sbjct: 298 ----YKLMKFRRSNAGKNYNQTPIVRVGDRVDADEILADGPAMEGGELALGQNPLIAFMT 353

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYNFED++ I+ER+V +DV+TSIHIEE +  ARDTKLGPEEITR+IPNV E+ LKN+D
Sbjct: 354 WDGYNFEDAIAINERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALKNLD 413

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GII +GAEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 414 EFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGG 473

Query: 938 TVVDVRIFNRHGID 951
            V +V+I+ R G D
Sbjct: 474 IVQNVKIYTREGGD 487



 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 119/439 (27%), Positives = 176/439 (40%), Gaps = 85/439 (19%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  + +        KN ++  I+ VG  V   D ++          +   +  L A    
Sbjct: 296  DKYKLMKFRRSNAGKNYNQTPIVRVGDRV-DADEILADGPAMEGGELALGQNPLIAFMTW 354

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI------SVEREQIELLARDKD- 972
               +  D            V D    + H  + +  +            +I  +  D   
Sbjct: 355  DGYNFEDAIAIN----ERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALK 410

Query: 973  --DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      +  +IL G+    G         L   +  E  R    +      +
Sbjct: 411  NLDEFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAR----EVRDTSLR 466

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V      +                 KI   + GD++ PGV ++V+V++A KR +Q GDKM
Sbjct: 467  VPHGGGGIVQNV-------------KIYTREGGDELAPGVNQMVRVYIAQKRKLQVGDKM 513

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ + HLG A   LG 
Sbjct: 514  AGRHGNKGTVSIVIPEEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLDLHLGMAARELGI 573

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + S + D   + DI                                          T +
Sbjct: 574  HVASPVFDGARDDDIWDALKEAGLPSDGK----------------------------TIL 605

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +DG                           TGE FD  + VG +Y +KL+HMV DK+++R
Sbjct: 606  YDG--------------------------RTGEAFDNRIAVGVMYYMKLSHMVDDKIHSR 639

Query: 1271 STGSYSLVTQQPLGGKSNR 1289
            S G YSLVTQQPLGGK+  
Sbjct: 640  SIGPYSLVTQQPLGGKAQF 658


>gi|313799161|gb|ADR82160.1| RNA polymerase beta subunit [Lactobacillus equi]
          Length = 657

 Score =  445 bits (1145), Expect = e-122,   Method: Composition-based stats.
 Identities = 294/494 (59%), Positives = 373/494 (75%), Gaps = 9/494 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D  +V PQ LIN +PVV+++ EFF S
Sbjct: 1   GNRRIRSVGELLQNQFRIGLTRMERVVRERMSIQDTATVTPQQLINIRPVVASIKEFFGS 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L  +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQTNPLGELTHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL+SSL+S+ RVN YGFIETPYR+V     KVT+ + YL+A EE+N  +AQANS L++D
Sbjct: 121 IGLISSLSSYGRVNRYGFIETPYRRVSWDTHKVTDKIDYLTADEEDNYVVAQANSPLNDD 180

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           GSF  ++V  R   E I V  +K+D++D SPKQVV++A + IPFLENDDSNR LMG NMQ
Sbjct: 181 GSFVNDVVMARAEEENIEVSIDKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQ 240

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL++  AP VGTG+E   A  +G A++A  AG+VE VDA  I +R  +  LD    
Sbjct: 241 RQAVPLIQPHAPLVGTGIEYKAAHDAGDAVIADHAGVVEYVDAREIRVRREDATLDK--- 297

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               Y+LMKF+RSN     NQ P+V+VGD V  ++I+ADGP+ + G+LALG+N L+AFM 
Sbjct: 298 ----YKLMKFRRSNAGKNYNQTPIVRVGDRVDADEILADGPAMEGGELALGQNPLIAFMT 353

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYNFED++ I+ER+V +DV+TSIHIEE +  ARDTKLGPEEITR+IPNV E+ LKN+D
Sbjct: 354 WDGYNFEDAIAINERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALKNLD 413

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GII +GAEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 414 EFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGG 473

Query: 938 TVVDVRIFNRHGID 951
            V +V+I+ R G D
Sbjct: 474 IVQNVKIYTREGGD 487



 Score =  281 bits (720), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 119/438 (27%), Positives = 176/438 (40%), Gaps = 85/438 (19%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +  + +        KN ++  I+ VG  V   D ++          +   +  L A    
Sbjct: 296  DKYKLMKFRRSNAGKNYNQTPIVRVGDRV-DADEILADGPAMEGGELALGQNPLIAFMTW 354

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI------SVEREQIELLARDKD- 972
               +  D            V D    + H  + +  +            +I  +  D   
Sbjct: 355  DGYNFEDAIAIN----ERLVKDDVYTSIHIEEMDSEARDTKLGPEEITREIPNVGEDALK 410

Query: 973  --DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+      +  +IL G+    G         L   +  E  R    +      +
Sbjct: 411  NLDEFGIIRIGAEVKDGDILVGKVTPKGMTELSAEERLLHAIFGEKAR----EVRDTSLR 466

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V      +                 KI   + GD++ PGV ++V+V++A KR +Q GDKM
Sbjct: 467  VPHGGGGIVQNV-------------KIYTREGGDELAPGVNQMVRVYIAQKRKLQVGDKM 513

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG VS ++P EDMPF+ DGTP+DI+L+P+GVPSRMN+GQ+ + HLG A   LG 
Sbjct: 514  AGRHGNKGTVSIVIPEEDMPFMPDGTPIDIMLSPMGVPSRMNIGQVLDLHLGMAARELGI 573

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             + S + D   + DI                                          T +
Sbjct: 574  HVASPVFDGARDDDIWDALKEAGLPSDGK----------------------------TIL 605

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +DG                           TGE FD  + VG +Y +KL+HMV DK+++R
Sbjct: 606  YDG--------------------------RTGEAFDNRIAVGVMYYMKLSHMVDDKIHSR 639

Query: 1271 STGSYSLVTQQPLGGKSN 1288
            S G YSLVTQQPLGGK+ 
Sbjct: 640  SIGPYSLVTQQPLGGKAQ 657


>gi|326649342|gb|AEA02129.1| RNA polymerase beta subunit [Rhizobium borbori]
          Length = 310

 Score =  445 bits (1145), Expect = e-122,   Method: Composition-based stats.
 Identities = 200/311 (64%), Positives = 243/311 (78%), Gaps = 1/311 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEFDPPKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQSVFKSVFPITDFSGASMLEFVSYEFDPPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTMNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEILSTFY K  Y + G+ W  P +   L  G K+ + L+D DTGE VIE+GKKLT  
Sbjct: 181 DGEEILSTFYTKSTYERDGEGWRVPFNPQAL-KGTKIVADLIDADTGEVVIEAGKKLTPR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           LL+ L++KG+K L  T+D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +    
Sbjct: 240 LLRQLQDKGLKALKATNDELYGNYLAEDIVNYATGEIYLEAGDEIDEKTLPIILSNGFDG 299

Query: 344 IPILYVDSVNN 354
            P+L +D VN 
Sbjct: 300 NPVLGIDHVNV 310


>gi|331029431|gb|AEC49865.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6053]
          Length = 305

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 174/303 (57%), Positives = 227/303 (74%), Gaps = 1/303 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           SYD FLM++     R +E L+A F+S FPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SYDQFLMVDEPTAGRLDEALKAVFRSGFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGE Y EAG+ I EKSL  
Sbjct: 240 AGKKLTVRQARQLQEKGLKALRMSDEELVGXYLAEDLVNPKTGEXYAEAGEEITEKSLNV 299

Query: 336 IFH 338
           +  
Sbjct: 300 LXE 302


>gi|315360835|gb|ADU05391.1| RNA polymerase beta subunit [Sinorhizobium sp. CCBAU 05699]
          Length = 296

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 193/295 (65%), Positives = 237/295 (80%), Gaps = 1/295 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPI  FSGA+MLEFVSYEF+PPKFDV++C  RDLTYA PLK+TLRLI
Sbjct: 2   RPDEGLQAVFKSVFPIKDFSGASMLEFVSYEFEPPKFDVEECRQRDLTYAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQ++YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEDTGAKSIKDIKEQNVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 122 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + GD W  P    D + G K  S ++D +TGE V+E+GKKLT  LL+ L+
Sbjct: 182 ETFYTKSLYQRDGDGWRVPFQP-DALKGQKAVSEMIDAETGEVVVETGKKLTPRLLRQLQ 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           EKG+K L  T D L G Y+AED+VN ETGEIY+EAGD IDEK+L  I  +   +I
Sbjct: 241 EKGLKALKATDDDLYGNYLAEDVVNFETGEIYLEAGDEIDEKTLPVILEAGFDEI 295


>gi|35396495|gb|AAQ84767.1| RpoB [Bosea massiliensis]
          Length = 229

 Score =  445 bits (1144), Expect = e-122,   Method: Composition-based stats.
 Identities = 146/232 (62%), Positives = 176/232 (75%), Gaps = 3/232 (1%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWA  GLGK+I + ++ Y+   DI  LR+  + V       E I+  D++ ++ + +
Sbjct: 61   THLGWAAAGLGKQIGAALDAYRKGHDIKALRASFDAVYEDN---EIIASMDENELVEMGQ 117

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + GVP++TPVF+GA E  I  +L  A L  SGQS LYDG TGEPFDR VTVGYIYMLK
Sbjct: 118  NLRRGVPIATPVFNGAKEADIERLLEQAGLHSSGQSTLYDGRTGEPFDRKVTVGYIYMLK 177

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 178  LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 229


>gi|35396497|gb|AAQ84768.1| RpoB [Bradyrhizobium liaoningense]
          Length = 229

 Score =  444 bits (1143), Expect = e-122,   Method: Composition-based stats.
 Identities = 151/232 (65%), Positives = 179/232 (77%), Gaps = 3/232 (1%)

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
            A+KR IQ GDKMAGRHGNKG+VS+I+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI E
Sbjct: 1    AVKRKIQPGDKMAGRHGNKGVVSKIVPIEDMPFLEDGTHADIVLNPLGVPSRMNVGQILE 60

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            THLGWAC GLGK+I   ++ Y +  DI PL+  L+KV G     E I   +D+ +L +  
Sbjct: 61   THLGWACAGLGKRIGQTVDAYLSKQDIKPLKETLKKVYGED---ETIKSLNDNELLELGH 117

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                GVP++TPVFDGA E  I  ML++A LD SGQS +YDG TG+PFDR VTVGYIYMLK
Sbjct: 118  NLSRGVPIATPVFDGAKEADIEEMLKLAGLDASGQSTVYDGRTGDPFDRKVTVGYIYMLK 177

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            L+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY 
Sbjct: 178  LHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 229


>gi|118411129|ref|YP_874523.1| DNA-directed RNA polymerase beta chain [Thalassiosira pseudonana]
 gi|125987645|sp|A0T0R1|RPOB_THAPS RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|116739876|gb|ABK20746.1| DNA-directed RNA polymerase beta chain [Thalassiosira pseudonana]
          Length = 1386

 Score =  444 bits (1142), Expect = e-122,   Method: Composition-based stats.
 Identities = 172/584 (29%), Positives = 259/584 (44%), Gaps = 64/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       +L+   P  G   E+ + +   MV       +  S+   +  ++     
Sbjct: 837  MGSNMQRQSVPLLLPQKPIVGTGLENQIALDSGMVINAQRAGIVESVTANKIIILED--- 893

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G                  I+   I+  G +V  G +L         S ++  + +L A
Sbjct: 894  SGRHYKYDLQKYQRSNQETCINHRPIVWEGEKVKSGQMLTDGPG-IISSELSLGQNVLVA 952

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     V   +       R+ I+ +  +   E+    +      D Q
Sbjct: 953  YMPWQGYNFEDAILINERLVYEDIFTSIHIERYEIEIDRTAEMSEQTTNNIPNLSISDVQ 1012

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             + +  I +              P       ++  D   + P S+  +            
Sbjct: 1013 NLNEDGIVT--------IGTFVKPGDILVGKIIPKDDSEQLPESKLLRAIFG-------- 1056

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGDKMAGRH 1094
               K   +TS  + E  +   IE + +            +++F+A  R IQ GDK+AGRH
Sbjct: 1057 AKAKGVRDTSFRMPEGEYGRVIETLTFNRRTKLAYKFEKIQIFIAQIRKIQVGDKIAGRH 1116

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKGI+SRILP +DMPFL DGTPVDI+LNPLGVPSRMNVGQ++E  LG A   L ++ K 
Sbjct: 1117 GNKGIISRILPRQDMPFLPDGTPVDIILNPLGVPSRMNVGQLYECLLGLAGHKLNRRFKI 1176

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            L  D               ++ G       I+     + +   E W              
Sbjct: 1177 LPFD---------------EMYGPEVSRILINKKLRQASIENDEAW-------------- 1207

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                      + +    G+ +L DG TG+ FD P+TVG  YMLKL H+V DK+++R+TG 
Sbjct: 1208 ----------LFNPYSPGKMVLLDGRTGKEFDNPITVGNAYMLKLIHLVDDKMHSRATGP 1257

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW ++ +GA++ L+E+LTIKSDD+ GR     SI+ 
Sbjct: 1258 YSLVTQQPLGGKAQHGGQRFGEMEVWALEGFGASFTLKELLTIKSDDMQGRNETLNSIIK 1317

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            G     +G PESF VLV+E++++GL +        +S +  EI 
Sbjct: 1318 GQPIPTSGVPESFKVLVQELRSIGLDLSTYRIDEFSSNQSYEIE 1361



 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 287/760 (37%), Positives = 428/760 (56%), Gaps = 45/760 (5%)

Query: 225  SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG- 283
            +++I S+ Y    +      + +  +  +       S + +  +  + +    K +    
Sbjct: 364  NDKIKSSLYFTNSFK-ELIKFKYNFTKKEKDKKRNQSQATIFKNKTKYLKTKSKIIQYKD 422

Query: 284  --LLKSLKEKGVKFLGITSDCLCGLY---------------VAEDIVNGETGEIYIEAGD 326
              L++ + +K  +   + +  L   Y               +++  +  +  EI I+   
Sbjct: 423  DHLIRDIYKKKYEEKELYTATLIPEYGSWIRFGFQKNTKINISKYPIKNQEDEIIIQLDK 482

Query: 327  VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            V  +  +  +    + D+ I      +   Y    ++T+             +++R    
Sbjct: 483  VTQKPIIHLLKEMGVTDLEICQNLQNSEFFYFNKPILTNSIHQPN-------KLLRFNLN 535

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
              +    S F+ + FD   Y L  +GR K+N RL+++    +  I  EDI AII  L+ L
Sbjct: 536  KNYYKNISEFSRI-FDPSYYRLGKIGRSKLNNRLDINLSKRITTITYEDIFAIIDKLITL 594

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               K   DDID+L NRRVRSVGE+L+N +R+G  R+ R ++ + +      +      + 
Sbjct: 595  STAKQISDDIDHLKNRRVRSVGELLQNLFRIGFQRLLRKLRSQTNKTYSSQLS-----SF 649

Query: 507  KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
              V + + EFF +SQLSQ  +  N LS +TH RR+S LG GG  R R    +RD+HP+HY
Sbjct: 650  NIVGATIKEFFGASQLSQYMDQTNPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHY 709

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEEN 624
            GRICP ET EG N+GL++SLT+ ARVN  GF+ETP+ +V +GKV    + +YL+A  E+ 
Sbjct: 710  GRICPIETPEGQNVGLIASLTTCARVNESGFLETPFWRVINGKVIKNRNPIYLTADIEDF 769

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
              IA A+ S +++   T+ L+  R   + + V   ++DFI  SP QVVS+AASLIPF E+
Sbjct: 770  YKIAPADISTNQENYLTKNLIPVRYKQDFLTVTPSEVDFIAVSPIQVVSVAASLIPFFEH 829

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
            DD+NR LMG NMQRQ+VPLL  + P VGTG+E+ +A  SG  I A+RAGIVE V A +I+
Sbjct: 830  DDANRALMGSNMQRQSVPLLLPQKPIVGTGLENQIALDSGMVINAQRAGIVESVTANKII 889

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            I    G           Y L K+QRSNQ TC+N RP+V  G++V+   ++ DGP     +
Sbjct: 890  ILEDSGR-------HYKYDLQKYQRSNQETCINHRPIVWEGEKVKSGQMLTDGPGIISSE 942

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            L+LG+N+LVA+MPW GYNFED++LI+ER+V ED+FTSIHIE +E+    T    E+ T +
Sbjct: 943  LSLGQNVLVAYMPWQGYNFEDAILINERLVYEDIFTSIHIERYEIEIDRTAEMSEQTTNN 1002

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            IPN+S   ++N++E GI+ +G  V PGDILVGKI PK +S   PE KLLRAIFG KA  V
Sbjct: 1003 IPNLSISDVQNLNEDGIVTIGTFVKPGDILVGKIIPKDDSEQLPESKLLRAIFGAKAKGV 1062

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            RDTS R+P G  G V++   FNR    + + +   E+ QI
Sbjct: 1063 RDTSFRMPEGEYGRVIETLTFNR----RTKLAYKFEKIQI 1098



 Score =  139 bits (350), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 42/144 (29%), Positives = 64/144 (44%), Gaps = 22/144 (15%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           +PD IE+Q+ S+  F+           +GL     +   I  FS     +L    Y    
Sbjct: 7   LPDFIEMQRVSFCWFIA----------QGLNEELNTFSRIYDFSQNTEYVLFGQEYSLVK 56

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLPLMTKDG 142
           P +++         Y+  L I L             K    IK  S + + +LPLMT   
Sbjct: 57  PIYNIVRAKKYTANYSAQLVIPL---------EVRNKKTNIIKYHSKFPIINLPLMTSSA 107

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFD 166
           TFVI G +R++VSQ+ RSPG++F+
Sbjct: 108 TFVINGCERVIVSQIIRSPGVYFE 131


>gi|212292057|gb|ACJ24143.1| RNA polymerase beta subunit [Rhizobium sp. CCBAU 83477]
          Length = 300

 Score =  443 bits (1139), Expect = e-121,   Method: Composition-based stats.
 Identities = 195/296 (65%), Positives = 236/296 (79%), Gaps = 1/296 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 5   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 64

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 65  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 124

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 125 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 184

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 185 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 243

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           +KG+K L    D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP
Sbjct: 244 DKGLKALKAGDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILSNGFDEIP 299


>gi|226348059|gb|ACO50383.1| RNA polymerase beta subunit [Agrobacterium rhizogenes]
          Length = 292

 Score =  442 bits (1138), Expect = e-121,   Method: Composition-based stats.
 Identities = 194/291 (66%), Positives = 238/291 (81%), Gaps = 1/291 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQ+ FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+T
Sbjct: 2   PKGGRPDEGLQSVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEILSTFY K +Y + GD W  P +A  L  GAK  + ++D DTGE V+E GKKLT  LL
Sbjct: 182 EEILSTFYTKSLYERSGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVEGGKKLTPRLL 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           + L++KG+K L  T + L GL++AEDIVN +TGEIY+EAGD IDEK+L  I
Sbjct: 241 RQLQDKGLKALKATDEDLYGLFLAEDIVNFQTGEIYLEAGDEIDEKTLPVI 291


>gi|299830351|ref|YP_003734566.1| RNA polymerase beta subunit [Kryptoperidinium foliaceum]
 gi|297385053|gb|ADI40351.1| RNA polymerase beta subunit [Kryptoperidinium foliaceum]
          Length = 1394

 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 169/581 (29%), Positives = 258/581 (44%), Gaps = 58/581 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI-EEFEVMARDTKLGP 858
                       ++    P  G   E+ + I   M      + I        +    K+G 
Sbjct: 845  MGSNMQRQSVPLIFPQKPIVGTGLENQIAIDSGMTLNAQVSGIVSSVTANKIVIQNKVGK 904

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            + I +    +       I+   I+  G ++  G IL         S +   + +L A   
Sbjct: 905  KIIYKLQKYLRSNQQTCINHRPIVWKGEKIKSGQILTDGP-AITTSELALGQNVLVAYMP 963

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   +       R+ ID +  S + E+    +      +     
Sbjct: 964  WQGYNFEDAILISERLVYDDIFTSIHIERYKIDIDRNSETSEQTMKMIPNLSLSE----- 1018

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                    ++ L     V+     K   +L   +IS     Q  +  +         + +
Sbjct: 1019 --------VKHLNNDGIVTVGTFVKPGDILVGKVISNNTAEQLPESKLLRAIFGAKAKGV 1070

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            K     S  + +  +   IE + +            + VF+A  R IQ GDK+AGRHGNK
Sbjct: 1071 KDN---SYRMPDGEYGRVIETVTFNRRTKLTYKFEKIYVFIAQIRKIQVGDKIAGRHGNK 1127

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+SRIL  +DMPFL DGTP+D++LNPLGVPSRMNVGQ++E  LG A   L  + K L  
Sbjct: 1128 GIISRILARQDMPFLPDGTPIDVILNPLGVPSRMNVGQLYECLLGLAGDKLNSRFKILPF 1187

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D               ++ G       I+     + ++  E W                 
Sbjct: 1188 D---------------EMYGLEMSRILINKKLRQASIKRNEGW----------------- 1215

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                   + +    G+ +L DG TG+ F+ P+TVG  YMLKL H+V DK++AR+TG YSL
Sbjct: 1216 -------LFNPYAPGKMVLIDGRTGKEFENPITVGNAYMLKLIHLVDDKIHARATGPYSL 1268

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPL GK+  GGQR GEMEVW ++ +GAA+ L+E+LTIKSDD+ GR     +IV G  
Sbjct: 1269 ITQQPLRGKAQHGGQRFGEMEVWALEGFGAAFTLKELLTIKSDDMQGRNETLNAIVKGQK 1328

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              + G PESF VL++E++++GL +        +S+K  E+ 
Sbjct: 1329 IPQFGIPESFKVLLQELRSIGLDMSTYKIENFSSSKRYEVE 1369



 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 272/723 (37%), Positives = 408/723 (56%), Gaps = 24/723 (3%)

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
            P I +S         +   +           +   T   + +   ++ +   K  +EK +
Sbjct: 388  PTIYFSNSLKEQFKYVFGKEKFTYKPERHKYLKTKTQFLLYQKDHEIKTNYHKKYEEKDL 447

Query: 294  KFLGITSDCLCGLYV---AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                +  +   G ++    +  +     +  I+  +      L++I    I  + +L   
Sbjct: 448  YSATLIPEY--GSWIRFGFQKNMKINPYKYPIKNQEEEIVIQLDKINQKPI--LSLLKEM 503

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALL---DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + +    +N   +D     + +L+     ++ +   D               FD + Y 
Sbjct: 504  GLTDLEIYQNLHFSDFFYFTQPSLINSKQFHQPLARFDFDLEYFKNISEFSRIFDPNYYR 563

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            L  VGRVKMN  LNL   + ++ I  EDI AI   L++L   K   DDID+L NRRVRSV
Sbjct: 564  LGRVGRVKMNHHLNLQLSERLQIITYEDIFAITDKLINLTISKAVPDDIDHLKNRRVRSV 623

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            GE+L+N +R+G  R+ R ++ + + VD   ++  +++N     + + EFF SSQLSQ  +
Sbjct: 624  GELLQNLFRIGFQRLVRKLRNQTNKVDSGYLLSFNIVN-----ATIREFFGSSQLSQYLD 678

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N LS +TH RR+S LG GG  R R    +RD+HP+HYGRICP ET EG N+GL++SLT
Sbjct: 679  QTNPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVGLIASLT 738

Query: 588  SFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            + ARVN  GF+ETP+ +V +GKV  T + +YL+A  E+   IA A+ + + +    +  +
Sbjct: 739  TCARVNKLGFLETPFWRVINGKVIKTGNPIYLTADIEDLYKIAPADIATNHENYLVKNSI 798

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R   + + V   ++DFI  S  QVVS+AASLIPF E+DD+NR LMG NMQRQ+VPL+ 
Sbjct: 799  PIRYKQDFVNVSPSEVDFIAISTVQVVSVAASLIPFFEHDDANRALMGSNMQRQSVPLIF 858

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             + P VGTG+E+ +A  SG  + A+ +GIV  V A +IVI++  G          IY+L 
Sbjct: 859  PQKPIVGTGLENQIAIDSGMTLNAQVSGIVSSVTANKIVIQNKVGKKI-------IYKLQ 911

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            K+ RSNQ TC+N RP+V  G++++   I+ DGP+    +LALG+N+LVA+MPW GYNFED
Sbjct: 912  KYLRSNQQTCINHRPIVWKGEKIKSGQILTDGPAITTSELALGQNVLVAYMPWQGYNFED 971

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            ++LISER+V +D+FTSIHIE +++         E+  + IPN+S   +K+++  GI+ VG
Sbjct: 972  AILISERLVYDDIFTSIHIERYKIDIDRNSETSEQTMKMIPNLSLSEVKHLNNDGIVTVG 1031

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
              V PGDILVGK+     +   PE KLLRAIFG KA  V+D S R+P G  G V++   F
Sbjct: 1032 TFVKPGDILVGKVISNNTAEQLPESKLLRAIFGAKAKGVKDNSYRMPDGEYGRVIETVTF 1091

Query: 946  NRH 948
            NR 
Sbjct: 1092 NRR 1094



 Score =  136 bits (343), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 44/176 (25%), Positives = 70/176 (39%), Gaps = 27/176 (15%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV- 77
           K   I  +PD + +Q+ S+  F+           +GL         I  FS     E+V 
Sbjct: 4   KMNYINALPDFLAMQRVSFCWFIT----------QGLNEELALFSKIHDFSQNT--EYVM 51

Query: 78  ---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MG 133
               Y    P + +         Y   L I +             K+I  I+  + + + 
Sbjct: 52  FGEEYNLIKPPYSLLIARKYSGNYRAQLVIPI---------EVRNKTINSIRYHNQFPII 102

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG-RASLSGKLLYACRIIPDQ 188
            LPLMT   TF+I G +R++VSQ+ RSPGI+F+  K  +     K   +  I   +
Sbjct: 103 TLPLMTTYATFIINGCERVIVSQIIRSPGIYFEKPKNQKTQKQFKRKLSTDIHKLR 158


>gi|212292063|gb|ACJ24146.1| RNA polymerase beta subunit [Rhizobium sp. CCBAU 83309]
          Length = 301

 Score =  442 bits (1137), Expect = e-121,   Method: Composition-based stats.
 Identities = 193/294 (65%), Positives = 233/294 (79%), Gaps = 1/294 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 6   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 65

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 66  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 125

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 126 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 185

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 186 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 244

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           +KG+K L    D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +    
Sbjct: 245 DKGLKALKAGDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILSNGSTS 298


>gi|302892877|ref|XP_003045320.1| hypothetical protein NECHADRAFT_70495 [Nectria haematococca mpVI
            77-13-4]
 gi|256726245|gb|EEU39607.1| hypothetical protein NECHADRAFT_70495 [Nectria haematococca mpVI
            77-13-4]
          Length = 1261

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 235/1441 (16%), Positives = 427/1441 (29%), Gaps = 324/1441 (22%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFSG------AAMLE 75
            L+  Q  S+D F              +Q        I+       +  G         ++
Sbjct: 39   LVSQQTDSFDEFTQTT----------IQDLVNEYSVISLDQPNPPSPPGVSIALRRYEIK 88

Query: 76   FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR------------LIVFDV 113
            F S     P               +C  R+LTYA PL I +             L   D 
Sbjct: 89   FGSVMVSRPTISETDGTVTSLLPYECRDRNLTYASPLYIKITKKVSVAVEKEVPLHEMDE 148

Query: 114  DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
            D+    K   +   + ++  +L    + G                         D+G+A 
Sbjct: 149  DQQAEYKRTGENPTKLVW--EL---EESG------------------------DDEGKAD 179

Query: 174  LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
                             W       KD++ V      K+P+        + SE   + F 
Sbjct: 180  D---------------SW-------KDMVFV-----GKLPIMVKSKICHLSSEHDDNLFL 212

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG------------EQVIESGKKLT 281
                   +G ++    S   L+   + ++++V +                  +E G +L 
Sbjct: 213  VNECPYDQGGYFVINGSEKVLIAQERSAANIVQVFKKAQPSPYTYTAEIRSALEKGSRLI 272

Query: 282  SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            S ++  L  KG    G     +    +     +     ++   G V DE  L  I +   
Sbjct: 273  SSMMLKLYGKGDSARGGFGQTI-HTTLPFVKADLPVAIVFRALGVVSDEDILNHICYDRT 331

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +      A+          +DR+ AL  I +                      
Sbjct: 332  DSQMLEMLRPCIEEAF--------CVQDREVALDFIGKR--------------------G 363

Query: 402  DSDKYDLSTVGRVKMNMRL-------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            + D+  L    RV++   +       ++   +     +   +  ++  L+    G+   D
Sbjct: 364  NRDQAGLGREKRVRVAKDILQKETLPHISQSEGSETRKAFFLGYMVHKLLQCALGRREPD 423

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSA 512
            D D+ G +R+   G +L   +R  + RM   +   +               I    + + 
Sbjct: 424  DRDHFGKKRLDLAGPLLAKLFRGIVRRMNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNG 483

Query: 513  VCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            +     +               +SQ+       S ++H RR +      + R     + R
Sbjct: 484  LKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKPR 539

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYL 617
             +H TH+G +CPAET EG   GLV +L+    V+     E     + +   +V  +   L
Sbjct: 540  QLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINRGMEVVEEYEPL 599

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAA 676
                    ++      +  D       V        +      + D  D   K       
Sbjct: 600  RYPHATKIFVNGVWCGVHSDPKHLVSQVLDTRRKSYLQYEVSLVRDIRDREFKVFSDAGR 659

Query: 677  SLIPFLENDD-----SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
             + P           S        + +  V  L  E           +           R
Sbjct: 660  VMRPVFTVQQEDDHESGIAKGALVLTKDLVNKLAKEQAEPPEDPSMKIGWE-----GLIR 714

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK---FQRSNQNTCVNQRPLVKVGDEV 788
            AG +E +DA       +    +     +D+YR+ K       +     N+R   K     
Sbjct: 715  AGTIEYLDAEEEETAMICMTPED----LDLYRMQKAGYVVDDDNTDDPNRRLKTKTNPTT 770

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                     PS  LG       +  + +P+  +N          M  + +     +  + 
Sbjct: 771  HMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYS 821

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                            +  +             +       +  
Sbjct: 822  RRM---------------------------DTMANILYYPQKPLATTRSMEFLKFRELPA 854

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    +F R   D+ ++      E  E   
Sbjct: 855  GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTEVFEKPF 913

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +           +       +  G           K+  +  +      R+   Q     
Sbjct: 914  QQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTTVHQRRDIS 973

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +      + +                       ++ VKV V   +  Q GD
Sbjct: 974  TPLRSTENGIVDSVIVTVNA--------------------DNVKYVKVRVRTTKIPQIGD 1013

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L       
Sbjct: 1014 KFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHAIPSRMTIAHLIECLLSKVSTLE 1073

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +                                                       +T
Sbjct: 1074 GMEGD-----------------------------------------------------AT 1080

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F     ++++ +LR       G  I+Y+G TG      V  G  Y  +L HMV DK++
Sbjct: 1081 P-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLRAQVFFGPTYYQRLRHMVDDKIH 1139

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD    R  V
Sbjct: 1140 ARARGPVQIMTRQPVEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSD--AFRVHV 1197

Query: 1329 YESIVAG---------------------NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             E  V G                         +   P +  +L +E+Q++ ++  +  SR
Sbjct: 1198 CE--VCGLMTPIANLSKQSFECRPCKNKTKIAQIHIPYAAKLLFQELQSMNIAARMFTSR 1255

Query: 1368 T 1368
            +
Sbjct: 1256 S 1256


>gi|212292067|gb|ACJ24148.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
          Length = 301

 Score =  442 bits (1136), Expect = e-121,   Method: Composition-based stats.
 Identities = 192/294 (65%), Positives = 233/294 (79%), Gaps = 1/294 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 6   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 65

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 66  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 125

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 126 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 185

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 186 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 244

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +
Sbjct: 245 DKGLKALKAADDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGVILANGFDE 298


>gi|299830556|ref|YP_003735004.1| DNA-directed RNA polymerase beta subunit [Durinskia baltica]
 gi|297384920|gb|ADI40219.1| DNA-directed RNA polymerase beta subunit [Durinskia baltica]
          Length = 1385

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 170/581 (29%), Positives = 258/581 (44%), Gaps = 58/581 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI-EEFEVMARDTKLGP 858
                       ++    P  G   E+ + +   M      + I        +    K G 
Sbjct: 836  MGSNMQRQSVPLIFPQKPIVGTGLENQIAVDSGMTLNAQVSGIVSSVTANKIIIKDKFGK 895

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            + I +    +       I+   I+  G  +  G IL         S +   + LL A   
Sbjct: 896  KIIYKLQKYLRSNQQTCINHRPIVWKGESIKSGQILTDGPAITN-SELALGQNLLVAYMP 954

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  L     V   V       R+ I+ +  S   E+    +      + + + 
Sbjct: 955  WQGYNFEDAILISERLVYNDVFTSIHIERYKIEIDRNSEMSEQTTKMIPNLSLSEVKHLN 1014

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D  I      ++ G     G        V+S++   + P S+  +     +         
Sbjct: 1015 DDGI------VMVGTFVKPGDILV--GKVISNNTAEQLPESKLLRAIFGAKAKGVK---- 1062

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGV-LRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                + S  + +  +   IE + +            + VF+A  R IQ GDK+AGRHGNK
Sbjct: 1063 ----DNSYRMPDGEYGRVIETVTFNRRTKLTYKFEKIYVFIAQIRKIQVGDKIAGRHGNK 1118

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+SRIL  +DMPFL DGTP+DI+LNPLGVPSRMNVGQ++E  LG A   L  + K L  
Sbjct: 1119 GIISRILARQDMPFLPDGTPIDIILNPLGVPSRMNVGQLYECLLGLAGDKLNSRFKILPF 1178

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D               ++ G       I+     + ++  + W                 
Sbjct: 1179 D---------------EMYGLEMSRILINKKLRQASMKRNQSW----------------- 1206

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                   + +    G+ +L DG TG+ F+ P+TVG  YMLKL H+V DK++AR+TG YSL
Sbjct: 1207 -------LFNPYAPGKMVLIDGRTGKEFENPITVGNAYMLKLIHLVDDKIHARATGPYSL 1259

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQPL GK+  GGQR GEMEVW ++ +GAA+ L+E+LTIKSDD+ GR     +IV G  
Sbjct: 1260 ITQQPLRGKAQHGGQRFGEMEVWALEGFGAAFTLKELLTIKSDDMQGRNETLNAIVKGQK 1319

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              + G PESF VL++E++++GL +        +S+K  EI 
Sbjct: 1320 IPQFGIPESFKVLLQELRSIGLDMSTYKIEKFSSSKRYEIE 1360



 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 271/727 (37%), Positives = 406/727 (55%), Gaps = 32/727 (4%)

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
            P I +S         +   +           +   T   + +   ++ +   K  +EK +
Sbjct: 379  PTIYFSNSLKDQFKYVFGKNKFTYKSERHKYLKTKTQLLLYKKDHEIKTNYHKKYEEKDL 438

Query: 294  KFLGITSDCL----------CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                +  +              +   +  +  +  E+ I+   +  +  L  +    + D
Sbjct: 439  YSATLIPEYGSWIRFSFQKNIKINPYKYPIKNQEDEVIIQLDKINQKPVLSLLKEMGLTD 498

Query: 344  IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            + I + +    + +  N  +   +K  K       + +   + +             FD 
Sbjct: 499  LEI-HQNLQYADFFYFNKPLVINSKQFK-------QPISRFESNLEYFKNISEFSRIFDP 550

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + Y L  VGR+K+N RLNL   + ++ I  EDI AI   L++L   K   DDID+L NRR
Sbjct: 551  NYYRLGRVGRLKINNRLNLQLSERLQIITYEDIFAITDKLINLTISKAVPDDIDHLKNRR 610

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            VRSVGE+L+N +R+G  R+ R ++ + + VD   ++  +++N     + + EFF SSQLS
Sbjct: 611  VRSVGELLQNLFRIGFQRLVRKLRNQTNKVDAGYLLSFNIVN-----ATIREFFGSSQLS 665

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  +  N LS +TH RR+S LG GG  R R    +RD+HP+HYGRICP ET EG N+GL+
Sbjct: 666  QYLDQTNPLSSLTHRRRISGLGPGGFDRDRISFAVRDIHPSHYGRICPIETPEGQNVGLI 725

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +SLT+ ARVN  GF+ETP+ +V +GKV  T + +YL+A  E+   IA A+ + + +    
Sbjct: 726  ASLTTCARVNKLGFLETPFWRVINGKVIKTGNPIYLTADIEDLYKIAPADIATNSENYLV 785

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +  +  R   + I V   ++DFI  S  QVVS+AASLIPF E+DD+NR LMG NMQRQ+V
Sbjct: 786  KNTIPIRYKQDFINVSPAEVDFIAISTVQVVSVAASLIPFFEHDDANRALMGSNMQRQSV 845

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL+  + P VGTG+E+ +A  SG  + A+ +GIV  V A +I+I+   G          I
Sbjct: 846  PLIFPQKPIVGTGLENQIAVDSGMTLNAQVSGIVSSVTANKIIIKDKFGKKI-------I 898

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y+L K+ RSNQ TC+N RP+V  G+ ++   I+ DGP+    +LALG+N+LVA+MPW GY
Sbjct: 899  YKLQKYLRSNQQTCINHRPIVWKGESIKSGQILTDGPAITNSELALGQNLLVAYMPWQGY 958

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFED++LISER+V  DVFTSIHIE +++         E+ T+ IPN+S   +K++++ GI
Sbjct: 959  NFEDAILISERLVYNDVFTSIHIERYKIEIDRNSEMSEQTTKMIPNLSLSEVKHLNDDGI 1018

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG  V PGDILVGK+     +   PE KLLRAIFG KA  V+D S R+P G  G V++
Sbjct: 1019 VMVGTFVKPGDILVGKVISNNTAEQLPESKLLRAIFGAKAKGVKDNSYRMPDGEYGRVIE 1078

Query: 942  VRIFNRH 948
               FNR 
Sbjct: 1079 TVTFNRR 1085



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 44/176 (25%), Positives = 70/176 (39%), Gaps = 27/176 (15%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV- 77
           K   I  +PD + +Q+ S+  F+           +GL         I  FS     E++ 
Sbjct: 4   KINYINALPDFLAMQRVSFCWFIT----------QGLNEELALFSKIQDFSQNT--EYIM 51

Query: 78  ---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MG 133
               Y    P + +         Y   L I +             K+I  I+ Q+ + + 
Sbjct: 52  FSEEYSLIKPPYSLLIARKYSGNYKAQLVIPI---------EVRNKTINSIRYQNQFPII 102

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG-RASLSGKLLYACRIIPDQ 188
            LPLMT   TF+I G +R++VSQ+ RSPGI+F+  K  +     K      I   +
Sbjct: 103 TLPLMTTYATFIINGCERVIVSQIIRSPGIYFEKSKNQKNQKQFKRKLTTDIHKLR 158


>gi|212292061|gb|ACJ24145.1| RNA polymerase beta subunit [Rhizobium fabae]
          Length = 304

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 192/294 (65%), Positives = 233/294 (79%), Gaps = 1/294 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 8   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 67

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 68  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 127

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 128 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 187

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 188 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 246

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +
Sbjct: 247 DKGLKALKAGDDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDE 300


>gi|222093443|gb|ACM43498.1| RNA polymerase beta subunit [Mycoplasma gallopavonis]
          Length = 969

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 298/843 (35%), Positives = 461/843 (54%), Gaps = 61/843 (7%)

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF----DSKDIIHVRIDRRRKV 212
           L RSPG ++     R   S  L     I+P  G W+++       S D + V++D+ + +
Sbjct: 1   LIRSPGAYYGLGV-RNKQSDDLFNKLEILPRIGSWLEVSHKVTSSSIDTVKVKVDKNKNI 59

Query: 213 PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA---DLMVGAKVSSSLVDIDT 269
            + +FL + G+ ++ +   F    +  +         ++    +  +          +  
Sbjct: 60  NLATFLGSFGLTAKTMEELFGTSDLLLETLKKDKIMSNSELSPEEKIDMCQEELFRGLRK 119

Query: 270 GEQVIESGK-KLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETGEI 320
           G+++ E  K  L  G+L   K   +   G           D +   Y+AED++   + E+
Sbjct: 120 GDRISEDAKLSLIPGILFDKKRYNLSETGRYMLNKKLSLVDRITNTYLAEDLIAKNSDEV 179

Query: 321 YIEAGDVIDEKSLEEIFH------SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
             + G  ID K  +EI         E   IP +  + V +    +N  +  + K  K  +
Sbjct: 180 LFKKGTFIDIKIAKEIQEKFESGILESVKIPKIDAEFVYHKVIKQNKDLKKRIKIIKVKV 239

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
               ++M  G      +                               D     +H+   
Sbjct: 240 YPSMKLMESGVDPILVIGN-----------------------------DPKSVEQHLLIS 270

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           DI+A I    +L  G G  DD D+L N+R+ SVGE+L+ Q  + L ++E+  +ER+ + +
Sbjct: 271 DIVAAINYYFNLTAGIGQDDDPDSLTNKRIVSVGELLEGQLSVALSKLEKITRERMGAKE 330

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            D V  +++ N K V + +  FF +S+LSQ  + +N L+ +++ RR+++LG GG+ R  A
Sbjct: 331 PDKVTAKNVTNNKLVTNQMKTFFNTSKLSQFMDQINPLAEVSNKRRVTSLGPGGLNRDTA 390

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-ND 613
             E+RDVH THYGRICP ET EG NIGL+ +  +FA+VN  GF++TPY KV +G V  ND
Sbjct: 391 QFEVRDVHSTHYGRICPIETPEGPNIGLILNYATFAKVNELGFLKTPYFKVNNGVVDYND 450

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YL+A EE     AQ++  +DE+       +  R     I+     +DFI+ S KQ+VS
Sbjct: 451 VRYLTAAEEIGYSFAQSSVRVDENNKIVVPTLTVRRDYNYIIATPYDVDFIEVSSKQIVS 510

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEAP V TG+E+ +AK S   IVAK AG
Sbjct: 511 VAAAAIPFLENDDANRALMGSNMQRQAVPLLQAEAPLVATGIEADIAKYSSYNIVAKNAG 570

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V  VD  +I I+      +      D Y L  F+RSNQ T + QRP+V VG +V + D+
Sbjct: 571 EVVFVDGSKIHIKY-PSPKEEGKFITDKYTLRNFERSNQGTLIQQRPIVHVGQKVEKGDL 629

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           + DG S   G++ALG+N+LV F  W+GYN+ED+++I+ER+V +DVFTSIHIEE  +  R 
Sbjct: 630 LVDGSSFKDGEMALGKNLLVGFSTWNGYNYEDAVIINERLVKDDVFTSIHIEEQTIQFRS 689

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           ++ G +E+T DIPNVS+  L+++DE GI+ VG+EV PGD+LVG+ +PKGE   + EEKLL
Sbjct: 690 SRAGDDELTNDIPNVSKYSLRHLDENGIVRVGSEVMPGDVLVGRTSPKGEENPSQEEKLL 749

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-------GIDKNERSISVEREQIEL 966
            AI  +++ + +DTSL+V +G +GTV+ V + +R        GIDK  +    ++ +I++
Sbjct: 750 MAILQQRSSNKKDTSLKVKNGHNGTVIHVEVLSRDKGDVLEEGIDKIVKVSIAQKRKIKV 809

Query: 967 LAR 969
             +
Sbjct: 810 GDK 812



 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 133/420 (31%), Positives = 184/420 (43%), Gaps = 67/420 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  GD+LV   + K +  M   + LL         +  D  +     V   V 
Sbjct: 617  IVHVGQKVEKGDLLVDGSSFK-DGEMALGKNLLVGFSTWNGYNYEDAVIINERLVKDDVF 675

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E    +          LD N   R+   +   + + G  
Sbjct: 676  -TSIHIEEQTIQFRSSRAGDDELTNDIPNVSKYSLRHLDENGIVRVGSEVMPGDVLVGRT 734

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++          +L           
Sbjct: 735  SPKGEENPSQE--EKLLMAILQQRSSNKKDTSLKVKNGHNGTVIHVEVLSRD-------- 784

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDK+AGRHGNKG++S +LP EDMP+L+DGTP+D+
Sbjct: 785  -KGDVLEEGIDKIVKVSIAQKRKIKVGDKVAGRHGNKGVISIVLPEEDMPYLEDGTPLDV 843

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   LG K  +   D     DI               
Sbjct: 844  MLNPQGVPSRMNIGQILEIHLGMAARKLGVKFVTPSFDGVKKPDIEVALEEAG------- 896

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + IL D +
Sbjct: 897  ------------------------------------------LDKSG-----KQILIDPI 909

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 910  TGRKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 969


>gi|323343166|ref|ZP_08083397.1| DNA-directed RNA polymerase subunit beta [Erysipelothrix
            rhusiopathiae ATCC 19414]
 gi|322463230|gb|EFY08425.1| DNA-directed RNA polymerase subunit beta [Erysipelothrix
            rhusiopathiae ATCC 19414]
          Length = 1372

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 321/768 (41%), Positives = 438/768 (57%), Gaps = 63/768 (8%)

Query: 232  FYPKIVYSQRG---DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG----L 284
            F     Y             L   + + G  ++S + DI  G  V E G  +T       
Sbjct: 316  FLDPRRYDLNKAGRYKIHKKLEVYNRVNGTVLTSDIKDI-NGNVVFEKGTHITRRDDVLK 374

Query: 285  LKSLKEKGVKFLGITSDCLCG----LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
            L+ +  +G          +        +  D      G I  +  D  D +  E      
Sbjct: 375  LREVLREGGHMNVFPLKNIFSAPDVRDITVDGTIHLVGRILSKDIDGDDFEF-ERGTVLT 433

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD--------------- 385
              DI  L  + +     I    V     +    L    R+   G                
Sbjct: 434  ASDIETLKGEDIQIYTGIMAKEVVVTKDNVWAVLNYSQRLYTVGRMLDASGSDMMSAKGN 493

Query: 386  ------------VSTFSVAESMFNFLFFD------------SDKYDLSTVGRVKMNMRLN 421
                               E +      D             + +        ++   + 
Sbjct: 494  LVADRFTPNYNVPKINKTNEKLIVDSLEDGPVTMWLVGAAMQELFVAQEDDETEIVKIIG 553

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
            +D   +   I   DI A     ++  +G G  DDID LGNRR+R+VGE+++NQ+R+GL R
Sbjct: 554  IDPLLEKTTIVASDIYATYSYFLNFIDGVGNEDDIDQLGNRRIRTVGELIQNQFRIGLSR 613

Query: 482  MERSIKERISSV-DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            MER +KER+S   D  ++ P++L N +P+ + V EFF SSQLSQ  + +N L+ +T+ RR
Sbjct: 614  MERVVKERMSISSDSSNLTPKNLTNVRPLTAMVKEFFSSSQLSQFMDQLNPLAELTNKRR 673

Query: 541  LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            +SALG GG+ R RAG E+RDVH +HYGRICP ET EG NIGL+S+LTS+ +++ YGFI+T
Sbjct: 674  ISALGPGGLTRDRAGFEVRDVHTSHYGRICPIETPEGPNIGLISNLTSYGKIDKYGFIQT 733

Query: 601  PYRKVC-DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            PYR V  DGKVT D++YLSA +E    IAQAN    +D     E V  R  GE IL  R+
Sbjct: 734  PYRIVTPDGKVTEDIIYLSADDEFEYVIAQANEV--QDHKLVNEEVVVRYRGENILAHRD 791

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             ++ ID SPKQ+VS+A + IPFLENDD++R LMG NMQRQAVPLLK  +PFVGTG+E  +
Sbjct: 792  TVELIDVSPKQIVSVATAAIPFLENDDASRALMGANMQRQAVPLLKPNSPFVGTGIEHRI 851

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            AK SG+A++    GIV  VDA R+++    G           Y L KF+RSNQ TC+NQ+
Sbjct: 852  AKDSGSAVICHEDGIVSYVDANRVIVNGESGKE-------RTYLLQKFRRSNQGTCINQK 904

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            PLV +G++V   DI+ADGPS   G+LALG+N+ VAFM W+GYN+ED++++SER+V EDV+
Sbjct: 905  PLVALGEKVSNGDILADGPSMQNGELALGQNVTVAFMTWNGYNYEDAIIMSERLVKEDVY 964

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TSIHIEE+ +  R+TKLGPEEITRDIPNVSE   +++D  GI+ +GAEV  GDILVGK+T
Sbjct: 965  TSIHIEEYTLEVRETKLGPEEITRDIPNVSEVACRHLDARGIVMIGAEVKEGDILVGKVT 1024

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            PKG+S ++PEEKLL AIFGEK+ +VRD SL+VP G SG V D++IF+R
Sbjct: 1025 PKGQSEISPEEKLLLAIFGEKSREVRDNSLKVPHGGSGIVQDIKIFSR 1072



 Score =  441 bits (1134), Expect = e-121,   Method: Composition-based stats.
 Identities = 172/529 (32%), Positives = 241/529 (45%), Gaps = 69/529 (13%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
            + G E                I++  ++ +G +V+ GDIL    +      +   + +  
Sbjct: 880  ESGKERTYLLQKFRRSNQGTCINQKPLVALGEKVSNGDILADGPS-MQNGELALGQNVTV 938

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            A       +  D  +     V   V        + ++  E  +  E      + RD  + 
Sbjct: 939  AFMTWNGYNYEDAIIMSERLVKEDVYTSIHIEEYTLEVRETKLGPEE-----ITRDIPNV 993

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              +  R++ +R   ++ G     G     K T      IS   +     F  +  +V+ N
Sbjct: 994  SEVACRHLDAR-GIVMIGAEVKEGDILVGKVTPKGQSEISPEEKLLLAIFGEKSREVRDN 1052

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +          +      KI     G D+PPGV   VKV++  KR I  GDKMAGRH
Sbjct: 1053 SLKVPHGGSGIVQDI------KIFSRAEGHDLPPGVSESVKVYIVQKRKIHEGDKMAGRH 1106

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG++S+ILP EDMP+++DGTPVDI+LNPLGVPSRMN+GQI E HLG A   L  K  +
Sbjct: 1107 GNKGVISKILPVEDMPYMEDGTPVDIMLNPLGVPSRMNIGQILELHLGIAAKNLNIKFAT 1166

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             + D     ++  +                                              
Sbjct: 1167 SVFDGIETDELFNIMKEGNVSPDGKMVL-------------------------------- 1194

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                             GQ       TGE +D  ++VG +YMLKL+HM+ DK++AR+TG 
Sbjct: 1195 ---------------YDGQ-------TGERYDERISVGVMYMLKLSHMIDDKLHARATGP 1232

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YSLVTQQPLGGK+  GGQR GEMEVW + AYGAA  LQE+LTIKSDDV GRT+ Y +I  
Sbjct: 1233 YSLVTQQPLGGKAQNGGQRFGEMEVWALYAYGAANTLQEILTIKSDDVNGRTKTYAAIQN 1292

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKC 1383
            G D  E G PESF VL  E+QAL L +   +   +     E + D ++ 
Sbjct: 1293 GEDIPEPGIPESFRVLKHELQALALDVKFLDENKEEI--KESLVDGDEE 1339



 Score =  286 bits (731), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 89/386 (23%), Positives = 168/386 (43%), Gaps = 77/386 (19%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G    R+ + +    +++P+L+E+Q  +Y+ F           NEGL   F  ++PI ++
Sbjct: 13  GNKATRRDYSQVSGTLELPNLVEIQTDAYEWF----------KNEGLFEVFNEIYPIQSY 62

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI--K 126
           +    L+F+ Y F  PK++VD+C  R+  YA PL+ T+RL           K   ++  K
Sbjct: 63  NENVKLKFIDYSFGEPKYNVDECRSREANYAAPLRATMRL-------EVINKQTGEVIEK 115

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           E+ +++GDLPLMT+ GTF+I G +R++VSQ+ RSPG +F  +      +G+  +   +IP
Sbjct: 116 EEEVFLGDLPLMTETGTFIINGAERVIVSQIVRSPGAYFKSEND--DKTGRDTFMSELIP 173

Query: 187 DQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSFLMALGMDSE--------------- 226
            +G W++   D +      +I++++DR+R +  T    + G+  +               
Sbjct: 174 SRGTWLEFMSDDRKAANGRVINMKVDRKRTIVSTILFKSFGLSLDLQEGEDAFDTHSFKT 233

Query: 227 -------------EILS----TF--------------YPKIVYSQRGDFWCFPLSAADLM 255
                        E +      F              YP+IV S   D       +  +M
Sbjct: 234 FLNAMNLPVYDEWEEIDSEKREFLTLYALLYTAFFGNYPEIVNSLVLDKTVTFEDSLRVM 293

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSG---LLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
              + +  +   D G   + + K L      L K+ + K  K L +  + + G  +  DI
Sbjct: 294 YENQRADEIPTTD-GAINLMNAKFLDPRRYDLNKAGRYKIHKKLEVY-NRVNGTVLTSDI 351

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFH 338
            +     ++ +   +     + ++  
Sbjct: 352 KDINGNVVFEKGTHITRRDDVLKLRE 377



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 74/204 (36%), Gaps = 6/204 (2%)

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
            F  +       D +   L  +       +S      +     ++  +K T       K 
Sbjct: 153 YFKSENDDKTGRDTFMSELIPSRGTWLEFMSDDRKAANGRVINMKVDRKRTIVSTILFKS 212

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            G+       +     +  +  +N     +Y E  + ID +  E +         +LY  
Sbjct: 213 FGLSLDLQEGEDAFDTHSFKTFLNAMNLPVYDE-WEEIDSEKREFLTLY-----ALLYTA 266

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
              N   I N+LV DK    +D+L  +Y   R  ++ T   A ++ N  F D  +YDL+ 
Sbjct: 267 FFGNYPEIVNSLVLDKTVTFEDSLRVMYENQRADEIPTTDGAINLMNAKFLDPRRYDLNK 326

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKE 434
            GR K++ +L +    +   +  +
Sbjct: 327 AGRYKIHKKLEVYNRVNGTVLTSD 350


>gi|212292065|gb|ACJ24147.1| RNA polymerase beta subunit [Rhizobium leguminosarum]
          Length = 302

 Score =  441 bits (1135), Expect = e-121,   Method: Composition-based stats.
 Identities = 193/294 (65%), Positives = 234/294 (79%), Gaps = 1/294 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 7   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 66

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 67  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 126

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 127 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 186

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 187 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 245

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           +KG+K L    D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +
Sbjct: 246 DKGLKALKAGDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGIILSNGFDE 299


>gi|212292059|gb|ACJ24144.1| RNA polymerase beta subunit [Rhododendron catawbiense]
          Length = 299

 Score =  441 bits (1134), Expect = e-121,   Method: Composition-based stats.
 Identities = 193/298 (64%), Positives = 234/298 (78%), Gaps = 1/298 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+T
Sbjct: 2   PKGGRPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVT 61

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 62  LRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFF 121

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD 
Sbjct: 122 DHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDG 181

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           EEIL TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL
Sbjct: 182 EEILDTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLL 240

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           + L +KG+K L    D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +
Sbjct: 241 RQLSDKGLKALKAGDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILSNGFDE 298


>gi|212292055|gb|ACJ24142.1| RNA polymerase beta subunit [Rhizobium sp. CCBAU 83476]
          Length = 298

 Score =  441 bits (1133), Expect = e-121,   Method: Composition-based stats.
 Identities = 193/294 (65%), Positives = 234/294 (79%), Gaps = 1/294 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLI
Sbjct: 5   RPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLI 64

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 65  VFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDK 124

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEIL
Sbjct: 125 GKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEIL 184

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+ L 
Sbjct: 185 DTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLRQLS 243

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           +KG+K L    D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +
Sbjct: 244 DKGLKALKAGDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLGVILSNGFDE 297


>gi|226348057|gb|ACO50382.1| RNA polymerase beta subunit [Rhizobium lusitanum]
          Length = 291

 Score =  440 bits (1132), Expect = e-121,   Method: Composition-based stats.
 Identities = 192/292 (65%), Positives = 237/292 (81%), Gaps = 1/292 (0%)

Query: 55  LQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           LQA F+SVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK+TLRLIVFD+D
Sbjct: 1   LQAVFRSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLKVTLRLIVFDID 60

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
           E TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  
Sbjct: 61  EDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHS 120

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD EEILSTFY 
Sbjct: 121 SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGEEILSTFYT 180

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K +Y + GD W  P +A  L  GAK  + ++D DTGE V+E GKKLT  LL+ L++KG+K
Sbjct: 181 KSLYQRSGDGWRIPFNAETL-KGAKTVTDMIDADTGEVVVEGGKKLTPRLLRQLQDKGLK 239

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L  T + L GL++AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+
Sbjct: 240 ALKATDEELYGLFLAEDIVNLRTGEIYLEAGDEIDEKTLPVILKAGFEEIPV 291


>gi|226348055|gb|ACO50381.1| RNA polymerase beta subunit [Rhizobium sullae]
          Length = 297

 Score =  440 bits (1131), Expect = e-121,   Method: Composition-based stats.
 Identities = 193/297 (64%), Positives = 235/297 (79%), Gaps = 1/297 (0%)

Query: 44  NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLK 103
                 RP+EGLQA FKSVFPIT FSGA+MLEFVSYEF+PPKFDVD+C  RDLTYA PLK
Sbjct: 1   EEPKGGRPDEGLQAVFKSVFPITDFSGASMLEFVSYEFEPPKFDVDECRQRDLTYAAPLK 60

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +TLRLIVFD+DE TGAKSIKDIKEQS+YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+
Sbjct: 61  VTLRLIVFDIDEDTGAKSIKDIKEQSVYMGDMPLMTNNGTFIVNGTERVIVSQMHRSPGV 120

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PV+S LMALGM
Sbjct: 121 FFDHDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVSSLLMALGM 180

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D EEIL TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  
Sbjct: 181 DGEEILDTFYTKSLYKRDGEGWRIPFQPETL-KGAKAITEMVDADTGEVVVEAGKKLTPR 239

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           LL++L +KG+K L  T D L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  + 
Sbjct: 240 LLRTLSDKGLKALKATDDDLYGNYLAEDIVNYSTGEIYLEAGDEIDEKTLPVILANG 296


>gi|215400714|ref|YP_002327475.1| RNA polymerase beta subunit [Vaucheria litorea]
 gi|194441164|gb|ACF70892.1| RNA polymerase beta subunit [Vaucheria litorea]
          Length = 1092

 Score =  440 bits (1131), Expect = e-120,   Method: Composition-based stats.
 Identities = 187/595 (31%), Positives = 271/595 (45%), Gaps = 68/595 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +L    P  G   E  + I       +  T I            K   E
Sbjct: 549  MGSNMQRQAVPLLWPQKPVVGTGLEAQIAIDSTTGILNYHTGIVTSV-TANEIIVKSIKE 607

Query: 860  EITRDIPNVSEEGLKNIDEC------GIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            +   +      E  +  ++        I+  G  VN G IL        E  +   + L 
Sbjct: 608  KSFSEYRCYKVEKYRRSNQNTCVNQKAIVWPGQLVNSGQILADGP-ATDEGELALGQNLT 666

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD--- 970
             A    +  +  D  L     VS  +V + +F    I+K E +I   R  +E +      
Sbjct: 667  VAYMPWEGYNYEDAIL-----VSERLVLLDLFTSIHIEKYEIAIRNTRSGMEEITSQIPN 721

Query: 971  -KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              +     LD N   R   ++   + + G    K +    SD +    +     F ++ E
Sbjct: 722  VNEHSIRNLDENGLIRKGSLVEPYDILVG----KVTPKDKSDELPPEGKLMKAIFGLKTE 777

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             V+     +    +     +    K        GD++  G++ +V+VF+A  R ++ GDK
Sbjct: 778  TVRDTSLRVPKGIKGRVIDILLLSKE------NGDEVAQGIVNLVQVFIAEVRKVKIGDK 831

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +AGRHGNKGI+S+ILP EDMP+L DG  +DI+ NPLGVPSRMNVGQIFE  LG+A   L 
Sbjct: 832  IAGRHGNKGIISKILPIEDMPYLPDGKIIDIIFNPLGVPSRMNVGQIFECLLGFAGDNLN 891

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            K+ K L  D               ++  + +    I++   ++ L+  + W         
Sbjct: 892  KRFKILPFD---------------EMYSSEASRILINNKLKEAALKTKKSWLFNEY---- 932

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                  G+ +L DG TGE FD P+ VG  Y+LKL H+V DK++A
Sbjct: 933  --------------------SPGKVLLKDGRTGENFDNPILVGKTYILKLIHLVDDKLHA 972

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RS G YSL+TQQPLGGKS +GGQR GEMEVW ++A+GAAY LQE+LT+KSDD+ GR  V 
Sbjct: 973  RSIGPYSLITQQPLGGKSQKGGQRFGEMEVWALEAFGAAYTLQELLTVKSDDIQGRNNVL 1032

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN--SRTKNSAKMEEIPDFNK 1382
             +IV G    + G PESF VL++E++ALGL I             K +E+  FN 
Sbjct: 1033 YAIVKGQPIPKPGVPESFKVLLRELRALGLDITTHQIMKLKTGQTKSKEVDLFND 1087



 Score =  413 bits (1061), Expect = e-112,   Method: Composition-based stats.
 Identities = 286/736 (38%), Positives = 426/736 (57%), Gaps = 23/736 (3%)

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           E++  F        +               G         I+  E++I +    + GL  
Sbjct: 83  ELIDQFLTNTKTILKKQKILLCEIPLMTNKGT------FIINGVERIIVNQLVRSPGLYY 136

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
             + K  +   I S  +     A      ++  I++             +   +++   I
Sbjct: 137 KKESKKNQSYDIYSATIITNRGAWLTFELKSDLIWVRINKKEKIPINVFLAGLDLKTQEI 196

Query: 347 --------LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                     ++S+N           D  K  +  L   Y      ++   +    +   
Sbjct: 197 YQTIKNYKFLINSINKTKLEFEKKYADGRKKNEK-LEKTYNKT--EEILAIAEIRDLICS 253

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
              +   YDL  +GR+K+N +L+L+    +R +  +DI+ II  L+++R   G +DDID+
Sbjct: 254 QILNPKYYDLGEIGRIKINKKLDLNLSLSIRTLTLKDILKIIDSLIEIRLYNGEVDDIDS 313

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L NRRVR VGE+++ Q R+GL R++R+  E++S+ D+D      +IN +P+++ + EFF 
Sbjct: 314 LINRRVRCVGELIQLQIRIGLNRLKRNTIEKLSTCDLDEFRANTVINTRPLIAVLNEFFG 373

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           SSQLSQ  +  N L+ +TH RR+SALG GG+         RD+HPT YGR+CP +T EG 
Sbjct: 374 SSQLSQFMDETNPLAELTHKRRISALGPGGLNTEHVTFSTRDIHPTQYGRLCPVQTPEGK 433

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDE 636
           N GL+SSL S+A++N YGFIETP+ KV D +V   +  VYLSA +E+   IA A+  L  
Sbjct: 434 NAGLISSLASYAKINHYGFIETPFFKVIDAQVFKKIIPVYLSAEQEKLYKIAPADIKLTN 493

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           D    + ++  R   E  L  R +++F+  SP Q++SIAA+LIPFLE+DD+NR LMG NM
Sbjct: 494 DDYIEKYIIPVRYNEEFTLATRHEVEFVAISPVQIISIAAALIPFLEHDDANRALMGSNM 553

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPLL  + P VGTG+E+ +A  S   I+    GIV  V A  I+++S++     S 
Sbjct: 554 QRQAVPLLWPQKPVVGTGLEAQIAIDSTTGILNYHTGIVTSVTANEIIVKSIKE---KSF 610

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           S    Y++ K++RSNQNTCVNQ+ +V  G  V    I+ADGP+TD G+LALG+N+ VA+M
Sbjct: 611 SEYRCYKVEKYRRSNQNTCVNQKAIVWPGQLVNSGQILADGPATDEGELALGQNLTVAYM 670

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
           PW GYN+ED++L+SER+V  D+FTSIHIE++E+  R+T+ G EEIT  IPNV+E  ++N+
Sbjct: 671 PWEGYNYEDAILVSERLVLLDLFTSIHIEKYEIAIRNTRSGMEEITSQIPNVNEHSIRNL 730

Query: 877 DECGIICVGAEVNPGDILVGKITPKGES-PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           DE G+I  G+ V P DILVGK+TPK +S  + PE KL++AIFG K   VRDTSLRVP G+
Sbjct: 731 DENGLIRKGSLVEPYDILVGKVTPKDKSDELPPEGKLMKAIFGLKTETVRDTSLRVPKGI 790

Query: 936 SGTVVDVRIFNRHGID 951
            G V+D+ + ++   D
Sbjct: 791 KGRVIDILLLSKENGD 806



 Score =  221 bits (562), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 77/340 (22%), Positives = 148/340 (43%), Gaps = 33/340 (9%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSY 79
            I ++PDL+E+QK+S+  FL           +GL         I   +G   L+     Y
Sbjct: 6   HITNLPDLLEIQKSSFCWFLS----------KGLPQELSKFSSIFDLTGDLELKIYGNEY 55

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI-KEQSIYMGDLPLM 138
           +F  P+F       + LTY++ + I + LI           + K I K+Q I + ++PLM
Sbjct: 56  KFKKPEFSHLIAKQKKLTYSIKVYIFIELI------DQFLTNTKTILKKQKILLCEIPLM 109

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  GTF+I G++RI+V+QL RSPG+++  +  +       +Y+  II ++G W+  E   
Sbjct: 110 TNKGTFIINGVERIIVNQLVRSPGLYYKKESKKNQSYD--IYSATIITNRGAWLTFEL-K 166

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
            D+I VRI+++ K+P+  FL  L + ++EI  T        +   F    ++   L    
Sbjct: 167 SDLIWVRINKKEKIPINVFLAGLDLKTQEIYQTI-------KNYKFLINSINKTKLEFEK 219

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           K +      +  E+     +++ +  +  +++     +        G      I      
Sbjct: 220 KYADGRKKNEKLEKTYNKTEEILA--IAEIRDLICSQILNPKYYDLGEIGRIKINKKLDL 277

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            + +    +  +  L+ I      +I +   +  + ++ I
Sbjct: 278 NLSLSIRTLTLKDILKIIDSLI--EIRLYNGEVDDIDSLI 315


>gi|322699819|gb|EFY91578.1| DNA-dependent RNA polymerase II beta subunit [Metarhizium acridum
            CQMa 102]
          Length = 1263

 Score =  439 bits (1130), Expect = e-120,   Method: Composition-based stats.
 Identities = 225/1430 (15%), Positives = 429/1430 (30%), Gaps = 301/1430 (21%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFSG------AAMLE 75
            L+  Q  S+D F              +Q        IT       + +G         ++
Sbjct: 40   LVSQQTDSFDEFTQTT----------IQDLVNEYSTITLDQPNPPSAAGEKVALRRYEIK 89

Query: 76   FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKD 124
            F +     P               +C  R+LTYA PL I + + +   V++    K + D
Sbjct: 90   FGTVMVSRPTISETDGTVTSLLPYECRDRNLTYASPLYINITKKVSRAVEQDIPLKELDD 149

Query: 125  IKEQSI-YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             + + +   G++P  TK                      +    +      +GK      
Sbjct: 150  AQREELKRTGEMP--TK---------------------LVWEVEESAEDDDTGK------ 180

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
                         D K+++ V      K+P+        +  E+  S F        +G 
Sbjct: 181  -----------SEDWKNMVFV-----GKLPIMVKSKICHLSREQEDSLFMVNECPYDQGG 224

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTG------------EQVIESGKKLTSGLLKSLKEK 291
            ++    S   L+   + ++++V +                  +E G +L S L   L  K
Sbjct: 225  YFVINGSEKVLIAQERSAANIVQVFKKAQPSPYTYTAEIRSALEKGSRLISSLTLKLYGK 284

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            G    G     +    +     +     ++   G V DE  L  I +       +  +  
Sbjct: 285  GDSARGGFGQTI-HTTLPFVKSDLPIAIVFRALGVVSDEDILNHICYDRKDSQMLEMLRP 343

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                A+          +DR+ AL  I +                      + D+  L   
Sbjct: 344  CIEEAF--------CVQDREVALDFIGKR--------------------GNRDQAGLGRD 375

Query: 412  GRVKMNMRL-------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
             RV++   +       ++   +     +   +  ++  L+    G+   DD D+ G +R+
Sbjct: 376  KRVRVAKDILQKETLPHISQTEGSETRKAFFLGYMVHKLLQCALGRREPDDRDHFGKKRL 435

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R  + RM   +    R              I    + + +     +   
Sbjct: 436  DLAGPLLAKLFRGIIRRMNTELSNYLRRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNW 495

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 496  GDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLV 551

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L+    V+     E     + +   +V  +   L        ++
Sbjct: 552  CPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMINRGMEVVEEYEPLRYPHATKIFV 611

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  + +D       V        +      + +  D   K        + P      
Sbjct: 612  NGVWVGVHQDPKHLVSQVLDTRRKSYLQYEVSLVREIRDQEFKIFSDAGRVMRPVFTVQQ 671

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             +    G       +                             RAG VE +DA      
Sbjct: 672  EDDPETGIEKGHLVLTKDLVNKLAKEQAEPPEDPSEKIGWEGLIRAGAVEYLDAEEEETA 731

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +    +         +       +    +N+R   K              PS  LG   
Sbjct: 732  MICMTPEDLELYRLQ-KAGVALDDDIGDDLNKRLKTKTNPTTHMYTHCEIHPSMILG--- 787

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N          M  + +     +  +                   
Sbjct: 788  ----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM--------------- 826

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 827  ------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 874

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ ++         E+  +      + +    Y +L
Sbjct: 875  SVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNY---TEVFEKPFHQSTLRMKHGTYDKL 930

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  +  +      R+   Q       ++     +     
Sbjct: 931  DDDGIVAPGVRVSGEDIIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVI 990

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             + +                       ++ VKV V   +  Q GDK A RHG KG +   
Sbjct: 991  LTVNA--------------------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVT 1030

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF ++G   DI++NP  +PSRM +  + E  L       G +            
Sbjct: 1031 YRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD---------- 1080

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     ++++ +L
Sbjct: 1081 -------------------------------------------ATP-FTDVTVDSVSELL 1096

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            R       G  I+Y+G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+
Sbjct: 1097 RKHGYQSRGFEIMYNGHTGKKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPV 1156

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------------ 1324
             G++  GG R GEME  C+ A+GAA  L+E L   SD       ++ G            
Sbjct: 1157 EGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSDAFRVHICEICGLMTPIANLSKQS 1216

Query: 1325 ------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  + +            +   P +  +L +E+Q++ ++  +  +R+
Sbjct: 1217 FECRPCKNKT--------KIAQIHIPYAAKLLFQELQSMNIAARMFTNRS 1258


>gi|108796876|ref|YP_636174.1| beta subunit of RNA polymerase [Pseudendoclonium akinetum]
 gi|88909629|sp|Q3ZJ93|RPOB_PSEAK RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|56159574|gb|AAV80598.1| beta subunit of RNA polymerase [Pseudendoclonium akinetum]
          Length = 2178

 Score =  439 bits (1130), Expect = e-120,   Method: Composition-based stats.
 Identities = 182/750 (24%), Positives = 307/750 (40%), Gaps = 71/750 (9%)

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVV-------SIAASLIPFLENDDSNRVLMGCN 695
            E           ++    + + +  P+  +       +    +I      +   V  G  
Sbjct: 1487 EYAINDKKRRVEIINSSSLFYNNLIPQNYILNNYHRSNQDTYMIHRPLVQEGQWVEKGDI 1546

Query: 696  MQRQAV---PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            +   +V     L      +   +         A ++++R    +   ++   I   E ++
Sbjct: 1547 LADSSVSVQGELSIGQNILVGYIPWEGYNFEDAVLISERLIFDDLYTSLH--IERYEVEI 1604

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS-TDLGDLALGRNM 811
              +  G++           +   ++   + K+G  V+  DI+    +      L    N+
Sbjct: 1605 RDTQFGLEQITNQIPNEKGEYDYIDSNGIAKIGTWVKEGDILVGKIAPIGQKKLTAYENL 1664

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            L   +        D+ L   R V       IH+ E     +          + +    ++
Sbjct: 1665 LYDILNKEIPKTRDTSLRVPRGV---TGRVIHV-EIVETTKKKGNDSSIFAKSLKFPKKQ 1720

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             LK +                 +  K   K +S     +     +   ++   ++   + 
Sbjct: 1721 KLKRV---------TSPEYWYPVNTKKDQKVQSFSFKNKSEKLFLTPVQSYFNKEAKTKN 1771

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P   S      +      + +N+R      +++    +++  +   L   I     +   
Sbjct: 1772 PKLNSPFFYLNKRNPDFNLKRNKR----IAKEMYFFNKNEKIKLSTLQIKIKGLEKKEFS 1827

Query: 992  GQNAVSG-PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
                +       +K+   +  +        W      ++   RN    +           
Sbjct: 1828 FPKILKARFSLLQKAQTANLKIEKFLDDKFWNNVNYSNKNFSRNGSQKENSNADGLQFYN 1887

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
               K K + +Q  +       + V +++A KR +Q GDK+AGRHGNKGI+S ILP +DMP
Sbjct: 1888 PLKKTKTKVLQPMEKTSFSGPQKVHIYLAEKRKLQIGDKIAGRHGNKGIISNILPRQDMP 1947

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L DGTP+DIVLNPLGVPSRMNVGQI E  LG A   L +  K    D            
Sbjct: 1948 YLSDGTPLDIVLNPLGVPSRMNVGQILECLLGMAGYYLKQNFKIQPFD------------ 1995

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
               ++ G  +    +     ++ ++  + W                        + + + 
Sbjct: 1996 ---EIYGCEASRSLVYSKLYEARIKTGQDW------------------------LFNANH 2028

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G++ L+DG TG+ F +PVTVG  Y+LKL H+V DK++ARSTG YSLVTQQPL G+S +G
Sbjct: 2029 PGKTRLFDGRTGDCFKQPVTVGVAYILKLIHLVDDKIHARSTGPYSLVTQQPLRGRSKQG 2088

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVL 1350
            GQR+GEMEVW ++ +GAAY+LQE+LTIKSDD+ GR +V  SI+        G PESF VL
Sbjct: 2089 GQRVGEMEVWALEGFGAAYILQEILTIKSDDLKGRNQVMNSILNNKPV-NFGLPESFKVL 2147

Query: 1351 VKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            V+E+Q+L L I +   R   +     I +F
Sbjct: 2148 VRELQSLCLDIAIYRYRENGTPTKININNF 2177



 Score =  397 bits (1020), Expect = e-108,   Method: Composition-based stats.
 Identities = 215/762 (28%), Positives = 351/762 (46%), Gaps = 86/762 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEF 81
             IPD + +Q++S+  FL            GL   FK+   IT  +    + F    Y+ 
Sbjct: 63  FKIPDFLNIQRSSFRQFL----------KSGLITEFKNCKSITNSNQTFEVFFYAEHYKL 112

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           + PK+     + +  +Y+  L + ++L  +           +++  Q + + +LPLMTK+
Sbjct: 113 NRPKWTPKQAILKKKSYSSQLYLPIQLSNY---------QTEEVHLQWVLLANLPLMTKN 163

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD-SKD 200
           G F++ G  R++++Q+ RSPG++F     +   + K +Y+   I  +G W+ +E D  K 
Sbjct: 164 GHFILNGCPRVLMNQIVRSPGVYFR----KVVKNQKTVYSADFIAQRGSWLRLEVDTKKG 219

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
            I  ++ +  K+P+ +FL ALG+    IL+              +               
Sbjct: 220 DIWAKLKKTPKIPIFTFLRALGLTLP-ILN-----NSIDFAKLRYLLQFKEESKRSKKIK 273

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
                 I+    ++E        LLKSLK+                              
Sbjct: 274 DFLGPGINNSLDIVE-----FRSLLKSLKKY----------------------------- 299

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                              +          +     ++   + T   +   +    +Y  
Sbjct: 300 ----------------MKPKPAKKSSKKQKTKKIKKWLTPFVCTTYFQSLLELCQKLYPQ 343

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
            +  ++    +A+      F +   YDLS +GR K+N +L +  P +   +  +D++   
Sbjct: 344 KKFLEL-DPKLAQKFLFRKFQNPRTYDLSILGREKINKKLGISIPLEKTILTSQDVLFAC 402

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
             L+DL  G    DDID+L NR+++  GE+++ Q   GL+R+E+ I+E++     DS   
Sbjct: 403 LFLMDLLQGLVISDDIDDLKNRKIKPSGELIQTQLSTGLIRLEKIIREKLKQPKQDSDSF 462

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            +L + KP+  A  +FF ++ LSQL +  N+LS ITH RRLS+LG GG+ R  AG+ +R 
Sbjct: 463 SNLFSVKPLNQAFRDFFGTNPLSQLMDQTNALSEITHKRRLSSLGPGGINRETAGMAIRG 522

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLS 618
           +HPTHYGRICP ET EG N GLV+S T F+ +N   FIETP+ K+  G +    +    S
Sbjct: 523 IHPTHYGRICPIETPEGQNAGLVNSFTIFSHLNTKSFIETPFYKMYKGFILKNKNPFLFS 582

Query: 619 AMEEENRYIAQANSSLDEDGS-FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           + +E N  +A  +              +  R   E   V R +I+FI  SP Q++SIA S
Sbjct: 583 SDQERNLVLAPGDIQTSLFHFLPPGVPIPSRQFKEFKRVSRNEINFIAVSPIQMISIATS 642

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE++D NR LMG NMQRQAVP ++   P VGTG+ES V    G  +  +++G V  
Sbjct: 643 LIPFLEHNDGNRALMGSNMQRQAVPTVRPSKPIVGTGLESRVISDVGHGLQVQKSGFVSY 702

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           VD  +I+I S +    P           K +    N  + Q+
Sbjct: 703 VDGNKIIIYSKKRIDQPFFFDTKKLHFPKKKVPFLNLDLQQQ 744


>gi|221059854|ref|XP_002260572.1| DNA-directed RNA polymerase [Plasmodium knowlesi strain H]
 gi|193810646|emb|CAQ42544.1| DNA-directed RNA polymerase, putative [Plasmodium knowlesi strain H]
          Length = 1401

 Score =  439 bits (1129), Expect = e-120,   Method: Composition-based stats.
 Identities = 223/1423 (15%), Positives = 416/1423 (29%), Gaps = 361/1423 (25%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L++    SY++F+   I              KS            +EF+      P    
Sbjct: 235  LVKQHIESYNYFIKHEIKTIMNATT--NKILKS-----DIDEHFYVEFLDIFVGRPLVEE 287

Query: 86   ------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                       C  RDLTY+ P+ + +  +          K    I++ ++ +G LP+M 
Sbjct: 288  NMIETNLTPQICRQRDLTYSAPIYVDVEYV----------KGSNIIRKNNVEIGRLPVML 337

Query: 140  ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                      G F++KG +R+++ Q   S               
Sbjct: 338  RSDICILNNKSEEELMKLGECPYDPGGYFIVKGTERVLLMQEQLSKN------------- 384

Query: 176  GKLLYACRIIPDQGLWMDIEFDSKDIIHVRID--------------RRRKVP-------- 213
                   RII        +E D K  I   I               +  K+         
Sbjct: 385  -------RII--------VEMDIKHNICATITSTTAESKSRCAIVYKNNKLYLKHNSFIE 429

Query: 214  ---VTSFLMALGMDSEE---------------ILSTFYP--KIVYSQRGDFWCF---PLS 250
               V   L A+G +S++               IL + Y           D   +    + 
Sbjct: 430  DIGVCIILRAMGYESDQEIFQMIGSHRNYLNGILLSLYDLYSENIKTNLDALLYIGKKIR 489

Query: 251  AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
               L  G   S     +   + +IE G    S +L S  ++  K+          L +  
Sbjct: 490  PRLLAKGFFSSMKEKQVKNEKDIIEEGLDFLSRVLLSHIQQKNKYDFRNKARCICLMI-R 548

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +++    +  ++  D    K LE            LY           +  ++   +  
Sbjct: 549  RVLDSANNKNELDDKDYYGNKRLELAGQLISLLFEDLYKRFYFTLKKQIDQTLSKYMQSN 608

Query: 371  KDALLDIYRVMRPGDVSTFSVAES-MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
              + L     +       F      +       +       + R KM           + 
Sbjct: 609  YTSKLKYSGNVNETYPDVFRSLPKDIITRGMQAAISTGNWNIKRFKMEKSGVSQVLSRLS 668

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
             I    ++  +    +          +       +             GL++    +   
Sbjct: 669  FIACIGMMTRLNSQFEKGRKVSGPRALQPSQWGVLCPCDTPEGESC--GLVKNLALMTHV 726

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG- 548
             +  + +  + + L       S         +        N +    H +    + +   
Sbjct: 727  TNDNENNEHLIEILYTLGVEDSDSLTGEEMYKEGIFFVIFNGILLGVHKKPRIFMRRIRC 786

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKV 605
            + R     +   ++     +     T  G     +  + +            +E      
Sbjct: 787  LRRYGKIGQFVSIYDNFLHKAIYISTDGGRLCRPLIIVENGKSKLTQEHILSLENGTINF 846

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             D   ++ + ++   E+ N  IA   S +  + S                         +
Sbjct: 847  FDLLKSSVIEWIDVNEQNNLLIALNESDISINTSHL-----------------------E 883

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
              P  ++ + A LIP+  ++ S R    C M +QA+                        
Sbjct: 884  IDPLTILGVVAGLIPYPNHNQSPRNTYQCAMGKQAIGA---------------------- 921

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                               I   +     +   + +Y               Q+PLVK  
Sbjct: 922  -------------------IGYNQFVRCDTLLYLLVYP--------------QKPLVKS- 947

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                           +   L  G+N +VA M + GY+ ED++++++  +       + + 
Sbjct: 948  ---------KTIEFINFEKLPAGQNAIVAVMSFGGYDIEDAIVMNKSSIDRGFGRCMSLR 998

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +  V  +    G  ++    P                           L      + +  
Sbjct: 999  KHAVELKKYFNGSNDLVLPSP---------------------------LAISKMQERQEK 1031

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
               E+         +A + RD    V +G    V + +                      
Sbjct: 1032 RRQEKLSQSQDKQRQAKEERDH---VENGAGTNVDEQK---------------------- 1066

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               +  + E  I   +       +  G     G     K +  +             +  
Sbjct: 1067 ---KFHNKE--IKKYHALDMDGVVSIGYLLKEGQVYINKYSPRNVKD----HVKDISKID 1117

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            + D K                   +  + + I+KI +        L++ K+ +   R  +
Sbjct: 1118 LNDLKANEI-------------KYKSVYPSYIDKIIF--TENAEGLKIYKIIMRQTRLPE 1162

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK + RHG KG+V  ++  EDMPF + G   D+++NP G PSRM VG++ E     + 
Sbjct: 1163 LGDKFSSRHGQKGVVGLLVNQEDMPFTESGICPDLIMNPHGFPSRMTVGKLLELVASKSA 1222

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
            V  G+     I       +                                         
Sbjct: 1223 VLDGELKYGSIFSGTPFEE----------------------------------------- 1241

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +++ +F                 + S + +LY GLTGEP +  + +G IY  KL HMV D
Sbjct: 1242 MASILF-------------KYGFNCSSKELLYSGLTGEPLETYIFMGPIYYQKLKHMVQD 1288

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DV- 1322
            K++AR+ G   L+T+QP  G+S  GG RLGEME  C+ AYG + +L E L + SD  DV 
Sbjct: 1289 KIHARARGPRQLLTRQPTEGRSKEGGLRLGEMERDCLIAYGVSNLLLERLMLSSDVCDVY 1348

Query: 1323 ----VGRTRVYESI----VAGNDTFETGTPESFNVLVKEMQAL 1357
                 G    Y++        +       P +  +L +E+Q +
Sbjct: 1349 ICEDCG-MMGYDTYCTFCQKCDKNALVKMPYACKLLFQELQTM 1390


>gi|300728451|ref|ZP_07061813.1| DNA-directed RNA polymerase, beta subunit [Prevotella bryantii B14]
 gi|299774370|gb|EFI71000.1| DNA-directed RNA polymerase, beta subunit [Prevotella bryantii B14]
          Length = 541

 Score =  439 bits (1129), Expect = e-120,   Method: Composition-based stats.
 Identities = 279/527 (52%), Positives = 375/527 (71%), Gaps = 6/527 (1%)

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            D R + KEDIIAIIK L+ L N + T+DDID+L NRRVR+VGE L NQ+ +GL RM R+
Sbjct: 1   MDTRVLTKEDIIAIIKYLIKLVNSQATVDDIDHLSNRRVRTVGEQLANQFSIGLARMSRT 60

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           I+ER++  D +   P DLINAK + S +  FF ++ LSQ  +  N L+ +TH RRLSALG
Sbjct: 61  IRERMNVRDNEVFTPTDLINAKTISSVINSFFGTNPLSQFMDQTNPLAEVTHKRRLSALG 120

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVH THYGR+CP E+ EG NIGL+SSL  +A +N  GFIETPYRKV
Sbjct: 121 PGGLTRERAGFEVRDVHYTHYGRLCPIESPEGPNIGLISSLCVYATINELGFIETPYRKV 180

Query: 606 CDGKV---TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            +G V     DVV+LSA EEE + I Q N+ L+ DG+F  ++V CR   +  +V  E +D
Sbjct: 181 NNGVVDMDNEDVVFLSAEEEEGKIIGQGNAPLNVDGTFIRKVVKCRQDADYPVVTPENVD 240

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D +P+Q+ S++A LIPFLE+DD +R LMGCNM RQAVPLL  EAP VGTG+E  V + 
Sbjct: 241 YMDVAPQQIASVSACLIPFLEHDDGHRALMGCNMMRQAVPLLHNEAPIVGTGLEKQVCED 300

Query: 723 SGAAIVAKRAGIVEQVDAIRIVI---RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           S   + A+  G+++ VDA  I I   R+ E +       +  YR+ KF+R+NQN  V+ R
Sbjct: 301 SRTQVTAEGEGVIDYVDATTIRILYDRTEEDEFVSFEPALKEYRIPKFRRTNQNMVVDLR 360

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+   G  V++ DI+ +G +T+ G+LALGRN+LVA++PW GYN+ED+++ISERM+ EDV 
Sbjct: 361 PICSKGQRVKKGDILTEGYATENGELALGRNLLVAYIPWKGYNYEDAVVISERMIREDVL 420

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS+H++E+ +  R+TK G EE T DIPNVSEE  K++D+ GII VGA V PGDIL+GKI+
Sbjct: 421 TSVHVDEYSLDVRETKRGVEEFTNDIPNVSEEATKDLDDNGIIRVGARVEPGDILIGKIS 480

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           PKGES  +PEEKLLRAIFG+KA DV+D+SL+    +SG  V +R  +
Sbjct: 481 PKGESDPSPEEKLLRAIFGDKAGDVKDSSLKANPSLSGVCVSIRNCS 527


>gi|325283024|ref|YP_004255565.1| DNA-directed RNA polymerase subunit beta [Deinococcus proteolyticus
           MRP]
 gi|324314833|gb|ADY25948.1| DNA-directed RNA polymerase subunit beta [Deinococcus proteolyticus
           MRP]
          Length = 1145

 Score =  439 bits (1129), Expect = e-120,   Method: Composition-based stats.
 Identities = 297/612 (48%), Positives = 405/612 (66%), Gaps = 26/612 (4%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +  +ALL ++ V+RPGD      A      L  D  +YDL   GR KMN +L      +
Sbjct: 232 MNADEALLRLFTVLRPGDPPKRDKATQYLYGLLADPRRYDLGEPGRFKMNTKLGTWQRSE 291

Query: 428 VRHIR-------KEDIIAIIKILVDLRNGKGTI-----------------DDIDNLGNRR 463
              +         E ++  I+ L+ L+NG  T+                 DDID+LGNRR
Sbjct: 292 PTLLSFRDGQFYDEGLVDTIRYLMALQNGVETVTLGADADGVAQEVRVYEDDIDHLGNRR 351

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           VR+VGE+L +Q R+G+ RM R ++ER+   + D+  P  L+N +P+V+A+ EFF  SQLS
Sbjct: 352 VRTVGELLADQLRVGMGRMARGVRERMLLGNPDAATPTKLVNNRPIVAAMREFFGRSQLS 411

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q ++  N LS + H RR+SALG GG+ R RAG ++RDVH THYGRICP ET EG NIGL+
Sbjct: 412 QFKDQTNPLSDLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPIETPEGANIGLI 471

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           SSL+S+++VN  GFIE PYR+V  G V+  V Y++A  E+   IAQANS L++DG+F EE
Sbjct: 472 SSLSSYSKVNPLGFIEAPYRRVEGGVVSEHVEYMTADIEDRFVIAQANSPLNDDGTFAEE 531

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            V  R  G+ +L     ++++D SPKQ+VSI  SLIPFLE+DD+NR LMG NMQ QAVPL
Sbjct: 532 RVLARKQGDPLLYDPADVEYMDVSPKQIVSINTSLIPFLEHDDANRALMGSNMQSQAVPL 591

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD--PSTSGVDI 761
           ++AE+P VGTG+E  V   SG ++V    G V  VD+  I I+  E   +    T  V +
Sbjct: 592 VRAESPSVGTGVEERVVTDSGTSVVTDVTGEVIYVDSRNIQIKLTEDAPELGMKTGNVQM 651

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + L++F RSNQ T ++Q P+V+VG++V +  +IADGP++  G LALG+N+ +A MP+ G+
Sbjct: 652 FELVRFTRSNQGTNLDQHPIVEVGEQVTKGQVIADGPASQFGRLALGQNITIAIMPFDGF 711

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++ ISE +V +D +TSIHIE+ E+ ARDTKLGPE+ITRDIP +SE  L+++DE GI
Sbjct: 712 NFEDAICISEGLVRKDFYTSIHIEKDEIEARDTKLGPEKITRDIPGLSEAALRDLDEDGI 771

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + VGAEV PGDILVGK + KGES  +PEE+LLR+IFGEKA +V+DTSLRV SG  G VV 
Sbjct: 772 VRVGAEVKPGDILVGKTSFKGESEPSPEERLLRSIFGEKAREVKDTSLRVQSGQGGIVVK 831

Query: 942 VRIFNRHGIDKN 953
              F R     +
Sbjct: 832 TVRFRRGDEGVD 843



 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 182/560 (32%), Positives = 267/560 (47%), Gaps = 40/560 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMAR----- 852
                  +    ++ A  P  G   E+ ++      +V++     I+++   +  +     
Sbjct: 580  MGSNMQSQAVPLVRAESPSVGTGVEERVVTDSGTSVVTDVTGEVIYVDSRNIQIKLTEDA 639

Query: 853  ---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                 K G  ++   +         N+D+  I+ VG +V  G ++           +   
Sbjct: 640  PELGMKTGNVQMFELVRFTRSNQGTNLDQHPIVEVGEQVTKGQVIADGP-ASQFGRLALG 698

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + +  AI      +  D        +S  +V    +    I+K+E      +   E + R
Sbjct: 699  QNITIAIMPFDGFNFEDAIC-----ISEGLVRKDFYTSIHIEKDEIEARDTKLGPEKITR 753

Query: 970  DK----DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            D     +     LD +   R+   +   + + G   FK  +  S +      RS + + A
Sbjct: 754  DIPGLSEAALRDLDEDGIVRVGAEVKPGDILVGKTSFKGESEPSPE--ERLLRSIFGEKA 811

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
             + +     V+S +                   +   G D+ PGV  +V+V+VA KR +Q
Sbjct: 812  REVKDTSLRVQSGQGGIVVKTVRFR--------RGDEGVDLKPGVREMVRVYVAQKRQLQ 863

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK+A RHGNKG+VS+ILP EDMP+L DGTPVD+V NPLGVPSRMN+GQI ETHLG   
Sbjct: 864  VGDKVANRHGNKGVVSKILPPEDMPYLADGTPVDLVFNPLGVPSRMNLGQILETHLGEVA 923

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               GKK  + + D      I  +      +       E   D D      +    K GV 
Sbjct: 924  RLTGKKFVTPVFDSVTEAKIKDMLEEQADL-RLSQRKEDGFDTDKREEEVLDRAAKLGV- 981

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +S P       E     LR   L  +G+S+L+DG TGE    PV VG +Y++KL HMV D
Sbjct: 982  ISEP------GEDYEGALRQ--LSRTGKSVLFDGRTGEAISGPVVVGTMYVMKLYHMVED 1033

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTG YSL+TQQPLGGK+  GGQR GEMEVW ++AYGAA+ L+EMLTIKSDD+ GR
Sbjct: 1034 KLHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIDGR 1093

Query: 1326 TRVYESIVAGNDTFETGTPE 1345
               Y+SIV G    ++  PE
Sbjct: 1094 DAAYQSIVKGEQVADSTIPE 1113



 Score =  266 bits (681), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/235 (36%), Positives = 131/235 (55%), Gaps = 23/235 (9%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA----- 71
           FG+  E+I +PDL EVQ  S+  FL    AP ER N GL++AF+ VFPI   +       
Sbjct: 10  FGEIAEVIPLPDLTEVQVQSFQAFLQEGKAPSERTNFGLESAFREVFPI-DETEKGRSTG 68

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            +L+++ Y    P +  ++C  +DLTY  P+   L+LI  D            IKE  ++
Sbjct: 69  LVLDYLEYRLGDPPYSPEECREKDLTYQAPMYAKLQLIHKDSGL---------IKEDQVF 119

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD--QG 189
           +GDLPLMT+DG+F+I G  R+V+SQ+HRSPG++F           K LY+  IIP   +G
Sbjct: 120 LGDLPLMTEDGSFIINGADRVVISQIHRSPGVYFTSS----YKGLKKLYSAAIIPMPKRG 175

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
            W+++E+ + D++ ++++ +RK PV+  L  LGMD  +I   F          D 
Sbjct: 176 PWIELEW-AGDMLEMKVN-KRKFPVSLLLRVLGMDDAQIRELFSEFDADIALEDK 228


>gi|322711689|gb|EFZ03262.1| DNA-dependent RNA polymerase II beta subunit [Metarhizium anisopliae
            ARSEF 23]
          Length = 1262

 Score =  438 bits (1127), Expect = e-120,   Method: Composition-based stats.
 Identities = 232/1435 (16%), Positives = 440/1435 (30%), Gaps = 311/1435 (21%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFSG------AAMLE 75
            L+  Q  S+D F              +Q        IT       + +G         ++
Sbjct: 39   LVSQQTDSFDEFTQTT----------IQDLVNEYSTITLDQPNPPSAAGEKVALRRYEIK 88

Query: 76   FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKD 124
            F +     P               +C  R+LTYA PL I + + +   V++    K + D
Sbjct: 89   FGTVMVSRPTISETDGTVTSLLPYECRDRNLTYASPLYINITKKVSRAVEQDIPLKELDD 148

Query: 125  IKEQSI-YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             + + +   G++P  TK            +V +L  S     D D G++           
Sbjct: 149  AQREELKRTGEMP--TK------------LVWELEESA---EDDDTGKSE---------- 181

Query: 184  IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
                         D K+++ V      K+P+        +  E+  S F        +G 
Sbjct: 182  -------------DWKNMVFV-----GKLPIMVKSKICHLSREQEDSLFMVNECPYDQGG 223

Query: 244  FWCFPLSAADLMVGAKVSSSLVDIDTG------------EQVIESGKKLTSGLLKSLKEK 291
            ++    S   L+   + ++++V +                  +E G +L S L   L  K
Sbjct: 224  YFVINGSEKVLIAQERSAANIVQVFKKAQPSPYTYTAEIRSALEKGSRLISSLSLKLYGK 283

Query: 292  GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            G    G     +    +     +     ++   G V DE  L  I +       +  +  
Sbjct: 284  GDSARGGFGQTI-HTTLPFVKSDLPIAIVFRALGVVSDEDILNHICYDRKDSQMLEMLRP 342

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                A+          +DR+ AL  I +                      + D+  L   
Sbjct: 343  CIEEAF--------CVQDREVALDFIGKR--------------------GNRDQAGLGRD 374

Query: 412  GRVKMNMRL-------NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
             RV++   +       ++   +     +   +  ++  L+    G+   DD D+ G +R+
Sbjct: 375  KRVRVAKDILQKETLPHISQTEGSETRKAFFLGYMVHKLLQCALGRREPDDRDHFGKKRL 434

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R  + RM   +    R              I    + + +     +   
Sbjct: 435  DLAGPLLAKLFRGIIRRMNTELSNYLRRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNW 494

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 495  GDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLV 550

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L+    V+     E     + +   +V  +   L        ++
Sbjct: 551  CPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMINRGMEVVEEYEPLRYPHATKIFV 610

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  + +D       V        +      + +  D   K        + P      
Sbjct: 611  NGVWVGVHQDPKHLVSQVLDTRRKSYLQYEVSLVREIRDQEFKIFSDAGRVMRPVFTVQQ 670

Query: 687  SNRVLMGCN-----MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             +    G       + ++ V  L  E           +           RAG VE +DA 
Sbjct: 671  EDDPETGIEKGHLVLTKELVNKLAKEQAEPPEDPSEKIGWE-----GLIRAGAVEYLDAE 725

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +         +       +    +N+R   K              PS  
Sbjct: 726  EEETSMICMTPEDLELYRLQ-KAGVALDDDIGDDLNKRLKTKTNPTTHMYTHCEIHPSMI 784

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +     +  +              
Sbjct: 785  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------- 825

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 826  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 868

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ ++         E+  +      + +   
Sbjct: 869  YNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNY---TEVFEKPFHQSTLRMKHG 924

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  +  +      R+   Q       ++     +
Sbjct: 925  TYDKLDDDGIVAPGVRVSGEDIIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGI 984

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                  + +                       ++ VKV V   +  Q GDK A RHG KG
Sbjct: 985  VDSVILTVNA--------------------DNVKYVKVRVRTTKIPQIGDKFASRHGQKG 1024

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF ++G   DI++NP  +PSRM +  + E  L       G +       
Sbjct: 1025 TIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD----- 1079

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     ++
Sbjct: 1080 ------------------------------------------------ATP-FTDVTVDS 1090

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            ++ +LR       G  I+Y+G TG+     V  G  Y  +L HMV DK++AR+ G   ++
Sbjct: 1091 VSELLRKHGYQSRGFEIMYNGHTGKKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIM 1150

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------- 1324
            T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD       ++ G       
Sbjct: 1151 TRQPVEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSDAFRVHICEICGLMTPIAN 1210

Query: 1325 -----------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                       + +            +   P +  +L +E+Q++ ++  +  +R+
Sbjct: 1211 LSKQSFECRPCKNKT--------KIAQIHIPYAAKLLFQELQSMNIAARMFTNRS 1257


>gi|269930907|gb|ACZ54188.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 441

 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 337/442 (76%), Positives = 386/442 (87%), Gaps = 1/442 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           GAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV 
Sbjct: 241 GAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVH 299

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           VGD V + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIH
Sbjct: 300 VGDRVEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIH 359

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           IEEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITPKGE
Sbjct: 360 IEEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIIYIGAEVQPGDILVGKITPKGE 419

Query: 904 SPMTPEEKLLRAIFGEKAVDVR 925
           SPMTPEEKLLRAIFGEKA DVR
Sbjct: 420 SPMTPEEKLLRAIFGEKASDVR 441


>gi|224178086|ref|YP_002600950.1| beta subunit of RNA polymerase [Pyramimonas parkeae]
 gi|215882753|gb|ACJ71126.1| beta subunit of RNA polymerase [Pyramimonas parkeae]
          Length = 1064

 Score =  438 bits (1126), Expect = e-120,   Method: Composition-based stats.
 Identities = 174/574 (30%), Positives = 252/574 (43%), Gaps = 77/574 (13%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       +L    P  G   E  +      V       +  S + EE  V      
Sbjct: 559  MGSNMQRQAVPILSPERPLVGTGLEGQVARDSGTVLLSKKSGLVISTNSEEIHVSYSKDS 618

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                 I              I +   +CVG  V  GD+L        +  +   + +L A
Sbjct: 619  RSNYIIHPLQRYQRSNQATCISQRPSVCVGDWVQEGDLLAD-GAATSKGELALGKNVLVA 677

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE--REQIELLARDKDD 973
                +  +  D  L     V   +       R+ ++  +  I +E     +  +  +  D
Sbjct: 678  YMPWEGYNFEDAILISERLVYENIYTSIHIERYEVEARQTKIGIEIFTRNLPHVENELTD 737

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ--FAVQDEKV 1031
                           +L G     G     K T        + P  +  +  F  ++  V
Sbjct: 738  HL--------DENGLVLPGSWVEGGDILVGKITPKGE--FDQTPEKRLLRAIFQQKEPDV 787

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q +   +    +     +  +                     V++F+A KR IQ GDK+A
Sbjct: 788  QDSSLRVPNGVKGRVIYVRPKKN------------------TVRIFLAEKRKIQVGDKIA 829

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGIVS ILP +DMPFL+DGTPVD+VLNPLGVPSRMNVGQ+FE  LG A   L + 
Sbjct: 830  GRHGNKGIVSNILPIQDMPFLQDGTPVDMVLNPLGVPSRMNVGQVFECLLGLAGKYLNQS 889

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +K +  D               ++ G  +    +     ++  +  ++W      +    
Sbjct: 890  MKVIPFD---------------EMYGKETSRGLVYRKLYEARRKTKKKWLFEPAFA---- 930

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                                G++ L+DG TGE FD+PV  GY YMLKL H+V DK++ARS
Sbjct: 931  --------------------GKTRLFDGRTGEVFDQPVLTGYPYMLKLVHLVDDKIHARS 970

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            TG YSLVTQQPLGG++  GGQRLGEMEVW ++ YGAAY+LQE+LT+KSDD+ GR  +  +
Sbjct: 971  TGPYSLVTQQPLGGRAKHGGQRLGEMEVWALEGYGAAYLLQELLTVKSDDMQGRNDILHA 1030

Query: 1332 IVA-GNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            I+  G    + G PESF VL+ E+++L L I + 
Sbjct: 1031 IIKGGTHLPQPGCPESFKVLISELRSLCLDIRIY 1064



 Score =  433 bits (1113), Expect = e-118,   Method: Composition-based stats.
 Identities = 274/584 (46%), Positives = 401/584 (68%), Gaps = 13/584 (2%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           D+K ALL ++  +RP    T   A  +    F + ++YDL  +GR+++N +L +      
Sbjct: 227 DQKSALLKLHFKLRPDRPGTLRSASDLLESRFMNPNRYDLGRLGRIRLNKKLRILGNPTA 286

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             +R EDI+A +  LV+L  G G +DDID+L NRR+R+ GE+++NQ R+G  R+E+ I+E
Sbjct: 287 TVLRPEDILAAVDYLVNLEFGMGKVDDIDDLKNRRIRTSGELIQNQIRIGFSRLEKMIRE 346

Query: 489 RISSVDI-------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +++ ++        +S +P   I+ KP+V ++ EFF SSQLSQ  +  N L+ ITH RRL
Sbjct: 347 KMTEIEPINGLTIAESFLPTRFIHPKPMVGSLREFFGSSQLSQYMDQTNPLAEITHKRRL 406

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           S+LG GG+++ RAG+ +R++HP+HYGRICP ET EG N GLVSSLT++A++N+ GF+E P
Sbjct: 407 SSLGPGGLSKDRAGMAVREIHPSHYGRICPIETPEGGNAGLVSSLTTYAKINSSGFLECP 466

Query: 602 YRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           + KV +G+V       +LSA +EEN +++  +  + ++    +E +  R   E      +
Sbjct: 467 FYKVNNGEVKKKEGPYFLSAEQEENTFVSPGDLFISKENKLCQEKIPTRYKKEFGTSSPK 526

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++ FI  SP Q++S+A SLIPFLE+DD+NRVLMG NMQRQAVP+L  E P VGTG+E  V
Sbjct: 527 QVQFIGISPIQMISVATSLIPFLEHDDANRVLMGSNMQRQAVPILSPERPLVGTGLEGQV 586

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +++K++G+V   ++  I +         S S   I+ L ++QRSNQ TC++QR
Sbjct: 587 ARDSGTVLLSKKSGLVISTNSEEIHVSY----SKDSRSNYIIHPLQRYQRSNQATCISQR 642

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V VGD V+  D++ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER+V E+++
Sbjct: 643 PSVCVGDWVQEGDLLADGAATSKGELALGKNVLVAYMPWEGYNFEDAILISERLVYENIY 702

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIE +EV AR TK+G E  TR++P+V  E   ++DE G++  G+ V  GDILVGKIT
Sbjct: 703 TSIHIERYEVEARQTKIGIEIFTRNLPHVENELTDHLDENGLVLPGSWVEGGDILVGKIT 762

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           PKGE   TPE++LLRAIF +K  DV+D+SLRVP+GV G V+ VR
Sbjct: 763 PKGEFDQTPEKRLLRAIFQQKEPDVQDSSLRVPNGVKGRVIYVR 806



 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 81/459 (17%), Positives = 167/459 (36%), Gaps = 33/459 (7%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI--TAFSGAAMLEF 76
           K  +   +PDL+ +Q+ S+  FL           +G Q   + + PI     +    + F
Sbjct: 3   KMTKDFKLPDLVGIQRESFFSFL----------EKGFQEEIQRISPICCENETEKTKIYF 52

Query: 77  VSYEFD--PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
            + E +   P     + +++ LTY+  + + L++  F  +E    KS    K Q +++G+
Sbjct: 53  YANEVEWRHPILLPQEAIFKSLTYSTAVYVPLQIFSFPHEEGIPRKS----KRQKVFLGE 108

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  GTF+I G  R++V+Q+ RS GI++     +        Y   I+ ++G W+ I
Sbjct: 109 IPLMTGKGTFIINGSSRVIVNQIVRSAGIYYKPQLDKD---NNKTYLGSILSNRGSWLRI 165

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG-DFWCFPLSAAD 253
           E D   ++ V+ID+ RK+P+  FL ALG+  ++I  +       ++              
Sbjct: 166 ETDKNALVWVKIDKIRKIPIFVFLYALGLTQKQINESLRHSTFLNKSLWKQAEMEEEEPP 225

Query: 254 LMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           +   + +      +       + S   L      +     +  LG          +    
Sbjct: 226 IDQKSALLKLHFKLRPDRPGTLRSASDLLESRFMNPNRYDLGRLGRIRLNKKLRILGNPT 285

Query: 313 VNGETGEIYIEAGDVIDE--------KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
                 E  + A D +            ++++ +  IR    L  + +         ++ 
Sbjct: 286 ATVLRPEDILAAVDYLVNLEFGMGKVDDIDDLKNRRIRTSGELIQNQIRIGFSRLEKMIR 345

Query: 365 DKNKDRKDAL-LDIYRVMRPGDVSTF-SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
           +K  + +    L I     P        +  S+  F         +     +        
Sbjct: 346 EKMTEIEPINGLTIAESFLPTRFIHPKPMVGSLREFFGSSQLSQYMDQTNPLAEITHKRR 405

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            +      + K+     ++ +     G+    +    GN
Sbjct: 406 LSSLGPGGLSKDRAGMAVREIHPSHYGRICPIETPEGGN 444


>gi|331029429|gb|AEC49864.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6028]
          Length = 305

 Score =  437 bits (1125), Expect = e-120,   Method: Composition-based stats.
 Identities = 175/304 (57%), Positives = 227/304 (74%), Gaps = 1/304 (0%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRD 95
           S D FLM++     R +E LQA  +SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R 
Sbjct: 1   SXDQFLMVDEPTGRRLDERLQAVSRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRG 60

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVS 155
           +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTFV+ G +R++VS
Sbjct: 61  MTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFVVNGTERVIVS 120

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT 215
           Q+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVT
Sbjct: 121 QMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVT 180

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S + ALG+D E+ILSTFY KI Y +  D W  P  A +   G    + L+D DTG+ V+E
Sbjct: 181 SLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLE 239

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           +GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL  
Sbjct: 240 AGKKLTVRQARQLQEKGLKGLRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLXV 299

Query: 336 IFHS 339
           +   
Sbjct: 300 LNEQ 303


>gi|330369320|gb|AEC12050.1| RNA polymerase beta subunit [Bradyrhizobium sp. CCBAU 23303]
          Length = 295

 Score =  437 bits (1124), Expect = e-120,   Method: Composition-based stats.
 Identities = 166/295 (56%), Positives = 227/295 (76%), Gaps = 1/295 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 2   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 61

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 62  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 121

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 122 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 181

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+
Sbjct: 182 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQ 240

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           EKG+K L ++ + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++
Sbjct: 241 EKGLKALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEHGYKEL 295


>gi|157777933|gb|ABV70119.1| DNA-directed RNA polymerase beta subunit [Heterosigma akashiwo]
          Length = 1117

 Score =  435 bits (1119), Expect = e-119,   Method: Composition-based stats.
 Identities = 182/599 (30%), Positives = 254/599 (42%), Gaps = 75/599 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       +L    P  G   E  +    R+V+  + T   I ++    +       
Sbjct: 528  MGANMQRQAVPLLYPRKPIVGTGIESQVAFDSRLVN--IATKPGIVKYVSSQQIDIKNIE 585

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +   + I          +++  ++ VG  +  G ++      +    +   + L  A 
Sbjct: 586  GEKIAYKLIKYRPSNQDTCLNQRPLVWVGQSIKTGQVIADGPGTQ-SGELALGQNLTVAY 644

Query: 917  FGEKAVD------VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +      V D  +      S  + +     +      +   S      E   ++
Sbjct: 645  MPWQGYNYEDAILVSDKLVYQNLFTSIHIEECETEVQQTKTGEQVITSDIPLVSEKNCKN 704

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+    Y    +IL G+    G        +  + L+      +         +
Sbjct: 705  L-DENGIIKVGKYVYPGDILVGKITPKGEID----QLPEAKLLKAIFGFKTPDMRDSSLR 759

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V   +                    KI K      +  GV   ++VF+A    +Q GDK+
Sbjct: 760  VPGGLSG-------------RVLDIKIFKKPKPGKV-FGVGSKIRVFIAQISKLQVGDKI 805

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SRILP +DMPFL DGT VDI+LNPLGVPSRMNVGQIFE  LG A   L K
Sbjct: 806  AGRHGNKGVISRILPHQDMPFLPDGTSVDIILNPLGVPSRMNVGQIFECLLGLAGDQLNK 865

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K L  D     + S +    +                                     
Sbjct: 866  RFKILPFDEMYQNEASRILINQKLKDAAKKQN---------------------------- 897

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                        L  A     G+ +L DG TGE FD PV VG  Y+LKL H+V DK++AR
Sbjct: 898  ---------KPWLFSAY--SPGKILLSDGRTGEKFDNPVLVGRSYILKLAHLVEDKIHAR 946

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSL+TQQP+GGKS  GGQR GEMEVW ++A+GAAY LQE+LTIKSDD+ GR  V  
Sbjct: 947  STGPYSLITQQPVGGKSQNGGQRFGEMEVWALEAFGAAYTLQELLTIKSDDMQGRDDVLN 1006

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSID-----LENSRTKNSAKMEEIPDFNKCE 1384
            SIV G +  ++  PESF VL++E+ ALGL I       EN   KN     EI      E
Sbjct: 1007 SIVCGQEIPKSSIPESFKVLMRELNALGLDITTYKVMFENETNKNCLIKNEINLMQTYE 1065



 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 291/679 (42%), Positives = 415/679 (61%), Gaps = 26/679 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIY---IEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           L   ++ L    V+   +  + G       +          E+   S    +  L ++  
Sbjct: 141 LYYKAEFLNNNIVSTVTIIAQRGSWLKFEFDKNGYWVRIDKEK-KISIFDFLEGLNINDE 199

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
              + +++     K K  ++ L       R  D    ++ E +      D + Y L  +G
Sbjct: 200 EILSGLKSIAPLLKYKKTQEILK------RNNDPDLKNLIEKI-----TDPNSYSLGIIG 248

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R+ +N RL L+    V  +   DI  II   +  R+     DDID+L NRR+R+VGE++ 
Sbjct: 249 RLNLNRRLGLNISTRVHTLTIHDIFGIIDFFLSARSFV--PDDIDDLRNRRIRAVGELIT 306

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           +Q  +GL R+ER+I ER +      ++P+ L+NA+P++SA+ EFF SSQLS   +  N L
Sbjct: 307 SQCEIGLNRLERNILERTNFSGSVRILPKTLVNARPIMSAIQEFFNSSQLSHYMDQTNLL 366

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S   + RR+SALG GG+   R  V  RD+HPT YGR+CP ET EG N+GLVS+L S+AR+
Sbjct: 367 SETANKRRISALGPGGLNADRVTVAARDIHPTQYGRLCPIETPEGQNVGLVSTLASYARI 426

Query: 593 NAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N  GFI+TPY +V +GK+     ++YL+A +EEN  IA A+   D+DG   ++ +  R  
Sbjct: 427 NRNGFIQTPYFRVENGKILTQQPLIYLTAEQEENLKIAPADVKRDQDGYLVDDFIVTRFN 486

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E I+ P + +DFI  S  Q++S+AASLIPFLE+DD+NR LMG NMQRQAVPLL    P 
Sbjct: 487 QEFIITPSKLVDFISVSVIQIISVAASLIPFLEHDDANRALMGANMQRQAVPLLYPRKPI 546

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+ES VA  S    +A + GIV+ V + +I I+++EG+          Y+L+K++ S
Sbjct: 547 VGTGIESQVAFDSRLVNIATKPGIVKYVSSQQIDIKNIEGEKIA-------YKLIKYRPS 599

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC+NQRPLV VG  ++   +IADGP T  G+LALG+N+ VA+MPW GYN+ED++L+S
Sbjct: 600 NQDTCLNQRPLVWVGQSIKTGQVIADGPGTQSGELALGQNLTVAYMPWQGYNYEDAILVS 659

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +++V +++FTSIHIEE E   + TK G + IT DIP VSE+  KN+DE GII VG  V P
Sbjct: 660 DKLVYQNLFTSIHIEECETEVQQTKTGEQVITSDIPLVSEKNCKNLDENGIIKVGKYVYP 719

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGKITPKGE    PE KLL+AIFG K  D+RD+SLRVP G+SG V+D++IF +   
Sbjct: 720 GDILVGKITPKGEIDQLPEAKLLKAIFGFKTPDMRDSSLRVPGGLSGRVLDIKIFKKPKP 779

Query: 951 DKNERSISVEREQIELLAR 969
            K     S  R  I  +++
Sbjct: 780 GKVFGVGSKIRVFIAQISK 798



 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 117/250 (46%), Gaps = 30/250 (12%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS-GAAML-----EF 76
           I  +PD +E+Q++S+  FL+          +GL     S+ PI   +     L     EF
Sbjct: 7   ITKLPDFLEIQRSSFCWFLL----------KGLSYELNSLSPIIDVNVKRVKLKLYPQEF 56

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK--DIKEQSIYMGD 134
           V     P +         D TY V + +   +I  D +     K  +  DIKE+ +++G 
Sbjct: 57  V---LKPGRTTPICAKQNDSTYGVRIFLPAEVIYCDTESKYPTKKNRLEDIKEK-VFIGQ 112

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  G+F++ G +R++V+Q+ R PG+++  +     L+  ++    II  +G W+  
Sbjct: 113 IPLMTSTGSFIVNGCERVIVNQIIRCPGLYYKAEF----LNNNIVSTVTIIAQRGSWLKF 168

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI---LSTFYPKIVYSQRGDFWCFPLSA 251
           EFD      VRID+ +K+ +  FL  L ++ EEI   L +  P + Y +  +        
Sbjct: 169 EFDKNGY-WVRIDKEKKISIFDFLEGLNINDEEILSGLKSIAPLLKYKKTQEILKRNNDP 227

Query: 252 ADLMVGAKVS 261
               +  K++
Sbjct: 228 DLKNLIEKIT 237


>gi|189095359|ref|YP_001936372.1| RNA polymerase beta subunit [Heterosigma akashiwo]
 gi|157694702|gb|ABV65978.1| DNA-directed RNA polymerase beta subunit [Heterosigma akashiwo]
          Length = 1121

 Score =  435 bits (1119), Expect = e-119,   Method: Composition-based stats.
 Identities = 182/599 (30%), Positives = 254/599 (42%), Gaps = 75/599 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       +L    P  G   E  +    R+V+  + T   I ++    +       
Sbjct: 528  MGANMQRQAVPLLYPRKPIVGTGIESQVAFDSRLVN--IATKPGIVKYVSSQQIDIKNIE 585

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +   + I          +++  ++ VG  +  G ++      +    +   + L  A 
Sbjct: 586  GEKIAYKLIKYRPSNQDTCLNQRPLVWVGQSIKTGQVIADGPGTQ-SGELALGQNLTVAY 644

Query: 917  FGEKAVD------VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +      V D  +      S  + +     +      +   S      E   ++
Sbjct: 645  MPWQGYNYEDAILVSDKLVYQNLFTSIHIEECETEVQQTKTGEQVITSDIPLVSEKNCKN 704

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+    Y    +IL G+    G        +  + L+      +         +
Sbjct: 705  L-DENGIIKVGKYVYPGDILVGKITPKGEID----QLPEAKLLKAIFGFKTPDMRDSSLR 759

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V   +                    KI K      +  GV   ++VF+A    +Q GDK+
Sbjct: 760  VPGGLSG-------------RVLDIKIFKKPKPGKV-FGVGSKIRVFIAQISKLQVGDKI 805

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SRILP +DMPFL DGT VDI+LNPLGVPSRMNVGQIFE  LG A   L K
Sbjct: 806  AGRHGNKGVISRILPHQDMPFLPDGTSVDIILNPLGVPSRMNVGQIFECLLGLAGDQLNK 865

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K L  D     + S +    +                                     
Sbjct: 866  RFKILPFDEMYQNEASRILINQKLKDAAKKQN---------------------------- 897

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                        L  A     G+ +L DG TGE FD PV VG  Y+LKL H+V DK++AR
Sbjct: 898  ---------KPWLFSAY--SPGKILLSDGRTGEKFDNPVLVGRSYILKLAHLVEDKIHAR 946

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSL+TQQP+GGKS  GGQR GEMEVW ++A+GAAY LQE+LTIKSDD+ GR  V  
Sbjct: 947  STGPYSLITQQPVGGKSQNGGQRFGEMEVWALEAFGAAYTLQELLTIKSDDMQGRDDVLN 1006

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSID-----LENSRTKNSAKMEEIPDFNKCE 1384
            SIV G +  ++  PESF VL++E+ ALGL I       EN   KN     EI      E
Sbjct: 1007 SIVCGQEIPKSSIPESFKVLMRELNALGLDITTYKVMFENETNKNCLIKNEINLMQTYE 1065



 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 291/679 (42%), Positives = 415/679 (61%), Gaps = 26/679 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIY---IEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           L   ++ L    V+   +  + G       +          E+   S    +  L ++  
Sbjct: 141 LYYKAEFLNNNIVSTVTIIAQRGSWLKFEFDKNGYWVRIDKEK-KISIFDFLEGLNINDE 199

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
              + +++     K K  ++ L       R  D    ++ E +      D + Y L  +G
Sbjct: 200 EILSGLKSIAPLLKYKKTQEILK------RNNDPDLKNLIEKI-----TDPNSYSLGIIG 248

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R+ +N RL L+    V  +   DI  II   +  R+     DDID+L NRR+R+VGE++ 
Sbjct: 249 RLNLNRRLGLNISTRVHTLTIHDIFGIIDFFLSARSFV--PDDIDDLRNRRIRAVGELIT 306

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           +Q  +GL R+ER+I ER +      ++P+ L+NA+P++SA+ EFF SSQLS   +  N L
Sbjct: 307 SQCEIGLNRLERNILERTNFSGSVRILPKTLVNARPIMSAIQEFFNSSQLSHYMDQTNLL 366

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S   + RR+SALG GG+   R  V  RD+HPT YGR+CP ET EG N+GLVS+L S+AR+
Sbjct: 367 SETANKRRISALGPGGLNADRVTVAARDIHPTQYGRLCPIETPEGQNVGLVSTLASYARI 426

Query: 593 NAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N  GFI+TPY +V +GK+     ++YL+A +EEN  IA A+   D+DG   ++ +  R  
Sbjct: 427 NRNGFIQTPYFRVENGKILTQQPLIYLTAEQEENLKIAPADVKRDQDGYLVDDFIVTRFN 486

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E I+ P + +DFI  S  Q++S+AASLIPFLE+DD+NR LMG NMQRQAVPLL    P 
Sbjct: 487 QEFIITPSKLVDFISVSVIQIISVAASLIPFLEHDDANRALMGANMQRQAVPLLYPRKPI 546

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+ES VA  S    +A + GIV+ V + +I I+++EG+          Y+L+K++ S
Sbjct: 547 VGTGIESQVAFDSRLVNIATKPGIVKYVSSQQIDIKNIEGEKIA-------YKLIKYRPS 599

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQ+TC+NQRPLV VG  ++   +IADGP T  G+LALG+N+ VA+MPW GYN+ED++L+S
Sbjct: 600 NQDTCLNQRPLVWVGQSIKTGQVIADGPGTQSGELALGQNLTVAYMPWQGYNYEDAILVS 659

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +++V +++FTSIHIEE E   + TK G + IT DIP VSE+  KN+DE GII VG  V P
Sbjct: 660 DKLVYQNLFTSIHIEECETEVQQTKTGEQVITSDIPLVSEKNCKNLDENGIIKVGKYVYP 719

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GDILVGKITPKGE    PE KLL+AIFG K  D+RD+SLRVP G+SG V+D++IF +   
Sbjct: 720 GDILVGKITPKGEIDQLPEAKLLKAIFGFKTPDMRDSSLRVPGGLSGRVLDIKIFKKPKP 779

Query: 951 DKNERSISVEREQIELLAR 969
            K     S  R  I  +++
Sbjct: 780 GKVFGVGSKIRVFIAQISK 798



 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 117/250 (46%), Gaps = 30/250 (12%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS-GAAML-----EF 76
           I  +PD +E+Q++S+  FL+          +GL     S+ PI   +     L     EF
Sbjct: 7   ITKLPDFLEIQRSSFCWFLL----------KGLSYELNSLSPIIDVNVKRVKLKLYPQEF 56

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK--DIKEQSIYMGD 134
           V     P +         D TY V + +   +I  D +     K  +  DIKE+ +++G 
Sbjct: 57  V---LKPGRTTPICAKQNDSTYGVRIFLPAEVIYCDTESKYPTKKNRLEDIKEK-VFIGQ 112

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  G+F++ G +R++V+Q+ R PG+++  +     L+  ++    II  +G W+  
Sbjct: 113 IPLMTSTGSFIVNGCERVIVNQIIRCPGLYYKAEF----LNNNIVSTVTIIAQRGSWLKF 168

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI---LSTFYPKIVYSQRGDFWCFPLSA 251
           EFD      VRID+ +K+ +  FL  L ++ EEI   L +  P + Y +  +        
Sbjct: 169 EFDKNGY-WVRIDKEKKISIFDFLEGLNINDEEILSGLKSIAPLLKYKKTQEILKRNNDP 227

Query: 252 ADLMVGAKVS 261
               +  K++
Sbjct: 228 DLKNLIEKIT 237


>gi|207108181|ref|ZP_03242343.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            HPKX_438_CA4C1]
          Length = 577

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 281/575 (48%), Positives = 392/575 (68%), Gaps = 10/575 (1%)

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVV 510
            IDD D+LGNRR+R+VGE+L N+   GL++M+++IK++++++    DS+MP DL+N+K + 
Sbjct: 2    IDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMIT 61

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            S + EFF   QLSQ  +  N LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRIC
Sbjct: 62   STIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRIC 121

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P ET EG NIGL+++L++F RVN  GFIE PY+KV DGKV  + +YL+A++E++  IA A
Sbjct: 122  PIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 181

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            ++ +DE+G+   +L+  R  GE +L  + K+  +D S   +V +AASLIPFLE+DD+NR 
Sbjct: 182  STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRA 241

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            LMG NMQRQAVPLL+++AP VGTG+E ++A+ S  AI A RAG+VE++D+  I I     
Sbjct: 242  LMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGES- 300

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                  + +D Y L K  R+NQNT  NQ P+VKVGD+V    IIADGPS D G+LALG+N
Sbjct: 301  ---KEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKN 357

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            + VAFMPW+GYNFED++++SER+  +D+FTS HI E EV AR+ K G EE T DIP+V E
Sbjct: 358  VRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGAEEFTADIPDVKE 417

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            E L ++DE GI+ VG  V+ G ILVGK +PKGE   TPEE+LLRAIFG+KA  V + SL 
Sbjct: 418  EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLY 477

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
             P  + GTV+DV++F + G +K+ R +S   E+   L  +  D   +L+R    R+  +L
Sbjct: 478  CPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLL 537

Query: 991  CG----QNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
                  +      K +K+   +  + I+   R   
Sbjct: 538  SQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTL 572


>gi|548822|sp|P36440|RPOB_HETCA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|452825|emb|CAA53450.1| RNA polymerase beta subunit [Heterosigma carterae]
          Length = 1116

 Score =  435 bits (1118), Expect = e-119,   Method: Composition-based stats.
 Identities = 182/599 (30%), Positives = 253/599 (42%), Gaps = 75/599 (12%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       +L    P  G   E  +    R+V+  + T   I ++    +       
Sbjct: 527  MGANMQRQAVPLLYPRKPIVGTGIESQVAFDSRLVN--IATKPGIVKYVSSQQIDIKNIE 584

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G +   + I          +++  ++ VG  +  G ++      +    +   + L  A 
Sbjct: 585  GEKIAYKLIKYRPSNQDTCLNQRPLVWVGQSIKTGQVIADGPGTQ-SGELALGQNLTVAY 643

Query: 917  FGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +  D  L            S  + +     +      +   S      E   ++
Sbjct: 644  MPWQGYNYEDAILVSDKLDIQNLFTSIHIEECETEVQQTKTGEQVITSDIPLVSEKNCKN 703

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+    Y    +IL G+    G        +  + L+      +         +
Sbjct: 704  L-DENGIIKVGKYVYPGDILVGKITPKGEID----QLPEAKLLKAIFGFKTPDMRDSSLR 758

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V   +                    KI K      +  GV   ++VF+A    +Q GDK+
Sbjct: 759  VPGGLSG-------------RVLDIKIFKKPKPGKV-FGVGSKIRVFIAQISKLQVGDKI 804

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++SRILP +DMPFL DGT VDI+LNPLGVPSRMNVGQIFE  LG A   L K
Sbjct: 805  AGRHGNKGVISRILPHQDMPFLPDGTSVDIILNPLGVPSRMNVGQIFECLLGLAGDQLNK 864

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            + K L  D     + S +    +                                     
Sbjct: 865  RFKILPFDEMYQNEASRILINQKLKDAAKKQN---------------------------- 896

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                        L  A     G+ +L DG TGE FD PV VG  Y+LKL H+V DK++AR
Sbjct: 897  ---------KPWLFSAY--SPGKILLSDGRTGEKFDNPVLVGRSYILKLAHLVEDKIHAR 945

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            STG YSL+TQQP+GGKS  GGQR GEMEVW ++A+GAAY LQE+LTIKSDD+ GR  V  
Sbjct: 946  STGPYSLITQQPVGGKSQNGGQRFGEMEVWALEAFGAAYTLQELLTIKSDDMQGRDDVLN 1005

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSID-----LENSRTKNSAKMEEIPDFNKCE 1384
            SIV G +  ++  PESF VL++E+ ALGL I       EN   KN     EI      E
Sbjct: 1006 SIVCGQEIPKSSIPESFKVLMRELNALGLDITTYKVMFENETNKNCLIKNEINLMQTYE 1064



 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 65/252 (25%), Positives = 114/252 (45%), Gaps = 35/252 (13%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS-GAAML-----EF 76
           I  +PD +E+Q++S+  FL+          +GL     S+ PI   +     L     EF
Sbjct: 7   ITKLPDFLEIQRSSFCWFLL----------KGLSYELNSLSPIIDVNVKRVKLKLYPQEF 56

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK--DIKEQSIYMGD 134
           V     P +         D TY V + +   +I  D +     K  +  DIKE+ +++G 
Sbjct: 57  V---LKPGRTTPICAKQNDSTYGVRIFLPAEVIYCDTESKYPTKKNRLEDIKEK-VFIGQ 112

Query: 135 LPLMTKDGTFVIKGIQ--RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           +PLMT  G+F++ G +  R   +Q+ R PG+++  +     L+  ++    II  +G W+
Sbjct: 113 IPLMTSTGSFIVNGCEGYR---NQIIRCPGLYYKAEF----LNNNIVSTVTIIAQRGSWL 165

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI---LSTFYPKIVYSQRGDFWCFPL 249
             EFD      VRID+ +K+ +  FL  L ++ EEI   L +  P + Y +  +      
Sbjct: 166 KFEFDKNGY-WVRIDKEKKISIFDFLEGLNINDEEILSGLKSIAPLLKYKKTQEILKRNN 224

Query: 250 SAADLMVGAKVS 261
                 +  K++
Sbjct: 225 DPDLKNLIEKIT 236


>gi|306569701|gb|ADN03345.1| RNA polymerase beta subunit [Bradyrhizobium liaoningense]
          Length = 292

 Score =  434 bits (1116), Expect = e-119,   Method: Composition-based stats.
 Identities = 166/292 (56%), Positives = 223/292 (76%), Gaps = 1/292 (0%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
           +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVF
Sbjct: 2   DEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVF 61

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           D+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+
Sbjct: 62  DIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGK 121

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILST
Sbjct: 122 THSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILST 181

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EK
Sbjct: 182 FYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEK 240

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           G+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     ++
Sbjct: 241 GLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKE 292


>gi|306569705|gb|ADN03347.1| RNA polymerase beta subunit [Bradyrhizobium yuanmingense]
          Length = 291

 Score =  434 bits (1115), Expect = e-119,   Method: Composition-based stats.
 Identities = 166/292 (56%), Positives = 223/292 (76%), Gaps = 1/292 (0%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
           +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVF
Sbjct: 1   DEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVF 60

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           D+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+
Sbjct: 61  DIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGK 120

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILST
Sbjct: 121 THSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILST 180

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EK
Sbjct: 181 FYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEK 239

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           G+K L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     ++
Sbjct: 240 GLKALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKE 291


>gi|229662009|gb|ACQ84444.1| DNA-dependent RNA polymerase II beta subunit [Epichloe festucae]
          Length = 1261

 Score =  433 bits (1113), Expect = e-118,   Method: Composition-based stats.
 Identities = 225/1428 (15%), Positives = 412/1428 (28%), Gaps = 297/1428 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFSG------AAMLE 75
            L+  Q  S+D F              +Q        IT       +  G         ++
Sbjct: 38   LVSQQTDSFDEFTQTT----------IQDLVNEYSTITLDQPNPPSPPGIKIALRRYEIK 87

Query: 76   FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
            F +     P               +C  R+LTYA PL I +             K +   
Sbjct: 88   FGTVMVSRPTISETDGTVTSLLPYECRDRNLTYASPLYINI------------TKKVSAA 135

Query: 126  KEQSIYMGDLPL--MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
             E+ +     PL  M                +Q           +  +   +        
Sbjct: 136  IEREV-----PLHEMDD--------------AQ---------QAEYAKTGEN-------- 159

Query: 184  IIPDQGLWMDIEF----------DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
              P + +W   E           D K+++ V      K+P+        +  E   S F 
Sbjct: 160  --PTKLIWEQEESPEDDDAGKSEDWKNMVFV-----GKLPIMVKSKICHLSRETDESLFM 212

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG------------EQVIESGKKLT 281
                   +G ++    S   L+   + ++++V +                  +E G +L 
Sbjct: 213  VNECPYDQGGYFVINGSEKVLIAQERSAANIVQVFKKAQPSPFTYTAEIRSALEKGSRLI 272

Query: 282  SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            S L   L  KG    G     +    +     +     ++   G V DE  L  I +   
Sbjct: 273  SSLQLKLYGKGDSARGGFGQTI-HTTLPFVKSDLPIAIVFRALGVVSDEDILNHICYDRK 331

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +      A+          +DR+ AL  I +                 N    
Sbjct: 332  DSQMLEMLRPCIEEAF--------CVQDREVALDFIGKR---------------GNRDQA 368

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
               +     V +  +           +     +   +  ++  L+    G+   DD D+ 
Sbjct: 369  GLGREKRVRVAKDILQKETLPHISQTEGSETRKAFFLGYMVHKLLQCALGRREPDDRDHF 428

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R  + RM   +    R              I    + + +    
Sbjct: 429  GKKRLDLAGPLLAKLFRGIVRRMNNELSNYLRRCVEGNRHFNLAVGIKPGTLSNGLKYSL 488

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 489  ATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKPRQLHNT 544

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L+    V+     E     + +   +V  +   L     
Sbjct: 545  HWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINRGMEVVEEYEPLRYPHA 604

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      + +D       V        +      + +  D   K        + P 
Sbjct: 605  TKIFVNGTWVGVHQDPKHLVSQVLDTRRKSYLQYEVSLVREIRDQEFKIFSDAGRVMRPV 664

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                  +    G       +               S             RAG VE +DA 
Sbjct: 665  FTVQQEDDPETGIEKGHLVLSKELVNKLAKEQAEPSEDPSEKIGWEGLIRAGAVEYLDAE 724

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +         +       +    +N+R   +              PS  
Sbjct: 725  EEETSMICMTPEDLELYRLQ-KAGVALDDDIGDDLNRRLKTRTNPTTHMYTHCEIHPSMI 783

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +     +  +              
Sbjct: 784  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------- 824

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 825  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 867

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ ++      E  E               +
Sbjct: 868  YNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYD 926

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   +  G           K+  +  +      R+   Q       ++     +   
Sbjct: 927  KLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDS 986

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
               + +                       ++ VKV V   +  Q GDK A RHG KG + 
Sbjct: 987  VILTVNA--------------------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF ++G   DI++NP  +PSRM +  + E  L       G +          
Sbjct: 1027 VTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD-------- 1078

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     ++++ 
Sbjct: 1079 ---------------------------------------------ATP-FTDVTVDSVSE 1092

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +LR       G  I+Y+G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+Q
Sbjct: 1093 LLRKHGYQSRGFEIMYNGHTGKKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQ 1152

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG------ 1335
            P+ G++  GG R GEME  C+ A+GAA  L+E L   SD    R  V E  + G      
Sbjct: 1153 PVEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSD--AFRVHVCE--ICGLMTPIA 1208

Query: 1336 ---------------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                               +   P +  +L +E+Q++ ++  +  +R+
Sbjct: 1209 NLSKQSFECRPCKNKTKIAQIHIPYAAKLLFQELQSMNIAARMFTNRS 1256


>gi|11467788|ref|NP_050839.1| RNA polymerase beta subunit [Nephroselmis olivacea]
 gi|17433259|sp|Q9TL06|RPOB_NEPOL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|5880717|gb|AAD54810.1|AF137379_33 beta subunit of RNA polymerase [Nephroselmis olivacea]
          Length = 1109

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 177/505 (35%), Positives = 251/505 (49%), Gaps = 73/505 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            II +   V  GD+L    +  G   +   + LL A    +  +  D  L     +   + 
Sbjct: 666  IIPLHTPVIRGDLLADGSSTSG-GQIALGKNLLVAYMPWEGYNFEDAILISERLIYDDLY 724

Query: 941  DVRIFNRHGIDK-------NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
                  R+ ++         E + S+  E  + L     DE+ I+ R  +    ++L G+
Sbjct: 725  TSLHIERYEVETQHTKLGPEEITKSIVHETDDKLPYRWLDERGIVMRGAWVEPGDVLIGK 784

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                  K       L   +  + P+     F     +V + V                  
Sbjct: 785  ITPKEEKELTPELRLVYAIFGKRPKG----FRDTSLRVPQGV------------------ 822

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                 ++     +     +VV V+V  +R IQ GDKMAGRHGNKGIVSRI+P +DMP+L+
Sbjct: 823  ---RGRVVDVRMIRDEDTKVVHVYVCQQRQIQVGDKMAGRHGNKGIVSRIVPRQDMPYLQ 879

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVD+VLNPLGVPSRMNVGQ+FE  LG A   LG+++K    D               
Sbjct: 880  DGTPVDMVLNPLGVPSRMNVGQVFECLLGLAGQRLGQQLKVRAFD--------------- 924

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
            ++ G  +    + +   ++       W          FD                +  G+
Sbjct: 925  EMYGAEASRHLVYNKLHEASEVTGHHWL---------FD---------------PNHPGK 960

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            S L DG TG+ FD+ VT+G  YMLKL H V DK++AR+TG YSL+TQQPLGG+S RGGQR
Sbjct: 961  SRLIDGRTGDMFDQAVTIGQAYMLKLIHQVDDKIHARATGPYSLITQQPLGGRSKRGGQR 1020

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
            LGEMEVW  + +GAAY LQE+LT+KSDD+ GR  +  ++V G    E GTPESF V+++E
Sbjct: 1021 LGEMEVWAFEGFGAAYTLQELLTVKSDDMQGRNEIMSAMVQGRQLPEMGTPESFKVMIRE 1080

Query: 1354 MQALGLSIDLENSRTKNSAKMEEIP 1378
            +QAL L I + + R+K + K EEI 
Sbjct: 1081 LQALCLDIGIYH-RSKMTFKTEEID 1104



 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 262/597 (43%), Positives = 380/597 (63%), Gaps = 25/597 (4%)

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           DAL  +Y  + P        A  +      D+ +YD+  VGRVK+N +L L  P+ V  +
Sbjct: 236 DALFHLYTKLSPDKPGNTLTARRVLYEKLMDAKRYDVGLVGRVKLNKKLKLPVPEHVHTL 295

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
           R  D +A    L+ L  G+G +DDID+L NRRVR  GE++++Q R+GL R+ER+++ RIS
Sbjct: 296 RPVDFLAATDYLIGLEYGRGQVDDIDHLKNRRVRCAGELIQSQLRIGLNRLERTMQGRIS 355

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
               +      L+N KPV++A+ EFF S+ LSQ  +  N L+ +TH RRLS+LG GG+++
Sbjct: 356 RP-GELPGMSSLMNPKPVMAALREFFGSNPLSQFMDQTNPLAELTHKRRLSSLGPGGLSQ 414

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG+ +R++HP+ YGRICP ET EG N GL+ S+ ++AR+N YG +E P+ +V +GKV 
Sbjct: 415 DRAGMAVREIHPSQYGRICPIETPEGPNAGLIGSMATYARLNQYGGLECPFYQVVEGKVL 474

Query: 612 ND--VVYLSAMEEE-------------NRYIAQANSSLDED----GSFTEELVFCRCAGE 652
            +   ++L+A +E+                +A A      D     +  +  +  R   E
Sbjct: 475 YEFGPIFLTAEQEDQVTVVAGDILDQRKLMVAVAEGRDPLDPAVRPTLPDRPLILRSRQE 534

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                   ++++  +P Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLLK EAP +G
Sbjct: 535 FHTGSFRDVNYVGIAPTQMISVATSLIPFLEHDDANRALMGSNMQRQAVPLLKTEAPIIG 594

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL---DPSTSGVDIYRLMKFQR 769
           TG+E+ VA  +G  + +   GIV  VDA RIV+ + +  L              L  +QR
Sbjct: 595 TGLEAQVAADAGGVVQSPFEGIVVYVDATRIVVSTSKSKLALSKKRKIHESNVFLQVYQR 654

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQ TC++QRP++ +   V R D++ADG ST  G +ALG+N+LVA+MPW GYNFED++LI
Sbjct: 655 SNQGTCIHQRPIIPLHTPVIRGDLLADGSSTSGGQIALGKNLLVAYMPWEGYNFEDAILI 714

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG--LKNIDECGIICVGAE 887
           SER++ +D++TS+HIE +EV  + TKLGPEEIT+ I + +++    + +DE GI+  GA 
Sbjct: 715 SERLIYDDLYTSLHIERYEVETQHTKLGPEEITKSIVHETDDKLPYRWLDERGIVMRGAW 774

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           V PGD+L+GKITPK E  +TPE +L+ AIFG++    RDTSLRVP GV G VVDVR+
Sbjct: 775 VEPGDVLIGKITPKEEKELTPELRLVYAIFGKRPKGFRDTSLRVPQGVRGRVVDVRM 831



 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 63/266 (23%), Positives = 117/266 (43%), Gaps = 29/266 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           +PDLI +Q+ S+  FL            GL      V P+T       L    Y    PK
Sbjct: 17  LPDLISIQRDSFLLFL----------ERGLATELSHVTPLTGSHFRITLCSHGYRLKRPK 66

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
             + + +++  +Y+  L + +       +        ++ + QS++MGD+PLMT  G F+
Sbjct: 67  VSIQEAVYQATSYSAALYVNV-------ETNQSNLGTQETQIQSVWMGDIPLMTSRGHFI 119

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           I G  R+VV+Q+ RSPGI+F     +     + ++   II ++G W+ +E D   +I VR
Sbjct: 120 INGSSRVVVNQIVRSPGIYFKEMIDQKH---RRMFQASIISNRGSWVRLETDVDGMIWVR 176

Query: 206 IDRRRKVPVTSFLMALGMDSEEIL------STFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           +D+ +K+ +   L A+G+  + I          +  +        W   +     ++   
Sbjct: 177 MDKAKKISILIVLEAMGLSKKTIFRSLKSPEFLFKALQQLLAKKRWQDKVYE---LIPQS 233

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLL 285
            + +L  + T     + G  LT+  +
Sbjct: 234 TTDALFHLYTKLSPDKPGNTLTARRV 259


>gi|269930793|gb|ACZ54131.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 439

 Score =  432 bits (1110), Expect = e-118,   Method: Composition-based stats.
 Identities = 335/440 (76%), Positives = 384/440 (87%), Gaps = 1/440 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VG
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVG 299

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D + + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIE
Sbjct: 300 DLIEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIE 359

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           EFEV ARDTKLGPEEITRDIPNV+EE L+N+D+ GII +GAEV P DILVGKITPKGESP
Sbjct: 360 EFEVAARDTKLGPEEITRDIPNVAEEALRNLDQAGIIYIGAEVQPADILVGKITPKGESP 419

Query: 906 MTPEEKLLRAIFGEKAVDVR 925
           MTPEEKLLRAIFGEKA DVR
Sbjct: 420 MTPEEKLLRAIFGEKASDVR 439


>gi|108773039|ref|YP_635949.1| beta subunit of RNA polymerase fragment b [Scenedesmus obliquus]
 gi|122179537|sp|Q1KVX5|RPOB2_SCEOB RecName: Full=DNA-directed RNA polymerase subunit beta C-terminal
            section; AltName: Full=PEP; AltName: Full=Plastid-encoded
            RNA polymerase subunit beta C-terminal section; Short=RNA
            polymerase subunit beta C-terminal section
 gi|88696605|gb|ABD48231.1| beta subunit of RNA polymerase fragment b [Scenedesmus obliquus]
          Length = 565

 Score =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 174/498 (34%), Positives = 246/498 (49%), Gaps = 50/498 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  GD+L    +  G      +   +  +  E         +           
Sbjct: 96   MVREGDWVQSGDLLADCASSLGGELCLGKNIFIAYMPWEGYNYEDAILISQRLVTEDVYT 155

Query: 941  DVRIFNRHGIDKN----ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             V I +     KN    +  I+ +   I    ++  DE+ I+    +    +IL G+   
Sbjct: 156  SVHIESYEVETKNTKLGKEQITNKIPDIPEKEKNHLDERGIVKLGTFVHEGQILVGKVTP 215

Query: 997  SGPK---GFKK--STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
               K   G++K   T+L  +LI     S      ++ + V+  + +    +  ++  L  
Sbjct: 216  IQKKYRSGYEKLLYTILEKELIPMRDSSLRTPKGLKAKVVEIKILNFSWNFAPTEKTLPS 275

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
              + K  K              V+V++A KR IQ GDKMAGRHGNKGIVS+ILP +DMPF
Sbjct: 276  PIQQKK-KNSKILLKKQRKPERVQVYLAEKRKIQVGDKMAGRHGNKGIVSKILPIQDMPF 334

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+D+VLNPLGVPSRMNVGQI+E  LG A   L    +    D             
Sbjct: 335  LPDGTPLDMVLNPLGVPSRMNVGQIYECLLGLASKYLNHYYRIQAFD------------- 381

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
              ++ G  +          ++ L+  ++W                        + +    
Sbjct: 382  --EIYGPHASRSFTFAKLYEARLKTNQKW------------------------LFNPCYP 415

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  ++DG TGEP+D PVTVG  YMLKL H+V DK++ARSTG YSLVTQQPL G+S  GG
Sbjct: 416  GKMQIFDGQTGEPYDSPVTVGIAYMLKLVHLVDDKIHARSTGPYSLVTQQPLRGRSKYGG 475

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QRLGEMEVW I+AYGAA++L EMLTIKSDD+ GR  ++ +I+     +  GTPESF VL+
Sbjct: 476  QRLGEMEVWAIEAYGAAFILLEMLTIKSDDISGRMTLWSNILLNMPIY-IGTPESFKVLI 534

Query: 1352 KEMQALGLSIDLENSRTK 1369
             E+QAL L + L     K
Sbjct: 535  CELQALCLDMGLFQLNKK 552



 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 93/220 (42%), Positives = 148/220 (67%), Gaps = 1/220 (0%)

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y L K+QRSNQ+T + QRP+V+ GD V+  D++AD  S+  G+L LG+N+ +A+MPW GY
Sbjct: 77  YSLQKYQRSNQDTLIVQRPMVREGDWVQSGDLLADCASSLGGELCLGKNIFIAYMPWEGY 136

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++LIS+R+V+EDV+TS+HIE +EV  ++TKLG E+IT  IP++ E+   ++DE GI
Sbjct: 137 NYEDAILISQRLVTEDVYTSVHIESYEVETKNTKLGKEQITNKIPDIPEKEKNHLDERGI 196

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + +G  V+ G ILVGK+TP  +   +  EKLL  I  ++ + +RD+SLR P G+   VV+
Sbjct: 197 VKLGTFVHEGQILVGKVTPIQKKYRSGYEKLLYTILEKELIPMRDSSLRTPKGLKAKVVE 256

Query: 942 VRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDR 980
           ++I N        E+++    +Q +  ++    +Q   +R
Sbjct: 257 IKILNFSWNFAPTEKTLPSPIQQKKKNSKILLKKQRKPER 296


>gi|22086503|gb|AAM90662.1|AF401092_1 RNA polymerase beta subunit [Ehrlichia ruminantium]
          Length = 519

 Score =  430 bits (1106), Expect = e-118,   Method: Composition-based stats.
 Identities = 295/520 (56%), Positives = 393/520 (75%), Gaps = 1/520 (0%)

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
               KDAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L LD  +
Sbjct: 1   IYRMKDALFEIYKVLRSGESPSLDTMKAFFDGLFFEKERYDLSTVGRIKLNDHLGLDISE 60

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           DV  + K+DII +IK +   +     +DDID+LGNRRVRSVGE ++NQ+R+  ++  + I
Sbjct: 61  DVTVLTKDDIIHVIKKVSIAKRWGRFVDDIDHLGNRRVRSVGEFIENQFRIRYIKTGKMI 120

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            + +SSV+ D+ M  D +N K + + + +FF SSQLSQ  +  N LS +TH RRLSALG 
Sbjct: 121 MDYMSSVNFDNAMLCDFVNPKVLATVLKDFFSSSQLSQFMDQTNPLSEVTHKRRLSALGP 180

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+PYRKV 
Sbjct: 181 GGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIESPYRKVD 240

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE++D+ID 
Sbjct: 241 NGVVTDKVEYLLAMQESNYYIADASATLDENNRFVDDMLYCRHDGNFVMVKREQVDYIDV 300

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP VGTGMES+VA  S   
Sbjct: 301 SPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLVGTGMESIVAAGSSTV 360

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           ++AKR+GIV +VD + IVIR+ + + +    GVDIY L KFQRSN NTC+NQ+PLVK GD
Sbjct: 361 VLAKRSGIVHRVDGLYIVIRAFDKEKNEY-LGVDIYNLRKFQRSNHNTCINQKPLVKPGD 419

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            VR ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFTSIHIEE
Sbjct: 420 YVRENDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFTSIHIEE 479

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           FE + RDT LGPE+I R IP+V+E+ L ++D+ GI+ VGA
Sbjct: 480 FECVVRDTALGPEKIMRSIPDVNEDSLSHLDDVGIVNVGA 519


>gi|215254181|gb|ACJ64095.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 439

 Score =  430 bits (1105), Expect = e-117,   Method: Composition-based stats.
 Identities = 283/439 (64%), Positives = 347/439 (79%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+S
Sbjct: 1   ERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRIS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  L PRE   
Sbjct: 121 RRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQ 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  
Sbjct: 181 YMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNVAVD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V
Sbjct: 241 SGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+I
Sbjct: 301 MPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKG
Sbjct: 361 HIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKG 420

Query: 903 ESPMTPEEKLLRAIFGEKA 921
           E+ +TPEEKLLRAIFGEKA
Sbjct: 421 ETQLTPEEKLLRAIFGEKA 439


>gi|269991247|emb|CAX12425.1| DNA-directed RNA polymerase beta chain [Fucus vesiculosus]
          Length = 1123

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 169/580 (29%), Positives = 261/580 (45%), Gaps = 55/580 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA---RDTKL 856
                       +L    P  G   E  +    ++V  ++                 +  +
Sbjct: 582  MGSNMQRQAVPLLYPKKPIIGTGIEHQIASDSQVVIINLLNGTVNYASSDQIIILDNENV 641

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  ++              I++  +I  G  V PG I+       G   +   + LL A 
Sbjct: 642  GNSKVYFLDKYRRSNQETIINQKPLIWAGEIVKPGQIIADGPGTDG-GELALGQNLLVAY 700

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  +  D  L     +   +       R+ +   + + ++E   I + + +      
Sbjct: 701  MPWEGYNYEDAILVSEKLIHNDLFTSIHIERYELQLMDNNTNIEEITITIPSIEAKAICN 760

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +    I  +      G    SG     K T +  +      +     F ++  + +    
Sbjct: 761  LDKNGIIKK------GTFVKSGDILVGKITPIVEEEELPESKLLRAIFNIKSPEPEDTSL 814

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +          ++   ++K      GD++  GV   V + +A  + I+ GDK++GRHGN
Sbjct: 815  RVPNGVSGRVIEVQTASRDK------GDNLESGVYEWVCISIAQTKKIKIGDKLSGRHGN 868

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S+++P  DMPFL DGT +D++LNPLGVPSRMNVGQIFE  LG+A   L ++ K L 
Sbjct: 869  KGVISKLIPTCDMPFLPDGTIIDVILNPLGVPSRMNVGQIFECLLGFAGDYLNQRFKVLP 928

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D     + S +                     + ++ + A +        T +F+    
Sbjct: 929  FDEMYRSNASRI-------------------LVNKTLKKAAYKTNK-----TWLFNK--- 961

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G+  L DG TGE F+ PV VG  Y+LKL H+V  K++ARSTGSYS
Sbjct: 962  ------------SSPGKIPLIDGRTGELFNNPVLVGKPYILKLIHLVDKKMHARSTGSYS 1009

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            L+TQQPLGGKS  GGQR GEMEVW ++A+G AY LQE+LTIKSDD+ GR  V+ +I+ G 
Sbjct: 1010 LITQQPLGGKSKHGGQRFGEMEVWALEAFGVAYTLQELLTIKSDDINGRHEVFNAIINGR 1069

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
               E G PESF VL++E+ ALGL I     R  NS +++ 
Sbjct: 1070 PIPEPGVPESFKVLLRELNALGLDITTHQLRKSNSEEIKS 1109



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 252/637 (39%), Positives = 363/637 (56%), Gaps = 37/637 (5%)

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           +Y    N     ++    +     K      +       +        + N    +   Y
Sbjct: 205 IYQTVQNYEFLRKSVQSLNSAVYEKMFQKANFESYNKSILIVILRVRELINERILNKSFY 264

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
           DL  VGR+K+N +L ++ P ++R +   D++  I  L+ +      +DDIDNL NRRVR 
Sbjct: 265 DLGEVGRIKLNKKLGINLPLNIRILTPLDVLKTIDKLISISFYNEKLDDIDNLENRRVRC 324

Query: 467 VGEMLKNQYRLGLLRMERSI------------------------------KERISSVDID 496
           VGE+L+ Q R+ L R++++I                               +       +
Sbjct: 325 VGELLQLQIRVALNRLKKNITTSEKLTSDMFRVKNIRKTILSKQIESTNKIQTEEKYTEN 384

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           ++MP  LI +K + S + EFF  S LSQ  + +N+L+++TH RR+S+LG GG+       
Sbjct: 385 TLMPSSLITSKVLTSTIREFFGLSPLSQYFDEINALAQLTHKRRISSLGPGGLNSEHVSF 444

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--V 614
             RD+HPT YGR+CP ET EG   GL+SSL + A++N YGFI TP+ +V  GKV  +   
Sbjct: 445 AARDIHPTQYGRLCPIETPEGQRAGLISSLATHAKINQYGFITTPFFRVYKGKVLKESTP 504

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +YL+A +E    +A A+  L +D  F  + V  R   E I+V    +DFI  SP Q+++ 
Sbjct: 505 IYLTAEKENIYRVASADVLLTKDYFFETQYVPVRFYNEFIVVNSTTVDFIAVSPIQIIAA 564

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            ASLIPFLE+DD+NR LMG NMQRQAVPLL  + P +GTG+E  +A  S   I+    G 
Sbjct: 565 GASLIPFLEHDDANRALMGSNMQRQAVPLLYPKKPIIGTGIEHQIASDSQVVIINLLNGT 624

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V    + +I+I   E   +       +Y L K++RSNQ T +NQ+PL+  G+ V+   II
Sbjct: 625 VNYASSDQIIILDNENVGNS-----KVYFLDKYRRSNQETIINQKPLIWAGEIVKPGQII 679

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGP TD G+LALG+N+LVA+MPW GYN+ED++L+SE+++  D+FTSIHIE +E+   D 
Sbjct: 680 ADGPGTDGGELALGQNLLVAYMPWEGYNYEDAILVSEKLIHNDLFTSIHIERYELQLMDN 739

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
               EEIT  IP++  + + N+D+ GII  G  V  GDILVGKITP  E    PE KLLR
Sbjct: 740 NTNIEEITITIPSIEAKAICNLDKNGIIKKGTFVKSGDILVGKITPIVEEEELPESKLLR 799

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           AIF  K+ +  DTSLRVP+GVSG V++V+  +R   D
Sbjct: 800 AIFNIKSPEPEDTSLRVPNGVSGRVIEVQTASRDKGD 836



 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 72/363 (19%), Positives = 143/363 (39%), Gaps = 32/363 (8%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV- 77
           K    + +PDL EVQ+ S+  FL           EG+   F     I   +  + +E + 
Sbjct: 9   KQKFPLVLPDLSEVQRLSFCWFLT----------EGIPEEFTDYPSI--LNKKSGIELII 56

Query: 78  ---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
               Y+   P F++   L +   + + + + + L   +V +    +      ++ ++ G+
Sbjct: 57  YGQEYKIHYPNFNILSALQKKGNFNLRIYVLMSLKKREVIKNGTLQPEDFSFKERVFFGE 116

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDH-DKGRASLSGKLLYACRIIPDQGLWMD 193
           +PLMT+ GTF+  G +R++VSQ+ RSPG+++    K +     K+ Y   II   G W+ 
Sbjct: 117 IPLMTEKGTFLFNGCERVIVSQIIRSPGLYYRRLQKEK-----KVFYEGTIISKHGSWLT 171

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
            E +   +I V+ID++ K+P+  FL+   ++  EI    Y  +   +        L++A 
Sbjct: 172 FELEYN-LIWVKIDKQYKIPINWFLVGFFLEENEI----YQTVQNYEFLRKSVQSLNSAV 226

Query: 254 LMVG-AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK--GVKFLGITSDCLCGLYVAE 310
                 K +    +      ++   + +   +L         V  + +       L +  
Sbjct: 227 YEKMFQKANFESYNKSILIVILRVRELINERILNKSFYDLGEVGRIKLNKKLGINLPLNI 286

Query: 311 DIVNG--ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
            I+        I          + L++I + E R +  +            N L  +   
Sbjct: 287 RILTPLDVLKTIDKLISISFYNEKLDDIDNLENRRVRCVGELLQLQIRVALNRLKKNITT 346

Query: 369 DRK 371
             K
Sbjct: 347 SEK 349


>gi|113170437|ref|YP_717229.1| RpoB [Ostreococcus tauri]
 gi|122235247|sp|Q0P3M6|RPOB_OSTTA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|112806844|emb|CAL36351.1| RpoB [Ostreococcus tauri]
          Length = 1088

 Score =  427 bits (1098), Expect = e-117,   Method: Composition-based stats.
 Identities = 160/489 (32%), Positives = 232/489 (47%), Gaps = 54/489 (11%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             ++   ++     V  GD L        +  +     +L      +  +  D  L     
Sbjct: 649  CLNHKPLVEANTWVEAGDCLAD-NAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERL 707

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V   V      +R+ +         E    ++      DE  ++    +    ++L G+ 
Sbjct: 708  VYDDVFTSIHISRYEVSTARLREGQEYFTNQVDRNQYLDEFGVVKIGTWVEAGDVLVGKI 767

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +          + L   +     R+           V   +  ++ +++     +ED   
Sbjct: 768  SPQPDSDNDPESRLLRAIFGGVARNTKTTSYCLSSGVSGRILDVRCEFKRQTKNIEDE-- 825

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                               V V++  KR +Q GDK+AGRHGNKGIVS ILP  DMP+L+ 
Sbjct: 826  ------------SIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQS 873

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G  +D+VLNPLGVPSRMNVGQIFE  LG A   L +  K L  D     ++S        
Sbjct: 874  GKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSR------- 926

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                      +  Y   S L   ++W                        +   +  G+S
Sbjct: 927  --------GFVYHYLYKSRLLTQQKW------------------------LFKPNSPGKS 954

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            I++DG TG  FD+PVTVGY Y+LKL H+V DK++ARSTG YSLVTQQPLGG+S +GGQRL
Sbjct: 955  IVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRL 1014

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW ++ +GAAYVLQE+LTIKSDD++GR R + S++ G    ++G PESF VLV E+
Sbjct: 1015 GEMEVWALEGFGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSEL 1074

Query: 1355 QALGLSIDL 1363
            + L L + +
Sbjct: 1075 RGLCLDMSI 1083



 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 254/705 (36%), Positives = 376/705 (53%), Gaps = 45/705 (6%)

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
              ++G +   ++     G ++       +   +     D + +  +     +    +  
Sbjct: 145 QFDKQGNRTHLVSFLSAYGSWL---RFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDT 201

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           +        A        D      +A+L +   + P   +T           FF+  +Y
Sbjct: 202 IVGALKYPEALDPTLKEVDWKLTTDEAILLLMSRLFPNRPATVLRGRKFLFNQFFNPRRY 261

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNRRVR 465
            LS VGR ++N +  + +      +  +D +A +  L+   NG+   +DDID+L NRR R
Sbjct: 262 SLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEFLDDIDHLKNRRAR 321

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP------QDLINAKPVVSAVCEFFCS 519
             GE+++ Q+RLGL R+ER I  RIS  +I    P        LI  + + S   EFF S
Sbjct: 322 LAGELIQTQFRLGLNRLERVIYNRISDENILRKTPGALGSLNSLIRTQVLASVFQEFFGS 381

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +QLSQ  +  N L+ ITH RRLS+LG GG+ R RAG+ +R +HP++YGRICP ET EG N
Sbjct: 382 NQLSQFMDQTNPLAEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKN 441

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDE 636
            GLV S+ +F ++N  GF+E+PY K+     T   N    LSA  EE+  +AQ +  L  
Sbjct: 442 AGLVGSIATFTQINKNGFLESPYYKLISESNTPDRNGFFLLSAFYEEDTVVAQGDVDLS- 500

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                   +  R   +      ++I+F+   P Q +SIA SLIPFLE+DD+NR LMG NM
Sbjct: 501 -----NFRIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNM 555

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI----------- 745
           QRQAV LL++E PFVGTG+E+ V +  GA IVAK+   +  VDA RI             
Sbjct: 556 QRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIDYFTPVIGDTNLI 615

Query: 746 ----RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                + E     +    +   L  +QRSNQ+TC+N +PLV+    V   D +AD  +T 
Sbjct: 616 DYQNLTAEDVFASNQFKHNTIWLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATA 675

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALGRN+L+ +MPW GYNFED++L+SER+V +DVFTSIHI  +EV     + G E  
Sbjct: 676 KGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLREGQEYF 735

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
           T  +     +  + +DE G++ +G  V  GD+LVGKI+P+ +S   PE +LLRAIFG  A
Sbjct: 736 TNQV-----DRNQYLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFGGVA 790

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
            + + TS  + SGVSG ++DVR   +       ++ ++E E IE 
Sbjct: 791 RNTKTTSYCLSSGVSGRILDVRCEFK------RQTKNIEDESIES 829



 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 105/799 (13%), Positives = 235/799 (29%), Gaps = 75/799 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGAAMLEFV--- 77
           +P+ ++ Q+ S+ +FL            G++       PI      + S      F+   
Sbjct: 10  LPNFLDSQRDSFRYFL----------ETGIREELDFFSPIVGQSLGSSSKRPTDRFISVS 59

Query: 78  ----SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                + F  P +   + + +  TY   L + + +    ++               +   
Sbjct: 60  FHSKDFYFKKPHYTPQEAVQKLGTYKSSLIVPVHVYSKYLNLNATFP---------VAFC 110

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           DLPLMT+ GTF++ G  R++V Q+ R PG++      +    G   +    +   G W+ 
Sbjct: 111 DLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQ---GNRTHLVSFLSAYGSWLR 167

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVY-SQRGDFWCFPLSA 251
            E D K ++   ID  RKVPVT FL ALG   + I+    YP+ +  + +   W      
Sbjct: 168 FETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDTIVGALKYPEALDPTLKEVDWKLTTDE 227

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCG 305
           A L++ +++             +  G+K       + +   +  +G              
Sbjct: 228 AILLLMSRL------FPNRPATVLRGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKT 281

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL--YVDSVNNNAYIRNTLV 363
            ++     +      Y+   +  + + L++I H + R   +    + +       R   V
Sbjct: 282 KHLTLTPQDALAALDYLLRCENGETEFLDDIDHLKNRRARLAGELIQTQFRLGLNRLERV 341

Query: 364 TDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                  ++ L      +      + T  +A     F   +     +     +       
Sbjct: 342 IYNRISDENILRKTPGALGSLNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKR 401

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +      + ++    I++ +     G+    +     N  +           + G L 
Sbjct: 402 RLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLE 461

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
                    S+    +         +            S       + +  +  T     
Sbjct: 462 SPYYKLISESNTPDRNGFFLLSAFYEEDTVVAQGDVDLSNFRIPTRNKSQFTENTVQE-- 519

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +   G+   +       + P              +      SL    R      +E  
Sbjct: 520 --INFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAVSLLRSERPFVGTGLEAH 577

Query: 602 YRKVCDGKVTND----VVYLSAMEEENR--YIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             +     +       + Y+ A   +     I   N    ++ +  +     +     I 
Sbjct: 578 VTRDIGATIVAKQNSYISYVDAQRIDYFTPVIGDTNLIDYQNLTAEDVFASNQFKHNTIW 637

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +   +    D        + A+      +  ++              +L          M
Sbjct: 638 LTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGY-------M 690

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                    A +V++R    +   +I I    V              ++ +      N  
Sbjct: 691 PWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLREGQEYFTNQVDR------NQY 744

Query: 776 VNQRPLVKVGDEVRRNDII 794
           +++  +VK+G  V   D++
Sbjct: 745 LDEFGVVKIGTWVEAGDVL 763


>gi|215254213|gb|ACJ64111.1| RNA polymerase beta subunit [Vibrio ponticus]
          Length = 437

 Score =  427 bits (1097), Expect = e-117,   Method: Composition-based stats.
 Identities = 279/437 (63%), Positives = 344/437 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D++++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR
Sbjct: 1   RVERAVKERLSLGDLEAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT++V YLSA+EE    IAQAN+ L EDG+F EEL+  R  GE  L PRE 
Sbjct: 121 PYRRVVDGVVTDEVDYLSAIEEGQFVIAQANTVLTEDGTFAEELITARQKGESGLHPREH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
             ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  +A
Sbjct: 181 AQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTGIERNIA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP
Sbjct: 241 VDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT
Sbjct: 301 CVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           +IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TP
Sbjct: 361 TIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTP 420

Query: 901 KGESPMTPEEKLLRAIF 917
           KGE+ +TPEEKLLRAIF
Sbjct: 421 KGETQLTPEEKLLRAIF 437


>gi|124805562|ref|XP_001350475.1| DNA-directed RNA polymerase III subunit, putative [Plasmodium
            falciparum 3D7]
 gi|23496598|gb|AAN36155.1|AE014845_10 DNA-directed RNA polymerase III subunit, putative [Plasmodium
            falciparum 3D7]
          Length = 1450

 Score =  426 bits (1096), Expect = e-116,   Method: Composition-based stats.
 Identities = 221/1442 (15%), Positives = 417/1442 (28%), Gaps = 350/1442 (24%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
            L++    SY++F+   I              KS            +EF+      P    
Sbjct: 255  LVKQHIESYNYFIKREIKTIMNATT--NKIIKS-----DIDEHFYVEFLDITVGTPSVEE 307

Query: 85   -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                 K     C  RDLTY+ P+ + +  +          K    I + ++ +G LP+M 
Sbjct: 308  NMIETKLTPQICRQRDLTYSAPIYVDVEYV----------KGNSIITKNNVEIGRLPVML 357

Query: 140  ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                      G F++KG +R+++ Q   S               
Sbjct: 358  RSDICVLNNKSEEELMKLGECPYDPGGYFIVKGTERVLLMQEQLSKN------------- 404

Query: 176  GKLLYACRIIPDQGLWMDIEFDSKDIIHVRID--------------RRRKVP-------- 213
                   RII        +E D K  I   I               +  K+         
Sbjct: 405  -------RII--------VEMDIKHNICATITSTTAESKSRCAIVYKNNKLYLKHNSFIE 449

Query: 214  ---VTSFLMALGMDSE-EILSTFYPKIV---------YSQRGDFWCFPLSAADLMVGAKV 260
               V   L A+G +S+ EI                  Y    +     L A   +     
Sbjct: 450  DIGVCIILRAMGYESDQEIFQMIGSHKNYVNGILLSLYELYNENIKTNLDALLYIGKKIR 509

Query: 261  SSSLVD----------IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
               L            +   + +IE G    S +L S  ++  K+          L +  
Sbjct: 510  PRLLAKGFFSSMKEKQVKNEKDIIEEGLDFLSRVLLSHIQQKSKYDFRNKARCICLMI-R 568

Query: 311  DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +++    +  I+  D    K LE            LY        Y       D+   +
Sbjct: 569  RVLDSANNKNEIDDKDYYGNKRLELAGQLISLLFEDLYKRF-----YFTLKKQIDQTLSK 623

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVR 429
                    ++   G+    +  +   N       +   + +     N  R  ++     +
Sbjct: 624  YMQSNYNSKLRSTGNNMNDNYPDVFRNLPKDIITRGMQTAISTGNWNIKRFKMEKSGVSQ 683

Query: 430  HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML-KNQYRLGLLRMERSIKE 488
             + +   IA I ++  L +       +      +    G +   +        + +++  
Sbjct: 684  VLSRLSFIACIGMMTRLNSQFEKGRKVSGPRALQPSQWGVLCPCDTPEGESCGLVKNLAL 743

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS---QLEEHVNSLSRITHTRRLSALG 545
                 + +      +     +     +     ++         +N +    H R    + 
Sbjct: 744  MTHVTNDNENNENLIEILYTLGVEDSDSLTGEEIYKEGVFFVILNGILLGVHKRPQKFMQ 803

Query: 546  -QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETP 601
                + R     +   ++           T  G     +  + +            +E  
Sbjct: 804  RIRYLRRYGKIGQFVSIYDNFLHNAIYISTDGGRLCRPLIIIENGKSKLLPQHIKALENG 863

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                 D   ++ + ++   E+ N  IA   S +                           
Sbjct: 864  TINFFDLLKSSVIEWIDVNEQNNLLIALNESDISLS-----------------------T 900

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              ++  P  ++ + A LIP+  ++ S R    C M +QA+                    
Sbjct: 901  THLEIDPLTILGVVAGLIPYPNHNQSPRNTYQCAMGKQAIGA------------------ 942

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                   I   +     +   + +Y               Q+PL
Sbjct: 943  -----------------------IGYNQFVRCDTLLYLLVYP--------------QKPL 965

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK                 +   L  G+N +VA M + GY+ ED++++++  +       
Sbjct: 966  VKS----------KTIEFINFEKLPAGQNAIVAVMSFCGYDIEDAIVMNKSSIDRGFGRC 1015

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            + + +  V  +    G  +I    P V  +  +   E  I          D +      K
Sbjct: 1016 MSLRKHSVELKKYFNGSNDIVLPSPLVINKLQQQRKEREIKSEIKNEKEKDGI------K 1069

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
             E      +           V   D   +   G      + +   +   +K+ R      
Sbjct: 1070 QEHHHNNIDSKNNKSSYNNNVSKIDNVKKDSYGHKNISNESKDDIKKMANKDIR------ 1123

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
                                   +   +     A  G    K+  +  +    +  +   
Sbjct: 1124 -----------------------KYHSLDMDGVASIGY-LIKEGQLYVNKFSPKNIKDHV 1159

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                  D             ++ ++   +  + + I+KI +        L++ K+ +   
Sbjct: 1160 KDIGKVD----------INDFKINEIKYKSVYPSYIDKIIF--TENSEGLKLYKIIMRQT 1207

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK + RHG KG+V  ++  EDMPF + G   D+++NP G PSRM VG++ E   
Sbjct: 1208 RLPELGDKFSSRHGQKGVVGLLVNQEDMPFTESGICPDLIMNPHGFPSRMTVGKLLELVA 1267

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
              A V  G+     I       +I+ +         +                 +     
Sbjct: 1268 SKAAVMDGEYKYGSIFSGTPFEEIAEILFRYGFNCSSK---------------ELLYSGL 1312

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +G P+ T                                        + +G IY  KL H
Sbjct: 1313 TGEPLET---------------------------------------YIFMGPIYYQKLKH 1333

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV DK++AR+ G   L+T+QP  G+S  GG RLGEME  C+ AYG + +L E L + SD 
Sbjct: 1334 MVQDKIHARARGPRQLLTRQPTEGRSKEGGLRLGEMERDCLIAYGVSNLLLERLMLSSD- 1392

Query: 1322 VVGRTRVYESIV----------------AGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V     VY  I                   +       P +  +L +E+Q + +   +  
Sbjct: 1393 VC---NVY--ICEDCGMMGYDLYCTFCKKCDKNIVIQMPYACKLLFQELQTMNVFPKIIV 1447

Query: 1366 SR 1367
              
Sbjct: 1448 KE 1449


>gi|260748886|gb|ACX48755.1| RNA polymerase beta subunit [Mesorhizobium sp. AC21a2]
 gi|260748888|gb|ACX48756.1| RNA polymerase beta subunit [Mesorhizobium sp. AC21c2]
          Length = 284

 Score =  426 bits (1095), Expect = e-116,   Method: Composition-based stats.
 Identities = 179/279 (64%), Positives = 221/279 (79%), Gaps = 1/279 (0%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            FKSVFPI+ FSG++MLEFV YEF+ PKFDVD+C  RDLTYA PLK+TLRLIVFD+DE T
Sbjct: 1   VFKSVFPISDFSGSSMLEFVKYEFEGPKFDVDECRQRDLTYAAPLKVTLRLIVFDIDEDT 60

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
           GAKSIKDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGK
Sbjct: 61  GAKSIKDIKEQDVYMGDMPLMTSNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGK 120

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           LL+A R+IP +G W+DIEFDSKD++H RIDRRRK+PVTS LMALGMD EEILSTFY KI 
Sbjct: 121 LLFAARVIPYRGSWLDIEFDSKDVVHARIDRRRKIPVTSLLMALGMDGEEILSTFYNKIT 180

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           Y + GD W  P +      G K    LVD DTGE V+E+GKK+T+   + L EKG+K + 
Sbjct: 181 YKRAGDHWRIPFNVE-RFRGLKAVGDLVDADTGEIVVEAGKKITARQARQLGEKGLKAIK 239

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
            T + L G Y+AEDIVN  TGEI++EAGD IDEK+L+ +
Sbjct: 240 ATDEDLLGNYLAEDIVNYATGEIFLEAGDEIDEKTLKVL 278


>gi|246880790|gb|ACS95102.1| beta subunit of RNA polymerase fragment 2 [Dunaliella salina]
          Length = 924

 Score =  425 bits (1092), Expect = e-116,   Method: Composition-based stats.
 Identities = 153/407 (37%), Positives = 213/407 (52%), Gaps = 43/407 (10%)

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP-RSQWWQFAVQ 1027
            +    +  I   N+ S   E     +     K            +  +   SQ   +  +
Sbjct: 521  KILSQQNKISSENLRSGTREGTKNFSLGQNNKIVLSGKFSGQSRVINFSNFSQLSSYTKK 580

Query: 1028 DEKVQRNVESLKVQYETSKSILE--DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              K  R + +L+   +     L+   + KNK EK  +        +  + +++A KR IQ
Sbjct: 581  FRKNPRVLRTLQTLVDGQLKNLKIMKKLKNKAEKGGFVSTKSIKDIETIHIYLAEKRKIQ 640

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDKM+GRHGNKGIVS+ILP +DMPFL DGTP+D+VLNPLGVPSRMNVGQI+E  LG A 
Sbjct: 641  VGDKMSGRHGNKGIVSQILPMQDMPFLPDGTPIDMVLNPLGVPSRMNVGQIYECLLGLAG 700

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG+  K    D               ++ G  +    +     ++  +   +W     
Sbjct: 701  KYLGEHYKISSFD---------------EIYGPEASRSFVFSKLYEARCKTGFKW----- 740

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                               + +    G+  LYDG TG+ + +PVTVG  YML+L HMV D
Sbjct: 741  -------------------LFNPQYPGKIRLYDGRTGDCYHQPVTVGQSYMLRLVHMVDD 781

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ RSTG YSLVTQQPL G+S +GGQRLGEMEVW ++ YGAA+ L EMLT+KSDD+ GR
Sbjct: 782  KIHMRSTGPYSLVTQQPLRGRSKQGGQRLGEMEVWALEGYGAAFTLLEMLTVKSDDLTGR 841

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
              ++ +++   D    GTPE+F VL+ E+QAL L I L    T N+ 
Sbjct: 842  MTLWSNLILNKDL-TIGTPEAFKVLICELQALCLDIGLYRYNTTNAP 887



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 46/101 (45%), Positives = 69/101 (68%)

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
              +        Y+L  F RSNQ+TC+  +P V  GD V+  D + D  ++  G+L+LG+
Sbjct: 83  NFNNKVVPKKTEYKLETFHRSNQDTCLTHKPAVFEGDWVQSGDFLTDCANSVGGELSLGQ 142

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           N+ +A+MPW GYNFED++LISER+VS+D+FTS+HIE +E+ 
Sbjct: 143 NIFIAYMPWEGYNFEDAILISERLVSDDLFTSVHIERYEIE 183



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 106/240 (44%), Gaps = 37/240 (15%)

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            EEITRDIP+V+ E + ++D  GI+ +G+ V  GDILVGKITP  +   TP +KLL  I  
Sbjct: 257  EEITRDIPDVTPEEICHLDSFGIVKIGSIVEEGDILVGKITPINKKDFTPYQKLLYTILD 316

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN---------------ERSISVEREQ 963
            ++    RD+SLR P G+   V+D++IF + G                   +RS  +E+ +
Sbjct: 317  KQIRPYRDSSLRAPKGIKAKVIDIKIFVKPGSVVRSPFAYSSKFLKTDPPKRSSKLEKSK 376

Query: 964  IELLARDKDDEQVIL---------------------DRNIYSRLMEILCGQNAVSGPKGF 1002
               +    +++                          RN Y +L++ +   + ++     
Sbjct: 377  KVRVKARSEEKSFDFSSPKKNNLIVRSSPVKAAPKQKRNAYLQLLKKISSSSNLNKFIHI 436

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
            KK    ++ +   + +    Q ++ +   +      + V+   +K ++      KI ++ 
Sbjct: 437  KKGFNQTNKMRHVFLQDMQSQQSLDNLNYLNSLNSFIPVRAAPTKKLIAREGNYKINEVN 496


>gi|331029435|gb|AEC49867.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6145]
          Length = 289

 Score =  424 bits (1091), Expect = e-116,   Method: Composition-based stats.
 Identities = 166/283 (58%), Positives = 218/283 (77%), Gaps = 1/283 (0%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVFD+DE T
Sbjct: 1   VFRSVFPISNFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEET 60

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
           GAKS+KDIKEQ++YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGK
Sbjct: 61  GAKSVKDIKEQNVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGK 120

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV 237
           LL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY KI 
Sbjct: 121 LLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQILSTFYKKIT 180

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           Y +  D W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L 
Sbjct: 181 YKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRQARQLQEKGLKALR 239

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
           ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +   +
Sbjct: 240 MSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKVLNEQD 282


>gi|221327614|gb|ACM17474.1| RNA polymerase beta subunit [Acholeplasma sp. DM-2009]
 gi|221327616|gb|ACM17475.1| RNA polymerase beta subunit [Acholeplasma sp. DM-2009]
 gi|221327618|gb|ACM17476.1| RNA polymerase beta subunit [Acholeplasma sp. DM-2009]
 gi|221327620|gb|ACM17477.1| RNA polymerase beta subunit [Acholeplasma sp. DM-2009]
          Length = 1223

 Score =  424 bits (1091), Expect = e-116,   Method: Composition-based stats.
 Identities = 307/769 (39%), Positives = 447/769 (58%), Gaps = 68/769 (8%)

Query: 249  LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            ++  +      V  ++V++ TGE ++E+G  LT  + ++L          +   L     
Sbjct: 280  ITPIEYAKEIIVEQNIVNLLTGEVIVEAGSVLTPEVRQTLLVNREGLNYASLRYL--RTF 337

Query: 309  AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
             +  +      +    G  + ++   +I+ ++     +  +      A     ++ D  +
Sbjct: 338  IDHDILLADDSVLFYEGTEVTDEVYFQIYENKQNLKSLEDLKYATVYAKQDIDILEDYRR 397

Query: 369  DRK-DALLDIYRVMRPGDVSTFSVAESMFNFLF---FDSDKYDLSTVGRVKMNMR----- 419
                ++  D   +M  G   T      +         +  KY L    + +   +     
Sbjct: 398  HESVESQRDHKPIMYCGYEITDENLLELQINRNKLDENVIKYFLVAGKKGEFYRKESQRR 457

Query: 420  ------------------------LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                                    +  D+ +   HI   DIIA I   ++L +G G IDD
Sbjct: 458  ATFVEVIQIKAAKDAKDDKDVIELIGHDSRETRLHITVSDIIASISYYLNLYDGVGKIDD 517

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            ID+L NRR+R +GE+LKNQ+R+GL ++E++IK+++S+ D      Q LIN KP+ +++ E
Sbjct: 518  IDHLSNRRLRLIGELLKNQFRIGLAKLEKNIKDKMSTADAKEASLQSLINIKPLTASLKE 577

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF SSQLSQ  + +N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGRICP ET 
Sbjct: 578  FFGSSQLSQFMDQINPLAELTQKRRVSALGTGGLARDRAGVEVRDVHESHYGRICPIETP 637

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-----GKVTNDVVYLSAMEEENRYIAQA 630
            EG +IGL+SSL S+A+V+ YGFI+TPY KV         VT++ VY +A EEE+  IA A
Sbjct: 638  EGPSIGLISSLASYAKVDQYGFIQTPYLKVDKSDPEHPFVTSEYVYFTAGEEEHHIIASA 697

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            +S  DE+G F  E V  R  G+    P +K+D++D SPKQ+VS+A S IPFLE+DD++R 
Sbjct: 698  DSQTDENGHFKTETVIGRFMGDTRSYPSKKVDYMDVSPKQIVSVATSSIPFLEHDDASRA 757

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            LMG NMQRQAVPLL  ++P VGTG+E   AK SG+AIVA   G+V   D  +IVI     
Sbjct: 758  LMGANMQRQAVPLLVPDSPIVGTGIEYRSAKDSGSAIVAHVDGVVTYADGRKIVIAVKPE 817

Query: 751  DLDPSTSG----------------------------VDIYRLMKFQRSNQNTCVNQRPLV 782
                +T G                             + Y L +F RSNQ+T + Q+P+V
Sbjct: 818  ASIKTTRGKLVYDKDTEFNWEAYDQIRQAKMTDLLRFETYPLTQFLRSNQDTSILQKPIV 877

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            ++G+++ + D+IADGPS + G+LALGRN++VAFM W GYN+ED++++SE +V  DV+TSI
Sbjct: 878  QIGEKIDKGDVIADGPSINKGELALGRNVVVAFMTWEGYNYEDAVIMSEDLVKNDVYTSI 937

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI+E +V +RDTKLG EEITR+IPNVS + LK +D+ G++  G EV  GDILVGKITPKG
Sbjct: 938  HIDEHQVESRDTKLGKEEITREIPNVSPDALKFLDDRGVVIPGTEVKEGDILVGKITPKG 997

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            ++  TPEEKLL+AIF EKA +VRDTSL+VP G  G V  ++ F++   D
Sbjct: 998  QTEPTPEEKLLQAIFNEKAREVRDTSLKVPHGGGGIVHSIQYFSKSNGD 1046



 Score =  298 bits (763), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 129/451 (28%), Positives = 202/451 (44%), Gaps = 77/451 (17%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
             A+ T L   E       +      +I +  I+ +G +++ GD++    +   +  +   
Sbjct: 845  QAKMTDLLRFETYPLTQFLRSNQDTSILQKPIVQIGEKIDKGDVIADGPS-INKGELALG 903

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELL 967
              ++ A    +  +  D  +     V   V      + H ++  +  +  E    +I  +
Sbjct: 904  RNVVVAFMTWEGYNYEDAVIMSEDLVKNDVYTSIHIDEHQVESRDTKLGKEEITREIPNV 963

Query: 968  ARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            + D     D++ ++      +  +IL G+    G         L   + +E  R      
Sbjct: 964  SPDALKFLDDRGVVIPGTEVKEGDILVGKITPKGQTEPTPEEKLLQAIFNEKAR------ 1017

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          ++            GD++ PGV  V++V++  KR I
Sbjct: 1018 -----EVRDTSLKVPHGGGGIVHSIQY------FSKSNGDELGPGVNEVIRVYIVKKRKI 1066

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG++S+ILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 1067 SEGDKMAGRHGNKGVISKILPREDMPYMADGTPVDIMLNPLGVPSRMNIGQVLEIHLGMA 1126

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG K+ + + D                          ++  D + V+  A     G 
Sbjct: 1127 AKKLGIKVATPVFDG-------------------------LTQLDLEQVMAEAGMASDGK 1161

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             V                             LYDG TGEP++  V+VG +YM+KL+HMV 
Sbjct: 1162 QV-----------------------------LYDGRTGEPYENRVSVGVMYMIKLSHMVD 1192

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            DK++ARS G Y+LVTQQP+GGK+  GGQR G
Sbjct: 1193 DKLHARSVGPYTLVTQQPMGGKAQNGGQRFG 1223



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 77/224 (34%), Gaps = 27/224 (12%)

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCF 247
           G W++ E  +K+I + ++DR +KV +T+ L A G D  EEI   F     Y +  D    
Sbjct: 1   GAWLEYEMGAKNIFYGKLDRSKKVSLTALLQAFGFDGIEEIKKLF---PTYKKMLDETFK 57

Query: 248 PLSAADLMVGAKVSSSLV-DIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITSD---- 301
                 ++        L   +  GE++ + + K+     L   +   ++ +G        
Sbjct: 58  KDEKEGILSSDTAIEDLYSKLRQGEKIPVSAAKEFVRTRLFDSRRYDLEEVGRYKFKQKL 117

Query: 302 CLCGL-----------------YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            +                      A+D+++  T  I +    ++D  S+E +        
Sbjct: 118 DITNRLMTIAQGITAPNQPAIYKYAQDVIDPVTKAILVAKDQIVDVASVELLSQHRDALR 177

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            ++     +      N +   K  D  +       +  P D   
Sbjct: 178 KVVLSKESSLQNESENEVFGIKTSDLFEQYAKDDILYIPADAKE 221



 Score = 42.8 bits (99), Expect = 0.47,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 44/119 (36%), Gaps = 2/119 (1%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+      I +I  L+                +       A+ D+Y  +R G+    S 
Sbjct: 29  LLQAFGFDGIEEIKKLFPTYKKMLDETFKKDEKEGILSSDTAIEDLYSKLRQGEKIPVSA 88

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           A+       FDS +YDL  VGR K   +L++        + I   +  AI K   D+ +
Sbjct: 89  AKEFVRTRLFDSRRYDLEEVGRYKFKQKLDITNRLMTIAQGITAPNQPAIYKYAQDVID 147


>gi|153846293|ref|ZP_01993851.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ3810]
 gi|149744937|gb|EDM56283.1| DNA-directed RNA polymerase, beta subunit [Vibrio parahaemolyticus
            AQ3810]
          Length = 278

 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 147/256 (57%), Positives = 189/256 (73%), Gaps = 5/256 (1%)

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
            K+  + +F+ K  KI  GDD+ PGVL++VKV++A+KR IQ GDKMAGRHGNKG++S+I P
Sbjct: 2    KADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINP 61

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ + G PVDIVLNPLGVPSRMN+GQI E HLG A  G+G KI  ++   K   ++
Sbjct: 62   VEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGDKINQMV---KEQQEL 118

Query: 1166 SPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            +  R FL+KV   G       I+   DD V  + +  + G+P++TPVFDGA E +I ++L
Sbjct: 119  AKFREFLQKVYDLGDTRQKVDIASLSDDEVRTLIKNLRGGLPIATPVFDGAPEASIKALL 178

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
             +ADL  SGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPL
Sbjct: 179  ELADLPTSGQLTLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 238

Query: 1284 GGKSNRGGQRLGEMEV 1299
            GGK+  GGQR GEMEV
Sbjct: 239  GGKAQFGGQRFGEMEV 254


>gi|115350033|ref|YP_764419.1| beta subunit of RNA polymerase [Stigeoclonium helveticum]
 gi|122165129|sp|Q06SE7|RPOB1_STIHE RecName: Full=DNA-directed RNA polymerase subunit beta N-terminal
           section; AltName: Full=PEP; AltName:
           Full=Plastid-encoded RNA polymerase subunit beta
           N-terminal section; Short=RNA polymerase subunit beta
           N-terminal section
 gi|98990247|gb|ABF60214.1| beta subunit of RNA polymerase [Stigeoclonium helveticum]
          Length = 696

 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 233/742 (31%), Positives = 366/742 (49%), Gaps = 70/742 (9%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML----EFV 77
           E   IPD +E+Q+ S+  FL            GL        PIT       +    E+ 
Sbjct: 4   EKYFIPDFVELQRRSFQRFL----------ETGLIEELNKRNPITNSQKDLEILLYPEY- 52

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y+  PP+++  D +    TY+  L +  +L           +  K I  + + +GD+PL
Sbjct: 53  -YKLAPPRWNSLDAILLSKTYSCRLYVPAQLT---------NRKTKQIMFKWVQLGDIPL 102

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL---YACRIIPDQGLWMDI 194
           M+K G FV+ G  R++++Q+ R PG++F   +     S K L   YA   I  +G W+ +
Sbjct: 103 MSKRGHFVVNGAARVIINQIVRGPGLYFSEIQYNVDSSKKTLVRRYAAEFISMRGTWLRL 162

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
             D + +I   + +  K+P+  FL+ +G+ +E+IL  F       +    +   L   +L
Sbjct: 163 SIDKEKMIWAELKKTPKIPLVWFLLGMGL-TEKIL--FQSLTQPKRLLYNYLDYLKIDNL 219

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            +  K  +         + +    KL S  +K+LK        +  +             
Sbjct: 220 AIDVKSQNDAFAKRALLRELLLKSKLNSSNIKTLKNSKDFKPLLLVND------------ 267

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                IY E     ++++     +S+  D+     D      Y  N+ +         AL
Sbjct: 268 -----IYSEMHSYKEKENRRYPLNSQNGDLA----DEKEKIPYYANSSLK--------AL 310

Query: 375 LDIYRVMRPGDVST-------FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
             IY  +      T           +      F +   YDL   GR+ +N +L+L  P  
Sbjct: 311 ELIYSKITNTKKITNLNKKFFAKQGQKWIFKKFMNPRTYDLGLHGRLSLNKKLSLSLPLS 370

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            R +   D++   + L+ +  G    DDIDNL NRRVR+  ++++ Q  +GLLR+E++I+
Sbjct: 371 QRTLTMYDVLVATEHLLRVEQGLLGTDDIDNLKNRRVRTSSDLIQMQIGIGLLRLEKNIR 430

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            + +++           + KP+  A+ EFF ++ LSQ  + +N L+ +TH RRL+ LG G
Sbjct: 431 SKFTTIKG-VPKINYFFSTKPLNGALKEFFGTNPLSQFMDMINPLAEMTHKRRLTTLGPG 489

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           GV+R  A +++R +HPTHYGRICP ET EG N GLV++LT+FARVN  G IETP+ KV  
Sbjct: 490 GVSRDTATMDIRGIHPTHYGRICPVETPEGKNAGLVNALTTFARVNPEGLIETPFYKVYK 549

Query: 608 GKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
           G+V       YLSA +EE   IA  + +L + G   + L+  R   E   V R  +DF+ 
Sbjct: 550 GQVQKKAGFFYLSAEKEEKAIIAAGDLNLSKTGFLPKGLIPVRKFDEFTKVLRNYVDFMS 609

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SP Q++S+A SL+PFLE+DD+NR LMG NMQRQAVPL+++E   VGTG+E+ +A  SG 
Sbjct: 610 VSPLQMISVATSLVPFLEHDDANRALMGANMQRQAVPLVRSEQAIVGTGIETRIASDSGH 669

Query: 726 AIVAKRAGIVEQVDAIRIVIRS 747
            I AK  G+V  V   +I I +
Sbjct: 670 VIRAKAGGLVGYVSGQKIRIYT 691


>gi|145340678|ref|XP_001415447.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144575670|gb|ABO93739.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 1174

 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 185/1055 (17%), Positives = 338/1055 (32%), Gaps = 198/1055 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +          N ++       ++A +   + +    +     A  +         KY 
Sbjct: 280  DILEHIVYDLADNEMMEMLRPSIEEAFVIQSQEVALDFIGKRGSAVGV---SREKRIKYA 336

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +      +  +I  L+    G+   DD D+ GN+R+   
Sbjct: 337  KEILQKELLPHVGVREDCETKK---AYFLGYMIHRLLLCSLGRRPEDDRDHYGNKRLDLG 393

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R    ++ + ++   +        +  Q  I AK +   +     +      
Sbjct: 394  GPLLAQLFRQLFRKLTKDVRLYCQRCIDSGKEIQLQLAIKAKTITQGLKYSLATGNWGSQ 453

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   ++  S ++H RR+++     + R     + R +H + +G ICPAE
Sbjct: 454  GAADIRAGVSQVLNRLSYSSTLSHLRRINS----PIGREGKLAKPRQLHNSLWGMICPAE 509

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG  +GLV +L   A V+     E     + +  + N      ++  E+  I      
Sbjct: 510  TPEGQAVGLVKNLALMALVSVGSPSEPILEFLDEWTMENLEEISPSLIAESTKIFLNGVW 569

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ---VVSIAASLIPFLENDDSNRV 690
            +    +  + +   R    +  +        D   K+            P    +D  ++
Sbjct: 570  VGVHRNPADLVRTLRKLRRQCDIDSSVSVVHDIRLKELRLYTDYGRCTRPLFIVEDDQKL 629

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
             +                    TG       +SG          +E VD        +  
Sbjct: 630  KIKKQHIELLTEKDV-------TGYTWNELVTSG---------FIEYVDTEEEETTMISM 673

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
             +D   +G                 V Q   V +             PS  LG       
Sbjct: 674  TIDDLVAGRH--------------AVEQNTGVAIN-----YTHCEIHPSMILG------- 707

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +  + +P+  +N          M  + +     +       R   LG        P V+ 
Sbjct: 708  ICASIIPFPDHNQSPRNTYQSAMGKQAMG----MYVTNYQIRMDTLGYVMFYPQKPLVTT 763

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              ++ +                             +      + AI      +  D+ L 
Sbjct: 764  RAMEYL-------------------------HFRELPAGCNAVVAIMCYTGYNQEDSVLM 798

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
              S +   +    ++ R   D+ ++  S+ RE+ E   RD          +       I 
Sbjct: 799  NQSAIDRGLF-RSLYYRSFKDEEKKQGSLSREEFERPDRDTCLGMRHGTYDKLDDDGLIC 857

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  L  D  +   +          +     ++  +        +  
Sbjct: 858  PGTRVSGDDIIIGKTAPLPEDDTAVLSK------RFSKKDCSTGMKHAETGIIDQVLL-- 909

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                LR VK+ V   R  Q GDK + RHG KG V      EDMP
Sbjct: 910  --------------TTNDQGLRFVKLRVRSMRTPQVGDKFSSRHGQKGTVGMTYTQEDMP 955

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                   
Sbjct: 956  FTCEGITPDIIVNPHAIPSRMTIGQLVECIMGKVAACMGKEGD----------------- 998

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     E I+SML      +
Sbjct: 999  ------------------------------------ATP-FTPVTAEDISSMLHKCGYQK 1021

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G  ++Y+G TG   D  + +G  Y  +L HMV DK+++R  G   ++T+QP+ G+S  G
Sbjct: 1022 RGNEVMYNGHTGRMLDAQIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPMEGRSRDG 1081

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAGN 1336
            G R GEME  CI ++GAA  L+E L  +SD     V            + + +E      
Sbjct: 1082 GLRFGEMERDCIMSHGAASFLKERLMDQSDAYRIHVCQKCGLIAVANLKNQTFEC---CK 1138

Query: 1337 DTFE------TGTPESFNVLVKEMQALGLSIDLEN 1365
            +  E         P +  +L +E+ ++ ++  L  
Sbjct: 1139 NPSERTSVVQVMVPYACKLLFQELMSMAIAPRLIT 1173



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 106/824 (12%), Positives = 242/824 (29%), Gaps = 110/824 (13%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFS----GAAMLEFVSYEF 81
           L+  Q  S++ F+   +         ++          P             + F     
Sbjct: 32  LVRQQLDSFNEFIQHTMQEIVDEMREIELTPE--HQHMPGQDIDSMEKKTYKISFNQIYL 89

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             P               +   R+LTY+ PL + +   V  V         K+I  ++ +
Sbjct: 90  SKPMVTEADGYTTTLFPKEARLRNLTYSAPLYVDMVKEVTTVQPDGETTVEKEILNKN-F 148

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDH 167
           +G +P+M                         + G FVI G ++++++Q   S    +  
Sbjct: 149 IGKVPIMLRSDYCSLHGHTDKELTELGECPYDEGGYFVINGSEKVLIAQERMSTNHVYVF 208

Query: 168 DKGRASLSGKLLYAC--RIIPDQGLWMDIEF-----------DSKDII-----HVRIDRR 209
           +K       K ++    R  P++G                  D+   I     ++R D  
Sbjct: 209 EK---KQPSKFMWQAECRSQPERGSRGASSCVMRQLHAPGTKDAPGPIRCTLPYIRTD-- 263

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL      +  ++  +     +  A ++   +V+   +   
Sbjct: 264 --IPIFVVFRALGFVADKDILEHIVYDLADNEMMEMLRPSIEEAFVIQSQEVALDFIGKR 321

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                +   K++     + L+++ +  +G+  DC          +      + + +    
Sbjct: 322 GSAVGVSREKRIKYAK-EILQKELLPHVGVREDCETKKAYFLGYMIH---RLLLCSLGRR 377

Query: 329 DEKSLEEIFHSEIRD-IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            E   +   +  +    P+L          +   +     +          ++       
Sbjct: 378 PEDDRDHYGNKRLDLGGPLLAQLFRQLFRKLTKDVRLYCQRCIDSGKEIQLQLAIKAKTI 437

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDL 446
           T  +  S+    +      D+       +N      T   +R I         +     L
Sbjct: 438 TQGLKYSLATGNWGSQGAADIRAGVSQVLNRLSYSSTLSHLRRINSPIGREGKLAKPRQL 497

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            N    +         +      ++KN   + L+ +    +  +  +D  ++   + I+ 
Sbjct: 498 HNSLWGMICPAETPEGQAVG---LVKNLALMALVSVGSPSEPILEFLDEWTMENLEEISP 554

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
             +  +   F     +       + +  +   RR   +           ++   ++  + 
Sbjct: 555 SLIAESTKIFLNGVWVGVHRNPADLVRTLRKLRRQCDIDSSVSVVHDIRLKELRLYTDYG 614

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
               P    E      +        +      +       +   +  + Y+   EEE   
Sbjct: 615 RCTRPLFIVEDDQKLKIKKQH----IELLTEKDVTGYTWNELVTSGFIEYVDTEEEETTM 670

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           I+             ++LV  R A E+           +  P  ++ I AS+IPF +++ 
Sbjct: 671 ISM----------TIDDLVAGRHAVEQNTGVAINYTHCEIHPSMILGICASIIPFPDHNQ 720

Query: 687 SNRVLMGCNMQRQAVPLL----------------KAEAPFVGT-GMESVVAKSSGAAIVA 729
           S R      M +QA+ +                   + P V T  ME +  +   A   A
Sbjct: 721 SPRNTYQSAMGKQAMGMYVTNYQIRMDTLGYVMFYPQKPLVTTRAMEYLHFRELPAGCNA 780

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
             A +          +   +  +D        YR  K +   Q 
Sbjct: 781 VVAIMCYTGYNQEDSVLMNQSAIDRGLFRSLYYRSFKDEEKKQG 824


>gi|82914537|ref|XP_728803.1| DNA-directed RNA polymerase subunit beta [Plasmodium yoelii yoelii
            str. 17XNL]
 gi|23485337|gb|EAA20368.1| DNA-directed RNA polymerase, beta subunit [Plasmodium yoelii yoelii]
          Length = 1312

 Score =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 185/1046 (17%), Positives = 343/1046 (32%), Gaps = 169/1046 (16%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            D        + R ++   +      + R  +   I  +I  L+    G+   DD D+ G 
Sbjct: 355  DKRILYAKELLRKEVLPHMGTGPGVESR--KSYFIGYMINRLLLAELGRIKEDDRDHFGK 412

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFF 517
            +R+   G ++ + +     +M + +K R+    ID+  P D    + +   +   +    
Sbjct: 413  KRLDIAGPLMASSFATYFRKMAKDVK-RVLQRQIDNNKPFDVAGAIRSCSQITQGMQYQL 471

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               ++Q+   +   S ++H RRL+      + R     + R +H T
Sbjct: 472  ATGNWGKDKDGKVIRTGVAQVLNRLTYSSCLSHLRRLNT----PLGREGKMAKPRQLHNT 527

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G ICP ET EG ++GLV +L+    ++        Y  + +      +  +     + 
Sbjct: 528  HWGMICPFETPEGQSVGLVKNLSLMCDISVGTSTNNIYEFLTE-WGLESLDEVPPQLMKE 586

Query: 625  RYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            +     N       +  + L+      R   +         D      K       ++ P
Sbjct: 587  KVKLFLNGKWVGCFNQIDNLIETLYELRRRCDISPEASIVRDVNSKEIKIFTDSGRAMRP 646

Query: 681  FLEN--------------------------------DDSNRVLMGCNMQRQAVPLLKAEA 708
                                                 +     + C  +   +  +  + 
Sbjct: 647  LYVVKNVGGKNKLKLTKEHIKNATKYPDKYNWDYFIQEGIIEYIDCEEEETTMISMFIDD 706

Query: 709  PFVGTGM--ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLM 765
               GTG        +   + I+   A I+   D  +    + +  +     G+      +
Sbjct: 707  LKTGTGYYNNYTHCEIHPSLILGVCASIIPFSDHNQSPRNTYQSAMSKQAMGIYVTNFNI 766

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +           Q+PLV                     DL  G N +VA M + GYN ED
Sbjct: 767  RLDTLAHLLYYPQKPLV----------CTKATEYLHFKDLPAGINAIVAIMCYTGYNQED 816

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECG 880
            S+++++  +   +F S+    +    +       E       R +  +       +++ G
Sbjct: 817  SLIMNQSSIDRGLFRSVFYRTYTSEEKQQGSLIIESFEKPSIRVVKGLKRGDYTKLEDDG 876

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +I  G  V   DI++GK++P  +            I   K  +   ++    +    TV 
Sbjct: 877  LIAPGIRVLGDDIIIGKVSPSIDDEE-------DIIIQRKIPNTSLSTSNNKNIYDTTVG 929

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I +   +  N    S           D   E  + DR             + ++   
Sbjct: 930  SDNISSNSSVMGNPSYGS--------TMLDAGSEPNVNDRYTSGSSSVGSDTSSRINSVS 981

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            G   +T+++      Y  +       +D +V           +  K       ++    +
Sbjct: 982  GQSHTTLVTGAESDRYGSTTGATIR-EDVEVPTLTIRTTNAMKQYKKDCSLSIRSNENGV 1040

Query: 1061 QWGDDMPPG--VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 +       +  KV V   R  Q GDK A RHG KG +      EDMPF  DGT  
Sbjct: 1041 IDTVMLSSNSRGNKFAKVKVRSVRIPQIGDKFASRHGQKGTIGITYRMEDMPFTSDGTFP 1100

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE-KVIG 1177
            DI++NP  VPSRM +G + E   G      G +  +         +IS     L  +  G
Sbjct: 1101 DIIMNPHAVPSRMTIGHLVECLAGKVAAIEGGEGDATPFSKITVQEISERLHRLGYEKYG 1160

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                                 +G+    
Sbjct: 1161 NDILYNG---------------------------------------------HNGKM--- 1172

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
                       + +G  +  +L HMV DK++ARS G  +++T+QP  G+S  GG R GEM
Sbjct: 1173 -------LTSKIFIGPTFYQRLKHMVEDKIHARSRGPLTMITRQPTEGRSRDGGLRFGEM 1225

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVAG--NDTFET 1341
            E  C+ ++G+A +L+E L  +SD       D+ G           YE  +     +  + 
Sbjct: 1226 ERDCMISHGSAKMLKERLFEESDAYRVHVCDICGLCCVADINKNAYECTICNSKTNISQI 1285

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSR 1367
              P +  +L +E+  + +   L    
Sbjct: 1286 YIPYACKLLFQELMTMAIYPKLVLED 1311



 Score =  165 bits (417), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 107/833 (12%), Positives = 216/833 (25%), Gaps = 146/833 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----------AFSGA--AMLE 75
           L+  Q  SY+ F+   +          Q        I              +      L+
Sbjct: 51  LVNQQIESYNDFIEYRM----------QEIIDEHPNIEIKPQPQYRPDKDENNNIIYSLK 100

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F     D P FD            +   R+LTY+  + I +    + VDE T  + +   
Sbjct: 101 FGQLSLDRPFFDEKNLINKNLWPQEARLRNLTYSSAIYIDIEQSTYIVDENTKKQIL--- 157

Query: 126 KEQSIY----MGDLPLMTKD------------------------GTFVIKGIQRIVVSQL 157
           KE+ +Y    +G +PLM K                         G F++ G ++++V+Q 
Sbjct: 158 KEKFVYERINLGRIPLMLKSMFCWTKGLPDNDISDMGECSLDQGGYFIVNGGEKVLVAQE 217

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR--------- 208
            R         K +   S K  +   I       M+ +  +     V++           
Sbjct: 218 -RMANNFIYVFK-KKHSS-KFGWIAEIR----SQME-KSQATSAFSVKMKTKSGSRGSGG 269

Query: 209 ----------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
                           R ++ V     ALG  S+ +IL      +      +     L  
Sbjct: 270 SGKSSGGLLVATLPYIRTEISVGILFRALGCTSDRDILQRIVYDLNDKMMINILKETLEE 329

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-------KFLGITSDCLC 304
                   +    +            K++     K L  K V         +        
Sbjct: 330 CIDYPTQDICLDYIGKRGPTVGASRDKRILY--AKELLRKEVLPHMGTGPGVESRKSYFI 387

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  +   ++  E G I  +  D   +K L+             +     +   +    + 
Sbjct: 388 GYMINRLLL-AELGRIKEDDRDHFGKKRLDIAGPLMASSFATYFRKMAKDVKRVLQRQID 446

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           +          D+   +R     T  +   +    +       +   G  ++  RL   +
Sbjct: 447 NNKP------FDVAGAIRSCSQITQGMQYQLATGNWGKDKDGKVIRTGVAQVLNRLTYSS 500

Query: 425 PDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 R          +     L N    +         +   + + L     + +   
Sbjct: 501 CLSHLRRLNTPLGREGKMAKPRQLHNTHWGMICPFETPEGQSVGLVKNLSLMCDISVGTS 560

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
             +I E ++      +   D +  + +   V  F     +    +  N +  +   RR  
Sbjct: 561 TNNIYEFLT---EWGLESLDEVPPQLMKEKVKLFLNGKWVGCFNQIDNLIETLYELRRRC 617

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPA---ETSEGHNIGLVSSLTSFARVNAYGFIE 599
            +            +   +       + P    +   G N   ++               
Sbjct: 618 DISPEASIVRDVNSKEIKIFTDSGRAMRPLYVVKNVGGKNKLKLTKEHIKNATKYPDKYN 677

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
             Y           + Y+   EEE   I+     L     +                   
Sbjct: 678 WDYFI-----QEGIIEYIDCEEEETTMISMFIDDLKTGTGYYNNY--------------- 717

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV--GTGMES 717
                +  P  ++ + AS+IPF +++ S R      M +QA+ +                
Sbjct: 718 --THCEIHPSLILGVCASIIPFSDHNQSPRNTYQSAMSKQAMGIYVTNFNIRLDTLAHLL 775

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
              +       A      + + A    I ++      +     I       R 
Sbjct: 776 YYPQKPLVCTKATEYLHFKDLPAGINAIVAIMCYTGYNQEDSLIMNQSSIDRG 828


>gi|260505966|gb|ACX42381.1| RNA polymerase subunit beta [Diplorickettsia massiliensis]
          Length = 227

 Score =  423 bits (1087), Expect = e-115,   Method: Composition-based stats.
 Identities = 138/224 (61%), Positives = 172/224 (76%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNPLGVPSRMNVGQ+ ETHLGWA  GLG KI  ++++ K   +I    S + 
Sbjct: 1    DGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAKGLGLKIGKMLDERKDLQEIRSFLSQIY 60

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                  +    +    D+ +L +A+  ++GVP++TPVFDG  E  I  MLR+ADL ESGQ
Sbjct: 61   NDNPQAAQKVDLEQLPDNELLELAKNLRNGVPMATPVFDGVTELEIKRMLRLADLPESGQ 120

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            ++LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR
Sbjct: 121  AVLYDGRTGERFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR 180

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
             GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV G+ 
Sbjct: 181  FGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKMYKNIVDGDH 224


>gi|122939099|gb|ABM69131.1| DNA-directed RNA polymerase beta chain [Rhizobium leguminosarum bv.
            viciae USDA 2370]
 gi|126797629|gb|ABO27346.1| DNA-directed RNA polymerase beta chain [Rhizobium indigoferae]
          Length = 224

 Score =  422 bits (1086), Expect = e-115,   Method: Composition-based stats.
 Identities = 157/224 (70%), Positives = 188/224 (83%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G++I  LI+ YKANG+I PLR  +  V+GTG   E++ ++DDDSVLR+A+Q
Sbjct: 61   HLGWACAGMGRQIGELIDAYKANGNIEPLRKTIGDVVGTGPKAEQVHEFDDDSVLRLADQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            WK GV ++TPVFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  WKRGVSIATPVFDGANEADVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|295661506|ref|XP_002791308.1| DNA-directed RNA polymerase II subunit RPB2 [Paracoccidioides
            brasiliensis Pb01]
 gi|226280870|gb|EEH36436.1| DNA-directed RNA polymerase II subunit RPB2 [Paracoccidioides
            brasiliensis Pb01]
          Length = 1258

 Score =  422 bits (1084), Expect = e-115,   Method: Composition-based stats.
 Identities = 198/1133 (17%), Positives = 362/1133 (31%), Gaps = 178/1133 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFAKGDTSKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 594  QVSPNATKVFVNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKEIPADLDPEERRERYFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +         +     N+R    +  +     
Sbjct: 713  GVVEYVDAEEEETIMIVMTPEDLEMSKQVQAGYNLPEEDHTD-RNRRVRSNLSQKTHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 814

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 815  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 914

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ D                +E  Q
Sbjct: 915  LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPD---------------AEELGQ 959

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  KV   T     E    +++      DD+     + VKV     +  Q GDK A 
Sbjct: 960  RTKQHTKVDVSTPLRSTESGIVDQVLISTSNDDL-----KFVKVRTRTTKIPQIGDKFAS 1014

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L       G + 
Sbjct: 1015 RHGQKGTIGITYRQEDMPFTREGITPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1074

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1075 D-----------------------------------------------------ATP-FT 1080

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+ +LR       G  ++Y+G TG      + +G  Y  +L HMV DK++AR+ 
Sbjct: 1081 DVTVDSISGLLREHGYQSRGFEVMYNGHTGRKLVAQIFLGPTYYQRLRHMVDDKIHARAR 1140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGR 1325
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1141 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICGL 1200

Query: 1326 TRVYESIVAGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1201 MTPIAKLKKGDFECRACKNKNKISQVHIPYAAKLLFQELMSMNIAARMFTKRS 1253



 Score =  184 bits (467), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 112/804 (13%), Positives = 232/804 (28%), Gaps = 146/804 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTLAPSEDEVDPVV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDE------- 115
             P               +   R+LTYA PL + +         RLI    D        
Sbjct: 95  ARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLISERDDADQDEQDN 154

Query: 116 -------------FTGAKSIKDIKEQSIYMGDLPLMTKD--------------------- 141
                           A +  + +E+++++G +P+M K                      
Sbjct: 155 DEDRRNRGTYLHWEPKALNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQALYNWNECPY 214

Query: 142 ---GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF 196
              G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  + 
Sbjct: 215 DSGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQL 271

Query: 197 DSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYS 239
             K  +  + D  +                 +P+     ALG +  E+IL+        +
Sbjct: 272 SIK--LFAKGDTSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDT 329

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +     +    ++   +V+   +          + +K        ++++ +  +  +
Sbjct: 330 PMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQS 389

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                      G  V   ++    G   ++  D   +K L+           IL++    
Sbjct: 390 EGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVTK 448

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +        V    +   +  +    +       +  +  ++    + +  K   S  G 
Sbjct: 449 DLYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAGV 501

Query: 414 VKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM 470
            ++  R    +      R          I     L N   G +   +    +    V  +
Sbjct: 502 SQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 561

Query: 471 LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               Y       E  I    + +   ++   PQ   NA  V      F     +    + 
Sbjct: 562 ALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRDP 615

Query: 529 VNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + +S +   RR + +  +  + R     E        R   P       P   + G  +
Sbjct: 616 SHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSLV 675

Query: 581 GLVSSLTSF-------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                +          A ++     E  Y        +  V Y+ A EEE   I      
Sbjct: 676 LSKEHIHKLEADKEIPADLDPEERRER-YFGWDGLVKSGVVEYVDAEEEETIMIVMTPED 734

Query: 634 LDEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L+              +     R     +          +  P  ++ I AS+IPF +++
Sbjct: 735 LEMSKQVQAGYNLPEEDHTDRNRRVRSNLSQKTHTWTHCEIHPSMILGICASIIPFPDHN 794

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAP 709
            S R      M +QA+ +      
Sbjct: 795 QSPRNTYQSAMGKQAMGVFLTNFD 818


>gi|304561666|gb|ADM43695.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561668|gb|ADM43696.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561672|gb|ADM43698.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561674|gb|ADM43699.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561676|gb|ADM43700.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561678|gb|ADM43701.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 444

 Score =  421 bits (1083), Expect = e-115,   Method: Composition-based stats.
 Identities = 172/488 (35%), Positives = 258/488 (52%), Gaps = 55/488 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  E+I +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEKIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDSVM 499
             D++ + 
Sbjct: 437 IQDVNEIT 444


>gi|304561570|gb|ADM43647.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561572|gb|ADM43648.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561574|gb|ADM43649.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561576|gb|ADM43650.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 444

 Score =  421 bits (1083), Expect = e-115,   Method: Composition-based stats.
 Identities = 173/488 (35%), Positives = 259/488 (53%), Gaps = 55/488 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS+ ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDSVM 499
             D++ + 
Sbjct: 437 IQDVNEIT 444


>gi|260944180|ref|XP_002616388.1| hypothetical protein CLUG_03629 [Clavispora lusitaniae ATCC 42720]
 gi|238850037|gb|EEQ39501.1| hypothetical protein CLUG_03629 [Clavispora lusitaniae ATCC 42720]
          Length = 858

 Score =  421 bits (1083), Expect = e-115,   Method: Composition-based stats.
 Identities = 178/973 (18%), Positives = 317/973 (32%), Gaps = 164/973 (16%)

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDID 496
            ++  L+     +   DD D+ G +R+   G +L + +RL   ++ R I    +    +  
Sbjct: 1    MVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLASLFRLLFKKLTRDIYNYMQRCVENDK 60

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSA 543
                   + ++ +   +     +               +SQ+       S ++H RR + 
Sbjct: 61   EFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSARAGVSQVLNRYTYSSTLSHLRRTNT 120

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                 + R     + R +H TH+G +CPAET EG   GLV +L+  + ++     E    
Sbjct: 121  ----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTASEPILY 176

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
             + +  +     Y+ +   +   +      +       + +   R    +  +  E    
Sbjct: 177  FLEEWGMEPLEDYVPSNSPDCTRVFVNGVWVGTHREPAQLVDTMRRLRRKGDISPEVSII 236

Query: 664  IDASP---KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
             D      K          P    DD        ++  Q   +            E    
Sbjct: 237  RDIREREFKIFTDAGRVYRPLFIVDDDPESETKGDLVLQKEHI---HKLINSEYDEYDEE 293

Query: 721  KSSGAAIVAK--RAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
              + A   +     G+VE VDA      +I     DL+ S S +   +    Q   Q   
Sbjct: 294  SQANAYTWSSLVNDGVVEYVDAEEEETIMIAMTPDDLEASKSSLSETQQKSLQLEEQELD 353

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              +R                  PS  LG  A       + +P+  +N          M  
Sbjct: 354  PAKRIKPTYTSSTHTFTHCEIHPSMILGVAA-------SIIPFPDHNQSPRNTYQSAMGK 406

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   + +  + V                               +  +           
Sbjct: 407  QAMG--VFLTNYSVRM---------------------------DTMANILYYPQKPLATT 437

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +   +  + AI      +  D+ +   S +   +    +F R  +D  +R
Sbjct: 438  RSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFRSYMDLEKR 496

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                  + +E   +    + + L    Y +L +   I  G           K+T +  D 
Sbjct: 497  QGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGVRVSGEDIIIGKTTPIPPDT 553

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                 R+Q+                 K    T     E    +++     GD       +
Sbjct: 554  EELGQRTQYHT---------------KRDASTPLRSTESGIVDQVLLTTNGD-----GAK 593

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV +   +  Q GDK A RHG KG +      EDMPF   G   D+++NP  +PSRM 
Sbjct: 594  FVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFSAQGIVPDLIINPHAIPSRMT 653

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            V  + E  L       G +                                         
Sbjct: 654  VAHLIECLLSKVSSLSGLEGD--------------------------------------- 674

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          ++P F     EA++ +LR       G  ++Y+G TG+     V  G
Sbjct: 675  --------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMYNGHTGKKLMAQVFFG 719

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+GAA  L+
Sbjct: 720  PTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLK 779

Query: 1313 EMLTIKSD-------DVVGRTRVYESIVAGN----------DTFETGTPESFNVLVKEMQ 1355
            E L   SD        + G   V  ++              + ++   P +  +L +E+ 
Sbjct: 780  ERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQIHIPYAAKLLFQELM 839

Query: 1356 ALGLSIDLENSRT 1368
            A+ +S  L   R+
Sbjct: 840  AMNISPRLYTERS 852


>gi|304561480|gb|ADM43602.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561484|gb|ADM43604.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561486|gb|ADM43605.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561488|gb|ADM43606.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561490|gb|ADM43607.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561494|gb|ADM43609.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561496|gb|ADM43610.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561498|gb|ADM43611.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561500|gb|ADM43612.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561502|gb|ADM43613.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561504|gb|ADM43614.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561506|gb|ADM43615.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561508|gb|ADM43616.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561512|gb|ADM43618.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561516|gb|ADM43620.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561522|gb|ADM43623.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561524|gb|ADM43624.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561526|gb|ADM43625.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561530|gb|ADM43627.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561532|gb|ADM43628.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561540|gb|ADM43632.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561552|gb|ADM43638.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561554|gb|ADM43639.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561556|gb|ADM43640.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561558|gb|ADM43641.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561560|gb|ADM43642.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561578|gb|ADM43651.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561580|gb|ADM43652.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561584|gb|ADM43654.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561586|gb|ADM43655.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561588|gb|ADM43656.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561590|gb|ADM43657.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561592|gb|ADM43658.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561594|gb|ADM43659.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561596|gb|ADM43660.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561598|gb|ADM43661.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561600|gb|ADM43662.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561602|gb|ADM43663.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561604|gb|ADM43664.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561606|gb|ADM43665.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561608|gb|ADM43666.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561610|gb|ADM43667.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561612|gb|ADM43668.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561614|gb|ADM43669.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561616|gb|ADM43670.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561618|gb|ADM43671.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561640|gb|ADM43682.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561642|gb|ADM43683.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561644|gb|ADM43684.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561646|gb|ADM43685.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561648|gb|ADM43686.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561650|gb|ADM43687.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561708|gb|ADM43716.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561716|gb|ADM43720.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561718|gb|ADM43721.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561720|gb|ADM43722.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561722|gb|ADM43723.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561724|gb|ADM43724.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561726|gb|ADM43725.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561728|gb|ADM43726.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561730|gb|ADM43727.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561732|gb|ADM43728.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561734|gb|ADM43729.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561736|gb|ADM43730.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561738|gb|ADM43731.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561740|gb|ADM43732.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561742|gb|ADM43733.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561744|gb|ADM43734.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561748|gb|ADM43736.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561750|gb|ADM43737.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561752|gb|ADM43738.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561754|gb|ADM43739.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561756|gb|ADM43740.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561758|gb|ADM43741.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561760|gb|ADM43742.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561762|gb|ADM43743.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561764|gb|ADM43744.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561766|gb|ADM43745.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561768|gb|ADM43746.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561770|gb|ADM43747.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561772|gb|ADM43748.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561784|gb|ADM43754.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561786|gb|ADM43755.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561788|gb|ADM43756.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561790|gb|ADM43757.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561792|gb|ADM43758.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561794|gb|ADM43759.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561796|gb|ADM43760.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561798|gb|ADM43761.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561804|gb|ADM43764.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561806|gb|ADM43765.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561810|gb|ADM43767.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561818|gb|ADM43771.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561820|gb|ADM43772.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561826|gb|ADM43775.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561836|gb|ADM43780.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561838|gb|ADM43781.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561840|gb|ADM43782.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561842|gb|ADM43783.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561844|gb|ADM43784.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561846|gb|ADM43785.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561848|gb|ADM43786.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561850|gb|ADM43787.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561852|gb|ADM43788.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561854|gb|ADM43789.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561856|gb|ADM43790.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561858|gb|ADM43791.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 444

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 173/488 (35%), Positives = 258/488 (52%), Gaps = 55/488 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDSVM 499
             D++ + 
Sbjct: 437 IQDVNEIT 444


>gi|225680527|gb|EEH18811.1| DNA-directed RNA polymerase II subunit RPB2 [Paracoccidioides
            brasiliensis Pb03]
 gi|226292836|gb|EEH48256.1| DNA-directed RNA polymerase II subunit RPB2 [Paracoccidioides
            brasiliensis Pb18]
          Length = 1258

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 198/1133 (17%), Positives = 362/1133 (31%), Gaps = 178/1133 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFAKGDTSKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 594  QVSPNATKVFVNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKEIPADLDPEERRERYFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +         +     N+R    +  +     
Sbjct: 713  GVVEYVDAEEEETIMIVMTPEDLEMSKQVQAGYNLPEEDHTD-RNRRVRSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 814

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 815  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 914

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ D                +E  Q
Sbjct: 915  LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPD---------------AEELGQ 959

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  KV   T     E    +++      DD+     + VKV     +  Q GDK A 
Sbjct: 960  RTKQHTKVDVSTPLRSTESGIVDQVLISTSNDDL-----KFVKVRTRTTKIPQIGDKFAS 1014

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L       G + 
Sbjct: 1015 RHGQKGTIGITYRQEDMPFTREGITPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1074

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1075 D-----------------------------------------------------ATP-FT 1080

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+ +LR       G  ++Y+G TG      + +G  Y  +L HMV DK++AR+ 
Sbjct: 1081 DVTVDSISGLLREHGYQSRGFEVMYNGHTGRKLVAQIFLGPTYYQRLRHMVDDKIHARAR 1140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGR 1325
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1141 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICGL 1200

Query: 1326 TRVYESIVAGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1201 MTPIAKLKKGDFECRACKNKNKISQVHIPYAAKLLFQELMSMNIAARMFTKRS 1253



 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 112/804 (13%), Positives = 232/804 (28%), Gaps = 146/804 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTLAPSEDEVDPVV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDE------- 115
             P               +   R+LTYA PL + +         RLI    D        
Sbjct: 95  ARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLISERDDADQDEQDN 154

Query: 116 -------------FTGAKSIKDIKEQSIYMGDLPLMTKD--------------------- 141
                           A +  + +E+++++G +P+M K                      
Sbjct: 155 DEDRRNRGTYLHWEPKALNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQALYNWNECPY 214

Query: 142 ---GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF 196
              G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  + 
Sbjct: 215 DSGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQL 271

Query: 197 DSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYS 239
             K  +  + D  +                 +P+     ALG +  E+IL+        +
Sbjct: 272 SIK--LFAKGDTSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDT 329

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +     +    ++   +V+   +          + +K        ++++ +  +  +
Sbjct: 330 PMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQS 389

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                      G  V   ++    G   ++  D   +K L+           IL++    
Sbjct: 390 EGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVTK 448

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +        V    +   +  +    +       +  +  ++    + +  K   S  G 
Sbjct: 449 DLYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAGV 501

Query: 414 VKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM 470
            ++  R    +      R          I     L N   G +   +    +    V  +
Sbjct: 502 SQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 561

Query: 471 LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               Y       E  I    + +   ++   PQ   NA  V      F     +    + 
Sbjct: 562 ALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRDP 615

Query: 529 VNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + +S +   RR + +  +  + R     E        R   P       P   + G  +
Sbjct: 616 SHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSLV 675

Query: 581 GLVSSLTSF-------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                +          A ++     E  Y        +  V Y+ A EEE   I      
Sbjct: 676 LSKEHIHKLEADKEIPADLDPEERRER-YFGWDGLVKSGVVEYVDAEEEETIMIVMTPED 734

Query: 634 LDEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L+              +     R     +          +  P  ++ I AS+IPF +++
Sbjct: 735 LEMSKQVQAGYNLPEEDHTDRNRRVRSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHN 794

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAP 709
            S R      M +QA+ +      
Sbjct: 795 QSPRNTYQSAMGKQAMGVFLTNFD 818


>gi|126797631|gb|ABO27347.1| DNA-directed RNA polymerase beta chain [Rhizobium gallicum]
 gi|149211739|gb|ABR22223.1| DNA-dependent RNA polymerase beta chain [Rhizobium yanglingense]
 gi|149211741|gb|ABR22224.1| DNA-dependent RNA polymerase beta chain [Rhizobium mongolense]
 gi|149211745|gb|ABR22226.1| DNA-dependent RNA polymerase beta chain [Rhizobium loessense]
          Length = 224

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 159/224 (70%), Positives = 185/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GK+I  LI  YKANG+I PLR  +  V+G G   E++ D+DDDSVLR+A+Q
Sbjct: 61   HLGWACAGMGKQIGDLIEAYKANGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVLRLADQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            WK GV ++TPVFDGA E  +N MLR+A L +SGQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  WKRGVSIATPVFDGAHEGDVNEMLRLAGLKDSGQSTLYDGRTGEQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|190694885|gb|ACE88987.1| RNA polymerase subunit beta [Rhodobium gokarnense]
          Length = 404

 Score =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 258/405 (63%), Positives = 316/405 (78%), Gaps = 1/405 (0%)

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
           SPG+ FDHDKG+   SGKLL+A RIIP +G W+DIEFD+KDI+H RIDRRRK+PVTS + 
Sbjct: 1   SPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLMF 60

Query: 220 ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           ALG+DSEEIL TFY +I+Y++ GD W  P  A   M G K +S L+D  TGE V+E+G+K
Sbjct: 61  ALGLDSEEILDTFYQRILYTRSGDGWQMPYDAQ-RMKGFKPTSDLIDAKTGEVVVEAGRK 119

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +T+ L + L EKGV+ L ++ + LCG Y+AEDIVN ETGEIY EAGD I EK L+     
Sbjct: 120 ITARLARQLGEKGVEALKVSDEELCGHYLAEDIVNAETGEIYAEAGDEITEKMLQGFIER 179

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
              +IP+L +D VN   YIRNTL  DKN+ R++AL DIYRVMRPG+  T   AE+MF+ L
Sbjct: 180 GYDEIPVLDIDHVNTGGYIRNTLAVDKNEAREEALFDIYRVMRPGEPPTLETAEAMFHSL 239

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
           FFD ++YDLS VGRVKMNMRL+L   D VR +R+ED++A+IK LVDLR+GKG IDDIDNL
Sbjct: 240 FFDPERYDLSAVGRVKMNMRLDLKCEDTVRVLRREDVLAVIKTLVDLRDGKGEIDDIDNL 299

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF S
Sbjct: 300 GNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGS 359

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPT
Sbjct: 360 SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPT 404


>gi|255073731|ref|XP_002500540.1| predicted protein [Micromonas sp. RCC299]
 gi|226515803|gb|ACO61798.1| predicted protein [Micromonas sp. RCC299]
          Length = 1178

 Score =  421 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 194/1085 (17%), Positives = 345/1085 (31%), Gaps = 225/1085 (20%)

Query: 320  IYIEAGDVIDEKSLEEI-FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            ++   G V D+  LE + +  E  ++  L  +S+     I++  V         AL  I 
Sbjct: 276  VFRALGFVADKDILEHLVYDFEDHEMMQLLRNSIEEAQVIQSQDV---------ALDFIG 326

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            +      V           +      K  L  VG             +     +   +  
Sbjct: 327  KRGSAVGV----TRPKRIQYAREILQKELLPHVG-----------VNEGCETKKAYFLGY 371

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I+  L+    G+   DD D+ GN+R+   G ++   +R    ++ + ++           
Sbjct: 372  IVNRLLLCALGRKKEDDRDHFGNKRMDLSGPLIAMLFRQLFRKVTKDVRLYSQRCIDSGK 431

Query: 499  MPQDL--INAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSAL 544
              Q    + AK + S +     +              +SQ+   ++  S ++H RRL++ 
Sbjct: 432  DIQLTLAVKAKTITSGLKYSLATGNWGAQGAQDIRAGVSQVLNRLSFSSTLSHLRRLNS- 490

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R     + R +H +H+G +CPAET EG  +GLV +L+    V+  G    P  +
Sbjct: 491  ---PIGREGKLAKPRQLHNSHWGMVCPAETPEGQAVGLVKNLSLMCLVS-VGSPSAPLLE 546

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE------EILVPR 658
              +     ++  +S     N      N           +LV               +   
Sbjct: 547  FLEEWSMENLEEISPSVIVNATKIFVNGVWVGVHREPAQLVQTLRNLRRKLDITIEVGVV 606

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I   +             +  +E++          M  +           V TG    
Sbjct: 607  HDIALRELRLYTDYGRCIRPLFIVEDNHLVIKKKDIQMLYEKEITGYTWNDLVATGCI-- 664

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                             E VD        +   +D                        Q
Sbjct: 665  -----------------EYVDTEEEETTMIAMTIDELVG--------------------Q 687

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            R   + G            PS  LG       +  + +P+  +N                
Sbjct: 688  RINAEPGGVKHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRN----------- 729

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
                    ++       +G       I               +  V        +    +
Sbjct: 730  -------TYQSAMGKQAMGMYVTNFQIRM-----------DTLAYVLFYPQKPLVTTRAM 771

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +     ++  I      +  D+ +   S +   +    IF R   D+ ++  S
Sbjct: 772  EHLHFRELPAGVNVVVGIMCYTGYNQEDSVIMNQSSIDRGLF-RSIFYRSFKDEEKKQGS 830

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E++E  +RD          +       I  G           K++ L          
Sbjct: 831  LTKEELERPSRDTTLGMRHGTYDKLDDDGLICPGTRVSGEDIIIGKTSPL---------- 880

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    +D+    +    K    T     E    +++             LR VK+ V
Sbjct: 881  -------PEDDPSAVSKRFTKRDCSTGMKNSETGIIDQVLL-----TTNDQGLRFVKIRV 928

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG +      EDMPF  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 929  RSCRTPQVGDKFSSRHGQKGTIGMTYTQEDMPFTCEGIVPDIIVNPHAIPSRMTIGQLVE 988

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+                                               
Sbjct: 989  CLMGKVAAMMGKEGD--------------------------------------------- 1003

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     E+I+ ML M    + G  ++Y+G TG   +  + +G  Y  +
Sbjct: 1004 --------ATP-FTPVTVESISDMLHMCGYQKRGNEVMYNGHTGRKLEAKIFLGPTYYQR 1054

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R  G   ++T+QP+ G+S  GG R GEME  CI ++GAA  L+E L  +
Sbjct: 1055 LKHMVDDKIHSRGRGPVQILTRQPMEGRSRDGGLRFGEMERDCIISHGAAAFLKERLMDQ 1114

Query: 1319 SD----DV---VG-------RTRVYESIVAGNDTFE------TGTPESFNVLVKEMQALG 1358
            SD     V    G       + + +E      +  E         P +  +L +E+ ++ 
Sbjct: 1115 SDAYRIHVCETCGLIAVANLKNQTFEC---CKNPSERTKVVQVMMPYACKLLFQELMSMA 1171

Query: 1359 LSIDL 1363
            ++  L
Sbjct: 1172 VAPRL 1176



 Score =  206 bits (524), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 136/975 (13%), Positives = 287/975 (29%), Gaps = 161/975 (16%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGA----AMLEFVSYEFD 82
           L   Q  S++ F+   +    DE  +  ++   +   P     G       +EF      
Sbjct: 32  LARQQLDSFNEFIQHTMQEIVDEMSDFTIEPE-EQHMPGEEADGKGKKKYKVEFKQIYLS 90

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITL---RLIVFDVDEFTGAKSIKDIKEQS 129
            P               +   R+LTY+ PL I +    +   D  + T  K I+ I  + 
Sbjct: 91  KPMVTEADGMTSTLFPKEARLRNLTYSAPLYIDMAKSTITTTDEIDATTGKYIETIDTEE 150

Query: 130 ---IYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
              ++ G +P+M                         + G F+I G ++++++Q   S  
Sbjct: 151 YPKVFFGKVPIMLRSQYCSLHDHTDKELTELGECPYDEGGYFIINGSEKVLIAQEKMSTN 210

Query: 163 IHFDHDKGRASLSGKLLYAC--RIIPDQGLWMDIEFDS--------KD---IIHVRIDRR 209
             +  +K       K ++    R  P+ G        +        KD   +I V I   
Sbjct: 211 HVYVFEK---RQPSKYMWVAECRSSPESGARAASSCMARLCHAPGTKDEAGVISVTIPYI 267

Query: 210 RK-VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           R  +P+     ALG  ++ +IL          +        +  A ++    V+   +  
Sbjct: 268 RTEIPLFVVFRALGFVADKDILEHLVYDFEDHEMMQLLRNSIEEAQVIQSQDVALDFIGK 327

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G+   C          +      + + A   
Sbjct: 328 RGSAVGVTRPKRIQYAR-EILQKELLPHVGVNEGCETKKAYFLGYI---VNRLLLCALGR 383

Query: 328 IDEKSLEEIFHSEIR-DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
             E   +   +  +    P++ +        +   +     +           +      
Sbjct: 384 KKEDDRDHFGNKRMDLSGPLIAMLFRQLFRKVTKDVRLYSQRCIDSGKDIQLTLAVKAKT 443

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVD 445
            T  +  S+    +      D+       +N      T   +R +         +     
Sbjct: 444 ITSGLKYSLATGNWGAQGAQDIRAGVSQVLNRLSFSSTLSHLRRLNSPIGREGKLAKPRQ 503

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   + L+ +       +  ++  S+   + I+
Sbjct: 504 LHNSHWGMVCPAETPEGQAVG---LVKNLSLMCLVSVGSPSAPLLEFLEEWSMENLEEIS 560

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +V+A   F     +    E    +  + + RR   +           +    ++  +
Sbjct: 561 PSVIVNATKIFVNGVWVGVHREPAQLVQTLRNLRRKLDITIEVGVVHDIALRELRLYTDY 620

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
              I P    E +++ +         +      E       D   T  + Y+   EEE  
Sbjct: 621 GRCIRPLFIVEDNHLVIKKK-----DIQMLYEKEITGYTWNDLVATGCIEYVDTEEEETT 675

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA             +ELV  R   E   V        +  P  ++ I AS+IPF +++
Sbjct: 676 MIAM----------TIDELVGQRINAEPGGVK-HMYTHCEIHPSMILGICASIIPFPDHN 724

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R      M +QA+ +                                          
Sbjct: 725 QSPRNTYQSAMGKQAMGMYVTNFQI----------------------------------- 749

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                    + + V  Y       +     ++ R              +  G +  +G +
Sbjct: 750 ------RMDTLAYVLFYPQKPLVTTRAMEHLHFR-------------ELPAGVNVVVGIM 790

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD- 864
                     +  +  + +  +          +F     +E +     TK   E  +RD 
Sbjct: 791 CYTGYNQEDSVIMNQSSIDRGL-------FRSIFYRSFKDEEKKQGSLTKEELERPSRDT 843

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+IC G  V+  DI++GK +P  E   +            K    
Sbjct: 844 TLGMRHGTYDKLDDDGLICPGTRVSGEDIIIGKTSPLPEDDPSAVS---------KRFTK 894

Query: 925 RDTSLRVPSGVSGTV 939
           RD S  + +  +G +
Sbjct: 895 RDCSTGMKNSETGII 909


>gi|304561662|gb|ADM43693.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561664|gb|ADM43694.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 442

 Score =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 172/486 (35%), Positives = 257/486 (52%), Gaps = 55/486 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  E+I +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEKIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDS 497
             D++ 
Sbjct: 437 IQDVNE 442


>gi|304561562|gb|ADM43643.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561564|gb|ADM43644.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 442

 Score =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 173/486 (35%), Positives = 258/486 (53%), Gaps = 55/486 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS+ ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDS 497
             D++ 
Sbjct: 437 IQDVNE 442


>gi|304561518|gb|ADM43621.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561520|gb|ADM43622.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561534|gb|ADM43629.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561536|gb|ADM43630.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561538|gb|ADM43631.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561542|gb|ADM43633.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561544|gb|ADM43634.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561546|gb|ADM43635.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561548|gb|ADM43636.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561550|gb|ADM43637.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561620|gb|ADM43672.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561622|gb|ADM43673.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561626|gb|ADM43675.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561628|gb|ADM43676.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561630|gb|ADM43677.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561632|gb|ADM43678.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561634|gb|ADM43679.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561636|gb|ADM43680.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561638|gb|ADM43681.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561652|gb|ADM43688.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561654|gb|ADM43689.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561658|gb|ADM43691.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561660|gb|ADM43692.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561680|gb|ADM43702.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561682|gb|ADM43703.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561684|gb|ADM43704.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561686|gb|ADM43705.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561688|gb|ADM43706.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561690|gb|ADM43707.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561700|gb|ADM43712.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561710|gb|ADM43717.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561712|gb|ADM43718.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561774|gb|ADM43749.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561776|gb|ADM43750.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561778|gb|ADM43751.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561780|gb|ADM43752.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561782|gb|ADM43753.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561802|gb|ADM43763.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561808|gb|ADM43766.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561812|gb|ADM43768.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561814|gb|ADM43769.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561816|gb|ADM43770.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561822|gb|ADM43773.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561824|gb|ADM43774.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 442

 Score =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 173/486 (35%), Positives = 257/486 (52%), Gaps = 55/486 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDIDS 497
             D++ 
Sbjct: 437 IQDVNE 442


>gi|304561832|gb|ADM43778.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 441

 Score =  420 bits (1079), Expect = e-115,   Method: Composition-based stats.
 Identities = 173/485 (35%), Positives = 257/485 (52%), Gaps = 55/485 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVDID 496
             D++
Sbjct: 437 IQDVN 441


>gi|304561670|gb|ADM43697.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 440

 Score =  420 bits (1079), Expect = e-115,   Method: Composition-based stats.
 Identities = 172/483 (35%), Positives = 255/483 (52%), Gaps = 55/483 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  E+I +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEKIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVD 494
             D
Sbjct: 437 IQD 439


>gi|304561568|gb|ADM43646.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 440

 Score =  420 bits (1079), Expect = e-114,   Method: Composition-based stats.
 Identities = 173/483 (35%), Positives = 256/483 (53%), Gaps = 55/483 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS+ ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVD 494
             D
Sbjct: 437 IQD 439


>gi|304561800|gb|ADM43762.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 444

 Score =  420 bits (1079), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/488 (35%), Positives = 257/488 (52%), Gaps = 55/488 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+ Q+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQXQFRIGLARLERVVKERMT 436

Query: 492 SVDIDSVM 499
             D++ + 
Sbjct: 437 IQDVNEIT 444


>gi|304561510|gb|ADM43617.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561514|gb|ADM43619.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561656|gb|ADM43690.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561692|gb|ADM43708.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561694|gb|ADM43709.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561698|gb|ADM43711.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561702|gb|ADM43713.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561704|gb|ADM43714.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561714|gb|ADM43719.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561830|gb|ADM43777.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 440

 Score =  420 bits (1079), Expect = e-114,   Method: Composition-based stats.
 Identities = 173/483 (35%), Positives = 255/483 (52%), Gaps = 55/483 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436

Query: 492 SVD 494
             D
Sbjct: 437 IQD 439


>gi|169616566|ref|XP_001801698.1| hypothetical protein SNOG_11456 [Phaeosphaeria nodorum SN15]
 gi|160703211|gb|EAT81164.2| hypothetical protein SNOG_11456 [Phaeosphaeria nodorum SN15]
          Length = 1252

 Score =  419 bits (1078), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/995 (17%), Positives = 319/995 (32%), Gaps = 163/995 (16%)

Query: 419  RLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +   D     + + +      +I  L+    G+   DD D+ G +R+   G ++ N +R+
Sbjct: 370  KFARDIMQKDKTLAKPTFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRI 429

Query: 478  GLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------L 522
              L++ + + +  +           Q  + A  + + +     +               +
Sbjct: 430  LFLKLTKDVFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGV 489

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ+       S ++H RR +      V R     + R +H +H+G +CPAET EG   GL
Sbjct: 490  SQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGL 545

Query: 583  VSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            V +L+    V+          +    + ++  +       E    ++      +      
Sbjct: 546  VKNLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQ 605

Query: 641  TEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQ 697
               +V        +      I D  D   K        + P    EN+ +          
Sbjct: 606  LVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKPNRNQLVFD 665

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDP 754
            R+    L  E     T      A  +      K   + G++E +DA       +    + 
Sbjct: 666  REISNRLVKEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPED 725

Query: 755  STSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                      L   +R+N      +R   K    +         P+  LG       +  
Sbjct: 726  LDEWRGMKMGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICA 778

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +  ++      +                        
Sbjct: 779  SIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRMETMMN------------------- 819

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                      V             +       +   +  + AI      +  D+ +   S
Sbjct: 820  ----------VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 869

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R   ++ +R   +    +E   +    + + L    Y +L +   + 
Sbjct: 870  SIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVA 925

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +++D      ++           ++     +  Q         
Sbjct: 926  PGVRVSGDDIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ--------- 976

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                LR VKV     +  Q GDK A RHG KG +      EDMP
Sbjct: 977  -----------VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMP 1025

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+V+NP  +PSRM +  + E  L       G++                   
Sbjct: 1026 FTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD----------------- 1068

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     + I+ +L  A   +
Sbjct: 1069 ------------------------------------ATP-FTEVTVDEISDLLEQAGYQK 1091

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G  I+Y+G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  G
Sbjct: 1092 RGFEIMYNGHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDG 1151

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG-------- 1335
            G R GEME  C+ A+GAA  L+E L   SD       D+ G      SI  G        
Sbjct: 1152 GLRFGEMERDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCH 1211

Query: 1336 --NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1212 NKTRISQIHIPYAAKLLFQELLAMNIATRMFTDRS 1246



 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 160/1165 (13%), Positives = 318/1165 (27%), Gaps = 226/1165 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++V   DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVVEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GNVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  --D---------------IIHV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
              D                 +     I  +++VP+     ALG+   EEILS        
Sbjct: 271  WADTSLGNPGQGKRAPGPFAYAMLPYI--KQEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +          + +      LK  ++   K   +
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRG------ANQGTRDRRLKFARDIMQKDKTL 382

Query: 299  TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAY 357
                  G  +   ++    G    +  D   +K L+           IL++  + +   Y
Sbjct: 383  AKPTFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKDVFKY 441

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            ++  + +  + + + A+           + T  +  S+    + D  K   +  G  ++ 
Sbjct: 442  LQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKAGVSQVL 493

Query: 418  MRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
             R    +      R          +     L N    +         +   + + L    
Sbjct: 494  NRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 553

Query: 476  RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             + +      I + +S  ++  +   D                   +    +    +S +
Sbjct: 554  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQQLVSVV 610

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
               RR   L             +RD+    +     A         + ++ T   R    
Sbjct: 611  QELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKPNRNQLV 663

Query: 596  GFIETPYRKVCDGKVTND------------------------VVYLSAMEEENRYIAQAN 631
               E   R V +   ++                         + YL A EEE   I  + 
Sbjct: 664  FDREISNRLVKEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSP 723

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              LDE       L                                          S R  
Sbjct: 724  EDLDEWRGMKMGLPT----------------------------------------SERAN 743

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            +G    R+  P          T  E   A   G       A I+   D  +    + +  
Sbjct: 744  LGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRNTYQSA 797

Query: 752  LDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            +     GV      ++ +         Q+PL                      +L  G+N
Sbjct: 798  MGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQN 847

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DI 865
             +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D 
Sbjct: 848  AIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADT 907

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              +       +D+ G++  G  V+  DI++GK  P         ++L +        DV 
Sbjct: 908  LRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLHTKRDVS 963

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVILDRNIYS 984
                   +G+   V+              R+ + +  QI +  A     +  I       
Sbjct: 964  TPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQE 1022

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKVQRNVES 1037
             +     G             + ++   + E   S+      Q+       E     +  
Sbjct: 1023 DMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVTVDEISD 1082

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQW 1062
            L  Q    K   E  +     K   
Sbjct: 1083 LLEQAGYQKRGFEIMYNGHTGKKMR 1107


>gi|302857290|ref|XP_002959835.1| hypothetical protein VOLCADRAFT_71834 [Volvox carteri f. nagariensis]
 gi|300254184|gb|EFJ39100.1| hypothetical protein VOLCADRAFT_71834 [Volvox carteri f. nagariensis]
          Length = 293

 Score =  419 bits (1076), Expect = e-114,   Method: Composition-based stats.
 Identities = 148/307 (48%), Positives = 183/307 (59%), Gaps = 41/307 (13%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V +++A KR IQ GDKMAGRHGNKGI+SRILP +DMPFL DGT VDIVLNPLGVPSRMNV
Sbjct: 4    VHIYLAEKRKIQVGDKMAGRHGNKGIISRILPRQDMPFLPDGTSVDIVLNPLGVPSRMNV 63

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQI+E  LG A   LG+  K    D               ++ G  +    +     D+ 
Sbjct: 64   GQIYECLLGLAGRYLGEHYKIPPFD---------------EMYGADASRSFVLSKLYDAR 108

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
             +    W          FD                +  G+  L+DG   E FD+ VTVG 
Sbjct: 109  KKTGLNWL---------FD---------------PNHPGKIRLFDGRNSECFDQTVTVGI 144

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y+LKL HMV DK++ARSTG YSLVTQQPL G+S +GGQRLGEMEVW I+ YGAA+VL E
Sbjct: 145  AYVLKLVHMVDDKLHARSTGPYSLVTQQPLRGRSKQGGQRLGEMEVWAIEGYGAAFVLSE 204

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT-KNSA 1372
            MLTIKSDD+ GR  ++++++  ND    G+PESF VLV E+QAL L I L      K   
Sbjct: 205  MLTIKSDDMTGRQNLWKNLIENNDIS-LGSPESFKVLVCELQALCLDIGLFRKNGIKQDI 263

Query: 1373 KMEEIPD 1379
             +  + D
Sbjct: 264  NLINLED 270


>gi|95115793|gb|ABF56191.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. triticae]
          Length = 1262

 Score =  419 bits (1076), Expect = e-114,   Method: Composition-based stats.
 Identities = 170/987 (17%), Positives = 315/987 (31%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIVDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSHAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ S          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T         +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDSDTRAGWSDTDIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTNERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLIINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 144/1046 (13%), Positives = 288/1046 (27%), Gaps = 220/1046 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
           L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38  LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
              P               +   R+LTY+  +   +          +++    DE     
Sbjct: 95  LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVAEGEDEDMEVT 154

Query: 121 SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
           +       IK +            +++G LP+M +                         
Sbjct: 155 NTVGGPTQIKWEREDVPMDDEAARVFIGKLPVMLRSELCHLRNQTDEALFAFNECPYDQG 214

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
           G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215 GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GPIPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200 --D---------------IIHV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
             D                 +     I  + +VP+     ALG+   EEILS        
Sbjct: 271 WADNSLANPGQGKRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329 TQMLELLKPSIEEGAVVQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                         +     +  +   D  D            + + +           +
Sbjct: 387 KEGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDH------FGKKRLDL-------AGPLV 433

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            N       K  KD    + R +     + F+V  ++   +  +  KY L   G      
Sbjct: 434 ANLFRILFLKLTKDVFKYLQRCVESS--TDFNVQMAVKASIITNGLKYSL-ATGNWGDQK 490

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           +         + + +    + +  L        R+GK       +  +  +    E  + 
Sbjct: 491 KAASAKAGVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEG 550

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q    +  +       + S     V      N + +         + + +++  +   + 
Sbjct: 551 QACGLVKNLSLMCYVSVGSDATPIVDFMSQRNMQLLEEYDQNQ--NPEATKVFVNGVWVG 608

Query: 534 RITHTRRLSALGQGGVARARAGVEM---RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             +H ++L ++ Q          EM   RD+    +     A         + ++ +   
Sbjct: 609 VHSHAQQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKPN 668

Query: 591 RVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENRY 626
           R       E   R V +   ++                         + YL A EEE   
Sbjct: 669 RNQLVFDREISNRLVKEQLDSDTRAGWSDTDIADNTYGWKGLIQDGVIEYLDAEEEETAM 728

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           I  +   LDE       L                                          
Sbjct: 729 ITFSPEDLDEWRGMKMGLPTNE-------------------------------------- 750

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             R  +G    R+  P          T  E   A   G       A I+   D  +    
Sbjct: 751 --RANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRN 802

Query: 747 SVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           + +  +     GV      ++ +         Q+PL                      +L
Sbjct: 803 TYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFREL 852

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-- 863
             G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     
Sbjct: 853 PAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKP 912

Query: 864 ---DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              D   +       +D+ G++  G  V+  DI++GK  P         +K         
Sbjct: 913 TRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAQELGQKT-------T 965

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFN 946
               RD S  + S  +G V  V    
Sbjct: 966 LHTKRDVSTPLRSTENGIVDQVLFTT 991


>gi|154279576|ref|XP_001540601.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Ajellomyces
            capsulatus NAm1]
 gi|150412544|gb|EDN07931.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Ajellomyces
            capsulatus NAm1]
          Length = 1743

 Score =  419 bits (1076), Expect = e-114,   Method: Composition-based stats.
 Identities = 197/1133 (17%), Positives = 365/1133 (32%), Gaps = 178/1133 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG          +    +     +     ++   G V DE  L
Sbjct: 746  VEKGSRILSQLSIKLFGKGDTSKSGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 804

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 805  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 853

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 854  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 902

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 903  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 962

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 963  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 1018

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 1019 RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 1078

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 1079 QVSPNATKVFVNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 1138

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 1139 RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVK-S 1197

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +   +         + N   N+R    +  +     
Sbjct: 1198 GVVEYVDAEEEETIMIVMTPEDLETSKQLQAGFSLPEEDNND-PNRRVRSTLSQKTHTWT 1256

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 1257 HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 1299

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 1300 TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNA 1340

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 1341 IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 1399

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ +                +E  Q
Sbjct: 1400 LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQ 1444

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 1445 RTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1499

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1500 RHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1559

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1560 D-----------------------------------------------------ATP-FT 1565

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1566 DVTVDSISSLLREHGYQSRGFEVMYNGYTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1625

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGR 1325
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1626 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICGL 1685

Query: 1326 TRVYESIVAGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1686 MTPIAKLKKGDFECRACKNKNKISQVHIPYAAKLLFQELMSMNIAARMFTKRS 1738



 Score =  184 bits (468), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 109/802 (13%), Positives = 229/802 (28%), Gaps = 142/802 (17%)

Query: 29   LIEVQKASYDHFLMMNIAPDERP------NEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
            L+  Q  S+D F+   +            ++ L  A   + P+        L+F +    
Sbjct: 523  LVSQQLDSFDEFISTTMQELVEEQGQVTLDQTLAPAEDKIDPVV--LRRYELKFGTVMLA 580

Query: 83   PPKFD----------VDDCLWRDLTYAVPLKITL---------RLI---------VFDVD 114
             P               +   R+LTYA PL + +         RLI           D D
Sbjct: 581  RPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLIAERDDAEQGEEDND 640

Query: 115  EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
            E   ++              + +E+++++G +P+M K                       
Sbjct: 641  EERRSRGTYLHWEPKALNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQSLYNWNECPYD 700

Query: 142  --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
              G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 701  SGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 757

Query: 198  SKDIIHVRIDRRRK----------------VPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
             K  +  + D  +                 +P+     ALG +  E+IL+        + 
Sbjct: 758  IK--LFGKGDTSKSGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 815

Query: 241  RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
              +     +    ++   +V+   +          + +K        ++++ +  +  + 
Sbjct: 816  MLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQSE 875

Query: 300  -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                      G  V   ++    G   ++  D   +K L+           IL++    +
Sbjct: 876  GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVTKD 934

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                    V    +   +  +    +       +  +  ++    + +  K   S  G  
Sbjct: 935  LYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAGVS 987

Query: 415  KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
            ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 988  QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 1047

Query: 472  KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                       E  I    + +   ++   PQ   NA  V      F     +    +  
Sbjct: 1048 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRDPS 1101

Query: 530  NSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIG 581
            + +S +   RR + +  +  + R     E        R   P       P   + G  + 
Sbjct: 1102 HLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSLVL 1161

Query: 582  LVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                +                     Y        +  V Y+ A EEE   I      L+
Sbjct: 1162 SKEHIHKLEADKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLE 1221

Query: 636  EDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                          +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 1222 TSKQLQAGFSLPEEDNNDPNRRVRSTLSQKTHTWTHCEIHPSMILGICASIIPFPDHNQS 1281

Query: 688  NRVLMGCNMQRQAVPLLKAEAP 709
             R      M +QA+ +      
Sbjct: 1282 PRNTYQSAMGKQAMGVFLTNFD 1303


>gi|304561528|gb|ADM43626.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561624|gb|ADM43674.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 441

 Score =  418 bits (1075), Expect = e-114,   Method: Composition-based stats.
 Identities = 173/485 (35%), Positives = 256/485 (52%), Gaps = 55/485 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  + 
Sbjct: 1   LEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLEN 50

Query: 84  -PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ G
Sbjct: 51  NPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEKG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI+
Sbjct: 102 TFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDIV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K  
Sbjct: 159 YVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK-- 216

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAEDI 312
                +  GE   +ES K L   L    K   +  +G             +  L  A+ I
Sbjct: 217 ----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKKI 272

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           VN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N            
Sbjct: 273 VNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT---------- 320

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
             +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I 
Sbjct: 321 --VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNIT 376

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++ 
Sbjct: 377 KDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMTI 436

Query: 493 VDIDS 497
            D++ 
Sbjct: 437 QDVNE 441


>gi|308798899|ref|XP_003074229.1| DNA-directed RNA polymerase (ISS) [Ostreococcus tauri]
 gi|116000401|emb|CAL50081.1| DNA-directed RNA polymerase (ISS) [Ostreococcus tauri]
          Length = 999

 Score =  418 bits (1075), Expect = e-114,   Method: Composition-based stats.
 Identities = 192/1100 (17%), Positives = 348/1100 (31%), Gaps = 236/1100 (21%)

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
                +     +     ++   G V D+  LE I                       N ++
Sbjct: 99   IRCTLPYIRTDIPIFVVFRALGFVADKDILEHIC-----------------YDLADNEMM 141

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
                   ++A +   + +    +     A  +         KY    + +  +      +
Sbjct: 142  EMLRPSIEEAFVIQSQEVALDFIGKRGSAVGV---SREKRIKYAKEILQKELLPHVGVRE 198

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
              +  +      +  +I  L+    G+   DD D+ GN+R+   G +L   +R    ++ 
Sbjct: 199  DCETKK---AYFLGYMIHRLLLCSLGRRPEDDRDHYGNKRLDLGGPLLAQLFRQLFRKLT 255

Query: 484  RSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHV 529
            + ++   +        +  Q  I AK +   +     +              +SQ+   +
Sbjct: 256  KDVRLYCQRCIDSGKEIQLQLAIKAKTITQGLKYSLATGNWGSQGAQDIRAGVSQVLNRL 315

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            +  S ++H RR+++     + R     + R +H + +G ICPAET EG  +GLV +L   
Sbjct: 316  SYSSTLSHLRRINS----PIGREGKLAKPRQLHNSLWGMICPAETPEGQAVGLVKNLALM 371

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            A V+     E     + +  + N      ++  E+  I      +       + +   R 
Sbjct: 372  ALVSVGSPSEPILEFLDEWTMENLEEISPSLIAESTKIFLNGVWVGVHRDPADLVRTLRK 431

Query: 650  AGEEILVPREKIDFIDASPKQ---VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
               +  V        D   K+            P    DD  ++ +              
Sbjct: 432  LRRQCDVDSSVSVVHDIRLKELRLYTDYGRCTRPLFIVDDDQKLRIKKQHIELLTEKDV- 490

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                  TG       +SG          +E VD        +   +D   +         
Sbjct: 491  ------TGYSWNELVTSG---------FIEYVDTEEEETTMISMTIDDLAA--------- 526

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      +++  V +     R       PS  LG       +  + +P+  +N    
Sbjct: 527  -----ARQSADRKTGVAI-----RYTHCEIHPSMILG-------ICASIIPFPDHNQSPR 569

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
                  M  + +     +       R   LG        P V+   ++ +          
Sbjct: 570  NTYQSAMGKQAMG----MYVTNYQIRMDTLGYVLFYPQKPLVTTRAMEYL---------- 615

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                               +      + AI      +  D+ L   S +   +    ++ 
Sbjct: 616  ---------------HFRELPAGCNAVVAIMCYTGYNQEDSVLMNQSAIDRGLF-RSLYY 659

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  S+ RE+ E   RD            Y +L +     ++    K F K  
Sbjct: 660  RSFKDEEKKQGSLSREEFERPDRDTCLGMRH---GTYDKLDDDGLIYDSAVLSKRFSKKD 716

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
              +    +E            D                                      
Sbjct: 717  CSTGMKHAETGIIDQVLLTTND-------------------------------------- 738

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VK+ V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP  
Sbjct: 739  --QGLRFVKLRVRSMRTPQVGDKFSSRHGQKGTVGMTYTQEDMPFTCEGITPDIIVNPHA 796

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +GQ+ E  +G     +GK+                                   
Sbjct: 797  IPSRMTIGQLVECIMGKVAACMGKEGD--------------------------------- 823

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E I++ML      + G  ++Y+G TG   D
Sbjct: 824  --------------------ATP-FTPVTAEDISTMLHKCGYQKRGNEVMYNGHTGRMLD 862

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G  Y  +L HMV DK+++R  G   ++T+QP+ G+S  GG R GEME  CI ++G
Sbjct: 863  AQIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPMEGRSRDGGLRFGEMERDCIMSHG 922

Query: 1307 AAYVLQEMLTIKSD----DVVG----------RTRVYESIVAGNDTFE------TGTPES 1346
            AA  L+E L  +SD     V            + + +E      +  E         P +
Sbjct: 923  AASFLKERLMDQSDAYRIHVCQKCGLIAVANLKNQTFEC---CKNPSERTSVVQVMVPYA 979

Query: 1347 FNVLVKEMQALGLSIDLENS 1366
              +L +E+ ++ ++  L  +
Sbjct: 980  CKLLFQELMSMAIAPRLITA 999



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 84/680 (12%), Positives = 206/680 (30%), Gaps = 67/680 (9%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC--RIIPDQG 189
           +G+ P   + G FVI G ++++++Q   S    +  +K       K ++    R  P++G
Sbjct: 20  LGECPY-DEGGYFVINGSEKVLIAQERMSTNHVYVFEK---KQPSKFMWQAECRSQPERG 75

Query: 190 LWMDIEF-----------DSKDII-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTF 232
                             D+   I     ++R D    +P+     ALG  ++ +IL   
Sbjct: 76  SRGASSCVMRQMHAVGTKDAPGPIRCTLPYIRTD----IPIFVVFRALGFVADKDILEHI 131

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
              +  ++  +     +  A ++   +V+   +        +   K++     + L+++ 
Sbjct: 132 CYDLADNEMMEMLRPSIEEAFVIQSQEVALDFIGKRGSAVGVSREKRIKYAK-EILQKEL 190

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD-IPILYVDS 351
           +  +G+  DC          +      + + +     E   +   +  +    P+L    
Sbjct: 191 LPHVGVREDCETKKAYFLGYMIH---RLLLCSLGRRPEDDRDHYGNKRLDLGGPLLAQLF 247

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                 +   +     +          ++       T  +  S+    +      D+   
Sbjct: 248 RQLFRKLTKDVRLYCQRCIDSGKEIQLQLAIKAKTITQGLKYSLATGNWGSQGAQDIRAG 307

Query: 412 GRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
               +N      T   +R I         +     L N    +         +      +
Sbjct: 308 VSQVLNRLSYSSTLSHLRRINSPIGREGKLAKPRQLHNSLWGMICPAETPEGQAVG---L 364

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           +KN   + L+ +    +  +  +D  ++   + I+   +  +   F     +    +  +
Sbjct: 365 VKNLALMALVSVGSPSEPILEFLDEWTMENLEEISPSLIAESTKIFLNGVWVGVHRDPAD 424

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +  +   RR   +           ++   ++  +     P    +      +       
Sbjct: 425 LVRTLRKLRRQCDVDSSVSVVHDIRLKELRLYTDYGRCTRPLFIVDDDQKLRIKKQH--- 481

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            +      +       +   +  + Y+   EEE   I+             ++L   R +
Sbjct: 482 -IELLTEKDVTGYSWNELVTSGFIEYVDTEEEETTMISM----------TIDDLAAARQS 530

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL------ 704
            +       +    +  P  ++ I AS+IPF +++ S R      M +QA+ +       
Sbjct: 531 ADRKTGVAIRYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGMYVTNYQI 590

Query: 705 ----------KAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                       + P V T  ME +  +   A   A  A +          +   +  +D
Sbjct: 591 RMDTLGYVLFYPQKPLVTTRAMEYLHFRELPAGCNAVVAIMCYTGYNQEDSVLMNQSAID 650

Query: 754 PSTSGVDIYRLMKFQRSNQN 773
                   YR  K +   Q 
Sbjct: 651 RGLFRSLYYRSFKDEEKKQG 670


>gi|125987641|sp|Q1ACN6|RPOB_CHAVU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1074

 Score =  418 bits (1075), Expect = e-114,   Method: Composition-based stats.
 Identities = 164/498 (32%), Positives = 244/498 (48%), Gaps = 53/498 (10%)

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I          + +  I+     V  G++L    +  G   ++    +L A    +  + 
Sbjct: 612  INYERSNQNTCLHQKPIVKKDDYVKKGELLADASSTLG-GEISLGNNILVAYMPWEGYNF 670

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  L     ++  ++   I+    I+K E  +++     E + +        L RN+  
Sbjct: 671  EDAVL-----INERLIYEDIYTSIHIEKYEIEVNMTSLGPEKITKKIPHLSEYLLRNL-D 724

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                IL G    +G     K T          P  +    A+   K     E+       
Sbjct: 725  VNGLILLGSWVKTGDVLVGKLTPREPGESLRLPEGRLLH-AIFGIKASSFFETCLKVAPG 783

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            ++  + D     +  ++  + +    ++ V +++  KR IQ GDK+AGRHGNKG++SRIL
Sbjct: 784  AEGRVID-----VRWVESANKLTQKYIKTVNIYILQKRKIQVGDKIAGRHGNKGVISRIL 838

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+++DGTP+D+VL+PLGVPSRMN+GQIFE  LG A   L K  + +  D +   +
Sbjct: 839  PREDMPYIQDGTPIDMVLSPLGVPSRMNLGQIFECLLGLAGESLKKHYRIMPFDERHERE 898

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             S   +F E                                     F G      +S L 
Sbjct: 899  ASRKLAFSELYQAKK-------------------------------FTG------HSWLF 921

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                D  G+S L+DG TG+ F+  +TVG  Y+LKL H V DK++ARSTG YS+VTQQPLG
Sbjct: 922  E--PDTPGKSQLFDGRTGQTFENAITVGKAYILKLIHQVDDKIHARSTGPYSMVTQQPLG 979

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-T 1343
            GK+ RGGQR+GEMEVW ++ +GAAY LQE+LT KSDD+ GR     +IV GN   +   T
Sbjct: 980  GKARRGGQRMGEMEVWALEGFGAAYTLQELLTRKSDDMKGRNEALGAIVTGNLIPKPNTT 1039

Query: 1344 PESFNVLVKEMQALGLSI 1361
            PESF +L++E++ L L+I
Sbjct: 1040 PESFKLLMRELRCLCLNI 1057



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 249/613 (40%), Positives = 361/613 (58%), Gaps = 15/613 (2%)

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV-MRPGDVSTFSVAESMFN 397
              +D+  L        +Y+     T      ++A++++YR         +FS       
Sbjct: 189 LNWKDLEKLISRPSLLLSYLSKEKRT--PYSPEEAIIELYRHSCSVSGEISFSENIRKEL 246

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
           +  F   + ++ ++GR+ +N +LNLD P++ R +  +D+IA I  L++       +DDID
Sbjct: 247 YHKFFKIRCEIGSIGRLNINKKLNLDIPEEERFLVPQDLIAAINSLIEKSFKIVNLDDID 306

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
           +L NRRV  + +ML++Q R+ L R++R I    R  +   +   PQ L+  KP+V+   E
Sbjct: 307 HLKNRRVHLIADMLQSQVRIALNRLKRMIAEVMRGINKRKNLPNPQSLVTPKPLVATFQE 366

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF S  L Q  +  N L+ ITH RR+S+LG GG+ +  A   +RD+HP+HYG+ICP ET 
Sbjct: 367 FFGSHPLCQFMDQTNPLAEITHKRRISSLGPGGLTQKTATFNVRDIHPSHYGKICPIETP 426

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSS 633
           EG N GLVSSL   A +N  GFIE+P+ K+   +        +L + +EE   I      
Sbjct: 427 EGQNAGLVSSLAILANINQNGFIESPFLKLHKNEYKQLTGSEHLCSEQEEYYRITTGE-H 485

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             E      +    R   E        + F D  P Q  SIA SLIPFLE+DD+NR LMG
Sbjct: 486 SRETAEKKGKPTPIRYRQEFSATAFHFLHFRDILPIQYFSIATSLIPFLEHDDANRALMG 545

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ E P VGTG+E  VA  S A +++K  G V+ VD   I IRS     +
Sbjct: 546 SNMQRQAVPLLRPEKPIVGTGLEGQVALDSAALVLSKIEGKVDFVDGRNINIRSNIVINE 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +  +  Y     +RSNQNTC++Q+P+VK  D V++ +++AD  ST  G+++LG N+LV
Sbjct: 606 FFSFQLINY-----ERSNQNTCLHQKPIVKKDDYVKKGELLADASSTLGGEISLGNNILV 660

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+MPW GYNFED++LI+ER++ ED++TSIHIE++E+    T LGPE+IT+ IP++SE  L
Sbjct: 661 AYMPWEGYNFEDAVLINERLIYEDIYTSIHIEKYEIEVNMTSLGPEKITKKIPHLSEYLL 720

Query: 874 KNIDECGIICVGAEVNPGDILVGKITP--KGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
           +N+D  G+I +G+ V  GD+LVGK+TP   GES   PE +LL AIFG KA    +T L+V
Sbjct: 721 RNLDVNGLILLGSWVKTGDVLVGKLTPREPGESLRLPEGRLLHAIFGIKASSFFETCLKV 780

Query: 932 PSGVSGTVVDVRI 944
             G  G V+DVR 
Sbjct: 781 APGAEGRVIDVRW 793



 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 71/358 (19%), Positives = 146/358 (40%), Gaps = 37/358 (10%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM- 73
             F KN +I  +PD I +Q  S+  F+           +GL   F+    I   SG    
Sbjct: 1   MKFEKNTDIFILPDFIRIQLESFHRFI----------EKGLLEEFQRFPVIRDSSGELSY 50

Query: 74  -LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            L    Y+   P F+  + +++  TY+  L +  ++     ++          K + I +
Sbjct: 51  FLNGKRYKLQEPSFNEQEAIYQASTYSSELYVPAQITHTKSEK---------TKSEIILI 101

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G++P+MT  G F+I G  R++V+Q+ RSPG+++  +         + Y+C  I + G  +
Sbjct: 102 GNIPIMTARGNFIINGASRVIVNQILRSPGLYYGSELD---AQANITYSCTFISEWGGRL 158

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            +E D+K  I VR+ ++RK+PV   L+A+G++ +++                      + 
Sbjct: 159 KLEMDNKRRIWVRLSKKRKIPVLLLLLAMGLNWKDLEKL--------ISRPSLLLSYLSK 210

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           +         +++++      +      +  + K L  K  K          G       
Sbjct: 211 EKRTPYSPEEAIIELYRHSCSVSGEISFSENIRKELYHKFFKIRCEIGS--IGRLNINKK 268

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           +N +  E   E   ++ +  +  I     +   I+ +D +++    R  L+ D  + +
Sbjct: 269 LNLDIPE---EERFLVPQDLIAAINSLIEKSFKIVNLDDIDHLKNRRVHLIADMLQSQ 323


>gi|164660997|ref|XP_001731621.1| hypothetical protein MGL_0889 [Malassezia globosa CBS 7966]
 gi|159105522|gb|EDP44407.1| hypothetical protein MGL_0889 [Malassezia globosa CBS 7966]
          Length = 1197

 Score =  418 bits (1075), Expect = e-114,   Method: Composition-based stats.
 Identities = 174/1052 (16%), Positives = 323/1052 (30%), Gaps = 174/1052 (16%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             V       +    ++       ++A +   R +    +        +     F    Y 
Sbjct: 285  DVLQHICYDFNDTQMLEMLKPCIEEAFVIQDREVALDFIGRRGTTTGL---SRFKRTAYA 341

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +         +     +      ++  L+     +  IDD D+ G +R+   
Sbjct: 342  QEILQKEMLPHISM---SEGSNTKKAYFFGYMVHRLLLAALDRREIDDRDHFGKKRLDLA 398

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R I    +    D      Q  +    + + +     +      
Sbjct: 399  GPLLSGLFRMLFRKVTRDIYRHLQRCVEDQREFHLQAAVRHATITNGLRYSLATGNWGDQ 458

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 459  KKAMQSKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGMVCPA 514

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN- 631
            ET EG   GLV +L+  + ++           + +  +T+ +    A  +  +       
Sbjct: 515  ETPEGQACGLVKNLSLMSNISVGTPSAPIVEFLEEFGLTSLIDMQGADPKATKVFVNGVW 574

Query: 632  -SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              + D+ G   + L   R   +         D  +   +        L P    D  +  
Sbjct: 575  LGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIREKELRIYTDAGRLLRPLFIVDQPSMT 634

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            L+      +A+     E      G +      SG                I  +    E 
Sbjct: 635  LLIKRHHVEALNEETGE------GWDWTRLVQSGV---------------IEYLDTEEEE 673

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
             +    S  D+ +  +++ +N        P                 P        L   
Sbjct: 674  TVLICMSPYDLEQSREYKATNG-----HMP-----------------PDMSDATRRLRSA 711

Query: 811  MLVAFMPWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
               A   W       +M++     ++            ++       +G       I   
Sbjct: 712  HTFAADTWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQIRM- 770

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 771  ----------DTMANILYYPQKPLATTRAMEHLRFRELPAGQNAIVAILCYSGYNQEDSV 820

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    ++ R   D  ++   +  E+ E   RD                  
Sbjct: 821  IMNQSAIDRGLF-RSLYYRTFQDMEKKVGVITMEEFEKPTRDTAIRLKHGTYEKLDVDGL 879

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +  G           K+  L  D                DE   R+    K    T    
Sbjct: 880  VPPGTRVSGEDIIIGKTAPLPPD---------------SDELGMRSKMHTKKDVSTPMKS 924

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
             E    +++     G        + VKV V   R  Q GDK A RHG KG +      ED
Sbjct: 925  TESGIIDQVLITTNG-----EGAKFVKVRVRSTRVPQVGDKFASRHGQKGTIGITYRQED 979

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  +PSRM +G + E  L       G++                 
Sbjct: 980  MPFTCEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGD--------------- 1024

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     + ++ +L     
Sbjct: 1025 --------------------------------------ATP-FTDLTVKGVSDILFSLGF 1045

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G  ++Y+G TG      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S 
Sbjct: 1046 QSRGLEVMYNGHTGRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSR 1105

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVA 1334
             GG R GEME  C+ ++G A  L+E +   SD       D+ G       R   +E    
Sbjct: 1106 DGGLRFGEMERDCMISHGMANFLKERMYDASDAYRLHICDLCGLTAVANLRKSTFECRAC 1165

Query: 1335 GND--TFETGTPESFNVLVKEMQALGLSIDLE 1364
             N     +   P +  +L +E+ ++G++  L 
Sbjct: 1166 RNRSAISQIHIPYAAKLLFQELMSMGIASRLY 1197



 Score =  185 bits (470), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 142/1019 (13%), Positives = 298/1019 (29%), Gaps = 198/1019 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL----------QAAFKSVFPITAFSGAAMLEFVS 78
           L+  Q  S++ F+   +      ++ L          QA           +    +EF  
Sbjct: 28  LVRQQIDSFNEFMSNTVQELVEESKSLTLEQSDQHTGQA--------EDKTRRYEIEFGQ 79

Query: 79  YEFDPPKFD----------VDDCLWRDLTYAVPLKITLR---LIVFDVDEFTGA------ 119
              + P+              +   R+LTY+  L + +    L+  + DE          
Sbjct: 80  IYMNKPQQTEADGSTAPLFPQEARQRNLTYSAGLHVDVSQKVLVKGEEDELDENGDQLWI 139

Query: 120 --KSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIV 153
              + ++I ++ +Y+G +P+M                           G F+I G ++++
Sbjct: 140 PDPTQEEIVDEKVYLGKVPIMLHSHFCWLTDLPDEGKYSLNECPFDSGGYFIINGSEKVL 199

Query: 154 VSQLHR--------------SPGIHFDHDKGRASLSGKLLYACRI---IPDQGLWMDIEF 196
           ++Q  R              SP       +      GK +   ++     ++      E 
Sbjct: 200 IAQE-RMAANHVYVFSKAPPSPITFLAEIRSAVERGGKTISTMQVKLFSRNR------EK 252

Query: 197 DSKDII-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
              + I     ++R D    +P+     ALG+  + ++L         +Q  +     + 
Sbjct: 253 SLNNTIKATLPYIRND----IPIVIVFRALGVVPDRDVLQHICYDFNDTQMLEMLKPCIE 308

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLC 304
            A ++   +V+   +    G     S  K T+   + L+++ +  + ++           
Sbjct: 309 EAFVIQDREVALDFIGRR-GTTTGLSRFKRTAYAQEILQKEMLPHISMSEGSNTKKAYFF 367

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  V   ++        I+  D   +K L+           +L+     +        V 
Sbjct: 368 GYMVHRLLL-AALDRREIDDRDHFGKKRLDLAGPLLSGLFRMLFRKVTRDIYRHLQRCVE 426

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D+ +    A +            T  +  S+    + D  K   S  G  ++  R    +
Sbjct: 427 DQREFHLQAAVRHA-------TITNGLRYSLATGNWGDQKKAMQSKAGVSQVLNRYTFAS 479

Query: 425 PDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 R          I     L N    +         +      ++KN   +  + +
Sbjct: 480 TLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLSLMSNISV 536

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                  +  ++   +     +      +    F     L   ++    +  +   RR  
Sbjct: 537 GTPSAPIVEFLEEFGLTSLIDMQGADPKATKV-FVNGVWLGTHDDPGQLVDTLRDLRRKD 595

Query: 543 AL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            +  +  V R     E+R ++      + P    +  ++ L+        +N        
Sbjct: 596 DISHEVSVVRDIREKELR-IYTDAGRLLRPLFIVDQPSMTLLIKRHHVEALNEETGEGWD 654

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED--------GSFTEELVFCRCAGEE 653
           + ++    V   + YL   EEE   I  +   L++             +     R     
Sbjct: 655 WTRLVQSGV---IEYLDTEEEETVLICMSPYDLEQSREYKATNGHMPPDMSDATRRLRSA 711

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                +     +  P  ++ + AS+IPF +++ S R      M +QA+ +          
Sbjct: 712 HTFAADTWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQI--- 768

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                    + A I+      +    A+  +          +   +  Y           
Sbjct: 769 ------RMDTMANILYYPQKPLATTRAMEHLRFRELPAGQNAIVAILCYSG--------- 813

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ            + +I +  + D G            M                 
Sbjct: 814 --YNQ-----------EDSVIMNQSAIDRGLFRSLYYRTFQDMEK--------------- 845

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
                   I +EEFE   RDT             +     + +D  G++  G  V+  DI
Sbjct: 846 ----KVGVITMEEFEKPTRDTA----------IRLKHGTYEKLDVDGLVPPGTRVSGEDI 891

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           ++GK  P     + P+   L      K    +D S  + S  SG +  V I       K
Sbjct: 892 IIGKTAP-----LPPDSDELG--MRSKMHTKKDVSTPMKSTESGIIDQVLITTNGEGAK 943


>gi|108773283|ref|YP_635711.1| RNA polymerase beta subunit [Chara vulgaris]
 gi|77157939|gb|ABA61980.1| beta subunit of RNA polymerase [Chara vulgaris]
          Length = 1091

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 164/498 (32%), Positives = 244/498 (48%), Gaps = 53/498 (10%)

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I          + +  I+     V  G++L    +  G   ++    +L A    +  + 
Sbjct: 629  INYERSNQNTCLHQKPIVKKDDYVKKGELLADASSTLG-GEISLGNNILVAYMPWEGYNF 687

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  L     ++  ++   I+    I+K E  +++     E + +        L RN+  
Sbjct: 688  EDAVL-----INERLIYEDIYTSIHIEKYEIEVNMTSLGPEKITKKIPHLSEYLLRNL-D 741

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                IL G    +G     K T          P  +    A+   K     E+       
Sbjct: 742  VNGLILLGSWVKTGDVLVGKLTPREPGESLRLPEGRLLH-AIFGIKASSFFETCLKVAPG 800

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            ++  + D     +  ++  + +    ++ V +++  KR IQ GDK+AGRHGNKG++SRIL
Sbjct: 801  AEGRVID-----VRWVESANKLTQKYIKTVNIYILQKRKIQVGDKIAGRHGNKGVISRIL 855

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+++DGTP+D+VL+PLGVPSRMN+GQIFE  LG A   L K  + +  D +   +
Sbjct: 856  PREDMPYIQDGTPIDMVLSPLGVPSRMNLGQIFECLLGLAGESLKKHYRIMPFDERHERE 915

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             S   +F E                                     F G      +S L 
Sbjct: 916  ASRKLAFSELYQAKK-------------------------------FTG------HSWLF 938

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                D  G+S L+DG TG+ F+  +TVG  Y+LKL H V DK++ARSTG YS+VTQQPLG
Sbjct: 939  E--PDTPGKSQLFDGRTGQTFENAITVGKAYILKLIHQVDDKIHARSTGPYSMVTQQPLG 996

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-T 1343
            GK+ RGGQR+GEMEVW ++ +GAAY LQE+LT KSDD+ GR     +IV GN   +   T
Sbjct: 997  GKARRGGQRMGEMEVWALEGFGAAYTLQELLTRKSDDMKGRNEALGAIVTGNLIPKPNTT 1056

Query: 1344 PESFNVLVKEMQALGLSI 1361
            PESF +L++E++ L L+I
Sbjct: 1057 PESFKLLMRELRCLCLNI 1074



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 249/613 (40%), Positives = 361/613 (58%), Gaps = 15/613 (2%)

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV-MRPGDVSTFSVAESMFN 397
              +D+  L        +Y+     T      ++A++++YR         +FS       
Sbjct: 206 LNWKDLEKLISRPSLLLSYLSKEKRT--PYSPEEAIIELYRHSCSVSGEISFSENIRKEL 263

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
           +  F   + ++ ++GR+ +N +LNLD P++ R +  +D+IA I  L++       +DDID
Sbjct: 264 YHKFFKIRCEIGSIGRLNINKKLNLDIPEEERFLVPQDLIAAINSLIEKSFKIVNLDDID 323

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
           +L NRRV  + +ML++Q R+ L R++R I    R  +   +   PQ L+  KP+V+   E
Sbjct: 324 HLKNRRVHLIADMLQSQVRIALNRLKRMIAEVMRGINKRKNLPNPQSLVTPKPLVATFQE 383

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF S  L Q  +  N L+ ITH RR+S+LG GG+ +  A   +RD+HP+HYG+ICP ET 
Sbjct: 384 FFGSHPLCQFMDQTNPLAEITHKRRISSLGPGGLTQKTATFNVRDIHPSHYGKICPIETP 443

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSS 633
           EG N GLVSSL   A +N  GFIE+P+ K+   +        +L + +EE   I      
Sbjct: 444 EGQNAGLVSSLAILANINQNGFIESPFLKLHKNEYKQLTGSEHLCSEQEEYYRITTGE-H 502

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             E      +    R   E        + F D  P Q  SIA SLIPFLE+DD+NR LMG
Sbjct: 503 SRETAEKKGKPTPIRYRQEFSATAFHFLHFRDILPIQYFSIATSLIPFLEHDDANRALMG 562

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ E P VGTG+E  VA  S A +++K  G V+ VD   I IRS     +
Sbjct: 563 SNMQRQAVPLLRPEKPIVGTGLEGQVALDSAALVLSKIEGKVDFVDGRNINIRSNIVINE 622

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +  +  Y     +RSNQNTC++Q+P+VK  D V++ +++AD  ST  G+++LG N+LV
Sbjct: 623 FFSFQLINY-----ERSNQNTCLHQKPIVKKDDYVKKGELLADASSTLGGEISLGNNILV 677

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           A+MPW GYNFED++LI+ER++ ED++TSIHIE++E+    T LGPE+IT+ IP++SE  L
Sbjct: 678 AYMPWEGYNFEDAVLINERLIYEDIYTSIHIEKYEIEVNMTSLGPEKITKKIPHLSEYLL 737

Query: 874 KNIDECGIICVGAEVNPGDILVGKITP--KGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
           +N+D  G+I +G+ V  GD+LVGK+TP   GES   PE +LL AIFG KA    +T L+V
Sbjct: 738 RNLDVNGLILLGSWVKTGDVLVGKLTPREPGESLRLPEGRLLHAIFGIKASSFFETCLKV 797

Query: 932 PSGVSGTVVDVRI 944
             G  G V+DVR 
Sbjct: 798 APGAEGRVIDVRW 810



 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 71/358 (19%), Positives = 146/358 (40%), Gaps = 37/358 (10%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM- 73
             F KN +I  +PD I +Q  S+  F+           +GL   F+    I   SG    
Sbjct: 18  MKFEKNTDIFILPDFIRIQLESFHRFI----------EKGLLEEFQRFPVIRDSSGELSY 67

Query: 74  -LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            L    Y+   P F+  + +++  TY+  L +  ++     ++          K + I +
Sbjct: 68  FLNGKRYKLQEPSFNEQEAIYQASTYSSELYVPAQITHTKSEK---------TKSEIILI 118

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G++P+MT  G F+I G  R++V+Q+ RSPG+++  +         + Y+C  I + G  +
Sbjct: 119 GNIPIMTARGNFIINGASRVIVNQILRSPGLYYGSELD---AQANITYSCTFISEWGGRL 175

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
            +E D+K  I VR+ ++RK+PV   L+A+G++ +++                      + 
Sbjct: 176 KLEMDNKRRIWVRLSKKRKIPVLLLLLAMGLNWKDLEKL--------ISRPSLLLSYLSK 227

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           +         +++++      +      +  + K L  K  K          G       
Sbjct: 228 EKRTPYSPEEAIIELYRHSCSVSGEISFSENIRKELYHKFFKIRCEIGS--IGRLNINKK 285

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           +N +  E   E   ++ +  +  I     +   I+ +D +++    R  L+ D  + +
Sbjct: 286 LNLDIPE---EERFLVPQDLIAAINSLIEKSFKIVNLDDIDHLKNRRVHLIADMLQSQ 340


>gi|304561828|gb|ADM43776.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 439

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 173/482 (35%), Positives = 254/482 (52%), Gaps = 55/482 (11%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP 83
           +++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  + 
Sbjct: 1   LEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLEN 50

Query: 84  -PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ G
Sbjct: 51  NPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEKG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI+
Sbjct: 102 TFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDIV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K  
Sbjct: 159 YVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK-- 216

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAEDI 312
                +  GE   +ES K L   L    K   +  +G             +  L  A+ I
Sbjct: 217 ----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKKI 272

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           VN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N            
Sbjct: 273 VNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT---------- 320

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
             +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I 
Sbjct: 321 --VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNIT 376

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++ 
Sbjct: 377 KDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMTI 436

Query: 493 VD 494
            D
Sbjct: 437 QD 438


>gi|126797641|gb|ABO27352.1| DNA-directed RNA polymerase beta chain [Agrobacterium rhizogenes]
 gi|149211737|gb|ABR22222.1| DNA-dependent RNA polymerase beta chain [Rhizobium tropici CIAT 899]
          Length = 224

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 155/224 (69%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G++I  LI  YKA+G+I PLR  ++ V+G G  ++ + +YDD SVLR+A+Q
Sbjct: 61   HLGWACAGMGRQIGELIEAYKASGNIEPLRKTIDLVVGDGPKSDDVHEYDDASVLRLADQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            WK GV ++TPVFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  WKRGVSIATPVFDGAGEADVNHMLAMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|95115795|gb|ABF56192.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. triticae]
 gi|95115797|gb|ABF56193.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. triticae]
          Length = 1262

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/987 (17%), Positives = 316/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ S          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTTERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  198 bits (503), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 156/1171 (13%), Positives = 317/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++V   DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVVEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GNVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  --D---------------IIHV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
              D                 +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WADNSLGGPGQGKRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + +S  ++  +   D                   +    +  
Sbjct: 558  NLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +S +   RR   L             +RD+    +     A         + ++ +  
Sbjct: 615  QLVSVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       E   R V +   ++                         + YL A EEE  
Sbjct: 668  NRNQLVFDREISNRLVKEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPTTE------------------------------------- 750

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
               R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 751  ---RANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  NTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|304561582|gb|ADM43653.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561696|gb|ADM43710.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
 gi|304561834|gb|ADM43779.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 436

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/480 (35%), Positives = 254/480 (52%), Gaps = 55/480 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMT 436


>gi|126797639|gb|ABO27351.1| DNA-directed RNA polymerase beta chain [Agrobacterium rhizogenes]
          Length = 224

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 155/224 (69%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G++I  LI  YKA+G+I PLR  ++ V+G G  ++ + +YDD SVLR+A+Q
Sbjct: 61   HLGWACAGMGRQIGELIEAYKASGNIEPLRKTIDMVVGDGPKSDDVHEYDDASVLRLADQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            WK GV ++TPVFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  WKRGVSIATPVFDGAGEADVNEMLVMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|294659491|ref|XP_002770594.1| DEHA2G07502p [Debaryomyces hansenii CBS767]
 gi|199434003|emb|CAR65929.1| DEHA2G07502p [Debaryomyces hansenii]
          Length = 1232

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 178/983 (18%), Positives = 321/983 (32%), Gaps = 158/983 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 363  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 422

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 423  DIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 482

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 483  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 538

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 539  SCISVGTSSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRN 598

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLI----PFLENDDSNRVLMGCNMQRQAVPLLK 705
                  +  E     D   K+      +       F+ +DD+     G    ++      
Sbjct: 599  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDDAESETKGELKLKKENVHKL 658

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDIY 762
              A +   G +      S +++V    GIVE VDA      +I     DL+ S S +   
Sbjct: 659  INAEYDDFGDDPDSLSYSWSSLV--NDGIVEYVDAEEEETIMIAMTPEDLETSRSTLSET 716

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                 Q   Q     +R  +K    +         PS  LG  A       + +P+  +N
Sbjct: 717  EQKDMQLEEQEVDPAKR--IKPTLGLHTFTHCEIHPSMILGVAA-------SIIPFPDHN 767

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      M  + +   + +  + V                               + 
Sbjct: 768  QSPRNTYQSAMGKQAMG--VFLTNYAVRM---------------------------DTMA 798

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 799  NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-R 857

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +F R  +D  +R      E  E   R                   I  G          
Sbjct: 858  SLFFRSYMDLEKRQGMKALETFEKPTRSDTLRLRHGTYEKLDDDGLIAPGVRVSGEDIII 917

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+T +  D      R+Q+         ++     +  Q               +     
Sbjct: 918  GKTTPIPPDAEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------VLLTTN 962

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            GD       + VKV +   +  Q GDK A RHG KG +      EDMPF   G   D+++
Sbjct: 963  GD-----GAKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFTSQGVVPDLII 1017

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM V  + E  L       G +                               
Sbjct: 1018 NPHAIPSRMTVAHLIECLLSKVSSLSGLEGD----------------------------- 1048

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    ++P F     EA++ +LR       G  ++Y+G TG
Sbjct: 1049 ------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMYNGHTG 1083

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+
Sbjct: 1084 KKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCM 1143

Query: 1303 QAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFETGTPE 1345
             A+GAA  L+E L   SD        + G   V  ++              + ++   P 
Sbjct: 1144 IAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQIHIPY 1203

Query: 1346 SFNVLVKEMQALGLSIDLENSRT 1368
            +  +L +E+ A+ +S  L   R+
Sbjct: 1204 AAKLLFQELMAMNISPRLYTERS 1226



 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 149/1008 (14%), Positives = 303/1008 (30%), Gaps = 162/1008 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------AAMLEFVSYEFD 82
           L+  Q  S+D F+   I      +  L        P    S          + F      
Sbjct: 38  LVSQQLDSFDEFIETTIQELVWEDSHL--ILDQ--PAQHTSEDDHENRRYEITFGKIYIS 93

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE----FTGAKSIKDIKEQ 128
            P               +   R+LTY+ PL + +   V   D+        + +++  E 
Sbjct: 94  KPTQTEGDGTTHPMFPQEARLRNLTYSSPLYVDMTKKVLKSDDNNRVDNELEWVEEKIED 153

Query: 129 S-----IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
                 +Y+G +P+M +                         G FVI G ++++++Q  R
Sbjct: 154 EGPQTKVYLGKVPIMLRSKFCMLRGLGEHEFYELKECPYDMGGYFVINGSEKVLIAQE-R 212

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID-----RRRK- 211
           S          + +    + +   I    ++G  +      K  ++ R D     R  K 
Sbjct: 213 SAANI--VQVFKKAAPSPISHIAEIRSAIEKGSRLISSMQIK--LYGRDDKGTSGRTIKA 268

Query: 212 --------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                   +P+     ALG+  + +IL          Q  +     +    ++   +V+ 
Sbjct: 269 TLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQEREVAL 328

Query: 263 SLVD------IDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDCLCGLYVAEDIVN 314
             +       I   +++  +   L   LL ++  +E            +    +   +  
Sbjct: 329 DFIGRRGVLGIRREKRIQYAKDILQKELLPNITQEEGFETRKAFFLGYMVNRLLLCALER 388

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDA 373
            E      +  D   +K L+           IL+   + +   Y++  +  DK  +   A
Sbjct: 389 KEP-----DDRDHFGKKRLDLAGPLLANLFRILFKKLTKDIYNYMQRCVENDKEFNLTLA 443

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHI 431
           +             T  +  S+    + +  K   S  G  ++  R    +      R  
Sbjct: 444 V--------KSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTN 495

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   I     L N    +         +      ++KN   +  + +  S +  + 
Sbjct: 496 TPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTSSEPILY 552

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            ++   + P +         +   F     +    E  + +  + + RR   +       
Sbjct: 553 FLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRNLRRRGDISPEVSII 612

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                +   +         P    +              + N +  I   Y         
Sbjct: 613 RDIREKEFKIFTDAGRVYRPLFIVDDDAESETKGELKLKKENVHKLINAEY-----DDFG 667

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D   LS           + SSL  DG                      ++++DA  ++ 
Sbjct: 668 DDPDSLS----------YSWSSLVNDG---------------------IVEYVDAEEEET 696

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAK 730
           + IA +      +  +       +MQ +   +  A+      G+      +   + I+  
Sbjct: 697 IMIAMTPEDLETSRSTLSETEQKDMQLEEQEVDPAKRIKPTLGLHTFTHCEIHPSMILGV 756

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            A I+   D  +    + +  +     GV      ++           Q+PL        
Sbjct: 757 AASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYAVRMDTMANILYYPQKPL-------- 808

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA   + GYN EDSM++++  +   +F S+    +  
Sbjct: 809 --ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMD 866

Query: 850 MARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + +   +   E        D   +     + +D+ G+I  G  V+  DI++GK TP    
Sbjct: 867 LEKRQGMKALETFEKPTRSDTLRLRHGTYEKLDDDGLIAPGVRVSGEDIIIGKTTPI--- 923

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           P   EE   R     +    RD S  + S  SG V  V +       K
Sbjct: 924 PPDAEELGQRT----QYHTKRDASTPLRSTESGIVDQVLLTTNGDGAK 967


>gi|95115799|gb|ABF56194.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
          Length = 1262

 Score =  418 bits (1074), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/987 (17%), Positives = 316/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ S          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 156/1171 (13%), Positives = 318/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++V   DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVVEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  TTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GSVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  ---DII--------------HV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
               + +              +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WSENSLGGSGQGKRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + +S  ++  +   D                   +    +  
Sbjct: 558  NLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +S +   RR   L             +RD+    +     A         + ++ +  
Sbjct: 615  QLVSVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       E   R V +    +                         + YL A EEE  
Sbjct: 668  NRNQLVFDREISNRLVKEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPT--------------------------------------- 748

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             S R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 749  -SERANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  NTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|303315773|ref|XP_003067891.1| DNA-directed RNA polymerase II, putative [Coccidioides posadasii C735
            delta SOWgp]
 gi|240107567|gb|EER25746.1| DNA-directed RNA polymerase II, putative [Coccidioides posadasii C735
            delta SOWgp]
          Length = 1258

 Score =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 198/1216 (16%), Positives = 386/1216 (31%), Gaps = 207/1216 (17%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYS------QRGDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L         IL       +Y+        G ++    S   L+   + + ++
Sbjct: 187  KMP--IMLK----SKYCILKDLGEHALYNWNECPYDSGGYFIINGSEKVLIAQERSAGNI 240

Query: 265  VDIDTGEQ------------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            V +                  +E G ++ S L   L  KG    G     +    +    
Sbjct: 241  VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLSIKLFAKGDSSKGGFGPTIRST-LPYIK 299

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +     ++   G V DE  L  I +       +  +       ++         +DR+ 
Sbjct: 300  TDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFV--------IQDREV 351

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL  I +    G   T    E    +      K  L  +              +     +
Sbjct: 352  ALDFISKR---GSSPTSMNHEKRVRYARDIIQKEFLPHI-----------SQSEGSETRK 397

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RI 490
               +  ++  L+    G+  +DD D+ G +R+   G +L N +R+  +R+ + + +  + 
Sbjct: 398  AFFLGYMVHKLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQR 457

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITH 537
                   +     + A  +   +     +               +SQ+       S ++H
Sbjct: 458  CVETNRQLYLNIGVKASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSH 517

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR +      + R     + R +H TH+G +CPAET EG   GLV +L     +     
Sbjct: 518  LRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTP 573

Query: 598  IET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             E    +    + +V  +     +      ++      +  D S     V        I 
Sbjct: 574  SEPIIDFMIQRNMEVLEEFEPQVSPNSTKIFVNGVWVGVHRDPSHLVSTVQSLRRRNMIS 633

Query: 656  VPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                 + D  D   K          P F+ ++D      G  +  +           +  
Sbjct: 634  HEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVLTKEHIRKLEADKEIPA 693

Query: 714  GMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
             ++    +          ++G+VE VDA      ++   + P    V       +     
Sbjct: 694  DLDPEERRERYYGWDGLVKSGVVEYVDAEEEE--TIMIVMSPEDLEVSKQYQAGYIPEED 751

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             +  N+R   K+  +          PS  LG       +  + +P+  +N          
Sbjct: 752  TSDPNRRVRSKLSQKAHTWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSA 804

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            M  + +                     E   +I    ++ L                   
Sbjct: 805  MGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA------------------ 836

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 +       +   +  + AI      +  D+ +   S +   +     +  +    
Sbjct: 837  -TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT--- 892

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLS 1009
             +    +    +E   +    + + +    Y ++ +   +  G           K+  L+
Sbjct: 893  -DSEKMIGLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLA 951

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +                +E  QR  +  K+   T     E    +++            
Sbjct: 952  PE---------------SEELGQRTKQHTKLDVSTPLRSTESGIVDQVLV-----STSNE 991

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             L+ VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PS
Sbjct: 992  DLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTFRQEDMPFTREGIVPDLIINPHAIPS 1051

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 1052 RMTIAHLIECQLSKVSSLRGYEGD------------------------------------ 1075

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++S+LR       G  ++Y+G TG      +
Sbjct: 1076 -----------------ATP-FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQI 1117

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+ 
Sbjct: 1118 FLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASA 1177

Query: 1310 VLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFETGTPESFNVLVK 1352
             L+E L   SD       D+ G       +  G+             +   P +  +L +
Sbjct: 1178 FLKERLFDVSDPFRIHICDICGLMTPIAKLKKGDFECRACKNKNKISQVHIPYAAKLLFQ 1237

Query: 1353 EMQALGLSIDLENSRT 1368
            E+ ++ ++  +   R+
Sbjct: 1238 ELMSMNIAARMYTKRS 1253



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 105/802 (13%), Positives = 231/802 (28%), Gaps = 142/802 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              L+F +     
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTIAPDEDDPDPVMVRRYELKFGTVMLAR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDV-------------------D 114
           P               +   R+LTYA PL + +   + +                    D
Sbjct: 97  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKKIAEGRERSLAERDEDDDEPDAKGD 156

Query: 115 EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
           E   A+              +  E++I++G +P+M K                       
Sbjct: 157 EERRARGTYLQWEPKALPEDEADEENIFIGKMPIMLKSKYCILKDLGEHALYNWNECPYD 216

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 217 SGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 273

Query: 198 SKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D  +                 +P+     ALG +  E+IL+        + 
Sbjct: 274 IK--LFAKGDSSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 331

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +          + +K        ++++ +  +  + 
Sbjct: 332 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQSE 391

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V + ++    G   ++  D   +K L+           +L++    +
Sbjct: 392 GSETRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 450

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 451 LYKYVQRCVETNRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 503

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 504 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 563

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
              Y       E  I    + +   ++   PQ   N+  +      F     +    +  
Sbjct: 564 LMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKI------FVNGVWVGVHRDPS 617

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +S +   RR + +                      R   P       P   + G  + 
Sbjct: 618 HLVSTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 677

Query: 582 LVSSL-------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
               +          A ++     E  Y        +  V Y+ A EEE   I  +   L
Sbjct: 678 TKEHIRKLEADKEIPADLDPEERRER-YYGWDGLVKSGVVEYVDAEEEETIMIVMSPEDL 736

Query: 635 DEDGSFTEELV-------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +    +    +         R    ++          +  P  ++ I AS+IPF +++ S
Sbjct: 737 EVSKQYQAGYIPEEDTSDPNRRVRSKLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAP 709
            R      M +QA+ +      
Sbjct: 797 PRNTYQSAMGKQAMGVFLTNFD 818


>gi|303273466|ref|XP_003056094.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226462178|gb|EEH59470.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 1172

 Score =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 184/1098 (16%), Positives = 354/1098 (32%), Gaps = 206/1098 (18%)

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
              +       E G I +    +  +  L  +F +      +   D + +  Y  N     
Sbjct: 239  RMLHSPGTKMEPGCIRVTLPYIRTDIPLFVVFRALG---FVADKDILEHIVYDFNDHDAM 295

Query: 366  K--NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            +      ++AL    + +    +     A  +         KY    + +  +     + 
Sbjct: 296  ELLRPSIEEALPIQSKKVALDYIGKRGSAVGV---SREKRIKYAQDILQKELLPH---VG 349

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
              ++    +   +  I+  L+    G+   DD D+ GN+R+   G ++   +R    ++ 
Sbjct: 350  VDEECETRKAYYLGYIVHRLLLCALGRRNEDDRDHFGNKRMDLAGPLIAILFRQLFRKLT 409

Query: 484  RSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHV 529
            + ++   +        +     + AK + S +     +              +SQ+   +
Sbjct: 410  KDVRLYCQRCVDSGKEIQLTLAVKAKTITSGLKYSLATGNWGAQGAQDIRAGVSQVLNRL 469

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            +  S ++H RRL++     + R     + R +H +H+G +CPAET EG   GLV +L+  
Sbjct: 470  SFSSTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLM 525

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            A V+  G   +P  +  +     ++  +S     +      N           +LV    
Sbjct: 526  ALVS-VGSPSSPVLEFLEEWTMENLEEISPSVISHATKIFVNGVWVGVHRDPADLVRTLR 584

Query: 650  AGEEILVPREKIDFIDASPKQVVSI----AASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                 +    ++  +     Q + +       + P    +D    +   N++      + 
Sbjct: 585  ELRRKVDITTEVGIVHDIRLQELRLYTDYGRCIRPLFIVEDQRMKIKKRNIEMLQEKDI- 643

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                   TG       SSG          +E VD        +   ++       +    
Sbjct: 644  -------TGFTWNDLVSSGC---------IEYVDTEEEETTMISMTIEDLVQARLLANNE 687

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
               +     C                      PS  LG       +  + +P+  +N   
Sbjct: 688  TSVQHMYTHC-------------------EIHPSMILG-------ICGSIIPFPDHNQ-- 719

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                S R   +       +  +    +                       +    +  V 
Sbjct: 720  ----SPRNTYQSAMGKQAMGMYVTNFQ-----------------------LRMDTLAYVL 752

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                   +    +       +     ++  I      +  D+ +   S +   +    IF
Sbjct: 753  FYPQKPLVTTRAMEHLHFRELPAGVNVVVGIMCYTGYNQEDSVIMNQSSIDRGLF-RSIF 811

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R   D+ ++  S+ +E +E  + +              +   I  G           K+
Sbjct: 812  YRSFKDEEKKQGSLTKEDLECPSPETTLGMRHGTYGKLDKDGLICPGTRVSGEDIIIGKT 871

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            + L                   D+    +    K    T     E    +++        
Sbjct: 872  SPL-----------------PDDDPSAASNRFTKRDCSTGMKNSETGIIDQVLL-----T 909

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VK+ V   R  Q GDK + RHG KG +      EDMPF  +G   DI++NP 
Sbjct: 910  TNDQGLRFVKIRVRSCRTPQVGDKFSSRHGQKGTIGMTYTQEDMPFTCEGVVPDIIVNPH 969

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 970  AIPSRMTIGQLVECLMGKVAAMMGKEGD-------------------------------- 997

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     E I+ ML      + G  ++Y+G TG   
Sbjct: 998  ---------------------ATP-FTPVTVENISDMLHQCGYQKRGNEVMYNGHTGRKL 1035

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  + +G  Y  +L HMV DK+++R  G   ++T+QP+ G+S  GG R GEME  CI ++
Sbjct: 1036 EAKIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPMEGRSRDGGLRFGEMERDCIISH 1095

Query: 1306 GAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAGNDTFE------TGTPE 1345
            GAA  L+E L  +SD     V            + + +E      +  E         P 
Sbjct: 1096 GAAAFLKERLMDQSDAYRVHVCQTCGLIAVANLKNQTFEC---CKNPSERMKVVQVLLPY 1152

Query: 1346 SFNVLVKEMQALGLSIDL 1363
            +  +L +E+ ++ ++  L
Sbjct: 1153 ACKLLFQELMSMAVAPRL 1170



 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 125/987 (12%), Positives = 273/987 (27%), Gaps = 190/987 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L   Q  S++ F+   +                +                          
Sbjct: 31  LARQQLDSFNEFIQHAMQEI---------VVDEMSSFELEPEQQHVPGEEGEGGEKKTYK 81

Query: 74  LEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           + F       P               +   R+LTY+ PL + +   V  V   +      
Sbjct: 82  ISFKQIYLSKPMVTEADGMTSTLFPKEARLRNLTYSAPLYVDMEKTVTTVTLDSQKTEEV 141

Query: 124 DIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHR 159
           + K   +++G +P+M                         + G F+I G ++++++Q   
Sbjct: 142 E-KINKVFIGKVPIMLRSEYCSLHDHTDKELTELGECPYDEGGYFIINGSEKVLIAQEKM 200

Query: 160 SPG---IHFDHDKGR---------ASLSGKLLYA---CRIIPDQGLWMDIEFDSKDIIHV 204
           S     +       +         +  SG    +    R++   G  M+       + ++
Sbjct: 201 SSNHVYVFKKRQPSKYMWVAECRSSPESGARAASACVARMLHSPGTKMEPGCIRVTLPYI 260

Query: 205 RIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           R D    +P+     ALG  ++ +IL             +     +  A  +   KV+  
Sbjct: 261 RTD----IPLFVVFRALGFVADKDILEHIVYDFNDHDAMELLRPSIEEALPIQSKKVALD 316

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +        +   K++       L+++ +  +G+  +C          +      + + 
Sbjct: 317 YIGKRGSAVGVSREKRIKYAQ-DILQKELLPHVGVDEECETRKAYYLGYIVH---RLLLC 372

Query: 324 AGDVIDEKSLEEIFHSEIR----DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           A    +E   +   +  +      I IL+                      K+  L +  
Sbjct: 373 ALGRRNEDDRDHFGNKRMDLAGPLIAILFRQLFRKLTKDVRLYCQRCVDSGKEIQLTLAV 432

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIA 438
                   T  +  S+    +      D+       +N      T   +R +        
Sbjct: 433 K---AKTITSGLKYSLATGNWGAQGAQDIRAGVSQVLNRLSFSSTLSHLRRLNSPIGREG 489

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +         +      ++KN   + L+ +       +  ++  ++
Sbjct: 490 KLAKPRQLHNSHWGMVCPAETPEGQACG---LVKNLSLMALVSVGSPSSPVLEFLEEWTM 546

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVE 557
              + I+   +  A   F     +    +  + +  +   RR   +  + G+       E
Sbjct: 547 ENLEEISPSVISHATKIFVNGVWVGVHRDPADLVRTLRELRRKVDITTEVGIVHDIRLQE 606

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R ++  +   I P    E   + +        +               D   +  + Y+
Sbjct: 607 LR-LYTDYGRCIRPLFIVEDQRMKIKKRNIEMLQEKDITG-----FTWNDLVSSGCIEYV 660

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EEE   I+             E+LV  R         +      +  P  ++ I  S
Sbjct: 661 DTEEEETTMISM----------TIEDLVQARLLANNETSVQHMYTHCEIHPSMILGICGS 710

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 711 IIPFPDHNQSPRNTYQSAMGKQAMGMYVTNFQL--------------------------- 743

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-----VKVGDEVRRND 792
                            + + V  Y       +     ++ R L     V VG       
Sbjct: 744 --------------RMDTLAYVLFYPQKPLVTTRAMEHLHFRELPAGVNVVVGIMCYTGY 789

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
              D         ++ R +  +       + E        +  ED+         E  + 
Sbjct: 790 NQEDSVIM--NQSSIDRGLFRSIFYRSFKDEEKK---QGSLTKEDL---------ECPSP 835

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           +T LG          +       +D+ G+IC G  V+  DI++GK +P  +   +     
Sbjct: 836 ETTLG----------MRHGTYGKLDKDGLICPGTRVSGEDIIIGKTSPLPDDDPSAASN- 884

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                       RD S  + +  +G +
Sbjct: 885 --------RFTKRDCSTGMKNSETGII 903


>gi|326484701|gb|EGE08711.1| DNA-dependent RNA polymerase II RPB140 [Trichophyton equinum CBS
            127.97]
          Length = 1258

 Score =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 190/1137 (16%), Positives = 371/1137 (32%), Gaps = 186/1137 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDI 1197

Query: 1323 VGRTRVYESIV-AGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G      + V  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1198 CG-LMTPIAKVKKGDFECRACRNKNKISQVHIPYAAKLLFQELASMNIAARMYTKRS 1253



 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 144/1050 (13%), Positives = 300/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEPDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  + Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|82621735|gb|ABB86549.1| second largest subunit of RNA polymerase II [Phaeosphaeria nodorum]
 gi|95115801|gb|ABF56195.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
 gi|95115803|gb|ABF56196.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
 gi|95115805|gb|ABF56197.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
 gi|95115807|gb|ABF56198.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
 gi|95115809|gb|ABF56199.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
 gi|95115811|gb|ABF56200.1| RNA polymerase II second largest subunit [Phaeosphaeria nodorum]
          Length = 1262

 Score =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 171/987 (17%), Positives = 316/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ +          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 158/1171 (13%), Positives = 319/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++V   DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVVEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GNVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  --D---------------IIHV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
              D                 +     I  +++VP+     ALG+   EEILS        
Sbjct: 271  WADTSLGNPGQGKRAPGPFAYAMLPYI--KQEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + +S  ++  +   D                   +    +  
Sbjct: 558  NLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +S +   RR   L             +RD+    +     A         + ++ T  
Sbjct: 615  QLVSVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       E   R V +   ++                         + YL A EEE  
Sbjct: 668  NRNQLVFDREISNRLVKEQLDSDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPT--------------------------------------- 748

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             S R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 749  -SERANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  NTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|326475036|gb|EGD99045.1| DNA-dependent RNA polymerase II RPB140 [Trichophyton tonsurans CBS
            112818]
          Length = 1258

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 190/1137 (16%), Positives = 371/1137 (32%), Gaps = 186/1137 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLLSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDI 1197

Query: 1323 VGRTRVYESIV-AGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G      + V  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1198 CG-LMTPIAKVKKGDFECRACRNKNKISQVHIPYAAKLLFQELASMNIAARMYTKRS 1253



 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 144/1052 (13%), Positives = 301/1052 (28%), Gaps = 222/1052 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEPDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDII------------------HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVY 238
            K +                   +++ D    +P+     ALG +  E+IL+        
Sbjct: 273 IKLLSKGDSAKGGFGPTIRSTLPYIKTD----IPIVVVFRALGVVSDEDILNHICYDRND 328

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +   +     +    ++   +V+   +       +  + +K        ++++ +  +  
Sbjct: 329 TPMLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQ 388

Query: 299 T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           +           G  V   ++    G   ++  D   +K L+           +L++   
Sbjct: 389 SEGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLT 447

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +        V    +   +  +    +       T  +  ++    + +  K   S  G
Sbjct: 448 KDLYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAG 500

Query: 413 RVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGE 469
             ++  R    +      R          I     L N   G +   +    +    V  
Sbjct: 501 VSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 560

Query: 470 MLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           +            E  I    + +   ++   PQ   N+  V      F     +    +
Sbjct: 561 LALMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRD 614

Query: 528 HVNSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             + +  +   RR + +                      R   P       P   + G  
Sbjct: 615 PAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSL 674

Query: 580 IGLVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           + +   +    A       ++   R+           +  + Y+ A EEE   I      
Sbjct: 675 VLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPED 734

Query: 634 LDEDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L+    +         +     R     +          +  P  ++ I AS+IPF +++
Sbjct: 735 LEASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHN 794

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R      M +QA+ +         T  E  +   +                      
Sbjct: 795 QSPRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL------------------- 828

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                                           Q+PL                      +L
Sbjct: 829 -----------------------------YYPQKPL----------ATTRSMEFLKFREL 849

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----- 860
             G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     
Sbjct: 850 PAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKP 909

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           +  D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     + 
Sbjct: 910 MRSDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH 964

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                D S  + S  SG V  V +   +   K
Sbjct: 965 --TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|41179041|ref|NP_958397.1| RNA polymerase beta subunit II [Chlamydomonas reinhardtii]
 gi|41017748|sp|Q8HTL7|RPOB2_CHLRE RecName: Full=DNA-directed RNA polymerase subunit beta C-terminal
            section; AltName: Full=PEP; AltName: Full=Plastid-encoded
            RNA polymerase subunit beta C-terminal section; Short=RNA
            polymerase subunit beta C-terminal section
 gi|24209934|gb|AAN41267.1| RNA polymerase beta'' subunit [Chlamydomonas reinhardtii]
 gi|28269764|tpg|DAA00942.1| TPA_inf: RNA polymerase beta subunit II [Chlamydomonas reinhardtii]
 gi|213517422|gb|ACJ50128.1| RNA polymerase beta subunit II [Chlamydomonas reinhardtii]
          Length = 626

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 164/497 (32%), Positives = 234/497 (47%), Gaps = 50/497 (10%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  GD+L    +  G   +     ++ A    +  +  D  L     V   +  
Sbjct: 116  VKEGDWVEVGDLLADSASSIG-GELAIGHNIIVAYMPWEGYNYEDAILINERLVYEDIYT 174

Query: 942  VRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                 R+ +   E  +  E+       I        D+  I     +    +IL G+   
Sbjct: 175  SIHIERYEVTTKETKLGFEQITREIPDISENEIKHLDKTGIAKIGSWVEEGDILVGKITP 234

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS-ILEDRFKN 1055
               K       L   +  +   +         + ++ NV ++ +          + +   
Sbjct: 235  FNIKTLTPQQKLLYKIFDKQLSTTKDSSLRAPKGIKANVININILARQKIQINTKSKNTG 294

Query: 1056 KIEKIQWGDDMPPGVLR---VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            K  K          ++     + +++A KR +Q GDKMAGRHGNKGIVSRILP +DMPFL
Sbjct: 295  KGSKPPRASKAQNTMVSQPSYIHIYLAEKRKMQVGDKMAGRHGNKGIVSRILPRQDMPFL 354

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DG  VDIVLNPLGVPSRMNVGQI+E  LG A   LG+  K    D              
Sbjct: 355  PDGAAVDIVLNPLGVPSRMNVGQIYECLLGLAGRYLGEHYKIPPFD-------------- 400

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
             ++ G  +    +     ++  +   +W                        + D +  G
Sbjct: 401  -EMYGADASRSFVLSKLYEARKKTGLKW------------------------LLDPNHPG 435

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L+DG   E FD+ VTVG  Y+LKL HMV DK++ARSTG YSLVTQQPL G+S +GGQ
Sbjct: 436  KIRLFDGRNSECFDQTVTVGIAYVLKLVHMVDDKMHARSTGPYSLVTQQPLRGRSKQGGQ 495

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            RLGEMEVW I+ YGAA+VL EMLTIKSDD+ GR  ++++++   +    G+PESF VL+ 
Sbjct: 496  RLGEMEVWAIEGYGAAFVLSEMLTIKSDDMTGRQNLWKNLIENKEIS-LGSPESFKVLIC 554

Query: 1353 EMQALGLSIDLENSRTK 1369
            E+QAL L I L     +
Sbjct: 555  ELQALCLDIGLFRKNKE 571



 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 95/196 (48%), Positives = 139/196 (70%)

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y L  + RSNQ+TC+  +P VK GD V   D++AD  S+  G+LA+G N++VA+MPW GY
Sbjct: 96  YNLETYHRSNQDTCLIHKPAVKEGDWVEVGDLLADSASSIGGELAIGHNIIVAYMPWEGY 155

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++LI+ER+V ED++TSIHIE +EV  ++TKLG E+ITR+IP++SE  +K++D+ GI
Sbjct: 156 NYEDAILINERLVYEDIYTSIHIERYEVTTKETKLGFEQITREIPDISENEIKHLDKTGI 215

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
             +G+ V  GDILVGKITP     +TP++KLL  IF ++    +D+SLR P G+   V++
Sbjct: 216 AKIGSWVEEGDILVGKITPFNIKTLTPQQKLLYKIFDKQLSTTKDSSLRAPKGIKANVIN 275

Query: 942 VRIFNRHGIDKNERSI 957
           + I  R  I  N +S 
Sbjct: 276 INILARQKIQINTKSK 291


>gi|126797637|gb|ABO27350.1| DNA-directed RNA polymerase beta chain [Rhizobium tropici]
          Length = 224

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 155/224 (69%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G++I  LI  YKA+G+I PLR  ++ V+G G  ++ + +YDD SVLR+A+Q
Sbjct: 61   HLGWACAGMGRQIGELIEAYKASGNIEPLRQTIDMVVGDGPKSDDVHEYDDASVLRLADQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            WK GV ++TPVFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  WKRGVSIATPVFDGAGEVDVNEMLEMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|95115791|gb|ABF56190.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. triticae]
          Length = 1262

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 171/987 (17%), Positives = 316/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ +          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 156/1171 (13%), Positives = 317/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++    DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVAEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GSVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  ---DII--------------HV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
               + +              +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WSENSLGGSGQGKRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + +S  ++  +   D                   +    +  
Sbjct: 558  NLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +S +   RR   L             +RD+    +     A         + ++ T  
Sbjct: 615  QLVSVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPTKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       E   R V +    +                         + YL A EEE  
Sbjct: 668  NRNQLVFDREISNRLVKEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPT--------------------------------------- 748

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             S R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 749  -SERANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  NTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|315041535|ref|XP_003170144.1| DNA-directed RNA polymerase [Arthroderma gypseum CBS 118893]
 gi|311345178|gb|EFR04381.1| DNA-directed RNA polymerase [Arthroderma gypseum CBS 118893]
          Length = 1258

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 190/1137 (16%), Positives = 371/1137 (32%), Gaps = 186/1137 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPADLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDI 1197

Query: 1323 VGRTRVYESIV-AGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G      + V  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1198 CG-LMTPIAKVKKGDFECRACRNKNKISQVHIPYAAKLLFQELASMNIAARMYTKRS 1253



 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 144/1050 (13%), Positives = 300/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEHDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  + Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPADLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|150951109|ref|XP_001387366.2| DNA-dependent RNA polymerase II [Scheffersomyces stipitis CBS 6054]
 gi|149388327|gb|EAZ63343.2| DNA-dependent RNA polymerase II [Pichia stipitis CBS 6054]
          Length = 1232

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 169/990 (17%), Positives = 320/990 (32%), Gaps = 158/990 (15%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 361  EEGFESRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFRKLTK 420

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 421  DIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 480

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 481  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 536

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
              ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 537  TCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHRDPANLVDTMRS 596

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                  +  E     D   K             P    DD        +++ Q   +   
Sbjct: 597  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDEAESETKGDLKLQKEHVHNL 656

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
             +       +     +S         G+VE VDA       +    +   +  +      
Sbjct: 657  LSSEYDEYEDPDNEGASYTWSSLINDGVVEYVDAEEEETIMIAMTPEDLEASKNAITETP 716

Query: 767  FQRSNQNTCVNQRPLVKV--GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             +   +   ++    +K                PS  LG  A       + +P+  +N  
Sbjct: 717  DKSVLEEQELDPAKRIKPTFSAATHTFTHCEIHPSMILGVAA-------SIIPFPDHNQS 769

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +   + +  + V                               +  +
Sbjct: 770  PRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DTMANI 800

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +       +   +  + AI      +  D+ +   S +   +    +
Sbjct: 801  LYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSL 859

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKG 1001
            F R  +D  +R      + +E   +    + + L    Y +L +   I  G         
Sbjct: 860  FFRTYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGVRVSGEDII 916

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+T +  D      R+Q+         ++     +  Q               +    
Sbjct: 917  IGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------VLLTT 961

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD       + VKV +   +  Q GDK A RHG KG +      EDMPF   G   D++
Sbjct: 962  NGD-----GAKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFTAQGIVPDLI 1016

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM V  + E  L       G +                              
Sbjct: 1017 INPHAIPSRMTVAHLIECLLSKVSSLSGLEGD---------------------------- 1048

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     ++P F     EA++ +LR       G  ++Y+G T
Sbjct: 1049 -------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMYNGHT 1082

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C
Sbjct: 1083 GKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDC 1142

Query: 1302 IQAYGAAYVLQEMLTIKSD----DVVGR---TRVYESIVAGN----------DTFETGTP 1344
            + A+GAA  L+E L   SD     V G      V  ++              + ++   P
Sbjct: 1143 MIAHGAAGFLKERLMEASDAFRVHVCGMCGLMTVIANLKKNQFECRSCKNKTNIYQIHIP 1202

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             +  +L +E+ A+ +S  +   R++NS ++
Sbjct: 1203 YAAKLLFQELMAMNISPRMYTERSQNSIRV 1232



 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/783 (13%), Positives = 223/783 (28%), Gaps = 127/783 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------AAMLEFVSYEFD 82
           L+  Q  S+D F+   I      +  L        P    S          + F      
Sbjct: 36  LVSQQLDSFDEFIETTIQELVWEDSHL--ILDQ--PAQHTSEDDHENRRYEITFGKIYIS 91

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVD---------EFTGAKSIK 123
            P               +   R+LTY+ PL + +   VF  D         E+   K   
Sbjct: 92  KPMQTEGDGTTHPMFPQEARLRNLTYSSPLYVDMTKKVFKSDDNRRKENELEWVEEKVED 151

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
           +  +Q +++G +P+M +                         G FVI G ++++++Q  R
Sbjct: 152 EEPQQKVFLGKVPIMLRSKFCMLRDLGEHEFFELKECPYDMGGYFVINGSEKVLIAQE-R 210

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------RRRK 211
           S          + +    + +   I    ++G  +      K  ++ R D      R  K
Sbjct: 211 SAANI--VQVFKKAAPSPISHVAEIRSALEKGSRLISSMQIK--LYGR-DEKGTSGRTIK 265

Query: 212 ---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                    +P+     ALG+  + +IL          Q  +     +    ++   +V+
Sbjct: 266 ATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQEREVA 325

Query: 262 SSLV------DIDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDCLCGLYVAEDIV 313
              +       I   +++  +   L   LL ++  +E            +    +   + 
Sbjct: 326 LDFIGRRGVLGIRREKRIQYAKDILQKELLPNITQEEGFESRKAFFLGYMVNRLLLCALE 385

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKD 372
             E      +  D   +K L+           IL+   + +   Y++  +  DK  +   
Sbjct: 386 RKEP-----DDRDHFGKKRLDLAGPLLANLFRILFRKLTKDIYNYMQRCVENDKEFNLTL 440

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RH 430
           A+             T  +  S+    + +  K   S  G  ++  R    +      R 
Sbjct: 441 AV--------KSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRT 492

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                    I     L N    +         +      ++KN   +  + +    +  +
Sbjct: 493 NTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMTCISVGTPSEPIL 549

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
             ++   + P +         +   F     +    +  N +  +   RR   +      
Sbjct: 550 YFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHRDPANLVDTMRSLRRRGDISPEVSI 609

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEG------------HNIGLVSSLTSFARVNAYGFI 598
                 +   +         P    +                 + + L+S          
Sbjct: 610 IRDIREKEFKIFTDAGRVYRPLFIVDDEAESETKGDLKLQKEHVHNLLSSEYDEYEDPDN 669

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-----------EELVFC 647
           E              V Y+ A EEE   IA     L+   +             +EL   
Sbjct: 670 EGASYTWSSLINDGVVEYVDAEEEETIMIAMTPEDLEASKNAITETPDKSVLEEQELDPA 729

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +                +  P  ++ +AAS+IPF +++ S R      M +QA+ +    
Sbjct: 730 KRIKPTFSAATHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN 789

Query: 708 APF 710
              
Sbjct: 790 YSV 792


>gi|95115789|gb|ABF56189.1| RNA polymerase II second largest subunit [Phaeosphaeria sp. S-93-48]
          Length = 1262

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 172/987 (17%), Positives = 316/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVSVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN+ S          R+    L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKPNRNQLVFDREISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRKTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 155/1171 (13%), Positives = 318/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++    DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVAEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GNVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  ---DII--------------HV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
               + +              +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WAENSLGGPGQGKRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + +S  ++  +   D                   +    +  
Sbjct: 558  NLSLMCYVSVGSDATPIIDFMSQRNMQLLEEYDQNQNPEATKVF---VNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +S +   RR   L             +RD+    +     A         + ++ +  
Sbjct: 615  QLVSVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENNPSKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       E   R V +    +                         + YL A EEE  
Sbjct: 668  NRNQLVFDREISNRLVKEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPT--------------------------------------- 748

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             S R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 749  -SERANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            ++ +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  KTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|331124046|gb|AEC53811.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 439

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 205/442 (46%), Positives = 299/442 (67%), Gaps = 3/442 (0%)

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
           IP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +   
Sbjct: 1   IPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKDQT 60

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
               L   D + G   S  +     G+  +E G+++T+  ++ L++ GV  + +  + + 
Sbjct: 61  LLMELVP-DRLRGETASFDIE--ANGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEYIV 117

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G   ++D +N  TGEI + A   I  ++L  +  +  + + +L+ + +++  ++  TL  
Sbjct: 118 GKVASKDYINEATGEIIVNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETLRI 177

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D   DR  AL++IYR+MRPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  + 
Sbjct: 178 DSTVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGRED 237

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER
Sbjct: 238 AQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVER 297

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SAL
Sbjct: 298 AVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISAL 357

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+
Sbjct: 358 GPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRR 417

Query: 605 VCDGKVTNDVVYLSAMEEENRY 626
           V DG VT++V YLSA+EE    
Sbjct: 418 VVDGVVTDEVDYLSAIEEGQFV 439


>gi|296818239|ref|XP_002849456.1| DNA-dependent RNA polymerase II RPB140 [Arthroderma otae CBS 113480]
 gi|238839909|gb|EEQ29571.1| DNA-dependent RNA polymerase II RPB140 [Arthroderma otae CBS 113480]
          Length = 1258

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 195/1134 (17%), Positives = 367/1134 (32%), Gaps = 180/1134 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFAKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVVEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDSNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGLTVVERFEKPMRSDT 914

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K++ L+ +                +E  Q
Sbjct: 915  LRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEELGQ 959

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 960  RTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1014

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1015 RHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEG 1074

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1075 D-----------------------------------------------------ATP-FT 1080

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1081 DVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGR 1325
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1141 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDICG- 1199

Query: 1326 TRVYESIV-AGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                 + V  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1200 LMTPIAKVKKGDFECRACRNKNKISQVHIPYAAKLLFQELASMNIAARMYTKRS 1253



 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 145/1050 (13%), Positives = 300/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPGDDEQDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDDEEEEVEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRSRGTYLHWERKPTLEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFAKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  V Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDSNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMVGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|89515252|gb|ABD75455.1| DNA-directed RNA polymerase beta chain [Ensifer adhaerens]
 gi|126797613|gb|ABO27338.1| DNA-directed RNA polymerase beta chain [Ensifer adhaerens]
          Length = 224

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 153/224 (68%), Positives = 180/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYKAGADIQPLRDTIDSVIGSGPKGEPIKQYDDASIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  SGQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEQAGLKVSGQSTLYDGRTGDQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|89515264|gb|ABD75461.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
 gi|89515266|gb|ABD75462.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
 gi|89515268|gb|ABD75463.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
 gi|89515270|gb|ABD75464.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
 gi|126797615|gb|ABO27339.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
 gi|126797617|gb|ABO27340.1| DNA-directed RNA polymerase beta chain [Sinorhizobium terangae]
          Length = 224

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 154/224 (68%), Positives = 185/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y  NGDI+PLR+ ++ VIG+G   E I +YDD+SV+R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYHENGDIAPLRATIDDVIGSGPKGEPIKNYDDESVVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS L+DG TGEPFDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLNKAGLKVTGQSTLFDGRTGEPFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|327298359|ref|XP_003233873.1| DNA-dependent RNA polymerase II RPB140 [Trichophyton rubrum CBS
            118892]
 gi|326464051|gb|EGD89504.1| DNA-dependent RNA polymerase II RPB140 [Trichophyton rubrum CBS
            118892]
          Length = 1258

 Score =  416 bits (1070), Expect = e-113,   Method: Composition-based stats.
 Identities = 190/1137 (16%), Positives = 372/1137 (32%), Gaps = 186/1137 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTSMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   + +
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNV 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDI 1197

Query: 1323 VGRTRVYESIV-AGN----------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G      + V  G+             +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1198 CG-LMTPIAKVKKGDFECRACRNRNKISQVHIPYAAKLLFQELASMNIAARMYTKRS 1253



 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 144/1050 (13%), Positives = 301/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEPDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTS 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  + Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N++VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNVIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|89515272|gb|ABD75465.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515274|gb|ABD75466.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515276|gb|ABD75467.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515278|gb|ABD75468.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515280|gb|ABD75469.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515282|gb|ABD75470.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
 gi|89515284|gb|ABD75471.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
          Length = 224

 Score =  416 bits (1070), Expect = e-113,   Method: Composition-based stats.
 Identities = 154/224 (68%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y  NGDI+PLR+ ++ VIG+G   E I  YDD+SV+R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYHENGDIAPLRATIDDVIGSGPKGEPIKQYDDESVVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS L+DG TGEPFDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLNKAGLKVTGQSTLFDGRTGEPFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|95115813|gb|ABF56201.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
 gi|95115815|gb|ABF56202.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
 gi|95115817|gb|ABF56203.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
 gi|95115823|gb|ABF56206.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
 gi|95115825|gb|ABF56207.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
          Length = 1262

 Score =  416 bits (1070), Expect = e-113,   Method: Composition-based stats.
 Identities = 172/987 (17%), Positives = 314/987 (31%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDASPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVTVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN  S          R     L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENSPSKPNRNQLVFDRDISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T      A  +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 155/1171 (13%), Positives = 319/1171 (27%), Gaps = 228/1171 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++    DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVAEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GSVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  ---DII--------------HV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
               + +              +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WSENSLGGPGQGRRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +      
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACG--- 554

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++KN   +  + +       I  +   ++   +  +      A   F     +    +  
Sbjct: 555  LVKNLSLMCYVSVGSDASPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              ++ +   RR   L             +RD+    +     A         + +S +  
Sbjct: 615  QLVTVVQELRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVENSPSKP 667

Query: 590  ARVNAYGFIETPYRKVCDGKVTND------------------------VVYLSAMEEENR 625
             R       +   R V +    +                         + YL A EEE  
Sbjct: 668  NRNQLVFDRDISNRLVKEQLDHDTRAGWSDADIADNTYGWKGLIQDGVIEYLDAEEEETA 727

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I  +   LDE       L                                         
Sbjct: 728  MITFSPEDLDEWRGMKMGLPT--------------------------------------- 748

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             S R  +G    R+  P          T  E   A   G       A I+   D  +   
Sbjct: 749  -SERANLGKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746  RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802  NTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
            L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864  ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D   +       +D+ G++  G  V+  DI++GK  P         ++L +     
Sbjct: 912  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLH 967

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVIL 978
               DV        +G+   V+              R+ + +  QI +  A     +  I 
Sbjct: 968  TKRDVSTPLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIG 1026

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKV 1031
                   +     G             + ++   + E   S+      Q+       E  
Sbjct: 1027 ITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVT 1086

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
               +  L  Q    K   E  +     K   
Sbjct: 1087 VDEISDLLEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|89515248|gb|ABD75453.1| DNA-directed RNA polymerase beta chain [Sinorhizobium arboris LMG
            14919]
          Length = 224

 Score =  416 bits (1069), Expect = e-113,   Method: Composition-based stats.
 Identities = 153/224 (68%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y+A+GDI+PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYQASGDIAPLRQTIDDVIGSGPKGEPIKQYDDESIIRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|126797585|gb|ABO27324.1| DNA-directed RNA polymerase beta chain [Sinorhizobium arboris]
          Length = 224

 Score =  416 bits (1069), Expect = e-113,   Method: Composition-based stats.
 Identities = 152/224 (67%), Positives = 184/224 (82%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GK+I ++++ Y+A+GDI+PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKRIGAMLDAYQASGDIAPLRQTIDDVIGSGPKGEPIKQYDDESIIRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|171677674|ref|XP_001903788.1| hypothetical protein [Podospora anserina S mat+]
 gi|170936905|emb|CAP61564.1| unnamed protein product [Podospora anserina S mat+]
          Length = 1278

 Score =  416 bits (1069), Expect = e-113,   Method: Composition-based stats.
 Identities = 195/1129 (17%), Positives = 347/1129 (30%), Gaps = 174/1129 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  K     G  ++ +  + +     +     ++   G V DE  L
Sbjct: 285  LEKGSRLISSLQMKLHTKASNEKGRLANTVS-VTLPYVREDVSLAIVFRALGIVSDEDIL 343

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A+          +DR+ AL  I +    G+ +      
Sbjct: 344  NHICYDRKDTQMLEALRPCIEEAF--------CIQDREIALDFIGKR---GNGNMGQNRM 392

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +          K  L  +              +     +   +  ++  L+    G+   
Sbjct: 393  NRIRAAKDLLQKEMLPHI-----------SQTEGCETRKAFFLGYMVNKLLQCALGRRDT 441

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R  + RM + +    +              I A  + +
Sbjct: 442  DDRDHFGKKRLDLAGPLLAKLFRGVVRRMTQDLMGYMKRCLDTNKHFTLALGIKANTLTN 501

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            A+     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 502  ALKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKP 557

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    V+     +    +       V  +   
Sbjct: 558  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPADPIVDFMTARGMDVLEEYEP 617

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            L A      ++      +  D      LV        I      +  I     ++ S A 
Sbjct: 618  LRAPNATKVFVNGTWVGVHNDPKQLVTLVQDLRRKNVISFEVSLVRDIREREFKIFSDAG 677

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             ++  L   +          + Q +      A                      ++G +E
Sbjct: 678  RVMRPLFTVEQEEKGNHGVEKGQLILNKDHIARLQRDKELGKYHPDYWGWQGLLKSGAIE 737

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA       +                + F     +   N R   KV            
Sbjct: 738  YLDAEEEETTMICMTPQDLDDFRMT--KLGFHIETTSGQGNNRIRTKVNKTTHMYTHCEI 795

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             P+  LG       +  + +P+  +N          M  + +     +  +         
Sbjct: 796  HPAMLLG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM----- 841

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 842  ----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 879

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D  +R      E  E   R       
Sbjct: 880  LCYSGYNQEDSVVMNQSSIDRGIF-RSLFFRSYTDCEKRVGINIVEMFEKPTRGDTLRLK 938

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +       I  G           K++ ++ D                 E  QR  +
Sbjct: 939  HGTYDKLDADGIIAPGIRVSGEDIIIGKTSPINPD---------------NAELGQRQQQ 983

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +K    T     E    + +      D      +R VKV V   +  Q GDK A RHG 
Sbjct: 984  HVKRDASTPLRSTESGIVDSVVLTTNQD-----GMRYVKVRVRTTKIPQIGDKFASRHGQ 1038

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G +     
Sbjct: 1039 KGTIGLTYRMEDMPFTAEGITPDIIINPHAIPSRMTIAHLVECLLSKVATLKGLEGD--- 1095

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                              +TP F     
Sbjct: 1096 --------------------------------------------------ATP-FTDVTV 1104

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++++ +LR       G  ILY G TG         G  Y  +L HMV DK++AR+ G   
Sbjct: 1105 DSVSDLLREQGYQSRGFEILYHGHTGRKLRAQCFFGPTYYQRLRHMVDDKIHARARGPVQ 1164

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVY 1329
            ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD       ++ G     
Sbjct: 1165 IMTRQPVEGRARDGGLRFGEMERDCMIAHGAASFLKERLFEVSDAYRVHICEICGLMTPI 1224

Query: 1330 ESIVA-------GND---TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             ++           +     +   P +  +L +E+ ++G++  +  SR+
Sbjct: 1225 ANLTKQSFECRPCKNKTKIAQVHMPYAAKLLFQELMSMGIASRMFTSRS 1273


>gi|89515256|gb|ABD75457.1| DNA-directed RNA polymerase beta chain [Sinorhizobium medicae]
 gi|89515258|gb|ABD75458.1| DNA-directed RNA polymerase beta chain [Sinorhizobium meliloti]
 gi|89515260|gb|ABD75459.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kummerowiae]
 gi|126797597|gb|ABO27330.1| DNA-directed RNA polymerase beta chain [Sinorhizobium meliloti]
 gi|126797599|gb|ABO27331.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kummerowiae]
 gi|126797601|gb|ABO27332.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kummerowiae]
 gi|126797603|gb|ABO27333.1| DNA-directed RNA polymerase beta chain [Sinorhizobium medicae]
 gi|126797605|gb|ABO27334.1| DNA-directed RNA polymerase beta chain [Sinorhizobium medicae]
          Length = 224

 Score =  416 bits (1069), Expect = e-113,   Method: Composition-based stats.
 Identities = 153/224 (68%), Positives = 181/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYKAGADIQPLRDTIDSVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEQAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|126797587|gb|ABO27325.1| DNA-directed RNA polymerase beta chain [Sinorhizobium arboris]
          Length = 224

 Score =  416 bits (1068), Expect = e-113,   Method: Composition-based stats.
 Identities = 153/224 (68%), Positives = 183/224 (81%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI +++  Y+A+GDI+PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLEAYQASGDIAPLRQTIDDVIGSGPKGEPIKQYDDESIIRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGETFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|89515254|gb|ABD75456.1| DNA-directed RNA polymerase beta chain [Ensifer adhaerens]
 gi|126797593|gb|ABO27328.1| DNA-directed RNA polymerase beta chain [Ensifer adhaerens]
 gi|126797595|gb|ABO27329.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. CFN_EC1002]
          Length = 224

 Score =  416 bits (1068), Expect = e-113,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 181/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGQKIGAMLDAYKAGADIQPLRDTIDSVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEQAGLKVTGQSTLYDGRTGDQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|3549619|gb|AAC34596.1| RNA polymerase beta subunit [Shewanella putrefaciens]
          Length = 245

 Score =  416 bits (1068), Expect = e-113,   Method: Composition-based stats.
 Identities = 117/250 (46%), Positives = 167/250 (66%), Gaps = 6/250 (2%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               ++   R+RK FGK P+++DIP L+ +Q  S+  F       D     GL+AAF+SV
Sbjct: 1   MVYSYSEKKRIRKDFGKRPQVLDIPYLLSIQLDSFKKF----TDQDPTGERGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI +FSG + L++VSY+   P FDV +C  R +TY+ PL++ LR++++D +   G  ++
Sbjct: 57  FPIKSFSGNSELQYVSYKLGEPVFDVKECQIRGVTYSAPLRVKLRMVLYDREAAAG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMGD+PLMT +GTFVI G +R++VSQLHRSPG+ FDHD+G+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGDIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
           RIIP +G W+D EFD KD + VRIDRRRK+P T  L AL   ++EIL  F+ ++ +  + 
Sbjct: 175 RIIPYRGSWLDFEFDPKDALFVRIDRRRKLPATIILRALEYSTQEILDLFFERVEFKIKK 234

Query: 243 DFWCFPLSAA 252
           D     L  +
Sbjct: 235 DTLVMTLVLS 244


>gi|95115819|gb|ABF56204.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
 gi|95115821|gb|ABF56205.1| RNA polymerase II second largest subunit [Phaeosphaeria avenaria f.
            sp. avenaria]
          Length = 1262

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 171/987 (17%), Positives = 313/987 (31%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +           Q  + A  + + +     +               +SQ+     
Sbjct: 448  VFKYLQRCVESSTDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +       E    ++      +         +V   
Sbjct: 564  YVSVGSDASPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQQLVTVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLK 705
                 +      I D  D   K        + P    EN  S          R     L 
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENSPSKPNRNQLVFDRDISNRLV 683

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DI 761
             E     T         +      K   + G++E +DA       +    +         
Sbjct: 684  KEQLDHDTRAGWSDTDIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPEDLDEWRGMK 743

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L   +R+N      +R   K    +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPTSERANLGKERLRRIKPKPDPRIHAYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNYALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTEVTVDEISDLLEQAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRVQVFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G      SI  G              + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIASIKKGMYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 157/1164 (13%), Positives = 319/1164 (27%), Gaps = 214/1164 (18%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF----PITAFS----GAAMLEFVSYE 80
            L+  Q  SYD F   N   D     G             P             ++F    
Sbjct: 38   LVSQQLDSYDEF-TRNTIQDIVKENG--TVILEQNTPYDPDEDSDPIIKRRYEIKFGRVY 94

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITL----------RLIVFDVDEFTGAK 120
               P               +   R+LTY+  +   +          +++    DE     
Sbjct: 95   LARPTHTEGDGTTVALFPHEARLRNLTYSGAMLADISNRIMVAKETQVVAEGEDEDMEVT 154

Query: 121  SI----KDIKEQS-----------IYMGDLPLMTKD------------------------ 141
            +       IK +            +++G LP+M +                         
Sbjct: 155  NTVGGPTQIKWEREDVPMDEESARVFIGKLPVMLRSELCHLRNQSDEALFAFNECPYDQG 214

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
            G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 215  GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GSVPWTAEIRSAVEKGTRLISSFNIK 270

Query: 200  ---DII--------------HV---RIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
               + +              +     I  + +VP+     ALG+   EEILS        
Sbjct: 271  WSENSLGGPGQGRRAPGPFAYAMLPYI--KTEVPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +      Q     +   +  +  ++ + +  +  
Sbjct: 329  TQMLELLKPSIEEGAVIQDRETALDFIAKRGANQGTRDRRLKFARDI--MQREFLPHISQ 386

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLVANLFRILFLKLT 445

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + +  + + + A+           + T  +  S+    + D  K   +  
Sbjct: 446  KDVFKYLQRCVESSTDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 497

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +      
Sbjct: 498  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACG--- 554

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++KN   +  + +       I  +   ++   +  +      A   F     +    +  
Sbjct: 555  LVKNLSLMCYVSVGSDASPIIDFMSQRNMQLLEEYDQNQNPEATKVFVNGVWVGVHSQAQ 614

Query: 530  NSLSRITHTRRLSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH--- 578
              ++ +   RR   L  +  + R     E        R + P       P++ +      
Sbjct: 615  QLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENSPSKPNRNQLVF 674

Query: 579  -----NIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                 N  +   L    R       I               + YL A EEE   I  +  
Sbjct: 675  DRDISNRLVKEQLDHDTRAGWSDTDIADNTYGWKGLIQDGVIEYLDAEEEETAMITFSPE 734

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             LDE       L                                          S R  +
Sbjct: 735  DLDEWRGMKMGLPT----------------------------------------SERANL 754

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G    R+  P          T  E   A   G       A I+   D  +    + +  +
Sbjct: 755  GKERLRRIKPKPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRNTYQSAM 808

Query: 753  DPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                 GV      ++ +         Q+PL                      +L  G+N 
Sbjct: 809  GKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNA 858

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIP 866
            +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D  
Sbjct: 859  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTL 918

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             +       +D+ G++  G  V+  DI++GK  P         ++L +        DV  
Sbjct: 919  RLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADA----QELGQKTTLHTKRDVST 974

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI-ELLARDKDDEQVILDRNIYSR 985
                  +G+   V+              R+ + +  QI +  A     +  I        
Sbjct: 975  PLRSTENGIVDQVL-FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQED 1033

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD-------EKVQRNVESL 1038
            +     G             + ++   + E   S+      Q+       E     +  L
Sbjct: 1034 MPFTSEGLTPDLVINPHAIPSRMTIAHLVECLLSKVGAITGQEGDATPFTEVTVDEISDL 1093

Query: 1039 KVQYETSKSILEDRFKNKIEKIQW 1062
              Q    K   E  +     K   
Sbjct: 1094 LEQAGYQKRGFEIMYNGHTGKKMR 1117


>gi|261196850|ref|XP_002624828.1| DNA-directed RNA polymerase II polypeptide [Ajellomyces dermatitidis
            SLH14081]
 gi|239596073|gb|EEQ78654.1| DNA-directed RNA polymerase II polypeptide [Ajellomyces dermatitidis
            SLH14081]
          Length = 1258

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 200/1133 (17%), Positives = 367/1133 (32%), Gaps = 178/1133 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            IE G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  IEKGSRILSQLSIKLFGKGDASKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 594  QVSPNATKVFVNGVWVGVHRDPSHLVNTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +   +         + N   N+R    +  +     
Sbjct: 713  GVVEYVDAEEEETIMIVMTPEDLETSKQLQAGFSLPEEDNND-PNRRVRSTLSQKTHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQAAMGKQAMGV----------FL 814

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 815  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNS 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 914

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ +                +E  Q
Sbjct: 915  LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQ 959

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 960  RTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1014

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1015 RHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1074

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1075 D-----------------------------------------------------ATP-FT 1080

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1081 DVTVDSISSLLREHGYQSRGFEVMYNGYTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG- 1324
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1141 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICGL 1200

Query: 1325 -------RTRVYESIV-AGND-TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                   +   +E       +   +   P +  +L +E+ ++ ++  L   R+
Sbjct: 1201 MTPIAKLKKSDFECRACKNKNKISQVHIPYAAKLLFQELMSMNIAARLFTKRS 1253



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/803 (13%), Positives = 229/803 (28%), Gaps = 144/803 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          + P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTLAPSEDEIDPVV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDEFTGAK-- 120
             P               +   R+LTYA PL + +         RLI    D   G +  
Sbjct: 95  ARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLIAERDDAEQGEEDH 154

Query: 121 ------------------SIKDIKEQSIYMGDLPLMTKD--------------------- 141
                             +  + +E+++++G +P+M K                      
Sbjct: 155 DEERRSRGTYLHWEPKPLNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQSLYNWNECPY 214

Query: 142 ---GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF 196
              G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  + 
Sbjct: 215 DSGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAIEKGSRILSQL 271

Query: 197 DSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYS 239
             K  +  + D  +                 +P+     ALG +  E+IL+        +
Sbjct: 272 SIK--LFGKGDASKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDT 329

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +     +    ++   +V+   +          + +K        ++++ +  +  +
Sbjct: 330 PMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQS 389

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                      G  V   ++    G   ++  D   +K L+           IL++    
Sbjct: 390 EGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVTK 448

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +        V    +   +  +    +       +  +  ++    + +  K   S  G 
Sbjct: 449 DLYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAGV 501

Query: 414 VKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM 470
            ++  R    +      R          I     L N   G +   +    +    V  +
Sbjct: 502 SQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 561

Query: 471 LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               Y       E  I    + +   ++   PQ   NA  V      F     +    + 
Sbjct: 562 ALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRDP 615

Query: 529 VNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + ++ +   RR + +  +  + R     E        R   P       P   + G  +
Sbjct: 616 SHLVNTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSLV 675

Query: 581 GLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                +                     Y        +  V Y+ A EEE   I      L
Sbjct: 676 LSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDL 735

Query: 635 DEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +              +     R     +          +  P  ++ I AS+IPF +++ 
Sbjct: 736 ETSKQLQAGFSLPEEDNNDPNRRVRSTLSQKTHTWTHCEIHPSMILGICASIIPFPDHNQ 795

Query: 687 SNRVLMGCNMQRQAVPLLKAEAP 709
           S R      M +QA+ +      
Sbjct: 796 SPRNTYQAAMGKQAMGVFLTNFD 818


>gi|149211753|gb|ABR22230.1| DNA-dependent RNA polymerase beta chain [Sinorhizobium chiapanecum]
 gi|149211755|gb|ABR22231.1| DNA-dependent RNA polymerase beta chain [Sinorhizobium chiapanecum]
 gi|149211757|gb|ABR22232.1| DNA-dependent RNA polymerase beta chain [Sinorhizobium chiapanecum]
 gi|149211759|gb|ABR22233.1| DNA-dependent RNA polymerase beta chain [Sinorhizobium chiapanecum]
          Length = 224

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 154/224 (68%), Positives = 183/224 (81%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y  NGDI PLR+ ++ VIG+G   E I  YDD+SV+R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYHENGDIKPLRATIDDVIGSGPKGEPIKQYDDESVVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS L+DG TGEPFDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLNKAGLKVTGQSTLFDGRTGEPFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|168027816|ref|XP_001766425.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162682334|gb|EDQ68753.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1185

 Score =  415 bits (1067), Expect = e-113,   Method: Composition-based stats.
 Identities = 178/1054 (16%), Positives = 339/1054 (32%), Gaps = 193/1054 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 282  DILEHICYDFSDTAMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 338

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G G  DD D+ GN+R+   
Sbjct: 339  KEILQKEMLPHVGVGEFCETKK---AYFFGYIIHRLLLCAIG-GAEDDRDHYGNKRLDLA 394

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ + ++   +    +   +     + AK + S +     +      
Sbjct: 395  GPLLGGLFRMLFRKLTKDVRGYLQKCVDNGKEINLAYAVKAKTITSGLKYSLATGNWGQA 454

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 455  NTAGVRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 510

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L   A +            + +    N        EE +  +   ++ 
Sbjct: 511  TPEGQACGLVKNLALMAYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPNSTK 563

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V     L       D  R    
Sbjct: 564  IFVNGLWVGIHRNPELLVRTLRQLRRQV---DVNTEVGVVRDIRLKELRLYTDYGRCSRP 620

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+                +   A  + + +         +  I  V+ + +
Sbjct: 621  LFIVEKQRLLI--------------KKQDVRALQMKESSENSWYDLVSKGFIEYVDTEEE 666

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R+N     +                    PS  LG       +  
Sbjct: 667  ETTMISMTIADLVNARNNPEEAYS-----------DTYTHCEIHPSMILG-------VCG 708

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 709  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 741

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 742  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 799

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ ++  ++ +E+ E   R+          +          G 
Sbjct: 800  SIDRGFF-RSIFYRSYRDEEKKQGTLIKEEFERPNRENTTGMRHGSYDKLDDDGLAPPGT 858

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T L                  QD+   +     K    T     E   
Sbjct: 859  RVSGEDVIIGKTTPL-----------------PQDDNASQAQRYTKRDQSTCLRHSESGM 901

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ +
Sbjct: 902  IDQVLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQ 956

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 957  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 996

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 997  ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1022

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1023 EVMYNGHTGRRLTAHIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1082

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV---VG-------RTRVYESIVAG---- 1335
             GEME  C+ A+GAA+ L+E L  +SD     V    G       +   YE    G    
Sbjct: 1083 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCEHCGIIAIANLKKNTYEC--RGCKNN 1140

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             D  +   P +  +L +E+ ++ ++  +     K
Sbjct: 1141 TDIVQVHIPYACKLLFQELMSMAIAPRMFTKELK 1174



 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 115/835 (13%), Positives = 244/835 (29%), Gaps = 129/835 (15%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G QA    V           + F
Sbjct: 33  LVRQQLDSFDEFIQNTMQEIVDESSDIEIRPESQHNPGRQAEIGDV--------TYKINF 84

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   V    E    ++ ++  
Sbjct: 85  GQIYLSKPMMTEADGETATLWPKAARLRNLTYSAPLYVDVTKFVTRKTEDGEEETEQEDL 144

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG 162
            + +Y+G +P+M +                         G F+I G ++++++Q   S  
Sbjct: 145 SK-VYIGKVPIMLRSRYCTLFENSDKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTN 203

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR------------ 208
            ++      +     K  Y   +        + +      + VR+  R            
Sbjct: 204 HVY----VFKKRQPNKYCYVAEVR----SMAENQNRPPSGMFVRMLSRAGAKGGSSGQYI 255

Query: 209 -------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
                  R ++P+     ALG  ++ +IL         +   +     L  A ++   +V
Sbjct: 256 RATLPYIRTEIPIIVVFRALGFVADKDILEHICYDFSDTAMMELLRPSLEEAFVIQNQQV 315

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +   +        +   K++     + L+++ +  +G+   C          +      +
Sbjct: 316 ALDYIGKRGSTVGVTREKRIKYAK-EILQKEMLPHVGVGEFCETKKAYFFGYIIH---RL 371

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            + A    ++              P+L          +   +     K   +        
Sbjct: 372 LLCAIGGAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTKDVRGYLQKCVDNGKEINLAY 431

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAI 439
                  T  +  S+    +  ++   +       +N      T   +R +         
Sbjct: 432 AVKAKTITSGLKYSLATGNWGQANTAGVRAGVSQVLNRLTYASTLSHLRRLNSPIGREGK 491

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +         +      ++KN   +  + +  +    +  ++  S  
Sbjct: 492 LAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMAYITVGSAANPILEFLEEWSTE 548

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM 558
             + I+   + ++   F     +         +  +   RR   +  + GV R     E+
Sbjct: 549 NFEEISPAVIPNSTKIFVNGLWVGIHRNPELLVRTLRQLRRQVDVNTEVGVVRDIRLKEL 608

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           R ++  +     P    E   + +         V A    E+      D      + Y+ 
Sbjct: 609 R-LYTDYGRCSRPLFIVEKQRLLIKKQ-----DVRALQMKESSENSWYDLVSKGFIEYVD 662

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EEE   I+              +LV  R   E      +     +  P  ++ +  S+
Sbjct: 663 TEEEETTMISM----------TIADLVNARNNPE--EAYSDTYTHCEIHPSMILGVCGSI 710

Query: 679 IPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAK 721
           IPF +++ S R      M +QA+                 L   + P V T  ME +  +
Sbjct: 711 IPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFR 770

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              A I A  A            +   +  +D        YR  + +   Q T +
Sbjct: 771 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKQGTLI 825


>gi|126797583|gb|ABO27323.1| DNA-directed RNA polymerase beta chain [Sinorhizobium fredii]
          Length = 224

 Score =  415 bits (1066), Expect = e-113,   Method: Composition-based stats.
 Identities = 152/224 (67%), Positives = 181/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ YKA  DI PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYKAGSDIQPLRDTIDSVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEQAGLKVTGQSTLYDGRTGDQFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|126797635|gb|ABO27349.1| DNA-directed RNA polymerase beta chain [Rhizobium galegae]
          Length = 223

 Score =  415 bits (1066), Expect = e-113,   Method: Composition-based stats.
 Identities = 143/224 (63%), Positives = 181/224 (80%), Gaps = 1/224 (0%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HL WAC G+GK+I +++ +Y+ + DI+ L+  L +   + ++ E ++ +DDDS++R+AEQ
Sbjct: 61   HLAWACAGMGKRIGAMLEEYRKSNDITDLKKELTEAYQSEANAE-VASFDDDSLVRLAEQ 119

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K G+ ++TPVFDGA E  + +ML  A LD SGQS+LYDG TGE FDR VTVGY+YM+KL
Sbjct: 120  SKRGLSIATPVFDGAHEPDVAAMLTKAGLDPSGQSVLYDGRTGEQFDRKVTVGYMYMIKL 179

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 180  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 223


>gi|89515262|gb|ABD75460.1| DNA-directed RNA polymerase beta chain [Sinorhizobium saheli]
 gi|126797607|gb|ABO27335.1| DNA-directed RNA polymerase beta chain [Sinorhizobium saheli]
 gi|126797609|gb|ABO27336.1| DNA-directed RNA polymerase beta chain [Sinorhizobium saheli]
 gi|126797611|gb|ABO27337.1| DNA-directed RNA polymerase beta chain [Sinorhizobium saheli]
          Length = 224

 Score =  415 bits (1066), Expect = e-113,   Method: Composition-based stats.
 Identities = 152/224 (67%), Positives = 183/224 (81%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y  NGDI+PLR+ ++ VIG+G   E I  YDD S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYYDNGDIAPLRTTIDDVIGSGPKGEPIKQYDDASIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML+ A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLQKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|254798673|ref|YP_003058290.1| beta subunit of RNA polymerase [Parachlorella kessleri]
 gi|229915621|gb|ACQ90964.1| beta subunit of RNA polymerase [Parachlorella kessleri]
          Length = 1312

 Score =  415 bits (1066), Expect = e-113,   Method: Composition-based stats.
 Identities = 139/304 (45%), Positives = 179/304 (58%), Gaps = 40/304 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V++ +  KR IQ GDKMAGRHGNKGI+S+ILPC+DMP+L DG P+DIVLNPLGVPSRMN
Sbjct: 1041 RVRIALLQKRNIQVGDKMAGRHGNKGIISKILPCQDMPYLPDGNPIDIVLNPLGVPSRMN 1100

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQI E+ LG+A   L +  K  + D K                G  +    +     ++
Sbjct: 1101 VGQILESLLGFAGKYLHESYKIELFDEK---------------FGAEASRSLVYSKLYEA 1145

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             L+ A  W                        + +    G+  L+DG TGE FD+PVTVG
Sbjct: 1146 SLKTANPW------------------------LFEPQHPGKIKLFDGRTGESFDQPVTVG 1181

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y YMLKL H+V DK++AR+TG YS VTQQP+ G++  GGQRLGEMEVW +QAYGAAY LQ
Sbjct: 1182 YAYMLKLIHLVDDKIHARATGPYSAVTQQPVRGRARNGGQRLGEMEVWALQAYGAAYTLQ 1241

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            E+LTIKSDD+ GR      I       + G PESF VL++E+Q+L  ++ +     K   
Sbjct: 1242 ELLTIKSDDIDGRKEAVFRIYTNRSL-KFGQPESFKVLLRELQSLCFNLQIYKYDKKTQI 1300

Query: 1373 KMEE 1376
               E
Sbjct: 1301 IKPE 1304



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 133/474 (28%), Positives = 209/474 (44%), Gaps = 17/474 (3%)

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            V T   A+  F    ++    ++  +GR +   +L          +  +DI    K  +
Sbjct: 278 QVVTDQTAQEFFLKNVWNYKNRNIGYLGRKQFREKLGSTLSITETWLTADDISLATKASL 337

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L   +   DDIDNL N+RVR  GE L ++   GL   E  +  + S++ I S       
Sbjct: 338 KLLCNEQVADDIDNLDNKRVRGCGEFLYDELNSGLQEFEHVLNRKFSNISISSKNSIFGN 397

Query: 505 NA------------KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
                         K +  +   FF    LSQ  +  N L+  TH RRL+ LG GGV+  
Sbjct: 398 ECATFWRFNRSLLSKYISKSWKNFFTGGTLSQFMDETNPLAETTHKRRLTVLGPGGVSGK 457

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           +  +++R +HPT+YGR+CP ET EG N GLV+S T + + N+ G +ETP+ +V  G++  
Sbjct: 458 QTTIQIRGIHPTYYGRLCPIETPEGQNAGLVNSFTVYTQRNSQGILETPFFEVYKGQIQK 517

Query: 613 DV--VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++   YLS   E    +A A+  L       +  +  R   +       +I        Q
Sbjct: 518 ELKAHYLSPQTESYLVLAPADICLSPWNQLPKTDLPVRKNWKFEYTIWNQISKQSIGLLQ 577

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL+ E   V TG+E+ V       I + 
Sbjct: 578 MISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPENALVSTGLETRVISDVNHGIRSS 637

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC-VNQRPLVKVGDEVR 789
           + G +  V + +  I+  +G+        +  +  K +    N    N+  L+K    V 
Sbjct: 638 KTGYITAVSSTK--IQLYKGNYVKDKQNGNTNKNSKIRSFFNNASVFNKFSLLKKYKAVN 695

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           +         T L   +  +         +   F+   +         V   IH
Sbjct: 696 QKQKQQKKFFTHLTFFSKTQTFNYFLHYHNHKYFDSKKIYQVTGFHFPVVIPIH 749



 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 110/249 (44%), Gaps = 27/249 (10%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+F+  +  ++ IPDLI++Q+ S+ +FL   +    +  +        +F  +      +
Sbjct: 21  RRFYYNDLYVL-IPDLIDIQRNSFQNFLQCGLFRSLKKKK------SFIFRKSIHKLEIV 73

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           L     +F  P+ D    L    TY   + I + L+ F           K  K + I +G
Sbjct: 74  LFPEWIQFKKPELDSKKALHFGKTYGSYIYIPV-LVKFS--------GWKKNKLEWILLG 124

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            LPL+TK G F+I GI R+V+ Q+ R+PGI+      +  ++       RI+P+QG W++
Sbjct: 125 FLPLLTKQGHFIINGIPRVVLHQMIRNPGIYILSKDSKTRVA-----TIRIVPEQGSWIN 179

Query: 194 IEFDSKDIIHV--RIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           I  D K  I +  R  R+ K+ V  FL ALG    EI        +       +   L  
Sbjct: 180 ITIDKKYRIWITTRFLRK-KISVLIFLQALGFSLSEIYKNLGYSELLQVS---FVKELQP 235

Query: 252 ADLMVGAKV 260
            +     ++
Sbjct: 236 DEKTRNDRI 244



 Score =  130 bits (327), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 94/231 (40%), Positives = 139/231 (60%), Gaps = 11/231 (4%)

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                 S      Y L  +QR+NQ+TC+ QRP +K GD V+  DIIADG ++  G LALG+
Sbjct: 819  KKQKSSIKKEYSYSLDNYQRTNQSTCITQRPNLKEGDWVQITDIIADGSASAGGKLALGK 878

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP--- 866
            N+L+A++PW GYNFED++LIS++++ +DVFTS+HI+ +EV  ++T+ G E IT  +P   
Sbjct: 879  NVLIAYVPWEGYNFEDAILISDKLLEKDVFTSLHIDYYEVEVKNTQYGLETITNKVPLEI 938

Query: 867  ---NVSEEGLKNIDECGIICVGAEVNPGDILVGKI---TPKGESPMTPEEKLLRAIFGEK 920
               +     L+ ++  G+I +G+ V  GD LVGKI   +PKG S     EKL   I+   
Sbjct: 939  DASSKDILQLQRLNSNGLIEIGSWVEEGDYLVGKISPLSPKGPSIYKQYEKLYNVIWQRD 998

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI--SVEREQIELLAR 969
                ++TSLRVP GV G V+DV+I      D    +   ++ R +I LL +
Sbjct: 999  NPTFKNTSLRVPKGVEGFVLDVQILPPKETDVLPLAPKNAILRVRIALLQK 1049


>gi|149211743|gb|ABR22225.1| DNA-dependent RNA polymerase beta chain [Rhizobium undicola]
          Length = 223

 Score =  414 bits (1065), Expect = e-113,   Method: Composition-based stats.
 Identities = 148/224 (66%), Positives = 179/224 (79%), Gaps = 1/224 (0%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HL WAC G+G+KI  ++ DY+ + DIS L+  L  V  + S  E +S +DDD+++R+AEQ
Sbjct: 61   HLAWACAGMGRKIGQMLEDYRKHLDISALKETLTDVYSSQSQDE-VSKFDDDALVRLAEQ 119

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K GV ++TPVFDGA E  ++ ML  A LD SGQS+LYDG TGE FDR VTVGY+YM+KL
Sbjct: 120  SKRGVSIATPVFDGAHESDVSEMLTKAGLDPSGQSVLYDGRTGEAFDRRVTVGYMYMIKL 179

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 180  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 223


>gi|239609658|gb|EEQ86645.1| DNA-directed RNA polymerase II polypeptide [Ajellomyces dermatitidis
            ER-3]
 gi|327357696|gb|EGE86553.1| DNA-directed RNA polymerase [Ajellomyces dermatitidis ATCC 18188]
          Length = 1258

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 200/1133 (17%), Positives = 367/1133 (32%), Gaps = 178/1133 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            IE G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  IEKGSRILSQLSIKLFGKGDASKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 594  QVSPNATKVFVNGVWVGVHRDPSHLVNTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +   +         + N   N+R    +  +     
Sbjct: 713  GVVEYVDAEEEETIMIVMTPEDLETSKQLQAGFSLPEEDNND-PNRRVRSTLSQKTHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQAAMGKQAMGV----------FL 814

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 815  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNS 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 914

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ +                +E  Q
Sbjct: 915  LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQ 959

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 960  RTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1014

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1015 RHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1074

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1075 D-----------------------------------------------------ATP-FT 1080

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1081 DVTVDSISSLLREHGYQSRGFEVMYNGYTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG- 1324
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G 
Sbjct: 1141 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICGL 1200

Query: 1325 -------RTRVYESIV-AGND-TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                   +   +E       +   +   P +  +L +E+ ++ ++  L   R+
Sbjct: 1201 MTPIAKLKKSDFECRACKNKNKISQVHIPYAAKLLFQELMSMNIAARLFTKRS 1253



 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 108/803 (13%), Positives = 229/803 (28%), Gaps = 144/803 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          + P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTLAPSEDEIDPVV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDEFTGAK-- 120
             P               +   R+LTYA PL + +         RLI    D   G +  
Sbjct: 95  ARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLIAERDDAEQGEEDH 154

Query: 121 ------------------SIKDIKEQSIYMGDLPLMTKD--------------------- 141
                             +  + +E+++++G +P+M K                      
Sbjct: 155 DEERRSRGTYLHWEPKPLNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQSLYNWNECPY 214

Query: 142 ---GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF 196
              G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  + 
Sbjct: 215 DSGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAIEKGSRILSQL 271

Query: 197 DSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYS 239
             K  +  + D  +                 +P+     ALG +  E+IL+        +
Sbjct: 272 SIK--LFGKGDASKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDT 329

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +     +    ++   +V+   +          + +K        ++++ +  +  +
Sbjct: 330 PMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQS 389

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                      G  V   ++    G   ++  D   +K L+           IL++    
Sbjct: 390 EGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVTK 448

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +        V    +   +  +    +       +  +  ++    + +  K   S  G 
Sbjct: 449 DLYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAGV 501

Query: 414 VKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM 470
            ++  R    +      R          I     L N   G +   +    +    V  +
Sbjct: 502 SQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 561

Query: 471 LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               Y       E  I    + +   ++   PQ   NA  V      F     +    + 
Sbjct: 562 ALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRDP 615

Query: 529 VNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + ++ +   RR + +  +  + R     E        R   P       P   + G  +
Sbjct: 616 SHLVNTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSLV 675

Query: 581 GLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                +                     Y        +  V Y+ A EEE   I      L
Sbjct: 676 LSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDL 735

Query: 635 DEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +              +     R     +          +  P  ++ I AS+IPF +++ 
Sbjct: 736 ETSKQLQAGFSLPEEDNNDPNRRVRSTLSQKTHTWTHCEIHPSMILGICASIIPFPDHNQ 795

Query: 687 SNRVLMGCNMQRQAVPLLKAEAP 709
           S R      M +QA+ +      
Sbjct: 796 SPRNTYQAAMGKQAMGVFLTNFD 818


>gi|229544477|gb|ACQ76417.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 134/237 (56%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  GLG++I  L+   +    +S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGLGQRIGDLL---QQQAKVSELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLEQGVPYATPVFDGASEAEIKDMLALAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|149244118|ref|XP_001526602.1| DNA-directed RNA polymerase II polypeptide 2 [Lodderomyces
            elongisporus NRRL YB-4239]
 gi|146448996|gb|EDK43252.1| DNA-directed RNA polymerase II polypeptide 2 [Lodderomyces
            elongisporus NRRL YB-4239]
          Length = 1238

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 177/985 (17%), Positives = 316/985 (32%), Gaps = 162/985 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 365  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 424

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 425  DIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 484

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 485  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 540

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC-- 647
            + ++  G    P            +   +     +      N            LV    
Sbjct: 541  SCIS-VGTPSDPILSFLRDWGLEPLEDYTPANSPDVTRVFVNGVWVGVHREPASLVDYMR 599

Query: 648  --RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R  G+         D  +   K          P    DD        +++ Q   + +
Sbjct: 600  DLRRNGDISPEVSLIRDIREKEFKIFTDAGRVYRPLFIVDDKPDSATKGDLKLQKEHVNQ 659

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDI 761
                      E     +      +  + GIVE VDA      +I     DL+ S S +  
Sbjct: 660  LLESSYEGYDEDDEDAAPKYTWSSLVKEGIVEYVDAEEEETIMIAMTPDDLEASKSSLTE 719

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             +    Q   Q     +R                  PS  LG  A       + +P+  +
Sbjct: 720  TQQQNLQMEEQELDPAKRIKPTNSSNTHTFTHCEIHPSMILGVAA-------SIIPFPDH 772

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +   + +  + V                               +
Sbjct: 773  NQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DTM 803

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 804  ANILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF- 862

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D  +R      + +E   +    + + L    Y +L +   I  G      
Sbjct: 863  RSLFFRSYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGVRVSGE 919

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T +  D      R+Q+         ++     +  Q               + 
Sbjct: 920  DIIIGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------VL 964

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 965  LTTNGD-----GAKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFTSEGVVP 1019

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +                           
Sbjct: 1020 DLIINPHAIPSRMTVAHLIECLLSKVSALSGLEGD------------------------- 1054

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     EA++ +LR       G  ++Y+
Sbjct: 1055 ----------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMYN 1085

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME
Sbjct: 1086 GHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEME 1145

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFET 1341
              C+ A+GAA  L+E L   SD        V G   V  ++              + ++ 
Sbjct: 1146 RDCMIAHGAAGFLKERLMEASDAFRVHVCGVCGLMSVIANLKKNQFECRSCKNKTNIYQI 1205

Query: 1342 GTPESFNVLVKEMQALGLSIDLENS 1366
              P +  +L +E+ A+ ++  L   
Sbjct: 1206 HIPYAAKLLFQELMAMNITPRLYTE 1230



 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 155/1018 (15%), Positives = 291/1018 (28%), Gaps = 178/1018 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL---QAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+   I      +  L   Q A  +       +    + F       P 
Sbjct: 40  LVSQQLDSFDEFIESTIQELVWEDSHLILDQPAQHTSEKDHD-NKRYEINFGKIYISKPT 98

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI---------KDIK 126
                         +   R+LTY+ P+ + +   VF  D+     +           + K
Sbjct: 99  QTEGDGTTHPMFPQEARLRNLTYSSPIYVDMTKRVFTSDDNKRIDNELEWHEIDVEGEKK 158

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG 162
              +Y+G +P+M +                         G FVI G ++++++Q  RS  
Sbjct: 159 TSKVYLGKVPIMLRSKFCMLRDLGEHEFYELKECPYDMGGYFVINGSEKVLIAQE-RSAA 217

Query: 163 IHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------RRRK--- 211
                   + +    + +   I    ++G  +      K  ++ R D      R  K   
Sbjct: 218 NI--VQVFKKAAPSPISHVAEIRSAIEKGSRLISSMQIK--LYGR-DEKGTSARTIKATL 272

Query: 212 ------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                 +P+     ALG+  + +IL          Q  +     +    ++   +V+   
Sbjct: 273 PYIKEDIPIVIVFRALGIVPDGDILEHICYDQNDWQMLEMLKPCVEEGFVIQEREVALDF 332

Query: 265 VD------IDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDCLCGLYVAEDIVNGE 316
           +       I   +++  +   L   LL ++  +E            +    +   +   E
Sbjct: 333 IGRRGVLGIRREKRIQYAKDILQKELLPNITQEEGFETRKAFFLGYMVNRLLLCALERKE 392

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALL 375
                 +  D   +K L+           IL+   + +   Y++  +  DK  +   A+ 
Sbjct: 393 P-----DDRDHFGKKRLDLAGPLLANLFRILFKKLTKDIYNYMQRCVENDKEFNLTLAV- 446

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + +  K   S  G  ++  R    +      R    
Sbjct: 447 -------KSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTP 499

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       +S +
Sbjct: 500 IGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTPSDPILSFL 556

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
               + P +             F     +    E  + +  +   RR   +     + R 
Sbjct: 557 RDWGLEPLEDYTPANSPDVTRVFVNGVWVGVHREPASLVDYMRDLRRNGDISPEVSLIRD 616

Query: 553 RAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY--- 602
               E        R   P       P   ++G        +      +  G+ E      
Sbjct: 617 IREKEFKIFTDAGRVYRPLFIVDDKPDSATKGDLKLQKEHVNQLLESSYEGYDEDDEDAA 676

Query: 603 --RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
                        V Y+ A EEE   IA     L+   S   E        EE  +   K
Sbjct: 677 PKYTWSSLVKEGIVEYVDAEEEETIMIAMTPDDLEASKSSLTETQQQNLQMEEQELDPAK 736

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
                 S                                             T  E   +
Sbjct: 737 RIKPTNSSNTHTF---------------------------------------THCEIHPS 757

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQR 779
              G A     A I+   D  +    + +  +     GV      ++           Q+
Sbjct: 758 MILGVA-----ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYSVRMDTMANILYYPQK 812

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL                      +L  G+N +VA   + GYN EDSM++++  +   +F
Sbjct: 813 PL----------ATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 862

Query: 840 TSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S+    +  + +   +   E        D   +     + +D+ G+I  G  V+  DI+
Sbjct: 863 RSLFFRSYMDLEKRQGMKALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGVRVSGEDII 922

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK TP    P   EE   R     +    RD S  + S  SG V  V +       K
Sbjct: 923 IGKTTPI---PPDTEELGQRT----QYHTKRDASTPLRSTESGIVDQVLLTTNGDGAK 973


>gi|209395051|gb|ACI45333.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395054|gb|ACI45335.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395060|gb|ACI45339.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  414 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  GLG++I  L+   +    +S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGLGQRIGDLL---QQQAKVSELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A                
Sbjct: 58   EDLAQLSDADLLSMAANLEQGVPYATPVFDGASEAEIKDMLALAYPEEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|146418277|ref|XP_001485104.1| hypothetical protein PGUG_02833 [Meyerozyma guilliermondii ATCC 6260]
          Length = 1291

 Score =  414 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 178/988 (18%), Positives = 317/988 (32%), Gaps = 162/988 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L + +R+   ++ +
Sbjct: 416  DEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLASLFRILFKKLTK 475

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 476  DIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 535

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 536  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 591

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 592  SCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRS 651

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQ---RQAVPL 703
                  +  E     D   K             P    DD         ++        L
Sbjct: 652  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDDPESETKGELKLQKEHIHKL 711

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVD 760
            L AE        E    +           G+VE VDA      +I     DL+ S S + 
Sbjct: 712  LNAEYSEEYATNEFGEEEGPYGWSSLVNDGVVEYVDAEEEETIMIAMTPEDLEASKSSLT 771

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              +    Q   Q     +R                  PS  LG  A       + +P+  
Sbjct: 772  ATQQKSLQLEEQELDPAKRIKPTNSSTTSTFTHCEIHPSMILGVAA-------SIIPFPD 824

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 825  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 855

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 856  MANILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 915

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L +   I  G     
Sbjct: 916  -RSLFFRTYMDLEKRQGM---KALETFEKPLRSDTLRLKHGTYEKLDDDGLIAPGIRVSG 971

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T +  D      R+Q+         ++     +  Q               +
Sbjct: 972  EDIIIGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 1016

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG V      EDMPF   G  
Sbjct: 1017 LLTTNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTVGVTYRHEDMPFTSQGIV 1071

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +                          
Sbjct: 1072 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGLEGD------------------------ 1107

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         ++P F     EA++ +LR       G  ++Y
Sbjct: 1108 -----------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMY 1137

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
             G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1138 HGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1197

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFE 1340
            E  C+ A+GAA  L+E L   SD        V G   V  ++              + ++
Sbjct: 1198 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGVCGLMSVIANLKKNQFECRSCKNKTNIYQ 1257

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ A+ +S  L   R+
Sbjct: 1258 IHIPYAAKLLFQELMAMNISPRLYTERS 1285


>gi|126797625|gb|ABO27344.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. Le39]
 gi|126797627|gb|ABO27345.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. Lc56]
          Length = 224

 Score =  414 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 179/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI +++  Y  +GDI PLR  ++ V+G G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLEAYHESGDIKPLRQTIDDVMGAGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLNKAGLKVTGQSTLYDGRTGEAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|89515250|gb|ABD75454.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kostiense]
 gi|126797589|gb|ABO27326.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kostiense]
 gi|126797591|gb|ABO27327.1| DNA-directed RNA polymerase beta chain [Sinorhizobium kostiense]
          Length = 224

 Score =  414 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 181/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI ++++ Y  NGDI PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGRKIGAMLDAYHDNGDIKPLRDTIDDVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS L+DG TGE FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNQMLEKAGLKVTGQSTLFDGRTGEAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|89515244|gb|ABD75451.1| DNA-directed RNA polymerase beta chain [Sinorhizobium fredii]
 gi|89515246|gb|ABD75452.1| DNA-directed RNA polymerase beta chain [Sinorhizobium xinjiangense]
 gi|126797579|gb|ABO27321.1| DNA-directed RNA polymerase beta chain [Sinorhizobium xinjiangense]
 gi|126797581|gb|ABO27322.1| DNA-directed RNA polymerase beta chain [Sinorhizobium fredii]
 gi|126797621|gb|ABO27342.1| DNA-directed RNA polymerase beta chain [Sinorhizobium fredii NGR234]
 gi|126797623|gb|ABO27343.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. GRX8]
          Length = 224

 Score =  413 bits (1062), Expect = e-112,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 182/224 (81%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI ++++ Y  +GDI PLR+ ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLDAYHESGDIKPLRTTIDDVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|190694875|gb|ACE88982.1| RNA polymerase subunit beta [Afifella marina]
 gi|190694879|gb|ACE88984.1| RNA polymerase subunit beta [Afifella marina]
          Length = 393

 Score =  413 bits (1062), Expect = e-112,   Method: Composition-based stats.
 Identities = 242/394 (61%), Positives = 302/394 (76%), Gaps = 1/394 (0%)

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTS 216
           +HRSPG+ FDHDKG+   SGKLL+A RIIP +G W+DIEFD+KD++H RIDRRRK+PVTS
Sbjct: 1   MHRSPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDIEFDAKDVVHARIDRRRKIPVTS 60

Query: 217 FLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
            LMALGMD EEILSTFY  +  ++  + W  P     L  G K S   VD  +GE V+E+
Sbjct: 61  LLMALGMDGEEILSTFYDIVTATRGDNGWIVPFDPEKL-RGTKASEDYVDAASGEVVVEA 119

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           GKK+T+ L + L EKGVK L ++ + + G Y+ EDIVN ETGEIY EAGD + EK L+++
Sbjct: 120 GKKITARLARQLVEKGVKSLVVSDEQVLGRYLGEDIVNFETGEIYAEAGDEVSEKMLDQL 179

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                 +I +L +D VN  AY+RNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF
Sbjct: 180 RELNREEIALLEIDHVNVGAYMRNTLAADKNESREDALFDIYRVMRPGEPPTIETAEAMF 239

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
             LFFD ++YDLS VGRVKMNMRL+L T D +R +RKEDI+A+I++L+DLR+G+G IDDI
Sbjct: 240 QSLFFDPERYDLSAVGRVKMNMRLDLQTEDTMRVLRKEDILAVIRMLLDLRDGRGEIDDI 299

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           DNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EF
Sbjct: 300 DNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREF 359

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           F SSQLSQ  +  N LS ITH RRLSALG GG+ 
Sbjct: 360 FGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLT 393


>gi|328725316|ref|XP_003248426.1| PREDICTED: DNA-directed RNA polymerase subunit beta-like, partial
           [Acyrthosiphon pisum]
          Length = 504

 Score =  413 bits (1061), Expect = e-112,   Method: Composition-based stats.
 Identities = 278/461 (60%), Positives = 356/461 (77%), Gaps = 3/461 (0%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R R
Sbjct: 1   DTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVT 611
           AG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV     +VT
Sbjct: 61  AGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVNIETNQVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YL+A EE++  +AQANS LDE G F ++ V CR  G+    P+E++D++D SPKQV
Sbjct: 121 DRIDYLTADEEDSYVVAQANSVLDETGKFVDDEVLCRFRGDNTTKPKERMDYMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAA+VAK 
Sbjct: 181 VSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVTARDSGAAVVAKY 240

Query: 732 AGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            G VE V+A  I++R + E +     + +D Y L KF+RSN  TC NQRP++  GD V +
Sbjct: 241 KGRVEHVEAKEILVRRIVEENGKEIETELDRYPLSKFKRSNSGTCYNQRPIIASGDIVTK 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            +I+ADGPS +LG++ALGRN++V FM W GYN+ED++++SER+V +DV+TSIH+EE+E  
Sbjct: 301 GEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHVEEYESE 360

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           ARDTKLGPEEITRDIPNVS+  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE
Sbjct: 361 ARDTKLGPEEITRDIPNVSDNALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEE 420

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 421 RLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGD 461



 Score = 92.1 bits (227), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 41/160 (25%), Positives = 67/160 (41%), Gaps = 5/160 (3%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI---YSRLMEILCGQNAVSGPKGFKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I       ++ L  +  V      K   +L
Sbjct: 345  KDDVYTSIHVEEYESEARDTKLGPEEITRDIPNVSDNALKNLDDRGIVYVGAEVKDGDIL 404

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDD-M 1066
               +  +       +  +           ++                 K+   + GDD +
Sbjct: 405  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDSL 464

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
             PGV ++V+V++  KR I  GDKM GRHGNKG++SRILP 
Sbjct: 465  SPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISRILPE 504


>gi|209395045|gb|ACI45329.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  413 bits (1061), Expect = e-112,   Method: Composition-based stats.
 Identities = 133/237 (56%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +     S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QQQAKASELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLQQGVPYATPVFDGASEAEIKDMLALAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|89515242|gb|ABD75450.1| DNA-directed RNA polymerase beta chain [Sinorhizobium americanum]
 gi|126797575|gb|ABO27319.1| DNA-directed RNA polymerase beta chain [Sinorhizobium americanum]
 gi|126797577|gb|ABO27320.1| DNA-directed RNA polymerase beta chain [Sinorhizobium americanum]
          Length = 224

 Score =  413 bits (1061), Expect = e-112,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 180/224 (80%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI +++  Y  +GDI PLR  ++ VIG+G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLEAYHESGDIKPLRQTIDDVIGSGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|126797619|gb|ABO27341.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. BR816]
          Length = 224

 Score =  413 bits (1061), Expect = e-112,   Method: Composition-based stats.
 Identities = 150/224 (66%), Positives = 179/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI +++  Y  +GDI PLR  ++ V+G G   E I  YDD+S++R+AEQ
Sbjct: 61   HLGWACAGMGKKIGAMLEAYHESGDIKPLRQTIDDVMGAGPKGEPIKQYDDESIVRLAEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKL
Sbjct: 121  TRRGVSIATPVFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|190346609|gb|EDK38735.2| hypothetical protein PGUG_02833 [Meyerozyma guilliermondii ATCC 6260]
          Length = 1291

 Score =  412 bits (1060), Expect = e-112,   Method: Composition-based stats.
 Identities = 178/988 (18%), Positives = 317/988 (32%), Gaps = 162/988 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L + +R+   ++ +
Sbjct: 416  DEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLASLFRILFKKLTK 475

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 476  DIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 535

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 536  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 591

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 592  SCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRS 651

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQ---RQAVPL 703
                  +  E     D   K             P    DD         ++        L
Sbjct: 652  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDDPESETKGELKLQKEHIHKL 711

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVD 760
            L AE        E    +           G+VE VDA      +I     DL+ S S + 
Sbjct: 712  LNAEYSEEYATNEFGEEEGPYGWSSLVNDGVVEYVDAEEEETIMIAMTPEDLEASKSSLT 771

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              +    Q   Q     +R                  PS  LG  A       + +P+  
Sbjct: 772  ATQQKSLQLEEQELDPAKRIKPTNSSTTSTFTHCEIHPSMILGVAA-------SIIPFPD 824

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 825  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 855

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 856  MANILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 915

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L +   I  G     
Sbjct: 916  -RSLFFRTYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGIRVSG 971

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T +  D      R+Q+         ++     +  Q               +
Sbjct: 972  EDIIIGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 1016

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG V      EDMPF   G  
Sbjct: 1017 LLTTNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTVGVTYRHEDMPFTSQGIV 1071

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +                          
Sbjct: 1072 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGLEGD------------------------ 1107

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         ++P F     EA++ +LR       G  ++Y
Sbjct: 1108 -----------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMY 1137

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
             G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1138 HGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1197

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFE 1340
            E  C+ A+GAA  L+E L   SD        V G   V  ++              + ++
Sbjct: 1198 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGVCGLMSVIANLKKNQFECRSCKNKTNIYQ 1257

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ A+ +S  L   R+
Sbjct: 1258 IHIPYAAKLLFQELMAMNISPRLYTERS 1285


>gi|66806179|ref|XP_636812.1| RNA polymerase II core subunit [Dictyostelium discoideum AX4]
 gi|74896933|sp|Q54J75|RPB2_DICDI RecName: Full=DNA-directed RNA polymerase II subunit rpb2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
 gi|60465215|gb|EAL63310.1| RNA polymerase II core subunit [Dictyostelium discoideum AX4]
          Length = 1170

 Score =  412 bits (1060), Expect = e-112,   Method: Composition-based stats.
 Identities = 158/984 (16%), Positives = 310/984 (31%), Gaps = 202/984 (20%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +      I   L+     +  +DD D+  N+R+   G +L   +R    
Sbjct: 348  HVSVAEFYETKKAFYFGYITHRLLLASLERRPLDDRDHFANKRLDLAGPLLGTLFRQLFK 407

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS------------SQLSQLE 526
            ++ + ++   +         +    + +K + S +     +            S ++Q+ 
Sbjct: 408  KLTKDVRLYLQRCIDKDKEFIASSAVKSKTITSGLKYSLATGNWGSSKSGGTKSGVAQVL 467

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
              +   S ++H RRL+      + R     + R +H TH+G +CP+ET EG   GLV +L
Sbjct: 468  NRLTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTHWGIVCPSETPEGQACGLVKNL 523

Query: 587  TSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA-NSSLDEDGSFTEE 643
               + ++     +     + +       ++  LS++    +         +         
Sbjct: 524  AMMSYISVGSASQPILEFLEEWTTENLEEISDLSSIFSATKIFVNGMWVGIHHQPDKLLS 583

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             +       ++ V    + D  +   +          P     D+   +   ++ +    
Sbjct: 584  TLRLLRRCGDVSVEVSVVRDIREKELRLYTDPGRCCRPLFVVQDNKVQIKKQHINKLINN 643

Query: 703  LLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
                    +  G+ E + A+     ++A               +   +    P+   V  
Sbjct: 644  DEYKWQDLLSEGIVEYIDAEEEETVLIA---------------MTPEDLVPMPNEQIVHT 688

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y                                   PS  LG       +  + +P+  +
Sbjct: 689  Y-----------------------------THCEIHPSMILG-------ICCSIIPFPDH 712

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +   ++I  ++                           +    +
Sbjct: 713  NQSPRNTYQAAMGKQAMG--VYITNYQ---------------------------LRMDTM 743

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V        +    +       +   + +  AI      +  D+ +   S +   +  
Sbjct: 744  AHVLFYPQKPLVTTRSMEYLHFRELPAGQNVCVAIACYSGYNQEDSVILNQSAIDRGLF- 802

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R   D+ ++  S+  E  E   RD                  +  G         
Sbjct: 803  RSMFYRAYKDEQKKQTSLMEEVFEKPERDTCAGMRHGSYEKIDDDGLVAPGVRVAGDDII 862

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+T L        P+++          ++ +   +  Q                    
Sbjct: 863  IGKTTPLPPSDDDLGPKTRRHTKRDSSTALRSSETGIVDQVIL----------------- 905

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      +  KV V   R  Q GDK + RHG KG        ED+PF  +G   DI+
Sbjct: 906  ---TTSGEGFKFCKVRVRSMRVPQIGDKFSSRHGQKGTCGMAYRQEDLPFTVEGIVPDII 962

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +GQ+ E  LG      G +                              
Sbjct: 963  VNPHAIPSRMTIGQLIECLLGKVSASTGDEGD---------------------------- 994

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     EAI+  L       +G  ++Y+G T
Sbjct: 995  -------------------------ATP-FTDVTVEAISQALHKIGYQMTGHEVMYNGHT 1028

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G   D  + +G  Y  +L HMV DK+++RS G   ++T+QP+ G+S  GG R GEME  C
Sbjct: 1029 GRRMDAQIFIGPTYYQRLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLRFGEMERDC 1088

Query: 1302 IQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV----------AGND---TFET 1341
            + ++GAA  L+E L  +SD       D+ G      +I              +     + 
Sbjct: 1089 MISHGAAQFLKERLFDQSDSYRVHICDICG----LIAIANLKKNSFECRRCKNKTQISQI 1144

Query: 1342 GTPESFNVLVKEMQALGLSIDLEN 1365
              P +  +L +E+ ++ ++  +  
Sbjct: 1145 RMPYAAKLLFQELMSMSIAPRMFT 1168



 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 136/997 (13%), Positives = 284/997 (28%), Gaps = 192/997 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L+  Q  S+D F+   +          Q       PIT                      
Sbjct: 36  LVRQQLDSFDEFIQNTM----------QEIIDESPPITLRPESQHHPGQAVVSNNVSTFS 85

Query: 74  LEFVSYEFDPPK---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           ++F       P             +    R+LTY+ PL + +   V    +  G +   D
Sbjct: 86  VKFGQIYLSKPTAEIDGVSQQVTPNQARIRNLTYSAPLFVDITKTVMTGSKSKGDERRTD 145

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + I++G +P+M +                         G F+I G ++++++Q   +
Sbjct: 146 EVLKRIFIGKVPIMLRSQYCMLNEADDRDLTTMGECSFDQGGYFIINGSEKVLIAQEKMN 205

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIP--DQGLW------MDIEFDSKD--------IIH 203
              ++      + S   K  Y   I    + G        + +  ++          + +
Sbjct: 206 NNHVY----VFKKSPPSKYSYVAEIRSCQETGSRPTSTMYLKMLHNTNKGPVGIKATVPY 261

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           ++ D    VPV     ALG  ++ +IL         +Q  D     L  + ++   +V+ 
Sbjct: 262 IKQD----VPVIIVFRALGFVADKDILEHICYDFKDAQMMDLMRPSLEESFVIQSQEVAL 317

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             +            +   +   + L+++ +  + +              +   T  + +
Sbjct: 318 DYLGKRGSTMGTREQRIKFAR--EVLQKEMLPHVSVAEFYETKKAFYFGYI---THRLLL 372

Query: 323 EAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            + +       +   +  +    P+L          +   +     +        I    
Sbjct: 373 ASLERRPLDDRDHFANKRLDLAGPLLGTLFRQLFKKLTKDVRLYLQRCIDKDKEFIASSA 432

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAII 440
                 T  +  S+    +  S      +     +N      T   +R +         +
Sbjct: 433 VKSKTITSGLKYSLATGNWGSSKSGGTKSGVAQVLNRLTFASTLSHLRRLNTPIGREGKL 492

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    I         +   + + L     + +    + I E +     +++  
Sbjct: 493 AKPRQLHNTHWGIVCPSETPEGQACGLVKNLAMMSYISVGSASQPILEFLEEWTTENL-- 550

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           +++ +   + SA   F     +    +    LS +   RR   +            +   
Sbjct: 551 EEISDLSSIFSATKIFVNGMWVGIHHQPDKLLSTLRLLRRCGDVSVEVSVVRDIREKELR 610

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           ++        P    + + + +     +    N          K  D      V Y+ A 
Sbjct: 611 LYTDPGRCCRPLFVVQDNKVQIKKQHINKLINNDE-------YKWQDLLSEGIVEYIDAE 663

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   IA     L    +                         +  P  ++ I  S+IP
Sbjct: 664 EEETVLIAMTPEDLVPMPNEQ---------------IVHTYTHCEIHPSMILGICCSIIP 708

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 709 FPDHNQSPRNTYQAAMGKQAMGVYITNYQL------------------------------ 738

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y               Q+PLV                  
Sbjct: 739 -----------RMDTMAHVLFYP--------------QKPLV----------TTRSMEYL 763

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N+ VA   + GYN EDS+++++  +   +F S+    ++   +      EE
Sbjct: 764 HFRELPAGQNVCVAIACYSGYNQEDSVILNQSAIDRGLFRSMFYRAYKDEQKKQTSLMEE 823

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           +           +     + ID+ G++  G  V   DI++GK TP   S           
Sbjct: 824 VFEKPERDTCAGMRHGSYEKIDDDGLVAPGVRVAGDDIIIGKTTPLPPSDDDLG------ 877

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               +    RD+S  + S  +G V  V +       K
Sbjct: 878 -PKTRRHTKRDSSTALRSSETGIVDQVILTTSGEGFK 913


>gi|133872300|gb|ABO40220.1| RNA polymerase beta subunit [Candidatus Liberibacter americanus]
          Length = 273

 Score =  412 bits (1060), Expect = e-112,   Method: Composition-based stats.
 Identities = 213/273 (78%), Positives = 251/273 (91%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKG+VFNGLGR RKFFG+ PEIIDIPDL+EVQ+ASYD FLM++   D RPNEGLQ AF+
Sbjct: 1   MAKGIVFNGLGRERKFFGRIPEIIDIPDLVEVQRASYDKFLMIDHPSDSRPNEGLQDAFR 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFP+TAFSGAAMLEFVSYEF+PPKFDV+DCL R+LTY+ PLKI LRLIVFD+DEFTGAK
Sbjct: 61  SVFPVTAFSGAAMLEFVSYEFEPPKFDVEDCLRRNLTYSAPLKIILRLIVFDIDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
           SIKDIKEQS+YMGD+PLMT+DGTFVI G  R+VVSQ+HRSPGI FDHDKGRASLSGKLLY
Sbjct: 121 SIKDIKEQSVYMGDIPLMTEDGTFVINGTPRVVVSQVHRSPGILFDHDKGRASLSGKLLY 180

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
           ACRIIP+ GLW+DIEFD+KDIIH+R+DRRRK+PVTSFLMALGMD EEILSTFY K+ Y++
Sbjct: 181 ACRIIPNMGLWLDIEFDTKDIIHMRVDRRRKIPVTSFLMALGMDHEEILSTFYSKVSYTK 240

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
           +GD+W FPLS+A++M+G+K+S +L+DI+TGE V
Sbjct: 241 KGDYWSFPLSSAEIMIGSKLSYNLIDINTGEVV 273


>gi|190694883|gb|ACE88986.1| RNA polymerase subunit beta [Afifella pfennigii]
          Length = 391

 Score =  412 bits (1059), Expect = e-112,   Method: Composition-based stats.
 Identities = 247/392 (63%), Positives = 303/392 (77%), Gaps = 1/392 (0%)

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFL 218
           RSPG+ FDHDKG+   SGKLL+A RIIP +G W+DIEFD+KDI+H RIDRRRK+PVTS L
Sbjct: 1   RSPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLL 60

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           MALGMD EEILSTFY  I  +++GD W  P  A  L  G K     VD ++GE V+E+GK
Sbjct: 61  MALGMDGEEILSTFYDHITVTRQGDGWILPFDAEKL-RGTKAEQDYVDAESGEIVVEAGK 119

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           K+T+ L K L EKGVK L I  + L G Y+AEDIVN ETGEIY EAG+ I +K L +   
Sbjct: 120 KITARLAKQLAEKGVKALAIAEEQLIGRYLAEDIVNYETGEIYAEAGEEISDKMLAQFAE 179

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             + ++P+L +D VN  AY+RNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ 
Sbjct: 180 IGLNELPVLEIDHVNVGAYMRNTLAADKNESREDALFDIYRVMRPGEPPTIETAEAMFHS 239

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
           LFFD ++YDLS VGRVKMNMRL+L+  D VR +R+EDI+A+I+ L+DLR+G+G IDDIDN
Sbjct: 240 LFFDPERYDLSAVGRVKMNMRLDLEADDTVRVLRREDILAVIRTLLDLRDGRGEIDDIDN 299

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           LGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF 
Sbjct: 300 LGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFG 359

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           SSQLSQ  +  N LS ITH RRLSALG GG+ 
Sbjct: 360 SSQLSQFMDQTNPLSEITHKRRLSALGPGGLT 391


>gi|149211751|gb|ABR22229.1| DNA-dependent RNA polymerase beta chain [Mesorhizobium amorphae]
          Length = 224

 Score =  412 bits (1059), Expect = e-112,   Method: Composition-based stats.
 Identities = 152/224 (67%), Positives = 178/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI  LI+ YKA GDI PLR  LE  +      E + +YDD+SV+R++EQ
Sbjct: 61   HLGWACAGMGRKIGELIDAYKAGGDIKPLRKTLESFMPANDRNEPVREYDDESVVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVSIATPVFDGAHEADINVMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|229544474|gb|ACQ76415.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  412 bits (1059), Expect = e-112,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 163/237 (68%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  GLG++I   +   +    +S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGLGQRIGDXL---QQQAKVSELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A                
Sbjct: 58   EDLAQLSDADLLSMAANLEQGVPYATPVFDGASEAEIKDMLALAYPEEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ L+L+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLRLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|149211749|gb|ABR22228.1| DNA-dependent RNA polymerase beta chain [Mesorhizobium tianshanense]
          Length = 224

 Score =  412 bits (1058), Expect = e-112,   Method: Composition-based stats.
 Identities = 152/224 (67%), Positives = 177/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI  LI+ YK  GDI PLR  LE  +      E + DYDD+SV+R++EQ
Sbjct: 61   HLGWACAGMGRKIGELIDAYKTGGDIKPLRKTLESFMPANDRNEPVRDYDDESVVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVAIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|149211747|gb|ABR22227.1| DNA-dependent RNA polymerase beta chain [Mesorhizobium ciceri]
          Length = 224

 Score =  412 bits (1058), Expect = e-112,   Method: Composition-based stats.
 Identities = 154/224 (68%), Positives = 178/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI  LI+ YKA GDI PLR  LE  I      E + DYDD+S++R++EQ
Sbjct: 61   HLGWACAGMGKKIGELIDTYKAAGDIKPLRKTLESFIPANDRNEPVRDYDDESIVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVSIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|126797647|gb|ABO27355.1| DNA-directed RNA polymerase beta chain [Mesorhizobium plurifarium]
          Length = 224

 Score =  412 bits (1058), Expect = e-112,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 178/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI  LI+ YK  GDI PLR  LE  +      E I +YDD+S++R++EQ
Sbjct: 61   HLGWACAGMGRKIGELIDAYKGGGDIKPLRKTLESFMPANDRNEPIREYDDESIVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVSIATPVFDGAHEADINTMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|154304837|ref|XP_001552822.1| hypothetical protein BC1G_09004 [Botryotinia fuckeliana B05.10]
 gi|150853866|gb|EDN29058.1| hypothetical protein BC1G_09004 [Botryotinia fuckeliana B05.10]
          Length = 1207

 Score =  412 bits (1058), Expect = e-112,   Method: Composition-based stats.
 Identities = 227/1363 (16%), Positives = 418/1363 (30%), Gaps = 266/1363 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
            L+  Q  S+D F+   +      N   Q       P ++           ++F +     
Sbjct: 38   LVSQQLDSFDEFVQTTMQELVEENS--QLTLDQNNPPSSHDNPIALRRYEIKFGTIMLSR 95

Query: 84   PKFD----------VDDCLWRDLTYAVPLKITLRL-IVFDVDEFTGAKSIKDIKEQSIYM 132
            P               +   R+LTY+ PL I +       V+       + D  EQ   M
Sbjct: 96   PAMTEGDGSTQVMLPQEARLRNLTYSSPLYIEMTKSTQVAVERPVPLNELDD--EQEAEM 153

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
                         + G +       H +  +    D       G  L      P+     
Sbjct: 154  -------------VNGGE-------HPTRLVWEYEDGDPEGPKGAPL------PE----- 182

Query: 193  DIEFDSKDIIHVRIDRRRKVPVTS-----FLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
                       V I    K+P+        L   G+D +E    +        +G ++  
Sbjct: 183  ----------QVYI---GKLPMMLKSEFCILK--GLDEDE---LYGWNECPYDQGGYFII 224

Query: 248  PLSAADLMVGAKVSSSLVDIDTG------------EQVIESGKKLTSGLLKSLKEKGVKF 295
              S   L+   + ++++V +                  +E G +L S L   L +KG   
Sbjct: 225  NGSEKVLIAQERSAANIVQVFKKPANSAVSYLAEIRSALEKGSRLISSLQIKLYDKGDSN 284

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
             G          +     +     ++   G V DE  L  I +       +  +      
Sbjct: 285  RGGFGKT-VKSTLPYIKADIPIAIVFRALGVVSDEDILNHICYDRNDTQMLEMLKPCIEE 343

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
            A++         +DR+ AL  I +        T    +    +      K  L  + +  
Sbjct: 344  AFV--------IQDREVALDFIGKRGN----GTSLTRDKRIKYARDIMQKELLPHISQK- 390

Query: 416  MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                      +     +   +  ++  L+    G+   DD D+ G +R+   G +L   +
Sbjct: 391  ----------EGSETRKAFFLGYMVHKLLQCALGRRETDDRDHFGKKRLDLAGPLLAKLF 440

Query: 476  RLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------ 521
            R    R+   +    +    +         + +  + + +     +              
Sbjct: 441  RNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAASSTA 500

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 501  GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 556

Query: 581  GLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L    +  V         +    + +V  +   L A      ++      +  D 
Sbjct: 557  GLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVGIHRDP 616

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN-DDSNRVLMGCNM 696
            +   + V        I      I +  D   K          P L   +D +    G  +
Sbjct: 617  AHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNDPDSANKGNLV 676

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGA--AIVAKRAGIVEQVDAIRI---VIRSVEGD 751
              +       +   +   M+      +G          G+VE +DA      +I     D
Sbjct: 677  LNKDHIRRLEDDQLLPANMDKDEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPED 736

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            LD S      Y++    R +++  +N+R    +             PS  LG       +
Sbjct: 737  LDISRQLQAGYQI----RPDESGDLNKRVKAPINPTAHVWTHCEIHPSMILG-------I 785

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N                        ++       +G      D+      
Sbjct: 786  CASIIPFPDHNQSPRNC------------------YQSAMGKQAMGVFLTNFDVRM---- 823

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                     +  +             +       +   +  + AI      +  D+ +  
Sbjct: 824  -------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMN 876

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--- 988
             S +   +    +F R   D+ +R   +    +E   +    + + L +  Y +L +   
Sbjct: 877  QSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLKQGTYDKLDDDGI 932

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +  G           K+  ++ D                +E  QR    +K    T    
Sbjct: 933  VAPGVRVTGADIIIGKTAPIAPD---------------SEEMGQRTKAHVKRDASTPLRS 977

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
             E    +++             LR VKV +   +  Q GDK A RHG KG +      +D
Sbjct: 978  TESGLVDQVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYMQQD 1032

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF ++G   D+++NP  +PSRM +  + E  L       G +  +          +S L
Sbjct: 1033 MPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKL 1092

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                     LR       G  +                      
Sbjct: 1093 -------------------------LRAHGYHSRGFEIM--------------------- 1106

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G +    G         V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++ 
Sbjct: 1107 -YHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDKIHARARGPVQILTRQPVEGRAR 1158

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG 1324
             GG R GEME  C+ ++GA+  L+E L   SD       D+ G
Sbjct: 1159 DGGLRFGEMERDCMISHGASAFLKERLFEVSDAFRVHICDICG 1201


>gi|209395129|gb|ACI45385.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LR+FL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QQQAKVSELRNFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLRQGVPYATPVFDGASEAEIKDMLMLAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVTGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|126797633|gb|ABO27348.1| DNA-directed RNA polymerase beta chain [Rhizobium huautlense]
          Length = 223

 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 146/224 (65%), Positives = 182/224 (81%), Gaps = 1/224 (0%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HL WAC G+GK+I  ++ +YK + DI+ L+  L  V  + ++ E ++++DD+S++R+AEQ
Sbjct: 61   HLAWACAGMGKRIGQMLEEYKKSSDITDLKRELRDVYESMANDE-VANFDDESLVRLAEQ 119

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             K GV ++TPVFDGA E  + SML+ A LD SGQS+LYDG TGE FDR VTVGY+YM+KL
Sbjct: 120  SKRGVSIATPVFDGAHEPDVASMLKKAGLDPSGQSVLYDGRTGEAFDRKVTVGYMYMIKL 179

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            NH+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 180  NHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 223


>gi|291336400|gb|ADD95957.1| DNA directed RNA polymerase beta subunit putative [uncultured
            organism MedDCM-OCT-S04-C1]
          Length = 1203

 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 199/1145 (17%), Positives = 390/1145 (34%), Gaps = 164/1145 (14%)

Query: 258  AKVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
             +V  S+ D+      +E  K+         + S K+   K L +      G+ + +   
Sbjct: 190  ERVLISMEDLAPNRVTVEINKRYAKKTEVAKIFSQKDGMRKPLTVEKRRD-GMLMVKIST 248

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
             G T    +     +  ++ +E+F +             N N    N           +A
Sbjct: 249  AGTTAIPVVLLMRALGIENDQELFQAIAGPTETFKFIVANINEVKDN--EEYTVDSLDEA 306

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
               + +    G    +  A      +    D+  L  +G              + R  + 
Sbjct: 307  HQWLEKKFAAGQQKEYREA-----RVTQLLDRELLPHLGDQ-----------TEDRKKKA 350

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--IS 491
              +  I++ ++++       +D D+  N+RVR  G+++++ +R+ + ++ R +K +    
Sbjct: 351  IFLGRIVRQVLEMAITSRKPNDKDHYANKRVRLAGDLVEDLFRVSMGQLARDLKYQLERH 410

Query: 492  SVDIDSVMPQDLINAKPVVSAVC-------EFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                  +     +    + S +             S +SQL +    LS ++H RR+++ 
Sbjct: 411  HNRKRELKITSCLRPDVLTSKIMHALATGNWVGGRSGVSQLLDRTTYLSALSHMRRVTS- 469

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R++   E RD+HPT +GR+CP ET EG N GLV +      ++     ET  R 
Sbjct: 470  ---PLVRSQPHFEARDLHPTQWGRLCPNETPEGQNCGLVKNAAQMIDISEA-VPETEIR- 524

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
                   +++      +  N      N  +       + LV            R ++   
Sbjct: 525  ----SRLDEMDVFQPDDWTNGDRIHVNGDIYGIHKRGKNLVTQFKNARRRGAIRPEVSIR 580

Query: 665  DASPKQVVSIAASL----IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
              S    + I         P L   D    L   +++  +   +          +E + A
Sbjct: 581  YDSQNNDIFINTDKGRILRPVLILYDGAPRLTQKHLEMVSSGEMTFTDLVNEGVVEWIDA 640

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            +      ++ R   +        V    +    P +     +                  
Sbjct: 641  EEEEDLYISPRPFTLP-----EAVPEGNKFAGRPVSHSTITW------------------ 677

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             + +G+       +    +   GD  +     +  +     +      I  ++V     +
Sbjct: 678  -LNLGEPGATTAKLQADITMPNGDKEVA----IFDVDLLYTSEHTHCEIDPQLVLGVCAS 732

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   E     R T  G   + +    +     +   +  +  +             +  
Sbjct: 733  LIPYPEHNSTPRVT--GGTAMVKQSLGLPSANYRLRPDTRL-HILHYPQRSITYTQAMDT 789

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                     +  + A+      +++D  +   S V    +    FNR    +  R    +
Sbjct: 790  TKFDSRPGGQNFIVAVMSLHGYNMQDAVIINRSCV-QRALGRSTFNRTYNAERRRFPGGQ 848

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++IE+     ++ + +     Y      L G       K  +   VL           +
Sbjct: 849  VDEIEIPGTGLEEVKGLKPVGSYDH----LEGDGLPHPEKYLEGGDVLVGKT----SPPR 900

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            + +       +Q          E  +S +  R   K               R+V+  V  
Sbjct: 901  FLEETGAGAFLQAQ--------ERRESSMPIRHGEKGWVDNVYVTESLDSGRLVRCMVRS 952

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             +  + GDK A RHG KG++ R++  EDMPF +DG   D+++NP  +PSRM V  + E  
Sbjct: 953  HKVPEVGDKFASRHGQKGVIGRLVNEEDMPFTRDGIVPDLIINPHAIPSRMTVAHVLEMI 1012

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G++I       +  G +                   + +  D +   V    
Sbjct: 1013 GGKVGSLEGRRIDGTAFRGEKEGSLRDSL---------------VRNGYDHTGREVMMNG 1057

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G      +F                                       VG IY  KL+
Sbjct: 1058 ETGETYPAEIF---------------------------------------VGCIYYQKLH 1078

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVS K++ARS G   ++T+QP  G++ +GG R GEME  C+ A+GA+ V+++ L  +SD
Sbjct: 1079 HMVSGKIHARSRGRVQILTRQPTEGRARQGGLRFGEMERDCLIAHGASMVIKDRLLDESD 1138

Query: 1321 DV-------VGRT-------RVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLE 1364
             +        G         R Y S + G+  + ++  T  +F +L+ EM++LG+++ LE
Sbjct: 1139 GIDLFVCAQSGHVAWFDPKRRTYVSPIHGDGAEVYKVQTSYAFKLLLDEMKSLGVAMRLE 1198

Query: 1365 NSRTK 1369
                +
Sbjct: 1199 LEDRR 1203



 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 143/1015 (14%), Positives = 286/1015 (28%), Gaps = 169/1015 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV-----FPITAFSG----------AAM 73
           L+  Q ASYD  +        R     +   +S+       +   +G            +
Sbjct: 14  LVNHQLASYDDCIPTGDNSVSRM----EKIVRSIRVGTDEEVEDENGGLVKLDVIDQDII 69

Query: 74  LEFVSYEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           +   + +   P               +C  R LTY  P+++   +    V          
Sbjct: 70  IRVKNIQLGEPTIREADGSDHPSSPMECRLRKLTYMSPVRMDFTIYRNGVPGQP------ 123

Query: 124 DIKEQSIYMGDLPLMT-------------------------------------------K 140
              E+ + +G++P+M                                             
Sbjct: 124 ---EKGVQVGNMPIMVRSRRCNLHANHIAGDRVLHPTTSDEDQKMWDELLRVKGEDPLDP 180

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW---MDIEFD 197
            G F+I G +R+++S    +P         R +   K     +I   +      + +E  
Sbjct: 181 GGYFIINGTERVLISMEDLAPNRVTVEINKRYA---KKTEVAKIFSQKDGMRKPLTVEKR 237

Query: 198 SKDIIHVRIDR--RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLM 255
              ++ V+I       +PV   + ALG+++++ L  F      ++   F    ++     
Sbjct: 238 RDGMLMVKISTAGTTAIPVVLLMRALGIENDQEL--FQAIAGPTETFKFIVANINEVKDN 295

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
               V S        E+   +G++      +  +    + L    D           +  
Sbjct: 296 EEYTVDSLDEAHQWLEKKFAAGQQKEYREARVTQLLDRELLPHLGDQTEDRKKKAIFLGR 355

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD--SVNNNAYIRNTLVTDKNKDRKDA 373
              ++   A         +   +  +R    L  D   V+     R+     +    +  
Sbjct: 356 IVRQVLEMAITSRKPNDKDHYANKRVRLAGDLVEDLFRVSMGQLARDLKYQLERHHNRKR 415

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L I   +RP DV T  +  ++    +          + R      L+       R    
Sbjct: 416 ELKITSCLRP-DVLTSKIMHALATGNWVGGRSGVSQLLDRTTYLSALSHMR----RVTSP 470

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                      DL   +      +     +   + +       +     E  I+ R    
Sbjct: 471 LVRSQPHFEARDLHPTQWGRLCPNETPEGQNCGLVKNAAQMIDISEAVPETEIRSR--LD 528

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           ++D   P D  N   +      +         +   N +++  + RR  A+      R  
Sbjct: 529 EMDVFQPDDWTNGDRIHVNGDIYG------IHKRGKNLVTQFKNARRRGAIRPEVSIRYD 582

Query: 554 AGVEMRDVHPTHYGRICPAET-SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           +      ++      + P     +G        L           + +      D     
Sbjct: 583 SQNNDIFINTDKGRILRPVLILYDGAPRLTQKHLE---------MVSSGEMTFTDLVNEG 633

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA-SPKQV 671
            V ++ A EEE+ YI+    +L E        V          V    I +++   P   
Sbjct: 634 VVEWIDAEEEEDLYISPRPFTLPE-------AVPEGNKFAGRPVSHSTITWLNLGEPGAT 686

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA---IV 728
            +   + I     D              A+  +        T  E       G     I 
Sbjct: 687 TAKLQADITMPNGDK-----------EVAIFDVDLLYTSEHTHCEIDPQLVLGVCASLIP 735

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                   +V     +++   G    +         ++           QR +       
Sbjct: 736 YPEHNSTPRVTGGTAMVKQSLGLPSAN-------YRLRPDTRLHILHYPQRSITY----- 783

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                     +T       G+N +VA M  HGYN +D+++I+   V   +  S     + 
Sbjct: 784 -----TQAMDTTKFDSRPGGQNFIVAVMSLHGYNMQDAVIINRSCVQRALGRSTFNRTYN 838

Query: 849 VMARDTKLGP-EEITRDIPNVSE-------EGLKNIDECGIICVGAEVNPGDILVGKITP 900
              R    G  +EI      + E           +++  G+      +  GD+LVGK +P
Sbjct: 839 AERRRFPGGQVDEIEIPGTGLEEVKGLKPVGSYDHLEGDGLPHPEKYLEGGDVLVGKTSP 898

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
                 T     L+      A + R++S+ +  G  G V +V +       +  R
Sbjct: 899 PRFLEETGAGAFLQ------AQERRESSMPIRHGEKGWVDNVYVTESLDSGRLVR 947


>gi|223590257|sp|A5DHT2|RPB2_PICGU RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
          Length = 1236

 Score =  411 bits (1057), Expect = e-112,   Method: Composition-based stats.
 Identities = 178/988 (18%), Positives = 317/988 (32%), Gaps = 162/988 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L + +R+   ++ +
Sbjct: 361  DEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLASLFRILFKKLTK 420

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 421  DIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 480

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 481  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 536

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 537  SCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRS 596

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQ---RQAVPL 703
                  +  E     D   K             P    DD         ++        L
Sbjct: 597  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDDPESETKGELKLQKEHIHKL 656

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVD 760
            L AE        E    +           G+VE VDA      +I     DL+ S S + 
Sbjct: 657  LNAEYSEEYATNEFGEEEGPYGWSSLVNDGVVEYVDAEEEETIMIAMTPEDLEASKSSLT 716

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              +    Q   Q     +R                  PS  LG  A       + +P+  
Sbjct: 717  ATQQKSLQLEEQELDPAKRIKPTNSSTTSTFTHCEIHPSMILGVAA-------SIIPFPD 769

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 770  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 800

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 801  MANILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 860

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L +   I  G     
Sbjct: 861  -RSLFFRTYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGIRVSG 916

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T +  D      R+Q+         ++     +  Q               +
Sbjct: 917  EDIIIGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 961

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG V      EDMPF   G  
Sbjct: 962  LLTTNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTVGVTYRHEDMPFTSQGIV 1016

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +                          
Sbjct: 1017 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGLEGD------------------------ 1052

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         ++P F     EA++ +LR       G  ++Y
Sbjct: 1053 -----------------------------ASP-FTDVTAEAVSKLLREHGYQSRGFEVMY 1082

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
             G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1083 HGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1142

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFE 1340
            E  C+ A+GAA  L+E L   SD        V G   V  ++              + ++
Sbjct: 1143 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGVCGLMSVIANLKKNQFECRSCKNKTNIYQ 1202

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ A+ +S  L   R+
Sbjct: 1203 IHIPYAAKLLFQELMAMNISPRLYTERS 1230


>gi|190694881|gb|ACE88985.1| RNA polymerase subunit beta [Rhodobium orientis]
          Length = 393

 Score =  411 bits (1056), Expect = e-112,   Method: Composition-based stats.
 Identities = 247/394 (62%), Positives = 304/394 (77%), Gaps = 1/394 (0%)

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTS 216
           +HRSPG+ FDHDKG+   SGKLL+A RIIP +G W+DIEFD+KDI+H RIDRRRK+PVTS
Sbjct: 1   MHRSPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTS 60

Query: 217 FLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
            + ALG+DSEEIL TFY  IVY++ G+ W  P  A   M G K +S L+D  TGE V+E+
Sbjct: 61  LMFALGLDSEEILDTFYQHIVYTRAGEGWQMPYDAQ-RMKGFKPTSDLIDAKTGEVVVEA 119

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           G+K+T+ L + L EKGV+ L ++ + LCG Y+A DIVN ETGEIY EAGD I EK+L   
Sbjct: 120 GRKITARLARQLGEKGVEALKVSDEELCGHYLAGDIVNPETGEIYAEAGDEITEKTLAGF 179

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                 +I +L +D VN   YIRNTL  DKN+ R++AL DIYRVMRPG+  T   AE+MF
Sbjct: 180 IERGYDEITVLDIDHVNTGGYIRNTLAVDKNEAREEALFDIYRVMRPGEPPTLETAEAMF 239

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           + LFFD ++YDLS VGRVKMNMRL+L   D VR +R+ED++A+IK LVDLR+GKG IDDI
Sbjct: 240 HSLFFDPERYDLSAVGRVKMNMRLDLKCEDTVRVLRREDVLAVIKTLVDLRDGKGEIDDI 299

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           DNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EF
Sbjct: 300 DNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREF 359

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           F SSQLSQ  +  N LS ITH RRLSALG GG+ 
Sbjct: 360 FGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLT 393


>gi|126797645|gb|ABO27354.1| DNA-directed RNA polymerase beta chain [Mesorhizobium mediterraneum]
          Length = 224

 Score =  411 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 177/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+G+KI  LI+ YK  GDI PLR  LE  +      E I +YDD+S++R++EQ
Sbjct: 61   HLGWACAGMGRKIGDLIDAYKTAGDIKPLRKTLESFMPANDRNEPIREYDDESIVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVSIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|331268125|ref|YP_004347774.1| beta subunit of RNA polymerase [Chlorella variabilis]
 gi|325296302|gb|ADZ05022.1| beta subunit of RNA polymerase [Chlorella variabilis]
          Length = 1358

 Score =  411 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 166/490 (33%), Positives = 232/490 (47%), Gaps = 53/490 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+     V  GDIL           ++  + +L A    +  +  D  L     V   + 
Sbjct: 895  ILSETMWVEKGDILAD-GAASTRGKLSIGQNVLVAYVPWEGYNFEDAILISQRLVHQDIF 953

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+       +ER   ++  +  +  + +L     +    +  G     G  
Sbjct: 954  TSLHIDHYDIEVKNTQHGLERITNQIPLKIDESTRDLLKIEKLNSRGLVEIGSWVEEGDY 1013

Query: 1001 GFKKSTVLSSD-LISEYPRSQWWQFAVQDEKVQRNVESLK-----VQYETSKSILEDRFK 1054
               K++ L+      E+   + +   +Q EK      SL+       +     IL  +  
Sbjct: 1014 LVGKTSPLNPKGPSVEHQYEKLYNVIMQREKTNFRNTSLRVPKGVEGFVLDVQILPSQEP 1073

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +     +  D +       V+V +  +R IQ GDKMAGRHGNKGIVS ILP  DMP+L D
Sbjct: 1074 DVAALAEKNDIL------RVRVVLLQRRRIQVGDKMAGRHGNKGIVSTILPRHDMPYLPD 1127

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DIVLNPLGVPSRMNVGQI E  LG A   L +   + + D +   + S    + + 
Sbjct: 1128 GTPIDIVLNPLGVPSRMNVGQILECLLGLAGKYLQESYTTNLFDEQFGAEASRSLVYSKL 1187

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                      KSG P                 L        G+ 
Sbjct: 1188 ---------------------YEASIKSGNP----------------WLFE--PHHPGKI 1208

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L+DG TG PFD+P+T+G  Y+LKL H+V DK++AR+TG YS VTQQP+ G+S  GGQRL
Sbjct: 1209 QLFDGRTGIPFDQPITIGCAYILKLVHLVDDKIHARATGPYSAVTQQPVRGRSRNGGQRL 1268

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GEMEVW +QAYGAAY L E+LT+KSDDV GR +    I  GN    +G PESF VL++E+
Sbjct: 1269 GEMEVWALQAYGAAYTLHELLTLKSDDVEGRKQAVVRIY-GNKPLNSGRPESFKVLLREL 1327

Query: 1355 QALGLSIDLE 1364
            QAL   + L 
Sbjct: 1328 QALCFDLQLY 1337



 Score =  273 bits (698), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 197/754 (26%), Positives = 314/754 (41%), Gaps = 132/754 (17%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           K +       +IP++I+VQ+ S+  F+            G + AF++    +  +    +
Sbjct: 10  KHYSGFEFSTEIPNIIDVQRQSFYSFI----------ENGFKEAFQNSLCFSTMTHDLEI 59

Query: 75  ----EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
               EF+ ++   P F+ +       TY   + I +            +K    +K + +
Sbjct: 60  LFFPEFIQFQ--KPDFNKNQAFVLGKTYGSSVYIPV---------GIKSKLSSSLKVEWL 108

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G LPLMTK G FVI GI R+V+ Q+ R+PGI+      R   +       RI+P++G 
Sbjct: 109 LIGVLPLMTKQGHFVINGIPRVVLHQMVRNPGIYTIPRDSRTQTA-----TVRIVPEKGG 163

Query: 191 WMDIEFDSKDIIHVRIDR--RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           W+++  D K+ I     R  RRKV +  FL ALG+   +I   F          + +   
Sbjct: 164 WINLTIDKKNRIWFS-TRTLRRKVSLLIFLQALGLSLGQI---FLRLEHSKILSNSYVND 219

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           LSA                   ++ +E+     +   K L   G++    T +       
Sbjct: 220 LSAP----------------QKQEFVENLSLGKTRHDKILIRAGLEEHPATQEE------ 257

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
                                                 LY   +  + Y R+  +TDK  
Sbjct: 258 ----------------------------------AWRYLYAHFLEYSPYARDESLTDKAA 283

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                        R    +T    E++            L  +GR +   ++    P D 
Sbjct: 284 -------------RDFFWNTLWNKETLI-----------LGKIGRQQFRDKVGSIEPLDQ 319

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             +  EDI+   + L+ L   +   D+ID+L  +R+R   E L  Q   G+   E     
Sbjct: 320 YSLTVEDILGATQALLKLIYKERLGDEIDSLTQKRIRGCNEFLLEQLVRGIKEFEIFFTR 379

Query: 489 RIS--------SVDIDSVMPQDLINA----KPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +I+        + D + + P    N     K V  A   FF S  L+Q  +  N L+  T
Sbjct: 380 KINTLPVTKPGTPDHNPLEPLWRQNKAVFSKSVSKAWKSFFTSGTLAQFMDQTNPLAEAT 439

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY- 595
           H RRL+ LG GGV   +  +++R +HPT+YGR+CP ET EG N GLV+S T  + ++   
Sbjct: 440 HKRRLTVLGPGGVNSKQTTIQIRGIHPTYYGRLCPIETPEGQNAGLVNSFTVLSTLSKDL 499

Query: 596 -GFIETPYRKVCDGKVTNDVVYL--SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
            G I+TP+ +V   +V   +  L  S  +E +   A A+  L       +  +  R    
Sbjct: 500 AGTIKTPFYQVYKRQVQKTLPPLSVSPRQESSLIGAPADIGLTSWNLLPKIPLPVRKELI 559

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                  +I+       Q +S+A SLIPFLE+DD+NR LMG NMQRQAVPL   +AP VG
Sbjct: 560 FDYDVSTRINTQSVGILQNISVATSLIPFLEHDDANRALMGSNMQRQAVPLANPQAPLVG 619

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           TG+E+ V       I   ++G + QV ++ I I 
Sbjct: 620 TGLETRVVCDVNHGIQVSQSGYITQVTSMGIKIM 653



 Score =  139 bits (350), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 85/238 (35%), Positives = 138/238 (57%), Gaps = 12/238 (5%)

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +   +P       Y L ++QR+NQ+TC++QRP++     V + DI+ADG ++  G L++G
Sbjct: 863  QNLTNPKFKNYKTYNLTRYQRTNQSTCISQRPILSETMWVEKGDILADGAASTRGKLSIG 922

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +N+LVA++PW GYNFED++LIS+R+V +D+FTS+HI+ +++  ++T+ G E IT  IP  
Sbjct: 923  QNVLVAYVPWEGYNFEDAILISQRLVHQDIFTSLHIDHYDIEVKNTQHGLERITNQIPLK 982

Query: 869  SEEGLK------NIDECGIICVGAEVNPGDILVGKITPKGESPMTPE---EKLLRAIFGE 919
             +E  +       ++  G++ +G+ V  GD LVGK +P      + E   EKL   I   
Sbjct: 983  IDESTRDLLKIEKLNSRGLVEIGSWVEEGDYLVGKTSPLNPKGPSVEHQYEKLYNVIMQR 1042

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
            +  + R+TSLRVP GV G V+DV+I      D    +   E+  I  +       + I
Sbjct: 1043 EKTNFRNTSLRVPKGVEGFVLDVQILPSQEPDV---AALAEKNDILRVRVVLLQRRRI 1097


>gi|163784549|ref|ZP_02179405.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880182|gb|EDP73830.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
          Length = 709

 Score =  411 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 218/699 (31%), Positives = 352/699 (50%), Gaps = 77/699 (11%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           +RK   +  E I  PDL+ V K S++ F+  N  P ER N+GL+  F++ FP    +G  
Sbjct: 12  LRKSLKRKEEAIAPPDLLHVVKNSFESFVQFNKNPYERENKGLENLFRTSFPFLDPNGQI 71

Query: 73  MLEFVSYEFD--------------------------------PPKFDVDDCLWRDLTYAV 100
            L +++YE                                    K  VD+C ++ LTY+ 
Sbjct: 72  ELRYIAYEVGDWECGNCRSELPNDVVGGVGVKCPNCGGTLIYKEKHTVDECKYKGLTYSA 131

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
           PL++ L L+V  ++  TG    K  K++ +Y GD+PL+TK G F+I G +R+VVSQL RS
Sbjct: 132 PLRVLLELVVNQLNPETGEIIPKFTKKEKVYFGDIPLLTKYGHFIINGSERVVVSQLIRS 191

Query: 161 PGIHFDHDKGRASLS-GKLLYACRIIPDQGLWMDIEFDSK-DIIHVRIDRRRKVPVTSFL 218
            GI F+  + +   +  +++Y   IIP++G  ++ E+ +  +    +IDR RKV  T+ L
Sbjct: 192 SGIFFEGKEDKTKDTLTRIIYKGSIIPEKGSRLEFEYATNVEHFFAKIDR-RKVIGTTVL 250

Query: 219 MALGMDSE-EILSTFYPKIV--YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
            A G+D+  +IL +FY + V  +  +           ++ +    +  +      ++  E
Sbjct: 251 RAFGLDTTYKILKSFYGEDVQRFVVKDGKLIDVDKNLEVALEELSNDEIFITFLADEEDE 310

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET---GEIYIEAGDVIDEKS 332
            GKK+T      ++ + ++     +       +A D +       G I IE       K 
Sbjct: 311 KGKKITVRQEIHVEPEKLEKYLSDNRIEIEEVIAIDPLVFRKSPYGNILIETLKKDQPKI 370

Query: 333 LEEIFHSEIRDIPIL------YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            ++    +   + I          +++  A++R      +         D+ +V R    
Sbjct: 371 NKDFTFQDAARVEIYRKMRPTDTAAIDPKAFLRRANELFETMFFDPQRYDLSKVGRVKIN 430

Query: 387 STFSVAESMFNFLFFDS---------------------------DKYDLSTVGRVKM-NM 418
           +           L  D+                           D+  L  +   K   +
Sbjct: 431 AKVHSIPKTIKPLDLDTLLEKYPPLVLDEDVKVGKEVIKKGTKIDQEILEKLKNAKFKEI 490

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           ++N    ++ R ++  DII I+K L++LR GK  +DDI +LGNRRVR VGE+L+ Q R+G
Sbjct: 491 KVNAYLDEEARFLQLVDIINIVKYLLELRLGKKQLDDIAHLGNRRVRPVGELLEAQARVG 550

Query: 479 LLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           + RM ++ K+R++++DI+  +V P + IN + +  ++ EF    QLSQ  +  N L+ +T
Sbjct: 551 VARMNKAFKDRLATIDIEDPNVKPGNFINPRYLTGSILEFLKGGQLSQFMDQANPLAELT 610

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R  A  E+RDVHPTHYGR+CP ET EG NIGLVSS+T ++ +N  G
Sbjct: 611 HKRRLSALGPGGLTRDSAKFEIRDVHPTHYGRVCPIETPEGQNIGLVSSMTVYSTLNELG 670

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           F+ TPYRKV +GKVTN++ YL+A +EE   IAQAN+ +D
Sbjct: 671 FLVTPYRKVVNGKVTNEIEYLAAYDEEKYVIAQANAPID 709


>gi|209395021|gb|ACI45313.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 134/237 (56%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRRGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|126797643|gb|ABO27353.1| DNA-directed RNA polymerase beta chain [Mesorhizobium loti]
          Length = 224

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 151/224 (67%), Positives = 177/224 (79%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q GDKMAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ET
Sbjct: 1    VKRKMQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWAC G+GKKI  LI  YK+ GDI PLR  LE  +      E + +YDD+S++R++EQ
Sbjct: 61   HLGWACAGMGKKIGELIETYKSAGDIKPLRKTLESFMPANDRNEPVREYDDESIVRLSEQ 120

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + GV ++TPVFDGA E  IN ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL
Sbjct: 121  MRRGVSIATPVFDGAHEADINIMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKL 180

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  HHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 224


>gi|304561706|gb|ADM43715.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 425

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 165/467 (35%), Positives = 243/467 (52%), Gaps = 55/467 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS  ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSNLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIG 423


>gi|209395018|gb|ACI45311.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395093|gb|ACI45361.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395096|gb|ACI45363.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  410 bits (1053), Expect = e-111,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 167/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     + LR FL+KV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGQRIGDML---QQQAKAAELRKFLDKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D+ ++ +A   + G+P +TPVFDGA EE I  ML++A  DE            
Sbjct: 58   EDLAQLCDEELVAMAAHLRHGMPYATPVFDGASEEEIKDMLKIAYPDEIAQRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|242824711|ref|XP_002488312.1| DNA-dependent RNA polymerase II RPB140 [Talaromyces stipitatus ATCC
            10500]
 gi|218713233|gb|EED12658.1| DNA-dependent RNA polymerase II RPB140 [Talaromyces stipitatus ATCC
            10500]
          Length = 1256

 Score =  410 bits (1053), Expect = e-111,   Method: Composition-based stats.
 Identities = 190/1135 (16%), Positives = 361/1135 (31%), Gaps = 182/1135 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 259  VEKGSRILSQLSLKLFAKGDSSKGGFGPTIR-SSLPYIKTDIPIVIVFRALGVVSDEDIL 317

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    +
Sbjct: 318  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSQTSMSHD 366

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 367  RRVRYAREIMQKEFLPHI-----------SQSEGSETRKAFFLGYMVHKLLQCALGRRDV 415

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    R+ R +    +        V+    +    +  
Sbjct: 416  DDRDHFGKKRLDLAGPLLATLFRTLFTRVTRDLTRYVQRCVETNREVVLNVGLKPATLTG 475

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 476  GLKYALATGNWGEQKKAMSSKAGVSQVLSRYTFASTLSHLRRTNT----PIGRDGKIAKP 531

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 532  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCSITVGSPSEPIVDFMIQRNMEVLEEFEP 591

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L        ++      +  D +     V        I      + D  D   K      
Sbjct: 592  LVTPHATKVFVNGVWVGIHRDPAHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 651

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P    D+  R     ++   +  +  L+A+             +         ++G
Sbjct: 652  RVCRPLFVIDNDPRSENCGSLVLNKDHIRRLEADRELPPDLDPEERREQYYGWEGLVKSG 711

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            ++E VDA       +    +       +         N +     R ++           
Sbjct: 712  VIEYVDAEEEETIMIAMSPEDLEISKQLQAGYAMPEDNSDPNKRVRSVLS--QRAHIWTH 769

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 770  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLT 812

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E   +I    ++ L                        +       +   +  +
Sbjct: 813  NFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNAI 853

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +     +  +   + +  +      IE   +    
Sbjct: 854  VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTEAERKLGLQ----TIEKFEKPMRS 909

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + + +  Y ++ +   +  G           K+  L+ +                +E 
Sbjct: 910  DTLGMRKGTYDKIEDDGLVAPGVRVTGEDIIIGKTAPLAPE---------------SEEL 954

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR     KV   T     E    +++      D      LR+VKV +   +  Q GDK 
Sbjct: 955  GQRTKAHTKVDVSTPLRATESGIVDQVLLTTGNDP----DLRLVKVRMRTTKIPQIGDKF 1010

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 1011 ASRHGQKGTIGITYRHEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 1070

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +                                                       +TP 
Sbjct: 1071 EGD-----------------------------------------------------ATP- 1076

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F     ++++ +LR       G  ++Y+G TG+     V +G  Y  +L HMV DK++AR
Sbjct: 1077 FTDVTVDSVSRLLREHGYQSRGFEVMYNGHTGKKLKAQVFLGPTYYQRLRHMVDDKIHAR 1136

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVV 1323
            + G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D  
Sbjct: 1137 ARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDC 1196

Query: 1324 G--------RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            G        +  ++E  +  N     +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1197 GLMTPIAKLKKGLFECRLCNNKHRISQVHIPYAAKLLFQELAAMNIAARMFTDRS 1251



 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 142/1041 (13%), Positives = 299/1041 (28%), Gaps = 200/1041 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              +++ +     
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTIDQTITPNEDEIDPVVIRRYEIKYGTIMLAR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITL--RLI------VFDVDEFTGAKSIKD- 124
           P F             +   R+LTYA PL + +  RL       V D D        ++ 
Sbjct: 97  PSFSEINGAATLLLPMEARHRNLTYASPLYLNVQRRLTEGRERKVADRDGEGLGDENEEQ 156

Query: 125 ---------------IKEQSI---YMGDLPLMTKD------------------------G 142
                          I E+     Y+G +P+M K                         G
Sbjct: 157 KPGGTYLEWEEKPLVISEEEAKGCYIGRIPIMLKSKYCLLRDLSEQSLYNWNECPYDSGG 216

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKD 200
            F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   K 
Sbjct: 217 YFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLSLK- 272

Query: 201 IIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGD 243
            +  + D  +                 +P+     ALG +  E+IL+        +   +
Sbjct: 273 -LFAKGDSSKGGFGPTIRSSLPYIKTDIPIVIVFRALGVVSDEDILNHICYDRNDTPMLE 331

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT---- 299
                +    ++   +V+   +      Q   S  +      + ++++ +  +  +    
Sbjct: 332 MLKPCIEEGFVIQDREVALDFISKRGSSQTSMSHDRRVRYAREIMQKEFLPHISQSEGSE 391

Query: 300 --SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                  G  V + ++    G   ++  D   +K L+            L+     +   
Sbjct: 392 TRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLATLFRTLFTRVTRDLTR 450

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                V    +      + +   ++P  + T  +  ++    + +  K   S  G  ++ 
Sbjct: 451 YVQRCVETNRE------VVLNVGLKPATL-TGGLKYALATGNWGEQKKAMSSKAGVSQVL 503

Query: 418 MRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
            R    +      R          I     L N    +         +   + + L    
Sbjct: 504 SRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMC 563

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            + +      I + +   +++ +   + +                 +    +  + +S +
Sbjct: 564 SITVGSPSEPIVDFMIQRNMEVLEEFEPLVTPHATKVF---VNGVWVGIHRDPAHLVSTV 620

Query: 536 THTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVS 584
              RR + +  +  + R     E        R   P       P   + G    N   + 
Sbjct: 621 QSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPRSENCGSLVLNKDHIR 680

Query: 585 SLTSFARVNAYGFIE---TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS-- 639
            L +   +      E     Y        +  + Y+ A EEE   IA +   L+      
Sbjct: 681 RLEADRELPPDLDPEERREQYYGWEGLVKSGVIEYVDAEEEETIMIAMSPEDLEISKQLQ 740

Query: 640 -----FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  +     +     +          +  P  ++ I AS+IPF +++ S R     
Sbjct: 741 AGYAMPEDNSDPNKRVRSVLSQRAHIWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 800

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                   D     + ++      
Sbjct: 801 AMGKQAMGVFLTNF------------------------------DQRMETMANILYYPQK 830

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             +       +KF+                G   + + +I +  S D G           
Sbjct: 831 PLATTRSMEFLKFRELPAGQNAIVAIACYSG-YNQEDSVIMNQSSIDRGLFRSLFY---- 885

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
                    E  + +              IE+FE   R   LG          + +    
Sbjct: 886 ---RTYTEAERKLGLQ------------TIEKFEKPMRSDTLG----------MRKGTYD 920

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            I++ G++  G  V   DI++GK  P     + PE + L      KA    D S  + + 
Sbjct: 921 KIEDDGLVAPGVRVTGEDIIIGKTAP-----LAPESEELGQR--TKAHTKVDVSTPLRAT 973

Query: 935 VSGTVVDVRIFNRHGIDKNER 955
            SG V   ++    G D + R
Sbjct: 974 ESGIV--DQVLLTTGNDPDLR 992


>gi|304561566|gb|ADM43645.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 424

 Score =  410 bits (1053), Expect = e-111,   Method: Composition-based stats.
 Identities = 165/467 (35%), Positives = 244/467 (52%), Gaps = 55/467 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++PDLIEVQK SY  FL           EGL+  F+ + PI +F+G   LEFV Y  +
Sbjct: 1   VLEMPDLIEVQKKSYKWFL----------EEGLREVFREISPIESFTGNLALEFVDYRLE 50

Query: 83  P-PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ V++C  RD TYAVP+K+ +RL           +   +IKE  ++MGD PLMT+ 
Sbjct: 51  NNPKYSVEECKDRDTTYAVPMKVKVRLT---------NRETGEIKESEVFMGDFPLMTEK 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF+I G +R++VSQL RSPG++++    +    GK L +  +IP++G W++ E DS DI
Sbjct: 102 GTFIINGAERVIVSQLVRSPGVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDI 158

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           ++VRIDR RKVPVT  L ALG  ++ +IL     +       D          L+   K 
Sbjct: 159 VYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK- 217

Query: 261 SSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAED 311
                 +  GE   +ES K L   L    K   +  +G             +  L  A+ 
Sbjct: 218 -----RLRPGEPPTVESAKSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKK 272

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IVN  TGEI +E G+ I ++  EEI +  I  + +L    V     I N           
Sbjct: 273 IVNPVTGEILVEEGEKISKEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT--------- 321

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              +DI +   P DVS+ ++ E++   L    +  D  +     +N   N       ++I
Sbjct: 322 ---VDINKYPMPYDVSSLNIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNI 376

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            K+DIIA I   ++L +G G+IDDID+LGNRR+RSVGE+L+NQ+R+G
Sbjct: 377 TKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLRSVGELLQNQFRIG 423


>gi|212545975|ref|XP_002153141.1| DNA-dependent RNA polymerase II RPB140 [Penicillium marneffei ATCC
            18224]
 gi|210064661|gb|EEA18756.1| DNA-dependent RNA polymerase II RPB140 [Penicillium marneffei ATCC
            18224]
          Length = 1254

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 190/1135 (16%), Positives = 361/1135 (31%), Gaps = 182/1135 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 257  VEKGSRILSQLSLKLFAKGDSSKGGFGPTIR-SSLPYIKTDIPIVIVFRALGVVSDEDIL 315

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    +
Sbjct: 316  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSQTSMSHD 364

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 365  RRVRYAREIMQKEFLPHI-----------SQSEGSETRKAFFLGYMVHKLLQCALGRRDV 413

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    R+ R +    +        V+    +    +  
Sbjct: 414  DDRDHFGKKRLDLAGPLLATLFRTLFTRVTRDLTRYVQRCVETNREVVLNVGLKPATLTG 473

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 474  GLKYALATGNWGEQKKAMSSKAGVSQVLSRYTFASTLSHLRRTNT----PIGRDGKIAKP 529

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 530  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCSITVGSPSEPIVDFMIQRNMEVLEEFEP 589

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L        ++      +  D +     V        I      + D  D   K      
Sbjct: 590  LVTPHATKVFVNGVWVGVHRDPAHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 649

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P    D+  R     ++   +  +  L+A+             +         ++G
Sbjct: 650  RVCRPLFVIDNDPRSENCGSLVLNKDHIRRLEADRELPPDLDPEERREQYYGWEGLVKSG 709

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            ++E VDA       +    +       +         N +     R ++           
Sbjct: 710  VIEYVDAEEEETIMIAMSPEDLEISKQLQAGYTLPEDNNDPNKRVRSVLS--QRAHIWTH 767

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 768  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLT 810

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E   +I    ++ L                        +       +   +  +
Sbjct: 811  NFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNAI 851

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +     +  +   + +  +      IE   +    
Sbjct: 852  VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTEAERKLGLQ----TIEKFEKPMRS 907

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + + +  Y ++ +   +  G           K+  L+ +                +E 
Sbjct: 908  DTLGMRKGTYDKIEDDGLVAPGVRVTGEDIIIGKTAPLAPE---------------SEEL 952

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR     KV   T     E    +++      D      LR+VKV +   +  Q GDK 
Sbjct: 953  GQRTKAHTKVDVSTPLRATESGIVDQVLLTTGNDP----DLRLVKVRMRTTKIPQIGDKF 1008

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 1009 ASRHGQKGTIGITYRHEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 1068

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +                                                       +TP 
Sbjct: 1069 EGD-----------------------------------------------------ATP- 1074

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F     ++++ +LR       G  ++Y+G TG+     V +G  Y  +L HMV DK++AR
Sbjct: 1075 FTDVTVDSVSRLLREHGYQSRGFEVMYNGHTGKKLKAQVFLGPTYYQRLRHMVDDKIHAR 1134

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVV 1323
            + G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D  
Sbjct: 1135 ARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDC 1194

Query: 1324 G--------RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            G        +  ++E  +  N     +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1195 GLMTPIAKLKKGLFECRLCNNKHRISQVHIPYAAKLLFQELAAMNIAARMFTDRS 1249



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 140/1039 (13%), Positives = 297/1039 (28%), Gaps = 198/1039 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              +++ +     
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTIDQTITPNEDEIDPVVIRRYEIKYGTIMLAR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDEFTGAKSIK- 123
           P F             +   R+LTYA PL + +         R  V    E    +  K 
Sbjct: 97  PSFSEINGAATLLLPMEARHRNLTYASPLYLNVQRRLTEGRERKAVDREGEGDENEEQKP 156

Query: 124 ------------DIKEQSI---YMGDLPLMTKD------------------------GTF 144
                        + E+     Y+G +P+M K                         G F
Sbjct: 157 GGTYLDWEEKPLVVSEEEAKGCYIGRIPIMLKSKYCLLRDLSEQSLYNWNECPYDSGGYF 216

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDII 202
           +I G ++++++Q  RS G        + +      Y   I    ++G  +  +   K  +
Sbjct: 217 IINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYIAEIRSAVEKGSRILSQLSLK--L 271

Query: 203 HVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFW 245
             + D  +                 +P+     ALG +  E+IL+        +   +  
Sbjct: 272 FAKGDSSKGGFGPTIRSSLPYIKTDIPIVIVFRALGVVSDEDILNHICYDRNDTPMLEML 331

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------ 299
              +    ++   +V+   +      Q   S  +      + ++++ +  +  +      
Sbjct: 332 KPCIEEGFVIQDREVALDFISKRGSSQTSMSHDRRVRYAREIMQKEFLPHISQSEGSETR 391

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
                G  V + ++    G   ++  D   +K L+            L+     +     
Sbjct: 392 KAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLATLFRTLFTRVTRDLTRYV 450

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              V    +      + +   ++P  + T  +  ++    + +  K   S  G  ++  R
Sbjct: 451 QRCVETNRE------VVLNVGLKPATL-TGGLKYALATGNWGEQKKAMSSKAGVSQVLSR 503

Query: 420 LNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
               +      R          I     L N    +         +   + + L     +
Sbjct: 504 YTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCSI 563

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +      I + +   +++ +   + +                 +    +  + +S +  
Sbjct: 564 TVGSPSEPIVDFMIQRNMEVLEEFEPLVTPHATKVF---VNGVWVGVHRDPAHLVSTVQS 620

Query: 538 TRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVSSL 586
            RR + +  +  + R     E        R   P       P   + G    N   +  L
Sbjct: 621 LRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPRSENCGSLVLNKDHIRRL 680

Query: 587 TSFARVNAYGFIE---TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS---- 639
            +   +      E     Y        +  + Y+ A EEE   IA +   L+        
Sbjct: 681 EADRELPPDLDPEERREQYYGWEGLVKSGVIEYVDAEEEETIMIAMSPEDLEISKQLQAG 740

Query: 640 ---FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                +     +     +          +  P  ++ I AS+IPF +++ S R      M
Sbjct: 741 YTLPEDNNDPNKRVRSVLSQRAHIWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 800

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                                   D     + ++        
Sbjct: 801 GKQAMGVFLTNF------------------------------DQRMETMANILYYPQKPL 830

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           +       +KF+                G   + + +I +  S D G             
Sbjct: 831 ATTRSMEFLKFRELPAGQNAIVAIACYSG-YNQEDSVIMNQSSIDRGLFRSLFY------ 883

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                  E  + +              IE+FE   R   LG          + +     I
Sbjct: 884 -RTYTEAERKLGLQ------------TIEKFEKPMRSDTLG----------MRKGTYDKI 920

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           ++ G++  G  V   DI++GK  P     + PE + L      KA    D S  + +  S
Sbjct: 921 EDDGLVAPGVRVTGEDIIIGKTAP-----LAPESEELGQR--TKAHTKVDVSTPLRATES 973

Query: 937 GTVVDVRIFNRHGIDKNER 955
           G V   ++    G D + R
Sbjct: 974 GIV--DQVLLTTGNDPDLR 990


>gi|209395090|gb|ACI45359.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 167/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FL+KV  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASHGIGQRIGDML---QQQAKASELRKFLDKVYNSCGRA 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   ++ ++ +A   + GVP +TPVFDGA E  I  ML++A  DE            
Sbjct: 58   EDLTQLSEEDLVAMAGNLQHGVPYATPVFDGASEAEIKDMLKIAYPDEIAQRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G  T E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGVHTIEAGMPESFNV 234


>gi|331029423|gb|AEC49861.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
          Length = 285

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 161/272 (59%), Positives = 209/272 (76%), Gaps = 1/272 (0%)

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           FSG +MLEFV YEF+PPK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAKS+KDIKE
Sbjct: 1   FSGTSMLEFVRYEFEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAKSVKDIKE 60

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q +YMGD+PLMT +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP 
Sbjct: 61  QDVYMGDIPLMTMNGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPY 120

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
           +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY KI Y +  D W  
Sbjct: 121 RGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQILSTFYKKITYKRTKDGWRV 180

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
           P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ + L G Y
Sbjct: 181 PFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRQARQLQEKGLKALRMSDEELVGNY 239

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +AED+VN +TGEIY EAG+ I EKSL+ +   
Sbjct: 240 LAEDLVNPKTGEIYAEAGEEITEKSLKVLNEQ 271


>gi|209395066|gb|ACI45343.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395069|gb|ACI45345.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QQQAKVSELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLTQLSDADLLSMAANLQQGVPYATPVFDGASEAEIKDMLALAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG +G+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRSGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395057|gb|ACI45337.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 163/237 (68%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  GLG++I  L+   +    +S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGLGQRIGDLL---QQQAKVSELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A                
Sbjct: 58   EDLAQLSDADLLSMAANLEQGVPYATPVFDGASEAEIKDMLALAYPEEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+  YDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYPYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395084|gb|ACI45355.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 168/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FL+KV  +   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASHGIGQRIGDML---QQQAKASELRKFLDKVYNSCGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   ++ ++ +A   + GVP +TPVFDGA E  I  ML++A  DE            
Sbjct: 58   EDLTQLSEEDLVAMAGNLQHGVPYATPVFDGASEAEIKDMLKIAYPDEIAQRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G  T E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGGHTIEAGMPESFNV 234


>gi|68300802|gb|AAY89343.1| RNA polymerase II second largest subunit [Antirrhinum majus]
          Length = 1198

 Score =  409 bits (1052), Expect = e-111,   Method: Composition-based stats.
 Identities = 184/1082 (17%), Positives = 350/1082 (32%), Gaps = 190/1082 (17%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            IY     +  E  +  IF + +  +    +       +  + ++       ++A +   +
Sbjct: 269  IYATLPYIRTEVPIIIIFRA-LGFVADKDILEHICYDFNDSKMMELLRPFLEEAFVIQNQ 327

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +    +       S          KY    + R  +      +  +  +         I
Sbjct: 328  QVA---LDYIGKRGSTIGVTRDKRIKYAREILQREMLPHVGTEEYCETKK---AYYFGYI 381

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDS 497
            I  L+    G+   DD D+  N+R+   G +L   +R+   ++ R ++  +     +   
Sbjct: 382  INRLLLCALGRRPEDDRDHYANKRLDLAGPLLAGLFRMLFRKLTRDVRSYVQKCVDNGKD 441

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSALG 545
            V  Q  I AK + S +     +              +SQ+   +   S ++H RRL++  
Sbjct: 442  VNLQFAIKAKTITSGLKYSIATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-- 499

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
               + R     + R +H +H+G +CPAET EG   GLV +L     +            +
Sbjct: 500  --PIGREGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFL 557

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             +    N        EE +  +    + +  +G++             +   R ++   D
Sbjct: 558  DEWSTEN-------FEEISPAVIPQATKIFVNGNWIGIHRNPELLVRTLRQLRRQV---D 607

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             + +  +     L       D  R      +  +   ++K +            +     
Sbjct: 608  VNTEVGIIRDIHLKELRLYTDYGRCSRPLFIVDKQRLVIKKKDILALQ---QRESADEYG 664

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                 R G VE VD             + +T        +   R N +   +        
Sbjct: 665  WHDLVRNGSVEYVDTEE----------EETTMISMTINDLINSRHNPDAAYS-------- 706

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                        PS  LG       +  + +P+  +N          M  + +   I++ 
Sbjct: 707  ---ETYTHCEIHPSLVLG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVT 754

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             ++                           +    +  V        +    +       
Sbjct: 755  NYQ---------------------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQ 787

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +      + AI      +  D+ +   S +        +F R   D+ ++  ++ +E   
Sbjct: 788  LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFG 846

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               RD          +          G           K+T  + D              
Sbjct: 847  CPNRDNTMGMRHGSYDKLEDDGFAPPGTRVSGDDVIIGKTTPFTPDE------------- 893

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                   +N+   +  + +S    E    +++      D +     R VKV +   R  Q
Sbjct: 894  ------NQNIRFTRQDHSSSLRHSESGVVDQVLLTTNADGL-----RFVKVRIRSVRIPQ 942

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK + RHG KG +      +DMP+  +G   DI++NP  +PSRM +GQ+ E  +G   
Sbjct: 943  IGDKFSSRHGQKGTIGMTYTQDDMPWSIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVA 1002

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +GK+                                                      
Sbjct: 1003 AHMGKEGD---------------------------------------------------- 1010

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
             +TP F     + I+  L        G   +Y+G TG P    + +G  Y  +L HMV D
Sbjct: 1011 -ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRPLTSMIFLGPTYYQRLKHMVDD 1068

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----D 1321
            K+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD     
Sbjct: 1069 KIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRVH 1128

Query: 1322 VVGRTRV----------YE--SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            V  R  +          YE  S     D  +   P +  +L++E+ ++ ++  L  +  K
Sbjct: 1129 VCERCGLMGIANLKKHSYECRSCKNKTDIVQIYIPYACKLLIQELMSMAIAPRLLTNDVK 1188

Query: 1370 NS 1371
            + 
Sbjct: 1189 SV 1190



 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 132/990 (13%), Positives = 271/990 (27%), Gaps = 199/990 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFSGA-------AML 74
           L+  Q  S+D F+   +          Q        I           G          +
Sbjct: 47  LVRQQLDSFDEFIQNTM----------QEIVDESSNIEIRPESQHNPGGNSDFAEAMYRI 96

Query: 75  EFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            F       P     D             R+LTY+ PL + +   V           + +
Sbjct: 97  SFGQIYLSKPMMTESDGETNTLFPKAARLRNLTYSSPLYVDVTKRVVKKGFDCE--EVTE 154

Query: 125 IKE-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
            +E   +++G +P+M +                         G F++ G ++++++Q   
Sbjct: 155 TQEFAKVFIGKVPIMLRSSYCSLYHLPEKDLMDLGECPYDQGGYFIVNGSEKVLIAQEKM 214

Query: 160 SPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI------DR---- 208
           S   ++      +     K  Y   +        + +  +   + VR+       R    
Sbjct: 215 STNHVY----VFKKRQPNKYSYVAEVR----SIAESQNKAPSGMFVRMLSRSGAKRGTSG 266

Query: 209 ----------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                     R +VP+     ALG  ++ +IL         S+  +     L  A ++  
Sbjct: 267 QYIYATLPYIRTEVPIIIIFRALGFVADKDILEHICYDFNDSKMMELLRPFLEEAFVIQN 326

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +        +   K++     + + ++ +     T +                
Sbjct: 327 QQVALDYIGKRGSTIGVTRDKRI--KYAREILQREMLPHVGTEEYCETKKAY--YFGYII 382

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A     E   +   +  +    P+L          +   + +   K   +    
Sbjct: 383 NRLLLCALGRRPEDDRDHYANKRLDLAGPLLAGLFRMLFRKLTRDVRSYVQKCVDNGKDV 442

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKED 435
             +        T  +  S+    +  ++           +N      T   +R +     
Sbjct: 443 NLQFAIKAKTITSGLKYSIATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIG 502

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +     L N    +         +      ++KN   +  + +  +    +  +D 
Sbjct: 503 REGKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLDE 559

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARA 554
            S    + I+   +  A   F   + +         +  +   RR   +  + G+ R   
Sbjct: 560 WSTENFEEISPAVIPQATKIFVNGNWIGIHRNPELLVRTLRQLRRQVDVNTEVGIIRDIH 619

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             E+R    T YGR             ++      A        E       D      V
Sbjct: 620 LKELR--LYTDYGRCSRPLFIVDKQRLVIKKKDILALQQRESADEYG---WHDLVRNGSV 674

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            Y+   EEE   I+              +L+  R   +      E     +  P  V+ +
Sbjct: 675 EYVDTEEEETTMISM----------TINDLINSRHNPD--AAYSETYTHCEIHPSLVLGV 722

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                           R   
Sbjct: 723 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDT 762

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           +  V                                       Q+PLV            
Sbjct: 763 LAYV-----------------------------------LYYPQKPLV----------TT 777

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                     L  G N +VA   + GYN EDS+++++  +    F S+    +    +  
Sbjct: 778 RAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKM 837

Query: 855 KLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               +E        +   +       +++ G    G  V+  D+++GK TP         
Sbjct: 838 GTLVKEDFGCPNRDNTMGMRHGSYDKLEDDGFAPPGTRVSGDDVIIGKTTPFTPDE---- 893

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                          +D S  +    SG V
Sbjct: 894 -------NQNIRFTRQDHSSSLRHSESGVV 916


>gi|255717775|ref|XP_002555168.1| KLTH0G02970p [Lachancea thermotolerans]
 gi|238936552|emb|CAR24731.1| KLTH0G02970p [Lachancea thermotolerans]
          Length = 1220

 Score =  409 bits (1051), Expect = e-111,   Method: Composition-based stats.
 Identities = 237/1406 (16%), Positives = 436/1406 (31%), Gaps = 289/1406 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
            L+  Q  S++ F+                                            + +
Sbjct: 39   LVSQQLDSFNQFIN-------------------------------------------YTI 55

Query: 89   DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL----PLMTKD-GT 143
             D +  D T           ++ +       ++    ++  I  G +    P MT+  G 
Sbjct: 56   QDSIVEDST-----------LILEQLAQHTTEADNISRKYEISFGKIYLAKPSMTESDG- 103

Query: 144  FVIKGIQRIVVS-----QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW---MDIE 195
                      VS     Q  R   + +    G      K  Y    IP + L    +D E
Sbjct: 104  ----------VSHAMYPQEARLRNLTYAS--GLFVEIRKRTYEAVDIPGRDLKYEVIDEE 151

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR------GDFWCFPL 249
             +  D   + I R     V   L         +L       +Y  +      G ++    
Sbjct: 152  SEMSDESKIFIGR-----VPIMLR----SKYCLLDELTESDLYKLKECPFDMGGYFIING 202

Query: 250  SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
            S   L+   + + ++V +   ++   S     +  ++S  EKG +F+      L G   +
Sbjct: 203  SEKVLIAQERSAGNIVQVF--KKSAPSPISHIAE-IRSALEKGSRFISTLQVKLYGREGS 259

Query: 310  EDIVNGETG-EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT-DKN 367
             +     T   I  +   VI  ++L  I   EI +     V+       ++  +      
Sbjct: 260  TNRTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLELLKPCVEEGFVI 319

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +DR+ AL  I R              +          +Y    + +  +     L+  + 
Sbjct: 320  QDRETALDFIGRR------------GTALGIKKEKRIQYAKDILQKEFLPHITQLEGFES 367

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +      +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ R I 
Sbjct: 368  RK---AFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTRDIL 424

Query: 488  --ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSL 532
               + S  +      +  + A  + + +     +               +SQ+       
Sbjct: 425  RFMQRSVEEAKDFNLKLAVKATTITAGLKYALATGNWGEQKKAMTSRAGVSQVLNRYTYS 484

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + +
Sbjct: 485  STLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI 540

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAG 651
            +  G    P     +      +      +  +      N           +LV   R   
Sbjct: 541  S-VGTDPLPIITFLNEWGMEPLEDYVPHQSPDATRVFVNGVWHGIHRNPAKLVDTIRKLR 599

Query: 652  EEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP--LLKA 706
             +  V  E     D   K             P    D++    +     R+     L+  
Sbjct: 600  RKGDVTSEVSIVRDIREKELKIFTDAGRVYRPLFIVDENEETGVKELKLRKGHIRKLMMT 659

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYR 763
            E   +  G E      + ++++ +  G+VE +DA       I     DLDP+    D   
Sbjct: 660  EYQDIEGGFEEEDINYTWSSLLNE--GLVEYIDAEEEETILIAMQHEDLDPTIEAADPEE 717

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             +   +  +    +                    PS  LG  A       + +P+  +N 
Sbjct: 718  ELDPAKRIKAIHHS-----------STFTHCEIHPSMILGVAA-------SIIPFPDHNQ 759

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +   + +  + V                               +  
Sbjct: 760  SPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DTMAN 790

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 791  ILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RS 849

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  +D+ +R      E  E   R           +       I  G           
Sbjct: 850  LFFRSYMDQEKRIGMSITESFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGDDMIIG 909

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+T +  D      R+ +         ++     +  Q                      
Sbjct: 910  KTTPIPPDAEELGQRTAFHSKRDASTPLRSTENGIVDQVLI------------------- 950

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 951  -TTNQEGLKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYRREDMPFTAEGVVPDLIIN 1009

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 1010 PHAIPSRMTVAHLIECLLSKVAALSGNEGD------------------------------ 1039

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   ++P F     + I+ +LR       G  ++Y+G TG+
Sbjct: 1040 -----------------------ASP-FTDITVDGISRLLREHGYQSRGFEVMYNGHTGK 1075

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
                 +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ 
Sbjct: 1076 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMI 1135

Query: 1304 AYGAAYVLQEMLTIKSD----DVVG-----------RTRVYESIVAG----NDTFETGTP 1344
            A+GAA  L+E L   SD     + G           +   +E    G     D ++   P
Sbjct: 1136 AHGAAAFLKERLMEASDAFRVHICGVCGLMTVVAKLKHNQFEC--RGCKNKIDIYQIHIP 1193

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKN 1370
             +  +L +E+ A+ ++  L   R+++
Sbjct: 1194 YAAKLLFQELMAMNIAPRLYTDRSRD 1219


>gi|320582153|gb|EFW96371.1| DNA-directed RNA polymerase II [Pichia angusta DL-1]
          Length = 1275

 Score =  409 bits (1050), Expect = e-111,   Method: Composition-based stats.
 Identities = 166/988 (16%), Positives = 302/988 (30%), Gaps = 156/988 (15%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++         +   +  I+  L+     +   DD D+ G +R+   G +L N +R+   
Sbjct: 399  HISQDSGYETNKAYFLGYIVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFR 458

Query: 481  RMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ R I    +      D       + +  + S +     +               +SQ+
Sbjct: 459  KLSRDIYRYMQRCIERGDDFNIVSAVKSNTITSGLKYSLATGNWGEQKKAMSSRAGVSQV 518

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 519  LNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKN 574

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L+  A  +     E     + +  +     Y    E +N      N +          LV
Sbjct: 575  LSLMACASVGSASEPITYLLEEWGLEPLSDYE-PQEHKNATRVFLNGNWVGTHRDPAMLV 633

Query: 646  FCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                          ++    D  +   K          P    D+         ++    
Sbjct: 634  ETMRQLRRSGTISPEVSLIRDIREREFKIFTDAGRIYRPLFIVDNDPDSEHKGELKLTKE 693

Query: 702  PLLKAEAPFVGTGMESVVAKSSGA----AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               K     V   ++       G              +     I  +    E  +  + S
Sbjct: 694  HCRKILDREVEEIVQDEEFDDEGQPLGPVQRVFGWDSLLSNGIIEYLDAEEEETVLIAMS 753

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
              D+      +       ++    +K   +          PS  LG  A       + +P
Sbjct: 754  PEDLISSASAEVQKAERDLDPAKRIKNVVKAHSFTHCEIHPSMILGVAA-------SIIP 806

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +   + +  + V                            
Sbjct: 807  FPDHNQSPRNTYQSAMGKQAMG--VFLTNYSVRM-------------------------- 838

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  + AI      +  D+ +   S +  
Sbjct: 839  -DTMANILYYPQKPLAKTQSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDR 897

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +    +F R  +D+  RS     E+ E   R                   I  G     
Sbjct: 898  GLF-RSLFFRSYMDQERRSGISVVEEFEKPMRSSTLGFKQGTYEKLDDDGLIAPGVRVSG 956

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  +  D      R+++         ++     +  Q                
Sbjct: 957  DDIIIGKTVPIPPDTEELGQRTKYHTKRDASTPLRTTESGIVDQVLL------------- 1003

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         L+  KV +   +  Q GDK A RHG KG +      EDMPF   G  
Sbjct: 1004 -------TTNAEGLKFAKVRMRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTAQGIV 1056

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +                          
Sbjct: 1057 PDLIINPHAIPSRMTVAHLIECLLSKVASMRGYEGD------------------------ 1092

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     +A++ +LR       G  ++Y
Sbjct: 1093 -----------------------------ATP-FTDLTVDAVSKLLRENGYQSRGFEVMY 1122

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            +G TG+     V  G  Y  +L HMV DK++AR+ G Y  +T+QP+ G++  GG R GEM
Sbjct: 1123 NGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPYQNLTRQPMEGRARDGGLRFGEM 1182

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFE 1340
            E  C+ A+GAA  L+E L   SD        + G   V  ++              + ++
Sbjct: 1183 ERDCMIAHGAAGFLKERLMDSSDAFRVHICGICGLMSVIANLKKNQFECKSCKNKTNIYQ 1242

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ ++ ++  L   ++
Sbjct: 1243 IHIPYAAKLLFQELMSMNIAPRLYTQKS 1270



 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 146/1083 (13%), Positives = 305/1083 (28%), Gaps = 254/1083 (23%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGL------QAAFKSVFPITAFSGAAMLEFVSYEFD 82
            L+  Q  S++ F+  +I      ++ L      Q   +        +    + F      
Sbjct: 34   LVSQQLDSFEEFIESSIQELVLEDKKLILDQPAQHITED----DDVNRRYEITFGDIFLS 89

Query: 83   PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK--------- 123
             P               +   R+LTY+ PL + ++ +V +  +     + +         
Sbjct: 90   KPSQTEADGTTSTLLPQEARLRNLTYSAPLYVEMKKMVKESIDDDDVVTTQVVWYREGEI 149

Query: 124  -------------------------DIKE--------------QSIYMGDLPLMTKD--- 141
                                     DI E              Q+I++G +P+M K    
Sbjct: 150  TRYRNGEIEQDEMVIMPPNFDDDSDDIIEERHGIKVHRSGAESQTIFIGKVPIMLKSKFC 209

Query: 142  ---------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
                                 G F+I G ++++++Q  RS          + S    + +
Sbjct: 210  SLYGLSEDELYEIRECPFDMGGYFIINGSEKVLIAQE-RSAANI--VQVFKKSPPSPVSH 266

Query: 181  ACRIIP--DQGLWMDIEF-------------------DSKDII-HVRIDRRRKVPVTSFL 218
               +    ++G  +                         K  + +++ D    +P+    
Sbjct: 267  IAELRSALEKGSRLISSIQVKLARGGASNFKSGGVGRSIKATLPYIKAD----IPIVIVF 322

Query: 219  MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
             ALG+  + +IL          Q  +     +    L+   +V+   +        I+  
Sbjct: 323  RALGVIEDGDILQHICYDENDWQMLEMLKPCIEEGFLIQSQEVALDYIGRRGNSIGIKKE 382

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
            +++       L+ + +  +   S            +      + + A +  +    +   
Sbjct: 383  RRIQYAK-DILQREFLPHISQDSGYETNKAYFLGYI---VNRLLLCALERKEPDDRDHFG 438

Query: 338  HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
               +                + N       K  +D    + R +  GD   F++  ++ +
Sbjct: 439  KKRLDL----------AGPLLANLFRILFRKLSRDIYRYMQRCIERGD--DFNIVSAVKS 486

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGT 452
                   KY L   G      +         + + +    + +  L        R+GK  
Sbjct: 487  NTITSGLKYSL-ATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLA 545

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMERSIKERISSVDIDSVMPQDLI 504
                 +  +  +    E  + Q          +    +  + +     ++   + P    
Sbjct: 546  KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMACASVGSASEPITYLLEEWGLEPLSDY 605

Query: 505  NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEM----- 558
              +   +A   F   + +    +    +  +   RR   +     + R     E      
Sbjct: 606  EPQEHKNATRVFLNGNWVGTHRDPAMLVETMRQLRRSGTISPEVSLIRDIREREFKIFTD 665

Query: 559  --RDVHPTHYGRICPAETSEGHNIGL-----------VSSLTSFARVNAYGFIETPYRKV 605
              R   P       P    +G                V  +      +  G    P ++V
Sbjct: 666  AGRIYRPLFIVDNDPDSEHKGELKLTKEHCRKILDREVEEIVQDEEFDDEGQPLGPVQRV 725

Query: 606  CDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGS---FTEELVFCRCAGEEILVPRE 659
                       + YL A EEE   IA +   L    S      E         + +V   
Sbjct: 726  FGWDSLLSNGIIEYLDAEEEETVLIAMSPEDLISSASAEVQKAERDLDPAKRIKNVVKAH 785

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                 +  P  ++ +AAS+IPF +++ S R      M +QA+ +                
Sbjct: 786  SFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYSV--------- 836

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                               + + +  Y      ++     +  R
Sbjct: 837  --------------------------------RMDTMANILYYPQKPLAKTQSMEYLKFR 864

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                                    +L  G+N +VA   + GYN EDSM++++  +   +F
Sbjct: 865  ------------------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 900

Query: 840  TSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             S+    +    R + +   E     +        +   + +D+ G+I  G  V+  DI+
Sbjct: 901  RSLFFRSYMDQERRSGISVVEEFEKPMRSSTLGFKQGTYEKLDDDGLIAPGVRVSGDDII 960

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +GK  P    P   EE   R     K    RD S  + +  SG V  V +       K  
Sbjct: 961  IGKTVPI---PPDTEELGQRT----KYHTKRDASTPLRTTESGIVDQVLLTTNAEGLKFA 1013

Query: 955  RSI 957
            +  
Sbjct: 1014 KVR 1016


>gi|209395102|gb|ACI45367.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  408 bits (1049), Expect = e-111,   Method: Composition-based stats.
 Identities = 133/237 (56%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR  LEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKLLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|330796313|ref|XP_003286212.1| RNA polymerase II core subunit [Dictyostelium purpureum]
 gi|325083799|gb|EGC37242.1| RNA polymerase II core subunit [Dictyostelium purpureum]
          Length = 1169

 Score =  408 bits (1048), Expect = e-111,   Method: Composition-based stats.
 Identities = 161/984 (16%), Positives = 316/984 (32%), Gaps = 203/984 (20%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +      I+  L+     +  +DD D+  N+R+   G +L   +R    
Sbjct: 349  HVSVAEFYETKKAFYFGYIVHRLLLASLERRPLDDRDHFANKRLDLAGPLLGTLFRQLFK 408

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS------------SQLSQLE 526
            ++ + ++   +         +P   + +K + S +     +            S ++Q+ 
Sbjct: 409  KLTKDVRLYLQRCIDKDKEFIPSSAVKSKTITSGLKYSLATGNWGSSKSGGTKSGVAQVL 468

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
              +   S ++H RRL+      + R     + R +H TH+G +CP+ET EG   GLV +L
Sbjct: 469  NRLTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTHWGIVCPSETPEGQACGLVKNL 524

Query: 587  TSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA-NSSLDEDGSFTEE 643
            +  + ++     +     + +       ++  LS++    +         +         
Sbjct: 525  SMMSYISVGSASQPILEFLEEWTTENLEEISDLSSIFTATKIFVNGMWVGIHHQPDKLLG 584

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             +       ++ V    + D  +   +          P     D+   +   ++ +    
Sbjct: 585  TLRLLRRCGDVSVEVSVVRDIREKELRLYTDPGRCCRPLFVVQDNKLQVKKHHISKLINN 644

Query: 703  --LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
                K +       +E + A+     ++A               +   +     +   V 
Sbjct: 645  SDEYKWQDLLNEGIIEYIDAEEEETVLIA---------------MTPDDLVPLANEQIVH 689

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             Y                                   PS  LG       +  + +P+  
Sbjct: 690  TY-----------------------------THCEIHPSMILG-------VCCSIIPFPD 713

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   ++I  ++                           +    
Sbjct: 714  HNQSPRNTYQAAMGKQAMG--VYITNYQ---------------------------LRMDT 744

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  V        +    +       +   +    AI      +  D+ +   S +   + 
Sbjct: 745  MAHVLFYPQKPLVTTRSMEYLHFRELPAGQNACVAIACYSGYNQEDSVILNQSAIDRGLF 804

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++  S+  EQ E   RD                  +  G        
Sbjct: 805  -RSMFYRAYKDEQKKQTSLMEEQFEKPDRDTCAGMRHGSYEKIDEDGLVAPGVRVAGDDI 863

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+T L                  +D+   +     K    T+    E+   +++   
Sbjct: 864  IIGKTTPLP---------------PQEDDLGPKTRRHTKRDSSTALRSSENGIVDQVILT 908

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G        +  KV V   R  Q GDK + RHG KG        ED+P+  +G   DI
Sbjct: 909  TSG-----EGFKFCKVRVRSMRVPQIGDKFSSRHGQKGTCGMAYRQEDLPWTVEGIVPDI 963

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V+NP  +PSRM +GQ+ E  LG      G +                             
Sbjct: 964  VVNPHAIPSRMTIGQLIECLLGKVSASTGDEGD--------------------------- 996

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     EAI+  L       +G  ++Y+G 
Sbjct: 997  --------------------------ATP-FTDVTVEAISQALHKVGYQMTGHEVMYNGH 1029

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG   D  + +G  Y  +L HMV DK+++RS G   ++T+QP+ G+S  GG R GEME  
Sbjct: 1030 TGRRMDAQIFIGPTYYQRLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLRFGEMERD 1089

Query: 1301 CIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV----------AGND---TFE 1340
            C+ ++G+A  L+E L  +SD       D+ G      +I              +     +
Sbjct: 1090 CMISHGSAAFLRERLFDQSDHYRVHVCDICG----LIAIANLKKNSFECRRCKNKTQISQ 1145

Query: 1341 TGTPESFNVLVKEMQALGLSIDLE 1364
               P +  +L +E+ ++ ++  + 
Sbjct: 1146 VRMPYAAKLLFQELMSMSIAPRMF 1169



 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 136/997 (13%), Positives = 278/997 (27%), Gaps = 190/997 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L+  Q  S+D F+   +          Q       PIT                      
Sbjct: 36  LVRQQLDSFDEFIQNTM----------QEIIDESPPITLRPEAQHHPGQTQIQNTVSTFS 85

Query: 74  LEFVSYEFDPPK---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK- 123
           ++F       P             +    R+LTY+ PL + +   V    +    +  + 
Sbjct: 86  VKFGQIYLSKPTAEIDGVSQQVTPNQARIRNLTYSAPLFVDITKTVMTGPKGKIEEQRRN 145

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
           D   + +++G +P+M +                         G FVI G ++++++Q   
Sbjct: 146 DELLKRVFIGKVPIMLRSQYCMLYEATDRDLTTMGECPFDQGGYFVINGSEKVLIAQEKM 205

Query: 160 SPG-IHFDHDKGRASLSGKLLYACRIIP--DQGLW------MDIEFDSKD--------II 202
           +   ++      + S   K  Y   I    + G        + +  ++          I 
Sbjct: 206 NNNHVY----VFKKSPPSKYSYVAEIRSCQETGSRPTSTMYLKMLHNTNKGPVGIKATIP 261

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    VPV     ALG  ++ +IL         +Q  D     L  + ++   +V+
Sbjct: 262 YIKQD----VPVIIVFRALGFVADKDILEHICYDFNDAQMMDLMRPSLEESFVIQSQEVA 317

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +            +   +   + L+++ +  + +              +      + 
Sbjct: 318 LDYLGKRGSTIGTREQRIKFAR--EVLQKEMLPHVSVAEFYETKKAFYFGYIVHRL--LL 373

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                   +              P+L          +   +     +        I    
Sbjct: 374 ASLERRPLDDRDHFANKRLDLAGPLLGTLFRQLFKKLTKDVRLYLQRCIDKDKEFIPSSA 433

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAII 440
                 T  +  S+    +  S      +     +N      T   +R +         +
Sbjct: 434 VKSKTITSGLKYSLATGNWGSSKSGGTKSGVAQVLNRLTFASTLSHLRRLNTPIGREGKL 493

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    I         +   + + L     + +    + I E +     +++  
Sbjct: 494 AKPRQLHNTHWGIVCPSETPEGQACGLVKNLSMMSYISVGSASQPILEFLEEWTTENLEE 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
              ++     +              +      +     R      +  V R     E+R 
Sbjct: 554 ISDLS-SIFTATKIFVNGMWVGIHHQPDKLLGTLRLLRRCGDVSVEVSVVRDIREKELR- 611

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           ++        P    + + + +     S    N+         K  D      + Y+ A 
Sbjct: 612 LYTDPGRCCRPLFVVQDNKLQVKKHHISKLINNSD------EYKWQDLLNEGIIEYIDAE 665

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   IA             ++LV                   +  P  ++ +  S+IP
Sbjct: 666 EEETVLIAM----------TPDDLVPLANEQ-----IVHTYTHCEIHPSMILGVCCSIIP 710

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 711 FPDHNQSPRNTYQAAMGKQAMGVYITNYQL------------------------------ 740

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y               Q+PLV                  
Sbjct: 741 -----------RMDTMAHVLFYP--------------QKPLV----------TTRSMEYL 765

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N  VA   + GYN EDS+++++  +   +F S+    ++   +      EE
Sbjct: 766 HFRELPAGQNACVAIACYSGYNQEDSVILNQSAIDRGLFRSMFYRAYKDEQKKQTSLMEE 825

Query: 861 ITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                       +     + IDE G++  G  V   DI++GK TP     + P+E  L  
Sbjct: 826 QFEKPDRDTCAGMRHGSYEKIDEDGLVAPGVRVAGDDIIIGKTTP-----LPPQEDDLG- 879

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               +    RD+S  + S  +G V  V +       K
Sbjct: 880 -PKTRRHTKRDSSTALRSSENGIVDQVILTTSGEGFK 915


>gi|331029433|gb|AEC49866.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6144]
          Length = 285

 Score =  408 bits (1048), Expect = e-111,   Method: Composition-based stats.
 Identities = 162/280 (57%), Positives = 212/280 (75%), Gaps = 1/280 (0%)

Query: 54  GLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV 113
           GLQA   SVFPI+ FSG +ML FV YEF+ PK+DVD+C    +T+A PLK TLRLIVFD+
Sbjct: 1   GLQAVSGSVFPISDFSGTSMLGFVRYEFEQPKYDVDECRQPGMTFAAPLKGTLRLIVFDI 60

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+  
Sbjct: 61  DEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTH 120

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
            SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY
Sbjct: 121 SSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFY 180

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
            KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+
Sbjct: 181 KKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGL 239

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           K L +  + L G YVAED+VN +TGEI+ EAG+ I +K +
Sbjct: 240 KALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLM 279


>gi|258596921|ref|XP_001349662.2| DNA-directed RNA polymerase II second largest subunit, putative
            [Plasmodium falciparum 3D7]
 gi|254688481|gb|AAC71932.3| DNA-directed RNA polymerase II second largest subunit, putative
            [Plasmodium falciparum 3D7]
          Length = 1340

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 179/1063 (16%), Positives = 336/1063 (31%), Gaps = 171/1063 (16%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            +        + R ++   +      + +  +   I  +I  L+    G+   DD D+ G 
Sbjct: 351  EKRILYAKELLRKEVLPHMGTHPGVESK--KSYFIGYMINRLLLAELGRIKEDDRDHFGK 408

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD----LINAKPVVSAVCEFF 517
            +R+   G ++ + +     +M + ++ R+    ID+  P D    + +   +   +    
Sbjct: 409  KRLDIAGPLMASSFSTYFRKMAKDVR-RVLQRQIDNNKPFDVAGAIRSCSQITQGMQYQL 467

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               ++Q+   +   S ++H RRL+      + R     + R +H T
Sbjct: 468  ATGNWGKDKDGKVIRTGVAQVLNRLTYSSCLSHLRRLNT----PLGREGKMAKPRQLHNT 523

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G ICP ET EG ++GLV +L+    ++        Y  + +      +  +     + 
Sbjct: 524  HWGMICPFETPEGQSVGLVKNLSLMCDISVGTSTNNIYEFLTEW-GLESLDEVPPELMKE 582

Query: 625  RYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            +     N       +  + L+      R   +         D      K       ++ P
Sbjct: 583  KVKLFLNGKWVGCFNQIDNLIETLYELRRRCDISPEASIVRDVNSKEIKIFTDSGRAMRP 642

Query: 681  FLEN--------------------------------DDSNRVLMGCNMQRQAVPLLKAEA 708
                                                 +     + C  +   +  +  + 
Sbjct: 643  LYVVKNVNGENKLKLTKEHVNNIEKYPETYNWDYLIQEGIIEYIDCEEEETTMISMFIDD 702

Query: 709  PFVGTGM--ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLM 765
               GTG        +   + I+   A I+   D  +    + +  +     G+      +
Sbjct: 703  LKTGTGYYNNFTHCEIHPSLILGVCASIIPFSDHNQSPRNTYQSAMGKQAMGIYVTNFNI 762

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +           Q+PLV                     +L  G N +VA M + GYN ED
Sbjct: 763  RLDTLAHLLYYPQKPLV----------CTKVMEYLRFRELPAGINAIVAIMCYTGYNQED 812

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECG 880
            S+++++  +   +F S+    +    +       E       R + N+       +D+ G
Sbjct: 813  SLIMNQSSIDRGLFRSVFYRTYTSEEKQQGSLIIESFEKPSVRVVKNLKRGDYTKLDDDG 872

Query: 881  I-----------ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
            +           I +G      D     I  K  +  +  +   +        +  + ++
Sbjct: 873  LIAPGIRVLGDDIIIGKVSPNIDDEDDIIIEKRNTSSSSIQIYNKDSISNNNSNNSNNNM 932

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +S         + +    +    S   + +     +             S     
Sbjct: 933  NNMSNMSNMSNIRSSISSNLSFSSNIGSSNVLDTLPDSPINNTYNNNNNININSSSNNYS 992

Query: 990  LCG-----QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            L G      +  S    F       S   +    +        D ++     S     + 
Sbjct: 993  LHGAASVTSSTPSSTTIFSSGQTAGSSNSNTKYGTTIVSSTKDDTEIPTLTISSTNVLKQ 1052

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPG--VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             K       ++    +     +       +  KV V   R  Q GDK A RHG KG +  
Sbjct: 1053 YKKDCSLSLRSNENGVIDTVMLSSNSRGNKFAKVKVRSVRIPQIGDKFASRHGQKGTIGI 1112

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF   G   DI++NP  VPSRM +G + E   G      G +  +        
Sbjct: 1113 TYRTEDMPFSSLGIFPDIIMNPHAVPSRMTIGHLVECLTGKVAAIEGGEGDATPFSKITV 1172

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             +IS     L                                           E+  N M
Sbjct: 1173 QEISQKLHNLGY-----------------------------------------EKYGNEM 1191

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L             Y+G  G      + +G  Y  +L HMV DK++ARS G  +++T+QP
Sbjct: 1192 L-------------YNGHNGRMLKSKIFIGPTYYQRLKHMVEDKIHARSRGPLTMITRQP 1238

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------------DVVGRT 1326
              G+S  GG R GEME  C+ ++G+A +L+E L  +SD                D+    
Sbjct: 1239 TEGRSRDGGLRFGEMERDCMISHGSAKMLKERLFEESDAYRVHVCDNCGLCCIADIN--K 1296

Query: 1327 RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              YE  V     +  +   P +  +L +E+  + +   L    
Sbjct: 1297 NAYECTVCNSKTNISQIYLPYACKLLFQELMTMAIYPKLVLED 1339



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 121/866 (13%), Positives = 237/866 (27%), Gaps = 152/866 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----------AFSGA--AMLE 75
           L+  Q  SY+ F+   +          Q        I              +      L+
Sbjct: 49  LVNQQIESYNDFIEYRM----------QEIIDEHPKIEIRPQPQYRTDRDENDNIIYSLK 98

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F     D P +D            +   R+LTY+  + I +    + +DE T    +K+ 
Sbjct: 99  FGQLSLDRPFYDEKNLSNKNLWPQEARLRNLTYSSAIYIDIEQSTYIIDEVTKKPVLKEK 158

Query: 126 -KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + I +G +PLM K                         G F++ G ++++V+Q  R 
Sbjct: 159 FIYERINLGRIPLMLKSMFCWTKGLPENEIADMGECSYDQGGYFIVNGGEKVLVAQE-RM 217

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK--------- 211
                   K +     K  +   I       M+    +     V++ + R          
Sbjct: 218 ANNFIYVFKKKQPS--KFGWVAEIR----SQMERSQATSG-FSVKM-KTRSGGSQYGSNK 269

Query: 212 ---------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
                          + V     ALG  S+ +IL             +     L      
Sbjct: 270 SGGQLVATLPYIRTEISVGILFRALGCTSDRDILQRIVYDFNDKLMINALRETLEECIEY 329

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-----KFLGI--TSDCLCGLYV 308
               V    +        + + ++      K L  K V        G+        G  +
Sbjct: 330 PTQDVCLDFIGKRG--PTVGASREKRILYAKELLRKEVLPHMGTHPGVESKKSYFIGYMI 387

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
              ++  E G I  +  D   +K L+             +     +   +    + +   
Sbjct: 388 NRLLL-AELGRIKEDDRDHFGKKRLDIAGPLMASSFSTYFRKMAKDVRRVLQRQIDNNKP 446

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                  D+   +R     T  +   +    +       +   G  ++  RL   +    
Sbjct: 447 ------FDVAGAIRSCSQITQGMQYQLATGNWGKDKDGKVIRTGVAQVLNRLTYSSCLSH 500

Query: 429 --RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             R          +     L N    +         +   + + L     + +     +I
Sbjct: 501 LRRLNTPLGREGKMAKPRQLHNTHWGMICPFETPEGQSVGLVKNLSLMCDISVGTSTNNI 560

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            E ++      +   D +  + +   V  F     +    +  N +  +   RR   +  
Sbjct: 561 YEFLT---EWGLESLDEVPPELMKEKVKLFLNGKWVGCFNQIDNLIETLYELRRRCDISP 617

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                     +   +       + P    +  N      LT     N   + ET      
Sbjct: 618 EASIVRDVNSKEIKIFTDSGRAMRPLYVVKNVNGENKLKLTKEHVNNIEKYPET--YNWD 675

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
                  + Y+   EEE   I+     L     +                        + 
Sbjct: 676 YLIQEGIIEYIDCEEEETTMISMFIDDLKTGTGYYNNF-----------------THCEI 718

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPF 710
            P  ++ + AS+IPF +++ S R      M +QA+                 L   + P 
Sbjct: 719 HPSLILGVCASIIPFSDHNQSPRNTYQSAMGKQAMGIYVTNFNIRLDTLAHLLYYPQKPL 778

Query: 711 VGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           V T  ME +  +   A I A  A +          +   +  +D        YR    + 
Sbjct: 779 VCTKVMEYLRFRELPAGINAIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSVFYRTYTSEE 838

Query: 770 SNQNTCVN---QRPLVKVGDEVRRND 792
             Q + +    ++P V+V   ++R D
Sbjct: 839 KQQGSLIIESFEKPSVRVVKNLKRGD 864


>gi|325092558|gb|EGC45868.1| DNA-dependent RNA polymerase II RPB140 [Ajellomyces capsulatus H88]
          Length = 1307

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 194/1079 (17%), Positives = 349/1079 (32%), Gaps = 168/1079 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 363  VEKGSRILSQLSIKLFGKGDTSKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 421

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 422  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 470

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 471  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 519

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  + S
Sbjct: 520  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSS 579

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 580  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 635

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 636  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 695

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 696  QVSPNATKVFVNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 755

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 756  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVK-S 814

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +   +         + N   N+R    +  +     
Sbjct: 815  GVVEYVDAEEEETIMIVMTPEDLETSKQLQAGFSLPEEDNND-PNRRVRSTLSQKTHTWT 873

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 874  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 916

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 917  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNA 957

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 958  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 1016

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ +                +E  Q
Sbjct: 1017 LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQ 1061

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 1062 RTKQHTKIDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1116

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1117 RHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1176

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1177 D-----------------------------------------------------ATP-FT 1182

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1183 DVTVDSISSLLREHGYQSRGFEVMYNGYTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1242

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG 1324
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G
Sbjct: 1243 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICG 1301



 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 110/804 (13%), Positives = 230/804 (28%), Gaps = 146/804 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERP------NEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           L+  Q  S+D F+   +            ++ L  A   + P+        L+F +    
Sbjct: 140 LVSQQLDSFDEFISTTMQELVEEQGQVTLDQTLAPAEDEIDPVV--LRRYELKFGTVMLA 197

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITL---------RLI---------VFDVD 114
            P               +   R+LTYA PL + +         RLI           D D
Sbjct: 198 RPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLIAERDDAEQGEEDND 257

Query: 115 EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
           E   ++              + +E+++++G +P+M K                       
Sbjct: 258 EERRSRGTYLHWEPKALNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQSLYNWNECPYD 317

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 318 SGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 374

Query: 198 SK-----DII-------------HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVY 238
            K     D               +++ D    +P+     ALG +  E+IL+        
Sbjct: 375 IKLFGKGDTSKGGFGPTIRSTLPYIKTD----IPIVVVFRALGVVSDEDILNHICYDRND 430

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +   +     +    ++   +V+   +          + +K        ++++ +  +  
Sbjct: 431 TPMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQ 490

Query: 299 T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           +           G  V   ++    G   ++  D   +K L+           IL++   
Sbjct: 491 SEGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVT 549

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +        V    +   +  +    +       +  +  ++    + +  K   S  G
Sbjct: 550 KDLYKYVQRCVETNRQLYLNIGVKASTL-------SSGLKYALATGNWGEQKKAASSKAG 602

Query: 413 RVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGE 469
             ++  R    +      R          I     L N   G +   +    +    V  
Sbjct: 603 VSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 662

Query: 470 MLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           +            E  I    + +   ++   PQ   NA  V      F     +    +
Sbjct: 663 LALMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRD 716

Query: 528 HVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHN 579
             + +S +   RR + +  +  + R     E        R   P       P   + G  
Sbjct: 717 PSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSL 776

Query: 580 IGLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           +     +                     Y        +  V Y+ A EEE   I      
Sbjct: 777 VLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPED 836

Query: 634 LDEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L+              +     R     +          +  P  ++ I AS+IPF +++
Sbjct: 837 LETSKQLQAGFSLPEEDNNDPNRRVRSTLSQKTHTWTHCEIHPSMILGICASIIPFPDHN 896

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAP 709
            S R      M +QA+ +      
Sbjct: 897 QSPRNTYQSAMGKQAMGVFLTNFD 920


>gi|50293059|ref|XP_448959.1| hypothetical protein [Candida glabrata CBS 138]
 gi|51701949|sp|Q6FLD5|RPB2_CANGA RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
 gi|49528272|emb|CAG61929.1| unnamed protein product [Candida glabrata]
          Length = 1223

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 174/977 (17%), Positives = 314/977 (32%), Gaps = 164/977 (16%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ + I    +
Sbjct: 372  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTKDIFRYMQ 431

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             +  + +    +  INAK + S +     +               +SQ+       S ++
Sbjct: 432  RTVEEANDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 491

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++   
Sbjct: 492  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGA 547

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGE 652
                    + +  +     Y+   +  +      N              E L   R  G+
Sbjct: 548  DPMPIITFLSEWGMEPLEDYV-PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 606

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLK-AEAPF 710
                     D  +   K          P F+  DD         +++  V  L   E   
Sbjct: 607  INPEVSMIRDIREQELKIFTDAGRVYRPLFIVEDDEELGRKELKVRKGHVAKLMATEYQD 666

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            +  G E     +  + +     G+VE +DA       +    +          + K    
Sbjct: 667  IEGGFEDAEDYTWSSLL---NEGLVEYIDAEEEESILIAMQPEDLEPTAVEQDIPK---- 719

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                 V+    +KV             PS  LG  A       + +P+  +N        
Sbjct: 720  ---ENVDLAKRIKVTHHATTFTHCEIHPSMILGVAA-------SIIPFPDHNQSPRNTYQ 769

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              M  + +   +    F +                               +  +      
Sbjct: 770  SAMGKQAMGVFLTNYNFRMDT-----------------------------MANILYYPQK 800

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                   +       +   +  + AI      +  D+ +   S +   +    +F R  +
Sbjct: 801  PLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFRSYM 859

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            D+ ++      E  E   R           +       I  G           K+T ++ 
Sbjct: 860  DQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDEDGLIAPGVRVSGEDIIIGKTTPIAP 919

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            D      R+ +         ++     +  Q                             
Sbjct: 920  DEEELGQRTAYHSKRDASTPLRSTENGIVDQVLI--------------------TTNQDG 959

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSR
Sbjct: 960  LKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR 1019

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M V  + E  L       G +                                       
Sbjct: 1020 MTVAHLIECLLSKVAALSGNEGD------------------------------------- 1042

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                            ++P F     E I+ +LR       G  ++Y+G TG+     + 
Sbjct: 1043 ----------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIF 1085

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
             G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+GAA  
Sbjct: 1086 FGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAAF 1145

Query: 1311 LQEMLTIKSD----DVVGRTRVYESIVA----------GND---TFETGTPESFNVLVKE 1353
            L+E L   SD     + G   +   I             ++    ++   P +  +L +E
Sbjct: 1146 LKERLMEASDAFRVHICGICGLMSVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQE 1205

Query: 1354 MQALGLSIDLENSRTKN 1370
            + A+ ++  L   R+++
Sbjct: 1206 LMAMNITPRLYTDRSRD 1222



 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/1010 (13%), Positives = 283/1010 (28%), Gaps = 175/1010 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ-AAFKSVFPITAF-SGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   +      +  L               S    + F       P  
Sbjct: 41  LVSQQLDSFNQFVDYTLQDIISEDSTLILEQLAQHTTEQDNISRKYEISFGKIYVTKPMV 100

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-------- 128
           +            +   R+LTY+  L + +    ++  +  G    +D+  Q        
Sbjct: 101 NESDGVTHALYPQEARLRNLTYSSGLFVDVTKRTYEAVDVPG----RDLNYQLIAEESEE 156

Query: 129 -----SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
                 +++G LP+M +                         G F+I G ++++++Q  R
Sbjct: 157 DSESGKVFIGRLPIMLRSKNCYLSDATESDLYKLKECPFDMGGYFIINGSEKVLIAQE-R 215

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID---RRRK--- 211
           S G        + +    + +   I    ++G         K  ++ R     R  K   
Sbjct: 216 SAGNI--VQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK--LYGRESSSARTIKATL 271

Query: 212 ------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                 +P+     ALG+  + EIL      +   Q  +     +    ++   + +   
Sbjct: 272 PYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDF 331

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
           +        I+  K++       L+++ +  +                +      + + A
Sbjct: 332 IGRRGTALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCA 387

Query: 325 GDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            D  D+   +      +    P+L          +   +     +  ++A     ++   
Sbjct: 388 LDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTKDIFRYMQRTVEEANDFNMKLAIN 447

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
               T  +  ++    + +  K   S  G  ++  R    +      R          + 
Sbjct: 448 AKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLA 507

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +         +      ++KN   +  + +       I+ +    + P 
Sbjct: 508 KPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGADPMPIITFLSEWGMEPL 564

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           +         A   F               +  +   RR   +            +   +
Sbjct: 565 EDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREQELKI 624

Query: 562 HPTHYGRICPAETSE------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-----V 610
                    P    E         + +     +      Y  IE  +    D        
Sbjct: 625 FTDAGRVYRPLFIVEDDEELGRKELKVRKGHVAKLMATEYQDIEGGFEDAEDYTWSSLLN 684

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDE---DGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              V Y+ A EEE+  IA     L+    +    +E V      +            +  
Sbjct: 685 EGLVEYIDAEEEESILIAMQPEDLEPTAVEQDIPKENVDLAKRIKVTH-HATTFTHCEIH 743

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ +AAS+IPF +++ S R      M +QA+ +      F                 
Sbjct: 744 PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNF----------------- 786

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + +  Y       +     +  R        
Sbjct: 787 ------------------------RMDTMANILYYPQKPLGTTRAMEYLKFR-------- 814

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA   + GYN EDSM++++  +   +F S+    +
Sbjct: 815 ----------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSY 858

Query: 848 EVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
               +   +   E        +   +       +DE G+I  G  V+  DI++GK TP  
Sbjct: 859 MDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDEDGLIAPGVRVSGEDIIIGKTTPIA 918

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                  ++             RD S  + S  +G V  V I       K
Sbjct: 919 PDEEELGQRTAY-------HSKRDASTPLRSTENGIVDQVLITTNQDGLK 961


>gi|229544480|gb|ACQ76419.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 136/237 (57%), Positives = 167/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV  T   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNTRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAERKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395111|gb|ACI45373.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LRSFL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QQQAKVSELRSFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLRQGVPYATPVFDGASEAEIKDMLMLAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT+VYESIV G    E G P+SFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVTGRTKVYESIVKGEHAIEAGMPKSFNV 234


>gi|222084087|ref|YP_002519540.1| RNA polymerase beta chain [Keteleeria davidiana]
 gi|220983639|dbj|BAH11405.1| RNA polymerase beta chain [Keteleeria davidiana]
          Length = 1076

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDPHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE  LG A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLLGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 239/695 (34%), Positives = 384/695 (55%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIHYRLELDHNRINYIYTGTLISDWGRRLKLEIDVGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     ++         ++R++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTCYPERFLFLLRKKKGRREREEYLWSKENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++   +  +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENDIFLLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVQIGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A+++  G +++P+ K+ +  +  ++VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKISHCGSLQSPFYKISERSIEENMVYLLPGEG 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  SI  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSIGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E  VA  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQVALDSGSVAIATQEGGIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +                       + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 V--------NITSSVNGDTVRTESVMYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDPHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 65/271 (23%), Positives = 119/271 (43%), Gaps = 29/271 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTEK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  RLI          ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPARLI---------RRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGIH+  +     ++   +Y   +I D G  + +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIHYRLELDHNRIN--YIYTGTLISDWGRRLKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R+RK+ +   L A+G++ EEIL        +              + +      
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTCYPERFLFLLRKKKGRREREEYLWSK--E 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +++++       +      +  L K L+EK 
Sbjct: 227 NAILEFYKKLYCVSGDLVFSESLCKELQEKF 257


>gi|45198922|ref|NP_985951.1| AFR404Cp [Ashbya gossypii ATCC 10895]
 gi|51701974|sp|Q753Q4|RPB2_ASHGO RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
 gi|44984951|gb|AAS53775.1| AFR404Cp [Ashbya gossypii ATCC 10895]
          Length = 1222

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 172/983 (17%), Positives = 317/983 (32%), Gaps = 174/983 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ R I    +
Sbjct: 369  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTRDILRFMQ 428

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             S  +      +  + A  + + +     +               +SQ+       S ++
Sbjct: 429  RSVEEAKDFNLKLAVKATTITAGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 488

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++  G
Sbjct: 489  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS-VG 543

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEIL 655
                P     +      +      +  +      N            LV   R    +  
Sbjct: 544  TDPVPIITFLNEWGMEPLEDYVPHQSPDATRVFVNGVWHGIHRNPARLVDTIRKLRRKGD 603

Query: 656  VPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQ---AVPLLKAEAP 709
            +  E     D   K             P     D+       +++ +      L+  E  
Sbjct: 604  ITAEVSIVRDIREKELKIFTDAGRVYRPLFVVADTQHADGHKDLKVRKGHIRKLMLTEYQ 663

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             +  G E      +  +++    GIVE +DA       +    +     V        Q 
Sbjct: 664  DIEGGFEDEDINYTWTSLL--NDGIVEYIDAEEEETILIAMQQEDLDPSV-------PQT 714

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
             + +  ++    +K              PS  LG  A       + +P+  +N       
Sbjct: 715  VDPSDELDPARRIKAIHHSNTFTHCEIHPSMILGVAA-------SVIPFPDHNQSPRNTY 767

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +   + +  + V                               +  +     
Sbjct: 768  QSAMGKQAMG--VFLTNYNVRM---------------------------DTMANILYYPQ 798

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    +       +   +  + AI      +  D+ +   S +   +    +F R  
Sbjct: 799  KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDSGLF-RSLFFRSY 857

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKST 1006
            +D+ +R   +     E   +      + +    Y +L +   I  G           K+T
Sbjct: 858  MDQEKR---IGMSITESFEKPHRTNTLRMKHGTYEKLDDDGLIAPGVRVSGDDIIIGKTT 914

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  D      R+ +         ++     +  Q                         
Sbjct: 915  PIPPDAEELGQRTAFHSKRDASTPLRSTENGIVDQVLI--------------------TT 954

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  
Sbjct: 955  NQEGLKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYRREDMPFTAEGVVPDLIINPHA 1014

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM V  + E  L       G +                                   
Sbjct: 1015 IPSRMTVAHLIECLLSKVAALSGNEGD--------------------------------- 1041

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                ++P F     + I+ +LR       G  ++Y+G TG+   
Sbjct: 1042 --------------------ASP-FTDITVDGISKLLREHGYQSRGFEVMYNGHTGKKLM 1080

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+G
Sbjct: 1081 AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHG 1140

Query: 1307 AAYVLQEMLTIKSD----DVVG-----------RTRVYESIVAG----NDTFETGTPESF 1347
            AA  L+E L   SD     + G           +   +E    G     D ++   P + 
Sbjct: 1141 AAAFLKERLMEASDAFRVHICGICGLMTVVAKLKHNQFEC--RGCKNKIDIYQVHIPYAA 1198

Query: 1348 NVLVKEMQALGLSIDLENSRTKN 1370
             +L +E+ A+ ++  L   R+++
Sbjct: 1199 KLLFQELMAMNIAPRLYTDRSRD 1221



 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 141/1008 (13%), Positives = 289/1008 (28%), Gaps = 170/1008 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL--QAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   I      +  L  +   +        S    + F       P  
Sbjct: 39  LVSQQLDSFNQFINYTIQDLILEDSTLILEQLAQHTTEADNISRKYEISFGKIYLAKPSM 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVF--------DVDEFTGAKSIKDIKEQ 128
                        +   R+LTYA  L + ++   +        D+      +  +D +E 
Sbjct: 99  TESDGVSHAMYPQEARLRNLTYASGLFVEIKKRTYEAVDIPGRDLKYEIIQEESEDTEEG 158

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIH 164
            I++G +P+M +                         G F+I G ++++++Q  RS G  
Sbjct: 159 KIFIGRVPIMLRSKYCLLDDLSESDLYRLKECPFDMGGYFIINGSEKVLIAQE-RSAGNI 217

Query: 165 FDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR---IDRRRK-------- 211
                 + S    + +   I    ++G         K  ++ R     R  K        
Sbjct: 218 --VQVFKKSAPSPISHIAEIRSALEKGSRFISTLQVK--LYGREGSTSRTIKATLPYIKQ 273

Query: 212 -VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            +P+     ALG+  + EIL          Q  +     +    ++   + +   +    
Sbjct: 274 DIPIVIIFRALGIIPDGEILEHICYDQNDWQMLEMLKPCVEEGFVIQDRETALDFIGRRG 333

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
               I+  K++       L+++ +  +                +      + + A D  D
Sbjct: 334 TALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCALDRKD 389

Query: 330 EKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           +   +      +    P+L          +   ++    +  ++A     ++       T
Sbjct: 390 QDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTRDILRFMQRSVEEAKDFNLKLAVKATTIT 449

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDL 446
             +  ++    + +  K   S  G  ++  R    +      R          +     L
Sbjct: 450 AGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQL 509

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            N    +         +      ++KN   +  + +       I+ ++   + P +    
Sbjct: 510 HNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTDPVPIITFLNEWGMEPLEDYVP 566

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                A   F               +  I   RR   +            +   +     
Sbjct: 567 HQSPDATRVFVNGVWHGIHRNPARLVDTIRKLRRKGDITAEVSIVRDIREKELKIFTDAG 626

Query: 567 GRICPA-------ETSEGHNIGLVSSLTSFARVNAYGFIETPY------RKVCDGKVTND 613
               P              ++ +         +  Y  IE  +                 
Sbjct: 627 RVYRPLFVVADTQHADGHKDLKVRKGHIRKLMLTEYQDIEGGFEDEDINYTWTSLLNDGI 686

Query: 614 VVYLSAMEEENRYIAQ----ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           V Y+ A EEE   IA      + S+ +    ++EL   R                +  P 
Sbjct: 687 VEYIDAEEEETILIAMQQEDLDPSVPQTVDPSDELDPARRIKAIH--HSNTFTHCEIHPS 744

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ +AAS+IPF +++ S R      M +QA+ +                          
Sbjct: 745 MILGVAASVIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV------------------- 785

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 786 ----------------------RMDTMANILYYPQKPLGTTRAMEYLKFR---------- 813

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA   + GYN EDSM++++  +   +F S+    +  
Sbjct: 814 --------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDSGLFRSLFFRSYMD 859

Query: 850 MARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +   +   E        +   +     + +D+ G+I  G  V+  DI++GK TP    
Sbjct: 860 QEKRIGMSITESFEKPHRTNTLRMKHGTYEKLDDDGLIAPGVRVSGDDIIIGKTTPI--- 916

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           P   EE   R  F       RD S  + S  +G V  V I       K
Sbjct: 917 PPDAEELGQRTAF----HSKRDASTPLRSTENGIVDQVLITTNQEGLK 960


>gi|225562623|gb|EEH10902.1| DNA-dependent RNA polymerase II RPB140 [Ajellomyces capsulatus
            G186AR]
          Length = 1307

 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 193/1079 (17%), Positives = 348/1079 (32%), Gaps = 168/1079 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 363  VEKGSRILSQLSIKLFGKGDTSKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 421

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 422  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPTSMNHE 470

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 471  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 519

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 520  DDRDHFGKKRLDLAGPLLANLFRILFMRVTKDLYKYVQRCVETNRQLYLNIGVKASTLSG 579

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 580  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 635

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 636  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 695

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D S     V        I      + D  D   K      
Sbjct: 696  QVSPNATKVFVNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 755

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+  +D      G  +  ++ +  L+A+         E    +  G   + K +
Sbjct: 756  RVCRPLFVVENDPKSENCGSLVLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVK-S 814

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +   +   +         + N   N+R    +  +     
Sbjct: 815  GVVEYVDAEEEETIMIVMTPEDLETSKQLQAGFSLPEEDNND-PNRRVRSTLSQKTHTWT 873

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 874  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 916

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 917  TNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNA 957

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R   
Sbjct: 958  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGMTVVERFEKPMRSDT 1016

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       +  G           K+  L+ +                +E  Q
Sbjct: 1017 LRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQ 1061

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK A 
Sbjct: 1062 RTKQHTKIDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFAS 1116

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 1117 RHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 1176

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 1177 D-----------------------------------------------------ATP-FT 1182

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                ++I+S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ 
Sbjct: 1183 DVTVDSISSLLREHGYQSRGFEVMYNGYTGRKLVAQVFLGPTYYQRLRHMVDDKIHARAR 1242

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG 1324
            G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ G
Sbjct: 1243 GPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDICG 1301



 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 110/804 (13%), Positives = 230/804 (28%), Gaps = 146/804 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERP------NEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           L+  Q  S+D F+   +            ++ L  A   + P+        L+F +    
Sbjct: 140 LVSQQLDSFDEFISTTMQELVEEQGQVTLDQTLAPAEDEIDPVV--LRRYELKFGTVMLA 197

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITL---------RLI---------VFDVD 114
            P               +   R+LTYA PL + +         RLI           D D
Sbjct: 198 RPSVTEGDGATSIMLPQEARLRNLTYASPLYLGITKRVTEGRERLIAERDDAEQGEEDND 257

Query: 115 EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
           E   ++              + +E+++++G +P+M K                       
Sbjct: 258 EERRSRGTYLHWEPKALNEDEPEEENVFIGRMPIMLKSKYCILKDLNEQSLYNWNECPYD 317

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 318 SGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 374

Query: 198 SK-----DII-------------HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVY 238
            K     D               +++ D    +P+     ALG +  E+IL+        
Sbjct: 375 IKLFGKGDTSKGGFGPTIRSTLPYIKTD----IPIVVVFRALGVVSDEDILNHICYDRND 430

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +   +     +    ++   +V+   +          + +K        ++++ +  +  
Sbjct: 431 TPMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQ 490

Query: 299 T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           +           G  V   ++    G   ++  D   +K L+           IL++   
Sbjct: 491 SEGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRILFMRVT 549

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +        V    +   +  +    +       +  +  ++    + +  K   S  G
Sbjct: 550 KDLYKYVQRCVETNRQLYLNIGVKASTL-------SGGLKYALATGNWGEQKKAASSKAG 602

Query: 413 RVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGE 469
             ++  R    +      R          I     L N   G +   +    +    V  
Sbjct: 603 VSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 662

Query: 470 MLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           +            E  I    + +   ++   PQ   NA  V      F     +    +
Sbjct: 663 LALMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNATKV------FVNGVWVGVHRD 716

Query: 528 HVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHN 579
             + +S +   RR + +  +  + R     E        R   P       P   + G  
Sbjct: 717 PSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVENDPKSENCGSL 776

Query: 580 IGLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           +     +                     Y        +  V Y+ A EEE   I      
Sbjct: 777 VLSKEHIHKLEADKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPED 836

Query: 634 LDEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L+              +     R     +          +  P  ++ I AS+IPF +++
Sbjct: 837 LETSKQLQAGFSLPEEDNNDPNRRVRSTLSQKTHTWTHCEIHPSMILGICASIIPFPDHN 896

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAP 709
            S R      M +QA+ +      
Sbjct: 897 QSPRNTYQSAMGKQAMGVFLTNFD 920


>gi|325186944|emb|CCA21488.1| PREDICTED: hypothetical protein [Albugo laibachii Nc14]
          Length = 1234

 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 195/1134 (17%), Positives = 368/1134 (32%), Gaps = 203/1134 (17%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G + TS +   + ++      I+ + +    +     +     I+   G V D + L
Sbjct: 272  VEHGVRPTSTMYVQMYQRSGGKSAISGNQIR-AVIPYIRQDIPVVIIFRALGFVADREIL 330

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E I +         + D      +  +       ++++ AL  I R              
Sbjct: 331  EHICYD--------FTDVELMERFKPSLEEAFVIQEQEVALDFIGRR------------G 370

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            S  N    D  +Y    + +  +      D  +  +      +  ++  L+    G+   
Sbjct: 371  SAINVGKADRIRYAQDILQKEMLPHVGVEDHNETKK---AYFLGYVVHKLLMCSLGRIGE 427

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ GN+R+   G +L + +R+   ++ + +K   +    +         I ++ + +
Sbjct: 428  DDRDHYGNKRLDLAGPLLGSLFRILFKKLTKDVKTYLQKCVDNGKDFNLTLAIRSRTITN 487

Query: 512  AVCEFFCSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
             +     +             +SQ+   +   S ++H RRL+      + R     + R 
Sbjct: 488  GLRYSLATGNWGMQKTASKAGVSQVLNRLTYASSLSHLRRLNT----PLGREGKQAQPRQ 543

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G ICPAET EG  +GLV +L   A ++  G  + P  +  +   T ++      
Sbjct: 544  LHNTHWGMICPAETPEGQAVGLVKNLALMAYIS-VGSPQAPILEFLEEWATENL------ 596

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            EE    I   ++ +  +G++       R   E +   R     +D   +  V        
Sbjct: 597  EEIKPQIIPHSTKIFVNGNWVG---VHREPNELVRTLRSLRRCVDIDAEVSVIRDLMNRE 653

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                 D+ RV     +  +   LL+ E                             ++  
Sbjct: 654  LRIYTDAGRVCRPLFIVEENQLLLQKEQVV---------------------KLQNHKITN 692

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             R      +G ++   +  +   ++  +  +            VG   ++       PS 
Sbjct: 693  YRWHNLLTDGVVELIDTEEEEVCMIAMEPKD------------VGLGTQQYTHCEIHPSM 740

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N       S R   +       +  +    R        
Sbjct: 741  ILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYCSNFRARM----- 782

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  V        +    +       +      +  I    
Sbjct: 783  ------------------DTMANVLNYPQKPLVTTRAMEFLHFRELPSGINAIVGIASYT 824

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +     +  +   +  +S         L++  ++ E+   D 
Sbjct: 825  GYNQEDSLIMNQSAIDRGLFRSTFYRCYVDQERNKSPHGGSAATALVSNCEEFEKPSRDN 884

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +  R        + +         T +S + I     S         E         K 
Sbjct: 885  CLGLRHGS----YHKLDADGLVAPGTRVSGNDIIIGKTSPL----PVSEDSSLEQRHQKR 936

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               TS    E+   + +      D       +  KV     R  Q GDK A RHG KG +
Sbjct: 937  DASTSLRSHENGIIDSVMLTTNAD-----GFKFTKVRFRNIRIPQIGDKFASRHGQKGTI 991

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM VG + E  LG      G +         
Sbjct: 992  GMTYRQEDMPFTLEGITPDIIVNPHAIPSRMTVGHLIECLLGKVSSQTGDEGD------- 1044

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     +AI 
Sbjct: 1045 ----------------------------------------------ATP-FTDVTVQAIA 1057

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L        G  +LY G TG P    + +G  +  +L HMV DK+++RS G  +++T+
Sbjct: 1058 DTLHNLGYQRHGNEVLYSGHTGRPLTAQIFIGPTFYQRLKHMVDDKIHSRSRGPVTMLTR 1117

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RT 1326
            QP+ G++  GG R+GEME  C+ ++G+A  L + L   SD       D+ G       R 
Sbjct: 1118 QPMEGRAREGGLRMGEMERDCLISHGSANFLMDRLFANSDAYRVHVCDICGIIAIANLRK 1177

Query: 1327 RVYE--SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
              +E  +        +   P S  +L +E+ ++ ++  L      N        
Sbjct: 1178 MTFECRNCRNKTQISQLHIPYSCKLLFQELMSMSIAPRLFTLGNPNLGVRHSSD 1231



 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 137/1016 (13%), Positives = 286/1016 (28%), Gaps = 217/1016 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS-GA--------AMLEFVSY 79
           L+  Q  S+D F+   +      +  ++     + P   ++ G          +++F   
Sbjct: 73  LVRQQLDSFDEFIQNTMQELVDDSRHIR-----INPEAQYTPGQAKAATDTIYVIQFGQI 127

Query: 80  EFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK--------S 121
               P               +   R+LTY+ PL + +    F  +     K         
Sbjct: 128 YLSKPTMTEADGSTSVMFPHEARLRNLTYSAPLYVDVVCQKFQANATGPTKIEEMEPYDQ 187

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL 157
           ++  KE   ++G +P+M +                         G F+I G ++++++Q 
Sbjct: 188 VETPKE---FIGMVPIMLRSQYCVLTHKTDKELTELNECVYDQGGYFLINGSEKVLIAQE 244

Query: 158 -----H----RSPGI--------------------------HFDHDKGRASLSGKLLYAC 182
                H    R  G+                           +    G++++SG  + A 
Sbjct: 245 RMSNNHVYCFRKSGVSKYSWVCETRSHVEHGVRPTSTMYVQMYQRSGGKSAISGNQIRA- 303

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP                ++R D    +PV     ALG  ++ EIL          + 
Sbjct: 304 -VIP----------------YIRQD----IPVVIIFRALGFVADREILEHICYDFTDVEL 342

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG----LLKSLKEKGVKFLG 297
            + +   L  A ++   +V+   +        +    ++         + L   GV+   
Sbjct: 343 MERFKPSLEEAFVIQEQEVALDFIGRRGSAINVGKADRIRYAQDILQKEMLPHVGVEDHN 402

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNA 356
            T       YV   ++    G I  +  D    K L+           IL+   + +   
Sbjct: 403 ETKKAYFLGYVVHKLLMCSLGRIGEDDRDHYGNKRLDLAGPLLGSLFRILFKKLTKDVKT 462

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           Y++  +   K+ +   A+             T  +  S+    +        + V +V  
Sbjct: 463 YLQKCVDNGKDFNLTLAIR--------SRTITNGLRYSLATGNWGMQKTASKAGVSQVLN 514

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
            +          R                L N    +         +      ++KN   
Sbjct: 515 RLTYASSLSHLRRLNTPLGREGKQAQPRQLHNTHWGMICPAETPEGQAVG---LVKNLAL 571

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +  + +       +  ++  +    + I  + +  +   F   + +    E    +  + 
Sbjct: 572 MAYISVGSPQAPILEFLEEWATENLEEIKPQIIPHSTKIFVNGNWVGVHREPNELVRTLR 631

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             RR   +                ++        P    E + + L        +V    
Sbjct: 632 SLRRCVDIDAEVSVIRDLMNRELRIYTDAGRVCRPLFIVEENQLLLQKE-----QVVKLQ 686

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             +    +  +      V  +   EEE   IA     +                      
Sbjct: 687 NHKITNYRWHNLLTDGVVELIDTEEEEVCMIAMEPKDVGLGTQ----------------- 729

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              +    +  P  ++ I AS+IPF +++ S R      M +QA+ +  +          
Sbjct: 730 ---QYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYCS---------N 777

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                 + A ++      +    A+  +          +  G+  Y          +  +
Sbjct: 778 FRARMDTMANVLNYPQKPLVTTRAMEFLHFRELPSGINAIVGIASYTGY---NQEDSLIM 834

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ  + +               ST         +      P  G      +   E     
Sbjct: 835 NQSAIDR-----------GLFRSTFYRCY---VDQERNKSPHGGSAATALVSNCE----- 875

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                    EFE  +RD  LG          +       +D  G++  G  V+  DI++G
Sbjct: 876 ---------EFEKPSRDNCLG----------LRHGSYHKLDADGLVAPGTRVSGNDIIIG 916

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K +P   S  +  E         +    RD S  + S  +G +  V +       K
Sbjct: 917 KTSPLPVSEDSSLE---------QRHQKRDASTSLRSHENGIIDSVMLTTNADGFK 963


>gi|6324725|ref|NP_014794.1| Rpb2p [Saccharomyces cerevisiae S288c]
 gi|2507349|sp|P08518|RPB2_YEAST RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; AltName: Full=B150; AltName:
            Full=DNA-directed RNA polymerase II 140 kDa polypeptide
 gi|14278325|pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 gi|14278336|pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 gi|14278366|pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
 gi|20150714|pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
            The Inhibitor Alpha Amanitin
 gi|30749617|pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
 gi|30749738|pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
 gi|34810554|pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
 gi|46015416|pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
 gi|46015781|pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
 gi|56965912|pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
            Matched Nucleotide
 gi|56965924|pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
            Mismatched Nucleotide
 gi|56966108|pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
 gi|56966122|pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
 gi|56966132|pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 gi|56966142|pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
 gi|56966152|pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
 gi|58177165|pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 gi|61679445|pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
 gi|61679462|pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With Substrate
            Analogue Gmpcpp
 gi|61679503|pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-Tfiis Complex
 gi|61679516|pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 gi|83754244|pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 gi|110590855|pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
 gi|122920062|pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 gi|122920077|pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
            Dgtp
 gi|122920092|pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
            Gmpcpp
 gi|122921031|pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
            2'dutp
 gi|122921067|pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
            Gmpcpp
 gi|122921083|pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
            Dutp
 gi|122921098|pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 gi|122921110|pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
            112006
 gi|134104675|pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
 gi|134104690|pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
 gi|134104711|pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
 gi|134104723|pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
 gi|134104735|pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
 gi|146387185|pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
 gi|160877774|pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
            Complex
 gi|161172228|pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
            Scaffold
 gi|161172241|pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
            Delta Virus-Derived Rna Stem Loop
 gi|190613463|pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
            Elongation Complex
 gi|194368735|pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
            With The Inhibitor Alpha-Amanitin
 gi|224983591|pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 gi|239781917|pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 gi|239781930|pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 gi|239781943|pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 gi|239781956|pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
            Mismatch
 gi|239781969|pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 gi|239781983|pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 gi|239781996|pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 gi|239782009|pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
 gi|240104512|pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
            Active Site
 gi|254839442|pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
            Mismatch
 gi|254839457|pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
            Mismatch
 gi|254839472|pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
 gi|254839487|pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
            Mismatch And A Frayed Rna 3'-Uridine
 gi|254839502|pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
 gi|254839517|pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
 gi|254839532|pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
            Mismatch And A Frayed Rna 3'-Guanine
 gi|257471947|pdb|3I4M|B Chain B, 8-Oxoguanine Containing Rna Polymerase Ii Elongation Complex
            D
 gi|257471962|pdb|3I4N|B Chain B, 8-Oxoguanine Containing Rna Polymerase Ii Elongation Complex
            E
 gi|266618766|pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
 gi|269914553|pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 gi|295982476|pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
 gi|295982489|pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
 gi|325053964|pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
 gi|325053979|pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
 gi|326634539|pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
            Subunit
 gi|1293711|gb|AAC49637.1| Rpb2p polymerase [Saccharomyces cerevisiae]
 gi|1420379|emb|CAA99357.1| RPB2 [Saccharomyces cerevisiae]
 gi|151945769|gb|EDN64010.1| RNA polymerase B [Saccharomyces cerevisiae YJM789]
 gi|256272775|gb|EEU07746.1| Rpb2p [Saccharomyces cerevisiae JAY291]
 gi|259149634|emb|CAY86438.1| Rpb2p [Saccharomyces cerevisiae EC1118]
 gi|285815031|tpg|DAA10924.1| TPA: Rpb2p [Saccharomyces cerevisiae S288c]
          Length = 1224

 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 175/980 (17%), Positives = 317/980 (32%), Gaps = 171/980 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ + I    +
Sbjct: 374  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQ 433

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             +  +      +  INAK + S +     +               +SQ+       S ++
Sbjct: 434  RTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 493

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++   
Sbjct: 494  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT 549

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGE 652
                    + +  +     Y+   +  +      N              E L   R  G+
Sbjct: 550  DPMPIITFLSEWGMEPLEDYV-PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 608

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP--LLKAEAPF 710
                     D  +   K          P    +D   +       R+     L+  E   
Sbjct: 609  INPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQD 668

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRLMKF 767
            +  G E V   +  + +     G+VE +DA       I     DL+P+ +  +    +  
Sbjct: 669  IEGGFEDVEEYTWSSLL---NEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDP 725

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             +            ++V             PS  LG  A       + +P+  +N     
Sbjct: 726  AK-----------RIRVSHHATTFTHCEIHPSMILGVAA-------SIIPFPDHNQSPRN 767

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
                 M  + +   + +  + V                               +  +   
Sbjct: 768  TYQSAMGKQAMG--VFLTNYNVRM---------------------------DTMANILYY 798

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                      +       +   +  + AI      +  D+ +   S +   +    +F R
Sbjct: 799  PQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFR 857

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +D+ ++      E  E   R           +       I  G           K+T 
Sbjct: 858  SYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP 917

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +S D      R+ +         ++     +  Q                          
Sbjct: 918  ISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQ--------------------VLVTTN 957

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
               L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +
Sbjct: 958  QDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI 1017

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V  + E  L       G +                                    
Sbjct: 1018 PSRMTVAHLIECLLSKVAALSGNEGD---------------------------------- 1043

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                               ++P F     E I+ +LR       G  ++Y+G TG+    
Sbjct: 1044 -------------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMA 1083

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+GA
Sbjct: 1084 QIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGA 1143

Query: 1308 AYVLQEMLTIKSD----DVVGRTRVYESIVA----------GND---TFETGTPESFNVL 1350
            A  L+E L   SD     + G   +   I             ++    ++   P +  +L
Sbjct: 1144 ASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL 1203

Query: 1351 VKEMQALGLSIDLENSRTKN 1370
             +E+ A+ ++  L   R+++
Sbjct: 1204 FQELMAMNITPRLYTDRSRD 1223



 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 131/1004 (13%), Positives = 290/1004 (28%), Gaps = 164/1004 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL--QAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   +      +  L  +   +        S    + F       P  
Sbjct: 43  LVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 102

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS------- 129
           +            +   R+LTY+  L + ++   ++  +  G +   ++  +        
Sbjct: 103 NESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSES 162

Query: 130 --IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGI 163
             +++G LP+M +                         G F+I G ++++++Q  RS G 
Sbjct: 163 GKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE-RSAGN 221

Query: 164 HFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR---IDRRRK------- 211
                  + +    + +   I    ++G         K  ++ R     R  K       
Sbjct: 222 I--VQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK--LYGREGSSARTIKATLPYIK 277

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG+  + EIL      +   Q  +     +    ++   + +   +   
Sbjct: 278 QDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRR 337

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                I+  K++       L+++ +  +                +      + + A D  
Sbjct: 338 GTALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCALDRK 393

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           D+   +      +    P+L          +   +     +  ++A     ++       
Sbjct: 394 DQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTI 453

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   S  G  ++  R    +      R          +     
Sbjct: 454 TSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQ 513

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   +  + +       I+ +    + P +   
Sbjct: 514 LHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYV 570

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                 A   F               +  +   RR   +            +   +    
Sbjct: 571 PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDA 630

Query: 566 YGRICPAETSEG------HNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-----VTNDV 614
                P    E         + +     +      Y  IE  +  V +           V
Sbjct: 631 GRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLV 690

Query: 615 VYLSAMEEENRYIAQANSSL-DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            Y+ A EEE+  IA     L   + +   +L         +          +  P  ++ 
Sbjct: 691 EYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILG 750

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AAS+IPF +++ S R      M +QA+ +                              
Sbjct: 751 VAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV----------------------- 787

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + +  Y       +     +  R              
Sbjct: 788 ------------------RMDTMANILYYPQKPLGTTRAMEYLKFR-------------- 815

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDSM++++  +   +F S+    +    + 
Sbjct: 816 ----------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKK 865

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   +       +D+ G+I  G  V+  D+++GK TP      +P
Sbjct: 866 YGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPI-----SP 920

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +E+ L       +   RD S  + S  +G V  V +       K
Sbjct: 921 DEEELGQRTAYHSK--RDASTPLRSTENGIVDQVLVTTNQDGLK 962


>gi|301101902|ref|XP_002900039.1| DNA-directed RNA polymerase II 135 kDa polypeptide [Phytophthora
            infestans T30-4]
 gi|262102614|gb|EEY60666.1| DNA-directed RNA polymerase II 135 kDa polypeptide [Phytophthora
            infestans T30-4]
          Length = 1202

 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 197/1121 (17%), Positives = 364/1121 (32%), Gaps = 203/1121 (18%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G + TS +   + +KG     IT + +    +     +     I+   G V D + L
Sbjct: 244  VEHGVRPTSTMYVQMYQKGGGKSAITGNQIR-AVIPYIRQDIPVVIIFRALGFVADREIL 302

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E I +         + D+     +  +       ++++ AL  I R              
Sbjct: 303  EHICYD--------FSDAELMERFKSSLEEAFVIQEQEVALDFIGRR------------G 342

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            S  N    D  +Y    + +  +      D  +  +      +  ++  L+    G+   
Sbjct: 343  SAINVSKADRIRYAQDILQKEMLPHVGVEDHNETKK---AYFLGYVVHKLLMCSLGRIGE 399

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ GN+R+   G +L   +R+   ++ + +K   +    +         I ++ + +
Sbjct: 400  DDRDHYGNKRLDLAGPLLGGLFRILFKKLTKDVKSFLQKCVDNGKDFNLTLAIRSRTITN 459

Query: 512  AVCEFFCSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
             +     +             +SQ+   +   S ++H RRL+      + R     + R 
Sbjct: 460  GLRYSLATGNWGMQKSASKAGVSQVLNRLTYASSLSHLRRLNT----PLGREGKQAQPRQ 515

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G ICPAET EG  +GLV +L   A ++  G  + P  +  +   T ++      
Sbjct: 516  LHNTHWGMICPAETPEGQAVGLVKNLALMAYIS-VGSPQAPILEFLEEWATENL------ 568

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            EE    I   ++ +  +G++       R   E I   R     +D   +  V        
Sbjct: 569  EEIKPQIIPHSTKIFVNGNWVG---VHREPNELIRTLRSLRRCVDIDAEVSVIRDLMNKE 625

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                 D+ RV     +      LL+ E                             ++  
Sbjct: 626  LRIYTDAGRVCRPLFIVEDNQLLLQKEQVV---------------------KLQNHKITN 664

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             R      +G ++   +  +   ++  +  +            VG   + +      PS 
Sbjct: 665  YRWHNLLTDGVVELIDTEEEEVCMIAMEPKD------------VGTGSQIHTHCEIHPSM 712

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N       S R   +       +  +    R        
Sbjct: 713  ILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYCSNFRARM----- 754

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  V        +    +       +      +  I    
Sbjct: 755  ------------------DTMANVLNYPQKPLVTTRAMEYLHFRELPSGINAIVGIASYT 796

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +         +  +   +  +S           A  ++ E+   + 
Sbjct: 797  GYNQEDSLIMNQSAIDRGFFRSTFYRCYIDQERNKSPHGGPGGGAGGANCEEFEKPSREN 856

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +  R        + +         T +S + I     S       Q E         K 
Sbjct: 857  CLGLRHGS----YHKLDNDGLVAPGTRVSGNDIIIGKTSPL----PQSEDSSLEQRHQKR 908

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T+    E+   + +      D       +  KV     R  Q GDK A RHG KG +
Sbjct: 909  DASTALRSHENGIIDSVMLTTNAD-----GFKFTKVRFRNIRVPQIGDKFASRHGQKGTI 963

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DIV+NP  +PSRM VG + E  LG      G +         
Sbjct: 964  GMTYRQEDMPFTVEGITPDIVVNPHAIPSRMTVGHLVECLLGKVSSQTGDEGD------- 1016

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     +AI 
Sbjct: 1017 ----------------------------------------------ATP-FTDVTVQAIA 1029

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L      + G  ++Y G TG      + +G  +  +L HMV DK+++RS G  +++T+
Sbjct: 1030 DTLHNLGYQKHGNEVMYSGHTGRRLTAQIFIGPTFYQRLKHMVDDKIHSRSRGPVTMLTR 1089

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RT 1326
            QP+ G++  GG R+GEME  C+ ++G+A  L + L   SD       D+ G       R 
Sbjct: 1090 QPMEGRAREGGLRMGEMERDCLISHGSANFLMDRLFANSDAYRVHVCDICGIIAIANLRK 1149

Query: 1327 RVYESIV--AGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
              +E           +   P S  +L +E+ A+ ++  L  
Sbjct: 1150 MTFECRTCRNKTQISQVHIPYSCKLLFQELMAMSIAPRLFT 1190



 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 135/1030 (13%), Positives = 281/1030 (27%), Gaps = 245/1030 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP---------ITAFSGAAMLEFVSY 79
           L+  Q  S+D F+   +      +  ++     + P          T       + F   
Sbjct: 45  LVRQQLDSFDEFIQNTMQELVDDSRSIR-----INPEAQYAPGQAKTNTDTIYNISFGQI 99

Query: 80  EFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK--------S 121
               P               +   R+LTY+ PL + +    +       A          
Sbjct: 100 YLSKPTMTEADGSTSVMFPHEARLRNLTYSAPLYVDVVCQKYQAPSSGPANLEDMEPYDQ 159

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL 157
           ++  KE   ++G +P+M +                         G F+I G ++++++Q 
Sbjct: 160 VETPKE---FIGMVPIMLRSQYCVLTHKTDKELTELNECVYDQGGYFIINGSEKVLIAQE 216

Query: 158 HRSPG-IH----------------------------------FDHDKGRASLSGKLLYAC 182
             S   ++                                  +    G+++++G  + A 
Sbjct: 217 RMSNNHVYCFRKNAASKYSWVCETRSHVEHGVRPTSTMYVQMYQKGGGKSAITGNQIRA- 275

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
            +IP                ++R D    +PV     ALG  ++ EIL         ++ 
Sbjct: 276 -VIP----------------YIRQD----IPVVIIFRALGFVADREILEHICYDFSDAEL 314

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG----LLKSLKEKGVKFLG 297
            + +   L  A ++   +V+   +        +    ++         + L   GV+   
Sbjct: 315 MERFKSSLEEAFVIQEQEVALDFIGRRGSAINVSKADRIRYAQDILQKEMLPHVGVEDHN 374

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
            T       YV   ++    G I  +  D    K L+           IL+     +   
Sbjct: 375 ETKKAYFLGYVVHKLLMCSLGRIGEDDRDHYGNKRLDLAGPLLGGLFRILFKKLTKDVKS 434

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                  D  KD    L    R +  G      +  S+    +        + V +V   
Sbjct: 435 FLQKC-VDNGKDFNLTLAIRSRTITNG------LRYSLATGNWGMQKSASKAGVSQVLNR 487

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
           +          R                L N    +         +      ++KN   +
Sbjct: 488 LTYASSLSHLRRLNTPLGREGKQAQPRQLHNTHWGMICPAETPEGQAVG---LVKNLALM 544

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             + +       +  ++  +    + I  + +  +   F   + +    E    +  +  
Sbjct: 545 AYISVGSPQAPILEFLEEWATENLEEIKPQIIPHSTKIFVNGNWVGVHREPNELIRTLRS 604

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR   +            +   ++        P    E + + L        +V     
Sbjct: 605 LRRCVDIDAEVSVIRDLMNKELRIYTDAGRVCRPLFIVEDNQLLLQKE-----QVVKLQN 659

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +    +  +      V  +   EEE   IA     +                       
Sbjct: 660 HKITNYRWHNLLTDGVVELIDTEEEEVCMIAMEPKDVG--------------------TG 699

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            +     +  P  ++ I AS+IPF +++ S R      M +QA+ +  +           
Sbjct: 700 SQIHTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYCSNFR-------- 751

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                                + + V  Y       +     ++
Sbjct: 752 ---------------------------------ARMDTMANVLNYPQKPLVTTRAMEYLH 778

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            R                        +L  G N +V    + GYN EDS+++++  +   
Sbjct: 779 FR------------------------ELPSGINAIVGIASYTGYNQEDSLIMNQSAIDRG 814

Query: 838 VFTSIHIEEFEVMARDTK-----------LGPEEITRD----IPNVSEEGLKNIDECGII 882
            F S     +    R+                EE  +        +       +D  G++
Sbjct: 815 FFRSTFYRCYIDQERNKSPHGGPGGGAGGANCEEFEKPSRENCLGLRHGSYHKLDNDGLV 874

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             G  V+  DI++GK +P  +S  +  E         +    RD S  + S  +G +  V
Sbjct: 875 APGTRVSGNDIIIGKTSPLPQSEDSSLE---------QRHQKRDASTALRSHENGIIDSV 925

Query: 943 RIFNRHGIDK 952
            +       K
Sbjct: 926 MLTTNADGFK 935


>gi|190694877|gb|ACE88983.1| RNA polymerase subunit beta [Rhodopseudomonas julia]
          Length = 393

 Score =  407 bits (1045), Expect = e-111,   Method: Composition-based stats.
 Identities = 241/394 (61%), Positives = 301/394 (76%), Gaps = 1/394 (0%)

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTS 216
           +HRSPG+ FDHDKG+   SGKLL+A RIIP +G W+DIEFD++D++H RIDRRRK+PVTS
Sbjct: 1   MHRSPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDIEFDAEDVVHARIDRRRKIPVTS 60

Query: 217 FLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
            LMALGMD EEILSTFY     ++  + W  P     L  G K S   VD  +GE V+E+
Sbjct: 61  LLMALGMDGEEILSTFYDIGTATRGDNGWIVPFDPEKL-RGTKASEDYVDAASGEVVVEA 119

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           GKK+T+ L + L EKGVK L ++ + + G Y+ EDIVN ETGEIY EAGD I EK L+++
Sbjct: 120 GKKITARLARQLVEKGVKSLMVSDEQVLGRYLGEDIVNFETGEIYAEAGDEISEKMLDQL 179

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                 ++ +L +D VN  AY+RNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF
Sbjct: 180 RELNRDELALLEIDHVNVGAYMRNTLAADKNESREDALFDIYRVMRPGEPPTIETAEAMF 239

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
             LFFD ++YDLS VGRVKMNMRL+L T D +R +RKEDI+A+I++L+DLR+G+G IDDI
Sbjct: 240 QSLFFDPERYDLSAVGRVKMNMRLDLQTEDTMRVLRKEDILAVIRMLLDLRDGRGEIDDI 299

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           DNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EF
Sbjct: 300 DNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREF 359

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           F SSQLSQ  +  N LS ITH RRLSALG GG+ 
Sbjct: 360 FGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLT 393


>gi|28202149|ref|NP_777390.1| RNA polymerase beta subunit [Anthoceros formosae]
 gi|41017708|sp|Q85BW1|RPOB_ANTFO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|27807851|dbj|BAC55326.1| RNA polymerase beta subunit [Anthoceros formosae]
 gi|27807944|dbj|BAC55416.1| RNA polymerase beta subunit [Anthoceros formosae]
          Length = 1071

 Score =  407 bits (1045), Expect = e-110,   Method: Composition-based stats.
 Identities = 179/584 (30%), Positives = 254/584 (43%), Gaps = 63/584 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +        G   E    +    V   V T      +    R T L  E
Sbjct: 545  MGFNMQRQAVPLSKPEKCIVGTGLESQTALDSGSVI--VATEGGRISYTDGRRITLLTKE 602

Query: 860  EI--TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            +   T+ +          I E   I +   V  G IL       G   +   + +L A  
Sbjct: 603  KEVETKLVIYQRSNNSTCIHEKPRIQLREYVKKGQILADGRATAG-GELALGKNILVAYM 661

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  L     +   +       R+ I+    S   ER   E+   D +     
Sbjct: 662  PWEGYNFEDAILISERLIHEDIYTSIHIERYEIEARVTSQGPERITREIPHLD-NYLLRH 720

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ--FAVQDEKVQRNV 1035
            LD +       +L G    +G     K T   ++     P  +  Q  F +Q    +   
Sbjct: 721  LDES-----GLVLPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVVTAKETC 775

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              + +        ++  ++ K                +V V++  KR IQ GDK+AGRHG
Sbjct: 776  LKVPLGGRGRVIDIKWIYQEK---------TSTTYAEIVHVYILQKREIQVGDKVAGRHG 826

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+S+ILP +DMP+L+DGTPVD+VL+PLGVPSRMNVGQIFE  LG A   L K  +  
Sbjct: 827  NKGIISKILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQIFECLLGLAGDFLQKHYRVT 886

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D +   + S    F E    +           D+                        
Sbjct: 887  PFDERYEREASRKLVFSELHEASRQTANPWLFESDN------------------------ 922

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                            G+S L DG TG+ F+ PVT+G  YMLKL H V DK++ARS+G Y
Sbjct: 923  ---------------PGKSGLLDGRTGDIFEEPVTIGKAYMLKLIHQVDDKIHARSSGPY 967

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            +LVTQQPL GKS RGGQR+GEMEVW ++ +GAAY L+EMLTIKSD +  R  V  +IV G
Sbjct: 968  ALVTQQPLRGKSRRGGQRVGEMEVWALEGFGAAYTLEEMLTIKSDHIQARFEVLRAIVTG 1027

Query: 1336 NDTFETGT-PESFNVLVKEMQALGLSID-LENSRTKNSAKMEEI 1377
                +  T PESF +LV+E+++L L++D +  S  +   K ++I
Sbjct: 1028 ELIPKPETAPESFRLLVRELRSLALNLDHIIVSEKELRIKFKDI 1071



 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 243/592 (41%), Positives = 373/592 (63%), Gaps = 13/592 (2%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           ++     +  +  +DA++++Y+ +   G    FS + S      F   + +L  +GR+ +
Sbjct: 208 MKRKTKKEHLQSTEDAIVELYKQIYCIGGDLNFSESISKELQKKFFQQRCELGKIGRLNL 267

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           N +LNLD P++   +  +D++A +  L+ +R G G  DDID+L NRRVRSV ++L++Q +
Sbjct: 268 NKKLNLDVPENENFLLPQDLLAAVDYLIKIRFGIGVPDDIDHLKNRRVRSVTDLLQDQLK 327

Query: 477 LGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           L L R+E SI++  R ++       P+ L+ + P+++   EFF S  LSQ  +  N L+ 
Sbjct: 328 LALNRLENSIRQAIRGANRREHLPTPKSLVTSTPLITTFKEFFGSHPLSQFLDQTNPLTE 387

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           + H RRLS+LG GG+ R  A  ++RD+HP+HYGRICP ETSEG N GLV+SL   A+V+ 
Sbjct: 388 VVHKRRLSSLGPGGLTRRTASFQVRDIHPSHYGRICPIETSEGMNAGLVASLAIHAKVDN 447

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           +G +E+P+ K+       D+ +LSA E+EN +IA  N       +  E++   R   E +
Sbjct: 448 WGSLESPFYKISGVSEEEDMTFLSAGEDENYHIATGNCLALNQTNQEEQVTPARYRQEFV 507

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                +I+     P Q  SI  SLIPFLE++D+NR LMG NMQRQAVPL K E   VGTG
Sbjct: 508 ATAWNQINLRSIFPLQYFSIGTSLIPFLEHNDANRALMGFNMQRQAVPLSKPEKCIVGTG 567

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +ES  A  SG+ IVA   G +   D  RI + + E +++         +L+ +QRSN +T
Sbjct: 568 LESQTALDSGSVIVATEGGRISYTDGRRITLLTKEKEVET--------KLVIYQRSNNST 619

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C++++P +++ + V++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER++
Sbjct: 620 CIHEKPRIQLREYVKKGQILADGRATAGGELALGKNILVAYMPWEGYNFEDAILISERLI 679

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TSIHIE +E+ AR T  GPE ITR+IP++    L+++DE G++  G+ V  GD+L
Sbjct: 680 HEDIYTSIHIERYEIEARVTSQGPERITREIPHLDNYLLRHLDESGLVLPGSWVETGDVL 739

Query: 895 VGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           VGK+TP+        PE KLL+AIFG + V  ++T L+VP G  G V+D++ 
Sbjct: 740 VGKLTPQETEESLRAPEGKLLQAIFGIQVVTAKETCLKVPLGGRGRVIDIKW 791



 Score =  206 bits (524), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 93/519 (17%), Positives = 186/519 (35%), Gaps = 43/519 (8%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           K  E+  +P+  E+Q   +  F+            GL         I         +  S
Sbjct: 5   KKIELFVLPEFTEIQFEGFHRFI----------KYGLVKELNDFPKIEDTDQEFEFQLFS 54

Query: 79  --YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
             Y+   P  +  D +++ +TY+  L +  +L           +    +K+Q +++G +P
Sbjct: 55  RQYQLAEPPIEERDAIYQSITYSSDLYVPAQLT---------ERKKGRVKKQIVFLGSIP 105

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LM   GTFV+ G+ R++++Q+ RSPGI+++ +  R   +G  +Y   II D G  + +E 
Sbjct: 106 LMNSQGTFVVNGVARVIINQILRSPGIYYNSELDR---NGIPIYTGTIISDWGRRLKLEI 162

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDFWCFPLSAADLM 255
           D K  I  RI ++RKV +   L+A+G+D EEIL +  YPK++              +   
Sbjct: 163 DGKTRIWARISKKRKVSILVLLLAMGLDIEEILGNVCYPKLLLGCMKRKTKKEHLQSTED 222

Query: 256 VGAKVSSSLVDIDTGEQVIES-GKKLTSGLLKSLKEKG-------VKFLGITSDCLCGLY 307
              ++   +  I       ES  K+L     +   E G        K L +         
Sbjct: 223 AIVELYKQIYCIGGDLNFSESISKELQKKFFQQRCELGKIGRLNLNKKLNLDVPENENFL 282

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN--NNAYIRNTLVTD 365
           + +D++      +      +     ++ + +  +R +  L  D +    N    +     
Sbjct: 283 LPQDLL-AAVDYLIKIRFGIGVPDDIDHLKNRRVRSVTDLLQDQLKLALNRLENSIRQAI 341

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           +  +R++ L     ++    + T    +  F            + +  V    RL+   P
Sbjct: 342 RGANRREHLPTPKSLVTSTPLIT--TFKEFFGSHPLSQFLDQTNPLTEVVHKRRLSSLGP 399

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
             +        +  I       +  G I  I+         V  +  +        +E  
Sbjct: 400 GGLTRRTASFQVRDIH-----PSHYGRICPIETSEGMNAGLVASLAIHAKVDNWGSLESP 454

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             +     + + +        +    A       +Q +Q
Sbjct: 455 FYKISGVSEEEDMTFLSAGEDENYHIATGNCLALNQTNQ 493


>gi|209395036|gb|ACI45323.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  406 bits (1044), Expect = e-110,   Method: Composition-based stats.
 Identities = 137/237 (57%), Positives = 168/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+FE HLGWA  G+G++I  ++   +     S LR FLEKV  T   T
Sbjct: 1    NPLGVPSRMNIGQVFEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNTRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAERKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|169844839|ref|XP_001829140.1| DNA-dependent RNA polymerase II second largest subunit [Coprinopsis
            cinerea okayama7#130]
 gi|116509880|gb|EAU92775.1| DNA-dependent RNA polymerase II second largest subunit [Coprinopsis
            cinerea okayama7#130]
          Length = 1222

 Score =  406 bits (1044), Expect = e-110,   Method: Composition-based stats.
 Identities = 187/1171 (15%), Positives = 362/1171 (30%), Gaps = 195/1171 (16%)

Query: 233  YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            Y    Y          ++   +        +         + E  +       K++ +  
Sbjct: 201  YDSGGYFIINGSEKVLIAQERMATNHVYVFAKAQPSPINFLAEI-RSAVERGGKTISQFQ 259

Query: 293  VKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            VK      +   G      +    V+     ++   G + D   LE I +       +  
Sbjct: 260  VKMFHRNQERSLGNVMKATIPYIKVDIPIWVVFRALGVISDRDILEHICYDMQDAQMLEM 319

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +    ++ ++         +DR+ AL  I        +                  +Y  
Sbjct: 320  LKPCIDDGFV--------IQDREVALDFIGNRGTTTGLP------------RDRRIRYAQ 359

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              + +  +      +  +  +         +I  L+     +  +DD D+ G +R+   G
Sbjct: 360  EILQKEMLPHISMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAG 416

Query: 469  EMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----- 521
             +L N +R+   ++ + +    +              +  + + + +     +       
Sbjct: 417  PLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLATGNWGDQK 476

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+       S ++H RR +      + R     + R +H TH+G +CPAE
Sbjct: 477  KSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAE 532

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L   A ++   +       + +  + +         EEN +     + 
Sbjct: 533  TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSTTPCTK 584

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +       R     +   ++     D SP+  V             D+ RV   
Sbjct: 585  VFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRP 641

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +      +L+ +        E+   +         ++GIVE +DA       +    +
Sbjct: 642  LFIVENQQLVLQKKHVRWLANSENDDGEE-WKWENLIKSGIVELLDAEEEETVMICMTPE 700

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                     R  +      +   +    +K G            PS  LG       +  
Sbjct: 701  DLE---VSRRQSEGMEIQDHEDYDPAARLKAGTHAHTWTHCEIHPSMILG-------ICA 750

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N                        ++       +G       I        
Sbjct: 751  SIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM------ 786

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 787  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNSIVAILCYSGYNQEDSVIVNQS 841

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D  ++S   + E+ E   R+          +       I  G 
Sbjct: 842  SIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGT 900

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
            N         K+  +  D      R++          ++     +  Q            
Sbjct: 901  NVTGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI--------- 951

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                              + VKV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 952  -----------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIAYRQEDMPFTA 1000

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +G + E  L      +G +                      
Sbjct: 1001 EGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD-------------------- 1040

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     E +++ LR       G 
Sbjct: 1041 ---------------------------------ATP-FTDLTVEGVSTFLRQRGYQSRGL 1066

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y G TG      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S  GG R
Sbjct: 1067 EVMYHGHTGRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLR 1126

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGNDTFETG---- 1342
             GEME  C+ ++G A  L+E L   SD       D+ G T +  + +    +FE      
Sbjct: 1127 FGEMERDCMISHGIAGFLKERLFDASDAYRLHVCDICGLTAI--ANLK-KQSFECRACKN 1183

Query: 1343 --------TPESFNVLVKEMQALGLSIDLEN 1365
                     P +  +L +E+Q++ ++  L  
Sbjct: 1184 KTACSQLYIPYAAKLLFQELQSMNIAARLYT 1214



 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 137/1005 (13%), Positives = 294/1005 (29%), Gaps = 194/1005 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA----FSG-------AAMLEFV 77
           L+  Q  S+D F+   +      N  L         I       +G          ++F 
Sbjct: 47  LVRQQLDSFDEFVQNTMQELVDENSDL---------ILDQADQHTGQAGDMTRRYEIKFG 97

Query: 78  SYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR---LIVFDVDEFTGAKSIKD 124
                 P               +   R+LTY+ PL I +R   L+  +     G  + + 
Sbjct: 98  QIYLSRPTVTEADGSVVPVFPQEARLRNLTYSAPLYIEMRKRVLVGREDPAVPGDITWEA 157

Query: 125 IKEQ------SIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
             E        I++G +P+M +                         G F+I G +++++
Sbjct: 158 EHEDTDGDAAKIWIGKVPIMLRSSFCILHELRDQDLYDLNECPYDSGGYFIINGSEKVLI 217

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK-----------DI 201
           +Q   +    +   K + S      +   I    ++G     +F  K           ++
Sbjct: 218 AQERMATNHVYVFAKAQPSPIN---FLAEIRSAVERGGKTISQFQVKMFHRNQERSLGNV 274

Query: 202 I-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +     ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++
Sbjct: 275 MKATIPYIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVI 330

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVA 309
              +V+   +        +   +++     + L+++ +  + +            G  + 
Sbjct: 331 QDREVALDFIGNRGTTTGLPRDRRIRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMIH 389

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNK 368
             ++        ++  D   +K L+           +L+   + +   Y++  + T K  
Sbjct: 390 RLLL-AALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEF 448

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           +   A+             T  +  S+    + D  K   S  G  ++  R    +    
Sbjct: 449 NLSLAV--------KHQTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSH 500

Query: 429 --RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             R          I     L N    +         +      ++KN   +  + +    
Sbjct: 501 LRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMACISVGSYS 557

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
              I  ++   +      NA         F     +    +  N +  I   RR   +  
Sbjct: 558 APVIEFLEEWGLE-SLEENAHSTTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISP 616

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                         ++        P    E   + L      +   +     E    K  
Sbjct: 617 EVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLVLQKKHVRWLANSENDDGEE--WKWE 674

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL------VPREK 660
           +   +  V  L A EEE   I      L+     +E +        +             
Sbjct: 675 NLIKSGIVELLDAEEEETVMICMTPEDLEVSRRQSEGMEIQDHEDYDPAARLKAGTHAHT 734

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 735 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI---------- 784

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 785 -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 812

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 813 -----------------------ELPAGQNSIVAILCYSGYNQEDSVIVNQSSIDRGLFR 849

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       I++ G+I  G  V   DI++
Sbjct: 850 SIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGTNVTGEDIII 909

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           GK  P         E+L +        DV        +G+   V+
Sbjct: 910 GKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 950


>gi|209395039|gb|ACI45325.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  406 bits (1044), Expect = e-110,   Method: Composition-based stats.
 Identities = 134/237 (56%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAERKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDVVGRT+VY SIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVVGRTKVYGSIVKGEHAIEAGMPESFNV 234


>gi|254567802|ref|XP_002491011.1| RNA polymerase II second largest subunit B150, part of central core
            [Pichia pastoris GS115]
 gi|238030808|emb|CAY68731.1| RNA polymerase II second largest subunit B150, part of central core
            [Pichia pastoris GS115]
 gi|328352458|emb|CCA38857.1| DNA-directed RNA polymerase III subunit C2 [Pichia pastoris CBS 7435]
          Length = 1227

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 161/987 (16%), Positives = 301/987 (30%), Gaps = 160/987 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   
Sbjct: 356  HITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFR 415

Query: 481  RMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ R I    +              + +  + S +     +               +SQ+
Sbjct: 416  KLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQV 475

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 476  LNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKN 531

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L+  + ++     E     + +      +      +         N            LV
Sbjct: 532  LSLLSGISIGSPSEPIINFLEEW-GMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLV 590

Query: 646  FCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                          ++    D  +   K    +     P    +D         ++    
Sbjct: 591  STMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKE 650

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV---EQVDAIRIVIRSVEGDLDPSTSG 758
             + K +  +    M     +                 E VD       ++   + P    
Sbjct: 651  HIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEE--TIMIAMTPEDLQ 708

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                   +   ++    +                     PS  LG  A       + +P+
Sbjct: 709  TRSLEQKEIDLNDTAKRIKPEMSTSSH---HTFTHCEIHPSMILGVAA-------SIIPF 758

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N          M  + +   + +  + V                             
Sbjct: 759  PDHNQSPRNTYQSAMGKQAMG--VFLTNYNVRM--------------------------- 789

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 790  DTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRG 849

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R                   I  G      
Sbjct: 850  LF-RSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGD 908

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T +  D      R+++         ++     +  Q                 
Sbjct: 909  DIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLL-------------- 954

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 955  ------TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVP 1008

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +                           
Sbjct: 1009 DLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGD------------------------- 1043

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     +A++++LR       G  ++Y+
Sbjct: 1044 ----------------------------ATP-FTDLTVDAVSNLLRDNGYQSRGFEVMYN 1074

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME
Sbjct: 1075 GHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEME 1134

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFET 1341
              C+ A+GAA  L+E L   SD        + G   V  ++              + ++ 
Sbjct: 1135 RDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQL 1194

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  L   R+
Sbjct: 1195 HIPYAAKLLFQELMAMNIAPRLYTERS 1221


>gi|68300804|gb|AAY89344.1| RNA polymerase II second largest subunit [Petunia x hybrida]
          Length = 1203

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 182/1058 (17%), Positives = 343/1058 (32%), Gaps = 187/1058 (17%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + +     +    ++       ++A +   + +    +       S   F      KY 
Sbjct: 301  DILAHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGFSRERRIKYA 357

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + R  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 358  KEILQREMLPHVGTREYCETKK---AYYFGYIIHRLLLCVLGRRPEDDRDHYGNKRLDLA 414

Query: 468  GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +         V  Q  I AK + S +     +      
Sbjct: 415  GPLLGGLFRMLFRKLTRDVRSYVQKCVDSGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 474

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 475  NAAGTRAGVSQVLNRLTFASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 530

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 531  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 583

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V    +L       D  R    
Sbjct: 584  IFVNGCWVGIHRNPDLLVRTLRQLRRQV---DVNTEVGVVRNINLKELRLYTDYGRCSRP 640

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   ++K +            ++ SG        G +E VD             +
Sbjct: 641  LFIVDKKKLIIKKKDILAL--QLRDSSEDSG-WHDLXAKGFIEYVDTEE----------E 687

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N +   +                    PS  LG       +  
Sbjct: 688  ETTMIAMTINDLTNSRLNPSEAYS-----------ETYTHCEIHPSLILG-------VCA 729

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 730  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 785

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 786  EHL-------------------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQS 820

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 821  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRENTMGMRHGSYDKLDDDGFAPPGT 879

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S                  D+   ++    +  + TS    E   
Sbjct: 880  RVSGDDVIIGKTTPISQ-----------------DDAQGQSARYTRKDHSTSLRHSETGI 922

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK+ +   R  Q GDK + RHG KG +      EDMP+  
Sbjct: 923  VDQVLLTTNADGL-----RFVKIRMRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWTM 977

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 978  EGITPDIIVNPHAIPSRMTIGQLVECVMGKVAAHMGKEGD-------------------- 1017

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1018 ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1043

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1044 ERMYNGHTGRILTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1103

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV---VGRTRV--YESI------VAGN-D 1337
             GEME  C+ A+GAA+ L+E L  +SD     V    G   +   + I           D
Sbjct: 1104 FGEMERDCMIAHGAAHFLKERLFDQSDAYRIHVCQQCGLIAIANLKKISFECRSCKNKTD 1163

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
              +   P +  +L++E+ ++ ++  +     K S   +
Sbjct: 1164 IVQVYIPYACKLLIQELMSMAIAPRMLTKEVKPSNGKK 1201



 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 131/994 (13%), Positives = 281/994 (28%), Gaps = 205/994 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGA-AML 74
           L+  Q  S+D F+   +          Q        I               F      +
Sbjct: 52  LVRQQLDSFDEFIQNTM----------QEIVDETADIEIRPESQHNPARQSDFVDTIYKI 101

Query: 75  EFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +F       P     D             R+LTY+ PL + +R  V           + +
Sbjct: 102 KFTQIYLSRPMMTESDGETNTLFPKAARLRNLTYSSPLYVDVRKEVIKKGHDYE--EVSE 159

Query: 125 IKE-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
            +E   +++G +P+M +                         G F++ G ++++++Q   
Sbjct: 160 CQEFTKVFIGKVPIMLRSSYCSLYNLSEKDLTELGECPYDQGGYFIVNGSEKVLIAQEKM 219

Query: 160 SPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK------- 211
           S   ++      +     K  Y   +        + +  +   + VR+  R         
Sbjct: 220 SSNHVY----VFKKRQPNKYAYVAEVR----SIAEGQTKAPSTMFVRMLSRSNAKVGSSG 271

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        +P+     ALG  ++ +IL+        +Q  +     L  A ++  
Sbjct: 272 QYIKATLPYIKNEIPIIIVFRALGFVADKDILAHICYDFADTQMMELLRPSLEEAFVIQN 331

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSG----LLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
            +V+   +            +++         + L   G +    T       Y+   ++
Sbjct: 332 QQVALDYIGKRGSTVGFSRERRIKYAKEILQREMLPHVGTREYCETKKAYYFGYIIHRLL 391

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKD 372
               G    +  D    K L+           +L+   + +  +Y++  + + K+ + + 
Sbjct: 392 LCVLGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDSGKDVNLQF 451

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI- 431
           A+             T  +  S+    +  ++           +N      T   +R + 
Sbjct: 452 AI--------KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTFASTLSHLRRLN 503

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +  +    + 
Sbjct: 504 SPIGREGKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILE 560

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVA 550
            ++  S    + I+   +  +   F     +         +  +   RR   +  + GV 
Sbjct: 561 FLEEWSTENFEEISPAVIPQSTKIFVNGCWVGIHRNPDLLVRTLRQLRRQVDVNTEVGVV 620

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R     E+R ++  +     P    +   + +        ++              D   
Sbjct: 621 RNINLKELR-LYTDYGRCSRPLFIVDKKKLIIKKKDILALQLRDSSEDSG----WHDLXA 675

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + Y+   EEE   IA   + L        E               E     +  P  
Sbjct: 676 KGFIEYVDTEEEETTMIAMTINDLTNSRLNPSE------------AYSETYTHCEIHPSL 723

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ + AS+IPF +++ S R      M +QA+ +      F                    
Sbjct: 724 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF-------------------- 763

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R   +  V                                       Q+PLV        
Sbjct: 764 RMDTLAYV-----------------------------------LYYPQKPLV-------- 780

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                         L  G N +VA   + GYN EDS+++++  +    F S+    +   
Sbjct: 781 --TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE 838

Query: 851 ARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +      +E        +   +       +D+ G    G  V+  D+++GK TP  +  
Sbjct: 839 EKKMGTLVKEDFGRPDRENTMGMRHGSYDKLDDDGFAPPGTRVSGDDVIIGKTTPISQDD 898

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    A         +D S  +    +G V
Sbjct: 899 ---------AQGQSARYTRKDHSTSLRHSETGIV 923


>gi|209395072|gb|ACI45347.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 134/237 (56%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV  T   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVRTSELRKFLEKVYNTRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     G+P +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGMPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|68300799|gb|AAY89342.1| RNA polymerase II second largest subunit [Nicotiana sylvestris]
          Length = 1203

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 182/1066 (17%), Positives = 335/1066 (31%), Gaps = 203/1066 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + +     +    ++       ++A +   + +    +       S   F      KY 
Sbjct: 301  DILAHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGFTRERRIKYA 357

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + R  +      +  +  +         II  L+    G+   DD D+ GB+R+   
Sbjct: 358  KEILQREMLPHVGTREYCETKK---AYYFGYIIHRLLLCVLGRRPEDDRDHYGBKRLDLA 414

Query: 468  GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +         V  Q  I AK + S +     +      
Sbjct: 415  GPLLGGLFRMLFRKLTRDVRSYVQKCVDSGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 474

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 475  NAAGTRAGVSQVLNRLTFASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 530

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 531  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 583

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V    +L       D  R    
Sbjct: 584  IFVNGCWVGIHRNPDLLVRTLRQLRRQV---DVNTEVGVVRNINLKELRLYTDYGRCSRP 640

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   ++K +        E   ++ SG        G +E VD             +
Sbjct: 641  LFIVEKKKLIIKKKDIIALQMRE--SSEDSG-WHDLVAKGFIEYVDTEE----------E 687

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 688  ETTMIAMTINDLTNSRLNPEEAYS-----------ETYTHCEIHPSLILG-------VCA 729

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 730  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 785

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 786  EHL-------------------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQS 820

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 821  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRENTMGMRHGSYDKLDDDGFAPPGT 879

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S D     P                       +Y         R 
Sbjct: 880  RVSGDDVIIGKTTPISQDDAQGQP----------------------ARYTQKDHSTSLRH 917

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                   Q         LR VK+ +   R  Q GDK + RHG KG +      EDMP+  
Sbjct: 918  SETGIVDQVLLTTNADGLRFVKIRMRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWNI 977

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 978  EGITPDIIVNPHAIPSRMTIGQLVECIMGKVAAHMGKEGD-------------------- 1017

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1018 ---------------------------------ATP-FTDVTVDNISKALHRCGYQMRGF 1043

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1044 ERMYNGHTGRVLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1103

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------------------RTRVY 1329
             GEME  C+ A+GAA+ L+E L  +SD     V                      R +  
Sbjct: 1104 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCQQCGLIAIANLKKMSFECRSCRNKT- 1162

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
                   D  +   P +  +L++E+ ++ ++  +     K S+  +
Sbjct: 1163 -------DNVQVYIPYACKLLIQELMSMAIAPRMLTKEPKPSSGKK 1201



 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 136/994 (13%), Positives = 288/994 (28%), Gaps = 206/994 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGA-AML 74
           L+  Q  S+D F+   +          Q        I               F      +
Sbjct: 53  LVRQQLDSFDEFIQNTM----------QEIVDETANIEIRPESQHNPSRQPDFVETIYKI 102

Query: 75  EFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +F       P     D             R+LTY+ PL + ++  V          +   
Sbjct: 103 KFTQIYLSRPMMTESDGETNTLFPKAARLRNLTYSSPLYVDVKKEVIKKGHDYEEVTENQ 162

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + +++G +P+M +                         G F++ G ++++++Q   S
Sbjct: 163 EFTK-VFIGKVPIMLRSSYCSLYNLSEKDLTELGECPYDQGGYFIVNGSEKVLIAQEKMS 221

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-------- 211
              ++      +     K  Y   +        + +  +   + VR+  R          
Sbjct: 222 SNHVY----VFKKRQPNKYAYVAEVR----SIAEGQNKAPSSMFVRMLSRSNAKGASGQY 273

Query: 212 -----------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                      +P+     ALG  ++ +IL+        +Q  +     L  A ++   +
Sbjct: 274 IRATLPYIRAEIPIIVVFRALGFVADKDILAHICYDFADTQMMELLRPSLEEAFVIQNQQ 333

Query: 260 VSSSLVDID------TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           V+   +         T E+ I+  K++     + L   G +    T       Y+   ++
Sbjct: 334 VALDYIGKRGSTVGFTRERRIKYAKEILQR--EMLPHVGTREYCETKKAYYFGYIIHRLL 391

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKD 372
               G    +  D   +K L+           +L+   + +  +Y++  + + K+ + + 
Sbjct: 392 LCVLGRRPEDDRDHYGBKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDSGKDVNLQF 451

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI- 431
           A+             T  +  S+    +  ++           +N      T   +R + 
Sbjct: 452 AI--------KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTFASTLSHLRRLN 503

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +  +    + 
Sbjct: 504 SPIGREGKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILE 560

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVA 550
            ++  S    + I+   +  +   F     +         +  +   RR   +  + GV 
Sbjct: 561 FLEEWSTENFEEISPAVIPQSTKIFVNGCWVGIHRNPDLLVRTLRQLRRQVDVNTEVGVV 620

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R     E+R ++  +     P    E   + +        ++         +  V  G  
Sbjct: 621 RNINLKELR-LYTDYGRCSRPLFIVEKKKLIIKKKDIIALQMRESSEDSGWHDLVAKGF- 678

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + Y+   EEE   IA              +L   R   E      E     +  P  
Sbjct: 679 ---IEYVDTEEEETTMIAM----------TINDLTNSRLNPE--EAYSETYTHCEIHPSL 723

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ + AS+IPF +++ S R      M +QA+ +      F                    
Sbjct: 724 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF-------------------- 763

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R   +  V                                       Q+PLV        
Sbjct: 764 RMDTLAYV-----------------------------------LYYPQKPLV-------- 780

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                         L  G N +VA   + GYN EDS+++++  +    F S+    +   
Sbjct: 781 --TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE 838

Query: 851 ARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +      +E        +   +       +D+ G    G  V+  D+++GK TP  +  
Sbjct: 839 EKKMGTLVKEDFGRPDRENTMGMRHGSYDKLDDDGFAPPGTRVSGDDVIIGKTTPISQDD 898

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    A         +D S  +    +G V
Sbjct: 899 ---------AQGQPARYTQKDHSTSLRHSETGIV 923


>gi|229544483|gb|ACQ76421.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 136/237 (57%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV  T   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGVML---QQQVKASELRKFLEKVYNTRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAERKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFGRPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|228016687|gb|ACP51515.1| RNA polymerase beta subunit [Pinus aristata]
          Length = 1075

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 163/497 (32%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YMLKL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMLKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 231/640 (36%), Positives = 356/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELNNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|156598002|gb|ABU85267.1| RNA polymerase beta subunit [Cycas micronesica]
          Length = 1066

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 166/497 (33%), Positives = 234/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 622  VRRGEYVKKGQILADGAATVG-GELSLGKNILVAHMPWEGYNFEDAILISERLVYEDIYT 680

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+GI     S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 681  SFHIERYGIVTCMTSQGPERITKEIPHLDAHL-LRHLDGN-----GLVMLGSWVETGDVL 734

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   ++     P  +  Q     +        L+V       +++ R+ +K E   
Sbjct: 735  VGKLTPQPAEESLRAPEGRLLQAIFGIQVSTARESCLRVPIGRRGRVIDVRWIHKEE--N 792

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
            +GD+       VV V++  KR IQ GDK+AGRHGNKGI+S+ILP +DMP+L+DGT VD+V
Sbjct: 793  FGDNAE-----VVHVYILQKRKIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTSVDMV 847

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGV SRMNVGQIFE   G A   + +  +    D +   + S    F  ++ G    
Sbjct: 848  LNPLGVLSRMNVGQIFECLPGLAGNLMNRHYRITPFDERYEREASRKLVF-PELYGASER 906

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T                           VF+                +  G++ L DG T
Sbjct: 907  TANPW-----------------------VFE---------------PNHPGKNRLIDGRT 928

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT G  YM KL H V DK++ARS+G Y+LVTQQPL GKS RGGQR+GEMEVW 
Sbjct: 929  GDTFEQPVTTGKAYMPKLIHQVDDKIHARSSGPYALVTQQPLRGKSKRGGQRVGEMEVWA 988

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALG-- 1358
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G      GT PESF +LV+E+++L   
Sbjct: 989  LEGFGVAYILQEMLTLKSDHIGARHEVLGAIITGGPIPRPGTAPESFRLLVRELRSLAPK 1048

Query: 1359 LSIDLENSRTKNSAKME 1375
            L   +         + E
Sbjct: 1049 LDHAIIYENDFQIDRKE 1065



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 233/605 (38%), Positives = 356/605 (58%), Gaps = 15/605 (2%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
              I  +L+ +  + +K+A+ + Y+ +    GD+              F   + +L  +G
Sbjct: 200 YPKILLSLLKEYLRSKKNAISEFYKKLYCVSGDLVFSESLCKELRK-KFLQQRCELGKIG 258

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R   N +LNLD P++      +D++A +   + ++ G GT+DD+D+L NRR+RSV ++L+
Sbjct: 259 RRNPNQKLNLDIPENEIFSLPQDVLAAVDYSIRVKFGMGTLDDMDHLKNRRIRSVADLLQ 318

Query: 473 NQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           NQ+ L L R+E +++  I           P +L+ + P+ +   +FF S  LSQ  +  N
Sbjct: 319 NQFGLALGRLENAVRRTIRRATKRKCLPTPNNLVTSTPLTTTFQDFFGSHPLSQFLDQTN 378

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            L+ I H R+LS LG GG+    A   +RD+HP+HYGRICP ETSEG N GLV+SL   A
Sbjct: 379 PLTEIVHRRKLSYLGPGGLTGRTASSRIRDIHPSHYGRICPIETSEGMNAGLVASLAIRA 438

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R+   G +++P+ K+ +      +VYLS+ E+E   IA  NS     G   E++   R  
Sbjct: 439 RIGHCGSLQSPFHKISERSEEEHMVYLSSGEDEYYRIATGNSLALNQGIREEQVTPARYR 498

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E + +  E+I F    P Q  S+  SLIPFLE++D+NR LMG NMQRQAVPL + E   
Sbjct: 499 QEFLAIAWEQIHFRSIFPFQYFSVGVSLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCI 558

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SG+A +A + G +  +DA +I                    L+ +QRS
Sbjct: 559 VGTGLEGQAAPDSGSAAIATQGGRITYIDAGKIT--------SSVDGDTVGTELVTYQRS 610

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N NTC++Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA MPW GYNFED++LIS
Sbjct: 611 NNNTCMHQKPRVRRGEYVKKGQILADGAATVGGELSLGKNILVAHMPWEGYNFEDAILIS 670

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED++TS HIE + ++   T  GPE IT++IP++    L+++D  G++ +G+ V  
Sbjct: 671 ERLVYEDIYTSFHIERYGIVTCMTSQGPERITKEIPHLDAHLLRHLDGNGLVMLGSWVET 730

Query: 891 GDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           GD+LVGK+TP+        PE +LL+AIFG +    R++ LRVP G  G V+DVR  ++ 
Sbjct: 731 GDVLVGKLTPQPAEESLRAPEGRLLQAIFGIQVSTARESCLRVPIGRRGRVIDVRWIHKE 790

Query: 949 GIDKN 953
               +
Sbjct: 791 ENFGD 795



 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 137/317 (43%), Gaps = 30/317 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL    ++   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLIEELQNFPKIEDTDQEIESQLFGNKYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + +++ LTY+  L +  RLI          ++ + I++Q++ +G+LPLM   GT
Sbjct: 62  PLIKERNAVYQSLTYSSELYVPARLI---------QRNSRKIQKQTVLIGNLPLMNSQGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+ RSPGI++  +      SG  LY   II D G    +E D K  I 
Sbjct: 113 FVVNGISRIVVNQILRSPGIYYSSEPD---QSGITLYTSTIISDWGGRSKLEIDGKTRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAK--V 260
            R+ ++RK+ +   L A+G +  EIL    YPKI+ S   ++     +A          V
Sbjct: 170 ARVSKKRKISIPILLSAMGSNLGEILDNVCYPKILLSLLKEYLRSKKNAISEFYKKLYCV 229

Query: 261 SSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKF--LGITSDCLCGLYVAEDIVNGET 317
           S  LV  ++  +++ +   +    L K  +    +   L I  + +  L          +
Sbjct: 230 SGDLVFSESLCKELRKKFLQQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDYS 289

Query: 318 GEIYIEAGDVIDEKSLE 334
             +    G + D   L+
Sbjct: 290 IRVKFGMGTLDDMDHLK 306


>gi|302780123|ref|XP_002971836.1| hypothetical protein SELMODRAFT_148107 [Selaginella moellendorffii]
 gi|300160135|gb|EFJ26753.1| hypothetical protein SELMODRAFT_148107 [Selaginella moellendorffii]
          Length = 1178

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 182/1055 (17%), Positives = 335/1055 (31%), Gaps = 191/1055 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 275  DILEHICYDFSDTAMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 331

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 332  KDILQKEMLPHVGVGEYCETKK---AYFFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 388

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L + +R    ++ + ++   +    +   V     + AK + S +     +      
Sbjct: 389  GPLLGSLFRQLFRKLTKDVRAYLQKCVDNGKEVNLAYAVKAKTITSGLKYSLATGNWGQA 448

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RR   L        R   + R +H +H+G +CPAE
Sbjct: 449  NSGNARAGVSQVLNRLTYASTLSHLRR---LNSPIGREGRLLAKPRQLHNSHWGMMCPAE 505

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L   A +            + +    N        EE +  +    + 
Sbjct: 506  TPEGQACGLVKNLALMAYITVGSAANPILVFLEEWSTEN-------FEEISPAVIPNATK 558

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G++           + +   R ++   D + +  V     L       D  R    
Sbjct: 559  IFVNGAWVGIHREPEHLVKTLRQLRRQV---DVNTEVGVVRDIRLKELRLYTDYGRCSRP 615

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+                    A    +           +  I  V+ + +
Sbjct: 616  LFIVEKQRLLI--------------KKSDIRALQQKEAGENGWHELVSKGFIEYVDTEEE 661

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 662  ETTMISMTISDLVNARLNPEEAYS-----------DTYTHCEIHPSMILG-------VCG 703

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 704  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 736

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 737  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 794

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ +++ ++ +E+ E   R+          +          G 
Sbjct: 795  SIDRGFF-RSIFYRSYRDEEKKAGTLVKEEFERPNRETTTGMRHGSYDKLDDDGIAPPGT 853

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T L                 VQDE   +     K    T     E   
Sbjct: 854  RVSGEDVIIGKTTPL-----------------VQDETGTQAQRYSKRDQSTCLRHSESGM 896

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK  V   R  Q GDK + RHG KG +      EDMPF +
Sbjct: 897  IDQVLLTTNADGL-----RFVKTRVRSIRIPQIGDKFSSRHGQKGTIGMTYTQEDMPFTQ 951

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 952  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAALMGKEGD-------------------- 991

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L   +    G 
Sbjct: 992  ---------------------------------ATP-FTDVTVDNISKALHKCNYQLRGF 1017

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1018 ETMYNGHTGRRLSAMIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1077

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-----SIVA-GNDTFET------ 1341
             GEME  C+ A+GAA+ L+E L  +SD    R  V E     +I     +TFE       
Sbjct: 1078 FGEMERDCMIAHGAAHFLKERLFDQSD--AYRVHVCEHCGLIAIANLKKNTFECRSCKNK 1135

Query: 1342 ------GTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                    P +  +L +E+ A+ ++  +     K 
Sbjct: 1136 TEIVQVHIPYACKLLFQELMAMAIAPRMFMKEVKK 1170



 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 136/991 (13%), Positives = 284/991 (28%), Gaps = 198/991 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSG--AAM 73
           L+  Q  S+D F+   +          Q        I               +SG     
Sbjct: 25  LVRQQLDSFDEFIQNTM----------QEIVDESSEIEIKPESQHNPGRNNEYSGETTFK 74

Query: 74  LEFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           ++F       P     D             R+LTY+ PL   +   V    E     + +
Sbjct: 75  IKFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYADIIKYVTRKGEDGEEDTEQ 134

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
           + +   +++G +P+M +                         G F+I G ++++++Q   
Sbjct: 135 E-ELPKVFIGKVPIMLRSSYCTLYQNSDKDLTELGECPYDQGGYFIINGSEKVLIAQEKM 193

Query: 160 SPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR--------- 209
           S   ++      +     K  Y   +        + +      + VR+  R         
Sbjct: 194 STNHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPASSMFVRMLSRAGAKAGSSG 245

Query: 210 -----------RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                      +++P+     ALG  ++ +IL         +   +     L  A ++  
Sbjct: 246 QYIRATLPYIKQEIPIIVVFRALGFVADKDILEHICYDFSDTAMMELLRPSLEEAFVIQN 305

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +        +   K++       L+++ +  +G+   C          +    
Sbjct: 306 QQVALDYIGKRGSTVGVTREKRIKYAK-DILQKEMLPHVGVGEYCETKKAYFFGYIIH-- 362

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A     E   +   +  +    P+L          +   +     K   +    
Sbjct: 363 -RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGSLFRQLFRKLTKDVRAYLQKCVDNGKEV 421

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR--KE 434
                      T  +  S+    +  ++  +        +N      T   +R +     
Sbjct: 422 NLAYAVKAKTITSGLKYSLATGNWGQANSGNARAGVSQVLNRLTYASTLSHLRRLNSPIG 481

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
               ++     L N    +         +      ++KN   +  + +  +    +  ++
Sbjct: 482 REGRLLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMAYITVGSAANPILVFLE 538

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
             S    + I+   + +A   F   + +    E  + +  +   RR   +  + GV R  
Sbjct: 539 EWSTENFEEISPAVIPNATKIFVNGAWVGIHREPEHLVKTLRQLRRQVDVNTEVGVVRDI 598

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E+R ++  +     P    E   + +  S      + A    E       +      
Sbjct: 599 RLKELR-LYTDYGRCSRPLFIVEKQRLLIKKS-----DIRALQQKEAGENGWHELVSKGF 652

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E      +     +  P  ++ 
Sbjct: 653 IEYVDTEEEETTMISM----------TISDLVNARLNPE--EAYSDTYTHCEIHPSMILG 700

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +  S+IPF +++ S R      M +QA+ +                           R  
Sbjct: 701 VCGSIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMD 740

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  V                                       Q+PLV           
Sbjct: 741 TLAYV-----------------------------------LYYPQKPLV----------T 755

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N +VA   + GYN EDS+++++  +    F SI    +    + 
Sbjct: 756 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKK 815

Query: 854 TK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              L  EE  R        +       +D+ GI   G  V+  D+++GK TP  +     
Sbjct: 816 AGTLVKEEFERPNRETTTGMRHGSYDKLDDDGIAPPGTRVSGEDVIIGKTTPLVQDE--- 872

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                      +    RD S  +    SG +
Sbjct: 873 ------TGTQAQRYSKRDQSTCLRHSESGMI 897


>gi|228017376|gb|ACP52193.1| RNA polymerase beta subunit [Larix occidentalis]
          Length = 1076

 Score =  406 bits (1043), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 239/695 (34%), Positives = 377/695 (54%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIYYRLELDHNRINYIYTGTLISDWGRRSKLEIDVGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     +           DR++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPERFFFLLKKKKGKWDREEYLWSRENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + S   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKSTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A+++  G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIDHCGSLQSPFYKISERSREEHMVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  N      G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNYLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                  L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 T--------NITSSVNGDTVRTELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 122/298 (40%), Gaps = 25/298 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDKEIESRLFGNEYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + I 
Sbjct: 113 FVVNGIYRIVVNQILISPGIYYRLELDHNRIN--YIYTGTLISDWGRRSKLEIDVGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+ R+RK+ +   L A+G++ EEIL        +              + +      ++
Sbjct: 171 ARVSRKRKISIPVLLSAMGLNLEEILDNTRYPERFFFLLKKKKGKWDREEYLWSR--ENA 228

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           +++       +      +  L K L+EK  +               +  ++    EI+
Sbjct: 229 ILEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNQKLNLDIPENEIF 286


>gi|209395078|gb|ACI45351.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +       LR FL +V  +   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGQRIGDML---QQQAKAGELREFLHEVYNSRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D+ ++ +AE   + VP +TPVFDGA EE I  MLR+A                
Sbjct: 58   ENLAQLSDEELVAMAENLTNDVPYATPVFDGASEEEIKDMLRIAYPDDIARRKGLTPTRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGHMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|307683667|dbj|BAJ19812.1| RNA polymerase beta chain [Picea morrisonicola]
          Length = 1076

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 237/695 (34%), Positives = 377/695 (54%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+    +    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIYYRSELDHNRINYIYTGTLISDWGRRSKLEIDVGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     +           +R++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPEKFFFLLKKKKGRWEREEYIWSKEKAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIGQCGSLQSPFYKISERSREEHMVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFQPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +                      L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 V--------NITSSVNGDTVRTELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRTPIGGRGRVIDVRWINRVDDSGD 805



 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 73/341 (21%), Positives = 142/341 (41%), Gaps = 37/341 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDKEIESRLFGNEYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY   L +  R         +  ++   I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSLTYYSELYVPAR---------SIRRNSSKIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + I 
Sbjct: 113 FVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKI----------VYSQRGDFWCFPLSAA 252
            R+ R+RK+ +   L A+G++ EEIL  T YP+            + +    W    +  
Sbjct: 171 ARVSRKRKISIPVLLSAMGLNLEEILDNTRYPEKFFFLLKKKKGRWEREEYIWSKEKAIL 230

Query: 253 DLMVGAK-VSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
           +       VS  LV  ++  +++ E   +    L K  +    + L +         + +
Sbjct: 231 EFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNQKLNLDIPENEIFSLPQ 290

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 291 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 330


>gi|302507686|ref|XP_003015804.1| hypothetical protein ARB_06116 [Arthroderma benhamiae CBS 112371]
 gi|291179372|gb|EFE35159.1| hypothetical protein ARB_06116 [Arthroderma benhamiae CBS 112371]
          Length = 1205

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 184/1082 (17%), Positives = 352/1082 (32%), Gaps = 174/1082 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDI 1197

Query: 1323 VG 1324
             G
Sbjct: 1198 CG 1199



 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 144/1050 (13%), Positives = 300/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEPDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  + Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|257042527|gb|ACV32801.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  325 bits (833), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 209/630 (33%), Positives = 312/630 (49%), Gaps = 24/630 (3%)

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR--PGDVS 387
           E+ L+   + +     +   +      Y+           R+ A+L+ Y+ +    GD+ 
Sbjct: 193 EEILDNTHYPKRFXFLLKKKERWEREEYLW---------SREKAILEFYKKLYCVSGDLV 243

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
            FS +        F     +L  +GR  +N +LNLD P++                    
Sbjct: 244 -FSESXXXXXXXKFFXXXCELGKIGRRNLNQKLNLDIPENEIFSXXXXXXXXXXXXXXXX 302

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
                              V ++L+                                   
Sbjct: 303 XXXXXXXXXXXXXXXXXXXVADLLQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 362

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                  +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+HP++YG
Sbjct: 363 XXXXXXXDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIHPSYYG 422

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--MEEENR 625
           RICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL     E+E  
Sbjct: 423 RICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYLLPGEDEDEYY 482

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIPFLE++
Sbjct: 483 RIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIPFLEHN 542

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA+    
Sbjct: 543 DANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV---- 598

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                              + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L
Sbjct: 599 ----NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGEL 654

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           +LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+I
Sbjct: 655 SLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREI 714

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVD 923
           P++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +   
Sbjct: 715 PHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVST 774

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            R++ LR P G  G V+DVR  NR     +
Sbjct: 775 ARESCLRAPIGGKGRVIDVRWINRVDDSGD 804


>gi|237688456|ref|YP_002905075.1| RNA polymerase beta subunit [Picea sitchensis]
 gi|226875285|gb|ACO89024.1| RNA polymerase beta subunit [Picea sitchensis]
          Length = 1076

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNSMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 200/695 (28%), Positives = 311/695 (44%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+    +    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIYYRSELDHNRINYIYTGTLISDWGRRSKLEIDVGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTL-------VTDKNKDRKDALLDIYRVMR-- 382
           S+  +  +   ++  +  ++                            A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPEKIFFLLKKKKGRWERXXXXXXXXXAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++               
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSXXXXXXXXXXX 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
                                                                       
Sbjct: 299 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
                         F               + I H R+LS LG GG+    A    RD+H
Sbjct: 359 XXXXXXXXXXXXXXFXXXXXXXXXXXXXXXTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIGQCGSLQSPFYKISERSREEHMVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFQPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +                      L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 V--------NITSSVNGDTVRTELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRTPIGGRGRVIDVRWINRVDDSGD 805



 Score =  152 bits (383), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 48/153 (31%), Positives = 82/153 (53%), Gaps = 11/153 (7%)

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            YE   P     D +++ LTY   L +  R         +  ++   I++Q++++G++PL
Sbjct: 56  EYELAEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSSKIQKQTVFLGNIPL 106

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           M   GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D
Sbjct: 107 MNSHGTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEID 164

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILS 230
             + I  R+ R+RK+ +   L A+G++ EEIL 
Sbjct: 165 VGERIWARVSRKRKISIPVLLSAMGLNLEEILD 197


>gi|209395030|gb|ACI45319.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395120|gb|ACI45379.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 163/237 (68%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR F EKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVRTSELRKFPEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     G+P +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGMPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q  LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QVFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|215254201|gb|ACJ64105.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 403

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 257/403 (63%), Positives = 315/403 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +E
Sbjct: 61  NSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           L+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 LITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPT 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           LKA+ P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY 
Sbjct: 181 LKADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYN 240

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNF
Sbjct: 241 LTKYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNF 300

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           EDS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ 
Sbjct: 301 EDSILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVY 360

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D
Sbjct: 361 IGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKD 403


>gi|134079870|emb|CAK41002.1| unnamed protein product [Aspergillus niger]
          Length = 1256

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 181/1065 (16%), Positives = 350/1065 (32%), Gaps = 166/1065 (15%)

Query: 346  ILYVDSVNNNAYIRNT-LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +   D +N+  Y RN   + +  K   +    I       +V+   +A+   +    + +
Sbjct: 311  VSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDR----EVALDFIAKRGSSQSSMNHE 366

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +        ++     ++   +     +   +  ++  L+    G+  +DD D+ G +R+
Sbjct: 367  RRVRYAREIMQKEFLPHISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRL 426

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   R+ R ++   +        +     I A  +   +     +   
Sbjct: 427  DLAGPLLANLFRVLFTRVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNW 486

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 487  GEQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 542

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +            ++
Sbjct: 543  CPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFV 602

Query: 628  AQANSSLDEDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLEND 685
                  +  D +     ++  R             D  +   K          P F+ ++
Sbjct: 603  NGVWVGIHRDPAHLVNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDN 662

Query: 686  DSNRVLMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI- 743
            D      G  +  ++ +  L+ +             +         ++G+VE VDA    
Sbjct: 663  DPKSENCGSLVLNKEHIRKLEQDKDLPPDLDPEDRRERYFGWDGLVKSGVVEYVDAEEEE 722

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             I  V    D   S          +    +     R ++    +          PS  LG
Sbjct: 723  TIMIVMTPEDLEISKQLQAGYALPEEELHDPNKRVRSILS--QKAHTWTHCEIHPSMILG 780

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +                     E   
Sbjct: 781  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMA 823

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            +I    ++ L                        +       +   +  + AI      +
Sbjct: 824  NILYYPQKPLA-------------------TTRSMEFLRFRELPAGQNAIVAIACYSGYN 864

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R   D  +         +E   +    + + + +  Y
Sbjct: 865  QEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGL---TVVERFEKPMRSDTIGMRKGTY 920

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L E   I  G           K+  L+ +                +E  QR     K+
Sbjct: 921  DKLDEDGIIAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKL 965

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++      DD+     + VKV +   +  Q GDK A RHG KG +
Sbjct: 966  DVSTPLRSTENGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTI 1020

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF ++G   D+++NP  +PSRM +  + E  L       G +         
Sbjct: 1021 GITYRQEDMPFTREGVCPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------- 1073

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     ++I+
Sbjct: 1074 ----------------------------------------------ATP-FTDVTVDSIS 1086

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+
Sbjct: 1087 RLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTR 1146

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV 1333
            QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D  G       + 
Sbjct: 1147 QPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPVAKLK 1206

Query: 1334 AG----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G          +   +   P +  +L +E+ ++ ++  +  +R+
Sbjct: 1207 KGLFECRLCNNKHRISQVHIPYAAKLLFQELASMNIAARMFTNRS 1251



 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 149/1044 (14%), Positives = 301/1044 (28%), Gaps = 209/1044 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPSEDEVDPVV--VRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVF--------DVDEFTGAKSIK 123
             P               +   R+LTYA PL + +   +         D D+   A+S +
Sbjct: 95  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGVTKKIMEGRERLVADRDDDDMAESTE 154

Query: 124 D-------------------IKEQSIYMGDLPLMTKD----------------------- 141
           D                    KE+++++G +P+M K                        
Sbjct: 155 DKKAHGTYLQWEQKELPADQAKEETVFIGKMPIMLKSKYCILKDLSEQALYNWNECPYDS 214

Query: 142 -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
            G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   
Sbjct: 215 GGYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSL 271

Query: 199 KDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQR 241
           K  +  + D                 +  +P+     ALG +  E+IL+        +  
Sbjct: 272 K--LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPM 329

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-- 299
            +     +    ++   +V+   +      Q   + ++      + ++++ +  +  +  
Sbjct: 330 LEMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKEFLPHISQSEG 389

Query: 300 ----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                    G  V   ++    G   ++  D   +K L+           +L+     + 
Sbjct: 390 SETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD- 447

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  V    +  ++  L+I          T  +  ++    + +  K   +  G  +
Sbjct: 448 ---LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASAKAGVSQ 501

Query: 416 MNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLK 472
           +  R    +      R          I     L N   G +   +    +    V  +  
Sbjct: 502 VLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 561

Query: 473 NQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
             Y       E  I    + +   ++   PQ   NA  V      F     +    +  +
Sbjct: 562 MCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPAH 615

Query: 531 SLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGL 582
            ++ +   RR + +  +  + R     E        R   P       P   + G  +  
Sbjct: 616 LVNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLN 675

Query: 583 VSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              +    +                Y        +  V Y+ A EEE   I      L+ 
Sbjct: 676 KEHIRKLEQDKDLPPDLDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEI 735

Query: 637 DGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                        E     +     +          +  P  ++ + AS+IPF +++ S 
Sbjct: 736 SKQLQAGYALPEEELHDPNKRVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSP 795

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                   + A I+      +    ++  +    
Sbjct: 796 RNTYQSAMGKQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRE 846

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 +   +  Y              NQ            + +I +  S D G     
Sbjct: 847 LPAGQNAIVAIACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS- 883

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
               + +  +        + + ER              FE   R   +G  +        
Sbjct: 884 ----LFYRTYTDSEKMVGLTVVER--------------FEKPMRSDTIGMRK-------- 917

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +DE GII  G  V+  DI++GK  P     + PE + L      KA    D S
Sbjct: 918 --GTYDKLDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVS 968

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  +G V  V +   +   K
Sbjct: 969 TPLRSTENGIVDQVLVSTSNDDLK 992


>gi|68300807|gb|AAY89345.1| RNA polymerase II second largest subunit [Solanum lycopersicum]
          Length = 1205

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 182/1065 (17%), Positives = 341/1065 (32%), Gaps = 203/1065 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             + +     +    ++       ++A +   + +    +       S   F      KY 
Sbjct: 306  DILAHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGFTREKRIKYA 362

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + R  +      +  +  +         II  L+    G+   DD D+  N+R+   
Sbjct: 363  KEILQREMLPHVGTREYCETKK---AYYFGYIIHRLLLCVLGRRPEDDRDHYANKRLDLA 419

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +         V  Q  I AK + S +     +      
Sbjct: 420  GPLLGGLFRMLFRKLTRDVRSYVQKCVDGGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 479

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 480  NAAGTRAGVSQVLNRLTFASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 535

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 536  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 588

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V    +L       D  R    
Sbjct: 589  IFVNGCWVGIHRNPDLLVRTLRQLRRQV---DVNTEVGVVRNINLKELRLYTDYGRCSRP 645

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +    +K          E   ++ SG        G +E VD             +
Sbjct: 646  LFIVDKKRLRIKKNDIIALQMRE--SSEDSG-WHDLVAKGFIEYVDTEE----------E 692

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N +                        PS  LG       +  
Sbjct: 693  ETTMIAMTINDLTNSRVNPDEAYA-----------ETYTHCEIHPSLILG-------VCA 734

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 735  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 790

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 791  EHL-------------------------HFRQLPAGINAIVAITCYSGYNQEDSVIMNQS 825

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    +F R   D+ ++  ++ +E      R+        + +          G 
Sbjct: 826  SIDRGLF-RSLFFRSYRDEEKKMGTLVKEDFGRPDREHTMGMRHGNYDKLEDDGFAPPGT 884

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S                  DE   ++    +  + TS    E   
Sbjct: 885  RVSGDDVIIGKTTPISQ-----------------DEAQGQSARYTRKDHSTSLRHSETGI 927

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK+ +   R  Q GDK + RHG KG +      EDMP+  
Sbjct: 928  VDQVLLTTNADGL-----RFVKIRMRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWSA 982

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 983  EGITPDIIVNPHAIPSRMTIGQLVECIMGKVAAHIGKEGD-------------------- 1022

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+  L        G 
Sbjct: 1023 ---------------------------------ATP-FTDVTVDSISRTLHNCGYQMRGF 1048

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1049 ERMYNGHTGRVLPAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1108

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------------------RTRVY 1329
             GEME  C+ A+GAA+ L+E L  +SD     V                      R +  
Sbjct: 1109 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCQQCGLMAIANLKKMSFECRSCRNKT- 1167

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
                   D  +   P +  +L++E+ ++ ++  +     K S + 
Sbjct: 1168 -------DNVQVYIPYACKLLIQELMSMAIAPRMLTKELKPSNRK 1205



 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 133/994 (13%), Positives = 287/994 (28%), Gaps = 206/994 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGA-AML 74
           L+  Q  S+D F+   +          Q        I               F      +
Sbjct: 58  LVRQQLDSFDEFIQNTM----------QEIVDETADIEIRPESQHNPSRQPDFVETIYKI 107

Query: 75  EFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           +F       P     D             R+LTY+ PL + ++  V          +   
Sbjct: 108 KFTQIYLSRPMMTESDGETNTLFPKAARLRNLTYSSPLYVDVKKEVIKKGHDYEEVTENQ 167

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + +++G +P+M +                         G F++ G ++++++Q   S
Sbjct: 168 EFTK-VFIGKVPIMLRSSYCSLYNLSEKDLTELGECPYDQGGYFIVNGSEKVLIAQEKMS 226

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-------- 211
              ++      +     K  Y   +        + +  +   + VR+  R          
Sbjct: 227 SNHVY----VFKKRQPNKYAYVAEVR----SISEGQNKAPSGMFVRMLSRSNSKGAYGQY 278

Query: 212 -----------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                      +P+     ALG  ++ +IL+        +Q  +     L  A ++   +
Sbjct: 279 IRATLPYIRTEIPIIVVFRALGFVADKDILAHICYDFADTQMMELLRPSLEEAFVIQNQQ 338

Query: 260 VSSSLVDID------TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           V+   +         T E+ I+  K++     + L   G +    T       Y+   ++
Sbjct: 339 VALDYIGKRGSTVGFTREKRIKYAKEILQR--EMLPHVGTREYCETKKAYYFGYIIHRLL 396

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKD 372
               G    +  D    K L+           +L+   + +  +Y++  +   K+ + + 
Sbjct: 397 LCVLGRRPEDDRDHYANKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDGGKDVNLQF 456

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI- 431
           A+             T  +  S+    +  ++           +N      T   +R + 
Sbjct: 457 AI--------KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTFASTLSHLRRLN 508

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +  +    + 
Sbjct: 509 SPIGREGKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILE 565

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVA 550
            ++  S    + I+   +  +   F     +         +  +   RR   +  + GV 
Sbjct: 566 FLEEWSTENFEEISPAVIPQSTKIFVNGCWVGIHRNPDLLVRTLRQLRRQVDVNTEVGVV 625

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R     E+R ++  +     P    +   + +  +     ++         +  V  G  
Sbjct: 626 RNINLKELR-LYTDYGRCSRPLFIVDKKRLRIKKNDIIALQMRESSEDSGWHDLVAKGF- 683

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + Y+   EEE   IA   + L       +E               E     +  P  
Sbjct: 684 ---IEYVDTEEEETTMIAMTINDLTNSRVNPDE------------AYAETYTHCEIHPSL 728

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ + AS+IPF +++ S R      M +QA+ +      F                    
Sbjct: 729 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF-------------------- 768

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R   +  V                                       Q+PLV        
Sbjct: 769 RMDTLAYV-----------------------------------LYYPQKPLV-------- 785

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                         L  G N +VA   + GYN EDS+++++  +   +F S+    +   
Sbjct: 786 --TTRAMEHLHFRQLPAGINAIVAITCYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYRDE 843

Query: 851 ARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +      +E            +       +++ G    G  V+  D+++GK TP  +  
Sbjct: 844 EKKMGTLVKEDFGRPDREHTMGMRHGNYDKLEDDGFAPPGTRVSGDDVIIGKTTPISQDE 903

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    A         +D S  +    +G V
Sbjct: 904 ---------AQGQSARYTRKDHSTSLRHSETGIV 928


>gi|302781178|ref|XP_002972363.1| hypothetical protein SELMODRAFT_172903 [Selaginella moellendorffii]
 gi|300159830|gb|EFJ26449.1| hypothetical protein SELMODRAFT_172903 [Selaginella moellendorffii]
          Length = 1178

 Score =  405 bits (1042), Expect = e-110,   Method: Composition-based stats.
 Identities = 180/1055 (17%), Positives = 334/1055 (31%), Gaps = 191/1055 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 275  DILEHICYDFSDTAMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 331

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 332  KDILQKEMLPHVGVGEYCETKK---AYFFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 388

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L + +R    ++ + ++   +    +   V     + AK + S +     +      
Sbjct: 389  GPLLGSLFRQLFRKLTKDVRAYLQKCVDNGKEVNLAYAVKAKTITSGLKYSLATGNWGQA 448

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RR   L        R   + R +H +H+G +CPAE
Sbjct: 449  NSGNARAGVSQVLNRLTYASTLSHLRR---LNSPIGREGRLLAKPRQLHNSHWGMMCPAE 505

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L   A +            + +    N        EE +  +    + 
Sbjct: 506  TPEGQACGLVKNLALMAYITVGSAANPILVFLEEWSTEN-------FEEISPAVIPNATK 558

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G++           + +   R ++   D + +  V     L       D  R    
Sbjct: 559  IFVNGAWVGIHREPEHLVKTLRQLRRQV---DVNTEVGVVRDIRLKELRLYTDYGRCSRP 615

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+                    A    +           +  I  V+ + +
Sbjct: 616  LFIVEKQRLLI--------------KKSDIRALQQKEAGENGWHELVSKGFIEYVDTEEE 661

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 662  ETTMISMTISDLVNARLNPEEAYS-----------DTYTHCEIHPSMILG-------VCG 703

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 704  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 736

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 737  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 794

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ +++ ++ +E+ E   R+          +          G 
Sbjct: 795  SIDRGFF-RSIFYRSYRDEEKKAGTLVKEEFERPNRETTTGMRHGSYDKLDDDGIAPPGT 853

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T L+                  DE   +     K    T     E   
Sbjct: 854  RVSGEDVIIGKTTPLAQ-----------------DETGTQAQRYSKRDQSTCLRHSESGM 896

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK  V   R  Q GDK + RHG KG +      EDMPF +
Sbjct: 897  IDQVLLTTNADGL-----RFVKTRVRSIRIPQIGDKFSSRHGQKGTIGMTYTQEDMPFTQ 951

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 952  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAALMGKEGD-------------------- 991

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L   +    G 
Sbjct: 992  ---------------------------------ATP-FTDVTVDNISKALHKCNYQLRGF 1017

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1018 ETMYNGHTGRRLSAMIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1077

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-----SIVA-GNDTFET------ 1341
             GEME  C+ A+GAA+ L+E L  +SD    R  V E     +I     +TFE       
Sbjct: 1078 FGEMERDCMIAHGAAHFLKERLFDQSD--AYRVHVCEHCGLIAIANLKKNTFECRSCKNK 1135

Query: 1342 ------GTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                    P +  +L +E+ A+ ++  +     K 
Sbjct: 1136 TEIVQVHIPYACKLLFQELMAMAIAPRMFMKEVKK 1170



 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 136/991 (13%), Positives = 284/991 (28%), Gaps = 198/991 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSG--AAM 73
           L+  Q  S+D F+   +          Q        I               +SG     
Sbjct: 25  LVRQQLDSFDEFIQNTM----------QEIVDESSEIEIKPESQHNPGRNNEYSGETTFK 74

Query: 74  LEFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           ++F       P     D             R+LTY+ PL   +   V    E     + +
Sbjct: 75  IKFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYADIIKYVTRKGEDGEEDTEQ 134

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
           + +   +++G +P+M +                         G F+I G ++++++Q   
Sbjct: 135 E-ELPKVFIGKVPIMLRSSYCTLYQNSDKDLTELGECPYDQGGYFIINGSEKVLIAQEKM 193

Query: 160 SPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR--------- 209
           S   ++      +     K  Y   +        + +      + VR+  R         
Sbjct: 194 STNHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPASSMFVRMLSRAGAKAGSSG 245

Query: 210 -----------RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                      +++P+     ALG  ++ +IL         +   +     L  A ++  
Sbjct: 246 QYIRATLPYIKQEIPIIVVFRALGFVADKDILEHICYDFSDTAMMELLRPSLEEAFVIQN 305

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +        +   K++       L+++ +  +G+   C          +    
Sbjct: 306 QQVALDYIGKRGSTVGVTREKRIKYAK-DILQKEMLPHVGVGEYCETKKAYFFGYIIH-- 362

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A     E   +   +  +    P+L          +   +     K   +    
Sbjct: 363 -RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGSLFRQLFRKLTKDVRAYLQKCVDNGKEV 421

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR--KE 434
                      T  +  S+    +  ++  +        +N      T   +R +     
Sbjct: 422 NLAYAVKAKTITSGLKYSLATGNWGQANSGNARAGVSQVLNRLTYASTLSHLRRLNSPIG 481

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
               ++     L N    +         +      ++KN   +  + +  +    +  ++
Sbjct: 482 REGRLLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMAYITVGSAANPILVFLE 538

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
             S    + I+   + +A   F   + +    E  + +  +   RR   +  + GV R  
Sbjct: 539 EWSTENFEEISPAVIPNATKIFVNGAWVGIHREPEHLVKTLRQLRRQVDVNTEVGVVRDI 598

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E+R ++  +     P    E   + +  S      + A    E       +      
Sbjct: 599 RLKELR-LYTDYGRCSRPLFIVEKQRLLIKKS-----DIRALQQKEAGENGWHELVSKGF 652

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E      +     +  P  ++ 
Sbjct: 653 IEYVDTEEEETTMISM----------TISDLVNARLNPE--EAYSDTYTHCEIHPSMILG 700

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +  S+IPF +++ S R      M +QA+ +                           R  
Sbjct: 701 VCGSIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMD 740

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  V                                       Q+PLV           
Sbjct: 741 TLAYV-----------------------------------LYYPQKPLV----------T 755

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N +VA   + GYN EDS+++++  +    F SI    +    + 
Sbjct: 756 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKK 815

Query: 854 TK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              L  EE  R        +       +D+ GI   G  V+  D+++GK TP  +     
Sbjct: 816 AGTLVKEEFERPNRETTTGMRHGSYDKLDDDGIAPPGTRVSGEDVIIGKTTPLAQDE--- 872

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                      +    RD S  +    SG +
Sbjct: 873 ------TGTQAQRYSKRDQSTCLRHSESGMI 897


>gi|317033268|ref|XP_001395161.2| DNA-directed RNA polymerase II subunit RPB2 [Aspergillus niger CBS
            513.88]
          Length = 1231

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 181/1065 (16%), Positives = 350/1065 (32%), Gaps = 166/1065 (15%)

Query: 346  ILYVDSVNNNAYIRNT-LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +   D +N+  Y RN   + +  K   +    I       +V+   +A+   +    + +
Sbjct: 286  VSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDR----EVALDFIAKRGSSQSSMNHE 341

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +        ++     ++   +     +   +  ++  L+    G+  +DD D+ G +R+
Sbjct: 342  RRVRYAREIMQKEFLPHISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRL 401

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   R+ R ++   +        +     I A  +   +     +   
Sbjct: 402  DLAGPLLANLFRVLFTRVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNW 461

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 462  GEQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 517

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +            ++
Sbjct: 518  CPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFV 577

Query: 628  AQANSSLDEDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLEND 685
                  +  D +     ++  R             D  +   K          P F+ ++
Sbjct: 578  NGVWVGIHRDPAHLVNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDN 637

Query: 686  DSNRVLMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI- 743
            D      G  +  ++ +  L+ +             +         ++G+VE VDA    
Sbjct: 638  DPKSENCGSLVLNKEHIRKLEQDKDLPPDLDPEDRRERYFGWDGLVKSGVVEYVDAEEEE 697

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             I  V    D   S          +    +     R ++    +          PS  LG
Sbjct: 698  TIMIVMTPEDLEISKQLQAGYALPEEELHDPNKRVRSILS--QKAHTWTHCEIHPSMILG 755

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +                     E   
Sbjct: 756  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMA 798

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            +I    ++ L                        +       +   +  + AI      +
Sbjct: 799  NILYYPQKPLA-------------------TTRSMEFLRFRELPAGQNAIVAIACYSGYN 839

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R   D  +         +E   +    + + + +  Y
Sbjct: 840  QEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGL---TVVERFEKPMRSDTIGMRKGTY 895

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L E   I  G           K+  L+ +                +E  QR     K+
Sbjct: 896  DKLDEDGIIAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKL 940

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++      DD+     + VKV +   +  Q GDK A RHG KG +
Sbjct: 941  DVSTPLRSTENGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTI 995

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF ++G   D+++NP  +PSRM +  + E  L       G +         
Sbjct: 996  GITYRQEDMPFTREGVCPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------- 1048

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     ++I+
Sbjct: 1049 ----------------------------------------------ATP-FTDVTVDSIS 1061

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +LR       G  ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+
Sbjct: 1062 RLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTR 1121

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV 1333
            QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D  G       + 
Sbjct: 1122 QPVEGRARDGGLRFGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPVAKLK 1181

Query: 1334 AG----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G          +   +   P +  +L +E+ ++ ++  +  +R+
Sbjct: 1182 KGLFECRLCNNKHRISQVHIPYAAKLLFQELASMNIAARMFTNRS 1226



 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 147/1019 (14%), Positives = 297/1019 (29%), Gaps = 184/1019 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPSEDEVDPVV--VRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD--IKEQS 129
             P               +   R+LTYA PL + +   + +  E   A    D   KE++
Sbjct: 95  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGVTKKIMEGRERLVADRDDDDMAKEET 154

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHF 165
           +++G +P+M K                         G F+I G ++++++Q  RS G   
Sbjct: 155 VFIGKMPIMLKSKYCILKDLSEQALYNWNECPYDSGGYFIINGSEKVLIAQE-RSAGN-- 211

Query: 166 DHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDR--------------- 208
                + +      Y   I    ++G  +  +   K  +  + D                
Sbjct: 212 TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLK--LFAKGDSAKGGFGPTIRSTLPY 269

Query: 209 -RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
            +  +P+     ALG +  E+IL+        +   +     +    ++   +V+   + 
Sbjct: 270 VKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDREVALDFIA 329

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEI 320
                Q   + ++      + ++++ +  +  +           G  V   ++    G  
Sbjct: 330 KRGSSQSSMNHERRVRYAREIMQKEFLPHISQSEGSETRKAFFLGYMV-HRLLQCALGRR 388

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            ++  D   +K L+           +L+     +        V    +  ++  L+I   
Sbjct: 389 DVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD----LQRYVQRCVETNREIYLNIG-- 442

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                  T  +  ++    + +  K   +  G  ++  R    +      R         
Sbjct: 443 -IKASTLTGGLKYALATGNWGEQKKAASAKAGVSQVLSRYTYASTLSHLRRTNTPIGRDG 501

Query: 439 IIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDI 495
            I     L N   G +   +    +    V  +    Y       E  I    + +   +
Sbjct: 502 KIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVL 561

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARA 554
           +   PQ   NA  V      F     +    +  + ++ +   RR + +  +  + R   
Sbjct: 562 EEFEPQVTPNATKV------FVNGVWVGIHRDPAHLVNTMLSLRRRNMISHEVSLIRDIR 615

Query: 555 GVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN------AYGFIETP 601
             E        R   P       P   + G  +     +    +                
Sbjct: 616 EREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKEHIRKLEQDKDLPPDLDPEDRRER 675

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS--------FTEELVFCRCAGEE 653
           Y        +  V Y+ A EEE   I      L+              E     +     
Sbjct: 676 YFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQLQAGYALPEEELHDPNKRVRSI 735

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           +          +  P  ++ + AS+IPF +++ S R      M +QA+ +          
Sbjct: 736 LSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT------- 788

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                    + A I+      +    ++  +          +   +  Y           
Sbjct: 789 --NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSG--------- 837

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ            + +I +  S D G         + +  +        + + ER 
Sbjct: 838 --YNQ-----------EDSVIMNQSSIDRGLFRS-----LFYRTYTDSEKMVGLTVVER- 878

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
                        FE   R   +G  +               +DE GII  G  V+  DI
Sbjct: 879 -------------FEKPMRSDTIGMRK----------GTYDKLDEDGIIAPGVRVSGEDI 915

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           ++GK  P     + PE + L      KA    D S  + S  +G V  V +   +   K
Sbjct: 916 IIGKTAP-----LAPEAEELGQR--TKAHTKLDVSTPLRSTENGIVDQVLVSTSNDDLK 967


>gi|307683573|dbj|BAJ19765.1| RNA polymerase beta chain [Larix decidua]
          Length = 1076

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTMGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 239/695 (34%), Positives = 377/695 (54%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIYYRLELDHNRINYIYTGTLISDWGRRSKLEIDVGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     +           DR++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPERFFFLLKKKKGKWDREEYLWSRENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + S   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKSTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A+++  G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIDHCGSLQSPFYKISERSREEHMVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  N      G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNYLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                  L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 T--------NITSSVNGDTVRTELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 124/300 (41%), Gaps = 29/300 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRLELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R+RK+ +   L A+G++ EEIL        +              + +      
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTRYPERFFFLLKKKKGKWDREEYLWSR--E 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           +++++       +      +  L K L+EK  +               +  ++    EI+
Sbjct: 227 NAILEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNQKLNLDIPENEIF 286


>gi|228016564|gb|ACP51394.1| RNA polymerase beta subunit [Abies firma]
          Length = 1076

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRKGEFVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 232/695 (33%), Positives = 372/695 (53%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +        + GE          + 
Sbjct: 120 RIVVNQILISPGIHYRLELDHNRINYIYTGTLISDWGRRSKFEIDAGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIR-------NTLVTDKNKDRKDALLDIYRVM--R 382
           S+  +  +   ++  +  ++     ++             +    +++A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILNNTRYPKIFLFLLKNKKGKREREEYLWSKENAILEFYKKLYCI 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNKKLNLDIPENDIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I            
Sbjct: 299 LIGVKIGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRXXXXX 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
                       +FF         +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 XXXXXXXXXXXQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A+++  G +++P+ K+ +  +  ++VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKISHCGSLQSPFYKISERSIEENIVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  SI  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSIGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           + I     E  +   +        + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 VNITSSVNEDTVRTES--------VMYQRSNTNTCTHQKPQVRKGEFVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 78/343 (22%), Positives = 144/343 (41%), Gaps = 41/343 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDKEIESRLFGNEYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+  SPGIH+  +     ++   +Y   +I D G     E D+ + I 
Sbjct: 113 FVVNGIYRIVVNQILISPGIHYRLELDHNRIN--YIYTGTLISDWGRRSKFEIDAGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDFWCFPLSAADLMVGAK--- 259
            R+ R+RK+ +   L A+G++ EEIL +T YPKI      +          L        
Sbjct: 171 ARVSRKRKISIPVLLSAMGLNLEEILNNTRYPKIFLFLLKNKKGKREREEYLWSKENAIL 230

Query: 260 --------VSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKF--LGITSDCLCGLYV 308
                   +S  LV  ++  +++ E   +    L K  +    K   L I  + +    +
Sbjct: 231 EFYKKLYCISGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNKKLNLDIPENDIF--SL 288

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +D++      I ++ G       ++ + +  IR +  L  + 
Sbjct: 289 PQDVLAAVDYLIGVKIGM-GTLDDIDHLRNRRIRSVADLLQNQ 330


>gi|119177838|ref|XP_001240650.1| hypothetical protein CIMG_07813 [Coccidioides immitis RS]
          Length = 1152

 Score =  405 bits (1041), Expect = e-110,   Method: Composition-based stats.
 Identities = 196/1163 (16%), Positives = 372/1163 (31%), Gaps = 199/1163 (17%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYS------QRGDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L         IL       +Y+        G ++    S   L+   + + ++
Sbjct: 134  KMP--IMLK----SKYCILKDLGEHALYNWNECPYDSGGYFIINGSEKVLIAQERSAGNI 187

Query: 265  VDIDTGEQ------------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            V +                  +E G ++ S L   L  KG    G     +    +    
Sbjct: 188  VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLSIKLFAKGDSSKGGFGPTIRST-LPYIK 246

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +     ++   G V DE  L  I +       +  +       ++         +DR+ 
Sbjct: 247  TDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFV--------IQDREV 298

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL  I +    G   T    E    +      K  L  +              +     +
Sbjct: 299  ALDFISKR---GSSPTSMNHEKRVRYARDIIQKEFLPHI-----------SQSEGSETRK 344

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RI 490
               +  ++  L+    G+  +DD D+ G +R+   G +L N +R+  +R+ + + +  + 
Sbjct: 345  AFFLGYMVHKLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQR 404

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITH 537
                   +     + A  +   +     +               +SQ+       S ++H
Sbjct: 405  CVETNRQLYLNIGVKASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSH 464

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR +      + R     + R +H TH+G +CPAET EG   GLV +L     +     
Sbjct: 465  LRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTP 520

Query: 598  IET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             E    +    + +V  +     +      ++      +  D S     V        I 
Sbjct: 521  SEPIIDFMIQRNMEVLEEFEPQVSPNSTKIFVNGVWVGVHRDPSHLVSTVQSLRRRNMIS 580

Query: 656  VPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-V 711
                 + D  D   K          P    D+  +     ++   ++ +  L+A+     
Sbjct: 581  HEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVLTKEHIHKLEADKEIPA 640

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                E    +  G   + K +G+VE VDA      ++   + P    V       +    
Sbjct: 641  DLDPEERRERYYGWDGLVK-SGVVEYVDAEEEE--TIMIVMSPEDLEVSKQYQAGYIPEE 697

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
              +  N+R   K+  +          PS  LG       +  + +P+  +N         
Sbjct: 698  DTSDPNRRVRSKLSQKAHTWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQS 750

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             M  + +                     E   +I    ++ L                  
Sbjct: 751  AMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA----------------- 783

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
                  +       +   +  + AI      +  D+ +   S +   +     +  +   
Sbjct: 784  --TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT-- 839

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVL 1008
              +    +    +E   +    + + +    Y ++ +   +  G           K+  L
Sbjct: 840  --DSEKMIGLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPL 897

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + +                +E  QR  +  K+   T     E    +++           
Sbjct: 898  APE---------------SEELGQRTKQHTKLDVSTPLRSTESGIVDQVLV-----STSN 937

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              L+ VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +P
Sbjct: 938  EDLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTFRQEDMPFTREGIVPDLIINPHAIP 997

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +  + E  L       G +                                     
Sbjct: 998  SRMTIAHLIECQLSKVSSLRGYEGD----------------------------------- 1022

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                              +TP F     ++++S+LR       G  ++Y+G TG      
Sbjct: 1023 ------------------ATP-FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQ 1063

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+
Sbjct: 1064 IFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGAS 1123

Query: 1309 YVLQEMLTIKSD-------DVVG 1324
              L+E L   SD       D+ G
Sbjct: 1124 AFLKERLFDVSDPFRVHICDICG 1146



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 98/755 (12%), Positives = 215/755 (28%), Gaps = 136/755 (18%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDV------- 113
              L+F +     P               +   R+LTYA PL + +   + +        
Sbjct: 31  RYELKFGTVMLARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKKIAEGRERSLAE 90

Query: 114 ------------DEFTGAKSI-----------KDIKEQSIYMGDLPLMTKD--------- 141
                       DE   A+              +  E++I++G +P+M K          
Sbjct: 91  RDEDDDEPDAKGDEERRARGTYLQWEPKALPEDEADEENIFIGKMPIMLKSKYCILKDLG 150

Query: 142 ---------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
                          G F+I G ++++++Q  RS G        + +      Y   I  
Sbjct: 151 EHALYNWNECPYDSGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRS 207

Query: 187 --DQGLWMDIEFDSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEE 227
             ++G  +  +   K  +  + D  +                 +P+     ALG +  E+
Sbjct: 208 AVEKGSRILSQLSIK--LFAKGDSSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDED 265

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           IL+        +   +     +    ++   +V+   +          + +K        
Sbjct: 266 ILNHICYDRNDTPMLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDI 325

Query: 288 LKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           ++++ +  +  +           G  V + ++    G   ++  D   +K L+       
Sbjct: 326 IQKEFLPHISQSEGSETRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLA 384

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
               +L++    +        V    +   +  +    +       T  +  ++    + 
Sbjct: 385 NLFRVLFMRLTKDLYKYVQRCVETNRQLYLNIGVKASTL-------TGGLKYALATGNWG 437

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDN 458
           +  K   S  G  ++  R    +      R          I     L N   G +   + 
Sbjct: 438 EQKKAASSKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAET 497

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEF 516
              +    V  +    Y       E  I    + +   ++   PQ   N+  +      F
Sbjct: 498 PEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKI------F 551

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGR 568
                +    +  + +S +   RR + +                      R   P     
Sbjct: 552 VNGVWVGVHRDPSHLVSTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVD 611

Query: 569 ICPAETSEGHNIGLVSSLTSF-------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
             P   + G  +     +          A ++     E  Y        +  V Y+ A E
Sbjct: 612 NDPKSENSGSLVLTKEHIHKLEADKEIPADLDPEERRER-YYGWDGLVKSGVVEYVDAEE 670

Query: 622 EENRYIAQANSSLDEDGSFTEELV-------FCRCAGEEILVPREKIDFIDASPKQVVSI 674
           EE   I  +   L+    +    +         R    ++          +  P  ++ I
Sbjct: 671 EETIMIVMSPEDLEVSKQYQAGYIPEEDTSDPNRRVRSKLSQKAHTWTHCEIHPSMILGI 730

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            AS+IPF +++ S R      M +QA+ +      
Sbjct: 731 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFD 765


>gi|330922612|ref|XP_003299905.1| hypothetical protein PTT_11005 [Pyrenophora teres f. teres 0-1]
 gi|311326219|gb|EFQ92000.1| hypothetical protein PTT_11005 [Pyrenophora teres f. teres 0-1]
          Length = 1262

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 163/987 (16%), Positives = 325/987 (32%), Gaps = 162/987 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +    +      Q  + A  + + +     +               +SQ+     
Sbjct: 448  VYKYLQRCVENNQDFNVQMAVKASTITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +     + +    ++      +  +      +V   
Sbjct: 564  YVSVGSDATPIVDFMTQRNMQLLEEYDQNQSPDATKVFVNGVWVGVHSNAQQLVTVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLK 705
                 +      I D  D   K        + P    ++  R     ++   ++    LK
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENDVRKPNRNHLIFTKEISNKLK 683

Query: 706  AEAPFVGTGM---ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            +E           E  V +++       + G+VE +DA       +    +      ++ 
Sbjct: 684  SEQMEASQRQGWSEEEVEQATYGWRGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMK 743

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGD-EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              +     +       R L  + D  +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPMTDHSLEGSQRLRRLKPLPDPRIHSYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNFALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIATDAAELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLIINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + ++ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTDVTVDQVSQLLENAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     + +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRTQIFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIV--AGNDTFET 1341
              C+ A+GAA  L+E L   SD       D+ G        +  +YE           + 
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICGLMSPIANLKKNLYECRPCHNKTRISQI 1229

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  +   R+
Sbjct: 1230 HIPYAAKLLFQELLAMNIATRMFTDRS 1256



 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 143/1041 (13%), Positives = 280/1041 (26%), Gaps = 221/1041 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF----------KSVFPITAFSGAAMLEFVS 78
           L+  Q  SYD F   N   D     G  +            +   PI        ++F  
Sbjct: 40  LVSQQLDSYDEF-TRNTIQDIVKENG--SVILEQNQPYNPDEEDNPI--IKRRYEMKFGR 94

Query: 79  YEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVF----------DVDEFTG 118
                P               +   R+LTY+  +   +   V           D DE   
Sbjct: 95  VYLARPTHTEGDGTTVQLYPHEARLRNLTYSGAMLADIENRVMVAREGRDPEADDDEEME 154

Query: 119 AKSIK---DIKEQS------------IYMGDLPLMTKD---------------------- 141
                    I+ +             +++G LP+M +                       
Sbjct: 155 GGYTGGQNQIRWERENMSSDDGAAARVFIGKLPVMLRSELCHLRAQSDADLFALNECPYD 214

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+
Sbjct: 215 QGGYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFN 270

Query: 198 SK---DII-----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKI 236
            K   + +                 +++ D    VP+     ALG+   EEILS      
Sbjct: 271 IKWAENSLAGPGKRIPGPFAYATLPYIKAD----VPMAIVFRALGIVSDEEILSHIVFDR 326

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             +Q  +     +    ++   + +   +            +   +  +  ++ + +  +
Sbjct: 327 NDTQTLELLKPSIEEGSVVQDRETALDFIAKRGANSGTRDRRLKFARDI--MQREFLPHI 384

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
                           +     +  +   D  D            + + +          
Sbjct: 385 SQKEGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDH------FGKKRLDL-------AGP 431

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            I N       K  KD    + R +       F+V  ++      +  KY L   G    
Sbjct: 432 LIANLFRILFLKLTKDVYKYLQRCVENNQ--DFNVQMAVKASTITNGLKYSL-ATGNWGD 488

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEML 471
             +         + + +    + +  L        R+GK       +  +  +    E  
Sbjct: 489 QKKAASAKAGVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETP 548

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE--------FFCSSQLS 523
           + Q    +  +       + S     V      N + +              F     + 
Sbjct: 549 EGQACGLVKNLSLMCYVSVGSDATPIVDFMTQRNMQLLEEYDQNQSPDATKVFVNGVWVG 608

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   ++ +   RR   L  +  + R     E + +       + P    E      
Sbjct: 609 VHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVVENDVRKP 667

Query: 583 VSSLTSFAR-VNAYGFIETPYRKVCDGKVTNDVV----------------YLSAMEEENR 625
             +   F + ++     E        G    +V                 YL A EEE  
Sbjct: 668 NRNHLIFTKEISNKLKSEQMEASQRQGWSEEEVEQATYGWRGLIQDGVVEYLDAEEEETA 727

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            I  +   L+E       L     + E                                 
Sbjct: 728 MITFSPEDLEEWREMKMGLPMTDHSLE--------------------------------- 754

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                  G    R+  PL         T  E   A   G       A I+   D  +   
Sbjct: 755 -------GSQRLRRLKPLPDPRIH-SYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746 RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802 NTYQSAMGKQAMGVALTNFALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
           L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852 LPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864 ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               D   +       +D+ G++  G  V+  DI++GK  P      T   +L +     
Sbjct: 912 PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIA----TDAAELGQKTTLH 967

Query: 920 KAVDVRDTSLRVPSGVSGTVV 940
              DV        +G+   V+
Sbjct: 968 TKRDVSTPLRSTENGIVDQVL 988


>gi|229544492|gb|ACQ76427.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 134/237 (56%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW + AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALGAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395126|gb|ACI45383.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 129/237 (54%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGW   G+G++I  +    +     S LR FL+KV  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWPSHGIGQRIGDM---XQQQAKASELRKFLDKVYNSCGRA 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   ++ ++ +A   + GVP +TPVFDGA E  I  ML++A  DE            
Sbjct: 58   EDLTQLSEEDLVAMAGNLQHGVPYATPVFDGASEAEIKDMLKIAYPDEIAQRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+  DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLADDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G  T E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHTIEAGMPESFNV 234


>gi|225446351|ref|XP_002274051.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|147841183|emb|CAN72948.1| hypothetical protein VITISV_033708 [Vitis vinifera]
 gi|302143287|emb|CBI21848.3| unnamed protein product [Vitis vinifera]
          Length = 1193

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 178/1055 (16%), Positives = 336/1055 (31%), Gaps = 193/1055 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 289  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 345

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 346  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 402

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 403  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 462

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 463  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 518

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 519  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 571

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 572  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 628

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                +   A  + +        D   +  I  V+ + 
Sbjct: 629  LFIVEKQRLLI--------------KKRDIRALQLRESPEDGGWHDLVSKGFIEYVDTEE 674

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 675  EETTMISMTINDLISARLNPEEAYS-----------ETYTHCEIHPSLILG-------VC 716

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 717  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 750

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 751  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 807

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 808  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 866

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T +S                  D+   +     +  + TS    E  
Sbjct: 867  TRVSGEDVIIGKTTPISQ-----------------DDSQGQASRYTRRDHSTSLRHSESG 909

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 910  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 964

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 965  VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 1005

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 1006 ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 1030

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG 
Sbjct: 1031 FETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGL 1090

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR----------TRVYESIVAG--- 1335
            R GEME  C+ A+GAA+ L+E L  +SD     V  R             +E    G   
Sbjct: 1091 RFGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIAIANLKKNSFEC--RGCKN 1148

Query: 1336 -NDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
              D  +   P +  +L +E+ A+ ++  +     K
Sbjct: 1149 KTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEVK 1183



 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 134/992 (13%), Positives = 282/992 (28%), Gaps = 201/992 (20%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G Q+ F              + F
Sbjct: 40  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGRQSDFLET--------IYKISF 91

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   +           + + +
Sbjct: 92  GQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRIIKKGHDLE--EVTETQ 149

Query: 127 E-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
           E   +++G +P+M +                         G F+I G ++++++Q   S 
Sbjct: 150 EFTKVFIGKVPIMLRSSYCTVYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMST 209

Query: 162 G-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR----------- 208
             ++      +     K  Y   +        + +      + VR+  R           
Sbjct: 210 NHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQY 261

Query: 209 --------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                   R ++P+     ALG  ++ +IL         +Q  +     L  A ++   +
Sbjct: 262 IRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQ 321

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
           V+   +        +   K++     + L+++ +  +G+   C          +      
Sbjct: 322 VALDYIGKRGSTVGVTREKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---R 377

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           + + A     E   +   +  +    P+L          +   +     K   +      
Sbjct: 378 LLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNL 437

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDII 437
           +        T  +  S+    +  ++           +N      T   +R +       
Sbjct: 438 QFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGRE 497

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             +     L N    +         +      ++KN   +  + +  +    +  ++  S
Sbjct: 498 GKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWS 554

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGV 556
               + I+   +  +   F     +         +  +   RR   +  + GV R     
Sbjct: 555 TENFEEISPAVIPQSTKIFVNGCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLK 614

Query: 557 EMRDVHPTHYGRICPAETSEGH----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           E+R ++  +     P    E          + +L         G+         D     
Sbjct: 615 ELR-LYTDYGRCSRPLFIVEKQRLLIKKRDIRALQLRESPEDGGW--------HDLVSKG 665

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +L+  R   E      E     +  P  ++
Sbjct: 666 FIEYVDTEEEETTMISM----------TINDLISARLNPE--EAYSETYTHCEIHPSLIL 713

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 714 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 753

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 754 DTLAYV-----------------------------------LYYPQKPLV---------- 768

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 769 TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 828

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 829 KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD-- 886

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  +         RD S  +    SG V
Sbjct: 887 -------SQGQASRYTRRDHSTSLRHSESGMV 911


>gi|209395048|gb|ACI45331.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LR FL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGERIGELL---QQQAKVSELRRFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG---------- 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  +E+           
Sbjct: 58   ENLALLSDADLLAMAGNLQQGVPYATPVFDGASEAEIKDMLELAYPEETARRRGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|307683479|dbj|BAJ19718.1| RNA polymerase beta chain [Pseudotsuga sinensis var. wilsoniana]
          Length = 1076

 Score =  405 bits (1040), Expect = e-110,   Method: Composition-based stats.
 Identities = 156/497 (31%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     +   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLIYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D    + + +  +      ++ G    +G   
Sbjct: 691  SFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLGENGL------VMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        + V+V  KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TIHVYVLQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/695 (33%), Positives = 375/695 (53%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIYYRLELDHNRINYIYTGTLISDWGRRSKLEIDGGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     ++          +R++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTHYPERFLFLLKKKKGKWEREEYLWSRENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVQIGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + S   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKSTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIGHCGSLQSPFYKISERSREEHMVYLLPGED 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  N      G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNYLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                   + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 T--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER++ ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLIYEDIYTSFHIVRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++ E G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLGENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 122/298 (40%), Gaps = 25/298 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDKEIESRLFGNEYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY   L +  R         +  ++   I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSLTYYSELYVPAR---------SIRRNSNQIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + I 
Sbjct: 113 FVVNGIYRIVVNQILISPGIYYRLELDHNRIN--YIYTGTLISDWGRRSKLEIDGGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
            R+ R+RK+ +   L A+G++ EEIL   +    +              + +      ++
Sbjct: 171 ARVSRKRKISIPVLLSAMGLNLEEILDNTHYPERFLFLLKKKKGKWEREEYLWSR--ENA 228

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           +++       +      +  L K L+EK  +               +  ++    EI+
Sbjct: 229 ILEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNQKLNLDIPENEIF 286


>gi|313183939|ref|YP_004021793.1| RNA polymerase beta subunit [Equisetum arvense]
 gi|281371659|gb|ADA63592.1| RNA polymerase beta subunit [Equisetum arvense]
          Length = 1071

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 159/507 (31%), Positives = 235/507 (46%), Gaps = 63/507 (12%)

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            E + +   ++++ L  + +   +  G  +  G   VG         +     +L A    
Sbjct: 612  ERSNNNTCMNQKPL--LCKDKFLRQGQIIADGASTVG-------GELALGRNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +   +       R+ I+ +  S   E+   E+   +       LD
Sbjct: 663  EGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSQGPEKLTREIPHLNNH-ILRHLD 721

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             N   +L     G    +G     K T L        P  +  Q     E +      LK
Sbjct: 722  ENGLVKL-----GSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                     ++ R  +        D +       + +F+  KR IQ GDK+AGRHGNKGI
Sbjct: 777  -----VPVGVKGRVIDIRWVFHEDDFINFSD--TIHIFILQKRKIQVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L++GTPVD++L+PLGVPSRMNVGQIFE  LG A   L K  + +  D 
Sbjct: 830  ISKILPRQDMPYLQNGTPVDMILSPLGVPSRMNVGQIFECLLGLAGNFLNKHYRIIPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F  ++      T     ++                              
Sbjct: 890  RYEREASRKLVF-SELYDASKQTSNPWLFE------------------------------ 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     D  G+S L DG TGE F++ VTVG  YM+KL H V DK++ARS+G Y+LVT
Sbjct: 919  --------PDHPGKSQLLDGRTGESFNQTVTVGKAYMMKLIHQVDDKIHARSSGPYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQP+ GKS RGGQRLGEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G    
Sbjct: 971  QQPVRGKSRRGGQRLGEMEVWALEGFGVAYILQEMLTTKSDHIQARYEVLGAILTGKPIP 1030

Query: 1340 ETG--TPESFNVLVKEMQALGLSIDLE 1364
            +     PESF +LV+E+++L L++  +
Sbjct: 1031 KPNNSVPESFRLLVRELRSLALNLTCD 1057



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 241/632 (38%), Positives = 364/632 (57%), Gaps = 14/632 (2%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            I+              +    ++   I    +                   +DAL+++Y
Sbjct: 167 RIWARVSKKRKVSIFILLLAIGLKPRDIFNGFNYPEILIKFFKRQVRDIHSVEDALVELY 226

Query: 379 RVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           + +    GDV    +        FF   +++L  +GR   N +L LD P +   +  +DI
Sbjct: 227 KSLYSITGDVLFSELIYKDLQKKFF-RQRFELGQIGRRNFNKKLELDVPKNEYFLLPQDI 285

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
           +A +  L+      GT+DDID+L NRRVRSV ++L++Q RL L R+E  I+   + ++  
Sbjct: 286 LAAVDHLIKANYRIGTLDDIDHLKNRRVRSVADLLQDQLRLSLERLELLIRQTMQEATKQ 345

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
              + P+ L+ + P ++   EFF S  LSQ  +  N LS I H R++SALG GG+ R  A
Sbjct: 346 KHFLTPEKLVTSTPFITTFKEFFGSHPLSQFMDQTNPLSEIVHKRKVSALGPGGLTRRTA 405

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              +RD+HP+HYGR+CP ETSEG N GL+SSL  +A++  YG +++P+ K+ +      +
Sbjct: 406 SFRVRDIHPSHYGRLCPIETSEGMNAGLISSLGIYAQLKKYGSLQSPFYKISNISDEEQI 465

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V LS  ++E   IA  +      G+  E+    R   E + +P  +++F    P Q  S+
Sbjct: 466 VQLSPNQDERYRIATGSFLAASWGAQEEQFTSARYQQEFLTIPWSQVNFRSFFPLQFFSV 525

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             SLIPFLE++D+NR LMG NMQRQAVPL K E   VGTG+E   A  SG+ + ++R G 
Sbjct: 526 GTSLIPFLEHNDANRALMGSNMQRQAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGK 585

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           +  +D  +I +   E              L+ ++RSN NTC+NQ+PL+     +R+  II
Sbjct: 586 LIYIDGEKITLFVDEETSINK-------NLLSYERSNNNTCMNQKPLLCKDKFLRQGQII 638

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADG ST  G+LALGRN+LVA+MPW GYNFED++LISER++ ED+FTS HIE +E+    T
Sbjct: 639 ADGASTVGGELALGRNILVAYMPWEGYNFEDAILISERLIYEDIFTSFHIERYEINVSFT 698

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKL 912
             GPE++TR+IP+++   L+++DE G++ +G+ V  GD+LVGK+TP         PE KL
Sbjct: 699 SQGPEKLTREIPHLNNHILRHLDENGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKL 758

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           L+AIFG + ++ R+T L+VP GV G V+D+R 
Sbjct: 759 LQAIFGTEVINARETCLKVPVGVKGRVIDIRW 790



 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 76/431 (17%), Positives = 148/431 (34%), Gaps = 30/431 (6%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--A 72
              GK       P+   +Q      FL +        ++G+     S   I         
Sbjct: 1   MSTGKKQGTFVPPEFGRIQSE---EFLRL-------VDQGIVDELTSFPKIEDGEKDCEF 50

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            L    Y          D ++   TY+  L +  +L           +  + IK Q + +
Sbjct: 51  RLFGEEYRLTESIVQEQDAIYECSTYSSDLYVLAQLT---------NRKNRTIKRQVVLL 101

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G LPLMT  G F+I G+ R+VVSQ+ RSPGI++  +       G  LY   II + G  +
Sbjct: 102 GSLPLMTSQGFFIINGVARVVVSQILRSPGIYYSRELDHK---GFPLYTGTIISNLGGRL 158

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSA 251
            +E D K  I  R+ ++RKV +   L+A+G+   +I + F YP+I+            S 
Sbjct: 159 KLELDKKARIWARVSKKRKVSIFILLLAIGLKPRDIFNGFNYPEILIKFFKRQVRDIHSV 218

Query: 252 ADLMVG--AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL--- 306
            D +V     + S   D+   E + +  +K        L + G +      +        
Sbjct: 219 EDALVELYKSLYSITGDVLFSELIYKDLQKKFFRQRFELGQIGRRNFNKKLELDVPKNEY 278

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
           ++    +      +      +     ++ + +  +R +  L  D +  +      L+   
Sbjct: 279 FLLPQDILAAVDHLIKANYRIGTLDDIDHLKNRRVRSVADLLQDQLRLSLERLELLIRQT 338

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            ++       +            +  +  F            + +  +    +++   P 
Sbjct: 339 MQEATKQKHFLTPEKLVTSTPFITTFKEFFGSHPLSQFMDQTNPLSEIVHKRKVSALGPG 398

Query: 427 DVRHIRKEDII 437
            +        +
Sbjct: 399 GLTRRTASFRV 409


>gi|302698289|ref|XP_003038823.1| DNA-dependent RNA polymerase II second largest subunit [Schizophyllum
            commune H4-8]
 gi|300112520|gb|EFJ03921.1| DNA-dependent RNA polymerase II second largest subunit [Schizophyllum
            commune H4-8]
          Length = 1204

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 197/1208 (16%), Positives = 360/1208 (29%), Gaps = 219/1208 (18%)

Query: 211  KVPVT------SFLMALGMDSEEILST---FYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            KVP+              +  +EI       Y    Y          ++   +       
Sbjct: 157  KVPIMLRSAFCILNK---LSDQEIYDLNECPYDSGGYFIINGSEKVLIAQERMATNHVYV 213

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI----VNGET 317
             +         + E  +       K++ +  VK    T +   G  +   I    V+   
Sbjct: 214  FAKAQPSPINFLAEI-RSAVEKGGKTISQFQVKMFHRTKERSMGNVIKATIPYIKVDIPI 272

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
              ++     + D   L+ I +       +  +    ++ ++              AL  I
Sbjct: 273  WVVFRALNVISDRDILDHICYESTDPQMLELLKPCIDDGFVIQEREV--------ALDFI 324

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                            +          +Y    + +  +      +  +  +        
Sbjct: 325  ------------GNRGTTTGLNRERRVRYAQEILQKELLPHVSMAEGSESKK---AYFFG 369

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDI 495
             ++  L+     +  +DD D+ G +R+   G +L   +R+   +M + +    +      
Sbjct: 370  YMVHRLLLAALERRELDDRDHFGKKRLDLAGPLLAGLFRMLFRKMTKDVYRYLQKCVESN 429

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I    +   +     +               +SQ+       S ++H RR +
Sbjct: 430  KDFNLNLAIKHHTISQGLKYSLATGNWGDQKKAGAAKAGVSQVLNRYTYASTLSHLRRCN 489

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
                  + R     + R +H TH+G +CPAET EG   GLV +L+  A ++  G I  P 
Sbjct: 490  T----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACIS-VGSISAPV 544

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                       +   +   E        N           +LV                 
Sbjct: 545  IDFLQEWNLESLEENARSSEATFTKVFVNGVWMGVHRDPAKLVETIRRLRRKD------- 597

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
              D S +  V             D+ RV     +      LL+       T         
Sbjct: 598  --DISQEVSVVRDIREKELRVYTDAGRVCRPLFIVENQSLLLEKHHVHALT---QGAKWD 652

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S       + GI+E +DA       +    +   +          Q++ +   +    + 
Sbjct: 653  SLV-----KQGIIELLDAEEEETVMIAMTPEDLENSRMTPEERAAQQAEEEVDMTATKVA 707

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFT 840
                           PS  LG       +  + +P+  +N          M  +   +F 
Sbjct: 708  HTMANTHTWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGIFL 760

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +  I                               +    +  +             +  
Sbjct: 761  TNFI-------------------------------LRMDTMANILYYPQKPLATTRSMEY 789

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +   +  + AI      +  D+ +   S +   +    I+ R   D  +   SV 
Sbjct: 790  LKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRGYTDMEK--KSVG 846

Query: 961  REQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E   +   D  + +    Y +L +   I  G           K+  +  D      
Sbjct: 847  MMPTEEFEKPSRDNTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPD------ 900

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      +E  QR     +    T     E    +++      D       ++++V 
Sbjct: 901  ---------SEELGQRTKNHTRRDVSTPLKSTESGIIDQVLLTTNED-----GKKLIRVR 946

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK A RHG KG +      EDMPF   G   DIV+NP  +PSRM +G + 
Sbjct: 947  VRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAQGIVPDIVINPHAIPSRMTIGHLV 1006

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L      +G +                                              
Sbjct: 1007 ECLLSKVATLIGNEGD-------------------------------------------- 1022

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                     +TP F     EA++  L      + G  ++Y G TG      V +G  Y  
Sbjct: 1023 ---------ATP-FTDLTVEAVSKSLAAKGFQQRGLEVMYHGHTGRKLQAQVYLGPTYYQ 1072

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            +L HMV DK+++R+ G   ++T+QP+ G+S  GG R GEME  C+ ++G A  L+E L  
Sbjct: 1073 RLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCMISHGIAGFLKERLFD 1132

Query: 1318 KSD-------DVVGRTRVYESIVAGNDTFETG------------TPESFNVLVKEMQALG 1358
             SD       D+ G T +  + +    +FE               P +  +L +E+QA+ 
Sbjct: 1133 ASDAYRLHVCDICGLTAI--ANLK-KQSFECRACKNKTACSQLYIPYAAKLLFQELQAMN 1189

Query: 1359 LSIDLENS 1366
            ++  L  +
Sbjct: 1190 IAPRLYTT 1197


>gi|321470077|gb|EFX81055.1| hypothetical protein DAPPUDRAFT_102782 [Daphnia pulex]
          Length = 1174

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 174/1089 (15%), Positives = 337/1089 (30%), Gaps = 211/1089 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G ++   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLMAFLFRALFKTLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGME 716
             + D  D   +          P L  ++   +L   +  M +Q   +  +    V TG+ 
Sbjct: 603  MVRDIQDREIRIYTDAGRICRPLLIVENCKLLLKKRHVDMLKQREYINFSWQELVATGV- 661

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                              VE +D +      +    +    G D Y              
Sbjct: 662  ------------------VEYIDTLEEETAMIAMSPEDLRQGKDAYCTTY---------- 693

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                                 P+  LG       +  + +P+  +N          M  +
Sbjct: 694  ---------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQ 731

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +   ++I  F                           ++    +  V        +   
Sbjct: 732  AMG--VYITNF---------------------------HVRMDTLAHVLQYPQKPLVTTR 762

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +      + AI      +  D+ +   S V         F  +   +++RS
Sbjct: 763  SMEYLRFRELPAGINSVVAILSYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDQESKRS 822

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLI 1013
               E    E   +   D    +   IY +L +   I  G           K+  L     
Sbjct: 823  ADQE----ETFEKPFRDHCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITL----- 873

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                            +   ++ES   ++    +    R        Q    +     + 
Sbjct: 874  ---------------PENDDDLESTTKKFSKRDASTFLRHSETGIVDQVMLTLNAEGNKF 918

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +
Sbjct: 919  CKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTI 978

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G + E   G      G+                                           
Sbjct: 979  GHLIECLQGKVSANKGEIGD---------------------------------------- 998

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         +TP  D  + + I+++L+       G  +LY+G TG   +  V +G 
Sbjct: 999  -------------ATPFNDAVNVQKISNLLQEYGYHLRGNEVLYNGHTGRKLNAQVFLGP 1045

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E
Sbjct: 1046 TYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRE 1105

Query: 1314 MLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQ 1355
             L   SD     V            R   +E    G        +   P +  +L +E+ 
Sbjct: 1106 RLFEVSDPYRIHVCNLCGIIAVANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELM 1163

Query: 1356 ALGLSIDLE 1364
            ++ ++  L 
Sbjct: 1164 SMNIAPRLM 1172



 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 144/984 (14%), Positives = 286/984 (29%), Gaps = 191/984 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +            +L+F       P  
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPAIDLQAEAQHSSGEVENPPRYVLKFEQIYLSKPTH 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +   V    E        + + Q  ++G +P
Sbjct: 99  WEKDGAPTAMMPNEARLRNLTYSAPLYVDITKTVHKEGEEQV-----ETQHQKTFIGKIP 153

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 154 IMLRSTYCLLNGMNDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 212

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  Y   I       ++        ++V +  R     +K               
Sbjct: 213 ----GKFAYKTEIR----SCLEHSSRPTSTLYVNMLARGGQGIKKSAIGQRIIAILPYIK 264

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 265 QEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGAR 324

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 325 GARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRREL 382

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+   +          +        +       +  
Sbjct: 383 DDRDHYGNKRLDLAGPLMAFLFRALFKTLMKEVRMYAQKFIDRGKDFNLE-------LAI 435

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
              + T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 436 KTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 495

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 496 AKPRQLHNTLWGMVCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 552

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 553 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMVRDIQDREI 612

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
              T  GRIC         +     L     V+     E       +   T  V Y+  +
Sbjct: 613 RIYTDAGRIC----RPLLIVENCKLLLKKRHVDMLKQREYINFSWQELVATGVVEYIDTL 668

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   IA +   L +                            +  P  ++ + AS+IP
Sbjct: 669 EEETAMIAMSPEDLRQG----------------KDAYCTTYTHCEIHPAMILGVCASIIP 712

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 713 FPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------ 742

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y               Q+PLV                  
Sbjct: 743 -----------RMDTLAHVLQYP--------------QKPLV----------TTRSMEYL 767

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE
Sbjct: 768 RFRELPAGINSVVAILSYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDQESKRSADQEE 827

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                       +       +D+ GII  G  V+  D+++GK     E+    E      
Sbjct: 828 TFEKPFRDHCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENDDDLESTT--- 884

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
               K    RD S  +    +G V
Sbjct: 885 ----KKFSKRDASTFLRHSETGIV 904


>gi|242910198|ref|YP_002970636.1| RNA polymerase b-subunit [Alsophila spinulosa]
 gi|218454867|gb|ACK77204.1| RNA polymerase b-subunit [Alsophila spinulosa]
          Length = 1082

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 154/482 (31%), Positives = 221/482 (45%), Gaps = 54/482 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G+++       G   +     +L A    +  +  D  L     +   +  
Sbjct: 638  VMPGELLKGGEVVADGAATVG-GELALGRNILVAYMPWEGYNSEDAVLISERSIYEDIST 696

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 RH ++    +   ER   E+   D       LD N       +  G    +G   
Sbjct: 697  SFHIERHEVEVCATNQGPERVTKEIPQLD-SYALRHLDNN-----GLVESGSWVEAGDVS 750

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T          P  +  Q           + + +            R  +      
Sbjct: 751  VGKLTPQEGADSLRAPEGRLSQ-----AISGIQLVNARESCLKVPIGRRGRVIDVRWVYP 805

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
              D M      V+ +++  KR IQ GDK+AGRHGNKGIVS+ILP +DMP+L+DGTPVD++
Sbjct: 806  EDDTMNDS--EVIHIYILQKRKIQVGDKIAGRHGNKGIVSKILPRQDMPYLQDGTPVDMI 863

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            L+PLGVPSRMNVGQIFE  LG A   L    + +  D +   + S    F E        
Sbjct: 864  LSPLGVPSRMNVGQIFECLLGLAGEFLKTHYRIVPFDERYEREASRKLVFSELC------ 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                           GA     N  L     +  G+S L DG T
Sbjct: 918  -------------------------------GASTGTRNPWLFE--PEHPGKSRLIDGRT 944

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++P+T+G  Y++KL H V DK++ARS+G Y+LVTQQPL G+S RGGQR+GEMEVW 
Sbjct: 945  GDPFEQPITIGKAYIMKLIHQVDDKIHARSSGPYALVTQQPLKGRSRRGGQRVGEMEVWA 1004

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-TPESFNVLVKEMQALGLS 1360
             +  G +Y LQEMLTIKSD +  R +V  +I  G    +    PESF +LV+E++ +GL+
Sbjct: 1005 SEGLGVSYTLQEMLTIKSDHIQARYKVPSAITTGKPIHKPNTVPESFRLLVRELRCMGLN 1064

Query: 1361 ID 1362
            ++
Sbjct: 1065 LE 1066



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 242/713 (33%), Positives = 388/713 (54%), Gaps = 21/713 (2%)

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           G  + +G+ + L  + ++  GI  +      G+      V  + G  +    D  D   +
Sbjct: 115 GTFIINGIARVLINQILRSPGIYYNRESDQKGVSAYTSTVISDRGGRFKSEMDKRDRIWV 174

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD-----------RKDALLDIYRVMR 382
                 ++  + +L    ++    ++N        +            +DA++++Y+ + 
Sbjct: 175 RISKKRKVSILILLIAMGLSRKDILQNVRYPKIFSNILKKQKWDIESPEDAIVELYKQLY 234

Query: 383 PGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
                    +ES+       F   + +L  +GR   N++L LD P+    +  +D++A  
Sbjct: 235 SATDVDIVFSESIVKELQKRFFQHRCELGRIGRRNSNIKLALDVPETEHFLLPQDVLAAA 294

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSV 498
              +++  G G +DDID+L NRRVRSV ++L+ Q +L L R+E  I++  R +      +
Sbjct: 295 DHSIEISYGMGNLDDIDHLKNRRVRSVADLLQEQLKLALNRLENPIRQNLRRAVRRKRPL 354

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            P+ L+ + PV++   EFF S  LSQ  +  N LS + H RRLS+LG GG+ R  A  + 
Sbjct: 355 TPRVLVTSVPVITTSKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSLGPGGLTRRTASFQA 414

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RD+H +HYGRICP ETSEG N GL+SSL   A+V+  G +++PY K+ +      +V LS
Sbjct: 415 RDIHFSHYGRICPIETSEGMNAGLISSLAIQAKVSNSGSLQSPYLKMSESSEEEQLVDLS 474

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             E++   +A  N  + E  +   E++  R   E + V  E++DF    P Q  SI ASL
Sbjct: 475 PAEDDYYRVATENLLISEWRTREREVIPVRYRQEFLSVLWEQVDFRSIHPLQYFSIGASL 534

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF+E++D+NR LMG  MQRQAVPL K E   VGTG+E  VA  SG   V++R G ++ +
Sbjct: 535 IPFIEHNDANRALMGSTMQRQAVPLFKPERCIVGTGLEGQVASDSGGVAVSEREGRIQYI 594

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           D  +I + + + +    +      RL  ++RSN NTC++Q+  V  G+ ++  +++ADG 
Sbjct: 595 DGNKITLSTTDEESGEKSLNTTDTRLRIYERSNNNTCIHQKSTVMPGELLKGGEVVADGA 654

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +T  G+LALGRN+LVA+MPW GYN ED++LISER + ED+ TS HIE  EV    T  GP
Sbjct: 655 ATVGGELALGRNILVAYMPWEGYNSEDAVLISERSIYEDISTSFHIERHEVEVCATNQGP 714

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAI 916
           E +T++IP +    L+++D  G++  G+ V  GD+ VGK+TP+  +     PE +L +AI
Sbjct: 715 ERVTKEIPQLDSYALRHLDNNGLVESGSWVEAGDVSVGKLTPQEGADSLRAPEGRLSQAI 774

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIELLA 968
            G + V+ R++ L+VP G  G V+DVR  +       +   I +   Q   + 
Sbjct: 775 SGIQLVNARESCLKVPIGRRGRVIDVRWVYPEDDTMNDSEVIHIYILQKRKIQ 827



 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 91/554 (16%), Positives = 192/554 (34%), Gaps = 49/554 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +P+L  +Q   ++ F+          NE L    K+   I           +S  Y+   
Sbjct: 16  LPELARIQFEGFNRFV----------NERLLEELKNFPKIEDTDKEVESRSISEQYQLTE 65

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P  +  D  ++ +TY+    +  +L              + ++E+++ +G +P M   GT
Sbjct: 66  PSVEERDAAYQCVTYSSDPYVPAQLTRNRD---------RIVQEEAVRLGAIPWMNSQGT 116

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI R++++Q+ RSPGI+++ +  +  +S    Y   +I D+G     E D +D I 
Sbjct: 117 FIINGIARVLINQILRSPGIYYNRESDQKGVSA---YTSTVISDRGGRFKSEMDKRDRIW 173

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD---LMVGAK 259
           VRI ++RKV +   L+A+G+  ++IL    YPKI  +          S  D    +    
Sbjct: 174 VRISKKRKVSILILLIAMGLSRKDILQNVRYPKIFSNILKKQKWDIESPEDAIVELYKQL 233

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLL----KSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
            S++ VDI   E +++  +K          +  +      L +         + +D++  
Sbjct: 234 YSATDVDIVFSESIVKELQKRFFQHRCELGRIGRRNSNIKLALDVPETEHFLLPQDVLAA 293

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
               I I    + +   ++ + +  +R +  L  + +          +    +       
Sbjct: 294 ADHSIEIS-YGMGNLDDIDHLKNRRVRSVADLLQEQLKLALNRLENPIRQNLRRAVRRKR 352

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +   +    V   + ++  F            + +  +    RL+   P  +       
Sbjct: 353 PLTPRVLVTSVPVITTSKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSLGPGGLTRRTASF 412

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               I       +  G I  I+         +  +          ++  S   +   + +
Sbjct: 413 QARDIHF-----SHYGRICPIETSEGMNAGLISSLAI------QAKVSNSGSLQSPYLKM 461

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
                ++ +              +  L   E        I    R        ++     
Sbjct: 462 SESSEEEQLVDLSPAEDDYYRVATENLLISEWRTREREVIPVRYRQEF-----LSVLWEQ 516

Query: 556 VEMRDVHPTHYGRI 569
           V+ R +HP  Y  I
Sbjct: 517 VDFRSIHPLQYFSI 530


>gi|222625458|gb|EEE59590.1| hypothetical protein OsJ_11898 [Oryza sativa Japonica Group]
          Length = 1218

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 189/1094 (17%), Positives = 344/1094 (31%), Gaps = 209/1094 (19%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V D+  LE I +       +  +      A++         
Sbjct: 294  LPYIRADIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV--- 350

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 AL  I +       +     E    +      K  L  VG             + 
Sbjct: 351  -----ALDYIGKR----GATVGVTKEKRIKYAKEILQKEMLPHVG-----------VGEF 390

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
                +      II  L+    G+   DD D+ GN+R+   G +L   +R+   ++ R ++
Sbjct: 391  CETKKAYYFGYIIHRLLMCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVR 450

Query: 488  ERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLS 533
              +     +   V  Q  I AK + S +     +              +SQ+   +   S
Sbjct: 451  SYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYAS 510

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ++H RRL++     + R     + R +H +H+G +CPAET EG   GLV +L     + 
Sbjct: 511  TLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYIT 566

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                       + +    N        EE +  +    + +  +G +           + 
Sbjct: 567  VGSAANPILEFLEEWGTEN-------FEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKT 619

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +   R +I   D + +  V     L       D  R      +      L+         
Sbjct: 620  LRRLRRQI---DVNTEVGVVRDIRLKELRLYTDYGRCSRPLFIVENQRLLI--------- 667

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                   +   A    +           +  I  ++ + + +T        +   R N  
Sbjct: 668  -----KKRHIRALQQRETPEEGWHDLVAKGFIEYIDTEEEETTMISMTINDLIGARHNPE 722

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               +                    PS  LG       +  + +P+  +N          M
Sbjct: 723  EAYS-----------ETYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSAM 764

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              + +   I++  ++                           +    +  V        +
Sbjct: 765  GKQAMG--IYVTNYQ---------------------------LRMDTLAYVLYYPQKPLV 795

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
                +       +      + AI      +  D+ +   S +        +F R   D+ 
Sbjct: 796  TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEE 854

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            ++  ++ +E+     R+          +          G           K++ +     
Sbjct: 855  KKMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPI----- 909

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                         QD+   +     K  + TS    E    +++      D +     R 
Sbjct: 910  ------------PQDDAQGQATRYTKRDHSTSLRHSESGMVDQVLLTTNADGL-----RF 952

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +
Sbjct: 953  VKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTI 1012

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E  +G     +GK+                                          
Sbjct: 1013 GQLIECIMGKVAAHMGKEGD---------------------------------------- 1032

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         +TP F     + I+  L        G   +Y+G TG      + +G 
Sbjct: 1033 -------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGP 1078

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E
Sbjct: 1079 TYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAFFLKE 1138

Query: 1314 MLTIKSDDVVGRTRVYE-----SIV---------AG----NDTFETGTPESFNVLVKEMQ 1355
             L  +SD    R  V E     +I           G     D  +   P +  +L +E+ 
Sbjct: 1139 RLFDQSD--AYRVHVCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELM 1196

Query: 1356 ALGLSIDLENSRTK 1369
            A+ ++  +     K
Sbjct: 1197 AMAIAPRMLTQDNK 1210



 Score =  255 bits (650), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 136/987 (13%), Positives = 284/987 (28%), Gaps = 192/987 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G QA F              + F
Sbjct: 68  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGRQAEFAETL--------HKISF 119

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   V            + ++
Sbjct: 120 GQIYLSKPMMTEADGETATLFPKSARLRNLTYSAPLYVDVSYRVMKKGHDCEE-VTETME 178

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG 162
              +++G +P+M +                         G F+I G ++++++Q   S  
Sbjct: 179 YPKVFIGKVPIMLRSSYCTLFQQSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTN 238

Query: 163 -IHFDHDKGRASLSGKLLYACRIIP-----DQGLWMDIEFD-----SKD----------I 201
            ++      +     K  Y   +       ++              +K           +
Sbjct: 239 HVY----VFKKRQPNKYAYVAEVRSMAENQNRPASSMFVRMLSRAGAKGGSSGQYIRATL 294

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
            ++R D    +P+     ALG  ++ +IL         +Q  +     L  A ++   +V
Sbjct: 295 PYIRAD----IPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV 350

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +   +        +   K++     + L+++ +  +G+   C          +      +
Sbjct: 351 ALDYIGKRGATVGVTKEKRIKYAK-EILQKEMLPHVGVGEFCETKKAYYFGYIIH---RL 406

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + A     E   +   +  +    P+L          +   + +   K   +      +
Sbjct: 407 LMCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQ 466

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIA 438
                   T  +  S+    +  +++          +N      T   +R +        
Sbjct: 467 FAIKAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREG 526

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +         +      ++KN   +  + +  +    +  ++    
Sbjct: 527 KLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWGT 583

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVE 557
              + I+   +  A   F     +         +  +   RR   +  + GV R     E
Sbjct: 584 ENFEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQIDVNTEVGVVRDIRLKE 643

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R ++  +     P    E   + +         + A    ETP     D      + Y+
Sbjct: 644 LR-LYTDYGRCSRPLFIVENQRLLIKKR-----HIRALQQRETPEEGWHDLVAKGFIEYI 697

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EEE   I+              +L+  R   E      E     +  P  ++ + AS
Sbjct: 698 DTEEEETTMISM----------TINDLIGARHNPE--EAYSETYTHCEIHPSLILGVCAS 745

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                           R   +  
Sbjct: 746 IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAY 785

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V                                       Q+PLV               
Sbjct: 786 V-----------------------------------LYYPQKPLV----------TTRAM 800

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                  L  G N +VA   + GYN EDS+++++  +    F S+    +    +     
Sbjct: 801 EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTL 860

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +E        +   +       +D+ G+   G  V+  D+++GK +P  +         
Sbjct: 861 VKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDD------- 913

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             A         RD S  +    SG V
Sbjct: 914 --AQGQATRYTKRDHSTSLRHSESGMV 938


>gi|257042699|gb|ACV32967.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  404 bits (1039), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 215/640 (33%), Positives = 326/640 (50%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DD                                          
Sbjct: 293 AAVDYLIGVKFGMGTLDDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF S  LSQ  +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 XXXXXXXXXXXXXXXFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 100/245 (40%), Gaps = 24/245 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEXXXXXXXXXLFGNEYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++  TY                  +   + + I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSXTY---------YSEXXXXARSXXXNSRKIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q   SPGI++  +     ++   +Y   +I D G    +E D  + I 
Sbjct: 113 FVVNGIYRIVVNQXXISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +  
Sbjct: 171 ARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAILE 230

Query: 263 SLVDI 267
               +
Sbjct: 231 FYKKL 235


>gi|320031539|gb|EFW13500.1| DNA-dependent RNA polymerase II RPB140 [Coccidioides posadasii str.
            Silveira]
          Length = 1205

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 193/1162 (16%), Positives = 368/1162 (31%), Gaps = 197/1162 (16%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYS------QRGDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L         IL       +Y+        G ++    S   L+   + + ++
Sbjct: 187  KMP--IMLK----SKYCILKDLGEHALYNWNECPYDSGGYFIINGSEKVLIAQERSAGNI 240

Query: 265  VDIDTGEQ------------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            V +                  +E G ++ S L   L  KG    G     +    +    
Sbjct: 241  VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLSIKLFAKGDSSKGGFGPTIRST-LPYIK 299

Query: 313  VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
             +     ++   G V DE  L  I +       +  +       ++         +DR+ 
Sbjct: 300  TDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFV--------IQDREV 351

Query: 373  ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            AL  I +    G   T    E    +      K  L  +              +     +
Sbjct: 352  ALDFISKR---GSSPTSMNHEKRVRYARDIIQKEFLPHI-----------SQSEGSETRK 397

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RI 490
               +  ++  L+    G+  +DD D+ G +R+   G +L N +R+  +R+ + + +  + 
Sbjct: 398  AFFLGYMVHKLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQR 457

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITH 537
                   +     + A  +   +     +               +SQ+       S ++H
Sbjct: 458  CVETNRQLYLNIGVKASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSH 517

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RR +      + R     + R +H TH+G +CPAET EG   GLV +L     +     
Sbjct: 518  LRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTP 573

Query: 598  IET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             E    +    + +V  +     +      ++      +  D S     V        I 
Sbjct: 574  SEPIIDFMIQRNMEVLEEFEPQVSPNSTKIFVNGVWVGVHRDPSHLVSTVQSLRRRNMIS 633

Query: 656  VPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                 + D  D   K          P F+ ++D      G  +  +           +  
Sbjct: 634  HEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVLTKEHIRKLEADKEIPA 693

Query: 714  GMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
             ++    +          ++G+VE VDA      ++   + P    V       +     
Sbjct: 694  DLDPEERRERYYGWDGLVKSGVVEYVDAEEEE--TIMIVMSPEDLEVSKQYQAGYIPEED 751

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             +  N+R   K+  +          PS  LG       +  + +P+  +N          
Sbjct: 752  TSDPNRRVRSKLSQKAHTWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSA 804

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            M  + +                     E   +I    ++ L                   
Sbjct: 805  MGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA------------------ 836

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 +       +   +  + AI      +  D+ +   S +   +     +  +    
Sbjct: 837  -TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT--- 892

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLS 1009
             +    +    +E   +    + + +    Y ++ +   +  G           K+  L+
Sbjct: 893  -DSEKMIGLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVAPGVRVSGEDIIIGKTAPLA 951

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +                +E  QR  +  K+   T     E    +++            
Sbjct: 952  PE---------------SEELGQRTKQHTKLDVSTPLRSTESGIVDQVLV-----STSNE 991

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             L+ VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PS
Sbjct: 992  DLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTFRQEDMPFTREGIVPDLIINPHAIPS 1051

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 1052 RMTIAHLIECQLSKVSSLRGYEGD------------------------------------ 1075

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++S+LR       G  ++Y+G TG      +
Sbjct: 1076 -----------------ATP-FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQI 1117

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+ 
Sbjct: 1118 FLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASA 1177

Query: 1310 VLQEMLTIKSD-------DVVG 1324
             L+E L   SD       D+ G
Sbjct: 1178 FLKERLFDVSDPFRIHICDICG 1199



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 105/802 (13%), Positives = 231/802 (28%), Gaps = 142/802 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              L+F +     
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTIAPDEDDPDPVMVRRYELKFGTVMLAR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDV-------------------D 114
           P               +   R+LTYA PL + +   + +                    D
Sbjct: 97  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKKIAEGRERSLAERDEDDDEPDAKGD 156

Query: 115 EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
           E   A+              +  E++I++G +P+M K                       
Sbjct: 157 EERRARGTYLQWEPKALPEDEADEENIFIGKMPIMLKSKYCILKDLGEHALYNWNECPYD 216

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 217 SGGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 273

Query: 198 SKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D  +                 +P+     ALG +  E+IL+        + 
Sbjct: 274 IK--LFAKGDSSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 331

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +          + +K        ++++ +  +  + 
Sbjct: 332 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQSE 391

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V + ++    G   ++  D   +K L+           +L++    +
Sbjct: 392 GSETRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 450

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 451 LYKYVQRCVETNRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 503

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 504 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 563

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
              Y       E  I    + +   ++   PQ   N+  +      F     +    +  
Sbjct: 564 LMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKI------FVNGVWVGVHRDPS 617

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +S +   RR + +                      R   P       P   + G  + 
Sbjct: 618 HLVSTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 677

Query: 582 LVSSL-------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
               +          A ++     E  Y        +  V Y+ A EEE   I  +   L
Sbjct: 678 TKEHIRKLEADKEIPADLDPEERRER-YYGWDGLVKSGVVEYVDAEEEETIMIVMSPEDL 736

Query: 635 DEDGSFTEELV-------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +    +    +         R    ++          +  P  ++ I AS+IPF +++ S
Sbjct: 737 EVSKQYQAGYIPEEDTSDPNRRVRSKLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAP 709
            R      M +QA+ +      
Sbjct: 797 PRNTYQSAMGKQAMGVFLTNFD 818


>gi|302668317|ref|XP_003025731.1| hypothetical protein TRV_00102 [Trichophyton verrucosum HKI 0517]
 gi|291189857|gb|EFE45120.1| hypothetical protein TRV_00102 [Trichophyton verrucosum HKI 0517]
          Length = 1205

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 182/1071 (16%), Positives = 349/1071 (32%), Gaps = 167/1071 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 261  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 319

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 320  NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 368

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 369  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 417

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 418  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 477

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 478  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 533

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 534  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNMEVLEEFEP 593

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 594  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 653

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 654  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 712

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 713  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 771

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 772  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 823

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 824  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 855

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 856  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 911

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 912  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 956

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 957  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 1011

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 1012 FASRHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1071

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 1072 YEGD-----------------------------------------------------ATP 1078

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     ++++S+LR       G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 1079 -FTDVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHA 1137

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            R+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD
Sbjct: 1138 RARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSD 1188



 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 144/1050 (13%), Positives = 300/1050 (28%), Gaps = 218/1050 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     ++V P              L+F +     
Sbjct: 37  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTVPPSDDEPDPVVLRRYELKFGTVMLAR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 96  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSERDEEEEEIEEKGD 155

Query: 116 ------------FTGAKSIKDIKEQSIYMGDLPLMTKD---------------------- 141
                               + +E++I++G +P+M K                       
Sbjct: 156 EERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLGEQALYNWNECPYD 215

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 216 SGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLS 272

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 273 IK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 330

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +       +  + +K        ++++ +  +  + 
Sbjct: 331 MLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDIIQKEFLPHISQSE 390

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L++    +
Sbjct: 391 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKD 449

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +   +  +    +       T  +  ++    + +  K   S  G  
Sbjct: 450 LYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVS 502

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 503 QVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 562

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                      E  I    + +   ++   PQ   N+  V      F     +    +  
Sbjct: 563 LMCCITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKV------FVNGVWVGVHRDPA 616

Query: 530 NSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           + +  +   RR + +                      R   P       P   + G  + 
Sbjct: 617 HLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVDNDPKSENSGSLVL 676

Query: 582 LVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +   +    A       ++   R+           +  + Y+ A EEE   I      L+
Sbjct: 677 VKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEEETIMIVMTPEDLE 736

Query: 636 EDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               +         +     R     +          +  P  ++ I AS+IPF +++ S
Sbjct: 737 ASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQS 796

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +         T  E  +   +                        
Sbjct: 797 PRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL--------------------- 828

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PL                      +L  
Sbjct: 829 ---------------------------YYPQKPL----------ATTRSMEFLKFRELPA 851

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E     + 
Sbjct: 852 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERFEKPMR 911

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK +P     + PE + L     +   
Sbjct: 912 SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPEAEELGQRTKQH-- 964

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              D S  + S  SG V  V +   +   K
Sbjct: 965 TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 994


>gi|254581920|ref|XP_002496945.1| ZYRO0D11770p [Zygosaccharomyces rouxii]
 gi|238939837|emb|CAR28012.1| ZYRO0D11770p [Zygosaccharomyces rouxii]
          Length = 1224

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 193/1178 (16%), Positives = 369/1178 (31%), Gaps = 176/1178 (14%)

Query: 240  QRGDFWCFPLSAADLMVGAKVSSS---LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
            +  + +    + +DL    +          I+  E+V+ + ++    +++  K+     +
Sbjct: 175  RSKNCYLSDATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPI 234

Query: 297  GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS----V 352
               ++      + +      T ++ + A +    ++++       +DIPI+ +      +
Sbjct: 235  SHVAE--IRSALEKGSRFISTLQVKLFAREGNSSRTIKATLPYIKQDIPIVIIFRALGII 292

Query: 353  NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             +   + +      +    + L               ++             K       
Sbjct: 293  PDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYA 352

Query: 413  RVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            R  +           +     +   +  +I  L+     +   DD D+ G +R+   G +
Sbjct: 353  RDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRRDQDDRDHFGKKRLDLAGPL 412

Query: 471  LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L   ++    ++ R I    + +  +      +  INAK + S +     +         
Sbjct: 413  LAQLFKTLFRKLTRDIFRYMQRTVEEAKDFNMKLAINAKTITSGLKYALATGNWGEQKKA 472

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 473  MSSRAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETP 528

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG   GLV +L+  + ++           + +  +     Y+   +         N    
Sbjct: 529  EGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYI-PHQSPEATRVFVNGVWH 587

Query: 636  EDGSF----TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                      E L   R  G+         D  +   K          P    DD   + 
Sbjct: 588  GVHRNPARLMETLRTLRRKGDINPEVSMVRDIREKELKIFTDAGRVYRPLFIVDDDETLN 647

Query: 692  MGCNMQRQAVP--LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                  R+     L+  E   +  G E                G+VE +DA        E
Sbjct: 648  RKELRIRKGHISKLMATEYQDIEGGFE---DSEEYTWTSLLNDGLVEYIDAE------EE 698

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
              +  S    D+  + +   +  +  + +R  +K              PS  LG  A   
Sbjct: 699  ETILISMQPEDLEPVQENTFNEDDDDLARR--IKATHHATTFTHCEVHPSMILGVAA--- 753

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
                + +P+  +N          M  + +   + +  + V                    
Sbjct: 754  ----SIIPFPDHNQSPRNTYQAAMGKQAMG--VFLTNYNVRM------------------ 789

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 790  ---------DTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI 840

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +   +    +F R  +D+ ++      E  E   R           +       I
Sbjct: 841  MNQSSIDRGLF-RSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI 899

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+T +S D      R+ +         ++     +  Q        
Sbjct: 900  APGVRVSGEDIIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQILI----- 954

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                 L+ VKV V   +  Q GDK A RHG KG +      EDM
Sbjct: 955  ---------------TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYGREDM 999

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   D+++NP  +PSRM V  + E  L       G +                  
Sbjct: 1000 PFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGD---------------- 1043

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                 ++P F     E I+ +LR     
Sbjct: 1044 -------------------------------------ASP-FTDITVEGISKLLREHGYQ 1065

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G  ++Y+G TG+     +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  
Sbjct: 1066 SRGFEVMYNGHTGKKLMSQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRD 1125

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN------ 1336
            GG R GEME  C+ A+GAA  L+E L   SD        + G   V   +          
Sbjct: 1126 GGLRFGEMERDCMIAHGAAAFLKERLMEASDAFRVHICGICGLMSVVAKLNHNQFECRGC 1185

Query: 1337 ----DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                D ++   P +  +L +E+ A+ ++  L   R+K+
Sbjct: 1186 DNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSKD 1223


>gi|257042614|gb|ACV32885.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 232/640 (36%), Positives = 357/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++          
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTXXGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++Y  ICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYXXICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395108|gb|ACI45371.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+G++ E HLGWA  G+G++I  L+   +    +S LRSFL++V  +    
Sbjct: 1    NPLGVPSRMNIGRVLEVHLGWARKGIGQRIGDLL---QQQAKVSELRSFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLRQGVPYATPVFDGASEAEIKDMLMLAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVTGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|29565582|ref|NP_817162.1| RNA polymerase beta subunit [Pinus koraiensis]
 gi|41017711|sp|Q85X54|RPOB_PINKO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|29469681|gb|AAO74009.1| RNA polymerase beta subunit [Pinus koraiensis]
 gi|257042642|gb|ACV32912.1| RNA polymerase beta subunit [Pinus monticola]
 gi|257042727|gb|ACV32994.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/640 (36%), Positives = 360/640 (56%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|166034413|gb|ABY78983.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. ITTG S11]
          Length = 214

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 148/214 (69%), Positives = 177/214 (82%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            ++I  ++  YKA+G+I PLR  +  V+G G   E++ D+DDDSVLR+A+QWK GV ++TP
Sbjct: 61   RQIGDMLEAYKASGNIEPLRKTIGDVVGDGPKAEQVKDFDDDSVLRLADQWKRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N+ML +A L ESGQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAHEGDVNAMLALAGLKESGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|257042584|gb|ACV32856.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 232/640 (36%), Positives = 356/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGAXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                 + +    +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 XXXXXXVTSTLFKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|309322404|ref|YP_003934484.1| RNA polymerase beta chain [Cathaya argyrophylla]
 gi|307683330|dbj|BAJ19637.1| RNA polymerase beta chain [Cathaya argyrophylla]
          Length = 1076

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 160/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SLHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GIVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGL- 1359
            ++ +G AY+LQEMLT+KSD +  R +V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNKVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1360 -SIDLENSRTKNSAKME 1375
             +  + + +     + E
Sbjct: 1059 SNHAIISEKDFQIDREE 1075



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/626 (37%), Positives = 354/626 (56%), Gaps = 15/626 (2%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
           +LEEI  +       L++       + R   +  + K   +    +Y V   GD+     
Sbjct: 191 NLEEILDNTRYPERFLFLLKKKKGRWEREEYLWSREKAILEFYKKLYCV--SGDLVFSES 248

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
                   FF   + +L  +GR   N +LNLD P++      +D++A +  L+ ++ G G
Sbjct: 249 LCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVLAAVDYLIGVKFGMG 307

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
           T+DDID+L NRR+RSV ++L+NQ+RL L R+E +I+  I         PQ+L+ +  + +
Sbjct: 308 TLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAIRRTIHRAIKRRSTPQNLVTSTILKN 367

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
              +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+HP++YGRICP
Sbjct: 368 TFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIHPSYYGRICP 427

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--MEEENRYIAQ 629
            +TSEG N GLV+S +  A++   G +++P+ K+ +      +VYL     E+E   IA 
Sbjct: 428 IDTSEGMNAGLVASSSIHAKIGHCGSLQSPFYKISERSREEHMVYLLPGEDEDEYYRIAT 487

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            N      G   E++   R   E I++  E+I F    P Q  S+  SLIPFLE++D+NR
Sbjct: 488 GNYLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPLQYFSVGVSLIPFLEHNDANR 547

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA+        
Sbjct: 548 ALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV-------- 599

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                        +L+ + RSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+
Sbjct: 600 NITSSVNGDTVRTKLVIYNRSNTNTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGK 659

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVA+MPW GYNFED++LISER+V ED++TS+HI  + +    T  GPE ITR+IP++ 
Sbjct: 660 NVLVAYMPWEGYNFEDAILISERLVYEDIYTSLHIVRYRIEICMTSQGPERITREIPHLD 719

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDT 927
              L+++DE GI+ +G+ +  GD+LVGK+TP+        PE +LL+ IFG +    R+ 
Sbjct: 720 AHSLRHLDENGIVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTAREN 779

Query: 928 SLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LR P G  G V+DVR  NR     +
Sbjct: 780 CLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 122/300 (40%), Gaps = 29/300 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          N+GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------NQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYKSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+   PGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILIGPGIYYRSELEHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R+RK+ +   L A+G++ EEIL        +              + +      
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKKGRWEREEYLWSR--E 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            ++++       +      +  L K L+EK  +               +  ++    EI+
Sbjct: 227 KAILEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNPNQKLNLDIPENEIF 286


>gi|229544489|gb|ACQ76425.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 133/237 (56%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVRTSELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     G+P +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGMPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLRHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395114|gb|ACI45375.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
 gi|209395117|gb|ACI45377.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 138/237 (58%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +     S LR FLE V  +   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QEQAKASELRKFLEVVYNSRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            EK+    DD +L +A Q K GVP +TPVFDGA E  I  ML +A                
Sbjct: 58   EKLELLSDDELLTMAAQLKDGVPYATPVFDGASEAEIKDMLEIAYPEAIAQRMGLTPTRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|317155939|ref|XP_001825469.2| DNA-directed RNA polymerase II subunit RPB2 [Aspergillus oryzae
            RIB40]
          Length = 1221

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 172/988 (17%), Positives = 322/988 (32%), Gaps = 160/988 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 349  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 408

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 409  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASAKAGVSQV 468

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 469  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 524

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     V      E    +    + +V  +            ++      +  D +    
Sbjct: 525  LALMCYVTVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGIHRDPAHLVN 584

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMGCNMQRQA 700
             +        I      I D  +   K          P   ++ND  +    G  + ++ 
Sbjct: 585  TMQSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGGLVLNKEH 644

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            +  L+ +             +         R+G+VE VDA       +    +       
Sbjct: 645  IRKLEQDKELPPDLDPEDRRERYFGWDGLVRSGVVEYVDAEEEETIMISMTPEDLEISKQ 704

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            +           +     R ++    +          PS  LG       +  + +P+  
Sbjct: 705  LQAGYALPEEELDPNKRVRSILS--QKAHTWTHCEIHPSMILG-------VCASIIPFPD 755

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +                     E   +I    ++ L       
Sbjct: 756  HNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA------ 799

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 800  -------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVVMNQSSIDRGLF 846

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D  +         +E   +    + + + +  Y +L E   I  G     
Sbjct: 847  -RSLFYRTYTDSEKMVGL---TVVERFEKPMRQDTIGMRKGTYDKLDEDGIIAPGVRVSG 902

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  L+ D                +E  QR     K+   T     E    +++
Sbjct: 903  EDIIIGKTAPLAPD---------------AEELGQRTKAHTKLDVSTPLRSTESGIVDQV 947

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                  DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 948  LVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSREGVA 1002

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+V+NP  +PSRM +  + E  L       G +                          
Sbjct: 1003 PDLVINPHAIPSRMTIAHLIECQLSKVSALRGFEGD------------------------ 1038

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  ++Y
Sbjct: 1039 -----------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEVMY 1068

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            +G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEM
Sbjct: 1069 NGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEM 1128

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFE 1340
            E  C+ A+GA+  L+E L   SD       D  G       +  G          +   +
Sbjct: 1129 ERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPVAKLKKGLFECRLCNNKHRISQ 1188

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ ++ ++  +  +R+
Sbjct: 1189 VHIPYAAKLLFQELASMNIAARMFTNRS 1216



 Score =  196 bits (497), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 144/1024 (14%), Positives = 297/1024 (29%), Gaps = 189/1024 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 23  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPDEDEVDPVV--VRRYELKFGTVML 79

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFT-------GAKSIKD 124
             P               +   R+LTYA PL + +   + +  E +         +  +D
Sbjct: 80  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERSVADRDDEEIEEDED 139

Query: 125 IKEQS-IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
            K Q  +++G +P+M K                         G F+I G ++++++Q  R
Sbjct: 140 RKAQETVFIGKVPIMLKSKYCILKDLSEQALYNWNECPYDSGGYFIINGSEKVLIAQE-R 198

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDR--------- 208
           S G        + +      Y   I    ++G  +  +   K  +  + D          
Sbjct: 199 SAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLK--LFAKGDSAKGGFGPTI 254

Query: 209 -------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
                  +  +P+     ALG +  E+IL+        +   +     +    ++   +V
Sbjct: 255 RSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDREV 314

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVN 314
           +   +      Q   + ++      + ++++ +  +  +           G  V   ++ 
Sbjct: 315 ALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGSETRKAFFLGYMV-HRLLQ 373

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              G   ++  D   +K L+           +L+     +        V    +  ++  
Sbjct: 374 CALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD----LQRYVQRCVETNREIY 429

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
           L+I          T  +  ++    + +  K   +  G  ++  R    +      R   
Sbjct: 430 LNIG---IKASTLTGGLKYALATGNWGEQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT 486

Query: 433 KEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
                  I     L N   G +   +    +    V  +    Y       E  I    +
Sbjct: 487 PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSEPIIDFMIQ 546

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGG 548
            +   ++   PQ   NA  V      F     +    +  + ++ +   RR + +  +  
Sbjct: 547 RNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPAHLVNTMQSLRRRNMISHEVS 600

Query: 549 VARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN------AY 595
           + R     E        R   P       P   + G  +     +    +          
Sbjct: 601 LIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGGLVLNKEHIRKLEQDKELPPDLDP 660

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS-------FTEELVFCR 648
                 Y        +  V Y+ A EEE   I+     L+             EEL   +
Sbjct: 661 EDRRERYFGWDGLVRSGVVEYVDAEEEETIMISMTPEDLEISKQLQAGYALPEEELDPNK 720

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +          +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 721 RVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT-- 778

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                         + A I+      +    ++  +          +   +  Y      
Sbjct: 779 -------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSG---- 827

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                   NQ                    S  +   ++ R +  +       + E  + 
Sbjct: 828 -------YNQE------------------DSVVMNQSSIDRGLFRSLFYRTYTDSEKMVG 862

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +              +E FE   R   +G          + +     +DE GII  G  V
Sbjct: 863 L------------TVVERFEKPMRQDTIG----------MRKGTYDKLDEDGIIAPGVRV 900

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           +  DI++GK  P         ++        KA    D S  + S  SG V  V +   +
Sbjct: 901 SGEDIIIGKTAPLAPDAEELGQRT-------KAHTKLDVSTPLRSTESGIVDQVLVSTSN 953

Query: 949 GIDK 952
              K
Sbjct: 954 DDLK 957


>gi|257042782|gb|ACV33047.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 183/591 (30%), Positives = 271/591 (45%), Gaps = 15/591 (2%)

Query: 369 DRKDALLDIYRVMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            R+ A+L+ Y+ +    GD+             FF   + +L  +GR  +N +LNLD P+
Sbjct: 223 SREKAILEFYKKLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPE 281

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +                       GT+                                 
Sbjct: 282 NEIFSXXXXXXXXXXXXXXXXXXMGTLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 341

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
                                       +FF S  LSQ  +  N                
Sbjct: 342 XXXXXXXXXXXXXXXXXXXXXXXXXXXXDFFGSHPLSQFLDQTNPXXXXXXXXXXXXXXX 401

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                           P++YGRI P +T    N GLV        +   G +++P+ K+ 
Sbjct: 402 XXXXXXXXXXXXXXXXPSYYGRIXPIDTXXXMNAGLVXXXXXXXXIXXCGSLQSPFYKIS 461

Query: 607 DGKVTNDVVYLSA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           +      +VYL     E+E   IA  NS     G   E++   R   E I++  E+I F 
Sbjct: 462 ERSREEHMVYLLPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFR 521

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              P Q  S+  SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG
Sbjct: 522 SIFPFQYFSVGVSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSG 581

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  +A + G +E +DA+                       + +QRSN NTC +Q+P V+ 
Sbjct: 582 SVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQ 633

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI
Sbjct: 634 GECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHI 693

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   
Sbjct: 694 VRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTE 753

Query: 905 PM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
               TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 754 ESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804


>gi|228017004|gb|ACP51827.1| RNA polymerase beta subunit [Pinus canariensis]
          Length = 1077

 Score =  404 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 633  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 691

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 692  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 745

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 746  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 803

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 804  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 858

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 859  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 918

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 919  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 939

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 940  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 999

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 1000 LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1059

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1060 LNHAIISEKNFQIDREE 1076



 Score =  359 bits (920), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 234/688 (34%), Positives = 367/688 (53%), Gaps = 23/688 (3%)

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           ++ G+    +    +   I +  L   +     +  + GE          + S+  +  +
Sbjct: 128 ISPGIYYRSELDHNRINYIYTGTLISDWGRRSKLEIDVGERIWARVSRKQKISIPVLLSA 187

Query: 340 EIRDIPILYVD--------SVNNNAYIRNTLVTDKNKDRKDALLDIYRVM--RPGDVSTF 389
              ++  +  +         +            +    R+ A+L+ Y+ +    GD+   
Sbjct: 188 MGLNLEEILDNTRYPERFLFLLKKKKKERWEREEYLWSREKAILEFYKKLYCISGDLVFS 247

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
                     FF   + +L  +GR  +N +LNLD P++      +D++A +  L+ ++ G
Sbjct: 248 ESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVLAAVDYLIGVKFG 306

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I         PQ+L+ +  +
Sbjct: 307 MGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRRSTPQNLVTSTLL 366

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +   +FF         +  N    I H R+LS LG GG+    A    RD+HP++YGRI
Sbjct: 367 KNTFQDFFGXXXXXXXXDQTNPXXEIAHGRKLSHLGPGGLTGRTASFRTRDIHPSYYGRI 426

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--MEEENRYI 627
           CP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     E+E   I
Sbjct: 427 CPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYLLPGEDEDEYYRI 486

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIPFLE++D+
Sbjct: 487 ATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVGVSLIPFLEHNDA 546

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA+      
Sbjct: 547 NRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV------ 600

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                            + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+L
Sbjct: 601 --NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSL 658

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP+
Sbjct: 659 GKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPH 718

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVR 925
           +    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R
Sbjct: 719 LDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTAR 778

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           +  LR P G  G V+DVR  NR     +
Sbjct: 779 ENCLRAPIGGKGRVIDVRWINRVDDSGD 806



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 55/209 (26%), Positives = 101/209 (48%), Gaps = 27/209 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS 230
           I  R+ R++K+ +   L A+G++ EEIL 
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILD 197


>gi|228016620|gb|ACP51449.1| RNA polymerase beta subunit [Pinus albicaulis]
          Length = 1075

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 229/640 (35%), Positives = 353/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N      H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNXXXDFFGXXXXXXXXDQTNPXXXXAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|166034411|gb|ABY78982.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. CFN ESH34]
          Length = 214

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 150/214 (70%), Positives = 178/214 (83%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            ++I  LI  YKANG+I PLR  +  V+G G   E++ D+DDDSVLR+A+QWK GV ++TP
Sbjct: 61   RQIGELIEAYKANGNIEPLRKTIGDVVGDGPKAEQVQDFDDDSVLRLADQWKRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA+E  +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGANEADVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|324986355|ref|YP_004276227.1| RNA polymerase beta subunit [Pinus lambertiana]
 gi|323514204|gb|ADX89751.1| RNA polymerase beta subunit [Pinus lambertiana]
          Length = 1075

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 230/640 (35%), Positives = 355/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +F          +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFXXXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|215254215|gb|ACJ64112.1| RNA polymerase beta subunit [Vibrio hepatarius]
 gi|215254219|gb|ACJ64114.1| RNA polymerase beta subunit [Vibrio hepatarius]
          Length = 404

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 255/402 (63%), Positives = 314/402 (78%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 2   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLIN 61

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E G+F+EEL
Sbjct: 62  SLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEQGTFSEEL 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE  L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L
Sbjct: 122 ITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           KA+ P VGTG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L
Sbjct: 182 KADKPLVGTGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNL 241

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFE
Sbjct: 242 TKYTRSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFE 301

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           DS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +
Sbjct: 302 DSILVSERVVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYI 361

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+ 
Sbjct: 362 GAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKT 403


>gi|257042555|gb|ACV32828.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 231/640 (36%), Positives = 354/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                 + +    +   +FF S  LSQ  +  N L+ I   R LS LG GG+    A   
Sbjct: 353 XXXXXXVXSTLFKNTFQDFFGSHPLSQFLDQTNPLTEIXXXRXLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|50303683|ref|XP_451784.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640916|emb|CAH02177.1| KLLA0B05577p [Kluyveromyces lactis]
          Length = 1221

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 165/980 (16%), Positives = 307/980 (31%), Gaps = 168/980 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ R I    +
Sbjct: 368  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTRDILRFMQ 427

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             S  +      +  + A  + + +     +               +SQ+       S ++
Sbjct: 428  RSVEEAKDFNLKLAVKATTITAGLKYALATGNWGEQKKSMSSRAGVSQVLNRYTYSSTLS 487

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++  G
Sbjct: 488  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS-VG 542

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEIL 655
                P     +      +      +  +      N           +LV   R    +  
Sbjct: 543  TDPLPIITFLNEWGMEPLEDYIPHQSPDATRVFVNGVWHGIHRNPAKLVDTIRKLRRKGD 602

Query: 656  VPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQAV--PLLKAEAPF 710
            +  E     D   K             P    D++          ++     L+  E   
Sbjct: 603  ITPEVSIVRDIREKELKIFTDAGRVYRPLFIVDENPETGRKELKVKKGHVRKLMLTEYQD 662

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            +  G +     +          G+VE +DA       +    +     +      +    
Sbjct: 663  IEGGFDDEEEMN-YTWTSLLNEGLVEYIDAEEEETILIAMQHEDLDPALLPVADSEDDLD 721

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                       ++              PS  LG  A       + +P+  +N        
Sbjct: 722  PARR-------IRAIHNSNIFTHCEIHPSMILGVAA-------SVIPFPDHNQSPRNTYQ 767

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              M  + +   + +  + V                               +  +      
Sbjct: 768  SAMGKQAMG--VFLTNYNVRM---------------------------DTMANILYYPQK 798

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                   +       +   +  + AI      +  D+ +   S +   +    +F R  +
Sbjct: 799  PLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFRSYM 857

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTV 1007
            D+ +R   +     E   +      + +    Y +L +   I  G           K+T 
Sbjct: 858  DQEKR---IGMSITESFEKPHRTNTLRMKHGTYDKLDDDGLIAPGVRVSGDDMIIGKTTP 914

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +  D      R+ +         ++     +  Q                          
Sbjct: 915  IPPDAEELGQRTAFHSKRDASTPLRSTENGIVDQVLI--------------------TTN 954

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
               L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +
Sbjct: 955  QEGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRTEDMPFTAEGVVPDLIINPHAI 1014

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V  + E  L       G +                                    
Sbjct: 1015 PSRMTVAHLIECLLSKVAALSGNEGD---------------------------------- 1040

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                               ++P F     + I+ +LR       G  ++Y+G TG+    
Sbjct: 1041 -------------------ASP-FTDITVDGISRLLREHGYQSRGFEVMYNGHTGKKLMA 1080

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+GA
Sbjct: 1081 QIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGA 1140

Query: 1308 AYVLQEMLTIKSD----DVVGRTRVYESIVAGND-------------TFETGTPESFNVL 1350
            A  L+E L   SD     + G   +   +                   ++   P +  +L
Sbjct: 1141 AAFLKERLMEASDAFRVHICGICGLMSVVAKLKHNQFECRSCKNKIDIYQVHIPYAAKLL 1200

Query: 1351 VKEMQALGLSIDLENSRTKN 1370
             +E+ A+ ++  L   R+K+
Sbjct: 1201 FQELMAMNIAPRLYTDRSKD 1220



 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 140/1009 (13%), Positives = 288/1009 (28%), Gaps = 171/1009 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ-AAFKSVFPITAF-SGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   I      +  L           T   S    + F       P  
Sbjct: 37  LVSQQLDSFNQFINYTIQDLILEDSTLILEQLAQHTTETDNISRKYEISFGKIYLAKPSM 96

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA---------KSIKDIKE 127
                        +   R+LTYA  L + ++   +   +  G          +S ++ + 
Sbjct: 97  TESDGVSHAMYPQEARLRNLTYASGLFVEIQKRTYQAIDIPGRDLKYEIITEESEENEEN 156

Query: 128 QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGI 163
             I++G +P+M +                         G F+I G ++++++Q  RS G 
Sbjct: 157 NKIFIGRVPIMLRSKYCLLDDLTESDLYRLKECPFDMGGYFIINGSEKVLIAQE-RSAGN 215

Query: 164 HFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR---IDRRRK------- 211
                  + S    + +   I    ++G         K  ++ R     R  K       
Sbjct: 216 I--VQVFKKSAPSPISHIAEIRSALEKGSRFISTLQVK--LYGREGSTSRTIKATLPYIK 271

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG+  + EIL      +   Q  +     +    ++   + +   +   
Sbjct: 272 QDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEEGFVIQDRETALDFIGRR 331

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                I+  K++       L+++ +  +                +      + + A D  
Sbjct: 332 GTALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCALDRK 387

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           D+   +      +    P+L          +   ++    +  ++A     ++       
Sbjct: 388 DQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTRDILRFMQRSVEEAKDFNLKLAVKATTI 447

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   S  G  ++  R    +      R          +     
Sbjct: 448 TAGLKYALATGNWGEQKKSMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQ 507

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   +  + +       I+ ++   + P +   
Sbjct: 508 LHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTDPLPIITFLNEWGMEPLEDYI 564

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                 A   F               +  I   RR   +            +   +    
Sbjct: 565 PHQSPDATRVFVNGVWHGIHRNPAKLVDTIRKLRRKGDITPEVSIVRDIREKELKIFTDA 624

Query: 566 YGRICPAET------SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-------N 612
                P         +    + +         +  Y  IE  +    +   T        
Sbjct: 625 GRVYRPLFIVDENPETGRKELKVKKGHVRKLMLTEYQDIEGGFDDEEEMNYTWTSLLNEG 684

Query: 613 DVVYLSAMEEENRYIAQ----ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V Y+ A EEE   IA      + +L       ++L   R                +  P
Sbjct: 685 LVEYIDAEEEETILIAMQHEDLDPALLPVADSEDDLDPARRIRAIH--NSNIFTHCEIHP 742

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ +AAS+IPF +++ S R      M +QA+ +                         
Sbjct: 743 SMILGVAASVIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV------------------ 784

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                                     + + +  Y       +     +  R         
Sbjct: 785 -----------------------RMDTMANILYYPQKPLGTTRAMEYLKFR--------- 812

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          +L  G+N +VA   + GYN EDSM++++  +   +F S+    + 
Sbjct: 813 ---------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYM 857

Query: 849 VMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              +   +   E        +   +       +D+ G+I  G  V+  D+++GK TP   
Sbjct: 858 DQEKRIGMSITESFEKPHRTNTLRMKHGTYDKLDDDGLIAPGVRVSGDDMIIGKTTPI-- 915

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P   EE   R  F       RD S  + S  +G V  V I       K
Sbjct: 916 -PPDAEELGQRTAF----HSKRDASTPLRSTENGIVDQVLITTNQEGLK 959


>gi|228017123|gb|ACP51944.1| RNA polymerase beta subunit [Pinus cembra]
          Length = 1075

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 229/640 (35%), Positives = 353/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+      +   +           +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTXTLFKNTXXDXXGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395042|gb|ACI45327.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 163/237 (68%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +     S LRSFLE+V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDLL---QQQAKASELRSFLEEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  DE            
Sbjct: 58   EDLAQLSDADLLSMAANLQQGVPYATPVFDGASEAEIKDMLALAYPDEIARRKGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TG+ F+RP T+GY++ LKL+H+V DK+ AR TG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGDRFERPTTIGYMHYLKLHHLVDDKMRARPTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|157279408|dbj|BAF80154.1| RNA polymerase beta subunit [Vibrio penaeicida]
          Length = 448

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 268/448 (59%), Positives = 348/448 (77%)

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
           RPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K
Sbjct: 1   RPGEPPTKEAAEALFESLFFAEERYDLSTVGRMKFNSSIEREDALEQGTLDEVDIIEVMK 60

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
            L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQ
Sbjct: 61  KLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQ 120

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           DLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDV
Sbjct: 121 DLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDV 180

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           H THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++
Sbjct: 181 HVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIQ 240

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E    IAQANS L E+G+F EELV  R  GE  L PR+++D++D +  QVVS+AASLIPF
Sbjct: 241 EGQFIIAQANSGLTEEGTFVEELVTARQKGESGLHPRDQVDYMDVATNQVVSVAASLIPF 300

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
           LE+DD+NR LMG NMQRQAVP L+A+ P VGTG+E  VA  SG   VAKR G+++ VDA 
Sbjct: 301 LEHDDANRALMGANMQRQAVPTLRADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDAS 360

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTD
Sbjct: 361 RIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTVLPGEPVARGDVLADGPSTD 420

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           LG+LALG+NM +AFMPW+GYNFEDS+L+
Sbjct: 421 LGELALGQNMRIAFMPWNGYNFEDSILV 448


>gi|228016058|gb|ACP50896.1| RNA polymerase beta subunit [Pinus rzedowskii]
          Length = 1075

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNSMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 229/640 (35%), Positives = 353/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N      H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGXXXXXXXXDQTNPXXXXAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|331029443|gb|AEC49871.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 6395]
          Length = 268

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 150/258 (58%), Positives = 196/258 (75%), Gaps = 1/258 (0%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+T
Sbjct: 8   PXGGRLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVT 67

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ F
Sbjct: 68  LRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFF 127

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           DHDKG+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D 
Sbjct: 128 DHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGIDG 187

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           E ILSTFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT G  
Sbjct: 188 EAILSTFYKKILYKRTKEAWRVPFDA-NRFRGYSTVTDLIDADTGKVVLEAGKKLTLGAD 246

Query: 286 KSLKEKGVKFLGITSDCL 303
           + L++KG K L    + L
Sbjct: 247 RQLQQKGXKALRSPGEAL 264


>gi|69216916|gb|AAZ03992.1| RNA polymerase beta chain [Ginkgo biloba]
          Length = 1072

 Score =  403 bits (1036), Expect = e-109,   Method: Composition-based stats.
 Identities = 164/581 (28%), Positives = 239/581 (41%), Gaps = 60/581 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LG 857
                       +        G   E  + +    V   +       E+      T    G
Sbjct: 546  MGSNMQRQAIPLFQPEKCITGTGLEGQVALDSGSV--TIAIQEGRIEYTDAENITFSFNG 603

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                T  +          + +   +  G  V  G IL        E  ++P + +L A  
Sbjct: 604  DTIGTELVLYQRSNKNTCMHQKPRVRQGECVKKGQILAD-GAATVEGELSPGKNILVAYM 662

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  L     V   +       RHGI     S   ER   E+   D       
Sbjct: 663  PWEGYNFEDAILISERLVYEDIYTSFHIERHGIRTCMTSQGPERITKEIPHLDAHL-LRH 721

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD N       ++ G    +G     K T    +     P  +  +           V +
Sbjct: 722  LDEN-----GLVMLGSWIETGDVLVGKLTPQKEEESLCAPEGRLLRTIFG-----IQVST 771

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             +            R  +     +   +        V V++  KR IQ GDK+AGRHGNK
Sbjct: 772  ARESCLRVPIGGRGRVIDVRWIHEE--ENSGDNAETVHVYILQKRKIQVGDKVAGRHGNK 829

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+S++LP +DMP+ ++GTPVD+V NPLGVPSRMNVGQIFE   G A   + K  +    
Sbjct: 830  GIISKVLPRQDMPYSQNGTPVDMVFNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPF 889

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              +   + S    F E    +                               VF+     
Sbjct: 890  GERYEREASRKLVFPELYRASEQTANPW------------------------VFE----- 920

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                       D  G++ L DG TG+ F++PVT+G  Y+ KL H V DK++ARS+G Y+L
Sbjct: 921  ----------PDHPGKNRLIDGRTGDLFEQPVTIGKAYIPKLIHQVDDKIHARSSGPYAL 970

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPL GKS RGGQR+GEMEVW ++  G AY+ QEMLT+KSD ++ R  V  +I+ G  
Sbjct: 971  VTQQPLRGKSKRGGQRVGEMEVWALEGSGVAYISQEMLTLKSDHIIARHEVLGAIITGEP 1030

Query: 1338 TFETG-TPESFNVLVKEMQALG--LSIDLENSRTKNSAKME 1375
              + G  PESF +LV+E+++L   L+  + + +     K E
Sbjct: 1031 IPKPGTVPESFRLLVRELRSLAPELNHAIISEKDFQIDKKE 1071



 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 226/599 (37%), Positives = 344/599 (57%), Gaps = 15/599 (2%)

Query: 361 TLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                  +  ++A+L+ ++ +    GD+                  + +L  +GR   N 
Sbjct: 212 QKRKKYLRSEENAILEFHKKLYCVGGDLVFSESLCKELQKKSL-QQRCELGRIGRRNPNQ 270

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
           +LNLD P++      +D++A     + ++ G GT+DD+D+L N+R+RSV ++L+NQ+ L 
Sbjct: 271 KLNLDIPENEIFSLPQDVLAAADYSIRVKFGMGTLDDMDHLKNKRIRSVADLLQNQFGLA 330

Query: 479 LLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           L R+  S++  I           P++L+ + P+ +   +FF    LSQ  +  N L+   
Sbjct: 331 LGRLVNSVRRTIRRATKCKCLPTPKNLVTSTPLTTTFQDFFGLHPLSQFLDQTNPLTEAV 390

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R+LS LG GG+ R  A   +RD+HP+HYGRICP ETSEG N GLV+SL   A++   G
Sbjct: 391 HRRKLSYLGPGGLTRRTASFRIRDIHPSHYGRICPIETSEGINAGLVASLAIHAKIGHCG 450

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            + +P+ K+ +G     +VY S  E+E   IA  NS     G   E++   R   E + +
Sbjct: 451 SLRSPFHKISEGSKEEHMVYPSPGEDEYYRIATGNSLALNQGIQEEQVTPARYRQEFLAI 510

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            RE+I F    P Q  S+  SLIPFLE++D+NR LMG NMQRQA+PL + E    GTG+E
Sbjct: 511 AREQIHFRSIFPFQYFSVGVSLIPFLEHNDANRALMGSNMQRQAIPLFQPEKCITGTGLE 570

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SG+  +A + G +E  DA        E              L+ +QRSN+NTC+
Sbjct: 571 GQVALDSGSVTIAIQEGRIEYTDA--------ENITFSFNGDTIGTELVLYQRSNKNTCM 622

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +Q+P V+ G+ V++  I+ADG +T  G+L+ G+N+LVA+MPW GYNFED++LISER+V E
Sbjct: 623 HQKPRVRQGECVKKGQILADGAATVEGELSPGKNILVAYMPWEGYNFEDAILISERLVYE 682

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D++TS HIE   +    T  GPE IT++IP++    L+++DE G++ +G+ +  GD+LVG
Sbjct: 683 DIYTSFHIERHGIRTCMTSQGPERITKEIPHLDAHLLRHLDENGLVMLGSWIETGDVLVG 742

Query: 897 KITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           K+TP+ E      PE +LLR IFG +    R++ LRVP G  G V+DVR  +      +
Sbjct: 743 KLTPQKEEESLCAPEGRLLRTIFGIQVSTARESCLRVPIGGRGRVIDVRWIHEEENSGD 801



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 77/338 (22%), Positives = 141/338 (41%), Gaps = 35/338 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP   ++Q   +  F+          ++GL     +   I          L    Y+   
Sbjct: 12  IPGFGQIQFEGFCRFI----------DQGLIEELSNFPEIEYTDQEIESRLSGKKYKSAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P  +  + +++ LTY+  L +  RLI          K+ + I++Q++++G++PLM   GT
Sbjct: 62  PLIEERNAVYQSLTYSSELYVPARLI---------QKNRRKIQKQTVFLGNIPLMNSRGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV Q+ RSPGI++  + G    +G  +Y   II D G    +E D K  I 
Sbjct: 113 FVVNGISRIVVDQILRSPGIYYSSEPG---HNGIAIYTGTIISDWGGRPKLEIDGKTRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY------SQRGDFWCFPLSAADLMVG 257
            R+ R++KV +   L A+G + EEIL       ++       Q+   +      A L   
Sbjct: 170 ARVSRKQKVSIPVLLSAMGSNFEEILDNVCYPEIFLSFLNGRQKRKKYLRSEENAILEFH 229

Query: 258 AKVSSSLVDIDTGEQVIES--GKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
            K+     D+   E + +    K L     L +  +    + L +         + +D++
Sbjct: 230 KKLYCVGGDLVFSESLCKELQKKSLQQRCELGRIGRRNPNQKLNLDIPENEIFSLPQDVL 289

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                 I ++   +     ++ + +  IR +  L  + 
Sbjct: 290 AAADYSIRVK-FGMGTLDDMDHLKNKRIRSVADLLQNQ 326


>gi|228017503|gb|ACP52318.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 228/640 (35%), Positives = 349/640 (54%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 XXXXXXXXXXXXXXXXXDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228017630|gb|ACP52443.1| RNA polymerase beta subunit [Pinus peuce]
          Length = 1075

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  357 bits (916), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 228/640 (35%), Positives = 348/640 (54%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                             FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 XXXXXXXXXXXXXXXFQXFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 138/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D+ + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDAGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|108773040|ref|YP_635950.1| beta subunit of RNA polymerase fragment a [Scenedesmus obliquus]
 gi|122179536|sp|Q1KVX4|RPOB1_SCEOB RecName: Full=DNA-directed RNA polymerase subunit beta N-terminal
           section; AltName: Full=PEP; AltName:
           Full=Plastid-encoded RNA polymerase subunit beta
           N-terminal section; Short=RNA polymerase subunit beta
           N-terminal section
 gi|88696606|gb|ABD48232.1| beta subunit of RNA polymerase fragment a [Scenedesmus obliquus]
          Length = 726

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 205/742 (27%), Positives = 350/742 (47%), Gaps = 44/742 (5%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IPDL+E+Q+  + + L           +G+        PIT F     + F    Y    
Sbjct: 8   IPDLVEIQRQGFFYLL----------EKGIIEEISKRNPITCFEKQIEIFFYPQYYRLTK 57

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P + +   ++   +Y     I ++L           +  K I  + I +   PLMT  G 
Sbjct: 58  PFYSIQQAIFYKKSYVSKFYIPVQLT---------DRKTKRIFLKWILLAHFPLMTNRGH 108

Query: 144 FVIKGIQRIVVSQLHRSPGIHFD---HDKGRASLSGK-----LLYACRIIPDQGLWMDIE 195
           F++ G  R++++QL RSPGI+F    H+      S K       +   II  +G W+ IE
Sbjct: 109 FLLNGSARVIINQLVRSPGIYFRENMHEIFSNKWSEKPSTTFRRFYADIICLKGTWLRIE 168

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLM 255
            D    +  ++ +  K+P+  FL+ +G+  + IL++ Y  +   Q        +  +   
Sbjct: 169 CDKDFSMWAKMKKGPKIPLLWFLLGMGLSEKYILNSVYKPMNLLQSFTKEMEKMQKSKSS 228

Query: 256 VGAKVSSSLVDIDTGEQVIESGK-KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
              K           EQ+ +  K K T      LK+   K        + G    +    
Sbjct: 229 KELKYPYISSTKQAWEQIQKLFKLKKTLRKFSFLKKNEEK----PKTFIFGQSSTKIEAK 284

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
               + +    + +  ++     + +   +   +      N   +     +K +      
Sbjct: 285 VVFSD-FAAFNNSVKRENTVFASNDDTFLVQTSFETKKKKNTRKKENFQKNKTQKTTKLS 343

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           L          +  + +    F   F +   YDL   GR  +N +L L  P +   +   
Sbjct: 344 LQNKEKRVASKLEAYELGRKWFANKFMNPRTYDLGKQGRWLINKKLGLTIPLEQTTLTAL 403

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK------- 487
           D++     L+ + +G   IDDID+L N+RVR+ GE L+  + +GL+R+E+SI+       
Sbjct: 404 DVLTATDSLMKIEDGFFEIDDIDHLKNKRVRTAGEALQEIFSIGLIRLEKSIRLKLNGNG 463

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           ++             L++ +P+  A  EFF +  LSQ  + +N L+ ITH RRLS+LG G
Sbjct: 464 QQSFFQKTSFFNFDSLMSTRPINGAFREFFGTHPLSQFMDQINPLAEITHKRRLSSLGPG 523

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           GV+R  A + +R +HP+HYGRICP ET EG N GLV+S+T++++++ +G++E+P+ KV  
Sbjct: 524 GVSRDTATLAIRGIHPSHYGRICPIETPEGKNTGLVNSITTYSKISFHGYLESPFYKVYK 583

Query: 608 GKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
           G+V  +  V YLS  ++++   A  + +L   G   ++ +  R     + +   K+  + 
Sbjct: 584 GQVQRNLGVFYLSPDKDDHFQTATPDLNLTPLGFLPKKPIPVRIGKRFVRMKTHKLALMG 643

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SP Q++S+A S IPFLE+DD+NR LMG NMQRQAVPL++ E P +GTG+E+ V   SG 
Sbjct: 644 VSPLQMISVATSFIPFLEHDDANRALMGSNMQRQAVPLIRPERPLIGTGLEARVVSDSGH 703

Query: 726 AIVAKRAGIVEQVDAIRIVIRS 747
           AI+AK +G +      +I + +
Sbjct: 704 AILAKTSGYIVYSSGSKIYLYT 725


>gi|209395075|gb|ACI45349.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +       LR FL +V  +   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGQRIGDML---QQQAKAGELREFLHEVYNSRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D+ ++ +AE   +GVP +TPVFDGA EE I  MLR+A                
Sbjct: 58   ENLAQLSDEELVAMAENLTNGVPYATPVFDGASEEEIKDMLRIAYPDDIARRKGLTPTRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGHMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GE+EVW ++AYGAAYVLQEMLT+KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEVEVWALEAYGAAYVLQEMLTVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|22086501|gb|AAM90661.1|AF401091_1 RNA polymerase beta subunit [Ehrlichia canis]
          Length = 475

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 276/475 (58%), Positives = 365/475 (76%), Gaps = 1/475 (0%)

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            KDAL +IY+V+R G+  +    ++ F+ LFF+ ++YDLSTVGR+K+N  L L+  +D+ 
Sbjct: 2   MKDALFEIYKVLRSGESPSLDTIKAFFDGLFFEKERYDLSTVGRIKLNDHLGLNVSEDIT 61

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            + K+DII +IK LV LR+G+G++DDID+LGNRRVRSVGE ++NQ+R+G+LR+ER I + 
Sbjct: 62  VLTKDDIIHVIKKLVLLRDGEGSVDDIDHLGNRRVRSVGEFIENQFRIGILRLERMIMDY 121

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +SSV+ D+ MP   ++      +   F  SSQLSQ  +  N LS +TH RRLSALG GG+
Sbjct: 122 MSSVNFDNAMPCRFLSILDFSYSFKRFLYSSQLSQFMDQTNPLSEVTHKRRLSALGPGGL 181

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R RAG E+RDVHPTHYGRICP ET EG NIGL+SSL  +AR+N +GFIE+PYRKV  G 
Sbjct: 182 TRERAGFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYARINKHGFIESPYRKVDKGV 241

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  G  ++V RE++D+ID SPK
Sbjct: 242 VTDKVEYLLAMQESNYYIADASATLDENNQFVDDMLYCRHDGNFVMVKREEVDYIDVSPK 301

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP +GTGMES+VA  SG  ++A
Sbjct: 302 QIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPLIGTGMESIVAAGSGTVVLA 361

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           KR GIV +VD + IVIR+ + + +    GVD+Y L KFQRSN NTC+NQRPLVK GD V+
Sbjct: 362 KRGGIVHRVDGLYIVIRAFDQEKNEY-LGVDVYNLRKFQRSNHNTCINQRPLVKPGDYVK 420

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            ND+IADG + D G+LALG+N+LVAFM W GYNFEDS++IS  +V +DVFTSIHI
Sbjct: 421 ANDVIADGSAIDQGELALGKNVLVAFMSWQGYNFEDSIVISSEVVKKDVFTSIHI 475


>gi|309322337|ref|YP_003934188.1| RNA polymerase beta chain [Cedrus deodara]
 gi|307683263|dbj|BAJ19571.1| RNA polymerase beta chain [Cedrus deodara]
          Length = 1076

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 159/497 (31%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G I+       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQIMADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHILRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMKKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 237/695 (34%), Positives = 379/695 (54%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIHYRLELDHNRINYIYTGTLISDWGRRSKLEIDMGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     ++         ++R++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKKGRREREEYLWSKENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENDIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ+
Sbjct: 299 LIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQN 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           L+ +  + +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A    RD+H
Sbjct: 359 LVTSTLLKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIGHCGSLQSPFYKISERSREEHMVYLLPGEG 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVLAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +                       + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 V--------NITSSVYGDTVRTESVMYQRSNTNTCTHQKPKVRQGECVKKGQIMADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHILRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 116/271 (42%), Gaps = 29/271 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFV----------DQGLMEELHNFPKIEDTDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q +++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQIVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGIH+  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIHYRLELDHNRIN--YIYTGTLISDWGRRSKLEIDMGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R+RK+ +   L A+G++ EEIL        +              + +      
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKKGRREREEYLWSK--E 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +++++       +      +  L K L+EK 
Sbjct: 227 NAILEFYKKLYCVSGDLVFSESLCKELQEKF 257


>gi|257042670|gb|ACV32939.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 214/640 (33%), Positives = 329/640 (51%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ                       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQXXXXXXXXXXXXXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                 + +    +   +FF S  LSQ  +  N L+ I                      
Sbjct: 353 XXXXXXVTSTLFKNTFQDFFGSHPLSQFLDQTNPLTEIAXXXXXXXXXXXXXXXXXXXXX 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
               HP++YGRICP +TSEG N GLV S    A++   G +++P+ K+ +      +VYL
Sbjct: 413 XXXXHPSYYGRICPIDTSEGMNAGLVXSXXIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228016122|gb|ACP50959.1| RNA polymerase beta subunit [Pinus sibirica]
          Length = 1075

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  347 bits (891), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 221/640 (34%), Positives = 340/640 (53%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N              G GG+    A   
Sbjct: 353 XXXXXXXXXXXXXXTXQDFFGXXXXXXXXDQTNPXXXXXXXXXXXXXGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|238498864|ref|XP_002380667.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus flavus NRRL3357]
 gi|83774211|dbj|BAE64336.1| unnamed protein product [Aspergillus oryzae]
 gi|220693941|gb|EED50286.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus flavus NRRL3357]
          Length = 1254

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 172/988 (17%), Positives = 322/988 (32%), Gaps = 160/988 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 382  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 441

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 442  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASAKAGVSQV 501

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 502  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 557

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     V      E    +    + +V  +            ++      +  D +    
Sbjct: 558  LALMCYVTVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGIHRDPAHLVN 617

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMGCNMQRQA 700
             +        I      I D  +   K          P   ++ND  +    G  + ++ 
Sbjct: 618  TMQSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGGLVLNKEH 677

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            +  L+ +             +         R+G+VE VDA       +    +       
Sbjct: 678  IRKLEQDKELPPDLDPEDRRERYFGWDGLVRSGVVEYVDAEEEETIMISMTPEDLEISKQ 737

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            +           +     R ++    +          PS  LG       +  + +P+  
Sbjct: 738  LQAGYALPEEELDPNKRVRSILS--QKAHTWTHCEIHPSMILG-------VCASIIPFPD 788

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +                     E   +I    ++ L       
Sbjct: 789  HNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA------ 832

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 833  -------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVVMNQSSIDRGLF 879

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D  +         +E   +    + + + +  Y +L E   I  G     
Sbjct: 880  -RSLFYRTYTDSEKMVGL---TVVERFEKPMRQDTIGMRKGTYDKLDEDGIIAPGVRVSG 935

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  L+ D                +E  QR     K+   T     E    +++
Sbjct: 936  EDIIIGKTAPLAPD---------------AEELGQRTKAHTKLDVSTPLRSTESGIVDQV 980

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                  DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 981  LVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSREGVA 1035

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+V+NP  +PSRM +  + E  L       G +                          
Sbjct: 1036 PDLVINPHAIPSRMTIAHLIECQLSKVSALRGFEGD------------------------ 1071

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  ++Y
Sbjct: 1072 -----------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEVMY 1101

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            +G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEM
Sbjct: 1102 NGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEM 1161

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG----------NDTFE 1340
            E  C+ A+GA+  L+E L   SD       D  G       +  G          +   +
Sbjct: 1162 ERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPVAKLKKGLFECRLCNNKHRISQ 1221

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ ++ ++  +  +R+
Sbjct: 1222 VHIPYAAKLLFQELASMNIAARMFTNRS 1249



 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 143/1042 (13%), Positives = 294/1042 (28%), Gaps = 207/1042 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPDEDEVDPVV--VRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE---------------- 115
             P               +   R+LTYA PL + +   + +  E                
Sbjct: 95  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERSVADRDDEEIEEDED 154

Query: 116 ----------FTGAKSIKDIKEQSIYMGDLPLMTKD------------------------ 141
                               KE+++++G +P+M K                         
Sbjct: 155 RKARGTYLQWEQKELPADQAKEETVFIGKVPIMLKSKYCILKDLSEQALYNWNECPYDSG 214

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
           G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   K
Sbjct: 215 GYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLK 271

Query: 200 DIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRG 242
             +  + D                 +  +P+     ALG +  E+IL+        +   
Sbjct: 272 --LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPML 329

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT--- 299
           +     +    ++   +V+   +      Q   + ++      + ++++ +  +  +   
Sbjct: 330 EMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGS 389

Query: 300 ---SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
                   G  V   ++    G   ++  D   +K L+           +L+     +  
Sbjct: 390 ETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD-- 446

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 V    +  ++  L+I          T  +  ++    + +  K   +  G  ++
Sbjct: 447 --LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASAKAGVSQV 501

Query: 417 NMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKN 473
             R    +      R          I     L N   G +   +    +    V  +   
Sbjct: 502 LSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALM 561

Query: 474 QYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            Y       E  I    + +   ++   PQ   NA  V      F     +    +  + 
Sbjct: 562 CYVTVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPAHL 615

Query: 532 LSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLV 583
           ++ +   RR + +  +  + R     E        R   P       P   + G  +   
Sbjct: 616 VNTMQSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGGLVLNK 675

Query: 584 SSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             +    +                Y        +  V Y+ A EEE   I+     L+  
Sbjct: 676 EHIRKLEQDKELPPDLDPEDRRERYFGWDGLVRSGVVEYVDAEEEETIMISMTPEDLEIS 735

Query: 638 GS-------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                      EEL   +     +          +  P  ++ + AS+IPF +++ S R 
Sbjct: 736 KQLQAGYALPEEELDPNKRVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRN 795

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                   + A I+      +    ++  +      
Sbjct: 796 TYQSAMGKQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELP 846

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               +   +  Y              NQ                    S  +   ++ R 
Sbjct: 847 AGQNAIVAIACYSG-----------YNQE------------------DSVVMNQSSIDRG 877

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +  +       + E  + +              +E FE   R   +G            +
Sbjct: 878 LFRSLFYRTYTDSEKMVGL------------TVVERFEKPMRQDTIGM----------RK 915

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +DE GII  G  V+  DI++GK  P         ++        KA    D S  
Sbjct: 916 GTYDKLDEDGIIAPGVRVSGEDIIIGKTAPLAPDAEELGQRT-------KAHTKLDVSTP 968

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V +   +   K
Sbjct: 969 LRSTESGIVDQVLVSTSNDDLK 990


>gi|228016816|gb|ACP51642.1| RNA polymerase beta subunit [Pinus attenuata]
          Length = 1074

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE  LG A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLLGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  342 bits (876), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 223/640 (34%), Positives = 341/640 (53%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERFLFLLKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +            
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAXXXXXXXXXXXX 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N             LG GG+    A   
Sbjct: 352 XXXXXXXXXXXXXXXXQDFFGXXXXXXXXDQTNXXXXXXXXXXXXHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGVQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/341 (19%), Positives = 139/341 (40%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + +++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKMQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDFWCFPL--------SA 251
           I  R+ R++K+ +   L  +G++ EEIL    +  + ++  + + W              
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERFLFLLKKERWEREEYLWSREKAIL 228

Query: 252 ADLMVGAKVSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                   +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|269930843|gb|ACZ54156.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 406

 Score =  403 bits (1035), Expect = e-109,   Method: Composition-based stats.
 Identities = 303/407 (74%), Positives = 352/407 (86%), Gaps = 1/407 (0%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSAL
Sbjct: 1   AIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +
Sbjct: 121 IIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SG
Sbjct: 181 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           AA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV V
Sbjct: 241 AAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHV 299

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V + DIIADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHI
Sbjct: 300 GDRVEKGDIIADGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHI 359

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           EEFEV ARDTKLGPEEITRDIPNV+EE L+N+DE GII +GAEV PG
Sbjct: 360 EEFEVAARDTKLGPEEITRDIPNVAEEALRNLDEAGIIYIGAEVQPG 406


>gi|300707573|ref|XP_002995989.1| hypothetical protein NCER_100983 [Nosema ceranae BRL01]
 gi|239605241|gb|EEQ82318.1| hypothetical protein NCER_100983 [Nosema ceranae BRL01]
          Length = 1143

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 181/1080 (16%), Positives = 350/1080 (32%), Gaps = 214/1080 (19%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            IY   G + D++  + I  +   ++  L  +S+  +A +++  V         AL  I +
Sbjct: 245  IYRALGFLSDKEITDHIITTNDDEMFDLLKESILESAVVQDQNV---------ALDYIGK 295

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
               P                      +    + +  +      +  +  +      +  +
Sbjct: 296  RAAP------------VGSSREKRINFAKDLLAKELLPHIGTQEFCETKK---AYFLGYM 340

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM--ERSIKERISSVDIDS 497
            ++ L+ +  G+   DD D+ G +R+   G +L + +R    ++  E +   +        
Sbjct: 341  VQKLLLVALGRKREDDRDHYGKKRMDLAGPLLASLFRSLYKKLCSETAKHMQKCIEGGRD 400

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSAL 544
                  + A  +         +               ++Q+    N +S ++H RR++  
Sbjct: 401  FNIALGLKASTIAQGFRYAIATGNWGDQAHAMQSKAGVAQVLNRYNFVSTLSHLRRVNT- 459

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + +     + R +H TH+G ICPAET EG   GLV +L+  A ++     E     
Sbjct: 460  ---PIEKEGKLAKPRQLHNTHWGMICPAETPEGQACGLVKNLSLMAYISVGSSSEPIVEF 516

Query: 605  VCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI- 661
            + +   +   ++ +L        ++      + ED  +    +       EI      I 
Sbjct: 517  LEECGLESLEEISHLQLQNATKVFVNGVWVGIHEDPEYLISSLRMLRRTLEIDKEVSIIR 576

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D  +   K          P     ++   +      ++ +             +E +  +
Sbjct: 577  DIREKEIKIQSDSGRPCRPLFVVKNNKLCIDEAYSNKEEIKRCTWNDFIENGLIEFLDVE 636

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                +++A     +  V                           K  R++++  +N    
Sbjct: 637  EEEVSMIAMSPDQLNSV--------------------------KKDLRASEDLNINY--- 667

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                            P+T LG       +  + +P+  +N          MV + +   
Sbjct: 668  ----------THCEIHPATILG-------ICASVIPFPDHNQSPRNTYQSAMVKQAMGI- 709

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                                              +    +  +        +    +   
Sbjct: 710  ----------------------------YATNFMLRMDTLSNILFYPQKPLVTTKSMEYI 741

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                + P +  + AI      +  D+ +   S +   +     F R   D+   +     
Sbjct: 742  RFKELPPGQNAIVAIASYTGYNQEDSIIMNQSAIDRGLF-RSFFYRTYTDQENTTRPGTH 800

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+     R +      L+ +       I  G           K + +     S      +
Sbjct: 801  EEFCKPLRSEVIRMRNLNYSKLDNDGIIPTGTRVTGDDVLIGKVSPILDPERSTKGNPVY 860

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                            LK    TS    ED F + +              +  KV V   
Sbjct: 861  ----------------LKKDSSTSMRRTEDGFVDSVIVTNK------EGYKFAKVKVRSC 898

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK A RH  KG V   L  EDMPF  +G   DI++NP  +PSRM +G + E  +
Sbjct: 899  RIPQMGDKFASRHAQKGTVGITLNQEDMPFTSEGIVPDIIINPHAIPSRMTIGHLIECLM 958

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G  C   G++                                                  
Sbjct: 959  GKTCALTGEEGD------------------------------------------------ 970

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +TP F+G   + I+  L+  +  + G  ++Y+G+TG      + +G  Y  +L H
Sbjct: 971  -----ATP-FNGVTVDNISEKLKEYNYQQRGFEVMYNGMTGHKLRAQIYIGPTYYQRLKH 1024

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK++AR+ G   ++T+QP+ G+S  GG R GEME  CI ++GA+  L+E L   SD 
Sbjct: 1025 MVDDKIHARAKGPLQILTRQPVEGRSRDGGLRFGEMERDCIISHGASAFLKERLMDVSDP 1084

Query: 1321 ------DVVG----RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                  D+ G     T+ Y     G     +      P +F +L++E+  + ++  ++  
Sbjct: 1085 YTCCICDLCGLIAIDTKRYNE-CKGCNNRTNLSLVEIPYAFKLLIQELMGMNIAPRIKTE 1143



 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 145/987 (14%), Positives = 280/987 (28%), Gaps = 186/987 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------AFSGAAMLEFVSY 79
           L+  Q  S+D F+   +          Q        IT                L+F   
Sbjct: 23  LVGQQIDSFDQFVKTKM----------QEVIDESPLITVQSTLSAGNETRKKITLKFGQI 72

Query: 80  EFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
               P               ++   RD+TY   L I    IV   +  +G   +   +  
Sbjct: 73  YVSKPPSYTEADGTTITLTPNEARLRDITYLSQLYID---IVKTTESESG--VVDQHRYS 127

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIH 164
            I  G LP+M K                         G F+I G ++++++Q   +    
Sbjct: 128 RIPFGSLPVMVKSSYCSTYKLSEEELIKIGECEYDVGGYFIINGSEKVIIAQERMASNTI 187

Query: 165 FDHDKGRASLSGKLLYACRI--IPDQGLWMDIEFDSK-----DIIHVRID-RRRKVPVTS 216
           +     + S      +   I  +P++G         K     ++I V I   ++++P+  
Sbjct: 188 Y---VFKKSQPASYSHYAEIRSVPEKGAKNPSAVSLKLCRNPNVIRVSIPYAKQEIPLFI 244

Query: 217 FLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
              ALG    +EI           +  D     +  + ++    V+   +          
Sbjct: 245 IYRALGFLSDKEITDHII-TTNDDEMFDLLKESILESAVVQDQNVALDYIGKRAAPVGSS 303

Query: 276 SGKKLTSGLLKSLKEKGV-------KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             K++     K L  K +       +F         G  V + ++    G    +  D  
Sbjct: 304 REKRINF--AKDLLAKELLPHIGTQEFCETKKAYFLGYMVQKLLL-VALGRKREDDRDHY 360

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
            +K ++            LY    +  A      +    +D   AL      +  G    
Sbjct: 361 GKKRMDLAGPLLASLFRSLYKKLCSETAKHMQKCIE-GGRDFNIALGLKASTIAQGFRYA 419

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            +            S       + R      L+       R     +    +     L N
Sbjct: 420 IATGNWGDQAHAMQSKAGVAQVLNRYNFVSTLSHLR----RVNTPIEKEGKLAKPRQLHN 475

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +         +      ++KN   +  + +  S +  +  ++   +   + I+   
Sbjct: 476 THWGMICPAETPEGQACG---LVKNLSLMAYISVGSSSEPIVEFLEECGLESLEEISHLQ 532

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + +A   F     +   E+    +S +   RR        +   +    +RD+       
Sbjct: 533 LQNATKVFVNGVWVGIHEDPEYLISSLRMLRRT-------LEIDKEVSIIRDIREKEIKI 585

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
              +         + ++             E       D      + +L   EEE   IA
Sbjct: 586 QSDSGRPCRPLFVVKNNKLCIDEA-YSNKEEIKRCTWNDFIENGLIEFLDVEEEEVSMIA 644

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
            +   L+                             +  P  ++ I AS+IPF +++ S 
Sbjct: 645 MSPDQLNSVKKDLRASEDLNINY----------THCEIHPATILGICASVIPFPDHNQSP 694

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 695 RNTYQSAMVKQAMGIYATNFML-------------------------------------- 716

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + S +  Y               Q+PLV                     +L  G
Sbjct: 717 ---RMDTLSNILFYP--------------QKPLV----------TTKSMEYIRFKELPPG 749

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----- 863
           +N +VA   + GYN EDS+++++  +   +F S     +      T+ G  E        
Sbjct: 750 QNAIVAIASYTGYNQEDSIIMNQSAIDRGLFRSFFYRTYTDQENTTRPGTHEEFCKPLRS 809

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           ++  +       +D  GII  G  V   D+L+GK++P  +          R+  G     
Sbjct: 810 EVIRMRNLNYSKLDNDGIIPTGTRVTGDDVLIGKVSPILDPE--------RSTKGNPVYL 861

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            +D+S  +     G V  V + N+ G 
Sbjct: 862 KKDSSTSMRRTEDGFVDSVIVTNKEGY 888


>gi|257042754|gb|ACV33020.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 1075

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 212/640 (33%), Positives = 320/640 (50%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +   A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VXXXAXGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                         T+DDID+L NRR+R                                
Sbjct: 293 XXXXXXXXXXXXMXTLDDIDHLRNRRIRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                        +   +FF S  LSQ  +  N L+ I H          G+    A   
Sbjct: 353 XXXXXXXXXXLFKNTFQDFFGSHPLSQFLDQTNPLTEIAHGXXXXXXXPXGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  135 bits (339), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 96/245 (39%), Gaps = 24/245 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           IP+  ++Q   +  F+          ++GL     +   I               YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDXXXXXXXXXXXYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ L     L +  R         +  ++ + I++Q++++G++PLM   GT
Sbjct: 62  PFIKERDAVYQSLXXXSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSHGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+  SPGI++  +     ++   +Y              E D  + I 
Sbjct: 113 FVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGXXXXXXXXXXXXEIDVGERIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R+RK+ +     A G++ EEIL  T YPK           +            +  
Sbjct: 171 ARVSRKRKISIPVXXXAXGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAILE 230

Query: 263 SLVDI 267
               +
Sbjct: 231 FYKKL 235


>gi|237688588|ref|YP_002905205.1| RNA polymerase beta subunit [Pinus gerardiana]
 gi|226876049|gb|ACO89305.1| RNA polymerase beta subunit [Pinus gerardiana]
          Length = 1075

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 228/640 (35%), Positives = 352/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +                    +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFXXXXXXXXXXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVS+L+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSALSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|67904266|ref|XP_682389.1| hypothetical protein AN9120.2 [Aspergillus nidulans FGSC A4]
 gi|40742763|gb|EAA61953.1| hypothetical protein AN9120.2 [Aspergillus nidulans FGSC A4]
          Length = 1028

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 181/992 (18%), Positives = 333/992 (33%), Gaps = 169/992 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 157  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 216

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     + A  V   +     +               +SQ+
Sbjct: 217  RVTRDLQRYVQRCVESDREIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQV 276

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 277  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 332

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +    S   E
Sbjct: 333  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVE 392

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQA 700
             +        I      I D  +   K          P    D+  +     N+   ++ 
Sbjct: 393  TMQALRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEH 452

Query: 701  VPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA      +I     DL+ S 
Sbjct: 453  IRKLEEDKELPPDMDPEDRRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 511

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y L +     Q+     R ++               PS  LG       +  + +
Sbjct: 512  QLQAGYALPE----EQDPNKRVRSILS--QRAHTWTHCEIHPSMILG-------VCASII 558

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 559  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 606

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 607  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 649

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +     +  +    ++    V    +E   +    + + + +  Y +L E   +  G 
Sbjct: 650  RGLFRSLFYRTY----SDSEKMVGLTVVERFEKPMRSDTIGMRKGTYDKLDEDGIVNPGV 705

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ D                +E  QR     K+   T     E+  
Sbjct: 706  RVSGEDIIIGKTAPLAPD---------------AEELGQRTKNHTKLDVSTPLRSTENGI 750

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV + M +  Q GDK A RHG KG +      EDMPF +
Sbjct: 751  VDQVLVTTTPDSL-----RSVKVRMRMTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTR 805

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 806  EGVTPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD-------------------- 845

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+ +LR       G 
Sbjct: 846  ---------------------------------ATP-FTDVTVDSISRLLREHGYQSRGF 871

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 872  EVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 931

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND- 1337
             GEME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N  
Sbjct: 932  FGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKH 991

Query: 1338 -TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
               +   P +  +L +E+ A+ +S  +  +R+
Sbjct: 992  RISQVHIPYAAKLLFQELAAMNISARMFTNRS 1023



 Score =  107 bits (266), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 105/777 (13%), Positives = 217/777 (27%), Gaps = 104/777 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+   E+IL+        +   +     +    ++   +V+
Sbjct: 68  YIKAD----IPIVIVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDREVA 123

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              +      Q   + ++      + ++++ +  +  +           G  V   ++  
Sbjct: 124 LDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGSETRKAFFLGYMV-HRLLQC 182

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
             G   ++  D   +K L+           +L+     +        +    +   ++  
Sbjct: 183 ALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD--------LQRYVQRCVESDR 234

Query: 376 DIY-RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
           +IY  V       T  +  ++    + +  K   +  G  ++  R    +      R   
Sbjct: 235 EIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT 294

Query: 433 KEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
                  I     L N   G +   +    +    V  +    Y       E  I    +
Sbjct: 295 PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQ 354

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +   ++   PQ   NA  V           Q S L E + +L R        +L +   
Sbjct: 355 RNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVETMQALRRRNMISHEVSLIRDIR 414

Query: 550 ARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN------AYGFIETP 601
            R         R   P       P   + G+ +     +                     
Sbjct: 415 EREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEHIRKLEEDKELPPDMDPEDRRER 474

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAGEEIL 655
           Y        +  V Y+ A EEE   I      L+            EE    +     + 
Sbjct: 475 YFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQLQAGYALPEEQDPNKRVRSILS 534

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                    +  P  ++ + AS+IPF +++ S R      M +QA+ +            
Sbjct: 535 QRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT--------- 585

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                  + A I+      +    ++  +          +   +  Y             
Sbjct: 586 NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSG----------- 634

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            NQ            + +I +  S D G         + +  +        + + ER   
Sbjct: 635 YNQ-----------EDSVIMNQSSIDRGLFRS-----LFYRTYSDSEKMVGLTVVER--- 675

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                      FE   R   +G  +               +DE GI+  G  V+  DI++
Sbjct: 676 -----------FEKPMRSDTIGMRK----------GTYDKLDEDGIVNPGVRVSGEDIII 714

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         E+L +       +DV        +G+   V+     +     K
Sbjct: 715 GKTAPLAPDA----EELGQRTKNHTKLDVSTPLRSTENGIVDQVLVTTTPDSLRSVK 767


>gi|57504729|ref|ZP_00370783.1| DNA-directed RNA polymerase, beta subunit (rpoB) [Campylobacter
           coli RM2228]
 gi|57019385|gb|EAL56083.1| DNA-directed RNA polymerase, beta subunit (rpoB) [Campylobacter
           coli RM2228]
          Length = 409

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 141/412 (34%), Positives = 230/412 (55%), Gaps = 24/412 (5%)

Query: 10  LGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS 69
             R+R  F    + I+IP+L+++QKAS+D+FL +          G++  FKS+FPI    
Sbjct: 7   RNRLRVDFSNISKQIEIPNLLQLQKASFDYFLNLE-----NGESGIEKVFKSIFPIHDPQ 61

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQ 128
               LE+VS E   PK+ + +C+ R LTY+V LK+ +RL + + DE TG K  IKDIKEQ
Sbjct: 62  NRLSLEYVSSEIGKPKYTIRECMERGLTYSVNLKMKIRLTLHEKDEKTGEKVGIKDIKEQ 121

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            IY+ ++PLMT   +F+I G++R+VV+QLHRSPG+ F  ++    ++ KL+Y  +IIPD+
Sbjct: 122 EIYIREIPLMTDRVSFIINGVERVVVNQLHRSPGVIFKEEESSTVVN-KLVYTAQIIPDR 180

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G W+  E+D+KD+++VRI++RRKVPVT    ALG   ++I+  FYP      + D +   
Sbjct: 181 GSWLYFEYDAKDVLYVRINKRRKVPVTMLFRALGYKKQDIIKLFYPIQTIHVKKDKFLTE 240

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
            + +D M   ++   + D + G  + ++GK+LT    + L + G+K++    + L   Y+
Sbjct: 241 FNPSDFM--DRIEYDIKD-EKGNIIHQAGKRLTKKKAEQLIKDGLKWIEYPVEILLNRYL 297

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A  I++ E+GE+  ++  ++DE  L +I     +   I    +   +A I N+   D   
Sbjct: 298 ANPIIDKESGEVLFDSLTLLDESKLAKIKEQ--KSFEIANDLANGVDAAIINSFAQDNET 355

Query: 369 ------------DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                       +   A + IY+VMRPG+      A++  N LF       L
Sbjct: 356 LKLLKQSENIDDENDLAAIRIYKVMRPGEPVVKDAAKAFVNDLFLILKDMIL 407


>gi|324986498|ref|YP_004276368.1| RNA polymerase beta subunit [Pinus nelsonii]
 gi|323522686|gb|ADX94934.1| RNA polymerase beta subunit [Pinus nelsonii]
          Length = 1075

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIKTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 230/640 (35%), Positives = 355/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRI P +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRIFPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGNTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|237688656|ref|YP_002905272.1| RNA polymerase beta subunit [Pinus krempfii]
 gi|226951114|gb|ACO94177.1| RNA polymerase beta subunit [Pinus krempfii]
          Length = 1075

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 231/640 (36%), Positives = 355/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFXXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA                        + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDA--------LNITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395033|gb|ACI45321.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 133/237 (56%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E H GWA  G+G++I  ++   +     S LR FLEKV  T   T
Sbjct: 1    NPLGVPSRMNIGQVLEVHXGWAGKGIGQRIGDML---QQQVRTSELRRFLEKVYNTRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     G+P +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGMPYATPVFDGAPEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|209395087|gb|ACI45357.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+G   E HLGWA  G+G++I  ++   +     S LR FL+KV  +   T
Sbjct: 1    NPLGVPSRMNIGLALEVHLGWASHGIGQRIGDML---QQQAKASELRKFLDKVYNSCGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   ++ ++ +A   + GVP +TPVFDGA E     ML++A  DE            
Sbjct: 58   EDLTQLSEEDMVAMAGNLQHGVPYATPVFDGASEAEFKDMLKIAYPDEIAQRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G  T E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHTIEAGMPESFNV 234


>gi|70906409|gb|AAZ14928.1| DNA-dependent RNA polymerase II second largest subunit [Coprinellus
            disseminatus]
          Length = 1241

 Score =  402 bits (1034), Expect = e-109,   Method: Composition-based stats.
 Identities = 167/1001 (16%), Positives = 324/1001 (32%), Gaps = 171/1001 (17%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 369  RERRIRYAQEILQKEMLPHISMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 425

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ + +    +              +  + + + +    
Sbjct: 426  GKKRLDLAGPLLAGLFRMLFRKLTKDVYRYLQKCVETHKEFNLTLAVKQQTITNGLKYSL 485

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 486  ATGNWGDQKKTMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 541

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 542  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 593

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 594  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 650

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIRI 743
             D+ RV     +      LL+ +   +G   + V  +          ++G++E +DA   
Sbjct: 651  TDAGRVCRPLFIVENQQLLLQKKH--IGWLNDGVDDQGEPYKWENLIKSGVIELLDAEEE 708

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +            +   ++       R  +K G            PS  LG
Sbjct: 709  ETVMISMTPEDLDISRRQAEGEETPENDAEFDPAAR--LKAGTHAHTWTHCEIHPSMILG 766

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 767  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 801

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 802  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 850

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    ++ R  +D  ++S +++ E+ E   RD          +  
Sbjct: 851  QEDSVIMNQSSIDRGLF-RSMYYRSYMDLEKKSGALQLEEFEKPTRDTTLRMKHGTYDKI 909

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G N         K+  +  D      R++          ++     +  Q  
Sbjct: 910  EDDGFIAPGTNVTGEDIIIGKTAPIPPDSEELGQRTRAHTRRDVSTPLKSTENGIVDQVL 969

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 970  I--------------------TTNAEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 1009

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +            
Sbjct: 1010 YRQEDMPFTCEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------- 1059

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     EA+++ L
Sbjct: 1060 -------------------------------------------ATP-FTDLTVEAVSNFL 1075

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            R       G  ++Y G TG      V +G  Y  +L HMV DK+++R+ G   ++T+QP+
Sbjct: 1076 RQKGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 1135

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN 1336
             G+S  GG R GEME  C+ ++G A  L+E L   SD       D+ G T +  + +   
Sbjct: 1136 EGRSRDGGLRFGEMERDCMISHGIAGFLKERLFEASDAYRLHVCDICGLTAI--ANLK-K 1192

Query: 1337 DTFETG------------TPESFNVLVKEMQALGLSIDLEN 1365
             +FE               P +  +L +E+Q++ ++  L  
Sbjct: 1193 QSFECRACKNKTACSQLYIPYAAKLLFQELQSMNIAARLYT 1233



 Score =  221 bits (564), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 136/1014 (13%), Positives = 285/1014 (28%), Gaps = 190/1014 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL------QAAFKSVFPITAFSGAAMLEFVSYEFD 82
           L+  Q  S+D F+   +      N  L      Q         T  +    ++F      
Sbjct: 65  LVRQQLDSFDEFVQNTMQELVDENADLILDQADQHTGHD----TDMTRRYEIKFGQIYLS 120

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK---EQS 129
            P               +   R+LTY+ PL + ++  V  +          DI+   EQ 
Sbjct: 121 RPTVTEADGSVFPLFPQEARLRNLTYSSPLYVEMKKRVL-IGREDPDGVPGDIQWETEQE 179

Query: 130 -------IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL- 157
                  I++G +P+M +                         G F+I G ++++++Q  
Sbjct: 180 DTGEPEKIWIGKVPIMLRSSFCILHQLRDNELYDLNECPYDSGGYFIINGSEKVLIAQER 239

Query: 158 ------------HRSPGIHFDHDKGRASLSGKLLYACRIIPD-QGLWMDIEFDSKDII-- 202
                         SP       +      GK +   ++    +      E    +++  
Sbjct: 240 MATNHVYVFAKAQPSPINFLAEIRSAVEKGGKTISQFQVKMFHRNQ----ERSMGNVMKA 295

Query: 203 ---HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
              ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   
Sbjct: 296 TIPYIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDR 351

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDI 312
           +V+   +        +   +++     + L+++ +  + +            G  +   +
Sbjct: 352 EVALDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMIHRLL 410

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           +         +      ++              +    + +   Y++  + T K  +   
Sbjct: 411 LAALERRELDDRDHFGKKRLDLAGPLLAGLFRMLFRKLTKDVYRYLQKCVETHKEFNLTL 470

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RH 430
           A+             T  +  S+    + D  K   S  G  ++  R    +      R 
Sbjct: 471 AVKQ--------QTITNGLKYSLATGNWGDQKKTMSSKAGVSQVLNRYTYASTLSHLRRC 522

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                    I     L N    +         +      ++KN   +  + +       I
Sbjct: 523 NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSCISVGSYSAPVI 579

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
             ++   +      NA         F     +    +  N +  I   RR   +      
Sbjct: 580 EFLEEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSV 638

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
                     ++        P    E   + L      +         E    K  +   
Sbjct: 639 VRDIRERELRLYTDAGRVCRPLFIVENQQLLLQKKHIGWLNDGVDDQGEP--YKWENLIK 696

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDF 663
           +  +  L A EEE   I+     LD      E         E                  
Sbjct: 697 SGVIELLDAEEEETVMISMTPEDLDISRRQAEGEETPENDAEFDPAARLKAGTHAHTWTH 756

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +  P  ++ I AS+IPF +++ S R      M +QA+ +                    
Sbjct: 757 CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------- 803

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                          + + +  Y       +     +  R    
Sbjct: 804 ----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR---- 831

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +L  G+N +VA + + GYN EDS+++++  +   +F S++
Sbjct: 832 --------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMY 871

Query: 844 IEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  + + +     E            +       I++ G I  G  V   DI++GK 
Sbjct: 872 YRSYMDLEKKSGALQLEEFEKPTRDTTLRMKHGTYDKIEDDGFIAPGTNVTGEDIIIGKT 931

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P         ++        +A   RD S  + S  +G V  V I       K
Sbjct: 932 APIPPDSEELGQRT-------RAHTRRDVSTPLKSTENGIVDQVLITTNAEGQK 978


>gi|115385276|ref|XP_001209185.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Aspergillus
            terreus NIH2624]
 gi|114196877|gb|EAU38577.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Aspergillus
            terreus NIH2624]
          Length = 1256

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 176/990 (17%), Positives = 328/990 (33%), Gaps = 163/990 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 383  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 442

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 443  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASAKAGVSQV 502

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 503  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 558

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 559  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGIHRDPAHLVN 618

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ-RQA 700
             +        I      I D  +   K          P F+ ++D      G  +  ++ 
Sbjct: 619  TMSSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKEH 678

Query: 701  VPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI-VIRSVEGDLDPSTSG 758
            +  L+ +         E    +  G   + K +G+VE VDA     I  V    D   S 
Sbjct: 679  IRKLEQDKELPPDLDPEERRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 737

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                     +    +     R ++    +          PS  LG       +  + +P+
Sbjct: 738  QLQAGYALPEEELHDPNKRVRSILS--QKAHTWTHCEIHPSMILG-------VCASIIPF 788

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N                        ++       +G      D    +   L     
Sbjct: 789  PDHNQSPRN------------------TYQSAMGKQAMGVFLTNFDQRMETMANL----- 825

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
                               +       +   +  + AI      +  D+ +   S +   
Sbjct: 826  ------LYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 879

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D  +         +E   +    + + + +  Y +L E   I  G   
Sbjct: 880  LF-RSLFYRTYTDSEKMVGL---TVVERFEKPMRSDTIGMRKGTYDKLDEDGIIAPGVRV 935

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  L+ +                +E  QR     K+   T     E    +
Sbjct: 936  SGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKLDVSTPLRSTESGIVD 980

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 981  QVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 1035

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 1036 VAPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD---------------------- 1073

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++I+ +LR       G  +
Sbjct: 1074 -------------------------------ATP-FTDVTVDSISRLLREHGYQSRGFEV 1101

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R G
Sbjct: 1102 MYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFG 1161

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND--T 1338
            EME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N    
Sbjct: 1162 EMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKHRI 1221

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             +   P +  +L +E+ ++ ++  +  +R+
Sbjct: 1222 SQVHIPYAAKLLFQELASMNIAARMFTNRS 1251



 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 150/1044 (14%), Positives = 299/1044 (28%), Gaps = 209/1044 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V PI        L+F +   
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPNEDEVDPIV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVFDVDEFTGAKSI 122
             P               +   R+LTYA PL + +         RL+    +E  G    
Sbjct: 95  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERLVADRNEEEMGEPVE 154

Query: 123 K------------------DIKEQSIYMGDLPLMTKD----------------------- 141
                                KE+++++G +P+M K                        
Sbjct: 155 DRKSQGTYLQWEQKELPPDQAKEETVFIGKMPIMLKSKYCILKDLSEQALYNWNECPYDS 214

Query: 142 -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
            G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   
Sbjct: 215 GGYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSL 271

Query: 199 KDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQR 241
           K  +  + D                 +  +P+     ALG +  E+IL+        +  
Sbjct: 272 K--LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPM 329

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-- 299
            +     +    ++   +V+   +      Q   + ++      + ++++ +  +  +  
Sbjct: 330 LEMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEG 389

Query: 300 ----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                    G  V   ++    G   ++  D   +K L+           +L+     + 
Sbjct: 390 SETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD- 447

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  V    +  ++  L+I          T  +  ++    + +  K   +  G  +
Sbjct: 448 ---LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASAKAGVSQ 501

Query: 416 MNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLK 472
           +  R    +      R          I     L N   G +   +    +    V  +  
Sbjct: 502 VLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 561

Query: 473 NQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
             Y       E  I    + +   ++   PQ   NA  V      F     +    +  +
Sbjct: 562 MCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPAH 615

Query: 531 SLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGL 582
            ++ ++  RR + +  +  + R     E        R   P       P   + G  +  
Sbjct: 616 LVNTMSSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLN 675

Query: 583 VSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              +    +                Y        +  V Y+ A EEE   I      L+ 
Sbjct: 676 KEHIRKLEQDKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEI 735

Query: 637 DGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                        E     +     +          +  P  ++ + AS+IPF +++ S 
Sbjct: 736 SKQLQAGYALPEEELHDPNKRVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSP 795

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                   D     + ++
Sbjct: 796 RNTYQSAMGKQAMGVFLTNF------------------------------DQRMETMANL 825

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                   +       ++F+                G   + + +I +  S D G     
Sbjct: 826 LYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSG-YNQEDSVIMNQSSIDRGLFRS- 883

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
               + +  +        + + ER              FE   R   +G  + T D    
Sbjct: 884 ----LFYRTYTDSEKMVGLTVVER--------------FEKPMRSDTIGMRKGTYD---- 921

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +DE GII  G  V+  DI++GK  P     + PE + L      KA    D S
Sbjct: 922 ------KLDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVS 968

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  SG V  V +   +   K
Sbjct: 969 TPLRSTESGIVDQVLVSTSNDDLK 992


>gi|324986427|ref|YP_004276298.1| RNA polymerase beta subunit [Pinus monophylla]
 gi|323522522|gb|ADX94864.1| RNA polymerase beta subunit [Pinus monophylla]
          Length = 1075

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 231/640 (36%), Positives = 356/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +    +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLFKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTNYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228017069|gb|ACP51891.1| RNA polymerase beta subunit [Cedrus deodara]
          Length = 1076

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 159/497 (31%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G I+       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 632  VRQGECVKKGQIMADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 690

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 691  SFHILRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 744

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 745  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 802

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 803  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 857

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D +   + S    F E    +   
Sbjct: 858  LNPLGVPSRMNVGQIFECLPGLAGNLMKKHYRITPFDERYEREASRKLVFPELYKASEQT 917

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 918  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 938

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V DK++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 939  GDVFEQPVTIGKAYMSKLSHQVDDKIHARSSGPYARVTQQPLRGKSKRGGQRVGEMEVWA 998

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 999  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1058

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1059 LNHAIISEKDFQIDREE 1075



 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 230/695 (33%), Positives = 368/695 (52%), Gaps = 22/695 (3%)

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           +++ +   ++ G+   L+    +   I +  L   +     +  + GE          + 
Sbjct: 120 RIVVNQILISPGIHYRLELDHNRINYIYTGTLISDWGRRSKLEIDMGERIWARVSRKRKI 179

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD-------ALLDIYRVMR-- 382
           S+  +  +   ++  +  ++     ++         ++R++       A+L+ Y+ +   
Sbjct: 180 SIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKKGRREREEYLWSKENAILEFYKKLYCV 239

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            GD+             FF   + +L  +GR   N +LNLD P++      +D++A +  
Sbjct: 240 SGDLVFSESLCKELQEKFF-RQRCELGKIGRRNPNQKLNLDIPENDIFSLPQDVLAAVDY 298

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E +++  I         PQ 
Sbjct: 299 LIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVRRTIHRATKRRSTPQX 358

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
              +    +   +FF         +  N      H R+LS LG GG+    A    RD+H
Sbjct: 359 XXXSTLXKNTFQDFFGXXXXXXXXDQTNPXXXXAHGRKLSHLGPGGLTGRTASFRTRDIH 418

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA--M 620
           P++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL     
Sbjct: 419 PSYYGRICPIDTSEGMNAGLVASLSIHAKIGHCGSLQSPFYKISERSREEHMVYLLPGEG 478

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+  SLIP
Sbjct: 479 EDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVLAWEQIHFRSIFPFQYFSVGVSLIP 538

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA
Sbjct: 539 FLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDA 598

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +                       + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T
Sbjct: 599 V--------NITSSVYGDTVRTESVMYQRSNTNTCTHQKPKVRQGECVKKGQIMADGAAT 650

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE 
Sbjct: 651 VGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHILRYRIEICMTSQGPER 710

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFG 918
           ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+        PE +LL+ IFG
Sbjct: 711 ITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFG 770

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            +    R+  LR P G  G V+DVR  NR     +
Sbjct: 771 IEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 805



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 116/271 (42%), Gaps = 29/271 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFV----------DQGLMEELHNFPKIEDTDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q +++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQIVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGIH+  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIHYRLELDHNRIN--YIYTGTLISDWGRRSKLEIDMGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R+RK+ +   L A+G++ EEIL        +              + +      
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKKGRREREEYLWSK--E 226

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +++++       +      +  L K L+EK 
Sbjct: 227 NAILEFYKKLYCVSGDLVFSESLCKELQEKF 257


>gi|228016179|gb|ACP51015.1| RNA polymerase beta subunit [Pinus squamata]
          Length = 1075

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 226/640 (35%), Positives = 347/640 (54%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+          +FF         +  N           S LG GG+    A   
Sbjct: 353 STPQNLVTXXXXXXXXXDFFGXXXXXXXXDQTNPXXXXXXXXXXSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228017566|gb|ACP52380.1| RNA polymerase beta subunit [Pinus parviflora var. pentaphylla]
          Length = 1075

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  340 bits (872), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 217/640 (33%), Positives = 335/640 (52%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++          
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N                       A   
Sbjct: 353 XXXXXXXXXXXXXXXXXDFFGXXXXXXXXDQTNPXXXXXXXXXXXXXXXXXXXXRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|108710089|gb|ABF97884.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative,
            expressed [Oryza sativa Japonica Group]
 gi|125545063|gb|EAY91202.1| hypothetical protein OsI_12811 [Oryza sativa Indica Group]
          Length = 1222

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 189/1094 (17%), Positives = 344/1094 (31%), Gaps = 209/1094 (19%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V D+  LE I +       +  +      A++         
Sbjct: 298  LPYIRADIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV--- 354

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 AL  I +       +     E    +      K  L  VG             + 
Sbjct: 355  -----ALDYIGKR----GATVGVTKEKRIKYAKEILQKEMLPHVG-----------VGEF 394

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
                +      II  L+    G+   DD D+ GN+R+   G +L   +R+   ++ R ++
Sbjct: 395  CETKKAYYFGYIIHRLLMCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVR 454

Query: 488  ERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLS 533
              +     +   V  Q  I AK + S +     +              +SQ+   +   S
Sbjct: 455  SYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYAS 514

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ++H RRL++     + R     + R +H +H+G +CPAET EG   GLV +L     + 
Sbjct: 515  TLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYIT 570

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                       + +    N        EE +  +    + +  +G +           + 
Sbjct: 571  VGSAANPILEFLEEWGTEN-------FEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKT 623

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +   R +I   D + +  V     L       D  R      +      L+         
Sbjct: 624  LRRLRRQI---DVNTEVGVVRDIRLKELRLYTDYGRCSRPLFIVENQRLLI--------- 671

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                   +   A    +           +  I  ++ + + +T        +   R N  
Sbjct: 672  -----KKRHIRALQQRETPEEGWHDLVAKGFIEYIDTEEEETTMISMTINDLIGARHNPE 726

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               +                    PS  LG       +  + +P+  +N          M
Sbjct: 727  EAYS-----------ETYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSAM 768

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              + +   I++  ++                           +    +  V        +
Sbjct: 769  GKQAMG--IYVTNYQ---------------------------LRMDTLAYVLYYPQKPLV 799

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
                +       +      + AI      +  D+ +   S +        +F R   D+ 
Sbjct: 800  TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEE 858

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            ++  ++ +E+     R+          +          G           K++ +     
Sbjct: 859  KKMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPI----- 913

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                         QD+   +     K  + TS    E    +++      D +     R 
Sbjct: 914  ------------PQDDAQGQATRYTKRDHSTSLRHSESGMVDQVLLTTNADGL-----RF 956

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +
Sbjct: 957  VKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTI 1016

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E  +G     +GK+                                          
Sbjct: 1017 GQLIECIMGKVAAHMGKEGD---------------------------------------- 1036

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         +TP F     + I+  L        G   +Y+G TG      + +G 
Sbjct: 1037 -------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGP 1082

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E
Sbjct: 1083 TYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAFFLKE 1142

Query: 1314 MLTIKSDDVVGRTRVYE-----SIV---------AG----NDTFETGTPESFNVLVKEMQ 1355
             L  +SD    R  V E     +I           G     D  +   P +  +L +E+ 
Sbjct: 1143 RLFDQSD--AYRVHVCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELM 1200

Query: 1356 ALGLSIDLENSRTK 1369
            A+ ++  +     K
Sbjct: 1201 AMAIAPRMLTQDNK 1214



 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 136/987 (13%), Positives = 284/987 (28%), Gaps = 192/987 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G QA F              + F
Sbjct: 72  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGRQAEFAETL--------HKISF 123

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   V            + ++
Sbjct: 124 GQIYLSKPMMTEADGETATLFPKSARLRNLTYSAPLYVDVSYRVMKKGHDCEE-VTETME 182

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG 162
              +++G +P+M +                         G F+I G ++++++Q   S  
Sbjct: 183 YPKVFIGKVPIMLRSSYCTLFQQSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTN 242

Query: 163 -IHFDHDKGRASLSGKLLYACRIIP-----DQGLWMDIEFD-----SKD----------I 201
            ++      +     K  Y   +       ++              +K           +
Sbjct: 243 HVY----VFKKRQPNKYAYVAEVRSMAENQNRPASSMFVRMLSRAGAKGGSSGQYIRATL 298

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
            ++R D    +P+     ALG  ++ +IL         +Q  +     L  A ++   +V
Sbjct: 299 PYIRAD----IPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV 354

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +   +        +   K++     + L+++ +  +G+   C          +      +
Sbjct: 355 ALDYIGKRGATVGVTKEKRIKYAK-EILQKEMLPHVGVGEFCETKKAYYFGYIIH---RL 410

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + A     E   +   +  +    P+L          +   + +   K   +      +
Sbjct: 411 LMCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQ 470

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIA 438
                   T  +  S+    +  +++          +N      T   +R +        
Sbjct: 471 FAIKAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREG 530

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +         +      ++KN   +  + +  +    +  ++    
Sbjct: 531 KLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWGT 587

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVE 557
              + I+   +  A   F     +         +  +   RR   +  + GV R     E
Sbjct: 588 ENFEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQIDVNTEVGVVRDIRLKE 647

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R ++  +     P    E   + +         + A    ETP     D      + Y+
Sbjct: 648 LR-LYTDYGRCSRPLFIVENQRLLIKKR-----HIRALQQRETPEEGWHDLVAKGFIEYI 701

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EEE   I+              +L+  R   E      E     +  P  ++ + AS
Sbjct: 702 DTEEEETTMISM----------TINDLIGARHNPE--EAYSETYTHCEIHPSLILGVCAS 749

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                           R   +  
Sbjct: 750 IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAY 789

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V                                       Q+PLV               
Sbjct: 790 V-----------------------------------LYYPQKPLV----------TTRAM 804

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                  L  G N +VA   + GYN EDS+++++  +    F S+    +    +     
Sbjct: 805 EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTL 864

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +E        +   +       +D+ G+   G  V+  D+++GK +P  +         
Sbjct: 865 VKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDD------- 917

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             A         RD S  +    SG V
Sbjct: 918 --AQGQATRYTKRDHSTSLRHSESGMV 942


>gi|41179042|ref|NP_958398.1| RNA polymerase beta subunit I [Chlamydomonas reinhardtii]
 gi|41017747|sp|Q8HTL6|RPOB1_CHLRE RecName: Full=DNA-directed RNA polymerase subunit beta N-terminal
           section; AltName: Full=PEP; AltName:
           Full=Plastid-encoded RNA polymerase subunit beta
           N-terminal section; Short=RNA polymerase subunit beta
           N-terminal section
 gi|24209933|gb|AAN41266.1| RNA polymerase beta' subunit [Chlamydomonas reinhardtii]
 gi|28269765|tpg|DAA00943.1| TPA_inf: RNA polymerase beta subunit I [Chlamydomonas reinhardtii]
 gi|213517423|gb|ACJ50129.1| RNA polymerase beta subunit I [Chlamydomonas reinhardtii]
          Length = 822

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 226/759 (29%), Positives = 350/759 (46%), Gaps = 107/759 (14%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPK 85
           D +E+Q+ S+   L           +G+   F    PIT       + F    Y+  PP+
Sbjct: 126 DFVEIQRNSFFTLL----------EKGIIEEFSKRNPITNSKKTMEIFFYPDYYQLTPPE 175

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           +     + +  +Y   L I ++L           KS   IK + +Y+GD+PLMTK G F+
Sbjct: 176 YSPSQAIIKSKSYTSKLYIPVQLT---------DKSKNIIKLKWVYIGDIPLMTKRGHFI 226

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK---------LLYACRIIPDQGLWMDIEF 196
           + G  R++V+Q+ RSPGI++   K   + S K           Y   +I ++G W+ IE 
Sbjct: 227 LNGCARVIVNQMVRSPGIYY-QKKIYENFSNKWSEKPENTFTRYFADLICNRGTWLRIEM 285

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           D  + I  ++ R  K+P+  FL+A+G+  + +L T     +     D          L  
Sbjct: 286 DKYNKIWAQMKRVPKIPIMWFLIAVGLTDKIVLKTVMDSKILLYNLDEDPLNPRKKPLPY 345

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                ++   I     ++ + K       K + E              G   ++     +
Sbjct: 346 VKTPPAAWSAIYN---IVFAKKIKAQEKAKKMLELT-----------EGNPSSKSQTKNK 391

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           T                     S  +    L V +        N     +  D + AL  
Sbjct: 392 T---------------------SASKKSKTLNVANTKGKTPAENIKTLSELIDLEKALFL 430

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
                R                 F +   YDL  VGRV  N +L L    D+  +  +D+
Sbjct: 431 KSEQGR-----------KWIFNKFMNPRTYDLGKVGRVNFNRKLKLSISQDITTLTPQDL 479

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           +A    L+ +  G   +DDID+L NRRVR+ GE+++ Q  +GL+R+E++I+E+++     
Sbjct: 480 LAATNNLILVSKGLRELDDIDHLKNRRVRTSGELIQIQIGVGLVRLEKTIREKMTYASGL 539

Query: 497 SVMPQDLI----------------------------NAKPVVSAVCEFFCSSQLSQLEEH 528
           S +P                                N KP   A+ EFF +S LSQ  + 
Sbjct: 540 SSLPSQKFAFRSSKQRNQSPVGDAENATQLTIGNLINTKPFNGALREFFGTSPLSQFMDQ 599

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
           +N L+ +TH RRLS++G GGV R  A + +R +HP+HYGRICP ET EG N GLV+SLT+
Sbjct: 600 INPLAELTHKRRLSSMGPGGVTRDSATLAIRGIHPSHYGRICPVETPEGKNTGLVNSLTA 659

Query: 589 FARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +ARVNA G+IETP+ +V  G+V     + + SA +EE   +   +    E G   +  + 
Sbjct: 660 YARVNAAGYIETPFYRVYKGQVQKKTGLYFFSAKQEEKIKLGAPDLYTSEIGFLPKASIP 719

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   +   + R +I ++  +P Q++SIA SLIPF E+DD+NR LMG NMQRQAVP+LK 
Sbjct: 720 VRIVEDFTKISRNEIQYVGVAPIQMISIATSLIPFFEHDDANRALMGSNMQRQAVPILKP 779

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           + P VGTG+E+     SG  I AK +GIV    +  I+I
Sbjct: 780 QRPIVGTGLEARAVSDSGHVITAKSSGIVMYTSSKEIII 818


>gi|228017310|gb|ACP52128.1| RNA polymerase beta subunit [Pinus lambertiana]
          Length = 1075

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  359 bits (922), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 229/640 (35%), Positives = 351/640 (54%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+            +FF         +  N L+ I   R+LS LG GG+    A   
Sbjct: 353 STPQNXXXXXXXXXXXXDFFGXXXXXXXXDQTNPLTEIAXXRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|156835986|ref|XP_001642238.1| hypothetical protein Kpol_186p2 [Vanderwaltozyma polyspora DSM 70294]
 gi|156112711|gb|EDO14380.1| hypothetical protein Kpol_186p2 [Vanderwaltozyma polyspora DSM 70294]
          Length = 1223

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 176/982 (17%), Positives = 316/982 (32%), Gaps = 173/982 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ + I    +
Sbjct: 371  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLGQLFKTLFRKLTKDIFRYMQ 430

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             +  + +    +  INAK + S +     +               +SQ+       S ++
Sbjct: 431  RTVEEANDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 490

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++   
Sbjct: 491  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT 546

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGE 652
                    + +  +     Y+   +  +      N              E L   R  G+
Sbjct: 547  DPMPIITFLSEWGMEPLEDYV-PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 605

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLK-AEAPF 710
                     D  +   K          P F+  +D         +++  +  L   E   
Sbjct: 606  INPEVSMIRDIREKELKIFTDAGRVYRPLFIVENDEQLGHKELKVRKGHIARLMATEYQD 665

Query: 711  VGTGMESVVAKSSGAAIVAK--RAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRLM 765
            +  G E      S     +     G+VE +DA       I     DLDP     ++    
Sbjct: 666  IEGGFE-----DSEEYTWSSLLNEGLVEYIDAEEEETILIAMQPEDLDPVQEEEEMEVDE 720

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                + +   V+                    PS  LG  A       + +P+  +N   
Sbjct: 721  NVDTAKRIRSVHHAT---------TFTHCEIHPSMILGVAA-------SIIPFPDHNQSP 764

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                   M  + +   + +  + V                               +  + 
Sbjct: 765  RNTYQSAMGKQAMG--VFLTNYNVRM---------------------------DTMANIL 795

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                        +       +   +  + AI      +  D+ +   S +   +    +F
Sbjct: 796  YYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLF 854

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R  +D+ ++      E  E   R           +       I  G           K+
Sbjct: 855  FRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGSYDKLDDDGLIAPGVRVSGEDIIIGKT 914

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T +S D      R+ +         ++     +  Q                        
Sbjct: 915  TPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLI--------------------T 954

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP 
Sbjct: 955  TNQDGLKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYGREDMPFTAEGIVPDLIINPH 1014

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM V  + E  L       G +                                  
Sbjct: 1015 AIPSRMTVAHLIECLLSKVAALSGNEGD-------------------------------- 1042

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 ++P F     E I+ +LR       G  ++Y+G TG+  
Sbjct: 1043 ---------------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKL 1080

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+
Sbjct: 1081 MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAH 1140

Query: 1306 GAAYVLQEMLTIKSD----DVVGRTRVYESIVA----------GND---TFETGTPESFN 1348
            GAA  L+E L   SD     + G   +   I             ++    ++   P +  
Sbjct: 1141 GAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAK 1200

Query: 1349 VLVKEMQALGLSIDLENSRTKN 1370
            +L +E+ A+ ++  L   R+++
Sbjct: 1201 LLFQELMAMNITPRLYADRSRD 1222



 Score =  231 bits (590), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 137/1007 (13%), Positives = 290/1007 (28%), Gaps = 168/1007 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL--QAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   +      +  L  +   +        S    + F       P  
Sbjct: 40  LVSQQLDSFNQFVDYTLQDIISEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA---------KSIKDIKE 127
           +            +   R+LTY+  L + +    ++  +  G          +S +D + 
Sbjct: 100 NESDGVTHALYPQESRLRNLTYSSGLFVDVNKRTYEAVDVPGRDLNYQLIAEESEEDNEN 159

Query: 128 QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGI 163
             +++G LP+M +                         G F+I G ++++++Q  RS G 
Sbjct: 160 DKVFIGRLPIMLRSKNCYLSDATESDLYKLKECPFDMGGYFIINGSEKVLIAQE-RSAGN 218

Query: 164 HFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR---IDRRRK------- 211
                  + +    + +   I    ++G         K  ++ R     R  K       
Sbjct: 219 I--VQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK--LYGREGSSTRTIKATLPYIK 274

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG+  + EIL      +   Q  +     +    ++   + +   +   
Sbjct: 275 QDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRR 334

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                I+  K++       L+++ +  +                +      + + A D  
Sbjct: 335 GTALGIKKEKRIQYAR-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCALDRK 390

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           D+   +      +    P+L          +   +     +  ++A     ++       
Sbjct: 391 DQDDRDHFGKKRLDLAGPLLGQLFKTLFRKLTKDIFRYMQRTVEEANDFNMKLAINAKTI 450

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   S  G  ++  R    +      R          +     
Sbjct: 451 TSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQ 510

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   +  + +       I+ +    + P +   
Sbjct: 511 LHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYV 567

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                 A   F               +  +   RR   +            +   +    
Sbjct: 568 PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDA 627

Query: 566 YGRICPAETSEG------HNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-----VTNDV 614
                P    E         + +     +      Y  IE  +    +           V
Sbjct: 628 GRVYRPLFIVENDEQLGHKELKVRKGHIARLMATEYQDIEGGFEDSEEYTWSSLLNEGLV 687

Query: 615 VYLSAMEEENRYIAQANSSLD----EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            Y+ A EEE   IA     LD    E+    +E V        +          +  P  
Sbjct: 688 EYIDAEEEETILIAMQPEDLDPVQEEEEMEVDENVDTAKRIRSVH-HATTFTHCEIHPSM 746

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ +AAS+IPF +++ S R      M +QA+ +                           
Sbjct: 747 ILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV-------------------- 786

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + +  Y       +     +  R           
Sbjct: 787 ---------------------RMDTMANILYYPQKPLGTTRAMEYLKFR----------- 814

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G+N +VA   + GYN EDSM++++  +   +F S+    +   
Sbjct: 815 -------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ 861

Query: 851 ARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +   +   E        +   +       +D+ G+I  G  V+  DI++GK TP     
Sbjct: 862 EKKYGMSITETFEKPQRTNTLRMKHGSYDKLDDDGLIAPGVRVSGEDIIIGKTTPI---- 917

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +P+E+ L       +   RD S  + S  +G V  V I       K
Sbjct: 918 -SPDEEELGQRTAYHSK--RDASTPLRSTENGIVDQVLITTNQDGLK 961


>gi|228016753|gb|ACP51580.1| RNA polymerase beta subunit [Pinus armandii]
          Length = 1075

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNLMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 211/640 (32%), Positives = 327/640 (51%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           + +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E ++           
Sbjct: 293 SAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N                           
Sbjct: 353 XXXXXXXXXXXXXXXXQDFFGXXXXXXXXDQTNXXXXXXXXXXXXXXXXXXXXXXXXXFX 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
                  +YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 XXXXXXXYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 138/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D+++     I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLSAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|70794968|gb|AAZ08458.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum]
          Length = 1207

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 175/1050 (16%), Positives = 328/1050 (31%), Gaps = 187/1050 (17%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +  N ++       ++A +   + +    +       S          +Y 
Sbjct: 305  DILEHICYEFTDNKMMDLLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTKEKRIRYA 361

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + R  +      +  +  +         II  L+    G+   DD D+  N+R+   
Sbjct: 362  KEILQREMLPHVGTGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYANKRLDLA 418

Query: 468  GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +     +   V  Q  I AK + S +     +      
Sbjct: 419  GPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 478

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 479  NSAGSRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 534

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 535  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPLATK 587

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V     L       D  R    
Sbjct: 588  IFVNGCWVGIHRNPELLVRTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDCGRCSRP 644

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +    +K +        ES         +     G +E VD        +   ++
Sbjct: 645  LFIVEKQKLQIKKKDILALQQRESPEEVGWHDLVA---KGYIEYVDTEEEETTMISMTIN 701

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
              TS                                        PS  LG       +  
Sbjct: 702  DLTSARLCPDDA---------------------YSETYTHCEIHPSLILG-------VCA 733

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 734  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 766

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 767  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 824

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ ++  ++ +E      R+          +          G 
Sbjct: 825  SIDRGFF-RSIFYRSYRDEEKKMGTLVKEDFGCPNRENTMGMRHGSYDKLDDDGFAPPGT 883

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++                  D+   +     +  + T     E   
Sbjct: 884  RVAGEDVIIGKTTPIAP-----------------DDAQGQTARYTRRDHSTCLRHSESGM 926

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK+ +   R  Q GDK + RHG KG +      EDMP+  
Sbjct: 927  VDQVLLTTNADGL-----RFVKMRMRSIRIPQIGDKFSSRHGQKGTIGMAYTQEDMPWTI 981

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 982  EGICPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 1021

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1022 ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1047

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG P    + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1048 ERMYNGHTGRPLTYTIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1107

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV----------------AGND 1337
             GEME  C+ A+GAA+ L+E L  +SD           IV                   D
Sbjct: 1108 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCALCGIVAIANLKKNSFECRHCKNKTD 1167

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              +   P +  +L++E+ A+ ++  L    
Sbjct: 1168 IVQVYIPYACKLLLQELMAMAIAPRLLTKD 1197



 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 134/988 (13%), Positives = 274/988 (27%), Gaps = 193/988 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G Q+ F  +           + F
Sbjct: 56  LVRQQLDSFDEFIQNTMQEIVDEAADIEIKPESQHNPGRQSDFVEMV--------YRISF 107

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   V           + + +
Sbjct: 108 GQIYLSKPMMTESDGETASLFPKAARLRNLTYSSPLYVDVTKRVVKKGHDCE--EVTETQ 165

Query: 127 E-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
           E   +++G +P+M +                         G F+I G ++++++Q   S 
Sbjct: 166 EFTKVFIGKVPIMLRSSYCSLYQTSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMST 225

Query: 162 G-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR------------ 208
             ++      +     K  Y   +        + +      + VR+              
Sbjct: 226 NHVY----VFKIRQPNKYAYVSEVR----SMAESQNRPPSGMFVRMVSSSSAKGGSSGQY 277

Query: 209 --------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                   R ++P+     ALG  ++ +IL     +   ++  D     L  A ++   +
Sbjct: 278 IRATLPYIRTEIPIVVVFRALGFVADKDILEHICYEFTDNKMMDLLRPSLEEAFVIQNQQ 337

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
           V+   +        +   K++     K + ++ +     T +                  
Sbjct: 338 VALDYIGKRGSTVGVTKEKRI--RYAKEILQREMLPHVGTGEYCETKKAYYFGYIIHR-- 393

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           + + A     E   +   +  +    P+L          +   + +   K   +      
Sbjct: 394 LLLCALGRRPEDDRDHYANKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVNL 453

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDII 437
           +        T  +  S+    +  ++           +N      T   +R +       
Sbjct: 454 QFAIKAKTITSGLKYSLATGNWGQANSAGSRAGVSQVLNRLTYASTLSHLRRLNSPIGRE 513

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             +     L N    +         +      ++KN   +  + +  +    +  ++  S
Sbjct: 514 GKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWS 570

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGV 556
               + I+   +  A   F     +         +  +   RR   +  + GV R     
Sbjct: 571 TENFEEISPAVIPLATKIFVNGCWVGIHRNPELLVRTLRQLRRQVDVNTEVGVIRDIRLK 630

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+R ++        P    E   +  +      A        E       D      + Y
Sbjct: 631 ELR-LYTDCGRCSRPLFIVEKQKLQ-IKKKDILALQQRESPEEVG---WHDLVAKGYIEY 685

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +   EEE   I+   + L       ++               E     +  P  ++ + A
Sbjct: 686 VDTEEEETTMISMTINDLTSARLCPDD------------AYSETYTHCEIHPSLILGVCA 733

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                           R   + 
Sbjct: 734 SIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLA 773

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            V                                       Q+PLV              
Sbjct: 774 YV-----------------------------------LYYPQKPLV----------TTRA 788

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                   L  G N +VA   + GYN EDS+++++  +    F SI    +    +    
Sbjct: 789 MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKMGT 848

Query: 857 GPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
             +E        +   +       +D+ G    G  V   D+++GK TP           
Sbjct: 849 LVKEDFGCPNRENTMGMRHGSYDKLDDDGFAPPGTRVAGEDVIIGKTTPIAPDD------ 902

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
              A         RD S  +    SG V
Sbjct: 903 ---AQGQTARYTRRDHSTCLRHSESGMV 927


>gi|215254203|gb|ACJ64106.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 400

 Score =  402 bits (1033), Expect = e-109,   Method: Composition-based stats.
 Identities = 255/400 (63%), Positives = 312/400 (78%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL
Sbjct: 61  SLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADEL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L
Sbjct: 121 ITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           KA+ P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L
Sbjct: 181 KADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNL 240

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFE
Sbjct: 241 TKYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFE 300

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           DS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +
Sbjct: 301 DSILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYI 360

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV
Sbjct: 361 GAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDV 400


>gi|228016876|gb|ACP51701.1| RNA polymerase beta subunit [Pinus ayacahuite]
          Length = 1075

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  352 bits (903), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 225/640 (35%), Positives = 345/640 (53%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N        R+LS LG GG+    A   
Sbjct: 353 XXXXXXXXXXXXXXXXXDFFGXXXXXXXXDQTNPXXXXXXXRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228017244|gb|ACP52063.1| RNA polymerase beta subunit [Pinus flexilis]
          Length = 1075

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  360 bits (924), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 228/640 (35%), Positives = 349/640 (54%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L  +E +++  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGHLEDTVRRTIHGATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+            +FF         +  N      H R+LS LG GG+    A   
Sbjct: 353 STPQNXXXXXXXXXXXXDFFGXXXXXXXXDQTNPXXXXXHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395063|gb|ACI45341.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LR FL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGERIGELL---QQQAKVSELRRFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG---------- 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  +E+           
Sbjct: 58   ENLALLSDADLLAMAGNLQQGVPYATPVFDGASEAEIKDMLELAYPEETARRRGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV  RT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVASRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|228017696|gb|ACP52508.1| RNA polymerase beta subunit [Pinus pinaster]
          Length = 1075

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKNFQIDREE 1074



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 234/640 (36%), Positives = 358/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + E     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCISGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLLKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/342 (19%), Positives = 136/342 (39%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELYNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYHSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +        K +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIKYIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +   L A+G++ EEIL  T YP+           +            +
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCISGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228016244|gb|ACP51079.1| RNA polymerase beta subunit [Pinus strobus]
          Length = 1075

 Score =  402 bits (1032), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GAVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKDFQIDREE 1074



 Score =  335 bits (859), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 219/640 (34%), Positives = 335/640 (52%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + +     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCVSGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L                  
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLTLGXXXXXXXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N L+     R+LS           A   
Sbjct: 353 XXXXXXXXXXXXXXXXXDFFGXXXXXXXXDQTNPLTXXXXGRKLSXXXXXXXXXXTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
             D+HP++YGRICP +TSEG N GLVSSL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TXDIHPSYYGRICPIDTSEGMNAGLVSSLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P V+ G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+       TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 804



 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 70/342 (20%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDTDK--EIEFSLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI RIVV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRIVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R+RK+ +   L A+G++ EEIL  T YPK           +            +
Sbjct: 169 IWARVSRKRKISIPVLLSAMGLNLEEILDNTHYPKRFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCVSGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395105|gb|ACI45369.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  401 bits (1031), Expect = e-109,   Method: Composition-based stats.
 Identities = 131/237 (55%), Positives = 166/237 (70%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LR FL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGERIGELL---QQQAKVSELRRFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG---------- 1232
            E ++   D  +L +A   + GVP +TPVFDGA E  I  ML +A  +E+           
Sbjct: 58   ENLALLSDADLLAMAGNLQQGVPYATPVFDGASEAEIKDMLELAYPEETARRRGLTPSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVEGEHAIEAGMPESFNV 234


>gi|313635048|gb|EFS01405.1| DNA-directed RNA polymerase subunit beta [Listeria seeligeri FSL
           N1-067]
          Length = 380

 Score =  401 bits (1031), Expect = e-109,   Method: Composition-based stats.
 Identities = 118/389 (30%), Positives = 195/389 (50%), Gaps = 41/389 (10%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK--------EK 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF---HSEIRDIPILY 348
            +       + L    +AE +V+ ETGEI    GD++D ++L++I     + +    +  
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRP 336

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            D V  ++ +  ++      D +  +  I
Sbjct: 337 TDGVMEDSVLVQSIKIYAPNDEEKEINII 365



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/83 (38%), Positives = 50/83 (60%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211 IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           ++VGR K+N +L+L      + +
Sbjct: 271 ASVGRYKINKKLHLKNRLFNQTL 293


>gi|255520705|ref|ZP_05387942.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J1-175]
          Length = 372

 Score =  401 bits (1031), Expect = e-109,   Method: Composition-based stats.
 Identities = 118/389 (30%), Positives = 195/389 (50%), Gaps = 41/389 (10%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK--------EK 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF---HSEIRDIPILY 348
            +       + L    +AE +V+ ETGEI    GD++D ++L++I     + +    +  
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRP 336

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            D V  ++ +  ++      D +  +  I
Sbjct: 337 TDGVMEDSVLVQSIKIYAPNDEEKEINII 365



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/83 (38%), Positives = 50/83 (60%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211 IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           ++VGR K+N +L+L      + +
Sbjct: 271 ASVGRYKINKKLHLKNRLFNQTL 293


>gi|307103930|gb|EFN52187.1| hypothetical protein CHLNCDRAFT_59036 [Chlorella variabilis]
          Length = 1175

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 180/1141 (15%), Positives = 352/1141 (30%), Gaps = 194/1141 (17%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
               I+  E+V+ + +++ +  +   ++         ++C   +  +   V+    ++   
Sbjct: 187  YFVINGSEKVLIAQERMANNHVYVFRKSQPSKYAYVAECRSVVEGSTRTVSTMQVKMLSR 246

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVD----SVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            AG     + +         DIPIL +      V +   + + +    +    +AL     
Sbjct: 247  AGQKGAGQCIRASIPYVRADIPILIIFRALGFVADKDILEHIVYDFGDTTMMEALRPSIE 306

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK--EDII 437
               P      ++           + +       R  +   L      +     K      
Sbjct: 307  EAFPIQSQEVALDYIGKRGSTIGATRNARIQYARELLQKELLPHVGMEEFCETKKAYFFG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDI 495
             +I  L+ +  G+   DD D+ GN+R+   G +L N +R    ++ + ++   +      
Sbjct: 367  YVIHRLLLVALGRREEDDRDHYGNKRLDLGGPLLANLFRQLFRKLSKDVRGYVQKCVDKG 426

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSA 543
              +     IN   +   +     +              +SQ+   +   S ++H RR+++
Sbjct: 427  KEINLTSAINKDTITRGLRYSLATGNWGVVGAGEVRPGVSQVLNRLTYASTLSHLRRINS 486

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                 + R     + R +H + +G ICPAET EG   GLV +L     ++          
Sbjct: 487  ----PIGREGKIAKPRQLHNSQWGMICPAETPEGQACGLVKNLALMTYISVGCASNPVLD 542

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
             + +   T D+  +S            N          + LV    A    +    ++  
Sbjct: 543  FLQEWA-TEDLEEISPSVIPKATKIFVNGVWVGIHRDPQTLVETLRAMRRQVDISTEVGV 601

Query: 664  IDASPKQVVSI----AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +     Q + +         P    +D           +     +        TG     
Sbjct: 602  VHDIRLQELRLYTDYGRCCRPLFIVEDQA--------VKVKKRDIINLQNREETGFTWQS 653

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
               +G                    I  V+ + + +T        ++  R  ++      
Sbjct: 654  MIEAGY-------------------IEYVDVEEEETTMIAMFINDLRLARIAEDAATASS 694

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                    +         P+  LG       +  + +P+  +N          M  + + 
Sbjct: 695  --------IALYTHCEIHPAMILG-------VCASIVPFPDHNQSPRNTYQSAMGKQAMG 739

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                +       R    G        P V+   ++ +                       
Sbjct: 740  ----MYVTNYQVRMDTQGYVLFYPQKPLVTTRNMEYL----------------------- 772

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +      + AI      +  D+++   S +   +    IF R    + ++  S+
Sbjct: 773  --HFRELPAGINTIVAIACYSGYNQEDSTMMNQSSIDRGIF-RSIFFRSYKTEEKKQGSL 829

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E IE   R+          +          G           K++ +  D        
Sbjct: 830  VQESIERPNREITAGTRHGTYDKLDDDGIAPPGTRVSGDDIVIGKTSPIPDDG------- 882

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                              L  +Y    +    R                   R VK+ V 
Sbjct: 883  ----------------SGLPQRYSKKDASTALRHSESGMIDSVLVTTGADGQRFVKMRVR 926

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              R  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +G + E 
Sbjct: 927  SVRIPQVGDKFASRHGQKGTIGITYTQEDMPFSAEGISPDLIINPHAIPSRMTIGHLVEA 986

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             +      +GK+                                                
Sbjct: 987  LMSKVAACMGKEGD---------------------------------------------- 1000

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   +TP F     + I++ L        G  ++Y+G TG      + +   Y  +L
Sbjct: 1001 -------ATP-FTSVTVDNISAALHRCGYQSRGWEVMYNGHTGRQLQAQIFLNPTYYQRL 1052

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK+++R  G   ++T+QP+ G++  GG R GEME  CI ++GAA  L+E L  +S
Sbjct: 1053 KHMVDDKIHSRGRGPVQILTRQPVEGRARDGGLRFGEMERDCIISHGAAAFLKERLYDQS 1112

Query: 1320 D-------DVVG--------RTRVYESIVAGND-TFETGTPESFNVLVKEMQALGLSIDL 1363
            D        V G        + + Y +         +   P +  +L +E+ A+ ++  +
Sbjct: 1113 DAYRVHVCSVCGLIAVANLKKNQFYCTACKNTTGIVQVFIPYACKLLFQELMAMCIAPRM 1172

Query: 1364 E 1364
             
Sbjct: 1173 I 1173



 Score =  229 bits (583), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 140/1009 (13%), Positives = 277/1009 (27%), Gaps = 221/1009 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L+  Q  S++ F+          N  LQ        I+                      
Sbjct: 35  LVRQQLDSFNDFI----------NTSLQEIVDENKLISITPQSQHVPGMQVEDDVEKIFE 84

Query: 74  LEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
           +EF       P F             +   R+LTYA PL + +      V    G++ ++
Sbjct: 85  VEFGQIYLSKPVFIEADGETAVLFPKEARLRNLTYAAPLYVDIE-RRDKVVHSDGSEEVE 143

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL-- 157
                 +++GD+P+M +                         G FVI G ++++++Q   
Sbjct: 144 VTPYPKVFLGDVPIMLRSDYCNLSGRSERDLCDLGECPYDQGGYFVINGSEKVLIAQERM 203

Query: 158 -----------HRSPGIHFDHDKGRASLSGKLLYACRI------------------IPDQ 188
                        S   +    +     S + +   ++                  IP  
Sbjct: 204 ANNHVYVFRKSQPSKYAYVAECRSVVEGSTRTVSTMQVKMLSRAGQKGAGQCIRASIP-- 261

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
                         +VR D    +P+     ALG  ++ +IL         +   +    
Sbjct: 262 --------------YVRAD----IPILIIFRALGFVADKDILEHIVYDFGDTTMMEALRP 303

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            +  A  +   +V+   +             ++     + L +K +       +      
Sbjct: 304 SIEEAFPIQSQEVALDYIGKRGSTIGATRNARIQY--ARELLQKELLPHVGMEEFCETKK 361

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD-IPILYVDSVNNNAYIRNTLVTDK 366
                       + + A    +E   +   +  +    P+L          +   +    
Sbjct: 362 AYFFGYVIHR--LLLVALGRREEDDRDHYGNKRLDLGGPLLANLFRQLFRKLSKDVRGYV 419

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            K                D  T  +  S+    +      ++       +N      T  
Sbjct: 420 QKCVDKGKEINLTSAINKDTITRGLRYSLATGNWGVVGAGEVRPGVSQVLNRLTYASTLS 479

Query: 427 DVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +R I         I     L N +  +         +      ++KN   +  + +  +
Sbjct: 480 HLRRINSPIGREGKIAKPRQLHNSQWGMICPAETPEGQACG---LVKNLALMTYISVGCA 536

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
               +  +   +    + I+   +  A   F     +    +    +  +   RR   + 
Sbjct: 537 SNPVLDFLQEWATEDLEEISPSVIPKATKIFVNGVWVGIHRDPQTLVETLRAMRRQVDIS 596

Query: 546 -QGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
            + GV       E+R    T YGR C P    E   + +         +N     ET + 
Sbjct: 597 TEVGVVHDIRLQELR--LYTDYGRCCRPLFIVEDQAVKVKKR----DIINLQNREETGF- 649

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-D 662
                     + Y+   EEE   IA           F  +L   R A +        +  
Sbjct: 650 TWQSMIEAGYIEYVDVEEEETTMIAM----------FINDLRLARIAEDAATASSIALYT 699

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ + AS++PF +++ S R      M +QA+ +                   
Sbjct: 700 HCEIHPAMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGMYVTNYQV------------ 747

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                   R      V                                       Q+PLV
Sbjct: 748 --------RMDTQGYV-----------------------------------LFYPQKPLV 764

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                        +       +L  G N +VA   + GYN EDS ++++  +   +F SI
Sbjct: 765 ----------TTRNMEYLHFRELPAGINTIVAIACYSGYNQEDSTMMNQSSIDRGIFRSI 814

Query: 843 HIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               ++   +      +E                    +D+ GI   G  V+  DI++GK
Sbjct: 815 FFRSYKTEEKKQGSLVQESIERPNREITAGTRHGTYDKLDDDGIAPPGTRVSGDDIVIGK 874

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            +P  +                +    +D S  +    SG +  V +  
Sbjct: 875 TSPIPDD----------GSGLPQRYSKKDASTALRHSESGMIDSVLVTT 913


>gi|119489058|ref|XP_001262829.1| DNA-dependent RNA polymerase II RPB140 [Neosartorya fischeri NRRL
            181]
 gi|119410987|gb|EAW20932.1| DNA-dependent RNA polymerase II RPB140 [Neosartorya fischeri NRRL
            181]
          Length = 1255

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 180/992 (18%), Positives = 336/992 (33%), Gaps = 169/992 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 384  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 443

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 444  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASSKAGVSQV 503

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 504  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 559

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-TE 642
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 560  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRDPAHLVN 619

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ-RQA 700
             ++  R             D  +   K          P F+ ++D      G  +  ++ 
Sbjct: 620  TMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKEH 679

Query: 701  VPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA      +I     DL+ S 
Sbjct: 680  IRKLEQDKELPADLDPEDRRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 738

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y L +    N+      R ++    +          PS  LG       +  + +
Sbjct: 739  QLQAGYALPEEDDPNKRV----RSILS--QKAHTWTHCEIHPSMILG-------VCASII 785

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 786  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 833

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 834  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 876

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R   D  +         +E   +    + + + +  Y +L E   I  G 
Sbjct: 877  RGLF-RSLFYRTYTDTEKMVGL---TVVERFEKPMRSDTIGMRKGTYDKLDEDGIIAPGV 932

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ +                +E  QR     K+   T     E+  
Sbjct: 933  RVSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKLDVSTPLRSTENGI 977

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF +
Sbjct: 978  VDQVLVSTSNDDL-----KFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTR 1032

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 1033 EGVSPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD-------------------- 1072

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+ +LR       G 
Sbjct: 1073 ---------------------------------ATP-FTDVTVDSISRLLREHGYQSRGF 1098

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 1099 EVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 1158

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND- 1337
             GEME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N  
Sbjct: 1159 FGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKH 1218

Query: 1338 -TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
               +   P +  +L +E+ A+ ++  +  +R+
Sbjct: 1219 RISQVHIPYAAKLLFQELAAMNIAARMFTNRS 1250



 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 152/1042 (14%), Positives = 300/1042 (28%), Gaps = 206/1042 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------AAMLEFVSYEFD 82
           L+  Q  S+D F+   +  +    +G Q       P +             L+F +    
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQG-QVTLDQTLPPSDDEDDPVVLRRYELKFGTVMLS 95

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITL---------RLIVF--------DVDE 115
            P               +   R+LTYA PL + +         RLI          D DE
Sbjct: 96  RPSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERLIADRDEDDVAPDADE 155

Query: 116 FTGAKSI-----------KDIKEQSIYMGDLPLMTKD----------------------- 141
              A+                KE+++++G +P+M K                        
Sbjct: 156 DRKARGTYLQWEQKELPADQAKEETVFIGKMPIMLKSKYCILKDLSEQALYNWNECPYDS 215

Query: 142 -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
            G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   
Sbjct: 216 GGYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSL 272

Query: 199 KDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQR 241
           K  +  + D                 +  +P+     ALG +  E+IL+        +  
Sbjct: 273 K--LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPM 330

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-- 299
            +     +    ++   +V+   +      Q   + ++      + ++++ +  +  +  
Sbjct: 331 LEMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEG 390

Query: 300 ----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                    G  V   ++    G   ++  D   +K L+           +L+     + 
Sbjct: 391 SETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD- 448

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  V    +  ++  L+I          T  +  ++    + +  K   S  G  +
Sbjct: 449 ---LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASSKAGVSQ 502

Query: 416 MNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLK 472
           +  R    +      R          I     L N   G +   +    +    V  +  
Sbjct: 503 VLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 562

Query: 473 NQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
             Y       E  I    + +   ++   PQ   NA  V      F     +    +  +
Sbjct: 563 MCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGVHRDPAH 616

Query: 531 SLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGL 582
            ++ +   RR + +  +  + R     E        R   P       P   + G  +  
Sbjct: 617 LVNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLN 676

Query: 583 VSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              +    +                Y        +  V Y+ A EEE   I      L+ 
Sbjct: 677 KEHIRKLEQDKELPADLDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEI 736

Query: 637 DGSFT------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                      EE    +     +          +  P  ++ + AS+IPF +++ S R 
Sbjct: 737 SKQLQAGYALPEEDDPNKRVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRN 796

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                   + A I+      +    ++  +      
Sbjct: 797 TYQSAMGKQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELP 847

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               +   +  Y              NQ            + +I +  S D G       
Sbjct: 848 AGQNAIVAIACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS--- 882

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             + +  +        + + ER              FE   R   +G            +
Sbjct: 883 --LFYRTYTDTEKMVGLTVVER--------------FEKPMRSDTIGM----------RK 916

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +DE GII  G  V+  DI++GK  P     + PE + L      KA    D S  
Sbjct: 917 GTYDKLDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVSTP 969

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  +G V  V +   +   K
Sbjct: 970 LRSTENGIVDQVLVSTSNDDLK 991


>gi|39945464|ref|XP_362269.1| hypothetical protein MGG_04714 [Magnaporthe oryzae 70-15]
 gi|145011262|gb|EDJ95918.1| hypothetical protein MGG_04714 [Magnaporthe oryzae 70-15]
          Length = 1276

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 214/1415 (15%), Positives = 424/1415 (29%), Gaps = 262/1415 (18%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------AAMLEFVSYEFD 82
            L+  Q  SY+ F    I         L     +  P   F G         +   +    
Sbjct: 44   LVSQQIDSYNEFTTSTIQGIVDEYSVL--TLDNPNPPDTFEGKPIRLRRYEIMLGNILVT 101

Query: 83   PPKFD----------VDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKDIKEQSIY 131
             P               +C  R+LTY+ PL + L + +   V+E      + D + +   
Sbjct: 102  QPTVKETDGKVSTLVPYECRDRNLTYSCPLYVKLTKKVNVAVEEDIPLHELNDEQREE-- 159

Query: 132  MGDLPLMTKDGTFVIKGIQRIVVSQLHRS----PGIHFDHDKGRASLSGKLLYACRIIPD 187
                                     + R+      I ++ D+ ++    + +        
Sbjct: 160  -------------------------MQRTNEHPTTIRWELDRDKSHNPDEKISG------ 188

Query: 188  QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
                   E  + D+I++      K+PV        + S+     F        +G ++  
Sbjct: 189  -------EKMA-DMIYI-----GKIPVMVKSRICYLRSQPESELFLLNECPYDQGGYFII 235

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
              S   L+   + ++++V +       +  K L    ++S  EKG + +   +  L    
Sbjct: 236  NGSEKVLIAQERSAANIVQVFKK---AQPNKYLYQAEIRSALEKGSRLVSTLTMKLTSKG 292

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
             +     G+T  + +         ++       + D  IL    ++ N      ++    
Sbjct: 293  DSTRGSFGQTIHLNLPYTSGDLPIAIVFRALGVVSDEDILNHIVLDKND---TQMLEMLR 349

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP-- 425
               ++A     R     +V+   +A+ +       + ++    V R  +           
Sbjct: 350  PSIEEAFCIQDR-----EVALDFIAKRVGKDGGHSNSRHLRLKVARDILQKDTLPHISQA 404

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +   +  ++  ++    G+  +DD D+ G +R+   G +L   +R  + ++   
Sbjct: 405  EGCETRKAFFLGYMVHKILQCALGRRDVDDRDHFGKKRLDLAGPLLAKLFRGIIRKLTND 464

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            +    R              +    + + +     +               +SQ+     
Sbjct: 465  MMGGLRRCIDAGRDFDLTASLKPNTLTNGLKYSLATGNWGDQKKAASSTAGVSQVLNRYT 524

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+   
Sbjct: 525  FASTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC 580

Query: 591  RVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+     E  Y  +      V  +    ++      +I      +        +LV+  
Sbjct: 581  MVSVGTPAEPIYDFLVARGMDVLEEYEPSNSSSTSKIFINGTWVGVANKIEELVDLVYDL 640

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                 +      I D  +   +        + P    +  +    G              
Sbjct: 641  RRKSRVDPEVSLIHDVREGEFRIFSDAGRVMRPLFVVNQKDDPRTGAQ------------ 688

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                           +G+ ++ K        D    +    EG         D    +  
Sbjct: 689  ---------------AGSLVLTKEHVAKLHADKDNNLSPGDEGHYGWQGLKSDGVLDLMD 733

Query: 768  QRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                +   +   P  L K          + +  + D  D+    N  +        + E 
Sbjct: 734  AEQEETAMICMSPSDLDKFRALKFGGATLDELEAFDKNDINRRLNTKINPTTHMYTHCEI 793

Query: 826  S----MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
                 + I   ++            ++       +G                 N     +
Sbjct: 794  HPSMLLGICASIIPFPDHNQSPRNCYQSAMGKQAMGFFLTN-----------YNRRMDTM 842

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 843  ANILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSTIDRGLF- 901

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   D  +R        +E   +    + + L +  Y +L +   +  G      
Sbjct: 902  RSLFFRSYTDSEKRVGI---NMVEKFEKPFRADTLRLKQGTYDKLEDDGIVAPGTRVSGE 958

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  + +D                 E  QR V+  K    T     E    +++ 
Sbjct: 959  DIIIGKTAPIPAD---------------NQELGQRTVQHTKRDASTPLRSTESGIVDQVI 1003

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     + VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 1004 VTTNQDGL-----KYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFTREGITP 1058

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +  +          +S L    E    +
Sbjct: 1059 DIIINPHAIPSRMTIAHLIECLLSKVATLKGMEGDATPFTEVTVDSVSNLLR--EHGYQS 1116

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                 G +    
Sbjct: 1117 RGFEVL---------------------------------------------YHGHT---- 1127

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G         V  G  Y  +L HMV DK++AR+ G  +++T+QP+ G++  GG R GEME
Sbjct: 1128 GR---KLRAQVFFGPTYYQRLRHMVDDKIHARARGPVNIMTRQPVEGRARDGGLRFGEME 1184

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVG---------------------RTRVYESIV 1333
              C+ A+GAA  L+E L   SD     + G                     R +      
Sbjct: 1185 RDCMIAHGAASFLKERLFEVSDAFRAHICGICGLMTPIADLTRKTFECRPCRNKT----- 1239

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1240 ---KIAQVHIPYAAKLLFQELASMNIATRMFTERS 1271


>gi|228016374|gb|ACP51207.1| RNA polymerase beta subunit [Pinus thunbergii]
          Length = 1075

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKNFQIDREE 1074



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 234/640 (36%), Positives = 358/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + E     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCISGDLVFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLLKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPKIHQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 804



 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/342 (19%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +   L A+G++ EEIL  T YP+           +            +
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCISGDLVFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|209395024|gb|ACI45315.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 132/237 (55%), Positives = 163/237 (68%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E H GWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHXGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EVLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEM T+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMHTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|313639728|gb|EFS04488.1| DNA-directed RNA polymerase subunit beta [Listeria seeligeri FSL
           S4-171]
          Length = 386

 Score =  401 bits (1030), Expect = e-109,   Method: Composition-based stats.
 Identities = 118/389 (30%), Positives = 195/389 (50%), Gaps = 41/389 (10%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK--------EK 291
             +      +   L+           +  GE   +++ + L        K          
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF---HSEIRDIPILY 348
            +       + L    +AE +V+ ETGEI    GD++D ++L++I     + +    +  
Sbjct: 277 KINKKLHLKNRLFNQTLAETLVDPETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRP 336

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            D V  ++ +  ++      D +  +  I
Sbjct: 337 TDGVMEDSVLVQSIKIYAPNDEEKEINII 365



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/83 (38%), Positives = 50/83 (60%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211 IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           ++VGR K+N +L+L      + +
Sbjct: 271 ASVGRYKINKKLHLKNRLFNQTL 293


>gi|121709250|ref|XP_001272355.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus clavatus NRRL 1]
 gi|119400504|gb|EAW10929.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus clavatus NRRL 1]
          Length = 1257

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 179/992 (18%), Positives = 335/992 (33%), Gaps = 167/992 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 384  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 443

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 444  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASSKAGVSQV 503

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 504  LSRYTYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 559

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-TE 642
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 560  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRDPAHLVN 619

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ-RQA 700
             ++  R             D  +   K          P F+ ++D      G  +  ++ 
Sbjct: 620  TMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGSLVLNKEH 679

Query: 701  VPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAI---RIVIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA     I+I     DL+ S 
Sbjct: 680  IRKLEQDKELPPDLDPEERRERYFGWDGLVK-SGVVEYVDAEEEEHIMISMTPEDLEISK 738

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y L   +    +     R ++               PS  LG       +  + +
Sbjct: 739  QLQAGYAL--PEEELNDPNKRVRSILS--QRAHTWTHCEIHPSMILG-------VCASII 787

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 788  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 835

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 836  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 878

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R   D  +         +E   +    + + + +  Y +L E   I  G 
Sbjct: 879  RGLF-RSMFYRTYTDTEKMVGL---TVVERFEKPMRSDTIGMRKGTYDKLDEDGIIAPGV 934

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ +                +E  QR     K+   T     E+  
Sbjct: 935  RVSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKLDVSTPLRSTENGI 979

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF +
Sbjct: 980  VDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTR 1034

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 1035 EGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------- 1074

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++++ +LR       G 
Sbjct: 1075 ---------------------------------ATP-FTDVTVDSVSRLLREHGYQSRGF 1100

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 1101 EVMYNGHTGRKMVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 1160

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND- 1337
             GEME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N  
Sbjct: 1161 FGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKH 1220

Query: 1338 -TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
               +   P +  +L +E+ A+ ++  +  +R+
Sbjct: 1221 RISQVHIPYAAKLLFQELAAMNIAARMFTNRS 1252



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 153/1045 (14%), Positives = 304/1045 (29%), Gaps = 210/1045 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---LQAAF----KSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+   +  +    +G   L          V P+        L+F +   
Sbjct: 38  LVSQQLDSFDEFVSSTMQ-ELVEEQGQVTLDQTLPPADDEVDPVV--LRRYELKFGTVML 94

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITL---------RLI--------VFDVD 114
             P               +   R+LTYA PL + +         RLI        V D D
Sbjct: 95  SRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERLIADREDDETVPDAD 154

Query: 115 EFTGAKSI-----------KDIKEQSIYMGDLPLMTKD---------------------- 141
           E   A+                KE+++++G +P+M K                       
Sbjct: 155 EDRKARGTYLQWEQKELPADQAKEETVFIGKMPIMLKSKYCILKDLSEQALYNWNECPYD 214

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +  
Sbjct: 215 SGGYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLS 271

Query: 198 SKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQ 240
            K  +  + D                 +  +P+     ALG +  E+IL+        + 
Sbjct: 272 LK--LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTP 329

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT- 299
             +     +    ++   +V+   +      Q   + ++      + ++++ +  +  + 
Sbjct: 330 MLEMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSE 389

Query: 300 -----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++    G   ++  D   +K L+           +L+     +
Sbjct: 390 GSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD 448

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V    +  ++  L+I          T  +  ++    + +  K   S  G  
Sbjct: 449 ----LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASSKAGVS 501

Query: 415 KMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEML 471
           ++  R    +      R          I     L N   G +   +    +    V  + 
Sbjct: 502 QVLSRYTYSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 561

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
              Y       E  I    + +   ++   PQ   NA  V      F     +    +  
Sbjct: 562 LMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGVHRDPA 615

Query: 530 NSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIG 581
           + ++ +   RR + +  +  + R     E        R   P       P   + G  + 
Sbjct: 616 HLVNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVIDNDPKSENCGSLVL 675

Query: 582 LVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               +    +                Y        +  V Y+ A EEE+  I+     L+
Sbjct: 676 NKEHIRKLEQDKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEEEHIMISMTPEDLE 735

Query: 636 EDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                         E     +     +          +  P  ++ + AS+IPF +++ S
Sbjct: 736 ISKQLQAGYALPEEELNDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQS 795

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +                   + A I+      +    ++  +   
Sbjct: 796 PRNTYQSAMGKQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFR 846

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  +   +  Y              NQ            + +I +  S D G    
Sbjct: 847 ELPAGQNAIVAIACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS 884

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                + +  +        + + ER              FE   R   +G          
Sbjct: 885 -----MFYRTYTDTEKMVGLTVVER--------------FEKPMRSDTIG---------- 915

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           + +     +DE GII  G  V+  DI++GK  P     + PE + L      KA    D 
Sbjct: 916 MRKGTYDKLDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDV 968

Query: 928 SLRVPSGVSGTVVDVRIFNRHGIDK 952
           S  + S  +G V  V +   +   K
Sbjct: 969 STPLRSTENGIVDQVLVSTSNDDLK 993


>gi|228017182|gb|ACP52002.1| RNA polymerase beta subunit [Pinus leiophylla var. chihuahuana]
          Length = 1074

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
               +                        VF                 D  G+  L DG T
Sbjct: 916  ANPL------------------------VF---------------GPDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    ++ T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKSDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 219/640 (34%), Positives = 336/640 (52%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERFLFLLKKERGEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +            +DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 292 AAVDXXXXXXXXXXXLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATXXX 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  +     +FF            N              G GG+    A   
Sbjct: 352 STPQNLVTSTLLXXXXXDFFGXXXXXXXXXXTNXXXXXXXXXXXXXXGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N      L+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAXXXXXLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E+    R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQTTPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 121/300 (40%), Gaps = 31/300 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R++K+ +   L  +G++ EEIL        Y +R  F                 
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILD----NTRYPERFLFLLKKERGEREEYLWSRE 224

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            ++++       I      +  L K L+EK  +               +  ++    EI+
Sbjct: 225 KAILEFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIF 284


>gi|228015990|gb|ACP50829.1| RNA polymerase beta subunit [Pinus resinosa]
          Length = 1075

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKNFQIDREE 1074



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 232/640 (36%), Positives = 352/640 (55%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + E     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCISGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+          +FF         +  N      H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTXXXXXXXXXDFFGXXXXXXXXDQTNXXXXXXHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSINGDTVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 705 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 804



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/342 (19%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +   L A+G++ EEIL  T YP+           +            +
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCISGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|255556051|ref|XP_002519060.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis]
 gi|223541723|gb|EEF43271.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis]
          Length = 1194

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 181/1060 (17%), Positives = 335/1060 (31%), Gaps = 191/1060 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       +          KY 
Sbjct: 290  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGATVGVTKEKRIKYA 346

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 347  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 403

Query: 468  GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +     +   V  Q  I AK + S +     +      
Sbjct: 404  GPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 463

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H + +G +CPAE
Sbjct: 464  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAE 519

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 520  TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPAVIPQATK 572

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +       R     +   R     +D + +  V     L       D  R    
Sbjct: 573  IFVNGCWVG---IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRP 629

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K +       + ++  + S     ++  G  + V   +  I  ++ + +
Sbjct: 630  LFIVEKQRLLIKKKD------IHALQQRES-----SEEGGWHDLV--AKGFIEYIDTEEE 676

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 677  ETTMISMTIHDLVQARINPEEAYS-----------DTYTHCEIHPSLILG-------VCA 718

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 719  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 774

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 775  EHL-------------------------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 809

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R           +          G 
Sbjct: 810  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGT 868

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +                       Q   +    +Y      +  R 
Sbjct: 869  RVSGEDVIIGKTTPI----------------------AQEEAQGQSARYTRRDHSISLRH 906

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                   Q         LR VKV V   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 907  SETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 966

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 967  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 1006

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1007 ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1032

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1033 ETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1092

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR----------TRVYESIVAG---- 1335
             GEME  C+ A+GAA+ L+E L  +SD     V  R             +E    G    
Sbjct: 1093 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIAIANLKKNSFEC--RGCKNK 1150

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             D  +   P +  +L +E+ A+ ++  +     K +   +
Sbjct: 1151 TDIVQVHIPYACKLLFQELMAMAIAPRMLTKDVKPTKDQK 1190



 Score =  238 bits (606), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 137/989 (13%), Positives = 286/989 (28%), Gaps = 195/989 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 41  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 91

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 92  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 151

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 152 FTK--VFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 209

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR---------- 208
              ++      +     K  Y   +        + +      + VR+  R          
Sbjct: 210 TNHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPPSTMFVRMLSRTSAKGGSSGQ 261

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 262 YIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQ 321

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +V+   +        +   K++     + L+++ +  +G+   C          +     
Sbjct: 322 QVALDYIGKRGATVGVTKEKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH--- 377

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   + +   K   +     
Sbjct: 378 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVN 437

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 438 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 497

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +      ++KN   +  + +  +    +  ++  
Sbjct: 498 EGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEW 554

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
                + I+   +  A   F     +    +    +  +   RR   +  + GV R    
Sbjct: 555 GTENFEEISPAVIPQATKIFVNGCWVGIHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRL 614

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+R ++  +     P    E   + L+      A        E       D      + 
Sbjct: 615 KELR-IYTDYGRCSRPLFIVEKQRL-LIKKKDIHALQQRESSEEGG---WHDLVAKGFIE 669

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE   I+              +LV  R   E      +     +  P  ++ + 
Sbjct: 670 YIDTEEEETTMISM----------TIHDLVQARINPE--EAYSDTYTHCEIHPSLILGVC 717

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +      F                    R   +
Sbjct: 718 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------RMDTL 757

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             V                                       Q+PLV             
Sbjct: 758 AYV-----------------------------------LYYPQKPLV----------TTR 772

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    L  G N +VA   + GYN EDS+++++  +    F S+    +    +   
Sbjct: 773 AMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 832

Query: 856 LGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +E        +   +       +D+ G+   G  V+  D+++GK TP  +       
Sbjct: 833 TLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQEE----- 887

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               A         RD S+ +    +G V
Sbjct: 888 ----AQGQSARYTRRDHSISLRHSETGIV 912


>gi|237688519|ref|YP_002905137.1| RNA polymerase beta subunit [Pinus contorta]
 gi|226875348|gb|ACO89086.1| RNA polymerase beta subunit [Pinus contorta]
          Length = 1074

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGTPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 230/640 (35%), Positives = 354/640 (55%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERFLFLLKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R++ ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLKDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +                  N    I H R+LS LG GG+    A   
Sbjct: 352 STPQNLVTSTLLKNTFXXXXXXXXXXXXXXXTNXXXXIAHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPKIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHLLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/341 (19%), Positives = 141/341 (41%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDFWCFPL--------SA 251
           I  R+ R++K+ +   L  +G++ EEIL    +  + ++  + + W              
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERFLFLLKKERWEREEYLWSREKAIL 228

Query: 252 ADLMVGAKVSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                   +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|209395099|gb|ACI45365.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGV SRMN+GQ+ E HLGWA  G+G++I  ++   +     + LR FL+KV      T
Sbjct: 1    NPLGVLSRMNIGQVLEVHLGWASKGIGQRIGDML---QQQAKAAELRKFLDKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----------SG 1232
            E ++   D+ ++ +A   + G+P +TPVFDGA EE I  ML++A  DE            
Sbjct: 58   EDLAQLCDEELVAMAAHLRHGMPYATPVFDGASEEEIKDMLKIAYPDEIAQRKGPTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEMLT+KSDDV GRT+VYESIV G    E G P SFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPGSFNV 234


>gi|300728450|ref|ZP_07061812.1| DNA-directed RNA polymerase, beta subunit [Prevotella bryantii B14]
 gi|299774369|gb|EFI70999.1| DNA-directed RNA polymerase, beta subunit [Prevotella bryantii B14]
          Length = 331

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 132/379 (34%), Positives = 190/379 (50%), Gaps = 55/379 (14%)

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETS 1045
             ++  G    +G +   K +  ++  +               DE   + ++ L + Y   
Sbjct: 7    GKVSQGVKDYTGAEIITKGSKFTTVALKNLEYDGVESNNWTGDEHTDKLIQKLIMNYIRK 66

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               L+   K +   I  GDD+P G+L++ KV++A KR IQ GDK+AGRHGNK        
Sbjct: 67   YKQLDAELKRRKFAITIGDDLPSGILQMAKVYIAKKRKIQVGDKLAGRHGNK-------- 118

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
                     G    IV        RM                     + +          
Sbjct: 119  ---------GIVSKIV--------RM---------------------EDMPFLEDGRP-- 138

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                  ++ V+       +++       +  A   K GV  +TP+FDGA  + ++     
Sbjct: 139  ------VDLVLNPMGVPSRMNLGQIFEAILGAAGKKLGVKFATPIFDGAKLDDLSEWTDK 192

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            A L     + ++DG TGE FD+P T+G  Y LKL HMV DK++ARS G YSL+TQQPLGG
Sbjct: 193  AGLPRLCSTHIFDGETGEQFDQPATIGMTYFLKLGHMVEDKMHARSIGPYSLITQQPLGG 252

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPE 1345
            K+  GGQR GEMEVW ++A+GA++VLQE+LTIKSDDVVGR++ YE+IV G+     G PE
Sbjct: 253  KAQFGGQRFGEMEVWALEAFGASHVLQEVLTIKSDDVVGRSKAYEAIVKGDAMPTPGIPE 312

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
            S NVL+ E++ LGLSI L+
Sbjct: 313  SLNVLLHELRGLGLSIKLD 331


>gi|228016303|gb|ACP51137.1| RNA polymerase beta subunit [Pinus taeda]
          Length = 1074

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 234/640 (36%), Positives = 360/640 (56%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERFLFLLKKERGEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF         +  N L+ I H R+LS LG GG+    A   
Sbjct: 352 STPQNLVTSTLLKNTFQDFFGXXXXXXXXDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 121/300 (40%), Gaps = 31/300 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           I  R+ R++K+ +   L  +G++ EEIL        Y +R  F                 
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILD----NTRYPERFLFLLKKERGEREEYLWSRE 224

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            ++++       I      +  L K L+EK  +               +  ++    EI+
Sbjct: 225 KAILEFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIF 284


>gi|7524615|ref|NP_042369.1| RNA polymerase beta subunit [Pinus thunbergii]
 gi|1173150|sp|P41607|RPOB_PINTH RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|1262609|dbj|BAA04326.1| RNA polymerase beta subunit [Pinus thunbergii]
          Length = 1075

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK++GRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVSGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKNFQIDREE 1074



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 238/640 (37%), Positives = 361/640 (56%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + E     +          Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTRYPERFLFLLKKKGRWEREEYLW---------SREKAILEFYK 233

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCISGDLVFSESLCKELQKKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIRRATKRR 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A   
Sbjct: 353 STPQNLVTSTLLKNTFQDFFGSHPLSQFLDQTNPLTEIAHGRKLSHLGPGGLTGRTASFR 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 705 QGPERITREIPHLDAHLLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 804



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/341 (19%), Positives = 132/341 (38%), Gaps = 38/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +   L A+G++ EEIL  T YP+           +            +
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKGRWEREEYLWSREKAI 228

Query: 261 SSSLVD---IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
                    I       ES  K         + +  K      +    L + E+ +    
Sbjct: 229 LEFYKKLYCISGDLVFSESLCKELQKKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 318 GEIYIE-------AGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            ++             +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|228017445|gb|ACP52261.1| RNA polymerase beta subunit [Pinus merkusii]
          Length = 1075

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 631  IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 689

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 690  SFHIVRYRIEICMTSQGPERITREIPHLDAH-PLRHLDEN-----GLVMLGSWIETGDVL 743

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 744  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 801

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 802  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 856

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 857  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 916

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 917  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 937

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 938  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 997

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 998  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1057

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + E
Sbjct: 1058 LNHAIISEKNFQIDREE 1074



 Score =  341 bits (874), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 221/640 (34%), Positives = 340/640 (53%), Gaps = 24/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +  E+ L+   + E     +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLW---------SREKAILEFYK 233

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+             FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 234 KLYCISGDLVFSESLCKELQEKFF-RQRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 292

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++           
Sbjct: 293 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVXXXXXXXXXXX 352

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                      + +   +FF         +  N L+ I                  A   
Sbjct: 353 XXXXXXXXXXXLKNTFQDFFGXXXXXXXXDQTNPLTEIAXXXXXXXXXXXXXTGRTAXXX 412

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 413 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 472

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 473 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 532

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 533 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 592

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 593 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILA 644

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 645 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 704

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 705 QGPERITREIPHLDAHPLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 764

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 765 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 804



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/342 (19%), Positives = 137/342 (40%), Gaps = 40/342 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL     +   I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHNFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D  + 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVGER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +   L A+G++ EEIL  T YP+           +            +
Sbjct: 169 IWARVSRKQKISIPVLLSAMGLNLEEILDNTRYPERFLFLLKKKERWEREEYLWSREKAI 228

Query: 261 SSSLVDI-----------DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
                 +              +++ E   +    L K  +    + L +         + 
Sbjct: 229 LEFYKKLYCISGDLVFSESLCKELQEKFFRQRCELGKIGRRNLNQKLNLDIPENEIFSLP 288

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 QDVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 329


>gi|44889502|gb|AAS48373.1| RNA polymerase II [Cochliobolus heterostrophus]
          Length = 1208

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 177/1089 (16%), Positives = 345/1089 (31%), Gaps = 183/1089 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY----VAEDIVNGETGEIYIEAGDVID 329
            +E G +L S       E  +         + G +    +     +     ++   G V D
Sbjct: 259  VEKGTRLISSFNIKWAENSLAG---PGKRIPGPFAYATLPYIKADVPMAIVFRALGIVSD 315

Query: 330  EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            E+ L  I +       +  +        +         +DR+ AL  I +          
Sbjct: 316  EEILSHIVYDRTDTQMLELLKPSIEEGSV--------VQDRETALDFIAKRGANSGTKDR 367

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +  +          +  L  + +            +     +      +I  L+    G
Sbjct: 368  RLKFA-----RDIMQREFLPHISQK-----------EGQDTRKAYFFGYMIHRLLQCVLG 411

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAK 507
            +   DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  + A 
Sbjct: 412  RRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYLQRCVENNQDFNVQMAVKAS 471

Query: 508  PVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             + + +     +               +SQ+       S ++H RR +      V R   
Sbjct: 472  IITNGLKYSLATGNWGDQKXAASAXAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGK 527

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTN 612
              + R +H +H+G +CPAET EG   GLV +L+    V+          +    + ++  
Sbjct: 528  LAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLE 587

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQV 671
            +       +    ++      +  +      +V        +      I D  D   K  
Sbjct: 588  EYDQNQNPDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIF 647

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
                  + P    ++  R     ++   ++    LKAE     T       +   A    
Sbjct: 648  TDAGRVMRPLFVVENDIRKPNRNHLIFTKEISNKLKAEQQETSTRQGWSQEEVEQATYGW 707

Query: 730  K---RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVG 785
            +   + G+VE +DA       +    +      +    L   +RS +     +R   +  
Sbjct: 708  RGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMKMGLPAAERSTEGKDRLRRLKPQPD 767

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +         P+  LG       +  + +P+  +N          M  + +  ++   
Sbjct: 768  PRIHAYTHCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNF 820

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
               +                                  V             +       
Sbjct: 821  ALRMETMMN-----------------------------VLYYPQKPLATTRSMEYLKFRE 851

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E
Sbjct: 852  LPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLE 907

Query: 966  LLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
               +    + + L    Y +L +   +  G           K+  +++D      ++   
Sbjct: 908  QFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAQELGQKTTLH 967

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    ++     +  Q                             LR VKV     +
Sbjct: 968  TKRDVSTPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRTTK 1007

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L 
Sbjct: 1008 VPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVTPDLIINPHAIPSRMTIAHLVECLLS 1067

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G++                                                   
Sbjct: 1068 KVGAITGQEGD------------------------------------------------- 1078

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                +TP F     + I+ +L  A   + G  I+Y+G TG+     + +G  Y  +L HM
Sbjct: 1079 ----ATP-FTDVTVDQISQLLEDAGYQKRGFEIMYNGHTGKKLRTQIFLGPTYYQRLRHM 1133

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-- 1320
            V DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD  
Sbjct: 1134 VDDKIHARARGPLQILTRQPVEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFTVSDAY 1193

Query: 1321 -----DVVG 1324
                 D+ G
Sbjct: 1194 TVHVCDICG 1202



 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 138/1041 (13%), Positives = 287/1041 (27%), Gaps = 212/1041 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS----VFPITAFS----GAAMLEFVSYE 80
           L+  Q  SYD F   N   D     G  +          P    +        ++F    
Sbjct: 40  LVSQQLDSYDEF-TRNTIQDIVKENG--SVILEQNTPYNPDEDDNPIIKRRYEIKFGRVY 96

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVF----------DVDEFTGAK 120
              P               +   R+LTY+  +   +   +           D DE     
Sbjct: 97  LARPTHTEGDGTTVQLYPHEARLRNLTYSGAMLADIENRIMVAREGRDPEGDEDEDMEGG 156

Query: 121 SIK---DIKEQS------------IYMGDLPLMTKD------------------------ 141
                  I+ +             +++G LP+M +                         
Sbjct: 157 YTGGASQIRWEREDMPMDDGTAARVFIGKLPVMLRSELCHLRAQSDADLFALNECPYDQG 216

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
           G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+ K
Sbjct: 217 GYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFNIK 272

Query: 200 ---DII-----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
              + +                 +++ D    VP+     ALG+   EEILS        
Sbjct: 273 WAENSLAGPGKRIPGPFAYATLPYIKAD----VPMAIVFRALGIVSDEEILSHIVYDRTD 328

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +Q  +     +    ++   + +   +         +  +   +  +  ++ + +  +  
Sbjct: 329 TQMLELLKPSIEEGSVVQDRETALDFIAKRGANSGTKDRRLKFARDI--MQREFLPHISQ 386

Query: 299 T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                       G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 387 KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLT 445

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            +   Y++  +  +++ + + A+           + T  +  S+    + D      +  
Sbjct: 446 KDVYKYLQRCVENNQDFNVQMAV--------KASIITNGLKYSLATGNWGDQKXAASAXA 497

Query: 412 GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
           G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 498 GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 557

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            L     + +      I + ++  ++  +   D                   +       
Sbjct: 558 NLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQNPDATKVF---VNGVWVGVHSNAQ 614

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             ++ +   RR   L  +  + R     E + +       + P    E        +   
Sbjct: 615 QLVTVVQELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVVENDIRKPNRNHLI 673

Query: 589 FAR-------------VNAYGF----IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
           F +                 G+    +E              V YL A EEE   I  + 
Sbjct: 674 FTKEISNKLKAEQQETSTRQGWSQEEVEQATYGWRGLIQDGVVEYLDAEEEETAMITFSP 733

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             L+E       L                                          + R  
Sbjct: 734 EDLEEWREMKMGLPA----------------------------------------AERST 753

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            G +  R+  P          T  E   A   G       A I+   D  +    + +  
Sbjct: 754 EGKDRLRRLKPQPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRNTYQSA 807

Query: 752 LDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +     GV      ++ +         Q+PL                      +L  G+N
Sbjct: 808 MGKQAMGVALTNFALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQN 857

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DI 865
            +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D 
Sbjct: 858 AIVAIATYGGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADT 917

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G++  G  V+  DI++GK  P         +K             R
Sbjct: 918 LRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAQELGQKT-------TLHTKR 970

Query: 926 DTSLRVPSGVSGTVVDVRIFN 946
           D S  + S  +G V  V    
Sbjct: 971 DVSTPLRSTENGIVDQVLFTT 991


>gi|209395081|gb|ACI45353.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+   HLGWA  G+G++I  ++   +       LR FL +V  +   T
Sbjct: 1    NPLGVPSRMNIGQVLVVHLGWASKGIGQRIGDML---QQQAKAGELREFLHEVYNSRGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL----------DESG 1232
            E ++   D+ ++ +AE   +GVP +TPVFDGA EE I  MLR+A                
Sbjct: 58   ENLAQLSDEELVAMAENLTNGVPYATPVFDGASEEEIKDMLRIAYPDDIARRKGLTPTRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGHMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGAAYVLQEML +KSDDVVGRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGAAYVLQEMLAVKSDDVVGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|228016940|gb|ACP51764.1| RNA polymerase beta subunit [Pinus banksiana]
          Length = 1074

 Score =  400 bits (1027), Expect = e-108,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    +  T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKPDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 232/640 (36%), Positives = 358/640 (55%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERFLFLLKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R++ ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLKDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF         +  N    I H R+LS LG GG+    A   
Sbjct: 352 STPQNLVTSTLLKNTFQDFFGXXXXXXXXDQTNXXXXIAHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPKIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHLLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/341 (19%), Positives = 141/341 (41%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +     ++   +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELDHNRIN--YIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDFWCFPL--------SA 251
           I  R+ R++K+ +   L  +G++ EEIL    +  + ++  + + W              
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERFLFLLKKERWEREEYLWSREKAIL 228

Query: 252 ADLMVGAKVSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                   +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|259485464|tpe|CBF82508.1| TPA: DNA-directed RNA polymerase Fragment (EC 2.7.7.6)
            [Source:UniProtKB/TrEMBL;Acc:Q9UV95] [Aspergillus
            nidulans FGSC A4]
          Length = 1252

 Score =  400 bits (1027), Expect = e-108,   Method: Composition-based stats.
 Identities = 181/992 (18%), Positives = 333/992 (33%), Gaps = 169/992 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 381  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 440

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     + A  V   +     +               +SQ+
Sbjct: 441  RVTRDLQRYVQRCVESDREIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQV 500

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 501  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 556

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +    S   E
Sbjct: 557  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVE 616

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQA 700
             +        I      I D  +   K          P    D+  +     N+   ++ 
Sbjct: 617  TMQALRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEH 676

Query: 701  VPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA      +I     DL+ S 
Sbjct: 677  IRKLEEDKELPPDMDPEDRRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 735

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y L +     Q+     R ++               PS  LG       +  + +
Sbjct: 736  QLQAGYALPE----EQDPNKRVRSILS--QRAHTWTHCEIHPSMILG-------VCASII 782

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 783  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 830

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 831  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 873

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +     +  +    ++    V    +E   +    + + + +  Y +L E   +  G 
Sbjct: 874  RGLFRSLFYRTY----SDSEKMVGLTVVERFEKPMRSDTIGMRKGTYDKLDEDGIVNPGV 929

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ D                +E  QR     K+   T     E+  
Sbjct: 930  RVSGEDIIIGKTAPLAPD---------------AEELGQRTKNHTKLDVSTPLRSTENGI 974

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV + M +  Q GDK A RHG KG +      EDMPF +
Sbjct: 975  VDQVLVTTTPDSL-----RSVKVRMRMTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTR 1029

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 1030 EGVTPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD-------------------- 1069

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+ +LR       G 
Sbjct: 1070 ---------------------------------ATP-FTDVTVDSISRLLREHGYQSRGF 1095

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 1096 EVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 1155

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND- 1337
             GEME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N  
Sbjct: 1156 FGEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKH 1215

Query: 1338 -TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
               +   P +  +L +E+ A+ +S  +  +R+
Sbjct: 1216 RISQVHIPYAAKLLFQELAAMNISARMFTNRS 1247



 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 144/1035 (13%), Positives = 298/1035 (28%), Gaps = 192/1035 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              L+F +     
Sbjct: 38  LVSQQLDSFDEFISSTLQ-ELVEEQGQVTLDQTIPPSEDEVDPVVVRRYELKFGTVMLSR 96

Query: 84  P----------KFDVDDCLWRDLTYAVPLKITLRLIVFD---------VDEFTGAKSIK- 123
           P               +   R++TYA PL + ++  + +          D+  G +  K 
Sbjct: 97  PMAMEGDGAATIMLPHEARLRNMTYASPLYLGIKKKIMEGRERMVGDRDDDDMGNEDRKA 156

Query: 124 ---------------DIKEQSIYMGDLPLMTKD------------------------GTF 144
                            KE+++++G +P+M K                         G F
Sbjct: 157 TGTYLQWEEMALPPDQAKEETVHIGKMPIMLKSKYCLLRDLGEQALYDWNECPYDSGGYF 216

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD----- 197
           +I G ++++++Q  RS G        + +      Y   I    ++G  +  +       
Sbjct: 217 IINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLKLFG 273

Query: 198 ----SKDII---------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGD 243
               +K            +++ D    +P+     ALG+   E+IL+        +   +
Sbjct: 274 KGDSAKGGFGPTIRSTLPYIKAD----IPIVIVFRALGVVSDEDILNHICYDRNDTPMLE 329

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT---- 299
                +    ++   +V+   +      Q   + ++      + ++++ +  +  +    
Sbjct: 330 MLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGSE 389

Query: 300 --SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                  G  V   ++    G   ++  D   +K L+           +L+     +   
Sbjct: 390 TRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD--- 445

Query: 358 IRNTLVTDKNKDRKDALLDIY-RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                +    +   ++  +IY  V       T  +  ++    + +  K   +  G  ++
Sbjct: 446 -----LQRYVQRCVESDREIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQV 500

Query: 417 NMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKN 473
             R    +      R          I     L N   G +   +    +    V  +   
Sbjct: 501 LSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALM 560

Query: 474 QYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            Y       E  I    + +   ++   PQ   NA  V           Q S L E + +
Sbjct: 561 CYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVETMQA 620

Query: 532 LSRITHTRRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           L R        +L +    R         R   P       P   + G+ +     +   
Sbjct: 621 LRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEHIRKL 680

Query: 590 ARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-- 641
                             Y        +  V Y+ A EEE   I      L+        
Sbjct: 681 EEDKELPPDMDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQLQAG 740

Query: 642 ----EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               EE    +     +          +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 741 YALPEEQDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMG 800

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                   + A I+      +    ++  +          +  
Sbjct: 801 KQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIV 851

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y              NQ            + +I +  S D G         + +  
Sbjct: 852 AIACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS-----LFYRT 884

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           +        + + ER              FE   R   +G  + T D           +D
Sbjct: 885 YSDSEKMVGLTVVER--------------FEKPMRSDTIGMRKGTYD----------KLD 920

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GI+  G  V+  DI++GK  P         E+L +       +DV        +G+  
Sbjct: 921 EDGIVNPGVRVSGEDIIIGKTAPLAPDA----EELGQRTKNHTKLDVSTPLRSTENGIVD 976

Query: 938 TVVDVRIFNRHGIDK 952
            V+     +     K
Sbjct: 977 QVLVTTTPDSLRSVK 991


>gi|70982424|ref|XP_746740.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus fumigatus Af293]
 gi|66844364|gb|EAL84702.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus fumigatus Af293]
 gi|159123019|gb|EDP48139.1| DNA-dependent RNA polymerase II RPB140 [Aspergillus fumigatus A1163]
          Length = 1255

 Score =  400 bits (1027), Expect = e-108,   Method: Composition-based stats.
 Identities = 176/991 (17%), Positives = 330/991 (33%), Gaps = 167/991 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 384  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 443

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 444  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASSKAGVSQV 503

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 504  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 559

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-TE 642
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 560  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRDPAHLVN 619

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ-RQA 700
             ++  R             D  +   K          P F+ ++D      G  +  +  
Sbjct: 620  TMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKDH 679

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTS 757
            +  L+ +             +         ++G+VE VDA      +I     DL+ S  
Sbjct: 680  IRKLEQDKELPADLDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQ 739

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                Y         +    N+R    +  +          PS  LG       +  + +P
Sbjct: 740  LQAGYA------LPEEDDPNKRVRSVLSQKAHTWTHCEIHPSMILG-------VCASIIP 786

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +                     E   +I    ++ L    
Sbjct: 787  FPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA--- 833

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
                                +       +   +  + AI      +  D+ +   S +  
Sbjct: 834  ----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDR 877

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   D  +         +E   +    + + + +  Y +L E   I  G  
Sbjct: 878  GLF-RSLFYRTYTDSEKMVGL---TVVERFEKPMRSDTIGMRKGTYDKLDEDGIIAPGVR 933

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L+ +                +E  QR     K+   T     E+   
Sbjct: 934  VSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKLDVSTPLRSTENGIV 978

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF ++
Sbjct: 979  DQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRE 1033

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G +                       
Sbjct: 1034 GVSPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD--------------------- 1072

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP F     ++I+ +LR       G  
Sbjct: 1073 --------------------------------ATP-FTDVTVDSISRLLREHGYQSRGFE 1099

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 1100 VMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRF 1159

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAGND-- 1337
            GEME  C+ A+GA+  L+E L   SD       D  G        +  ++E  +  N   
Sbjct: 1160 GEMERDCMIAHGASAFLKERLFDVSDPFRVHICDDCGLMTPIAKLKKGLFECRLCNNKHR 1219

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
              +   P +  +L +E+ A+ ++  +  +R+
Sbjct: 1220 ISQVHIPYAAKLLFQELAAMNIAARMFTNRS 1250



 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 145/1041 (13%), Positives = 296/1041 (28%), Gaps = 204/1041 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              L+F +     
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQGQVTLDQTLPPSEDEDDPVVLRRYELKFGTVMLSR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE------------------ 115
           P               +   R+LTYA PL + +   + +  E                  
Sbjct: 97  PSVTEGDGATTIMLPQEARLRNLTYASPLYLGITKRIMEGRERLIADRDEDDAAPDADED 156

Query: 116 ----------FTGAKSIKDIKEQSIYMGDLPLMTKD------------------------ 141
                               KE+++++G +P+M K                         
Sbjct: 157 RKARGTYLQWEQKELPPDQAKEETVFIGKMPIMLKSKYCILKDLSEQALYNWNECPYDSG 216

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK 199
           G F+I G ++++++Q  RS G        + +      Y   I    ++G  +  +   K
Sbjct: 217 GYFIINGSEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLK 273

Query: 200 DIIHVRIDR----------------RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRG 242
             +  + D                 +  +P+     ALG +  E+IL+        +   
Sbjct: 274 --LFAKGDSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPML 331

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT--- 299
           +     +    ++   +V+   +      Q   + ++      + ++++ +  +  +   
Sbjct: 332 EMLKPCIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGS 391

Query: 300 ---SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
                   G  V   ++    G   ++  D   +K L+           +L+     +  
Sbjct: 392 ETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD-- 448

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                 V    +  ++  L+I          T  +  ++    + +  K   S  G  ++
Sbjct: 449 --LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASSKAGVSQV 503

Query: 417 NMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKN 473
             R    +      R          I     L N   G +   +    +    V  +   
Sbjct: 504 LSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALM 563

Query: 474 QYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            Y       E  I    + +   ++   PQ   NA  V      F     +    +  + 
Sbjct: 564 CYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGVHRDPAHL 617

Query: 532 LSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLV 583
           ++ +   RR + +  +  + R     E        R   P       P   + G  +   
Sbjct: 618 VNTMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNK 677

Query: 584 SSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             +    +                Y        +  V Y+ A EEE   I      L+  
Sbjct: 678 DHIRKLEQDKELPADLDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEIS 737

Query: 638 GSFT------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                     EE    +     +          +  P  ++ + AS+IPF +++ S R  
Sbjct: 738 KQLQAGYALPEEDDPNKRVRSVLSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNT 797

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +QA+ +                   + A I+      +    ++  +       
Sbjct: 798 YQSAMGKQAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPA 848

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              +   +  Y              NQ            + +I +  S D G        
Sbjct: 849 GQNAIVAIACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS---- 882

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            + +  +        + + ER              FE   R   +G  +           
Sbjct: 883 -LFYRTYTDSEKMVGLTVVER--------------FEKPMRSDTIGMRK----------G 917

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +DE GII  G  V+  DI++GK  P     + PE + L      KA    D S  +
Sbjct: 918 TYDKLDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVSTPL 970

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            S  +G V  V +   +   K
Sbjct: 971 RSTENGIVDQVLVSTSNDDLK 991


>gi|255709707|gb|ACU30744.1| DNA-directed RNA polymerase beta chain [Pseudomonas sp. In5]
          Length = 409

 Score =  399 bits (1026), Expect = e-108,   Method: Composition-based stats.
 Identities = 245/407 (60%), Positives = 319/407 (78%)

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N 
Sbjct: 2   ENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNP 61

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR
Sbjct: 62  LSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYAR 121

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   
Sbjct: 122 TNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLN 181

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P V
Sbjct: 182 EFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLV 241

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSN
Sbjct: 242 GTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSN 301

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           QNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SE
Sbjct: 302 QNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSE 361

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           R+V ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E  L  +DE
Sbjct: 362 RVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDE 408


>gi|326436004|gb|EGD81574.1| DNA-directed RNA polymerase II polypeptide [Salpingoeca sp. ATCC
            50818]
          Length = 1193

 Score =  399 bits (1026), Expect = e-108,   Method: Composition-based stats.
 Identities = 182/1154 (15%), Positives = 357/1154 (30%), Gaps = 191/1154 (16%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------------TSDCLCGLYVAED 311
               I+  E+V+ + +K+    +   ++K  K+L +                L    +   
Sbjct: 180  YFIINGSEKVLLAQEKMAPNTVFVFEKKDPKYLFVTEIKSVLERSPRPPSSLLVKLLRGS 239

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
                 +G +       + +     +    +       +       +    ++        
Sbjct: 240  QSAARSGPVLHVTLPYVRQDVPVVVVFRALGFEDDRSILEHIIYDFNDMEMMEMLKPSLD 299

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +A +   R     DV+   + +          ++        ++  +  ++         
Sbjct: 300  EAFVIQNR-----DVALDWIGKRAVQSPAISKERRIHYAKDILQKELLPHIGLGPHCETK 354

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ER 489
            +   +  ++   +     +  +DD D+ GN+R+   G +    +R     + + ++   +
Sbjct: 355  KAFFLGYMVHRTLQAALRRRQLDDRDHYGNKRLDMSGPLTGFLFRTLFRNVTKELRSYIQ 414

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
                  + +     +N+K + S +   F +               +SQ+   +   S ++
Sbjct: 415  KKLNRSEEIKLSAGLNSKQIESGLRYSFATGNWGTQAKAFEARAGVSQVLNRLTFASTLS 474

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RRL++     + R     + R +H TH+G ICPAET EGH +GLV +L   A V   G
Sbjct: 475  HLRRLNS----PIERTGKIAKPRQLHNTHWGYICPAETPEGHAVGLVKNLALMASVTVGG 530

Query: 597  FIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQ-ANSSLDEDGSFTEELVFCRCAGEE 653
                    +     +  +D+   S + +  +     A   +  +       +      + 
Sbjct: 531  DATPVLELLNSIGMESLDDLASRSVIRDTTKIFVNGAWVGIHMEPEEVVRNLHLCRRTQA 590

Query: 654  ILVPREKIDFIDASPK--QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             ++  E   F D   +   V S +  L   L   +   +    +   Q    L  +    
Sbjct: 591  DMIQSEVSIFRDIREREIHVYSDSGRLTRPLLIVEKPELDDTFHDGTQQQQTLALKKQ-- 648

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                  +    S A   A  A           ++  ++ + + +T         +     
Sbjct: 649  -----HLEKLQSAAMQNAFEATYSWSDLVREGLVEYIDVNEEDTTMIAMTPDDFEMSDEQ 703

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
               C                      PS  LG       +  + +P+  +N       S 
Sbjct: 704  DLYCTTY-------------THCEIHPSMILG-------ICASIIPFPDHNQ------SP 737

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R   +       +  +                           +I    +  V       
Sbjct: 738  RNTYQSAMGKQAMGIYTTNF-----------------------HIRLDTLAHVLYYPQQP 774

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             +    +       +      + AI      +  D+ +     V   +    +F R    
Sbjct: 775  LVKTRSMDYMYFKDLPAGINAIVAIMCYTGYNQEDSVIMNKCAVDRGLF-RSVFYRSYAS 833

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              E +      ++    +   +    +  + Y +L +                 T ++ D
Sbjct: 834  SEENT----GREVIKFEKPSRETCAGMRNSNYGKLED----------DGLIAPGTSVTGD 879

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                          ++        +S   ++E     +  R        Q    M P   
Sbjct: 880  -------DAIIGRTMELPPNAEARDSRLARFEKLDKSVFLRASENGIIDQVMVAMGPKGT 932

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R VK+ V   R  Q GDK A RHG KG        EDMPF   G   DI++NP  +PSRM
Sbjct: 933  RFVKIRVRSIRVPQIGDKFASRHGQKGTCGMQYSQEDMPFTCQGITPDIIVNPHAIPSRM 992

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E  LG      G                                          
Sbjct: 993  TIGHLIECLLGKVGCLEGAFGD-------------------------------------- 1014

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP F       + S L   +  + G  +LY+G TG      V  
Sbjct: 1015 ---------------ATP-FIEVTVNEVASALEAHNFHKYGNEVLYNGFTGRKMQAQVFF 1058

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+G+A  L
Sbjct: 1059 GPTYYQRLKHMVDDKIHARARGPLQILTKQPVEGRSRDGGLRFGEMERDCMIAHGSAQFL 1118

Query: 1312 QEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFETGTPESFNVLVKEM 1354
            +E L   SD       D+ G   +  ++                 +   P +  +L +E+
Sbjct: 1119 RERLFEVSDPYRIHVCDICGLICI-ANLNKNELECKACSNTTRVSQVRIPYACKLLFQEL 1177

Query: 1355 QALGLSIDLENSRT 1368
             ++ ++  +    +
Sbjct: 1178 MSMCIAPRIMTDNS 1191



 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 130/1022 (12%), Positives = 281/1022 (27%), Gaps = 195/1022 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+DHF+   I      +  L+   K   P    +      +  ++F       
Sbjct: 35  LVRQQLDSFDHFIQYGIQDAVEKSPALEIEAK---PQYTTNEFEEPPSYSVKFCEVSLSK 91

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           P              +D   R+LTY   + +       +  +     +        +++G
Sbjct: 92  PTHYEEDGTSHFLYPNDARLRNLTYWSEMFVEAEETYRETQDSEPETTTTS-----VHLG 146

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F+I G ++++++Q   +P  +     
Sbjct: 147 KIPIMLRSKFCLLNGKLNDDLYNLNECPLDPGGYFIINGSEKVLLAQEKMAPNTVFVFEK 206

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RKVPV--TSF---- 217
           K       K L+   I       ++        + V++ R      R  PV   +     
Sbjct: 207 KDP-----KYLFVTEI----KSVLERSPRPPSSLLVKLLRGSQSAARSGPVLHVTLPYVR 257

Query: 218 --------LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
                     ALG + +  IL          +  +     L  A ++    V+   +   
Sbjct: 258 QDVPVVVVFRALGFEDDRSILEHIIYDFNDMEMMEMLKPSLDEAFVIQNRDVALDWIGKR 317

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             +    S ++        L+++ +  +G+   C          +   T +  +    + 
Sbjct: 318 AVQSPAISKERRIHYAKDILQKELLPHIGLGPHCETKKAFFLGYMVHRTLQAALRRRQLD 377

Query: 329 DEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           D      + +  S      +      N    +R+ +    N+  +   + +   +    +
Sbjct: 378 DRDHYGNKRLDMSGPLTGFLFRTLFRNVTKELRSYIQKKLNRSEE---IKLSAGLNSKQI 434

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVD 445
            +              +  ++        +N      T   +R +    +    I     
Sbjct: 435 ESGLRYSFATGNWGTQAKAFEARAGVSQVLNRLTFASTLSHLRRLNSPIERTGKIAKPRQ 494

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N                  + + L     + +      + E ++S+ ++S+   DL +
Sbjct: 495 LHNTHWGYICPAETPEGHAVGLVKNLALMASVTVGGDATPVLELLNSIGMESL--DDLAS 552

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PT 564
              +      F   + +    E    +  +   RR  A            +  R++H  +
Sbjct: 553 RSVIRDTTKIFVNGAWVGIHMEPEEVVRNLHLCRRTQADMIQSEVSIFRDIREREIHVYS 612

Query: 565 HYGRI-CPAETSEGHN---------------IGLVSSLTSFARVNAYGFIETPYRKVCDG 608
             GR+  P    E                        L            E  Y    D 
Sbjct: 613 DSGRLTRPLLIVEKPELDDTFHDGTQQQQTLALKKQHLEKLQSAAMQNAFEATY-SWSDL 671

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+   EE+   IA      +                +E  +        +  P
Sbjct: 672 VREGLVEYIDVNEEDTTMIAMTPDDFE--------------MSDEQDLYCTTYTHCEIHP 717

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ I AS+IPF +++ S R      M +QA+ +                         
Sbjct: 718 SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYTTNFHI------------------ 759

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV--GD 786
                                     + + V  Y                 PLVK    D
Sbjct: 760 -----------------------RLDTLAHVLYYPQQ--------------PLVKTRSMD 782

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            +   D+ A   +            ++ +  ++    EDS+++++  V   +F S+    
Sbjct: 783 YMYFKDLPAGINAI---------VAIMCYTGYNQ---EDSVIMNKCAVDRGLFRSVFYRS 830

Query: 847 FEVMARDTKLGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           +     +T     +  +        +       +++ G+I  G  V   D ++G+     
Sbjct: 831 YASSEENTGREVIKFEKPSRETCAGMRNSNYGKLEDDGLIAPGTSVTGDDAIIGRTM--- 887

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
              + P  +   +         +   LR         V V +  +       R  S+   
Sbjct: 888 --ELPPNAEARDSRLARFEKLDKSVFLRASENGIIDQVMVAMGPKGTRFVKIRVRSIRVP 945

Query: 963 QI 964
           QI
Sbjct: 946 QI 947


>gi|172072925|ref|YP_001806686.1| RNA polymerase beta subunit [Cryptomeria japonica]
 gi|171854944|dbj|BAG16684.1| RNA polymerase beta subunit [Cryptomeria japonica]
 gi|239794312|dbj|BAH73309.1| RNA polymerase beta subunit [Cryptomeria japonica]
 gi|239794395|dbj|BAH73391.1| RNA polymerase beta subunit [Cryptomeria japonica]
          Length = 1083

 Score =  399 bits (1025), Expect = e-108,   Method: Composition-based stats.
 Identities = 158/499 (31%), Positives = 232/499 (46%), Gaps = 56/499 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G I+       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 635  VRQGEYVKRGQIIADSAATAG-GELSLGKNILVAYMPWEGYNFEDAILISERLVYQDIFT 693

Query: 942  VRIFNRH--GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                 R+  G+    +   V   +I  L          LD N       ++ G    +G 
Sbjct: 694  SFQIVRYEIGVYFTNQGPEVITREIPHLDAYL---LRHLDEN-----GLVMIGSWIETGD 745

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K  + + +             A+ D K     E+    +   K +       +  +
Sbjct: 746  VLVGKLILEAEEDSLLNTPEGKLLQALFDIKAPTGKENC---FRVPKGVKGRVIDVRCFQ 802

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                DD    ++  V V++  KR IQ GDK+AGRHGNKGI+S+ILP +DMP+L++GTPVD
Sbjct: 803  EFEEDDYLGDIVEKVHVYILQKRKIQVGDKVAGRHGNKGIISKILPRQDMPYLQNGTPVD 862

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +VLNPLGVPSRMNVGQIFE  LG A   + K  +    D +   + S    F E    + 
Sbjct: 863  MVLNPLGVPSRMNVGQIFECLLGLAGKLMNKHYRLAPFDERYEREASRKLVFSELYKASE 922

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                          VF+                D  G+  L DG
Sbjct: 923  QTANPW------------------------VFE---------------PDHPGKHRLIDG 943

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG+ F++PVT+G  Y+ KL H V DK++ARS+G Y+LVTQQPL GKS+RGGQR+GEMEV
Sbjct: 944  RTGKVFEQPVTIGIAYISKLCHQVDDKIHARSSGPYTLVTQQPLKGKSHRGGQRVGEMEV 1003

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP-ESFNVLVKEMQALG 1358
            W +Q +G AY+L EMLT+KSD +  R +++ +I  G    +  TP ESF +L +E+++L 
Sbjct: 1004 WALQGFGVAYILHEMLTLKSDHMDTREKIFGAIFNGEPMPKPSTPTESFRLLSRELRSLA 1063

Query: 1359 LSID--LENSRTKNSAKME 1375
            L ++  + +       K E
Sbjct: 1064 LELNHTILSEIDFQIDKKE 1082



 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 222/589 (37%), Positives = 337/589 (57%), Gaps = 14/589 (2%)

Query: 371 KDALLDIYRVMRPGDVSTFSVA---ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           ++A+L++Y+ +   D          +       F   K  L   GR   N +L+LD P++
Sbjct: 225 EEAILELYKELYISDEIEKENCEFSDIYEKVRAFFRMKCALGKNGRRNPNKKLSLDIPEN 284

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
                  D++A +  L+ +R G GT DDID+L NR +RSV ++L+ Q R  L+    +I+
Sbjct: 285 EIFSLPHDVLAAVDYLIKVRFGTGTPDDIDHLQNRYIRSVADLLQEQLRFALIDFREAIE 344

Query: 488 ER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +    +S +    +   L    P+     +FF    LSQ  +  N L+ I H+R++S+LG
Sbjct: 345 KTILSASTNPKKRITNKLETLIPLTETFQDFFGLHPLSQFLDQTNPLAEIVHSRKVSSLG 404

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+    +    RD+HP+HYGRICP  TSEG N+GL+ SL+ +A +  YG +++P+ ++
Sbjct: 405 PGGLTSRTSTFRTRDIHPSHYGRICPITTSEGINVGLIGSLSIYATLGHYGSLQSPFYRL 464

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            +      +VYL   E+E   IA  NS     G   E+    R   E +    ++I F  
Sbjct: 465 SERSNEEQMVYLLPGEDEYYRIATGNSLALNQGVPEEQFTPARFQQEFLFFAWDQIHFRS 524

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P Q  S+   LIPF+E++D+NR LMG NMQRQAVPL++ E   VGTG+E   A  SG+
Sbjct: 525 IFPSQYFSVGVCLIPFIEHNDANRALMGSNMQRQAVPLVQPEKCIVGTGLEGQAALDSGS 584

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             +AK+ G ++ +D   I I S     +  T  +       +QRSN +TC++Q+P V+ G
Sbjct: 585 VAIAKQGGKIKYIDGENITITSSVARNNIETELIL------YQRSNSDTCMHQKPRVRQG 638

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           + V+R  IIAD  +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V +D+FTS  I 
Sbjct: 639 EYVKRGQIIADSAATAGGELSLGKNILVAYMPWEGYNFEDAILISERLVYQDIFTSFQIV 698

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +E+    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+  + E  
Sbjct: 699 RYEIGVYFTNQGPEVITREIPHLDAYLLRHLDENGLVMIGSWIETGDVLVGKLILEAEED 758

Query: 906 M---TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
               TPE KLL+A+F  KA   ++   RVP GV G V+DVR F     D
Sbjct: 759 SLLNTPEGKLLQALFDIKAPTGKENCFRVPKGVKGRVIDVRCFQEFEED 807



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 84/448 (18%), Positives = 162/448 (36%), Gaps = 39/448 (8%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVS 78
             I  IP+  ++Q   +D F+           +GL         I +       +L    
Sbjct: 7   KGIFTIPEFGKIQLEGFDRFI----------EQGLIEELNKFSKIESPKKKRKFLLFGNE 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI-YMGDLPL 137
           Y+   P     D ++  LTY   L +  RLI          K+ + IK + I Y+GD+PL
Sbjct: 57  YKLTEPSIKERDAVYMSLTYHCQLYVPARLI-------KKTKTREKIKNRMILYLGDIPL 109

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE-F 196
           M   GTFVI G  R+VV+Q+ RSPGI++  ++     SG ++Y   II D G    +E  
Sbjct: 110 MNSKGTFVINGNYRVVVNQILRSPGIYYTWER---KPSGNIIYIGTIISDWGGRSRLEIK 166

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST-----F------YPKIVYSQRGDFW 245
                I +R+ R++K+ V  FL+A+G++S++I +      F      Y    Y   G   
Sbjct: 167 KKTKKIWIRVSRKKKISVLLFLLAMGLNSKDIFNYKNILAFFKYSEEYYTYFYWYGGKEE 226

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
                  +L +  ++     +     + + +  ++   L K+ +    K L +       
Sbjct: 227 AILELYKELYISDEIEKENCEFSDIYEKVRAFFRMKCALGKNGRRNPNKKLSLDIPENEI 286

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +  D++      I +          ++ + +  IR +  L  + +    +        
Sbjct: 287 FSLPHDVLAAVDYLIKV-RFGTGTPDDIDHLQNRYIRSVADLLQEQLR---FALIDFREA 342

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             K    A  +  + +     +   + E+  +F         L     +   +     + 
Sbjct: 343 IEKTILSASTNPKKRITNKLETLIPLTETFQDFFGLHPLSQFLDQTNPLAEIVHSRKVSS 402

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +         + +     G+   
Sbjct: 403 LGPGGLTSRTSTFRTRDIHPSHYGRICP 430


>gi|330369316|gb|AEC12048.1| RNA polymerase beta subunit [Bradyrhizobium sp. CCBAU 051161]
 gi|330369318|gb|AEC12049.1| RNA polymerase beta subunit [Bradyrhizobium sp. CCBAU 25541]
 gi|330369322|gb|AEC12051.1| RNA polymerase beta subunit [Bradyrhizobium sp. CCBAU 45502]
          Length = 238

 Score =  399 bits (1025), Expect = e-108,   Method: Composition-based stats.
 Identities = 144/239 (60%), Positives = 187/239 (78%), Gaps = 1/239 (0%)

Query: 50  RPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           R +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLI
Sbjct: 1   RLDEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLI 60

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
           VFD+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDK
Sbjct: 61  VFDIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDK 120

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           G+   SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E IL
Sbjct: 121 GKTHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAIL 180

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           STFY KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L
Sbjct: 181 STFYKKILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQL 238


>gi|11134656|sp|Q42877|RPB2_SOLLC RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2; AltName: Full=DNA-directed RNA polymerase II 135 kDa
            polypeptide
 gi|1049068|gb|AAC49273.1| RNA polymerase II subunit 2 [Solanum lycopersicum]
          Length = 1191

 Score =  399 bits (1025), Expect = e-108,   Method: Composition-based stats.
 Identities = 178/1054 (16%), Positives = 333/1054 (31%), Gaps = 191/1054 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       +          KY 
Sbjct: 287  DILEHICYDFNDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGATVGVTREKRIKYA 343

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 344  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 400

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 401  GPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 460

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H + +G +CPAE
Sbjct: 461  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAE 516

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 517  TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPAVIPQATK 569

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G++       R     +   R     +D + +  V     L       D  R    
Sbjct: 570  IFVNGTWVG---IHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRP 626

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   ++K +   + T      +   G        G +E +D        +   ++
Sbjct: 627  LFIVEKQRLMIKKKD--IQTLQ-QRESPDEGGWHDLVAKGYIEYIDTEEEETTMISMTIN 683

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                              +   D  +D  +      +L   +  
Sbjct: 684  DLVQA----------------------------RLNPGDAYSDTYTHCEIHPSLILGVCA 715

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 716  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 771

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 772  EHL-------------------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQS 806

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R           +          G 
Sbjct: 807  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGT 865

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S                  D+   +     +  + TS    E   
Sbjct: 866  RVSGEDVIIGKTTPISQ-----------------DDAQGQASRYTRKDHSTSLRHSETGM 908

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 909  VDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 963

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 964  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 1003

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1004 ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1029

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1030 ETMYNGHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1089

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR----------TRVYESIVAG---- 1335
             GEME  C+ A+GAA+ L+E L  +SD     V  R             +E    G    
Sbjct: 1090 FGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIAIANLKKNSFEC--RGCKNK 1147

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
             D  +   P +  +L +E+ A+ ++  +     K
Sbjct: 1148 TDIVQVHIPYACKLLFQELMAMAIAPRMLTKDVK 1181



 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 134/993 (13%), Positives = 284/993 (28%), Gaps = 203/993 (20%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 38  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIN 88

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 89  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 148

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 149 FTK--VFIGKVPIMLRSSYCTLYQNSEKDLTELGECPLDQGGYFIINGSEKVLIAQEKMS 206

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR---------- 208
              ++      +     K  +   +        D +      + VR+  R          
Sbjct: 207 TNHVY----VFKKRQPNKYAFVAEVR----SMADTQNRPPSTMFVRMLSRTSAKGGSSGQ 258

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 259 YIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFNDTQMMELLRPSLEEAFVIQNQ 318

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +V+   +        +   K++     + L+++ +  +G+   C          +     
Sbjct: 319 QVALDYIGKRGATVGVTREKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH--- 374

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   +     K   +     
Sbjct: 375 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVN 434

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 435 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 494

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +      ++KN   +  + +  +    +  ++  
Sbjct: 495 EGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEW 551

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
                + I+   +  A   F   + +    +    +  +   RR   +  + GV R    
Sbjct: 552 GTENFEEISPAVIPQATKIFVNGTWVGIHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRL 611

Query: 556 VEMRDVHPTHYGRICPAETSE----GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            E+R ++  +     P    E          + +L      +  G+         D    
Sbjct: 612 KELR-IYTDYGRCSRPLFIVEKQRLMIKKKDIQTLQQRESPDEGGW--------HDLVAK 662

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+              +LV  R          +     +  P  +
Sbjct: 663 GYIEYIDTEEEETTMISM----------TINDLVQARLNP--GDAYSDTYTHCEIHPSLI 710

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +      F                    R
Sbjct: 711 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------R 750

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 751 MDTLAYV-----------------------------------LYYPQKPLV--------- 766

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N +VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 767 -TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 825

Query: 852 RDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E            +       +D+ G+   G  V+  D+++GK TP  +   
Sbjct: 826 KKMGTLVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD- 884

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   A         +D S  +    +G V
Sbjct: 885 --------AQGQASRYTRKDHSTSLRHSETGMV 909


>gi|190333344|gb|AAS67502.2| DNA-dependent RNA polymerase II second largest subunit [Meyerozyma
            guilliermondii]
          Length = 1219

 Score =  399 bits (1025), Expect = e-108,   Method: Composition-based stats.
 Identities = 175/977 (17%), Positives = 312/977 (31%), Gaps = 162/977 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L + +R+   ++ +
Sbjct: 361  DEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLASLFRILFKKLTK 420

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 421  DIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 480

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 481  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 536

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + +  +     Y+ +   ++  +      +         +   R 
Sbjct: 537  SCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVNGVWVGTHREPAHLVDTMRS 596

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQ---RQAVPL 703
                  +  E     D   K             P    DD         ++        L
Sbjct: 597  LRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDDPESETKGELKLQKEHIHKL 656

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVD 760
            L AE        E    +           G+VE VDA      +I     DL+ S S + 
Sbjct: 657  LNAEYSEEYATNEFGEEEGPYGWSSLVNDGVVEYVDAEEEETIMIAMTPEDLEASKSSLT 716

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              +    Q   Q     +R                  PS  LG  A       + +P+  
Sbjct: 717  ATQQKSLQLEEQELDPAKRIKPTNSSTTSTFTHCEIHPSMILGVAA-------SIIPFPD 769

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 770  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 800

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 801  MANILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 860

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L +   I  G     
Sbjct: 861  -RSLFFRTYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGIRVSG 916

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T +  D      R+Q+         ++     +  Q               +
Sbjct: 917  EDIIIGKTTPIPPDTEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 961

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG V      EDMPF   G  
Sbjct: 962  LLTTNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTVGVTYRHEDMPFTSQGIV 1016

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +                          
Sbjct: 1017 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGLEGD------------------------ 1052

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         ++P+ D    EA++ +LR       G  ++Y
Sbjct: 1053 -----------------------------ASPLTD-VTAEAVSKLLREHGYQSRGFEVMY 1082

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
             G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1083 HGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1142

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAGN----------DTFE 1340
            E  C+ A+GAA  L+E L   SD        V G   V  ++              + ++
Sbjct: 1143 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGVCGLMSVIANLKKNQFECRSCKNKTNIYQ 1202

Query: 1341 TGTPESFNVLVKEMQAL 1357
               P +  +L +E  A+
Sbjct: 1203 VHIPYAAKLLFQESMAM 1219


>gi|166034423|gb|ABY78988.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. ITTG S7]
          Length = 214

 Score =  399 bits (1025), Expect = e-108,   Method: Composition-based stats.
 Identities = 149/214 (69%), Positives = 178/214 (83%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            ++I  LI  YKA+G+I PLR  ++ V+G G+ ++++ DYDD SVLR+A+QWK GV ++TP
Sbjct: 61   RQIGELIEAYKASGNIEPLRKTIDMVVGDGTKSDEVRDYDDASVLRLADQWKRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAGEADVNEMLAMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|126165904|ref|YP_209551.2| RNA polymerase beta subunit [Huperzia lucidula]
          Length = 1078

 Score =  399 bits (1024), Expect = e-108,   Method: Composition-based stats.
 Identities = 165/512 (32%), Positives = 242/512 (47%), Gaps = 61/512 (11%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
              G    T+ I          + +   + +G  +  G IL      +G       + +L 
Sbjct: 609  NGGGTINTKLITYQRSNNNTCMHQKPRVNLGEYLKEGQILADGAATEG-GEPASGKNILV 667

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            A    +  +  D  L     ++  ++   +F    I+K E    +     E+L R    E
Sbjct: 668  AYMPWEGYNFEDAVL-----INECLIYENVFTSIHIEKYEVEARITLNGPEILTR----E 718

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               LD      L E   +L G    +G     K T    +   + P     Q        
Sbjct: 719  IPHLDDYFLRHLDENGLVLPGSWVETGDVIVGKLTPRDPEESLKIPEGNLLQAIFG---- 774

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
              ++ + +          + +  +        D+        + V++  KR I+ GDK+A
Sbjct: 775  -IDITATRETCLKVPPGGKGQVIDVRSVYPEDDNQYRN---FIYVYILQKREIKVGDKVA 830

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+S+ILP EDMP+L+DGTP++++L+PLGVPSRMNVGQIFE  LG A   L + 
Sbjct: 831  GRHGNKGIISKILPREDMPYLQDGTPIEMILSPLGVPSRMNVGQIFECLLGLAGGFLKRH 890

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             + +  D +   + S    F E                                      
Sbjct: 891  YRVIPFDERYEREASRKLVFSELNK----------------------------------- 915

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A E+  N  L    LD  G+S+L DG TGE F +P+T+G  YMLKL H V DK++ARS
Sbjct: 916  --AGEQTTNPWLFE--LDNPGKSLLIDGRTGEIFQQPITIGKAYMLKLIHQVDDKIHARS 971

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            +G YSLVTQQPL G+S  GGQR+GEMEVW ++ +GA+Y+LQEMLTIKSD +  R ++  +
Sbjct: 972  SGPYSLVTQQPLKGRSRMGGQRVGEMEVWALEGFGASYILQEMLTIKSDHIQARQKIINN 1031

Query: 1332 IVAGNDTFET-GTPESFNVLVKEMQALGLSID 1362
            IVAG    +   TPESF +L +E++ L L++D
Sbjct: 1032 IVAGEPVDKPETTPESFRLLARELRCLALNLD 1063



 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 228/641 (35%), Positives = 360/641 (56%), Gaps = 23/641 (3%)

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN--NAYIRNTLVTDKNKDRKDAL 374
              I+           L  +    + +  IL         +  IR     +  + +++A+
Sbjct: 168 NNRIWFRIDKKHKVSILLLLLAMGLNEEKILDTVHYPEVMSDIIREAKDEENIEWKENAV 227

Query: 375 LDIYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            ++Y  +          +  +F      F   K++L  +GR  +N +LNL+ P D   + 
Sbjct: 228 SELYEQIFGTTDEEDVESYDIFEELKKEFFEPKFELGRIGRFNINKKLNLNVPKDEIFLL 287

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +D++A I   + LR G GT DD+D+L N+R+RSV + L+N+++L L R+   +  RI+ 
Sbjct: 288 PKDVLAAIDYSIKLRIGVGTFDDVDHLKNKRIRSVADFLQNRFKLALERLGDLVHRRINR 347

Query: 493 VDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +     +P    L+ + P++    EFF S  LSQ  +  N L+++ H RR S+LG GG+ 
Sbjct: 348 LTRRKRVPTIGSLVTSDPLLKTFKEFFGSYPLSQFLDQTNPLTQVIHKRRFSSLGPGGLT 407

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET----PYRKVC 606
           +  A ++ RD+HP+ YGRICP ETSEG N GL+SS+  +A ++ +GF+++     Y +V 
Sbjct: 408 KRIASIKARDIHPSIYGRICPIETSEGMNAGLISSMAIYASIDHWGFLQSTLHKEYDEVL 467

Query: 607 DGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             +   D+  +SA  EE   IA     +   E+    E     +   E +    ++I   
Sbjct: 468 FEEQNQDMADVSA--EEYFRIATEACLAVSPEEDENKEIFTVAQLQQEFLTTSWDRIKLR 525

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
             SP Q  S+    IP  E++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG
Sbjct: 526 IISPLQYFSVGVCPIPSFEHNDANRALMGSNMQRQAVPLFEPERCIVGTGLEGQAASDSG 585

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           + ++A++ G V+ VD   I +            G    +L+ +QRSN NTC++Q+P V +
Sbjct: 586 SVVIAEQGGKVDYVDGKEITLLVN-------GGGTINTKLITYQRSNNNTCMHQKPRVNL 638

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ ++   I+ADG +T+ G+ A G+N+LVA+MPW GYNFED++LI+E ++ E+VFTSIHI
Sbjct: 639 GEYLKEGQILADGAATEGGEPASGKNILVAYMPWEGYNFEDAVLINECLIYENVFTSIHI 698

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           E++EV AR T  GPE +TR+IP++ +  L+++DE G++  G+ V  GD++VGK+TP+   
Sbjct: 699 EKYEVEARITLNGPEILTREIPHLDDYFLRHLDENGLVLPGSWVETGDVIVGKLTPRDPE 758

Query: 905 PMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                PE  LL+AIFG      R+T L+VP G  G V+DVR
Sbjct: 759 ESLKIPEGNLLQAIFGIDITATRETCLKVPPGGKGQVIDVR 799



 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 91/506 (17%), Positives = 173/506 (34%), Gaps = 67/506 (13%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM- 73
               +N +I  +PD  ++Q  ++  F+          N+G+     +   I         
Sbjct: 1   MDLEQNEDIYVLPDFRKIQLEAFHRFI----------NQGIMEELDNFPKIEDTDQEFEF 50

Query: 74  -LEFVSYEFDPPKFDVDDCLWRDL-TYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
            L    Y    P     D L+  + T +  L +  RL           +    +KEQ+++
Sbjct: 51  QLFGEKYYLLEPSVKEGDSLYESIITNSCKLYVPARLT---------QRKKGKVKEQTVF 101

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +G++PLM+  GTFVI GI R++++Q+ RSPGI++  +K          Y   II + G  
Sbjct: 102 IGNIPLMSSQGTFVINGIARVIINQMLRSPGIYYKSEKDP-DSGEITTYTATIISNWGER 160

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           + +E D+ + I  RID++ KV +   L+A+G++ E+IL T +   V S          + 
Sbjct: 161 LQLELDANNRIWFRIDKKHKVSILLLLLAMGLNEEKILDTVHYPEVMSDIIREAKDEENI 220

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
                        +   T E+ +ES           + E+  K        L G     +
Sbjct: 221 EWKENAVSELYEQIFGTTDEEDVESY---------DIFEELKKEFFEPKFEL-GRIGRFN 270

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN---------NAYIRNTL 362
           I       +  +   ++ +  L  I +S    I +   D V++           +++N  
Sbjct: 271 INKKLNLNVPKDEIFLLPKDVLAAIDYSIKLRIGVGTFDDVDHLKNKRIRSVADFLQNRF 330

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTF-------SVAESMFNFLFFDSDKYDLSTVGRVK 415
                +        I R+ R   V T         + ++   F         L     + 
Sbjct: 331 KLALERLGDLVHRRINRLTRRKRVPTIGSLVTSDPLLKTFKEFFGSYPLSQFLDQTNPLT 390

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD------------------ID 457
             +     +      + K       + +     G+    +                  ID
Sbjct: 391 QVIHKRRFSSLGPGGLTKRIASIKARDIHPSIYGRICPIETSEGMNAGLISSMAIYASID 450

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRME 483
           + G  +     E  +  +      M 
Sbjct: 451 HWGFLQSTLHKEYDEVLFEEQNQDMA 476


>gi|257076606|ref|ZP_05570967.1| DNA-directed RNA polymerase subunit B [Ferroplasma acidarmanus fer1]
          Length = 1195

 Score =  399 bits (1024), Expect = e-108,   Method: Composition-based stats.
 Identities = 204/1191 (17%), Positives = 418/1191 (35%), Gaps = 194/1191 (16%)

Query: 225  SEEILSTFYPK----IVYSQRGDFWCFPLSAAD------LMVGAKVSSSLVDIDTGEQVI 274
            SE+ L  +  K    I  ++            D      +    +V  SL D+   + ++
Sbjct: 153  SEQNLDLYIEKNNGPIDETRENKLRYVDEDPTDPGGYFIIGGSERVIVSLEDLAPNKILV 212

Query: 275  ESGKKLTSGL----LKSLKEKGVKFLGITS--DCLCGLYVAEDIVNGETGEIYIEAGDVI 328
            E  +K  S +    + S K      + +    D +  + +   +       I ++A  + 
Sbjct: 213  EYEEKYDSRVEVAKIFSQKSGFRALISMEKGSDGIINVSIP-TVAGTIPLVILMKALGID 271

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             +  + E  +++ R  P++Y +  ++       L  +   + +DAL  + +    G    
Sbjct: 272  KDVDIHEAIYTDPRMDPLIYANIEDSRNL--KILPPNGINNNEDALSYLEKRFAAGQAKE 329

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            F                  ++ +    +   L  D  D ++  +   +  + + L++L  
Sbjct: 330  FRDK--------------KITQMLDRALLPHLGDDVSDRLK--KAIYLGRMARSLLELNL 373

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK- 507
            G   +DD D+  N+R++  G++L   +R     + + +K ++          +     + 
Sbjct: 374  GMRHVDDKDHYANKRIKLSGDLLDELFRNAFQSVMKDLKYQLEKTYNKKRGIRLRPAVRQ 433

Query: 508  --------PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
                      ++        + +SQL +  +++S ++H RR+ +     + R++   E R
Sbjct: 434  DLLTQKVLHSMATGNWIGGRTGVSQLLDRTSNMSTLSHLRRIIS----PLTRSQPHFEAR 489

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            D+HPT +GRICP ET EG N GLV + +    V      +    ++ +     D+  ++ 
Sbjct: 490  DLHPTQWGRICPNETPEGQNCGLVKNASLIINVTQGIDPDIVMEELQNM----DIHEVTK 545

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             E   R     +     +                 L     + +   + + +++     +
Sbjct: 546  EEASGRIYLNGDFIGYHNDPAILTDTIRNLRRSGKLSNEVNVKYDSNTNEVIINCDRGRL 605

Query: 680  PFL-ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQ 737
                   +  + +M   M  +           + +G +E + A+    A ++        
Sbjct: 606  RRPLFVVNEGKTVMNEEMLEKLRMGEYTVNDLISSGAIEWLDAEEEENAYISVFPFEFPD 665

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                   +   +     +    D+           + C              +       
Sbjct: 666  NCPDCGKVLYRDNVTWINPGNSDVTLEC-------DECHAH----------FKGTNNLSM 708

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T    D ++   ++ + +P+  +N    + I+  M+ +    SI + +     R    
Sbjct: 709  DHTHCEIDASMILGVVASLIPYPEHNSSPRITIASAMIKQ----SIGLPQANYRIRTDTR 764

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G       IP V+ +                          +           +  + AI
Sbjct: 765  GHLLHYPQIPLVTTKV-------------------------MDFIKYRRKPAGQNFVVAI 799

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +++D  +   + +   +     F  +  ++       E            D+  
Sbjct: 800  VSYHGYNMQDAIIMNKASIERGLGRSSFFRTYTAEERRYPGGQE------------DKFE 847

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            I   ++     E        +G    +     S  L+ +    ++ +     E+    + 
Sbjct: 848  IPSHDVLGARAEEYYKNLDENGIIFPESKVEGSDVLVGKTSPPRFLE-----EENADKLG 902

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L+     S   +       ++ +     +     R++KV V   R  Q GDK A RHG 
Sbjct: 903  PLRR--RESSVTVRPTESGYVDNVFL--TVSESNSRIIKVKVRSDRIPQPGDKFASRHGQ 958

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++  +   EDMPF +DG   D++ NP  VPSRM         LG     +G K+ ++ 
Sbjct: 959  KGVIGYVAAQEDMPFTEDGIIPDLLFNPHSVPSRMT--------LGHVLEMMGAKVSTM- 1009

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                         SG  + + +FDG  E
Sbjct: 1010 ---------------------------------------------SGENIDSTIFDGEPE 1024

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
             ++   L+     ESG  ++YDG+TG+ F+  + +G IY  KL+HMV+ K +ARS G   
Sbjct: 1025 RSLREQLKKYGFRESGNEVMYDGITGKKFEVDIFMGVIYYQKLHHMVASKFHARSRGPVQ 1084

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----VVG-------- 1324
            ++T+QP  G+S +GG R GEME   + A+GA+ V+++ L  +SD     V G        
Sbjct: 1085 ILTRQPTEGRSRQGGLRFGEMERDTLIAHGASMVIKDRLLDQSDGTILYVCGNPTCGHIA 1144

Query: 1325 ----RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
                R         GN  + +   T  +F ++  E+ ++G+ + LE    K
Sbjct: 1145 IYDFRKGTLRCPACGNTGNIYPIETSYAFKLMRDELSSMGIVMRLELGDMK 1195



 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 139/921 (15%), Positives = 260/921 (28%), Gaps = 189/921 (20%)

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT------ 139
               +   RDL Y  P+ + LR++     E    +    IK     +G++P+M       
Sbjct: 102 ITPQEARLRDLNYMAPIMLRLRIV-----EDGIERDANTIK-----IGEIPVMVRSKICT 151

Query: 140 ----------------------------------KDGTFVIKGIQRIVVSQLHRSPGIHF 165
                                               G F+I G +R++VS    +P    
Sbjct: 152 LSEQNLDLYIEKNNGPIDETRENKLRYVDEDPTDPGGYFIIGGSERVIVSLEDLAPNKIL 211

Query: 166 DHDKGRASL--------SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTS 216
              + +           S K  +   I  ++G           II+V I      +P+  
Sbjct: 212 VEYEEKYDSRVEVAKIFSQKSGFRALISMEKGS--------DGIINVSIPTVAGTIPLVI 263

Query: 217 FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
            + ALG+D + +I    Y         D   +        +     + + + +     +E
Sbjct: 264 LMKALGIDKDVDIHEAIYTDPR----MDPLIYANIEDSRNLKILPPNGINNNEDALSYLE 319

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             K+  +G  K  ++K +  +    D     ++ +D+ +     IY+        + L  
Sbjct: 320 --KRFAAGQAKEFRDKKITQML---DRALLPHLGDDVSDRLKKAIYLGRMARSLLE-LNL 373

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                             +   +            KD    + +            A   
Sbjct: 374 GMRHVDDKDHYANKRIKLSGDLLDELFRNAFQSVMKDLKYQLEKTYNKKRGIRLRPA--- 430

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                           G             D  R      +  + +I+  L   +   + 
Sbjct: 431 VRQDLLTQKVLHSMATGNWIGGRTGVSQLLD--RTSNMSTLSHLRRIISPLTRSQPHFEA 488

Query: 456 ID-NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVV 510
            D +          E  + Q   GL++    I      +D D VM +    D+       
Sbjct: 489 RDLHPTQWGRICPNETPEGQ-NCGLVKNASLIINVTQGIDPDIVMEELQNMDIHEVTKEE 547

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           ++   +     +    +       I + RR   L      +  +      ++        
Sbjct: 548 ASGRIYLNGDFIGYHNDPAILTDTIRNLRRSGKLSNEVNVKYDSNTNEVIINCDRGRLRR 607

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P          +   +    R+  Y         V D   +  + +L A EEEN YI+  
Sbjct: 608 PLFVVNEGKTVMNEEMLEKLRMGEYT--------VNDLISSGAIEWLDAEEEENAYISVF 659

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKI---------------------DFIDASPK 669
                 D       V  R     I      +                        +    
Sbjct: 660 PFEFP-DNCPDCGKVLYRDNVTWINPGNSDVTLECDECHAHFKGTNNLSMDHTHCEIDAS 718

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + ASLIP+ E++ S R+ +   M +Q++ L +A                       
Sbjct: 719 MILGVVASLIPYPEHNSSPRITIASAMIKQSIGLPQANYRI------------------- 759

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    +   +  Y               Q PLV       
Sbjct: 760 ----------------------RTDTRGHLLHYP--------------QIPLV------- 776

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                             G+N +VA + +HGYN +D++++++  +   +  S     +  
Sbjct: 777 ---TTKVMDFIKYRRKPAGQNFVVAIVSYHGYNMQDAIIMNKASIERGLGRSSFFRTYTA 833

Query: 850 MARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             R    G E+      +      +EE  KN+DE GII   ++V   D+LVGK +P    
Sbjct: 834 EERRYPGGQEDKFEIPSHDVLGARAEEYYKNLDENGIIFPESKVEGSDVLVGKTSPPRFL 893

Query: 905 PMTPEEKLLRAIFGEKAVDVR 925
                +KL      E +V VR
Sbjct: 894 EEENADKLGPLRRRESSVTVR 914


>gi|228015921|gb|ACP50761.1| RNA polymerase beta subunit [Pinus ponderosa]
          Length = 1074

 Score =  398 bits (1023), Expect = e-108,   Method: Composition-based stats.
 Identities = 161/497 (32%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    ++ T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKSDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 234/640 (36%), Positives = 359/640 (56%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +L  +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERYLFLLKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF            N L+ I H R+LS LG GG+    A   
Sbjct: 352 STPQNLVTSTLLKNTFQDFFGXXXXXXXXXXTNPLTEIAHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P ++ G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 66/341 (19%), Positives = 139/341 (40%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDFWCFPL--------SA 251
           I  R+ R++K+ +   L  +G++ EEIL    +  + ++  + + W              
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERYLFLLKKERWEREEYLWSREKAIL 228

Query: 252 ADLMVGAKVSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                   +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|68053052|sp|Q5SCX8|RPOB_HUPLU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|50660025|gb|AAT80747.1| RNA polymerase beta subunit [Huperzia lucidula]
          Length = 1080

 Score =  398 bits (1023), Expect = e-108,   Method: Composition-based stats.
 Identities = 165/512 (32%), Positives = 242/512 (47%), Gaps = 61/512 (11%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
              G    T+ I          + +   + +G  +  G IL      +G       + +L 
Sbjct: 611  NGGGTINTKLITYQRSNNNTCMHQKPRVNLGEYLKEGQILADGAATEG-GEPASGKNILV 669

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            A    +  +  D  L     ++  ++   +F    I+K E    +     E+L R    E
Sbjct: 670  AYMPWEGYNFEDAVL-----INECLIYENVFTSIHIEKYEVEARITLNGPEILTR----E 720

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               LD      L E   +L G    +G     K T    +   + P     Q        
Sbjct: 721  IPHLDDYFLRHLDENGLVLPGSWVETGDVIVGKLTPRDPEESLKIPEGNLLQAIFG---- 776

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
              ++ + +          + +  +        D+        + V++  KR I+ GDK+A
Sbjct: 777  -IDITATRETCLKVPPGGKGQVIDVRSVYPEDDNQYRN---FIYVYILQKREIKVGDKVA 832

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGI+S+ILP EDMP+L+DGTP++++L+PLGVPSRMNVGQIFE  LG A   L + 
Sbjct: 833  GRHGNKGIISKILPREDMPYLQDGTPIEMILSPLGVPSRMNVGQIFECLLGLAGGFLKRH 892

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
             + +  D +   + S    F E                                      
Sbjct: 893  YRVIPFDERYEREASRKLVFSELNK----------------------------------- 917

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
              A E+  N  L    LD  G+S+L DG TGE F +P+T+G  YMLKL H V DK++ARS
Sbjct: 918  --AGEQTTNPWLFE--LDNPGKSLLIDGRTGEIFQQPITIGKAYMLKLIHQVDDKIHARS 973

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
            +G YSLVTQQPL G+S  GGQR+GEMEVW ++ +GA+Y+LQEMLTIKSD +  R ++  +
Sbjct: 974  SGPYSLVTQQPLKGRSRMGGQRVGEMEVWALEGFGASYILQEMLTIKSDHIQARQKIINN 1033

Query: 1332 IVAGNDTFET-GTPESFNVLVKEMQALGLSID 1362
            IVAG    +   TPESF +L +E++ L L++D
Sbjct: 1034 IVAGEPVDKPETTPESFRLLARELRCLALNLD 1065



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 228/641 (35%), Positives = 360/641 (56%), Gaps = 23/641 (3%)

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN--NAYIRNTLVTDKNKDRKDAL 374
              I+           L  +    + +  IL         +  IR     +  + +++A+
Sbjct: 170 NNRIWFRIDKKHKVSILLLLLAMGLNEEKILDTVHYPEVMSDIIREAKDEENIEWKENAV 229

Query: 375 LDIYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            ++Y  +          +  +F      F   K++L  +GR  +N +LNL+ P D   + 
Sbjct: 230 SELYEQIFGTTDEEDVESYDIFEELKKEFFEPKFELGRIGRFNINKKLNLNVPKDEIFLL 289

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            +D++A I   + LR G GT DD+D+L N+R+RSV + L+N+++L L R+   +  RI+ 
Sbjct: 290 PKDVLAAIDYSIKLRIGVGTFDDVDHLKNKRIRSVADFLQNRFKLALERLGDLVHRRINR 349

Query: 493 VDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +     +P    L+ + P++    EFF S  LSQ  +  N L+++ H RR S+LG GG+ 
Sbjct: 350 LTRRKRVPTIGSLVTSDPLLKTFKEFFGSYPLSQFLDQTNPLTQVIHKRRFSSLGPGGLT 409

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET----PYRKVC 606
           +  A ++ RD+HP+ YGRICP ETSEG N GL+SS+  +A ++ +GF+++     Y +V 
Sbjct: 410 KRIASIKARDIHPSIYGRICPIETSEGMNAGLISSMAIYASIDHWGFLQSTLHKEYDEVL 469

Query: 607 DGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             +   D+  +SA  EE   IA     +   E+    E     +   E +    ++I   
Sbjct: 470 FEEQNQDMADVSA--EEYFRIATEACLAVSPEEDENKEIFTVAQLQQEFLTTSWDRIKLR 527

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
             SP Q  S+    IP  E++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG
Sbjct: 528 IISPLQYFSVGVCPIPSFEHNDANRALMGSNMQRQAVPLFEPERCIVGTGLEGQAASDSG 587

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           + ++A++ G V+ VD   I +            G    +L+ +QRSN NTC++Q+P V +
Sbjct: 588 SVVIAEQGGKVDYVDGKEITLLVN-------GGGTINTKLITYQRSNNNTCMHQKPRVNL 640

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ ++   I+ADG +T+ G+ A G+N+LVA+MPW GYNFED++LI+E ++ E+VFTSIHI
Sbjct: 641 GEYLKEGQILADGAATEGGEPASGKNILVAYMPWEGYNFEDAVLINECLIYENVFTSIHI 700

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           E++EV AR T  GPE +TR+IP++ +  L+++DE G++  G+ V  GD++VGK+TP+   
Sbjct: 701 EKYEVEARITLNGPEILTREIPHLDDYFLRHLDENGLVLPGSWVETGDVIVGKLTPRDPE 760

Query: 905 PMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                PE  LL+AIFG      R+T L+VP G  G V+DVR
Sbjct: 761 ESLKIPEGNLLQAIFGIDITATRETCLKVPPGGKGQVIDVR 801



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 90/500 (18%), Positives = 171/500 (34%), Gaps = 67/500 (13%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVS 78
            +I  +PD  ++Q  ++  F+          N+G+     +   I          L    
Sbjct: 9   EDIYVLPDFRKIQLEAFHRFI----------NQGIMEELDNFPKIEDTDQEFEFQLFGEK 58

Query: 79  YEFDPPKFDVDDCLWRDL-TYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
           Y    P     D L+  + T +  L +  RL           +    +KEQ++++G++PL
Sbjct: 59  YYLLEPSVKEGDSLYESIITNSCKLYVPARLT---------QRKKGKVKEQTVFIGNIPL 109

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           M+  GTFVI GI R++++Q+ RSPGI++  +K          Y   II + G  + +E D
Sbjct: 110 MSSQGTFVINGIARVIINQMLRSPGIYYKSEKDP-DSGEITTYTATIISNWGERLQLELD 168

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           + + I  RID++ KV +   L+A+G++ E+IL T +   V S          +       
Sbjct: 169 ANNRIWFRIDKKHKVSILLLLLAMGLNEEKILDTVHYPEVMSDIIREAKDEENIEWKENA 228

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
                  +   T E+ +ES           + E+  K        L G     +I     
Sbjct: 229 VSELYEQIFGTTDEEDVESY---------DIFEELKKEFFEPKFEL-GRIGRFNINKKLN 278

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN---------NAYIRNTLVTDKNK 368
             +  +   ++ +  L  I +S    I +   D V++           +++N       +
Sbjct: 279 LNVPKDEIFLLPKDVLAAIDYSIKLRIGVGTFDDVDHLKNKRIRSVADFLQNRFKLALER 338

Query: 369 DRKDALLDIYRVMRPGDVSTF-------SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                   I R+ R   V T         + ++   F         L     +   +   
Sbjct: 339 LGDLVHRRINRLTRRKRVPTIGSLVTSDPLLKTFKEFFGSYPLSQFLDQTNPLTQVIHKR 398

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD------------------IDNLGNRR 463
             +      + K       + +     G+    +                  ID+ G  +
Sbjct: 399 RFSSLGPGGLTKRIASIKARDIHPSIYGRICPIETSEGMNAGLISSMAIYASIDHWGFLQ 458

Query: 464 VRSVGEMLKNQYRLGLLRME 483
                E  +  +      M 
Sbjct: 459 STLHKEYDEVLFEEQNQDMA 478


>gi|119719204|ref|YP_919699.1| DNA-directed RNA polymerase subunit B [Thermofilum pendens Hrk 5]
 gi|119524324|gb|ABL77696.1| DNA-directed RNA polymerase, subunit B' [Thermofilum pendens Hrk 5]
          Length = 1130

 Score =  398 bits (1023), Expect = e-108,   Method: Composition-based stats.
 Identities = 185/1041 (17%), Positives = 344/1041 (33%), Gaps = 225/1041 (21%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              ++AL  I   + PG                   D+  L  +GR               
Sbjct: 271  TPEEALDYIGSRVSPGQPRNVR-----IERAQAVLDENLLPHIGRGPA-----------A 314

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R  +   +  ++  L++L+ G    DD D+L N+R+R  GE++   +R    ++ + +  
Sbjct: 315  RISKAFFVGQMVSRLLELKLGMRGPDDKDHLANKRIRQAGELIAQVFRSAFRQLVKEMTY 374

Query: 489  RISSVDIDSVMPQ---------DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             I      +                     ++        + +SQ+ +  N LS I+H R
Sbjct: 375  SIERHTSKTRDINLVSIVRPDIITERLNHALATGNWVGGRTGVSQILDRTNYLSTISHLR 434

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            R+ +     ++R +   E R++HPT +GR+CP E+ EG N GLV  L   A ++     +
Sbjct: 435  RVVS----PLSRTQPHFEARELHPTQWGRLCPVESPEGQNCGLVKHLALLATLSNGTDEK 490

Query: 600  TPY------------RKVCDGKVTNDVVYLSA----MEEENRYIAQANSSLDEDGSFTEE 643
              Y             K     ++   VYL+       E+ + +A+    L  +G  + E
Sbjct: 491  QVYDLLVGRLGVVPVEKTVGKNISGARVYLNGRLIGYVEDGKGLAETLRKLRREGRISHE 550

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +     + E  +   +           V   A  +   L   ++    +           
Sbjct: 551  VNVAFYSHEYTVGGVK----GRIEEVYVNCDAGRIRRPLIVVENGEPRLKHEHVELLRKG 606

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                +  +  G+                   VE +DA       +               
Sbjct: 607  EWTWSDLIENGI-------------------VEYLDAEEEENAYI--------------- 632

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                                V +   ++  +   P+  LG +A+        +P+  YN 
Sbjct: 633  -----------------ATDVSELTPQHTHLEIVPAAILGIIAMT-------IPFIEYNQ 668

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  +    S+ I  +    R             P V       +    +  
Sbjct: 669  SPRNSYQAAMAKQ----SLGIPHYNFKLRMDPRMHVMYYPQKPLVKTRIFDLLPLDNLPY 724

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                                        ++ A+      +++D  +   + +   +    
Sbjct: 725  -------------------------GTNMVVAVLTGGGYNIQDAVVINKAAIERGMSRSV 759

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             F         R+   E  +      D+ ++  +    +  +  +     + V G    +
Sbjct: 760  FF---------RTYEAEERRYPGGLEDRFEKPSLEKDLLDVKPPQAYEAIDPVDGIAYVE 810

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    ++S     +++   ++           +V  +   + L  R   K    +  
Sbjct: 811  AELYGGQAVVSRTSPPRFYTSTLEP----------RVMTKRKDTSLLLRHGEKGIIDRVF 860

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                PG +++ KV V   RP + GDK A RHG KG+V  ++P EDMPF ++G   D+++N
Sbjct: 861  IMESPGGIKLAKVRVRDLRPTELGDKFASRHGQKGVVGMLVPQEDMPFTEEGITPDLIIN 920

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM VGQ+ E   G A    G++I +   +  +  +I  +               
Sbjct: 921  PHAIPSRMTVGQLLEAITGKAAALAGRRIDATAFEPPSLDEIREILR------------- 967

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                          E    GV                                    TGE
Sbjct: 968  -----SYGFRSDGKEVLYDGV------------------------------------TGE 986

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              +  + +G +Y  KL+H+V+DK++AR+ G   ++T+QP  G++  GG R GEME  C+ 
Sbjct: 987  KLEAEIFIGVVYYEKLHHLVADKMHARARGRVQILTRQPTEGRAREGGLRFGEMEKDCLV 1046

Query: 1304 AYGAAYVLQEMLTIKSDDVV--------------GRTRVYESIVAGND--TFETGTPESF 1347
             +GA+ +L+E L   SD                  R       V G+           +F
Sbjct: 1047 GHGASMLLRERLLESSDKTTIWVCENCGYMGWFDARKNTPVCPVCGDKGRLSPVEVSYAF 1106

Query: 1348 NVLVKEMQALGLSIDLENSRT 1368
             +L++E+  LGLS+ L     
Sbjct: 1107 KLLLQELTGLGLSVRLILKDK 1127



 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 161/982 (16%), Positives = 283/982 (28%), Gaps = 198/982 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S++ FL            GLQ     V  I   S    ++F   E   P F  
Sbjct: 28  LVRQHLDSFNAFL----------ERGLQEIVDEVGGIKVESQGVEIKFGKIEVGQPTFRE 77

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                          R++TYA PL +T+ L V   +  T          +S+Y+G LP+M
Sbjct: 78  ADGSDLALTPMIARLRNITYAAPLYLTMTLYVDGEERRT----------ESVYIGSLPIM 127

Query: 139 TKD-------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
            K                          G F++ G +R++V Q   S             
Sbjct: 128 VKSKKCVLYGLKSEDEIVKYGEDPYDPGGYFIVNGSERVIVMQEDLSVN---RVLVDYGG 184

Query: 174 LSGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEI 228
            SG + +  ++       +   + +E     +I+        K+PV   + ALG+ +++ 
Sbjct: 185 ASGSVTHTAKVFSVAAGQR-SPLTVERTKDGMIYASFPACPSKIPVVVLMRALGLKTDQE 243

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI-DTGEQVIESGKKLTSGLLK- 286
           ++       Y+   D          LM  +K++++  +  D     +  G+     + + 
Sbjct: 244 IA-------YAIGNDPIIQQEFLPVLMEQSKIAATPEEALDYIGSRVSPGQPRNVRIERA 296

Query: 287 --SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIR 342
              L E  +  +G               +     E+ +      D+  L  + I  +   
Sbjct: 297 QAVLDENLLPHIGRGPAARISKAFFVGQMVSRLLELKLGMRGPDDKDHLANKRIRQAGEL 356

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              +           +  ++    +K R   L+ I R     D+ T  +  ++    +  
Sbjct: 357 IAQVFRSAFRQLVKEMTYSIERHTSKTRDINLVSIVRP----DIITERLNHALATGNWVG 412

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
                   + R      ++       R +             +L   +            
Sbjct: 413 GRTGVSQILDRTNYLSTISHLR----RVVSPLSRTQPHFEARELHPTQWGRLCPVESPEG 468

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +   + + L     L     E+ +      V    V+P +    K +  A        +L
Sbjct: 469 QNCGLVKHLALLATLSNGTDEKQV--YDLLVGRLGVVPVEKTVGKNISGARVYLNG--RL 524

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM----RDVHPTHYGRICPAETSEGH 578
               E    L+      R        V  A    E                C A      
Sbjct: 525 IGYVEDGKGLAETLRKLRREGRISHEVNVAFYSHEYTVGGVKGRIEEVYVNCDAGRIRRP 584

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            I + +             +        D      V YL A EEEN YIA   S L    
Sbjct: 585 LIVVENGEPRLKH-EHVELLRKGEWTWSDLIENGIVEYLDAEEEENAYIATDVSELTPQH 643

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++  P  ++ I A  IPF+E + S R      M +
Sbjct: 644 -----------------------THLEIVPAAILGIIAMTIPFIEYNQSPRNSYQAAMAK 680

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           Q++ +                                                       
Sbjct: 681 QSLGI-----------------------------------------PHYNFKLRMDPRMH 699

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           V  Y               Q+PLVK                  L +L  G NM+VA +  
Sbjct: 700 VMYYP--------------QKPLVKTRIF----------DLLPLDNLPYGTNMVVAVLTG 735

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-------PNVSEE 871
            GYN +D+++I++  +   +  S+    +E   R    G E+                 +
Sbjct: 736 GGYNIQDAVVINKAAIERGMSRSVFFRTYEAEERRYPGGLEDRFEKPSLEKDLLDVKPPQ 795

Query: 872 GLKNIDE-CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
             + ID   GI  V AE+  G  +V + +P      T E +++           +DTSL 
Sbjct: 796 AYEAIDPVDGIAYVEAELYGGQAVVSRTSPPRFYTSTLEPRVM--------TKRKDTSLL 847

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           +  G  G +  V I    G  K
Sbjct: 848 LRHGEKGIIDRVFIMESPGGIK 869


>gi|170591608|ref|XP_001900562.1| DNA-directed RNA polymerase II second largest subunit [Brugia malayi]
 gi|158592174|gb|EDP30776.1| DNA-directed RNA polymerase II second largest subunit, putative
            [Brugia malayi]
          Length = 1185

 Score =  398 bits (1023), Expect = e-108,   Method: Composition-based stats.
 Identities = 172/1084 (15%), Positives = 330/1084 (30%), Gaps = 202/1084 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G   I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 269  GPKIIAILPYIKQEIPVMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 328

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 329  EQNVALNFIGARGAKPGV---TKEQRIKYAREILQKEMLPHVGISDFCETKK---AYFLG 382

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             ++  L+    G+  +DD D++GN+R+   G +L   +R     + + ++         +
Sbjct: 383  YMVHRLLLAALGRRELDDRDHMGNKRLDLAGPLLAFLFRALFRNLLKEVRLTAQKYINKN 442

Query: 498  --VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
               M    +    +   +     +               +SQ+   +   + ++H RR +
Sbjct: 443  GDFMLDLCVKTPLITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRCN 502

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++     E   
Sbjct: 503  S----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPIL 558

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    +V   +  +    ++  A   +  D       L   R   + I+    
Sbjct: 559  EFLEEWSMENLEEVAPTAIADATKIFVNGAWVGIHRDPEQLMTTLKKLRREMDIIVSEVS 618

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             + D  D   +          P L  ++    L   ++ +             G  +E +
Sbjct: 619  MVRDIRDREIRIYTDAGRVCRPLLIVENQKLALKRKHIDQLKDNSYTWSELVAGGVVELI 678

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             A      ++A     +                                           
Sbjct: 679  DAMEEETVMLAMMPEDL------------------------------------------- 695

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                K G            P+  LG       +  + +P+  +N       S R   +  
Sbjct: 696  ----KAGGYCDTYTHCEIHPAMILG-------VCASIIPFPDHNQ------SPRNTYQSA 738

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
                 +  +                           ++    +  V        +    +
Sbjct: 739  MGKQAMGVYTTNF-----------------------HVRMDTLAHVLYYPQKPLVTTRSM 775

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                 + +      + AI      +  D+ +   SG+   +    +F R   D+     +
Sbjct: 776  EYLRFNELPAGINAIVAILSYTGYNQEDSIIMNQSGIDRGLF-RSVFYRSYRDQEANLDN 834

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
               E IE   RDK         +       I  G           K              
Sbjct: 835  ANEELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGK-------------- 880

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   +     + ++++   +Y    +    R        Q    +     + VK+ V
Sbjct: 881  ------TISLPDTEDDLDAAIKRYTKKDASTFLRSSETGIVDQVMLTLNTDGNKFVKIRV 934

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG +  +   EDMPF  +G   DI++NP  VPSRM +G + E
Sbjct: 935  RSVRLPQIGDKFASRHGQKGTMGMMYRQEDMPFTNEGITPDIIINPHAVPSRMTIGHLIE 994

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 995  CLQGKLSANKGEIGD--------------------------------------------- 1009

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L+       G  I+Y+G TG      V +G  Y  +
Sbjct: 1010 --------ATPFNDTVNVQKISNLLQEYGYHLRGNEIMYNGHTGRKLTIQVFLGPTYYQR 1061

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   
Sbjct: 1062 LKHMVDDKIHSRARGPVQMMNRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEV 1121

Query: 1319 SD--DV-----VG-------RTRVYESIV--AGNDTFETGTPESFNVLVKEMQALGLSID 1362
            SD   V      G       RT  +E               P +  +L +E+ ++ ++  
Sbjct: 1122 SDPYHVYICNNCGLIVVANLRTNSFECKACRNKTQVSAFRIPYACKLLFQELMSMSIAPR 1181

Query: 1363 LENS 1366
            L  S
Sbjct: 1182 LMVS 1185



 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 153/1012 (15%), Positives = 302/1012 (29%), Gaps = 212/1012 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-----PITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+ MN+    ++ P   LQ+  +        PI        L+F     
Sbjct: 41  LVRQQLDSFDEFIQMNVQRIVEDSPPVELQSEVQHFSGDVENPI-----KFALKFDQIYL 95

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             P              ++   R+LTY+ PL I +   +    E       K+ K + ++
Sbjct: 96  SKPTHWEKDGAPTPMMPNEARLRNLTYSSPLYIDITKTMTRSGEEP-----KETKYEKVF 150

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G FVI G ++++++Q   +   ++  
Sbjct: 151 VGKIPIMLRSSYCMLANMSDRDLSELNECPLDPGGYFVINGSEKVLIAQEKMATNTVYVF 210

Query: 167 HDKGRASLSGKLLYACRIIP-----------DQGLWMDIEFDSKDIIHVRIDRR-----R 210
             K      GK  Y                      +++       + V +  R     +
Sbjct: 211 SMKD-----GKYTYKTECRSCLENSRQVLKQYFLSILEV-TRPTSTLWVNMLPRGGGGSK 264

Query: 211 K-----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
           K                 +PV     ALG  S+ +IL          +  +     L  A
Sbjct: 265 KSAMGPKIIAILPYIKQEIPVMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEA 324

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYV 308
            ++    V+ + +     +  +   +++         + L   G+     T       Y+
Sbjct: 325 FVIQEQNVALNFIGARGAKPGVTKEQRIKYAREILQKEMLPHVGISDFCETKKAYFLGYM 384

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
              ++    G   ++  D +  K L+            L+ + +          +     
Sbjct: 385 VHRLLLAALGRRELDDRDHMGNKRLDLAGPLLAFLFRALFRNLLKEVRLTAQKYINKNGD 444

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
              D  +          + T  +A S+    + D  K   S  G  ++  RL        
Sbjct: 445 FMLDLCV-------KTPLITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSH 497

Query: 429 --RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             R          +     L N +  +         +   + + L     + +  +   I
Sbjct: 498 LRRCNSPIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPI 557

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            E +    ++++   + +    +  A   F   + +    +    ++ +   RR   +  
Sbjct: 558 LEFLEEWSMENL---EEVAPTAIADATKIFVNGAWVGIHRDPEQLMTTLKKLRREMDIIV 614

Query: 547 GGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             V+  R   +      T  GR+C P    E   + L        + N+Y + E     V
Sbjct: 615 SEVSMVRDIRDREIRIYTDAGRVCRPLLIVENQKLALKRKHIDQLKDNSYTWSELVAGGV 674

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                   V  + AMEEE   +A     L   G                    +     +
Sbjct: 675 --------VELIDAMEEETVMLAMMPEDLKAGG------------------YCDTYTHCE 708

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ + AS+IPF +++ S R      M +QA+ +                      
Sbjct: 709 IHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV--------------- 753

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + V  Y               Q+PLV   
Sbjct: 754 --------------------------RMDTLAHVLYYP--------------QKPLV--- 770

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G N +VA + + GYN EDS+++++  +   +F S+   
Sbjct: 771 -------TTRSMEYLRFNELPAGINAIVAILSYTGYNQEDSIIMNQSGIDRGLFRSVFYR 823

Query: 846 EFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +     +     EE            +       +DE GII  G  V+  D+++GK   
Sbjct: 824 SYRDQEANLDNANEELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTIS 883

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++    +  +       K    +D S  + S  +G V  V +      +K
Sbjct: 884 LPDTEDDLDAAI-------KRYTKKDASTFLRSSETGIVDQVMLTLNTDGNK 928


>gi|108796736|ref|YP_636566.1| RNA polymerase beta subunit [Zygnema circumcarinatum]
 gi|88909648|sp|Q32RG0|RPOB_ZYGCR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|61393720|gb|AAX45862.1| beta subunit of RNA polymerase [Zygnema circumcarinatum]
          Length = 1063

 Score =  398 bits (1023), Expect = e-108,   Method: Composition-based stats.
 Identities = 157/486 (32%), Positives = 235/486 (48%), Gaps = 54/486 (11%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             + +  I+  G  V  G  L+   +   +  +   + +L A    +  +  D  L     
Sbjct: 610  CLHQRPIVECGETVQKGQ-LIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERL 668

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   V       R+  +  E + ++E    ++   +    + + +  + S       G  
Sbjct: 669  IYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVLRHLDETGVVS------LGAW 722

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G     K T   S+ +   P S+  Q  +  +        LKV       +++ R+ 
Sbjct: 723  VETGDVLVGKLTAKQSEGLLHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWI 782

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +       D+   G  +V+ V++  +R IQ GDK+AGRHGNKG+VSRILP +DMP+L+D
Sbjct: 783  TR-------DNHLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQD 835

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD+VL+PLGVPSRMNVGQ+FE  LG A   L +  + +  D +   + S    F  +
Sbjct: 836  GTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDERYGRESSRKLVF-SE 894

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            +      T     ++                                       D  G+S
Sbjct: 895  LYKASQTTNYPWIFE--------------------------------------PDSPGKS 916

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L+DG TGE F++PVTVG  YM KL H V DK++ARSTG Y+LVTQQP+ G+S +GGQR+
Sbjct: 917  RLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRV 976

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKE 1353
            GEMEVW  Q +GAA VLQE+LT KSD    R     +IV GN   +  GT +   VL++E
Sbjct: 977  GEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLVPKPIGTSDCLGVLIRE 1036

Query: 1354 MQALGL 1359
            +Q LG+
Sbjct: 1037 LQCLGI 1042



 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 219/591 (37%), Positives = 339/591 (57%), Gaps = 10/591 (1%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             +DA +D+ + ++    +T                 Y+L  +GR+ +N RLNL   +  
Sbjct: 208 CVEDAKIDLCKRLKLKQKTTQIELGVTDPIYSLFLKPYELGRMGRLNLNKRLNLRVSEFE 267

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
             +R +D+I     LV + NG G++DDID+L ++RV+ V ++   Q  + L ++  ++  
Sbjct: 268 ILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLNMALKKLNVAVHT 327

Query: 489 RISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            ++ ++     +  + ++++  + +    F  S QLSQ  +  N LS I H R+LS LG 
Sbjct: 328 NLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGP 387

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+    A   +RD+HP+ YGRICP +T+EG N G+V+S T  A +   G I+T   KVC
Sbjct: 388 GGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVC 447

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
              +   V+ +   E+E   IA  +  +  + S   + +  +   E + +  ++I F + 
Sbjct: 448 TNSMQGHVIDMLPGEDEYSTIATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNT 507

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P    S+   LIPFLE+DD+ R LMG NMQRQAVPLLK E P VGTG+ES VA  SG  
Sbjct: 508 LPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLERPIVGTGIESQVALDSGTV 567

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I A +   +  VDA +I     +         +    L+ ++RSN  TC++QRP+V+ G+
Sbjct: 568 ITAVQECKIHNVDATQIAYVPKDSF------ELLYINLLNYERSNNATCLHQRPIVECGE 621

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V++  +IADG +T  G+LALG+N+LVA+MPW GYNFED++LI+ER++ EDV+TS+HIE 
Sbjct: 622 TVQKGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIER 681

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE--S 904
           +E  AR+T    E IT+ IP+++   L+++DE G++ +GA V  GD+LVGK+T K     
Sbjct: 682 YEAEARETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSEGL 741

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
             TPE KLL+ I G +A   +DT L+VP+   G V+DVR   R       R
Sbjct: 742 LHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITRDNHLLGHR 792



 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/190 (27%), Positives = 90/190 (47%), Gaps = 28/190 (14%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS--YEFDP 83
           +PD  ++Q  S+ HFL             L+   +    I   +     + +   Y  + 
Sbjct: 13  LPDFKQIQIDSFRHFLTDL----------LRLELQRFGTIKHANQQLEFKLLGELYRLEI 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           PKF+  + +++  TY+  L     L+          K    I++Q++++G +PLM+  GT
Sbjct: 63  PKFNEREAVYQSATYSSNLYAPAYLV---------DKKRGIIQKQTVFLGSIPLMSARGT 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FVI+G+ R +VSQL RSPGI++        LS + +Y   II + G    +E D +  + 
Sbjct: 114 FVIRGVSRCIVSQLLRSPGIYYT-------LSVQGVYTATIICNSGKSFKLELDRQGCLW 166

Query: 204 VRIDRRRKVP 213
           VR+ R  K P
Sbjct: 167 VRVGRNSKAP 176


>gi|73975069|ref|XP_860865.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            11 [Canis familiaris]
          Length = 1180

 Score =  398 bits (1022), Expect = e-108,   Method: Composition-based stats.
 Identities = 168/1083 (15%), Positives = 326/1083 (30%), Gaps = 191/1083 (17%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
              + +  +    ++   +  +    ++      + +D       +       +I+     
Sbjct: 543  EFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVSM 602

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
            I  I     ++ + A  +   L   +  ++L+      Q           +         
Sbjct: 603  IRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYRPILELYLWQDL 662

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             +SG           E +D +      +    D        Y                  
Sbjct: 663  VASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY------------------ 695

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                             PS  LG       +  + +P+  +N          M  + +  
Sbjct: 696  -------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG- 740

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             ++I  F                           ++    +  V        +    +  
Sbjct: 741  -VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSMEY 772

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S V        +F R   ++  +    +
Sbjct: 773  LRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGFDQ 831

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             E  E   R+          +       I  G           K+  L            
Sbjct: 832  EEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL------------ 879

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                     + +  +E    +Y         R        Q    +     +  K+ V  
Sbjct: 880  --------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRS 931

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E  
Sbjct: 932  VRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECL 991

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G+                                                  
Sbjct: 992  QGKVSANKGEIGD----------------------------------------------- 1004

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +L 
Sbjct: 1005 ------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLK 1058

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   SD
Sbjct: 1059 HMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1118

Query: 1321 ----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSID 1362
                 V            RT  YE    G            P +  +L +E+ ++ ++  
Sbjct: 1119 PYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIAPR 1176

Query: 1363 LEN 1365
            + +
Sbjct: 1177 MMS 1179



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 141/1006 (14%), Positives = 289/1006 (28%), Gaps = 203/1006 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +          
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVSMIRDI 606

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVT 611
                 ++        P    E   + L        +    N Y  I   Y    D   +
Sbjct: 607 REREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYRPILELY-LWQDLVAS 665

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V Y+  +EEE   +A     L E                  +         +  P  +
Sbjct: 666 GVVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMI 709

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                            
Sbjct: 710 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV--------------------- 748

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                  + + V  Y               Q+PLV         
Sbjct: 749 --------------------RMDTLAHVLYYP--------------QKPLV--------- 765

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA   + GYN EDS++++   V    F S+    ++   
Sbjct: 766 -TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQE 824

Query: 852 RDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                  EE+           +       +D+ G+I  G  V+  D+++GK     E+  
Sbjct: 825 SKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENED 884

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             E          +    RD S  + +  +G V  V +       K
Sbjct: 885 ELEGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 923


>gi|312079478|ref|XP_003142191.1| DNA-directed RNA polymerase II second largest subunit [Loa loa]
 gi|307762647|gb|EFO21881.1| DNA-directed RNA polymerase II second largest subunit [Loa loa]
          Length = 1171

 Score =  398 bits (1022), Expect = e-108,   Method: Composition-based stats.
 Identities = 172/1084 (15%), Positives = 330/1084 (30%), Gaps = 202/1084 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G   I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 255  GPKIIAILPYIKQEIPVMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 314

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 315  EQNVALNFIGARGAKPGV---TKEQRIKYAKEILQKEMLPHVGISDFCETKK---AYFLG 368

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             ++  L+    G+  +DD D++GN+R+   G +L   +R     + + ++         +
Sbjct: 369  YMVHRLLLAALGRRELDDRDHMGNKRLDLAGPLLAFLFRALFRNLLKEVRLTAQKYINKN 428

Query: 498  --VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
               M    +    +   +     +               +SQ+   +   + ++H RR +
Sbjct: 429  GDFMLDLCVKTPLITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRCN 488

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++     E   
Sbjct: 489  S----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPIL 544

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    +V   +  +    ++  A   +  D       L   R   + I+    
Sbjct: 545  EFLEEWSMENLEEVAPTAIADATKIFVNGAWVGIHRDPEQLMTTLKKLRREMDIIVSEVS 604

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             + D  D   +          P L  ++    L   ++ +             G  +E +
Sbjct: 605  MVRDIRDREIRIYTDAGRVCRPLLIVENQKLALKRKHIDQLKDNSYTWSELVAGGVVELI 664

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             A      ++A     +                                           
Sbjct: 665  DAMEEETVMLAMMPEDL------------------------------------------- 681

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                K G            P+  LG       +  + +P+  +N       S R   +  
Sbjct: 682  ----KAGGYCDTYTHCEIHPAMILG-------VCASIIPFPDHNQ------SPRNTYQSA 724

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
                 +  +                           ++    +  V        +    +
Sbjct: 725  MGKQAMGVYTTNF-----------------------HVRMDTLAHVLYYPQKPLVTTRSM 761

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                 + +      + AI      +  D+ +   SG+   +    +F R   D+     +
Sbjct: 762  EYLRFNELPAGINAIVAILSYTGYNQEDSIIMNQSGIDRGLF-RSVFYRSYRDQEANLDN 820

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
               E IE   RDK         +       I  G           K              
Sbjct: 821  ANEELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGK-------------- 866

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   +     + ++++   +Y    +    R        Q    +     + VK+ V
Sbjct: 867  ------TISLPDTEDDLDATIKRYTKKDASTFLRSSETGIVDQVMLTLNTDGNKFVKIRV 920

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG +  +   EDMPF  +G   DI++NP  VPSRM +G + E
Sbjct: 921  RSVRLPQIGDKFASRHGQKGTMGMMYRQEDMPFTNEGITPDIIINPHAVPSRMTIGHLIE 980

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 981  CLQGKLSANKGEIGD--------------------------------------------- 995

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L+       G  I+Y+G TG      V +G  Y  +
Sbjct: 996  --------ATPFNDTVNVQKISNLLQEYGYHLRGNEIMYNGHTGRKLTIQVFLGPTYYQR 1047

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   
Sbjct: 1048 LKHMVDDKIHSRARGPVQMMNRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEV 1107

Query: 1319 SD--DV-----VG-------RTRVYESIV--AGNDTFETGTPESFNVLVKEMQALGLSID 1362
            SD   V      G       RT  +E               P +  +L +E+ ++ ++  
Sbjct: 1108 SDPYHVYICNNCGLIVVANLRTNSFECKACRNKTQVSAFRIPYACKLLFQELMSMSIAPR 1167

Query: 1363 LENS 1366
            L  S
Sbjct: 1168 LMVS 1171



 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 155/1003 (15%), Positives = 304/1003 (30%), Gaps = 208/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-----PITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F+ MN+    ++ P   LQ+  +        PI        L+F     
Sbjct: 41  LVRQQLDSFDEFIQMNVQRIVEDSPPVELQSEVQHFSGDVENPI-----KFALKFDQIYL 95

Query: 82  DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             P              ++   R+LTY+ PL I +   +  + E       K+ K + ++
Sbjct: 96  SKPTHWEKDGAPTPMMPNEARLRNLTYSSPLYIDITKTMTRIGEEP-----KETKYEKVF 150

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G FVI G ++++++Q   +   ++  
Sbjct: 151 VGKIPIMLRSSYCMLANMSDRDLSELNECPLDPGGYFVINGSEKVLIAQEKMATNTVYVF 210

Query: 167 HDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------- 211
             K      GK  Y   CR        ++        + V +  R     +K        
Sbjct: 211 SMKD-----GKYTYKTECR------SCLENSSRPTSTLWVNMLPRGGGGSKKSAMGPKII 259

Query: 212 ---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                    +PV     ALG  S+ +IL          +  +     L  A ++    V+
Sbjct: 260 AILPYIKQEIPVMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVA 319

Query: 262 SSLVDIDTGEQVIESGKKLTSG----LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            + +     +  +   +++         + L   G+     T       Y+   ++    
Sbjct: 320 LNFIGARGAKPGVTKEQRIKYAKEILQKEMLPHVGISDFCETKKAYFLGYMVHRLLLAAL 379

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G   ++  D +  K L+            L+ + +          +        D  +  
Sbjct: 380 GRRELDDRDHMGNKRLDLAGPLLAFLFRALFRNLLKEVRLTAQKYINKNGDFMLDLCV-- 437

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKED 435
                   + T  +A S+    + D  K   S  G  ++  RL          R      
Sbjct: 438 -----KTPLITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRCNSPIG 492

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +     L N +  +         +   + + L     + +  +   I E +    +
Sbjct: 493 REGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEEWSM 552

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           +++   + +    +  A   F   + +    +    ++ +   RR   +    V+  R  
Sbjct: 553 ENL---EEVAPTAIADATKIFVNGAWVGIHRDPEQLMTTLKKLRREMDIIVSEVSMVRDI 609

Query: 556 VEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            +      T  GR+C P    E   + L        + N+Y + E     V        V
Sbjct: 610 RDREIRIYTDAGRVCRPLLIVENQKLALKRKHIDQLKDNSYTWSELVAGGV--------V 661

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             + AMEEE   +A     L   G                    +     +  P  ++ +
Sbjct: 662 ELIDAMEEETVMLAMMPEDLKAGG------------------YCDTYTHCEIHPAMILGV 703

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                               
Sbjct: 704 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV------------------------ 739

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                               + + V  Y               Q+PLV            
Sbjct: 740 -----------------RMDTLAHVLYYP--------------QKPLV----------TT 758

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  G N +VA + + GYN EDS+++++  +   +F S+    +     + 
Sbjct: 759 RSMEYLRFNELPAGINAIVAILSYTGYNQEDSIIMNQSGIDRGLFRSVFYRSYRDQEANL 818

Query: 855 KLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               EE            +       +DE GII  G  V+  D+++GK     ++    +
Sbjct: 819 DNANEELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTISLPDTEDDLD 878

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +       K    +D S  + S  +G V  V +      +K
Sbjct: 879 ATI-------KRYTKKDASTFLRSSETGIVDQVMLTLNTDGNK 914


>gi|255955085|ref|XP_002568295.1| Pc21g12680 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211590006|emb|CAP96165.1| Pc21g12680 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 1255

 Score =  398 bits (1022), Expect = e-108,   Method: Composition-based stats.
 Identities = 177/993 (17%), Positives = 329/993 (33%), Gaps = 169/993 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L + +R    
Sbjct: 382  HISQNEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFT 441

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ + ++   +        +     I A  +   +     +               +SQ+
Sbjct: 442  RVTKDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASAKAGVSQV 501

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 502  LSRYTFASSLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 557

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +  D S    
Sbjct: 558  LALMCYITVGTPAEPIVDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGIHRDPSHLVT 617

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAV 701
             +        I      I D  +   K          P F+ ++D      G  +  +  
Sbjct: 618  TMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVIDNDPKSENSGGLVLNKEH 677

Query: 702  PLLKAEAPFVGTGM---ESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPS 755
                     + T M   E          +V  R+G VE VDA      +I     DL+ S
Sbjct: 678  IRKLEADKDLPTDMAPEERREQYFGWDGLV--RSGAVEYVDAEEEETIMIVMTPEDLEIS 735

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                  Y L   + S+ N  V  R ++               PS  LG       +  + 
Sbjct: 736  RQLQAGYALPDDETSDPNKRV--RSILS--QRAHTWTHCEIHPSMILG-------VCASI 784

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N          M  + +                     E   +I    ++ L  
Sbjct: 785  IPFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFSQRMETMANILYYPQKPLA- 833

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                                  +       +   +  + AI      +  D+ +   S +
Sbjct: 834  ------------------TTRSMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSI 875

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +     +  +   +      V  + +E   +    + + + +  Y +L E   +  G
Sbjct: 876  DRGLFRSLFYRTYADTE----KMVGLQVVERFEKPMRLDTLGMRKGTYDKLDEDGIVAPG 931

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  L++D                +E  QR     K+   T     E+ 
Sbjct: 932  VRVSGEDIIIGKTAPLAAD---------------AEELGQRTKAHTKIDVSTPLRSTENG 976

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 977  IVDQVLISTGNDDL-----KFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFT 1031

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   D+++NP  +PSRM +  + E  L       G +                     
Sbjct: 1032 REGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD------------------- 1072

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     ++++ +LR       G
Sbjct: 1073 ----------------------------------ATP-FTDVTVDSVSRLLREHGYQSRG 1097

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ++++G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG 
Sbjct: 1098 FEVMFNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGL 1157

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG---------- 1335
            R GEME  C+ A+GA+  L+E L   SD       D  G       +  G          
Sbjct: 1158 RFGEMERDCMIAHGASSFLKERLFDVSDPFRVHICDDCGLMTPVAKLKKGLFECRLCNNK 1217

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +   +   P +  +L +E+ ++ ++  +   R+
Sbjct: 1218 HRISQVHIPYAAKLLFQELASMNIAARMFTDRS 1250



 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 150/1044 (14%), Positives = 293/1044 (28%), Gaps = 210/1044 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFK--------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+   +  +    +G Q             + PI        L+F +  
Sbjct: 38  LVSQQLDSFDEFISSTMQ-ELVEEQG-QVVLDQTLPPSEDEIEPIV--VRRYELKFGTVM 93

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD------ 124
              P               +   R+LTYA PL + +   + +  E  G  +  D      
Sbjct: 94  LSRPSVTEGDGATTIMLPQEARLRNLTYASPLYLGVTKKIMEGREKIGKPTDDDDNEGES 153

Query: 125 --------------------IKEQSIYMGDLPLMTKD----------------------- 141
                               +KE+++++G +P+M K                        
Sbjct: 154 DPKTQGTYLEWETKQLPQEQMKEETVFIGKMPIMLKSKYCILKDLNESSLYAWNECPYDS 213

Query: 142 -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF-- 196
            G FVI G ++++++Q  RS G        + +      Y   I    ++G  M      
Sbjct: 214 GGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYIAEIRSAVEKGSRMLSSLTL 270

Query: 197 -------DSKDII---------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYS 239
                   +K            +V+ D    +P+     ALG+   E+IL+        +
Sbjct: 271 KLFAKGDSAKGGFGPTIRSTLPYVKAD----IPIVVVFRALGVVSDEDILNHICYDRNDT 326

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
              +     +    ++   +V+   +      Q   +  +        ++++ +  +   
Sbjct: 327 PMLEMLKPCIEEGFVIQDREVALDFIAKRGSSQSNLNHDRRVRYARDIMQKELLPHISQN 386

Query: 300 ------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
                      G  V   ++    G   ++  D   +K L+            L+     
Sbjct: 387 EGSETRKAFFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTK 445

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           +        V    +  ++  L+I          T  +  ++    + +  K   +  G 
Sbjct: 446 D----LQRYVQRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASAKAGV 498

Query: 414 VKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM 470
            ++  R    +      R          I     L N   G +   +    +    V  +
Sbjct: 499 SQVLSRYTFASSLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 558

Query: 471 LKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
               Y       E       + +   ++   PQ   NA  V      F     +    + 
Sbjct: 559 ALMCYITVGTPAEPIVDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDP 612

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA---------ETSEGHN 579
            + ++ + + RR + +                +         P          E S G  
Sbjct: 613 SHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVIDNDPKSENSGGLV 672

Query: 580 IGLVSSLTSFARVNAYGFI-----ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           +         A  +    +        Y        +  V Y+ A EEE   I      L
Sbjct: 673 LNKEHIRKLEADKDLPTDMAPEERREQYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDL 732

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +                                       A   +P  E  D N+ +   
Sbjct: 733 EISRQLQ---------------------------------AGYALPDDETSDPNKRVRSI 759

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             QR                      +   + I+   A I+   D  +    + +  +  
Sbjct: 760 LSQR---------------AHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGK 804

Query: 755 STSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
              GV       + +         Q+PL                      +L  G+N +V
Sbjct: 805 QAMGVFLTNFSQRMETMANILYYPQKPL----------ATTRSMEFLRFRELPAGQNAIV 854

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A   + GYN EDS+++++  +   +F S+    +    +   L   E        D   +
Sbjct: 855 AIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFEKPMRLDTLGM 914

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            +     +DE GI+  G  V+  DI++GK  P         ++        KA    D S
Sbjct: 915 RKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAADAEELGQRT-------KAHTKIDVS 967

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  +G V  V I   +   K
Sbjct: 968 TPLRSTENGIVDQVLISTGNDDLK 991


>gi|215254207|gb|ACJ64108.1| RNA polymerase beta subunit [Vibrio neptunius]
          Length = 396

 Score =  398 bits (1022), Expect = e-108,   Method: Composition-based stats.
 Identities = 255/396 (64%), Positives = 313/396 (79%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E G+F +EL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLSEHGTFADELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VG
Sbjct: 121 SALHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
           ILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTS
Sbjct: 361 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTS 396


>gi|215254173|gb|ACJ64091.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 398

 Score =  397 bits (1021), Expect = e-108,   Method: Composition-based stats.
 Identities = 257/398 (64%), Positives = 313/398 (78%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R
Sbjct: 61  FARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITAR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ 
Sbjct: 121 QKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADK 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ 
Sbjct: 181 PLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYT 240

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L
Sbjct: 241 RSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSIL 300

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV
Sbjct: 301 VSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEV 360

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D
Sbjct: 361 KGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKD 398


>gi|228016505|gb|ACP51336.1| RNA polymerase beta subunit [Pinus torreyana subsp. torreyana]
          Length = 1074

 Score =  397 bits (1021), Expect = e-108,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 238/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            IC G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  ICQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    ++ T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKSDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 231/640 (36%), Positives = 355/640 (55%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERYLFLFKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
             PQ+L+ +  + +   +FF         +  N      H R+LS LG GG+    A   
Sbjct: 352 STPQNLVTSTLLKNTFQDFFGXXXXXXXXDQTNXXXXXXHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQICQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  178 bits (451), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 67/341 (19%), Positives = 139/341 (40%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS---------TFYPKIVYSQRGDFWCFPLSAA 252
           I  R+ R++K+ +   L  +G++ EEIL            + K  + +    W    +  
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERYLFLFKKERWEREEYLWSREKAIL 228

Query: 253 DLMVGAK-VSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
           +       +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|166034419|gb|ABY78986.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. CFN ESH10]
 gi|166034421|gb|ABY78987.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. CFN ESH27]
          Length = 214

 Score =  397 bits (1020), Expect = e-108,   Method: Composition-based stats.
 Identities = 149/214 (69%), Positives = 179/214 (83%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            ++I  LI+ YKA+G+I PLR  ++ V+G G  ++++ +YDDDSVLR+A+QWK GV ++TP
Sbjct: 61   RQIGELIDAYKASGNIEPLRQTIDMVVGDGPKSDEVHEYDDDSVLRLADQWKRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAGEVDVNEMLAMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|166034415|gb|ABY78984.1| DNA-directed RNA polymerase beta chain [Ensifer mexicanus]
          Length = 214

 Score =  397 bits (1020), Expect = e-108,   Method: Composition-based stats.
 Identities = 147/214 (68%), Positives = 176/214 (82%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            KKI ++++ Y  NGDI+PLR+ ++ VIG+G   E I  YDD+SV+R+AEQ + GV ++TP
Sbjct: 61   KKIGAMLDAYHENGDIAPLRATIDDVIGSGPKGEPIKQYDDESVVRLAEQTRRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N ML  A L  +GQS L+DG TGEPFDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAVEADVNEMLNKAGLKVTGQSTLFDGRTGEPFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|172211|gb|AAA68096.1| RNA polymerase II 48 kd subunit [Saccharomyces cerevisiae]
          Length = 1224

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 174/980 (17%), Positives = 316/980 (32%), Gaps = 171/980 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ + I    +
Sbjct: 374  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQ 433

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             +  +      +  INAK + S +     +               +SQ+       S ++
Sbjct: 434  RTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 493

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++   
Sbjct: 494  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT 549

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGE 652
                    + +  +     Y+   +  +      N              E L   R  G+
Sbjct: 550  DPMPIITFLSEWGMEPLEDYV-PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 608

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP--LLKAEAPF 710
                     D  +   K          P    +D   +       R+     L+  E   
Sbjct: 609  INPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQD 668

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRLMKF 767
            +  G E V   +  + +     G+VE +DA       I     DL+P+ +  +    +  
Sbjct: 669  IEGGFEDVEEYTWSSLL---NEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDP 725

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             +            ++V             PS  LG  A       + +P+  +N     
Sbjct: 726  AK-----------RIRVSHHATTFTHCEIHPSMILGVAA-------SIIPFPDHNQSPRN 767

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
                 M  + +   + +  + V                               +  +   
Sbjct: 768  TYQSAMGKQAMG--VFLTNYNVRM---------------------------DTMANILYY 798

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                      +       +   +  + AI      +  D+ +   S +   +    +F R
Sbjct: 799  PQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFR 857

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +D+ ++      E  E   R           +       I  G           K+T 
Sbjct: 858  SYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP 917

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +S D      R+ +         ++     +  Q                          
Sbjct: 918  ISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQ--------------------VLVTTN 957

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
               L+ VKV V   +  Q GDK A RHG KG +      EDMPF +     D+++NP  +
Sbjct: 958  QDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTRRRYVPDLIINPHAI 1017

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V  + E  L       G +                                    
Sbjct: 1018 PSRMTVAHLIECLLSKVAALSGNEGD---------------------------------- 1043

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                               ++P F     E I+ +LR       G  ++Y+G TG+    
Sbjct: 1044 -------------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMA 1083

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C+ A+GA
Sbjct: 1084 QIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGA 1143

Query: 1308 AYVLQEMLTIKSD----DVVGRTRVYESIVA----------GND---TFETGTPESFNVL 1350
            A  L+E L   SD     + G   +   I             ++    ++   P +  +L
Sbjct: 1144 ASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL 1203

Query: 1351 VKEMQALGLSIDLENSRTKN 1370
             +E+ A+ ++  L   R+++
Sbjct: 1204 FQELMAMNITPRLYTDRSRD 1223



 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 131/1004 (13%), Positives = 290/1004 (28%), Gaps = 164/1004 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGL--QAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S++ F+   +      +  L  +   +        S    + F       P  
Sbjct: 43  LVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 102

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS------- 129
           +            +   R+LTY+  L + ++   ++  +  G +   ++  +        
Sbjct: 103 NESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSES 162

Query: 130 --IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGI 163
             +++G LP+M +                         G F+I G ++++++Q  RS G 
Sbjct: 163 GKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE-RSAGN 221

Query: 164 HFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR---IDRRRK------- 211
                  + +    + +   I    ++G         K  ++ R     R  K       
Sbjct: 222 I--VQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVK--LYGREGSSARTIKATLPYIK 277

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG+  + EIL      +   Q  +     +    ++   + +   +   
Sbjct: 278 QDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRR 337

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                I+  K++       L+++ +  +                +      + + A D  
Sbjct: 338 GTALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFF---LGYMINRLLLCALDRK 393

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           D+   +      +    P+L          +   +     +  ++A     ++       
Sbjct: 394 DQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTI 453

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   S  G  ++  R    +      R          +     
Sbjct: 454 TSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQ 513

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   +  + +       I+ +    + P +   
Sbjct: 514 LHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYV 570

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                 A   F               +  +   RR   +            +   +    
Sbjct: 571 PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDA 630

Query: 566 YGRICPAETSEG------HNIGLVSSLTSFARVNAYGFIETPYRKVCDGK-----VTNDV 614
                P    E         + +     +      Y  IE  +  V +           V
Sbjct: 631 GRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLV 690

Query: 615 VYLSAMEEENRYIAQANSSL-DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            Y+ A EEE+  IA     L   + +   +L         +          +  P  ++ 
Sbjct: 691 EYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILG 750

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AAS+IPF +++ S R      M +QA+ +                              
Sbjct: 751 VAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV----------------------- 787

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + +  Y       +     +  R              
Sbjct: 788 ------------------RMDTMANILYYPQKPLGTTRAMEYLKFR-------------- 815

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDSM++++  +   +F S+    +    + 
Sbjct: 816 ----------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKK 865

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   +       +D+ G+I  G  V+  D+++GK TP      +P
Sbjct: 866 YGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPI-----SP 920

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +E+ L       +   RD S  + S  +G V  V +       K
Sbjct: 921 DEEELGQRTAYHSK--RDASTPLRSTENGIVDQVLVTTNQDGLK 962


>gi|228016441|gb|ACP51273.1| RNA polymerase beta subunit [Pinus torreyana subsp. insularis]
          Length = 1074

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 162/497 (32%), Positives = 238/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            IC G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 630  ICQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 688

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 689  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 742

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 743  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 800

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP +DMP+L++G PVD+V
Sbjct: 801  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLPRQDMPYLQNGIPVDMV 855

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMNVGQIFE   G A   + K  +    D K   + S    F E    +   
Sbjct: 856  LNPLGVPSRMNVGQIFECLPGLAGNPMNKHYRITPFDEKYEREASRKLVFPELYKASEQT 915

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                D  G+  L DG T
Sbjct: 916  ANPW------------------------VFE---------------PDHPGKHRLIDGRT 936

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PVT+G  YM KL+H V +K++ARS+G Y+ VTQQPL GKS RGGQR+GEMEVW 
Sbjct: 937  GDVFEQPVTIGKAYMSKLSHQVDEKIHARSSGPYARVTQQPLRGKSKRGGQRIGEMEVWA 996

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G    ++ T PESF +L++E+++L L 
Sbjct: 997  LEGFGVAYILQEMLTLKSDHIRTRNEVLGAIITGGPIPKSDTAPESFRLLIRELRSLALE 1056

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  + + +     + +
Sbjct: 1057 LNHAIISEKNFQIDREK 1073



 Score =  350 bits (898), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 228/640 (35%), Positives = 347/640 (54%), Gaps = 25/640 (3%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +    +  E+ L+       R + +   +      Y+           R+ A+L+ Y+
Sbjct: 183 VLLSGMGLNLEEILDN-TRYPERYLFLFKKERWEREEYLW---------SREKAILEFYK 232

Query: 380 VM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD++            FF   + +L  +GR  +N +LNLD P++      +D++
Sbjct: 233 KLHCISGDLAFSESLCKELQEKFF-RKRCELGKIGRRNLNQKLNLDIPENEIFSLPQDVL 291

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +  L+ ++ G GT+DDID+L NRR+RSV ++L+NQ+RL L R+E ++K  I       
Sbjct: 292 AAVDYLIGVKFGMGTLDDIDHLRNRRIRSVADLLQNQFRLALGRLEDAVKRTIHRATKRR 351

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                            +FF         +  N      H R+LS LG GG+    A   
Sbjct: 352 STXXXXXXXXXXXXXXQDFFGXXXXXXXXDQTNXXXXXAHGRKLSHLGPGGLTGRTASFR 411

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+HP++YGRICP +TSEG N GLV+SL+  A++   G +++P+ K+ +      +VYL
Sbjct: 412 TRDIHPSYYGRICPIDTSEGMNAGLVASLSIHAKIGDCGSLQSPFYKISERSREEHMVYL 471

Query: 618 SA--MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                E+E   IA  NS     G   E++   R   E I++  E+I F    P Q  S+ 
Sbjct: 472 LPGEDEDEYYRIATGNSLALNQGIQEEQITPARYRQEFIVIAWEQIHFRSIFPFQYFSVG 531

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E    GTG+E   A  SG+  +A + G +
Sbjct: 532 VSLIPFLEHNDANRALMGSNMQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRI 591

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           E +DA+                       + +QRSN NTC +Q+P +  G+ V++  I+A
Sbjct: 592 EYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQKPQICQGECVKKGQILA 643

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI  + +    T 
Sbjct: 644 DGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTS 703

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL
Sbjct: 704 QGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLL 763

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           + IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 764 QTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 803



 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 67/341 (19%), Positives = 139/341 (40%), Gaps = 39/341 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP+  ++Q   +  F+          ++GL         I        +EF      YE 
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLMEELHDFPKIEDIDK--EIEFRLFGNEYEL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D +++ LTY   L +  R         +  ++ + I++Q++++G++PLM   
Sbjct: 60  AEPFIKERDAVYQSLTYYSELYVPAR---------SIRRNSRKIQKQTVFLGNIPLMNSH 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFV+ GI R+VV+Q+  SPGI++  +          +Y   +I D G    +E D ++ 
Sbjct: 111 GTFVVNGIYRVVVNQILISPGIYYRSELD--HNRIHYIYTGTLISDWGRRSKLEIDVRER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILS---------TFYPKIVYSQRGDFWCFPLSAA 252
           I  R+ R++K+ +   L  +G++ EEIL            + K  + +    W    +  
Sbjct: 169 IWARVSRKQKISIPVLLSGMGLNLEEILDNTRYPERYLFLFKKERWEREEYLWSREKAIL 228

Query: 253 DLMVGAK-VSSSLVDIDT-GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
           +       +S  L   ++  +++ E   +    L K  +    + L +         + +
Sbjct: 229 EFYKKLHCISGDLAFSESLCKELQEKFFRKRCELGKIGRRNLNQKLNLDIPENEIFSLPQ 288

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           D++      I ++   +     ++ + +  IR +  L  + 
Sbjct: 289 DVLAAVDYLIGVK-FGMGTLDDIDHLRNRRIRSVADLLQNQ 328


>gi|16486|emb|CAA79528.1| RNA polymerase II second largest subunit [Arabidopsis thaliana]
          Length = 1188

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 187/1044 (17%), Positives = 335/1044 (32%), Gaps = 198/1044 (18%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM---------NMR 419
                A   +  ++RP     F +   +    +       +      ++          M 
Sbjct: 294  CYDFADTQMMELLRPSLEEAFVIQNQLVALDYIGKRGATVGVTKEKRIKYARDILQKEML 353

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L +   +     +      II  L+    G+   DD D+ GN+R+   G +L   +R+  
Sbjct: 354  LYVGIGEHCETKKAYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLF 413

Query: 480  LRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQL 525
             ++ R ++  +     +   V  Q  I AK + S +     +              +SQ+
Sbjct: 414  RKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQV 473

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   S ++H RRL++     + R     + R +H + +G +CPAET EG   GLV +
Sbjct: 474  LNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKN 529

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L     +            + +    N        EE +  +    + +  +G +     
Sbjct: 530  LALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPSVIPQATKIFVNGMWVG--- 579

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R     +   R     +D + +  V     L       D  R      +      L+K
Sbjct: 580  VHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVDNQKLLIK 639

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                     + ++  + S     A+  G    V   +  I  ++ + + +T        +
Sbjct: 640  KRD------IYALQQRES-----AEEDGWHHLV--AKGFIEYIDTEEEETTMISMTISDL 686

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
               R                            PS  LG       +  + +P+  +N   
Sbjct: 687  VQARLRPEEAYT-----------ENYTHCEIHPSLILG-------VCASIIPFPDHNQSP 728

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                   M  + +     I       R   L         P V+   ++++         
Sbjct: 729  RNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL--------- 775

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                                +      + AI      +  D+ +   S +        +F
Sbjct: 776  ----------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLF 818

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R   D+ ++  ++ +E      R           +          G           K+
Sbjct: 819  FRSYRDEEKKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKT 878

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T +S                  DE   ++    +  +  S    E    +++      D 
Sbjct: 879  TPISQ-----------------DEAQGQSSRYTRRDHSISLRHSETGMVDQVLLTTNADG 921

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 922  L-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGVTPDIIVNPH 976

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 977  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 1004

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 1005 ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 1042

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 1043 TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 1102

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------NDTFETG------------TPE 1345
            GAA+ L+E L  +SD    R  V E  V G         ++FE               P 
Sbjct: 1103 GAAHFLKERLFDQSD--AYRVHVCE--VCGLIAIANLKKNSFECRGCKNKTDIVQVYIPY 1158

Query: 1346 SFNVLVKEMQALGLSIDLENSRTK 1369
            +  +L +E+ ++ ++  +     K
Sbjct: 1159 ACKLLFQELMSMAIAPRMLTKHLK 1182



 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 143/993 (14%), Positives = 286/993 (28%), Gaps = 203/993 (20%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 39  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 89

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 90  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 149

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 150 FTK--VFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 207

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR----------- 208
              ++      +     K  Y   +        + +      + VR+             
Sbjct: 208 TNHVY----VFKKRQPNKYAYVGEVR----SMAENQNRPPSTMFVRMLARASAKGGSSGQ 259

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 260 YIRCTLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQ 319

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            V+   +        +   K++         + L   G+     T       Y+   ++ 
Sbjct: 320 LVALDYIGKRGATVGVTKEKRIKYARDILQKEMLLYVGIGEHCETKKAYYFGYIIHRLLL 379

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDA 373
              G    +  D    K L+           +L+   + +  +Y++  +   K  + + A
Sbjct: 380 CALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQFA 439

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-R 432
           +             T  +  S+    +  ++           +N      T   +R +  
Sbjct: 440 I--------KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 491

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N +  +         +      ++KN   +  + +  +    +  
Sbjct: 492 PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEF 548

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVAR 551
           ++       + I+   +  A   F     +    +    +  +   RR   +  + GV R
Sbjct: 549 LEEWGTENFEEISPSVIPQATKIFVNGMWVGVHRDPDMLVKTLRRLRRRVDVNTEVGVVR 608

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                E+R    T YGR         +   L+     +A        E            
Sbjct: 609 DIRLKELR--IYTDYGRCSRPLFIVDNQKLLIKKRDIYALQQRESAEEDG---WHHLVAK 663

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+              +LV  R   EE     E     +  P  +
Sbjct: 664 GFIEYIDTEEEETTMISM----------TISDLVQARLRPEEAYT--ENYTHCEIHPSLI 711

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +      F                    R
Sbjct: 712 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------R 751

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 752 MDTLAYV-----------------------------------LYYPQKPLV--------- 767

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N +VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 768 -TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 826

Query: 852 RDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E            +       +D+ G+   G  V+  D+++GK TP  +   
Sbjct: 827 KKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE- 885

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   A         RD S+ +    +G V
Sbjct: 886 --------AQGQSSRYTRRDHSISLRHSETGMV 910


>gi|166034425|gb|ABY78989.1| DNA-directed RNA polymerase beta chain [Rhizobium sp. CFN ESH23]
          Length = 214

 Score =  397 bits (1019), Expect = e-107,   Method: Composition-based stats.
 Identities = 149/214 (69%), Positives = 178/214 (83%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            ++I  LI  YKA+G+I PLR  ++ V+G G  ++++ +YDDDSVLR+A+QWK GV ++TP
Sbjct: 61   RQIGDLIEAYKASGNIEPLRKTIDMVVGDGPKSDEVHEYDDDSVLRLADQWKRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAGEVDVNEMLAMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|6606105|gb|AAF19065.1|AF107793_1 DNA-dependent RNA polymerase II RPB140 [Emericella nidulans]
          Length = 1009

 Score =  396 bits (1018), Expect = e-107,   Method: Composition-based stats.
 Identities = 171/927 (18%), Positives = 309/927 (33%), Gaps = 152/927 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 161  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 220

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     + A  V   +     +               +SQ+
Sbjct: 221  RVTRDLQRYVQRCVESDREIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQV 280

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 281  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 336

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +    S   E
Sbjct: 337  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVE 396

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQA 700
             +        I      I D  +   K          P    D+  +     N+   ++ 
Sbjct: 397  TMQALRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEH 456

Query: 701  VPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA      +I     DL+ S 
Sbjct: 457  IRKLEEDKELPPDMDPEDRRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 515

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y L +     Q+     R ++               PS  LG       +  + +
Sbjct: 516  QLQAGYALPE----EQDPNKRVRSILS--QRAHTWTHCEIHPSMILG-------VCASII 562

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 563  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 610

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 611  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 653

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +     +  +    ++    V    +E   +    + + + +  Y +L E   +  G 
Sbjct: 654  RGLFRSLFYRTY----SDSEKMVGLTVVERFEKPMRSDTIGMRKGTYDKLDEDGIVNPGV 709

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ D                +E  QR     K+   T     E+  
Sbjct: 710  RVSGEDIIIGKTAPLAPD---------------AEELGQRTKNHTKLDVSTPLRSTENGI 754

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV + M +  Q GDK A RHG KG +      EDMPF +
Sbjct: 755  VDQVLVTTTPDSL-----RSVKVRMRMTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTR 809

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 810  EGVTPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD-------------------- 849

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+ +LR       G 
Sbjct: 850  ---------------------------------ATP-FTDVTVDSISRLLREHGYQSRGF 875

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 876  EVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 935

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             GEME  C+ A+GA+  L+E L   SD
Sbjct: 936  FGEMERDCMIAHGASAFLKERLFDVSD 962



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 113/851 (13%), Positives = 238/851 (27%), Gaps = 127/851 (14%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD--------- 197
            ++++++Q  RS G        + +      Y   I    ++G  +  +           
Sbjct: 1   SEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLKLFGKGDS 57

Query: 198 SKDII---------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
           +K            +++ D    +P+     ALG+   E+IL+        +   +    
Sbjct: 58  AKGGFGPTIRSTLPYIKAD----IPIVIVFRALGVVSDEDILNHICYDRNDTPMLEMLKP 113

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SD 301
            +    ++   +V+   +      Q   + ++      + ++++ +  +  +        
Sbjct: 114 CIEEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGSETRKA 173

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              G  V   ++    G   ++  D   +K L+           +L+     +       
Sbjct: 174 FFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD------- 225

Query: 362 LVTDKNKDRKDALLDIY-RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +    +   ++  +IY  V       T  +  ++    + +  K   +  G  ++  R 
Sbjct: 226 -LQRYVQRCVESDREIYLNVGLKASTVTQGLRYALATGNWGEQKKAASAKAGVSQVLSRY 284

Query: 421 NLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
              +      R          I     L N   G +   +    +    V  +    Y  
Sbjct: 285 TYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT 344

Query: 478 GLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
                E  I    + +   ++   PQ   NA  V           Q S L E + +L R 
Sbjct: 345 VGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRQPSHLVETMQALRRR 404

Query: 536 THTRRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
                  +L +    R         R   P       P   + G+ +     +       
Sbjct: 405 NMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGNLVLNKEHIRKLEEDK 464

Query: 594 ------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------ 641
                         Y        +  V Y+ A EEE   I      L+            
Sbjct: 465 ELPPDMDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQLQAGYALP 524

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           EE    +     +          +  P  ++ + AS+IPF +++ S R      M +QA+
Sbjct: 525 EEQDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 584

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            +                   + A I+      +    ++  +          +   +  
Sbjct: 585 GVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIAC 635

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y              NQ            + +I +  S D G         + +  +   
Sbjct: 636 YSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS-----LFYRTYSDS 668

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
                + + ER              FE   R   +G  +               +DE GI
Sbjct: 669 EKMVGLTVVER--------------FEKPMRSDTIGMRK----------GTYDKLDEDGI 704

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +  G  V+  DI++GK  P         E+L +       +DV        +G+   V+ 
Sbjct: 705 VNPGVRVSGEDIIIGKTAPLAPDA----EELGQRTKNHTKLDVSTPLRSTENGIVDQVLV 760

Query: 942 VRIFNRHGIDK 952
               +     K
Sbjct: 761 TTTPDSLRSVK 771


>gi|94987715|ref|YP_595816.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
            MGAS9429]
 gi|94541223|gb|ABF31272.1| DNA-directed RNA polymerase beta chain [Streptococcus pyogenes
            MGAS9429]
          Length = 249

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 119/274 (43%), Positives = 153/274 (55%), Gaps = 54/274 (19%)

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+   
Sbjct: 1    MPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW-- 58

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                       D   E           +
Sbjct: 59   -------------------------------------------DTVREA---------GM 66

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
            D   +++LYDG TGEPFD  V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+ 
Sbjct: 67   DSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQ 126

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFN 1348
             GGQR GEMEVW ++AYGA+ VLQE+LT KSDDV GR + YE+I  G    + G PESF 
Sbjct: 127  FGGQRFGEMEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFR 186

Query: 1349 VLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNK 1382
            VLVKE+Q+LGL + + +         +     + 
Sbjct: 187  VLVKELQSLGLDMRVLDEDDNEVELRDLDEGEDD 220


>gi|209395123|gb|ACI45381.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 130/237 (54%), Positives = 164/237 (69%), Gaps = 13/237 (5%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  L+   +    +S LR FL++V  +    
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWASKGIGERIGELL---QQQAKVSELRRFLDEVYNSRGRK 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG---------- 1232
            E ++   D  +L +A   + GVP +TPVFDGA E     ML +A  +E+           
Sbjct: 58   ENLALLSDADLLAMAGNLQQGVPYATPVFDGASEAENKDMLELAYPEETARRRGLTSSRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+GY++ LKL+H+V DK+ ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAYLYDGRTGERFERPTTIGYMHYLKLHHLVDDKMRARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            R GEMEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  RFGEMEVWALEAYGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 234


>gi|324120604|dbj|BAJ78693.1| RNA polymerase II second largest subunit [Thermobia domestica]
          Length = 1175

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 170/1087 (15%), Positives = 330/1087 (30%), Gaps = 206/1087 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLKYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  D+   +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVDNGKLLLKKRHIDMLKEREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F  +   +++R
Sbjct: 763  RSMEYLRFRELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKR 822

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                E EQ E   R+          +       I  G           K           
Sbjct: 823  FCDQE-EQFERPTRNTCQGMRNAIYDKLDDDGIIAPGVRVSGDDVVIGK----------- 870

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                      + D +    +E    +Y    +    R        Q    +     +  K
Sbjct: 871  -------TITLPDNE--DELEGTTKRYTKRDASTFLRNSETGIVDQVMITLNSEGYKFCK 921

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 922  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGH 981

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 982  LIECLQGKVSANKGEIGD------------------------------------------ 999

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G  Y
Sbjct: 1000 -----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLGPTY 1048

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L
Sbjct: 1049 YQRLKHMVDDKIHSRARGPLQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERL 1108

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            R   +E    G        +   P +  +L +E+ ++
Sbjct: 1109 FEVSDPYRIHVCNFCGLIAIANLRNSTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSM 1166

Query: 1358 GLSIDLE 1364
             ++  L 
Sbjct: 1167 NIAPRLM 1173



 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 142/994 (14%), Positives = 290/994 (29%), Gaps = 184/994 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKTVIKEGEDPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                 K  Y   I       ++        + V         I +              
Sbjct: 213 S-----KYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  L+  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLKYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    +   + L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVDNGKLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNYHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT- 862
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRFCDQEEQFE 831

Query: 863 ----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 RPTRNTCQGMRNAIYDKLDDDGIIAPGVRVSGDDVVIGKTITLPDNEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K    RD S  + +  +G V  V I       K
Sbjct: 886 -KRYTKRDASTFLRNSETGIVDQVMITLNSEGYK 918


>gi|15234572|ref|NP_193902.1| NRPB2; DNA binding / DNA-directed RNA polymerase [Arabidopsis
            thaliana]
 gi|21542437|sp|P38420|RPB2_ARATH RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2; AltName: Full=DNA-directed RNA polymerase II 135 kDa
            polypeptide; AltName: Full=Protein EMBRYO DEFECTIVE 1989
 gi|4455279|emb|CAB36815.1| DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain
            [Arabidopsis thaliana]
 gi|7268968|emb|CAB81278.1| DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain
            [Arabidopsis thaliana]
          Length = 1188

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 188/1044 (18%), Positives = 332/1044 (31%), Gaps = 198/1044 (18%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD-------KYDLSTVGRVKMNMRLN 421
                A   +  ++RP     F +   +    +           K       R  +   + 
Sbjct: 294  CYDFADTQMMELLRPSLEEAFVIQNQLVALDYIGKRGATVGVTKEKRIKYARDILQKEML 353

Query: 422  LDTPDDVRHIRK--EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
                       K       II  L+    G+   DD D+ GN+R+   G +L   +R+  
Sbjct: 354  PHVGIGEHCETKKAYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLF 413

Query: 480  LRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQL 525
             ++ R ++  +     +   V  Q  I AK + S +     +              +SQ+
Sbjct: 414  RKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQV 473

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   S ++H RRL++     + R     + R +H + +G +CPAET EG   GLV +
Sbjct: 474  LNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKN 529

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L     +            + +    N        EE +  +    + +  +G +     
Sbjct: 530  LALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPSVIPQATKIFVNGMWVG--- 579

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R     +   R     +D + +  V     L       D  R      +      L+K
Sbjct: 580  VHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVDNQKLLIK 639

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                     + ++  + S     A+  G    V   +  I  ++ + + +T        +
Sbjct: 640  KRD------IYALQQRES-----AEEDGWHHLV--AKGFIEYIDTEEEETTMISMTISDL 686

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
               R                            PS  LG       +  + +P+  +N   
Sbjct: 687  VQARLRPEEAYT-----------ENYTHCEIHPSLILG-------VCASIIPFPDHNQSP 728

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                   M  + +     I       R   L         P V+   ++++         
Sbjct: 729  RNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL--------- 775

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                                +      + AI      +  D+ +   S +        +F
Sbjct: 776  ----------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLF 818

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R   D+ ++  ++ +E      R           +          G           K+
Sbjct: 819  FRSYRDEEKKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKT 878

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T +S                  DE   ++    +  +  S    E    +++      D 
Sbjct: 879  TPISQ-----------------DEAQGQSSRYTRRDHSISLRHSETGMVDQVLLTTNADG 921

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 922  L-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGVTPDIIVNPH 976

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 977  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 1004

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 1005 ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 1042

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 1043 TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 1102

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------NDTFETG------------TPE 1345
            GAA+ L+E L  +SD    R  V E  V G         ++FE               P 
Sbjct: 1103 GAAHFLKERLFDQSD--AYRVHVCE--VCGLIAIANLKKNSFECRGCKNKTDIVQVYIPY 1158

Query: 1346 SFNVLVKEMQALGLSIDLENSRTK 1369
            +  +L +E+ ++ ++  +     K
Sbjct: 1159 ACKLLFQELMSMAIAPRMLTKHLK 1182



 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 140/989 (14%), Positives = 282/989 (28%), Gaps = 195/989 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 39  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 89

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 90  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 149

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 150 FTK--VFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 207

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR----------- 208
              ++      +     K  Y   +        + +      + VR+             
Sbjct: 208 TNHVY----VFKKRQPNKYAYVGEVR----SMAENQNRPPSTMFVRMLARASAKGGSSGQ 259

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 260 YIRCTLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQ 319

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
            V+   +        +   K++       L+++ +  +GI   C          +     
Sbjct: 320 LVALDYIGKRGATVGVTKEKRIKYAR-DILQKEMLPHVGIGEHCETKKAYYFGYIIH--- 375

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   + +   K   +     
Sbjct: 376 RLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVN 435

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 436 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 495

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +      ++KN   +  + +  +    +  ++  
Sbjct: 496 EGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEW 552

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
                + I+   +  A   F     +    +    +  +   RR   +  + GV R    
Sbjct: 553 GTENFEEISPSVIPQATKIFVNGMWVGVHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRL 612

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+R    T YGR         +   L+     +A        E              + 
Sbjct: 613 KELR--IYTDYGRCSRPLFIVDNQKLLIKKRDIYALQQRESAEEDG---WHHLVAKGFIE 667

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE   I+              +LV  R   EE     E     +  P  ++ + 
Sbjct: 668 YIDTEEEETTMISM----------TISDLVQARLRPEEAYT--ENYTHCEIHPSLILGVC 715

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +      F                    R   +
Sbjct: 716 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------RMDTL 755

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             V                                       Q+PLV             
Sbjct: 756 AYV-----------------------------------LYYPQKPLV----------TTR 770

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    L  G N +VA   + GYN EDS+++++  +    F S+    +    +   
Sbjct: 771 AMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 830

Query: 856 LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +E            +       +D+ G+   G  V+  D+++GK TP  +       
Sbjct: 831 TLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE----- 885

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               A         RD S+ +    +G V
Sbjct: 886 ----AQGQSSRYTRRDHSISLRHSETGMV 910


>gi|50346774|ref|YP_053147.1| RNA polymerase beta subunit [Nymphaea alba]
 gi|68053165|sp|Q6EW56|RPOB_NYMAL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|50250319|emb|CAF28585.1| RNA polymerase beta subunit [Nymphaea alba]
          Length = 1071

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 138/396 (34%), Positives = 207/396 (52%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 721  LDRNGIVMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 780

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 781  GGRGRVIDVRWGQKKG----GSIYNP---EMIRVYISQKRKIKVGDKVAGRHGNKGIISK 833

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQ+FE  LG A   LG+  +    D +  
Sbjct: 834  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQMFECSLGLAGDLLGRHYRITPFDERYE 893

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 894  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 919

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YMLKL H V DK++ RS+G Y+LVTQQP
Sbjct: 920  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMLKLIHQVDDKIHGRSSGHYALVTQQP 974

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 975  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPE 1034

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 GAPESFRLLVRELRSLSLELNHFLVSEKNFQINRKE 1070



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 231/662 (34%), Positives = 369/662 (55%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +  E          + S+  +  +    +  +  +     
Sbjct: 144 ISVYTGTIISDWGGRSELEIDRKERIWARVSRKQKISILVLSSAMGSSLREILDNVCYPE 203

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 204 IFLSFPNEKEKKKIGSKENAILEFYQKFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 262

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 263 GRRNMNQRLNLDIPPNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 322

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   P++L+ + P+ +    FF    LSQ+ +  
Sbjct: 323 QDQFGLALVRLENVVRGTICGAIRHKLIPTPRNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 383 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARV  +G IETP+ ++ +      +VYLS   +E   +A  NS     G   EE+   R 
Sbjct: 443 ARVGDWGSIETPFYEISERSKEEQMVYLSPSRDEYYMVAAGNSLALTRGIQEEEVGPARY 502

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I   +  P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503 RQEFLTIAWEQIHLRNIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 562

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+R G +   DA +IV+                  L+ +QR
Sbjct: 563 IVGTGLERQAALDSGGSAIAEREGKIIYTDAEKIVLSGN--------GDTISIPLVMYQR 614

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q+P V  G  +++  I+ADG +T  G+LALG+N+ VA+MPW GYN ED++LI
Sbjct: 615 SNKNTWMHQKPQVHRGKYLKKGQILADGAATVGGELALGKNVSVAYMPWEGYNSEDAVLI 674

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V 
Sbjct: 675 SERLVYDDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEPYLLRNLDRNGIVMLGSWVE 734

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 735 TGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWGQK 794

Query: 948 HG 949
            G
Sbjct: 795 KG 796



 Score =  168 bits (425), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 106/233 (45%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     SY+ 
Sbjct: 13  IPGFSQIQFEGFCRFI----------DQGLMEELHQFPKIEDTDQ--EIEFQLFGESYQL 60

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  +TY+  L +   LI          ++ ++++EQ++ +G++PLM   
Sbjct: 61  VEPLIKERDAVYESITYSSELYVPAGLIW---------RTGRNMQEQTVLLGNIPLMNSL 111

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++        +S   +Y   II D G   ++E D K+ 
Sbjct: 112 GTSIVNGIYRIVINQILQSPGIYYSTGLDHNGIS---VYTGTIISDWGGRSELEIDRKER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G    EIL    YP+I  S   +     + + +
Sbjct: 169 IWARVSRKQKISILVLSSAMGSSLREILDNVCYPEIFLSFPNEKEKKKIGSKE 221


>gi|150251451|ref|YP_001312184.1| RNA polymerase beta chain [Cycas taitungensis]
 gi|158513731|sp|A6H5F9|RPOB_CYCTA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|149941501|dbj|BAF64925.1| RNA polymerase beta chain [Cycas taitungensis]
          Length = 1072

 Score =  396 bits (1017), Expect = e-107,   Method: Composition-based stats.
 Identities = 163/497 (32%), Positives = 232/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 628  VRRGEYVKKGQILADGAATVG-GELSLGKNILVAHMPWEGYNFEDAILISERLVYEDIYT 686

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+GI     S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 687  SFHIERYGIVTCMTSQGPERITKEIPHLDAHL-LRHLDGN-----GLVMLGSWVETGDVL 740

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   ++     P  +  Q     +        L+V       +++ R+ +K E   
Sbjct: 741  VGKLTPQPAEESLRAPEGRLLQAIFGIQVSSARESCLRVPIGGRGRVIDVRWIHKEE--N 798

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
            +GD+       VV V++  KR IQ GDK+AGR GNKGI+S+ILP +DMP+L+DGT VD+V
Sbjct: 799  FGDNAE-----VVHVYIFQKRKIQVGDKVAGRLGNKGIISKILPRQDMPYLQDGTSVDMV 853

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGV SRMNVGQIFE   G A   + +  +    D +   + S  +    ++ G    
Sbjct: 854  LNPLGVLSRMNVGQIFECLPGLAGNLMNRHYRITPFDERYEREASR-KPVFPELYGASEQ 912

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T                           VF+                +  G++ L DG T
Sbjct: 913  TANPW-----------------------VFE---------------PNHPGKNRLIDGRT 934

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+  ++PVT G  YM KL H V DK++ARS+G Y+LVTQQPL GKS RGGQR+GEMEVW 
Sbjct: 935  GDTLEQPVTTGKAYMPKLIHQVDDKIHARSSGPYALVTQQPLRGKSKRGGQRVGEMEVWA 994

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALG-- 1358
            ++ +G AY+LQEMLT+KSD +  R  V  +I+ G      GT PESF +LV+E+++L   
Sbjct: 995  LEGFGVAYILQEMLTLKSDHIGARHEVLGAIITGGPIPRPGTAPESFRLLVRELRSLAPE 1054

Query: 1359 LSIDLENSRTKNSAKME 1375
            L   +         + E
Sbjct: 1055 LDHAIIYENDFQIDRKE 1071



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 237/640 (37%), Positives = 364/640 (56%), Gaps = 26/640 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I + A      + L+ + +   +    L  +      Y+R          +K+A+L+ Y+
Sbjct: 182 ILLSAMGSNLGEILDNVCY--PKIFLSLLTERQEQKEYLR---------SKKNAILEFYK 230

Query: 380 VMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            +    GD+              F   + +L  +GR   N +LNLD P++      +D++
Sbjct: 231 KLYCVSGDLVFSESLCKELRK-KFLQQRCELGKIGRRNPNQKLNLDIPENEIFSLPQDVL 289

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A +   + ++ G GT+DD+D+L NRR+RSV ++L+NQ+ L L R+E +++  I       
Sbjct: 290 AAVDYSIRVKFGMGTLDDMDHLKNRRIRSVADLLQNQFGLALGRLENAVRRTIRRATKRK 349

Query: 498 V--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
               P +L+ + P+ +   +FF S  LSQ  +  N L+ I H R+LS LG GG+    A 
Sbjct: 350 CLPTPNNLVTSTPLTTTFQDFFGSHPLSQFLDQTNPLTEIVHRRKLSYLGPGGLTGRTAS 409

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             +RD+HP+HYGRICP ETSEG N GLV+SL   AR+   G +++P+ K+ +      +V
Sbjct: 410 SRIRDIHPSHYGRICPIETSEGMNAGLVASLAIRARIGHCGSLQSPFHKISERSEEEHMV 469

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLS+ E+E   IA  N      G   E++   R   E + +  E+I F    P Q  S+ 
Sbjct: 470 YLSSGEDEYYRIATGNYLALNQGIREEQVTPARYRQEFLAIAWEQIHFRSIFPFQYFSVG 529

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +
Sbjct: 530 VSLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIATQGGRI 589

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             +DA +I                    L+ +QRSN NTC++Q+P V+ G+ V++  I+A
Sbjct: 590 TYIDAGKIT--------SSVDGDTVGTELVTYQRSNNNTCMHQKPRVRRGEYVKKGQILA 641

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T 
Sbjct: 642 DGAATVGGELSLGKNILVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTS 701

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLL 913
            GPE IT++IP++    L+++D  G++ +G+ V  GD+LVGK+TP+        PE +LL
Sbjct: 702 QGPERITKEIPHLDAHLLRHLDGNGLVMLGSWVETGDVLVGKLTPQPAEESLRAPEGRLL 761

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           +AIFG +    R++ LRVP G  G V+DVR  ++     +
Sbjct: 762 QAIFGIQVSSARESCLRVPIGGRGRVIDVRWIHKEENFGD 801



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/299 (24%), Positives = 129/299 (43%), Gaps = 31/299 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP+  ++Q   +  F+          ++GL    ++   I          L    YE   
Sbjct: 12  IPEFGKIQFEGFCRFI----------DQGLIEELQNFPKIEDTDQEIESQLFGNKYELAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + +++ LTY+  L +  RLI          ++ + I++Q++ +G+LPLM   GT
Sbjct: 62  PLIKERNAVYQSLTYSSELYVPARLI---------QRNSRKIQKQTVLIGNLPLMNSQGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FV+ GI RIVV+Q+ RSPGI++  +      SG  LY   II D G    +E D K  I 
Sbjct: 113 FVVNGISRIVVNQILRSPGIYYSSEPD---QSGITLYTSTIISDWGGRSKLEIDGKTRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ ++RK+ +   L A+G +  EIL    YPKI  S             + +   K  +
Sbjct: 170 ARVSKKRKISIPILLSAMGSNLGEILDNVCYPKIFLSL----LTERQEQKEYLRSKK--N 223

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           ++++       +      +  L K L++K ++               +  ++    EI+
Sbjct: 224 AILEFYKKLYCVSGDLVFSESLCKELRKKFLQQRCELGKIGRRNPNQKLNLDIPENEIF 282


>gi|73975071|ref|XP_860899.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            12 [Canis familiaris]
          Length = 1174

 Score =  395 bits (1016), Expect = e-107,   Method: Composition-based stats.
 Identities = 177/1081 (16%), Positives = 331/1081 (30%), Gaps = 194/1081 (17%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 254  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 313

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 314  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 367

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 368  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 427

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 428  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 487

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 488  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 543

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              + +  + N        E     IA A + +  +G +             +   R +  
Sbjct: 544  EFLEEWSMENL------EEISPAAIADA-TKIFVNGCWVGIHKDPEQLMNTLRKLRRQ-- 594

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D  P   +             D+ R+     +  +   LL  +   +    E      
Sbjct: 595  -MDIIPDVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLL--KKRHIDQLKEREYNNY 651

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S   +VA  +G+VE +D +      +    D        Y                    
Sbjct: 652  SWQDLVA--SGVVEYIDTLEEETVMLAMTPDDLQEKEVAY-------------------- 689

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           PS  LG       +  + +P+  +N          M  + +   +
Sbjct: 690  -----CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--V 735

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +I  F                           ++    +  V        +    +    
Sbjct: 736  YITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSMEYLR 768

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +      + AI      +  D+ +   S V        +F R   ++  +    + E
Sbjct: 769  FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGFDQEE 827

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   R+          +       I  G           K+  L              
Sbjct: 828  VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL-------------- 873

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                   + +  +E    +Y         R        Q    +     +  K+ V   R
Sbjct: 874  ------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVR 927

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E   G
Sbjct: 928  IPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG 987

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G+                                                    
Sbjct: 988  KVSANKGEIGD------------------------------------------------- 998

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +L HM
Sbjct: 999  ----ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHM 1054

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-- 1320
            V DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   SD  
Sbjct: 1055 VDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPY 1114

Query: 1321 --DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               V            RT  YE    G            P +  +L +E+ ++ ++  + 
Sbjct: 1115 QVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172

Query: 1365 N 1365
            +
Sbjct: 1173 S 1173



 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 138/1004 (13%), Positives = 288/1004 (28%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV---------------- 204
            ++ F     + + +G+    CR        ++        I V                
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGEAGSHAI 253

Query: 205 --RIDR-----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
             RI       +++VP+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 254 GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 313

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              V+ + +     +  +   K++     + L+++ +  +G++  C          +   
Sbjct: 314 EQNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH- 371

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              + + A    +    +   +  +    P+L          +   +     K       
Sbjct: 372 --RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKD 429

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
               +     + +  +  S+    + D  K   +  G  ++  RL   +      R    
Sbjct: 430 FNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSP 489

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 +     L N    +                ++KN   +  + +       +  +
Sbjct: 490 IGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFL 546

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S+   + I+   +  A   F     +   ++    ++ +   RR   +         
Sbjct: 547 EEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVSMIRD 606

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|189197211|ref|XP_001934943.1| DNA-directed RNA polymerase II subunit RPB2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
 gi|187980891|gb|EDU47517.1| DNA-directed RNA polymerase II subunit RPB2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
          Length = 1208

 Score =  395 bits (1016), Expect = e-107,   Method: Composition-based stats.
 Identities = 156/933 (16%), Positives = 306/933 (32%), Gaps = 152/933 (16%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 388  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKD 447

Query: 486  IKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            + +  +    +      Q  + A  + + +     +               +SQ+     
Sbjct: 448  VYKYLQRCVENNQDFNVQMAVKASTITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 507

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 508  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 563

Query: 591  RVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +     + +    ++      +  +      +V   
Sbjct: 564  YVSVGSDATPIVDFMTQRNMQLLEEYDQNQSPDATKVFVNGVWVGVHSNAQQLVTVVQEL 623

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLK 705
                 +      I D  D   K        + P    ++  R     ++   ++    LK
Sbjct: 624  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENDVRKPNRNHLIFTKEISNKLK 683

Query: 706  AEAPFVGTGM---ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            +E           E  V +++       + G+VE +DA       +    +      ++ 
Sbjct: 684  SEQMEANQRQGWSEEEVEQATYGWRGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMK 743

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGD-EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              +     +       R L  + D  +         P+  LG       +  + +P+  +
Sbjct: 744  MGLPMTDHSLEGSQRLRRLKPLPDPRIHSYTHCEIHPAMILG-------ICASIIPFPDH 796

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +  ++      +                                
Sbjct: 797  NQSPRNTYQSAMGKQAMGVALTNFALRMETMMN--------------------------- 829

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 830  --VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLF- 886

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 887  RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGD 943

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      ++           ++     +  Q                 
Sbjct: 944  DIIIGKTAPIATDAAELGQKTTLHTKRDVSTPLRSTENGIVDQ----------------- 986

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 987  ---VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLTP 1043

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G++                           
Sbjct: 1044 DLIINPHAIPSRMTIAHLVECLLSKVGAITGQEGD------------------------- 1078

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + ++ +L  A   + G  I+Y+
Sbjct: 1079 ----------------------------ATP-FTDVTVDQVSQLLENAGYQKRGFEIMYN 1109

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG+     + +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME
Sbjct: 1110 GHTGKKMRTQIFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRFGEME 1169

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD-------DVVG 1324
              C+ A+GAA  L+E L   SD       D+ G
Sbjct: 1170 RDCMIAHGAAAFLKERLFTVSDAYTVHVCDICG 1202



 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 143/1041 (13%), Positives = 280/1041 (26%), Gaps = 221/1041 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF----------KSVFPITAFSGAAMLEFVS 78
           L+  Q  SYD F   N   D     G  +            +   PI        ++F  
Sbjct: 40  LVSQQLDSYDEF-TRNTIQDIVKENG--SVILEQNQPYNPDEEDNPI--IKRRYEMKFGR 94

Query: 79  YEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVF----------DVDEFTG 118
                P               +   R+LTY+  +   +   V           D DE   
Sbjct: 95  VYLARPTHTEGDGTTVQLYPHEARLRNLTYSGAMLADIENRVMVAREGRDPDADDDEEME 154

Query: 119 AKSIK---DIKEQS------------IYMGDLPLMTKD---------------------- 141
                    I+ +             +++G LP+M +                       
Sbjct: 155 GGYTGGQNQIRWERENMSSDDGAAARVFIGKLPVMLRSELCHLRAQSDADLFALNECPYD 214

Query: 142 --GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFD 197
             G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F+
Sbjct: 215 QGGYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFN 270

Query: 198 SK---DII-----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKI 236
            K   + +                 +++ D    VP+     ALG+   EEILS      
Sbjct: 271 IKWAENSLAGPGKRIPGPFAYATLPYIKAD----VPMAIVFRALGIVSDEEILSHIVFDR 326

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
             +Q  +     +    ++   + +   +            +   +  +  ++ + +  +
Sbjct: 327 NDTQTLELLKPSIEEGSVVQDRETALDFIAKRGANSGTRDRRLKFARDI--MQREFLPHI 384

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
                           +     +  +   D  D            + + +          
Sbjct: 385 SQKEGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDH------FGKKRLDL-------AGP 431

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            I N       K  KD    + R +       F+V  ++      +  KY L   G    
Sbjct: 432 LIANLFRILFLKLTKDVYKYLQRCVENNQ--DFNVQMAVKASTITNGLKYSL-ATGNWGD 488

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEML 471
             +         + + +    + +  L        R+GK       +  +  +    E  
Sbjct: 489 QKKAASAKAGVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETP 548

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE--------FFCSSQLS 523
           + Q    +  +       + S     V      N + +              F     + 
Sbjct: 549 EGQACGLVKNLSLMCYVSVGSDATPIVDFMTQRNMQLLEEYDQNQSPDATKVFVNGVWVG 608

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   ++ +   RR   L  +  + R     E + +       + P    E      
Sbjct: 609 VHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVVENDVRKP 667

Query: 583 VSSLTSFAR-VNAYGFIETPYRKVCDGKVTNDVV----------------YLSAMEEENR 625
             +   F + ++     E        G    +V                 YL A EEE  
Sbjct: 668 NRNHLIFTKEISNKLKSEQMEANQRQGWSEEEVEQATYGWRGLIQDGVVEYLDAEEEETA 727

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            I  +   L+E       L     + E                                 
Sbjct: 728 MITFSPEDLEEWREMKMGLPMTDHSLE--------------------------------- 754

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                  G    R+  PL         T  E   A   G       A I+   D  +   
Sbjct: 755 -------GSQRLRRLKPLPDPRIH-SYTHCEIHPAMILGIC-----ASIIPFPDHNQSPR 801

Query: 746 RSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            + +  +     GV      ++ +         Q+PL                      +
Sbjct: 802 NTYQSAMGKQAMGVALTNFALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRE 851

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
           L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 852 LPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEK 911

Query: 864 ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               D   +       +D+ G++  G  V+  DI++GK  P      T   +L +     
Sbjct: 912 PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIA----TDAAELGQKTTLH 967

Query: 920 KAVDVRDTSLRVPSGVSGTVV 940
              DV        +G+   V+
Sbjct: 968 TKRDVSTPLRSTENGIVDQVL 988


>gi|60393870|sp|Q85FM7|RPOB_ADICA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|48995173|gb|AAP29384.3| RNA polymerase beta chain [Adiantum capillus-veneris]
          Length = 1071

 Score =  395 bits (1016), Expect = e-107,   Method: Composition-based stats.
 Identities = 141/465 (30%), Positives = 216/465 (46%), Gaps = 58/465 (12%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIELLARDK-----DDEQVIL 978
            ++  +           D  + +   I ++  + + +E+ ++E+ A ++       +   L
Sbjct: 654  KNILVAYMPWEGYNFEDAVLISERLIYEDIFTSLHIEKHEVEICATNQGPERVTKQISQL 713

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            D  +   L +   +  G    +G     K T       S  P  +  Q           +
Sbjct: 714  DGYLLRHLDDDGLVELGSWVEAGDVLVGKLTPQEGASSSRVPEGRLLQAIFG-----IQL 768

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             + +            R  +        D      L V+ +++  +R IQ GDK+AGRHG
Sbjct: 769  VNARESCLRVPIGGRGRVIDVRWVYPEDDATND--LEVIHIYILQRRKIQVGDKIAGRHG 826

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGIVS+I+P +DMP+L++GTPVD++L+PLGVPSRMNVGQIFE  LG A   L    + +
Sbjct: 827  NKGIVSKIVPRQDMPYLQNGTPVDMILSPLGVPSRMNVGQIFECLLGLAGEFLETHYRVV 886

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D +   + S    F E                                          
Sbjct: 887  PFDERYEREASRKLVFAELHEAGARTNNPW------------------------------ 916

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                     + +    G+S L DG TG+PF + +T G  Y++KL H V DK++ARS+G Y
Sbjct: 917  ---------LFEPSHPGKSRLIDGRTGDPFGQSITTGKAYIMKLIHQVDDKIHARSSGPY 967

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            +LVTQQPL GKS RGGQR+GEMEVW ++ +G +Y LQEMLT KSD +  R +   +I+ G
Sbjct: 968  ALVTQQPLKGKSRRGGQRIGEMEVWALEGFGVSYTLQEMLTTKSDHIQARYKALSAIMTG 1027

Query: 1336 NDTFET-GTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
                +    PESF +LV+E++ +GL+  LE +         E  +
Sbjct: 1028 KPVCKPKTVPESFRLLVRELRCMGLN--LERNFISEEDLGREFEN 1070



 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 248/660 (37%), Positives = 382/660 (57%), Gaps = 11/660 (1%)

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              I++             +    +    IL                 +  +  +DA+++
Sbjct: 157 RNRIWVRISKKKKISIFILLVAMGLCKRDILQNSRYPRIFSNMFKRQKESIESPEDAIVE 216

Query: 377 IYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           +Y+ +     +    +ES+F      F   + +L  +GR  +N++L LD P+    +  +
Sbjct: 217 LYKHLYSATDADVFFSESIFRELQKRFFQHRCELGRIGRRNLNIKLTLDVPETESFLLPQ 276

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-- 492
           DI+A    LV++  G+G +DDID+L NRRVRSV ++L+ Q +L L R+E  I++ +S   
Sbjct: 277 DILAAADHLVEISYGEGKLDDIDHLKNRRVRSVADLLQEQLKLALNRLENLIRQNLSRAV 336

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
               ++ P+ L+   PV++A  EFF S  LSQ  +  N LS + H RRLS++G GG+ R 
Sbjct: 337 RRKRAITPRGLVTPVPVIAAFKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRR 396

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            A  + RD+H +HYGRICP ETSEG N GL+SSL   A VN  G + +PY ++ D     
Sbjct: 397 TASFQARDIHFSHYGRICPIETSEGMNAGLISSLAIQAGVNTSGSLGSPYLEMSDSSGEE 456

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V LS  E++   +A  N  L E     +E++  R   E + V  E++DF    P    
Sbjct: 457 QLVNLSPAEDDYYRVASENLLLSEWRGSEKEIIPVRYQQEFLSVLWEQVDFRSIHPLHHF 516

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           SI ASLIPF+E++D+NR LMG  MQRQAVPL+K E   VGTG+ES VA  SG+  ++++ 
Sbjct: 517 SIGASLIPFIEHNDANRALMGSTMQRQAVPLIKPERCIVGTGLESQVALDSGSVAISEQD 576

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVGDEVRRN 791
           G V  +D  RI +  +        +       +K F+RSN NTC++Q+P V +G+ +R  
Sbjct: 577 GKVCYIDGNRIELSLIHEAKKNKLAQPTTIEELKIFERSNNNTCMHQKPAVSLGELLRGG 636

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER++ ED+FTS+HIE+ EV  
Sbjct: 637 EIVADGAATVRGELALGKNILVAYMPWEGYNFEDAVLISERLIYEDIFTSLHIEKHEVEI 696

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PE 909
             T  GPE +T+ I  +    L+++D+ G++ +G+ V  GD+LVGK+TP+  +  +  PE
Sbjct: 697 CATNQGPERVTKQISQLDGYLLRHLDDDGLVELGSWVEAGDVLVGKLTPQEGASSSRVPE 756

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +LL+AIFG + V+ R++ LRVP G  G V+DV    R    +++ +  +E   I +L R
Sbjct: 757 GRLLQAIFGIQLVNARESCLRVPIGGRGRVIDV----RWVYPEDDATNDLEVIHIYILQR 812



 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/283 (25%), Positives = 130/283 (45%), Gaps = 34/283 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVS----YE 80
           +P+L ++Q   +  F+   +         L+      FP I        +EF S    Y+
Sbjct: 4   LPELAQIQFKGFSRFVHQKL---------LKEL--ENFPKIEDTDK--EVEFRSIGNQYQ 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P  +  D  ++ +TY+  L +  +LI          K  + ++E+ + +G +P M  
Sbjct: 51  LTEPSLEERDAAYQCITYSADLYVPAQLIC---------KEDQIVQEEDVRLGSIPWMNS 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I GI R++VSQ+ RSPGI+++ +       G L Y   +I DQG    +E D ++
Sbjct: 102 GGTFIINGIARVLVSQILRSPGIYYNRESD---QRGILAYTSTVISDQGGRFKLEIDGRN 158

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIV---YSQRGDFWCFPLSAADLMV 256
            I VRI +++K+ +   L+A+G+   +IL ++ YP+I    + ++ +    P  A   + 
Sbjct: 159 RIWVRISKKKKISIFILLVAMGLCKRDILQNSRYPRIFSNMFKRQKESIESPEDAIVELY 218

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
               S++  D+   E +    +K        L   G + L I 
Sbjct: 219 KHLYSATDADVFFSESIFRELQKRFFQHRCELGRIGRRNLNIK 261


>gi|73975079|ref|XP_861018.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            16 [Canis familiaris]
          Length = 1173

 Score =  395 bits (1016), Expect = e-107,   Method: Composition-based stats.
 Identities = 177/1081 (16%), Positives = 331/1081 (30%), Gaps = 194/1081 (17%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              + +  + N        E     IA A + +  +G +             +   R +  
Sbjct: 543  EFLEEWSMENL------EEISPAAIADA-TKIFVNGCWVGIHKDPEQLMNTLRKLRRQ-- 593

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +D  P   +             D+ R+     +  +   LL  +   +    E      
Sbjct: 594  -MDIIPDVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLL--KKRHIDQLKEREYNNY 650

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            S   +VA  +G+VE +D +      +    D        Y                    
Sbjct: 651  SWQDLVA--SGVVEYIDTLEEETVMLAMTPDDLQEKEVAY-------------------- 688

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           PS  LG       +  + +P+  +N          M  + +   +
Sbjct: 689  -----CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--V 734

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +I  F                           ++    +  V        +    +    
Sbjct: 735  YITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSMEYLR 767

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +      + AI      +  D+ +   S V        +F R   ++  +    + E
Sbjct: 768  FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGFDQEE 826

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   R+          +       I  G           K+  L              
Sbjct: 827  VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL-------------- 872

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                   + +  +E    +Y         R        Q    +     +  K+ V   R
Sbjct: 873  ------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVR 926

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E   G
Sbjct: 927  IPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG 986

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G+                                                    
Sbjct: 987  KVSANKGEIGD------------------------------------------------- 997

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +L HM
Sbjct: 998  ----ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHM 1053

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-- 1320
            V DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   SD  
Sbjct: 1054 VDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPY 1113

Query: 1321 --DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               V            RT  YE    G            P +  +L +E+ ++ ++  + 
Sbjct: 1114 QVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1171

Query: 1365 N 1365
            +
Sbjct: 1172 S 1172



 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 138/1003 (13%), Positives = 287/1003 (28%), Gaps = 204/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +          
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVSMIRDI 606

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
                 ++        P    E   + L         ++     E       D   +  V
Sbjct: 607 REREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVV 661

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            Y+  +EEE   +A     L E                  +         +  P  ++ +
Sbjct: 662 EYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILGV 705

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                               
Sbjct: 706 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------ 741

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                               + + V  Y               Q+PLV            
Sbjct: 742 -----------------RMDTLAHVLYYP--------------QKPLV----------TT 760

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  G N +VA   + GYN EDS++++   V    F S+    ++      
Sbjct: 761 RSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 820

Query: 855 KLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               EE+           +       +D+ G+I  G  V+  D+++GK     E+    E
Sbjct: 821 GFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELE 880

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                     +    RD S  + +  +G V  V +       K
Sbjct: 881 GT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 916


>gi|16488|emb|CAA79527.1| RNA polymerase II second largest subunit [Arabidopsis thaliana]
          Length = 1188

 Score =  395 bits (1016), Expect = e-107,   Method: Composition-based stats.
 Identities = 187/1044 (17%), Positives = 334/1044 (31%), Gaps = 198/1044 (18%)

Query: 369  DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM---------NMR 419
                A   +  ++RP     F +   +    +       +      ++          M 
Sbjct: 294  CYDFADTQMMELLRPSLEEAFVIQNQLVALDYIGKRGATVGVTKEKRIKYARDILQKEML 353

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
            L +   +     +      II  L+    G+   DD D+ GN+R+   G +L   +R+  
Sbjct: 354  LYVGIGEHCETKKAYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLF 413

Query: 480  LRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQL 525
             ++ R ++  +     +   V  Q  I AK + S +     +              +SQ+
Sbjct: 414  RKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQV 473

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   S ++H RRL++     + R     + R +H + +G +CPAET EG   GLV +
Sbjct: 474  LNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKN 529

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L     +            + +    N        EE +  +    + +  +G +     
Sbjct: 530  LALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPSVIPQATKIFVNGMWVG--- 579

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R     +   R     +D + +  V     L       D  R      +      L+K
Sbjct: 580  VHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVDNQKLLIK 639

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                     + ++  + S     A+  G    V   +  I  ++ + + +T        +
Sbjct: 640  KRD------IYALQQRES-----AEEDGWHHLV--AKGFIEYIDTEEEETTMISMTISDL 686

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
               R                            PS  LG       +  + +P+  +N   
Sbjct: 687  VQARLRPEEAYT-----------ENYTHCEIHPSLILG-------VCASIIPFPDHNQSP 728

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                   M  + +     I       R   L         P V+   ++++         
Sbjct: 729  RNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL--------- 775

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                                +        AI      +  D+ +   S +        +F
Sbjct: 776  ----------------HFRQLPAGINANVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLF 818

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R   D+ ++  ++ +E      R           +          G           K+
Sbjct: 819  FRSYRDEEKKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKT 878

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T +S                  DE   ++    +  +  S    E    +++      D 
Sbjct: 879  TPISQ-----------------DEAQGQSSRYTRRDHSISLRHSETGMVDQVLLTTNADG 921

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 922  L-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGVTPDIIVNPH 976

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 977  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 1004

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 1005 ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 1042

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 1043 TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 1102

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------NDTFETG------------TPE 1345
            GAA+ L+E L  +SD    R  V E  V G         ++FE               P 
Sbjct: 1103 GAAHFLKERLFDQSD--AYRVHVCE--VCGLIAIANLKKNSFECRGCKNKTDIVQVYIPY 1158

Query: 1346 SFNVLVKEMQALGLSIDLENSRTK 1369
            +  +L +E+ ++ ++  +     K
Sbjct: 1159 ACKLLFQELMSMAIAPRMLTKHLK 1182



 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 143/993 (14%), Positives = 285/993 (28%), Gaps = 203/993 (20%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 39  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 89

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 90  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 149

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 150 FTK--VFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 207

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR----------- 208
              ++      +     K  Y   +        + +      + VR+             
Sbjct: 208 TNHVY----VFKKRQPNKYAYVGEVR----SMAENQNRPPSTMFVRMLARASAKGGSSGQ 259

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 260 YIRCTLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQ 319

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
            V+   +        +   K++         + L   G+     T       Y+   ++ 
Sbjct: 320 LVALDYIGKRGATVGVTKEKRIKYARDILQKEMLLYVGIGEHCETKKAYYFGYIIHRLLL 379

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDA 373
              G    +  D    K L+           +L+   + +  +Y++  +   K  + + A
Sbjct: 380 CALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQFA 439

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-R 432
           +             T  +  S+    +  ++           +N      T   +R +  
Sbjct: 440 I--------KAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS 491

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N +  +         +      ++KN   +  + +  +    +  
Sbjct: 492 PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEF 548

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVAR 551
           ++       + I+   +  A   F     +    +    +  +   RR   +  + GV R
Sbjct: 549 LEEWGTENFEEISPSVIPQATKIFVNGMWVGVHRDPDMLVKTLRRLRRRVDVNTEVGVVR 608

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                E+R    T YGR         +   L+     +A        E            
Sbjct: 609 DIRLKELR--IYTDYGRCSRPLFIVDNQKLLIKKRDIYALQQRESAEEDG---WHHLVAK 663

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+              +LV  R   EE     E     +  P  +
Sbjct: 664 GFIEYIDTEEEETTMISM----------TISDLVQARLRPEEAYT--ENYTHCEIHPSLI 711

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +      F                    R
Sbjct: 712 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------R 751

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 752 MDTLAYV-----------------------------------LYYPQKPLV--------- 767

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N  VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 768 -TTRAMEHLHFRQLPAGINANVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 826

Query: 852 RDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E            +       +D+ G+   G  V+  D+++GK TP  +   
Sbjct: 827 KKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE- 885

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   A         RD S+ +    +G V
Sbjct: 886 --------AQGQSSRYTRRDHSISLRHSETGMV 910


>gi|121720605|ref|YP_001001526.1| RNA polymerase beta subunit [Nuphar advena]
 gi|69216918|gb|AAZ03993.1| RNA polymerase beta chain [Nuphar advena]
 gi|84682196|gb|ABC60450.1| RNA polymerase beta subunit [Nuphar advena]
          Length = 1071

 Score =  395 bits (1015), Expect = e-107,   Method: Composition-based stats.
 Identities = 138/396 (34%), Positives = 207/396 (52%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 721  LDRNGIVMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 780

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 781  GGRGRVIDVRWGQKRG----GSIYNP---EMIRVYISQKRKIKVGDKVAGRHGNKGIISK 833

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQ+FE  LG A   LG+  +    D +  
Sbjct: 834  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQMFECSLGLAGDLLGRHYRITPFDERYE 893

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 894  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 919

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YMLKL H V DK++ RS+G Y+LVTQQP
Sbjct: 920  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMLKLIHQVDDKIHGRSSGHYALVTQQP 974

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 975  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPE 1034

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 GAPESFRLLVRELRSLSLELNHFLVSEKNFQINRKE 1070



 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 229/662 (34%), Positives = 368/662 (55%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +  E          + S+  +  +    +  +  +     
Sbjct: 144 ISVYTGTIISDWGGRSELEIDRKERIWARVSRKQKISILVLPSAMGSSLREILDNVCYPE 203

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 204 IFLSFPNEKEKKKIGSKENAILEFYQKFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 262

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 263 GRRNMNQRLNLDIPQNNTFLLPRDVLAAADHLIGIKFGMGTLDDMNHLKNKRIRSVADLL 322

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LSQ+ +  
Sbjct: 323 QDQFGLALVRLENVVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 383 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARV  +G IETP+ ++ +      +VYLS   +E   +A  NS     G   EE+   R 
Sbjct: 443 ARVGDWGSIETPFYEISERSKEEQMVYLSPSRDEYYMVAAGNSLALNRGIQEEEVGPARY 502

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I   +  P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503 RQEFLTIAWEQIHLRNIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 562

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+R G +   DA +I++                  L+ +QR
Sbjct: 563 IVGTGLERQAALDSGGSAIAEREGKIIYTDAEKIILSGN--------GDTISIPLVMYQR 614

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q+P V  G  +++  I+ADG +T  G+LALG+N+ VA+MPW GYN ED++L+
Sbjct: 615 SNKNTWMHQKPQVHRGKYLKKGQILADGAATVGGELALGKNVSVAYMPWEGYNSEDAVLV 674

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V 
Sbjct: 675 SERLVYDDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEPYLLRNLDRNGIVMLGSWVE 734

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 735 TGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWGQK 794

Query: 948 HG 949
            G
Sbjct: 795 RG 796



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 106/233 (45%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     SY+ 
Sbjct: 13  IPGFSQIQFEGFCRFI----------DQGLMEELHQFPKIEDTDQ--EIEFKLFGESYQL 60

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  +TY+  L +   LI          ++ ++++EQ++ +G++PLM   
Sbjct: 61  VEPLIKERDAVYESITYSSELYVPAGLIW---------RTGRNMQEQTVLLGNIPLMNSS 111

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++        +S   +Y   II D G   ++E D K+ 
Sbjct: 112 GTSIVNGIYRIVINQILQSPGIYYGTGLDHNGIS---VYTGTIISDWGGRSELEIDRKER 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G    EIL    YP+I  S   +     + + +
Sbjct: 169 IWARVSRKQKISILVLPSAMGSSLREILDNVCYPEIFLSFPNEKEKKKIGSKE 221


>gi|297799890|ref|XP_002867829.1| hypothetical protein ARALYDRAFT_492703 [Arabidopsis lyrata subsp.
            lyrata]
 gi|297313665|gb|EFH44088.1| hypothetical protein ARALYDRAFT_492703 [Arabidopsis lyrata subsp.
            lyrata]
          Length = 1188

 Score =  395 bits (1015), Expect = e-107,   Method: Composition-based stats.
 Identities = 184/1056 (17%), Positives = 338/1056 (32%), Gaps = 195/1056 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   +++    +       +          KY 
Sbjct: 288  DILEHICYDFADTQMMELLRPSLEEAFVIQNQLVA---LDYIGKRGATVGVTKEKRIKYA 344

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 345  KDILQKEMLPHVGIGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 401

Query: 468  GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++  +     +   V  Q  I AK + S +     +      
Sbjct: 402  GPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQA 461

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H + +G +CPAE
Sbjct: 462  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAE 517

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 518  TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPSVIPQATK 570

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +       R     +   R     +D + +  V     L       D  R    
Sbjct: 571  IFVNGMWVG---VHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRP 627

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +      L+K         + ++  + S     A+  G    V   +  I  ++ + +
Sbjct: 628  LFIVDNQRLLIKKRD------IYALQQRES-----AEEDGWHHLV--AKGFIEYIDTEEE 674

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R                            PS  LG       +  
Sbjct: 675  ETTMISMTISDLVQARLRPEEAYT-----------ENYTHCEIHPSLILG-------VCA 716

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +     I       R   L         P V+   +
Sbjct: 717  SIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 772

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +++                             +      + AI      +  D+ +   S
Sbjct: 773  EHL-------------------------HFRQLPAGINAIVAISCYSGYNQEDSVIMNQS 807

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R           +          G 
Sbjct: 808  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGT 866

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S                  DE   ++    +  +  S    E   
Sbjct: 867  RVSGEDVIIGKTTPISQ-----------------DEAQGQSSRYTRRDHSISLRHSETGM 909

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 910  VDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTI 964

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 965  EGVTPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 1004

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 1005 ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 1030

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG P    + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 1031 ERMYNGHTGRPLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1090

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------NDTFETG--- 1342
             GEME  C+ A+GAA+ L+E L  +SD    R  V E  V G         ++FE     
Sbjct: 1091 FGEMERDCMIAHGAAHFLKERLFDQSD--AYRVHVCE--VCGLIAIANLKKNSFECRGCK 1146

Query: 1343 ---------TPESFNVLVKEMQALGLSIDLENSRTK 1369
                      P +  +L +E+ ++ ++  +     K
Sbjct: 1147 NKTDIVQVYIPYACKLLFQELMSMAIAPRMLTKHLK 1182



 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 138/989 (13%), Positives = 278/989 (28%), Gaps = 195/989 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 39  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 89

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 90  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 149

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 150 FTK--VFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 207

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR----------- 208
              ++      +     K  Y   +        + +      + VR+             
Sbjct: 208 TNHVY----VFKKRQPNKYAYVGEVR----SMAENQNRPPSTMFVRMLARASAKGGSSGQ 259

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 260 YIRCTLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQ 319

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
            V+   +        +   K++     K + +K +       +                 
Sbjct: 320 LVALDYIGKRGATVGVTKEKRI--KYAKDILQKEMLPHVGIGEYCETKKAYYFGYIIHR- 376

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   + +   K   +     
Sbjct: 377 -LLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKEVN 435

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 436 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 495

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +      ++KN   +  + +  +    +  ++  
Sbjct: 496 EGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEW 552

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
                + I+   +  A   F     +    +    +  +   RR   +  + GV R    
Sbjct: 553 GTENFEEISPSVIPQATKIFVNGMWVGVHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRL 612

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+R    T YGR         +   L+     +A        E              + 
Sbjct: 613 KELR--IYTDYGRCSRPLFIVDNQRLLIKKRDIYALQQRESAEEDG---WHHLVAKGFIE 667

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE   I+              +LV  R   EE     E     +  P  ++ + 
Sbjct: 668 YIDTEEEETTMISM----------TISDLVQARLRPEEAYT--ENYTHCEIHPSLILGVC 715

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +      F                    R   +
Sbjct: 716 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------RMDTL 755

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             V                                       Q+PLV             
Sbjct: 756 AYV-----------------------------------LYYPQKPLV----------TTR 770

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    L  G N +VA   + GYN EDS+++++  +    F S+    +    +   
Sbjct: 771 AMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 830

Query: 856 LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +E            +       +D+ G+   G  V+  D+++GK TP  +       
Sbjct: 831 TLVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE----- 885

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               A         RD S+ +    +G V
Sbjct: 886 ----AQGQSSRYTRRDHSISLRHSETGMV 910


>gi|215254211|gb|ACJ64110.1| RNA polymerase beta subunit [Vibrio ponticus]
          Length = 396

 Score =  395 bits (1014), Expect = e-107,   Method: Composition-based stats.
 Identities = 256/396 (64%), Positives = 310/396 (78%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L EDG+F EEL+  R
Sbjct: 61  FARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANTVLTEDGTFAEELITAR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ 
Sbjct: 121 QKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADK 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ 
Sbjct: 181 PLVGTGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYT 240

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L
Sbjct: 241 RSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSIL 300

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV
Sbjct: 301 VSERVVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEV 360

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV
Sbjct: 361 KGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDV 396


>gi|156598158|gb|ABU85343.1| RNA polymerase beta subunit [Elaeis oleifera]
          Length = 1067

 Score =  395 bits (1014), Expect = e-107,   Method: Composition-based stats.
 Identities = 162/579 (27%), Positives = 255/579 (44%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   + +        I         +  G  
Sbjct: 541  MSSNMQRQAVPLSRSEKCIVGTGLERQTALDSGVSAIAEHEGKIIYTDPHKIILSSNGDT 600

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 601  ISIPLVMYQRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVG-GELALGKNILVAYMPW 659

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +  L 
Sbjct: 660  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLL 714

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  R   ++ G    +G     K T  +++  S  P  +  +  +  +       SLK
Sbjct: 715  RNL-DRNGIVMLGSWVETGDILVGKLTPQTANESSYSPEDRLLRVILGIQVSTAKETSLK 773

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 774  LPIGGRGRVIDVRWIQKK----GGSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGI 826

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L K  +    D 
Sbjct: 827  ISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKKHYRIAPFDE 886

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E                                    VF+       
Sbjct: 887  RYEQEASRKLVFSELYEACKQTKNPW------------------------VFE------- 915

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 916  --------PEYPGKSRIFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVT 967

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 968  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIVGGTVP 1027

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1028 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1066



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/691 (34%), Positives = 380/691 (54%), Gaps = 20/691 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E     + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 135 ELDNNGISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLRKILD 194

Query: 350 DSVNNNAYIRNTLVTDKNK-DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKY 406
           +      ++       K    +++A+L+ Y+      GD              FF   + 
Sbjct: 195 NVCYPEIFLSFPNDKRKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRC 253

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
           +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RS
Sbjct: 254 ELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRS 313

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQ 524
           V ++L++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ
Sbjct: 314 VADLLQDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQ 373

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           + +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ 
Sbjct: 374 VLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIG 433

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL    R+  +G IE+P+ ++        VVYLS   +E   +A  NS     G   E++
Sbjct: 434 SLAIHVRIGHWGSIESPFYEISQRSKEAQVVYLSPNRDEYYMVAAGNSLALNRGIQEEQV 493

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL 
Sbjct: 494 VPARYRQEFLTIAWEQIHLRSFFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLS 553

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           ++E   VGTG+E   A  SG + +A+  G +   D  +I++ S                L
Sbjct: 554 RSEKCIVGTGLERQTALDSGVSAIAEHEGKIIYTDPHKIILSSN--------GDTISIPL 605

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           + +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN E
Sbjct: 606 VMYQRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVGGELALGKNILVAYMPWEGYNSE 665

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++LISER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ +
Sbjct: 666 DAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLLRNLDRNGIVML 725

Query: 885 GAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           G+ V  GDILVGK+TP+   ES  +PE++LLR I G +    ++TSL++P G  G V+DV
Sbjct: 726 GSWVETGDILVGKLTPQTANESSYSPEDRLLRVILGIQVSTAKETSLKLPIGGRGRVIDV 785

Query: 943 RIFNRHGIDKNE----RSISVEREQIELLAR 969
           R   + G         R    ++ +I++  +
Sbjct: 786 RWIQKKGGSSYNPEMIRVYISQKREIKVGDK 816



 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 75/335 (22%), Positives = 136/335 (40%), Gaps = 34/335 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS-YEFDPP 84
           IP   ++Q   +  F+          N+GL   F     I        L FV  Y+   P
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLTEEFHKFPKIEDQEIEFKL-FVETYKLVEP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
                D ++  LTY+  L +   LI          K+ +D+++Q++++G++PLM   GTF
Sbjct: 61  LIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQKQTVFIGNIPLMNSLGTF 111

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  I  
Sbjct: 112 IVNGIYRIVINQILQSPGIYYRSELD---NNGISVYTSTIISDWGGRSELEIDRKARIWA 168

Query: 205 RIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           R+ R++K+ +     A+G +  +IL    YP+I  S   D      S  + ++      +
Sbjct: 169 RVSRKQKISILVLSSAMGSNLRKILDNVCYPEIFLSFPNDKRKKIGSKENAILEFYQQFA 228

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            V  D      ES  K         + +  +      +    L + ++       ++   
Sbjct: 229 CVGGDP--VFSESLCKELQKKFFQQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAA 286

Query: 324 AGD-------VIDEKSLEEIFHSEIRDIPILYVDS 351
           A         +     +  + +  IR +  L  D 
Sbjct: 287 ADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 321


>gi|156372267|ref|XP_001628960.1| predicted protein [Nematostella vectensis]
 gi|156215949|gb|EDO36897.1| predicted protein [Nematostella vectensis]
          Length = 1182

 Score =  395 bits (1014), Expect = e-107,   Method: Composition-based stats.
 Identities = 174/1085 (16%), Positives = 332/1085 (30%), Gaps = 203/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  + +   I ++    I    +  +    +       +    ++        +A +  
Sbjct: 257  GQRIVGSLPYIKQEIPIMIVFRALGFVADRDILEHIIYDFEDQEMMEMVKPSLDEAFVIQ 316

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 317  EQNVALNFIGSRGARPGV---TKERRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 370

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 371  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFRNLMKEVRMYAQKFIDRG 430

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  +  K +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 431  KDFNIELALKPKVITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 490

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H TH+G ICPAET EGH +GLV +L   A ++         
Sbjct: 491  S----PIGREGKLAKPRQLHNTHWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 546

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  ++            N          ++L+      R   + I+   
Sbjct: 547  EFMEEW-TMENLEEITPSAINTSTKIFVNGCWVGIHRDPDQLMSTLRKLRRRMDIIVSEV 605

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              +        ++ S A  +   L   ++ ++L+  N   Q                E  
Sbjct: 606  SMVRDFREREIRIYSDAGRICRPLLIVENQKLLLKKNHIDQLK--------------ERE 651

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
              + S   +VA        V+    V+ ++  D                           
Sbjct: 652  YNEYSWQELVANGIVEYIDVNEEETVMVAMTPDE-------------------------- 685

Query: 779  RPLVKVGD-EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
              LV+ G             PS  LG       +  + +P+  +N          M  + 
Sbjct: 686  --LVEKGQAYCSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQA 736

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +   ++I  +                           ++    +  V        +    
Sbjct: 737  MG--VYITNY---------------------------HVRMDTLAHVLYYPQKPLVTTRS 767

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +      + AI      +  D S+ + +      +   +F R   D+  +  
Sbjct: 768  MEYLRFRELPAGINAIVAIASYTGYNQED-SVIMNASAIDRGLYRSVFYRSYRDQESKKG 826

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
              + E  E   RD          +       I  G           K+  L         
Sbjct: 827  LDQEETFEKPTRDAVQGMRNASYDKLDEDGLIAPGIRVSGDDVIVGKTVTL--------- 877

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                             +E    +Y    +    R        Q    +     +  K+ 
Sbjct: 878  -----------PDNDDELEGTARKYSKKDASTFLRPSETGIVDQVMVTINQEGFKFTKIK 926

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK A RHG KG        EDMPF  +G   D+++NP  +PSRM +G + 
Sbjct: 927  VRSVRVPQIGDKFASRHGQKGTCGITYRQEDMPFTCEGLSPDVIINPHAIPSRMTIGHLI 986

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E   G      G+                                               
Sbjct: 987  ECLQGKVSANKGEIGD-------------------------------------------- 1002

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                     +TP  D  + + I+ +L        G  +LY G TG   +  V +G  Y  
Sbjct: 1003 ---------ATPFNDAVNVQKISQLLNDYGYHLRGNEVLYSGFTGRKLNTQVFLGPTYYQ 1053

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            +L HMV DK+++R+ G   ++T+QP+ G+S  GG R GEME  C+ A+G+A  L E L  
Sbjct: 1054 RLKHMVDDKIHSRARGPLQILTRQPMEGRSRDGGLRFGEMERDCMIAHGSAQFLNERLFE 1113

Query: 1318 KSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGL 1359
             SD     V            R   +E    G            P +  +L +E+ ++ +
Sbjct: 1114 VSDPYSCHVCNLCGLIAIANLRNNTFEC--RGCKNKTQVSRIRMPYAAKLLFQELMSMSI 1171

Query: 1360 SIDLE 1364
            +  + 
Sbjct: 1172 APRMM 1176



 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 144/999 (14%), Positives = 297/999 (29%), Gaps = 195/999 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  + +   T      +L+F       P  
Sbjct: 43  LVRQQLDSFDEFIQMSVQRIVEDSPEIDLQAESQHMTSDTEIPARFVLKFEQIYLSKPTH 102

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ P  + +       +E     +   +     ++G +P
Sbjct: 103 WEKDGAPSPMMPNEARLRNLTYSAPFYVDITKTRIKDNEEPQVTTHSKM-----FIGKIP 157

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 158 IMLRSTYCLLNGLLDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSKKDS 217

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-----------------RI-----DRR 209
                K  Y   I       ++        + V                 RI       +
Sbjct: 218 -----KYSYTAEIR----SCLEHSSRPTSTMWVSMLAKGSSGGRRSAIGQRIVGSLPYIK 268

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           +++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 269 QEIPIMIVFRALGFVADRDILEHIIYDFEDQEMMEMVKPSLDEAFVIQEQNVALNFIGSR 328

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   +++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 329 GARPGVTKERRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRREL 386

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +  D    K L+            L+ +       Y +  +   K+ + + AL       
Sbjct: 387 DDRDHYGNKRLDLAGPLLAFLFRGLFRNLMKEVRMYAQKFIDRGKDFNIELAL------- 439

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               V T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 440 -KPKVITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGREGK 498

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  ++ 
Sbjct: 499 LAKPRQLHNTHWGMICPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFMEEWTME 555

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    + ++   F     +    +    +S +   RR   +    V+  R   E  
Sbjct: 556 NLEEITPSAINTSTKIFVNGCWVGIHRDPDQLMSTLRKLRRRMDIIVSEVSMVRDFRERE 615

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               +  GRIC P    E   + L  +      ++     E       +      V Y+ 
Sbjct: 616 IRIYSDAGRICRPLLIVENQKLLLKKN-----HIDQLKEREYNEYSWQELVANGIVEYID 670

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EEE   +A     L E G                          +  P  ++ + AS+
Sbjct: 671 VNEEETVMVAMTPDELVEKG----------------QAYCSTYTHCEIHPSMILGVCASI 714

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 715 IPFPDHNQSPRNTYQSAMGKQAMGVYITNYHV---------------------------- 746

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + V  Y               Q+PLV                
Sbjct: 747 -------------RMDTLAHVLYYP--------------QKPLV----------TTRSME 769

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G N +VA   + GYN EDS++++   +   ++ S+    +        L  
Sbjct: 770 YLRFRELPAGINAIVAIASYTGYNQEDSVIMNASAIDRGLYRSVFYRSYRDQESKKGLDQ 829

Query: 859 EEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           EE         +  +       +DE G+I  G  V+  D++VGK     ++    E    
Sbjct: 830 EETFEKPTRDAVQGMRNASYDKLDEDGLIAPGIRVSGDDVIVGKTVTLPDNDDELEGTAR 889

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +          +D S  +    +G V  V +       K
Sbjct: 890 K-------YSKKDASTFLRPSETGIVDQVMVTINQEGFK 921


>gi|324120668|dbj|BAJ78725.1| RNA polymerase II second largest subunit [Stichotrema asahinai]
          Length = 1173

 Score =  395 bits (1014), Expect = e-107,   Method: Composition-based stats.
 Identities = 174/999 (17%), Positives = 308/999 (30%), Gaps = 197/999 (19%)

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ G
Sbjct: 334  EKRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYG 390

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFC 518
            N+R+   G +L   +R     + + ++               +  +  + +   +     
Sbjct: 391  NKRLDLGGPLLSFLFRGMFKNLIKEVRLYAQKFVDRGKDFNIELAVKTRIISDGLRYSLA 450

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+   +   S ++H RR+++     + R     + R +H T 
Sbjct: 451  TGNWADQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTL 506

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEE 623
            +G ICPAET EG  +GLV +L   A ++           + +  +    ++   S  +  
Sbjct: 507  WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSSIADST 566

Query: 624  NRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
              ++      +  D       L   R   + I+     + D  D   +          P 
Sbjct: 567  KIFVNGCWVGIHRDPELLMSTLRKLRRQMDIIVSEVSMVRDIRDREIRIYTDAGRICRPL 626

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA- 740
            L  D   R+LM                  V           SG           E +D  
Sbjct: 627  LIVDSEGRLLMKKKDIDLLKDRDYGWQSLVS----------SGVV---------EYIDTL 667

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                I       D   +  D Y            C N                    PS 
Sbjct: 668  EEETIMIAMTPNDLRQNRDDTY------------CANF-------------THCEIHPSM 702

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   ++I  F             
Sbjct: 703  ILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------- 740

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                          ++    +  V    +   +    +       +      + AI    
Sbjct: 741  --------------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYT 786

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V        +F R   D   R +  + EQ E   R           
Sbjct: 787  GYNQEDSIIINASAVERGFF-RSVFYRSYRDAEVRRLGDQDEQFEKPNRLTCQGMRHAIY 845

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  L  +                    +  +ES+  
Sbjct: 846  DKLDEDGIIAPGVRVSGDDVVIGKTITLMEN--------------------EDELESVTK 885

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            +Y    +    R        Q    +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 886  KYTKRDASTFLRRSETGVVDQVMLTLNAEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 945

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 946  GIQYRQEDMPFTSEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD------- 998

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 999  ----------------------------------------------ATPFNDAVNVQKIS 1012

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +L+    +  G  I+Y+G TG   +  + +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1013 HLLQEYGYNLRGNEIMYNGYTGRKINAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILVR 1072

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QPL G++  GG R GEME  C  ++GAA  L+E L   SD     V            R 
Sbjct: 1073 QPLEGRARDGGLRFGEMERDCQISHGAAQFLRERLFTVSDPYRIHVCNLCGLIVIANLRN 1132

Query: 1327 RVYESI-VAGN-DTFETGTPESFNVLVKEMQALGLSIDL 1363
              +E           +   P +  +L++E+ A+ +S  +
Sbjct: 1133 NTFECKSCKNKTQISQVHLPYASKLLMQELMAMLISPRI 1171



 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 137/983 (13%), Positives = 282/983 (28%), Gaps = 190/983 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  SYD F+ M++      +  ++    A      I       +L+F       P 
Sbjct: 40  LVRQQLDSYDEFIQMSVQRVVEDSPVIEIVAEAQHLAGEIENP-PRYLLKFEQIYLSKPT 98

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E    K          ++G +
Sbjct: 99  HWEKDGAPSPLVPNEARLRNLTYSAPLYVDISKTIIRDGEDPIYKPHTKT-----FIGKI 153

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                             F+I G ++++++Q   +   ++    K 
Sbjct: 154 PIMLRSTYCLLNGMTDRDLTELNECPFDPGAYFIINGSEKVLIAQEKMATNTVYVFAMKD 213

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-----------------RIDR----- 208
                GK  Y   I       ++        + V                 RI       
Sbjct: 214 -----GKFAYKTEIR----SCLEHSSRPTSTLWVNMLARGGQVGKRNSVGQRIIAILPYI 264

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    ++ + +  
Sbjct: 265 KQEIPIMVVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNIALNFIGA 324

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 325 RGARPGVTKEKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 380

Query: 328 IDEKSLEEIFHSEIRD-IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 381 RELDDRDHYGNKRLDLGGPLLSFLFRGMFKNLIKEVRLYAQKFVDRGKDFNIELAVKTRI 440

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            +  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 441 ISDGLRYSLATGNWADQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 500

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 501 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 557

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  +   F     +    +    +S +   RR   +    V+  R   +      T
Sbjct: 558 APSSIADSTKIFVNGCWVGIHRDPELLMSTLRKLRRQMDIIVSEVSMVRDIRDREIRIYT 617

Query: 565 HYGRICP---AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
             GRIC       SEG  +     +      +                 +  V Y+  +E
Sbjct: 618 DAGRICRPLLIVDSEGRLLMKKKDIDLLKDRDYG---------WQSLVSSGVVEYIDTLE 668

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           EE   IA   + L ++                           +  P  ++ + AS+IPF
Sbjct: 669 EETIMIAMTPNDLRQNR---------------DDTYCANFTHCEIHPSMILGVCASIIPF 713

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            +++ S R      M +QA+ +                                      
Sbjct: 714 PDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------- 742

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                        + + V  Y                +PLV                   
Sbjct: 743 ----------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLR 768

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEE 860
             +L  G N +VA + + GYN EDS++I+   V    F S+    + +   R      E+
Sbjct: 769 FRELPAGINSIVAILCYTGYNQEDSIIINASAVERGFFRSVFYRSYRDAEVRRLGDQDEQ 828

Query: 861 ITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             +        +       +DE GII  G  V+  D+++GK     E+    E       
Sbjct: 829 FEKPNRLTCQGMRHAIYDKLDEDGIIAPGVRVSGDDVVIGKTITLMENEDELESVT---- 884

Query: 917 FGEKAVDVRDTSLRVPSGVSGTV 939
              K    RD S  +    +G V
Sbjct: 885 ---KKYTKRDASTFLRRSETGVV 904


>gi|194209129|ref|XP_001916826.1| PREDICTED: similar to DNA-directed RNA polymerase II subunit RPB2
            (RNA polymerase II subunit B2) (DNA-directed RNA
            polymerase II subunit B) (RNA polymerase II subunit 2)
            (DNA-directed RNA polymerase II 140 kDa polypeptide)
            [Equus caballus]
          Length = 1174

 Score =  394 bits (1013), Expect = e-107,   Method: Composition-based stats.
 Identities = 174/1085 (16%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 Q  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLQLAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
             ++     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLQLAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|242038711|ref|XP_002466750.1| hypothetical protein SORBIDRAFT_01g013470 [Sorghum bicolor]
 gi|241920604|gb|EER93748.1| hypothetical protein SORBIDRAFT_01g013470 [Sorghum bicolor]
          Length = 1218

 Score =  394 bits (1013), Expect = e-107,   Method: Composition-based stats.
 Identities = 186/1080 (17%), Positives = 339/1080 (31%), Gaps = 196/1080 (18%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V D+  LE I +       +  +      A++         
Sbjct: 309  LPYIRADIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV--- 365

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 AL  I +       +     E    +      K  L  VG             + 
Sbjct: 366  -----ALDYIGKR----GATVGVTREKRIKYAKEILQKEMLPHVG-----------VGEF 405

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
                +      II  L+    G+   DD D+ GN+R+   G +L   +R+  +   + + 
Sbjct: 406  CETKKAYYFGYIIHRLLMCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMC-VDNGKEVN 464

Query: 488  ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
             + +              A        +    + +SQ+   +   S ++H RRL++    
Sbjct: 465  LQFAIKAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYASTLSHLRRLNS---- 520

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
             + R     + R +H +H+G +CPAET EG   GLV +L     +            + +
Sbjct: 521  PIGREGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEE 580

Query: 608  GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                N        EE +  +    + +  +G +           + +   R +I   D +
Sbjct: 581  WGTEN-------FEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQI---DVN 630

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
             +  V     L       D  R      +      L+K          E           
Sbjct: 631  TEVGVVRDIRLKELRLYTDYGRCSRPLFIVEGQRLLIKKAHIIALQHRE----------- 679

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                 G  E V   +  I  ++ + + +T        +   R N     +          
Sbjct: 680  -TPDEGWHELVS--KGYIEYIDTEEEETTMISMTISDLHNARHNPEDAYS---------- 726

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                      PS  LG       +  + +P+  +N          M  + +   I++  +
Sbjct: 727  -ETYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNY 776

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            +                           +    +  V        +    +       + 
Sbjct: 777  Q---------------------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLP 809

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
                 + AI      +  D+ +   S +        +F R   D+ ++  ++ +E+    
Sbjct: 810  AGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEEFGRP 868

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             R+          +          G           K++ +                  Q
Sbjct: 869  NRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPI-----------------PQ 911

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D+   +     K  + TS    E    +++      D +     R VKV +   R  Q G
Sbjct: 912  DDAQGQASRYSKRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIG 966

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     
Sbjct: 967  DKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAQ 1026

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            +G++                                                       +
Sbjct: 1027 MGREGD-----------------------------------------------------A 1033

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TP F     + I+  L   +    G   +Y+G TG      + +G  Y  +L HMV DK+
Sbjct: 1034 TP-FTDVTVDNISKALHRCNYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRLKHMVDDKI 1092

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            ++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD    R  
Sbjct: 1093 HSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAFFLKERLFDQSD--AYRVH 1150

Query: 1328 VYE-----SIV---------AG----NDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            V E     +I           G     D  +   P +  +L +E+ A+ ++  +     K
Sbjct: 1151 VCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTHDMK 1210



 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 139/986 (14%), Positives = 282/986 (28%), Gaps = 205/986 (20%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           L+  Q  S+D F+               I P+ + N G QA F              + F
Sbjct: 83  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGRQAEFAETL--------HKISF 134

Query: 77  VSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P     D             R+LTY+ PL + +   V            +   
Sbjct: 135 GQIYLSKPMMTEADGETATLFPKSARLRNLTYSAPLYVDVSYRVMKKGHDCEE-VTETAD 193

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG 162
              +++G +P+M +                         G F+I G ++++++Q   S  
Sbjct: 194 YPKVFIGKVPIMLRSSYCTLYQQSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTN 253

Query: 163 -IHFDHDKGRASLSGKLLYACRIIP-----DQGLWMDIEFD-----SKD----------I 201
            ++      +     K  Y   +       ++              +K           +
Sbjct: 254 HVY----VFKKRQPNKFAYVAEVRSMAENQNRPASSMFVRMLSRAGAKGGSSGQYIRATL 309

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
            ++R D    +P+     ALG  ++ +IL         +Q  +     L  A ++   +V
Sbjct: 310 PYIRAD----IPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV 365

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +   +        +   K++     + L+++ +  +G+   C          +      +
Sbjct: 366 ALDYIGKRGATVGVTREKRIKYAK-EILQKEMLPHVGVGEFCETKKAYYFGYIIH---RL 421

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            + A     E   +   +        L +         R  +   K  + + A+      
Sbjct: 422 LMCALGRRAEDDRDHYGNKR------LDLAGPLLGGLFRMCVDNGKEVNLQFAI------ 469

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAI 439
                  T  +  S+    +  +++          +N      T   +R +         
Sbjct: 470 --KAKTITSGLKYSLATGNWGQANQAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGK 527

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +         +      ++KN   +  + +  +    +  ++     
Sbjct: 528 LAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWGTE 584

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM 558
             + I+   +  A   F     +         +  +   RR   +  + GV R     E+
Sbjct: 585 NFEEISPAVIPQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQIDVNTEVGVVRDIRLKEL 644

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           R ++  +     P    EG  + +       A + A    ETP     +      + Y+ 
Sbjct: 645 R-LYTDYGRCSRPLFIVEGQRLLIKK-----AHIIALQHRETPDEGWHELVSKGYIEYID 698

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EEE   I+   S L             R   E      E     +  P  ++ + AS+
Sbjct: 699 TEEEETTMISMTISDLH----------NARHNPE--DAYSETYTHCEIHPSLILGVCASI 746

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                           R   +  V
Sbjct: 747 IPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV 786

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                                                  Q+PLV                
Sbjct: 787 -----------------------------------LYYPQKPLV----------TTRAME 801

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                 L  G N +VA   + GYN EDS+++++  +    F S+    +    +      
Sbjct: 802 HLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLV 861

Query: 859 EE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           +E        +   +       +D+ G+   G  V+  D+++GK +P  +          
Sbjct: 862 KEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDD-------- 913

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTV 939
            A         RD S  +    SG V
Sbjct: 914 -AQGQASRYSKRDHSTSLRHSESGMV 938


>gi|73975077|ref|XP_860990.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            15 [Canis familiaris]
          Length = 1179

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 171/1085 (15%), Positives = 323/1085 (29%), Gaps = 196/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I    
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVS 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
               D  +   +          P L  +    +L   ++ +         + F        
Sbjct: 602  MIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSEFFF--FSWQ 659

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 660  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 694

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 695  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 738

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 739  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 769

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 770  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 828

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 829  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 878

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +E    +Y         R        Q    +     +  K+ V
Sbjct: 879  ----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 928

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 929  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 988

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 989  CLQGKVSANKGEIGD--------------------------------------------- 1003

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 1004 --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1055

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1056 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1115

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1116 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1173

Query: 1361 IDLEN 1365
              + +
Sbjct: 1174 PRMMS 1178



 Score =  241 bits (614), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 139/1004 (13%), Positives = 288/1004 (28%), Gaps = 200/1004 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +          
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIPDVSMIRDI 606

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI-ETPYRKVCDGKVTND 613
                 ++        P    E   + L        +   Y    E  +    D   +  
Sbjct: 607 REREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSEFFFFSWQDLVASGV 666

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 667 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 710

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 711 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 747

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 748 ------------------RMDTLAHVLYYP--------------QKPLV----------T 765

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 766 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 825

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 826 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 885

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 886 EGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 922


>gi|292559501|ref|YP_003540923.1| DNA-directed RNA polymerase beta chain [Phoenix dactylifera]
 gi|290790909|gb|ADD63164.1| DNA-directed RNA polymerase beta chain [Phoenix dactylifera]
 gi|294620569|gb|ADF28138.1| DNA-directed RNA polymerase beta chain [Phoenix dactylifera]
          Length = 1068

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 162/579 (27%), Positives = 255/579 (44%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   + +        I         +  G  
Sbjct: 542  MSSNMQRQAVPLSRSEKCIVGTGLERQTALDSGVSAIAEHEGKIIYTDPHKIILSSNGDT 601

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 602  ISIPLVMYQRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVG-GELALGKNILVAYMPW 660

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +  L 
Sbjct: 661  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLL 715

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  R   ++ G    +G     K T  +++  S  P  +  +  +  +       SLK
Sbjct: 716  RNL-DRNGIVMLGSWVETGDILVGKLTPQTANESSYSPEDRLLRVILGIQVSTAKETSLK 774

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 775  LPIGGRGRVIDVRWIQKK----GGSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGI 827

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L K  +    D 
Sbjct: 828  ISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKKHYRIAPFDE 887

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E                                    VF+       
Sbjct: 888  RYEQEASRKLVFSELYEACKQTKNPW------------------------VFE------- 916

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 917  --------PEYPGKSRIFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVT 968

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 969  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIVGGTVP 1028

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1029 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1067



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 238/692 (34%), Positives = 382/692 (55%), Gaps = 21/692 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E     + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 135 ELDNNGISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLRKILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 195 NVCYPEIFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSDSLCKELQKKFF-QQR 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 313

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LS
Sbjct: 314 SVADLLQDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLS 373

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 374 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 433

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL    R+  +G IE+P+ ++        VVYLS   +E   +A  NS     G   E+
Sbjct: 434 GSLAIHVRIGHWGSIESPFYEISQRSKEAQVVYLSPNRDEYYMVAAGNSLALNRGIQEEQ 493

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  EKI F    P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 494 VVPARYRQEFLTIAWEKIHFRSFFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 553

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E   A  SG + +A+  G +   D  +I++ S                
Sbjct: 554 SRSEKCIVGTGLERQTALDSGVSAIAEHEGKIIYTDPHKIILSSN--------GDTISIP 605

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 606 LVMYQRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVGGELALGKNILVAYMPWEGYNS 665

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ 
Sbjct: 666 EDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLLRNLDRNGIVM 725

Query: 884 VGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+   ES  +PE++LLR I G +    ++TSL++P G  G V+D
Sbjct: 726 LGSWVETGDILVGKLTPQTANESSYSPEDRLLRVILGIQVSTAKETSLKLPIGGRGRVID 785

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   + G         R    ++ +I++  +
Sbjct: 786 VRWIQKKGGSSYNPEMIRVYISQKREIKVGDK 817



 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 109/230 (47%), Gaps = 25/230 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS-YEFDPP 84
           IP   ++Q   +  F+          N+GL   F     I        L FV  Y+   P
Sbjct: 12  IPAFSQIQFEGFYRFI----------NQGLTEEFHKFPKIEDQEIEFKL-FVETYKLVEP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
                D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GTF
Sbjct: 61  LIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTVFIGNIPLMNSLGTF 111

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  I  
Sbjct: 112 IVNGIYRIVINQILQSPGIYYRSELD---NNGISVYTSTIISDWGGRSELEIDRKARIWA 168

Query: 205 RIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           R+ R++K+ +     A+G +  +IL    YP+I  S   D     + + +
Sbjct: 169 RVSRKQKISILVLSSAMGSNLRKILDNVCYPEIFLSFPNDKEKKKIGSKE 218


>gi|324120676|dbj|BAJ78729.1| RNA polymerase II second largest subunit [Stenopsyche marmorata]
          Length = 1174

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 251  GQRIIAIVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 310

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 311  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 364

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 365  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 424

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 425  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 484

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 485  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 540

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 541  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 600

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  D+   +L   +  M ++      +    V +G+ 
Sbjct: 601  MIRDIRDREIRIYTDAGRICRPLLIVDNGILLLKKRHIDMLKERDLNNYSWQVLVASGVV 660

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 661  EYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------- 692

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 693  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 729

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 730  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 760

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V            +   K+  
Sbjct: 761  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF---YRSYKDSE 817

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 818  SKRIGDQE-EQFEKPTRTTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITL---- 872

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    ++    +Y    +    R        Q    +     +
Sbjct: 873  ----------------PENDDELDGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 916

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 917  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 976

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 977  IGHLIECIQGKVSSNKGEIGD--------------------------------------- 997

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 998  --------------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQVFLG 1043

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1044 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1103

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1104 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1161

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1162 MSMNIAPRLM 1171



 Score =  238 bits (607), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 287/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 37  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHASGEIETP-PHYLLKFEQIYLSKPT 95

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 96  HWEKDGAAAAMMPNEARLRNLTYSAPLYVDITKTIVKEGEDPI-----ETQHQKTFIGKI 150

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 151 PIMLRSTYCLLNGLIDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 210

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  +   I       ++        + V +  R     +K              
Sbjct: 211 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMSRGGQSIKKNAIGQRIIAIVPYI 261

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 262 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 321

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 322 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 377

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 378 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 437

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 438 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 497

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 498 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 554

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 555 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 614

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    +   + L         ++     +           +  V Y+  +EEE
Sbjct: 615 DAGRICRPLLIVDNGILLLKKR-----HIDMLKERDLNNYSWQVLVASGVVEYIDTLEEE 669

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 670 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 714

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 715 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 741

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 742 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 769

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 770 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGDQEEQFE 829

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    +         
Sbjct: 830 KPTRTTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDGTT------ 883

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 884 -KRYTKRDASTFLRNSETGIV 903


>gi|324500827|gb|ADY40377.1| DNA-directed RNA polymerase II subunit RPB2 [Ascaris suum]
          Length = 1173

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 177/1086 (16%), Positives = 336/1086 (30%), Gaps = 204/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 255  GQRIIAILPYIKQEIPIMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 314

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      I 
Sbjct: 315  EQNVALNFIGARGAKPGV---TKEQRIKYAKEILQKEMLPHVGISDFCETKK---AYFIG 368

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             ++  L+    G+  +DD D++GN+R+   G +L   +R     + + ++         +
Sbjct: 369  YMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFKNLLKEVRLTAQKYINKN 428

Query: 498  --VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
               +    +    +   +     +               +SQ+   +   + ++H RR +
Sbjct: 429  GDFILDACVKTSTITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRCN 488

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++     E   
Sbjct: 489  S----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPIL 544

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    +V   +  +    ++  A   +  D       L   R   + I+    
Sbjct: 545  EFLEEWSMENLEEVAPSAIADATKIFVNGAWVGIHRDPEQLMSTLKKLRREMDIIVSEVS 604

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGM-E 716
             + D  D   +          P L  ++   VL   ++ + +      A +  V  G+ E
Sbjct: 605  MVRDIRDREIRIYTDAGRVCRPLLIVENQKLVLKKKHIDQLKDTNDNYAWSDLVAGGVVE 664

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             + A      ++A     +                                         
Sbjct: 665  LIDAMEEETVMLAMMPEDL----------------------------------------- 683

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                  K G            P+  LG       +  + +P+  +N       S R   +
Sbjct: 684  ------KAGGYCDTYTHCEIHPAMILG-------VCASIIPFPDHNQ------SPRNTYQ 724

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                   +  +                           ++    +  V        +   
Sbjct: 725  SAMGKQAMGVYTTNF-----------------------HVRMDTLAHVLYYPQKPLVTTR 761

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +     + +      + AI      +  D+ +   SG+   +    +F R   D+    
Sbjct: 762  SMEYLRFNELPAGINAIVAILSYTGYNQEDSVIMNQSGIDRGLF-RSVFYRSYRDQEANL 820

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
             +   E IE   RDK         +       I  G           K            
Sbjct: 821  DNANEELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGK------------ 868

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                     +    V+ ++E+   +Y    +    R        Q    +     + VK+
Sbjct: 869  --------TISLPDVEDDLEANTKKYTKRDASTFLRSSETGIVDQVMLTLNTDGNKFVKI 920

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             V   R  Q GDK A RHG KG +  +   EDMPF  +G   DI++NP  VPSRM +G +
Sbjct: 921  RVRSVRLPQIGDKFASRHGQKGTMGIMYRQEDMPFTNEGITPDIIINPHAVPSRMTIGHL 980

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E   G      G+                                              
Sbjct: 981  IECLQGKLSANKGEIGD------------------------------------------- 997

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                      +TP  D  + + I+++L        G  I+Y+G TG      V +G  Y 
Sbjct: 998  ----------ATPFNDTVNVQKISNLLSEYGYHLRGNEIMYNGHTGHKLTTQVFLGPTYY 1047

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L 
Sbjct: 1048 QRLKHMVDDKIHSRARGPVQMMNRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLF 1107

Query: 1317 IKSD--DV-----VG-------RTRVYESIV--AGNDTFETGTPESFNVLVKEMQALGLS 1360
              SD   V      G       RT  +E               P +  +L +E+ ++ ++
Sbjct: 1108 EVSDPYHVYVCNNCGLIVIANLRTNTFECKACRNKTQVSAIRIPYACKLLFQELMSMSIA 1167

Query: 1361 IDLENS 1366
              L  S
Sbjct: 1168 PRLMVS 1173



 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 153/998 (15%), Positives = 295/998 (29%), Gaps = 197/998 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFP-ITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ MN+    ++ P   LQ+  +     I   +    L+        P 
Sbjct: 42  LVRQQLDSFDEFIQMNVQRIVEDSPPVELQSEVQHFSGDIENPT-KFALKLDQIYLSKPT 100

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E       K+ K + +++G +
Sbjct: 101 HWEKDGAPTPMMPNEARLRNLTYSSPLYVDITKTVSRDGEDP-----KESKYEKVFVGKI 155

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 156 PIMLRSSYCMLSNMSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 215

Query: 171 RASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHV----RIDRRRK------------- 211
                GK  Y   CR        ++        + V    R    +K             
Sbjct: 216 -----GKYAYKTECR------SCLENSSRPTSTLWVNMMARGGSTKKSAMGQRIIAILPY 264

Query: 212 ----VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               +P+     ALG  S+ +IL          +  +     L  A ++    V+ + + 
Sbjct: 265 IKQEIPIMIVFRALGFVSDHDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIG 324

Query: 267 IDTGEQVIESGKKLTSG----LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
               +  +   +++         + L   G+     T       Y+   ++    G   +
Sbjct: 325 ARGAKPGVTKEQRIKYAKEILQKEMLPHVGISDFCETKKAYFIGYMVHRLLLAALGRREL 384

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D I  K L+            L+ + +          +        DA +       
Sbjct: 385 DDRDHIGNKRLDLAGPLLAFLFRALFKNLLKEVRLTAQKYINKNGDFILDACV------- 437

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
                T  +A S+    + D  K   S  G  ++  RL          R          +
Sbjct: 438 KTSTITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRCNSPIGREGKL 497

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N +  +         +   + + L     + +  +   I E +    ++++  
Sbjct: 498 AKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEEWSMENL-- 555

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + +    +  A   F   + +    +    +S +   RR   +    V+  R   +   
Sbjct: 556 -EEVAPSAIADATKIFVNGAWVGIHRDPEQLMSTLKKLRREMDIIVSEVSMVRDIRDREI 614

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GR+C P    E   + L        +     +         D      V  + A
Sbjct: 615 RIYTDAGRVCRPLLIVENQKLVLKKKHIDQLKDTNDNYA------WSDLVAGGVVELIDA 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           MEEE   +A     L   G                    +     +  P  ++ + AS+I
Sbjct: 669 MEEETVMLAMMPEDLKAGG------------------YCDTYTHCEIHPAMILGVCASII 710

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 711 PFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV----------------------------- 741

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + V  Y               Q+PLV                 
Sbjct: 742 ------------RMDTLAHVLYYP--------------QKPLV----------TTRSMEY 765

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G N +VA + + GYN EDS+++++  +   +F S+    +     +     E
Sbjct: 766 LRFNELPAGINAIVAILSYTGYNQEDSVIMNQSGIDRGLFRSVFYRSYRDQEANLDNANE 825

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E            +       +DE GII  G  V+  D+++GK     +     E     
Sbjct: 826 ELIEKPTRDKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTISLPDVEDDLEANT-- 883

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                K    RD S  + S  +G V  V +      +K
Sbjct: 884 -----KKYTKRDASTFLRSSETGIVDQVMLTLNTDGNK 916


>gi|73975075|ref|XP_860963.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            14 [Canis familiaris]
          Length = 1175

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 165/1086 (15%), Positives = 323/1086 (29%), Gaps = 202/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
              + +  +    ++   +  +    ++      + +D       +        +    + 
Sbjct: 543  EFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQTVLSFYWKV 602

Query: 661  IDFIDASPKQVVSIAAS---LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                D   +++     +     P L  +    +L   ++ +                   
Sbjct: 603  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN--------YSW 654

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                +SG           E +D +      +    D        Y               
Sbjct: 655  QDLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY--------------- 690

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
                                PS  LG       +  + +P+  +N          M  + 
Sbjct: 691  ----------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQA 733

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +   ++I  F                           ++    +  V        +    
Sbjct: 734  MG--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRS 764

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +      + AI      +  D+ +   S V        +F R   ++  +  
Sbjct: 765  MEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKG 823

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
              + E  E   R+          +       I  G           K+  L         
Sbjct: 824  FDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL--------- 874

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                        + +  +E    +Y         R        Q    +     +  K+ 
Sbjct: 875  -----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIR 923

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + 
Sbjct: 924  VRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLI 983

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E   G      G+                                               
Sbjct: 984  ECLQGKVSANKGEIGD-------------------------------------------- 999

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                     +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  
Sbjct: 1000 ---------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQ 1050

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L  
Sbjct: 1051 RLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFE 1110

Query: 1318 KSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGL 1359
             SD     V            RT  YE    G            P +  +L +E+ ++ +
Sbjct: 1111 ASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSI 1168

Query: 1360 SIDLEN 1365
            +  + +
Sbjct: 1169 APRMMS 1174



 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 145/1005 (14%), Positives = 295/1005 (29%), Gaps = 206/1005 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR + L          
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQTVLSFYWKVSMIR 606

Query: 555 GVEMRDVHP-THYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            +  R++   T  GRIC P    E   + L         ++     E       D   + 
Sbjct: 607 DIREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASG 661

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V Y+  +EEE   +A     L E                  +         +  P  ++
Sbjct: 662 VVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMIL 705

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                             
Sbjct: 706 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV---------------------- 743

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                 + + V  Y               Q+PLV          
Sbjct: 744 -------------------RMDTLAHVLYYP--------------QKPLV---------- 760

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                      +L  G N +VA   + GYN EDS++++   V    F S+    ++    
Sbjct: 761 TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQES 820

Query: 853 DTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 EE+           +       +D+ G+I  G  V+  D+++GK     E+   
Sbjct: 821 KKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDE 880

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            E          +    RD S  + +  +G V  V +       K
Sbjct: 881 LEGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 918


>gi|324120606|dbj|BAJ78694.1| RNA polymerase II second largest subunit [Isolepisma japonica]
          Length = 1176

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 169/1090 (15%), Positives = 331/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLKYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             + D  D   +          P L  D+   +L   +  M ++           V +G+ 
Sbjct: 603  MVRDIRDREIRIYTDAGRICRPLLIVDNGRLLLKKRHIDMLKEREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPEDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAIACYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   IY +L +   I  G           K        
Sbjct: 820  SKRICDQE-EQFEKPTRTTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGK-------- 870

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D      +E    +Y    +    R        Q    +     +
Sbjct: 871  ----------TITLPDND--DELEGTTKRYTKRDASTFLRNSETGIVDQVMITLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPLQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANMRNSTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 143/994 (14%), Positives = 291/994 (29%), Gaps = 184/994 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIVAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  L+  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLKYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMVRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    +   + L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVDNGRLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAIACYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRICDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 KPTRTTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPDNDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K    RD S  + +  +G V  V I       K
Sbjct: 886 -KRYTKRDASTFLRNSETGIVDQVMITLNSEGYK 918


>gi|114594588|ref|XP_001136218.1| PREDICTED: DNA directed RNA polymerase II polypeptide B isoform 1
            [Pan troglodytes]
 gi|297673507|ref|XP_002814802.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like isoform 3
            [Pongo abelii]
          Length = 1099

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 178  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 237

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 238  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 291

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 292  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 351

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 352  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 411

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 412  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 467

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 468  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 526

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 527  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 579

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 580  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 614

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 615  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 658

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 659  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 689

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 690  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 748

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 749  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 798

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 799  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 848

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 849  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 908

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 909  CLQGKVSANKGEIGD--------------------------------------------- 923

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 924  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 975

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 976  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1035

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1036 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1093

Query: 1361 IDLEN 1365
              + +
Sbjct: 1094 PRMMS 1098



 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 135/950 (14%), Positives = 277/950 (29%), Gaps = 183/950 (19%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
             +L+F       P              ++   R+LTY+ PL + +   V    E     
Sbjct: 8   RYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-- 65

Query: 121 SIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQ 156
                + Q  ++G +P+M                           G F+I G ++++++Q
Sbjct: 66  ---QTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 122

Query: 157 LHRSPG-IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR----- 209
              +   ++ F     + + +G+    CR        ++        I V +  R     
Sbjct: 123 EKMATNTVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGA 172

Query: 210 RK-----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +K                 VP+     ALG  S+ +IL          +  +     L  
Sbjct: 173 KKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDE 232

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           A ++    V+ + +     +  +   K++     + L+++ +  +G++  C         
Sbjct: 233 AFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLG 291

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDR 370
            +      + + A    +    +   +  +    P+L          +   +     K  
Sbjct: 292 YMVH---RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 348

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
                    +     + +  +  S+    + D  K   +  G  ++  RL   +      
Sbjct: 349 DRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLR 408

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R          +     L N    +                ++KN   +  + +      
Sbjct: 409 RLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSP 465

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            +  ++  S+   + I+   +  A   F     +   ++    ++ +   RR   +    
Sbjct: 466 ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE 525

Query: 549 VARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           V+  R   E      T  GRIC P    E   + L         ++     E       D
Sbjct: 526 VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQD 580

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              +  V Y+  +EEE   +A     L E                  +         +  
Sbjct: 581 LVASGVVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIH 624

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ + AS+IPF +++ S R      M +QA+ +                        
Sbjct: 625 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------- 667

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + V  Y               Q+PLV     
Sbjct: 668 ------------------------RMDTLAHVLYYP--------------QKPLV----- 684

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G N +VA   + GYN EDS++++   V    F S+    +
Sbjct: 685 -----TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY 739

Query: 848 EVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           +          EE+           +       +D+ G+I  G  V+  D+++GK     
Sbjct: 740 KEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLP 799

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E+    E          +    RD S  + +  +G V  V +       K
Sbjct: 800 ENEDELEST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 842


>gi|324120674|dbj|BAJ78728.1| RNA polymerase II second largest subunit [Papilio polytes]
          Length = 1176

 Score =  394 bits (1012), Expect = e-107,   Method: Composition-based stats.
 Identities = 170/1090 (15%), Positives = 330/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAIVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKERRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   +    ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVENGALLLKKKHIDHLKERDYNNYGWQNLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A     + Q                                      
Sbjct: 663  EYIDTLEEETVMIAMSPDDLAQ-------------------------------------- 684

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                  VK              P+  LG       +  + +P+  +N          M  
Sbjct: 685  ------VKEYAYCSTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         +  +   +++R
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKR 822

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                E    E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 823  LGDQE----EQFEKPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITL---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    +Y    +    R        Q    +     +
Sbjct: 875  ----------------PENDDELEGTTRRYTKRDASTFLRNSETGIVDQVMVTLNREGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECIQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+S+L+       G  ++Y+G TG   +  V +G
Sbjct: 1000 --------------ATPFNDAVNVQKISSLLQEYGYHLRGNEVMYNGHTGRKINAQVFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  245 bits (625), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 143/1008 (14%), Positives = 294/1008 (29%), Gaps = 212/1008 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------AFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDSPPIELQAEAQHSSGEIETPPKYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +   +E        + +
Sbjct: 89  DQIYLSKPTHWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKENEEPI-----ETQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q I++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKIFIGKIPIMLRSTYCLLSNLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR----- 208
            ++    K      GK  Y   I       ++        + V         I +     
Sbjct: 204 TVYVFSMKD-----GKYAYKTEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQ 254

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    ++++P+     ALG  ++ +IL          +  +     L  A ++   
Sbjct: 255 RIIAIVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQ 314

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDI 312
            V+ + +        +   +++     + L+++ +  +G++           G  V   +
Sbjct: 315 NVALNFIGARGARPGVTKERRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLL 373

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           +    G   ++  D    K L+            L+ + +          +        +
Sbjct: 374 L-AALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRGKDFNLE 432

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RH 430
                  +     + T  +  S+    + D  K   +  G  ++  RL   +      R 
Sbjct: 433 -------LAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRV 485

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                    +     L N    +                ++KN   +  + +       +
Sbjct: 486 NSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPIL 542

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
             ++  S+   + I    +  A   F     +    +    ++ +   RR   +    V+
Sbjct: 543 EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 551 RARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R   +      T  GRIC P    E   + L         ++     +       +  
Sbjct: 603 MIRDIRDREIRIYTDAGRICRPLLIVENGALLLKKK-----HIDHLKERDYNNYGWQNLV 657

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            +  V Y+  +EEE   IA +   L +   +                        +  P 
Sbjct: 658 ASGVVEYIDTLEEETVMIAMSPDDLAQVKEY---------------AYCSTYTHCEIHPA 702

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +                          
Sbjct: 703 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------- 743

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + V  Y                +PLV       
Sbjct: 744 ----------------------RMDTLAHVLYYP--------------HKPLV------- 760

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G N +VA + + GYN EDS++++   V    F S+    ++ 
Sbjct: 761 ---TTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKD 817

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                    EE            +       +D+ GII  G  V+  D+++GK     E+
Sbjct: 818 SESKRLGDQEEQFEKPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITLPEN 877

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               E    R          RD S  + +  +G V  V +       K
Sbjct: 878 DDELEGTTRR-------YTKRDASTFLRNSETGIVDQVMVTLNREGYK 918


>gi|73975081|ref|XP_861044.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            17 [Canis familiaris]
          Length = 1099

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 172/1085 (15%), Positives = 325/1085 (29%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 178  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 237

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 238  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 291

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 292  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 351

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 352  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 411

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 412  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 467

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 468  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 526

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 527  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 579

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 580  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 614

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 615  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 658

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 659  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 689

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 690  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 748

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 749  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 798

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +E    +Y         R        Q    +     +  K+ V
Sbjct: 799  ----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 848

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 849  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 908

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 909  CLQGKVSANKGEIGD--------------------------------------------- 923

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 924  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 975

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 976  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1035

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1036 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1093

Query: 1361 IDLEN 1365
              + +
Sbjct: 1094 PRMMS 1098



 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 135/950 (14%), Positives = 277/950 (29%), Gaps = 183/950 (19%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
             +L+F       P              ++   R+LTY+ PL + +   V    E     
Sbjct: 8   RYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-- 65

Query: 121 SIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQ 156
                + Q  ++G +P+M                           G F+I G ++++++Q
Sbjct: 66  ---QTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 122

Query: 157 LHRSPG-IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR----- 209
              +   ++ F     + + +G+    CR        ++        I V +  R     
Sbjct: 123 EKMATNTVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGA 172

Query: 210 RK-----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +K                 VP+     ALG  S+ +IL          +  +     L  
Sbjct: 173 KKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDE 232

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           A ++    V+ + +     +  +   K++     + L+++ +  +G++  C         
Sbjct: 233 AFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLG 291

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDR 370
            +      + + A    +    +   +  +    P+L          +   +     K  
Sbjct: 292 YMVH---RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 348

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
                    +     + +  +  S+    + D  K   +  G  ++  RL   +      
Sbjct: 349 DRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLR 408

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R          +     L N    +                ++KN   +  + +      
Sbjct: 409 RLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSP 465

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            +  ++  S+   + I+   +  A   F     +   ++    ++ +   RR   +    
Sbjct: 466 ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE 525

Query: 549 VARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           V+  R   E      T  GRIC P    E   + L         ++     E       D
Sbjct: 526 VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQD 580

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              +  V Y+  +EEE   +A     L E                  +         +  
Sbjct: 581 LVASGVVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIH 624

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ + AS+IPF +++ S R      M +QA+ +                        
Sbjct: 625 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------- 667

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + V  Y               Q+PLV     
Sbjct: 668 ------------------------RMDTLAHVLYYP--------------QKPLV----- 684

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G N +VA   + GYN EDS++++   V    F S+    +
Sbjct: 685 -----TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY 739

Query: 848 EVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           +          EE+           +       +D+ G+I  G  V+  D+++GK     
Sbjct: 740 KEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLP 799

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E+    E          +    RD S  + +  +G V  V +       K
Sbjct: 800 ENEDELEGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 842


>gi|194378878|dbj|BAG57990.1| unnamed protein product [Homo sapiens]
          Length = 1099

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 327/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 178  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 237

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 238  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 291

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 292  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 351

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 352  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 411

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 412  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 467

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 468  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 526

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 527  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 579

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 580  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 614

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 615  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 658

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 659  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 689

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V  +     +F R   ++  +   
Sbjct: 690  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRSFF-RSVFYRSYKEQESKKGF 748

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 749  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 798

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 799  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 848

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 849  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 908

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 909  CLQGKVSANKGEIGD--------------------------------------------- 923

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 924  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 975

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 976  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1035

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1036 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1093

Query: 1361 IDLEN 1365
              + +
Sbjct: 1094 PRMMS 1098



 Score =  223 bits (567), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 135/950 (14%), Positives = 277/950 (29%), Gaps = 183/950 (19%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
             +L+F       P              ++   R+LTY+ PL + +   V    E     
Sbjct: 8   RYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-- 65

Query: 121 SIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQ 156
                + Q  ++G +P+M                           G F+I G ++++++Q
Sbjct: 66  ---QTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 122

Query: 157 LHRSPG-IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR----- 209
              +   ++ F     + + +G+    CR        ++        I V +  R     
Sbjct: 123 EKMATNTVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGA 172

Query: 210 RK-----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +K                 VP+     ALG  S+ +IL          +  +     L  
Sbjct: 173 KKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDE 232

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           A ++    V+ + +     +  +   K++     + L+++ +  +G++  C         
Sbjct: 233 AFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLG 291

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDR 370
            +      + + A    +    +   +  +    P+L          +   +     K  
Sbjct: 292 YMVH---RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 348

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
                    +     + +  +  S+    + D  K   +  G  ++  RL   +      
Sbjct: 349 DRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLR 408

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R          +     L N    +                ++KN   +  + +      
Sbjct: 409 RLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSP 465

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            +  ++  S+   + I+   +  A   F     +   ++    ++ +   RR   +    
Sbjct: 466 ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE 525

Query: 549 VARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           V+  R   E      T  GRIC P    E   + L         ++     E       D
Sbjct: 526 VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQD 580

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              +  V Y+  +EEE   +A     L E                  +         +  
Sbjct: 581 LVASGVVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIH 624

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ + AS+IPF +++ S R      M +QA+ +                        
Sbjct: 625 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------- 667

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + V  Y               Q+PLV     
Sbjct: 668 ------------------------RMDTLAHVLYYP--------------QKPLV----- 684

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G N +VA   + GYN EDS++++   V    F S+    +
Sbjct: 685 -----TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRSFFRSVFYRSY 739

Query: 848 EVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           +          EE+           +       +D+ G+I  G  V+  D+++GK     
Sbjct: 740 KEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLP 799

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E+    E          +    RD S  + +  +G V  V +       K
Sbjct: 800 ENEDELEST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 842


>gi|297673503|ref|XP_002814800.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like isoform 1
            [Pongo abelii]
          Length = 1167

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 246  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 305

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 306  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 359

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 360  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 419

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 420  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 480  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 535

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 536  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 594

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 595  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 647

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 648  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 682

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 683  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 726

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 727  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 757

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 758  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 816

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 817  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 866

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 867  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 916

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 917  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 976

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 977  CLQGKVSANKGEIGD--------------------------------------------- 991

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 992  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1043

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1044 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1103

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1104 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1161

Query: 1361 IDLEN 1365
              + +
Sbjct: 1162 PRMMS 1166



 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 32  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 81

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 82  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 136

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 137 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 196

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 197 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 246

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 247 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 306

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 307 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 363

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 364 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 422

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 423 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 482

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 483 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 539

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 540 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 599

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 600 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 654

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 655 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 698

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 699 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 735

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 736 ------------------RMDTLAHVLYYP--------------QKPLV----------T 753

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 754 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 813

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 814 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 873

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 874 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 910


>gi|302488402|ref|NP_001019632.2| DNA-directed RNA polymerase II subunit RPB2 [Danio rerio]
          Length = 1174

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 173/1086 (15%), Positives = 325/1086 (29%), Gaps = 201/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKERRIKYAKEVLQKEVLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + I+          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         +             
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFY------------- 811

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              R   E  ++   D++ I ++           G       K      +     +S    
Sbjct: 812  --RSYKEQESKKGFDQEEIFEKPTRE----TCQGMRHAIYDKLDDDGLIAPGVRVSG--E 863

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   V   +    ++S   +Y         R        Q    +     +  K+ V
Sbjct: 864  DVIIGKTVTLPENDDELDSTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM VG + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTVGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + ++++L        G  +LY+G TG      + VG  Y  +
Sbjct: 999  --------ATPFNDAVNVQKVSNLLSEYGYHLRGNEVLYNGFTGRKLTSQIFVGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLKERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGLMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLENS 1366
              +  S
Sbjct: 1169 PRMMTS 1174



 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 143/1003 (14%), Positives = 294/1003 (29%), Gaps = 203/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHTSGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +    E       +  +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDGEEQ-----QQTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLSGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMMARGGQGVKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   +++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKERRIKYAK-EVLQKEVLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             E      T  GRIC         +     L     ++     E       D   +  V
Sbjct: 607 IREREIRIYTDAGRIC----RPLLIVEKQKLLLKRRHIDQLKEREYNNYSWQDLVASGVV 662

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            Y+  +EEE   +A     L E G                +         +  P  ++ +
Sbjct: 663 EYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILGV 706

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                               
Sbjct: 707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------ 742

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                               + + V  Y               Q+PLV            
Sbjct: 743 -----------------RMDTLAHVLYYP--------------QKPLV----------TT 761

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  G N +VA   + GYN EDS++++   V    F S+    ++      
Sbjct: 762 RSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821

Query: 855 KLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               EEI           +       +D+ G+I  G  V+  D+++GK     E+    +
Sbjct: 822 GFDQEEIFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGEDVIIGKTVTLPENDDELD 881

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                     +    RD S  + +  +G V  V +       K
Sbjct: 882 ST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|215254175|gb|ACJ64092.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 391

 Score =  394 bits (1011), Expect = e-107,   Method: Composition-based stats.
 Identities = 249/391 (63%), Positives = 305/391 (78%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+
Sbjct: 61  LSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LK
Sbjct: 121 TARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLK 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           A+ P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L 
Sbjct: 181 ADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLT 240

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFED
Sbjct: 241 KYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFED 300

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           S+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +G
Sbjct: 301 SILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIG 360

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           AEV  GDILVGK+TPKGE+ +TPEEKLLRAI
Sbjct: 361 AEVKGGDILVGKVTPKGETQLTPEEKLLRAI 391


>gi|73975065|ref|XP_860805.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            9 [Canis familiaris]
          Length = 1182

 Score =  393 bits (1010), Expect = e-107,   Method: Composition-based stats.
 Identities = 176/1092 (16%), Positives = 331/1092 (30%), Gaps = 203/1092 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 249  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 308

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 309  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 362

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 363  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 422

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 423  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 482

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 483  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 538

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 539  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 597

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM--- 715
              I  I     ++ + A  +   L   +  ++L+      Q     + E   VG G    
Sbjct: 598  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQEHK--QREQQAVGEGEAGS 655

Query: 716  ----ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                +     +SG           E +D +      +    D        Y         
Sbjct: 656  PLNKDWQDLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY--------- 697

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                                      PS  LG       +  + +P+  +N         
Sbjct: 698  ----------------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQS 734

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             M  + +   ++I  F                           ++    +  V       
Sbjct: 735  AMGKQAMG--VYITNF---------------------------HVRMDTLAHVLYYPQKP 765

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             +    +       +      + AI      +  D+ +   S V        +F R   +
Sbjct: 766  LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKE 824

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  +    + E  E   R+          +       I  G           K+  L   
Sbjct: 825  QESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL--- 881

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                              + +  +E    +Y         R        Q    +     
Sbjct: 882  -----------------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGY 924

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            +  K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM
Sbjct: 925  KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRM 984

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E   G      G+                                         
Sbjct: 985  TIGHLIECLQGKVSANKGEIGD-------------------------------------- 1006

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP  D  + + I+++L        G  +LY+G TG      + +
Sbjct: 1007 ---------------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFI 1051

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L
Sbjct: 1052 GPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFL 1111

Query: 1312 QEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKE 1353
            +E L   SD     V            RT  YE    G            P +  +L +E
Sbjct: 1112 RERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQE 1169

Query: 1354 MQALGLSIDLEN 1365
            + ++ ++  + +
Sbjct: 1170 LMSMSIAPRMMS 1181



 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 146/1007 (14%), Positives = 294/1007 (29%), Gaps = 203/1007 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-------------RID 207
            ++ F     + + +G+    CR        ++        I V             RI 
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQSAIGQRIV 253

Query: 208 R-----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                 +++VP+     ALG  S+ +IL          +  +     L  A ++    V+
Sbjct: 254 ATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVA 313

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            + +     +  +   K++     + L+++ +  +G++  C          +      + 
Sbjct: 314 LNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH---RLL 369

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A    +    +   +  +    P+L          +   +     K           +
Sbjct: 370 LAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLEL 429

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                + +  +  S+    + D  K   +  G  ++  RL   +      R         
Sbjct: 430 AIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDG 489

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +                ++KN   +  + +       +  ++  S+
Sbjct: 490 KLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSM 546

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
              + I+   +  A   F     +   ++    ++ +   RR   +    V+  R   E 
Sbjct: 547 ENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIRER 606

Query: 559 RDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFAR-------VNAYGFIETPYRKVCDGKV 610
                T  GRIC P    E   + L                V          +   D   
Sbjct: 607 EIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQEHKQREQQAVGEGEAGSPLNKDWQDLVA 666

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           +  V Y+  +EEE   +A     L E                  +         +  P  
Sbjct: 667 SGVVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSM 710

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ + AS+IPF +++ S R      M +QA+ +                           
Sbjct: 711 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV-------------------- 750

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + V  Y               Q+PLV        
Sbjct: 751 ---------------------RMDTLAHVLYYP--------------QKPLV-------- 767

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G N +VA   + GYN EDS++++   V    F S+    ++  
Sbjct: 768 --TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQ 825

Query: 851 ARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                   EE+           +       +D+ G+I  G  V+  D+++GK     E+ 
Sbjct: 826 ESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENE 885

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              E          +    RD S  + +  +G V  V +       K
Sbjct: 886 DELEGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 925


>gi|281352499|gb|EFB28083.1| hypothetical protein PANDA_006563 [Ailuropoda melanoleuca]
          Length = 1168

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 172/1085 (15%), Positives = 325/1085 (29%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 247  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 306

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 307  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 360

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 361  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 420

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 421  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 480

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 481  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 536

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 537  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 595

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 596  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 648

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 649  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 683

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 684  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 727

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 728  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 758

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 759  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 817

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 818  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 867

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +E    +Y         R        Q    +     +  K+ V
Sbjct: 868  ----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 917

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 918  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 977

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 978  CLQGKVSANKGEIGD--------------------------------------------- 992

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 993  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1044

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1045 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1104

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1105 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1162

Query: 1361 IDLEN 1365
              + +
Sbjct: 1163 PRMMS 1167



 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 33  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 82

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 83  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 137

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 138 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 197

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 198 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 247

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 248 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 307

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 308 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 364

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 365 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 423

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 424 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 483

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 484 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 540

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 541 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 600

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 601 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 655

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 656 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 699

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 700 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 736

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 737 ------------------RMDTLAHVLYYP--------------QKPLV----------T 754

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 755 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 814

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 815 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 874

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 875 EGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 911


>gi|166034417|gb|ABY78985.1| DNA-directed RNA polymerase beta chain [Sinorhizobium sp. ITTG S8]
          Length = 214

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 143/214 (66%), Positives = 171/214 (79%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPIEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            KKI +++  Y  +GDI PLR  ++ V+G G   E I  YDD+S++R+AEQ + GV ++TP
Sbjct: 61   KKIGAMLEAYHESGDIKPLRQTIDDVMGAGPKGEPIKQYDDESIVRLAEQTRRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  +N ML  A L  +GQS LYDG TG+ FDR VTVGYIYMLKLNH+V DK++A
Sbjct: 121  VFDGAVEADVNEMLEKAGLKVTGQSTLYDGRTGDAFDRQVTVGYIYMLKLNHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|326200273|gb|ADZ52312.1| RNA polymerase beta subunit [Asclepias syriaca]
          Length = 1069

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 156/497 (31%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   ++  + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VHRGKYIKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNSEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              IF    I K E    V  +  E + ++    +  L RN+  +   ++ G    +G   
Sbjct: 680  DDIFTSFHIRKYEIQTHVTSQGPERVTKEIPYLEAHLLRNL-DKKGIVMLGSWVETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIRKRG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 796  -GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S L+DG T
Sbjct: 912  GNPW------------------------VFE---------------PEYPGKSRLFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GNAFEQPVLIGNSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRARQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSDD+  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDDIRARQEVLGTTMVGGTIPNPKDAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLISEKNFQINRKE 1069



 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 231/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSQLEIDRKARIWARVSRKQKISILVLSSAMGSNLREIIENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K + +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 FFLSFLNDKERKKIRSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENAVRGTIGGAIRHKLIPTPQNLVTSTALTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GGV    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKFSYLGPGGVTGRTASFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         EELV  R 
Sbjct: 442 ARIGHWGSLESPFFEISERSTGMQMLYLSPGRDEYYMVAWGNSLALNQDIQEEELVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI  SLIPF+E++D+NR LM  NMQRQA+PL ++E  
Sbjct: 502 RQEFLTIAWEQIHLRSIFPFQYFSIGTSLIPFIEHNDANRALMSSNMQRQAIPLYRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G V   D  +I++                  L+ ++R
Sbjct: 562 IVGTGLERQAALDSGALSIAEREGKVVYTDVDKILLSVN--------GDTLSIPLVLYER 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V  G  +++  I+ADG +T  G+L+LG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPRVHRGKYIKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +D+FTS HI ++E+    T  GPE +T++IP +    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYDDIFTSFHIRKYEIQTHVTSQGPERVTKEIPYLEAHLLRNLDKKGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIRK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 RGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DRGLPEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYELLTYSSELYVSAGLIW---------KTSRDVQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G    +E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSQLEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EI+    YP+   S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREIIENVCYPEFFLSFLNDKERKKIRSKE 220


>gi|73975073|ref|XP_860930.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            13 [Canis familiaris]
          Length = 1180

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 172/1086 (15%), Positives = 325/1086 (29%), Gaps = 197/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              I D  +   +          P L  +    +L   ++ +         + F       
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSEFFF--FSW 659

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                +SG           E +D +      +    D        Y               
Sbjct: 660  QDLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY--------------- 695

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
                                PS  LG       +  + +P+  +N          M  + 
Sbjct: 696  ----------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQA 738

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +   ++I  F                           ++    +  V        +    
Sbjct: 739  MG--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRS 769

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +      + AI      +  D+ +   S V        +F R   ++  +  
Sbjct: 770  MEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKG 828

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
              + E  E   R+          +       I  G           K+  L         
Sbjct: 829  FDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL--------- 879

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                        + +  +E    +Y         R        Q    +     +  K+ 
Sbjct: 880  -----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIR 928

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + 
Sbjct: 929  VRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLI 988

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E   G      G+                                               
Sbjct: 989  ECLQGKVSANKGEIGD-------------------------------------------- 1004

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                     +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  
Sbjct: 1005 ---------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQ 1055

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L  
Sbjct: 1056 RLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFE 1115

Query: 1318 KSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGL 1359
             SD     V            RT  YE    G            P +  +L +E+ ++ +
Sbjct: 1116 ASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSI 1173

Query: 1360 SIDLEN 1365
            +  + +
Sbjct: 1174 APRMMS 1179



 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 147/1005 (14%), Positives = 295/1005 (29%), Gaps = 201/1005 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFI-ETPYRKVCDGKVTN 612
             E      T  GRIC P    E   + L        +   Y    E  +    D   + 
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSEFFFFSWQDLVASG 666

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V Y+  +EEE   +A     L E                  +         +  P  ++
Sbjct: 667 VVEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMIL 710

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                             
Sbjct: 711 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV---------------------- 748

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                 + + V  Y               Q+PLV          
Sbjct: 749 -------------------RMDTLAHVLYYP--------------QKPLV---------- 765

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                      +L  G N +VA   + GYN EDS++++   V    F S+    ++    
Sbjct: 766 TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQES 825

Query: 853 DTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 EE+           +       +D+ G+I  G  V+  D+++GK     E+   
Sbjct: 826 KKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDE 885

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            E          +    RD S  + +  +G V  V +       K
Sbjct: 886 LEGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 923


>gi|324120616|dbj|BAJ78699.1| RNA polymerase II second largest subunit [Phraortes illepidus]
          Length = 1150

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAIMPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKTLMKEVRMYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   +  M +            V +G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVENGKLLLKKRHIDMLKDREYNNYGWQVLVASGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               + + +   +   +    Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MMTEDMKHEKEYAYCTTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V    +   +  
Sbjct: 707  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPHKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 738  RSMEYLRFRELPAGINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 795  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGK-------- 845

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D +    +E    ++    +    R        Q    +     +
Sbjct: 846  ----------TITLPDNE--DELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNAEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 894  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 975  --------------ATPFNDAVNVQKISALLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1139 MAMNIAPRLM 1148



 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 287/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    +        + + Q  ++G +
Sbjct: 73  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDGDEPM-----ESQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 187

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 188 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAIMPYI 238

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 239 KQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVIQEQNVALNFIGA 298

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 299 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 354

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 355 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKTLMKEVRMYAQKFIDRGKDFNLELAIKTKI 414

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 415 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 474

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 475 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 531

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 532 APSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 591

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L         ++     E           +  V Y+  +EEE
Sbjct: 592 DAGRICRPLLIVENGKLLLKKR-----HIDMLKDREYNNYGWQVLVASGVVEYIDTLEEE 646

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA                +      E+           +  P  ++ + AS+IPF +
Sbjct: 647 TVMIAM---------------MTEDMKHEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 691

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 692 HNQSPRNTYQSAMGKQAMGVYITNYHV--------------------------------- 718

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 719 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 746

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 747 ELPAGINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 806

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 807 KPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITLPDNEDELEGTT------ 860

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 861 -KRFTKRDASTFLRNSETGIV 880


>gi|194270592|gb|ACF36842.1| RNA polymerase beta subunit [Enterococcus sp. CSL 7544-3]
          Length = 594

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 252/424 (59%), Positives = 319/424 (75%), Gaps = 9/424 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+
Sbjct: 1   NPLSELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSY 60

Query: 590 ARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           A+VN YGFIETPYR+V   +GKVT  + YL+A EE++  +AQANS L+EDGSF EELV  
Sbjct: 61  AKVNKYGFIETPYRRVDRANGKVTEHIDYLTADEEDHYMVAQANSPLNEDGSFAEELVMA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V  EK+D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL++  
Sbjct: 121 RIQSENLEVSIEKVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIQPR 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTGME   A  SGAA++ K  G+VE VDA  I +R   G LD        Y ++KF
Sbjct: 181 SPIVGTGMEYKAAHDSGAALLCKHDGVVEYVDAKEIRVRRNNGALDK-------YNVIKF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T  NQRP+V +G+ V   D +ADG S + G++ALG+N+LVAFM W GYN+ED++
Sbjct: 234 HRSNAGTSYNQRPIVSLGEIVEAGDTLADGSSMEQGEMALGQNVLVAFMTWEGYNYEDAI 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++S R+V +DV+TSIHIEE+E  ARDTKLGPEEITR++PNV ++ LK++DE GII +GAE
Sbjct: 294 IMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITRELPNVGDDALKDLDEMGIIRIGAE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R
Sbjct: 354 VKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTR 413

Query: 948 HGID 951
              D
Sbjct: 414 EAGD 417



 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 139/449 (30%), Positives = 191/449 (42%), Gaps = 79/449 (17%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +    I         + ++  I+ +G  V  GD L    +   +  M   + +
Sbjct: 219  RRNNGALDKYNVIKFHRSNAGTSYNQRPIVSLGEIVEAGDTLADGSS-MEQGEMALGQNV 277

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA---- 968
            L A    +  +  D  +     V   V        +  +  +  +  E    EL      
Sbjct: 278  LVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITRELPNVGDD 337

Query: 969  --RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE  I+      +  ++L G+    G         L   +  E  R      ++
Sbjct: 338  ALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKARE-VRDTSL 395

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +       +                    KI   + GD++ PGV  +V+V++  KR I  
Sbjct: 396  RVPHGGGGI----------------VHDVKIFTREAGDELAPGVNMLVRVYIVQKRKINE 439

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A  
Sbjct: 440  GDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAR 499

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  + + + D     D+                                         
Sbjct: 500  SLGIHVATPVFDGADEDDVW---------------------------------------- 519

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                   A           ADL    ++ILYDG TGEPFD  ++VG +YMLKL HMV DK
Sbjct: 520  -------ATVAE-------ADLARDAKTILYDGRTGEPFDNRISVGVMYMLKLAHMVDDK 565

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 566  LHARSIGPYSLVTQQPLGGKAQFGGQRFG 594


>gi|23512288|gb|AAH38472.1| Polymerase (RNA) II (DNA directed) polypeptide B [Mus musculus]
          Length = 1167

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 325/1085 (29%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 246  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 305

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 306  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 359

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 360  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 419

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 420  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 480  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 535

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 536  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 594

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 595  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 647

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 648  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 682

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 683  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 726

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 727  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 757

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 758  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 816

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+                  I  G           K+  L          
Sbjct: 817  DQEEVFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 866

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 867  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 916

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 917  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 976

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 977  CLQGKVSANKGEIGD--------------------------------------------- 991

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 992  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1043

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1044 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1103

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1104 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1161

Query: 1361 IDLEN 1365
              + +
Sbjct: 1162 PRMMS 1166



 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 32  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 81

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 82  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 136

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 137 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 196

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 197 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 246

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 247 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 306

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 307 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 363

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 364 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 422

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 423 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 482

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 483 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 539

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 540 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 599

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 600 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 654

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 655 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 698

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 699 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 735

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 736 ------------------RMDTLAHVLYYP--------------QKPLV----------T 753

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 754 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 813

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +     + +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 814 KGFDQEEVFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 873

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 874 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 910


>gi|194379208|dbj|BAG58155.1| unnamed protein product [Homo sapiens]
          Length = 1167

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 246  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 305

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 306  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 359

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 360  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 419

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 420  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 479

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 480  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 535

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 536  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 594

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 595  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 647

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 648  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 682

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 683  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 726

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 727  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 757

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 758  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 816

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 817  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 866

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 867  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 916

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 917  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 976

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 977  CLQGKVSANKGEIGD--------------------------------------------- 991

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 992  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1043

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1044 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1103

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1104 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1161

Query: 1361 IDLEN 1365
              + +
Sbjct: 1162 PRMMS 1166



 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 32  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 81

Query: 77  VSYEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 82  EQIYLSKPTHRERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 136

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 137 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 196

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 197 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 246

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 247 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 306

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 307 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 363

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 364 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 422

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 423 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 482

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 483 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 539

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 540 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 599

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 600 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 654

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 655 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 698

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 699 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 735

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 736 ------------------RMDTLAHVLYYP--------------QKPLV----------T 753

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 754 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 813

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 814 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 873

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 874 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 910


>gi|162606010|ref|XP_001713520.1| DNA-directed RNA polymerase II second largest subunit [Guillardia
            theta]
 gi|13794440|gb|AAK39815.1|AF165818_23 DNA-directed RNA polymerase II second largest subunit [Guillardia
            theta]
          Length = 1206

 Score =  393 bits (1010), Expect = e-106,   Method: Composition-based stats.
 Identities = 194/1174 (16%), Positives = 371/1174 (31%), Gaps = 206/1174 (17%)

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             F              + +         +  +           ++           S+ +
Sbjct: 195  IFQKNENLRNTIKIKNYTVEGYLYFAECRSVADYSKWSPSLLTVKVCLCPYKDQKFSIFK 254

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
            K +KF       L G +    ++       Y +    I        F +EI  +  +  D
Sbjct: 255  KNLKFNS-PEIFLSGGFYLRMMLP------YFKKDIPITWIFKALGFENEIEILDYICYD 307

Query: 351  SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            S + +       + + +K      L I   +   + +  ++ + +         K+    
Sbjct: 308  SQDEDLISIVRYIVEDDKISTQNSLSISCPILDQETALAAIGQHVSKGPQGIRIKFAYEV 367

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            + +  +               +      II  L+  + GK  +DD D+ G +R+ +VG +
Sbjct: 368  LQKEFLPHI---GIGQGFELRKGYFFGYIINKLISTQIGKRKMDDRDHYGYKRLDTVGPL 424

Query: 471  LKNQYRLGLLRMERSIKERISSVDID---SVMPQDLINAKPVVSAVCEFFCSSQL----- 522
            L   +R  L ++ +  K  +             +D   +  V + +     +        
Sbjct: 425  LSQLFRQLLGKVLKEFKTNVQKKIHRLDKKFELKDFFKSNYVTTGIQYALSTGNWGTDKQ 484

Query: 523  ------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                  SQ+   ++  S ++H RR+++    G        + R +H +H+G ICP ET E
Sbjct: 485  SLRTGISQVLNRLSYSSTLSHLRRVNSPSAKG----NKITKPRHLHNSHWGYICPVETPE 540

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            GH+ GLV +L   A +           K+ +         L ++EE N    +++  +  
Sbjct: 541  GHSCGLVKNLALTAMITIGTSPLFIIEKLENLG-------LESLEEYNSDKLKSSFKVFV 593

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +G +                P   I  +    ++ +      I   + D           
Sbjct: 594  NGCWIG----------THKNPFALISKMKIYRRRNIFSEEISIILDDYDK---------- 633

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                               E  +   SG  I        E +  I    + +    D   
Sbjct: 634  -------------------EIKIFSDSGRVIRPLLIINEENIIKINNKQKYLHNLTDD-- 672

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                           Q+   N + L++ G  + V   +      S         +N+   
Sbjct: 673  ---------------QSIYSNFQQLLEEGILEYVDPEEEETCLISMFYN-FKYLKNLHTQ 716

Query: 815  FMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +       S++  +   ++            ++       +G      D        
Sbjct: 717  KIKYTHCELHPSVILGVCASLIPFCDHNQSPRNTYQAAMGKQAIGINVSNYDFRM----- 771

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +        +    +              + AI      +  D+ +   
Sbjct: 772  ------DTMCHILYYPQKPLVCTKSMNFIKFKDFPNGINAIVAIACYGGYNQEDSIIMSQ 825

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +   +     F R+  D  +     ++E  E+      +   I           I  G
Sbjct: 826  DSIDRGLF-RSFFFRNYKDVEKIKFGGKKETFEIPNWKSCNGIKIHSYEKLDLDGLIGEG 884

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +   S      K+             +  +    +D ++      +K    +S    E  
Sbjct: 885  KKVNSNDIIIGKT-----------CPTNLFDNNNEDLRLLGKNLKIKTDCSSSIKNFETG 933

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +K+   +          R+VK+ +   R  Q GDK A RHG KGI+  I    +MPF 
Sbjct: 934  VVDKVILAK-----SDEGFRLVKIRIRSVRLPQIGDKFASRHGQKGIIGMIYRQVNMPFS 988

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            + G   DI++NP  +PSRM +G + E  L  A    G +                     
Sbjct: 989  EQGISPDIIMNPHAIPSRMTIGHLLECLLSKAVSMKGIEGDG------------------ 1030

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               TP F+  + E I + L   + D++G
Sbjct: 1031 -----------------------------------TP-FERQNMEDIMNFLEKNNFDKNG 1054

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ILY+G  G+     + +G  Y  KL HMV DK+++R+ G   ++T+QP+ G+S  GG 
Sbjct: 1055 WEILYNGFNGKRIKSLIFMGPTYYQKLKHMVEDKIHSRARGPIQILTRQPVEGRSREGGL 1114

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV---AGNDTFET- 1341
            R GEME  C+ ++GAA  L++ L  +SD       D  G       IV      + FE  
Sbjct: 1115 RFGEMERDCMISHGAAIFLKDRLFDQSDPFGIYVCDFCG------FIVVSNKKQNNFECR 1168

Query: 1342 -----------GTPESFNVLVKEMQALGLSIDLE 1364
                         P +F +L++E+ +L + + L 
Sbjct: 1169 NCSNRSMISFIRIPYAFKLLIQELMSLSVGVRLI 1202



 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 107/793 (13%), Positives = 231/793 (29%), Gaps = 158/793 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA------------AMLEF 76
           L++ Q  S+++F+   +          Q     + PIT +                ++  
Sbjct: 24  LVDQQINSFNNFIQNTM----------QDIIDDMPPITVYIDNDPGNDDLLSKIRMVIRL 73

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P +            ++   R+LTY+ PL   +             KSI  I 
Sbjct: 74  GQLHLSKPTYIEDDGLVHNLVPNEARLRNLTYSSPLYCEIS-----TSIIKNEKSIDYIL 128

Query: 127 EQ---SIYMGDLPLM------------------------TKDGTFVIKGIQRIVVSQLHR 159
           +Q    I +G +P+M                           G F++ G ++++V+Q   
Sbjct: 129 KQFSEKILIGRIPIMIKSKFCILSNLDIKCLKNLGECPDDPGGYFIVNGSEKVIVAQEQL 188

Query: 160 SPG-IHFDHD--------KGRASLSGKLLYACR--------------------IIPDQGL 190
           S   ++            K +       LY                       + P +  
Sbjct: 189 SWNKVYIFQKNENLRNTIKIKNYTVEGYLYFAECRSVADYSKWSPSLLTVKVCLCPYKDQ 248

Query: 191 WMDIEFDSKDI------------IHVRI---DRRRKVPVTSFLMALGMDSE-EILSTFYP 234
                   K++             ++R+     ++ +P+T    ALG ++E EIL     
Sbjct: 249 --KFSIFKKNLKFNSPEIFLSGGFYLRMMLPYFKKDIPITWIFKALGFENEIEILDYICY 306

Query: 235 K---------IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
                     + Y    D      S +         ++L  I         G ++     
Sbjct: 307 DSQDEDLISIVRYIVEDDKISTQNSLSISCPILDQETALAAIGQHVSKGPQGIRI-KFAY 365

Query: 286 KSLKEKGVKFLGI------TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           + L+++ +  +GI            G Y+   +++ + G+  ++  D    K L+ +   
Sbjct: 366 EVLQKEFLPHIGIGQGFELRKGYFFG-YIINKLISTQIGKRKMDDRDHYGYKRLDTVGPL 424

Query: 340 EIRDIPIL--YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
             +    L   V         +     DK  + KD     Y         T  +  ++  
Sbjct: 425 LSQLFRQLLGKVLKEFKTNVQKKIHRLDKKFELKDFFKSNY--------VTTGIQYALST 476

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             +    +   + + +V   +  +       R          I     L N         
Sbjct: 477 GNWGTDKQSLRTGISQVLNRLSYSSTLSHLRRVNSPSAKGNKITKPRHLHNSHWGYICP- 535

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                       ++KN     ++ +  S    I  ++   +   +  N+  + S+   F 
Sbjct: 536 --VETPEGHSCGLVKNLALTAMITIGTSPLFIIEKLENLGLESLEEYNSDKLKSSFKVFV 593

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
               +   +     +S++   RR +   +          +   +       I P      
Sbjct: 594 NGCWIGTHKNPFALISKMKIYRRRNIFSEEISIILDDYDKEIKIFSDSGRVIRPLLIINE 653

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NI  +++   +         ++ Y           + Y+   EEE   I+         
Sbjct: 654 ENIIKINNKQKYLH--NLTDDQSIYSNFQQLLEEGILEYVDPEEEETCLISMF------- 704

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                   +     + +   + K    +  P  ++ + ASLIPF +++ S R      M 
Sbjct: 705 --------YNFKYLKNLHTQKIKYTHCELHPSVILGVCASLIPFCDHNQSPRNTYQAAMG 756

Query: 698 RQAVPLLKAEAPF 710
           +QA+ +  +   F
Sbjct: 757 KQAIGINVSNYDF 769


>gi|4505941|ref|NP_000929.1| DNA-directed RNA polymerase II subunit RPB2 [Homo sapiens]
 gi|157822127|ref|NP_001099472.1| DNA-directed RNA polymerase II subunit RPB2 [Rattus norvegicus]
 gi|114594586|ref|XP_517275.2| PREDICTED: DNA directed RNA polymerase II polypeptide B isoform 2
            [Pan troglodytes]
 gi|296196473|ref|XP_002745851.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2 [Callithrix
            jacchus]
 gi|297292842|ref|XP_001083325.2| PREDICTED: DNA-directed RNA polymerase II subunit RPB2 isoform 1
            [Macaca mulatta]
 gi|297673513|ref|XP_002814803.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like isoform 4
            [Pongo abelii]
 gi|401012|sp|P30876|RPB2_HUMAN RecName: Full=DNA-directed RNA polymerase II subunit RPB2; AltName:
            Full=DNA-directed RNA polymerase II 140 kDa polypeptide;
            AltName: Full=DNA-directed RNA polymerase II subunit B;
            AltName: Full=RNA polymerase II subunit 2; AltName:
            Full=RNA polymerase II subunit B2
 gi|36122|emb|CAA45124.1| RNA polymerase II 140 kDa subunit [Homo sapiens]
 gi|254869|gb|AAB23139.1| RNA polymerase II second largest subunit, RNA polymerase B second
            largest subunit [human, HeLa cells, Peptide, 1174 aa]
 gi|33870592|gb|AAH23503.2| Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa [Homo
            sapiens]
 gi|119625924|gb|EAX05519.1| polymerase (RNA) II (DNA directed) polypeptide B, 140kDa [Homo
            sapiens]
 gi|149035168|gb|EDL89872.1| polymerase (RNA) II (DNA directed) polypeptide B (predicted) [Rattus
            norvegicus]
 gi|158260669|dbj|BAF82512.1| unnamed protein product [Homo sapiens]
 gi|168277428|dbj|BAG10692.1| DNA-directed RNA polymerase II subunit RPB2 [synthetic construct]
          Length = 1174

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|327279896|ref|XP_003224691.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Anolis
            carolinensis]
          Length = 1174

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 174/1085 (16%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGIAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIKV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGLMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHATGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVVKEGEDQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCQLNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMICPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                          +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEKGI----------------AYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|154707850|ref|NP_001092552.1| DNA-directed RNA polymerase II subunit RPB2 [Bos taurus]
 gi|73975053|ref|XP_532382.2| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            2 [Canis familiaris]
 gi|301765482|ref|XP_002918158.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like
            [Ailuropoda melanoleuca]
 gi|148744083|gb|AAI42268.1| POLR2B protein [Bos taurus]
 gi|296486557|gb|DAA28670.1| DNA directed RNA polymerase II polypeptide B [Bos taurus]
          Length = 1174

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 172/1085 (15%), Positives = 325/1085 (29%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +E    +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|126331583|ref|XP_001362455.1| PREDICTED: similar to RNA polymerase II 140 kDa subunit [Monodelphis
            domestica]
          Length = 1174

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHATGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|166034405|gb|ABY78979.1| DNA-directed RNA polymerase beta chain [Mesorhizobium sp. CFN ESH26]
 gi|166034407|gb|ABY78980.1| DNA-directed RNA polymerase beta chain [Mesorhizobium sp. CFN ESH5]
          Length = 214

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 146/214 (68%), Positives = 170/214 (79%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +KI  LI+ YK  GDI PLR  LE  +      E I DYDD+S++R++EQ + GV ++TP
Sbjct: 61   RKIGELIDAYKGGGDIKPLRKTLESFMPANDRNEPIRDYDDESIVRLSEQMRRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++A
Sbjct: 121  VFDGAHEVDINTMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|324120612|dbj|BAJ78697.1| RNA polymerase II second largest subunit [Ephemera japonica]
          Length = 1179

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 168/1092 (15%), Positives = 333/1092 (30%), Gaps = 212/1092 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 257  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 316

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 317  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 370

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+     +  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 371  YMVHRLLLAALSRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 430

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 431  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 490

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 491  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 546

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   + ++    ++      +  D       L   R   + I+    
Sbjct: 547  EFLEEWSMENLEEIAPSAILDATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVS 606

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ + +L   +  M +            V +G+ 
Sbjct: 607  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKVHIDMLKDRDYNNYGWQFLVSSGVV 666

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   + + +   +    Y             
Sbjct: 667  EYIDTLEEETVMIA---------------MSPDDLNHEKEYAYCTTY------------- 698

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 699  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 735

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V        +  
Sbjct: 736  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTT 766

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         +      K++ 
Sbjct: 767  RSMEYLRFRELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSIFY---RSYKDQE 823

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   IY +L +   I  G           K+  L    
Sbjct: 824  SKKIGDQE-EQFEKPNRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVIIGKTITL---- 878

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    +Y    +    R        Q    +     +
Sbjct: 879  ----------------PENDDELEGSTKKYVKRDASTFLRNSETGIVDQVMITLNSEGYK 922

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 923  FSKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 982

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 983  IGHLIECLQGKVSANKGEIGD--------------------------------------- 1003

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+S+L+       G  ++Y+G TG   +  + +G
Sbjct: 1004 --------------ATPFNDAVNVQKISSLLQEYGYHLRGNEVMYNGHTGRKINAQIFLG 1049

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1050 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1109

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1110 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1167

Query: 1355 QALGLSIDLENS 1366
             ++ ++  L   
Sbjct: 1168 MSMNIAPRLMVE 1179



 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 147/995 (14%), Positives = 298/995 (29%), Gaps = 186/995 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I +      L+F       P 
Sbjct: 43  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIESP-PKYFLKFEQIYLSKPT 101

Query: 86  FD----------VDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                        ++   R+LTY+ PL + + +L+V D +      +  + + Q  ++G 
Sbjct: 102 HWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKLVVKDGE------NTVETQHQKTFIGK 155

Query: 135 LPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDK 169
           +P+M                           G F+I G ++++++Q   +   ++    K
Sbjct: 156 IPIMLRSTYCLLSGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAMK 215

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR------------- 208
                 GK  Y   I        +        + V         I +             
Sbjct: 216 D-----GKFAYKAEIR----SCQEHSSRPTSTLWVNMMARSGQSIKKSAIGQRIIAILPY 266

Query: 209 -RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
            ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + + 
Sbjct: 267 IKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIG 326

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
                  +   K++     + L+++ +  +G++  C          +      + + A  
Sbjct: 327 ARGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALS 382

Query: 327 VIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
             +    +   +  +    P+L          +   +     K           +     
Sbjct: 383 RRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTK 442

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKIL 443
           + T  +  S+    + D  K   +  G  ++  RL   +      R          +   
Sbjct: 443 IITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKP 502

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
             L N    +                ++KN   +  + +       +  ++  S+   + 
Sbjct: 503 RQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEE 559

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           I    ++ A   F     +    +    +S +   RR   +    V+  R   +      
Sbjct: 560 IAPSAILDATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIY 619

Query: 564 THYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
           T  GRIC P    E  ++ L         ++     +           +  V Y+  +EE
Sbjct: 620 TDAGRICRPLLIVENGSLLLKK-----VHIDMLKDRDYNNYGWQFLVSSGVVEYIDTLEE 674

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   IA +   L                 E+           +  P  ++ + AS+IPF 
Sbjct: 675 ETVMIAMSPDDL---------------NHEKEYAYCTTYTHCEIHPAMILGVCASIIPFP 719

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +                                       
Sbjct: 720 DHNQSPRNTYQSAMGKQAMGVYITNFHV-------------------------------- 747

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                       + + V  Y               Q+PLV                    
Sbjct: 748 ---------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRF 774

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +L  G N +VA   + GYN EDS++++   V    F SI    ++          EE  
Sbjct: 775 RELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSIFYRSYKDQESKKIGDQEEQF 834

Query: 863 RD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                     +       +D+ GII  G  V+  D+++GK     E+    E    + + 
Sbjct: 835 EKPNRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVIIGKTITLPENDDELEGSTKKYVK 894

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                  RD S  + +  +G V  V I       K
Sbjct: 895 -------RDASTFLRNSETGIVDQVMITLNSEGYK 922


>gi|324120632|dbj|BAJ78707.1| RNA polymerase II second largest subunit [Euborellia plebeja]
          Length = 1174

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 252  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 311

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 312  EQNVALNFIGARGARPGV---TREKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 365

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 366  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 425

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 426  KDFNLDLAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 485

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 486  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 541

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 542  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 601

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ + +L   +  M ++           V +G+ 
Sbjct: 602  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHIDMLKEREYNNYGWQVLVASGVV 661

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 662  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 693

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 694  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 730

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 731  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 761

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 762  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDSE 818

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 819  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGLRVSGDDVVIGKTITL---- 873

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             + +  ++    +Y    +    R        Q    +     +
Sbjct: 874  ----------------PENEDELDGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 917

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 918  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 977

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 978  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 998

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 999  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1044

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1045 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1104

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1105 ERLFEVSDPYRIHVCNLCGLIAIANMRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1162

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1163 MSMNIAPRLM 1172



 Score =  240 bits (612), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 139/981 (14%), Positives = 290/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  + +   I       +L+F       P 
Sbjct: 38  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTAGEIENP-PRYLLKFEQIYLSKPT 96

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 97  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDKEEPI-----ETQHQKTFIGKI 151

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 152 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 211

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 212 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 262

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 263 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 322

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 323 RGARPGVTREKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 378

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 379 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKI 438

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 439 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 498

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 499 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 555

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 556 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 615

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     E           +  V Y+  +EEE
Sbjct: 616 DAGRICRPLLIVENGSLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 670

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 671 TVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 715

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 716 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 742

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 743 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 770

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 771 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDSESKRIGDQEEQFE 830

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    +         
Sbjct: 831 KPTRQTCQGMRNALYDKLDDDGIISPGLRVSGDDVVIGKTITLPENEDELDGTT------ 884

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 885 -KRYTKRDASTFLRNSETGIV 904


>gi|194386684|dbj|BAG61152.1| unnamed protein product [Homo sapiens]
          Length = 1083

 Score =  393 bits (1009), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 162  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 221

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 222  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 275

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 276  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 335

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 336  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 395

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 396  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 451

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 452  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 510

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 511  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 563

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 564  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 598

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 599  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 642

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 643  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 673

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 674  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 732

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 733  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIISKTVTL---------- 782

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 783  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 832

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 833  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 892

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 893  CLQGKVSANKGEIGD--------------------------------------------- 907

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 908  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 959

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 960  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1019

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1020 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1077

Query: 1361 IDLEN 1365
              + +
Sbjct: 1078 PRMMS 1082



 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 131/920 (14%), Positives = 269/920 (29%), Gaps = 173/920 (18%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----------- 139
              R+LTY+ PL + +   V    E          + Q  ++G +P+M            
Sbjct: 22  ARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQHQKTFIGKIPIMLRSTYCLLNGLT 76

Query: 140 -------------KDGTFVIKGIQRIVVSQLHRSPG-IH-FDHDKGRASLSGKLLYACRI 184
                          G F+I G ++++++Q   +   ++ F     + + +G+    CR 
Sbjct: 77  DRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGE----CR- 131

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRR-----RK-----------------VPVTSFLMALG 222
                  ++        I V +  R     +K                 VP+     ALG
Sbjct: 132 -----SCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALG 186

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
             S+ +IL          +  +     L  A ++    V+ + +     +  +   K++ 
Sbjct: 187 FVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIK 246

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + L+++ +  +G++  C          +      + + A    +    +   +  +
Sbjct: 247 YAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGRRELDDRDHYGNKRL 302

Query: 342 RDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
               P+L          +   +     K           +     + +  +  S+    +
Sbjct: 303 DLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNW 362

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            D  K   +  G  ++  RL   +      R          +     L N    +     
Sbjct: 363 GDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAE 422

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                      ++KN   +  + +       +  ++  S+   + I+   +  A   F  
Sbjct: 423 TPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVN 479

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-PAETSEG 577
              +   ++    ++ +   RR   +    V+  R   E      T  GRIC P    E 
Sbjct: 480 GCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEK 539

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L         ++     E       D   +  V Y+  +EEE   +A     L E 
Sbjct: 540 QKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEK 594

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                            +         +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 595 ----------------EVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMG 638

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 639 KQAMGVYITNFHV-----------------------------------------RMDTLA 657

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            V  Y               Q+PLV                     +L  G N +VA   
Sbjct: 658 HVLYYP--------------QKPLV----------TTRSMEYLRFRELPAGINSIVAIAS 693

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEG 872
           + GYN EDS++++   V    F S+    ++          EE+           +    
Sbjct: 694 YTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAI 753

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+I  G  V+  D+++ K     E+    E          +    RD S  + 
Sbjct: 754 YDKLDDDGLIAPGVRVSGDDVIISKTVTLPENEDELEST-------NRRYTKRDCSTFLR 806

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           +  +G V  V +       K
Sbjct: 807 TSETGIVDQVMVTLNQEGYK 826


>gi|324120648|dbj|BAJ78715.1| RNA polymerase II second largest subunit [Cryptotympana facialis]
          Length = 1175

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 169/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ + +L   ++   ++           V +G+ 
Sbjct: 603  IIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHIDNLKERDYNNYGWQVLVSSGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETTMIA---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F  +   +++R
Sbjct: 763  RSMEYLRFRELPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKR 822

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                E    E   +        +   IY +L +   I  G           K+  L    
Sbjct: 823  VGDQE----EQFEKPTRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTMTL---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                               +  +E    +Y    +    R        Q    +     +
Sbjct: 875  ----------------PDNEDELEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGISPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSANKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFIG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  239 bits (609), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 287/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEDPI-----ETQHQKSFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    +  +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     +           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGSLLLKKR-----HIDNLKERDYNNYGWQVLVSSGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TTMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKRVGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 KPTRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTMTLPDNEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYTKRDASTFLRNSETGIV 905


>gi|226958589|ref|NP_722493.2| DNA-directed RNA polymerase II subunit RPB2 [Mus musculus]
 gi|51702009|sp|Q8CFI7|RPB2_MOUSE RecName: Full=DNA-directed RNA polymerase II subunit RPB2; AltName:
            Full=DNA-directed RNA polymerase II 140 kDa polypeptide;
            AltName: Full=DNA-directed RNA polymerase II subunit B;
            AltName: Full=RNA polymerase II subunit 2; AltName:
            Full=RNA polymerase II subunit B2
 gi|148705989|gb|EDL37936.1| polymerase (RNA) II (DNA directed) polypeptide B [Mus musculus]
          Length = 1174

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 325/1085 (29%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+                  I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  238 bits (607), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +     + +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|297292844|ref|XP_002804166.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2 isoform 2
            [Macaca mulatta]
          Length = 1083

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 162  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 221

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 222  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 275

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 276  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 335

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 336  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 395

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 396  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 451

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 452  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 510

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 511  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 563

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 564  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 598

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 599  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 642

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 643  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 673

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 674  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 732

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 733  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 782

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 783  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 832

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 833  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 892

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 893  CLQGKVSANKGEIGD--------------------------------------------- 907

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 908  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 959

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 960  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1019

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1020 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1077

Query: 1361 IDLEN 1365
              + +
Sbjct: 1078 PRMMS 1082



 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 132/920 (14%), Positives = 270/920 (29%), Gaps = 173/920 (18%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----------- 139
              R+LTY+ PL + +   V    E          + Q  ++G +P+M            
Sbjct: 22  ARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQHQKTFIGKIPIMLRSTYCLLNGLT 76

Query: 140 -------------KDGTFVIKGIQRIVVSQLHRSPG-IH-FDHDKGRASLSGKLLYACRI 184
                          G F+I G ++++++Q   +   ++ F     + + +G+    CR 
Sbjct: 77  DRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGE----CR- 131

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRR-----RK-----------------VPVTSFLMALG 222
                  ++        I V +  R     +K                 VP+     ALG
Sbjct: 132 -----SCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALG 186

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
             S+ +IL          +  +     L  A ++    V+ + +     +  +   K++ 
Sbjct: 187 FVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIK 246

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + L+++ +  +G++  C          +      + + A    +    +   +  +
Sbjct: 247 YAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGRRELDDRDHYGNKRL 302

Query: 342 RDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
               P+L          +   +     K           +     + +  +  S+    +
Sbjct: 303 DLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNW 362

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            D  K   +  G  ++  RL   +      R          +     L N    +     
Sbjct: 363 GDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAE 422

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                      ++KN   +  + +       +  ++  S+   + I+   +  A   F  
Sbjct: 423 TPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVN 479

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-PAETSEG 577
              +   ++    ++ +   RR   +    V+  R   E      T  GRIC P    E 
Sbjct: 480 GCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEK 539

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L         ++     E       D   +  V Y+  +EEE   +A     L E 
Sbjct: 540 QKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEK 594

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                            +         +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 595 ----------------EVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMG 638

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 639 KQAMGVYITNFHV-----------------------------------------RMDTLA 657

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            V  Y               Q+PLV                     +L  G N +VA   
Sbjct: 658 HVLYYP--------------QKPLV----------TTRSMEYLRFRELPAGINSIVAIAS 693

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEG 872
           + GYN EDS++++   V    F S+    ++          EE+           +    
Sbjct: 694 YTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAI 753

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+I  G  V+  D+++GK     E+    E          +    RD S  + 
Sbjct: 754 YDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEST-------NRRYTKRDCSTFLR 806

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           +  +G V  V +       K
Sbjct: 807 TSETGIVDQVMVTLNQEGYK 826


>gi|108796838|ref|YP_636411.1| RNA polymerase beta subunit [Staurastrum punctulatum]
 gi|88909641|sp|Q32RW5|RPOB_STAPU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|61393606|gb|AAX45747.1| beta subunit of RNA polymerase [Staurastrum punctulatum]
          Length = 1068

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 156/510 (30%), Positives = 240/510 (47%), Gaps = 56/510 (10%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             K   ++    I          I +   + +G  V  G +L       G   +   + +L
Sbjct: 598  DKDNVQQKFNLITYERSNNGTCIHQRPTVKIGFSVRKGQLLADGSATVG-GELALGKNVL 656

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  L     V+  +       R+ I   E   ++E   I        D
Sbjct: 657  VAYMPWEGYNFEDAVLISDRLVNEDIYTSIHIQRYEISVQE---NIEGFDIITREIPHVD 713

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            + ++   +    +     G     G     K   L +  +   P  +  Q     + +  
Sbjct: 714  KYLLRHLDYRGIIK---IGAWVEPGDVLVGKLAPLEAPHLLRSPEGKLLQAIFGVQAITT 770

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                LK+    +  +++ R+  +           P  +  + V++  KR IQ GDK+AGR
Sbjct: 771  RESCLKLPAGGTGRVIDVRWIEQQG---------PSGVSSLHVYILQKRKIQVGDKVAGR 821

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VSRILP EDMP+++DGTP+D+VL+PLGVPSRMNVGQ+FE  LG A   L    +
Sbjct: 822  HGNKGVVSRILPREDMPYMQDGTPIDMVLSPLGVPSRMNVGQLFECLLGLAGSYLNNHYR 881

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +  D +   + S    F  ++      T     ++                        
Sbjct: 882  IMPFDERFEREASRKLVF-SELYKARKFTGYPWLFE------------------------ 916

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                           +  G+S L+DG TGE F++ +TVG  YM+KL HMV +K++ARS+G
Sbjct: 917  --------------PNSPGKSSLFDGRTGEIFEQSITVGKAYMMKLIHMVDEKIHARSSG 962

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             Y+LVTQQPL G+SN+GGQR+GEMEVW  + +GAAY+LQE+LTIKSD V GR++V  +IV
Sbjct: 963  PYALVTQQPLRGRSNKGGQRVGEMEVWAFEGFGAAYMLQEILTIKSDHVKGRSQVRGAIV 1022

Query: 1334 AGNDTFET-GTPESFNVLVKEMQALGLSID 1362
            A     +    P+ F +L++E++ LG+ I 
Sbjct: 1023 AKESIPKPIDPPDCFRLLIRELRCLGIEIK 1052



 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 223/590 (37%), Positives = 346/590 (58%), Gaps = 23/590 (3%)

Query: 374 LLDIYRVMRPGDVSTFSVAESMF---NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           L+ +Y+ + PG       A  +        + +  Y L T GR+ +N RLNL+       
Sbjct: 215 LIALYKQL-PGPKKVKPKANPLIISEQIQQWCAQVYKLGTSGRLNLNRRLNLNFSKSNDS 273

Query: 431 IRKEDIIAIIKILVDLRN-------GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           +  +D+IA  ++LV +         GK + DDID+L N+ V SV EML+ Q  L L+ ++
Sbjct: 274 LLPQDLIAAAELLVKMSLLHPGPKGGKDSSDDIDHLKNKHVISVAEMLRKQLSLCLIDLQ 333

Query: 484 RSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
             ++   R        + P+ ++ ++P+     +FF S +L Q  +  N L+ + H R+L
Sbjct: 334 IQVRRAIRRGISSKRILSPRSMMISRPLTQMFNQFFGSHELIQFLDQTNPLAEMAHKRKL 393

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           S LG GG+ R  A    RD+HP+HYGRIC  ETSEG N G++ SL+  ARV++ G IE P
Sbjct: 394 SLLGPGGLTRRTASFRTRDIHPSHYGRICTIETSEGMNAGVIPSLSICARVDSEGVIENP 453

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             K+         VY+ A  +E   I   N          E     +   E + +  ++I
Sbjct: 454 LHKIGGNIKEQYTVYVRAGRDERLKIGTNNCLAIGQKGQ-ERSTSTQYQQEFVSMSWDQI 512

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           +     P Q  +I ASLIPFLE++D+ R LMG +MQRQAVPL+K E   VGTG+E+ ++ 
Sbjct: 513 NLRSILPIQYFAIGASLIPFLEHNDATRTLMGSSMQRQAVPLVKPEKSIVGTGIEAHISL 572

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +++ + G ++ VD  +IV+   +              L+ ++RSN  TC++QRP 
Sbjct: 573 DSGTVLISLKDGKIKYVDGKQIVLVDKDNVQQKF-------NLITYERSNNGTCIHQRPT 625

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK+G  VR+  ++ADG +T  G+LALG+N+LVA+MPW GYNFED++LIS+R+V+ED++TS
Sbjct: 626 VKIGFSVRKGQLLADGSATVGGELALGKNVLVAYMPWEGYNFEDAVLISDRLVNEDIYTS 685

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHI+ +E+  ++   G + ITR+IP+V +  L+++D  GII +GA V PGD+LVGK+ P 
Sbjct: 686 IHIQRYEISVQENIEGFDIITREIPHVDKYLLRHLDYRGIIKIGAWVEPGDVLVGKLAPL 745

Query: 902 GESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
               +  +PE KLL+AIFG +A+  R++ L++P+G +G V+DVR   + G
Sbjct: 746 EAPHLLRSPEGKLLQAIFGVQAITTRESCLKLPAGGTGRVIDVRWIEQQG 795



 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 53/206 (25%), Positives = 94/206 (45%), Gaps = 29/206 (14%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           +PD +++Q  S+  FL             +         I   +     + +   Y    
Sbjct: 8   LPDFLQIQIESFRRFLHNC----------IFEELSKFPIIYDSNQGIEFKLIPEKYLLTE 57

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P F   + +++  TY+  L + ++L +            K  + Q++ +G LPLMT  GT
Sbjct: 58  PLFTEREAVYKFTTYSSDLYVPIQLTL---------TKEKKSRIQTVCLGSLPLMTPQGT 108

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP-DQGLWMDIEFDSKDII 202
           FVI G+   +V+Q+ R+PGI++        L+   +Y   I+  D    + +E D K  +
Sbjct: 109 FVINGVSWTIVNQILRNPGIYYV-------LNRNGMYTATILCLDVDKRLRLEIDKKGRL 161

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEI 228
            VRI+ R K+P+   L+ALG+D  +I
Sbjct: 162 SVRINNRHKIPLVFLLIALGLDINDI 187


>gi|297673505|ref|XP_002814801.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like isoform 2
            [Pongo abelii]
          Length = 1083

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 162  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 221

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 222  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 275

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 276  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 335

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 336  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 395

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 396  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 451

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 452  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 510

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 511  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 563

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 564  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 598

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 599  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 642

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 643  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 673

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 674  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 732

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 733  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 782

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 783  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 832

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 833  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 892

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 893  CLQGKVSANKGEIGD--------------------------------------------- 907

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 908  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 959

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 960  LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1019

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1020 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1077

Query: 1361 IDLEN 1365
              + +
Sbjct: 1078 PRMMS 1082



 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 132/920 (14%), Positives = 270/920 (29%), Gaps = 173/920 (18%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----------- 139
              R+LTY+ PL + +   V    E          + Q  ++G +P+M            
Sbjct: 22  ARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQHQKTFIGKIPIMLRSTYCLLNGLT 76

Query: 140 -------------KDGTFVIKGIQRIVVSQLHRSPG-IH-FDHDKGRASLSGKLLYACRI 184
                          G F+I G ++++++Q   +   ++ F     + + +G+    CR 
Sbjct: 77  DRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGE----CR- 131

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRR-----RK-----------------VPVTSFLMALG 222
                  ++        I V +  R     +K                 VP+     ALG
Sbjct: 132 -----SCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALG 186

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
             S+ +IL          +  +     L  A ++    V+ + +     +  +   K++ 
Sbjct: 187 FVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIK 246

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + L+++ +  +G++  C          +      + + A    +    +   +  +
Sbjct: 247 YAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGRRELDDRDHYGNKRL 302

Query: 342 RDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
               P+L          +   +     K           +     + +  +  S+    +
Sbjct: 303 DLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNW 362

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            D  K   +  G  ++  RL   +      R          +     L N    +     
Sbjct: 363 GDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAE 422

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                      ++KN   +  + +       +  ++  S+   + I+   +  A   F  
Sbjct: 423 TPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVN 479

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-PAETSEG 577
              +   ++    ++ +   RR   +    V+  R   E      T  GRIC P    E 
Sbjct: 480 GCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEK 539

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L         ++     E       D   +  V Y+  +EEE   +A     L E 
Sbjct: 540 QKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEK 594

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                            +         +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 595 ----------------EVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMG 638

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 639 KQAMGVYITNFHV-----------------------------------------RMDTLA 657

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            V  Y               Q+PLV                     +L  G N +VA   
Sbjct: 658 HVLYYP--------------QKPLV----------TTRSMEYLRFRELPAGINSIVAIAS 693

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEG 872
           + GYN EDS++++   V    F S+    ++          EE+           +    
Sbjct: 694 YTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAI 753

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+I  G  V+  D+++GK     E+    E          +    RD S  + 
Sbjct: 754 YDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEST-------NRRYTKRDCSTFLR 806

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           +  +G V  V +       K
Sbjct: 807 TSETGIVDQVMVTLNQEGYK 826


>gi|215254205|gb|ACJ64107.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 392

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 253/392 (64%), Positives = 309/392 (78%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VG
Sbjct: 121 SGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           ILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV
Sbjct: 361 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDV 392


>gi|166034409|gb|ABY78981.1| DNA-directed RNA polymerase beta chain [Mesorhizobium sp. CFN ESH18]
          Length = 214

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 145/214 (67%), Positives = 170/214 (79%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT  DIVLNPLGVPSRMNVGQI ETHLGWAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +KI  LI+ YK  GDI PLR  LE  +      E I +YDD+S++R++EQ + GV ++TP
Sbjct: 61   RKIGELIDAYKGGGDIKPLRKTLESFMPANDRNEPIREYDDESIVRLSEQMRRGVSIATP 120

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  IN+ML  A L  SGQS LYDG TGEPFDR VT+GYIYMLKL+H+V DK++A
Sbjct: 121  VFDGAHEVDINTMLEQAGLHTSGQSQLYDGRTGEPFDRKVTMGYIYMLKLHHLVDDKIHA 180

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 181  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 214


>gi|166034427|gb|ABY78990.1| DNA-directed RNA polymerase beta chain [Agrobacterium sp. ITTG S2]
 gi|166034429|gb|ABY78991.1| DNA-directed RNA polymerase beta chain [Agrobacterium sp. ITTG S10]
 gi|167375134|gb|ABZ79325.1| DNA-directed RNA polymerase beta chain [Agrobacterium sp. CFN_ERSH16]
          Length = 213

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 139/214 (64%), Positives = 173/214 (80%), Gaps = 1/214 (0%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VSRI+P EDMPFL+DGT VDI LNPLGVPSRMNVGQI ETHL WAC G+G
Sbjct: 1    MAGRHGNKGVVSRIVPVEDMPFLEDGTHVDICLNPLGVPSRMNVGQILETHLAWACAGMG 60

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            KKI  ++ +Y+   DIS LRS L ++  + ++ E +  +DDDS++++AE+ K GV ++TP
Sbjct: 61   KKIGEMLEEYRKTMDISELRSELTEIYASEANDE-VQRFDDDSLVKLAEEAKRGVSIATP 119

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VFDGA E  + +ML+ A L ESGQS+LYDG TGEPFDR VTVGY+YM+KLNH+V DK++A
Sbjct: 120  VFDGAHEPDVAAMLKKAGLHESGQSVLYDGRTGEPFDRKVTVGYMYMIKLNHLVDDKIHA 179

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            RS G YSLVTQQPLGGK+  GGQR GEMEVW ++
Sbjct: 180  RSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 213


>gi|324120624|dbj|BAJ78703.1| RNA polymerase II second largest subunit [Nomadacris japonica]
          Length = 1173

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 176/1087 (16%), Positives = 336/1087 (30%), Gaps = 206/1087 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 251  GQRIVAILPYIKQEIPIIIAFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQ 310

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + T      +         KY    + +  +      D  +  +      + 
Sbjct: 311  EQNVALNFIGTRGARPGV---TKERRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 364

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 365  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 424

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 425  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 484

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 485  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 540

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 541  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 600

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             I D  D   +          P L  ++ + +L   ++ R                 E  
Sbjct: 601  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHIDRLK---------------ERD 645

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                    +VA+  G+VE +D +      +   LD                         
Sbjct: 646  YDNYGWQMLVAE--GVVEYIDTLEEETVMIAMSLDDLRHD-------------------- 683

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                K       +      P+  LG       +  + +P+  +N          M  + +
Sbjct: 684  ----KSYAYCSTHTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 732

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V    +   +    +
Sbjct: 733  G--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSM 763

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         F      K+  S  
Sbjct: 764  EYLRFRELPAGINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAESKR 820

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            +  ++ E   +        +   +Y +L +   I  G           K           
Sbjct: 821  IGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGK----------- 868

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                      + D +    +E    +Y    +    R        Q    +     +  K
Sbjct: 869  -------TITLPDNE--DELEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCK 919

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 920  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGH 979

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 980  LIECLQGKVSSNKGEIGD------------------------------------------ 997

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+S+L+       G  ++Y+G TG   +  V +G  Y
Sbjct: 998  -----------ATPFNDAVNVQKISSLLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTY 1046

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L
Sbjct: 1047 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERL 1106

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            R   +E    G        +   P +  +L +E+ A+
Sbjct: 1107 FEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMAM 1164

Query: 1358 GLSIDLE 1364
             ++  L 
Sbjct: 1165 NIAPRLM 1171



 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 133/981 (13%), Positives = 284/981 (28%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  +   I       +L+F       P 
Sbjct: 37  LVRQQLDSFDEFIQMSVQRIVEDSPQIELQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 95

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +             +   +   Q  ++G +
Sbjct: 96  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDI-----LKRVEKHKEEPVETLHQKTFIGKI 150

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 151 PIMLRSTYCLLSTLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 210

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 211 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIVAILPYI 261

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 262 KQEIPIIIAFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGT 321

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   +++     + L+++ +  +G++  C          +      + + A   
Sbjct: 322 RGARPGVTKERRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 377

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 378 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 437

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 438 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 497

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 498 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 554

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 555 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 614

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     +              V Y+  +EEE
Sbjct: 615 DAGRICRPLLIVENGSLLLKKR-----HIDRLKERDYDNYGWQMLVAEGVVEYIDTLEEE 669

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 670 TVMIAMSLDDL---------------RHDKSYAYCSTHTHCEIHPAMILGVCASIIPFPD 714

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 715 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 741

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 742 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 769

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 770 ELPAGINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 829

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 830 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDNEDELEGTT------ 883

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 884 -KRYTKRDASTFLRNSETGIV 903


>gi|194033330|ref|YP_002000391.1| beta subunit of RNA polymerase fragment 2 [Oedogonium cardiacum]
 gi|156619054|gb|ABU88205.1| RNA polymerase beta subunit [Oedogonium cardiacum]
 gi|186968947|gb|ACC97270.1| beta subunit of RNA polymerase fragment 2 [Oedogonium cardiacum]
          Length = 739

 Score =  392 bits (1008), Expect = e-106,   Method: Composition-based stats.
 Identities = 143/372 (38%), Positives = 198/372 (53%), Gaps = 55/372 (14%)

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S    ++  +F  ++   +    ++       +     + K+K       D+    VL
Sbjct: 408  LLSNMNFTKLKKFYRKNNNQELTERTINKTNIKLQFQKLRQKKDKKFYSINNDEAEQNVL 467

Query: 1072 RV---------------VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                             + V++A KR IQ GDK+AGRHGNKGIVS+ILP +DMP+L DG+
Sbjct: 468  PRKKDFSLNLFNSKPFTIHVYLAEKRKIQVGDKIAGRHGNKGIVSKILPIQDMPYLADGS 527

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
             VD+VLNPLGVPSRMNVGQI+E  LG A   LG+  + L  D K   + S    F  K+ 
Sbjct: 528  FVDLVLNPLGVPSRMNVGQIYECLLGLAGYYLGEYYRILPFDEKIGEEASRSFVF-SKLY 586

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
              G  T     +D  +                                       G++ L
Sbjct: 587  EAGMKTGNYWLFDPKN--------------------------------------PGKTYL 608

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TGE F++ V +GY Y+LKL H+V DK+++RSTG YS VTQQPL G+S +GGQRLGE
Sbjct: 609  FDGRTGEKFEQQVMIGYAYILKLVHLVDDKIHSRSTGPYSAVTQQPLRGRSKQGGQRLGE 668

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++ YGAA+ L E+LTIKSDD +GR  +++SI+   +     TPESF VLV E++A
Sbjct: 669  MEVWALEGYGAAFTLLELLTIKSDDKIGRLTIWDSILRQKEIS-IKTPESFKVLVCELKA 727

Query: 1357 LGLSIDLENSRT 1368
            L   I +     
Sbjct: 728  LCFDIGIFRKNK 739



 Score =  130 bits (328), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 82/187 (43%), Positives = 129/187 (68%), Gaps = 2/187 (1%)

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y L  + RSNQ+TC+  RP +  G+ V+  DI+AD  S+  G+LA+G+N+L+A+MPW GY
Sbjct: 11  YHLENYHRSNQDTCLVHRPTINEGNWVQPGDILADCSSSKNGELAIGQNILIAYMPWEGY 70

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED+MLIS+R+V ++++TSIHIE +E+   +T+ G E+IT+++ ++  E L ++D+ GI
Sbjct: 71  NYEDAMLISDRLVYDEIYTSIHIERYEISIEETQFGFEKITKELYDLPGENLSHLDKNGI 130

Query: 882 ICVGAEVNPGDILVGKITPKGES-PMTPEEKLLRAIFGEKAVDV-RDTSLRVPSGVSGTV 939
             +G+ +  GDILVGK+TP  +    +  EKLL  I G K  +  +DTSLRVP G+   V
Sbjct: 131 TVLGSWLKEGDILVGKVTPTDKKVKYSNYEKLLYDILGTKKQNKGKDTSLRVPKGLEAKV 190

Query: 940 VDVRIFN 946
           + + I +
Sbjct: 191 ITIEILS 197


>gi|215254187|gb|ACJ64098.1| RNA polymerase beta subunit [Vibrio brasiliensis]
          Length = 390

 Score =  392 bits (1007), Expect = e-106,   Method: Composition-based stats.
 Identities = 248/390 (63%), Positives = 306/390 (78%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E+G+F EEL+ 
Sbjct: 61  SAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEEGTFAEELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE  L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA
Sbjct: 121 ARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K
Sbjct: 181 DKPLVGTGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTK 240

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           + RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS
Sbjct: 241 YTRSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDS 300

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GA
Sbjct: 301 ILVSERVVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGA 360

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           EV  GDILVGK+TPKGE+ +TPEEKLLRAI
Sbjct: 361 EVKGGDILVGKVTPKGETQLTPEEKLLRAI 390


>gi|224049409|ref|XP_002192218.1| PREDICTED: polymerase (RNA) II (DNA directed) polypeptide B, 140kDa
            [Taeniopygia guttata]
          Length = 1174

 Score =  392 bits (1007), Expect = e-106,   Method: Composition-based stats.
 Identities = 172/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGY 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   ++         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 147/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEDQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGYDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|324120594|dbj|BAJ78688.1| RNA polymerase II second largest subunit [Metriocampa sp. 44]
          Length = 1176

 Score =  392 bits (1007), Expect = e-106,   Method: Composition-based stats.
 Identities = 169/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 254  GQRIIAIVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQ 313

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 314  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 367

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 368  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRG 427

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 428  KDFNLELAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 487

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 488  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 543

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 544  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVS 603

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +     L   +  M ++           V +G+ 
Sbjct: 604  MIRDIRDREIRIYTDAGRICRPLLIVEGGKLSLKKRHIEMLKEREYNNYGWQDLVASGVV 663

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 664  EYIDTLEEETVMIA---------------MSPEDLRQDKEYAYCTTY------------- 695

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 696  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 732

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V        +  
Sbjct: 733  QAMG--VYITNF---------------------------HVRMDTLAHVLFYPQKPLVTT 763

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         +  +   + +R
Sbjct: 764  RSMEYLRFRELPAGINSIVAIACYTGYNQEDSVIMNTSAVERGFFRSVFYRAYKDQECKR 823

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S   E    E   +   +    +   IY +L +   I  G           K+       
Sbjct: 824  SGDQE----EQFEKPTRESCQGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKT------- 872

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D++    +E    ++    +    R        Q    +     +
Sbjct: 873  ---------ITLPITDDE----LEGTTKRFSKRDASTFLRNSETGIVDQVMVTLNNEGYK 919

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 920  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 979

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 980  IGHLIECLQGKVSANKGEIGD--------------------------------------- 1000

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1001 --------------ATPFNDTVNVQKISNLLQEYGYQLRGNEVMYNGQTGRKINAQIFLG 1046

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1047 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1106

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1107 ERLFEVSDPYRVHVCNLCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1164

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1165 MAMNIAPRLM 1174



 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 148/1004 (14%), Positives = 293/1004 (29%), Gaps = 204/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+ M++    ++ P   LQA  +         P        +L+F    
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTTGEVENPP------RYLLKFEQIY 93

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              P              ++   R+LTY+ PL + +   +    E        + + Q  
Sbjct: 94  LSKPTHWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKSIVKEGEEAV-----ETQHQKT 148

Query: 131 YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
           ++G +P+M                           G F+I G ++++++Q   +   ++ 
Sbjct: 149 FIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV 208

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------- 211
              K      GK  Y   I       ++        + V +  R     +K         
Sbjct: 209 FSMKD-----GKYAYKSEIR----SCLEHSSRPTSTLWVNMLARGGQSIKKSAIGQRIIA 259

Query: 212 --------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                   +P+     ALG  ++ +IL          +  +     L  A ++    V+ 
Sbjct: 260 IVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVAL 319

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGE 316
           + +        +   K++     + L+++ +  +G++           G  V   ++   
Sbjct: 320 NFIGARGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AA 377

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            G   ++  D    K L+            L+ + +          +        +    
Sbjct: 378 LGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRGKDFNLE---- 433

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + T  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 434 ---LAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPI 490

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 491 GRDGKLAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLE 547

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I    +  A   F     +    +    +S +   RR   +    V+  R 
Sbjct: 548 EWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRD 607

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             +      T  GRIC P    EG  + L        +       E       D   +  
Sbjct: 608 IRDREIRIYTDAGRICRPLLIVEGGKLSLKKRHIEMLK-----EREYNNYGWQDLVASGV 662

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   IA +   L                 ++           +  P  ++ 
Sbjct: 663 VEYIDTLEEETVMIAMSPEDL---------------RQDKEYAYCTTYTHCEIHPAMILG 707

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 708 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 744

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 745 ------------------RMDTLAHVLFYP--------------QKPLV----------T 762

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 763 TRSMEYLRFRELPAGINSIVAIACYTGYNQEDSVIMNTSAVERGFFRSVFYRAYKDQECK 822

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE            +       +D+ GII  G  V+  D+++GK      +    
Sbjct: 823 RSGDQEEQFEKPTRESCQGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITLPITDDEL 882

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          K    RD S  + +  +G V  V +   +   K
Sbjct: 883 EGTT-------KRFSKRDASTFLRNSETGIVDQVMVTLNNEGYK 919


>gi|153868486|ref|ZP_01998391.1| DNA-directed RNA polymerase, beta subunit [Beggiatoa sp. SS]
 gi|152144194|gb|EDN71609.1| DNA-directed RNA polymerase, beta subunit [Beggiatoa sp. SS]
          Length = 195

 Score =  392 bits (1007), Expect = e-106,   Method: Composition-based stats.
 Identities = 114/194 (58%), Positives = 150/194 (77%)

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            ++K+  +    E ++   D  +L +A+    GVP++TPVFDGA E+ I  ML +A L ++
Sbjct: 1    MDKIYNSSGKQEDLNSLTDSEILELAKNLSHGVPMATPVFDGASEQEIKFMLELAALPKT 60

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GQ+ LYDG TGE F+R VTVGY+YMLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GG
Sbjct: 61   GQATLYDGRTGEAFERSVTVGYMYMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGG 120

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGA+Y LQEMLT+KSDDV GRT++Y++IV G+   E G PESFNVLV
Sbjct: 121  QRFGEMEVWALEAYGASYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLV 180

Query: 1352 KEMQALGLSIDLEN 1365
            KE+++LG+ I+LE 
Sbjct: 181  KEIRSLGIDIELEQ 194


>gi|73975067|ref|XP_860838.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            10 [Canis familiaris]
          Length = 1166

 Score =  392 bits (1007), Expect = e-106,   Method: Composition-based stats.
 Identities = 170/1081 (15%), Positives = 323/1081 (29%), Gaps = 196/1081 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 248  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 307

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 308  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 361

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 362  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 421

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 422  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 481

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 482  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 537

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              + +  + N      A   +   I      +       + +   R    ++ +    I 
Sbjct: 538  EFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSMIR 597

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             I     ++ + A  +   L   +  ++L+      Q                      +
Sbjct: 598  DIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQDLVA 650

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG           E +D +      +    D        Y                    
Sbjct: 651  SGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY-------------------- 681

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           PS  LG       +  + +P+  +N          M  + +   +
Sbjct: 682  -----CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--V 727

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +I  F                           ++    +  V        +    +    
Sbjct: 728  YITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSMEYLR 760

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +      + AI      +  D+ +   S V        +F R   ++  +    + E
Sbjct: 761  FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGFDQEE 819

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   R+          +       I  G           K+  L              
Sbjct: 820  VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL-------------- 865

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                   + +  +E    +Y         R        Q    +     +  K+ V   R
Sbjct: 866  ------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVR 919

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E   G
Sbjct: 920  IPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG 979

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G+                                                    
Sbjct: 980  KVSANKGEIGD------------------------------------------------- 990

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +L HM
Sbjct: 991  ----ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHM 1046

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-- 1320
            V DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   SD  
Sbjct: 1047 VDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPY 1106

Query: 1321 --DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               V            RT  YE    G            P +  +L +E+ ++ ++  + 
Sbjct: 1107 QVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1164

Query: 1365 N 1365
            +
Sbjct: 1165 S 1165



 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 140/998 (14%), Positives = 293/998 (29%), Gaps = 201/998 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI------------IHVRIDR 208
            ++ F     + + +G+    CR        ++      +             I  RI  
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTNNLKIKSLKKKSGAIGQRIVA 253

Query: 209 -----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                +++VP+     ALG  S+ +IL          +  +     L  A ++    V+ 
Sbjct: 254 TLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVAL 313

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
           + +     +  +   K++     + L+++ +  +G++  C          +      + +
Sbjct: 314 NFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLL 369

Query: 323 EAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            A    +    +   +  +    P+L          +   +     K           + 
Sbjct: 370 AALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELA 429

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + +  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 430 IKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGK 489

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 490 LAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 546

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I+   +  A   F     +   ++    ++ +   RR   +    + R     E+R
Sbjct: 547 NLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDI-IVSMIRDIREREIR 605

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++        P    E   + L         ++     E       D   +  V Y+  
Sbjct: 606 -IYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVVEYIDT 659

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   +A     L E                  +         +  P  ++ + AS+I
Sbjct: 660 LEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILGVCASII 703

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 704 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------------- 734

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + V  Y               Q+PLV                 
Sbjct: 735 ------------RMDTLAHVLYYP--------------QKPLV----------TTRSMEY 758

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G N +VA   + GYN EDS++++   V    F S+    ++          E
Sbjct: 759 LRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQE 818

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E+           +       +D+ G+I  G  V+  D+++GK     E+    E     
Sbjct: 819 EVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGT--- 875

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                +    RD S  + +  +G V  V +       K
Sbjct: 876 ----NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 909


>gi|324120640|dbj|BAJ78711.1| RNA polymerase II second largest subunit [Blattella nipponica]
          Length = 1175

 Score =  392 bits (1006), Expect = e-106,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 331/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGVTKDR---RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +    +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGGTLLLKKRHVDMLKEKEYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +  +D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPEDLRVDKEYAYCQTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 820  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGK-------- 870

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D      +E    ++    +    R        Q    +     +
Sbjct: 871  ----------TITLPDND--DELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYAIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMSIAPRLM 1173



 Score =  247 bits (631), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 141/981 (14%), Positives = 291/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   +++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKDRRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  L+  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    EG  + L         V+     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVEGGTLLLKKR-----HVDMLKEKEYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++     +     +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RVDKEYAYCQTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDNDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRFTKRDASTFLRNSETGIV 905


>gi|198418494|ref|XP_002128916.1| PREDICTED: similar to POLR2B protein [Ciona intestinalis]
          Length = 1173

 Score =  392 bits (1006), Expect = e-106,   Method: Composition-based stats.
 Identities = 165/1054 (15%), Positives = 321/1054 (30%), Gaps = 202/1054 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++        +A +   + +    + +      +         KY 
Sbjct: 283  DILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGV---TKEKRIKYA 339

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+   
Sbjct: 340  REILQKEMLPHVGISDFCETKK---AYFLGYMVHRLLSAALGRRELDDRDHYGNKRLDLA 396

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R     + + ++               +  I  + +   +     +      
Sbjct: 397  GPLLAFLFRGLFRNLMKEVRLYAQKFIDRGKDFNLELAIKTRIITDGLKYSLATGNWGDQ 456

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+   +   S ++H RRL++     + R     + R +H + +G ICPA
Sbjct: 457  KKAHQARAGVSQVLNRLTYASTLSHLRRLNS----PIGRDGKLAKPRQLHNSLWGMICPA 512

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EGH +GLV +L   A ++           + +     ++  +S     N      N 
Sbjct: 513  ETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWS-MENLEEISPSAIANATKIFVNG 571

Query: 633  SLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                     E+L+      R   + I+     +  I     ++ + A  +   L   ++ 
Sbjct: 572  CWVGIHRDPEQLMNTLRKLRRQMDIIVSEVSMVRDIREREIRIYTDAGRICRPLLIVENQ 631

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            ++L+      Q      +               +SG           E +D +      +
Sbjct: 632  KLLLKTRHIDQLKEDYNS--------YSWQDLVASGVV---------EYIDPLEEETIML 674

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +      + Y                                   P+  LG     
Sbjct: 675  AMFPEDLQDKGEQY-------------------------CSTYTHCEIHPAMILG----- 704

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N          M  + +   ++I  F                     
Sbjct: 705  --VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF--------------------- 739

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  ++    +  V        +    +       +      + AI      +  D+ 
Sbjct: 740  ------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINAIVAISTYTGYNQEDSI 793

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S V        +F R   D   +S   + E  E   R           +       
Sbjct: 794  IVNKSSVDRGFF-RSVFYRSYKDAENKSAYDQEETFERPERSFCTGMRHAIYDKLDDDGL 852

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +  G           K+ +L                     + +  +E    +++     
Sbjct: 853  VSPGIRVSGDDVVIGKTVML--------------------PENEDELEGTTQRFKKRDVS 892

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
               R        Q    +     +  K+ V   R  Q GDK A RHG KG        ED
Sbjct: 893  TFLRTSETGIVDQVMISINQDGYKFTKIRVRSVRVPQIGDKFASRHGQKGTCGITYRAED 952

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   D+++NP  +PSRM +G + E   G      G+                  
Sbjct: 953  MPFTSEGVQPDLIVNPHAIPSRMTIGHLIECIQGKVSANKGEIGD--------------- 997

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP  D  + + I+++L     
Sbjct: 998  --------------------------------------ATPFNDTVNVQKISNLLHEYGY 1019

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             + G  +LY+G TG   +  V  G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S 
Sbjct: 1020 QQRGNEVLYNGHTGRKLNTQVFFGPTYYQRLKHMVDDKIHSRARGPVQILNRQPMEGRSR 1079

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVA 1334
             GG R GEME  C  A+GAA  L+E L   SD     V            R+  +E    
Sbjct: 1080 DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYRVHVCNLCGLIAIANLRSHTFEC--R 1137

Query: 1335 G----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            G        +   P +  +L +E+ ++ ++  + 
Sbjct: 1138 GCKNKTHISQVRMPYACKLLFQELMSMSIAPRMM 1171



 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 145/996 (14%), Positives = 294/996 (29%), Gaps = 190/996 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +      +     +L+F       P  
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDAPIIELQAESQHTSTEVSVPTKYLLKFEQIYLSKPTH 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +   V   +         + + Q  ++G +P
Sbjct: 99  WEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVVKHEAQPV-----ETQHQKTFIGKIP 153

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 154 IMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFKKKDS 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-----------------RIDR-----R 209
                K  +   I   +   ++        + V                 RI       R
Sbjct: 214 -----KYAFTSEI---RSS-LENSSRPTSSMWVNMLARGGQGVKKSAIGQRITAIIPYIR 264

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           +++P+     ALG  S+ +IL          +  +     L  A ++    V+ + +   
Sbjct: 265 QEIPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGSR 324

Query: 269 TGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
             +  +   K++         + L   G+     T       Y+   +++   G   ++ 
Sbjct: 325 GAKPGVTKEKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLSAALGRRELDD 384

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
            D    K L+            L+ + +          +        +       +    
Sbjct: 385 RDHYGNKRLDLAGPLLAFLFRGLFRNLMKEVRLYAQKFIDRGKDFNLE-------LAIKT 437

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKI 442
            + T  +  S+    + D  K   +  G  ++  RL   +      R          +  
Sbjct: 438 RIITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTYASTLSHLRRLNSPIGRDGKLAK 497

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              L N    +                ++KN   +  + +       +  ++  S+   +
Sbjct: 498 PRQLHNSLWGMICPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLE 554

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            I+   + +A   F     +    +    ++ +   RR   +    V+  R   E     
Sbjct: 555 EISPSAIANATKIFVNGCWVGIHRDPEQLMNTLRKLRRQMDIIVSEVSMVRDIREREIRI 614

Query: 563 PTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            T  GRIC P    E   + L +      + +             D   +  V Y+  +E
Sbjct: 615 YTDAGRICRPLLIVENQKLLLKTRHIDQLKEDYNS------YSWQDLVASGVVEYIDPLE 668

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           EE   +A     L + G                          +  P  ++ + AS+IPF
Sbjct: 669 EETIMLAMFPEDLQDKGEQ----------------YCSTYTHCEIHPAMILGVCASIIPF 712

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            +++ S R      M +QA+ +                                      
Sbjct: 713 PDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------- 741

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                        + + V  Y               Q+PLV                   
Sbjct: 742 ----------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLR 767

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +L  G N +VA   + GYN EDS+++++  V    F S+    ++     +    EE 
Sbjct: 768 FRELPAGINAIVAISTYTGYNQEDSIIVNKSSVDRGFFRSVFYRSYKDAENKSAYDQEET 827

Query: 862 T-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      +       +D+ G++  G  V+  D+++GK     E+    E    R  
Sbjct: 828 FERPERSFCTGMRHAIYDKLDDDGLVSPGIRVSGDDVVIGKTVMLPENEDELEGTTQR-- 885

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   RD S  + +  +G V  V I       K
Sbjct: 886 -----FKKRDVSTFLRTSETGIVDQVMISINQDGYK 916


>gi|57530101|ref|NP_001006448.1| DNA-directed RNA polymerase II subunit RPB2 [Gallus gallus]
 gi|53127025|emb|CAG31004.1| hypothetical protein RCJMB04_1i14 [Gallus gallus]
          Length = 1174

 Score =  392 bits (1006), Expect = e-106,   Method: Composition-based stats.
 Identities = 172/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGY 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   ++         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 295/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHATGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEDQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGYDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRFTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|291401757|ref|XP_002717206.1| PREDICTED: DNA directed RNA polymerase II polypeptide B [Oryctolagus
            cuniculus]
          Length = 1174

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1085 (15%), Positives = 326/1085 (30%), Gaps = 201/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 823

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + E  E   R+          +       I  G           K+  L          
Sbjct: 824  DQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL---------- 873

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +ES   +Y         R        Q    +     +  K+ V
Sbjct: 874  ----------PENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFLGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLEN 1365
              + +
Sbjct: 1169 PRMMS 1173



 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|209879223|ref|XP_002141052.1| RNA polymerase beta subunit [Cryptosporidium muris RN66]
 gi|209556658|gb|EEA06703.1| RNA polymerase beta subunit, putative [Cryptosporidium muris RN66]
          Length = 1184

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 176/975 (18%), Positives = 319/975 (32%), Gaps = 185/975 (18%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---E 488
            +   I  ++  L     G+   DD D+ G +R+   G ++   +     +M + ++   +
Sbjct: 347  KAYFIGYMVHRLCMGALGRVPEDDRDHFGKKRLDLAGPLVAASFGQSFRKMMKDMRRLLQ 406

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
            R      +  +   + +A  +   +   F +               ++Q+   +   S +
Sbjct: 407  RNIDNGKEFDVAGVIRSASYITQTLQYQFATGNWGKDRDGKIVRTGVAQVLSRLTFASAL 466

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            ++ RRL+      + R     + R +H TH+G ICPAET EGH +GLV +L     ++  
Sbjct: 467  SYLRRLNT----PLGREGTLAKPRQLHNTHWGMICPAETPEGHAVGLVKNLALMCEIS-V 521

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL----DEDGSFTEELVFCRCAG 651
            G+     R   D    + +  +   + +++     N +     D+       L   R +G
Sbjct: 522  GYRPFAIRTFLDEWGMDSIDEVPPEDIKDKIKVFLNGNWVGCFDDSEDSITNLRMIRRSG 581

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E        +D ++   K       S+ P     +   + +  +     + +   E    
Sbjct: 582  EIPYETSIVLDVVNREVKLFTDAGRSMRPLYIVGEDGELKIRKSHIATLLGIKMPENN-- 639

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL--DPSTSGVDIYRLMKFQR 769
                              +   I+ +VD     I         D   SG+  Y   + + 
Sbjct: 640  ----------------SNEDMKILSEVDLPEGGISRDSDFTWDDLIKSGIIEYIDCEEEE 683

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            +              G            PS  LG       +  + +P+  +N     + 
Sbjct: 684  TAMIAMFMNDLRDARG-YCSTYTHCEIHPSLILG-------ICASIIPFPDHNQSPRNVY 735

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +   ++   + V                                  V     
Sbjct: 736  QSAMGKQAMG--VYTSNYNVRMDTLG---------------------------YVLYYPQ 766

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
               +    +T      +      +  I      +  D+ +   S +   +     F  + 
Sbjct: 767  KPLVTTRAMTYMRFRELPAGINCIVGIMCYSGYNQEDSLIMNQSSIDRGLFRSVFFRTYV 826

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIY---SRLMEILCGQNAVSGPKGFKKST 1006
             ++      +    IE       DE   L    Y    R   I  G   +       K  
Sbjct: 827  SEE----KQIGSNLIEAFELPNPDEVSGLRFGNYGNLDRDGLIEPGNRVLGDDIIIGKFG 882

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +       ++  +   +D  +      L+         +     +K  K       
Sbjct: 883  PIPPEERD----NRIERLTKRDCSI-----GLRSSEHGVVDEVLLSTNSKGVKFT----- 928

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                    KV V   R    GDK A RHG KG +      EDMPF +DG   DI++NP  
Sbjct: 929  --------KVKVRTIRVPHIGDKFASRHGQKGTIGITYRMEDMPFTQDGIVPDIIMNPHA 980

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +G + E  LG  C   G +                                   
Sbjct: 981  IPSRMTIGHLIECILGKTCAIEGMEGD--------------------------------- 1007

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E I++ L  A    +G  ++Y+G TG   +
Sbjct: 1008 --------------------ATP-FTKVTVEEISNRLHAAGFQRNGNEVMYNGHTGRQLE 1046

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G  Y  +L HMV DK++AR+ G+ +++T+QP  G+S  GG R GEME  C+ ++G
Sbjct: 1047 SRIFIGPTYYQRLKHMVDDKIHARAKGAITMLTRQPREGRSREGGLRFGEMERDCMISHG 1106

Query: 1307 AAYVLQEMLTIKSDDVVGRTRV----------------YESIVAGN--DTFETGTPESFN 1348
            AA +L+E L  + D    R  V                YE  V  N     +   P +  
Sbjct: 1107 AAKMLKERLFDQCD--AYRVHVCELCGLICTADLGKQHYECKVCSNKSQISQVCLPYACK 1164

Query: 1349 VLVKEMQALGLSIDL 1363
            +L++E+ A+ +   L
Sbjct: 1165 LLLQELMAMSIYPRL 1179



 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 143/1025 (13%), Positives = 293/1025 (28%), Gaps = 217/1025 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+M            LQ       PI                S   +L+
Sbjct: 28  LVSQQLESFNDFIMYK----------LQEIVDEHPPIVIIPQPQYRPDEQIDTSIQYVLK 77

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P  +            +   R LTYA P+ +     ++ + E      + + 
Sbjct: 78  FGQLSLSRPSVEEREGVARGLWPSEARLRSLTYASPVFVDAEQKIYRMHEDGTQTLLHET 137

Query: 126 KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
               + +  +P+M +                         G F+I G++++++ Q  R  
Sbjct: 138 TYSRLPLAKIPIMLRSEYCWTHNISERELQSAGECIYDQGGYFIINGMEKVLIGQE-RMA 196

Query: 162 G--IHFDHDKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSK-------DII----HVRID 207
              ++    K       K  +   +  ++ G+     F  K        ++    ++R D
Sbjct: 197 NNFVYLFQKK----QPSKYTWIAEVRSNREGMQATSGFSVKLRGGSQGQVVATLPYIRTD 252

Query: 208 RRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               +P+     ALG +  ++IL         SQ        L         +V    + 
Sbjct: 253 ----IPIAILFRALGVLSDKDILLRCVYDFSDSQMLAILRPSLEETFEFSSQEVCLDFIG 308

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEI 320
                      K++     + L+ + +  +G+T           G  V    + G  G +
Sbjct: 309 KRGPTVGAIREKRIQYAR-ELLEREVLPHVGVTIGCEFRKAYFIGYMVHRLCM-GALGRV 366

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             +  D   +K L+             +   + +   +    + +  +       D+  V
Sbjct: 367 PEDDRDHFGKKRLDLAGPLVAASFGQSFRKMMKDMRRLLQRNIDNGKE------FDVAGV 420

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
           +R     T ++        +       +   G  ++  RL   +      R         
Sbjct: 421 IRSASYITQTLQYQFATGNWGKDRDGKIVRTGVAQVLSRLTFASALSYLRRLNTPLGREG 480

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +                ++KN   +  + +        + +D   +
Sbjct: 481 TLAKPRQLHNTHWGMICPAETPEGHAVG---LVKNLALMCEISVGYRPFAIRTFLDEWGM 537

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
              D +  + +   +  F   + +   ++  +S++ +   RR   +              
Sbjct: 538 DSIDEVPPEDIKDKIKVFLNGNWVGCFDDSEDSITNLRMIRRSGEIPYETSIVLDVVNRE 597

Query: 559 RDVHPTHYGRICP----------------AETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
             +       + P                  T  G  +   +S      ++     E   
Sbjct: 598 VKLFTDAGRSMRPLYIVGEDGELKIRKSHIATLLGIKMPENNSNEDMKILSEVDLPEGGI 657

Query: 603 RK-----VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +       D   +  + Y+   EEE   IA   + L +   +                 
Sbjct: 658 SRDSDFTWDDLIKSGIIEYIDCEEEETAMIAMFMNDLRDARGY----------------- 700

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++ S R +    M +QA+ +  +           
Sbjct: 701 CSTYTHCEIHPSLILGICASIIPFPDHNQSPRNVYQSAMGKQAMGVYTSNYNV------- 753

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                        R   +  V                                       
Sbjct: 754 -------------RMDTLGYV-----------------------------------LYYP 765

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PLV                     +L  G N +V  M + GYN EDS+++++  +   
Sbjct: 766 QKPLV----------TTRAMTYMRFRELPAGINCIVGIMCYSGYNQEDSLIMNQSSIDRG 815

Query: 838 VFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +       E        ++  +      N+D  G+I  G  V   D
Sbjct: 816 LFRSVFFRTYVSEEKQIGSNLIEAFELPNPDEVSGLRFGNYGNLDRDGLIEPGNRVLGDD 875

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P       PEE+  R     K    RD S+ + S   G V +V +       K
Sbjct: 876 IIIGKFGPI-----PPEERDNRIERLTK----RDCSIGLRSSEHGVVDEVLLSTNSKGVK 926

Query: 953 NERSI 957
             +  
Sbjct: 927 FTKVK 931


>gi|324120626|dbj|BAJ78704.1| RNA polymerase II second largest subunit [Euconocephalus varius]
          Length = 1175

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 169/1090 (15%), Positives = 335/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKTLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H + +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNSLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +  + +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGGSLLLKKKHIDMLKEREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFF---RSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+ +L    
Sbjct: 820  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTIML---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             + +  +E    ++    +    R        Q    +     +
Sbjct: 875  ----------------PETEDELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1164 MAMNIAPRLM 1173



 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 141/981 (14%), Positives = 292/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  + +   I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHISGEIENP-PHYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIEKEGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGS 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKTLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  ++  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNSLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    EG ++ L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVEGGSLLLKKK-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTIMLPETEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRFTKRDASTFLRNSETGIV 905


>gi|47208444|emb|CAF93098.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1217

 Score =  391 bits (1005), Expect = e-106,   Method: Composition-based stats.
 Identities = 178/1096 (16%), Positives = 342/1096 (31%), Gaps = 151/1096 (13%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 226  GQRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 285

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 286  EQNVALNFIGSRGAKPGV---TKERRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 339

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + I+          
Sbjct: 340  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRG 399

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 400  KDFNLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVN 459

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 460  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 515

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 516  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 574

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 575  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREYNN-------YSWQ 627

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 628  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 662

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 663  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 706

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 707  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 737

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   ++  +   
Sbjct: 738  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF-RSVFYRSYKEQESKKGF 796

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS---- 1014
             + E  E   R+                  I  G           K+  L  +       
Sbjct: 797  DQEEIFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGEDVIIGKTVTLPENEDELDGT 856

Query: 1015 -----EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
                 +   S + + +      Q  V   +  Y+  K  +  R  +           P  
Sbjct: 857  NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVSRRHLHLTRLRSSPGFKPSR 916

Query: 1070 VLR-VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            +L     + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +P
Sbjct: 917  MLSHSCSLQVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIP 976

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM VG + E   G                  +   +  L   +  ++   +    +   
Sbjct: 977  SRMTVGHLIECLQGKV------------WTSTSTLHLPELHCSVPLILVAANTGWAVLYQ 1024

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                  +V+   K  +  +TP  D  + + ++++L        G  +LY+G TG      
Sbjct: 1025 LFPVSFQVSAN-KGEIGDATPFNDAVNVQKVSNLLSEYGYHLRGNEVLYNGFTGRKLTSQ 1083

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA
Sbjct: 1084 IFIGPTYYQRLKHMVDDKIHSRARGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAA 1143

Query: 1309 YVLQEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVL 1350
              L+E L   SD     V            RT  YE    G            P +  +L
Sbjct: 1144 QFLKERLFEASDPYQVHVCNLCGLMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLL 1201

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++ ++  +  S
Sbjct: 1202 FQELMSMSIAPRMMTS 1217



 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 144/1004 (14%), Positives = 291/1004 (28%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 12  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHTSGEVEEPPRYLLKF 61

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +    E          +
Sbjct: 62  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKEGEDQI-----QTQ 116

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 117 HQKTFIGKIPIMLRSTYCLLSGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 176

Query: 163 -IHFDHDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--- 211
            ++    K       K  Y   CR        ++        I V +  R     +K   
Sbjct: 177 TVYVFAKKDS-----KYAYTSECR------SCLENSSRPTSTIWVSMMARGGQGVKKSAI 225

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         VP+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 226 GQRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 285

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              V+ + +     +  +   +++     + L+++ +  +G++  C          +   
Sbjct: 286 EQNVALNFIGSRGAKPGVTKERRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH- 343

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              + + A    +    +   +  +    P+L          +   +     K       
Sbjct: 344 --RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRGKD 401

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
               +     + +  +  S+    + D  K   +  G  ++  RL   +      R    
Sbjct: 402 FNLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVNSP 461

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 +     L N    +                ++KN   +  + +       +  +
Sbjct: 462 IGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFL 518

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R
Sbjct: 519 EEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIR 578

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E      T  GRIC         +     L     ++     E       D   +  
Sbjct: 579 DIREREIRIYTDAGRIC----RPLLIVEKQKLLLKRRHIDQLKEREYNNYSWQDLVASGV 634

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                +         +  P  ++ 
Sbjct: 635 VEYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILG 678

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 679 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 715

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 716 ------------------RMDTLAHVLYYP--------------QKPLV----------T 733

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 734 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 793

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EEI           +     + +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 794 KGFDQEEIFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGEDVIIGKTVTLPENEDEL 853

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +          +    RD S  + +  +G V  V +       K
Sbjct: 854 DGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 890


>gi|310792957|gb|EFQ28418.1| RNA polymerase Rpb2 [Glomerella graminicola M1.001]
          Length = 1259

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 198/1228 (16%), Positives = 373/1228 (30%), Gaps = 213/1228 (17%)

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D KD+I   I R   +P+        + SE+    F        +G ++    S   L+ 
Sbjct: 184  DMKDMIF--IGR---MPIMVKSKICHLSSEQEDDLFMLNECPYDQGGYFIINGSEKVLIA 238

Query: 257  GAKVSSSLVDIDTG------------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
              + ++++V +                  +E G +L S ++  L  KG    G     + 
Sbjct: 239  QERSAANIVQVFKKAQPSPYSYTAEIRSALEKGSRLISSMMLKLYSKGDAAKGGYGQTI- 297

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
               +     +     ++   G V DE  L  I +       +  +      A+       
Sbjct: 298  HCSLPYVKADLPIAIVFRALGVVSDEDILNHICYDRNDSQMLEMLRPCIEEAF------- 350

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
               +DR+ AL  I +     ++                  K  L  +             
Sbjct: 351  -CIQDREVALDFIGKRGSNHNIPRE----KRVRTAKDILQKETLPHI-----------SQ 394

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+    G+   DD D+ G +R+   G +L   +R  + RM +
Sbjct: 395  SEGSETRKAFFLGYMVHKLLQCALGRRDTDDRDHFGKKRLDLAGPLLAKLFRNIVRRMNQ 454

Query: 485  SIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             +                   +  + + + +     +               +SQ+    
Sbjct: 455  ELSGHLKRCVESNRQFSLTLGVKPQTLSNGLKYSLATGNWGDQKKAMSSTAGVSQVLNRY 514

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 515  TFASTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 570

Query: 590  ARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              V+     E    Y      +V  +   L        ++      + +D       V  
Sbjct: 571  CYVSVGTPAEPIIDYMIQRGMEVLEEYEPLRYPNATKVFLNGVWVGVHQDPRILVPDVQG 630

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                               S +  +        F    D+ RV+    +  Q+   +  +
Sbjct: 631  TRRRNV------------ISHEVSLVRDIRDREFKIFSDAGRVMRPVFVVEQSANGIVPQ 678

Query: 708  APFV---GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
               V    T  E    + +     A +        A   VI  ++ + + +         
Sbjct: 679  GSLVLQKATVNEMREQQENPPDNPADKITWESL--AHSGVIEYLDAEEEETAMICMTPED 736

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            ++  R                   ++  ++ D        L    N           +  
Sbjct: 737  LEIYRLQ-----------------KQGQVVEDNADGPNSRLKTKINPTTHMYTHCEIHPS 779

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
              + I   ++            ++       +G                       +  +
Sbjct: 780  MLLGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRM-----------DTMANI 828

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +       +   +  + AI      +  D+ +   S +   +    +
Sbjct: 829  LYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSL 887

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKG 1001
            F R   D  +R        +E   +    + + L    Y +L +   +  G         
Sbjct: 888  FFRSYTDCEKRVGI---NLVEQFEKPFRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDII 944

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K++ +S D                 E  QR  + +K    T     E+   +++    
Sbjct: 945  IGKTSPISPD---------------NAELGQRTTQHVKRDASTPLRSTENGIVDQVIVTT 989

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
              D +     R VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 990  NQDGL-----RYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTAEGITPDII 1044

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G +  +          +S L    ++   +   
Sbjct: 1045 INPHAIPSRMTIAHLIECLLSKVSTLKGMEGDATPFTDVTVDSVSQLLR--DQGYQSRGF 1102

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                             +G +    G  
Sbjct: 1103 EIM---------------------------------------------YNGHT----GR- 1112

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
                   V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C
Sbjct: 1113 --KLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRFGEMERDC 1170

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG---------------------NDTFE 1340
            + A+GAA  L+E L   SD    R  V E  + G                         +
Sbjct: 1171 MIAHGAASFLKERLFEVSD--AFRVHVCE--ICGLMTPIANLSKQSFECRPCKNKTKIAQ 1226

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+Q++ ++  +  +R+
Sbjct: 1227 IHIPYAAKLLFQELQSMNIAARMFTNRS 1254



 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 106/799 (13%), Positives = 216/799 (27%), Gaps = 136/799 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F    +          Q       P++            ++F +     
Sbjct: 39  LVSQQVDSFDEFTSSTVQELIDEYS--QITLDQPNPMSDSDKVIALRRYEVKFGTVMVSR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIV----------FDVDEFTGA---- 119
           P               +C  R+LTYA PL + +   V           ++DE        
Sbjct: 97  PSITEADGKVTTLLPYECRDRNLTYASPLYVKITKKVSIAVEKPIPLNELDEEQQDELAN 156

Query: 120 ----------------------KSIKDIKEQSIYMGDLPLMTKD---------------- 141
                                 K+  D  +  I++G +P+M K                 
Sbjct: 157 TGEHPTKLEWEEEESGEDYGADKNKSDDMKDMIFIGRMPIMVKSKICHLSSEQEDDLFML 216

Query: 142 --------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLW 191
                   G F+I G ++++++Q  RS          + +      Y   I    ++G  
Sbjct: 217 NECPYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKAQPSPYSYTAEIRSALEKGSR 273

Query: 192 MDIEFDSK------------------DIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTF 232
           +      K                   + +V+ D    +P+     ALG +  E+IL+  
Sbjct: 274 LISSMMLKLYSKGDAAKGGYGQTIHCSLPYVKAD----LPIAIVFRALGVVSDEDILNHI 329

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEK 291
                 SQ  +     +  A  +   +V+   +        I   K++     K  L+++
Sbjct: 330 CYDRNDSQMLEMLRPCIEEAFCIQDREVALDFIGKRGSNHNIPREKRV--RTAKDILQKE 387

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +  +  +             +  +   +   A    D    +      +     L    
Sbjct: 388 TLPHISQSEGSETRKAFFLGYMVHK---LLQCALGRRDTDDRDHFGKKRLDLAGPLLAKL 444

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA--ESMFNFLFFDSDKYDLS 409
             N     N  ++   K   ++    + +       T S     S+    + D  K   S
Sbjct: 445 FRNIVRRMNQELSGHLKRCVESNRQ-FSLTLGVKPQTLSNGLKYSLATGNWGDQKKAMSS 503

Query: 410 TVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           T G  ++  R    +      R          +     L N    +         +   +
Sbjct: 504 TAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGL 563

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            + L     + +      I + +    ++ +   + +                 +   ++
Sbjct: 564 VKNLSLMCYVSVGTPAEPIIDYMIQRGMEVLEEYEPLRYPNATKVF---LNGVWVGVHQD 620

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE---GHNIGLVS 584
               +  +  TRR + +                +       + P    E      +   S
Sbjct: 621 PRILVPDVQGTRRRNVISHEVSLVRDIRDREFKIFSDAGRVMRPVFVVEQSANGIVPQGS 680

Query: 585 SLTSFARVNAYGFIETP-------YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +   A VN     +                  +  + YL A EEE   I      L+  
Sbjct: 681 LVLQKATVNEMREQQENPPDNPADKITWESLAHSGVIEYLDAEEEETAMICMTPEDLEIY 740

Query: 638 GSFTEELV-------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
               +  V              +I          +  P  ++ I AS+IPF +++ S R 
Sbjct: 741 RLQKQGQVVEDNADGPNSRLKTKINPTTHMYTHCEIHPSMLLGICASIIPFPDHNQSPRN 800

Query: 691 LMGCNMQRQAVPLLKAEAP 709
                M +QA+        
Sbjct: 801 TYQSAMGKQAMGFFLTNYS 819


>gi|260807868|ref|XP_002598730.1| hypothetical protein BRAFLDRAFT_282817 [Branchiostoma floridae]
 gi|229284004|gb|EEN54742.1| hypothetical protein BRAFLDRAFT_282817 [Branchiostoma floridae]
          Length = 1137

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 167/1014 (16%), Positives = 312/1014 (30%), Gaps = 187/1014 (18%)

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +   +    +    +  +     V  +  L            K   +A++   V     
Sbjct: 278  FIGVKVRRSRWGGPKRTRVEEAREVLHSTILAHVPVVKFNFRLKCVYLALMVRRVVQAQA 337

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLIN 505
            +  +DD D  GN+R+   G++L   +     +    +K+            Q      + 
Sbjct: 338  QDRVDDRDYYGNKRLELAGQLLALLFEDLFKKFNAELKKIADQTIPKPRAAQFDIVKHMR 397

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVE 557
               + + +     +   +     ++         RLS +   G+         + R    
Sbjct: 398  QDQITNGLVNAISTGNWTVKRFKMDRAGVTQVLSRLSFISALGMMTRISSQFEKTRKVSG 457

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
             R + P+ +G +CP++T EG   GLV +L     +      +   R   +  V  DV  L
Sbjct: 458  PRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEQPIQRLAFNLGV-EDVHLL 516

Query: 618  SAME--EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            S  E   ++ Y+   N ++       + L+             E +        + V+IA
Sbjct: 517  SGEELNSQDSYLVMLNGNILGVICDHQHLIRSFRKMRRAGYINEFVSICPNHEHRCVNIA 576

Query: 676  AS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            +       P++   +   ++   +++         E       +E +             
Sbjct: 577  SDAGRVCRPYIIVTNGRPMVTNRHIEELTKGYRAFEDFLREGLVEYLDVNEENDC----- 631

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                  +      I   +                         C      V   D     
Sbjct: 632  -----NITLYEADITREDETTLE-----------------HLQCF-----VSCRDT---- 660

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
              +   P T LG       +    +P+  +N          M  + +        +    
Sbjct: 661  THLEIEPFTILG-------VCAGLIPYPHHNQSPRNTYQCAMGKQAMGAIG----YNQHN 709

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R   L    +    P V  + ++ ID                            +   + 
Sbjct: 710  RIDTLLYLLVFPQRPMVKTKTIELID-------------------------YEKLPAGQN 744

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
               A+      D+ D  +   S V        ++ +      +R  +   +++     D 
Sbjct: 745  ATVAVMSYSGYDIEDALILNKSSVDRGFGRCLVYRKQNCTL-KRYSNQTFDRVMGPMVDA 803

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               + I    I         G+   +      KS    +                     
Sbjct: 804  ATRKPIWRHEILDVDGICAPGERVQNKQVLVNKSMPKQT-------------------MN 844

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                   + +Y+      +    + +E +    +       ++K+ +   R  + GDK +
Sbjct: 845  PVQTPGQQPEYQDVPITYKGPVDSYVETVLVSSNQEEAF--LIKMLLRQTRRPEIGDKFS 902

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG+   I+  EDMPF   G   DI++NP G PSRM VG++ E   G         
Sbjct: 903  SRHGQKGVCGLIVNQEDMPFTDQGICPDIIMNPHGFPSRMTVGKLMELLAGK-------- 954

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                         A   +      T  F
Sbjct: 955  ---------------------------------------------AGVLEGKFHYGT-AF 968

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             G+  + +   L     +  G+  L  G+TGEP +  +  G +Y  KL HMV DK++AR+
Sbjct: 969  GGSKVKDVCEELVQHGFNYQGKDYLTSGITGEPLNAYIYTGPVYYQKLKHMVLDKIHARA 1028

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTR 1327
             G  +++T+QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G   
Sbjct: 1029 KGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDQFEVDVCG--- 1085

Query: 1328 VYESIVAG-----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
              E  + G            +      P +  +L +E+Q++ ++  L+  +   
Sbjct: 1086 --ECGLLGYSGWCQYCKSSRNVSSLKMPYACKLLFQELQSMNIAPRLKLVKYNE 1137



 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 114/761 (14%), Positives = 219/761 (28%), Gaps = 154/761 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE +         ++       L++++     P    
Sbjct: 31  LVKQHIDSFNYFINVEIKKIMKANEKI---------VSDADPNFYLKYLNIYVGMPDVEE 81

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + +   ++ +G +P+M
Sbjct: 82  GFNITKPIAPHECRLRDMTYSAPITVDIEYT----------RGNQRVVRNNLPIGRMPIM 131

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S              
Sbjct: 132 LRSSNCVLTGKSPSELAKLKECPLDPGGYFLVKGVEKVILIQEQLSKN------------ 179

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-----DRRRK------------------ 211
                   R+I        +E D K +I   +     +R+ K                  
Sbjct: 180 --------RMI--------VETDRKGLISCSVTSSTHERKTKTYVVQKNAKYFLKHNTFT 223

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIV--------YSQRGDFWCFPLSAADLMVGAKV 260
             +P+     A+G++S+ EI+                  +      F    A   +G KV
Sbjct: 224 EDIPIAIAFKAMGVESDQEIVQLIGTDARTMAAVAPSLEECHKAQVFTQKQALRFIGVKV 283

Query: 261 SSSLVDIDTGEQVIESGKKLTSG-LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
             S        +V E+ + L S  L      K    L      L    V +         
Sbjct: 284 RRSRWGGPKRTRVEEAREVLHSTILAHVPVVKFNFRLKCVYLALMVRRVVQAQAQDR--- 340

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
             ++  D    K LE            L+         I +  +         A  DI +
Sbjct: 341 --VDDRDYYGNKRLELAGQLLALLFEDLFKKFNAELKKIADQTIPKPR----AAQFDIVK 394

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            MR                   ++      TV R KM+          +  I    ++  
Sbjct: 395 HMRQDQ----------ITNGLVNAISTGNWTVKRFKMDRAGVTQVLSRLSFISALGMMTR 444

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I    +          +       +    +  + +    +  +         S +     
Sbjct: 445 ISSQFEKTRKVSGPRSLQPSQWG-MLCPSDTPEGEACGLVKNLALMTHITTDSEEQPIQR 503

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI---THTRRLSALGQGGVARARAGV 556
               +  + V     E   S     +  + N L  I    H  R        + RA    
Sbjct: 504 LAFNLGVEDVHLLSGEELNSQDSYLVMLNGNILGVICDHQHLIR----SFRKMRRAGYIN 559

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTND 613
           E   + P H  R     +  G        +T+   +     IE     YR   D      
Sbjct: 560 EFVSICPNHEHRCVNIASDAGRVCRPYIIVTNGRPMVTNRHIEELTKGYRAFEDFLREGL 619

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YL   EE +  I    + +  +   T E + C        V       ++  P  ++ 
Sbjct: 620 VEYLDVNEENDCNITLYEADITREDETTLEHLQC-------FVSCRDTTHLEIEPFTILG 672

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLL-KAEAPFVGT 713
           + A LIP+  ++ S R    C M +QA+  +   +   + T
Sbjct: 673 VCAGLIPYPHHNQSPRNTYQCAMGKQAMGAIGYNQHNRIDT 713


>gi|186885817|gb|ACC93316.1| RNA polymerase beta subunit [Carthamus tinctorius]
          Length = 1024

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 142/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   A    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGAERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +             ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VHSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IVS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  364 bits (935), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 255/828 (30%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P     +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQTNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLESMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKAFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSFLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   DA +I++                  L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKILYTDADKILLSGN--------GDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGAERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR  +    
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVHSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            D+ +++  +     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 750  DETDKTERIRVYILQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLITERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|221120338|ref|XP_002163509.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 1426

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 174/1085 (16%), Positives = 333/1085 (30%), Gaps = 203/1085 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 258  GQRIIATIPYICQEIPIMIVFRALGFVSDRDILEHIIYDFTDQEMMEMVKPSLDEAFVVQ 317

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + T      +         KY    + +  +      D  +  +      + 
Sbjct: 318  EQNVALNFIGTRGARPGV---TKEKRIKYAREILQKEMLPHVGTSDFCETKK---AYFLG 371

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDI 495
             ++  ++    G+  +DD D+ GN+R+   G +L   +R     + + ++   +      
Sbjct: 372  YMVHRILLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDKG 431

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 432  KDFKIELAIKTKTITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 491

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R       R +H TH+G ICPAET EG  +GLV +L   A ++         
Sbjct: 492  S----PIGRDGKLARPRQLHNTHWGMICPAETPEGQAVGLVKNLALMAYISVGSQPSPIL 547

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----AGEEILVPR 658
              + +     ++  +S    ++      N          E+L+          + I+   
Sbjct: 548  EFLEEWA-MENLEEISPSAIKDATKIFVNGCWVGIHRDPEQLILTLRRLRRQMDIIVSEV 606

Query: 659  EKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM 715
              + D  D   +          P L  ++   +L   ++   ++           V  G+
Sbjct: 607  SMVRDIRDKEIRIYTDAGRVCRPLLIVENQKLLLKKSHVDQLKEREMNNFGWQDLVSKGV 666

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                               VE +D        +   L+        Y             
Sbjct: 667  -------------------VEYIDVNEEETAMIAMSLEDLEEREHKYSSTY--------- 698

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  PS  LG       +  + +P+  +N          M  
Sbjct: 699  ----------------THSEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 735

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V        +  
Sbjct: 736  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTT 766

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D S+ + +      +   +F R   D+  R
Sbjct: 767  RSMDFLKFRELPAGINSIVAIASYTGYNQED-SVLLNASAINRGLYRSVFYRSYRDEESR 825

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                + E+ E   RD+         +       I  G           K+  L  D    
Sbjct: 826  KGLDQEEKFEKPNRDETTGMRAAIYDKLDDDGLIPPGSRVSGDDVIIGKTVTLPDDEDET 885

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              +++ ++       ++ +   +  Q   + +                        +  K
Sbjct: 886  DSQAKHFKKRDASTFLRASETGIVDQVMLTINE--------------------EGYKFCK 925

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
              V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 926  NKVRSVRIPQIGDKFASRHGQKGTCGITYRQEDMPFTCEGISPDIIINPHAIPSRMTIGH 985

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 986  LIECLQGKVSANKGEIGD------------------------------------------ 1003

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + ++S+L+       G  +LY+G TG   +  V +G  Y
Sbjct: 1004 -----------ATPFNDAVNVQLVSSLLQEYGYHLRGNEVLYNGFTGRKLNAQVFLGPTY 1052

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++T+QP+ G+S  GG R GEME  C  A+GAA  L E L
Sbjct: 1053 YQRLKHMVDDKIHSRARGPVQILTRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLNERL 1112

Query: 1316 TIKSD----DVVG----------RTRVYE--SIVAGNDTFETGTPESFNVLVKEMQALGL 1359
               SD     V            R   +E  S        +   P +  +L +E+ ++ +
Sbjct: 1113 FEASDAYRVHVCNLCGLIAIANLRNNTFECRSCKNKTQVSQIRIPYACKLLFQELMSMSI 1172

Query: 1360 SIDLE 1364
            +  + 
Sbjct: 1173 APRMM 1177



 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 136/957 (14%), Positives = 275/957 (28%), Gaps = 197/957 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGA-------AMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI       ++           L+F
Sbjct: 43  LVRQQLDSFDEFIQMSV----------QRIVEESPPIELQAETQYTENEIEEPTRYQLKF 92

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +    +    +      
Sbjct: 93  EQIYLSKPTHWEKDGAPKPMMPNEARLRNLTYSAPLYVDISKTITRSGQEPETEE----- 147

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
              IY+G +P+M                           G F+I G ++++++Q   +  
Sbjct: 148 HSKIYIGKIPIMLRSTYCVLSGLVDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATN 207

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV----------------- 204
            ++  H K       K  Y+C I       ++        + +                 
Sbjct: 208 TVYVFHKKDS-----KYAYSCEIR----SCLEQSSRPTSTMFISMLAKGGGGGAKKSAIG 258

Query: 205 -RIDRR-----RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
            RI        +++P+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 259 QRIIATIPYICQEIPIMIVFRALGFVSDRDILEHIIYDFTDQEMMEMVKPSLDEAFVVQE 318

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +        +   K++     + + +K +     TSD           +    
Sbjct: 319 QNVALNFIGTRGARPGVTKEKRI--KYAREILQKEMLPHVGTSDFCETKKAY--FLGYMV 374

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             I + A    +    +   +  +    P+L          +   +     K        
Sbjct: 375 HRILLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDKGKDF 434

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +       T  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 435 KIELAIKTKTITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 494

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +         +      ++KN   +  + +       +  ++
Sbjct: 495 GRDGKLARPRQLHNTHWGMICPAETPEGQAVG---LVKNLALMAYISVGSQPSPILEFLE 551

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             ++   + I+   +  A   F     +    +    +  +   RR   +    V+  R 
Sbjct: 552 EWAMENLEEISPSAIKDATKIFVNGCWVGIHRDPEQLILTLRRLRRQMDIIVSEVSMVRD 611

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             +      T  GR+C P    E   + L  S      V+     E       D      
Sbjct: 612 IRDKEIRIYTDAGRVCRPLLIVENQKLLLKKS-----HVDQLKEREMNNFGWQDLVSKGV 666

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+   EEE   IA +   L+                E            +  P  ++ 
Sbjct: 667 VEYIDVNEEETAMIAMSLEDLE----------------EREHKYSSTYTHSEIHPSMILG 710

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 711 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 747

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 748 ------------------RMDTLAHVLYYP--------------QKPLV----------T 765

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS+L++   ++  ++ S+    +      
Sbjct: 766 TRSMDFLKFRELPAGINSIVAIASYTGYNQEDSVLLNASAINRGLYRSVFYRSYRDEESR 825

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             L  EE        +   +       +D+ G+I  G+ V+  D+++GK     +  
Sbjct: 826 KGLDQEEKFEKPNRDETTGMRAAIYDKLDDDGLIPPGSRVSGDDVIIGKTVTLPDDE 882


>gi|324120634|dbj|BAJ78708.1| RNA polymerase II second largest subunit [Forficula hiromasai]
          Length = 1174

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 166/1090 (15%), Positives = 335/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 252  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 311

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 312  EQNVALNFIGARGARPGV---TREKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 365

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 366  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 425

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 426  KDFNLDLAIKTKIITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVN 485

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 486  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 541

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 542  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 601

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ N +L   +  M ++           V +G+ 
Sbjct: 602  MIRDIRDREIRIYTDAGRICRPLLIVENGNLLLKKHHIDMLKEREHNNYGWQVLVASGVV 661

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 662  EYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------- 693

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 694  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 730

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 731  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 761

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V   +     +  +   +++R
Sbjct: 762  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGLFRSVFYRSYKDSESKR 821

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            +   E    E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 822  NGDQE----EQFEKPTRQTCQGMRNALYDKLDDDGIISPGLRVSGDDVVIGKTITL---- 873

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             + +  ++    +Y    +    R        Q    +     +
Sbjct: 874  ----------------PENEDELDGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 917

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 918  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 977

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 978  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 998

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 999  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1044

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1045 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1104

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     +            R   +E    G        +   P +  +L +E+
Sbjct: 1105 ERLFEVSDPYRIHICNLCGLIAIANMRNNTFEC--KGCKNKTQISQVKLPYAAKLLFQEL 1162

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1163 MSMNIAPRLM 1172



 Score =  241 bits (616), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 289/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  +   I       +L+F       P 
Sbjct: 38  LVRQQLDSFDEFIQMSVQRIVEDSPQIELQAEAQHTAGEIENP-PKYLLKFEQIYLSKPT 96

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 97  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDKEEPI-----ETQHQKTFIGKI 151

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 152 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 211

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 212 -----GKYAYKSEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 262

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 263 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 322

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 323 RGARPGVTREKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 378

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 379 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKI 438

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  ++  G  ++  RL   +      R          +    
Sbjct: 439 ITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 498

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 499 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 555

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 556 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 615

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L         ++     E           +  V Y+  +EEE
Sbjct: 616 DAGRICRPLLIVENGNLLLKKH-----HIDMLKEREHNNYGWQVLVASGVVEYIDTLEEE 670

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 671 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 715

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 716 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 742

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 743 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 770

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V   +F S+    ++          EE   
Sbjct: 771 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGLFRSVFYRSYKDSESKRNGDQEEQFE 830

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    +         
Sbjct: 831 KPTRQTCQGMRNALYDKLDDDGIISPGLRVSGDDVVIGKTITLPENEDELDGTT------ 884

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 885 -KRYTKRDASTFLRNSETGIV 904


>gi|324120646|dbj|BAJ78714.1| RNA polymerase II second largest subunit [Gynaikothrips ficorum]
          Length = 1150

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 166/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKEKRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRALFKNLMKEVRMYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   N+   ++           V +G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVENGQLLLKKRNIDQLKERDYNNYGWQMLVASGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   + + D   +    Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MSPDDLNQDKEYAYCTTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 707  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   + V            +   K+  
Sbjct: 738  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNATAVERGFFRSVF---YRSYKDAE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 795  SKRIGDQE-EQFEKPNRSNCQGMRNALYDKLDDDGIIAPGLRVSGDDVVIGKTITL---- 849

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    ++    +    R        Q    +     +
Sbjct: 850  ----------------PETDDELEGTTRRHTKRDASTFLRNSETGIVDQVMLTLNSEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 894  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 975  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1139 MSMSIAPRLM 1148



 Score =  236 bits (603), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 137/992 (13%), Positives = 286/992 (28%), Gaps = 206/992 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+ M++    ++ P   LQA  +         P        +L+F    
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTTGEVETPP------RYLLKFEQIY 67

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              P              ++   R+LTY+ PL + +   +    E               
Sbjct: 68  LSKPTHWEKDGAPSAMMPNEARLRNLTYSAPLYVDITKTIIREGEDQVVTQNPKT----- 122

Query: 131 YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
           ++G +P+M                           G F+I G ++++++Q   +   ++ 
Sbjct: 123 FIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV 182

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR--------- 208
              K      GK  Y   I       ++        + V         I +         
Sbjct: 183 FAMKD-----GKFAYKSEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIA 233

Query: 209 -----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ 
Sbjct: 234 ILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVAL 293

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGE 316
           + +        +   K++     + L+++ +  +G++           G  V   ++   
Sbjct: 294 NFIGARGARPGVTKEKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AA 351

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            G   ++  D    K L+            L+ + +          +        +    
Sbjct: 352 LGRRELDDRDHYGNKRLDLAGPLLAFLFRALFKNLMKEVRMYAQKFIDRGKDFNLE---- 407

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + T  +  S+    + D  K  ++  G  ++  RL   +      R     
Sbjct: 408 ---LAIKTKIITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVNSPI 464

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 465 GRDGKLAKPRQLHNTLWGMVCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLE 521

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I    +  A   F     +    +    ++ +   RR   +    V+    
Sbjct: 522 EWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMI-- 579

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY--RKVCDGKVTN 612
               RD+          A       + + +      + N     E  Y          + 
Sbjct: 580 ----RDIRDREIRIYTDAGRICRPLLIVENGQLLLKKRNIDQLKERDYNNYGWQMLVASG 635

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V Y+  +EEE   IA +   L                 ++           +  P  ++
Sbjct: 636 VVEYIDTLEEETVMIAMSPDDL---------------NQDKEYAYCTTYTHCEIHPAMIL 680

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                             
Sbjct: 681 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV---------------------- 718

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                 + + V  Y                +PLV          
Sbjct: 719 -------------------RMDTLAHVLYYP--------------HKPLV---------- 735

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                      +L  G N +VA + + GYN EDS++++   V    F S+    ++    
Sbjct: 736 TTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNATAVERGFFRSVFYRSYKDAES 795

Query: 853 DTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 EE        +   +       +D+ GII  G  V+  D+++GK     E+   
Sbjct: 796 KRIGDQEEQFEKPNRSNCQGMRNALYDKLDDDGIIAPGLRVSGDDVVIGKTITLPETDDE 855

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            E    R          RD S  + +  +G V
Sbjct: 856 LEGTTRR-------HTKRDASTFLRNSETGIV 880


>gi|186885819|gb|ACC93317.1| RNA polymerase beta subunit [Centaurea melitensis]
          Length = 1024

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 142/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   A    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGAERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +             ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VHSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IVS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  360 bits (924), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLESMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKAFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   DA +I++                  L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKILYTDADKILLSGN--------GDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKTQVQQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGAERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR  +    
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVHSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            D+ +++  +     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 750  DETDKTERIRVYILQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLITERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|324120602|dbj|BAJ78692.1| RNA polymerase II second largest subunit [Nipponatelura sp. 66-1]
          Length = 1175

 Score =  391 bits (1004), Expect = e-106,   Method: Composition-based stats.
 Identities = 171/1086 (15%), Positives = 328/1086 (30%), Gaps = 204/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAISDATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGME 716
             I D  D   +          P L  ++ + +L   +  M ++           V  G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVENGHLLLKKKHIDMLKEKEYNNYGWQVLVAQGV- 661

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                              VE +D +      +    D                       
Sbjct: 662  ------------------VEYIDTLEEETVMIAMTPDDLRQD------------------ 685

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                  K              P+  LG       +  + +P+  +N          M  +
Sbjct: 686  ------KEYAYCTNYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQ 732

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +   ++I  F                           ++    +  V    +   +   
Sbjct: 733  AMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTR 763

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +      + AI      +  D+ +   S V        +F R   D   + 
Sbjct: 764  SMEYLRFRELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFF-RSVFFRSYKDAESKG 822

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
            +  + EQ E  +R           +       I  G           K+  L        
Sbjct: 823  MGDQEEQFEKPSRTTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITL-------- 874

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                         +    +E    +Y    +    R        Q    +     +  K+
Sbjct: 875  ------------PENDDELEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKI 922

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G +
Sbjct: 923  RVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHL 982

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E   G      G+                                              
Sbjct: 983  IECLQGKVSSNKGEIGD------------------------------------------- 999

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                      +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G  Y 
Sbjct: 1000 ----------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQIFLGPTYY 1049

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L 
Sbjct: 1050 QRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERLF 1109

Query: 1317 IKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALG 1358
              SD     V            R   +E    G        +   P +  +L +E+ ++ 
Sbjct: 1110 EVSDPYRVHVCNFCGIIAIANLRNNTFEC--KGCKNKTQISQIRLPYAAKLLFQELMSMN 1167

Query: 1359 LSIDLE 1364
            ++  L 
Sbjct: 1168 IAPRLM 1173



 Score =  236 bits (603), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 285/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    +        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDGDEPV-----ETQNQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I        +        + V         I +              
Sbjct: 213 -----GKYAFKSEIR----SCQEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAISDATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     E              V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGHLLLKKK-----HIDMLKEKEYNNYGWQVLVAQGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA     L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMTPDDL---------------RQDKEYAYCTNYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKGMGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPSRTTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYTKRDASTFLRNSETGIV 905


>gi|149390346|ref|YP_001294344.1| RNA polymerase beta subunit [Dioscorea elephantipes]
 gi|158513762|sp|A6MMJ9|RPOB_DIOEL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|148668038|gb|ABR01422.1| RNA polymerase beta subunit [Dioscorea elephantipes]
          Length = 1070

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 161/563 (28%), Positives = 260/563 (46%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++      ++E     I+ +  +++                  ++    +
Sbjct: 562  IVGTGLERQTALDSGVSAIAEREGKIIYTDTHKIIFSSNGDTMSIPLVMYQRSNKNTCMH 621

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                  +  G  +  G IL    T  G   +   + +L A    +  +  D  L     +
Sbjct: 622  QKPQ--VPRGKCIKKGQILADGATTVG-GELALGKNVLVAHMPWEGYNSEDAVL-----I 673

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E + ++    +  L RN+  R   ++ G   
Sbjct: 674  SERLVYEDIYTSFYIRKYEIQTHVTSQGPERITKEIPHLEDHLLRNL-DRNGIVMLGSWI 732

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  ++   S  P  +  +  +  +       SLK+       +++ R+  
Sbjct: 733  ETGDILVGKLTPQTATESSYAPEDRLLRAILGIQVSTAKETSLKLSIGGRGRVIDVRWIQ 792

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG
Sbjct: 793  KR----GGSIYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDG 845

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 846  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKRHYRIAPFDERYEQEASRKLVFSELY 905

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 906  SASKQTKNPW------------------------VFE---------------PEYPGKSR 926

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 927  IFDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 986

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+
Sbjct: 987  EMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIVGGTVPNPEDAPESFRLLVREL 1046

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1047 RSLALELNHFLVSEKNFQINRKE 1069



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 233/662 (35%), Positives = 366/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILY-VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I+           L  +         IL  V          N     K   +++A+L+ 
Sbjct: 167 RIWARVSRKQKISILVLLSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKENAILEF 226

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD              FF   + +L  +GR   N RLNLD P     +   D
Sbjct: 227 YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNTNQRLNLDIPQKNTFLLPRD 285

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           ++A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 286 VLAAADHLIRMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENGVRGTICGAIR 345

Query: 496 DSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             ++P  ++L+ +    +    FF    LSQ+ +  N L++I H RRLS LG GG+    
Sbjct: 346 HKLIPNPKNLVTSTSFTTTYESFFGLHPLSQVLDRTNPLTQIAHGRRLSYLGPGGLTGRT 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G IE+P+ ++ +      
Sbjct: 406 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGHWGSIESPFYEISERSKKAQ 465

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E+I      P Q  S
Sbjct: 466 MIYLSPSRDEYYMVAAGNSLALNRGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFS 525

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG + +A+R G
Sbjct: 526 IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQTALDSGVSAIAEREG 585

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D  +I+  S                L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 586 KIIYTDTHKIIFSSN--------GDTMSIPLVMYQRSNKNTCMHQKPQVPRGKCIKKGQI 637

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N+LVA MPW GYN ED++LISER+V ED++TS +I ++E+    
Sbjct: 638 LADGATTVGGELALGKNVLVAHMPWEGYNSEDAVLISERLVYEDIYTSFYIRKYEIQTHV 697

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE IT++IP++ +  L+N+D  GI+ +G+ +  GDILVGK+TP+  +  +  PE++
Sbjct: 698 TSQGPERITKEIPHLEDHLLRNLDRNGIVMLGSWIETGDILVGKLTPQTATESSYAPEDR 757

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELL 967
           LLRAI G +    ++TSL++  G  G V+DVR   + G      +  R    ++ +I++ 
Sbjct: 758 LLRAILGIQVSTAKETSLKLSIGGRGRVIDVRWIQKRGGSIYNPEMIRVYISQKREIKVG 817

Query: 968 AR 969
            +
Sbjct: 818 DK 819



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------NQGLMEELHKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ + ++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTSRAMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            +I GI RIV++Q+ ++PG+++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIINGIYRIVINQILQNPGVYYRSELDHNGIS---VYTSTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +   L A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLLSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|295311724|ref|YP_003587460.1| RNA polymerase beta subunit [Oncidium Gower Ramsey]
 gi|254833101|gb|ACT83104.1| RNA polymerase beta subunit [Oncidium Gower Ramsey]
          Length = 1070

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 155/497 (31%), Positives = 245/497 (49%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D  L     ++  +V 
Sbjct: 626  VQRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAVL-----INERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E + +D    +  L RN+  R   ++ G    +G   
Sbjct: 680  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEAHLLRNL-DRNGIVMLGSWIETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  ++  +S  P  +  +  +  +       SL++       +++ R+ ++     
Sbjct: 739  VGKLTPQTASELSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK---- 794

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V
Sbjct: 795  ---GVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L K  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGDLLKKHYRIGPFDERYEQEASRKLVFSELYEASKKT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 912  KNPW------------------------VFE---------------PEYPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GDLFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G    +  G PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGATIIGATVPKPEGAPESFRLLVRELRSLSLE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLVSEKNFQMDRKE 1069



 Score =  368 bits (945), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 235/686 (34%), Positives = 383/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 143 ISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNIREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y       GD              FF   + +L  +
Sbjct: 203 IFLSFPNDKEKKKIGSKENAILEFYLQFACVGGDPVFSESLCKELQKKFF-QQRCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNLD P +   +   D++A +  L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNINRRLNLDIPQNNTFLLPRDLLAAVDHLIRMKLGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENTVRGTICGAIRHKLIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKWSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            +V  +G IE+P+ ++ D      +VYLS   +E   +A  NS     G   +++V  R 
Sbjct: 442 VKVGYWGSIESPFYELSDRSKEAQMVYLSPNRDEYYMVAAGNSLALNRGIQEQQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEEIRLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+R G +   D  +I+  S                L+ +QR
Sbjct: 562 IVGTGLEGQTALDSGISAIAERKGKIIYTDTQKIIFSSN--------GDTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKTQVQRGKYIKKGQILAGGVATAGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+V ED++TS HI ++E+    T  GPE IT+DIP++    L+N+D  GI+ +G+ + 
Sbjct: 674 NERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEAHLLRNLDRNGIVMLGSWIE 733

Query: 890 PGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+  S +  TPE++LLRAI G +    ++TSLR+P G  G V+DVR  +R
Sbjct: 734 TGDILVGKLTPQTASELSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHR 793

Query: 948 HGID----KNERSISVEREQIELLAR 969
            G+     +  R    ++ +I++  +
Sbjct: 794 KGVSNSNPEKIRVYISQKREIKVGDK 819



 Score =  169 bits (428), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLTEEFHKFQKIEDRDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ ++++EQ++++G++P+M   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAVLIW---------KTGRNMQEQTVFLGNIPIMNSFGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELEHNGIS---VYTSTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNIREILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|324120644|dbj|BAJ78713.1| RNA polymerase II second largest subunit [Thrips palmi]
          Length = 1150

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 164/1090 (15%), Positives = 331/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKEKRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRALFKNLMKEVRMYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   N+   ++           V +G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVENGQLLLKKRNIDQLKERDYNNYGWQMLVASGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V    +   +  
Sbjct: 707  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPHKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   + V            +   K+  
Sbjct: 738  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNATAVERGFFRSVF---YRSYKDAE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +   +    +   IY +L +   I  G           K+  L    
Sbjct: 795  SKRIGDQE-EQFEKPNRNNCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPETD 853

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                  ++          ++ +   +  Q                        +     +
Sbjct: 854  DDLDGTTRRHTKRDASTFLRNSETGIVDQVML--------------------TLNSEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 894  FCKIRVRSVRIPQIGDKFASRHGQKGTCGVQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+ +L+       G  ++Y+G TG   +  V +G
Sbjct: 975  --------------ATPFNDAVNVQKISQLLQDYGYHLRGNEVMYNGHTGRKINAQVFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1139 MSMNIAPRLM 1148



 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 139/987 (14%), Positives = 290/987 (29%), Gaps = 196/987 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 73  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEEPI-----ETQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 187

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y C I       ++        + V         I +              
Sbjct: 188 -----GKFAYKCEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 238

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 239 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 298

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   K++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 299 RGARPGVTKEKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 356

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        +       + 
Sbjct: 357 LDDRDHYGNKRLDLAGPLLAFLFRALFKNLMKEVRMYAQKFIDRGKDFNLE-------LA 409

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K  L+  G  ++  RL   +      R          
Sbjct: 410 IKTKIITDGLRYSLATGNWGDQKKAHLARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 469

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 470 LAKPRQLHNTLWGMVCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 526

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+        R
Sbjct: 527 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMI------R 580

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY--RKVCDGKVTNDVVYL 617
           D+          A       + + +      + N     E  Y          +  V Y+
Sbjct: 581 DIRDREIRIYTDAGRICRPLLIVENGQLLLKKRNIDQLKERDYNNYGWQMLVASGVVEYI 640

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +EEE   IA +   L                 ++           +  P  ++ + AS
Sbjct: 641 DTLEEETVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCAS 685

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 686 IIPFPDHNQSPRNTYQSAMGKQAMGVYITNYHV--------------------------- 718

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            + + V  Y                +PLV               
Sbjct: 719 --------------RMDTLAHVLYYP--------------HKPLV----------TTRSM 740

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G N +VA + + GYN EDS++++   V    F S+    ++         
Sbjct: 741 EYLRFRELPAGINSIVAILCYTGYNQEDSVILNATAVERGFFRSVFYRSYKDAESKRIGD 800

Query: 858 PEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            EE        +   +       +D+ GII  G  V+  D+++GK     E+    +   
Sbjct: 801 QEEQFEKPNRNNCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPETDDDLDGTT 860

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            R          RD S  + +  +G V
Sbjct: 861 RR-------HTKRDASTFLRNSETGIV 880


>gi|324120620|dbj|BAJ78701.1| RNA polymerase II second largest subunit [Galloisiana yuasai]
          Length = 1175

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 171/1090 (15%), Positives = 331/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  D  N +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVDGGNLLLKKRHIDMLKEREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 820  SKRIGDQE-EQFEKPTRLTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITL---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    +Y    +    R        Q    +     +
Sbjct: 875  ----------------PENDDELEGATKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  I+++G TG      + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEIMFNGHTGRKISAQIFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     +            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHICNFCGIIAIANMRNNTFEC--KGCKNKTQISQVKLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1164 MAMNIAPRLM 1173



 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 140/981 (14%), Positives = 291/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +   +E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTILKENEEPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I       ++        + V         I +              
Sbjct: 213 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    +G N+ L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVDGGNLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRLTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPENDDELEGAT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYTKRDASTFLRNSETGIV 905


>gi|332148560|dbj|BAK20129.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 330

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 146/381 (38%), Positives = 197/381 (51%), Gaps = 62/381 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 6    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 63

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 64   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 123

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 124  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 183

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 184  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 237

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 238  ----------------------TVLYDG--------------------------RTGEPF 249

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 250  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 309

Query: 1306 GAAYVLQEMLTIKSDDVVGRT 1326
            GAAY LQE+LT+KSDDVVGR 
Sbjct: 310  GAAYTLQEILTVKSDDVVGRV 330



 Score =  120 bits (301), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 82/122 (67%), Positives = 100/122 (81%)

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV 
Sbjct: 1   SERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVK 60

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR  
Sbjct: 61  DGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRED 120

Query: 950 ID 951
            D
Sbjct: 121 GD 122


>gi|324120670|dbj|BAJ78726.1| RNA polymerase II second largest subunit [Eretes sticticus]
          Length = 1174

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 167/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 252  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 311

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 312  EQNVALNFIGARGAKPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 365

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 366  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKG 425

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 426  KDFNLDLAIKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 485

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 486  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 541

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 542  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 601

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ N +L   +  M ++           V +G+ 
Sbjct: 602  MIRDIRDREIRIYTDAGRICRPLLIVENGNLLLKKRHIDMLKEREYNNYGWQVLVASGVV 661

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 662  EYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------- 693

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 694  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 730

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 731  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 761

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         +  +   +++R
Sbjct: 762  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDAESKR 821

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                E    E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 822  LGDQE----EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITL---- 873

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    ++    +Y    +    R        Q    +     +
Sbjct: 874  ----------------PENDDELDGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 917

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 918  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 977

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 978  IGHLIECIQGKVSANKGEIGD--------------------------------------- 998

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 999  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1044

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1045 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1104

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1105 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1162

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1163 MSMNIAPRLM 1172



 Score =  244 bits (624), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 142/981 (14%), Positives = 289/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 38  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 96

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 97  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPI-----ETQHQKTFIGKI 151

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 152 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAMKD 211

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  Y   I       ++        + V +  R     +K              
Sbjct: 212 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQAIKKAAIGQRIIAILPYI 262

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 263 KQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 322

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
              +  +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 323 RGAKPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 378

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 379 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKGKDFNLDLAIKTKM 438

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 439 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 498

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 499 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 555

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 556 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 615

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L         ++     E           +  V Y+  +EEE
Sbjct: 616 DAGRICRPLLIVENGNLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 670

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 671 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 715

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 716 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 742

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 743 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 770

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 771 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDAESKRLGDQEEQFE 830

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    +         
Sbjct: 831 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPENDDELDGTT------ 884

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 885 -KRYTKRDASTFLRNSETGIV 904


>gi|324120664|dbj|BAJ78723.1| RNA polymerase II second largest subunit [Inocellia japonica]
          Length = 1175

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 173/1087 (15%), Positives = 331/1087 (30%), Gaps = 206/1087 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIRQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLDLAIKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ N +L   +  M +            V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVENGNLLLKKSHVDMLKDREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +  + Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPEDLRQDKENAYCNTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V        +F R   D   +
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFF-RSVFYRSYKDSESK 821

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             I  + EQ E   R           +       I  G           K+ +L       
Sbjct: 822  RIGDQEEQFEKPTRQTCQGMRNAHYDKLDDDGIISPGIRVSGDDVVIGKTIML------- 874

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                          + +  +E    +Y    +    R        Q    +     +  K
Sbjct: 875  -------------PENEDELEGTTKRYTKRDASTFLRNSETGVVDQVMLTLNSEGYKFCK 921

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 922  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGH 981

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 982  LIECIQGKVSSNKGEIGD------------------------------------------ 999

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G  Y
Sbjct: 1000 -----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTY 1048

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L
Sbjct: 1049 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERL 1108

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            +   +E    G        +   P +  +L +E+ A+
Sbjct: 1109 FEVSDPYRIHVCNFCGLIAIANLKNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMAM 1166

Query: 1358 GLSIDLE 1364
             ++  L 
Sbjct: 1167 NIAPRLM 1173



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 142/981 (14%), Positives = 289/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSAEIETP-PHYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    +        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDGDDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR--------IDR-------------- 208
                 K  Y   I       ++        + V         I +              
Sbjct: 213 S-----KYAYKAEIR----SCLEHSSRPTSSLWVNMMARGGQAIKKAAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           R+++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 RQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKM 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L  S      V+     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGNLLLKKS-----HVDMLKDREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RQDKENAYCNTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRQTCQGMRNAHYDKLDDDGIISPGIRVSGDDVVIGKTIMLPENEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYTKRDASTFLRNSETGVV 905


>gi|324120642|dbj|BAJ78712.1| RNA polymerase II second largest subunit [Reticulitermes speratus]
          Length = 1150

 Score =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 170/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKDKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRIYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +  N +L   +  M ++           V +G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVEGGNLLLKKRHIDMLKEREYNNYGWQVLVASGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 707  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 738  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RAYKDAE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 795  SKRIGDQE-EQFEKPTRTTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITL---- 849

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                               +  +E    ++    +    R        Q    +     +
Sbjct: 850  ----------------PDTEDELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 894  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 975  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1139 MAMNIAPRLM 1148



 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 142/986 (14%), Positives = 292/986 (29%), Gaps = 194/986 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 73  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPI-----ETQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 187

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I       ++        + V         I +              
Sbjct: 188 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 238

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 239 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 298

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   K++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 299 RGARPGVTKDKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 356

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        +       + 
Sbjct: 357 LDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRIYAQKFIDRGKDFNLE-------LA 409

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 410 IKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 469

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 470 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 526

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 527 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 586

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               T  GRIC P    EG N+ L         ++     E           +  V Y+ 
Sbjct: 587 IRIYTDAGRICRPLLIVEGGNLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYID 641

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            +EEE   IA +   L                 ++           +  P  ++ + AS+
Sbjct: 642 TLEEETVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASI 686

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 687 IPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV---------------------------- 718

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + V  Y                +PLV                
Sbjct: 719 -------------RMDTLAHVLYYP--------------HKPLV----------TTRSME 741

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G N +VA + + GYN EDS++++   V    F S+    ++          
Sbjct: 742 YLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRAYKDAESKRIGDQ 801

Query: 859 EEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           EE            +       +D+ GII  G  V+  D+++GK     ++    E    
Sbjct: 802 EEQFEKPTRTTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDTEDELEGTT- 860

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 K    RD S  + +  +G V
Sbjct: 861 ------KRFTKRDASTFLRNSETGIV 880


>gi|324120656|dbj|BAJ78719.1| RNA polymerase II second largest subunit [Metylophorus sp. E-43]
          Length = 1176

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 170/1089 (15%), Positives = 336/1089 (30%), Gaps = 208/1089 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 252  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 311

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 312  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 365

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++   +      
Sbjct: 366  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMFAQKFIDRG 425

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 426  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 485

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 486  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 541

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 542  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 601

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC--NMQRQAVPLLKAEAPFVGTGME 716
             I D  D   +          P L  ++   +L     NM ++           V +G+ 
Sbjct: 602  MIRDIRDREIRIYTDAGRICRPLLIVENGQLLLKRNHVNMLKEREFNNYGWQVLVASGV- 660

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                              VE +D +      +  +LD    G +                
Sbjct: 661  ------------------VEYIDTLEEETVMIAMNLDDLRGGQE---------------- 686

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                  K       +      P+  LG       +  + +P+  +N          M  +
Sbjct: 687  ------KEYAYCSTHTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQ 733

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +   ++I  +                           ++    +  V    +   +   
Sbjct: 734  AMG--VYITNY---------------------------HVRMDTLAHVLFYPHKPLVTTR 764

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +      + AI      +  D+ +   S V            +   K+  S
Sbjct: 765  SMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRS---CFYRSYKDSES 821

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLI 1013
              +  ++ E   +        +   +Y +L +   I  G           K+  L     
Sbjct: 822  KRIGDQE-EQFEKPTRQTCQGMRNAMYDKLDDDGIITPGVRVSGDDVVIGKTITL----- 875

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                                ++E    ++    +    R        Q    +     + 
Sbjct: 876  ---------------PDTDDDLEGTTRRFTKRDASTFLRNSETGCVDQVMLTLNAEGYKF 920

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +
Sbjct: 921  CKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTI 980

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G + E   G      G+                                           
Sbjct: 981  GHLIECLQGKVSANKGEIGD---------------------------------------- 1000

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G 
Sbjct: 1001 -------------ATPFNDAVNVQKISTLLQEYGYHLRGNELMYNGHTGRKINAQVFLGP 1047

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E
Sbjct: 1048 TYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRE 1107

Query: 1314 MLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQ 1355
             L   SD     V            R   +E    G        +   P +  +L +E+ 
Sbjct: 1108 RLFEVSDPYRIHVCNLCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELM 1165

Query: 1356 ALGLSIDLE 1364
            ++ ++  L 
Sbjct: 1166 SMNIAPRLM 1174



 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 144/985 (14%), Positives = 289/985 (29%), Gaps = 190/985 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +            +L+F       P  
Sbjct: 38  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIEHPPHYLLKFEQIYLSKPTH 97

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +   +    E        + + Q  ++G +P
Sbjct: 98  WEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEEPI-----ETQHQKSFIGKIP 152

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 153 IMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 211

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR--------------R 209
               GK  Y   I       ++        + V         I +              +
Sbjct: 212 ----GKYAYKTEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYIK 263

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           +++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 264 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGAR 323

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 324 GARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRREL 381

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 382 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMFAQKFIDRGKDFNLE-------LAI 434

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
              + T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 435 KTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 494

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 495 AKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 551

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 552 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 611

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E   + L  +      VN     E           +  V Y+  
Sbjct: 612 RIYTDAGRICRPLLIVENGQLLLKRN-----HVNMLKEREFNNYGWQVLVASGVVEYIDT 666

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA     L             R   E+           +  P  ++ + AS+I
Sbjct: 667 LEEETVMIAMNLDDL-------------RGGQEKEYAYCSTHTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNYHV----------------------------- 744

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + V  Y                +PLV                 
Sbjct: 745 ------------RMDTLAHVLFYP--------------HKPLV----------TTRSMEY 768

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G N +VA + + GYN EDS++++   V    F S     ++          E
Sbjct: 769 LRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSCFYRSYKDSESKRIGDQE 828

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E            +       +D+ GII  G  V+  D+++GK     ++    E    R
Sbjct: 829 EQFEKPTRQTCQGMRNAMYDKLDDDGIITPGVRVSGDDVVIGKTITLPDTDDDLEGTTRR 888

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                     RD S  + +  +G V
Sbjct: 889 -------FTKRDASTFLRNSETGCV 906


>gi|332148566|dbj|BAK20132.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148586|dbj|BAK20142.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 329

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 146/381 (38%), Positives = 197/381 (51%), Gaps = 62/381 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 5    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 62

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 63   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 122

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 123  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 182

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 183  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 236

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 237  ----------------------TVLYDG--------------------------RTGEPF 248

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 249  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 308

Query: 1306 GAAYVLQEMLTIKSDDVVGRT 1326
            GAAY LQE+LT+KSDDVVGR 
Sbjct: 309  GAAYTLQEILTVKSDDVVGRV 329



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 81/121 (66%), Positives = 99/121 (81%)

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV  
Sbjct: 1   ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKD 60

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   
Sbjct: 61  GDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDG 120

Query: 951 D 951
           D
Sbjct: 121 D 121


>gi|215254195|gb|ACJ64102.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 389

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 247/389 (63%), Positives = 303/389 (77%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G F +EL+ 
Sbjct: 61  SAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAALTEEGGFADELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA
Sbjct: 121 ARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K
Sbjct: 181 DKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTK 240

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           + RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS
Sbjct: 241 YTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDS 300

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GA
Sbjct: 301 ILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGA 360

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRA 915
           EV  GDILVGK+TPKGE+ +TPEEKLLRA
Sbjct: 361 EVKGGDILVGKVTPKGETQLTPEEKLLRA 389


>gi|126022812|ref|NP_904091.2| RNA polymerase beta subunit [Amborella trichopoda]
 gi|158518417|sp|P60282|RPOB_AMBTC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1072

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 722  LDRNGIVMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRVILGIQVSTAKETCLKLPI 781

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K                 ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 782  GGRGRVIDVRWIQKK-------GASSYNPEKIRVYISQKREIKVGDKVAGRHGNKGIISK 834

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 835  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRITPFDERYE 894

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 895  QEASRKLVFPELYEASKRTANPW------------------------VFE---------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YMLKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMLKLIHQVDDKIHGRSSGHYALVTQQP 975

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G    +  
Sbjct: 976  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQELLGTTIVGGTIPKPE 1035

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L +   L + +     + E
Sbjct: 1036 GAPESFRLLVRELRSLALELKHFLVSEKNFQINRKE 1071



 Score =  361 bits (927), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 230/634 (36%), Positives = 354/634 (55%), Gaps = 21/634 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V       Y  N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NVCYPEILLYFPNEKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKRFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLN+D P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRQNMNQRLNIDIPQNNTFLLPRDVLAATDHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I           PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENVVRGTICGAIRHKFIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDEDGSFT 641
            SL   AR+  +G I +P+ ++ +      +VYLS   +E   +  A  NS         
Sbjct: 436 GSLAIHARIGDWGSIRSPFYEISERSKEEQMVYLSPRRDEYYMVMVAAGNSLALNQDIQD 495

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E ID     P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 496 EQVVPARYRQEFVTIAWEHIDLRSIYPLQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 555

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG + +A+  G V   D         E  L         
Sbjct: 556 PLSRSEKCIVGTGLERQAALDSGGSAIAQHEGKVIYTD--------TEKILLSGNGDTIS 607

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V     V++  ++ADG +T  G+LALG+N+LVA MPW GY
Sbjct: 608 IPLLMYQRSNKNTCMHQKPQVHRDKYVKKGQVLADGAATVGGELALGKNVLVAHMPWEGY 667

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V  D++TS HI ++E+    T  GPE+IT +IP++    L+N+D  GI
Sbjct: 668 NFEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSHGPEKITNEIPHLEAHLLRNLDRNGI 727

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GD+LVGK+TP+     +  PE++LLR I G +    ++T L++P G  G V
Sbjct: 728 VMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRVILGIQVSTAKETCLKLPIGGRGRV 787

Query: 940 VDVRIFNRHG----IDKNERSISVEREQIELLAR 969
           +DVR   + G      +  R    ++ +I++  +
Sbjct: 788 IDVRWIQKKGASSYNPEKIRVYISQKREIKVGDK 821



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 70/337 (20%), Positives = 132/337 (39%), Gaps = 35/337 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 12  IPGFSQIQFEGFCRFV----------DQGLAEELHKFPKIEDTDQ--EIEFQLLVETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LT++  L +   LI          K  +D++EQ++++G++PLM   
Sbjct: 60  AEPLIKERDAVYESLTHSSELYVPAGLIW---------KVGRDMQEQTVFIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D+G   ++E D K  
Sbjct: 111 GTFIVNGIYRIVINQILQSPGIYYSSELDHNGIS---VYTGTIISDRGGRSELEIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +     A+G +  EIL    YP+I+     +     + + +  +    
Sbjct: 168 IWARVSRKQKISILVLPSAMGSNLREILDNVCYPEILLYFPNEKEKKKIGSKENAILEFY 227

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVN 314
                            K+L     +   E G       +  L         ++    V 
Sbjct: 228 QQFSCVGGDPVFSESLCKELQKRFFQQRCELGRIGRQNMNQRLNIDIPQNNTFLLPRDVL 287

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
             T  +      +     +  + +  IR +  L  D 
Sbjct: 288 AATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324


>gi|332148554|dbj|BAK20126.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148562|dbj|BAK20130.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148564|dbj|BAK20131.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148568|dbj|BAK20133.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148582|dbj|BAK20140.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 331

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 146/381 (38%), Positives = 197/381 (51%), Gaps = 62/381 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 7    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 64

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 65   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 124

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 125  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 184

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 185  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 238

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 239  ----------------------TVLYDG--------------------------RTGEPF 250

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 251  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 310

Query: 1306 GAAYVLQEMLTIKSDDVVGRT 1326
            GAAY LQE+LT+KSDDVVGR 
Sbjct: 311  GAAYTLQEILTVKSDDVVGRV 331



 Score =  121 bits (304), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 82/123 (66%), Positives = 101/123 (82%)

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV
Sbjct: 1   MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEV 60

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR 
Sbjct: 61  KDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRE 120

Query: 949 GID 951
             D
Sbjct: 121 DGD 123


>gi|324120614|dbj|BAJ78698.1| RNA polymerase II second largest subunit [Isonychia japonica]
          Length = 1150

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 171/1092 (15%), Positives = 333/1092 (30%), Gaps = 212/1092 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+     +  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALSRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   + ++    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAILDATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++SN +L   +  M +            V +G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVENSNLLLKKRHIDMLKDRDYNNYGWQFLVSSGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MSPEDLHHDKEYAYCTTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V        +  
Sbjct: 707  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V            +   K++ 
Sbjct: 738  RSMEYLRFRELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSIF---YRSYKDQE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   IY +L +   I  G           K+  L    
Sbjct: 795  SKRIGDQE-EQFEKPNRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVIIGKTITL---- 849

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    +Y    +    R        Q    +     +
Sbjct: 850  ----------------PENDDELEGTTKRYTKRDASTFLRNSETGIVDQVMITLNSEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DIV+NP  +PSRM 
Sbjct: 894  FSKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIVINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSANKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+S+L+       G  ++Y+G TG   +  + +G
Sbjct: 975  --------------ATPFNDAVNVQKISSLLQEYGYHLRGNEVMYNGHTGRKINAQIFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLENS 1366
             ++ ++  L   
Sbjct: 1139 MSMNIAPRLMVE 1150



 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 149/994 (14%), Positives = 292/994 (29%), Gaps = 184/994 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        D + Q  ++G +
Sbjct: 73  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVVKEGEDPI-----DTQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAMKD 187

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I        +        + V         I +              
Sbjct: 188 -----GKFAYKAEIR----SCQEHSSRPTSTLWVNMMARSGQSIKKSAIGQRIIAILPYI 238

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 239 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 298

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 299 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALSR 354

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 355 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 414

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 415 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 474

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 475 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 531

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               ++ A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 532 APSAILDATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 591

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L        +   Y      +        +  V Y+  +EEE
Sbjct: 592 DAGRICRPLLIVENSNLLLKKRHIDMLKDRDYNNYGWQFLV-----SSGVVEYIDTLEEE 646

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L  D  +                        +  P  ++ + AS+IPF +
Sbjct: 647 TVMIAMSPEDLHHDKEY---------------AYCTTYTHCEIHPAMILGVCASIIPFPD 691

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 692 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 718

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y               Q+PLV                     
Sbjct: 719 --------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRFR 746

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F SI    ++          EE   
Sbjct: 747 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSIFYRSYKDQESKRIGDQEEQFE 806

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 807 KPNRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVIIGKTITLPENDDELEGTT------ 860

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K    RD S  + +  +G V  V I       K
Sbjct: 861 -KRYTKRDASTFLRNSETGIVDQVMITLNSEGYK 893


>gi|331029425|gb|AEC49862.1| RNA polymerase beta subunit [Bradyrhizobium sp. SEMIA 696]
          Length = 270

 Score =  390 bits (1002), Expect = e-106,   Method: Composition-based stats.
 Identities = 151/259 (58%), Positives = 198/259 (76%), Gaps = 1/259 (0%)

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
           F+PPK+DVD+C  R +T+A PLK+TLRLIVFD+DE TGAKS+KDIKEQ +YMGD+PLMT 
Sbjct: 1   FEPPKYDVDECRQRGMTFAAPLKVTLRLIVFDIDEETGAKSVKDIKEQDVYMGDIPLMTM 60

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
           +GTFV+ G +R++VSQ+HRSPG+ FDHDKG+   SGKLL+A R+IP +G W+DIEFD+KD
Sbjct: 61  NGTFVVNGTERVIVSQMHRSPGVFFDHDKGKTHSSGKLLFAARVIPYRGSWLDIEFDAKD 120

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I+  RIDRRRK+PVTS + ALG+D E+ILSTFY KI Y +  D W  P  A +   G   
Sbjct: 121 IVFARIDRRRKLPVTSLMYALGLDGEQILSTFYKKITYKRTKDGWRVPFDA-NRFRGYST 179

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
            + L+D DTG+ V+E+GKKLT    + L+EKG+K L ++ + L G Y+AED+VN +TGEI
Sbjct: 180 VNDLIDADTGKVVLEAGKKLTVRQARQLQEKGLKALRMSDEELVGNYLAEDLVNPKTGEI 239

Query: 321 YIEAGDVIDEKSLEEIFHS 339
           Y EAG+ I EKSL+ +   
Sbjct: 240 YAEAGEEITEKSLKVLNEQ 258


>gi|324120608|dbj|BAJ78695.1| RNA polymerase II second largest subunit [Epiophlebia superstes]
          Length = 1175

 Score =  390 bits (1002), Expect = e-105,   Method: Composition-based stats.
 Identities = 165/1000 (16%), Positives = 313/1000 (31%), Gaps = 203/1000 (20%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+
Sbjct: 337  KYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYGNKRL 393

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R     + + ++               +  I  K +   +     +   
Sbjct: 394  DLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNW 453

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+   +   S ++H RR+++     + R     + R +H T +G I
Sbjct: 454  GDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWGMI 509

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYI 627
            CPAET EG  +GLV +L   A ++           + +  +    ++   +  +    ++
Sbjct: 510  CPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFV 569

Query: 628  AQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
                  +  D       L   R   + I+     I D  D   +          P L  +
Sbjct: 570  NGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLIVE 629

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +   +L   +++                     V  +SG           E +D      
Sbjct: 630  NGTLLLKKRHIEMLKEREYNNYG--------WQVLVASGVV---------EYIDT----- 667

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               E  +  + S  D+ +  ++                              P+  LG  
Sbjct: 668  -LEEETVMIAMSPEDLRQEKEYA------------------YCSTYTHCEIHPAMILG-- 706

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   ++I  F                  
Sbjct: 707  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------------ 741

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     ++    +  V    +   +    +       +      + AI      +  
Sbjct: 742  ---------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSVVAIACYTGYNQE 792

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V         +  +   +++R    E    E   +        +   IY +
Sbjct: 793  DSVIMNASAVERGFFRSVFYRSYKDQESKRVGDQE----EQFEKPTRATCQGMRNAIYDK 848

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   I  G           K+  L                     +    +E    ++
Sbjct: 849  LDDDGIIAPGVRVSGDDVVIGKTITL--------------------PENDDELEGTTKRF 888

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                +    R        Q    +     +  K+ V   R  Q GDK A RHG KG    
Sbjct: 889  TKRDASTFLRNSETGIVDQVMITLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGI 948

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E   G      G+            
Sbjct: 949  QYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--------- 999

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP  D  + + I+S+
Sbjct: 1000 --------------------------------------------ATPFNDAVNVQKISSL 1015

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L+       G  ++Y+G TG   +  + +G  Y  +L HMV DK+++R+ G   ++ +QP
Sbjct: 1016 LQEYGYQLRGNEVMYNGHTGRKINAQIFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQP 1075

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRV 1328
            + G++  GG R GEME  C  A+GAA  L+E L   SD     V            R   
Sbjct: 1076 MEGRARDGGLRFGEMERDCQIAHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANLRNNT 1135

Query: 1329 YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1136 FEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1173



 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 144/994 (14%), Positives = 289/994 (29%), Gaps = 184/994 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVAKEGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I       ++        + V         I +              
Sbjct: 213 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMARCGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRVKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L        +       E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGTLLLKKRHIEMLK-----EREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RQEKEYAYCSTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFYRSYKDQESKRVGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVVIGKTITLPENDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K    RD S  + +  +G V  V I       K
Sbjct: 886 -KRFTKRDASTFLRNSETGIVDQVMITLNSEGYK 918


>gi|34481621|emb|CAD45099.1| RNA polymerase beta subunit [Amborella trichopoda]
          Length = 1078

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 728  LDRNGIVMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRVILGIQVSTAKETCLKLPI 787

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K                 ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 788  GGRGRVIDVRWIQKK-------GASSYNPEKIRVYISQKREIKVGDKVAGRHGNKGIISK 840

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 841  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRITPFDERYE 900

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 901  QEASRKLVFPELYEASKRTANPW------------------------VFE---------- 926

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YMLKL H V DK++ RS+G Y+LVTQQP
Sbjct: 927  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMLKLIHQVDDKIHGRSSGHYALVTQQP 981

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G    +  
Sbjct: 982  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQELLGTTIVGGTIPKPE 1041

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L +   L + +     + E
Sbjct: 1042 GAPESFRLLVRELRSLALELKHFLVSEKNFQINRKE 1077



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 230/634 (36%), Positives = 354/634 (55%), Gaps = 21/634 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V       Y  N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 203 NVCYPEILLYFPNEKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKRFF-QQR 261

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLN+D P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 262 CELGRIGRQNMNQRLNIDIPQNNTFLLPRDVLAATDHLIGMKFGMGTLDDMNHLKNKRIR 321

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I           PQ+L+ + P+ +    FF    LS
Sbjct: 322 SVADLLQDQFGLALVRLENVVRGTICGAIRHKFIPTPQNLVTSTPLTTTYESFFGLHPLS 381

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 382 QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 441

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDEDGSFT 641
            SL   AR+  +G I +P+ ++ +      +VYLS   +E   +  A  NS         
Sbjct: 442 GSLAIHARIGDWGSIRSPFYEISERSKEEQMVYLSPRRDEYYMVMVAAGNSLALNQDIQD 501

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E ID     P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 502 EQVVPARYRQEFVTIAWEHIDLRSIYPLQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 561

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG + +A+  G V   D         E  L         
Sbjct: 562 PLSRSEKCIVGTGLERQAALDSGGSAIAQHEGKVIYTD--------TEKILLSGNGDTIS 613

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V     V++  ++ADG +T  G+LALG+N+LVA MPW GY
Sbjct: 614 IPLLMYQRSNKNTCMHQKPQVHRDKYVKKGQVLADGAATVGGELALGKNVLVAHMPWEGY 673

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V  D++TS HI ++E+    T  GPE+IT +IP++    L+N+D  GI
Sbjct: 674 NFEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSHGPEKITNEIPHLEAHLLRNLDRNGI 733

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GD+LVGK+TP+     +  PE++LLR I G +    ++T L++P G  G V
Sbjct: 734 VMLGSWVETGDVLVGKLTPQTAKESSYAPEDRLLRVILGIQVSTAKETCLKLPIGGRGRV 793

Query: 940 VDVRIFNRHG----IDKNERSISVEREQIELLAR 969
           +DVR   + G      +  R    ++ +I++  +
Sbjct: 794 IDVRWIQKKGASSYNPEKIRVYISQKREIKVGDK 827



 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 70/337 (20%), Positives = 132/337 (39%), Gaps = 35/337 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 18  IPGFSQIQFEGFCRFV----------DQGLAEELHKFPKIEDTDQ--EIEFQLLVETYQL 65

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LT++  L +   LI          K  +D++EQ++++G++PLM   
Sbjct: 66  AEPLIKERDAVYESLTHSSELYVPAGLIW---------KVGRDMQEQTVFIGNIPLMNSL 116

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D+G   ++E D K  
Sbjct: 117 GTFIVNGIYRIVINQILQSPGIYYSSELDHNGIS---VYTGTIISDRGGRSELEIDRKAR 173

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +     A+G +  EIL    YP+I+     +     + + +  +    
Sbjct: 174 IWARVSRKQKISILVLPSAMGSNLREILDNVCYPEILLYFPNEKEKKKIGSKENAILEFY 233

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVN 314
                            K+L     +   E G       +  L         ++    V 
Sbjct: 234 QQFSCVGGDPVFSESLCKELQKRFFQQRCELGRIGRQNMNQRLNIDIPQNNTFLLPRDVL 293

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
             T  +      +     +  + +  IR +  L  D 
Sbjct: 294 AATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 330


>gi|291190610|ref|NP_001167150.1| DNA-directed RNA polymerase II subunit RPB2 [Salmo salar]
 gi|223648370|gb|ACN10943.1| DNA-directed RNA polymerase II subunit RPB2 [Salmo salar]
          Length = 1174

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 172/1086 (15%), Positives = 325/1086 (29%), Gaps = 201/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKERRIKYAKEVLQKEVLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + I+          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKGVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYSHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         +             
Sbjct: 765  EYLRFRELPAGINSIVAIAAYTGYNQEDSVIMNRSAVDRGFFRSVFY------------- 811

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              R   E  ++   D++ I ++           G       K      +     +S    
Sbjct: 812  --RSYKEQESKKGFDQEEIFEKPTRE----TCSGMRHAIYDKLDDDGLIAPGVRVSG--E 863

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   V   +    ++S   +Y         R        Q    +     +  K+ V
Sbjct: 864  DVIIGKTVTLPETDDELDSTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM VG + E
Sbjct: 924  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTVGHLIE 983

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 984  CLQGKVSANKGEIGD--------------------------------------------- 998

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + ++++L        G  +LY+G TG      + +G  Y  +
Sbjct: 999  --------ATPFNDAVNVQKVSNLLSEYGYHLRGNEVLYNGFTGRKITSQIFLGPTYYQR 1050

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1051 LKHMVDDKIHSRARGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1110

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1111 SDPYQVHVCNLCGLMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1168

Query: 1361 IDLENS 1366
              +  S
Sbjct: 1169 PRMMTS 1174



 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 143/1003 (14%), Positives = 293/1003 (29%), Gaps = 203/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHTSGEVEDPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKEGEDQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLSGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSSIWVSMMARGGQGVKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVSTLPYIRQEVPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   +++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKERRIKYAK-EVLQKEVLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEIRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDVKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             E      T  GRIC         +     L     ++     E       D   +  V
Sbjct: 607 IREREIRIYTDAGRIC----RPLLIVEKQKLLLKRRHIDQLKEREYNNYSWQDLVASGVV 662

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            Y+  +EEE   +A     L E G                +         +  P  ++ +
Sbjct: 663 EYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYSHCEIHPSMILGV 706

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                               
Sbjct: 707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------ 742

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                               + + V  Y               Q+PLV            
Sbjct: 743 -----------------RMDTLAHVLYYP--------------QKPLV----------TT 761

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  G N +VA   + GYN EDS++++   V    F S+    ++      
Sbjct: 762 RSMEYLRFRELPAGINSIVAIAAYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821

Query: 855 KLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               EEI           +       +D+ G+I  G  V+  D+++GK     E+    +
Sbjct: 822 GFDQEEIFEKPTRETCSGMRHAIYDKLDDDGLIAPGVRVSGEDVIIGKTVTLPETDDELD 881

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                     +    RD S  + +  +G V  V +       K
Sbjct: 882 ST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|115605014|ref|YP_784465.1| RNA polymerase beta subunit [Piper cenocladum]
 gi|122164370|sp|Q06GR8|RPOB_PIPCE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|112253743|gb|ABI14464.1| RNA polymerase beta subunit [Piper cenocladum]
          Length = 1070

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/497 (31%), Positives = 242/497 (48%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VSRGKCIKKGQILANGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E + ++    +  L RN+  R   ++ G    +G   
Sbjct: 680  EDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLLRNL-DRNGIVMLGSWVETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  ++   S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V+++ KR ++ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V
Sbjct: 796  -GSSYNP---ETIRVYISQKREMKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   LG+  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGDFLGRHYRVAPFDERYEQEASRKLVFSELYEASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 912  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PFD+PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GDPFDQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-TPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G      G  PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRSRQEVLGTTIVGGTIANPGDAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLLSEKDFQIHRKE 1069



 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 228/610 (37%), Positives = 350/610 (57%), Gaps = 15/610 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   R++A+L+ Y+      GD              FF  
Sbjct: 195 LENVRYPEIFLSFLNERDKKKIGSRENAILEFYQQFACVGGDPVFSESLCRELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+ S LG GG+    A   +RD+H +HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHTSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   ARV  +G I+TP+ ++ +      +VYLS   +E   +A  NS     G   
Sbjct: 434 LIGSLAIHARVGPWGSIKTPFYEISERSKRLQLVYLSPSVDEYHMVAAGNSLALNRGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E+ V  R   E + +  E+I      P Q  S+ ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQAVPARYRQEFLTIAWEQIHLRSIFPFQYFSMGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG + +++R G V           + +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGVSAISEREGKVIYT--------NTDKIILSGNGDTIT 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V  G  +++  I+A+G +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMHQKTQVSRGKCIKKGQILANGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI
Sbjct: 666 NFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLETHLLRNLDRNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHG 949
           +DVR   + G
Sbjct: 786 IDVRWIQKKG 795



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP+  ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPEFSQIQFEGFCRFI----------DWGLAEELHKFPKIEDTDQEIEFQLFVETYQLAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K  KD++EQ++++G++PLM+  G 
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KPGKDMQEQTVFIGNIPLMSSLGI 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELD---HNGIFIYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVSSSAMGSNLREILENVRYPEIFLSFLNERDKKKIGSRE 220


>gi|18860303|ref|NP_569621.1| RNA polymerase beta subunit [Psilotum nudum]
 gi|41017771|sp|Q8WI24|RPOB_PSINU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|18389456|dbj|BAB84208.1| RNA polymerase subunit beta [Psilotum nudum]
          Length = 1066

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 245/654 (37%), Positives = 375/654 (57%), Gaps = 13/654 (1%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            I+           +  +    +    IL      N             K  +DA++++Y
Sbjct: 167 RIWARISKERKFSIITLLLALGLTRKDILNGVCYPNILLDLWKRQDKDIKSSEDAIIELY 226

Query: 379 RVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           + +       TFS +            +++L  +GR   N +LNL+ P++   +  +D++
Sbjct: 227 KNLYCVSGDVTFSESIRKELQRKLFKQRFELGQIGRRNPNNKLNLNVPENESFLLPQDLL 286

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--VDI 495
           A I  L+ ++ G GT+DDID+L NRRVRSV   L+ Q RL L  +E SI++ +       
Sbjct: 287 AAIDYLIGIKYGIGTLDDIDHLKNRRVRSVANFLQGQLRLALTHLENSIRQTMHKAIKRK 346

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            S+ P+ L+ + P+++   EFF S  LSQ  +  N L+ + H RRLS LG GG+ R  A 
Sbjct: 347 RSLTPKGLVISTPLLTTFKEFFGSHPLSQFLDQTNPLAEMIHKRRLSTLGPGGLTRRTAS 406

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            ++RD+HP++YGRICP ETSEG N GL++SL   ARVN YG++ + +  + D      +V
Sbjct: 407 FQVRDIHPSYYGRICPIETSEGINAGLITSLALHARVNDYGYLHSSFYNISDD--EEHIV 464

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLS  E+E   IA  N      G+  +++   R   E + +  E++ F    P Q  SI 
Sbjct: 465 YLSPAEDEYYRIATGNQLASNWGTQEKQVTLARYRQEFLTIAWEQVHFRSLFPLQYFSIG 524

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE++D+NR LMG +MQRQAVPLLK E   VGTG+E  VA  SG+   + + G +
Sbjct: 525 ASLIPFLEHNDANRALMGSHMQRQAVPLLKPEKCIVGTGLEGQVALDSGSVTRSTQEGQI 584

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             VD  +I +   + +   +        L+ ++RSN  TC+ +RP++  G  ++   ++A
Sbjct: 585 VYVDGAKITLSLNDNETIDTE-------LITYKRSNNKTCIKERPIISTGTYLKEGQLLA 637

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+LA GRN+LVA+MPW GYNFED++LISER++SED+FTS+HIE +E+  R T 
Sbjct: 638 DGTATVGGELAPGRNILVAYMPWEGYNFEDAILISERLISEDIFTSLHIERYEIEVRITN 697

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            G EEIT+DIP++    L+++D  G++ +G+ V  GD+LVGK+TP+ +S   PE KLL+A
Sbjct: 698 QGIEEITKDIPHLDSYVLRHLDSNGLVVLGSWVETGDVLVGKLTPQEDSLRAPEGKLLQA 757

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI-DKNERSISVEREQIELLA 968
           IFG +  D +++ L+VP G  G V+D R   +  I   N ++I +   Q   + 
Sbjct: 758 IFGIQVADTKESCLKVPIGGQGRVIDARWVYKENILINNAKTIHIYILQKRKIR 811



 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 163/574 (28%), Positives = 240/574 (41%), Gaps = 85/574 (14%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFT-SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
               G   E  + +    V+       I   +   +           T  I          
Sbjct: 558  CIVGTGLEGQVALDSGSVTRSTQEGQIVYVDGAKITLSLNDNETIDTELITYKRSNNKTC 617

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            I E  II  G  +  G +L       G   + P   +L A    +  +  D  L     +
Sbjct: 618  IKERPIISTGTYLKEGQLLADGTATVG-GELAPGRNILVAYMPWEGYNFEDAILISERLI 676

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +       R+ I+    +  +E    ++   D       LD N       ++ G   
Sbjct: 677  SEDIFTSLHIERYEIEVRITNQGIEEITKDIPHLD-SYVLRHLDSN-----GLVVLGSWV 730

Query: 996  VSGPKGFKKSTVLSSDLI--SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             +G     K T     L           +   V D K       LKV       +++ R+
Sbjct: 731  ETGDVLVGKLTPQEDSLRAPEGKLLQAIFGIQVADTKESC----LKVPIGGQGRVIDARW 786

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K   +           + + +++  KR I+ GDK+AGRHGNKGIVS+ILP +DMP L+
Sbjct: 787  VYKENIL-------INNAKTIHIYILQKRKIRVGDKVAGRHGNKGIVSKILPRQDMPHLQ 839

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVD++L+PLGVPSRMNVGQIFE  LG A   + +  +    D +   + S    F E
Sbjct: 840  DGTPVDMILSPLGVPSRMNVGQIFECLLGLAGDFMQRHYRITPFDERFEREASRKLVFSE 899

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                    A E+  N  L   D    G+
Sbjct: 900  LCE-------------------------------------ASEKTRNPWLFEPDYP--GK 920

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            S L DG TG+ F++PVTVG  YM+KL H V DK++ARS+G Y+L+TQQPL          
Sbjct: 921  SRLIDGRTGDTFEQPVTVGKAYMMKLIHQVDDKIHARSSGPYALITQQPL---------- 970

Query: 1294 LG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
                          EMEVW ++++GAAY+LQEMLT+KSD +  R +V  +IV G    + 
Sbjct: 971  --RGRSRRGGQRVGEMEVWALESFGAAYILQEMLTLKSDHIQARYKVLGAIVTGKPIPKP 1028

Query: 1342 G-TPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
               PESF +LV+E+++L L+++      K+  + 
Sbjct: 1029 NSVPESFRLLVRELRSLALNLNYFLISEKDLERE 1062



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/268 (26%), Positives = 115/268 (42%), Gaps = 34/268 (12%)

Query: 32  VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV----SYEFDPPKFD 87
           +Q   +  F+          N+GL         I        +EF+     Y+   P   
Sbjct: 18  IQYEGFKRFI----------NQGLMEELLKFPKIQDADQ--EVEFLLVGDQYKLREPSIK 65

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
             D +++ +TY+  L +  RL           K  + I+EQ ++MG +PLMT  GTF+I 
Sbjct: 66  EKDAVYKCVTYSSELYVPARLT---------QKRNRRIREQILFMGSIPLMTSQGTFIIN 116

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G+ R++V+Q+ RSPGI +  +     +    LY   II + G    +E D +  I  RI 
Sbjct: 117 GVTRVLVNQIVRSPGIFYSREPDHKRI---PLYTGTIISNWGGRFKLEIDGRMRIWARIS 173

Query: 208 RRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRG--DFWCFPLSAADLMVGAKVSSSL 264
           + RK  + + L+ALG+  ++IL+   YP I+       D        A + +   +    
Sbjct: 174 KERKFSIITLLLALGLTRKDILNGVCYPNILLDLWKRQDKDIKSSEDAIIELYKNLYCVS 233

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKG 292
            D+   E +    K+L   L K   E G
Sbjct: 234 GDVTFSESI---RKELQRKLFKQRFELG 258


>gi|237831495|ref|XP_002365045.1| DNA-directed RNA polymerase II subunit RPB2, putative [Toxoplasma
            gondii ME49]
 gi|211962709|gb|EEA97904.1| DNA-directed RNA polymerase II subunit RPB2, putative [Toxoplasma
            gondii ME49]
 gi|221487105|gb|EEE25351.1| DNA-directed RNA polymerase II subunit, putative [Toxoplasma gondii
            GT1]
 gi|221506791|gb|EEE32408.1| DNA-directed RNA polymerase II subunit, putative [Toxoplasma gondii
            VEG]
          Length = 1259

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 175/1003 (17%), Positives = 324/1003 (32%), Gaps = 191/1003 (19%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              +        + R ++   +  +   + +  +   I  ++  L+    G+   DD D+ 
Sbjct: 404  QREKRIQYARELLRKEVLPHVGTEVGCENK--KAFYIGYMVHRLLLADLGRINQDDRDHF 461

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ---DLINAKPVVSAVCEF 516
            G +R+   G ++   +     +M + ++  +               + +A  +   +   
Sbjct: 462  GKKRLDMAGPLIAASFGTLYRKMIKDVRRILQRQVDHGKSFDVAGAIRSASQITQGLQYQ 521

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               ++Q+   +   S ++H RRL+      + R     + R +H 
Sbjct: 522  IATGNWGKDKEGKIVRTGVAQVLNRLTFASALSHLRRLNT----PLGREGKMAKPRQLHN 577

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G ICPAET EG  +GLV +L   + ++      T +  + +    + +  ++    +
Sbjct: 578  THWGMICPAETPEGQAVGLVKNLALMSDISVGSATNTVHEFLVEW-GLDPLEEMTPDVIK 636

Query: 624  NRYIAQANSSL----DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             R     N S     DE     + L   R   +         D ++   K       ++ 
Sbjct: 637  ERVKVFVNGSWVGCFDEADVLCQTLRQLRRRCDISSETSIVRDLVNREVKIFTDAGRAMR 696

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P    D+  R L+   M+R  +  L                K   +       GI+E VD
Sbjct: 697  PLFVVDEGTRDLV---MKRCHLEEL------------QRRGKDEKSWGYLMEKGIIEFVD 741

Query: 740  AIR---IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                   +I     D+         Y   +                              
Sbjct: 742  CEEEETCMIAMFVEDIRSEKRQAFPYTHCEIH---------------------------- 773

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                     +L   +  + +P+  +N       S R V +       +  +         
Sbjct: 774  --------PSLILGVCASIIPFPDHNQ------SPRNVYQSAMGKQAMGVYTSSF----- 814

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      N   + L ++                +    +       +      + AI
Sbjct: 815  ----------NHRMDTLAHL--------LYYPQKPLVCTRAMEFLRFRELPAGINAIVAI 856

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R    +  +  S+  E  E  + +      
Sbjct: 857  LCYSGYNQEDSLIMSQSSIDRGLF-RSVFYRTYCSEERQQGSLMVESFEPPSIEHVQGMK 915

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
              D +       +  G   +       K++ L  D       +      V     +R   
Sbjct: 916  RGDYSKLDADGLVEPGSRVLGDDVIIGKTSPLFDDDTGMPGGAGAGPGGVPSPFAKRK-- 973

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                        L       ++++    +        VKV     R  Q+GDK A RHG 
Sbjct: 974  ------RDCSLCLRSSETGVVDQVMLSVNNRGSRFTKVKV--RSVRIPQTGDKFASRHGQ 1025

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF ++G   D+++NP  VPSRM +G + E  LG      G       
Sbjct: 1026 KGTIGITYRTEDMPFNEEGITPDLIMNPHAVPSRMTIGHLVECLLGKTAAIFG------- 1078

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                          G   +TP F+G   
Sbjct: 1079 ----------------------------------------------GEGDATP-FNGYAV 1091

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
              I++ L     +  G   LY G TG      +  G  Y  +L HMV DK++AR+ G  +
Sbjct: 1092 LDISNRLHSLGYERFGNERLYHGHTGRHLPSLIFFGPTYYQRLKHMVDDKIHARARGPVT 1151

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV- 1328
            ++T+QP+ GKS  GG R GEME  C+ ++GAA++L+E L  +SD       D+ G     
Sbjct: 1152 MLTRQPMEGKSREGGLRFGEMERDCMISHGAAHMLKERLFEQSDAYRVHVCDICGLVCTA 1211

Query: 1329 ------YESIVAGND--TFETGTPESFNVLVKEMQALGLSIDL 1363
                  +E  +  N     +   P +  +L++E+ A+ +   L
Sbjct: 1212 DLSRGNFECKLCDNKSRISQICIPYACKLLLQELMAMCIYPRL 1254



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 110/809 (13%), Positives = 221/809 (27%), Gaps = 152/809 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+             +Q       PI                +    L+
Sbjct: 104 LVNQQLESFNDFVSYK----------IQEIIDEHPPIEIRPTPQYRPEEEVESNVIYRLK 153

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKD 124
                 + P  +            +   R+LTY+ PL + +    + VD  TG  + +  
Sbjct: 154 MDQLSLNRPSVEEKEGISKHLWPYEARTRNLTYSSPLYVDVEQTTYTVDPETGAERLVDQ 213

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
           +    + +G +P+M K                         G F+I G ++++V+Q   +
Sbjct: 214 VTYSRVLLGRIPMMLKSAYCWTKDLPEHDLADVGECAYDQGGYFIINGGEKVLVAQERMA 273

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSKDIIHVRIDRR----RK---- 211
               F +   +   S K  +   +   + G+     F  K        R     RK    
Sbjct: 274 SN--FVYVFQKKQPS-KFGWVAEVRSQKEGMQATSGFAVKKR-----SRTGGEGRKGGRP 325

Query: 212 --------------VPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +P+     ALG +   +IL     ++ Y  +       +  +    
Sbjct: 326 GGQIVAALPYIRTEIPIVILFRALGCISDRDIL----LRVAYDLKDPQLIALMKPSLEEG 381

Query: 257 GAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKGVKF-------LGITSDCLCGLY 307
               S  +     G+    + + ++      + L  K V                  G  
Sbjct: 382 FDYSSQDVCLDFIGKRGPTVGAQREKRIQYARELLRKEVLPHVGTEVGCENKKAFYIGYM 441

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V   ++  + G I  +  D   +K L+            LY   + +   I    V    
Sbjct: 442 VHRLLL-ADLGRINQDDRDHFGKKRLDMAGPLIAASFGTLYRKMIKDVRRILQRQVDHGK 500

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                   D+   +R     T  +   +    +    +  +   G  ++  RL   +   
Sbjct: 501 SF------DVAGAIRSASQITQGLQYQIATGNWGKDKEGKIVRTGVAQVLNRLTFASALS 554

Query: 428 V--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              R          +     L N    +         +      ++KN   +  + +  +
Sbjct: 555 HLRRLNTPLGREGKMAKPRQLHNTHWGMICPAETPEGQAVG---LVKNLALMSDISVGSA 611

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
                  +    + P + +    +   V  F   S +   +E       +   RR   + 
Sbjct: 612 TNTVHEFLVEWGLDPLEEMTPDVIKERVKVFVNGSWVGCFDEADVLCQTLRQLRRRCDIS 671

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                          +       + P    +     LV        +   G  E      
Sbjct: 672 SETSIVRDLVNREVKIFTDAGRAMRPLFVVDEGTRDLVMKRCHLEELQRRGKDEKS---W 728

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                   + ++   EEE   IA     +  +                           +
Sbjct: 729 GYLMEKGIIEFVDCEEEETCMIAMFVEDIRSEKRQAFPY-----------------THCE 771

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAP 709
             P  ++ + AS+IPF +++ S R +    M +QA+                 L   + P
Sbjct: 772 IHPSLILGVCASIIPFPDHNQSPRNVYQSAMGKQAMGVYTSSFNHRMDTLAHLLYYPQKP 831

Query: 710 FVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
            V T  ME +  +   A I A  A +   
Sbjct: 832 LVCTRAMEFLRFRELPAGINAIVAILCYS 860


>gi|295065718|ref|YP_003587658.1| RNA polymerase beta subunit [Anomochloa marantoidea]
 gi|251765242|gb|ACT15396.1| RNA polymerase beta subunit [Anomochloa marantoidea]
          Length = 1077

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 125/306 (40%), Positives = 178/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 810  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 869

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE  LG A   L K  +    D +   + S    F E    +              
Sbjct: 870  VGQIFECSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 922

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 923  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 950

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 951  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVKGRAKQGGQRVGEMEVWALEGFGVAHILQ 1010

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1011 EILTYKSDHLIARQELLNATIRGRGVPNHEDPPESFRVLVRELRSLALELNHSLVSEKNF 1070

Query: 1370 NSAKME 1375
               K E
Sbjct: 1071 QVNKEE 1076



 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 225/614 (36%), Positives = 353/614 (57%), Gaps = 26/614 (4%)

Query: 373 ALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           A+L+ Y+      GD+             FF   K +L  +GR  +N RLNLD P +   
Sbjct: 222 AILEFYQQFACVGGDLVFSESLCEELQKKFFS-QKCELGRIGRRNINRRLNLDIPQNNTF 280

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           +   D++A    L+ ++ G G  DD D  +L N+R+RSV ++L++Q+ L L R++ ++++
Sbjct: 281 LLPRDVLAATDHLIGMQFGMGIRDDDDMNHLKNKRIRSVADLLQDQFGLALGRLQHAVQK 340

Query: 489 RISS--VDIDSVMPQDLINAKPVVSA----VCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            I    +      PQ L+      +        FF +  LSQ+ +  N L++  H R++S
Sbjct: 341 TICRVFIRQSKPTPQILVTPTSTSTLLITTYETFFGTYPLSQVFDQTNPLTQTVHGRKVS 400

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-YGFIETP 601
            LG GG+    A    RD+HP+HYGRICP +TSEG N+GL  SL   AR++  +G IE+P
Sbjct: 401 CLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEGINVGLTGSLAIHARIDPSWGSIESP 460

Query: 602 YRKV---CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           + ++      K    V+YLS   +E   IA  NS     G   E++V  R   E + +  
Sbjct: 461 FYEISEKEKDKKERQVLYLSPNRDEYYMIAAGNSLSLNQGIQEEQVVPARYRQEFLTIAW 520

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           E+I      P Q  SI  SLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  
Sbjct: 521 EQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMSSNMQRQAVPLFRSEKCIVGTGLERQ 580

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            A  S  +++A+R G +   D+ +I++ S                L+   RSN+NTC++Q
Sbjct: 581 TALDSRVSVIAEREGKIISADSHKIILSSN--------GKTLSIPLVVHWRSNKNTCMHQ 632

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +P V+ G  +++  I+A+G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED+
Sbjct: 633 KPRVRQGKCIKKGQILAEGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 692

Query: 839 FTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +TS HI ++E+    T  GP E+IT++IP++ E  L+N+   G++ +G+ V  GDILVGK
Sbjct: 693 YTSFHIRKYEIETATTSEGPAEKITKEIPHLGEHLLRNLGINGVVMLGSWVETGDILVGK 752

Query: 898 ITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           +T +  +  +   E  LLRAI G +    ++TSL++P G  G V+DV+   R+ +D   R
Sbjct: 753 LTAQIANEPSYLAETGLLRAILGLEVSTAKETSLKLPIGGRGRVIDVKWIQRNPLDIMVR 812

Query: 956 SISVEREQIELLAR 969
              +++ +I++  +
Sbjct: 813 VYILQKREIKVGDK 826



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 103/221 (46%), Gaps = 27/221 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDP 83
           IP   ++Q   +  F+          N+GL         I         + V   Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELDKFPTIEDTDHEIAFQLVAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++PLM   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPLMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+IKGI RIV++Q+ +SPGI++  +     +S   +Y   +I D G   ++  D K+ + 
Sbjct: 111 FIIKGIYRIVINQILQSPGIYYRSELDHKGIS---IYTGTLISDWGGRSELALDKKERVW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGD 243
            R+ R++K+ +     A+G +  EIL    YP+I  S   D
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFLND 208


>gi|290489620|gb|ADD31194.1| RNA polymerase beta subunit protein [Nerium oleander]
          Length = 1070

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 155/497 (31%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   ++  + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VQRGKYIKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 680  EDIYTSFHIRKYEIQTHVTSQGPERVTNEIPHLEAHLLRNL-DKKGIVMLGSWVETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKRG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V+++ KR IQ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 796  -GSSYNP---ETIRVYISQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 912  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GNPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTILGGTIPNPEDAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 374/662 (56%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GGV    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKLSYLGPGGVTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYRVAAGNSLALNQDIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G V   D  +I++                  L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALSIAEREGKVVYTDTDKILLSVN--------GDTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPRVQRGKYIKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTNEIPHLEAHLLRNLDKKGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HG 949
            G
Sbjct: 794 RG 795



 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLAEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERNAVYELLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|323148898|ref|YP_004222453.1| RNA polymerase beta subunit [Smilax china]
 gi|308742589|gb|ADO33440.1| RNA polymerase beta subunit [Smilax china]
          Length = 1060

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 249/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +        G   E    +   + +        I         +  G  
Sbjct: 534  MSSNMQRQAVPLSRPEKCIVGTGLERQTALDSGLSAIAEHEGKIIYTDTHKIVISSNGDT 593

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 594  INIPLVMYQRSNKNTCMHQKPQVQRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 652

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +  L 
Sbjct: 653  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAYLL 707

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  R   +  G    +G     K T  +++  S  P  +  +  +  +       SLK
Sbjct: 708  RNL-DRNGIVRLGSWIEAGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLK 766

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K                +++V+V  KR I+ GDK+AGRHGNKGI
Sbjct: 767  LPIGGRGRVIDVRWIQKR-------GSSSYNPEMIRVYVLQKREIKVGDKVAGRHGNKGI 819

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+ +DGT VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 820  ISKILPRQDMPYFQDGTTVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKRHYRIAPFDE 879

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 880  RYEQEASRKLVFPELYEASKQTKNPW------------------------VFE------- 908

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 909  --------PEYPGKSRIFDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGPYALVT 960

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 961  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIVGGTVP 1020

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1021 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1059



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 231/686 (33%), Positives = 379/686 (55%), Gaps = 23/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 135 ISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 194

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 195 IFLSFLNGKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 253

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN R NLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 254 GRRNMNRRFNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 313

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 314 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRT 373

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R++S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 374 NPLTQIVHGRKVSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 433

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+  +G I++P+ ++   +    +VYL    +E   +A  NS     G   E++V  R 
Sbjct: 434 VRIGRWGSIDSPFFEIASKET--QMVYLPPSRDEYYMVAAGNSLALNRGIQEEQVVPARY 491

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL + E  
Sbjct: 492 RQEFLTVAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRPEKC 551

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+  G +   D  +IVI S                L+ +QR
Sbjct: 552 IVGTGLERQTALDSGLSAIAEHEGKIIYTDTHKIVISSN--------GDTINIPLVMYQR 603

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 604 SNKNTCMHQKPQVQRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNSEDAVLI 663

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ +G+ + 
Sbjct: 664 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAYLLRNLDRNGIVRLGSWIE 723

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+  +  +  PE++LLRAI G +    ++TSL++P G  G V+DVR   +
Sbjct: 724 AGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWIQK 783

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 784 RGSSSYNPEMIRVYVLQKREIKVGDK 809



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------NQGLVEEFHKFPKIEDTDQEIEFQLFVERYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI+         K+ +DI+EQ++++G++PLM   GT
Sbjct: 54  PLIKERDAVYESLTYSSELYVPAGLIL---------KTGRDIQEQTVFIGNIPLMNSLGT 104

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 105 FIVNGIYRIVINQILQSPGIYYHSELDHNGIS---VYTSTIISDWGGRSELEIDRKARIW 161

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +
Sbjct: 162 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNGKEKKKIGSKE 212


>gi|186885855|gb|ACC93335.1| RNA polymerase beta subunit [Echinops ritro]
          Length = 1024

 Score =  390 bits (1001), Expect = e-105,   Method: Composition-based stats.
 Identities = 141/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 427/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKAFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   DA +I++                  L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTDADKILLSGN--------GDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRQGKCIKKGQILAYGSATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++  +     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  166 bits (420), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 91/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +            I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRRS-------YIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|323149074|ref|YP_004222638.1| RNA polymerase beta subunit [Anthriscus cerefolium]
 gi|289645567|gb|ADD13630.1| RNA polymerase beta subunit [Anthriscus cerefolium]
          Length = 1070

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 157/580 (27%), Positives = 254/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   +++        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVLAIAEHEGKVIYTDTDKILLSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G  ++          +   + +  A    
Sbjct: 604  LNIPLVMYQRSNKNTCMHQKPQVQRGKYIKKGQ-ILAYGAATVGGELALGKNVSVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T       S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKRG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEA 1218
            +   + S    F E    +                            +TP VF+      
Sbjct: 890  RYEQEASRKLVFSELYQASKQT-------------------------ATPWVFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R +V  + + G   
Sbjct: 970  TQQPLRGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQQVLGTTIIGEAI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++    + +T    + E
Sbjct: 1030 PNPQDAPESFRLLVRELRSLALELNHFFVSEKTFKIKRKE 1069



 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 227/686 (33%), Positives = 375/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   K +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQKCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RL+LD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV +++
Sbjct: 262 GRRNLNRRLHLDISQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLI 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L+R+E  I+  I       ++P  Q+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQLGLALVRLENVIRGTIGGALRHKLIPSPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++  +G +E+P+ ++        ++YLS  ++E   +A  N      G   E++V  R 
Sbjct: 442 AKIGRWGSLESPFYEISQRSKGARMLYLSPGKDEYYMVAAGNPLALNQGLQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + V  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTVAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G V   D         +  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVLAIAEHEGKVIYTD--------TDKILLSGNGDTLNIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+ VA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPQVQRGKYIKKGQILAYGAATVGGELALGKNVSVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T++IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            G+ILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 RGGSSYNPEMIRVYISQKREIKVGDK 819



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/336 (20%), Positives = 134/336 (39%), Gaps = 31/336 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFM----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYKLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L I+  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PFIKERDAVYESLTYSSELYISAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKSRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQ 229

Query: 263 ------SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   V  ++  + ++         L  +  + +             ++    +   
Sbjct: 230 FACVGGDPVFSESLCKELQKKFFQQKCELGKIGRRNLNRRLHLDISQNNTFLLPRDILAA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
              +      +     +  + +  IR +  L  D +
Sbjct: 290 ADHLIGMKFGMGTLDDMNHLKNKRIRSVADLIQDQL 325


>gi|242009479|ref|XP_002425513.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative
            [Pediculus humanus corporis]
 gi|212509368|gb|EEB12775.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative
            [Pediculus humanus corporis]
          Length = 1175

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 167/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKERRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++   +      
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMFAQKFIDRG 426

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV ++   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNIALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC--NMQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +    +L     NM ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGGQLLLKKNHVNMLKEREYNNFGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V    +   ++ 
Sbjct: 732  QAMG--VYITNY---------------------------HVRMDTLAHVLFYPHKPLVIT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V            +   K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVF---YRSYKDSE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 820  SKRIGDQE-EQFEKPNRQTCQGMRNAMYDKLDDDGIIAPGVRVSGDDVIIGK-------- 870

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D      +E    +Y    +    R        Q    +     +
Sbjct: 871  ----------TITLPDND--DELEGATKRYTKRDASTFLRNSETGCVDQVMITLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNELMYNGHTGRKINAQVFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  245 bits (625), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 148/999 (14%), Positives = 296/999 (29%), Gaps = 194/999 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDTPIIDLQAEAQHASGEIENP-PHYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + K Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKKIIKEGEDPI-----ETKHQKSFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   +++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 324 RGARPGVTKERRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 381

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        +       + 
Sbjct: 382 LDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMFAQKFIDRGKDFNLE-------LA 434

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 435 IKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 494

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 495 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNIALMAYISVGSQPSPILEFLEEWSME 551

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 552 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 611

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               T  GRIC P    EG  + L  +      VN     E           +  V Y+ 
Sbjct: 612 IRIYTDAGRICRPLLIVEGGQLLLKKN-----HVNMLKEREYNNFGWQVLVASGVVEYID 666

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            +EEE   IA +   L                 ++           +  P  ++ + AS+
Sbjct: 667 TLEEETVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASI 711

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 712 IPFPDHNQSPRNTYQSAMGKQAMGVYITNYHV---------------------------- 743

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + V  Y                +PLV          I     
Sbjct: 744 -------------RMDTLAHVLFYP--------------HKPLV----------ITRSME 766

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G N +VA + + GYN EDS++++   V    F S+    ++          
Sbjct: 767 YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFYRSYKDSESKRIGDQ 826

Query: 859 EEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           EE            +       +D+ GII  G  V+  D+++GK     ++    E    
Sbjct: 827 EEQFEKPNRQTCQGMRNAMYDKLDDDGIIAPGVRVSGDDVIIGKTITLPDNDDELEGAT- 885

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 K    RD S  + +  +G V  V I       K
Sbjct: 886 ------KRYTKRDASTFLRNSETGCVDQVMITLNSEGYK 918


>gi|324120638|dbj|BAJ78710.1| RNA polymerase II second largest subunit [Tenodera aridifolia]
          Length = 1175

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNIALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKG 426

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +  + +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGGSLLLKKRHIDMLKEREYNNYGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        +++               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETVMIS---------------MSPDDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 820  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGK-------- 870

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D +    +E    ++    +    R        Q    +     +
Sbjct: 871  ----------TITLPDNE--DELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1164 MAMNIAPRLM 1173



 Score =  244 bits (623), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 138/981 (14%), Positives = 291/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    ++ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNIALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K  ++  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHMARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    EG ++ L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVEGGSLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              I+ +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMISMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDNEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRFTKRDASTFLRNSETGIV 905


>gi|209360637|gb|ACI42989.1| RNA polymerase beta subunit [Mycoplasma synoviae]
          Length = 904

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 150/463 (32%), Positives = 211/463 (45%), Gaps = 67/463 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V+
Sbjct: 509  IVKVGDHVKEGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVL 567

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+      +   S S E      +          LD     ++   +   + + G  
Sbjct: 568  -TSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRI 626

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V++          +L           
Sbjct: 627  SPKGEENPSQE--EKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVLSR--------- 675

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  ++KV++A KR I+ GDKMAGRHGNKG++S ILP EDMP L+DGTP+DI
Sbjct: 676  ENGDILEDGLDSIIKVYIAQKRKIKVGDKMAGRHGNKGVISIILPEEDMPHLEDGTPLDI 735

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D      I  L            
Sbjct: 736  MLNPQGVPSRMNIGQVLEMHLGMAAKKLGTKFVTPSFDGIKKETIEDLLQEAN------- 788

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + ++ D +
Sbjct: 789  ------------------------------------------LDKSG-----KQVVIDPI 801

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD P++VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 802  TGEKFDNPISVGVIYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 861

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
             +++YGA+ +LQE+LT KSDD+  R  VY+++V  +     G 
Sbjct: 862  ALESYGASNILQEILTYKSDDIYSRNLVYKALVNDSAIPNPGM 904



 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/714 (36%), Positives = 406/714 (56%), Gaps = 38/714 (5%)

Query: 267 IDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGET 317
           I  G+++ E  K+ L SG+L   K   +   G           + +   Y+A+ +V+   
Sbjct: 12  IRKGDRISEESKRSLLSGMLFDKKRYNLSKTGRYMLNNKLSLVERITNTYLAQKVVSHLG 71

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
                + G  +  +  +EI  S           S  +   I N    D           +
Sbjct: 72  NT--FDVGTYVTYEIAKEIQESFEAKAK--DNKSNLHLEKIPNINPDDVYYKINKDNKSL 127

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +    +  +    +M                        +  D      H+   DII
Sbjct: 128 NKRINIARIKIWPTKRAMDANETPSE---------------VIGNDPKATEEHLLLSDII 172

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A I   ++L  G G  DD D+L N+R+ SVGE+L+ + R+ LL++E++ +ER+ + + D 
Sbjct: 173 AAISYYLNLTVGIGQDDDPDSLMNKRIVSVGELLEGELRIALLKLEKATRERMGAKEPDK 232

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +  +++ N K + + +  FF +S+L+Q  + +N L+ I++ RR+++LG GG+ R  A  E
Sbjct: 233 ITAKNVTNNKLITNQMKTFFNTSKLAQFMDQINPLAEISNKRRVTSLGPGGLNRDTAQFE 292

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVY 616
           +RDVH THYGRICP ET EG NIGL+ +   ++ VN  GF++TPY KV DG V  NDV Y
Sbjct: 293 VRDVHSTHYGRICPIETPEGPNIGLILNYAIYSTVNELGFLQTPYYKVNDGVVDYNDVRY 352

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L++ EE     AQ++  +++     +E +  +     I+   + IDF++ S KQ+VS+AA
Sbjct: 353 LTSYEEIGYAFAQSSVHVNDKNEIIDEQITIKKDYNYIIGSPKDIDFLEVSSKQIVSVAA 412

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           + IPFLEN+D+NR LMG NMQRQAVPL++AEAP V TG+E+ +AK S   IVA   G V 
Sbjct: 413 AAIPFLENNDANRALMGSNMQRQAVPLIEAEAPLVATGIEADIAKFSSYNIVANNDGEVI 472

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VD  +I +R        +   +D Y L  F++SNQ T + Q+P+VKVGD V+  D++ D
Sbjct: 473 YVDGTKIQVR--------TAKKIDTYNLKNFEKSNQGTIIQQKPIVKVGDHVKEGDLLVD 524

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G S   G++ALG+N+LV F  W+GYNFED+++I+ER+V +DV TSI+IEE  +  R +K 
Sbjct: 525 GSSFKDGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVLTSIYIEEQTIQFRISKS 584

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             + +TRDIPNVS+  ++N+DE GII VG+EV  GD+LVG+I+PKGE   + EEKLL AI
Sbjct: 585 SEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRISPKGEENPSQEEKLLNAI 644

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-SVEREQIELLAR 969
           F ++  + +DTSL+V +G +GTV+ V + +R   D  E  + S+ +  I    +
Sbjct: 645 FNQRPQNYKDTSLKVKNGHNGTVIHVEVLSRENGDILEDGLDSIIKVYIAQKRK 698


>gi|289065081|ref|YP_003433967.1| RNA polymerase beta subunit [Typha latifolia]
 gi|69216922|gb|AAZ03995.1| RNA polymerase beta chain [Typha latifolia]
 gi|281371764|gb|ADA63691.1| RNA polymerase beta subunit [Typha latifolia]
          Length = 1072

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 148/444 (33%), Positives = 227/444 (51%), Gaps = 50/444 (11%)

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   I+    I K E    V  +  E + ++    +  L RN+  R   ++ G  
Sbjct: 675  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNL-DRNGIVMLGSW 733

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G     K T  +++  S  P  +  +  +  +       SLK+       +++ R+ 
Sbjct: 734  VETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWI 793

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K E    G         +++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+D
Sbjct: 794  QKKE----GSSYNS---EMIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQD 846

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E 
Sbjct: 847  GTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKRHYRIAPFDERYEQEASRKLVFSEL 906

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
               +                               VF+                +  G+S
Sbjct: 907  YEASKQTKNPW------------------------VFE---------------PEYPGKS 927

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+
Sbjct: 928  RIFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRV 987

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKE 1353
            GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E
Sbjct: 988  GEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIIGGRVTKPEDAPESFRLLVRE 1047

Query: 1354 MQALGLSID--LENSRTKNSAKME 1375
            +++L L ++  L + +     + E
Sbjct: 1048 LRSLALELNHFLVSEKNFQINRKE 1071



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/688 (34%), Positives = 385/688 (55%), Gaps = 23/688 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALARLENAVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            R+  +G IE+P+ ++ +     +  +VYLS   +E   +A  NS     G   E++V  
Sbjct: 442 VRIGHWGSIESPFYEISERSKEKESQMVYLSPNRDEYYMVAAGNSLALNRGIQEEQVVPA 501

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502 RYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              VGTG+E   A  SG +++A+ AG +   D  +I++ S E  +           L+ +
Sbjct: 562 KCIVGTGLERQTALDSGVSVIAEHAGKIIYTDTHKIILSSNENTI--------SIPLVMY 613

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++
Sbjct: 614 QRSNKNTCMHQKPQVWRGKSIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAV 673

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ +G+ 
Sbjct: 674 LISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDRNGIVMLGSW 733

Query: 888 VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           V  GDILVGK+TP+  +  +  PE++LLRAI G +    ++TSL++P G  G V+DVR  
Sbjct: 734 VETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWI 793

Query: 946 NRH----GIDKNERSISVEREQIELLAR 969
            +        +  R   +++ +I++  +
Sbjct: 794 QKKEGSSYNSEMIRVYILQKREIKVGDK 821



 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL A F+    I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLTAEFQKFPKIEDTDQEIEFKLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTVFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|262090292|ref|YP_002364492.2| RNA polymerase beta subunit [Festuca arundinacea]
 gi|261410433|gb|ACJ70749.2| RNA polymerase beta subunit [Festuca arundinacea]
          Length = 1079

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 126/306 (41%), Positives = 178/306 (58%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++L     KN 
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIPNHEDPPESFRVLVRELRSLALELNLFLVSEKNF 1069

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1070 QVNRED 1075



 Score =  346 bits (887), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 230/700 (32%), Positives = 381/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    +    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTSSFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKV----CDGKVTNDVVYLSAMEEENRYIAQANS 632
            N+GL  SL   AR++  +G IE+P+ ++       K +  V+YLS  ++E   IA  NS
Sbjct: 434 INVGLTGSLAIHARIDHLWGSIESPFYEISAEKAKKKKSRQVIYLSPNKDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKILSTDSHKILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+N C++Q+  V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTLSIPLVNHRRSNKNNCMHQKSRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++   
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEAH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D  G++ +G+ V   DILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDRNGVVRLGSWVETSDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQREPLDIMVRVYILQKREIKVGDK 825



 Score =  167 bits (424), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+ L         I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQALAEELDKFPAIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|222093455|gb|ACM43504.1| RNA polymerase beta subunit [Mycoplasma synoviae]
          Length = 907

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 150/463 (32%), Positives = 211/463 (45%), Gaps = 67/463 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V+
Sbjct: 512  IVKVGDHVKEGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVL 570

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+      +   S S E      +          LD     ++   +   + + G  
Sbjct: 571  -TSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRI 629

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V++          +L           
Sbjct: 630  SPKGEENPSQE--EKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVLSR--------- 678

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  ++KV++A KR I+ GDKMAGRHGNKG++S ILP EDMP L+DGTP+DI
Sbjct: 679  ENGDILEDGLDSIIKVYIAQKRKIKVGDKMAGRHGNKGVISIILPEEDMPHLEDGTPLDI 738

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D      I  L            
Sbjct: 739  MLNPQGVPSRMNIGQVLEMHLGMAAKKLGTKFVTPSFDGIKKETIEDLLQEAN------- 791

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + ++ D +
Sbjct: 792  ------------------------------------------LDKSG-----KQVVIDPI 804

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD P++VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 805  TGEKFDNPISVGVIYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 864

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT 1343
             +++YGA+ +LQE+LT KSDD+  R  VY+++V  +     G 
Sbjct: 865  ALESYGASNILQEILTYKSDDIYSRNLVYKALVNDSAIPNPGM 907



 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/714 (36%), Positives = 407/714 (57%), Gaps = 38/714 (5%)

Query: 267 IDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGET 317
           I  G+++ E  K+ L SG+L   K   +   G           + +   Y+A+ +V+   
Sbjct: 15  IRKGDRISEESKRSLLSGMLFDKKRYNLSKTGRYMLNNKLSLVERITNTYLAQKVVSHLG 74

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
                + G  +  +  +EI  S           S  +   I N    D           +
Sbjct: 75  NT--FDVGTYVTYEIAKEIQESFEAKAK--DNKSNLHLEKIPNINPDDVYYKINKDNKSL 130

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +    +  +    +M   +                    +  D      H+   DII
Sbjct: 131 NKRINIARIKIWPTKRAMDANVTPSE---------------VIGNDPKATEEHLLLSDII 175

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A I   ++L  G G  DD D+L N+R+ SVGE+L+ + R+ LL++E++ +ER+ + + D 
Sbjct: 176 AAISYYLNLTVGIGQDDDPDSLMNKRIVSVGELLEGELRIALLKLEKATRERMGAKEPDK 235

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +  +++ N K + + +  FF +S+L+Q  + +N L+ I++ RR+++LG GG+ R  A  E
Sbjct: 236 ITAKNVTNNKLITNQMKTFFNTSKLAQFMDQINPLAEISNKRRVTSLGPGGLNRDTAQFE 295

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVY 616
           +RDVH THYGRICP ET EG NIGL+ +   ++ VN  GF++TPY KV DG V  NDV Y
Sbjct: 296 VRDVHSTHYGRICPIETPEGPNIGLILNYAIYSTVNELGFLQTPYYKVNDGVVDYNDVRY 355

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L++ EE     AQ++  +++     +E +  +     I+   + IDF++ S KQ+VS+AA
Sbjct: 356 LTSYEEIGYAFAQSSVHVNDKNEIIDEQITIKKDYNYIIGSPKDIDFLEVSSKQIVSVAA 415

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           + IPFLEN+D+NR LMG NMQRQAVPL++AEAP V TG+E+ +AK S   IVA   G V 
Sbjct: 416 AAIPFLENNDANRALMGSNMQRQAVPLIEAEAPLVATGIEADIAKFSSYNIVANNDGEVI 475

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VD  +I +R        +   +D Y L  F++SNQ T + Q+P+VKVGD V+  D++ D
Sbjct: 476 YVDGTKIQVR--------TAKKIDTYNLKNFEKSNQGTIIQQKPIVKVGDHVKEGDLLVD 527

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G S   G++ALG+N+LV F  W+GYNFED+++I+ER+V +DV TSI+IEE  +  R +K 
Sbjct: 528 GSSFKDGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVLTSIYIEEQTIQFRISKS 587

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             + +TRDIPNVS+  ++N+DE GII VG+EV  GD+LVG+I+PKGE   + EEKLL AI
Sbjct: 588 SEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRISPKGEENPSQEEKLLNAI 647

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-SVEREQIELLAR 969
           F ++  + +DTSL+V +G +GTV+ V + +R   D  E  + S+ +  I    +
Sbjct: 648 FNQRPQNYKDTSLKVKNGHNGTVIHVEVLSRENGDILEDGLDSIIKVYIAQKRK 701


>gi|186885815|gb|ACC93315.1| RNA polymerase beta subunit [Brachylaena elliptica]
 gi|186885915|gb|ACC93365.1| RNA polymerase beta subunit [Oldenburgia grandis]
          Length = 1024

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 141/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 424/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKAFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++  +     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|324120678|dbj|BAJ78730.1| RNA polymerase II second largest subunit [Panorpa takenouchii]
          Length = 1172

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 250  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVVQ 309

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 310  EQNVALNFIGARGARPGV---TKDKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 363

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 364  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKG 423

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 424  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRIN 483

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 484  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 539

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 540  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVS 599

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ N +L   +  M ++           V +G+ 
Sbjct: 600  MIRDIRDREIRIYTDAGRICRPLLIVENRNLLLKKRHVDMLKERDYNNYGWQVLVASGVV 659

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 660  EYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------- 691

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 692  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 728

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V        +  
Sbjct: 729  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPMKPLVTT 759

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         +  +   + +R
Sbjct: 760  RSMEYLRFRELPAGINTIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSETKR 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                E    E   +        +   +Y +L E   I  G           K+  L    
Sbjct: 820  LGDQE----EQFEKPTRQSCQGMRNALYDKLDEDGIIAPGIRVSGDDVIIGKTITL---- 871

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    ++    +    R        Q    +     +
Sbjct: 872  ----------------PENDDELEGTTKRHTKRDASTFLRNSETGIVDQVMLTLNSEGYK 915

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 916  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 975

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 976  IGHLIECIQGKLGANKGEIGD--------------------------------------- 996

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 997  --------------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQVFLG 1042

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1043 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1102

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R+  +E    G        +   P +  +L +E+
Sbjct: 1103 ERLFEVSDPYRIHVCNFCGLIAIANLRSNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1160

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1161 MSMNIAPRLM 1170



 Score =  196 bits (498), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 104/747 (13%), Positives = 227/747 (30%), Gaps = 107/747 (14%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 36  LVRQQLDSFDEFIQMSVQRIVEDSPAIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 94

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    + +      + + Q  ++G +
Sbjct: 95  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTIVQDGKDSV-----ETQHQKSFIGKI 149

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 150 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 209

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 210 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 260

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 261 KQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVVQEQNVALNFIGA 320

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 321 RGARPGVTKDKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 376

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 377 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDKGKDFNLELAIKTKI 436

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 437 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRINSPIGRDGKLAKPR 496

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 497 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 553

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    +S +   RR   +    V+  R   +      T
Sbjct: 554 APSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 613

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L         V+     +           +  V Y+  +EEE
Sbjct: 614 DAGRICRPLLIVENRNLLLKKR-----HVDMLKERDYNNYGWQVLVASGVVEYIDTLEEE 668

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 669 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 713

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           ++ S R      M +QA+ +       
Sbjct: 714 HNQSPRNTYQSAMGKQAMGVYITNYHV 740


>gi|186885963|gb|ACC93389.1| RNA polymerase beta subunit [Tarchonanthus camphoratus]
          Length = 1024

 Score =  389 bits (1000), Expect = e-105,   Method: Composition-based stats.
 Identities = 141/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 254/834 (30%), Positives = 424/834 (50%), Gaps = 43/834 (5%)

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
            E     + + +  +   +     +  +             + S+  +  +   +I  +  
Sbjct: 95   ELNDNEISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILE 154

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDL 408
            +      ++       K   +++A+L+ Y+     +    FS + S      F   + +L
Sbjct: 155  NVCYPELFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCEL 214

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV 
Sbjct: 215  GGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVA 274

Query: 469  EMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            ++L+ Q+ L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ 
Sbjct: 275  DLLQEQFGLALVRLENMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKAFFRLHPLSQVL 334

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
            +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL
Sbjct: 335  DRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSL 394

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
               AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V 
Sbjct: 395  AIHARIGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVP 454

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++
Sbjct: 455  ARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQS 514

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E   VGTG+E   A  SGA  +A+  G +   D         +  L           L+ 
Sbjct: 515  EKCIVGTGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLVM 566

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            +QRSN+NTC+ Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED+
Sbjct: 567  YQRSNKNTCMPQKPQVRQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDA 626

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+
Sbjct: 627  VLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGS 683

Query: 887  EVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
             V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR 
Sbjct: 684  WVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRW 743

Query: 945  FNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA- 995
                  D+ +++  +     ++ +I++  +      ++ +I        +  +  G+   
Sbjct: 744  VQSSKTDETDKTERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVD 803

Query: 996  -----VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLK 1039
                 +  P       +  S L ++     + ++ A  DE+ ++            E+ K
Sbjct: 804  MVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASK 863

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                      E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 864  QTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +     +S   +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELNDNEIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|291241363|ref|XP_002740582.1| PREDICTED: DNA directed RNA polymerase II polypeptide B-like
            [Saccoglossus kowalevskii]
          Length = 1175

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 166/1087 (15%), Positives = 325/1087 (29%), Gaps = 207/1087 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  + A   I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVAALPYIRQEIPIMIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKERRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DI 495
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRHLFKNLMKEVRIYAQKFIDKG 426

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIITDGLKYSLATGNWGEQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R       R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLARPRQLHNTLWGMICPAETPEGQAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  E    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAASAINEATKIFVNGCWVGIHRDPEQLMNTLKKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             + D  +   +          P L  +    +L   +  M ++      +    V +G+ 
Sbjct: 603  MVRDIREKEIRIYTDAGRICRPLLIVEKQKLLLKKKHIDMLKEREYNNYSWQDLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A                   +   +        Y             
Sbjct: 663  EYIDTLEEETVMLAMTP----------------DDLQEKGMGYCSTY------------- 693

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  PS  LG       +  + +P+  +N          M  
Sbjct: 694  ----------------THCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 730

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V        +  
Sbjct: 731  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPQKPLVTT 761

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V        +F R   D+  +
Sbjct: 762  RSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNLSAVERGFF-RSVFYRSYRDQESK 820

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                + E  E   R+      +   +       I  G           K+  L       
Sbjct: 821  KGLDQEEVFEKPDRESCQGMRMAVYDKLDDDGIIAPGSRVSGDDVLIGKTVTL------- 873

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                          +    +E    ++    S    R        Q    +     +  K
Sbjct: 874  -------------PENDDELEGTTRRFTKRDSSTFMRRTETGIVDQVMVSINQEGYKFCK 920

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 921  IKIRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTAEGITPDIIINPHAIPSRMTIGH 980

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 981  LIECLQGKVSANKGEIGD------------------------------------------ 998

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L        G  +LY+G TG      + +G  Y
Sbjct: 999  -----------ATPFNDTVNVQKISNLLHEYGYHLRGNEVLYNGFTGRKLGTQIFIGPTY 1047

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  ++GAA  L+E L
Sbjct: 1048 YQRLKHMVDDKIHSRARGPLQILNRQPMEGRSRDGGLRFGEMERDCQISHGAAQFLRERL 1107

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            R   +E    G        +   P +  +L +E+ ++
Sbjct: 1108 FEVSDPYRVHVCNLCGLIAIANLRNNTFEC--RGCKNKTQISQIRLPYACKLLFQELMSM 1165

Query: 1358 GLSIDLE 1364
             ++  + 
Sbjct: 1166 SIAPRMM 1172



 Score =  242 bits (617), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 146/1008 (14%), Positives = 296/1008 (29%), Gaps = 213/1008 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI   +               +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDSPPIELQAEATHTTIEVEVPTRYILKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   +    +       ++ +
Sbjct: 89  EQIYLSKPTHWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGDEP-----QETQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        + V +  R     RK    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLEHSSRPTSTLWVHMMARGGQGVRKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        +P+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVAALPYIRQEIPIMIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAED 311
             V+ + +        +   +++     + L+++ +  +G++           G  V   
Sbjct: 314 QNVALNFIGARGARPGVTKERRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRL 372

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           ++    G   ++  D    K L+            L+ + +          +        
Sbjct: 373 LL-AALGRRELDDRDHYGNKRLDLAGPLLAFLFRHLFKNLMKEVRIYAQKFIDKGKDFNL 431

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--R 429
           +       +     + T  +  S+    + +  K   +  G  ++  RL   +      R
Sbjct: 432 E-------LAIKTRIITDGLKYSLATGNWGEQKKAHQARAGVSQVLNRLTFASTLSHLRR 484

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                     +     L N    +         +      ++KN   +  + +       
Sbjct: 485 LNSPIGRDGKLARPRQLHNTLWGMICPAETPEGQAVG---LVKNLALMAYISVGSQPSPI 541

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +  ++  S+   + I A  +  A   F     +    +    ++ +   RR   +    V
Sbjct: 542 LEFLEEWSMENLEEIAASAINEATKIFVNGCWVGIHRDPEQLMNTLKKLRRQMDIIVSEV 601

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
           +  R   E      T  GRIC         +     L     ++     E       D  
Sbjct: 602 SMVRDIREKEIRIYTDAGRIC----RPLLIVEKQKLLLKKKHIDMLKEREYNNYSWQDLV 657

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            +  V Y+  +EEE   +A     L E G                +         +  P 
Sbjct: 658 ASGVVEYIDTLEEETVMLAMTPDDLQEKG----------------MGYCSTYTHCEIHPS 701

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +                          
Sbjct: 702 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNYHV------------------- 742

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + V  Y               Q+PLV       
Sbjct: 743 ----------------------RMDTLAHVLYYP--------------QKPLV------- 759

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G N +VA   + GYN EDS++++   V    F S+    +  
Sbjct: 760 ---TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNLSAVERGFFRSVFYRSYRD 816

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                 L  EE+           +       +D+ GII  G+ V+  D+L+GK     E+
Sbjct: 817 QESKKGLDQEEVFEKPDRESCQGMRMAVYDKLDDDGIIAPGSRVSGDDVLIGKTVTLPEN 876

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               E    R          RD+S  +    +G V  V +       K
Sbjct: 877 DDELEGTTRR-------FTKRDSSTFMRRTETGIVDQVMVSINQEGYK 917


>gi|11466500|ref|NP_044749.1| RNA polymerase subunit beta [Reclinomonas americana]
 gi|2258330|gb|AAD11864.1| RNA polymerase subunit beta [Reclinomonas americana]
          Length = 1478

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 257/1060 (24%), Positives = 453/1060 (42%), Gaps = 79/1060 (7%)

Query: 13   VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            +R  F    EI+ IP+L+++ K+SY++FL   +   +R + G+Q+  K  F      G +
Sbjct: 15   LRLGFSSINEIVPIPNLLKISKSSYNNFLQRFVPYSKRLDVGIQSLLKKYF------GNS 68

Query: 73   MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
               F+ Y F   + + D+CL   LTY++PL + L++ + D  + T  K          Y+
Sbjct: 69   ---FICYSFGVSEKNPDECLENGLTYSIPLYVFLKVNMKDNVKDTIKKY---------YI 116

Query: 133  GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G++PL+T  G+F+I G++  V++QL R  G++ +  K       K     R +  + + +
Sbjct: 117  GEIPLLTDSGSFIINGVENTVINQLVRDSGVYINKSKSPFI---KTSLKIRGLKGRSIQL 173

Query: 193  DIEFDSKDIIHVRIDRRRKVP------------VTSFLMALGMDSEEILSTF-YPKIVYS 239
            D  +D  + I  +ID +  +             +   L +  +  +EI  TF Y    Y 
Sbjct: 174  DYFYD--NFIGQKIDTKTLISGKNLNQNITHQEIDKLLDSFKISFKEIGETFTYSITEYK 231

Query: 240  QRGDFWCFPLSAADL------MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                 W    +  ++           + S+ +  D           + + ++ +      
Sbjct: 232  YCNMGWFIDFNWKEISKYRFIKKNKNIISTSLSFDNNLLANNDYISILNTVVNNKFISND 291

Query: 294  KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
            KFL      L      + I   E           +  K    +   +  D   L  +   
Sbjct: 292  KFLNHDLFLLDIYKDNKSIFIIENTNDDFSYPLELLNKVGSHLSSFKNSDFLFLIENKNI 351

Query: 354  NNAYIRNTLVTDKNKDRKDALLDI---YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            N  YI   L    +  R    + I    + +     S   +    F         + L  
Sbjct: 352  NYQYIFINLKEQPDSIRNSLQVVIESKKKKLLMFFNSKHVLKNDFFLEKDVLFHNFKLGP 411

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG--NRRVRSVG 468
            +GR+K+N++  L+  +    +   D   I++ L+ +  G    D  +     NRR  ++G
Sbjct: 412  IGRLKINLKFGLN--EKKEELTSIDFTRILRYLIQIDKGFIENDIYEEQSLLNRRFNNIG 469

Query: 469  EMLKNQYRLGLLRMERS-IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            E L +     L+  E S           + ++ + + N +     +  +   S L Q  E
Sbjct: 470  EHLYSCLSDYLISKEDSKYSVSKEDYIKNQMLFKKINNCRNAFYFLIRYLNKSSLCQYTE 529

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N+LS + HTR++S +G GG+      +EMRDVH + YG+ICP ET EG ++G+V++L+
Sbjct: 530  QANALSYLGHTRKVSIMGPGGLKNDNISLEMRDVHISTYGKICPIETPEGKSVGVVNNLS 589

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL-VF 646
             + R N    +ETPY  V +  VTN + YL+  EE+   IA A   L +DGSF     ++
Sbjct: 590  LYTRTNTLFQLETPYIFVKENFVTNIIHYLTPQEEKYYKIAHATEVLKKDGSFLNTKEIY 649

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            CR     I V  + +D+I+ S  Q+ S++AS+IPFLE++D NR LMG NMQ+QAVPLL  
Sbjct: 650  CRYLHSLITVDSKNVDYIEMSSGQITSLSASMIPFLEHNDGNRALMGSNMQKQAVPLLNL 709

Query: 707  EAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRIVIRSVEGDL------DPST 756
            E   +GTG+E ++ +     S   ++ K         +I  +++    ++      D   
Sbjct: 710  EKSLIGTGIEGIIGRDFFNISKNLLLEKMTNENVFGISILKILKKENKNIIFSQFVDLFI 769

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                +Y  +K + SNQ T ++ + + K    +  N+I   G S    +L+LG N+LV F 
Sbjct: 770  KNHFLYSTIKHKNSNQKTDIDFKYVNKKNINIFENNIDNIGYSIKNNELSLGNNVLVGFT 829

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
              +G+ FEDS++ISER+V ++ F SIH+E ++ M    K   E I   +          +
Sbjct: 830  SMNGHTFEDSIVISERIVRDNYFQSIHLEVYKTMEMYEKDSQEIIRNFL------STDFL 883

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D  G+I +G  V   DIL+GK   +       +  +       K               S
Sbjct: 884  DVDGVIHLGTNVCTNDILIGKEKRQLLLSEKNKLIVYDKSIRYKNKKKGVVIQIAKFFDS 943

Query: 937  GTVVDVRIFNRHGIDKNERSIS--VEREQIELL----------ARDKDDEQVILDRNIYS 984
               ++        + K+  S+   + +E+   L                +  I  + I  
Sbjct: 944  LVDLNKHYITTSNLQKSTESLLSYIYKEEKIRLMFLSYLFFIFKNKYKYDLGIKKKIILD 1003

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
             L   L  +   S    + K+ +  ++L  +      ++ 
Sbjct: 1004 DLNIHLNQKMNWSFSSFYTKTILYRNNLNIKLNFDLIYKM 1043



 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 144/397 (36%), Positives = 219/397 (55%), Gaps = 12/397 (3%)

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            R IY R  +       ++      K   +       Y      +  +  E          
Sbjct: 1088 REIYKRNKK--NDFVLLNIKMSLSKVFFIDLKKKIPYSMEFLLKNFILQEMYILLFLYYI 1145

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR------VVKVFVAMKRPIQSGDKMAGR 1093
             +Y      + +  +  ++K     +     L+      +VKV VA K  IQ GDK+ GR
Sbjct: 1146 KEYNKQNFNVFENDQIFVQKKTKSINKKKDCLKNNYSLRMVKVVVACKHNIQVGDKLTGR 1205

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            +GNKG++SRIL  EDMP+L+DGTP+DIVL+PLGV SRMN+GQ+ E HLG A V L KK++
Sbjct: 1206 YGNKGVISRILSLEDMPYLRDGTPLDIVLSPLGVSSRMNIGQLLECHLGLAGVELSKKLQ 1265

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
             +I  Y     +   R +L  +         ++  +D  ++ + +    G+P+STP+F+ 
Sbjct: 1266 QIIQTY---DIVGKSRKYLSMLYRNKKELLLLNSLNDSQIICLFKNISHGIPISTPIFNS 1322

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A+   I+++LR++ L+   +  + DG+TG   D  VTVGY+YM+KLNH++  K++ RSTG
Sbjct: 1323 ANNFDIDNLLRISGLNIQSKVTIIDGITGVVLDNKVTVGYMYMMKLNHLIDHKIHGRSTG 1382

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             Y+++TQQ   GKS  GGQRLGEMEVW +QAYGAAY LQEMLT KSD  + R+   ++ +
Sbjct: 1383 PYNIITQQASKGKSRNGGQRLGEMEVWALQAYGAAYTLQEMLTFKSDSTISRSSFLQNFI 1442

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
             G  T     P +F +L  E++ LG+ ++    R+  
Sbjct: 1443 RGK-TSRIDIPRTFKLLRDELRVLGMELNFIVKRSNE 1478


>gi|324120628|dbj|BAJ78705.1| RNA polymerase II second largest subunit [Teleogryllus emma]
          Length = 1174

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 171/1087 (15%), Positives = 328/1087 (30%), Gaps = 206/1087 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 252  GQRIIAVLPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 311

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 312  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 365

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 366  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 425

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 426  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 485

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 486  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 541

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 542  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 601

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             I D  D   +          P L  ++ N +L   ++                      
Sbjct: 602  MIRDIRDREIRIYTDAGRICRPLLIVENGNLLLKKRHIDMLKEREYNNFG--------WQ 653

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            V  +SG           E +D +      +    D                         
Sbjct: 654  VLVASGVV---------EYIDTLEEETVMIAMSPDDLRQE-------------------- 684

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                K              P+  LG       +  + +P+  +N          M  + +
Sbjct: 685  ----KEYAYCMTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V    +   +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         F      K+  S  
Sbjct: 765  EYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAESKR 821

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            +  ++ E   +        +   +Y +L +   I  G           K           
Sbjct: 822  IGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGK----------- 869

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                      + D +    +E    +Y    +    R        Q    +     +  K
Sbjct: 870  -------TITLPDNE--DELEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCK 920

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 921  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGH 980

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 981  LIECLQGKVSSNKGEIGD------------------------------------------ 998

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G  Y
Sbjct: 999  -----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLGPTY 1047

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L
Sbjct: 1048 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERL 1107

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            R   +E    G        +   P +  +L +E+ A+
Sbjct: 1108 FEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMAM 1165

Query: 1358 GLSIDLE 1364
             ++  L 
Sbjct: 1166 NIAPRLM 1172



 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 141/981 (14%), Positives = 289/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 38  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 96

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 97  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIKDGEEPI-----ETQHQKTFIGKI 151

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 152 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 211

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 212 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAVLPYI 262

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 263 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 322

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 323 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 378

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 379 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 438

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 439 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 498

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 499 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 555

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 556 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 615

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  N+ L         ++     E           +  V Y+  +EEE
Sbjct: 616 DAGRICRPLLIVENGNLLLKKR-----HIDMLKEREYNNFGWQVLVASGVVEYIDTLEEE 670

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 671 TVMIAMSPDDL---------------RQEKEYAYCMTYTHCEIHPAMILGVCASIIPFPD 715

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 716 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 742

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 743 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 770

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 771 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 830

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 831 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDNEDELEGTT------ 884

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 885 -KRYTKRDASTFLRNSETGIV 904


>gi|332148584|dbj|BAK20141.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 328

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 146/380 (38%), Positives = 197/380 (51%), Gaps = 62/380 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 5    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 62

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 63   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 122

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 123  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 182

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 183  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 236

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 237  ----------------------TVLYDG--------------------------RTGEPF 248

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 249  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 308

Query: 1306 GAAYVLQEMLTIKSDDVVGR 1325
            GAAY LQE+LT+KSDDVVGR
Sbjct: 309  GAAYTLQEILTVKSDDVVGR 328



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 81/121 (66%), Positives = 99/121 (81%)

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV  
Sbjct: 1   ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKD 60

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   
Sbjct: 61  GDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDG 120

Query: 951 D 951
           D
Sbjct: 121 D 121


>gi|224179481|ref|YP_002601004.1| beta subunit of RNA polymerase [Monomastix sp. OKE-1]
 gi|217314524|gb|ACK36867.1| beta subunit of RNA polymerase [Monomastix sp. OKE-1]
          Length = 2108

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 186/641 (29%), Positives = 273/641 (42%), Gaps = 115/641 (17%)

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            N+  + +P      +  ++ ++   +     S      +   +D+    E  + ++P   
Sbjct: 1374 NIFRSLVPGEYLTRDLDIVTNKTSRNSGNENS----TLKTSTKDSLEALE--SINLPPKL 1427

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKIT--------------------PKGESPMTPE 909
               L+++D  GII  G  V  GDIL+GK+                      K ++   PE
Sbjct: 1428 PPKLRHLDANGIIKPGTWVQEGDILLGKLQIGPKDNLNNFDIKAQNTPFAQKIQTLPFPE 1487

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE--RSISVEREQIELL 967
             +LL AIF  +      T     S + G  +    F     +K     S   ++EQI   
Sbjct: 1488 YRLLLAIFDLQNRTPDKTLPTQTSNLEGGKLWPTTFGEKLSEKESTLPSSQDKKEQIIGE 1547

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 +E      +  S     L  QN  S     + +  L +   S        Q    
Sbjct: 1548 KSLSSEEGERSPLSDLSAYKNTLPSQNFGSELTSGQDTLNLLAAEKSSNSGLFAHQIKNT 1607

Query: 1028 DEKVQRNVESLKVQY--ETSKSILEDRFKN------------------------------ 1055
              KV   V+   + Y  +   SI + R K                               
Sbjct: 1608 SFKVGIGVKGRVLDYVVDGRISIFDGRQKANQNLPPRGSRETPPGLWPSQREEREGRGGR 1667

Query: 1056 ----KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                +  K   G+         V +F+A K+ IQ GDKM+GRHGNKGIVS ILP +DMP+
Sbjct: 1668 TPFLEKHKTLIGEGFIQSAATSVSIFLAHKKRIQLGDKMSGRHGNKGIVSLILPPQDMPY 1727

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L+DG PVD+VLNPLGVPSRMNVGQ+ ET  G +     K  + +  D +     S  ++ 
Sbjct: 1728 LQDGKPVDVVLNPLGVPSRMNVGQVLETLFGLSAFYSHKVYRIMPFDERIAPSQSIEKNT 1787

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM-LRMADLDE 1230
            L++         + S       LR  +  K+GVP             I+ + L+      
Sbjct: 1788 LQENASLSLSRPETSRSLVYGHLRKLKT-KAGVP--------PKRAEISELGLQKGGYPR 1838

Query: 1231 S-------------------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            +                   G++ L+DG TGE F +P  VGY YM KL H+V DK++ARS
Sbjct: 1839 TLKSIKKGSQLNWLFDPNNPGKTHLFDGRTGEIFYQPALVGYSYMFKLIHLVDDKIHARS 1898

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT----- 1326
            TG YSLVTQQPLGG+S +GGQRLGEMEVW ++ +G A +LQE LT+KSD++  R      
Sbjct: 1899 TGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGTASILQEFLTVKSDEIYSRNNFLFH 1958

Query: 1327 ---RVYESIVAGNDTFETGTPESF-------NVLVKEMQAL 1357
               R +ES+    +       ESF        V  +E+++L
Sbjct: 1959 LMRRNWESLEKNEN-------ESFARDAIKARVAGEELRSL 1992



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 144/621 (23%), Positives = 246/621 (39%), Gaps = 133/621 (21%)

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
               +  K I     Y GD+PLMT+ G+F+I G  R++V+Q+ R P ++F   K +    
Sbjct: 356 ERSTRQKKQIF--WFYFGDIPLMTERGSFIINGAPRVLVNQIIRCPSVYF---KVKLDQK 410

Query: 176 GKLLYACRIIPDQGLWMDIEFDS-KDIIHVRIDRRRKVPVTSFLMALGM--DSEEILSTF 232
            +  Y    + + G W+ +E D   + +  RID+  + P    LM LG   DSE + S  
Sbjct: 411 NRRSYTASFLSEYGSWLRLETDRLSNRLWARIDKSPRFPADILLMGLGYVLDSENLNSVK 470

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAK---------VSSSLVDIDTGEQVIESGKKLTSG 283
           Y       + +         + +V  K          +S+L             K LT+ 
Sbjct: 471 YGLSKNEFKLNAQTLSFGKENKVVINKNIVKNSIFETASTLNSTFPASPFTSLKKYLTAK 530

Query: 284 LLKSLKEKGVKFLGITSDCL---------------------CGLYVAEDIVNGETGEIYI 322
            ++  +E          +                        G  +++ + +    + + 
Sbjct: 531 YIQVYQENNNLPTRQHDEREVQRPPRNGGEGSVGRTPFLDWIGKGLSKGLQSTAGEKQFA 590

Query: 323 EAGDVIDEKSLEEIFHSEIRDI---------------------PILYVDSVNNNAYIRNT 361
           +  + ++ K + +  +     +                      I    S   N   +NT
Sbjct: 591 KLLNKVENKKISKEQNYLWSSVSARLAEPKISSIQSPRPVLSGSIGKKFSSTKNFVFKNT 650

Query: 362 LVTDKNKDRK---------------DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           +  D  +  +                AL  +++   PG  ++     S F   F +  +Y
Sbjct: 651 VENDNTRTPRRTNAGSKSGITINTATALQALWKKCNPGRWTSALGCYSFFYNKFLNPKRY 710

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG-------TIDDIDNL 459
            +  VGR+++N RL  +    +  +  ED++     L +L+            +DDID+L
Sbjct: 711 SIGRVGRIRLNKRLRRNPECKIPTLTPEDVLLAFHYLTELKIADAKENTFSLELDDIDHL 770

Query: 460 GNRRVRSVGEMLKNQYRLGLLRME-RSIKERISSVDIDSVMPQDLINAK----------- 507
            NRRVR  GE+L+NQ+RL L R+   +I+ + +  +I + + Q     +           
Sbjct: 771 KNRRVRLPGEILQNQFRLALSRIPYSAIRLQDNKTNIRNEVLQQREKVQRPQGVPLEGRV 830

Query: 508 ----------------------------------------PVVSAVCEFFCSSQLSQLEE 527
                                                      S + E F + QLSQ  +
Sbjct: 831 GRSPPSGEAKKVEQNQNSIRKNFDSVSSSRSEDSVPPGIPAFQSTLRELFNTGQLSQYMD 890

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ ITH RRLS+LG GGV R +AG  +R++HP+H+GRICP ET EG N GLV SL 
Sbjct: 891 QTNPLAEITHKRRLSSLGPGGVGRDQAGFAVREIHPSHFGRICPIETPEGQNAGLVGSLA 950

Query: 588 SFARVNAYGFIETPYRKVCDG 608
           S+AR+N  GF+++P   + + 
Sbjct: 951 SYARINDDGFLQSPALPIENQ 971



 Score =  137 bits (346), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 98/303 (32%), Positives = 154/303 (50%), Gaps = 57/303 (18%)

Query: 610  VTNDVVYLSAMEEENRYIAQANS---------SLDEDGSFTEELVFCRCAGEEILVPREK 660
            V  ++   S+  E+  Y+   ++          +  + S    +   R   E + +    
Sbjct: 1048 VRQNISLFSSELEDEIYVCTGDTLNPCLLNTSKIVANTSLFPPVFPVRHKQEFLTINSTD 1107

Query: 661  ---------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                       F    P Q++SIA SLIPFLE+DD+NR LMG NMQRQAVP +  E  FV
Sbjct: 1108 ALQFIQAPTKLFTGICPIQLISIATSLIPFLEHDDANRALMGSNMQRQAVPFMTPEKAFV 1167

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE---------------------- 749
            GTG+E   A+ S   ++A  +G +  VD+  I +++ +                      
Sbjct: 1168 GTGLELQAARDSSTLVLADESGQILFVDSQSIKLKTEKHGRTFSELRSPPGTKGQRPQWG 1227

Query: 750  -----------------GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                              +    +  +  Y L  F  SNQ+TC+ QRP V++G+ V +  
Sbjct: 1228 KLSLDLKDQSAHPIEFSPERGGFSKEISSYELTDFTPSNQSTCLKQRPAVEIGEWVEKGS 1287

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            ++ADG  T  G++ALG+N+L+A+MPW GYNFED+++I+ER+V ED++TS+H+E F+V  R
Sbjct: 1288 LLADGSGTRDGEVALGKNVLLAYMPWEGYNFEDAIVINERLVFEDIYTSVHVERFDVDVR 1347

Query: 853  DTK 855
            +TK
Sbjct: 1348 NTK 1350



 Score = 41.2 bits (95), Expect = 1.3,   Method: Composition-based stats.
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 1343 TPESFNVLVKEMQALGLSI 1361
             PESF VL+ E+ AL LS+
Sbjct: 2084 VPESFRVLINELHALCLSV 2102


>gi|186885805|gb|ACC93310.1| RNA polymerase beta subunit [Atractylis cancellata]
          Length = 1024

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 141/460 (30%), Positives = 218/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +             V+V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VHSSKTDETDKTERVRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAAFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 257/828 (31%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREIIENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNEKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +        PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWIPTPQNLVNSTPLTGTYKTFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +G     ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISEGSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   DA +I++                  L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHGGKIIYTDADKILLSGN--------GDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P ++ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQIRQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN---R 947
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR  +    
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVHSSKT 749

Query: 948  HGIDKNERSIS--VEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
               DK ER     +++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTERVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAAFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 56/203 (27%), Positives = 98/203 (48%), Gaps = 12/203 (5%)

Query: 69  SGAAMLEF--VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           +     EF    Y+   P     D ++  LTY+  L ++ RLI  +          + I+
Sbjct: 1   NQEIDFEFFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQ 53

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           EQ I +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II 
Sbjct: 54  EQRILIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIIS 110

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
           D G  +++E D K  I VR+ R++K+ +   L A+G++  EI+       ++    +   
Sbjct: 111 DWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREIIENVCYPELFLSFLNEKK 170

Query: 247 FPLSAADLMVGAKVSSSLVDIDT 269
              S  + ++      + V+ D 
Sbjct: 171 KIGSKENAILEFYQQFACVEGDP 193


>gi|134110814|ref|XP_775871.1| hypothetical protein CNBD2790 [Cryptococcus neoformans var.
            neoformans B-3501A]
 gi|50258537|gb|EAL21224.1| hypothetical protein CNBD2790 [Cryptococcus neoformans var.
            neoformans B-3501A]
          Length = 1245

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 168/983 (17%), Positives = 309/983 (31%), Gaps = 162/983 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++ T +     +   +  ++  L     G+  +DD D+ GN+R+   G ++   + +   
Sbjct: 390  HVSTAEGFESKKAYFLGYMVHRLCMAALGRKELDDRDHFGNKRLDLAGPLMAEMFNVVFG 449

Query: 481  RMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ----------LSQLEEH 528
            ++   +   +               I    +   +     +            +SQ+   
Sbjct: 450  KLREDMYRYLKKCVEQNKEFALNMAIRPNTITDGLKYALATGNWGKRDNTRAGVSQVLNR 509

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L  
Sbjct: 510  YTFASTLSHLRRTNT----PIGRDSKAAKPRQLHNTHWGMVCPAETPEGSACGLVKNLAL 565

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             + ++   +       + +  + +   Y  A      ++      +  D       +   
Sbjct: 566  MSYISVGSYSAPVMEFLEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQM 625

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              G ++      + D  +   +          P    D   + L         +  +  E
Sbjct: 626  RRGGQLKYEVSIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQMADE 685

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRL 764
                           SGA       GIVE VDA       I     DL  + +    + L
Sbjct: 686  GLL------------SGAWDKLLSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHEL 733

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            ++ + ++     +    +K     ++   +   PS  LG       +  + +P+  +N  
Sbjct: 734  VRDRAAHNLESFDPAARIKSTVWSQQYTHMEIHPSMILG-------VCASIVPFPDHNQS 786

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +   +                                 +    ++ V
Sbjct: 787  PRNTYQSAMGKQAMGVCL-----------------------------TNYQLRMDTMVNV 817

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +     S +   +  + AI      +  D+ +   S +   +    +
Sbjct: 818  LYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSL 876

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPKG 1001
            + R   D  +    V+ E IE   R++         + Y++L     +  G N       
Sbjct: 877  YFRSYTDTEKMKGMVKAETIEKPDRNETLRMKHGTGDRYAKLDVDGLVAPGTNVNGDDIL 936

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  L  D      R+Q                  K    T     E    +++    
Sbjct: 937  IGKTAPLPEDSEELGQRTQLHT---------------KRDISTPLKSTEQGVVDQVMLST 981

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G          VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 982  NG-----EGNMFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDII 1036

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L       G +  +          +S +     K   +   
Sbjct: 1037 INPHAIPSRMTIGHLVECLLSKVSTLTGAEGDATPFTELTVEAVSKVLR--AKGYQSRGF 1094

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                              G +    G  
Sbjct: 1095 EVL---------------------------------------------YHGHT----GR- 1104

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
                   V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  C
Sbjct: 1105 --KLQAQVYFGPTYYQRLKHMVDDKIHARARGPLQILTRQPVEGRSRDGGLRFGEMERDC 1162

Query: 1302 IQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAG-NDTFETGTPE 1345
            + ++G A  L+E +   SD       DV G        +   Y S+        +   P 
Sbjct: 1163 MISHGIAGFLKERMYDSSDAFRIHVCDVCGLMAVANLKKQEFYCSVCRNSTQISQVYIPY 1222

Query: 1346 SFNVLVKEMQALGLSIDLENSRT 1368
            +  +L +E+QA+ ++  +     
Sbjct: 1223 AAKLLFQELQAMNIACRMYGETD 1245



 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 126/1028 (12%), Positives = 273/1028 (26%), Gaps = 187/1028 (18%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
            L+  Q  S++ F+   +          Q        +T              +    + F
Sbjct: 66   LVRQQLESFNEFIENTM----------QEIVDDHSRLTLDQFTQYTGVAGDETRRYEISF 115

Query: 77   VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLI------VFDVDEFTGAK 120
                                   +   R+LTY+ PL + ++        V D  E     
Sbjct: 116  GQIYLARVNHTEMDGRTNMLFPQEARLRNLTYSAPLYVDIKKRTLTASGVDDPVEADWQP 175

Query: 121  SIKD------IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
            ++ D       +E+   +G +P+M +                         G F+I G +
Sbjct: 176  AVGDDGEVEGAEEEKTSIGKVPVMVRSNFCLLHGLPDDQCHEIGECPYDQGGYFIISGSE 235

Query: 151  RIVVSQLHRSPG-------------IHFDHDKGRASLSGKLLYACRIIPD-QGLWMDIEF 196
            +++++Q   +                +F     +    G++     +    +        
Sbjct: 236  KVLIAQERMATNHVFVFLKAAPARFTYFAEINSQKEKGGRVANHTEVRMYARASGTTGGV 295

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
                + + ++D    +P+     ALG+  + ++LS            +     +      
Sbjct: 296  IRVSLPYTKVD----IPLVVVFRALGIVPDRDVLSHICFGAEDEALLEMLQPSIEE---- 347

Query: 256  VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
                 S ++ D DT    I  G++         + +   F  +  + L  +  AE   + 
Sbjct: 348  -----SFAVQDRDTALDFI--GRRGQHEKAPRAQRQRAAFDILHKEFLPHVSTAEGFESK 400

Query: 316  ETGEIYIEAGDVID----EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +   +      +       K L++  H   + + +           +   L  D  +  K
Sbjct: 401  KAYFLGYMVHRLCMAALGRKELDDRDHFGNKRLDLAGPLMAEMFNVVFGKLREDMYRYLK 460

Query: 372  DALLDIYRV-MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
              +       +              +     +  K D +  G  ++  R    +      
Sbjct: 461  KCVEQNKEFALNMAIRPNTITDGLKYALATGNWGKRDNTRAGVSQVLNRYTFASTLSHLR 520

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            R        +       L N    +             + + L     + +      + E
Sbjct: 521  RTNTPIGRDSKAAKPRQLHNTHWGMVCPAETPEGSACGLVKNLALMSYISVGSYSAPVME 580

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
                  ++    +DL   +   +A   F     +    +     + +   RR   L    
Sbjct: 581  F-----LEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQMRRGGQLKYEV 635

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                        ++        P    +     L        R++               
Sbjct: 636  SIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQMADEGLLSGAWDKL 695

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRCAGEEILVPR-------- 658
                 V Y+ A EEE   IA     L          ELV  R A                
Sbjct: 696  LSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHELVRDRAAHNLESFDPAARIKSTV 755

Query: 659  --EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
              ++   ++  P  ++ + AS++PF +++ S R      M +QA+ +             
Sbjct: 756  WSQQYTHMEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGVCLTNYQL------ 809

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                  +   ++      +    ++  +  S       +   +  Y              
Sbjct: 810  ---RMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSG-----------Y 855

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ            + +I +  S D G         + F  +        M+ +E +   
Sbjct: 856  NQ-----------EDSVIMNQSSIDRGLFRS-----LYFRSYTDTEKMKGMVKAETIEKP 899

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            D   ++            K G             +    +D  G++  G  VN  DIL+G
Sbjct: 900  DRNETL----------RMKHGT-----------GDRYAKLDVDGLVAPGTNVNGDDILIG 938

Query: 897  KITPKGESPMTPEEKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRH 948
            K  P  E      ++        +          V D  +   +G     V +R+   R 
Sbjct: 939  KTAPLPEDSEELGQRTQLHTKRDISTPLKSTEQGVVDQVMLSTNGEGNMFVKIRVRSTRV 998

Query: 949  GIDKNERS 956
                ++ +
Sbjct: 999  PQIGDKFA 1006


>gi|332148576|dbj|BAK20137.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 333

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 146/380 (38%), Positives = 197/380 (51%), Gaps = 62/380 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 10   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 67

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 68   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 127

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 128  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 187

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 188  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 241

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 242  ----------------------TVLYDG--------------------------RTGEPF 253

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 254  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 313

Query: 1306 GAAYVLQEMLTIKSDDVVGR 1325
            GAAY LQE+LT+KSDDVVGR
Sbjct: 314  GAAYTLQEILTVKSDDVVGR 333



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 82/126 (65%), Positives = 104/126 (82%)

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +G
Sbjct: 1   AIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIG 60

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++F
Sbjct: 61  AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVF 120

Query: 946 NRHGID 951
           NR   D
Sbjct: 121 NREDGD 126


>gi|324120622|dbj|BAJ78702.1| RNA polymerase II second largest subunit [Karoophasma biedouwense]
          Length = 1176

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 170/1089 (15%), Positives = 333/1089 (30%), Gaps = 210/1089 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAVLPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGME 716
             I D  D   +          P L  ++ + +L   +  M ++           V     
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHIDMLKEREYNNYGWQVLVA---- 658

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                  SG           E +D         E  +  + S  D+ +  ++         
Sbjct: 659  ------SGVV---------EYIDT------LEEETVMIAMSPEDLRQEKEYA-------- 689

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                                 P+  LG       +  + +P+  +N          M  +
Sbjct: 690  ----------YCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQ 732

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +   ++I  F                           ++    +  V    +   +   
Sbjct: 733  AMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTR 763

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +      + AI      +  D+ +   S V         F      K+  S
Sbjct: 764  SMEYLRFRELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAES 820

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLI 1013
              +  ++ E   +        +   +Y +L +   I  G           K+  L     
Sbjct: 821  KRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITL----- 874

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                            +    +E    ++    +    R        Q    +     + 
Sbjct: 875  ---------------PENDDELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKF 919

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
             K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +
Sbjct: 920  CKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTI 979

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G + E   G      G+                                           
Sbjct: 980  GHLIECLQGKVSANKGEIGD---------------------------------------- 999

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         +TP  D  + + I+++L+       G  ++Y+G TG      + +G 
Sbjct: 1000 -------------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKISAQIFLGP 1046

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+E
Sbjct: 1047 TYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRE 1106

Query: 1314 MLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQ 1355
             L   SD     V            R   +E    G        +   P +  +L +E+ 
Sbjct: 1107 RLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELM 1164

Query: 1356 ALGLSIDLE 1364
            ++ ++  L 
Sbjct: 1165 SMNIAPRLM 1173



 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 141/981 (14%), Positives = 289/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAVLPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGSLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPENDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRFTKRDASTFLRNSETGIV 905


>gi|215254177|gb|ACJ64093.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 389

 Score =  389 bits (999), Expect = e-105,   Method: Composition-based stats.
 Identities = 251/389 (64%), Positives = 306/389 (78%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  
Sbjct: 61  RCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQK 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P 
Sbjct: 121 GESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPL 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RS
Sbjct: 181 VGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRS 240

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           NQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+S
Sbjct: 241 NQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVS 300

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  
Sbjct: 301 ERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKG 360

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGE 919
           GDILVGK+TPKGE+ +TPEEKLLRAIFGE
Sbjct: 361 GDILVGKVTPKGETQLTPEEKLLRAIFGE 389


>gi|156573716|gb|ABU85190.1| RNA polymerase beta subunit [Anethum graveolens]
          Length = 1070

 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 253/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   +++        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVLAIAEHEGKVIYTDTDKILLSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G  ++          +   + +L A    
Sbjct: 604  INIPLVMYQRSNKNTCMHQKPRVQRGKYIKKGQ-ILAYGAATVGGELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T       S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEA 1218
            +   + S    F E    +                            +TP VF+      
Sbjct: 890  RYEQEASRKLVFSELYQASKQT-------------------------ATPWVFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G   
Sbjct: 970  TQQPLRGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGAI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++    + +T    + E
Sbjct: 1030 PNPQDAPESFRLLVRELRSLALELNHFFVSEKTFKIKRKE 1069



 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 228/686 (33%), Positives = 376/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   K +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQKCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RL+LD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV +++
Sbjct: 262 GRRNMNRRLHLDISQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLI 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L+R+E  I+  I       ++P  Q+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQLGLALVRLENVIRGTICGALRHKLIPAPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++  +G +E+P+ ++        ++YLS  ++E   +A  N      G   E++V  R 
Sbjct: 442 AKIGRWGSLESPFYEISHRSKGARMLYLSPGKDEYYMVASGNPLALNQGLQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G V   D         +  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVLAIAEHEGKVIYTD--------TDKILLSGNGDTINIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPRVQRGKYIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T++IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            G+ILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 RGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 69/336 (20%), Positives = 134/336 (39%), Gaps = 31/336 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFM----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L I+  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYISAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQ 229

Query: 263 ------SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                   V  ++  + ++         L  +  + +             ++    +   
Sbjct: 230 FACVGGDPVFSESLCKELQKKFFQQKCELGKIGRRNMNRRLHLDISQNNTFLLPRDILAA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
              +      +     +  + +  IR +  L  D +
Sbjct: 290 ADHLIGMKFGMGTLDDMNHLKNKRIRSVADLIQDQL 325


>gi|313183814|ref|YP_004021657.1| RNA polymerase beta subunit [Prunus persica]
 gi|309321426|gb|ADO64967.1| RNA polymerase beta subunit [Prunus persica]
          Length = 1070

 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +  +      +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKVVYTYTDKIVLSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LNIPLVIYQRSNKNTCMHQNPQVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V     E +  +    +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYGDIYTSFHIRKYEIQTHVTSNGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   +  G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVRLGSWVKTGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  VSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYEASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALELNHFLVSEKNFQIKRKE 1069



 Score =  368 bits (944), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 230/634 (36%), Positives = 357/634 (56%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVVSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  VGR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRVGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q  L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQLGLALVRLENMVRGTICGAIKHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   A++  +G +E+P+ ++ +      ++YLS  ++E   +A  NS     G   
Sbjct: 434 LIGSLAIHAKIGYWGSLESPFYEISERSKKVRMLYLSPSKDEYYMVAAGNSLALNRGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + V  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPTRYRQEFLTVEWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  VA  SG   +A+  G V             +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKVVYT--------YTDKIVLSGNGDTLN 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVIYQRSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI
Sbjct: 666 NSEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSNGPERITNEIPHLEAHLLRNLDKNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VRLGSWVKTGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKKGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 70/336 (20%), Positives = 131/336 (38%), Gaps = 31/336 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+           +GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------EQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PVIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RI+++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRILINQILQSPGIYYRSELDHNGIS---VYTGIIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQ 229

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGE 316
                          K+L     +   E G       +  L         ++    +   
Sbjct: 230 FACVGGDPVVSESLCKELQKKFFQQRCELGRVGRRNMNRRLNLDIPQNNTFLLPRDILAA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
              +      +     +  + +  IR +  L  D +
Sbjct: 290 ADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQL 325


>gi|6606113|gb|AAF19069.1|AF107797_1 DNA-dependent RNA polymerase II RPB140 [Capronia mansonii]
          Length = 1029

 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 178/1016 (17%), Positives = 331/1016 (32%), Gaps = 178/1016 (17%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +   + + + +    +        R  +   +  ++  L+    G+   DD D+LG 
Sbjct: 144  HERQKHATDILQKEFLPHIGQGPDATAR--KAFFLGYMVNRLLKCALGRAEPDDRDHLGK 201

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP--VVSAVCEFFCS 519
            +R+   G ++ N +RL   +  +     +            +   K   + S +     +
Sbjct: 202  KRLDLAGPLMTNLFRLQFDKATKDFYRYMQKRVESGQPINIMAGFKHPIITSGLKYSLAT 261

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +A     + R     + R +H TH+
Sbjct: 262  GNWGDQKKLDKAKAGVSQVLSRYTFSSTLSHLRRTNA----PIGREGKIAKPRQLHNTHW 317

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + V            + +  +T  V    A+E+    
Sbjct: 318  GYVCPAETPEGQACGLVKNLSLMSMVTNSYETGP----LLNYVMTKHVE---ALEDWEPR 370

Query: 627  IAQANSSLDEDGSF-------TEELVFCRCAGEEILVPREKIDF-IDASPKQVVSIAAS- 677
            +    + +  DG +        + LV          V    +    D   K+      S 
Sbjct: 371  LNPRATKIFVDGVWFAVVLRDPKRLVDDLRKLRRKGVFDSHVSLVWDIREKEFKISGDSG 430

Query: 678  ----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                 +  +E D S+  L    + ++ +  L   A    +G +               +G
Sbjct: 431  RIVRPLFVVETDRSSENLGNLVLNKEHINKLDQTAYLKESGFQWTDEIRPYGWTDLLESG 490

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE +DA       +    +        +  M+ +  +     N  PL+           
Sbjct: 491  VVEYLDAEEEETAMICMTPEALADSKARWLGMEIENEDDPLRRN-DPLLNPHAHTF--TH 547

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 548  CEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLT 590

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E   +I    ++ L                        +       +   +  +
Sbjct: 591  NFDQRMETMANILYYPQKPLAR-------------------TMAMDYLKFRELPAGQNAI 631

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +     +  +     +   SV    +E   +    
Sbjct: 632  VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQ----DSEKSVGHSVVEQFEKPTRS 687

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y ++ E   +  G           K+  ++ D                +E 
Sbjct: 688  DTLRLKHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPD---------------AEEL 732

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR  + +K    T     E    +++              R  KV V   +  Q GDK 
Sbjct: 733  GQRLKQHIKRDVSTPLRSTESGIVDQVML-----TTTAEGHRFAKVRVRTTKVPQIGDKF 787

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 788  ASRHGQKGTIGITYRHEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGD 847

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +                                                       +TP 
Sbjct: 848  EGD-----------------------------------------------------ATP- 853

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F       ++ +LR       G  ++Y+G TG      V +G  Y  +L HMV DK+++R
Sbjct: 854  FTKVTVTQVSELLRTMGYQSRGFEVMYNGHTGRKMVAQVFLGPTYYQRLRHMVDDKIHSR 913

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVV 1323
            + G   ++T+QP+ G++  GG R GEME  C+ A+GA+  L+E L   SD       D+ 
Sbjct: 914  ARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASSFLKERLFDVSDPFRVHVCDIC 973

Query: 1324 GRTRVYESIVAG----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            G   V   +             N   +   P +  +L +E+ A+ ++  L   R++
Sbjct: 974  GLMTVIAKLKKNTFECKNCNNKNKISQIYLPYAAKLLFQELWAMNIAARLYTKRSR 1029



 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 115/861 (13%), Positives = 239/861 (27%), Gaps = 159/861 (18%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      +   I    D+G  M  +   K  +  R+
Sbjct: 1   SEKVLIAQE-RSAGNI--VQVFQKAAPAPFTHLAEIRSVIDRGARMMSQCTVK--LFRRV 55

Query: 207 D-----------R------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           D           R      ++ +P+     AL + S+ +IL          +  D     
Sbjct: 56  DGPEGTKIDNPIRVQLPYVKQDIPLVIVFRALDIVSDADILEKICFDQSDKEMMDMLMGS 115

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           L     + GA ++   +        ++S ++        L+++ +  +G   D       
Sbjct: 116 LQEGQPIQGADLARDFIARRGNVPSLKSHER-QKHATDILQKEFLPHIGQGPDATARKAF 174

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               +      +   A    +    + +    +                + N      +K
Sbjct: 175 F---LGYMVNRLLKCALGRAEPDDRDHLGKKRLDL----------AGPLMTNLFRLQFDK 221

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             KD    + + +  G           F      S        G      +L+       
Sbjct: 222 ATKDFYRYMQKRVESGQPINIMAG---FKHPIITSGLKYSLATGNWGDQKKLDKAKAGVS 278

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R GK       +  +       E  + Q   GL++  
Sbjct: 279 QVLSRYTFSSTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC-GLVKNL 337

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL----------EEHVNSLS 533
             +    +S +   ++   +      +                          +    + 
Sbjct: 338 SLMSMVTNSYETGPLLNYVMTKHVEALEDWEPRLNPRATKIFVDGVWFAVVLRDPKRLVD 397

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE--GHNIGLVSSLTSFAR 591
            +   RR                +   +       + P    E    +  L + + +   
Sbjct: 398 DLRKLRRKGVFDSHVSLVWDIREKEFKISGDSGRIVRPLFVVETDRSSENLGNLVLNKEH 457

Query: 592 VNAYGFIETPYRKVCDGKVTNDV--------------VYLSAMEEENRYIAQANSSLDED 637
           +N     +T Y K    + T+++               YL A EEE   I     +L + 
Sbjct: 458 INKLD--QTAYLKESGFQWTDEIRPYGWTDLLESGVVEYLDAEEEETAMICMTPEALADS 515

Query: 638 G------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                      E    R     +          +  P  ++ + AS+IPF +++ S R  
Sbjct: 516 KARWLGMEIENEDDPLRRNDPLLNPHAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNT 575

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +QA+ +                                                
Sbjct: 576 YQSAMGKQAMGVFLTNF-----------------------------------------DQ 594

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              + + +  Y      R+     +                           +L  G+N 
Sbjct: 595 RMETMANILYYPQKPLARTMAMDYL------------------------KFRELPAGQNA 630

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIP 866
           +VA   + GYN EDS+++++  +   +F S+    ++   +       E        D  
Sbjct: 631 IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDSEKSVGHSVVEQFEKPTRSDTL 690

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +       IDE GI+  G  V+  DI++GK  P         ++L + I        RD
Sbjct: 691 RLKHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPDAEELGQRLKQHIK-------RD 743

Query: 927 TSLRVPSGVSGTVVDVRIFNR 947
            S  + S  SG V  V +   
Sbjct: 744 VSTPLRSTESGIVDQVMLTTT 764


>gi|290489624|gb|ADD31196.1| RNA polymerase beta subunit protein [Rhododendron simsii]
          Length = 1064

 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 135/392 (34%), Positives = 199/392 (50%), Gaps = 51/392 (13%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +      K T       S Y        AV D      V + K   
Sbjct: 720  LDKNGIVMLGSWVKTDDILVGKLTPQMVKEESLYAPEDRLLRAVLD----IQVSTFKETC 775

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                + +  R  +        D+        ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 776  LKLPTGVRGRVIDVRWIESSIDN-----PETIRVYILQKREIKVGDKVAGRHGNKGIISK 830

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  + +  D +  
Sbjct: 831  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIVPFDERYE 890

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 891  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 916

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S L++G TG+ F++PV +G  Y+LKL H V DK++ARS+G Y+LVTQQP
Sbjct: 917  -----PEYPGKSRLFNGRTGDSFEQPVIIGKSYILKLIHQVDDKIHARSSGPYALVTQQP 971

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD    R +VY+++++G       
Sbjct: 972  LRGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHTRTRRKVYDTMLSGGIMPNPK 1031

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNS 1371
            G PESF +LV+E+++L L +   L + +    
Sbjct: 1032 GAPESFELLVRELRSLALELKHFLISEKNFQI 1063



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 227/657 (34%), Positives = 370/657 (56%), Gaps = 28/657 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I   A      + LE + + E     +   D +                 +++A+L+ Y+
Sbjct: 182 ILSSAMGSNLREILENLCYPETFLSFLNDNDKIEIG-------------SKENAILEFYQ 228

Query: 380 VMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
                G+   FS +   +    F   + +L  +GR  MN RLNL+ P +   +   DI+A
Sbjct: 229 QFTCVGEDLVFSESLCEYLQKKFFQQRCELGRIGRRNMNRRLNLNIPQNNIFLLPRDILA 288

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +  L+ ++ G  T+DD+++L N+R+RSV ++L++Q  L L+R+E  ++E I       +
Sbjct: 289 AVDHLIGIKFGMVTLDDMNHLKNKRIRSVADLLQDQLGLALVRLENVVEESICGAIRHKL 348

Query: 499 --MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
              PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    A  
Sbjct: 349 ISTPQNLVTSTPLTTTYESFFGLHPLSQVFDRTNPLTQIVHGRKFSYLGPGGLTGRTASF 408

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            +R++HP++YGRICP +TSEG N+GL+ SL+  ARV  +GF+E+P+ ++ +      ++Y
Sbjct: 409 RIRNIHPSYYGRICPIDTSEGINVGLIGSLSIHARVGHWGFLESPFFEISEKSKKGRMLY 468

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LS + +E   +A  NS      S  E+ V  R   E + +  E++      P Q  SI  
Sbjct: 469 LSPVIDEYYMLASGNSLSLSQDSQEEQFVPARYRQEFLTIAWERVHLRCIFPFQYFSIGV 528

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPF+E++D+ R LM  NMQRQAVPL ++E   VGTG+E   A  SGA ++A+  G + 
Sbjct: 529 SLIPFIEHNDATRALMSSNMQRQAVPLFRSEKCIVGTGLERQAALDSGALVIAEHEGKII 588

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             D  +IV+                  L+ +QRSN+NTC++Q+P V  G  +++  I+AD
Sbjct: 589 YTDTDKIVLSGN--------GDTLSIPLVMYQRSNKNTCMHQKPQVPQGRWIKKGQILAD 640

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+LALG+N+LVA+MPW GYN ED++LI+ER+V   ++TS  I ++E+    T  
Sbjct: 641 GAATVGGELALGKNLLVAYMPWEGYNSEDAVLINERLVYGAIYTSFQIWKYEIQVYVTNE 700

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP---KGESPMTPEEKLL 913
           GPE +T  IP++    L+N+D+ GI+ +G+ V   DILVGK+TP   K ES   PE++LL
Sbjct: 701 GPERVTNKIPHLKAHKLRNLDKNGIVMLGSWVKTDDILVGKLTPQMVKEESLYAPEDRLL 760

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIELLAR 969
           RA+   +    ++T L++P+GV G V+DVR   +     +  R   +++ +I++  +
Sbjct: 761 RAVLDIQVSTFKETCLKLPTGVRGRVIDVRWIESSIDNPETIRVYILQKREIKVGDK 817



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL+        I        +EF     +Y+ 
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLREELYKFRKIENPDE--EIEFQLFAETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L ++  LI          KS   ++EQ+I++G++PLM   
Sbjct: 60  LDPLIKERDAVYESLTYSSQLYVSAGLIC---------KSSVTMQEQTIFIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++   + + + +G L Y   II D G  +++  D K  
Sbjct: 111 GTSIVNGIYRIVINQILQSPGIYY---RSKLNHNGILAYTGTIISDWGGRLELAIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP+   S   D     + + +
Sbjct: 168 IWARVSRKQKISILILSSAMGSNLREILENLCYPETFLSFLNDNDKIEIGSKE 220


>gi|186885907|gb|ACC93361.1| RNA polymerase beta subunit [Macledium zeyheri]
          Length = 1024

 Score =  389 bits (998), Expect = e-105,   Method: Composition-based stats.
 Identities = 140/460 (30%), Positives = 220/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMGVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q         +  ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETDKIEKIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 252/778 (32%), Positives = 412/778 (52%), Gaps = 74/778 (9%)

Query: 207 DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47  DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LRSPGIYY 92

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 93  QSELNDNGISVYTGTIISDWGGRL------ELEIDRKAKIWVRVSRQQKLSIL------- 139

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 140 ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 181

Query: 377 IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+     +    FS + S      F   + +L  +GR  MN RLNLD P++   +   D
Sbjct: 182 FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPENNTFLLPRD 241

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 242 ILAAADRLIRIKFGMGTLDDLNHLKNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 301

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302 HNWIPTPQNLVNSTPLTGTYKTFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 361

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 362 ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSKEAR 421

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482 IGASLIPFVEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 541

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 542 KIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCIHQKPQVRQGKCIKKGQI 593

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 651

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
              GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652 -NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 710

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           LLR I G      ++T L++P G  G V+DVR        K + +  +E+ ++ +L +
Sbjct: 711 LLRTILGMGVYTSKETCLKLPIGGRGRVIDVRWV---QSSKTDETDKIEKIRVYILQK 765



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLGEPLIKEKDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKAKIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|2654279|emb|CAA47069.1| DNA-directed RNA polymerase [Euplotes octocarinatus]
          Length = 1194

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 173/1052 (16%), Positives = 330/1052 (31%), Gaps = 197/1052 (18%)

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            + +++   +        +    +A+        P      +++            + +  
Sbjct: 303  NCISDKEILDRICYDSTDSHMMEAMRASLEEGTPFLTQEDALSYIGSRGTAGGVGREERI 362

Query: 410  TVGRVKMNMRLNLDTPDDVRH--IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               R  +                 +   I  +   L++   G+   DD D+ G +R+   
Sbjct: 363  RHAREILKRHFLPHVSTKDSCESQKSYFIGYMCHRLLNAHLGRIKEDDRDHYGKKRLDMA 422

Query: 468  GEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R    R  +      +  +   DS+          +   +     +      
Sbjct: 423  GSLLGMLFRNLFRRFVKEAGRYLKAQADKGDSLNITKAFKKDIISDGLKYALATGNWGTN 482

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+   +   S ++H RRL+      + ++    + R +H TH+G +CPA
Sbjct: 483  AAGEVSKTGVSQVLNRLTFASTLSHLRRLNT----PLQKSGKLTKPRQLHNTHWGMVCPA 538

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L+  A V+     E   R++ +   T ++V +S  +         N 
Sbjct: 539  ETPEGQACGLVKNLSLMAFVSVGSAAER-LREILENYGTENLVSISPSDIHESTKVFVNG 597

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                  + +E+L+         L+  ++I               S++  + N +      
Sbjct: 598  CWIGIHNESEDLINNIKLMRRALLIPKEI---------------SIVRDIPNREVKFYTD 642

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +QR    +         T +               R    E+ D++       EG +
Sbjct: 643  HGRVQRPLFIVDDNRLILKKTHV--------------VRLQDHERSDSMNFDDTLKEGLV 688

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +      +   ++     +          ++  +           PS  LG       + 
Sbjct: 689  EFLDVEEEETSMIAMNVGD----------LENRNYCSTYTHCEIHPSMILG-------VC 731

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   ++   +++                       
Sbjct: 732  ASIIPFPDHNQSPRNCYQSAMGKQAMG--VYCSNYQIRM--------------------- 768

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  V        ++   +       + P    + AI      +  D+ +   
Sbjct: 769  ------DTLAHVLYYPQKPLVVARSLDFPHVKELPPGCDSIVAITCYTGYNQVDSVIMSQ 822

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            + +           R    KN   I V  E++          +   D         I  G
Sbjct: 823  APIDRG------CFRSVFYKNIFEIPVRVERLLRYPDSTVVGRRNGDYTKLDIDGLIFPG 876

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            +N +       K+ +              +   + D          +            R
Sbjct: 877  KNVLGDDIIIGKTAL----------PRNLFNDEMDD----------QTNLIKKDDSTSLR 916

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K                  KV +   R  Q GDK A RHG KG V      ED+PF 
Sbjct: 917  HSEKGIIDSVILTSNEEGDSFTKVKMRAIRIPQIGDKFASRHGQKGTVGMTYRQEDIPFT 976

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   DI++NP  +PSRM +G + E          G++                     
Sbjct: 977  QEGIIPDIIVNPHAIPSRMTIGHLIECLASKVACFKGEEGD------------------- 1017

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     E I++ L      + G
Sbjct: 1018 ----------------------------------ATP-FQDVTVEHISNDLHRLGYQKRG 1042

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ++YDG TG   D  + +G  Y  +L HMV DK+++RS G   ++T+QP  G+S  GG 
Sbjct: 1043 NEVMYDGWTGRKMDTMIFLGPTYYQRLKHMVDDKIHSRSRGPLQILTRQPTEGRSRHGGL 1102

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVAG--- 1335
            R GEME  C+ ++GAA  L+E L   SD        + G       R + Y  +  G   
Sbjct: 1103 RFGEMERDCMVSHGAARFLKERLFDVSDCYTVHVCRICGLICEANLRQQKY--LCRGCQN 1160

Query: 1336 -NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              +  + G P +  +L +E+ A+ ++  +  S
Sbjct: 1161 STNICQVGLPYACKLLFQELMAMQIAPRMITS 1192



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 134/1014 (13%), Positives = 277/1014 (27%), Gaps = 243/1014 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF-----------V 77
           L+  Q +S+D FL   +      N  +     S+ P         L+F           +
Sbjct: 50  LVSQQISSFDRFLSYTVQDIVTENNTI-----SIQP--------ELQFAPGSMNESRENI 96

Query: 78  SYEF--------DPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
            Y+         + P+F            ++   R+LTY   L + ++     V++    
Sbjct: 97  KYDIILGQVRVNEKPRFKEFDDKYNVIFPNEARLRNLTYQTSLYVEVKKQDKVVEQDGSE 156

Query: 120 KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
             I +  E+ +YMG +P+M +                         G F+I G ++++V+
Sbjct: 157 VIIDEQTEKEVYMGKVPVMVRSGFCSLNGIDESERWEMKECFHDQGGYFIINGGEKVIVA 216

Query: 156 ---------------Q--------LHRS--------PGIHFDHDKGR------ASLSGKL 178
                          Q          RS        P         +       S SG  
Sbjct: 217 HERMANNFVYVFHKKQPSKFSWVAEVRSQVDASNRPPNQFSIKMYSKGQRRAGGSFSGGK 276

Query: 179 LYACRI---IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYP 234
           ++   +   IP                         +PV     AL  +  +EIL     
Sbjct: 277 IFGQTLCASIPYINA--------------------DIPVAILFRALNCISDKEILDRICY 316

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID------TGEQVIESGKKLTSGLLKSL 288
               S   +     L      +  + + S +           E+ I   +++        
Sbjct: 317 DSTDSHMMEAMRASLEEGTPFLTQEDALSYIGSRGTAGGVGREERIRHAREILKRH-FLP 375

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
                           G Y+   ++N   G I  +  D   +K L+            L+
Sbjct: 376 HVSTKDSCESQKSYFIG-YMCHRLLNAHLGRIKEDDRDHYGKKRLDMAGSLLGMLFRNLF 434

Query: 349 VDSVNN-NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
              V     Y++       + +   A           D+ +  +  ++    +  +   +
Sbjct: 435 RRFVKEAGRYLKAQADKGDSLNITKAF--------KKDIISDGLKYALATGNWGTNAAGE 486

Query: 408 LSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           +S  G  ++  RL   +      R          +     L N    +         +  
Sbjct: 487 VSKTGVSQVLNRLTFASTLSHLRRLNTPLQKSGKLTKPRQLHNTHWGMVCPAETPEGQAC 546

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            + + L     + +      ++E + +   ++++         +  +   F     +   
Sbjct: 547 GLVKNLSLMAFVSVGSAAERLREILENYGTENLVSIS---PSDIHESTKVFVNGCWIGIH 603

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            E  + ++ I   RR   + +               +  H     P    + + + L  +
Sbjct: 604 NESEDLINNIKLMRRALLIPKEISIVRDIPNREVKFYTDHGRVQRPLFIVDDNRLILKKT 663

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
                +        +      D      V +L   EEE   IA     L+          
Sbjct: 664 HVVRLQD----HERSDSMNFDDTLKEGLVEFLDVEEEETSMIAMNVGDLENRN------- 712

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                              +  P  ++ + AS+IPF +++ S R      M +QA+ +  
Sbjct: 713 -----------YCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNCYQSAMGKQAMGVYC 761

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           +                                                + + V  Y   
Sbjct: 762 SNYQI-----------------------------------------RMDTLAHVLYYP-- 778

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                       Q+PLV          +        + +L  G + +VA   + GYN  D
Sbjct: 779 ------------QKPLV----------VARSLDFPHVKELPPGCDSIVAITCYTGYNQVD 816

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           S+++S+  +    F S+  +    +    +         +          +D  G+I  G
Sbjct: 817 SVIMSQAPIDRGCFRSVFYKNIFEIPVRVERLLRYPDSTVVGRRNGDYTKLDIDGLIFPG 876

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             V   DI++GK          P       +  +  +  +D S  +     G +
Sbjct: 877 KNVLGDDIIIGKTA-------LPRNLFNDEMDDQTNLIKKDDSTSLRHSEKGII 923


>gi|73975063|ref|XP_860777.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            8 [Canis familiaris]
          Length = 1173

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 178/1088 (16%), Positives = 333/1088 (30%), Gaps = 208/1088 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        I+N+   +K  R   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSAIYNKV-FEKPTR--- 820

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             E  Q+  L   ++   V +   IY +L +   I  G           K+  L       
Sbjct: 821  -ETCQVIFLLSYRNRAIVGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTL------- 872

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                          + +  +E    +Y         R        Q    +     +  K
Sbjct: 873  -------------PENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCK 919

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 920  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGH 979

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 980  LIECLQGKVSANKGEIGD------------------------------------------ 997

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L        G  +LY+G TG      + +G  Y
Sbjct: 998  -----------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTY 1046

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L
Sbjct: 1047 YQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERL 1106

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            RT  YE    G            P +  +L +E+ ++
Sbjct: 1107 FEASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSM 1164

Query: 1358 GLSIDLEN 1365
             ++  + +
Sbjct: 1165 SIAPRMMS 1172



 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 151/1003 (15%), Positives = 298/1003 (29%), Gaps = 204/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS-IHIEEFEVMAR 852
                     +L  G N +VA   + GYN EDS++++   V    F S I+ + FE   R
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSAIYNKVFEKPTR 820

Query: 853 DTKLGP---EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           +T           R I  +       +D+ G+I  G  V+  D+++GK     E+    E
Sbjct: 821 ETCQVIFLLSYRNRAIVGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELE 880

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                     +    RD S  + +  +G V  V +       K
Sbjct: 881 GT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 916


>gi|324120618|dbj|BAJ78700.1| RNA polymerase II second largest subunit [Aposthonia japonica]
          Length = 1150

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 167/1090 (15%), Positives = 335/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 228  GQRIIAILPYIRQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 287

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 288  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 341

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 342  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLTKEVRMYAQKFIDRG 401

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 402  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 461

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 462  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPAPIL 517

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 518  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 577

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ + +L   +  M ++           V  G+ 
Sbjct: 578  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHVDMLKEREYNNYGWQVLVAQGVV 637

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               + + +   D   +  + Y             
Sbjct: 638  EYIDTLEEETVMIA---------------MSTDDLKQDKEFAYCNTY------------- 669

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 670  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 706

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 707  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 737

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 738  RSMEYLRFRELPAGINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFF---RSYKDAE 794

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 795  SKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGK-------- 845

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D +    +E    ++    +    R        Q    +     +
Sbjct: 846  ----------TITLPDNE--DELEGSTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 893

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 894  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 953

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 954  IGHLIECLQGKVSANKGEIGD--------------------------------------- 974

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 975  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1021 PTYYQRLKHMVDDKIHSRARGPLQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1080

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R+  +E    G        +   P +  +L +E+
Sbjct: 1081 ERLFEVSDPYRIHVCNFCGLIAIANLRSNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1138

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1139 MSMNIAPRLM 1148



 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 145/977 (14%), Positives = 294/977 (30%), Gaps = 176/977 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHASGEIETP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 73  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVRDGEEPI-----ETQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 187

Query: 171 RASLSGKLLYACRIIPDQGL---WMDI-----EFDSKDIIHVRIDR-----RRKVPVTSF 217
                   + +C+    +     W+++     +   K  I  RI       R+++P+   
Sbjct: 188 GKYAYKTEIRSCQEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYIRQEIPIMIV 247

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
             ALG  ++ +IL          +  +     L  A ++    V+ + +        +  
Sbjct: 248 FRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTK 307

Query: 277 GKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            K++     + L+++ +  +G++           G  V   ++    G   ++  D    
Sbjct: 308 EKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRELDDRDHYGN 365

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
           K L+            L+ +            +        +       +     + T  
Sbjct: 366 KRLDLAGPLLAFLFRGLFKNLTKEVRMYAQKFIDRGKDFNLE-------LAIKTKIITDG 418

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           +  S+    + D  K   +  G  ++  RL   +      R          +     L N
Sbjct: 419 LRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQLHN 478

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +                ++KN   +  + +       +  ++  S+   + I    
Sbjct: 479 TLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPAPILEFLEEWSMENLEEIAPSA 535

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           +  A   F     +    +    ++ +   RR   +    V+  R   +      T  GR
Sbjct: 536 IADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGR 595

Query: 569 IC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           IC P    E  ++ L         V+     E              V Y+  +EEE   I
Sbjct: 596 ICRPLLIVENGSLLLKKR-----HVDMLKEREYNNYGWQVLVAQGVVEYIDTLEEETVMI 650

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A +   L +D  F                        +  P  ++ + AS+IPF +++ S
Sbjct: 651 AMSTDDLKQDKEF---------------AYCNTYTHCEIHPAMILGVCASIIPFPDHNQS 695

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +                                            
Sbjct: 696 PRNTYQSAMGKQAMGVYITNFHV------------------------------------- 718

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  + + V  Y                +PLV                     +L  
Sbjct: 719 ----RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFRELPA 750

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD--- 864
           G N +VA + + GYN EDS++++   V    F S+    ++          EE       
Sbjct: 751 GINSVVAILCYTGYNQEDSVIMNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFEKPTR 810

Query: 865 --IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                +       +D+ GII  G  V+  D+++GK     ++    E          K  
Sbjct: 811 QTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTITLPDNEDELEGST-------KRF 863

Query: 923 DVRDTSLRVPSGVSGTV 939
             RD S  + +  +G V
Sbjct: 864 TKRDASTFLRNSETGIV 880


>gi|69216914|gb|AAZ03991.1| RNA polymerase beta chain [Acorus americanus]
          Length = 1068

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 160/563 (28%), Positives = 257/563 (45%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++      ++E     IH +  +++   +  G       +          
Sbjct: 560  IVGTGLERQAALDSGVSAIAECEGKIIHTDTHKIVL--SGHGDTISIPLVMYQRSNKNTC 617

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +   +  G  +  G IL       G   +   + +L A    +  +  D  L     +
Sbjct: 618  MHQNPQVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----I 671

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E +  +    +  L RN+  R   +  G   
Sbjct: 672  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNL-DRNGIVALGSWV 730

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  +++  S  P  +  +  +  +        LK+       +++ R+  
Sbjct: 731  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 790

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG
Sbjct: 791  KKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDG 843

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 844  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELY 903

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 904  EASKQTANPW------------------------VFE---------------PEYPGKSR 924

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 925  IFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 984

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+
Sbjct: 985  EMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVREL 1044

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1045 RSLALELNHFLVSEKNFQINRKE 1067



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 260/831 (31%), Positives = 429/831 (51%), Gaps = 44/831 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 140  ISVYTSTIISDWGGRSELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 199

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 200  IFLSFLNDREKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 258

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 259  GRRNMNRRLNLDIPQSNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 318

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +++  I       +   PQ+L+++  + +    FF    LSQ+ +  
Sbjct: 319  QDQFGLALVRLENAVRGTICGAIRHKLILTPQNLVSSTSLTTTYESFFGLHPLSQVLDRT 378

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 379  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 438

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-LDEDGSFTEELVFCR 648
            AR+  +G IE+P+ +V        +V+LS   +E   +A  NS  L+  G   E++V  R
Sbjct: 439  ARIGHWGSIESPFYEVYQRSKETKMVFLSPSRDEYYTVATGNSLALNRGGIQEEQIVPAR 498

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E 
Sbjct: 499  YRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEK 558

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +Q
Sbjct: 559  CIVGTGLERQAALDSGVSAIAECEGKIIHTDTHKIVL--------SGHGDTISIPLVMYQ 610

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 611  RSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 670

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V
Sbjct: 671  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNLDRNGIVALGSWV 730

Query: 889  NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              GDILVGK+TP+  +  +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 731  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 790

Query: 947  RHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------Q 993
            + G         R    ++ +I++  +   +   + I+ + +  + M  L          
Sbjct: 791  KKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVF 850

Query: 994  NAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQY 1042
            N +  P       +    L ++     + ++ A  DE+ ++            E+ K   
Sbjct: 851  NPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTA 910

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 911  NPWVFEPEYPGKSRIFDGRTGDPFEQPVL-IGKSYIL-KLIHQVDDKIHGR 959



 Score =  184 bits (467), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL   F     I         + FV  Y+   
Sbjct: 9   IPGFSQIQFEGFCRFI----------DQGLMEEFHKFPKIEDTDQEIEFQLFVERYQLVE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 59  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 110 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKSRIW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 167 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDREKKKIGSKE 217


>gi|324120630|dbj|BAJ78706.1| RNA polymerase II second largest subunit [Oyamia lugubris]
          Length = 1175

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 167/1090 (15%), Positives = 331/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  +  N +L   +  M ++           V +G+ 
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGGNLLLKKRHVDMLKEREYNNFGWQVLVASGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 663  EYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V            +   K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF---YRSYKDAE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K        
Sbjct: 820  SKRIGDQE-EQFEKPTRATCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGK-------- 870

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                         + D +    +E    +Y    +    R        Q    +     +
Sbjct: 871  ----------TITLPDNE--DELEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDM F  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTAEGLTPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSANKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 143/981 (14%), Positives = 290/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTRI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    EG N+ L         V+     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVEGGNLLLKKR-----HVDMLKEREYNNFGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     ++    E         
Sbjct: 832 KPTRATCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTITLPDNEDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYTKRDASTFLRNSETGIV 905


>gi|209360635|gb|ACI42988.1| RNA polymerase beta subunit [Acholeplasma sp. N93]
          Length = 699

 Score =  388 bits (997), Expect = e-105,   Method: Composition-based stats.
 Identities = 257/522 (49%), Positives = 354/522 (67%), Gaps = 31/522 (5%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R +GE+LKNQ+R+GL R E++IK+++S+ +     P +++N  P+V A+  FF SS
Sbjct: 1   NRRLRLIGELLKNQFRIGLARAEKNIKDKMSTTNFADATPSNIMNMTPLVGAIKTFFGSS 60

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + +N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +I
Sbjct: 61  QLSQFMDQINPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSI 120

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDG-----KVTNDVVYLSAMEEENRYIAQANSSLD 635
           GL+SSL ++A+V+ YGFI+TP+ KV         VT + VYL+A EE+++ IA A S ++
Sbjct: 121 GLISSLATYAKVDKYGFIQTPFLKVVKNEKGEPMVTQEYVYLTANEEQDQVIASAASPVN 180

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           EDG+F E  V  R  GE  +     + ++D SPKQ+VS+A + IPFLE+DD++R LMG N
Sbjct: 181 EDGTFIENRVIARSNGETAIFDASNVTYMDVSPKQLVSVATASIPFLEHDDASRALMGAN 240

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV------- 748
           MQRQAVPLL+  +P VGTG+E   AK SGA +VA+ +G V  VDA +I+I          
Sbjct: 241 MQRQAVPLLQPTSPIVGTGIEYRAAKDSGAVVVAQTSGYVTYVDAKKIIITKEPIEDIKV 300

Query: 749 -----------------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                            +   D      + Y L++F RSNQ+T + QRP+V  G+ + + 
Sbjct: 301 AGQPIYTVGGEFNYAIAKKLYDYGLGENETYELIQFLRSNQDTLILQRPIVAQGEWIDKG 360

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D+IADGPSTD G+LALGRN+ VAFM W GYN+ED++++ E +V  DV+TSIHI+E+E+  
Sbjct: 361 DVIADGPSTDKGELALGRNVTVAFMTWEGYNYEDAVIMCEDLVKNDVYTSIHIDEYEIET 420

Query: 852 RDTK--LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           RD K   G EEITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP+
Sbjct: 421 RDLKQSNGKEEITREIPNVGQEAVKYLDERGIIVPGSEVKEGDILVGKITPKGAFEPTPQ 480

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKL+ A+ G+KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 481 EKLIHAVIGDKAKEFRDSSLRVPHGGGGVVQSVQYFSKKNGD 522



 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 131/443 (29%), Positives = 196/443 (44%), Gaps = 65/443 (14%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            D  LG  E    I  +       I +  I+  G  ++ GD++    +   +  +     +
Sbjct: 322  DYGLGENETYELIQFLRSNQDTLILQRPIVAQGEWIDKGDVIADGPST-DKGELALGRNV 380

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
              A    +  +  D  +     V   V      + + I+  +   S  +E+I     +  
Sbjct: 381  TVAFMTWEGYNYEDAVIMCEDLVKNDVYTSIHIDEYEIETRDLKQSNGKEEITREIPNVG 440

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
             E V            I+ G     G     K T   +      P+ +     + D+  +
Sbjct: 441  QEAV----KYLDERGIIVPGSEVKEGDILVGKITPKGA--FEPTPQEKLIHAVIGDKAKE 494

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                SL+V +     +   ++ +K      GD +PPGV   ++V++A KR I  GDKMAG
Sbjct: 495  FRDSSLRVPHGGGGVVQSVQYFSKKN----GDQLPPGVNEQIRVYIAKKRKITEGDKMAG 550

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++S+ILP EDMP+L DGTPVDI+LNPLGVPSRMN+GQI E HLG +   LG K+
Sbjct: 551  RHGNKGVISKILPREDMPYLADGTPVDIMLNPLGVPSRMNIGQILEIHLGISAKRLGIKV 610

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D+  +                                           D
Sbjct: 611  ATPVFDGVTDEDLKEIMK-----------------------------------------D 629

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
               E    + L             YDG TGE +   ++VG +YM+KL+HMV DK++AR+ 
Sbjct: 630  AGIEPDGKTTL-------------YDGRTGEAYQNRISVGVMYMIKLSHMVDDKLHARNV 676

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLG 1295
            G Y+LVTQQP+GGK+  GGQR G
Sbjct: 677  GPYTLVTQQPMGGKAQNGGQRFG 699


>gi|324120610|dbj|BAJ78696.1| RNA polymerase II second largest subunit [Mnais pruinosa pruinosa]
          Length = 1175

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 164/1000 (16%), Positives = 313/1000 (31%), Gaps = 203/1000 (20%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+
Sbjct: 337  KYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYGNKRL 393

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R     + + ++               +  I  K +   +     +   
Sbjct: 394  DLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNW 453

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+   +   S ++H RR+++     + R     + R +H T +G I
Sbjct: 454  GDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWGMI 509

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYI 627
            CPAET EG  +GLV +L   A ++           + +  +    ++   +  +    ++
Sbjct: 510  CPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFV 569

Query: 628  AQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
                  +  D       L   R   + I+     I D  D   +          P L  +
Sbjct: 570  NGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLIVE 629

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +   +L   +++                     V  +SG           E +D      
Sbjct: 630  NGTLLLKKRHIEMLKEREYNNYG--------WQVLVASGVV---------EYIDT----- 667

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               E  +  + S  D+ +  ++                              P+  LG  
Sbjct: 668  -LEEETVMIAMSPEDLRQEKEYA------------------YCTTYTHCEIHPAMILG-- 706

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   ++I  F                  
Sbjct: 707  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------------ 741

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     ++    +  V    +   +    +       +      + AI      +  
Sbjct: 742  ---------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSVVAIACYTGYNQE 792

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V         +  +   +++R    E    E   +        +   IY +
Sbjct: 793  DSVIMNASAVERGFFRSVFYRSYKDQESKRVGDQE----EQFEKPTRATCQGMRNAIYDK 848

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   I  G           K+  L                     +    +E    ++
Sbjct: 849  LDDDGIIAPGVRVSGDDVVIGKTITL--------------------PENDDELEGTTKRF 888

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                +    R        Q    +     +  K+ V   R  Q GDK A RHG KG    
Sbjct: 889  TKRDASTFLRNSETGIVDQVMITLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGI 948

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E   G      G+            
Sbjct: 949  QYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIECLQGKVSSNKGEIGD--------- 999

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP  D  + + I+S+
Sbjct: 1000 --------------------------------------------ATPFNDAVNVQKISSL 1015

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L+       G  ++++G TG   +  + +G  Y  +L HMV DK+++R+ G   ++ +QP
Sbjct: 1016 LQEYGYQLRGNEVMFNGHTGRKINAQIFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQP 1075

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRV 1328
            + G++  GG R GEME  C  A+GAA  L+E L   SD     V            R   
Sbjct: 1076 MEGRARDGGLRFGEMERDCQIAHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANLRNNT 1135

Query: 1329 YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1136 FEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1173



 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 144/994 (14%), Positives = 289/994 (29%), Gaps = 184/994 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVAKEGEEPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I       ++        + V         I +              
Sbjct: 213 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRVKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L        +       E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGTLLLKKRHIEMLK-----EREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFYRSYKDQESKRVGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPTRATCQGMRNAIYDKLDDDGIIAPGVRVSGDDVVIGKTITLPENDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            K    RD S  + +  +G V  V I       K
Sbjct: 886 -KRFTKRDASTFLRNSETGIVDQVMITLNSEGYK 918


>gi|219673994|ref|YP_002456479.1| RNA polymerase beta subunit [Trifolium subterraneum]
 gi|193788963|gb|ACF20559.1| RNA polymerase beta subunit [Trifolium subterraneum]
          Length = 1070

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T    +  S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDILVGKLTPQMENESSYAPEDRLLRAILGIQVSASKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+ +K E               ++++++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIHKKE-------ASSDHPETIQIYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD+V NPLGVPSRMN+GQ+ E  LG A   L +  +    D +  
Sbjct: 833  ILSRQDMPYLQDGRPVDMVFNPLGVPSRMNIGQLLECSLGLAGSKLNRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYEASKETSNPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S L+DG TG PF++PV +G  Y+LKL H V DK++ RSTG Y+LVTQQP
Sbjct: 921  -------YPGKSRLFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSTGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++N+GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V E+ + G    +  
Sbjct: 974  LKGRANQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHINARQEVLETTINGGTIPKPV 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKDFQMQRKE 1069



 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 232/682 (34%), Positives = 375/682 (54%), Gaps = 18/682 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTATIISDWGGRLELEMDRKARIWARVSRKQKISILVLSSAMGSNLSEILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N    +K   +++A+L+ YR      GD              FF   + +L  +
Sbjct: 203 IFLSFLNEREEEKIGSKENAILEFYRQFACVGGDPIFPESLCEELQKKFF-QQRCELGGI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLN+D P++   +   DI+     L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNIDIPENNPFLLPRDILTAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  I+  IS          PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENIIRGTISGAIRYKWIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+++ H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQLVHGRKWSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G IE+P+ ++ +      ++YLS   +E   +A  N          E++V  R 
Sbjct: 442 ARIGRWGSIESPFYEISERSKRIRMLYLSPSRDEYYMVATGNYLALNRDIQEEQIVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D  +IV+                  L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIVYKDTDKIVLFGN--------GNALSIPLIIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  V+R  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKSQVEKGKCVKRGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED+FTS HI ++E+    T  GPE IT  IP++    L+++D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIFTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLLRHLDKNGIVILGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+ E+  +  PE++LLRAI G +    ++T L++P G  G V+DVR  ++
Sbjct: 734 TGDILVGKLTPQMENESSYAPEDRLLRAILGIQVSASKETCLKLPIGGRGRVIDVRWIHK 793

Query: 948 HGIDKN-ERSISVEREQIELLA 968
                +   +I +   Q   + 
Sbjct: 794 KEASSDHPETIQIYISQKREIK 815



 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 105/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P L ++Q   +  F+          + GL         +         + FV  Y+   
Sbjct: 12  LPGLNQIQFEGFCRFI----------DRGLTEELLKFPKVEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+    I+  LI          K+   I+EQ I++G++PLM   GT
Sbjct: 62  PSIKEKDAVYESLTYSSEFYISAGLIW---------KNSSAIQEQIIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI R+V++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRVVINQILQSPGIYYRSELDHNGIS---VYTATIISDWGGRLELEMDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFLSFLNEREEEKIGSKE 220


>gi|316969378|gb|EFV53485.1| DNA-directed RNA polymerase II subunit RPB2 [Trichinella spiralis]
          Length = 1190

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 168/992 (16%), Positives = 313/992 (31%), Gaps = 197/992 (19%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+
Sbjct: 361  KYAREILQKETLPHVGISDFCETKK---AYFLGYMVHRLLLAAMGRRELDDRDHYGNKRL 417

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--- 521
               G +    ++  L  ++  +  +           +  +    +   +     +     
Sbjct: 418  DLAGPL--GLFKNLLKEVK--MVAQRYINKTGDFNLELCVRTGILTKGLQYSLATGNWGD 473

Query: 522  ----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                      +SQ+   +   + ++H RRL++     + R     + R +H T +G ICP
Sbjct: 474  QKKAHQTRAGVSQVLNRLTYAATLSHLRRLNS----PIGREGKLAKPRQLHNTLWGMICP 529

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQ 629
            AET EG  +GLV +L   A ++     E     + +  +    +V   +       ++  
Sbjct: 530  AETPEGQAVGLVKNLALMAYISVGSQQEPILEFLEEWSMETLEEVAPSAISATTKIFVNG 589

Query: 630  ANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDS 687
            A   +  +       L   R   + ++     + D  D   +          P L  +D 
Sbjct: 590  AWVGIHREPQQLMATLRKLRRQMDIVVSEVSMVRDIRDREIRIYTDAGRICRPLLIVEDQ 649

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
              +L   +++            +            S     +    I    +   ++  +
Sbjct: 650  RLLLKKNHIENLKRRNESNGHGW------------SELVANSIVEYIDTMEEETIMLAMT 697

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             +   D      D Y                                   PS  LG    
Sbjct: 698  PDDLQDRGVGYCDTY-----------------------------THCEIHPSMILG---- 724

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +     I       R   L         P 
Sbjct: 725  ---VCASIIPFPDHNQSPRNTYQSAMGKQAMG----IYTTNFHVRMDTLAHVLWYPQKPL 777

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V+   ++ +                           + +      + AI      +  D+
Sbjct: 778  VTTRSMEYL-------------------------RFNELPAGINSIVAILSYTGYNQEDS 812

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    IF R   D+     +   E IE   R                  
Sbjct: 813  VIMNSSSIDRGMF-RSIFYRSYRDQESSREARNEETIEKPTR------------------ 853

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +I  G       K      V     +S           ++D       +      + + +
Sbjct: 854  QICQGMRNAVYHKLDDDGIVSPGTRVSGDDVIIGKTIMLEDTDDSSTTKRSSK--KDAST 911

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
             L       ++++     +     + VKV V   R  Q GDK A RHG KG +  I   E
Sbjct: 912  FLRASETGIVDQVML--SVNADGNKFVKVRVRSIRIPQIGDKFASRHGQKGTIGMIYRQE 969

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   DI++NP  +PSRM +G + E   G      G+                 
Sbjct: 970  DMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANRGEIGD-------------- 1015

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP  D  + + ++S+L+   
Sbjct: 1016 ---------------------------------------ATPFNDSVNVQKVSSLLQEYG 1036

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G  ++Y G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S
Sbjct: 1037 YHLRGNEVMYSGFTGRKLNTQVFIGPTYYQRLKHMVDDKIHSRARGPLQMMARQPMEGRS 1096

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIV 1333
              GG R GEME  C  A+GAA+ L+E L   SD        + G       RT  YE   
Sbjct: 1097 RDGGLRFGEMERDCQIAHGAAHFLKERLFEVSDPYTVYVCKICGIIAIANSRTGHYECRT 1156

Query: 1334 --AGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                        P +  +L +E+ ++ ++  +
Sbjct: 1157 CRNKTKISRVNIPYACKLLFQELTSMCIAPRM 1188



 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 103/763 (13%), Positives = 228/763 (29%), Gaps = 143/763 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT----AF--SG----AAMLEFVS 78
           L+  Q  S+D F+ M++          Q   +   P+          G       ++F  
Sbjct: 61  LVRQQLDSFDEFIQMSV----------QKLVEDSPPVEIQLEDHGAQGLSETKFSIKFEQ 110

Query: 79  YEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                P              ++   R+LTY+ PL + +   +   +E          K +
Sbjct: 111 IYLSKPTHWEKDGAPAPLMPNEARLRNLTYSAPLYVDITKTIAKSNEEPL-----IAKYE 165

Query: 129 SIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-I 163
            +++G +P+M                           G F+I G ++++++Q   +   +
Sbjct: 166 KVFIGKIPIMLRSTYCLLNRLSERDLTDLNECPLDPGGYFIINGSEKVLIAQEKMATNTV 225

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR---------RK--- 211
           +    K       K  +           ++        + V +  R         +K   
Sbjct: 226 YVFSLKD-----NKFAFKAECR----SCLESSSRPTSTLWVNMYARGGGHGAANTKKQLM 276

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +PV     ALG  S+ +IL         ++  +     L  A ++ 
Sbjct: 277 GQRIVVNLPYVKQELPVIVVFRALGFVSDRDILEHIVYDFDDAEMMEMVKPSLDEAFVIQ 336

Query: 257 GAKVSSSLVDID------TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              V+ + +         T E+ ++  +++     ++L   G+     T       Y+  
Sbjct: 337 EQSVALNFIGSRGVQPGITREKRVKYAREILQK--ETLPHVGISDFCETKKAYFLGYMVH 394

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            ++    G   ++  D    K L+            L+ + +     +    +       
Sbjct: 395 RLLLAAMGRRELDDRDHYGNKRLDLAGPLG------LFKNLLKEVKMVAQRYINKTGDFN 448

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
            +  +          + T  +  S+    + D  K   +  G  ++  RL          
Sbjct: 449 LELCVR-------TGILTKGLQYSLATGNWGDQKKAHQTRAGVSQVLNRLTYAATLSHLR 501

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R          +     L N    +         +      ++KN   +  + +    + 
Sbjct: 502 RLNSPIGREGKLAKPRQLHNTLWGMICPAETPEGQAVG---LVKNLALMAYISVGSQQEP 558

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            +  ++  S+   + +    + +    F   + +    E    ++ +   RR   +    
Sbjct: 559 ILEFLEEWSMETLEEVAPSAISATTKIFVNGAWVGIHREPQQLMATLRKLRRQMDIVVSE 618

Query: 549 VARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           V+  R   +      T  GRIC P    E   + L  +       N     E+      +
Sbjct: 619 VSMVRDIRDREIRIYTDAGRICRPLLIVEDQRLLLKKNHIE----NLKRRNESNGHGWSE 674

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
               + V Y+  MEEE   +A     L + G                +   +     +  
Sbjct: 675 LVANSIVEYIDTMEEETIMLAMTPDDLQDRG----------------VGYCDTYTHCEIH 718

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           P  ++ + AS+IPF +++ S R      M +QA+ +       
Sbjct: 719 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYTTNFHV 761


>gi|325117477|emb|CBZ53029.1| DNA-directed RNA polymerase subunit beta [Neospora caninum Liverpool]
          Length = 1260

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 173/1005 (17%), Positives = 322/1005 (32%), Gaps = 196/1005 (19%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              +        + R ++   +  +   + +  +   I  ++  L+    G+   DD D+ 
Sbjct: 406  QREKRIQYARELLRKEVLPHVGTEAGCENK--KAFFIGYMVHRLLLADLGRINQDDRDHF 463

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ---DLINAKPVVSAVCEF 516
            G +R+   G ++   +     +M + ++  +               + +A  +   +   
Sbjct: 464  GKKRLDMAGPLIAASFGTLYRKMIKDVRRILQRQVDHGKSFDVAGAIRSASQITQGLQYQ 523

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               ++Q+   +   S ++H RRL+      + R     + R +H 
Sbjct: 524  IATGNWGKDKEGKIVRTGVAQVLNRLTFASALSHLRRLNT----PLGREGKMAKPRQLHN 579

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G ICPAET EG  +GLV +L   + ++      T +  + +    + +  ++    +
Sbjct: 580  THWGMICPAETPEGQAVGLVKNLALMSDISVGSATNTVHEFLVEW-GLDPLEEMTPDVIK 638

Query: 624  NRYIAQANSSL----DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             R     N S     DE     + L   R   +         D ++   K       ++ 
Sbjct: 639  ERVKVFVNGSWVGCFDEADVLCQTLRQLRRRCDISSETSIVRDLVNREVKIFTDAGRAMR 698

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P    D+  R L+   M+R  +  L                K   +       GI+E VD
Sbjct: 699  PLFVVDEGTRDLV---MKRGHLEEL------------QRRGKDEKSWGYLMEKGIIEFVD 743

Query: 740  AIR---IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                   +I     D+         Y   +                              
Sbjct: 744  CEEEETCMIAMFVEDIRSEKRLAFPYTHCEIH---------------------------- 775

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                     +L   +  + +P+  +N       S R V +       +  +         
Sbjct: 776  --------PSLILGVCASIIPFPDHNQ------SPRNVYQSAMGKQAMGVYTSSF----- 816

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      N   + L ++                +    +       +      + AI
Sbjct: 817  ----------NHRMDTLAHL--------LYYPQKPLVCTRAMEFLRFRELPAGINAIVAI 858

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R    +  +  S+  E  E  + +      
Sbjct: 859  LCYSGYNQEDSLIMSQSSIDRGLF-RSVFYRTYCSEERQQGSLMVESFEPPSIEHVQGMK 917

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
              D +       +  G   +       K++ +  D                       + 
Sbjct: 918  RGDYSKLDADGLVEPGSRVLGDDVIIGKTSPIFDDD-------------AGMPGAAAGIA 964

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMP--PGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             +   +   K       ++    +     +       R  KV V   R  Q+GDK A RH
Sbjct: 965  GVPSPFAKRKRDCSLCLRSSETGVVDQVMLSVNSRGSRFTKVKVRSVRIPQTGDKFASRH 1024

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF ++G   D+++NP  VPSRM +G + E  LG      G     
Sbjct: 1025 GQKGTIGITYRTEDMPFNEEGITPDLIMNPHAVPSRMTIGHLVECLLGKTAAIFG----- 1079

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                            G   +TP F+G 
Sbjct: 1080 ------------------------------------------------GEGDATP-FNGY 1090

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                I++ L     +  G   LY G TG      V  G  Y  +L HMV DK++AR+ G 
Sbjct: 1091 AVLDISNRLHSLGYERFGNERLYHGHTGRHLPSLVFFGPTYYQRLKHMVDDKIHARARGP 1150

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTR 1327
             +++T+QP+ GKS  GG R GEME  C+ ++GAA++L+E L  +SD       D+ G   
Sbjct: 1151 VTMLTRQPMEGKSREGGLRFGEMERDCMISHGAAHMLKERLFEQSDAYRVHVCDICGLVC 1210

Query: 1328 V-------YESIVAGND--TFETGTPESFNVLVKEMQALGLSIDL 1363
                    +E  +  N     +   P +  +L++E+  + +   L
Sbjct: 1211 TADLSRGNFECKLCDNKSRISQICIPYACKLLLQELMTMCIYPRL 1255



 Score =  169 bits (428), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 108/809 (13%), Positives = 222/809 (27%), Gaps = 151/809 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+             +Q       PI                +    L+
Sbjct: 105 LVNQQLESFNDFVSYK----------IQEIIDEHPPIEIKPTPQYRPEEEVESNVIYRLK 154

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG-AKSIKD 124
                 + P  +            +   R+LTY+ PL + +    + VD  TG  + +  
Sbjct: 155 MDQLSLNRPSVEEKEGISKHLWPYEARTRNLTYSSPLYVDVEQTTYTVDPETGVERLVDQ 214

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
           +    + +G +P+M K                         G F+I G ++++V+Q   +
Sbjct: 215 VTYSRVLLGRIPMMLKSAYCWTKDLPEHDLADVGECAYDQGGYFIINGGEKVLVAQERMA 274

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSKDII----------------- 202
               F +   +   S K  +   +   + G+     F  K                    
Sbjct: 275 SN--FVYVFQKKQPS-KFGWVAEVRSQKEGMQATSGFAVKKRSRTGEGRGAKGGRPGGQI 331

Query: 203 -----HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                ++R +    +P+     ALG +   +IL     ++ Y  +       +  +    
Sbjct: 332 VAALPYIRTE----IPIVILFRALGCISDRDIL----LRVAYDLKDPQLISLMKPSLEEG 383

Query: 257 GAKVSSSLVDIDTGE--QVIESGKKLTSGLLKSLKEKGV-------KFLGITSDCLCGLY 307
               S  +     G+    + + ++      + L  K V                  G  
Sbjct: 384 FDYGSQDVCLDFIGKRGPTVGAQREKRIQYARELLRKEVLPHVGTEAGCENKKAFFIGYM 443

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V   ++  + G I  +  D   +K L+            LY   + +   I    V    
Sbjct: 444 VHRLLL-ADLGRINQDDRDHFGKKRLDMAGPLIAASFGTLYRKMIKDVRRILQRQVDHGK 502

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                   D+   +R     T  +   +    +    +  +   G  ++  RL   +   
Sbjct: 503 SF------DVAGAIRSASQITQGLQYQIATGNWGKDKEGKIVRTGVAQVLNRLTFASALS 556

Query: 428 V--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              R          +     L N    +         +      ++KN   +  + +  +
Sbjct: 557 HLRRLNTPLGREGKMAKPRQLHNTHWGMICPAETPEGQAVG---LVKNLALMSDISVGSA 613

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
                  +    + P + +    +   V  F   S +   +E       +   RR   + 
Sbjct: 614 TNTVHEFLVEWGLDPLEEMTPDVIKERVKVFVNGSWVGCFDEADVLCQTLRQLRRRCDIS 673

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                          +       + P    +     LV        +   G  E      
Sbjct: 674 SETSIVRDLVNREVKIFTDAGRAMRPLFVVDEGTRDLVMKRGHLEELQRRGKDEKS---W 730

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                   + ++   EEE   IA     +  +                           +
Sbjct: 731 GYLMEKGIIEFVDCEEEETCMIAMFVEDIRSEKRLAFPY-----------------THCE 773

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAP 709
             P  ++ + AS+IPF +++ S R +    M +QA+                 L   + P
Sbjct: 774 IHPSLILGVCASIIPFPDHNQSPRNVYQSAMGKQAMGVYTSSFNHRMDTLAHLLYYPQKP 833

Query: 710 FVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
            V T  ME +  +   A I A  A +   
Sbjct: 834 LVCTRAMEFLRFRELPAGINAIVAILCYS 862


>gi|161622302|ref|YP_001586174.1| RNA polymerase beta subunit [Acorus americanus]
 gi|182676548|sp|A9LYH7|RPOB_ACOAM RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|160369845|gb|ABX38736.1| RNA polymerase beta subunit [Acorus americanus]
          Length = 1083

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 160/563 (28%), Positives = 257/563 (45%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++      ++E     IH +  +++   +  G       +          
Sbjct: 575  IVGTGLERQAALDSGVSAIAECEGKIIHTDTHKIVL--SGHGDTISIPLVMYQRSNKNTC 632

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +   +  G  +  G IL       G   +   + +L A    +  +  D  L     +
Sbjct: 633  MHQNPQVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----I 686

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E +  +    +  L RN+  R   +  G   
Sbjct: 687  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNL-DRNGIVALGSWV 745

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  +++  S  P  +  +  +  +        LK+       +++ R+  
Sbjct: 746  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 805

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG
Sbjct: 806  KKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDG 858

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 859  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELY 918

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 919  EASKQTANPW------------------------VFE---------------PEYPGKSR 939

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 940  IFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 999

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+
Sbjct: 1000 EMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVREL 1059

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1060 RSLALELNHFLVSEKNFQINRKE 1082



 Score =  369 bits (948), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 260/831 (31%), Positives = 429/831 (51%), Gaps = 44/831 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 155  ISVYTSTIISDWGGRSELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 214

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 215  IFLSFLNDREKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 273

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 274  GRRNMNRRLNLDIPQSNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 333

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +++  I       +   PQ+L+++  + +    FF    LSQ+ +  
Sbjct: 334  QDQFGLALVRLENAVRGTICGAIRHKLILTPQNLVSSTSLTTTYESFFGLHPLSQVLDRT 393

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 394  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 453

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-LDEDGSFTEELVFCR 648
            AR+  +G IE+P+ +V        +V+LS   +E   +A  NS  L+  G   E++V  R
Sbjct: 454  ARIGHWGSIESPFYEVYQRSKETKMVFLSPSRDEYYTVATGNSLALNRGGIQEEQIVPAR 513

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E 
Sbjct: 514  YRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEK 573

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +Q
Sbjct: 574  CIVGTGLERQAALDSGVSAIAECEGKIIHTDTHKIVL--------SGHGDTISIPLVMYQ 625

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 626  RSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 685

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V
Sbjct: 686  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNLDRNGIVALGSWV 745

Query: 889  NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              GDILVGK+TP+  +  +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 746  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 805

Query: 947  RHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------Q 993
            + G         R    ++ +I++  +   +   + I+ + +  + M  L          
Sbjct: 806  KKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVF 865

Query: 994  NAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQY 1042
            N +  P       +    L ++     + ++ A  DE+ ++            E+ K   
Sbjct: 866  NPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTA 925

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 926  NPWVFEPEYPGKSRIFDGRTGDPFEQPVL-IGKSYIL-KLIHQVDDKIHGR 974



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL   F     I         + FV  Y+   
Sbjct: 24  IPGFSQIQFEGFCRFI----------DQGLMEEFHKFPKIEDTDQEIEFQLFVERYQLVE 73

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 74  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 124

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 125 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKSRIW 181

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 182 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDREKKKIGSKE 232


>gi|324120600|dbj|BAJ78691.1| RNA polymerase II second largest subunit [Petrobiellus takunagae]
          Length = 1151

 Score =  388 bits (996), Expect = e-105,   Method: Composition-based stats.
 Identities = 162/1008 (16%), Positives = 309/1008 (30%), Gaps = 209/1008 (20%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ 
Sbjct: 307  REKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHY 363

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFF 517
            GN+R+   G +L   +R     + + ++               +  I  K +   +    
Sbjct: 364  GNKRLDLAGPLLAFLFRGMFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSL 423

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+   +   S ++H RR+++     + R     + R +H T
Sbjct: 424  ATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNT 479

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEE 622
             +G ICPAET EG  +GLV +L   A ++           + +  +    ++   +  + 
Sbjct: 480  LWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADA 539

Query: 623  ENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
               ++      +  D       L   R   + I+     I D  D   +          P
Sbjct: 540  TKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRP 599

Query: 681  FLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQ 737
             L  ++   +L   +  M ++           V +  +E +        ++A        
Sbjct: 600  LLIVENGRLLLKKRHVDMLKEREYNNYGWQDLVASSAVEYIDTLEEETVMIA-------- 651

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                   +   +   D   +    Y                                   
Sbjct: 652  -------MSLDDLRQDKEYAYCTTY-----------------------------THCEIH 675

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            P+  LG       +  + +P+  +N          M  + +   ++I  F          
Sbjct: 676  PAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------- 716

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                             ++    +  V        +    +       +      + AI 
Sbjct: 717  -----------------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSVVAIA 759

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S V            +   +++R    E    E   +        
Sbjct: 760  CYTGYNQEDSVIMNASAVERGFFRSVFMRAYKDSESKRVGDQE----EQFEKPTRQTCQG 815

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            +   IY +L +   I  G           K+  L                     +    
Sbjct: 816  MRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITL--------------------PENDDE 855

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +E    +Y    +    R        Q    +     +  K+ V   R  Q GDK A RH
Sbjct: 856  LEGTTKRYTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRH 915

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG        EDMPF  +G   DI++NP  +PSRM +G + E   G      G+    
Sbjct: 916  GQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIECLQGKVSSNKGEIGD- 974

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP  D  
Sbjct: 975  ----------------------------------------------------ATPFNDAV 982

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            + + I+++L+       G  ++++G +G   +  V +G  Y  +L HMV DK+++R+ G 
Sbjct: 983  NVQKISALLQEYGYQLRGNEVMFNGHSGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGP 1042

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG------ 1324
              ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L   SD     V        
Sbjct: 1043 VQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERLFEVSDPYRIHVCNFCGLIA 1102

Query: 1325 ----RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                R   +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1103 IANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1148



 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 146/981 (14%), Positives = 291/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 14  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 72

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 73  HWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKTVVKDGEDPI-----ETQHQKTFIGKI 127

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 128 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 187

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  Y   I       ++        + V +  R     +K              
Sbjct: 188 -----GKYAYKSEIR----SCLEHSSRPTSTLWVNMLARGGQSVKKSSVGQKIIAILPYI 238

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 239 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGG 298

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
              +  +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 299 RGAKPGVTREKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 354

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 355 RELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 414

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 415 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 474

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 475 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 531

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    +S +   RR   +    V+  R   +      T
Sbjct: 532 APSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 591

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L         V+     E       D   ++ V Y+  +EEE
Sbjct: 592 DAGRICRPLLIVENGRLLLKKR-----HVDMLKEREYNNYGWQDLVASSAVEYIDTLEEE 646

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 647 TVMIAMSLDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 691

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 692 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 718

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y               Q+PLV                     
Sbjct: 719 --------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRFR 746

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+ +  ++          EE   
Sbjct: 747 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFMRAYKDSESKRVGDQEEQFE 806

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 807 KPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITLPENDDELEGTT------ 860

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 861 -KRYTKRDASTFLRNSETGIV 880


>gi|308745991|ref|YP_003934550.1| RNA polymerase beta subunit [Cheilanthes lindheimeri]
 gi|302375424|gb|ADL29798.1| RNA polymerase beta subunit [Cheilanthes lindheimeri]
          Length = 1076

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 132/373 (35%), Positives = 183/373 (49%), Gaps = 47/373 (12%)

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G    +G     K T       S  P  +  Q           + + +           
Sbjct: 734  LGSWVETGDVSVGKLTPQEGASSSRVPEGRLLQAIFG-----IQLVNARESCLKVPIGGR 788

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
             R  +        D        V+ +++  +R IQ GDK+AGRHGNKGIVS+ILP +DMP
Sbjct: 789  GRVIDVRWVYPEDDTTNDS--EVIHIYILQRRKIQVGDKIAGRHGNKGIVSKILPRQDMP 846

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L+DGTPVD++L+PLGVPSRMNVGQIFE  LG A   L    + +  D +   + S    
Sbjct: 847  YLQDGTPVDMILSPLGVPSRMNVGQIFECLLGLAGEFLETHYRIVPFDERYEREASRKLV 906

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
            F E                                                   + +   
Sbjct: 907  FAELHEAGARTNNPW---------------------------------------LFEPSH 927

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+S L DG TG+ F +P+T G  Y++KL H V DK++ARS+G Y+LVTQQPL GKS RG
Sbjct: 928  PGKSRLIDGRTGDSFGQPITTGKAYIMKLIHQVDDKIHARSSGPYALVTQQPLKGKSRRG 987

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-TPESFNV 1349
            GQR+GEMEVW  + +G +Y LQEMLT KSD +  R +V  +I  G    +    PESF +
Sbjct: 988  GQRVGEMEVWASEGFGVSYTLQEMLTTKSDHIQARYKVPSAITTGRPVHKPNTVPESFRL 1047

Query: 1350 LVKEMQALGLSID 1362
            LV+E++ +GL+++
Sbjct: 1048 LVRELRRMGLNLE 1060



 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 262/719 (36%), Positives = 402/719 (55%), Gaps = 27/719 (3%)

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           G  + +G+ + L  + ++  GI  +      GL      V  + G  +    D  D+  +
Sbjct: 103 GTFVINGIARVLVNQILRSPGIYYNRESDQKGLPAYTSTVISDWGGRFKPEMDRRDKIWI 162

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRN-----------TLVTDKNKDRKDALLDIYRVMR 382
                 +I  + +L    +     +RN               +  +  +DA+ ++Y+   
Sbjct: 163 RISKKRKISILILLVSMGLGKRDILRNARYPKIFPNMSKKQKEIIESPEDAIAELYKHPY 222

Query: 383 PGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
               +  S +ES+F      F   + +L  +GR   N++L LD P+    +  +DI+A  
Sbjct: 223 SAADANLSFSESIFKELQKRFFQHRCELGRIGRRNPNIKLTLDVPETEYFLLPQDILAAA 282

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--VDIDSV 498
              +++  GKG +DDID+L NRRVRSV ++L+ Q +L   R+E SI++ +S       ++
Sbjct: 283 DHSIEISYGKGKLDDIDHLKNRRVRSVADLLQEQLKLASNRLENSIRQNLSRAVRRKRAI 342

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            P+ L+   PV++A  EFF S  LSQ  +  N LS + H RRLS++G GG+ R  A  + 
Sbjct: 343 TPRGLVTPAPVIAAFKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRRTASFQA 402

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RD+H +HYGRICP ETSEG N GL+SSL   A V+  G +++PY ++ D      +V LS
Sbjct: 403 RDIHFSHYGRICPIETSEGMNAGLISSLAIQAGVSNSGSLQSPYLEMSDSSGEEQLVDLS 462

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             E++   IA  N  L +  +   EL+  R   E + VP E++DF    P    SI ASL
Sbjct: 463 PAEDDYYRIATENLLLPDWRASERELIPVRYQQEFLSVPWEQVDFRSIHPLHHFSIGASL 522

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF+E++D+NR LMG  MQRQAVPL+K E   VGTG+ES VA  SG+  ++ R G ++ +
Sbjct: 523 IPFIEHNDANRALMGSTMQRQAVPLVKPERCIVGTGLESQVASDSGSVTISGRVGKIQYI 582

Query: 739 DAIRIVI------RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           D  RI +      RS E      +S +    L  ++RSN NTC++Q+P V  G+ +R  +
Sbjct: 583 DGNRIELSPIHEARSNESARLIISSDIINIELKIYERSNNNTCMHQKPAVSRGELLRSGE 642

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           I+ADG +T  G+ ALGRN+LVA+MPW GYNFED++LISER++ ED+FTS HIE+ EV   
Sbjct: 643 IVADGAATARGEPALGRNILVAYMPWEGYNFEDAVLISERLIYEDIFTSFHIEKHEVEIC 702

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEE 910
            T  GPE +T+ IP V    L+++D+ G++ +G+ V  GD+ VGK+TP+  +  +  PE 
Sbjct: 703 ATNQGPERVTKQIPQVDSHALRHLDDNGLVELGSWVETGDVSVGKLTPQEGASSSRVPEG 762

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIELLA 968
           +LL+AIFG + V+ R++ L+VP G  G V+DVR  +       +   I +   Q   + 
Sbjct: 763 RLLQAIFGIQLVNARESCLKVPIGGRGRVIDVRWVYPEDDTTNDSEVIHIYILQRRKIQ 821



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 77/432 (17%), Positives = 147/432 (34%), Gaps = 39/432 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVS----YE 80
           +P+L  +Q   +  F+   +         L+      FP I        +EF S    Y+
Sbjct: 4   LPELARIQFEGFSRFVHKRL---------LEEL--ENFPKIEDTDK--EVEFRSIGNRYQ 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P  +  D  ++ +TY+    + ++LI  +          + ++E+ + +G +P M  
Sbjct: 51  LAEPSVEERDAAYQCITYSADPYVPVQLICNED---------RVVQEEDVRLGSIPWMNS 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTFVI GI R++V+Q+ RSPGI+++ +       G   Y   +I D G     E D +D
Sbjct: 102 RGTFVINGIARVLVNQILRSPGIYYNRESD---QKGLPAYTSTVISDWGGRFKPEMDRRD 158

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
            I +RI ++RK+ +   L+++G+   +IL +  YPKI  +          S  D  +   
Sbjct: 159 KIWIRISKKRKISILILLVSMGLGKRDILRNARYPKIFPNMSKKQKEIIESPED-AIAEL 217

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                   D      ES  K         + +  +      +    L V E        +
Sbjct: 218 YKHPYSAADANLSFSESIFKELQKRFFQHRCELGRIGRRNPNIKLTLDVPETEYFLLPQD 277

Query: 320 IYIEAGD-------VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           I   A               ++ + +  +R +  L  + +   +      +         
Sbjct: 278 ILAAADHSIEISYGKGKLDDIDHLKNRRVRSVADLLQEQLKLASNRLENSIRQNLSRAVR 337

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
               I            +  +  F            + +  +    RL+   P  +    
Sbjct: 338 RKRAITPRGLVTPAPVIAAFKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRRT 397

Query: 433 KEDIIAIIKILV 444
                  I    
Sbjct: 398 ASFQARDIHFSH 409


>gi|30352026|ref|NP_848052.1| RNA polymerase beta subunit [Adiantum capillus-veneris]
          Length = 1071

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 123/295 (41%), Positives = 170/295 (57%), Gaps = 40/295 (13%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              L V+ +++  +R IQ GDK+AGRHGNKGIVS+I+P +DMP+L++GTPVD++L+PLGVP
Sbjct: 800  NDLEVIHIYILQRRKIQVGDKIAGRHGNKGIVSKIVPRQDMPYLQNGTPVDMILSPLGVP 859

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRMNVGQIFE  LG A        + +  D +   + S                      
Sbjct: 860  SRMNVGQIFECLLGLAGEFSETHYRVVPFDERYEREASRKLV------------------ 901

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                              + P   GA     N  L        G+S L DG TG+PF + 
Sbjct: 902  -----------------FAEPHEAGARTN--NPWLFE--PSHPGKSRLIDGRTGDPFGQS 940

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +T G  Y++KL H V DK++ARS+G Y+LVTQQPL GKS RGGQR+GEMEVW  + +G +
Sbjct: 941  ITTGKAYIMKLIHQVDDKIHARSSGPYALVTQQPLKGKSRRGGQRIGEMEVWASEGFGVS 1000

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID 1362
            Y LQEMLT KSD +  R +   +I+ G    +    PESF +LV+E++ +GL+++
Sbjct: 1001 YTLQEMLTTKSDHIQARYKALSAIMTGKPVCKPKTVPESFRLLVRELRRMGLNLE 1055



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 244/660 (36%), Positives = 374/660 (56%), Gaps = 11/660 (1%)

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
              I++             +    +    IL                 +  +  +DA+ +
Sbjct: 157 RNRIWVRISKKKKISIFILLVAMGLCKRDILQNSRYPRIFSNMFKRQKESIESPEDAIAE 216

Query: 377 IYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           +Y+ +     +    +ES+F      F   + +L  +GR  +N++L LD P+    +  +
Sbjct: 217 LYKHLYSATDADVFFSESIFRELXKRFFQHRCELGRIGRRNLNIKLTLDVPETESFLLPQ 276

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-- 492
           DI+A     V++  G+G +DDID+L NRRVRSV ++L+ Q +L   R+E  I+  +S   
Sbjct: 277 DILAAADHSVEISYGEGKLDDIDHLKNRRVRSVADLLQEQLKLAPNRLENLIRXNLSRAV 336

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
               ++ P+ L+   PV++A  EFF S  LSQ  +  N LS + H RRLS++G GG+ R 
Sbjct: 337 RRKRAITPRGLVTPVPVIAAFKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRR 396

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
            A  + RD+H +HYGRICP ETSEG N GL+SSL   A VN  G + +PY ++ D     
Sbjct: 397 TASFQARDIHFSHYGRICPIETSEGMNAGLISSLAIQAGVNTSGSLGSPYLEMSDSSGEE 456

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            +V LS  E++   +A  N  L E     +E++  R   E + V  E++DF    P    
Sbjct: 457 QLVNLSPAEDDYYRVASENLLLSEWRGSEKEIIPVRYQQEFLSVLWEQVDFRSIHPLHHF 516

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           SI ASLIPF+E++D+NR LMG   QRQAVPL+K E   VGTG+ES VA  SG+  ++++ 
Sbjct: 517 SIGASLIPFIEHNDANRALMGSTTQRQAVPLIKPERCIVGTGLESQVALDSGSVAISEQD 576

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVGDEVRRN 791
           G V  +D  RI +  +        +       +K F+RSN NTC++Q+P V +G+ +R  
Sbjct: 577 GKVCYIDGNRIELSLIHEAKKNKLAQPTTIEELKIFERSNNNTCMHQKPAVSLGELLRGG 636

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER++ ED+FTS+HIE+ EV  
Sbjct: 637 EIVADGAATVRGELALGKNILVAYMPWEGYNFEDAVLISERLIYEDIFTSLHIEKHEVEI 696

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PE 909
             T  GPE +T+ I  +    L+++D+ G++  G+ V  GD+LVGK+TP+  +  +  PE
Sbjct: 697 CATNQGPERVTKQISQLDGYLLRHLDDDGLVESGSWVEAGDVLVGKLTPQEGASSSRVPE 756

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + L+AIFG + V+ R++ LRVP G  G V DV    R    +++ +  +E   I +L R
Sbjct: 757 GRSLQAIFGIQLVNARESCLRVPIGGRGRVTDV----RWVYPEDDATNDLEVIHIYILQR 812



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 85/435 (19%), Positives = 158/435 (36%), Gaps = 45/435 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVS----YE 80
           +P+L ++Q   +  F+   +         L+      FP I        +EF S    Y+
Sbjct: 4   LPELAQIQFKGFSRFVHQKL---------LKEL--ENFPKIEDTDK--EVEFXSIGNQYQ 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P  +  D  ++ +TY+    +   LI          K  + ++E+ + +G +P M  
Sbjct: 51  LTEPSLEERDAAYQCITYSADPYVPAXLIC---------KEDQIVQEEDVRLGSIPWMNS 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I GI R++VSQ+ RSPGI+++ +       G L Y    I DQG    +E D ++
Sbjct: 102 GGTFIINGIARVLVSQILRSPGIYYNRESD---QRGILAYTSTAISDQGGRFKLEIDGRN 158

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIV---YSQRGDFWCFPLSAADLMV 256
            I VRI +++K+ +   L+A+G+   +IL ++ YP+I    + ++ +    P  A   + 
Sbjct: 159 RIWVRISKKKKISIFILLVAMGLCKRDILQNSRYPRIFSNMFKRQKESIESPEDAIAELY 218

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
               S++  D+   E +     K        L   G + L I       L V E      
Sbjct: 219 KHLYSATDADVFFSESIFRELXKRFFQHRCELGRIGRRNLNIK----LTLDVPETESFLL 274

Query: 317 TGEIYIEAGD-------VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             +I   A               ++ + +  +R +  L  + +         L+      
Sbjct: 275 PQDILAAADHSVEISYGEGKLDDIDHLKNRRVRSVADLLQEQLKLAPNRLENLIRXNLSR 334

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
                  I        V   +  +  F            + +  +    RL+   P  + 
Sbjct: 335 AVRRKRAITPRGLVTPVPVIAAFKEFFGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLT 394

Query: 430 HIRKEDIIAIIKILV 444
                     I    
Sbjct: 395 RRTASFQARDIHFSH 409


>gi|290489650|gb|ADD31209.1| RNA polymerase beta subunit protein [Staphylea colchica]
          Length = 1070

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 252/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +        G   E  +++   + +        I         +     
Sbjct: 544  MSSNMQRQAVPLSRPEKCIVGTGLERQVVLDSGVSAIAEHEGKIIYTDTDKIILSGNRDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          I +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LSIPLVMYQRSNKNTCIHQNSQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPRVAKESSYAPEDRLLRAILAIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKK----GGSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYEASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRIGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALDLNHFLVSEKNFQINRKE 1069



 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 251/778 (32%), Positives = 404/778 (51%), Gaps = 41/778 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   +++A+L+ Y+ +    GD              FF  
Sbjct: 195  LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQLACVGGDPVFSESLCKELQKKFFH- 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             K +L  +GR  MN  LNLD P     +   DI+A   +L+ ++ G GT+DD+++L N+R
Sbjct: 254  QKCELGRIGRRNMNQSLNLDIPQYNTFLLPRDILAATDLLIGMKFGMGTLDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314  IRSVADLLQDQFGLALVRLENVVRGTIYGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ SL   AR+  +G +E+P+ ++ +      ++Y S   +E   +A  NS         
Sbjct: 434  LIGSLAIHARIGHWGSLESPFYEISERSKKVRMLYFSPNRDEYYMVAAGNSLALNRSIQE 493

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            EE+V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494  EEVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL + E   VGTG+E  V   SG + +A+  G +   D  +I++      L         
Sbjct: 554  PLSRPEKCIVGTGLERQVVLDSGVSAIAEHEGKIIYTDTDKIILSGNRDTL--------S 605

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L+ +QRSN+NTC++Q   V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606  IPLVMYQRSNKNTCIHQNSQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGY 665

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI
Sbjct: 666  NFEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGI 725

Query: 882  ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            + +G+ V  GDILVGK+TP+     +  PE++LLRAI   +    ++T L++P G  G V
Sbjct: 726  VMLGSWVETGDILVGKLTPRVAKESSYAPEDRLLRAILAIQVSTSKETCLKLPIGGRGRV 785

Query: 940  VDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCG 992
            +DVR   + G         R    ++ +I++  +      ++ +I        +  +  G
Sbjct: 786  IDVRWIQKKGGSSYNPEMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDG 845

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------V 1035
            +            + ++   I E           + ++ A  DE+ ++            
Sbjct: 846  RPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELY 905

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            E+ K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  EASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 75/335 (22%), Positives = 139/335 (41%), Gaps = 31/335 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDPDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ I++G++PLMT  GT
Sbjct: 62  PLIKERDAVYDSLTYSSELYVSAGLIW---------KTNRDMQEQKIFIGNIPLMTSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKAKIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD---LMVGAK 259
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +   L    +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQ 229

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY---VAEDIVNGE 316
           ++    D    E + +  +K        L   G + +  + +     Y   +    +   
Sbjct: 230 LACVGGDPVFSESLCKELQKKFFHQKCELGRIGRRNMNQSLNLDIPQYNTFLLPRDILAA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           T  +      +     +  + +  IR +  L  D 
Sbjct: 290 TDLLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324


>gi|186885953|gb|ACC93384.1| RNA polymerase beta subunit [Stenopadus talaumifolius]
          Length = 1026

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 158/562 (28%), Positives = 246/562 (43%), Gaps = 58/562 (10%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +    ++        I         +  G       +          I
Sbjct: 519  CIVGTGLERQAALDSGALAIAEHEGKIIYTDTDKILLSGNGDTLSIPLVMYQRSNKNTCI 578

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G  ++          +   + +L A    +  +  D  L     +S
Sbjct: 579  HQKPQVRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----IS 632

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    
Sbjct: 633  ERLVYEDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVE 691

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T       S  P  +  +  +           LK+       +++ R+  K
Sbjct: 692  TGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK 751

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                             ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 752  KR---------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 802

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E   
Sbjct: 803  PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYE 862

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                             T VF+                +  G+S +
Sbjct: 863  ASKQTAN------------------------TWVFE---------------PEYPGKSRI 883

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQPL G++ +GGQR+GE
Sbjct: 884  FDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQPLKGRAKQGGQRVGE 943

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 944  MEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELR 1003

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +T    + E
Sbjct: 1004 SLALELNHFLVSEKTFQINRKE 1025



 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 261/804 (32%), Positives = 414/804 (51%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCIHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K    T     E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANTWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|156598352|gb|ABU85436.1| RNA polymerase beta subunit [Musa acuminata]
          Length = 1070

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 147/444 (33%), Positives = 225/444 (50%), Gaps = 50/444 (11%)

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +S  +V   I+    I K E    V  +  E + ++    +  L RN+  R   ++ G  
Sbjct: 673  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNL-DRNGVVMLGSW 731

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G     K T  +++  S  P  +  +  +  +       SLK+       +++ R+ 
Sbjct: 732  VETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWI 791

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K      G         +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+D
Sbjct: 792  RKK----GGSCYNS---EMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQD 844

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E 
Sbjct: 845  GTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKRHYRIAPFDERYEQEASRKLVFSEL 904

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
               +                               VF+                +  G+S
Sbjct: 905  YEASKQTKNPW------------------------VFE---------------PEYPGKS 925

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+
Sbjct: 926  RIFDGRTGNPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRV 985

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKE 1353
            GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E
Sbjct: 986  GEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGATIIGGRVSNPEDAPESFRLLVRE 1045

Query: 1354 MQALGLSID--LENSRTKNSAKME 1375
            +++L L ++  L + +     + E
Sbjct: 1046 LRSLALELNHFLVSEKNFQINRKE 1069



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 381/686 (55%), Gaps = 18/686 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 140 ISVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILILSSAMGSNLREILDNVCYPE 199

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 200 IFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 258

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RS+ ++L
Sbjct: 259 GRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGIKFGMGTLDDMNHLKNKRIRSIADLL 318

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 319 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRT 378

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 379 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 438

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E++V  R 
Sbjct: 439 VRIGHWGSIESPFYEISERSKEAQIVYLSPNRDEYYMVAAGNSLALNRGIQEEQVVPARY 498

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 499 RQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSERC 558

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+  G +   D  +I++ S        +  + IY     QR
Sbjct: 559 IVGTGLERQTALDSGVSAIAEHEGKIIYTDPHKIILSSNGDTTISISIPLVIY-----QR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT++IP++    L+N+D  G++ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDRNGVVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+  +  +  PE++LLRAI G +    ++TSL++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWIRK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSCYNSEMIRVYISQKREIKVGDK 819



 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          NEGL   F     I         + FV  Y+   
Sbjct: 9   IPGFSQIQFEGFCRFI----------NEGLTEEFHKFPKIEDTDQEIEFKLFVERYQLVE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P  +  D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 59  PLINERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTVFIGNIPLMNSLGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 110 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKARIW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 167 ARVSRKQKISILILSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKE 217


>gi|301353339|ref|YP_003795572.1| RNA polymerase beta subunit [Pteridium aquilinum subsp. aquilinum]
 gi|301016257|gb|ADK47544.1| RNA polymerase beta subunit [Pteridium aquilinum subsp. aquilinum]
          Length = 1071

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 147/498 (29%), Positives = 221/498 (44%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G     G+ ++                +L A    +  +  D  L     +   +  
Sbjct: 627  VSPGELPKSGE-VIADGAATVRGESALGRNILVAYMPWEGYNFEDAVLISECSIYEDIST 685

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ ++    +   E+   ++   D    + + D  +         G    +G   
Sbjct: 686  SFHIERYEVEVCATNQGPEKVTKQIPQLDSHALRHLDDNGLVE------SGSWVEAGDVS 739

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  Q           + + +          + R  +      
Sbjct: 740  VGKLTPQEGAGSSRAPEGRSLQ-----AISGIQLVNARESCLKVPIGGKGRVIDVGWVYP 794

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
              D        V+ +++  KR IQ GDK+AGRHGNKGIVS++LP +DMP+L+DGTPVD++
Sbjct: 795  EDDTSNDS--EVIHIYILQKRKIQVGDKVAGRHGNKGIVSKVLPRQDMPYLQDGTPVDMI 852

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            L+PLGVPSRMNVGQIFE  LG A        + +  D +   + S    F E        
Sbjct: 853  LSPLGVPSRMNVGQIFECLLGLAGEFPETHYRIVPLDERYEREASRKLVFSEPYR----- 907

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                            A   + N  L     D  G+S L DG T
Sbjct: 908  --------------------------------ASVSSHNPWLFE--PDHPGKSRLIDGRT 933

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G PF +P+T+G  Y++KL H V DK++ARS+G Y+LVTQQPL G+S RGGQR+GEMEVW 
Sbjct: 934  GNPFAQPITIGKAYIMKLIHQVDDKIHARSSGPYALVTQQPLKGRSRRGGQRVGEMEVWA 993

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG-TPESFNVLVKEMQALGLS 1360
             + +G +Y  QEMLTIKSD +  R +V  +I+ G    +    PESF + V+E++ +GL+
Sbjct: 994  SEGFGVSYTSQEMLTIKSDHIQARYKVPSAIMTGKPVHKPNTVPESFRLPVRELRCMGLN 1053

Query: 1361 ID----LENSRTKNSAKM 1374
            ++    LE    + S  +
Sbjct: 1054 LEHSFILEEDLGRESESI 1071



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 237/715 (33%), Positives = 387/715 (54%), Gaps = 22/715 (3%)

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKS 332
            G  + +G+ + L  + ++  GI  +      G+      V  + G  +    D  D+  
Sbjct: 102 KGTFIINGIARVLVNQILRSPGIYYNRESDQKGVSAYTSTVISDRGGRFKPEMDRKDKIW 161

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR-----------KDALLDIYRVM 381
           +      +I  + +L    ++    ++N        +            +DA+ ++Y+  
Sbjct: 162 VRISKKRKISILILLIAMGLSKKDILQNVRYPKIFSNILKKHKGAVESSEDAIAELYKHP 221

Query: 382 RPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                +  + +ES+F      F   + +L  +GR  +N++L LD P+    +  +D++A 
Sbjct: 222 YSATDADITFSESIFKELQKRFFQHRRELGRIGRRNLNIKLTLDVPETEHFLLPQDVLAA 281

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--VDIDS 497
               +++  G G +DDID+L NRRVRSV ++ + Q +L   R+E SI++ +S       +
Sbjct: 282 ADHSIEISYGMGNLDDIDHLKNRRVRSVADLPQEQLKLASNRLENSIRQNLSRAVRRKRA 341

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + P+ L+   PV++   EF  S  LSQ  +  N LS + H RRLS++G GG+ R  A  +
Sbjct: 342 ITPRGLVTPAPVIATFKEFSGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRRTASFQ 401

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            RD+H +HYGRICP ETSEG N GL+SSL   A+V+  G +++PY K+ +      +V  
Sbjct: 402 ARDIHFSHYGRICPIETSEGMNAGLISSLAIQAKVSNSGSLQSPYPKMSESFEEEHLVDS 461

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           S  E++   +A  NS + +  +  +ELV  R   E + V  E++DF    P    SI AS
Sbjct: 462 SPTEDDYYRVATENSLISDWRTREKELVPVRYQQEFLSVLWEQVDFRSIHPLHYFSIGAS 521

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPF+E++D+N  L G  MQRQAVPL+K +   VGTG+ES VA  SG+  V+ + G ++ 
Sbjct: 522 LIPFIEHNDANCALTGSTMQRQAVPLVKPDRCIVGTGLESQVALDSGSVAVSGQEGQIQY 581

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           +D  RI + ++                +K ++RSN NTC++Q+  V  G+  +  ++IAD
Sbjct: 582 IDGNRIELSTIHEATSDEKILRVTNNKLKIYERSNNNTCIHQKSTVSPGELPKSGEVIAD 641

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+ ALGRN+LVA+MPW GYNFED++LISE  + ED+ TS HIE +EV    T  
Sbjct: 642 GAATVRGESALGRNILVAYMPWEGYNFEDAVLISECSIYEDISTSFHIERYEVEVCATNQ 701

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLR 914
           GPE++T+ IP +    L+++D+ G++  G+ V  GD+ VGK+TP+  +  +  PE + L+
Sbjct: 702 GPEKVTKQIPQLDSHALRHLDDNGLVESGSWVEAGDVSVGKLTPQEGAGSSRAPEGRSLQ 761

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIELLA 968
           AI G + V+ R++ L+VP G  G V+DV   +       +   I +   Q   + 
Sbjct: 762 AISGIQLVNARESCLKVPIGGKGRVIDVGWVYPEDDTSNDSEVIHIYILQKRKIQ 816



 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 91/556 (16%), Positives = 185/556 (33%), Gaps = 53/556 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEF----VSYE 80
           +P+L  +Q   +  F+   +         L+      FP I        +EF      Y+
Sbjct: 4   LPELARIQFEGFSRFVHERL---------LEEL--ENFPKIEDTDK--EVEFRSISKQYQ 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P  +  D  ++ +TY+  L + ++L           +  + ++E+ + +G +P M  
Sbjct: 51  LAEPSVEERDAAYQCVTYSADLYVPVQLT---------RREDRVVQEEDVRLGSIPWMNS 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I GI R++V+Q+ RSPGI+++ +  +  +S    Y   +I D+G     E D KD
Sbjct: 102 KGTFIINGIARVLVNQILRSPGIYYNRESDQKGVSA---YTSTVISDRGGRFKPEMDRKD 158

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKI---VYSQRGDFWCFPLSAADLMV 256
            I VRI ++RK+ +   L+A+G+  ++IL    YPKI   +  +          A   + 
Sbjct: 159 KIWVRISKKRKISILILLIAMGLSKKDILQNVRYPKIFSNILKKHKGAVESSEDAIAELY 218

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIV 313
               S++  DI   E + +  +K      + L   G + L I           ++    V
Sbjct: 219 KHPYSATDADITFSESIFKELQKRFFQHRRELGRIGRRNLNIKLTLDVPETEHFLLPQDV 278

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                     +  + +   ++ + +  +R +  L  + +   +      +          
Sbjct: 279 LAAADHSIEISYGMGNLDDIDHLKNRRVRSVADLPQEQLKLASNRLENSIRQNLSRAVRR 338

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
              I            +  +               + +  +    RL+   P  +     
Sbjct: 339 KRAITPRGLVTPAPVIATFKEFSGSHPLSQFLDQTNPLSEMVHKRRLSSVGPGGLTRRTA 398

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I       +  G I  I+         +  +           ++    +   S 
Sbjct: 399 SFQARDIHF-----SHYGRICPIETSEGMNAGLISSLAIQAKVSNSGSLQSPYPKMSESF 453

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + ++            A      S                          Q  ++   
Sbjct: 454 EEEHLVDSSPTEDDYYRVATENSLISDW-----------RTREKELVPVRYQQEFLSVLW 502

Query: 554 AGVEMRDVHPTHYGRI 569
             V+ R +HP HY  I
Sbjct: 503 EQVDFRSIHPLHYFSI 518


>gi|289152658|gb|ADC84225.1| RNA polymerase beta subunit [Prevotella nigrescens ATCC 33563]
          Length = 222

 Score =  387 bits (994), Expect = e-105,   Method: Composition-based stats.
 Identities = 136/278 (48%), Positives = 166/278 (59%), Gaps = 58/278 (20%)

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K+AGRHGNKGIVS+++  EDMPFL+DG  VD+VLNP+GVPSRMN+GQIFE  LG A   L
Sbjct: 1    KLAGRHGNKGIVSKVVRVEDMPFLEDGRAVDLVLNPMGVPSRMNLGQIFEAILGAAGYKL 60

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-- 1206
            G K  + I D     D+                                   K+G+P   
Sbjct: 61   GVKFSTPIFDGAKLEDLKEWTD------------------------------KAGLPPMC 90

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            ST ++DG                           TGE FD+P TVG  Y LKL HMV DK
Sbjct: 91   STYIYDGE--------------------------TGERFDQPATVGITYFLKLGHMVEDK 124

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT 1326
            ++ARS G YSL+TQQPLGGK+  GGQR GEMEVW I+A+GA++VLQE+LTIKSDDVVGR+
Sbjct: 125  MHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAIEAFGASHVLQEILTIKSDDVVGRS 184

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            + YESIV G      G PES NVL+ E++ LGLSI L+
Sbjct: 185  KAYESIVKGEPMPMPGIPESLNVLLHELRGLGLSIKLD 222


>gi|186885841|gb|ACC93328.1| RNA polymerase beta subunit [Dicoma sp. JLP-2008]
 gi|186885843|gb|ACC93329.1| RNA polymerase beta subunit [Dicoma capensis]
          Length = 1024

 Score =  387 bits (994), Expect = e-105,   Method: Composition-based stats.
 Identities = 140/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMGVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETDKTEKIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 274/927 (29%), Positives = 462/927 (49%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LRSPGIYY 92

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 93   QSELNDNGISVYTGTIISDWGGRL------ELEIDRKAKIWVRVSRQQKLSIL------- 139

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 140  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 181

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P++   +   D
Sbjct: 182  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPENNTFLLPRD 241

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 242  ILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 301

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302  HNWIPTPQNLVNSTPLTGTYKTFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 361

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 362  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSKEAR 421

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E+  A  SGA  +A+  G
Sbjct: 482  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEAQAALDSGALAIAEHEG 541

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 542  KIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCIHQKPRVPQGKCIKKGQI 593

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  -NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 710

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G      ++T L++P G  G V+DVR       D+ +++  +     ++ +I++
Sbjct: 711  LLRTILGMGVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETDKTEKIRVYILQKREIKV 770

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 771  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGG 830

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 831  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPF 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 891  EQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  166 bits (420), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKAKIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|197131670|gb|ACH47353.1| RNA polymerase beta subunit [Erodium chrysanthum]
          Length = 1200

 Score =  387 bits (994), Expect = e-105,   Method: Composition-based stats.
 Identities = 125/307 (40%), Positives = 181/307 (58%), Gaps = 42/307 (13%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V++  KR I+ GDK+AGRHGNKGI+SRILP +DMP+L+DG P+D+V NPLGVPSRM
Sbjct: 932  EMIRVYILQKREIKVGDKVAGRHGNKGIISRILPRQDMPYLQDGKPIDMVFNPLGVPSRM 991

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A V L +  +    D +   + S    F E    +             
Sbjct: 992  NVGQIFECSLGLAGVLLERHYRVGPFDERYEQEASRKLVFSELHEASKQTGNPW------ 1045

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S L+DG TG+ F+ PV V
Sbjct: 1046 ------------------VFE---------------PEYPGKSRLFDGRTGDAFEEPVLV 1072

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RSTG Y+ +TQQP+ G++ RGGQR+GEMEVW ++ +G A++L
Sbjct: 1073 GQPYILKLIHQVDDKIHGRSTGPYTSLTQQPVKGRARRGGQRVGEMEVWALEGFGVAHIL 1132

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD +  R +V+++++ G +  +  G PESF VLV+E+++L L ++  L + + 
Sbjct: 1133 QEMLTYKSDHLRTRAQVFDTVIIGGEMPKAEGAPESFRVLVRELRSLALELNHFLVSEKN 1192

Query: 1369 KNSAKME 1375
                + E
Sbjct: 1193 FQMNRKE 1199



 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 227/660 (34%), Positives = 359/660 (54%), Gaps = 19/660 (2%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           G I+           L  +    +    IL  V          +  V      ++ A+L+
Sbjct: 301 GRIWARVSRKQKISILLLLSAMGLNLSEILENVCYPEIFLSFLDKKVRKIIGSKETAILE 360

Query: 377 IYRVMRPG----DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            Y+         D              FF   + +L  +GR  MN RLNL        + 
Sbjct: 361 FYQQFVGVGVGGDPVLSDSLCEELQKKFF-RQRCELGRIGRRNMNRRLNLAISQKNTFLL 419

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             DI+A    L++++ G GT+DD+++L N+R+RSV ++ ++Q  L L+R+E+ +K  I  
Sbjct: 420 PRDILAATDHLIEMKFGMGTLDDMNHLKNKRIRSVADLFQDQLGLALIRLEKVVKRSIRG 479

Query: 493 VDIDSVM--PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           V    ++  PQ+L+ + P  +    FF    LSQ+ +  N L++I H R+ S LG GG+ 
Sbjct: 480 VIKGELLLRPQNLVTSTPFQTTYESFFGLHPLSQVLDETNPLTQIVHGRKWSFLGPGGLT 539

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE-TPYRKVCDGK 609
              A   +RD+HP++YGRIC  +TSEG N+GL  SL   AR+ A+G +E   Y      K
Sbjct: 540 GRTASFRIRDIHPSYYGRICTIDTSEGINVGLSGSLAIHARIGAFGSLESPFYEISKKSK 599

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               ++ LS+  +E   I   NS         E++V  R   E + +  E++      P 
Sbjct: 600 GAPQILSLSSRRDEYCMIGTGNSLALNGVFQEEQIVSARYRQEFLTIAWEQVHLRSIFPF 659

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q  SI ASLIPF+E++D+NR LM  NMQRQAV L ++E   VGTG+E  VA  SG  ++ 
Sbjct: 660 QYFSIGASLIPFIEHNDANRALMSSNMQRQAVALSRSEKCIVGTGLEGQVALDSGVPLLT 719

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           + AG +  +   +I++                  L+ +QRSN+NTC++Q+P V+ G  ++
Sbjct: 720 EHAGKILSIHTDKILLAGN--------GTTLSIPLVMYQRSNKNTCIHQKPQVRRGKCMK 771

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           +  I+ADG ST  G+LALG+N+LVA+MPW GYNFED++LISER+V ED+ TS HI ++E+
Sbjct: 772 KGQILADGASTVGGELALGKNLLVAYMPWEGYNFEDAVLISERLVYEDILTSFHIRKYEI 831

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
               T  GPE+IT+ IP++  + L+N+D+ G++ +G+ V  GD+LVGK++P+      PE
Sbjct: 832 EIHVTSQGPEKITQKIPHLRPDLLRNLDKNGVVILGSWVEGGDVLVGKLSPQLA--QAPE 889

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +L+ A+FG +    R+T L++P G  G VVDVR    +   +  R   +++ +I++  +
Sbjct: 890 ARLVDALFGTQIATSRETCLKLPRGGRGRVVDVRWIRSNPEREMIRVYILQKREIKVGDK 949



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 59/282 (20%), Positives = 117/282 (41%), Gaps = 20/282 (7%)

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
           +   P     D ++  LTY+  L ++  LI               +++Q I +G++PLM 
Sbjct: 192 KLVEPLIKERDAIYECLTYSSELYVSAGLIWKRTGYS--------MQKQRILIGNIPLMN 243

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             G F++ G+ R+VV+Q+ +SPGI++   + +    G  +Y   II D G  +++E D K
Sbjct: 244 SLGIFIVNGMYRMVVNQILQSPGIYY---RSKLDYKGFCVYTGTIISDWGGRLELEIDRK 300

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGA 258
             I  R+ R++K+ +   L A+G++  EIL    YP+I  S         + + +  +  
Sbjct: 301 GRIWARVSRKQKISILLLLSAMGLNLSEILENVCYPEIFLSFLDKKVRKIIGSKETAILE 360

Query: 259 KVSSSLVDIDTGEQVIESG--KKLTSGLLKSLKEKGVKFLGITSDCLC------GLYVAE 310
                +     G+ V+     ++L     +   E G       +  L         ++  
Sbjct: 361 FYQQFVGVGVGGDPVLSDSLCEELQKKFFRQRCELGRIGRRNMNRRLNLAISQKNTFLLP 420

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
             +   T  +      +     +  + +  IR +  L+ D +
Sbjct: 421 RDILAATDHLIEMKFGMGTLDDMNHLKNKRIRSVADLFQDQL 462


>gi|186885925|gb|ACC93370.1| RNA polymerase beta subunit [Pasaccardoa grantii]
          Length = 1024

 Score =  387 bits (994), Expect = e-105,   Method: Composition-based stats.
 Identities = 140/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMGVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQNSKTDETDKTEKIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  SI+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGSIIFGETI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 274/927 (29%), Positives = 461/927 (49%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LRSPGIYY 92

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 93   QSELNDNGISVYTGTIISDWGGRL------ELEIDRKAKIWVRVSRQQKLSIL------- 139

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 140  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 181

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 182  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 241

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 242  ILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 301

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302  HNWIPTPQNLVNSTPLTGTYKTFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 361

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 362  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSNETR 421

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 541

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 542  KIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCIHQKPRVQQGKCIKKGQI 593

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594  LAYGAATVDGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  -NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 710

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G      ++T L++P G  G V+DVR       D+ +++  +     ++ +I++
Sbjct: 711  LLRTILGMGVYTSKETCLKLPIGGRGRVIDVRWVQNSKTDETDKTEKIRVYILQKREIKV 770

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 771  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGG 830

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 831  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPF 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 891  EQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLRKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ RSPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILRSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKAKIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|332148588|dbj|BAK20143.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|332148594|dbj|BAK20146.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|332148596|dbj|BAK20147.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|332148600|dbj|BAK20149.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 324

 Score =  387 bits (993), Expect = e-105,   Method: Composition-based stats.
 Identities = 145/379 (38%), Positives = 196/379 (51%), Gaps = 62/379 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 2    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVNDGD 59

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 60   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 119

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 120  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 179

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 180  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 233

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 234  ----------------------TVLYDG--------------------------RTGEPF 245

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 246  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 305

Query: 1306 GAAYVLQEMLTIKSDDVVG 1324
            GAAY LQE+LT+KSDDVVG
Sbjct: 306  GAAYTLQEILTVKSDDVVG 324



 Score =  114 bits (286), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 80/118 (67%), Positives = 97/118 (82%)

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+
Sbjct: 1   VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDL 60

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 118


>gi|308161806|gb|EFO64240.1| DNA-directed RNA polymerase subunit B' [Giardia lamblia P15]
          Length = 1239

 Score =  387 bits (993), Expect = e-105,   Method: Composition-based stats.
 Identities = 209/1424 (14%), Positives = 431/1424 (30%), Gaps = 307/1424 (21%)

Query: 31   EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYE---------- 80
            +    S++H L + I    R N  L  A               +E V  +          
Sbjct: 36   KHHLDSFNHLLDVTIPAIIRENSLLVVA-------KHPQFHLRIEKVDVKQVSQGSSKLA 88

Query: 81   -------FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                            +C  R++TYA P+ I +R    +       K         I +G
Sbjct: 89   SSSAGSGVG---LTPHECRQRNMTYAAPITIDVRCKASNKSSVQYYK--------DICIG 137

Query: 134  DLPLMT------------------------KDGTFVIKGIQRIVV--SQLHRSPGIHFDH 167
             +P+M                           G F+++G ++ ++   Q+  +  +    
Sbjct: 138  YIPIMLRSNRCILTNKSRKQQAFLQECPDDPGGYFIVRGAEKSILLAEQMTMNRIV---- 193

Query: 168  DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI--IHVRIDRRRKVPVTSFLMALGMDS 225
              GR +     +       ++     + + +K    IH + +++  +P+ +   A+G   
Sbjct: 194  -VGRNADGNVEVTVASNTTERKSRCAVLYKNKKFYLIHNKFNKKP-IPIVTVFKAMGF-- 249

Query: 226  EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
                             D     L   D +    +S S+ +    +              
Sbjct: 250  ---------------VNDVTVLSLIGTDQLFLDYMSLSVQECSNDKIYT----------- 283

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY--IEAGDVIDEKSLEEIFHSEIRD 343
               +E+ +K+L    D +          N  T  +    +A        L     S I  
Sbjct: 284  ---QEQALKYLA---DRIIVRTYTNANSNFSTSPVATAAKASVESARDCLAHFVLSHIPV 337

Query: 344  IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +  L +     +   + +     +      +         G  +T     S        S
Sbjct: 338  VERLNLQQAAQHVLPQTSTPAGSSVSAGADM---------GTATTGGSGRSGSANAAAKS 388

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNR 462
                 +++G   +    +L        + K   +A +     L + G    D  D +GN+
Sbjct: 389  ALGSGASMGASTIGSATSLTNAARFNWLPKAVYLATMIRRAILFDFGVIKGDSKDFVGNK 448

Query: 463  RVRSVGEMLKNQYRLGLLRM-ERSIKERISSVDIDSVMPQDLINAKPVV----SAVCEFF 517
            ++ + G++L+  +      +    +++  + +  D     DL N   V     S +   F
Sbjct: 449  KIETAGDLLELIFDDAFKTLLAHMVRKVDNILRSDRNRGTDLTNYDIVSLVDSSIITRAF 508

Query: 518  CSS----------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
             ++                 +SQ+   ++ +S +    RLS+       +A      R +
Sbjct: 509  NTAISTGNWKIEKIGVDRVGVSQVLSRLSYISALGQVTRLSST----FDKAMKSSGPRML 564

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            + +  G  CP++T EG ++G+V +L+  AR++     ++  + +           +S   
Sbjct: 565  NFSQMGIFCPSDTPEGESVGIVKNLSIMARISKDESTDSISKLL-----------MSIGV 613

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+       ++     G         +    + ++    I       K  +S   S    
Sbjct: 614  EDLASCWSGDTFSLGYGYMVFLNGTIKGVIAKDMLKGFIITLRTFRRKGYISYLTSFHFN 673

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             E+             R  + +   +       +E ++       +     G VE +D  
Sbjct: 674  DEHQAVYINCDSGRACRPLLIVENGKLMLTRNDIELLMDNQ-KCFVDLIYEGKVEYLDVN 732

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +  D    T                     Q    ++        ++   P   
Sbjct: 733  EAKNAYIAMDTKDLTP--------------------QHTHCEIESYTLLGYVVGLIPYPH 772

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                         +    G     ++  ++                              
Sbjct: 773  HNQSP-----RNCYQCSMGKQASGAIAFNQ------------------------------ 797

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                    E  +  +D                    +   G   +   +     +    +
Sbjct: 798  ----LERFETAMFLLD---------YPQRPLTSTKILKLTGYERLPAGQNATVCVMSYSS 844

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE---RSISVEREQIELLARDKDDEQVIL 978
             D+ D  +   + +        I+     + N    +S+   ++ +    +D   +    
Sbjct: 845  FDIEDALILNRNAIDRGFGRCSIYRSISTELNSIGSKSVDGIKDILLGPPKDHLKQYEGY 904

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                   L  +  G +  +G     K   +++                  E ++  +E+ 
Sbjct: 905  HAIEDDGLCAV--GAHLKTGDIVINKGRHITNIPGLSDGTEATVSLIKSPESLKSPLETT 962

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                          + +K+     GD        ++KV     R  + GDK + RHG KG
Sbjct: 963  T-------------YIDKVLVTTNGD-----GNMLIKVLTREPRRPEVGDKFSSRHGQKG 1004

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +   I+P  D+PF   G   D+++NP G PSRM V ++ E     +    G++       
Sbjct: 1005 VCGLIVPQSDLPFTSQGIVPDLIMNPHGYPSRMTVAKLLELLSNKSGCFRGEQTDGTCFR 1064

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             K +                                                        
Sbjct: 1065 TKTDETFL--------------------------------------------------AE 1074

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   LR+A    SG+ +LY GLTG+     +  G IY  KL HMV DK+++R TG  +++
Sbjct: 1075 LYDSLRVAGFSYSGKDVLYSGLTGDVIPVYIFNGPIYYQKLKHMVKDKIHSRGTGPITML 1134

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD-------VVG-----RT 1326
            T+QP  G+   GG R+GEME  C  +YGA+ +L E   + SDD         G     + 
Sbjct: 1135 TRQPTEGRRVHGGLRMGEMERDCAISYGASALLLERFMLSSDDFLAYVCETCGLFSYEKN 1194

Query: 1327 RVYESIVA--GNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                      G D  +   P +  ++++E+ ++G+ + ++   +
Sbjct: 1195 GALWCPTCQSGKDVVKIRIPYAAKLMIQELISMGVLVRMQLEDS 1238


>gi|139390340|ref|YP_001122938.1| RNA polymerase beta subunit [Aethionema cordifolium]
 gi|158513599|sp|A4QJA7|RPOB_AETCO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286133|dbj|BAF49762.1| RNA polymerase beta subunit [Aethionema cordifolium]
          Length = 1073

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/498 (30%), Positives = 236/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L      +  +  D  L     +S  +V 
Sbjct: 629  VRRGKCIKKGQILADGAATVG-GELALGKNILVGYMPWEGYNFEDAVL-----ISECLVY 682

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 683  GNIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 740

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 741  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKG-- 798

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 799  --GSSYNP---EKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 853

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 854  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 913

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 914  TANPW------------------------VFE---------------PEYPGKSRIFDGR 934

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 935  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 994

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L
Sbjct: 995  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLAL 1054

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1055 DLNHFLVSEKNFQINRKE 1072



 Score =  357 bits (915), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 248/757 (32%), Positives = 405/757 (53%), Gaps = 42/757 (5%)

Query: 369  DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             +++A+L+ Y+      GD              FF   + +L  +GR  +N RLNL  P 
Sbjct: 218  SKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRIGRRNINWRLNLTIPQ 276

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L R+E  +
Sbjct: 277  NNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLQNKRIRSVADLLQDQFGLALARLENVV 336

Query: 487  KERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            K  I       +   PQ+L+ A P+ +    FF    LSQ+ +  N L++I H R+LS L
Sbjct: 337  KGTICGAIKHKLIPTPQNLVTATPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYL 396

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            G GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ +
Sbjct: 397  GPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGDWGSLESPFYE 456

Query: 605  VCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            + +      +   +LS  ++E   IA  NS     G   E+ V  R   E + +  E++ 
Sbjct: 457  LFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVH 516

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                 P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  
Sbjct: 517  LRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVALD 576

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SG   +A++ G +   D  +I++     +            L+++QRSN+NTC++Q+P V
Sbjct: 577  SGVPAIAEQEGKILYTDTKKIILSGYGDNTLG-------IPLIRYQRSNKNTCMHQKPQV 629

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            + G  +++  I+ADG +T  G+LALG+N+LV +MPW GYNFED++LISE +V  +++TS 
Sbjct: 630  RRGKCIKKGQILADGAATVGGELALGKNILVGYMPWEGYNFEDAVLISECLVYGNIYTSF 689

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+ 
Sbjct: 690  HIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQV 749

Query: 903  ESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERS 956
                +  PE++LLRAI G +    ++T L++P G  G V+DVR   + G      +  R 
Sbjct: 750  AKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSYNPEKIRV 809

Query: 957  ISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
               ++ +I++  +      ++ +I        +  +  G+            + ++   I
Sbjct: 810  YISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQI 869

Query: 1014 SEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNK 1056
             E           + ++ A  DE+ ++            E+ K          E   K++
Sbjct: 870  FECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSR 929

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 930  IFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 964



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEEVSKFPKIEDIDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKQIGSKE 220


>gi|114107125|ref|YP_740109.1| RNA polymerase beta subunit [Daucus carota]
 gi|122233840|sp|Q0G9X0|RPOB_DAUCA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|113200900|gb|ABI32416.1| RNA polymerase beta subunit [Daucus carota]
          Length = 1070

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   +++        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVLAIAEHEGKVIYTDTDKILLSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G  ++          +   + +L A    
Sbjct: 604  LNIPLVMYQRSNKNTCMHQKPQVQRGKYIKKGQ-ILAYGAATIGGELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E + R+    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTREIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T       S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKR----VGSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEA 1218
            +   + S    F E    +                            +TP VF+      
Sbjct: 890  RYEQEASRKLVFSELYQASKQT-------------------------ATPWVFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G   
Sbjct: 970  TQQPLRGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGAI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++    + +T    + E
Sbjct: 1030 PNPEDAPESFRLLVRELRSLALELNHFFVSEKTFKIKRKE 1069



 Score =  349 bits (895), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 229/686 (33%), Positives = 375/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   K +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQKCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RL LD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV +++
Sbjct: 262 GRRNMNRRLRLDISQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLI 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L+R+E  I+  I       ++P  Q+L+ + P+ S    FF    LSQ+ +  
Sbjct: 322 QDQLGLALVRLENMIRGTIGGALRHKLIPSPQNLVTSTPLTSTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++   G +E+P+ ++        ++YLS  ++E   +A  N      G   E++V  R 
Sbjct: 442 AKIGRGGSLESPFYEISQRSKGARMLYLSPGKDEYYMVAAGNPLALNQGLQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G V   D         +  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVLAIAEHEGKVIYTD--------TDKILLSGNGDTLNIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPQVQRGKYIKKGQILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +TR+IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTREIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            G+ILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGEILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 H----GIDKNERSISVEREQIELLAR 969
                   +  R   +++ +I++  +
Sbjct: 794 RVGSSYNPETIRVYILQKREIKVGDK 819



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFM----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+    I+  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSEFYISAGLIW---------KTSRDMQEQTIFLGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|139390144|ref|YP_001123717.1| RNA polymerase beta subunit [Lobularia maritima]
 gi|158513985|sp|A4QLI6|RPOB_LOBMA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286921|dbj|BAF50541.1| RNA polymerase beta subunit [Lobularia maritima]
          Length = 1072

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 157/579 (27%), Positives = 252/579 (43%), Gaps = 58/579 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIILSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   ++  + +L A    
Sbjct: 606  FSIPLIMYQRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVG-GELSLGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S ++V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISESLVYDDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EKIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYQASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLATTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKM 1374
             +    PESF +LV+E+++L L ++  L + +     + 
Sbjct: 1032 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRK 1070



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 229/688 (33%), Positives = 380/688 (55%), Gaps = 23/688 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYKQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQLGLALARLENVVKGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442 ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502 RYRQEFLTIAWEEVHLRSILPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              VGTG+E  VA  SG   +A+  G +   D  +I++                  L+ +
Sbjct: 562 KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIILSGN--------GDTFSIPLIMY 613

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++
Sbjct: 614 QRSNKNTCMHQKPQVRRGKYIKKGQILADGAATVGGELSLGKNILVAYMPWEGYNFEDAV 673

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE +V +D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674 LISESLVYDDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888 VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734 VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946 NRHG----IDKNERSISVEREQIELLAR 969
            + G      +  R    ++ +I++  +
Sbjct: 794 QKKGGSSYNPEKIRVYISQKREIKVGDK 821



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|332148592|dbj|BAK20145.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148602|dbj|BAK20150.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148606|dbj|BAK20152.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 324

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 145/379 (38%), Positives = 196/379 (51%), Gaps = 62/379 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 2    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 59

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 60   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 119

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 120  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 179

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 180  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 233

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 234  ----------------------TVLYDG--------------------------RTGEPF 245

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 246  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 305

Query: 1306 GAAYVLQEMLTIKSDDVVG 1324
            GAAY LQE+LT+KSDDVVG
Sbjct: 306  GAAYTLQEILTVKSDDVVG 324



 Score =  115 bits (288), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 79/118 (66%), Positives = 96/118 (81%)

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV  GD+
Sbjct: 1   VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDL 60

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 118


>gi|324120636|dbj|BAJ78709.1| RNA polymerase II second largest subunit [Zorotypus sp. 154-1]
          Length = 1173

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 251  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 310

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 311  EQNVALNFIGSRGARPGV---TREKRIKYAKEILQKEMLPHVGVSDFCETKK---AYFLG 364

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 365  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRG 424

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 425  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 484

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 485  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 540

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 541  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRREMDIIVSEVS 600

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++ + +L   +  M +            V +G+ 
Sbjct: 601  MIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKRHIDMLKDREYNNYGWQVLVSSGLV 660

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 661  EYIDTLEEETVMIA---------------MSPDDLRQDKEYAYCTTY------------- 692

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 693  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 729

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 730  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 760

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 761  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFF---RSYKDAE 817

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   +Y +L +   I  G           K+  L    
Sbjct: 818  SKRIGDQE-EQFEKPNRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTMTLH--- 873

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    ++    +    R        Q    +     +
Sbjct: 874  -----------------ETDDELEGTTKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYK 916

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 917  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMT 976

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 977  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 997

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 998  --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1043

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1044 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1103

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1104 ERLFEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQIRLPYAAKLLFQEL 1161

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1162 MAMNIAPRLM 1171



 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 137/981 (13%), Positives = 287/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  +   I       +L+F       P 
Sbjct: 37  LVRQQLDSFDEFIQMSVQRIVEDSPQIELQAEAQHTTGEIETP-PRYLLKFEQIYLSKPT 95

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 96  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVRDGEDPI-----EAQHQKTFIGKI 150

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 151 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 210

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 211 -----GKYAYKSEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 261

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 262 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGS 321

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 322 RGARPGVTREKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 377

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 378 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLELAIKTKI 437

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 438 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 497

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 498 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 554

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 555 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRREMDIIVSEVSMIRDIRDREIRIYT 614

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L         ++     E           +  V Y+  +EEE
Sbjct: 615 DAGRICRPLLIVENGSLLLKKR-----HIDMLKDREYNNYGWQVLVSSGLVEYIDTLEEE 669

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 670 TVMIAMSPDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 714

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 715 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 741

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 742 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 769

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 770 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKRIGDQEEQFE 829

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 830 KPNRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTMTLHETDDELEGTT------ 883

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 884 -KRFTKRDASTFLRNSETGIV 903


>gi|332148578|dbj|BAK20138.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 328

 Score =  387 bits (993), Expect = e-104,   Method: Composition-based stats.
 Identities = 145/379 (38%), Positives = 196/379 (51%), Gaps = 62/379 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 6    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 63

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 64   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 123

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 124  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 183

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 184  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 237

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 238  ----------------------TVLYDG--------------------------RTGEPF 249

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 250  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 309

Query: 1306 GAAYVLQEMLTIKSDDVVG 1324
            GAAY LQE+LT+KSDDVVG
Sbjct: 310  GAAYTLQEILTVKSDDVVG 328



 Score =  120 bits (301), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 82/122 (67%), Positives = 100/122 (81%)

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV 
Sbjct: 1   SERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVK 60

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR  
Sbjct: 61  DGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRED 120

Query: 950 ID 951
            D
Sbjct: 121 GD 122


>gi|186885837|gb|ACC93326.1| RNA polymerase beta subunit [Cyclolepis genistoides]
          Length = 1028

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 138/396 (34%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGTGVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKK----RGSSSKP---ERIHVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  S + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGSTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 260/806 (32%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIAIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGQT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCLKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI--FNRHGIDKNER--SISVEREQIELL 967
            LLR I G      ++T L++P G  G V+DVR     R    K ER     +++ +I++ 
Sbjct: 716  LLRTILGTGVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIHVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 57/184 (30%), Positives = 95/184 (51%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TNRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|218192606|gb|EEC75033.1| hypothetical protein OsI_11126 [Oryza sativa Indica Group]
          Length = 870

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 162/573 (28%), Positives = 256/573 (44%), Gaps = 67/573 (11%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--------GPEEITRDI 865
            + +P+  +N  +  L+S  M  +       I E E     T          G       +
Sbjct: 353  SLIPFIEHNDANRALMSSNMQRQADSRVSVIAEREGKIISTNSHKILLSSSGKTISIPLV 412

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +        + +   +  G  +  G+IL       G   +   + +L A    +  ++ 
Sbjct: 413  THRRSNKNTCMHQKPRVPRGKSIKKGEILAEGAATVG-GELALGKNVLVAYMPWEGYNLE 471

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  L     V   +       ++ I  +  S     +  + +   ++     LDRN   +
Sbjct: 472  DAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHLLRNLDRNGVVK 531

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
            L     G    +G     K T   +   S    +   +     E       SLK+     
Sbjct: 532  L-----GSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLKLPIGGR 586

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
              +++        K    D +      +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP
Sbjct: 587  GRVID-------VKWIQRDPLGI----MVRVYILQKREIKVGDKVAGRHGNKGIISKILP 635

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE+ LG A   L K  +    D +   + 
Sbjct: 636  RQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDERYEQEA 695

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S    F E    +                               VF+             
Sbjct: 696  SRKLVFSELYEASKQTKNPW------------------------VFE------------- 718

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
               +  G+S ++DG TG+PF++PV +G  Y+LKL H V +K++ RSTG YSLVTQQP+ G
Sbjct: 719  --PEYPGKSRIFDGRTGDPFEQPVLIGKSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRG 776

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTP 1344
            ++ +GGQR+GEMEVW ++ +G A++LQE+LT KSD ++ R  +  + + G         P
Sbjct: 777  RAKQGGQRIGEMEVWALEGFGVAHILQEILTYKSDHLIARQEILNATIWGKRVPNHEDPP 836

Query: 1345 ESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            ESF VLV+E+++L L ++  L + +     + E
Sbjct: 837  ESFRVLVRELRSLALELNHFLVSQKNFQVNREE 869



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 216/639 (33%), Positives = 347/639 (54%), Gaps = 47/639 (7%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 11  NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 69

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 70  CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 129

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV------CEFF 517
           +RSV ++L++Q+ L L R++ ++++ I  V I    P       P  +++        FF
Sbjct: 130 IRSVADLLQDQFGLALGRLQHAVQKTIRRVLIRQSKPTPQTLVTPTSTSILLITTYETFF 189

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 190 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 249

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 250 INVGLTGSLAIHARIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 309

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 310 SLNRCIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 369

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQA                      S  +++A+R G +   ++ +I++        
Sbjct: 370 SNMQRQA---------------------DSRVSVIAEREGKIISTNSHKILL-------- 400

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++ +I+A+G +T  G+LALG+N+LV
Sbjct: 401 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGEILAEGAATVGGELALGKNVLV 460

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYN ED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 461 AYMPWEGYNLEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 520

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 521 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 580

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +    R   +++ +I++  +
Sbjct: 581 LPIGGRGRVIDVKWIQRDPLGIMVRVYILQKREIKVGDK 619


>gi|186885831|gb|ACC93323.1| RNA polymerase beta subunit [Chuquiraga spinosa]
          Length = 1024

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 137/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 674  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 733

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G +  P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 734  GGRGRVIDVRWVQKKG----GSNYNP---ERIHVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +   +                           VF+          
Sbjct: 847  QEASRKLVFSELYEASKQTSNPW------------------------VFE---------- 872

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RSTG Y+LVTQQP
Sbjct: 873  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSTGHYALVTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 928  LRGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 254/806 (31%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             ++           L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 121  RVWARVSRNQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKENAILEF 180

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 181  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 239

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L++++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 240  ILAAADRLIEIKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGALR 299

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+   P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 300  HKLIATPQNLVTLTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 359

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 360  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 419

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   +++V  R   E + +  E++        Q  S
Sbjct: 420  MLYLSPGRDEYYMVAAGNSLALNQGIQEKQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 479

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG   +A+  G
Sbjct: 480  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGTLAIAEHEG 539

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V  G  +++   
Sbjct: 540  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVGRGKCIKKGQS 591

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 592  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQPHV 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 711

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELL 967
            LLRAI G +    ++T L++P G  G V+DVR   + G      +      +++ +I++ 
Sbjct: 712  LLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSNYNPERIHVYILQKREIKVG 771

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 772  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 831

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 832  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTSNPWVFEPEYPGKSRIFDGRTGDPFE 891

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 892  QPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 54/180 (30%), Positives = 91/180 (50%), Gaps = 16/180 (8%)

Query: 76  FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           FV  Y+   P     D +++ LTY+  L ++  LI                KEQ+I++G+
Sbjct: 9   FVETYQLVEPLIQEGDAVYKSLTYSSELYVSAGLIWKTSR-----------KEQTIFIGN 57

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S    Y   II D G  +++
Sbjct: 58  IPLMNSLGAFIVNGIYRIVINQILQSPGIYYQSELDHNGISA---YIGTIISDWGGRLEL 114

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  +  R+ R +K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 115 EIDRKVRVWARVSRNQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKE 174


>gi|324120598|dbj|BAJ78690.1| RNA polymerase II second largest subunit [Pedetontus unimaculatus]
          Length = 1176

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 162/1007 (16%), Positives = 309/1007 (30%), Gaps = 209/1007 (20%)

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ G
Sbjct: 333  EKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYG 389

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFC 518
            N+R+   G +L   +R     + + ++               +  I  K +   +     
Sbjct: 390  NKRLDLAGPLLAFLFRGMFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLA 449

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+   +   S ++H RR+++     + R     + R +H T 
Sbjct: 450  TGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTL 505

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEE 623
            +G ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +  
Sbjct: 506  WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT 565

Query: 624  NRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
              ++      +  D       L   R   + I+     I D  D   +          P 
Sbjct: 566  KIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPL 625

Query: 682  LENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQV 738
            L  ++   +L   +  M ++           V +  +E +        ++A         
Sbjct: 626  LIVENGRLLLKKRHVDMLKEREYNNYGWQDLVASSAVEYIDTLEEETVMIA--------- 676

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                  +   +   D   +    Y                                   P
Sbjct: 677  ------MSLDDLRQDKEYAYCTTY-----------------------------THCEIHP 701

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +  LG       +  + +P+  +N          M  + +   ++I  F           
Sbjct: 702  AMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF----------- 741

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                            ++    +  V        +    +       +      + AI  
Sbjct: 742  ----------------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSVVAIAC 785

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S V            +   +++R    E    E   +        +
Sbjct: 786  YTGYNQEDSVIMNASAVERGFFRSVFMRAYKDSESKRVGDQE----EQFEKPTRQTCQGM 841

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
               IY +L +   I  G           K+  L                     +    +
Sbjct: 842  RNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITL--------------------PENDDEL 881

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E    +Y    +    R        Q    +     +  K+ V   R  Q GDK A RHG
Sbjct: 882  EGTTRRYTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHG 941

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG        EDMPF  +G   DI++NP  +PSRM +G + E   G      G+     
Sbjct: 942  QKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIECLQGKVSSNKGEIGD-- 999

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP  D  +
Sbjct: 1000 ---------------------------------------------------ATPFNDAVN 1008

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + I+++L+       G  ++++G +G   +  V +G  Y  +L HMV DK+++R+ G  
Sbjct: 1009 VQKISALLQEYGYQLRGNEVMFNGHSGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPV 1068

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG------- 1324
             ++ +QP+ G++  GG R GEME  C  A+GAA  L+E L   SD     V         
Sbjct: 1069 QILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERLFEVSDPYRIHVCNFCGLIAI 1128

Query: 1325 ---RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               R   +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1129 ANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1173



 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 146/981 (14%), Positives = 291/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKTVVKDGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  Y   I       ++        + V +  R     +K              
Sbjct: 213 -----GKYAYKSEIR----SCLEHSSRPTSTLWVNMLARGGQSVKKSSVGQKIIAILPYI 263

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGG 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
              +  +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGAKPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    +S +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L         V+     E       D   ++ V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGRLLLKKR-----HVDMLKEREYNNYGWQDLVASSAVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSLDDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y               Q+PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+ +  ++          EE   
Sbjct: 772 ELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFMRAYKDSESKRVGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E    R    
Sbjct: 832 KPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITLPENDDELEGTTRR---- 887

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
                 RD S  + +  +G V
Sbjct: 888 ---YTKRDASTFLRNSETGIV 905


>gi|290489652|gb|ADD31210.1| RNA polymerase beta subunit protein [Trochodendron aralioides]
          Length = 1070

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/579 (27%), Positives = 252/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVSAIAEHEGKIIYTDTDKIILSGNGET 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          +++   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  RNIPLVIYERSNKNTCMNQKPQVQRGKYIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITSEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  R   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DRNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQISTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFPELYEASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTVP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  + + +     + E
Sbjct: 1031 NPEDAPESFRLLVRELRSLALELNHFIVSEKNFQINRKE 1069



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 252/776 (32%), Positives = 408/776 (52%), Gaps = 41/776 (5%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
             V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197  NVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256  CELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
            SV ++L++Q+ L L+R+E +++  IS      +   PQ+L+ + P+ +    FF    LS
Sbjct: 316  SVADLLQDQFGLALIRLENAVRGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+ +  N+L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376  QVLDRTNALTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   E+
Sbjct: 436  GSLAIHARIGHWGSLESPFYEISERSKEVRMIYLSPSRDEYYTVAAGNSLALNQGIQEEQ 495

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496  VVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             ++E   VGTG+E   A  SG + +A+  G +   D  +I++       +          
Sbjct: 556  SRSEKCIVGTGLERQAALDSGVSAIAEHEGKIIYTDTDKIILSGNGETRNI--------P 607

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+ ++RSN+NTC+NQ+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 608  LVIYERSNKNTCMNQKPQVQRGKYIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNS 667

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ 
Sbjct: 668  EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITSEIPHLEAHLLRNLDRNGIVM 727

Query: 884  VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728  LGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQISTSKETCLKLPIGGRGRVID 787

Query: 942  VRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
            VR   + G         R    ++ +I++  +      ++ +I        +  +  G  
Sbjct: 788  VRWIQKKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTP 847

Query: 995  AVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VES 1037
                       + ++   I E           + ++ A  DE+ ++            E+
Sbjct: 848  VDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFPELYEA 907

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 908  SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 961



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|332148572|dbj|BAK20135.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148574|dbj|BAK20136.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148580|dbj|BAK20139.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 329

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 145/379 (38%), Positives = 196/379 (51%), Gaps = 62/379 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 7    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 64

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 65   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 124

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 125  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 184

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 185  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 238

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 239  ----------------------TVLYDG--------------------------RTGEPF 250

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 251  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 310

Query: 1306 GAAYVLQEMLTIKSDDVVG 1324
            GAAY LQE+LT+KSDDVVG
Sbjct: 311  GAAYTLQEILTVKSDDVVG 329



 Score =  121 bits (304), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 82/123 (66%), Positives = 101/123 (82%)

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV
Sbjct: 1   MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEV 60

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR 
Sbjct: 61  KDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRE 120

Query: 949 GID 951
             D
Sbjct: 121 DGD 123


>gi|290489638|gb|ADD31203.1| RNA polymerase beta subunit protein [Gunnera manicata]
          Length = 1070

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 160/579 (27%), Positives = 252/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVSAIAEHEGKIIYTDTDKIILSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +T  + LL A    
Sbjct: 604  LSIPLVMYERSNKNTCMHQKPQVQRGNCIKKGQILADGAATVG-GELTLGKNLLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAYLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKK----RGSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYEASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 249/830 (30%), Positives = 421/830 (50%), Gaps = 43/830 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  ++    
Sbjct: 143  ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNACYPE 202

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLNDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P +   +   DI+A    L+ +R G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNMNQRLNLDIPQNNTFLLPRDILAAADHLIGMRFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442  ARIGHWGSLESPFYEISERSKKVRMLYLSPSRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502  RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E   A  SG + +A+  G +   D         +  +           L+ ++R
Sbjct: 562  IVGTGLERQAALDSGVSAIAEHEGKIIYTD--------TDKIILSGNGDTLSIPLVMYER 613

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN+NTC++Q+P V+ G+ +++  I+ADG +T  G+L LG+N+LVA+MPW GYN ED++LI
Sbjct: 614  SNKNTCMHQKPQVQRGNCIKKGQILADGAATVGGELTLGKNLLVAYMPWEGYNSEDAVLI 673

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674  SERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAYLLRNLDKNGIVMLGSWVE 733

Query: 890  PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734  TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948  H----GIDKNERSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                    +  R    ++ +I++  +      ++ +I        +  +  G+       
Sbjct: 794  KRGSSYNPEMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFN 853

Query: 1001 GFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQYE 1043
                 + ++   I E           + ++ A  DE+ ++            E+ K    
Sbjct: 854  PLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTAN 913

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                  E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  PWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 961



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 111/236 (47%), Gaps = 25/236 (10%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS- 78
            E+  IP   ++Q   +  F+          ++GL         I         + FV  
Sbjct: 7   EEMSTIPGFSQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVET 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  +TY+  L ++  LI          K+ +D++EQ+I++G++P+M
Sbjct: 57  YQLVEPLIKERDAVYESITYSSELYVSAGLIW---------KTSRDMQEQTIFLGNIPIM 107

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D 
Sbjct: 108 NSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDR 164

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWCFPLSAAD 253
           K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 165 KARIWARVSRKQKISILVLSSAMGSNLREILDNACYPEIFLSFLNDKEKKKIGSKE 220


>gi|68164795|ref|YP_247591.1| RNA polymerase beta subunit [Cucumis sativus]
 gi|67511390|emb|CAJ00750.1| RNA polymerase beta chain [Cucumis sativus]
          Length = 1071

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 206/396 (52%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L++G PVD+V NPLGVPSRMNVGQIFE  LG A   L +  + +  D +  
Sbjct: 833  ILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIVPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +    +                          VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTAKSPW-----------------------VFE---------- 919

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 920  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 974

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 975  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1034

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             TPESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 DTPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1070



 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/634 (36%), Positives = 362/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  +N RLNLD P++   + + DI+A    L+ L+ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNLNQRLNLDIPENNTFLLQRDILAAADHLIGLKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTFESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +ETP+ ++ +      ++YLS   +E   +A  NS     G   
Sbjct: 434 LIGSLAIHARIGHWGSLETPFYEISERSKKVRMLYLSPSRDEYYMVATGNSLALNPGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQIVPARYRQEFLTIEWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  VA+ SG A +A+  G +   D         +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQVARDSGVAAIAEHGGKIIYTD--------TDKIIFSGNGYTRR 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC+ Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMQQKSQVHQGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER++ ED++TS HI ++E+    T  GPE IT +IP++    L N+D+ GI
Sbjct: 666 NFEDAVLISERLIYEDIYTSFHIRKYEIQTHVTSHGPERITNEIPHLEARLLCNLDKNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKKGGSSYNPEIIRVYISQKREIKVGDK 819



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPAFNQIQFEGFCRFI----------DHGLTEELSKFPKIEDTDQEIEFQLFVETYKLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTRRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ G+ RIV+SQ+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGLYRIVISQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|186885809|gb|ACC93312.1| RNA polymerase beta subunit [Barnadesia spinosa]
          Length = 1024

 Score =  386 bits (992), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 580  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 633

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 634  EDIYTSFHIRKYEIQPHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 692

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 693  VGKLTPQMVKESSYAPEDRLLRAILGIQVFTSKETCLKLPIGGRGRVIDVRWVQKK---- 748

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 749  RGSSYNP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 805

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 806  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 865

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 866  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 886

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RSTG Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 887  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSTGHYALVTQQPLRGRAKQGGQRVGEMEVWA 946

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 947  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1006

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1007 LNHFLVSEKTFQINRKE 1023



 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 258/806 (32%), Positives = 416/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 121  RIWARVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKENAILEF 180

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 181  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 239

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L++++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 240  ILAAADRLIEMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGALR 299

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+   P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 300  HKLIATPQNLVTLTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 359

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 360  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 419

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 420  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 479

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 480  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 539

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 540  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 591

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 592  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQPHV 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 711

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH----GIDKNERSISVEREQIELL 967
            LLRAI G +    ++T L++P G  G V+DVR   +        +  R   +++ +I++ 
Sbjct: 712  LLRAILGIQVFTSKETCLKLPIGGRGRVIDVRWVQKKRGSSYNPERIRVYILQKREIKVG 771

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 772  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 831

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 832  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 891

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 892  QPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 55/180 (30%), Positives = 92/180 (51%), Gaps = 16/180 (8%)

Query: 76  FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           FV  Y+   P     D +++ LTY+  L ++  LI                KEQ+I++G+
Sbjct: 9   FVETYQLVEPLIKEGDAVYKSLTYSSELYVSAGLIWKTSR-----------KEQTIFIGN 57

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S    Y   II D G  +++
Sbjct: 58  IPLMNSLGAFIVNGIYRIVINQILQSPGIYYQSELDHNGISA---YIGTIISDWGGRLEL 114

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  I  R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 115 EIDRKVRIWARVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKE 174


>gi|215254185|gb|ACJ64097.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 383

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 241/383 (62%), Positives = 297/383 (77%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+
Sbjct: 61  LSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LK
Sbjct: 121 TARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLK 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           A+ P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L 
Sbjct: 181 ADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLT 240

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFED
Sbjct: 241 KYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFED 300

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           S+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +G
Sbjct: 301 SILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIG 360

Query: 886 AEVNPGDILVGKITPKGESPMTP 908
           AEV  GDILVGK+TPKGE+ +TP
Sbjct: 361 AEVKGGDILVGKVTPKGETQLTP 383


>gi|324120654|dbj|BAJ78718.1| RNA polymerase II second largest subunit [Uroleucon
            nigrotuberculatum]
          Length = 1177

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 166/1093 (15%), Positives = 334/1093 (30%), Gaps = 212/1093 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 254  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 313

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 314  EQNVALNFIGSRGARPGV---TKDKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 367

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 368  YMVHRLLLASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 427

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 428  KDFNLDLAIKTKLITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 487

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 488  S----PIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 543

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   + ++    ++      +  D       L   R   + I+    
Sbjct: 544  EFLEEWSMENLEEIAPSAIVDATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVS 603

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   ++   ++           V  G+ 
Sbjct: 604  IIRDIRDREIRIYTDAGRICRPLLIVENGKLLLKKRHIDSLKERDYNNYGWQVLVSNGVV 663

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   +   +    Y             
Sbjct: 664  EYIDTLEEETTMIA---------------MSPDDLRQEKEYAYCTTY------------- 695

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 696  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 732

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 733  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 763

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 764  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFF---RSYKDSE 820

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E+  +        +   IY +L +   I  G           K+  L    
Sbjct: 821  SKRIGDQE-EVFEKPNRQSCQGMRNAIYDKLDDDGIISPGLRVSGDDVIIGKTMTL---- 875

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                               +  +E    +Y         R        Q    +     +
Sbjct: 876  ----------------PDNEDELEGTTKKYSKRDCSTFLRNSETGLIDQVLLTLNSEGYK 919

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V  +R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 920  FCKIRVRSERIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 979

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 980  IGHLIECLQGKVSANKGEIGD--------------------------------------- 1000

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G +G   +  V +G
Sbjct: 1001 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGFSGRKINAQVFLG 1046

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  A+GAA  L+
Sbjct: 1047 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLR 1106

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     +            R   +E    G        +   P +  +L +E+
Sbjct: 1107 ERLFEVSDPYRIHICNFCGLIAIANLRNNTFEC--KGCKNKTQISQVKLPYAAKLLFQEL 1164

Query: 1355 QALGLSIDLENSR 1367
             ++ ++  L  + 
Sbjct: 1165 MSMNIAPRLMVTN 1177



 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 141/987 (14%), Positives = 293/987 (29%), Gaps = 196/987 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  + +   I        ++F       P 
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPQIELQAESQHTHGEI-DTPTKYQIKFEQIYLSKPT 98

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRL-IVFDVDEFTGAKSIKDIKEQSIYMGD 134
                        ++   R+LTY+ PL + +   ++ D +E    +  K       ++G 
Sbjct: 99  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVIKDGEEPVVTQHSKS------FIGK 152

Query: 135 LPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDK 169
           +P+M                           G F+I G ++++++Q   +   ++    K
Sbjct: 153 IPIMLRSTYCLLFGLNDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMK 212

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR------------- 208
                 GK  +   I       ++        + V         I +             
Sbjct: 213 D-----GKYAFKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPY 263

Query: 209 -RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
            ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + + 
Sbjct: 264 IKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIG 323

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEI 320
                  +   K++     + L+++ +  +G++           G  V   ++    G  
Sbjct: 324 SRGARPGVTKDKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRR 381

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            ++  D    K L+            L+ + +          +        D       +
Sbjct: 382 ELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLD-------L 434

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                + T  +  S+    + D  K   +  G  ++  RL   +      R         
Sbjct: 435 AIKTKLITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDG 494

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +                ++KN   +  + +       +  ++  S+
Sbjct: 495 KLAKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSM 551

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
              + I    +V A   F     +    +    +  +   RR   +    V+  R   + 
Sbjct: 552 ENLEEIAPSAIVDATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDR 611

Query: 559 RDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
                T  GRIC P    E   + L         +++    +              V Y+
Sbjct: 612 EIRIYTDAGRICRPLLIVENGKLLLKKR-----HIDSLKERDYNNYGWQVLVSNGVVEYI 666

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +EEE   IA +   L                 E+           +  P  ++ + AS
Sbjct: 667 DTLEEETTMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCAS 711

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 712 IIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------- 744

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            + + V  Y                +PLV               
Sbjct: 745 --------------RMDTLAHVLYYP--------------HKPLV----------TTRSM 766

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G N +VA + + GYN EDS++++   V    F S+    ++         
Sbjct: 767 EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFFRSYKDSESKRIGD 826

Query: 858 PEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            EE+           +       +D+ GII  G  V+  D+++GK     ++    E   
Sbjct: 827 QEEVFEKPNRQSCQGMRNAIYDKLDDDGIISPGLRVSGDDVIIGKTMTLPDNEDELEGTT 886

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  K    RD S  + +  +G +
Sbjct: 887 -------KKYSKRDCSTFLRNSETGLI 906


>gi|209360643|gb|ACI42992.1| RNA polymerase beta subunit [Mycoplasma synoviae]
          Length = 903

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 150/462 (32%), Positives = 211/462 (45%), Gaps = 67/462 (14%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V+
Sbjct: 509  IVKVGDHVKEGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVL 567

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+      +   S S E      +          LD     ++   +   + + G  
Sbjct: 568  -TSIYIEEQTIQFRISKSSEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRI 626

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V++          +L           
Sbjct: 627  SPKGEENPSQE--EKLLNAIFNQRPQNYKDTSLKVKNGHNGTVIHVEVLSR--------- 675

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  ++KV++A KR I+ GDKMAGRHGNKG++S ILP EDMP L+DGTP+DI
Sbjct: 676  ENGDILEDGLDSIIKVYIAQKRKIKVGDKMAGRHGNKGVISIILPEEDMPHLEDGTPLDI 735

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D      I  L            
Sbjct: 736  MLNPQGVPSRMNIGQVLEMHLGMAAKKLGTKFVTPSFDGIKKETIEDLLQEAN------- 788

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + ++ D +
Sbjct: 789  ------------------------------------------LDKSG-----KQVVIDSI 801

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE FD P++VG IYMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 802  TGEKFDNPISVGVIYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFGEMETW 861

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
             +++YGA+ +LQE+LT KSDD+  R  VY+++V  +     G
Sbjct: 862  ALESYGASNILQEILTYKSDDIYSRNLVYKALVNDSAIPNPG 903



 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/714 (36%), Positives = 407/714 (57%), Gaps = 38/714 (5%)

Query: 267 IDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGET 317
           I  G+++ E  K+ L SG+L   K   +   G           + +   Y+A+ +V+   
Sbjct: 12  IRKGDRISEESKRSLLSGMLFDKKRYNLSKTGRYMLNNKLSLVERITNTYLAQKVVSHLG 71

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
                + G  +  +  +EI  S           S  +   I N    D           +
Sbjct: 72  NT--FDVGTYVTYEIAKEIQESFEAKAK--DNKSNLHLEKIPNINPDDVYYKINKDNKSL 127

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +    +  +    +M   +                    +  D      H+   DII
Sbjct: 128 NKRINIARIKIWPTKRAMDANVTPSE---------------VIGNDPKATEEHLLLSDII 172

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A I   ++L  G G  DD D+L N+R+ SVGE+L+ + R+ LL++E++ +ER+ + + D 
Sbjct: 173 AAISYYLNLTVGIGQDDDPDSLMNKRIVSVGELLEGELRIALLKLEKATRERMGAKEPDK 232

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +  +++ N K + + +  FF +S+L+Q  + +N L+ I++ RR+++LG GG+ R  A  E
Sbjct: 233 ITAKNVTNNKLITNQMKTFFNTSKLAQFMDQINPLAEISNKRRVTSLGPGGLNRDTAQFE 292

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVY 616
           +RDVH THYGRICP ET EG NIGL+ +   ++ VN  GF++TPY KV DG V  NDV Y
Sbjct: 293 VRDVHSTHYGRICPIETPEGPNIGLILNYAIYSTVNELGFLQTPYYKVNDGVVDYNDVRY 352

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L++ EE     AQ++  +++     +E +  +     I+   + IDF++ S KQ+VS+AA
Sbjct: 353 LTSYEEIGYAFAQSSVHVNDKNEIIDEQITIKKDYNYIIGSPKDIDFLEVSSKQIVSVAA 412

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           + IPFLEN+D+NR LMG NMQRQAVPL++AEAP V TG+E+ +AK S   IVA   G V 
Sbjct: 413 AAIPFLENNDANRALMGSNMQRQAVPLIEAEAPLVATGIEADIAKFSSYNIVANNDGEVI 472

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VD  +I +R        +   +D Y L  F++SNQ T + Q+P+VKVGD V+  D++ D
Sbjct: 473 YVDGTKIQVR--------TAKKIDTYNLKNFEKSNQGTIIQQKPIVKVGDHVKEGDLLVD 524

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G S   G++ALG+N+LV F  W+GYNFED+++I+ER+V +DV TSI+IEE  +  R +K 
Sbjct: 525 GSSFKDGEMALGKNLLVGFTTWNGYNFEDAIIINERLVKDDVLTSIYIEEQTIQFRISKS 584

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             + +TRDIPNVS+  ++N+DE GII VG+EV  GD+LVG+I+PKGE   + EEKLL AI
Sbjct: 585 SEDIMTRDIPNVSKYSMRNLDEFGIIKVGSEVVAGDVLVGRISPKGEENPSQEEKLLNAI 644

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-SVEREQIELLAR 969
           F ++  + +DTSL+V +G +GTV+ V + +R   D  E  + S+ +  I    +
Sbjct: 645 FNQRPQNYKDTSLKVKNGHNGTVIHVEVLSRENGDILEDGLDSIIKVYIAQKRK 698


>gi|159106854|ref|YP_001531273.1| RNA polymerase beta subunit [Lolium perenne]
 gi|182676568|sp|A8Y9G0|RPOB_LOLPR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|158934388|emb|CAO85966.1| RNA polymerase beta subunit [Lolium perenne]
          Length = 1076

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1069

Query: 1370 NSAKME 1375
               + E
Sbjct: 1070 QVTREE 1075



 Score =  350 bits (898), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 233/700 (33%), Positives = 381/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    +    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTSSFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKV----CDGKVTNDVVYLSAMEEENRYIAQANS 632
            N+GL  SL   AR+N  +G IE+P+ ++       K +  VVYLS   +E   IA  NS
Sbjct: 434 INVGLTGSLAIHARINHLWGSIESPFYEISAEKAKKKKSRQVVYLSPNRDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  SG +++A+R G +   D+ +I++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSGVSVIAEREGKILSTDSHKILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+N C++Q+  V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTLSIPLVNHRRSNKNNCMHQKSRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++   
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEAH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D  G++ +G+ V   DILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDRNGVVRLGSWVETSDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 825



 Score =  167 bits (424), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+ L         I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQALAEELNKFPAIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|324120650|dbj|BAJ78716.1| RNA polymerase II second largest subunit [Anacanthocoris striicornis]
          Length = 1175

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 168/1090 (15%), Positives = 333/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKERRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   +++  ++           V +G+ 
Sbjct: 603  IIRDIRDREIRIYTDAGRICRPLLIVENGQLLLKKRHIENLKERDYNNYGWQVLVSSGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               I   +   D   +    Y             
Sbjct: 663  EYIDTLEEETTMIA---------------ISPEDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  F                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F  +   +++R
Sbjct: 763  RSMEYLRFRELPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKR 822

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
                E    E   +        +   IY +L +   I  G           K+  L    
Sbjct: 823  VGDQE----EQFEKPMRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITL---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    ++    +    R        Q    +     +
Sbjct: 875  ----------------PENDDELEGTTKKFTKRDASTFLRNSETGIVDQVMLTLNAEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLSPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSANKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNLCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             ++ ++  L 
Sbjct: 1164 MSMNIAPRLM 1173



 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 137/980 (13%), Positives = 284/980 (28%), Gaps = 182/980 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +            +L+F       P  
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEVETPPRYLLKFEQIYLSKPTH 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +   +    E        + + Q  ++G +P
Sbjct: 99  WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTIIREGEEPI-----ESQHQKSFIGKIP 153

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 154 IMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 212

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR--------------R 209
               GK  Y   I       ++        + V         I +              +
Sbjct: 213 ----GKFAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYIK 264

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           +++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 265 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGAR 324

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                +   +++     + L+++ +  +G++  C          +      + + A    
Sbjct: 325 GARPGVTKERRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGRR 380

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +    +   +  +    P+L          +   +     K           +     + 
Sbjct: 381 ELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKII 440

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   +  G  ++  RL   +      R          +     
Sbjct: 441 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQ 500

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +                ++KN   +  + +       +  ++  S+   + I 
Sbjct: 501 LHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIA 557

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +  A   F     +    +    +  +   RR   +    V+  R   +      T 
Sbjct: 558 PSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIYTD 617

Query: 566 YGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            GRIC P    E   + L         +      +           +  V Y+  +EEE 
Sbjct: 618 AGRICRPLLIVENGQLLLKKR-----HIENLKERDYNNYGWQVLVSSGVVEYIDTLEEET 672

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA +   L                 ++           +  P  ++ + AS+IPF ++
Sbjct: 673 TMIAISPEDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPDH 717

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           + S R      M +QA+ +                                         
Sbjct: 718 NQSPRNTYQSAMGKQAMGVYITNFHV---------------------------------- 743

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                     + + V  Y                +PLV                     +
Sbjct: 744 -------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFRE 772

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           L  G N +VA   + GYN EDS++++   V    F S+    ++          EE    
Sbjct: 773 LPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFFRSYKDAESKRVGDQEEQFEK 832

Query: 865 -----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                   +       +D+ GII  G  V+  D+++GK     E+    E          
Sbjct: 833 PMRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENDDELEGTT------- 885

Query: 920 KAVDVRDTSLRVPSGVSGTV 939
           K    RD S  + +  +G V
Sbjct: 886 KKFTKRDASTFLRNSETGIV 905


>gi|186885909|gb|ACC93362.1| RNA polymerase beta subunit [Mutisia retrorsa]
          Length = 1028

 Score =  386 bits (991), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRQGKCIKKGQ-ILAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRQGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|114329648|ref|YP_740467.1| RNA polymerase beta subunit [Citrus sinensis]
 gi|122166191|sp|Q09MI6|RPOB_CITSI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|113952614|gb|ABI49012.1| RNA polymerase beta subunit [Citrus sinensis]
          Length = 1070

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/580 (27%), Positives = 249/580 (42%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLVRSEKCIVGTGLEPQVALDSGVPAIAEHEGKIIYTDIDKIVLSGNGNT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G +L       G   +   + +L A    
Sbjct: 604  YSIPLIMYQRSNKNTCMHQKPQVGRGKCIKKGQVLADGAATVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  ++   I+    I K E    V  +  E +  +    E  +L
Sbjct: 663  EGYNFEDAVL-----ISERLIYRDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEARLL 717

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T  ++   S  P  +  +  +  +        L
Sbjct: 718  RN--LDKNGIVMLGSWVETGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTSKETCL 775

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P     + V+++ KR I+ GDK+AGRHGNKG
Sbjct: 776  KLPIGGRGRVIDVRWVQKKG----GSSYNP---ETICVYISQKREIKVGDKVAGRHGNKG 828

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IVS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 829  IVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLNRHYRIAPFD 888

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 889  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF+ PV +G  Y+LKL H V DKV+ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEEPVLIGKPYILKLIHQVDDKVHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 970  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGETI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +LV+E+++L L ++  + + +     K E
Sbjct: 1030 PNPEDAPESFRLLVRELRSLALELNHFVVSEKNFQINKKE 1069



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 233/668 (34%), Positives = 376/668 (56%), Gaps = 17/668 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E G   + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELGHNGISVYTGTIISDWGGRFELEIDRKARIWARVSRKQKVSILVLSAAMGSNLREILE 196

Query: 350 DSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++      +K K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NICYPEIFLSFLTNKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFFH-QR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNL+ P +   +   D++A +  L+ L+ G GT+DD+++L N+R+R
Sbjct: 256 CELGKIGRRNMNQRLNLNIPQNNTFLLPRDVLAAVDHLIGLKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLS 523
           SV  +L++Q+ L L+R+E  I+  I       +MP  Q+L+ + P+ +    FF    LS
Sbjct: 316 SVANLLQDQFGLALVRLENVIRGTICGAIRHKLMPTPQNLVTSTPLTTTYDSFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     GS  E+
Sbjct: 436 GSLAIHARIGYWGSLESPFYEIFEKSKKVRMLYLSPSRDEYYMVAAGNSLALNQGSPEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 VVPTRYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +++E   VGTG+E  VA  SG   +A+  G +   D  +IV+                  
Sbjct: 556 VRSEKCIVGTGLEPQVALDSGVPAIAEHEGKIIYTDIDKIVLSGN--------GNTYSIP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  +++  ++ADG +T  G+LALG+N+LVA+MPW GYNF
Sbjct: 608 LIMYQRSNKNTCMHQKPQVGRGKCIKKGQVLADGAATVGGELALGKNILVAYMPWEGYNF 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER++  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 668 EDAVLISERLIYRDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEARLLRNLDKNGIVM 727

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728 LGSWVETGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942 VRIFNRHG 949
           VR   + G
Sbjct: 788 VRWVQKKG 795



 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++   TY+  L ++  LI          KS  D++EQ+I++G++PLM   GT
Sbjct: 62  PLLKERDAVYESFTYSSELYVSAGLIW---------KSRGDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  + G   +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELGHNGIS---VYTGTIISDWGGRFELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++KV +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKVSILVLSAAMGSNLREILENICYPEIFLSFLTNKEKKKIGSKE 220


>gi|227438078|gb|ACP30538.1| RNA polymerase beta subunit [Mycoplasma sp. Phocoena C-269]
          Length = 670

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 245/493 (49%), Positives = 348/493 (70%), Gaps = 2/493 (0%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ SVGE+L+NQ  +G  +ME++ +ER+SS +++ + P+++ N K V + + +FF S
Sbjct: 2   MNKRIVSVGELLQNQLNVGFAKMEKNTRERLSSKEVEKITPKNITNNKLVYNQIKQFFNS 61

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ +++ RRL++LG GG+ R  A  E+RDVHPTHYGRICP ET EG N
Sbjct: 62  SKLSQFMDQINPLAELSNKRRLTSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPN 121

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +L S+ARVN +GF+ETPY  V DG V  ++  YL+A EE      Q+++ + ED 
Sbjct: 122 IGLILNLASYARVNDFGFLETPYFAVEDGVVDYSEPCYLTAAEETGHKFVQSSTPVGEDN 181

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              ++ V  R  G+ + +  E++DFID S KQ+ S+AAS IPFLENDD+NR LMG NMQR
Sbjct: 182 RLIDDFVIARYNGDYMKIAAEEVDFIDVSSKQMTSLAASCIPFLENDDANRALMGSNMQR 241

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL AEAP VGTG+ES +AK S + I   + G V  VD  +I I++ E   +     
Sbjct: 242 QAVPLLIAEAPLVGTGIESEIAKFSFSNITCDKEGEVVYVDGNQIHIKTEEDKPNR-KGH 300

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           VD Y L  F+RSNQ + +NQ P+VKVGD + +  IIADGPS   G+L+LG+N++VAF  W
Sbjct: 301 VDKYYLRVFERSNQGSIINQNPVVKVGDHIEKGQIIADGPSCSNGELSLGKNVVVAFSTW 360

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           HGYN+ED+++ISER+V +DV+TSIHIEE  +  R++K G + +T DIPN S    +++DE
Sbjct: 361 HGYNYEDAVIISERLVKDDVYTSIHIEEHTLQFRNSKAGNDVLTTDIPNASNNSKRHLDE 420

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ VG+EV PGDILVG+++PKG+   +PEEKLL AIF +K  +++DTSL+V +G SGT
Sbjct: 421 NGIVTVGSEVEPGDILVGRVSPKGDENPSPEEKLLSAIFSKKTPNLKDTSLKVKNGHSGT 480

Query: 939 VVDVRIFNRHGID 951
           ++   I +R   D
Sbjct: 481 IIAREIISRENGD 493



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 111/327 (33%), Positives = 147/327 (44%), Gaps = 71/327 (21%)

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +   DE  I+         +IL G+ +  G +       L S + S+   +         
Sbjct: 415  KRHLDENGIVTVGSEVEPGDILVGRVSPKGDENPSPEEKLLSAIFSKKTPNLKDT----- 469

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                          +            +I   + GD +  GV  +VKV+VA KR I+ GD
Sbjct: 470  ------------SLKVKNGHSGTIIAREIISRENGDILEDGVEMIVKVWVAQKRKIKVGD 517

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++S +LP EDMP+++DGTPVDI+LNP GVPSRMN+GQ+ E HLG A   L
Sbjct: 518  KMAGRHGNKGVISIVLPVEDMPYMEDGTPVDIMLNPQGVPSRMNIGQVLELHLGMAARSL 577

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G K  + + D      I+                                          
Sbjct: 578  GVKFATQVFDGINKDQITDCLEEAGLPKNGKMKLI------------------------- 612

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
               DG                            GEPFD+ ++VG +YMLKL+HMV DK++
Sbjct: 613  ---DGIT--------------------------GEPFDKEISVGVMYMLKLSHMVDDKMH 643

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 644  ARSIGPYSLITQQPLGGKSQNGGQRFG 670


>gi|186885911|gb|ACC93363.1| RNA polymerase beta subunit [Nassauvia pygmaea]
          Length = 1028

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/562 (28%), Positives = 247/562 (43%), Gaps = 56/562 (9%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +    ++        I         +  G       I          +
Sbjct: 519  CIVGTGLERQAALDSGALAIAEHEGKIIYTDTDKILLSGNGDTLSIPLIMYQRSNKNTCM 578

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G  ++          +   + +L A    +  +  D  L     +S
Sbjct: 579  HQKPQVRRGKCIKKGQ-ILAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVL-----IS 632

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    
Sbjct: 633  ERLVYEDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVE 691

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T       S  P  +  +  +           LK+       +++ R+  K
Sbjct: 692  TGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK 751

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 752  K----RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 804

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E   
Sbjct: 805  PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYE 864

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 865  ASKQTANPW------------------------VFE---------------PEYPGKSRI 885

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GE
Sbjct: 886  FDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGE 945

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 946  MEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELR 1005

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +T    + E
Sbjct: 1006 SLALELNHFLVSEKTFQINRKE 1027



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 415/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+D++++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADHLIGIKFGMGTLDNMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS  ++E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGKDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|118430292|ref|YP_874726.1| RNA polymerase beta subunit [Agrostis stolonifera]
 gi|125987640|sp|A1E9Z8|RPOB_AGRST RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|118201201|gb|ABK79570.1| RNA polymerase beta subunit [Agrostis stolonifera]
          Length = 1076

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1069

Query: 1370 NSAKME 1375
               + E
Sbjct: 1070 QINREE 1075



 Score =  351 bits (900), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 236/700 (33%), Positives = 383/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKV----CDGKVTNDVVYLSAMEEENRYIAQANS 632
            N+GL  SL   AR++  +G IE+P+ ++       K    VVYLS   +E   IA  NS
Sbjct: 434 INVGLTGSLAIHARIDHLWGSIESPFYEISAEKAKKKKARQVVYLSPNRDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIVSTDSHKILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTISIPLVNHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E 
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 825



 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+ L         I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQALAEELDKFPIIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|290790839|gb|ADD63095.1| RNA polymerase beta subunit [Microlaena stipoides]
          Length = 1067

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 247/579 (42%), Gaps = 59/579 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +  R+          I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILLSSSGKT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 + +        + +   +  G  V  G IL       G   +   + +L A    
Sbjct: 604  ISIPLVTHRRSNKNTCMHQKLRVPRGKSVKKGQILAEGAATVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     V   +       ++ I  +  S     +  + +   ++     LD
Sbjct: 663  EGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHLLRNLD 722

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN   +L     G    +G     K T   +   S    +   +     E       SLK
Sbjct: 723  RNGVVKL-----GSWVETGDILVGKLTPQVTSESSYIAEAGLLRAIFGLEVSTSKETSLK 777

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++        K    D +      +V+V++  KR I+ GDK+AGRHGNKGI
Sbjct: 778  LSIGGRGRVID-------VKWIQRDPLDI----MVRVYILQKREIKVGDKVAGRHGNKGI 826

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE+ LG A   L K  +    D 
Sbjct: 827  ISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLKKHYRIAPFDE 886

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 887  RYEQEASRKLVFSELYEASKQTKNPW------------------------VFE------- 915

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V +K++ RSTG YSLVT
Sbjct: 916  --------PEYPGKSRIFDGRTGDPFEQPVLIGKSYILKLIHQVDEKIHGRSTGPYSLVT 967

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQP+ G++ +GGQR+GEMEVW ++ +G A++LQE+LT KSD ++ R  +  + + G    
Sbjct: 968  QQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQEILTYKSDHLIARQEILNATIWGKRVP 1027

Query: 1340 E-TGTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF VLV+E+++L L ++  L + +     + E
Sbjct: 1028 NHEDPPESFRVLVRELRSLALELNHFLVSEKNFQVNREE 1066



 Score =  347 bits (890), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 234/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 127 ELDHKGIFIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 186

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 187 NVSYPEIFLSFLNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 245

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 246 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 305

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 306 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 365

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 366 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 425

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 426 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 485

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 486 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 545

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 546 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL-------- 597

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+  V  G  V++  I+A+G +T  G+LALG+N+LV
Sbjct: 598 SSSGKTISIPLVTHRRSNKNTCMHQKLRVPRGKSVKKGQILAEGAATVGGELALGKNILV 657

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 658 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 717

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 718 LRNLDRNGVVKLGSWVETGDILVGKLTPQVTSESSYIAEAGLLRAIFGLEVSTSKETSLK 777

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +  G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 778 LSIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 816



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 103/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 54  PSIKEKDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 102

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +       G  +Y   II D G   ++  D K+ I 
Sbjct: 103 FIINGIYRIVINQILLSPGIYYRSELDHK---GIFIYTGTIISDWGGRSELAIDKKERIW 159

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 160 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFLNAKEKKRIESKEKAI 213


>gi|158518563|sp|Q3V542|RPOB_ACOCL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1071

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/563 (28%), Positives = 257/563 (45%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++      ++E     I+ +  +++   +  G       +          
Sbjct: 563  IVGTGLERQAALDSGVSAIAECEGKIIYTDTHKIVL--SGHGDTISIPLVMYQRSNKNTC 620

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +   +  G  +  G IL       G   +   + +L A    +  +  D  L     +
Sbjct: 621  MHQNPQVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----I 674

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E +  +    +  L RN+  R   +  G   
Sbjct: 675  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNL-DRNGIVALGSWV 733

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  +++  S  P  +  +  +  +        LK+       +++ R+  
Sbjct: 734  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 793

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG
Sbjct: 794  KKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDG 846

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 847  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELY 906

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 907  EASKQTANPW------------------------VFE---------------PEYPGKSR 927

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 928  IFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 987

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+
Sbjct: 988  EMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVREL 1047

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1048 RSLALELNHFLVSEKNFQINRKE 1070



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 260/831 (31%), Positives = 429/831 (51%), Gaps = 44/831 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTSTIISDWGGRSELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLNDREKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNMNRRLNLDIPQSNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +++  I       +   PQ+L+++  + +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALVRLENAVRGTICGAIRHKLILTPQNLVSSTSLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-LDEDGSFTEELVFCR 648
            AR+  +G IE+P+ +V        +V+LS   +E   +A  NS  L+  G   E++V  R
Sbjct: 442  ARIGHWGSIESPFYEVYQRSKETKMVFLSPSRDEYYTVATGNSLALNRGGIQEEQIVPAR 501

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E 
Sbjct: 502  YRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEK 561

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +Q
Sbjct: 562  CIVGTGLERQAALDSGVSAIAECEGKIIYTDTHKIVL--------SGHGDTISIPLVMYQ 613

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 614  RSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 673

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V
Sbjct: 674  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNLDRNGIVALGSWV 733

Query: 889  NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              GDILVGK+TP+  +  +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 734  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 793

Query: 947  RHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------Q 993
            + G         R    ++ +I++  +   +   + I+ + +  + M  L          
Sbjct: 794  KKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVF 853

Query: 994  NAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQY 1042
            N +  P       +    L ++     + ++ A  DE+ ++            E+ K   
Sbjct: 854  NPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTA 913

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 914  NPWVFEPEYPGKSRIFDGRTGDPFEQPVL-IGKSYIL-KLIHQVDDKIHGR 962



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL   F     I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLMEEFHKFPKIEDTDQEIEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKSRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDREKKKIGSKE 220


>gi|186885827|gb|ACC93321.1| RNA polymerase beta subunit [Chimantaea humilis]
 gi|186885959|gb|ACC93387.1| RNA polymerase beta subunit [Stomatochaeta condensata]
          Length = 1026

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 157/562 (27%), Positives = 245/562 (43%), Gaps = 58/562 (10%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +    ++        I         +  G       +          I
Sbjct: 519  CIVGTGLERQAALDSGALAIAEHEGKIIYTDTDKILLSGNGDTLSIPLVMYQRSNKNTCI 578

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G  ++          +   + +L A    +  +  D  L     +S
Sbjct: 579  HQKPQVRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----IS 632

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    
Sbjct: 633  ERLVYEDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVE 691

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T       S  P  +  +  +           LK+       +++ R+  K
Sbjct: 692  TGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK 751

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                             ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 752  KR---------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 802

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E   
Sbjct: 803  PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYE 862

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 863  ASKQTANPW------------------------VFE---------------PEYPGKSRI 883

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQPL G++ +GGQR+GE
Sbjct: 884  FDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQPLKGRAKQGGQRVGE 943

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 944  MEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELR 1003

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +T    + E
Sbjct: 1004 SLALELNHFLVSEKTFQINRKE 1025



 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 260/804 (32%), Positives = 413/804 (51%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCIHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885973|gb|ACC93394.1| RNA polymerase beta subunit [Wunderlichia mirabilis]
          Length = 1026

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 152/497 (30%), Positives = 234/497 (47%), Gaps = 58/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPEKVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKR--- 753

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 754  ------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 807

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 808  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 867

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 868  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 888

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 889  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQPLKGRAKQGGQRVGEMEVWA 948

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 949  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1008

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1009 LNHFLVSEKTFQINRKE 1025



 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 260/804 (32%), Positives = 420/804 (52%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L++
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEL 184

Query: 378  YRVMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            ++      GD +      +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  HQQFAWVEGDPAFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +G     
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISEGSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D  +I++                  L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTDTDKILLSVN--------GDTLSIPLVMYQRSNKNTCIHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE++T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885839|gb|ACC93327.1| RNA polymerase beta subunit [Dasyphyllum reticulatum]
          Length = 1024

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 580  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 633

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 634  EDIYTSFHIRKYEIQPHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 692

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 693  VGKLTPQMVKESSYAPEDRLLRAILGIQVFTSKETCLKLPIGGRGRVIDVRWVQKKG--- 749

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 750  -GSSYNP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 805

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 806  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 865

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 866  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 886

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RSTG Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 887  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSTGHYALVTQQPLRGRAKQGGQRVGEMEVWA 946

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 947  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPEDAPESFRLLVRELRSLALE 1006

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1007 LNHFLVSEKTFQINRKE 1023



 Score =  370 bits (950), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 258/806 (32%), Positives = 416/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L  +    +    IL  V          N     K   +++A+ + 
Sbjct: 121  RIWARVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKENAIFEF 180

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 181  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 239

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L++++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 240  ILAAADRLIEMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGALR 299

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+   P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 300  HKLIATPQNLVTLTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 359

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 360  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 419

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 420  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 479

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 480  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 539

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 540  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 591

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 592  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQPHV 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 711

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELL 967
            LLRAI G +    ++T L++P G  G V+DVR   + G      +  R   +++ +I++ 
Sbjct: 712  LLRAILGIQVFTSKETCLKLPIGGRGRVIDVRWVQKKGGSSYNPERIRVYILQKREIKVG 771

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 772  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 831

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 832  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 891

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 892  QPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 55/180 (30%), Positives = 92/180 (51%), Gaps = 16/180 (8%)

Query: 76  FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           FV  Y+   P     D +++ LTY+  L ++  LI                KEQ+I++G+
Sbjct: 9   FVETYQLVEPLIKEGDAVYKSLTYSSELYVSAGLIWKTSR-----------KEQTIFIGN 57

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S    Y   II D G  +++
Sbjct: 58  IPLMNSLGAFIVNGIYRIVINQILQSPGIYYQSELDHNGISA---YIGTIISDWGGRLEL 114

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  I  R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 115 EIDRKVRIWARVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKE 174


>gi|156065749|ref|XP_001598796.1| hypothetical protein SS1G_00885 [Sclerotinia sclerotiorum 1980]
 gi|154691744|gb|EDN91482.1| hypothetical protein SS1G_00885 [Sclerotinia sclerotiorum 1980 UF-70]
          Length = 1267

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 182/1069 (17%), Positives = 345/1069 (32%), Gaps = 167/1069 (15%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +       S+        
Sbjct: 315  VSDEDILNHICYDRNDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGNGTSL---TRDKR 371

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             KY    + +  +      +  +  +      +  ++  L+    G+   DD D+ G +R
Sbjct: 372  IKYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHKLLQCALGRRETDDRDHFGKKR 428

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    R+   +    +    +         + +  + + +     +  
Sbjct: 429  LDLAGPLLAKLFRNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGN 488

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 489  WGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 544

Query: 569  ICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L    +  V         +    + +V  +   L A      +
Sbjct: 545  VCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVF 604

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN- 684
            +      +  D +   + V        I      I +  D   K          P L   
Sbjct: 605  VNGVWVGVHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVID 664

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA--AIVAKRAGIVEQVDAIR 742
            +D +    G  +  +       +   + + M+       G          G+VE +DA  
Sbjct: 665  NDPDSPNKGNLVLNKDHIRRLEDDQSLPSNMDKDEKVHHGYYGFQGLINDGVVEYLDAEE 724

Query: 743  I---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                +I     DLD S      Y++    R + +  +N+R    +             PS
Sbjct: 725  EETVMITMTPEDLDISRQLQAGYQI----RPDDSGDLNKRVKAPINPTAHVWTHCEIHPS 780

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N  +S+            T      ++       +G  
Sbjct: 781  MILG-------ICASIIPFPDHNQANSVA-----------TKSPRNCYQSAMGKQAMGVF 822

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D+               +  +             +       +   +  + AI   
Sbjct: 823  LTNFDVRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCY 871

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L 
Sbjct: 872  SGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLK 927

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +  Y +L +   +  G           K+  ++ D                +E  QR   
Sbjct: 928  QGTYEKLDDDGIVAPGVRVTGADIIIGKTAPIAPD---------------SEEMGQRTKA 972

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +K    T     E    +++             LR VKV +   +  Q GDK A RHG 
Sbjct: 973  HVKRDASTPLRSTESGLVDQVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQ 1027

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      +DMPF ++G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 1028 KGTIGITYMQQDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGLEGDATP 1087

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L                         LR       G  +          
Sbjct: 1088 FTEVTVDSVSKL-------------------------LRAHGYHSRGFEIM--------- 1113

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G +    G         V +G  Y  +L HMV DK++AR+ G   
Sbjct: 1114 -------------YHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDKIHARARGPVQ 1153

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVY 1329
            ++T+QP+ G++  GG R GEME  C+ ++GA+  L+E L   SD       D+ G     
Sbjct: 1154 ILTRQPVEGRARDGGLRFGEMERDCMISHGASAFLKERLFEVSDAFRVHICDICGLMTPI 1213

Query: 1330 ESIVAG----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
              I  G              +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1214 AKINTGSFECRPCKNKTKISQIHIPYAAKLLFQELAAMNIATRMFTKRS 1262



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 134/1046 (12%), Positives = 277/1046 (26%), Gaps = 228/1046 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +      N   Q       P ++           ++F +     
Sbjct: 38  LVSQQIDSFDEFVQTTMQELVEENS--QLTLDQNNPPSSNDNPIALRRYEIKFGTIMLSR 95

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITL--------------------------- 106
           P               +   R+LTY+ PL I +                           
Sbjct: 96  PAMTEGDGSTQVMLPQEARLRNLTYSSPLYIEMTKSTQVAVERPVPLNELDDEQEADLAN 155

Query: 107 ------RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------- 141
                 RL+    D            E  +Y+G LP+M K                    
Sbjct: 156 GGEHPTRLVWEYEDGDPDGAKGGPAPE-RVYVGKLPMMLKSEYCFLKNCDEDDLYGWNEC 214

Query: 142 -----GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDI 194
                G F+I G ++++++Q  RS          +   +  + Y   I    ++G  +  
Sbjct: 215 PYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKPANQAVSYLAEIRSALEKGSRLIS 271

Query: 195 EFDSKDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIV 237
               K  ++ + D  R                 +P+     ALG +  E+IL+       
Sbjct: 272 SLQIK--LYDKGDSGRGGFGKTVKSTLPYIKQDIPIAIVFRALGVVSDEDILNHICYDRN 329

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +Q  +     +  A ++   +V+   +        +   K++     + + +K +    
Sbjct: 330 DTQMLEMLKPCIEEAFVIQDREVALDFIGKRGNGTSLTRDKRI--KYARDIMQKEL---- 383

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
                          ++ + G    +A  +              R+              
Sbjct: 384 ------------LPHISQKEGSETRKAFFLGYMVHKLLQCALGRRETDDRDHFGKKRLDL 431

Query: 358 IRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
               L        +    D+YR + R  + +               +        G    
Sbjct: 432 AGPLLAKLFRNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGD 491

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEML 471
             +    T    + + +    + +  L        R+GK       +  +  +    E  
Sbjct: 492 QKKAASSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETP 551

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLS 523
           + Q    +  +       + +     V      N + +         +A   F     + 
Sbjct: 552 EGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVG 611

Query: 524 QLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETS 575
              +  + +  +   RR   +  +  + R     E        R   P       P   +
Sbjct: 612 VHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNDPDSPN 671

Query: 576 EGHNIGLVSSL-------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +G+ +     +       +  + ++    +   Y           V YL A EEE   I 
Sbjct: 672 KGNLVLNKDHIRRLEDDQSLPSNMDKDEKVHHGYYGFQGLINDGVVEYLDAEEEETVMIT 731

Query: 629 QANSSLDEDG--------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                LD              +     +     I          +  P  ++ I AS+IP
Sbjct: 732 MTPEDLDISRQLQAGYQIRPDDSGDLNKRVKAPINPTAHVWTHCEIHPSMILGICASIIP 791

Query: 681 FLENDDS-------NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           F +++ +        R      M +QA+ +               V   + A I+     
Sbjct: 792 FPDHNQANSVATKSPRNCYQSAMGKQAMGVFLT---------NFDVRMDTMANILYYPQK 842

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +    ++  +          +   +  Y              NQ               
Sbjct: 843 PLATTRSMEFLKFRELPAGQNAIVAIMCYSG-----------YNQE-------------- 877

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                S  +   ++ R +  +       + E  + ++     E  + S            
Sbjct: 878 ----DSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPYRS------------ 921

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                     D   + +   + +D+ GI+  G  V   DI++GK  P         ++  
Sbjct: 922 ----------DTLKLKQGTYEKLDDDGIVAPGVRVTGADIIIGKTAPIAPDSEEMGQRT- 970

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 KA   RD S  + S  SG V
Sbjct: 971 ------KAHVKRDASTPLRSTESGLV 990


>gi|290489604|gb|ADD31186.1| RNA polymerase beta subunit protein [Antirrhinum majus]
          Length = 1070

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVVLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---EMIRVYISQKREIKVGDKIAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASQRTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  368 bits (945), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 240/668 (35%), Positives = 374/668 (55%), Gaps = 26/668 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR-------NTLVTDKNKDRK 371
           EI  +A         ++I    +     L +  + +N Y         N     K   ++
Sbjct: 161 EIDRKARIWARVSRKQKISILVLSSAMGLNLREILDNVYYPEIFLSFLNDKERKKIGSKE 220

Query: 372 DALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           +A+L+ Y+      GD              FF   + +L  +GR  MN RLNLD P +  
Sbjct: 221 NAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPLNNT 279

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +   DI+A    L+ L+ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  
Sbjct: 280 FLLPRDILAAADHLIGLKFGMGTLDDMNHLKNKRIRSVSDLLQDQFGLSLVRLENVVRGT 339

Query: 490 ISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           I       +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+LS LG G
Sbjct: 340 ICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPG 399

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +
Sbjct: 400 GLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARMGHWGSLESPFYEISE 459

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 ++YL    +E   +A  NS         E++V  R   E + +  E++      
Sbjct: 460 RSTGLRLLYLPPGRDEYYMLAAGNSLALNQDIQEEQVVPARYRQEFLTIAWEQVHLRSIF 519

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  
Sbjct: 520 PFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGALA 579

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +A+R G +  +D         +  L           L+ +QRSN+NTC++Q+P V+ G  
Sbjct: 580 IAERGGKIVYID--------TDKILFSGNGETRSIPLVMYQRSNKNTCMHQKPQVQRGKC 631

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LISER+V ED++TS HI ++
Sbjct: 632 IKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIYTSFHIRKY 691

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESP 905
           E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES 
Sbjct: 692 EIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVVLGSWVETGDILVGKLTPQMVKESS 751

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVER 961
             PE++LLRAI G +    ++T L++P G  G V+DVR   + G         R    ++
Sbjct: 752 YAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKRGGSSYNPEMIRVYISQK 811

Query: 962 EQIELLAR 969
            +I++  +
Sbjct: 812 REIKVGDK 819



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 111/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++  LI          K+ +D+++Q+I +G++PLM   GT
Sbjct: 62  PLIRERNAVYESLTYSSELYVSAGLIW---------KTSRDMQDQTILIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL   +YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILDNVYYPEIFLSFLNDKERKKIGSKE 220


>gi|196009726|ref|XP_002114728.1| DNA directed RNA polymerase II polypeptide B [Trichoplax adhaerens]
 gi|190582790|gb|EDV22862.1| DNA directed RNA polymerase II polypeptide B [Trichoplax adhaerens]
          Length = 1196

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 175/1073 (16%), Positives = 343/1073 (31%), Gaps = 191/1073 (17%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  + A   ++++    +    +  +    +       +    L+        +A +  
Sbjct: 255  GQKIVAAIPYVNQEIPIMVVFRALGFVADRDILEHIIYDFDDPELMEMVKPSLDEAFVIQ 314

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 315  EQNVALNYIGSRGSRSGV---TKEKRIKYAREILQKEMLPHVGISDYCETKK---AYFLG 368

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
             ++  L+    G+  +DD D+ GN+R      +LK   ++   +   + ++    + I +
Sbjct: 369  YMVHRLLLTALGRREVDDRDHYGNKR--LFRNLLKE-VKMYAQKFVDNGRDFNLELAIKT 425

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ----LSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             +  D +          +   + Q    +SQ+   +  +S ++H RRL++     + R  
Sbjct: 426  KIITDGLRYSLATGNWGDQKKAHQSRAGVSQVLNRLTFVSTLSHLRRLNS----PIGRDG 481

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                 R +H TH+G ICPAET EG  +GLV +L   A ++           + +  + N 
Sbjct: 482  KLARPRQLHNTHWGMICPAETPEGQAVGLVKNLALMAYISVGSQPSPILEFLEEWSMEN- 540

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
                  +EE +     + + +  +G +             +   R ++D         + 
Sbjct: 541  ------LEEVSHSALASATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDV--------IV 586

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR-- 731
               S++  + + +         + R  + +   +       +ES+           +   
Sbjct: 587  SEVSMVRDIRDREIRIYTDAGRICRPLLIVENQKLVLKKNHIESMKTADDYEVFGWQDLI 646

Query: 732  -AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              GIVE VD +      +    D  T+GV                          +  R 
Sbjct: 647  ANGIVEYVDTLEEETVMIAMTPDYLTAGV--------------------------NYCRT 680

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   PS  LG       +  + +P+  +N       S R   +       +  +   
Sbjct: 681  YTHCEIHPSMILG-------VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYTTN 727

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                    ++    +  V        +    +       +    
Sbjct: 728  F-----------------------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGI 764

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +     +   +    +F R   D+         E  E  +++
Sbjct: 765  NTIVAIASYTGYNQEDSIIMNRGAIDRGLF-RSVFYRSYRDQESSGDFNSEEIFEKPSKE 823

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
                      +       +  G     G     K+ +L  D  +    ++ +        
Sbjct: 824  TCSGMHNAMYDKLDDDGLVAPGTRVSGGDIVIGKTALLPEDADALGDTNKRFVKRDASTG 883

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            ++ +   +  Q   +                          +  KV V   R  Q GDK 
Sbjct: 884  LRSSESGIVDQVLLTV--------------------SQEGYKFTKVRVRSVRIPQIGDKF 923

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E   G      G+
Sbjct: 924  ASRHGQKGTCGITYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGE 983

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
                                                                    +TP 
Sbjct: 984  IGD-----------------------------------------------------ATPF 990

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
             D    + I+S+L        G  +LY+G TG   +  V +G  Y  +L HMV DK++AR
Sbjct: 991  NDTLTVQKISSLLSDYGYHLRGNEVLYNGFTGRKLNTQVFLGPTYYQRLKHMVDDKIHAR 1050

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVV 1323
            + G    +T+QP+ G++  GG R GEME  C  ++GAA  L+E L   SD       ++ 
Sbjct: 1051 ARGPLQNLTRQPMQGRARDGGLRFGEMERDCQISHGAAQFLRERLYDASDPYIVHMCNLC 1110

Query: 1324 G-------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            G       R   YE    G        +   P +  +L +E+ ++ L+  + +
Sbjct: 1111 GLVAVANLRNDTYEC--KGCRNKTRISQVRIPYACKLLFQELMSMSLAPRIMS 1161



 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 146/982 (14%), Positives = 281/982 (28%), Gaps = 201/982 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   +Q   +        S    L+F       P F
Sbjct: 41  LVRQQLDSFDEFIQMSVQRIVEDSPQIDIQGETQHHSSEEQQSVRYQLKFDQIYLSKPTF 100

Query: 87  -------DVD---DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                            R+LTY+ PL + +   +   +     K          ++G +P
Sbjct: 101 WEKDGSPTPMMSNQARLRNLTYSAPLYVDITKTITKGNNEPEVKCHPKT-----FIGKIP 155

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHR-SPGIHFDHDKGR 171
           +M +                         G F+I G ++++++Q    S  ++    K  
Sbjct: 156 IMLRSTYCLLHNMADHALTELNECPLDVGGYFIINGSEKVLIAQEKMASNTVYVFQKKES 215

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
                K  Y   I        +        + V +  R     +K               
Sbjct: 216 -----KYAYVAEIR----SVTENSSRPTSTLWVSMLARGGGTSKKSVIGQKIVAAIPYVN 266

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 267 QEIPIMVVFRALGFVADRDILEHIIYDFDDPELMEMVKPSLDEAFVIQEQNVALNYIGSR 326

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                +   K++     + + +K +      SD                     +A  + 
Sbjct: 327 GSRSGVTKEKRI--KYAREILQKEMLPHVGISDYCETK----------------KAYFLG 368

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN---TLVTDKNKDRKDALLDIYRVMRPGD 385
                  +     R++     D   N    RN    +     K   +       +     
Sbjct: 369 YMVHRLLLTALGRREVD--DRDHYGNKRLFRNLLKEVKMYAQKFVDNGRDFNLELAIKTK 426

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKIL 443
           + T  +  S+    + D  K   S  G  ++  RL   +      R          +   
Sbjct: 427 IITDGLRYSLATGNWGDQKKAHQSRAGVSQVLNRLTFVSTLSHLRRLNSPIGRDGKLARP 486

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
             L N    +         +      ++KN   +  + +       +  ++  S+   + 
Sbjct: 487 RQLHNTHWGMICPAETPEGQAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEE 543

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           ++   + SA   F     +    +    +S +   RR   +    V+  R   +      
Sbjct: 544 VSHSALASATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDVIVSEVSMVRDIRDREIRIY 603

Query: 564 THYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
           T  GRIC P    E   + L  +       +     +       D      V Y+  +EE
Sbjct: 604 TDAGRICRPLLIVENQKLVLKKNHIE----SMKTADDYEVFGWQDLIANGIVEYVDTLEE 659

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   IA     L    ++                        +  P  ++ + AS+IPF 
Sbjct: 660 ETVMIAMTPDYLTAGVNYCRTY-----------------THCEIHPSMILGVCASIIPFP 702

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +                                       
Sbjct: 703 DHNQSPRNTYQSAMGKQAMGVYTTNFHV-------------------------------- 730

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                       + + V  Y               Q+PLV                    
Sbjct: 731 ---------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRF 757

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +L  G N +VA   + GYN EDS++++   +   +F S+    +           EEI 
Sbjct: 758 RELPAGINTIVAIASYTGYNQEDSIIMNRGAIDRGLFRSVFYRSYRDQESSGDFNSEEIF 817

Query: 863 RD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                     +       +D+ G++  G  V+ GDI++GK     E      +   R + 
Sbjct: 818 EKPSKETCSGMHNAMYDKLDDDGLVAPGTRVSGGDIVIGKTALLPEDADALGDTNKRFVK 877

Query: 918 GEKAVDVRDTSLRVPSGVSGTV 939
                  RD S  + S  SG V
Sbjct: 878 -------RDASTGLRSSESGIV 892


>gi|7525025|ref|NP_051051.1| RNA polymerase beta subunit [Arabidopsis thaliana]
 gi|5881686|dbj|BAA84377.1| RNA polymerase beta subunit [Arabidopsis thaliana]
          Length = 1072

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKKG----GSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1032 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 253/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV                   L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|215254189|gb|ACJ64099.1| RNA polymerase beta subunit [Vibrio chagasii]
          Length = 390

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 241/386 (62%), Positives = 301/386 (77%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N  S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPWSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E+G+F +EL+ 
Sbjct: 61  SAFARCNDYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANTVLTEEGTFADELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE  L PR+ +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA
Sbjct: 121 ARQKGESGLHPRDHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K
Sbjct: 181 DKPLVGTGIERNIAVDSGVTAVAKRGGMIQSVDASRIVVKVNEDELVPGEAGIDIYNLTK 240

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           + RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS
Sbjct: 241 YTRSNQNTCINQRPTVLPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDS 300

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GA
Sbjct: 301 ILVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGA 360

Query: 887 EVNPGDILVGKITPKGESPMTPEEKL 912
           EV  GDILVGK+TPKGE+ +TPEEKL
Sbjct: 361 EVKGGDILVGKVTPKGETQLTPEEKL 386


>gi|161784184|ref|YP_001595500.1| RNA polymerase beta subunit [Lemna minor]
 gi|182676567|sp|A9L988|RPOB_LEMMI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|88696762|gb|ABD48487.1| RNA polymerase beta subunit [Lemna minor]
          Length = 1072

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 160/579 (27%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   +          I         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVSVIAEHEGKVISTDTHQIVFSGNGNT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  V  G IL       G   +   + +L A    
Sbjct: 606  LNIPLVMYQRSNKNTCMHQKPQVQRGKYVKKGQILADGAATVG-GELALGKNVLVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    +  +  E +  +    +  L 
Sbjct: 665  EGYNFEDAVL-----ISERLVYSDIYTSFHIRKYEIQTHMTSQGPERITNEIPHLEAHLL 719

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  R   ++ G    +G     K T   ++  S  P  +  +  +  +       SLK
Sbjct: 720  RNL-DRNGIVMLGSWVETGDILVGKLTPQIANESSYAPEDRLLRAILGIQVSTAKETSLK 778

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P    +++V++  KR I+ GDK+AGRHGNKGI
Sbjct: 779  LPIGGRGRVIDVRWIQKK----GGSSYNP---EIIRVYILQKREIKVGDKVAGRHGNKGI 831

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 832  ISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLNRHYRIAPFDE 891

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 892  RYEQEASRKLVFSELYEASKQTKNPW------------------------VFE------- 920

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++ V +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 921  --------PEYPGKSKIFDGRTGDPFEQAVLIGKSYILKLIHQVDDKIHGRSSGHYALVT 972

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 973  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIV 1032

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1033 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 267/808 (33%), Positives = 421/808 (52%), Gaps = 44/808 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILY-VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 167  RIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKKKIGSKENAILEF 226

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 227  YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNINQRLNLDIPHNNTFLLPRD 285

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            ++A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E +++  IS    
Sbjct: 286  VLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENAVRGTISGAIR 345

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+ +  + +    FF    LSQ+ +  N L++I H R+LS LG GGV    
Sbjct: 346  HKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGVTGRT 405

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G IETP+ ++ +     +
Sbjct: 406  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGHWGSIETPFYEISERSKEKE 465

Query: 614  --VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
              ++YLS   +E   IA  NS     G   E++V  R   E + +  E++      P Q 
Sbjct: 466  ARMIYLSPSRDEYYMIAAGNSLALNRGIQEEQVVPARYRQEFLTIAWEQVHLRSIFPFQY 525

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
             SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG +++A+ 
Sbjct: 526  FSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVSVIAEH 585

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G V   D  +IV       L+          L+ +QRSN+NTC++Q+P V+ G  V++ 
Sbjct: 586  EGKVISTDTHQIVFSGNGNTLNI--------PLVMYQRSNKNTCMHQKPQVQRGKYVKKG 637

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER+V  D++TS HI ++E+  
Sbjct: 638  QILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYSDIYTSFHIRKYEIQT 697

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PE 909
              T  GPE IT +IP++    L+N+D  GI+ +G+ V  GDILVGK+TP+  +  +  PE
Sbjct: 698  HMTSQGPERITNEIPHLEAHLLRNLDRNGIVMLGSWVETGDILVGKLTPQIANESSYAPE 757

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIE 965
            ++LLRAI G +    ++TSL++P G  G V+DVR   + G         R   +++ +I+
Sbjct: 758  DRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWIQKKGGSSYNPEIIRVYILQKREIK 817

Query: 966  LLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP----- 1017
            +  +      ++ +I        +  +  G             + ++   I E       
Sbjct: 818  VGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAG 877

Query: 1018 --RSQWWQFAVQDEKVQRNVES---LKVQYETSKS-------ILEDRFKNKIEKIQWGDD 1065
               ++ ++ A  DE+ ++           YE SK          E   K+KI   + GD 
Sbjct: 878  DLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPWVFEPEYPGKSKIFDGRTGDP 937

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                VL + K ++  K   Q  DK+ GR
Sbjct: 938  FEQAVL-IGKSYIL-KLIHQVDDKIHGR 963



 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLMEEFNKFPKIEDTDQEIEFKLFVETYQLAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D+KEQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVLAGLIW---------KTNRDMKEQTVFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|75755651|ref|YP_319757.1| RNA polymerase beta subunit [Acorus calamus]
 gi|74381701|emb|CAI53786.1| RNA polymerase beta subunit [Acorus calamus]
          Length = 1083

 Score =  385 bits (990), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/563 (28%), Positives = 257/563 (45%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++      ++E     I+ +  +++   +  G       +          
Sbjct: 575  IVGTGLERQAALDSGVSAIAECEGKIIYTDTHKIVL--SGHGDTISIPLVMYQRSNKNTC 632

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +   +  G  +  G IL       G   +   + +L A    +  +  D  L     +
Sbjct: 633  MHQNPQVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----I 686

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E +  +    +  L RN+  R   +  G   
Sbjct: 687  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNL-DRNGIVALGSWV 745

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  +++  S  P  +  +  +  +        LK+       +++ R+  
Sbjct: 746  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 805

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG
Sbjct: 806  KKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDG 858

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 859  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELY 918

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 919  EASKQTANPW------------------------VFE---------------PEYPGKSR 939

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 940  IFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 999

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+
Sbjct: 1000 EMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVREL 1059

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1060 RSLALELNHFLVSEKNFQINRKE 1082



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 260/831 (31%), Positives = 429/831 (51%), Gaps = 44/831 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 155  ISVYTSTIISDWGGRSELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 214

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 215  IFLSFLNDREKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 273

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 274  GRRNMNRRLNLDIPQSNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 333

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +++  I       +   PQ+L+++  + +    FF    LSQ+ +  
Sbjct: 334  QDQFGLALVRLENAVRGTICGAIRHKLILTPQNLVSSTSLTTTYESFFGLHPLSQVLDRT 393

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 394  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 453

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-LDEDGSFTEELVFCR 648
            AR+  +G IE+P+ +V        +V+LS   +E   +A  NS  L+  G   E++V  R
Sbjct: 454  ARIGHWGSIESPFYEVYQRSKETKMVFLSPSRDEYYTVATGNSLALNRGGIQEEQIVPAR 513

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E 
Sbjct: 514  YRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEK 573

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +Q
Sbjct: 574  CIVGTGLERQAALDSGVSAIAECEGKIIYTDTHKIVL--------SGHGDTISIPLVMYQ 625

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 626  RSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 685

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V
Sbjct: 686  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNLDRNGIVALGSWV 745

Query: 889  NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              GDILVGK+TP+  +  +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 746  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 805

Query: 947  RHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------Q 993
            + G         R    ++ +I++  +   +   + I+ + +  + M  L          
Sbjct: 806  KKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVF 865

Query: 994  NAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQY 1042
            N +  P       +    L ++     + ++ A  DE+ ++            E+ K   
Sbjct: 866  NPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTA 925

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 926  NPWVFEPEYPGKSRIFDGRTGDPFEQPVL-IGKSYIL-KLIHQVDDKIHGR 974



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL   F     I         + FV  Y+   
Sbjct: 24  IPGFSQIQFEGFCRFI----------DQGLMEEFHKFPKIEDTDQEIEFQLFVERYQLVE 73

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 74  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 124

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 125 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKSRIW 181

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 182 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDREKKKIGSKE 232


>gi|186885927|gb|ACC93371.1| RNA polymerase beta subunit [Perezia purpurata]
          Length = 1028

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-EKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNLNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KILYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+++ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLEKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|139388902|ref|YP_001123629.1| RNA polymerase beta subunit [Lepidium virginicum]
 gi|158513978|sp|A4QL98|RPOB_LEPVR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286832|dbj|BAF50453.1| RNA polymerase beta subunit [Lepidium virginicum]
          Length = 1072

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIIFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1032 PKPDDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 253/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I+                   L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIIFSGN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|158518592|sp|Q4VZP1|RPOB_CUCSA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|74027093|gb|AAZ94643.1| RNA polymerase beta subunit [Cucumis sativus]
 gi|115432796|gb|ABI97409.1| RNA polymerase beta subunit [Cucumis sativus]
 gi|115498295|gb|ABI98737.1| RNA polymerase beta subunit [Cucumis sativus]
          Length = 1070

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 205/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L++G PVD+V NPLGVPSRMNVGQIFE  LG A   L +  + +  D +  
Sbjct: 833  ILPREDMPYLQNGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIVPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTASPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             TPESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DTPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/634 (36%), Positives = 362/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  +N RLNLD P++   + + DI+A    L+ L+ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNLNQRLNLDIPENNTFLLQRDILAAADHLIGLKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTFESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +ETP+ ++ +      ++YLS   +E   +A  NS     G   
Sbjct: 434 LIGSLAIHARIGHWGSLETPFYEISERSKKVRMLYLSPSRDEYYMVATGNSLALNPGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQIVPARYRQEFLTIEWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  VA+ SG A +A+  G +   D         +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQVARDSGVAAIAEHGGKIIYTD--------TDKIIFSGNGYTRR 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC+ Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMQQKSQVHQGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER++ ED++TS HI ++E+    T  GPE IT +IP++    L N+D+ GI
Sbjct: 666 NFEDAVLISERLIYEDIYTSFHIRKYEIQTHVTSHGPERITNEIPHLEARLLCNLDKNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKKGGSSYNPEIIRVYISQKREIKVGDK 819



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPAFNQIQFEGFCRFI----------DHGLTEELSKFPKIEDTDQEIEFQLFVETYKLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTRRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ G+ RIV+SQ+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGLYRIVISQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|167950015|ref|ZP_02537089.1| DNA-directed RNA polymerase, beta subunit [Endoriftia persephone
            'Hot96_1+Hot96_2']
          Length = 256

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 125/209 (59%), Positives = 156/209 (74%), Gaps = 3/209 (1%)

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G PVDIVLNPLGVPSRMNVGQ+ ETHLG+A  G+G+KI +++   +A   ++ LR FL+K
Sbjct: 1    GEPVDIVLNPLGVPSRMNVGQVLETHLGFAAKGVGRKIGAML---QAQAKVAELREFLDK 57

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
            V  T    E +    D+ V+ +    + GVP++TPVFDGA E  I+ ML +  L +SGQ 
Sbjct: 58   VYNTSGKREDLDSLTDEEVVTLCGNLREGVPMATPVFDGAHESEIHHMLELGGLPQSGQL 117

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L+DG TG+ F+R VTVGY+YMLKLNH+V DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 118  TLFDGRTGDAFERQVTVGYMYMLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 177

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
            GEMEVW  +AYGAAY LQEMLT+KSDDV 
Sbjct: 178  GEMEVWAWEAYGAAYTLQEMLTVKSDDVQ 206


>gi|222139883|ref|YP_002519950.1| RNA polymerase beta chain [Ephedra equisetina]
 gi|220983551|dbj|BAH11318.1| RNA polymerase beta chain [Ephedra equisetina]
          Length = 1100

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 164/592 (27%), Positives = 264/592 (44%), Gaps = 63/592 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +L       G   E  + +  R++      +  I+E  +   D+K    
Sbjct: 546  MGSNMQRQAVPLLQPEKCIVGTGLEGQVALDSRIL------ATSIQEGRIEYFDSKTIVS 599

Query: 860  EITRDIPNVSEEGLKNIDECGIICV------GAEVNPGDILVGKITPKGESPMTPEEKLL 913
             + R       E  +  +   +I        G  V  G  +    T  G   +   + +L
Sbjct: 600  SLNRKTIETILEIYQRSNSNILIHQKPQVNQGNYVKRGQFMADGSTTIG-GELCLGKNIL 658

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV---EREQIELLARD 970
             A    +  +  D  L     +   +       R+          +   E  QIE  +  
Sbjct: 659  VAYMPWQGYNFEDAILINERLIYEEIFTSFHITRYETMIYMAECEILTKEIPQIEAYSLR 718

Query: 971  KDDEQVILDRNIYSRLMEILCGQ-NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
              DE  I+    + +  ++L G+    S  +  +   +     +   PR++        +
Sbjct: 719  HLDENGIVRVGSWIQPGDVLVGKLKPRSSQEVLRFPELRLLQDLFCTPRTKETCLKANGK 778

Query: 1030 KVQRNVESLKVQ--YETSKSILEDRFKNKIEKIQWGDDMPPGVL--RVVKVFVAMKRPIQ 1085
                +V  +K+Q  ++ +         +  +  +  D   PG      V V++  KR IQ
Sbjct: 779  GRVIDVNWIKLQTLWQDNLRKSHHEDDDIEDDFEKNDQTDPGENDSEKVHVYILQKRKIQ 838

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK+AGRHGNKGI+S++L  ++MPFL++G PVD++LNPLGVPSRMNVGQIFE  LG A 
Sbjct: 839  VGDKVAGRHGNKGIISKVLSRQEMPFLQNGKPVDMILNPLGVPSRMNVGQIFECLLGLAG 898

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              + K+ +    D +   + S    F E    +                           
Sbjct: 899  TLMNKQYRIPPFDERYEQEASRKLVFNELHKASEQTVNPW-------------------- 938

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                VF+               L+  G++ ++DG TGE  ++PVTVG  YM+KL H V D
Sbjct: 939  ----VFE---------------LEHLGKTKIFDGKTGEILEQPVTVGKAYMMKLIHQVYD 979

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K++ARSTGSY+ +TQQP+ GKS  GGQRLGEMEVW ++++G A +LQEMLT+KSD +  R
Sbjct: 980  KMHARSTGSYARITQQPVQGKSKGGGQRLGEMEVWALESFGVASILQEMLTVKSDHLKTR 1039

Query: 1326 TRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLSID--LENSRTKNSAKM 1374
            T++  SI+ G+   +  T  ESF VL++E+++L L ++  + + +       
Sbjct: 1040 TKILRSILDGHSVPKAETATESFRVLIRELRSLALELNHTIISEKNFQIENK 1091



 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 220/699 (31%), Positives = 348/699 (49%), Gaps = 31/699 (4%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN----AYIRNTLVTDKNKDRKDALL 375
            +++          L  +F   ++   +LY             I N  +  K   +   +L
Sbjct: 159  LWVRISRKKKVSILVFLFTMGLKIEEVLYNTYNLTGFEGWELIWNEKMKQKLSRKGGPIL 218

Query: 376  DIYRVMRPGDVSTFSVAESMF---NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
              Y  +      +   A S F       F S + +L  +GR  +N +LNLD PD+   + 
Sbjct: 219  TFYEELESMKCDSSDFAFSEFLYKKLTNFISKRCELGRIGRRNLNQKLNLDIPDNEIFLL 278

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             +D++AI+  L+ +  G GTID+ID+L NR   SV + LK +  L L R++  I++ + +
Sbjct: 279  PQDVLAIVDYLIKVSYGLGTIDNIDHLQNRHFCSVSDFLKKEVGLALNRVKVLIQKNMQT 338

Query: 493  VDIDSVM-------PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            ++I           P+    +  +   +  FF    LSQ  E  N L+ I H R++S LG
Sbjct: 339  IEILENTQNKQIMFPEFPFISTQLTRTLKHFFGLHPLSQFLEQTNPLAEILHGRKVSFLG 398

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
             GG+    A    RD+HP++YGR CP  T EG N GL++SL +   V+ +GF+++P+  V
Sbjct: 399  PGGLTERTASFRARDIHPSYYGRFCPINTPEGQNAGLIASLANSVNVDDFGFLKSPFYNV 458

Query: 606  CDGKVTND-VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
                  +  V YL   E++N  IA  N    +     ++    +   + + V  E+I F 
Sbjct: 459  TKKSNEDHMVSYLLPNEDKNYRIALENLLAVDHKLPEKKNTPTQYRQDFLSVAWEQIHFR 518

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
               P Q  SI  SLIPFLE++D+ R LMG NMQRQAVPLL+ E   VGTG+E  VA  S 
Sbjct: 519  SILPLQYFSIGVSLIPFLEHNDATRALMGSNMQRQAVPLLQPEKCIVGTGLEGQVALDSR 578

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                + + G +E  D+  IV       ++          L  +QRSN N  ++Q+P V  
Sbjct: 579  ILATSIQEGRIEYFDSKTIVSSLNRKTIET--------ILEIYQRSNSNILIHQKPQVNQ 630

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G+ V+R   +ADG +T  G+L LG+N+LVA+MPW GYNFED++LI+ER++ E++FTS HI
Sbjct: 631  GNYVKRGQFMADGSTTIGGELCLGKNILVAYMPWQGYNFEDAILINERLIYEEIFTSFHI 690

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              +E M        E +T++IP +    L+++DE GI+ VG+ + PGD+LVGK+ P+   
Sbjct: 691  TRYETMI--YMAECEILTKEIPQIEAYSLRHLDENGIVRVGSWIQPGDVLVGKLKPRSSQ 748

Query: 905  P--MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
                 PE +LL+ +F       R     + +   G V+DV       + ++    S   +
Sbjct: 749  EVLRFPELRLLQDLFC----TPRTKETCLKANGKGRVIDVNWIKLQTLWQDNLRKSHHED 804

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                   +K+D+    + +     + IL  +    G K 
Sbjct: 805  DDIEDDFEKNDQTDPGENDSEKVHVYILQKRKIQVGDKV 843



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 80/382 (20%), Positives = 148/382 (38%), Gaps = 36/382 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVS-YEFDP 83
           IPD  ++Q   +  F+  +I                 FP I+         F   Y+   
Sbjct: 6   IPDFSQIQMKGFFRFIEKDIFEKLVD-----------FPQISNTEKEVKFFFGKNYKIME 54

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS-IYMGDLPLMTKDG 142
           P     + +++  T++    +    I +           K +K +  IY+GD+PLM   G
Sbjct: 55  PPTTERNAVYQRFTFSSKFYVPGIFIYW-----------KQMKRKRMIYLGDIPLMNDHG 103

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TFVI G  R+VV+Q+ RSPGI++  ++ +A      +Y   +I D G  +  E D K  +
Sbjct: 104 TFVINGNYRVVVNQIIRSPGIYYSLEQKKAGN----IYTGTLISDCGERLKFEIDIKKKL 159

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            VRI R++KV +  FL  +G+  EE+L   Y    +      W   +       G  + +
Sbjct: 160 WVRISRKKKVSILVFLFTMGLKIEEVLYNTYNLTGFEGWELIWNEKMKQKLSRKGGPILT 219

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
              +       +ES K  +S    S          I+  C  G     ++      +I  
Sbjct: 220 FYEE-------LESMKCDSSDFAFSEFLYKKLTNFISKRCELGRIGRRNLNQKLNLDIPD 272

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
               ++ +  L  + +       +  +D++++        V+D  K      L+  +V+ 
Sbjct: 273 NEIFLLPQDVLAIVDYLIKVSYGLGTIDNIDHLQNRHFCSVSDFLKKEVGLALNRVKVLI 332

Query: 383 PGDVSTFSVAESMFNFLFFDSD 404
             ++ T  + E+  N      +
Sbjct: 333 QKNMQTIEILENTQNKQIMFPE 354


>gi|262400793|gb|ACY66282.1| RNA polymerase beta subunit [Brassica napus]
          Length = 1072

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/535 (29%), Positives = 246/535 (45%), Gaps = 60/535 (11%)

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI--ICVGAEVNPGDILVGKITPKGES 904
            +    +    G E        + +   KN        +  G  +  G IL       G  
Sbjct: 591  YTDTEKIILSGNENTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-G 649

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   + +L A    +  +  D  L     +S  +V   I+    I K E    V  +  
Sbjct: 650  ELALGKNILVAYMPWEGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGP 704

Query: 965  ELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            E + ++    E  +L      +   ++ G    +G     K T   +   S  P  +  +
Sbjct: 705  ERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLR 762

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              +  +        LK+       +++ R+  K      G    P    +++V+++ KR 
Sbjct: 763  AILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKRE 815

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG 
Sbjct: 816  IKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGL 875

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   L +  +    D +   + S    F E    +                         
Sbjct: 876  AGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------------------ 917

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                  VF+                +  G+S ++DG TG+PF++PV +G  Y+LKL H V
Sbjct: 918  ------VFE---------------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQV 956

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD + 
Sbjct: 957  DDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIR 1016

Query: 1324 GRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             R  V  + + G    +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1017 ARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 251/832 (30%), Positives = 422/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A   + +       T+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADLPIPNFIPIKTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELVEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I++   E  L           L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIILSGNENTL--------SIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSQFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYELLTYSSELYVSAGLIW---------KTNRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI R+V++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRVVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|313199695|ref|YP_004021309.1| RNA polymerase beta subunit [Theobroma cacao]
 gi|309321259|gb|ADO64802.1| RNA polymerase beta subunit [Theobroma cacao]
 gi|328924776|gb|ADO64882.2| RNA polymerase beta subunit [Theobroma cacao]
          Length = 1070

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 161/580 (27%), Positives = 258/580 (44%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LSIPLVMYQRSNKNTCMHQTPRVQRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEA 1218
            +   + S    F                         +E +++G   + P VF+      
Sbjct: 890  RYEQEASRKLVF-------------------------SELYEAGKQTANPWVFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 970  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1030 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 253/830 (30%), Positives = 423/830 (50%), Gaps = 43/830 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNL+ P +   +   DI++    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNMNQRLNLNIPQNNTFLLPRDILSAADQLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442  ARIGHWGSLESPFYKIFERSKKAQMLYLSPSRDEYYMVATGNSLALNQGIQEEQVVPARY 501

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502  RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E  VA  SG   +A   G +   D         +  +           L+ +QR
Sbjct: 562  IVGTGLERQVALDSGVPAIADHEGKIISTD--------TDKIILSGNGDTLSIPLVMYQR 613

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614  SNKNTCMHQTPRVQRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890  PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734  TGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948  HGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
             G         R    ++ +I++  +      ++ +I        +  +  G+       
Sbjct: 794  KGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFN 853

Query: 1001 GFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQYE 1043
                 + ++   I E           + ++ A  DE+ ++            E+ K    
Sbjct: 854  PLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEAGKQTAN 913

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                  E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  PWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFYGFM----------DRGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSKDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|186885923|gb|ACC93369.1| RNA polymerase beta subunit [Pachylaena atriplicifolia]
          Length = 1028

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERITNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N +LNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRKLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|317046165|ref|YP_004072454.1| RNA polymerase beta subunit [Corynocarpus laevigata]
 gi|309252882|gb|ADO60302.1| RNA polymerase beta subunit [Corynocarpus laevigata]
          Length = 1070

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 204/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  + +  D +  
Sbjct: 833  ILPREDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIVPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTASPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 234/662 (35%), Positives = 367/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I+           L  +         IL  V          N     K   +++A+L+ 
Sbjct: 167 RIWARVSRKQKISILVLLSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 226

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD              FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 227 YQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNLNRRLNLDIPQNNTFLLPRD 285

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 286 ILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENMVRGTICGAIR 345

Query: 496 DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 346 HKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRT 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 406 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGHWGSLESPFYEISERSKKVR 465

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++      P Q  S
Sbjct: 466 MLYLSPSRDEYYMVATGNSLALNRGIQEEQVVPARYRQEFLTIEWEQVHLRSIFPFQYFS 525

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  SG   +A+  G
Sbjct: 526 IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPALAEHGG 585

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D  +IV+                  L+ +QRSN+NTC++Q+  V+ G  +++  I
Sbjct: 586 KIIYTDTDKIVLSGN--------GYTRSIPLVMYQRSNKNTCMHQKSQVQQGKCIKKGQI 637

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N++VA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 638 LADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHV 697

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++
Sbjct: 698 TSHGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDR 757

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   + G         R    ++ +I++ 
Sbjct: 758 LLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPEMIRVYISQKREIKVG 817

Query: 968 AR 969
            +
Sbjct: 818 DK 819



 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 111/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSARLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV+SQ+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVISQILQSPGIYYRSELDHKGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +   L A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLLSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|186885967|gb|ACC93391.1| RNA polymerase beta subunit [Trixis divaricata]
          Length = 1028

 Score =  385 bits (989), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKKGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLLGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++Y S   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYFSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATAGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKKGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLEKYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|139387244|ref|YP_001123365.1| RNA polymerase beta subunit [Capsella bursa-pastoris]
 gi|158513957|sp|A4QKI4|RPOB_CAPBU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286565|dbj|BAF50189.1| RNA polymerase beta subunit [Capsella bursa-pastoris]
          Length = 1072

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1032 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  360 bits (925), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 254/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV                   L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|160689642|gb|ABX45679.1| RNA polymerase subunit beta [Bacillus sonorensis]
          Length = 321

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 143/377 (37%), Positives = 194/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGA--EVKDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E HLG A   LG  + S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 80/117 (68%), Positives = 96/117 (82%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAEV  GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAEVKDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNREDGD 117


>gi|186885913|gb|ACC93364.1| RNA polymerase beta subunit [Nouelia insignis]
          Length = 1026

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 199/396 (50%), Gaps = 51/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K                 ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKKR---------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 788

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 789  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 848

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 849  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQP
Sbjct: 875  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQP 929

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 930  LKGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 989

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 990  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1025



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 259/804 (32%), Positives = 413/804 (51%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++ +    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYGIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885899|gb|ACC93357.1| RNA polymerase beta subunit [Leucomeris spectabilis]
          Length = 1026

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 199/396 (50%), Gaps = 51/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K                 ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKKR---------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 788

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 789  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 848

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 849  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQP
Sbjct: 875  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQP 929

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 930  LKGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 989

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 990  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1025



 Score =  370 bits (950), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 258/804 (32%), Positives = 412/804 (51%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  +   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPAQYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++ +    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYGIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP +    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPQIEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|153805632|ref|YP_001382217.1| RNA polymerase beta chain [Leptosira terrestris]
 gi|160175226|sp|A6YGE0|RPOB2_LEPTE RecName: Full=DNA-directed RNA polymerase subunit beta C-terminal
            section; AltName: Full=PEP; AltName: Full=Plastid-encoded
            RNA polymerase subunit beta C-terminal section; Short=RNA
            polymerase subunit beta C-terminal section
 gi|134270163|gb|ABO69352.1| RNA polymerase beta chain [Leptosira terrestris]
          Length = 880

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 142/391 (36%), Positives = 204/391 (52%), Gaps = 56/391 (14%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  D   I+    + +  +I+  +    GP        L + ++ +             +
Sbjct: 529  DHLDNDGIIKLGTWVKPGDIIVSKLRPIGPHNPTPLEKLVAAILKKKFDDYKNAAFYTPK 588

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             V   +  +                  +E      D+    +  V+ ++  KR I  GDK
Sbjct: 589  DVYGRIVGI----------------EILEPKNLPSDVEYSGIGRVEFYLVDKRRIFVGDK 632

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKGI+S ILP +DMP+L DGTPVD+VLNPLGVPSRMNVGQ+FET LG A   L 
Sbjct: 633  MAGRHGNKGIISNILPKQDMPYLPDGTPVDMVLNPLGVPSRMNVGQVFETLLGLAGKYLH 692

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +  K    D               +V G  +    +     ++ L+  + W         
Sbjct: 693  QHFKVTPFD---------------EVYGPEASRSLVYSKLYEARLKTDQNW--------- 728

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            +FD                   G++ ++DG TG  FD+ VT GY YMLKL H+V  K++A
Sbjct: 729  IFD---------------PKSPGKTRIFDGQTGANFDQAVTAGYAYMLKLIHLVDHKIHA 773

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY 1329
            RSTG Y+LVTQQP+ G+S  GGQRLGEME W ++A+GA+Y LQEM+TIKSDD++GRT+V+
Sbjct: 774  RSTGPYALVTQQPVRGRSRAGGQRLGEMEFWALEAFGASYNLQEMMTIKSDDILGRTQVF 833

Query: 1330 ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
            +SI+       +  PESF V + E+++LG++
Sbjct: 834  DSILNSKPIQNSH-PESFRVFINELRSLGVN 863



 Score = 90.9 bits (224), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 11/249 (4%)

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           +   D   +  + Y L  + RSNQ TC+ QRP VK+G+ V++ D + D  ++  G+LALG
Sbjct: 45  DKARDVYRAHENSYFLDHYIRSNQATCITQRPSVKLGEWVQKGDFLCDTTASSAGELALG 104

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +N+LVA+MPWHGYNFED++L++E ++  D++TS+H+E+FE+   +T  GPE I       
Sbjct: 105 KNILVAYMPWHGYNFEDAILVNETLIIYDIYTSLHLEKFEIEIENTNWGPEIIKLSDWMF 164

Query: 869 SEEG---LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           S++                   V    I +G +    ++ +  + KLL        +   
Sbjct: 165 SDKRDSLYGKELFTQETTKQTYVKEKQITIGVL---KQAFLRRKGKLLINRRFISKIHKY 221

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE---LLARDKDDEQVILDRNI 982
           +        V       +      I+KN +   + R  IE    L+     +    +  I
Sbjct: 222 EFLTNQRFVVPQ--FRYQQTLFQQINKNPKKQLISRSIIENSNQLSIYNKPKIRFTNNVI 279

Query: 983 YSRLMEILC 991
            S+L + L 
Sbjct: 280 SSKLFKPLI 288



 Score = 59.7 bits (143), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/105 (29%), Positives = 51/105 (48%)

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            V +    ++D  GII +G  V PGDI+V K+ P G    TP EKL+ AI  +K  D ++
Sbjct: 522 FVQKNNYDHLDNDGIIKLGTWVKPGDIIVSKLRPIGPHNPTPLEKLVAAILKKKFDDYKN 581

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
            +   P  V G +V + I     +  +     + R +  L+ + +
Sbjct: 582 AAFYTPKDVYGRIVGIEILEPKNLPSDVEYSGIGRVEFYLVDKRR 626


>gi|186885937|gb|ACC93376.1| RNA polymerase beta subunit [Proustia cuneifolia]
          Length = 1028

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENLARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|23011160|ref|ZP_00051607.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 419

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 285/404 (70%), Positives = 331/404 (81%), Gaps = 1/404 (0%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRRVRSVGE+++NQYR+GLLRMER+I+ER+SSVDIDSVMP DLINAKP  +AV EFF SS
Sbjct: 1   NRRVRSVGELMENQYRVGLLRMERAIRERMSSVDIDSVMPHDLINAKPAAAAVREFFGSS 60

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NI
Sbjct: 61  QLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 120

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL ++ARVN YGFIE PYRKV DG+VT+DVVYLSAMEE    +AQANS LD DG F
Sbjct: 121 GLINSLATYARVNQYGFIEAPYRKVFDGRVTSDVVYLSAMEEGRYTVAQANSILDADGRF 180

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           TE+LV CR AG+ ++VP  +I+ ID SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQA
Sbjct: 181 TEDLVSCRRAGDFVMVPANEINMIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQA 240

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL++AEAP VGTGME  VA+ SGAAI AKR G+V+QVDA R+VIR+ E     + SGVD
Sbjct: 241 VPLIRAEAPLVGTGMEQAVARDSGAAITAKRTGVVDQVDATRVVIRATEETQASA-SGVD 299

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           IY L+KFQRSNQNTC+ QRPLVKVGD + + DIIADGPST LG+LALGRN+LVAFMPW+G
Sbjct: 300 IYNLLKFQRSNQNTCITQRPLVKVGDLIAKGDIIADGPSTQLGELALGRNVLVAFMPWNG 359

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           YNFEDS+LISER+V +DVFTSIHIEEFEV  R      E     
Sbjct: 360 YNFEDSILISERIVRDDVFTSIHIEEFEVRPRYQVGQKELPGIP 403


>gi|290489610|gb|ADD31189.1| RNA polymerase beta subunit protein [Ehretia acuminata]
          Length = 1070

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 233/686 (33%), Positives = 377/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRPELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+     L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILTAADHLIGLKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYMVAAGNSLALNQDIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+  G +   D         +  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEGEGKIISTD--------TDKILLSGNGNTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRPELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|324120666|dbj|BAJ78724.1| RNA polymerase II second largest subunit [Chrysoperla nipponensis]
          Length = 1175

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 165/1087 (15%), Positives = 324/1087 (29%), Gaps = 206/1087 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLDLAIKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             I D  D   +          P +  ++ + +L   ++                      
Sbjct: 603  MIRDIRDREIRIYTDAGRISRPLIIVENGSLLLKKSHIDMLKDREYNNYG--------WQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                SG            + +   I I   +       +    Y                
Sbjct: 655  GLVGSGVV----EYIDTLEEETTMIAISPDDLRNSKEYAYCSTY---------------- 694

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               P+  LG       +  + +P+  +N          M  + +
Sbjct: 695  -------------THCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAM 734

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V    +   +    +
Sbjct: 735  G--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSM 765

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V            +   K+  S  
Sbjct: 766  EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF---YRSYKDSESKR 822

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            +  ++ E   +        +   +Y +L +   I  G           K+  L       
Sbjct: 823  IGEQE-EQFEKPTRQTCSGMRHALYDKLDDDGIISPGVRVSGDDVVIGKTMTL------- 874

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                          + +  +E    +Y    +    R        Q    +     +  K
Sbjct: 875  -------------PENEDELEGTTKRYTKRDASTFLRNSETGVVDQVMLTLNSEGYKFCK 921

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G 
Sbjct: 922  IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGH 981

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G      G+                                             
Sbjct: 982  LIECIQGKVSSNKGEIGD------------------------------------------ 999

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP  D  + + I+++L+       G  ++Y+G TG   +  V  G  Y
Sbjct: 1000 -----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFFGPTY 1048

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R+ G   ++ +QP  G++  GG R GEME  C  ++GAA  L+E L
Sbjct: 1049 YQRLKHMVDDKIHSRARGPLQILVRQPSEGRARDGGLRFGEMERDCQISHGAAQFLRERL 1108

Query: 1316 TIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQAL 1357
               SD     V            R   +E    G        +   P +  +L +E+ ++
Sbjct: 1109 FEVSDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSM 1166

Query: 1358 GLSIDLE 1364
             ++  L 
Sbjct: 1167 NIAPRLM 1173



 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 137/987 (13%), Positives = 287/987 (29%), Gaps = 196/987 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+ M++    ++ P   LQA  +         P        +L+F    
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIELQAEAQHTSGEMENPP------RYLLKFEQIY 92

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              P              ++   R+LTY+ PL + +   +    E          + Q  
Sbjct: 93  LSKPTHWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEEPIV-----TQHQKT 147

Query: 131 YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
           ++G +P+M                           G F+I G ++++++Q   +   ++ 
Sbjct: 148 FIGKIPIMLRSSFCLLSKLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV 207

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR--------- 208
              K      GK  +   I       ++        + V         I +         
Sbjct: 208 FSMKD-----GKYAFKSEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKAAIGQRIIA 258

Query: 209 -----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ 
Sbjct: 259 ILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVAL 318

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
           + +        +   K++     + L+++ +  +G++  C          +      + +
Sbjct: 319 NFIGARGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLL 374

Query: 323 EAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            A    +    +   +  +    P+L          +   +     K           + 
Sbjct: 375 AALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLA 434

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 435 IKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 494

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 495 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 551

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVE 557
             + I    +  A   F     +    +    ++ +   RR     + +  + R     E
Sbjct: 552 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 611

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R ++        P    E  ++ L  S      ++     E           +  V Y+
Sbjct: 612 IR-IYTDAGRISRPLIIVENGSLLLKKS-----HIDMLKDREYNNYGWQGLVGSGVVEYI 665

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +EEE   IA +   L                  +           +  P  ++ I AS
Sbjct: 666 DTLEEETTMIAISPDDL---------------RNSKEYAYCSTYTHCEIHPAMILGICAS 710

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 711 IIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------- 743

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            + + V  Y                +PLV               
Sbjct: 744 --------------RMDTLAHVLYYP--------------HKPLV----------TTRSM 765

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G N +VA + + GYN EDS++++   V    F S+    ++         
Sbjct: 766 EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGE 825

Query: 858 PEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            EE            +       +D+ GII  G  V+  D+++GK     E+    E   
Sbjct: 826 QEEQFEKPTRQTCSGMRHALYDKLDDDGIISPGVRVSGDDVVIGKTMTLPENEDELEGTT 885

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  K    RD S  + +  +G V
Sbjct: 886 -------KRYTKRDASTFLRNSETGVV 905


>gi|290790771|gb|ADD63028.1| RNA polymerase beta subunit [Potamophila parviflora]
          Length = 1067

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 800  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 859

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 860  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 912

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 913  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 940

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 941  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1000

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1001 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1060

Query: 1370 NSAKME 1375
               + E
Sbjct: 1061 QVNREE 1066



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 236/699 (33%), Positives = 384/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 127 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 186

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 187 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 245

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 246 CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 305

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV------CEFF 517
           +RSV ++L++Q+ L L R++ ++++ I  V I  + P       P  +++        FF
Sbjct: 306 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIHQLKPTPQTLVTPTSTSILLITTYETFF 365

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 366 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 425

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 426 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKQKKERQVVYLSPNRDEYYMIAAGNSL 485

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 486 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 545

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 546 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL-------- 597

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 598 SSSGKAISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 657

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 658 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 717

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 718 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 777

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 778 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 816



 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ R I               +++Q+I +G++P+M   GT
Sbjct: 54  PSIKERDAVYESLTYSSELYVSARFIFGFN-----------VQKQTISIGNIPIMNSLGT 102

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 103 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 159

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 160 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 213


>gi|114329738|ref|YP_740557.1| RNA polymerase beta subunit [Platanus occidentalis]
 gi|122166043|sp|Q09G54|RPOB_PLAOC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|114054376|gb|ABI49770.1| RNA polymerase beta subunit [Platanus occidentalis]
          Length = 1070

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G I+       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VRRGKFIKKGQIVADGAATVG-GELALGKNVLVAYMPWEGYNSEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  R   ++ G    +G   
Sbjct: 680  GDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNL-DRNGIVMLGSWVETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   +   S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     + V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTP+D+V
Sbjct: 796  -GSSYNP---ETICVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPIDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYKASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 912  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPSPEDAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLVSEKNFQINRKE 1069



 Score =  369 bits (948), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 226/608 (37%), Positives = 351/608 (57%), Gaps = 15/608 (2%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALIRLENVVRGTICGAIKHKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L+++ H R+LS LG GG+    A   +RD+H +HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQMVHGRKLSYLGPGGLTGRTASFRIRDIHSSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL  +AR+  +G +E+P+ ++ D      ++YLS   +E   +A  NS         E+
Sbjct: 436 GSLAIYARIGHWGSLESPFYEISDRSKEVQMLYLSPSRDEYYMVAAGNSLALNQSIPEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++ F    P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 VVPARYRQEFLTIAWEQVHFRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E   A  SG + +A+  G +   D  +I++                  
Sbjct: 556 SQSEKCIVGTGLERQAALDSGVSTIAEHEGKIIYTDTDKIILLGN--------GDTLSIP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC+ Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 608 LVMYQRSNKNTCMYQKPQVRRGKFIKKGQIVADGAATVGGELALGKNVLVAYMPWEGYNS 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ 
Sbjct: 668 EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDRNGIVM 727

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728 LGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942 VRIFNRHG 949
           VR   + G
Sbjct: 788 VRWIQKKG 795



 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  + +   LI          K  +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSEVYVPAGLIW---------KPGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSESDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|332148590|dbj|BAK20144.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|332148598|dbj|BAK20148.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|332148604|dbj|BAK20151.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 324

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 144/379 (37%), Positives = 195/379 (51%), Gaps = 62/379 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 2    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVNDGD 59

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 60   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 119

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 120  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 179

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 180  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 233

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 234  ----------------------TVLYDG--------------------------RTGEPF 245

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 246  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 305

Query: 1306 GAAYVLQEMLTIKSDDVVG 1324
            GAAY LQE+LT+KSDDVV 
Sbjct: 306  GAAYTLQEILTVKSDDVVA 324



 Score =  114 bits (286), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 80/118 (67%), Positives = 97/118 (82%)

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+
Sbjct: 1   VKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDL 60

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  LVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 118


>gi|91983984|ref|YP_567068.1| RNA polymerase beta subunit [Vitis vinifera]
 gi|122242805|sp|Q0ZJ28|RPOB_VITVI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|91701642|gb|ABE47526.1| RNA polymerase beta subunit [Vitis vinifera]
          Length = 1070

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D K  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDEKYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 249/778 (32%), Positives = 402/778 (51%), Gaps = 41/778 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   ++ A+L+ Y+      GD              FF  
Sbjct: 195  LENVCYPEIFLSFLNDKEKKKIGSKESAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  +GR  +N RLNLD P +   +  +DI+A    L+ ++ G G +DD+++L N+R
Sbjct: 254  QRCELGRIGRRNINRRLNLDIPQNNTFLLPQDILAAADHLIGMKFGMGILDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + PV +    FF    
Sbjct: 314  IRSVADLLQDQFGLALIRLENVVRGTICGAIRHKLIPTPQNLVTSTPVTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   
Sbjct: 434  LIGSLAIHARIGHWGSLESPFYEISERSKKVRMLYLSPSRDEYYMVAAGNSLALNQGIQE 493

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494  EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL ++E   VGTG+E   A  SG  ++A+  G +   D         +  +         
Sbjct: 554  PLSRSEKCIVGTGLERQAALDSGVPVIAEHEGKIVYTD--------TDKIILSGNGDTLS 605

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L+ +QRSN+NTC++Q+  V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606  IPLVMYQRSNKNTCMHQKAQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N ED++LISER+V  D++TS HI ++E+    T  GPE IT  IP++    L+N+D+ GI
Sbjct: 666  NSEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNKIPHLEAHLLRNLDKNGI 725

Query: 882  ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726  VILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940  VDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCG 992
            +DVR   + G         R    ++ +I++  +      ++ +I        +  +  G
Sbjct: 786  IDVRWIQKKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDG 845

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------V 1035
            +            + ++   I E           + ++ A  DEK ++            
Sbjct: 846  RPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDEKYEQEASRKLVFSELY 905

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            E+ K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  EASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ G+ RIV++Q+ +SPGI++  +     +S   +Y   I+ D G  +++E D K  I 
Sbjct: 113 SIVNGLYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIVSDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|14017562|ref|NP_114249.1| RNA polymerase beta subunit [Triticum aestivum]
 gi|15214264|sp|Q9XPS7|RPOB_WHEAT RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|4958867|dbj|BAA78040.1| RNA polymerase subunit beta [Triticum aestivum]
 gi|13928195|dbj|BAB47024.1| RNA polymerase beta subunit [Triticum aestivum]
          Length = 1076

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1069

Query: 1370 NSAKME 1375
               + E
Sbjct: 1070 QVNREE 1075



 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 237/700 (33%), Positives = 383/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTND----VVYLSAMEEENRYIAQANS 632
            N+GL  SL   AR++  +G IE+P+ ++   K        VVYLS   +E   IA  NS
Sbjct: 434 INVGLTGSLAIHARIDHLWGSIESPFYEISAEKAKEKKERQVVYLSPNRDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  S  +I+A+R G +   D+ +I++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSIIAEREGKIISTDSHKILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTISIPLVNHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E 
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 825



 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+ L         I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQALAEELDKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|186885795|gb|ACC93305.1| RNA polymerase beta subunit [Adenocaulon bicolor]
 gi|186885903|gb|ACC93359.1| RNA polymerase beta subunit [Lophopappus cuneatus]
          Length = 1028

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|118430378|ref|YP_874643.1| RNA polymerase beta subunit [Hordeum vulgare subsp. vulgare]
 gi|158512662|sp|A1E9I1|RPOB_HORVU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|118201032|gb|ABK79403.1| RNA polymerase beta subunit [Hordeum vulgare subsp. vulgare]
          Length = 1076

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1069

Query: 1370 NSAKME 1375
               + E
Sbjct: 1070 QVNREE 1075



 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 236/700 (33%), Positives = 384/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTND----VVYLSAMEEENRYIAQANS 632
            N+GL  SL   AR++  +G IE+P+ ++   K        VVYLS   +E   IA  NS
Sbjct: 434 INVGLTGSLAIHARIDHLWGSIESPFYEISAEKAKEKKERQVVYLSPNRDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTISIPLVNHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E 
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D+ G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDKNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 825



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+ L         I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFFRFI----------NQALAEELDKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|116201245|ref|XP_001226434.1| hypothetical protein CHGG_08507 [Chaetomium globosum CBS 148.51]
 gi|88177025|gb|EAQ84493.1| hypothetical protein CHGG_08507 [Chaetomium globosum CBS 148.51]
          Length = 1182

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 186/1070 (17%), Positives = 329/1070 (30%), Gaps = 169/1070 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  KG    G  ++ +  + +     +   G ++   G V DE  L
Sbjct: 223  LEKGSRLISSLQMKLHSKGSPEKGRLANTVS-VTLPYVREDVSLGIVFRALGIVSDEDIL 281

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A+          +DR+ AL  I +              
Sbjct: 282  NHICYDRTDTQMLEALRPCIEEAF--------CIQDREIALDFIGKR---------GNGN 324

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +  N +       DL     ++  M  ++   +     +   +  ++  L+    G+   
Sbjct: 325  AGQNRMNRVRAAKDL-----LQKEMLPHISQTEGCETRKAFFLGYMVHRLLQCALGRRDP 379

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R  + RM + +    +       +      I    + +
Sbjct: 380  DDRDHFGKKRLDLPGPLLAKLFRNVIRRMTQDLMSYMKRCIDTNKNFSLPLGIKHSTLTN 439

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 440  GLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKP 495

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    V+     +    +      +V  +   
Sbjct: 496  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPADPIVEFMIARGMEVLEEYEP 555

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L        ++      + +D      LV        I      + D  D   K      
Sbjct: 556  LRYPNATKVFVNGTWVGVHQDPKHLVTLVQGLRRKNVISFEVSLVRDIRDREFKIFSDAG 615

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
              + P    +       G  M    +                             ++G +
Sbjct: 616  RVMRPLFTVEQEPNGESGAEMGALILNKDH-IGRLKMDAELGKYHPDYWGWQGLLKSGAI 674

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR--SNQNTCVNQRPLVKVGDEVRRNDI 793
            E +DA       +          +D +R  K  R   + +   N R   K          
Sbjct: 675  EYLDAEEEETVMICMTPQD----LDQFRARKMGRIEPDNSGLGNNRIKTKPNPTTHMYTH 730

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +     +  +      
Sbjct: 731  CEIHPSMLLG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM-- 779

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 780  -------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 814

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D  +R      EQ E    ++ D
Sbjct: 815  VAIACYSGYNQEDSVIMNQSSIDRGIF-RSLFFRSYTDCEKRVGINIVEQFEKP--NRSD 871

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
                L  + Y +L     +  G           K+  ++ D      RS           
Sbjct: 872  TLR-LKHSTYDKLDADGIVAPGIRVSGEDIIIGKTCPINPDNAELGQRSN---------- 920

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 + +K    T     E    +++      D      +R VKV V   +  Q GDK 
Sbjct: 921  -----QHVKRDASTPLRSTESGIIDQVVMTTNQD-----GMRYVKVRVRTTKVPQIGDKF 970

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G 
Sbjct: 971  ASRHGQKGTIGVTYRQEDMPFTAEGITPDIIINPHAIPSRMTIAHLIECLLSKVSTLKGM 1030

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +                              ++      +LR       G  +    
Sbjct: 1031 EGDATPFT-------------------------DVTVDSVSDLLREHGYQSRGFEIM--- 1062

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                                 G +    G         +  G  Y  +L HMV DK++AR
Sbjct: 1063 -------------------YHGHT----GR---KLRSQIFFGPTYYQRLRHMVDDKIHAR 1096

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            + G   ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD
Sbjct: 1097 ARGPLQIMTRQPVEGRARDGGLRFGEMERDCMIAHGAASFLKERLFEVSD 1146



 Score =  136 bits (342), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 104/754 (13%), Positives = 212/754 (28%), Gaps = 112/754 (14%)

Query: 29  LIEVQKASYDHFLMMNIAP-----DERPNEGLQA--AFKSVFPITAFSGAAMLEFVSYEF 81
           L+  Q  S+D F    I        +R    +    A K +            E+++   
Sbjct: 62  LVAQQIDSFDEFTSTTIQSLVDEVTKRARVAINEEVALKDM----DEEQQ---EYMARTG 114

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           + PK                   T+R    D     G+    + K   I++G LP+M K 
Sbjct: 115 EAPK-------------------TIRWEEEDTGPTEGSGKGGEDKGDLIFLGKLPVMVKS 155

Query: 142 ------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                                   G F+I G ++++++Q  RS          +    G 
Sbjct: 156 QVCHLAGEDDESLFLLNECPYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKPPGGS 212

Query: 178 LLYACRIIP--DQGLWMDIEFDSK-------------DII-----HVRIDRRRKVPVTSF 217
           + Y   I    ++G  +      K             + +     +VR D    V +   
Sbjct: 213 VSYQAEIRSALEKGSRLISSLQMKLHSKGSPEKGRLANTVSVTLPYVRED----VSLGIV 268

Query: 218 LMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
             ALG+   E+IL+        +Q  +     +  A  +   +++   +    G      
Sbjct: 269 FRALGIVSDEDILNHICYDRTDTQMLEALRPCIEEAFCIQDREIALDFIGKR-GNGNAGQ 327

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
            +       K L +K +      ++           +      +   A    D    +  
Sbjct: 328 NRMNRVRAAKDLLQKEMLPHISQTEGCETRKAF--FLGYMVHRLLQCALGRRDPDDRDHF 385

Query: 337 FHSEIRD-IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
               +    P+L     N    +   L++   +           +       T  +  S+
Sbjct: 386 GKKRLDLPGPLLAKLFRNVIRRMTQDLMSYMKRCIDTNKNFSLPLGIKHSTLTNGLKYSL 445

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTI 453
               + D  K   ST G  ++  R    +      R          +     L N    +
Sbjct: 446 ATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGL 505

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                    +   + + L     + +      I E + +  ++ +   + +         
Sbjct: 506 VCPAETPEGQACGLVKNLSLMCYVSVGTPADPIVEFMIARGMEVLEEYEPLRYPNATKVF 565

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM-------RDVHPTH 565
                 + +   ++  + ++ +   RR + +  +  + R     E        R + P  
Sbjct: 566 ---VNGTWVGVHQDPKHLVTLVQGLRRKNVISFEVSLVRDIRDREFKIFSDAGRVMRPLF 622

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAY---GFIETPYRKVCDGKVTNDVVYLSAMEE 622
                P   S      L+ +     R+      G     Y        +  + YL A EE
Sbjct: 623 TVEQEPNGESGAEMGALILNKDHIGRLKMDAELGKYHPDYWGWQGLLKSGAIEYLDAEEE 682

Query: 623 ENRYIAQANSSLDEDGSFTEELVF-------CRCAGEEILVPREKIDFIDASPKQVVSIA 675
           E   I      LD+  +     +              +           +  P  ++ I 
Sbjct: 683 ETVMICMTPQDLDQFRARKMGRIEPDNSGLGNNRIKTKPNPTTHMYTHCEIHPSMLLGIC 742

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           AS+IPF +++ S R      M +QA+        
Sbjct: 743 ASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYS 776


>gi|186885825|gb|ACC93320.1| RNA polymerase beta subunit [Chaptalia nutans]
          Length = 1028

 Score =  385 bits (988), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  370 bits (950), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADHLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEIYERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G+  E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGTQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+  V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLNIPLVMYQRSNKNTCMHQKTQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885897|gb|ACC93356.1| RNA polymerase beta subunit [Leucheria thermarum]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVIYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSMGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885865|gb|ACC93340.1| RNA polymerase beta subunit [Gerbera piloselloides]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 152/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + ++    + E
Sbjct: 1011 LNHFLVSEKSFQINRKE 1027



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADHLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEIYERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGLQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG   +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGTLAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLNIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885891|gb|ACC93353.1| RNA polymerase beta subunit [Hyaloseris rubicunda]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL   +   G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQILAYGLATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RDSSSKPEKIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N         +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKNIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYSD--------TDKILLSGNGNTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGLATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRDSSSKPEKIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 95/184 (51%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKEKDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---HNGIAVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKNI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885823|gb|ACC93319.1| RNA polymerase beta subunit [Chaetanthera pentacaenoides]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWGEKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A V L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGVLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSGGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 258/808 (31%), Positives = 418/808 (51%), Gaps = 42/808 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD   +    +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFYESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADGLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   +++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGIDEYYMVAAGNSLALNQGIQEQQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG   +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGTLAIAQYEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L  S  G+    L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDMILLSSHGGILRIPLVLYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWGEKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGVL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              V+ + K ++  K   Q  DK+ GR G
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGRSG 921



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  CMGKIPLMNSRGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|139389942|ref|YP_001123542.1| RNA polymerase beta subunit [Draba nemorosa]
 gi|158513971|sp|A4QL11|RPOB_DRANE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286744|dbj|BAF50366.1| RNA polymerase beta subunit [Draba nemorosa]
          Length = 1072

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/498 (30%), Positives = 238/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 628  VRRGQCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 682  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 739

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 740  LVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 796

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 797  -GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 852

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 853  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 912

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 913  TANPW------------------------VFE---------------PEYPGKSRIFDGR 933

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 934  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 993

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L
Sbjct: 994  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLAL 1053

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1054 ELNHFLVSEKNFQINRQE 1071



 Score =  355 bits (911), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 251/832 (30%), Positives = 422/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINSRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++        +   +LS  ++E   IA  NS         E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFCKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRDIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I++                  L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILSTDTEKIILSGN--------GNTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGQCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  + ++  LI          K+ ++++EQ I++G++PLM   G 
Sbjct: 62  PLIKERDAVYESLTYSSEIYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGI 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|269930801|gb|ACZ54135.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 423

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 307/424 (72%), Positives = 365/424 (86%), Gaps = 1/424 (0%)

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
              AE+MF+ LFFD ++YDLS VGRVKMN+R++L+ PD VR +R+EDI+A++K+LV+LR+
Sbjct: 1   IDTAEAMFHSLFFDPERYDLSAVGRVKMNLRMDLNCPDTVRVLRQEDILAVVKMLVELRD 60

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           G+G IDDIDNLGNRRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP
Sbjct: 61  GRGEIDDIDNLGNRRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKP 120

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
             +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR
Sbjct: 121 AAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 180

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           ICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+A
Sbjct: 181 ICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVA 240

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+N
Sbjct: 241 QANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDAN 300

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ 
Sbjct: 301 RALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVSAKRSGIVDQVDATRIVIRAT 360

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           E  LDPS SGVDIYRL KFQRSNQ+TC+NQRPLV VGD V + DIIADGPSTDLGDLALG
Sbjct: 361 ED-LDPSKSGVDIYRLQKFQRSNQSTCINQRPLVHVGDLVEKGDIIADGPSTDLGDLALG 419

Query: 809 RNML 812
           RN+L
Sbjct: 420 RNVL 423


>gi|186885793|gb|ACC93304.1| RNA polymerase beta subunit [Adenocaulon chilense]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  KGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLXSEKTFQINRKE 1027



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKKGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|330850611|ref|YP_004376492.1| RNA polymerase beta subunit [Ptilidium pulcherrimum]
 gi|302024740|gb|ADK89586.1| RNA polymerase beta subunit [Ptilidium pulcherrimum]
          Length = 1063

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 238/615 (38%), Positives = 369/615 (60%), Gaps = 15/615 (2%)

Query: 360 NTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           N  + ++    ++A++++Y+ +    GD+             FF   + +L  +GR+ +N
Sbjct: 203 NKKLKEQPSSTEEAIVELYKQLYSLSGDIVFSESIRKELQKKFF-QQRCELGKMGRLNLN 261

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            +LNLD P++   +  +DI+A +  L+ L+ G G +DDIDNL NRRV SV ++L+NQ +L
Sbjct: 262 EKLNLDVPENETFLLPQDILAAVDYLIKLKFGIGKLDDIDNLKNRRVCSVADLLQNQLKL 321

Query: 478 GLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            L R+E SI++  R  +       P+ L+   P++    EFF S  LSQ  +  N L+ +
Sbjct: 322 ALNRLENSIRQILRGVTKRKRLPTPKSLVTPTPLIKTFKEFFGSHPLSQFLDQTNPLTEM 381

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            H RRLS+LG GG+ R  AG ++RD+HP+HYGRICP ETSEG N GL+ SL   A +N  
Sbjct: 382 VHKRRLSSLGPGGLTRRTAGFQVRDIHPSHYGRICPIETSEGMNAGLIGSLAIHAEINIL 441

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G +E+P+ K+ +    + +  LSA E+E   IA  N    +  S  E +   R   + + 
Sbjct: 442 GCLESPFYKISELSEEDKIFNLSAGEDEYYRIATGNCLALDQKSPEERITPARYRQDFVA 501

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +  E++      P Q  S+ ASLIPFLE++D+NR LMG NMQRQAVPLLK E   VGTG+
Sbjct: 502 IAWEQVHLRSIFPLQYFSVGASLIPFLEHNDANRALMGSNMQRQAVPLLKTEKCIVGTGI 561

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG+  V+ + G +  +++ +I +   + +++          L+ +QRSN +TC
Sbjct: 562 EGQTALDSGSVTVSIKGGKIHSINSEKITLSLNKKEINT--------NLIIYQRSNNSTC 613

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           ++Q+P       +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER++ 
Sbjct: 614 IHQKPQRNGKVYIKKGQILADGAATSKGELALGKNLLVAYMPWEGYNFEDAILISERLIY 673

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           ED++TSIHIE +E+ AR T  G E+ T++IP++    L+++D+ G +  GA V  GD+LV
Sbjct: 674 EDIYTSIHIERYEIEARVTSQGAEKFTKEIPHLDHYLLRHLDKNGFVLTGAWVETGDVLV 733

Query: 896 GKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           GK+TP+     +  PE KLL+AIFG +  + ++T L+VP G  G V+DVR   R     +
Sbjct: 734 GKLTPQETEETSRAPEGKLLQAIFGIQVANSKETCLKVPIGGKGRVIDVRSIYREDSSND 793

Query: 954 ERSISVEREQIELLA 968
            + I +   Q   + 
Sbjct: 794 AKIIHIYVSQRRKIQ 808



 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/460 (32%), Positives = 215/460 (46%), Gaps = 81/460 (17%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I ++  + I +ER +IE       A     E   L
Sbjct: 647  KNLLVAYMPWEGYNFEDAILISERLIYEDIYTSIHIERYEIEARVTSQGAEKFTKEIPHL 706

Query: 979  DRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            D  +     +   +L G    +G     K T   ++  S  P  +  Q     +      
Sbjct: 707  DHYLLRHLDKNGFVLTGAWVETGDVLVGKLTPQETEETSRAPEGKLLQAIFGIQVANSKE 766

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R            +      +++ ++V+ +R IQ GDK+AGRHG
Sbjct: 767  TCLKVPIGGKGRVIDVR--------SIYREDSSNDAKIIHIYVSQRRKIQVGDKVAGRHG 818

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+S+ILP +DMPFL++GTP+D++L+PLGVPSRMNVGQIFE  LG A   L K  + +
Sbjct: 819  NKGIISKILPRQDMPFLQNGTPIDMILSPLGVPSRMNVGQIFECLLGLAGYFLNKNYRII 878

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D +   + S    F E                                        A 
Sbjct: 879  PFDERYEREASRKLVFSELYE-------------------------------------AS 901

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E+ +N  L        G+S L+DG TGE F++P+T G  YMLKL H V DK++ARS+G Y
Sbjct: 902  EKTVNPWLFE--PANPGKSRLFDGRTGEIFEQPITTGKAYMLKLIHQVDDKIHARSSGPY 959

Query: 1276 SLVTQQPL------------GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
            +LVTQQPL                        EMEVW ++ +G AY+LQEMLTIKSD + 
Sbjct: 960  ALVTQQPLRGRSRRGGQRVG------------EMEVWALEGFGVAYILQEMLTIKSDHIR 1007

Query: 1324 GRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLSID 1362
             R  V  +IV G    E  T PESF +LV+E+++L L I+
Sbjct: 1008 ARYEVLGAIVTGEPIPEPKTAPESFKLLVRELRSLALKIN 1047



 Score =  199 bits (505), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 126/305 (41%), Gaps = 28/305 (9%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----V 77
           EI  +P+   +Q   ++ F+           +GL     +   I        LEF     
Sbjct: 2   EIFVLPEFGRIQFEGFNRFIS----------KGLIEELINFPRIEDIDE--ELEFRIFGE 49

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y+   P     D +++ +TY+  L +  RL           K    I++Q +++G +PL
Sbjct: 50  QYQLTEPFLKERDAIYKSITYSSDLYVPARLT---------QKREGKIQKQRVFLGSIPL 100

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           M   GTFV+ G+ R++++Q+ RSPGI+++ +  R   +G   Y   +I + G  + +E D
Sbjct: 101 MNSQGTFVVNGVARVIINQILRSPGIYYNSELDR---NGITTYTGTLISNWGGRLKLEID 157

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           +K  I  RI ++RKV +   L A G++ ++IL +      +    +       ++     
Sbjct: 158 AKRRIWARISKKRKVSILILLSATGLNLKQILISVCYPKFFLDSINKKLKEQPSSTEEAI 217

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            ++   L  +       ES +K         + +  K   +  +    L V E+      
Sbjct: 218 VELYKQLYSLSGDIVFSESIRKELQKKFFQQRCELGKMGRLNLNEKLNLDVPENETFLLP 277

Query: 318 GEIYI 322
            +I  
Sbjct: 278 QDILA 282


>gi|139388086|ref|YP_001123278.1| RNA polymerase beta subunit [Barbarea verna]
 gi|158513637|sp|A4QK97|RPOB_BARVE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286477|dbj|BAF50102.1| RNA polymerase beta subunit [Barbarea verna]
          Length = 1072

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYERSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1032 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 253/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV                   L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            +RSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  ERSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDH--EIEFQLFMETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   
Sbjct: 60  VEPLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 111 GTSIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 168 IWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|186885889|gb|ACC93352.1| RNA polymerase beta subunit [Hyalis argentea]
 gi|186885893|gb|ACC93354.1| RNA polymerase beta subunit [Ianthopappus corymbosus]
          Length = 1026

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 200/396 (50%), Gaps = 51/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K                 ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKKR---------GSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 788

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 789  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 848

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 849  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YSL+TQQP
Sbjct: 875  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYSLLTQQP 929

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 930  LKGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 989

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T +  + E
Sbjct: 990  DAPESFRLLVRELRSLALELNHFLVSEKTFHINRKE 1025



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 260/804 (32%), Positives = 414/804 (51%), Gaps = 40/804 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +G     
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISEGSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++ +    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYGIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--VEREQIELLAR 969
            LLR I G +    ++T L++P G  G V+DVR   +    K ER     +++ +I++  +
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSKPERIRVYILQKREIKVGDK 775

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRS 1019
                  ++ +I        +  +  G+        +  P       +  S L ++     
Sbjct: 776  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLD 835

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 836  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 895

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 896  VI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885851|gb|ACC93333.1| RNA polymerase beta subunit [Doniophyton anomalum]
          Length = 1024

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/482 (31%), Positives = 230/482 (47%), Gaps = 54/482 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  L           +   + +L A    +  +  D  L     +S  +V 
Sbjct: 580  VRRGKCIKKGQSL-AYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 633

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 634  EDIYTSFHIRKYEIQPHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 692

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 693  VGKLTPQLVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWAQKKG--- 749

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G D  P     + V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 750  -GSDYNP---ERIHVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 805

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 806  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 865

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            +                           VF+                +  G+S ++DG T
Sbjct: 866  SNPW------------------------VFE---------------PEYPGKSRIFDGRT 886

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RSTG Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 887  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSTGHYALVTQQPLRGRAKQGGQRVGEMEVWA 946

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 947  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPEDAPESFRLLVRELRSLALE 1006

Query: 1361 ID 1362
            ++
Sbjct: 1007 LN 1008



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 263/894 (29%), Positives = 439/894 (49%), Gaps = 43/894 (4%)

Query: 233  YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID--TGEQVIESGKKLTSGLLKSLKE 290
            Y   +Y   G  W        + +G     + +      G   I   + L S  +    E
Sbjct: 32   YSSELYVSAGLIWKTSSKEQTIFIGNIPLMNSLGAFIVNGIYRIVINQILQSPGIYYQSE 91

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                 +      +   +     +  +             + S+  +  +   +I  +  +
Sbjct: 92   LDHNGISAYIGTIISDWGGRLELEIDRKVRIWARVSRNQKLSILVLLSAMGLNIREILEN 151

Query: 351  SVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYD 407
                  ++      DK K   +++A+L+ Y+     G    FS + S      F   + +
Sbjct: 152  VCYPEIFLSFLNDKDKKKIGSKENAILEFYQQFACVGGDPVFSESLSKDLQKKFFQQRCE 211

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV
Sbjct: 212  LGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSV 271

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
             ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+
Sbjct: 272  ADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQV 331

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ S
Sbjct: 332  LDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGS 391

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   E++V
Sbjct: 392  LAIHARIGRWGSLESPFYEISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVV 451

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL +
Sbjct: 452  PARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQ 511

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            +E   VGTG+E   A  SG   +A+  G +   D         +  L           L+
Sbjct: 512  SEKCIVGTGLERQAALDSGTLAIAEHEGKIISSD--------TDKILLSGNGDTLSIPLV 563

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
             +QRSN+NTC++Q+P V+ G  +++   +A G +T  G+LALG+N+LVA+MPW GYNFED
Sbjct: 564  MYQRSNKNTCMHQKPQVRRGKCIKKGQSLAYGAATVGGELALGKNVLVAYMPWEGYNFED 623

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            ++LISER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G
Sbjct: 624  AVLISERLVYEDIYTSFHIRKYEIQPHVTSQGPERVTNEIPHLEAHLLRNLDKNGIVMLG 683

Query: 886  AEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            + V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR
Sbjct: 684  SWVETGDILVGKLTPQLVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVR 743

Query: 944  IFNRHG----IDKNERSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA- 995
               + G      +      +++ +I++  +      ++ +I        +  +  G+   
Sbjct: 744  WAQKKGGSDYNPERIHVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVD 803

Query: 996  -----VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLK 1039
                 +  P       +  S L ++     + ++ A  DE+ ++            E+ K
Sbjct: 804  MVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASK 863

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                      E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 864  QTSNPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/180 (30%), Positives = 91/180 (50%), Gaps = 16/180 (8%)

Query: 76  FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           FV  Y+   P     D +++ LTY+  L ++  LI                KEQ+I++G+
Sbjct: 9   FVETYQLVEPLIQEGDAVYKSLTYSSELYVSAGLIWKTSS-----------KEQTIFIGN 57

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S    Y   II D G  +++
Sbjct: 58  IPLMNSLGAFIVNGIYRIVINQILQSPGIYYQSELDHNGISA---YIGTIISDWGGRLEL 114

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  I  R+ R +K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 115 EIDRKVRIWARVSRNQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKDKKKIGSKE 174


>gi|186885789|gb|ACC93302.1| RNA polymerase beta subunit [Acourtia turbinata]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKK----RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 413/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLESMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P  + G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQFQRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSEXDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885965|gb|ACC93390.1| RNA polymerase beta subunit [Trichocline boecheri]
          Length = 1030

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 157/562 (27%), Positives = 247/562 (43%), Gaps = 56/562 (9%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +    ++        I         +  G       +          +
Sbjct: 521  CIVGTGLERQAALDSGALAIAEHEGKIIYTDTDKILLSGNGDTINIPLVMYQRSNKNTCM 580

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G  ++          +   + +L A    +  +  D  L     +S
Sbjct: 581  HQKPQVRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----IS 634

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    
Sbjct: 635  ERLVYEDIYTSFHIRKYEIQIHVTSQGPERVTYEIPHLEAHLLRNL-DKNGIVMLGSWVE 693

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T       S  P  +  +  +           LK+       +++ R+  K
Sbjct: 694  TGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK 753

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 754  K----RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 806

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E   
Sbjct: 807  PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIGPFDERYEQEASRKLVFSELYE 866

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 867  ASKQTANPW------------------------VFE---------------PEYPGKSRI 887

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GE
Sbjct: 888  FDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGE 947

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 948  MEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELR 1007

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +T    + E
Sbjct: 1008 SLALELNHFLVSEKTFQINRKE 1029



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 234/664 (35%), Positives = 367/664 (55%), Gaps = 22/664 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR+ +N RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRLNINRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEIYERSKRAR 423

Query: 614 --VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q 
Sbjct: 424 ARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQY 483

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+ 
Sbjct: 484 FSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEH 543

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++ 
Sbjct: 544 EGKIIYTD--------TDKILLSGNGDTINIPLVMYQRSNKNTCMHQKPQVRRGKCIKKG 595

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+  
Sbjct: 596 QILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI 655

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPE 909
             T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE
Sbjct: 656 HVTSQGPERVTYEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPE 715

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIE 965
           ++LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I+
Sbjct: 716 DRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIK 775

Query: 966 LLAR 969
           +  +
Sbjct: 776 VGDK 779



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|139389256|ref|YP_001123022.1| RNA polymerase beta subunit [Aethionema grandiflorum]
 gi|158513606|sp|A4QJJ1|RPOB_AETGR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286218|dbj|BAF49846.1| RNA polymerase beta subunit [Aethionema grandiflorum]
          Length = 1073

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 238/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 629  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 682

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E + ++    +  L RN+  +   ++ G    +G   
Sbjct: 683  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGHLLRNL-DKNGIVMLGSWVETGDIL 741

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   +   S  P  +  +  +  +        LK+       +++  +  K     
Sbjct: 742  VGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVGWVQKKG--- 798

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 799  -GSSYNP---EKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 854

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 855  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 914

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 915  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 935

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW 
Sbjct: 936  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWA 995

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L 
Sbjct: 996  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPKPEDAPESFRLLVRELRSLALD 1055

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1056 LNHFLVSEKNFQINRKE 1072



 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 251/832 (30%), Positives = 424/832 (50%), Gaps = 44/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL  P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLTIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L R+E  +K  I       +   PQ+L+ A P+ +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALARLENVVKGTICGAIKHKLIPTPQNLVTATPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A++ G +   D  +I++     +            L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEQEGKILYTDTKKIILSGNGDNTLG-------IPLIMY 614

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+  V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 615  QRSNKNTCMHQKSQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 674

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 675  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGHLLRNLDKNGIVMLGSW 734

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DV   
Sbjct: 735  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVGWV 794

Query: 946  NRHG----IDKNERSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G      +  R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 795  QKKGGSSYNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 854

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 855  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 914

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 915  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 964



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEEVSKFPKIEDIDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ + ++EQ I++G++PLM   GT
Sbjct: 62  PLRKERDAVYESLTYSSELYVSAGLIW---------KTSRKMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|186885847|gb|ACC93331.1| RNA polymerase beta subunit [Dinoseris salicifolia]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 151/497 (30%), Positives = 234/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RDSSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 257/806 (31%), Positives = 414/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N         +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKNIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD +      +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPAFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYSD--------TDKILLSGNGNTLSIPLVMYQRSNKNTCMHQKPHVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRDSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 95/184 (51%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKEKDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---HNGIAVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKNI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885943|gb|ACC93379.1| RNA polymerase beta subunit [Richterago amplexifolia]
          Length = 1028

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K ++              ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVRKKKR-------SSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+ KL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYIFKLIHQVDDKIHVRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLIRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++ALL+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENALLEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVEGDPVFSEYLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIAIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGTICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N  P+      FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 304 YKWIPTPQKLVNPSPLKGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKFSFLGPGGLTGQT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRAILGMRVYTSKETCLKLPIGGRGRVIDVRWVRKKKRSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y    P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYHLVEPLIKERDAVYKSLTYSSALYVSARLIWKTDRR-------RNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G L+Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---PNGILVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|156598504|gb|ABU85510.1| RNA polymerase beta subunit [Passiflora biflora]
          Length = 1068

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/493 (31%), Positives = 235/493 (47%), Gaps = 56/493 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G +L       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VQPGKFLKKGQVLADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I     I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 680  EDILTSFYIRKYEIQTHVTSQGSEKITNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P ++        +        LK+       +++ R+  K E   
Sbjct: 739  VGKLTPQMGKESSYSPENRLLGAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKE--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG  VD+V
Sbjct: 796  -GYRYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGGTVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPLDERYEQEASRKLVFSELYEASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            +                           VF+                +  G+S L+DG T
Sbjct: 912  SNPW------------------------VFE---------------PEYPGKSRLFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F++P+ +G  Y+LKL H VSDK++ARS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GDSFEQPILIGRPYILKLIHQVSDKIHARSSGPYTLVTQQPLRGRARKGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G +++LQEMLTIKSD +  R  V  + ++G    +    PESF +LV+E+++L L 
Sbjct: 993  LEGFGVSHILQEMLTIKSDHIRARQEVLGTTISGRIIPKAEDAPESFRLLVRELRSLSLE 1052

Query: 1361 ID--LENSRTKNS 1371
            +   L + +    
Sbjct: 1053 LKNFLISEKNFQI 1065



 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 229/692 (33%), Positives = 385/692 (55%), Gaps = 21/692 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + +    +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ESNYKGILVYVGTIISDWGGRVELQIDRKRRMWVRVSRKQKISILVLSSAMGLNLKEILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N    ++   +++A+L+ Y+      GD              FF   K
Sbjct: 197 NVCYPEIFLSFLNDKEKNEIGSKENAILEFYQQFTCVGGDPVFSESLCKELQKKFF-QQK 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L T+GR+ MN RLNL  P +   +   DI+A    L++++ G  T  D+++L N+R+R
Sbjct: 256 CELGTIGRLNMNERLNLHIPHNNIFLLPRDILAAADHLIEMKLGMDTPSDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  +K  +S      +   P++L+   P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENVVKRTLSRAVKQKLIPTPKNLVTPIPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H RRLS LG GG+    A   MR++HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIFHARRLSYLGPGGLTARTASFGMRNIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SLT  A++  +G +E+P+ ++ +G     ++YLS+  +E   IA  N      G+  E+
Sbjct: 436 GSLTIHAKIGHWGSLESPFLEISEGSKKGRMLYLSSNRDEYYMIATGNYLALNRGAREEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  +   E + +  +++      P Q  SI  SLIPF+E++D+ R LM  NMQRQAVPL
Sbjct: 496 VVSAQHRQEFLTIAWDQVHLRSFFPFQYFSIGVSLIPFIEHNDATRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +++E   VGTG+E  VA+ SG   +A+ AG +   D  +I++                  
Sbjct: 556 VRSEKCIVGTGLERQVARDSGVPAIAEHAGKIISTDIDKILLSRN--------RYTLSIP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+  V+ G  +++  ++ADG +T  G+LALG+N+LVA+MPW GYNF
Sbjct: 608 LVVYQRSNKNTCMHQKTQVQPGKFLKKGQVLADGAATVGGELALGKNILVAYMPWEGYNF 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V ED+ TS +I ++E+    T  G E+IT +IP++    L+N+D+ GI+ 
Sbjct: 668 EDAVLISERLVYEDILTSFYIRKYEIQTHVTSQGSEKITNEIPHLEAHLLRNLDKNGIVM 727

Query: 884 VGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+   ES  +PE +LL AIFG +    ++T L++P G  G V+D
Sbjct: 728 LGSWVETGDILVGKLTPQMGKESSYSPENRLLGAIFGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   +    +      R   +++ +I++  +
Sbjct: 788 VRWIQKKEGYRYNPETIRVYILQKREIKVGDK 819



 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 81/438 (18%), Positives = 161/438 (36%), Gaps = 36/438 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL+        +         + FV  Y+   
Sbjct: 12  IPAFNQIQFEGFCRFI----------DQGLREELSKFPKMEDGDEEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K  +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAALIW---------KGSRDMQEQTLFLGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +       G L+Y   II D G  ++++ D K  + 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSESNYK---GILVYVGTIISDWGGRVELQIDRKRRMW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VR+ R++K+ +     A+G++ +EIL    YP+I  S   D     + + +  +      
Sbjct: 170 VRVSRKQKISILVLSSAMGLNLKEILENVCYPEIFLSFLNDKEKNEIGSKENAILEFYQQ 229

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                          K+L     +   E G       ++ L  L++  + +     +I  
Sbjct: 230 FTCVGGDPVFSESLCKELQKKFFQQKCELGTIGRLNMNERL-NLHIPHNNIFLLPRDILA 288

Query: 323 EAGD-------VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
            A         +     +  + +  IR +  L  D           +V           L
Sbjct: 289 AADHLIEMKLGMDTPSDMNHLKNKRIRSVADLLQDQFGLALVRLENVVKRTLSRAVKQKL 348

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
                     +   +  ES F            + + ++    RL+   P     +    
Sbjct: 349 IPTPKNLVTPIPLTTTYESFFGLHPLSQVLDRTNPLTQIFHARRLSYLGPGG---LTART 405

Query: 436 IIAIIKILVDLRNGKGTI 453
               ++ +     G+   
Sbjct: 406 ASFGMRNIHPSHYGRICP 423


>gi|149390434|ref|YP_001294262.1| RNA polymerase beta subunit [Illicium oligandrum]
 gi|147917387|gb|ABQ52511.1| RNA polymerase beta subunit [Illicium oligandrum]
          Length = 1062

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 205/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 712  LDKNGIVMLGSWVETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 771

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 772  GGRGRVIDVRWIQKK----RGSSSNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 824

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLG+PSRMNVGQ+FE  +G A   L +  + +  D +  
Sbjct: 825  ILPRQDMPYLQDGTPVDMVFNPLGIPSRMNVGQMFECSIGLAGNLLNRHYRIIPFDERYE 884

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 885  QEASRKLVFPELYKASKQTANPW------------------------VFE---------- 910

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YM+KL H V DK++ RS+G Y+LVTQQP
Sbjct: 911  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMMKLIHQVDDKIHGRSSGHYALVTQQP 965

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++  GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 966  LRGRAKHGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPD 1025

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L ++  L + ++    + E
Sbjct: 1026 GAPESFRLLVRELRSLALELNHFLVSEKSFQINRKE 1061



 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/632 (36%), Positives = 356/632 (56%), Gaps = 19/632 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 189 NVCYPEIFLSFPNDKEKKKIGSKENAVLEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 247

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 248 CELGRIGRRNMNQRLNLDIPQNSTFLLPRDVLAAADHLIGMKFGMGTLDDLNHLKNKRIR 307

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 308 SVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 367

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 368 QVLDRTNPLTQIVHGRKWSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 427

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E+
Sbjct: 428 GSLAIHARIGDWGSIESPFYEISERLKEEQMVYLSPRRDEYYMVAAGNSLALNRGIQEEQ 487

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 488 VVPARYRQEFLTIAWEQIHLRSIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 547

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             +E   VGTG+E   A  SG + +A+  G +   D  +IV+                  
Sbjct: 548 SHSEKCIVGTGLERQAALDSGGSAIAEHEGKITYTDTEKIVLSGN--------GDTISIP 599

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  V++  I+ADG +   G+LALG+N+LVA+MPW GYN 
Sbjct: 600 LVMYQRSNKNTCMHQKPQVHRGKCVKKGQILADGAAIIGGELALGKNILVAYMPWEGYNS 659

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 660 EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVM 719

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 720 LGSWVETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVID 779

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   +     +     R    ++ +I++  +
Sbjct: 780 VRWIQKKRGSSSNPETIRVYISQKREIKVGDK 811



 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 56/226 (24%), Positives = 106/226 (46%), Gaps = 25/226 (11%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDPPKFDV 88
           ++Q   +  F+          ++GL         +         + FV  Y+   P    
Sbjct: 9   QIQFEGFCKFI----------DQGLAEELHKFPKMEDTDQEMEFQLFVETYQLVEPLIKE 58

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
            D ++  LTY+  L ++  LI          ++ +D+++Q++++G++PLM   GT ++ G
Sbjct: 59  RDAVYESLTYSSELYVSAGLIW---------RAGRDMRKQTVFIGNIPLMNSLGTSLVNG 109

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
           I RIVV+Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I  R+ R
Sbjct: 110 IYRIVVNQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIWARVSR 166

Query: 209 RRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           ++K+ +     A+G +  +IL    YP+I  S   D     + + +
Sbjct: 167 KQKISILVPSSAMGSNLRDILDNVCYPEIFLSFPNDKEKKKIGSKE 212


>gi|186885787|gb|ACC93301.1| RNA polymerase beta subunit [Acicarpha spathulata]
          Length = 1026

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 676  LDKNGIVMLGSWVETGDILVGKLTPQMGKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 735

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 736  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYILQKREIKVGDKVAGRHGNKGIISK 788

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 789  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 848

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 849  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 875  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 929

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 930  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARREVLGTTIIGGTIPNPE 989

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 990  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1025



 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 260/806 (32%), Positives = 415/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 123  RIWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 182

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 183  YQQFACVGGDPVFSESLCKDLQKKFF-LQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 241

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 242  ILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGALR 301

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+LS LG GGV    
Sbjct: 302  HKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGVTGRT 361

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 362  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 421

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPTRYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEPQAALDSGALAIAEHEG 541

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 542  KIIYTD--------TDKILLSGNGDALSIPLVMYQRSNKNTCMHQKPQVWRGKCIKKGQI 593

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594  VAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHV 653

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 654  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMGKESSYAPEDR 713

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLRAI G +    ++T L++P G  G V+DVR   + G         R   +++ +I++ 
Sbjct: 714  LLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPEMIRVYILQKREIKVG 773

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 774  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 833

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 834  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 893

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 894  QPVI-IGKPYIL-KLIHQVDDKIHGR 917



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/180 (31%), Positives = 97/180 (53%), Gaps = 14/180 (7%)

Query: 76  FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           FV  Y+   P     D ++  LTY+  L I+  LI          K+ ++++EQ+I++G+
Sbjct: 9   FVETYQLVEPPIKERDAVYESLTYSSELYISAGLI---------GKTSRNMQEQTIFIGN 59

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S    Y   II D G  +++
Sbjct: 60  IPLMNSLGTFIVNGIYRIVINQILQSPGIYYRPELDHNGISA---YTGTIISDWGGRLEL 116

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  I  R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 117 EIDRKARIWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSFLNDKEKKKIGSKE 176


>gi|139389793|ref|YP_001123454.1| RNA polymerase beta subunit [Crucihimalaya wallichii]
 gi|158513964|sp|A4QKS3|RPOB_CRUWA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286655|dbj|BAF50278.1| RNA polymerase beta subunit [Crucihimalaya wallichii]
          Length = 1072

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/498 (30%), Positives = 238/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 628  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 682  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 739

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 740  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 796

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 797  -GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 852

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 853  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 912

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 913  TANPW------------------------VFE---------------PEYPGKSRIFDGR 933

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 934  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 993

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L
Sbjct: 994  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLAL 1053

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1054 ELNHFLVSEKNFQINRKE 1071



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 255/832 (30%), Positives = 425/832 (51%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINSRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV  S                L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSSN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMEEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|91090964|ref|XP_974653.1| PREDICTED: similar to AGAP003648-PA [Tribolium castaneum]
 gi|270013197|gb|EFA09645.1| hypothetical protein TcasGA2_TC011771 [Tribolium castaneum]
          Length = 1175

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 166/1091 (15%), Positives = 331/1091 (30%), Gaps = 214/1091 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + T      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNIALNFIGTRGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLDLAIKTKLITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  ++     N      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEIAPSAIANATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEV 601

Query: 659  EKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM 715
              I D  D   +          P L  ++   +L   +  M ++           V +G+
Sbjct: 602  SMIRDIRDREIRIYTDAGRICRPLLIVENGTLLLKKRHIDMLKEREYNNYGWQVLVASGV 661

Query: 716  -ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
             E +        ++A               +   +   +   +    Y            
Sbjct: 662  VEYIDTLEEETVMIA---------------MSPDDLRQEKEYAYCTTY------------ 694

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
                                   P+  LG       +  + +P+  +N          M 
Sbjct: 695  -----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMG 730

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             + +   ++I  F                           ++    +  V    +   + 
Sbjct: 731  KQAMG--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVT 761

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S V            +   K+ 
Sbjct: 762  TRSMEYLRFRELPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVF---YRSYKDA 818

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSD 1011
             S  +  ++ E   +        +   +Y +L +   I  G           K+  L   
Sbjct: 819  ESKRIGDQE-EQFEKPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTMTL--- 874

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                              +    ++    ++    +    R        Q    +     
Sbjct: 875  -----------------PENDDELDGTTKRFTKRDASTFLRNSETGVVDQVMLTLNSEGY 917

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            +  K+ V   R  Q GDK A RHG KG        EDM F  +G   DI++NP  +PSRM
Sbjct: 918  KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMIFTCEGLTPDIIINPHAIPSRM 977

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E   G      G+                                         
Sbjct: 978  TIGHLIECIQGKVSANKGEIGD-------------------------------------- 999

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP  D  + + I+++L+       G  ++Y+G TG   +  + +
Sbjct: 1000 ---------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQIFL 1044

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L
Sbjct: 1045 GPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFL 1104

Query: 1312 QEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKE 1353
            +E L   SD     V            R   +E    G        +   P +  +L +E
Sbjct: 1105 RERLFEVSDQYRIHVCNFCGLIAIANMRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQE 1162

Query: 1354 MQALGLSIDLE 1364
            + ++ ++  L 
Sbjct: 1163 LMSMNIAPRLM 1173



 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 139/981 (14%), Positives = 288/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     +   S   +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGELENPS-RYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  +   I       ++        + V +  R     +K              
Sbjct: 213 -----GKYAFKSEIR----SCLEHSSRPTSTLWVNMMARGGQAIKKAAIGQRIIAILPYI 263

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    ++ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNIALNFIGT 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKL 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               + +A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIANATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L         ++     E           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGTLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E+           +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFYRSYKDAESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    +         
Sbjct: 832 KPTRQTCQGMRNALYDKLDDDGIIAPGIRVSGDDVVIGKTMTLPENDDELDGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRFTKRDASTFLRNSETGVV 905


>gi|73975059|ref|XP_860708.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            6 [Canis familiaris]
          Length = 1162

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 169/1085 (15%), Positives = 321/1085 (29%), Gaps = 213/1085 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGAKPGV---TKEKRIKYAKEVLQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 427  KDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EGH +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N          E+L+      R   + I+   
Sbjct: 543  EFLEEWS-MENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEV 601

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              I  I     ++ + A  +   L   +  ++L+      Q                   
Sbjct: 602  SMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNN-------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLAMTPDDLQEKEVAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 734  G--VYITNF---------------------------HVRMDTLAHVLYYPQKPLVTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         +  +   ++++   
Sbjct: 765  EYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFD 824

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             E    +        +  I D+     L  I  G           K+             
Sbjct: 825  QEEVFEKPTRETCQGKHAIYDKLDDDGL--IAPGVRVSGDDVIIGKT------------- 869

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                                  +Y         R        Q    +     +  K+ V
Sbjct: 870  ------------------GTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 911

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 912  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIE 971

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 972  CLQGKVSANKGEIGD--------------------------------------------- 986

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L        G  +LY+G TG      + +G  Y  +
Sbjct: 987  --------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQR 1038

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L+E L   
Sbjct: 1039 LKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEA 1098

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            RT  YE    G            P +  +L +E+ ++ ++
Sbjct: 1099 SDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPYACKLLFQELMSMSIA 1156

Query: 1361 IDLEN 1365
              + +
Sbjct: 1157 PRMMS 1161



 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 145/1008 (14%), Positives = 293/1008 (29%), Gaps = 205/1008 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEE----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP---- 905
                EE     TR+           +D+ G+I  G  V+  D+++GK            
Sbjct: 821 KGFDQEEVFEKPTRETCQGKHAIYDKLDDDGLIAPGVRVSGDDVIIGKTGTNRRYTKRDC 880

Query: 906 ----MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                T E  ++  +      +           V    +  +  +RHG
Sbjct: 881 STFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHG 928


>gi|253729547|ref|YP_003029730.1| RpoB [Bambusa oldhamii]
 gi|246367057|gb|ACS94668.1| RpoB [Bambusa oldhamii]
          Length = 1075

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1009 EILTYKSDHLIARQGILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1370 NSAKME 1375
               + E
Sbjct: 1069 QVNREE 1074



 Score =  350 bits (899), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 236/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKVSILVLSSAMGSNLREILD 194

Query: 350 D--SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +           N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEILLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALDRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKV---CDGKVTNDVVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++      K    VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKEKQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPWGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFFRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++KV +     A+G +  EIL    YP+I+ S         + + +  +
Sbjct: 168 ARVSRKQKVSILVLSSAMGSNLREILDNVSYPEILLSFPNAKEKKRIESKEKAI 221


>gi|215254167|gb|ACJ64088.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 382

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 241/382 (63%), Positives = 297/382 (77%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+ 
Sbjct: 61  SAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA
Sbjct: 121 ARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           + P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K
Sbjct: 181 DKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTK 240

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           + RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS
Sbjct: 241 YTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDS 300

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GA
Sbjct: 301 ILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGA 360

Query: 887 EVNPGDILVGKITPKGESPMTP 908
           EV  GDILVGK+TPKGE+ +TP
Sbjct: 361 EVKGGDILVGKVTPKGETQLTP 382


>gi|186885833|gb|ACC93324.1| RNA polymerase beta subunit [Cnicothamnus lorentzii]
          Length = 1028

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K  +              ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVRKKRR-------SSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+ KL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYIFKLIHQVDDKIHVRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLIRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++ALL+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENALLEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVEGDPVFSEYLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAANRLIAIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGTICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N  P+      FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 304 YKWIPTPQKLVNPSPLKGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKFSFLGPGGLTGQT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYSD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRAILGMRVYTSKETCLKLPIGGRGRVIDVRWVRKKRRSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y    P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYHLVEPLIKERDAVYKSLTYSSALYVSARLIWKTDRR-------RNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G L+Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---PNGILVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|158514217|sp|A6MMT6|RPOB_ILLOL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1070

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 205/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKK----RGSSSNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLG+PSRMNVGQ+FE  +G A   L +  + +  D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGIPSRMNVGQMFECSIGLAGNLLNRHYRIIPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFPELYKASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  YM+KL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYMMKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++  GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKHGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPD 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L ++  L + ++    + E
Sbjct: 1034 GAPESFRLLVRELRSLALELNHFLVSEKSFQINRKE 1069



 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 230/632 (36%), Positives = 356/632 (56%), Gaps = 19/632 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NVCYPEIFLSFPNDKEKKKIGSKENAVLEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNMNQRLNLDIPQNSTFLLPRDVLAAADHLIGMKFGMGTLDDLNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKWSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E+
Sbjct: 436 GSLAIHARIGDWGSIESPFYEISERLKEEQMVYLSPRRDEYYMVAAGNSLALNRGIQEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 VVPARYRQEFLTIAWEQIHLRSIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             +E   VGTG+E   A  SG + +A+  G +   D  +IV+                  
Sbjct: 556 SHSEKCIVGTGLERQAALDSGGSAIAEHEGKITYTDTEKIVLSGN--------GDTISIP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  V++  I+ADG +   G+LALG+N+LVA+MPW GYN 
Sbjct: 608 LVMYQRSNKNTCMHQKPQVHRGKCVKKGQILADGAAIIGGELALGKNILVAYMPWEGYNS 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 668 EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVM 727

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728 LGSWVETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVID 787

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   +     +     R    ++ +I++  +
Sbjct: 788 VRWIQKKRGSSSNPETIRVYISQKREIKVGDK 819



 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 56/226 (24%), Positives = 106/226 (46%), Gaps = 25/226 (11%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDPPKFDV 88
           ++Q   +  F+          ++GL         +         + FV  Y+   P    
Sbjct: 17  QIQFEGFCKFI----------DQGLAEELHKFPKMEDTDQEMEFQLFVETYQLVEPLIKE 66

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
            D ++  LTY+  L ++  LI          ++ +D+++Q++++G++PLM   GT ++ G
Sbjct: 67  RDAVYESLTYSSELYVSAGLIW---------RAGRDMRKQTVFIGNIPLMNSLGTSLVNG 117

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
           I RIVV+Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I  R+ R
Sbjct: 118 IYRIVVNQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIWARVSR 174

Query: 209 RRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           ++K+ +     A+G +  +IL    YP+I  S   D     + + +
Sbjct: 175 KQKISILVPSSAMGSNLRDILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|255961373|ref|YP_003097566.1| RNA polymerase beta subunit [Dendrocalamus latiflorus]
 gi|255040250|gb|ACT99910.1| RNA polymerase beta subunit [Dendrocalamus latiflorus]
          Length = 1075

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1009 EILTYKSDHLIARQGILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1370 NSAKME 1375
               + E
Sbjct: 1069 QVNREE 1074



 Score =  351 bits (900), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 236/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 D--SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +           N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEILLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALDRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKV---CDGKVTNDVVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++      K    VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKEKQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPWGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFFRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I+ S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEILLSFPNAKEKKRIESKEKAI 221


>gi|186885849|gb|ACC93332.1| RNA polymerase beta subunit [Dolichlasium lagascae]
          Length = 1028

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  368 bits (945), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 416/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNL  P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGRIGRRNMNRRLNLAIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L++++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 244  ILAAADRLIEIKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGALK 303

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+   P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKLIATPQNLVTLTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLEKYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|290489640|gb|ADD31204.1| RNA polymerase beta subunit protein [Heuchera sanguinea]
          Length = 1072

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 722  LDKNGIVRLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQISTSKETCLKLPI 781

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 782  GGKGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 834

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 835  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 894

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 895  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 975

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 976  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1035

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1036 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 251/780 (32%), Positives = 403/780 (51%), Gaps = 43/780 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195  LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESVCKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  VGR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254  QRCELGRVGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314  IRSVADLLQDQFGLALVRLENVVRGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+LS LG GG+    A   +RD+H +HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDRTNPLTQIVHARKLSYLGPGGLTGRTASFRIRDIHSSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGS 639
            L+ SL   AR+  +G +E+P+ ++ + + +  V   YLS   +E   IA  NS     G 
Sbjct: 434  LIGSLAIHARIGHWGSLESPFYEISESERSKKVRMLYLSPSRDEYYMIAAGNSLALNQGI 493

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQ
Sbjct: 494  QEEQVVPARYRQEFLSIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQ 553

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            AVPL ++E   VGTG+E   A  SG   +A+  G +   D         +  +       
Sbjct: 554  AVPLSRSEKCIVGTGLERQAALDSGVPAIAEHEGKIIYTD--------TDKIILSGNGNT 605

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                L+ ++RSN+NTC++Q+P V  G  +++  I+ADG +   G+LALG+N+LVA+MPW 
Sbjct: 606  LSIPLIMYERSNKNTCMHQKPQVHRGKCIKKGQILADGAAIVGGELALGKNVLVAYMPWE 665

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYN ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ 
Sbjct: 666  GYNSEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKN 725

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            GI+ +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G
Sbjct: 726  GIVRLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQISTSKETCLKLPIGGKG 785

Query: 938  TVVDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEIL 990
             V+DVR   + G         R    ++ +I++  +      ++ +I        +  + 
Sbjct: 786  RVIDVRWIQKKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQ 845

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN--------- 1034
             G+            + ++   I E           + ++ A  DE+ ++          
Sbjct: 846  DGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSE 905

Query: 1035 -VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E+ K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  LYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|187233923|gb|ACD01208.1| RNA polymerase beta subunit [Phyllostachys propinqua]
          Length = 1075

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 124/308 (40%), Positives = 179/308 (58%), Gaps = 46/308 (14%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE---TGTPESFNVLVKEMQALGLSID--LENSR 1367
            E+LT KSD ++ R  +  + + G           PESF VLV+E+++L L ++  L + +
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEYP--PESFRVLVRELRSLALELNHFLVSEK 1066

Query: 1368 TKNSAKME 1375
                 + E
Sbjct: 1067 NFQVNREE 1074



 Score =  354 bits (908), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 235/699 (33%), Positives = 383/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLKEILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVTHRRSNKNTCMHQKPRVLRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G + +EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLKEILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|48478763|ref|YP_024371.1| RNA polymerase beta subunit [Saccharum hybrid cultivar SP-80-3280]
 gi|50812518|ref|YP_054621.1| RNA polymerase beta subunit [Saccharum officinarum]
 gi|68053153|sp|Q6ENX3|RPOB_SACOF RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|48478665|gb|AAT44685.1| RNA polymerase beta chain [Saccharum hybrid cultivar SP80-3280]
 gi|49659502|dbj|BAD27283.1| RNA polymerase beta subunit [Saccharum hybrid cultivar NCo 310]
          Length = 1075

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 125/306 (40%), Positives = 177/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 RVNRED 1074



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 235/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISICTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  VGR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRVGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  L+Q+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLAQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISSDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVAHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT+ IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKQIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R   D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPFDIMVRVYILQKREIKVGDK 824



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 103/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERNAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +    II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---ICTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|92090945|sp|Q6L3A7|RPOB_SACHY RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1075

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 125/306 (40%), Positives = 177/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 RVNRED 1074



 Score =  352 bits (902), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 235/669 (35%), Positives = 368/669 (55%), Gaps = 27/669 (4%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILY-VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I+           L  +    +    IL  V          N     + + ++ A+L+ 
Sbjct: 165 RIWARVSRKQKISILVLLSAMGLNLREILDNVSYPEIFLSFLNAKEKKRIESKEKAILEF 224

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD+             FF   K +L  VGR  MN RLNLD P +   +   D
Sbjct: 225 YQQFACVGGDLVFSESLCEELQKKFF-QQKCELGRVGRRNMNRRLNLDIPQNNTFLLPRD 283

Query: 436 IIAIIKILVDLRNGKGTIDDID--NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERIS 491
           ++A    L+ ++ G G +DD D  +L N+R+RSV ++L++Q+ L L R++ +++   R  
Sbjct: 284 VLAATDHLIGMKFGTGILDDDDMNHLKNKRIRSVADLLQDQFGLALGRLQHAVQKTIRRV 343

Query: 492 SVDIDSVMPQDLINAKP----VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            +      PQ L+        +++    FF +  L+Q+ +  N L++  H R++S LG G
Sbjct: 344 FIRQSKPTPQTLVTPTSTSILLITTYETFFGTYPLAQVFDQTNPLTQTVHGRKVSCLGPG 403

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN-AYGFIETPYRKVC 606
           G+    A    RD+HP+HYGRICP +TSEG N+GL  SL   AR++  +G IE+P+ ++ 
Sbjct: 404 GLTGRTASFRSRDIHPSHYGRICPIDTSEGINVGLTGSLAIHARIDHWWGSIESPFYEIS 463

Query: 607 DGKVTND---VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           +         VVYLS   +E   IA  NS     G   E++V  R   E + +  E+I  
Sbjct: 464 EKAKEKKERQVVYLSPNRDEYYMIAAGNSLSLNQGIQEEQVVPARYRQEFLTIAWEQIHV 523

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
               P Q  SI  SLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  S
Sbjct: 524 RSIFPFQYFSIGGSLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQTALDS 583

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             +++A+R G +   D+ +I++         S+       L+  +RSN+NTC++Q+P V 
Sbjct: 584 RVSVIAEREGKIISSDSHKILL--------SSSGKTISIPLVAHRRSNKNTCMHQKPRVP 635

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            G  +++  I+A+G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS H
Sbjct: 636 RGKSIKKGQILAEGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFH 695

Query: 844 IEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           I ++E+    T  G  E+IT+ IP++ E  L+N+D  G++ +G+ V  GDILVGK+TP+ 
Sbjct: 696 IRKYEIQTDTTSQGSAEKITKQIPHLEEHLLRNLDRNGVVRLGSWVETGDILVGKLTPQI 755

Query: 903 ESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            S  +   E  LLRAIFG +    ++TSL++P G  G V+DV+   R   D   R   ++
Sbjct: 756 ASESSYIAEAGLLRAIFGLEVSTSKETSLKLPIGGRGRVIDVKWIQRDPFDIMVRVYILQ 815

Query: 961 REQIELLAR 969
           + +I++  +
Sbjct: 816 KREIKVGDK 824



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 106/234 (45%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERNAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +    II D G  +++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---ICTGTIISDWGGRLELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +   L A+G++  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLLSAMGLNLREILDNVSYPEIFLSFLNAKEKKRIESKEKAI 221


>gi|324120662|dbj|BAJ78722.1| RNA polymerase II second largest subunit [Protohermes grandis]
          Length = 1175

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 169/1084 (15%), Positives = 328/1084 (30%), Gaps = 200/1084 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                    I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLDLAIKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRIN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             I D  D   +          P L  ++   +L   ++                      
Sbjct: 603  MIRDIRDREIRIYTDSGRICRPLLIVENGKLLLKKRHIDMLKEREYNNYG--------WQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            V  +SG           E +D         E  +  + S  D+    ++           
Sbjct: 655  VLVASGVV---------EYIDT------LEEETVMIAMSPEDLRHEKEYA---------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                        +       +  LG       +  + +P+  +N          M  + +
Sbjct: 690  --------YCTTHTHCEIHAAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 734

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V    +   +    +
Sbjct: 735  G--VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSM 765

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   D   + I 
Sbjct: 766  EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFF-RSVFYRSYKDSESKRIG 824

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + EQ E   R           +       I  G           K+  L          
Sbjct: 825  DQEEQFEKPTRQTCQGMRNAHYDKLDDDGIISPGIRVSGDDVVIGKTITL---------- 874

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       + +  +E    ++    +    R        Q    +     +  K+ V
Sbjct: 875  ----------PENEDELEGTTKRFTKRDASTFLRNSETGVVDQVMLTLNSEGYKFCKIRV 924

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 925  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIE 984

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 985  CIQGKVSSNKGEIGD--------------------------------------------- 999

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L+       G  ++Y+G TG   +  + +G  Y  +
Sbjct: 1000 --------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQIFLGPTYYQR 1051

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   
Sbjct: 1052 LKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEV 1111

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            R   +E    G        +   P +  +L +E+ ++ ++
Sbjct: 1112 SDPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIA 1169

Query: 1361 IDLE 1364
              L 
Sbjct: 1170 PRLM 1173



 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 144/986 (14%), Positives = 288/986 (29%), Gaps = 194/986 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  Y   I       ++        + V +  R     +K              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQAIKKAAIGQRIIAILPYI 263

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   K++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 324 RGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 381

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        D       + 
Sbjct: 382 LDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLD-------LA 434

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 435 IKTKMITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRINSPIGRDGK 494

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 495 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 551

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 552 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 611

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               T  GRIC P    E   + L         ++     E           +  V Y+ 
Sbjct: 612 IRIYTDSGRICRPLLIVENGKLLLKKR-----HIDMLKEREYNNYGWQVLVASGVVEYID 666

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            +EEE   IA +   L                 E+           +     ++ + AS+
Sbjct: 667 TLEEETVMIAMSPEDL---------------RHEKEYAYCTTHTHCEIHAAMILGVCASI 711

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 712 IPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV---------------------------- 743

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + V  Y                +PLV                
Sbjct: 744 -------------RMDTLAHVLYYP--------------HKPLV----------TTRSME 766

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G N +VA + + GYN EDS++++   V    F S+    ++          
Sbjct: 767 YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGDQ 826

Query: 859 EEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           EE            +       +D+ GII  G  V+  D+++GK     E+    E    
Sbjct: 827 EEQFEKPTRQTCQGMRNAHYDKLDDDGIISPGIRVSGDDVVIGKTITLPENEDELEGTT- 885

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 K    RD S  + +  +G V
Sbjct: 886 ------KRFTKRDASTFLRNSETGVV 905


>gi|187763097|ref|YP_001876572.1| RNA polymerase beta subunit [Welwitschia mirabilis]
 gi|163311627|gb|ABY26785.1| RNA polymerase beta subunit [Welwitschia mirabilis]
          Length = 1108

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 155/506 (30%), Positives = 227/506 (44%), Gaps = 73/506 (14%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  +  G IL       G   +   + +L A    +  +  D  L     +   ++ 
Sbjct: 635  INQGKYIKKGQILADGAVTVG-GEICLGKNILVAYMPWQGYNFEDAILISERLIYEDILT 693

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+             ++I  L          LD N   R+     G     G   
Sbjct: 694  SFHITRYETTICTTECETLTKKIPQLDPYL---LRHLDENGLVRV-----GSWVQPGDVL 745

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ---YETSKSILEDRFKNKIE 1058
              K    S +  S +P  +  Q        +        +    + +   LE  +++ +E
Sbjct: 746  VGKLKPRSPEEFSRFPELRLLQDIFCTPPTKETCLRAGGKGQVIDLNWIKLETLWEDDLE 805

Query: 1059 KIQWGDDMP---------------------PGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            K+   ++                             V V++  KR IQ GDK+AGRHGNK
Sbjct: 806  KVHQENEEDDDTEDFYDDTIYEKVYPIDHVYSDSEKVHVYLLQKRQIQVGDKVAGRHGNK 865

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            GI+S +LP +DMP+L++G  VD+VLNPLGVPSRMNVGQIFE  LG A     K  +    
Sbjct: 866  GIISVVLPRQDMPYLQNGVSVDMVLNPLGVPSRMNVGQIFECLLGLAGTLTNKHYRIPPF 925

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
            D +   + S    F E    +                               VF+     
Sbjct: 926  DERYEQEASRKLVFSELYKASEQTANPW------------------------VFE----- 956

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                      L+  G++ ++DG TGE F++PVT+G  YM+KL H V DK++ARSTGSY+ 
Sbjct: 957  ----------LEHLGKTKIFDGRTGEIFEQPVTIGKAYMMKLIHQVEDKMHARSTGSYAR 1006

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            +TQQP+ GKS  GGQRLGEMEVW ++++G A +LQEMLT+KSD +  R +V +SI+ G  
Sbjct: 1007 ITQQPVQGKSKGGGQRLGEMEVWALESFGVACILQEMLTVKSDHMEARKKVLKSILDGRS 1066

Query: 1338 TFETGT-PESFNVLVKEMQALGLSID 1362
              +  T  ESF VL++E+++L L I 
Sbjct: 1067 VPKANTATESFRVLIRELRSLALEIQ 1092



 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 204/585 (34%), Positives = 319/585 (54%), Gaps = 27/585 (4%)

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNF---LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           A+L  Y  +     ++  +A S F     + F S +  L  +GR  +N +LNL+ P++  
Sbjct: 223 AILTFYEELDSIKCNSKDLAFSEFLSKKLINFLSKRCKLGRIGRQNLNKKLNLEIPENEI 282

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +  +D++AI++ L+ L  G GT D+ID+L NRR  SV + LK +  + L  ++  I+E 
Sbjct: 283 FLLPQDVLAIVEYLIKLSYGVGTFDNIDHLQNRRFCSVADFLKKEVGIALDNVKVLIQEI 342

Query: 490 ISSVDIDSVM-------PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           + +++I++          +  + +  +   +  FF    LSQ  E  N L+ I H R++S
Sbjct: 343 MQTIEIENQNKRIILPEFEFFLVSTEITKTLNHFFGLHPLSQFLEQTNPLAEILHARKVS 402

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            LG GG+    A    RD+HP++YGR CP  T EG N GL++SL   A+V+  G +E+P+
Sbjct: 403 FLGPGGLTEQTASFRARDIHPSYYGRFCPINTPEGQNAGLIASLAISAKVDNSGSLESPF 462

Query: 603 RKVCDGKVTND-VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            K+ +       + YL   E+E+  IA  N    +     ++    +   E + +  E+I
Sbjct: 463 YKIAEKTKKEQLISYLLPSEDESYRIALGNFLAVDQKIPEKKNTPTQYRQEFLSIAWEQI 522

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            F    P Q  SI  SLIPFLE++D+ R LMG NMQRQAVP L+ E   VGTG+ES VA 
Sbjct: 523 HFRSILPFQYFSIGVSLIPFLEHNDATRALMGSNMQRQAVPPLQPEKCIVGTGLESQVAL 582

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   ++K+ G ++ +DA  I        +  S        L  +QRSN NT + Q+P 
Sbjct: 583 DSGNLAISKQEGRIKYIDAETI--------ISSSKGNTTQIELQTYQRSNSNTLMYQKPH 634

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           +  G  +++  I+ADG  T  G++ LG+N+LVA+MPW GYNFED++LISER++ ED+ TS
Sbjct: 635 INQGKYIKKGQILADGAVTVGGEICLGKNILVAYMPWQGYNFEDAILISERLIYEDILTS 694

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            HI  +E          E +T+ IP +    L+++DE G++ VG+ V PGD+LVGK+ P+
Sbjct: 695 FHITRYETTI--CTTECETLTKKIPQLDPYLLRHLDENGLVRVGSWVQPGDVLVGKLKPR 752

Query: 902 GESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                +  PE +LL+ IF             + +G  G V+D+  
Sbjct: 753 SPEEFSRFPELRLLQDIFCTPPTK----ETCLRAGGKGQVIDLNW 793



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 77/382 (20%), Positives = 149/382 (39%), Gaps = 33/382 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F +  E+  IP+  ++Q   +  F+           +GLQ        I         
Sbjct: 1   MQFEEKKEMFTIPEFGQIQLEGFCRFI----------EQGLQEKLFQFPKIENTKKGLEF 50

Query: 75  EFVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            F   Y+   P  +  D +++ LTY+    +    + +           K + ++ IY+G
Sbjct: 51  FFGKNYKIIEPSINERDAVYQRLTYSSKFYVPGFFVYWK----------KILSKKMIYLG 100

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           ++PLM   GTFVI G  R+VV+QL R+PGI++  ++ R       +    +I D G  + 
Sbjct: 101 EIPLMNNKGTFVINGNYRVVVNQLIRNPGIYYSLERKRTGN----ICTSTLISDCGGRLK 156

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW-CFPLSAA 252
            E D +  I VR+ R++KV +  F   +G++ EEIL+       Y +  + W     +  
Sbjct: 157 FELDREKNIWVRVSRKKKVSILVFFFVMGLNIEEILN----NTCYLKGFEGWGLICNNKK 212

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                ++   +++        ++S K  +  L  S          ++  C  G    +++
Sbjct: 213 LKKKLSRQRGAILTFYEE---LDSIKCNSKDLAFSEFLSKKLINFLSKRCKLGRIGRQNL 269

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                 EI      ++ +  L  + +       +   D++++    R   V D  K    
Sbjct: 270 NKKLNLEIPENEIFLLPQDVLAIVEYLIKLSYGVGTFDNIDHLQNRRFCSVADFLKKEVG 329

Query: 373 ALLDIYRVMRPGDVSTFSVAES 394
             LD  +V+    + T  +   
Sbjct: 330 IALDNVKVLIQEIMQTIEIENQ 351


>gi|186885853|gb|ACC93334.1| RNA polymerase beta subunit [Duidaea pinifolia]
          Length = 1028

 Score =  384 bits (986), Expect = e-104,   Method: Composition-based stats.
 Identities = 151/497 (30%), Positives = 234/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMGKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RDSSSKPESIRVYILQKREIKVGDKIAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDPPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/661 (35%), Positives = 369/661 (55%), Gaps = 18/661 (2%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           Y+     G    FS + S      F   + +L  +GR  MN RLNLD P +   +   DI
Sbjct: 185 YQQFACVGGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDI 244

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
           +A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +   
Sbjct: 245 LAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKH 304

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    A
Sbjct: 305 NWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTA 364

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      +
Sbjct: 365 TFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGARM 424

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  SI
Sbjct: 425 LYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSI 484

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G 
Sbjct: 485 GASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEGK 544

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I+
Sbjct: 545 IIYSD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQIL 596

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    T
Sbjct: 597 AYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHVT 656

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKL 912
             GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++L
Sbjct: 657 SQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMGKESSYAPEDRL 716

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELLA 968
           LR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++  
Sbjct: 717 LRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRDSSSKPESIRVYILQKREIKVGD 776

Query: 969 R 969
           +
Sbjct: 777 K 777



 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKEKDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---HNGIAVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|290489632|gb|ADD31200.1| RNA polymerase beta subunit protein [Cornus florida]
          Length = 1070

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNLQINRKE 1069



 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 238/686 (34%), Positives = 379/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSDSLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ ++ +      V+YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHLGSLESPFYEISERPKKVRVLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+  G +   D  +IV+                  L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEHEGKIVYTDTDKIVLSGN--------GNTISIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  ++R  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPRVQGGKCIKRGQILADGAATVGGELALGKNILVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V EDV+TS HI ++EV    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDVYTSFHIRKYEVQTHVTSQGPERVTSEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 RGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP+  ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPEFNQIQFEGFCRFI----------DRGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI R+V++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRVVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|186885869|gb|ACC93342.1| RNA polymerase beta subunit [Gochnatia hypoleuca]
          Length = 1028

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K  +              ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVRKKRR-------SSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+ KL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYIFKLIHQVDDKIHVRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLIRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++ALL+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENALLEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVEGDPVFSEYLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIAIKFGMGTLDDMNHLKNKRIRSVADLLREQFGLALVRLENMARGTICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N  P+      FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 304 YKWIPTPQKLVNPSPLKGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKFSFLGPGGLTGQT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRAILGMRVYTSKETCLKLPIGGRGRVIDVRWVRKKRRSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y    P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYHLVEPLIKERDAVYKSLTYSSALYVSARLIWKTDRR-------RNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G L+Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---PNGILVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|307697295|gb|ADN86102.1| RNA polymerase beta subunit [Chasmanthium latifolium]
          Length = 1075

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 125/306 (40%), Positives = 177/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 QVNRED 1074



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 236/699 (33%), Positives = 383/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKEKIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  VGR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRVGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSKVSVIAEREGKIISSDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVAHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELERFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKEKIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|149390532|ref|YP_001294176.1| RNA polymerase beta subunit [Buxus microphylla]
 gi|158513756|sp|A6MM28|RPOB_BUXMI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|146762277|gb|ABQ45241.1| RNA polymerase beta subunit [Buxus microphylla]
          Length = 1070

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 134/395 (33%), Positives = 205/395 (51%), Gaps = 49/395 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  +S   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQTSKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G +  P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSNYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L++GTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQNGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y++KL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYIMKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKM 1374
             TPESF +LV+E+++L L ++  L + +     + 
Sbjct: 1034 DTPESFRLLVRELRSLALELNHFLVSEKNFQINRK 1068



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 415/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILY-VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L            IL  V          N     K   +++A+L+ 
Sbjct: 167  RIWARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKENAILEF 226

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 227  YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 285

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E +++  I     
Sbjct: 286  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENAVRGTICGAIR 345

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 346  HKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRT 405

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 406  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGHWGSLESPFYEISERSKKVR 465

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS  ++E   +A  NS     G   E++V  R   E + +  E++      P Q  S
Sbjct: 466  MLYLSPSKDEYYMVAAGNSLSLNKGIQEEQVVPARYRQEFLTIAWEQVHLRSIFPFQYFS 525

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG + +A+  G
Sbjct: 526  IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGVSAIAEHEG 585

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D        ++  +           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 586  KIIYTD--------IDKIILSGNGDTLRIPLVMYQRSNKNTCMHQKPQVQRGKCIKKGQI 637

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADG +T  G+LALG+N+LVA+MPW GYN ED++LISE +V  D++TS HI ++E+    
Sbjct: 638  LADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISECLVYRDIYTSFHIRKYEIQTHV 697

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
            T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++
Sbjct: 698  TSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQTSKESSYAPEDR 757

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLRAI G +    ++T L++P G  G V+DVR   + G         R    ++ +I++ 
Sbjct: 758  LLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSNYNPETIRVYISQKREIKVG 817

Query: 968  AR--DKDDEQVILDRNIYSRLMEILCG-------QNAVSGPKGFKKSTVLSSDL-ISEYP 1017
             +   +   + I+ + +  + M  L          N +  P       +    L ++   
Sbjct: 818  DKVAGRHGNKGIISKILPRQDMPYLQNGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGGL 877

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 878  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 937

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++ MK   Q  DK+ GR
Sbjct: 938  QPVI-IGKSYI-MKLIHQVDDKIHGR 961



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 109/236 (46%), Gaps = 25/236 (10%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS- 78
            E+  IP   ++Q   +  F+          ++GL         I         + FV  
Sbjct: 7   EEMSTIPGFSQIQFEGFCRFI----------DQGLMEELYKFPKIEDTDQEIEFQLFVET 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L +   LI          K+ ++++EQ+I++G++PLM
Sbjct: 57  YQLAEPLIKERDAVYESLTYSSELYVPAGLIW---------KTSRNMQEQTIFIGNIPLM 107

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GT ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D 
Sbjct: 108 NSLGTSIVNGIYRIVINQILQSPGIYYRSELD---HNGTSVYTGTIISDWGGRSELEIDR 164

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 165 KARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|139389634|ref|YP_001123191.1| RNA polymerase beta subunit [Arabis hirsuta]
 gi|158513575|sp|A4QK10|RPOB_ARAHI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286389|dbj|BAF50015.1| RNA polymerase beta subunit [Arabis hirsuta]
          Length = 1072

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 154/498 (30%), Positives = 238/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 628  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 682  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 739

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 740  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 796

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 797  -GGTSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 852

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 853  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 912

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 913  TANPW------------------------VFE---------------PEYPGKSRIFDGR 933

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 934  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 993

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L
Sbjct: 994  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLAL 1053

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1054 ELNHFLVSEKNFQINRKE 1071



 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 251/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS         E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKEARIRMLFLSPSQDEYYMIAAGNSLALNRDIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E+++     P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVNLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I++                  L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILSTDTEKIIL--------SGDGNTISIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGTSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   G 
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGI 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|324120652|dbj|BAJ78717.1| RNA polymerase II second largest subunit [Bemisia tabaci]
          Length = 1176

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 169/1090 (15%), Positives = 332/1090 (30%), Gaps = 212/1090 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKDKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNMELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTGM- 715
             I D  D   +          P L  ++   +L   ++   +Q           V +G+ 
Sbjct: 603  IIRDIRDREIRIYTDAGRICRPLLIVENQTLLLKRSHVDNLKQRDYNNYKWQELVSSGVV 662

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +        ++A               +   +   D   +    Y             
Sbjct: 663  EYIDTLEEETTMIA---------------MSPEDLRQDKEYAYCTTY------------- 694

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                                  P+  LG       +  + +P+  +N          M  
Sbjct: 695  ----------------THCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGK 731

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   ++I  +                           ++    +  V    +   +  
Sbjct: 732  QAMG--VYITNY---------------------------HVRMDTLAHVLYYPHKPLVTT 762

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S V         F      K+  
Sbjct: 763  RSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFF---RSYKDSE 819

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDL 1012
            S  +  ++ E   +        +   IY +L +   I  G           K+  L    
Sbjct: 820  SKRIGDQE-EQFEKPNRSTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITL---- 874

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                             +    +E    +Y    +    R        Q    +     +
Sbjct: 875  ----------------PENDDELEGTTKRYSKRDASTFLRNSETGIVDQVMLTLNSEGYK 918

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
              K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM 
Sbjct: 919  FCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLAPDIIINPHAIPSRMT 978

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 979  IGHLIECLQGKVSSNKGEIGD--------------------------------------- 999

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+++L+       G  ++Y+G +G   +  V +G
Sbjct: 1000 --------------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHSGRKINAQVFLG 1045

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+
Sbjct: 1046 PTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLR 1105

Query: 1313 EMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEM 1354
            E L   SD     V            R   +E    G        +   P +  +L +E+
Sbjct: 1106 ERLFEVSDPYRIHVCNYCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQEL 1163

Query: 1355 QALGLSIDLE 1364
             A+ ++  L 
Sbjct: 1164 MAMNIAPRLM 1173



 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 140/981 (14%), Positives = 288/981 (29%), Gaps = 184/981 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIETP-PRYLLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    +       +       ++G +
Sbjct: 98  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVIKDGQEPVVTEHEKS-----FIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTFCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKDKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNMELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    +  +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   +     L   + V+     +    K  +   +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENQTL-----LLKRSHVDNLKQRDYNNYKWQELVSSGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 ++           +  P  ++ + AS+IPF +
Sbjct: 672 TTMIAMSPEDL---------------RQDKEYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNYHV--------------------------------- 743

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y                +PLV                     
Sbjct: 744 --------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFR 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE   
Sbjct: 772 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFFRSYKDSESKRIGDQEEQFE 831

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +D+ GII  G  V+  D+++GK     E+    E         
Sbjct: 832 KPNRSTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENDDELEGTT------ 885

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + +  +G V
Sbjct: 886 -KRYSKRDASTFLRNSETGIV 905


>gi|12644277|sp|P46818|RPOB_SINAL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|5457427|emb|CAB48411.1| RNA polymerase A beta subunit [Sinapis alba]
          Length = 1078

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 138/415 (33%), Positives = 211/415 (50%), Gaps = 52/415 (12%)

Query: 965  ELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            E + ++    E  +L      +   ++ G    +G     K T   +   S  P  +  +
Sbjct: 711  ERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLR 768

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              +  +        LK+       +++ R+  K      G    P    +++V+++ KR 
Sbjct: 769  AILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKRE 821

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG 
Sbjct: 822  IKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGL 881

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   L +  +    D +   + S    F E    +                         
Sbjct: 882  AGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------------------ 923

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                  VF+                +  G+S ++DG TG+PF++PV +G  Y+LKL H V
Sbjct: 924  ------VFE---------------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQV 962

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD + 
Sbjct: 963  DDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIR 1022

Query: 1324 GRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             R  V  + + G    +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1023 ARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1077



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 254/832 (30%), Positives = 427/832 (51%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 149  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 208

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 209  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 267

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 268  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 327

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  I       ++P  Q+L+ + P+ +    FF    LSQ+ +  
Sbjct: 328  QDQLGLALARLENVVKGTIGGAIRHKLIPPTQNLVTSTPLTTTYESFFGFHPLSQVLDRT 387

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 388  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 447

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E++V  
Sbjct: 448  ARIGDWGSLESPFYELVEKSKKAQIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQVVPA 507

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 508  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 567

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I++   E  L           L+ +
Sbjct: 568  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIILSGNENTL--------SIPLIMY 619

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 620  QRSNKNTCMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAV 679

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 680  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 739

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 740  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 799

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 800  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 859

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 860  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 919

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 920  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 969



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 18  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 67

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 68  PLIKERDAVYESLTYSSELYVSAGLIW---------KTNRNMQEQRIFIGNIPLMNSLGT 118

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI R+V++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 119 SIVNGIYRVVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 175

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 176 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 226


>gi|220983464|dbj|BAH11233.1| RNA polymerase beta chain [Welwitschia mirabilis]
          Length = 1108

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 157/507 (30%), Positives = 229/507 (45%), Gaps = 75/507 (14%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  +  G IL       G   +   + +L A    +  +  D  L     +   ++ 
Sbjct: 635  INQGKYIKKGQILADGAVTVG-GEICLGKNILVAYMPWQGYNFEDAILISERLIYEDILT 693

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+             ++I  L          LD N   R+     G     G   
Sbjct: 694  SFHITRYETTICTTECETLTKKIPQLDPYL---LRHLDENGLVRV-----GSWVQPGDVL 745

Query: 1002 FKKSTVLSSDLISEYPRSQWWQF------------------------AVQDEKVQRN-VE 1036
              K    S +  S +P  +  Q                          ++ E +  + +E
Sbjct: 746  VGKLKPRSPEEFSRFPELRLLQDLFCTPPTKETCLRAGGKGQVIDLNWIKLETLWEDDLE 805

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  + E      +       EK+   D +     + V V++  KR IQ GDK+AGRHGN
Sbjct: 806  KVHQENEEDDDTEDFYDDTIYEKVYPIDHVYSDSEK-VHVYLLQKRQIQVGDKVAGRHGN 864

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KGI+S +LP +DMP+L++G  VD+VLNPLGVPSRMNVGQIFE  LG A     K  +   
Sbjct: 865  KGIISVVLPRQDMPYLQNGVSVDMVLNPLGVPSRMNVGQIFECLLGLAGTLTNKHYRIPP 924

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D +   + S    F E    +                               VF+    
Sbjct: 925  FDERYEQEASRKLVFSELYKASEQTANPW------------------------VFE---- 956

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                       L+  G++ ++DG TGE F++PVT+G  YM+KL H V DK++ARSTGSY+
Sbjct: 957  -----------LEHLGKTKIFDGRTGEIFEQPVTIGKAYMMKLIHQVEDKMHARSTGSYA 1005

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
             +TQQP+ GKS  GGQRLGEMEVW ++++G A +LQEMLT+KSD +  R +V +SI+ G 
Sbjct: 1006 RITQQPVQGKSKGGGQRLGEMEVWALESFGVACILQEMLTVKSDHMEARKKVLKSILDGR 1065

Query: 1337 DTFETGT-PESFNVLVKEMQALGLSID 1362
               +  T  ESF VL++E+++L L I 
Sbjct: 1066 SVPKANTATESFRVLIRELRSLALEIQ 1092



 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 203/585 (34%), Positives = 319/585 (54%), Gaps = 27/585 (4%)

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNF---LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           A+L  Y  +     ++  +A S F     + F S +  L  +GR  +N +LNL+ P++  
Sbjct: 223 AILTFYEELDSIKCNSKDLAFSEFLSKKLINFLSKRCKLGRIGRQNLNKKLNLEIPENEI 282

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +  +D++AI++ L+ L  G GT D+ID+L NRR  SV + LK +  + L  ++  I+E 
Sbjct: 283 FLLPQDVLAIVEYLIKLSYGVGTFDNIDHLQNRRFCSVADFLKKEVGIALDNVKVLIQEI 342

Query: 490 ISSVDIDSVM-------PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           + +++I++          +  + +  +   +  FF    LSQ  E  N L+ I H R++S
Sbjct: 343 MQTIEIENQNKRIILPEFEFFLVSTEITKTLNHFFGLHPLSQFLEQTNPLAEILHARKVS 402

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            LG GG+    A    RD+HP++YGR CP  T EG N GL++SL   A+V+  G +E+P+
Sbjct: 403 FLGPGGLTEQTASFRARDIHPSYYGRFCPINTPEGQNAGLIASLAISAKVDNSGSLESPF 462

Query: 603 RKVCDGKVTND-VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            K+ +       + YL   E+E+  IA  N    +     ++    +   E + +  E+I
Sbjct: 463 YKIAEKTKKEQLISYLLPSEDESYRIALGNFLAVDQKIPEKKNTPTQYRQEFLSIAWEQI 522

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            F    P Q  SI  SLIPFLE++D+ R LMG NMQRQAVP L+ E   VGTG+ES VA 
Sbjct: 523 HFRSILPFQYFSIGVSLIPFLEHNDATRALMGSNMQRQAVPPLQPEKCIVGTGLESQVAL 582

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   ++K+ G ++ +DA  I        +  S        L  +QRSN NT + Q+P 
Sbjct: 583 DSGNLAISKQEGRIKYIDAETI--------ISSSKGSTTQIELQTYQRSNSNTLMYQKPH 634

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           +  G  +++  I+ADG  T  G++ LG+N+LVA+MPW GYNFED++LISER++ ED+ TS
Sbjct: 635 INQGKYIKKGQILADGAVTVGGEICLGKNILVAYMPWQGYNFEDAILISERLIYEDILTS 694

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            HI  +E          E +T+ IP +    L+++DE G++ VG+ V PGD+LVGK+ P+
Sbjct: 695 FHITRYETTI--CTTECETLTKKIPQLDPYLLRHLDENGLVRVGSWVQPGDVLVGKLKPR 752

Query: 902 GESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                +  PE +LL+ +F             + +G  G V+D+  
Sbjct: 753 SPEEFSRFPELRLLQDLFCTPPTK----ETCLRAGGKGQVIDLNW 793



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 77/382 (20%), Positives = 149/382 (39%), Gaps = 33/382 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F +  E+  IP+  ++Q   +  F+           +GLQ        I         
Sbjct: 1   MQFEEKKEMFTIPEFGQIQLEGFCRFI----------EQGLQEKLFQFPKIENTKKGLEF 50

Query: 75  EFVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            F   Y+   P  +  D +++ LTY+    +    + +           K + ++ IY+G
Sbjct: 51  FFGKNYKIIEPSINERDAVYQRLTYSSKFYVPGFFVYWK----------KILSKKMIYLG 100

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           ++PLM   GTFVI G  R+VV+QL R+PGI++  ++ R       +    +I D G  + 
Sbjct: 101 EIPLMNNKGTFVINGNYRVVVNQLIRNPGIYYSLERKRTGN----ICTSTLISDCGGRLK 156

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW-CFPLSAA 252
            E D +  I VR+ R++KV +  F   +G++ EEIL+       Y +  + W     +  
Sbjct: 157 FELDREKNIWVRVSRKKKVSILVFFFVMGLNIEEILN----NTCYLKGFEGWGLICNNKK 212

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
                ++   +++        ++S K  +  L  S          ++  C  G    +++
Sbjct: 213 LKKKLSRQRGAILTFYEE---LDSIKCNSKDLAFSEFLSKKLINFLSKRCKLGRIGRQNL 269

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                 EI      ++ +  L  + +       +   D++++    R   V D  K    
Sbjct: 270 NKKLNLEIPENEIFLLPQDVLAIVEYLIKLSYGVGTFDNIDHLQNRRFCSVADFLKKEVG 329

Query: 373 ALLDIYRVMRPGDVSTFSVAES 394
             LD  +V+    + T  +   
Sbjct: 330 IALDNVKVLIQEIMQTIEIENQ 351


>gi|296936663|gb|ADH94335.1| RNA polymerase beta subunit [Syzygium cumini]
          Length = 1072

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 137/405 (33%), Positives = 206/405 (50%), Gaps = 51/405 (12%)

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            E  IL      +   ++ G    +G     K T  ++   S  P  +  +  +  +    
Sbjct: 715  EAHILRN--LDKNGIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTS 772

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                LK+       +++ R+  K      G +  P     + V++  KR I+ GDK+AGR
Sbjct: 773  KETCLKLPIGGRGRVIDVRWIQKKG----GSNYNP---ETICVYILQKREIKVGDKVAGR 825

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +
Sbjct: 826  HGNKGIISKILPIQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYR 885

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                D +   + S    F E    +                               VF+ 
Sbjct: 886  IAPFDERYEQEASRKLVFSELYEASQQTANPW------------------------VFE- 920

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                           +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G
Sbjct: 921  --------------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSG 966

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + +
Sbjct: 967  HYALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTI 1026

Query: 1334 AGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             G    +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1027 IGGTIPKPEDAPESFRLLVRELRSLSLELNHFLVSEKNFQINRKE 1071



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 229/612 (37%), Positives = 353/612 (57%), Gaps = 17/612 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  +K  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVKGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGS 639
           L+ SL   AR+   G +E+P+ ++ +   +  V   YLS   +E   +A  NS     G 
Sbjct: 434 LIGSLAIHARIGQGGSLESPFYEISERSKSKRVRMFYLSPSRDEYYMVAAGNSLALNQGI 493

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E+ V  R   E + +  E+++     P Q  SI ASLIPF+E++D+NR LM  NMQRQ
Sbjct: 494 QEEQGVPARYRQEFLTIAWEQVNLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQ 553

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL ++E   VGTG+E   A  SG   +A+  G +   +  +I++              
Sbjct: 554 AVPLSRSEKCIVGTGLERQAALDSGVTAIAEHEGKIIYTNTDKIILLGN--------GDT 605

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
               L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA++PW 
Sbjct: 606 LSIPLVMYQRSNKNTCMHQKPQVPRGKCIKKGQILADGGATVGGELALGKNVLVAYLPWE 665

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++LISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ 
Sbjct: 666 GYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHILRNLDKN 725

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           GI+ +G+ V  GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G
Sbjct: 726 GIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRG 785

Query: 938 TVVDVRIFNRHG 949
            V+DVR   + G
Sbjct: 786 RVIDVRWIQKKG 797



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  VPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTYA  L ++  LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYASELYVSAGLIW---------KTSRDMQEQTLFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|118614482|ref|YP_899397.1| RNA polymerase beta subunit [Sorghum bicolor]
 gi|125987644|sp|A1E9R4|RPOB_SORBI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|118201116|gb|ABK79486.1| RNA polymerase beta subunit [Sorghum bicolor]
          Length = 1075

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 125/306 (40%), Positives = 177/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 RVNRED 1074



 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 235/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  VGR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRVGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  L+Q+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLAQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISSDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVAHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT+ IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKQIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R   D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPFDIMVRVYILQKREIKVGDK 824



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERNAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|563343|emb|CAA57814.1| RNA polymerase subunit beta [Sinapis alba]
          Length = 1078

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 138/415 (33%), Positives = 211/415 (50%), Gaps = 52/415 (12%)

Query: 965  ELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            E + ++    E  +L      +   ++ G    +G     K T   +   S  P  +  +
Sbjct: 711  ERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLR 768

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              +  +        LK+       +++ R+  K      G    P    +++V+++ KR 
Sbjct: 769  AILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKRE 821

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG 
Sbjct: 822  IKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGL 881

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A   L +  +    D +   + S    F E    +                         
Sbjct: 882  AGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------------------ 923

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                  VF+                +  G+S ++DG TG+PF++PV +G  Y+LKL H V
Sbjct: 924  ------VFE---------------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQV 962

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD + 
Sbjct: 963  DDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIR 1022

Query: 1324 GRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             R  V  + + G    +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1023 ARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1077



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 254/832 (30%), Positives = 427/832 (51%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 149  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 208

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 209  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 267

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 268  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 327

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  I       ++P  Q+L+ + P+ +    FF    LSQ+ +  
Sbjct: 328  QDQLGLALARLENVVKGTIGGAIRHKLIPPTQNLVTSTPLTTTYESFFGFHPLSQVLDRT 387

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 388  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 447

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E++V  
Sbjct: 448  ARIGDWGSLESPFYELVEKSKKAQIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQVVPA 507

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 508  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 567

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +I++   E  L           L+ +
Sbjct: 568  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIILSGNENTL--------SIPLIMY 619

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 620  QRSNKNTCMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAV 679

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 680  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 739

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 740  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 799

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 800  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 859

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 860  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 919

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 920  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 969



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 18  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 67

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 68  PLIKERDAVYESLTYSSELYVSAGLIW---------KTNRNMQEQRIFIGNIPLMNSLGT 118

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI R+V++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 119 SIVNGIYRVVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 175

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 176 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 226


>gi|68053043|sp|Q5QA72|RPOB_ACOGR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|56122473|gb|AAV74361.1| RpoB [Acorus gramineus]
          Length = 1071

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/547 (28%), Positives = 252/547 (46%), Gaps = 58/547 (10%)

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
              ++E     I+ +  +++   +  G       +          + +   +  G  +  G
Sbjct: 579  SAIAECEGKIIYTDTHKIVL--SGHGDTISIPLVMYQRSNKNTCMHQNPQVRRGKCIKKG 636

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             IL       G   +   + +L A    +  +  D  L     +S  +V   I+    I 
Sbjct: 637  QILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVYEDIYTSFHIR 690

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K E    V  +  E +  +    +  L RN+  R   +  G    +G     K T  +++
Sbjct: 691  KYEIQTHVTSQGPERITHEIPHLEAHLLRNL-DRNGIVALGSWVETGDILVGKLTPQTAN 749

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              S  P  +  +  +  +        LK+       +++ R+  K      G    P   
Sbjct: 750  ESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQKKG----GSSYNP--- 802

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DGTPVD+V NPLGVPSRM
Sbjct: 803  ETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVFNPLGVPSRM 862

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 863  NVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------ 916

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S ++DG TG+PF++PV +
Sbjct: 917  ------------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLI 943

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G A++L
Sbjct: 944  GKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVAHIL 1003

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD +  R  V  + + G         PESF +LV+E+++L L ++  L + + 
Sbjct: 1004 QEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALELNHFLVSEKN 1063

Query: 1369 KNSAKME 1375
                + E
Sbjct: 1064 FQINRKE 1070



 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 254/831 (30%), Positives = 422/831 (50%), Gaps = 44/831 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTSTIISDWGGRSELEIDRKSRIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356  AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLNDREKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNMNRRLNLDIPQSNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +++  I       +   PQ+L+++  + +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALVRLENAVRGTICGAIRHKLILTPQNLVSSTSLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS-LDEDGSFTEELVFCR 648
            AR+  +G IE+P+ +V        +V+LS   +E   +A  NS  L+  G   E++V  R
Sbjct: 442  ARIGHWGSIESPFYEVYQRSKETKMVFLSPSRDEYYTVATGNSLALNRGGIQEEQIVPAR 501

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++  
Sbjct: 502  YRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSXX 561

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                       A  SG + +A+  G +   D  +IV+                  L+ +Q
Sbjct: 562  XXXXXXXXXXAALDSGVSAIAECEGKIIYTDTHKIVL--------SGHGDTISIPLVMYQ 613

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 614  RSNKNTCMHQNPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 673

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V
Sbjct: 674  ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITHEIPHLEAHLLRNLDRNGIVALGSWV 733

Query: 889  NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              GDILVGK+TP+  +  +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 734  ETGDILVGKLTPQTANESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQ 793

Query: 947  RHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------Q 993
            + G         R    ++ +I++  +   +   + I+ + +  + M  L          
Sbjct: 794  KKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVF 853

Query: 994  NAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQY 1042
            N +  P       +    L ++     + ++ A  DE+ ++            E+ K   
Sbjct: 854  NPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTA 913

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 914  NPWVFEPEYPGKSRIFDGRTGDPFEQPVL-IGKSYIL-KLIHQVDDKIHGR 962



 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL   F     I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFV----------DQGLMEEFHKFPKIEDTDQEIEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTSTIISDWGGRSELEIDRKSRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDREKKKIGSKE 220


>gi|139389088|ref|YP_001123806.1| RNA polymerase beta subunit [Nasturtium officinale]
 gi|158513992|sp|A4QLS5|RPOB_NASOF RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134287011|dbj|BAF50630.1| RNA polymerase beta subunit [Nasturtium officinale]
          Length = 1072

 Score =  384 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 158/580 (27%), Positives = 252/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYERSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RH--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYKASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1032 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  359 bits (922), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 230/688 (33%), Positives = 378/688 (54%), Gaps = 23/688 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQLGLALSRLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442 ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYFMIAAGNSLALNRGIQEEQAVPA 501

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502 RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              VGTG+E  VA  SG   +A+  G +   D  +IV                   L+ +
Sbjct: 562 KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGN--------GDTLSIPLIMY 613

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614 ERSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+++D+ GI+ +G+ 
Sbjct: 674 LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRHLDKNGIVMLGSW 733

Query: 888 VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734 VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946 NRHGIDKNE----RSISVEREQIELLAR 969
            + G         R    ++ +I++  +
Sbjct: 794 QKKGGSSYNPEIIRVYISQKREIKVGDK 821



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDH--EIEFQLFMETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   
Sbjct: 60  VEPLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 111 GTSIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 168 IWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|186885791|gb|ACC93303.1| RNA polymerase beta subunit [Richterago angustifolia]
          Length = 1028

 Score =  383 bits (984), Expect = e-104,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K ++              ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVRKKKR-------SSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+ KL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYIFKLIHQVDDKIHVRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTLPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L +  T    + E
Sbjct: 992  DAPESFRLLIRELRSLALELNHFLVSEETFQINRKE 1027



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++ALL+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENALLEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVEGDPVFSEYLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIAIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGTICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N  P+      FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 304 YKWIPTPQKLVNPSPLKGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKFSFLGPGGLTGQT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRAILGMRVYTSKETCLKLPIGGRGRVIDVRWVRKKKRSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y    P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYHLVEPLIKERDAVYKSLTYSSALYVSARLIWKTDRR-------RNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G L+Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---PNGILVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|158291888|ref|XP_313416.3| AGAP003648-PA [Anopheles gambiae str. PEST]
 gi|157017504|gb|EAA08858.3| AGAP003648-PA [Anopheles gambiae str. PEST]
          Length = 1175

 Score =  383 bits (984), Expect = e-104,   Method: Composition-based stats.
 Identities = 163/1002 (16%), Positives = 305/1002 (30%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 335  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYGNK 391

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I  K +   +     + 
Sbjct: 392  RLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATG 451

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 452  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 507

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENR 625
             ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +    
Sbjct: 508  MICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKI 567

Query: 626  YIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D       L   R   + I+     I D  D   +          P L 
Sbjct: 568  FVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLI 627

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             ++ + +L   ++                      V  +SG           E +D +  
Sbjct: 628  VENGSLLLRKNHIDMLKDRDYNNYG--------WQVLVASGVV---------EYIDTLEE 670

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +                                  K              P+  LG
Sbjct: 671  ETVMIAMTPYDLKQD------------------------KEYAYCTTYTHCEIHPAMILG 706

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 707  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 741

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 742  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 790

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V            +   K+  S  +  ++ E   +        +   +Y
Sbjct: 791  QEDSVILNASAVERGFFRSVF---YRSYKDSESKRIGDQE-EQFEKPNRQTCQGMRNALY 846

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L E   I  G           K+  L                     +   +++    
Sbjct: 847  DKLDEDGIIAPGLRVSGDDVVIGKTITL--------------------PETDDDLDGTTK 886

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            +Y         R        Q    +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 887  RYTKRDGSTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 946

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 947  GIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECIQGKLGSNKGEIGD------- 999

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1000 ----------------------------------------------ATPFNDAVNVQKIS 1013

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1014 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1073

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     V            R 
Sbjct: 1074 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANLRN 1133

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ A+ ++  L 
Sbjct: 1134 NTFEC--KGCKNKTQISQVKLPYAAKLLFQELMAMNIAPRLM 1173



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 100/747 (13%), Positives = 224/747 (29%), Gaps = 107/747 (14%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  S   I   +   +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPAIELTAEAQHSSGEIENPT-RYLLKFDQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +        +        + + Q  ++G +
Sbjct: 98  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKLVEGQDPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKTEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRVIAILPYV 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E  ++ L  +     +   Y               +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENGSLLLRKNHIDMLKDRDYNN-----YGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA     L +D  +                        +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMTPYDLKQDKEY---------------AYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           ++ S R      M +QA+ +       
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV 743


>gi|215254217|gb|ACJ64113.1| RNA polymerase beta subunit [Vibrio hepatarius]
          Length = 381

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 243/381 (63%), Positives = 300/381 (78%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E G+F+EEL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLTEQGTFSEELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VG
Sbjct: 121 SGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKITPKGESPMTPEEKLL 913
           ILVGK+TPKGE+ +TPEEKLL
Sbjct: 361 ILVGKVTPKGETQLTPEEKLL 381


>gi|114329960|ref|YP_740642.1| RNA polymerase beta subunit [Nandina domestica]
 gi|122165969|sp|Q09FW9|RPOB_NANDO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|114054462|gb|ABI49855.1| RNA polymerase beta subunit [Nandina domestica]
          Length = 1070

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDRNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+ +K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIHKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF +PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFAQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 227/634 (35%), Positives = 358/634 (56%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           I  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 IDNVCYPEIFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNLD P ++  +   D++A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLNLDIPHNITFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L ++R+E +++  I       +   P +L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLAMVRLENAVRGTIGGAIRQKLIPTPHNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +E P+ ++ +      V+YLS   +E   +   NS     G   
Sbjct: 434 LIGSLAIHARIGHWGSLERPFYEISERSKGVRVIYLSPSIDEYYMVTAGNSLALNHGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E+I      P Q  S+ ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQIQLRSIFPFQYFSVGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG + +A+  G +   D         +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGVSAIAEHEGKIIYTD--------TDKIILSGNGATLS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMHQKPQVSRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI
Sbjct: 666 NFEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDRNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR  ++ G         R    ++ +I++  +
Sbjct: 786 IDVRWIHKKGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 105/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DRGLMEELNKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +   LTY   L +   LI          K+ KDI+EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVHESLTYCSELYVPAGLIW---------KTGKDIQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G + +EI+    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLKEIIDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|325126857|ref|YP_004286094.1| RNA polymerase beta subunit [Fragaria vesca subsp. vesca]
 gi|324022769|gb|ADY15343.1| RNA polymerase beta subunit [Fragaria vesca subsp. vesca]
          Length = 1070

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 250/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVTAIAEHEGKIIYTDTDKIILSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G +L       G   +   + +L A    
Sbjct: 604  LNIPLVIYQRSNKNTCMHQKPQVQRGKCIKKGQVLADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V     E +  +    +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYGDIYTSFHIRKYEIQTHVTSNGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   +  G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVRLGSWVKTGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  VSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYEASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPADAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 230/620 (37%), Positives = 362/620 (58%), Gaps = 19/620 (3%)

Query: 360 NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           N     K   +++A+L+ Y+      GD              FF   + +L  +GR  MN
Sbjct: 209 NDKEKKKIGSKENAILEFYQQFACVGGDPVVSESLCKELQKKFF-QQRCELGRIGRRNMN 267

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L
Sbjct: 268 RRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGL 327

Query: 478 GLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I
Sbjct: 328 SLVRLENMVRGTICGAIKHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQI 387

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A++  +
Sbjct: 388 VHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKIGYW 447

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G +E+P+ ++ +      ++YLS  ++E   IA  NS     G   E++V  R   E + 
Sbjct: 448 GSLESPFYEISERSKKVRMLYLSPSKDEYYMIAAGNSLGLNRGIQEEQVVPARYRQEFLT 507

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+
Sbjct: 508 VEWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGL 567

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E  VA  SG   +A+  G +   D  +I++      L+          L+ +QRSN+NTC
Sbjct: 568 ERQVALDSGVTAIAEHEGKIIYTDTDKIILSGNGDTLNI--------PLVIYQRSNKNTC 619

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           ++Q+P V+ G  +++  ++ADG +T  G+LALG+N+LVA+MPW GYN ED++LISER+V 
Sbjct: 620 MHQKPQVQRGKCIKKGQVLADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISERLVY 679

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILV
Sbjct: 680 GDIYTSFHIRKYEIQTHVTSNGPERITNEIPHLEAHLLRNLDKNGIVRLGSWVKTGDILV 739

Query: 896 GKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           GK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   + G    
Sbjct: 740 GKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSY 799

Query: 954 E----RSISVEREQIELLAR 969
                R    ++ +I++  +
Sbjct: 800 NPETIRVYISQKREIKVGDK 819



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 72/337 (21%), Positives = 133/337 (39%), Gaps = 35/337 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP L ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQ--EIEFQLFGETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   
Sbjct: 60  VEPLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 111 GTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGIIISDWGGRLELEIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +  +    
Sbjct: 168 IWARVSRKQKISILVLSSAMGSNLREILENARYPEIFLSFLNDKEKKKIGSKENAILEFY 227

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVN 314
                            K+L     +   E G       +  L         ++    + 
Sbjct: 228 QQFACVGGDPVVSESLCKELQKKFFQQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDIL 287

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                +      +     +  + +  IR +  L  D 
Sbjct: 288 AAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324


>gi|227438084|gb|ACP30540.1| RNA polymerase beta subunit [Streptococcus sp. CSL 7508]
          Length = 595

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 245/425 (57%), Positives = 314/425 (73%), Gaps = 9/425 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S
Sbjct: 1   HNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSS 60

Query: 589 FARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +  +N YGFI+TPYRKV      VT D+ +L+A EE+   +AQANS L+EDG+F EE+V 
Sbjct: 61  YGHLNKYGFIQTPYRKVDKETGVVTRDIEWLTADEEDEYTVAQANSILNEDGTFAEEIVM 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G     P   +D++D SPKQVV++A + IPFLEN+DSNR LMG NMQRQAVPL+  
Sbjct: 121 GRHQGNNQEFPISAVDYVDVSPKQVVAVATACIPFLENNDSNRALMGANMQRQAVPLIDP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +AP VGTGME   A  SGAA++A+  G V   DA ++ +R  +G       G+D+Y++ K
Sbjct: 181 KAPLVGTGMEYQAAHDSGAAVIAQNDGKVIYSDADKVEVRREDG-------GLDVYQITK 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSN  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED+
Sbjct: 234 FRRSNSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TS+H+EEFE   RDTKLG EEITR+IPNV EE LK++DE G+I +GA
Sbjct: 294 VIMSERLVKDDVYTSVHLEEFESETRDTKLGAEEITREIPNVGEEALKDLDEMGVIRIGA 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DVRIF 
Sbjct: 354 EVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVRIFT 413

Query: 947 RHGID 951
           R   D
Sbjct: 414 RANGD 418



 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 149/649 (22%), Positives = 239/649 (36%), Gaps = 82/649 (12%)

Query: 652  EEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            +        + +        +       I  + N  S   L      +     +  E   
Sbjct: 24   DRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDKETGV 83

Query: 711  VGTGMESVVA--KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            V   +E + A  +       A      +   A  IV+   +G+          Y  +  +
Sbjct: 84   VTRDIEWLTADEEDEYTVAQANSILNEDGTFAEEIVMGRHQGNNQEFPISAVDYVDVSPK 143

Query: 769  R--SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            +  +    C+           +  ND        ++   A+      A +   G  ++ +
Sbjct: 144  QVVAVATACIP---------FLENNDSNRALMGANMQRQAVPLIDPKAPLVGTGMEYQAA 194

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
                  +++++    I+ +  +V  R    G +                 ++  ++ VG 
Sbjct: 195  HDSGAAVIAQNDGKVIYSDADKVEVRREDGGLDVYQI-TKFRRSNSGTAYNQRTLVKVGD 253

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             V  GD +    +      M   +  + A    +  +  D  +         V D    +
Sbjct: 254  VVEKGDFIADGPS-MENGEMALGQNPIVAYMTWEGYNFEDAVIM----SERLVKDDVYTS 308

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
             H  +    +   +    E+     +  +  L       +  I  G     G     K T
Sbjct: 309  VHLEEFESETRDTKLGAEEITREIPNVGEEALKD--LDEMGVIRIGAEVKEGDILVGKVT 366

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                  +S   R     F  +  +V+     +    +     +      +I     GD++
Sbjct: 367  PKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------RIFTRANGDEL 420

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              GV  +V+V++A KR ++ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLG
Sbjct: 421  QSGVNMLVRVYIAQKRKVKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLG 480

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG  + + + D     D+                     
Sbjct: 481  VPSRMNIGQVMELHLGMAARTLGVHMATPVFDGATAEDLWETVKEAGMDSDAK------- 533

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 T ++DG                           TGEPFD
Sbjct: 534  ---------------------TVLYDG--------------------------RTGEPFD 546

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
              V+VG +YM+KL+HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 547  NRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFG 595


>gi|69216924|gb|AAZ03996.1| RNA polymerase beta chain [Yucca schidigera]
          Length = 1069

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 159/563 (28%), Positives = 261/563 (46%), Gaps = 58/563 (10%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +   G   + ++     +++E     I+ +  +++   +  G       +          
Sbjct: 562  IVGTGLERQTALDSGVSVIAEREGKIIYTDTHKIIF--SSNGDTISIPLVMYQRSNKNTC 619

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +   +  G  +  G IL       G   +   + +L A    +  +  D  L     +
Sbjct: 620  MHQKPQVQQGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNSEDAVL-----I 673

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            S  +V   I+    I K E    V  +  E + ++    +  L RN+  R   ++ G   
Sbjct: 674  SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNL-DRNGIVMLGSWI 732

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T  +++  S  P  +  +  +  +       SLK+       +++ R+  
Sbjct: 733  EAGDILVGKLTPQAANESSYAPEDRLLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWIQ 792

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG
Sbjct: 793  KK----GGSSYNP---ERIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDG 845

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E  
Sbjct: 846  TPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLKRHYRIAPFDERYEQEASRKLVFSELY 905

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                               VF+                +  G+S 
Sbjct: 906  EASKQTKNPW------------------------VFE---------------PEYPGKSK 926

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 927  IFDGRTGDPFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVG 986

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  +  + + G         PESF +LV+E+
Sbjct: 987  EMEVWALEGFGVAHILQEMLTYKSDHIRARQELLGATIIGGTVPNPEDAPESFRLLVREL 1046

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1047 RSLALELNHFLVSEKNFQINRKE 1069



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 266/806 (33%), Positives = 422/806 (52%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPILY-VDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I+           L            IL  V          N     K   +++A+L+ 
Sbjct: 167  RIWARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFSNDKEKKKIGSKENAILEF 226

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 227  YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRD 285

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
            ++A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E +I+  I     
Sbjct: 286  LLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALVRLENAIRGTICGAIR 345

Query: 496  DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              +   PQ+L+ +  + +    FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 346  HKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 405

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G IE+P+ ++ +      
Sbjct: 406  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGHWGSIESPFYEISERSKKAQ 465

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E+I F    P Q  S
Sbjct: 466  MIYLSPNRDEYYMVAAGNSLALNRGIQEEQVVPARYRQEFLTIAWEQIHFRSIFPFQYFS 525

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG +++A+R G
Sbjct: 526  IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQTALDSGVSVIAEREG 585

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D  +I+  S                L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 586  KIIYTDTHKIIFSSN--------GDTISIPLVMYQRSNKNTCMHQKPQVQQGKCIKKGQI 637

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +ADG +T  G+LALG+N+LVA+MPW GYN ED++LISER+V ED++TS HI ++E+    
Sbjct: 638  LADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIYTSFHIRKYEIQTHV 697

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
            T  GPE IT++IP++    L+N+D  GI+ +G+ +  GDILVGK+TP+  +  +  PE++
Sbjct: 698  TSQGPERITKEIPHLEAHLLRNLDRNGIVMLGSWIEAGDILVGKLTPQAANESSYAPEDR 757

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELL 967
            LLRAI G +    ++TSL++P G  G V+DVR   + G      +  R    ++ +I++ 
Sbjct: 758  LLRAILGIQVSTAKETSLKLPIGGRGRVIDVRWIQKKGGSSYNPERIRVYISQKREIKVG 817

Query: 968  AR--DKDDEQVILDRNIYSRLMEILCG-------QNAVSGPKGFKKSTVLSSDL-ISEYP 1017
             +   +   + I+ + +  + M  L          N +  P       +    L ++   
Sbjct: 818  DKVAGRHGNKGIISKILSRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDL 877

Query: 1018 RSQWWQFAVQDEKVQRNVES---LKVQYETSKS-------ILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++           YE SK          E   K+KI   + GD   
Sbjct: 878  LKRHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPWVFEPEYPGKSKIFDGRTGDPFE 937

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              VL + K ++  K   Q  DK+ GR
Sbjct: 938  QPVL-IGKSYIL-KLIHQVDDKIHGR 961



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------NQGLAEEFHKFPKIEDRDQEMEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++++++++G +PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQQKTVFIGTIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D +  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELD---HNGNSVYTSTIISDWGGRSELEIDRRTRIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFSNDKEKKKIGSKE 220


>gi|332148556|dbj|BAK20127.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|332148570|dbj|BAK20134.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 328

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 144/378 (38%), Positives = 195/378 (51%), Gaps = 62/378 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 7    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 64

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 65   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 124

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 125  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 184

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 185  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 238

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 239  ----------------------TVLYDG--------------------------RTGEPF 250

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 251  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 310

Query: 1306 GAAYVLQEMLTIKSDDVV 1323
            GAAY LQE+LT+KSDDVV
Sbjct: 311  GAAYTLQEILTVKSDDVV 328



 Score =  121 bits (304), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 82/123 (66%), Positives = 101/123 (82%)

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV
Sbjct: 1   MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEV 60

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR 
Sbjct: 61  KDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRE 120

Query: 949 GID 951
             D
Sbjct: 121 DGD 123


>gi|290489608|gb|ADD31188.1| RNA polymerase beta subunit protein [Dillenia indica]
          Length = 1072

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 156/579 (26%), Positives = 253/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   +++        I         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVTLDSGVLTIAEHEGNIIYTDTAKILLSGNGDI 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  RSIPLVMYQRSNKNTCMHQKPQVQWGKYIKKGQILADGAATVG-GELALGKNVLVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   ++    I K E    V  +  E +  +    +  L 
Sbjct: 665  EGYNSEDAVL-----ISERMVYGDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 719

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 720  RNL-DKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLK 778

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 779  LPIGGRGRVIDVRWIRKKG----GYSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 831

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+ILP +DMP+ +DG+PVD+V NPLGVPSRMNVGQIFE  LG A   L +  + L  D 
Sbjct: 832  VSKILPRQDMPYFQDGSPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLNRHYRILPFDE 891

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F  ++      T     ++ +                            
Sbjct: 892  RYEQEASRKLVF-SELYKASKQTANPWIFEPE---------------------------- 922

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                        G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 923  ----------YPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 972

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 973  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1032

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1033 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFRINRKE 1071



 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 232/694 (33%), Positives = 375/694 (54%), Gaps = 23/694 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELDHKGISVYTGAIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGANLKAILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NVYYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  +N RLNLD P +   +   DI+A    L+ L+ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNINRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENLVRGTICGAIRHKLLPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFT 641
            SL    R+  +G +E+P+      + +  V   YLS   +E   +A  NS     G   
Sbjct: 436 GSLAIHTRIGHWGSLESPFYDYEISEKSKKVRMLYLSPSGDEYYMVAAGNSLALNHGIQE 495

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++   R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 496 EQVAPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 555

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  V   SG   +A+  G +   D  +I++             +  
Sbjct: 556 PLSRSEKCIVGTGLERQVTLDSGVLTIAEHEGNIIYTDTAKILLSGN--------GDIRS 607

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 608 IPLVMYQRSNKNTCMHQKPQVQWGKYIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 667

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISERMV  DV+TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI
Sbjct: 668 NSEDAVLISERMVYGDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGI 727

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 728 VMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 787

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 788 IDVRWIRKKGGYSYNPETIRVYISQKREIKVGDK 821



 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 112/237 (47%), Gaps = 26/237 (10%)

Query: 21  PEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS 78
            E++  IP   ++Q   +  F+          ++GL         I         + FV 
Sbjct: 6   NEVMSTIPGFNQIQFEGFCRFI----------DQGLAEELSKFPKIEDTDQEIEFQLFVE 55

Query: 79  -YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PL
Sbjct: 56  TYQLVEPLIKERDAVYESLTYSSELYVSAGLIW---------KTNRDMQEQTIFIGNIPL 106

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           M   GT +I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D
Sbjct: 107 MNSLGTSIINGIYRIVINQILQSPGIYYRSELDHKGIS---VYTGAIISDWGGRSELEID 163

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWCFPLSAAD 253
            K  I  R+ R++K+ +     A+G + + IL   +YP+I  S   D     + + +
Sbjct: 164 RKARIWARVSRKQKISILVLSSAMGANLKAILENVYYPEIFLSFLNDKEKKKIGSKE 220


>gi|91208894|ref|YP_538927.1| RNA polymerase beta subunit [Gossypium hirsutum]
 gi|109903858|sp|Q2L8Z9|RPOB_GOSHI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|85687408|gb|ABC73620.1| RNA polymerase beta subunit [Gossypium hirsutum]
          Length = 1070

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDA 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LGIPLVMYQRSNKNTCMHQTARVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWVQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQ+FE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQLFECSLGLAGSLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYQASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGGPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNL+ P +   +   DI+A    L+ ++ G G +DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNQRLNLNIPQNNTFLLPRDILAAADRLIGMKFGMGPLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYKIFERSKKAQMLYLSPSRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A   G +   D  +I++      L           L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDALGI--------PLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q   V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQTARVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCGFM----------DRGLTEELYKFPKIEDTEQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSKDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|325210922|ref|YP_004285996.1| RNA polymerase beta subunit [Gossypium thurberi]
 gi|290775784|gb|ADD62280.1| RNA polymerase beta subunit [Gossypium thurberi]
          Length = 1070

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDA 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LGIPLVMYQRSNKNTCMHQTARVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWVQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQ+FE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQLFECSLGLAGSLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYQASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGGPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 233/686 (33%), Positives = 379/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNQRLNLNIPQNNTFLLPRDILAAADRLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYKIFERSKKAQMLYLSPSRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A   G +   D  +I++      L           L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDALGI--------PLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q   V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQTARVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCGFM----------DRGLTEELYKFPKIEDTEQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSKDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|290489630|gb|ADD31199.1| RNA polymerase beta subunit protein [Bulnesia arborea]
          Length = 1070

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 154/523 (29%), Positives = 242/523 (46%), Gaps = 56/523 (10%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G       I          I +   +  G  +  G +L    +  G   +   + +L A
Sbjct: 600  NGNTLNIPLIMYQRSNKNTCIHQKARVQYGKWIKKGQLLADGASTVG-GELALGKNILVA 658

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    +
Sbjct: 659  YMPWEGYNFEDAVL-----ISERLVYENIYTSFHIRKYEIQTHVTSQGPEKITKEIPHLE 713

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              L RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +      
Sbjct: 714  AHLLRNL-DKNGIVMLGSWVETGDVLVGKLTPQMTKESSYAPEDRLLRAILGIQVSTSKE 772

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LK+       +++ R+  K      G    P    +++V++  KR I+ GDK+AGRHG
Sbjct: 773  TCLKLPIGGRGRVIDVRWIQKK----GGSSYNP---EIIRVYILQKREIKVGDKVAGRHG 825

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+S+IL  +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +  
Sbjct: 826  NKGIISKILTRQDMPYLQDGRCVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIA 885

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D +   + S    F E    +                               VF+   
Sbjct: 886  PFDERYEKEASRKLVFSELYEASKQTANPW------------------------VFE--- 918

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                         +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y
Sbjct: 919  ------------PEYPGKSKIFDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHY 966

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            +LVTQQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G
Sbjct: 967  ALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIG 1026

Query: 1336 NDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1027 GTIPKPQDAPESFRLLVRELRSLALELNHFLVSEKNLKMTRKE 1069



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 256/778 (32%), Positives = 415/778 (53%), Gaps = 41/778 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195  LENVCYPEMFLSFLNDKEKKKIGSKENAILEFYQQFASVGGDPVFSESLCKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  +GR  MN+R NLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254  QRCELGKIGRRNMNLRFNLDIPQNNTFLLPRDILAATDHLIGIKFGIGTLDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q  L L+R+E  IK  IS      +   PQ+L+ + P+ +    FF    
Sbjct: 314  IRSVSDLLQDQLGLALVRLENVIKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVFDRTNPLTQIVHGRKLSYLGPGGLTARTANFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ SL   AR+  +G +E+P+ ++ +      ++ LS   +E   IA  NS         
Sbjct: 434  LIGSLAIHARIGHWGSLESPFYEISEQSKKVRILSLSPNRDEYYMIAAGNSLALNRDIQE 493

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E++V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494  EQVVPARYRQEFLTIAWERIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL ++E   VGTG+E   A  SG  +++++ G +   D  ++V+ +    L+        
Sbjct: 554  PLSQSEKCIVGTGLERQAALDSGVPVISEQEGKIIYSDTKKVVLSTNGNTLNI------- 606

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L+ +QRSN+NTC++Q+  V+ G  +++  ++ADG ST  G+LALG+N+LVA+MPW GY
Sbjct: 607  -PLIMYQRSNKNTCIHQKARVQYGKWIKKGQLLADGASTVGGELALGKNILVAYMPWEGY 665

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFED++LISER+V E+++TS HI ++E+    T  GPE+IT++IP++    L+N+D+ GI
Sbjct: 666  NFEDAVLISERLVYENIYTSFHIRKYEIQTHVTSQGPEKITKEIPHLEAHLLRNLDKNGI 725

Query: 882  ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            + +G+ V  GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726  VMLGSWVETGDVLVGKLTPQMTKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940  VDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCG 992
            +DVR   + G         R   +++ +I++  +      ++ +I        +  +  G
Sbjct: 786  IDVRWIQKKGGSSYNPEIIRVYILQKREIKVGDKVAGRHGNKGIISKILTRQDMPYLQDG 845

Query: 993  ------QNAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------V 1035
                   N +  P       +    L ++     + ++ A  DE+ ++            
Sbjct: 846  RCVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEKEASRKLVFSELY 905

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            E+ K          E   K+KI   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 906  EASKQTANPWVFEPEYPGKSKIFDGRTGDPFEQPVL-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 75/342 (21%), Positives = 147/342 (42%), Gaps = 32/342 (9%)

Query: 21  PEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS 78
            E++  IP L ++Q   +  F+          + GL         I         + FV 
Sbjct: 6   NEVMSTIPGLNQIQFEGFCKFI----------DRGLIEELYKFQKIEDADQEIEFQLFVE 55

Query: 79  -YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y+   P     D +++ LTY+  L ++  LI          K+++ ++EQ+I++G++PL
Sbjct: 56  TYKLVEPSITERDAIYQSLTYSSELHVSAGLIW---------KTVRGMQEQTIFIGNIPL 106

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           M   GTF++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D
Sbjct: 107 MNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---HNGIPVYIGTIISDWGGRLELEID 163

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD--- 253
            K  I  R+ R++K+ +     A+G++  EIL    YP++  S   D     + + +   
Sbjct: 164 RKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPEMFLSFLNDKEKKKIGSKENAI 223

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAE 310
           L    + +S   D    E + +  +K        L + G + + +  +        ++  
Sbjct: 224 LEFYQQFASVGGDPVFSESLCKELQKKFFQQRCELGKIGRRNMNLRFNLDIPQNNTFLLP 283

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
             +   T  +      +     +  + +  IR +  L  D +
Sbjct: 284 RDILAATDHLIGIKFGIGTLDDMNHLKNKRIRSVSDLLQDQL 325


>gi|116617100|ref|YP_817474.1| RNA polymerase beta subunit [Coffea arabica]
 gi|122153613|sp|A0A327|RPOB_COFAR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|116242156|gb|ABJ89671.1| RNA polymerase beta subunit [Coffea arabica]
          Length = 1066

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 235/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   ++  + +L A    +  +  D  L     +S  +V 
Sbjct: 622  VQRGKCIKKGQILADAAATVG-GELSLGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 675

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 676  EDIYTSFHIRKYEIQTHVTSQGPERVTNEIPHLEAHLLRNL-DKSGIVMLGSWVETGDIL 734

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 735  VGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKG--- 791

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG PVD+V
Sbjct: 792  -GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISKILTRQDMPYLQDGRPVDMV 847

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +   
Sbjct: 848  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYQASKQT 907

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF              A+    G+S ++DG T
Sbjct: 908  ANPW------------------------VF-------------EAEYP--GKSRIFDGRT 928

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 929  GNPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 988

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 989  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPEDAPESFRLLVRELRSLALE 1048

Query: 1361 ID--LENSRTKNSAKME 1375
            +   L + +     + E
Sbjct: 1049 LKHFLISEKNFRIHRKE 1065



 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 234/686 (34%), Positives = 381/686 (55%), Gaps = 25/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNPFLLPRDILAAADHLIGLKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDGT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +GF+E+P+ ++ + +V     +L    +E   +A  NS         +++V  R 
Sbjct: 442 ARIGHWGFLESPFYEISERRVL----FLLPGRDEYYKVAAGNSLALNQDIQEKQVVPARY 497

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 498 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 557

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G V   D         +  L     G     L+ +QR
Sbjct: 558 IVGTGLEQQAALDSGALSIAEREGKVLYTD--------TDKILLSGNGGTLSIPLVMYQR 609

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+AD  +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 610 SNKNTCMHQKPRVQRGKCIKKGQILADAAATVGGELSLGKNVLVAYMPWEGYNFEDAVLI 669

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 670 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERVTNEIPHLEAHLLRNLDKSGIVMLGSWVE 729

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 730 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 789

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 790 KGGSSYNPEMIRVYISQKREIKVGDK 815



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLAEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYELLTYSSELYVSAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ G+ RI+++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGVYRILINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|229577746|ref|YP_002836082.1| RNA polymerase beta subunit [Megaleranthis saniculifolia]
 gi|226933874|gb|ACO92007.1| RNA polymerase beta subunit [Megaleranthis saniculifolia]
          Length = 1071

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 721  LDRNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 780

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 781  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 833

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 834  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRISPFDERYE 893

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 894  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 919

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 920  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 974

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 975  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTISNPE 1034

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1070



 Score =  367 bits (942), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 254/779 (32%), Positives = 405/779 (51%), Gaps = 42/779 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            I  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195  IDNVCYPEIFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  +GR  MN RLNLD P ++  +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254  QRCELGRIGRRNMNRRLNLDIPQNITFLLPRDILAAADHLIRMKFGMGTLDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E +++  I       +   P +L+ + P+ +    FF    
Sbjct: 314  IRSVADLLQDQFGLALVRLENAVRGTIGGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSF 640
            L+ SL   AR+  +G +E P+ ++ D       VVYLS   +E   +A  NS     G  
Sbjct: 434  LIGSLAIHARIGHWGSLERPFYEISDKSTKELRVVYLSPSRDEYYMVAAGNSLALNQGIQ 493

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             E++V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQA
Sbjct: 494  EEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQA 553

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            VPL ++E   VGTG+E   A  SG + +A+  G +   D  +I++               
Sbjct: 554  VPLSRSEKCIVGTGLERQAALDSGVSAIAEHEGKIVYTDTDKIMLSGN--------GDTL 605

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               L+ +QRSN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N++VA+MPW G
Sbjct: 606  SIPLVMYQRSNKNTCMHQKTRVPRGKCIKKGQILADGAATVGGELALGKNVVVAYMPWEG 665

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YNFED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  G
Sbjct: 666  YNFEDAVLISERLVYGDIYTSFHIRKYEIKTHVTSQGPERITNEIPHLEAHLLRNLDRNG 725

Query: 881  IICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            I+ +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G 
Sbjct: 726  IVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGR 785

Query: 939  VVDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILC 991
            V+DVR   + G         R    ++ +I++  +      ++ +I        +  +  
Sbjct: 786  VIDVRWIQKKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQD 845

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN---------- 1034
            G             + ++   I E           + ++ +  DE+ ++           
Sbjct: 846  GTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRISPFDERYEQEASRKLVFSEL 905

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             E+ K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  YEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 962



 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 104/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +    I          K+ +D +EQ+I++G +PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGFIW---------KTGRDTQEQTIFIGKIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EI+    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREIIDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|160689608|gb|ABX45662.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689644|gb|ABX45680.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689646|gb|ABX45681.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689672|gb|ABX45694.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689682|gb|ABX45699.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689684|gb|ABX45700.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689710|gb|ABX45713.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
 gi|160689720|gb|ABX45718.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 321

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/377 (37%), Positives = 194/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVNDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 79/117 (67%), Positives = 96/117 (82%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|42795545|gb|AAS46111.1| RNA polymerase beta chain [Oryza sativa Japonica Group]
 gi|42795609|gb|AAS46174.1| RNA polymerase beta chain [Oryza sativa Japonica Group]
 gi|290790564|gb|ADD62824.1| RNA polymerase beta subunit [Oryza sativa Japonica Group]
 gi|290790633|gb|ADD62892.1| RNA polymerase beta subunit [Oryza meridionalis]
 gi|290790702|gb|ADD62960.1| RNA polymerase beta subunit [Oryza australiensis]
          Length = 1067

 Score =  383 bits (984), Expect = e-103,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 800  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 859

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 860  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 912

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 913  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 940

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 941  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1000

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1001 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSQKNF 1060

Query: 1370 NSAKME 1375
               + E
Sbjct: 1061 QVNREE 1066



 Score =  348 bits (893), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 232/699 (33%), Positives = 382/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 127 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLKEILD 186

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 187 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 245

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 246 CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 305

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 306 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 365

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 366 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 425

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 426 INVGLTGSLAIHARIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 485

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 486 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 545

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   ++ +I++        
Sbjct: 546 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTNSHKILL-------- 597

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 598 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 657

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 658 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 717

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 718 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 777

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 778 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 816



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I         +     Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEISFQLFAKGYQLLE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 54  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 102

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 103 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 159

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G + +EIL    YP+I  S         + + +  +
Sbjct: 160 ARVSRKQKISILVLSSAMGSNLKEILDNVSYPEIFLSFPNAKEKKRIESKEKAI 213


>gi|225544116|ref|YP_002720104.1| rpoB [Jatropha curcas]
 gi|224979557|gb|ACN72684.1| rpoB [Jatropha curcas]
          Length = 1072

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 136/427 (31%), Positives = 210/427 (49%), Gaps = 52/427 (12%)

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            R   ++            +E   L+ ++     +   ++ G    +G     K     + 
Sbjct: 691  RKYEIQTHVTSQGPEKITNEIPHLEAHLLRNLDKNGIVILGSWVETGDILVGKLRPQMAK 750

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              S  P  +  +  +  +        LK+       +++ R+  K      G    P   
Sbjct: 751  ESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKG----GSSYNP--- 803

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRM
Sbjct: 804  ETIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRM 863

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 864  NVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------ 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S ++DG TG+PF++PV +
Sbjct: 918  ------------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVII 944

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G +++L
Sbjct: 945  GKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVSHIL 1004

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L +D  L + + 
Sbjct: 1005 QEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLALELDHFLVSEKN 1064

Query: 1369 KNSAKME 1375
                + E
Sbjct: 1065 FQINRKE 1071



 Score =  365 bits (938), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 251/804 (31%), Positives = 419/804 (52%), Gaps = 52/804 (6%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            +   A  +   + LE +      +I + +++  +            K   +++A+L+ Y+
Sbjct: 182  VLSSAMGLNLREILENVC---CPEIFLSFLNLNDKG--------KKKMGSKENAILEFYQ 230

Query: 380  VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                  GD              FF   + +L  +GR+ MN RLNLD P +   +   DI+
Sbjct: 231  QFTCVGGDPVFSESLCKELQKKFF-QQRCELGRIGRLNMNRRLNLDIPHNNTFLLPRDIL 289

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I       
Sbjct: 290  AAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALIRLENVVRGTIWGAIRHK 349

Query: 498  V--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    A 
Sbjct: 350  LIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTAS 409

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
              +RD+HP+HYGRICP +TSEG N+GL+ SL   A++  +G +E+P+  + +G     ++
Sbjct: 410  FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKIGYWGSLESPFYGISEGSKKARML 469

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            YLS   EE   +A  NS     G   E++   R   E + +  E++      P Q  SI 
Sbjct: 470  YLSPNREEYYRVAAGNSLALNRGVQEEQVAPARYRQEFLTIAWEQVHLRSIFPFQYFSIG 529

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  V+  SG   +A+  G +
Sbjct: 530  ASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVSLDSGVPAIAEHEGKI 589

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
               D        ++  +           L+ +QRSN+NTC++Q+  V+ G  +++  ++A
Sbjct: 590  IYTD--------IDKIILSGNGDTLRIPLVMYQRSNKNTCMHQKTQVQRGKCIKKGQVLA 641

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            DG +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    T 
Sbjct: 642  DGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTS 701

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLL 913
             GPE+IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+ P+     +  PE++LL
Sbjct: 702  QGPEKITNEIPHLEAHLLRNLDKNGIVILGSWVETGDILVGKLRPQMAKESSYAPEDRLL 761

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
            RAI G +    ++T L++P G  G V+DVR   + G         R   +++ +I++  +
Sbjct: 762  RAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIRVYILQKREIKVGDK 821

Query: 970  ---DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP-------RS 1019
                  ++ +I        +  +  G+            + ++   I E           
Sbjct: 822  VAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLD 881

Query: 1020 QWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            + ++ A  DE+ ++            E+ K          E   K++I   + GD     
Sbjct: 882  RHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQP 941

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGR 1093
            V+ + K ++  K   Q  DK+ GR
Sbjct: 942  VI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 72/339 (21%), Positives = 136/339 (40%), Gaps = 37/339 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         +         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCGFI----------DQGLTEELYKFPKMEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  I 
Sbjct: 113 FIINGIYRIVINQILQSPGIYYRSELD---HNGIPVYTGTIISDWGGRVELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY----SQRGDFWCFPLSAADLMVGAK 259
            R+ R++K+ +     A+G++  EIL       ++    +          S  + ++   
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCCPEIFLSFLNLNDKGKKKMGSKENAILEFY 229

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
              + V  D      ES  K         + +  +   +  +    L +  +       +
Sbjct: 230 QQFTCVGGDP--VFSESLCKELQKKFFQQRCELGRIGRLNMNRRLNLDIPHNNTFLLPRD 287

Query: 320 IYIEAGD-------VIDEKSLEEIFHSEIRDIPILYVDS 351
           I   A         +     +  + +  IR +  L  D 
Sbjct: 288 ILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 326


>gi|89142868|emb|CAJ76105.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKTVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   EI++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKREIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|160689600|gb|ABX45658.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689602|gb|ABX45659.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689604|gb|ABX45660.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689606|gb|ABX45661.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689610|gb|ABX45663.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689614|gb|ABX45665.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689616|gb|ABX45666.1| RNA polymerase subunit beta [Bacillus mojavensis]
 gi|160689618|gb|ABX45667.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689620|gb|ABX45668.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689624|gb|ABX45670.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689626|gb|ABX45671.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689628|gb|ABX45672.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689630|gb|ABX45673.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689632|gb|ABX45674.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689634|gb|ABX45675.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689636|gb|ABX45676.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689638|gb|ABX45677.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689640|gb|ABX45678.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689648|gb|ABX45682.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689650|gb|ABX45683.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689652|gb|ABX45684.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689654|gb|ABX45685.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689656|gb|ABX45686.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689658|gb|ABX45687.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689660|gb|ABX45688.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689662|gb|ABX45689.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689666|gb|ABX45691.1| RNA polymerase subunit beta [Bacillus mojavensis]
 gi|160689668|gb|ABX45692.1| RNA polymerase subunit beta [Bacillus mojavensis]
 gi|160689670|gb|ABX45693.1| RNA polymerase subunit beta [Bacillus tequilensis]
 gi|160689676|gb|ABX45696.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689678|gb|ABX45697.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689680|gb|ABX45698.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689686|gb|ABX45701.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689688|gb|ABX45702.1| RNA polymerase subunit beta [Bacillus subtilis subsp. inaquosorum]
 gi|160689690|gb|ABX45703.1| RNA polymerase subunit beta [Bacillus subtilis subsp. spizizenii]
 gi|160689692|gb|ABX45704.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689694|gb|ABX45705.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689696|gb|ABX45706.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689698|gb|ABX45707.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689700|gb|ABX45708.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689702|gb|ABX45709.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689704|gb|ABX45710.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689706|gb|ABX45711.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689708|gb|ABX45712.1| RNA polymerase subunit beta [Bacillus mojavensis]
 gi|160689712|gb|ABX45714.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689714|gb|ABX45715.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689716|gb|ABX45716.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689718|gb|ABX45717.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689724|gb|ABX45720.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689726|gb|ABX45721.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689732|gb|ABX45724.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689734|gb|ABX45725.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|160689736|gb|ABX45726.1| RNA polymerase subunit beta [Bacillus subtilis]
 gi|293627267|gb|ADE58308.1| RNA polymerase beta subunit [Bacillus subtilis subsp. inaquosorum]
          Length = 321

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/377 (37%), Positives = 194/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 78/117 (66%), Positives = 95/117 (81%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV  GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|32487328|emb|CAE05903.1| OSJNBa0061C08.10 [Oryza sativa Japonica Group]
 gi|57834097|emb|CAE04762.3| OSJNBa0079C19.3 [Oryza sativa Japonica Group]
          Length = 1067

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 800  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 859

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 860  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 912

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 913  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 940

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 941  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1000

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1001 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSQKNF 1060

Query: 1370 NSAKME 1375
               + E
Sbjct: 1061 QVNREE 1066



 Score =  348 bits (893), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 232/699 (33%), Positives = 382/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 127 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLKEILD 186

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 187 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 245

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 246 CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 305

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 306 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 365

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 366 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 425

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 426 INVGLTGSLAIHARIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 485

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 486 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 545

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   ++ +I++        
Sbjct: 546 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTNSHKILL-------- 597

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 598 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNILV 657

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 658 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 717

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 718 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 777

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 778 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 816



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I         +     Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEISFQLFAKGYQLLE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 54  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 102

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 103 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 159

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G + +EIL    YP+I  S         + + +  +
Sbjct: 160 ARVSRKQKISILVLSSAMGSNLKEILDNVSYPEIFLSFPNAKEKKRIESKEKAI 213


>gi|11466777|ref|NP_039373.1| RNA polymerase beta subunit [Oryza sativa Japonica Group]
 gi|50233961|ref|YP_052739.1| RNA polymerase beta subunit [Oryza nivara]
 gi|109156587|ref|YP_654206.1| RNA polymerase beta subunit [Oryza sativa Indica Group]
 gi|68053142|sp|Q6ENI4|RPOB_ORYNI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|148839636|sp|P0C501|RPOB_ORYSA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|148839637|sp|P0C502|RPOB_ORYSI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|148839638|sp|P0C503|RPOB_ORYSJ RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|11971|emb|CAA33986.1| RNA polymerase beta subunit [Oryza sativa Japonica Group]
 gi|42795479|gb|AAS46046.1| RNA polymerase beta chain [Oryza sativa Indica Group]
 gi|49614985|dbj|BAD26768.1| RNA polymerase beta subunit [Oryza nivara]
          Length = 1075

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 179/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSQKNF 1068

Query: 1370 NSAKME 1375
               + E
Sbjct: 1069 QVNREE 1074



 Score =  348 bits (893), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 232/699 (33%), Positives = 382/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLKEILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   ++ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTNSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I         +     Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEISFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G + +EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLKEILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|224003383|ref|XP_002291363.1| DNA directed RNA polymerase II, second largest subunit [Thalassiosira
            pseudonana CCMP1335]
 gi|220973139|gb|EED91470.1| DNA directed RNA polymerase II, second largest subunit [Thalassiosira
            pseudonana CCMP1335]
          Length = 1196

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 163/1042 (15%), Positives = 317/1042 (30%), Gaps = 196/1042 (18%)

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            ++       ++A +   + +    +     A  +      D  +Y    + +  +     
Sbjct: 305  MMDLFRPSLEEAFVIQKQEVALDFIGRRGSARDV---TKDDRIRYAAGILQKEVLPHVGT 361

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
             +  +  +      +   +  L+  + G+   DD D+ G +R+   G +L   +R+   +
Sbjct: 362  EEHCETKK---GFFLGYAVHKLLMCKLGRADEDDRDHFGKKRLDLAGPLLGGLFRVLFRK 418

Query: 482  MERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-----------LSQLEEH 528
            + + +++ +     +         I +  +   +     +             +SQ+   
Sbjct: 419  LTKDVRKHLQRCLDEGKHFNIGAAIKSNHISDGLKYSLATGNWGDKGNTSKAGVSQVLNR 478

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            +   S ++H RR +      +AR     + R +H +H+G +CPAET EG  +GLV ++  
Sbjct: 479  LTYASSLSHLRRSNT----PLARTGKQAKPRQLHNSHWGMVCPAETPEGQAVGLVKNMAL 534

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYL-SAMEEENRYIAQANSSLDEDGSFTEELVFC 647
             A +            + +    N    L S + E N      N +        ++LV  
Sbjct: 535  MAYITTGTSQVPVMEFLEEFSTENLTDILPSVIAEPNTCKIFVNGNWVGIHRDPKQLVHT 594

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPL 703
              +   ++    ++  +   P+  V I         P     D     +  +   Q   +
Sbjct: 595  FRSLRRMIDIDAEVSIVRDIPESEVRIYTDAGRICRPLFIVTDQELA-IKKHHISQLQGV 653

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
               +     T +                 G+VE VD        +  +       V    
Sbjct: 654  SPDQKKLTWTDLLME--------------GLVEYVDTEEEETTMIAMEPKDLDMTVGEPY 699

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
               +                              PS  LG       +  + +P+  +N 
Sbjct: 700  STTY------------------------THCEIHPSMILG-------ICASIIPFPDHNQ 728

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +   I+   ++V                               +  
Sbjct: 729  SPRNTYQSAMGKQAMG--IYASNYQVRM---------------------------DTMAH 759

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            V             +       +     ++ AI      +  D+ +   S +   +    
Sbjct: 760  VLHYPQKPLCTTRAMEFLHFRELPSGVNVVVAIMIYTGYNQEDSLIMNQSAIDRGLFRSS 819

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +   +   S+                    L+   + R        +   G K   
Sbjct: 820  YYRCYNDQEKSSSVGS---------------VGALNSEFFER-----PAFDNCKGMKTGD 859

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               +    L+S   R       +        + +   +Y         +           
Sbjct: 860  YGKLDDDGLVSPGTRVSGDDVLIGKTAPMDAIANTPSRYTKRDCSTSMKANENGIVDNVL 919

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R  KV +   R  Q GDK A RHG KG +      EDMPF  +G   DI++N
Sbjct: 920  ISTTKEGYRFTKVRIRNVRIPQVGDKFASRHGQKGTIGMTYRQEDMPFTCEGIVPDIIVN 979

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM + Q+ E  LG   V  G +                                
Sbjct: 980  PHAIPSRMTIAQLIECILGKVAVFQGCEGD------------------------------ 1009

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     + I+  L        G   +Y G TG 
Sbjct: 1010 -----------------------ATP-FTDVHVDDISKRLHAMGYQRHGNEAMYQGHTGR 1045

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P +  V +G  +  +L H+V DKV++R+ G  +++T+QPL G++  GG R+GEME  C+ 
Sbjct: 1046 PLNARVFIGPTFYQRLKHLVDDKVHSRARGPVAMLTRQPLEGRARDGGLRMGEMERDCLI 1105

Query: 1304 AYGAAYVLQEMLTIKSD----DVVGR----------TRVYESIVA---GND--TFETGTP 1344
             +G A  +++     SD     +  R             YE       G      +   P
Sbjct: 1106 THGCANFIRDRFFCNSDQYRIHICERCGLTAQSNLKKMTYECRTPTCVGLPYKICQVEIP 1165

Query: 1345 ESFNVLVKEMQALGLSIDLENS 1366
             +  +L +E+Q++ +S  +   
Sbjct: 1166 YACKLLFQELQSMCISPRIYTE 1187



 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 128/1013 (12%), Positives = 283/1013 (27%), Gaps = 207/1013 (20%)

Query: 29  LIEVQKASYDHFLMMN------------IAPDERPNEGLQAA-FKSVFPITAFSGA-AML 74
           L+  Q  S+D F+               ++P+ +   G   A F       + +     +
Sbjct: 26  LVRQQLDSFDEFIQNTMQELVDDSGSIRVSPEIQHLVGYDEANFDETM--NSTTKKVFEV 83

Query: 75  EFVSYEFDPPK----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT------- 117
           +F       P               +   R+LTYA PL + + +  + V           
Sbjct: 84  KFGQVYLSKPTTVEKDGTVTNMFPHEARLRNLTYAAPLYVDVTMNEYRVGNDVNVGDPAE 143

Query: 118 ---GAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
                 S ++ +++  ++G +P+M +                         G FVI G +
Sbjct: 144 DMGEPVSTEEARKE--FLGYVPIMLRSLFCVLSDKDDAQLADLGECIYDQGGYFVINGSE 201

Query: 151 RIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR- 208
           +++V+Q   S   ++    K  +  S        +I  +   ++        +++++ + 
Sbjct: 202 KVIVAQERMSNNHVYAFKKKQPSKFSW-------VIETR-SQVENSTRPTSTLYIQMYQK 253

Query: 209 ------------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
                             R  +PV     ALG  ++ +I+      +   +  D +   L
Sbjct: 254 GGKGAIEGNQIRSTLPYIRTDIPVVIIFRALGYVADRDIIEHVVYDLTDGEMMDLFRPSL 313

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCG 305
             A ++   +V+   +      + +    ++         + L   G +    T      
Sbjct: 314 EEAFVIQKQEVALDFIGRRGSARDVTKDDRIRYAAGILQKEVLPHVGTEEHCETKKGFFL 373

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
            Y    ++  + G    +  D   +K L+           +L+         +   +   
Sbjct: 374 GYAVHKLLMCKLGRADEDDRDHFGKKRLDLAGPLLGGLFRVLFRK-------LTKDVRKH 426

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             +   +            +  +  +  S+    + D      + V +V   +       
Sbjct: 427 LQRCLDEGKHFNIGAAIKSNHISDGLKYSLATGNWGDKGNTSKAGVSQVLNRLTYASSLS 486

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              R                L N    +         +   + + +     +     +  
Sbjct: 487 HLRRSNTPLARTGKQAKPRQLHNSHWGMVCPAETPEGQAVGLVKNMALMAYITTGTSQVP 546

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           + E +     +++    L +     +    F   + +    +    +      RR+  + 
Sbjct: 547 VMEFLEEFSTENLT-DILPSVIAEPNTCKIFVNGNWVGIHRDPKQLVHTFRSLRRMIDID 605

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
                          ++        P        + +     S  +       +      
Sbjct: 606 AEVSIVRDIPESEVRIYTDAGRICRPLFIVTDQELAIKKHHISQLQ---GVSPDQKKLTW 662

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            D  +   V Y+   EEE   IA     LD                             +
Sbjct: 663 TDLLMEGLVEYVDTEEEETTMIAMEPKDLD---------------MTVGEPYSTTYTHCE 707

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R      M +QA+ +  +                   
Sbjct: 708 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYASNYQV--------------- 752

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + V  Y               Q+PL    
Sbjct: 753 --------------------------RMDTMAHVLHYP--------------QKPLC--- 769

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G N++VA M + GYN EDS+++++  +   +F S +  
Sbjct: 770 -------TTRAMEFLHFRELPSGVNVVVAIMIYTGYNQEDSLIMNQSAIDRGLFRSSYYR 822

Query: 846 EFEVMARDTKLGP----------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +    + + +G                +   +       +D+ G++  G  V+  D+L+
Sbjct: 823 CYNDQEKSSSVGSVGALNSEFFERPAFDNCKGMKTGDYGKLDDDGLVSPGTRVSGDDVLI 882

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           GK  P      TP                RD S  + +  +G V +V I    
Sbjct: 883 GKTAPMDAIANTP-----------SRYTKRDCSTSMKANENGIVDNVLISTTK 924


>gi|290489642|gb|ADD31205.1| RNA polymerase beta subunit protein [Liquidambar styraciflua]
          Length = 1070

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+++DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYVQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPK 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 225/634 (35%), Positives = 359/634 (56%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RL+L+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLDLNIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   
Sbjct: 434 LIGSLAIHARIGRWGSLESPFYEISERSKKVRMLYLSPSRDEYYMVAAGNSLALNQGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG  ++A+  G +   D         +  +         
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGIPVLAEHEGKIVYTD--------TDKIILSGNGDTLS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V+    +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMHQKPQVQRSKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISE +V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI
Sbjct: 666 NFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKRGGSSYNPEMIRVYISQKREIKVGDK 819



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          KS  D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KSSGDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---IYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|186885873|gb|ACC93344.1| RNA polymerase beta subunit [Gongylolepis benthamiana]
          Length = 1028

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 151/497 (30%), Positives = 235/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMGKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK----- 751

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
              +         ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 752  --NRDSSSKPESIRVYILQKREIKVGDKIAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDPPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 260/806 (32%), Positives = 416/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNQRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            D     PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  DKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYSD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMGKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIE-- 965
            LLR I G +    ++T L++P G  G V+DVR   ++    ++    R   +++ +I+  
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKNRDSSSKPESIRVYILQKREIKVG 775

Query: 966  -LLARDKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
              +A    ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKIAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QPVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKEKDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---HNGIAVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|89142820|emb|CAJ76081.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142830|emb|CAJ76086.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            TGE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KTGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|186885861|gb|ACC93338.1| RNA polymerase beta subunit [Felicia heterophylla]
          Length = 1024

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/460 (30%), Positives = 218/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVILGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTNETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            IVS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IVSKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 843  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 872

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 873  ---------PESPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++  GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKNGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P     +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQTNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKIYERSKGARMLYLSPGTDEYYMVAAGNSLALNRGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + V  E++        Q  S+ ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTVAWEQVHLRSIFSFQYFSVGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKTRVRRGKCIKKGQILACGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEVHLLRNLDKNGIVILGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            ++ E++ S+     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 750  NETEKTESIRVYILQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|139389410|ref|YP_001123107.1| RNA polymerase beta subunit [Olimarabidopsis pumila]
 gi|158513625|sp|A4QJS5|RPOB_OLIPU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|134286304|dbj|BAF49931.1| RNA polymerase beta subunit [Olimarabidopsis pumila]
          Length = 1072

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 153/498 (30%), Positives = 237/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 628  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 682  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 739

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 740  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 796

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 797  -GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 852

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 853  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 912

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 913  TANPW------------------------VFE---------------PEYPGKSRIFDGR 933

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 934  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 993

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L
Sbjct: 994  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPESFRLLVRELRSLAL 1053

Query: 1360 SID--LENSRTKNSAKME 1375
             ++    + +     + E
Sbjct: 1054 ELNHFFVSEKNFQINRKE 1071



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 254/832 (30%), Positives = 426/832 (51%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVSYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV+          +       L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVL--------SGSGDTLTIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERNAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVSYPEIFLSFLTDKEKKKIGSKE 220


>gi|89142818|emb|CAJ76080.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142834|emb|CAJ76088.1| RNA polymerase, beta subunit [Corallococcus exiguus]
 gi|89142846|emb|CAJ76094.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142872|emb|CAJ76107.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142874|emb|CAJ76108.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   EI++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKREIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|160689722|gb|ABX45719.1| RNA polymerase subunit beta [Bacillus atrophaeus]
 gi|160689728|gb|ABX45722.1| RNA polymerase subunit beta [Bacillus atrophaeus]
          Length = 321

 Score =  383 bits (983), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/381 (37%), Positives = 188/381 (49%), Gaps = 70/381 (18%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEILCGQNAVSGPKG 1001
            K++   S+  E+ E  ARD       + R+I                I  G     G   
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVNDGDLL 60

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T      ++   R     F  +  +V+     +          +      K+   +
Sbjct: 61   VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDV------KVFNRE 114

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+
Sbjct: 115  DGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIM 174

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+                
Sbjct: 175  LNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK-- 232

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                      T ++DG                           T
Sbjct: 233  --------------------------TVLYDG--------------------------RT 240

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW 
Sbjct: 241  GEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 300

Query: 1302 IQAYGAAYVLQEMLTIKSDDV 1322
            ++AYGAAY LQE+LT+KSDDV
Sbjct: 301  LEAYGAAYTLQEILTVKSDDV 321



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 80/117 (68%), Positives = 96/117 (82%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEVN GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVNDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|298705314|emb|CBJ49004.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 1277

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 171/1044 (16%), Positives = 328/1044 (31%), Gaps = 193/1044 (18%)

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
               +    ++       ++A +   +V+    +     A ++      +   Y    + R
Sbjct: 382  VYDFSDTDMMEKFRPSLEEADVIQNQVVAQDFIGKRGSAVNVGRNERIN---YAKGLLQR 438

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
              +         +  +      +  ++  L+    G+   DD D+ G +R+   G +L  
Sbjct: 439  EFLPHVGIGAGTEAKKV---FFLGYMVHKLLMCSLGRLEEDDRDHYGKKRLDLAGALLAG 495

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ +++++  ++        +    I ++ +   +     +            
Sbjct: 496  LFRQLFRKLTQNVRKYLQLCLDKGTQFVVGTAIKSQFITDGLKYSLATGNWGDKKTATKA 555

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+   +   S ++H RRL+      + R     + R +H TH+G ICPAET EG  +
Sbjct: 556  GVSQVLNRLTYASALSHLRRLNT----PLGREGKQAKPRQLHNTHWGFICPAETPEGQAV 611

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN-SSLDEDGS 639
            GLV +L   A ++    +      + +  + N        E     IAQ N + +  +G+
Sbjct: 612  GLVKNLALMAYISVGCSLSPILEFLEEWAMENL------DEIAPHMIAQTNCTKVFVNGN 665

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            +       R     +     +   +D   +  V             D+ RV       R 
Sbjct: 666  WVG---VHRDPNRLVQTLVHQRRALDIDVEVSVVRDIKGRELRLYTDAGRV------CRP 716

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
               +           +  +   + G   +  + G+VE +D       ++     DL+ S 
Sbjct: 717  LFVVENNRLRIRKKHINDLHDPNYGWTNL-MQQGVVEYIDTEEEETTMVAMEPKDLEESG 775

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y                                   PS  LG       +  + +
Sbjct: 776  GYSSTY-----------------------------THCEIHPSMILG-------VCASII 799

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  +                            +
Sbjct: 800  PFPDHNQ------SPRNTYQSAMGKQAMGIY-----------------------ASNYQL 830

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +     ++  I      +  D+ +   S V 
Sbjct: 831  RMDTLAHVLHYPEKPLVTTRAMEHLHFRELPSGFNVIVGIMVYSGYNQEDSLIMNQSAVD 890

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +     F                   E   R   D  V+   +      E   G    
Sbjct: 891  RGLFRSSFFRTLN-------------DQEKAGRGMGDMAVLSAESFERPARENTAGMKHG 937

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +  K  +   V     +S           +                + S +++       
Sbjct: 938  NYDKLEEDGLVAPGTRVSGTDVLIGKTTPLGGGVAGVTGGPGHRSKKDSSTVMRSHEDGI 997

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            ++++           +  KV +   R  Q GDK A RHG KG +      EDMP+  DG 
Sbjct: 998  VDRVML--TTNQEGFKFCKVRIRNVRVPQIGDKFASRHGQKGTIGMTYRQEDMPWSIDGI 1055

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM + Q+ E  LG   V  G +                         
Sbjct: 1056 VPDIIVNPHAIPSRMTIAQLIECLLGKVGVLTGTEGD----------------------- 1092

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F       ++S L      + G  ++
Sbjct: 1093 ------------------------------ATP-FTDVTVANVSSTLHKIGFQKHGNEVM 1121

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y G TG   +  V +G  +  +L H+V DK+++RS G    +T+QP+ G+   GG R+GE
Sbjct: 1122 YSGHTGRMLNTKVFLGPTFYQRLKHLVDDKIHSRSRGPVMNLTRQPMEGRGRDGGLRMGE 1181

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESI-VAGN-DTFE 1340
            ME  C+ ++G A  L++ L I SD       D  G       R   +E     G  D  +
Sbjct: 1182 MERDCLISHGCANFLRDRLFINSDAYRVHVCDKCGLIAVANLRKMSFECRGCKGKSDVSQ 1241

Query: 1341 TGTPESFNVLVKEMQALGLSIDLE 1364
               P +  +L +E+ A+ ++  + 
Sbjct: 1242 IHVPYACKLLFQELMAMCIAPRMF 1265



 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 138/1013 (13%), Positives = 286/1013 (28%), Gaps = 211/1013 (20%)

Query: 29   LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAF-SGAAMLEFVSYEFDPPK 85
            L+  Q  S+D FL   +           +    +   P          + F       P 
Sbjct: 121  LVRQQLDSFDEFLQSTMHELVSSAGEIKITPELQ-YMPGQDTVRRTFQINFGQVYLAKPT 179

Query: 86   ----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK----------DI 125
                          +   R+LTY  PL   +    ++ D    ++             + 
Sbjct: 180  AREKDGSLTSMFPHEARLRNLTYNSPLYCDISCKTYEADVGDRSQEDGEGLEAEEERENP 239

Query: 126  KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
            KE   ++G +P+M +                         G FVI G ++++++    S 
Sbjct: 240  KE---FLGWVPIMLRSSFCVLVNRTDKELTELGECIYDQGGYFVINGSEKVLIANERMST 296

Query: 162  G-IHFDHDKGRASLSGKLLYACRIIP---DQG---LWMDIEFDSKD-------------- 200
              ++      +     K  +   I     + G     M ++  +K               
Sbjct: 297  NHVY----CFKKRQPSKFTWTSEIRSFVDNSGRPPSSMFLQMYAKGTQHSKVNGGHIRAQ 352

Query: 201  IIHVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
            + ++R D    VPV     ALG  +++ IL         +   + +   L  AD++    
Sbjct: 353  LPYIRTD----VPVVLVFRALGYTNDKAILEHIVYDFSDTDMMEKFRPSLEEADVIQNQV 408

Query: 260  VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIV 313
            V+   +        +   +++       L+ + +  +GI            G  V + ++
Sbjct: 409  VAQDFIGKRGSAVNVGRNERINYAK-GLLQREFLPHVGIGAGTEAKKVFFLGYMVHKLLM 467

Query: 314  NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                G +  +  D   +K L+            L+     N        +    +     
Sbjct: 468  -CSLGRLEEDDRDHYGKKRLDLAGALLAGLFRQLFRKLTQNVRKYLQLCLDKGTQF---- 522

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
               +          T  +  S+    + D      + V +V   +          R    
Sbjct: 523  ---VVGTAIKSQFITDGLKYSLATGNWGDKKTATKAGVSQVLNRLTYASALSHLRRLNTP 579

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                        L N              +      ++KN   +  + +  S+   +  +
Sbjct: 580  LGREGKQAKPRQLHNTHWGFICPAETPEGQAVG---LVKNLALMAYISVGCSLSPILEFL 636

Query: 494  DIDSVMPQDLINAKPV--VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVA 550
            +  ++   D I    +   +    F   + +    +    +  + H RR   +  +  V 
Sbjct: 637  EEWAMENLDEIAPHMIAQTNCTKVFVNGNWVGVHRDPNRLVQTLVHQRRALDIDVEVSVV 696

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R   G E+R ++        P    E + + +     +      YG+         +   
Sbjct: 697  RDIKGRELR-LYTDAGRVCRPLFVVENNRLRIRKKHINDLHDPNYGW--------TNLMQ 747

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
               V Y+   EEE   +A     L+E G +                        +  P  
Sbjct: 748  QGVVEYIDTEEEETTMVAMEPKDLEESGGY-----------------SSTYTHCEIHPSM 790

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            ++ + AS+IPF +++ S R      M +QA+ +  +                        
Sbjct: 791  ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYASNYQL-------------------- 830

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                    + + V  Y       +     ++ R           
Sbjct: 831  ---------------------RMDTLAHVLHYPEKPLVTTRAMEHLHFR----------- 858

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                         +L  G N++V  M + GYN EDS+++++  V   +F S         
Sbjct: 859  -------------ELPSGFNVIVGIMVYSGYNQEDSLIMNQSAVDRGLFRSSFFRTLNDQ 905

Query: 851  ARDTKLGPEE-----------ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +  +   +               +   +       ++E G++  G  V+  D+L+GK T
Sbjct: 906  EKAGRGMGDMAVLSAESFERPARENTAGMKHGNYDKLEEDGLVAPGTRVSGTDVLIGKTT 965

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P G                      +D+S  + S   G V  V +       K
Sbjct: 966  PLGGGVAGVTGGPGH-------RSKKDSSTVMRSHEDGIVDRVMLTTNQEGFK 1011


>gi|89142822|emb|CAJ76082.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142826|emb|CAJ76084.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 192/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   EI++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKREIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + NL+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFNLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|160689730|gb|ABX45723.1| RNA polymerase subunit beta [Bacillus pumilus]
          Length = 321

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/377 (37%), Positives = 194/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGA--EVKDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  115 bits (287), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 79/117 (67%), Positives = 95/117 (81%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|324120672|dbj|BAJ78727.1| RNA polymerase II second largest subunit [Lucidina biplagiata]
          Length = 1175

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 157/1007 (15%), Positives = 308/1007 (30%), Gaps = 209/1007 (20%)

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ G
Sbjct: 333  EKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYG 389

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFC 518
            N+R+   G +L   +R     + + ++                  I  K +   +     
Sbjct: 390  NKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKLITDGLRYSLA 449

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+   +   S ++H RR+++     + R     + R +H T 
Sbjct: 450  TGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTL 505

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEE 623
            +G ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +  
Sbjct: 506  WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT 565

Query: 624  NRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
              ++      +  D       L   R   + I+     I D  D   +          P 
Sbjct: 566  KIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPL 625

Query: 682  LENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQV 738
            L  ++   +L   +  M ++           V  G+ E +        ++A         
Sbjct: 626  LIVENGQLLLKKRHIDMLKEREYNNYGWQVLVAQGVVEYIDTLEEETVMIA--------- 676

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                  I   +   +   +    Y                                   P
Sbjct: 677  ------ISPDDLRQEKDYAYCTTY-----------------------------THCEIHP 701

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +  LG       +  + +P+  +N          M  + +   ++I  F           
Sbjct: 702  AMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF----------- 741

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                            ++    +  V    +   +    +       +      + AI  
Sbjct: 742  ----------------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAIAC 785

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S V            +   K+     +  ++ E   +        +
Sbjct: 786  YTGYNQEDSVILNASAVERGFFRSVF---YRSYKDSECKRIGDQE-EQFEKPTRQTCQGM 841

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
               +Y +L +   I  G           K+  L                     +    +
Sbjct: 842  RNALYDKLDDDGIISPGIRVSGDDVVIGKTMTL--------------------PENDDEL 881

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            +    ++    +    R        Q    +     +  K+ V   R  Q GDK A RHG
Sbjct: 882  DGTTKKFSKRDASTFLRNSETGVVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHG 941

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG        EDM F  +G   DI++NP  +PSRM +G + E   G      G+     
Sbjct: 942  QKGTCGIQYRQEDMIFTCEGITPDIIINPHAIPSRMTIGHLIECIQGKVSANKGEIGD-- 999

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP  D  +
Sbjct: 1000 ---------------------------------------------------ATPFNDAVN 1008

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + I+++L+       G  ++Y+G TG   +  + +G  Y  +L HMV DK+++R+ G  
Sbjct: 1009 VQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQIFLGPTYYQRLKHMVDDKIHSRARGPV 1068

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG------- 1324
             ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +         
Sbjct: 1069 QILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHICNFCGLIAI 1128

Query: 1325 ---RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               R   +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1129 ANLRNNTFEC--KGCKNKTQISQIRLPYAAKLLFQELMSMNIAPRLM 1173



 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 141/980 (14%), Positives = 284/980 (28%), Gaps = 182/980 (18%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +            +L+F       P  
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEVENPPRYLLKFEQIYLSKPTH 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +   +    E        + + Q  ++G +P
Sbjct: 99  WEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEEPI-----ETQHQKTFIGKIP 153

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 154 IMLRSTYCLLSGLTDRDLMELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAMKD- 212

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 213 ----GKYAFKSEIR----SCLEHSSRPTSTLWVNMMARGGQAIKKAAIGQRIIAILPYIK 264

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +PV     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 265 QEIPVMVVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGAR 324

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                +   K++     + L+++ +  +G++  C          +      + + A    
Sbjct: 325 GARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGRR 380

Query: 329 DEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +    +   +  +    P+L          +   +     K           +     + 
Sbjct: 381 ELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLDLAIKTKLI 440

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   +  G  ++  RL   +      R          +     
Sbjct: 441 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQ 500

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +                ++KN   +  + +       +  ++  S+   + I 
Sbjct: 501 LHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIA 557

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +  A   F     +    +    +S +   RR   +    V+  R   +      T 
Sbjct: 558 PSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYTD 617

Query: 566 YGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            GRIC P    E   + L         ++     E              V Y+  +EEE 
Sbjct: 618 AGRICRPLLIVENGQLLLKKR-----HIDMLKEREYNNYGWQVLVAQGVVEYIDTLEEET 672

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA +   L                 E+           +  P  ++ + AS+IPF ++
Sbjct: 673 VMIAISPDDL---------------RQEKDYAYCTTYTHCEIHPAMILGVCASIIPFPDH 717

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           + S R      M +QA+ +                                         
Sbjct: 718 NQSPRNTYQSAMGKQAMGVYITNFHV---------------------------------- 743

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                     + + V  Y                +PLV                     +
Sbjct: 744 -------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYLRFRE 772

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           L  G N +VA   + GYN EDS++++   V    F S+    ++          EE    
Sbjct: 773 LPAGINSIVAIACYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSECKRIGDQEEQFEK 832

Query: 865 -----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                   +       +D+ GII  G  V+  D+++GK     E+    +          
Sbjct: 833 PTRQTCQGMRNALYDKLDDDGIISPGIRVSGDDVVIGKTMTLPENDDELDGTT------- 885

Query: 920 KAVDVRDTSLRVPSGVSGTV 939
           K    RD S  + +  +G V
Sbjct: 886 KKFSKRDASTFLRNSETGVV 905


>gi|34581975|gb|AAQ75923.1| RpoB [Trilisa paniculata]
          Length = 826

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 46/396 (11%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+          D+        V+V++  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 533  GGRGRVIDVRWVR----SSKTDETEKTESIRVRVYILQKREIKVGDKVAGRHGNKGIVSK 588

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 589  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 648

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 649  QEASRKLVF-SELYEASKQTVNPWIFEPE------------------------------- 676

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 677  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 729

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 730  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 789

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 790  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 825



 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 247/727 (33%), Positives = 394/727 (54%), Gaps = 44/727 (6%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  +N RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNLNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYQV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ D      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISDRSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLYQSEKCIVGTGLEGQAALDSGALAIAEHEGNIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LI ER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWDGYNFEDAVLIGERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-------EREQIELLAR--DKDDEQVILDRNIYS 984
            G  G V+DVR       D+ E++ S+       ++ +I++  +   +   + I+ + +  
Sbjct: 533  GGRGRVIDVRWVRSSKTDETEKTESIRVRVYILQKREIKVGDKVAGRHGNKGIVSKILPR 592

Query: 985  RLMEILCG-------QNAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN-- 1034
            + M  L          N +  P       +  S L ++     + ++ A  DE+ ++   
Sbjct: 593  QDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEAS 652

Query: 1035 --------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                     E+ K          E   K++I   + GD     V+ + K ++  K   Q 
Sbjct: 653  RKLVFSELYEASKQTVNPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQV 710

Query: 1087 GDKMAGR 1093
             DK+ GR
Sbjct: 711  DDKIHGR 717


>gi|312381454|gb|EFR27200.1| hypothetical protein AND_06234 [Anopheles darlingi]
          Length = 1954

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 153/943 (16%), Positives = 291/943 (30%), Gaps = 189/943 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 335  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYGNK 391

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I  K +   +     + 
Sbjct: 392  RLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATG 451

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 452  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 507

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENR 625
             ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +    
Sbjct: 508  MICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKI 567

Query: 626  YIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D       L   R   + I+     I D  D   +          P L 
Sbjct: 568  FVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLI 627

Query: 684  NDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDA 740
             +  + +L   +  M +            V +G+ E +        ++A           
Sbjct: 628  VEGGSLLLRKHHIDMLKDRDYNNYGWQVLVASGVVEYIDTLEEETVMIA----------- 676

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +   +   D   +    Y                                   P+ 
Sbjct: 677  ----MTPYDLKQDKEYAYCTTY-----------------------------THCEIHPAM 703

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   ++I  F             
Sbjct: 704  ILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------- 741

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                          ++    +  V        +    +       +      + AI    
Sbjct: 742  --------------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYT 787

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V         +      K+  S  +  ++ E   +        +  
Sbjct: 788  GYNQEDSVILNASAVERGFFRSVFY---RSYKDSESKRIGDQE-EQFEKPNRQTCQGMRN 843

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
             +Y +L E   I  G           K+  L          ++ +        ++ +   
Sbjct: 844  ALYDKLDEDGIIAPGLRVSGDDVVIGKTITLPETDDDLDGTTKRFTKRDGSTFLRNSETG 903

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                        +     +  K+ V   R  Q GDK A RHG K
Sbjct: 904  IVDQVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQK 943

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G        EDMPF  +G   DI++NP  +PSRM +G + E   G      G+       
Sbjct: 944  GTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECIQGKLGSNKGEIGD---- 999

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP  D  + +
Sbjct: 1000 -------------------------------------------------ATPFNDAVNVQ 1010

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I++ L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   +
Sbjct: 1011 KISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQI 1070

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            + +QP+ G++  GG R GEME  C  ++GAA  L+E L   SD
Sbjct: 1071 LVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSD 1113



 Score =  248 bits (633), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 142/989 (14%), Positives = 292/989 (29%), Gaps = 200/989 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  S   I   +   +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPAIELTAEAQHSSGEIENPT-RYLLKFDQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +        +        + + Q  ++G +
Sbjct: 98  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKIVEGQDPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKTEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRVIAILPYV 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   K++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 324 RGARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 381

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        +       + 
Sbjct: 382 LDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLE-------LA 434

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 435 IKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 494

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 495 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 551

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 552 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 611

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVV 615
               T  GRIC P    EG ++ L        +    N YG+       V        V 
Sbjct: 612 IRIYTDAGRICRPLLIVEGGSLLLRKHHIDMLKDRDYNNYGWQVLVASGV--------VE 663

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+  +EEE   IA     L +D  +                        +  P  ++ + 
Sbjct: 664 YIDTLEEETVMIAMTPYDLKQDKEY---------------AYCTTYTHCEIHPAMILGVC 708

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +                                
Sbjct: 709 ASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------- 743

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                              + + V  Y +     +     +  R                
Sbjct: 744 ----------------RMDTLAHVLYYPMKPLVTTRSMEYLRFR---------------- 771

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G N +VA + + GYN EDS++++   V    F S+    ++       
Sbjct: 772 --------ELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRI 823

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              EE            +       +DE GII  G  V+  D+++GK     E+    + 
Sbjct: 824 GDQEEQFEKPNRQTCQGMRNALYDKLDEDGIIAPGLRVSGDDVVIGKTITLPETDDDLDG 883

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    K    RD S  + +  +G V
Sbjct: 884 TT-------KRFTKRDGSTFLRNSETGIV 905


>gi|324120658|dbj|BAJ78720.1| RNA polymerase II second largest subunit [Neocolochelyna itoi]
          Length = 1175

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 168/1086 (15%), Positives = 334/1086 (30%), Gaps = 204/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + T      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGTRGARPGV---TKEKRIKYAREILQKEMLPHVGISDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLSASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I  I     ++ + A  +   L   +   +L+                          V
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVEGQNLLLKKRHIDMLKERDYTNYG-------WQV 655

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
              +SG           E +D         E  +  + S  D+ +  ++            
Sbjct: 656  LVASGVV---------EYIDT------LEEETVMIAMSPEDLRQEKEYA----------- 689

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                              P+  LG       +  + +P+  +N          M  + + 
Sbjct: 690  -------YCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG 735

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              ++I  F                           ++    +  V    +   +    + 
Sbjct: 736  --VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSME 766

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +      + AI      +  D+ +   S V            +   K+  S  +
Sbjct: 767  YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVF---YRSYKDSESKRI 823

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
              ++ E   +        +   IY +L +   I  G           K+  L        
Sbjct: 824  GDQE-EQFEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITL-------- 874

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                         +    ++S   ++    +    R        Q    +     +  K+
Sbjct: 875  ------------PETDDELDSATKRFTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKI 922

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G +
Sbjct: 923  RVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFSCEGLTPDIIINPHAIPSRMTIGHL 982

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E   G      G+                                              
Sbjct: 983  IECIQGKVSANKGEIGD------------------------------------------- 999

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                      +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G  Y 
Sbjct: 1000 ----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTYY 1049

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L 
Sbjct: 1050 QRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLF 1109

Query: 1317 IKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALG 1358
              SD     +            R   +E    G        +   P +  +L +E+ A+ 
Sbjct: 1110 EVSDPYRIHICNFCGLIAIANLRNNTFEC--KGCKNKTQISQIRLPYAAKLLFQELMAMN 1167

Query: 1359 LSIDLE 1364
            ++  L 
Sbjct: 1168 IAPRLM 1173



 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 143/984 (14%), Positives = 287/984 (29%), Gaps = 190/984 (19%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I        L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIENPVRHL-LKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDAEDPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  Y   I       ++        + V         I +              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWVNMMAKSGASIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGT 323

Query: 268 DTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
                 +   K++         + L   G+     T       Y+   +++   G   ++
Sbjct: 324 RGARPGVTKEKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLSASLGRRELD 383

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+            L+ + +          +        +       +   
Sbjct: 384 DRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLE-------LAIK 436

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
             + T  +  S+    + D  K   +  G  ++  RL   +      R          + 
Sbjct: 437 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLA 496

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +                ++KN   +  + +       +  ++  S+   
Sbjct: 497 KPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENL 553

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           + I    +  A   F     +    +    ++ +   RR   +    V+  R   +    
Sbjct: 554 EEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIR 613

Query: 562 HPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
             T  GRIC P    EG N+ L         ++     +           +  V Y+  +
Sbjct: 614 IYTDAGRICRPLLIVEGQNLLLKKR-----HIDMLKERDYTNYGWQVLVASGVVEYIDTL 668

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   IA +   L                 E+           +  P  ++ + AS+IP
Sbjct: 669 EEETVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIP 713

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 714 FPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------ 743

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y                +PLV                  
Sbjct: 744 -----------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYL 768

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE
Sbjct: 769 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGDQEE 828

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                       +       +D+ GII  G  V+  D+++GK     E+    +      
Sbjct: 829 QFEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPETDDELDSAT--- 885

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
               K    RD S  + +  +G V
Sbjct: 886 ----KRFTKRDASTFLRNSETGIV 905


>gi|89142844|emb|CAJ76093.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 190/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQSNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|89142828|emb|CAJ76085.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142832|emb|CAJ76087.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142850|emb|CAJ76096.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142852|emb|CAJ76097.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142854|emb|CAJ76098.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142856|emb|CAJ76099.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142858|emb|CAJ76100.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142860|emb|CAJ76101.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142862|emb|CAJ76102.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142864|emb|CAJ76103.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 190/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|269930797|gb|ACZ54133.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 436

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 304/432 (70%), Positives = 364/432 (84%), Gaps = 1/432 (0%)

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFF
Sbjct: 6   DQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFHSLFF 65

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           D ++YDLS VGRVKMN+R++L+ PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGN
Sbjct: 66  DPERYDLSAVGRVKMNLRMDLNCPDTVRVLRQEDILAVVKMLVELRDGRGEIDDIDNLGN 125

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQ
Sbjct: 126 RRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQ 185

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIG
Sbjct: 186 LSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIG 245

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FT
Sbjct: 246 LINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFT 305

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAV
Sbjct: 306 EEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAV 365

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL++AEAPFVGTGMESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 366 PLVRAEAPFVGTGMESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 424

Query: 762 YRLMKFQRSNQN 773
           YRL KFQRSNQ+
Sbjct: 425 YRLQKFQRSNQS 436


>gi|89142848|emb|CAJ76095.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 279/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   EI++  +L++D+ N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKREIKEFKVLFIDNHNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|108802635|ref|YP_636291.1| RNA polymerase beta subunit [Eucalyptus globulus subsp. globulus]
 gi|88909138|sp|Q49L06|RPOB_EUCGG RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|60460801|gb|AAX21021.1| RNA polymerase beta subunit [Eucalyptus globulus subsp. globulus]
          Length = 1072

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 722  LDKNGIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 781

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G +  P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 782  GGRGRVIDVRWIQKKG----GSNYNP---ETICVYILQKREIKVGDKVAGRHGNKGIISK 834

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 835  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 894

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 895  QEASRKLVFSELYEASQQTANPW------------------------VFE---------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 975

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 976  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPK 1035

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1036 DAPESFRLLVRELRSLSLELNHFLVSEKNFQINRKE 1071



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 229/612 (37%), Positives = 353/612 (57%), Gaps = 17/612 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  +K  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVKGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGS 639
           L+ SL   AR+   G +E+P+ ++ +   +  V   YLS   +E   IA  NS       
Sbjct: 434 LIGSLAIHARIGQGGSLESPFYEISERSKSKKVRMLYLSPSRDEYYMIAAGNSLALNQRI 493

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E++V  R   E + +  E+++     P Q  SI ASLIPF+E++D+NR LM  NMQRQ
Sbjct: 494 QEEQVVPARYRQEFLTIAWEQVNLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQ 553

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL ++E   VGTG+E   A  SG   +A+  G +   +  +I++              
Sbjct: 554 AVPLSRSEKCIVGTGLERQAALDSGVTAIAEHEGKIIYTNTDKIILLGN--------GDT 605

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
               L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA++PW 
Sbjct: 606 LSIPLVMYQRSNKNTCMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYLPWE 665

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++LISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ 
Sbjct: 666 GYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKN 725

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           GI+ +G+ V  GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G
Sbjct: 726 GIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRG 785

Query: 938 TVVDVRIFNRHG 949
            V+DVR   + G
Sbjct: 786 RVIDVRWIQKKG 797



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELIKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTLFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|89142816|emb|CAJ76079.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142842|emb|CAJ76092.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + NL+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFNLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|332022245|gb|EGI62560.1| DNA-directed RNA polymerase II subunit RPB2 [Acromyrmex echinatior]
          Length = 1178

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 161/1061 (15%), Positives = 326/1061 (30%), Gaps = 212/1061 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++        +A +   + +    + T      +         KY 
Sbjct: 286  DILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGTRGAKPGV---TKEKRIKYA 342

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+   
Sbjct: 343  REILQKEMLPHVGISDFCETKK---AYFLGYMVHRLLSASLGRRELDDRDHYGNKRLDLA 399

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R     + + ++               +  I  K +   +     +      
Sbjct: 400  GPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQ 459

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+   +   S ++H RR+++     + R     + R +H T +G +CPA
Sbjct: 460  KKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWGMLCPA 515

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
            ET EG  +GLV +L   A ++           + +  +    ++   +  +    ++   
Sbjct: 516  ETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGC 575

Query: 631  NSSLDEDGSFTE-ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D       L   R   + I+     +  I     ++ + A  +   L   +   
Sbjct: 576  WVGIHRDPDQLMATLRKLRRQMDIIVSEVSMVRDIRDREIRIYTDAGRISRPLLIVEGQN 635

Query: 690  VLMGC---NMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +L+     NM ++           VG+G+ E +        ++A               +
Sbjct: 636  LLLQTRHINMLKERDYNNDGWQELVGSGVVEYIDTLEEETVMIA---------------M 680

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               +   +   +    Y                                   P+  LG  
Sbjct: 681  SPDDLRQEKEYAYCTTY-----------------------------THCEIHPAMILG-- 709

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   ++I  F                  
Sbjct: 710  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------------ 744

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     ++    +  V    +   +    +       +      + AI      +  
Sbjct: 745  ---------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQE 795

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V         +      K   S  +  ++ E   +        +   IY +
Sbjct: 796  DSVILNASAVERGFFRSVFY---RSYKESESKKIGDQE-EQFEKPSRLTCSGMRNAIYDK 851

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   I  G           K+  L          ++ +        ++ +   +  Q 
Sbjct: 852  LDDDGIIAPGIRVSGDDVIIGKTITLPETDDELDSTTKRFTKRDASTFLRNSETGIVDQV 911

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                   +     +  K+ V   R  Q GDK A RHG KG    
Sbjct: 912  ML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGI 951

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E   G      G+            
Sbjct: 952  QYRQEDMPFSSEGLTPDIIINPHAIPSRMTIGHLIECIQGKVSANKGEIGD--------- 1002

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP  D  + + I+++
Sbjct: 1003 --------------------------------------------ATPFNDAVNVQKISTL 1018

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +QP
Sbjct: 1019 LQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQP 1078

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRV 1328
            + G++  GG R GEME  C  ++GAA  L+E L   SD     +            R   
Sbjct: 1079 MEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHICNFCGLIAIANLRNNT 1138

Query: 1329 YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            +E    G        +   P +  +L +E+ A+ ++  L  
Sbjct: 1139 FEC--KGCKNKTQIAQIRLPYAAKLLFQELMAMNIAPRLMT 1177



 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 136/985 (13%), Positives = 286/985 (29%), Gaps = 192/985 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  +   I        L+F       P 
Sbjct: 42  LVRQQLDSFDEFIEMSVQRIVEDSPQIELQAEAQHTTGEIEKPVKHL-LKFEQIYLSKPT 100

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 101 HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIEKDGEDPV-----ETQHQKTFIGKI 155

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 156 PIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 215

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDR-------------- 208
                GK  Y   I       ++        +           I +              
Sbjct: 216 -----GKYAYKAEIR----SCLEHSSRPTSTLWINMMAKSGASIKKSAIGQRIIAIIPYI 266

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 267 KQEIPIMVVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGT 326

Query: 268 DTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
              +  +   K++         + L   G+     T       Y+   +++   G   ++
Sbjct: 327 RGAKPGVTKEKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLSASLGRRELD 386

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+            L+ + +          +        +       +   
Sbjct: 387 DRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLE-------LAIK 439

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
             + T  +  S+    + D  K   +  G  ++  RL   +      R          + 
Sbjct: 440 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLA 499

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +                ++KN   +  + +       +  ++  S+   
Sbjct: 500 KPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENL 556

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVEMR 559
           + I    +  A   F     +    +    ++ +   RR     + +  + R     E+R
Sbjct: 557 EEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMVRDIRDREIR 616

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++        P    EG N+ L +       +N     +       +   +  V Y+  
Sbjct: 617 -IYTDAGRISRPLLIVEGQNLLLQTR-----HINMLKERDYNNDGWQELVGSGVVEYIDT 670

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L                 E+           +  P  ++ + AS+I
Sbjct: 671 LEEETVMIAMSPDDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASII 715

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 716 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------------- 746

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + V  Y                +PLV                 
Sbjct: 747 ------------RMDTLAHVLYYP--------------HKPLV----------TTRSMEY 770

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G N +VA + + GYN EDS++++   V    F S+    ++          E
Sbjct: 771 LRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKESESKKIGDQE 830

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E            +       +D+ GII  G  V+  D+++GK     E+    +     
Sbjct: 831 EQFEKPSRLTCSGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITLPETDDELDSTT-- 888

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                K    RD S  + +  +G V
Sbjct: 889 -----KRFTKRDASTFLRNSETGIV 908


>gi|160689664|gb|ABX45690.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 321

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 126/270 (46%), Positives = 158/270 (58%), Gaps = 54/270 (20%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 106  HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 165

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 166  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 225

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 226  GMSRDAK----------------------------TVLYDG------------------- 238

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                    TGEPFD  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 239  -------RTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQ 291

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            R GEMEVW ++AYGAAY LQE+LT+KSDDV
Sbjct: 292  RFGEMEVWALEAYGAAYTLQEILTVKSDDV 321



 Score =  112 bits (280), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 77/117 (65%), Positives = 95/117 (81%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+T +HIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+L
Sbjct: 1   KDDVYTHLHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|89142836|emb|CAJ76089.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 190/420 (45%), Positives = 281/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+ +TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDEKTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|309322441|ref|YP_003933954.1| RNA polymerase beta subunit [Eucalyptus grandis]
 gi|308223275|gb|ADO23583.1| RNA polymerase beta subunit [Eucalyptus grandis]
          Length = 1072

 Score =  382 bits (982), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 722  LDKNGIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 781

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G +  P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 782  GGRGRVIDVRWIQKKG----GSNYNP---ETICVYILQKREIKVGDKVAGRHGNKGIISK 834

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 835  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 894

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 895  QEASRKLVFSELYEASQQTANPW------------------------VFE---------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 975

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 976  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPK 1035

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1036 DAPESFRLLVRELRSLSLELNHFLVSEKNFQINRKE 1071



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 229/612 (37%), Positives = 353/612 (57%), Gaps = 17/612 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  +K  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVKGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGS 639
           L+ SL   AR+   G +E+P+ ++ +   +  V   YLS   +E   IA  NS       
Sbjct: 434 LIGSLAIHARIGQGGSLESPFYEISERSKSKKVRMLYLSPSRDEYYMIAAGNSLALNQRI 493

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E++V  R   E + +  E+++     P Q  SI ASLIPF+E++D+NR LM  NMQRQ
Sbjct: 494 QEEQVVPARYRQEFLTIAWEQVNLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQ 553

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL ++E   VGTG+E   A  SG   +A+  G +   +  +I++              
Sbjct: 554 AVPLSRSEKCIVGTGLERQAALDSGVTTIAEHEGKIIYTNTDKIILLGN--------GDT 605

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
               L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA++PW 
Sbjct: 606 LSIPLVMYQRSNKNTCMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYLPWE 665

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED++LISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ 
Sbjct: 666 GYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKN 725

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           GI+ +G+ V  GD+LVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G
Sbjct: 726 GIVMLGSWVEAGDVLVGKLTPQTAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRG 785

Query: 938 TVVDVRIFNRHG 949
            V+DVR   + G
Sbjct: 786 RVIDVRWIQKKG 797



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQNLFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|70794986|gb|AAZ08467.1| RNA polymerase II second largest subunit [Linanthus californicus]
          Length = 733

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 153/873 (17%), Positives = 276/873 (31%), Gaps = 169/873 (19%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            ++SQ+   +   S ++H RRL++     + R     + R +H + +G +CPAET EG   
Sbjct: 10   EVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQAC 65

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L     +            + +    N        EE +  +    + +  +G +
Sbjct: 66   GLVKNLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPAVIPQATKIFVNGCW 118

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   R     +D + +  V     L       D  R      +    
Sbjct: 119  VG---IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVENQ 175

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDLDPSTSGV 759
              L+                +   A    +        D   +  I  ++ + + +T   
Sbjct: 176  RLLI--------------KKRDIQALQQRESPEDGGWHDLVSKGYIEYIDTEEEETTMIS 221

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +   R+N+    +                    PS  LG       +  + +P+ 
Sbjct: 222  MTINDLVSARANKKEAYS-----------DTYTHCEIHPSLILG-------VCASIIPFP 263

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     I       R   L         P V+   ++++   
Sbjct: 264  DHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL--- 316

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                                      +      + AI      +  D+ +   S +    
Sbjct: 317  ----------------------HFRELPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGF 354

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D+ ++  ++ +E      R           +          G       
Sbjct: 355  F-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGED 413

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T ++ D  ++   +  +        ++ +   +  Q                  
Sbjct: 414  VIIGKTTPIAPDEATQGGPAARYTKRDHSTSLRHSETGIVDQVLL--------------- 458

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   D
Sbjct: 459  -----TTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGICPD 513

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +GQ+ E  +G     +GK+                            
Sbjct: 514  IIVNPHAIPSRMTIGQLIECIMGKVAAXMGKEGD-------------------------- 547

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     + I+  L        G   +Y+G
Sbjct: 548  ---------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNG 579

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME 
Sbjct: 580  HTGRRLPAXIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMER 639

Query: 1300 WCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIV---------AG----NDTFETG 1342
             C+ A+GAA+ L+E L  +SD     V  R     +I           G     D  +  
Sbjct: 640  DCMIAHGAAHFLKERLFDQSDAYRVHVCERCG-LVAIANLKKNSFECRGCKNKTDIVQVH 698

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             P +  +L +E+ ++ ++  +     K +   +
Sbjct: 699  IPYACKLLFQELMSMAIAPRMMTKDIKQAKDQK 731


>gi|194132101|gb|ACF33355.1| RNA polymerase beta subunit [Gonystylus bancanus]
          Length = 1072

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 204/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   S   S  P  +  +  +  +        LK+  
Sbjct: 722  LDKNGIVMLGSWVETGDILVGKLTPQLSKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 781

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 782  GGRGRVIDVRWIQKKG----GSAYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 834

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 835  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 894

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 895  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYVLKLIHQVDDKIHGRSSGHYALVTQQP 975

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 976  LRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1035

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + +
Sbjct: 1036 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKK 1071



 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 229/687 (33%), Positives = 376/687 (54%), Gaps = 21/687 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + +    +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYMGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFN-FLFFDSDKYDLST 410
            ++         K + +++A+L+ Y+      GD                F   + +L  
Sbjct: 203 IFLSFLTNKEKKKIRSKENAILEFYQQFSCVGGDPVFSESLCLCKELQKKFFHQRCELGR 262

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +GR  MN RLNL+ P +   +   DI+A    L+ ++ G GT+DD ++L  +R+RSV ++
Sbjct: 263 IGRRNMNQRLNLNIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDTNHLKKKRIRSVADL 322

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ + 
Sbjct: 323 LQDQFGLALVRLESVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDR 382

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL  
Sbjct: 383 TNPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAI 442

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R
Sbjct: 443 HARIGHWGSLESPFYKIFERSKKERMLYLSPNRDEYYMVAAGNSLALNQGIQEEQVVPAR 502

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL  +E 
Sbjct: 503 YRQEFLTITWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSCSEK 562

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+E  VA  SGA  +A+  G +   D  + ++ +                L+ +Q
Sbjct: 563 CIVGTGLERQVALDSGALAIAEHEGKIIYTDIDKTILSAN--------GDALSIPLVMYQ 614

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 615 RSNKNTCMHQTPRVRRGKCMKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVL 674

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V ED++TS HI ++E+    T  GPE IT ++P++    L+N+D+ GI+ +G+ V
Sbjct: 675 ISERLVYEDIYTSFHIRKYEIQTHMTSQGPERITNEVPHLETHLLRNLDKNGIVMLGSWV 734

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 735 ETGDILVGKLTPQLSKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQ 794

Query: 947 RHG----IDKNERSISVEREQIELLAR 969
           + G      +  R    ++ +I++  +
Sbjct: 795 KKGGSAYNPEMIRVYISQKREIKVGDK 821



 Score =  167 bits (424), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQVFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K  +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSGLYVSAGLIW---------KPSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ G+ RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGLYRIVINQILQSPGIYYRSELDHNGIS---VYMGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTNKEKKKIRSKE 220


>gi|11466679|ref|NP_039275.1| RNA polymerase beta subunit [Marchantia polymorpha]
 gi|133415|sp|P06272|RPOB_MARPO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|11647|emb|CAA28061.1| rpoB [Marchantia polymorpha]
          Length = 1065

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 240/640 (37%), Positives = 376/640 (58%), Gaps = 15/640 (2%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN--AYIRNTLVTDKNKDRKDALLD 376
            I+           L  +    +    IL           +I+     +     +DA+++
Sbjct: 161 RIWARISKKRKVSILVLLLAMGLNLQNILDSVCYPKIFLEFIKKNTKKEYPNSTEDAIVE 220

Query: 377 IYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           +Y+ +   G    FS +        F   + +L  +GR+ +N +LNL+ P++   +  +D
Sbjct: 221 LYKHLYCIGGDLFFSESIRKELQKKFFQQRCELGKIGRLNLNKKLNLNVPENEIFVLPQD 280

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSV 493
           I+A +  L+ L+ G GTIDDID+L NRRV SV ++L++Q +L L R+E S+    R ++ 
Sbjct: 281 ILAAVDYLIKLKFGIGTIDDIDHLKNRRVCSVADLLQDQLKLALNRLENSVLFFFRGATK 340

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 P+ L+ + P++    EFF S  LSQ  +  N L+ I H RRLS+LG GG+ R  
Sbjct: 341 RKRLPTPKSLVTSTPLIMTFKEFFGSHPLSQFLDQTNPLTEIVHKRRLSSLGPGGLTRRT 400

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A  ++RD+H +HYGRICP ETSEG N GL++SL   A+++  G +E+P+ K+       +
Sbjct: 401 ASFQVRDIHASHYGRICPIETSEGMNAGLIASLAIHAKISILGCLESPFYKISKLSNLEE 460

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++ LSA E+E   IA  N    +  S  E++   R   + + +  E++      P Q  S
Sbjct: 461 IINLSAAEDEYYRIATGNCLALDQNSQEEQITPARYRQDFVAIAWEQVHLRSIFPLQYFS 520

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE++D+NR LMG NMQRQAVPLLK E   VGTG+ES  A  SG+  V+   G
Sbjct: 521 VGASLIPFLEHNDANRALMGSNMQRQAVPLLKPEKCIVGTGIESQTALDSGSVTVSSHGG 580

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +E +D  +I++   +  +D          L+ +QRSN +TC++Q+P V+    +++  I
Sbjct: 581 KIEYLDGNQIILSLKKKKIDK--------NLIIYQRSNNSTCMHQKPKVEKQKYIKKGQI 632

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N+LVA+MPW GYNFED++LI+ER++ ED++TSIHIE +E+ AR 
Sbjct: 633 LADGAATANGELALGKNILVAYMPWEGYNFEDAILINERLIYEDIYTSIHIERYEIEARV 692

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE+ T +IP++ +  L+++D+ GI+  G+ V  GD+LVGK+TP+        PE K
Sbjct: 693 TSQGPEKFTNEIPHLDDYLLRHLDQNGIVLTGSWVETGDVLVGKLTPQETEENLRAPEGK 752

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LL+AIFG +    ++T L+VP G  G V+D+R+ ++    
Sbjct: 753 LLQAIFGIQVATSKETCLKVPPGGRGRVIDIRLISQEDNS 792



 Score =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 158/534 (29%), Positives = 231/534 (43%), Gaps = 88/534 (16%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
              G  E       +     K ID+  II         +       PK E     ++  + 
Sbjct: 578  HGGKIEYLDGNQIILSLKKKKIDKNLIIYQ----RSNNSTCMHQKPKVEKQKYIKKGQIL 633

Query: 915  AIFGEKAVD----VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE---- 965
            A     A       ++  +           D  + N   I ++  + I +ER +IE    
Sbjct: 634  ADGAATANGELALGKNILVAYMPWEGYNFEDAILINERLIYEDIYTSIHIERYEIEARVT 693

Query: 966  -LLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
                    +E   LD  +   L +   +L G    +G     K T   ++     P  + 
Sbjct: 694  SQGPEKFTNEIPHLDDYLLRHLDQNGIVLTGSWVETGDVLVGKLTPQETEENLRAPEGKL 753

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             Q           V + K            R  +   ++   +D      +++ +++  K
Sbjct: 754  LQAIFG-----IQVATSKETCLKVPPGGRGRVID--IRLISQEDNSANTAQIIHIYILQK 806

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDK+AGRHGNKGI+S+ILP +DMPFL+DGTP+D++L+PLGVPSRMNVGQIFE  L
Sbjct: 807  RKIQIGDKVAGRHGNKGIISKILPRQDMPFLQDGTPIDMILSPLGVPSRMNVGQIFECLL 866

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   L K  + +  D +   + S    F E    +   T                   
Sbjct: 867  GLAGSFLHKNYRIIPFDERYEREASRKLVFSELYKASKKTTNPW---------------- 910

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                   + + D  G++ L DG TGE F++P+T+G  YMLKL H
Sbjct: 911  -----------------------LFEPDNPGKNRLIDGRTGEIFEQPITIGKAYMLKLIH 947

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG------------EMEVWCIQAYGAAY 1309
             V DK++ARS+G Y+LVTQQPL                        EMEVW ++ +G AY
Sbjct: 948  QVDDKIHARSSGPYALVTQQPL------------RGRSRRGGQRVGEMEVWALEGFGVAY 995

Query: 1310 VLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLSID 1362
            +LQEMLTIKSD +  R  V  +IV G    +  T PESF +LV+E+++L L I+
Sbjct: 996  ILQEMLTIKSDHIRARYEVLGAIVTGEPIPKPNTAPESFKLLVRELRSLALEIN 1049



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 107/791 (13%), Positives = 238/791 (30%), Gaps = 77/791 (9%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEF--VS 78
           EI  +P+  ++Q   ++ F+          N+GL     S FPI          +     
Sbjct: 2   EIFILPEFGKIQFEGFNRFI----------NQGLSEEL-SNFPIIEDIDQEFEFQIFGEQ 50

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D +++ +TY+  + +  +L      +              +++G +PLM
Sbjct: 51  YKLAEPLLKERDAVYQSITYSSDVYVPAQLTQKKKGKIQKQI---------VFLGSIPLM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GTFV+ G+ R++++Q+ RSPGI+++ +      +G  +Y   +I + G  + +E D 
Sbjct: 102 NSQGTFVVNGVARVIINQILRSPGIYYNSELD---HNGIPIYTGTLISNWGGRLKLEIDG 158

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVG 257
           K  I  RI ++RKV +   L+A+G++ + IL +  YPKI               +     
Sbjct: 159 KTRIWARISKKRKVSILVLLLAMGLNLQNILDSVCYPKIFLEFIKKNTKKEYPNSTEDAI 218

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK----------FLGITSDCLCGLY 307
            ++   L  I       ES +K         + +  K           L +  + +    
Sbjct: 219 VELYKHLYCIGGDLFFSESIRKELQKKFFQQRCELGKIGRLNLNKKLNLNVPENEIF--- 275

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
           V    +      +      +     ++ + +  +  +  L  D +          V    
Sbjct: 276 VLPQDILAAVDYLIKLKFGIGTIDDIDHLKNRRVCSVADLLQDQLKLALNRLENSVLFFF 335

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           +                        +  F            + +  +    RL+      
Sbjct: 336 RGATKRKRLPTPKSLVTSTPLIMTFKEFFGSHPLSQFLDQTNPLTEIVHKRRLS---SLG 392

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME-RSI 486
              + +      ++ +     G+    +     N  + +   +      LG L      I
Sbjct: 393 PGGLTRRTASFQVRDIHASHYGRICPIETSEGMNAGLIASLAIHAKISILGCLESPFYKI 452

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE---HVNSLSRITHTRRLSA 543
            +  +  +I ++   +    +           +SQ  Q+       + ++       L +
Sbjct: 453 SKLSNLEEIINLSAAEDEYYRIATGNCLALDQNSQEEQITPARYRQDFVAIAWEQVHLRS 512

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           +         A +     H     R       +   + L+                    
Sbjct: 513 IFPLQYFSVGASLIPFLEHNDAN-RALMGSNMQRQAVPLLKPEKCIVGTGIESQTALDSG 571

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V        + YL           Q   SL +       +++ R      +  + K++ 
Sbjct: 572 SVTVSSHGGKIEYLDGN--------QIILSLKKKKIDKNLIIYQRSNNSTCMHQKPKVEK 623

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
                K  +    +         +  + +G N+    +P             E ++ +  
Sbjct: 624 QKYIKKGQILADGAATA------NGELALGKNILVAYMPWEGYNFEDAILINERLIYEDI 677

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
             +I  +R  I  +V +                        +          ++Q  +V 
Sbjct: 678 YTSIHIERYEIEARVTS---------------QGPEKFTNEIPHLDDYLLRHLDQNGIVL 722

Query: 784 VGDEVRRNDII 794
            G  V   D++
Sbjct: 723 TGSWVETGDVL 733


>gi|81301554|ref|YP_398851.1| RNA polymerase beta subunit [Nicotiana tomentosiformis]
 gi|88909146|sp|Q33C46|RPOB_NICTO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|80750913|dbj|BAE47989.1| RNA polymerase beta subunit [Nicotiana tomentosiformis]
          Length = 1070

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 198/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLLI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 230/660 (34%), Positives = 370/660 (56%), Gaps = 32/660 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +   A  +   + LE + + EI    +   +                   +++A+L+ Y+
Sbjct: 182 VLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIG-------------SKENAILEFYQ 228

Query: 380 VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                 GD              FF   + +L  +GR  MN RLNLD P +   +   DI+
Sbjct: 229 QFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDIL 287

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A    L+ L+ G G +DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I       
Sbjct: 288 AAADHLIGLKFGMGALDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGAIRHK 347

Query: 498 V--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    A 
Sbjct: 348 LIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTAS 407

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             +RD+HP+HYGRICP +TSEG N+GL+ SL   A++  +G +E+P+ ++ +      ++
Sbjct: 408 FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKIGHWGSLESPFYEISERSTGVRML 467

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLS   +E   +A  NS         E++V  R   E + +  E++      P Q  SI 
Sbjct: 468 YLSPGRDEYYMVAAGNSLALNRDIQEEQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIG 527

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+R G V
Sbjct: 528 ASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGALAIAEREGRV 587

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              +  +I++             +    L+ +QRSN+NTC++Q+  V  G  +++  I+A
Sbjct: 588 VYTNTDKILLAGN--------GDILSIPLVIYQRSNKNTCMHQKLQVPRGKCIKKGQILA 639

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+LALG+N+LVA+MPW GYN ED++LISER+V ED++TS HI ++E+    T 
Sbjct: 640 DGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIYTSFHIRKYEIQTHVTS 699

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLL 913
            GPE++T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++LL
Sbjct: 700 QGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLL 759

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           RAI G +    ++T L++  G  G V+DVR   + G         R   +++ +I++  +
Sbjct: 760 RAILGIQVSTSKETCLKLLIGGRGRVIDVRWIQKRGGSSYNPETIRVYILQKREIKVGDK 819



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+ ++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTFFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIGSKE 220


>gi|122893982|ref|YP_001004178.1| RNA polymerase beta subunit [Ranunculus macranthus]
 gi|69216920|gb|AAZ03994.1| RNA polymerase beta chain [Ranunculus macranthus]
 gi|85540796|gb|ABC70748.1| RNA polymerase beta subunit [Ranunculus macranthus]
          Length = 1070

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDRNGIVMLGSWVETGDILVGKLTPQIAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVVDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGNLLDRHYRISPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYQASKQTGNPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIMGGTISNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 233/634 (36%), Positives = 361/634 (56%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           I  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 IDNVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  +N RLNLD P ++  +   DI+A    L+ ++ G GT+DD+++L N+R
Sbjct: 254 QRCELGRIGRRNINRRLNLDIPQNITFLLPRDIVAAADHLIRMKFGMGTLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTIGGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +E P+ ++ +      VVYLS  ++E   +A  NS     G   
Sbjct: 434 LIGSLAIHARIGHWGSLERPFYEISEKSKEVRVVYLSPSKDEYYMVAAGNSLALNRGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTITWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  VA  SG + +A+  G +   D  +I++                
Sbjct: 554 PLCRSEKCIVGTGLERQVALDSGVSAIAEHEGKIIYTDTDKIMLSGN--------GDTLS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V     +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVMYQRSNKNTCMHQKPRVPRSKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LI+ER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI
Sbjct: 666 NFEDAVLINERLVYRDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDRNGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQIAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VDVR   + G         R    ++ +I++  +
Sbjct: 786 VDVRWIQKKGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLAEELSKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P  +  D ++  LTY+  L +   LI          K+ +D +EQ+I++G +PLM   GT
Sbjct: 62  PLINERDAVYESLTYSSELYVPAGLIW---------KNGRDTQEQTIFIGKIPLMNSFGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIINGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EI+    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREIIDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|89142824|emb|CAJ76083.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 279/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   EI++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKREIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + NL+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFNLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P  + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PATAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|89142886|emb|CAJ76114.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 192/420 (45%), Positives = 277/420 (65%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLEFKGSTEEILNYYYATETIYLQSAQDFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            TGE +++  +K T   +K L+   +K L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KTGELIVKKNRKFTRAAIKKLEAAKMKTLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + +  ++E+    I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQDKVDELLKRNIKEFKVLFIDNLNVGPYLRETLMLDKIETPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F  LFF+ ++YDLS VGR+K+N +  L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETAINLFTNLFFNPERYDLSKVGRLKLNFKFGLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|315275959|ref|ZP_07869515.1| DNA-directed RNA polymerase, beta subunit [Listeria marthii FSL
           S4-120]
 gi|313615689|gb|EFR88983.1| DNA-directed RNA polymerase, beta subunit [Listeria marthii FSL
           S4-120]
          Length = 279

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 101/301 (33%), Positives = 159/301 (52%), Gaps = 30/301 (9%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGIT 299
             +      +   L+           +  GE   +++ + L        K   +  +G  
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRY 276

Query: 300 S 300
            
Sbjct: 277 K 277



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/69 (43%), Positives = 44/69 (63%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 211 IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 270

Query: 409 STVGRVKMN 417
           ++VGR K+N
Sbjct: 271 ASVGRYKIN 279


>gi|290489648|gb|ADD31208.1| RNA polymerase beta subunit protein [Quercus nigra]
          Length = 1073

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 723  LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYTPEDRLLRAILGIQVSASKETCLKLPI 782

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K         +       + V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 783  GGRGRVIDVRWVQKK-------GVSSYNPEKIHVYISQKREIKVGDKVAGRHGNKGIISK 835

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   LG+  +    D +  
Sbjct: 836  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLGRHYRIAPFDERYE 895

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VFD          
Sbjct: 896  QEASRKLVFSELYEASKQTANPW------------------------VFD---------- 921

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S + DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 922  -----PEYPGKSRILDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 976

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G    +  
Sbjct: 977  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEILGTTIIGRTIPKPE 1036

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1037 DAPESFRLLVRELRSLALELNHFLVSEKNFQMNRKE 1072



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 236/670 (35%), Positives = 377/670 (56%), Gaps = 14/670 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E     + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELDNTGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     K   +++A+L+ Y+      GD              FF   K
Sbjct: 197 NVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQK 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P ++  +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNMNQRLNLDIPQNIPFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ + L R+E  I+  I       +   PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGVALFRLENMIRGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +GF+E+P+ ++ +      ++YLS   +E   +A  NS     G   E+
Sbjct: 436 GSLAIHARIGHWGFLESPFYEISERSKKVRMLYLSPSRDEYSIVASGNSLGLNRGIQEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + V  E++        Q  S+ ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 VVPVRYRQEFLTVEWEQVHLRSIFTFQYFSVGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E  VA  SGA  +A+  G +  +DA +I++             +    
Sbjct: 556 SRSEKCIVGTGLERQVALDSGALAIAEHEGKIISIDADKILL-----SGKVDKGDIISIP 610

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 611 LIMYQRSNKNTCMHQKPRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNS 670

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 671 EDAVLISERLVYGDIYTSFHIRKYEIQTYVTSYGPERITNEIPHLKAYLLRNLDKNGIVM 730

Query: 884 VGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+   ES  TPE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 731 LGSWVETGDILVGKLTPQVAKESSYTPEDRLLRAILGIQVSASKETCLKLPIGGRGRVID 790

Query: 942 VRIFNRHGID 951
           VR   + G+ 
Sbjct: 791 VRWVQKKGVS 800



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 25/239 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-F 76
           G+N  +  IP   ++Q   +  F+          ++GL         +   +     + F
Sbjct: 4   GRNEGMYTIPGFNQIQFEGFCRFI----------DQGLTEELYKFPKMEDINQEIEFQLF 53

Query: 77  VS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           V  Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++
Sbjct: 54  VETYQLVEPVIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNI 104

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLM   GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E
Sbjct: 105 PLMNSLGTSIVNGIYRIVINQILQSPGIYYRSELDNTGIS---VYTGTIISDWGGRLELE 161

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            D K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 162 IDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|11465946|ref|NP_054488.1| RNA polymerase beta subunit [Nicotiana tabacum]
 gi|78102523|ref|YP_358664.1| RNA polymerase beta subunit [Nicotiana sylvestris]
 gi|133424|sp|P06271|RPOB_TOBAC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|88909145|sp|Q3C1G7|RPOB_NICSY RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|11781|emb|CAA31238.1| unnamed protein product [Nicotiana tabacum]
 gi|11822|emb|CAA77346.1| RNA polymerase beta subunit [Nicotiana tabacum]
 gi|77799550|dbj|BAE46639.1| RNA polymerase beta subunit [Nicotiana sylvestris]
          Length = 1070

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 198/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 229/686 (33%), Positives = 380/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      ++ K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLSDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYMVAAGNSLALNQDIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G V   +  +I++             +    L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEREGRVVYTNTDKILLAGN--------GDILSIPLVIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKLQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 794 RGGSSYNPETIRVYILQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIGSKE 220


>gi|89142814|emb|CAJ76078.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142838|emb|CAJ76090.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142840|emb|CAJ76091.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 190/420 (45%), Positives = 279/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
             GE +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KAGELIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|17552304|ref|NP_498047.1| RNA Polymerase II (B) subunit family member (rpb-2) [Caenorhabditis
            elegans]
 gi|2507348|sp|Q10578|RPB2_CAEEL RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
 gi|532805|gb|AAA21158.1| Rna polymerase ii (b) subunit protein 2 [Caenorhabditis elegans]
          Length = 1193

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 165/1095 (15%), Positives = 333/1095 (30%), Gaps = 209/1095 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 259  GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFNDPEMMEMVKPSLDEAFVIQ 318

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +     +   +     +   I 
Sbjct: 319  EQNVALNFIGARGAKPGV---TREQRIKYAREILQKELLPH---VGVSEHCETKKAFFIG 372

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDI 495
             ++  L+    G+  +DD D++GN+R+   G +L   +R     + + ++   +      
Sbjct: 373  YMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRSLFRNLLKEMRMTAQKYINKN 432

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
            D       +    +   +     +               +SQ+   +   + ++H RR +
Sbjct: 433  DDFALDVCVKTSTITRGLTYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRAN 492

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++     E   
Sbjct: 493  S----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPIL 548

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N +        ++L+      R   + I+   
Sbjct: 549  EFLEEWS-MENLEEVSPSAIADATKIFVNGAWVGIHREPDQLMTTLKKLRRQMDIIVSEV 607

Query: 659  EKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL----KAEAPFVGT 713
              + D  D   +          P L  ++    L   ++ +             +  VG 
Sbjct: 608  SMVRDIRDREIRIYTDAGRVCRPLLIVENQKLALKKRHIDQLKEAADEANKYTWSDLVGG 667

Query: 714  GM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            G+ E + +     +++A     +                                     
Sbjct: 668  GVVELIDSMEEETSMIAMMPEDL------------------------------------- 690

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                      + G     +      P+  LG       +  + +P+  +N       S R
Sbjct: 691  ----------RSGGYCDTHTHCEIHPAMILG-------VCASIIPFPDHNQ------SPR 727

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
               +       +  +                           ++    +  V        
Sbjct: 728  NTYQSAMGKQAMGVYTTNF-----------------------HVRMDTLAHVLYYPQKPL 764

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    +     + +      + AI      +  D+ +   S +   +    +F R   D 
Sbjct: 765  VTTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLF-RSVFYRSYRDN 823

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
                 +   E IE   R+K         +       I  G           K+  L    
Sbjct: 824  EANLDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVAL---- 879

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                              +  ++++   +Y    +    R        Q    +     +
Sbjct: 880  ----------------PDIDDDLDASGKKYPKRDASTFLRSSETGIVDQVMLSLNSDGNK 923

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VK+ +   R  Q GDK A RHG KG +  +   EDMPF  +G   DI++NP  VPSRM 
Sbjct: 924  FVKIRMRSVRLPQIGDKFASRHGQKGTMGIMYRQEDMPFTAEGLTPDIIINPHAVPSRMT 983

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+                                          
Sbjct: 984  IGHLIECLQGKLSANKGEIGD--------------------------------------- 1004

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP  D  + + I+ +L        G  ++Y+G TG+     +  G
Sbjct: 1005 --------------ATPFNDTVNVQKISGLLCEYGYHLRGNEVMYNGHTGKKLTTQIFFG 1050

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GA   L+
Sbjct: 1051 PTYYQRLKHMVDDKIHSRARGPIQMMNRQPMEGRARDGGLRFGEMERDCQISHGATQFLR 1110

Query: 1313 EMLTIKSD--DV-----VG-------RTRVYESIV--AGNDTFETGTPESFNVLVKEMQA 1356
            E L   SD   V      G       RT  +E               P +  +L +E+ +
Sbjct: 1111 ERLFEVSDPYHVYVCNNCGLIVVANLRTNSFECKACRNKTQVSAVRIPYACKLLFQELMS 1170

Query: 1357 LGLSIDLENSRTKNS 1371
            + ++  L     ++ 
Sbjct: 1171 MSIAPRLMVKPRQSK 1185



 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 151/1006 (15%), Positives = 297/1006 (29%), Gaps = 210/1006 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA------------AMLEF 76
           L+  Q  S+D F+ MN+          Q   +   P+   S                L+F
Sbjct: 46  LVRQQLDSFDEFVQMNV----------QRIVEDSPPVELQSENQHLGTDMENPAKFSLKF 95

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTYA PL + +  +V   D  T     K   
Sbjct: 96  NQIYLSKPTHWEKDGAPMPMMPNEARLRNLTYASPLYVDITKVVTRDDSATEKVYDK--- 152

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
              +++G +P+M                           G FVI G ++++++Q   +  
Sbjct: 153 ---VFVGKVPVMLRSSYCMLSNMTDRDLTELNECPLDPGGYFVINGSEKVLIAQEKMATN 209

Query: 163 -IHFDHDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--- 211
            ++    K      GK  +   CR        ++        + V +  R     +K   
Sbjct: 210 TVYVFSMKD-----GKYAFKTECR------SCLENSSRPTSTMWVNMLARGGGGGKKTAM 258

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +P+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 259 GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFNDPEMMEMVKPSLDEAFVIQ 318

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              V+ + +     +  +   +++     + L+++ +  +G++  C          +   
Sbjct: 319 EQNVALNFIGARGAKPGVTREQRIKYAR-EILQKELLPHVGVSEHCETKKAFFIGYMVHR 377

Query: 317 TGEIYIEAGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +   ++ D   +  + +  +      +      N    +R T     NK+   AL
Sbjct: 378 LLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRSLFRNLLKEMRMTAQKYINKNDDFAL 437

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
               +        T  +  S+    + D  K   S  G  ++  RL          R   
Sbjct: 438 DVCVK----TSTITRGLTYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRANS 493

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N +  +         +   + + L     + +  +   I E +  
Sbjct: 494 PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEE 553

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++++   + ++   +  A   F   + +    E    ++ +   RR   +    V+  
Sbjct: 554 WSMENL---EEVSPSAIADATKIFVNGAWVGIHREPDQLMTTLKKLRRQMDIIVSEVSMV 610

Query: 553 RAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           R   +      T  GR+C P    E   + L        +       E       D    
Sbjct: 611 RDIRDREIRIYTDAGRVCRPLLIVENQKLALKKRHIDQLK---EAADEANKYTWSDLVGG 667

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  + +MEEE   IA     L   G                    +     +  P  +
Sbjct: 668 GVVELIDSMEEETSMIAMMPEDLRSGG------------------YCDTHTHCEIHPAMI 709

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                            
Sbjct: 710 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV--------------------- 748

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                  + + V  Y               Q+PLV         
Sbjct: 749 --------------------RMDTLAHVLYYP--------------QKPLV--------- 765

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA + + GYN EDS++++   +   +F S+    +    
Sbjct: 766 -TTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLFRSVFYRSYRDNE 824

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     EE            +       +DE GII  G  V+  D+++GK     +   
Sbjct: 825 ANLDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVALPDIDD 884

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +    +          RD S  + S  +G V  V +      +K
Sbjct: 885 DLDASGKKYPK-------RDASTFLRSSETGIVDQVMLSLNSDGNK 923


>gi|331218393|ref|XP_003321874.1| DNA-directed RNA polymerase II subunit RPB2 [Puccinia graminis f. sp.
            tritici CRL 75-36-700-3]
 gi|309300864|gb|EFP77455.1| DNA-directed RNA polymerase II subunit RPB2 [Puccinia graminis f. sp.
            tritici CRL 75-36-700-3]
          Length = 1122

 Score =  382 bits (981), Expect = e-103,   Method: Composition-based stats.
 Identities = 206/1314 (15%), Positives = 402/1314 (30%), Gaps = 266/1314 (20%)

Query: 88   VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
             ++   R+LTY+ PL + +          +   +  +                       
Sbjct: 13   PNEARLRNLTYSSPLYVDM--------SKSNKLATGE----------------------- 41

Query: 148  GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
                             FD +      +G+ +Y            D++ D K+   + I 
Sbjct: 42   -----------------FDEE------TGEPIYIAD---------DVDNDEKNSTQIYI- 68

Query: 208  RRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR------GDFWCFPLSAADLMVGAKVS 261
               KVP    L         IL       +Y         G ++    S   L+   +++
Sbjct: 69   --GKVP--IMLR----SEFCILDKLEDPGLYELNECPFDQGGYFVINGSEKVLIAQERMA 120

Query: 262  SS--LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
            ++   V    G   +E G K  S +   +   G K             +     +     
Sbjct: 121  ANHVYVFAKAGPLAVEKGSKTVSSMQVKM-YGGHKAEKAGGGATIKTTLPYIRNDIPIVV 179

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            ++   G + D+  LE I +          +     +++          ++++ AL  I R
Sbjct: 180  VFRALGIIPDKDILEHICYDRNDTAMFEMLKPCLEDSF--------PIQEQEVALDFIGR 231

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                   +T    E    +      K  L  +              +  +  +      +
Sbjct: 232  R----GTATGLSREKRLKYAEEILQKEMLPHI-----------SMSEGQQGKKAYFFGYM 276

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DS 497
            I  L+     +  +DD D+ G +R+   G +L   +R+   ++ + +   +         
Sbjct: 277  IHRLLLAALDRRDLDDRDHFGKKRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVEMQKP 336

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSAL 544
                  + +  + + +     +               +SQ+       S ++H RR +  
Sbjct: 337  FNLNAAVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT- 395

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R     + R +H +H+G +CPAET EG   GLV +L   + ++  G    P  +
Sbjct: 396  ---PIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYIS-VGSPSAPIVE 451

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
              +      +   S+       +   N           EL+                   
Sbjct: 452  FLEEWGMESLDEFSSDMSNGTKV-FVNGVWQGVHRAPAELLDTIKRLR---------RCG 501

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMES------ 717
            D  P+  V             D  RV     +      LLK E   ++  G E+      
Sbjct: 502  DIEPEVSVMRDVRERELRVFTDGGRVCRPLFIVENQQLLLKKEHIEWLSNGCETAEEDQD 561

Query: 718  --VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                A   G      +      V     +    E  +    +  ++ +  ++Q + Q   
Sbjct: 562  AGEEAADDGVPFGWSQLVARGIV---EYLDAEEEETVMICMTPEELEQSREYQETGQVPK 618

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
             N  P  +    ++ N  +     T      A+   +  + +P+  +N       S R  
Sbjct: 619  ENYDPAAR----LKGNTSMYSHTWTHCEIHPAMILGICASIIPFPDHNQ------SPRNT 668

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +       +  +    R                            +  +          
Sbjct: 669  YQSAMGKQAMGVYLTNFRTRM-----------------------DTMANILYYPQKPLAT 705

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     + R  +D+ +
Sbjct: 706  TRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSFYYRSYMDQEK 764

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R+ +++ E+ E   RD          +       I  G           K+  +  D   
Sbjct: 765  RAGALQMEEFEKPTRDSTLRLKHGTYDKLDDDGIITPGTRVSGDDIIIGKTAPIPKD--- 821

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         +E  QR     K          E+   +++      D +     + V
Sbjct: 822  ------------SEELGQRMKTHTKRDVSMPLKSTENGIIDQVLVTTNQDGL-----KFV 864

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  ++GDK A RHG KG V  +   EDMPF  +G   DI++NP  +PSRM +G
Sbjct: 865  KVRIRSTRIPETGDKFASRHGQKGTVGILYRQEDMPFTSEGVCPDIIINPHAIPSRMTIG 924

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +  +          IS L    +K   +                
Sbjct: 925  HLVECLLSKVSTITGNEGDATPFSEVTVEAISALLK--DKGYQSRGLEIM---------- 972

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                            F+G                 +G+                 +G  
Sbjct: 973  ----------------FNG----------------HTGK----------KLRAQCYLGPT 990

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  +L HMV+DK+++R+ G   ++T+QP+ G+S  GG R GEME  C+ ++G A  L+E 
Sbjct: 991  YYQRLKHMVNDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCMISHGIAGFLKER 1050

Query: 1315 LTIKSD-------DVVGRTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGL 1359
            +   SD       D  G   +  + +     +  +   P +  +L +E+Q++ +
Sbjct: 1051 MFDVSDAYRVHVCDFCGMVAI--ANLKKQSFEFSQVYIPYAAKLLFQELQSMNI 1102


>gi|34582147|gb|AAQ76037.1| RpoB [Zinnia juniperifolia]
          Length = 825

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 474  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 533

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 534  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 587

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 588  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 647

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 648  QEASRKLVF-SELYSASKQTANPWIFEPE------------------------------- 675

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 676  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 728

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 729  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 788

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 789  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 824



 Score =  355 bits (912), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 244/726 (33%), Positives = 392/726 (53%), Gaps = 43/726 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSL 634
            EG N+GL+ SL   AR+  +G +E+P+ ++ +       ++YLS   +E   +A  NS  
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYQISERSKKGAQMLYLSPGRDEYYMVAAGNSLA 243

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
               G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  
Sbjct: 244  LNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSS 303

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L  
Sbjct: 304  NMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLS 355

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                     L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA
Sbjct: 356  GNGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVA 415

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            +MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+
Sbjct: 416  YMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLR 472

Query: 875  NIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P
Sbjct: 473  NLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLP 532

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYS 984
             G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I       
Sbjct: 533  IGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQ 592

Query: 985  RLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN--- 1034
             +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++    
Sbjct: 593  DMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASR 652

Query: 1035 -------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                     + K          E   K++I   + GD     V+ + K ++  K   Q  
Sbjct: 653  KLVFSELYSASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVD 710

Query: 1088 DKMAGR 1093
            DK+ GR
Sbjct: 711  DKIHGR 716


>gi|290489636|gb|ADD31202.1| RNA polymerase beta subunit protein [Ficus sp. Moore 315]
          Length = 1070

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 204/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKKGIVMLGSWVETGDILVGKLTPQIAKESSYAPEDRLLRAILGIQISTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K E    G    P     ++V+++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKE----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ R +G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRCSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTMIGGPIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            G PESF +LV+E+++L L ++  L + +     + +
Sbjct: 1034 GAPESFRLLVRELRSLALELNHFLVSEKNFQINRKD 1069



 Score =  364 bits (935), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 237/662 (35%), Positives = 374/662 (56%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I+      +    L  +    +    IL  V          N     K K +++A+L+ 
Sbjct: 167 RIWARVSRKLKISILVLLSAMGLNLREILENVCYPEIFLSFLNDKEKKKIKSKENAILEF 226

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 227 YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGKIGRRNMNRRLNLDIPQNNTFLLPRD 285

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           I+A    L+ ++ G G +DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I     
Sbjct: 286 ILAAADHLIGMKFGMGILDDMNHLKNKRIRSVADLLQDQFALALVRLENMVRGTICGAIR 345

Query: 496 DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             +   PQ+L+ +  + +    FF    LSQ+ +  N L++I H R++S LG GG+    
Sbjct: 346 HKLIPTPQNLLTSTTLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKVSYLGPGGLTGRT 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  ARV  +G +E+P+ ++ +      
Sbjct: 406 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARVGCWGSLESPFYEISERSKKVR 465

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS  ++E   +A  NS     GS  E++V  R   E + +  E++      P Q  S
Sbjct: 466 ILYLSPSKDEYYMVAAGNSLALNLGSQEEQVVPARYRQEFLTIEWEQVHLRSIFPFQYFS 525

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  SGA  +A+  G
Sbjct: 526 IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLECQVALDSGAPTIAEHEG 585

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D  +I++      L           L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 586 KIIYTDTKKIILSGNRDTL--------SIPLVIYQRSNKNTCMHQKPQVAQGKCIKKGQI 637

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N+LVA+MPW GYNFED++LI+ER+V ED++TS HI ++E+    
Sbjct: 638 LADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLINERLVYEDIYTSFHIRKYEIQTHV 697

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++
Sbjct: 698 TSHGPERITNEIPHLEAHLLRNLDKKGIVMLGSWVETGDILVGKLTPQIAKESSYAPEDR 757

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH----GIDKNERSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +        +  R    ++ +I++ 
Sbjct: 758 LLRAILGIQISTSKETCLKLPIGGRGRVIDVRWIQKKEGSSYNPETIRVYISQKREIKVG 817

Query: 968 AR 969
            +
Sbjct: 818 DK 819



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 96/528 (18%), Positives = 178/528 (33%), Gaps = 39/528 (7%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS- 78
            E+  IP   ++Q   +  F+          ++GL         I         + FV  
Sbjct: 7   EEMSTIPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVET 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM
Sbjct: 57  YQLVEPLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLM 107

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D 
Sbjct: 108 NSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDR 164

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           K  I  R+ R+ K+ +   L A+G++  EIL       ++    +        +      
Sbjct: 165 KARIWARVSRKLKISILVLLSAMGLNLREILENVCYPEIFLSFLNDKEKKKIKSKENAIL 224

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +       +       ES  K         + +  K      +    L + ++       
Sbjct: 225 EFYQQFACVGGDPVFSESLCKELQKKFFQQRCELGKIGRRNMNRRLNLDIPQNNTFLLPR 284

Query: 319 EIYIEAGDVIDE-------KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +I   A  +I           +  + +  IR +  L  D           +V        
Sbjct: 285 DILAAADHLIGMKFGMGILDDMNHLKNKRIRSVADLLQDQFALALVRLENMVRGTICGAI 344

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
              L           +  +  ES F            + + ++    +++   P  +   
Sbjct: 345 RHKLIPTPQNLLTSTTLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKVSYLGPGGLT-- 402

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER---SIKE 488
                 A  +I     +  G I  ID      V  +G +  +        +E     I E
Sbjct: 403 ---GRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARVGCWGSLESPFYEISE 459

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           R   V I  + P                   SQ  Q+         +T
Sbjct: 460 RSKKVRILYLSPSKDEYYMVAAGNSLALNLGSQEEQVVPARYRQEFLT 507


>gi|170042980|ref|XP_001849183.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Culex
            quinquefasciatus]
 gi|167866385|gb|EDS29768.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Culex
            quinquefasciatus]
          Length = 1176

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 161/1002 (16%), Positives = 305/1002 (30%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I  K +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENR 625
             ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +    
Sbjct: 509  MICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKI 568

Query: 626  YIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D       L   R   + I+     I D  D   +          P L 
Sbjct: 569  FVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLI 628

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             ++ + +L   ++                      V  +SG           E +D +  
Sbjct: 629  VENGSLLLRKNHVDMLKERDYNNYG--------WQVLVASGVV---------EYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +                                  K              P+  LG
Sbjct: 672  ETVMIAMTPYDLKQD------------------------KEYAYCTTYTHCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V            +   K+  S  +  ++ E   +        +   +Y
Sbjct: 792  QEDSVILNASAVERGFFRSVF---YRSYKDSESKKIGDQE-EQFEKPNRQTCQGMRNALY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L                     +   +++    
Sbjct: 848  DKLDDDGIIAPGLRVSGDDVVIGKTITL--------------------PETDDDLDGTTK 887

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            +Y         R        Q    +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 888  RYSKRDGSTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLTPDIIINPHAIPSRMTIGHLIECIQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     V            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1135 NTFEC--KGCKNKTQISQVKLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 101/752 (13%), Positives = 227/752 (30%), Gaps = 117/752 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQ---AAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++      +  ++    A  +   I   +   +L+F       P 
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELTAEAQHTTGDIETPT-RYVLKFDQIYLSKPT 98

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +        +        + + Q  ++G +
Sbjct: 99  HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKIVEGQDPV-----ETQHQKTFIGKI 153

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 154 PIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 213

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH----VR----IDR-------------- 208
                GK  Y   I       ++        +      R    I +              
Sbjct: 214 -----GKYAYKSEIR----SCLEHSSRPTSTLWCNMMARGGQSIKKSAIGQRVIAILPYV 264

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 265 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGA 324

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                 +   K++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 325 RGARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AALGRRE 382

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K L+            L+ + +          +        +       + 
Sbjct: 383 LDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRMYAQKFIDRGKDFNLE-------LA 435

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 436 IKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGK 495

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 496 LAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSME 552

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 553 NLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDRE 612

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               T  GRIC P    E  ++ L  +      V+     +           +  V Y+ 
Sbjct: 613 IRIYTDAGRICRPLLIVENGSLLLRKN-----HVDMLKERDYNNYGWQVLVASGVVEYID 667

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            +EEE   IA     L +D  +                        +  P  ++ + AS+
Sbjct: 668 TLEEETVMIAMTPYDLKQDKEY---------------AYCTTYTHCEIHPAMILGVCASI 712

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           IPF +++ S R      M +QA+ +       
Sbjct: 713 IPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|160689612|gb|ABX45664.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 321

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/377 (37%), Positives = 193/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVNDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMTKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 79/117 (67%), Positives = 96/117 (82%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|34581933|gb|AAQ75895.1| RpoB [Helianthus annuus]
          Length = 824

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 246/725 (33%), Positives = 394/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYQISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM CN
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVQLRSIFAFQYFSIGASLIPFIEHNDANRALMSCN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|66363138|ref|XP_628535.1| RNA polymerase beta subunit [Cryptosporidium parvum Iowa II]
 gi|46229549|gb|EAK90367.1| RNA polymerase beta subunit [Cryptosporidium parvum Iowa II]
          Length = 1177

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 175/974 (17%), Positives = 324/974 (33%), Gaps = 196/974 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---E 488
            +   I  ++  L     G+   DD D+ G +R+   G ++   +     +M + ++   +
Sbjct: 355  KAYFIGYMVHKLCLGALGRVPEDDRDHFGKKRLDLAGPLVAASFGQCFRKMMKDVRRLLQ 414

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
            R      +  +   + +A  +   +   F +               +SQ+   +   S +
Sbjct: 415  RNIDNGKEFDVAGVIRSASYITQTIQYQFATGNWGKDKDGKIIRTGVSQVLSRLTFTSAL 474

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            ++ RRL+      + R     + R +H TH+G ICPAET EGH++GLV +L     ++  
Sbjct: 475  SYLRRLNT----PLGREGKFAKPRQLHNTHWGMICPAETPEGHSVGLVKNLALMCEIS-V 529

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL----DEDGSFTEELVFCRCAG 651
            G+     R   D    + +  +     + +     N +     D+       L   R +G
Sbjct: 530  GYRPYAIRTFLDEWGMDSIDEIPPEGIKRKIKVFLNGNWVGCFDDSEDSISNLRMIRRSG 589

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E        +D ++   K       S+ P     +         +++  +  L  E P  
Sbjct: 590  EIPYETSIVLDVVNREVKLFTDSGRSMRPLYIVGE----DGDLKIKKSHINSLLNENPSF 645

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               ME      +   +V               +I  ++ + + ++        ++  R  
Sbjct: 646  DEKMEDEKHDYTWDDLV------------NTGIIEYIDCEEEETSMIAMFINDLRIDRG- 692

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                                      PS  LG       +  + +P+  +N     +   
Sbjct: 693  ---------------YCSTYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNVYQS 730

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             M  + +   ++   + V                                  V       
Sbjct: 731  AMGKQAMG--VYTSNYNVRMDTLG---------------------------YVLYYPQKP 761

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             +    +T      +      +  I      +  D+ +   S +   +     F  +  +
Sbjct: 762  LVTTRAMTYMRFRELPAGINCIVGIMCYSGYNQEDSLIMNQSSIDRGLFRSVFFRTYVSE 821

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPKGFKKSTVL 1008
            +      V    IE       +E   L    Y  L     I  G   +       K   +
Sbjct: 822  E----KQVGSNLIEAFELPNPEEVSGLRFGNYGNLDLDGLIEPGNRVLGDDIIIGKVGPI 877

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + +       ++  +   +D  V      ++         +     +K            
Sbjct: 878  NPEDRD----TRIQKLTKRDCSV-----GIRTSEHGVVDEVLLSTNSK------------ 916

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              ++  KV V   R    GDK A RHG KG +      EDMPF +DG   DI++NP  +P
Sbjct: 917  -GVKFAKVKVRTIRIPHVGDKFASRHGQKGTIGITYRTEDMPFTQDGIIPDIIMNPHAIP 975

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +G + E  LG AC   G +                                     
Sbjct: 976  SRMTIGHLIECLLGKACAIQGLEGD----------------------------------- 1000

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                              +TP F     E I+S L  +   ++G  ++Y+G TG+  +  
Sbjct: 1001 ------------------ATP-FTKITVEEISSRLHSSGFQKNGNEVMYNGHTGKRLESR 1041

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G  Y  +L HMV DK++AR+ G+ +++T+QP  G++  GG R GEME  C+ ++GAA
Sbjct: 1042 IFIGPTYYQRLKHMVDDKIHARARGAVTMLTRQPREGRAREGGLRFGEMERDCMISHGAA 1101

Query: 1309 YVLQEMLTIKSDDVVGRTRVYE-----SIVA-GNDTFETG------------TPESFNVL 1350
             +L+E L  + D    R  V E      I   G   FE               P +  +L
Sbjct: 1102 KMLKERLFDQCD--AYRVHVCEMCGLICIADLGKQHFECNACNNKSRISQICLPYACKLL 1159

Query: 1351 VKEMQALGLSIDLE 1364
            ++E+ A+ +   L 
Sbjct: 1160 LQELMAMSIYPRLH 1173



 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 143/1011 (14%), Positives = 290/1011 (28%), Gaps = 202/1011 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+M            LQ       PI                    +L+
Sbjct: 34  LVNQQLESFNDFIMYK----------LQEIVDEHPPIIITPQSQYRPDEQIDTKVRYVLK 83

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P  +           ++   R+LTY+ P+ +     V+ +++      + + 
Sbjct: 84  FGQLSLSRPSVEEREGVARGLWPNEARLRNLTYSSPVFVDAEQKVYKLEDDGSETLVYET 143

Query: 126 KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
               + +  +P+M +                         G F+I G+++++V Q  R  
Sbjct: 144 VYSRLPLAKIPIMLRSEYCWTHNISERELQSAGECVYDQGGYFIINGMEKVLVGQE-RMA 202

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSK---------DII----HVRID 207
              F +   +   S K  +   I  ++ G+     F  K          I+    ++R D
Sbjct: 203 NN-FVYLFQKNQPS-KYTWIAEIRSNREGMQATSGFSVKLRGSDGNQGQIVATLPYIRTD 260

Query: 208 RRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               +P+     ALG +  ++ILS        +Q        L          V    + 
Sbjct: 261 ----IPIAILFRALGVLSDKDILSRCVYDFNDTQMLALLRPSLEETFEFFSQDVCLDFIG 316

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT------SDCLCGLYVAEDIVNGETGE 319
                  + + ++      K L EK  +  +G+T           G  V +  + G  G 
Sbjct: 317 KRG--PTVGAAREKRIQYAKELFEKELLPHVGVTSGSESRKAYFIGYMVHKLCL-GALGR 373

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +  +  D   +K L+             +   + +   +    + +  +       D+  
Sbjct: 374 VPEDDRDHFGKKRLDLAGPLVAASFGQCFRKMMKDVRRLLQRNIDNGKE------FDVAG 427

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDII 437
           V+R     T ++        +       +   G  ++  RL   +      R        
Sbjct: 428 VIRSASYITQTIQYQFATGNWGKDKDGKIIRTGVSQVLSRLTFTSALSYLRRLNTPLGRE 487

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                   L N    +                ++KN   +  + +        + +D   
Sbjct: 488 GKFAKPRQLHNTHWGMICPAETPEGHSVG---LVKNLALMCEISVGYRPYAIRTFLDEWG 544

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +   D I  + +   +  F   + +   ++  +S+S +   RR   +             
Sbjct: 545 MDSIDEIPPEGIKRKIKVFLNGNWVGCFDDSEDSISNLRMIRRSGEIPYETSIVLDVVNR 604

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVT 611
              +       + P           +      + +N           E       D   T
Sbjct: 605 EVKLFTDSGRSMRPLYIVGEDGDLKIKKSHINSLLNENPSFDEKMEDEKHDYTWDDLVNT 664

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   IA   + L  D  +                        +  P  +
Sbjct: 665 GIIEYIDCEEEETSMIAMFINDLRIDRGY-----------------CSTYTHCEIHPSLI 707

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R +    M +QA+ +  +                        R
Sbjct: 708 LGVCASIIPFPDHNQSPRNVYQSAMGKQAMGVYTSNYNV--------------------R 747

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 748 MDTLGYV-----------------------------------LYYPQKPLV--------- 763

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +V  M + GYN EDS+++++  +   +F S+    +    
Sbjct: 764 -TTRAMTYMRFRELPAGINCIVGIMCYSGYNQEDSLIMNQSSIDRGLFRSVFFRTYVSEE 822

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +       E        ++  +      N+D  G+I  G  V   DI++GK+ P      
Sbjct: 823 KQVGSNLIEAFELPNPEEVSGLRFGNYGNLDLDGLIEPGNRVLGDDIIIGKVGPINPEDR 882

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
               + L           RD S+ + +   G V +V +       K  +  
Sbjct: 883 DTRIQKL---------TKRDCSVGIRTSEHGVVDEVLLSTNSKGVKFAKVK 924


>gi|160177574|sp|A7M958|RPOB_CUSRE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1070

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 152/497 (30%), Positives = 230/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G      E  +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VRRGQFIKKGQILAG-GAATVEGELALGKSVLVAYMPWEGYNFEDAVL-----ISECLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              IF    I K E  I +  +  E +  +    +  L RN+  +   +L G     G   
Sbjct: 680  EDIFTSFHIKKYEIQIHMTTQGPEKVTNEIPHLEAHLIRNL-DKNGIVLQGSWVEPGDVL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       +  P  +  +  +           LKV       +++ R+  K     
Sbjct: 739  VGKLTPQVVKESAYAPEDRLLRAILGIPVSASKETCLKVPIGARGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG  VD+V
Sbjct: 796  -GYGYNP---EKIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRSVDLV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S  +    ++      
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR-KIVFSELYEASKQ 910

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T     ++ +                                        G+S ++DG T
Sbjct: 911  TANPWAFEPE--------------------------------------YPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F+ PV +G  Y+LKL H V DK++ RS G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GKTFEHPVLIGKPYILKLIHQVDDKIHGRSIGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPSPKNAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            +   L + +     + E
Sbjct: 1053 LTHFLVSEKNFQVNRKE 1069



 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 230/660 (34%), Positives = 372/660 (56%), Gaps = 32/660 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A  +   + LE + + EI    +   +                   +++A+L+ Y+
Sbjct: 182 VLLSAMGLNLREILENVCYPEILLSFLRDKEKKKIG-------------SKENAILEFYK 228

Query: 380 VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                 GD              FF   + +L  +GR  MN RL+LD P +   +   DI+
Sbjct: 229 KFACVGGDPLFSESLCKELQNKFF-QQRCELGRIGRRNMNRRLHLDIPHNNTFLLPRDIL 287

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS--SVDI 495
                L+ L+ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E +++  +       
Sbjct: 288 EATDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQFGLALVRLENAVQGTLCGAIRHK 347

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
               PQ+L+ +  + +    FF    LSQ+ +  N L++I H R++S+LG GG+    A 
Sbjct: 348 RIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDGTNPLTQIVHARKVSSLGPGGLTGRTAS 407

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ D      V+
Sbjct: 408 FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGNWGSLESPFYEISDRLTGVRVL 467

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LS   +E   +A  NS         +++V  R   E + +  E+++     P Q  SI 
Sbjct: 468 HLSPGRDEYYMVAAGNSLALNQDIQEDQVVPARYRQEFLTIAWEQVNLRSIFPFQYFSIG 527

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VGTGME   A  SG+  +A+R G V
Sbjct: 528 ASLIPFIEHNDANRALMSSNMQRQAVPLTWSEKCIVGTGMERQAALDSGSLAIAEREGRV 587

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D  +I++                  L+ +QRSN+NTC+ Q+P V+ G  +++  I+A
Sbjct: 588 IYTDTEKILV--------SGDGKTINIPLVMYQRSNKNTCMYQQPQVRRGQFIKKGQILA 639

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            G +T  G+LALG+++LVA+MPW GYNFED++LISE +V ED+FTS HI+++E+    T 
Sbjct: 640 GGAATVEGELALGKSVLVAYMPWEGYNFEDAVLISECLVYEDIFTSFHIKKYEIQIHMTT 699

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE++T +IP++    ++N+D+ GI+  G+ V PGD+LVGK+TP+   ES   PE++LL
Sbjct: 700 QGPEKVTNEIPHLEAHLIRNLDKNGIVLQGSWVEPGDVLVGKLTPQVVKESAYAPEDRLL 759

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELLAR 969
           RAI G      ++T L+VP G  G V+DVR   + G      +  R   +++ +I++  +
Sbjct: 760 RAILGIPVSASKETCLKVPIGARGRVIDVRWIQKKGGYGYNPEKIRVYILQKREIKVGDK 819



 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 75/335 (22%), Positives = 137/335 (40%), Gaps = 31/335 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQLEGFCRFI----------DQGLMEELSKFQKIEDIDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G LP+M   GT
Sbjct: 62  PLIKERDAVYDSLTYSSELYVSAGLI---------RKASKDMQEQTIFIGSLPIMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  + 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELD---QNGISVYTGTIISDWGGRLELEIDRKARVW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +   L A+G++  EIL    YP+I+ S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLLSAMGLNLREILENVCYPEILLSFLRDKEKKKIGSKENAILEFYKK 229

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGE 316
                          K+L +   +   E G       +  L         ++    +   
Sbjct: 230 FACVGGDPLFSESLCKELQNKFFQQRCELGRIGRRNMNRRLHLDIPHNNTFLLPRDILEA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           T  +      +     +  + +  IR +  L  D 
Sbjct: 290 TDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQ 324


>gi|34581818|gb|AAQ75819.1| RpoB [Athroisma gracile subsp. psyllioides]
          Length = 824

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQNSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLNRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  360 bits (925), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 246/725 (33%), Positives = 394/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQNSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++    ++ ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLNRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|28261709|ref|NP_783224.1| RNA polymerase beta subunit [Atropa belladonna]
 gi|41017766|sp|Q8S8X9|RPOB_ATRBE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|20068323|emb|CAC88036.1| RNA polymerase beta subunit [Atropa belladonna]
          Length = 1070

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 229/686 (33%), Positives = 379/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      ++ K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLSDKERKKIGSKENAILEFYQQFACVSGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYMVAAGNSLALNRDIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G V   +  +I++             +    L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEREGRVVYTNTDKILLAGN--------GDILSIPLVIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKLQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 RGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIGSKE 220


>gi|290489612|gb|ADD31190.1| RNA polymerase beta subunit protein [Ilex cornuta]
          Length = 1070

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 157/579 (27%), Positives = 248/579 (42%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +    ++        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGALAISEHEGKIIYTDTDKIFLSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LSIPLVMYQRSNKNTCMHQKTQVRRGKCIKKGQILADGTATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPEKVTNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T       S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEHRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     + V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKG----GSSYNP---ETICVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD++ NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMIFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYEASTQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 NPEDAPESFRLLVRELRSLALELNHFLVSEKNFQITRKE 1069



 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/662 (34%), Positives = 368/662 (55%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +  +  +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGKSELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I           PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKFIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      V+YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSKGVRVLYLSPHRDEYYMVAAGNSLALNQGIPEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +++  G +   D         +              L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAISEHEGKIIYTD--------TDKIFLSGNGDTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKTQVRRGKCIKKGQILADGTATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE +LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEHRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HG 949
            G
Sbjct: 794 KG 795



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D+++Q+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQDQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            +I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIINGIYRIVINQILQSPGIYYKSELDHNGIS---VYTGTIISDWGGKSELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|156618818|ref|YP_001430100.1| RNA polymerase beta subunit [Cuscuta reflexa]
 gi|156556003|emb|CAM98386.1| RNA polymerase beta chain [Cuscuta reflexa]
          Length = 1070

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 152/497 (30%), Positives = 230/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G      E  +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VRRGQFIKKGQILAG-GAATVEGELALGKSVLVAYMPWEGYNSEDAVL-----ISECLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              IF    I K E  I +  +  E +  +    +  L RN+  +   +L G     G   
Sbjct: 680  EDIFTSFHIKKYEIQIHMTTQGPEKVTNEIPHLEAHLIRNL-DKNGIVLQGSWVEPGDVL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       +  P  +  +  +           LKV       +++ R+  K     
Sbjct: 739  VGKLTPQVVKESAYAPEDRLLRAILGIPVSASKETCLKVPIGARGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG  VD+V
Sbjct: 796  -GYGYNP---EKIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRSVDLV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S  +    ++      
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR-KIVFSELYEASKQ 910

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T     ++ +                                        G+S ++DG T
Sbjct: 911  TANPWAFEPE--------------------------------------YPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+ F+ PV +G  Y+LKL H V DK++ RS G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GKTFEHPVLIGKPYILKLIHQVDDKIHGRSIGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPSPKNAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            +   L + +     + E
Sbjct: 1053 LTHFLVSEKNFQVNRKE 1069



 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 224/611 (36%), Positives = 358/611 (58%), Gaps = 19/611 (3%)

Query: 369 DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +++A+L+ Y+      GD              FF   + +L  +GR  MN RL+LD P 
Sbjct: 218 SKENAILEFYKKFACVGGDPLFSESLCKELQNKFF-QQRCELGRIGRRNMNRRLHLDIPH 276

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   +   DI+     L+ L+ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E ++
Sbjct: 277 NNTFLLPRDILEATDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQFGLALVRLENAV 336

Query: 487 KERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +  +           PQ+L+ +  + +    FF    LSQ+ +  N L++I H R++S+L
Sbjct: 337 QGTLCGAIRHKRIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDGTNPLTQIVHARKVSSL 396

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ +
Sbjct: 397 GPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGNWGSLESPFYE 456

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + D      V++LS   +E   +A  NS         +++V  R   E + +  E+++  
Sbjct: 457 ISDRLTGVRVLHLSPGRDEYYMVAAGNSLALNQDIQEDQVVPARYRQEFLTIAWEQVNLR 516

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VGTGME   A  SG
Sbjct: 517 SIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLTWSEKCIVGTGMERQAALDSG 576

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
           +  +A+R G V   D  +I++                  L+ +QRSN+NTC+ Q+P V+ 
Sbjct: 577 SLAIAEREGRVIYTDTEKILV--------SGDGKTINIPLVMYQRSNKNTCMYQQPQVRR 628

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G  +++  I+A G +T  G+LALG+++LVA+MPW GYN ED++LISE +V ED+FTS HI
Sbjct: 629 GQFIKKGQILAGGAATVEGELALGKSVLVAYMPWEGYNSEDAVLISECLVYEDIFTSFHI 688

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--G 902
           +++E+    T  GPE++T +IP++    ++N+D+ GI+  G+ V PGD+LVGK+TP+   
Sbjct: 689 KKYEIQIHMTTQGPEKVTNEIPHLEAHLIRNLDKNGIVLQGSWVEPGDVLVGKLTPQVVK 748

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSIS 958
           ES   PE++LLRAI G      ++T L+VP G  G V+DVR   + G      +  R   
Sbjct: 749 ESAYAPEDRLLRAILGIPVSASKETCLKVPIGARGRVIDVRWIQKKGGYGYNPEKIRVYI 808

Query: 959 VEREQIELLAR 969
           +++ +I++  +
Sbjct: 809 LQKREIKVGDK 819



 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 73/335 (21%), Positives = 133/335 (39%), Gaps = 31/335 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQLEGFCRFI----------DQGLMEELSKFQKIEDIDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G LP+M   GT
Sbjct: 62  PLIKERDAVYDSLTYSSELYVSAGLI---------RKASKDMQEQTIFIGSLPIMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  + 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELD---QNGISVYTGTIISDWGGRSELEIDRKARVW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G +  EIL    YP+I+ S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEILLSFLRDKEKKKIGSKENAILEFYKK 229

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGE 316
                          K+L +   +   E G       +  L         ++    +   
Sbjct: 230 FACVGGDPLFSESLCKELQNKFFQQRCELGRIGRRNMNRRLHLDIPHNNTFLLPRDILEA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           T  +      +     +  + +  IR +  L  D 
Sbjct: 290 TDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQ 324


>gi|34581972|gb|AAQ75921.1| RpoB [Layia heterotricha]
          Length = 824

 Score =  382 bits (980), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 247/725 (34%), Positives = 392/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQTNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE IT +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERITNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|34582012|gb|AAQ75947.1| RpoB [Oyedaea verbesinoides]
          Length = 824

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 245/725 (33%), Positives = 393/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E + +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENTARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+  + +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYNISERSKEAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTIRIPLVMYQRSNKNTCMHQKPQVRQGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|290489606|gb|ADD31187.1| RNA polymerase beta subunit protein [Aucuba japonica]
          Length = 1070

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDLFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     K E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINKKE 1069



 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 236/686 (34%), Positives = 381/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGIKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLYPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYKISERSTGVRILYLSPGRDEYYRVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G +   D         +  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEREGKIIYTD--------TDKILLSGNGETLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPQVQRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIKTHVTSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSAELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|34582021|gb|AAQ75953.1| RpoB [Perityle lindheimeri]
          Length = 824

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 246/725 (33%), Positives = 393/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|147722|gb|AAA24581.1| RNA polymerase beta subunit (rpoB) (EC 2.7.7.6) [Escherichia coli]
 gi|147725|gb|AAA24583.1| RNA polymerase beta subunit (rpoB) (EC 2.7.7.6) [Escherichia coli]
          Length = 200

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 117/200 (58%), Positives = 151/200 (75%)

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                    +         +S + D+ V+R+AE  + G+P++TPVFDGA E  I  +L++ 
Sbjct: 1    EFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG 60

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
            DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK
Sbjct: 61   DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGK 120

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   E G PES
Sbjct: 121  AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPES 180

Query: 1347 FNVLVKEMQALGLSIDLENS 1366
            FNVL+KE+++LG++I+LE+ 
Sbjct: 181  FNVLLKEIRSLGINIELEDE 200


>gi|126165914|ref|YP_358570.2| RNA polymerase beta subunit [Phalaenopsis aphrodite subsp. formosana]
 gi|158518566|sp|Q3BAP8|RPOB_PHAAO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1070

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 151/498 (30%), Positives = 238/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G         +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VQRGKYIKKGQILAGGAA-TAGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      R   ++ G    +G  
Sbjct: 680  KDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEARLLRN--LDRNGIVMLGSWIETGDI 737

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++   S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 738  LVGKLTPQTASESSYAPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRR--- 794

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DGTPVD+
Sbjct: 795  ----GVSNSNPERIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDM 850

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L K  +    D +   + S    F E    +  
Sbjct: 851  VFNPLGVPSRMNVGQIFECSLGLAGDLLKKHYRIGPFDERYEQEASRKLVFSELYEASKK 910

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 911  TKNPW------------------------VFE---------------PEYPGKSRIFDGR 931

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW
Sbjct: 932  TGDLFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVW 991

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  +++ G         PESF +LV+E+++L L
Sbjct: 992  ALEGFGVAHILQEMLTYKSDHIRARQEVLGAMIIGATVPNPESAPESFRLLVRELRSLSL 1051

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1052 ELNHFLVSEKNFQMDRKE 1069



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 230/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 143 VSVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNIREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNLD P +   +   D++A +  L+ ++ G GT+DD+ +L N+R+RSV ++L
Sbjct: 262 GRQNLNRRLNLDIPQNNTFLLPRDLLAAVDHLIGMKLGMGTLDDMSHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENTVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKWSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLMGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            +V  +G IE+P+  + +      +VYLS   +E   +A  NS         +++V  R 
Sbjct: 442 VKVGYWGSIESPFYGLSERSKEAQMVYLSPNRDEYYMVAAGNSLALNRDIQEQQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEEIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG +++A+  G +   D         +     S        L+ +QR
Sbjct: 562 IVGTGLEGQTALDSGVSVIAECKGKIIYTD--------TQKIFLSSNGDTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC+NQ+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMNQKTQVQRGKYIKKGQILAGGAATAGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +D++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ +G+ + 
Sbjct: 674 SERLVYKDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEARLLRNLDRNGIVMLGSWIE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+  S  +  PE++LLRAI G +    ++TSLR+P G  G V+DVR  +R
Sbjct: 734 TGDILVGKLTPQTASESSYAPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHR 793

Query: 948 HGID----KNERSISVEREQIELLAR 969
            G+     +  R    ++ +I++  +
Sbjct: 794 RGVSNSNPERIRVYISQKREIKVGDK 819



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLTEEFHKFQKIEDRDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ ++++EQ++++G++P+M   GT
Sbjct: 62  PLITERDAVYESLTYSSELYVPAVLIW---------KTGRNMQEQTVFIGNIPIMNSFGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQIVQSPGIYYRSELE---HNGVSVYTSTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNIREILDNVCYPEIFLSFPNDKEKKKIGSKE 220


>gi|255730467|ref|XP_002550158.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Candida
            tropicalis MYA-3404]
 gi|240132115|gb|EER31673.1| DNA-directed RNA polymerase II 140 kDa polypeptide [Candida
            tropicalis MYA-3404]
          Length = 1240

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 169/989 (17%), Positives = 317/989 (32%), Gaps = 163/989 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L   +R+   ++ +
Sbjct: 364  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLAGLFRILFKKLTK 423

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 424  DIYNYMQRCVENDSDFNLTLAVKSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRY 483

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 484  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 539

Query: 590  ARVNAYGFIETP--YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++     E    + +    +V  D V  +A +    ++      +  D +   + V  
Sbjct: 540  TCISVGSSSEPILGFLRDFGLEVLEDYVPSNAPDSTRIFVNGVWVGVHRDPAQLVDYVRD 599

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV------LMGCNMQRQA 700
                 +I      I D  +   K          P    DD+         ++     R+ 
Sbjct: 600  LRRSGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNEDSPTKGDLMITKEHIRKL 659

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            V     +             K + +++V++  GIVE VDA       +    D   +   
Sbjct: 660  VAEDMDDDELEEDEEGGESRKYTWSSLVSE--GIVEYVDAEEEETIMIAMSPDDVKASKS 717

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWH 819
                 + Q                   ++          T      ++   +  + +P+ 
Sbjct: 718  TMSESEQQELQLQEQEL-----DPAKRIKPTTSSNTHTYTHCEIHPSMILGVAASIIPFP 772

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +   + +  + V                              
Sbjct: 773  DHNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------D 803

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 804  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAVVAIACYSGYNQEDSMIMNQSSIDRGL 863

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAV 996
                +F R  +D  +R      + +E   +    + + L    Y +L E   I  G    
Sbjct: 864  F-RSLFFRSYMDLEKRQGM---KLLETFEKPSRSDTLRLKHGTYEKLDEDGLIAPGIRVS 919

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T + +D                +E  QR +   K    T     E    ++
Sbjct: 920  GEDIIIGKTTPIPAD---------------TEELGQRTLHHSKRDASTPLRSTESGIVDQ 964

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +     GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 965  VLLTTNGD-----GSKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGI 1019

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM V  + E  L       G +  +          I+ L    E   
Sbjct: 1020 VPDLIINPHAIPSRMTVAHLIECLLSKVSSLSGFEGDASPFTDVTAEAIAKLLR--EHGY 1077

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +       +                                            +G+ ++
Sbjct: 1078 QSRGFEVMYNG------------------------------------------HTGKKLM 1095

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
                        V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GE
Sbjct: 1096 ----------AQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGE 1145

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIV-------------AGNDTF 1339
            ME  C+ A+GAA  L+E L   SD     V G   +   I                 + +
Sbjct: 1146 MERDCMIAHGAAGFLKERLMEASDAFRVHVCGMCGLMSVIANLKKNQFECRSCKNKTNIY 1205

Query: 1340 ETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +   P +  +L +E+ A+ +S  L   R+
Sbjct: 1206 QIHIPYAAKLLFQELMAMNISPRLYTERS 1234



 Score =  215 bits (547), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 141/1036 (13%), Positives = 290/1036 (27%), Gaps = 210/1036 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-----ITAF-SGAAMLEFVSYEFD 82
           L+  Q  S+D F+  +I      +  L        P     +    +    +EF      
Sbjct: 38  LVSQQLDSFDEFVETSIQELVWEDSHL--ILDQ--PAQHTSVADHKNKRYEIEFGKIYIS 93

Query: 83  PPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS--- 129
                            +   R+LTY+ PL + +    F+ D+     +  + +E     
Sbjct: 94  KTSQTEGDGTTHSVFPQEARLRNLTYSSPLYVDMTKRKFESDDNKRKDNELEWEEIEVDD 153

Query: 130 -------IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH 158
                  +++G +P+M +                         G FVI G ++++++Q  
Sbjct: 154 KEGPQSKVFLGKVPIMLRSKFCMLNGLAEHEFYELKECPYDMGGYFVINGSEKVLIAQE- 212

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------RRR 210
           RS          + +    + +   I    ++G  +      K  ++ R D      R  
Sbjct: 213 RSAANI--VQVFKKAAPSPISHVAEIRSALEKGSRLISSMQIK--LYGR-DEKGVAGRTI 267

Query: 211 K---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           K         +P+     ALG+  + +IL          Q  +     +    ++   +V
Sbjct: 268 KATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQEREV 327

Query: 261 SSSLV------DIDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDCLCGLYVAEDI 312
           +   +       I   +++  +   L   LL ++  +E            +    +   +
Sbjct: 328 ALDFIGRRGVLGIRREKRIQYAKDILQKELLPNITQEEGFETRKAFFLGYMVNRLLLCAL 387

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRK 371
              E      +  D   +K L+           IL+   + +   Y++  +  D + +  
Sbjct: 388 ERKEP-----DDRDHFGKKRLDLAGPLLAGLFRILFKKLTKDIYNYMQRCVENDSDFNLT 442

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--R 429
            A+             T  +  S+    + +  K   S  G  ++  R    +      R
Sbjct: 443 LAV--------KSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRYTYSSTLSHLRR 494

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                     I     L N    +         +      ++KN   +  + +  S +  
Sbjct: 495 TNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMTCISVGSSSEPI 551

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +  +    +   +         +   F     +    +    +  +   RR   +     
Sbjct: 552 LGFLRDFGLEVLEDYVPSNAPDSTRIFVNGVWVGVHRDPAQLVDYVRDLRRSGDISPEVS 611

Query: 550 ARARAGVEMRDVHPTHYGRICP----------------AETSEGHNIGLVSSLTSFARVN 593
                  +   +         P                  T E     +   +       
Sbjct: 612 IIRDIREKEFKIFTDAGRVYRPLFIVDDNEDSPTKGDLMITKEHIRKLVAEDMDDDELEE 671

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-------- 645
                E+             V Y+ A EEE   IA +   +    S   E          
Sbjct: 672 DEEGGESRKYTWSSLVSEGIVEYVDAEEEETIMIAMSPDDVKASKSTMSESEQQELQLQE 731

Query: 646 ----FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                 +                +  P  ++ +AAS+IPF +++ S R      M +QA+
Sbjct: 732 QELDPAKRIKPTTSSNTHTYTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAM 791

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            +                                                   + + +  
Sbjct: 792 GVFLTNYSV-----------------------------------------RMDTMANILY 810

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y       +     +  R                        +L  G+N +VA   + GY
Sbjct: 811 YPQKPLATTRSMEYLKFR------------------------ELPAGQNAVVAIACYSGY 846

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNI 876
           N EDSM++++  +   +F S+    +  + +   +   E        D   +     + +
Sbjct: 847 NQEDSMIMNQSSIDRGLFRSLFFRSYMDLEKRQGMKLLETFEKPSRSDTLRLKHGTYEKL 906

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE G+I  G  V+  DI++GK TP         ++ L           RD S  + S  S
Sbjct: 907 DEDGLIAPGIRVSGEDIIIGKTTPIPADTEELGQRTLH-------HSKRDASTPLRSTES 959

Query: 937 GTVVDVRIFNRHGIDK 952
           G V  V +       K
Sbjct: 960 GIVDQVLLTTNGDGSK 975


>gi|89142880|emb|CAJ76111.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 189/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLHFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +G+ +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGDLIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|186885961|gb|ACC93388.1| RNA polymerase beta subunit [Syncarpha vestita]
          Length = 1016

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 665  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 724

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 725  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIVSK 778

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVDIV NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 779  ILPRQDMPYLQDGRPVDIVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 838

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 839  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 866

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 867  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 919

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 920  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 979

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 980  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1015



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 276/927 (29%), Positives = 463/927 (49%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 39   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 84

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + I TG  + + G +L       L+      + +       L +        
Sbjct: 85   QSELNDNGISIYTGTIISDWGGRL------ELEIDRKARIWVRVSRQQKLSIL------- 131

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 132  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 173

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 174  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 233

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 234  ILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 293

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 294  HNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 353

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 354  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGPWGSLESPFYKISERSKGAR 413

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   +++V  R   E + +  E++        Q  S
Sbjct: 414  MLYLSPGRDEYYMVAAGNSLALNQGIQEQQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 473

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 474  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 533

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         E  L           L+ +QRSN+NT ++Q+  V  G  +++  +
Sbjct: 534  KILYTD--------TEKILLSGNGDTLRIPLVMYQRSNKNTSMHQKSQVPRGKCIKKGQV 585

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 586  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 643

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 644  -NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 702

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +I++
Sbjct: 703  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKV 762

Query: 967  LAR--DKDDEQVILDRNIYSRLMEILCG-------QNAVSGPKGFKKSTVLSSDL-ISEY 1016
              +   +   + I+ + +  + M  L          N +  P       +  S L ++  
Sbjct: 763  GDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDIVFNPLGVPSRMNVGQIFESSLGLAGD 822

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 823  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPF 882

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 883  EQPVI-IGKPYIL-KLIHQVDDKIHGR 907



 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/170 (32%), Positives = 91/170 (53%), Gaps = 11/170 (6%)

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I +G +PLM
Sbjct: 5   YQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTILIGKIPLM 57

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D 
Sbjct: 58  TSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISIYTGTIISDWGGRLELEIDR 114

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 KARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 164


>gi|11467182|ref|NP_043015.1| RNA polymerase beta subunit [Zea mays]
 gi|133414|sp|P16023|RPOB_MAIZE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|12480|emb|CAA35195.1| unnamed protein product [Zea mays]
 gi|902212|emb|CAA60276.1| RNA polymerase beta subunit [Zea mays]
          Length = 1075

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 176/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGAPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRMPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 QVNRED 1074



 Score =  353 bits (905), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 235/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  VGR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRVGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  L+Q+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLAQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAQREGKIISSDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVAHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT+ IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKQIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R   D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPFDIMVRVYILQKREIKVGDK 824



 Score =  168 bits (425), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++ RLI              D+++++I +G++P+M   GT
Sbjct: 62  PSIKERNAVYESLTYSSELYVSARLIFGF-----------DVQKETISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|89142876|emb|CAJ76109.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142878|emb|CAJ76110.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142882|emb|CAJ76112.1| RNA polymerase, beta subunit [Corallococcus coralloides]
 gi|89142890|emb|CAJ76116.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 189/420 (45%), Positives = 280/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +G+ +++  +K T   +K L+   +  L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGDLIVKKNRKFTRAAIKKLEAAKMTKLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|182684897|ref|YP_001836644.1| hypothetical protein SPCG_1926 [Streptococcus pneumoniae CGSP14]
 gi|182630231|gb|ACB91179.1| hypothetical protein SPCG_1926 [Streptococcus pneumoniae CGSP14]
          Length = 377

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 112/363 (30%), Positives = 178/363 (49%), Gaps = 33/363 (9%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A   V  G  R R+ F +  E++D+P+LIE+Q  S+  FL          + GL+  F+
Sbjct: 14  LAGHDVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFKAFL----------DHGLKEVFE 63

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
            V PI+ F+    LEFV YE   PK+ +++    D +Y+ P+ +T RLI          K
Sbjct: 64  DVLPISNFTDTMELEFVGYEIKEPKYTLEEARIHDASYSAPIFVTFRLI---------NK 114

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
              +IK Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG++F+    +   +GK+ Y
Sbjct: 115 ETGEIKTQEVFFGDFPIMTEMGTFIINGGERIIVSQLVRSPGVYFN---DKVDKNGKVGY 171

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTFYPKIVYS 239
              +IP++G W+++E DSKDI + RIDR RK+P T+ + ALG    +EI   F    +  
Sbjct: 172 GSTVIPNRGAWLELESDSKDITYTRIDRTRKIPFTTLVRALGFSGDDEIFDIFGDSELVR 231

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGI 298
              +      +  D      +      +  GE    ES + L        +   +  +G 
Sbjct: 232 NTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPKTAESSRSLLVARFFDPRRYDLAAVGR 290

Query: 299 T--------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                       L    +AE +V+ ETGEI +EAG ++    +E I      D+  +   
Sbjct: 291 YKINKKLNVKTRLLNQTIAEPLVDPETGEILVEAGTIMTRSVIESIESHLDGDLNKIVYI 350

Query: 351 SVN 353
             +
Sbjct: 351 PND 353



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/169 (22%), Positives = 65/169 (38%), Gaps = 4/169 (2%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYI 322
           I+ GE++I S    + G+  + K      +G  S  +        +  D  +     I  
Sbjct: 140 INGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELESDSKDITYTRIDR 199

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
                         F  +     I     +  N   ++      +    +AL +IY  +R
Sbjct: 200 TRKIPFTTLVRALGFSGDDEIFDIFGDSELVRNTVEKDIHKNPMDSRTDEALKEIYERLR 259

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           PG+  T   + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 260 PGEPKTAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTI 308


>gi|52694169|emb|CAG30614.1| DNA-directed RNA polymerase beta chain [Pseudomonas aeruginosa]
          Length = 383

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 234/383 (61%), Positives = 299/383 (78%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  
Sbjct: 121 VVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEEITRDIP 866
           I+E   +ARDTKLGPEEIT DIP
Sbjct: 361 IQELTCVARDTKLGPEEITADIP 383


>gi|119368491|ref|YP_913179.1| RNA polymerase beta subunit [Gossypium barbadense]
 gi|125987642|sp|A0ZZ27|RPOB_GOSBA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|119224853|dbj|BAF41239.1| RNA polymerase beta subunit [Gossypium barbadense]
          Length = 1070

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/579 (27%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDA 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LGIPLVMYQRSNKNTCMHQTARVRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWVQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQ+FE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQLFECSLGLAGSLLDRHHRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 890  RYEQEASRKLVFSELYQASKQTANPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSRIFDGRTGGPFEQPVIIGKPYILKLIHQVDDKIHGRSSGYYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNL+ P +   +   DI+A    L+ ++ G G +DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNQRLNLNIPQNNTFLLPRDILAAADRLIGMKFGMGPLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYKIFERSKKAQMLYLSPSRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A   G +   D  +I++      L           L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIADHEGKIISTDTDKIILSGNGDALGI--------PLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q   V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQTARVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCGFM----------DRGLTEELYKFPKIEDTEQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSKDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|34581930|gb|AAQ75893.1| RpoB [Helenium bigelovii]
          Length = 824

 Score =  381 bits (979), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFRLNRKE 823



 Score =  358 bits (919), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 244/725 (33%), Positives = 393/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNVYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V E+++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEEIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ +++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|160689674|gb|ABX45695.1| RNA polymerase subunit beta [Bacillus amyloliquefaciens]
          Length = 321

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 142/376 (37%), Positives = 193/376 (51%), Gaps = 62/376 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVNDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RTGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDD 1321
            GAAY LQE+LT+KSDD
Sbjct: 305  GAAYTLQEILTVKSDD 320



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 79/117 (67%), Positives = 96/117 (82%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEVN GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVNDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|91208980|ref|YP_538840.1| RNA polymerase beta subunit [Solanum bulbocastanum]
 gi|109914397|sp|Q2MIJ5|RPOB_SOLBU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|84371887|gb|ABC56205.1| RNA polymerase beta subunit [Solanum bulbocastanum]
          Length = 1070

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKKGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 227/634 (35%), Positives = 363/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++++L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKERKKIGSKENSILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN +LNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRKLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSPPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL+  AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434 LIGSLSIHARIGHWGSLESPFYEISERSTGVRMLYLSPGSDEYYMVAAGNSLALNRDIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SGA  +A+R G +   +  +I++             +  
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGALAIAEREGRIVYTNTDKILLAGN--------GDILS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVIYQRSNKNTCMHQKLRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI
Sbjct: 666 NSEDAVLISERLVYEDIYTSFHIRKYEIHTHVTSQGPEKVTNEIPHLEAHLLRNLDKKGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKRGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|89280627|ref|YP_514844.1| RNA polymerase beta subunit [Solanum lycopersicum]
 gi|109904147|sp|Q2MIA8|RPOB_SOLLC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|84371975|gb|ABC56292.1| RNA polymerase beta subunit [Solanum lycopersicum]
 gi|89241663|emb|CAJ32385.1| RNA polymerase beta chain [Solanum lycopersicum]
          Length = 1070

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKKGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 227/634 (35%), Positives = 363/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++++L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKERKKIGSKENSILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN +LNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRKLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSPPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL+  AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434 LIGSLSIHARIGHWGSLESPFYEISERSTGVRMLYLSPGSDEYYMVAAGNSLALNRDIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SGA  +A+R G +   +  +I++             +  
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGALAIAEREGRIVYTNTHKILLAGN--------GDILS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVIYQRSNKNTCMHQKFRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI
Sbjct: 666 NSEDAVLISERLVYEDIYTSFHIRKYEIHTHVTSQGPEKVTNEIPHLEAHLLRNLDKKGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKRGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|158518554|sp|Q0G9M7|RPOB_LIRTU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1070

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 204/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYSASKQTANPWVFEPEC------------------------------ 921

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 922  --------PGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   R++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFPNDKEKKKIGSRENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSIESPFYEISERSKEVQMVYLSPSRDEYYMVAAGNSLALNWGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +QR
Sbjct: 562 IVGTGLECQAALDSGVSAIAEHEGKIVYTDTDKIVLSGN--------GDTISIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ + 
Sbjct: 674 SERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWIE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPEMIRVYISQKREIKVGDK 819



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTVFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSRE 220


>gi|108773122|ref|YP_635631.1| RNA polymerase beta subunit [Solanum tuberosum]
 gi|88656796|gb|ABD47049.1| RNA polymerase beta subunit [Solanum tuberosum]
          Length = 1070

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKKGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 228/634 (35%), Positives = 364/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++++L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKERKKIGSKENSILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN +LNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRKLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSPPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL+  AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434 LIGSLSIHARIGHWGSLESPFYEISERSTGVRMLYLSPGSDEYYMVAAGNSLALNRDIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SGA  +A+R G +   +  +I++             +  
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGALAIAEREGRIVYTNTDKILLAGN--------GDILS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 IPLVIYQRSNKNTCMHQKLRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI
Sbjct: 666 NFEDAVLISERLVYEDIYTSFHIRKYEIHTHVTSQGPEKVTNEIPHLEAHLLRNLDKKGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKRGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|88909640|sp|Q2VEI4|RPOB_SOLTU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|82754621|gb|ABB90035.1| RNA polymerase beta chain [Solanum tuberosum]
          Length = 1070

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKKGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 226/634 (35%), Positives = 364/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++++L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKERKKIGSKENSILEFYQQFACVGGDPVFSESLCKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN +LNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R
Sbjct: 254 QRCELGRIGRRNMNRKLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSPPLTTTYESFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL+  AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434 LIGSLSIHARIGHWGSLESPFYEISERSTGVRMLYLSPGSDEYYMVAAGNSLALNRDIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SGA  +A+R G +   +  +I++             +  
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGALAIAEREGRIVYTNTDKILLAGN--------GDILS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V  G  +++  I+ADG +T  G+LALG+N+LVA++PW GY
Sbjct: 606 IPLVIYQRSNKNTCMHQKLRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYIPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LI+ER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI
Sbjct: 666 NFEDAVLITERLVYEDIYTSFHIRKYEIHTHVTSQGPEKVTNEIPHLEAHLLRNLDKKGI 725

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G         R    ++ +I++  +
Sbjct: 786 IDVRWIQKRGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKERKKIGSKE 220


>gi|186885951|gb|ACC93383.1| RNA polymerase beta subunit [Sonchus oleraceus]
          Length = 1024

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 138/460 (30%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L K  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDKHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTVNPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       +   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKQIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDQTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKILYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDKHYRIAPFDERYEQEASRKLVFSELYEASKQTVNPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPPIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKQI 172


>gi|34581954|gb|AAQ75909.1| RpoB [Inula britannica]
          Length = 824

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VQNSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 248/725 (34%), Positives = 394/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  VGR  MN RLNLD P++   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGVGRRNMNRRLNLDIPENNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         E  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTD--------TEKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVQNSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|156538773|ref|XP_001607902.1| PREDICTED: similar to ENSANGP00000011389 [Nasonia vitripennis]
          Length = 1175

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 172/1083 (15%), Positives = 337/1083 (31%), Gaps = 198/1083 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIRQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGSRGARPGV---TKERRIKYAREILQKETLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLSASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R       R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLARPRQLHNTLWGMLCPAETPEGQAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              + +  + N        E     IA A + +  +G +             +   R ++D
Sbjct: 543  EFLEEWSMENL------EEIAPSAIADA-TKIFVNGCWVGIHRDPDQLMATLRKLRRQMD 595

Query: 663  FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                  +  +             D+ R+     +    + LL  +   +    E      
Sbjct: 596  I--IVSEVSMVRDIRDREIRIYTDAGRISRPLLIVENQLLLL--KKRHIEMLKERDYNND 651

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                +V++  G+VE +D         E  +  + S  D+ +  ++               
Sbjct: 652  GWQELVSQ--GVVEYIDT------LEEETVMIAMSPEDLRQEKEYA-------------- 689

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           P+  LG       +  + +P+  +N          M  + +   +
Sbjct: 690  ----YCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--V 736

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +I  F                           ++    +  V    +   +    +    
Sbjct: 737  YITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSMEYLR 769

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +      + AI      +  D+ +   S V         +  +   + +R   VE  
Sbjct: 770  FRELPAGINSIVAILCYTGYNQEDSIILNTSAVERGFFRSVFYRSYKDSETKRLGDVE-- 827

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              E   +        +   IY +L E   I  G           K+  L          +
Sbjct: 828  --EQFEKPNRQTCQGMRNAIYDKLDEDGIISPGIRVSGDDVIIGKTMTLPETDDDLDSST 885

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            + +        ++ +   +  Q                        +     +  K+ V 
Sbjct: 886  KRFTKRDASTFLRNSETGIVDQVML--------------------TLNSEGYKFCKIRVR 925

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E 
Sbjct: 926  SVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGMTPDIIINPHAIPSRMTIGHLIEC 985

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
              G      G+                                                 
Sbjct: 986  IQGKVSANKGEIGD---------------------------------------------- 999

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   +TP  D  + + I+++L        G  I+Y+G TG   +  V +G  Y  +L
Sbjct: 1000 -------ATPFNDAVNVQKISTLLMEYGYQLRGNEIMYNGHTGRKINAQVFLGPTYYQRL 1052

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   S
Sbjct: 1053 KHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVS 1112

Query: 1320 D----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSI 1361
            D     V            R   +E    G        +   P +  +L +E+ ++ ++ 
Sbjct: 1113 DPYRIHVCNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAP 1170

Query: 1362 DLE 1364
             L 
Sbjct: 1171 RLM 1173



 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 142/988 (14%), Positives = 289/988 (29%), Gaps = 198/988 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    +E P   LQA  +     I   +   + +F       P 
Sbjct: 39  LVRQQLDSFDEFIEMSVQRIVEESPQIDLQAEAQHRTGDIETPTRHLV-KFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEPT-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSIKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                GK  Y   I       ++        + + +  +     +K              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPVSTLWINMMSKSGAAIKKSAIGQRIIAILPYI 263

Query: 212 ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 RQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGS 323

Query: 268 DTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
                 +   +++         ++L   GV     T       Y+   +++   G   ++
Sbjct: 324 RGARPGVTKERRIKYAREILQKETLPHVGVSDFCETKKAYFLGYMVHRLLSASLGRRELD 383

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+            L+ + +          +        +       +   
Sbjct: 384 DRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLE-------LAIK 436

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
             + T  +  S+    + D  K   +  G  ++  RL   +      R          + 
Sbjct: 437 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLA 496

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +         +      ++KN   +  + +       +  ++  S+   
Sbjct: 497 RPRQLHNTLWGMLCPAETPEGQAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENL 553

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVEMR 559
           + I    +  A   F     +    +    ++ +   RR     + +  + R     E+R
Sbjct: 554 EEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMVRDIRDREIR 613

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVVY 616
            ++        P    E   + L        +    N  G+ E   + V        V Y
Sbjct: 614 -IYTDAGRISRPLLIVENQLLLLKKRHIEMLKERDYNNDGWQELVSQGV--------VEY 664

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +  +EEE   IA +   L                 E+           +  P  ++ + A
Sbjct: 665 IDTLEEETVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCA 709

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 710 SIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV-------------------------- 743

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + V  Y                +PLV              
Sbjct: 744 ---------------RMDTLAHVLYYP--------------HKPLV----------TTRS 764

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G N +VA + + GYN EDS++++   V    F S+    ++        
Sbjct: 765 MEYLRFRELPAGINSIVAILCYTGYNQEDSIILNTSAVERGFFRSVFYRSYKDSETKRLG 824

Query: 857 GPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
             EE            +       +DE GII  G  V+  D+++GK     E+    +  
Sbjct: 825 DVEEQFEKPNRQTCQGMRNAIYDKLDEDGIISPGIRVSGDDVIIGKTMTLPETDDDLDSS 884

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   K    RD S  + +  +G V
Sbjct: 885 T-------KRFTKRDASTFLRNSETGIV 905


>gi|186885845|gb|ACC93330.1| RNA polymerase beta subunit [Dimorphotheca sinuata]
          Length = 1024

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 135/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE---QIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +    R+   QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKHEIQINRGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ ++      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVKW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  + + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFIVSEKTFQLNRKE 1023



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A +
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHASI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSQGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  S+ ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSVGASLIPFIEHNDANRALMSSNMQRQAVPLSHSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D  +I +                  L+++QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKILYTDTDKIHLSGN--------GDTLSIPLVRYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRQGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI + E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKHEIQINR---GPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DV+       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVKWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     VL + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVL-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 55/178 (30%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRC-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +P+MT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPVMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|58802775|gb|AAW82495.1| RNA polymerase beta chain [Phalaenopsis aphrodite subsp. formosana]
          Length = 1091

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 151/498 (30%), Positives = 238/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G         +   + +L A    +  +  D  L     +S  +V 
Sbjct: 647  VQRGKYIKKGQILAGGAA-TAGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 700

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      R   ++ G    +G  
Sbjct: 701  KDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEARLLRN--LDRNGIVMLGSWIETGDI 758

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++   S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 759  LVGKLTPQTASESSYAPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRR--- 815

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DGTPVD+
Sbjct: 816  ----GVSNSNPERIRVYISQKREIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGTPVDM 871

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L K  +    D +   + S    F E    +  
Sbjct: 872  VFNPLGVPSRMNVGQIFECSLGLAGDLLKKHYRIGPFDERYEQEASRKLVFSELYEASKK 931

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G+S ++DG 
Sbjct: 932  TKNPW------------------------VFE---------------PEYPGKSRIFDGR 952

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW
Sbjct: 953  TGDLFEQPVLIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVW 1012

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  +++ G         PESF +LV+E+++L L
Sbjct: 1013 ALEGFGVAHILQEMLTYKSDHIRARQEVLGAMIIGATVPNPESAPESFRLLVRELRSLSL 1072

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1073 ELNHFLVSEKNFQMDRKE 1090



 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 230/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 164 VSVYTSTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNIREILDNVCYPE 223

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 224 IFLSFPNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGKI 282

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNLD P +   +   D++A +  L+ ++ G GT+DD+ +L N+R+RSV ++L
Sbjct: 283 GRQNLNRRLNLDIPQNNTFLLPRDLLAAVDHLIGMKLGMGTLDDMSHLKNKRIRSVADLL 342

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 343 QDQFGLALVRLENTVRGTICGAIRHKLIPTPQNLVTSTSLTTTYESFFGLHPLSQVLDRT 402

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 403 NPLTQIVHGRKWSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLMGSLAIH 462

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            +V  +G IE+P+  + +      +VYLS   +E   +A  NS         +++V  R 
Sbjct: 463 VKVGYWGSIESPFYGLSERSKEAQMVYLSPNRDEYYMVAAGNSLALNRDIQEQQVVPARY 522

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 523 RQEFLTIAWEEIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 582

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG +++A+  G +   D         +     S        L+ +QR
Sbjct: 583 IVGTGLEGQTALDSGVSVIAECKGKIIYTD--------TQKIFLSSNGDTLSIPLVMYQR 634

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC+NQ+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 635 SNKNTCMNQKTQVQRGKYIKKGQILAGGAATAGGELALGKNVLVAYMPWEGYNFEDAVLI 694

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V +D++TS HI ++E+    T  GPE IT++IP++    L+N+D  GI+ +G+ + 
Sbjct: 695 SERLVYKDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEARLLRNLDRNGIVMLGSWIE 754

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+  S  +  PE++LLRAI G +    ++TSLR+P G  G V+DVR  +R
Sbjct: 755 TGDILVGKLTPQTASESSYAPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHR 814

Query: 948 HGID----KNERSISVEREQIELLAR 969
            G+     +  R    ++ +I++  +
Sbjct: 815 RGVSNSNPERIRVYISQKREIKVGDK 840



 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          N+GL   F     I         + FV  Y+   
Sbjct: 33  IPGFSQIQFEGFCRFI----------NQGLTEEFHKFQKIEDRDQEIEFQLFVETYQLVE 82

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ ++++EQ++++G++P+M   GT
Sbjct: 83  PLITERDAVYESLTYSSELYVPAVLIW---------KTGRNMQEQTVFIGNIPIMNSFGT 133

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  I 
Sbjct: 134 SIVNGIYRIVINQIVQSPGIYYRSELE---HNGVSVYTSTIISDWGGRSELEIDRKARIW 190

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 191 ARVSRKQKISILVLSSAMGSNIREILDNVCYPEIFLSFPNDKEKKKIGSKE 241


>gi|169142709|ref|YP_001687136.1| RNA polymerase beta subunit [Oenothera argillicola]
 gi|169143030|ref|YP_001687450.1| RNA polymerase beta subunit [Oenothera parviflora]
 gi|159792947|gb|ABW98703.1| RNA polymerase beta subunit [Oenothera argillicola]
 gi|159895556|gb|ABX10120.1| RNA polymerase beta subunit [Oenothera parviflora]
          Length = 1072

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/397 (33%), Positives = 204/397 (51%), Gaps = 50/397 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ- 1041
              +   ++ G    +G     K T   ++  S Y   +    A+   ++  + E+     
Sbjct: 721  LDKNGIVMMGSWVEAGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLP 780

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                  +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S
Sbjct: 781  IGGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIIS 833

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG+A   L +  +    D + 
Sbjct: 834  KILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGFAGDLLERHYRIAPFDERY 893

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              + S    F E    +                               VF+         
Sbjct: 894  EQEASRKLVFSELYEASKQTANPW------------------------VFE--------- 920

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+S L+DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+ VTQQ
Sbjct: 921  ------PEYPGKSRLFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYARVTQQ 974

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    + 
Sbjct: 975  PLRGRAKQGGQRVGEMEVWALEGFGVAHLLQEMLTYKSDHIRARQGVLGTTILGGTIPKP 1034

Query: 1342 -GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
               PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 EDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 227/687 (33%), Positives = 375/687 (54%), Gaps = 22/687 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 144 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 203

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N         +++A+L+ Y+      GD           +  FF   + +L  +
Sbjct: 204 MFLSFLNEKEKKTIGSKENAILEFYQQFSCVGGDPVFSESLCKELHTKFF-QQRCELGRI 262

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD ++L N+R+RSV ++L
Sbjct: 263 GRQNMNRRLNLDIPQHNTFLLPRDILAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLL 322

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LSQ+ +  
Sbjct: 323 QDQFGLALVRLESVVRRTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   MRD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 383 NPLTQIVHGRKLSYLGPGGLTARTASFRMRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ ++ +      ++Y S   +E   +A  NS     G   E++V  R 
Sbjct: 443 ARIGRGGSLESPFYEISERSNKGRMLYFSPSRDEYYMVAAGNSLALNRGIQEEQVVPARY 502

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  +++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503 RQEFLTLAWDQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSERC 562

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   +  SG   +A+R G V   ++ +I++          +       L+ +Q 
Sbjct: 563 IVGTGLERQASLDSGVTAIAEREGKVIYTNSDKIIL--------SGSGDTLSIPLVMYQG 614

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 615 SNKNTWMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 674

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 675 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMMGSWVE 734

Query: 890 PGDILVGKITPKGESPMT---PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            G+ILVGK+TP+     +   PEE+LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 735 AGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLPIGGRGRVIDVRWIQ 794

Query: 947 RHGIDKNE----RSISVEREQIELLAR 969
           + G         R   +++ +I++  +
Sbjct: 795 KRGGSSYNPETIRVYILQKREIKVGDK 821



 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 28/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I   +    +EF     +Y  
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDDTDQ-EIEFQLFVETYHL 60

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L I+  LI          KS +D+++Q+I++G++PLM   
Sbjct: 61  VEPLIKERDAVYELLTYSSELYISAGLIW---------KSSRDMQKQTIFIGNIPLMNSL 111

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 112 GTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKAR 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP++  S   +     + + +
Sbjct: 169 IWARVSRKQKISILVLSSAMGSNLREILENVCYPEMFLSFLNEKEKKTIGSKE 221


>gi|167391797|ref|YP_001671675.1| RNA polymerase beta subunit [Carica papaya]
 gi|166344124|gb|ABY86774.1| RNA polymerase beta chain [Carica papaya]
          Length = 1070

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVRLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QESSRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYTLKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 234/686 (34%), Positives = 381/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLNIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVKGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +      ++YLS  ++E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGDWGSLESPFYKIFEKSKKARMLYLSPSKDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D  +I++      L+          L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIVSTDTDKIILSGNGDTLNI--------PLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQTPQVRGGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI  +E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYGDIYTSFHIRRYEIQTHVTSQGPERITNEIPHLEGHLLRNLDKNGIVRLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPEMIRVYISQKREIKVGDK 819



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ G+ RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGLYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|114107038|ref|YP_740194.1| RNA polymerase beta subunit [Liriodendron tulipifera]
 gi|113200986|gb|ABI32501.1| RNA polymerase beta subunit [Liriodendron tulipifera]
          Length = 1079

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 204/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 729  LDKNGIVMLGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 788

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 789  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 841

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 842  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 901

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 902  QEASRKLVF-SELYSASKQTANPWVFEPEC------------------------------ 930

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 931  --------PGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 982

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 983  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1042

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1043 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1078



 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 152 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 211

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   R++A+L+ Y+      GD              FF   + +L  +
Sbjct: 212 IFLSFPNDKEKKKIGSRENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 270

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 271 GRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 330

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 331 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 390

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 391 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 450

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E++V  R 
Sbjct: 451 ARIGHWGSIESPFYEISERSKEVQMVYLSPSRDEYYMVAAGNSLALNWGIQEEQVVPARY 510

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 511 RQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 570

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+  G +   D  +IV+                  L+ +QR
Sbjct: 571 IVGTGLECQAALDSGVSAIAEHEGKIVYTDTDKIVLSGN--------GDTISIPLVMYQR 622

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 623 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 682

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ + 
Sbjct: 683 SERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWIE 742

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 743 TGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVIDVRWIQK 802

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 803 KGGSSYNPEMIRVYISQKREIKVGDK 828



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 21  IPGFSQIQFEGFCRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLVE 70

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 71  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTVFIGNIPLMNSLGT 121

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 122 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 178

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 179 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSRE 229


>gi|89142866|emb|CAJ76104.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 189/420 (45%), Positives = 279/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +G+ +++  +K T   +K L+   +  L I  D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGDLIVKKNRKFTRAAIKKLEAAKMTKLPIDVDELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPGD  
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|268574492|ref|XP_002642223.1| C. briggsae CBR-RPB-2 protein [Caenorhabditis briggsae]
          Length = 1194

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/988 (15%), Positives = 314/988 (31%), Gaps = 206/988 (20%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   I  ++  L+    G+  +DD D++GN+R+   G +L   +R    
Sbjct: 357  HVGVSEHCETKKAFFIGYMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFR 416

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
             + + ++   +      D       +    +   +     +               +SQ+
Sbjct: 417  NLLKEMRMTAQKYINKNDDFALDVCVKTSTITRGLAYSLATGNWGDQKKAHQSRAGVSQV 476

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   + ++H RR ++     + R     + R +H T +G +CPAET EG  +GLV +
Sbjct: 477  LNRLTYTATLSHLRRANS----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKN 532

Query: 586  LTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L   A ++     E     + +  +    +V   +  +    ++  A   +  +     +
Sbjct: 533  LALMAYISVGSLPEPILEFLEEWSMENLEEVSPSAIADATKIFVNGAWVGIHREPELLMD 592

Query: 644  -LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM---QR 698
             L   R   + I+     + D  D   +          P L  +     L   ++   + 
Sbjct: 593  TLKKLRRQMDIIVSEVSMVRDIRDREIRIYTDAGRVCRPLLIVEKQKLALRKRHIDLLKD 652

Query: 699  QAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                     +  VG G+ E + +     +++A     +                      
Sbjct: 653  VDETKKYTWSDLVGNGVVELIDSMEEETSMIAMMPEDL---------------------- 690

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                                     + G            P+  LG       +  + +P
Sbjct: 691  -------------------------RSGGYCDTYTHCEIHPAMILG-------VCASIIP 718

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N       S R   +       +  +                           ++ 
Sbjct: 719  FPDHNQ------SPRNTYQSAMGKQAMGVYTTNF-----------------------HVR 749

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  V        +    +     + +      + AI      +  D+ +   S +  
Sbjct: 750  MDTLAHVLYYPQKPLVTTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDR 809

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   D      +++    EL+ +   ++   +  ++Y +L E   I  G  
Sbjct: 810  GLF-RSVFYRSYRDNEA---NIDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMR 865

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L                      +  ++++   +Y    +    R  
Sbjct: 866  VSGDDVIIGKTVAL--------------------PDIDDDLDATGKKYPKRDASTFLRSS 905

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  Q    +     + VK+ +   R  Q GDK A RHG KG +  +   EDMPF  +
Sbjct: 906  ETGIVDQVMLSLNNDGNKFVKIRMRSVRLPQIGDKFASRHGQKGTMGIMYRQEDMPFTAE 965

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  VPSRM +G + E   G      G+                        
Sbjct: 966  GLTPDIIINPHAVPSRMTIGHLIECLQGKLSANKGEIGD--------------------- 1004

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP  D  + + I+ +L        G  
Sbjct: 1005 --------------------------------ATPFNDTVNVQKISGLLCEYGYHLRGNE 1032

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++Y+G TG+     +  G  Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R 
Sbjct: 1033 VMYNGHTGKKLTTQIFFGPTYYQRLKHMVDDKIHSRARGPIQMMNRQPMEGRARDGGLRF 1092

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD--DV-----VG-------RTRVYESIV--AGNDT 1338
            GEME  C  ++GA   L+E L   SD   V      G       RT  +E          
Sbjct: 1093 GEMERDCQISHGATQFLRERLFEVSDPYHVYVCNNCGLIVVANLRTNSFECKACRNKTQV 1152

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENS 1366
                 P +  +L +E+ ++ ++  L   
Sbjct: 1153 SAVRIPYACKLLFQELMSMSIAPRLMVK 1180



 Score =  228 bits (582), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 152/1006 (15%), Positives = 302/1006 (30%), Gaps = 211/1006 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA------------AMLEF 76
           L+  Q  S+D F+ MN+          Q   +   P+   S                L+F
Sbjct: 47  LVRQQLDSFDEFVQMNV----------QRIVEDSPPVELQSENQHLGNDMENPAKFSLKF 96

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTYA PL + +  +V      T  +S+ +  
Sbjct: 97  NQIYLSKPTHWEKDGAPMPMMPNEARLRNLTYASPLYVDITKVV------TRDESVNEKV 150

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            + +++G +P+M                           G FVI G ++++++Q   +  
Sbjct: 151 YEKVFVGKVPVMLRSSYCMLSNMTDRDLTELNECPLDPGGYFVINGSEKVLIAQEKMATN 210

Query: 163 -IHFDHDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--- 211
            ++    K      GK  +   CR        ++        + V +  R     +K   
Sbjct: 211 TVYVFSMKD-----GKYAFKTECR------SCLENSSRPTSTMWVNMLARGGGGGKKTAM 259

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +P+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 260 GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFEDPEMMEMVKPSLDEAFVIQ 319

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              V+ + +     +  +   +++     + L+++ +  +G++  C          +   
Sbjct: 320 EQNVALNFIGARGAKPGVTREQRIKYAR-EILQKELLPHVGVSEHCETKKAFFIGYMVHR 378

Query: 317 TGEIYIEAGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +   ++ D   +  + +  +      +      N    +R T     NK+   AL
Sbjct: 379 LLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFRNLLKEMRMTAQKYINKNDDFAL 438

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
               +        T  +A S+    + D  K   S  G  ++  RL          R   
Sbjct: 439 DVCVK----TSTITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRANS 494

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N +  +         +   + + L     + +  +   I E +  
Sbjct: 495 PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEE 554

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++++   + ++   +  A   F   + +    E    +  +   RR   +    V+  
Sbjct: 555 WSMENL---EEVSPSAIADATKIFVNGAWVGIHREPELLMDTLKKLRRQMDIIVSEVSMV 611

Query: 553 RAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           R   +      T  GR+C P    E   + L        +       ET      D    
Sbjct: 612 RDIRDREIRIYTDAGRVCRPLLIVEKQKLALRKRHIDLLKD----VDETKKYTWSDLVGN 667

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  + +MEEE   IA     L   G                    +     +  P  +
Sbjct: 668 GVVELIDSMEEETSMIAMMPEDLRSGG------------------YCDTYTHCEIHPAMI 709

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                            
Sbjct: 710 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV--------------------- 748

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                  + + V  Y               Q+PLV         
Sbjct: 749 --------------------RMDTLAHVLYYP--------------QKPLV--------- 765

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA + + GYN EDS++++   +   +F S+    +    
Sbjct: 766 -TTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLFRSVFYRSYRDNE 824

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     EE            +       +DE GII  G  V+  D+++GK     +   
Sbjct: 825 ANIDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVALPDIDD 884

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +    +          RD S  + S  +G V  V +   +  +K
Sbjct: 885 DLDATGKKYPK-------RDASTFLRSSETGIVDQVMLSLNNDGNK 923


>gi|307208700|gb|EFN85990.1| DNA-directed RNA polymerase II subunit RPB2 [Harpegnathos saltator]
          Length = 1123

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 162/1059 (15%), Positives = 325/1059 (30%), Gaps = 206/1059 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++        +A +   + +    + T      +         KY 
Sbjct: 231  DILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGTRGARAGV---TKEKRIKYA 287

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+   
Sbjct: 288  REILQKEMLPHVGISDFCETKK---AYFLGYMVHRLLSASLGRRELDDRDHYGNKRLDLA 344

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R     + + ++               +  I  K +   +     +      
Sbjct: 345  GPLLAFLFRALFKNLMKEVRLYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQ 404

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+   +   S ++H RR+++     + R     + R +H T +G +CPA
Sbjct: 405  KKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWGMLCPA 460

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
            ET EG  +GLV +L   A ++           + +  +    ++   +  +    ++   
Sbjct: 461  ETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGC 520

Query: 631  NSSLDEDGSFTE-ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D       L   R   + I+     I  I     ++ + A  +   L   +   
Sbjct: 521  WVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRISRPLLIVEGQN 580

Query: 690  VLMGCN---MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +L+      M ++           VG+G+ E +        ++A               +
Sbjct: 581  LLLKKRHIDMLKERDYNNDGWQELVGSGVVEYIDTLEEETVMIA---------------M 625

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               +   +   +    Y                                   P+  LG  
Sbjct: 626  SPDDLRQEKEYAYCTTY-----------------------------THCEIHPAMILG-- 654

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   ++I  F                  
Sbjct: 655  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------------ 689

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     ++    +  V    +   +    +       +      + AI      +  
Sbjct: 690  ---------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQE 740

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V        +F R   +   + I  + EQ E  +R           +    
Sbjct: 741  DSVILNASAVERGFF-RSVFYRSYKEAESKKIGDQEEQFEKPSRLTCQGMRNAIYDKLDD 799

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  L          ++ +        ++ +   +  Q    
Sbjct: 800  DGIIAPGIRVSGDDVIIGKTITLPETDDELDSTTKRFTKRDASTFLRNSETGIVDQVML- 858

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                +     +  K+ V   R  Q GDK A RHG KG       
Sbjct: 859  -------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYR 899

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E   G      G+               
Sbjct: 900  QEDMPFSCEGLTPDIIINPHAIPSRMTIGHLIECIQGKVSANKGEIGD------------ 947

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP  D  + + I+++L+ 
Sbjct: 948  -----------------------------------------ATPFNDAVNVQKISTLLQE 966

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +QP+ G
Sbjct: 967  YGYQLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEG 1026

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYES 1331
            ++  GG R GEME  C  ++GAA  L+E L   SD     +            R   +E 
Sbjct: 1027 RARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHICNFCGLIAIANLRNNTFEC 1086

Query: 1332 IVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
               G        +   P +  +L +E+ A+ ++  L  +
Sbjct: 1087 --KGCKNKTQISQIRLPYAAKLLFQELMAMNIAPRLMTT 1123



 Score =  225 bits (574), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 131/949 (13%), Positives = 269/949 (28%), Gaps = 195/949 (20%)

Query: 65  ITAFSGAAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVD 114
           I        L+F       P              ++   R+LTY+ PL + +   +    
Sbjct: 26  IENPVRHL-LKFEQIYLSKPTHWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIMKDG 84

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQ 150
           E        + + Q  ++G +P+M                           G F+I G +
Sbjct: 85  EEPI-----ETQHQKTFIGKIPIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSE 139

Query: 151 RIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH------ 203
           +++++Q   +   ++    K      GK  Y   I       ++        +       
Sbjct: 140 KVLIAQEKMATNTVYVFSMKD-----GKYAYKAEIR----SCLEHSSRPTSTLWINMMAK 190

Query: 204 --VRIDR--------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
               I +              ++++P+     ALG  ++ +IL          +  +   
Sbjct: 191 SGASIKKSAIGQRIVAIIPYVKQEIPIMVVFRALGFVADRDILEHIIYDFDDPEMMEMVK 250

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDC 302
             L  A ++    V+ + +        +   K++         + L   G+     T   
Sbjct: 251 PSLDEAFVIQEQNVALNFIGTRGARAGVTKEKRIKYAREILQKEMLPHVGISDFCETKKA 310

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
               Y+   +++   G   ++  D    K L+            L+ + +          
Sbjct: 311 YFLGYMVHRLLSASLGRRELDDRDHYGNKRLDLAGPLLAFLFRALFKNLMKEVRLYAQKF 370

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
           +        +       +     + T  +  S+    + D  K   +  G  ++  RL  
Sbjct: 371 IDRGKDFNLE-------LAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTF 423

Query: 423 DTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +      R          +     L N    +                ++KN   +  +
Sbjct: 424 ASTLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYI 480

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            +       +  ++  S+   + I    +  A   F     +    +    ++ +   RR
Sbjct: 481 SVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRR 540

Query: 541 L--SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAY 595
                + +  + R     E+R ++        P    EG N+ L        +    N  
Sbjct: 541 QMDIIVSEVSMIRDIRDREIR-IYTDAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNND 599

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G+ E           +  V Y+  +EEE   IA +   L                 E+  
Sbjct: 600 GWQELV--------GSGVVEYIDTLEEETVMIAMSPDDL---------------RQEKEY 636

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                    +  P  ++ + AS+IPF +++ S R      M +QA+ +            
Sbjct: 637 AYCTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----- 691

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                                  + + V  Y             
Sbjct: 692 ------------------------------------RMDTLAHVLYYP------------ 703

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              +PLV                     +L  G N +VA + + GYN EDS++++   V 
Sbjct: 704 --HKPLV----------TTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVE 751

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNP 890
              F S+    ++          EE            +       +D+ GII  G  V+ 
Sbjct: 752 RGFFRSVFYRSYKEAESKKIGDQEEQFEKPSRLTCQGMRNAIYDKLDDDGIIAPGIRVSG 811

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            D+++GK     E+    +          K    RD S  + +  +G V
Sbjct: 812 DDVIIGKTITLPETDDELDSTT-------KRFTKRDASTFLRNSETGIV 853


>gi|164597817|ref|NP_084686.2| RNA polymerase beta subunit [Oenothera elata subsp. hookeri]
 gi|169142944|ref|YP_001687366.1| RNA polymerase beta subunit [Oenothera biennis]
 gi|172045800|sp|Q9MTM5|RPOB_OENEH RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|159793117|gb|ABW98871.1| RNA polymerase beta subunit [Oenothera biennis]
 gi|162423684|emb|CAB67151.2| RNA polymerase beta subunit [Oenothera elata subsp. hookeri]
          Length = 1072

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/397 (33%), Positives = 204/397 (51%), Gaps = 50/397 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ- 1041
              +   ++ G    +G     K T   ++  S Y   +    A+   ++  + E+     
Sbjct: 721  LDKNGIVMMGSWVEAGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLP 780

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                  +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S
Sbjct: 781  IGGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIIS 833

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG+A   L +  +    D + 
Sbjct: 834  KILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGFAGDLLERHYRIAPFDERY 893

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              + S    F E    +                               VF+         
Sbjct: 894  EQEASRKLVFSELYEASKQTANPW------------------------VFE--------- 920

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+S L+DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+ VTQQ
Sbjct: 921  ------PEYPGKSRLFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYARVTQQ 974

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    + 
Sbjct: 975  PLRGRAKQGGQRVGEMEVWALEGFGVAHLLQEMLTYKSDHIRARQGVLGTTILGGTIPKP 1034

Query: 1342 -GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
               PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 EDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 226/687 (32%), Positives = 376/687 (54%), Gaps = 22/687 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 144 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 203

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N         +++A+L+ Y+      GD           +  FF   + +L  +
Sbjct: 204 MFLSFLNEKEKKTIGSKENAILEFYQQFSCVGGDPVFSESLCKELHTKFF-QQRCELGRI 262

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD ++L N+R+RSV ++L
Sbjct: 263 GRQNMNRRLNLDIPQHNTFLLPRDILAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLL 322

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LSQ+ +  
Sbjct: 323 QDQFGLALVRLESVVRRTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   MRD+HP++YGRICP +TSEG N+GL+ SL   
Sbjct: 383 NPLTQIVHGRKLSYLGPGGLTARTASFRMRDIHPSYYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ ++ +      ++Y S   +E   +A  NS     G   E++V  R 
Sbjct: 443 ARIGRGGSLESPFYEISERSNKGRMLYFSPSRDEYYMVAAGNSLALNRGIQEEQVVPARY 502

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  +++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503 RQEFLTLAWDQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSERC 562

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   +  SG   +A+R G +   ++ +I++          +       L+ +QR
Sbjct: 563 IVGTGLERQASLDSGVTAIAEREGKIIYTNSDKIIL--------SGSGDTLSIPLVMYQR 614

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 615 SNKNTWMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 674

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 675 SERLVYEDIYTSFHIRKYEMQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMMGSWVE 734

Query: 890 PGDILVGKITPKGESPMT---PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            G+ILVGK+TP+     +   PEE+LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 735 AGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLPIGGRGRVIDVRWIQ 794

Query: 947 RHGIDKNE----RSISVEREQIELLAR 969
           + G         R   +++ +I++  +
Sbjct: 795 KRGGSSYNPETIRVYILQKREIKVGDK 821



 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 28/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I   +    +EF     +Y  
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDDTDQ-EIEFQLFVETYHL 60

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L I+  LI          KS +D+++Q+I++G++PLM   
Sbjct: 61  VEPLIKERDAVYELLTYSSELYISAGLIW---------KSSRDMQKQTIFIGNIPLMNSL 111

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 112 GTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKAR 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP++  S   +     + + +
Sbjct: 169 IWARVSRKQKISILVLSSAMGSNLREILENVCYPEMFLSFLNEKEKKTIGSKE 221


>gi|34582033|gb|AAQ75961.1| RpoB [Phaneroglossa bolusii]
          Length = 824

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      ++            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 533  GGRGRVIDVRW------VRSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 587  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 646

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 647  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 675  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 727

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 728  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 787

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 788  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 247/725 (34%), Positives = 394/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGTRMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIVYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    L+ +QRSN+NTC++Q+PLV+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NGDTLRIPLVMYQRSNKNTCMHQKPLVRRGKCIKKGQILAYGAATIGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       GPE +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSR 985
            G  G V+DVR       D+ E++ S+     ++ +I++  +      ++ +I        
Sbjct: 533  GGRGRVIDVRWVRSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQD 592

Query: 986  LMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            +  +  G+        +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|186885797|gb|ACC93306.1| RNA polymerase beta subunit [Ainsliaea apiculata]
          Length = 1024

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------YPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGTIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    ++ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRVIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---HQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (416), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   NFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|307182559|gb|EFN69752.1| DNA-directed RNA polymerase II subunit RPB2 [Camponotus floridanus]
          Length = 1178

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 163/1057 (15%), Positives = 324/1057 (30%), Gaps = 206/1057 (19%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++        +A +   + +    + T      +         KY 
Sbjct: 286  DILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGTRGAKPGV---TKEKRIKYA 342

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+R+   
Sbjct: 343  REILQKEMLPHVGISDFCETKK---AYFLGYMVHRLLSASLGRRELDDRDHYGNKRLDLA 399

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R     + + ++               +  I  K +   +     +      
Sbjct: 400  GPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQ 459

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+   +   S ++H RR+++     + R     + R +H T +G +CPA
Sbjct: 460  KKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWGMLCPA 515

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQA 630
            ET EG  +GLV +L   A ++           + +  +    ++   +  +    ++   
Sbjct: 516  ETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGC 575

Query: 631  NSSLDEDGSFTE-ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D       L   R   + I+     I  I     ++ + A  +   L   +   
Sbjct: 576  WVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRISRPLLIVEGQN 635

Query: 690  VLMGCN---MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +L+      M ++           VG+G+ E +        ++A               +
Sbjct: 636  LLLKKRHIDMLKERDYNNDGWQELVGSGVVEYIDTLEEETVMIA---------------M 680

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               +   D   +    Y                                   P+  LG  
Sbjct: 681  SPDDLKQDKEYAYCTTY-----------------------------THCEIHPAMILG-- 709

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   ++I  F                  
Sbjct: 710  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------------ 744

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     ++    +  V    +   +    +       +      + AI      +  
Sbjct: 745  ---------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQE 795

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V        +F R   +   + I  + EQ E  +R           +    
Sbjct: 796  DSVILNASAVERGFF-RSVFYRSYKEAESKKIGDQEEQFEKPSRLTCQGMRNAIYDKLDD 854

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  L          ++ +        ++ +   +  Q    
Sbjct: 855  DGIIAPGIRVSGDDVIIGKTITLPETDDELDSTTKRFTKRDASTFLRNSETGIVDQVML- 913

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                +     +  K+ V   R  Q GDK A RHG KG       
Sbjct: 914  -------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYR 954

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E   G      G+               
Sbjct: 955  QEDMPFSCEGLTPDIIINPHAIPSRMTIGHLIECIQGKVSANKGEIGD------------ 1002

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP  D  + + I+++L+ 
Sbjct: 1003 -----------------------------------------ATPFNDAVNVQKISTLLQE 1021

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +QP+ G
Sbjct: 1022 YGYQLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEG 1081

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYES 1331
            ++  GG R GEME  C  ++GAA  L+E L   SD     +            R   +E 
Sbjct: 1082 RARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHICNFCGLIAIANLRNNTFEC 1141

Query: 1332 IVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
               G        +   P +  +L +E+ A+ ++  L 
Sbjct: 1142 --KGCKNKTQISQIRLPYAAKLLFQELMAMNIAPRLM 1176



 Score =  239 bits (609), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 141/988 (14%), Positives = 290/988 (29%), Gaps = 198/988 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  + +   I        L+F       P 
Sbjct: 42  LVRQQLDSFDEFIEMSVQRIVEDSPQIDLQAEAQHTTGEIENPVRHL-LKFEQIYLSKPT 100

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 101 HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPV-----ETQHQKTFIGKI 155

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 156 PIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 215

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDR-------------- 208
                GK  Y   I       ++        +           I +              
Sbjct: 216 -----GKYAYKAEIR----SCLEHSSRPTSTLWINMMAKSGASIKKSAIGQRIIAIIPYI 266

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 267 KQEIPIMVVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGT 326

Query: 268 DTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
              +  +   K++         + L   G+     T       Y+   +++   G   ++
Sbjct: 327 RGAKPGVTKEKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLSASLGRRELD 386

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+            L+ + +          +        +       +   
Sbjct: 387 DRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLE-------LAIK 439

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
             + T  +  S+    + D  K   +  G  ++  RL   +      R          + 
Sbjct: 440 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLA 499

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +                ++KN   +  + +       +  ++  S+   
Sbjct: 500 KPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENL 556

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVEMR 559
           + I    +  A   F     +    +    ++ +   RR     + +  + R     E+R
Sbjct: 557 EEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRDREIR 616

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVVY 616
            ++        P    EG N+ L        +    N  G+ E           +  V Y
Sbjct: 617 -IYTDAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNNDGWQELV--------GSGVVEY 667

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +  +EEE   IA +   L +D  +                        +  P  ++ + A
Sbjct: 668 IDTLEEETVMIAMSPDDLKQDKEY---------------AYCTTYTHCEIHPAMILGVCA 712

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 713 SIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV-------------------------- 746

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + V  Y                +PLV              
Sbjct: 747 ---------------RMDTLAHVLYYP--------------HKPLV----------TTRS 767

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G N +VA + + GYN EDS++++   V    F S+    ++        
Sbjct: 768 MEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKEAESKKIG 827

Query: 857 GPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
             EE            +       +D+ GII  G  V+  D+++GK     E+    +  
Sbjct: 828 DQEEQFEKPSRLTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVIIGKTITLPETDDELDST 887

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   K    RD S  + +  +G V
Sbjct: 888 T-------KRFTKRDASTFLRNSETGIV 908


>gi|186885875|gb|ACC93345.1| RNA polymerase beta subunit [Gorteria diffusa]
          Length = 1024

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 218/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERLTNEIPHLEVH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMPFL+DG P+D+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPFLQDGRPIDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 256/828 (30%), Positives = 427/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   +  L  +GR 
Sbjct: 161  LFLSFLNDKKKMGSKENAILEFYQQFACVEGDPVFSESLSKDLLKKFFQQRCVLGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERLTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            D+ E++ S+     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPFLQDGRPIDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 91/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L +  RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVAARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKM 172


>gi|186885929|gb|ACC93372.1| RNA polymerase beta subunit [Pertya scandens]
          Length = 1024

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------YPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGXIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYKQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  YMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++L+SER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLVSER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|169142859|ref|YP_001687282.1| RNA polymerase beta subunit [Oenothera glazioviana]
 gi|159895471|gb|ABX10036.1| RNA polymerase beta subunit [Oenothera glazioviana]
          Length = 1072

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 134/397 (33%), Positives = 204/397 (51%), Gaps = 50/397 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ- 1041
              +   ++ G    +G     K T   ++  S Y   +    A+   ++  + E+     
Sbjct: 721  LDKNGIVMMGSWVEAGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLP 780

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                  +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S
Sbjct: 781  IGGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIIS 833

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG+A   L +  +    D + 
Sbjct: 834  KILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGFAGDLLERHYRIAPFDERY 893

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              + S    F E    +                               VF+         
Sbjct: 894  EQEASRKLVFSELYEASKQTANPW------------------------VFE--------- 920

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+S L+DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+ VTQQ
Sbjct: 921  ------PEYPGKSRLFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYARVTQQ 974

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    + 
Sbjct: 975  PLRGRAKQGGQRVGEMEVWALEGFGVAHLLQEMLTYKSDHIRARQGVLGTTILGGTIPKP 1034

Query: 1342 -GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
               PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1035 EDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1071



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 226/687 (32%), Positives = 376/687 (54%), Gaps = 22/687 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 144 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 203

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N         +++A+L+ Y+      GD           +  FF   + +L  +
Sbjct: 204 MFLSFLNEKEKKTIGSKENAILEFYQQFSCVGGDPVFSESLCKELHTKFF-QQRCELGRI 262

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD ++L N+R+RSV ++L
Sbjct: 263 GRQNMNRRLNLDIPQHNTFLLPRDILAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLL 322

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LSQ+ +  
Sbjct: 323 QDQFGLALVRLESVVRRTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   MRD+HP++YGRICP +TSEG N+GL+ SL   
Sbjct: 383 NPLTQIVHGRKLSYLGPGGLTARTASFRMRDIHPSYYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ ++ +      ++Y S   +E   +A  NS     G   E++V  R 
Sbjct: 443 ARIGRGGSLESPFYEISERSNKGRMLYFSPSRDEYYMVAAGNSLALNRGIQEEQVVPARY 502

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  +++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503 RQEFLTLAWDQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSERC 562

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   +  SG   +A+R G +   ++ +I++          +       L+ +QR
Sbjct: 563 IVGTGLERQASLDSGVTAIAEREGKIIYTNSDKIIL--------SGSGDTLSIPLVMYQR 614

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 615 SNKNTWMHQKPQVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 674

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 675 SERLVYEDIYTSFHIRKYEMQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMMGSWVE 734

Query: 890 PGDILVGKITPKGESPMT---PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            G+ILVGK+TP+     +   PEE+LLRAI G +    ++T L++P G  G V+DVR   
Sbjct: 735 AGEILVGKLTPQMAEEESSYAPEERLLRAILGIQISTSKETCLKLPIGGRGRVIDVRWIQ 794

Query: 947 RHGIDKNE----RSISVEREQIELLAR 969
           + G         R   +++ +I++  +
Sbjct: 795 KRGGSSYNPETIRVYILQKREIKVGDK 821



 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 110/233 (47%), Gaps = 28/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          ++GL         I   +    +EF     +Y  
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDDTDQ-EIEFQLFVETYHL 60

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L I+  LI          KS +D+++Q+I++G++PLM   
Sbjct: 61  VEPLIKERDAVYELLTYSSELYISAGLIW---------KSSRDMQKQTIFIGNIPLMNSL 111

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  
Sbjct: 112 GTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKAR 168

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EIL    YP++  S   +     + + +
Sbjct: 169 IWARVSRKQKISILVLSSAMGSNLREILENVCYPEMFLSFLNEKEKKTIGSKE 221


>gi|324120660|dbj|BAJ78721.1| RNA polymerase II second largest subunit [Vespa analis insularis]
          Length = 1175

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 165/1086 (15%), Positives = 331/1086 (30%), Gaps = 204/1086 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAIIPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + T      +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGTRGARPGV---TKEKRIKYAREILQKEMLPHVGISDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLSASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVS 602

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             I  I     ++ + A  +   L   +   +L+                           
Sbjct: 603  MIRDIRDREIRIYTDAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNNDG-------WQE 655

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
               SG           E +D         E  +  + S  D+ +  ++            
Sbjct: 656  LVGSGVV---------EYIDT------LEEETVMIAMSPEDLRQEKEYA----------- 689

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                              P+  LG       +  + +P+  +N          M  + + 
Sbjct: 690  -------YCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG 735

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              ++I  F                           ++    +  V    +   +    + 
Sbjct: 736  --VYITNF---------------------------HVRMDTLAHVLYYPHKPLVTTRSME 766

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +      + AI      +  D+ +   S V         +      K+  S  +
Sbjct: 767  YLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFY---RSYKDSESKRI 823

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
              ++ E   +        +   IY +L +   I  G           K+  L        
Sbjct: 824  GDQE-EQFEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPETDDELD 882

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
              ++ +        ++ +   +  Q                        +     +  K+
Sbjct: 883  STTKRFTKRDASTFLRNSETGIVDQVML--------------------TLNSEGYKFCKI 922

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G +
Sbjct: 923  RVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFSCEGLTPDIIINPHAIPSRMTIGHL 982

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E   G      G+                                              
Sbjct: 983  IECIQGKVSANKGEIGD------------------------------------------- 999

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                      +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G  Y 
Sbjct: 1000 ----------ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTYY 1049

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L 
Sbjct: 1050 QRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLF 1109

Query: 1317 IKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALG 1358
              SD     +            R   +E    G        +   P +  +L +E+ A+ 
Sbjct: 1110 EVSDPYRIHICNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMAMN 1167

Query: 1359 LSIDLE 1364
            ++  L 
Sbjct: 1168 IAPRLM 1173



 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 141/988 (14%), Positives = 287/988 (29%), Gaps = 198/988 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I        L+F       P 
Sbjct: 39  LVRQQLDSFDEFIEMSVQRIVEDSPQIDLQAEAQHTSGEIENPVRHL-LKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIEKDGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDR-------------- 208
                GK  Y   I       ++        +           I +              
Sbjct: 213 -----GKYAYKAEIR----SCLEHSSRPTSTLWINMMAKSGASIKKSAIGQRIIAIIPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGT 323

Query: 268 DTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
                 +   K++         + L   G+     T       Y+   +++   G   ++
Sbjct: 324 RGARPGVTKEKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLSASLGRRELD 383

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+            L+ + +          +        +       +   
Sbjct: 384 DRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRLYAQKFIDRGKDFNLE-------LAIK 436

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
             + T  +  S+    + D  K   +  G  ++  RL   +      R          + 
Sbjct: 437 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLA 496

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +                ++KN   +  + +       +  ++  S+   
Sbjct: 497 KPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENL 553

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVEMR 559
           + I    +  A   F     +    +    ++ +   RR     + +  + R     E+R
Sbjct: 554 EEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRDREIR 613

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVVY 616
            ++        P    EG N+ L        +    N  G+ E           +  V Y
Sbjct: 614 -IYTDAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNNDGWQELV--------GSGVVEY 664

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +  +EEE   IA +   L                 E+           +  P  ++ + A
Sbjct: 665 IDTLEEETVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCA 709

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 710 SIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV-------------------------- 743

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + V  Y                +PLV              
Sbjct: 744 ---------------RMDTLAHVLYYP--------------HKPLV----------TTRS 764

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G N +VA + + GYN EDS++++   V    F S+    ++        
Sbjct: 765 MEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIG 824

Query: 857 GPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
             EE            +       +D+ GII  G  V+  D+++GK     E+    +  
Sbjct: 825 DQEEQFEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPETDDELDST 884

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   K    RD S  + +  +G V
Sbjct: 885 T-------KRFTKRDASTFLRNSETGIV 905


>gi|309357401|emb|CAP35692.2| CBR-RPB-2 protein [Caenorhabditis briggsae AF16]
          Length = 1215

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 158/988 (15%), Positives = 314/988 (31%), Gaps = 206/988 (20%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   I  ++  L+    G+  +DD D++GN+R+   G +L   +R    
Sbjct: 378  HVGVSEHCETKKAFFIGYMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFR 437

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
             + + ++   +      D       +    +   +     +               +SQ+
Sbjct: 438  NLLKEMRMTAQKYINKNDDFALDVCVKTSTITRGLAYSLATGNWGDQKKAHQSRAGVSQV 497

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   + ++H RR ++     + R     + R +H T +G +CPAET EG  +GLV +
Sbjct: 498  LNRLTYTATLSHLRRANS----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKN 553

Query: 586  LTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L   A ++     E     + +  +    +V   +  +    ++  A   +  +     +
Sbjct: 554  LALMAYISVGSLPEPILEFLEEWSMENLEEVSPSAIADATKIFVNGAWVGIHREPELLMD 613

Query: 644  -LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM---QR 698
             L   R   + I+     + D  D   +          P L  +     L   ++   + 
Sbjct: 614  TLKKLRRQMDIIVSEVSMVRDIRDREIRIYTDAGRVCRPLLIVEKQKLALRKRHIDLLKD 673

Query: 699  QAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                     +  VG G+ E + +     +++A     +                      
Sbjct: 674  VDETKKYTWSDLVGNGVVELIDSMEEETSMIAMMPEDL---------------------- 711

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                                     + G            P+  LG       +  + +P
Sbjct: 712  -------------------------RSGGYCDTYTHCEIHPAMILG-------VCASIIP 739

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N       S R   +       +  +                           ++ 
Sbjct: 740  FPDHNQ------SPRNTYQSAMGKQAMGVYTTNF-----------------------HVR 770

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  V        +    +     + +      + AI      +  D+ +   S +  
Sbjct: 771  MDTLAHVLYYPQKPLVTTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDR 830

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   D      +++    EL+ +   ++   +  ++Y +L E   I  G  
Sbjct: 831  GLF-RSVFYRSYRDNEA---NIDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMR 886

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L                      +  ++++   +Y    +    R  
Sbjct: 887  VSGDDVIIGKTVAL--------------------PDIDDDLDATGKKYPKRDASTFLRSS 926

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  Q    +     + VK+ +   R  Q GDK A RHG KG +  +   EDMPF  +
Sbjct: 927  ETGIVDQVMLSLNNDGNKFVKIRMRSVRLPQIGDKFASRHGQKGTMGIMYRQEDMPFTAE 986

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  VPSRM +G + E   G      G+                        
Sbjct: 987  GLTPDIIINPHAVPSRMTIGHLIECLQGKLSANKGEIGD--------------------- 1025

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP  D  + + I+ +L        G  
Sbjct: 1026 --------------------------------ATPFNDTVNVQKISGLLCEYGYHLRGNE 1053

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++Y+G TG+     +  G  Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R 
Sbjct: 1054 VMYNGHTGKKLTTQIFFGPTYYQRLKHMVDDKIHSRARGPIQMMNRQPMEGRARDGGLRF 1113

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD--DV-----VG-------RTRVYESIV--AGNDT 1338
            GEME  C  ++GA   L+E L   SD   V      G       RT  +E          
Sbjct: 1114 GEMERDCQISHGATQFLRERLFEVSDPYHVYVCNNCGLIVVANLRTNSFECKACRNKTQV 1173

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENS 1366
                 P +  +L +E+ ++ ++  L   
Sbjct: 1174 SAVRIPYACKLLFQELMSMSIAPRLMVK 1201



 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 152/1006 (15%), Positives = 302/1006 (30%), Gaps = 211/1006 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA------------AMLEF 76
           L+  Q  S+D F+ MN+          Q   +   P+   S                L+F
Sbjct: 68  LVRQQLDSFDEFVQMNV----------QRIVEDSPPVELQSENQHLGNDMENPAKFSLKF 117

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTYA PL + +  +V      T  +S+ +  
Sbjct: 118 NQIYLSKPTHWEKDGAPMPMMPNEARLRNLTYASPLYVDITKVV------TRDESVNEKV 171

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            + +++G +P+M                           G FVI G ++++++Q   +  
Sbjct: 172 YEKVFVGKVPVMLRSSYCMLSNMTDRDLTELNECPLDPGGYFVINGSEKVLIAQEKMATN 231

Query: 163 -IHFDHDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--- 211
            ++    K      GK  +   CR        ++        + V +  R     +K   
Sbjct: 232 TVYVFSMKD-----GKYAFKTECR------SCLENSSRPTSTMWVNMLARGGGGGKKTAM 280

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +P+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 281 GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFEDPEMMEMVKPSLDEAFVIQ 340

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              V+ + +     +  +   +++     + L+++ +  +G++  C          +   
Sbjct: 341 EQNVALNFIGARGAKPGVTREQRIKYAR-EILQKELLPHVGVSEHCETKKAFFIGYMVHR 399

Query: 317 TGEIYIEAGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +   ++ D   +  + +  +      +      N    +R T     NK+   AL
Sbjct: 400 LLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFRNLLKEMRMTAQKYINKNDDFAL 459

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
               +        T  +A S+    + D  K   S  G  ++  RL          R   
Sbjct: 460 DVCVK----TSTITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRANS 515

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N +  +         +   + + L     + +  +   I E +  
Sbjct: 516 PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEE 575

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++++   + ++   +  A   F   + +    E    +  +   RR   +    V+  
Sbjct: 576 WSMENL---EEVSPSAIADATKIFVNGAWVGIHREPELLMDTLKKLRRQMDIIVSEVSMV 632

Query: 553 RAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           R   +      T  GR+C P    E   + L        +       ET      D    
Sbjct: 633 RDIRDREIRIYTDAGRVCRPLLIVEKQKLALRKRHIDLLKD----VDETKKYTWSDLVGN 688

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  + +MEEE   IA     L   G                    +     +  P  +
Sbjct: 689 GVVELIDSMEEETSMIAMMPEDLRSGG------------------YCDTYTHCEIHPAMI 730

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                            
Sbjct: 731 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV--------------------- 769

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                  + + V  Y               Q+PLV         
Sbjct: 770 --------------------RMDTLAHVLYYP--------------QKPLV--------- 786

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA + + GYN EDS++++   +   +F S+    +    
Sbjct: 787 -TTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLFRSVFYRSYRDNE 845

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     EE            +       +DE GII  G  V+  D+++GK     +   
Sbjct: 846 ANIDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVALPDIDD 905

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +    +          RD S  + S  +G V  V +   +  +K
Sbjct: 906 DLDATGKKYPK-------RDASTFLRSSETGIVDQVMLSLNNDGNK 944


>gi|186885821|gb|ACC93318.1| RNA polymerase beta subunit [Centratherum punctatum]
          Length = 1024

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKRQIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTVNPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 231/686 (33%), Positives = 374/686 (54%), Gaps = 16/686 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L   GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGTGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   ARV
Sbjct: 341 TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++L+SER
Sbjct: 573 NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLVSER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISVEREQIELLARDKDDEQV 976
           D+ E++ S+    ++       D+  
Sbjct: 750 DETEKTESIRVYILQKRQIKVGDKVA 775



 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYKLAEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885871|gb|ACC93343.1| RNA polymerase beta subunit [Gochnatia hiriartiana]
          Length = 1028

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K  +              ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVRKKRR-------SSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRM+VGQIFE+ LG A   L +  +    D +  
Sbjct: 791  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMDVGQIFESSLGLAGGLLDRHYRIAPFDERYE 850

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 851  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 876

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+ KL H V DK++ RS+G YSL+TQQP
Sbjct: 877  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYIFKLIHQVDDKIHVRSSGHYSLLTQQP 931

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ RGGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 932  LKGRAKRGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPE 991

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L + +T    + E
Sbjct: 992  DAPESFRLLIRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++ALL+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENALLEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVEGDPVFSEYLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIAIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGTICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N  P+      FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 304 YKWIPTPQKLVNPSPLKGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKFSFLGPGGLTGQT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGMNVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SG   +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGTLAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G+ +++  I
Sbjct: 544 KIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGNCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++++    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYQIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRAILGMRVYTSKETCLKLPIGGRGRVIDVRWVRKKRRSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y    P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYHLVEPLIKERDAVYKSLTYSSALYVSARLIWKTDRR-------RNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLM   GTF++ GI RIV++Q+ +SPGI++  +      +G L+Y   II D G 
Sbjct: 58  SIGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELD---PNGILVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885857|gb|ACC93336.1| RNA polymerase beta subunit [Eremanthus erythropappus]
          Length = 1024

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKRQIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTSNPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 375/686 (54%), Gaps = 16/686 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   ARV
Sbjct: 341 TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573 NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISVEREQIELLARDKDDEQV 976
           D+ E++ S+    ++       D+  
Sbjct: 750 DETEKTESIRVYILQKRQIKVGDKVA 775



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYKLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|160689622|gb|ABX45669.1| RNA polymerase subunit beta [Bacillus vallismortis]
          Length = 321

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 142/377 (37%), Positives = 194/377 (51%), Gaps = 62/377 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 1    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 58

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 59   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 118

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 119  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 178

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 179  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 232

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           +GEPF
Sbjct: 233  ----------------------TVLYDG--------------------------RSGEPF 244

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 245  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 304

Query: 1306 GAAYVLQEMLTIKSDDV 1322
            GAAY LQE+LT+KSDDV
Sbjct: 305  GAAYTLQEILTVKSDDV 321



 Score =  114 bits (286), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 78/117 (66%), Positives = 95/117 (81%)

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV  GD+L
Sbjct: 1   KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLL 60

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 117


>gi|186885901|gb|ACC93358.1| RNA polymerase beta subunit [Sinclairia palmeri]
          Length = 1024

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQINRKE 1023



 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L   GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGSGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885957|gb|ACC93386.1| RNA polymerase beta subunit [Stokesia laevis]
          Length = 1024

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILIGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 230/684 (33%), Positives = 378/684 (55%), Gaps = 21/684 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   ARV
Sbjct: 341 TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +           + +  L           L+ ++RSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYT--------NTDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573 NTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           IL+GK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILIGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISV-----EREQIELLAR 969
           D+ E++ S+     ++ +I++  +
Sbjct: 750 DETEKTESIRVYILQKREIKVGDK 773



 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 54/178 (30%), Positives = 90/178 (50%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPG ++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGFYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++  D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|326909380|ref|YP_004327649.1| RNA polymerase beta subunit [Hevea brasiliensis]
 gi|308523494|gb|ADO33544.1| RNA polymerase beta subunit [Hevea brasiliensis]
          Length = 1070

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKK----GGSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG     L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLTGDLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G +++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVSHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 249/778 (32%), Positives = 409/778 (52%), Gaps = 41/778 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195  LENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFTCVGGDPIFSESLCKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  +GR+ MN RLNLD P +   +   DI+A    L++++ G GT+DD+++L N+R
Sbjct: 254  QRCELGKIGRLNMNRRLNLDIPHNNTFLLPRDILAAADRLIEMKFGMGTLDDMNHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314  IRSVADLLQDQFGLALIRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ SL   A++  +G +E+P+ ++ +G     + YLS   EE   +A  N      G   
Sbjct: 434  LIGSLAIHAKIGHWGSLESPFYEISEGSKKVRMFYLSPNREEYYMVAAGNYLALNRGVQE 493

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +++   R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494  KQVAPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL ++E   VGTG+E  VA  SG   +A+  G +   D        ++  +         
Sbjct: 554  PLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKIIYTD--------IDKIILSGNGDTLR 605

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L+ +QRSN+NTC++Q+  ++ G  +++  ++ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606  IPLVMYQRSNKNTCMHQKTQLRRGKCIKKGQVLADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            NFED++LISER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI
Sbjct: 666  NFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGI 725

Query: 882  ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726  VMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940  VDVRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCG 992
            +DVR   + G         R   +++ +I++  +      ++ +I        +  +  G
Sbjct: 786  IDVRWIQKKGGSSYNPETIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDG 845

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------V 1035
            +            + ++   I E           + ++ A  DE+ ++            
Sbjct: 846  RPVDMVFNPLGVPSRMNVGQIFECSLGLTGDLLDRHYRIAPFDERYEQEASRKLVFSELY 905

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            E+ K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  EASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 111/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  +TY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESITYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 FIINGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRVELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|52694283|emb|CAG37981.1| RNA polymerase beta subunit [Pseudomonas pseudoalcaligenes]
          Length = 387

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 237/387 (61%), Positives = 306/387 (79%), Gaps = 1/387 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPRE 659
           PYR V +GKVT+++V+LSA+EE +  IAQA+++L++   S++ ELV  R   E  +   E
Sbjct: 121 PYRVVKEGKVTDEIVFLSAIEEADHVIAQASATLNDKRASWSTELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVNDNEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDQVSRGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIP 866
           T+IHI+E   +ARDTKLGPEEI+ DIP
Sbjct: 361 TTIHIQELTCVARDTKLGPEEISSDIP 387


>gi|61992021|gb|AAX58142.1| RNA polymerase beta subunit [Lactuca sativa]
          Length = 1070

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 655  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 714

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 715  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 774

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 775  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 828

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 829  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 888

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 889  ERYEQEASRKLVF-SELYEASKQTVNPWIFEPE--------------------------- 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 921  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 970  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 1030 PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1069



 Score =  358 bits (918), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 270/930 (29%), Positives = 456/930 (49%), Gaps = 94/930 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 83   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 128

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 129  QSELNDNGISVYTGTIISDWGGRL------ELEIDRKTRIWVRVSRQQKLSIL------- 175

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I +         ++ A ++
Sbjct: 176  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKQIGSKENAILEFYQQFACVE 226

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFF----DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
               V    +  +  + +  F                   GR  MN RLNLD P +   + 
Sbjct: 227  GDPVF--SESLSKDLQKKFFQQRCELGGIGRPAAQAWAAGRRNMNRRLNLDIPQNNTFLL 284

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERI 490
              DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     
Sbjct: 285  PRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYA 344

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +     +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+ 
Sbjct: 345  ALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLT 404

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
               A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +   
Sbjct: 405  ARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSK 464

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
               ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q
Sbjct: 465  GARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQ 524

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
              SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+
Sbjct: 525  YFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAE 584

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
              G +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++
Sbjct: 585  HEGEIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCMHQKPQVQRGKCIKK 636

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
              I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+ 
Sbjct: 637  GQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQ 696

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTP 908
                  G E +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   P
Sbjct: 697  I---NQGSERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAP 753

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQ 963
            E++LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +
Sbjct: 754  EDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKRE 813

Query: 964  IELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-I 1013
            I++  +      ++ +I        +  +  G+        +  P       +  S L +
Sbjct: 814  IKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGL 873

Query: 1014 SEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            +     + ++ A  DE+ ++            E+ K          E   K++I   + G
Sbjct: 874  AGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTVNPWIFEPESPGKSRIFDGRTG 933

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            D     V+ + K ++  K   Q  DK+ GR
Sbjct: 934  DPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 961



 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 23/225 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--AAMLEFVSYEFDP 83
           IP   ++Q   +  F+          ++GL         I   +      L    Y+   
Sbjct: 4   IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTNQEIDFELFLERYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI  +          + I+EQ+I +G +PLMT  G 
Sbjct: 54  PSIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTILIGKIPLMTSLGA 106

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  I 
Sbjct: 107 FIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGGRLELEIDRKTRIW 163

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 164 VRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKQI 208


>gi|52694137|emb|CAG30598.1| DNA-directed RNA polymerase beta chain [Pseudomonas chlororaphis]
          Length = 389

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 237/389 (60%), Positives = 308/389 (79%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E
Sbjct: 121 SPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKGQLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           T+IHI+E   +ARDTKLGPEEIT DIPNV
Sbjct: 361 TTIHIQELTCVARDTKLGPEEITADIPNV 389


>gi|186885859|gb|ACC93337.1| RNA polymerase beta subunit [Erigeron tenuis]
          Length = 1024

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIVSK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 847  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 872

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 873  -----PESPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 256/828 (30%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNEKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKIDEKSKGARMLYLSPGTDEYYMVAAGNSLALNRGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+R G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEREGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKTQVRRGKCIKKGQILACGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            D+ E++ S+     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  VFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 119/288 (41%), Gaps = 19/288 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            +++E D K  I VR+ R++K+ +   L A+G++  EIL       ++    +      S
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNEKKKIGS 174

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             + ++      + V+ D      ES  K         + +         +    L + +
Sbjct: 175 KENAILEFYQQFACVEGDP--VFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQ 232

Query: 311 DIVNGETGEIYIEA-------GDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +       +I   A         +     +  + +  IR +  L  + 
Sbjct: 233 NNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280


>gi|110227071|ref|YP_665550.1| RNA polymerase beta subunit [Populus alba]
 gi|122237048|sp|Q14FG5|RPOB_POPAL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|109945509|dbj|BAE97197.1| RNA polymerase beta chain [Populus alba]
          Length = 1070

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 157/580 (27%), Positives = 258/580 (44%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLARSEKCIVGTGLERQVALDSGVPAIAEHEGKIIYTDIDKIILSGNGYT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G +L       G   +   + +L A    
Sbjct: 604  VSIPLVMYQRSNKNTCMHQKTQVQRGKCIKRGQVLADGAATVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   ++    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILIGKLTPQLAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPTGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGGPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLARHYRVAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEA 1218
            +   + S    F                         +E +++G   + P VF+      
Sbjct: 890  RYEQEASRKLVF-------------------------SELYEAGKQTANPWVFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V+DK++ RS+G Y+LV
Sbjct: 919  ---------PECPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVADKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G +++LQEMLT KSD +  R  V  + ++G   
Sbjct: 970  TQQPLRGRAKQGGQRVGEMEVWALEGFGVSHILQEMLTYKSDHIRARQEVLGTTISGRTI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +    PESF +LV+E+++L L +   L + +     + E
Sbjct: 1030 PKPEDAPESFRLLVRELRSLALELKHFLISEKNFQINRKE 1069



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 230/686 (33%), Positives = 379/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRVELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   R++A+L+ Y+      G               FF   + +L  +
Sbjct: 203 IFLSFLSDKEKKKIGSRENAILEFYQQFTCVGGGPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR+ MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRLNMNQRLNLDIPHNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALIRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SLT  
Sbjct: 382 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLTIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++   G +E+P+ ++        ++YLS   +E   IA  N      G+  E++V  R 
Sbjct: 442 AKIGHLGSLESPFYEISARSKKVRMLYLSPNRDEYYMIAAGNCLALNRGAREEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVRLRSFFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLARSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D        ++  +           L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIIYTD--------IDKIILSGNGYTVSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  ++R  ++ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKTQVQRGKCIKRGQVLADGAATVGGELALGKNILVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V EDV+TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDIL+GK+TP+     +  PE++LLRAI G +    ++T L++P+G  G V+DVR   +
Sbjct: 734 TGDILIGKLTPQLAKESSYAPEDRLLRAILGIQVSTSKETCLKLPTGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYILQKREIKVGDK 819



 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLAEELYKFPKIEDRDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSGGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELNHNGIS---VYTGTIISDWGGRVELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKEKKKIGSRE 220


>gi|195446199|ref|XP_002070673.1| GK12191 [Drosophila willistoni]
 gi|194166758|gb|EDW81659.1| GK12191 [Drosophila willistoni]
          Length = 1176

 Score =  380 bits (976), Expect = e-102,   Method: Composition-based stats.
 Identities = 163/1004 (16%), Positives = 316/1004 (31%), Gaps = 203/1004 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDAENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              +E    G        +   P +  +L +E+ ++ ++  L  S
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVS 1176



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|195392246|ref|XP_002054770.1| RNA polymerase II 140kD subunit [Drosophila virilis]
 gi|194152856|gb|EDW68290.1| RNA polymerase II 140kD subunit [Drosophila virilis]
          Length = 1176

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 163/1004 (16%), Positives = 316/1004 (31%), Gaps = 203/1004 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDAENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              +E    G        +   P +  +L +E+ ++ ++  L  S
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVS 1176



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 223/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGMDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E   + L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|186885811|gb|ACC93313.1| RNA polymerase beta subunit [Berkheya purpurea]
          Length = 1024

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 218/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 252/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A++
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
             G+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  PGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 93/178 (52%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L F  Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFFERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|215254193|gb|ACJ64101.1| RNA polymerase beta subunit [Vibrio harveyi]
 gi|215254197|gb|ACJ64103.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 377

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 239/377 (63%), Positives = 294/377 (77%)

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N
Sbjct: 1   EVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCN 60

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G F +EL+  R  GE 
Sbjct: 61  EYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAALTEEGGFADELITARQKGES 120

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGT
Sbjct: 121 GLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGT 180

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQN
Sbjct: 181 GIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQN 240

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+
Sbjct: 241 TCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERV 300

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDI
Sbjct: 301 VQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDI 360

Query: 894 LVGKITPKGESPMTPEE 910
           LVGK+TPKGE+ +TPEE
Sbjct: 361 LVGKVTPKGETQLTPEE 377


>gi|52220802|ref|YP_086958.1| RNA polymerase beta subunit [Panax ginseng]
 gi|68053101|sp|Q68S14|RPOB_PANGI RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|51235305|gb|AAT98501.1| RNA polymerase beta subunit [Panax ginseng]
          Length = 1071

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/397 (33%), Positives = 206/397 (51%), Gaps = 51/397 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 721  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 780

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 781  GGRGRVIDVRWIQKRG----GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISK 833

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVP RMNVGQIFE  LG A   L +  +    D +  
Sbjct: 834  ILPRQDMPYLQDGRPVDMVFNPLGVPPRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 893

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEAINS 1221
             + S    F                         +E +++G   + P VF+         
Sbjct: 894  QEASRKLVF-------------------------SELYEAGKQTANPWVFE--------- 919

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQ
Sbjct: 920  ------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQ 973

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G      
Sbjct: 974  PLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNP 1033

Query: 1342 -GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
               PESF +LV+E+++L L ++    + +     + E
Sbjct: 1034 QDAPESFRLLVRELRSLALELNHFFVSEKNFQINRKE 1070



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 253/830 (30%), Positives = 425/830 (51%), Gaps = 43/830 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 144  ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 203

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 204  IFLSFLTDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 262

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNLD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 263  GRRNMNRRLNLDISQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 322

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 323  QDQFGLALVRLENVVRGTICGALRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 382

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 383  NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 442

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR+  +G +E+P+ ++ +      ++YLS  ++E   +A  NS     G   E++V  R 
Sbjct: 443  ARIGRWGSLESPFYEISERSKGARMLYLSPGKDEYYMVAAGNSLALNQGIQEEQVVPARY 502

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 503  RQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 562

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E   A  SGA  +A+  G +   D         +  L           L+ +QR
Sbjct: 563  IVGTGLERQAAIDSGALAIAEHEGKIIYTD--------TDKILLSGNGNTLSIPLVIYQR 614

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 615  SNKNTCMHQKPQVQRGKCIKKGQILAHGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 674

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 675  SERLVYEDIYTSFHIRKYEIKTHVTSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVE 734

Query: 890  PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 735  TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 794

Query: 948  HGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA----- 995
             G         R    ++ +I++  +      ++ +I        +  +  G+       
Sbjct: 795  RGGSSYNPEMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFN 854

Query: 996  -VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYE 1043
             +  P       +    L ++     + ++ A  DE+ ++            E+ K    
Sbjct: 855  PLGVPPRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEAGKQTAN 914

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                  E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 915  PWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 962



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 111/239 (46%), Gaps = 25/239 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-F 76
           GKN  +  IP   ++Q   +  F+          ++GL         I         + F
Sbjct: 5   GKNEGMSTIPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLF 54

Query: 77  VS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           V  Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I+ G++
Sbjct: 55  VETYQLVEPLIKERDAVYESLTYSSELYVSAGLIW---------KTGRDMQEQTIFFGNI 105

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLM   GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E
Sbjct: 106 PLMNSLGTSIVNGIYRIVINQVLQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELE 162

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            D K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 163 IDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKIGSKE 221


>gi|194745991|ref|XP_001955468.1| GF16238 [Drosophila ananassae]
 gi|190628505|gb|EDV44029.1| GF16238 [Drosophila ananassae]
          Length = 1176

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 163/1004 (16%), Positives = 316/1004 (31%), Gaps = 203/1004 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              +E    G        +   P +  +L +E+ ++ ++  L  S
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVS 1176



 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 225/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +        +        + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGQDPI-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|52694131|emb|CAG30595.1| DNA-directed RNA polymerase beta chain [Pseudomonas taetrolens]
          Length = 390

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 236/390 (60%), Positives = 306/390 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED F
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEIT DIPNV 
Sbjct: 361 TTIHIQELTCVARDTKLGPEEITADIPNVG 390


>gi|153831494|ref|ZP_01984161.1| DNA-directed RNA polymerase beta chain [Vibrio cholerae 623-39]
 gi|148873024|gb|EDL71159.1| DNA-directed RNA polymerase beta chain [Vibrio cholerae 623-39]
          Length = 313

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 199/313 (63%), Gaps = 5/313 (1%)

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           LRL++FD D   G  ++KDIKEQ +YMG++PLMT++GTFVI G +R++VSQLHRSPG+ F
Sbjct: 5   LRLVIFDKDAPAG--TVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFF 62

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS 225
           D DKG+   SGK+LY  RIIP +G W+D EFD KD ++VRIDRRRK+P +  L ALG  S
Sbjct: 63  DSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRALGKTS 122

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            EIL  F+ K+ +  +       L    L  G   +  +     G+  +E G+++T+  +
Sbjct: 123 AEILDIFFEKVNFEVKDQTLMMELVPERL-RGETATFDIE--ADGKVYVEKGRRVTARHI 179

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + L++ GV F+ +  + + G   A+D VN  TGE+ I A   I  ++L  +  +  + + 
Sbjct: 180 RQLEKDGVNFIEVPVEYIVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLE 239

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L+ + +++  ++  TL  D   DR  AL++IYR+MRPG+  T   AES+F  LFF +++
Sbjct: 240 VLFTNDLDHGPFMSETLRVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAER 299

Query: 406 YDLSTVGRVKMNM 418
           YDLSTVGR+K N 
Sbjct: 300 YDLSTVGRMKFNS 312


>gi|290489628|gb|ADD31198.1| RNA polymerase beta subunit protein [Berberidopsis corallina]
          Length = 1070

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 154/497 (30%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VRRGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNSEDAVL-----ISERLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E + ++    +  L RN+  +   ++ G    +G   
Sbjct: 680  GDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLLRNL-DKNGIVMLGSWVEAGDIL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   +   S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIPKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P    +++V+++ KR I+ GDK+AGRHGNKGIVS+ILP +DMP+L+DG PVD+V
Sbjct: 796  -GSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGRPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG     L +  +    D +   + S    F E    +   
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLTGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 911

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 912  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A +LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVANILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPEDAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLVSEKNFQINRKE 1069



 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 226/686 (32%), Positives = 375/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A +  L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAVDHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSKKVRMLYLSPSRDEYYMVAAGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL + E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRPEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G +           + +  +           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVLAIAEHEGKIIYT--------ATDKIILSGNGDTLSIPLLMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE +T++IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYGDIYTSFHIRKYEIQTHVTSQGPERVTKEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 AGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIPK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPEMIRVYISQKREIKVGDK 819



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELFKFPKIEDTDQEIEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERNAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|186885879|gb|ACC93347.1| RNA polymerase beta subunit [Gymnarrhena micrantha]
          Length = 1024

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 200/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMQVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTGNPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------YPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 248/828 (29%), Positives = 418/828 (50%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +        
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILETVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE-SMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +  T      S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDTVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRS  
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKILYTD--------TDKILLSGNGDTLRIPLIMYQRSXX 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             TC++ +P ++ G  +++  I+A G +T  G+L LG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  XTCMHHKPQIRRGKCIKKGQILAYGAATVDGELTLGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMQVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTGNPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 58/178 (32%), Positives = 93/178 (52%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          K I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------KYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL T  YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILETVCYPELFLSFLNDKKKI 172


>gi|195145272|ref|XP_002013620.1| GL24239 [Drosophila persimilis]
 gi|198452242|ref|XP_001358686.2| GA16485 [Drosophila pseudoobscura pseudoobscura]
 gi|194102563|gb|EDW24606.1| GL24239 [Drosophila persimilis]
 gi|198131848|gb|EAL27829.2| GA16485 [Drosophila pseudoobscura pseudoobscura]
          Length = 1176

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 162/1002 (16%), Positives = 315/1002 (31%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|195109863|ref|XP_001999501.1| GI23040 [Drosophila mojavensis]
 gi|193916095|gb|EDW14962.1| GI23040 [Drosophila mojavensis]
          Length = 1176

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 163/1004 (16%), Positives = 316/1004 (31%), Gaps = 203/1004 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDAENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMPFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              +E    G        +   P +  +L +E+ ++ ++  L  S
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVS 1176



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 223/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGMDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E   + L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|186885935|gb|ACC93375.1| RNA polymerase beta subunit [Pluchea carolinensis]
          Length = 1024

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/397 (33%), Positives = 205/397 (51%), Gaps = 50/397 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLNRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEAINS 1221
             + S    F                         +E +++G   + P +F+         
Sbjct: 847  QEASRKLVF-------------------------SELYEAGKQTANPWIFE--------- 872

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                   +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQ
Sbjct: 873  ------PESPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQ 926

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET 1341
            PL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G      
Sbjct: 927  PLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTP 986

Query: 1342 -GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
               PESF + V+E+++L L ++  L + +T    + E
Sbjct: 987  EDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E  VA  SG   +A+  G +   D  +I++                  ++ +QRSN+
Sbjct: 521  TGLEGQVALDSGTLAIAEHEGKIIYTDLDKILLSGN--------GDTLRIPVVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+  V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKTQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++    ++ ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEAGKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P  +  D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIEERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|169794065|ref|YP_001718429.1| RNA polymerase beta subunit [Manihot esculenta]
 gi|157695877|gb|ABV66146.1| RNA polymerase beta subunit [Manihot esculenta]
          Length = 1070

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAVLGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKK----GGSCYNP---ERICVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G +++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVSHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQITRKE 1069



 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 225/662 (33%), Positives = 371/662 (56%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRVELEIDRKARIWARVSRKQKISILVLSSAMGLNLKEILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFTCVGGDPIFSESLCKELQKKFF-QQRCELGKI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR+ MN +LNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRLNMNRKLNLDIPHNNTFLLPRDILAAADRLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALIRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++  +G +E+P+ ++ +G     + YLS   EE   +A  NS     G   E++   R 
Sbjct: 442 AKIGYWGSLESPFYEISEGSKKVRMFYLSPNREEYYMVAAGNSLALNRGVQEEQVAPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWERVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D        ++  +           L+++QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIIYTD--------IDKIILSGNGDTLRIPLVRYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  ++ G  +++  ++ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKTQLRRGKCIKKGQVLADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRA+ G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAVLGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HG 949
            G
Sbjct: 794 KG 795



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 76/337 (22%), Positives = 139/337 (41%), Gaps = 35/337 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKEKDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 FIINGIYRIVINQILQSPGIYYRSELEHNGIS---VYTGTIISDWGGRVELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G++ +EIL    YP+I  S   D     + + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQ 229

Query: 263 SLVDIDTGEQVI-ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
                  G+ +  ES  K         + +  K   +  +    L +  +       +I 
Sbjct: 230 --FTCVGGDPIFSESLCKELQKKFFQQRCELGKIGRLNMNRKLNLDIPHNNTFLLPRDIL 287

Query: 322 IEA-------GDVIDEKSLEEIFHSEIRDIPILYVDS 351
             A         +     +  + +  IR +  L  D 
Sbjct: 288 AAADRLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324


>gi|295137021|ref|YP_003587568.1| RNA polymerase beta subunit [Pisum sativum]
 gi|293338593|gb|ADE43566.1| RNA polymerase beta subunit [Pisum sativum]
          Length = 1070

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 129/396 (32%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+ +K      G    P     + ++++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIHKKA----GSSYNP---ETIHIYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQI E  LG A   L +  +    D +  
Sbjct: 833  ILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQILECSLGLAGSMLNRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYEASKQTSNPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG  F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -------YPGKSRIFDGRTGNAFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LKGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTIPKPV 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKDFQIQRKE 1069



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 234/682 (34%), Positives = 376/682 (55%), Gaps = 18/682 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + S  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYSGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLSEILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ YR      GD        +     FF   + +L  +
Sbjct: 203 IFLSFLNEKEEKKIGSKENAILEFYRQFACVGGDPIFPESLCTELQTKFF-QQRCELGGI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLN++ P++   +   DI+     L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNINIPENNTFLLPRDILTAADHLIRMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  I+  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLEHIIRGTICGAIRSKLRPTPQNLVTSTPLTTTYESFFGLHPLSQVLDLT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS+LG GG+    A   MRD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSSLGPGGLTGRTASFRMRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G IE+P+ ++ +      ++YLS   +E   +A  N      G   E++V  R 
Sbjct: 442 ARIGRWGSIESPFYEISERSKRIRMLYLSPSRDEYYMVATGNFLALNRGIQEEQIVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D  +I++          +       L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIVYNDTHKILL--------FGSGNALSIPLIIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC +Q+  V+ G  V++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCRHQKSQVQKGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT  IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNQIPHLEAHLLRNLDKNGIVILGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FN 946
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR    
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIHK 793

Query: 947 RHGIDKNERSISVEREQIELLA 968
           + G   N  +I +   Q   + 
Sbjct: 794 KAGSSYNPETIHIYISQKREIK 815



 Score =  179 bits (453), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 111/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P L ++Q   +  F+          + GL         I      +  + FV  Y+   
Sbjct: 12  LPGLNQIQFEGFCRFI----------DRGLTEELLKFPKIEDTDQESEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L I+  LI          K+ +DI+EQ I++G++PLM   GT
Sbjct: 62  PSIKEKDAVYESLTYSSELYISAGLIW---------KNSRDIQEQIIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y+  II D G  +++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYSGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLSEILDNVCYPEIFLSFLNEKEEKKIGSKE 220


>gi|134093189|ref|YP_001109491.1| RNA polymerase beta subunit [Populus trichocarpa]
 gi|158513642|sp|A4GYQ0|RPOB_POPTR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|133712051|gb|ABO36694.1| RNA polymerase beta chain [Populus trichocarpa]
          Length = 1070

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 155/579 (26%), Positives = 251/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I         +  G  
Sbjct: 544  MSSNMQRQAVPLARSEKCIVGTGLERQVALDSGVPAIAEHEGKIIYTDIDKIILSGNGYT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G +L       G   +   + +L A    
Sbjct: 604  VSIPLVMYQRSNKNTCMHQKTQVQRGKCIKRGQVLADGAATVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   ++    I K E    V  +  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVMLGSWVETGDILIGKLTPQLAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPTGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGAPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRVAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E                                    VF+       
Sbjct: 890  RYEQEASRKLVFSELYEAGKQTGNPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF++PV +G  Y+LKL H V+DK++ RS+G Y+LVT
Sbjct: 919  --------PECPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVADKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G +++LQEMLT KSD +  R  V  + ++G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVSHILQEMLTYKSDHIRARQEVLGTTISGRTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L +   L + +     + E
Sbjct: 1031 KPEDAPESFRLLVRELRSLALELKHFLISEKNFQINRKE 1069



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 230/686 (33%), Positives = 379/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRVELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   R++A+L+ Y+      G               FF   + +L  +
Sbjct: 203 IFLSFLSDKEKKKIGSRENAILEFYQQFTCVGGGPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR+ MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRLNMNQRLNLDIPHNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALIRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SLT  
Sbjct: 382 NPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLTIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A++   G +E+P+ ++        ++YLS   +E   IA  N      G+  E++V  R 
Sbjct: 442 AKIGHLGSLESPFYEISARSKKVRMLYLSPNRDEYYMIAAGNCLALNRGAREEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVRLRSFFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLARSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D        ++  +           L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIIYTD--------IDKIILSGNGYTVSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  ++R  ++ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKTQVQRGKCIKRGQVLADGAATVGGELALGKNILVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V EDV+TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDVYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDIL+GK+TP+     +  PE++LLRAI G +    ++T L++P+G  G V+DVR   +
Sbjct: 734 TGDILIGKLTPQLAKESSYAPEDRLLRAILGIQVSTSKETCLKLPTGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYILQKREIKVGDK 819



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 110/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLAEELYKFPKIEDRDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSGGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELNHNGIS---VYTGTIISDWGGRVELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKEKKKIGSRE 220


>gi|89142888|emb|CAJ76115.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 277/420 (65%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVSDTAKKNPLEFKGSTEEILNYYYATETIYLQSAQDFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            TGE +++  +K T   +K L+   +K L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KTGELIVKKNRKFTRAAIKKLEAAKMKTLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + +  ++E+    I++  +L++D++N   Y+R TL+ DK +  + ++++IYR +RPGD  
Sbjct: 180 VSQDKVDELLKRNIKEFKVLFIDNLNVGPYLRETLMLDKLETPEQSIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F  LFF+ ++YDLS VGR+K+N +  L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETAINLFTNLFFNPERYDLSKVGRLKLNFKFGLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|186885931|gb|ACC93373.1| RNA polymerase beta subunit [Platycarphella carlinoides]
          Length = 1024

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTGETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGTDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILASGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
             + E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  GETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885947|gb|ACC93381.1| RNA polymerase beta subunit [Scolymus maculatus]
          Length = 1023

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 672  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 731

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 732  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 785

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 786  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 845

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 846  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 873

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 874  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 926

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 927  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 986

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 987  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1022



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 272/927 (29%), Positives = 461/927 (49%), Gaps = 99/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 92

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 93   QSELNDNGISVYTGTIISDWGGRL------ELEIDRKTRIWVRVSRQQKLSIL------- 139

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +    ++ + +++                   +++A+L+
Sbjct: 140  ---VLLSAMGLNIREILENVCY---PELFLSFLNDKKIG-------------SKENAILE 180

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 181  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 240

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L R+E   +     +  
Sbjct: 241  ILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALARLENMARGNIYAALK 300

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 301  HNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 360

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 361  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAR 420

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 421  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 480

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 481  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 540

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 541  KIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCMHQKPQVQRGKCIKKGQI 592

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 593  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 650

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 651  -NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 709

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +I++
Sbjct: 710  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKV 769

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 770  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGG 829

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 830  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPF 889

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 890  EQPVI-IGKPYIL-KLIHQVDDKIHGR 914



 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 66/285 (23%), Positives = 120/285 (42%), Gaps = 14/285 (4%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D      
Sbjct: 115 RLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKIGSK 174

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GL 306
             A L    + +    D    E + +  +K        L   G + +    +        
Sbjct: 175 ENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNT 234

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           ++    +      +      +     +  + +  IR +  L  + 
Sbjct: 235 FLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 279


>gi|324120596|dbj|BAJ78689.1| RNA polymerase II second largest subunit [Lepidocampa weberi]
          Length = 1179

 Score =  380 bits (975), Expect = e-102,   Method: Composition-based stats.
 Identities = 160/1004 (15%), Positives = 306/1004 (30%), Gaps = 203/1004 (20%)

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ G
Sbjct: 337  EKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLAALGRRELDDRDHYG 393

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFC 518
            N+R+   G +L   +R     + + ++               +  I  + +   +     
Sbjct: 394  NKRLDLAGPLLAFLFRGLFKNLLKEVRIYSQKFIDRGKDFNLELAIKTRIITDGLRYSLA 453

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+   +   S ++H RR+++     + R     + R +H T 
Sbjct: 454  TGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTL 509

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEE 623
            +G ICPAET EG  +GLV +L   A ++           + +  +    ++   +  +  
Sbjct: 510  WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT 569

Query: 624  NRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
              ++      +  D       L   R   + I+     I D  D   +          P 
Sbjct: 570  KIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPL 629

Query: 682  LENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQV 738
            L  +     L   +  M ++           V +G+ E +        ++A         
Sbjct: 630  LIVEGGRLALKKRHIEMLKEREYNNYGWQDLVASGVVEYIDTLEEETVMIA--------- 680

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                  +   +   D   +    Y                                   P
Sbjct: 681  ------MSPEDLRQDKEYAYCTTY-----------------------------THCEIHP 705

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +  LG       +  + +P+  +N          M  + +   ++I  F           
Sbjct: 706  AMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF----------- 745

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                            ++    +  V        +    +       +      + AI  
Sbjct: 746  ----------------HVRMDTLAHVLFYPQKPLVTTRSMEYLRFRELPAGINSVVAIAC 789

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S V         +  +   + +RS   E EQ E   ++        
Sbjct: 790  YTGYNQEDSVIMNASAVERGFFRSVFYRSYKDQECKRSGDQE-EQFEKPTKETCQGMRNA 848

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +       I  G           K+  L                     +    +E  
Sbjct: 849  IYDKLDEDGIIAPGIRVSGDDVIIGKTITL--------------------PENDDELEGT 888

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              ++    +    R        Q    +     +  K+ V   R  Q GDK A RHG KG
Sbjct: 889  TRRFTKRDASTFLRNSETGIVDQVMVTLNAEGYKFCKIRVRSVRIPQIGDKFASRHGQKG 948

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                    EDM F  +G   DI++NP  +PSRM +G + E   G      G+        
Sbjct: 949  TCGIQYRQEDMIFTCEGLTPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD----- 1003

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP  D  + + 
Sbjct: 1004 ------------------------------------------------ATPFNDTVNVQK 1015

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I+++L+       G  ++Y+G +G   +  + +G  Y  +L HMV DK+++R+ G   ++
Sbjct: 1016 ISNLLQEYGYQLRGNEVMYNGQSGRKINAQIFLGPTYYQRLKHMVDDKIHSRARGPVQIL 1075

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG---------- 1324
             +QP+ G++  GG R GEME  C  A+GAA  L+E L   SD     V            
Sbjct: 1076 VRQPMEGRARDGGLRFGEMERDCQIAHGAAQFLRERLFEVSDPYRIHVCNLCGLIAIANL 1135

Query: 1325 RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            R   +E    G        +   P +  +L +E+ A+ ++  + 
Sbjct: 1136 RNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMAMNIAPRMM 1177



 Score =  249 bits (635), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 149/991 (15%), Positives = 290/991 (29%), Gaps = 204/991 (20%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+ M++    ++ P   LQA  +         P        +L+F    
Sbjct: 43  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTTGEVETPP------RYLLKFEQIY 96

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              P              ++   R+LTY+ PL + +   V    E        + + Q  
Sbjct: 97  LSKPTHWEKDGAPTPMMPNEARLRNLTYSAPLYVDITKSVIKEGEEAI-----ETQHQKT 151

Query: 131 YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
           ++G +P+M                           G F+I G ++++++Q   +   ++ 
Sbjct: 152 FIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV 211

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------- 211
              K      GK  Y   I       ++        + V +  R     +K         
Sbjct: 212 FSMKD-----GKYAYKAEIR----SCLEHSSRPTSTLWVNMLARGGQSIKKSAIGQRIIA 262

Query: 212 --------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                   +P+     ALG  ++ +IL          +  +     L  A ++    V+ 
Sbjct: 263 VVPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVAL 322

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGE 316
           + +        +   K++     + L+++ +  +G++           G  V   ++   
Sbjct: 323 NFIGARGARPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AA 380

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            G   ++  D    K L+            L+ + +          +        +    
Sbjct: 381 LGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLLKEVRIYSQKFIDRGKDFNLE---- 436

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + T  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 437 ---LAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPI 493

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 494 GRDGKLAKPRQLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLE 550

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I    +  A   F     +    +    +S +   RR   +    V+  R 
Sbjct: 551 EWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMSTLRKLRRQMDIIVSEVSMIRD 610

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             +      T  GRIC P    EG  + L        +       E       D   +  
Sbjct: 611 IRDREIRIYTDAGRICRPLLIVEGGRLALKKRHIEMLK-----EREYNNYGWQDLVASGV 665

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   IA +   L                 ++           +  P  ++ 
Sbjct: 666 VEYIDTLEEETVMIAMSPEDL---------------RQDKEYAYCTTYTHCEIHPAMILG 710

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 711 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 747

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 748 ------------------RMDTLAHVLFYP--------------QKPLV----------T 765

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 766 TRSMEYLRFRELPAGINSVVAIACYTGYNQEDSVIMNASAVERGFFRSVFYRSYKDQECK 825

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE            +       +DE GII  G  V+  D+++GK     E+    
Sbjct: 826 RSGDQEEQFEKPTKETCQGMRNAIYDKLDEDGIIAPGIRVSGDDVIIGKTITLPENDDEL 885

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           E    R          RD S  + +  +G V
Sbjct: 886 EGTTRR-------FTKRDASTFLRNSETGIV 909


>gi|223245|prf||0612199A polymerase beta,RNA
          Length = 384

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 117/218 (53%), Positives = 156/218 (71%)

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                    +         +S + D+ V+R+AE  + G+P++TPVFDGA E  I  +L++ 
Sbjct: 9    EFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG 68

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
            DL  SGQ  LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK
Sbjct: 69   DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGK 128

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPES 1346
            +  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRT++Y++IV GN   E G PES
Sbjct: 129  AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPES 188

Query: 1347 FNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
            FNVL+KE+++LG++I+LE+        ++   +  + +
Sbjct: 189  FNVLLKEIRSLGINIELEDQMKDLLKFLKAQTETEEFD 226


>gi|11497516|ref|NP_054924.1| RNA polymerase beta subunit [Spinacia oleracea]
 gi|133421|sp|P11703|RPOB_SPIOL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|7636097|emb|CAB88717.1| RNA polymerase beta subunit [Spinacia oleracea]
          Length = 1070

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVRLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     + V+++ KR I+ GDK+AGRHGNKGI+SR
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIHVYISQKREIKVGDKVAGRHGNKGIISR 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD++ NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILLRQDMPYLQDGRPVDMIFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + R     +ME
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSERNFQINRME 1069



 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 231/662 (34%), Positives = 374/662 (56%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKDLQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P++   +   DI+A    L+ ++ G GT+DD+++L ++R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPENNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKHKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTISGAIRHKLIPTPQNLVTSTPLTTTFESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+PY ++ +      ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGPWGSLESPYYEISERSKRVQMLYLSPSRDEYYMLASGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++ F      Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHFRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   +  +IV+                  L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVLAIAEHEGKIIYTNTDKIVLLGN--------GNTVSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P +  G  V++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKPQIPRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE++T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTYVTSQGPEKVTSEIPHLEAHLLRNLDKNGIVRLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HG 949
            G
Sbjct: 794 KG 795



 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         +         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFWRFI----------DQGLTEELSKFPKMEDTDQEIEFQLFVETYQLAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ+I +G++PLM   GT
Sbjct: 62  PLIKEKDAVYESLTYSSELYVSAGLIW---------KTRREMQEQTILIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|283794960|ref|YP_003359351.1| RNA polymerase beta subunit [Olea europaea]
 gi|330850735|ref|YP_004376413.1| RNA polymerase beta subunit [Olea europaea subsp. europaea]
 gi|281428679|gb|ADA69918.1| RNA polymerase beta subunit [Olea europaea]
 gi|291059245|gb|ADD72081.1| RNA polymerase beta subunit [Olea europaea]
 gi|328795425|emb|CBR30306.1| RNA polymerase beta subunit [Olea europaea subsp. europaea]
          Length = 1070

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++++++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRIYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG +G PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRSGNPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 238/682 (34%), Positives = 377/682 (55%), Gaps = 18/682 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L++L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIELKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       ++P  Q+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPIPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYMVAAGNSLALNQDIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL + E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRPEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA  +A+R G +   D         E  L           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGALAIAEREGKIIYTD--------TEKILFSGNGDTLSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVQRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQIHVTSQGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FN 946
            GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V+DVR    
Sbjct: 734 TGDILVGKLTPQMVKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 947 RHGIDKNERSISVEREQIELLA 968
           R G   N  +I +   Q   + 
Sbjct: 794 RGGSSYNPETIRIYISQKREIK 815



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVERYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSGGLIW---------KTSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDKERKKIGSKE 220


>gi|186885877|gb|ACC93346.1| RNA polymerase beta subunit [Gundelia tournefortii]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 424/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P     +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQSNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+L LG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELTLGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|294874302|ref|XP_002766888.1| RNA polymerase beta subunit, putative [Perkinsus marinus ATCC 50983]
 gi|239868263|gb|EEQ99605.1| RNA polymerase beta subunit, putative [Perkinsus marinus ATCC 50983]
          Length = 1171

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 157/964 (16%), Positives = 305/964 (31%), Gaps = 177/964 (18%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   I  ++  L+  + G+   DD D+ G +R+   G ++   +     ++ +  K  + 
Sbjct: 348  KAYFIGYMVHRLLLGQLGRIAEDDRDHFGKKRMDMAGPLMAASFAQLFRKLVQDSKRILQ 407

Query: 492  SVDIDSVMP---QDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
                          + +A  +   +     +               +SQ+   +  +S +
Sbjct: 408  RQVDSGRHFDLNSAIRSASSITDGLRYQLATGNWGIDKSGKSVRTGVSQVLNRLTFMSTM 467

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            +H RR++      + R+    + R +H TH+G ICPAET EG  +GLV ++     +   
Sbjct: 468  SHLRRMNT----PLERSGKLAKPRQLHNTHWGMICPAETPEGQAVGLVKNIALMCTITVG 523

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                  Y  + +     ++  ++  + ++      N       +    L           
Sbjct: 524  SLPNVVYDFL-NEWGLENLDEINPSQIKHMTKVFLNGQWVGMHADATMLCE--------- 573

Query: 656  VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                     D   K+ +    S+I  L+ ++      G    R    +    +  +    
Sbjct: 574  ------TLRDLRRKRDIDPEVSIIRDLQANELRIFTDGGRACRPLYVVQPPPSQKLCIKR 627

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E          + A R  ++        ++              +   +  F    +N  
Sbjct: 628  EH---------VEALRRMLLNNEHGGWDMLVEEGLVEYIDAEEEETCMVAMFVDDLRNA- 677

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              QR   K              PS  LG       +  + +P+  +N       S R   
Sbjct: 678  --QRRKSKASSYCHTYTHCEIHPSLILG-------VCASIIPFPDHNQ------SPRNTY 722

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +       +  +                                 +  V        +  
Sbjct: 723  QSAMGKQAMGVYATNFNMRI-----------------------DTMAHVLNYPQKPLVGT 759

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG-IDKNE 954
              +       +      + AI      +  D+ +   S +    +    F  +   +K +
Sbjct: 760  RAMEYLRFRELPAGNNAIVAIMTYSGYNQEDSLIMNASSIDRGFMRSVHFKSYMADEKRQ 819

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +  VE  +    ++    ++   D +       I  G           K + + +    
Sbjct: 820  GAQVVEEFRAPSWSKTYAMKRG--DYSKLDNDGLINPGTRVHGDDILIGKVSPIPNQTDE 877

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            E    +  ++  +D  V                 L+      ++++     +     +  
Sbjct: 878  E---GRIQKYTERDCSV----------------ALKGADNGVVDQVML--SVNARGHKFT 916

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            K+ V   R    GDK A RHG KG +      EDMPF + G   DI++NP  VPSRM +G
Sbjct: 917  KIRVRTLRVPTIGDKFASRHGQKGTMGISYRQEDMPFTQFGVVPDIIMNPHAVPSRMTIG 976

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  LG   +  G++                                           
Sbjct: 977  HLVECLLGKVGLLSGEEGD----------------------------------------- 995

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                        +TP F       I + L        G+ ++Y+G TG      + +G  
Sbjct: 996  ------------ATP-FSQVTVHEIMARLHELGFQRQGREVMYNGHTGLRLPAKIFIGPT 1042

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  +L HMV DK+++R+ G   ++T+QP+ G+   GG R GEME  C+ ++GAA  L+E 
Sbjct: 1043 YYQRLKHMVEDKIHSRARGPMQMLTRQPMEGRGREGGLRFGEMERDCMISHGAAKFLKER 1102

Query: 1315 LTIKSD-------DVVGRTRV-------YESIV-AGNDTFETGTPESFNVLVKEMQALGL 1359
            L   SD       D  G   +       YE      +   +   P +  +L +E+  + +
Sbjct: 1103 LFDISDAYRVHVCDNCGMFAIANLYKNHYECRACKNSTISQVHIPYACKLLFQELMTMSI 1162

Query: 1360 SIDL 1363
               L
Sbjct: 1163 MPKL 1166



 Score =  209 bits (532), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 142/964 (14%), Positives = 282/964 (29%), Gaps = 203/964 (21%)

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPPK----------FDVDDCLWRDLTYAVPLKITLRLI 109
            S FP         +EF     + P              +    R+LTY+ P+ + +   
Sbjct: 62  DSSFP---------VEFGQLSLNKPTVEEVDGAMTSLTPNQARLRNLTYSSPVYVNVTQT 112

Query: 110 VF---DVDEFTGAKS-IKDIKEQSIYMGDLPLMTKD------------------------ 141
            +   D D+    K  I +     I +G +P+M K                         
Sbjct: 113 TYALADPDDPNSEKQLISEDSYSKILIGRIPMMLKSEYCWLKNQTERGLVEMGECVFDQG 172

Query: 142 GTFVIKGIQRIVVSQLHRSPG--IHFDHDK----------------GRASLSGKLLYACR 183
           G F+I G ++++++ + R     ++    K                G  S SG   ++ +
Sbjct: 173 GYFIINGSEKVLIA-MERMANNFVYCFQKKQPAKYTWICEIRSQAEGMLSTSG---FSVK 228

Query: 184 IIPDQGLWMDIEFDSKDII-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIV 237
           ++ + G        ++  I     ++  D    +PV     ALG  S+ E++        
Sbjct: 229 MLANLGGR----SAARGQIVCSMPYINAD----IPVVILFRALGCVSDREVIERIVYDFS 280

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK------ 291
            +Q        +  A  ++  +V+   +        I + K       K L +K      
Sbjct: 281 DTQMMFLLRPSIEEAMPIMSQEVALDFIAKRG--PTIGTSKSGRIQYAKELLQKELLPHL 338

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           GVK            Y+   ++ G+ G I  +  D   +K ++            L+   
Sbjct: 339 GVKQYCEPRKAYFIGYMVHRLLLGQLGRIAEDDRDHFGKKRMDMAGPLMAASFAQLFRKL 398

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           V ++  I    V            D+   +R     T  +   +    +           
Sbjct: 399 VQDSKRILQRQVDSGRHF------DLNSAIRSASSITDGLRYQLATGNWGIDKSGKSVRT 452

Query: 412 GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
           G  ++  RL   +      R     +    +     L N    +         +   + +
Sbjct: 453 GVSQVLNRLTFMSTMSHLRRMNTPLERSGKLAKPRQLHNTHWGMICPAETPEGQAVGLVK 512

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +     + +  +   + + ++   ++++   D IN   +      F     +    +  
Sbjct: 513 NIALMCTITVGSLPNVVYDFLNEWGLENL---DEINPSQIKHMTKVFLNGQWVGMHADAT 569

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
                +   RR   +             +RD+             +      +    +  
Sbjct: 570 MLCETLRDLRRKRDIDP-------EVSIIRDLQANELRIFTDGGRACRPLYVVQPPPSQK 622

Query: 590 ARVNAYGFIETPYRKVCDGKV--------TNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
             +     +E   R + + +            V Y+ A EEE   +A           F 
Sbjct: 623 LCIKRE-HVEALRRMLLNNEHGGWDMLVEEGLVEYIDAEEEETCMVAM----------FV 671

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           ++L   +    +           +  P  ++ + AS+IPF +++ S R      M +QA+
Sbjct: 672 DDLRNAQRRKSKASSYCHTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 731

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
                                                     V  +       + + V  
Sbjct: 732 G-----------------------------------------VYATNFNMRIDTMAHVLN 750

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q+PLV                     +L  G N +VA M + GY
Sbjct: 751 YP--------------QKPLVG----------TRAMEYLRFRELPAGNNAIVAIMTYSGY 786

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNI 876
           N EDS++++   +      S+H + +    +       E  R         +       +
Sbjct: 787 NQEDSLIMNASSIDRGFMRSVHFKSYMADEKRQGAQVVEEFRAPSWSKTYAMKRGDYSKL 846

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D  G+I  G  V+  DIL+GK++P      T EE     I      D         +GV 
Sbjct: 847 DNDGLINPGTRVHGDDILIGKVSPIP--NQTDEE---GRIQKYTERDCSVALKGADNGVV 901

Query: 937 GTVV 940
             V+
Sbjct: 902 DQVM 905


>gi|186885863|gb|ACC93339.1| RNA polymerase beta subunit [Gamochaeta pensylvanica]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 278/927 (29%), Positives = 463/927 (49%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 92

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + I TG  + + G +L       L+      + +       L +        
Sbjct: 93   QSELNDNGISIYTGTIISDWGGRL------ELEIDRKARIWVRVSRQQKLSIL------- 139

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 140  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 181

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 182  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 241

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 242  ILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 301

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302  HNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 361

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +ETP+ K+ +      
Sbjct: 362  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLETPFYKISERSKGAR 421

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   +++V  R   E + +  E++        Q  S
Sbjct: 422  MLYLSPGRDEYYMVAAGNSLALNQGIQEQQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 541

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         E  L           L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 542  KILYTD--------TEKILLSGNGDTLRIPLVMYQRSNKNTCMHQKPQVPRGKCIKKGQI 593

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  -NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 710

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +I++
Sbjct: 711  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKV 770

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 771  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGD 830

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 831  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPF 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 891  EQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYKLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISIYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885971|gb|ACC93393.1| RNA polymerase beta subunit [Warionia saharae]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (936), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 255/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNNKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKIYERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGHTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 119/288 (41%), Gaps = 19/288 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            +++E D K  I VR+ R++K+ +   L A+G++  EIL       ++    +      S
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNNKKKIGS 174

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
             + ++      + V+ D      ES  K         + +         +    L + +
Sbjct: 175 KENAILEFYQQFACVEGDP--VFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQ 232

Query: 311 DIVNGETGEIYIEA-------GDVIDEKSLEEIFHSEIRDIPILYVDS 351
           +       +I   A         +     +  + +  IR +  L  + 
Sbjct: 233 NNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280


>gi|94502478|ref|YP_588104.1| RNA polymerase beta subunit [Helianthus annuus]
 gi|122179585|sp|Q1KXX2|RPOB_HELAN RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|88656882|gb|ABD47133.1| RNA polymerase beta subunit [Helianthus annuus]
          Length = 1060

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 709  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 768

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 769  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 822

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 823  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 882

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 883  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 910

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 911  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 963

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 964  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 1023

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 1024 DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1059



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 275/927 (29%), Positives = 464/927 (50%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 83   DRRRYIQEQTILIGKIPIMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 128

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + + TG  + + G +L       L+      + +       L +        
Sbjct: 129  QSELNDNGISVYTGTIISDWGGRL------ELEIDRKARIWVRVSRQQKLSIL------- 175

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 176  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 217

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 218  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 277

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 278  ILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 337

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 338  HNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 397

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 398  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYQISERSKGAQ 457

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 458  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVQLRSIFAFQYFS 517

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 518  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 577

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 578  KIFYTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 629

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 630  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 687

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 688  -NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 746

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +I++
Sbjct: 747  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKV 806

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 807  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGD 866

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 867  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPF 926

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 927  EQPVI-IGKPYIL-KLIHQVDDKIHGR 951



 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 107/225 (47%), Gaps = 23/225 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IP   ++Q   +  F+          ++GL         I   +     EF    Y+   
Sbjct: 4   IPGFNQIQFEGFCRFI----------DQGLAEELSKFPKIEDTNQEIDFEFFLERYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI  +          + I+EQ+I +G +P+MT  G 
Sbjct: 54  PLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTILIGKIPIMTSLGA 106

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  I 
Sbjct: 107 FIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGGRLELEIDRKARIW 163

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 164 VRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 208


>gi|186885969|gb|ACC93392.1| RNA polymerase beta subunit [Ursinia speciosa]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 198/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYASKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +             ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VPSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTVNPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 252/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             +N RLNLD P   + +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NLNRRLNLDIPQSNKFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A++
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YL+   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLAPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLIMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYASKETCLKLPIGGRGRVIDVRWVPSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTVNPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885803|gb|ACC93309.1| RNA polymerase beta subunit [Arctotis hirsuta]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKAESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIKARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKAESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/178 (32%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          K I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------KYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885917|gb|ACC93366.1| RNA polymerase beta subunit [Oncosiphon grandiflorum]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   ++ A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKETAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A++
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS  ++E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGTRMLYLSPGKDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLIMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVDGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P  +  D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLINERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|149390260|ref|YP_001294090.1| RNA polymerase beta subunit [Chloranthus spicatus]
 gi|158513759|sp|A6MMB4|RPOB_CHLSC RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|146744180|gb|ABQ43252.1| RNA polymerase beta subunit [Chloranthus spicatus]
          Length = 1070

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 156/580 (26%), Positives = 250/580 (43%), Gaps = 58/580 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E    +   +          I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLEHQAALDSGVSVIAEHEGKIIYTETNKIVFSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          + +   +  G  +  G IL G  +  G   +   + +L A    
Sbjct: 604  ISIPLVMYQRSNKNTCMHQNPQVQRGKCIKKGQILAGGASTVG-GELALGKNILVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 663  EGYNSEDAVL-----ISERLVYGDIYTSFHIRKYEIKTHVTSQGPERITKEIPHLEANLL 717

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T  ++   S  P  +  +  +  +        L
Sbjct: 718  RN--LDKNGIVMLGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTTRETCL 775

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 776  KLPIGGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKG 828

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 829  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFD 888

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 889  ERYEQEASRKLVFPELYEASKQTANPW------------------------VFE------ 918

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 919  ---------PEYPGKSRIFDGRTGDPFEQPVIMGKSYILKLIHQVDDKIHGRSSGHYALV 969

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G   
Sbjct: 970  TQQPLRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTI 1029

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF +L++E+++L L ++  L + +     + E
Sbjct: 1030 LNPEDAPESFRLLIRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 252/776 (32%), Positives = 404/776 (52%), Gaps = 41/776 (5%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
             V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197  NVCYPEIFLSFPNDKEKKKFGSKENAILEFYQQFACVGGDPIFSESLCKELQKKFF-QQR 255

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256  CELGRIGRRNMNRRLNLDIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
            SV ++L++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 316  SVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 375

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376  QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             SL   AR+  +G IE+P+ ++ +      +VYLS   +E   +A  NS     G   E+
Sbjct: 436  GSLAIHARIGHWGSIESPFYEIYERSKEVQMVYLSPSRDEYYMVAAGNSLALNQGIQEEQ 495

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496  VVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             ++E   VGTG+E   A  SG +++A+  G +   +  +IV                   
Sbjct: 556  SRSEKCIVGTGLEHQAALDSGVSVIAEHEGKIIYTETNKIVFSGN--------GDTISIP 607

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+ +QRSN+NTC++Q P V+ G  +++  I+A G ST  G+LALG+N+LVA+MPW GYN 
Sbjct: 608  LVMYQRSNKNTCMHQNPQVQRGKCIKKGQILAGGASTVGGELALGKNILVAYMPWEGYNS 667

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            ED++LISER+V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ 
Sbjct: 668  EDAVLISERLVYGDIYTSFHIRKYEIKTHVTSQGPERITKEIPHLEANLLRNLDKNGIVM 727

Query: 884  VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +G+ +  GDILVGK+TP+     +  PE++LLRAI G +    R+T L++P G  G V+D
Sbjct: 728  LGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTTRETCLKLPIGGRGRVID 787

Query: 942  VRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
            VR   + G         R    ++ +I++  +      ++ +I        +  +  G+ 
Sbjct: 788  VRWIQKKGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRP 847

Query: 995  AVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VES 1037
                       + ++   I E           + ++ A  DE+ ++            E+
Sbjct: 848  VDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFPELYEA 907

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 908  SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-MGKSYIL-KLIHQVDDKIHGR 961



 Score =  172 bits (435), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTSRDMQEQTVFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D       + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKFGSKE 220


>gi|186885785|gb|ACC93300.1| RNA polymerase beta subunit [Achillea millefolium]
          Length = 1024

 Score =  379 bits (974), Expect = e-102,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   A++
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS  ++E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGTRMLYLSPGKDEYYMLAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLIMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVDGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P  +  D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLINERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|313183985|ref|YP_004021142.1| RNA polymerase beta subunit [Castanea mollissima]
 gi|309321512|gb|ADO65052.1| RNA polymerase beta subunit [Castanea mollissima]
          Length = 1073

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 200/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 723  LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYTPEDRLLRAILGIQVSTSKETCLKLPI 782

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K         +       + V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 783  GGRGRVIDVRWVQKK-------GVSSYNPEKIHVYISQKREIKVGDKVAGRHGNKGIISK 835

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   LG+  +    D +  
Sbjct: 836  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLGRHYRIAPFDERYE 895

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VFD          
Sbjct: 896  QEASRKLVFSELYEASKQTANPW------------------------VFD---------- 921

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S + DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 922  -----PEYPGKSRILDGRTGDPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 976

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G    +  
Sbjct: 977  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEILGTTIIGRTIPKPE 1036

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1037 DAPESFRLLVRELRSLALELNHFLVSEKNFQMNRKE 1072



 Score =  367 bits (943), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 237/675 (35%), Positives = 378/675 (56%), Gaps = 14/675 (2%)

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +  L E     + + +  +   +     +  +             + S+  +  +   ++
Sbjct: 132 IYYLSELDNTGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNL 191

Query: 345 PILYVDSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLF 400
             +  +      ++   N     K   +++A+L+ Y+      GD              F
Sbjct: 192 REILENVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKF 251

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           F   K +L  +GR  MN RLNLD P ++  +   DI+A    L+ ++ G GT+DD+++L 
Sbjct: 252 F-QQKCELGRIGRRNMNQRLNLDIPQNIPFLLPRDILAAADHLIGMKFGMGTLDDMNHLK 310

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFC 518
           N+R+RSV ++L++Q+ + L R+E  I+  I       +   PQ+L+ + P+ +    FF 
Sbjct: 311 NKRIRSVADLLQDQFGVALFRLENMIRGTIGGAIRHKLIPTPQNLVTSTPLTTTYESFFG 370

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
              LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG 
Sbjct: 371 LHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGI 430

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           N+GL+ SL   AR+  +GF+E+P+ ++ +      ++YLS   +E   +A  NS     G
Sbjct: 431 NVGLIGSLAIHARIGHWGFLESPFYEISERSKKVRMLYLSPSRDEYSIVASGNSLGLNRG 490

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              E++V  R   E + V  E++        Q  S+ ASLIPF+E++D+NR LM  NMQR
Sbjct: 491 IQEEQVVPVRYRQEFLTVEWERVHLRSIFTFQYFSVGASLIPFIEHNDANRALMSSNMQR 550

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL ++E   VGTG+E  VA  SGA  +A+  G +   DA +I++             
Sbjct: 551 QAVPLSRSEKCIVGTGLERQVALDSGALAIAEHEGKIISTDADKILL-----SGKVDKGD 605

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +    L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW
Sbjct: 606 IISIPLIMYQRSNKNTCMHQKPRVPRGKCIKKGQILADGAATVGGELALGKNVLVAYMPW 665

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+
Sbjct: 666 EGYNSEDAVLISERLVYGDIYTSFHIRKYEIQTHVTSYGPERITNEIPHLKAYLLRNLDK 725

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            GI+ +G+ V  GDILVGK+TP+   ES  TPE++LLRAI G +    ++T L++P G  
Sbjct: 726 NGIVMLGSWVETGDILVGKLTPQVAKESSYTPEDRLLRAILGIQVSTSKETCLKLPIGGR 785

Query: 937 GTVVDVRIFNRHGID 951
           G V+DVR   + G+ 
Sbjct: 786 GRVIDVRWVQKKGVS 800



 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 25/239 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-F 76
           G+N  +  IP   ++Q   +  F+          ++GL         +   +     + F
Sbjct: 4   GRNEGMYTIPGFNQIQFEGFCRFI----------DQGLTEELYKFPKMEDINQEIEFQLF 53

Query: 77  VS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           V  Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++
Sbjct: 54  VETYQLVEPVIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNI 104

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLM   GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E
Sbjct: 105 PLMNSLGTSIVNGIYRIVINQILQSPGIYYLSELDNTGIS---VYTGTIISDWGGRLELE 161

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            D K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 162 IDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|183217728|ref|YP_001837347.1| RNA polymerase beta subunit [Guizotia abyssinica]
 gi|179366243|gb|ACB86514.1| RNA polymerase beta subunit [Guizotia abyssinica]
          Length = 1060

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 200/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 709  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 768

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 769  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 822

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG+PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 823  ILPRQDMPYLQDGSPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 882

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 883  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 910

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 911  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 963

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 964  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 1023

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 1024 DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1059



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 258/828 (31%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 137  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 196

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 197  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 256

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 257  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 316

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 317  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 376

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 377  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 436

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 437  GRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 496

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 497  FLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 556

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G V   D         +  L           L+ +QRSN+
Sbjct: 557  TGLEGQAALDSGALAIAEHEGKVFYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 608

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 609  NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 668

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 669  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 725

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 726  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 785

Query: 951  DKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QNAV 996
            D+ E++ S+     ++ +I++  +   +   + I+ + +  + M  L          N +
Sbjct: 786  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGSPVDMVFNPL 845

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 846  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 905

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 951



 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 23/225 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--AAMLEFVSYEFDP 83
           IP   ++Q   +  F+          ++GL         I   +      L    Y+   
Sbjct: 4   IPGFNQIQFEGFCRFI----------DQGLAEELSKFPKIEDTNQEIDFELFLERYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI  +          + I+EQ+I +G +PLMT  G 
Sbjct: 54  PLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTILIGKIPLMTSLGA 106

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  I 
Sbjct: 107 FIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGGRLELEIDRKARIW 163

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 164 VRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 208


>gi|290489616|gb|ADD31192.1| RNA polymerase beta subunit protein [Meliosma aff. cuneifolia Moore
            333]
          Length = 1070

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDRNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+ I++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKGIIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPA 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 227/686 (33%), Positives = 371/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLKEILDNVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD   +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDISQNNTFLLPRDVLAAGDQLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I           P +L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKWIPTPHNLVTSTPLTTTYESFFGLHPLSQVLDQT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      +VYLS   +E   +A  NS         EE+V  R 
Sbjct: 442 ARIGHWGSLESPFYEISERSKKVRMVYLSPSRDEYYIVAAGNSLALNQNVQEEEVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG + +A+  G +   D        ++  +           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVSAIAEHEGKIIYTD--------IDKIILSGNGDTLKIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVPRGKCMKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ V 
Sbjct: 674 SERLVYGDIYTSFHIRKYEIQTHVTNQGPERITNEIPHLEVHLLRNLDRNGIVMLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R    ++ +I++  +
Sbjct: 794 KGGSSYNPETIRVYISQKREIKVGDK 819



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCKFI----------DQGLTEELYKFPKIEDPDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PFIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RI+++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRILINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G + +EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLKEILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|149637929|ref|XP_001508364.1| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Ornithorhynchus anatinus]
          Length = 1113

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 167/996 (16%), Positives = 306/996 (30%), Gaps = 179/996 (17%)

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                    K  +     +  +  L      +     K    A++   V L  G   +DD 
Sbjct: 275  RMWGGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDR 334

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSA 512
            D  GN+R+   G++L   +     +    +K+    V       Q      +    + + 
Sbjct: 335  DYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNG 394

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPT 564
            +     +   S     ++         RLS +   G+         + R     R + P+
Sbjct: 395  MVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPS 454

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +G +CP++T EG   GLV +L     +      + P  K+ +     DV  L   EE +
Sbjct: 455  QWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIVKLANNLGVEDVNLL-CGEELS 512

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N  L         ++              +  +I+       ++    +     
Sbjct: 513  Y----PNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCV----- 563

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                    G  + R  + + K +       ME +              G     D +   
Sbjct: 564  ---YISSDGGRLCRPYIIVKKQKPAVTDKHMEELA------------QGYRNFEDFLHES 608

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +       + +   + +Y     + +                                 +
Sbjct: 609  LVEYLDVNEENDCNIALYEHTINKDTTHLEI----------------------------E 640

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +    +P+  +N          M  + + T      +    R   L        
Sbjct: 641  PFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG----YNQRNRIDTLMYLLAYPQ 696

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             P V  + ++ ID                            +   +    A+      D+
Sbjct: 697  KPMVKTKTIELID-------------------------FEKLPAGQNATVAVMSYSGYDI 731

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +   + +        ++        +R  +   +++     D    + I    I  
Sbjct: 732  EDALVLNKASLDRGFGRCLVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILD 790

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                   G+   +      KS                 Q  ++   V +       QY+ 
Sbjct: 791  ADGICSPGEKVENKQVLVNKSMP------------TVTQIPLEGSNVPQQ-----PQYKD 833

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 +    + IEK+    +       ++K+ +   R  + GDK + RHG KG+   I+
Sbjct: 834  VPITYKGATDSYIEKVMISSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 891

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPF   G   DI++NP G PSRM VG++ E   G                      
Sbjct: 892  PQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGK--------------------- 930

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                            A          T  F G+  + +   L 
Sbjct: 931  --------------------------------AGVLDGKFHYGT-AFGGSKVKDVCEDLV 957

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  
Sbjct: 958  RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTE 1017

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAG 1335
            G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G+  +            
Sbjct: 1018 GRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKS 1077

Query: 1336 N-DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            +        P +  +L +E+Q++ +   L+ S+   
Sbjct: 1078 SCHVSSLRIPYACKLLFQELQSMNIIPRLKLSKYNE 1113



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 115/947 (12%), Positives = 275/947 (29%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 19  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 69

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 70  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 119

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 120 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 178

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 179 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIAIIFKAMGVESDQEIVQMI 235

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  +E  ++L + 
Sbjct: 236 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKMEEARELLAS 295

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 296 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 348

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 349 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 406

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 407 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 457

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V   + +  + V     E      + 
Sbjct: 458 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLANNLGVEDVNLLCGEELSYPNVF 517

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 518 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 576

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  +     +   YR   D    + V YL   EE +  IA            
Sbjct: 577 IIVKKQKPAVTDKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 625

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 626 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 673

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 674 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 693

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 D   L  G+N  VA M + G
Sbjct: 694 ---------------YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSG 728

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 729 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 788

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 789 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 835


>gi|157325522|ref|YP_001468300.1| RNA polymerase beta subunit [Ipomoea purpurea]
 gi|182676565|sp|A7Y3B9|RPOB_IPOPU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|157056750|gb|ABV02340.1| RNA polymerase beta subunit [Ipomoea purpurea]
          Length = 1067

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 198/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T       S  P  +  +  +  +        LKV  
Sbjct: 717  LDKNGIVKQGSWVETGDVLVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKVPI 776

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P    +++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 777  GGRGRVIDVRWIQKKG----GSSYNP---EMIRVYILQKREIKVGDKVAGRHGNKGIISK 829

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMN+GQIFE  LG A   L +  +    D +  
Sbjct: 830  ILPRQDMPYLQDGRSVDLVFNPLGVPSRMNLGQIFECSLGLAGSLLDRHYRIAPFDERYE 889

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S  +    ++      T     ++ +                               
Sbjct: 890  QEASR-KVVFSELYEASKQTANPWAFEPE------------------------------- 917

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 918  -------YPGKSRIFDGRTGNPFEQPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 970

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 971  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPK 1030

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 DAPESFRLLVRELRSLALELNHFLVSEKNFQIHRKE 1066



 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 228/686 (33%), Positives = 382/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 140 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 199

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMR--PGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 200 IFLSFLSDKEKKKIGSKENAILEFYQQFACVDGDPIFSESLWKELQKKFF-QQRCELGRI 258

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   D++A    L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 259 GRRNMNRRLNLDIPQNNTFLLPRDLLAAADHLIGLKFGMGTLDDMNHLQNKRIRSVADLL 318

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 319 QDQFGLALVRLENAVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 378

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S+LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 379 NPLTQIVHGRKFSSLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 438

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         +++V  R 
Sbjct: 439 ARIGHWGSLESPFYEISERSTGVRMLYLSPGRDEYYMVAAGNSLALNQDIQEDQVVPARY 498

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 499 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 558

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SGA ++A+R G V   D         +  L           L+ ++R
Sbjct: 559 IVGTGVERQAALDSGALVIAEREGRVVYTD--------TDKILFSGDGETLSIPLVMYKR 610

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 611 SNKNTCMHQKPQVQRGKCIKKGQILADGAATVEGELALGKNVLVAYMPWEGYNSEDAVLI 670

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI+++E+    T  GPE++T +IP++    ++N+D+ GI+  G+ V 
Sbjct: 671 SERLVYEDIYTSFHIKKYEIQTHVTSQGPEKVTNEIPHLEAHFIRNLDKNGIVKQGSWVE 730

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+     +  PE++LLRAI G +    ++T L+VP G  G V+DVR   +
Sbjct: 731 TGDVLVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKVPIGGRGRVIDVRWIQK 790

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 791 KGGSSYNPEMIRVYILQKREIKVGDK 816



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 9   IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDIDQEIEFQLFVETYQLVE 58

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI          K+ +D++EQ+I++G +PLM   GT
Sbjct: 59  PLIKERDAVYDSLTYSSELYVSARLIW---------KTSRDMQEQTIFIGSIPLMNSQGT 109

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 110 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 166

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 167 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLSDKEKKKIGSKE 217


>gi|52694125|emb|CAG30592.1| DNA-directed RNA polymerase beta chain [Pseudomonas synxantha]
          Length = 391

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 236/390 (60%), Positives = 307/390 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 181

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 182 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 241

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 242 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 301

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED F
Sbjct: 302 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRF 361

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEIT DIPNV 
Sbjct: 362 TTIHIQELTCVARDTKLGPEEITADIPNVG 391


>gi|68475107|ref|XP_718439.1| hypothetical protein CaO19.10857 [Candida albicans SC5314]
 gi|68475648|ref|XP_718172.1| hypothetical protein CaO19.3349 [Candida albicans SC5314]
 gi|46439928|gb|EAK99240.1| hypothetical protein CaO19.3349 [Candida albicans SC5314]
 gi|46440204|gb|EAK99513.1| hypothetical protein CaO19.10857 [Candida albicans SC5314]
 gi|238879352|gb|EEQ42990.1| DNA-directed RNA polymerase II polypeptide 2 [Candida albicans WO-1]
          Length = 1234

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 174/988 (17%), Positives = 319/988 (32%), Gaps = 165/988 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 362  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 421

Query: 485  SIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I   +     +         + ++ +   +     +               +SQ+    
Sbjct: 422  DIYNYMQRCVENGGDFNVTLAVKSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRY 481

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 482  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 537

Query: 590  ARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++     E     + D   +V  D V  +A +    ++      +  D +   + +  
Sbjct: 538  TCISVGTPSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRE 597

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLL 704
                 ++      I D  +   K          P    DD+          + ++ V  L
Sbjct: 598  LRRSGDLSPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPDSETKGELKITKEHVKQL 657

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDI 761
                       +   ++ + +++VA   GIVE VDA      +I     D+  S + V  
Sbjct: 658  LRSDELDEDDEDYENSRYTWSSLVA--DGIVEYVDAEEEETIMIAMTPDDVKASKNSVSE 715

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHG 820
                K Q   Q            G  ++          T      ++   +  + +P+  
Sbjct: 716  SEQQKIQLEEQEL--------DPGKRIKPTTSGNTHTYTHCEIHPSMILGVAASIIPFPD 767

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 768  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 798

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 799  MANILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 858

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L E   I  G     
Sbjct: 859  -RSLFFRSYMDIEKRQGM---KALETFEKPTRSDTLRLKHGTYEKLDEDGLIAPGVRVSG 914

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T + +D      R+Q+         ++     +  Q               +
Sbjct: 915  EDIIIGKTTPIPADAEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 959

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 960  LLTTNGD-----GSKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFTAEGIV 1014

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +  +          IS L         
Sbjct: 1015 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGFEGDASPFTDVTTEQISTLLR------- 1067

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                              V     +G  +   VF                          
Sbjct: 1068 --------DHGYQSRGFEVMYNGHTGKKLMAQVF-------------------------- 1093

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
                          G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1094 -------------FGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1140

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIV-------------AGNDTFE 1340
            E  C+ A+GAA  L+E L   SD     V G   +   I                 + ++
Sbjct: 1141 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGMCGLMSVIANLKKNQFECRSCKNKTNIYQ 1200

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               P +  +L +E+ A+ +S  L   R+
Sbjct: 1201 IHIPYAAKLLFQELMAMNISPRLYTERS 1228



 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 143/1037 (13%), Positives = 290/1037 (27%), Gaps = 218/1037 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-----------FSGAAMLEFV 77
           L+  Q  S+D F+  +I      +  L         I              +    + F 
Sbjct: 38  LVSQQLDSFDEFVETSIQELVWEDSHL---------ILDQPAQHTSEKDHENKRYEITFG 88

Query: 78  SYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR-LIVFDVDEFTGAKSIKDIK 126
                 P               +   R+LTY+ PL + +   +    D       ++ I+
Sbjct: 89  KIYISKPSQTEGDGSTHAVFPQEARLRNLTYSSPLYVDMTSKVFKSDDNKRKDNELEWIQ 148

Query: 127 EQ-------SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
           E+        +++G +P+M +                         G FVI G ++++++
Sbjct: 149 EEPDKDTETKVFLGKVPIMLRSKFCMLRDLAEHEFYELKECPYDMGGYFVINGSEKVLIA 208

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------ 207
           Q  RS          + +    + +   I    ++G  +      K  ++ R D      
Sbjct: 209 QE-RSAANI--VQVFKKAAPSPISHVAEIRSAIEKGSRLISSMQIK--LYGR-DEKGVSG 262

Query: 208 RRRK---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           R  K         +P+     ALG+  + +IL          Q  +     +    ++  
Sbjct: 263 RTIKATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQE 322

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +    G   I   K++     K + +K +       +           +    
Sbjct: 323 REVALDFIGRR-GVLGIRREKRIQY--AKDILQKELLPNITQEEGFETRKAF--FLGYMV 377

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             + + A +  +    +      +                + N       K  KD    +
Sbjct: 378 NRLLLCALERKEPDDRDHFGKKRLDL----------AGPLLANLFRILFKKLTKDIYNYM 427

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            R +  G    F+V  ++ +    D  +Y L   G      +         + + +    
Sbjct: 428 QRCVENGG--DFNVTLAVKSQTITDGLRYSL-ATGNWGEQRKAMSSRAGVSQVLNRYTYS 484

Query: 438 AIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMER 484
           + +  L        R+GK       +  +  +    E  + Q          +  + +  
Sbjct: 485 STLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCISVGT 544

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             +  +  +    +   +         +   F     +    +    +  +   RR   L
Sbjct: 545 PSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRELRRSGDL 604

Query: 545 GQG-GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR----V 592
                + R     E        R   P       P   ++G        +    R     
Sbjct: 605 SPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPDSETKGELKITKEHVKQLLRSDELD 664

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 E              V Y+ A EEE   IA     +    +   E    +   E
Sbjct: 665 EDDEDYENSRYTWSSLVADGIVEYVDAEEEETIMIAMTPDDVKASKNSVSESEQQKIQLE 724

Query: 653 EILVPR------------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  +                    +  P  ++ +AAS+IPF +++ S R      M +QA
Sbjct: 725 EQELDPGKRIKPTTSGNTHTYTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA 784

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                                                   + + + 
Sbjct: 785 MGVFLTNYSV-----------------------------------------RMDTMANIL 803

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA   + G
Sbjct: 804 YYPQKPLGTTRSMEYLKFR------------------------ELPAGQNAIVAIACYSG 839

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDSM++++  +   +F S+    +  + +   +   E        D   +     + 
Sbjct: 840 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDIEKRQGMKALETFEKPTRSDTLRLKHGTYEK 899

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G+I  G  V+  DI++GK TP         ++        +    RD S  + S  
Sbjct: 900 LDEDGLIAPGVRVSGEDIIIGKTTPIPADAEELGQRT-------QYHTKRDASTPLRSTE 952

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG V  V +       K
Sbjct: 953 SGIVDQVLLTTNGDGSK 969


>gi|186885939|gb|ACC93377.1| RNA polymerase beta subunit [Psacalium paucicapitatum]
          Length = 1024

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      ++            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VRSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (938), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 255/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVRSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885949|gb|ACC93382.1| RNA polymerase beta subunit [Senecio polypodioides]
          Length = 1024

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      ++            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VRSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 255/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K  +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKNSERSKGTRMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIVYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVRRGKCIKKGQILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVRSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (410), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885895|gb|ACC93355.1| RNA polymerase beta subunit [Jungia polita]
          Length = 1028

 Score =  379 bits (973), Expect = e-102,   Method: Composition-based stats.
 Identities = 155/562 (27%), Positives = 245/562 (43%), Gaps = 56/562 (9%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +    ++        I         +  G       +          +
Sbjct: 519  CIVGTGLERQAALDSGALAIAEHEGKIIYTDTDKILVSGNGDTLSIPLVMYQRSNKNTCM 578

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G  ++          +   + +L A    +  +  D  L     +S
Sbjct: 579  HQKPQVQRGKCIKKGQ-ILAYGAATVGGELPLGKNVLVAYMPWEGYNFEDAVL-----IS 632

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    
Sbjct: 633  ERLVYEDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVE 691

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T       S  P  +  +  +           LK+       +++ R+  K
Sbjct: 692  TGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQK 751

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG 
Sbjct: 752  K----RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILARQDMPYLQDGR 804

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E   
Sbjct: 805  PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYE 864

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 865  ASKQTANPW------------------------VFE---------------PEYPGKSRI 885

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++ V +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GE
Sbjct: 886  FDGRTGDPFEQLVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGE 945

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 946  MEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELR 1005

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +T    + E
Sbjct: 1006 SLALELNHFLVSEKTFQINRKE 1027



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 256/806 (31%), Positives = 415/806 (51%), Gaps = 42/806 (5%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378  YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185  YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNLNRRLNLDIPQNNTFLLPRD 243

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244  ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                  PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304  HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364  ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERAKGAR 423

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPTRYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D  +I++                  L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544  KIIYTDTDKILVSGN--------GDTLSIPLVMYQRSNKNTCMHQKPQVQRGKCIKKGQI 595

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+L LG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596  LAYGAATVGGELPLGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
            T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656  TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
            LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968  AR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYP 1017
             +      ++ +I        +  +  G+        +  P       +  S L ++   
Sbjct: 776  DKVAGRHGNKGIISKILARQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGL 835

Query: 1018 RSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + ++ A  DE+ ++            E+ K          E   K++I   + GD   
Sbjct: 836  LDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFE 895

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              V+ + K ++  K   Q  DK+ GR
Sbjct: 896  QLVI-IGKPYIL-KLIHQVDDKIHGR 919



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKESDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|159161245|ref|YP_001542523.1| RNA polymerase beta subunit [Cuscuta exaltata]
 gi|182676562|sp|A8W3B6|RPOB_CUSEX RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|158938670|gb|ABW83687.1| RNA polymerase beta subunit [Cuscuta exaltata]
          Length = 1070

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 229/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL        E  +   + +L A    +  +  D  L     +S  +V 
Sbjct: 626  VRRGQFIKKGQILAD-GAATVEGELALGKSVLVAYMPWEGYNYEDAVL-----ISECLVY 679

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              IF    I K E    V  +  E +  +    +  L RN+  +   +L G     G   
Sbjct: 680  EDIFTSFHIRKYEIQTHVTTQGPEKVTNEIPHLEAHLIRNL-DKNGIVLQGSWVEPGDVL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +  +        LKV       +++ R+  K     
Sbjct: 739  VGKLTPQVVKESSYAPEDRLLRAILGIQVSASKETCLKVPIGGRGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG  VD+V
Sbjct: 796  -GYGYNP---EKIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRSVDLV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S  +    ++      
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR-KIVFSELYEASKQ 910

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T     ++ +                                        G+S ++DG T
Sbjct: 911  TANPWAFEPE--------------------------------------YPGKSRIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F+ PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GNTFEHPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIRARQEVLGTTIVGGTIPNPKNAPESFRLLVRELRSLALE 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            +   L + +     K E
Sbjct: 1053 LTHFLVSEKNFQVNKRE 1069



 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 225/686 (32%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREIIENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 ILLSFLRDKEKKKIGSKENAILEFYKKFACVGGDPLFSESLCKELQNKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RL+LD P +   +   DI+    +L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLHLDIPQNNTFLLPRDILEATDLLIGLKFGMGTLDDMNHLQNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++++ L L+R+E +++  I           PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 322 QDKFGLALVRLENAVQGTICGAIHHKKIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R++S+LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHARKVSSLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+  +G +E+P+ K+ D      V++LS   +E   +A  NS         + +V  R 
Sbjct: 442 VRIGNWGSLESPFFKISDRLTGVRVLHLSPGRDEYYMVAAGNSLALNQDIQEDLVVPARF 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E+++     P Q  SI  SLIPF+E++D+NR LM  NMQRQAVPL  +E  
Sbjct: 502 RQEFLTIAWEQVNLRSIFPFQYFSIGTSLIPFIEHNDANRALMSSNMQRQAVPLAWSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG+  +A+R G V   D  +I++                  L+ +QR
Sbjct: 562 IVGTGVERQAALDSGSLAIAEREGRVIYTDTEKILV--------SGDGKTISIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC+ Q+P V+ G  +++  I+ADG +T  G+LALG+++LVA+MPW GYN+ED++LI
Sbjct: 614 SNKNTCMYQQPQVRRGQFIKKGQILADGAATVEGELALGKSVLVAYMPWEGYNYEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SE +V ED+FTS HI ++E+    T  GPE++T +IP++    ++N+D+ GI+  G+ V 
Sbjct: 674 SECLVYEDIFTSFHIRKYEIQTHVTTQGPEKVTNEIPHLEAHLIRNLDKNGIVLQGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           PGD+LVGK+TP+     +  PE++LLRAI G +    ++T L+VP G  G V+DVR   +
Sbjct: 734 PGDVLVGKLTPQVVKESSYAPEDRLLRAILGIQVSASKETCLKVPIGGRGRVIDVRWIQK 793

Query: 948 HG----IDKNERSISVEREQIELLAR 969
            G      +  R   +++ +I++  +
Sbjct: 794 KGGYGYNPEKIRVYILQKREIKVGDK 819



 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP L ++Q   +  F+          ++GL         I        +EF     +Y+ 
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFQKIEDIDQ--EIEFQLFAETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+  L ++  LI          K+ KD++EQ I++G +P+M   
Sbjct: 60  VEPLIKERDAVYDSLTYSSELYVSAGLI---------RKASKDMQEQKIFIGSIPIMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  
Sbjct: 111 GTSIVNGIYRIVINQILQSPGIYYRSELD---QNGISVYTGTIISDWGGRSELEIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G +  EI+    YP+I+ S   D     + + +
Sbjct: 168 IWARVSRKQKISILVLSSAMGSNLREIIENVCYPEILLSFLRDKEKKKIGSKE 220


>gi|81176237|ref|YP_398316.1| RNA polymerase beta subunit [Lactuca sativa]
 gi|85700397|sp|Q56P13|RPOB_LACSA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|78675155|dbj|BAE47581.1| RNA polymerase beta subunit [Lactuca sativa]
 gi|88656970|gb|ABD47220.1| RNA polymerase beta subunit [Lactuca sativa]
          Length = 1060

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 645  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 704

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 705  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 764

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 765  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 818

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 819  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFD 878

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 879  ERYEQEASRKLVF-SELYEASKQTVNPWIFEPE--------------------------- 910

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 911  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 959

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 960  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 1019

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 1020 PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1059



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 253/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 137  ISVYTGTIISDWGGRLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 196

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       +   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 197  LFLSFLNDKKQIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 256

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 257  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 316

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 317  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 376

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 377  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 436

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 437  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 496

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 497  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 556

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 557  TGLEGQAALDSGALAIAEHEGEIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 608

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 609  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 668

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 669  LVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 725

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 726  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 785

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 786  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 845

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 846  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTVNPW 905

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 906  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 951



 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 23/225 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--AAMLEFVSYEFDP 83
           IP   ++Q   +  F+          ++GL         I   +      L    Y+   
Sbjct: 4   IPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTNQEIDFELFLERYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI  +          + I+EQ+I +G +PLMT  G 
Sbjct: 54  PSIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTILIGKIPLMTSLGA 106

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E D K  I 
Sbjct: 107 FIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGGRLELEIDRKTRIW 163

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 164 VRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKQI 208


>gi|89142870|emb|CAJ76106.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 188/420 (44%), Positives = 278/420 (66%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVGDTAKKNPLDFKGSTEEILNYYYATETIYLQSAADFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            +G+ +++  +K T   +K L+   +  L I  D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KSGDLIVKKNRKFTRAAIKKLEAAKMTKLPIDVDELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+   +I++  +L++D++N   Y+R TL+ DK +  + A+++IYR +RPG   
Sbjct: 180 VSQEKVDELLKRDIKEFKVLFIDNLNVGPYLRETLMLDKIESPEQAIMEIYRRLRPGHPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F+ LFF+ ++YDLS VGR+K+N + +L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETATNLFSNLFFNPERYDLSKVGRLKLNFKFSLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|186885975|gb|ACC93395.1| RNA polymerase beta subunit [Youngia japonica]
          Length = 1024

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/396 (32%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTVNPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  + + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFIVSEKTFQINRKE 1023



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 252/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       +   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKQIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V +D++TS HI ++E+       G E +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYDDIYTSFHIRKYEIQI---NQGTERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTVNPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPPIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKTRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKQI 172


>gi|260677410|ref|YP_003208178.1| RNA polymerase beta subunit [Coix lacryma-jobi]
 gi|209361348|gb|ACI43263.1| RNA polymerase beta subunit [Coix lacryma-jobi]
          Length = 1075

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 124/306 (40%), Positives = 176/306 (57%), Gaps = 40/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++  STG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 949  KSYILKLIHQVDEKIHGHSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 1008

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++      KN 
Sbjct: 1009 EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1068

Query: 1372 AKMEEI 1377
                E 
Sbjct: 1069 QVNRED 1074



 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 236/699 (33%), Positives = 381/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  L   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTLISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEEVQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  VGR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRVGRRNMNRRLNLDIPQNNTFLLPRDVLAATDHLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  L+Q+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLAQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G IE+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSIESPFYEISEKAKEKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNQGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISSDSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVAHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT+ IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKQIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R   D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPFDIMVRVYILQKREIKVGDK 824



 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     + ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERNAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   +I D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTLISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|241948201|ref|XP_002416823.1| DNA-dependent RNA polymerase II component, putative [Candida
            dubliniensis CD36]
 gi|223640161|emb|CAX44408.1| DNA-dependent RNA polymerase II component, putative [Candida
            dubliniensis CD36]
          Length = 1234

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 171/985 (17%), Positives = 318/985 (32%), Gaps = 159/985 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 362  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 421

Query: 485  SIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I   +     +         + ++ +   +     +               +SQ+    
Sbjct: 422  DIYNYMQRCVENGGDFNVTLAVKSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRY 481

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 482  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 537

Query: 590  ARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++     E     + D   +V  D V  +A +    ++      +  D +   + +  
Sbjct: 538  TCISVGTPSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRE 597

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLL 704
                 ++      I D  +   K          P    DD+          + ++ +  L
Sbjct: 598  LRRSGDLSPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPESETKGELKITKEHIKQL 657

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                       +    + + +++VA   GIVE VDA       +    D   +  D    
Sbjct: 658  LRSDELDEDDEDYDNTRYTWSSLVA--DGIVEYVDAEEEETIMIAMTPDDVKASKDSVSE 715

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYNF 823
             + Q+  Q       P    G  ++     +    T      ++   +  + +P+  +N 
Sbjct: 716  SE-QQKIQLEEQELDP----GKRIKPTTSGSTHTYTHCEIHPSMILGVAASIIPFPDHNQ 770

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +   + +  + V                               +  
Sbjct: 771  SPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DTMAN 801

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 802  ILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RS 860

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +D  +R      + +E   +    + + L    Y +L E   I  G        
Sbjct: 861  LFFRSYMDIEKRQGM---KALETFEKPTRSDTLRLKHGTYEKLDEDGLIAPGVRVSGEDI 917

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+T + +D      R+Q+         ++     +  Q               +   
Sbjct: 918  IIGKTTPIPADAEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------VLLT 962

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 963  TNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFTAEGIVPDL 1017

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM V  + E  L       G +  +          IS L            
Sbjct: 1018 IINPHAIPSRMTVAHLIECLLSKVSSLSGFEGDASPFTDVTTEQISTLLR---------- 1067

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                           V     +G  +   VF                             
Sbjct: 1068 -----DHGYQSRGFEVMYNGHTGKKLMAQVF----------------------------- 1093

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
                       G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME  
Sbjct: 1094 ----------FGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERD 1143

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIV-------------AGNDTFETGT 1343
            C+ A+GAA  L+E L   SD     V G   +   I                 + ++   
Sbjct: 1144 CMIAHGAAGFLKERLMEASDAFRVHVCGMCGLMSVIANLKKNQFECRSCKNKTNIYQIHI 1203

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
            P +  +L +E+ A+ +S  L   R+
Sbjct: 1204 PYAAKLLFQELMAMNISPRLYTERS 1228



 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 142/1037 (13%), Positives = 289/1037 (27%), Gaps = 218/1037 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-----------FSGAAMLEFV 77
           L+  Q  S+D F+  +I      +  L         I              +    + F 
Sbjct: 38  LVSQQLDSFDEFVETSIQELVWEDSHL---------ILDQPAQHTSEKDHENKRYEITFG 88

Query: 78  SYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR-LIVFDVDEFTGAKSIKDIK 126
                 P               +   R+LTY+ PL + +   +    D       ++ I+
Sbjct: 89  KIYISKPSQTEGDGSTHAVFPQEARLRNLTYSSPLYVDMTSKVFKSDDNKRKDNELEWIQ 148

Query: 127 EQ-------SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
           E+        +++G +P+M +                         G FVI G ++++++
Sbjct: 149 EEPDKDTETKVFLGKVPIMLRSKFCMLRDLAEHEFYELKECPYDMGGYFVINGSEKVLIA 208

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------ 207
           Q  RS          + +    + +   I    ++G  +      K  ++ R D      
Sbjct: 209 QE-RSAANI--VQVFKKAAPSPISHVAEIRSAIEKGSRLISSMQIK--LYGR-DEKGVSG 262

Query: 208 RRRK---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           R  K         +P+     ALG+  + +IL          Q  +     +    ++  
Sbjct: 263 RTIKATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQE 322

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +    G   I   K++     K + +K +       +           +    
Sbjct: 323 REVALDFIGRR-GVLGIRREKRIQY--AKDILQKELLPNITQEEGFETRKAF--FLGYMV 377

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             + + A +  +    +      +                + N       K  KD    +
Sbjct: 378 NRLLLCALERKEPDDRDHFGKKRLDL----------AGPLLANLFRILFKKLTKDIYNYM 427

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            R +  G    F+V  ++ +    D  +Y L   G      +         + + +    
Sbjct: 428 QRCVENGG--DFNVTLAVKSQTITDGLRYSL-ATGNWGEQRKAMSSRAGVSQVLNRYTYS 484

Query: 438 AIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMER 484
           + +  L        R+GK       +  +  +    E  + Q          +  + +  
Sbjct: 485 STLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCISVGT 544

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             +  +  +    +   +         +   F     +    +    +  +   RR   L
Sbjct: 545 PSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRELRRSGDL 604

Query: 545 GQG-GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR----V 592
                + R     E        R   P       P   ++G        +    R     
Sbjct: 605 SPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPESETKGELKITKEHIKQLLRSDELD 664

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 +              V Y+ A EEE   IA     +        E    +   E
Sbjct: 665 EDDEDYDNTRYTWSSLVADGIVEYVDAEEEETIMIAMTPDDVKASKDSVSESEQQKIQLE 724

Query: 653 EILVPR------------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  +                    +  P  ++ +AAS+IPF +++ S R      M +QA
Sbjct: 725 EQELDPGKRIKPTTSGSTHTYTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA 784

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                                                   + + + 
Sbjct: 785 MGVFLTNYSV-----------------------------------------RMDTMANIL 803

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA   + G
Sbjct: 804 YYPQKPLGTTRSMEYLKFR------------------------ELPAGQNAIVAIACYSG 839

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDSM++++  +   +F S+    +  + +   +   E        D   +     + 
Sbjct: 840 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDIEKRQGMKALETFEKPTRSDTLRLKHGTYEK 899

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G+I  G  V+  DI++GK TP         ++        +    RD S  + S  
Sbjct: 900 LDEDGLIAPGVRVSGEDIIIGKTTPIPADAEELGQRT-------QYHTKRDASTPLRSTE 952

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG V  V +       K
Sbjct: 953 SGIVDQVLLTTNGDGAK 969


>gi|285310164|emb|CBH41063.1| DNA-directed RNA polymerase beta subunit [Pseudomonas
           nitroreducens]
          Length = 386

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 237/386 (61%), Positives = 306/386 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V +G V++D+V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +
Sbjct: 121 YRVVKEGLVSDDIVFLSAIEEADHVIAQASATLNEKGELIDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+ GD+V R+DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+
Sbjct: 301 VQKGDQVSRSDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTT 360

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN 867
           IHI+E   +ARDTKLGPEEIT DIPN
Sbjct: 361 IHIQELTCVARDTKLGPEEITADIPN 386


>gi|255024261|ref|ZP_05296247.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J1-208]
          Length = 269

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 100/293 (34%), Positives = 156/293 (53%), Gaps = 30/293 (10%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
             +      +   L+           +  GE   +++ + L        K   
Sbjct: 223 TLEKDNTDNAEKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYD 269



 Score = 49.7 bits (117), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/59 (40%), Positives = 35/59 (59%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YD
Sbjct: 211 IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYD 269


>gi|167519879|ref|XP_001744279.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777365|gb|EDQ90982.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1166

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 189/1143 (16%), Positives = 347/1143 (30%), Gaps = 233/1143 (20%)

Query: 271  EQVIESGKKLTSGLLKSLKE--KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
              ++E   + TS ++  +     G      T   +    +     +     ++   G   
Sbjct: 210  RSIVEDSNRPTSTMMVKMLRGGSGGTKGRATFGRVIHASLPYIRQDIPVVVLFRALGFED 269

Query: 329  DEKSLEEIFHS--EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            D   LE I +   ++  + +L              +  D    R  A + + + MR    
Sbjct: 270  DRSILEHIIYDFDDMEMMELLKPSLDEAFVVQTREVALDLIGRRSMAAVGMSKDMR---- 325

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                     F       +      VG      +         R ++              
Sbjct: 326  -------VRFARDILQKEMLPHIGVGPQCEQAKAFFLGYMVHRTLQAALR---------- 368

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLI 504
               +  +DD D+ GN+R+   G ++   +R    ++ + +  K           M   L+
Sbjct: 369  ---RRELDDRDHYGNKRLDLAGSLVAYLFRTLFKQLTKKLTRKVTDLVNRNHKFMVITLL 425

Query: 505  NAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            + + + S +     +               +SQ+   +   S ++H RRL++     + R
Sbjct: 426  DVEILGSGLRYSLATGNWGDQKKAHEARAGVSQVLNRLTFASTLSHLRRLNS----PIDR 481

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 + R +H TH+G ICPAET EGH +GLV +L+  A +            V D    
Sbjct: 482  TGKIAKPRQLHNTHWGYICPAETPEGHAVGLVKNLSLMASLTVGSDDTP----VHDLLGA 537

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            + + YL             +         T   VF       I    +++          
Sbjct: 538  SGLDYL-------------DRLPSRSAIKTATKVFVNGNWVGIHSHPDEL---------- 574

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            V+     +    +  ++ V +  N++ +                E  +   SG     + 
Sbjct: 575  VTTMRQYLLDAAHSVASEVSIFRNIRER----------------EVHIVTDSGRTT--RP 616

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              IV + DA R         +    +    +             + QR +V   + +  N
Sbjct: 617  LLIVNKDDANRCRFALKNSHVMALRNDQMSWTH-----------LVQRGVV---EYIDVN 662

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEV 849
            +      + D G L            +       SM+  I   ++            ++ 
Sbjct: 663  EEETTMIAMDQGTLEETSYCN----TYTHCEIHPSMILSICASIIPFPDHNQSPRNTYQS 718

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                  +G                 ++    +  V        +    +     + +   
Sbjct: 719  AMGKQAMGVYITN-----------FHVRMDTLAHVLYYPQRPLVQTRSMNYLRFAELPAG 767

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
               +  I      +  D+ +     V   +     +  +       S   ER +I  + +
Sbjct: 768  INAIVGIMTYTGYNQEDSVIMNRYSVERGLFRSVFYRSYAA-----SEHSERGEIIKIDK 822

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
               +  + + R  Y +L +     + +  P             + E P            
Sbjct: 823  PSRENCIGMRRANYDKLED-----DGIVAPGIRVSGDDAIVGRLLELP------------ 865

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              +   ++   ++E     L  R             +     + VK+ V   R  Q GDK
Sbjct: 866  --EATRQASGGRFEKRDKSLFLRSSESGIIDGVMISVNQKGEKFVKIRVRSVRTPQIGDK 923

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG        EDMPF   G   DI++NP  +PSRM +G + E  LG +    G
Sbjct: 924  FASRHGQKGTCGMQYAQEDMPFAASGVVPDIIVNPHAIPSRMTIGHLIECLLGKSASHSG 983

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                                                                     +TP
Sbjct: 984  TIGD-----------------------------------------------------ATP 990

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F   +   +  +L   +    G  ++Y+G TG      V +G  Y  +L HMV DK++A
Sbjct: 991  -FTKVNVTDVADILEGYNFQRYGNEVMYNGFTGRKMQAQVFLGPTYYQRLKHMVDDKIHA 1049

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DV 1322
            R+ G    +T+QP+ G+S  GG R GEME  C+ A+GAA  L+E L   SD       DV
Sbjct: 1050 RARGPLQNLTRQPMEGRSRDGGLRFGEMERDCMIAHGAAQFLRERLFEVSDPYSLHVCDV 1109

Query: 1323 VG-----------------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             G                 R                  P +  +L +E+  + +   +  
Sbjct: 1110 CGLPCVAKLEKNEFECTRCRNST--------RVSRIRLPYACKLLFQELMTMSVVPRMMT 1161

Query: 1366 SRT 1368
              +
Sbjct: 1162 DDS 1164



 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 148/1018 (14%), Positives = 293/1018 (28%), Gaps = 231/1018 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP-KFD 87
           L+  Q  S+DHF+   +          Q   K+  PI    G   L+++S E + P K  
Sbjct: 26  LVRQQLDSFDHFITYTV----------QKIIKNSPPIE-VQGR--LQYLSNEIEEPPKHT 72

Query: 88  ------------------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
                                    +DC  R+LTY   ++  +   V             
Sbjct: 73  ISFGQAGFALPQHKEEDGNYDHVFPNDCRLRNLTYQSLMQCEITHTV-----EQKNPETG 127

Query: 124 DIKEQSIYMGDLPLMT-------------------------KDGTFVIKGIQRIVVSQLH 158
           ++      +G +P+M                            G F+I G ++++++Q  
Sbjct: 128 EVTTTPALLGKVPMMLRSKYCTLNKMETFRDFYDINECPLDPGGYFIINGSEKVLIAQEK 187

Query: 159 RSPG-IHFDHDKGRAS-------------------------------LSGKLLYACRIIP 186
            +   ++    K                                     G+  +  R+I 
Sbjct: 188 MAGNTVYVFEKKDSKHMFVTEMRSIVEDSNRPTSTMMVKMLRGGSGGTKGRATF-GRVI- 245

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
                         + ++R D    +PV     ALG + +  IL          +  +  
Sbjct: 246 -----------HASLPYIRQD----IPVVVLFRALGFEDDRSILEHIIYDFDDMEMMELL 290

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              L  A ++   +V+  L+   +   V  S           L+++ +  +G+   C   
Sbjct: 291 KPSLDEAFVVQTREVALDLIGRRSMAAVGMSKDMRVRFARDILQKEMLPHIGVGPQCEQA 350

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
                  +   T +  +   ++ D      +        +  L+              VT
Sbjct: 351 KAFFLGYMVHRTLQAALRRRELDDRDHYGNKRLDLAGSLVAYLFRTLFKQLTKKLTRKVT 410

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D        ++     +   ++    +  S+    + D  K   +  G  ++  RL   +
Sbjct: 411 DLVNRNHKFMVIT---LLDVEILGSGLRYSLATGNWGDQKKAHEARAGVSQVLNRLTFAS 467

Query: 425 PDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 R     D    I     L N                     ++KN   +  L +
Sbjct: 468 TLSHLRRLNSPIDRTGKIAKPRQLHNTHWGYICPAETPEGHAVG---LVKNLSLMASLTV 524

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                     +    +   D + ++  +    + F +     +  H +    +T  R+  
Sbjct: 525 GSDDTPVHDLLGASGLDYLDRLPSRSAIKTATKVFVNGN--WVGIHSHPDELVTTMRQY- 581

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS---SLTSFARVNAYGF-I 598
            L     + A      R++       +  +  +    + +     +   FA  N++   +
Sbjct: 582 -LLDAAHSVASEVSIFRNIREREVHIVTDSGRTTRPLLIVNKDDANRCRFALKNSHVMAL 640

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
                          V Y+   EEE   IA    +L+E                      
Sbjct: 641 RNDQMSWTHLVQRGVVEYIDVNEEETTMIAMDQGTLEE------------------TSYC 682

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                 +  P  ++SI AS+IPF +++ S R      M +QA+ +               
Sbjct: 683 NTYTHCEIHPSMILSICASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV-------- 734

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                                               + + V  Y               Q
Sbjct: 735 ---------------------------------RMDTLAHVLYYP--------------Q 747

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV+                    +L  G N +V  M + GYN EDS++++   V   +
Sbjct: 748 RPLVQ----------TRSMNYLRFAELPAGINAIVGIMTYTGYNQEDSVIMNRYSVERGL 797

Query: 839 FTSIHIEEF---EVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
           F S+    +   E   R   +  ++ +R +   +       +++ GI+  G  V+  D +
Sbjct: 798 FRSVFYRSYAASEHSERGEIIKIDKPSRENCIGMRRANYDKLEDDGIVAPGIRVSGDDAI 857

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VG++    E+                  + RD SL + S  SG +  V I      +K
Sbjct: 858 VGRLLELPEATRQASGG---------RFEKRDKSLFLRSSESGIIDGVMISVNQKGEK 906


>gi|156084492|ref|XP_001609729.1| DNA-directed RNA polymerase, beta subunit family protein [Babesia
            bovis]
 gi|154796981|gb|EDO06161.1| DNA-directed RNA polymerase, beta subunit family protein [Babesia
            bovis]
          Length = 1207

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 165/1004 (16%), Positives = 304/1004 (30%), Gaps = 226/1004 (22%)

Query: 407  DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
                + R      +  +   + R  +   +  ++  L+  R G+   DD D+ G +R+  
Sbjct: 380  YAKDLLRQHFLPHVGTEPGCESR--KCYFLGYMVHRLLLSRLGRIPEDDRDHFGKKRLDL 437

Query: 467  VGEMLKNQYRLGLLRMERS---IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
             G ++ + +     +M +    I ++      +  +   + +A  +   +     +    
Sbjct: 438  AGSLMASSFGTLFRKMVKDTKRILQQQIDSGREFDVAGAVRSATQITHGLQYQLLTGNWG 497

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+   +   S ++H RRL+      + R     + R +H TH+G IC
Sbjct: 498  RDRDGKVVRTGVSQVLNRLTFASYLSHLRRLNT----PLGREGKIAKPRQLHNTHWGMIC 553

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIA 628
            PAET EG  +GLV +L     ++      T    +C+  +   ++V      +    +I 
Sbjct: 554  PAETPEGQAVGLVKNLALMCFISVGTAASTINEFLCEWGMDSLDEVPPEVIKDRIKIFIN 613

Query: 629  QANS-SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                   DE  S  + L+  R  G          D +    K       ++ P L  ++ 
Sbjct: 614  GTWVGCFDEAESLVKTLLELRRRGNIAAETSIVCDIVSQEVKIFTDAGRAMRPLLIVENG 673

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            N + +      +           +           SG           E VD     +  
Sbjct: 674  NTLAITKTDIARLDNNECNWDGLI----------ESGVV---------EYVDCEEEEMCM 714

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +    +   +                                        PS  LG    
Sbjct: 715  IAMFAEDLKNNST--------------------------YCNTYTHCEIHPSMILG---- 744

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+   N       S R   +       +  +                    
Sbjct: 745  ---VCASIIPFPDQNQ------SPRNTYQSAMGKQAMGVYATNF---------------- 779

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                   N+    +  +        +    +       +      + AI      +  D+
Sbjct: 780  -------NLRMDPLSHLLYYPQKPLVCTRSMEFLRFRELPAGINAIVAIMCYTGYNQEDS 832

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL- 986
             +   S +   +        +  ++      V    +E   R      V L R  Y++L 
Sbjct: 833  LIMNQSSIDRGLFRSAFNRTYVSEE----KHVGSTVVERFERPNPATCVGLKRGDYTKLD 888

Query: 987  --MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                +  G   +       +++  + +      +         +  V   V         
Sbjct: 889  ADGLVQPGSRVLGDDVIIGRTSACNDEEDENLRQDCSCCLRTSENGVVDTVLI------- 941

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       R  KV V   R  Q GDK A RHG KG +    
Sbjct: 942  --------------------SSNAKGSRFAKVKVRSIRVPQIGDKFASRHGQKGTIGMTY 981

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              ED+PF  +G   DI++NP  VPSRM +G + E  +G      G +             
Sbjct: 982  RTEDLPFTCEGIVPDIIMNPHAVPSRMTIGHLVECLVGKVGACCGMEGD----------- 1030

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     + +   L 
Sbjct: 1031 ------------------------------------------ATP-FSKLTVQHVAERLF 1047

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                 + G   L+ G TGE     + +G  Y  +L HMV DK++AR+ G  +++T+QP  
Sbjct: 1048 ECGYGKHGNEALHCGFTGEMIVSKIFIGPTYYQRLKHMVEDKIHARARGPVTMLTRQPTE 1107

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR--------------- 1325
            G+S  GG R GEME  C+ ++GAA +L+E L  +SD     V  R               
Sbjct: 1108 GRSRDGGLRFGEMERDCMISHGAAKMLKERLFDQSDAFRIHVCDRCGLCCVADLNRNNFE 1167

Query: 1326 -----TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                  +         +  +   P +  +L++E+ A+ +   L 
Sbjct: 1168 CTACDNKT--------NISQVTIPYACKLLIQELMAMAIYPKLL 1203



 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 105/842 (12%), Positives = 227/842 (26%), Gaps = 158/842 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT----------AFSGA---AMLE 75
           L+  Q  S++ F+   +          Q       PI                     L+
Sbjct: 74  LVHQQIESFNDFVTYRM----------QETIDQHPPIEITPQPQYHPEDERENNIVYKLK 123

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
           F     + P  +            +   R+LTY+  + + +    +  DE T  +++++ 
Sbjct: 124 FGQLSLNKPCVEEMAGVLKHIWPQEARLRNLTYSSQIYVDIEQKTYLRDENTNTETLQET 183

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
           I    I +G +P+M K                         G F++ G +R+++ Q  R 
Sbjct: 184 ITYPRIELGRIPMMLKSAYCWTKDISEDDLADVGECPFDEGGYFIVNGGERVLIGQE-RM 242

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE--------------------FDSKD 200
              +    K +     K      I        +                      F S  
Sbjct: 243 ANNYIYIFKKKQPS--KYSLVAEIR----SQPEFSQGTTPFSIMMKSTSGIAGNRFKSHG 296

Query: 201 II-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            +     +++ D    +P+     ALG  ++ +IL     +IVY          +  +  
Sbjct: 297 QLVGSIPYLKSD----IPIAILFRALGCVADRDILQ----RIVYDFEDKQMLTLMRPSLE 348

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-----------SDCL 303
                 +  +     G++    G  L + +     +  ++   +                
Sbjct: 349 ETADYSTQEMCLDFIGKRGPTVGAPLETRV--QYAKDLLRQHFLPHVGTEPGCESRKCYF 406

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  V   +++   G I  +  D   +K L+            L+   V +   I    +
Sbjct: 407 LGYMVHRLLLS-RLGRIPEDDRDHFGKKRLDLAGSLMASSFGTLFRKMVKDTKRILQQQI 465

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
               +       D+   +R     T  +   +    +       +   G  ++  RL   
Sbjct: 466 DSGREF------DVAGAVRSATQITHGLQYQLLTGNWGRDRDGKVVRTGVSQVLNRLTFA 519

Query: 424 TPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
           +      R          I     L N    +         +      ++KN   +  + 
Sbjct: 520 SYLSHLRRLNTPLGREGKIAKPRQLHNTHWGMICPAETPEGQAVG---LVKNLALMCFIS 576

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +  +       +    +   D +  + +   +  F   + +   +E  + +  +   RR 
Sbjct: 577 VGTAASTINEFLCEWGMDSLDEVPPEVIKDRIKIFINGTWVGCFDEAESLVKTLLELRRR 636

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA----RVNAYGF 597
             +            +   +       + P    E  N   ++            N  G 
Sbjct: 637 GNIAAETSIVCDIVSQEVKIFTDAGRAMRPLLIVENGNTLAITKTDIARLDNNECNWDGL 696

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           IE+             V Y+   EEE   IA     L  + ++                 
Sbjct: 697 IES-----------GVVEYVDCEEEEMCMIAMFAEDLKNNSTYCNTY------------- 732

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG--TGM 715
                  +  P  ++ + AS+IPF + + S R      M +QA+ +              
Sbjct: 733 ----THCEIHPSMILGVCASIIPFPDQNQSPRNTYQSAMGKQAMGVYATNFNLRMDPLSH 788

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                +       +       ++ A    I ++      +     I       R    + 
Sbjct: 789 LLYYPQKPLVCTRSMEFLRFRELPAGINAIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSA 848

Query: 776 VN 777
            N
Sbjct: 849 FN 850


>gi|312217766|emb|CBX97713.1| similar to DNA-dependent RNA polymerase II second largest subunit
            [Leptosphaeria maculans]
          Length = 1360

 Score =  379 bits (972), Expect = e-102,   Method: Composition-based stats.
 Identities = 160/995 (16%), Positives = 317/995 (31%), Gaps = 177/995 (17%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +      +I  L+    G+   DD D+ G +R+   G ++ N +R+  L++ + 
Sbjct: 485  EGQDTRKAYFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKD 544

Query: 486  I--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            +    +           Q  + A  + + +     +               +SQ+     
Sbjct: 545  VFKYLQRCVESNQDFNVQMAVKASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 604

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      V R     + R +H +H+G +CPAET EG   GLV +L+   
Sbjct: 605  YASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMC 660

Query: 591  RVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+          +    + ++  +     + +    ++      +  +      +V   
Sbjct: 661  YVSVGSDASPIIDFMTQRNMQLLEEYDQNQSPDATKIFVNGVWVGVHSNPHQLVSVVQEL 720

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVL-----MGCNMQRQAV 701
                 +      I D  D   K        + P F+  +D  +           + R+  
Sbjct: 721  RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVIENDIRKPNRHQLIFTKEISRKLT 780

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
               + +    G   E + A + G      + G++E +DA       +    +   +  D+
Sbjct: 781  YEQETQDQRQGWSEEDIAAATYG-WKGLIQDGVIEYLDAEEEETAMITFSPEDLDAWRDM 839

Query: 762  ----YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                    +  +  +    + +P  K    V         P+  LG       +  + +P
Sbjct: 840  KTGRAPDERRLKDPKFRLSSIKP--KPDTRVHAYTHCEIHPAMILG-------ICASIIP 890

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +  ++      +                            
Sbjct: 891  FPDHNQSPRNTYQSAMGKQAMGVALTNYALRMETMMN----------------------- 927

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
                  V             +       +   +  + AI      +  D+ +   S +  
Sbjct: 928  ------VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIMNQSSIDR 981

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   ++ +R   +    +E   +    + + L    Y +L +   +  G  
Sbjct: 982  GLF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVR 1037

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +++D      ++           ++     +  Q             
Sbjct: 1038 VSGDDIIIGKTAPIATDAQELGQKTTLHTKRDVSTPLRSTENGIVDQ------------- 1084

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            LR VKV     +  Q GDK A RHG KG +      EDMPF ++
Sbjct: 1085 -------VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSRE 1137

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G++  +          IS        
Sbjct: 1138 GLTPDLIINPHAIPSRMTIAHLVECLLSKVGAIEGREGDATPFTDITVDQIS-------- 1189

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                              +L      K G  +                        +G +
Sbjct: 1190 -----------------EILESKGYQKRGFEIM----------------------YNGHT 1210

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   G+     + +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 1211 -------GKKMRTQIFLGPTYYQRLRHMVDDKIHARARGPLQILTRQPVEGRARDGGLRF 1263

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIV----AGND------ 1337
            GEME  C+ A+GAA  L+E L   SD       D+ G      S +     G        
Sbjct: 1264 GEMERDCMIAHGAAAFLKERLFTVSDAYTVHVCDICG----LMSPIAQLKKGQYECRPCQ 1319

Query: 1338 ----TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                  +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1320 NKTRISQIHIPYAAKLLFQELLAMNIATRMFTDRS 1354



 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 136/1051 (12%), Positives = 289/1051 (27%), Gaps = 231/1051 (21%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--------AAMLEFVSYE 80
            L+  Q  SYD F   N   D     G  +           +            + F    
Sbjct: 137  LVSQQLDSYDEF-TRNTIQDIVKENG--SVILEQNTPYDPNEDENPIIKRRYEITFGRVY 193

Query: 81   FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD------ 124
               P               +   R+LTY+  +   +   +    E       +D      
Sbjct: 194  LARPTHTEGDGTTVQLYPHEARLRNLTYSGAMLADISNRIMVAREHNAMVEGEDDDLDGG 253

Query: 125  --------IK--------EQS----IYMGDLPLMTKD----------------------- 141
                    I+        E+     +++G LP+M +                        
Sbjct: 254  YTAGGATQIRWEREDMPGEEEAAARVFIGKLPVMLRSELCHLRNQSDADLFALNECPYDQ 313

Query: 142  -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
             G FVI G ++++++Q  RS        + +    G + +   I    ++G  +   F  
Sbjct: 314  GGYFVINGSEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFTI 369

Query: 199  K---DII----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVY 238
            K   + +                +V+ +    +P+     ALG+   EEILS        
Sbjct: 370  KWAENSLAGGKRVPGPFAYATLPYVKSE----IPMAIVFRALGIVSDEEILSHIVYDRTD 425

Query: 239  SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +Q  +     +    ++   + +   +     +Q  +  +   +  +  ++ + +  +  
Sbjct: 426  TQMLELLKPSIEEGSVVQDRESALDFIARRGAQQATKDRRLKFARDI--MQREFLPHISQ 483

Query: 299  T------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-S 351
                        G  +   ++    G    +  D   +K L+           IL++  +
Sbjct: 484  KEGQDTRKAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLT 542

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +   Y++  + ++++ + + A+           + T  +  S+    + D  K   +  
Sbjct: 543  KDVFKYLQRCVESNQDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKA 594

Query: 412  GRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            G  ++  R    +      R          +     L N    +         +   + +
Sbjct: 595  GVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVK 654

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L     + +      I + ++  ++  +   D   +               +       
Sbjct: 655  NLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQSPDATKIF---VNGVWVGVHSNPH 711

Query: 530  NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG----------- 577
              +S +   RR   L  +  + R     E + +       + P    E            
Sbjct: 712  QLVSVVQELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVIENDIRKPNRHQLI 770

Query: 578  --HNIGLVSSLTSFARVNAYGFIETPY----RKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
                I    +     +    G+ E                  + YL A EEE   I  + 
Sbjct: 771  FTKEISRKLTYEQETQDQRQGWSEEDIAAATYGWKGLIQDGVIEYLDAEEEETAMITFSP 830

Query: 632  SSLDEDGSFTEELVFCRCAGEEILV-----------PREKIDFIDASPKQVVSIAASLIP 680
              LD                ++                      +  P  ++ I AS+IP
Sbjct: 831  EDLDAWRDMKTGRAPDERRLKDPKFRLSSIKPKPDTRVHAYTHCEIHPAMILGICASIIP 890

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            F +++ S R      M +QA+ +                                     
Sbjct: 891  FPDHNQSPRNTYQSAMGKQAMGVALTNYAL------------------------------ 920

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                          +   V  Y       +     +  R                     
Sbjct: 921  -----------RMETMMNVLYYPQKPLATTRSMEYLKFR--------------------- 948

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E
Sbjct: 949  ---ELPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLE 1005

Query: 861  ITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                    D   +       +D+ G++  G  V+  DI++GK  P         +K    
Sbjct: 1006 QFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIATDAQELGQKT--- 1062

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                     RD S  + S  +G V  V    
Sbjct: 1063 ----TLHTKRDVSTPLRSTENGIVDQVLFTT 1089


>gi|115604926|ref|YP_784378.1| RNA polymerase beta subunit [Drimys granadensis]
 gi|122164449|sp|Q06H05|RPOB_DRIGR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|112032654|gb|ABH88289.1| RNA polymerase beta subunit [Drimys granadensis]
          Length = 1071

 Score =  378 bits (971), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/390 (34%), Positives = 203/390 (52%), Gaps = 49/390 (12%)

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            ++ G    +G     K T  ++   S  P  +  +  +  +        LK+       +
Sbjct: 727  VMLGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRV 786

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            ++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +D
Sbjct: 787  IDVRWIQK----GGGSSYNP---EMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQD 839

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S  
Sbjct: 840  MPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRK 899

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
              F E    +                               VF+                
Sbjct: 900  LVFPELYEASKQTANPW------------------------VFE---------------P 920

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
            +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ 
Sbjct: 921  EYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAK 980

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESF 1347
            +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G         PESF
Sbjct: 981  QGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPEDAPESF 1040

Query: 1348 NVLVKEMQALGLSID--LENSRTKNSAKME 1375
             +LV+E+++L L ++  L + +     + E
Sbjct: 1041 RLLVRELRSLALELNHFLVSEKNFQIHRKE 1070



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 253/776 (32%), Positives = 401/776 (51%), Gaps = 40/776 (5%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
             V          N     K   R++A+L+ Y+      GD              FF   +
Sbjct: 197  NVCYPEIFLSFPNEKEKKKIGSRENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256  CELGRIGRRNMNWRLNLDIPQNNLFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
            SV ++L++Q+ L L+R+E  ++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 316  SVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 375

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376  QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             SL   AR+   G IE+P+ ++         VYLS   +E   +A  NS     G   E+
Sbjct: 436  GSLAIHARIGYLGSIESPFYEISQRSKEVQTVYLSPNRDEYYMVAAGNSLALNQGIQEEQ 495

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496  VVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             ++E   VGTG+E   A  SG + +A++ G +   D  +IV+                  
Sbjct: 556  SRSEKCIVGTGLERQAALDSGVSAIAEQDGKIIYTDTDKIVLSGNGDTAIS-------IP 608

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LV++MPW GYNF
Sbjct: 609  LVIYQRSNKNTCMHQKPQVPRGKCLKKGQILADGAATVGGELALGKNVLVSYMPWEGYNF 668

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ 
Sbjct: 669  EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDINGIVM 728

Query: 884  VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +G+ +  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 729  LGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVID 788

Query: 942  VRIFNRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
            VR   + G         R    ++ +I++  +      ++ +I        +  +  G  
Sbjct: 789  VRWIQKGGGSSYNPEMIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTP 848

Query: 995  AVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VES 1037
                       + ++   I E           + ++ A  DE+ ++            E+
Sbjct: 849  VDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFPELYEA 908

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 909  SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 962



 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y    
Sbjct: 12  IPGFSQIQFEGFFRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVDTYRLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGSIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFPNEKEKKKIGSRE 220


>gi|52694285|emb|CAG37982.1| RNA polymerase beta subunit [Pseudomonas fragi]
          Length = 387

 Score =  378 bits (971), Expect = e-102,   Method: Composition-based stats.
 Identities = 235/387 (60%), Positives = 304/387 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDATRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT
Sbjct: 301 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPN 867
           +IHI+E   +ARDTKLGPEEIT DIPN
Sbjct: 361 TIHIQELTCVARDTKLGPEEITADIPN 387


>gi|194033140|ref|YP_002000478.1| RNA polymerase beta subunit [Brachypodium distachyon]
 gi|193075548|gb|ACF08631.1| RNA polymerase beta subunit [Brachypodium distachyon]
          Length = 1076

 Score =  378 bits (971), Expect = e-102,   Method: Composition-based stats.
 Identities = 123/306 (40%), Positives = 178/306 (58%), Gaps = 42/306 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 809  MVRVYILQKREIKVGDKVAGRHGNKGIISKILTRQDMPYLQDGTPVDVVFNPLGVPSRMN 868

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 869  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKETKNPW------- 921

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 922  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 949

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 950  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRVGEMEVWALEGFGVAHILQ 1009

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID--LENSRTK 1369
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++  L + +  
Sbjct: 1010 EILTYKSDHLIARQEILNATIWGKRIANHEDPPESFRVLVRELRSLALELNHFLVSEKNF 1069

Query: 1370 NSAKME 1375
               + E
Sbjct: 1070 QVNREE 1075



 Score =  348 bits (892), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 236/700 (33%), Positives = 383/700 (54%), Gaps = 29/700 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++ G G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDVLAATDQLIGMKFGTGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV------CEFF 517
           +RSV ++L++Q+ L L R++ ++++ I  V I    P       P  +++        FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPHTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GAYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTND----VVYLSAMEEENRYIAQANS 632
            N+GL  SL   A+++  +G +E+P+ ++   K        VVYLS   +E   IA  NS
Sbjct: 434 INVGLTGSLAIHAKIDHLWGSVESPFYEISAEKAKEKKERQVVYLSPNRDEYYMIAAGNS 493

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM
Sbjct: 494 LSLNQGIQEEQVVPARYRQEFLTIVWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALM 553

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   D+ RI++       
Sbjct: 554 SSNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTDSHRILL------- 606

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+L
Sbjct: 607 -SSSGKTISIPLVNHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVL 665

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEE 871
           VA+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E 
Sbjct: 666 VAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEH 725

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSL 929
            L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL
Sbjct: 726 LLRNLDRNGVVRLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSL 785

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 KLPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 825



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFLTIKDPDHEIAFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|34582099|gb|AAQ76005.1| RpoB [Tagetes erecta]
          Length = 824

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 136/460 (29%), Positives = 218/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI   +    +E   L+ +
Sbjct: 409  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGSERVTNEIPHLEVH 468

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 469  LLRNLDKNGIVMLGSWVETGDILVGKLTPQIVKESSYAPEDRLLRTILGMRVYTSKETCL 528

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 529  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 582

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 583  IISKILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 642

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 643  ERYEQEASRKLVF-SELYEASKQTTNPWIFEPE--------------------------- 674

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 675  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 723

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 724  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 783

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 784  PTPADAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 823



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 243/725 (33%), Positives = 394/725 (54%), Gaps = 42/725 (5%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
               F   + +L  +GR  MN +LNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4    QKKFFQQRCELGGIGRRNMNRKLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64   HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
            FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124  FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG N+GL+ SL   A++  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184  EGINVGLIGSLAIHAKIGRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
              G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244  NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
            MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D         +  L   
Sbjct: 304  MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTD--------TDKILLSG 355

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             +      L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 356  NADTLRIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAY 415

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            MPW GYNFED++LISER+V ED++TS HI ++E+       G E +T +IP++    L+N
Sbjct: 416  MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI---NQGSERVTNEIPHLEVHLLRN 472

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPS 933
            +D+ GI+ +G+ V  GDILVGK+TP+     +  PE++LLR I G +    ++T L++P 
Sbjct: 473  LDKNGIVMLGSWVETGDILVGKLTPQIVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 532

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISV-----EREQIELLAR--DKDDEQVILDRNIYSRL 986
            G  G V+DVR       D+ E++ S+     ++ +I++  +   +   + I+ + +  + 
Sbjct: 533  GGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILSRQD 592

Query: 987  MEILCG-------QNAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN---- 1034
            M  L          N +  P       +  S L ++     + ++ A  DE+ ++     
Sbjct: 593  MPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRK 652

Query: 1035 ------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   E+ K          E   K++I   + GD     V+ + K ++  K   Q  D
Sbjct: 653  LVFSELYEASKQTTNPWIFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDD 710

Query: 1089 KMAGR 1093
            K+ GR
Sbjct: 711  KIHGR 715


>gi|110288943|gb|ABB47303.2| DNA-directed RNA polymerase beta chain, putative [Oryza sativa
            Japonica Group]
          Length = 1382

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 122/291 (41%), Positives = 173/291 (59%), Gaps = 40/291 (13%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 624  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 683

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 684  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQETSRKLVFSELYEASKQTKNPW------- 736

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF+ PV +G
Sbjct: 737  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEHPVLIG 764

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 765  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 824

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFE-TGTPESFNVLVKEMQALGLSID 1362
            E+LT KSD ++ R  +  + + G         PESF VLV+E+++L L ++
Sbjct: 825  EILTYKSDHLIARQEILNATIWGKRVPNHEDPPESFRVLVRELRSLALELN 875



 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 226/639 (35%), Positives = 361/639 (56%), Gaps = 26/639 (4%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 11  NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 69

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 70  CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 129

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 130 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 189

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 190 GTYPLSQVFDQTNPLTQTVHWRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 249

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL    R++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 250 INVGLTGSLAIHVRIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 309

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 310 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 369

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   ++ +I++        
Sbjct: 370 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTNSHKILL-------- 421

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 422 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 481

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ +  
Sbjct: 482 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEKHL 541

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 542 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 601

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 602 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 640


>gi|324120680|dbj|BAJ78731.1| RNA polymerase II second largest subunit [Ctenocephalides felis]
          Length = 1175

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 169/1084 (15%), Positives = 325/1084 (29%), Gaps = 200/1084 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVVQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGARPGV---TKDKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             I D  D   +          P L  ++   +L   ++                T     
Sbjct: 603  MIRDIRDREIRIYTDAGRICRPLLIVENRTLLLKKRHIDMLKERDY--------TNYGWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            V  +SG           E +D +      +    D                         
Sbjct: 655  VLVASGVV---------EYIDTLEEETVMIAMSPDDLRQE-------------------- 685

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                +              P+  LG       +  + +P+  +N          M  + +
Sbjct: 686  ----RAYAYCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 734

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               ++I  F                           ++    +  V        +    +
Sbjct: 735  G--VYITNF---------------------------HVRMDTLAHVLYYPMKPLVTTRSM 765

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        +F R   D   + + 
Sbjct: 766  EYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFF-RSVFYRSYKDSETKRMG 824

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + EQ E   R           +       I  G           K+  L          
Sbjct: 825  DQEEQFEKPNRQTCQGMRNALYDKLDEDGIIAPGIRVSGDDVIIGKTITL---------- 874

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                       +    +E    ++    +    R        Q    +     +  K+ V
Sbjct: 875  ----------PENDDELEGTTKRHTKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRV 924

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E
Sbjct: 925  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGLMPDIIINPHAIPSRMTIGHLIE 984

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+                                                
Sbjct: 985  CIQGKLGANKGEIGD--------------------------------------------- 999

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G  Y  +
Sbjct: 1000 --------ATPFNDAVNVQKISTLLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQR 1051

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   
Sbjct: 1052 LKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEV 1111

Query: 1319 SD----DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLS 1360
            SD     V            R+  +E    G        +   P +  +L +E+ ++ ++
Sbjct: 1112 SDPYRIHVCNFCGLIAIANLRSNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIA 1169

Query: 1361 IDLE 1364
              L 
Sbjct: 1170 PRLM 1173



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 100/747 (13%), Positives = 224/747 (29%), Gaps = 107/747 (14%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPAIDLQAEAQHTSGEIENP-PRYVLKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    +        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIIMDGKDPV-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV--------RIDR-------------- 208
                GK  +   I       ++        + V         I +              
Sbjct: 213 -----GKFAFKAEIR----SCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAILPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDQEMMEMVKPSLDEAFVVQEQNVALNFIGA 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++     + L+++ +  +G++  C          +      + + A   
Sbjct: 324 RGARPGVTKDKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVH---RLLLAALGR 379

Query: 328 IDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +    +   +  +    P+L          +   +     K           +     +
Sbjct: 380 RELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKI 439

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 440 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 499

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 500 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 556

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 557 APSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVSMIRDIRDREIRIYT 616

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L         ++     +           +  V Y+  +EEE
Sbjct: 617 DAGRICRPLLIVENRTLLLKKR-----HIDMLKERDYTNYGWQVLVASGVVEYIDTLEEE 671

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA +   L                 E            +  P  ++ + AS+IPF +
Sbjct: 672 TVMIAMSPDDL---------------RQERAYAYCTTYTHCEIHPAMILGVCASIIPFPD 716

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           ++ S R      M +QA+ +       
Sbjct: 717 HNQSPRNTYQSAMGKQAMGVYITNFHV 743


>gi|186885799|gb|ACC93307.1| RNA polymerase beta subunit [Ainsliaea macrocephala]
          Length = 1024

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 198/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDYVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------YPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGTIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 425/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLSIPLVMYQRSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC+ Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMPQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---HQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ +++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETDKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDYVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   NFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|186885885|gb|ACC93350.1| RNA polymerase beta subunit [Heterolepis aliena]
          Length = 1024

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 199/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLSLELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 254/828 (30%), Positives = 426/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYETS 1045
              P       +  S L ++     + ++ A  DE+ ++            E+ K      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPESPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  163 bits (412), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPPIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|52694135|emb|CAG30597.1| DNA-directed RNA polymerase beta chain [Pseudomonas marginalis]
          Length = 389

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 235/389 (60%), Positives = 306/389 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           T+IHI+E   +ARDTKLGPEEIT DIPNV
Sbjct: 361 TTIHIQELTCVARDTKLGPEEITADIPNV 389


>gi|52694287|emb|CAG37983.1| RNA polymerase beta subunit [Pseudomonas fragi]
          Length = 387

 Score =  378 bits (970), Expect = e-102,   Method: Composition-based stats.
 Identities = 235/387 (60%), Positives = 304/387 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT
Sbjct: 301 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPN 867
           +IHI+E   +ARDTKLGPEEIT DIPN
Sbjct: 361 TIHIQELTCVARDTKLGPEEITADIPN 387


>gi|297837963|ref|XP_002886863.1| hypothetical protein ARALYDRAFT_893971 [Arabidopsis lyrata subsp.
            lyrata]
 gi|297332704|gb|EFH63122.1| hypothetical protein ARALYDRAFT_893971 [Arabidopsis lyrata subsp.
            lyrata]
          Length = 1763

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 155/560 (27%), Positives = 244/560 (43%), Gaps = 56/560 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +         +  G  
Sbjct: 546  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDT 605

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  +  G IL       G   +   + +L A    
Sbjct: 606  LSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPW 664

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVIL 978
            +  +  D  L     +S  +V   I+    I K E    V  +  E + ++    E  +L
Sbjct: 665  EGYNFEDAVL-----ISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLL 719

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                  +   ++ G    +G     K T   +   S  P  +  +  +  +        L
Sbjct: 720  RN--LDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCL 777

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+  K      G    P    +++V+++ KR I+ GDK+AGRHGNKG
Sbjct: 778  KLPIGGRGRVIDVRWVQKK----GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKG 830

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 831  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +                               VF+      
Sbjct: 891  ERYEQEASRKLVFSELYEASKQTANPW------------------------VFE------ 920

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 921  ---------PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 971

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G   
Sbjct: 972  TQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTI 1031

Query: 1339 FET-GTPESFNVLVKEMQAL 1357
             +    PESF +LV+E+++L
Sbjct: 1032 PKPEDAPESFRLLVRELRSL 1051



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 254/832 (30%), Positives = 424/832 (50%), Gaps = 45/832 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q  L L R+E  +K  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382  NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442  ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502  RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               VGTG+E  VA  SG   +A+  G +   D  +IV                   L+ +
Sbjct: 562  KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGN--------GDTLSIPLIMY 613

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614  QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674  LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888  VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734  VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946  NRHGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             + G         R    ++ +I++  +      ++ +I        +  +  G+     
Sbjct: 794  QKKGGSSYNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 853

Query: 999  PKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQ 1041
                   + ++   I E           + ++ A  DE+ ++            E+ K  
Sbjct: 854  FNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                    E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  ANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 963



 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELSKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQIIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|114804257|ref|YP_762253.1| RNA polymerase beta subunit [Morus indica]
 gi|122166813|sp|Q09X25|RPOB_MORIN RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|78100309|gb|ABB20950.1| RNA polymerase beta subunit [Morus indica]
          Length = 1070

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQISISKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ R +G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRCSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTMVGGPIPKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + +
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKD 1069



 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 233/662 (35%), Positives = 367/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I+           L  +    +    IL  V                K K +++A+L+ 
Sbjct: 167 RIWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSFLKDKEKKKIKSKENAILEF 226

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 227 YQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNTTFLLPRD 285

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           I+A    L+ ++ G G +DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  +     
Sbjct: 286 ILAAADHLIGMKFGMGILDDMNHLKNKRIRSVADLLQDQFGLALVRLENMVRGTMCGAIR 345

Query: 496 DSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             +   PQ+L+ +  + +    FF    LSQ+ +  N L++I H R+ S LG GG+    
Sbjct: 346 HKLIPTPQNLVTSTTLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKASYLGPGGLTGRT 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 406 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGHWGSLESPFYEISERSKKVR 465

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     GS  E++V  R   E + +  E++      P Q  S
Sbjct: 466 MLYLSPSIDEYYMVAAGNSLALNRGSQEEQVVPARYRQEFLTIEWEQVHLRSIFPFQYFS 525

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  SG   +A+  G
Sbjct: 526 IGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLECQVALDSGVPTIAEHQG 585

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D  +I++      L           L+ +QRSN+NTC++Q+P V  G  +++  I
Sbjct: 586 KIIYTDTEKIILSGNRDTL--------SIPLVIYQRSNKNTCMHQKPQVSRGKCIKKGQI 637

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N+LVA+MPW GYN ED++LI+ER+V ED++TS HI ++E+    
Sbjct: 638 LADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLINERLVYEDIYTSFHIRKYEIHTHV 697

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE IT +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++
Sbjct: 698 TSHGPERITNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDR 757

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLRAI G +    ++T L++P G  G V+DVR   + G         R    ++ +I++ 
Sbjct: 758 LLRAILGIQISISKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIRVYISQKREIKVG 817

Query: 968 AR 969
            +
Sbjct: 818 DK 819



 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 106/220 (48%), Gaps = 24/220 (10%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS- 78
            EI  IP   ++Q   +  F+          ++GL         I         + FV  
Sbjct: 7   EEISTIPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVET 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM
Sbjct: 57  YQLVEPLIKERDAVYESLTYSSELYVSAGLIW---------KTSRDMQEQTIFIGNIPLM 107

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D 
Sbjct: 108 NSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDR 164

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
           K  I  R+ R++K+ +   L A+G++  EIL       ++
Sbjct: 165 KARIWARVSRKQKISILVLLSAMGLNLREILENVCYPEIF 204


>gi|186885887|gb|ACC93351.1| RNA polymerase beta subunit [Hoplophyllum spinosum]
          Length = 1009

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 130/381 (34%), Positives = 194/381 (50%), Gaps = 46/381 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++                   P F           
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFE-------------------PEF----------- 875

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 876  --------PGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID 1362
              PESF + V+E+++L L ++
Sbjct: 988  DAPESFRLFVRELRSLALELN 1008



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 257/828 (31%), Positives = 428/828 (51%), Gaps = 43/828 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221  NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475  YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
            + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281  FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341  TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
              +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401  GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461  FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521  TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYERSNK 572

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573  NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633  LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893  ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690  ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951  DKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------V 996
            D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        +
Sbjct: 750  DETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPL 809

Query: 997  SGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRNVES---LKVQYETSKSI---- 1048
              P       +  S L ++     + ++ A  DE+ ++           YE SK      
Sbjct: 810  GVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW 869

Query: 1049 -LEDRF--KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              E  F  K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 870  IFEPEFPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|41017685|sp|Q7YJX8|RPOB_CALFG RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|32399371|emb|CAD28713.1| RNA polymerase beta subunit [Calycanthus floridus var. glaucus]
          Length = 1060

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G     G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 710  LDKNGIVMLGSWIERGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 769

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V +  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 770  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVSILQKREIKVGDKVAGRHGNKGIVSK 822

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQ+FE  LG A   L K  +    D +  
Sbjct: 823  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQMFECSLGLAGYLLDKHYRIAPFDERYE 882

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 883  QEASRKLVFPELYSASKQTVNPW------------------------VFE---------- 908

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 909  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 963

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G    +  
Sbjct: 964  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGATIIGGTIPKPE 1023

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1024 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1059



 Score =  367 bits (941), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 228/632 (36%), Positives = 362/632 (57%), Gaps = 21/632 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     K   R++A+L+ Y+      GD              FF   +
Sbjct: 189 NVCYPEIFLSFPNDKEKKKIGSRENAILEFYKQFACVGGDPVFSESLCKELQKKFF-QQR 247

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLN+D P +   +   D++A++  L+ ++ G GT+DD+++L N+R+R
Sbjct: 248 CELGRIGRRNMNRRLNIDIPQNNTFLLPRDVLAVVDHLIGMKFGMGTLDDMNHLKNKRIR 307

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E +++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 308 SVADLLQDQFGLALVRLENAVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 367

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 368 QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 427

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +   + ++VYL    +E   +A  NS     G   E+
Sbjct: 428 GSLAIHARIGHWGSIESPFYEISEK--SKEIVYLPPSRDEYYMVAAGNSLALNRGIQEEQ 485

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 486 VVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 545

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E   A  SG + +A+  G +   D  +IV+                  
Sbjct: 546 SRSEKCIVGTGLEGQAALDSGVSAIAEHEGKIIYTDTDKIVLSGN--------RDTISIP 597

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA MPW GYN 
Sbjct: 598 LVMYQRSNKNTCMHQKPRVPRGKCIKKGQILADGAATVGGELALGKNVLVAHMPWEGYNS 657

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER++  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 658 EDAVLISERLIYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVM 717

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ +  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 718 LGSWIERGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVID 777

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   + G         R   +++ +I++  +
Sbjct: 778 VRWIQKKGGSSYNPETIRVSILQKREIKVGDK 809



 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 4   IPGFSQIQFEGFCRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLVE 53

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   G 
Sbjct: 54  PLIKERDAVYESLTYSSELYVSAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGN 104

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 105 SIVSGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRPELEIDRKARIW 161

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 162 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSRE 212


>gi|5514652|emb|CAA29180.2| RNA polymerase [Drosophila melanogaster]
          Length = 1123

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 157/1005 (15%), Positives = 310/1005 (30%), Gaps = 209/1005 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 283  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 339

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 340  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 399

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 400  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 455

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENR 625
             +CPAET EG  +GLV +L   A ++           + +  +    ++   +  +    
Sbjct: 456  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKI 515

Query: 626  YIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D       L   R   + I+     I D  D   +          P L 
Sbjct: 516  FVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLI 575

Query: 684  NDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDA 740
             ++ + +L   +  M ++      +    V +G+ E +        ++A           
Sbjct: 576  VENGSLLLKKTHVEMLKERDYNNYSWQVLVASGVVEYMYTLEEETVMIA----------- 624

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +   +   D   +    Y                                   P+ 
Sbjct: 625  ----MSPYDLKQDKDYAYCTTY-----------------------------THCEIHPAM 651

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   ++I  F             
Sbjct: 652  ILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF------------- 689

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                          ++    +  V        +    +       +      + AI    
Sbjct: 690  --------------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYT 735

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V         +  +   +N+R    E    E   +        +  
Sbjct: 736  GYNQEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRN 791

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   I  G           K+  L  +       ++ +        ++ +   
Sbjct: 792  AHYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETG 851

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                        +     +  K+ V   R  Q GDK A RHG K
Sbjct: 852  IVDQVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQK 891

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G        EDM F  +G   DI++NP  +PSRM +G + E   G      G+       
Sbjct: 892  GTCGIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD---- 947

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP  D  + +
Sbjct: 948  -------------------------------------------------ATPFNDAVNVQ 958

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I++ L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   +
Sbjct: 959  KISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQI 1018

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------- 1324
            + +QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +           
Sbjct: 1019 LVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIAN 1078

Query: 1325 -RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             R   +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1079 LRNNTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1121



 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 93/707 (13%), Positives = 206/707 (29%), Gaps = 113/707 (15%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              L+F       P              ++   R+LTY+ PL + +              
Sbjct: 31  RFSLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-- 88

Query: 121 SIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQ 156
              + + Q  ++G +P+M                           G F+I G ++++++Q
Sbjct: 89  ---ETQHQKTFIGKIPIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQ 145

Query: 157 LHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----R 210
              +   ++    K      GK  +   I       ++        + V +  R     +
Sbjct: 146 EKMATNTVYVFSMKD-----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIK 196

Query: 211 K-----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
           K                 +P+     ALG  ++ +IL          +  +     L  A
Sbjct: 197 KSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEA 256

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGL 306
            ++    V+ + +        +   K++     + L+++ +  +G++           G 
Sbjct: 257 FVVQEQNVALNFIGARGARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGY 315

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
            V   ++    G   ++  D    K L+            L+ + +          +   
Sbjct: 316 MVHRLLL-ASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRG 374

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
                +       +    ++ T  +  S+    + D  K   +  G  ++  RL   +  
Sbjct: 375 KDFNLE-------LAIKTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTL 427

Query: 427 DV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               R          +     L N    +                ++KN   +  + +  
Sbjct: 428 SHLRRVNSPIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGS 484

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                +  ++  S+   + I    +  A   F     +    +    ++ +   RR   +
Sbjct: 485 QPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDI 544

Query: 545 GQGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
               V+  R   +      T  GRIC P    E  ++ L  +     +   Y        
Sbjct: 545 IVSEVSMIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----Y 599

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                  +  V Y+  +EEE   IA +   L +D                          
Sbjct: 600 SWQVLVASGVVEYMYTLEEETVMIAMSPYDLKQDK---------------DYAYCTTYTH 644

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            +  P  ++ + AS+IPF +++ S R      M +QA+ +       
Sbjct: 645 CEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 691


>gi|89142884|emb|CAJ76113.1| RNA polymerase, beta subunit [Corallococcus coralloides]
          Length = 419

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 191/420 (45%), Positives = 274/420 (65%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVSDTAKKNPLEFKGSTEEILNYYYATETIYLQSAQDFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            TGE +++  +K T   +K L+   +K L I +D L     A D+V+  TGE+ +E  + 
Sbjct: 120 KTGELIVKKNRKFTRAAIKKLEAAKMKTLPIDADELFTKVSAYDVVDENTGEVILECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + +  ++E+    I++  +L++D++N   Y+R TL+ DK +  +   + IYR +RPGD  
Sbjct: 180 VSQDKVDELLKRNIKEFKVLFIDNLNVGPYLRETLMLDKIETPEGPNIGIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F  LFF+ ++YDLS VGR+K+N +  L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETAINLFTNLFFNPERYDLSKVGRLKLNFKFGLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|68053016|sp|Q589C0|RPOB_SILLA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|62149315|dbj|BAD93457.1| RNA polymerase beta chain [Silene latifolia]
          Length = 1070

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVRLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     + V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIHVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T +   ++ +                               
Sbjct: 893  QEASRKLVF-SELYQASKQTSEPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -------YPGKSRIFDGRTGDLFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQDVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +L++E+++L L ++  L + +T    +ME
Sbjct: 1034 DAPESFRLLIRELRSLALELNHFLVSEKTFQINRME 1069



 Score =  365 bits (938), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 226/662 (34%), Positives = 367/662 (55%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLKEILDNVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      DK     +++A+L+ Y+      GD              FF   K +L  +
Sbjct: 203 IFLSFLNDKDKKNFGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQKCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ K+ +      +++LS   +E   ++  NS     G   E++V  R 
Sbjct: 442 ARIGLLGSLESPFYKISERSAMVQMLFLSPSIDEYYMVSTGNSLALNQGIQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G +   D         +  +      +    L+ +QR
Sbjct: 562 IVGTGLERQAALDSGILAIAEHEGKILYTD--------TDKIIFSGNGDIQSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q P +  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQNPRIPRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++++    T  GPE +T +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYDIQTYVTSQGPERVTSEIPHLEAHLLRNLDKNGIVRLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948 HG 949
            G
Sbjct: 794 KG 795



 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 73/335 (21%), Positives = 135/335 (40%), Gaps = 31/335 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCQFI----------DQGLPEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY+  L ++  LI          K+ ++I+EQ+I +G++PLM   GT
Sbjct: 62  PVIKEKDAVYKSLTYSSELYVSAGLIW---------KTGREIQEQTILIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 FLVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G + +EIL    YP+I  S   D       + +  +      
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLKEILDNVCYPEIFLSFLNDKDKKNFGSKENAILEFYQQ 229

Query: 263 SLV---DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGE 316
                 D    E + +  +K        L   G + +    +        ++    +   
Sbjct: 230 FACVGGDPVFSESLCKELQKKFFQQKCELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAA 289

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           T  +      +     +  + +  IR +  L  D 
Sbjct: 290 TDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324


>gi|45545313|gb|AAS67504.1| DNA-dependent RNA polymerase II second largest subunit [Candida
            tropicalis]
          Length = 1020

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 161/978 (16%), Positives = 309/978 (31%), Gaps = 163/978 (16%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L   +R+   ++ +
Sbjct: 161  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLAGLFRILFKKLTK 220

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 221  DIYNYMQRCVENDSDFNLTLAVKSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRY 280

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 281  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 336

Query: 590  ARVNAYGFIETP--YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++     E    + +    +V  D V  +A +    ++      +  D +   + V  
Sbjct: 337  TCISVGSSSEPILGFLRDFGLEVLEDYVPSNAPDSTRIFVNGVWVGVHRDPAQLVDYVRD 396

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV------LMGCNMQRQA 700
                 +I      I D  +   K          P    DD+         ++     R+ 
Sbjct: 397  LRRSGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNEDSPTKGDLMITKEHIRKL 456

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            V     +             K + +++V++   +   VDA       +    D   +   
Sbjct: 457  VAEDMDDDELEEDEEGGESRKYTWSSLVSEGIVV--YVDAEEEETIMIAMSPDDVKASKS 514

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWH 819
                 + Q                   ++          T      ++   +  + +P+ 
Sbjct: 515  TMSESEQQELQLQEQEL-----DPAKRIKPTTSSNTHTYTHCEIHPSMILGVAASIIPFP 569

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +   + +  + V                              
Sbjct: 570  DHNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------D 600

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 601  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAVVAIACYSGYNQEDSMIMNQSSIDRGL 660

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAV 996
                +F R  +D  +R      + +E   +    + + L    Y +L E   I  G    
Sbjct: 661  F-RSLFFRSYMDLEKRQGM---KLLETFEKPSRSDTLRLKHGTYEKLDEDGLIAPGIRVS 716

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T + +D                +E  QR +   K    T     E    ++
Sbjct: 717  GEDIIIGKTTPIPAD---------------TEELGQRTLHHSKRDASTPLRSTESGIVDQ 761

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +     GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 762  VLLTTNGD-----GSKFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGI 816

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM V  + E  L       G +  +          I+ L    E   
Sbjct: 817  VPDLIINPHAIPSRMTVAHLIECLLSKVSSLSGFEGDASPFTDVTAEAIAKLLR--EHGY 874

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +       +                                            +G+ ++
Sbjct: 875  QSRGFEVMYNG------------------------------------------HTGKKLM 892

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
                        V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GE
Sbjct: 893  ----------AQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGE 942

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD----DVVGR---TRVYESIVAGN----------DTF 1339
            ME  C+ A+GAA  L+E L   SD     V G      V  ++              + +
Sbjct: 943  MERDCMIAHGAAGFLKERLMEASDAFRVHVCGMCGLMSVIANLKKNQFECRSCKNKTNIY 1002

Query: 1340 ETGTPESFNVLVKEMQAL 1357
            +   P +  +L +E  ++
Sbjct: 1003 QIHIPYAAKLLFQEFMSM 1020



 Score =  136 bits (342), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 115/866 (13%), Positives = 240/866 (27%), Gaps = 156/866 (18%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          + +    + +   I    ++G  +      K  ++ R 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKAAPSPISHVAEIRSALEKGSRLISSMQIK--LYGR- 54

Query: 207 D------RRRK---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           D      R  K         +P+     ALG+  + +IL          Q  +     + 
Sbjct: 55  DEKGVAGRTIKATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVE 114

Query: 251 AADLMVGAKVSSSLV------DIDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDC 302
              ++   +V+   +       I   +++  +   L   LL ++  +E            
Sbjct: 115 EGFVIQEREVALDFIGRRGVLGIRREKRIQYAKDILQKELLPNITQEEGFETRKAFFLGY 174

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNT 361
           +    +   +   E      +  D   +K L+           IL+   + +   Y++  
Sbjct: 175 MVNRLLLCALERKEP-----DDRDHFGKKRLDLAGPLLAGLFRILFKKLTKDIYNYMQRC 229

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +  D + +   A+             T  +  S+    + +  K   S  G  ++  R  
Sbjct: 230 VENDSDFNLTLAV--------KSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRYT 281

Query: 422 LDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
             +      R          I     L N    +         +      ++KN   +  
Sbjct: 282 YSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMTC 338

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           + +  S +  +  +    +   +         +   F     +    +    +  +   R
Sbjct: 339 ISVGSSSEPILGFLRDFGLEVLEDYVPSNAPDSTRIFVNGVWVGVHRDPAQLVDYVRDLR 398

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICP----------------AETSEGHNIGLV 583
           R   +            +   +         P                  T E     + 
Sbjct: 399 RSGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNEDSPTKGDLMITKEHIRKLVA 458

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             +            E+             VVY+ A EEE   IA +   +    S   E
Sbjct: 459 EDMDDDELEEDEEGGESRKYTWSSLVSEGIVVYVDAEEEETIMIAMSPDDVKASKSTMSE 518

Query: 644 LV------------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                           +                +  P  ++ +AAS+IPF +++ S R  
Sbjct: 519 SEQQELQLQEQELDPAKRIKPTTSSNTHTYTHCEIHPSMILGVAASIIPFPDHNQSPRNT 578

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +QA+ +                                                
Sbjct: 579 YQSAMGKQAMGVFLTNYSV----------------------------------------- 597

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              + + +  Y       +     +  R                        +L  G+N 
Sbjct: 598 RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNA 633

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIP 866
           +VA   + GYN EDSM++++  +   +F S+    +  + +   +   E        D  
Sbjct: 634 VVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDLEKRQGMKLLETFEKPSRSDTL 693

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +     + +DE G+I  G  V+  DI++GK TP         ++ L           RD
Sbjct: 694 RLKHGTYEKLDEDGLIAPGIRVSGEDIIIGKTTPIPADTEELGQRTLH-------HSKRD 746

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDK 952
            S  + S  SG V  V +       K
Sbjct: 747 ASTPLRSTESGIVDQVLLTTNGDGSK 772


>gi|89142892|emb|CAJ76117.1| RNA polymerase, beta subunit [Corallococcus macrosporus]
          Length = 419

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 189/420 (45%), Positives = 276/420 (65%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y       +           +L+ G + +  +   
Sbjct: 61  GAVPDTAKKNPLEFKGSTEEILNYYYATETIYLQSSEDFEKSVELELLPGQRATRDI-KT 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
             G+ +++  +K T   +K L+   +K L I +D L     A D+V+  TG + +E  + 
Sbjct: 120 KAGDLIVKKNRKFTRAAIKKLEAAKMKTLPIDADELFTKVSAYDVVDENTGVVLLECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ +EE+    I++  +L++D++N   Y+R TL+ DK +  + ++++IYR +RPGD  
Sbjct: 180 VSQEKVEELLKHGIKEFKVLFIDNLNVGPYLRETLMLDKLETPEQSIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F  LFF+ ++YDLS VGR+K+N +  L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETAINLFTNLFFNPERYDLSKVGRLKLNFKFGLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|89142894|emb|CAJ76118.1| RNA polymerase, beta subunit [Myxococcus xanthus]
          Length = 419

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 189/420 (45%), Positives = 274/420 (65%), Gaps = 15/420 (3%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G  FDHDKG++  SGKLLY  RIIP +G W+D EFD KD+++VRIDRRRK+P T  + AL
Sbjct: 1   GAFFDHDKGKSHSSGKLLYNARIIPYRGSWIDFEFDHKDLLYVRIDRRRKLPATVLIRAL 60

Query: 222 GM--------------DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           G                +EEIL+ +Y                   +L+ G + +  +   
Sbjct: 61  GAVPDTAKKNPLEFKGSTEEILNYYYATETIYLHSAEEFEKSVELELLPGQRATRDI-KA 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            TGE +++  +K T   +K L+   +K L I +D L     A D+V    G + +E  + 
Sbjct: 120 KTGELIVKKNRKFTRAAIKKLEAAKMKTLPIDADELFTKVSAYDVVEETNGVVLLECNEE 179

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           + ++ ++E+    I++  +L++D++N   Y+R TL+ DK +  + ++++IYR +RPGD  
Sbjct: 180 VTQEKVDELLKHGIKEFKVLFIDNLNVGPYLRETLMLDKLETPEQSIMEIYRRLRPGDPP 239

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T   A ++F  LFF+ ++YDLS VGR+K+N +  L+ P D + + K DI+ +I+ L+DL+
Sbjct: 240 TPETAINLFTNLFFNPERYDLSKVGRLKLNFKFGLEEPLDGQILTKRDILEVIRYLIDLK 299

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NGKGTIDDID+LGNRRVR+VGE+L+NQYR+GL+RMER+IKER+S  +I+++MP DLINAK
Sbjct: 300 NGKGTIDDIDHLGNRRVRAVGELLENQYRIGLVRMERAIKERMSLQEIETLMPHDLINAK 359

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV + + EFF SSQLSQ  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYG
Sbjct: 360 PVTAVIKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 419


>gi|90595843|ref|NP_862746.2| RNA polymerase beta subunit [Calycanthus floridus var. glaucus]
          Length = 1069

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 135/396 (34%), Positives = 201/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G     G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 719  LDKNGIVMLGSWIERGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTAKETCLKLPI 778

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V +  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 779  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVSILQKREIKVGDKVAGRHGNKGIVSK 831

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQ+FE  LG A   L K  +    D +  
Sbjct: 832  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQMFECSLGLAGYLLDKHYRIAPFDERYE 891

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 892  QEASRKLVFPELYSASKQTVNPW------------------------VFE---------- 917

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 918  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 972

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G    +  
Sbjct: 973  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGATIIGGTIPKPE 1032

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1033 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1068



 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 228/632 (36%), Positives = 362/632 (57%), Gaps = 21/632 (3%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
            V          N     K   R++A+L+ Y+      GD              FF   +
Sbjct: 198 NVCYPEIFLSFPNDKEKKKIGSRENAILEFYKQFACVGGDPVFSESLCKELQKKFF-QQR 256

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLN+D P +   +   D++A++  L+ ++ G GT+DD+++L N+R+R
Sbjct: 257 CELGRIGRRNMNRRLNIDIPQNNTFLLPRDVLAVVDHLIGMKFGMGTLDDMNHLKNKRIR 316

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E +++  I       +   P +L+ + P+ +    FF    LS
Sbjct: 317 SVADLLQDQFGLALVRLENAVRGTICGAIRHKLIPTPHNLVTSTPLTTTYESFFGLHPLS 376

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 377 QVLDRTNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 436

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +   + ++VYL    +E   +A  NS     G   E+
Sbjct: 437 GSLAIHARIGHWGSIESPFYEISEK--SKEIVYLPPSRDEYYMVAAGNSLALNRGIQEEQ 494

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E+I      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 495 VVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 554

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E   A  SG + +A+  G +   D  +IV+                  
Sbjct: 555 SRSEKCIVGTGLEGQAALDSGVSAIAEHEGKIIYTDTDKIVLSGN--------RDTISIP 606

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA MPW GYN 
Sbjct: 607 LVMYQRSNKNTCMHQKPRVPRGKCIKKGQILADGAATVGGELALGKNVLVAHMPWEGYNS 666

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER++  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ 
Sbjct: 667 EDAVLISERLIYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDKNGIVM 726

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ +  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 727 LGSWIERGDILVGKLTPQAAKESSYAPEDRLLRAILGIQVSTAKETCLKLPIGGRGRVID 786

Query: 942 VRIFNRHGIDKNE----RSISVEREQIELLAR 969
           VR   + G         R   +++ +I++  +
Sbjct: 787 VRWIQKKGGSSYNPETIRVSILQKREIKVGDK 818



 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 13  IPGFSQIQFEGFCRFI----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLVE 62

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   G 
Sbjct: 63  PLIKERDAVYESLTYSSELYVSAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGN 113

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 114 SIVSGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRPELEIDRKARIW 170

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 171 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFPNDKEKKKIGSRE 221


>gi|290489618|gb|ADD31193.1| RNA polymerase beta subunit protein [Nelumbo nucifera]
          Length = 1070

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 136/396 (34%), Positives = 203/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDRNGIVMLGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIRVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIINPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLVSEKNFQINRKE 1069



 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 251/776 (32%), Positives = 403/776 (51%), Gaps = 41/776 (5%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
             V          N     K   +++A+L+ Y+      GD              FF   +
Sbjct: 197  NVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             +L  +GR  +N RLNLD P     +   D++A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256  CELGRIGRRNINRRLNLDIPQKNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
            SV ++L++Q+ L L+R+E +++  IS      +   PQ+L+ + P+ +    FF    LS
Sbjct: 316  SVADLLQDQFGLALVRLENAVRGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376  QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             SL   AR+  +G +E+P+ ++ +      +VYLS   +E   +A  NS         E+
Sbjct: 436  GSLAIHARIGHWGSLESPFYEISERSKEVRIVYLSPSRDEYYMVAAGNSLALNQSIQEEQ 495

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496  VVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             ++E   VGTG+E   A  SG + +A+  G +   D         +  +           
Sbjct: 556  SRSEKCIVGTGLECQAALDSGVSAIAEHEGKIIYTD--------TDKIILSGNGDTLSIP 607

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 608  LIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNS 667

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
            ED++LISER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ 
Sbjct: 668  EDAVLISERLVYGDIYTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDRNGIVM 727

Query: 884  VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728  LGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942  VRIFNRHGIDKNE----RSISVEREQI---ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            VR   + G         R    ++ +I   + +A    ++ +I        +  +  G  
Sbjct: 788  VRWIQKKGGSSYNPETIRVYISQKREIRVGDKVAGRHGNKGIISKILPRQDMPYLQDGTP 847

Query: 995  AVSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VES 1037
                       + ++   I E           + ++ A  DE+ ++            E+
Sbjct: 848  VDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEA 907

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 908  SKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 961



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P  +  D ++  LTY+  L +   LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLINERDAVYESLTYSSELYVPAGLIW---------KTGRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVPSSAMGSNLREILDNVCYPEIFLSFLNDKEKKKIGSKE 220


>gi|50549809|ref|XP_502376.1| YALI0D03718p [Yarrowia lipolytica]
 gi|49648244|emb|CAG80564.1| YALI0D03718p [Yarrowia lipolytica]
          Length = 1229

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 160/1071 (14%), Positives = 323/1071 (30%), Gaps = 183/1071 (17%)

Query: 348  YVDSVNNNAYIRNTLVT--DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
              D + +  Y  N            ++A +   R +    +     A  +         +
Sbjct: 286  DGDILEHICYDNNDWQMLEMLKPCIEEAFVIQDREVALDYIGRRGSAVGV---NRERRVR 342

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            Y    + +  +         +     +   +  ++  ++ +  G+   DD D+ G +R+ 
Sbjct: 343  YARDILQKELLPHITQ---EEGFETRKAYFLGYMVHRMLLVALGRKEPDDRDHFGKKRLD 399

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G ++   +R+   ++ + I   +               + +  + + +     +    
Sbjct: 400  LAGPLMAGIFRMLFKKLTKDIYRYMLKCVETNKDFNLTLAVKSNTITNGLKYSLATGNWG 459

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 460  DQKKAMSSRAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 515

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIA 628
            PAET EG   GLV +L+  + ++           + +  +    D V  +       ++ 
Sbjct: 516  PAETPEGQACGLVKNLSLMSCISVGTPSFPIINFLDEWGMEPLEDYVPHTHTTSTRVFVN 575

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDS 687
                 +  D +   +++       +I      I D  +   +          P    +++
Sbjct: 576  GVWVGVHRDATQLTDMIKSLRRMGDIESEVSIIRDIREKEIRIFTDAGRVYRPLFVVENN 635

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVG----TGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
                    +  Q   + + +          G E    K++G   +               
Sbjct: 636  PDAERKGELVLQKDHIYQLQQQMAEQAETEGDEGKGDKNTGWNWLV-----------DNG 684

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            VI  ++G+ + +         ++F R  Q         +     V+          T   
Sbjct: 685  VIEYIDGEEEETVMIAMTPEDLEFSRQMQAGVEMPEDELDPARRVKPAYNPHSHTWTHCE 744

Query: 804  -DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
               ++   +L + +P+  +N          M  + +   + +  ++V             
Sbjct: 745  IHPSMILGILASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM----------- 791

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 792  ----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGY 835

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R  +D+  R      E+ E   R           + 
Sbjct: 836  NQEDSVVMNQSSIDRGLF-RSLFFRSYMDQERRVGMSVVEEFEKPTRADTLRMKHGTYDK 894

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  +  G           K+  +  D      R+++         ++     +  Q 
Sbjct: 895  LDDDGLVCPGVRVSGEDIIIGKTAPIPPDAEELGQRTKYHTKRDASTPLRSTENGIVDQV 954

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        LR VKV +   +  Q GDK A RHG KG +  
Sbjct: 955  LL--------------------TTNQEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGV 994

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM V  + E  L       G +  +        
Sbjct: 995  TYRHEDMPFSAEGVVPDIIINPHAIPSRMTVAHLIECLLSKVSCLSGLEGDATPFTDVTV 1054

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS L         +                                            
Sbjct: 1055 DAISKLLR--SHGYQSRGFEVMYHG----------------------------------- 1077

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    +G+ I+              +G  Y  +L HMV DK++AR+ G   ++T+QP
Sbjct: 1078 -------HTGKKIM----------AQCFLGPTYYQRLRHMVDDKIHARARGPVQILTRQP 1120

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG-------------- 1324
            + G+S  GG R GEME  C+ A+GAA  L+E L   SD     V G              
Sbjct: 1121 VEGRSREGGLRFGEMERDCMIAHGAAAFLKERLMEASDAFRIHVCGVCGSMNVIANLKKN 1180

Query: 1325 -------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                   R +           ++   P +  +L +E+ A+ ++  L + R+
Sbjct: 1181 QFECRSCRNKT--------KIYQVQIPYAAKLLFQELMAMNIAPRLFSDRS 1223



 Score =  198 bits (504), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 144/1016 (14%), Positives = 287/1016 (28%), Gaps = 203/1016 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS----VFPITAFSGAAMLEFVSYEFDPP 84
           L+  Q  S+D F+   I      +  L            P    +    + F       P
Sbjct: 34  LVSQQLDSFDEFIETTIQELVWEDRTL--ILDQPAQHTTPNDNQNKRFEITFGKIYLSRP 91

Query: 85  KFD----------VDDCLWRDLTYAVPLKITLRL-IVFDVDEFTG-------AKSIKDIK 126
                          +   R+LTY+ PL + ++  ++F +D+               +++
Sbjct: 92  TMTEADGSTHPMYPQEARARNLTYSSPLYVDMKKRVLFSIDDPARPEADVVWNPIPGEVE 151

Query: 127 E--QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
           E    +Y+G +P+M +                         G FVI G ++++++Q  RS
Sbjct: 152 EPVSKVYIGKVPIMLRSKFCILRGLRENDLYELNECPYDQGGYFVINGSEKVLIAQE-RS 210

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK--------------DIIHV 204
                     + +    + +   I    ++G  +      K               + +V
Sbjct: 211 AANI--VQVFKKAAPSPISHVAEIRSAVEKGSRLISSMQIKMFGRSDKGPVTIKAALPYV 268

Query: 205 RIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           R D    +P+     ALG+  + +IL          Q  +     +  A ++   +V+  
Sbjct: 269 RAD----IPIVVVFRALGVVPDGDILEHICYDNNDWQMLEMLKPCIEEAFVIQDREVALD 324

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +        +   +++     + + +K +                   +  E G    +
Sbjct: 325 YIGRRGSAVGVNRERRV--RYARDILQKEL----------------LPHITQEEGFETRK 366

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A  +        +     ++                  +        K    DIYR M  
Sbjct: 367 AYFLGYMVHRMLLVALGRKEPDDRDHFGKKRLDLAGPLMAGIFRMLFKKLTKDIYRYMLK 426

Query: 384 GDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++  ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 427 CVETNKDFNLTLAVKSNTITNGLKYSL-ATGNWGDQKKAMSSRAGVSQVLNRYTFASTLS 485

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMERSIKE 488
            L        R+GK       +  +  +    E  + Q          +  + +      
Sbjct: 486 HLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTPSFP 545

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQG 547
            I+ +D   + P +        ++   F     +    +       I   RR+  +  + 
Sbjct: 546 IINFLDEWGMEPLEDYVPHTHTTSTRVFVNGVWVGVHRDATQLTDMIKSLRRMGDIESEV 605

Query: 548 GVARARAGVEMRD-------VHPTHYGRICPAETSEGHNIGLVSSLTSFAR--------- 591
            + R     E+R          P       P    +G  +     +    +         
Sbjct: 606 SIIRDIREKEIRIFTDAGRVYRPLFVVENNPDAERKGELVLQKDHIYQLQQQMAEQAETE 665

Query: 592 -VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-------EE 643
                G   T +  + D  V   + Y+   EEE   IA     L+             +E
Sbjct: 666 GDEGKGDKNTGWNWLVDNGV---IEYIDGEEEETVMIAMTPEDLEFSRQMQAGVEMPEDE 722

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           L   R                +  P  ++ I AS+IPF +++ S R      M +QA+ +
Sbjct: 723 LDPARRVKPAYNPHSHTWTHCEIHPSMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGV 782

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                          V   + A I+                            +      
Sbjct: 783 FLT---------NYDVRMDTMANILY---------------------YPQKPLATTRSME 812

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            +KF+            L   G             S  +   ++ R +  +       + 
Sbjct: 813 FLKFRELPAGQNAIVAILCYSG--------YNQEDSVVMNQSSIDRGLFRSLFFRSYMDQ 864

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           E  + +S             +EEFE   R           D   +       +D+ G++C
Sbjct: 865 ERRVGMS------------VVEEFEKPTR----------ADTLRMKHGTYDKLDDDGLVC 902

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  DI++GK  P    P   EE   R     K    RD S  + S  +G V
Sbjct: 903 PGVRVSGEDIIIGKTAPI---PPDAEELGQRT----KYHTKRDASTPLRSTENGIV 951


>gi|186885835|gb|ACC93325.1| RNA polymerase beta subunit [Corymbium glabrum]
          Length = 1024

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 135/460 (29%), Positives = 217/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS---ISVEREQIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +   I     QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      ++            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VRSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+ F++PV +G  Y+LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDSFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 255/829 (30%), Positives = 427/829 (51%), Gaps = 45/829 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101  ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356  AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTVGR 413
             ++       K   +++A+L+ Y+     +      +ES+F      F   + +L  +GR
Sbjct: 161  LFLSFLNDKKKIGSKENAILEFYQQFACVE-GDPGFSESLFKDLQKKFFQQRCELGGIGR 219

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
              MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ 
Sbjct: 220  RNMNRRLNLDIPQNNTFLLLRDILAAADHLIRIKFGMGTLDDMNHLQNKRIRSVADLLQE 279

Query: 474  QYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            Q+ L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N 
Sbjct: 280  QFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNP 339

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR
Sbjct: 340  LTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAR 399

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            +  +G +E+P+ ++ +      V+YLS   +E   +A  NS     G   E++V  R   
Sbjct: 400  IGRWGSLESPFYQIYEKSKGARVLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQ 459

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   V
Sbjct: 460  EFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIV 519

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E   A  SGA  +A+  G +   D         +  L           L+ +QRSN
Sbjct: 520  GTGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRIPLVMYQRSN 571

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            +NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISE
Sbjct: 572  KNTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISE 631

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  G
Sbjct: 632  RLVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETG 688

Query: 892  DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            DILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR      
Sbjct: 689  DILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVRSSK 748

Query: 950  IDKNERSISV-----EREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNA------ 995
             D+ E++ S+     ++ +I++  +      ++ +I        +  +  G+        
Sbjct: 749  TDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNP 808

Query: 996  VSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYET 1044
            +  P       +  S L ++     + ++ A  DE+ ++            E+ K     
Sbjct: 809  LGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANP 868

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                 E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 869  WIFEPESPGKSRIFDGRTGDSFEQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 107/226 (47%), Gaps = 21/226 (9%)

Query: 69  SGAAMLEF--VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           +     EF    Y+   P     D ++  LTY+  L ++ RLI  +          + I+
Sbjct: 1   NQEIDFEFFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQ 53

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           EQ+I MG +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II 
Sbjct: 54  EQTILMGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIIS 110

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWC 246
           D G  +++E D K  I VR+ R++K+ +   L A+G++  EIL       ++    +   
Sbjct: 111 DWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKK 170

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
              S  + ++      + V+ D G          +  L K L++K 
Sbjct: 171 KIGSKENAILEFYQQFACVEGDPG---------FSESLFKDLQKKF 207


>gi|330369324|gb|AEC12052.1| RNA polymerase beta subunit [Bradyrhizobium sp. CCBAU 23332]
          Length = 218

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/219 (61%), Positives = 174/219 (79%), Gaps = 1/219 (0%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVF 111
           +EGLQA F+SVFPI+ FSG +MLEFV YEF+ PK+DVD+C  R +T+A PLK+TLRLIVF
Sbjct: 1   DEGLQAVFRSVFPISDFSGTSMLEFVRYEFEQPKYDVDECRQRGMTFAAPLKVTLRLIVF 60

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           D+DE TGAKS+KDIKEQ +YMGD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG+
Sbjct: 61  DIDEETGAKSVKDIKEQDVYMGDIPLMTMNGTFIVNGTERVIVSQMHRSPGVFFDHDKGK 120

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILST
Sbjct: 121 THSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILST 180

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           FY +I+Y +  + W  P  A +   G    + L+D DTG
Sbjct: 181 FYKRILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTG 218


>gi|215254199|gb|ACJ64104.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 376

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 235/376 (62%), Positives = 290/376 (77%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FRDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++L E+G+F +EL
Sbjct: 61  SLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAALTEEGTFADEL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L
Sbjct: 121 ITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           KA+ P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L
Sbjct: 181 KADKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNL 240

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFE
Sbjct: 241 TKYTRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFE 300

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           DS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +
Sbjct: 301 DSILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYI 360

Query: 885 GAEVNPGDILVGKITP 900
           GAEV  GDILVGK+TP
Sbjct: 361 GAEVKGGDILVGKVTP 376


>gi|290489634|gb|ADD31201.1| RNA polymerase beta subunit protein [Euonymus americanus]
          Length = 1072

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/427 (31%), Positives = 206/427 (48%), Gaps = 52/427 (12%)

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            R   ++       +    +E   L+ ++     +   +  G    +G     K T   + 
Sbjct: 691  RKYEIQAHVTSQGSERITNEIPHLEAHLLRNLDKNGIVALGSWVETGDILVGKLTPQMAK 750

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              S  P  +  +  +  +        LK+       +++ R+  K               
Sbjct: 751  ESSYAPEDRLLRAILGIQVSSSKETCLKLPTGGRGRVIDVRWVQKK-------GGSDSNP 803

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V++  KR I+ GDK+AGRHGNKGIVS+ILP +DMP+L+DG  VD+V NPLGVPSRM
Sbjct: 804  ETIRVYILQKREIKVGDKVAGRHGNKGIVSKILPRQDMPYLQDGGTVDMVFNPLGVPSRM 863

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 864  NVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------ 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S ++DG TG PF++PV +
Sbjct: 918  ------------------VFE---------------PEYPGKSRIFDGRTGNPFEQPVII 944

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G +++L
Sbjct: 945  GKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRIGEMEVWALEGFGVSHIL 1004

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L L ++    + + 
Sbjct: 1005 QEMLTYKSDHIKARQEVLGTTIVGGTIPKPEDAPESFRLLVRELRSLALELNHFFVSEKN 1064

Query: 1369 KNSAKME 1375
                + E
Sbjct: 1065 FQINRKE 1071



 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 229/694 (32%), Positives = 375/694 (54%), Gaps = 23/694 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E     + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 EADHNGISVYTGSIISDWGGRFELEIDRKARIWARVSRKQKISILVLSSAMGLNLREILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     K   ++ A+L+ Y+      GD              FF   +
Sbjct: 197 NVCYPEIFLSFLNEKEKKKIGSKETAILEFYQQFTCVGGDPVFSESLCKELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNMNQRLNLDLPPTNTFLLPRDILAAADYLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   PQ L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENMVRGTICGAIRHKLIPTPQSLVPSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++  H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQTVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            SL   A++   G +E+P+ ++ +      N + YLS   +E   IA  NS     G   
Sbjct: 436 GSLAIHAKIGHCGSLESPFYEIFEESKSKKNRMFYLSPNRDEYCMIAAGNSLALSRGIQE 495

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 496 EQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 555

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG E  VA  SG +++A+  G +   D  +I +   E         +  
Sbjct: 556 PLSQSEKCIVGTGAERQVALDSGVSVIAEHEGRIIYTDTDKIFLLGNED--------IFN 607

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+  V+    +++  I+ DG +T  G+L LG+N+LVA+MPW GY
Sbjct: 608 IPLVVYQRSNKNTCMHQKGRVQRDKCIKKGQILGDGAATVGGELTLGKNILVAYMPWEGY 667

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISERM+  D++TS HI ++E+ A  T  G E IT +IP++    L+N+D+ GI
Sbjct: 668 NSEDAVLISERMIYGDIYTSFHIRKYEIQAHVTSQGSERITNEIPHLEAHLLRNLDKNGI 727

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P+G  G V
Sbjct: 728 VALGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSSSKETCLKLPTGGRGRV 787

Query: 940 VDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           +DVR   + G   +     R   +++ +I++  +
Sbjct: 788 IDVRWVQKKGGSDSNPETIRVYILQKREIKVGDK 821



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 107/233 (45%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP   ++Q   +  F+          + GL         I        +EF     +Y+ 
Sbjct: 12  IPGFNQIQFEGFCRFI----------DHGLTEELYKFPKIEDTEQ--EIEFQLFAETYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  +TY+  L ++ RLI          K+ +DI++Q+++ G++PLM   
Sbjct: 60  VEPLIKERDAVYEAITYSSELYVSARLIW---------KTSRDIQKQTLFFGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++ GI R  ++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  
Sbjct: 111 GTSIVNGIYRTAINQILQSPGIYYRSEADHNGIS---VYTGSIISDWGGRFELEIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G++  EIL    YP+I  S   +     + + +
Sbjct: 168 IWARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLNEKEKKKIGSKE 220


>gi|308487676|ref|XP_003106033.1| CRE-RPB-2 protein [Caenorhabditis remanei]
 gi|308254607|gb|EFO98559.1| CRE-RPB-2 protein [Caenorhabditis remanei]
          Length = 1207

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 159/997 (15%), Positives = 307/997 (30%), Gaps = 210/997 (21%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   I  ++  L+    G+  +DD D++GN+R+   G +L   +R    
Sbjct: 363  HVGVSEHCETKKAFFIGYMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFR 422

Query: 481  RMERS----------IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------- 521
             + +           +  +      D       +    +   +     +           
Sbjct: 423  NLLKEKMITSCIQMRMTAQKYINKNDDFALDVCVKTSTITRGLAYSLATGNWGDQKKAHQ 482

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+   +   + ++H RR ++     + R     + R +H T +G +CPAET EG
Sbjct: 483  SRAGVSQVLNRLTYTATLSHLRRANS----PIGREGKLAKPRQLHNTQWGMVCPAETPEG 538

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
              +GLV +L   A ++     E     + +     ++  +S     +      N +    
Sbjct: 539  QAVGLVKNLALMAYISVGSLPEPILEFLEEWS-MENLEEVSPSAIADATKIFVNGAWVGI 597

Query: 638  GSFTEELVFC----RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                ++L+      R   + I+     + D  D   +          P L  +D    L 
Sbjct: 598  HREPDQLMTTLKKLRRQMDIIVSEVSMVRDIRDREIRIYTDAGRVCRPLLIVEDQKLALR 657

Query: 693  GCNMQRQAVP---LLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              ++ +            +  VG G+ E + +     +++A     +             
Sbjct: 658  KRHIDQLKDIDEANKYTWSDLVGGGVVELIDSMEEETSMIAMMPEDL------------- 704

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                              + G     +      P+  LG     
Sbjct: 705  ----------------------------------RSGVYCDTHTHCEIHPAMILG----- 725

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N       S R   +       +  +                     
Sbjct: 726  --VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYTTNF----------------- 760

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  ++    +  V        +    +     + +      + AI      +  D+ 
Sbjct: 761  ------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSV 814

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D      +   E IE   R+K         +       
Sbjct: 815  IMNNSAIDRGLF-RSVFYRSYRDNEANLDNANEELIEKPTREKCSGMRHSLYDKLDEDGI 873

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  L                      +  ++++   +Y    + 
Sbjct: 874  ISPGMRVSGDDVIIGKTVAL--------------------PDIDDDLDATGKKYPKRDAS 913

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
               R        Q    +     + VK+ +   R  Q GDK A RHG KG +  +   ED
Sbjct: 914  TFLRSSETGIVDQVMLSLNNDGNKFVKIRMRSVRLPQIGDKFASRHGQKGTMGIMYRQED 973

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  VPSRM +G + E   G      G+                  
Sbjct: 974  MPFTAEGLTPDIIINPHAVPSRMTIGHLIECLQGKLSANKGEIGD--------------- 1018

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP  D  + + I+ +L     
Sbjct: 1019 --------------------------------------ATPFNDTVNVQKISGLLCEYGY 1040

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G  ++Y+G TG+     +  G  Y  +L HMV DK+++R+ G   ++ +QP+ G++ 
Sbjct: 1041 HLRGNEVMYNGHTGKKLTTQIFFGPTYYQRLKHMVDDKIHSRARGPIQMMNRQPMEGRAR 1100

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DV-----VG-------RTRVYESIV- 1333
             GG R GEME  C  ++GA   L+E L   SD   V      G       RT  +E    
Sbjct: 1101 DGGLRFGEMERDCQISHGATQFLRERLFEVSDPYHVYVCNNCGLIVVANLRTNSFECKAC 1160

Query: 1334 -AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
                       P +  +L +E+ ++ ++  L     +
Sbjct: 1161 RNKTQVSAVRIPYACKLLFQELMSMSIAPRLMVKPQQ 1197



 Score =  226 bits (575), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 157/1013 (15%), Positives = 300/1013 (29%), Gaps = 217/1013 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA------------AMLEF 76
           L+  Q  S+D F+ MN+          Q   +   P+   S                L+F
Sbjct: 53  LVRQQLDSFDEFVQMNV----------QRIVEDSPPVELQSENQHLGNDMENPAKFSLKF 102

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTYA PL + +  +V   D      S+ +  
Sbjct: 103 NQIYLSKPTHWEKDGAPMPMMPNEARLRNLTYASPLYVDITKVVTRDD------SVNEKV 156

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            + +++G +P+M                           G FVI G ++++++Q   +  
Sbjct: 157 YEKVFVGKVPVMLRSSYCMLSNMTDRDLTELNECPLDPGGYFVINGSEKVLIAQEKMATN 216

Query: 163 -IHFDHDKGRASLSGKLLYA--CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--- 211
            ++    K      GK  +   CR        ++        + V +  R     +K   
Sbjct: 217 TVYVFSMKD-----GKYAFKTECR------SCLENSSRPTSTMWVNMLARGGGGGKKTAM 265

Query: 212 --------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                         +P+     ALG  S+ +IL          +  +     L  A ++ 
Sbjct: 266 GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFDDPEMMEMVKPSLDEAFVIQ 325

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDI 312
              V+ + +     +  +   +++         + L   GV     T       Y+   +
Sbjct: 326 EQNVALNFIGARGAKPGVTREQRIKYAREILQKELLPHVGVSEHCETKKAFFIGYMVHRL 385

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY-----IRNTLVTDKN 367
           +    G   ++  D I  K L+            L+ + +          +R T     N
Sbjct: 386 LLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRALFRNLLKEKMITSCIQMRMTAQKYIN 445

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           K+   AL    +        T  +A S+    + D  K   S  G  ++  RL       
Sbjct: 446 KNDDFALDVCVK----TSTITRGLAYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLS 501

Query: 428 V--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              R          +     L N +  +         +   + + L     + +  +   
Sbjct: 502 HLRRANSPIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEP 561

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           I E +    ++++   + ++   +  A   F   + +    E    ++ +   RR   + 
Sbjct: 562 ILEFLEEWSMENL---EEVSPSAIADATKIFVNGAWVGIHREPDQLMTTLKKLRRQMDII 618

Query: 546 QGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
              V+  R   +      T  GR+C P    E   + L        +       E     
Sbjct: 619 VSEVSMVRDIRDREIRIYTDAGRVCRPLLIVEDQKLALRKRHIDQLKD----IDEANKYT 674

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      V  + +MEEE   IA     L                     V  +     
Sbjct: 675 WSDLVGGGVVELIDSMEEETSMIAMMPEDLRS------------------GVYCDTHTHC 716

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ + AS+IPF +++ S R      M +QA+ +                     
Sbjct: 717 EIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYTTNFHV-------------- 762

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         + + V  Y               Q+PLV  
Sbjct: 763 ---------------------------RMDTLAHVLYYP--------------QKPLV-- 779

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                              +L  G N +VA + + GYN EDS++++   +   +F S+  
Sbjct: 780 --------TTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLFRSVFY 831

Query: 845 EEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +     +     EE            +       +DE GII  G  V+  D+++GK  
Sbjct: 832 RSYRDNEANLDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTV 891

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +    +          RD S  + S  +G V  V +   +  +K
Sbjct: 892 ALPDIDDDLDATGKKYPK-------RDASTFLRSSETGIVDQVMLSLNNDGNK 937


>gi|52694143|emb|CAG30601.1| DNA-directed RNA polymerase beta chain [Pseudomonas graminis]
          Length = 389

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/389 (59%), Positives = 304/389 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASAAMNDKKILIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           +IHI+E   +ARDTKLGPE+I+ DIPNV 
Sbjct: 361 TIHIQELTCVARDTKLGPEKISADIPNVG 389


>gi|34501436|ref|NP_904223.1| RNA polymerase beta subunit [Physcomitrella patens subsp. patens]
 gi|41017602|sp|P60283|RPOB_PHYPA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|34494806|dbj|BAC85073.1| RNA polymerase beta subunit [Physcomitrella patens subsp. patens]
          Length = 1085

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/626 (37%), Positives = 367/626 (58%), Gaps = 17/626 (2%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
           ++++I  S       L                 D   +    L  I   +   +     +
Sbjct: 202 TIKQILDSVCSSKIFLDFLKEKKKKKEHLQSTEDAMVELYKQLYYIGGDLLFSESIRKEL 261

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            +  F        + +L  +GR+ +N +L+LD P++   +  +DI+A I  L+ ++ G G
Sbjct: 262 QKKFFQ------QRCELGKIGRLNVNKKLSLDIPENEFFLLPQDILAAIDYLIKIKFGIG 315

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPV 509
           T+DDID+L NRR+RSV ++L++Q +L L+R+E S++   R ++     + P++LI   P+
Sbjct: 316 TLDDIDHLKNRRIRSVADLLQDQLKLALIRLENSVRQVMRRTTKRKRLLSPKNLITQTPL 375

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           ++   EFF S  LSQ  +  NSL+ I H RRLS+LG GGV R  AG ++RD+H +HY RI
Sbjct: 376 IATFKEFFGSHPLSQFLDQTNSLAEIVHKRRLSSLGPGGVTRRTAGFQVRDIHFSHYTRI 435

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ETSEG N GL++SL   A VN +GF+E+P+ K+        ++ LSA E+E   IA 
Sbjct: 436 CPIETSEGMNAGLIASLAIHANVNNWGFLESPFYKISKNVKEEKIINLSAGEDEYYRIAT 495

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            N    + G+   ++   R   E + +  E+I      P Q  S+  SLIPFLE++D+NR
Sbjct: 496 GNCLALDQGTQKIQITPARYRQEFLAIAWEQIHLRSIYPLQYFSVGVSLIPFLEHNDANR 555

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVPL+K E   VGTG+ES VA  SG  ++ K++  +   D  +I + +  
Sbjct: 556 ALMGSNMQRQAVPLIKLEKCIVGTGLESQVALDSGNVMITKQSEKIMYTDGKKISLLNNT 615

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            +   +        L+ +QRSN +TC++Q+P V     +++  ++ DG +   G+L LG+
Sbjct: 616 NETVNT-------HLIIYQRSNNSTCIHQKPQVISKKFLKKGQVLTDGAAILKGELTLGK 668

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVA+MPW GYNFED++LISER++ ED++TSIHIE +E+ +R+T  GPE+IT++IP++ 
Sbjct: 669 NILVAYMPWEGYNFEDAILISERLIYEDIYTSIHIERYEIESRNTNQGPEKITKEIPHLE 728

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDT 927
              L+++D+ G++  G+ V  GD+LVGK+TP+        PE KLL+AIFG +  + ++T
Sbjct: 729 NSVLRHLDKNGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVTNAKET 788

Query: 928 SLRVPSGVSGTVVDVRIFNRHGIDKN 953
            L+VP    G V+DV   ++     N
Sbjct: 789 CLKVPLNGKGRVIDVIWISKKENSSN 814



 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/477 (30%), Positives = 221/477 (46%), Gaps = 82/477 (17%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIELLA-----RDKDDEQVIL 978
            ++  +           D  + +   I ++  + I +ER +IE             E   L
Sbjct: 668  KNILVAYMPWEGYNFEDAILISERLIYEDIYTSIHIERYEIESRNTNQGPEKITKEIPHL 727

Query: 979  DRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++     +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 728  ENSVLRHLDKNGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVTNAKE 787

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++  + +K E             +++ V++A KR IQ GDK+AGRHG
Sbjct: 788  TCLKVPLNGKGRVIDVIWISKKE-------NSSNYEKIIHVYIAQKRKIQVGDKVAGRHG 840

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGI+S+ILP +DMP+L+DGTP+D+VL+PLGVPSRMNVGQIFE  LG A   LGK  +  
Sbjct: 841  NKGIISKILPRQDMPYLQDGTPIDMVLSPLGVPSRMNVGQIFECLLGLAGYFLGKHYRIT 900

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              D K   + S    F  ++      T  +  ++ ++                       
Sbjct: 901  PFDEKYEREASRKLVF-SELYKASKKTGNLWLFEPEN----------------------- 936

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                            G+S L +G TGE F++ VTVG  YMLKL H V DK++ARS+G Y
Sbjct: 937  ---------------PGKSRLLNGRTGEIFEQAVTVGKAYMLKLIHQVDDKIHARSSGPY 981

Query: 1276 SLVTQQPLGGKSNRGGQRLG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
            +LVTQQPL                        EMEVW ++ +G AY+LQEMLTIKSD + 
Sbjct: 982  ALVTQQPL------------RGRSRRGGQRVGEMEVWALEGFGVAYILQEMLTIKSDHIH 1029

Query: 1324 GRTRVYESIVAGNDTFETGT-PESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             R  V  +I+ G    +  T PESF +LV+E+++L L  +L+++         +  D
Sbjct: 1030 ARYEVLGAIITGEPIPKPKTAPESFLLLVRELRSLSL--ELDHAVIFEKNLNIKFKD 1084



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 122/789 (15%), Positives = 265/789 (33%), Gaps = 76/789 (9%)

Query: 24  IDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVS--YE 80
             +P+L ++Q  SY +F+  N+  +             +FP I   +     E ++  Y+
Sbjct: 23  FSLPELRQIQFKSYYYFIYKNLISELN-----------IFPEIFDLNQEFQFELLNKEYK 71

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P+       +   TY+  L +T RL+          K   +I++Q+I++G +PL+  
Sbjct: 72  LIKPEKTTI--KFHYNTYSSDLYVTCRLL--------RRKKKIEIQKQTIFIGSIPLIDY 121

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
             TF I  + R++++Q+ RSPGI+++ +     +S   +Y   II D G  + +E DSK 
Sbjct: 122 QSTFRINSVTRVIINQILRSPGIYYNSELDHNGIS---IYTGTIISDWGGRLKLEIDSKT 178

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILS------TFYPKIVYSQRGDFWCFPLSAADL 254
            I  RI ++RKV +   L+A+G+  ++IL        F   +   ++          A +
Sbjct: 179 RIWARISKKRKVSILVLLLAMGLTIKQILDSVCSSKIFLDFLKEKKKKKEHLQSTEDAMV 238

Query: 255 MVGAKVSS----SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +  ++       L      +++ +   +    L K  +    K L +         + +
Sbjct: 239 ELYKQLYYIGGDLLFSESIRKELQKKFFQQRCELGKIGRLNVNKKLSLDIPENEFFLLPQ 298

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           DI+      I I+   +     ++ + +  IR +  L  D +          V    +  
Sbjct: 299 DILAAIDYLIKIK-FGIGTLDDIDHLKNRRIRSVADLLQDQLKLALIRLENSVRQVMRRT 357

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
                 +            +  +  F            +++  +    RL+   P  V  
Sbjct: 358 TKRKRLLSPKNLITQTPLIATFKEFFGSHPLSQFLDQTNSLAEIVHKRRLSSLGPGGVTR 417

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                 +  I      R     I  I+         +  +  +        +E    +  
Sbjct: 418 RTAGFQVRDIHFSHYTR-----ICPIETSEGMNAGLIASLAIHANVNNWGFLESPFYKIS 472

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +V  + ++     N              + L+   +      +IT  R         +A
Sbjct: 473 KNVKEEKII-----NLSAGEDEYYRIATGNCLA--LDQGTQKIQITPARYRQEF----LA 521

Query: 551 RARAGVEMRDVHPTHY-----GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            A   + +R ++P  Y       I   E ++ +   + S++   A          P  K+
Sbjct: 522 IAWEQIHLRSIYPLQYFSVGVSLIPFLEHNDANRALMGSNMQRQA---------VPLIKL 572

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
               V   +    A++  N  I + +  +     +T+             V    I +  
Sbjct: 573 EKCIVGTGLESQVALDSGNVMITKQSEKIM----YTDGKKISLLNNTNETVNTHLIIYQR 628

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
           ++    +     +I          +  G  + +     L      +   M         A
Sbjct: 629 SNNSTCIHQKPQVISKKFLKKGQVLTDGAAILK---GELTLGKNILVAYMPWEGYNFEDA 685

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            ++++R    +   +I I  R      + +     I + +    ++    +++  LV  G
Sbjct: 686 ILISERLIYEDIYTSIHIE-RYEIESRNTNQGPEKITKEIPHLENSVLRHLDKNGLVIPG 744

Query: 786 DEVRRNDII 794
             V   D++
Sbjct: 745 SWVETGDVL 753


>gi|290489644|gb|ADD31206.1| RNA polymerase beta subunit protein [Oxalis latifolia]
          Length = 1070

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   S   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVVLGSWVETGDILVGKLTPQMSKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+ +K      G    P     + V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDIRWIHKKG----GSSYNP---EKISVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I P +DMP+L+DG P+D+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  IFPRQDMPYLQDGKPIDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++P+ +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPIIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G +++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRIGEMEVWALEGFGVSHILQEMLTYKSDHIRARQEVLGTTIIGGTISKPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLISEKNFQINRKE 1069



 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 230/662 (34%), Positives = 371/662 (56%), Gaps = 17/662 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRVELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N         +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLNDKEKKTIGSKENAILEFYQQFTCVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNQRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ S    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTSTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++  H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQTVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P+ K+ +G     ++YLS   +E   +A  NS     G   E++V  R 
Sbjct: 442 ARIGHWGSLESPFYKISEGSKKVRMLYLSPNIDEYYMLAAGNSLALNRGFQEEQVVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPLQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G V   D  +IV+                  L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVLAIAEHGGKVIYTDTDKIVLSEN--------GDTFSIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P  + G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L+
Sbjct: 614 SNKNTCMHQKPQAQRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLV 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE IT +IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYGDIYTSFHIRKYEIQTHLTSQGPERITNEIPHLEAHLLRNLDKNGIVVLGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D+R  ++
Sbjct: 734 TGDILVGKLTPQMSKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDIRWIHK 793

Query: 948 HG 949
            G
Sbjct: 794 KG 795



 Score =  162 bits (409), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         +         + FV  ++   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DRGLTEELYKFPKMEDTDQEIEFQLFVETHQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY+  L ++  LI          K+ ++++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYKSLTYSSELYVSAGLIW---------KTCRNMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRVELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNDKEKKTIGSKE 220


>gi|222093449|gb|ACM43501.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
          Length = 821

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/680 (38%), Positives = 408/680 (60%), Gaps = 29/680 (4%)

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D +   Y+A+D        I ++  D   E  +     + I +   + + +      I+N
Sbjct: 1   DRIITTYLAQD--------IVLKNVDPTMEAKILYPKGTYITNDIAIEIQNAFKEGLIKN 52

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             + D           +Y  +   +        ++     F S K       +  +   +
Sbjct: 53  IDLKDYGITSD-----VYGKLLDTNPK-LKNRMNIIGIYIFKSKKAMEKDGEKHFV---I 103

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             D      H+   DI+AII    +L    G  DD D+L N+R+ SVGE+L NQ  +GLL
Sbjct: 104 GNDPTSVENHLLISDIVAIINYYFNLNENIGRDDDPDSLINKRIVSVGELLLNQLNIGLL 163

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +ME++ +E++SS +I  + P+++ N K + + +  FF SS+LSQ  +  N LS I+  R+
Sbjct: 164 KMEKNTREKMSSKEISRITPKNITNNKMIQNQIKTFFNSSKLSQFMDQTNPLSEISTKRK 223

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A+V+ YGF++T
Sbjct: 224 ITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYAKVDEYGFLQT 283

Query: 601 PYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY KV +G V  +  VYL+A EE NR  AQ++ S+DE+G  T+E V  +   +  +V  +
Sbjct: 284 PYFKVTNGIVDFSQPVYLTAHEEINRTFAQSSISIDENGKITDEQVIVKSNFDYNVVSPK 343

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D+ID S KQ+ S+AAS IPFLEN+D+NR LMG NMQRQAVPLL AEAP V TG+E+ +
Sbjct: 344 EVDYIDVSSKQMTSLAASSIPFLENNDANRALMGSNMQRQAVPLLFAEAPLVATGIEADI 403

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           AK S   + +   G V  VD  +I I+    D       +  Y+L  F+++NQ T ++Q 
Sbjct: 404 AKFSPNNLKSTVDGEVVFVDGSQIKIK----DSASEKGSIKTYQLKTFEKTNQGTVISQS 459

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+VK+GD+V + D+I+D  S   G++ALG+N+LV F  W+GYN+ED++++SER+V +DVF
Sbjct: 460 PIVKMGDKVLKGDLISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE  +  R +K G +++T DIPN S +  +++DE GI+ +G+EV  GDILVG+++
Sbjct: 520 TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRVS 579

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           PKG+  ++P EKLL  IF +K  + +DTSL+V +G  GTV+DV I +R          +V
Sbjct: 580 PKGDENISPAEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSREN-------RNV 632

Query: 960 EREQIELLARDKDDEQVILD 979
             E+I+++ +    ++  + 
Sbjct: 633 LEEEIDMMIKVYVAQKRKIK 652



 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 129/428 (30%), Positives = 186/428 (43%), Gaps = 67/428 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L+   +   +  M   + +L         +  D  +     V   V 
Sbjct: 461  IVKMGDKVLKGD-LISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  +S + + +    +       +  LD N   R+   +   + + G  
Sbjct: 520  -TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRV 578

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K    +S    +E   +  +   + +EK          Q       +  R    +   
Sbjct: 579  SPKGDENISP---AEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSRENRNV--- 632

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   +  ++KV+VA KR I+ GDKMAGRHGNKG++SR+LP EDMP+L+DGTP+DI
Sbjct: 633  -----LEEEIDMMIKVYVAQKRKIKVGDKMAGRHGNKGVISRVLPVEDMPYLEDGTPLDI 687

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  S + D     DI       +       
Sbjct: 688  ILNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVSPVFDGVKKADIMDALEEAKLPRTGKM 747

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VFD                            
Sbjct: 748  K----------------------------VFDPT-------------------------- 753

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D  ++VG +YM KL+HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 754  TGEKIDNEISVGVMYMFKLSHMVDDKMHSRSIGPYSLITQQPLGGKSQNGGQRFGEMETW 813

Query: 1301 CIQAYGAA 1308
             +++YGAA
Sbjct: 814  ALESYGAA 821


>gi|323148822|ref|YP_004221915.1| RNA polymerase beta subunit [Erodium carvifolium]
 gi|316926286|gb|ADU58139.1| RNA polymerase beta subunit [Erodium carvifolium]
          Length = 1116

 Score =  377 bits (967), Expect = e-101,   Method: Composition-based stats.
 Identities = 155/562 (27%), Positives = 246/562 (43%), Gaps = 57/562 (10%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E  + +   +          I         +  G       +          I
Sbjct: 608  CIVGTGLEGQVALDSGVPLITEHAGKIISIHTDKILLSGNGDTLSIPLVMYQRSNKNTCI 667

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G IL       G   +   + LL A    +  +  D  L     +S
Sbjct: 668  HQKPQVRRGKCIKKGQILADGAATVG-GELALGKNLLVAYMPWEGYNFEDAVL-----IS 721

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I     I K E  I V  +  E + +     +  L RN+  +   ++ G    
Sbjct: 722  ERLVYEDILTSFHIRKYEIEIHVTSQGPEKITKKIPYLRTHLLRNL-DKSGIVILGSW-- 778

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                  ++  +L   L  +  +    +    D      + + +            R  + 
Sbjct: 779  -----VEEGDILVGKLRPQLAQDLAPEDRFVDAVFGTQIATSRATCLKLPRGGRGRVIDV 833

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                   +   P     ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 834  RWIRSNPERESPER-ERIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGK 892

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+D+V NPLGVPSRMNVGQIFE  LG A V L +  +    D +   + S    F E   
Sbjct: 893  PLDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDERYEQEASRKLVFSELHE 952

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 953  ASKQTGNPW------------------------VFE---------------PEYPGKSRI 973

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV VG  Y+LKL H V DK++ RS+G Y+ VTQQPL G++ RGGQR+GE
Sbjct: 974  FDGRTGDPFEQPVLVGQPYILKLIHQVDDKIHGRSSGPYASVTQQPLRGRAKRGGQRVGE 1033

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G A++LQEMLT KSD +  R +++ + + G +  +    PESF +LV+E++
Sbjct: 1034 MEVWALEGFGVAHILQEMLTYKSDHLRTRDKIFGTTIIGGEMPKAEDAPESFRLLVRELR 1093

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +     + E
Sbjct: 1094 SLALELNHFLVSEKNFQMNRKE 1115



 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 224/686 (32%), Positives = 368/686 (53%), Gaps = 16/686 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 184 ELDHKGILVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILE 243

Query: 350 DSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++      +K K   +++A+L+ Y+      GD              FF   +
Sbjct: 244 NVCYPEIFLAFLDDKEKEKIGSKENAILEFYQQFVCVGGDPVFSDSLCKELQNKFF-RQR 302

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  +N RLNLD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 303 CELGRIGRRNINRRLNLDISQNNTFLLPRDILAATDHLIGIKFGMGTLDDMNHLKNKRIR 362

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E+ +K  I       +   PQ+ + + P+ +    FF    LS
Sbjct: 363 SVADLLQDQFGLALIRLEKVVKRAIRGAIKGKLIPTPQNFVTSTPLKTTYESFFGLHPLS 422

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP++YGRIC  +TSEG N+GL+
Sbjct: 423 QVLDETNPLTQIVHGRKWSFLGPGGLTGRTASFRIRDIHPSYYGRICTIDTSEGINVGLI 482

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G +E+P+ ++        ++YLS+  +E   I   NS    +    E+
Sbjct: 483 GSLAIHARIGDFGSLESPFYEISAKSKRARILYLSSRRDEYCMIGTGNSLALNESFQEEQ 542

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV L
Sbjct: 543 IVTARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVAL 602

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E  VA  SG  ++ + AG +  +          +  L           
Sbjct: 603 SRSEKCIVGTGLEGQVALDSGVPLITEHAGKIISIH--------TDKILLSGNGDTLSIP 654

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNF
Sbjct: 655 LVMYQRSNKNTCIHQKPQVRRGKCIKKGQILADGAATVGGELALGKNLLVAYMPWEGYNF 714

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V ED+ TS HI ++E+    T  GPE+IT+ IP +    L+N+D+ GI+ 
Sbjct: 715 EDAVLISERLVYEDILTSFHIRKYEIEIHVTSQGPEKITKKIPYLRTHLLRNLDKSGIVI 774

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           +G+ V  GDILVGK+ P+    + PE++ + A+FG +    R T L++P G  G V+DVR
Sbjct: 775 LGSWVEEGDILVGKLRPQLAQDLAPEDRFVDAVFGTQIATSRATCLKLPRGGRGRVIDVR 834

Query: 944 IFNRHGIDKNERSISVEREQIELLAR 969
              R   ++        R  I     
Sbjct: 835 WI-RSNPERESPERERIRVYISQKRE 859



 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 107/267 (40%), Gaps = 50/267 (18%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERP---NEGLQAAFKSV--------FP-ITAFSGAAM 73
           IP L ++Q   +  F+   +  +       EG    F  +        FP I  F     
Sbjct: 12  IPGLNQIQFEGFCRFVDQGLREELYKFPTVEGFIEDFLDIEDFLDIEDFPDIEDFLNEVE 71

Query: 74  LEFVS------------------Y--------EFDPPKFDVDDCLWRDLTYAVPLKITLR 107
            +                     Y        +   P     D ++  LTY+  L ++  
Sbjct: 72  EDLEKDIDVDEDVDEDIDEDVDVYFRLFAETSKLVEPLIKERDAVYESLTYSSELYVSAG 131

Query: 108 LIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDH 167
           LI               +++Q I +G++PLM   G F++ G+ R++V+Q+ +SPGI++  
Sbjct: 132 LIWKRKGYS--------MQKQRILIGNIPLMNSLGIFIVNGMYRMIVNQILQSPGIYYRS 183

Query: 168 DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE 227
           +       G L+Y   II D G  +++E D K  I  R+ R++K+ +     A+G +  E
Sbjct: 184 ELDHK---GILVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLRE 240

Query: 228 ILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           IL    YP+I  +   D     + + +
Sbjct: 241 ILENVCYPEIFLAFLDDKEKEKIGSKE 267


>gi|186885883|gb|ACC93349.1| RNA polymerase beta subunit [Hesperomannia arbuscula]
          Length = 1024

 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 131/396 (33%), Positives = 198/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S + DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRILDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF + V+E+++L L ++  L + +T    + E
Sbjct: 988  DAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 231/684 (33%), Positives = 378/684 (55%), Gaps = 21/684 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341 TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +   D         +  L           L+ ++RSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYTD--------TDKILLSGNGDTLRISLVMYERSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573 NTCIHQKPQVQRGTCIKKGQIVAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI ++E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISV-----EREQIELLAR 969
           D+ E++ S+     ++ +I++  +
Sbjct: 750 DETEKTESIRVYILQKREIKVGDK 773



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|290973756|ref|XP_002669613.1| DNA-directed RNA polymerase II [Naegleria gruberi]
 gi|284083163|gb|EFC36869.1| DNA-directed RNA polymerase II [Naegleria gruberi]
          Length = 1233

 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 160/980 (16%), Positives = 318/980 (32%), Gaps = 203/980 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   I  ++  L+    G+  +DD D+ GN+R+   G +L+  +     ++ + ++  + 
Sbjct: 414  KAYFIGYMVHRLLLGALGRRPLDDRDHYGNKRLELAGGLLQGLFLQLFKKVVKEMESTLK 473

Query: 492  SVDIDSVMPQDLI--NAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITH 537
               + S         N + +   +     +              ++Q+   +   S ++H
Sbjct: 474  KSILKSSEIDVAPAVNKRTITKGLQYSLATGNWGVQGSRDIRAGVAQVLNRLTYTSTLSH 533

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             RRL+      + R+      R +H T +G ICPAET EG   GLV +L   + +   G 
Sbjct: 534  LRRLNT----PIERSGKQAAPRQLHNTQWGVICPAETPEGGACGLVKNLALMSYIT-VGT 588

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC------AG 651
             +T   K+ D    N +  L   +         N          +ELV          A 
Sbjct: 589  DKTHISKMLDELGINKLHELDESDLNKYTKVFLNGMWMGVHHTPDELVKHLRVLRRTGAV 648

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
            +  +     +   +          A  +  ++ D     +   ++Q      +  +    
Sbjct: 649  DMQVSIVRDVREREVRIWCDSGRCARPLFIVDRDHDTLFIKNQHVQALRENTMNWDNLLE 708

Query: 712  GTGMESVVAKSSGAAIVAK--RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
               +E +  +   + ++A   R  + ++  A     R                       
Sbjct: 709  QGLVELIDTEEEESIMIAMDFRELVEKRSSANEGKSR----------------------- 745

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                           G   +        PS  LG L        + +P+  +N       
Sbjct: 746  --------------KGGSRQPYTHAEIHPSMILGILG-------SIIPFPDHNQ------ 778

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            S R   +       +  +    +                            +  V     
Sbjct: 779  SPRNTYQSAMGKQAMGVYITNFQQRM-----------------------DTLAHVLYYPQ 815

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
               +    +       +   +  + AI      +  D+ +   S +   +     +  + 
Sbjct: 816  RPLVTTQPMEYLRFGELPAGQNAVVAIACYSGYNQEDSVIMNQSAIDRGLFRSVFYRTYS 875

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKST 1006
              + ++   +    +E   + K D    +  + Y +L +   I  G           K+ 
Sbjct: 876  DHERKKGNFL----LENFEKPKRDTTAGMKTSTYEKLEDDGIIAPGVRVSGSDIIIGKTV 931

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L  +                    Q+     ++   T     E+   +           
Sbjct: 932  PLPEE-----------------SAKQKTSRQTRLDMSTPLRSNENGIVD-----TVVVTT 969

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + VK+ V + R  Q GDK + RHG KG        ED+PF ++G   DI++NP  
Sbjct: 970  DSEGFKFVKIKVRVVRIPQIGDKFSSRHGQKGTCGITYRQEDLPFTREGIVPDIIVNPHA 1029

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM VGQ+ E  LG      G +                                   
Sbjct: 1030 IPSRMTVGQLIECLLGKISSLSGNEGD--------------------------------- 1056

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F  A+    + ML      +    ++++G TG   +
Sbjct: 1057 --------------------ATP-FTDANVNYFSEMLHSLGYQKRANEVMFNGHTGRKLE 1095

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G  Y  +L HMV DK+++R+ G    +T+QP+ G++  GG R GEME  C+ ++G
Sbjct: 1096 AQIFIGPTYYQRLKHMVDDKIHSRARGPLQNLTRQPVEGRARDGGLRFGEMERDCMISHG 1155

Query: 1307 AAYVLQEMLTIKSD-------DVVGRTRVYESIVA--------GND---TFETGTPESFN 1348
            +A  L+E L   SD       +V G   +  + +          ++     +   P +F 
Sbjct: 1156 SAAWLKERLFQVSDEYRVHICNVCG--MMATANIKQQQFKCDACDNKTSFSQVFIPYAFK 1213

Query: 1349 VLVKEMQALGLSIDLENSRT 1368
            ++++E+ A+ L++ +  +  
Sbjct: 1214 LMIQELMAMNLAVRIITATE 1233



 Score =  200 bits (509), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 140/1013 (13%), Positives = 287/1013 (28%), Gaps = 215/1013 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-------------TAFSGA---- 71
           L+  Q  S++ F+             +Q   +    I                       
Sbjct: 68  LVRQQLDSFNVFIQQT----------IQELVEGTSEIMLSSSASYKVGQKRDQQQNQPQF 117

Query: 72  -AMLEFVSYEFDPPKFD-------------VDDCLWRDLTYAVPLKITL-RLIVFDVDEF 116
              ++F       P  D              +D   R+LTY+ PL + +    +      
Sbjct: 118 KYNIKFGQIYLSRPTVDTKSEQIEAYSSVYPNDARLRNLTYSSPLYVDIHEKKITLRPGS 177

Query: 117 TGAKSIKDIKEQS-------------IYMGDLPLMTKD---------------------- 141
           T       + E+              I +G +P+M +                       
Sbjct: 178 TANIYTAQVGEEDTDDFIVQSKIHNQIPLGSIPIMLRSVYCMLSEVQDVTDVGECPFDSG 237

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP-----DQ---GLWMD 193
           G F+I G ++++++Q   +     +H         K  Y   I        +   G ++ 
Sbjct: 238 GYFIINGGEKVIIAQERMAT----NHVYVFKKAMSKFSYVAEIRSSQEGGYRAPSGFFIK 293

Query: 194 IEF---DSKDII---------HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
           +E    + K  I         ++R D    +P+     AL   ++ EI+      +   Q
Sbjct: 294 MEPKQGNKKGGIGGLIHATIPYIRQD----IPIVILFRALSCQADKEIIKHIIYNLNDGQ 349

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI-- 298
             +     L  A  ++   V+   +    G  +  S +K  +   + L+++ +  +GI  
Sbjct: 350 MMELLRPSLEEAVAVLSNTVALDYIGKR-GNTLGASQEKRMNHAEEILQKEMLPHVGIGD 408

Query: 299 ----TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                     G  V   ++         +     +++        +   + +        
Sbjct: 409 TSYDRKAYFIGYMVHRLLLGALGRRPLDDRDHYGNKRLELAGGLLQGLFLQLFKKVVKEM 468

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            + ++ +++     D   A+             T  +  S+    +      D+      
Sbjct: 469 ESTLKKSILKSSEIDVAPAV--------NKRTITKGLQYSLATGNWGVQGSRDIRAGVAQ 520

Query: 415 KMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            +N      T   +R +    +          L N +  +                ++KN
Sbjct: 521 VLNRLTYTSTLSHLRRLNTPIERSGKQAAPRQLHNTQWGVICPAETPEGGACG---LVKN 577

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
              +  + +          +D   +     ++   +      F     +         + 
Sbjct: 578 LALMSYITVGTDKTHISKMLDELGINKLHELDESDLNKYTKVFLNGMWMGVHHTPDELVK 637

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS-FARV 592
            +   RR  A+             +RDV        C +         +     + F + 
Sbjct: 638 HLRVLRRTGAV-------DMQVSIVRDVREREVRIWCDSGRCARPLFIVDRDHDTLFIKN 690

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                +        +      V  +   EEE+  IA     L E  S   E    +    
Sbjct: 691 QHVQALRENTMNWDNLLEQGLVELIDTEEEESIMIAMDFRELVEKRSSANEGKSRKGGSR 750

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
           +           +  P  ++ I  S+IPF +++ S R      M +QA+ +         
Sbjct: 751 QPY------THAEIHPSMILGILGSIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFQ--- 801

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                                                     + + V  Y          
Sbjct: 802 --------------------------------------QRMDTLAHVLYYP--------- 814

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                QRPLV                    G+L  G+N +VA   + GYN EDS+++++ 
Sbjct: 815 -----QRPLV----------TTQPMEYLRFGELPAGQNAVVAIACYSGYNQEDSVIMNQS 859

Query: 833 MVSEDVFTSIHIEEFEVMARDTKL----GPEEITRDIP-NVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    R          E+  RD    +     + +++ GII  G  
Sbjct: 860 AIDRGLFRSVFYRTYSDHERKKGNFLLENFEKPKRDTTAGMKTSTYEKLEDDGIIAPGVR 919

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P       PEE   +    +  +D+        +G+  TVV
Sbjct: 920 VSGSDIIIGKTVP------LPEESAKQKTSRQTRLDMSTPLRSNENGIVDTVV 966


>gi|186885921|gb|ACC93368.1| RNA polymerase beta subunit [Osteospermum asperulum]
          Length = 1024

 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 137/460 (29%), Positives = 219/460 (47%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE---QIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +    R+   QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKHEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +  +        L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMQVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+       +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYTLKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFRLNRKE 1023



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 233/684 (34%), Positives = 377/684 (55%), Gaps = 21/684 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   ARV
Sbjct: 341 TQIVHGRKLSYLGPGGLTARIATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGTRMLYLSPGRDEYYMVAAGNSLALNQGIPEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSNSEKSIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +   D  +I +                  L+ +QRSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYTDTDKIHLSGN--------GNTLRIPLVMYQRSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573 NTCMHQKPQVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI + E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKHEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILVGKLTPQMVKESSYAPEDRLLRTILGMQVYTSKETCLKLPIGGRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISV-----EREQIELLAR 969
           D+ E++ S+     ++ +I++  +
Sbjct: 750 DETEKTESIRVYILQKREIKVGDK 773



 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRC-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELT---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|52694139|emb|CAG30599.1| DNA-directed RNA polymerase beta chain [Pseudomonas mucidolens]
          Length = 389

 Score =  376 bits (966), Expect = e-101,   Method: Composition-based stats.
 Identities = 234/389 (60%), Positives = 304/389 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            +IHI+E   +ARDTKLGPEEIT DIPNV
Sbjct: 361 PTIHIQELTCVARDTKLGPEEITADIPNV 389


>gi|222093451|gb|ACM43502.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
 gi|222093453|gb|ACM43503.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
 gi|222355886|gb|ACM48575.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
 gi|222355888|gb|ACM48576.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
 gi|222355890|gb|ACM48577.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
 gi|222355892|gb|ACM48578.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
          Length = 821

 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/680 (38%), Positives = 408/680 (60%), Gaps = 29/680 (4%)

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D +   Y+A+D        I ++  D   E  +     + I +   + + +      I+N
Sbjct: 1   DRIITTYLAQD--------IVLKNVDPTMEAKILYPKGTYITNDIAIEIQNAFKEGLIKN 52

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             + D           +Y  +   +        ++     F S K       +  +   +
Sbjct: 53  IDLKDYGITSD-----VYGKLLDTNPK-LKNRMNIIGIYIFKSKKAMEKDGEKHFV---I 103

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             D      H+   DI+AII    +L    G  DD D+L N+R+ SVGE+L NQ  +GLL
Sbjct: 104 GNDPTSVENHLLISDIVAIINYYFNLNENIGRDDDPDSLINKRIVSVGELLLNQLNIGLL 163

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +ME++ +E++SS +I  + P+++ N K + + +  FF SS+LSQ  +  N LS I+  R+
Sbjct: 164 KMEKNTREKMSSKEISRITPKNITNNKMIQNQIKTFFNSSKLSQFMDQTNPLSEISTKRK 223

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A+V+ YGF++T
Sbjct: 224 ITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYAKVDEYGFLQT 283

Query: 601 PYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY KV +G V  +  VYL+A EE NR  AQ++ S+DE+G  T+E V  +   +  +V  +
Sbjct: 284 PYFKVTNGIVDFSQPVYLTAHEEINRTFAQSSISIDENGKITDEQVIVKSNFDYNVVSPK 343

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D+ID S KQ+ S+AAS IPFLEN+D+NR LMG NMQRQAVPLL AEAP V TG+E+ +
Sbjct: 344 EVDYIDVSSKQMTSLAASSIPFLENNDANRALMGSNMQRQAVPLLFAEAPLVATGIEADI 403

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           AK S   + +   G V  VD  +I I+    D       +  Y+L  F+++NQ T ++Q 
Sbjct: 404 AKFSPNNLKSTVDGEVVFVDGSQIKIK----DSASEKGSIKTYQLKTFEKTNQGTVISQS 459

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+VK+GD+V + D+I+D  S   G++ALG+N+LV F  W+GYN+ED++++SER+V +DVF
Sbjct: 460 PIVKMGDKVLKGDLISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE  +  R +K G +++T DIPN S +  +++DE GI+ +G+EV  GDILVG+++
Sbjct: 520 TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRVS 579

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           PKG+  ++P EKLL  IF +K  + +DTSL+V +G  GTV+DV I +R   +       V
Sbjct: 580 PKGDENISPAEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSRENGN-------V 632

Query: 960 EREQIELLARDKDDEQVILD 979
             E+I+++ +    ++  + 
Sbjct: 633 LEEEIDMMIKVYVAQKRKIK 652



 Score =  323 bits (829), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 131/428 (30%), Positives = 193/428 (45%), Gaps = 67/428 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L+   +   +  M   + +L         +  D  +     V   V 
Sbjct: 461  IVKMGDKVLKGD-LISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  +S + + +    +       +  LD N   R+   +   + + G  
Sbjct: 520  -TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRV 578

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K    +S    +E   +  +   + +EK       +K  ++ +   +E      I   
Sbjct: 579  SPKGDENISP---AEKLLNGIFNQKISNEKDTSL--KVKNGHQGTVIDVE------ILSR 627

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + G+ +   +  ++KV+VA KR I+ GDKMAGRHGNKG++SR+LP EDMP+L+DGTP+DI
Sbjct: 628  ENGNVLEEEIDMMIKVYVAQKRKIKVGDKMAGRHGNKGVISRVLPVEDMPYLEDGTPLDI 687

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  S + D     DI       +       
Sbjct: 688  ILNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVSPVFDGVKKADIMDALEEAKLPRTGKM 747

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VFD                            
Sbjct: 748  K----------------------------VFDPT-------------------------- 753

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D  ++VG +YM KL+HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 754  TGEKIDNEISVGVMYMFKLSHMVDDKMHSRSIGPYSLITQQPLGGKSQNGGQRFGEMETW 813

Query: 1301 CIQAYGAA 1308
             +++YGAA
Sbjct: 814  ALESYGAA 821


>gi|290489646|gb|ADD31207.1| RNA polymerase beta subunit protein [Plumbago auriculata]
          Length = 1067

 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 136/427 (31%), Positives = 211/427 (49%), Gaps = 55/427 (12%)

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            R   ++            +E   L+ ++     +   ++ G    +G     K T   + 
Sbjct: 689  RKYEIQTHVTSQGPEKLTNEIPHLEAHLLRNLDKNGIVMIGSWVETGDILVGKLTPQMTK 748

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
              S  P  +  +  +  +        LK+       +++ R+         G    P   
Sbjct: 749  ESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRW-------IGGSSSNP--- 798

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRM
Sbjct: 799  ETIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRM 858

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 859  NVGQIFECSLGLAGELLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW------ 912

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+               L+  G+S ++DG TG+PF++ V +
Sbjct: 913  ------------------VFE---------------LESPGKSRIFDGRTGDPFEQLVII 939

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G A++L
Sbjct: 940  GNPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVAHIL 999

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD +  R  +  + + G         PESF +LV+E+++L L ++  L + + 
Sbjct: 1000 QEMLTYKSDHIRARQEILGTTIIGGTLPNPEDAPESFRLLVRELRSLALELNHFLVSEKN 1059

Query: 1369 KNSAKME 1375
               ++ME
Sbjct: 1060 LRISRME 1066



 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 255/804 (31%), Positives = 418/804 (51%), Gaps = 57/804 (7%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            +   A  +   + LE I + EI    +   +  N                +++A+L+ Y+
Sbjct: 182  VLSSAMGLNLREILENICYPEILFSFLTDKEKKNFG-------------SKENAILEFYQ 228

Query: 380  VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                  GD              FF   + +L  +GR  MN RLNLD P++   +   DI+
Sbjct: 229  QFACVGGDPVFSESLWKELQTKFF-QQRCELGRIGRRNMNQRLNLDIPENNTFLLPRDIL 287

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            A   +L+ ++ G  TIDD+D+L N+R+RSV ++L++Q+ L L+R+E  ++  I       
Sbjct: 288  AAADLLIGIKFGMDTIDDMDHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGAIRHK 347

Query: 498  V--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
                PQ+L+ + P+++    FF    LSQ+ +  N L++I H R+LS+LG GG+    A 
Sbjct: 348  FIPTPQNLVTSTPLITTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSSLGPGGLTGRTAS 407

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
              +RD+HP+HYGRICP +TSEG N+GL+ SL   A++   G +E+P+ ++        ++
Sbjct: 408  FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAKIGFLGSLESPFYEISGKSKKVQML 467

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            YLS+  +E   +A  NS     G   E +V  R   E +    E++ F    P Q  SI 
Sbjct: 468  YLSSRRDEYYIVATGNSLALSQGIQEEGVVPARYRQEFLTSAWEQVHFRSIFPFQYFSIG 527

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VGTG+E   A  SG   +A++ G +
Sbjct: 528  ASLIPFIEHNDANRALMSSNMQRQAVPLSHSEKCIVGTGLERQAALDSGVLAIAEQEGKI 587

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
               D  +I++ S                L+ +QRSN+NTC++Q+P +  G  +++  I+A
Sbjct: 588  ISTDTDKIILSSN--------GYTLSVPLVMYQRSNKNTCMHQKPQIPKGKCIKKGQILA 639

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            DG +T  G+LALG+N+LVA+MPW GYNFED++LISER+   D++TS HI ++E+    T 
Sbjct: 640  DGAATVGGELALGKNILVAYMPWEGYNFEDAVLISERLAYGDIYTSFHIRKYEIQTHVTS 699

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLL 913
             GPE++T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+     +  PE++LL
Sbjct: 700  QGPEKLTNEIPHLEAHLLRNLDKNGIVMIGSWVETGDILVGKLTPQMTKESSYAPEDRLL 759

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF-NRHGIDKNERSISVEREQIELLAR--- 969
            RAI G +    ++T L++P G  G V+DVR         +  R   +++ +I++  +   
Sbjct: 760  RAILGIQVSTSKETCLKLPIGGRGRVIDVRWIGGSSSNPETIRVYILQKREIKVGDKVAG 819

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP-------RSQWW 1022
               ++ +I        +  +  G+            + ++   I E           + +
Sbjct: 820  RHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGELLDRHY 879

Query: 1023 QFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + A  DE+ ++            E+ K         LE   K++I   + GD       +
Sbjct: 880  RIAPFDERYEQEASRKLVFSELYEASKQTANPWVFELESPGKSRIFDGRTGDPFE----Q 935

Query: 1073 VVKV---FVAMKRPIQSGDKMAGR 1093
            +V +   ++  K   Q  DK+ GR
Sbjct: 936  LVIIGNPYIL-KLIHQVDDKIHGR 958



 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 114/240 (47%), Gaps = 29/240 (12%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF-- 76
           +N  +  IP   ++Q   +  F+          ++GL         I        +EF  
Sbjct: 5   RNESVSTIPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDRDQ--EIEFQL 52

Query: 77  --VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
              +Y+   P     D ++  LTY+  L ++  LI          K  +D++EQ+I++G+
Sbjct: 53  FAEAYQLVEPLLKERDAVYESLTYSSELYVSAGLIW---------KMSRDMQEQTIFIGN 103

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++
Sbjct: 104 IPLMNSLGTFIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRSEL 160

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           E D K  I  R+ R++K+ +     A+G++  EIL    YP+I++S   D       + +
Sbjct: 161 EIDRKARIWARVSRKQKISILVLSSAMGLNLREILENICYPEILFSFLTDKEKKNFGSKE 220


>gi|159161152|ref|YP_001542439.1| RNA polymerase beta subunit [Ceratophyllum demersum]
 gi|182676556|sp|A8SE86|RPOB_CERDE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|148508435|gb|ABQ81442.1| RNA polymerase beta subunit [Ceratophyllum demersum]
 gi|227481111|emb|CAP62490.1| RNA polymerase beta subunit [Ceratophyllum demersum]
          Length = 1070

 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 133/396 (33%), Positives = 202/396 (51%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R   +  G    +G     K T  ++   S  P  +  +  +  +        LK+  
Sbjct: 720  LDRNGIVRLGSWIETGDILVGKLTPQTAKESSYAPEDRLLRAILGVQVSTAKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DGTP+D+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILARQDMPYLQDGTPIDMVFNPLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +   +                           VF+          
Sbjct: 893  QEASRKLVFPELYEASKQTSNPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGDPFEQPVIIGKSYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++ QEMLT KSD +  R  V  + + G       
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHISQEMLTYKSDHIRARQEVLGTTIIGGTIPNPE 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLALELNHFLISDKNFQINRKE 1069



 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 258/830 (31%), Positives = 425/830 (51%), Gaps = 43/830 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILDNVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      D+ K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203  IFLSFLNDKDRKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN RLNL+ P +   +   D++A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262  GRRNMNQRLNLNIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E +I+  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALVRLENAIRGTISGAIKHKLIPTPQNLVTSTPLTTTFESFFGLHPLSQVLDRT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L++I H R+ S LG GGV    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTQIVHGRKSSYLGPGGVTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            A++  +G IETP+ ++ +      +VYL    +E   +A  NS     G   E++V  R 
Sbjct: 442  AKIGFWGSIETPFYEISEKSKEAQIVYLPPSRDEYSMVAAGNSLALNRGIQEEQVVPARY 501

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E + +  EKI      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502  RQEFLTIAWEKIHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLFRSEKC 561

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E  VA  SG + +A+  G +   D  +IV+ +                L+ +QR
Sbjct: 562  IVGTGLERQVALDSGVSAIAEHEGKILYTDTDKIVLSAN--------GDTISIPLVMYQR 613

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN+NTC++Q+P V+    +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614  SNKNTCMHQKPQVQRNKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SERMV ED+FTS HI ++E+    T  GPE IT +IP++    L+N+D  GI+ +G+ + 
Sbjct: 674  SERMVYEDIFTSFHIRKYEIQTHVTSQGPERITNEIPHLEAHLLRNLDRNGIVRLGSWIE 733

Query: 890  PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734  TGDILVGKLTPQTAKESSYAPEDRLLRAILGVQVSTAKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948  HGIDKNE----RSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
             G         R    ++ +I++  +      ++ +I        +  +  G        
Sbjct: 794  KGGSSYNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILARQDMPYLQDGTPIDMVFN 853

Query: 1001 GFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESLKVQYE 1043
                 + ++   I E           + ++ A  DE+ ++            E+ K    
Sbjct: 854  PLGVPSRMNVGQIFECSLGLAGDLLDRHYRIAPFDERYEQEASRKLVFPELYEASKQTSN 913

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                  E   K++I   + GD     V+ + K ++  K   Q  DK+ GR
Sbjct: 914  PWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKSYIL-KLIHQVDDKIHGR 961



 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  FL          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFSQIQFEGFCRFL----------DQGLTEELHKFPKIEDTDQEIEFQLFVETYQLAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L +   LI          K+ +D++EQ++++G++PLM   GT
Sbjct: 62  PLIKEKDAIYESLTYSSELYVPAGLIW---------KNGRDMQEQTVFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILDNVCYPEIFLSFLNDKDRKKIGSKE 220


>gi|169142779|ref|YP_001687204.1| RNA polymerase beta subunit [Aneura mirabilis]
 gi|153973805|gb|ABS54465.1| RNA polymerase beta subunit [Aneura mirabilis]
          Length = 1065

 Score =  376 bits (965), Expect = e-101,   Method: Composition-based stats.
 Identities = 231/594 (38%), Positives = 351/594 (59%), Gaps = 13/594 (2%)

Query: 366 KNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           K +  ++A ++ YR + R G   TFS +        F   + +L   GR  +N +  +D 
Sbjct: 210 KARSTEEATVEPYRQLYRVGTDITFSESLRRDLQKKFFRHRCELGKTGRSNLNEKFAIDI 269

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           P++   +  +D++A +   +  + G GTID+ID+L NRR+ SV  +L+NQ +L L R+E 
Sbjct: 270 PENETSLLPQDVLAAVDYPIKPKLGIGTIDNIDHLKNRRICSVANLLQNQLKLALNRLEH 329

Query: 485 SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           SI+   + ++       P+ L+++ P++    EFF S  LSQ  +  N L+ I H RRLS
Sbjct: 330 SIRQIFQGTTKRKRLPTPRALVSSTPLMITFKEFFGSHPLSQFLDQTNPLTEIVHKRRLS 389

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           +LG GG+ R  A  ++RD+HP+HYGRICP ETSEG N GL+ SL   A +N+ G +E+P+
Sbjct: 390 SLGPGGLTRRTASFQVRDIHPSHYGRICPIETSEGMNAGLIGSLAIHAGINSSGRLESPF 449

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+ +    + +   SA  +E   IA  N    +     E++   R   + + +  E++ 
Sbjct: 450 YKISESYKEDRIYNPSAGRDECYRIATGNFLALDRRGREEQITPARYRQDFVAIAWEQVH 509

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           F    P Q  SI ASLIPFLE++D+NR LMG NMQRQAVPLL++E   VGTG+ES  A  
Sbjct: 510 FRSIFPSQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLLRSEKCIVGTGVESQTASD 569

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  I +   G +  V + +I +     +++         + + +Q +N  TC++Q+P  
Sbjct: 570 SGGTIASIWGGRISFVSSNQITLSMNGKEMNT--------KPISYQSTNNGTCMHQKPRD 621

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                V+R  I+ADG +T  G+LALG+N+ VA+MPW GYNFED++LIS+R V ED +TSI
Sbjct: 622 DEEVYVKRGQILADGAATAKGELALGKNVSVAYMPWEGYNFEDAILISDRSVYEDTYTSI 681

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIE++ + AR T  G E+ TR+IP++    L+++D  G   +G+ V  GDILVGK+TP+ 
Sbjct: 682 HIEKYVIEARVTSQGVEKFTREIPHLDNYLLRHLDRNGFATIGSWVETGDILVGKLTPQE 741

Query: 903 --ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
             E+   PE KLL+AIFG +     +T LRVP G  G V+D+R  +R  I  ++
Sbjct: 742 IKETSRAPEGKLLQAIFGIQITTSEETCLRVPIGGRGRVIDIRSISREDITSDD 795



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 142/472 (30%), Positives = 204/472 (43%), Gaps = 80/472 (16%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++ S+           D  + +   + ++  + I +E+  IE             E   L
Sbjct: 648  KNVSVAYMPWEGYNFEDAILISDRSVYEDTYTSIHIEKYVIEARVTSQGVEKFTREIPHL 707

Query: 979  DRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            D  +     R      G    +G     K T       S  P  +  Q     +      
Sbjct: 708  DNYLLRHLDRNGFATIGSWVETGDILVGKLTPQEIKETSRAPEGKLLQAIFGIQITTSEE 767

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              L+V       +++      I  I   D        ++ V+V  +R IQ GDK+AGRHG
Sbjct: 768  TCLRVPIGGRGRVID------IRSISREDITSDDA-EIIHVYVPQQRKIQIGDKIAGRHG 820

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKGIVS ILP +DMPFL++G P+D++L+PLGVPSRMNVGQI E  LG A   L K  +  
Sbjct: 821  NKGIVSEILPRQDMPFLQNGVPMDMILSPLGVPSRMNVGQILECLLGLAGYFLNKNYRIT 880

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
             +D +   + S    F  ++      T     ++                          
Sbjct: 881  PSDERYEQESSRKLVF-SELYRASEITSNPWLFE-------------------------- 913

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                         +  G++ L DG TGE F++PVT G  YMLKL H V DK++ARS+G Y
Sbjct: 914  ------------PNNPGKNRLLDGRTGEAFEQPVTTGIAYMLKLIHQVDDKIHARSSGPY 961

Query: 1276 SLVTQQPLGGKSNRGGQRLG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
            +LVTQQPL                        EMEVW ++ +G +Y+LQEMLT KSD + 
Sbjct: 962  ALVTQQPL------------RGRSRRGGQRVGEMEVWALEGFGVSYILQEMLTTKSDHIR 1009

Query: 1324 GRTRVYESIVAGNDTFETG-TPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             R  V  +IV G    +    PESF +LV+E+++L L I    +  KN    
Sbjct: 1010 ARYEVLGAIVTGEPVHKPDTVPESFKLLVRELRSLALGIGHNTTSEKNLELR 1061



 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 91/559 (16%), Positives = 192/559 (34%), Gaps = 50/559 (8%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-Y 79
           + + +P+   +Q   ++ F+           +GL     +   I           F   Y
Sbjct: 2   QTLVLPEFGRIQFEGFNRFIT----------QGLSEELTNFPKIEDTERELQFRIFGDEY 51

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               P F+  + +++ +TY+  L +  RL+          +   +++ Q++++G +PLM 
Sbjct: 52  ILTEPLFEEKNAVYQSVTYSSDLYVPARLLY---------RRGGEVRRQTVFLGSIPLMN 102

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF++ GI R++V+Q+ RSPGI+++ +  R   +G  +Y    I + G  + +E D K
Sbjct: 103 SQGTFIVNGIARVIVNQILRSPGIYYNSESDR---NGVSVYTGTFISNWGGRLKLEIDGK 159

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEEIL-STFYPKIVYSQRGDF-------WCFPLSA 251
             +  RI ++RKV V   L A+G+D E+I+ S  YPKI+    G+             + 
Sbjct: 160 ARVWARISKKRKVSVLVLLSAMGLDFEKIVASICYPKILLESVGEGTGGEKARSTEEATV 219

Query: 252 ADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                  +V + +   ++  + + +   +    L K+ +    +   I         + +
Sbjct: 220 EPYRQLYRVGTDITFSESLRRDLQKKFFRHRCELGKTGRSNLNEKFAIDIPENETSLLPQ 279

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           D++             +    +++ + +  I  +  L  + +          +    +  
Sbjct: 280 DVL-AAVDYPIKPKLGIGTIDNIDHLKNRRICSVANLLQNQLKLALNRLEHSIRQIFQGT 338

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
                                 +  F            + +  +    RL+   P  +  
Sbjct: 339 TKRKRLPTPRALVSSTPLMITFKEFFGSHPLSQFLDQTNPLTEIVHKRRLSSLGPGGLTR 398

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                 +  I       +  G I  I+         +G +  +       R+E    +  
Sbjct: 399 RTASFQVRDIH-----PSHYGRICPIETSEGMNAGLIGSLAIHAGINSSGRLESPFYKIS 453

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            S   D +        +      C    +       +      +IT  R         VA
Sbjct: 454 ESYKEDRIYNPSAGRDE------CYRIATGNFLA-LDRRGREEQITPARYRQDF----VA 502

Query: 551 RARAGVEMRDVHPTHYGRI 569
            A   V  R + P+ Y  I
Sbjct: 503 IAWEQVHFRSIFPSQYFSI 521


>gi|215254209|gb|ACJ64109.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
          Length = 376

 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 238/376 (63%), Positives = 293/376 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++F
Sbjct: 1   NPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+E+G+F +EL+  R 
Sbjct: 61  ARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEEGTFADELITARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P
Sbjct: 121 KGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKP 180

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ R
Sbjct: 181 LVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTR 240

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+
Sbjct: 241 SNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILV 300

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 301 SERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVK 360

Query: 890 PGDILVGKITPKGESP 905
            GDILVGK+TPKGE+ 
Sbjct: 361 GGDILVGKVTPKGETQ 376


>gi|115391894|ref|YP_778482.1| RNA polymerase beta subunit [Jasminum nudiflorum]
 gi|122164981|sp|Q06RD9|RPOB_JASNU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|110456215|gb|ABG74620.1| RNA polymerase beta subunit [Jasminum nudiflorum]
          Length = 1064

 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 136/424 (32%), Positives = 215/424 (50%), Gaps = 54/424 (12%)

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R   ++    E +  +    +  L RN+  +   ++ G    +G     K   L+ +++ 
Sbjct: 691  RKYEIQTAGTERITNEIPHLEAHLLRNL-DKNGIVMLGSWVETGAILVGK---LTPEVVK 746

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            E P ++        + V   V + K            R  +     + GD+  P     +
Sbjct: 747  ESPANRLV-----YDIVGIQVSTSKDTCLKLPIGGRGRVIDVRWIQKRGDNDNP---ETI 798

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            +++++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVG
Sbjct: 799  RIYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVG 858

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            QIFE  LG A   L +  + +  D +   + S    F E    +   T            
Sbjct: 859  QIFECSLGLAGGLLDRHYRIVPFDERYEQEASRKLVFSELYEASKQTTNPW--------- 909

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                           VF+                +  G+S ++DG +G PF++P+ +G  
Sbjct: 910  ---------------VFE---------------PEYPGKSRIFDGRSGNPFEQPILIGKP 939

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y+LKL H V DK++ RS G+Y+ +TQQPL G++  GGQR+GEMEVW ++ +G A++LQEM
Sbjct: 940  YILKLIHQVDDKIHGRSVGNYTHITQQPLRGRAKGGGQRVGEMEVWALEGFGVAHILQEM 999

Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNS 1371
            LT KSD +  R ++  + + G         PESF VLV+E+++L L ++  L + +    
Sbjct: 1000 LTYKSDHIRARQKIPGTTMIGGTIPNPEDAPESFRVLVRELRSLALELNHFLVSEKNFQI 1059

Query: 1372 AKME 1375
             + E
Sbjct: 1060 NRKE 1063



 Score =  355 bits (911), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 229/687 (33%), Positives = 369/687 (53%), Gaps = 22/687 (3%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E     + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELDHNEISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLKEILD 196

Query: 350 DSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++      ++ K   +++A+L+ Y+      GD              FF   +
Sbjct: 197 NVFYPEIFLSFLKDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQTKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   DI+A    L++ + G GT+DD+++L N+R+R
Sbjct: 256 CELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIEQKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV----MPQDLINAKPVVSAVCEFFCSSQ 521
           SV ++L++Q  L L+R+E  ++E I             PQ+L+ + P+ +    FF S  
Sbjct: 316 SVADLLQDQLGLALVRLEDEVRETICGPIRHKWRTTPHPQNLVTSTPLTTTYESFFGSHP 375

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+ S L  GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 376 LSQVLDQTNPLTQIVHGRKWSYLDPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 435

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   A++  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 436 LIGSLAIHAKIGHWGSLESPFYEISERSTGVQMLYLSPGRDEYYTVAAGNSLALNQDIQE 495

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           EE+V  R   E + +  E++ F    P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 496 EEVVPARYRQEFLTIAWEQVHFRSILPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 555

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL + E   VGTG+E  VA  SGA  +A+R G +   D         E  L         
Sbjct: 556 PLSRPEKCIVGTGLERQVALDSGALAIAEREGKIVSTD--------TEKILFSGNGDTLS 607

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +Q SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 608 IPLVMYQSSNKNTCMHQKPQVQRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 667

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISER+V ED++TS HI ++E+       G E IT +IP++    L+N+D+ GI
Sbjct: 668 NSEDAVLISERLVYEDIYTSFHIRKYEIQT----AGTERITNEIPHLEAHLLRNLDKNGI 723

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + +G+ V  G ILVGK+TP+     +P  +L+  I G +    +DT L++P G  G V+D
Sbjct: 724 VMLGSWVETGAILVGKLTPEVVKE-SPANRLVYDIVGIQVSTSKDTCLKLPIGGRGRVID 782

Query: 942 VRIFNRHGIDKNERSISVEREQIELLA 968
           VR   + G + N  +I +   Q   + 
Sbjct: 783 VRWIQKRGDNDNPETIRIYISQKREIK 809



 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 110/233 (47%), Gaps = 29/233 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF----VSYEF 81
           IP L ++Q   +  F+          ++GL         I        +EF      Y+ 
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTDQ--EIEFQLFMERYQL 59

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P     D ++  LTY+    ++  LI          K+ +D++EQ+I +G++PLM   
Sbjct: 60  VEPLRKERDAVYESLTYSSEFYVSAGLIW---------KTSRDMQEQTILIGNIPLMNSL 110

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GT ++KGI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  
Sbjct: 111 GTSIVKGIYRIVINQILQSPGIYYRSELDHNEIS---VYTGTIISDWGGRSELEIDRKAR 167

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWCFPLSAAD 253
           I  R+ R++K+ +     A+G + +EIL   FYP+I  S   D     + + +
Sbjct: 168 IWARVSRKQKISILVLSSAMGSNLKEILDNVFYPEIFLSFLKDKERKKIGSKE 220


>gi|290489626|gb|ADD31197.1| RNA polymerase beta subunit protein [Ximenia americana]
          Length = 1075

 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 132/396 (33%), Positives = 199/396 (50%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   +  G    +G     K T   +  +S  P  +  +  +  +        LK+  
Sbjct: 725  LDKNGIVKPGSWVETGDILVGKLTPQRAKGLSYVPEDRLLRVILGIQAATSKETCLKLPI 784

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V+++ KR IQ GDK+AGRHGNKGI+S+
Sbjct: 785  GGRGRVIDVRWSQKK----RGSSYNP---ETIRVYISQKREIQVGDKVAGRHGNKGIISK 837

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG P D+  NPLGVPSRMNVGQIFE  LG A   L +  + +  D +  
Sbjct: 838  ILPRQDMPYLQDGRPADMGFNPLGVPSRMNVGQIFECSLGLAGDLLNRHYRIVPFDERYE 897

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 898  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 923

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS G Y++VTQQP
Sbjct: 924  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSGGHYAIVTQQP 978

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEME+W ++ +G AY+LQEMLT KSD +  R  V  + + G       
Sbjct: 979  LRGRAKQGGQRVGEMEIWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTISNPE 1038

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L +   L + +     + E
Sbjct: 1039 DAPESFRLLVRELRSLALELKHCLVSEKNFQINRRE 1074



 Score =  364 bits (933), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 256/837 (30%), Positives = 427/837 (51%), Gaps = 48/837 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +  E          + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRSELEIDRKERIWARVSRKQKISILVLSSTMGSNLREILENVCYPE 202

Query: 356  AYIRNTLVTDKNKDR---KDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLST 410
             ++    + +K K     ++A+L+ Y+      GD +            FF   K +L  
Sbjct: 203  IFLSFLNLNEKEKKMGSKENAILEFYQQFACVGGDPAFSESLCKELQKKFF-QQKCELGR 261

Query: 411  VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            +GR  MN +LNLD P +   +   DI+A +  L+ ++ G GT DD+++L N+R+RSV ++
Sbjct: 262  IGRRNMNRKLNLDIPQNNTFLLPRDILAAVDHLIGIKFGMGTRDDMNHLKNKRIRSVADL 321

Query: 471  LKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+++    FF    LSQ+ + 
Sbjct: 322  LQDQFGLALVRLENVVRRTICGAIRHKLIPTPQNLVTSTPLITTYESFFGLYPLSQVLDQ 381

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             N L++I H R+ S LG GG+    A   +RD+HP+HYG ICP +TSEG N+GL+ SL  
Sbjct: 382  TNPLTQIVHGRKSSYLGPGGLTGRTASFRIRDIHPSHYGCICPIDTSEGINVGLIGSLAI 441

Query: 589  FARVNAYGFIETPYRKV----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
             AR+  +G +E+ +  V       K    ++YLS+ ++E   IA  NS     G   E++
Sbjct: 442  HARIGHWGSLESLFYDVYEISERSKKKIRMLYLSSSKDEYYMIAAGNSLALNQGIQEEQV 501

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL 
Sbjct: 502  VPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLF 561

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            ++E   VGTG+E   A  SG   +A+R G +   D  +IV+                  L
Sbjct: 562  RSEKCIVGTGLECQAALDSGVPAIAERGGKIIYTDTDKIVLSGN--------GDTLSIPL 613

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            + +QRSN+ TC++Q+P V+    +++  I+ADG +T  G+LALG+N+LVA+MPW GYN E
Sbjct: 614  VMYQRSNKKTCMHQKPQVQRDKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSE 673

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
            D++LISER+V ED++TS HI+++E+    T  GPE IT +IP +    L+N+D+ GI+  
Sbjct: 674  DAILISERLVYEDIYTSFHIQKYEIQTHVTSQGPERITNEIPYLETHLLRNLDKNGIVKP 733

Query: 885  GAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            G+ V  GDILVGK+TP+    ++  PE++LLR I G +A   ++T L++P G  G V+DV
Sbjct: 734  GSWVETGDILVGKLTPQRAKGLSYVPEDRLLRVILGIQAATSKETCLKLPIGGRGRVIDV 793

Query: 943  RIFNRHGIDKNE----RSISVEREQI---ELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            R   +           R    ++ +I   + +A    ++ +I        +  +  G+ A
Sbjct: 794  RWSQKKRGSSYNPETIRVYISQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPA 853

Query: 996  VSGPKGFKKSTVLSSDLISEYP-------RSQWWQFAVQDEKVQRN----------VESL 1038
              G       + ++   I E          ++ ++    DE+ ++            E+ 
Sbjct: 854  DMGFNPLGVPSRMNVGQIFECSLGLAGDLLNRHYRIVPFDERYEQEASRKLVFSELYEAS 913

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            K          E   K++I   + GD     V+ + K ++  K   Q  DK+ GR G
Sbjct: 914  KQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI-IGKPYIL-KLIHQVDDKIHGRSG 968



 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 105/236 (44%), Gaps = 29/236 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP    +Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNHIQFEGFCRFI----------DQGLTEELYKFPKIGDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
                 + ++  LTY+  L +   LI          K+ +DI+EQ+I++G++PLM   GT
Sbjct: 62  SLIKERNAVYESLTYSSELYVYAGLIW---------KTNRDIQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K+ I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRPELNHNGIS---VYTGTIISDWGGRSELEIDRKERIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
            R+ R++K+ +      +G +  EIL       ++          L+  +  +G+K
Sbjct: 170 ARVSRKQKISILVLSSTMGSNLREILENVCYPEIFL-----SFLNLNEKEKKMGSK 220


>gi|11467044|ref|NP_041951.1| RNA polymerase beta subunit [Euglena gracilis]
 gi|133397|sp|P23579|RPOB_EUGGR RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|311709|emb|CAA35052.1| RNA polymerase subunit [Euglena gracilis]
 gi|415794|emb|CAA50138.1| RNA polymerase subunit [Euglena gracilis]
          Length = 1082

 Score =  375 bits (964), Expect = e-101,   Method: Composition-based stats.
 Identities = 144/417 (34%), Positives = 209/417 (50%), Gaps = 57/417 (13%)

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL---SSDLISEYPRSQWWQFAVQDEK 1030
            E+++ +    S  M+           KG   S  +   S   I     +   +   + + 
Sbjct: 705  ERLVFEDIFTSIHMKKFKTFIVNDEKKGENISMFIPNASLKTIKNLKNNGIIKIGSEIKA 764

Query: 1031 VQRNVESLKVQYET--SKSILEDRFKNKIEK-------------IQWGDDMPPGVLRVVK 1075
                +  +KV+ +      +L   F NK+ K             +   + +       V 
Sbjct: 765  QDVLIGRIKVKLKNTPKNKMLIAFFGNKVRKDVSLRSPRSLVGIVTSVEILCKKSNCSVL 824

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + VA KR IQ GDK+AGRHGNKGI+S+I+P  DMPFL DGTPVD++LNPLG+PSRMNVGQ
Sbjct: 825  IHVAEKRRIQIGDKIAGRHGNKGIISKIVPSIDMPFLPDGTPVDMILNPLGIPSRMNVGQ 884

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            +FE+ L  + + L ++ K    D               +V  + +    +    +++  R
Sbjct: 885  VFESLLNLSSLFLKERYKIQPFD---------------EVQTSMNSKSFVYKKLNEARKR 929

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              + W                        + + +  G++ LYDG    PFD PV  GY Y
Sbjct: 930  TKKDW------------------------LFNPNYPGKAFLYDGRNCRPFDHPVAFGYAY 965

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
            +LKL HMV DK++AR TG YS VTQQPL GKS  GGQR GEMEVW I+ +GAAY+LQE+L
Sbjct: 966  ILKLIHMVKDKIHARVTGPYSSVTQQPLRGKSKNGGQRFGEMEVWAIEGFGAAYLLQELL 1025

Query: 1316 TIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            TIKSDDV+ R+    S++ G    +   PE+F + + EMQ+L + I +  +  K   
Sbjct: 1026 TIKSDDVLNRSEALFSLINGTYFSKPNIPEAFKLFILEMQSLCIDIKIFTNNYKKFD 1082



 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 231/794 (29%), Positives = 385/794 (48%), Gaps = 62/794 (7%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
           + F  +  Y               +  G K       I +     E   +    +  +L 
Sbjct: 84  NMFLVRNKYILFAKIPLMTEKGTFIFNGNKRIMVNQIIRSPGVYFEKN-RYNDSIFATLI 142

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                +L    D   G++V  D +      I            L+ +  S  +    L  
Sbjct: 143 PTFGSWLTFKIDQDEGIFVKVDKIKTAIPLINF----------LKCLGLSRKKFFLYLN- 191

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV-STFSVAESMFNFLFFDSDKYDL 408
                +     TL   ++   +    + Y++  P +V   F  A       F D  KYDL
Sbjct: 192 -----DPIFIETLQESESYGIRLEFFEFYKIFFPNEVNVRFGNARKFLRSKFMDPRKYDL 246

Query: 409 STVGRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             VGR ++N ++   +     R ++ ED++ I   L++L+ G    D+ID+L N+ VRS+
Sbjct: 247 GEVGRFRVNTKIYRSEFFQSNRTLQPEDVLGIAHYLIELKKGMIPFDEIDDLKNKLVRSI 306

Query: 468 GEMLKNQYRLGLLRMERSIKERI----SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           GE+L++Q+R+ L  +E S+KE++     +    +       N+  + + + +FF  + LS
Sbjct: 307 GELLQSQFRIILNELESSLKEKLIFLYKNPSEKTFRLSRFFNSYFITNRIRKFFSVNPLS 366

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           QL +  NSLS +TH R+LS  G  G+ + R  +++R+++ + YGR+CP ETSEG N GL+
Sbjct: 367 QLLDDTNSLSELTHKRKLSPFGPNGLNKERTKLDVREINTSQYGRVCPIETSEGKNAGLI 426

Query: 584 SSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            SL    RV+ YGF+E+P+ KV     +    + ++S+ +E+   +A  +       +  
Sbjct: 427 LSLAKDVRVDKYGFLESPFYKVLRGKIETNKGIYFISSAQEKYFTVAPFDVFRSSQSNLL 486

Query: 642 --EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +L+  + +        + IDFI  S  Q  S+   L+PFLE++D+NRVLMG NMQRQ
Sbjct: 487 DKNKLLGVKRSKIFSYSFSKNIDFISISTDQFTSLGTGLVPFLEHNDANRVLMGSNMQRQ 546

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE---------- 749
           ++ LL+ E PF+ TG E+++ + S A ++AK +G V      +IVI+  E          
Sbjct: 547 SLILLEKEVPFIKTGREALINRESDATVLAKSSGKVIYSSLKKIVIQEEEYCANIEFFNK 606

Query: 750 -----------------GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                       IY L   ++SN    + + P+V  G+ VR+  
Sbjct: 607 NYSFFNLLGCLNEISQKNFKLIKKVNQKIYFLESPKKSNHGVYIQKIPIVHEGEWVRKGQ 666

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           IIADG ST  G + LG+N+LVA++ W GYNFED+++ISER+V ED+FTSIH+++F+    
Sbjct: 667 IIADGMSTLRGGICLGKNVLVAYLGWEGYNFEDAVIISERLVFEDIFTSIHMKKFKTFIV 726

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           + +   E I+  IPN S + +KN+   GII +G+E+   D+L+G+I  K +   TP+ K+
Sbjct: 727 NDEKKGENISMFIPNASLKTIKNLKNNGIIKIGSEIKAQDVLIGRI--KVKLKNTPKNKM 784

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
           L A FG K    +D SLR P  + G V  V I  +    K+  S+ +   +   +     
Sbjct: 785 LIAFFGNKVR--KDVSLRSPRSLVGIVTSVEILCK----KSNCSVLIHVAEKRRIQIGDK 838

Query: 973 DEQVILDRNIYSRL 986
                 ++ I S++
Sbjct: 839 IAGRHGNKGIISKI 852



 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/334 (17%), Positives = 128/334 (38%), Gaps = 48/334 (14%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +L+++Q+ S+  FL   +  + R    ++      F I+  +       V Y+   PK  
Sbjct: 10  NLLDIQRNSFRSFLKKGLVEELRK---IKDIAHEGFRISFQTDN-----VKYK--KPKIS 59

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
            +  L    TY++ + I + +   ++           ++ + I    +PLMT+ GTF+  
Sbjct: 60  AEFALKNGETYSLSVHIPVEVTYNNMFL---------VRNKYILFAKIPLMTEKGTFIFN 110

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +RI+V+Q+ RSPG++F+    +   +  +     +IP  G W+  + D  + I V++D
Sbjct: 111 GNKRIMVNQIIRSPGVYFE----KNRYNDSIF--ATLIPTFGSWLTFKIDQDEGIFVKVD 164

Query: 208 RRRK-VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS--- 263
           + +  +P+ +FL  LG+           K  +    D             G ++      
Sbjct: 165 KIKTAIPLINFLKCLGLSR---------KKFFLYLNDPIFIETLQESESYGIRLEFFEFY 215

Query: 264 -LVDIDTGEQVIESGKKLTSGLLKSLKEKGV---------KFLGITSDCLCGLYVAEDIV 313
            +   +       + +K         ++  +           +  +        +  + V
Sbjct: 216 KIFFPNEVNVRFGNARKFLRSKFMDPRKYDLGEVGRFRVNTKIYRSEFFQSNRTLQPEDV 275

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            G    +      +I    ++++ +  +R I  L
Sbjct: 276 LGIAHYLIELKKGMIPFDEIDDLKNKLVRSIGEL 309


>gi|197131674|gb|ACH47355.1| RNA polymerase beta subunit [Geranium carolinianum]
          Length = 1113

 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 155/562 (27%), Positives = 242/562 (43%), Gaps = 63/562 (11%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E  + +   +          I         +  G       +          I
Sbjct: 611  CIVGTGLEGQVALDSGVPLITEHAGKVISIHTDKILLSGNGDTLSIPLVMYQRSNKNTCI 670

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G IL       G   +   + LL A    +  +  D  L     +S
Sbjct: 671  HQKPQVRRGKCMKKGQILADGAATVG-GELALGKNLLVAYMPWEGYNFEDAVL-----IS 724

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V  +  E + +       +L      +   ++ G    
Sbjct: 725  ERLVYEDIYTSFHIRKYEIQIHVTSQGPEKVTKKIPLRAHLLRN--LDKNGVVILGSWVE 782

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T   +  +S   +     F  Q    +     L          +     N 
Sbjct: 783  AGDILVGKLTPQLAQDLSPADQFVDAVFGTQLATSRETCLKLPRGGRGRVIDVRWIRSNP 842

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                             ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 843  KR-------------ERIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGK 889

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+D+V NPLGVPSRMNVGQIFE  LG A V L +  +    D +   + S    F E   
Sbjct: 890  PIDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDERYEQEASRKLVFSELHE 949

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 950  ASKQTGNPW------------------------VFE---------------PEYPGKSRI 970

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV VG  Y+LKL H V DK++ RS G Y+ VTQQP+ G++ RGGQR+GE
Sbjct: 971  FDGRTGDPFEQPVIVGQPYILKLIHQVDDKIHGRSNGPYASVTQQPIRGRAKRGGQRVGE 1030

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G A++LQEMLT KSD +  R +++++ + G +  +    PESF +LV+E++
Sbjct: 1031 MEVWALEGFGVAHILQEMLTYKSDHLRTRDKIFDTTIVGGEMPKAEDAPESFRLLVRELR 1090

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +     + E
Sbjct: 1091 SLALELNHFLVSEKNFQMNRKE 1112



 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 222/686 (32%), Positives = 376/686 (54%), Gaps = 16/686 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K   + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 187 ELDHKGFWVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILE 246

Query: 350 DSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMR--PGDVSTFSVAESMFNFLFFDSDK 405
           +      ++      +K K   +++A+L+ Y+      GD              FF   +
Sbjct: 247 NVCYPEIFLAFLDDKEKEKMGSKENAILEFYQQFVCVDGDPVFSDSLCKELQNQFF-RQR 305

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  +N RLNLD   +   +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 306 CELGRIGRRNINRRLNLDISQNNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIR 365

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E+ ++  I       +   PQ+ + + P  +    FF    LS
Sbjct: 366 SVADLLQDQFGLALIRLEKVVRGAIGGAIKGKLIPTPQNFVTSTPFKTTYESFFGLHPLS 425

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+ S LG GG+    A   +RD+HP++YGRIC  +TSEG N+GL+
Sbjct: 426 QVLDETNPLTQIVHGRKWSFLGPGGLTGRTASFRIRDIHPSYYGRICTIDTSEGINVGLI 485

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G +E+P+ ++ +      ++YLS+  +E   I   NS    +G   E+
Sbjct: 486 GSLAIHARIGHFGSLESPFYEISEKSKRARILYLSSRRDEYCMIGTGNSLALNEGFQEEQ 545

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV L
Sbjct: 546 IVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVAL 605

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E  VA  SG  ++ + AG V  +          +  L           
Sbjct: 606 SRSEKCIVGTGLEGQVALDSGVPLITEHAGKVISIH--------TDKILLSGNGDTLSIP 657

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNF
Sbjct: 658 LVMYQRSNKNTCIHQKPQVRRGKCMKKGQILADGAATVGGELALGKNLLVAYMPWEGYNF 717

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V ED++TS HI ++E+    T  GPE++T+ IP +    L+N+D+ G++ 
Sbjct: 718 EDAVLISERLVYEDIYTSFHIRKYEIQIHVTSQGPEKVTKKIP-LRAHLLRNLDKNGVVI 776

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           +G+ V  GDILVGK+TP+    ++P ++ + A+FG +    R+T L++P G  G V+DVR
Sbjct: 777 LGSWVEAGDILVGKLTPQLAQDLSPADQFVDAVFGTQLATSRETCLKLPRGGRGRVIDVR 836

Query: 944 IFNRHGIDKNERSISVEREQIELLAR 969
               +   +  R    ++ +I++  +
Sbjct: 837 WIRSNPKRERIRVYISQKREIKVGDK 862



 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/280 (21%), Positives = 113/280 (40%), Gaps = 18/280 (6%)

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L ++  LI      +        +++Q+I +G++PLM
Sbjct: 106 YKLVEPLIKERDAVYESLTYSSELYVSAGLIWKRKGYY--------MQKQTILIGNIPLM 157

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              G F++ GI R+VV+Q+ +SPGI++  +       G  +Y   II D G  +++E D 
Sbjct: 158 NSLGIFIVNGIYRMVVNQILQSPGIYYRSELDHK---GFWVYTGTIISDWGGRLELEIDR 214

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVG 257
           K  I  R+ R++K+ +     A+G +  EIL    YP+I  +   D     + + +  + 
Sbjct: 215 KARIWARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLAFLDDKEKEKMGSKENAIL 274

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAED 311
                 +             K+L +   +   E G       +  L         ++   
Sbjct: 275 EFYQQFVCVDGDPVFSDSLCKELQNQFFRQRCELGRIGRRNINRRLNLDISQNNTFLLPR 334

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +   T  +      +     +  + +  IR +  L  D 
Sbjct: 335 DILAATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 374


>gi|52694145|emb|CAG30602.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           pseudoalcaligenes]
          Length = 384

 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/381 (61%), Positives = 301/381 (79%), Gaps = 1/381 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPRE 659
           PYR V +GKVT+++V+LSA+EE +  IAQA+++L++   S++ ELV  R   E  +   E
Sbjct: 121 PYRVVKEGKVTDEIVFLSAIEEADHVIAQASATLNDKRASWSTELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVNDNEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDQVSRGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEE 860
           T+IHI+E   +ARDTKLGPEE
Sbjct: 361 TTIHIQELTCVARDTKLGPEE 381


>gi|189162263|ref|YP_001936509.1| RNA polymerase beta subunit [Fagopyrum esculentum subsp. ancestrale]
 gi|166065349|gb|ABY79724.1| RNA polymerase beta subunit [Fagopyrum esculentum subsp. ancestrale]
          Length = 1070

 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 160/562 (28%), Positives = 251/562 (44%), Gaps = 56/562 (9%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +   +++        I         +  G       +          +
Sbjct: 561  CIVGTGLERQAALDSGVLAIAEHEGKIISTETDKIILSGNGYTLNIPLVMYQRSNKNTCM 620

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   I  G  +  G IL       G   +   + +L A    +  +  D  L     +S
Sbjct: 621  HQKARIRQGKCIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNFEDAVL-----IS 674

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E    V  +  E L  +    +  L RN+  +   ++ G    
Sbjct: 675  ERLVYGDIYTSFHIRKYEIQTHVTSQGPERLTNEIPHLEAHLLRNL-DKNGIVVLGAWVE 733

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T   +   S+ P  +  +  +  +        LK+   +   +++ R+  K
Sbjct: 734  AGDILVGKLTPQMAKESSDAPEDRLLRAILGIQVATSKETCLKLPIGSRGRVIDVRWIQK 793

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                             ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 794  K-------GSSSSNPETIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 846

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE  LG A   LG+  +    D +   + S    F E   
Sbjct: 847  PVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLGRHYRIAPFDERYEQEASRKLVFSELYE 906

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 907  ASKQTANPW------------------------VFE---------------PEYPGKSRI 927

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GE
Sbjct: 928  FDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGE 987

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G A++LQEMLT KSD +  R  V  + + G         PESF +LV+E++
Sbjct: 988  MEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPNPEDAPESFRLLVRELR 1047

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +     +ME
Sbjct: 1048 SLALELNYFLVSEKNLQINRME 1069



 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 227/686 (33%), Positives = 372/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTVISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   ++ A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKVGSKETAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L  +R+RSV ++L
Sbjct: 262 GRRNMNQRLNLDIPQNNTFLLPRDILAAADRLIGMKFGMGTLDDMNHLKKKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  IS      +   PQ+L+ + P+ +    F     LSQ+ +  
Sbjct: 322 QDQFGLALVRLENVVRGTISGAIRHKLIPTPQNLVTSIPLTTTYESFLGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+ ++G +E+P+ K+        ++YLS   +E   +A   S     G   E +V  R 
Sbjct: 442 ARIGSWGSLESPFYKIFGKSKRVQMLYLSPSRDEYYMVAAGTSLALNRGIPEEGIVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E +    E++ F    P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTSAWEEVHFRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E   A  SG   +A+  G +             +  +           L+ +QR
Sbjct: 562 IVGTGLERQAALDSGVLAIAEHEGKIIST--------ETDKIILSGNGYTLNIPLVMYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  ++ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 614 SNKNTCMHQKARIRQGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V  D++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +GA V 
Sbjct: 674 SERLVYGDIYTSFHIRKYEIQTHVTSQGPERLTNEIPHLEAHLLRNLDKNGIVVLGAWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734 AGDILVGKLTPQMAKESSDAPEDRLLRAILGIQVATSKETCLKLPIGSRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G   +     R    ++ +I++  +
Sbjct: 794 KGSSSSNPETIRVYISQKREIKVGDK 819



 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYKLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LT++  L ++  LI          K+ +D++E +I+  +LPLM   GT
Sbjct: 62  PLLKERDAVYESLTHSSELYVSAGLIW---------KTGRDMQEPTIFYWNLPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ GI RIV++Q+ +SPGI++  +     +S   +Y   +I D G   ++E D K  I 
Sbjct: 113 FIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTVISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLTDKEKKKVGSKE 220


>gi|17136444|ref|NP_476706.1| RNA polymerase II 140kD subunit [Drosophila melanogaster]
 gi|195329082|ref|XP_002031240.1| GM24152 [Drosophila sechellia]
 gi|12644108|sp|P08266|RPB2_DROME RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2; AltName: Full=DNA-directed RNA polymerase II 140 kDa
            polypeptide
 gi|7299847|gb|AAF55024.1| RNA polymerase II 140kD subunit [Drosophila melanogaster]
 gi|27819971|gb|AAO25022.1| LD22387p [Drosophila melanogaster]
 gi|194120183|gb|EDW42226.1| GM24152 [Drosophila sechellia]
          Length = 1176

 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/1002 (16%), Positives = 314/1002 (31%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDM F  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|215254221|gb|ACJ64115.1| RNA polymerase beta subunit [Vibrio rumoiensis]
          Length = 375

 Score =  375 bits (963), Expect = e-101,   Method: Composition-based stats.
 Identities = 232/375 (61%), Positives = 287/375 (76%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L++FAR N YGF+ETPYR+V DG VT +V YLSA+EE    IAQAN+ L ++G F +EL+
Sbjct: 61  LSAFARCNEYGFLETPYRRVVDGVVTEEVDYLSAIEEGQFVIAQANAHLTDEGRFADELI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  L PR+ ++++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LK
Sbjct: 121 TARQKGESGLHPRDHVNYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLK 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           A+ P +GTG+E  VA  SG   VAKR G V+ VDA RIVI+  E +L P  +G+DIY L 
Sbjct: 181 ADQPLLGTGIERNVAVDSGVTAVAKRGGTVQSVDASRIVIKVNEDELVPGEAGIDIYNLT 240

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFED
Sbjct: 241 KYTRSNQNTCINQRPTVLPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFED 300

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           S+L+SER+V ED FT+IHI+E   +ARDTKLG EE T DIPNV E  L  +DE GI+ +G
Sbjct: 301 SILVSERVVQEDRFTTIHIQELSCVARDTKLGSEEDTADIPNVGESALSKLDESGIVHIG 360

Query: 886 AEVNPGDILVGKITP 900
           AEV  GDIL+GK+TP
Sbjct: 361 AEVKGGDILLGKVTP 375


>gi|195501705|ref|XP_002097907.1| GE24221 [Drosophila yakuba]
 gi|194184008|gb|EDW97619.1| GE24221 [Drosophila yakuba]
          Length = 1176

 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/1002 (16%), Positives = 314/1002 (31%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDM F  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1135 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|195064711|ref|XP_001996619.1| GH19704 [Drosophila grimshawi]
 gi|193892751|gb|EDV91617.1| GH19704 [Drosophila grimshawi]
          Length = 1175

 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/1002 (16%), Positives = 314/1002 (31%), Gaps = 203/1002 (20%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 335  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 391

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 392  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 451

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 452  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 507

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 508  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 561

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 562  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 612

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 613  RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 670

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 671  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 706

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 707  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 741

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 742  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 790

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 791  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 846

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 847  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFAKRDASTFLRNSETGIVD 906

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 907  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 946

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDM F  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 947  GIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 999

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1000 ----------------------------------------------ATPFNDAVNVQKIS 1013

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1014 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1073

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1074 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1133

Query: 1327 RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1134 NTFEC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1173



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 223/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 39  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 98

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 99  WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 153

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 154 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 212

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 213 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 264

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 265 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 324

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 325 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 382

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 383 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 435

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 436 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 495

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 496 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 552

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 553 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 612

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E   + L  +     +   Y               +  V Y+  
Sbjct: 613 RIYTDAGRICRPLLIVENGTLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 667

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 668 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 712

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 713 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 743


>gi|52694133|emb|CAG30596.1| DNA-directed RNA polymerase beta chain [Pseudomonas cedrina]
          Length = 390

 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/389 (59%), Positives = 303/389 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKP   AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RVERAVKERLSMAESEGLMPQDLINAKPGAGAVKEFFGSSQLSQFMDQNNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 62  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 122 PYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 182 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 242 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 301

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V +D FT
Sbjct: 302 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQKDRFT 361

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVS 869
            IHI+E   +ARDTKLGPEEI+ DIPNV 
Sbjct: 362 PIHIQELTCVARDTKLGPEEISADIPNVG 390


>gi|229544495|gb|ACQ76429.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 222

 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 123/225 (54%), Positives = 153/225 (68%), Gaps = 13/225 (5%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGWA  G+G++I  ++   +     S LR FLEKV      TE ++   D+ + 
Sbjct: 1    QVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRTEDLAQLSDEELR 57

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEP 1244
             +A     GVP +TPVFDGA EE I  ML++A  D      G      Q+ LYDG TGE 
Sbjct: 58   VMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRTQAFLYDGRTGER 117

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 118  FERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 177

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            YGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  YGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 222


>gi|222093447|gb|ACM43500.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
          Length = 821

 Score =  375 bits (962), Expect = e-101,   Method: Composition-based stats.
 Identities = 264/680 (38%), Positives = 406/680 (59%), Gaps = 29/680 (4%)

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D +   Y+A+D        I ++  D   E  +       I +     + +      I+N
Sbjct: 1   DRIITTYLAQD--------IVLKNVDPTMEPKILYPKGIYITNDIANDIQNAFKEGLIKN 52

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             + D           +Y  +   +        ++     F S K       +  +   +
Sbjct: 53  IDLKDYGITSD-----VYGKLLDTNPK-LKNRMNIIGIYIFKSKKAMEKDGEKHFV---I 103

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             D      H+   DI+AII    +L    G  DD D+L N+R+ SVGE+L NQ  +GLL
Sbjct: 104 GNDPTSVENHLLISDIVAIINYYFNLNENIGRDDDPDSLINKRIVSVGELLLNQLNIGLL 163

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +ME++ +E++SS +I  + P+++ N K + + +  FF SS+LSQ  +  N LS I+  R+
Sbjct: 164 KMEKNTREKMSSKEISRITPKNITNNKMIQNQIKTFFNSSKLSQFMDQTNPLSEISTKRK 223

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A+V+ YGF++T
Sbjct: 224 ITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYAKVDEYGFLQT 283

Query: 601 PYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY KV +G V  +  VYL+A EE NR  AQ++ S+DE+G  T+E V  +   +  +V  +
Sbjct: 284 PYFKVTNGIVDFSQPVYLTAHEEINRTFAQSSISIDENGKITDEQVIVKSNFDYNVVSPK 343

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D+ID S KQ+ S+AAS IPFLEN+D+NR LMG NMQRQAVPLL AEAP V TG+E+ +
Sbjct: 344 EVDYIDVSSKQMTSLAASSIPFLENNDANRALMGSNMQRQAVPLLFAEAPLVATGIEADI 403

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           AK S   + +   G V  VD  +I I+    D       +  Y+L  F+++NQ T ++Q 
Sbjct: 404 AKFSPNNLKSTVDGEVVFVDGSQIKIK----DSASEKGSIKTYQLKTFEKTNQGTVISQS 459

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+VK+GD+V + D+I+D  S   G++ALG+N+LV F  W+GYN+ED++++SER+V +DVF
Sbjct: 460 PIVKMGDKVLKGDLISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE  +  R +K G +++T DIPN S E  +++DE GI+ +G+EV  GDILVG+++
Sbjct: 520 TSIHIEEQTIQFRKSKAGDDKLTADIPNASLESRRHLDENGIVRIGSEVVTGDILVGRVS 579

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           PKG+  ++P EKLL  IF +K  + +DTSL+V +G  GTV+DV I +R   +       V
Sbjct: 580 PKGDENISPAEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSRENGN-------V 632

Query: 960 EREQIELLARDKDDEQVILD 979
             E+I+++ +    ++  + 
Sbjct: 633 LEEEIDMMIKVYVAQKRKIK 652



 Score =  324 bits (830), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 131/428 (30%), Positives = 194/428 (45%), Gaps = 67/428 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L+   +   +  M   + +L         +  D  +     V   V 
Sbjct: 461  IVKMGDKVLKGD-LISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  +S + + +    +     + +  LD N   R+   +   + + G  
Sbjct: 520  -TSIHIEEQTIQFRKSKAGDDKLTADIPNASLESRRHLDENGIVRIGSEVVTGDILVGRV 578

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K    +S    +E   +  +   + +EK       +K  ++ +   +E      I   
Sbjct: 579  SPKGDENISP---AEKLLNGIFNQKISNEKDTSL--KVKNGHQGTVIDVE------ILSR 627

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + G+ +   +  ++KV+VA KR I+ GDKMAGRHGNKG++SR+LP EDMP+L+DGTP+DI
Sbjct: 628  ENGNVLEEEIDMMIKVYVAQKRKIKVGDKMAGRHGNKGVISRVLPVEDMPYLEDGTPLDI 687

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  S + D     DI       +       
Sbjct: 688  ILNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVSPVFDGVKKADIMDALEEAKLPRTGKM 747

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VFD                            
Sbjct: 748  K----------------------------VFDPT-------------------------- 753

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D  ++VG +YM KL+HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 754  TGEKIDNEISVGVMYMFKLSHMVDDKMHSRSIGPYSLITQQPLGGKSQNGGQRFGEMETW 813

Query: 1301 CIQAYGAA 1308
             +++YGAA
Sbjct: 814  ALESYGAA 821


>gi|194900689|ref|XP_001979888.1| GG16840 [Drosophila erecta]
 gi|190651591|gb|EDV48846.1| GG16840 [Drosophila erecta]
          Length = 1176

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/999 (16%), Positives = 311/999 (31%), Gaps = 197/999 (19%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E E  E   R           +  
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE-ENFEKPNRGTCQGMRNAHYDKL 850

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  L  +       ++ +        ++ +   +  Q  
Sbjct: 851  DDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVDQVM 910

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                  +     +  K+ V   R  Q GDK A RHG KG     
Sbjct: 911  L--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQ 950

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDM F  +G   DI++NP  +PSRM +G + E   G      G+             
Sbjct: 951  YRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD---------- 1000

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP  D  + + I++ L
Sbjct: 1001 -------------------------------------------ATPFNDAVNVQKISTFL 1017

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +QP+
Sbjct: 1018 QEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPM 1077

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVY 1329
             G++  GG R GEME  C  ++GAA  L+E L   SD     +            R   +
Sbjct: 1078 EGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRNNTF 1137

Query: 1330 ESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            E    G        +   P +  +L +E+ ++ ++  L 
Sbjct: 1138 EC--KGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|222093445|gb|ACM43499.1| RNA polymerase beta subunit [Mycoplasma pulmonis]
          Length = 821

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 263/680 (38%), Positives = 406/680 (59%), Gaps = 29/680 (4%)

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
           D +   Y+A+D        I ++  D   E  +       I +     + +      I+N
Sbjct: 1   DRIITTYLAQD--------IVLKNVDPTMEPKILYPKGIYITNDIANDIQNAFKEGLIKN 52

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             + D           +Y  +   +        ++     F S K       +  +   +
Sbjct: 53  IDLKDYGITSD-----VYGKLLDTNPK-LKNRMNIIGIYIFKSKKAMEKDGEKHFV---I 103

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
             D      H+   DI+AII    +L    G  DD D+L N+R+ SVGE+L NQ  +GLL
Sbjct: 104 GNDPTSVENHLLISDIVAIINYYFNLNENIGRDDDPDSLINKRIVSVGELLLNQLNIGLL 163

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           +ME++ +E++SS +I  + P+++ N K + + +  FF SS+LSQ  +  N LS I+  R+
Sbjct: 164 KMEKNTREKMSSKEISRITPKNITNNKMIQNQIKTFFNSSKLSQFMDQTNPLSEISTKRK 223

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++A+V+ YGF++T
Sbjct: 224 ITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATYAKVDEYGFLQT 283

Query: 601 PYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           PY KV +G V  +  VYL+A EE NR  AQ++ S+DE+G  T+E V  +   +  +V  +
Sbjct: 284 PYFKVTNGIVDFSQPVYLTAHEEINRTFAQSSISIDENGKITDEQVIVKSNFDYNVVSPK 343

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           ++D+ID S KQ+ S+AAS IPFLEN+D+NR LMG NMQRQAVPLL AEAP V TG+E+ +
Sbjct: 344 EVDYIDVSSKQMTSLAASSIPFLENNDANRALMGSNMQRQAVPLLFAEAPLVATGIEADI 403

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           AK S   + +   G V  VD  +I I+    D       +  Y+L  F+++NQ T ++Q 
Sbjct: 404 AKFSPNNLKSTVDGEVVFVDGSQIKIK----DSASEKGSIKTYQLKTFEKTNQGTVISQS 459

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+VK+GD+V + D+I+D  S   G++ALG+N+LV F  W+GYN+ED++++SER+V +DVF
Sbjct: 460 PIVKMGDKVLKGDLISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TSIHIEE  +  R +K G +++T DIPN S +  +++DE GI+ +G+EV  GDILVG+++
Sbjct: 520 TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRVS 579

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           PKG+  ++P EKLL  IF +K  + +DTSL+V +G  GTV+DV I +R   +       V
Sbjct: 580 PKGDENISPAEKLLNGIFNQKISNEKDTSLKVKNGHQGTVIDVEILSRENGN-------V 632

Query: 960 EREQIELLARDKDDEQVILD 979
             E+I+++ +    ++  + 
Sbjct: 633 LEEEIDMMIKVYVAQKRKIK 652



 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 131/428 (30%), Positives = 193/428 (45%), Gaps = 67/428 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L+   +   +  M   + +L         +  D  +     V   V 
Sbjct: 461  IVKMGDKVLKGD-LISDSSSFKDGEMALGKNVLVGFSTWNGYNYEDAIIVSERLVKDDVF 519

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  +S + + +    +       +  LD N   R+   +   + + G  
Sbjct: 520  -TSIHIEEQTIQFRKSKAGDDKLTADIPNASLKSRRHLDENGIVRIGSEVVTGDILVGRV 578

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K    +S    +E   +  +   + +EK       +K  ++ +   +E      I   
Sbjct: 579  SPKGDENISP---AEKLLNGIFNQKISNEKDTSL--KVKNGHQGTVIDVE------ILSR 627

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + G+ +   +  ++KV+VA KR I+ GDKMAGRHGNKG++SR+LP EDMP+L+DGTP+DI
Sbjct: 628  ENGNVLEEEIDMMIKVYVAQKRKIKVGDKMAGRHGNKGVISRVLPVEDMPYLEDGTPLDI 687

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  S + D     DI       +       
Sbjct: 688  ILNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVSPVFDGVKKADIMDALEEAKLPRTGKM 747

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VFD                            
Sbjct: 748  K----------------------------VFDPT-------------------------- 753

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGE  D  ++VG +YM KL+HMV DK+++RS G YSL+TQQPLGGKS  GGQR GEME W
Sbjct: 754  TGEKIDNEISVGVMYMFKLSHMVDDKMHSRSIGPYSLITQQPLGGKSQNGGQRFGEMETW 813

Query: 1301 CIQAYGAA 1308
             +++YGAA
Sbjct: 814  ALESYGAA 821


>gi|197294112|ref|YP_002149733.1| RNA polymerase beta subunit [Cicer arietinum]
 gi|197089800|gb|ACH41070.1| RNA polymerase beta subunit [Cicer arietinum]
          Length = 1070

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 155/579 (26%), Positives = 245/579 (42%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        I            G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKIIYNDTDKIILYGNGNA 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  V  G IL       G   +   + +L A    
Sbjct: 604  LSIPLIIYQRSNKNTCMHQKSQVQKGKCVKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V     E +       +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSPSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+ +K      G    P     + ++++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPVGGRGRVIDVRWIHKKA----GSSYNP---ETIHIYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D 
Sbjct: 830  VSKILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSMLNRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F  ++      T     ++ +                            
Sbjct: 890  RYEQEASRKLVF-SELYEASKQTSNPWIFEPE---------------------------- 920

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                        G+S ++DG TG  F++ V +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 921  ----------YPGKSGIFDGRTGNRFEQAVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLKGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPVDAPESFRLLVRELRSLALELNHFLVSEKDFQIQRKE 1069



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 236/682 (34%), Positives = 375/682 (54%), Gaps = 18/682 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTATIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLSEILENVCYPE 202

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K   +++A+L+ YR      GD        +     FF   + +L  +
Sbjct: 203 IFLSFLNEKEEKKIGSKENAILEFYRQFACVGGDPIFPESLCTELQKKFF-QQRCELGGI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+     L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNMNRRLNLDIPQNNTFLLPRDILTAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  I+  IS      +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENIIRGTISGALRYKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G IE+P+ ++ D      ++YLS   +E   +A  N      G   E++V  R 
Sbjct: 442 ARIGHWGSIESPFYEISDRSKRIQMLYLSPSRDEYYMVATGNFLALNRGIQEEQIVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG   +A+  G +   D  +I++                  L+ +QR
Sbjct: 562 IVGTGLERQVALDSGVPAIAEHEGKIIYNDTDKIILYGN--------GNALSIPLIIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+  V+ G  V++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKSQVQKGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI ++E+    T  GPE IT  IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 SERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLLRNLDKNGIVILGSWVE 733

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FN 946
            GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR    
Sbjct: 734 TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSPSKETCLKLPVGGRGRVIDVRWIHK 793

Query: 947 RHGIDKNERSISVEREQIELLA 968
           + G   N  +I +   Q   + 
Sbjct: 794 KAGSSYNPETIHIYISQKREIK 815



 Score =  172 bits (435), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  LPGLNQIQFEGFSRFI----------DRGLTEELLKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L I+  LI          K+ +DI+EQ I++G++PLM   GT
Sbjct: 62  PAIKEKDAVYESLTYSSELYISAGLIW---------KNSRDIQEQIIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTATIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFLSFLNEKEEKKIGSKE 220


>gi|52694271|emb|CAG37975.1| RNA polymerase beta subunit [Pseudomonas marginalis pv. pastinacae]
          Length = 391

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/390 (58%), Positives = 301/390 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPE 181

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 182 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 241

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 242 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 301

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 302 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 361

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEI    P   
Sbjct: 362 TTIHIQELTCVARDTKLGPEEIYCRHPERG 391


>gi|153012213|ref|YP_001381728.1| RNA polymerase beta subunit [Medicago truncatula]
          Length = 1070

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 154/579 (26%), Positives = 244/579 (42%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   + +        +            G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHAGKIVYNDTDKIILFGNGNS 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I          + +   +  G  V  G IL       G   +   + +L A    
Sbjct: 604  LSIPLIIYQRSNKNTCMHQKSRVHKGKCVKKGQILADGAATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    V     E +       +  L 
Sbjct: 663  EGYNSEDAVL-----ISERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G    +G     K T   +   S  P  +  +  +  +        LK
Sbjct: 718  RNL-DKNGIVILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     + ++++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKKA----GSSYNP---ETIHIYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQI E  LG A   L +  +    D 
Sbjct: 830  VSKILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQILECSLGLAGSMLNRHYRIAPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F  ++      T     ++ +                            
Sbjct: 890  RYEQEASRKLVF-SELYEASKQTSNPWIFEPE---------------------------- 920

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                        G+S ++DG TG  F++PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 921  ----------YPGKSGIFDGRTGNLFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLKGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTIP 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 KPVDAPESFRLLVRELRSLALELNHFLVSEKDFQIQRKE 1069



 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 238/688 (34%), Positives = 378/688 (54%), Gaps = 18/688 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELDHKGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLSEILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      +I   N     K   +++A+L+ YR      GD        +     FF   +
Sbjct: 197 NVCYPEIFISFLNEKEEKKIGSKENAILEFYRQFACVGGDPIFPESLCTELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLN+D P++   +   DI+     L+ ++ G GT+DD+++L N+R+R
Sbjct: 256 CELGGIGRRNMNRRLNIDIPENNTFLLPRDILTAADHLIGMKFGMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  I+  IS      +   PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENIIRGTISGAIRYKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +      ++YLS   +E   +A  N      G   E+
Sbjct: 436 GSLAIHARIGRWGSIESPFFEISERSKRIRMLYLSPSRDEYYMVATGNFLALNRGIQEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 IVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E  VA  SG   +A+ AG +   D  +I++                  
Sbjct: 556 SRSEKCIVGTGLERQVALDSGVPAIAEHAGKIVYNDTDKIILFGN--------GNSLSIP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ +QRSN+NTC++Q+  V  G  V++  I+ADG +T  G+LALG+N+LVA+MPW GYN 
Sbjct: 608 LIIYQRSNKNTCMHQKSRVHKGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNS 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LISER+V ED++TS HI ++E+    T  GPE IT  IP++    L+N+D+ GI+ 
Sbjct: 668 EDAVLISERLVYEDIYTSFHIRKYEIQTHVTSHGPERITNKIPHLEAHLLRNLDKNGIVI 727

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728 LGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942 VRI-FNRHGIDKNERSISVEREQIELLA 968
           VR    + G   N  +I +   Q   + 
Sbjct: 788 VRWIQKKAGSSYNPETIHIYISQKREIK 815



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  LPGLNQIQFEGFCRFI----------DRGLTEELFKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L I+  LI          K+ +DI+EQ I++G++PLM   GT
Sbjct: 62  PSIKEKDAVYESLTYSSELYISAGLIW---------KNSRDIQEQIIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHKGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   +     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFISFLNEKEEKKIGSKE 220


>gi|139387452|ref|YP_001122806.1| RNA polymerase beta subunit [Phaseolus vulgaris]
 gi|158513614|sp|A4GGA5|RPOB_PHAVU RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|112030974|gb|ABH88086.1| RNA polymerase beta subunit [Phaseolus vulgaris]
 gi|158187149|gb|ABW22782.1| RNA polymerase beta subunit [Phaseolus vulgaris]
          Length = 1070

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 256/830 (30%), Positives = 420/830 (50%), Gaps = 43/830 (5%)

Query: 296  LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
            + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143  ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILILLSAMGSNLSEILENVCYPE 202

Query: 356  AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             ++      DK K   +++A+L+ YR      GD              FF   + +L  +
Sbjct: 203  IFVSFLNDKDKKKIGSKENAILEFYRQFACVGGDPVFSESLWKELQKKFF-QQRCELGRI 261

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
            GR  MN +LNLD P +   +   DI+     L+ ++ G   +DDI++L N+R+RSV ++L
Sbjct: 262  GRRNMNQKLNLDIPQNNTFLLPRDILTAASHLIGMKFGMALLDDINHLKNKRIRSVADLL 321

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322  QDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDQT 381

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L+ I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382  NPLTEIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            AR+  +G IE+P+ ++ +      ++YLS   +E   +A  NS         E++V  R 
Sbjct: 442  ARIGIWGAIESPFFEISERSKRIRMLYLSPSIDEYYMVATGNSLALTRDIQEEQIVPARY 501

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502  RQEFLTIAWEQVHLRSIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             VGTG+E  VA  SG + +A   G +   D  RI +                  L  +QR
Sbjct: 562  IVGTGLECQVALDSGVSAIADHEGNIVYTDTDRIFLFVN--------GDTLSIPLTIYQR 613

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SN+NTC++Q+P V  G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614  SNKNTCMHQKPQVHRGKFIKKGQILADGAATVGGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED+FTS HI ++E+    T  G E IT  IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674  SERLVYEDIFTSFHIRKYEIQTHMTSYGSERITNKIPHLEANLLRNLDKNGIVILGSWVE 733

Query: 890  PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             GD+LVGK+TP+   ES  +PE++LLRAI G +    ++T L++P G  G V+DVR   +
Sbjct: 734  TGDVLVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793

Query: 948  HGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG-------QN 994
             G         R   +++ +I++  +   +   + I+ + +  + M  L          N
Sbjct: 794  KGGSSYNPETIRISILQKREIKVGDKVAGRHGNKGIVSKILSRQDMPYLQDGEPVDMVFN 853

Query: 995  AVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------VESLKVQYE 1043
             +  P       +    L +S     + ++    DE+ ++            E+ K    
Sbjct: 854  PLGVPSRMNVGQIFECSLGLSGGMLDKHYRITPFDERYEQEASRKLVFSELYEASKKTSN 913

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                  E   K+KI   + G+      + + K ++  K   Q  DK+ GR
Sbjct: 914  PWIFEPEYPGKSKIFDGRTGNSFKQPAI-MGKTYIL-KLIHQVDDKIHGR 961



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 144/497 (28%), Positives = 225/497 (45%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     V   +  
Sbjct: 626  VHRGKFIKKGQILADGAATVG-GELALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIFT 684

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 ++ I  +  S   ER       +    E  +L      +   ++ G    +G   
Sbjct: 685  SFHIRKYEIQTHMTSYGSERI----TNKIPHLEANLLRN--LDKNGIVILGSWVETGDVL 738

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T   +   S  P  +  +  +  +        LK+       +++ R+  K     
Sbjct: 739  VGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKG--- 795

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     +++ +  KR I+ GDK+AGRHGNKGIVS+IL  +DMP+L+DG PVD+V
Sbjct: 796  -GSSYNP---ETIRISILQKREIKVGDKVAGRHGNKGIVSKILSRQDMPYLQDGEPVDMV 851

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE  LG +   L K  +    D +   + S    F  ++      
Sbjct: 852  FNPLGVPSRMNVGQIFECSLGLSGGMLDKHYRITPFDERYEQEASRKLVF-SELYEASKK 910

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
            T     ++ +                                        G+S ++DG T
Sbjct: 911  TSNPWIFEPE--------------------------------------YPGKSKIFDGRT 932

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G  F +P  +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW 
Sbjct: 933  GNSFKQPAIMGKTYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWA 992

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+++L + 
Sbjct: 993  LEGFGVAHILQEMLTYKSDHIKTRQEVLGTTIIGGTIPKPTDAPESFRLLVRELRSLAME 1052

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +     + E
Sbjct: 1053 LNHFLVSEKNFRIHRKE 1069



 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 114/238 (47%), Gaps = 29/238 (12%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF---- 76
            E+  +P L ++Q   +  F+          + GL         I        +EF    
Sbjct: 7   EEMSTLPGLNQIQLEGFCRFI----------DRGLTEGLFKFPKIEDTDQ--EIEFQLFA 54

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
            +Y+   P  +  D ++  LTY+  L ++  LI          KS +DIK+Q+I++G++P
Sbjct: 55  ETYQLLEPLINEKDAVYESLTYSAELYVSTGLIW---------KSSRDIKKQTIFVGNIP 105

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LM   GT ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E 
Sbjct: 106 LMNSLGTSIVNGIYRIVINQILQSPGIYYRSELD---PNGISVYTGTIISDWGGRLELEI 162

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           D K  I  R+ R++K+ +   L A+G +  EIL    YP+I  S   D     + + +
Sbjct: 163 DKKARIWARVSRKQKISILILLSAMGSNLSEILENVCYPEIFVSFLNDKDKKKIGSKE 220


>gi|237664248|gb|ACR09678.1| RNA polymerase beta subunit [Pseudomonas sp. EBCL-Psp1]
          Length = 384

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 232/384 (60%), Positives = 300/384 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRDIP 866
           HI+E   +ARDTKLGPEEIT DIP
Sbjct: 361 HIQELTCVARDTKLGPEEITADIP 384


>gi|52694151|emb|CAG30605.1| DNA-directed RNA polymerase beta chain [Pseudomonas fuscovaginae]
          Length = 388

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 237/388 (61%), Positives = 305/388 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+D+V+LSA+EE +  IAQA+++++E     +EL   R   E  +   E 
Sbjct: 121 PYRVVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELEAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +IHI+E   +ARDTKLGPEEIT DIPNV
Sbjct: 361 TIHIQELTCVARDTKLGPEEITPDIPNV 388


>gi|52694281|emb|CAG37980.1| RNA polymerase beta subunit [Pseudomonas ficuserectae]
          Length = 386

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 232/386 (60%), Positives = 301/386 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     
Sbjct: 121 PYRVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELVDELVAVRHLNEFTVKAPAD 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIP 866
           +IHI+E   +ARDTKLGPEEIT DIP
Sbjct: 361 TIHIQELTCVARDTKLGPEEITADIP 386


>gi|323449816|gb|EGB05701.1| hypothetical protein AURANDRAFT_38329 [Aureococcus anophagefferens]
          Length = 1233

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 165/1069 (15%), Positives = 319/1069 (29%), Gaps = 221/1069 (20%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++        +A +   + +    +     A ++         +Y 
Sbjct: 331  DILEHVVYDFSDTEMMERLRPSLDEAFVIQNQTIALDFIGRRGSATNIGRSKRV---QYA 387

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  D  +      +  I+  L+     +   DD D+ G +R+   
Sbjct: 388  KELLQKEVLPHVGTEEQSDTKK---AFFVGYIVHKLLMCSLERIDEDDRDHYGKKRLDLA 444

Query: 468  GEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ + +    +    D         I ++ V   +     +      
Sbjct: 445  GPLLGGLFRMLFRKLTKDVLAYLQKCIDDGRDFNLASAIKSRVVTDGLRYSLATGNWGDR 504

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+   +   S ++H RRL+      + R     + R +H TH+G ICPAET
Sbjct: 505  KDASRAGVSQVLNRLTYASTLSHLRRLNT----PLGREGKQAKPRQLHNTHWGFICPAET 560

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE-----ENRYIAQ 629
             EG  +GLV +L   + V+  G  ++P  +  +     ++  +S            ++  
Sbjct: 561  PEGQAVGLVKNLALMSYVS-VGSPQSPILEFLEEWSMENLEEISPQTIADPGTTKIFVNG 619

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            +   +  D S  E  +       +I      +  I     +V + A  +   L   ++  
Sbjct: 620  SWVGVHRDPSTLESTLRSLRRQIDIDPEVSVVRDIKEKELRVYTDAGRVCRPLLIVEAAS 679

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             +     Q      L+     V   +        G   +  +  +               
Sbjct: 680  TVTRVRSQEATFQELRLRKSHVQKLVNG----DLGWTQLLVKGLVELIDTEEEETAMIAM 735

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
               D +      Y                                   PS  LG      
Sbjct: 736  IPSDLNEPYSSTY-----------------------------THCEIHPSMILG------ 760

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N       S R   +       +  +    +                 
Sbjct: 761  -ICGSIIPFPDHNQ------SPRNTYQSAMGKQAMGIYASNFQQRM-------------- 799

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  V             +       +      + AI      +  D+ +
Sbjct: 800  ---------DTLSHVLHYPQKPLATTRAMEHLHFRELPSGVNAIVAIMCYTGYNQEDSLI 850

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ--IELLARDKDDEQVILDRNIYSRLM 987
               + +   +     F R   DK       +  +   E   R   DE   +    Y ++ 
Sbjct: 851  MNQAAIDRGLF-RSTFYRTYSDKEHNKGIWDSPEYLQETFERPNRDECTAMRHGSYEKID 909

Query: 988  EI--------LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                      + G + + G       + L ++      R         +  +   V    
Sbjct: 910  SDGLVSPGVRVSGSDILVGKTSPSWHSGLKAERSGPSKRDSSTTMRPNESGLVDQVMLST 969

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                             ++  KV     R  Q GDK A RHG KG 
Sbjct: 970  NQ---------------------------DGMKFTKVRTRTIRIPQIGDKFASRHGQKGT 1002

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMP+ +DG   DI++NP  +PSRM +G + E          GK+        
Sbjct: 1003 IGMTYAQEDMPWTRDGVSPDIIVNPHAIPSRMTIGHLVECLQSKVGALTGKEGD------ 1056

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                           +TP F     + I
Sbjct: 1057 -----------------------------------------------ATP-FTDVSVDQI 1068

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L        G  ++Y G TG      V +G  +  +L H+V DK++ARS G  +++T
Sbjct: 1069 AGVLHELGYHRHGNEVMYSGHTGRIIHAKVFLGPTFYQRLKHLVDDKIHARSRGPVTMLT 1128

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------R 1325
            +QP+ G++  GG R+GEME  C+ ++G +  L++ +   SD     V            R
Sbjct: 1129 RQPMEGRARDGGLRMGEMERDCLISHGVSSFLRDRMFANSDPYSIHVCTLCGLIAHADLR 1188

Query: 1326 TRVY-----------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             R +            SIV          P +  +L +E+ A+ ++  +
Sbjct: 1189 KRAFWCNNKDCQHANSSIVR------VHIPYACKLLFQELMAMCIAPRI 1231



 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 161/1093 (14%), Positives = 300/1093 (27%), Gaps = 281/1093 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFK---SVFPIT---AFSGAAMLEFVSYEFD 82
           L+  Q  S+D F+  N   +   + G +   K      P       S   +L F      
Sbjct: 21  LVRQQLDSFDEFIQ-NTMQELVDDSG-ELVVKPEAQYAPGQLAATPSTYFVL-FNQVYVS 77

Query: 83  PPKFD----------VDDCLWRDLTY---------------AVPL--------------- 102
            P               +   R++TY               A PL               
Sbjct: 78  KPTATEKDGTTSNMFPHEARLRNMTYASPMYVDISCVEQKQASPLRQGCAAELEIHGDWY 137

Query: 103 ----------KITLRLIVFDVDEFTGAKSIKDIKEQSI---------------------- 130
                       T+   V      +G   I+ ++E  +                      
Sbjct: 138 PCVITKLSDGYATVTYEVVGPIH-SGDDQIQVVEEHHVDVSARVRLINGGSSTHRIDSPK 196

Query: 131 -YMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
            ++G +P+M +                         G FVI G +++VV+Q   S   ++
Sbjct: 197 EFLGYVPIMLRSRFCVLADKSDKELCELGECIYDQGGYFVINGSEKVVVAQERMSNNHVY 256

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR--------RKVPVTS 216
               K     S   +  CR   + G            I++++  +         ++ VT 
Sbjct: 257 CFRKKQPHKYS--WVVECRSHVEHGAR------PTSTIYMQMYNKAGRGQSQGNQIRVTL 308

Query: 217 -----------FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                         ALG  ++ +IL         ++  +     L  A ++    ++   
Sbjct: 309 PYVRVDVPVIVVFRALGFVADRDILEHVVYDFSDTEMMERLRPSLDEAFVIQNQTIALDF 368

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
           +        I   K++     K L +K V     T +                G I  + 
Sbjct: 369 IGRRGSATNIGRSKRVQY--AKELLQKEVLPHVGTEEQSDTKKAFFV------GYIVHKL 420

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
                E+  E+      +    L          +         K  KD L  + + +  G
Sbjct: 421 LMCSLERIDEDDRDHYGKKRLDL------AGPLLGGLFRMLFRKLTKDVLAYLQKCIDDG 474

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
               F++A ++ + +  D  +Y L+T        R +       + + +    + +  L 
Sbjct: 475 R--DFNLASAIKSRVVTDGLRYSLATG---NWGDRKDASRAGVSQVLNRLTYASTLSHLR 529

Query: 445 DL-----RNGKGTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRMERSIKERIS 491
            L     R GK       +  +       E        ++KN   +  + +       + 
Sbjct: 530 RLNTPLGREGKQAKPRQLHNTHWGFICPAETPEGQAVGLVKNLALMSYVSVGSPQSPILE 589

Query: 492 SVDIDSVMPQDLINAKPVVSAVCE--FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            ++  S+   + I+ + +        F   S +    +     S +   RR   +     
Sbjct: 590 FLEEWSMENLEEISPQTIADPGTTKIFVNGSWVGVHRDPSTLESTLRSLRRQIDIDPEVS 649

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS------LTSFARVNAYGFIETPYR 603
                  +   V+        P    E  +                 R +    +     
Sbjct: 650 VVRDIKEKELRVYTDAGRVCRPLLIVEAASTVTRVRSQEATFQELRLRKSHVQKLVNGDL 709

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 V   V  +   EEE   IA   S L+E                           
Sbjct: 710 GWTQLLVKGLVELIDTEEEETAMIAMIPSDLNEP-------------------YSSTYTH 750

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +  P  ++ I  S+IPF +++ S R      M +QA+ +  +                 
Sbjct: 751 CEIHPSMILGICGSIIPFPDHNQSPRNTYQSAMGKQAMGIYASNFQ-------------- 796

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                          + S V  Y       +     ++ R    
Sbjct: 797 ---------------------------QRMDTLSHVLHYPQKPLATTRAMEHLHFR---- 825

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +L  G N +VA M + GYN EDS+++++  +   +F S  
Sbjct: 826 --------------------ELPSGVNAIVAIMCYTGYNQEDSLIMNQAAIDRGLFRSTF 865

Query: 844 IEEFEVMARDTK---------LGPEEITRD-IPNVSEEGLKNIDECGIICVGAEVNPGDI 893
              +     +              E   RD    +     + ID  G++  G  V+  DI
Sbjct: 866 YRTYSDKEHNKGIWDSPEYLQETFERPNRDECTAMRHGSYEKIDSDGLVSPGVRVSGSDI 925

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK- 952
           LVGK +P   S +  E               RD+S  +    SG V  V +       K 
Sbjct: 926 LVGKTSPSWHSGLKAE---------RSGPSKRDSSTTMRPNESGLVDQVMLSTNQDGMKF 976

Query: 953 -NERSISVEREQI 964
              R+ ++   QI
Sbjct: 977 TKVRTRTIRIPQI 989


>gi|52694275|emb|CAG37977.1| RNA polymerase beta subunit [Pseudomonas fluorescens]
          Length = 391

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/390 (58%), Positives = 300/390 (76%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPE 181

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 182 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 241

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 242 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 301

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 302 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 361

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEI    P   
Sbjct: 362 TTIHIQELTCVARDTKLGPEEIYCRHPERG 391


>gi|52538129|emb|CAH19168.1| RNA polymerase beta-subunit [Pseudomonas cedrina]
          Length = 389

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 231/387 (59%), Positives = 302/387 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPE 181

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 182 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 241

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 242 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 301

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED F
Sbjct: 302 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRF 361

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIP 866
           T+IHI+E   +ARDTKLGPEEI    P
Sbjct: 362 TTIHIQELTCVARDTKLGPEEIYCRHP 388


>gi|124302897|ref|YP_001023692.1| RNA polymerase beta subunit [Angiopteris evecta]
 gi|158512822|sp|A2T324|RPOB_ANGEV RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|110628295|gb|ABG79591.1| RNA polymerase beta subunit [Angiopteris evecta]
          Length = 1070

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 241/633 (38%), Positives = 365/633 (57%), Gaps = 14/633 (2%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          +  +    +    IL      N          +  +  +DA++++
Sbjct: 166 KRIWVRLSKNRKVSIIILLLAMGLNMNDILKNVRYPNIFLRLFQRQAENIQSYEDAIVEL 225

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+ +    G++             FF   K++L   GR  +N +LNLD P +   +  +D
Sbjct: 226 YKNLYSAGGNLVFSDSICKELQTKFF-QQKFELGQFGRRNLNKKLNLDVPGNEHLLLPQD 284

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
           ++A +  L+ +  G GT+DDID+L NRRVRSV ++L+ Q  L L R+E  I++ I +V  
Sbjct: 285 LLAAVDYLIGVNYGIGTLDDIDDLKNRRVRSVADLLREQLGLALDRLEILIRQTIHTVAR 344

Query: 496 DS--VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               V P+ LI + P+ +   +FF S  LSQ  +  N L+ +TH RRLS+LG GG+ R  
Sbjct: 345 RKRLVTPKGLITSAPLTTIFQDFFGSHSLSQFLDQTNPLAELTHKRRLSSLGPGGLTRRT 404

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A  ++RD++P+HYGRICP ETSEG N GL++SL   A+VN  G + +P+ K+        
Sbjct: 405 ASFQVRDINPSHYGRICPIETSEGMNAGLIASLAIHAKVNDRGSLLSPFYKISKTLGEEH 464

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +VYLS+ E+E   IA  N+   +     E     R   E + +  ++I F    P Q  S
Sbjct: 465 IVYLSSEEDEYYRIATGNTLSLDREIREERATPARYRQEFLTIAWKQIHFRSIFPFQYFS 524

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I  SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+ES +A  SG+ +V+ + G
Sbjct: 525 IGTSLIPFLEHNDANRALMGSNMQRQAVPLSQPEKCIVGTGLESQIALDSGSVVVSNQDG 584

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  +D   I I           S +       ++RSN NTC++QRP+V  G+ +R+  +
Sbjct: 585 QIAYLDGETISILLQNEKTVDIKSII-------YERSNNNTCIHQRPVVSQGERLRKGQL 637

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALGRN+LVA+MPW GYNFED++LISER++ ED++TS HIE +E+    
Sbjct: 638 LADGTATVGGELALGRNILVAYMPWEGYNFEDAVLISERLIYEDIYTSFHIERYEINIYT 697

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEK 911
           T  GPE+IT++IP++    L+++D  G++  G+ V  GD+LVGK+TP+        PE K
Sbjct: 698 TSQGPEKITKEIPHLDSYVLRHLDNNGLVVPGSWVETGDVLVGKLTPQEAENSLRVPEGK 757

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           LL+AI G +  + R++ L+VP G  G V+DVR 
Sbjct: 758 LLQAISGIQLANTRESCLKVPIGGRGRVIDVRW 790



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 157/511 (30%), Positives = 228/511 (44%), Gaps = 78/511 (15%)

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            + I          I +  ++  G  +  G +L       G   +     +L A    +  
Sbjct: 607  KSIIYERSNNNTCIHQRPVVSQGERLRKGQLLADGTATVG-GELALGRNILVAYMPWEGY 665

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D  L     +   +       R+ I+    S   E+   E+   D       LD N 
Sbjct: 666  NFEDAVLISERLIYEDIYTSFHIERYEINIYTTSQGPEKITKEIPHLD-SYVLRHLDNN- 723

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  ++ G    +G     K T   ++     P  +  Q     +        LKV  
Sbjct: 724  ----GLVVPGSWVETGDVLVGKLTPQEAENSLRVPEGKLLQAISGIQLANTRESCLKVPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      I   D + P +  +V V++  KR IQ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRW------IYDEDTL-PNIANMVHVYILQKRKIQVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DGTPVD++L+PLGVPSRMNVGQIFE  LG A   L K  +    D +  
Sbjct: 833  ILPRQDMPYLQDGTPVDMILSPLGVPSRMNVGQIFECLLGLAGDILKKHYRITPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E                                        A +EA    
Sbjct: 893  REASRKLVFSELHE-------------------------------------ASQEAAIPW 915

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L     D  G+S L DG TG+ F++PVT+G  YM+KL H V DK++ARS+G Y+LVTQQP
Sbjct: 916  LFE--PDHPGKSRLIDGRTGDIFEQPVTIGKAYMMKLIHQVDDKIHARSSGPYALVTQQP 973

Query: 1283 LGGKSNRGGQRLG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE 1330
            L                        EMEVW ++ +G +Y+LQEMLTIKSD +  R+++  
Sbjct: 974  L------------RGRSRGGGQRVGEMEVWALEGFGVSYILQEMLTIKSDHIPARSKLLG 1021

Query: 1331 SIVAGNDTFETG-TPESFNVLVKEMQALGLS 1360
            SIV G    +    PESF +LV+E+++L ++
Sbjct: 1022 SIVTGKSIPKPNTVPESFRLLVRELRSLAVN 1052



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 99/225 (44%), Gaps = 29/225 (12%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF---- 76
            ++  +P+   +Q   +  F+  +          L     +   I        +EF    
Sbjct: 7   KKMFVLPEFGRIQFEGFQRFIHQD----------LVEELTNFPKIEDIDQ--EVEFRLFG 54

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
             Y    P     D +++  TY+  L +  +L+          +    I+ Q+++ G +P
Sbjct: 55  ERYRLTEPCIKERDAVYQSFTYSSDLYVPAQLM---------RRRNGRIQRQTVHFGSIP 105

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LM   GTFVI GI R+V++Q+ RSPGI++D +      +G  +Y   II D G     E 
Sbjct: 106 LMNSQGTFVINGIARVVINQILRSPGIYYDSELD---HNGNSIYTGTIISDWGGRFKSEI 162

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQ 240
           D K  I VR+ + RKV +   L+A+G++  +IL    YP I    
Sbjct: 163 DGKKRIWVRLSKNRKVSIIILLLAMGLNMNDILKNVRYPNIFLRL 207


>gi|52694221|emb|CAG30640.1| DNA-directed RNA polymerase beta chain [Pseudomonas flavescens]
 gi|52694401|emb|CAG38040.1| RNA polymerase beta subunit [Pseudomonas flavescens]
          Length = 379

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/379 (61%), Positives = 298/379 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + ++PQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLLPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVQEG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 121 KVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R    +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVANDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDVV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R DI+ADGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E  
Sbjct: 301 ARGDIMADGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPEEITRDIPN 867
            +ARDTKLGPEEI+ DIPN
Sbjct: 361 CVARDTKLGPEEISADIPN 379


>gi|295136939|ref|YP_003587772.1| RNA polymerase beta subunit [Lathyrus sativus]
 gi|293338661|gb|ADE43633.1| RNA polymerase beta subunit [Lathyrus sativus]
          Length = 1067

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 119/307 (38%), Positives = 173/307 (56%), Gaps = 42/307 (13%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              V+++++ KR I+ GDK+AGRHGNKGIVS+IL  +DMP+L+DG PVD+V NPLGVPSRM
Sbjct: 799  ETVQIYISQKREIKVGDKVAGRHGNKGIVSKILSRQDMPYLQDGRPVDMVFNPLGVPSRM 858

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI E  LG A   L +  +    D +   + S    F  ++      T     ++ +
Sbjct: 859  NVGQILECSLGLAGSMLNRHYRIAPFDERYEQEASRKLVF-SELYEASKQTSNPWIFEPE 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                    G+S ++DG TG PF++PV +
Sbjct: 918  --------------------------------------YPGKSRIFDGRTGNPFEQPVII 939

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++  GGQR+GEMEVW ++ +G A++L
Sbjct: 940  GKPYILKLIHQVDDKIHGRSSGHYALVTQQPLKGRAKGGGQRVGEMEVWALEGFGVAHIL 999

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRT 1368
            QEMLT KSD + GR  V  + + G    +     ESF +LV+E+++L L ++  L + + 
Sbjct: 1000 QEMLTYKSDHIKGRQEVLGTTIIGGTIPKPVDATESFRLLVRELRSLALELNHFLVSEKD 1059

Query: 1369 KNSAKME 1375
                + E
Sbjct: 1060 FQIQRKE 1066



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 236/748 (31%), Positives = 393/748 (52%), Gaps = 23/748 (3%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMV----GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           Y   +Y   G  W   L   + ++       ++S    I  G   I   + L S  +   
Sbjct: 76  YSSKLYISSGLIWKNSLDIQEQIIFIGNIPLMNSLGTFIVNGIYRIVVNQILQSPGIYYR 135

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            +     + + +  +   +     +  +             + S+  +  +   ++  + 
Sbjct: 136 SKLDHNGISVYTATIISDWGGRLELKMDRKARIWARVSRKQKISILVLSSAMGSNLSEIL 195

Query: 349 VDSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSD 404
            +      ++      ++     +++A+L+ YR      GD        +     FF   
Sbjct: 196 ANVCYPEIFLSCLTEEEEENIGSKENAILEFYRQFVCVGGDPIFSESLYTELQKKFF-KQ 254

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           K +L  +GR  MN RLN+D P++   +   DI+     L+ ++ G GT+D++++L N+R+
Sbjct: 255 KCELGGIGRRNMNRRLNMDIPENNTFLLPRDILTAADHLIGMKFGMGTLDNMNHLKNKRI 314

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI--NAKPVVSAVCEFFCSSQL 522
           RSV ++L++Q+ L L+R+E  I+E++     D ++P       + P+ +    FF    L
Sbjct: 315 RSVADLLQDQFGLALVRLENIIREKMCRAIRDKLIPTTENLVTSTPLTTTYESFFGLHPL 374

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ+ +  N LS+I H R+ S+LG GG+    A   +RD+HP++YGRICP +TSEG N+GL
Sbjct: 375 SQVFDQTNPLSQIVHGRKWSSLGPGGLTARTASFRIRDIHPSNYGRICPIDTSEGINVGL 434

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL   AR+  +G IE+P+ ++ +      ++YLS   +E   +A  N      G   E
Sbjct: 435 IGSLAIHARIGRWGSIESPFYEISERSKRIRMLYLSPRRDEYYMVATGNFLALTRGIQEE 494

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           ++V  R   E + +  E++     SP Q  SI ASLIPF+E++D+NR LM  NMQRQAVP
Sbjct: 495 QIVPARYRQEFLTIAWEQVHLRSISPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVP 554

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L ++E   VGTG+E  VA  SG   +A+  G +   D         +  +   +      
Sbjct: 555 LSRSEKCIVGTGLERHVALDSGVPAIAEHEGKIVYND--------TDKIILFGSGNALSI 606

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+ ++RSN+NTC++Q+  V+ G  V++  I+ADG +T  G+LALG+N+LVA+MPW GYN
Sbjct: 607 PLIIYKRSNKNTCMHQKSQVQKGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYN 666

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
            ED++LISER+V +D++TS HI ++E+    T  G E IT  IP++    L+N+D+ GI+
Sbjct: 667 SEDAVLISERLVYDDIYTSFHIRKYEIQTHVTSDGRERITNKIPHLEGYLLRNLDKNGIV 726

Query: 883 CVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+
Sbjct: 727 ILGSWVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVI 786

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLA 968
           DVR     G   N  ++ +   Q   + 
Sbjct: 787 DVRWI--QGSSYNPETVQIYISQKREIK 812



 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 74/345 (21%), Positives = 133/345 (38%), Gaps = 32/345 (9%)

Query: 17  FGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
           FG   E +  +P L ++Q   +  F+          + GL         I         +
Sbjct: 2   FGVGNEGMSTLPGLNQIQFEGFCRFI----------DRGLTEELLKFPKIEDPDQEMEFQ 51

Query: 76  -FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
            F   Y+   P     D ++  LTY+  L I+  LI          K+  DI+EQ I++G
Sbjct: 52  LFAETYQLVEPSIKEKDAVYELLTYSSKLYISSGLIW---------KNSLDIQEQIIFIG 102

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           ++PLM   GTF++ GI RIVV+Q+ +SPGI++   + +   +G  +Y   II D G  ++
Sbjct: 103 NIPLMNSLGTFIVNGIYRIVVNQILQSPGIYY---RSKLDHNGISVYTATIISDWGGRLE 159

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
           ++ D K  I  R+ R++K+ +     A+G +  EIL+      ++             + 
Sbjct: 160 LKMDRKARIWARVSRKQKISILVLSSAMGSNLSEILANVCYPEIFLSCLTEEEEENIGSK 219

Query: 254 LMVGAKVSSSLVDIDTGEQVIES-GKKLTSGLLKSLKEKGVKFLGITSDCL------CGL 306
                +     V +       ES   +L     K   E G       +  L         
Sbjct: 220 ENAILEFYRQFVCVGGDPIFSESLYTELQKKFFKQKCELGGIGRRNMNRRLNMDIPENNT 279

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           ++    +      +      +    ++  + +  IR +  L  D 
Sbjct: 280 FLLPRDILTAADHLIGMKFGMGTLDNMNHLKNKRIRSVADLLQDQ 324


>gi|52694273|emb|CAG37976.1| RNA polymerase beta subunit [Pseudomonas fluorescens]
          Length = 391

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/390 (58%), Positives = 301/390 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 181

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 182 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 241

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 242 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 301

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 302 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 361

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEI    P   
Sbjct: 362 TTIHIQELTCVARDTKLGPEEIYCRHPERG 391


>gi|119618187|gb|EAW97781.1| polymerase (RNA) III (DNA directed) polypeptide B, isoform CRA_b
            [Homo sapiens]
          Length = 1177

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 172/1001 (17%), Positives = 313/1001 (31%), Gaps = 137/1001 (13%)

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                    K  +     +  +  L      +     K    A++   V L  G   +DD 
Sbjct: 287  RMWGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDR 346

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSA 512
            D  GN+R+   G++L   +     +    +K+    V       Q      +    + + 
Sbjct: 347  DYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNG 406

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPT 564
            +     +   S     ++         RLS +   G+         + R     R + P+
Sbjct: 407  MVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPS 466

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +G +CP++T EG   GLV +L     +      + P  K+       DV  L   EE +
Sbjct: 467  QWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIVKLASNLGVEDVNLL-CGEELS 524

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA-ASLIPFLE 683
                     +  +G +  E    R   + +   R        +    +S        ++ 
Sbjct: 525  Y---PNVFLVFLNGGYIIETCVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYIS 581

Query: 684  NDDSNRVLMGCNMQRQAVPLLKA---EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            +D        C + ++    L     E   +    E+V+       I           ++
Sbjct: 582  SDGGRLCRYICRLLKRVFKNLFIFALERNRLVFIFETVLTSFI-VKINLIPNFEDFLHES 640

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
            +   +   E +             ++        C  + P          + + A   +T
Sbjct: 641  LVEYLDVNEENDCNIALYEHTINKLECSGMISAHCNLRLPG-SSNSPASASQVAATTDTT 699

Query: 801  DLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             L  +      +    +P+  +N          M  + + T      +    R   L   
Sbjct: 700  HLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG----YNQRNRIDTLMYL 755

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                  P V  +                          I       +   +    A+   
Sbjct: 756  LAYPQKPMVKTKT-------------------------IELIEFEKLPAGQNATVAVMSY 790

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               D+ D  +   + +        ++        +R  +   +++     D    + I  
Sbjct: 791  SGYDIEDALVLNKASLDRGFGRCLVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWR 849

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              I         G+   +      KS                 Q  ++   V +      
Sbjct: 850  HEILDADGICSPGEKVENKQVLVNKSMP------------TVTQIPLEGSNVPQQ----- 892

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             QY+      +    + IEK+    +       ++K+ +   R  + GDK + RHG KG+
Sbjct: 893  PQYKDVPITYKGATDSYIEKVMISSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGV 950

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
               I+P EDMPF   G   DI++NP G PSRM V        G     L  K   L   +
Sbjct: 951  CGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTV--------GKLIELLAGKAGVLDGRF 1002

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                               F G+  + +
Sbjct: 1003 HYGT----------------------------------------------AFGGSKVKDV 1016

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L     +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++T
Sbjct: 1017 CEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLT 1076

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE----- 1330
            +QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G+  +       
Sbjct: 1077 RQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWC 1136

Query: 1331 SIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                 +        P +  +L +E+Q++ +   L+ S+   
Sbjct: 1137 HYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLSKYNE 1177



 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 121/993 (12%), Positives = 271/993 (27%), Gaps = 231/993 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S              
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKN------------ 187

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR---K--------------VPVTSF 217
                   RII        +E D K  +   + R     K              +P+   
Sbjct: 188 --------RII--------VEADRKGAVGASVTRTNMAVKQGRFYLRHNTLSEDIPIVII 231

Query: 218 LMALGMDSE-EILSTFYPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
             A+G++S+ EI+     +              +       + A   +        +   
Sbjct: 232 FKAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGG 291

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
              +  IE  ++L +  +  L    VK     + C+    +   ++  +      +    
Sbjct: 292 GPKKTKIEEARELLASTI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYY 349

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            +++          + + +L+ D           +       ++ A  D+ + MR   ++
Sbjct: 350 GNKRL-----ELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQIT 404

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
              V     +   +   ++ +   G  ++  RL+  +   +            K+     
Sbjct: 405 NGMVNA--ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRS 462

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
                           +    +  + +    +  +           D   V     +  +
Sbjct: 463 LQ---------PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVE 513

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTH 565
            V     E      +  +  +   +      R    L      + RA    E   +    
Sbjct: 514 DVNLLCGEELSYPNVFLVFLNGGYIIETCVIRDHKKLVNTFRLMRRAGYINEFVSISTNL 573

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV-------------------- 605
             R     +  G     +  L      N + F     R V                    
Sbjct: 574 TDRCVYISSDGGRLCRYICRLLKRVFKNLFIFALERNRLVFIFETVLTSFIVKINLIPNF 633

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------ 659
            D    + V YL   EE +  IA        +      ++   C                
Sbjct: 634 EDFLHESLVEYLDVNEENDCNIAL--YEHTINKLECSGMISAHCNLRLPGSSNSPASASQ 691

Query: 660 -----KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                    ++  P  ++ + A LIP+  ++ S R    C M +QA+  +         G
Sbjct: 692 VAATTDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------G 742

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                   +   ++A                                             
Sbjct: 743 YNQRNRIDTLMYLLA--------------------------------------------- 757

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+P+VK                 +   L  G+N  VA M + GY+ ED++++++  +
Sbjct: 758 -YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASL 806

Query: 835 SEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVN 889
                  +  +  +    R T    +++   + + +          +D  GI   G +V 
Sbjct: 807 DRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVE 866

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              +LV K  P           + +    +   
Sbjct: 867 NKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 899


>gi|73975061|ref|XP_860737.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
            polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
            7 [Canis familiaris]
          Length = 1113

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 151/865 (17%), Positives = 263/865 (30%), Gaps = 175/865 (20%)

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             + +SQ+   +   S ++H RRL++     + R     + R +H T +G +CPAET EGH
Sbjct: 405  RAGVSQVLNRLTFASTLSHLRRLNS----PIGRDGKLAKPRQLHNTLWGMVCPAETPEGH 460

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             +GLV +L   A ++           + +  + N      A   +   I      +    
Sbjct: 461  AVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHK 520

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               + +   R    ++ +    I  I     ++ + A  +   L   +  ++L+      
Sbjct: 521  DPEQLMNTLRKLRRQMDIIVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHID 580

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            Q                      +SG           E +D +      +    D     
Sbjct: 581  QLKEREYNN-------YSWQDLVASGVV---------EYIDTLEEETVMLAMTPDDLQEK 624

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               Y                                   PS  LG       +  + +P+
Sbjct: 625  EVAY-------------------------CSTYTHCEIHPSMILG-------VCASIIPF 652

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N          M  + +   ++I  F                           ++  
Sbjct: 653  PDHNQSPRNTYQSAMGKQAMG--VYITNF---------------------------HVRM 683

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S V   
Sbjct: 684  DTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 743

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   ++  +    + E  E   R+          +       I  G      
Sbjct: 744  FF-RSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGD 802

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L                     + +  +E    +Y         R      
Sbjct: 803  DVIIGKTVTL--------------------PENEDELEGTNRRYTKRDCSTFLRTSETGI 842

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              Q    +     +  K+ V   R  Q GDK A RHG KG        EDMPF  +G   
Sbjct: 843  VDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITP 902

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E   G      G+                            
Sbjct: 903  DIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD------------------------- 937

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP  D  + + I+++L        G  +LY+
Sbjct: 938  ----------------------------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYN 969

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG      + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME
Sbjct: 970  GFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEME 1029

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFE 1340
              C  A+GAA  L+E L   SD     V            RT  YE    G         
Sbjct: 1030 RDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISL 1087

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
               P +  +L +E+ ++ ++  + +
Sbjct: 1088 VRMPYACKLLFQELMSMSIAPRMMS 1112



 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 143/997 (14%), Positives = 286/997 (28%), Gaps = 252/997 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI------------IHVRIDR 208
            ++ F     + + +G+    CR        ++      +             I  RI  
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTNNLKIKSLKKKSGAIGQRIVA 253

Query: 209 -----RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                +++VP+     ALG  S+ +IL          +  +     L  A ++    V+ 
Sbjct: 254 TLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVAL 313

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
           + +     +  +   K++     + L+++ +  +G++                       
Sbjct: 314 NFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDF--------------------- 351

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
                                            AY       D+ KD    L    R++ 
Sbjct: 352 ----------------------------CETKKAYFLGYKFIDRGKDFNLELAIKTRIIS 383

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
            G      +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 384 DG------LKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKL 437

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 438 AKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 494

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I+   +  A   F     +   ++    ++ +   RR   +    + R     E+R 
Sbjct: 495 LEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDI-IVSMIRDIREREIR- 552

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           ++        P    E   + L         ++     E       D   +  V Y+  +
Sbjct: 553 IYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGVVEYIDTL 607

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   +A     L E                  +         +  P  ++ + AS+IP
Sbjct: 608 EEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILGVCASIIP 651

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 652 FPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------ 681

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y               Q+PLV                  
Sbjct: 682 -----------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYL 706

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G N +VA   + GYN EDS++++   V    F S+    ++          EE
Sbjct: 707 RFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEE 766

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           +           +       +D+ G+I  G  V+  D+++GK     E+    E      
Sbjct: 767 VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGT---- 822

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               +    RD S  + +  +G V  V +       K
Sbjct: 823 ---NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 856


>gi|285310172|emb|CBH41067.1| DNA-directed RNA polymerase beta subunit [Pseudomonas
           citronellolis]
          Length = 381

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 231/381 (60%), Positives = 297/381 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G V++++V+LSA+EE +  IAQA+++LD  G   +ELV  R   E  +   E +  
Sbjct: 121 VVKEGLVSDEIVFLSAIEEADHVIAQASATLDAKGRLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD + R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDVIARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEEITRD 864
           I+E   +ARDTKLGPEEIT D
Sbjct: 361 IQELTCVARDTKLGPEEITAD 381


>gi|52694277|emb|CAG37978.1| RNA polymerase beta subunit [Pseudomonas fluorescens]
          Length = 390

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/390 (58%), Positives = 301/390 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEI    P   
Sbjct: 361 TTIHIQELTCVARDTKLGPEEIYCRHPERG 390


>gi|13518436|ref|NP_084796.1| RNA polymerase beta subunit [Lotus japonicus]
 gi|23822111|sp|Q9BBS9|RPOB_LOTJA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|13358977|dbj|BAB33194.1| RNA polymerase beta subunit [Lotus japonicus]
          Length = 1070

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 154/563 (27%), Positives = 245/563 (43%), Gaps = 58/563 (10%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E  + +    ++        I +          G       +          +
Sbjct: 561  CIVGTGLERQVALDSGTLAIAEHEGKIIYKDTNKIVLFGSGETLSVPLVIYRRSNKNTCM 620

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G IL       G   ++  + +L A    +  +  D  L     +S
Sbjct: 621  HQKSQVQRGKCIKRGQILADGAATVG-GELSLGKNVLVAYMPWEGYNSEDAVL-----IS 674

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELL-ARDKDDEQVILDRNIYSRLMEILCGQNA 995
              +V   I+    I K E    V     E +  +    E  +L      +   ++ G   
Sbjct: 675  DRLVYEDIYTSFHIRKYEIQTHVTSNGPERITNKIPHLEVHLLRN--LDKNGLVILGSWV 732

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G     K T   +   S  P  +  +  +  +        LK+       +++ R+ +
Sbjct: 733  EAGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWLH 792

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G    P     + +++  KR I+ GDK+AGRHGNKGIVS+IL  +DMP+L+DG
Sbjct: 793  KKG----GSGYNP---ETIHIYILQKREIKVGDKVAGRHGNKGIVSKILARQDMPYLQDG 845

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F  ++
Sbjct: 846  RPVDMVFNPLGVPSRMNVGQIFECSLGLAGDVLDRHYRIAPFDERYEQEASRKLVF-SEL 904

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                  T     ++ +                                        G+S 
Sbjct: 905  YQASKQTSNPWIFEPE--------------------------------------YPGKSR 926

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+G
Sbjct: 927  IFDGRTGTPFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALVTQQPLKGRAKQGGQRVG 986

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEM 1354
            EMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +    PESF +LV+E+
Sbjct: 987  EMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTISKPVDAPESFRLLVREL 1046

Query: 1355 QALGLSID--LENSRTKNSAKME 1375
            ++L L ++  L + +     + E
Sbjct: 1047 RSLALELNHFLVSEKNFRIHRKE 1069



 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 227/668 (33%), Positives = 368/668 (55%), Gaps = 17/668 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 137 ELDHKGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLNEILE 196

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     K   ++ A+L+ YR      GD              FF   +
Sbjct: 197 NVCYPEIFLSFLNDKEEKKIGSKESAILEFYRQFACVGGDPVFPESLCRELQKKFF-QQR 255

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P +   +   DI+     L+ ++   GT+DD+++L N+R+R
Sbjct: 256 CELGEIGRRNMNRRLNLDIPQNNTFLLPRDILTAADHLIGMKFRMGTLDDMNHLKNKRIR 315

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LS
Sbjct: 316 SVADLLQDQFGLALVRLENMVRGTICGAIRYKLIPTPQNLVTSTPLTTTYESFFGLHPLS 375

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+H +HYGRICP +TSEG N+GL+
Sbjct: 376 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHSSHYGRICPIDTSEGINVGLI 435

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+  +G IE+P+ ++ +      ++YLS   +E   IA  N      G+  E+
Sbjct: 436 GSLAIHARIGRWGSIESPFFEISERSKRIHMLYLSPSRDEYYMIATGNYLALNQGNQEEQ 495

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 496 IVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 555

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            ++E   VGTG+E  VA  SG   +A+  G +   D  +IV+          +       
Sbjct: 556 SQSEKCIVGTGLERQVALDSGTLAIAEHEGKIIYKDTNKIVL--------FGSGETLSVP 607

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L+ ++RSN+NTC++Q+  V+ G  ++R  I+ADG +T  G+L+LG+N+LVA+MPW GYN 
Sbjct: 608 LVIYRRSNKNTCMHQKSQVQRGKCIKRGQILADGAATVGGELSLGKNVLVAYMPWEGYNS 667

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++LIS+R+V ED++TS HI ++E+    T  GPE IT  IP++    L+N+D+ G++ 
Sbjct: 668 EDAVLISDRLVYEDIYTSFHIRKYEIQTHVTSNGPERITNKIPHLEVHLLRNLDKNGLVI 727

Query: 884 VGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +G+ V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+D
Sbjct: 728 LGSWVEAGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVID 787

Query: 942 VRIFNRHG 949
           VR  ++ G
Sbjct: 788 VRWLHKKG 795



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           +P L ++Q   +  F+          + GL         I         + FV  Y+   
Sbjct: 12  LPGLNQIQFEGFCRFI----------DRGLTEELFKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ K+I+EQ+I++G++PLM   GT
Sbjct: 62  PSIKEKDAVYESLTYSSELYVSAGLIW---------KNSKNIQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHKGIS---VYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLNEILENVCYPEIFLSFLNDKEEKKIGSKE 220


>gi|285310166|emb|CBH41064.1| DNA-directed RNA polymerase beta subunit [Pseudomonas
           nitroreducens]
          Length = 381

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 233/381 (61%), Positives = 301/381 (79%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G V++D+V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  
Sbjct: 121 VVKEGLVSDDIVFLSAIEEADHVIAQASATLNEKGQLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQ 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD+V R+DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDQVSRSDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEEITRD 864
           I+E   +ARDTKLGPEEIT D
Sbjct: 361 IQELTCVARDTKLGPEEITAD 381


>gi|52694269|emb|CAG37974.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. IV]
          Length = 390

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 230/390 (58%), Positives = 300/390 (76%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           T+IHI+E   +ARDTKLGPEEI    P   
Sbjct: 361 TTIHIQELTCVARDTKLGPEEIYCRHPERG 390


>gi|292494337|dbj|BAI94511.1| RNA polymerase beta subunit B [Pseudomonas indoloxydans]
          Length = 372

 Score =  374 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 227/372 (61%), Positives = 292/372 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 121 QVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 241 ARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 SRGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 361 CVARDTKLGPEE 372


>gi|237664250|gb|ACR09679.1| RNA polymerase beta subunit [Pseudomonas sp. EBCL-Psp2]
          Length = 384

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/384 (60%), Positives = 300/384 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPMVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRDIP 866
           HI+E   +ARDTKLGPEEIT DIP
Sbjct: 361 HIQELTCVARDTKLGPEEITADIP 384


>gi|52694141|emb|CAG30600.1| DNA-directed RNA polymerase beta chain [Pseudomonas lundensis]
          Length = 385

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 231/385 (60%), Positives = 302/385 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL Q  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLLQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKEGVVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDI 865
           +IHI+E   +ARDTKLGPEEIT DI
Sbjct: 361 TIHIQELTCVARDTKLGPEEITADI 385


>gi|52694289|emb|CAG37984.1| RNA polymerase beta subunit [Pseudomonas fuscovaginae]
          Length = 389

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/389 (60%), Positives = 302/389 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           +IHI+E   +ARDTKLGPEEI R  P   
Sbjct: 361 TIHIQELTCVARDTKLGPEEIYRRHPERG 389


>gi|269930799|gb|ACZ54134.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 425

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 295/422 (69%), Positives = 354/422 (83%), Gaps = 1/422 (0%)

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             I IL +D +N  AYIRNTL  DKN+ R+DAL DIYRVMRPG+  T   AE+MF+ LFF
Sbjct: 5   DQINILDIDHMNIGAYIRNTLKVDKNESRQDALFDIYRVMRPGEPPTIDTAEAMFHSLFF 64

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           D ++YDLS VGRVKMN+R++L+ PD VR +R+EDI+A++K+LV+LR+G+G IDDIDNLGN
Sbjct: 65  DPERYDLSAVGRVKMNLRMDLNCPDTVRVLRQEDILAVVKMLVELRDGRGEIDDIDNLGN 124

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RRVRSVGE+++NQYR+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQ
Sbjct: 125 RRVRSVGELMENQYRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQ 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS ITH RR SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIG
Sbjct: 185 LSQFMDQTNPLSEITHKRRFSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIG 244

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FT
Sbjct: 245 LINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFT 304

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAV
Sbjct: 305 EEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAV 364

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL++AEAPFVGTGMESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 365 PLVRAEAPFVGTGMESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 423

Query: 762 YR 763
           YR
Sbjct: 424 YR 425


>gi|52694129|emb|CAG30594.1| DNA-directed RNA polymerase beta chain [Pseudomonas savastanoi]
          Length = 387

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 231/387 (59%), Positives = 301/387 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +    
Sbjct: 121 SPYRVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPA 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIP 866
            +IHI+E   +ARDTKLGPEEIT DIP
Sbjct: 361 PTIHIQELTCVARDTKLGPEEITPDIP 387


>gi|186885945|gb|ACC93380.1| RNA polymerase beta subunit [Scaevola aemula]
          Length = 1027

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 129/396 (32%), Positives = 198/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  +    S     + +   +           LK+  
Sbjct: 676  LDKNGIVVLGSWVETGDVLVGKLTPQTEKESSYPLEDKLFYDVLGIPVYTLKETCLKLPI 735

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      IQ           +++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 736  GGRGRVIDVRW------IQKKKKDDSDSSYMIRVYILQKREIKVGDKVAGRHGNKGIISK 789

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG P+D+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 790  ILPRQDMPYLQDGRPLDMVFNPLGVPSRMNVGQIFESSLGLAGGFLDRHYRIAPFDERYE 849

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 850  QEASRKLVFSELYQASKQTANPW------------------------VFE---------- 875

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S + DG TG+PF++PV +G  Y+LKL H V DK++ RS G Y+ VTQQP
Sbjct: 876  -----PEYPGKSRILDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSRGPYASVTQQP 930

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            + G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G       
Sbjct: 931  VRGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQELIGTRIIGGRIPNPE 990

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 991  DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1026



 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 225/662 (33%), Positives = 363/662 (54%), Gaps = 19/662 (2%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            ++           L  +    +    IL  V        + N         +++A+L+ 
Sbjct: 123 RVWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSLLNDKEKKNIGSKENAILEF 182

Query: 378 YRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           Y+     G+   FS +        F   + +L  +GR  MN RLNLD P +   +   DI
Sbjct: 183 YQQFACVGEDPVFSESLCKELQQKFFQQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDI 242

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           +A    L+ ++ G GT+DD ++L N+R+RSV ++L++Q  L L+R+E  ++  I      
Sbjct: 243 LAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLLQDQLGLALVRLEDVVRGTICRALRQ 302

Query: 497 SVM--PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +   P++L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    A
Sbjct: 303 KLRRPPRNLLTSTPLTTTYESFFRLHPLSQVLDQTNPLTQIVHGRKFSYLGPGGLTARTA 362

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+  + +    + +
Sbjct: 363 SFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYAISERSKGSRM 422

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +YLS   +E   +A  NS     G   E++V  R   E + V  E++        Q  SI
Sbjct: 423 LYLSPDRDEYYMLAGGNSLALNQGIQDEQVVPARYRQEFLTVAWEQVHLRSLFSFQYFSI 482

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A++ G 
Sbjct: 483 GASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEQEGK 542

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           +             +  L           L+ +QRSN+ TC++Q+P V  G  +++   +
Sbjct: 543 IIYT--------KTDKILLSGNGHTLSIPLVMYQRSNKKTCMHQKPQVGRGKCIKKGQFL 594

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+  R T
Sbjct: 595 AYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHICKYEIQTRMT 654

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKL 912
             GPE +T +IP++    L+N+D+ GI+ +G+ V  GD+LVGK+TP+ E   +   E+KL
Sbjct: 655 SQGPERVTNEIPHLEGYLLRNLDKNGIVVLGSWVETGDVLVGKLTPQTEKESSYPLEDKL 714

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-----RSISVEREQIELL 967
              + G     +++T L++P G  G V+DVR   +   D ++     R   +++ +I++ 
Sbjct: 715 FYDVLGIPVYTLKETCLKLPIGGRGRVIDVRWIQKKKKDDSDSSYMIRVYILQKREIKVG 774

Query: 968 AR 969
            +
Sbjct: 775 DK 776



 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 55/176 (31%), Positives = 96/176 (54%), Gaps = 13/176 (7%)

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P       ++  LTY+  L I+ RLI          KSI++ +EQ I++G++PLM
Sbjct: 13  YQLVEPLITERAAVYASLTYSSRLYISARLIW---------KSIRNKREQRIFIGNIPLM 63

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           +  GTF++ G+ RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D 
Sbjct: 64  SSLGTFIVNGLYRIVINQILQSPGIYYRSELDHKGIS---VYTATIISDWGGRLELEIDR 120

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           K  +  R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 121 KARVWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSLLNDKEKKNIGSKE 176


>gi|52694291|emb|CAG37985.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. I]
          Length = 388

 Score =  373 bits (958), Expect = e-100,   Method: Composition-based stats.
 Identities = 230/386 (59%), Positives = 299/386 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIP 866
           +IHI+E   +ARDTKLGPEEI    P
Sbjct: 361 TIHIQELTCVARDTKLGPEEIYCRHP 386


>gi|71028664|ref|XP_763975.1| DNA-directed RNA polymerase II subunit [Theileria parva strain
            Muguga]
 gi|68350929|gb|EAN31692.1| DNA-directed RNA polymerase II subunit, putative [Theileria parva]
          Length = 1190

 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 166/984 (16%), Positives = 307/984 (31%), Gaps = 221/984 (22%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  +I  L+  + G+   DD ++ G +R+   G ++ + +     ++ + ++  + 
Sbjct: 379  KCFYLGYMIHRLLLNQLGRINEDDREHFGKKRLDLAGSLMASSFGTLFRKLAKDVERFLK 438

Query: 492  SVDIDSVMPQ---DLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
            +             + +   +   +     +               +SQ+   +   S +
Sbjct: 439  NQIDSGRSFDVAGAIKSCSQITQGLQYQLLTGNWGRDKDGNVVRTGVSQVLNRLTFASYL 498

Query: 536  THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
            +H RRL+      + R     + R +H TH+G ICPAET EG  +GLV +L     ++  
Sbjct: 499  SHLRRLNT----PLGREGKMAKPRQLHNTHWGMICPAETPEGQAVGLVKNLALMCYIS-V 553

Query: 596  GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAG 651
            G + +           + +  +S +  ++R     N +     +  + LV      R  G
Sbjct: 554  GSLSSTILDFLLEFGMDSLDEISPILIKDRVKIFLNGTWVGVFNQPDSLVNVLLELRRKG 613

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                      D +    K       S+ P    ++ NR+L+               +  +
Sbjct: 614  NISSETSIVRDIMSNEIKIFTDAGRSMRPLYIVEN-NRLLITKKHADMIENRQLTWSGLL 672

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
             TG+                   VE +D     I  +    D                  
Sbjct: 673  ETGV-------------------VEYIDCEEEEICMIAMFPDD----------------- 696

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                     LV   +           PS  LG       +  + +P+   N       S 
Sbjct: 697  ---------LVNNNNYCNSYTHCEIHPSMILG-------VCASIIPFPDQNQ------SP 734

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R   +       +  +                           N+    +  V       
Sbjct: 735  RNTYQSAMGKQAMGVYSTN-----------------------YNLRMDTLSHVLYYPQKP 771

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF-NRHGI 950
             +    +       +      + AI      +  D+ +   S +   +            
Sbjct: 772  LVCTRSMEFLRFRELPAGINSIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSVFNRTYSSE 831

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTV 1007
            +K   S  +E       + +  +    L R  YS+L     +  G   +       +S+ 
Sbjct: 832  EKYLGSTVIESFTKPTASGNFLN----LKRGDYSKLDNDGLVEPGSRVLGDDIIIGRSSP 887

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            + +D  +    S+          ++ N   +      + +                    
Sbjct: 888  VEADPNNPQYTSEMNLRMDCSCCLRPNENGVVDNVLLTVN-------------------- 927

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                +  KV V   R  Q GDK A RHG KG +      ED+PF  DG   DI++NP  V
Sbjct: 928  NKGCKFTKVKVRSIRVPQIGDKFASRHGQKGTIGMTFRMEDLPFTCDGIVPDIIMNPHAV 987

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E  LG     +G +                                    
Sbjct: 988  PSRMTIGHLIECLLGKVGSLVGMEGD---------------------------------- 1013

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                               +TP F     + I++ L        G    ++G TG     
Sbjct: 1014 -------------------ATP-FSKMTLDQISNRLFKCRYSRYGNEAFHNGFTGNLMAS 1053

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG  Y  +L HMV DK++AR+ G  +++T+QP  G+S  GG R GEME  C+ ++GA
Sbjct: 1054 KIFVGPTYYQRLKHMVEDKIHARARGPVTMLTRQPTEGRSREGGLRFGEMERDCMISHGA 1113

Query: 1308 AYVLQEMLTIKSD----DVVG--------------------RTRVYESIVAGNDTFETGT 1343
            A +L+E L  +SD     V                        +            +   
Sbjct: 1114 AKMLKERLFDQSDAYRVHVCNFCGLLSVANLNNSSFQCTACDNKT--------QISQVTI 1165

Query: 1344 PESFNVLVKEMQALGLSIDLENSR 1367
            P +  +L++E+ A+ +   L  + 
Sbjct: 1166 PYACKLLLQELMAMAIYPKLILTE 1189



 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 135/991 (13%), Positives = 284/991 (28%), Gaps = 221/991 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGA--------AMLE 75
           L+  Q  S++ F+   +          Q    +  PI       +             L+
Sbjct: 74  LVHQQIESFNDFITYRM----------QEIIDAHPPIEITPQPNYRPEEEEENSILYRLK 123

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F     + P  +            +   R+LTYA  + I +    F V+E          
Sbjct: 124 FGQLSLNKPSVEEKDGVFKHIWPQEARLRNLTYASQVYIDIEQETF-VNENGKLVQTDST 182

Query: 126 KEQSIYMGDLPLM------------------------TKDGTFVIKGIQRIVVSQLHRSP 161
               + +  +P+M                         + G FV+ G +R++++Q  R  
Sbjct: 183 VYPRVPLCRMPMMHKSSYCWTRGLNDRDLSDIGECVFDQGGYFVVNGGERVLIAQE-RMA 241

Query: 162 GIH---FDHDKGRASLSGKL---------LYACRI-IPDQGLWMDIEFDSKDII-----H 203
                 F+    + S   +L         + +  I I +    +     +K+ +     +
Sbjct: 242 NNFVYVFNKKNSKYSAVAQLRSQPDFIQGVTSLTIMISN--SQL-----TKNKMVAVLPY 294

Query: 204 VRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           +R D    +PV     ALG +   +IL         +Q        L             
Sbjct: 295 IRSD----IPVPILFRALGCISDRDILQRIVYDFSDTQMLSLMRASLEECKRGPTVGALH 350

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                   E +    ++     + +      K          G  +   ++N + G I  
Sbjct: 351 EERLNFAKETL----RRHFLPHVGTEVGSESKKC-----FYLGYMIHRLLLN-QLGRINE 400

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +  +   +K L+            L+   + +   +++N + + ++ D   A+    +  
Sbjct: 401 DDREHFGKKRLDLAGSLMASSFGTLFRKLAKDVERFLKNQIDSGRSFDVAGAIKSCSQ-- 458

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
                 T  +   +    +      ++   G  ++  RL   +      R          
Sbjct: 459 -----ITQGLQYQLLTGNWGRDKDGNVVRTGVSQVLNRLTFASYLSHLRRLNTPLGREGK 513

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L N    +         +   + + L     + +  +  +I + +    +DS+ 
Sbjct: 514 MAKPRQLHNTHWGMICPAETPEGQAVGLVKNLALMCYISVGSLSSTILDFLLEFGMDSL- 572

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             D I+   +   V  F   + +    +  + ++ +   RR   +               
Sbjct: 573 --DEISPILIKDRVKIFLNGTWVGVFNQPDSLVNVLLELRRKGNISSETSIVRDIMSNEI 630

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFA---RVNAYGFIETPYRKVCDGKVTNDVVY 616
            +       + P    E + + +           ++   G +E           T  V Y
Sbjct: 631 KIFTDAGRSMRPLYIVENNRLLITKKHADMIENRQLTWSGLLE-----------TGVVEY 679

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +   EEE   IA     L  + ++                        +  P  ++ + A
Sbjct: 680 IDCEEEEICMIAMFPDDLVNNNNYCNSY-----------------THCEIHPSMILGVCA 722

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF + + S R      M +QA+ +                                 
Sbjct: 723 SIIPFPDQNQSPRNTYQSAMGKQAMGVYSTNYNL-------------------------- 756

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + S V  Y               Q+PLV              
Sbjct: 757 ---------------RMDTLSHVLYYP--------------QKPLV----------CTRS 777

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G N +VA M + GYN EDS+++++  +   +F S+    +    +    
Sbjct: 778 MEFLRFRELPAGINSIVAIMCYTGYNQEDSLIMNQSSIDRGLFRSVFNRTYSSEEKYLGS 837

Query: 857 GPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              E            N+       +D  G++  G+ V   DI++G+ +P    P  P+ 
Sbjct: 838 TVIESFTKPTASGNFLNLKRGDYSKLDNDGLVEPGSRVLGDDIIIGRSSPVEADPNNPQY 897

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
                +         D S  +    +G V +
Sbjct: 898 TSEMNLR-------MDCSCCLRPNENGVVDN 921


>gi|320592188|gb|EFX04627.1| DNA-dependent RNA polymerase 2 rpb140 [Grosmannia clavigera kw1407]
          Length = 1266

 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 174/1063 (16%), Positives = 331/1063 (31%), Gaps = 164/1063 (15%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A     R     +V+   + +   N      
Sbjct: 323  VSDEDILNHICYDRNDSQMLEMLRPCIEEAFCIQDR-----EVALDFIGKRGQNSHGISR 377

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
                 +    ++  M  ++   +     +   +  ++  L+    G+  +DD D+ G +R
Sbjct: 378  KDRVRAARDILQKEMLPHISQSEGCETRKAFFLGYMVHKLLQCALGRRDVDDRDHFGKKR 437

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R  + +M + +                +  I  + + + +     +  
Sbjct: 438  LDLAGSLLAKLFRGIIRKMYQELMNHLKRCVDTGKHFDLRVGIRHQTLTNGLKYSLATGN 497

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 498  WGDQKKAMSSTAGVSQVLNRYTFSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGL 553

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L+    V+     E    +    + +V  +   L        +
Sbjct: 554  VCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVEFMIARNMEVLEEYEPLRYPNATKIF 613

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
            +  +   + +D      LV        I      + D  D   K        + P    +
Sbjct: 614  VNGSWVGVHQDPKHLVSLVQGLRRKGVIQSEVSLVRDIRDREFKIFSDAGRVMRPLFAIE 673

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
              +    G       +     +      G+     K  G   +     I E +DA     
Sbjct: 674  QEDNADSGVEKGMLVLTKEHVQRLDADEGLSKDDPKYFGWDGICDAGAI-EYLDAEEEET 732

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +               +  +N+R   K+             PS  LG  
Sbjct: 733  AMICMTPEDLDNYRMQKAGYVLPDETNDEDINKRVKTKMNPTTHMYTHCEIHPSMLLG-- 790

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G        
Sbjct: 791  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGFFLTNYPR 827

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  V             +       +   +  + AI      +  
Sbjct: 828  RM-----------DTMANVLYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 876

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D  +R        +E   +    + + L    Y +
Sbjct: 877  DSVIMNQSSIDRGLF-RSLFFRAYTDSEKRVGI---NFVETFEKPFRSDTLRLKHGTYDK 932

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   +  G           K++ ++ D                 E  QR    +K   
Sbjct: 933  LDDDGIVAPGVRVSGEDIIIGKTSPINPD---------------HQEMGQRTQAHVKRDA 977

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             T     E    +++      D++     R VKV V   +  Q GDK A RHG KG +  
Sbjct: 978  STPLRSTESGIIDQVVVTTNQDNL-----RYVKVRVRTTKIPQIGDKFASRHGQKGTIGV 1032

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +  + E  L       G +  +        
Sbjct: 1033 TYRSEDMPFTTEGILPDIIINPHAIPSRMTIAHLIECLLSKVATLKGMEGDATPFT---- 1088

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                  ++      +LR       G  +                
Sbjct: 1089 ---------------------DVTVDSVSGLLREHGYQSRGFEIM--------------- 1112

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G +    G         V  G  Y  +L HMV DK++AR+ G   ++T+QP
Sbjct: 1113 -------YHGHT----GR---KLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQP 1158

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVA- 1334
            + G++  GG R GEME  C+ A+GAA  L+E L   SD       ++ G      ++   
Sbjct: 1159 VEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSDAYRVHICEICGLMTPIANLTKQ 1218

Query: 1335 ------GND---TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                    +     +   P +  +L +E+ A+ ++  +   R+
Sbjct: 1219 SFECRPCKNKTRIAQVQIPYAAKLLFQELAAMNIAARMFTDRS 1261



 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 146/1051 (13%), Positives = 297/1051 (28%), Gaps = 217/1051 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS----GAAMLEFVSYEFDPP 84
            L+  Q  S++ F    +         L    +S  PI +          ++F +     P
Sbjct: 42   LVSQQIDSFNEFTTTTVQS-LIDEHSLLTLDQSNPPIASDRPVKLRRYEIKFGNIMVSKP 100

Query: 85   KF----------DVDDCLWRDLTYAVPLKITLRLIV----------FDVDEF-------T 117
            +F             +C  R+LTY+ P+   +   V           ++DE        T
Sbjct: 101  QFAEGDGRVSTLTPYECRDRNLTYSCPIYARITKKVSLAVDEPIPDDELDEEQIEEMQRT 160

Query: 118  GAKSIKDIKEQS-------------------IYMGDLPLMTKD----------------- 141
            G +  + + E+                    ++MG LP+M K                  
Sbjct: 161  GEQPTRIVWEEEPSDLPDYEKDKADEDMKDMVFMGRLPIMVKSKICHLAYEDEDGLFLLN 220

Query: 142  -------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWM 192
                   G F+I G ++++++Q  RS          + +   K  Y   I    ++G  +
Sbjct: 221  ECPYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKAQPSKFSYTAEIRSALEKGSRL 277

Query: 193  DIEFDSKDIIHVRIDRRR--------------K--VPVTSFLMALG-MDSEEILSTFYPK 235
                    ++  + D  R              K  +P+     ALG +  E+IL+     
Sbjct: 278  ISSLSI--MLVAKGDTGRGSFGQTVHTTLPYIKSELPIAVVFRALGVVSDEDILNHICYD 335

Query: 236  IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-- 293
               SQ  +     +  A  +   +V+   +    G+      +K      + + +K +  
Sbjct: 336  RNDSQMLEMLRPCIEEAFCIQDREVALDFIGKR-GQNSHGISRKDRVRAARDILQKEMLP 394

Query: 294  -----KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
                 +          G  V + ++    G   ++  D   +K L+       +    + 
Sbjct: 395  HISQSEGCETRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGSLLAKLFRGII 453

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                            D  K     +   ++ +  G      +  S+    + D  K   
Sbjct: 454  RKMYQELMNHLKRC-VDTGKHFDLRVGIRHQTLTNG------LKYSLATGNWGDQKKAMS 506

Query: 409  STVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            ST G  ++  R    +      R          +     L N    +         +   
Sbjct: 507  STAGVSQVLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG 566

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            + + L     + +      I E + + +++ +   + +               S +   +
Sbjct: 567  LVKNLSLMCYVSVGTPAEPIVEFMIARNMEVLEEYEPLRYPNATKIF---VNGSWVGVHQ 623

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE---------- 576
            +  + +S +   RR   +                +       + P    E          
Sbjct: 624  DPKHLVSLVQGLRRKGVIQSEVSLVRDIRDREFKIFSDAGRVMRPLFAIEQEDNADSGVE 683

Query: 577  -GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
             G  +     +            +  Y           + YL A EEE   I      LD
Sbjct: 684  KGMLVLTKEHVQRLDADEGLSKDDPKYFGWDGICDAGAIEYLDAEEEETAMICMTPEDLD 743

Query: 636  EDGSFTEELV---------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                     V           +    ++          +  P  ++ I AS+IPF +++ 
Sbjct: 744  NYRMQKAGYVLPDETNDEDINKRVKTKMNPTTHMYTHCEIHPSMLLGICASIIPFPDHNQ 803

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            S R      M +QA+       P                                     
Sbjct: 804  SPRNTYQSAMGKQAMGFFLTNYP------------------------------------- 826

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                    + + V  Y       +     +  R                        +L 
Sbjct: 827  ----RRMDTMANVLYYPQKPLATTRSMEYLKFR------------------------ELP 858

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----I 861
             G+N +VA + + GYN EDS+++++  +   +F S+    +    +   +   E      
Sbjct: 859  AGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLFFRAYTDSEKRVGINFVETFEKPF 918

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              D   +       +D+ GI+  G  V+  DI++GK +P         ++        +A
Sbjct: 919  RSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTSPINPDHQEMGQRT-------QA 971

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               RD S  + S  SG +  V +       +
Sbjct: 972  HVKRDASTPLRSTESGIIDQVVVTTNQDNLR 1002


>gi|209360641|gb|ACI42991.1| RNA polymerase beta subunit [Mycoplasma incognitus]
          Length = 665

 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 252/645 (39%), Positives = 390/645 (60%), Gaps = 18/645 (2%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
             N+R+ +VGE+L++Q  +GL+++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3    TNKRIVAVGELLQSQLNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNS 62

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63   SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
            IGL+ +  ++A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+ 
Sbjct: 123  IGLILNFATYAQVNKYGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENN 182

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               ++ +  R     I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183  KLVDKQLTMRHNYNYIIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQR 242

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVPLL  EAPFV TG+ES +AK S    VAK  G+VE VD  +I +R+ +G LD     
Sbjct: 243  QAVPLLIPEAPFVATGIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD----- 297

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               Y L  FQRSNQ+T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  +
Sbjct: 298  --TYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTY 355

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356  KGYNYEDAVILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDE 415

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GI+ +G+EV PGD+LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GT
Sbjct: 416  HGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGT 475

Query: 939  VVDVRIFNRHGIDKNERSIS-VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            V+ V + +R   D  E  I  + +  I +  + K  +++         +  +L  ++   
Sbjct: 476  VIGVDVLSRENGDALEDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPY 535

Query: 998  GPKGFKKSTVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR---- 1052
               G     +L+   +       Q  +  +     +   + +   ++  K          
Sbjct: 536  LEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDVTLE 595

Query: 1053 ----FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   K   I             V V   +K     GDKM  R
Sbjct: 596  AGLPLSGKQWLIDPITGNKLDKPVSVGVMYMLKLNHMVGDKMHSR 640



 Score =  304 bits (778), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 142/529 (26%), Positives = 222/529 (41%), Gaps = 86/529 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L+   P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+  GD
Sbjct: 271  FVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K    +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 330  LLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQF 388

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++++   +   A    DE  I+         ++L G+ +  G     +  
Sbjct: 389  RTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEE 447

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++                  QR +       +             +   + GD +
Sbjct: 448  KLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENGDAL 490

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 491  EDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 550

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG K  +   D     +I  +                  
Sbjct: 551  VPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV------------------ 592

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                          ++G+P+                        SG+  L D +TG   D
Sbjct: 593  ------------TLEAGLPL------------------------SGKQWLIDPITGNKLD 616

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 617  KPVSVGVMYMLKLNHMVGDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|215254223|gb|ACJ64116.1| RNA polymerase beta subunit [Vibrio sp. UST981101-002]
          Length = 373

 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 233/373 (62%), Positives = 290/373 (77%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E G+F EEL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTVLSEQGTFAEELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQR+A P L+A+ P VG
Sbjct: 121 SGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRRAGPTLRADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNIAVDSGVTAVAKRGGVIQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKITPKGESP 905
           ILVGK+TPKGE+ 
Sbjct: 361 ILVGKVTPKGETQ 373


>gi|229077401|ref|ZP_04210056.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock4-2]
 gi|228705906|gb|EEL58237.1| DNA-directed RNA polymerase subunit beta [Bacillus cereus Rock4-2]
          Length = 223

 Score =  373 bits (957), Expect = e-100,   Method: Composition-based stats.
 Identities = 100/179 (55%), Positives = 130/179 (72%)

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+ ++TPVFDGA EE +   +  A +    ++ILYDG TGEPFD  V+VG +YM+KL HM
Sbjct: 29   GIHIATPVFDGAREEDVWGTIEEAGMANDAKTILYDGRTGEPFDNRVSVGVMYMIKLAHM 88

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT+KSDDV
Sbjct: 89   VDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDV 148

Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
            VGR + YE+IV G +  E G PESF VL+KE+Q+LG+ + + +S        +   D +
Sbjct: 149  VGRVKTYEAIVKGENVPEPGVPESFKVLIKELQSLGMDVKMMSSDDTEIEMRDTEDDDD 207


>gi|91214141|ref|YP_538763.1| RNA polymerase beta subunit [Glycine max]
 gi|88984774|sp|Q8HVY5|RPOB_SOYBN RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|83595742|gb|ABC25123.1| RNA polymerase beta subunit [Glycine max]
          Length = 1070

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/686 (33%), Positives = 378/686 (55%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLSEILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      DK K   +++A+L+ YR      GD              FF   + +L  +
Sbjct: 203 IFVSFLNDKDKKKIGSKENAILEFYRQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN +LNLD P +   +   DI+     L+ ++ G G +DDI++L N+R+RSV ++L
Sbjct: 262 GRRNMNQKLNLDIPQNNTFLLPRDILTAADHLIGMKFGMGILDDINHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDQT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+ ++G IE+P+ ++ +      ++YLS   +E   +A  NS         E+ V  R 
Sbjct: 442 ARIGSWGSIESPFYEISERSKRIRMLYLSPSRDEYYMVATGNSLALNRDIQEEQTVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG + +A+  G +   +  RI +                  L  +QR
Sbjct: 562 IVGTGLERQVALDSGVSAIAEHEGNIIYTNTDRIFLFGN--------GDTLSIPLTIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVDGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+V ED++TS HI ++E+    T  G E IT  IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 NERLVYEDIYTSFHIRKYEIQTHMTSYGSERITNKIPHLEAHLLRNLDKNGIVILGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES  +PE++LLRAI G +    ++T L++P+G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPTGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 794 KGGSSYNPETIRIYILQKREIKVGDK 819



 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 128/396 (32%), Positives = 197/396 (49%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDILVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPT 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     +++++  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRIYILQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGMLERHYRITPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYEASKQTSNPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG  F +P  +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -------YPGKSKIFDGRTGNSFKQPAIMGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKTRQEVLGTTIIGGTIPKPT 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L + ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLAMELNHFLVSEKNFRIHRKE 1069



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 115/232 (49%), Gaps = 27/232 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLE-FVS-YEFD 82
           +P L ++Q   +  F+   +       EGL   FK  FP I         + FV  Y+  
Sbjct: 12  LPGLNQIQFEGFCRFIDRGLP------EGL---FK--FPKIEDTDQEIEFQLFVETYQLL 60

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            P  +  D ++  LTY+  L ++  LI          KS +DI+EQ+I++G++PLM   G
Sbjct: 61  EPLINEKDAVYESLTYSAELYVSAGLIW---------KSSRDIQEQTIFVGNIPLMNSLG 111

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           T ++ GI RIV++Q+ +SPGI++  +      SG  +Y   II D G  +++E D K  I
Sbjct: 112 TSIVNGIYRIVINQILQSPGIYYRSELD---PSGISVYTGTIISDWGGRLELEIDRKARI 168

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
             R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 169 WARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFVSFLNDKDKKKIGSKE 220


>gi|309322138|ref|YP_003934053.1| RNA polymerase beta subunit [Geranium palmatum]
 gi|197131678|gb|ACH47357.1| RNA polymerase beta subunit [Geranium palmatum]
 gi|300069231|gb|ADJ66352.1| RNA polymerase beta subunit [Geranium palmatum]
          Length = 1109

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 153/562 (27%), Positives = 242/562 (43%), Gaps = 63/562 (11%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E  + +   +          I         +  G       +          I
Sbjct: 607  CIVGTGLEGQVALDSAVPLITEHAGKVISIHTDKILLSGNGDTLSIPLVMYQGSNKNTCI 666

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G IL       G   +   + LL A    +  +  D  L     +S
Sbjct: 667  HQKPQVRRGKCMKKGQILADGAATVG-GELALGKNLLVAYMPWEGYNFEDAIL-----IS 720

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V R+  E + +       +L      +   ++ G    
Sbjct: 721  ERLVYEDIYTSFHIRKYEIKIHVTRQGPERVTKKIPLRAHLLRN--LDKNGVVILGSWVE 778

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T   +  +S   +         D      + + +            R  + 
Sbjct: 779  AGDILVGKLTPQLAQDLSPADK-------FLDALFSTQLATSRQTCLKLPRGRRGRVIDV 831

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                   +         ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 832  RWIRSNPER------ERIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGK 885

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+D+V NPLGVPSRMNVGQIFE  LG A V L +  +    D +   + S    F E   
Sbjct: 886  PIDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDERYEQEASRKLVFSELHE 945

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 946  ASKQTGNPW------------------------VFE---------------PEYPGKSRI 966

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV VG  Y+LKL H V DK++ R  G Y+ VTQQP+ G++ RGGQR+GE
Sbjct: 967  FDGRTGDPFEQPVIVGQPYILKLIHQVDDKIHGRYDGPYASVTQQPVRGRAKRGGQRVGE 1026

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G A++LQEMLT KSD +  R +++ + + G +  +    PESF +LV+E++
Sbjct: 1027 MEVWALEGFGVAHILQEMLTYKSDHLRTRDKIFGTTILGGEMPKAMDAPESFRLLVRELR 1086

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L + +     + E
Sbjct: 1087 SLALELNHFLVSEKNFQMNRKE 1108



 Score =  341 bits (875), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 221/687 (32%), Positives = 370/687 (53%), Gaps = 17/687 (2%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K   + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 182 ELDHKGFLVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLRDIIE 241

Query: 350 DSVNNNAYIRNTLVTDKNK--DRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDK 405
           +       +      +K K   +++A+L+ Y+  V   GD              FF   +
Sbjct: 242 NVCYPEILLAFLDDKEKGKIGSKENAILEFYQEFVCIGGDPVFSDSLCKELQNTFF-RQR 300

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  +N RLNLD   + + +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 301 CELGKIGRRNINRRLNLDISQNNKFLLPRDILAATDHLIGIKFGMGTLDDMNHLKNKRIR 360

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  IK  I       +   PQ+ + + P+ +    FF    LS
Sbjct: 361 SVADLLQDQFGLALIRLEEVIKGGIRGAIKGELIPTPQNFVTSTPLKTTYESFFGLHPLS 420

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVA-RARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           Q+ +  N L++I H R+ S LG GG+         +RD+HP++YGRIC  +TSEG N+GL
Sbjct: 421 QVLDETNPLTQIVHGRKWSFLGPGGLTTGQTPSFRIRDIHPSYYGRICTIDTSEGINVGL 480

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL   AR+  +  +E+P+ ++ +      ++YLS+  +E   I   NS    +G   E
Sbjct: 481 IGSLAVHARIGHFESLESPFFEISEKPKGARLLYLSSRRDEYCMIGTGNSLALNEGFQEE 540

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           ++V  R   E + +  E++      P Q  SI  SLIPF+E++D+NR LM  NMQRQAV 
Sbjct: 541 QIVPARYRQEFLTIAWEQVHLRSIFPFQYFSIGTSLIPFIEHNDANRALMSSNMQRQAVA 600

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L ++E   VGTG+E  VA  S   ++ + AG V  +          +  L          
Sbjct: 601 LSRSEKCIVGTGLEGQVALDSAVPLITEHAGKVISIH--------TDKILLSGNGDTLSI 652

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+ +Q SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN
Sbjct: 653 PLVMYQGSNKNTCIHQKPQVRRGKCMKKGQILADGAATVGGELALGKNLLVAYMPWEGYN 712

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           FED++LISER+V ED++TS HI ++E+    T+ GPE +T+ IP +    L+N+D+ G++
Sbjct: 713 FEDAILISERLVYEDIYTSFHIRKYEIKIHVTRQGPERVTKKIP-LRAHLLRNLDKNGVV 771

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +G+ V  GDILVGK+TP+    ++P +K L A+F  +    R T L++P G  G V+DV
Sbjct: 772 ILGSWVEAGDILVGKLTPQLAQDLSPADKFLDALFSTQLATSRQTCLKLPRGRRGRVIDV 831

Query: 943 RIFNRHGIDKNERSISVEREQIELLAR 969
           R    +   +  R    ++ +I++  +
Sbjct: 832 RWIRSNPERERIRVYISQKREIKVGDK 858



 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 113/280 (40%), Gaps = 18/280 (6%)

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y+   P     D ++  LTY+  L +   LI               +++Q+I +G++PLM
Sbjct: 101 YKLVEPLIKERDAVYESLTYSSELYVAAGLIWKRKGYS--------MQKQTILIGNIPLM 152

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              G F++ GI R+VV+Q+ +SPGI++  +       G L+Y   II D G  +++E D 
Sbjct: 153 NSLGIFIVNGIYRMVVNQILQSPGIYYRSELDHK---GFLVYTGTIISDWGGRLELEIDR 209

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVG 257
           K  I  R+ R++K+ +     A+G +  +I+    YP+I+ +   D     + + +  + 
Sbjct: 210 KARIWARVSRKQKISILVLSSAMGSNLRDIIENVCYPEILLAFLDDKEKGKIGSKENAIL 269

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAED 311
                 +             K+L +   +   E G       +  L         ++   
Sbjct: 270 EFYQEFVCIGGDPVFSDSLCKELQNTFFRQRCELGKIGRRNINRRLNLDISQNNKFLLPR 329

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +   T  +      +     +  + +  IR +  L  D 
Sbjct: 330 DILAATDHLIGIKFGMGTLDDMNHLKNKRIRSVADLLQDQ 369


>gi|52694295|emb|CAG37987.1| RNA polymerase beta subunit [Pseudomonas marginalis]
          Length = 388

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 230/388 (59%), Positives = 299/388 (77%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V D  VT+++V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +
Sbjct: 121 YRVVKDALVTDEIVFLSAIEEADHVIAQASATMNEKKVLVDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+
Sbjct: 301 VRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTT 360

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVS 869
           IHI+E   +ARDTKLGPEEI    P   
Sbjct: 361 IHIQELTCVARDTKLGPEEIYCRHPERG 388


>gi|215254183|gb|ACJ64096.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 372

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/372 (63%), Positives = 288/372 (77%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  
Sbjct: 61  AFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+
Sbjct: 121 RQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKAD 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P VGTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+
Sbjct: 181 KPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKY 240

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+
Sbjct: 241 TRSNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSI 300

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAE
Sbjct: 301 LVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAE 360

Query: 888 VNPGDILVGKIT 899
           V  GDILVGK+T
Sbjct: 361 VKGGDILVGKVT 372


>gi|83583681|gb|ABC24700.1| RNA polymerase beta subunit [Spiroplasma insolitum]
 gi|83583683|gb|ABC24701.1| RNA polymerase beta subunit [Spiroplasma insolitum]
 gi|83583691|gb|ABC24705.1| RNA polymerase beta subunit [Spiroplasma insolitum]
          Length = 592

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/474 (49%), Positives = 331/474 (69%), Gaps = 8/474 (1%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            ++A++NA+GFIETPYR+V D KVT +  YL+A +E+N  +AQAN  L + G   +E V  
Sbjct: 61   TYAKINAFGFIETPYRRVIDCKVTAENDYLTADQEKNYVVAQANIRLSDKGEILDEQVVA 120

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121  RFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLISPN 180

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E        G+  Y L  F
Sbjct: 181  SPYVGTGVEYAAARDSGLAIVSQYDGSVDYVDATRIVLKTKE--------GLKNYNLDTF 232

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233  VRSNQGTSLTHVPLVKHGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            ++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293  IVSERLVSEDVFTSIHIEEYTIERRQTKQGSEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353  VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
               + +   + V +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  EKYELSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDG 466



 Score =  311 bits (796), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 121/415 (29%), Positives = 188/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVKHGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGSEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 417  -----LSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  +            
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNEELIEIMEKAN------- 524

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      ++        + +L DG 
Sbjct: 525  ------------------------------------------MKNFG-----KEVLIDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +GE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 538  SGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 592


>gi|289066826|ref|YP_003434344.1| RNA polymerase beta subunit [Vigna radiata]
 gi|259020013|gb|ACV90211.1| RNA polymerase beta subunit [Vigna radiata]
          Length = 1070

 Score =  372 bits (956), Expect = e-100,   Method: Composition-based stats.
 Identities = 254/778 (32%), Positives = 406/778 (52%), Gaps = 41/778 (5%)

Query: 346  ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
            +  V          N     K   +++A+L+ YR      GD              FF  
Sbjct: 195  LENVCYPEIFVSFLNDKEKKKIGSKENAILEFYRQFACVGGDPVFSESLWKELQKKFF-Q 253

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             + +L  +GR  +N +LNLD P +   +   DI+     L+ ++ G   +DDI++L N+R
Sbjct: 254  QRCELGKIGRRNINQKLNLDIPQNNTFLLPRDILTAADHLIGMKFGMALLDDINHLKNKR 313

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
            +RSV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    
Sbjct: 314  IRSVADLLQDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP 373

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
            LSQ+ +  N L+ I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374  LSQVLDQTNPLTEIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582  LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            L+ SL   AR+  +G IE+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434  LIGSLAIHARIGIWGAIESPFFEISERSKRIRMLYLSPNIDEYYMVATGNSLALTRDIQE 493

Query: 642  EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E++V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494  EQIVPARYRQEFLTIAWEQVHLRSIYPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            PL ++E   VGTG+E  VA  SG + +A+  G +   D  RI +                
Sbjct: 554  PLSESEKCIVGTGLECQVALDSGVSAIAEHEGNIVYTDTDRIFLFVN--------GDTLS 605

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              L  +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GY
Sbjct: 606  IPLTIYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNVLVAYMPWEGY 665

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N ED++LISER+V ED+FTS HI ++E+    T  G E IT  IP++  + L+N+D+ GI
Sbjct: 666  NSEDAVLISERLVYEDIFTSFHIRKYEIQTHMTSYGSERITNKIPHLEAKLLRNLDKNGI 725

Query: 882  ICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            + +G+ V  GD+LVGK+TP+   ES  +PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726  VILGSWVETGDVLVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPIGGRGRV 785

Query: 940  VDVRIFNRHGIDKNE----RSISVEREQIELLAR--DKDDEQVILDRNIYSRLMEILCG- 992
            +DVR   + G         R   +++ +I++  +   +   + I+ + +  + M  L   
Sbjct: 786  IDVRWIQKKGGSSYNPETIRISILQKREIKVGDKVAGRHGNKGIVSKILSRQDMPYLQDG 845

Query: 993  ------QNAVSGPKGFKKSTVLSSDL-ISEYPRSQWWQFAVQDEKVQRN----------V 1035
                   N +  P       +    L +S     + ++    DE+ ++            
Sbjct: 846  GPVDMVFNPLGVPSRMNVGQIFECSLGLSGGMLDRHYRITPFDERYEQEASRKLVFSELY 905

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
            E+ K          E   K+KI   + G+      + + K ++  K   Q  DK+ GR
Sbjct: 906  EASKQTSNPWIFEPEYPGKSKIFDGRTGNSFKQPAI-MGKTYIL-KLIHQVDDKIHGR 961



 Score =  360 bits (925), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 128/396 (32%), Positives = 196/396 (49%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDVLVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     +++ +  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKKG----GSSYNP---ETIRISILQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG +   L +  +    D +  
Sbjct: 833  ILSRQDMPYLQDGGPVDMVFNPLGVPSRMNVGQIFECSLGLSGGMLDRHYRITPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYEASKQTSNPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG  F +P  +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -------YPGKSKIFDGRTGNSFKQPAIMGKTYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G+S +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKTRQEVLGTTIIGGTIPKPT 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L + ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLAMELNHFLISEKNFRIHRKE 1069



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 113/238 (47%), Gaps = 29/238 (12%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF---- 76
            E+  +P L ++Q   +  F+          + GL         I        +EF    
Sbjct: 7   EEMSTLPGLNQIQFEGFCRFI----------DRGLTEGLFKFPKIEDTDQ--EIEFQLFS 54

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
            +Y+   P  +  D ++  LTY+  L I+  LI          KS +DI++Q+I++G++P
Sbjct: 55  ETYQLLEPLINEKDAVYESLTYSAELYISAGLIW---------KSSRDIQKQTIFVGNIP 105

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LM   GT ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G  +++E 
Sbjct: 106 LMNSLGTSIVNGIYRIVINQILQSPGIYYRSELD---PNGISVYTGTIISDWGGRLELEI 162

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           D K  I  R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 163 DKKARIWARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFVSFLNDKEKKKIGSKE 220


>gi|219116262|ref|XP_002178926.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409693|gb|EEC49624.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 1212

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 161/1005 (16%), Positives = 310/1005 (30%), Gaps = 194/1005 (19%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII--AIIKILVDLRNGKGTIDDIDNL 459
            D  K D     +  +   +      +     K+       +  L+  R G+   DD D+ 
Sbjct: 355  DVTKEDRMRYAQAILQKEVLPHVGTEEHCETKKGFFIGYAVHKLLMCRLGRAEEDDRDHF 414

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ + +++ +     +         I +  +   +    
Sbjct: 415  GKKRLDLAGPLLGGLFRVLFRKLTKDVRKHLQRCLDEGKHFNIGAAIKSNHITDGLKYSL 474

Query: 518  CSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
             +             +SQ+   +   S ++H RR +      +AR     + R +H TH+
Sbjct: 475  ATGNWGDKGMATKAGVSQVLNRLTYASSLSHLRRCNT----PLARTGKQAKPRQLHNTHW 530

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG  +GLV +L   A +            + +    N    L +       
Sbjct: 531  GMVCPAETPEGQAVGLVKNLALMAYITTGTAQVPVLEFLEEFSTENLTDILPS------V 584

Query: 627  IAQANSS-LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA+ N+  +  +G++       +   E     R  +   D   +  +    +        
Sbjct: 585  IAEPNTCKIFVNGNWVGIHRDPKALEETFRSLRRMV---DIDAEVSIVRDIADKEVRIYT 641

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+ R+     + ++    +K        GM+    K +   ++ +        +     +
Sbjct: 642  DAGRICRPLFVVQEQKLAIKKHHIMQLQGMDPNEKKLTWTDLLMEGLVEYIDTEEEETTM 701

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             ++E +   S                                          PS  LG  
Sbjct: 702  VAMEPNDLDSDDSYSSTYT----------------------------HCEIHPSMILG-- 731

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I+   ++V                
Sbjct: 732  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYASNYQVRM-------------- 770

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  V             +       +      +  I      +  
Sbjct: 771  -------------DTMAHVLHYPQKPLCTTRAMEFLHFRELPSGVNCIVGILVYTGYNQE 817

Query: 926  DTSLRVPSGVSGTVVDVRIFNRH-GIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
            D+ +   S +   +     +  +   +K     ++     EL  +   D    +    Y 
Sbjct: 818  DSLILNQSAIDRGLFRSSYYRCYIDQEKASTVGTIGSLTSELFEKPSMDSTRGMKHGEYG 877

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   +  G           K+  + +                           +  +
Sbjct: 878  KLDDDGLVAPGTRVSGDDVLIGKTAPIDAT------------------------AGMPSR 913

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y         +                   R  KV +   R  Q GDK A RHG KG + 
Sbjct: 914  YSKRDCSTSMKANEHGIVDNVLISTTKEGYRFTKVRIRNVRTPQIGDKFASRHGQKGTIG 973

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DI++NP  +PSRM + Q+ E  LG   V  G +          
Sbjct: 974  MTYRQEDMPFTVEGIVPDIIVNPHAIPSRMTIAQLIECLLGKVVVFQGCEGD-------- 1025

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     E I++
Sbjct: 1026 ---------------------------------------------ATP-FTDVTVEDIST 1039

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L        G   LY G TG P +  V +G  +  +L H+V DKV++R+ G  +++T+Q
Sbjct: 1040 RLHAMGYQRHGNEALYQGHTGRPLNARVFIGPTFYQRLKHLVDDKVHSRARGPVAMLTRQ 1099

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR----------TR 1327
            PL G+S  GG R+GEME  C+  +G A  +++   + SD     +  R            
Sbjct: 1100 PLEGRSRDGGLRMGEMERDCLITHGCANFMRDRFFVNSDQYRIHICERCGLTAQANLKKM 1159

Query: 1328 VYE-----SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             YE      +       +   P +  +L++E+ ++ +   +    
Sbjct: 1160 TYECRSPMCVGRPTQICQVEIPYAAKLLLQELNSMCIQTRIYTKN 1204



 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 126/1009 (12%), Positives = 278/1009 (27%), Gaps = 201/1009 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-------------AMLE 75
           L+  Q  S+D F+  N   +   + G       +  +  +                  + 
Sbjct: 44  LVRQQLDSFDEFIQ-NTMQELVDDSGDIRVSPEIQHMVGYDDEAYDREQEKETKFVFEIH 102

Query: 76  FVSYEFDPPK-------FD---VDDCLWRDLTYAVPLKITLRL---------IVFDVDEF 116
           F       P               +   R++TY+ PL + + L          V D  E 
Sbjct: 103 FGQVYLSKPTTVEKDGTITNMFPHEARLRNMTYSAPLYVDVDLNQYQVGREVNVNDPSED 162

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
            G     +  ++  ++G +P+M +                         G FVI G +++
Sbjct: 163 LGEPVATEHAKKE-FLGYVPIMLRSLFCVLSDKDDADLSDLGECVYDQGGYFVINGSEKV 221

Query: 153 VVSQLHRSPG-IH-FD-----------HDKGRASLSGKLLYACRIIPD----QGLWMDIE 195
           +++Q   S   ++ F              + +   S + +    I       +G  ++  
Sbjct: 222 IIAQERLSNNHVYAFKKKQPSKFSWVIETRSQVENSTRPVSTLYIQMYHKGGRGA-IEGN 280

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
                + ++R D    +PV     ALG  ++ +I+      +   +  D +   L  A +
Sbjct: 281 QIRSTLPYIRTD----IPVVIIFRALGYVADRDIIEHVVYDLTDGEMMDLFRPSLEEAFV 336

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLL----KSLKEKGVKFLGITSDCLCGLYVAE 310
           +    V+   +      + +    ++         + L   G +    T       Y   
Sbjct: 337 IQRQDVALDFIGRRGSARDVTKEDRMRYAQAILQKEVLPHVGTEEHCETKKGFFIGYAVH 396

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            ++    G    +  D   +K L+           +L+         +   +     +  
Sbjct: 397 KLLMCRLGRAEEDDRDHFGKKRLDLAGPLLGGLFRVLFRK-------LTKDVRKHLQRCL 449

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
            +            +  T  +  S+    + D      + V +V   +          R 
Sbjct: 450 DEGKHFNIGAAIKSNHITDGLKYSLATGNWGDKGMATKAGVSQVLNRLTYASSLSHLRRC 509

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                          L N    +         +   + + L     +     +  + E +
Sbjct: 510 NTPLARTGKQAKPRQLHNTHWGMVCPAETPEGQAVGLVKNLALMAYITTGTAQVPVLEFL 569

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGV 549
                +++    L +     +    F   + +    +           RR+  +  +  +
Sbjct: 570 EEFSTENLT-DILPSVIAEPNTCKIFVNGNWVGIHRDPKALEETFRSLRRMVDIDAEVSI 628

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R  A  E+R ++        P    +   + +        +               D  
Sbjct: 629 VRDIADKEVR-IYTDAGRICRPLFVVQEQKLAIKKHHIMQLQ---GMDPNEKKLTWTDLL 684

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           +   V Y+   EEE   +A                       +            +  P 
Sbjct: 685 MEGLVEYIDTEEEETTMVAM-----------------EPNDLDSDDSYSSTYTHCEIHPS 727

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +  +                       
Sbjct: 728 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYASNYQV------------------- 768

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + V  Y               Q+PL        
Sbjct: 769 ----------------------RMDTMAHVLHYP--------------QKPLC------- 785

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G N +V  + + GYN EDS+++++  +   +F S +   +  
Sbjct: 786 ---TTRAMEFLHFRELPSGVNCIVGILVYTGYNQEDSLILNQSAIDRGLFRSSYYRCYID 842

Query: 850 MARDTKLGP----------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             + + +G           +        +       +D+ G++  G  V+  D+L+GK  
Sbjct: 843 QEKASTVGTIGSLTSELFEKPSMDSTRGMKHGEYGKLDDDGLVAPGTRVSGDDVLIGKTA 902

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           P   +   P                RD S  + +   G V +V I    
Sbjct: 903 PIDATAGMP-----------SRYSKRDCSTSMKANEHGIVDNVLISTTK 940


>gi|229544486|gb|ACQ76423.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 222

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 122/225 (54%), Positives = 153/225 (68%), Gaps = 13/225 (5%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGWA  G+G++I  ++   +     S LR FLEKV      TE ++   D+ + 
Sbjct: 1    QVLEVHLGWAGKGIGQRIGDML---QQQVRTSELRKFLEKVYNARGRTEDLAQLSDEELR 57

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------QSILYDGLTGEP 1244
             +A     G+P +TPVFDGA EE I  ML++A  D      G      Q+ LYDG TGE 
Sbjct: 58   VMATHLTQGMPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRTQAFLYDGRTGER 117

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F+RP T+GY++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++A
Sbjct: 118  FERPTTIGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 177

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            YGA+YVLQEMLT+KSDDV GRT+VYESIV G    E G PESFNV
Sbjct: 178  YGASYVLQEMLTVKSDDVAGRTKVYESIVKGEHAIEAGMPESFNV 222


>gi|52694293|emb|CAG37986.1| RNA polymerase beta subunit [Pseudomonas marginalis pv. pastinacae]
          Length = 388

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/388 (59%), Positives = 299/388 (77%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +
Sbjct: 121 YRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+
Sbjct: 301 VRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTT 360

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVS 869
           IHI+E   +ARDTKLGPEEI    P   
Sbjct: 361 IHIQELTCVARDTKLGPEEIYCRHPERG 388


>gi|52694301|emb|CAG37990.1| RNA polymerase beta subunit [Pseudomonas marginalis pv. alfalfae]
          Length = 384

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 231/384 (60%), Positives = 299/384 (77%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPGAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT I
Sbjct: 301 RKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTPI 360

Query: 843 HIEEFEVMARDTKLGPEEITRDIP 866
           HI+E   +ARDTKLGPEEIT DIP
Sbjct: 361 HIQELTCVARDTKLGPEEITADIP 384


>gi|156598653|gb|ABU85582.1| RNA polymerase beta subunit [Scaevola aemula]
          Length = 1071

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 129/396 (32%), Positives = 198/396 (50%), Gaps = 48/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T  +    S     + +   +           LK+  
Sbjct: 720  LDKNGIVVLGSWVETGDVLVGKLTPQTEKESSYPLEDKLFYDVLGIPVYTLKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      IQ           +++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRW------IQKKKKDDSDSSYMIRVYILQKREIKVGDKVAGRHGNKGIISK 833

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG P+D+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 834  ILPRQDMPYLQDGRPLDMVFNPLGVPSRMNVGQIFESSLGLAGGFLDRHYRIAPFDERYE 893

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 894  QEASRKLVFSELYQASKQTANPW------------------------VFE---------- 919

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S + DG TG+PF++PV +G  Y+LKL H V DK++ RS G Y+ VTQQP
Sbjct: 920  -----PEYPGKSRILDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSRGPYASVTQQP 974

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            + G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  +  + + G       
Sbjct: 975  VRGRAKKGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQELIGTRIIGGRIPNPE 1034

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L L ++  L + +T    + E
Sbjct: 1035 DAPESFRLLVRELRSLALELNHFLVSEKTFQINRKE 1070



 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 225/662 (33%), Positives = 363/662 (54%), Gaps = 19/662 (2%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            ++           L  +    +    IL  V        + N         +++A+L+ 
Sbjct: 167 RVWARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSLLNDKEKKNIGSKENAILEF 226

Query: 378 YRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           Y+     G+   FS +        F   + +L  +GR  MN RLNLD P +   +   DI
Sbjct: 227 YQQFACVGEDPVFSESLCKELQQKFFQQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDI 286

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           +A    L+ ++ G GT+DD ++L N+R+RSV ++L++Q  L L+R+E  ++  I      
Sbjct: 287 LAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLLQDQLGLALVRLEDVVRGTICRALRQ 346

Query: 497 SVM--PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            +   P++L+ + P+ +    FF    LSQ+ +  N L++I H R+ S LG GG+    A
Sbjct: 347 KLRRPPRNLLTSTPLTTTYESFFRLHPLSQVLDQTNPLTQIVHGRKFSYLGPGGLTARTA 406

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+  + +    + +
Sbjct: 407 SFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYAISERSKGSRM 466

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +YLS   +E   +A  NS     G   E++V  R   E + V  E++        Q  SI
Sbjct: 467 LYLSPDRDEYYMLAGGNSLALNQGIQDEQVVPARYRQEFLTVAWEQVHLRSLFSFQYFSI 526

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A++ G 
Sbjct: 527 GASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEQEGK 586

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           +             +  L           L+ +QRSN+ TC++Q+P V  G  +++   +
Sbjct: 587 IIYT--------KTDKILLSGNGHTLSIPLVMYQRSNKKTCMHQKPQVGRGKCIKKGQFL 638

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+  R T
Sbjct: 639 AYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHICKYEIQTRMT 698

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKL 912
             GPE +T +IP++    L+N+D+ GI+ +G+ V  GD+LVGK+TP+ E   +   E+KL
Sbjct: 699 SQGPERVTNEIPHLEGYLLRNLDKNGIVVLGSWVETGDVLVGKLTPQTEKESSYPLEDKL 758

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-----RSISVEREQIELL 967
              + G     +++T L++P G  G V+DVR   +   D ++     R   +++ +I++ 
Sbjct: 759 FYDVLGIPVYTLKETCLKLPIGGRGRVIDVRWIQKKKKDDSDSSYMIRVYILQKREIKVG 818

Query: 968 AR 969
            +
Sbjct: 819 DK 820



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 112/231 (48%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA--AMLEFVSYEFDP 83
           IP   ++Q   +  F+          ++GL+        I          L   +Y+   
Sbjct: 12  IPAFNQIQFEGFSRFI----------DQGLKEELSKFPKIEDRDQKIFFHLFRETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P       ++  LTY+  L I+ RLI          KSI++ +EQ I++G++PLM+  GT
Sbjct: 62  PLITERAAVYASLTYSSRLYISARLIW---------KSIRNKREQRIFIGNIPLMSSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F++ G+ RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  + 
Sbjct: 113 FIVNGLYRIVINQILQSPGIYYRSELDHKGIS---VYTATIISDWGGRLELEIDRKARVW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLLSAMGLNLREILENVCYPEIFLSLLNDKEKKNIGSKE 220


>gi|227438073|gb|ACP30536.1| RNA polymerase beta subunit [Mycoplasma iners]
          Length = 664

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/490 (47%), Positives = 344/490 (70%), Gaps = 8/490 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ SVGE+++NQ  + L ++E++ +ER+ + + D V P+++ N K V + +  FF S
Sbjct: 2   TNKRIVSVGELMQNQLNVVLTKLEKTTRERMGAKEPDKVNPKNVTNNKLVSTQMKTFFNS 61

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 62  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 121

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN YGF++TPY KV +G V    V YL+A EE   YIAQ+   +DE+ 
Sbjct: 122 IGLILNFATYAKVNEYGFLQTPYYKVENGVVNYEKVEYLTATEEIGFYIAQSTVKVDENN 181

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              ++ V  R     +L    +ID+I+ +  Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 182 RIIDKQVTMRHNYTYVLGEPTQIDYIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQR 241

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ EAPFV TG+ES +AK S A  VAK  G+VE VD  +I IR+  G  D     
Sbjct: 242 QAVPLLQTEAPFVATGLESAIAKYSSANFVAKNDGVVEYVDGSKIKIRNNNGKSDS---- 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y L  FQRSNQ+T V+QRPLVK+G EV++ D++ DG S   G+L+LG+N++VAF  +
Sbjct: 298 ---YSLRNFQRSNQDTVVHQRPLVKIGQEVKKGDLLVDGSSFKNGELSLGKNLVVAFTTY 354

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++ER+V EDV TSIHIEE  +  R +++G +E+T +IPNVS+  ++++DE
Sbjct: 355 KGYNYEDAIILNERLVKEDVLTSIHIEEHTIQFRTSRMGDDELTAEIPNVSKYSIRHLDE 414

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            G++ VG+EV PGD+LVG+++PKG+   + EEKLL +I G++  +V+DTSL+V +G  GT
Sbjct: 415 NGVVRVGSEVMPGDVLVGRVSPKGDDNPSQEEKLLSSILGQRLTNVKDTSLKVKNGHGGT 474

Query: 939 VVDVRIFNRH 948
           V+ V + +R 
Sbjct: 475 VIGVEVLSRD 484



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 147/524 (28%), Positives = 213/524 (40%), Gaps = 76/524 (14%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E ++   +   + 
Sbjct: 212  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQTEAPFVATGLESAIA--KYSSAN 269

Query: 837  DVFTSIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
             V  +  + E+   ++       G  +               + +  ++ +G EV  GD+
Sbjct: 270  FVAKNDGVVEYVDGSKIKIRNNNGKSDSYSLRNFQRSNQDTVVHQRPLVKIGQEVKKGDL 329

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LV   + K    ++  + L+ A    K  +  D  +     V   V+       H I   
Sbjct: 330  LVDGSSFKN-GELSLGKNLVVAFTTYKGYNYEDAIILNERLVKEDVLTSIHIEEHTIQF- 387

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD-- 1011
              S   + E    +          LD N   R+   +   + + G    K     S +  
Sbjct: 388  RTSRMGDDELTAEIPNVSKYSIRHLDENGVVRVGSEVMPGDVLVGRVSPKGDDNPSQEEK 447

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S     +         KV+       +  E        +F++ I+KI           
Sbjct: 448  LLSSILGQRLTNVKDTSLKVKNGHGGTVIGVEVLSRDSNAQFEDGIDKI----------- 496

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP+L+DGTPVD++LNP GVPSRM
Sbjct: 497  --VKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPYLEDGTPVDVMLNPQGVPSRM 554

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A   L  K  +   D     +I                          
Sbjct: 555  NIGQVLEIHLGMAARSLNCKFVTPTFDGIKKEEI-------------------------- 588

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                               F+   E  +          ESG+  L D +TG+ FD PV+V
Sbjct: 589  -------------------FNLIKEAKL---------PESGKQYLIDPITGKRFDNPVSV 620

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            G +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 621  GVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|83583679|gb|ABC24699.1| RNA polymerase beta subunit [Spiroplasma poulsonii]
          Length = 592

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/442 (51%), Positives = 319/442 (72%), Gaps = 8/442 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A++NA+GFIETPYR+V D KVT +  YL+A +E+N  +AQAN  L + G   +E V  
Sbjct: 61  TYAKINAFGFIETPYRRVIDCKVTAENDYLTADQEKNYVVAQANIRLSDKGEILDEQVVA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121 RFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLISPN 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E        G+  Y L  F
Sbjct: 181 SPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--------GLKNYNLDTF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233 VRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+VS+DVFTSIHIEE+ +  R TK G EEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293 IVSERLVSDDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353 VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948 HGIDKNERSISVEREQIELLAR 969
              + +   + V +  I    +
Sbjct: 413 EKYELSADVLEVIKIYIVQKRK 434



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 122/415 (29%), Positives = 188/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVKQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSDDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGGEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 417  -----LSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  +            
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNEELIEIMEKAN------- 524

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      ++        + +L DG 
Sbjct: 525  ------------------------------------------MKNFG-----KEVLIDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 538  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 592


>gi|209360649|gb|ACI42995.1| RNA polymerase beta subunit [Mycoplasma fermentans]
          Length = 665

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 251/645 (38%), Positives = 389/645 (60%), Gaps = 18/645 (2%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
             N+R+ +VGE+L++Q  +GL+++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3    TNKRIVAVGELLQSQLNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNS 62

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63   SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
            IGL+ +  ++A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+ 
Sbjct: 123  IGLILNFATYAQVNKYGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENN 182

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               ++ +  R     I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183  KLVDKQLTMRHNYNYIIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQR 242

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVPLL  EAPFV TG+ES +AK S    VAK  G+VE VD  +I +R+ +G LD     
Sbjct: 243  QAVPLLIPEAPFVATGIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD----- 297

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               Y L  FQRSNQ+T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  +
Sbjct: 298  --TYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTY 355

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356  KGYNYEDAVILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDE 415

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GI+ +G+EV PGD+LVG+++PK +   + EEKLL A+  ++ ++V+DTSL+V +G +GT
Sbjct: 416  HGIVRIGSEVVPGDVLVGRVSPKRDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGT 475

Query: 939  VVDVRIFNRHGIDKNERSIS-VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
            V+ V + +R   D  E  I  + +  I +  + K  +++         +  +L  ++   
Sbjct: 476  VIGVDVLSRENGDALEDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPY 535

Query: 998  GPKGFKKSTVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR---- 1052
               G     +L+   +       Q  +  +     +   + +   ++  K          
Sbjct: 536  LEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDVTLE 595

Query: 1053 ----FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   K   I             V V   +K     GDKM  R
Sbjct: 596  AGLPLSGKQWLIDPITGNKLDKPVSVGVMYMLKLNHMVGDKMHSR 640



 Score =  301 bits (770), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 141/529 (26%), Positives = 221/529 (41%), Gaps = 86/529 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L+   P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+  GD
Sbjct: 271  FVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K    +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 330  LLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQF 388

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++++   +   A    DE  I+         ++L G+ +        +  
Sbjct: 389  RTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKRDDNPSQEE 447

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++                  QR +       +             +   + GD +
Sbjct: 448  KLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENGDAL 490

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 491  EDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 550

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG K  +   D     +I  +                  
Sbjct: 551  VPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV------------------ 592

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                          ++G+P+                        SG+  L D +TG   D
Sbjct: 593  ------------TLEAGLPL------------------------SGKQWLIDPITGNKLD 616

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 617  KPVSVGVMYMLKLNHMVGDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|209360655|gb|ACI42998.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 664

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 241/517 (46%), Positives = 354/517 (68%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ KERIS+ DI+ + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQFRVGLIKLEKNTKERISTKDIEKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA+++ YGFI++PY  V +  V  ++  YL+A+EE     AQ+   + +D  
Sbjct: 123 GLILNLASFAKIDRYGFIQSPYFPVKNRIVDFSEPKYLTAIEEAGYTFAQSTVKI-KDNY 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ V  R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDKVIVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  E+P V TG+E+ VAK S   I AKR G+V+ VDA  I +           + +
Sbjct: 242 AVPVLFPESPLVATGVEADVAKFSSTNISAKRDGVVKYVDASVIKVMPT------GLNKL 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D+Y L  F+RSNQ T ++Q PLVKVGDE++  D++ DGPS   G+LALG+N+LV F  WH
Sbjct: 296 DVYHLRTFERSNQGTLIHQIPLVKVGDEIKEGDLLVDGPSMKDGELALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE 
Sbjct: 356 GYNYEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDEN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVKVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V + I +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAIDILSRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  304 bits (778), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 317  LVKVGDEIKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 435  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 483

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 484  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +    +       
Sbjct: 544  VLNPQGVPSRMNIGQILELHLGSAAKNLNTKFVTPIFDGITHNQIRDILEEAKMDTTGK- 602

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 603  ---------------------------TVVYD--------------------------GQ 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|209360633|gb|ACI42987.1| RNA polymerase beta subunit [Mycoplasma fermentans]
 gi|209360639|gb|ACI42990.1| RNA polymerase beta subunit [Mycoplasma fermentans]
          Length = 665

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/517 (45%), Positives = 356/517 (68%), Gaps = 10/517 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ +VGE+L++Q  +GL+++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3   TNKRIVAVGELLQSQLNVGLVKLEKTTRERMGAKEPDKVTPKNVTNNKLISTQMKTFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+ 
Sbjct: 123 IGLILNFATYAQVNKYGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              ++ +  R     I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183 KLVDKQLTMRHNYNYIIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL  EAPFV TG+ES +AK S    VAK  G+VE VD  +I +R+ +G LD     
Sbjct: 243 QAVPLLIPEAPFVATGIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD----- 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y L  FQRSNQ+T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  +
Sbjct: 298 --TYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTY 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356 KGYNYEDAVILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDE 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EV PGD+LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GT
Sbjct: 416 HGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGT 475

Query: 939 VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
           V+ V + +R     +     +E+     +A  +  + 
Sbjct: 476 VIGVDVLSRENG--DALEDGIEKIVKVSIAIKRKIKV 510



 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 142/529 (26%), Positives = 222/529 (41%), Gaps = 86/529 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L+   P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+  GD
Sbjct: 271  FVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K    +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 330  LLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQF 388

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++++   +   A    DE  I+         ++L G+ +  G     +  
Sbjct: 389  RTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEE 447

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++                  QR +       +             +   + GD +
Sbjct: 448  KLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENGDAL 490

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 491  EDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 550

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG K  +   D     +I  +                  
Sbjct: 551  VPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV------------------ 592

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                          ++G+P+                        SG+  L D +TG   D
Sbjct: 593  ------------TLEAGLPL------------------------SGKQWLIDPITGNKLD 616

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 617  KPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|186885933|gb|ACC93374.1| RNA polymerase beta subunit [Plazia daphnoides]
          Length = 1026

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 582  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 635

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 636  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 694

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 695  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 750

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 751  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 807

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 808  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 867

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 868  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 888

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 889  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 948

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 949  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1008

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1009 LNHFLVSEKTFQINRKE 1025



 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 232/662 (35%), Positives = 366/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 123 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFMNDKEKKKIGSKENAILEF 182

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 183 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 241

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    ++ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 242 ILAAADRVIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 301

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 361

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A  ++RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ +      
Sbjct: 362 ASFQIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGAR 421

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 541

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +           + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 542 KIIYT--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 593

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 653

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 654 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 713

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 714 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 773

Query: 968 AR 969
            +
Sbjct: 774 DK 775



 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 57/184 (30%), Positives = 95/184 (51%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 3   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 55

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 56  FMGKIPLMNSLGAFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 112

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 113 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFMNDKEKKKI 172

Query: 250 SAAD 253
            + +
Sbjct: 173 GSKE 176


>gi|52694393|emb|CAG38036.1| RNA polymerase beta subunit [Pseudomonas reptilovora]
          Length = 384

 Score =  372 bits (955), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/384 (59%), Positives = 299/384 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 PLVNKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITR 863
           T IHI+E   +ARDTKLGPEEI+ 
Sbjct: 361 TRIHIQELTCVARDTKLGPEEISC 384


>gi|195570991|ref|XP_002103487.1| GD18948 [Drosophila simulans]
 gi|194199414|gb|EDX12990.1| GD18948 [Drosophila simulans]
          Length = 1176

 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 160/1000 (16%), Positives = 313/1000 (31%), Gaps = 199/1000 (19%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ GN+
Sbjct: 336  RIKYAKEILQKEMLPHVGVSDFCETKK---AYFLGYMVHRLLLASLGRRELDDRDHYGNK 392

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I    +   +     + 
Sbjct: 393  RLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATG 452

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RR+++     + R     + R +H T +G
Sbjct: 453  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PIGRDGKLAKPRQLHNTLWG 508

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG  +GLV +L   A ++           + +  + N        E     I
Sbjct: 509  MLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENL------EEIAPSAI 562

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A A + +  +G +             +   R ++D        ++    S+I  + + + 
Sbjct: 563  ADA-TKIFVNGCWVGIHRDPEQLMATLRKLRRQMD--------IIVSEVSMIRDIRDREI 613

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS----SGAAIVAKRAGIVEQVDAIRI 743
                    + R  + +         T +E +  +     S   +VA  +G+VE +D +  
Sbjct: 614  RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVA--SGVVEYIDTLEE 671

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +           D      +                              P+  LG
Sbjct: 672  ETVMIAMSPYDLKQDKDYAYCTTY------------------------THCEIHPAMILG 707

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   ++I  F                
Sbjct: 708  -------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF---------------- 742

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                       ++    +  V        +    +       +      + AI      +
Sbjct: 743  -----------HVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYN 791

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S V         +  +   +N+R    E    E   +        +    Y
Sbjct: 792  QEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQE----ENFEKPHRGTCQGMRNAHY 847

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  L  +       ++ +        ++ +   +  
Sbjct: 848  DKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVD 907

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                        +     +  K+ V   R  Q GDK A RHG KG  
Sbjct: 908  QVML--------------------TLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTC 947

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDM F  +G   DI++NP  +PSRM +G + E   G      G+          
Sbjct: 948  GIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGD------- 1000

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP  D  + + I+
Sbjct: 1001 ----------------------------------------------ATPFNDAVNVQKIS 1014

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            + L+       G  ++Y+G TG   +  V +G  Y  +L HMV DK+++R+ G   ++ +
Sbjct: 1015 TFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVR 1074

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RT 1326
            QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +            R 
Sbjct: 1075 QPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRN 1134

Query: 1327 RVYESI-VAGN-DTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +E           +   P +  +L +E+ ++ ++  L 
Sbjct: 1135 NTFECKSCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLM 1174



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 103/751 (13%), Positives = 224/751 (29%), Gaps = 115/751 (15%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+ M++    ++ P   LQA  +             L+F       P  
Sbjct: 40  LVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTH 99

Query: 87  D----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++   R+LTY+ PL + +                 + + Q  ++G +P
Sbjct: 100 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV-----ETQHQKTFIGKIP 154

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G F+I G ++++++Q   +   ++    K  
Sbjct: 155 IMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD- 213

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------------- 211
               GK  +   I       ++        + V +  R     +K               
Sbjct: 214 ----GKYAFKTEIR----SCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIK 265

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +   
Sbjct: 266 QEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGAR 325

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYI 322
                +   K++     + L+++ +  +G++           G  V   ++    G   +
Sbjct: 326 GARPGVTKDKRIKYAK-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-ASLGRREL 383

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +  D    K L+            L+ + +          +        +       +  
Sbjct: 384 DDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLE-------LAI 436

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  S+    + D  K   +  G  ++  RL   +      R          +
Sbjct: 437 KTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKL 496

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +                ++KN   +  + +       +  ++  S+  
Sbjct: 497 AKPRQLHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMEN 553

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            + I    +  A   F     +    +    ++ +   RR   +    V+  R   +   
Sbjct: 554 LEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREI 613

Query: 561 VHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
              T  GRIC P    E  ++ L  +     +   Y               +  V Y+  
Sbjct: 614 RIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNN-----YSWQVLVASGVVEYIDT 668

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EEE   IA +   L +D                           +  P  ++ + AS+I
Sbjct: 669 LEEETVMIAMSPYDLKQDK---------------DYAYCTTYTHCEIHPAMILGVCASII 713

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           PF +++ S R      M +QA+ +       
Sbjct: 714 PFPDHNQSPRNTYQSAMGKQAMGVYITNFHV 744


>gi|167858189|gb|ACA04035.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858191|gb|ACA04036.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858193|gb|ACA04037.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858195|gb|ACA04038.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858197|gb|ACA04039.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858199|gb|ACA04040.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858201|gb|ACA04041.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858203|gb|ACA04042.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858205|gb|ACA04043.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858207|gb|ACA04044.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858209|gb|ACA04045.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858211|gb|ACA04046.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858213|gb|ACA04047.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858215|gb|ACA04048.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858217|gb|ACA04049.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858219|gb|ACA04050.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858221|gb|ACA04051.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858223|gb|ACA04052.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858225|gb|ACA04053.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858227|gb|ACA04054.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858229|gb|ACA04055.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858231|gb|ACA04056.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858233|gb|ACA04057.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858235|gb|ACA04058.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858237|gb|ACA04059.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858239|gb|ACA04060.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858241|gb|ACA04061.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858243|gb|ACA04062.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858245|gb|ACA04063.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858247|gb|ACA04064.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858249|gb|ACA04065.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858251|gb|ACA04066.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858253|gb|ACA04067.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858255|gb|ACA04068.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858257|gb|ACA04069.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858259|gb|ACA04070.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858261|gb|ACA04071.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858263|gb|ACA04072.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858265|gb|ACA04073.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858267|gb|ACA04074.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858269|gb|ACA04075.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858271|gb|ACA04076.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858273|gb|ACA04077.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858275|gb|ACA04078.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858277|gb|ACA04079.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858279|gb|ACA04080.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858281|gb|ACA04081.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858283|gb|ACA04082.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858285|gb|ACA04083.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858287|gb|ACA04084.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858289|gb|ACA04085.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858291|gb|ACA04086.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858293|gb|ACA04087.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858295|gb|ACA04088.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858297|gb|ACA04089.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858299|gb|ACA04090.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858301|gb|ACA04091.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858303|gb|ACA04092.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858305|gb|ACA04093.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858307|gb|ACA04094.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858309|gb|ACA04095.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858311|gb|ACA04096.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858313|gb|ACA04097.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858315|gb|ACA04098.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858317|gb|ACA04099.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858319|gb|ACA04100.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858321|gb|ACA04101.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858323|gb|ACA04102.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858325|gb|ACA04103.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858327|gb|ACA04104.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858329|gb|ACA04105.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858331|gb|ACA04106.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858333|gb|ACA04107.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858335|gb|ACA04108.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858337|gb|ACA04109.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858339|gb|ACA04110.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858341|gb|ACA04111.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858343|gb|ACA04112.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858345|gb|ACA04113.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858347|gb|ACA04114.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858349|gb|ACA04115.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858351|gb|ACA04116.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858353|gb|ACA04117.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858355|gb|ACA04118.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858357|gb|ACA04119.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858359|gb|ACA04120.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858361|gb|ACA04121.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858363|gb|ACA04122.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858365|gb|ACA04123.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858367|gb|ACA04124.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858369|gb|ACA04125.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858371|gb|ACA04126.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858373|gb|ACA04127.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858375|gb|ACA04128.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858377|gb|ACA04129.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858381|gb|ACA04131.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858383|gb|ACA04132.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858385|gb|ACA04133.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858387|gb|ACA04134.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858389|gb|ACA04135.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858391|gb|ACA04136.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858393|gb|ACA04137.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858395|gb|ACA04138.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858397|gb|ACA04139.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858399|gb|ACA04140.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858401|gb|ACA04141.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858403|gb|ACA04142.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858405|gb|ACA04143.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858407|gb|ACA04144.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858409|gb|ACA04145.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858411|gb|ACA04146.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858413|gb|ACA04147.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858415|gb|ACA04148.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858417|gb|ACA04149.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858419|gb|ACA04150.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858421|gb|ACA04151.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858423|gb|ACA04152.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858425|gb|ACA04153.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858427|gb|ACA04154.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858429|gb|ACA04155.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858431|gb|ACA04156.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858433|gb|ACA04157.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858435|gb|ACA04158.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858437|gb|ACA04159.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858439|gb|ACA04160.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858441|gb|ACA04161.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858443|gb|ACA04162.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858445|gb|ACA04163.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858447|gb|ACA04164.1| RNA polymerase beta subunit [Bacillus simplex]
 gi|167858449|gb|ACA04165.1| RNA polymerase beta subunit [Bacillus simplex]
          Length = 290

 Score =  372 bits (954), Expect = e-100,   Method: Composition-based stats.
 Identities = 102/318 (32%), Positives = 168/318 (52%), Gaps = 38/318 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++D+P+LIE+Q ASY  FL          + GL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLDLPNLIEIQTASYQWFL----------DVGLKEMFQDISPIEDFTGNLSLEFIDYSLA 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RL+          K   ++K+Q ++MGD PLMT+ G
Sbjct: 51  EPKYSVEETKERDVTYSAPLRVKVRLV---------NKETGEVKDQDVFMGDFPLMTETG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TFVI G +R++VSQL RSP ++++   G+   +GKL ++  +IP++G W++ E D+KD++
Sbjct: 102 TFVINGAERVIVSQLVRSPSVYYN---GKMDKNGKLGFSATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +VRIDR RK+P+T  + ALG  ++ EI+             +          L+      
Sbjct: 159 YVRIDRTRKLPITVLMRALGFGTDQEIIDLIGDNEYLRNTLEKDNTESVEKALL------ 212

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDI 312
                +  GE   +E+ K L        K           +       + L G  +AE +
Sbjct: 213 EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFGQRIAETL 272

Query: 313 VNGETGEIYIEAGDVIDE 330
           ++ ETGEI +E G ++D 
Sbjct: 273 IDPETGEIIVEKGTMLDR 290



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/188 (22%), Positives = 77/188 (40%), Gaps = 1/188 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  + K     
Sbjct: 73  KVRLVNKETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYNGKMDKNG 132

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            LG ++  +     A      +  ++     D   +  +  +  +         +D + +
Sbjct: 133 KLGFSATVIPNRG-AWLEYETDAKDVVYVRIDRTRKLPITVLMRALGFGTDQEIIDLIGD 191

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           N Y+RNTL  D  +  + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 192 NEYLRNTLEKDNTESVEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 251

Query: 415 KMNMRLNL 422
           K+N +L++
Sbjct: 252 KINKKLHI 259


>gi|83583667|gb|ABC24693.1| RNA polymerase beta subunit [Spiroplasma melliferum]
 gi|83583669|gb|ABC24694.1| RNA polymerase beta subunit [Spiroplasma melliferum]
 gi|83583671|gb|ABC24695.1| RNA polymerase beta subunit [Spiroplasma melliferum KC3]
          Length = 592

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/442 (52%), Positives = 320/442 (72%), Gaps = 8/442 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A++N+YGFIETPYR+V   KVT +  YL+A EE+N  +AQAN  L + G   +E V  
Sbjct: 61  TYAKINSYGFIETPYRRVIGCKVTMENDYLTADEEKNYVVAQANIRLSDKGEILDEQVVA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121 RFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLIAPN 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P+VGTG+E   A+ SG AIV++  GIV+ VDA RIV+++ E        G+  Y L  F
Sbjct: 181 SPYVGTGVEYAAARDSGLAIVSQYDGIVDFVDATRIVLKTKE--------GLKNYNLDTF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T +   PLV+ G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233 VRSNQGTSLTHVPLVRQGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293 IVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353 VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948 HGIDKNERSISVEREQIELLAR 969
              + +   + V +  I    +
Sbjct: 413 EKYELSADVLEVIKIYIVQKRK 434



 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 125/415 (30%), Positives = 190/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVRQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTPVDI
Sbjct: 417  -----LSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPVDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +            
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGMTNEELIEIMD---------- 521

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                    + ++        + +L DG 
Sbjct: 522  ---------------------------------------KAGMKNFG-----KEVLIDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD PV+VG +YMLKL+HMV DK++AR+ GSYSL+TQQPLGGK+  GGQR G
Sbjct: 538  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGSYSLITQQPLGGKAQNGGQRFG 592


>gi|332148558|dbj|BAK20128.1| RNA polymerase subunit beta [Bacillus subtilis]
          Length = 323

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 139/373 (37%), Positives = 190/373 (50%), Gaps = 62/373 (16%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V   D
Sbjct: 7    KDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGA--EVKDGD 64

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           K+   + GD+
Sbjct: 65   LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDE 124

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGTP+DI+LNPL
Sbjct: 125  LPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPL 184

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E H+G A   LG  I S + D     D+                    
Sbjct: 185  GVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAK------ 238

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           TGEPF
Sbjct: 239  ----------------------TVLYDG--------------------------RTGEPF 250

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AY
Sbjct: 251  DNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 310

Query: 1306 GAAYVLQEMLTIK 1318
            GAAY LQE+LT+K
Sbjct: 311  GAAYTLQEILTVK 323



 Score =  121 bits (304), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 82/123 (66%), Positives = 101/123 (82%)

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+D+ GII +GAEV
Sbjct: 1   MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEV 60

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G + DV++FNR 
Sbjct: 61  KDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNRE 120

Query: 949 GID 951
             D
Sbjct: 121 DGD 123


>gi|215254191|gb|ACJ64100.1| RNA polymerase beta subunit [Vibrio chagasii]
          Length = 374

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/374 (62%), Positives = 290/374 (77%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ L E+G+F +EL
Sbjct: 61  SLSAFARCNDYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANTVLTEEGTFADEL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE  L PR+ +D++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP L
Sbjct: 121 ITARQKGESGLHPRDHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           KA+ P VGTG+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L
Sbjct: 181 KADKPLVGTGIERNIAVDSGVTAVAKRGGMIQSVDASRIVVKVNEDELVPGEAGIDIYNL 240

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+ RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFE
Sbjct: 241 TKYTRSNQNTCINQRPTVLPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFE 300

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           DS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E GL  +DE GI+ +
Sbjct: 301 DSILVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITVDIPNVGEPGLSKLDESGIVYI 360

Query: 885 GAEVNPGDILVGKI 898
           GAEV  GDILVGK+
Sbjct: 361 GAEVKGGDILVGKV 374


>gi|115531906|ref|YP_784062.1| RNA polymerase beta subunit [Pelargonium x hortorum]
 gi|122164288|sp|Q06FW9|RPOB_PELHO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|112382060|gb|ABI17253.1| RNA polymerase beta subunit [Pelargonium x hortorum]
          Length = 1079

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 124/304 (40%), Positives = 177/304 (58%), Gaps = 44/304 (14%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V++  KR I+ GDK+AGRHGNKGIVS+ILP +DMP+L+DG P+D+V NPLGVPSRM
Sbjct: 804  ERIRVYILQKRKIKVGDKVAGRHGNKGIVSKILPIQDMPYLQDGRPLDMVFNPLGVPSRM 863

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 864  NVGQIFECSLGLAGGLLDRHYRIAPFDERYEEEASRKLVFSELYEASKQTGNPW------ 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+SI++DG TG+PF++PV V
Sbjct: 918  ------------------VFE---------------PEYPGKSIIFDGRTGDPFEQPVIV 944

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL H V DK++ RSTG YS VTQQP+ G++ RGGQR+GEMEVW +Q  G A++L
Sbjct: 945  GQSYILKLIHQVDDKIHGRSTGPYSRVTQQPVKGRARRGGQRVGEMEVWALQGLGVAHIL 1004

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFET---GTPESFNVLVKEMQALGLSID--LENS 1366
            +E+LT KSD +  R +++ +++ G    +      PESF +LV+E+++L L ++  L + 
Sbjct: 1005 EEILTYKSDHLTTRNQIFGTLLLGGALPKPEPEDRPESFRLLVRELRSLSLELNYFLVSK 1064

Query: 1367 RTKN 1370
              KN
Sbjct: 1065 NKKN 1068



 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 219/684 (32%), Positives = 366/684 (53%), Gaps = 19/684 (2%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
             +    +   +     +  +  E          + S+  +  +   ++  +  ++    
Sbjct: 147 FTVYIATIISDWGGRLKLEIDKKERIWARVSRKQKISILVLSSAMGSNLKEILENACYPE 206

Query: 356 AYIRNTLVTDK-NKDRKDALLDIYRVMRPGDVSTFSVAESMFN---FLFFDSDKYDLSTV 411
            ++   L  +   K++K A+L++Y   +       S+            F S K +L  V
Sbjct: 207 IFLALNLKKECGFKEKKYAILELYAKYKDFTEYKDSLDFDFLCETLRKTFFSHKCELGRV 266

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNLD       +  +DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 267 GRQNINRRLNLDISHKNTFLLPQDILAATNHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 326

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLI--NAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L R+E ++ + I        +P       + P+ +    FF    LS + +  
Sbjct: 327 QDQFGLALNRLEDAVCDTIGRAIAKDKIPTLRHLATSTPLTTTYESFFKLHPLSHVFDET 386

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I H R+ S LG GG+    A   +RD+HP++YGRICP +TSEG  +GL+  L + 
Sbjct: 387 NPLTHIVHGRKWSFLGPGGLTERTARFRVRDIHPSNYGRICPIDTSEGIKVGLIGYLATH 446

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+   G +E+P+ ++ +      ++ LS+ +EE   I   NS     G   E+++  R 
Sbjct: 447 ARIGDCGSLESPFYEMSEKSKRVRMLSLSSRKEEYYMIGTGNSLALNQGIQEEQIIPARY 506

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++ F    P Q  SI  SLIPFLE++D+ R LM  NMQRQAVPL ++E  
Sbjct: 507 RQEFLTIAWEEVHFRSVFPFQYFSIGVSLIPFLEHNDATRALMSSNMQRQAVPLSRSEKC 566

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG E  VA  SG  ++ + AG +      +I++      L           L+ FQR
Sbjct: 567 IVGTGFEGQVALDSGIPLITEHAGKIISTHTDKILLSVNGETLSS--------PLVLFQR 618

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NT ++Q P V  G+  ++  I+ADG +T  G+LALG+N+LV +MPW GYNFED++LI
Sbjct: 619 SNKNTWIHQTPQVSRGNCTKKGQILADGAATVGGELALGKNVLVGYMPWEGYNFEDAVLI 678

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI + E+    T  GPE+IT  IP++    L+N+D+ G++ +G+ V 
Sbjct: 679 SERLVYEDIYTSFHIRKCEIKIFMTMKGPEKITNQIPHIDPHLLRNLDKNGVVILGSWVE 738

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GDILVGK+TP+    ++PE++L+ A+F       R + L++P    G V+DVR  ++  
Sbjct: 739 AGDILVGKLTPEL-VELSPEKRLIEALFDAPIGTTRQSCLKLPIWGRGRVIDVRWIHKGS 797

Query: 950 IDKNE----RSISVEREQIELLAR 969
             ++     R   +++ +I++  +
Sbjct: 798 ASRSNPERIRVYILQKRKIKVGDK 821



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 75/346 (21%), Positives = 137/346 (39%), Gaps = 48/346 (13%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--------- 76
           IP L ++Q   +  FL          ++GL     S FP     G + LE+         
Sbjct: 12  IPALNQIQFEGFCRFL----------DQGLIEEL-SQFP----KGNSFLEYFRDEEIDFQ 56

Query: 77  ---VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
               +Y    P     D  +  LTY+  L ++   +  D          K  ++++I +G
Sbjct: 57  LFSKTYHLVKPLIKERDARYESLTYSSKLYVSAGFLWKD----------KRPQKKTICIG 106

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           +LPLM   GTF++ GI R+V++Q+ +SPGI++  +       G  +Y   II D G  + 
Sbjct: 107 NLPLMNSVGTFIVNGISRVVINQILQSPGIYYGSELDYQ---GFTVYIATIISDWGGRLK 163

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGDFWC----FP 248
           +E D K+ I  R+ R++K+ +     A+G + +EIL    YP+I  +      C      
Sbjct: 164 LEIDKKERIWARVSRKQKISILVLSSAMGSNLKEILENACYPEIFLALNLKKECGFKEKK 223

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---G 305
            +  +L    K  +   D    + + E+ +K        L   G + +    +       
Sbjct: 224 YAILELYAKYKDFTEYKDSLDFDFLCETLRKTFFSHKCELGRVGRQNINRRLNLDISHKN 283

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            ++    +   T  +      +     +  + +  IR +  L  D 
Sbjct: 284 TFLLPQDILAATNHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 329


>gi|52694303|emb|CAG37991.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. I]
          Length = 384

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/384 (59%), Positives = 297/384 (77%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+I
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRDIP 866
           HI+E   +ARDTKLGPEEI    P
Sbjct: 361 HIQELTCVARDTKLGPEEIYCRHP 384


>gi|321257963|ref|XP_003193762.1| DNA-dependent RNA polymerase II RPB140 [Cryptococcus gattii WM276]
 gi|317460232|gb|ADV21975.1| DNA-dependent RNA polymerase II RPB140, putative [Cryptococcus gattii
            WM276]
          Length = 1193

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 157/873 (17%), Positives = 276/873 (31%), Gaps = 150/873 (17%)

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             + +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 448  RAGVSQVLNRYTFASTLSHLRRTNT----PIGRDSKAAKPRQLHNTHWGMVCPAETPEGS 503

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV +L   + ++   +       + +  + +   Y  A      ++      +  D 
Sbjct: 504  ACGLVKNLALMSYISVGSYSAPVMEFLEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDA 563

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                  +     G ++      + D  +   +          P    D   + L      
Sbjct: 564  PTLHNNLLQMRRGGQLKYEVSIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDH 623

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDP 754
               +  L  E               SGA       GIVE VDA       I     DL  
Sbjct: 624  IDRIDQLADEGLL------------SGAWDKLLSEGIVEYVDAAEEETILIAMTPEDLVN 671

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            + +    + L++ + ++     +    +K     ++   +   PS  LG       +  +
Sbjct: 672  ARTAHSKHELVRDRAAHNLESFDPAARIKSTVWSQQYTHMEIHPSMILG-------VCAS 724

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +   +                                
Sbjct: 725  IIPFPDHNQSPRNTYQSAMGKQAMGVCL-----------------------------TNY 755

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +    ++ V             +     S +   +  + AI      +  D+ +   S 
Sbjct: 756  QLRMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSGYNQEDSVIMNQSS 815

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILC 991
            +   +    ++ R   D  +    V+ E IE   R++         + Y++L     +  
Sbjct: 816  IDRGLF-RSLYFRSYTDTEKMKGMVKAETIEKPDRNETLRMKHGTSDRYAKLDVDGLVAP 874

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G N         K+  L  D      R+Q                  K    T     E 
Sbjct: 875  GTNVNGDDILIGKTAPLPEDSEELGQRTQLHT---------------KRDISTPLKSTEQ 919

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++     G          VK+ V   R  Q GDK A RHG KG +      EDMPF
Sbjct: 920  GVVDQVMLSTNG-----EGNMFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPF 974

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   DI++NP  +PSRM +G + E  L       G +  +          +S +   
Sbjct: 975  TAEGLVPDIIINPHAIPSRMTIGHLVECLLSKVSTLTGAEGDATPFTELTVEAVSKVLR- 1033

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
              K   +                                                     
Sbjct: 1034 -AKGYQSRGFEVL---------------------------------------------YH 1047

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G +    G         V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG
Sbjct: 1048 GHT----GR---KLQAQVYFGPTYYQRLKHMVDDKIHARARGPLQILTRQPVEGRSRDGG 1100

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAG- 1335
             R GEME  C+ ++G A  L+E +   SD       D+ G        +   Y S+    
Sbjct: 1101 LRFGEMERDCMISHGIAGFLKERMYDSSDAFRIHVCDICGLMAVANLKKQEFYCSVCRNS 1160

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                +   P +  +L +E+QA+ ++  +     
Sbjct: 1161 TQISQVYIPYAAKLLFQELQAMNIACRMYGETD 1193



 Score =  138 bits (347), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 122/1028 (11%), Positives = 266/1028 (25%), Gaps = 240/1028 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L+  Q  S++ F+   +          Q        +T              +    + F
Sbjct: 67  LVRQQLESFNEFIENTM----------QEIVDDHSRLTLDQFTQYTGVAGDETRRYEISF 116

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR---LIVFDVDEFTGA---- 119
                                  +   R+LTY+ PL + ++   L    VD+   A    
Sbjct: 117 GQIYLARVNHTEMDGRTNMLFPQEARLRNLTYSAPLYVDIKKRTLTASGVDDPVEADWQP 176

Query: 120 -----KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
                  ++  +E+   +G +P+M +                         G F+I G +
Sbjct: 177 AVGDDGEVESAEEEKTSIGKVPVMVRSNFCLLHGLPDDQCHEIGECPYDQGGYFIISGSE 236

Query: 151 RIVVSQLHRSPG-------------IHFDHDKGRASLSGKLLYACRIIPD-Q-----GLW 191
           +++++Q   +                +F     +    G++     +    +     G  
Sbjct: 237 KVLIAQERMATNHVFVFLKAAPARFTYFAEINSQKEKGGRVANHTEVRMYARASGTTGGV 296

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           + +      + + ++D    +P+     ALG+  + ++LS            +     + 
Sbjct: 297 IRVS-----LPYTKVD----IPLVVVFRALGIVPDRDVLSHVCFGAEDEALLEMLQPSIE 347

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +  +     +   +                       ++         +  +       
Sbjct: 348 ESFAVQDRDTALDFIGRRG-----------------QHEKAPRAQRQRAAFDILHKEFLP 390

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            +   E  E                                 +  AY    +  ++NK  
Sbjct: 391 HVSTAEGFE---------------------------------SKKAYFLGYMCVEQNK-- 415

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
           + AL    R     +  T  +  ++    +    K D +  G  ++  R    +      
Sbjct: 416 EFALNMAIRP----NTVTDGLKYALATGNWG---KRDNTRAGVSQVLNRYTFASTLSHLR 468

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R        +       L N    +             + + L     + +      + E
Sbjct: 469 RTNTPIGRDSKAAKPRQLHNTHWGMVCPAETPEGSACGLVKNLALMSYISVGSYSAPVME 528

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
                 ++    +DL   +   +A   F     +    +     + +   RR   L    
Sbjct: 529 F-----LEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQMRRGGQLKYEV 583

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                       ++        P    +     L        R++               
Sbjct: 584 SIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQLADEGLLSGAWDKL 643

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRCAGEEILVPR-------- 658
                V Y+ A EEE   IA     L          ELV  R A                
Sbjct: 644 LSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHELVRDRAAHNLESFDPAARIKSTV 703

Query: 659 --EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             ++   ++  P  ++ + AS+IPF +++ S R      M +QA+ +             
Sbjct: 704 WSQQYTHMEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVCLTNYQL------ 757

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                 +   ++      +    ++  +  S       +   +  Y              
Sbjct: 758 ---RMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSG-----------Y 803

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ            + +I +  S D G         + F  +        M+ +E +   
Sbjct: 804 NQ-----------EDSVIMNQSSIDRGLFRS-----LYFRSYTDTEKMKGMVKAETIEKP 847

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D   ++            K G             +    +D  G++  G  VN  DIL+G
Sbjct: 848 DRNETL----------RMKHGT-----------SDRYAKLDVDGLVAPGTNVNGDDILIG 886

Query: 897 KITPKGESPMTPEEKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRH 948
           K  P  E      ++        +          V D  +   +G     V +R+   R 
Sbjct: 887 KTAPLPEDSEELGQRTQLHTKRDISTPLKSTEQGVVDQVMLSTNGEGNMFVKIRVRSTRV 946

Query: 949 GIDKNERS 956
               ++ +
Sbjct: 947 PQIGDKFA 954


>gi|297614612|gb|ADI48608.1| DNA-directed RNA polymerase beta chain [Shewanella algae]
          Length = 380

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/380 (61%), Positives = 293/380 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SAL
Sbjct: 1   AVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N+YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNSYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D  VT++V YLSA+EE    IAQAN  LD +G   EE V CR  GE   +    I ++
Sbjct: 121 VIDSVVTDEVEYLSAIEEGRYVIAQANIELDNEGRIVEEQVACRHKGESTFMRASDIQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  SG
Sbjct: 181 DVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   V
Sbjct: 241 VVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSV 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ V R D++ADGPSTDLGDLALG+NM VAFMPW+GYNFEDS+LISER+  ED FT+IHI
Sbjct: 301 GEPVVRGDVLADGPSTDLGDLALGQNMRVAFMPWNGYNFEDSILISERVAQEDRFTTIHI 360

Query: 845 EEFEVMARDTKLGPEEITRD 864
           +E   +ARDTKLG EEIT D
Sbjct: 361 QELSCIARDTKLGSEEITAD 380


>gi|197311434|gb|ACH61923.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 664

 Score =  371 bits (953), Expect = e-100,   Method: Composition-based stats.
 Identities = 244/517 (47%), Positives = 353/517 (68%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ KERIS+ DI+ + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQFRVGLIKLEKNTKERISTKDIEKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA+++ YGFI++PY  V D  V  ++  YL+A+EE     AQ+   + ++  
Sbjct: 123 GLILNLASFAKIDKYGFIQSPYFPVKDRVVDFSEPKYLTAIEEAGYTFAQSTVKI-KNNY 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ V  R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDKVIVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  E+P V TG+E+ VAK S   I AKR GIV+ VDA  I I           S +
Sbjct: 242 AVPVLFPESPLVATGVEADVAKFSSTNISAKRGGIVKYVDASVIKILPT------GLSKL 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVKVGDE++  D++ DGPS   G+LALG+N+LV F  WH
Sbjct: 296 DSYHLRTFERSNQGTLIHQIPLVKVGDEIKEGDLLVDGPSMKDGELALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE 
Sbjct: 356 GYNYEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDEN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVKVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V + I +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAIDILSRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  304 bits (778), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 128/415 (30%), Positives = 182/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 317  LVKVGDEIKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 435  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 483

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 484  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +    +  I    
Sbjct: 544  VLNPQGVPSRMNIGQILELHLGSAAKKLNTKFVTPIFDGITHNQIREILHEADMDITGK- 602

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 603  ---------------------------TVVYD--------------------------GK 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|83755175|gb|ABC46436.1| RNA polymerase beta subunit [Spiroplasma monobiae]
 gi|83755177|gb|ABC46437.1| RNA polymerase beta subunit [Spiroplasma monobiae]
          Length = 594

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/476 (49%), Positives = 333/476 (69%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV + KV + +  YL+A +E++  +AQAN +L EDG+  +E V 
Sbjct: 61   TYAKINEYGFIETPYRKVKNTKVISGEYEYLTADKEKDYVVAQANINLAEDGTILDEQVV 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+V  E +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVSPEDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG AIVA   GIV+ VD+ R+ I   +        G+  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAIVATADGIVKYVDSKRVTIEQKD--------GIKTYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FSRSNNGTAITHLPIVKLGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K +DE GI+ +G+
Sbjct: 293  VIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEVSKKYLDEDGIVAIGS 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  RADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468



 Score =  281 bits (720), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 121/419 (28%), Positives = 176/419 (42%), Gaps = 75/419 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLRVPSGVSGT 938
            I+ +G +V   DIL  G    KGE  +     +    + G    D    S R+      T
Sbjct: 247  IVKLGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAVIVSERIVIDDRFT 306

Query: 939  VVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             + +  +        +    + R+   I  +++   DE  I+      ++ +IL G+   
Sbjct: 307  SIHIDEYTIERRQTKQGPEEITRDIPNISEVSKKYLDEDGIVAIGSEVKVGDILVGKVTP 366

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                       L   +  E  R           +V    E +                 K
Sbjct: 367  KSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVKSI-------------K 409

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G D+P  +L ++KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGT
Sbjct: 410  RFSRADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGT 469

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +        
Sbjct: 470  PVDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVKEQELQDIMEEAGMDN 529

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                               DG   EA +                
Sbjct: 530  YGKVTLV----------------------------DGRTGEAFDK--------------- 546

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                       P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  -----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|186885905|gb|ACC93360.1| RNA polymerase beta subunit [Lycoseris crocata]
          Length = 1028

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 237/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWIQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++AR +G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHARCSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G        +PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGNTIIGGIIPTPEDSPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 233/662 (35%), Positives = 363/662 (54%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPGFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H  +LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGIKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+  + +      
Sbjct: 364 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYDISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   IA  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +           + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYT--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWIQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|83583687|gb|ABC24703.1| RNA polymerase beta subunit [Spiroplasma syrphidicola]
          Length = 592

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/442 (52%), Positives = 323/442 (73%), Gaps = 8/442 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A++N++GFIETPYRKV + KVT    YL+A EE+N  +AQAN  L + G   ++ V  
Sbjct: 61  TYAKINSFGFIETPYRKVVNNKVTAQNDYLTADEEKNYVVAQANIRLSDKGEILDDQVIA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE I+ PR+++D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121 RFQGENIIAPRDEVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLISPS 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P+VGTG+E   A+ SG AIV++  G V+ VDA +I++++ E        G+  Y L  F
Sbjct: 181 SPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATKIILKTKE--------GLKTYFLDTF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T +   PLVKVG +V +N I+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233 VRSNQGTSLTHVPLVKVGQKVEKNQILADGPSIEKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293 IVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353 VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948 HGIDKNERSISVEREQIELLAR 969
              +     + V +  I    +
Sbjct: 413 EKYELAADVLEVIKVYIVQKRK 434



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 126/415 (30%), Positives = 189/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V    IL    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVKVGQKVEKNQILADGPS-IEKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP L+DGTPVDI
Sbjct: 417  -----LAADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHLEDGTPVDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  + +          
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVATPVFDGMTNDELIEIMNKAN------- 524

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      ++        + +L DG 
Sbjct: 525  ------------------------------------------MKNFG-----KEVLVDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 538  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 592


>gi|186885955|gb|ACC93385.1| RNA polymerase beta subunit [Stifftia chrysantha]
          Length = 1028

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 150/497 (30%), Positives = 233/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RDSSSKPERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG     L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESSLGLGGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 366/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYSD--------TDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRDSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSSRLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|186885919|gb|ACC93367.1| RNA polymerase beta subunit [Onoseris hastata]
          Length = 1028

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 151/497 (30%), Positives = 234/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQSPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RTSSYKSERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD              FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCXDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ +      
Sbjct: 364 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS  ++E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGKDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLECQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +           + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYT--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T   PE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQSPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI--FNRHGIDKNERSIS--VEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR     R    K+ER     +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRTSSYKSERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D +++ LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYKSLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|83755173|gb|ABC46435.1| RNA polymerase beta subunit [Spiroplasma cantharicola]
          Length = 594

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 231/476 (48%), Positives = 333/476 (69%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV + KV   +  YL+A +E++  +AQAN +L EDG+  ++ V 
Sbjct: 61   TYAKINEYGFIETPYRKVKNTKVMSGEYEYLTADKEKDYVVAQANINLGEDGTILDDQVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+V  + +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVSPKDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG AIVA   GI++ VD+ ++V+   +        G+  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAIVATAPGIIKYVDSKKVVVEQKD--------GIKTYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FSRSNNGTALTHLPIVKIGDKVKARDILADGPSMENGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K +DE GI+ +GA
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGA 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  +    + ++ +++         + +IL  ++      G
Sbjct: 413  RVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468



 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 121/420 (28%), Positives = 177/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI---FGEKAVDVRDTSLRVPSGVSG 937
            I+ +G +V   DIL    +      +   + ++ A     G    D    S R+      
Sbjct: 247  IVKIGDKVKARDILADGPS-MENGELALGQNVVVAFTTWNGYNYEDAVIVSERIVIEDRF 305

Query: 938  TVVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            T + +  +        +    + R+   I   ++   DE  I+      ++ +IL G+  
Sbjct: 306  TSIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGAEVKVGDILVGKVT 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        L   +  E  R           +V    E +                 
Sbjct: 366  PKSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIIKSI------------- 408

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DG
Sbjct: 409  KRFSRVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +       
Sbjct: 469  TPVDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVKEQELQDIMKEAGMD 528

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ+ 
Sbjct: 529  NYGKVTLI-----------------------------------------------DGQT- 540

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GE FD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  ------GEAFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|52694171|emb|CAG30615.1| DNA-directed RNA polymerase beta chain [Pseudomonas coronafaciens]
          Length = 385

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/385 (60%), Positives = 300/385 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  
Sbjct: 121 VVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEEITRDIPNV 868
           I+E   +ARDTKLGPEEIT DIPNV
Sbjct: 361 IQELTCVARDTKLGPEEITADIPNV 385


>gi|215254179|gb|ACJ64094.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 368

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 234/368 (63%), Positives = 287/368 (77%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VG
Sbjct: 121 SGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKITP 900
           ILVGK+TP
Sbjct: 361 ILVGKVTP 368


>gi|328859896|gb|EGG09004.1| hypothetical protein MELLADRAFT_47615 [Melampsora larici-populina
            98AG31]
          Length = 1257

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 173/1101 (15%), Positives = 346/1101 (31%), Gaps = 199/1101 (18%)

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH--SEIRDIPILYVDSVNNNAYIRNT 361
                +     +     ++   G + D+  L+ I +  ++I    +L     ++       
Sbjct: 291  IKTTLPYIRNDIPIVVVFRALGIIPDKDILDHICYDRNDIDMFEMLKPCLEDSFPI---- 346

Query: 362  LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                  ++++ AL  I R       +T    E    +      K  L  +          
Sbjct: 347  ------QEQEVALDFIGRR----GTATGLSREKRLKYAEEILQKEMLPHI---------- 386

Query: 422  LDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                +  +  +      ++  L+     +  +DD D+ G +R+   G +L   +R+   +
Sbjct: 387  -SMSEGQQGKKAYFFGYMVHRLLLAALERRDLDDRDHFGKKRLDLAGPLLAGLFRMLFRK 445

Query: 482  MERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLE 526
            + + +   +               + +  + + +     +               +SQ+ 
Sbjct: 446  LTKDVYRHLQKCVEMQKPFNLNTAVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVL 505

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
                  S ++H RR +      + R     + R +H +H+G +CPAET EG   GLV +L
Sbjct: 506  NRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNL 561

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
               + ++  G    P  +  +      +   SA       +           S  E L  
Sbjct: 562  ALMSYIS-VGSPSAPIVEFLEEWGMESLDEFSADMATGTKVFVNGVWQGVHRSPAELLDT 620

Query: 647  CRCAGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             +       +  E     D   +             P    ++   +L   +++  +   
Sbjct: 621  IKRLRRCGDIEPEVSVVRDVRERELRVFTDGGRVCRPLFIVENQQLLLTKDHVEWLSNGY 680

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +       G   E        + +VAK  GIVE +DA        E  +    +  D+ +
Sbjct: 681  VTGTEDPNGIVPEDEGQPFGWSQLVAK--GIVEYLDAE------EEETVMICMTPEDLEQ 732

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYN 822
              ++Q + Q       P  +    ++ N  +     T      A+   +  + +P+  +N
Sbjct: 733  SREYQETGQVPKEVFDPAAR----LKGNTSMYSHTWTHCEIHPAMILGICASIIPFPDHN 788

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                   S R   +       +  +    R                            + 
Sbjct: 789  Q------SPRNTYQSAMGKQAMGVYLTNFRMRM-----------------------DTMA 819

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 820  NILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-R 878

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
              + R  +D+ +++ +++ E+ E  +R+                  I  G          
Sbjct: 879  SFYYRSYMDQEKKAGALQMEEFEKPSRENTLRLKHGTYEKLDDDGIITPGTRVSGDDIII 938

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+  +  D                +E  QR     K          E+   +++     
Sbjct: 939  GKTAPIPPD---------------SEELGQRMKTHTKRDVSMPLKSTENGIIDQVLITTN 983

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
             D +     + VKV +   R  ++GDK A RHG KG V  +   EDMPF  +G   DI++
Sbjct: 984  QDGL-----KFVKVRIRSTRIPETGDKFASRHGQKGTVGILYRQEDMPFTSEGICPDIII 1038

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +G + E  L       G +  +          IS L          G  +
Sbjct: 1039 NPHAIPSRMTIGHLVECLLSKVSTITGNEGDATPFSEVTVEAISSLLK------DNGYQS 1092

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                                             +G +    G   
Sbjct: 1093 RGLEIM-----------------------------------------YNGHT----GR-- 1105

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                    +G  Y  +L HMV+DK+++R+ G   ++T+QP+ G+S  GG R GEME  C+
Sbjct: 1106 -KLRAQCYLGPTYYQRLKHMVNDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCM 1164

Query: 1303 QAYGAAYVLQEMLTIKSD-------DVVG-----------------RTRVYESIVAGNDT 1338
             ++G A  L+E +   SD       D+ G                 R +           
Sbjct: 1165 ISHGIAGFLKERMFDVSDAYRVHVCDICGMVAIANLKKQSFECRACRNKT--------AI 1216

Query: 1339 FETGTPESFNVLVKEMQALGL 1359
             +   P +  +L +E+Q++ +
Sbjct: 1217 SQVYIPYAAKLLFQELQSMNI 1237



 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 140/1018 (13%), Positives = 279/1018 (27%), Gaps = 180/1018 (17%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG----AAMLEFVSYEFDP 83
           +L+  Q +S+D F+   +         L    +     T  +G       + F       
Sbjct: 58  NLVSQQISSFDGFVNTTMQELVDETGSL--ILEQSMQYTDKAGDLTKRYEISFGQIYLSR 115

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITL----RLIVFDVDEFTGAKS-------I 122
           P              ++   R+LTY+ PL + +    ++   + DE TG           
Sbjct: 116 PTMTESDGTVSPMFPNEARLRNLTYSAPLYVDMSKSNKVATGEFDEVTGEPIYISDDDDN 175

Query: 123 KDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH 158
            D     IY+G +P+M +                         G FVI G ++++++Q  
Sbjct: 176 PDKNSSQIYIGKVPIMLRSEFCILDKLDDRGLYDLNECPFDQGGYFVINGSEKVLIAQE- 234

Query: 159 R--------------SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD----IEFDSKD 200
           R              SP       +       K +   ++    G   +           
Sbjct: 235 RMAANHVYVFAKAAPSPISFLSEIRSAVEKGSKTVSTMQVKMFGGHKAEKAGGGATIKTT 294

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           + ++R D    +P+     ALG+  + +IL             +     L  +  +   +
Sbjct: 295 LPYIRND----IPIVVVFRALGIIPDKDILDHICYDRNDIDMFEMLKPCLEDSFPIQEQE 350

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
           V+   +    G     S +K      + L+++ +  + ++                    
Sbjct: 351 VALDFIGRR-GTATGLSREKRLKYAEEILQKEMLPHISMSEG---QQGKKAYFFGYMVHR 406

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           + + A +  D    +      +    P+L          +   +     K  +       
Sbjct: 407 LLLAALERRDLDDRDHFGKKRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVEMQKPFNL 466

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDI 436
                 +  T  +  S+    + D  K   +  G  ++  R    +      R       
Sbjct: 467 NTAVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNTPIGR 526

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              I     L N    +         +      ++KN   +  + +       +  ++  
Sbjct: 527 DGKIAKPRQLHNSHWGMVCPAETPEGQACG---LVKNLALMSYISVGSPSAPIVEFLEEW 583

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +   D  +A              Q          L  I   RR   +            
Sbjct: 584 GMESLDEFSADMATGTKVFVNGVWQ-GVHRSPAELLDTIKRLRRCGDIEPEVSVVRDVRE 642

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV------ 610
               V         P    E   + L      +         E P   V + +       
Sbjct: 643 RELRVFTDGGRVCRPLFIVENQQLLLTKDHVEWLSNGYVTGTEDPNGIVPEDEGQPFGWS 702

Query: 611 ----TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE-------LVFCRCAGEEILVPRE 659
                  V YL A EEE   I      L++   + E                    +   
Sbjct: 703 QLVAKGIVEYLDAEEEETVMICMTPEDLEQSREYQETGQVPKEVFDPAARLKGNTSMYSH 762

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                +  P  ++ I AS+IPF +++ S R      M +QA+ +                
Sbjct: 763 TWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNFRM--------- 813

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                              + + +  Y       +     +  R
Sbjct: 814 --------------------------------RMDTMANILYYPQKPLATTRSMEYLRFR 841

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                                   +L  G+N +VA + + GYN EDS+++++  +   +F
Sbjct: 842 ------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 877

Query: 840 TSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S +   +    +       E        +   +     + +D+ GII  G  V+  DI+
Sbjct: 878 RSFYYRSYMDQEKKAGALQMEEFEKPSRENTLRLKHGTYEKLDDDGIITPGTRVSGDDII 937

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P         +++       K    RD S+ + S  +G +  V I       K
Sbjct: 938 IGKTAPIPPDSEELGQRM-------KTHTKRDVSMPLKSTENGIIDQVLITTNQDGLK 988


>gi|186885801|gb|ACC93308.1| RNA polymerase beta subunit [Aphyllocladus spartioides]
          Length = 1028

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 153/497 (30%), Positives = 236/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKEICLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 233/662 (35%), Positives = 364/662 (54%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFMNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ +      
Sbjct: 364 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V+YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 VLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +           + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYT--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLR I G +    ++  L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKEICLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 57/184 (30%), Positives = 95/184 (51%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   G F++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGAFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFMNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|227809528|gb|ACP40983.1| RNA polymerase beta subunit [Mycoplasma orale]
          Length = 664

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 238/511 (46%), Positives = 352/511 (68%), Gaps = 9/511 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+++GL+++E++ KERI + +I+ + P+++ N KP+ + +  FF +S
Sbjct: 3   NKRIVTIGELLQNQFKIGLIKLEKNTKERIVTKEIEKITPKNVTNNKPIFNQMKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA+++ YGFI+TPY +V + KV  +  VYL+A+EE N  IAQ+  ++ ++G 
Sbjct: 123 GLILNLASFAKIDKYGFIQTPYFRVKNRKVDFSQPVYLTAIEELNVVIAQSTINV-KNGI 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +++V  R   E I    E +++I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDVVMARKDNEYIQAKAEDVNYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP++KAEAP V TG+E+ +AK S   + +   G V  VDA +I I +            
Sbjct: 242 AVPVIKAEAPLVATGVEADIAKYSSTNLRSNTTGKVTYVDANQIKILAD------GAKKA 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D+Y L  F+RSNQ T ++Q P+VKVGDE++  D++ DGPS   G++ALG+N+LV F  W+
Sbjct: 296 DVYNLRTFERSNQGTLIHQIPIVKVGDEIKEGDLLVDGPSMKDGEMALGKNVLVGFSTWN 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + ++E 
Sbjct: 356 GYNYEDAVILSERLVKDDVYTSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNED 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ +G+EV  GDILVG+ +PKGE   TPEEKL+ AIFG+K+ + +DTSL+V  G +GTV
Sbjct: 416 GIVRIGSEVTAGDILVGRTSPKGEENPTPEEKLMAAIFGQKSSNRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-HGIDKNERSISVEREQIELLAR 969
           VDV I +R  G    E    + +  I    +
Sbjct: 476 VDVEIISREDGGQLEEGVEKIIKVSIAQKRK 506



 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 121/420 (28%), Positives = 186/420 (44%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ VG E+  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 317  IVKVGDEIKEGDLLVDGPS-MKDGEMALGKNVLVGFSTWNGYNYEDAVILSERLVKDDVY 375

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +          E  ++ +   +   ++   +E  I+         +IL G+ +
Sbjct: 376  TSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSEVTAGDILVGRTS 435

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +       L + +  +   ++           +     +K  +  +   +E     
Sbjct: 436  PKGEENPTPEEKLMAAIFGQKSSNR-----------KDTSLKVKHGHNGTVVDVE----- 479

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I   + G  +  GV +++KV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DG
Sbjct: 480  -IISREDGGQLEEGVEKIIKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDG 538

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQ+ E HLG A   LG+K  + + D   +  I  +    +  
Sbjct: 539  TPLDMLLNPQGVPSRMNIGQVLELHLGQAAKNLGEKFVTPVFDGITHNQIKDILEEAKVN 598

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T V+ G                      
Sbjct: 599  PTGK----------------------------TVVYSGLT-------------------- 610

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 611  ------GEPFDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|52694173|emb|CAG30616.1| DNA-directed RNA polymerase beta chain [Pseudomonas fragi]
          Length = 381

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 229/381 (60%), Positives = 298/381 (78%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  
Sbjct: 121 VVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVR 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEEITRD 864
           I+E   +ARDTKLGPEEI+ D
Sbjct: 361 IQELTCVARDTKLGPEEISAD 381


>gi|306411065|gb|ADM86138.1| RNA polymerase beta chain [Onoseris ilicifolia]
          Length = 1017

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 150/497 (30%), Positives = 234/497 (47%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 573  VRQGKCIKKGQ-ILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 626

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I +  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 627  EDIYTSFHIRKYEIQIHMTSQSPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 685

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 686  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 741

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 742  ---RTSSSKSERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 798

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 799  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 858

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S ++DG T
Sbjct: 859  ANPW------------------------VFE---------------PEYPGKSRIFDGRT 879

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW 
Sbjct: 880  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVWA 939

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 940  LEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLALE 999

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1000 LNHFLVSEKTFQINRKE 1016



 Score =  354 bits (909), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 221/580 (38%), Positives = 340/580 (58%), Gaps = 16/580 (2%)

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 195 QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIGIKFGMGTLDDMN 254

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--VDIDSVMPQDLINAKPVVSAVCE 515
           +L N+R+RSV ++L+ Q+ L L+R+E   +  I           PQ L+N+ P+      
Sbjct: 255 HLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALKHKWIPTPQKLVNSTPLTGTYEV 314

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 315 FFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTS 374

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG N+GL+ SL    R+  +G +E+P+ ++ +      ++YLS   +E   +A  NS   
Sbjct: 375 EGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGARMLYLSPGRDEYYMVAAGNSLAL 434

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 435 NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSN 494

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +           + +  L   
Sbjct: 495 MQRQAVPLSQSEKCIVGTGLECQAALDSGALAIAEHEGKIIYT--------NTDKILLSG 546

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L+ +QRSN+NT ++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+
Sbjct: 547 NGDTLSIPLVMYQRSNKNTYMHQKPQVRQGKCIKKGQILAYGAATIGGELALGKNVLVAY 606

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER+V ED++TS HI ++E+    T   PE +T +IP++    L+N
Sbjct: 607 MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHMTSQSPERVTNEIPHLEAHLLRN 666

Query: 876 IDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LLR I G +    ++T L++P 
Sbjct: 667 LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 726

Query: 934 GVSGTVVDVRI--FNRHGIDKNERSIS--VEREQIELLAR 969
           G  G V+DVR     R    K+ER     +++ +I++  +
Sbjct: 727 GGRGRVIDVRWVQKKRTSSSKSERIRVYILQKREIKVGDK 766



 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 60/206 (29%), Positives = 102/206 (49%), Gaps = 13/206 (6%)

Query: 65  ITAFSG--AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           I   +      L    Y+   P     D +++ LTY+  L ++ RLI             
Sbjct: 2   IEDTNQEIDFQLFLERYQLVEPLIKERDAVYKSLTYSSELYVSARLIWK-------TSRR 54

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           ++I+EQ+I+MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y  
Sbjct: 55  RNIQEQTIFMGKIPLMNSMGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTG 111

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQR 241
            II D G  +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S  
Sbjct: 112 TIISDWGGRLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFL 171

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDI 267
            D     + + +  +     + L   
Sbjct: 172 NDKEKKKIGSKENSILEFYRNDLQKK 197


>gi|58266096|ref|XP_570204.1| DNA-dependent RNA polymerase II RPB140 [Cryptococcus neoformans var.
            neoformans JEC21]
 gi|57226437|gb|AAW42897.1| DNA-dependent RNA polymerase II RPB140, putative [Cryptococcus
            neoformans var. neoformans JEC21]
          Length = 1193

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 157/873 (17%), Positives = 276/873 (31%), Gaps = 150/873 (17%)

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             + +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 448  RAGVSQVLNRYTFASTLSHLRRTNT----PIGRDSKAAKPRQLHNTHWGMVCPAETPEGS 503

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV +L   + ++   +       + +  + +   Y  A      ++      +  D 
Sbjct: 504  ACGLVKNLALMSYISVGSYSAPVMEFLEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDA 563

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                  +     G ++      + D  +   +          P    D   + L      
Sbjct: 564  PTLHNNLLQMRRGGQLKYEVSIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDH 623

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDP 754
               +  +  E               SGA       GIVE VDA       I     DL  
Sbjct: 624  IDRIDQMADEGLL------------SGAWDKLLSEGIVEYVDAAEEETILIAMTPEDLVN 671

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            + +    + L++ + ++     +    +K     ++   +   PS  LG       +  +
Sbjct: 672  ARTAHSKHELVRDRAAHNLESFDPAARIKSTVWSQQYTHMEIHPSMILG-------VCAS 724

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +   +                                
Sbjct: 725  IVPFPDHNQSPRNTYQSAMGKQAMGVCL-----------------------------TNY 755

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +    ++ V             +     S +   +  + AI      +  D+ +   S 
Sbjct: 756  QLRMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSGYNQEDSVIMNQSS 815

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILC 991
            +   +    ++ R   D  +    V+ E IE   R++         + Y++L     +  
Sbjct: 816  IDRGLF-RSLYFRSYTDTEKMKGMVKAETIEKPDRNETLRMKHGTGDRYAKLDVDGLVAP 874

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G N         K+  L  D      R+Q                  K    T     E 
Sbjct: 875  GTNVNGDDILIGKTAPLPEDSEELGQRTQLHT---------------KRDISTPLKSTEQ 919

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++     G          VK+ V   R  Q GDK A RHG KG +      EDMPF
Sbjct: 920  GVVDQVMLSTNG-----EGNMFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPF 974

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   DI++NP  +PSRM +G + E  L       G +  +          +S +   
Sbjct: 975  TAEGLVPDIIINPHAIPSRMTIGHLVECLLSKVSTLTGAEGDATPFTELTVEAVSKVLR- 1033

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
              K   +                                                     
Sbjct: 1034 -AKGYQSRGFEVL---------------------------------------------YH 1047

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G +    G         V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG
Sbjct: 1048 GHT----GR---KLQAQVYFGPTYYQRLKHMVDDKIHARARGPLQILTRQPVEGRSRDGG 1100

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAG- 1335
             R GEME  C+ ++G A  L+E +   SD       DV G        +   Y S+    
Sbjct: 1101 LRFGEMERDCMISHGIAGFLKERMYDSSDAFRIHVCDVCGLMAVANLKKQEFYCSVCRNS 1160

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                +   P +  +L +E+QA+ ++  +     
Sbjct: 1161 TQISQVYIPYAAKLLFQELQAMNIACRMYGETD 1193



 Score =  137 bits (346), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 121/1028 (11%), Positives = 265/1028 (25%), Gaps = 240/1028 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L+  Q  S++ F+   +          Q        +T              +    + F
Sbjct: 67  LVRQQLESFNEFIENTM----------QEIVDDHSRLTLDQFTQYTGVAGDETRRYEISF 116

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLI------VFDVDEFTGAK 120
                                  +   R+LTY+ PL + ++        V D  E     
Sbjct: 117 GQIYLARVNHTEMDGRTNMLFPQEARLRNLTYSAPLYVDIKKRTLTASGVDDPVEADWQP 176

Query: 121 SIKD------IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
           ++ D       +E+   +G +P+M +                         G F+I G +
Sbjct: 177 AVGDDGEVEGAEEEKTSIGKVPVMVRSNFCLLHGLPDDQCHEIGECPYDQGGYFIISGSE 236

Query: 151 RIVVSQLHRSPG-------------IHFDHDKGRASLSGKLLYACRIIPD-Q-----GLW 191
           +++++Q   +                +F     +    G++     +    +     G  
Sbjct: 237 KVLIAQERMATNHVFVFLKAAPARFTYFAEINSQKEKGGRVANHTEVRMYARASGTTGGV 296

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           + +      + + ++D    +P+     ALG+  + ++LS            +     + 
Sbjct: 297 IRVS-----LPYTKVD----IPLVVVFRALGIVPDRDVLSHICFGAEDEALLEMLQPSIE 347

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            +  +     +   +                       ++         +  +       
Sbjct: 348 ESFAVQDRDTALDFIGRRG-----------------QHEKAPRAQRQRAAFDILHKEFLP 390

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
            +   E  E                                 +  AY    +  ++NK  
Sbjct: 391 HVSTAEGFE---------------------------------SKKAYFLGYMCVEQNK-- 415

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
           + AL    R     +  T  +  ++    +    K D +  G  ++  R    +      
Sbjct: 416 EFALNMAIRP----NTITDGLKYALATGNWG---KRDNTRAGVSQVLNRYTFASTLSHLR 468

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R        +       L N    +             + + L     + +      + E
Sbjct: 469 RTNTPIGRDSKAAKPRQLHNTHWGMVCPAETPEGSACGLVKNLALMSYISVGSYSAPVME 528

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
                 ++    +DL   +   +A   F     +    +     + +   RR   L    
Sbjct: 529 F-----LEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQMRRGGQLKYEV 583

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                       ++        P    +     L        R++               
Sbjct: 584 SIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQMADEGLLSGAWDKL 643

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRCAGEEILVPR-------- 658
                V Y+ A EEE   IA     L          ELV  R A                
Sbjct: 644 LSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHELVRDRAAHNLESFDPAARIKSTV 703

Query: 659 --EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             ++   ++  P  ++ + AS++PF +++ S R      M +QA+ +             
Sbjct: 704 WSQQYTHMEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGVCLTNYQL------ 757

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                 +   ++      +    ++  +  S       +   +  Y              
Sbjct: 758 ---RMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSG-----------Y 803

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           NQ            + +I +  S D G         + F  +        M+ +E +   
Sbjct: 804 NQ-----------EDSVIMNQSSIDRGLFRS-----LYFRSYTDTEKMKGMVKAETIEKP 847

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D   ++            K G             +    +D  G++  G  VN  DIL+G
Sbjct: 848 DRNETL----------RMKHGT-----------GDRYAKLDVDGLVAPGTNVNGDDILIG 886

Query: 897 KITPKGESPMTPEEKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRH 948
           K  P  E      ++        +          V D  +   +G     V +R+   R 
Sbjct: 887 KTAPLPEDSEELGQRTQLHTKRDISTPLKSTEQGVVDQVMLSTNGEGNMFVKIRVRSTRV 946

Query: 949 GIDKNERS 956
               ++ +
Sbjct: 947 PQIGDKFA 954


>gi|297614614|gb|ADI48609.1| DNA-directed RNA polymerase beta chain [Shewanella chilikensis]
 gi|297614616|gb|ADI48610.1| DNA-directed RNA polymerase beta chain [Shewanella sp. KJW27]
          Length = 379

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 232/376 (61%), Positives = 290/376 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SAL
Sbjct: 1   AVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N+YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNSYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D  VT++V YLSA+EE    IAQAN  LD +G   EE V CR  GE   +    I ++
Sbjct: 121 VIDSVVTDEVEYLSAIEEGRYVIAQANIELDNEGRIVEEQVACRHKGESTFMRASDIQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  SG
Sbjct: 181 DVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   V
Sbjct: 241 VVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSV 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ V R D++ADGPSTDLGDLALG+NM VAFMPW+GYNFEDS+LISER+  ED FT+IHI
Sbjct: 301 GEPVVRGDVLADGPSTDLGDLALGQNMRVAFMPWNGYNFEDSILISERVAQEDRFTTIHI 360

Query: 845 EEFEVMARDTKLGPEE 860
           +E   +ARDTKLG EE
Sbjct: 361 QELSCIARDTKLGSEE 376


>gi|52694163|emb|CAG30611.1| DNA-directed RNA polymerase beta chain [Pseudomonas grimontii]
          Length = 382

 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 228/382 (59%), Positives = 298/382 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F +I
Sbjct: 301 RKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFPTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRD 864
           HI+E   +ARDTKLGPEEI+ D
Sbjct: 361 HIQELTCVARDTKLGPEEISAD 382


>gi|83755169|gb|ABC46433.1| RNA polymerase beta subunit [Spiroplasma cantharicola]
          Length = 594

 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 232/476 (48%), Positives = 333/476 (69%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV + KV   +  YL+A +E++  +AQAN +L EDG+  ++ V 
Sbjct: 61   TYAKINEYGFIETPYRKVKNTKVMSGEYEYLTADKEKDYVVAQANINLGEDGTILDDQVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+V  + +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVSPKDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV+ VD+ ++VI   +        G+  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAVVATAPGIVKYVDSKKVVIEQKD--------GIKTYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FSRSNNGTALTHLPIVKIGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K +DE GI+ +GA
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGA 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  +    + ++ +++         + +IL  ++      G
Sbjct: 413  RVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468



 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 124/419 (29%), Positives = 178/419 (42%), Gaps = 75/419 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLRVPSGVSGT 938
            I+ +G +V   DIL  G    KGE  +     +    + G    D    S R+      T
Sbjct: 247  IVKIGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAVIVSERIVIEDRFT 306

Query: 939  VVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             + +  +        +    + R+   I   ++   DE  I+      ++ +IL G+   
Sbjct: 307  SIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGAEVKVGDILVGKVTP 366

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                       L   +  E  R           +V    E +                 K
Sbjct: 367  KSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIIKSI-------------K 409

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGT
Sbjct: 410  RFSRVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGT 469

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +        
Sbjct: 470  PVDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVKEQELQDIMEEAGMDN 529

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                                                   GQ+  
Sbjct: 530  YGKVTLI-----------------------------------------------DGQT-- 540

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 GE FD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  -----GEAFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|83583673|gb|ABC24696.1| RNA polymerase beta subunit [Spiroplasma phoeniceum]
 gi|83583675|gb|ABC24697.1| RNA polymerase beta subunit [Spiroplasma phoeniceum]
 gi|83583677|gb|ABC24698.1| RNA polymerase beta subunit [Spiroplasma phoeniceum]
          Length = 592

 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 231/442 (52%), Positives = 318/442 (71%), Gaps = 8/442 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A++N YGFIETPYR+V   KVT +  YL+A EE+N  +AQAN  L + G   +E V  
Sbjct: 61  TYAKINLYGFIETPYRRVIGCKVTMENDYLTADEEKNYVVAQANIRLSDKGEILDEQVVA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121 RFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLIAPN 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E V A+ SG AIV++  G V+ VDA RIV+++ E        G+  Y L  F
Sbjct: 181 SPHVGTGVEYVAARDSGLAIVSQYDGTVDFVDATRIVLKTKE--------GLKNYNLDTF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T +   PLV+ G ++ +  ++ADGPS D G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233 VRSNQGTSLTHVPLVRQGQKIEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293 IVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353 VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948 HGIDKNERSISVEREQIELLAR 969
              + +   + V +  I    +
Sbjct: 413 EKYELSADVLEVIKVYIVQKRK 434



 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 123/415 (29%), Positives = 189/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVRQGQKIEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 417  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +            
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGMTNKELIEIMD---------- 521

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                    + ++        + +L DG 
Sbjct: 522  ---------------------------------------KAGMKNFG-----KEVLIDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 538  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 592


>gi|227809526|gb|ACP40982.1| RNA polymerase beta subunit [Mycoplasma orale]
          Length = 664

 Score =  370 bits (949), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 238/511 (46%), Positives = 352/511 (68%), Gaps = 9/511 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+++GL+++E++ KERI + +I+ + P+++ N KP+ + +  FF +S
Sbjct: 3   NKRIVTIGELLQNQFKIGLIKLEKNTKERIVTKEIEKITPKNVTNNKPIFNQMKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA+++ YGFI+TPY +V + KV  +  VYL+A+EE N  IAQ+  ++ ++G 
Sbjct: 123 GLILNLASFAKIDKYGFIQTPYFRVKNRKVDFSQPVYLTAIEELNVVIAQSTINV-KNGI 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +++V  R   E I    E +++I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDVVMARKDNEYIQAKAEDVNYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP++KAEAP V TG+E+ +AK S   + +   G V  VDA +I I +            
Sbjct: 242 AVPVIKAEAPLVATGVEADIAKYSSTNLRSNTTGKVTYVDANQIKILAD------GAKKA 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D+Y L  F+RSNQ T ++Q P+VKVGDE++  D++ DGPS   G++ALG+N+LV F  W+
Sbjct: 296 DVYNLRTFERSNQGTLIHQIPIVKVGDEIKEGDLLVDGPSMKDGEMALGKNVLVGFSTWN 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + ++E 
Sbjct: 356 GYNYEDAVILSERLVKDDVYTSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNED 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ +G+EV  GDILVG+  PKGE   TPEEKL+ AIFG+K+ + +DTSL+V  G +GTV
Sbjct: 416 GIVRIGSEVTAGDILVGRTIPKGEENPTPEEKLMAAIFGQKSSNRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNRHGIDK-NERSISVEREQIELLAR 969
           VDV I +R   D+  E    + +  I    +
Sbjct: 476 VDVEIISREDGDQLEEGVEKIIKVSIAQKRK 506



 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 122/420 (29%), Positives = 186/420 (44%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ VG E+  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 317  IVKVGDEIKEGDLLVDGPS-MKDGEMALGKNVLVGFSTWNGYNYEDAVILSERLVKDDVY 375

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +          E  ++ +   +   ++   +E  I+         +IL G+  
Sbjct: 376  TSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSEVTAGDILVGRTI 435

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +       L + +  +   ++           +     +K  +  +   +E     
Sbjct: 436  PKGEENPTPEEKLMAAIFGQKSSNR-----------KDTSLKVKHGHNGTVVDVE----- 479

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I   + GD +  GV +++KV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DG
Sbjct: 480  -IISREDGDQLEEGVEKIIKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDG 538

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQ+ E HLG A   LG+K  + + D   +  I  +    +  
Sbjct: 539  TPLDMLLNPQGVPSRMNIGQVLELHLGQAAKNLGEKFVTPVFDGITHNQIKDILEEAKVN 598

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T V+ G                      
Sbjct: 599  PSGK----------------------------TVVYSGLT-------------------- 610

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 611  ------GEPFDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|255017837|ref|ZP_05289963.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL F2-515]
          Length = 224

 Score =  369 bits (948), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 95/241 (39%), Positives = 143/241 (59%), Gaps = 23/241 (9%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQ 240
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+           
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRN 222

Query: 241 R 241
            
Sbjct: 223 T 223


>gi|83583685|gb|ABC24702.1| RNA polymerase beta subunit [Spiroplasma chrysopicola]
          Length = 592

 Score =  369 bits (948), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 230/442 (52%), Positives = 323/442 (73%), Gaps = 8/442 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A++N++GFIETPYR+V + KVT    YL+A EE+N  +AQAN  L + G   ++ V  
Sbjct: 61  TYAKINSFGFIETPYRRVVNNKVTAQNDYLTADEEKNYVVAQANIRLSDRGEILDDQVIA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE I+ PR+++D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   
Sbjct: 121 RFQGENIIAPRDEVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLISPS 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P+VGTG+E   A+ SG AIV++  G V+ VDA +I++++ E        G+  Y L  F
Sbjct: 181 SPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATKIILKTKE--------GLKTYFLDTF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQ T +   PLVK+G +V +N I+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 233 VRSNQGTSLTHVPLVKLGQKVEKNQILADGPSIEKGELALGQNVVVAFTTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++ +G E
Sbjct: 293 IVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLVIIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R
Sbjct: 353 VKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPR 412

Query: 948 HGIDKNERSISVEREQIELLAR 969
              +     + V +  I    +
Sbjct: 413 EKYELAADVLEVIKVYIVQKRK 434



 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 125/415 (30%), Positives = 189/415 (45%), Gaps = 68/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G +V    IL    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 246  LVKLGQKVEKNQILADGPS-IEKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 305  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 358

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 359  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP L+DGTPVDI
Sbjct: 417  -----LAADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHLEDGTPVDI 471

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  + +          
Sbjct: 472  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVATPVFDGMTNDELIEIMNKAN------- 524

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      ++        + +L DG 
Sbjct: 525  ------------------------------------------MKNFG-----KEVLVDGR 537

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 538  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 592


>gi|292494335|dbj|BAI94510.1| RNA polymerase beta subunit B [Pseudomonas sp. HT-3]
          Length = 371

 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 227/371 (61%), Positives = 292/371 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 121 KVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 241 ARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R+DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 ARSDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPE 859
            +ARDTKLGPE
Sbjct: 361 CVARDTKLGPE 371


>gi|66351044|emb|CAI13207.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 385

 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 231/385 (60%), Positives = 299/385 (77%), Gaps = 1/385 (0%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V DG+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E
Sbjct: 122 SPYRVVKDGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+ ASLIPFLE+DD+NR LMG   ZRQAVP L+++ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVXASLIPFLEHDDANRALMGSXXZRQAVPTLRSDKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDATRIVVRVRDDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV+ GD V R DI+ADGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED F
Sbjct: 301 PLVRKGDVVARGDIMADGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRF 360

Query: 840 TSIHIEEFEVMARDTKLGPEEITRD 864
           T+IHI+E   ++RDTKLGPEEIT D
Sbjct: 361 TTIHIQELTCVSRDTKLGPEEITAD 385


>gi|294807308|ref|ZP_06766121.1| DNA-directed RNA polymerase, beta subunit [Bacteroides xylanisolvens
            SD CC 1b]
 gi|294445473|gb|EFG14127.1| DNA-directed RNA polymerase, beta subunit [Bacteroides xylanisolvens
            SD CC 1b]
          Length = 192

 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 117/246 (47%), Positives = 145/246 (58%), Gaps = 54/246 (21%)

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIVLNPLGVPSRMN+GQIFE         LG+  K+L                       
Sbjct: 1    DIVLNPLGVPSRMNIGQIFE-------AVLGRAGKTL----------------------- 30

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                    GV  +TP+FDGA  E ++     A L    ++ L D
Sbjct: 31   ------------------------GVKFATPIFDGATMEDLDQWTDKAGLPRYCKTYLCD 66

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TGE FD+  TVG  YMLKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEME
Sbjct: 67   GGTGEQFDQAATVGVTYMLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEME 126

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++ +GAA++LQE+LTIKSDDVVGR++ YE+IV G    + G PES NVL+ E++ LG
Sbjct: 127  VWALEGFGAAHILQEILTIKSDDVVGRSKAYEAIVKGEPMPQPGIPESLNVLLHELRGLG 186

Query: 1359 LSIDLE 1364
            LSI+LE
Sbjct: 187  LSINLE 192


>gi|306411069|gb|ADM86140.1| RNA polymerase beta chain [Urmenetea atacamensis]
          Length = 1028

 Score =  369 bits (948), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 153/498 (30%), Positives = 237/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I V  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHVTSQGPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRSSS 756

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 757  S-------KSERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                     +TP VF+                +  G+S ++DG 
Sbjct: 870  -------------------------ATPWVFE---------------PEYPGKSRIFDGR 889

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +GGQR+GEMEVW
Sbjct: 890  TGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQGGQRVGEMEVW 949

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L
Sbjct: 950  ALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRLLVRELRSLAL 1009

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +T    + E
Sbjct: 1010 ELNHFLVSEKTFQINRKE 1027



 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 233/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ +      
Sbjct: 364 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLECQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  +        + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYI--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI----FNRHGIDKNERSISVEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR      +     +  R   +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRSSSSKSERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|218458997|ref|ZP_03499088.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli Kim 5]
          Length = 309

 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 210/309 (67%), Positives = 266/309 (86%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            GESPMTPEEKLLRAIFGEKA DVRDTS+R+P G  GT+V+VR+FNRHG++K+ER++++ER
Sbjct: 1    GESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTIVEVRVFNRHGVEKDERAMAIER 60

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E+IE LA+D+DDEQ ILDRN+Y RL+++L GQ +++GPKGFKK T LS+ ++SEYPRSQW
Sbjct: 61   EEIERLAKDRDDEQAILDRNVYGRLIDMLRGQVSIAGPKGFKKGTELSNAVVSEYPRSQW 120

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            W FAV+DEKVQ  +E+L+ QY+ SKS LE RF +K+EK+Q GD+MPPGV+++VKVFVA+K
Sbjct: 121  WMFAVEDEKVQSELEALRGQYDESKSRLEQRFMDKVEKVQRGDEMPPGVMKMVKVFVAVK 180

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R IQ GDKMAGRHGNKG+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHL
Sbjct: 181  RKIQPGDKMAGRHGNKGVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHL 240

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            GWAC G+G++I  LI  YKANG+I PLR  +  V+G G   E++ ++DDDSVLR+A+QWK
Sbjct: 241  GWACAGMGRQIGELIEAYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDDSVLRLADQWK 300

Query: 1202 SGVPVSTPV 1210
             GV ++TPV
Sbjct: 301  RGVSIATPV 309


>gi|197131676|gb|ACH47356.1| RNA polymerase beta subunit [Geranium macrorrhizum]
          Length = 984

 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 151/562 (26%), Positives = 238/562 (42%), Gaps = 63/562 (11%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E  + +   +          I         +  G       +          I
Sbjct: 482  CIVGTGLEGQVALDSGVPLITEHAGKVISIHTDKILLSGNGDTLSIPLVMYQRSNKNTCI 541

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   +  G  +  G IL       G   +   + LL A       +  D  L     +S
Sbjct: 542  HQKPQVRQGKCMKKGQILADGAATVG-GELALGKNLLVAYMPWGGYNFEDAIL-----IS 595

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E  I V R+  E + +       +L      +   ++ G    
Sbjct: 596  ERLVYDDIYTSFHIRKYEIKIHVTRQGPERVTKKIPLRAHLLRN--LDKNGVVILGSWVE 653

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T   +  +S   +         D      + + +            R  + 
Sbjct: 654  AGDILVGKLTPQLAQDLSPVDK-------FVDALFGTQLATSRQTCLKLPRGRRGRVIDV 706

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                   +         + ++++ KR I+ GDK+AGRHGNKGI+S+I P +DMP+L+DG 
Sbjct: 707  RWIRSNPERD------RISIYISQKREIKVGDKVAGRHGNKGIISKISPRQDMPYLQDGK 760

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+D+V NPLGVPSRMNVGQIFE  LG A V L +  +    D +   + S    F E   
Sbjct: 761  PIDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDERYEQEASRKLVFSELHE 820

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +                               VF+                +  G+S +
Sbjct: 821  ASKQTGNPW------------------------VFE---------------PEYPGKSRI 841

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            +DG TG+PF++PV VG  Y+LKL H V DK++ R  G Y+ VTQQP+ G++ RGGQR+GE
Sbjct: 842  FDGRTGDPFEQPVIVGQPYILKLIHQVDDKIHGRCDGPYASVTQQPVRGRAKRGGQRVGE 901

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQ 1355
            MEVW ++ +G A++LQEMLT KSD +  R +++ + + G +  +    PESF +LV+E++
Sbjct: 902  MEVWALEGFGVAHILQEMLTYKSDHLRTRDKIFGTTIVGGEMPKAEDAPESFRLLVRELR 961

Query: 1356 ALGLSID--LENSRTKNSAKME 1375
            +L L ++  L +       + E
Sbjct: 962  SLALELNHFLVSENNFQMNRKE 983



 Score =  337 bits (865), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 221/641 (34%), Positives = 363/641 (56%), Gaps = 26/641 (4%)

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSV 391
           E I +    +I + ++D                   +++A+L+ Y+      GD      
Sbjct: 114 EIIENVCYPEIVLAFLDDKEKGKIG----------SKENAILEFYQQFVCVGGDTVFSDS 163

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
                   FF   + +L  +GR  +N RLNLD   +   +   DI+A    L+ ++ G G
Sbjct: 164 LCKELQNKFF-RQRCELGRIGRRNINRRLNLDISQNNTFLLPRDILAATDHLIGIKFGMG 222

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPV 509
            +DD+++L N+R+RSV ++L++Q+ L LLR+E  +K  I       +   P++ + + P 
Sbjct: 223 RLDDMNHLKNKRIRSVADLLQDQFGLALLRLEEVVKGGIRGAIKGELIPTPKNFVTSTPF 282

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +    FF    LSQ+ +  N L++I H R+ S LG GG+    A   +RD+HP++YGRI
Sbjct: 283 KTTYESFFGLHPLSQVLDETNPLTQIVHGRKWSFLGPGGLTGQTASFRIRDIHPSYYGRI 342

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           C  +TSEG N+GL+ SL   AR+  +G +E+ + ++ +      ++YLS+  +E   I  
Sbjct: 343 CTIDTSEGINVGLIGSLAIHARIGHFGSLESTFYEISEKSKGARLLYLSSRRDEYCMIGT 402

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            NS    +G   E++V  R   E + +  +++      P Q  SI ASLIPF+E++D+NR
Sbjct: 403 GNSLALNEGFQEEQVVPARYRQEFLTIAWDQVHLRSIFPFQYFSIGASLIPFIEHNDANR 462

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LM  NMQRQAV L ++E   VGTG+E  VA  SG  ++ + AG V  +          +
Sbjct: 463 ALMSSNMQRQAVALSRSEKCIVGTGLEGQVALDSGVPLITEHAGKVISIH--------TD 514

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
             L           L+ +QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+
Sbjct: 515 KILLSGNGDTLSIPLVMYQRSNKNTCIHQKPQVRQGKCMKKGQILADGAATVGGELALGK 574

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVA+MPW GYNFED++LISER+V +D++TS HI ++E+    T+ GPE +T+ IP + 
Sbjct: 575 NLLVAYMPWGGYNFEDAILISERLVYDDIYTSFHIRKYEIKIHVTRQGPERVTKKIP-LR 633

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
              L+N+D+ G++ +G+ V  GDILVGK+TP+    ++P +K + A+FG +    R T L
Sbjct: 634 AHLLRNLDKNGVVILGSWVEAGDILVGKLTPQLAQDLSPVDKFVDALFGTQLATSRQTCL 693

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISV-EREQIELLAR 969
           ++P G  G V+DVR   R   +++  SI + ++ +I++  +
Sbjct: 694 KLPRGRRGRVIDVRWI-RSNPERDRISIYISQKREIKVGDK 733



 Score =  122 bits (305), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 41/136 (30%), Positives = 74/136 (54%), Gaps = 4/136 (2%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
            K    +++Q+I +G++PLM   G F++ GI R+VV+Q+ +SPGI++  +       G  
Sbjct: 9   KKKGYSMQKQTILIGNIPLMNSLGIFILNGIYRMVVNQILQSPGIYYRSELDHK---GFF 65

Query: 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIV 237
           +Y   II D G  +++E D K  I  R+ R++K+ +     A+G +  EI+    YP+IV
Sbjct: 66  IYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREIIENVCYPEIV 125

Query: 238 YSQRGDFWCFPLSAAD 253
            +   D     + + +
Sbjct: 126 LAFLDDKEKGKIGSKE 141


>gi|167858379|gb|ACA04130.1| RNA polymerase beta subunit [Bacillus simplex]
          Length = 290

 Score =  369 bits (947), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 101/318 (31%), Positives = 168/318 (52%), Gaps = 38/318 (11%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++D+P+LIE+Q ASY  FL          + GL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLDLPNLIEIQTASYQWFL----------DVGLKEMFQDISPIEDFTGNLSLEFIDYSLA 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RL+          K   ++K+Q ++MGD PLMT+ G
Sbjct: 51  EPKYSVEETKERDVTYSAPLRVKVRLV---------NKETGEVKDQDVFMGDFPLMTETG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TFVI G +R++VSQL RSP ++++   G+   +GKL ++  +IP++G W++ E D+KD++
Sbjct: 102 TFVINGAERVIVSQLVRSPSVYYN---GKMDKNGKLGFSATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +VRIDR RK+P+T  + ALG  ++ E++             +          L+      
Sbjct: 159 YVRIDRTRKLPITVLMRALGFGTDQEVIDLIGDNEYLRNTLEKDNTESVEKALL------ 212

Query: 262 SSLVDIDTGE-QVIESGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDI 312
                +  GE   +E+ K L        K           +       + L G  +AE +
Sbjct: 213 EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFGQRIAETL 272

Query: 313 VNGETGEIYIEAGDVIDE 330
           ++ ETGEI +E G ++D 
Sbjct: 273 IDPETGEIIVEKGTMLDR 290



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/188 (22%), Positives = 77/188 (40%), Gaps = 1/188 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  + K     
Sbjct: 73  KVRLVNKETGEVKDQDVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYYNGKMDKNG 132

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            LG ++  +     A      +  ++     D   +  +  +  +         +D + +
Sbjct: 133 KLGFSATVIPNRG-AWLEYETDAKDVVYVRIDRTRKLPITVLMRALGFGTDQEVIDLIGD 191

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           N Y+RNTL  D  +  + ALL+IY  +RPG+  T   A+S+    FFD  +YDL+ VGR 
Sbjct: 192 NEYLRNTLEKDNTESVEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVGRY 251

Query: 415 KMNMRLNL 422
           K+N +L++
Sbjct: 252 KINKKLHI 259


>gi|83755171|gb|ABC46434.1| RNA polymerase beta subunit [Spiroplasma cantharicola]
          Length = 594

 Score =  369 bits (946), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 231/476 (48%), Positives = 334/476 (70%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV + KV + +  YL+A +E++  +AQAN +L EDG+  ++ V 
Sbjct: 61   TYAKINEYGFIETPYRKVKNTKVISGEYEYLTADKEKDYVVAQANINLGEDGTILDDQVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+V  + +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVSPKDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV+ VD+ ++V+   +        G+  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAVVATAPGIVKYVDSKKVVVEQKD--------GIKTYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FSRSNNGTALTHLPIVKIGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K +DE GI+ +GA
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGA 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  +    + ++ +++         + +IL  ++      G
Sbjct: 413  RVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468



 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 124/419 (29%), Positives = 178/419 (42%), Gaps = 75/419 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLRVPSGVSGT 938
            I+ +G +V   DIL  G    KGE  +     +    + G    D    S R+      T
Sbjct: 247  IVKIGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAVIVSERIVIEDRFT 306

Query: 939  VVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             + +  +        +    + R+   I   ++   DE  I+      ++ +IL G+   
Sbjct: 307  SIHIDEYTIERRQTKQGPEEITRDIPNISEASKKYLDEDGIVAIGAEVKVGDILVGKVTP 366

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                       L   +  E  R           +V    E +                 K
Sbjct: 367  KSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIIKSI-------------K 409

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGT
Sbjct: 410  RFSRVDGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGT 469

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +        
Sbjct: 470  PVDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVKEQELQDIMKEAGMDN 529

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                                                   GQ+  
Sbjct: 530  YGKVTLI-----------------------------------------------DGQT-- 540

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 GE FD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  -----GEAFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|297614618|gb|ADI48611.1| DNA-directed RNA polymerase beta chain [Shewanella sp. KJW23]
          Length = 379

 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 231/376 (61%), Positives = 289/376 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +++ER+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SAL
Sbjct: 1   AVRERLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N+YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNSYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D  VT++V YLSA+EE    IAQAN  LD +    EE V CR  GE   +    I ++
Sbjct: 121 VIDSVVTDEVEYLSAIEEGRYVIAQANIELDNESRIVEEQVACRHKGESTFMRASDIQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SP+Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  SG
Sbjct: 181 DVSPQQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             + AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   V
Sbjct: 241 VVVAAKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSV 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G+ V R D++ADGPSTDLGDLALG+NM VAFMPW+GYNFEDS+LISER+  ED FT+IHI
Sbjct: 301 GEPVVRGDVLADGPSTDLGDLALGQNMRVAFMPWNGYNFEDSILISERVAQEDRFTTIHI 360

Query: 845 EEFEVMARDTKLGPEE 860
           +E   +ARDTKLG EE
Sbjct: 361 QELSCIARDTKLGSEE 376


>gi|213408763|ref|XP_002175152.1| DNA-directed RNA polymerase II complex subunit Rpb2
            [Schizosaccharomyces japonicus yFS275]
 gi|212003199|gb|EEB08859.1| DNA-directed RNA polymerase II complex subunit Rpb2
            [Schizosaccharomyces japonicus yFS275]
          Length = 1210

 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 192/1210 (15%), Positives = 364/1210 (30%), Gaps = 210/1210 (17%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQR------GDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L      +  IL+      +Y         G ++    S   ++   + ++++
Sbjct: 154  KIP--IMLR----STFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANI 207

Query: 265  VDIDTGEQ--------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            V +              I S  +  S L+ S++ K +      S       +     +  
Sbjct: 208  VQVFRKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARSTENSGQTIKATLPYIRSDIP 267

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               ++   G V D   LE I +       +  +      A++         +D+  AL  
Sbjct: 268  IVVVFRALGVVPDRDILEHICYDPNDLQMLEMMKPCIEEAFV--------IQDKDVALDY 319

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            I +              S          +Y    + +  +     L   +     +   +
Sbjct: 320  IGKR------------GSTTGVTREKRLRYAHDILQKEMLPHITTL---EGFETRKAFFL 364

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
              ++  ++     +   DD D+ G +R+   G +L + +R+   +M R +    +     
Sbjct: 365  GYMVHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFKKMTRDVYKYMQKCVET 424

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRL 541
                     + +  + + +     +               +SQ+       S ++H RR 
Sbjct: 425  NREFNLTLAVKSNTITNGLRYSLATGNWGDQKRGLANRVGVSQVLNRYTFASTLSHLRRT 484

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            +      + R     + R +H TH+G +CPAET EG   GLV +L+  + V+        
Sbjct: 485  NT----PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPI 540

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
               + +  + +   Y  +       +      L             R     + +  E  
Sbjct: 541  IEFLEEWGMESLEDYNPSASPNATKVFVNGIWLGVHRDPVHLTETLRSLRRRLDISAEVS 600

Query: 662  DFIDASPKQVVSI-----AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
               D   K++            +  ++ND ++       ++++ +  L  +        E
Sbjct: 601  IVRDIREKELRLFTDAGRICRPLFIVDNDSNSDTKGELCIRKEHIQQLLEDRDRFDINAE 660

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                 SS  A     +G++E +DA       +    D            + Q        
Sbjct: 661  QRFGWSSLIA-----SGLIEYLDAEEEETVMIAMSPDDLELSRQANAGYEMQEELDPAK- 714

Query: 777  NQRPLVKV--GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
                 VK      V         P+  LG LA       + +P+  +N          M 
Sbjct: 715  ----RVKPAPNPHVHAWTHCEIHPAMILGILA-------SIIPFPDHNQSPRNTYQSAMG 763

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             + +   I++  ++V                               +  +          
Sbjct: 764  KQAMG--IYLTNYQVRM---------------------------DTMANILYYPQKPLAT 794

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +    IF R  +D+ +
Sbjct: 795  TRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQSSIDRGLF-RSIFYRTYMDQEK 853

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +      E+ E   R           +       I  G           K+  +  D   
Sbjct: 854  KIGMTVMEEFERPTRSTTLRMKHGTYDKLEDDGLIAPGTRVSGDDIIIGKTAPVPPDHEE 913

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+Q          ++     +  Q                             L+ V
Sbjct: 914  LGQRTQLHAKRDVSTPLRSTESGIVDQ--------------------VMVTTNQEGLKFV 953

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK A RHG KG +      EDMPF   G   DI++NP  +PSRM V 
Sbjct: 954  KVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVA 1013

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +  +          +S L                          
Sbjct: 1014 HLVECQLSKVSALSGLEGDATPFTEVTVEAVSKLLRSHG--------------------- 1052

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD--ESGQSILYDGLTGEPFDRPVTVG 1252
                                              +    G +    G         V +G
Sbjct: 1053 ----------------------------FHSRGFEVMYHGHT----GR---KLVAQVFLG 1077

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y  +L H+V DK++AR+ G   ++T+QP+ G+S  GG R GEME  C  ++G + VL+
Sbjct: 1078 PTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLR 1137

Query: 1313 EMLTIKSD-------DVVG-------RTRVYESIVAGNDTFETGT--PESFNVLVKEMQA 1356
            E L   SD       D+ G       +   YE     N T  +    P +  +L +E+ +
Sbjct: 1138 ERLFDCSDAYRVIVCDLCGLIAIASFKKNSYECRSCQNRTRFSQIYLPYAAKLLFQELMS 1197

Query: 1357 LGLSIDLENS 1366
            + ++  L   
Sbjct: 1198 MNIAPRLFTK 1207



 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 144/1020 (14%), Positives = 293/1020 (28%), Gaps = 194/1020 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L   Q +S+D F+   +          Q        +T             ++    + F
Sbjct: 30  LARQQLSSFDEFVQNTM----------QEIVDDDSTLTLDQYAQHTGAQGDYTRRYEINF 79

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFD-------VDEFTGA 119
                  P               +   R+LTY+ PL + +R  V         + E    
Sbjct: 80  GQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMRAQDSNVPIGEEIWL 139

Query: 120 KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
              +D +   +++G +P+M +                         G F+I G ++++++
Sbjct: 140 TEEEDDEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIA 199

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDII----------- 202
           Q  RS   +      +A+ S  + Y   I    ++G  +      K +            
Sbjct: 200 QE-RSA-ANIVQVFRKAAPS-PIAYVAEIRSALERGSRLISSMQIKLMARSTENSGQTIK 256

Query: 203 ----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
               ++R D    +P+     ALG+  + +IL          Q  +     +  A ++  
Sbjct: 257 ATLPYIRSD----IPIVVVFRALGVVPDRDILEHICYDPNDLQMLEMMKPCIEEAFVIQD 312

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+   +        +   K+L       L+++ +  +                +    
Sbjct: 313 KDVALDYIGKRGSTTGVTREKRLRYAH-DILQKEMLPHITTLEGFETRKAFFLGYMVH-- 369

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A +  +    +      +    P+L          +   +     K  +     
Sbjct: 370 -RMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFKKMTRDVYKYMQKCVETNREF 428

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +    +  T  +  S+    + D  +   + VG  ++  R    +      R     
Sbjct: 429 NLTLAVKSNTITNGLRYSLATGNWGDQKRGLANRVGVSQVLNRYTFASTLSHLRRTNTPI 488

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +         +      ++KN   +  + +       I  ++
Sbjct: 489 GRDGKLAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLSLMSYVSVGSPSAPIIEFLE 545

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
              +   +  N     +A   F     L    + V+    +   RR   +  +  + R  
Sbjct: 546 EWGMESLEDYNPSASPNATKVFVNGIWLGVHRDPVHLTETLRSLRRRLDISAEVSIVRDI 605

Query: 554 AGVEMRDVHPTHYGRIC---------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
              E+R    T  GRIC             ++G        +           I    R 
Sbjct: 606 REKELR--LFTDAGRICRPLFIVDNDSNSDTKGELCIRKEHIQQLLEDRDRFDINAEQRF 663

Query: 605 -VCDGKVTNDVVYLSAMEEENRYIAQANSSL------DEDGSFTEELVFCRCAGEEILVP 657
                  +  + YL A EEE   IA +   L      +      EEL   +         
Sbjct: 664 GWSSLIASGLIEYLDAEEEETVMIAMSPDDLELSRQANAGYEMQEELDPAKRVKPAPNPH 723

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++ S R      M +QA+ +              
Sbjct: 724 VHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQV------- 776

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                                + + +  Y       +     + 
Sbjct: 777 ----------------------------------RMDTMANILYYPQKPLATTRSMEYLK 802

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            R                        +L  G+N +VA + + GYN EDS+++++  +   
Sbjct: 803 FR------------------------ELPAGQNAIVAILCYSGYNQEDSIIMNQSSIDRG 838

Query: 838 VFTSIHIEEFEVMARDTKLG-PEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F SI    +    +   +   EE  R        +       +++ G+I  G  V+  D
Sbjct: 839 LFRSIFYRTYMDQEKKIGMTVMEEFERPTRSTTLRMKHGTYDKLEDDGLIAPGTRVSGDD 898

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P         ++        +    RD S  + S  SG V  V +       K
Sbjct: 899 IIIGKTAPVPPDHEELGQRT-------QLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLK 951


>gi|285310170|emb|CBH41066.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. CCUG
           53068]
          Length = 371

 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 224/370 (60%), Positives = 287/370 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGLV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++++V+LSA+EE +  IAQA+++LD  G   +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 SDEIVFLSAIEEADHVIAQASATLDAKGRLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD + R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVIAR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 302 GDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 361

Query: 851 ARDTKLGPEE 860
           ARDTKLGPEE
Sbjct: 362 ARDTKLGPEE 371


>gi|297614610|gb|ADI48607.1| DNA-directed RNA polymerase beta chain [Shewanella haliotis]
          Length = 375

 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 231/372 (62%), Positives = 286/372 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D++ +MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG
Sbjct: 1   RLSLGDLNELMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL++FAR N+YGF+ETPYRKV D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSTFARTNSYGFLETPYRKVIDS 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT++V YLSA+EE    IAQAN  LD +G   EE V CR  GE   +    I ++D SP
Sbjct: 121 VVTDEVEYLSAIEEGRYVIAQANIELDNEGRIVEEQVACRHKGESTFMRASDIQYMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +Q++S+AASLIPFLE+DD+NR LMG NMQRQAVP LK+E P VGTG+E  +A  SG  + 
Sbjct: 181 QQIISVAASLIPFLEHDDANRALMGANMQRQAVPTLKSEKPLVGTGIERTLAVDSGVVVA 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP   VG+ V
Sbjct: 241 AKRGGVIDYVDASRIVVKVNEDELRPGEAGIDIYNLTKYTRSNQNTCINQRPCCSVGEPV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R D++ADGPSTDLGDLALG+NM VAFMPW+GYNFEDS+LISER+  ED FT+IHI+E  
Sbjct: 301 VRGDVLADGPSTDLGDLALGQNMRVAFMPWNGYNFEDSILISERVAQEDRFTTIHIQELS 360

Query: 849 VMARDTKLGPEE 860
            +ARDTKLG EE
Sbjct: 361 CIARDTKLGSEE 372


>gi|52694211|emb|CAG30635.1| DNA-directed RNA polymerase beta chain [Pseudomonas alcaliphila]
          Length = 372

 Score =  369 bits (946), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 227/371 (61%), Positives = 292/371 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVNEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 122 KVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 242 ARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R+DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 ARSDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPE 859
            +ARDTKLGPE
Sbjct: 362 CVARDTKLGPE 372


>gi|52694407|emb|CAG38043.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 370

 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 230/371 (61%), Positives = 291/371 (78%), Gaps = 1/371 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DG+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDATRIVVRVRDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVARGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTK
Sbjct: 300 DGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRFTTIHIQELTCVSRDTK 359

Query: 856 LGPEEITRDIP 866
           LGPEEIT DIP
Sbjct: 360 LGPEEITADIP 370


>gi|213582658|ref|ZP_03364484.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E98-0664]
 gi|289812028|ref|ZP_06542657.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. AG3]
          Length = 163

 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 109/163 (66%), Positives = 137/163 (84%)

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +P++TPVFDGA E  I  +L++ DL  SGQ  L+DG TGE F+RPVTVGY+YMLKLNH+V
Sbjct: 1    MPIATPVFDGAKEAEIKELLKLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLV 60

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
             DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV 
Sbjct: 61   DDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 120

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            GRT++Y++IV GN   E G PESFNVL+KE+++LG++I+LE+ 
Sbjct: 121  GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 163


>gi|52694147|emb|CAG30603.1| DNA-directed RNA polymerase beta chain [Pseudomonas rhodesiae]
          Length = 381

 Score =  368 bits (945), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 227/380 (59%), Positives = 294/380 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKP   AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERVSMAESEGLMPQDLINAKPGAGAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPEE 860
            IHI+E   +ARDTKLGPEE
Sbjct: 361 PIHIQELTCVARDTKLGPEE 380


>gi|22711962|ref|NP_683774.1| RNA polymerase beta subunit [Chaetosphaeridium globosum]
 gi|41017759|sp|Q8MA12|RPOB_CHAGL RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
           Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
           subunit beta; Short=RNA polymerase subunit beta
 gi|22416966|gb|AAM96566.1| beta subunit of RNA polymerase [Chaetosphaeridium globosum]
          Length = 1070

 Score =  368 bits (944), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 242/632 (38%), Positives = 380/632 (60%), Gaps = 16/632 (2%)

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK--DRKDALLDIYRVMRP--GD 385
           ++ +  I       I +  +     +  I + ++  KN   ++KDA+L+IY+ +    GD
Sbjct: 176 KRKVSAIVLLLSMGIKLSDITRSIEHPAILDNILKKKNVLSNQKDAILEIYKQLFSAGGD 235

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
            +      S     FF   + ++  +GR  +N +L L+ PD+   +  EDI+A I  L+ 
Sbjct: 236 PNFSDNILSELQRTFF-QQRCEIGLIGRSNLNKKLGLNIPDEEIFLLPEDILATINYLIK 294

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDL 503
           L  G G++DDID+L NRRV+S+ + L  Q +  L ++E +I    +  S     + P+ L
Sbjct: 295 LSLGIGSLDDIDHLKNRRVKSISDFLSEQLKNALNKIENTIEQSIKNISKRKRILTPKSL 354

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           IN+  +++   +FF S  LSQ  +  NSL+ + H RR+S+LG GG+ R  A   +RD+HP
Sbjct: 355 INSGILLAFFKDFFGSHPLSQFLDQTNSLTELVHKRRISSLGPGGLTRRTASFHVRDIHP 414

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           +HYGRICP ETSEG N GLV+SL S A +N  GFIE+P+ ++ D  + +  ++LSA E+E
Sbjct: 415 SHYGRICPIETSEGMNAGLVASLASNATINTMGFIESPFYQLNDSSLFDKPIFLSAREDE 474

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IA  N    +     +++   R   E I  P    +     P Q  SI ASLIPFLE
Sbjct: 475 NFRIALGNRLAIDQEIQEKQITPARYKQEFINTPWSLANLRSIFPWQYFSIGASLIPFLE 534

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +DD+NR LMG NMQRQAVPLL  E P VGTG E+ +A+ SGA +++   G ++ +D+  I
Sbjct: 535 HDDANRALMGSNMQRQAVPLLITERPIVGTGFEANIARDSGAPLISNIDGKIQYLDSEFI 594

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            I  V+              L  +QRSN NTC++ R +V++   VR+  I+ADG +T  G
Sbjct: 595 EILGVDKKTYKLK-------LSNYQRSNNNTCIHHRAIVQLNQWVRKGQILADGATTIRG 647

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L+LGRN+LVA+MPW GYNFED++LIS+R++ +D++TSIHI+++E+  +    G ++IT+
Sbjct: 648 ELSLGRNILVAYMPWEGYNFEDAVLISDRLIYDDLYTSIHIQKYELEIKINHQGQDKITK 707

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKA 921
           DIP++ +  L+++DE G++ +G+ V  GD+L+GK++ +        PE KLL+AIFG + 
Sbjct: 708 DIPHIDKYFLRHLDENGLVTLGSWVEAGDVLIGKLSSQEREDSLKVPEGKLLQAIFGLQI 767

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            + RDTSL++P+G  G V+D++   +     +
Sbjct: 768 GNSRDTSLKLPAGGEGRVIDIQWIFQDEGGID 799



 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 155/531 (29%), Positives = 227/531 (42%), Gaps = 95/531 (17%)

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                     I    I+ +   V  G IL    T      ++    +L A    +  +  D
Sbjct: 611  YQRSNNNTCIHHRAIVQLNQWVRKGQILADGATTIR-GELSLGRNILVAYMPWEGYNFED 669

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD--KDDE--QVILDRNI 982
              L     +S  ++   ++    I K E  I +  +  + + +D    D+     LD N 
Sbjct: 670  AVL-----ISDRLIYDDLYTSIHIQKYELEIKINHQGQDKITKDIPHIDKYFLRHLDEN- 723

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ--FAVQDEKVQRNVESLKV 1040
                  +  G    +G     K +    +   + P  +  Q  F +Q    +     L  
Sbjct: 724  ----GLVTLGSWVEAGDVLIGKLSSQEREDSLKVPEGKLLQAIFGLQIGNSRDTSLKLPA 779

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E     ++  F+         D+        V V+V  KR IQ GDK+AGRHGNKGIV
Sbjct: 780  GGEGRVIDIQWIFQ---------DEGGIDSNNFVNVYVLQKRRIQVGDKIAGRHGNKGIV 830

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            S+IL   DMP+L++GT +D+VL+PLGVPSRMNVGQI E  LG+A   L K  +    D +
Sbjct: 831  SQILSRHDMPYLQNGTSIDMVLSPLGVPSRMNVGQILECLLGFAGKFLNKNYRITPFDER 890

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               + S  +  L ++      T      + ++                            
Sbjct: 891  YEREASR-KLVLSELHKAKKLTGYPWLLEPENA--------------------------- 922

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                       G+S L+DG TGE F++PVTVG  Y+LKL H V DK++ARSTG YSLVTQ
Sbjct: 923  -----------GKSRLFDGRTGETFNQPVTVGSAYILKLIHQVDDKIHARSTGPYSLVTQ 971

Query: 1281 QP-------------LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            QP                          EMEVW ++ +GAAY+LQEMLT+KSD +  R  
Sbjct: 972  QPVRGRSRGGGQRVG-------------EMEVWALEGFGAAYILQEMLTVKSDHIHSRYD 1018

Query: 1328 VYESIV-AGNDTFETGTPESFNVLVKEMQALGL---SIDLENSRTKNSAKM 1374
            V  +IV        T TPESF +L +E++ LG+    I++ +   +     
Sbjct: 1019 VLGAIVTGTTIKTPTTTPESFRLLARELRCLGIQINDIEIYHETLQKKEIE 1069



 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 73/445 (16%), Positives = 154/445 (34%), Gaps = 44/445 (9%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSY 79
           E   +PDL ++Q  ++ +FL             +    K+   I         +     +
Sbjct: 9   EKFTLPDLGKIQLQNFYNFLTKI----------IYKELKAFPKIYDSEHNFEFKIYPEEF 58

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               P  +  + +++ +TY+  L +T  L                 ++Q + +G +PL+T
Sbjct: 59  FLVEPILNERESIYKSITYSTELYVTAELNCIKNQTK---------QKQKVLLGHIPLIT 109

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
            +G+F+I GI R VVSQ+ RSPGI+F         + K +Y   II + G  + +E D +
Sbjct: 110 SNGSFIINGISRAVVSQILRSPGIYFGSQLD---SNSKCIYTATIISESGSRLKLEIDDR 166

Query: 200 DIIHVRIDRRRKVPVTSFLMALGMDSEE---------ILSTFYPKIVYSQRGDFWCFPLS 250
            +I  RI ++RKV     L+++G+   +         IL     K             + 
Sbjct: 167 KLIWARISKKRKVSAIVLLLSMGIKLSDITRSIEHPAILDNILKKKNVLSNQKDAILEIY 226

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
                 G   + S   +   ++     +     + +S   K +  L I  + +    +  
Sbjct: 227 KQLFSAGGDPNFSDNILSELQRTFFQQRCEIGLIGRSNLNKKL-GLNIPDEEIF---LLP 282

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKD 369
           + +      +   +  +     ++ + +  ++ I   L     N    I NT+       
Sbjct: 283 EDILATINYLIKLSLGIGSLDDIDHLKNRRVKSISDFLSEQLKNALNKIENTIEQSIKNI 342

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFF-DSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            K       R++ P  +    +  + F   F        L     +   +     +    
Sbjct: 343 SK-----RKRILTPKSLINSGILLAFFKDFFGSHPLSQFLDQTNSLTELVHKRRISSLGP 397

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI 453
             + +      ++ +     G+   
Sbjct: 398 GGLTRRTASFHVRDIHPSHYGRICP 422


>gi|226731989|gb|ACO82065.1| RNA polymerase beta subunit [Pseudomonas oryzihabitans]
          Length = 364

 Score =  368 bits (944), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 221/364 (60%), Positives = 284/364 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA+++++  G   +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNNKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI
Sbjct: 241 VIDSVDASRVVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVERSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM VAFMPW+GYNFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 301 LADGPSTDMGELALGQNMRVAFMPWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARD 360

Query: 854 TKLG 857
           TKLG
Sbjct: 361 TKLG 364


>gi|320166143|gb|EFW43042.1| DNA-directed RNA polymerase II subunit RPB2 [Capsaspora owczarzaki
            ATCC 30864]
          Length = 1729

 Score =  368 bits (944), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 149/967 (15%), Positives = 286/967 (29%), Gaps = 162/967 (16%)

Query: 355  NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              Y    ++       ++AL    +   P  +        +      +  +Y    + + 
Sbjct: 306  YDYQDQEMMEMLRFSLEEALPIQEQ---PVALDFIGKRGLVQGATRENRIRYAKEILQKE 362

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
             +      D  +  +         I+  L+    G+  +DD D+ GN+R    G ++   
Sbjct: 363  LLPHVGVTDHSETKK---AYFFGYIVHRLLQAALGRRELDDRDHYGNKRCDLAGALVGGL 419

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +RL   ++ + +K   +                AK +   +     +             
Sbjct: 420  FRLLFRKLIKDVKASLQKDVDKRHEFNLLAAFKAKIISDGLRYSLATGNWGDAKKAHESR 479

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+   +   S ++H RRL++     + R     + R +  T +G +CPAET EG  
Sbjct: 480  AGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLQNTQWGVMCPAETPEGQA 535

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L   A ++  G       +  +   T ++   +            N       +
Sbjct: 536  CGLVKNLALMAYIS-VGSPALHIIEFLEEWATENLEETTPQSILQSTKIFVNGCWVGIHA 594

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
               ELV                   D SP+  +             D+ R +    +   
Sbjct: 595  QANELVRTLAQLR---------QRTDISPEISIVPDIRERELRIYSDAGRAMRPLFVVED 645

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                ++ E            A++  A           ++     VI  ++   + +    
Sbjct: 646  ERLSIRRE----HIDALKQAAQADRAGEHIDNPMRWPEL-ITTGVIEYIDTQEEETRMIA 700

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 + + R               G     +      P+  LG       +  + +P+ 
Sbjct: 701  MHPEDLDYARREGR-----------GAYCSTHTHCEINPAMILG-------VCASIIPFP 742

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +   ++I  F+V             + +         + D  
Sbjct: 743  DHNQSPRNCYQSAMGKQAMG--VYISNFQVRLDTMSHTLYYPQKPLTTTRSMEYLHFD-- 798

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                                      +      + AI      +  D+ +   S +   +
Sbjct: 799  -------------------------SLPAGMNAIVAISVYSGYNQEDSVVMNQSAIDRGL 833

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                 +  +  +     + V  E+ E  + +          +       +  G       
Sbjct: 834  FRSLFYRSYKDEVKPAGLDVGDEEFEKPSLEIVAGMRHSSYDKLDADGLVAPGTRVSGDD 893

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T +  +                       +     +Y    +    R       
Sbjct: 894  FIIGKTTPIPDEK--------------------NELAQTMKRYRKRDASTALRSTENGIV 933

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                  +     R VKV V   R  Q GDK A RHG KG        EDMP+  +G   D
Sbjct: 934  DTVMLSVNEDGHRFVKVRVRGIRIPQIGDKFASRHGQKGTCGITYRQEDMPYNAEGITPD 993

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +G + E   G                                     
Sbjct: 994  IIINPHAIPSRMTIGHLIECLQGKVAA--------------------------------- 1020

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                    +  +TP       ++I  +L+       G  +L++G
Sbjct: 1021 --------------------LTGKIGDATPFNTDVTVKSIADLLKEFRYHPYGNEVLFNG 1060

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG+  +  V  G  Y  +L HMV DK+++R  G  + +T+QP+ G++  GG R GEME 
Sbjct: 1061 HTGKKMNTQVYFGPTYYQRLKHMVDDKIHSRQRGPLTNLTRQPVEGRARDGGLRFGEMER 1120

Query: 1300 WCIQAYG 1306
             C+  +G
Sbjct: 1121 DCL--HG 1125



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 109/755 (14%), Positives = 239/755 (31%), Gaps = 108/755 (14%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG----AAMLEFVSYEFDPP 84
           L+  Q  S+D F+ + I         L+   +  F             ++ F +     P
Sbjct: 51  LVRQQLDSFDDFISLTIPELISEQGTLELKVERQF--LDADEVAPPRYVVSFDNIFISHP 108

Query: 85  KFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                         ++   R+LTYA  L + L+  +F  DE    +  +      +Y+G 
Sbjct: 109 TITESDGYNHALFPNEARLRNLTYACRLYVNLKREMFRYDENGVEEPPEVKILDKVYLGQ 168

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP--GIHFDHD 168
           +P+M +                         G FVI G ++++++Q  R     ++  H 
Sbjct: 169 IPMMLRSKNCALFNKKDYELEKMNECPYDQGGYFVINGSEKVLIAQE-RMANNNVYVFHR 227

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI------------DR-------- 208
           K       K  Y   I       ++      + ++ ++            +R        
Sbjct: 228 K----PPAKYSYVAEIR----SALETGHRPANTLYTKMLTRGQSKGESAGNRIQCTLPYI 279

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           +  +P+     ALG  S+ ++L          +  +   F L  A  +    V+   +  
Sbjct: 280 KTDIPIVVVFRALGFVSDRDVLDHVIYDYQDQEMMEMLRFSLEEALPIQEQPVALDFIGK 339

Query: 268 D------TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
                  T E  I   K++    L  L   GV     T       Y+   ++    G   
Sbjct: 340 RGLVQGATRENRIRYAKEILQKEL--LPHVGVTDHSETKKAYFFGYIVHRLLQAALGRRE 397

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D    K  +           +L+   + +   ++ +L  D +K  +  LL  ++  
Sbjct: 398 LDDRDHYGNKRCDLAGALVGGLFRLLFRKLIKD---VKASLQKDVDKRHEFNLLAAFK-- 452

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
               + +  +  S+    + D+ K   S  G  ++  RL   +      R          
Sbjct: 453 --AKIISDGLRYSLATGNWGDAKKAHESRAGVSQVLNRLTYASTLSHLRRLNSPIGREGK 510

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L+N +  +         +      ++KN   +  + +       I  ++  +  
Sbjct: 511 LAKPRQLQNTQWGVMCPAETPEGQACG---LVKNLALMAYISVGSPALHIIEFLEEWATE 567

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             +    + ++ +   F     +    +    +  +   R+ + +               
Sbjct: 568 NLEETTPQSILQSTKIFVNGCWVGIHAQANELVRTLAQLRQRTDISPEISIVPDIREREL 627

Query: 560 DVHPTHYGRICPAETSEGHNIGL----VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            ++      + P    E   + +    + +L   A+ +  G       +  +   T  + 
Sbjct: 628 RIYSDAGRAMRPLFVVEDERLSIRREHIDALKQAAQADRAGEHIDNPMRWPELITTGVIE 687

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE R IA             E+L + R   E            + +P  ++ + 
Sbjct: 688 YIDTQEEETRMIAM----------HPEDLDYARR--EGRGAYCSTHTHCEINPAMILGVC 735

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           AS+IPF +++ S R      M +QA+ +  +    
Sbjct: 736 ASIIPFPDHNQSPRNCYQSAMGKQAMGVYISNFQV 770



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 32/88 (36%)

Query: 1301 CIQAYGAAYVLQEMLTIKSD-------DVVG-----------------RTRVYESIVAGN 1336
            C+ A+GAA  L+E L  +SD       D+ G                 R +         
Sbjct: 1640 CMIAHGAAQFLRERLFEQSDFSRVHVCDICGLIAIANLKKNEFECRACRNKT-------- 1691

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLE 1364
               +   P +  +L +E+ ++ ++  L 
Sbjct: 1692 QISQIFLPYAAKLLFQELMSMSIAPRLM 1719


>gi|170084317|ref|XP_001873382.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164650934|gb|EDR15174.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 942

 Score =  367 bits (943), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 156/937 (16%), Positives = 292/937 (31%), Gaps = 149/937 (15%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 130  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 186

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 187  GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 246

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 247  ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 302

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 303  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 354

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 355  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 411

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +   Q + L K    ++  G+               + GI+E +DA   
Sbjct: 412  TDAGRVCRPLFIVENQQLALQKKHVKWLSNGLNDDG--DEYKWEHLVKGGIIELLDAEEE 469

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +       +    ++       R  +K G            PS  LG
Sbjct: 470  ETVMISMTPEDLENSRLQQSGVDLHANDGEFDPAAR--LKAGTHAHTWTHCEIHPSMILG 527

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 528  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 562

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 563  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 611

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +  
Sbjct: 612  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKHGTYDKI 670

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R+Q          ++     +  Q  
Sbjct: 671  EDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTQTHTRRDVSTPLKSTESGIVDQVL 730

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 731  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 770

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 771  YRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 825

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 826  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 849

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                    G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+
Sbjct: 850  ------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 896

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G+S  GG R GEME  C+ ++G A  L+E L   SD
Sbjct: 897  EGRSRDGGLRFGEMERDCMISHGIAGFLKERLFEASD 933



 Score =  135 bits (340), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 99/777 (12%), Positives = 217/777 (27%), Gaps = 124/777 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+      LG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 60  YIKVD----IPIWVVFRGLGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 115

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + +              +      + 
Sbjct: 116 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 171

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 172 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLQKCV 221

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 222 --ETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 278

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 279 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAP 338

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 339 VIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVS 398

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR--VNAYGFIETPYRKVCD 607
                  +   ++        P    E   + L      +    +N  G       K   
Sbjct: 399 VVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLSNGLNDDGDE----YKWEH 454

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREK 660
                 +  L A EEE   I+     L+        +      GE               
Sbjct: 455 LVKGGIIELLDAEEEETVMISMTPEDLENSRLQQSGVDLHANDGEFDPAARLKAGTHAHT 514

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 515 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI---------- 564

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 565 -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 592

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 593 -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 629

Query: 841 SIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E        +   +       I++ G+I  G  V   DI++
Sbjct: 630 SIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAPGTGVAGEDIII 689

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 690 GKTAPIPPDSEELGQRT-------QTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 739


>gi|207081364|gb|ACI22950.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 380

 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 228/377 (60%), Positives = 295/377 (78%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV + V EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAGVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  
Sbjct: 121 VVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEE 860
           I+E   +ARDTKLGPEE
Sbjct: 361 IQELTCVARDTKLGPEE 377


>gi|52694153|emb|CAG30606.1| DNA-directed RNA polymerase beta chain [Pseudomonas orientalis]
          Length = 381

 Score =  367 bits (943), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 227/379 (59%), Positives = 296/379 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKP   AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPGAGAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT
Sbjct: 301 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFT 360

Query: 841 SIHIEEFEVMARDTKLGPE 859
           +IHI+E   +ARDTKLGPE
Sbjct: 361 TIHIQELTCVARDTKLGPE 379


>gi|99034134|ref|ZP_01314233.1| hypothetical protein Wendoof_01000976 [Wolbachia endosymbiont of
            Drosophila willistoni TSC#14030-0811.24]
          Length = 363

 Score =  367 bits (943), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 180/373 (48%), Positives = 254/373 (68%), Gaps = 12/373 (3%)

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            VGD V++ D+IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS  +V +D+FTSIH
Sbjct: 3    VGDYVKKGDVIADGPAINSGELALGKNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIH 62

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IEEF+ +  DT LG E+ITR IP V+EE L ++D+ GI+ +G  V PG ILVGK+TPK  
Sbjct: 63   IEEFDCVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPS 122

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              + PE KLL  IFGEK+ D  D+SL     V GTV+DV++F R G+++NER++ +++++
Sbjct: 123  LSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKE 182

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            I     ++D    +     Y  L ++L    +               +      R QWW 
Sbjct: 183  INDFEEERDYIINVTSEYFYDELKKLLINSGSQ------------DREKFDSIEREQWWG 230

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              ++++ +   V+SLK  ++   S    +FK K+EK+  G D+P GV   VKVF+A+K  
Sbjct: 231  IGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHS 290

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q GDKMAGRHGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMNVGQI ETH+GW
Sbjct: 291  LQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGW 350

Query: 1144 ACVGLGKKIKSLI 1156
            AC  LG+K+ +++
Sbjct: 351  ACRKLGEKVSNIL 363


>gi|313199657|ref|YP_004021273.1| RNA polymerase beta subunit [Isoetes flaccida]
 gi|291575386|gb|ADE18099.1| RNA polymerase beta subunit [Isoetes flaccida]
          Length = 1072

 Score =  367 bits (943), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 158/484 (32%), Positives = 225/484 (46%), Gaps = 65/484 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   + P + +L A    +  +  D+ L     +S  ++ 
Sbjct: 628  VNQGEYLERGQILADGGATVG-GELAPGKNILIAYMPWEGYNFEDSVL-----ISERLIH 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              IF    I K E    V     E  A +   +   LD      L +   +L G    +G
Sbjct: 682  EDIFTSIHIGKYEIGAHV---TPEGTAEEITRKIPHLDDYFLRHLDKSGLVLPGSWVETG 738

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQ--FAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                 K T   S+   + P     Q  F +     +     +          +   +   
Sbjct: 739  DVLVGKLTPRDSEESLKAPEGNSLQAIFGIDTTTTRETCLKVPPGGRGQVIDVRWIYPED 798

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              +            +VV V+V  +R I+ GDK+AGRHGNKGI+S+ILP +DMP+L++GT
Sbjct: 799  TSRYT----------KVVHVYVLQERKIRVGDKVAGRHGNKGIISKILPRQDMPYLQNGT 848

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            P+D++L+PLGVPSRMNVGQIFE  LG A   L +  + +  D +   +      F E   
Sbjct: 849  PIDMILSPLGVPSRMNVGQIFECVLGIAGDFLRRHYRVMPFDERYEREAPRKLVFPEPHE 908

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
             +       S                        F+               LD  G+S L
Sbjct: 909  ASRQTANPWS------------------------FE---------------LDNPGKSRL 929

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
             DG TG+ F++PVT+G  YM KL H V DK++ARS+G YS VTQQPL G+S RGGQR+GE
Sbjct: 930  IDGRTGDIFEQPVTIGKAYMPKLIHQVDDKIHARSSGPYSRVTQQPLRGRSKRGGQRVGE 989

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGT--PESFNVLVKEM 1354
            MEVW  + +G +++ QEMLTIKSD    R +V  +IVAG   +E     PESF +LV+E 
Sbjct: 990  MEVWAPEGFGVSHIPQEMLTIKSDHAETRQKVVSTIVAGEPIYEPEVITPESFRLLVREP 1049

Query: 1355 QALG 1358
            + L 
Sbjct: 1050 RCLA 1053



 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 230/690 (33%), Positives = 359/690 (52%), Gaps = 15/690 (2%)

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           +L+         T   +        +       I++             +    +    I
Sbjct: 135 NLERDPNGNPIYTGTIISNRGGRFKLEPDMKNRIWVRINRKQRISIRLLLLAMGLDTKEI 194

Query: 347 L-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           L  V   + ++           + R+ A+ ++Y+++   D        S  +   F   K
Sbjct: 195 LENVCYPDVSSDAFRKTKAKHIQSREYAISELYKLLYGTDEYLKFPDISEESQERFSQPK 254

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           ++   +GR+ +N +LNLD P +      +D++A+I   + +R G GT+DD+D+L N+ + 
Sbjct: 255 FEPGKIGRINLNKKLNLDVPKNEIFSLPKDMLAVIDYSIKVRIGVGTLDDMDHLKNKHIC 314

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLS 523
           SV +  K+Q RL   R E S++ R++       +P     + +  +++   EFF S  LS
Sbjct: 315 SVADSSKDQSRLASERSEDSVRGRMNRATQHKRVPTFGSPVTSSLLLTTFKEFFGSHPLS 374

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L++I H RRLS LG GG  R  A  ++RD HP+HYGR+CP ETSEG N G +
Sbjct: 375 QSLDQTNPLTQIVHRRRLSYLGPGGSIRRTASFQVRDTHPSHYGRVCPIETSEGMNAGPI 434

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL   A V+ +GF  +P+ K+ +      +   ++SA E+E   I              
Sbjct: 435 SSLALHASVDPWGFFGSPFYKISEILSEEGDTATHVSAEEDEYYRITTGTCLSVSQEDKE 494

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++   R   E + +   +I     SP Q   + A  IP LEN+D+NR  MG NMQRQAV
Sbjct: 495 EQVTAARYRQEIVTIAWNQIHLRSISPLQHFPVGAPPIPPLENNDANRASMGSNMQRQAV 554

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL K E   VGTG+E  VA  SG  +VA R G ++ +D  +I +   +G+   +   +  
Sbjct: 555 PLSKPEKCIVGTGLEGQVAPDSGTVVVAARGGKIDYIDGEKITLLVDDGNTIDTKLVI-- 612

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
                +QRSN +T ++Q+P V  G+ + R  I+ADG +T  G+LA G+N+L+A+MPW GY
Sbjct: 613 -----YQRSNNDTRMHQKPRVNQGEYLERGQILADGGATVGGELAPGKNILIAYMPWEGY 667

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECG 880
           NFEDS+LISER++ ED+FTSIHI ++E+ A  T  G  EEITR IP++ +  L+++D+ G
Sbjct: 668 NFEDSVLISERLIHEDIFTSIHIGKYEIGAHVTPEGTAEEITRKIPHLDDYFLRHLDKSG 727

Query: 881 IICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++  G+ V  GD+LVGK+TP+        PE   L+AIFG      R+T L+VP G  G 
Sbjct: 728 LVLPGSWVETGDVLVGKLTPRDSEESLKAPEGNSLQAIFGIDTTTTRETCLKVPPGGRGQ 787

Query: 939 VVDVRIFNRHGIDKNERSISVEREQIELLA 968
           V+DVR        +  + + V   Q   + 
Sbjct: 788 VIDVRWIYPEDTSRYTKVVHVYVLQERKIR 817



 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 114/804 (14%), Positives = 252/804 (31%), Gaps = 95/804 (11%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEF- 76
           KN EI  +P+  ++Q  ++  F+          ++GL     + FP I        +EF 
Sbjct: 5   KNGEIFVLPNFGKIQLEAFYRFV----------DQGLMEE-PNNFPCIEDTDE--EIEFR 51

Query: 77  ---VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                Y    P     D +   +TY+    +  +         +  K    IK Q++Y+G
Sbjct: 52  LFGEQYYLIEPLIGEKDAVCGSITYSPKSYVPAQ---------STQKGRGRIKRQTVYIG 102

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           ++PLM+  GTFV+ G  R+ ++Q+ RSPGI+ + ++     +G  +Y   II ++G    
Sbjct: 103 NIPLMSSQGTFVVNGTARVAINQILRSPGIYLNLERD---PNGNPIYTGTIISNRGGRFK 159

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP----KIVYSQRGDFWCFP- 248
           +E D K+ I VRI+R++++ +   L+A+G+D++EIL            + +         
Sbjct: 160 LEPDMKNRIWVRINRKQRISIRLLLLAMGLDTKEILENVCYPDVSSDAFRKTKAKHIQSR 219

Query: 249 ----LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                    L+ G        DI    Q   S  K   G +  +       L +  + + 
Sbjct: 220 EYAISELYKLLYGTDEYLKFPDISEESQERFSQPKFEPGKIGRINLNKKLNLDVPKNEIF 279

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
            L      V   + ++      V     ++ + +  I  +     DS  + + + +    
Sbjct: 280 SLPKDMLAVIDYSIKV---RIGVGTLDDMDHLKNKHICSVA----DSSKDQSRLASERSE 332

Query: 365 DKNKDRKDALLDIYRVMRPGDVST----FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           D  + R +      RV   G   T     +  +  F            + + ++    RL
Sbjct: 333 DSVRGRMNRATQHKRVPTFGSPVTSSLLLTTFKEFFGSHPLSQSLDQTNPLTQIVHRRRL 392

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +   P           +          +  G +  I+         +  +  +       
Sbjct: 393 SYLGPGGSIRRTASFQVRDTH-----PSHYGRVCPIETSEGMNAGPISSLALHASVDPWG 447

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS--------QLSQLEEHVNSL 532
                  +    +  +      +   +     +    C S        Q++        +
Sbjct: 448 FFGSPFYKISEILSEEGDTATHVSAEEDEYYRITTGTCLSVSQEDKEEQVTAARYRQEIV 507

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           +   +   L ++         A      +      R       +   + L          
Sbjct: 508 TIAWNQIHLRSISPLQHFPVGAPPIP-PLENNDANRASMGSNMQRQAVPLSKPEKCIVGT 566

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--VFCRCA 650
              G +      V        + Y+   +          + L +DG+  +    ++ R  
Sbjct: 567 GLEGQVAPDSGTVVVAARGGKIDYIDGEKI---------TLLVDDGNTIDTKLVIYQRSN 617

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            +  +  + +++  +   +  +                               L      
Sbjct: 618 NDTRMHQKPRVNQGEYLERGQILADGGA--------------------TVGGELAPGKNI 657

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           +   M         + ++++R    +   +I I    +   + P  +  +I R +     
Sbjct: 658 LIAYMPWEGYNFEDSVLISERLIHEDIFTSIHIGKYEIGAHVTPEGTAEEITRKIPHLDD 717

Query: 771 NQNTCVNQRPLVKVGDEVRRNDII 794
                +++  LV  G  V   D++
Sbjct: 718 YFLRHLDKSGLVLPGSWVETGDVL 741


>gi|6686323|sp|P50546|RPOB_ARATH RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
          Length = 1072

 Score =  367 bits (942), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 150/498 (30%), Positives = 235/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 628  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 681

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 682  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 739

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 740  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 796

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 797  -GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 852

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 853  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 912

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G++ ++DG 
Sbjct: 913  TANPW------------------------VFE---------------PEYPGKTRIFDGR 933

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V   ++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 934  TGDPFEQPVIIGKPYILKLIHQVDVIIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 993

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +     ESF +LV+E+++L L
Sbjct: 994  ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAQESFRLLVRELRSLAL 1053

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1054 ELNHFLVSEKNFQINRKE 1071



 Score =  360 bits (924), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 231/688 (33%), Positives = 378/688 (54%), Gaps = 23/688 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 203 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 262 GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQLGLALARLENVVKGTIGGAIRYKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 382 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 442 ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 501

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 502 RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 561

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              VGTG+E  VA  SG   +A+  G +   D  +IV+                  L+ +
Sbjct: 562 KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVLSGN--------GDTLSIPLIMY 613

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 614 QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 673

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 674 LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 733

Query: 888 VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 734 VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 793

Query: 946 NRHGIDKNE----RSISVEREQIELLAR 969
            + G         R    ++ +I++  +
Sbjct: 794 QKKGGSSYNPEIIRVYISQKREIKVGDK 821



 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFYRFI----------DQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 220


>gi|52694279|emb|CAG37979.1| RNA polymerase beta subunit [Pseudomonas amygdali]
          Length = 385

 Score =  367 bits (942), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 229/385 (59%), Positives = 298/385 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     
Sbjct: 121 PYRVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELVDELVAVRHLNEFTVKAPAD 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVACRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LV  GD V+R+DI+ADGPST++G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F 
Sbjct: 301 LVSKGDRVQRSDIMADGPSTNMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDPFP 360

Query: 841 SIHIEEFEVMARDTKLGPEEITRDI 865
           +IHI+E   +ARDTKLGPEEIT DI
Sbjct: 361 TIHIQELTCVARDTKLGPEEITADI 385


>gi|215254169|gb|ACJ64089.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|215254171|gb|ACJ64090.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 366

 Score =  367 bits (941), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 232/366 (63%), Positives = 285/366 (77%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARC 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE
Sbjct: 61  NEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L PRE   ++D +  QVVSIAASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VG
Sbjct: 121 SGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVG 180

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 181 TGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQ 240

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 241 NTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 300

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 301 VVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 360

Query: 893 ILVGKI 898
           ILVGK+
Sbjct: 361 ILVGKV 366


>gi|2196464|emb|CAA74024.1| DNA-dependent RNA polymerase subunit beta [Arabidopsis thaliana]
          Length = 1078

 Score =  367 bits (941), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 150/498 (30%), Positives = 235/498 (47%), Gaps = 58/498 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL       G   +   + +L A    +  +  D  L     +S  +V 
Sbjct: 634  VRRGKCIKKGQILADGAATVG-GELALGKNILVAYMPWEGYNFEDAVL-----ISECLVY 687

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + ++    E  +L      +   ++ G    +G  
Sbjct: 688  GDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRN--LDKNGIVMLGSWVETGDI 745

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T   +   S  P  +  +  +  +        LK+       +++ R+  K    
Sbjct: 746  LVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKK--- 802

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G    P    +++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+
Sbjct: 803  -GGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDM 858

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F E    +  
Sbjct: 859  VFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQ 918

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         VF+                +  G++ ++DG 
Sbjct: 919  TANPW------------------------VFE---------------PEYPGKTRIFDGR 939

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+PF++PV +G  Y+LKL H V   ++ RS+G Y+LVTQQPL G+S +GGQR+GEMEVW
Sbjct: 940  TGDPFEQPVIIGKPYILKLIHQVDVIIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVW 999

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGL 1359
             ++ +G A++LQEMLT KSD +  R  V  + + G    +     ESF +LV+E+++L L
Sbjct: 1000 ALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAQESFRLLVRELRSLAL 1059

Query: 1360 SID--LENSRTKNSAKME 1375
             ++  L + +     + E
Sbjct: 1060 ELNHFLVSEKNFQINRKE 1077



 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 231/688 (33%), Positives = 378/688 (54%), Gaps = 23/688 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 149 ISVYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 208

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 209 IFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFFH-QRCELGRI 267

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  +N RLNL+ P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L
Sbjct: 268 GRRNINWRLNLNIPQNNIFLLPRDILAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLL 327

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q  L L R+E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 328 QDQLGLALARLENVVKGTIGGAIRYKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRT 387

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL+  
Sbjct: 388 NPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIH 447

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           AR+  +G +E+P+ ++ +      +   +LS  ++E   IA  NS     G   E+ V  
Sbjct: 448 ARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPA 507

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E
Sbjct: 508 RYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSE 567

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              VGTG+E  VA  SG   +A+  G +   D  +IV+                  L+ +
Sbjct: 568 KCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVLSGN--------GDTLSIPLIMY 619

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           QRSN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++
Sbjct: 620 QRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAV 679

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           LISE +V  D++TS HI ++E+    T  GPE IT++IP++    L+N+D+ GI+ +G+ 
Sbjct: 680 LISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSW 739

Query: 888 VNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR  
Sbjct: 740 VETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWV 799

Query: 946 NRHGIDKNE----RSISVEREQIELLAR 969
            + G         R    ++ +I++  +
Sbjct: 800 QKKGGSSYNPEIIRVYISQKREIKVGDK 827



 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 18  IPGFNQIQFEGFYRFI----------DQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVE 67

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ I++G++PLM   GT
Sbjct: 68  PLIKERDAVYESLTYSSELYVSAGLIW---------KTSRNMQEQRIFIGNIPLMNSLGT 118

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I 
Sbjct: 119 SIVNGIYRIVINQILQSPGIYYQSELDHNGIS---VYTGTIISDWGGRLELEIDKKARIW 175

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 176 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKE 226


>gi|52694373|emb|CAG38026.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 373

 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 228/374 (60%), Positives = 290/374 (77%), Gaps = 1/374 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA R+V+R  +G+++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDASRVVVRVHDGEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVERGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTK
Sbjct: 300 DGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRFTTIHIQELTCVSRDTK 359

Query: 856 LGPEEITRDIPNVS 869
           LGPEEI R  P   
Sbjct: 360 LGPEEIYRRHPERG 373


>gi|83583689|gb|ABC24704.1| RNA polymerase beta subunit [Spiroplasma platyhelix]
          Length = 593

 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 234/446 (52%), Positives = 317/446 (71%), Gaps = 9/446 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ + + RRL+ALG GG++R RA +E+RDVH +HYGRICP+ET EG NIGL+S+L 
Sbjct: 1   QTNPLAELANKRRLTALGPGGLSRERASLEVRDVHYSHYGRICPSETPEGPNIGLISNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A+VN YGFIETPYRKV D KVT++V+YL+A +E++  IAQAN  LD       + V  
Sbjct: 61  TYAKVNEYGFIETPYRKVVDAKVTDEVLYLTAGDEKDYIIAQANIELDSHNVIKSKNVIA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G+ I+V   K+DFID SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+K E
Sbjct: 121 RNNGQNIIVSPSKVDFIDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLIKPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTG+E  VA+ SG AI+AK  G+++ VDA  I+++  +         V+ Y L KF
Sbjct: 181 APIVGTGVEYAVARDSGLAILAKNPGVIKYVDANEIIVQGEKE--------VNTYELSKF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  T ++   LVK+GD+V +  I+ADGPS   G+LALG+N++V FM W+GYN+ED++
Sbjct: 233 ERSNYGTGISHSTLVKIGDKVEKGQILADGPSMKDGELALGQNVIVGFMTWNGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +ISER+V +DV+TSIHIEE+ +  R TK G EEITR+IPN SE   K +D+ GI+ VG E
Sbjct: 293 IISERLVKDDVYTSIHIEEYTLERRRTKQGKEEITREIPNTSEIARKYLDDDGIVLVGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG++  TPEEKLL  ++GEK+ +V+D SLRVP+G +G V  V+ + R
Sbjct: 353 VKEGDILVGKVTPKGQTQPTPEEKLLSILYGEKSRNVKDNSLRVPNGGAGIVQSVKRYAR 412

Query: 948 -HGIDKNERSISVEREQIELLARDKD 972
             G +       +    I    + ++
Sbjct: 413 ADGYELPSEVEEIIHVYIVQKRKIRE 438



 Score =  308 bits (789), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 125/420 (29%), Positives = 184/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G +V  G IL    +   +  +   + ++         +  D  +     V   V 
Sbjct: 246  LVKIGDKVEKGQILADGPS-MKDGELALGQNVIVGFMTWNGYNYEDAIIISERLVKDDVY 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                   + +++       E    E      +AR   D+  I+      +  +IL G+  
Sbjct: 305  TSIHIEEYTLERRRTKQGKEEITREIPNTSEIARKYLDDDGIVLVGTEVKEGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L S L  E  R+     +++       +     +Y  +          
Sbjct: 365  PKGQTQPTPEEKLLSILYGEKSRN-VKDNSLRVPNGGAGIVQSVKRYARA---------- 413

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                   G ++P  V  ++ V++  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+DG
Sbjct: 414  ------DGYELPSEVEEIIHVYIVQKRKIREGDKMAGRHGNKGVISKVLPVEDMPFLEDG 467

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+          
Sbjct: 468  TPIDIMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGLKNDDLLN-------- 519

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                       I         D   +  
Sbjct: 520  -------------------------------------------IMKEANFNGFD---KVT 533

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LYDG+TGE FD  ++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 534  LYDGMTGEKFDNKISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 593


>gi|229915248|gb|ACQ90686.1| DNA-directed RNA polymerase beta chain [Marinobacterium sp. KW44]
          Length = 373

 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 228/372 (61%), Positives = 295/372 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + D++MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG
Sbjct: 1   RLSMAESDNLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YGF+ETPYR+V DG
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVFARTNDYGFLETPYRRVVDG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+D+ YLSA+EE    IAQA++++DE+   T+ELV  R   E  ++  E++ ++D SP
Sbjct: 121 QVTDDIDYLSAIEENKYIIAQASAAMDEERRLTDELVAVRHLNEFTVMGPERVQYMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E  VA+ SG  +V
Sbjct: 181 RQVVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGIERNVAQDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G++E VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR +V+ G+ V
Sbjct: 241 ARRGGVIESVDAARIVVRVHDDEVEAGDAGVDIYNLTKYVRSNQNTCINQRSIVRPGETV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R D++ADGPS DLG+LALG+NM +AFMPW+GYNFEDS+LISER+V ED FT+IHI+E  
Sbjct: 301 QRGDVMADGPSVDLGELALGQNMRIAFMPWNGYNFEDSILISERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 361 CVARDTKLGPEE 372


>gi|52538151|emb|CAH19177.1| RNA polymerase beta-subunit [Pseudomonas cedrina]
          Length = 376

 Score =  367 bits (941), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 225/376 (59%), Positives = 291/376 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITRDIP 866
           ARDTKLGPEEI    P
Sbjct: 361 ARDTKLGPEEIYCRHP 376


>gi|150964944|gb|ABR87005.1| DNA-directed RNA polymerase beta chain [Pseudomonas xiamenensis]
          Length = 375

 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 228/372 (61%), Positives = 286/372 (76%), Gaps = 1/372 (0%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPYRRVKDT 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++ +  DG   EELV  R   E  +   E++  +D SP
Sbjct: 122 VVTDEIVFLSAIEEADHVIAQASAEV-RDGKLVEELVAVRHMNEFSVKAPEEVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  SG  + 
Sbjct: 181 RQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVALDSGVCVT 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+V+ VDA RIVIR  + +++   +GVDIY L K+ RSNQNTC+NQRPLVK GD V
Sbjct: 241 ARRGGVVDSVDASRIVIRVNDDEVEAGEAGVDIYTLTKYTRSNQNTCINQRPLVKKGDVV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
              DI+ADG S D+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E  
Sbjct: 301 AIKDILADGSSVDMGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPEE 860
            ++RDTKLGPEE
Sbjct: 361 CVSRDTKLGPEE 372


>gi|81171075|gb|ABB58764.1| RNA polymerase beta subunit [Spiroplasma floricola]
 gi|82798474|gb|ABB91900.1| RNA polymerase beta subunit [Spiroplasma floricola]
          Length = 591

 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 234/474 (49%), Positives = 334/474 (70%), Gaps = 10/474 (2%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2    NPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590  ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A++N YGFIETPYRKV + KV   +  YL+A +E++  +AQAN +L EDG+  ++ V  R
Sbjct: 62   AKINEYGFIETPYRKVKNTKVMSGEYEYLTADKEKDYVVAQANINLAEDGTILDDQVIAR 121

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              G++I+V  + ID++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E+
Sbjct: 122  YRGDDIMVSPQDIDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPES 181

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            P VGTG+E   A+ SG A+VA  +GIV+ VD+ +IVI   +        G+  Y L  F 
Sbjct: 182  PIVGTGVEHEAARDSGDAVVATESGIVKYVDSKKIVIEQKD--------GIKTYDLNDFS 233

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+++
Sbjct: 234  RSNNGTAITHLPIVKIGDKVKAKDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAVI 293

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K +DE GI+ +G+EV
Sbjct: 294  VSERIVIEDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEVSKKYLDEDGIVAIGSEV 353

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
              GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+R 
Sbjct: 354  KVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFSRA 413

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
             G D     + + +  I    + ++ +++         + +IL  ++      G
Sbjct: 414  DGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDG 467



 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 120/417 (28%), Positives = 175/417 (41%), Gaps = 75/417 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLRVPSGVSGT 938
            I+ +G +V   DIL  G    KGE  +     +    + G    D    S R+      T
Sbjct: 246  IVKIGDKVKAKDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAVIVSERIVIEDRFT 305

Query: 939  VVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             + +  +        +    + R+   I  +++   DE  I+      ++ +IL G+   
Sbjct: 306  SIHIDEYTIERRQTKQGPEEITRDIPNISEVSKKYLDEDGIVAIGSEVKVGDILVGKVTP 365

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                       L   +  E  R           +V    E +                 K
Sbjct: 366  KSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIIKSI-------------K 408

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G D+P  +L ++KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGT
Sbjct: 409  RFSRADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGT 468

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +        
Sbjct: 469  PVDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVREQELQDIMHEAGMDN 528

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                               DG   EA +                
Sbjct: 529  YGKVKLI----------------------------DGRTGEAFDK--------------- 545

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                       P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR
Sbjct: 546  -----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQR 591


>gi|126460694|ref|YP_001056972.1| DNA-directed RNA polymerase subunit B [Pyrobaculum calidifontis JCM
            11548]
 gi|126250415|gb|ABO09506.1| DNA-directed RNA polymerase, subunit B' / DNA-directed RNA
            polymerase, subunit B' [Pyrobaculum calidifontis JCM
            11548]
          Length = 1127

 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 124/603 (20%), Positives = 218/603 (36%), Gaps = 97/603 (16%)

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             V+ GD     D +      +  D     N  +A  P    +    + I    +   + +
Sbjct: 603  RVRKGDLT--WDDLVKMGVVEYLDADEEENAHIAVDPRGDLSGYTHVEIIPSAILGAIAS 660

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   E     R+               S      +D  G   +        +    +  
Sbjct: 661  IIPYLEHNQSPRNQYEAAMAKQSLGLPQSNFLY-KLDSRG--HMLYYPERPIVTTRGLEL 717

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
             G S     +  + A+      ++ D  +   + V   +    +F R    + ++    E
Sbjct: 718  VGYSKRPAGQNAVVALLTYTGYNIEDAVILNKASVERGMF-RSVFYRTYETEEQKYPGGE 776

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++IE+                       + G           +  +   ++        
Sbjct: 777  EDRIEVPD-------------------SSVKGYRGPEAYSHLDEDGIAPPEVYVSSNEVL 817

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              + +          E +  +   +   +    K  ++++       P   ++VKV +  
Sbjct: 818  IGKTSPPRFYTTLETERILKERRDASVAVRRGEKGIVDRVII--TESPEGNKLVKVRLRE 875

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  + GDK A RHG KG+V  +L  EDMPF +DG   DI++NP  +PSRM VGQ+ E+ 
Sbjct: 876  LRIPELGDKFASRHGQKGVVGMLLRQEDMPFTEDGIVPDIIVNPHALPSRMTVGQLLESI 935

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G+ +                                                
Sbjct: 936  AGKVGAATGQLVD----------------------------------------------- 948

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP F+G  EE +  +L        G+ ++Y G+TGE     + +G +Y  KL+
Sbjct: 949  ------ATP-FEGVGEEDLRKLLLKLGFRWDGKEVMYSGITGEKLVADIFIGIVYYQKLH 1001

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK++AR+ G   ++T+QP  G+S  GG RLGEME   + A+GA+ +L E L   SD
Sbjct: 1002 HMVADKIHARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGASALLYERLVESSD 1061

Query: 1321 -------DVVG-------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLE 1364
                   ++ G       +T      + G+     +   P +F +L++E+ ALG+   LE
Sbjct: 1062 KYVMYVCELCGLPAYLDAKTNKPRCPIHGDTGQFAKVVVPYAFKLLLQELMALGIYPKLE 1121

Query: 1365 NSR 1367
             S 
Sbjct: 1122 LSE 1124



 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 119/732 (16%), Positives = 219/732 (29%), Gaps = 125/732 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFV 77
           L   Q  S++ FL   +          E   +GL+   + +   +P I    G+  L + 
Sbjct: 37  LANHQIKSFNDFLDKRLPRIVEEFKVVETEIKGLKLVLEKIEVGWPRIKESDGSESLIY- 95

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R+ TYA PL +T  L V D    T             Y+G+LP+
Sbjct: 96  ----------PMEARLRNATYAAPLYLTATLYVDDEPYVTETF----------YIGELPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGR 171
           M K                         G F+I G +R+++SQ  L     I+   DK  
Sbjct: 136 MVKSKRCNLTRLKPSEYAKKFEDPQDFGGYFIINGSERVIISQEDLVTDRPIYDVGDKPS 195

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILS 230
                K +     I  +   + +E +   +I+V +     K+P   ++ ALG++++E   
Sbjct: 196 VKFLAKTI--STGIGYR-STLTVELNKDGVIYVTLSAMPVKIPFPIYMKALGLETDE--- 249

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKL-TSGLLK 286
                +V +   D          L+   +V+      +D   G+  +   + +     L+
Sbjct: 250 ----DVVKAVSDDPDIQKELLPSLIAANQVAITREDALDYIGGKVAVGQPRPVRIERALQ 305

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L    +  LG T+                 G+I     +      L+           +
Sbjct: 306 LLDRYFLPHLGTTTPDEKKQQEIRLKKALMLGQIVKGLVE------LQLGRRKPDDKDHV 359

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +     T   +  ++    + +    G +        +           
Sbjct: 360 GNKRVRLVGDLMTQLFRTVFKQFLQELRSQLEKYYARGRIPHIQT---IVRPDIITERVR 416

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-NLGNRRVR 465
                G             D   ++     +   +++  L   +   +  D +       
Sbjct: 417 QALATGNWVGGKTGVSQILDRTNYLSTLSYL--RRVVSSLSRTQPHFEARDLHPTQWGRL 474

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
              E  + Q  +GL++    + E  + VD   V  Q L N   V                
Sbjct: 475 CAVETPEGQ-NVGLVKNLALLAEITTGVDEREVE-QLLYNLGTVPVLKAREDGIRGAEVY 532

Query: 526 EE------HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-CPAETSEGH 578
                   H N+   +   R L   G+       A +    +     GRI  P    E  
Sbjct: 533 LNGRLIGIHPNAEELVATVRSLRRQGKISDEINIAHINGSVLVNCDGGRIRRPLLVVENG 592

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            + L   +    R     +         D      V YL A EEEN +IA          
Sbjct: 593 RLKLTKDIVERVRKGDLTW--------DDLVKMGVVEYLDADEEENAHIAVD-------- 636

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++  P  ++   AS+IP+LE++ S R      M +
Sbjct: 637 ---------------PRGDLSGYTHVEIIPSAILGAIASIIPYLEHNQSPRNQYEAAMAK 681

Query: 699 QAVPLLKAEAPF 710
           Q++ L ++   +
Sbjct: 682 QSLGLPQSNFLY 693


>gi|313620908|gb|EFR92087.1| DNA-directed RNA polymerase, beta subunit [Listeria innocua FSL
           S4-378]
 gi|313625350|gb|EFR95144.1| DNA-directed RNA polymerase, beta subunit [Listeria innocua FSL
           J1-023]
          Length = 212

 Score =  366 bits (940), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 95/230 (41%), Positives = 143/230 (62%), Gaps = 23/230 (10%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILS 230
             +IP++G W++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+ 
Sbjct: 163 STVIPNRGAWLEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIID 212


>gi|52538131|emb|CAH19169.1| RNA polymerase beta-subunit [Pseudomonas orientalis]
 gi|52538137|emb|CAH19172.1| RNA polymerase beta-subunit [Pseudomonas orientalis]
          Length = 376

 Score =  366 bits (940), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 225/376 (59%), Positives = 291/376 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITRDIP 866
           ARDTKLGPEEI    P
Sbjct: 361 ARDTKLGPEEIYCRHP 376


>gi|52694239|emb|CAG30649.1| DNA-directed RNA polymerase beta chain [Pseudomonas agarici]
          Length = 375

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 226/375 (60%), Positives = 290/375 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++++++    T+ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DEIVFLSAIEEADHVIAQASATMNDKKILTDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAPR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+
Sbjct: 241 GGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRS 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +A
Sbjct: 301 DIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVA 360

Query: 852 RDTKLGPEEITRDIP 866
           RDTKLGPEEI R  P
Sbjct: 361 RDTKLGPEEIFRGHP 375


>gi|224458654|gb|ACN43190.1| RpoB [Bacillus sp. PS-207]
 gi|224458660|gb|ACN43193.1| RpoB [Bacillus sp. PS-122]
          Length = 251

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 95/279 (34%), Positives = 149/279 (53%), Gaps = 30/279 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           +MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYET 158

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           D+KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 DAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL 218

Query: 256 VGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV 293
                      +  GE   +E+ K L        K   +
Sbjct: 219 ------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 251



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 62/174 (35%), Gaps = 1/174 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 79  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 138

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 139 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 197

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL
Sbjct: 198 NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 251


>gi|197311418|gb|ACH61915.1| RNA polymerase beta subunit [Mycoplasma gateae]
 gi|197311420|gb|ACH61916.1| RNA polymerase beta subunit [Mycoplasma gateae]
 gi|197311422|gb|ACH61917.1| RNA polymerase beta subunit [Mycoplasma gateae]
 gi|197311424|gb|ACH61918.1| RNA polymerase beta subunit [Mycoplasma gateae]
          Length = 664

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 237/517 (45%), Positives = 349/517 (67%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ R+GL+++E++ +ERIS+ +   + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQLRIGLIKLEKNTRERISTKETSKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA ++ YGFI++PY KV + KV  +   YL+A+EE     AQ+  ++ E+  
Sbjct: 123 GLILNLASFADIDKYGFIKSPYFKVENKKVDFSRPHYLTAIEEAGYTFAQSTVNI-ENDL 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ V  R   E + VP E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IVDKAVMVRRDNEYLQVPAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  E+P V TG+E+ +A+ S   I+AK  G+V  VDA  I I          ++  
Sbjct: 242 AVPVLFPESPLVATGVEADIARYSSTNIIAKYDGVVSYVDANVIKITRE------GSTKK 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVK+G EV+  D++ DGPS   G++ALG+N+LV F  WH
Sbjct: 296 DSYYLRTFERSNQGTLIHQVPLVKLGQEVKAGDLLVDGPSMKDGEMALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G+N+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +D+ 
Sbjct: 356 GFNYEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDDN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVRVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V V + +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAVEVLSREQGDTLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 317  LVKLGQEVKAGDLLVDGPS-MKDGEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDDNGIVRVGSEVSAGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 435  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSR--------- 483

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 484  EQGDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + I D   +  I  +           S
Sbjct: 544  VLNPQGVPSRMNIGQVLELHLGLAAKKLGTKFVTPIFDGITHNQIKDILEEANINSSGKS 603

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DG                           
Sbjct: 604  V----------------------------VYDG--------------------------R 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|93009660|gb|ABE98142.1| RNA polymerase beta subunit [Spiroplasma culicicola]
          Length = 602

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 230/448 (51%), Positives = 315/448 (70%), Gaps = 10/448 (2%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++L+++AR+N +GFIETPYRKV  GKV      YL+A  E++  +AQAN  + EDG+  +
Sbjct: 61  NNLSTYARINEFGFIETPYRKVKSGKVILGQYEYLTADREKDYIVAQANIQIAEDGTILD 120

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E V  R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVP
Sbjct: 121 ESVIARYRGDDIMAAPIDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVP 180

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L+  E+P VGTG+E   A+ SG A+VA   GIV+ VDA  I I          + G+  Y
Sbjct: 181 LINPESPIVGTGVEHEAARDSGDAVVATEDGIVKYVDAKLISI--------EGSKGIKNY 232

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L  F RSN  T +   P+VKVGD+V   DI+ADGPS + G+LALG+N++VAF  W+GYN
Sbjct: 233 DLNDFNRSNNGTALTHLPIVKVGDKVNARDILADGPSMEKGELALGQNVVVAFTTWNGYN 292

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GI+
Sbjct: 293 YEDAVIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITREIPNISEASKKHLDEEGIV 352

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +G EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  +
Sbjct: 353 AIGTEVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI 412

Query: 943 RIFNR-HGIDKNERSISVEREQIELLAR 969
           + F+R  G D     + + +  +    +
Sbjct: 413 KRFSRADGYDLPADILEIIKIYVVQKRK 440



 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 128/422 (30%), Positives = 184/422 (43%), Gaps = 73/422 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +VN  DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 251  IVKVGDKVNARDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E   +  G     
Sbjct: 306  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIPNISEASKKHLDEEGIVAIGTEVKV 360

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 361  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 414

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 415  FSRADGYDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 474

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 475  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGLKVNTPVFEGVKENELQEIMEEAGMTNY 534

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                   
Sbjct: 535  GKVTLV----------------------------DGRTGEAF------------------ 548

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
                    D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR GEM
Sbjct: 549  --------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFGEM 600

Query: 1298 EV 1299
            EV
Sbjct: 601  EV 602


>gi|302030858|gb|ADK91818.1| RNA polymerase beta subunit [Mycoplasma arginini]
          Length = 664

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 234/517 (45%), Positives = 349/517 (67%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ +ERIS+ +   + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQFRIGLIKLEKNTRERISTKETSKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA ++ YGFI++PY +V + KV  +   YL+A+EE     AQ+   + E+  
Sbjct: 123 GLILNLASFADIDKYGFIKSPYFRVVNKKVDFSKPYYLTAIEEAGYSFAQSTVKI-ENDE 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ V  R   E + VP  ++DF+  S +Q+ SI+AS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IVDDFVMVRRDNEYLEVPANEVDFVGVSNRQMTSISASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  EAP V TG+E+ +AK S   I+AK  G+V  VDA  I+++         ++  
Sbjct: 242 AVPVLFPEAPLVATGVEADIAKYSSTNIIAKFDGVVTYVDANVIIVKRE------GSNKK 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVK+  EV+  D++ DGPS   G++ALG+N+LV F  WH
Sbjct: 296 DHYYLRTFERSNQGTLIHQVPLVKLNQEVKAGDLLVDGPSMKNGEMALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G+N+ED++++SER+V ++V+TSIHIEE  +  R +K G + +T DIPNVS    + +DE 
Sbjct: 356 GFNYEDAVVLSERLVKDNVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDEN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVRVGSEVSAGDILVGRTSPKGEENPTPEEKLMGAIFGQKTASRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V V + +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAVEVLSREFGDTLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 179/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  EV  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 317  LVKLNQEVKAGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDNV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDENGIVRVGSEVSAGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L   F       
Sbjct: 435  SPKGEENPTPE--EKLMGAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSREF------- 485

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 486  --GDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +           S
Sbjct: 544  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILEEANINSSGKS 603

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DG                           
Sbjct: 604  V----------------------------VYDG--------------------------R 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|221124107|ref|XP_002161911.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 1371

 Score =  366 bits (939), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 232/1490 (15%), Positives = 431/1490 (28%), Gaps = 300/1490 (20%)

Query: 30   IEVQKASYDHFLMMNIAP-DERPNEGLQAAFKSVFP--ITAFSGA-AMLEFVSYEFDPPK 85
            ++ Q  +   F+  +I   +     GL  A K + P       G  A +  +      P 
Sbjct: 21   LDNQNKALQEFIQPHIESFNYILENGLNEAVKLIIPQEFELPDGRRAEISILDCSIGTPV 80

Query: 86   FD------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
             D              +C  R  TY   L +TL+  +  V + +  KSI  +        
Sbjct: 81   VDDNNFTSKTQRVYPAECRERHCTYKAKLTVTLQWKINGVLQGSVTKSIAQV-------- 132

Query: 134  DLPLMTKD------------------------GTFVIKGIQ---RIVVSQ-------LHR 159
              P+M K                         G F++ GI+   R++V Q       + R
Sbjct: 133  --PVMVKSKNCSLANLTPAQLIEKHEEAEEWGGYFIVNGIEKILRMLVMQRRNYPLAMVR 190

Query: 160  ----SPGIHFDH--------DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
                S G  F           K ++     L Y        G +       K+   V   
Sbjct: 191  KSWKSRGPLFTEFGVSIRSIQKDQSGNINVLHYLTD-----GSFTLSFIHQKEQFFV--- 242

Query: 208  RRRKVPVTSFLMAL--------------G-----------------------MDSEEILS 230
                 P+   L AL              G                       +   ++L 
Sbjct: 243  -----PLALILKALTANSDQYIYKQLLHGKEDDIFFKDVVVNMLRTLNDENLLSQNDVLK 297

Query: 231  TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
                +         W      A  M    V   L  I     ++    +    L      
Sbjct: 298  YMGMRFRIKVNLPEWTSDEDIAKYMFQTCVLVHLEKITDKFNLLIYMTQKLFALANDKCA 357

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGE-----TGEIYIEAGDVIDEKS-LEEIFHSEIRDI 344
                   +  + L G +    ++        TG I  ++G  + + + +  +        
Sbjct: 358  AESPDNPMNHEVLLGGHTYLLVLKQMESFLATGNILSKSGLGLMQATGMSVVADKLNFMR 417

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             + +   ++  A+      T   K   +A   +  V  P       +   +      ++ 
Sbjct: 418  YLSHFRCIHRGAFFTEMRTTTVRKLLPEAWGFLCPVHTPDGAPCGLLNH-LAAACKVENT 476

Query: 405  KYDLSTVGRVKMNMRLNLDTPD---------------DVRHIRKEDIIAIIKILVDLRNG 449
            KY  S + ++ + + + L   D                V  +R      + K L   +  
Sbjct: 477  KYPTSDLIKLLVKLGMQLCDMDLGLASDSYSVLLDGCVVGRLRSHISEEVCKKLRVFKAL 536

Query: 450  KGTIDDIDN--LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            +  +       +   R +   +         + RM R ++      +    +        
Sbjct: 537  QKEMVPPTMEIIFIPRTKFASQYEGIFLFTDVARMIRPVR--NLLTNTVEYIGSFEQVYM 594

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
             +     E    +           LS +      S   Q            R+++    G
Sbjct: 595  DIAVYSDEIHAPTTTHMELNDCAMLSELATLTPYSDFNQSP----------RNMYQCQMG 644

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            +           +G           N    I+TP   +   K  ++         +N  +
Sbjct: 645  K---------QTMGTPCQALKHRSDNKMYKIQTPQAPLVRNKTYSEYGV------DNFPL 689

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
               N+ +          +  R     I      + + +           S +   +    
Sbjct: 690  GT-NAVVAVISYTVRFQIMARRKELTIAERERILVYHE--------EGYSQVQIAKKMKI 740

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            +R  +   +QR     +        +G      K     I                 IRS
Sbjct: 741  SRCCVQRTLQRYHESGVHTSKN--RSGRPKKTNKLQDREIKNISLSNRRY---TAEKIRS 795

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            V  + +         +    Q         ++PL++  ++++R +      +  +     
Sbjct: 796  VYNNFNEIKISTSTVKNRLKQVGLHGRVAARKPLLRPVNKIKRLNWAKRHENWSMEQWKN 855

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                  +     G         S+R V    +      E  ++      G   +      
Sbjct: 856  VLWTDESKFELFG---------SKRRVFVRRYAGERYSEECLVPTVKHGGGSVMVWGCFG 906

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                GL +  E  +             + +   + +   + E             D + T
Sbjct: 907  GENVGLIHRIEGIMTKE----------IYREILEQQVLPSGERLFPDQYVFMHDNDPKHT 956

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
            S    S +     D++      I  +    S +   IELL  + D +      +    L 
Sbjct: 957  SKICKSYLE----DLQTQEVLKIM-DWPPQSPDLNPIELLWEELDRKVRETQPSSRESLW 1011

Query: 988  EILCGQNAVSGPKGF---KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
             +L  Q     P+     ++S+   S L+ +       +F    +        +  +Y+T
Sbjct: 1012 NMLEEQWNAIQPEILRSDEESSTFKSGLLGKDGLPPIGRFMQHGDPYYSYYHIINGEYKT 1071

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             K    +       KI   D     +L+ V + + ++R    GDK A RHG KGI+S   
Sbjct: 1072 VKYKHMEPAYIDDIKILGSDKGDRELLK-VSIKLRIQRNPIIGDKFASRHGQKGILSVKW 1130

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P E+MPF + G   DI+ NP G PSRM +G + E+  G +    G    S    +     
Sbjct: 1131 PAENMPFTESGMIPDIIFNPHGFPSRMTIGMMIESMAGKSAALHGITHDSTPFIFSEKKP 1190

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             +                                                    +  +L 
Sbjct: 1191 AAHY--------------------------------------------------MGEILV 1200

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A  +  G   +Y G+ G+  D  + +G +Y  +L HMV+DK   RSTG    +T QP+ 
Sbjct: 1201 KAGYNYYGNERMYSGINGKEMDVDIFIGIVYYQRLRHMVADKYQVRSTGPVDNLTHQPVQ 1260

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTR---VYESIVA--- 1334
            G+  +GG R GEME   + A+G+ ++L + L   SD     V   T+   ++  IV    
Sbjct: 1261 GRKRQGGIRFGEMERDALIAHGSGFLLHDRLFNCSDRCETHVC--TKCGSIFTPIVRKPV 1318

Query: 1335 ---------------------GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                                 G+D  +   P  F  L+ E+ A+  +I L
Sbjct: 1319 THHDSLIGFNDRKWFCRVCGHGDDIQKMLVPYVFKYLIAELTAM--NIRL 1366


>gi|186885813|gb|ACC93314.1| RNA polymerase beta subunit [Brachyclados caespitosus]
          Length = 798

 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 231/662 (34%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR+ +N RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRLNINRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEIYERSKRAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  + +  I
Sbjct: 544 KIIYTD--------TDKILLSGNGDTINIPLVMYQRSNKNTCMHQKPQVRRGKCITKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +  G +T  G+LALG+N+LVA+MPW GY+FED++LI+ER+V ED++TS HI ++E+    
Sbjct: 596 LGYGAATVGGELALGKNVLVAYMPWEGYHFEDAVLITERLVYEDIYTSFHIRKYEIQIHV 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T  GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR   +     ++    R   +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRGSSSKPERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLGRYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 35/128 (27%), Positives = 56/128 (43%), Gaps = 7/128 (5%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 678  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 737

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 738  GGRGRVIDVRWVQKK----RGSSSKP---ERIRVYILQKREIKVGDKVAGRHGNKGIISK 790

Query: 1103 ILPCEDMP 1110
            ILP +DMP
Sbjct: 791  ILPRQDMP 798


>gi|83755181|gb|ABC46439.1| RNA polymerase beta subunit [Spiroplasma taiwanense]
          Length = 594

 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 229/476 (48%), Positives = 332/476 (69%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV + +V   +  YL+A +E+   +A+AN  + EDG+  ++ V 
Sbjct: 61   TYAKINEYGFIETPYRKVRNKQVILGEYEYLTADKEKEYVVAEANIKMSEDGTILDDQVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVNPADVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA + GIV+ VD+ +I I   +        G+ IY L  
Sbjct: 181  ESPIVGTGVEFEAARDSGDAVVATQDGIVKYVDSKKITIEQKD--------GIKIYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FSRSNNGTAITHLPIVKIGDKVKARDILADGPSMENGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++DE GI+ +GA
Sbjct: 293  VIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITRDIPNISEASKKHLDEDGIVAIGA 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  +    + ++ +++         + +IL  ++      G
Sbjct: 413  RADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDG 468



 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 125/418 (29%), Positives = 185/418 (44%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V   DIL    +      +   + ++ A       +  D  +         V+
Sbjct: 247  IVKIGDKVKARDILADGPS-MENGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   +   +       L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITRDIPNISEASKKHLDEDGIVAIGAEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG KI + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGLKINTPVFEGVKEKELLEIMEEAGM--- 527

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                + +   + +                         G+    
Sbjct: 528  --------------------DNYGKVILI------------------------DGK---- 539

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
               TGEPFD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 540  ---TGEPFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|145592515|ref|YP_001154517.1| DNA-directed RNA polymerase subunit beta [Pyrobaculum arsenaticum DSM
            13514]
 gi|145284283|gb|ABP51865.1| DNA-directed RNA polymerase, subunit B' / DNA-directed RNA
            polymerase, subunit B' [Pyrobaculum arsenaticum DSM
            13514]
          Length = 1127

 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 122/607 (20%), Positives = 215/607 (35%), Gaps = 105/607 (17%)

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             VK G+     D +      +  D     N  +A  P    +    + I    +   + +
Sbjct: 603  RVKRGELT--WDDLLKMGVVEYLDADEEENAHIAVDPEGDLSNYTHVEIIPSSILGAIAS 660

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   E     R+               S      +D  G   +        +    +  
Sbjct: 661  IIPFLEHNQSPRNQYEAAMAKQSLGLPQSNFLY-KLDSRG--HMLYYPERPIVTTRGLEL 717

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
             G S     +  + A+      ++ D  +   + V   +    +F R    + +R    E
Sbjct: 718  VGYSKRPAGQNAVVALLTYTGYNIEDAVILNKASVERGMF-RSVFYRTYETEEQRYPGGE 776

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
             ++IE+                       + G           +  +   ++        
Sbjct: 777  EDKIEIPD-------------------SSVKGYRGPEAYSHLDEDGIAPPEVYVSSSEVL 817

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
              + +          E +  +   +   +    K  ++++       P   ++VKV +  
Sbjct: 818  IGKTSPPRFYTTLETERILKERRDASVAVRRGEKGIVDRVIV--TESPEGNKLVKVRLRE 875

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  + GDK A RHG KG+V  +L  EDMPF ++G   DI++NP  +PSRM V Q+ E+ 
Sbjct: 876  LRIPELGDKFASRHGQKGVVGMLLRQEDMPFTEEGIVPDIIVNPHALPSRMTVAQLLESM 935

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G  +                                                
Sbjct: 936  AGKVGAATGNLVD----------------------------------------------- 948

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP F+G  EE +  +L        G+ ++Y G+TGE     + +G +Y  KL+
Sbjct: 949  ------ATP-FEGVKEEDLRKLLLKLGYKWDGKEVMYSGITGEKLVADIFIGIVYYQKLH 1001

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK++AR+ G   ++T+QP  G+S  GG RLGEME   + A+GA+ +L E L   SD
Sbjct: 1002 HMVADKIHARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGASALLYERLVESSD 1061

Query: 1321 DVVGRTRVY------------------ESIVAGN--DTFETGTPESFNVLVKEMQALGLS 1360
                +  +Y                  +  + G+     +   P +F +L++E+ ALG+ 
Sbjct: 1062 ----KYTMYVCELCGLPAYLDAKSNKPKCPIHGDTGQFAKVTVPYAFKLLLQELIALGIY 1117

Query: 1361 IDLENSR 1367
              LE S 
Sbjct: 1118 PKLELSE 1124



 Score =  178 bits (451), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 133/653 (20%), Positives = 241/653 (36%), Gaps = 92/653 (14%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R+DAL  I   +  G      V  ++        D+Y L  +G    + +   +     
Sbjct: 278 TREDALDYIGGKVAVGQPRPVRVERAL-----QLLDRYFLPHLGTTVPDEKKQQEIRLK- 331

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              +   +  I+K LV+L+ G+   DD D++ N+RVR VG+++   +R    ++ + ++ 
Sbjct: 332 ---KALMLGQIVKGLVELQLGRRKPDDKDHVANKRVRLVGDLMTQLFRTVFKQLLQELRS 388

Query: 489 RISSVDIDSVMPQ---------DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           ++        +P               +  ++        + +SQ+ +  N LS +++ R
Sbjct: 389 QLEKYYARGRIPHLQTIVRPDIITERVRQALATGNWVGGKTGVSQILDRTNYLSTLSYLR 448

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+ +     ++R +   E RD+HPT +GR+C  ET EG N+GLV +L   A +       
Sbjct: 449 RVVS----SLSRTQPHFEARDLHPTQWGRLCAVETPEGQNVGLVKNLALLAEITTGVDEN 504

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVP 657
                V    +   VV +    EE    A+   N  L       EELV    +       
Sbjct: 505 D----VEQMLLQQGVVPILKAREEGVRGAEVYLNGRLIGIHPEPEELVKTVRSLRRQGKI 560

Query: 658 REKIDFIDASPKQVVSIAASLI--PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            ++I+    +    V+     I  P L  +D    L    ++R     L  +       +
Sbjct: 561 SDEINIAYLNGVVYVNSDGGRIRRPLLVVEDGKLKLTKDIVERVKRGELTWDDLLKMGVV 620

Query: 716 ESVVAKSSGAAIVAKRAGIVEQV--------DAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           E + A     A +A                  +I   I S+   L+ + S  + Y     
Sbjct: 621 EYLDADEEENAHIAVDPEGDLSNYTHVEIIPSSILGAIASIIPFLEHNQSPRNQYEAAMA 680

Query: 768 QRSN---------------QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           ++S                      +RP+V                         G+N +
Sbjct: 681 KQSLGLPQSNFLYKLDSRGHMLYYPERPIV----------TTRGLELVGYSKRPAGQNAV 730

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP------ 866
           VA + + GYN ED++++++  V   +F S+    +E   +    G EE   +IP      
Sbjct: 731 VALLTYTGYNIEDAVILNKASVERGMFRSVFYRTYETEEQRYPGG-EEDKIEIPDSSVKG 789

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
               E   ++DE GI      V+  ++L+GK +P         E++L+        + RD
Sbjct: 790 YRGPEAYSHLDEDGIAPPEVYVSSSEVLIGKTSPPRFYTTLETERILK--------ERRD 841

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            S+ V  G  G V              +R I  E  +   L + +  E  I +
Sbjct: 842 ASVAVRRGEKGIV--------------DRVIVTESPEGNKLVKVRLRELRIPE 880



 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 105/732 (14%), Positives = 211/732 (28%), Gaps = 125/732 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFV 77
           L   Q  S++ FL   +          +   +GL+   + +   +P I    G+  L + 
Sbjct: 37  LASHQIKSFNDFLDKKLPRIVEDFKVVDTEIKGLKLVLEKIEVGWPRIKESDGSESLIY- 95

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R+ TY+ PL +T  L V D    T             Y+G+LP+
Sbjct: 96  ----------PMEARLRNATYSAPLYLTAVLYVDDEPYATETF----------YIGELPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGR 171
           M K                         G F+I G +R+++SQ  L     I+   DK  
Sbjct: 136 MVKSKRCNLTRLRPSEYPKRFEDPQDFGGYFIINGSERVIISQEDLVADRPIYDKGDKPS 195

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILS 230
                K +     I  +   + +E +   +I+  +     K+P   ++ ALG++++E   
Sbjct: 196 VKFLAKTI--STGIGYR-STLTVELNKDGVIYATLSAIPVKIPFPIYMKALGLETDE--- 249

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKLT-SGLLK 286
                +V +   D          L+V  +++      +D   G+  +   + +     L+
Sbjct: 250 ----DVVKAVSDDPDIQKELLPSLVVANQIAITREDALDYIGGKVAVGQPRPVRVERALQ 305

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L    +  LG T                  G+I     +      L+           +
Sbjct: 306 LLDRYFLPHLGTTVPDEKKQQEIRLKKALMLGQIVKGLVE------LQLGRRKPDDKDHV 359

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +     T   +  ++    + +    G +        +           
Sbjct: 360 ANKRVRLVGDLMTQLFRTVFKQLLQELRSQLEKYYARGRIPHLQT---IVRPDIITERVR 416

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-NLGNRRVR 465
                G             D   ++     +   +++  L   +   +  D +       
Sbjct: 417 QALATGNWVGGKTGVSQILDRTNYLSTLSYL--RRVVSSLSRTQPHFEARDLHPTQWGRL 474

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS-- 523
              E  + Q    +  +    +      + D           P++ A  E    +++   
Sbjct: 475 CAVETPEGQNVGLVKNLALLAEITTGVDENDVEQMLLQQGVVPILKAREEGVRGAEVYLN 534

Query: 524 -----QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                   E    +  +   RR   +             +  V+        P    E  
Sbjct: 535 GRLIGIHPEPEELVKTVRSLRRQGKISDE--INIAYLNGVVYVNSDGGRIRRPLLVVEDG 592

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            + L   +    +     +         D      V YL A EEEN +IA          
Sbjct: 593 KLKLTKDIVERVKRGELTW--------DDLLKMGVVEYLDADEEENAHIAVD-------- 636

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++  P  ++   AS+IPFLE++ S R      M +
Sbjct: 637 ---------------PEGDLSNYTHVEIIPSSILGAIASIIPFLEHNQSPRNQYEAAMAK 681

Query: 699 QAVPLLKAEAPF 710
           Q++ L ++   +
Sbjct: 682 QSLGLPQSNFLY 693


>gi|197311416|gb|ACH61914.1| RNA polymerase beta subunit [Mycoplasma gateae]
          Length = 664

 Score =  365 bits (938), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 237/517 (45%), Positives = 349/517 (67%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ R+GL+++E++ +ERIS+ +   + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQLRIGLIKLEKNTRERISTKETSKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA ++ YGFI++PY KV + KV  +   YL+A+EE     AQ+  ++ E+  
Sbjct: 123 GLILNLASFADIDKYGFIKSPYFKVENKKVDFSRPHYLTAIEEAGYTFAQSTVNI-ENDL 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ V  R   E + VP E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IVDKAVMVRRDNEYLQVPAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  E+P V TG+E+ +A+ S   I+AK  G+V  VDA  I I          ++  
Sbjct: 242 AVPVLFPESPLVATGVEADIARYSSTNIIAKYDGVVSYVDANVIKITRE------GSTKK 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVK+G EV+  D++ DGPS   G++ALG+N+LV F  WH
Sbjct: 296 DSYYLRTFERSNQGTLIHQVPLVKLGQEVKAGDLLVDGPSMKDGEMALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G+N+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +D+ 
Sbjct: 356 GFNYEDALVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDDN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVRVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V V + +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAVEVLSREQGDTLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 317  LVKLGQEVKAGDLLVDGPS-MKDGEMALGKNVLVGFTTWHGFNYEDALVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDDNGIVRVGSEVSAGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 435  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSR--------- 483

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 484  EQGDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + I D   +  I  +           S
Sbjct: 544  VLNPQGVPSRMNIGQVLELHLGLAAKKLGTKFVTPIFDGITHNQIKDILEEANINSSGKS 603

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DG                           
Sbjct: 604  V----------------------------VYDG--------------------------R 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|325969565|ref|YP_004245757.1| DNA-directed RNA polymerase subunit beta [Vulcanisaeta moutnovskia
            768-28]
 gi|323708768|gb|ADY02255.1| DNA-directed RNA polymerase subunit beta [Vulcanisaeta moutnovskia
            768-28]
          Length = 1141

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 190/1134 (16%), Positives = 351/1134 (30%), Gaps = 208/1134 (18%)

Query: 258  AKVSSSLVDIDTGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             +V  S  D+   +   + G K   + + K +         +T +      +        
Sbjct: 185  ERVIVSQEDLAPNKPFFDKGDKASITNVAKVISIGAGYKTTVTVERHRDGIIYVTFPAIA 244

Query: 317  T---GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
            T     I + A  +  ++ +          + +     + N                 DA
Sbjct: 245  TRIPFPIIMRALGLETDEDI---------VLAVSDDPDIQNELLPSLQFSVQIASTIDDA 295

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L  I   +  G                   D+Y L  +G             ++ R  + 
Sbjct: 296  LDFIGSKVAIGQPREVR-----IERAKQVLDRYFLPHLG-----------ATEEARVKKA 339

Query: 434  EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
              +  ++K ++++  G+   DD D++ N+RVR VG++L   +R    ++ + I++++   
Sbjct: 340  LLVGQMVKGVIEMYLGRRQPDDKDHIANKRVRLVGDLLAQLFRAVFKQVLQDIRQQLER- 398

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                                                       H  R        + RA 
Sbjct: 399  -------------------------------------------HYSRGKIPSLVTLVRAD 415

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN- 612
               E          RI  A  +     G         R N    +    R V +   T  
Sbjct: 416  IITE----------RIRHALATGNWIGGRTGVSQMLDRTNVLSTLSHLRRIVSNLSRTQP 465

Query: 613  --DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              +   L   +            L    +   +          +      ++  +     
Sbjct: 466  HFEARDLHPTQ---------WGRLCAIETPEGQNCGLVKNLALLSTITVGVNENEVEKML 516

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
                   ++P L+            +  + + +       VGT  E             +
Sbjct: 517  YDL---GVVPILKARKEGVKGTEVYLNGRLIGIHTEPEKLVGTVREMR-----------R 562

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            R  I  +++  RI    ++        G     L+  +             ++ G+    
Sbjct: 563  RGQISHEINIARIQNEYLDELRVNCDGGRLRRPLLIIEDGKPRLKPEHIERLRKGEWSWS 622

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            + I         GD     N LVA  P    +    M I   ++   V + I   E    
Sbjct: 623  DLISNGIIEYLDGD--EEENALVAINPEEDMSKYTHMEIIPSVMIGAVASVIPYAEHNQS 680

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R+               +    +  D  G   +        ++   +   G       +
Sbjct: 681  PRNIYEAAMAKQSLGFPAANYRFRM-DSRG--HLLIYPERPLVITRGMELNGYLGRPAGQ 737

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + A+      ++ D  +   S +    +   +F R    +  R    E ++IE+ + +
Sbjct: 738  NAVVALLTYTGYNMEDAVILNRSSIERG-MYRSVFFRTYETEQMRYPGGEEDRIEIPSAE 796

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
                               + G           +  ++S ++       +         +
Sbjct: 797  -------------------VRGYKGPEAYAHLDEDGIVSPEVF--VSGGEVLIGKTSPPR 835

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                     V      S +  R   K               ++VKV V   R  + GDK 
Sbjct: 836  FYGVYTEAVVSSARRDSSITVRRGEKGIVDSVVITETNEGYKLVKVKVRELRIPELGDKF 895

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG++  ++P +DMPF +DG   DI++NP  +PSRM VGQ+ E+  G      G 
Sbjct: 896  ASRHGQKGVMGMMIPMQDMPFTEDGITPDIIVNPHALPSRMTVGQLLESMAGKVAALRGL 955

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
             I                                                      +TP 
Sbjct: 956  TID-----------------------------------------------------ATP- 961

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F+G  EE +  +L  +     G+ ++Y GLTG   +  + +G +Y  KL+HMV+DK++AR
Sbjct: 962  FEGVTEEELRDLLIRSGFRWDGKEVMYSGLTGRKLEADIFIGVVYYQKLHHMVADKIHAR 1021

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DV 1322
            + G   ++T+QP  G+S  GG RLGEME   + A+GAA +L+E L   SD        D 
Sbjct: 1022 ARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGAAALLKERLVESSDKYVMYVCED- 1080

Query: 1323 VGRTRVYES-------IVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             G    Y++        + G+         P +F +L+ E+ +LG+   +E   
Sbjct: 1081 CGMIAWYDANKGKPVCPIHGDKGRIVRIVVPYAFKLLLHELMSLGIYPRIEAGD 1134



 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 115/730 (15%), Positives = 226/730 (30%), Gaps = 124/730 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+  Q  S++ F+             LQ        I        ++    E   P+   
Sbjct: 50  LVRHQIDSFNDFVEKK----------LQEVVNENSLIETEVKGLYIKLERIEVGKPRVRE 99

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R+LTYA PL +T+ L V D          +++  Q +Y+GDLP+M
Sbjct: 100 ADASEHILYPMEARLRNLTYAAPLYLTMVLYVND----------EEVDRQKVYIGDLPIM 149

Query: 139 ------------------------TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+I G +R++VSQ   +P   F     +AS+
Sbjct: 150 IKSKFCNLYGLKRQELISKLEDPDDPGGYFIINGSERVIVSQEDLAPNKPFFDKGDKASI 209

Query: 175 SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRID--RRRKVPVTSFLMALGMDSEEI 228
           +       ++I      +   + +E     II+V       R +P    + ALG++++E 
Sbjct: 210 TN----VAKVISIGAGYK-TTVTVERHRDGIIYVTFPAIATR-IPFPIIMRALGLETDE- 262

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS---SLVDIDTGEQVIESGKKLTSGLL 285
                  IV +   D          L    +++S     +D    +  I   +++     
Sbjct: 263 ------DIVLAVSDDPDIQNELLPSLQFSVQIASTIDDALDFIGSKVAIGQPREVRIERA 316

Query: 286 KS-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIR 342
           K  L    +  LG T +      +    +     E+Y+      D+  +  + +      
Sbjct: 317 KQVLDRYFLPHLGATEEARVKKALLVGQMVKGVIEMYLGRRQPDDKDHIANKRVRLVGDL 376

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              +           IR  L    ++ +  +L+ + R     D+ T  +  ++    +  
Sbjct: 377 LAQLFRAVFKQVLQDIRQQLERHYSRGKIPSLVTLVR----ADIITERIRHALATGNWIG 432

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGN 461
                   + R  +   L+      V ++ +       + L   + G+   I+  +    
Sbjct: 433 GRTGVSQMLDRTNVLSTLSHLRRI-VSNLSRTQPHFEARDLHPTQWGRLCAIETPEGQNC 491

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             V+++  +      +    +E+ + +         V+P      + V            
Sbjct: 492 GLVKNLALLSTITVGVNENEVEKMLYDL-------GVVPILKARKEGVKGTEVYLNGRLI 544

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-CPAETSEGHNI 580
               E      +     RR     +  +AR +             GR+  P    E    
Sbjct: 545 GIHTEPEKLVGTVREMRRRGQISHEINIARIQNEYLDELRVNCDGGRLRRPLLIIEDGKP 604

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            L        R   + +         D      + YL   EEEN  +A            
Sbjct: 605 RLKPEHIERLRKGEWSW--------SDLISNGIIEYLDGDEEENALVAINPEE------- 649

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                              K   ++  P  ++   AS+IP+ E++ S R +    M +Q+
Sbjct: 650 ----------------DMSKYTHMEIIPSVMIGAVASVIPYAEHNQSPRNIYEAAMAKQS 693

Query: 701 VPLLKAEAPF 710
           +    A   F
Sbjct: 694 LGFPAANYRF 703


>gi|186898005|gb|ACC93944.1| RNA polymerase beta subunit [Spiroplasma penaei]
          Length = 490

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 230/465 (49%), Positives = 326/465 (70%), Gaps = 8/465 (1%)

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            + RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L ++A++NA+G
Sbjct: 1    NKRRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLATYAKINAFG 60

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            FIETPYR+V D KVT +  YL+A +E+N  +AQAN  L + G   +E V  R  GE I+ 
Sbjct: 61   FIETPYRRVIDCKVTAENDYLTADQEKNYVVAQANIRLSDKGEILDEQVVARFQGENIIA 120

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+   +P+VGTG+E
Sbjct: 121  TRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLISPNSPYVGTGVE 180

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
               A+ SG AIV++  G V+ VDA RIV+++ E        G+  Y L  F RSNQ T +
Sbjct: 181  YAAARDSGLAIVSQYDGSVDYVDATRIVLKTKE--------GLKNYNLDTFVRSNQGTSL 232

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
               PLVK G +V +  ++ADGPS D G+LALG+N++VAF  W+GYN+ED++++SER+VSE
Sbjct: 233  THVPLVKHGQKVEKGQVLADGPSIDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSE 292

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            DVFTSIHIEE+ +  R TK G EEITR+IPN+S+   K +D+ G++ +G EV PGDILVG
Sbjct: 293  DVFTSIHIEEYTIERRQTKQGSEEITREIPNISQNARKFLDDDGLVIIGTEVKPGDILVG 352

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R   + +   
Sbjct: 353  KVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYELSADV 412

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            + V +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  LEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDG 457



 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 124/268 (46%), Gaps = 14/268 (5%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 237  LVKHGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 295

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 296  TSIHIEEYTIERRQTKQGSEEITREIPNISQNARKFLDDDGL------VIIGTEVKPGDI 349

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 350  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 407

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 408  -----LSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 462

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            +LNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 463  MLNPLGVPSRMNIGQVLEIHLGMAAKKL 490


>gi|307595330|ref|YP_003901647.1| DNA-directed RNA polymerase subunit B [Vulcanisaeta distributa DSM
            14429]
 gi|307550531|gb|ADN50596.1| DNA-directed RNA polymerase subunit B [Vulcanisaeta distributa DSM
            14429]
          Length = 1141

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 193/1139 (16%), Positives = 352/1139 (30%), Gaps = 218/1139 (19%)

Query: 258  AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             +V  S  D+   +   + G K +   +  +   G            G      +     
Sbjct: 185  ERVIVSQEDLAPNKPFYDKGDKASITHVAKVISIG-----------AGYKTTVTVERHRD 233

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN------TLVTDKNKDRK 371
            G IY+    +        I  +   +     V +V+++  I+N                 
Sbjct: 234  GIIYVTFPAIATRIPFPIIMRALGLETDEDIVLAVSDDPDIQNELLPSLQFSVQIASTVD 293

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            DAL  I   +  G                   D+Y L  +G           T +D R  
Sbjct: 294  DALDFIGSKVAIGQPREVR-----IERAKQVLDRYFLPHLG-----------TTEDARIK 337

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  ++K ++++  G+   DD D++ N+RVR VG+++   +R    ++ + I++++ 
Sbjct: 338  KALMVGQMVKGVIEMYLGRRQPDDKDHIANKRVRLVGDLMAQLFRAVFRQVLQDIRQQLE 397

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
                                                         H  R        + R
Sbjct: 398  R--------------------------------------------HYSRGKIPSLVTLVR 413

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            A    E          R+  A  +     G         R N    +    R V +   T
Sbjct: 414  ADIITE----------RVRHAIATGNWIGGRTGVSQMLDRTNIMSTLSHLRRVVSNLSRT 463

Query: 612  N---DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                +   L   +            L    +   +          +      +D  +   
Sbjct: 464  QPHFEARDLHPTQ---------WGRLCAIETPEGQNCGLVKNLALLSTITVGVDENEVEK 514

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
                     ++P L             +  + + +       V T  E            
Sbjct: 515  LLYDL---GVVPILRARKEGVKGTEVYLNGRLIGVHTEPDKLVSTIREMR---------- 561

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
             +R  I  +++  RI    ++        G     L+  +             ++ G+  
Sbjct: 562  -RRGQINHEINVARIRNEYLDEVRVNCDGGRLRRPLIIIENGKPKLRPEHVEKLRKGEWT 620

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
              + I         GD     N LVA  P    +    M +   ++   V + I   E  
Sbjct: 621  WSDLISNGIIEYLDGD--EEENALVAINPEEDMSKYTHMEVIPSVMIGAVASIIPYAEHN 678

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
               R+               +    +  D  G   +        ++   I   G      
Sbjct: 679  QSPRNIYEAAMAKQSLGFPAANYRFRM-DSRG--HLLIYPERPLVITRGIELNGYLERPA 735

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      ++ D  +   S +    +   +F R    +  R    E ++IE+ +
Sbjct: 736  GQNAVVALLTYTGYNMEDAVILNKSAIERG-MYRSVFFRTYETEQMRYPGGEEDRIEIPS 794

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
             +                   + G           +  ++S ++       +        
Sbjct: 795  AE-------------------VRGYKGPEAYAHLDEDGIVSPEVF--VSGGEVLIGKTSP 833

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
             +         V      S +  R   K               ++VKV V   R  + GD
Sbjct: 834  PRFYGVYTETVVSSARRDSSITVRRGEKGIVDSVVVTETNEGYKLVKVKVRELRIPELGD 893

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG++  ++P +DMPF +DG   DI++NP  +PSRM VGQ+ E+  G      
Sbjct: 894  KFASRHGQKGVMGMMIPMQDMPFTEDGITPDIIVNPHALPSRMTVGQLLESMAGKVAALR 953

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  I                                                      +T
Sbjct: 954  GVMID-----------------------------------------------------AT 960

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F+G  EE +  +L  +     G+ ++Y GLTG   +  + +G +Y  KL+HMV+DK++
Sbjct: 961  P-FEGVTEEELRDLLIRSGFRWDGKEVMYSGLTGRKLEADIFIGVVYYQKLHHMVADKIH 1019

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            AR+ G   ++T+QP  G+S  GG RLGEME   + A+GAA +L+E L   SD    R  +
Sbjct: 1020 ARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGAAALLRERLVESSD----RYVM 1075

Query: 1329 Y------------------ESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            Y                     + G+         P +F +L++E+ +LG+   +E   
Sbjct: 1076 YVCEDCGMIAWYDSNKGKPVCPIHGDKGRIVRVVVPYAFKLLLQELMSLGIYPRIEAGD 1134



 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 114/729 (15%), Positives = 227/729 (31%), Gaps = 122/729 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+  Q  S++ F+             LQ        I        ++    E   P+   
Sbjct: 50  LVRHQIDSFNDFVEKK----------LQEIVNENNIIETEVKGLYIKLERIEVGKPRVRE 99

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R+LTYA PL +T+ L V D          +++  Q +Y+GDLP+M
Sbjct: 100 ADASEHILYPMEARLRNLTYAAPLYLTMVLYVND----------EEVDRQKVYIGDLPIM 149

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+I G +R++VSQ   +P   F     +AS+
Sbjct: 150 VRSKFCNLYGLKRQELISKLEDPDDPGGYFIINGSERVIVSQEDLAPNKPFYDKGDKASI 209

Query: 175 SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRID--RRRKVPVTSFLMALGMDSEEI 228
           +    +  ++I      +   + +E     II+V       R +P    + ALG++++E 
Sbjct: 210 T----HVAKVISIGAGYK-TTVTVERHRDGIIYVTFPAIATR-IPFPIIMRALGLETDE- 262

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS---SLVDIDTGEQVIESGKKLTSGLL 285
                  IV +   D          L    +++S     +D    +  I   +++     
Sbjct: 263 ------DIVLAVSDDPDIQNELLPSLQFSVQIASTVDDALDFIGSKVAIGQPREVRIERA 316

Query: 286 KS-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIR 342
           K  L    +  LG T D      +    +     E+Y+      D+  +  + +      
Sbjct: 317 KQVLDRYFLPHLGTTEDARIKKALMVGQMVKGVIEMYLGRRQPDDKDHIANKRVRLVGDL 376

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              +           IR  L    ++ +  +L+ + R     D+ T  V  ++    +  
Sbjct: 377 MAQLFRAVFRQVLQDIRQQLERHYSRGKIPSLVTLVR----ADIITERVRHAIATGNWIG 432

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGN 461
                   + R  +   L+      V ++ +       + L   + G+   I+  +    
Sbjct: 433 GRTGVSQMLDRTNIMSTLSHLRRV-VSNLSRTQPHFEARDLHPTQWGRLCAIETPEGQNC 491

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             V+++  +      +    +E+ + +      + +         K  V     +     
Sbjct: 492 GLVKNLALLSTITVGVDENEVEKLLYDLGVVPILRA--------RKEGVKGTEVYLNGRL 543

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    E    +S I   RR        +        +R+ +       C         I 
Sbjct: 544 IGVHTEPDKLVSTIREMRRRG-----QINHEINVARIRNEYLDEVRVNCDGGRLRRPLII 598

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           + +      R      +        D      + YL   EEEN  +A             
Sbjct: 599 IENGKPKL-RPEHVEKLRKGEWTWSDLISNGIIEYLDGDEEENALVAINPEE-------- 649

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                             K   ++  P  ++   AS+IP+ E++ S R +    M +Q++
Sbjct: 650 ---------------DMSKYTHMEVIPSVMIGAVASIIPYAEHNQSPRNIYEAAMAKQSL 694

Query: 702 PLLKAEAPF 710
               A   F
Sbjct: 695 GFPAANYRF 703


>gi|52538163|emb|CAH19183.1| RNA polymerase beta-subunit [Pseudomonas gessardii]
          Length = 378

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 224/376 (59%), Positives = 289/376 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITRDIP 866
           ARDTKLGPEEI    P
Sbjct: 361 ARDTKLGPEEIYCRHP 376


>gi|52694201|emb|CAG30630.1| DNA-directed RNA polymerase beta chain [Pseudomonas azotoformans]
          Length = 374

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 225/374 (60%), Positives = 291/374 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D 
Sbjct: 121 DALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQE 360

Query: 847 FEVMARDTKLGPEE 860
              +ARDTKLGPEE
Sbjct: 361 LTCVARDTKLGPEE 374


>gi|207081360|gb|ACI22948.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 379

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 228/376 (60%), Positives = 295/376 (78%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +
Sbjct: 121 VKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 181 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  
Sbjct: 241 VCVVARRGGVIDSVDASRIVVRVADDEVEPVEAGVDIYNLTKYTRSNQNTCINQRPLVSK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI
Sbjct: 301 GDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHI 360

Query: 845 EEFEVMARDTKLGPEE 860
           +E   +ARDTKLGPEE
Sbjct: 361 QELTCVARDTKLGPEE 376


>gi|52694311|emb|CAG37995.1| RNA polymerase beta subunit [Pseudomonas sp. LMG 13978]
          Length = 378

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 226/377 (59%), Positives = 295/377 (78%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+ KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAGKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  
Sbjct: 121 VVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 KGDKVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIH 360

Query: 844 IEEFEVMARDTKLGPEE 860
           I+E   +ARDTKLGPEE
Sbjct: 361 IQELTCVARDTKLGPEE 377


>gi|52694159|emb|CAG30609.1| DNA-directed RNA polymerase beta chain [Pseudomonas caricapapayae]
          Length = 382

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 228/382 (59%), Positives = 296/382 (77%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     + 
Sbjct: 121 RVVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V E  FT+I
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEARFTTI 360

Query: 843 HIEEFEVMARDTKLGPEEITRD 864
           HI+E   +ARDTKLGPEEIT D
Sbjct: 361 HIQELTCVARDTKLGPEEITAD 382


>gi|18312085|ref|NP_558752.1| DNA-directed RNA polymerase subunit B [Pyrobaculum aerophilum str.
            IM2]
 gi|18159514|gb|AAL62934.1| DNA-directed RNA polymerase subunit B (rpoB) [Pyrobaculum aerophilum
            str. IM2]
          Length = 1127

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 125/606 (20%), Positives = 215/606 (35%), Gaps = 105/606 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD     D +      +  D     N  +A  P         + I    +   + + 
Sbjct: 604  VKRGDLT--WDDLVKMGVVEYLDADEEENAHIATDPRGNLTNYTHVEIIPSSILGAIASI 661

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R+               S      +D  G   +        +    +   
Sbjct: 662  IPYIEHNQSPRNQYEAAMAKQSLGLPQSNFLY-KLDSRG--HMLYYPERPIVTTRGLELI 718

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G S     +  + A+      ++ D  +   + V   +    +F R    + ++    E 
Sbjct: 719  GYSKRPAGQNAVVALLTYTGYNIEDAVILNKASVERGMF-RSVFYRTYETEEQKYPGGEE 777

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++IE+                       + G           +  +   ++         
Sbjct: 778  DRIEIPD-------------------SSVKGYRGPEAYSHLDEDGIAPPEVYVSSNEVLI 818

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + +          E +  +   +   +    K  ++K+       P   ++VKV +   
Sbjct: 819  GKTSPPRFYTTLEAERILKERRDASVAVRRGEKGIVDKVII--TESPEGNKLVKVRLREL 876

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  +L  EDMPF +DG   DI++NP  +PSRM V Q+ E+  
Sbjct: 877  RVPELGDKFASRHGQKGVVGMLLRQEDMPFTEDGIVPDIIVNPHALPSRMTVAQLLESIA 936

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+ I                                                 
Sbjct: 937  GKLGASTGQLID------------------------------------------------ 948

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +TP F+G  EE +  +L        G+ ++Y G+TGE     + +G +Y  KL+H
Sbjct: 949  -----ATP-FEGVKEEDLRKLLLKLGYKWDGKEVMYSGITGERLVADIFIGIVYYQKLHH 1002

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+DK++AR+ G   ++T+QP  G+S  GG RLGEME   + A+GA+ +L E L   SD 
Sbjct: 1003 MVADKIHARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGASALLHERLVESSD- 1061

Query: 1322 VVGRTRVY------------------ESIVAGN--DTFETGTPESFNVLVKEMQALGLSI 1361
               +  +Y                  +  + G+     +   P +F +L++E+ ALG+  
Sbjct: 1062 ---KYVMYVCELCGLPAYLDAKSNKPKCPIHGDTGQFAKVVVPYAFKLLLQELIALGIYP 1118

Query: 1362 DLENSR 1367
             LE S 
Sbjct: 1119 KLELSE 1124



 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 103/725 (14%), Positives = 207/725 (28%), Gaps = 111/725 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFV 77
           L   Q  S++ FL   +          E   +GL+   + +   +P I    G+  L + 
Sbjct: 37  LANHQIKSFNDFLDKKLPKIVEDFKVVETEIKGLKLVLEKIEVGWPRIKESDGSESLIY- 95

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R+ TY+ PL +T  L V D    T             Y+G+LP+
Sbjct: 96  ----------PMEARLRNATYSAPLYLTATLYVDDEPYATETF----------YIGELPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGR 171
           M K                         G F+I G +R+++SQ  L     I+   DK  
Sbjct: 136 MVKSKRCNLTRLRPSEYAKRFEDPQDFGGYFIINGSERVIISQEDLVADRPIYDKGDKPS 195

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILS 230
                K +     I  +   + +E +   +I+  +     K+P   ++ ALG++++E   
Sbjct: 196 VRFLAKTI--STGIGYR-STLTVELNKDGVIYATLSAMPVKIPFPIYMKALGLETDE--- 249

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKL-TSGLLK 286
                +V +   D          L+   +++      +D   G+  +   + +     L+
Sbjct: 250 ----DVVKAVSDDPEIQKELLPSLIAANQIAITREDALDYIGGKVAVGQPRPVRIERALQ 305

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L    +  LG T                  G+I     +      L            +
Sbjct: 306 LLDRYFLPHLGTTVPDEKKQQEIRLKKALMLGQIVKGLVE------LHLGRRKPDDKDHV 359

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +     T   +  ++    + +    G +        +           
Sbjct: 360 GNKRVRLVGDLMTQLFRTVLKQFLQELKSQLEKYYARGRIPHIQT---IVRPDIITERVR 416

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-NLGNRRVR 465
                G             D   ++     +   +++  L   +   +  D +       
Sbjct: 417 QALATGNWVGGKTGVSQILDRTNYLSTLSYL--RRVVSSLSRTQPHFEARDLHPTQWGRL 474

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
              E  + Q  +GL++    + E  + VD +  +   L N   +          S     
Sbjct: 475 CAVETPEGQ-NVGLVKNLALLAEITTGVD-EGEVEHMLYNMGVIPILKAREEGVSGAEVY 532

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                             +         +      V        C         + + + 
Sbjct: 533 LNGRLIGVHPNPEELAKTVRGLRRQGKISDEINIAVINGTVYVNCDGGRIRRPLLVVENG 592

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
                R      ++       D      V YL A EEEN +IA                 
Sbjct: 593 KLKLTR-EIVEKVKRGDLTWDDLVKMGVVEYLDADEEENAHIAT---------------- 635

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                  +          ++  P  ++   AS+IP++E++ S R      M +Q++ L +
Sbjct: 636 -------DPRGNLTNYTHVEIIPSSILGAIASIIPYIEHNQSPRNQYEAAMAKQSLGLPQ 688

Query: 706 AEAPF 710
           +   +
Sbjct: 689 SNFLY 693


>gi|222093441|gb|ACM43497.1| RNA polymerase beta subunit [Mycoplasma alvi]
          Length = 761

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 240/533 (45%), Positives = 347/533 (65%), Gaps = 31/533 (5%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS---------------------VM 499
           N+R++ + E+L  + + G+ RMER I+E+++  D  +                     + 
Sbjct: 1   NKRLKLINELLYGRVQTGMARMERYIREKLAIADGSNKNVEINEETGELVETDKQKTRLT 60

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            + ++N+KP    + +FF + QL+Q  +  N LS +T+ RR+SA+G GG++R    +++R
Sbjct: 61  IKSVVNSKPFQIVIRDFFNTHQLTQFLDQQNPLSELTNKRRISAMGPGGISREDPNLDIR 120

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVH +HYGRICP ET EG NIGL+ SL  +A +++ GF+ +PYRKV +GK+T++V YL+A
Sbjct: 121 DVHYSHYGRICPIETPEGMNIGLIMSLAFYATIDSNGFLMSPYRKVKNGKITDEVEYLTA 180

Query: 620 MEEENRYIAQ--ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           + E+   IA+  A+  +  DG   E+ V  R    + L   ++ID+ID +P+QVVSIAAS
Sbjct: 181 LREDEYIIAESSASMKIHADGLINEKEVIARYRSSQELYEPKRIDYIDVAPRQVVSIAAS 240

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLENDDS R LMG NMQRQA PLLK  AP VGTG+E  +A  SG AI+A   G +  
Sbjct: 241 LIPFLENDDSARALMGANMQRQATPLLKPYAPTVGTGVEYKIAHDSGMAIIANNDGKIVN 300

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           V   ++V+++ +G L         Y L KF++SNQNTC N  P+V +   ++  +++ADG
Sbjct: 301 VSNDKVVVQNNDGKLQ-------TYALTKFEKSNQNTCYNHSPIVSINQNIKAGEVLADG 353

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           PS   G+LALG+N+LVAF  W GYN+ED++++SER+  EDV+TSI I E+ V    T+ G
Sbjct: 354 PSMKNGELALGQNVLVAFTTWRGYNYEDAIIVSERLFREDVYTSITINEYTVQCVRTRNG 413

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITRDIPNVSE   + +DE GII VGAEV  GDILVGKI+PKG+  ++ EEKLL+AIF
Sbjct: 414 DEEITRDIPNVSESAKRYLDEDGIIMVGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIF 473

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFN-RHGIDKNERSISVEREQIELLAR 969
           GEK  ++R++SL+VP+G  GTV  VR FN     + ++  I + +  I    +
Sbjct: 474 GEKTKNIRESSLKVPNGGEGTVAAVRRFNIAKNDELDDDVIELVKVYIAQKRK 526



 Score =  344 bits (883), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 141/472 (29%), Positives = 207/472 (43%), Gaps = 48/472 (10%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +                +   I+ +   +  G++L    + K       +  L
Sbjct: 309  QNNDGKLQTYALTKFEKSNQNTCYNHSPIVSINQNIKAGEVLADGPSMKNGELALGQNVL 368

Query: 913  L-----RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIEL 966
            +     R    E A+ V +   R     S T+ +  +   R      E +  +    +  
Sbjct: 369  VAFTTWRGYNYEDAIIVSERLFREDVYTSITINEYTVQCVRTRNGDEEITRDI--PNVSE 426

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
             A+   DE  I+      +  +IL G+ +  G         L   +  E  +        
Sbjct: 427  SAKRYLDEDGIIMVGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIFGEKTK----NIRE 482

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
               KV    E                       I   D++   V+ +VKV++A KR IQ 
Sbjct: 483  SSLKVPNGGEGTVAAVR-------------RFNIAKNDELDDDVIELVKVYIAQKRKIQI 529

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK+AGRHGNKGIVS+I+P EDMP L+DGTPVDI+LNPLGVPSRMN+GQIFE HLG A  
Sbjct: 530  GDKVAGRHGNKGIVSKIVPIEDMPHLEDGTPVDIMLNPLGVPSRMNIGQIFEIHLGLAAR 589

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS---- 1202
             L KK                    L   I         ++  +  +  + +  K     
Sbjct: 590  ELAKKELIESVFVPNGDKYISDLFGLNLPIAKSLINTFKTNLKERKITNLEDAKKQVKTI 649

Query: 1203 ----------------GVPVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGE 1243
                               ++TPVF+G +   +  +++ A++D S   G+  L DG TGE
Sbjct: 650  DIDITLRQMGLSYDDLAYKIATPVFEGVNMGDLKEIMKEANIDTSKNFGKFKLIDGRTGE 709

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            PF++P+T+G +YMLKL+HMV DK+++R+ G YS +TQQPLGGKS  GGQR G
Sbjct: 710  PFEKPITIGVMYMLKLHHMVDDKIHSRAVGPYSKITQQPLGGKSQNGGQRFG 761


>gi|170784777|ref|YP_001718693.1| RNA polymerase beta subunit [Trachelium caeruleum]
 gi|156598804|gb|ABU85655.1| RNA polymerase beta subunit [Trachelium caeruleum]
 gi|157267525|gb|ABV26518.1| RNA polymerase beta subunit [Trachelium caeruleum]
          Length = 1070

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 159/579 (27%), Positives = 250/579 (43%), Gaps = 56/579 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +    ++        I         +  G  
Sbjct: 544  MSSNMQRQAVPLSRSEKCIVGTGLEGQVALDSGALALAQHEGKIIYTDTDKIFFSGNGDT 603

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          I +   +  G  +  G IL       G   +   + +L A    
Sbjct: 604  LSLPLVMYQRSNKNTCIHQKPQVQRGKCIKKGQILASGTATVG-GELALGKNVLVAYMPW 662

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     +S  +V   I+    I K E    +  E  E +  +    +  L 
Sbjct: 663  EGYNFEDAVL-----ISERLVYEDIYTSFHIRKYEIQTYMTSEGPERVTNEIPHLEAYLL 717

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            RN+  +   ++ G     G     K T    +  +  P  +  +  +  E        LK
Sbjct: 718  RNL-DKNGIVMLGSWVEEGDILVGKLTPQMVNESAYAPEDRLLRAILGIEVSTSKETCLK 776

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K      G    P     ++V+++ KR I+ GDK+AGRHGNKGI
Sbjct: 777  LPIGGRGRVIDVRWIQKR----VGSSYNP---ETIRVYISQKREIKVGDKVAGRHGNKGI 829

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D 
Sbjct: 830  ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIGPFDE 889

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E        +                           VF+       
Sbjct: 890  RYEQEASRKLVFSELYEAGKQTSNPW------------------------VFE------- 918

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S ++DG TG+PF +PV +G  Y+LKL H V DK++ RS+G Y+LVT
Sbjct: 919  --------PEYPGKSKIFDGRTGDPFQQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVT 970

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            QQPL G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    
Sbjct: 971  QQPLRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKARQEVLGTTIIGGTIL 1030

Query: 1340 ET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                 PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1031 NPEDAPESFRLLVRELRSLALELNHFLISEKNFQINRKE 1069



 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 227/634 (35%), Positives = 362/634 (57%), Gaps = 19/634 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N    +K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNDKEKNKIGSKENAILEFYKKFTGVGGDPIFSEYLYKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            + +L  +GR  MN RLNL  P +   +   DI+A +  L++++ G G +DD+++L N+R
Sbjct: 254 QRCELGRIGRQNMNRRLNLAIPQNNTFLLPRDILAAVDGLIEMKFGMGRLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP--QDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L+R+E+ ++  I       + P  Q+L+ +  + +    FF    
Sbjct: 314 IRSVADLLQDQFGLALVRLEKVVRSTICGALRHKLRPRPQNLVTSPLLTTTYDSFFGLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+G
Sbjct: 374 LSQVLDQTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SLT   R+  +G +E+P+ ++        ++YLS  ++E   +A  NS     G   
Sbjct: 434 LIGSLTIHVRIGRWGSLESPFYEISKRSKGARMLYLSPGQDEYYMVASGNSLALNQGIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E++        Q  SI ASLIPF+E++D++R LM  NMQRQAV
Sbjct: 494 EQVVPARYCQEFLTIAWEEVHLRSIFSFQYFSIGASLIPFIEHNDASRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E  VA  SGA  +A+  G +   D         +            
Sbjct: 554 PLSRSEKCIVGTGLEGQVALDSGALALAQHEGKIIYTD--------TDKIFFSGNGDTLS 605

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ +QRSN+NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GY
Sbjct: 606 LPLVMYQRSNKNTCIHQKPQVQRGKCIKKGQILASGTATVGGELALGKNVLVAYMPWEGY 665

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI
Sbjct: 666 NFEDAVLISERLVYEDIYTSFHIRKYEIQTYMTSEGPERVTNEIPHLEAYLLRNLDKNGI 725

Query: 882 ICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TP+   ES   PE++LLRAI G +    ++T L++P G  G V
Sbjct: 726 VMLGSWVEEGDILVGKLTPQMVNESAYAPEDRLLRAILGIEVSTSKETCLKLPIGGRGRV 785

Query: 940 VDVRIFNRH----GIDKNERSISVEREQIELLAR 969
           +DVR   +        +  R    ++ +I++  +
Sbjct: 786 IDVRWIQKRVGSSYNPETIRVYISQKREIKVGDK 819



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 111/239 (46%), Gaps = 27/239 (11%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAM--LE 75
           KN  +  IP   ++Q   +  F+          ++GL+    S FP I          L 
Sbjct: 5   KNEGMFTIPGFNQIQFEGFCRFI----------DQGLRDEL-SNFPKIEDPDQKMEFQLF 53

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
             +Y+   P     D ++  LTY+    ++  LI         +K  + +++Q+IY+G++
Sbjct: 54  METYQLVEPLIKERDAVYESLTYSSEFYVSAGLI---------SKIRRGMQKQTIYIGNI 104

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLM   GTF++ GI RIV++Q+ +SPGI+F  +      +G   Y   II D G   ++E
Sbjct: 105 PLMNSLGTFIVNGIYRIVINQIVQSPGIYFRSELD---HNGIASYTGTIISDWGGRSELE 161

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            D K  I  R+ R++K+ +     A+G    EIL    YP+I  S   D     + + +
Sbjct: 162 IDRKARIWARVSRKQKISILVLSSAMGSSLREILENVCYPEIFLSFLNDKEKNKIGSKE 220


>gi|83755163|gb|ABC46430.1| RNA polymerase beta subunit [Spiroplasma litorale]
 gi|83755165|gb|ABC46431.1| RNA polymerase beta subunit [Spiroplasma litorale]
          Length = 594

 Score =  365 bits (937), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 227/423 (53%), Positives = 312/423 (73%), Gaps = 9/423 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A++N YGFIETPYRKV + KV  +   YL+A +E+   +AQAN  + EDG+  ++ V 
Sbjct: 61  TYAKINEYGFIETPYRKVKNKKVILDQYEYLTADKEKEYVVAQANIKIAEDGTIIDDQVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMVNSSDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLIDP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG AIVA   G+V+ VD+ RIV+           +G+  Y L  
Sbjct: 181 ESPVVGTGVEFEAARDSGDAIVATEGGVVKYVDSKRIVV--------EQKNGIKNYDLND 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VKVGD+V++ DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FNRSNNGTAITHIPIVKVGDKVKKRDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK G EEITRDIPNVSE   KN+DE GI+ +G+
Sbjct: 293 VIVSERVVIDDRFTSIHIDEYTIERRQTKQGQEEITRDIPNVSEAIKKNLDEDGIVAIGS 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSIKRFS 412

Query: 947 RHG 949
           +  
Sbjct: 413 KAN 415



 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 127/418 (30%), Positives = 181/418 (43%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKKRDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   +   +   I   L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGQEEITRDIPNVSEAIKKNLDEDGIVAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L V+KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKANGHDLPADILEVIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG KI + + +     D+  + +       
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAQKLGIKISTPVFEGVKEEDLKDIMAEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                   
Sbjct: 531  GKVKLI----------------------------DGRTGEAF------------------ 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                    D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  --------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|226731987|gb|ACO82064.1| RNA polymerase beta subunit [Pseudomonas alcaligenes]
          Length = 362

 Score =  365 bits (936), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 219/362 (60%), Positives = 282/362 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D +VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTQVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA+++++  G   +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNAKGQLVDELVNVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVSRGDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARD 360

Query: 854 TK 855
           TK
Sbjct: 361 TK 362


>gi|328769515|gb|EGF79559.1| RNA polymerase II second largest subunit precursor [Batrachochytrium
            dendrobatidis JAM81]
          Length = 1312

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 143/826 (17%), Positives = 244/826 (29%), Gaps = 163/826 (19%)

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             +     CPAET EG   GLV +L+    +   G    P  +  +      +  +S    
Sbjct: 624  NSIVSHNCPAETPEGQACGLVKNLSLMGYIT-VGSPAPPILEFLEEWTMESLEEISPSTI 682

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                    N          ++LV         +         D SP+  V          
Sbjct: 683  PTATKIFLNGQWVGIHRDPDQLVSTLRRLRRSV---------DVSPEVSVVRDVRDRELR 733

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
               D+ R+     +      L+  +        + +  K   +       G+VE +D   
Sbjct: 734  LCTDAGRIARSLFVVTPEQSLVLTKEMVQQLHEDQIQWKDLLS------YGVVEYIDTEE 787

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D              +R    T   +   V   +           PS  L
Sbjct: 788  EETVMICMTPDDLAEARMAAAGQVVERHQVGTGRLKSATVYTRNY----THCEIHPSMIL 843

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N     +    M  + +                        
Sbjct: 844  G-------ICASIIPFPDHNQSPRNVYQSAMGKQAMG----------------------- 873

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                 ++   L+      +  +             +       +      + AI      
Sbjct: 874  ---LFLTNFQLRM---DTMSNILFYPQKPLATTRAMEFMHFRDLPAGINAVVAIACYSGY 927

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D+ ++   +  E +E  +RD            
Sbjct: 928  NQEDSLIMNQSSIDRGLF-RSLYYRVYMDQEKKVGMISTETLEKPSRDTTLRLKHGTYEK 986

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +++D      R+           ++     +  Q 
Sbjct: 987  LEDDGLIAPGVRVSGEDIIIGKTVPIAADSTELGQRTTMHTKRDASTPLKSTENGIVDQV 1046

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R    GDK A RHG KG V  
Sbjct: 1047 LI--------------------TTNQDGFKFVKVRVRSIRIPHMGDKFASRHGQKGTVGI 1086

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  DG   D+++NP  +PSRM +G + E  L       G +           
Sbjct: 1087 TYRTEDMPFTADGITPDLIINPHAIPSRMTIGHLVECLLSKVSTFTGDEGD--------- 1137

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     EAI+  
Sbjct: 1138 --------------------------------------------ATP-FTDVTVEAISQA 1152

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L+       G  +LY+G TG   +  V  G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 1153 LQGYGYQRRGFEVLYNGHTGRKLNAQVYTGPTYYQRLKHMVDDKIHSRARGPLQILTRQP 1212

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG----------- 1324
            + G+S  GG R GEME  C+ ++GAA  L+E L   SD       D  G           
Sbjct: 1213 VEGRSRDGGLRFGEMERDCMISHGAANFLKERLFDASDAYRVHVCDHCGLMAVANLKKNS 1272

Query: 1325 ------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                  R +            +   P +  +L +E+ A+ ++  L 
Sbjct: 1273 FECRSCRNKT--------QISQVYLPYACKLLFQELMAMNIAPRLM 1310



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 60/479 (12%), Positives = 126/479 (26%), Gaps = 47/479 (9%)

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
                   +E+          +L+       A      +   N            ++   
Sbjct: 515 WIKGSLFFIEQHRSKCQHAFELLHTGLGTKAAVSAEINMPHHNPSH---------MLNVK 565

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           ++ T    E  +       D+Y      R       +++     R     D   + +   
Sbjct: 566 EIPTAPADE--YITWIEFKDRYVHKESPRFVWVTIHSIEEAPAER---LYDFNTVSQNHS 620

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
              N   + +        +      ++KN   +G + +       +  ++  ++   + I
Sbjct: 621 FFANSIVSHNCPAETPEGQACG---LVKNLSLMGYITVGSPAPPILEFLEEWTMESLEEI 677

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +   + +A   F     +    +    +S +   RR   +             +RDV   
Sbjct: 678 SPSTIPTATKIFLNGQWVGIHRDPDQLVSTLRRLRRSVDVSP-------EVSVVRDVRDR 730

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                  A         +    +          +     +  D      V Y+   EEE 
Sbjct: 731 ELRLCTDAGRIARSLFVVTPEQSLVLTKEMVQQLHEDQIQWKDLLSYGVVEYIDTEEEET 790

Query: 625 RYIAQANSSLDEDGSFTEELVFCRC-----AGEEILVPREKIDFIDASPKQVVSIAASLI 679
             I      L E        V  R        +   V        +  P  ++ I AS+I
Sbjct: 791 VMICMTPDDLAEARMAAAGQVVERHQVGTGRLKSATVYTRNYTHCEIHPSMILGICASII 850

Query: 680 PFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKS 722
           PF +++ S R +    M +QA+                 L   + P   T  ME +  + 
Sbjct: 851 PFPDHNQSPRNVYQSAMGKQAMGLFLTNFQLRMDTMSNILFYPQKPLATTRAMEFMHFRD 910

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             A I A    I       +     +            +Y  +   +  +   ++   L
Sbjct: 911 LPAGINA-VVAIACYSGYNQEDSLIMNQSSIDRGLFRSLYYRVYMDQEKKVGMISTETL 968



 Score = 57.0 bits (136), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 59/153 (38%), Gaps = 19/153 (12%)

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDID 496
           +I  L+     +   DD D+ G +R+   G +L   +R+   ++ + +    +I+     
Sbjct: 1   MIHRLLLAALDRRETDDRDHFGKKRLDLAGPLLGGLFRMLFRKLTKDVSRYLQITMESGR 60

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSA 543
                  + +  + + +     +               +SQ+       S ++H RRL+ 
Sbjct: 61  EFNLSLAVKSSTITNGLKYSLATGNWGDQKKFMQARAGVSQVLNRYTFASTLSHLRRLNT 120

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                + R     + R +H TH+G +C +  +E
Sbjct: 121 ----PIGRDGKLAKPRQLHNTHWGMVCLSGDTE 149


>gi|52694409|emb|CAG38044.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 368

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 228/369 (61%), Positives = 289/369 (78%), Gaps = 1/369 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DG+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDATRIVVRVRDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVARGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM VAFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   ++RDTK
Sbjct: 300 DGPSTDMGELALGQNMRVAFMPWNGYNFEDSILLSERVVQEDRFTTIHIQELTCVSRDTK 359

Query: 856 LGPEEITRD 864
           LGPEEIT D
Sbjct: 360 LGPEEITAD 368


>gi|6606093|gb|AAF19059.1|AF107787_1 DNA-dependent RNA polymerase II RPB140 [Candida albicans]
          Length = 1210

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 169/970 (17%), Positives = 309/970 (31%), Gaps = 165/970 (17%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 362  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 421

Query: 485  SIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I   +     +         + ++ +   +     +               +SQ+    
Sbjct: 422  DIYNYMQRCVENGGDFNVTLAVKSQTITDGLRYSLATGNWGEQRKAMSSRAGVSQVLNRY 481

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 482  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 537

Query: 590  ARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++     E     + D   +V  D V  +A +    ++      +  D +   + +  
Sbjct: 538  TCISVGTPSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRE 597

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN--MQRQAVPLL 704
                 ++      I D  +   K          P    DD+          + ++ V  L
Sbjct: 598  LRRSGDLSPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPDSETKGELKITKEHVKQL 657

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDI 761
                       +   ++ + +++VA   GIVE VDA      +I     D+  S + V  
Sbjct: 658  LRSDELDEDDEDYENSRYTWSSLVA--DGIVEYVDAEEEETIMIAMTPDDVKASKNSVSE 715

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHG 820
                K Q   Q            G  ++          T      ++   +  + +P+  
Sbjct: 716  SEQQKIQLEEQEL--------DPGKRIKPTTSGNTHTYTHCEIHPSMILGVAASIIPFPD 767

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  + V                               
Sbjct: 768  HNQSPRNTYQSAMGKQAMG--VFLTNYSVRM---------------------------DT 798

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 799  MANILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 858

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +D  +R      + +E   +    + + L    Y +L E   I  G     
Sbjct: 859  -RSLFFRSYMDIEKRQGM---KALETFEKPTRSDTLRLKHGTYEKLDEDGLIAPGVRVSG 914

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+T + +D      R+Q+         ++     +  Q               +
Sbjct: 915  EDIIIGKTTPIPADAEELGQRTQYHTKRDASTPLRSTESGIVDQ---------------V 959

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 960  LLTTNGD-----GSKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFTAEGIV 1014

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM V  + E  L       G +  +          IS L         
Sbjct: 1015 PDLIINPHAIPSRMTVAHLIECLLSKVSSLSGFEGDASPFTDVTTEQISTLLR------- 1067

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                              V     +G  +   VF                          
Sbjct: 1068 --------DHGYQSRGFEVMYNGHTGKKLMAQVF-------------------------- 1093

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
                          G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEM
Sbjct: 1094 -------------FGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEM 1140

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIV-------------AGNDTFE 1340
            E  C+ A+GAA  L+E L   SD     V G   +   I                 + ++
Sbjct: 1141 ERDCMIAHGAAGFLKERLMEASDAFRVHVCGMCGLMSVIANLKKNQFECRSCKNKTNIYQ 1200

Query: 1341 TGTPESFNVL 1350
               P +  +L
Sbjct: 1201 IHIPYAAKLL 1210



 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 143/1037 (13%), Positives = 290/1037 (27%), Gaps = 218/1037 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-----------FSGAAMLEFV 77
           L+  Q  S+D F+  +I      +  L         I              +    + F 
Sbjct: 38  LVSQQLDSFDEFVETSIQELVWEDSHL---------ILDQPAQHTSEKDHENKRYEITFG 88

Query: 78  SYEFDPPKFD----------VDDCLWRDLTYAVPLKITLR-LIVFDVDEFTGAKSIKDIK 126
                 P               +   R+LTY+ PL + +   +    D       ++ I+
Sbjct: 89  KIYISKPSQTEGDGSTHAVFPQEARLRNLTYSSPLYVDMTSKVFKSDDNKRKDNELEWIQ 148

Query: 127 EQ-------SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
           E+        +++G +P+M +                         G FVI G ++++++
Sbjct: 149 EEPDKDTETKVFLGKVPIMLRSKFCMLRDLAEHEFYELKECPYDMGGYFVINGSEKVLIA 208

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRID------ 207
           Q  RS          + +    + +   I    ++G  +      K  ++ R D      
Sbjct: 209 QE-RSAANI--VQVFKKAAPSPISHVAEIRSAIEKGSRLISSMQIK--LYGR-DEKGVSG 262

Query: 208 RRRK---------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           R  K         +P+     ALG+  + +IL          Q  +     +    ++  
Sbjct: 263 RTIKATLPYIKEDIPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQE 322

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V+   +    G   I   K++     K + +K +       +           +    
Sbjct: 323 REVALDFIGRR-GVLGIRREKRIQY--AKDILQKELLPNITQEEGFETRKAF--FLGYMV 377

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             + + A +  +    +      +                + N       K  KD    +
Sbjct: 378 NRLLLCALERKEPDDRDHFGKKRLDL----------AGPLLANLFRILFKKLTKDIYNYM 427

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            R +  G    F+V  ++ +    D  +Y L   G      +         + + +    
Sbjct: 428 QRCVENGG--DFNVTLAVKSQTITDGLRYSL-ATGNWGEQRKAMSSRAGVSQVLNRYTYS 484

Query: 438 AIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMER 484
           + +  L        R+GK       +  +  +    E  + Q          +  + +  
Sbjct: 485 STLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCISVGT 544

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             +  +  +    +   +         +   F     +    +    +  +   RR   L
Sbjct: 545 PSEPILGFLRDYGLEVLEDYVPSNAPDSTRVFVNGVWVGVHRDPAALVDFMRELRRSGDL 604

Query: 545 GQG-GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR----V 592
                + R     E        R   P       P   ++G        +    R     
Sbjct: 605 SPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDNPDSETKGELKITKEHVKQLLRSDELD 664

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 E              V Y+ A EEE   IA     +    +   E    +   E
Sbjct: 665 EDDEDYENSRYTWSSLVADGIVEYVDAEEEETIMIAMTPDDVKASKNSVSESEQQKIQLE 724

Query: 653 EILVPR------------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           E  +                    +  P  ++ +AAS+IPF +++ S R      M +QA
Sbjct: 725 EQELDPGKRIKPTTSGNTHTYTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA 784

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                                                   + + + 
Sbjct: 785 MGVFLTNYSV-----------------------------------------RMDTMANIL 803

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA   + G
Sbjct: 804 YYPQKPLGTTRSMEYLKFR------------------------ELPAGQNAIVAIACYSG 839

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDSM++++  +   +F S+    +  + +   +   E        D   +     + 
Sbjct: 840 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDIEKRQGMKALETFEKPTRSDTLRLKHGTYEK 899

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G+I  G  V+  DI++GK TP         ++        +    RD S  + S  
Sbjct: 900 LDEDGLIAPGVRVSGEDIIIGKTTPIPADAEELGQRT-------QYHTKRDASTPLRSTE 952

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG V  V +       K
Sbjct: 953 SGIVDQVLLTTNGDGSK 969


>gi|225282|prf||1211235T RNA polymerase beta
          Length = 1000

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 234/660 (35%), Positives = 372/660 (56%), Gaps = 32/660 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +   A  +   + LE + + EI    +   +                   +++A+L+ Y+
Sbjct: 182 VLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIG-------------SKENAILEFYQ 228

Query: 380 VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                 GD              FF   + +L  +GR  MN RLNLD P +   +   DI+
Sbjct: 229 QFACVGGDPVFSESLCKELQKKFF-QQRCELGRIGRRNMNRRLNLDIPQNNTFLLPRDIL 287

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A    L+ L+ G G +DD+++L N+R+RSV ++L++Q+ L L+R+E  ++  I       
Sbjct: 288 AAADHLIGLKFGMGALDDMNHLKNKRIRSVADLLQDQFGLALVRLENVVRGTICGAIRHK 347

Query: 498 V--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           +   PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    A 
Sbjct: 348 LIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTAS 407

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      ++
Sbjct: 408 FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGHWGSLESPFYEISERSTGVRML 467

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLS   +E   +A  NS         E++V  R   E + +  E++      P Q  SI 
Sbjct: 468 YLSPGRDEYYMVAAGNSLALNQDIQEEQVVPARYRQEFLTIAWEQVHLRSIFPFQYFSIG 527

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+R G V
Sbjct: 528 ASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQAALDSGALAIAEREGRV 587

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              +  +I++             +    L+ +QRSN+NTC++Q+  V  G  +++  I+A
Sbjct: 588 VYTNTDKILLAGN--------GDILSIPLVIYQRSNKNTCMHQKLQVPRGKCIKKGQILA 639

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG +T  G+LALG+N+LVA+MPW GYN ED++LISER+V ED++TS HI ++E+    T 
Sbjct: 640 DGAATVGGELALGKNVLVAYMPWEGYNSEDAVLISERLVYEDIYTSFHIRKYEIQTHVTS 699

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLL 913
            GPE++T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++LL
Sbjct: 700 QGPEKVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLL 759

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE----RSISVEREQIELLAR 969
           RAI G +    ++T L++P G  G V+DVR   + G         R   +++ +I++  +
Sbjct: 760 RAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQKRGGSSYNPETIRVYILQKREIKVGDK 819



 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 110/327 (33%), Positives = 161/327 (49%), Gaps = 46/327 (14%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVMLGSWVETGDILVGKLTPQVVKESSYAPEDRLLRAILGIQVSTSKETCLKLPI 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 780  GGRGRVIDVRWIQKRG----GSSYNP---ETIRVYILQKREIKVGDKVAGRHGNKGIISK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 893  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 918

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 919  -----PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            L G++ +GGQR+GEMEVW ++ +G A+
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAH 1000



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRSELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G++  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKERKKIGSKE 220


>gi|68171622|ref|ZP_00544990.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998959|gb|EAM85642.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
          Length = 214

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 118/212 (55%), Positives = 157/212 (74%)

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S LR+FL +V       + I    D+ +L  AE+ + GVP++ PVF+G  +  I+++LR
Sbjct: 3    VSHLRNFLYQVYDGQDLKDNIQSMSDEDLLVFAERLRDGVPMAAPVFEGPKDSQISNLLR 62

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
            +ADLD SGQ  LYDG  GE FDR VTVGYIYMLKL+H+V DK++ARS G Y LVTQQPLG
Sbjct: 63   LADLDVSGQVDLYDGRIGEKFDRKVTVGYIYMLKLHHLVDDKIHARSVGPYGLVTQQPLG 122

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+VGR ++YESI+ G+  FE G P
Sbjct: 123  GKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIVGRVKIYESIIKGDSNFECGIP 182

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            ESFNV+VKE+++L L + L+  +   S ++++
Sbjct: 183  ESFNVMVKELRSLCLDVALKQDKDFLSNEVKD 214


>gi|281494510|gb|ADA72011.1| RNA polymerase subunit B [Acinetobacter sp. UA3]
          Length = 290

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 138/294 (46%), Positives = 190/294 (64%), Gaps = 5/294 (1%)

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE +
Sbjct: 1    KEEYKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLSSLELVDLLEIQPSDEAI 59

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +  ++   +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMA
Sbjct: 60   AERLTQIQTFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMA 119

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++
Sbjct: 120  GRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQ 179

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            I  ++   K   +I+ LR+FL+K+    G   E +    DD +L +A   ++GVP++TPV
Sbjct: 180  IDKML---KQQREIAELRAFLDKIYNKVGGEQEDLDSLTDDEILVLAGNLRAGVPLATPV 236

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            FDGA+E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V 
Sbjct: 237  FDGAEEGQIKELLELAELPRSGQTVLYDGRTGEKFDRPVTVGYMYMLKLNHLVD 290


>gi|52694385|emb|CAG38032.1| RNA polymerase beta subunit [Pseudomonas agarici]
          Length = 371

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 226/371 (60%), Positives = 289/371 (77%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++    T+ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNDKKILTDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAPRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+A
Sbjct: 241 DSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 301 DGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 360

Query: 856 LGPEEITRDIP 866
           LGPEEI R  P
Sbjct: 361 LGPEEIFRGHP 371


>gi|224458656|gb|ACN43191.1| RpoB [Bacillus sp. PS-250]
 gi|224458662|gb|ACN43194.1| RpoB [Bacillus sp. PS-188]
 gi|224458666|gb|ACN43196.1| RpoB [Bacillus sp. PS-231]
          Length = 250

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 95/278 (34%), Positives = 148/278 (53%), Gaps = 30/278 (10%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           +MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYET 158

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           D+KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 DAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL 218

Query: 256 VGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
                      +  GE   +E+ K L        K   
Sbjct: 219 ------EIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 250



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 61/173 (35%), Gaps = 1/173 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 79  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 138

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 139 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 197

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YD
Sbjct: 198 NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 250


>gi|186885881|gb|ACC93348.1| RNA polymerase beta subunit [Hecastocleis shockleyi]
          Length = 1023

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 124/312 (39%), Positives = 177/312 (56%), Gaps = 42/312 (13%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG PVD+V NPLG
Sbjct: 750  QSSKTERIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLG 809

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +        
Sbjct: 810  VPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPW- 868

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                   VF+                +  G+S ++DG TG+PF+
Sbjct: 869  -----------------------VFE---------------PEYPGKSRIFDGRTGDPFE 890

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
            +PV +G  Y+LKL H V DK++ RS+G YS +TQQPL G++ +GGQR+GEMEVW ++ +G
Sbjct: 891  QPVIIGKPYILKLIHQVDDKIHGRSSGQYSFLTQQPLKGRAKKGGQRVGEMEVWALEGFG 950

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--L 1363
             AY+LQEMLT KSD +  R  V  +I+ G         PESF +LV+E+++L L ++  L
Sbjct: 951  VAYILQEMLTYKSDHIRARQEVLGTIIIGGTIPIPEDAPESFRLLVRELRSLALELNHFL 1010

Query: 1364 ENSRTKNSAKME 1375
             + +T    + E
Sbjct: 1011 VSEKTFQINRKE 1022



 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 258/805 (32%), Positives = 415/805 (51%), Gaps = 38/805 (4%)

Query: 319  EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
             I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125  RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFFSFLNDKDKKKIGSKENAILEF 184

Query: 378  YRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            Y+     +    FS + S      F   + +L  +GR  MN RLNLD P +   +   DI
Sbjct: 185  YQQFACVEGDLVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDI 244

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
            +A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +    ++   
Sbjct: 245  LAAADRLIRIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNIYVALKH 304

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    A
Sbjct: 305  KWIPTPQKLVNSTPLTDTYQVFFRLHPLSQVLDGTNPLTQIVHGRKLSYLGPGGLTARTA 364

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
               +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      +
Sbjct: 365  TFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEISERSKGARM 424

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
             YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  SI
Sbjct: 425  PYLSPGRDEYYMVAAGNSLALNQGIHEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSI 484

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+R G 
Sbjct: 485  GASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEREGK 544

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +   D         +  L  S        L+++QRSN+NT ++Q+  V+ G  +++  I+
Sbjct: 545  IIYTD--------TDKILLSSNGDTLSIPLVRYQRSNKNTWMHQKAQVRRGKCIKKGQIL 596

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    T
Sbjct: 597  AYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHVT 656

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEKL 912
              GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++L
Sbjct: 657  NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMLKESSYAPEDRL 716

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR--- 969
            LR I G      ++T L++P G  G V+DVR       ++  R   +++ +I++  +   
Sbjct: 717  LRTILGMGVYTSKETCLKLPIGGRGRVIDVRWVQSSKTER-IRVYILQKREIKVGDKVAG 775

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEYPRSQWW 1022
               ++ +I        +  +  G+        +  P       +  S L ++     + +
Sbjct: 776  RHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHY 835

Query: 1023 QFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + A  DE+ ++            E+ K          E   K++I   + GD     V+ 
Sbjct: 836  RIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVI- 894

Query: 1073 VVKVFVAMKRPIQSGDKMAGR-HGN 1096
            + K ++  K   Q  DK+ GR  G 
Sbjct: 895  IGKPYIL-KLIHQVDDKIHGRSSGQ 918



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 99/184 (53%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLEKYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TNRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           ++G++PLMT  GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FIGNIPLMTSLGTFIVNGIYRIVINQILQSPGIYYRSELNHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I +S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFFSFLNDKDKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|302703649|gb|ADL62671.1| RNA polymerase beta subunit [Mycoplasma sp. 32328]
 gi|302703657|gb|ADL62675.1| RNA polymerase beta subunit [Mycoplasma sp. 31848]
 gi|302703659|gb|ADL62676.1| RNA polymerase beta subunit [Mycoplasma sp. 31948]
          Length = 665

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 236/520 (45%), Positives = 356/520 (68%), Gaps = 15/520 (2%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           ++ N+R+ SVGE+L NQ  + L ++E++ +ER+ + + + V  +++ N K + + +  FF
Sbjct: 1   SMVNKRIVSVGELLANQLNVALSKLEKTTRERMGAKEPEKVTAKNVTNNKLITNQMKTFF 60

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SS+LSQ  + +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG
Sbjct: 61  NSSKLSQFMDQINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEG 120

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDE 636
            NIGL+ +  ++A+VN  GF++TPY KV +G +  NDV YL+A EE     +Q++ ++DE
Sbjct: 121 PNIGLILNYATYAKVNEMGFLQTPYFKVNNGVIDYNDVRYLTASEEIGYKFSQSSVTVDE 180

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +    +EL+  R     ++    ++DFI+ S KQ+VS+AA  IPFLENDD+NR LMG NM
Sbjct: 181 NNRIVDELITIRHNYNYVIDKPSEVDFIEVSSKQMVSVAAGAIPFLENDDANRALMGSNM 240

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPLL+AEAP+V TG+E  +AK S   +VAK AG V  VD+ +I I++ +G  D   
Sbjct: 241 QRQAVPLLQAEAPYVATGIEGDIAKYSAYNLVAKNAGEVVYVDSQKIHIKNDKGTTDK-- 298

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y L  F+RSNQ T +NQ P+VK+GD+V   ++I DG S   G+LALG+N+LVAF 
Sbjct: 299 -----YVLRNFERSNQGTVINQIPIVKLGDKVEEGELIVDGSSFKNGELALGKNVLVAFT 353

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W+GYN+ED+++++E++V +DV+TSIHIEE  +  R++K G +++T  IPNVS+  L+N+
Sbjct: 354 TWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNSKAGDDKLTASIPNVSKYSLRNL 413

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ VG+EV PGD+LVG+++PKGE   T EEKLL AI  ++    RDTSL+V +G +
Sbjct: 414 DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLLMAILQQRPSSDRDTSLKVKNGHN 473

Query: 937 GTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           GTV+ V + +R        GIDK  +    ++ +I++  +
Sbjct: 474 GTVIGVEVLSRELGDVLEDGIDKIVKVSIAQKRKIKVGDK 513



 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 143/526 (27%), Positives = 225/526 (42%), Gaps = 82/526 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMVS 835
            Q   V  G      +  A+              +L A  P+     E  +    +  +V+
Sbjct: 214  QMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQAEAPYVATGIEGDIAKYSAYNLVA 273

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    ++++  ++  ++ K   ++        S +G   I++  I+ +G +V  G+++V
Sbjct: 274  KNAGEVVYVDSQKIHIKNDKGTTDKYVLRNFERSNQGTV-INQIPIVKLGDKVEEGELIV 332

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHG 949
               + K    +   + +L A       +  D  +            S  + +  I  R+ 
Sbjct: 333  DGSSFKN-GELALGKNVLVAFTTWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNS 391

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
               +++  +      +   R+  DE  I+         ++L G+ +  G +   +   L 
Sbjct: 392  KAGDDKLTASIPNVSKYSLRNL-DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLL 450

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              ++ + P S        D      V++          +L             GD +  G
Sbjct: 451  MAILQQRPSS--------DRDTSLKVKNGHNGTVIGVEVLSREL---------GDVLEDG 493

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP L+DGTPVDI+LNP GVPS
Sbjct: 494  IDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPHLEDGTPVDIMLNPQGVPS 553

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG A   LG K  +   D     DI                        
Sbjct: 554  RMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKQDI------------------------ 589

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
             ++ L  A   K+G  +                             L D +TGE FD PV
Sbjct: 590  -ENALEEAGLPKTGKQI-----------------------------LIDPVTGEKFDNPV 619

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +VG +YMLKLNHM+ DK++ RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 620  SVGVMYMLKLNHMIDDKMHGRSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|83755179|gb|ABC46438.1| RNA polymerase beta subunit [Spiroplasma taiwanense]
          Length = 594

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 225/444 (50%), Positives = 319/444 (71%), Gaps = 10/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A++N YGFIETPYRKV + +V      YL+A +E+   +A+AN  + EDG+  ++ V 
Sbjct: 61  TYAKINEYGFIETPYRKVRNKQVILGKYEYLTADKEKEYVVAEANIKMSEDGTILDDQVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMVNPADVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG A+VA + GIV+ VD+ +I I   +        G+ IY L  
Sbjct: 181 ESPIVGTGVEFEAARDSGDAVVATQDGIVKYVDSKKITIEQKD--------GIKIYDLND 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FSRSNNGTAITHLPIVKIGDKVKARDILADGPSMENGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK GPEE+TRDIPN+SE   K++DE GI+ +GA
Sbjct: 293 VIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEVTRDIPNISEASKKHLDEDGIVAIGA 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947 R-HGIDKNERSISVEREQIELLAR 969
           R  G D     + + +  +    +
Sbjct: 413 RADGHDLPADILEIIKVYVVQKRK 436



 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 125/418 (29%), Positives = 185/418 (44%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V   DIL    +      +   + ++ A       +  D  +         V+
Sbjct: 247  IVKIGDKVKARDILADGPS-MENGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   +   +       L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEVTRDIPNISEASKKHLDEDGIVAIGAEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG KI + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGLKINTPVFEGVKEKELLEIMEEAGM--- 527

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                + +   + +                         G+    
Sbjct: 528  --------------------DNYGKVILI------------------------DGK---- 539

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
               TGEPFD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 540  ---TGEPFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|84996571|ref|XP_953007.1| DNA-directed RNA polymerase II subunit [Theileria annulata strain
            Ankara]
 gi|65304003|emb|CAI76382.1| DNA-directed RNA polymerase II subunit, putative [Theileria annulata]
          Length = 1223

 Score =  365 bits (936), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 167/1003 (16%), Positives = 307/1003 (30%), Gaps = 240/1003 (23%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  +I  L+  + G+   DD ++ G +R+   G ++ + +     ++ + ++  + 
Sbjct: 393  KCFYLGYMIHRLLLNQLGRINEDDREHFGKKRLDLAGSLMASSFGTLFRKLAKDVERFLK 452

Query: 492  SVDIDSVMPQ---DLINAKPVVSAVCEFFCSS---------------------------- 520
            +             + +   +   +     +                             
Sbjct: 453  NQIDSGRSFDVAGAIKSCSQITQGLQYQLLTGTHSKIIKIKFILLKKFTIWNWGRDKDGN 512

Query: 521  ----QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+   +   S ++H RRL+      + R     + R +H TH+G ICPAET E
Sbjct: 513  VVRTGVSQVLNRLTFASYLSHLRRLNT----PLGREGKMAKPRQLHNTHWGMICPAETPE 568

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G  +GLV +L     ++  G + +           + +  +S +  ++R     N +   
Sbjct: 569  GQAVGLVKNLALMCYIS-VGSLSSTILDFLLEFGMDSLDEISPILIKDRVKIFLNGTWVG 627

Query: 637  DGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              +  + LV      R  G          D +    K       S+ P    ++ NR+L+
Sbjct: 628  VFNQPDSLVNVLLELRRKGNISSETSIVRDIMSNEIKIFTDSGRSMRPLYIVEN-NRLLI 686

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
                           +  + TG+                   VE +D     I  +    
Sbjct: 687  TKRHANMIENNQLTWSGLMETGV-------------------VEYIDCEEEEICMIAMFP 727

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            D                           LV   +           PS  LG       + 
Sbjct: 728  DD--------------------------LVNNNNYCNSYTHCEIHPSMILG-------VC 754

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+   N       S R   +       +  +                         
Sbjct: 755  ASIIPFPDQNQ------SPRNTYQSAMGKQAMGVYSTN---------------------- 786

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              N+    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 787  -YNLRMDTLSHVLYYPQKPLVCTRSMEFLRFRELPAGINSIVAIMCYTGYNQEDSLIMNQ 845

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD-EQVILDRNIYSRLME--- 988
            S +   +        +  ++      +    IE   +     + + L R  YS+L     
Sbjct: 846  SSIDRGLFRSVFNRTYSSEE----KYLGSTVIESFTKPTSTGKFLNLKRGDYSKLDNDGL 901

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G   +       +S+ + SD  +     +          ++ N   +      + + 
Sbjct: 902  IEPGSRVLGDDIIIGRSSPVESDPNNPQYTPEMNLRMDCSCCLRPNENGVVDNVLLTVN- 960

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   +  KV V   R  Q GDK A RHG KG +      ED
Sbjct: 961  -------------------NKGCKFTKVKVRSIRVPQIGDKFASRHGQKGTIGMTFRMED 1001

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            +PF  DG   DI++NP  VPSRM +G + E  LG     +G +                 
Sbjct: 1002 LPFTCDGIVPDIIMNPHAVPSRMTIGHLIECLLGKVGSLVGMEGD--------------- 1046

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     E I++ L     
Sbjct: 1047 --------------------------------------ATP-FSKMTLEQISNRLFKCRY 1067

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G    ++G TG      + VG  Y  +L HMV DK++AR+ G  +++T+QP  G+S 
Sbjct: 1068 SRYGNEAFHNGFTGNLMASKIFVGPTYYQRLKHMVEDKIHARARGPVTMLTRQPTEGRSR 1127

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG-------------------- 1324
             GG R GEME  C+ ++GAA +L+E L  +SD     V                      
Sbjct: 1128 EGGLRFGEMERDCMISHGAAKMLKERLFDQSDAYRVHVCNFCGLLSVANLNNSSFQCTAC 1187

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              +            +   P +  +L++E+ A+ +   L  + 
Sbjct: 1188 DNKT--------QISQVTIPYACKLLLQELMAMAIYPKLILTE 1222



 Score =  221 bits (562), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 136/1006 (13%), Positives = 287/1006 (28%), Gaps = 218/1006 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGA--------AMLE 75
           L+  Q  S++ F+   +          Q    S  PI       +             L+
Sbjct: 74  LVHQQIESFNDFITYRM----------QEIIDSHPPIEITPQPNYRPEEEVENSVVYKLK 123

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P  +            +   R+LTYA  + I +    + ++E          
Sbjct: 124 FGQLSLSKPSVEEKDGVFKHIWPQEARLRNLTYASQVYIDIEQETY-INEDGKLTQTDST 182

Query: 126 KEQSIYMGDLPLM------------------------TKDGTFVIKGIQRIVVSQLHRSP 161
               + +  +P+M                         + G FV+ G +R++++Q  R  
Sbjct: 183 VYPRVPLCRMPMMHKSSYCWTRGLNDQDLSDIGECVFDQGGYFVVNGGERVLIAQE-RMA 241

Query: 162 GIH---FDHDKGRASLSGKL---------LYACRI-IPDQGLWMDIEFDSKDII-----H 203
                 F+    + S   +L         + +  I I +    +     +K+ +     +
Sbjct: 242 NNFVYVFNKKNSKYSAVAQLRSQPDFIQGVTSLTIMISN--SQL-----TKNKMVAVLPY 294

Query: 204 VRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           +R D    +PV     ALG +   +IL         +Q        L         +   
Sbjct: 295 IRSD----IPVPILFRALGCISDRDILQRIVYDFSDTQMLSLMRSSLEECSEYTSQEQCL 350

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG------ITSDCLCGLYVAEDIVNGE 316
             +            ++L     ++L+   +  +G             G  +   ++N +
Sbjct: 351 DFIGKRGPTVGALQEERLNFAK-ETLRRHFLPHVGTEVGSESKKCFYLGYMIHRLLLN-Q 408

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALL 375
            G I  +  +   +K L+            L+   + +   +++N + + ++ D   A+ 
Sbjct: 409 LGRINEDDREHFGKKRLDLAGSLMASSFGTLFRKLAKDVERFLKNQIDSGRSFDVAGAIK 468

Query: 376 DI--------YRVMRPGDVSTFSVAESMFN-----FLFFDSDKYDLSTVGRVKMNMRLNL 422
                     Y+++         +   +           D D   + T     +N     
Sbjct: 469 SCSQITQGLQYQLLTGTHSKIIKIKFILLKKFTIWNWGRDKDGNVVRTGVSQVLNRLTFA 528

Query: 423 DTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                +R +         +     L N    +         +   + + L     + +  
Sbjct: 529 SYLSHLRRLNTPLGREGKMAKPRQLHNTHWGMICPAETPEGQAVGLVKNLALMCYISVGS 588

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +  +I + +    +DS+   D I+   +   V  F   + +    +  + ++ +   RR 
Sbjct: 589 LSSTILDFLLEFGMDSL---DEISPILIKDRVKIFLNGTWVGVFNQPDSLVNVLLELRRK 645

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +                +       + P    E + + +     +    N   +    
Sbjct: 646 GNISSETSIVRDIMSNEIKIFTDSGRSMRPLYIVENNRLLITKRHANMIENNQLTW---- 701

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                    T  V Y+   EEE   IA     L  + ++                     
Sbjct: 702 ----SGLMETGVVEYIDCEEEEICMIAMFPDDLVNNNNYCNSY----------------- 740

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +  P  ++ + AS+IPF + + S R      M +QA+ +                  
Sbjct: 741 THCEIHPSMILGVCASIIPFPDQNQSPRNTYQSAMGKQAMGVYSTNYNL----------- 789

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                            + S V  Y               Q+PL
Sbjct: 790 ------------------------------RMDTLSHVLYYP--------------QKPL 805

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V                     +L  G N +VA M + GYN EDS+++++  +   +F S
Sbjct: 806 V----------CTRSMEFLRFRELPAGINSIVAIMCYTGYNQEDSLIMNQSSIDRGLFRS 855

Query: 842 IHIEEFEVMARDTKLGPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +    +    +       E            N+       +D  G+I  G+ V   DI++
Sbjct: 856 VFNRTYSSEEKYLGSTVIESFTKPTSTGKFLNLKRGDYSKLDNDGLIEPGSRVLGDDIII 915

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           G+ +P    P  P+      +         D S  +    +G V +
Sbjct: 916 GRSSPVESDPNNPQYTPEMNLR-------MDCSCCLRPNENGVVDN 954


>gi|328777078|ref|XP_003249277.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase II
            subunit RPB2 [Apis mellifera]
          Length = 1154

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 166/1079 (15%), Positives = 323/1079 (29%), Gaps = 201/1079 (18%)

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
               +  KS   I  S I    I  +  +     I            +D L  I       
Sbjct: 236  WINMMAKSGASIKKSAIGQRIIAIIPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDP 295

Query: 385  DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            ++    V  S+            L+ +G      R  +     +++ R+     ++  + 
Sbjct: 296  EM-MEMVKPSLDEAFVIQEQNVALNFIG--TRGARPGVTKEKRIKYAREILQKEMLPHVG 352

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQD 502
                 +          N+R+   G +L   +R     + + ++               + 
Sbjct: 353  IRDFCETKKAYFLEFINKRLDLAGPLLAFXFRGLFKNLMKEVRLYAQKFIDRGKDFNLEL 412

Query: 503  LINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGV 549
             I  K +   +     +               +SQ+   +   S ++H RR+++     +
Sbjct: 413  AIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNS----PI 468

Query: 550  ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R     + R +H T +G +CPAET EG  +GLV +L   A ++           + +  
Sbjct: 469  GRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWS 528

Query: 610  V--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPREKIDFIDA 666
            +    ++   +  +    ++      +  D       L   R   + I+     I  I  
Sbjct: 529  MENLEEIAPSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRD 588

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
               ++ + A  +   L   +   +L+                              SG  
Sbjct: 589  REIRIYTDAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNNDG-------WQELVGSGVV 641

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                     E +D         E  +  + S  D+ +  ++                   
Sbjct: 642  ---------EYIDT------LEEETVMIAMSPEDLRQEKEYA------------------ 668

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                       P+  LG       +  + +P+  +N          M  + +   ++I  
Sbjct: 669  YCTTYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITN 719

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            F                           ++    +  V    +   +    +       +
Sbjct: 720  F---------------------------HVRMDTLAHVLYYPHKPLVTTRSMEYLRFREL 752

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
                  + AI      +  D+ +   S V         +      K+  S  +  ++ E 
Sbjct: 753  PAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFY---RSYKDSESKRIGDQE-EQ 808

Query: 967  LARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
              +        +   IY +L +   I  G           K+  L          ++ + 
Sbjct: 809  FEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPEADDELDSTTKRFT 868

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                   ++ +   +  Q                        +     +  K+ V   R 
Sbjct: 869  KRDASTFLRNSETGIVDQVML--------------------TLNSEGYKFCKIRVRSVRI 908

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E   G 
Sbjct: 909  PQIGDKFASRHGQKGTCGIQYRQEDMPFSCEGLTPDIIINPHAIPSRMTIGHLIECIQGK 968

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                 G+                                                     
Sbjct: 969  VSANKGEIGD-------------------------------------------------- 978

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +TP  D  + + I+++L+       G  ++Y+G TG   +  V +G  Y  +L HMV
Sbjct: 979  ---ATPFNDAVNVQKISTLLQEYGYQLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMV 1035

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
             DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   SD   
Sbjct: 1036 DDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYR 1095

Query: 1321 -DVVG----------RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +            R   +E    G        +   P +  +L +E+ A+ ++  L 
Sbjct: 1096 IHICNFCGLIAIANLRNNTFEC--KGCKNKTQISQIRLPYAAKLLFQELMAMNIAPRLM 1152



 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 138/984 (14%), Positives = 279/984 (28%), Gaps = 211/984 (21%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
           L+  Q  S+D F+ M++    ++ P   LQA  +     I        L+F       P 
Sbjct: 39  LVRQQLDSFDEFIEMSVQRIVEDSPQIDLQAEAQHTSGEIENPVRHL-LKFEQIYLSKPT 97

Query: 86  FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        ++   R+LTY+ PL + +   +    E        + + Q  ++G +
Sbjct: 98  HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEDPI-----ETQHQKTFIGKI 152

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153 PIMLRSKYCLLAGLSDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD 212

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDR-------------- 208
                GK  Y   I       ++        +           I +              
Sbjct: 213 -----GKYAYKSEIR----SCLEHSSRPTSTLWINMMAKSGASIKKSAIGQRIIAIIPYI 263

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++++P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264 KQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGT 323

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                 +   K++          + ++   +                        +  + 
Sbjct: 324 RGARPGVTKEKRI------KYAREILQKEMLPH------------------VGIRDFCET 359

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                LE I        P+L          +   +     K           +     + 
Sbjct: 360 KKAYFLEFINKRLDLAGPLLAFXFRGLFKNLMKEVRLYAQKFIDRGKDFNLELAIKTKII 419

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   +  G  ++  RL   +      R          +     
Sbjct: 420 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQ 479

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +                ++KN   +  + +       +  ++  S+   + I 
Sbjct: 480 LHNTLWGMLCPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIA 536

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL--SALGQGGVARARAGVEMRDVHP 563
              +  A   F     +    +    ++ +   RR     + +  + R     E+R ++ 
Sbjct: 537 PSAIADATKIFVNGCWVGIHRDPDQLMATLRKLRRQMDIIVSEVSMIRDIRDREIR-IYT 595

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVVYLSAM 620
                  P    EG N+ L        +    N  G+ E           +  V Y+  +
Sbjct: 596 DAGRISRPLLIVEGQNLLLKKRHIDMLKERDYNNDGWQELV--------GSGVVEYIDTL 647

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   IA +   L                 E+           +  P  ++ + AS+IP
Sbjct: 648 EEETVMIAMSPEDL---------------RQEKEYAYCTTYTHCEIHPAMILGVCASIIP 692

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 693 FPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------------ 722

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + V  Y                +PLV                  
Sbjct: 723 -----------RMDTLAHVLYYP--------------HKPLV----------TTRSMEYL 747

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G N +VA + + GYN EDS++++   V    F S+    ++          EE
Sbjct: 748 RFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSESKRIGDQEE 807

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                       +       +D+ GII  G  V+  D+++GK     E+    +      
Sbjct: 808 QFEKPTRQTCQGMRNAIYDKLDDDGIIAPGIRVSGDDVVIGKTITLPEADDELDSTT--- 864

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
               K    RD S  + +  +G V
Sbjct: 865 ----KRFTKRDASTFLRNSETGIV 884


>gi|312062818|emb|CAS03783.1| RNA polymerase beta subunit [Pseudomonas fluorescens]
          Length = 371

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 222/370 (60%), Positives = 288/370 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 302 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 361

Query: 851 ARDTKLGPEE 860
           ARDTKLGPEE
Sbjct: 362 ARDTKLGPEE 371


>gi|306411067|gb|ADM86139.1| RNA polymerase beta chain [Onoseris onoseroides]
          Length = 1028

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 235/662 (35%), Positives = 365/662 (55%), Gaps = 20/662 (3%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  MN RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADRLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ +      
Sbjct: 364 ASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHTRIGRWGSLESPFYEISERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLECQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +           + +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 544 KIIYT--------NTDKILLSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCIKKGQI 595

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 596 LAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQIHM 655

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
           T   PE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 656 TSQSPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 715

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI--FNRHGIDKNERSIS--VEREQIELL 967
           LLR I G +    ++T L++P G  G V+DVR     R    K+ER     +++ +I++ 
Sbjct: 716 LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKKRTSSSKSERIRVYILQKREIKVG 775

Query: 968 AR 969
            +
Sbjct: 776 DK 777



 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 149/497 (29%), Positives = 233/497 (46%), Gaps = 56/497 (11%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G  ++          +   + +L A    +  +  D  L     +S  +V 
Sbjct: 584  VRRGKCIKKGQ-ILAYGAATIGGELALGKNVLVAYMPWEGYNFEDAVL-----ISERLVY 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E  I +  +  E +  +    +  L RN+  +   ++ G    +G   
Sbjct: 638  EDIYTSFHIRKYEIQIHMTSQSPERVTNEIPHLEAHLLRNL-DKNGIVMLGSWVETGDIL 696

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T       S  P  +  +  +           LK+       +++ R+  K     
Sbjct: 697  VGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQKK---- 752

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                        ++V++  KR I+ GDK++GRHGNKGI+S+ILP +DMP+L+DG PVD+V
Sbjct: 753  ---RTSSSKSERIRVYILQKREIKVGDKVSGRHGNKGIISKILPRQDMPYLQDGRPVDMV 809

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    F E    +   
Sbjct: 810  FNPLGVPSRMNVGQIFESLLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQT 869

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                        VF+                +  G+S +YDG T
Sbjct: 870  ANPW------------------------VFE---------------PEYPGKSRIYDGRT 890

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+ QQPL G++ +GGQR+GEMEVW 
Sbjct: 891  GDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLPQQPLKGRAKQGGQRVGEMEVWA 950

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNVLVKEMQALGLS 1360
            ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +LV+E+++L L 
Sbjct: 951  LEGFGVAYILQEMLTYKSDHIRPRQEVLATTIIGGTIPTPEDPPESFRLLVRELRSLALE 1010

Query: 1361 ID--LENSRTKNSAKME 1375
            ++  L + +T    + E
Sbjct: 1011 LNHFLVSEKTFQINRKE 1027



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/184 (30%), Positives = 96/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D +++ LTY+    ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYKSLTYSSEFYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNIREILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|197205454|gb|AAZ81446.2| RNA polymerase beta subunit [Mycoplasma bovigenitalium]
          Length = 664

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 224/493 (45%), Positives = 342/493 (69%), Gaps = 8/493 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ ++GE+++N  ++GL ++E++ +ER+ + + D V P++  N K + + +  FF S
Sbjct: 2   TNKRIVAIGELIQNNLKVGLAKLEKTTRERMGAKEPDKVSPKNATNNKLISNQMKTFFNS 61

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 62  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 121

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A VN +GF++TPY +V +  V  ++ VYL+A +E    IAQ+   +DE+ 
Sbjct: 122 IGLILNYATYASVNEFGFLQTPYYRVENCVVNYSEPVYLTAADEMGYKIAQSTVKVDENN 181

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +  +  R      +   ++IDFI+ SP Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 182 RIIDTNITIRHNYTYQIASADEIDFIEVSPNQMVSVAAGCIPFLENDDANRALMGANMQR 241

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+AEAPFV TG+E+ +AK S    VA+  G+VE VD  +I IR+       + + 
Sbjct: 242 QAVPLLQAEAPFVATGIEADIAKYSSGNFVARNDGLVEYVDGKKIKIRN-------AKNA 294

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +D Y L  FQRSNQ+T V+Q+PLVK G EV++ D++ DG S   G+L+LG+N++VAF  +
Sbjct: 295 LDTYYLKNFQRSNQDTVVHQKPLVKEGQEVKKGDLLVDGASFKDGELSLGKNVVVAFSTY 354

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++ER+V +DVFTSIHIEE  +  R +K G +E+T D+PNVS+   +++DE
Sbjct: 355 KGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTADLPNVSKFATRHLDE 414

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G++V PGD+LVG+++PKG+   + EEKLL A+  ++   V+DTSL+V +G  GT
Sbjct: 415 FGIVRIGSDVTPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQQPVKDTSLKVKNGHGGT 474

Query: 939 VVDVRIFNRHGID 951
           V+ V + +R   D
Sbjct: 475 VIAVEVLSRENKD 487



 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 136/529 (25%), Positives = 209/529 (39%), Gaps = 86/529 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L A  P+     E  +   +     
Sbjct: 212  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLQAEAPFVATGIEADIA--KYSSGN 269

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + E+ V  +  K+   +   D   +      N D    +  ++  G EV  GD
Sbjct: 270  FVARNDGLVEY-VDGKKIKIRNAKNALDTYYLKNFQRSNQDTVVHQKPLVKEGQEVKKGD 328

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K +  ++  + ++ A    K  +  D  +            S  + +  I  
Sbjct: 329  LLVDGASFK-DGELSLGKNVVVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQF 387

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++ +   +   A    DE  I+         ++L G+ +  G     +  
Sbjct: 388  RTSKAGDDE-LTADLPNVSKFATRHLDEFGIVRIGSDVTPGDVLVGRVSPKGDDNPSQEE 446

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   ++ +  +          +     V++       +  +L    K         D +
Sbjct: 447  KLLLAVLQQRQQPV--------KDTSLKVKNGHGGTVIAVEVLSRENK---------DQL 489

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP L DGTPVD++LNP G
Sbjct: 490  EDGITKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPHLLDGTPVDVMLNPQG 549

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   L  K  +   D     +I  +                  
Sbjct: 550  VPSRMNIGQVLEIHLGMAARTLQTKFVTRPFDGIKKEEIYDVIEEANLPTTGKQILID-- 607

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                              P++   FD                                  
Sbjct: 608  ------------------PITGEKFD---------------------------------- 615

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
             PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 616  NPVSVGVMYMLKLNHMVDDKLHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|290751454|emb|CAQ16388.1| RNA polymerase beta subunit [Pseudomonas sp. R-26423]
          Length = 376

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 223/372 (59%), Positives = 291/372 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 5   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 64

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 65  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 124

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E++  +D SP
Sbjct: 125 VVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEEVTLMDVSP 184

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 185 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 244

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 245 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 304

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 305 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 364

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 365 CVARDTKLGPEE 376


>gi|161345233|gb|ABX64457.1| RpoB [Bacillus subtilis]
          Length = 249

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 95/277 (34%), Positives = 147/277 (53%), Gaps = 30/277 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+
Sbjct: 1   ARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFI 50

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+
Sbjct: 51  DYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPI 101

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D
Sbjct: 102 MTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETD 158

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           +KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+ 
Sbjct: 159 AKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDQALL- 217

Query: 257 GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
                     +  GE   +E+ K L        K   
Sbjct: 218 -----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 249



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 61/173 (35%), Gaps = 1/173 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 78  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 137

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 138 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 196

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YD
Sbjct: 197 NEYLRNTLDKDNTENSDQALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 249


>gi|290489622|gb|ADD31195.1| RNA polymerase beta subunit protein [Phoradendron serotinum]
          Length = 1072

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 118/321 (36%), Positives = 177/321 (55%), Gaps = 47/321 (14%)

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            I+ G    P    ++ ++++ KR I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG PVD
Sbjct: 793  IRRGYSYNP---EIICIYISQKRKIKVGDKVAGRHGNKGIISKILSRQDMPYLQDGRPVD 849

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +V NPLGVPSRMNVGQI E  LG A   L +  +    D +   + S    F  ++    
Sbjct: 850  MVFNPLGVPSRMNVGQILECSLGLAGGMLDRHYRIGPFDERYEQEASRKLVF-SELYNAS 908

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
            + T      + +                                        G+S ++DG
Sbjct: 909  NQTANPWVLEPE--------------------------------------YPGKSRIFDG 930

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
              G+ F++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEV
Sbjct: 931  RKGDIFEQPVLIGKSYILKLIHQVDDKIHGRSSGYYALVTQQPLRGRAKQGGQRVGEMEV 990

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT---FETGTPESFNVLVKEMQA 1356
            W ++ +G A++LQEMLT KSD +  R  V  + + G       +   PESF +LV+E+++
Sbjct: 991  WALEGFGVAHILQEMLTYKSDHMSARQEVLGTTIIGRTISSSPDDSVPESFRLLVRELRS 1050

Query: 1357 LGLSID--LENSRTKNSAKME 1375
            L L ++  L + +     + E
Sbjct: 1051 LALELNHFLVSEKNFRINRKE 1071



 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 219/676 (32%), Positives = 355/676 (52%), Gaps = 19/676 (2%)

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           +   +     +  +  E          + S+  +  +    +  +  +      ++    
Sbjct: 149 IISDWGGRSELEIDRKERIWVRVSRKQKMSILVLSSAMGSHLREILENVCYPEIFLSFLN 208

Query: 363 VTDKNK-DRKDALLDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             +K +  +++++L+ ++       D +             F   K +L  +GR  +N R
Sbjct: 209 DKEKKRGSKENSILEFFQQFACIGRDPAFSESFLCKELQNKFFQQKCELGKIGRRNLNRR 268

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           LNL  P +   +   DI+A    L+ ++ G GT+DD ++L N+R+RSV ++L++Q+ L L
Sbjct: 269 LNLHIPHNYLFLLPRDILAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLLQDQFGLAL 328

Query: 480 LRME---RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +R+E   R    R          PQ L+ +  + +    FF    LSQ+ +  N L++I 
Sbjct: 329 VRLENVVRGTICRSIRQHKWIPTPQHLVTSTSLTTTYESFFGLHPLSQVLDRTNPLTQIV 388

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAY 595
           H R+ S LG GG+    A  ++RD+HP+HYGRICP +TSEG ++GL+ S+  +AR+ +  
Sbjct: 389 HGRKSSYLGPGGLTGRTASFQIRDIHPSHYGRICPIDTSEGIHVGLIGSIAIYARMGDWG 448

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA-NSSLDEDGSFTEELVFCRCAGEEI 654
           G IETP+  + +      ++YLS   +E   I  A N+     G   E++V  R   E +
Sbjct: 449 GSIETPFYDISERSKKRQMLYLSPSIDEYYIIVSAGNNLALNQGLQEEQVVTARYRQEFL 508

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG
Sbjct: 509 TIAWEQVHLRSLFPSQYFSIGASLIPFIEHNDANRSLMSSNMQRQAVPLYQSEKCIVGTG 568

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A  SG   +A+  G          +I +    +           L+ +QRSN+NT
Sbjct: 569 LERQAALDSGVTAIAECGG---------KIIETNNKIILSGNGEYLSIPLVIYQRSNKNT 619

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C++Q P V     +++  I+ADG +   G+LALG+N+LV +MPW GYNFED++LISER+V
Sbjct: 620 CIHQNPQVWQDKYMKKGQIVADGAAIVGGELALGKNVLVTYMPWEGYNFEDAILISERLV 679

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TS HI ++E+    T  GPE IT +IP+     L+++D+ GI+ +G+ V  GDIL
Sbjct: 680 YEDIYTSFHIRKYEIQTHVTSRGPERITNEIPHFEAYLLRHLDKNGIVMLGSWVEEGDIL 739

Query: 895 VGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VGK+TP+     +  PE++LLRAI G +    ++T L++P G     V    + R G   
Sbjct: 740 VGKLTPQMTKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGGRGRVIDVRWIRRGYSY 799

Query: 953 NERSISVEREQIELLA 968
           N   I +   Q   + 
Sbjct: 800 NPEIICIYISQKRKIK 815



 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 73/338 (21%), Positives = 128/338 (37%), Gaps = 38/338 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          + GL         +         + FV   +   
Sbjct: 12  IPGFNQIQFEGFCRFM----------DLGLTEELYKFPKMEDTDQELEFQLFVETCQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
                 D ++  LTY+  L ++  LI          K  KD++EQ+I+ G +PLM   GT
Sbjct: 62  SSIKERDAVYESLTYSSELYVSAGLIW---------KPSKDMQEQTIFYGKIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +  +  +S        II D G   ++E D K+ I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELDQNGISV----TATIISDWGGRSELEIDRKERIW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           VR+ R++K+ +     A+G    EIL    YP+I  S   D      S  + ++      
Sbjct: 169 VRVSRKQKMSILVLSSAMGSHLREILENVCYPEIFLSFLNDKEKKRGSKENSILEFFQQF 228

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKG---------VKFLGITSDCLCGLYVAEDIV 313
           + +  D         K+L +   +   E G            L I  + L    +    +
Sbjct: 229 ACIGRDPAFSESFLCKELQNKFFQQKCELGKIGRRNLNRRLNLHIPHNYLF---LLPRDI 285

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                 +      +        + +  IR +  L  D 
Sbjct: 286 LAAADHLIGMKFGMGTLDDTNHLKNKRIRSVADLLQDQ 323


>gi|222093439|gb|ACM43496.1| RNA polymerase beta subunit [Mycoplasma maculosum]
          Length = 665

 Score =  364 bits (935), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 238/505 (47%), Positives = 358/505 (70%), Gaps = 10/505 (1%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           ++ N+R+ SVGE+L+NQ  +G+LR+E++ +ER+++ D + V P+++ N K V + +  FF
Sbjct: 1   SMTNKRIVSVGELLQNQLNVGILRLEKTTRERMTAKDPEKVTPKNITNNKLVSNQMKTFF 60

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SS+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG
Sbjct: 61  NSSKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEG 120

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDE 636
            NIGL+ +L  +A VN YGF++TPY KV +G V  + V YL+A +E    I Q+   ++E
Sbjct: 121 PNIGLILNLAIYAGVNEYGFLQTPYFKVNNGVVDYSTVEYLTAADEYGFNIGQSTVHVNE 180

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           D   T+E +  R     I+   + +D+I+ + +Q+VS+AA  IPFLENDD+NR LMG NM
Sbjct: 181 DNRITDEFLTIRKNYNYIIGTPKDVDYIEVASRQMVSVAAGCIPFLENDDANRALMGSNM 240

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQ+VPL++ EAPFV TG E+ +AK S A   AK+ GIVE  D  +I IR+ +G LD   
Sbjct: 241 QRQSVPLIETEAPFVATGTEADIAKYSAANFRAKQDGIVEFADGSKIKIRNKKGTLD--- 297

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y L  FQRSNQ+T ++QRPLVKVG EV+++D++ DG S   G+L+LG+N+LVAF 
Sbjct: 298 ----TYNLKNFQRSNQDTVIHQRPLVKVGQEVKKDDLLVDGSSFKNGELSLGKNLLVAFT 353

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            + G+N+ED+++++ER+V EDV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++
Sbjct: 354 TYKGFNYEDAVILNERLVKEDVLTSIHIEEQTIQFRTSKAGVDELTRDIPNVSKHSIRHL 413

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ VG+EV PGD+LVG+++PKG+   + EEKLL A+ G++ ++V+DTSL+V +G +
Sbjct: 414 DERGIVLVGSEVTPGDVLVGRVSPKGDDNPSQEEKLLSAVLGQRQMNVKDTSLKVKNGHN 473

Query: 937 GTVVDVRIFNRHGIDKNERSISVER 961
           GT++ V I +R    K++    +++
Sbjct: 474 GTIIGVEILSREN--KDQLEDGIDK 496



 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 133/526 (25%), Positives = 196/526 (37%), Gaps = 82/526 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V  G      +  A+              ++    P+     E  +   +   +  
Sbjct: 214  QMVSVAAGCIPFLENDDANRALMGSNMQRQSVPLIETEAPFVATGTEADIA--KYSAANF 271

Query: 838  VFTSIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                  I EF   ++     K G  +               I +  ++ VG EV   D+L
Sbjct: 272  RAKQDGIVEFADGSKIKIRNKKGTLDTYNLKNFQRSNQDTVIHQRPLVKVGQEVKKDDLL 331

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            V   + K    ++  + LL A    K  +  D  +     V   V+         I    
Sbjct: 332  VDGSSFKN-GELSLGKNLLVAFTTYKGFNYEDAVILNERLVKEDVLTSIHIEEQTIQFRT 390

Query: 955  RSISVER--EQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
                V+     I  +++      DE+ I+         ++L G+ +  G     +   L 
Sbjct: 391  SKAGVDELTRDIPNVSKHSIRHLDERGIVLVGSEVTPGDVLVGRVSPKGDDNPSQEEKLL 450

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            S ++                  QR +       +            +I   +  D +  G
Sbjct: 451  SAVLG-----------------QRQMNVKDTSLKVKNGHNGTIIGVEILSRENKDQLEDG 493

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM              P     
Sbjct: 494  IDKIVKVSIAVKRKIRVGDKMSGRHGNKGVVSVILPEEDM--------------PH---- 535

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
                    E                   D   N    P R  + +V+             
Sbjct: 536  -------LE--------------DGTPVDVMLNPQGVPSRMNIGQVL------------- 561

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
               +       K G    TPVFDG  +E I + +  A L  SG+ IL D +TGE  D+PV
Sbjct: 562  --EIHLGMAARKLGCKFVTPVFDGIKKEDIQAAIEEAGLPVSGKQILIDPITGEKIDKPV 619

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 620  SVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|197311430|gb|ACH61921.1| RNA polymerase beta subunit [Mycoplasma canadense]
          Length = 664

 Score =  364 bits (935), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 238/517 (46%), Positives = 347/517 (67%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ +ERIS+ +   + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQFRIGLIKLEKNTRERISTKETSKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA ++ YGFI++PY +V D KV  +   YL+A+EE     AQ+   + E+  
Sbjct: 123 GLILNLASFADIDKYGFIKSPYFRVKDKKVDFSKPYYLTAIEEAGYSFAQSTVRI-ENDE 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++LV  R   E + VP  ++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDLVMVRRDNEYLQVPANEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  EAP V TG+E+ +AK S   I+AK  G+V  VDA  I I          +   
Sbjct: 242 AVPVLFPEAPLVATGVEADIAKYSSTNIIAKYDGVVSYVDANVIKISRE------GSKKT 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVK+  E++  D++ DGPS   G++ALG+N+LV F  WH
Sbjct: 296 DSYYLRTFERSNQGTLIHQVPLVKLNQEIKAGDLLVDGPSMKNGEMALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G+N+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +DE 
Sbjct: 356 GFNYEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDEN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVRVGSEVSTGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKYGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V V + +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAVDVLSRELGDTLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 131/415 (31%), Positives = 186/415 (44%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  E+  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 317  LVKLNQEIKAGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDENGIVRVGSEVSTGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 435  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKYGHNGTVVAVDVLSREL------- 485

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 486  --GDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 544  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILE---------- 593

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               E  INS         SG+S++YDG 
Sbjct: 594  -----------------------------------EAKINS---------SGKSVVYDGR 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|221328711|gb|ACM17818.1| RNA polymerase subunit B [Pseudomonas sp. ICMP 11283]
          Length = 376

 Score =  364 bits (935), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 221/372 (59%), Positives = 286/372 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLIN KPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINFKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++ +     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMSDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|15778187|gb|AAL07334.1| rpoB [Glycine max]
          Length = 1070

 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 128/396 (32%), Positives = 197/396 (49%), Gaps = 49/396 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T   +   S  P  +  +  +  +        LK+  
Sbjct: 720  LDKNGIVILGSWVETGDILVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPT 779

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  K      G    P     +++++  KR I+ GDK+AGRHGNKGIVS+
Sbjct: 780  GGRGRVIDVRWIQKK----GGSSYNP---ETIRIYILQKREIKVGDKVAGRHGNKGIVSK 832

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            IL  +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 833  ILSRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGGMLERHYRITPFDERYE 892

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 893  QEASRKLVF-SELYEASKQTSNPWIFEPE------------------------------- 920

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG  F +P  +G  Y+LKL H V DK++ RS+G Y+LVTQQP
Sbjct: 921  -------YPGKSKIFDGRTGNSFKQPAIMGKPYILKLIHQVDDKIHGRSSGHYALVTQQP 973

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R  V  + + G    +  
Sbjct: 974  LRGRAKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIKTRQEVLGTTIIGGTIPKPT 1033

Query: 1342 GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              PESF +LV+E+++L + ++  L + +     + E
Sbjct: 1034 DAPESFRLLVRELRSLAMELNHFLVSEKNFRIHRKE 1069



 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 231/686 (33%), Positives = 377/686 (54%), Gaps = 21/686 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 143 ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLSEILENVCYPE 202

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      DK K   +++A+L+ YR      GD              FF   + +L  +
Sbjct: 203 IFVSFLNDKDKKKIGSKENAILEFYRQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 261

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN +LNLD P +   +   DI+     L+ ++ G G +DDI++L N+R+RSV ++L
Sbjct: 262 GRRNMNQKLNLDIPQNNTFLLPRDILTAADHLIGMKFGMGILDDINHLKNKRIRSVADLL 321

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 322 QDQFGLALVRLENMVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDQT 381

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+LS LG   +  A A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 382 NPLTQIVHGRKLSYLGLEDLTGATASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 441

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+ ++G IE+P+ ++ +      ++YLS   +E   +A  NS         E+ V  R 
Sbjct: 442 ARIGSWGSIESPFYEISERSKRIRMLYLSPSRDEYYMVATGNSLALNRDIQEEQTVPARY 501

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
             E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E  
Sbjct: 502 RQEFLTIAWEQVHLRSIFPFQYFSIGASLIPFIEHNDTNRALMSSNMQRQAVPLSQSEKC 561

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+E  VA  SG + +A+  G +   +  RI +                  L  +QR
Sbjct: 562 IVGTGLERQVALVSGVSAIAEHEGNIIYTNTDRIFLFGN--------GDTLSIPLTIYQR 613

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN+NTC++Q+P V+ G  +++  I+ADG +T  G+LALG+N+LVA+MPW GYN ED++LI
Sbjct: 614 SNKNTCMHQKPQVRRGKCIKKGQILADGAATVDGELALGKNVLVAYMPWEGYNSEDAVLI 673

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +ER+V ED++TS HI ++E+    T  G E IT  IP++    L+N+D+ GI+ +G+ V 
Sbjct: 674 NERLVYEDIYTSFHIRKYEIQTHMTSYGSERITNKIPHLEAHLLRNLDKNGIVILGSWVE 733

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GDILVGK+TP+   ES  +PE++LLRAI G +    ++T L++P+G  G V+DVR   +
Sbjct: 734 TGDILVGKLTPQMAKESSYSPEDRLLRAILGIQVSTSKETCLKLPTGGRGRVIDVRWIQK 793

Query: 948 HGIDKNE----RSISVEREQIELLAR 969
            G         R   +++ +I++  +
Sbjct: 794 KGGSSYNPETIRIYILQKREIKVGDK 819



 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP   ++Q   +  F+          ++GL         +         + FV  Y+   
Sbjct: 12  IPGFNQIQFEGFWRFI----------DQGLTEELSKFPKMEDTDQEIEFQLFVETYQLAE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ ++++EQ+I +G++PLM   GT
Sbjct: 62  PLIKEKDAVYESLTYSSELYVSAGLIW---------KTRREMQEQTILIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      SG  +Y   II D G  +++E D K  I 
Sbjct: 113 SIVNGIYRIVINQILQSPGIYYRSELD---PSGISVYTGTIISDWGGRLELEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLSEILENVCYPEIFVSFLNDKDKKKIGSKE 220


>gi|186885941|gb|ACC93378.1| RNA polymerase beta subunit [Relhania calycina]
          Length = 998

 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 276/927 (29%), Positives = 464/927 (50%), Gaps = 98/927 (10%)

Query: 207  DRRR----------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            DRRR          K+P+ + L A       I++  Y  ++           L +  +  
Sbjct: 47   DRRRYIQEQTILIGKIPLMTSLGAF------IVNGIYRIVINQI--------LQSPGIYY 92

Query: 257  GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             ++++ + + I TG  + + G +L       L+      + +       L +        
Sbjct: 93   QSELNDNGISIYTGTIISDWGGRL------ELEIDRKARIWVRVSRQQKLSIL------- 139

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               + + A  +   + LE + +      P L++  +N+   I           +++A+L+
Sbjct: 140  ---VLLSAMGLNIREILENVCY------PELFLSFLNDKKKIG---------SKENAILE 181

Query: 377  IYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
             Y+     +    FS + S      F   + +L  +GR  MN RLNL+ P +   +   D
Sbjct: 182  FYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLNIPQNNTFLLPRD 241

Query: 436  IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
            I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +     +  
Sbjct: 242  ILAAADHLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALK 301

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  PQ+L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 302  HNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTART 361

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
            A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ K+ +      
Sbjct: 362  ATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAR 421

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 422  MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 482  IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEG 541

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +   D         +  L           L+ +QRSN+NTC++Q+P V+ G  +++  I
Sbjct: 542  KIISTD--------TDKILLSGNGDTLRIPLVMYQRSNKNTCMHQKPQVRQGKCIKKGQI 593

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +A G +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI ++E+    
Sbjct: 594  LAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQI-- 651

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK--GESPMTPEEK 911
               GPE +T +IP++    L+N+D+ GI+ +G+ V  GDILVGK+TP+   ES   PE++
Sbjct: 652  -NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDR 710

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV-----EREQIEL 966
            LLR I G +    ++T L++P G  G V+DVR       D+ E++ S+     ++ +I++
Sbjct: 711  LLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEKTESIRVYILQKREIKV 770

Query: 967  LAR---DKDDEQVILDRNIYSRLMEILCGQNA------VSGPKGFKKSTVLSSDL-ISEY 1016
              +      ++ +I        +  +  G+        +  P       +  S L ++  
Sbjct: 771  GDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGD 830

Query: 1017 PRSQWWQFAVQDEKVQRN----------VESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
               + ++ A  DE+ ++            E+ K          E   K++I   + GD  
Sbjct: 831  LLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPESPGKSRIFDGRTGDPF 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               V+ + K ++  K   Q  DK+ GR
Sbjct: 891  EQPVI-IGKPYIL-KLIHQVDDKIHGR 915



 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 125/371 (33%), Positives = 185/371 (49%), Gaps = 46/371 (12%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P  +  +  +           LK+  
Sbjct: 673  LDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPI 732

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 733  GGRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISK 786

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +  
Sbjct: 787  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYE 846

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F  ++      T     ++ +                               
Sbjct: 847  QEASRKLVF-SELYEASKQTANPWIFEPE------------------------------- 874

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQP
Sbjct: 875  -------SPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQP 927

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET- 1341
            L G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G       
Sbjct: 928  LKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPE 987

Query: 1342 GTPESFNVLVK 1352
              PESF + V+
Sbjct: 988  DAPESFRLFVR 998



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISIYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|222093437|gb|ACM43495.1| RNA polymerase beta subunit [Mycoplasma maculosum]
          Length = 665

 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 238/505 (47%), Positives = 357/505 (70%), Gaps = 10/505 (1%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           ++ N+R+ SVGE+L+NQ  +G+LR+E++ +ER+++ D + V P+++ N K V + +  FF
Sbjct: 1   SMTNKRIVSVGELLQNQLNVGILRLEKTTRERMTAKDPEKVTPKNITNNKLVSNQMKTFF 60

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SS+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG
Sbjct: 61  NSSKLSQFMDQINPLAEISNERRITSLGPGGLNRYTAQFEVRDVHATHYGRICPIETPEG 120

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDE 636
            NIGL+ +L  +A VN YGF++TPY KV +G V  + V YL+A +E    I Q+   ++E
Sbjct: 121 PNIGLILNLAIYAGVNEYGFLQTPYFKVNNGVVDYSTVEYLTAADEYGFNIGQSTVHVNE 180

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           D   T+E +  R     I+     +D+I+ + +Q+VS+AA  IPFLENDD+NR LMG NM
Sbjct: 181 DNRITDEFLTIRKNYNYIIGTPRDVDYIEVASRQMVSVAAGCIPFLENDDANRALMGSNM 240

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQ+VPL++ EAPFV TG E+ +AK S A   AK+ GIVE  D  +I IR+ +G LD   
Sbjct: 241 QRQSVPLIETEAPFVATGTEADIAKYSAANFRAKQDGIVEFADGSKIKIRNKKGTLD--- 297

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y L  FQRSNQ+T ++QRPLVKVG EV+++D++ DG S   G+L+LG+N+LVAF 
Sbjct: 298 ----TYNLKNFQRSNQDTVIHQRPLVKVGQEVKKDDLLVDGSSFKNGELSLGKNLLVAFT 353

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            + G+N+ED+++++ER+V EDV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++
Sbjct: 354 TYKGFNYEDAVILNERLVKEDVLTSIHIEEQTIQFRTSKAGVDELTRDIPNVSKHSIRHL 413

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ VG+EV PGD+LVG+++PKG+   + EEKLL A+ G++ ++V+DTSL+V +G +
Sbjct: 414 DERGIVLVGSEVTPGDVLVGRVSPKGDDNPSQEEKLLSAVLGQRQMNVKDTSLKVKNGHN 473

Query: 937 GTVVDVRIFNRHGIDKNERSISVER 961
           GT++ V I +R    K++    +++
Sbjct: 474 GTIIGVEILSREN--KDQLEDGIDK 496



 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 133/526 (25%), Positives = 196/526 (37%), Gaps = 82/526 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q   V  G      +  A+              ++    P+     E  +   +   +  
Sbjct: 214  QMVSVAAGCIPFLENDDANRALMGSNMQRQSVPLIETEAPFVATGTEADIA--KYSAANF 271

Query: 838  VFTSIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                  I EF   ++     K G  +               I +  ++ VG EV   D+L
Sbjct: 272  RAKQDGIVEFADGSKIKIRNKKGTLDTYNLKNFQRSNQDTVIHQRPLVKVGQEVKKDDLL 331

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            V   + K    ++  + LL A    K  +  D  +     V   V+         I    
Sbjct: 332  VDGSSFKN-GELSLGKNLLVAFTTYKGFNYEDAVILNERLVKEDVLTSIHIEEQTIQFRT 390

Query: 955  RSISVER--EQIELLAR---DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
                V+     I  +++      DE+ I+         ++L G+ +  G     +   L 
Sbjct: 391  SKAGVDELTRDIPNVSKHSIRHLDERGIVLVGSEVTPGDVLVGRVSPKGDDNPSQEEKLL 450

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            S ++                  QR +       +            +I   +  D +  G
Sbjct: 451  SAVLG-----------------QRQMNVKDTSLKVKNGHNGTIIGVEILSRENKDQLEDG 493

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM              P     
Sbjct: 494  IDKIVKVSIAVKRKIRVGDKMSGRHGNKGVVSVILPEEDM--------------PH---- 535

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
                    E                   D   N    P R  + +V+             
Sbjct: 536  -------LE--------------DGTPVDVMLNPQGVPSRMNIGQVL------------- 561

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
               +       K G    TPVFDG  +E I + +  A L  SG+ IL D +TGE  D+PV
Sbjct: 562  --EIHLGMAARKLGCKFVTPVFDGIKKEDIQAAIEEAGLPVSGKQILIDPITGEKIDKPV 619

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 620  SVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|221328697|gb|ACM17811.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
 gi|221328703|gb|ACM17814.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 376

 Score =  364 bits (934), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 226/372 (60%), Positives = 291/372 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SP
Sbjct: 122 VVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|52694331|emb|CAG38005.1| RNA polymerase beta subunit [Pseudomonas pseudoalcaligenes]
          Length = 377

 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 227/375 (60%), Positives = 293/375 (78%), Gaps = 1/375 (0%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MP DLINAKPV + V EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPLDLINAKPVAAGVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFID 665
           +GKVT+++V+LSA+EE +  IAQA+++L++   S++ ELV  R   E  +   E +  +D
Sbjct: 121 EGKVTDEIVFLSAIEEADHVIAQASATLNDKRASWSTELVAVRHLNEFTVKAPEDVTLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG 
Sbjct: 181 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  G
Sbjct: 241 CVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D+V R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 DQVARGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQ 360

Query: 846 EFEVMARDTKLGPEE 860
           E   +ARDTKLGP+E
Sbjct: 361 ELTCVARDTKLGPKE 375


>gi|224458664|gb|ACN43195.1| RpoB [Bacillus sp. PS-202]
          Length = 250

 Score =  364 bits (934), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 95/278 (34%), Positives = 148/278 (53%), Gaps = 30/278 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+
Sbjct: 1   ARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFI 50

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+
Sbjct: 51  DYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPI 101

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D
Sbjct: 102 MTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETD 158

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           +KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+ 
Sbjct: 159 AKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL- 217

Query: 257 GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV 293
                     +  GE   +E+ K L        K   +
Sbjct: 218 -----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 250



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 62/174 (35%), Gaps = 1/174 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 78  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 137

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 138 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 196

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL
Sbjct: 197 NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 250


>gi|226525537|gb|ACO70965.1| DNA-directed RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 367

 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 229/364 (62%), Positives = 291/364 (79%)

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N L
Sbjct: 1   NQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPL 60

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ 
Sbjct: 61  SEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 120

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+ETPYRKV +G VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE
Sbjct: 121 NEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGE 180

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VG
Sbjct: 181 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVG 240

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME  VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQ
Sbjct: 241 TGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQ 300

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQ P V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+SER
Sbjct: 301 NTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSER 360

Query: 833 MVSE 836
           +V E
Sbjct: 361 VVQE 364


>gi|52694387|emb|CAG38033.1| RNA polymerase beta subunit [Pseudomonas agarici]
          Length = 370

 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 225/368 (61%), Positives = 288/368 (78%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++    T+ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNDKKILTDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAPRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+A
Sbjct: 241 DSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 301 DGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 360

Query: 856 LGPEEITR 863
           LGPEEI R
Sbjct: 361 LGPEEIFR 368


>gi|209360631|gb|ACI42986.1| RNA polymerase beta subunit [Mycoplasma sphenisci]
          Length = 665

 Score =  364 bits (933), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 226/517 (43%), Positives = 353/517 (68%), Gaps = 10/517 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ SVGE+LKNQ  LGL ++E++ +ER+ S D + + P+++ N K V + +  FF S
Sbjct: 3   MNKRIVSVGELLKNQLDLGLNKLEKTTRERMGSNDPEKIKPKNITNNKLVSNQMKTFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I+  RR+++LG GG++R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMDQINPLAEISTERRITSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGPN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN YG ++TPY KV +G V  + V YL+A++E    +AQ+   +D++ 
Sbjct: 123 IGLILNFATYAKVNKYGLLQTPYYKVENGVVNYDQVEYLTAVDEMGYKLAQSTIKVDDNN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              ++ +  R     ++ P E+ID+++ S KQ+ SIAAS IPFLENDD+NR LMG NMQR
Sbjct: 183 KIVDKQITARYNYVYVVCPPEEIDYMEVSSKQMTSIAASCIPFLENDDANRALMGANMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+AEAP + TG+E+ +AK S A + +   GI++ VD  +I IR          + 
Sbjct: 243 QAVPLLEAEAPLIATGIEADIAKYSAANLTSNCDGIIDYVDGEKIKIR-------KPNNT 295

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              ++L  FQRSNQ T ++Q+P+VK+G EV++ D++ DG S   G+++LG+N+LVAF  +
Sbjct: 296 TSTFKLKTFQRSNQGTLISQKPIVKIGQEVKKGDLLVDGSSFKDGEMSLGKNVLVAFSTY 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++ER+V +DVFTSIHIEE  +  R ++ G + +T D+PNVS+   +++DE
Sbjct: 356 NGYNYEDAVILNERLVKDDVFTSIHIEEQLIQFRTSRAGDDRLTADLPNVSKFATRHLDE 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EV+PGD+LVG+ +PKG+   + EEKLL AI  +K ++V+DTSL+V +G  GT
Sbjct: 416 HGIVRIGSEVSPGDVLVGRTSPKGDDNPSQEEKLLSAILQQKPLNVKDTSLKVKNGHGGT 475

Query: 939 VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
           V+   I +R    K+     +++     +A+ +  + 
Sbjct: 476 VIATEILDRDN--KDNLEDGIDKIVKVFIAQKRKIKV 510



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 131/421 (31%), Positives = 192/421 (45%), Gaps = 79/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ +G EV  GD+LV   + K +  M+  + +L A       +  D  +           
Sbjct: 318  IVKIGQEVKKGDLLVDGSSFK-DGEMSLGKNVLVAFSTYNGYNYEDAVILNERLVKDDVF 376

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     ++R ++ +   +   A    DE  I+         ++L G+ 
Sbjct: 377  TSIHIEEQLIQFRTSRAGDDR-LTADLPNVSKFATRHLDEHGIVRIGSEVSPGDVLVGRT 435

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L S ++ + P +      V+D  ++           T     +++  
Sbjct: 436  SPKGDDNPSQEEKLLSAILQQKPLN------VKDTSLKVKNGHGGTVIATEILDRDNK-- 487

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                     D++  G+ ++VKVF+A KR I+ GDKM+GRHGNKG+VS +LP EDMP L D
Sbjct: 488  ---------DNLEDGIDKIVKVFIAQKRKIKVGDKMSGRHGNKGVVSIVLPVEDMPHLAD 538

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD+VLNP GVPSRMN+GQ+ E HLG A   LG K  + + D     +I  L      
Sbjct: 539  GTPVDVVLNPQGVPSRMNIGQVLELHLGMAARSLGCKFVTPVFDGVKKDEIESLLEEAN- 597

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                            L  +      + 
Sbjct: 598  ------------------------------------------------LSKSG-----KQ 604

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +L + +TGE  D+PV+VG +YM KLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 605  VLINPITGEKLDKPVSVGVMYMFKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 664

Query: 1295 G 1295
            G
Sbjct: 665  G 665


>gi|221328713|gb|ACM17819.1| RNA polymerase subunit B [Pseudomonas sp. ICMP 11284]
          Length = 376

 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 222/372 (59%), Positives = 287/372 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++ +     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMSDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|294768456|gb|ADF36176.1| RNA polymerase beta subunit [Mycoplasma anatis]
 gi|294768458|gb|ADF36177.1| RNA polymerase beta subunit [Mycoplasma anatis]
          Length = 664

 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 234/520 (45%), Positives = 355/520 (68%), Gaps = 15/520 (2%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           ++ N+R+ SVGE+L NQ  + L ++E++ +ER+ + + + V  +++ N K + + +  FF
Sbjct: 1   SMVNKRIVSVGELLANQLNVALSKLEKTTRERMGAKEPEKVTAKNVTNNKLITNQMKTFF 60

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SS+LSQ  + +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG
Sbjct: 61  NSSKLSQFMDQINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEG 120

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDE 636
            NIGL+ +  ++A+VN  GF++TPY KV +G +  NDV YL+A EE     +Q++ ++DE
Sbjct: 121 PNIGLILNYATYAKVNEMGFLQTPYFKVNNGVIDYNDVRYLTASEEIGYKFSQSSVTVDE 180

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +    +EL+  R     ++    ++DFI+ S KQ+VS+AA  IPFLENDD+NR LMG NM
Sbjct: 181 NNKIVDELITIRHNYNYVIDKPSEVDFIEVSSKQMVSVAAGAIPFLENDDANRALMGSNM 240

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVPLL+ EAP+V TG+E  +AK S   +VAK AG V  VD+ +I I++ +G  D   
Sbjct: 241 QRQAVPLLQTEAPYVATGIEGDIAKYSAYNLVAKNAGEVIYVDSQKIHIKNDKGTTDK-- 298

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y L  F+RSNQ T +NQ P+VK+GD+V   ++I DG S   G+LALG+N+LVAF 
Sbjct: 299 -----YVLRNFERSNQGTVINQIPIVKLGDKVEEGELIVDGSSFKNGELALGKNVLVAFT 353

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W+GYN+ED+++++E++V +DV+TSIHIEE  +  R++K G +++T  IPNVS+  ++N+
Sbjct: 354 TWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNSKAGDDKLTASIPNVSKYSIRNL 413

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GI+ VG+EV PGD+LVG+++PKGE   T EEKLL AI  ++    RDTSL+V +G +
Sbjct: 414 DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLLMAILQQRPSSDRDTSLKVKNGHN 473

Query: 937 GTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           GTV+ V + +R        GIDK  +    ++ +I++  +
Sbjct: 474 GTVIGVEVLSRELGDVLEDGIDKIVKVSIAQKRKIKVGDK 513



 Score =  303 bits (776), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 143/525 (27%), Positives = 223/525 (42%), Gaps = 82/525 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMVS 835
            Q   V  G      +  A+              +L    P+     E  +    +  +V+
Sbjct: 214  QMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQTEAPYVATGIEGDIAKYSAYNLVA 273

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    I+++  ++  ++ K   ++        S +G   I++  I+ +G +V  G+++V
Sbjct: 274  KNAGEVIYVDSQKIHIKNDKGTTDKYVLRNFERSNQGTV-INQIPIVKLGDKVEEGELIV 332

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHG 949
               + K    +   + +L A       +  D  +            S  + +  I  R+ 
Sbjct: 333  DGSSFKN-GELALGKNVLVAFTTWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNS 391

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
               +++  +      +   R+  DE  I+         ++L G+ +  G +   +   L 
Sbjct: 392  KAGDDKLTASIPNVSKYSIRNL-DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLL 450

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              ++ + P S        D      V++          +L             GD +  G
Sbjct: 451  MAILQQRPSS--------DRDTSLKVKNGHNGTVIGVEVLSREL---------GDVLEDG 493

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP L+DGTPVDI+LNP GVPS
Sbjct: 494  IDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPHLEDGTPVDIMLNPQGVPS 553

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG A   LG K  +   D     DI                        
Sbjct: 554  RMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKQDI------------------------ 589

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
             ++ L  A   K+G  +                             L D +TGE FD PV
Sbjct: 590  -ENALEEAGLPKTGKQI-----------------------------LIDPVTGEKFDNPV 619

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +VG +YMLKLNHMV DK++ RS G YSL+TQQPLGGKS  GGQR 
Sbjct: 620  SVGVMYMLKLNHMVDDKMHGRSVGPYSLITQQPLGGKSQNGGQRF 664


>gi|226897636|gb|ACO90267.1| RNA polymerase beta subunit gene [Bacillus firmus]
          Length = 389

 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 237/389 (60%), Positives = 303/389 (77%), Gaps = 3/389 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+SF
Sbjct: 1   NPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSF 60

Query: 590 ARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           A+VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQAN+ L +DGSF +E V  
Sbjct: 61  AKVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQANALLGDDGSFLDEEVVA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ E
Sbjct: 121 RFKGENTVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMK 766
           AP VGTGME V  K SGAA++ K  GIVE V+A  + +R ++  D       +D YR++K
Sbjct: 181 APRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIKNVDGQEVKGDLDKYRMLK 240

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAFM W GYN+ED+
Sbjct: 241 FIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAFMTWDGYNYEDA 300

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII  GA
Sbjct: 301 IIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRTGA 360

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRA 915
           EV  GD+LVGK+TPKG + +T EE+LL A
Sbjct: 361 EVKDGDLLVGKVTPKGVTELTAEERLLHA 389


>gi|224458658|gb|ACN43192.1| RpoB [Bacillus sp. PS-97]
          Length = 249

 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 95/277 (34%), Positives = 148/277 (53%), Gaps = 30/277 (10%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ 
Sbjct: 1   RISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFID 50

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+M
Sbjct: 51  YSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+
Sbjct: 102 TDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDA 158

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+  
Sbjct: 159 KDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL-- 216

Query: 258 AKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV 293
                    +  GE   +E+ K L        K   +
Sbjct: 217 ----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 249



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 62/174 (35%), Gaps = 1/174 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 77  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 136

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 137 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 195

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YDL
Sbjct: 196 NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDL 249


>gi|52538167|emb|CAH19185.1| RNA polymerase beta-subunit [Pseudomonas rhodesiae]
          Length = 378

 Score =  364 bits (933), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 224/376 (59%), Positives = 288/376 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV  AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAGAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITRDIP 866
           ARDTKLGPEEI    P
Sbjct: 361 ARDTKLGPEEIYCRHP 376


>gi|221328705|gb|ACM17815.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 376

 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 226/372 (60%), Positives = 291/372 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SP
Sbjct: 122 VVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSISLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|52694325|emb|CAG38002.1| RNA polymerase beta subunit [Pseudomonas sp. LMG 13977]
          Length = 375

 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 225/374 (60%), Positives = 292/374 (78%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 2   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 61

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 62  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D 
Sbjct: 122 EGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 182 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 242 VVAPRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 301

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           +V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E
Sbjct: 302 KVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQE 361

Query: 847 FEVMARDTKLGPEE 860
              +ARDTKLGPEE
Sbjct: 362 LTCVARDTKLGPEE 375


>gi|161345231|gb|ABX64456.1| RpoB [Bacillus amyloliquefaciens]
          Length = 249

 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 95/277 (34%), Positives = 147/277 (53%), Gaps = 30/277 (10%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+
Sbjct: 1   ARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFI 50

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+
Sbjct: 51  DYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPI 101

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D
Sbjct: 102 MTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETD 158

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           +KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+ 
Sbjct: 159 AKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDQALL- 217

Query: 257 GAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
                     +  GE   +E+ K L        K   
Sbjct: 218 -----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 249



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 61/173 (35%), Gaps = 1/173 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 78  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 137

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 138 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 196

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YD
Sbjct: 197 NEYLRNTLDKDNTENSDQALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 249


>gi|209360659|gb|ACI43000.1| RNA polymerase beta subunit [Mycoplasma zalophidermidis]
          Length = 665

 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 233/503 (46%), Positives = 349/503 (69%), Gaps = 10/503 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ S+GE+++N  ++GL ++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3   TNKRIVSLGELVQNNLKVGLSKLEKTTRERMGAKEPDKVSPKNVTNNKLISNQMKTFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN +GF+ETPY +V +G V  ++ VYL+A +E    IAQ+   +DE+ 
Sbjct: 123 IGLILNFATYAKVNEFGFLETPYFRVDNGIVDYSEPVYLTAADEMGYKIAQSTVKVDENN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +  +  R      +   ++IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183 RIIDPQLTIRHNYTYQIGTADEIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ EAPFV TG+E+ +AK S    VA+  GIVE VD  +I IR+          G
Sbjct: 243 QAVPLLETEAPFVATGIEAEIAKYSSGNFVARNDGIVEFVDGKKIKIRND-------KKG 295

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +D Y L  FQRSNQ+T V+Q+PLV+ G EV++ D++ DG S   G+LALG+N+LVAF  +
Sbjct: 296 IDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGDLLVDGSSFKDGELALGKNVLVAFSTY 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++ER+V +DVFTSIHIEE  V  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356 NGYNYEDAVILNERLVKDDVFTSIHIEEQTVQFRTSKAGDDELTADIPNVSKFSTRHLDE 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ VG++V PGD+LVG+++PKG+   T EEKLL A+  ++   V+DTSL+V +G  GT
Sbjct: 416 HGIVRVGSDVAPGDVLVGRVSPKGDDNPTQEEKLLLAVLQQRQQAVKDTSLKVKNGHGGT 475

Query: 939 VVDVRIFNRHGIDKNERSISVER 961
           V+ V I +R    K++    +++
Sbjct: 476 VIGVEILSREN--KDQLEDGIDK 496



 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 140/531 (26%), Positives = 215/531 (40%), Gaps = 90/531 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEAPFVATGIEAEIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  I EF V  +  K+  ++   D  N+      N D    +  ++  G EV  GD
Sbjct: 271  FVARNDGIVEF-VDGKKIKIRNDKKGIDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K +  +   + +L A       +  D  +            S  + +  +  
Sbjct: 330  LLVDGSSFK-DGELALGKNVLVAFSTYNGYNYEDAVILNERLVKDDVFTSIHIEEQTVQF 388

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++ +   +   +    DE  I+         ++L G+ +  G     +  
Sbjct: 389  RTSKAGDDE-LTADIPNVSKFSTRHLDEHGIVRVGSDVAPGDVLVGRVSPKGDDNPTQEE 447

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG--D 1064
             L   ++                   +  +                    +E +     D
Sbjct: 448  KLLLAVL-------------------QQRQQAVKDTSLKVKNGHGGTVIGVEILSRENKD 488

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +  G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP L+DGT VD++LNP
Sbjct: 489  QLEDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPHLEDGTSVDVMLNP 548

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
             GVPSRMN+GQ+ E HLG A   L  K  + + D     +I  +                
Sbjct: 549  QGVPSRMNIGQVLEIHLGMAARSLKTKFVTRVFDGIKKEEIYDVIE-------------- 594

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                            ++G+P        A  + I                L + +TGE 
Sbjct: 595  ----------------EAGLP--------ATGKQI----------------LINPITGEK 614

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            FD PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 615  FDNPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|209360657|gb|ACI42999.1| RNA polymerase beta subunit [Mycoplasma zalophidermidis]
          Length = 665

 Score =  363 bits (932), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 233/503 (46%), Positives = 349/503 (69%), Gaps = 10/503 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ S+GE+++N  ++GL ++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3   TNKRIVSLGELVQNNLKVGLSKLEKTTRERMGAKEPDKVSPKNVTNNKLISNQMKTFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN +GF+ETPY +V +G V  ++ VYL+A +E    IAQ+   +DE+ 
Sbjct: 123 IGLILNFATYAKVNEFGFLETPYFRVDNGIVDYSEPVYLTAADEMGYKIAQSTVKVDENN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +  +  R      +   ++IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183 RIIDPQLTIRHNYTYQIGTADEIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ EAPFV TG+E+ +AK S    VA+  GIVE VD  +I IR+          G
Sbjct: 243 QAVPLLETEAPFVATGIEAEIAKYSSGNFVARNDGIVEFVDGKKIKIRND-------KKG 295

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +D Y L  FQRSNQ+T V+Q+PLV+ G EV++ D++ DG S   G+LALG+N+LVAF  +
Sbjct: 296 IDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGDLLVDGSSFKDGELALGKNVLVAFSTY 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++ER+V +DVFTSIHIEE  V  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356 NGYNYEDAVILNERLVKDDVFTSIHIEEQTVQFRTSKAGDDELTADIPNVSKFSTRHLDE 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ VG++V PGD+LVG+++PKG+   T EEKLL A+  ++   V+DTSL+V +G  GT
Sbjct: 416 HGIVRVGSDVAPGDVLVGRVSPKGDDNPTQEEKLLLAVLQQRQQAVKDTSLKVKNGHGGT 475

Query: 939 VVDVRIFNRHGIDKNERSISVER 961
           V+ V I +R    K++    +++
Sbjct: 476 VIGVEILSREN--KDQLEDGIDK 496



 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 126/531 (23%), Positives = 197/531 (37%), Gaps = 90/531 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEAPFVATGIEAEIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  I EF V  +  K+  ++   D  N+      N D    +  ++  G EV  GD
Sbjct: 271  FVARNDGIVEF-VDGKKIKIRNDKKGIDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K +  +   + +L A       +  D  +            S  + +  +  
Sbjct: 330  LLVDGSSFK-DGELALGKNVLVAFSTYNGYNYEDAVILNERLVKDDVFTSIHIEEQTVQF 388

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++ +   +   +    DE  I+         ++L G+ +  G     +  
Sbjct: 389  RTSKAGDDE-LTADIPNVSKFSTRHLDEHGIVRVGSDVAPGDVLVGRVSPKGDDNPTQEE 447

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG--D 1064
             L   ++                   +  +                    +E +     D
Sbjct: 448  KLLLAVL-------------------QQRQQAVKDTSLKVKNGHGGTVIGVEILSRENKD 488

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +  G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDM              P
Sbjct: 489  QLEDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDM--------------P 534

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
                         E                   D   N    P R  + +V+        
Sbjct: 535  H-----------LE--------------DGTPVDVMLNPQGVPSRMNIGQVL-------- 561

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                    +              T VFDG  +E I  ++  A L  +G+ IL + +TGE 
Sbjct: 562  -------EIHLGMAARSLKTKFVTRVFDGIKKEEIYDVIEEAGLPATGKQILINPITGEK 614

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            FD PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 615  FDNPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|92090449|gb|ABE73082.1| RNA polymerase beta subunit [Mesoplasma lactucae ATCC 49193]
          Length = 598

 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 228/425 (53%), Positives = 312/425 (73%), Gaps = 9/425 (2%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            + +N LS +T+ RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++
Sbjct: 1   MDQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHESHYGRICPIETPEGPNIGLINN 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           L ++A+VN YGFI TPYRKV +GK+  ND+ YL+A EE    IAQAN    +DG   +E 
Sbjct: 61  LATYAKVNEYGFITTPYRKVNNGKIDNNDIRYLTADEESKYIIAQANVRQSKDGDILDET 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  G++I+     +DFID SPKQ+ SIA + IPFLENDD+NR LMG NMQRQAVPLL
Sbjct: 121 VISRYKGDDIIANTADVDFIDVSPKQIFSIATACIPFLENDDANRALMGANMQRQAVPLL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
             +AP VGTG+E   A+ SG+A+VAK  GIV  VD+  I + + +        G   Y+L
Sbjct: 181 NPQAPLVGTGVEFEAARDSGSAVVAKEDGIVRYVDSKVITVETKD--------GTHTYQL 232

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           + F+RSN  T ++Q P+VKVGD+V++ +IIADGPS D G+LA+G+N++VAF  ++GYN+E
Sbjct: 233 INFERSNNGTAISQAPIVKVGDQVKKGEIIADGPSMDNGELAIGQNVVVAFTTYNGYNYE 292

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++++SER+  ED FTSIH++E+ +  R+TK G EEITR++PN+S+   K +DE GI+ +
Sbjct: 293 DAIIMSERVTQEDRFTSIHVDEYTIERRNTKQGEEEITRELPNISDNAKKYLDEDGIVAI 352

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G EV+ GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  V+ 
Sbjct: 353 GTEVHQGDILVGKVTPKGQVQLSPEDKLLNAIFGEKSRNVKDNSLRVPNGGDGIVQSVKR 412

Query: 945 FNRHG 949
           F R  
Sbjct: 413 FTRED 417



 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 130/422 (30%), Positives = 181/422 (42%), Gaps = 77/422 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ VG +V  G+I+    +      +   + ++ A       +  D  +           
Sbjct: 249  IVKVGDQVKKGEIIADGPS-MDNGELAIGQNVVVAFTTYNGYNYEDAIIMSERVTQEDRF 307

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                VD     R    + E  I+ E   I   A+   DE  I+         +IL G+  
Sbjct: 308  TSIHVDEYTIERRNTKQGEEEITRELPNISDNAKKYLDEDGIVAIGTEVHQGDILVGKVT 367

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L + +  E  R           +V    + +                 
Sbjct: 368  PKGQVQLSPEDKLLNAIFGEKSR----NVKDNSLRVPNGGDGIVQSV------------- 410

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K    + G D+ P +L V+KV++  KR IQ GDKM+GRHGNKG++SRILP EDMP L+DG
Sbjct: 411  KRFTREDGYDLAPDILEVIKVYIVQKRKIQEGDKMSGRHGNKGVISRILPIEDMPHLEDG 470

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   LG K+ + + +   + ++  +       
Sbjct: 471  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKLGVKVATPVFEGLTDEELDDIMKEAGMT 530

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                DGA                     
Sbjct: 531  NFGKVKLI----------------------------DGA--------------------- 541

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEP D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 542  -----TGEPMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 596

Query: 1296 EM 1297
            EM
Sbjct: 597  EM 598


>gi|313227690|emb|CBY22838.1| unnamed protein product [Oikopleura dioica]
          Length = 1187

 Score =  363 bits (931), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 158/980 (16%), Positives = 303/980 (30%), Gaps = 192/980 (19%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  ++    G+   DD D+ GN+R+   G +L   +R    
Sbjct: 351  HVGISEYCETKKAYFLGYMVNRILQAGLGRRGEDDRDHYGNKRMDLAGPLLAFLFRSLFK 410

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ +  +   +        +     I  K +   +     +               +SQ+
Sbjct: 411  KLTKDARIAAQKEIEKGKPMNVLTAIKTKIITDGLKYSLATGNWGDQQKASQCRPGVSQV 470

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   S ++H RRL++     V R     + R +H T +G +CPAET EGH +GLV +
Sbjct: 471  LNRLTYASSLSHLRRLNS----PVGRDGKLAKPRQLHSTQWGMVCPAETPEGHAVGLVKN 526

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L   + ++           + +     ++  ++     +      N          E+L+
Sbjct: 527  LALMSYISVGSQPSPILEFLEEWS-MENLEEITPNSISDATKIFVNGCWVGIHRDPEQLM 585

Query: 646  -FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
               R    ++ +   ++  +     + + I           D+ R+     +      LL
Sbjct: 586  GTLRKLRRQMDIIVSEVSMVRDIRNREIRIYT---------DAGRICRPLLIVEDQRLLL 636

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            K +           + K    +  +    I   V      +         +   V     
Sbjct: 637  KKD--------HLAMLKDPEYSNYSWTELIKAGVVEYIDTLEEETIMCAMTPDEVKKTDE 688

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            M + RS                           P+  LG       +  + +P+  +N  
Sbjct: 689  MAYCRSY--------------------THCEIHPAMILG-------VCASIVPFPDHNQS 721

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                                  ++       +G       I   +   +           
Sbjct: 722  PRN------------------TYQSAMGKQAVGVFVTNFQIRMDTMGNICF--------- 754

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                     +   +     S +      + A+      +  D+ +   + +        I
Sbjct: 755  --YPQKPLCVTRSMEYLRFSELPAGINTIVALSCYTGYNQEDSLIMNMASLDRG-FHRSI 811

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            + R   D   + I    E  E   R           +       I  G           K
Sbjct: 812  YYRGYRDTENKKILDPEETFEKPDRATTQGMRHAMYDKLEDDGLIAPGTRISGDDVMIGK 871

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                                A+QD      ++    +Y    + L  +   K        
Sbjct: 872  ------------------TIALQDGD--DALDPTAKKYTKKDASLFAKPTEKGIIDSVMV 911

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     + VK+ +   R  + GDK A RHG KG    +L CEDM F  DG   D+++NP
Sbjct: 912  TINEDGYKFVKIRLRSVRIPEVGDKFASRHGQKGTNGIMLRCEDMLFTPDGMQPDLIVNP 971

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +G +FE                                              
Sbjct: 972  HAIPSRMTIGHLFECLTSKVGA-------------------------------------- 993

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                            K  +  +TP       + ++ +L   +  + G  +LY G TG  
Sbjct: 994  ---------------IKGEIGDATPFNPSVTVQKVSDILHEYEYQQRGNEVLYSGFTGRK 1038

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
             +  V  G  Y  +L HMV+DK+++R+ G   L+ +QP+ G+S  GG R GEME  C  A
Sbjct: 1039 MNTQVFFGPTYYQRLKHMVNDKIHSRARGPVQLLNRQPMEGRSRDGGLRFGEMERDCQIA 1098

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------------------NDTFETGTP 1344
            +GA+  L+E L   SD      RV+   + G                     +  +   P
Sbjct: 1099 HGASQFLKERLFEVSDP----YRVHVCNLCGLICVANLTSNSFECRSCSNKTNISQVRMP 1154

Query: 1345 ESFNVLVKEMQALGLSIDLE 1364
             +  +L +E+ ++ ++  + 
Sbjct: 1155 YACKLLFQELMSMQIAPRMM 1174



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 111/830 (13%), Positives = 227/830 (27%), Gaps = 137/830 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG------------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +    I   S                ++F
Sbjct: 38  LVRQQLESFDEFITMSV----------QRIVEESPVIELQSEPNYNAGEPEEPTKYQIKF 87

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY  PL + +       D+    +     K
Sbjct: 88  EQIYLSKPTHWEVGTGPNPLMPNEARLRNLTYCAPLYVDINRTTIRSDDPRPHEE----K 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            + I++G +P+M                           G FVI G +++V++Q   +  
Sbjct: 144 HEKIFIGQIPIMLRSEYCLLSGLSDRDLTELNECPLDPGGYFVINGSEKVVIAQEKMANN 203

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGL---WMDIEFD------SKDII---------H 203
            ++    K           +C     +     W+++          K  I         +
Sbjct: 204 TVYVFEKKDSKYELTAECRSCLENSSRPTSTIWINLLARSGGTGVKKSAIGRRIAAILPY 263

Query: 204 VRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           V+ D     P+     ALG  S+ +IL             +     +  A ++    V+ 
Sbjct: 264 VKQDT----PIIIVFRALGFVSDRDILEHIVYDFDDPDMMEMVKPSIDEAFVIQEEAVAL 319

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             +        +   K++     K + +K +      S+           +      I  
Sbjct: 320 DFIGKRGARPGVTREKRM--KYAKEILQKELLPHVGISEYCETKKAY--FLGYMVNRILQ 375

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
                  E   +   +  +                +     +   K  KDA +   + + 
Sbjct: 376 AGLGRRGEDDRDHYGNKRMDL----------AGPLLAFLFRSLFKKLTKDARIAAQKEIE 425

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
            G       A      +  D  KY L   G      + +   P   + + +    + +  
Sbjct: 426 KGKPMNVLTAIK--TKIITDGLKYSL-ATGNWGDQQKASQCRPGVSQVLNRLTYASSLSH 482

Query: 443 LVDL-----RNGKGTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRMERSIKER 489
           L  L     R+GK       +     +    E        ++KN   +  + +       
Sbjct: 483 LRRLNSPVGRDGKLAKPRQLHSTQWGMVCPAETPEGHAVGLVKNLALMSYISVGSQPSPI 542

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +  ++  S+   + I    +  A   F     +    +    +  +   RR   +    V
Sbjct: 543 LEFLEEWSMENLEEITPNSISDATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEV 602

Query: 550 ARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           +  R          T  GRIC P    E   + L     +  +       E       + 
Sbjct: 603 SMVRDIRNREIRIYTDAGRICRPLLIVEDQRLLLKKDHLAMLK-----DPEYSNYSWTEL 657

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+  +EEE    A     + +                            +  P
Sbjct: 658 IKAGVVEYIDTLEEETIMCAMTPDEVKKTDEM---------------AYCRSYTHCEIHP 702

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG--TGMESVVAKSSGAA 726
             ++ + AS++PF +++ S R      M +QAV +            G      +     
Sbjct: 703 AMILGVCASIVPFPDHNQSPRNTYQSAMGKQAVGVFVTNFQIRMDTMGNICFYPQKPLCV 762

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +       ++ A    I ++      +     I  +    R    +  
Sbjct: 763 TRSMEYLRFSELPAGINTIVALSCYTGYNQEDSLIMNMASLDRGFHRSIY 812


>gi|118082917|ref|XP_416307.2| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Gallus gallus]
          Length = 1126

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 165/996 (16%), Positives = 310/996 (31%), Gaps = 179/996 (17%)

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              ++    K  +     +  +  L      +     K    A++   V L  G+  +DD 
Sbjct: 288  QRMWGGPKKTKMEEARELLASTILTHVLVKEFNFRAKCIYTAVMVRRVILAQGENKVDDR 347

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSA 512
            D  GN+R+   G++L   +     +    +K+    V       Q      +    + + 
Sbjct: 348  DYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQVIPKQRAAQFDVVKHMRQDQITNG 407

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPT 564
            +     +   S     ++         RLS +   G+         + R     R + P+
Sbjct: 408  MVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPS 467

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +G +CP++T EG   GLV +L     +      + P  K+       DV  L   EE +
Sbjct: 468  QWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIIKLASNLGVEDVNLL-CGEELS 525

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N  L         ++              +  +I+       +++   +    +
Sbjct: 526  Y----PNVFLVFLNGNILGVIRDHQKLVNTFRIMRRAGYINEFVSISTNLSDRCV--YIS 579

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D  R+     + ++  P +  +       ME +              G     D +   
Sbjct: 580  SDGGRLCRPYIIVKKQKPAVTNK------HMEELA------------QGYRNFEDFLHEG 621

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +       + +   + +Y     + +                                 +
Sbjct: 622  LVEYLDVNEENDCNIALYEHTINKDTTHLEI----------------------------E 653

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +    +P+  +N          M  + + T      +    R   L        
Sbjct: 654  PFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG----YNQRNRIDTLMYLLAYPQ 709

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             P V  + ++ ID                            +   +    A+      D+
Sbjct: 710  KPMVKTKTIELID-------------------------FEKLPAGQNATVAVMSYSGYDI 744

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +   + +        ++        +R  +   +++     D    + I    I  
Sbjct: 745  EDALVLNKASLDRGFGRCLVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILD 803

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                   G+   +      KS                 Q  ++   V +       QY+ 
Sbjct: 804  ADGICSPGEKVENKQVLVNKSMP------------TVTQTPLEGSSVPQQ-----PQYKD 846

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 +    + IEK+    +       ++K+ +   R  + GDK + RHG KG+   I+
Sbjct: 847  VPVTYKGATDSYIEKVMISSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 904

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPF   G   DI++NP G PSRM V        G     L  K   L   +     
Sbjct: 905  PQEDMPFCDTGICPDIIMNPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT- 955

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                          F G+  + +   L 
Sbjct: 956  ---------------------------------------------AFGGSKVKDVCEDLI 970

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  
Sbjct: 971  RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTE 1030

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAG 1335
            G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G+  +            
Sbjct: 1031 GRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKS 1090

Query: 1336 N-DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            +        P +  +L +E+Q++ +   L+ ++   
Sbjct: 1091 SCHVSSLRIPYACKLLFQELQSMNIIPRLKLAKYNE 1126



 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 128/955 (13%), Positives = 275/955 (28%), Gaps = 200/955 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 33  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGTPDVEE 83

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 84  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 133

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 134 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 192

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMALGMD 224
            G  + +               + K   ++ + + R           +P+     A+G++
Sbjct: 193 VGASVTSST------------HEKKSRTNMVVKQGRFYLRHNTLSEDIPIAIIFKAMGVE 240

Query: 225 SE-EILSTFYPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S+ EI+     +            +      F    A   +G KV    +     +  +E
Sbjct: 241 SDQEIVQMIGTEEHVMAAFAPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGPKKTKME 300

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             ++L +  +  L    VK     + C+    V    V    GE  ++  D    K LE 
Sbjct: 301 EARELLASTI--LTHVLVKEFNFRAKCIY-TAVMVRRVILAQGENKVDDRDYYGNKRLEL 357

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                      L+    +    I + ++  +      A  D+ + MR   ++   V    
Sbjct: 358 AGQLLSLLFEDLFKKFNSELKKIADQVIPKQR----AAQFDVVKHMRQDQITNGMVNA-- 411

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +   +   ++ +   G  ++  RL+  +   +            K+             
Sbjct: 412 ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ------ 465

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                   +    +  + +    +  +           D   +     +  + V     E
Sbjct: 466 ---PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLASNLGVEDVNLLCGE 522

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                 +  +  + N L  I   ++L    +  + RA    E   +      R     + 
Sbjct: 523 ELSYPNVFLVFLNGNILGVIRDHQKLVNTFRI-MRRAGYINEFVSISTNLSDRCVYISSD 581

Query: 576 EGHNIGL--VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            G       +      A  N     +   YR   D      V YL   EE +  IA    
Sbjct: 582 GGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHEGLVEYLDVNEENDCNIAL--- 638

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                                     +    ++  P  ++ + A LIP+  ++ S R   
Sbjct: 639 --------------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 678

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +         G        +   ++A                       
Sbjct: 679 QCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----------------------- 706

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    Q+P+VK                 D   L  G+N  
Sbjct: 707 -----------------------YPQKPMVK----------TKTIELIDFEKLPAGQNAT 733

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEE 871
           VA M + GY+ ED++++++  +       +  +  +    R T    +++   + + +  
Sbjct: 734 VAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATR 793

Query: 872 GLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                   +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 794 KPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQTPLEGSSVPQQPQYKDVP 848


>gi|212373943|emb|CAP09898.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35697]
          Length = 370

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 221/369 (59%), Positives = 287/369 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLG 857
            +ARDTKLG
Sbjct: 362 CVARDTKLG 370


>gi|221328709|gb|ACM17817.1| RNA polymerase subunit B [Pseudomonas sp. ICMP 5941]
          Length = 376

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 224/372 (60%), Positives = 290/372 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL+ SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIDSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++D+V+LSA+EE +  IAQA+++++E+    +ELV  R   E  +   E +  +D SP
Sbjct: 122 VVSDDIVFLSAIEEADHVIAQASAAMNENKQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCLNQRPLVSKGDKV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSISLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|52694329|emb|CAG38004.1| RNA polymerase beta subunit [Pseudomonas ficuserectae]
          Length = 376

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 224/374 (59%), Positives = 290/374 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D 
Sbjct: 121 EGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELVDELVAVRHLNEFTVKAPADVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQE 360

Query: 847 FEVMARDTKLGPEE 860
              +ARDTKLGPEE
Sbjct: 361 LTCVARDTKLGPEE 374


>gi|227809532|gb|ACP40985.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
          Length = 666

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 244/520 (46%), Positives = 359/520 (69%), Gaps = 13/520 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ +VGE+L+ Q+ LGLL++E++ KE++SS + D + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVAVGELLQKQFLLGLLKLEKNTKEKLSSKESDKINPKNITNNKPIYNQFKTFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN LS + + RR+++LG GG+ R  A  E+RDVH T+YGRICP ET EG NI
Sbjct: 63  KLSQFMDQVNPLSELANKRRITSLGPGGLNRETAQFEVRDVHSTYYGRICPIETPEGQNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L ++++ + +GFI+TPY  V +G V   +V +L+A++E     AQ++ ++DE+  
Sbjct: 123 GLILNLATYSKTDDFGFIQTPYFPVKNGVVNYGEVKWLTAVDEYGYTFAQSSVTIDENNK 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E +  R   + ++V  E+ID+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQ
Sbjct: 183 IIDEFITVRKDYQYLIVKPEEIDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL++AEAP +GTG+E  +AK +   I A  +GIV  VDA  I I+  +G+L+      
Sbjct: 243 AVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYVDAKTIKIKPFDGNLEE----- 297

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           DIY L  FQ+SNQ T +NQ P V+VG+ + +  ++ DGPST  G+LALG+N+LVAF  WH
Sbjct: 298 DIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTKDGELALGKNVLVAFTTWH 357

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++ISE++V +DVFTSIHIEE  +  R +K G + +T +IPN S    +++DE 
Sbjct: 358 GYNFEDAIIISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDEN 417

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EVN GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G +GTV
Sbjct: 418 GIVRVGSEVNTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGSNQKDTSLKVKHGDAGTV 477

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           +DV+I +R   D       +  + I+ + +    ++  + 
Sbjct: 478 IDVQIISRANGD-------ILEDGIDKIVKVFIAQKRKIK 510



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 125/414 (30%), Positives = 186/414 (44%), Gaps = 67/414 (16%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG  +  G ++    + K +  +   + +L A       +  D  +     V   V  
Sbjct: 320  VEVGETIEKGQLVCDGPSTK-DGELALGKNVLVAFTTWHGYNFEDAIIISEKLVKDDVF- 377

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I       +   S + +      +       +  LD N   R+   +   + + G   
Sbjct: 378  TSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDENGIVRVGSEVNTGDILVGRIS 437

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     + +        +       ++   +   SLKV++  + ++++     +I    
Sbjct: 438  PKGEDNPTPE-------EKLLNAIFGNKGSNQKDTSLKVKHGDAGTVID----VQIISRA 486

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD +  G+ ++VKVF+A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI+
Sbjct: 487  NGDILEDGIDKIVKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPYLEDGTPIDIL 546

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GV SRMN+GQ+ E HLG A   L  K  S + D   N  +  +             
Sbjct: 547  LNPQGVASRMNIGQVLELHLGMAAKKLNVKFVSPVFDGIKNESLDSIL------------ 594

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                              E           L ESG+  LYDG+T
Sbjct: 595  ---------------------------------KEAD---------LPESGRFTLYDGIT 612

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            G+ +D  V+VG +YMLKL HMV DK+ ARS G YSL++QQPLGGKS  GGQR G
Sbjct: 613  GKQYDSKVSVGVMYMLKLQHMVDDKINARSVGPYSLISQQPLGGKSQNGGQRFG 666


>gi|63054498|ref|NP_593101.2| RNA polymerase II complex subunit Rpb2 [Schizosaccharomyces pombe
            972h-]
 gi|19862286|sp|Q02061|RPB2_SCHPO RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2; AltName: Full=DNA-directed RNA polymerase II 138 kDa
            polypeptide
 gi|256599716|pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|256599728|pdb|3H0G|N Chain N, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|159883907|emb|CAB86470.2| RNA polymerase II complex subunit Rpb2 [Schizosaccharomyces pombe]
          Length = 1210

 Score =  363 bits (931), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 193/1210 (15%), Positives = 362/1210 (29%), Gaps = 204/1210 (16%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQR------GDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L      +  IL+      +Y         G ++    S   ++   + ++++
Sbjct: 154  KIP--IMLR----STFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANI 207

Query: 265  VDIDTGEQ--------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            V +              I S  +  S L+ S++ K +      S       +     +  
Sbjct: 208  VQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRATLPYIRSDIP 267

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               ++   G V D   LE I +       +  +      A++         +D+  AL  
Sbjct: 268  IVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFV--------IQDKDIALDY 319

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            I +              S          +Y    + +  +       T +     +   +
Sbjct: 320  IGKR------------GSTTGVTREKRLRYAHDILQKELLPHIT---TMEGFETRKAFFL 364

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
              +I  ++     +   DD D+ G +R+   G +L + +R+   +M R +    +     
Sbjct: 365  GYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVET 424

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRL 541
                     + +  + + +     +               +SQ+       S ++H RR 
Sbjct: 425  NREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRT 484

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            +      + R     + R +H TH+G +CPAET EG   GLV +L+  + V+  G    P
Sbjct: 485  NT----PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVS-VGSPSAP 539

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGEEILVP 657
              +  +      +   +     N      N             TE L   R   +     
Sbjct: 540  IIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEV 599

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRV--LMGCNMQRQAVPLLKAEAPFVGTGM 715
                D  +   +          P    D++          ++++ +  L  +        
Sbjct: 600  SIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDP 659

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E        A + +     ++  +   ++I     DL+ S      Y + +     Q   
Sbjct: 660  EQRFGW--TALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVK 717

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                P V               P+  LG LA       + +P+  +N          M  
Sbjct: 718  PAPNPHVH------AWTHCEIHPAMILGILA-------SIIPFPDHNQSPRNTYQSAMGK 764

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   +++  ++V                               +  +           
Sbjct: 765  QAMG--VYLTNYQVRM---------------------------DTMANILYYPQKPLATT 795

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +   +  + AI      +  D+ +   + +   +    IF R   D+ ++
Sbjct: 796  RSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF-RSIFYRTYTDQEKK 854

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                  E+ E   R           +       I  G           K+  +  D    
Sbjct: 855  IGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEEL 914

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R+Q          ++     +  Q                             L+ VK
Sbjct: 915  GQRTQLHAKRDVSTPLRSTESGIVDQ--------------------VMVTTNQEGLKFVK 954

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R  Q GDK A RHG KG +      EDMPF   G   DI++NP  +PSRM V  
Sbjct: 955  VRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAH 1014

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L       G +  +          +S L                 S         
Sbjct: 1015 LVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLR---------------SHGFQSRGFE 1059

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            V     +G  +   VF G                                         Y
Sbjct: 1060 VMYHGHTGRKLVAQVFLG---------------------------------------PTY 1080

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L H+V DK++AR+ G   ++T+QP+ G+S  GG R GEME  C  ++G + VL+E L
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140

Query: 1316 TIKSD-------DVVGRTRV-------YE--SIVAGNDTFETGTPESFNVLVKEMQALGL 1359
               SD       D+ G   +       YE  S        +   P +  +L +E+ ++ +
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200

Query: 1360 SIDLENSRTK 1369
            +  L     K
Sbjct: 1201 APRLFTKNHK 1210



 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 141/1020 (13%), Positives = 289/1020 (28%), Gaps = 194/1020 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L   Q  S+D F+   +          Q        +T              +    + F
Sbjct: 30  LARQQLFSFDEFVQNTM----------QEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINF 79

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFD-------VDEFTGA 119
                  P               +   R+LTY+ PL + +R  V         + E    
Sbjct: 80  GQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWL 139

Query: 120 KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
              +D +   +++G +P+M +                         G F+I G ++++++
Sbjct: 140 VEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIA 199

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDII----------- 202
           Q  RS          + +    + Y   I    ++G  +      K +            
Sbjct: 200 QE-RSAANI--VQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIR 256

Query: 203 ----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
               ++R D    +P+     ALG+  + +IL          Q  +     +  A ++  
Sbjct: 257 ATLPYIRSD----IPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQD 312

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             ++   +        +   K+L       L+++ +  +                +    
Sbjct: 313 KDIALDYIGKRGSTTGVTREKRLRYAH-DILQKELLPHITTMEGFETRKAFFLGYMIH-- 369

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A +  +    +      +    P+L          +   +     K  +     
Sbjct: 370 -RMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREF 428

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +    ++ T  +  S+    + D  +  ++ VG  ++  R    +      R     
Sbjct: 429 NLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPI 488

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +         +      ++KN   +  + +       I  ++
Sbjct: 489 GRDGKLAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLSLMSYVSVGSPSAPIIEFLE 545

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
              +   +  N     +A   F     L    +  +    +   RR   +  +  + R  
Sbjct: 546 EWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDI 605

Query: 554 AGVEMRDVHPTHYGRIC---------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
              E+R    T  GRIC         P     G        +           I+   R 
Sbjct: 606 REKELR--LFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRF 663

Query: 605 -VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF------TEELVFCRCAGEEILVP 657
                  +  + YL A EEE   IA +   L+            EEL   +         
Sbjct: 664 GWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPH 723

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++ S R      M +QA+ +              
Sbjct: 724 VHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQV------- 776

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                                + + +  Y       +     + 
Sbjct: 777 ----------------------------------RMDTMANILYYPQKPLATTRSMEYLK 802

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            R                        +L  G+N +VA + + GYN EDS+++++  +   
Sbjct: 803 FR------------------------ELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRG 838

Query: 838 VFTSIHIEEFEVMARDTKLG-PEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F SI    +    +   +   EE  R        +       +++ G+I  G  V+  D
Sbjct: 839 LFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGED 898

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P         ++        +    RD S  + S  SG V  V +       K
Sbjct: 899 IIIGKTAPIPLDHEELGQRT-------QLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLK 951


>gi|161345227|gb|ABX64454.1| RpoB [Bacillus subtilis]
          Length = 248

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 95/276 (34%), Positives = 147/276 (53%), Gaps = 30/276 (10%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ 
Sbjct: 1   RISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFID 50

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+M
Sbjct: 51  YSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+
Sbjct: 102 TDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDA 158

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+  
Sbjct: 159 KDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDQALL-- 216

Query: 258 AKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
                    +  GE   +E+ K L        K   
Sbjct: 217 ----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 248



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 61/173 (35%), Gaps = 1/173 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 77  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 136

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 137 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 195

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YD
Sbjct: 196 NEYLRNTLDKDNTENSDQALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 248


>gi|52694383|emb|CAG38031.1| RNA polymerase beta subunit [Pseudomonas agarici]
          Length = 366

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 223/365 (61%), Positives = 286/365 (78%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++    T+ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNDKKILTDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAPRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+A
Sbjct: 241 DSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 301 DGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 360

Query: 856 LGPEE 860
           LGPEE
Sbjct: 361 LGPEE 365


>gi|294768466|gb|ADF36181.1| RNA polymerase beta subunit [Mycoplasma sp. Mirounga ES2774-NAS]
          Length = 668

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 240/495 (48%), Positives = 347/495 (70%), Gaps = 8/495 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ R+GLL++E++ KE+I+  D+D +  +++ N KP+ + +  FF SS
Sbjct: 4   NKRIVTIGELLQNQLRIGLLKLEKNTKEKIAGKDLDKITARNVTNNKPIYNQMKSFFNSS 63

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 64  KLSQFMDQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNI 123

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-G 638
           GL+ ++ S+A+++ YGFI+TPY KV +G    +DV YL+A+EE N   AQ++ ++DE  G
Sbjct: 124 GLILNMASYAKIDEYGFIQTPYFKVNNGVADFDDVRYLTAIEEVNFTFAQSSINIDESTG 183

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E V CR   E I VPRE+ID++  S +Q+ SI+AS IPFLENDD+NR LMG NMQR
Sbjct: 184 KILDEKVICRKNNEYIEVPREEIDYMGVSSRQMTSISASAIPFLENDDANRALMGSNMQR 243

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+K EAP+V TG+E+ +A+ S + + A + G+V  VDA +I I+S       +   
Sbjct: 244 QAVPLIKPEAPYVATGVEADIARFSASNVRATKDGVVTYVDASQIKIQSE------NEKK 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             IY L  F+RSNQ T ++Q+PLV VG E++  D++ DGPS + G+LALG+N+LV F  W
Sbjct: 298 PTIYYLRTFERSNQGTVIHQKPLVHVGQEIKAGDLLTDGPSMEKGELALGKNVLVGFSTW 357

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++E++V EDV+TSIHIEE  +  R +K G + +T +IPN S    + + E
Sbjct: 358 YGYNYEDAVVLNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSEIPNASNRSKRFLTE 417

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GT
Sbjct: 418 DGIVRIGSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGT 477

Query: 939 VVDVRIFNRHGIDKN 953
           VV V +  R   D N
Sbjct: 478 VVAVDVLRRDTDDTN 492



 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 116/415 (27%), Positives = 175/415 (42%), Gaps = 66/415 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+L    +   +  +   + +L         +  D  +     V   V 
Sbjct: 320  LVHVGQEIKAGDLLTDGPS-MEKGELALGKNVLVGFSTWYGYNYEDAVVLNEKLVKEDV- 377

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  RS + +      +    +  +  L  +   R+   +   + + G  
Sbjct: 378  YTSIHIEEQTIQFRRSKAGDDILTSEIPNASNRSKRFLTEDGIVRIGSEVGPGDILVGRI 437

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V+        +  +L     +     
Sbjct: 438  SPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVLRRDTDD----- 490

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                ++  G+  +VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 491  ---TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPEEDMPYLEDGTPLDI 547

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  +  + + D  +   I  ++           
Sbjct: 548  LLNPQGVPSRMNIGQVLELHLGLAAKKLNCRFVTPVFDGISYKQIQEIQKEAGIDPSGKM 607

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SG+       
Sbjct: 608  TV-----------------------------------------------YSGK------- 613

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 614  TGKPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 668


>gi|83755153|gb|ABC46425.1| RNA polymerase beta subunit [Spiroplasma apis]
          Length = 594

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 232/477 (48%), Positives = 332/477 (69%), Gaps = 10/477 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N YGFIETPYRKV +GKV  N+  YL+A +E +  +AQAN  +D +G   ++ V 
Sbjct: 61   TYARINKYGFIETPYRKVENGKVLINEYEYLTADKERDYVVAQANIQIDANGKILDDSVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+VP   +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVPPMDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VAK  GIV+ VD+ +I +          +SGV  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAVVAKADGIVKYVDSRKITV--------EESSGVRNYVLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FNRSNNGTAITHIPIVKVGDKIKERDILADGPSMENGELALGQNLVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+I N+SE   K++DE GI  +G+
Sbjct: 293  VILSERVVIDDRFTSIHIDEYTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGS 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            R  G D     + + +  +    + ++ +++         + +IL  ++      G 
Sbjct: 413  RADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGV 469



 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 120/418 (28%), Positives = 173/418 (41%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++   DIL    +      +   + L+ A       +  D  +         V+
Sbjct: 247  IVKVGDKIKERDILADGPS-MENGELALGQNLVVAFTTWNGYNYEDAVIL----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E      G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP  ++G P
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGVP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVSTPVFEGVKENELIEIMEEAGMENY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVKLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPL GK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLSGKAQNGGQRFG 594


>gi|83755155|gb|ABC46426.1| RNA polymerase beta subunit [Spiroplasma apis]
          Length = 594

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 232/477 (48%), Positives = 332/477 (69%), Gaps = 10/477 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N YGFIETPYRKV +GKV  N+  YL+A +E +  +AQAN  +D +G   ++ V 
Sbjct: 61   TYARINKYGFIETPYRKVENGKVLINEYEYLTADKERDYVVAQANIQIDANGKILDDSVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+VP   +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVPPMDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VAK  GIV+ VD+ +I +          +SGV  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAVVAKADGIVKYVDSRKITV--------EESSGVRNYVLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FNRSNNGTAITHIPIVKVGDKIKERDILADGPSMENGELALGQNLVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+I N+SE   K++DE GI  +G+
Sbjct: 293  VILSERVVIDDRFTSIHIDEYTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGS 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            R  G D     + + +  +    + ++ +++         + +IL  ++      G 
Sbjct: 413  RADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGV 469



 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 121/418 (28%), Positives = 174/418 (41%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++   DIL    +      +   + L+ A       +  D  +         V+
Sbjct: 247  IVKVGDKIKERDILADGPS-MENGELALGQNLVVAFTTWNGYNYEDAVIL----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E      G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP  ++G P
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGVP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVSTPVFEGVKENELIEIMEEAGMENY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVKLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|83755151|gb|ABC46424.1| RNA polymerase beta subunit [Spiroplasma apis]
          Length = 594

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 232/477 (48%), Positives = 332/477 (69%), Gaps = 10/477 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N YGFIETPYRKV +GKV  N+  YL+A +E +  +AQAN  +D +G   ++ V 
Sbjct: 61   TYARINKYGFIETPYRKVENGKVLINEYEYLTADKERDYVVAQANIQIDANGKILDDSVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+VP   +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMVPPMDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VAK  GIV+ VD+ +I +          +SGV  Y L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAVVAKADGIVKYVDSRKITV--------EESSGVRNYVLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FNRSNNGTAITHIPIVKVGDKIKERDILADGPSMENGELALGQNLVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+I N+SE   K++DE GI  +G+
Sbjct: 293  VILSERVVIDDRFTSIHIDEYTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGS 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            R  G D     + + +  +    + ++ +++         + +IL  ++      G 
Sbjct: 413  RADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGV 469



 Score =  278 bits (710), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 121/418 (28%), Positives = 174/418 (41%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++   DIL    +      +   + L+ A       +  D  +         V+
Sbjct: 247  IVKVGDKIKERDILADGPS-MENGELALGQNLVVAFTTWNGYNYEDAVIL----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E      G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP  ++G P
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGVP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGIAAKKLGIKVSTPVFEGVKENELIEIMEEAGMENY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVKLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|161345223|gb|ABX64452.1| RpoB [Bacillus subtilis]
          Length = 247

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 95/275 (34%), Positives = 147/275 (53%), Gaps = 30/275 (10%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ 
Sbjct: 1   RISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFID 50

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+M
Sbjct: 51  YSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+
Sbjct: 102 TDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDA 158

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+  
Sbjct: 159 KDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDQALL-- 216

Query: 258 AKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEK 291
                    +  GE   +E+ K L        K  
Sbjct: 217 ----EIYERLRPGEPPTVENAKSLLDSRFFDPKRY 247



 Score = 48.5 bits (114), Expect = 0.007,   Method: Composition-based stats.
 Identities = 34/172 (19%), Positives = 60/172 (34%), Gaps = 1/172 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 77  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 136

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 137 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 195

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +Y
Sbjct: 196 NEYLRNTLDKDNTENSDQALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRY 247


>gi|186885829|gb|ACC93322.1| RNA polymerase beta subunit [Chrysanthemoides monilifera]
          Length = 1024

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 233/684 (34%), Positives = 377/684 (55%), Gaps = 21/684 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   ARV
Sbjct: 341 TQIVHGRKLSYLGPGGLTARIATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKISERSKGTRMLYLSPGRDEYYMVAAGNSLALNKGIPEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSNSEKSIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SGA  +A+  G +   D  +I +                  L+ +QRSN+
Sbjct: 521 TGLEGQAALDSGALAIAEHEGKIIYTDTDKIHLSGN--------GNTLRIPLVMYQRSNK 572

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC++Q+P V+ G  +++  I+A G +T  G+LALG+N+LVA+MPW GYNFED++LISER
Sbjct: 573 NTCMHQKPQVRRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISER 632

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI + E+       GPE +T +IP++    L+N+D+ GI+ +G+ V  GD
Sbjct: 633 LVYEDIYTSFHIRKHEIQI---NQGPERVTNEIPHLEAHLLRNLDKNGIVMLGSWVETGD 689

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           ILVGK+TP+   ES   PE++LLR I G +    ++T L++P G  G V+DVR       
Sbjct: 690 ILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGSRGRVIDVRWVQSSKT 749

Query: 951 DKNERSISV-----EREQIELLAR 969
           D+ E++ S+     ++ +I++  +
Sbjct: 750 DETEKTESIRVYILQKREIKVGDK 773



 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 133/460 (28%), Positives = 215/460 (46%), Gaps = 54/460 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE---QIELLARDKDDEQVILDRN 981
            ++  +           D  + +   + ++  +    R+   QI        +E   L+ +
Sbjct: 609  KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKHEIQINQGPERVTNEIPHLEAH 668

Query: 982  IY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     +   ++ G    +G     K T       S  P  +  +  +           L
Sbjct: 669  LLRNLDKNGIVMLGSWVETGDILVGKLTPQMVKESSYAPEDRLLRTILGMRVYTSKETCL 728

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+   +   +++ R+      +Q            ++V++  KR I+ GDK+AGRHGNKG
Sbjct: 729  KLPIGSRGRVIDVRW------VQSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKG 782

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG PVD+V NPLGV    NVGQIFE+ LG A   L +  +    D
Sbjct: 783  IISKILPRQDMPYLQDGRPVDMVFNPLGVLHERNVGQIFESSLGLAGDLLDRHYRIAPFD 842

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F  ++      T     ++ +                           
Sbjct: 843  ERYEQEASRKLVF-SELYEASKQTANPWIFEPE--------------------------- 874

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                         G+S ++DG TG+PF++PV +G  Y LKL H V DK++ RS+G YS +
Sbjct: 875  -----------SPGKSRIFDGRTGDPFEQPVIIGKPYTLKLIHQVDDKIHGRSSGRYSRL 923

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPL G++ +GGQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G   
Sbjct: 924  TQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRI 983

Query: 1339 FET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
                  PESF + V+E+++L L ++  L + +T    + E
Sbjct: 984  PTPEDAPESFRLFVRELRSLALELNHFLVSEKTFRLNRKE 1023



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 11/178 (6%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI  +          + I+EQ+I
Sbjct: 5   NFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRC-------RYIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
            +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G 
Sbjct: 58  LIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELT---DNGISVYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
            +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D    
Sbjct: 115 RLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKKKI 172


>gi|119872217|ref|YP_930224.1| DNA-directed RNA polymerase subunit B [Pyrobaculum islandicum DSM
            4184]
 gi|119673625|gb|ABL87881.1| DNA-directed RNA polymerase, subunit B' / DNA-directed RNA
            polymerase, subunit B' [Pyrobaculum islandicum DSM 4184]
          Length = 1127

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 127/602 (21%), Positives = 216/602 (35%), Gaps = 97/602 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ G+     D +      +  D     N  +A  P    +    + I    +   V + 
Sbjct: 604  VRRGELT--WDDLVKMGVIEYLDADEEENAYIATDPHDDLSKYTHVEIIPSAILGAVASI 661

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R+               S      +D  G   +        +    +   
Sbjct: 662  IPYLEHNQSPRNQYEAAMAKQSLGLPQSNFLY-KLDSRG--HMLYYPERPIVTTRGLELI 718

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G S     +  + A+      ++ D  +   + V   +    +F R    + ++    E 
Sbjct: 719  GYSKKPAGQNAVVALLTYTGYNMEDAIILNKAAVERGMF-RSVFYRTYETEEQKYPGGEE 777

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++IE+                       + G           +  +   ++         
Sbjct: 778  DKIEVPD-------------------SSVKGYRGPEAYSHLDEDGIAPPEVYVSSNEVII 818

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + +          E +  +   S   +    K  ++++       P   R+VKV +   
Sbjct: 819  GKTSPPRFYTTLETERILKERRDSSVAVRRGEKGIVDRVII--TESPEGNRLVKVRLREL 876

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  IL  EDMPF ++G   DI++NP  +PSRM VGQ+ E+  
Sbjct: 877  RIPELGDKFASRHGQKGVVGMILRHEDMPFTEEGIVPDIIVNPHALPSRMTVGQLLESIA 936

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG  +                                                 
Sbjct: 937  GKIGASLGALVD------------------------------------------------ 948

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +TP F+G  EE +  +L        G+ ++Y G+TGE     + +G +Y  KL+H
Sbjct: 949  -----ATP-FEGVKEEELRKLLMKLGYKWDGKEVMYSGITGEKLVADIFIGVVYYQKLHH 1002

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+DK++AR+ G   ++T+QP  G+S  GG RLGEME   + A+GA+ +L E L   SD 
Sbjct: 1003 MVADKIHARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGASALLYERLVESSDK 1062

Query: 1322 --------------VVGRTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                          +  RT      + G+     +   P +F +L++E+ ALG+   LE 
Sbjct: 1063 YTMYVCELCGLPAYLDARTNKPRCPIHGDTGQFAKVIVPYAFKLLLQELIALGIYPKLEL 1122

Query: 1366 SR 1367
            S 
Sbjct: 1123 SE 1124



 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 111/738 (15%), Positives = 226/738 (30%), Gaps = 137/738 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFV 77
           L   Q  S++ FL   +          E   +GL+   + +   +P I    G+  L + 
Sbjct: 37  LANHQIKSFNDFLDKKLPKIVEDFKVIETEIKGLKLVLERIEVGWPRIKESDGSESLIY- 95

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R+ TY+ PL +T  L V D    T             Y+G+LP+
Sbjct: 96  ----------PMEARLRNATYSAPLYLTATLYVDDEPYVTETF----------YIGELPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGR 171
           M K                         G F+I G +R+++SQ  L     I+   DK  
Sbjct: 136 MVKSKRCNLTRLKPSEYVKKFEDPQDFGGYFIINGSERVIISQEDLVTDRPIYDKGDKPS 195

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILS 230
                K +     I  +   + +E +   II+V +     K+P   ++ ALG++++E   
Sbjct: 196 VKYIAKTI--STGIGYR-STLVVELNKDGIIYVTLSAMPVKIPFPVYMKALGLETDE--- 249

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKLTSGLLKS 287
                +V +   D          L+   +++      +D   G+  +   K +       
Sbjct: 250 ----DVVKAVSDDPEIQKELLPSLIAANQIAITKEDALDFIGGKVAVGQPKPIRVEKALQ 305

Query: 288 L--------------KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           L               EK  + + +    + G  V + ++  + G    +  D +  K +
Sbjct: 306 LLDRYFLPHLGTTVPDEKKQQEIRLKKALMLGQIV-KGLIELDLGRRKPDDKDHVANKRV 364

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
             +     +    ++   +                        I  ++RP D+ T  V +
Sbjct: 365 RLVGDLMTQLFRTVFKQFLQELKSQLEKYYARGRIPH------IQTIVRP-DIITERVRQ 417

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GT 452
           ++    +          + R      L+      V  + +       + L   + G+   
Sbjct: 418 ALATGNWVGGKTGVSQILDRTNYMSTLSYLRRV-VSSLSRTQPHFEARDLHPTQWGRLCA 476

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           ++  +      V+++  + +    +    +E+ +    +   +  +  +D       V  
Sbjct: 477 VETPEGQNVGLVKNLALLAEITTGVDEGEVEQLLY---NLGVVPILKARDEGIRGAEVYI 533

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                                 +   RR   +                V+        P 
Sbjct: 534 NGRLIGIHP-----NPDELARTVRSLRRQGKISDE--INIAVLNNAVYVNCDGGRIRRPL 586

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
              E   + L   +    R     +         D      + YL A EEEN YIA    
Sbjct: 587 LVVENGKLKLTKEIVEKVRRGELTW--------DDLVKMGVIEYLDADEEENAYIAT--- 635

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                               +      K   ++  P  ++   AS+IP+LE++ S R   
Sbjct: 636 --------------------DPHDDLSKYTHVEIIPSAILGAVASIIPYLEHNQSPRNQY 675

Query: 693 GCNMQRQAVPLLKAEAPF 710
              M +Q++ L ++   +
Sbjct: 676 EAAMAKQSLGLPQSNFLY 693


>gi|52538149|emb|CAH19176.1| RNA polymerase beta-subunit [Pseudomonas monteilii]
          Length = 378

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 224/376 (59%), Positives = 288/376 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 SDDIVFLSAIEEADHVIAQASAAMNEKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA 
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAP 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            DI+ADGPSTD+G+LALG+NM +AFM W+G+ FEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 GDIMADGPSTDMGELALGQNMRIAFMAWNGFYFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITRDIP 866
           ARDTKLGPEEI    P
Sbjct: 361 ARDTKLGPEEIYCGHP 376


>gi|161345229|gb|ABX64455.1| RpoB [Bacillus subtilis]
          Length = 248

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 95/276 (34%), Positives = 147/276 (53%), Gaps = 30/276 (10%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ 
Sbjct: 1   RISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFID 50

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+M
Sbjct: 51  YSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIM 101

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           T  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+
Sbjct: 102 TDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDA 158

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+  
Sbjct: 159 KDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL-- 216

Query: 258 AKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKG 292
                    +  GE   +E+ K L        K   
Sbjct: 217 ----EIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 248



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 61/173 (35%), Gaps = 1/173 (0%)

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K+    +                    +    I+  E+VI S    +  +  S K     
Sbjct: 77  KVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNG 136

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
             G T+  +       +        +Y+             +          + +D +  
Sbjct: 137 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEI-LDLIGE 195

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           N Y+RNTL  D  ++   ALL+IY  +RPG+  T   A+S+ +  FFD  +YD
Sbjct: 196 NEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYD 248


>gi|52694307|emb|CAG37993.1| RNA polymerase beta subunit [Pseudomonas coronafaciens]
          Length = 376

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 222/376 (59%), Positives = 290/376 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDL NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLFNAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  
Sbjct: 121 VVKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F +IH
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFPTIH 360

Query: 844 IEEFEVMARDTKLGPE 859
           I+E   +ARDTKLGPE
Sbjct: 361 IQELTCVARDTKLGPE 376


>gi|254553681|gb|ACT67299.1| RNA polymerase beta subunit [Joinvillea plicata]
          Length = 863

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 236/691 (34%), Positives = 381/691 (55%), Gaps = 26/691 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + I +  +   +     +  +  E          + S+  +  +   ++  +  +     
Sbjct: 141 ISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLREILDNVSYPE 200

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++   N     K + ++ A+L+ Y+      GD+             FF   K +L  +
Sbjct: 201 IFLSFPNDKEKKKIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFFH-QKCELGRI 259

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRRVRSVGE 469
           GR  MN RLNLD P +   +   D++A    L+ ++ G GT+DD D  +L N+R+RSV +
Sbjct: 260 GRRNMNRRLNLDIPQNNTFLLPRDVLAAADHLIGMKFGMGTLDDDDMNHLKNKRIRSVAD 319

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL------INAKPVVSAVCEFFCSSQLS 523
           +L++Q+ L L R+E ++K+ I       + P           +  +++    FF +  LS
Sbjct: 320 LLQDQFGLALGRLEHAVKKTIRRAIRRKLKPTPKILVTPTSTSFLLITTYETFFGTYPLS 379

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++  H R+LS LG GG+    A    RD+HP+HYGRICP +TSEG N+GL 
Sbjct: 380 QVFDQTNPLTQTVHGRKLSYLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEGINVGLT 439

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
            SL   AR++ +G IE+P+ ++ +     +  VVYLS   +E   IA  NS     G   
Sbjct: 440 GSLAIHARIDHWGSIESPFYEISEKPKEKETQVVYLSPNRDEYYMIAAGNSLALNQGIQE 499

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM  NMQRQAV
Sbjct: 500 EQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMSSNMQRQAV 559

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SG +++A+R G +   D+  IV+ S              
Sbjct: 560 PLSRSEKCIVGTGLERQTALDSGVSVIAEREGKIISTDSHLIVLSSN--------GNTIS 611

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+   RSN+NTC++Q+P V+ G  +++  I+A+G +T  G+LALG+N+LVA+MPW GY
Sbjct: 612 IPLVVHWRSNKNTCMHQKPRVRRGKCIKKGQILAEGAATVGGELALGKNVLVAYMPWEGY 671

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECG 880
           N ED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  L+N+D  G
Sbjct: 672 NSEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSVEKITKEIPHLEEHLLRNLDING 731

Query: 881 IICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ V  GDILVGK+TP+ E+  +   E +LLRAI G +    ++TSL++P G  G 
Sbjct: 732 VVMLGSWVETGDILVGKLTPQIENESSYISEARLLRAILGLEVSTSKETSLKLPIGGRGR 791

Query: 939 VVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           V+DV+   R  +D   R   +++ +I++  +
Sbjct: 792 VIDVKWIQRDPLDIMVRVYILQKREIKVGDK 822



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 101/221 (45%), Gaps = 27/221 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--AAMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL         +          L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELHKFPKMEDTDHEMQFQLFAEGYQLVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI             +D++EQ+I +G++PLM   GT
Sbjct: 62  PSKKERDAVYESLTYSSELYVSAGLIWG-----------RDVQEQTISIGNIPLMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+ +SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILQSPGIYYRSELDHNGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGD 243
            R+ R++K+ +     A+G +  EIL    YP+I  S   D
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLREILDNVSYPEIFLSFPND 208



 Score =  124 bits (310), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 39/58 (67%), Positives = 51/58 (87%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGT VD+V NPLGVPSR
Sbjct: 806  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTSVDMVFNPLGVPSR 863


>gi|52694199|emb|CAG30629.1| DNA-directed RNA polymerase beta chain [Pseudomonas ficuserectae]
          Length = 376

 Score =  362 bits (930), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 224/374 (59%), Positives = 289/374 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D 
Sbjct: 121 EGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT IHI+E
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTRIHIQE 360

Query: 847 FEVMARDTKLGPEE 860
              +ARDTKLGPEE
Sbjct: 361 LTCVARDTKLGPEE 374


>gi|294768462|gb|ADF36179.1| RNA polymerase beta subunit [Mycoplasma sp. Mirounga ES2806-GEN]
          Length = 664

 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 232/503 (46%), Positives = 349/503 (69%), Gaps = 10/503 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ S+GE+++N  ++GL ++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 3   TNKRIVSLGELVQNNLKVGLSKLEKTTRERMGAKEPDKVSPKNVTNNKLISNQMKTFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++A+VN +GF+ETPY +V +G V  ++ VYL+A +E    IAQ+   +DE+ 
Sbjct: 123 IGLILNFATYAKVNEFGFLETPYFRVDNGIVDYSEPVYLTAADEMGYKIAQSTVKVDENN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +  +  R      +   ++IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183 RIIDPQLTIRHNYTYQIGTADEIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ EAPFV TG+E+ +AK S    VA+  GIVE VD  +I IR+          G
Sbjct: 243 QAVPLLETEAPFVATGIEAEIAKYSSGNFVARNDGIVEFVDGKKIKIRND-------KKG 295

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +D Y L  FQRSNQ+T V+Q+PLV+ G EV++ D++ DG S   G+LALG+N+LVAF  +
Sbjct: 296 IDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGDLLVDGSSFKDGELALGKNVLVAFTTY 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++ER+V +DVFTSIHIEE  V  R +K G +E+T DIPNVS+   +++DE
Sbjct: 356 NGYNYEDAVILNERLVKDDVFTSIHIEEQTVQFRTSKAGDDELTADIPNVSKFSTRHLDE 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            G++ VG++V PGD+LVG+++PKG+   T EEKLL A+  ++   V+DTSL+V +G  GT
Sbjct: 416 HGVVRVGSDVAPGDVLVGRVSPKGDDNPTQEEKLLLAVLQQRQQAVKDTSLKVKNGHGGT 475

Query: 939 VVDVRIFNRHGIDKNERSISVER 961
           V+ V I +R    K++    +++
Sbjct: 476 VIGVEILSREN--KDQLEDGIDK 496



 Score =  250 bits (638), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 130/522 (24%), Positives = 195/522 (37%), Gaps = 74/522 (14%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E  +   +     
Sbjct: 213  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEAPFVATGIEAEIA--KYSSGN 270

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  I EF V  +  K+  ++   D  N+      N D    +  ++  G EV  GD
Sbjct: 271  FVARNDGIVEF-VDGKKIKIRNDKKGIDTYNLKNFQRSNQDTVVHQKPLVREGQEVKKGD 329

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +LV   + K +  +   + +L A       +  D  +     V   V    I       +
Sbjct: 330  LLVDGSSFK-DGELALGKNVLVAFTTYNGYNYEDAVILNERLVKDDVF-TSIHIEEQTVQ 387

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               S + + E    +          LD +   R+   +   + + G    K     + + 
Sbjct: 388  FRTSKAGDDELTADIPNVSKFSTRHLDEHGVVRVGSDVAPGDVLVGRVSPKGDDNPTQEE 447

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                   Q  Q AV+D  ++                 E++           D +  G+ +
Sbjct: 448  KLLLAVLQQRQQAVKDTSLKVKNGHGGTVIGVEILSRENK-----------DQLEDGIDK 496

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDM              P        
Sbjct: 497  IVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDM--------------PH------- 535

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                 E                   D   N    P R  + +V+                
Sbjct: 536  ----LE--------------DGTPVDVMLNPQGVPSRMNIGQVL---------------E 562

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            +              T VFDG  +E I  ++  A L  +G+  L + +TGE FD PV+VG
Sbjct: 563  IHLGMAARSLKTKFVTRVFDGIKKEEIYDVIEEAGLPATGKQTLINPITGEKFDNPVSVG 622

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 623  VMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 664


>gi|326912147|ref|XP_003202415.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like
            [Meleagris gallopavo]
          Length = 1129

 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 165/1003 (16%), Positives = 308/1003 (30%), Gaps = 193/1003 (19%)

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              ++    K  +     +  +  L      +     K    A++   V L  G+  +DD 
Sbjct: 291  QRMWGGPKKTKMEEARELLASTILTHVLVKEFNFRAKCIYTAVMVRRVILAQGENKVDDR 350

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSA 512
            D  GN+R+   G++L   +     +    +K+    V       Q      +    + + 
Sbjct: 351  DYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQVIPKQRAAQFDVVKHMRQDQITNG 410

Query: 513  VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPT 564
            +     +   S     ++         RLS +   G+         + R     R + P+
Sbjct: 411  MVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPS 470

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +G +CP++T EG   GLV +L     +      + P  K+       DV  L   EE +
Sbjct: 471  QWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIIKLASNLGVEDVNLL-CGEELS 528

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N  L         ++              +  +I+       +++   +    +
Sbjct: 529  Y----PNVFLVFLNGNILGVIRDHQKLVNTFRIMRRAGYINEFVSISTNLSDRCV--YIS 582

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D  R+     + ++  P +  +       ME +              G     D +   
Sbjct: 583  SDGGRLCRPYIIVKKQKPAVTNK------HMEELA------------QGYRNFEDFLHEG 624

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +       + +   + +Y     + +                                 +
Sbjct: 625  LVEYLDVNEENDCNIALYEHTINKDTTHLEI----------------------------E 656

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +    +P+  +N          M  + + T      +    R   L        
Sbjct: 657  PFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG----YNQRNRIDTLMYLLAYPQ 712

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             P V  + ++ ID                            +   +    A+      D+
Sbjct: 713  KPMVKTKTIELID-------------------------FEKLPAGQNATVAVMSYSGYDI 747

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +   + +        ++        +R  +   +++     D    + I    I  
Sbjct: 748  EDALVLNKASLDRGFGRCLVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILD 806

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                   G+   +      KS                 Q  ++   V +       QY+ 
Sbjct: 807  ADGICSPGEKVENKQVLVNKSMP------------TVTQTPLEGSSVPQQ-----PQYKD 849

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 +    + IEK+    +       ++K+ +   R  + GDK + RHG KG+   I+
Sbjct: 850  VPVTYKGATDSYIEKVMISSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIV 907

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMPF   G   DI++NP G PSRM V        G     L  K   L   +     
Sbjct: 908  PQEDMPFCDTGICPDIIMNPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT- 958

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                          F G+  + +   L 
Sbjct: 959  ---------------------------------------------AFGGSKVKDVCEDLI 973

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  
Sbjct: 974  RHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTE 1033

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-------- 1336
            G+S  GG RLGEME  C+  YGA+ +L E L I SD        +E  V G         
Sbjct: 1034 GRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSG 1086

Query: 1337 ---------DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                            P +  +L +E+Q++ +   L+ ++   
Sbjct: 1087 WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLAKYNE 1129



 Score =  197 bits (502), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 127/946 (13%), Positives = 277/946 (29%), Gaps = 182/946 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 36  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGTPDVEE 86

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 87  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 136

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 137 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 195

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 196 VGASVTSST--HEKKSRTNLVV-KQGRFYLRHNTLSEDIPIAIIFKAMGVESDQEIVQMI 252

Query: 233 YPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
             +            +      F    A   +G KV    +     +  +E  ++L +  
Sbjct: 253 GTEEHVMAAFAPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGPKKTKMEEARELLAST 312

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +  L    VK     + C+    V    V    GE  ++  D    K LE          
Sbjct: 313 I--LTHVLVKEFNFRAKCIY-TAVMVRRVILAQGENKVDDRDYYGNKRLELAGQLLSLLF 369

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             L+    +    I + ++  +      A  D+ + MR   ++   V     +   +   
Sbjct: 370 EDLFKKFNSELKKIADQVIPKQR----AAQFDVVKHMRQDQITNGMVNA--ISTGNWSLK 423

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           ++ +   G  ++  RL+  +   +            K+                     +
Sbjct: 424 RFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWGM 474

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
               +  + +    +  +           D   +     +  + V     E      +  
Sbjct: 475 LCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLASNLGVEDVNLLCGEELSYPNVFL 534

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL-- 582
           +  + N L  I   ++L    +  + RA    E   +      R     +  G       
Sbjct: 535 VFLNGNILGVIRDHQKLVNTFRI-MRRAGYINEFVSISTNLSDRCVYISSDGGRLCRPYI 593

Query: 583 VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           +      A  N     +   YR   D      V YL   EE +  IA             
Sbjct: 594 IVKKQKPAVTNKHMEELAQGYRNFEDFLHEGLVEYLDVNEENDCNIAL------------ 641

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            +    ++  P  ++ + A LIP+  ++ S R    C M +QA+
Sbjct: 642 -----------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM 690

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
             +         G        +   ++A                                
Sbjct: 691 GTI---------GYNQRNRIDTLMYLLA-------------------------------- 709

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
                           Q+P+VK                 D   L  G+N  VA M + GY
Sbjct: 710 --------------YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSGY 745

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----I 876
           + ED++++++  +       +  +  +    R T    +++   + + +          +
Sbjct: 746 DIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEIL 805

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           D  GI   G +V    +LV K  P           + +    +   
Sbjct: 806 DADGICSPGEKVENKQVLVNKSMPTVTQTPLEGSSVPQQPQYKDVP 851


>gi|52694231|emb|CAG30645.1| DNA-directed RNA polymerase beta chain [Pseudomonas vancouverensis]
          Length = 370

 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 221/370 (59%), Positives = 287/370 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RA  E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAFFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEPYVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEE 860
           ARDTKLGPEE
Sbjct: 361 ARDTKLGPEE 370


>gi|222084193|ref|YP_002519787.1| RNA polymerase beta chain [Gnetum parvifolium]
 gi|158513793|sp|A6BM50|RPOB_GNEPA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|149941456|dbj|BAF64895.1| RNA polymerase beta subunit [Gnetum parvifolium]
 gi|220983530|dbj|BAH11298.1| RNA polymerase beta chain [Gnetum parvifolium]
          Length = 1108

 Score =  362 bits (929), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 129/360 (35%), Positives = 192/360 (53%), Gaps = 50/360 (13%)

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            S+   F   D +     +  +  Y+ ++  LE  +       Q  +         V V++
Sbjct: 795  SKLQAFCKDDLEKGHQDDDTEDIYDEAEDALEKVY-------QLNNYNLSSDSEKVHVYL 847

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
              KR IQ GDK+AGRHGNKGIVS +L  +DMPFL+ G  +D+VLNPL VPSRMNVGQIFE
Sbjct: 848  LEKRKIQVGDKVAGRHGNKGIVSIVLSRQDMPFLQSGISLDMVLNPLSVPSRMNVGQIFE 907

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              LG A   + K  +    D +   + S    F  ++      T     ++ + +     
Sbjct: 908  CLLGLAGT-MNKHYRIPPFDERYEQEASRKLVFY-ELYKASEQTANPWIFELEHL----- 960

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                                             G++ ++DG TGE F++PVT G  Y+LK
Sbjct: 961  ---------------------------------GKTQIFDGRTGEIFEQPVTTGNAYILK 987

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L H V+DK++ARSTG+Y+ +TQQP+ GKS  GGQRLGEMEVW ++++G AYVL+EMLT+K
Sbjct: 988  LIHQVNDKMHARSTGNYARITQQPVQGKSKGGGQRLGEMEVWALESFGVAYVLREMLTVK 1047

Query: 1319 SDDVVGRTRVYESIVAGNDTFETG-TPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +D +  R ++  SI+ G+   +     ESF VL KE+ +L L ++  + + +  N  ++E
Sbjct: 1048 ADHIRARKKILRSILDGHSVPKADSATESFRVLSKELNSLALELNHTIISGKYFNLDRIE 1107



 Score =  320 bits (821), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 214/678 (31%), Positives = 339/678 (50%), Gaps = 33/678 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN----AYIRNTLVTDKNKDRKDALL 375
           I+I      +   L   F   +    IL              I N  +  K   +K A+ 
Sbjct: 165 IWIRISRKKNVSILVFFFAMGLDIEEILKNTYYIKGFEGWGLICNEKLKHKLSRKKGAIF 224

Query: 376 DIYRVM-----RPGDVSTFSVAESMFNFL-FFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             Y  +         V + S++ES++     F S +  L  +GR  +N +LNL+ PD+  
Sbjct: 225 TFYEELGSRGDNNDFVFSESLSESLYKKFTNFLSKRCKLGRIGRRNLNKKLNLEIPDNEI 284

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME------ 483
            +  +D++AII  L+ +  G GT+D+ID+L NRR  SV ++LK +  L L R++      
Sbjct: 285 FLLPQDVLAIIDYLIKVSYGVGTVDNIDHLQNRRFFSVADLLKKEVGLALNRVKVLIQKT 344

Query: 484 -RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ++I+      +   ++P+  + +  +   +  FF    LSQ  E  NSL+ I H R++S
Sbjct: 345 MQTIEMLRKKQNKRIMLPEIPLVSTQITKTLKHFFGLHPLSQFLEQTNSLAEILHARKVS 404

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            LG GG+    A    RD+HP++YGR CP  T EG N GL++SL   AR+N        Y
Sbjct: 405 FLGPGGLTERTANFRARDIHPSYYGRFCPINTPEGQNAGLIASLAISARINFGFLESPFY 464

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                 +    +VYLS  E+    IA  N    +     ++    +   E + +  E+I 
Sbjct: 465 NVAKKYQKAKKIVYLSPSEDVYYRIALGNCLSVDQKIPEKKNTPTQYHQEFLSIAWEQIH 524

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           F    P Q  SI  SLIPFLE++D+ R LMG NMQRQAVP ++ E   VGTG+E  VA  
Sbjct: 525 FRCFLPLQYFSIGVSLIPFLEHNDATRALMGSNMQRQAVPSVQPEKCIVGTGLEGQVALD 584

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SGA  ++ + G ++  DA  IV                   L  +QRSN NT ++Q+   
Sbjct: 585 SGALAISTQEGRIQYSDAATIV--------SVLKGNTTQTELQIYQRSNSNTLMHQKTHA 636

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                VR+  I+ADG +   G++ LG+N+LVA+MPW GYNFED++LISE ++ +D+FTS 
Sbjct: 637 SQAKYVRKGQILADGAAMLGGEICLGKNILVAYMPWQGYNFEDAILISECLIYKDIFTSF 696

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HI  +E      +   E++TR+IP ++   L+++D+ G++ VG+ V PGD+LVGK+ P+ 
Sbjct: 697 HITRYETTICTAEC--EKMTREIPRLATYSLRHLDKNGLVRVGSWVQPGDVLVGKLRPRS 754

Query: 903 ESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
               +  PE +LL+ +F    +        + +   G V+DV         K++     +
Sbjct: 755 SEDFSRFPELRLLQDLFCTSPIK----ETCLRANGKGRVIDVNWSKLQAFCKDDLEKGHQ 810

Query: 961 REQIELLARDKDDEQVIL 978
            +  E +  + +D    +
Sbjct: 811 DDDTEDIYDEAEDALEKV 828



 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 85/394 (21%), Positives = 154/394 (39%), Gaps = 35/394 (8%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAM 73
             F +  E+  IP+  ++Q   +  F+  ++                 FP I        
Sbjct: 1   MQFDEKKEMFTIPEFGQIQLEGFCRFIEYDLLDKFVK-----------FPKIANTQK--E 47

Query: 74  LEFV---SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           +EF+   +Y+   P     D +++ LT++  L +    I ++  +               
Sbjct: 48  VEFLFDKNYKIIEPSIKEKDAVYQRLTFSSKLFVPAFFIYWNKIKKKKII---------- 97

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           Y+G++PLM  +GTF+I G  R+VV+QL RSPGI++  ++ R       +Y   +I D G 
Sbjct: 98  YLGEIPLMNNNGTFLINGNYRVVVNQLIRSPGIYYSLERKRTGN----IYTSTLISDCGG 153

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            +  E D K  I +RI R++ V +  F  A+G+D EEIL   Y    +   G        
Sbjct: 154 RLKFEIDIKQNIWIRISRKKNVSILVFFFAMGLDIEEILKNTYYIKGF--EGWGLICNEK 211

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
               +   K +      + G +   +    +  L +SL +K   FL  +  C  G     
Sbjct: 212 LKHKLSRKKGAIFTFYEELGSRGDNNDFVFSESLSESLYKKFTNFL--SKRCKLGRIGRR 269

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           ++      EI      ++ +  L  I +       +  VD++++    R   V D  K  
Sbjct: 270 NLNKKLNLEIPDNEIFLLPQDVLAIIDYLIKVSYGVGTVDNIDHLQNRRFFSVADLLKKE 329

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
               L+  +V+    + T  +     N      +
Sbjct: 330 VGLALNRVKVLIQKTMQTIEMLRKKQNKRIMLPE 363


>gi|227809530|gb|ACP40984.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
 gi|227809534|gb|ACP40986.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
          Length = 666

 Score =  362 bits (929), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 243/520 (46%), Positives = 358/520 (68%), Gaps = 13/520 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ +VGE+L+ Q+ LGLL++E++ KE++SS + D + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVAVGELLQKQFLLGLLKLEKNTKEKLSSKESDKINPKNITNNKPIYNQFKTFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN LS + + RR+++LG GG+ R  A  E+RDVH T+YGRICP ET EG NI
Sbjct: 63  KLSQFMDQVNPLSELANKRRITSLGPGGLNRETAQFEVRDVHSTYYGRICPIETPEGQNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L ++++ + +GFI+TPY  V +G V   +V +L+A++E     AQ++ ++DE+  
Sbjct: 123 GLILNLATYSKTDDFGFIQTPYFPVKNGVVNYGEVKWLTAVDEYGYTFAQSSVTIDENNK 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E +  R   + ++V  E+ID+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQ
Sbjct: 183 IIDEFITVRKDYQYLIVKPEEIDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL++AEAP +GTG+E  +AK +   I A  +GIV  VDA  I I+  + +L+      
Sbjct: 243 AVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYVDAKTIKIKPFDENLEE----- 297

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           DIY L  FQ+SNQ T +NQ P V+VG+ + +  ++ DGPST  G+LALG+N+LVAF  WH
Sbjct: 298 DIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTKDGELALGKNVLVAFTTWH 357

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++ISE++V +DVFTSIHIEE  +  R +K G + +T +IPN S    +++DE 
Sbjct: 358 GYNFEDAIIISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDEN 417

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EVN GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G +GTV
Sbjct: 418 GIVRVGSEVNTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGSNQKDTSLKVKHGDAGTV 477

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           +DV+I +R   D       +  + I+ + +    ++  + 
Sbjct: 478 IDVQIISRANGD-------ILEDGIDKIVKVFIAQKRKIK 510



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 136/500 (27%), Positives = 206/500 (41%), Gaps = 72/500 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ A  P  G   E  +            + I     +      K   E
Sbjct: 235  MGANMQRQAVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYV-DAKTIKIKPFDE 293

Query: 860  EITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             +  DI  +      N    I++   + VG  +  G ++    + K +  +   + +L A
Sbjct: 294  NLEEDIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTK-DGELALGKNVLVA 352

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                   +  D  +     V   V    I       +   S + +      +       +
Sbjct: 353  FTTWHGYNFEDAIIISEKLVKDDVF-TSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSK 411

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD N   R+   +   + + G    K     + +        +       ++   +  
Sbjct: 412  RHLDENGIVRVGSEVNTGDILVGRISPKGEDNPTPE-------EKLLNAIFGNKGSNQKD 464

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLKV++  + ++++     +I     GD +  G+ ++VKVF+A KR I+ GDKMAGRHG
Sbjct: 465  TSLKVKHGDAGTVID----VQIISRANGDILEDGIDKIVKVFIAQKRKIKVGDKMAGRHG 520

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S +LP EDMP+L+DGTP+DI+LNP GV SRMN+GQ+ E HLG A   L  K  S 
Sbjct: 521  NKGVISLVLPVEDMPYLEDGTPIDILLNPQGVASRMNIGQVLELHLGMAAKKLNVKFVSP 580

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D   N  +  +                                               
Sbjct: 581  VFDGIKNESLDSIL---------------------------------------------K 595

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E           L ESG+  LYDG+TG+ +D  V+VG +YMLKL HMV DK+ ARS G Y
Sbjct: 596  EAD---------LPESGRFTLYDGITGKQYDSKVSVGVMYMLKLQHMVDDKINARSVGPY 646

Query: 1276 SLVTQQPLGGKSNRGGQRLG 1295
            SL++QQPLGGKS  GGQR G
Sbjct: 647  SLISQQPLGGKSQNGGQRFG 666


>gi|83755167|gb|ABC46432.1| RNA polymerase beta subunit [Spiroplasma turonicum]
          Length = 594

 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 227/423 (53%), Positives = 311/423 (73%), Gaps = 9/423 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A++N YGFIETPYRKV + KV  +   YL+A +E+   +AQAN  + EDG+  ++ V 
Sbjct: 61  TYAKINEYGFIETPYRKVKNKKVYLDQYEYLTADKEKEYVVAQANIKMSEDGTILDDQVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMVNAADVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLIDP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG A+VA   GIV+ VD+ +I+I           + V  Y L  
Sbjct: 181 ESPVVGTGVEFEAARDSGDAVVATEDGIVKYVDSRKIIIEQN--------NVVKNYDLND 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VKVGD+V++ DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FNRSNNGTAITHIPIVKVGDKVKKRDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK G EEITRDIPNVSE   KN+DE GI+ +GA
Sbjct: 293 VIVSERVVIDDRFTSIHIDEYTIERRQTKQGQEEITRDIPNVSETVKKNLDEDGIVAIGA 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSIKRFS 412

Query: 947 RHG 949
           +  
Sbjct: 413 KAN 415



 Score =  281 bits (719), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 125/418 (29%), Positives = 180/418 (43%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKKRDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   +   +   +   L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGQEEITRDIPNVSETVKKNLDEDGIVAIGAEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L V+KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKANGHDLPADILEVIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG KI + + +     D+  + +       
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAQKLGVKISTPVFEGVKEQDLKEIMTEAGMTNF 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVKLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|52694347|emb|CAG38013.1| RNA polymerase beta subunit [Pseudomonas caricapapayae]
          Length = 372

 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 222/372 (59%), Positives = 288/372 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 121 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELVDELVAVRHLNEFTVKAPADVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 361 CVARDTKLGPEE 372


>gi|52538145|emb|CAH19174.1| RNA polymerase beta-subunit [Pseudomonas mandelii]
          Length = 375

 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 222/373 (59%), Positives = 288/373 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 360

Query: 851 ARDTKLGPEEITR 863
           ARD KLGPEEI  
Sbjct: 361 ARDPKLGPEEIYC 373


>gi|218554|dbj|BAA02600.1| RNA polymerase II second largest subunit [Schizosaccharomyces pombe]
          Length = 1210

 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 193/1210 (15%), Positives = 362/1210 (29%), Gaps = 204/1210 (16%)

Query: 211  KVPVTSFLMALGMDSEEILSTFYPKIVYSQR------GDFWCFPLSAADLMVGAKVSSSL 264
            K+P    L      +  IL+      +Y         G ++    S   ++   + ++++
Sbjct: 154  KIP--IMLR----STFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANI 207

Query: 265  VDIDTGEQ--------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
            V +              I S  +  S L+ S++ K +      S       +     +  
Sbjct: 208  VQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRATLPYIRSDIP 267

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               ++   G V D   LE I +       +  +      A++         +D+  AL  
Sbjct: 268  IVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFV--------IQDKDIALDY 319

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            I +              S          +Y    + +  +       T +     +   +
Sbjct: 320  IGKR------------GSTTGVTREKRLRYAHDILQKELLPHIT---TMEGFETRKAFFL 364

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
              +I  ++     +   DD D+ G +R+   G +L + +R+   +M R +    +     
Sbjct: 365  GYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVET 424

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRL 541
                     + +  + + +     +               +SQ+       S ++H RR 
Sbjct: 425  NREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRT 484

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            +      + R     + R +H TH+G +CPAET EG   GLV +L+  + V+  G    P
Sbjct: 485  NT----PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVS-VGSPSAP 539

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGEEILVP 657
              +  +      +   +     N      N             TE L   R   +     
Sbjct: 540  IIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEV 599

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRV--LMGCNMQRQAVPLLKAEAPFVGTGM 715
                D  +   +          P    D++          ++++ +  L  +        
Sbjct: 600  SIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDP 659

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E        A + +     ++  +   ++I     DL+ S      Y + +     Q   
Sbjct: 660  EQRFGW--TALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVK 717

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
                P V               P+  LG LA       + +P+  +N          M  
Sbjct: 718  PAPNPHVH------ARTHCEIHPAMILGILA-------SIIPFPDHNQSPRNTYQSAMGK 764

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +   +++  ++V                               +  +           
Sbjct: 765  QAMG--VYLTNYQVRM---------------------------DTMANILYYPQKPLATT 795

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +   +  + AI      +  D+ +   + +   +    IF R   D+ ++
Sbjct: 796  RSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF-RSIFYRTYTDQEKK 854

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                  E+ E   R           +       I  G           K+  +  D    
Sbjct: 855  IGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEEL 914

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R+Q          ++     +  Q                             L+ VK
Sbjct: 915  GQRTQLHAKRDVSTPLRSTESGIVDQ--------------------VMVTTNQEGLKFVK 954

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R  Q GDK A RHG KG +      EDMPF   G   DI++NP  +PSRM V  
Sbjct: 955  VRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAH 1014

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L       G +  +          +S L                 S         
Sbjct: 1015 LVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLR---------------SHGFQSRGFE 1059

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            V     +G  +   VF G                                         Y
Sbjct: 1060 VMYHGHTGRKLVAQVFLG---------------------------------------PTY 1080

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L H+V DK++AR+ G   ++T+QP+ G+S  GG R GEME  C  ++G + VL+E L
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140

Query: 1316 TIKSD-------DVVGRTRV-------YE--SIVAGNDTFETGTPESFNVLVKEMQALGL 1359
               SD       D+ G   +       YE  S        +   P +  +L +E+ ++ +
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200

Query: 1360 SIDLENSRTK 1369
            +  L     K
Sbjct: 1201 APRLFTKNHK 1210



 Score =  244 bits (623), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 139/1008 (13%), Positives = 286/1008 (28%), Gaps = 191/1008 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L   Q  S+D F+   +          Q        +T              +    + F
Sbjct: 30  LARQQLFSFDEFVQNTM----------QEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINF 79

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFD-------VDEFTGA 119
                  P               +   R+LTY+ PL + +R  V         + E    
Sbjct: 80  GQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWL 139

Query: 120 KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
              +D +   +++G +P+M +                         G F+I G ++++++
Sbjct: 140 VEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIA 199

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDII----------- 202
           Q  RS          + +    + Y   I    ++G  +      K +            
Sbjct: 200 QE-RSAANI--VQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIR 256

Query: 203 ----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
               ++R D    +P+     ALG+  + +IL          Q  +     +  A ++  
Sbjct: 257 ATLPYIRSD----IPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQD 312

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             ++   +        +   K+L       L+++ +  +                +    
Sbjct: 313 KDIALDYIGKRGSTTGVTREKRLRYAH-DILQKELLPHITTMEGFETRKAFFLGYMIH-- 369

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A +  +    +      +    P+L          +   +     K  +     
Sbjct: 370 -RMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREF 428

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +    ++ T  +  S+    + D  +  ++ VG  ++  R    +      R     
Sbjct: 429 NLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPI 488

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +         +      ++KN   +  + +       I  ++
Sbjct: 489 GRDGKLAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLSLMSYVSVGSPSAPIIEFLE 545

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
              +   +  N     +A   F     L    +  +    +   RR   +  +  + R  
Sbjct: 546 EWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDI 605

Query: 554 AGVEMRDVHPTHYGRIC---------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
              E+R    T  GRIC         P     G        +           I+   R 
Sbjct: 606 REKELR--LFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRF 663

Query: 605 -VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF------TEELVFCRCAGEEILVP 657
                  +  + YL A EEE   IA +   L+            EEL   +         
Sbjct: 664 GWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPH 723

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++ S R      M +QA+ +              
Sbjct: 724 VHARTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQV------- 776

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                                + + +  Y       +     + 
Sbjct: 777 ----------------------------------RMDTMANILYYPQKPLATTRSMEYLK 802

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            R                        +L  G+N +VA + + GYN EDS+++++  +   
Sbjct: 803 FR------------------------ELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRG 838

Query: 838 VFTSIHIEEFEVMARDTKLG-PEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F SI    +    +   +   EE  R        +       +++ G+I  G  V+  D
Sbjct: 839 LFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGED 898

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I++GK  P         E+L +        DV        SG+   V+
Sbjct: 899 IIIGKTAPI----PLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVM 942


>gi|52694345|emb|CAG38012.1| RNA polymerase beta subunit [Pseudomonas tolaasii]
          Length = 373

 Score =  362 bits (928), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 222/372 (59%), Positives = 288/372 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V E  FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEARFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|227438067|gb|ACP30535.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
          Length = 666

 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 242/520 (46%), Positives = 358/520 (68%), Gaps = 13/520 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ +VGE+L+ Q+ LGLL++E++ KE++SS + D + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVAVGELLQKQFLLGLLKLEKNTKEKLSSKESDKINPKNITNNKPIYNQFKTFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN LS + + RR+++LG GG+ R  A  E+RDVH T+YGRICP ET EG NI
Sbjct: 63  KLSQFMDQVNPLSELANKRRITSLGPGGLNRETAQFEVRDVHSTYYGRICPIETPEGQNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L ++++ + +GFI+TPY  V +G V   +V +L+A++E     AQ++ ++DE+  
Sbjct: 123 GLILNLATYSKTDDFGFIQTPYFPVKNGIVNYGEVKWLTAVDEYGYTFAQSSVTIDENNK 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++ +  R   + ++V  E+ID+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQ
Sbjct: 183 IIDQFITVRKDYQYLIVKPEEIDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL++AEAP +GTG+E  +AK +   I A  +GIV  VDA  I I+  + +L+      
Sbjct: 243 AVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYVDAKTIKIKPFDENLEE----- 297

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           DIY L  FQ+SNQ T +NQ P V+VG+ + +  ++ DGPST  G+LALG+N+LVAF  WH
Sbjct: 298 DIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTKDGELALGKNVLVAFTTWH 357

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++ISE++V +DVFTSIHIEE  +  R +K G + +T +IPN S    +++DE 
Sbjct: 358 GYNFEDAIIISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDEN 417

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EVN GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G +GTV
Sbjct: 418 GIVRVGSEVNTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGSNQKDTSLKVKHGDAGTV 477

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           +DV+I +R   D       +  + I+ + +    ++  + 
Sbjct: 478 IDVQIISRANGD-------ILEDGIDKIVKVFIAQKRKIK 510



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 136/500 (27%), Positives = 206/500 (41%), Gaps = 72/500 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ A  P  G   E  +            + I     +      K   E
Sbjct: 235  MGANMQRQAVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYV-DAKTIKIKPFDE 293

Query: 860  EITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             +  DI  +      N    I++   + VG  +  G ++    + K +  +   + +L A
Sbjct: 294  NLEEDIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTK-DGELALGKNVLVA 352

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                   +  D  +     V   V    I       +   S + +      +       +
Sbjct: 353  FTTWHGYNFEDAIIISEKLVKDDVF-TSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSK 411

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD N   R+   +   + + G    K     + +        +       ++   +  
Sbjct: 412  RHLDENGIVRVGSEVNTGDILVGRISPKGEDNPTPE-------EKLLNAIFGNKGSNQKD 464

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLKV++  + ++++     +I     GD +  G+ ++VKVF+A KR I+ GDKMAGRHG
Sbjct: 465  TSLKVKHGDAGTVID----VQIISRANGDILEDGIDKIVKVFIAQKRKIKVGDKMAGRHG 520

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S +LP EDMP+L+DGTP+DI+LNP GV SRMN+GQ+ E HLG A   L  K  S 
Sbjct: 521  NKGVISLVLPVEDMPYLEDGTPIDILLNPQGVASRMNIGQVLELHLGMAAKKLNVKFVSP 580

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D   N  +  +                                               
Sbjct: 581  VFDGIKNESLDSIL---------------------------------------------K 595

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E           L ESG+  LYDG+TG+ +D  V+VG +YMLKL HMV DK+ ARS G Y
Sbjct: 596  EAD---------LPESGRFTLYDGITGKQYDSKVSVGVMYMLKLQHMVDDKINARSVGPY 646

Query: 1276 SLVTQQPLGGKSNRGGQRLG 1295
            SL++QQPLGGKS  GGQR G
Sbjct: 647  SLISQQPLGGKSQNGGQRFG 666


>gi|224555847|gb|ACN56500.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 102/181 (56%), Positives = 130/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ + TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKIMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+QALGL + + N + +     +   D 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQALGLDMKVLNGKGQEVKMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|83699937|gb|ABC40945.1| RNA polymerase beta subunit [Spiroplasma velocicrescens]
          Length = 594

 Score =  361 bits (927), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 233/476 (48%), Positives = 328/476 (68%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N LS +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLSELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N +GFIETPYRKV  G+V  ++  YL+A +E++  +AQAN  + EDG+  +E V 
Sbjct: 61   TYARINKFGFIETPYRKVIKGRVIKDEYEYLTADKEKDFIVAQANIQIAEDGTILDESVV 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++++     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDMMANPIDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG AIVA   GIV  VDA  I +           SGV IY L  
Sbjct: 181  ESPIVGTGVEHEAARDSGDAIVASADGIVRYVDAKVIKV--------EEASGVKIYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F +SN  T +   P+VKVGD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FTKSNNGTAITHLPIVKVGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK G EEITR+IPN+SE   K++DE GI+ +G 
Sbjct: 293  VIVSERIVIDDRFTSIHIDEYTIERRQTKQGQEEITREIPNISEASKKHLDEEGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  RADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMDDG 468



 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 127/418 (30%), Positives = 185/418 (44%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKARDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGQEEITREIPNISEASKKHLDEEGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP + DGTP
Sbjct: 411  FSRADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMDDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     D+            
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGLKVNTPVFEGVKENDLV----------- 519

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                           +++ A     G    T                       G++   
Sbjct: 520  --------------EIMKEAGMENYGKVTLT----------------------DGRT--- 540

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
             G T   FD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  -GET---FDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|197311432|gb|ACH61922.1| RNA polymerase beta subunit [Mycoplasma canadense]
          Length = 664

 Score =  361 bits (927), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 237/517 (45%), Positives = 346/517 (66%), Gaps = 15/517 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ +ERIS+ +   + P+++ N KP+ +    FF +S
Sbjct: 3   NKRIVTIGELLQNQFRIGLIKLEKNTRERISTKETSKITPKNVTNNKPIFNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 63  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA ++ YGFI++PY +V D KV  +   YL+A+EE     AQ+   + E+  
Sbjct: 123 GLILNLASFADIDKYGFIKSPYFRVKDKKVDFSKPYYLTAIEEAGYSFAQSTVRI-ENDE 181

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             ++LV  R   E + VP  ++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 182 IIDDLVMVRRDNEYLQVPANEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 241

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+L  EAP V TG+E+ +AK S   I+AK  G+V  VDA  I I          +   
Sbjct: 242 AVPVLFPEAPLVATGVEADIAKYSSTNIIAKYDGVVSYVDANVIKISRE------GSKKT 295

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T ++Q PLVK+  E++  D++ DGPS   G++ALG+N+LV F  WH
Sbjct: 296 DSYYLRTFERSNQGTLIHQVPLVKLNQEIKAGDLLVDGPSMKNGEMALGKNVLVGFTTWH 355

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G+N+ED++++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +DE 
Sbjct: 356 GFNYEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDEN 415

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV+ GDILVG+ + KGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTV
Sbjct: 416 GIVRVGSEVSTGDILVGRTSQKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKYGHNGTV 475

Query: 940 VDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V V + +R        GI+K  +    ++ +I++  +
Sbjct: 476 VAVDVLSRELGDTLEDGIEKIVKVSIAQKRKIKVGDK 512



 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 131/415 (31%), Positives = 186/415 (44%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  E+  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 317  LVKLNQEIKAGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 374

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 375  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNHSKRFLDENGIVRVGSEVSTGDILVGRT 434

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 435  SQKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKYGHNGTVVAVDVLSREL------- 485

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 486  --GDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 543

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 544  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILE---------- 593

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               E  INS         SG+S++YDG 
Sbjct: 594  -----------------------------------EAKINS---------SGKSVVYDGR 609

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 610  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|209360653|gb|ACI42997.1| RNA polymerase beta subunit [Mycoplasma testudinis]
          Length = 760

 Score =  361 bits (927), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 234/508 (46%), Positives = 345/508 (67%), Gaps = 29/508 (5%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS--------------------VMP 500
           N+R++ + E+L+++ + G+LRM+R I+++++  D  +                    +  
Sbjct: 1   NKRLKLINELLRSRVQTGMLRMDRYIRDKLAIADGSNKNVELNEATGEMEETQKQTRLTI 60

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           + +IN+KP    + +FF + QL+Q  +  N L+ +T+ RR+SA+G GG++R    +++RD
Sbjct: 61  KSVINSKPFQLVIKDFFNTHQLTQFLDQQNPLAELTNKRRISAMGPGGISREDPNLDIRD 120

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VH +HYGRICP ET EG NIGL+ SL S+A +++ GF+ +PYRKV  G +T+    L+A+
Sbjct: 121 VHYSHYGRICPIETPEGMNIGLIMSLASYATIDSNGFLMSPYRKVEKGVITDKFERLTAL 180

Query: 621 EEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            E+   IA+A  N  L+E+G   ++ +  R    + L   +++D+ID +P+QVVSIAASL
Sbjct: 181 REDEYIIAEASANMKLNEEGKILDKEIIARYRSSQELYDPKRVDYIDVAPRQVVSIAASL 240

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDDS+R LMG NMQRQA PLLK  AP VGTG+E  +A  SG  I+AKR G V  V
Sbjct: 241 IPFLENDDSSRALMGANMQRQAAPLLKPYAPVVGTGVEYKIAHDSGMVILAKRDGEVVYV 300

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           D+  I ++  +G +D        Y+L KF +SNQNTC NQ P+V +G++V+++ I+ADG 
Sbjct: 301 DSTEIKVKGSDGKIDS-------YQLTKFLKSNQNTCYNQTPIVALGEKVKKSQILADGA 353

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +   G+LALG+N+L AF  W GYN+ED+++IS+R++ EDV+TSI+I E  V    TK G 
Sbjct: 354 AMRNGELALGQNILAAFTTWRGYNYEDAIIISDRLLQEDVYTSININEHTVQCVRTKNGD 413

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV+++  + +DE G+I VGAEV  GDILVGKI+PKG+  ++ EEKLL+AIFG
Sbjct: 414 EEITRDIPNVADDAKRYLDEDGVIMVGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIFG 473

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EK  ++R++SL+VP G  G V  VR F+
Sbjct: 474 EKTKNIRESSLKVPHGGDGVVAAVRRFS 501



 Score =  344 bits (882), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 143/520 (27%), Positives = 227/520 (43%), Gaps = 37/520 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGP 858
                       +L  + P  G   E  +     MV         +       +     G 
Sbjct: 254  MGANMQRQAAPLLKPYAPVVGTGVEYKIAHDSGMVILAKRDGEVVYVDSTEIKVKGSDGK 313

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +  +    +        ++  I+ +G +V    IL           +   + +L A   
Sbjct: 314  IDSYQLTKFLKSNQNTCYNQTPIVALGEKVKKSQILAD-GAAMRNGELALGQNILAAFTT 372

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  +  D  +     +   V      N H +    R+ + + E    +    DD +  L
Sbjct: 373  WRGYNYEDAIIISDRLLQEDVYTSININEHTVQC-VRTKNGDEEITRDIPNVADDAKRYL 431

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D +       I+ G     G     K +      +S   +     F  + + ++ +   +
Sbjct: 432  DED-----GVIMVGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIFGEKTKNIRESSLKV 486

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                +   + +      +   I  GD++   V+ +VKV+VA KR IQ GDK+AGRHGNKG
Sbjct: 487  PHGGDGVVAAV------RRFSIAKGDELGDDVIELVKVYVAQKRKIQIGDKLAGRHGNKG 540

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL---------- 1148
            IVS+I+P EDMP L+DGTP+DI+LNPLGVPSRMN+GQIFE HLG A  G+          
Sbjct: 541  IVSKIVPREDMPHLEDGTPIDILLNPLGVPSRMNIGQIFELHLGLAARGIARKELIKAAY 600

Query: 1149 ---GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV- 1204
               G+K    +         S + +  +   G  +     +      +         G+ 
Sbjct: 601  DTAGEKTLKKLFGLSTVAAKSLISTTKDYCKGKAAKNVDDALARIRPIDIDIILKLVGMT 660

Query: 1205 ------PVSTPVFDGADEEAINSMLRMADLDE---SGQSILYDGLTGEPFDRPVTVGYIY 1255
                   ++TPVF+G +   + +++  A +D     G+  L DG TGEPF++P++VG +Y
Sbjct: 661  YDDLSYKIATPVFEGVNMNDLKNIMAEAGIDSEKTHGKFKLIDGRTGEPFEKPISVGVMY 720

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            MLKL+HMV DK+++R+ G YS +TQQPLGGKS  GGQR G
Sbjct: 721  MLKLDHMVDDKIHSRAVGPYSKITQQPLGGKSQMGGQRFG 760


>gi|167385143|ref|XP_001737225.1| DNA-directed RNA polymerase II subunit RPB2 [Entamoeba dispar SAW760]
 gi|165900064|gb|EDR26512.1| DNA-directed RNA polymerase II subunit RPB2, putative [Entamoeba
            dispar SAW760]
          Length = 1170

 Score =  361 bits (927), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 179/1074 (16%), Positives = 330/1074 (30%), Gaps = 213/1074 (19%)

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
               +I +      +       +   +  ++    +DA   +      G+ S  +  E + 
Sbjct: 265  NDQKIVEAICFDENDNEMYNIVTTAIQANECTTTEDARRWL------GEHSKKTNKEGVI 318

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              +  +  K  L   G  K+   L      D    + + +  +    + +  GK   DD 
Sbjct: 319  EIVSENIQK--LQRDGTEKLKKDLLPHIGTDNFESKAQFLGYMTNHFLSVYTGKRNGDDR 376

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+L  +R+   G ++   ++  L RM ++ + ++        ++     ++   + S   
Sbjct: 377  DHLARKRMLMTGGLMMELFKNSLKRMMKTARAQLQKQLSSNKTLEYAKPLSFPTITSDFT 436

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA--------RAGVEMRDVHPTHY 566
            +   +    Q     +         RL+        R         R   + R +H T +
Sbjct: 437  KALGTGNWPQPGGKESRHGVAQVLSRLTFTSALAYLRKISSPVEGKRKTQKPRQLHNTQW 496

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEEN 624
            G ICPAET EG + GLV  L+  A++      E         D +   ++   +  +  N
Sbjct: 497  GYICPAETPEGESCGLVKMLSLMAQITVALQDEQVDEIKEALDCQYVCNINDCTGEKMNN 556

Query: 625  RYIAQANSSLDE----DGSFTEELVFCRCAGEEILVPREKID-----FIDASPKQVVSIA 675
                  N    +         EEL   R    +  V +           +          
Sbjct: 557  ITKVFLNGVWLKCSEQPQKLLEELKNYRKNSTKGKVKKVMSMVLDQLHKELRIYTDAGRC 616

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
               +  + N++ +  L   N+++  +  L +       G E                GI+
Sbjct: 617  TRPLFTVSNNNGHYTL---NLKQSQITELCSRLDNESNGTEKTKF-----WNNFLSKGII 668

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA    +  +        +                           G   +      
Sbjct: 669  EYVDADEEEMSMIAMFPSDLDNT-------------------------EGGSSKNYTHCE 703

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              P+  +G L        + +P+  +N       S R   +       I  +        
Sbjct: 704  IHPALVMGVLG-------SIIPFPDHNQ------SPRNTYQCAMGKQAIGVYA------- 743

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                         S   L+ +D  G   V        +            +      + A
Sbjct: 744  -------------SNYQLR-LDSLG--HVLFYPQKPLVSTRAAEYVKFGHIPAGINAIVA 787

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            +      +  D+ +     +   +     F     D    +   E  ++      +++ +
Sbjct: 788  VCCYSGYNQEDSVMMNQGSIDRGLFRSMAFKTFSED----AKKSETTELMFFKPSENNSE 843

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            +  D + Y ++                   T +  D I           A   E   + +
Sbjct: 844  ITEDISKYEKV----------DVDGILAPGTKVKPDDIL---------VAGFYENKNKTL 884

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            +   ++Y+  ++ + D         Q          + ++V +   R  Q GDK + RHG
Sbjct: 885  KDCSLRYKPRENGVVD---------QVVVTNAQSGTKYIRVKMRSIRIPQIGDKFSSRHG 935

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMPF  +G   DI++NP  +PSRM VGQ+ E         LGK     
Sbjct: 936  QKGTVGMTYRQEDMPFTIEGISPDIIMNPHAIPSRMTVGQLVEC-------LLGK----- 983

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                            V   TP      
Sbjct: 984  -----------------------------------------VGALVGDVQSGTPFQKDIT 1002

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + I   L        G   L+ G TG   D  V +G  Y  +L H+V DKV+ R+TG Y
Sbjct: 1003 VDKIGERLHKLKYQRRGYEALFSGHTGRKLDSLVYIGPTYYQRLKHLVDDKVHGRATGPY 1062

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            + +T+QPL G+S  GG RLGEME  C+ ++G + +L+E L + SD        Y+  V  
Sbjct: 1063 ATLTRQPLEGRSRDGGLRLGEMERDCMISHGVSSLLKERLFLASD-------KYQIYVCD 1115

Query: 1336 N-----------------------DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                                       +   P +  +L +E+ ++ +   +   
Sbjct: 1116 KCHMPAVANHKACTFQCSCCKDKTHISKVDIPYACKLLFQELMSMAVCPRIYTE 1169



 Score =  138 bits (348), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 102/761 (13%), Positives = 222/761 (29%), Gaps = 119/761 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-AMLEFVSYEFDPPKFD 87
           L++ Q +SY++F+             ++ +   V  I+A       +      F  PK  
Sbjct: 28  LVKQQLSSYNNFIKKVRDVITSDTTKIEISNAEVLGISANDEEEHTIVLTDPIFHFPKVS 87

Query: 88  ----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R LTYA  L++  +    D     G + I  + +  I    +P 
Sbjct: 88  TGSKASASLFPHEARLRSLTYACQLEVKAK----DTIRKNGTEEITTVPKIDI--ASIPS 141

Query: 138 MTKD-------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDK 169
           M K                          G F+IKG +++V++Q   +P    +    D+
Sbjct: 142 MLKSDVCRLKRCVTQPSMISKDECSFEQGGYFIIKGSEKVVIAQEKMAPNTVLVFEGSDQ 201

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDII--------HVRIDRRR---KVPVTSFL 218
            +    G +                   S D +        + ++D+ R   KVPV +  
Sbjct: 202 LKYPYEGNINSLA---------------SNDEVRTHKIRMDYPKLDKSRLKIKVPVLTLS 246

Query: 219 M------------ALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSS 262
                        ALG ++++ I+         ++  +     + A +        +   
Sbjct: 247 RMDCDVPVVLLFVALGYENDQKIVEAICFDENDNEMYNIVTTAIQANECTTTEDARRWLG 306

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                   E VIE   +    L +   EK +K   +              +   T     
Sbjct: 307 EHSKKTNKEGVIEIVSENIQKLQRDGTEK-LKKDLLPHIGTDNFESKAQFLGYMTNHFLS 365

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN--AYIRNTLVTDKNKDRKDALLDIYRV 380
                 +    + +    +     L ++   N+    ++      + +   +  L+  + 
Sbjct: 366 VYTGKRNGDDRDHLARKRMLMTGGLMMELFKNSLKRMMKTARAQLQKQLSSNKTLEYAKP 425

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +    +++                K     V +V   +          +     +     
Sbjct: 426 LSFPTITSDFTKALGTGNWPQPGGKESRHGVAQVLSRLTFTSALAYLRKISSPVEGKRKT 485

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG------LLRMERSIKERISSVD 494
           +    L N +                + +ML    ++        +   +   +     +
Sbjct: 486 QKPRQLHNTQWGYICPAETPEGESCGLVKMLSLMAQITVALQDEQVDEIKEALDCQYVCN 545

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           I+    + + N   V        CS Q  +L E + +  + +   ++  +    + +   
Sbjct: 546 INDCTGEKMNNITKVFLNGVWLKCSEQPQKLLEELKNYRKNSTKGKVKKVMSMVLDQLHK 605

Query: 555 GVEM-----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            + +     R   P           +       ++ L S     + G  +T +    +  
Sbjct: 606 ELRIYTDAGRCTRPLFTVSNNNGHYTLNLKQSQITELCSRLDNESNGTEKTKF--WNNFL 663

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               + Y+ A EEE   IA   S LD                       +     +  P 
Sbjct: 664 SKGIIEYVDADEEEMSMIAMFPSDLD----------------NTEGGSSKNYTHCEIHPA 707

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            V+ +  S+IPF +++ S R    C M +QA+ +  +    
Sbjct: 708 LVMGVLGSIIPFPDHNQSPRNTYQCAMGKQAIGVYASNYQL 748


>gi|212373983|emb|CAP09918.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35717]
          Length = 370

 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 220/369 (59%), Positives = 286/369 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPXDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLG 857
            +ARDTKLG
Sbjct: 362 CVARDTKLG 370


>gi|312985376|gb|ADR30831.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 102/181 (56%), Positives = 130/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ + TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKIMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSD
Sbjct: 79   HMVDDKIHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+QALGL + + N + +     +   D 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQALGLDMKVLNGKGQEVKMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|294768470|gb|ADF36183.1| RNA polymerase beta subunit [Mycoplasma sp. Mirounga ES2805-ORL]
          Length = 665

 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 247/632 (39%), Positives = 388/632 (61%), Gaps = 20/632 (3%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
             N+R+ SVGE+L NQ+ +GL ++E++ +ER+S+ + D V P+++ N K + + +  FF S
Sbjct: 3    TNKRIVSVGELLHNQFNVGLSKLEKTTRERMSAKEPDKVTPKNITNNKLISNQMKTFFNS 62

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S+LSQ  + +N LS I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63   SKLSQFMDQINPLSEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 122

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
            IGL+ +  S+A+ N +GF+ETPY KV DG V  ++V YL+A EE    I Q+   +D++G
Sbjct: 123  IGLILNFASYAKTNKFGFLETPYYKVNDGVVDYSEVEYLTASEEIGYKIVQSTVKVDDNG 182

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               ++ +  R     IL   + +D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 183  KLIDDSITMRYNYNYILGSSKDVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQR 242

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            QAVPLL+AEAP V TG+ES +AK S +   +K  G+VE VD  +I IR+ +G L+     
Sbjct: 243  QAVPLLEAEAPLVATGLESEIAKYSSSNFSSKSNGVVEYVDGEKIKIRNEKGTLE----- 297

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               Y L  F+RSNQ++ V+Q+P+VK G EV   D++ DG S   G+LALG+N++VAF  +
Sbjct: 298  --TYFLKNFERSNQDSVVHQKPIVKEGQEVSVGDLLVDGSSFKDGELALGKNVVVAFTTY 355

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
             GYN+ED+++++ER+V +DVFTSIHIEE  +  R ++ G +E+T +IPNVS+  ++++D 
Sbjct: 356  KGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRTSRAGDDELTSEIPNVSKHSIRHLDP 415

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             G++ VG+EV PGDILVG+++PKG+   +PEEK+L +I  ++ ++VRDTSL+V +G +GT
Sbjct: 416  YGVVRVGSEVVPGDILVGRVSPKGDDNPSPEEKMLSSILQQRQLNVRDTSLKVKNGHAGT 475

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            V+   I +R    K++    +++     +A  +  +        +     +         
Sbjct: 476  VISTEILSREN--KDQLEDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDM 533

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
            P   +  T +   L  +   S+     V +  +    + LK ++ T     +   K +I 
Sbjct: 534  P-YLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAAKQLKCKFVTPV--FDGIKKEEIF 590

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             +     +P    +   + +       +GDK 
Sbjct: 591  DVIKEAGLPETGKQ---ILI----DPITGDKF 615



 Score =  314 bits (805), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 148/562 (26%), Positives = 223/562 (39%), Gaps = 77/562 (13%)

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV-----NQRPLVKVGDEVRRNDIIAD 796
            +  ++  +       S    Y       S+++        NQ   V  G      +  A+
Sbjct: 173  QSTVKVDDNGKLIDDSITMRYNYNYILGSSKDVDYIEVAPNQMVSVAAGCIPFLENDDAN 232

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---D 853
                          +L A  P      E  +   +   S     S  + E+    +    
Sbjct: 233  RALMGSNMQRQAVPLLEAEAPLVATGLESEIA--KYSSSNFSSKSNGVVEYVDGEKIKIR 290

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
             + G  E               + +  I+  G EV+ GD+LV   + K +  +   + ++
Sbjct: 291  NEKGTLETYFLKNFERSNQDSVVHQKPIVKEGQEVSVGDLLVDGSSFK-DGELALGKNVV 349

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    K  +  D  +     V   V    I       +   S + + E    +      
Sbjct: 350  VAFTTYKGYNYEDAIILNERLVKDDVF-TSIHIEEQTIQFRTSRAGDDELTSEIPNVSKH 408

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                LD     R+   +   + + G    K     S +           +  +     QR
Sbjct: 409  SIRHLDPYGVVRVGSEVVPGDILVGRVSPKGDDNPSPE-----------EKMLSSILQQR 457

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             +       +            +I   +  D +  G+ ++VKV +A+KR I+ GDKM+GR
Sbjct: 458  QLNVRDTSLKVKNGHAGTVISTEILSRENKDQLEDGIDKIVKVSIAVKRKIKVGDKMSGR 517

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HGNKG+VS +LP EDMP+L+DGTPVD++LNP GVPSRMN+GQ+ E HLG A   L  K  
Sbjct: 518  HGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAAKQLKCKFV 577

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            + + D     +I                                             FD 
Sbjct: 578  TPVFDGIKKEEI---------------------------------------------FD- 591

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                    +++ A L E+G+ IL D +TG+ FD PV+VG +YMLKLNHMV DK++ARS G
Sbjct: 592  --------VIKEAGLPETGKQILIDPITGDKFDNPVSVGVMYMLKLNHMVDDKMHARSVG 643

Query: 1274 SYSLVTQQPLGGKSNRGGQRLG 1295
             YSL+TQQPLGGKS  GGQR G
Sbjct: 644  PYSLITQQPLGGKSQNGGQRFG 665


>gi|294768464|gb|ADF36180.1| RNA polymerase beta subunit [Mycoplasma sp. Mirounga ES2806-NAS]
          Length = 667

 Score =  361 bits (926), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 240/495 (48%), Positives = 347/495 (70%), Gaps = 8/495 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ R+GLL++E++ KE+I+  D+D +  +++ N KP+ + +  FF SS
Sbjct: 4   NKRIVTIGELLQNQLRIGLLKLEKNTKEKIAGKDLDKITARNVTNNKPIYNQMKSFFNSS 63

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 64  KLSQFMDQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNI 123

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-G 638
           GL+ ++ S+A+++ YGFI+TPY KV +G    ND+ YL+A+EE N   AQ++ ++DE  G
Sbjct: 124 GLILNMASYAKIDEYGFIQTPYFKVNNGVADFNDIRYLTAIEEINFTFAQSSINIDESTG 183

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E V CR   E I VPRE+ID++  S +Q+ SI+AS IPFLENDD+NR LMG NMQR
Sbjct: 184 KILDEKVMCRKNNEYIEVPREEIDYMGVSSRQMTSISASAIPFLENDDANRALMGSNMQR 243

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+K EAP+V TG+E+ +A+ S + + A + G+V  VDA +I I+S       +   
Sbjct: 244 QAVPLIKPEAPYVATGVEADIARFSASNVRATKDGVVTYVDASQIKIQSE------NEKK 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             IY L  F+RSNQ T ++Q+PLV VG E++  D++ DGPS + G+LALG+N+LV F  W
Sbjct: 298 PTIYYLRTFERSNQGTVIHQKPLVHVGQEIKVGDLLTDGPSMEKGELALGKNVLVGFSTW 357

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++++E++V EDV+TSIHIEE  +  R +K G + +T +IPN S    + + E
Sbjct: 358 YGYNYEDAVVLNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSEIPNASNRSKRFLTE 417

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GT
Sbjct: 418 DGIVRIGSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGT 477

Query: 939 VVDVRIFNRHGIDKN 953
           VV V +  R   D N
Sbjct: 478 VVAVDVLRRDTDDTN 492



 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 115/414 (27%), Positives = 174/414 (42%), Gaps = 66/414 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+L    +   +  +   + +L         +  D  +     V   V 
Sbjct: 320  LVHVGQEIKVGDLLTDGPS-MEKGELALGKNVLVGFSTWYGYNYEDAVVLNEKLVKEDV- 377

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  RS + +      +    +  +  L  +   R+   +   + + G  
Sbjct: 378  YTSIHIEEQTIQFRRSKAGDDILTSEIPNASNRSKRFLTEDGIVRIGSEVGPGDILVGRI 437

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V+        +  +L     +     
Sbjct: 438  SPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVLRRDTDD----- 490

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                ++  G+  +VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 491  ---TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPEEDMPYLEDGTPLDI 547

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  +  + + D  +   I  ++           
Sbjct: 548  LLNPQGVPSRMNIGQVLELHLGLAAKKLNCRFVTPVFDGISYKQIQEIQKEAGIDPSGKM 607

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SG+       
Sbjct: 608  TV-----------------------------------------------YSGK------- 613

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            TG+PFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 614  TGKPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 667


>gi|294768468|gb|ADF36182.1| RNA polymerase beta subunit [Mycoplasma sp. Mirounga ES2774-NASSP4]
          Length = 668

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 234/495 (47%), Positives = 339/495 (68%), Gaps = 8/495 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ R+GLL++E++ KE+I+  D+D +  +++ N KP+ + +  FF SS
Sbjct: 4   NKRIVTIGELLQNQLRIGLLKLEKNTKEKIAGKDLDKITARNVTNNKPIYNQMKTFFNSS 63

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 64  KLSQFMDQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNI 123

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-G 638
           GL+ ++ S+A+++ YGFI+TPY KV  G V  ND+ YL+A+EE N   AQ++ ++DE+ G
Sbjct: 124 GLILNMASYAKIDDYGFIQTPYFKVNKGIVDFNDIRYLTAIEEINFTFAQSSINIDENTG 183

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E V  R   E I + + +ID+I  S +Q+ SI+AS IPFLENDD+NR LMG NMQR
Sbjct: 184 EILDEKVMSRKNNEYIELDKTEIDYIGVSSRQMTSISASAIPFLENDDANRALMGSNMQR 243

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+K EAP V TG+E+ +AK S + + A + G+V  VDA  I I++           
Sbjct: 244 QAVPLIKPEAPLVATGVEADIAKFSASNVRATKDGVVTYVDANEIRIKNE------FEKK 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +Y L  F+RSNQ T ++Q+PLVK G  ++  D++ DGPS   G+LALG+N+LV F  W
Sbjct: 298 STVYYLRTFERSNQGTVIHQKPLVKAGQVIKAGDLLTDGPSMQNGELALGKNVLVGFSTW 357

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++E++V +DV+TSIHIEE  +  R +K G + +T +IPN S    + + E
Sbjct: 358 FGYNYEDAVILNEKLVKDDVYTSIHIEEQTIQFRRSKAGDDILTSEIPNASNRSKRFLGE 417

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GT
Sbjct: 418 DGIVIIGSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGT 477

Query: 939 VVDVRIFNRHGIDKN 953
           VV V +  R   D N
Sbjct: 478 VVAVDVLRRDTDDTN 492



 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 98/241 (40%), Positives = 125/241 (51%), Gaps = 54/241 (22%)

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            + + +     ++  G+  +VKV +A KR I+ GDKMAGRHGNKG+VS ILP EDMP+L D
Sbjct: 482  DVLRRDTDDTNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPEEDMPYLSD 541

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  S + D  +   I  ++     
Sbjct: 542  GTPLDILLNPQGVPSRMNIGQVLELHLGLAAKKLNCKFVSPVFDGISYKQIQEIQKEAGI 601

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                    +G+ 
Sbjct: 602  DTSGKMTV-----------------------------------------------YNGK- 613

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 614  ------TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 667

Query: 1295 G 1295
            G
Sbjct: 668  G 668


>gi|183584839|gb|ACC63862.1| RNA polymerase subunit B [Acinetobacter towneri]
          Length = 286

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 137/289 (47%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDMLSGLALVDLLEIQPSDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++   +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQTFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K   +I+ LR+FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA
Sbjct: 181  L---KQQREIAELRAFLDKIYNKVGGEQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAELPRSGQTVLYDGRTGEKFDRPVTVGYMYMLKLNHLV 286


>gi|183584835|gb|ACC63860.1| RNA polymerase subunit B [Acinetobacter tandoii]
          Length = 286

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 138/289 (47%), Positives = 189/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G  G K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLSGQESNGG-GGTKRGDKLSEDMLSGLELVDLLEIQPSDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA
Sbjct: 181  L---KQQREIAELRVFLDKIYNKVGGQQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A++  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELAEIPRSGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|156628204|gb|ABU89019.1| RNA polymerase beta subunit [Spiroplasma eriocheiris]
 gi|156628206|gb|ABU89020.1| RNA polymerase beta subunit [Spiroplasma sp. CRAYFISH]
 gi|156628208|gb|ABU89021.1| RNA polymerase beta subunit [Spiroplasma sp. SHRIMP]
          Length = 573

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 226/431 (52%), Positives = 315/431 (73%), Gaps = 8/431 (1%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRL+ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL+++L ++A++N++GFI
Sbjct: 1   RRLTALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINNLATYAKINSFGFI 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           ETPYRKV D KVT+   YL+A EE+N  +AQAN  L + G   ++ V  R  GE I+  R
Sbjct: 61  ETPYRKVIDNKVTSQNDYLTADEEKNYVVAQANIRLSDKGEILDDQVIARFQGENIIALR 120

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            ++D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+  ++P+VGTG+E  
Sbjct: 121 TEVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLINPQSPYVGTGVEYA 180

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            AK SG AIV++  G+++ VDA +I++++ E        G+  Y L  F RSNQ T +  
Sbjct: 181 AAKDSGLAIVSQYDGVIDFVDATKIILKTKE--------GLKTYNLDTFVRSNQGTSLTH 232

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            PLVK G +V +  I+ADGPS D G+LALG+N++VAF  W+GYN+ED++++SER+V++DV
Sbjct: 233 VPLVKQGQKVVKGQILADGPSIDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVADDV 292

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           FTSIHIEE+ +  R TK G EEITR+IPN+SE   K +D+ G++ +G EV PGDILVGK+
Sbjct: 293 FTSIHIEEYTIERRQTKQGAEEITREIPNISENARKFLDDDGLVIIGTEVKPGDILVGKV 352

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
           TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G V  ++ F R   +     + 
Sbjct: 353 TPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIVQAIKRFPREKYELAADVLE 412

Query: 959 VEREQIELLAR 969
           V +  I    +
Sbjct: 413 VVKVYIVQKRK 423



 Score =  293 bits (750), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 127/410 (30%), Positives = 185/410 (45%), Gaps = 74/410 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G IL    +   +  +   + ++ A       +  D  +         V 
Sbjct: 235  LVKQGQKVVKGQILADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIV----SERLVA 289

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D    + H  +      ++ER Q +  A +   E   +  N    L +   ++ G     
Sbjct: 290  DDVFTSIHIEE-----YTIERRQTKQGAEEITREIPNISENARKFLDDDGLVIIGTEVKP 344

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   +     F  + + V+ N   +    E     ++   + K 
Sbjct: 345  GDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIVQAIKRFPREKY 404

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            E       +   VL VVKV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP L+DGTP
Sbjct: 405  E-------LAADVLEVVKVYIVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHLEDGTP 457

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  L         
Sbjct: 458  VDIMLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNDELIELMD------- 510

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                       + ++        + IL 
Sbjct: 511  ------------------------------------------KAGMKNFG-----KEILV 523

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            DG TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+
Sbjct: 524  DGRTGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKA 573


>gi|212373961|emb|CAP09907.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35706]
          Length = 367

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 219/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 361 CVARDTK 367


>gi|83755185|gb|ABC46441.1| RNA polymerase beta subunit [Spiroplasma lampyridicola]
          Length = 594

 Score =  361 bits (926), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 229/476 (48%), Positives = 327/476 (68%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N +GFIETPYRKV +G V   +  YL+A +E +  +AQAN ++  DG   +E V 
Sbjct: 61   TYARINDFGFIETPYRKVKNGIVLNEEYEYLTADKERDYIVAQANINIGNDGKILDEEVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+    +ID++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMTSAREIDYLDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG AIVA   G+V  VD+ +I ++         ++G   Y L  
Sbjct: 181  ESPIVGTGVEYEAARDSGEAIVATEDGVVTYVDSKKITVK--------GSNGPKTYILAD 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVG++V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FNRSNSGTVITHLPIVKVGEKVKTKDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK G EEITR+IPNVSE   K +DE G+I +G+
Sbjct: 293  VIVSERIVQEDKFTSIHIDEYTLERRQTKQGHEEITREIPNVSEMSKKYLDEDGLIAIGS 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDIL+GKITPK ++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G V  ++ + 
Sbjct: 353  EVKSGDILIGKITPKSQTQLSPEDKLLQAIFGEKSRNVKDNSLRVPNGGDGIVQSIKRYK 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  REDGYDLPADILEIVKVFIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHTIDG 468



 Score =  281 bits (719), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 122/418 (29%), Positives = 182/418 (43%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V 
Sbjct: 247  IVKVGEKVKTKDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVQ 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ---VILDRNIYSRLMEILCGQNAVS 997
            + +  + H  +      ++ER Q +    +   E      + +        I  G    S
Sbjct: 302  EDKFTSIHIDE-----YTLERRQTKQGHEEITREIPNVSEMSKKYLDEDGLIAIGSEVKS 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    +     +      K 
Sbjct: 357  GDILIGKITPKSQTQLSPEDKLLQAIFGEKSRNVKDNSLRVPNGGDGIVQSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
             K + G D+P  +L +VKVF+  KR IQ GDKMAGRHGNKG++S+ILP EDMP   DGTP
Sbjct: 411  YKREDGYDLPADILEIVKVFIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHTIDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP G+PSRMN+GQ+ E HLG A   LG K+ + + +     ++  + +       
Sbjct: 471  VDIMLNPQGIPSRMNIGQVLEIHLGMAAKKLGIKVSTPVFEGVNEEELVDIMTEAGMTSY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
               +                              DG   E                  ++
Sbjct: 531  GKVNLI----------------------------DGRTGE------------------MF 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            D        +P++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  D--------KPISVGVMYMLKLSHMVDDKLHARNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|221328707|gb|ACM17816.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 376

 Score =  360 bits (925), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 225/372 (60%), Positives = 292/372 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ+ +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQVMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETREGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SP
Sbjct: 122 VVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S+R+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSISLSQRLVQEDRFTTIHIQELT 361

Query: 849 VMARDTKLGPEE 860
            +ARDTKLGPEE
Sbjct: 362 CVARDTKLGPEE 373


>gi|290751436|emb|CAQ16379.1| RNA polymerase beta subunit [Pseudomonas sp. R-26429]
          Length = 367

 Score =  360 bits (925), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 219/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 361 CVARDTK 367


>gi|94962313|gb|ABF48472.1| RNA polymerase beta subunit [Entomoplasma freundtii]
          Length = 595

 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 232/449 (51%), Positives = 320/449 (71%), Gaps = 10/449 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L
Sbjct: 1   DQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
             +A+VN +GFI TPYRKV +G +  ND+ YL+A EE N  I+Q++   D+DG   E+ V
Sbjct: 61  ACYAQVNEHGFITTPYRKVTNGVIDNNDIHYLTASEEGNYIISQSSIKQDDDGKILEKNV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE+++   + +D+ID SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPLL 
Sbjct: 121 VARYKGEDMIADVKDVDYIDVSPKQIVSIATSGIPFLENDDANRALMGANMQRQAVPLLN 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P VGTG+E   A+ SGAAIVA+   +V+ VD+  I           S  G+  Y L 
Sbjct: 181 PESPIVGTGIEFEAARDSGAAIVAEENALVKYVDSNLIT--------TESKEGIKTYTLA 232

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSN  T +  RP+VKVGD++ +  IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 233 SFERSNNGTALVHRPIVKVGDKIEKGQIIADGPSMDKGELAIGQNVVVAFTTYNGYNFED 292

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V ED FTSIHI+E+ +  R+TK G E+ITRD+PN+SE   K +D  GI+  G
Sbjct: 293 AIIMSERVVMEDRFTSIHIDEYSIERRNTKQGAEDITRDVPNISEAAKKYLDADGIVAPG 352

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F
Sbjct: 353 TEVKVGDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIKRF 412

Query: 946 NRHGIDKNERSISVEREQIELLARDKDDE 974
           +R     +  +  +E  +I ++ + K  E
Sbjct: 413 SREDGF-DLPADVLEVIKIYIVQKRKIQE 440



 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 124/420 (29%), Positives = 184/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPSGVSG 937
            I+ VG ++  G I+    +   +  +   + ++ A     G    D    S RV      
Sbjct: 248  IVKVGDKIEKGQIIADGPS-MDKGELAIGQNVVVAFTTYNGYNFEDAIIMSERVVMEDRF 306

Query: 938  TVVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            T + +  ++    +  + +  + R+   I   A+   D   I+      ++ +IL G+  
Sbjct: 307  TSIHIDEYSIERRNTKQGAEDITRDVPNISEAAKKYLDADGIVAPGTEVKVGDILVGKVT 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E +                 
Sbjct: 367  PKGQAQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSI------------- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K    + G D+P  VL V+K+++  KR IQ GDKM+GRHGNKG++SRILP EDMP L+DG
Sbjct: 410  KRFSREDGFDLPADVLEVIKIYIVQKRKIQEGDKMSGRHGNKGVISRILPIEDMPHLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   LG K+ + + +   + +++ + +     
Sbjct: 470  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKLGVKVATPVFEGLNDKELNEIMTEAGMT 529

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 530  NYGKVKLI-----------------------------------------------DGQ-- 540

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TG+  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  -----TGDVMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 595


>gi|52694223|emb|CAG30641.1| DNA-directed RNA polymerase beta chain [Pseudomonas avellanae]
          Length = 373

 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 217/366 (59%), Positives = 283/366 (77%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 6   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 65

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++
Sbjct: 66  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEI 125

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IAQA++++++     +E V  R   E  +     +  +D SPKQVVS+
Sbjct: 126 VFLSAIEESDHVIAQASAAMNDKQELIDERVAVRHLNEFTVKAPTDVTLMDVSPKQVVSV 185

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE++D+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 186 AASLIPFLEHNDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 245

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 246 IDSVDATRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 305

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED F +IHI+E   +ARDT
Sbjct: 306 ADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFPTIHIQELTCVARDT 365

Query: 855 KLGPEE 860
           KLGPEE
Sbjct: 366 KLGPEE 371


>gi|52694319|emb|CAG37999.1| RNA polymerase beta subunit [Pseudomonas tolaasii]
          Length = 375

 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 222/375 (59%), Positives = 290/375 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +
Sbjct: 121 VKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 181 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  
Sbjct: 241 VCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V E  FT+IHI
Sbjct: 301 GDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEARFTTIHI 360

Query: 845 EEFEVMARDTKLGPE 859
           +E   +AR TKLGPE
Sbjct: 361 QELTCVARHTKLGPE 375


>gi|212373987|emb|CAP09920.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35719]
          Length = 369

 Score =  360 bits (925), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 219/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 3   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 62

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 63  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 122

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 123 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 182

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 183 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 242

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 243 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 302

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 303 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELT 362

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 363 CVARDTK 369


>gi|83699939|gb|ABC40946.1| RNA polymerase beta subunit [Spiroplasma culicicola]
          Length = 594

 Score =  360 bits (924), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 229/444 (51%), Positives = 314/444 (70%), Gaps = 10/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++AR+N +GFIETPYRKV  GKV      YL+A  E++  +AQAN  + EDG+  +E V 
Sbjct: 61  TYARINEFGFIETPYRKVKSGKVILGQYEYLTADREKDYIVAQANIQIAEDGTILDESVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMAAPIDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG A+VA   GIV+ VDA  I I          + G+  Y L  
Sbjct: 181 ESPIVGTGVEHEAARDSGDAVVATEDGIVKYVDAKLISI--------EGSKGIKNYDLND 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VKVGD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FNRSNNGTALTHLPIVKVGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GI+ +G 
Sbjct: 293 VIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITREIPNISEASKKHLDEEGIVAIGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947 R-HGIDKNERSISVEREQIELLAR 969
           R  G D     + + +  +    +
Sbjct: 413 RADGYDLPADILEIIKIYVVQKRK 436



 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 123/418 (29%), Positives = 179/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKARDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIPNISEASKKHLDEEGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSRADGYDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGLKVNTPVFEGVKENELQEIMEEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                   
Sbjct: 531  GKVTLV----------------------------DGRTGEAF------------------ 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                    D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  --------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|197131672|gb|ACH47354.1| RNA polymerase beta subunit [Erodium texanum]
          Length = 1161

 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 119/342 (34%), Positives = 178/342 (52%), Gaps = 77/342 (22%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG P+D+V NPLGVPSRM
Sbjct: 858  ERIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGKPIDMVFNPLGVPSRM 917

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 918  NVGQIFECSLGLAGALLDRHYRVAPFDERYEQEASRKLVFSELHEASKQTGNPW------ 971

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S ++DG TG+PF++PV V
Sbjct: 972  ------------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVIV 998

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS------------------------ 1287
            G  Y+LKL H V DK++ RSTG Y+ +TQQP+ G++                        
Sbjct: 999  GQPYILKLIHQVDDKIHGRSTGHYTPLTQQPVKGRAKGGGPAGRRNGGLGSRGVWCCAYF 1058

Query: 1288 -----------NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
                         GGQR+GEMEVW ++ +G A++LQEMLT KSD +  R +++++   G 
Sbjct: 1059 LLHNNPLREGPRGGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHLRTRDKIFQTTSHGG 1118

Query: 1337 DTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            +  +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1119 EMPKAEDAPESFRLLVRELRSLALEMNHFLVSEKNFQMNRKE 1160



 Score =  344 bits (883), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 216/605 (35%), Positives = 352/605 (58%), Gaps = 13/605 (2%)

Query: 369 DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +++A+L+ Y+      GD              FF   + +L  +GR  +N RLNL    
Sbjct: 272 SKENAILEFYQQFVCVGGDPVFSDSLCKELQNQFF-RQRCELGRIGRRNINRRLNLAISQ 330

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSVG++L++Q RL L+R+E+ +
Sbjct: 331 NNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIRSVGDLLQDQLRLALIRLEKVV 390

Query: 487 KE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           K   R +        PQ+ + + P+ +    FF    LSQ+ +  N L++I H R+ S L
Sbjct: 391 KRAIREAMKGKLIPTPQNFVTSTPLKTTYESFFGLHPLSQVLDETNPLTQIVHGRKWSFL 450

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+    A    RD+HP++YGRIC  +TSEG N+GL+ SL   AR+  +G +E+P+ +
Sbjct: 451 GPGGLTGQTASFRRRDIHPSYYGRICTIDTSEGINVGLIGSLAIHARIGDFGSLESPFYE 510

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + +      ++YLS+  +E   I   NS    +    E++V  R   E + +  E++   
Sbjct: 511 ISEKSKRARILYLSSRRDEYCMIGIGNSLALNESFQEEQIVPARYRQEFLTIAWEQVHLR 570

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              P Q +SI  SLIPF+E++D+ R LM  NMQRQAV L ++E   VGTG+E  VA  SG
Sbjct: 571 SIFPFQYISIGVSLIPFIEHNDATRALMSSNMQRQAVALSRSEKCIVGTGLEGQVALDSG 630

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +++ + AG +  +          +  L           L+++QRSN+NTC++Q+P V+ 
Sbjct: 631 VSLITEHAGKIISIH--------TDKILLSGNGNTLSIPLVRYQRSNKNTCIHQQPQVRW 682

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G  +++  I+ADG ST  G+LALG+N+LVA+MPW GYNFED++LISER+V ED+ TS HI
Sbjct: 683 GKCIKKGQILADGASTVGGELALGKNLLVAYMPWEGYNFEDAVLISERLVYEDILTSFHI 742

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            ++E+    T  GPE++T  IP+++   L+N+ + G++ +G+ V  GDILVGK+ P+   
Sbjct: 743 RKYEIQIHVTNQGPEKVTNKIPHLAPHLLRNLGKNGVVILGSWVEAGDILVGKLRPRLAQ 802

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            ++PE++ + A+ G +    R T L+VP G  G V+DVR    +   ++ +  S ER ++
Sbjct: 803 DVSPEDRFVDALLGTQIATSRPTCLKVPRGGRGRVIDVRWIRSNPERESRKRKSRERIRV 862

Query: 965 ELLAR 969
            +  +
Sbjct: 863 YISQK 867



 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 69/379 (18%), Positives = 136/379 (35%), Gaps = 63/379 (16%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-------FVS 78
           IP L ++Q   +  F+   +  +      ++   K    I  F   A LE       F+ 
Sbjct: 12  IPGLNQIQFEGFCRFVDQGLREELSKFPTVEGLIKDFLDIEDFLDMANLEDLEDLEDFLD 71

Query: 79  Y--------------------------------------EFDPPKFDVDDCLWRDLTYAV 100
                                                  +   P     D ++  LTY+ 
Sbjct: 72  AVGQDLEKEVDEGIDIDEDVDEDVEKDVDVCFQLFAETSKLVEPLIKERDAVYESLTYSS 131

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            L ++  LI      +        +++Q+I +G++PLM   G F++ G+ R+VV+Q+ +S
Sbjct: 132 ELYVSAGLIWKRKGYY--------MQKQTILIGNIPLMNSWGVFIVNGMYRMVVNQILQS 183

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
           PGI++  +       G L+Y   II D G  +++E D K  I  R+ R++K+ +     A
Sbjct: 184 PGIYYRSELDHK---GILVYTGTIISDWGGRLELEIDRKGRIWARVSRKQKISILVLSSA 240

Query: 221 LGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           +G +  EIL    YP+++ +   D     + + +  +       +             K+
Sbjct: 241 MGSNLSEILENVCYPELLLAFLYDKENATIGSKENAILEFYQQFVCVGGDPVFSDSLCKE 300

Query: 280 LTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           L +   +   E G       +  L         ++    +   T  +      +     +
Sbjct: 301 LQNQFFRQRCELGRIGRRNINRRLNLAISQNNTFLLPRDILAATDHLIGMKFGMGTLDDM 360

Query: 334 EEIFHSEIRDIPILYVDSV 352
             + +  IR +  L  D +
Sbjct: 361 NHLKNKRIRSVGDLLQDQL 379


>gi|52694349|emb|CAG38014.1| RNA polymerase beta subunit [Pseudomonas corrugata]
          Length = 369

 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 220/369 (59%), Positives = 286/369 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + ++PQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLLPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTPIHIQELT 360

Query: 849 VMARDTKLG 857
            +ARDTKLG
Sbjct: 361 CVARDTKLG 369


>gi|221328699|gb|ACM17812.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 376

 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 225/363 (61%), Positives = 285/363 (78%)

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           VMPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E
Sbjct: 11  VMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFE 70

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+D+V+L
Sbjct: 71  VRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDDIVFL 130

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 131 SAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 190

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ 
Sbjct: 191 LIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDS 250

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADG
Sbjct: 251 VDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADG 310

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           PSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT IHI+E   +ARDTKLG
Sbjct: 311 PSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTPIHIQELTCVARDTKLG 370

Query: 858 PEE 860
           PEE
Sbjct: 371 PEE 373


>gi|290751442|emb|CAQ16382.1| RNA polymerase beta subunit [Pseudomonas sp. R-27199]
          Length = 367

 Score =  360 bits (924), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 219/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKGHLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQEXT 360

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 361 CVARDTK 367


>gi|67475595|ref|XP_653488.1| DNA-directed RNA polymerase subunit [Entamoeba histolytica HM-1:IMSS]
 gi|56470445|gb|EAL48102.1| DNA-directed RNA polymerase subunit, putative [Entamoeba histolytica
            HM-1:IMSS]
          Length = 1170

 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 178/1074 (16%), Positives = 330/1074 (30%), Gaps = 213/1074 (19%)

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
               +I +      +       +   +  ++    +DA   +      G+ S  +  E + 
Sbjct: 265  NDQKIVEAICFDENDNEMYNIVTTAIQANECTTTEDARRWL------GEHSKKTNKEGVI 318

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              +  +  K  L   G  K+   L      D    + + +  +    + +  GK   DD 
Sbjct: 319  EIVSENIQK--LQRDGTEKLKKDLLPHIGTDNFESKAQFLGYMTNHFLSVYTGKRNGDDR 376

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+L  +R+   G ++   ++  L RM ++ + ++        ++     ++   + +   
Sbjct: 377  DHLARKRMLMTGGLMMELFKNSLKRMMKTARAQLQKQLSSNKALEYAKPLSFPTITTDFT 436

Query: 515  EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA--------RAGVEMRDVHPTHY 566
            +   +    Q     +         RL+        R         R   + R +H T +
Sbjct: 437  KALGTGNWPQPGGKESRHGVAQVLSRLTFTSALAYLRKISSPVEGKRKTQKPRQLHNTQW 496

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEEN 624
            G ICPAET EG + GLV  L+  A++      E         D +   ++   +  +  N
Sbjct: 497  GYICPAETPEGESCGLVKMLSLMAQITVALQDEQVDEIKEALDCQYVCNINDCTGEKMNN 556

Query: 625  RYIAQANSSLDE----DGSFTEELVFCRCAGEEILVPREKID-----FIDASPKQVVSIA 675
                  N    +         EEL   R    +  V +           +          
Sbjct: 557  ITKVFLNGVWLKCSEQPQKLLEELKNYRKNSTKGKVKKVMSMVLDQLHKELRIYTDAGRC 616

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
               +  + N++ +  L   N+++  +  L +       G E                GI+
Sbjct: 617  TRPLFTVSNNNGHYTL---NLKQSQITELCSRLDNESNGTEKTKF-----WNNFLSKGII 668

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA    +  +        +                           G   +      
Sbjct: 669  EYVDADEEEMSMIAMFPSDLDNT-------------------------EGGSSKNYTHCE 703

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              P+  +G L        + +P+  +N       S R   +       I  +        
Sbjct: 704  IHPALVMGVLG-------SIIPFPDHNQ------SPRNTYQCAMGKQAIGVYA------- 743

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                         S   L+ +D  G   V        +            +      + A
Sbjct: 744  -------------SNYQLR-LDSLG--HVLFYPQKPLVSTRAAEYVKFGHIPAGINAIVA 787

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            +      +  D+ +     +   +     F     D    +   E  ++      +++ +
Sbjct: 788  VCCYSGYNQEDSVMMNQGSIDRGLFRSMAFKTFSED----AKKSETTELMFFKPSENNSE 843

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            +  D + Y ++                   T +  D I           A   E   + +
Sbjct: 844  ITEDISKYEKV----------DVDGILAPGTKVKPDDIL---------VAGFYENKNKTL 884

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            +   ++Y+  ++ + D         Q          + ++V +   R  Q GDK + RHG
Sbjct: 885  KDCSLRYKPRENGVVD---------QVVVTNAQSGTKYIRVKMRSIRIPQIGDKFSSRHG 935

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMPF  +G   DI++NP  +PSRM VGQ+ E         LGK     
Sbjct: 936  QKGTVGMTYRQEDMPFTIEGISPDIIMNPHAIPSRMTVGQLVEC-------LLGK----- 983

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                            V   TP      
Sbjct: 984  -----------------------------------------VGALVGDVQSGTPFQKDVT 1002

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + I   L        G   L+ G TG   D  V +G  Y  +L H+V DKV+ R+TG Y
Sbjct: 1003 VDRIGERLHKLKYQRRGYEALFSGHTGRKLDSLVYIGPTYYQRLKHLVDDKVHGRATGPY 1062

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG 1335
            + +T+QPL G+S  GG RLGEME  C+ ++G + +L+E L + SD        Y+  V  
Sbjct: 1063 ATLTRQPLEGRSRDGGLRLGEMERDCMISHGVSSLLKERLFLASD-------KYQIYVCD 1115

Query: 1336 N-----------------------DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                                       +   P +  +L +E+ ++ +   +   
Sbjct: 1116 KCHMPAVANHKACTFQCSCCKDKTHISKVDIPYACKLLFQELMSMAVCPRIYTE 1169



 Score =  137 bits (346), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 101/761 (13%), Positives = 219/761 (28%), Gaps = 119/761 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-AMLEFVSYEFDPPKFD 87
           L++ Q +SY++F+             ++ +   V  I+A       +      F  PK  
Sbjct: 28  LVKQQLSSYNNFIKKVRDVITSDTTKIEISNAEVLGISANDEEEHTIVLTDPIFHFPKVS 87

Query: 88  ----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R LTY+  L++  +  +            K      I +  +P 
Sbjct: 88  TGSKASASLFPHEARLRSLTYSCQLEVKAKDTIRKNGAEEITTVPK------IDIASIPS 141

Query: 138 MTKD-------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDK 169
           M K                          G F+IKG +++V++Q   +P    +    D+
Sbjct: 142 MLKSDVCRLKRCVTQPSMINKDECSFEQGGYFIIKGSEKVVIAQEKMAPNTVLVFEGSDQ 201

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDII--------HVRIDRRR---KVPVTSFL 218
            +    G +                   S D +        + ++D+ R   KVPV S  
Sbjct: 202 LKYPYEGNINSLA---------------SNDEVRTHKIRMDYPKLDKSRLKIKVPVLSLS 246

Query: 219 M------------ALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSS 262
                        ALG ++++ I+         ++  +     + A +        +   
Sbjct: 247 RMDCDVPVVLLFVALGYENDQKIVEAICFDENDNEMYNIVTTAIQANECTTTEDARRWLG 306

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                   E VIE   +    L +   EK +K   +              +   T     
Sbjct: 307 EHSKKTNKEGVIEIVSENIQKLQRDGTEK-LKKDLLPHIGTDNFESKAQFLGYMTNHFLS 365

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN--AYIRNTLVTDKNKDRKDALLDIYRV 380
                 +    + +    +     L ++   N+    ++      + +   +  L+  + 
Sbjct: 366 VYTGKRNGDDRDHLARKRMLMTGGLMMELFKNSLKRMMKTARAQLQKQLSSNKALEYAKP 425

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +    ++T                K     V +V   +          +     +     
Sbjct: 426 LSFPTITTDFTKALGTGNWPQPGGKESRHGVAQVLSRLTFTSALAYLRKISSPVEGKRKT 485

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG------LLRMERSIKERISSVD 494
           +    L N +                + +ML    ++        +   +   +     +
Sbjct: 486 QKPRQLHNTQWGYICPAETPEGESCGLVKMLSLMAQITVALQDEQVDEIKEALDCQYVCN 545

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           I+    + + N   V        CS Q  +L E + +  + +   ++  +    + +   
Sbjct: 546 INDCTGEKMNNITKVFLNGVWLKCSEQPQKLLEELKNYRKNSTKGKVKKVMSMVLDQLHK 605

Query: 555 GVEM-----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            + +     R   P           +       ++ L S     + G  +T +    +  
Sbjct: 606 ELRIYTDAGRCTRPLFTVSNNNGHYTLNLKQSQITELCSRLDNESNGTEKTKF--WNNFL 663

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               + Y+ A EEE   IA   S LD                       +     +  P 
Sbjct: 664 SKGIIEYVDADEEEMSMIAMFPSDLD----------------NTEGGSSKNYTHCEIHPA 707

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            V+ +  S+IPF +++ S R    C M +QA+ +  +    
Sbjct: 708 LVMGVLGSIIPFPDHNQSPRNTYQCAMGKQAIGVYASNYQL 748


>gi|212373969|emb|CAP09911.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35710]
          Length = 363

 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 218/363 (60%), Positives = 283/363 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARD 360

Query: 854 TKL 856
           TKL
Sbjct: 361 TKL 363


>gi|83699943|gb|ABC40948.1| RNA polymerase beta subunit [Spiroplasma tabanidicola]
          Length = 594

 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 239/524 (45%), Positives = 343/524 (65%), Gaps = 11/524 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVH +HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHTSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV +GKV  ++ VYL+A +E++  +AQAN   D+DG   +E V 
Sbjct: 61   TYAKINPYGFIETPYRKVLNGKVLKDEHVYLTADKEKDFIVAQANIQTDKDGKILDESVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV+ VD+  I I           +GV  Y L  
Sbjct: 181  ESPIVGTGVEYEAARDSGDAVVATEDGIVKYVDSKTITI--------EGKNGVKSYTLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+V+ N+I+ADGPS + G+LALG+N++VAF  W+GYNFED+
Sbjct: 233  FSRSNNGTAITHLPIVKVGDKVKANEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G 
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDSDGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            +  G D     + + +  +    + ++ +++         + +IL  ++      G    
Sbjct: 413  KAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTPVD 472

Query: 1006 TVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
             +L+   I       Q  +  +     + N++     +E  K  
Sbjct: 473  IMLNPQGIPSRMNIGQVLEIHLGMAAKKLNIKVATPVFEGVKED 516



 Score =  275 bits (703), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 118/418 (28%), Positives = 178/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   +IL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKANEILADGPS-MEKGELALGQNVVVAFTTWNGYNFEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            + R  + H  +      ++ER Q +    +   +   +  +    L     +  G     
Sbjct: 302  EDRFTSIHIDE-----YTLERRQTKQGPEEITRDIPNISESHKKHLDSDGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP G+PSRMN+GQ+ E HLG A   L  K+ + + +     D+  +         
Sbjct: 471  VDIMLNPQGIPSRMNIGQVLEIHLGMAAKKLNIKVATPVFEGVKEDDLKAIMDEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                   
Sbjct: 531  GKVKLI----------------------------DGRTGEAF------------------ 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                    D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  --------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|312985374|gb|ADR30830.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  360 bits (923), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 102/181 (56%), Positives = 129/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ + TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKIMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LT KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR  V+ESIV G    + G PESF VLVKE+QALGL + + N + +     +   D 
Sbjct: 139  DVRGRNNVFESIVKGQAIPKPGVPESFRVLVKELQALGLDMKVLNGKGQEVKMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|197131684|gb|ACH47360.1| RNA polymerase beta subunit [Pelargonium cotyledonis]
          Length = 1074

 Score =  359 bits (922), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 121/313 (38%), Positives = 175/313 (55%), Gaps = 48/313 (15%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
             +++V+++ KR I+ GDK++GRHGNKG+VS+ILP EDMP+L+DG P+D+V NPLGVPSRM
Sbjct: 800  EMIRVYISQKRQIKVGDKVSGRHGNKGVVSKILPREDMPYLQDGRPIDMVFNPLGVPSRM 859

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 860  NVGQIFECSLGLAGSLLDRHYRVAPFDERYEQEASRKLVFSELYEASKQTGNPW------ 913

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S + DG TG+ F++PV V
Sbjct: 914  ------------------VFE---------------PEYPGKSRILDGRTGDSFEQPVIV 940

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y+LKL+H V DK++ RSTG YSLVTQQP+ G++  GGQR+GEMEVW ++  G A++L
Sbjct: 941  GQSYILKLSHQVDDKIHGRSTGRYSLVTQQPVKGRALGGGQRVGEMEVWALEGLGVAHIL 1000

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETG-------TPESFNVLVKEMQALGLSID-- 1362
             EMLT KSD +  R +V  +++ G    +          PESF +LV+E++ L L ++  
Sbjct: 1001 HEMLTYKSDHLRTRKQVIGTLMIGGALSKPEPEDENEYAPESFRLLVRELRVLALELNHF 1060

Query: 1363 LENSRTKNSAKME 1375
            L + +     + E
Sbjct: 1061 LVSKKNFQMNRKE 1073



 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 218/656 (33%), Positives = 361/656 (55%), Gaps = 12/656 (1%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           G ++           L  +         I+  V          +    +    +++++L+
Sbjct: 170 GRLWARVSRKQKISILVLLSAMGSNLKDIIENVCYPEIFQAFLDKKFNENFGSKENSVLE 229

Query: 377 IYRVMRPGDVSTFSVAESMFN-FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           +Y+        T             F   +  L  +GR  +N RLNLD P ++  +   D
Sbjct: 230 LYQKFVDAGGYTELNDTIYIELRKKFFRQRCVLGRLGRQNINRRLNLDIPQNITFLLPRD 289

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSV 493
           I+A    L+ ++ G GT+DD+++L N+RVRSVG++L++Q+ L L R+E+++    + +  
Sbjct: 290 ILAATDHLIGMQFGMGTLDDMNHLKNKRVRSVGDLLQDQFGLALFRLEKAVNATIKKAFE 349

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                + Q+L+ + P+ +    FF  + LS + +  N LS+  H R+ S LG  G+    
Sbjct: 350 KKRRPILQNLVTSTPLTTTYESFFGLNPLSHILDGTNPLSQTVHRRKWSYLGPRGLTART 409

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A + +RD+HP++YGRICP +TSEG   GL  SL   AR+  +G +E+P  ++        
Sbjct: 410 ASIRIRDIHPSYYGRICPLDTSEGIKAGLTGSLAIHARIGDFGSLESPLYEISLKSKKIR 469

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS+ +EE   I   N+     G   E+++  R   E + +  +++      P Q  S
Sbjct: 470 MLYLSSRKEEYYMIGIGNALALNQGIQEEQMISARYRQEFLTIAWDQVHLRSVFPFQYFS 529

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I  SLIPFLE++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA+ SG  ++ + AG
Sbjct: 530 IGVSLIPFLEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLEGQVARDSGMTLITENAG 589

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +    A +I++      L           L+ ++RSN+NT ++Q P V  G   ++  +
Sbjct: 590 KIISTHADKILLSVNGETLSS--------PLVLYERSNRNTWIHQNPQVSRGKWTKKGQL 641

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER+V ED++TS HI + E+    
Sbjct: 642 LADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKCEIEIFV 701

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           T  GPE+ITR IP++ +  L+N+D+ G+  +G+ V  GDILVGK+TP+    + PE++L+
Sbjct: 702 TDKGPEKITRKIPHIDDHFLRNLDKNGVAILGSWVEAGDILVGKLTPQLVDELAPEKRLV 761

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            A+F       ++T L++P G  G V+DVR  ++    +  R    ++ QI++  +
Sbjct: 762 GALFDAPIAASKETCLKLPIGGRGRVIDVRWIHKGCNPEMIRVYISQKRQIKVGDK 817



 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 86/514 (16%), Positives = 175/514 (34%), Gaps = 44/514 (8%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY------ 79
           IP L ++Q   +  FL           EGL+      FP   F      E + +      
Sbjct: 12  IPRLNQIQIEGFHRFLA----------EGLREELSK-FPKGDFLKNWRDEDIDFQFFSEK 60

Query: 80  -EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                P     D ++  LTY+  L +               K+ + ++EQ++++G+LPLM
Sbjct: 61  SYLVEPLIKERDAIYESLTYSSELYV---------SAGFLWKNKRPMQEQTVFLGNLPLM 111

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
              GTF++ GI R+VV+Q+ +SPGI++  +       G  +Y   II D G  + ++ D 
Sbjct: 112 NSLGTFIVNGIHRVVVNQILQSPGIYYRSELDYK---GFTVYIATIISDCGGRLKLQIDR 168

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           K  +  R+ R++K+ +   L A+G + ++I+       ++    D        +      
Sbjct: 169 KGRLWARVSRKQKISILVLLSAMGSNLKDIIENVCYPEIFQAFLDKKFNENFGSKENSVL 228

Query: 259 KVSSSLVDID-----TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI- 312
           ++    VD            IE  KK        L   G + +    +      +   + 
Sbjct: 229 ELYQKFVDAGGYTELNDTIYIELRKKFFRQRC-VLGRLGRQNINRRLNLDIPQNITFLLP 287

Query: 313 --VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +   T  +      +     +  + +  +R +  L  D      +     V   N   
Sbjct: 288 RDILAATDHLIGMQFGMGTLDDMNHLKNKRVRSVGDLLQDQFGLALFRLEKAV---NATI 344

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           K A     R +    V++  +  +  +F   +   + L     +   +     +    R 
Sbjct: 345 KKAFEKKRRPILQNLVTSTPLTTTYESFFGLNPLSHILDGTNPLSQTVHRRKWSYLGPRG 404

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           +        I+ +     G+  I  +D     +    G +  +        +E  + E  
Sbjct: 405 LTARTASIRIRDIHPSYYGR--ICPLDTSEGIKAGLTGSLAIHARIGDFGSLESPLYEIS 462

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
                  ++       +  +  +      +Q  Q
Sbjct: 463 LKSKKIRMLYLSSRKEEYYMIGIGNALALNQGIQ 496


>gi|52694191|emb|CAG30625.1| DNA-directed RNA polymerase beta chain [Pseudomonas cannabina]
          Length = 377

 Score =  359 bits (922), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 219/368 (59%), Positives = 285/368 (77%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 10  ERLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 69

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V
Sbjct: 70  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEIV 129

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+A
Sbjct: 130 FLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVA 189

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 190 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVI 249

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+A
Sbjct: 250 DSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMA 309

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V +D FT+IHI+E   +ARDTK
Sbjct: 310 DGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQQDRFTTIHIQELTCVARDTK 369

Query: 856 LGPEEITR 863
           LG EEI  
Sbjct: 370 LGLEEIPP 377


>gi|212373967|emb|CAP09910.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35709]
          Length = 362

 Score =  359 bits (922), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 217/362 (59%), Positives = 282/362 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARD 360

Query: 854 TK 855
           TK
Sbjct: 361 TK 362


>gi|52694353|emb|CAG38016.1| RNA polymerase beta subunit [Pseudomonas coronafaciens]
          Length = 370

 Score =  359 bits (922), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 220/369 (59%), Positives = 285/369 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQ
Sbjct: 122 TEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +
Sbjct: 302 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCV 361

Query: 851 ARDTKLGPE 859
           ARDTKLGPE
Sbjct: 362 ARDTKLGPE 370


>gi|83699935|gb|ABC40944.1| RNA polymerase beta subunit [Spiroplasma chinense]
          Length = 594

 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 229/476 (48%), Positives = 327/476 (68%), Gaps = 10/476 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N LS +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLSELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++AR+N +GFIETPYRKV  G+V   +  YL+A +E++  +AQAN  + EDG+  +E V 
Sbjct: 61   TYARINKFGFIETPYRKVEKGRVIKGEYEYLTADKEKDFIVAQANIQIAEDGTILDESVV 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++++     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDMMASPIDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV  VD+  I +   +        G+  Y L  
Sbjct: 181  ESPIVGTGVEHESARDSGDAVVASADGIVRYVDSKLISVEGAD--------GIKNYDLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F +SN  T +   P+VKVGD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233  FNKSNNGTAITHLPIVKVGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GI+ +G 
Sbjct: 293  VIVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITREIPNISEASKKHLDEEGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
            R  G D     + + +  I    + ++ +++         + +IL  ++      G
Sbjct: 413  RADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDG 468



 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 124/418 (29%), Positives = 181/418 (43%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKARDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E   +  G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIPNISEASKKHLDEEGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSRADGHDLPADILEIIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     D+  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVNTPVFEGVKENDLVEIMEEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                                  G++   
Sbjct: 531  GKVKL-----------------------------------------------TDGRT--- 540

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                GE FD+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  ----GEAFDKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|221328701|gb|ACM17813.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 364

 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 224/361 (62%), Positives = 284/361 (78%)

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
           PQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+R
Sbjct: 1   PQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVR 60

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           DVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+D+V+LSA
Sbjct: 61  DVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDDIVFLSA 120

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           +EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AASLI
Sbjct: 121 IEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLI 180

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA+ SG  +VA+R G+++ VD
Sbjct: 181 PFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVARDSGVCVVARRGGVIDSVD 240

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPS
Sbjct: 241 ASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPS 300

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           TD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPE
Sbjct: 301 TDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPE 360

Query: 860 E 860
           E
Sbjct: 361 E 361


>gi|83755157|gb|ABC46427.1| RNA polymerase beta subunit [Spiroplasma montanense]
 gi|83755159|gb|ABC46428.1| RNA polymerase beta subunit [Spiroplasma montanense]
 gi|83755161|gb|ABC46429.1| RNA polymerase beta subunit [Spiroplasma montanense]
          Length = 594

 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 225/444 (50%), Positives = 316/444 (71%), Gaps = 10/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++AR+N +GFIETPYRKV +GKV  N+  YL+A +E +  +AQAN  ++ DG   +E V 
Sbjct: 61  TYARINKFGFIETPYRKVENGKVIPNEYEYLTADKERDYVVAQANIQINSDGKILDESVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+     +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMAAPSDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG A+VA   GIV+ VD+ RI +   +        G+  Y L  
Sbjct: 181 ESPIVGTGVEHEAARDSGDAVVATADGIVKFVDSKRITVEQSD--------GIKNYILND 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VKVGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FNRSNNGTAITHIPIVKVGDKIKDRDILADGPSMENGELALGQNLVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+I N+SE   K++DE GI  +G+
Sbjct: 293 VILSERVVIDDRFTSIHIDEYTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGS 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947 R-HGIDKNERSISVEREQIELLAR 969
           R  G D     + + +  +    +
Sbjct: 413 RADGHDLPADILEIIKVYVVQKRK 436



 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 122/418 (29%), Positives = 175/418 (41%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++   DIL    +      +   + L+ A       +  D  +         V+
Sbjct: 247  IVKVGDKIKDRDILADGPS-MENGELALGQNLVVAFTTWNGYNYEDAVIL----SERVVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +       L E      G     
Sbjct: 302  DDRFTSIHIDE-----YTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++KV+V  KR IQ GDKMAGRHGNKG++S+ILP EDMP  ++GTP
Sbjct: 411  FSRADGHDLPADILEIIKVYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHTENGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVSTPVFEGVKENELIEIMEEAGMENY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVTLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|197311436|gb|ACH61924.1| RNA polymerase beta subunit [Mycoplasma californicum]
          Length = 664

 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 229/503 (45%), Positives = 341/503 (67%), Gaps = 10/503 (1%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            N+R+ +VGE+++N  ++GL ++E++ +ER+ + + D V P+++ N K + + +  FF S
Sbjct: 2   TNKRIVAVGELVQNNLKVGLAKLEKTTRERMGAKEPDKVSPKNVTNNKLISNQMKTFFNS 61

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ    +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 62  SKLSQFMAQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPN 121

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ +  ++ARVN YG +ETPY +V  G +  ++ VYL+A  E    IAQ+   +DE+ 
Sbjct: 122 IGLILNFATYARVNEYGLLETPYYRVEKGVIDYSEPVYLTAAGEMGYKIAQSTVKVDENN 181

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E +  R      +   E IDF++ +P Q+VS+AA  IPFLENDD+NR LMG NMQR
Sbjct: 182 KIVDEQLTIRHNYTYEMGLAEDIDFVEVAPNQMVSVAAGCIPFLENDDANRALMGANMQR 241

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ EAPFV TG+ES +AK S    VAK  G+V+ VD  +I I++     +     
Sbjct: 242 QAVPLLETEAPFVATGIESEIAKYSSGNFVAKSDGVVDYVDGHKIKIKTNSNKNES---- 297

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y L  FQRSNQ+T V+Q+PLVK G  V++ D++ DG S   G+LALG+N+LVAF  +
Sbjct: 298 ---YTLKNFQRSNQDTVVHQKPLVKEGQVVKKGDLLVDGSSFKNGELALGKNVLVAFSTY 354

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++ER+V +DVFTSIHIEE  +  R++K G +E+T DIPNVS+   +++DE
Sbjct: 355 KGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRNSKAGNDELTSDIPNVSKYSTRHLDE 414

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ VG+EV PGD+LVG+++PKG+   + EEKLL A+  ++   V+DTSL+V +G  GT
Sbjct: 415 RGIVRVGSEVVPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQHPVKDTSLKVKNGHGGT 474

Query: 939 VVDVRIFNRHGIDKNERSISVER 961
           ++ V I +R    K+     +++
Sbjct: 475 IIGVEILDRQN--KDALEDGIDK 495



 Score =  244 bits (624), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 127/527 (24%), Positives = 199/527 (37%), Gaps = 82/527 (15%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMV 834
            NQ   V  G      +  A+              +L    P+     E  +    S   V
Sbjct: 212  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEAPFVATGIESEIAKYSSGNFV 271

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ++      +++  ++  + T     E               + +  ++  G  V  GD+L
Sbjct: 272  AKSDGVVDYVDGHKIKIK-TNSNKNESYTLKNFQRSNQDTVVHQKPLVKEGQVVKKGDLL 330

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRH 948
            V   + K    +   + +L A    K  +  D  +            S  + +  I  R+
Sbjct: 331  VDGSSFKN-GELALGKNVLVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRN 389

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                N+   S     +   +    DE+ I+         ++L G+ +  G     +   L
Sbjct: 390  SKAGNDELTSDI-PNVSKYSTRHLDERGIVRVGSEVVPGDVLVGRVSPKGDDNPSQEEKL 448

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               ++ +             +     V++          IL+ + K         D +  
Sbjct: 449  LLAVLQQRQHPV--------KDTSLKVKNGHGGTIIGVEILDRQNK---------DALED 491

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDM              P    
Sbjct: 492  GIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDM--------------PH--- 534

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
                     E                   D   N    P R  + +V+            
Sbjct: 535  --------LE--------------DGTPVDVMLNPQGVPSRMNIGQVL------------ 560

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                +       +      T VFDG  +EAI  +++ A L  +G+ IL D +TG  FD P
Sbjct: 561  ---EIHLGMAARELKTKFVTRVFDGIKKEAIYDVIQEAGLPITGKQILIDPITGNKFDNP 617

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            V+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 618  VSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 664


>gi|330040234|ref|XP_003239811.1| DNA-directed RNA polymerase II second largest subunit [Cryptomonas
            paramecium]
 gi|327206736|gb|AEA38913.1| DNA-directed RNA polymerase II second largest subunit [Cryptomonas
            paramecium]
          Length = 1209

 Score =  359 bits (921), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 171/1085 (15%), Positives = 341/1085 (31%), Gaps = 199/1085 (18%)

Query: 321  YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            Y ++   +        F  E   IP +  D+ N N       +   +    D L +    
Sbjct: 279  YFKSDVPVTWIFKALGFEDETEIIPYICYDNTNENLIELVRNILKDDHFVPDNLKNDCFR 338

Query: 381  MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
            +   + S   + + +F        +Y    + R  +     +         +      ++
Sbjct: 339  LDQ-ETSLALIGQHIFKASHGTRIRYAYEILQREFLPH---VGIGQGFELRKGFFFGYMV 394

Query: 441  KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE---RISSVDIDS 497
              L+ ++ G   +DD D+ G +R+ +V  +L   +R  + +  + ++    + ++++ ++
Sbjct: 395  NKLLLVQLGNKKVDDRDHYGYKRLDTVSPLLSVLFRQLVNKATKDLRMSLEKKTNLEKNT 454

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQ 546
                D+     + + +     +             +SQ+   +N +S ++H R++++ G 
Sbjct: 455  FQISDIFKFNLITTGMFYSLATGNWSTNGQTMKTGVSQVLNRINYMSTLSHLRKINSTGI 514

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                      + R +H T++G ICP ET EGH+ GLV +L   A +         +  + 
Sbjct: 515  N----VSKLTKPRQLHNTYWGLICPVETPEGHSCGLVKNLAISAYITLGSSSMPVFEFLE 570

Query: 607  DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE---KIDF 663
            + K+ N              I   +  +             RC        +E    I  
Sbjct: 571  ELKIKNFNEIKVQNIRFYYKIFLNDCWIGVYDKPDTIAKTLRCFRRSGNTNQELSVIIFH 630

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D   K          P + ++          + +                         
Sbjct: 631  KDKEIKIYTDAGRVCRPLIVSELVKFNKKNQYIVKSISVNQYNFDVL------------- 677

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                      I  +     ++   +   +D       +  +  F+             +K
Sbjct: 678  ---------TIGNKCTFTELIRNGLIEFIDAEEEKTCVIGMYVFEG------------IK 716

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              + +         PS  +G       +  +F+P+  +N          M  +    SI 
Sbjct: 717  NINNLITFTHFEIHPSMIMG-------ICASFIPFSHHNQSPRNTYQAAMGKQ----SIG 765

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I       R                            +  +        +    +     
Sbjct: 766  IYSLNFQHRM-------------------------DTMAHILYYPQKPLVTTRFLNYSAS 800

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
                     + A       +  D+ +     +   +    +F R   D+ ++  +  +E 
Sbjct: 801  KNFPNGINAIVATACYTGYNQEDSIIMSQDSIDRGLF-RSVFYRCYRDEEKKKTNGFKET 859

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E+  + +     I           +  G           K+   ++ +  +        
Sbjct: 860  FEIPNKSECIGLKIGSYEKLDLDGFVQEGSRISGEDVIIGKTVPFTNGISQKKILKFKKN 919

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
               + +        L    E             ++KI  G        R+VK+ +   R 
Sbjct: 920  PKYKKDA-----SILARNCEVGV----------VDKIMIGTSEY--GNRLVKIRIRSIRI 962

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             Q GDK A RHG KGI+       D+PF  +G   DI++NP  +PSRM +G ++E  L  
Sbjct: 963  PQVGDKFASRHGQKGILGMAYKQYDLPFTTEGMSPDIIMNPHAIPSRMTIGHVYECLLAK 1022

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                 G +                                                    
Sbjct: 1023 ISAISGIEGDG------------------------------------------------- 1033

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                TP F     E I   L+    D+SG   + +G TG+     + +G  Y  KL HMV
Sbjct: 1034 ----TP-FSSISIEKIMKHLKNYGYDKSGWEAMINGFTGKFLKNLIFIGPTYYQKLKHMV 1088

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
             DK+++RS G   ++T+QP+ G+S  GG R GEME  CI ++G+   L++ L  +SD   
Sbjct: 1089 DDKIHSRSRGPVQILTRQPVEGRSRYGGLRFGEMERDCILSHGSIVFLKDRLLDQSDPFV 1148

Query: 1321 ----DVVG-----------------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
                D+ G                   +++ S++          P +  +L++E+ AL +
Sbjct: 1149 IFVCDLCGLIAIGNRKLKIFECRSCDNKMFISLIK--------IPYACKLLLQELIALSI 1200

Query: 1360 SIDLE 1364
               + 
Sbjct: 1201 GPRMI 1205



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 125/978 (12%), Positives = 270/978 (27%), Gaps = 207/978 (21%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI---------TAFSGAA------ML 74
           I+ Q  S++ F+   +          Q     + PI         T F          +L
Sbjct: 26  IKQQLESFNDFVQNKM----------QDIVDDLPPIVVSYKVDKLTDFKENFLQNMKKIL 75

Query: 75  EFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLI-VFDVDEFTGAKSIK 123
                    P F            ++   R L+Y+ PL   + +  V   +E    + + 
Sbjct: 76  RLGQLHLSKPTFIEEDGVIHTLLPNEARLRSLSYSSPLYCDISVTTVNVTNEHEKERELN 135

Query: 124 DIKE-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH 158
             +E Q I +G +P+M K                         G F+I G ++++V+Q  
Sbjct: 136 FKQEKQKILLGRIPIMIKSRFCILDKLLPMTLQNLGECNLDLGGYFIINGSEKVIVAQEK 195

Query: 159 RSPG-IHFDHDKGRASLSGKLLY---------ACRIIPDQGLWMDIEFDSK--------- 199
            +   ++    K   +   K  +          CR I + G W       K         
Sbjct: 196 MAWNYVYVFEKKKENNSVDKSFFLDLKNLFFAECRSISEFGKWSPSLTIIKICLNKFRKK 255

Query: 200 -------------DIIHVRI---DRRRKVPVTSFLMALGMDSE-EILSTFYPKIV----Y 238
                           ++R+     +  VPVT    ALG + E EI+             
Sbjct: 256 KIAKKENSFSHFTGKFYIRVVLPYFKSDVPVTWIFKALGFEDETEIIPYICYDNTNENLI 315

Query: 239 SQRGDFWCFPLSAADLMVGA--KVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKF 295
               +         D +     ++         G+ + ++            L+ + +  
Sbjct: 316 ELVRNILKDDHFVPDNLKNDCFRLDQETSLALIGQHIFKASHGTRIRYAYEILQREFLPH 375

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFHSEIRDIPILYVDSVNN 354
           +GI              +  +   + +    V D      +   +    + +L+   VN 
Sbjct: 376 VGIGQGFELRKGFFFGYMVNKLLLVQLGNKKVDDRDHYGYKRLDTVSPLLSVLFRQLVNK 435

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
               ++  ++ + K   +        +   ++ T  +  S+    +  + +   + V +V
Sbjct: 436 AT--KDLRMSLEKKTNLEKNTFQISDIFKFNLITTGMFYSLATGNWSTNGQTMKTGVSQV 493

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
              +          +       ++ +     L N    +                ++KN 
Sbjct: 494 LNRINYMSTLSHLRKINSTGINVSKLTKPRQLHNTYWGLICP---VETPEGHSCGLVKNL 550

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                + +  S       ++   +   + I  + +      F     +   ++       
Sbjct: 551 AISAYITLGSSSMPVFEFLEELKIKNFNEIKVQNIRFYYKIFLNDCWIGVYDKPDTIAKT 610

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS-SLTSFARVN 593
           +   RR     Q          +   ++        P   SE       +  +     VN
Sbjct: 611 LRCFRRSGNTNQELSVIIFHKDKEIKIYTDAGRVCRPLIVSELVKFNKKNQYIVKSISVN 670

Query: 594 AYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            Y F            +      + ++ A EE+   I      + E       L+     
Sbjct: 671 QYNFDVLTIGNKCTFTELIRNGLIEFIDAEEEKTCVIGM---YVFEGIKNINNLIT---- 723

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                         +  P  ++ I AS IPF  ++ S R      M +Q++ +       
Sbjct: 724 ----------FTHFEIHPSMIMGICASFIPFSHHNQSPRNTYQAAMGKQSIGIYSLNFQ- 772

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                                                       + + +  Y        
Sbjct: 773 ----------------------------------------HRMDTMAHILYYP------- 785

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM---PWHGYNFEDSM 827
                  Q+PLV                  +        N + A +    + GYN EDS+
Sbjct: 786 -------QKPLV-------------TTRFLNYSASKNFPNGINAIVATACYTGYNQEDSI 825

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGII 882
           ++S+  +   +F S+    +    +    G +E        +   +     + +D  G +
Sbjct: 826 IMSQDSIDRGLFRSVFYRCYRDEEKKKTNGFKETFEIPNKSECIGLKIGSYEKLDLDGFV 885

Query: 883 CVGAEVNPGDILVGKITP 900
             G+ ++  D+++GK  P
Sbjct: 886 QEGSRISGEDVIIGKTVP 903


>gi|83699941|gb|ABC40947.1| RNA polymerase beta subunit [Spiroplasma lineolae]
          Length = 594

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 239/524 (45%), Positives = 343/524 (65%), Gaps = 11/524 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVH +HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHTSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV +GKV  ++ VYL+A +E++  +AQAN   D+DG   +E V 
Sbjct: 61   TYAKINPYGFIETPYRKVLNGKVLKDEHVYLTADKEKDFIVAQANIQTDKDGKILDESVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV+ VD+  I I           +GV  Y L  
Sbjct: 181  ESPIVGTGVEYEAARDSGDAVVATEDGIVKYVDSKTITI--------EGKNGVKSYTLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+V+ N+I+ADGPS + G+LALG+N++VAF  W+GYNFED+
Sbjct: 233  FSRSNNGTAITHLPIVKVGDKVKANEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G 
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDLDGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            +  G D     + + +  +    + ++ +++         + +IL  ++      G    
Sbjct: 413  KAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTPVD 472

Query: 1006 TVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
             +L+   I       Q  +  +     + N++     +E  K  
Sbjct: 473  IMLNPQGIPSRMNIGQVLEIHLGMAAKKLNLKVATPVFEGVKED 516



 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 120/419 (28%), Positives = 173/419 (41%), Gaps = 75/419 (17%)

Query: 881  IICVGAEVNPGDILV-GKITPKGESPMTPEEKLLRAIF-GEKAVDVRDTSLRVPSGVSGT 938
            I+ VG +V   +IL  G    KGE  +     +    + G    D    S R+      T
Sbjct: 247  IVKVGDKVKANEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAVIVSERIVIEDRFT 306

Query: 939  VVDVRIFNRHGIDKNERSISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             + +  +        +    + R+   I    +   D   I+      ++ +IL G+   
Sbjct: 307  SIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDLDGIVAIGTEVKVGDILVGKVTP 366

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                       L   +  E  R           +V    E +                 K
Sbjct: 367  KSQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIIKSI-------------K 409

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGT
Sbjct: 410  RFSKAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGT 469

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LNP G+PSRMN+GQ+ E HLG A   L  K+ + + +     D+  +        
Sbjct: 470  PVDIMLNPQGIPSRMNIGQVLEIHLGMAAKKLNLKVATPVFEGVKEDDLKAIMDEAGMTN 529

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                               DG   EA                  
Sbjct: 530  YGKVKLI----------------------------DGRTGEAF----------------- 544

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                     D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  ---------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|318603115|emb|CBJ04598.1| RNA polymerase beta subunit [Pseudomonas sp. R-38647]
          Length = 361

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 216/361 (59%), Positives = 281/361 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARD 360

Query: 854 T 854
           T
Sbjct: 361 T 361


>gi|83699949|gb|ABC40951.1| RNA polymerase beta subunit [Spiroplasma helicoides]
          Length = 594

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 229/444 (51%), Positives = 320/444 (72%), Gaps = 10/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++AR+N +GFIETPYR+V +GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V 
Sbjct: 61  TYARINEFGFIETPYRQVKNGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  
Sbjct: 181 ESPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSD 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VKVGD ++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FWRSNSGTAITHLPIVKVGDSIKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G 
Sbjct: 293 VIVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSIKRFS 412

Query: 947 R-HGIDKNERSISVEREQIELLAR 969
           +  G D     + + +  +    +
Sbjct: 413 KSDGHDLPADILEIIKIYVVQKRK 436



 Score =  280 bits (715), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 123/418 (29%), Positives = 179/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDSIKARDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++ER Q +    +   E   +  +    L E   I  G     
Sbjct: 302  DDRFTSIHIDE-----YTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKSDGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +     D+  + +       
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAKKLGIKVSTPVFEGVKEADLKDIMNEAGMENY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVKLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|290751434|emb|CAQ16378.1| RNA polymerase beta subunit [Pseudomonas sp. R-26735]
          Length = 368

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 218/367 (59%), Positives = 284/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 361

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 362 CVARDTK 368


>gi|212373993|emb|CAP09923.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35722]
 gi|290751438|emb|CAQ16380.1| RNA polymerase beta subunit [Pseudomonas sp. R-29016]
          Length = 367

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 218/367 (59%), Positives = 284/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 360

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 361 CVARDTK 367


>gi|212373955|emb|CAP09904.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35703]
          Length = 360

 Score =  359 bits (920), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 217/360 (60%), Positives = 281/360 (78%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+A
Sbjct: 241 DSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 301 DGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 360


>gi|83699945|gb|ABC40949.1| RNA polymerase beta subunit [Spiroplasma tabanidicola]
          Length = 594

 Score =  358 bits (919), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 239/524 (45%), Positives = 343/524 (65%), Gaps = 11/524 (2%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVH +HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHTSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV DGKV  ++ VYL+A +E++  +AQAN   D+DG   +E V 
Sbjct: 61   TYAKINPYGFIETPYRKVLDGKVLKDEHVYLTADKEKDFIVAQANIQTDKDGKILDESVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV+ VD+  I I           +G+  Y L  
Sbjct: 181  ESPIVGTGVEYEAARDSGDAVVATEDGIVKYVDSKTITI--------EGKNGIKSYTLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+V+ N+I+ADGPS + G+LALG+N++VAF  W+GYNFED+
Sbjct: 233  FSRSNNGTAITHLPIVKVGDKVKSNEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G 
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDSDGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            +  G D     + + +  +    + ++ +++         + +IL  ++      G    
Sbjct: 413  KAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTPVD 472

Query: 1006 TVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
             +L+   I       Q  +  +     + N++     +E  K  
Sbjct: 473  IMLNPQGIPSRMNIGQVLEIHLGMAAKKLNLKVATPVFEGVKED 516



 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 118/418 (28%), Positives = 178/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   +IL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKVKSNEILADGPS-MEKGELALGQNVVVAFTTWNGYNFEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            + R  + H  +      ++ER Q +    +   +   +  +    L     +  G     
Sbjct: 302  EDRFTSIHIDE-----YTLERRQTKQGPEEITRDIPNISESHKKHLDSDGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKAEGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP G+PSRMN+GQ+ E HLG A   L  K+ + + +     D+  +         
Sbjct: 471  VDIMLNPQGIPSRMNIGQVLEIHLGMAAKKLNLKVATPVFEGVKEDDLKAIMDEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                   
Sbjct: 531  GKVKLI----------------------------DGRTGEAF------------------ 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                    D+P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  --------DKPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|98991110|gb|ABF60573.1| RNA polymerase beta subunit [Mycoplasma pirum]
          Length = 750

 Score =  358 bits (919), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 236/518 (45%), Positives = 339/518 (65%), Gaps = 31/518 (5%)

Query: 476 RLGLLRMERSIKERISSVDIDS---------------------VMPQDLINAKPVVSAVC 514
           + G+ RMER I+E+++  D  +                     +  + ++N+KP    + 
Sbjct: 1   QTGMARMERYIREKLAIADGTNKNVEVNEETGEFVETDKQKTRLTIKSVVNSKPFQLVIR 60

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           +FF + QL+Q  +  N LS +T+ RR+SA+G GG++R    +++RDVH +HYGRICP ET
Sbjct: 61  DFFNTHQLTQFLDQQNPLSELTNKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIET 120

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA--QANS 632
            EG NIGL+ SL  +A ++  GF+ +PYRKV +GK+T++V YL+A+ E+   IA   A+ 
Sbjct: 121 PEGMNIGLIMSLAFYATIDNNGFLMSPYRKVKNGKITDEVEYLTALREDEYIIAGSSASM 180

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  DGS  ++ V  R    + L   + +D+ID +P+QVVSIAA LIPFLENDDS R LM
Sbjct: 181 KVSADGSIGDDQVIARYRSSQELYNPKLVDYIDVAPRQVVSIAAGLIPFLENDDSARALM 240

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA PLLK  AP VGTG+E  +A  SG AI+A+ +G V  V++ +IVI++ +G L
Sbjct: 241 GANMQRQATPLLKPYAPTVGTGVEYKIAHDSGMAIIAENSGKVVSVNSDKIVIKNDDGKL 300

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           D        Y L+KF++SNQNTC N  P+V+V  ++    ++ADGPS   G+LALG+N+L
Sbjct: 301 D-------NYSLVKFEKSNQNTCYNHTPIVEVNQKINAGQVVADGPSMKNGELALGQNVL 353

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W GYN+ED+++IS+R+  EDV+TSI I E+ V    T+ G EEITRDIPN+SE  
Sbjct: 354 VAFTTWRGYNYEDAIIISDRLFREDVYTSITINEYSVQCVRTRNGDEEITRDIPNISENA 413

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + +DE GII VGAEV  GDILVGKI+PKG+  ++ EEKLL+AIFGEK  ++R++SL+VP
Sbjct: 414 KRYLDEDGIIMVGAEVKEGDILVGKISPKGQVDLSVEEKLLQAIFGEKTKNIRESSLKVP 473

Query: 933 SGVSGTVVDVRIFN-RHGIDKNERSISVEREQIELLAR 969
           +G  G V  VR F+     + ++  I + +  I    +
Sbjct: 474 NGGDGIVAAVRRFSIAKNDELDDDVIELVKVYIVQKRK 511



 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 151/531 (28%), Positives = 228/531 (42%), Gaps = 51/531 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM-VSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L  + P  G   E  +     M +  +    +     + +      G 
Sbjct: 240  MGANMQRQATPLLKPYAPTVGTGVEYKIAHDSGMAIIAENSGKVVSVNSDKIVIKNDDGK 299

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +    +           +   I+ V  ++N G ++    + K    +   + +L A   
Sbjct: 300  LDNYSLVKFEKSNQNTCYNHTPIVEVNQKINAGQVVADGPSMKN-GELALGQNVLVAFTT 358

Query: 919  EKAVDVRDTSL------RVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQIELLARDK 971
             +  +  D  +      R     S T+ +  +   R      E +  +    I   A+  
Sbjct: 359  WRGYNYEDAIIISDRLFREDVYTSITINEYSVQCVRTRNGDEEITRDI--PNISENAKRY 416

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+      +  +IL G+ +  G         L   +  E  +           KV
Sbjct: 417  LDEDGIIMVGAEVKEGDILVGKISPKGQVDLSVEEKLLQAIFGEKTK----NIRESSLKV 472

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                + +                     I   D++   V+ +VKV++  KR IQ GDK+A
Sbjct: 473  PNGGDGIVAAVR-------------RFSIAKNDELDDDVIELVKVYIVQKRKIQIGDKIA 519

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKGIVS+I+P EDMP L+DGTPVDI+LNPLGVPSRMN+GQIFE HLG A   L KK
Sbjct: 520  GRHGNKGIVSKIVPVEDMPHLEDGTPVDIMLNPLGVPSRMNIGQIFEIHLGLAARELAKK 579

Query: 1152 IKSLINDYKANGDISPLRSFLE------------------KVIGTGSHTEKISDYDDDSV 1193
                        +       L                   K+        K+   D D  
Sbjct: 580  ELIQATFEPKGDEYISELFGLNLRSAKTLIQNFKSHLKERKISNAIDAKNKVKTIDIDIT 639

Query: 1194 LRVAEQWKSGV--PVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRP 1248
            LR +      +   ++TPVF+G +   +  +++ A++D +   G+  L DG TGE F++P
Sbjct: 640  LRQSGLSYDDLAYKIATPVFEGVNMGDLKDIMKEANIDTNKNFGKFKLIDGRTGEAFEKP 699

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            +TVG +YMLKL+HMV DK+++R+ G YS +TQQPLGGKS  GGQR GEMEV
Sbjct: 700  ITVGVMYMLKLDHMVDDKIHSRAVGPYSKITQQPLGGKSQNGGQRFGEMEV 750


>gi|290751440|emb|CAQ16381.1| RNA polymerase beta subunit [Pseudomonas sp. R-29008]
          Length = 371

 Score =  358 bits (919), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 218/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 5   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 64

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 65  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 124

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 125 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 184

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 185 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 244

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 245 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 304

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 305 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQEXT 364

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 365 CVARDTK 371


>gi|52694363|emb|CAG38021.1| RNA polymerase beta subunit [Pseudomonas pseudoalcaligenes]
          Length = 370

 Score =  358 bits (919), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 221/369 (59%), Positives = 285/369 (77%), Gaps = 1/369 (0%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +GKVT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGKVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           +V+LSA+EE +  IAQA+++L++   S++ ELV  R   E  +   E +  +D SPKQVV
Sbjct: 122 IVFLSAIEEADHVIAQASATLNDKRASWSTELVAVRHLNEFTVKAPEDVTLMDVSPKQVV 181

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R 
Sbjct: 182 SVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRG 241

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R D
Sbjct: 242 GVIDSVDATRIVVRVNDNEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVSRGD 301

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           I+ADGPSTD+G+LALG+NM VAFMPW+G+NFE  + +SER+V E  F +IHI+E   +AR
Sbjct: 302 IMADGPSTDMGELALGQNMRVAFMPWNGFNFEAPIHLSERVVQEARFPTIHIQELTCVAR 361

Query: 853 DTKLGPEEI 861
           DTKLGP E 
Sbjct: 362 DTKLGPAEN 370


>gi|183584741|gb|ACC63813.1| RNA polymerase subunit B [Acinetobacter ursingii DSM 16037]
 gi|190688700|gb|ACE86377.1| RpoB [Acinetobacter ursingii]
 gi|190688702|gb|ACE86378.1| RpoB [Acinetobacter ursingii]
 gi|190688704|gb|ACE86379.1| RpoB [Acinetobacter ursingii]
 gi|190688706|gb|ACE86380.1| RpoB [Acinetobacter ursingii]
 gi|190688708|gb|ACE86381.1| RpoB [Acinetobacter ursingii]
 gi|190688710|gb|ACE86382.1| RpoB [Acinetobacter ursingii]
 gi|190688712|gb|ACE86383.1| RpoB [Acinetobacter ursingii]
 gi|190688714|gb|ACE86384.1| RpoB [Acinetobacter ursingii]
          Length = 286

 Score =  358 bits (919), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 137/289 (47%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ++  G    K+   L+ DL+S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQDSNGGGTT-KRGDKLTEDLLSGLELVDLLEIQPSDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    I+ LR FL+K+    G   E ++   DD VL +A   + GVP++TPVFDGA
Sbjct: 181  LQQQRT---IAELRIFLDKIYNKVGGEQEDLNSLTDDEVLVLAGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|227438081|gb|ACP30539.1| RNA polymerase beta subunit [Mycoplasma canis]
          Length = 665

 Score =  358 bits (918), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 237/520 (45%), Positives = 347/520 (66%), Gaps = 14/520 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ SVGE+++ Q +L L ++E++ KERI + D++ V  +++ N K + +    FF +S
Sbjct: 3   NKRIVSVGELIEGQLQLALTKLEKTTKERIGAKDVEKVTAKNVTNNKLITNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 63  KLSQFMDQINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +  ++A+V+  GF++TPY KV +G V   DV YL+A EE    IAQ++  +DE+  
Sbjct: 123 GLILNFATYAKVDDKGFLKTPYYKVNNGVVDYEDVKYLTASEEFGYSIAQSSVRVDENNK 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E +  R          + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQ
Sbjct: 183 IIDEFLTIRRNYTYENGRSDDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPLL+ EAP + TG+E+ +AK S   +VAK AG V  VD  RI I+  E  +       
Sbjct: 243 AVPLLQTEAPLIATGIEADIAKYSSYNLVAKNAGKVTFVDGSRIHIQRKESTV------T 296

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T + QRPLV++GDEV   DI+ DG S   G+LALG+N+LV F  W+
Sbjct: 297 DKYTLRNFERSNQGTLIQQRPLVRIGDEVEVGDILTDGSSFKDGELALGKNVLVGFTTWN 356

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+++PN S+  L+N+D+ 
Sbjct: 357 GYNFEDAVIINERLVKNDVYTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDD 416

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV PGDILVG+++PKGE   + EEK+L AI G+++   +DTSL+V +G SGT+
Sbjct: 417 GIVKVGSEVYPGDILVGRVSPKGEENPSQEEKMLYAILGQRSPSTKDTSLKVKNGHSGTI 476

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
             V I +R   D       V  E IE + +    ++  + 
Sbjct: 477 THVEILSREKGD-------VLEEGIEKIVKVSIAQKRKIK 509



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 128/415 (30%), Positives = 180/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GDIL    + K +  +   + +L         +  D  +     V   V 
Sbjct: 318  LVRIGDEVEVGDILTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAVIINERLVKNDV- 375

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E  + +          LD +   ++   +   + + G  
Sbjct: 376  YTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDDGIVKVGSEVYPGDILVGRV 435

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++      T   IL           
Sbjct: 436  SPKGEENPSQE--EKMLYAILGQRSPSTKDTSLKVKNGHSGTITHVEILSR--------- 484

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 485  EKGDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 544

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  S   D     DI               
Sbjct: 545  MLNPQGVPSRMNIGQILELHLGMAARKLNVKFVSPSFDGVKKPDIEAALEEAG------- 597

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L         + +L D +
Sbjct: 598  ------------------------------------------LDKTG-----KQVLIDPI 610

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 611  TGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|315048479|ref|XP_003173614.1| DNA-directed RNA polymerase III subunit RPC2 [Arthroderma gypseum CBS
            118893]
 gi|311341581|gb|EFR00784.1| DNA-directed RNA polymerase III subunit RPC2 [Arthroderma gypseum CBS
            118893]
          Length = 1210

 Score =  358 bits (918), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 255  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 307

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 308  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLNIYTQQQALEYLGARIKI 360

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 361  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 411

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 412  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 471

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 472  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 531

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 532  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFT 590

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 591  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 643

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 644  FVSV--------FINHNQ------KCVHVSTDDGRICRPLIIVEKKRSRVTARHL----S 685

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 686  ALRNGTMDFDDFLSHGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 729

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 730  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 769

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 770  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 808

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 809  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR 868

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 869  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 916

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 917  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 967

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 968  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIVS 1027

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1028 GQFGYG-----------------------------------------------------T 1034

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1035 P-FGGSPVEEMSAILVNHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1093

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1094 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1153

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1154 SCGFMGYSGWCQRCKSSAGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1207

Query: 1373 K 1373
            +
Sbjct: 1208 R 1208



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 100 LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGAPRRT 149

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 150 DEEQSGIKIDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 199

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 200 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 259

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 260 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 308

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 309 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLNIYTQQQALEYLGARIKINRKASGFG 368

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 369 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 419

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 420 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 479

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 480 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 539

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 540 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFTLGAEDIQTV 599

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 600 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHVS 659

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 660 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSHGLVEYVDVNEENDANIAVY 719

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 720 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 756

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 757 TYQCAMGKQAIGAIANNQFL 776


>gi|83755183|gb|ABC46440.1| RNA polymerase beta subunit [Spiroplasma sabaudiense]
          Length = 594

 Score =  358 bits (918), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 226/423 (53%), Positives = 313/423 (73%), Gaps = 9/423 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLAELTNKRRLTALGPGGLSRERAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++AR+N YGFIETPYRKV + KV  +   YL+A +E +  +AQAN  +D+DG+  ++ V 
Sbjct: 61  TYARINEYGFIETPYRKVENKKVVPDKYEYLTADQERDFIVAQANIKIDKDGTILDDNVV 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+   E +D++D SPKQ+VSIA SLIPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIMANAEDVDYVDVSPKQIVSIATSLIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           ++P VGTG+E   A+ SG AIVA+  GIV+ +D+ +I + + E        G   Y L  
Sbjct: 181 QSPVVGTGVEFEAARDSGDAIVAREDGIVKFLDSRKITLETKE--------GPKHYVLSD 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P+VK+  +V++ DI+ADGPS + G+LALG+N++VAF  W+GYN+ED+
Sbjct: 233 FIRSNNGTAITHSPIVKLNQKVKKGDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K +DE GII +G+
Sbjct: 293 VIVSERIVIDDRFTSIHIDEYTIEKRQTKQGPEEITREIPNISEASKKYLDESGIIAIGS 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  +R F+
Sbjct: 353 EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIRRFS 412

Query: 947 RHG 949
           R  
Sbjct: 413 RAD 415



 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 124/418 (29%), Positives = 181/418 (43%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +  +V  GDIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKLNQKVKKGDILADGPS-MEKGELALGQNVVVAFTTWNGYNYEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D R  + H  +      ++E+ Q +    +   E   +       L E   I  G     
Sbjct: 302  DDRFTSIHIDE-----YTIEKRQTKQGPEEITREIPNISEASKKYLDESGIIAIGSEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      + 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSI------RR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L V+KVFV  KR IQ GDKMAGRHGNKG++S+ILP EDMP+++DGTP
Sbjct: 411  FSRADGYDLPADILEVIKVFVVQKRKIQEGDKMAGRHGNKGVISKILPVEDMPYMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP GVPSRMN+GQ+ E HLG A   LG K+ + + +   + ++  + +       
Sbjct: 471  VDIMLNPQGVPSRMNIGQVLEIHLGMAAEKLGIKVSTPVFEGLNDEELQDIMAEAGMKNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA +                 
Sbjct: 531  GKVTLI----------------------------DGRTGEAFDK---------------- 546

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                      P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 547  ----------PIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 594


>gi|327300783|ref|XP_003235084.1| DNA-directed RNA polymerase III [Trichophyton rubrum CBS 118892]
 gi|326462436|gb|EGD87889.1| DNA-directed RNA polymerase III [Trichophyton rubrum CBS 118892]
          Length = 1210

 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 255  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 307

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 308  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKI 360

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 361  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 411

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 412  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 471

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 472  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 531

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 532  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFT 590

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 591  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 643

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 644  FVSV--------FINHNQ------KCVHVSTDDGRICRPLIIVEKKRSRVTARHL----S 685

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 686  ALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 729

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 730  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 769

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 770  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 808

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 809  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR 868

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 869  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 916

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 917  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 967

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 968  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIIS 1027

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1028 GQFGYG-----------------------------------------------------T 1034

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1035 P-FGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1093

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1094 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1153

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1154 SCGFMGYSGWCQRCKSSVGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1207

Query: 1373 K 1373
            +
Sbjct: 1208 R 1208



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 100 LVKQHIDSYNYFVEVQ----------LRKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 149

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 150 DEEQSGIKADSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 199

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 200 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 259

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 260 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 308

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 309 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKINRKASGFG 368

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 369 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 419

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 420 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 479

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 480 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 539

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 540 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFTLGAEDIQTV 599

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 600 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHVS 659

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 660 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVY 719

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 720 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 756

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 757 TYQCAMGKQAIGAIANNQFL 776


>gi|227438075|gb|ACP30537.1| RNA polymerase beta subunit [Mycoplasma canis]
          Length = 665

 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 237/520 (45%), Positives = 347/520 (66%), Gaps = 14/520 (2%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ SVGE+++ Q +L L ++E++ KERI + D++ V  +++ N K + +    FF +S
Sbjct: 3   NKRIVSVGELIEGQLQLALTKLEKTTKERIGAKDVEKVTAKNVTNNKLITNQFKSFFNTS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 63  KLSQFMDQINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +  ++A+V+  GF++TPY KV +G V   DV YL+A EE    IAQ++  +DE+  
Sbjct: 123 GLILNFATYAKVDDKGFLKTPYYKVNNGVVDYEDVRYLTASEEFGYSIAQSSVRVDENNK 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E +  R          + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQ
Sbjct: 183 IIDEFLTIRRNYTYENGRSDDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPLL+ EAP + TG+E+ +AK S   +VAK AG V  VD  RI I+  E  +       
Sbjct: 243 AVPLLQTEAPLIATGIEADIAKYSSYNLVAKNAGKVTFVDGSRIHIQRKESTV------T 296

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D Y L  F+RSNQ T + QRPLV++GDEV   DI+ DG S   G+LALG+N+LV F  W+
Sbjct: 297 DKYTLRNFERSNQGTLIQQRPLVRIGDEVEVGDILTDGSSFKDGELALGKNVLVGFTTWN 356

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+++PN S+  L+N+D+ 
Sbjct: 357 GYNFEDAVIINERLVKNDVYTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDD 416

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ VG+EV PGDILVG+++PKGE   + EEK+L AI G+++   +DTSL+V +G SGT+
Sbjct: 417 GIVKVGSEVYPGDILVGRVSPKGEENPSQEEKMLYAILGQRSPSTKDTSLKVKNGHSGTI 476

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
             V I +R   D       V  E IE + +    ++  + 
Sbjct: 477 THVEILSREKGD-------VLEEGIEKIVKVSIAQKRKIK 509



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 128/415 (30%), Positives = 180/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GDIL    + K +  +   + +L         +  D  +     V   V 
Sbjct: 318  LVRIGDEVEVGDILTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAVIINERLVKNDV- 375

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E  + +          LD +   ++   +   + + G  
Sbjct: 376  YTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDDGIVKVGSEVYPGDILVGRV 435

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++      T   IL           
Sbjct: 436  SPKGEENPSQE--EKMLYAILGQRSPSTKDTSLKVKNGHSGTITHVEILSR--------- 484

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 485  EKGDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 544

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  S   D     DI               
Sbjct: 545  MLNPQGVPSRMNIGQILELHLGMAARKLNVKFVSPSFDGVKKPDIEAALEEAG------- 597

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L         + +L D +
Sbjct: 598  ------------------------------------------LDKTG-----KQVLIDPI 610

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 611  TGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 665


>gi|312985382|gb|ADR30834.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 100/181 (55%), Positives = 130/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ V TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKVMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE++T KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQELMTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+Q+LGL   + +++ +     +   D 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQSLGLDTKVLDAKGREVRMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|290751452|emb|CAQ16387.1| RNA polymerase beta subunit [Pseudomonas sp. R-26424]
          Length = 370

 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 218/367 (59%), Positives = 285/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINA PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 4   RLSMAESEGLMPQDLINAXPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 63

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 64  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 123

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SP
Sbjct: 124 VVTDEIVFLSAIEEADHVIAQASAAMNEKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 183

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 184 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 243

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 244 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVV 303

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 304 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 363

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 364 CVARDTK 370


>gi|90902246|gb|ABE01891.1| RNA polymerase beta subunit [Acholeplasma modicum]
          Length = 645

 Score =  358 bits (918), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 211/782 (26%), Positives = 320/782 (40%), Gaps = 145/782 (18%)

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q  + VN LS +T  RR+SALG GG+AR RAGVE+RDVH THYGRICP ET EG +IGL+
Sbjct: 1    QFMDQVNPLSELTQKRRVSALGTGGIARDRAGVEVRDVHNTHYGRICPIETPEGPSIGLI 60

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SSL+++++ + YGFI+TPY K+                          S LDE+G     
Sbjct: 61   SSLSTYSKADKYGFIQTPYFKLDL------------------------SRLDENGRPIPR 96

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            ++              +I+++ A  ++   IA++  P  EN D     +      +    
Sbjct: 97   VI-------------NEIEYLTADEEKDKVIASAATPLDENGDFVEKRIIGRHAGETNIY 143

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             + E     T M+    +    ++       +E  DA R ++ +                
Sbjct: 144  YRDEF----THMDVSPKQI--VSVSTATIPFLEHDDATRALMGAN--------------- 182

Query: 764  LMKFQRSNQNTCVNQRPLVKVG-DEVRRNDIIADGPSTDLGDLALGR--NMLVAFMPWHG 820
                QR        + P+V  G +     D  A   S   G +       +++   P   
Sbjct: 183  ---MQRQAVPLIAPESPIVGTGVEYRAAKDSGAVLVSNHEGYVTYVDAAKIVITKEPTEK 239

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
              F  ++L    +            E     R+      E+              I +  
Sbjct: 240  VKFAGNVLYDPEI--------GFNSEVARKLREYGQDDSEVYWLQKFNRSNQDTFILQKP 291

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G ++N GD L+          +     +  A       +  D  +         V 
Sbjct: 292  LVELGEKINVGD-LISDGASTENGELALGRNVTVAFMTWDGYNYEDAIIM----SEDLVK 346

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            +    + H  +       +E   I+  +    +E         +  ++ L  +  +    
Sbjct: 347  NDVYTSIHIDE-----YEIETRDIKTTSSSYQEEITREVPQASTDALKKLDSEGIIIVGS 401

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K+  +L                   +  +Q  +      Y  +   +       ++KI
Sbjct: 402  EVKEGDILVGK----ITPKGVNDPTPSERLIQSILGDKSRDYRDTSLRVPHGGGGIVQKI 457

Query: 1061 Q-----WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            Q      GD +PPGV + +KVFVA KR I  GDKMAGRHGNKG++S+ILP EDMP + DG
Sbjct: 458  QVYSKANGDILPPGVNKSIKVFVAQKRKITEGDKMAGRHGNKGVISKILPREDMPHMADG 517

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D   + ++  +       
Sbjct: 518  TPVDIMLNPLGVPSRMNIGQVLEIHLGMAAKKLGIKVATPVFDGVTDSELRAVMKEA--- 574

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                         DDD    +                                   G   
Sbjct: 575  -----------GLDDDGKTVL---------------------------------YDG--- 587

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE FD  ++VG +YM+KL+HMV DK++ARS G Y+LVTQQP+GGK+  GGQR G
Sbjct: 588  ----RTGEAFDNRISVGVMYMIKLSHMVDDKLHARSVGPYTLVTQQPMGGKAQNGGQRFG 643

Query: 1296 EM 1297
            EM
Sbjct: 644  EM 645


>gi|183584769|gb|ACC63827.1| RNA polymerase subunit B [Acinetobacter genomosp. 15TU]
          Length = 286

 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 183/289 (63%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS  L+S             DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEQLLSGLELVDLLDIQPSDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG +I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D+ +L+++   + GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELRDFLDKIYNKVGGQQEDLDSLTDEEILKLSGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A L  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAGLSRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|183584761|gb|ACC63823.1| RNA polymerase subunit B [Acinetobacter genomosp. 6]
          Length = 286

 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L G+ +  G    K+   L+ D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGKESNGGGTT-KRGDKLAEDMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSIEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    ++ LR FL+K+    G   E +    D+ VL++A   ++GVP++TPVFDGA
Sbjct: 181  LQQQRT---VAELRLFLDKIYNKVGGEQEDLDSLTDEEVLKLAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  SGQ  L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELAELPRSGQQTLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|326479873|gb|EGE03883.1| DNA-directed RNA polymerase III subunit RPC2 [Trichophyton equinum
            CBS 127.97]
          Length = 1210

 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 255  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 307

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 308  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKI 360

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 361  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 411

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 412  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 471

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 472  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 531

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 532  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFI 590

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 591  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 643

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 644  FVSV--------FINHNQ------KCVHISTDDGRICRPLIIVEKKRSRVTARHL----S 685

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 686  ALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 729

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 730  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 769

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 770  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 808

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 809  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSHSNGTKDRLVGPTR 868

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 869  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 916

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 917  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 967

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 968  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIIS 1027

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1028 GQFGYG-----------------------------------------------------T 1034

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1035 P-FGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1093

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1094 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1153

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1154 SCGFMGYSSWCQRCKSSVGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1207

Query: 1373 K 1373
            +
Sbjct: 1208 R 1208



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 100 LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 149

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 150 DEEQSGIKIDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 199

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 200 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 259

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 260 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 308

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 309 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKINRKASGFG 368

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 369 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 419

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 420 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 479

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 480 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 539

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 540 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFILGAEDIQTV 599

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 600 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHIS 659

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 660 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVY 719

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 720 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 756

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 757 TYQCAMGKQAIGAIANNQFL 776


>gi|312985378|gb|ADR30832.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 102/181 (56%), Positives = 129/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ V TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKVMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE++T KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEIMTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+QALGL   + N + +     +   D 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQALGLDTKVLNGKGQEVRMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|183584757|gb|ACC63821.1| RNA polymerase subunit B [Acinetobacter johnsonii]
          Length = 286

 Score =  357 bits (917), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLTGQESNGGGTT-KRGDKLSVDVLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEEIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   KA   +  LR FL+K+    G   E +    DD +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KAQRTVLELRGFLDKIYNKVGGEQEDLDSLTDDEILVLSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A++  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELANISRTGQTVLYDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584753|gb|ACC63819.1| RNA polymerase subunit B [Acinetobacter lwoffii]
          Length = 286

 Score =  357 bits (917), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 133/290 (45%), Positives = 187/290 (64%), Gaps = 5/290 (1%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   
Sbjct: 1    FKIFEEAARERVIRLLNGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEIQPVDEAIAER 59

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRH
Sbjct: 60   LTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRH 119

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG +I  
Sbjct: 120  GNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDK 179

Query: 1155 LINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            ++ + +    +  LR FL+K+    G   E +    D+ +L+++   ++GVP++TPVFDG
Sbjct: 180  MMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEILKLSGNLRAGVPLATPVFDG 236

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            A+E  I  +L++A L  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 237  AEEGQIKELLQLAGLSSTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|183584759|gb|ACC63822.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752489|gb|ADP09566.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752491|gb|ADP09567.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752493|gb|ADP09568.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752495|gb|ADP09569.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752497|gb|ADP09570.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752499|gb|ADP09571.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752501|gb|ADP09572.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752503|gb|ADP09573.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752505|gb|ADP09574.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752507|gb|ADP09575.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752509|gb|ADP09576.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752511|gb|ADP09577.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752513|gb|ADP09578.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752515|gb|ADP09579.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752517|gb|ADP09580.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752519|gb|ADP09581.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752521|gb|ADP09582.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
 gi|310752523|gb|ADP09583.1| RNA polymerase subunit B [Acinetobacter genomosp. 3]
          Length = 286

 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 131/289 (45%), Positives = 185/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L  +++S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLVEEVLSGLELVDLLEIQPADEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A +  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|83699947|gb|ABC40950.1| RNA polymerase beta subunit [Spiroplasma gladiatoris]
          Length = 594

 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 244/565 (43%), Positives = 355/565 (62%), Gaps = 22/565 (3%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              N L+ +T+ RRL+ALG GG++R RA +E+RDVH +HYGRICP ET EG NIGL+++L+
Sbjct: 1    QTNPLAELTNKRRLTALGPGGLSRDRAALEVRDVHTSHYGRICPIETPEGPNIGLINNLS 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++A++N YGFIETPYRKV  GKV  ++ VYL+A +E++  +AQAN    +DG   +E V 
Sbjct: 61   TYAKINKYGFIETPYRKVVKGKVLNDEHVYLTADKEKDFIVAQANIQTSKDGKILDESVI 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121  ARYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E+P VGTG+E   A+ SG A+VA   GIV  VD+  I I           +G   Y L  
Sbjct: 181  ESPIVGTGVEFEAARDSGDAVVASEDGIVRYVDSKTITI--------EGKNGPRSYTLND 232

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F RSN  T +   P+VKVGD+++ NDI+ADGPS + G+LALG+N++VAF  W+GYNFED+
Sbjct: 233  FYRSNNGTAITHLPIVKVGDKIKANDILADGPSMEKGELALGQNVVVAFTTWNGYNFEDA 292

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            +++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G 
Sbjct: 293  VIVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESNKKHLDSDGIVAIGT 352

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G +  ++ F+
Sbjct: 353  EVKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSIKRFS 412

Query: 947  R-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            +  G D     + + +  +    + ++ +++         + +IL  ++      G    
Sbjct: 413  KADGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTPVD 472

Query: 1006 TVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             +L+   I       Q  +  +        + + K+  + S  + E   ++ ++ I    
Sbjct: 473  IMLNPQGIPSRMNIGQVLEIHLG-------MAAKKLNLKVSTPVFEGVKEDDLKAIMD-- 523

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDK 1089
                G+    KV +   R  ++ DK
Sbjct: 524  --EAGMTNYGKVTLIDGRTGEAYDK 546



 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 119/418 (28%), Positives = 179/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++   DIL    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKVGDKIKANDILADGPS-MEKGELALGQNVVVAFTTWNGYNFEDAVIV----SERIVI 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            + R  + H  +      ++ER Q +    +   +   +  +    L     +  G     
Sbjct: 302  EDRFTSIHIDE-----YTLERRQTKQGPEEITRDIPNISESNKKHLDSDGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T  S   +S   +     F  +   V+ N   +    E     +      K 
Sbjct: 357  GDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIIKSI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  +L ++K++V  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP
Sbjct: 411  FSKADGHDLPADILEIIKIYVVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHMEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP G+PSRMN+GQ+ E HLG A   L  K+ + + +     D+  +         
Sbjct: 471  VDIMLNPQGIPSRMNIGQVLEIHLGMAAKKLNLKVSTPVFEGVKEDDLKAIMDEAGMTNY 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG   EA                  Y
Sbjct: 531  GKVTLI----------------------------DGRTGEA------------------Y 544

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            D        +P++VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  D--------KPISVGVMYMLKLSHMVDDKLHTRNIGPYSLITQQPLGGKAQNGGQRFG 594


>gi|300508136|dbj|BAJ10900.1| RNA polymerase beta subunit [Pseudomonas tuomuerensis]
          Length = 368

 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 216/357 (60%), Positives = 275/357 (77%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 6   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 65

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V  GKVT+++
Sbjct: 66  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNRYGFLESPYRVVKGGKVTDEI 125

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IAQA++ L+E G   EELV  R   E  +   E +  +D SPKQVVS+
Sbjct: 126 VFLSAIEESDHVIAQASAKLNEAGELVEELVNVRHLNEFTVKAPEDVTLMDVSPKQVVSV 185

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 186 AASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGV 245

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V R DI+
Sbjct: 246 IDSVDASRIVVRVNDAEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVNKGDVVARGDIM 305

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           ADGPSTD+G+LALG+N+ VAFMPW+G+NFEDS+ +SER+V ED  T+IHI+E   +A
Sbjct: 306 ADGPSTDMGELALGQNLRVAFMPWNGFNFEDSICLSERVVQEDRLTTIHIQELTCVA 362


>gi|83755187|gb|ABC46442.1| RNA polymerase beta subunit [Spiroplasma ixodetis]
 gi|83755189|gb|ABC46443.1| RNA polymerase beta subunit [Spiroplasma ixodetis]
 gi|83755191|gb|ABC46444.1| RNA polymerase beta subunit [Spiroplasma ixodetis]
          Length = 593

 Score =  357 bits (916), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 231/422 (54%), Positives = 309/422 (73%), Gaps = 8/422 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ + + RRL+ALG GG++R RA +E+RDVH +HYGRICP ET EG NIGL+++L 
Sbjct: 1   QTNPLAELANKRRLTALGPGGLSRDRASLEVRDVHYSHYGRICPIETPEGPNIGLINNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR+N YGFIETPYR+V  GK+TN++ YL+A EE+N  IAQAN  LD +       V  
Sbjct: 61  TYARINEYGFIETPYRQVIAGKITNEIKYLTAGEEKNYIIAQANIELDTNNVIKNNNVIA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G+ I+V   ++++ID SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PLLK +
Sbjct: 121 RSNGQNIIVGPNEVEYIDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLLKPQ 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P VGTG+E  VA+ SG AIVA   G+V+ VD+  I+I+S +         V  Y L +F
Sbjct: 181 TPIVGTGVEYAVARDSGLAIVANLPGVVQYVDSHEIIIKSEDE--------VATYELSRF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T V   PLVKVGD+V  N I+ADGPS   G+LALG+N+++AFM WHGYN+ED++
Sbjct: 233 ERSNQGTAVTHVPLVKVGDKVEVNQILADGPSMKDGELALGQNVIIAFMTWHGYNYEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +ISER+V +DV+TS+HIEE+ +  R TK G EEITR+IPN SE+  + +D+ GI+ +G E
Sbjct: 293 IISERLVKDDVYTSMHIEEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDEGIVLIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVGK+TPKG++  T EEKLL AIFGEK+ +V+D SLRVP+G +G +  ++ + R
Sbjct: 353 VKEGDILVGKVTPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIIQGIKRYKR 412

Query: 948 HG 949
             
Sbjct: 413 ED 414



 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 133/421 (31%), Positives = 187/421 (44%), Gaps = 79/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V    IL    +   +  +   + ++ A       +  D  +     V   V 
Sbjct: 246  LVKVGDKVEVNQILADGPS-MKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVY 304

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ++  +     E    +I    E   R  DDE  I+      +  +IL G+ 
Sbjct: 305  TSMHIEEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDE-GIVLIGTEVKEGDILVGKV 363

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L + +  E  R+               ++ +                
Sbjct: 364  TPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIIQGI---------------- 407

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K + G D+P  V  VVKVF+  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+D
Sbjct: 408  -KRYKREDGFDLPSEVEEVVKVFIVQKRKIREGDKMAGRHGNKGVISKVLPIEDMPFLED 466

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+  +    + 
Sbjct: 467  GTPVDIMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGAKNQDLLDIMKEAK- 525

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                FD                    + 
Sbjct: 526  -YND--------------------------------FD--------------------KL 532

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             LYDGLTGE F + ++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR 
Sbjct: 533  TLYDGLTGEKFAKKISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRF 592

Query: 1295 G 1295
            G
Sbjct: 593  G 593


>gi|326468641|gb|EGD92650.1| DNA-directed RNA polymerase III [Trichophyton tonsurans CBS 112818]
          Length = 1210

 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 255  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 307

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 308  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKI 360

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 361  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 411

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 412  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 471

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 472  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 531

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 532  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFI 590

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 591  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 643

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 644  FVSV--------FINHNQ------KCVHISTDDGRICRPLIIVEKKRSRVTARHL----S 685

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 686  ALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 729

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 730  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 769

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 770  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 808

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 809  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR 868

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 869  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 916

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 917  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 967

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 968  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIIS 1027

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1028 GQFGYG-----------------------------------------------------T 1034

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1035 P-FGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1093

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1094 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1153

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1154 SCGFMGYSSWCQRCKSSVGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1207

Query: 1373 K 1373
            +
Sbjct: 1208 R 1208



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 100 LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 149

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 150 DEEQSGIKIDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 199

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 200 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 259

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 260 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 308

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 309 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKINRKASGFG 368

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 369 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 419

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 420 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 479

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 480 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 539

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 540 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFILGAEDIQTV 599

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 600 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHIS 659

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 660 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVY 719

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 720 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 756

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 757 TYQCAMGKQAIGAIANNQFL 776


>gi|290751446|emb|CAQ16384.1| RNA polymerase beta subunit [Pseudomonas sp. R-26430]
          Length = 370

 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 217/370 (58%), Positives = 285/370 (77%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +  R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   LSRRLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D
Sbjct: 121 KEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG 
Sbjct: 181 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  G
Sbjct: 241 CVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           D V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 DRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 360

Query: 846 EFEVMARDTK 855
           E   +ARDTK
Sbjct: 361 ELTCVARDTK 370


>gi|302657001|ref|XP_003020234.1| hypothetical protein TRV_05698 [Trichophyton verrucosum HKI 0517]
 gi|291184045|gb|EFE39616.1| hypothetical protein TRV_05698 [Trichophyton verrucosum HKI 0517]
          Length = 1196

 Score =  357 bits (916), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 241  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 293

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 294  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKI 346

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 347  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 397

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 398  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 457

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 458  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 517

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 518  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFT 576

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 577  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 629

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 630  FVSV--------FINHNQ------KCVHVSTDDGRICRPLIIVEKKRSRVTARHL----S 671

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 672  ALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 715

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 716  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 755

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 756  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 794

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 795  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR 854

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 855  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 902

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 903  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 953

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 954  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIIS 1013

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1014 GQFGYG-----------------------------------------------------T 1020

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1021 P-FGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1079

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1080 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1139

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1140 SCGFMGYSGWCQRCKSSVGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1193

Query: 1373 K 1373
            +
Sbjct: 1194 R 1194



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 86  LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 135

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 136 DEEQSGIKVDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 185

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 186 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 245

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 246 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 294

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 295 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKINRKASGFG 354

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 355 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 405

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 406 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 465

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 466 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 525

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 526 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFTLGAEDIQTV 585

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 586 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHVS 645

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 646 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVY 705

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 706 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 742

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 743 TYQCAMGKQAIGAIANNQFL 762


>gi|52694381|emb|CAG38030.1| RNA polymerase beta subunit [Pseudomonas alcaligenes]
          Length = 372

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 223/372 (59%), Positives = 286/372 (76%), Gaps = 1/372 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D +VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTQVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +LSA+EE +  IAQA+++++    S++      R   E  +   E +  +D SPKQVVS+
Sbjct: 121 FLSAIEEADHVIAQASATMNAKRASWSTSWWTVRHLNEFTVKAPEDVTLMDVSPKQVVSV 180

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 181 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 240

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+
Sbjct: 241 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVSRGDIM 300

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDT
Sbjct: 301 ADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELPCVARDT 360

Query: 855 KLGPEEITRDIP 866
           KLGPEEI R  P
Sbjct: 361 KLGPEEIYRGHP 372


>gi|197131682|gb|ACH47359.1| RNA polymerase beta subunit [Sarcocaulon vanderietiae]
          Length = 1067

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 220/609 (36%), Positives = 346/609 (56%), Gaps = 13/609 (2%)

Query: 366 KNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
               +++A+L+ Y+     G+   FS +        F   + +L  +GR  +N RLNL  
Sbjct: 216 NIWSKENAILEFYQQFVCVGEDPVFSDSLYKELQKKFFRQRCELGRLGRRNINRRLNLAI 275

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+ER
Sbjct: 276 SQNNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQFGLALIRLER 335

Query: 485 SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            ++     +        PQ L+ + P+ S    FF    LSQ+ +  N L++I H R+ S
Sbjct: 336 VVEGAIGRALKHKWIPTPQSLVTSSPLASTYASFFGLHPLSQVLDGTNPLAQIVHGRKWS 395

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            LG GG+    A   +RD+HP++YGRIC  +TSEG  +GL      +AR+  YG +E+P+
Sbjct: 396 FLGPGGLTARTASFRIRDIHPSYYGRICTIDTSEGIKVGLRGDDLHYARIGHYGSLESPF 455

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            ++ D      ++YLS+  +E   I   NS     G   E++V  R   E + +  E++ 
Sbjct: 456 YEIPDKSKRARMLYLSSRRDEYCMIGTGNSLALNQGYQEEQIVPARYRQEFLTIAWEQVH 515

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  
Sbjct: 516 LRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLEGQVALD 575

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +    AG +  +          +  L           L+ ++RSN+NTC++Q+P V
Sbjct: 576 SGVPLRTDHAGKLISIH--------TDKILLSGNGDSLSIPLVMYERSNKNTCIHQKPQV 627

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + G  ++R  I+ADG +   G+LALG+N+LVA+MPW GYNFED++LISER+V E +FTS 
Sbjct: 628 QPGKCIKRGQILADGAAMVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEGIFTSF 687

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HI ++E+   +T  GPE IT  IP++    L+N+D+ G++ +G+ V  GDILVGK+TP+ 
Sbjct: 688 HIRKYEIQIDETSQGPERITNKIPHLEAHLLRNLDKTGVVILGSWVEAGDILVGKLTPQP 747

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN--RHGIDKNERSISVE 960
               +PE + + AIFG +    R T L++P G  G V+DVR     R    +  R    +
Sbjct: 748 AQESSPENRFVEAIFGPQIPTSRATCLKLPRGGRGRVIDVRWIPKGRPSNPERIRVYISQ 807

Query: 961 REQIELLAR 969
           + +I++  +
Sbjct: 808 KREIKVGDK 816



 Score =  353 bits (905), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 150/591 (25%), Positives = 232/591 (39%), Gaps = 84/591 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   +          I         +  G  
Sbjct: 545  MSSNMQRQAVPLSRSEKCIVGTGLEGQVALDSGVPLRTDHAGKLISIHTDKILLSGNGDS 604

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          I +   +  G  +  G IL           +   + +L A    
Sbjct: 605  LSIPLVMYERSNKNTCIHQKPQVQPGKCIKRGQILAD-GAAMVGGELALGKNVLVAYMPW 663

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     V   +       ++ I  +E S   ER       +    E  +L 
Sbjct: 664  EGYNFEDAVLISERLVYEGIFTSFHIRKYEIQIDETSQGPERI----TNKIPHLEAHLLR 719

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +   ++ G    +G     K T   +   S   R     F  Q    +     L 
Sbjct: 720  N--LDKTGVVILGSWVEAGDILVGKLTPQPAQESSPENRFVEAIFGPQIPTSRATCLKLP 777

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                             +  I  G    P     ++V+++ KR I+ GDK+AGRHGNKG+
Sbjct: 778  RGGRGRVID--------VRWIPKGRPSNP---ERIRVYISQKREIKVGDKVAGRHGNKGV 826

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A V L +  +    D 
Sbjct: 827  VSKILPRQDMPYLQDGKPVDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDE 886

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 887  RYEQEASRKLVFSELHEASKQTGNPW------------------------VFE------- 915

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S+L+DG TG+PF +PV VG  Y+LKL H V DK++ RS+G Y+++T
Sbjct: 916  --------PEYPGKSVLFDGRTGDPFQQPVIVGQPYILKLIHQVDDKIHGRSSGPYAIIT 967

Query: 1280 QQPLGGKSNRGGQRLG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            QQPL                        EMEVW ++ +G A++LQEMLT KSD +  R +
Sbjct: 968  QQPL------------RGRARRGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHLRTRQK 1015

Query: 1328 VYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            V+ + + G +  +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1016 VFGTTIIGGEIPKAKDAPESFRLLVRELRSLALDLNHFLLSEKNFQMNRKE 1066



 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 72/336 (21%), Positives = 136/336 (40%), Gaps = 32/336 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA---AMLEFVSYEFD 82
           IP L ++Q   +  F+          ++GL+        I           L   +Y+  
Sbjct: 12  IPGLNQIQFKGFCRFV----------DQGLREELSKFPKIEDPLDKDVDFRLFAETYQLV 61

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            P     D ++  LTY   L +   LI          KS + +++Q+I++G++PLM   G
Sbjct: 62  EPLIKERDAVYESLTYCSELYVCAGLIW---------KSKRPMQKQTIWIGNIPLMNSLG 112

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF++ GI R+VV+Q+ +SPGI++   + +    G L+Y   II D G  +++E D K  I
Sbjct: 113 TFLVNGIYRMVVNQILQSPGIYY---RSKLDHKGSLVYTGTIISDWGGRLELEIDRKARI 169

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVY-----SQRGDFWCFPLSAADLMV 256
             R+ R++K+ +     A+G +  EIL    YP+I+       +  + W    +  +   
Sbjct: 170 WARVSRKQKISILVLSSAMGSNLSEILENVRYPEILLAFLASKKNANIWSKENAILEFYQ 229

Query: 257 G-AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
               V    V  D+  + ++         L  L  + +      +      ++    +  
Sbjct: 230 QFVCVGEDPVFSDSLYKELQKKFFRQRCELGRLGRRNINRRLNLAISQNNTFLLPRDILA 289

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            T  +      +     +  + +  IR +  L  D 
Sbjct: 290 ATDHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 325


>gi|290751432|emb|CAQ16377.1| RNA polymerase beta subunit [Pseudomonas sp. R-26745]
          Length = 367

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 217/367 (59%), Positives = 284/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+   
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQXLT 360

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 361 CVARDTK 367


>gi|224555849|gb|ACN56501.1| RNA polymerase beta subunit [Oenococcus oeni]
 gi|312985380|gb|ADR30833.1| RNA polymerase beta subunit [Oenococcus oeni]
 gi|312985384|gb|ADR30835.1| RNA polymerase beta subunit [Oenococcus oeni]
 gi|312985386|gb|ADR30836.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 102/181 (56%), Positives = 129/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ V TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKVMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE++T KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEIMTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+QALGL   + N + +     +   D 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQALGLDTKVLNGKGQEVRMAQMDEDD 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|302505599|ref|XP_003014506.1| hypothetical protein ARB_07068 [Arthroderma benhamiae CBS 112371]
 gi|291178327|gb|EFE34117.1| hypothetical protein ARB_07068 [Arthroderma benhamiae CBS 112371]
          Length = 1196

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 181/1141 (15%), Positives = 353/1141 (30%), Gaps = 218/1141 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +    +   +    + +     I ++
Sbjct: 241  IVETDPKKEIVQASVTSSS-----HERKSKSYIIMKKGRIYLRH--NVLNDDIPIVILLK 293

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  + ++   + A      V      ++ AL  +   ++ 
Sbjct: 294  AMGIQSDKEMLLL-------VAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKI 346

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +      S F     +     +  +  V ++     D     + +    +  + + +
Sbjct: 347  NRKA------SGFGPARRNYVAEAIEAISSVIISHVQVQDMNFRPKAL---YVTHMARRV 397

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-------VDID 496
            +  +     +DD D +GN+R+   G++L   +     +    IK  I          +  
Sbjct: 398  LMAKLDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAF 457

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
               P   I+   +   +     +   S     +          RLS +   G+       
Sbjct: 458  DAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 517

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +C ++T EG   GLV +L     +      E P +K+   
Sbjct: 518  FEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTN-DEEEPVQKLVFT 576

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  +   E       Q    +  +GS        R     +   R        S 
Sbjct: 577  LGAEDIQTVGGRE----CFGQGAYIVFMNGSPIA---LTRRPKYFLNAFRRLRRMGRISE 629

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               V        F+ ++        C         +      V      V A+       
Sbjct: 630  FVSV--------FINHNQ------KCVHVSTDDGRICRPLIIVEKKRSRVTARHL----S 671

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A R G ++  D +   +       + + + + +Y       +                  
Sbjct: 672  ALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVYEREIDANTTH---------------- 715

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 716  -----LEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 755

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    ++          +    I       +  
Sbjct: 756  ---------------------IANNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPA 794

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +   +    
Sbjct: 795  GQNAMVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR 854

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                      +  +  R   +L      +  +      V  +    +   S        D
Sbjct: 855  ----------ENGVSIRKHGLLDNDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSD 902

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              +          Y     + +  + +K+           G  +++KV     R  + GD
Sbjct: 903  AGLPVKYNPTPQTY----KLPDYSYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGD 953

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+V  I    DMPF   G   DI++NP G PSRM VG++ E   G A +  
Sbjct: 954  KFSSRHGQKGVVGIIAEQADMPFTDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIIS 1013

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+                                                         T
Sbjct: 1014 GQFGYG-----------------------------------------------------T 1020

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            P F G+  E ++++L        G+  L  G+TGEP    V  G IY  KL HMV DK++
Sbjct: 1021 P-FGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMH 1079

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1080 SRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCE 1139

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
                        R +    +V          P +  +LV+E+ ++ +   L         
Sbjct: 1140 SCGFMGYSGWCQRCKSSVGVVK------MVIPYAAKLLVQELFSMNVVARLRLQDEFPED 1193

Query: 1373 K 1373
            +
Sbjct: 1194 R 1194



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 211/740 (28%), Gaps = 121/740 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 86  LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 135

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 136 DEEQSGIKVDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 185

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 186 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 245

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 246 PKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 294

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 295 MGIQSDKEMLLLVAGVDMEYQEDFAINFEEAVKLSIYTQQQALEYLGARIKINRKASGFG 354

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                  +   + +  + I+       +V    +N     +Y+    +     + ++  S
Sbjct: 355 PARRNYVAEAIEAISSVIIS-------HVQVQDMNFRPKALYV--THMARRVLMAKLDPS 405

Query: 340 EIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            + D   +           +         K   D  ++I +V++    +    A  +   
Sbjct: 406 LVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAYPVVAI 465

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 466 HGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 525

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +  +    G    + +++         D   P   +        +   
Sbjct: 526 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFTLGAEDIQTV 585

Query: 517 FCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                  Q      +N        R    L     + R     E   V   H  +     
Sbjct: 586 GGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFINHNQKCVHVS 645

Query: 574 TSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G     L+      +RV       +        D      V Y+   EE +  IA  
Sbjct: 646 TDDGRICRPLIIVEKKRSRVTARHLSALRNGTMDFDDFLSNGLVEYVDVNEENDANIAVY 705

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +D +                          ++  P  V+   A LIP+  ++ S R 
Sbjct: 706 EREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 742

Query: 691 LMGCNMQRQAVPLLKAEAPF 710
              C M +QA+  +      
Sbjct: 743 TYQCAMGKQAIGAIANNQFL 762


>gi|304322972|ref|YP_003795481.1| beta subunit of RNA polymerase [Floydiella terrestris]
 gi|270048171|gb|ACZ58466.1| beta subunit of RNA polymerase [Floydiella terrestris]
          Length = 808

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 198/780 (25%), Positives = 324/780 (41%), Gaps = 82/780 (10%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML----EFVSYEFD 82
           PD + +Q+ S+  FL           +GL   F    PIT  S    L    EF  Y+  
Sbjct: 9   PDFVSLQRKSFFRFL----------EKGLVEEFSKRSPITNISKGLKLCFYPEF--YKLV 56

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
           PPK++ +  +  D TY+  L + ++L  F           K+I  +  ++ DLPLMT  G
Sbjct: 57  PPKWNPNKAILYDRTYSAKLFVPVQLTSF---------KTKEIVFEWAFLCDLPLMTNRG 107

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDH----------DKGRASLSGKLLYACRIIPDQGLWM 192
            F++ G+ R++++Q+HR PGI++            +  R S S    Y   +I  +G W+
Sbjct: 108 HFLVNGVARVIINQIHRGPGIYYTKTTKKKEILDVETDRKSFSNLTRYYADVISMRGNWL 167

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL----------STFYPKIVYSQRG 242
            +  DSK+     + +  K+P+  FL+  G+  E I            +F   I+ S+  
Sbjct: 168 RLSVDSKNRFWAEMKKTPKIPLLWFLLGTGLRKETIFSKINNSSLLYDSFCNNILLSELD 227

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF------- 295
               F + +         S  L           + ++       + +   +         
Sbjct: 228 QEKYFYVDSTFSAHEKMSSLVLKGKQKNTGKKRNLREWFYKHFMNPRTYDLGPHGRLCIN 287

Query: 296 ----LGITSDCLCGLYVAEDIVN--GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
               L  T   L          +    T  +      +     ++ + +  +R       
Sbjct: 288 RKLGLSFTQSALLNKMSTLTPYDLLFATDYLLKLLAGLGTTDDIDNLKNRRVRTSSDFIQ 347

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDA------------------LLDIYRVMRP--GDVSTF 389
             +          + DK  D   A                       ++ +P   +    
Sbjct: 348 LQIGIGLVRLEKKIRDKLIDFLFAPSLPLKSNEKEKKKDALLKKKAEKLTKPASFEEKRK 407

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
                        + K                 ++  + + I  E    + K    +   
Sbjct: 408 LKNGKKKQGSQKTATKAKEKKGSNSSFKKTSEKNSKKNEKKIGSEKSSKLSKNSSKVSKS 467

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAK 507
               +D       + ++  +  K     G  + +++ +           ++   D INA+
Sbjct: 468 SQKKEDEKASSLSKKKASKKRSKAFETKGFDKEKKNFREAPEFLITRKKNLRISDFINAR 527

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            V  A+ EFF +S LSQ  + +N L+ ITH RR + LG GGV+   A + +R +HPTHYG
Sbjct: 528 YVNGALREFFGTSPLSQFLDQINPLAEITHKRRFTLLGPGGVSEDTATMAVRGIHPTHYG 587

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENR 625
           RICP ET EG N GLV++LT +ARVN+ G IETP+ KV   ++       +LS  +EE  
Sbjct: 588 RICPVETPEGKNAGLVNTLTGYARVNSDGLIETPFLKVFKSQIQKKKGFFFLSPEQEEKS 647

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + S+ + G   +  +  R  GE   V  + + F+  SP Q++S+A SL+PFLE+D
Sbjct: 648 VLATGDLSISKTGFLPKGFLPARSLGEFTKVSSKSVGFMSVSPIQLISVATSLVPFLEHD 707

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPL ++E P VGTG E+     SGAA+ AK  G V    A ++V+
Sbjct: 708 DANRALMGANMQRQAVPLARSEQPIVGTGTEAKAISDSGAAVRAKFGGFVCYASANKVVV 767


>gi|94962315|gb|ABF48473.1| RNA polymerase beta subunit [Entomoplasma lucivorax]
          Length = 595

 Score =  357 bits (915), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 235/467 (50%), Positives = 329/467 (70%), Gaps = 10/467 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L
Sbjct: 1   DQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVV-YLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           +++A+VN YGFI TPYRKV DG + ND+V YL+A EE N  I+Q+    D++G    + V
Sbjct: 61  STYAKVNEYGFITTPYRKVVDGVIQNDIVDYLTADEEHNFVISQSGVKQDDNGKILNKTV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G +++   E +D+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+ 
Sbjct: 121 VARFRGGDMIANTEDVDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIN 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P VGTG+E   A+ SGAAIVA  +GIV+ VD+  I +         S +G+  Y L 
Sbjct: 181 PESPIVGTGIEFEAARDSGAAIVAADSGIVKYVDSKIITV--------ESKNGIKTYELA 232

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F RSN  T +   PL+KVGD+V +  IIADGPS + G+LA+G+N++VAF  ++GYNFED
Sbjct: 233 DFNRSNNGTALLHSPLIKVGDKVEKGQIIADGPSMEQGELAIGQNVVVAFTTYNGYNFED 292

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +D FTSIHI+E+ +  R+TK+GPEEITR+IPN+SE   K +D  GI+  G
Sbjct: 293 AVIMSERVVMDDKFTSIHIDEYVIERRNTKIGPEEITREIPNISEAAKKFLDSDGIVAPG 352

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  GTV  ++ F
Sbjct: 353 TEVRVGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGTVQSIKRF 412

Query: 946 NR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
           +R  G D     + + +  I    + ++ +++         + +IL 
Sbjct: 413 SREDGYDLPADVLEIIKVYIVQKRKIQEGDKMSGRHGNKGVISKILP 459



 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 129/420 (30%), Positives = 182/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            +I VG +V  G I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 248  LIKVGDKVEKGQIIADGPS-MEQGELAIGQNVVVAFTTYNGYNFEDAVIMSERVVMDDKF 306

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                +D  +  R         I+ E   I   A+   D   I+      R+ +IL G+  
Sbjct: 307  TSIHIDEYVIERRNTKIGPEEITREIPNISEAAKKFLDSDGIVAPGTEVRVGDILVGKVT 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E                   
Sbjct: 367  PKGQTQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGTVQSI------------- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K    + G D+P  VL ++KV++  KR IQ GDKM+GRHGNKG++S+ILP EDMP L+DG
Sbjct: 410  KRFSREDGYDLPADVLEIIKVYIVQKRKIQEGDKMSGRHGNKGVISKILPVEDMPHLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            T VDI+LNP GVPSRMN+GQI E HLG A   LG KI + + +   + ++          
Sbjct: 470  TLVDILLNPQGVPSRMNIGQILEIHLGMAAQKLGVKIAAPVFEGLTSTEL---------- 519

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                     + I +    A +   G+  
Sbjct: 520  -----------------------------------------DDIMAE---AGMTNFGKVK 535

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L DG TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 536  LIDGQTGEVMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 595


>gi|183584747|gb|ACC63816.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752561|gb|ADP09602.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752563|gb|ADP09603.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752565|gb|ADP09604.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752567|gb|ADP09605.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752569|gb|ADP09606.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752571|gb|ADP09607.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752573|gb|ADP09608.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752575|gb|ADP09609.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|310752577|gb|ADP09610.1| RNA polymerase subunit B [Acinetobacter baumannii]
          Length = 286

 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPADEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D+ +L +A   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584751|gb|ACC63818.1| RNA polymerase subunit B [Acinetobacter junii]
          Length = 286

 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 137/289 (47%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGEKLSEDMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    I+ LRSFL+K+    G   E++    D+ + ++A   ++GVP++TPVFDGA
Sbjct: 181  L---KQQRTIAELRSFLDKIYNKVGGEQEQLDTLTDEEIFKLAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|290751444|emb|CAQ16383.1| RNA polymerase beta subunit [Pseudomonas sp. R-32840]
          Length = 371

 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 217/367 (59%), Positives = 284/367 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 5   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 64

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 65  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 124

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 125 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 184

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 185 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 244

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 245 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 304

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E  
Sbjct: 305 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELT 364

Query: 849 VMARDTK 855
            +ARDTK
Sbjct: 365 CVARDTK 371


>gi|209360645|gb|ACI42993.1| RNA polymerase beta subunit [Mycoplasma insons]
          Length = 751

 Score =  356 bits (914), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 239/523 (45%), Positives = 337/523 (64%), Gaps = 21/523 (4%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD------------IDSVMPQDLINAK 507
           GN+R+R + E+LK + +  +LR+E+ I+E++S+++             D++  + LIN K
Sbjct: 1   GNKRLRLISELLKGRIQTAMLRIEKFIREKMSNLEAKLSHLTKNENSKDNLTVKSLINTK 60

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           P    + EFF S QL Q  +  N LS +T+ R++SA+G GG+ R    +++RDVH +HYG
Sbjct: 61  PFQIVIKEFFNSHQLIQFIDQQNPLSELTNKRKISAMGPGGINREDPNLDIRDVHYSHYG 120

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           +ICP ET EG NIGL+ SL S+A+ +   F+ TPY KV DGK+T +VV+L+A  E+   +
Sbjct: 121 KICPIETPEGMNIGLIMSLASYAQSDENCFLTTPYFKVIDGKITEEVVWLTASREDEYVV 180

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A+A +  DE+ +     V  R   E       +ID+ID SP+QVVS+A+S IPFLENDD+
Sbjct: 181 AEATNQRDENNNLISP-VSARYRSESQKFDASEIDYIDISPRQVVSVASSCIPFLENDDA 239

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQA PLLK  AP VGTG E  +A  SG  +VAK  G+V +VD   I I++
Sbjct: 240 NRALMGANMQRQATPLLKPYAPLVGTGFEYKIAHDSGMVLVAKEDGVVTKVDGKTIEIQN 299

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                D        Y L K++RSNQ+TC NQ P+V++G++V+++  + DGP+   G+LAL
Sbjct: 300 KNKTTD-------TYTLTKYKRSNQDTCNNQTPIVRLGEKVKKDQSLVDGPAMQNGELAL 352

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N+LVAF  W GYN+ED++++S R+VSED++TSIHI E  +    TK G EEITR IPN
Sbjct: 353 GQNVLVAFTTWRGYNYEDAIILSSRLVSEDIYTSIHINEHSIECLRTKNGDEEITRQIPN 412

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           VS++  + +D  GII VGAEV  GDILVGK +PKG+   + EEKLL+AIF EK   V D+
Sbjct: 413 VSDDLKRYLDNDGIIMVGAEVREGDILVGKTSPKGQVDQSSEEKLLQAIFSEKIKPVNDS 472

Query: 928 SLRVPSGVSGTVVDVRIFN-RHGIDKNERSISVEREQIELLAR 969
           SL+VP G  G VV V+  +   G    +  I V +  I    +
Sbjct: 473 SLKVPHGGEGIVVGVKRLSVYEGNTLKDDVIEVIKVLIAQKRK 515



 Score =  350 bits (899), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 150/524 (28%), Positives = 231/524 (44%), Gaps = 44/524 (8%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV----SEDVFTSIHIEEFEVMARDTK 855
                       +L  + P  G  FE  +     MV     + V T +  +  E+     K
Sbjct: 244  MGANMQRQATPLLKPYAPLVGTGFEYKIAHDSGMVLVAKEDGVVTKVDGKTIEIQ---NK 300

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                +                ++  I+ +G +V     LV          +   + +L A
Sbjct: 301  NKTTDTYTLTKYKRSNQDTCNNQTPIVRLGEKVKKDQSLVDGP-AMQNGELALGQNVLVA 359

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                +  +  D  +     VS  +      N H I+   R+ + + E    +    DD +
Sbjct: 360  FTTWRGYNYEDAIILSSRLVSEDIYTSIHINEHSIEC-LRTKNGDEEITRQIPNVSDDLK 418

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD +       I+ G     G     K++       S   +     F+ + + V  + 
Sbjct: 419  RYLDND-----GIIMVGAEVREGDILVGKTSPKGQVDQSSEEKLLQAIFSEKIKPVNDSS 473

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +    E     +      K   +  G+ +   V+ V+KV +A KR IQ GDKMAGRHG
Sbjct: 474  LKVPHGGEGIVVGV------KRLSVYEGNTLKDDVIEVIKVLIAQKRKIQVGDKMAGRHG 527

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK---- 1151
            NKGIVSRI+P EDMP+L+DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   +G K    
Sbjct: 528  NKGIVSRIVPLEDMPYLEDGTPIDIMLNPLGVPSRMNIGQVLEMHLGLAARKIGFKKLIQ 587

Query: 1152 ---------IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                         +       +I  L    ++ +   + T +    +    + ++     
Sbjct: 588  MYYDPKTQLSDYTLTFGIYEENIKSLLKAFKEHVAELNITSEQQALEQLKDINLSIMLNK 647

Query: 1203 --------GVPVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTV 1251
                       V+TPVF G +   +  ++  A +D +   G+  L+DG+TGE F++P++V
Sbjct: 648  AGLMHEDLSFKVATPVFSGVNNNDLVEIMTEAGIDPTETKGKFTLFDGMTGEKFEKPISV 707

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            G +YMLKL+HMV DK++ARS G YS +TQQPLGGKS  GGQR G
Sbjct: 708  GVMYMLKLDHMVDDKIHARSVGPYSKITQQPLGGKSQNGGQRFG 751


>gi|161345225|gb|ABX64453.1| RpoB [Bacillus subtilis]
          Length = 227

 Score =  356 bits (914), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 89/240 (37%), Positives = 138/240 (57%), Gaps = 23/240 (9%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+
Sbjct: 1   ARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFI 50

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+
Sbjct: 51  DYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPI 101

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D
Sbjct: 102 MTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETD 158

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           +KD+++VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+ 
Sbjct: 159 AKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDQALLE 218


>gi|312136876|ref|YP_004004213.1| DNA-directed RNA polymerase, subunit b' [Methanothermus fervidus DSM
            2088]
 gi|311224595|gb|ADP77451.1| DNA-directed RNA polymerase, subunit B' [Methanothermus fervidus DSM
            2088]
          Length = 604

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 124/585 (21%), Positives = 202/585 (34%), Gaps = 94/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A            + I   ++       I         R+T     
Sbjct: 97   IEYLDAEEEENAYIAISEDELTEEHTHLEIDPAVMFGVSAGLIPYANHNSSPRNTMEAAM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S    +         +        +    +       M   +  + A+   
Sbjct: 157  AKQALGIYASNYKYR---TDTRSHLLFYPQIPLVRTRIMDINEYDKMPAGQNFVVAVLSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   S V    +    F R       R    + ++ E+  +        + 
Sbjct: 214  EGYNMEDALIINKSAVERG-LARSFFFRTYESSERRYPGGQEDKFEIPKKG-------IR 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                      L     ++      +  VL           +  +F    +          
Sbjct: 266  GYRSEDSYRHLDEDGIINPGTEVSQGDVLIGKTSPPRFLGEIDEFGTVSD---------- 315

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                  +S +  R   K               ++VKV V   R  + GDK A RHG KG+
Sbjct: 316  ---RRRESSVTVRPGEKGVVDTVILTESSEGNKLVKVKVRDGRVPELGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMPF +DG   D+++NP  +PSRM+VGQ+ E  LG      G++I       
Sbjct: 373  IGLIVPEEDMPFTEDGLVPDLIINPHAIPSRMSVGQMLEMLLGKGACFEGRRIDG----- 427

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                            TP F G  EE I
Sbjct: 428  ------------------------------------------------TP-FTGEKEEEI 438

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L+    +  G   +Y+G+TGE  +  + VG +Y  KL+HM +DKVYARS G   ++T
Sbjct: 439  KHVLKKYGFESEGLEAMYNGMTGEKIEAEIFVGVVYYQKLHHMTADKVYARSRGPVQILT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESI 1332
            +QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD       D  G   VY+ I
Sbjct: 499  RQPTEGRAREGGLRFGEMERDCLIAHGAALTLKERLLDESDKYEALVCDKCGMLAVYDKI 558

Query: 1333 -------VAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                   + G+  D +      +F +L+ E+++L +   L     
Sbjct: 559  HDKTYCPLCGDKSDIYPVEMSYAFKLLLDELRSLCIFPRLRLEDK 603



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 56/195 (28%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +     +   ++    +  I   RR   +                +         P    
Sbjct: 7   YLNGELVGTCKDPEKFVEEIRKKRREGKISHEVNIAYHPENNEVLIFTDPGRVRRPLIVV 66

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L        R     + +     V        + YL A EEEN YIA +   L 
Sbjct: 67  ENGKPKLTKEHIEKLRNGEITWNDLIKEGV--------IEYLDAEEEENAYIAISEDELT 118

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P  +  ++A LIP+  ++ S R  M   
Sbjct: 119 -----------------------EEHTHLEIDPAVMFGVSAGLIPYANHNSSPRNTMEAA 155

Query: 696 MQRQAVPLLKAEAPF 710
           M +QA+ +  +   +
Sbjct: 156 MAKQALGIYASNYKY 170


>gi|183584749|gb|ACC63817.1| RNA polymerase subunit B [Acinetobacter haemolyticus]
          Length = 286

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEIQPADEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSIEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP    G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDIHGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    I+ LR+FL+K+    G   E +    D+ VL++A   ++GVP++TPVFDGA
Sbjct: 181  LQQQRT---IAELRAFLDKIYNKVGGEQEDLDSLTDEEVLKLAGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELAELPRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|84490161|ref|YP_448393.1| DNA-directed RNA polymerase subunit B' [Methanosphaera stadtmanae DSM
            3091]
 gi|84373480|gb|ABC57750.1| RpoB1 [Methanosphaera stadtmanae DSM 3091]
          Length = 603

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 124/584 (21%), Positives = 205/584 (35%), Gaps = 93/584 (15%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A            + I    +       I         R+T     
Sbjct: 97   IEYIDAEEEENAYIAMFEDQLTEDHTHLEIDPSTMLGICAGIIPYANHNSSPRNTMEAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                    VS   L+         +  +     +    +           +  + AI   
Sbjct: 157  TKQALGLYVSNYNLR---TDTRAHLLHQPQMPVVKTKSMVSTEYDKRPSGQNFVVAILSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +   +     F R       R    + +  E           ++ 
Sbjct: 214  QGCNMEDALVMNKAALERGLGRSSFF-RSYEASERRYPGGQEDHFEYPE-------SMVR 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                  + + L     ++         VL              +F    E+ +    +++
Sbjct: 266  GYRSEEVYKHLDEDGLINPEVPVTSGDVLIGKTSPPRFLEDVDEFGTVAERRRETSVTVR 325

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                      E    +K+   +          ++ KV V   R  + GDK A RHG KG+
Sbjct: 326  HG--------EHGIVDKVMLTE-----TVEGSKLAKVKVRDHRQPEYGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P E+MPF ++G   D+++NP  +PSRM++GQI E   G A    G +I       
Sbjct: 373  LGLIVPQENMPFNENGMCPDLMINPHAIPSRMSIGQIIEMLAGKAGCMEGHRIDG----- 427

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                            TP F G  E+ I
Sbjct: 428  ------------------------------------------------TP-FTGVPEDEI 438

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L+    +  G+  LY+G+TGE F   + VG  Y  KL+HM SDKVYARS G   ++T
Sbjct: 439  KRLLKENGFETHGREQLYNGITGERFKAEIFVGVAYYQKLHHMTSDKVYARSRGPVQVLT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----VVG----------- 1324
            +QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD     + G           
Sbjct: 499  RQPTEGRAREGGLRFGEMERDCLIAHGAALALKERLLDESDKYEALLCGNCGRLAVRDKI 558

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R R Y +I    +TF      +F +L+ E+++L +S +L     
Sbjct: 559  RDRTYCAICGETETFPIEISYAFKLLLDELKSLCISPNLVLEDK 602



 Score = 50.8 bits (120), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 39/107 (36%), Gaps = 23/107 (21%)

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K  D      + Y+ A EEEN YIA     L ED                          
Sbjct: 87  KWFDLIHKGIIEYIDAEEEENAYIAMFEDQLTEDH-----------------------TH 123

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           ++  P  ++ I A +IP+  ++ S R  M   M +QA+ L  +    
Sbjct: 124 LEIDPSTMLGICAGIIPYANHNSSPRNTMEAGMTKQALGLYVSNYNL 170


>gi|197311428|gb|ACH61920.1| RNA polymerase beta subunit [Mycoplasma hyosynoviae]
          Length = 671

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 230/521 (44%), Positives = 349/521 (66%), Gaps = 9/521 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GL+++E++ KERI++ +ID + P+++ N KP+ +    FF +S
Sbjct: 1   NKRIVTIGELLQNQFRVGLIKLEKNTKERIATKEIDKITPKNVTNNKPIFNQFKSFFNTS 60

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NI
Sbjct: 61  KLSQFMDQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNI 120

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L SFA+++ YGFI+TPY KV D K+  ++  YL+A+EE    IAQ+   + ++  
Sbjct: 121 GLILNLASFAKIDKYGFIQTPYFKVKDRKIDFSEPKYLTAIEEMGAIIAQSTVRI-KNNM 179

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +E V  R   E I V   K+D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQ
Sbjct: 180 IIDEYVMARKDSEFIEVEASKVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQ 239

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-----GDLDP 754
           AVP++K EAP V TG+E+ +A+ S   + +   G V  +DA +I I   +          
Sbjct: 240 AVPIIKPEAPLVATGVEADIARYSSTNLRSTIDGTVTYIDADKIEITPDDFAETSTKSTK 299

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            +   +++ L  F+RSNQ T ++Q PLVK+G ++++ D++ DGPS   G+LALG+N+LV 
Sbjct: 300 KSKRPEVFYLRTFERSNQGTLIHQIPLVKLGQKIQKGDLLVDGPSMKDGELALGKNVLVG 359

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           F  WHGYN+ED++++SE++V +DV+TSIHIEE  +  R +K G + +T DIPN S    +
Sbjct: 360 FSTWHGYNYEDAVILSEKLVKDDVYTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKR 419

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +++ GI+ VG+EV  GDILVG+ +PKGE   TPEEKL+ AIF +K+   +DTSL+V  G
Sbjct: 420 FLNDQGIVRVGSEVIAGDILVGRTSPKGEENPTPEEKLMAAIFSQKSSQRKDTSLKVKHG 479

Query: 935 VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            +GTVV V + +R     ++    +E+     +A+ +  + 
Sbjct: 480 HNGTVVAVEVLSREFG--DQLEDGIEKIVKVSIAQKRKIQV 518



 Score =  290 bits (743), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 120/413 (29%), Positives = 178/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G ++  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 326  LVKLGQKIQKGDLLVDGPS-MKDGELALGKNVLVGFSTWHGYNYEDAVILSEKLVKDDV- 383

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L+     R+   +   + + G  
Sbjct: 384  YTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKRFLNDQGIVRVGSEVIAGDILVGRT 443

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q + Q +     V+        +  +L   F       
Sbjct: 444  SPKGEENPTPE--EKLMAAIFSQKSSQRKDTSLKVKHGHNGTVVAVEVLSREF------- 494

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 495  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSVVLPVEDMPYLEDGTPLDI 552

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + + D   +  I  +    +      S
Sbjct: 553  VLNPQGVPSRMNIGQVLELHLGLAAKKLGVKFVTPVFDGITHNQIKDILQEAKIDPSGKS 612

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +GQ       
Sbjct: 613  VV-----------------------------------------------YNGQ------- 618

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE  D P++VG +Y LKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 619  TGEKLDAPISVGIMYYLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 671


>gi|73697677|gb|AAZ81455.1| RNA polymerase beta subunit [Mycoplasma sp. ATCC 27369]
          Length = 595

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 222/415 (53%), Positives = 308/415 (74%), Gaps = 9/415 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K E+
Sbjct: 121 FNGDDYMARVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIKPES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L  ++
Sbjct: 181 PIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILSDYE 232

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED+++
Sbjct: 233 RSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIV 292

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN+SE+  +++D  GI+ +G EV
Sbjct: 293 MSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEV 352

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++
Sbjct: 353 KVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIK 407



 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 125/427 (29%), Positives = 186/427 (43%), Gaps = 80/427 (18%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 240  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 294

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 295  ERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 354

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 355  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 407

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 408  -----RFKAKSASNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPV 462

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP L+DGTPVDI+LNP GVPSRMN+GQI E HLG A   L +K+ + + +     ++ 
Sbjct: 463  EDMPHLEDGTPVDIILNPQGVPSRMNIGQILEIHLGMAAKKLNQKVITPVFEGLNEKELE 522

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
             + +                                                        
Sbjct: 523  EIMAEAGMTNYGKVTLI------------------------------------------- 539

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 GQ       TGEPFD+P+ VG +YMLKL+HMV DK++ R+ G YSL+TQQPLGGK
Sbjct: 540  ----DGQ-------TGEPFDKPIAVGVMYMLKLSHMVDDKIHTRNVGPYSLITQQPLGGK 588

Query: 1287 SNRGGQR 1293
            +  GGQR
Sbjct: 589  AQNGGQR 595


>gi|156628210|gb|ABU89022.1| RNA polymerase beta subunit [Spiroplasma mirum]
          Length = 571

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 223/428 (52%), Positives = 311/428 (72%), Gaps = 8/428 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           +ALG GG++R RAG+E+RDVH +HYGRICP ET EG NIGL++SL ++A++N++GFIETP
Sbjct: 2   TALGPGGLSRERAGLEVRDVHYSHYGRICPIETPEGPNIGLINSLATYAKINSFGFIETP 61

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRKV D KVT+   YL+A EE+N  +A AN  L + G   ++ V  R  GE I+  R ++
Sbjct: 62  YRKVIDNKVTSQNDYLTADEEKNYVVAHANIRLSDKGKILDDQVIARFQGENIIASRTEV 121

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PL+  ++P+VGTG+E   AK
Sbjct: 122 DYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLINPQSPYVGTGVEYAAAK 181

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG AIV++  G+++ VDA +I++++ E        G+  Y L  F RSNQ T +   PL
Sbjct: 182 DSGLAIVSQYDGVIDFVDATKIILKTKE--------GLKTYNLDTFVRSNQGTSLTHVPL 233

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK G +V +  I+ADGPS D G+LALG+N++VAF  W+GYN+ED++++SER+V++DVFTS
Sbjct: 234 VKQGQKVVKGQILADGPSIDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVADDVFTS 293

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIEE+ +  R TK G EEITR+IPN+SE   K +D+ G++ +G EV PGDILVGK+TPK
Sbjct: 294 IHIEEYTIERRQTKQGAEEITREIPNISENARKFLDDDGLVIIGTEVKPGDILVGKVTPK 353

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
           G++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G V  ++ F R   +     + V +
Sbjct: 354 GQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIVQAIKRFPREKYELAADVLEVVK 413

Query: 962 EQIELLAR 969
             I    +
Sbjct: 414 VYIVQKRK 421



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 127/410 (30%), Positives = 185/410 (45%), Gaps = 74/410 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G IL    +   +  +   + ++ A       +  D  +         V 
Sbjct: 233  LVKQGQKVVKGQILADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIV----SERLVA 287

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            D    + H  +      ++ER Q +  A +   E   +  N    L +   ++ G     
Sbjct: 288  DDVFTSIHIEE-----YTIERRQTKQGAEEITREIPNISENARKFLDDDGLVIIGTEVKP 342

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   +     F  + + V+ N   +    E     ++   + K 
Sbjct: 343  GDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIVQAIKRFPREKY 402

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            E       +   VL VVKV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP L+DGTP
Sbjct: 403  E-------LAADVLEVVKVYIVQKRKIQEGDKMAGRHGNKGVISKILPIEDMPHLEDGTP 455

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  L         
Sbjct: 456  VDIMLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNDELIELMD------- 508

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                       + ++        + IL 
Sbjct: 509  ------------------------------------------KAGMKNFG-----KEILV 521

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            DG TGE FD PV+VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+
Sbjct: 522  DGRTGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKA 571


>gi|80978863|gb|ABB54680.1| RNA polymerase beta subunit [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|80978865|gb|ABB54681.1| RNA polymerase beta subunit [Mycoplasma capricolum subsp.
           capricolum]
          Length = 596

 Score =  356 bits (913), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 222/415 (53%), Positives = 308/415 (74%), Gaps = 9/415 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 62  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K E+
Sbjct: 122 FNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIKPES 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L  ++
Sbjct: 182 PIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILSDYE 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED+++
Sbjct: 234 RSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIV 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN+SE+  +++D  GI+ +G EV
Sbjct: 294 MSERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             GD+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++
Sbjct: 354 KVGDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIK 408



 Score =  291 bits (744), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 126/427 (29%), Positives = 187/427 (43%), Gaps = 80/427 (18%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+ VG  V  G+I+    +   +  +   + ++ A       +  D  +      
Sbjct: 241  LTQSPIVKVGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVM----S 295

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLA---------RDKDDEQVILDRNIYSRL 986
               V+D R  + H  +      + ++ Q E+           +   D + I+      ++
Sbjct: 296  ERIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKV 355

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
             ++L G+    G         L   +  E  R           +V    E +    +   
Sbjct: 356  GDVLVGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--- 408

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 RFK K      G ++P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP 
Sbjct: 409  -----RFKAKSALNPDGIELPADIIEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPI 463

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMP L+DGTPVDI+LNP GVPSRMN+GQI E HLG A   L +K+ + + +     ++ 
Sbjct: 464  EDMPHLEDGTPVDIILNPQGVPSRMNIGQILEIHLGMAAKKLNQKVITPVFEGLNEKELE 523

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
             + +                                                        
Sbjct: 524  EIMAEAGMTNYGKVTLI------------------------------------------- 540

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                 GQ       TGEPFD+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK
Sbjct: 541  ----DGQ-------TGEPFDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGK 589

Query: 1287 SNRGGQR 1293
            +  GGQR
Sbjct: 590  AQNGGQR 596


>gi|294768460|gb|ADF36178.1| RNA polymerase beta subunit [Mycoplasma sp. Phocoena C-264-GEN]
          Length = 666

 Score =  355 bits (912), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 230/512 (44%), Positives = 346/512 (67%), Gaps = 9/512 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ ++GE+L+NQ+R+GLL++E++ +E+I + + D +  +++ N KP+ + +  FF SS
Sbjct: 4   NKRIVTIGELLQNQFRIGLLKLEKNTEEKIKTKETDKITARNVTNNKPIYNQMKSFFNSS 63

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 64  KLSQFMDQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNI 123

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLD-EDG 638
           GL+ +L S+A+++ YGFI++PY KV +G V  ND+VYL+A+EE N   AQ++ ++D E G
Sbjct: 124 GLILNLASYAKIDEYGFIQSPYFKVNNGVVDFNDIVYLTAIEETNYSFAQSSINIDTETG 183

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E V  R   E   + + +ID++  S +Q+ SI+AS IPFLENDD+NR LMG NMQR
Sbjct: 184 QILDEKVMARKNNEYTELNKNEIDYLGVSSRQMASISASAIPFLENDDANRALMGSNMQR 243

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL+K EAP V TG+E+ +AK S + + + +AGIV  VDA  I ++      +     
Sbjct: 244 QAVPLIKPEAPLVATGVEADIAKYSASNVRSTKAGIVTYVDAGVIKVKPDNEKKE----- 298

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              ++L  F+RSNQ T ++Q+P+V VG  +   D++ DGPS   G+LALGRN+LV F  W
Sbjct: 299 -FEFKLKTFERSNQGTVIHQKPIVNVGQRIEVGDLLTDGPSMQNGELALGRNVLVGFSTW 357

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED+++++ER+V +DV+TSIHI+E  +  R  K G + +T DIPN S    + ++E
Sbjct: 358 FGYNYEDAVILNERLVKDDVYTSIHIDEQVIQFRRAKAGEDILTADIPNASNRSKRFLNE 417

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            G++ VG+EV+ GDILVG+++PK E   +PEEKL+ AIFG K  +++DTSL+V  G  GT
Sbjct: 418 KGVVRVGSEVSAGDILVGRVSPKAEENPSPEEKLMSAIFGHKTSNLKDTSLKVKHGHGGT 477

Query: 939 VVDVRIFNRH-GIDKNERSISVEREQIELLAR 969
           VV V I +R  G    +   ++ +  I    +
Sbjct: 478 VVAVEILSREAGDQLEDGIETIVKISIAQKRK 509



 Score =  284 bits (727), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 119/414 (28%), Positives = 175/414 (42%), Gaps = 67/414 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  GD+L    +      +     +L         +  D  +     V   V 
Sbjct: 320  IVNVGQRIEVGDLLTDGPS-MQNGELALGRNVLVGFSTWFGYNYEDAVILNERLVKDDV- 377

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I     + +  R+ + E      +    +  +  L+     R+   +   + + G  
Sbjct: 378  YTSIHIDEQVIQFRRAKAGEDILTADIPNASNRSKRFLNEKGVVRVGSEVSAGDILVGRV 437

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +              ++D  +      +K  +  +   +E      I   
Sbjct: 438  SPKAEENPSPEEKLMSAIFGHKTSNLKDTSL-----KVKHGHGGTVVAVE------ILSR 486

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+  +VK+ +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 487  EAGDQLEDGIETIVKISIAQKRKIKVGDKMAGRHGNKGVVSIVLPEEDMPYLEDGTPLDI 546

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  S + D  +  +I  ++           
Sbjct: 547  LLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVSPVFDGISYKEIQEIQKEAGLSTTGKM 606

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V++G   E                       
Sbjct: 607  T----------------------------VYNGITGE----------------------- 615

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
               PFD+PV+VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 616  ---PFDQPVSVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 666


>gi|197311426|gb|ACH61919.1| RNA polymerase beta subunit [Mycoplasma agassizii]
          Length = 669

 Score =  355 bits (911), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 227/520 (43%), Positives = 342/520 (65%), Gaps = 10/520 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+R+ SVGE+L NQ+ +GL +ME++  E+IS+ +   + P+++ N K V + +  FF SS
Sbjct: 3   NKRIVSVGELLLNQFIIGLNKMEKNTLEKISAREASKITPKNVTNNKMVQNQIKTFFNSS 62

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +LSQ  +  N L+ I+  R++++LG GG+ R  A  E+RDVH THYGRICP ET EG NI
Sbjct: 63  KLSQFMDQTNPLAEISSKRKITSLGMGGLNRDTAQFEVRDVHTTHYGRICPIETPEGQNI 122

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS 639
           GL+ +L +FAR+N  GF+ETPY +V +G V  +  +YL++ EE + + AQ+  +LD++  
Sbjct: 123 GLILNLATFARINDLGFLETPYYRVNNGVVDASKPIYLTSYEELDLHFAQSTINLDDNNR 182

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +  V  +  GE  +V   ++D++  S  Q+ S+A+S IPFLEN+D+NR LMG NMQRQ
Sbjct: 183 IIDPKVTVKYNGEYTIVDATEVDYVSVSSNQMTSLASSCIPFLENNDANRALMGANMQRQ 242

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           +VPLL AEAP V TG+E+ +AK S A + A RAG V  VD   I I+        S +  
Sbjct: 243 SVPLLVAEAPNVATGIEADLAKYSSANVKANRAGKVIYVDGKEIKIQPFSDS--DSKTRT 300

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D+Y+L+ ++RSNQ T ++Q P+VKVGD V    II DG S   G++++G+N+LV F  + 
Sbjct: 301 DVYQLLSYERSNQGTVMSQTPIVKVGDTVEAGQIITDGSSFKNGEMSIGKNLLVGFSTFE 360

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYNFED+++I+ER+  +D  TSIHIEE  +  R  K G +E+T +IPNVS    +N+++ 
Sbjct: 361 GYNFEDAIIINERLFKDDTLTSIHIEEQSIQFRKLKAGDDELTAEIPNVSLRSRRNLNDE 420

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+ +G+EV PGDILVG+++P+G+   +P EKLL  IF +K    +DTSL+V +G  GTV
Sbjct: 421 GIVNIGSEVLPGDILVGRVSPRGDENTSPSEKLLNGIFNQKITTKKDTSLKVKNGHQGTV 480

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           +DV+I +R   DK E       + I+ + +    ++  + 
Sbjct: 481 IDVQILSRKFGDKLE-------DGIDKIVKVYIAQKRKIK 513



 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 111/417 (26%), Positives = 170/417 (40%), Gaps = 71/417 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  G I+    + K    M+  + LL      +  +  D  +           
Sbjct: 322  IVKVGDTVEAGQIITDGSSFKN-GEMSIGKNLLVGFSTFEGYNFEDAII----------- 369

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
               I  R   D    SI +E + I+    +  DDE      N+  R    L  +  V+  
Sbjct: 370  ---INERLFKDDTLTSIHIEEQSIQFRKLKAGDDELTAEIPNVSLRSRRNLNDEGIVNIG 426

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KIE 1058
                   +L   +      +      + +    + + + K      K+  +    + +I 
Sbjct: 427  SEVLPGDILVGRVSPRGDENTSPSEKLLNGIFNQKITTKKDTSLKVKNGHQGTVIDVQIL 486

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              ++GD +  G+ ++VKV++A KR I+ GDKMAGR+GNK                     
Sbjct: 487  SRKFGDKLEDGIDKIVKVYIAQKRKIKVGDKMAGRYGNK--------------------- 525

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
                   GV SR+                            + +       + L+ ++  
Sbjct: 526  -------GVISRI--------------------------VPEEDMPYLEDGTPLDVLLNP 552

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 +++      +        +G    +PVFDG   E I S L  A LD SG++ +YD
Sbjct: 553  QGVPSRMNIGQVFELHLGMVSRLTGAKFVSPVFDGIKWEDIQSELENAGLDRSGKTKIYD 612

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
              TG PFD PV+VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 613  PQTGLPFDHPVSVGMMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 669


>gi|212373949|emb|CAP09901.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35700]
          Length = 360

 Score =  355 bits (911), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 215/356 (60%), Positives = 277/356 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEE
Sbjct: 302 LALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEE 357


>gi|224555851|gb|ACN56502.1| RNA polymerase beta subunit [Oenococcus oeni]
          Length = 199

 Score =  355 bits (911), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 101/181 (55%), Positives = 129/181 (71%)

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G+ V TPVFDGA ++ I   L+ A LDE G+++LYDG TGE FD  ++VG ++ +KL 
Sbjct: 19   KLGIKVMTPVFDGASDDEIIDALKEAGLDEDGKTVLYDGQTGEAFDNRISVGVMHYMKLA 78

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE++T KSD
Sbjct: 79   HMVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEIMTYKSD 138

Query: 1321 DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDF 1380
            DV GR +V+ESIV G    + G PESF VLVKE+QALGL   + N + +     +   + 
Sbjct: 139  DVRGRNKVFESIVKGQAIPKPGVPESFRVLVKELQALGLDTKVLNGKGQEVRMAQMDEED 198

Query: 1381 N 1381
            N
Sbjct: 199  N 199


>gi|309322258|ref|YP_003934336.1| RNA polymerase beta subunit [Monsonia speciosa]
 gi|197131680|gb|ACH47358.1| RNA polymerase beta subunit [Monsonia speciosa]
 gi|300069351|gb|ADJ66471.1| RNA polymerase beta subunit [Monsonia speciosa]
          Length = 1067

 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 220/681 (32%), Positives = 360/681 (52%), Gaps = 13/681 (1%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + + +  +   +     +  +             + S+  +  +   ++  +  
Sbjct: 138 ELDHKGILVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLSSAMGSNLREILE 197

Query: 350 DSVNNNAYIRNTLVTDKNKDR--KDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKY 406
           +      ++              ++A+L+ Y+     G+   FS +        F   + 
Sbjct: 198 NVRYPEIFLSFLADKANANIWSKENAILEFYQQFVCVGEDPLFSDSLYKELQKKFFRQRC 257

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
           +L  +GR  +N RLNL        +   DI+A    L+ ++ G G +DD+++L N+R+RS
Sbjct: 258 ELGGLGRRNINRRLNLAISQSKTFLLPRDILAATDHLIGMKFGMGRLDDMNHLKNKRIRS 317

Query: 467 VGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           V ++L++Q+ L L+R+ER +      +        PQ L+   P+ S    FF    LSQ
Sbjct: 318 VADLLQDQFGLALIRLERVVTGAIGGALKHKWIRTPQSLVTPSPLASTYASFFGLHPLSQ 377

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           + +  N L++I H R+ S LG GG+    A   +RD+HP++YGRIC  +TSEG  +GL+ 
Sbjct: 378 VLDGTNPLAQIVHGRKWSFLGPGGLTARTASFRIRDIHPSYYGRICTIDTSEGIKVGLMG 437

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL   AR+  YG +E+P+ ++ +      ++YLS+  +E   I   NS     G   E++
Sbjct: 438 SLAIHARIGHYGSLESPFYEIPEKSKRARMLYLSSRRDEYSMIGTGNSLALNQGYQEEQI 497

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E + +  E++      P Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL 
Sbjct: 498 VPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLS 557

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           ++E   VGTG+E  VA  SG +++ + AG    +          +  L           L
Sbjct: 558 RSEKCIVGTGLEGQVALDSGVSLITEHAGKPISIH--------TDKILLSGNGDSLSIPL 609

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           + ++ SN+NTC++Q+P V+ G  +RR  ++ADG +T  G+LALG+N+LVA+MPW GYNFE
Sbjct: 610 VMYEGSNKNTCIHQKPQVQRGKCIRRGQVLADGAATVGGELALGKNVLVAYMPWEGYNFE 669

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++LISER+V E ++TS HI ++E+   +T  GPE IT+ IP++    L+N+D+ G++ +
Sbjct: 670 DAVLISERLVYEGIYTSFHIRKYEIQIDETSQGPERITKKIPHLEAHLLRNLDKNGVVIL 729

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+ V  GDILVGK+ P+      PE + + A+FG +    R   L++P G  G V+DVR 
Sbjct: 730 GSWVEAGDILVGKLRPQPAQESVPENRFVEAVFGPQIPTSRAACLKLPIGGRGRVIDVRW 789

Query: 945 FNRHGIDKNERSISVEREQIE 965
             + G    ER      ++ E
Sbjct: 790 SPKGGPSNPERIRVYISQKRE 810



 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 146/591 (24%), Positives = 236/591 (39%), Gaps = 84/591 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       +  +     G   E  + +   +          I         +  G  
Sbjct: 545  MSSNMQRQAVPLSRSEKCIVGTGLEGQVALDSGVSLITEHAGKPISIHTDKILLSGNGDS 604

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +          I +   +  G  +  G +L       G   +   + +L A    
Sbjct: 605  LSIPLVMYEGSNKNTCIHQKPQVQRGKCIRRGQVLADGAATVG-GELALGKNVLVAYMPW 663

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  +  D  L     V   +       ++ I  +E S   ER       +    E  +L 
Sbjct: 664  EGYNFEDAVLISERLVYEGIYTSFHIRKYEIQIDETSQGPERI----TKKIPHLEAHLLR 719

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 +   ++ G    +G        +         P +++ +     +        LK
Sbjct: 720  N--LDKNGVVILGSWVEAGDILV--GKLRPQPAQESVPENRFVEAVFGPQIPTSRAACLK 775

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            +       +++ R+  K           P     ++V+++ KR I+ GDK+AGRHGNKG+
Sbjct: 776  LPIGGRGRVIDVRWSPKGG---------PSNPERIRVYISQKREIKVGDKVAGRHGNKGV 826

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A V L +  +    D 
Sbjct: 827  VSKILPRQDMPYLQDGKPVDMVFNPLGVPSRMNVGQIFECSLGLAGVLLDRHYRVAPFDE 886

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   + S    F E    +                               VF+       
Sbjct: 887  RYEQEASRKLVFSELHEASKQTGNPW------------------------VFE------- 915

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                     +  G+S+L+DG TG+PF +PV VG  Y+LKL H V DK++ RS+G Y+++T
Sbjct: 916  --------PEYPGKSVLFDGRTGDPFQQPVIVGQPYILKLIHQVDDKIHGRSSGPYAIIT 967

Query: 1280 QQPLGGKSNRGGQRLG------------EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            QQPL                        EMEVW ++ +G A++LQEMLT KSD +  R +
Sbjct: 968  QQPL------------RGRARRGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHLRTRQK 1015

Query: 1328 VYESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            V+ + + G    +    PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1016 VFGTTIIGGAIPKAKDAPESFRLLVRELRSLALDLNHFLLSEKNFQMNRKE 1066



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 72/336 (21%), Positives = 131/336 (38%), Gaps = 32/336 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA---AMLEFVSYEFD 82
           IP L ++Q   +  F+          ++GL+        I           L   +Y+  
Sbjct: 12  IPGLNQIQFKGFSRFV----------DQGLREELSKFPKIEDPLDKDVDFRLFAETYQLV 61

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            P     D ++  LTY   L +               KS + +++Q+I++G++PLM   G
Sbjct: 62  EPLIKERDAVYESLTYCSELYV---------CAGFFCKSKRPMQKQTIWIGNIPLMNSLG 112

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I GI R+VV+Q+ +SPGI++  +       G L+Y   II D G  +++E D K  I
Sbjct: 113 TFLINGIYRMVVNQILQSPGIYYRSELDHK---GILVYTGTIISDWGGRLELEIDRKARI 169

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
             R+ R++K+ +     A+G +  EIL    YP+I  S   D     + + +  +     
Sbjct: 170 WARVSRKQKISILVLSSAMGSNLREILENVRYPEIFLSFLADKANANIWSKENAILEFYQ 229

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC------GLYVAEDIVNG 315
             +   +         K+L     +   E G       +  L         ++    +  
Sbjct: 230 QFVCVGEDPLFSDSLYKELQKKFFRQRCELGGLGRRNINRRLNLAISQSKTFLLPRDILA 289

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            T  +      +     +  + +  IR +  L  D 
Sbjct: 290 ATDHLIGMKFGMGRLDDMNHLKNKRIRSVADLLQDQ 325


>gi|183584767|gb|ACC63826.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752525|gb|ADP09584.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752527|gb|ADP09585.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752529|gb|ADP09586.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752531|gb|ADP09587.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752533|gb|ADP09588.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752535|gb|ADP09589.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752537|gb|ADP09590.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752539|gb|ADP09591.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752541|gb|ADP09592.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752543|gb|ADP09593.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752545|gb|ADP09594.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752547|gb|ADP09595.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752549|gb|ADP09596.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752551|gb|ADP09597.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752553|gb|ADP09598.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752555|gb|ADP09599.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|310752557|gb|ADP09600.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
          Length = 286

 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 136/289 (47%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E +    DD +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KEQRTVLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|66356606|ref|XP_625481.1| DNA-directed RNA polymerase beta subunit [Cryptosporidium parvum Iowa
            II]
 gi|46226475|gb|EAK87469.1| DNA-directed RNA polymerase beta subunit [Cryptosporidium parvum Iowa
            II]
          Length = 1287

 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 169/1001 (16%), Positives = 303/1001 (30%), Gaps = 186/1001 (18%)

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            L T+ RV ++    + T    + +    +  + K ++D       +DD D  GN+R+   
Sbjct: 423  LETLNRVLLSHIGTIYTDLHPKAL---FLCLMAKRVLDASEDNSLLDDKDYYGNKRIELA 479

Query: 468  GEMLKNQYRLGLLRM-----------------ERSIKERISSVDIDSVMPQDLINA---K 507
            G+++   +     R                   R   +  +  D  +    D        
Sbjct: 480  GQLISILFEDLFKRFSVLTKKQIDQTLIRYFQTRDASKAGTGRDDSNSTYPDCFRNLPTD 539

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMR 559
             +   +     +   S     +          R S +   G+         +AR     R
Sbjct: 540  IITRGMQTALSTGNWSIKRFRMERSGMTQVLTRFSYIASLGIMTRVDSQFEKARKVSGPR 599

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             + P+ +G +CP +T EG + GLV +L                                 
Sbjct: 600  ALQPSQWGILCPCDTPEGESCGLVKNLA-------------------------------- 627

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                                     +      + +      +   D S    +       
Sbjct: 628  ---------------------LTTHITTDHCPQYLTSLLFTLGVQDISSCSYLDFNTKQS 666

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
              L N+D      G N  ++   +    +     G+       +      +R G + Q  
Sbjct: 667  EKLSNEDLKNESSGKNNVKKHYYVSINGSLL---GVHRKPELLASQLRNLRRKGFIGQFV 723

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            +I             +  G     L+   +            +K G+ +  + I      
Sbjct: 724  SIFCN-HIHSSVQIATDGGRLCRPLIIVDQGVPRLKEEHIEQLKRGEIIFSDFISQGIL- 781

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D+    N+L+A    +  N    + I    +   V   I         R+T     
Sbjct: 782  -EWIDVNEENNLLIALRDENLTNETTHLEIDPLSILGVVSGLIPYPNHNQSPRNTYQC-- 838

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S    + +    ++ +             I       +   +    A+   
Sbjct: 839  -AMGKQVMGSVGFNQFLRCDSVLYLLVYPQKPLCKTRTIEMINFEQLPAGQNSSVAVMSF 897

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               D+ D  +   + V        +  R          ++E +++     ++    + + 
Sbjct: 898  AGYDIEDAIVMNKASVDRGFARCFVMKR---------QTIELQKLPNGLSERVVRPISVG 948

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                          + +           +S D I     S         +  Q ++    
Sbjct: 949  SGNTGNRRFSFKNDSILDNDGVCNVGVQVSEDDIIVNKMSPINTREYVGDPSQFDLSE-- 1006

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
              Y+ S    +    + I+++           ++ KV     R  + GDK + RHG KG+
Sbjct: 1007 --YKPSPVKYKGPTSSYIDRVIL--TENADGNQIYKVITRQTRRPELGDKFSSRHGQKGV 1062

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  I+  ED+PF + G   D+++NP G PSRM VG++ E     A V  G          
Sbjct: 1063 VGLIISQEDLPFSETGWCPDLIMNPHGFPSRMTVGKLLELISSKASVLDG---------- 1112

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                    ++ G       F G   E  
Sbjct: 1113 ---------------------------------------NYRYGT-----AFGGTPLEES 1128

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L       SG+  L  G TGE  +  + VG IY  KL HMV DK++AR  G   ++T
Sbjct: 1129 AKCLVEHGFHYSGKEYLTSGTTGEAIEAYIFVGPIYYQKLKHMVLDKMHARGRGPRQILT 1188

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG---- 1335
            +QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD       V+E+ V      
Sbjct: 1189 RQPTEGRSKDGGLRLGEMERDCLVAYGASNLLIERLMLNSD-------VFETNVCNQCGL 1241

Query: 1336 -------------NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                          D      P +  +L +E+QA+ +   +
Sbjct: 1242 FGYNNYCHYCKSSQDVSIIRLPYACKLLFQELQAMNVCPRI 1282



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 132/964 (13%), Positives = 283/964 (29%), Gaps = 177/964 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    SY++F+   I    R N       +S         +  +EF+      PK   
Sbjct: 123 LVKHHIDSYNYFVTTEIQSIVRANA--NRMIRS-----DVDPSFFIEFLDARVGMPKLEE 175

Query: 87  -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                      C  RD+TYA P+ + +  +  +            ++++++ +G +P+M 
Sbjct: 176 NMITVDLTPMMCRMRDITYAAPIFVDVDYVRGNTV----------VRKKNVEIGRIPVML 225

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                     G FV+KG ++ ++ Q   S       ++    L 
Sbjct: 226 RSKVCILHGKTAAEMVKLNECPHDPGGYFVVKGTEKAILMQEQLS------KNRIIVELD 279

Query: 176 GKLLYACRIIP---DQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILST 231
            K  Y   +     +      + F     +++R +    ++P+   L A+G+++E+    
Sbjct: 280 NKHNYCATVTSTTAESKSRTLVVF-KNGKLYLRHNSFSDEIPLCIVLKAMGIETEQ--EI 336

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F+         +     L             +L+ +    +        +S        +
Sbjct: 337 FFMIGNEPHHQEGIINSLQEVHQEGIFTQRQALLFMSKKAKSKFKSTFGSSRGFDKSNAE 396

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                            AE+    E G           +  LE +    +  I  +Y D 
Sbjct: 397 E---------------SAENSGFTEFGGSKSSLCGTSIDDVLETLNRVLLSHIGTIYTDL 441

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                ++        +    ++LLD         +    +A  +                
Sbjct: 442 HPKALFLCLMAKRVLDASEDNSLLDDKDYYGNKRI---ELAGQLI--------------- 483

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                   L  D       + K+ I   +      R+        D+  +        + 
Sbjct: 484 ------SILFEDLFKRFSVLTKKQIDQTLIRYFQTRDASKAGTGRDDSNSTYPDCFRNLP 537

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +    G+     +    I    ++                       S ++Q+    + 
Sbjct: 538 TDIITRGMQTALSTGNWSIKRFRME----------------------RSGMTQVLTRFSY 575

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           ++ +    R+ +       +AR     R + P+ +G +CP +T EG + GLV +L     
Sbjct: 576 IASLGIMTRVDS----QFEKARKVSGPRALQPSQWGILCPCDTPEGESCGLVKNLALTTH 631

Query: 592 VNAYG---------------FIETPYRKVCDGKVTNDVVYLSAMEE-------ENRYIAQ 629
           +                    I +      + K +  +       E       +  Y   
Sbjct: 632 ITTDHCPQYLTSLLFTLGVQDISSCSYLDFNTKQSEKLSNEDLKNESSGKNNVKKHYYVS 691

Query: 630 ANSSLDEDGSFTE----ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            N SL       E    +L   R  G          + I +S +          P +  D
Sbjct: 692 INGSLLGVHRKPELLASQLRNLRRKGFIGQFVSIFCNHIHSSVQIATDGGRLCRPLIIVD 751

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD------ 739
                L   ++++     +          +E +        ++A R   +          
Sbjct: 752 QGVPRLKEEHIEQLKRGEIIFSDFISQGILEWIDVNEENNLLIALRDENLTNETTHLEID 811

Query: 740 --AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIA 795
             +I  V+  +    + + S  + Y+    ++   +   NQ       +   V     + 
Sbjct: 812 PLSILGVVSGLIPYPNHNQSPRNTYQCAMGKQVMGSVGFNQFLRCDSVLYLLVYPQKPLC 871

Query: 796 DG---PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                   +   L  G+N  VA M + GY+ ED++++++  V         ++   +  +
Sbjct: 872 KTRTIEMINFEQLPAGQNSSVAVMSFAGYDIEDAIVMNKASVDRGFARCFVMKRQTIELQ 931

Query: 853 DTKLGPEEITRDIPNVSEEGLKN----------IDECGIICVGAEVNPGDILVGKITPKG 902
               G  E      +V      N          +D  G+  VG +V+  DI+V K++P  
Sbjct: 932 KLPNGLSERVVRPISVGSGNTGNRRFSFKNDSILDNDGVCNVGVQVSEDDIIVNKMSPIN 991

Query: 903 ESPM 906
               
Sbjct: 992 TREY 995


>gi|205277598|gb|ACI02066.1| RNA polymerase subunit B [Acinetobacter sp. 'isolate 30Bi']
          Length = 286

 Score =  355 bits (910), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 136/290 (46%), Positives = 186/290 (64%), Gaps = 5/290 (1%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I +     R++ +L GQ +  G    K+   L+ DL+S        +    DE +   
Sbjct: 1    FKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLTEDLLSGLELVDLLEIQPVDEGIAER 59

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRH
Sbjct: 60   LTQIQVFLKEKGIEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRH 119

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI  
Sbjct: 120  GNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDK 179

Query: 1155 LINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            ++   +    I+ LR FL+K+    G   E +    DD +L +++  + G+P++TPVFDG
Sbjct: 180  MLQQQRT---IAELRIFLDKIYNKVGGEQEDLDSLTDDEILALSKNLRKGIPLATPVFDG 236

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            ADE  I  +L +AD+  SGQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 237  ADEGQIKELLELADIPRSGQTVLFDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|124485982|ref|YP_001030598.1| DNA-directed RNA polymerase subunit B' [Methanocorpusculum labreanum
            Z]
 gi|124363523|gb|ABN07331.1| DNA-directed RNA polymerase, subunit B' [Methanocorpusculum labreanum
            Z]
          Length = 637

 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 116/585 (19%), Positives = 200/585 (34%), Gaps = 65/585 (11%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     ++ +A            + I   ++       +   E     R T     
Sbjct: 99   IEFIDAEEEDDLFIAVQESDLTPEHTHLEIDPSLILGIGAAHVPFPEHNASPRVTMGAGM 158

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+  D  G   +        +        G       +    AI   
Sbjct: 159  IKQALGFAQANMKLRP-DTRG--HMLHYAQVPMVHTQAAELIGSDNRPQGQNFCVAIISY 215

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + V   V     F R    +  R    + ++IEL   D         
Sbjct: 216  EGYNIEDALIFNKASVERGV-GRSHFFRTYEGEERRYPGGQVDRIELPEED--------- 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                      + G + +          +++ + +                +         
Sbjct: 266  ----------VQGSHGIGSYANLDVDGIINPETV--VNEKDVLIGKTSPPRFLEEPTGEL 313

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +  E  +        N+   +            R+VKV     R  + GDK A RHG KG
Sbjct: 314  IAVEKRRDTSITMRSNETGIVDTVIITESENSSRLVKVRTRDLRIPEIGDKFASRHGQKG 373

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +   I P E+MPF   G   D+V+NP  VPSRM +G + E   G A    G ++ +    
Sbjct: 374  VCGLITPQENMPFTAAGIAPDLVINPHAVPSRMTIGHMLEMIGGKAGALEGSRVNATSFR 433

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  I        +++      + +                              E+ 
Sbjct: 434  KTQVEKIFDSSFAQNRLLNDKEIGKDVKSSTLT-----------------------REQV 470

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L  A    +G+ ++YDG+TG  F   + +G IY  KL HMVS K++ARS G   ++
Sbjct: 471  LRHQLAEAGFAHTGREVMYDGITGRRFQADIYIGVIYYQKLYHMVSTKMHARSRGPVQVL 530

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYES 1331
            T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G   +Y++
Sbjct: 531  TRQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLDESDAVKQYVCARCGMVAMYDA 590

Query: 1332 -------IVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                   +  G   D +E     +F +L+ EM+++G++  L    
Sbjct: 591  KQKMTRCLACGAETDIYEVEMSYAFKLLLDEMKSMGIAPRLRLED 635



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 54/349 (15%), Positives = 107/349 (30%), Gaps = 35/349 (10%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G ++  Y    + +      ++S     +         ++ D       +     G   +
Sbjct: 16  GKVDDAYGFTRNFRQMRRSGHVSTEVNISYKDYSNEIVINTDRGRARRPLIVVENGVPAV 75

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            P +       +   +  ++   I F++                 + + +++     T +
Sbjct: 76  TPEDIEIVRSGAEDFMALVSQGKIEFID---------AEEEDDLFIAVQESDLTPEHTHL 126

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   +   G  I A      E   + R+ + +  G +  +         ++         
Sbjct: 127 EIDPSLILG--IGAAHVPFPEHNASPRVTMGA--GMIKQALGFAQANMKLRPDTRGHMLH 182

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q P+V                     +   G+N  VA + + GYN ED+++ ++  V 
Sbjct: 183 YAQVPMVH----------TQAAELIGSDNRPQGQNFCVAIISYEGYNIEDALIFNKASVE 232

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNP 890
             V  S     +E   R    G  +                   N+D  GII     VN 
Sbjct: 233 RGVGRSHFFRTYEGEERRYPGGQVDRIELPEEDVQGSHGIGSYANLDVDGIINPETVVNE 292

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            D+L+GK +P         E +            RDTS+ + S  +G V
Sbjct: 293 KDVLIGKTSPPRFLEEPTGELI-------AVEKRRDTSITMRSNETGIV 334


>gi|183584783|gb|ACC63834.1| RNA polymerase subunit B [Acinetobacter sp. NIPH 973]
 gi|310752599|gb|ADP09621.1| RNA polymerase subunit B [Acinetobacter sp. LUH 1471]
          Length = 286

 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 136/289 (47%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAARGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E +    DD +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KEQRTVLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584837|gb|ACC63861.1| RNA polymerase subunit B [Acinetobacter tjernbergiae]
          Length = 286

 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 134/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS+D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLTGQESNGG-GSTKRGDKLSADVLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E++    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|310752585|gb|ADP09614.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752587|gb|ADP09615.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752593|gb|ADP09618.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752595|gb|ADP09619.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
          Length = 286

 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L  D++S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLNGQESNGG-GSTKRGDKLVEDMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|310787933|gb|ADP24190.1| RNA polymerase subunit B [Acinetobacter soli]
          Length = 286

 Score =  354 bits (909), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 184/289 (63%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L  Q +  G    K+   LS D++S             DE +   +
Sbjct: 2    KIFEEAARERVVRLLTNQESNGGGTT-KRGDKLSEDMLSGLELVDLLDIQPTDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    I+ LR FL+K+    G   E +    D+ +L +A   + GVP++TPVFDGA
Sbjct: 181  LQQQRT---IAELRIFLDKIYNKVGGEQEDLDSLTDEEILVLAGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EENQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584833|gb|ACC63859.1| RNA polymerase subunit B [Acinetobacter gerneri]
          Length = 286

 Score =  354 bits (909), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS +L+S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEELLSGLELVDLLEIQPSDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDINGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    I+ LR FL+K+    G   E +    D+ +L ++   + GVP++TPVFDGA
Sbjct: 181  L---KEQRTIAELRVFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAELPRSGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|183584841|gb|ACC63863.1| RNA polymerase subunit B [Acinetobacter baylyi]
 gi|239949581|gb|ACS36587.1| RNA polymerase subunit B [Acinetobacter baylyi]
          Length = 286

 Score =  354 bits (909), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 134/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S             DE +   +
Sbjct: 2    KIFEEAARERIVRLLNGQESNGGGTT-KRGDKLSDDVLSGLELVDLLDIQPTDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    I+ LR FL+K+    G   E++    D+ +L +A   + GVP++TPVFDGA
Sbjct: 181  LQQQRT---IAELRIFLDKIYNKVGGEQEELDTLTDEEILVLAGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584831|gb|ACC63858.1| RNA polymerase subunit B [Acinetobacter bouvetii]
          Length = 286

 Score =  354 bits (908), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 185/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS +++S    +   +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEEVLSGLELADLLEIQPTDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG KI  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E +    DD +L ++   ++GVP++TPVFDGA
Sbjct: 181  M---KEQRTVLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|95020417|gb|ABF50733.1| RNA polymerase beta subunit [Entomoplasma luminosum]
          Length = 595

 Score =  354 bits (908), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 226/421 (53%), Positives = 311/421 (73%), Gaps = 9/421 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L
Sbjct: 1   DQINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVV-YLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           +++A+VN YGFI TPYRKV +G + ND++ YL+A EE N  I+QA    D++G+   + V
Sbjct: 61  STYAKVNEYGFITTPYRKVINGVIQNDIIDYLTADEEHNFIISQAGVKQDDNGTILNKTV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE+++   +++D+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+ 
Sbjct: 121 VARFRGEDMVANIDEVDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIN 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P VGTG+E   A+ SGAA+VA  +GI + VD+  I I         S  G+  Y L 
Sbjct: 181 PESPIVGTGIEFEAARDSGAAVVALESGIAKYVDSKLITI--------ESKKGIKTYELS 232

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F RSN  T +   P++KVGD+V +  IIADGPS + G+LA+G+N++VAF  ++GYNFED
Sbjct: 233 DFDRSNNGTALVHSPIIKVGDQVEKGQIIADGPSMEQGELAIGQNVVVAFTTYNGYNFED 292

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V ED FTSIHI+E+ +  R+TK+G EEITR+IPNVSE+  K +D  GI+  G
Sbjct: 293 AVIMSERVVMEDKFTSIHIDEYVIERRNTKIGIEEITREIPNVSEQAKKFLDADGIVAPG 352

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            EV  GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F
Sbjct: 353 TEVKVGDILVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQTIKRF 412

Query: 946 N 946
           +
Sbjct: 413 S 413



 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 126/420 (30%), Positives = 177/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            II VG +V  G I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 248  IIKVGDQVEKGQIIADGPS-MEQGELAIGQNVVVAFTTYNGYNFEDAVIMSERVVMEDKF 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I++    I +E    E       A+   D   I+      ++ +IL G+  
Sbjct: 307  TSIHIDEYVIERRNTKIGIEEITREIPNVSEQAKKFLDADGIVAPGTEVKVGDILVGKVT 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E +                 
Sbjct: 367  PKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQTI------------- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P GVL V+KV+V  KR IQ GDKM+GRHGNKG++S+IL  EDMP L+DG
Sbjct: 410  KRFSAADGFDLPAGVLEVIKVYVVQKRKIQEGDKMSGRHGNKGVISKILSIEDMPHLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +     ++  +       
Sbjct: 470  TPVDILLNPQGIPSRMNIGQILELHLGMAAQKLGVKIATPVFEGLTATELDEIMEEAGMT 529

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                DGA                     
Sbjct: 530  NFGKVKLI----------------------------DGA--------------------- 540

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TG+  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 541  -----TGDVMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 595


>gi|310752559|gb|ADP09601.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
          Length = 286

 Score =  354 bits (908), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 135/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS DL+S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    DD +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEILVLSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|124007163|gb|ABM87943.1| RNA polymerase beta subunit [Enterobacter aerogenes]
          Length = 315

 Score =  354 bits (908), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 165/323 (51%), Positives = 224/323 (69%), Gaps = 13/323 (4%)

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            +E   ++RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+
Sbjct: 1    QELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGET 60

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +TPEEKLLRAIFGEKA DV+D+SLRVP+GVSGTV+DV++F R G++K++R++ +E  Q+
Sbjct: 61   QLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQL 120

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            +   +D  +E  IL+  ++SR+  +L                   +D + + PR +W + 
Sbjct: 121  KQAKKDLSEELQILEAGLFSRIYAVLVAGGV-------------EADKLDKLPRDRWLEL 167

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             + DE+ Q  +E L  QY+  K   E + + K  KI  GDD+ PGVL++VKV++A+KR I
Sbjct: 168  GLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRI 227

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKG++S+I P EDMP   +GTPVDIVLNPLGVPSRMN+GQI ETHLG A
Sbjct: 228  QPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMA 287

Query: 1145 CVGLGKKIKSLINDYKANGDISP 1167
              G+G KI +++   +    +  
Sbjct: 288  AKGIGDKINAMLKQQQEVAKLRE 310


>gi|183584775|gb|ACC63830.1| RNA polymerase subunit B [Acinetobacter sp. NIPH 817]
 gi|310752597|gb|ADP09620.1| RNA polymerase subunit B [Acinetobacter sp. LUH 1470]
          Length = 286

 Score =  354 bits (908), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L  D++S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLKGQESNGG-GSTKRGDKLVEDMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584787|gb|ACC63836.1| RNA polymerase subunit B [Acinetobacter schindleri]
          Length = 286

 Score =  354 bits (908), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 182/289 (62%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S             DE +   +
Sbjct: 2    KIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLDIQPVDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    DD +L ++   + GVP++TPVFDGA
Sbjct: 181  LQEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|270119515|emb|CAY90190.2| RNA polymerase subunit B [Acinetobacter sp. G30]
          Length = 283

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 135/287 (47%), Positives = 187/287 (65%), Gaps = 5/287 (1%)

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            R    R++ +L  Q +  G    K+   L+ DL+S        +    DE +   +  ++
Sbjct: 1    RAARERIVRLLKDQQSNGG-GNTKRGDKLTEDLLSHLALVDLLEIQPNDEAIAERLTQIQ 59

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+
Sbjct: 60   VFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGV 119

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   
Sbjct: 120  VSHILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKMV--- 176

Query: 1160 KANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            K    I+ LR FL+K+    G   E++    D+ ++++A   ++GVP++TPVFDGA+E  
Sbjct: 177  KQQRTIAELREFLDKIYNKVGGEQEQLDTLTDEEIMKLAGNLRAGVPLATPVFDGAEEGQ 236

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            I  +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V D
Sbjct: 237  IKELLELAELPRSGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVDD 283


>gi|290751450|emb|CAQ16386.1| RNA polymerase beta subunit [Pseudomonas sp. R-33145]
          Length = 362

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 213/362 (58%), Positives = 279/362 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  B  S ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDXNBPXSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASAAMNDKNELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI E   +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIXELTCVARD 360

Query: 854 TK 855
           TK
Sbjct: 361 TK 362


>gi|239949583|gb|ACS36588.1| RNA polymerase subunit B [Acinetobacter baylyi]
          Length = 286

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S             DE +   +
Sbjct: 2    KIFEEAARERIVRLLNGQESNGGGTT-KRGDKLSDDVLSGLELVDLLDIQPTDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   +    I+ LR FL+K+    G   +++    D+ +L +A   + GVP++TPVFDGA
Sbjct: 181  LQQQRT---IAELRIFLDKIYNKVGGEQKELDTLTDEEILVLAGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  +GQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAELPRTGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|209360647|gb|ACI42994.1| RNA polymerase beta subunit [Mycoplasma conjunctivae]
          Length = 665

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 233/493 (47%), Positives = 328/493 (66%), Gaps = 9/493 (1%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKER-ISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           N+R+ SVGE+L+NQ+ + L ++E++ KE+  S  + D +  + +IN KP+ +    FF S
Sbjct: 3   NKRIVSVGELLQNQFLIALSKIEKNTKEKISSKGESDKITVKTVINNKPIYNQFKNFFNS 62

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  E +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG N
Sbjct: 63  SKLSQFMEQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHATHYGRICPVETPEGQN 122

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           IGL+ + + FA+ N YGFI TPY KV +  V  +   +L+A EE     AQ++ +++E  
Sbjct: 123 IGLILNFSVFAKTNPYGFILTPYYKVTNKVVDYSKPHWLTAAEEFGLAFAQSSIAINEKN 182

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               + V  R     ++V   ++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQR
Sbjct: 183 EIIADKVTVRKNQTYLVVDASQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQR 242

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLLK+EAP V TG+ES VA  S   I ++  G+V  VDA +IVI   E         
Sbjct: 243 QAVPLLKSEAPLVATGIESDVALYSSTNIRSEVDGVVSFVDAKKIVITDYEDKQ------ 296

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y L  F++SNQ T + Q P+VKVG  + + D+I DGPSTD G+LALG+N+LVAF  W
Sbjct: 297 -HTYFLRYFEKSNQETLIIQHPIVKVGQTINKGDLICDGPSTDNGELALGKNVLVAFSTW 355

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
           +GYN+ED+++ISE++V +DVFTSIHI+E  +  R +K G + +T D+PN S     ++D 
Sbjct: 356 YGYNYEDAIIISEKLVKDDVFTSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDA 415

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+ +G+EVN GDILVG+ +PKGE   TPE+KL+ AI+G+K +  +DTSLRV  G  GT
Sbjct: 416 NGIVRIGSEVNTGDILVGRTSPKGEDNPTPEDKLMSAIWGKKTLQQKDTSLRVKHGEGGT 475

Query: 939 VVDVRIFNRHGID 951
           V+DV+I +R   D
Sbjct: 476 VIDVQIISRDLGD 488



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 136/415 (32%), Positives = 188/415 (45%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +N GD++    +      +   + +L A       +  D  +     V   V 
Sbjct: 318  IVKVGQTINKGDLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 376

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    K   S +        L    +  +  LD N   R+   +   + + G  
Sbjct: 377  -TSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDANGIVRIGSEVNTGDILVGRT 435

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W +  +Q +     V+  +        I+           
Sbjct: 436  SPKGEDNPTPE--DKLMSAIWGKKTLQQKDTSLRVKHGEGGTVIDVQIISRDL------- 486

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++  GV  +VKV VA KR I+ GDKMAGRHGNKG+VS +LP EDMPFL+DGTPVDI
Sbjct: 487  --GDNLEDGVGMIVKVLVAQKRKIKVGDKMAGRHGNKGVVSIVLPVEDMPFLEDGTPVDI 544

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG+A   L  K  + + D      +  L            
Sbjct: 545  LLNPQGVPSRMNIGQVLELHLGFAAKKLNTKFVTPVFDGIKLETMQELFR---------- 594

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 595  --------------------EAGIP------------------------ESGKFTLYDGI 610

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD  V+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 611  TGQPFDNKVSVGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFG 665


>gi|183584803|gb|ACC63844.1| RNA polymerase subunit B [Acinetobacter venetianus]
 gi|187710936|gb|ACD14071.1| RNA polymerase subunit B [Acinetobacter venetianus]
 gi|187710938|gb|ACD14072.1| RNA polymerase subunit B [Acinetobacter venetianus]
 gi|187710942|gb|ACD14074.1| RNA polymerase subunit B [Acinetobacter venetianus]
          Length = 286

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEDVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E+++   D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELRDFLDKIYNKVGGEQEELNSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584745|gb|ACC63815.1| RNA polymerase subunit B [Acinetobacter parvus]
          Length = 286

 Score =  353 bits (907), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS++++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSAEVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|83699913|gb|ABC40933.1| RNA polymerase beta subunit [Mesoplasma tabanidae]
          Length = 598

 Score =  353 bits (907), Expect = 9e-95,   Method: Composition-based stats.
 Identities = 218/416 (52%), Positives = 300/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV +G + N+  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVINGVIQNEHEYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  IVA   GIV+ VDA +I +         S +G+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCIVATENGIVKYVDAKQITV--------ESKAGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD V    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSVEAGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D  GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVK 408



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 179/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSVEAGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIELPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSTDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|52694365|emb|CAG38022.1| RNA polymerase beta subunit [Pseudomonas viridiflava]
          Length = 368

 Score =  353 bits (907), Expect = 9e-95,   Method: Composition-based stats.
 Identities = 217/367 (59%), Positives = 285/367 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IA+A++++++     +ELV  R   E  +     +  +D SPKQVVS
Sbjct: 122 IVFLSAIEEADHVIARASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVS 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+  G  +VA+R G
Sbjct: 182 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDFGVCVVARRGG 241

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI
Sbjct: 242 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDI 301

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARD
Sbjct: 302 MADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARD 361

Query: 854 TKLGPEE 860
           TKLGP+E
Sbjct: 362 TKLGPKE 368


>gi|209360651|gb|ACI42996.1| RNA polymerase beta subunit [Mycoplasma amphoriforme A39]
          Length = 760

 Score =  353 bits (907), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 233/501 (46%), Positives = 333/501 (66%), Gaps = 29/501 (5%)

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS--------------------VMP 500
           N+R++ + E+L+ + + G+LR+ER IK++++  D  +                    +  
Sbjct: 1   NKRLKLINELLRTRVQTGMLRIERHIKDKLAIADGANKNTEFNEITGEFEEVEKPTRLTI 60

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           + +IN+KP    + +FF + QL+Q  +  N L+ +T+ RR+SA+G GG++R    +++RD
Sbjct: 61  KSVINSKPFQLVIKDFFNTHQLTQFLDQQNPLAELTNKRRISAMGPGGISREDPNLDIRD 120

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VH +HYGRICP ET EG NIGL+ SL  +A ++  GF+  PY KV DG +T+ V  L+A+
Sbjct: 121 VHYSHYGRICPIETPEGFNIGLIMSLAFYAEIDQNGFLMAPYYKVKDGVITDQVEKLTAL 180

Query: 621 EEENRYIAQANS--SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            E+   IA+A++   +D +G   ++ +  R    + L   +++D+ID +PKQVVSIA +L
Sbjct: 181 REDEYIIAEASASMKVDANGKIKDQGIIARYRSSQELYDPKQVDYIDVAPKQVVSIATNL 240

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDDS+R LMG NMQRQA PLLK  AP VGTG+E  +A  SG  I+AK  G V  V
Sbjct: 241 IPFLENDDSSRALMGANMQRQATPLLKPYAPVVGTGVEYKIAHDSGMVILAKNGGEVSYV 300

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           D+ +IVI++ EG  D        Y L+KFQ+SNQNT  NQ P+V VG++V +   IADG 
Sbjct: 301 DSHKIVIKTKEGTED-------YYSLIKFQKSNQNTSYNQVPIVTVGEKVEKFQTIADGA 353

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +   G+LALG+N+LVAF  W GYN+ED+++IS+R++ EDV+TSI I E  V    TK G 
Sbjct: 354 AMHNGELALGQNVLVAFTTWRGYNYEDAIIISDRLLKEDVYTSISINEHVVQCVRTKNGD 413

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV +E    +DE G+I +GAEV  GDILVGKI+PKG+  ++ EEKLL+AIFG
Sbjct: 414 EEITRDIPNVPDEAKLYLDEDGVIMIGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIFG 473

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
           EK  ++R++SL+VP G  G V
Sbjct: 474 EKTKNIRESSLKVPHGGDGVV 494



 Score =  340 bits (873), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 143/526 (27%), Positives = 234/526 (44%), Gaps = 49/526 (9%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV--SEDVFTSIHIEEFEVMARDTKLG 857
                       +L  + P  G   E  +     MV  +++     +++  +++ + TK G
Sbjct: 254  MGANMQRQATPLLKPYAPVVGTGVEYKIAHDSGMVILAKNGGEVSYVDSHKIVIK-TKEG 312

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
             E+    I         + ++  I+ VG +V      +          +   + +L A  
Sbjct: 313  TEDYYSLIKFQKSNQNTSYNQVPIVTVGEKVE-KFQTIADGAAMHNGELALGQNVLVAFT 371

Query: 918  GEKAVDVRDTSLRVPSGVSGTV-----VDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
              +  +  D  +     +   V     ++  +         +  I+ +   +   A+   
Sbjct: 372  TWRGYNYEDAIIISDRLLKEDVYTSISINEHVVQCVRTKNGDEEITRDIPNVPDEAKLYL 431

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  ++      +  +IL G+ +  G         L   +  E  ++           ++
Sbjct: 432  DEDGVIMIGAEVKEGDILVGKISPKGQVDLSAEEKLLQAIFGEKTKN-----------IR 480

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             +   +    +   + +          I  GD++   V+ +VKV++  KR IQ GDK+AG
Sbjct: 481  ESSLKVPHGGDGVVAAVH------RFNIARGDELGDDVIELVKVYIVQKRKIQIGDKLAG 534

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC------- 1145
            RHGNKGIVS+I+P EDMP L+DGTP+DIVLNPLGVPSRMN+GQIFE HLG A        
Sbjct: 535  RHGNKGIVSKIVPREDMPHLEDGTPIDIVLNPLGVPSRMNIGQIFELHLGLAARQIAQQE 594

Query: 1146 -----------VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
                         L K         K+    +        +        KI   D D +L
Sbjct: 595  LIKATFSHDGDKTLAKLFGLTSLGAKSLIKAAKEHCKSRNIKTHEEAINKIKAIDVDVIL 654

Query: 1195 RVAEQWKSGV--PVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPV 1249
            +     +  +   ++TPVF+G +   + +++  A +D     G+  L DG TGEPF++P+
Sbjct: 655  KQVGMSRDDLSYKIATPVFEGVNMNDLRTVMAEAGIDTEKTHGKFKLIDGRTGEPFEKPI 714

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +VG +YMLKL+HMV DKV++R+ G YS +TQQPLGG+S  GGQR G
Sbjct: 715  SVGVMYMLKLDHMVDDKVHSRAVGPYSKITQQPLGGRSQMGGQRFG 760


>gi|187710940|gb|ACD14073.1| RNA polymerase subunit B [Acinetobacter venetianus]
          Length = 286

 Score =  353 bits (907), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 188/289 (65%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEDVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKGYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E+++   D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELRDFLDKIYNKVGGEQEELNSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|312062816|emb|CAS03782.1| RNA polymerase beta subunit [Pseudomonas fluorescens]
          Length = 356

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 214/355 (60%), Positives = 276/355 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPE
Sbjct: 302 LALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPE 356


>gi|183584743|gb|ACC63814.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584773|gb|ACC63829.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584785|gb|ACC63835.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584793|gb|ACC63839.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584819|gb|ACC63852.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584821|gb|ACC63853.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584827|gb|ACC63856.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584843|gb|ACC63864.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
 gi|183584847|gb|ACC63866.1| RNA polymerase subunit B [Acinetobacter gyllenbergii]
          Length = 286

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEDVLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG K++ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKLEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KEQRTVLELRDFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|73697673|gb|AAZ81453.1| RNA polymerase beta subunit [Mycoplasma yeatsii GM274B]
          Length = 595

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 225/415 (54%), Positives = 309/415 (74%), Gaps = 9/415 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARV+ YGFI TPYRKV +     + V YL+A +E    IAQ+N   DE+G   +E+V  R
Sbjct: 61  ARVDEYGFITTPYRKVVNGVIQNDQVEYLTADKERKFVIAQSNVKQDENGKILDEMVVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G++ +   ++ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++ E+
Sbjct: 121 FNGDDYMARIDEIDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIRPES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTG+E   A+ SG A+VAK  GIV+ VD+  I I+          SG+  Y L  F+
Sbjct: 181 PFVGTGIEFEAARDSGEAVVAKEDGIVKYVDSKMISIQ--------GESGIKTYTLSDFE 232

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T + Q P+VK GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED+++
Sbjct: 233 RSNNGTSLTQAPIVKKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIV 292

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +D FTSIHI+E+ +  R+TK G EE+TR++PNVSE+  K++D  GI+ +G EV
Sbjct: 293 MSERVVMDDRFTSIHIDEYTIEVRNTKQGLEEVTREVPNVSEQAKKHLDSEGIVAIGTEV 352

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++
Sbjct: 353 KVGDILVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIK 407



 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 122/418 (29%), Positives = 178/418 (42%), Gaps = 72/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 245  IVKKGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVMSERVVMDDRF 303

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+       +E    E       A+   D + I+      ++ +IL G+  
Sbjct: 304  TSIHIDEYTIEVRNTKQGLEEVTREVPNVSEQAKKHLDSEGIVAIGTEVKVGDILVGKVT 363

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E +    +        RFK 
Sbjct: 364  PKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--------RFKA 411

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  ++ V+KV++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+DG
Sbjct: 412  KSASNPDGIDLPADIVEVIKVYIVQKRKIQEGDKMSGRHGNKGIISRILPVEDMPHLEDG 471

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   + +KI + + +     ++  + +     
Sbjct: 472  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKINEKIITPVFEGLNEKELDEIMAEAGMT 531

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    G+  
Sbjct: 532  NYGKVTLI-----------------------------------------------DGK-- 542

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                 TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR
Sbjct: 543  -----TGEAIDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGKAQNGGQR 595


>gi|183584829|gb|ACC63857.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752581|gb|ADP09612.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752583|gb|ADP09613.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752589|gb|ADP09616.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
          Length = 286

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 185/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L   ++S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLNGQESNGG-GSTKRGDKLVDGMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584825|gb|ACC63855.1| RNA polymerase subunit B [Acinetobacter genomosp. 14BJ]
          Length = 286

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 133/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L+ D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLTEDVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KEQRTVIELREFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|310752579|gb|ADP09611.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
 gi|310752591|gb|ADP09617.1| RNA polymerase subunit B [Acinetobacter calcoaceticus]
          Length = 286

 Score =  353 bits (906), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 132/289 (45%), Positives = 185/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L   ++S        +    DE +   +
Sbjct: 2    KIFEEAARERVIRLLNGQESNGG-GSTKRGDKLVEGMLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|270119513|emb|CAY90189.2| RNA polymerase subunit B [Acinetobacter sp. A1PC16]
          Length = 282

 Score =  353 bits (905), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 134/284 (47%), Positives = 186/284 (65%), Gaps = 5/284 (1%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              R++ +L  Q +  G    K+   L+ DL+S        +    DE +   +  ++V  
Sbjct: 2    RERIVRLLKDQQSNGG-GNTKRGDKLTEDLLSHLALVDLLEIQPNDEAIAERLTQIQVFL 60

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS 
Sbjct: 61   KEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSN 120

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   K  
Sbjct: 121  ILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKMV---KQQ 177

Query: 1163 GDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              I+ LR FL+K+    G   E++    D+ ++++A   ++GVP++TPVFDGA+E  I  
Sbjct: 178  RTIAELREFLDKIYNKVGGEQEQLDTLTDEEIMKLAGNLRAGVPLATPVFDGAEEGQIKE 237

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +L +A+L  SGQ++LYDG TGE FDRPVTVGY+YMLKLNH+V D
Sbjct: 238  LLELAELPRSGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVDD 281


>gi|183584797|gb|ACC63841.1| RNA polymerase subunit B [Acinetobacter genomosp. 15BJ]
 gi|183584801|gb|ACC63843.1| RNA polymerase subunit B [Acinetobacter genomosp. 16BJ]
          Length = 286

 Score =  353 bits (905), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 131/289 (45%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L+ D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLAEDVLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG K++ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKLEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VLELRDFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584795|gb|ACC63840.1| RNA polymerase subunit B [Acinetobacter genomosp. 14TU]
          Length = 286

 Score =  353 bits (905), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 134/289 (46%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEDVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    +  LR FL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  L---KEQRTVIELREFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|183584755|gb|ACC63820.1| RNA polymerase subunit B [Acinetobacter radioresistens]
          Length = 286

 Score =  353 bits (905), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 136/289 (47%), Positives = 186/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L  Q +  G    K+   LS +L+S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKDQVSNGG-GNTKRGEKLSEELLSGLELIDLLEIQPSDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTHGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS+ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NKGVVSQILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            +   K    I  LR FL+K+    G   E++    DD +L++A     GVP++TPVFDGA
Sbjct: 181  L---KQQRAIVELRDFLDKIYNKVGGEQEQLDTLTDDEILKLAGNLSKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +A+L  SGQ IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EEGQIKELLELAELPRSGQQILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|83699895|gb|ABC40924.1| RNA polymerase beta subunit [Mesoplasma chauliocola]
 gi|83699897|gb|ABC40925.1| RNA polymerase beta subunit [Mesoplasma chauliocola]
 gi|83699899|gb|ABC40926.1| RNA polymerase beta subunit [Mesoplasma grammopterae]
          Length = 598

 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 217/416 (52%), Positives = 300/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV +G + N+  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVINGVIQNEHEYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  IVA   GIV+ VDA +I +         S +G+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCIVATENGIVKYVDAKQITV--------ESKAGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD +    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSIEAGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D  GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVK 408



 Score =  298 bits (762), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 179/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSIEAGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSNDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|302703651|gb|ADL62672.1| RNA polymerase beta subunit [Mycoplasma fastidiosum]
          Length = 754

 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 222/526 (42%), Positives = 336/526 (63%), Gaps = 21/526 (3%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI-------------SSVDIDSVMPQDLI 504
           +LGN+R+R + E+L N+ ++ LLR+E+ I+E++             +  + + +  + LI
Sbjct: 1   HLGNKRMRLISELLCNRIQIALLRIEKFIREKMAASEVKMKNISLKNEGNTEQISVKSLI 60

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N KP    + EFF S QL+Q  +  N LS +T+ RR+SA+G GG+ R    +++RDVH +
Sbjct: 61  NTKPFQIIIKEFFNSHQLTQFIDQQNPLSELTNKRRISAMGPGGINRDDPNLDIRDVHYS 120

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           +YGRICP ET EG NIGL+ SL ++++++  GFI +PY KV +G +T+++ +L+A+ E+ 
Sbjct: 121 NYGRICPIETPEGMNIGLIMSLATYSQIDELGFITSPYYKVRNGVITDEIHWLTALREDE 180

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             I +A S  D+        V  R          + +D+ID +P QVVSI+ + IPFLEN
Sbjct: 181 YVITEAISPRDKKNKLLSP-VNARYRSFIESFEAKDVDYIDVNPCQVVSISTASIPFLEN 239

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQA PLL+  AP VGTG+E  +A+ SG A+VA+  GIV   D   + 
Sbjct: 240 DDANRALMGANMQRQATPLLRPYAPIVGTGLEYPIARDSGMALVAEEDGIVVAADGESLS 299

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R        +      + L+KF+RSNQ+T   Q P+V+ G+ +++  ++ADGP+   G+
Sbjct: 300 VRYE------NLGVNRCHHLVKFKRSNQDTSNTQTPIVRAGEAIQKGQVLADGPAMQNGE 353

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N+LVAF  W GYN+ED++++S R+V +D+FTSIHI+E  +    TK G EEITR 
Sbjct: 354 LALGQNVLVAFTTWSGYNYEDAIVLSSRLVQDDLFTSIHIDEHTIECLRTKNGDEEITRQ 413

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPN+S++  + +DE G+I VGAEV  GDILVGK +PK +   + EEKLL+AIF EK   V
Sbjct: 414 IPNISDDAKRYLDEDGVIIVGAEVYEGDILVGKTSPKAQVEQSSEEKLLQAIFSEKVKQV 473

Query: 925 RDTSLRVPSGVSGTVVDVRIFN-RHGIDKNERSISVEREQIELLAR 969
           +D+SL+VP G  G V  V+ F+ + G + N+  I + +  +    +
Sbjct: 474 KDSSLKVPHGGEGVVAAVKRFSVQSGNELNDDVIEIIKVFVAQKRK 519



 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 153/521 (29%), Positives = 231/521 (44%), Gaps = 38/521 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L  + P  G   E  +       +V+E+    +  +   +  R   LG
Sbjct: 247  MGANMQRQATPLLRPYAPIVGTGLEYPIARDSGMALVAEEDGIVVAADGESLSVRYENLG 306

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   +         +  +  I+  G  +  G +L           +   + +L A  
Sbjct: 307  VNRCHHLVKFKRSNQDTSNTQTPIVRAGEAIQKGQVLADGP-AMQNGELALGQNVLVAFT 365

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D  +     V   +      + H I+   R+ + + E    +    DD +  
Sbjct: 366  TWSGYNYEDAIVLSSRLVQDDLFTSIHIDEHTIEC-LRTKNGDEEITRQIPNISDDAKRY 424

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +       I+ G     G     K++  +    S   +     F+ + ++V+ +   
Sbjct: 425  LDED-----GVIIVGAEVYEGDILVGKTSPKAQVEQSSEEKLLQAIFSEKVKQVKDSSLK 479

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +    E   + +      K   +Q G+++   V+ ++KVFVA KR IQ GDKMAGRHGNK
Sbjct: 480  VPHGGEGVVAAV------KRFSVQSGNELNDDVIEIIKVFVAQKRKIQMGDKMAGRHGNK 533

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL--------- 1148
            GIVSRI+P EDMP L+DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   L         
Sbjct: 534  GIVSRIVPMEDMPHLEDGTPVDILLNPLGVPSRMNIGQVLEMHLGLAGRKLVLRELIKAY 593

Query: 1149 ---------GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
                     G+       +                +       EK+SD +   +L+    
Sbjct: 594  FNNTPTTQIGQMFGLRETNVVNLLKNFKEHIDEININTEKQALEKLSDVNLTMILKQTGL 653

Query: 1200 WKSGV--PVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYI 1254
                +   +STPVF G +   +  +++ A LD +   G+  LYDG TGE F+RP++VG  
Sbjct: 654  LTEDLIYKISTPVFSGVNHTDLIEIMKEAGLDPTINKGKFDLYDGRTGEKFERPISVGIS 713

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            YMLKL+HMV DK++ARS G YS +TQQPLGGKS  GGQR G
Sbjct: 714  YMLKLDHMVDDKIHARSVGPYSKITQQPLGGKSQNGGQRFG 754


>gi|318602995|emb|CBJ04575.1| RNA polymerase beta subunit [Pseudomonas sp. R-37194]
          Length = 357

 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 211/356 (59%), Positives = 275/356 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           +ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTC 356


>gi|83699933|gb|ABC40943.1| RNA polymerase beta subunit [Entomoplasma melaleucae]
          Length = 594

 Score =  352 bits (904), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 226/420 (53%), Positives = 310/420 (73%), Gaps = 9/420 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVV-YLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGFI TPYRKV +G + ND++ YL+A EE N  I+QA    D++G+   + V 
Sbjct: 61  TYAKVNEYGFITTPYRKVINGVIQNDIIDYLTADEEHNFIISQAGVKQDDNGTILNKTVV 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE+++   +++D+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARFRGEDMVANIDEVDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SGAA+VA  +GI + VD+  I I         S  G+  Y L  
Sbjct: 181 ESPIVGTGIEFEAARDSGAAVVALESGIAKYVDSKLITI--------ESKKGIKTYELSD 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F RSN  T +   P++KVGD+V +  IIADGPS + G+LA+G+N++VAF  ++GYNFED+
Sbjct: 233 FDRSNNGTALVHSPIIKVGDQVEKGQIIADGPSMEQGELAIGQNVVVAFTTYNGYNFEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V ED FTSIHI+E+ +  R+TK+G EEITR+IPNVSE+  K +D  GI+  G 
Sbjct: 293 VIMSERVVMEDKFTSIHIDEYVIERRNTKIGIEEITREIPNVSEQAKKFLDADGIVAPGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQTIKRFS 412



 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 126/420 (30%), Positives = 177/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            II VG +V  G I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 247  IIKVGDQVEKGQIIADGPS-MEQGELAIGQNVVVAFTTYNGYNFEDAVIMSERVVMEDKF 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I++    I +E    E       A+   D   I+      ++ +IL G+  
Sbjct: 306  TSIHIDEYVIERRNTKIGIEEITREIPNVSEQAKKFLDADGIVAPGTEVKVGDILVGKVT 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E +                 
Sbjct: 366  PKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQTI------------- 408

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P GVL V+KV+V  KR IQ GDKM+GRHGNKG++S+IL  EDMP L+DG
Sbjct: 409  KRFSAADGFDLPAGVLEVIKVYVVQKRKIQEGDKMSGRHGNKGVISKILSIEDMPHLEDG 468

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +     ++  +       
Sbjct: 469  TPVDILLNPQGIPSRMNIGQILELHLGMAAQKLGVKIATPVFEGLTATELDEIMEEAGMT 528

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                DGA                     
Sbjct: 529  NFGKVKLI----------------------------DGA--------------------- 539

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TG+  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 540  -----TGDVMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 594


>gi|83699905|gb|ABC40929.1| RNA polymerase beta subunit [Mesoplasma entomophilum]
 gi|83699907|gb|ABC40930.1| RNA polymerase beta subunit [Mesoplasma entomophilum]
 gi|83699909|gb|ABC40931.1| RNA polymerase beta subunit [Mesoplasma entomophilum]
 gi|83699911|gb|ABC40932.1| RNA polymerase beta subunit [Mesoplasma syrphidae]
          Length = 598

 Score =  352 bits (903), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 218/416 (52%), Positives = 300/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV DG + N+  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVIDGVIQNEHEYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  IVA   GIV+ VDA +I +         S +G+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCIVAAENGIVKYVDAKQITV--------ESKAGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD +    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSIEAGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D  GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVK 408



 Score =  298 bits (762), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 179/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSIEAGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSNDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|183584799|gb|ACC63842.1| RNA polymerase subunit B [Acinetobacter genomosp. 17BJ]
          Length = 286

 Score =  352 bits (903), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 134/289 (46%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   L+ D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLKGQESNGG-GSTKRGDKLAEDVLSGLELVDLLEIQPTDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E++    D  VL ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VIELREFLDKIYNKVGGEQEELDSLTDAEVLALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ+IL+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTILFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|83699921|gb|ABC40937.1| RNA polymerase beta subunit [Mesoplasma corruscae]
          Length = 598

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 215/454 (47%), Positives = 316/454 (69%), Gaps = 9/454 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY +V +G +  +  YL+A +E++  I+Q+N + DE     ++ V  
Sbjct: 61  TYAVVDDLGFITTPYLRVQNGVIQEEYDYLTADQEKDFVISQSNVNKDESNKILDKTVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +   E++ +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIANIEEVQYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIAPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTG+E   A+ SG A+VA ++G+V+ VD+ +I + S +        G   Y L  F
Sbjct: 181 APIVGTGIEFEAARDSGVAVVAAQSGVVKYVDSTQINVESKD--------GFKTYSLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  + + Q+P+VKVGD+V+  +IIADGPS D G+LA+G+N++VAF  ++GYNFED++
Sbjct: 233 DRSNNGSSIVQKPIVKVGDKVKAGEIIADGPSIDQGELAIGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IP VSE   K +D  GI+ +G E
Sbjct: 293 VMSERIIQEDKFTSVHIDEYVLEVRNTKQGLEEITSEIPQVSENAKKYLDSEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDIL+GK+TPKG+S ++PE+KLL AIFGEK+  V+D SLRVP+G  G V  ++ F +
Sbjct: 353 VKTGDILIGKVTPKGQSQLSPEDKLLHAIFGEKSRSVKDNSLRVPNGGEGIVQSIKRF-K 411

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
                N   I +  + +E++      ++ I + +
Sbjct: 412 AKSASNPDGIELSADVLEVIKIYIVQKRKIQEGD 445



 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 123/420 (29%), Positives = 182/420 (43%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  G+I+    +   +  +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDKVKAGEIIADGPS-IDQGELAIGQNVVVAFTTYNGYNFEDAIVMSERIIQEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++       +E       Q+   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGLEEITSEIPQVSENAKKYLDSEGIVAIGTEVKTGDILIGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          +V    E +    +        RFK 
Sbjct: 365  PKGQSQLSPEDKLLHAIFGEKSRS----VKDNSLRVPNGGEGIVQSIK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++   VL V+K+++  KR IQ GDKM+GRHGNKGI+S+ILP EDMP L+DG
Sbjct: 413  KSASNPDGIELSADVLEVIKIYIVQKRKIQEGDKMSGRHGNKGIISKILPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGLPSRMNFGQILEIHLGMAAKKLGVKIATPVFEGVNSQDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ+ 
Sbjct: 533  NYGKVTLI-----------------------------------------------DGQT- 544

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GE  D+P++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  ------GEAIDKPISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|73697643|gb|AAZ81438.1| RNA polymerase beta subunit [Mycoplasma cottewii]
          Length = 595

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 225/415 (54%), Positives = 308/415 (74%), Gaps = 9/415 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARV+ YGFI TPYRKV +     + V YL+A +E    IAQ+N   DE+G   +E+V  R
Sbjct: 61  ARVDEYGFITTPYRKVINGVIQNDQVEYLTADKERKFIIAQSNVKQDENGKILDEIVVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G++ +   ++ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++ E+
Sbjct: 121 FNGDDYMARIDEIDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIRPES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTG+E   A+ SG A+VAK  GIV+ VD+  I I           SG+  Y L  F+
Sbjct: 181 PFVGTGIEFEAARDSGEAVVAKEDGIVKYVDSKMISI--------EGQSGIKTYTLSDFE 232

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T + Q P+VK GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED+++
Sbjct: 233 RSNNGTSLTQAPIVKKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIV 292

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +D FTSIHI+E+ +  R+TK G EE+TR++PNVSE+  K++D  GI+ +G EV
Sbjct: 293 MSERVVMDDRFTSIHIDEYTIEVRNTKQGLEEVTREVPNVSEQAKKHLDSEGIVAIGTEV 352

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++
Sbjct: 353 KVGDILVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIK 407



 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 122/418 (29%), Positives = 178/418 (42%), Gaps = 72/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 245  IVKKGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVMSERVVMDDRF 303

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+       +E    E       A+   D + I+      ++ +IL G+  
Sbjct: 304  TSIHIDEYTIEVRNTKQGLEEVTREVPNVSEQAKKHLDSEGIVAIGTEVKVGDILVGKVT 363

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           +V    E +    +        RFK 
Sbjct: 364  PKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK--------RFKA 411

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  ++ V+KV++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+DG
Sbjct: 412  KSASNPDGIDLPADIVEVIKVYIVQKRKIQEGDKMSGRHGNKGIISRILPVEDMPHLEDG 471

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   + +KI + + +     ++  + +     
Sbjct: 472  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKINEKIITPVFEGLNEKELDEIMAEAGMT 531

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    G+  
Sbjct: 532  NYGKVTLI-----------------------------------------------DGK-- 542

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                 TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR
Sbjct: 543  -----TGEAIDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGKAQNGGQR 595


>gi|52694167|emb|CAG30613.1| DNA-directed RNA polymerase beta chain [Pseudomonas pertucinogena]
          Length = 370

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 218/365 (59%), Positives = 277/365 (75%), Gaps = 1/365 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV + V EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAGVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           +V D  VT+++V+LSA+EE +  IAQA++ +  DG   EELV  R   E  +   E++  
Sbjct: 121 RVKDTVVTDEIVFLSAIEEADHVIAQASAEV-RDGKLVEELVAVRHMNEFSVKAPEEVTL 179

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  S
Sbjct: 180 MDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVALDS 239

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  + A+R G+V+ VDA RIVIR  + +++   +GVDIY L+K+ RSNQNTC+NQRPLVK
Sbjct: 240 GVCVTARRGGVVDSVDASRIVIRVNDDEVEAGEAGVDIYTLIKYTRSNQNTCINQRPLVK 299

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            GD V   DI+A G S D+G+LALG+NM VAFMPW+GYNFEDS+LISER+V ED F++I 
Sbjct: 300 KGDVVAVKDILASGSSVDMGELALGQNMRVAFMPWNGYNFEDSILISERVVQEDRFSTIR 359

Query: 844 IEEFE 848
           I +  
Sbjct: 360 IHKLT 364


>gi|83699917|gb|ABC40935.1| RNA polymerase beta subunit [Entomoplasma lucivorax]
          Length = 598

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 217/416 (52%), Positives = 299/416 (71%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV D  + N+  YLSA EE+   I+Q+N + D +G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVIDCIIQNEHEYLSADEEKEYIISQSNVTKDANGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIAKVAEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SGA +VA   GIV+ VDA +I +           SG+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGACVVATENGIVKYVDAKQIAV--------EVKSGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD V    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSVEAGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D+ GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDQEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVK 408



 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 128/420 (30%), Positives = 180/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSVEAGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D++ I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDQEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSTDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEVIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|83699901|gb|ABC40927.1| RNA polymerase beta subunit [Mesoplasma coleopterae]
 gi|83699903|gb|ABC40928.1| RNA polymerase beta subunit [Mesoplasma coleopterae]
          Length = 598

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 217/416 (52%), Positives = 300/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV DG + N+  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVIDGVIQNEHEYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIAKVSEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  +VA   GIV+ VDA +I +         S +G+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCVVAAENGIVKYVDAKQITV--------ESKAGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD +    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSIEAGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D  GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVK 408



 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 179/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSIEAGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDNEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSNDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|98991114|gb|ABF60575.1| RNA polymerase beta subunit [Mycoplasma iowae]
          Length = 755

 Score =  352 bits (903), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 234/518 (45%), Positives = 337/518 (65%), Gaps = 24/518 (4%)

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVD------------IDSVMPQDLINAKPVVSAV 513
            + E+LK + + GL R+E+ I ++++  D              +V  + +IN KP     
Sbjct: 1   LIHELLKARSQAGLARIEKFINDKLAIADGANKVQEENEEARKAVTVKSIINTKPFQMTF 60

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF S QL+Q  +  N L+ +T+ RR+SA+G GG++R    +++RDVH +HYG+ICP E
Sbjct: 61  KEFFNSHQLTQFLDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHYSHYGKICPIE 120

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL+ SL S+A  +  GF+ TPYR V +G +T+++ +L+A+ E+   IA +N  
Sbjct: 121 TPEGMNIGLIMSLASYADADENGFLITPYRVVKNGVITDEIKWLTALREDEYVIACSNLH 180

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + +D  FTE+ V CR           K+D+ID +PKQVVSIAAS IPFLENDD+NR LMG
Sbjct: 181 V-KDNKFTEDSVLCRYRSSWDYFDVNKVDYIDIAPKQVVSIAASSIPFLENDDANRALMG 239

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE--QVDAIRIVIRSVEGD 751
            NMQRQA PL++  AP VGTG E  +A  SG AIV +   + E   VD            
Sbjct: 240 ANMQRQATPLIRPTAPIVGTGNEYKIAHDSGMAIVYEEDEVGEVKYVDGK--------KI 291

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           +  +  G   Y L+KF +SNQNTC N  P+V VGD+V++ + IADGPS + G+LALG+N 
Sbjct: 292 IIKNKKGEKQYDLLKFNKSNQNTCNNHMPIVNVGDKVKKYETIADGPSMNNGELALGQNA 351

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
           LVAF  W GYN+ED++++S+R+ +EDVFTSIHI E+ +    TK G EEITRD+PNVSE 
Sbjct: 352 LVAFTTWSGYNYEDAIILSKRLFNEDVFTSIHIVEYSIECLKTKNGDEEITRDVPNVSES 411

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             + +D+ G+I VGAEV  GD+LVGKI+PKG+  ++PEEKLL+AIFG+K+ + ++TSL+V
Sbjct: 412 SKRYLDDEGVIMVGAEVKEGDVLVGKISPKGQVELSPEEKLLQAIFGDKSKNYKETSLKV 471

Query: 932 PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           P G  GTV  ++ F +   D    +  +E+ ++ ++ +
Sbjct: 472 PHGGEGTVALIKRF-KVQDDYELNADVIEQIKVYVVQK 508



 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 147/514 (28%), Positives = 222/514 (43%), Gaps = 63/514 (12%)

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGP---------EEITRDIPNVSEEGLKNIDECG 880
            +E  ++ D   +I  EE EV       G          E+    +           +   
Sbjct: 261  NEYKIAHDSGMAIVYEEDEVGEVKYVDGKKIIIKNKKGEKQYDLLKFNKSNQNTCNNHMP 320

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V   + +    +      +   +  L A       +  D  +           
Sbjct: 321  IVNVGDKVKKYETIADGPS-MNNGELALGQNALVAFTTWSGYNYEDAIILSK-------- 371

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                  R   +    SI +    IE L  ++ D+E      N+       L  +  +   
Sbjct: 372  ------RLFNEDVFTSIHIVEYSIECLKTKNGDEEITRDVPNVSESSKRYLDDEGVIMVG 425

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK----- 1054
               K+  VL              + + +++ +Q         Y+ +   +    +     
Sbjct: 426  AEVKEGDVLVGK----ISPKGQVELSPEEKLLQAIFGDKSKNYKETSLKVPHGGEGTVAL 481

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K+Q   ++   V+  +KV+V  KR IQ GDKMAGRHGNKGI+S+I+P EDMP L+D
Sbjct: 482  IKRFKVQDDYELNADVIEQIKVYVVQKRKIQIGDKMAGRHGNKGIISKIVPIEDMPHLED 541

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG-KKIKSLINDYKANGDISPLRS--- 1170
            GTP+DI+LNPLGVPSRMN+GQI E HLG A   +  KK   +I + +     +       
Sbjct: 542  GTPIDIMLNPLGVPSRMNIGQILELHLGLAMRKISLKKQLEMIFNKEKPEAFTQWFGIDV 601

Query: 1171 --------------FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV--PVSTPVFDGA 1214
                            + +          +++D   VL  A   +  V   VSTPVF+G 
Sbjct: 602  DLSKILISKFKEVLKEKNITTLEQAENSFTEFDYSIVLSRAGISRDQVNYKVSTPVFEGV 661

Query: 1215 DEEAINSMLRMADLDE---------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
              + +   +  A +           +G+  L DG TGE FD  ++VG +YMLKL+HMV D
Sbjct: 662  KRDDLIEAMNEAGIKPLDPKTTNGKNGKFKLIDGRTGEYFDGDISVGIMYMLKLDHMVDD 721

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            K+++R+ G YS +TQQPLGGKS  GGQR GEMEV
Sbjct: 722  KIHSRAVGPYSKITQQPLGGKSQNGGQRFGEMEV 755


>gi|120407526|gb|AAY82000.2| RNA polymerase II second largest subunit [Coleochaete scutata]
          Length = 702

 Score =  352 bits (902), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 140/819 (17%), Positives = 252/819 (30%), Gaps = 163/819 (19%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   A ++           + +    N       +EE +       +
Sbjct: 2    ETPEGQACGLVKNLALMAYISVGSAAAPILEFLEEWTTEN-------LEEIHPNDIPNTT 54

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +G +           + +   R ++D               L  + +     R L 
Sbjct: 55   KIFVNGVWVGIHRDPDMLVKTLQKLRRQVDVNTEVGVVRDIRLKELRLYTDYGRCCRPLF 114

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              + QR  +     E     T    +  +  G   + +  G++E VD        +   +
Sbjct: 115  XVDNQRLVIKKHHIEELLDPT----LPDEDRGWNKLVE-LGLIEYVDTEEEETTMISMTI 169

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +   S                                        PS  LG       + 
Sbjct: 170  NDLVSARQNPEEA---------------------YSTTYTHCEIHPSMILG-------IC 201

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +    H                           + 
Sbjct: 202  ASIIPFPDHNQSPRNTYQSAMGKQAMGILCH---------------------------KL 234

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +   +   +C              +       +   +  +  I      +  D+ +   
Sbjct: 235  FRLAXDHXGVCPCTIPQKPLATTRAMEHLHFRQLPAGQNAIVGILCYSGYNQEDSVIMNQ 294

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        I  R   D+ ++  S+ +E+ E  +R+          +          G
Sbjct: 295  SSIDRGFF-RSISYRSYRDEEKKQGSLVKEEFEKPSRETVMGMRHGSYDKLDDDGIAPPG 353

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                +      K+T L                   D+  +      K    TS    E  
Sbjct: 354  TRVSAEDVIIGKTTPL------------------PDDGNEAARRFTKRDQSTSLKHSESG 395

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++             LR VK+ V   R  Q GDK A RHG KG V      EDMPF 
Sbjct: 396  MVDQVLL-----TTNDQGLRFVKMRVRSVRIPQIGDKFASRHGQKGTVGITYTQEDMPFT 450

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   DI++NP  +PSRM +G + E  LG     +G++                     
Sbjct: 451  QEGIVPDIIVNPHAIPSRMTIGHLIECLLGKVATHIGREGD------------------- 491

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 492  ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 516

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               +Y+G TG      + +G  Y  +L HMV DK+++R+ G   ++T+QP  G++  GG 
Sbjct: 517  FETMYNGHTGRKLQAQIFLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPAEGRAKDGGL 576

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG---------- 1335
            R GEME  C+ A+GAA+ ++E L  +SD       ++ G   +  ++  G          
Sbjct: 577  RFGEMERDCMIAHGAAHFMKERLFDQSDAYRVHVCEICGLIAI-ANLKKGTFECRGCKNK 635

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
             D  +   P +  +L +E+ A+ ++  +     K +   
Sbjct: 636  TDIVQVHIPYACKLLFQELMAMAIAPRMFTREEKANESE 674



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 75/477 (15%), Positives = 141/477 (29%), Gaps = 85/477 (17%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  +    + I+   + +    F     + 
Sbjct: 5   EGQACGLVKNLALMAYISVGSAAAPILEFLEEWTTENLEEIHPNDIPNTTKIFVNGVWVG 64

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R    T YGR C       +   +
Sbjct: 65  IHRDPDMLVKTLQKLRRQVDVNTEVGVVRDIRLKELR--LYTDYGRCCRPLFXVDNQRLV 122

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +        ++    +    R          + Y+   EEE   I+              
Sbjct: 123 IKKHHIEELLDP--TLPDEDRGWNKLVELGLIEYVDTEEEETTMISM----------TIN 170

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E            +  P  ++ I AS+IPF +++ S R      M +QA+ 
Sbjct: 171 DLVSARQNPE--EAYSTTYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 228

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +L  +          +     G          +    A+  +          +  G+  Y
Sbjct: 229 ILCHKLF-------RLAXDHXGVCPCTIPQKPLATTRAMEHLHFRQLPAGQNAIVGILCY 281

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                         NQ            + +I +  S D G                   
Sbjct: 282 SG-----------YNQ-----------EDSVIMNQSSIDRGFF----------------- 302

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
              S+        E    S+  EEFE  +R+T +G          +       +D+ GI 
Sbjct: 303 --RSISYRSYRDEEKKQGSLVKEEFEKPSRETVMG----------MRHGSYDKLDDDGIA 350

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             G  V+  D+++GK TP  +                +    RD S  +    SG V
Sbjct: 351 PPGTRVSAEDVIIGKTTPLPDDGN----------EAARRFTKRDQSTSLKHSESGMV 397


>gi|80978849|gb|ABB54673.1| RNA polymerase beta subunit [Mycoplasma putrefaciens]
          Length = 596

 Score =  352 bits (902), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 222/415 (53%), Positives = 311/415 (74%), Gaps = 9/415 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTND-VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARV+ YGFI TPYR+V +G + N+ + YL+A +E    IAQ+N   DE+G   +E+V  R
Sbjct: 62  ARVDEYGFITTPYRRVINGVIQNEQIEYLTADKERKFVIAQSNVKQDENGKILDEIVVSR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G++ +   ++I++ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++ E+
Sbjct: 122 FNGDDYMARVDEIEYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIRPES 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E   A+ SG AIVAK  GIV+ VD+  I ++          SG+  Y L  F+
Sbjct: 182 PIVGTGIEFEAARDSGEAIVAKEDGIVKYVDSKMISVQ--------GESGIKTYTLSDFE 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN  T + Q P+V+ GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED+++
Sbjct: 234 RSNNGTSLTQSPIVRKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIV 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +D FTSIHI+E+ +  R+TK G EE+TR++PNVSE+  K++D  GI+ +G EV
Sbjct: 294 MSERVVIDDRFTSIHIDEYTLEVRNTKQGLEEVTREVPNVSEQARKHLDLEGIVAIGTEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
             GDILVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++
Sbjct: 354 KVGDILVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGIVQSIK 408



 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 122/423 (28%), Positives = 180/423 (42%), Gaps = 72/423 (17%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            + +  I+  G  V  G+I+    +   +  +   + ++ A       +  D  +     V
Sbjct: 241  LTQSPIVRKGDVVKKGEIIADGPS-MDQGELAIGQNVVVAFSTYNGYNFEDAIVMSERVV 299

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEIL 990
                      + + ++       +E    E       AR   D + I+      ++ +IL
Sbjct: 300  IDDRFTSIHIDEYTLEVRNTKQGLEEVTREVPNVSEQARKHLDLEGIVAIGTEVKVGDIL 359

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+    G         L   +  E  R           +V    E +    +       
Sbjct: 360  VGKVTPKGQVQLSPEDKLLHAIFGEKSR----NVKDNSLRVPNGGEGIVQSIK------- 408

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
             RFK K      G D+P  ++ V+KV+V  KR IQ GDKM+GRHGNKGI+SRILP EDMP
Sbjct: 409  -RFKAKSSLNPDGIDLPADIVEVIKVYVVQKRKIQEGDKMSGRHGNKGIISRILPIEDMP 467

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             L+DGTPVDI+LNP GVPSRMN+GQI E HLG A   + +K+ + + +     ++  + +
Sbjct: 468  HLEDGTPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKINQKVITPVFEGLNEKELDEIMA 527

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                                        
Sbjct: 528  EAGMTNYGKVTLI----------------------------------------------- 540

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+       TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  G
Sbjct: 541  DGK-------TGEAIDKPIAVGVMYMLKLSHMVDDKIHARNVGPYSLITQQPLGGKAQNG 593

Query: 1291 GQR 1293
            GQR
Sbjct: 594  GQR 596


>gi|52694249|emb|CAG30654.1| DNA-directed RNA polymerase beta chain [Pseudomonas brenneri]
          Length = 361

 Score =  352 bits (902), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 212/361 (58%), Positives = 278/361 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDL+ AKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLLYAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SER+V ED F +IHI+    +ARD
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFPTIHIKGLTCVARD 360

Query: 854 T 854
           T
Sbjct: 361 T 361


>gi|83699923|gb|ABC40938.1| RNA polymerase beta subunit [Entomoplasma ellychniae]
          Length = 598

 Score =  352 bits (902), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 214/454 (47%), Positives = 316/454 (69%), Gaps = 9/454 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY +V +G +  +  YL+A +E++  I+Q+N + DE     ++ V  
Sbjct: 61  TYAVVDDLGFITTPYLRVQNGVIQEEYDYLTADQEKDFVISQSNVNKDESNKIFDKTVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +   E++ +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIANIEEVQYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIAPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP VGTG+E   A+ SG A+VA ++G+V+ VD+ +I + S +        G   Y L  F
Sbjct: 181 APIVGTGIEFEAARDSGVAVVAAQSGVVKYVDSTQINVESKD--------GFKTYSLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  + + Q+P+VKVGD+V+  +IIADGPS D G+LA+G+N++VAF  ++GYNFED++
Sbjct: 233 DRSNNGSSIVQKPIVKVGDKVKAGEIIADGPSIDQGELAIGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IP VSE   K +D  GI+ +G E
Sbjct: 293 VMSERIIQEDKFTSVHIDEYVLEVRNTKQGLEEITSEIPQVSENAKKYLDSEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDIL+GK+TPKG++ ++PE+KLL AIFGEK+  V+D SLRVP+G  G V  ++ F +
Sbjct: 353 VKTGDILIGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLRVPNGGEGIVQSIKRF-K 411

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
                N   I +  + +E++      ++ I + +
Sbjct: 412 AKSVSNPDGIELSADVLEVIKIYIVQKRKIQEGD 445



 Score =  294 bits (752), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 125/420 (29%), Positives = 185/420 (44%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  G+I+    +   +  +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDKVKAGEIIADGPS-IDQGELAIGQNVVVAFTTYNGYNFEDAIVMSERIIQEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++       +E       Q+   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGLEEITSEIPQVSENAKKYLDSEGIVAIGTEVKTGDILIGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          +V    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLRVPNGGEGIVQSIK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++   VL V+K+++  KR IQ GDKM+GRHGNKGI+S+ILP EDMP L+DG
Sbjct: 413  KSVSNPDGIELSADVLEVIKIYIVQKRKIQEGDKMSGRHGNKGIISKILPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGLPSRMNFGQILEIHLGMAAKKLGVKIATPVFEGVNSQDLDEIMAEAGM- 531

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                  E +     +                         GQ  
Sbjct: 532  ----------------------ENYGKVTLI------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|328870070|gb|EGG18445.1| RNA polymerase II core subunit [Dictyostelium fasciculatum]
          Length = 1565

 Score =  351 bits (901), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 108/509 (21%), Positives = 180/509 (35%), Gaps = 93/509 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +   + +  AI      +  D+ +   S
Sbjct: 1133 YQLRMDTMAHVLFYPQKPLVTTRSMEYLHFRELPAGQNVCVAIACYSGYNQEDSVILNQS 1192

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    +F R   D+ ++  S+  E  E   RD                  +  G 
Sbjct: 1193 AIDRGMF-RSMFYRSYKDEQKKQTSLMEETFEKPDRDTTVGMRHGSYEKIDEDGLVAPGI 1251

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T L                  +DE   +     K    T+    E+  
Sbjct: 1252 RVTGDDIIIGKTTPLP---------------PQEDELGPKTRRQSKKDSSTAMRSSENGV 1296

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++     GD +     +  KV V   R  Q GDK + RHG KG        ED+P+  
Sbjct: 1297 VDQVVLTTSGDGL-----KFTKVRVRSMRTPQIGDKFSSRHGQKGTCGMAYRQEDLPWTV 1351

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  LG      G +                      
Sbjct: 1352 EGVVPDIIVNPHAIPSRMTIGQLIECLLGKVSASTGDEGD-------------------- 1391

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     EAI+  L       +G 
Sbjct: 1392 ---------------------------------ATP-FTDVTVEAISQALHKIGYQMTGH 1417

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG   D  + +G  Y  +L HMV DK+++RS G   ++T+QP+ G+S  GG R
Sbjct: 1418 EVMYNGHTGRRMDAQIFIGPTYYQRLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLR 1477

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVAGND-- 1337
             GEME  C+ ++GAA  L+E L  +SD       D+ G       R   +E      +  
Sbjct: 1478 FGEMERDCMISHGAAQFLKERLFDQSDSYRVHICDICGLIAIANLRKNSFECR-RCKNKT 1536

Query: 1338 -TFETGTPESFNVLVKEMQALGLSIDLEN 1365
               +   P +  +L +E+ A+ ++  +  
Sbjct: 1537 QISQVKIPYAAKLLFQELMAMSIAPRMFT 1565



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 96/797 (12%), Positives = 228/797 (28%), Gaps = 140/797 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L+  Q  S+D F+   +          Q       PIT                ++    
Sbjct: 37  LVRQQLDSFDEFIQNTM----------QDIIDESPPITLKPETQHQPGQSQAHNYT-TFS 85

Query: 74  LEFVSYEFDPPK---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           ++F       P             +    R+LTY+ PL + +   +      T  +S+++
Sbjct: 86  IKFGQIYLSKPTSDIDGLTQSITPNQARIRNLTYSAPLYVDITKTL------TTKQSVEE 139

Query: 125 IKEQSIYMGDLPLMTKD---------------------------GTFVIKGIQRIVVSQL 157
              + I++G +P+M +                            G FVI G ++++++Q 
Sbjct: 140 EALEKIFIGKVPIMLRSKYCILSGDGDTSDTDLAMMGECPFDQGGYFVINGSEKVLIAQE 199

Query: 158 HRSPG-IHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDRR----- 209
             S   ++      + +   K  Y   I    + G            ++V++ ++     
Sbjct: 200 KMSHNHVY----VFKKTPPSKYSYVAEIRSCQETGSR------PTSTMYVKMLQKSSKGP 249

Query: 210 ---------RKV--PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                     K+  P+     ALG  ++ +IL         +Q  D     L  + ++  
Sbjct: 250 SGIKATIPYIKMDVPIVVIFRALGFVADKDILEHICYDFSDAQLMDLMRPSLEESFVIQN 309

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAED 311
            +V+   +            +   +   + L+++ +  + +            G  V   
Sbjct: 310 QEVALDYLGKRGSTVGTRDHRIKFAR--EVLQKEMLPHVSVEEYFETKKAYYFGYIVHRL 367

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           ++         +     +++              +    + +   +++  +   K     
Sbjct: 368 LLAALERRPLDDRDHFANKRLDLAGPLLGTLFRQLFKKLTKDVRMWLQRCIDKGKEFTPI 427

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            A+             T  +  S+    +  +     + V +V   +          R  
Sbjct: 428 SAI--------KPKTITSGLKYSLATGNWGAAHSGARAGVAQVLNRLTFASTLSHLRRLN 479

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    I         +   + + L     + +      I E + 
Sbjct: 480 TPIGREGKLAKPRQLHNTHWGIVCPSETPEGQACGLVKNLAMMAYISVGSASEPILEFLE 539

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
               +++  +++ +   +++A   F     +   ++  + L  +   R    +       
Sbjct: 540 EWSTENL--EEITDPSSILNATKIFVNGMWVGINKQPDHLLKTLRTLRGCGDVSVEVSIV 597

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                +   ++        P        + +  S      VN          K  D   +
Sbjct: 598 RDIREKEIRLYTDAGRCCRPLFVVRDSKLLIKKSHIQNLIVNPD-------YKWMDLITS 650

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I    S L +  + T                       +  P  +
Sbjct: 651 GLIEYIDTEEEETVMIGMNPSDLIQSHTETVT---------------HNYTHCEIHPSMI 695

Query: 672 VSIAASLIPFLENDDSNRVLMGC-NMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA 729
           + I  S+IPF +++ S R    C ++  Q      ++       + E VV       + +
Sbjct: 696 LGICCSIIPFPDHNQSPRNTYQCLSIDEQVTMADGSKRAIKDVKVGEYVVTFHPQTMVQS 755

Query: 730 KRAGIVEQVDAIRIVIR 746
               + + V      IR
Sbjct: 756 TTRVVNQYVRPTDKPIR 772



 Score =  105 bits (262), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 122/372 (32%), Gaps = 22/372 (5%)

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           ++   +     +      I+  L+     +  +DD D+  N+R+   G +L   +R    
Sbjct: 345 HVSVEEYFETKKAYYFGYIVHRLLLAALERRPLDDRDHFANKRLDLAGPLLGTLFRQLFK 404

Query: 481 RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-----------LSQLEE 527
           ++ + ++   +          P   I  K + S +     +             ++Q+  
Sbjct: 405 KLTKDVRMWLQRCIDKGKEFTPISAIKPKTITSGLKYSLATGNWGAAHSGARAGVAQVLN 464

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +   S ++H RRL+      + R     + R +H TH+G +CP+ET EG   GLV +L 
Sbjct: 465 RLTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTHWGIVCPSETPEGQACGLVKNLA 520

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-- 645
             A ++     E     + +    N           N      N          + L+  
Sbjct: 521 MMAYISVGSASEPILEFLEEWSTENLEEITDPSSILNATKIFVNGMWVGINKQPDHLLKT 580

Query: 646 --FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R  G+  +      D  +   +          P     DS  ++   ++Q   V  
Sbjct: 581 LRTLRGCGDVSVEVSIVRDIREKEIRLYTDAGRCCRPLFVVRDSKLLIKKSHIQNLIVNP 640

Query: 704 LKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
                  + +G +E +  +     ++      + Q     +       ++ PS       
Sbjct: 641 DYKWMDLITSGLIEYIDTEEEETVMIGMNPSDLIQSHTETVTHNYTHCEIHPSMILGICC 700

Query: 763 RLMKFQRSNQNT 774
            ++ F   NQ+ 
Sbjct: 701 SIIPFPDHNQSP 712



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/211 (19%), Positives = 75/211 (35%), Gaps = 22/211 (10%)

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                    +         ++           Q+PLV                     +L 
Sbjct: 1117 HNSAMGKQAMGVYITNYQLRMDTMAHVLFYPQKPLV----------TTRSMEYLHFRELP 1166

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
             G+N+ VA   + GYN EDS+++++  +   +F S+    ++   +      EE      
Sbjct: 1167 AGQNVCVAIACYSGYNQEDSVILNQSAIDRGMFRSMFYRSYKDEQKKQTSLMEETFEKPD 1226

Query: 867  N-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                  +     + IDE G++  G  V   DI++GK TP     + P+E  L      ++
Sbjct: 1227 RDTTVGMRHGSYEKIDEDGLVAPGIRVTGDDIIIGKTTP-----LPPQEDELGPKTRRQS 1281

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               +D+S  + S  +G V  V +       K
Sbjct: 1282 K--KDSSTAMRSSENGVVDQVVLTTSGDGLK 1310


>gi|116563578|gb|ABJ99805.1| RpoB [Bacillus subtilis subsp. subtilis]
          Length = 212

 Score =  351 bits (901), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDXALL 212


>gi|82798476|gb|ABB91901.1| RNA polymerase beta subunit [Acholeplasma multilocale]
          Length = 598

 Score =  351 bits (901), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 224/417 (53%), Positives = 308/417 (73%), Gaps = 11/417 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTN---DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           A+VN YGFI TPYR V DG + +   D+VYL+A EE N  IAQ+N   DE+G   +E+V 
Sbjct: 62  AKVNEYGFITTPYRPVIDGVINDNPADIVYLTADEERNFIIAQSNVQQDENGKILDEIVV 121

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++ +    +ID+ID SPKQ+VS+A + IPFLENDD+NR LMG NMQRQAVPLL  
Sbjct: 122 SRYRGDDYMASLPEIDYIDVSPKQIVSVATAAIPFLENDDANRALMGANMQRQAVPLLNP 181

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           ++P VGTG+E   A+ SG+A+VA   GIV+ VD+  I I         S +G   Y L  
Sbjct: 182 QSPIVGTGIEFEAARDSGSAVVATEDGIVKYVDSRIITI--------ESKNGAKTYTLSD 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSN  + +   P+V+ GD+V + +IIADGPS D G+LA+G+N++VAF  ++GYNFED+
Sbjct: 234 FERSNNGSSLVHFPIVRAGDKVNKGEIIADGPSMDKGELAIGQNVVVAFTTYNGYNFEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V ED FTS+HI+E+ +  R+TK G EE+TR+IPN+SE   K +DE GI+ +G 
Sbjct: 294 IIMSERVVMEDRFTSVHIDEYTIEVRNTKQGEEEVTREIPNISENAKKFLDEDGIVAIGT 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SL+VP+G  G V  V+
Sbjct: 354 EVKVGDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLKVPNGGEGIVQSVK 410



 Score =  290 bits (743), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 127/418 (30%), Positives = 179/418 (42%), Gaps = 72/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +VN G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 248  IVRAGDKVNKGEIIADGPS-MDKGELAIGQNVVVAFTTYNGYNFEDAIIMSERVVMEDRF 306

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+        E        I   A+   DE  I+      ++ +IL G+  
Sbjct: 307  TSVHIDEYTIEVRNTKQGEEEVTREIPNISENAKKFLDEDGIVAIGTEVKVGDILVGKVT 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           KV    E +    +        RFK 
Sbjct: 367  PKGQAQLSPEDKLLHAIFGEKSR----NVKDNSLKVPNGGEGIVQSVK--------RFKA 414

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++   V+ V+KV++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+DG
Sbjct: 415  KSPLNPEGIELAADVMEVIKVYIVQKRKIQEGDKMSGRHGNKGIISRILPIEDMPHLEDG 474

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   LG KI + + +     ++  + +     
Sbjct: 475  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGLNENELDEIMAEAGME 534

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 535  NYGKVKLI-----------------------------------------------DGQ-- 545

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                 TGE  D+P++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR
Sbjct: 546  -----TGEAIDKPISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQR 598


>gi|45545349|gb|AAS67522.1| DNA-dependent RNA polymerase II second largest subunit [Taphrina
            deformans]
          Length = 936

 Score =  351 bits (901), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 167/1042 (16%), Positives = 320/1042 (30%), Gaps = 163/1042 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            IE G KL S +   LK   V   G T        +     +     ++   G V D   L
Sbjct: 37   IEKGSKLISSMQIKLKAAKVGSTGQTIAA----TLPYVKTDIPIVIVFRALGVVPDRDIL 92

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            + I +       +  +      A++         +DR+ AL  I +              
Sbjct: 93   DHICYDAKDRQMLEMLKPCIEEAFV--------IQDREVALDFIGKR------------G 132

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            S          +Y    + +  +       T +     +   +  ++  L+     +   
Sbjct: 133  SAIGVTKEKRLRYAQDILQKEMLPHIT---TSEGFETRKAFFLGYMVHRLLLCALERRDP 189

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   R+ + I++ ++              +    + +
Sbjct: 190  DDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLPLAVKHTTITN 249

Query: 512  AVCEFFCSS-------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 250  GLRYSLATGTWGDQKKQMNARVGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 305

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL- 617
            R +H TH+G +CPAET EG   GLV +L   + V+           + +  + +   Y  
Sbjct: 306  RQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGMESLEDYNP 365

Query: 618  SAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            SA     +            + G   + L   R   +         D  +   +      
Sbjct: 366  SAGRPSTKIFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAG 425

Query: 676  ASLIP-FLENDD--SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P F+ +DD  + +   G  + ++      A +       E        +  +A+  
Sbjct: 426  RVCRPLFVVHDDESAEKSEAGSLVLKKEHVQRMAYSKEHPEDDEKFGWAQVLSNGIAEYL 485

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
               E+   +  +            +G       K ++         RP V     +    
Sbjct: 486  DAEEEETVMIAMTPDDLEATKHMMAGYVEPEDEKERKIAAEAAKRLRPAVNKAQHL--WT 543

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   + +  ++V   
Sbjct: 544  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQVRM- 593

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 594  --------------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNA 627

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  E+    + ++ E   R+  
Sbjct: 628  IVAILCYSGYNQEDSMIMNQSSIDRGLF-RSMFYRVYQDSEEKIDMNQAQEFEKPTRETT 686

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
             +     R+ Y +L +                 T +S + +     +   +     +   
Sbjct: 687  MKM---KRSTYDKLED----------DGLVAPGTRVSGEDVIVGKTAGLLKDENLADLAS 733

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R+    K    T     E    +K+      D       + VKV +   +  Q GDK A 
Sbjct: 734  RSATQTKRDVSTQLRSTEAGIIDKVMVSTNSD-----GHKFVKVRIRATKIPQIGDKFAS 788

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM V  + E  L       G + 
Sbjct: 789  RHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEG 848

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +                                   D +V  V+   +           
Sbjct: 849  DATPF-------------------------------TDVTVEAVSNNLR----------- 866

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G  I+Y+G TG      V +G  Y  +L H+V DK++AR+ 
Sbjct: 867  ------------EQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARAR 914

Query: 1273 GSYSLVTQQPLGGKSNRGGQRL 1294
            G   ++T+QP+ G++  GG R 
Sbjct: 915  GPMQILTRQPVEGRARDGGLRF 936



 Score =  145 bits (366), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 117/857 (13%), Positives = 243/857 (28%), Gaps = 142/857 (16%)

Query: 149 IQRIVVSQLHRSPG----IHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDII 202
            ++++++Q  RS      +       R +    + Y   I    ++G  +      K   
Sbjct: 1   SEKVIIAQE-RSAANMVQVF------RKAPPSPVSYLAEIRSAIEKGSKLISSMQIKLKA 53

Query: 203 ---------------HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
                          +V+ D    +P+     ALG+  + +IL          Q  +   
Sbjct: 54  AKVGSTGQTIAATLPYVKTD----IPIVIVFRALGVVPDRDILDHICYDAKDRQMLEMLK 109

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
             +  A ++   +V+   +        +   K+L     + + +K +     TS+     
Sbjct: 110 PCIEEAFVIQDREVALDFIGKRGSAIGVTKEKRL--RYAQDILQKEMLPHITTSEGFETR 167

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTD 365
                 +      + + A +  D    +      I    P+L          +   +   
Sbjct: 168 KAF--FLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQY 225

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
             K           +       T  +  S+    + D  K   + VG  ++  R    + 
Sbjct: 226 MTKCVDSGKEFNLPLAVKHTTITNGLRYSLATGTWGDQKKQMNARVGVSQVLNRYTYAST 285

Query: 426 DDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                R          I     L N    +         +      ++KN   +  + + 
Sbjct: 286 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLALMSYVSVG 342

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
            +    I  ++   +   +  N      +   F     L    +  + +  +   RR + 
Sbjct: 343 SASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNGVWLGVHSDPGHLVKTLRSLRRKTD 402

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRIC-------PAETSEGHNIGLVSSLTSFARV---N 593
           +    V+  R   E      T  GR+C         E++E    G +       +    +
Sbjct: 403 ISPE-VSVVRDIREKELRLFTDAGRVCRPLFVVHDDESAEKSEAGSLVLKKEHVQRMAYS 461

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                +                YL A EEE   IA     L+         V      E 
Sbjct: 462 KEHPEDDEKFGWAQVLSNGIAEYLDAEEEETVMIAMTPDDLEATKHMMAGYVEPEDEKER 521

Query: 654 -------------ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                        +   +      +  P  ++ I AS+IPF +++ S R      M +QA
Sbjct: 522 KIAAEAAKRLRPAVNKAQHLWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQA 581

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                                                   + + + 
Sbjct: 582 MGVFLTNYQV-----------------------------------------RMDTMANIL 600

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA + + G
Sbjct: 601 YYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILCYSG 636

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP----EEITRDIPN-VSEEGLKN 875
           YN EDSM++++  +   +F S+    ++       +      E+ TR+    +       
Sbjct: 637 YNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRSTYDK 696

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G++  G  V+  D++VGK     +      E L            RD S ++ S  
Sbjct: 697 LEDDGLVAPGTRVSGEDVIVGKTAGLLKD-----ENLADLASRSATQTKRDVSTQLRSTE 751

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G +  V +       K
Sbjct: 752 AGIIDKVMVSTNSDGHK 768


>gi|116563502|gb|ABJ99767.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563504|gb|ABJ99768.1| RpoB [Bacillus sp. 3EC1b2]
 gi|116563506|gb|ABJ99769.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563508|gb|ABJ99770.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563512|gb|ABJ99772.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563526|gb|ABJ99779.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563538|gb|ABJ99785.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563548|gb|ABJ99790.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563564|gb|ABJ99798.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563576|gb|ABJ99804.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563606|gb|ABJ99819.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563630|gb|ABJ99831.1| RpoB [Bacillus subtilis subsp. subtilis]
          Length = 212

 Score =  351 bits (901), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL 212


>gi|52694185|emb|CAG30622.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           multiresinivorans]
          Length = 358

 Score =  351 bits (901), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 216/358 (60%), Positives = 282/358 (78%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVGAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +G V++D+V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  +
Sbjct: 121 VKEGLVSDDIVFLSAIEEADHVIAQASATLNEKGQLIDELVAVRHLNEFTVKAPEDVTLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 181 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ 
Sbjct: 241 VCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           GD+V R+DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER+V ED FT+I
Sbjct: 301 GDQVSRSDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 358


>gi|58697061|ref|ZP_00372517.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
            endosymbiont of Drosophila simulans]
 gi|58536666|gb|EAL59965.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
            endosymbiont of Drosophila simulans]
          Length = 874

 Score =  351 bits (901), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 108/191 (56%), Positives = 143/191 (74%), Gaps = 4/191 (2%)

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            +  A + + GVPV+ PVF+G  +E I  +  +A LD SGQ++LYDG +GE FDR VTVGY
Sbjct: 1    IEFARKLRDGVPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGY 60

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +YMLKL+H+V  K++ARS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQE
Sbjct: 61   MYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQE 120

Query: 1314 MLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            MLT+KSDD+ GR ++YESI+ G+  FE G PESFNV++KE+++L L++DL     +N   
Sbjct: 121  MLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDL----KQNDVV 176

Query: 1374 MEEIPDFNKCE 1384
            +E+I   N  +
Sbjct: 177  IEDISHTNIAQ 187


>gi|116563554|gb|ABJ99793.1| RpoB [Bacillus mojavensis]
 gi|116563556|gb|ABJ99794.1| RpoB [Bacillus mojavensis]
 gi|116563582|gb|ABJ99807.1| RpoB [Bacillus mojavensis]
 gi|116563584|gb|ABJ99808.1| RpoB [Bacillus mojavensis]
 gi|116563586|gb|ABJ99809.1| RpoB [Bacillus mojavensis]
 gi|116563622|gb|ABJ99827.1| RpoB [Bacillus mojavensis]
 gi|116563634|gb|ABJ99833.1| RpoB [Bacillus subtilis subsp. spizizenii]
          Length = 212

 Score =  351 bits (901), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLVGENEYLRNTLDKDNTENSDKALL 212


>gi|302030855|gb|ADK91817.1| RNA polymerase beta subunit [Mycoplasma muris]
          Length = 761

 Score =  351 bits (901), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 224/526 (42%), Positives = 331/526 (62%), Gaps = 20/526 (3%)

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD-------------IDSVMPQDLI 504
           +LGN+R++ + E+LK + + GL R+E+ I ++++  D               ++  + +I
Sbjct: 1   HLGNKRLKLIHELLKARSQAGLARIEKFINDKLAIADGANKSQEENENEVKKTITVKSII 60

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N KP   +  EFF S QL+Q  +  N L+ +T+ RR+SA+G GG++R    +++RDVH +
Sbjct: 61  NTKPFQMSFKEFFNSHQLTQFLDQQNPLAELTNKRRISAMGPGGISREDPNLDIRDVHYS 120

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYG+ICP ET EG NIGL+ SL S+A V+  GF+ TPY  V +GKV + + +L+A++E+ 
Sbjct: 121 HYGKICPIETPEGMNIGLIMSLASYADVDENGFLITPYHVVENGKVIDKIEWLTALKEDE 180

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA ++  + +D  F  + V CR          +++D++D SPKQVVSIAAS IPFLEN
Sbjct: 181 YIIACSSPDI-KDNKFLNDKVLCRYRSSWEFFDAKRVDYLDISPKQVVSIAASSIPFLEN 239

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQA PL++  AP VGTG E  +A  SG A         ++ DA    
Sbjct: 240 DDANRALMGANMQRQATPLIRPHAPIVGTGNEYRIAHDSGMA-----YVYDQKEDATVKY 294

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +   +  L+  +  +  Y  +KF +SNQNTC NQ P+V + ++++    +ADGP+   G+
Sbjct: 295 VDGNKIKLETKSGSIIDYDFLKFNKSNQNTCNNQIPIVSIDEKIKYGQTLADGPAMQNGE 354

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
           LALG+N LVAF  W GYN+ED++++S R+  EDVFTSIHI E+ V     K G EEITRD
Sbjct: 355 LALGQNALVAFTTWSGYNYEDAIILSSRLFKEDVFTSIHIVEYTVECLRAKNGDEEITRD 414

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           +PNVSE   + +D+ GII VGAEV  GD+LVGKI+PKG+  ++ EEKLL+AIFG+K+ + 
Sbjct: 415 VPNVSETAKRYLDDEGIIMVGAEVKEGDVLVGKISPKGQVDLSSEEKLLQAIFGDKSKNH 474

Query: 925 RDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVEREQIELLAR 969
           ++TSL+VP G  GTV    R   +   + +   I   +  +    +
Sbjct: 475 KETSLKVPHGGEGTVAFVKRFKAQDDYELDADVIEQIKVYVVQKRK 520



 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 134/534 (25%), Positives = 221/534 (41%), Gaps = 57/534 (10%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKL 856
                       ++    P  G   E  +     M            ++    +   +TK 
Sbjct: 247  MGANMQRQATPLIRPHAPIVGTGNEYRIAHDSGMAYVYDQKEDATVKYVDGNKIKLETKS 306

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G       +           ++  I+ +  ++  G  L           +   +  L A 
Sbjct: 307  GSIIDYDFLKFNKSNQNTCNNQIPIVSIDEKIKYGQTLADGP-AMQNGELALGQNALVAF 365

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE------QIELLARD 970
                  +  D  + + S +    V   I       +  R+ + + E       +   A+ 
Sbjct: 366  TTWSGYNYEDAII-LSSRLFKEDVFTSIHIVEYTVECLRAKNGDEEITRDVPNVSETAKR 424

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              D++ I+      +  ++L G+ +  G         L   +  +  ++           
Sbjct: 425  YLDDEGIIMVGAEVKEGDVLVGKISPKGQVDLSSEEKLLQAIFGDKSKNHKETSLKVPHG 484

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             +  V  +                 K  K Q   ++   V+  +KV+V  KR IQ GDKM
Sbjct: 485  GEGTVAFV-----------------KRFKAQDDYELDADVIEQIKVYVVQKRKIQIGDKM 527

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL-- 1148
            AGRHGNKGI+S+I+P EDMP L+DGTP+DI+LNP+GVPSRMN+GQI E HLG+A   L  
Sbjct: 528  AGRHGNKGIISKIVPIEDMPHLEDGTPIDIMLNPVGVPSRMNIGQILELHLGYAMRKLTL 587

Query: 1149 ----------------GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                             +     +   +       L    +K+       ++ ++ D   
Sbjct: 588  SKILELVFAKAKLEEYKQWFGISVEVAETLNKHFNLLLKEKKITSLEQAKKEFTELDYTI 647

Query: 1193 VLRVAEQWKSGV--PVSTPVFDGADEEAINSMLRMADLD---------ESGQSILYDGLT 1241
            VL  A      +   V+TPVF+G +++ +  +++ A +D          +G+  L DG T
Sbjct: 648  VLTRAGISHDDITYKVATPVFEGVNKKDLQVIMKEAGIDPVSSPEGMGRNGKFKLIDGRT 707

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GE FD  +++G +Y+LKL+HMV DK+++R+ G YS +TQQPLGGKS  GGQR G
Sbjct: 708  GEYFDGDISIGVMYILKLDHMVDDKIHSRAVGPYSKITQQPLGGKSQNGGQRFG 761


>gi|156619303|gb|ABU88331.1| RNA polymerase beta subunit [Chlamydomonas moewusii]
          Length = 795

 Score =  351 bits (900), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 203/812 (25%), Positives = 340/812 (41%), Gaps = 105/812 (12%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--V 77
              +  +PD +E+Q+ S+   L           +GL   F    PIT+      + F   
Sbjct: 2   LNSVYYLPDFLEIQRQSFFTLL----------EKGLIDEFSKRNPITSKKKDVEVYFYPE 51

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y+   P +     + R  +Y   L + +++           K    I+ +  Y+G+LPL
Sbjct: 52  YYKLTLPTYSPRQAILRCKSYTSKLYMPVQITF---------KKTNTIRLKWAYIGNLPL 102

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL---------YACRIIPDQ 188
           MTK G F++ G  RI+V+Q+ RSPGI++  +K     + KL          Y   +I  +
Sbjct: 103 MTKRGHFILNGAPRIIVNQIIRSPGIYY-QEKLYERFTDKLSDKPNVTYKRYYADLICLR 161

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G W+ +E D    I  +  +  K+P+  +L+ +G+    IL++        Q    +   
Sbjct: 162 GTWLRLEIDRDKDIWAQTKKGPKIPIYWYLIGMGLSEHIILNSILEPQRILQNLAPFTLD 221

Query: 249 LSAADLMVGAKV---------SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
             +                      +++    + +E+    T+    SL  KG      +
Sbjct: 222 RKSTRKKRNDYSYVKNPPDAWKEIYLELSRSPKSVETSTSATTSKDNSLYSKGSTTKDES 281

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN--NAY 357
                    A + +  +   +  EA +   +    +  +    D+      + N      
Sbjct: 282 PRR-TNKVDARNALTSKKKSLQKEASEQGRKWLFNKFMNPRAYDLSRQGRAAFNRKLGLK 340

Query: 358 IRNTLVTDKNKDRKDALLDIYRV---MRPGDVSTFSVAESMFNFLFFDSDK-----YDLS 409
           I    +T   +D   A   + +V   ++P D         +         +       L 
Sbjct: 341 IDENQLTLTAQDLLSATDYLIKVEKGLKPIDDIDHLKNRRVRTSGELIQIQIGIAVVRLE 400

Query: 410 TVGRVKMNMRLNL------DTPDDVRHIRKEDIIAIIKILVDLRNGKGTID--------- 454
              R K+N           D P   R        +  + L  LR+  G I+         
Sbjct: 401 KTIREKINKTEMQFSFSLGDAPRTSRISSNFKKDSSTQKLKQLRSSTGLINDQIAPITTD 460

Query: 455 --------DIDNLGNRRVRSVGEMLK-----------------------------NQYRL 477
                    I+        +  E  +                             N  R 
Sbjct: 461 ITNFPTKQPIEFQTKNEDSTYVEFSRPVNPENSNIKSNSEKNLISSSGMVTTTTKNNTRA 520

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
              + +  +   +      ++   +LIN K   SA+ EFF +S LSQ  + +N L+ ITH
Sbjct: 521 STKKTKPLLFGNLQKNQTKTLNISNLINNKSFNSALREFFGTSPLSQFMDQINPLAEITH 580

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLS++G GGV R  A +E+R +HPTHYGRICP ET EG N GLV+SLT+++RVN+ G 
Sbjct: 581 KRRLSSMGPGGVTRDTATLEIRGIHPTHYGRICPVETPEGKNTGLVNSLTNYSRVNSLGI 640

Query: 598 IETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           +E+P+ +V  G V  ++   YLSA +EE   +  A+  +          +  R   +   
Sbjct: 641 LESPFYRVYKGMVQKNLGLFYLSAEQEEKTKLGAADLFVSSIDFLENNNIPVRIGEKFTK 700

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           + R  ++++  SP Q++SIA SLIPFLE+DD+NR LMG NMQRQAVP+++ E P VGTG+
Sbjct: 701 IHRNLVEYVGVSPTQMISIATSLIPFLEHDDANRALMGSNMQRQAVPVIRPERPIVGTGL 760

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           ES     SG  I ++ +G++  V + +I++R+
Sbjct: 761 ESRAVSDSGHVIQSRFSGVITYVSSDKIIVRT 792


>gi|194033333|ref|YP_002000410.1| beta subunit of RNA polymerase fragment 1 [Oedogonium cardiacum]
 gi|156619052|gb|ABU88204.1| RNA polymerase beta subunit [Oedogonium cardiacum]
 gi|186968950|gb|ACC97273.1| beta subunit of RNA polymerase fragment 1 [Oedogonium cardiacum]
          Length = 672

 Score =  351 bits (900), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 202/733 (27%), Positives = 338/733 (46%), Gaps = 95/733 (12%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPK 85
           D  E+Q+ S+ +FL            GL     +  PI          F    Y+   PK
Sbjct: 20  DFTELQRNSFLNFL----------KNGLIEELSNRNPIRNHKNNIEFIFYPEYYKLKRPK 69

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           ++V + +    +Y   L +  +L+          K+ K I+ + + +G+LPLMTK G F+
Sbjct: 70  WNVRESILLGKSYVAELYVPAQLM---------DKNNKKIQLKWVLIGNLPLMTKRGYFI 120

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL---------YACRIIPDQGLWMDIEF 196
           I G  R++++Q+ R PGI++     +     K           Y    +  +G W+ +  
Sbjct: 121 INGAARVIMNQIIRGPGIYYSEAIHQYDSFEKKNILMNQSFSRYYADFVSLRGYWLRLSV 180

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           D                                  F+              PL    L +
Sbjct: 181 DK-------------------------------DQFFWAE----MKKTPKIPLLWFLLAI 205

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
           G       ++     + I + K+L   L  SLK K    L +        ++  ++ N  
Sbjct: 206 G-------LNERLLFRYISNPKRLLHNLHNSLKSK--TQLALIKKLQKLQHIQLNVSN-- 254

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
                          ++E+   ++   I  +  +   +  Y  N L              
Sbjct: 255 ---------------NIEKKQKNKTHTIERVQKND-THTLYQYNFLPDSSLMAWDLISKK 298

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           + +  +   + +           F +   YD+ T+GR+ +N + NL        +   D+
Sbjct: 299 LVKKKKMSILKSQEQTRKWLFQRFMNPRSYDIGTIGRLALNKKFNLSISTKKHVLTPYDL 358

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           +     L+ +  G   +DDID+L NR++R+  E+++ Q  +GL+R+E+ IK+R++ + + 
Sbjct: 359 LFATDYLMKVEKGLKNLDDIDHLQNRKLRTASEIIQIQIGIGLIRLEKYIKDRLNQIKVF 418

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
               + LI  K + SA+ EFF +S LSQ  + +N L+ ITH RRL++LG GG+ +  A +
Sbjct: 419 P-KIESLITTKSLNSALTEFFGTSPLSQFMDQINPLAEITHKRRLTSLGPGGITKDNATM 477

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--V 614
            +R +HPTHYGRICP ET EG N GLV+S+T++A++N+ G IETP+ KV  G+V  +  +
Sbjct: 478 IIRGIHPTHYGRICPVETPEGKNAGLVNSITTYAKINSSGLIETPFYKVYKGQVMKNLGI 537

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            +LSA +EE      A+ +L   G   +  +  R     I   R ++ ++  SP Q++SI
Sbjct: 538 FFLSADDEEQINTVAADINLSAFGFLPKNYIPGRKKDNFIRFSRNQVHYMSISPIQMISI 597

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A SL+PF E+DD+NR LMG NMQRQAVPL++ + P VGTG+E      SG  I ++  GI
Sbjct: 598 ATSLVPFFEHDDANRALMGANMQRQAVPLIRPKRPIVGTGVEIRSVADSGHIIESRTGGI 657

Query: 735 VEQVDAIRIVIRS 747
           V  V A +I++ +
Sbjct: 658 VSYVSAKKIIVHT 670


>gi|116563612|gb|ABJ99822.1| RpoB [Bacillus subtilis subsp. subtilis]
          Length = 212

 Score =  350 bits (899), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLXGENEYLRNTLDKDNTENSDKALL 212


>gi|318603132|emb|CBJ04602.1| RNA polymerase beta subunit [Pseudomonas sp. R-38812]
          Length = 352

 Score =  350 bits (899), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 210/350 (60%), Positives = 272/350 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 3   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 62

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 63  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 122

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 123 HVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 182

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 183 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 242

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+
Sbjct: 243 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGE 302

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           LALG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARDT
Sbjct: 303 LALGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARDT 352


>gi|83699919|gb|ABC40936.1| RNA polymerase beta subunit [Mesoplasma chauliocola]
          Length = 598

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 219/416 (52%), Positives = 301/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV DG +  +  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVIDGVIQAEHEYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +   E++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIARVEEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  IVA   GIV+ VDA +I +         S SG+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCIVAVENGIVKYVDAKQITV--------ESKSGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD + +  IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSIEKGQIIADGPSVDNGELALGQNVVVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D  GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITAEIPNISDNAKKYLDSEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQSVQ 408



 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 129/420 (30%), Positives = 182/420 (43%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR-----VPSGV 935
            I+ VG  +  G I+    +      +   + ++ A       +  D  +      +    
Sbjct: 246  IVKVGDSIEKGQIIADGPS-VDNGELALGQNVVVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            +   +D  +       +    I+ E   I   A+   D + I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITAEIPNISDNAKKYLDSEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQSVQ--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP L+DG
Sbjct: 413  KSAANPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLEDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSNDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGEIIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|207081366|gb|ACI22951.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
 gi|207081368|gb|ACI22952.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 368

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 217/357 (60%), Positives = 278/357 (77%)

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +MPQDLI AKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E
Sbjct: 12  LMPQDLIIAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFE 71

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+D+V+L
Sbjct: 72  VRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDDIVFL 131

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 132 SAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 191

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ 
Sbjct: 192 LIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDS 251

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADG
Sbjct: 252 VDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADG 311

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           PSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT IHI+E   +ARDT
Sbjct: 312 PSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTPIHIQELPCVARDT 368


>gi|83699915|gb|ABC40934.1| RNA polymerase beta subunit [Entomoplasma melaleucae]
          Length = 598

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 217/416 (52%), Positives = 301/416 (72%), Gaps = 8/416 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +T+ RRL+ALG GG++R RA +E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLAELTNKRRLTALGPGGLSRDRASLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A V+  GFI TPY KV DG + N+  YLSA EE+   I+Q+N + DE+G   +E V  
Sbjct: 61  TYAIVDELGFIRTPYLKVIDGVIENEHQYLSADEEKEYIISQSNVTKDENGKILDETVVS 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++ +    ++ FID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVP +  E
Sbjct: 121 RYKGDDYIARVSEVQFIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPTIVPE 180

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +PFVGTG+E   A+ SG  +VA   GIV+ VDA +I +         + SG+  Y L  F
Sbjct: 181 SPFVGTGIEFEAARDSGVCVVATENGIVKYVDAKQIAV--------EAKSGIKTYTLANF 232

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  + + Q+P+VKVGD +    IIADGPS D G+LALG+N++VAF  ++GYNFED++
Sbjct: 233 ERSNNGSSIVQKPIVKVGDSIEAGQIIADGPSVDNGELALGQNVIVAFTTYNGYNFEDAI 292

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER++ ED FTS+HI+E+ +  R+TK G EEIT +IPN+S+   K +D+ GI+ +G E
Sbjct: 293 VMSERVIMEDKFTSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDQEGIVAIGTE 352

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           V  GDILVGK+TPKG++ ++PE+KLL AIFGEK+  V+D SL+VP+G  G V  V+
Sbjct: 353 VKTGDILVGKVTPKGQTQLSPEDKLLHAIFGEKSRSVKDNSLKVPNGGEGIVQAVK 408



 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 180/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  G I+    +      +   + ++ A       +  D  +     +     
Sbjct: 246  IVKVGDSIEAGQIIADGPS-VDNGELALGQNVIVAFTTYNGYNFEDAIVMSERVIMEDKF 304

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + ++        E        I   A+   D++ I+      +  +IL G+  
Sbjct: 305  TSVHIDEYVLEVRNTKQGAEEITSEIPNISDNAKKYLDQEGIVAIGTEVKTGDILVGKVT 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  RS          KV    E +    +        RFK 
Sbjct: 365  PKGQTQLSPEDKLLHAIFGEKSRS----VKDNSLKVPNGGEGIVQAVK--------RFKA 412

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G D+P  VL V+KV++  KR IQ GDKM+GRHGNKGI+S++LP EDMP LKDG
Sbjct: 413  KSATNPDGIDLPADVLEVIKVYIVQKRKIQEGDKMSGRHGNKGIISKVLPVEDMPHLKDG 472

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP G+PSRMN+GQI E HLG A   LG KI + + +   + D+  + +     
Sbjct: 473  TPVDILLNPQGIPSRMNIGQILEIHLGMAAKKLGVKIATPVFEGVNSNDLDEIMAEAGME 532

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 533  NYGKVKLI-----------------------------------------------DGQ-- 543

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TG+  D+P++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGK+  GGQR G
Sbjct: 544  -----TGDVIDKPISVGVMYMLKLSHMVDDKLHARSVGPYSLITQQPLGGKAQNGGQRFG 598


>gi|83699927|gb|ABC40940.1| RNA polymerase beta subunit [Mesoplasma syrphidae]
          Length = 599

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 217/417 (52%), Positives = 312/417 (74%), Gaps = 9/417 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDV-VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGFI TPYRKV +G + N++  YL+A EE N  IAQ+N   +E G   +E+V 
Sbjct: 61  TYAKVNEYGFITTPYRKVINGVIQNNIVEYLTADEERNFIIAQSNVQQEETGKILDEVVV 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++ +   +++D+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 SRYKGDDYMASLDELDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG+A+VA  +GIV+ VD+  I +         + SG+  Y L  
Sbjct: 181 ESPIVGTGIEFEAARDSGSAVVASESGIVKYVDSKIITV--------EAKSGIKTYTLSD 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           ++RSN  + +   P+VK GD+V++ +IIADGPS + G+LA+G+N++VAF  ++GYNFED+
Sbjct: 233 WERSNNGSALVHFPIVKAGDKVKKGEIIADGPSMEKGELAIGQNVVVAFSTYNGYNFEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V ED FTS+H++E+ +  R+TK G EE+TR+IPN+SE+  K +D  GI+ +G 
Sbjct: 293 IIMSERVVMEDRFTSVHVDEYTIEVRNTKQGEEEVTREIPNISEQAKKFLDLDGIVAIGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SL+VP+G  G V  ++
Sbjct: 353 EVKVGDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLKVPNGGEGIVQAIK 409



 Score =  294 bits (752), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 126/420 (30%), Positives = 177/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V  G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 247  IVKAGDKVKKGEIIADGPS-MEKGELAIGQNVVVAFSTYNGYNFEDAIIMSERVVMEDRF 305

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+        E        I   A+   D   I+      ++ +IL G+  
Sbjct: 306  TSVHVDEYTIEVRNTKQGEEEVTREIPNISEQAKKFLDLDGIVAIGTEVKVGDILVGKVT 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           KV    E +    +        RFK 
Sbjct: 366  PKGQAQLSPEDKLLHAIFGEKSR----NVKDNSLKVPNGGEGIVQAIK--------RFKA 413

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++   V+ V+KV++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+DG
Sbjct: 414  KSPLNPDGIELAADVMEVIKVYIVQKRKIQEGDKMSGRHGNKGIISRILPIEDMPHLEDG 473

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   LG KI + + +     ++  + +     
Sbjct: 474  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKLGAKIATPVFEGLNETELDEIMAEAGMD 533

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 534  NYGKVKLI-----------------------------------------------DGQ-- 544

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  -----TGEAIDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 599


>gi|212373981|emb|CAP09917.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35725]
          Length = 357

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 212/357 (59%), Positives = 278/357 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 357


>gi|83699931|gb|ABC40942.1| RNA polymerase beta subunit [Entomoplasma somnilux]
          Length = 594

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 225/444 (50%), Positives = 314/444 (70%), Gaps = 10/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A++N YGFI TPYRKV +      +V YL+A EE+N  I+QA+ + D  G  T++ V 
Sbjct: 61  TYAKINEYGFITTPYRKVVNGIIQNEEVHYLTADEEKNFMISQASVNQDATGKITDKTVI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++I+     ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 ARYRGDDIVTDILDIDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SGAA+VA  +GIV+ VD+  I I         + SG+  Y L  
Sbjct: 181 ESPIVGTGIEFEAARDSGAAVVATESGIVKYVDSRLITI--------EAKSGIKTYSLST 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSN  T +   P+VK GD+V +  IIADGPS + G+LA+G+N++VAF  ++GYNFED+
Sbjct: 233 FERSNNGTALIHFPIVKAGDKVDKGQIIADGPSMEKGELAIGQNVVVAFTTYNGYNFEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V ED FTS+HI+E+ +  R TK G E++TR++PNVSE   K +D  GI+ +G 
Sbjct: 293 VIMSERVVMEDRFTSVHIDEYVIERRSTKQGNEDVTRELPNVSEAAKKYLDSDGIVAIGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V  ++ F+
Sbjct: 353 EVKVGDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGDGIVQAIKRFS 412

Query: 947 -RHGIDKNERSISVEREQIELLAR 969
              G D     + + +  I    +
Sbjct: 413 AADGFDLPADVLEIIKVYIVQKRK 436



 Score =  291 bits (746), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 121/418 (28%), Positives = 176/418 (42%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V+ G I+    +   +  +   + ++ A       +  D  +         V+
Sbjct: 247  IVKAGDKVDKGQIIADGPS-MEKGELAIGQNVVVAFTTYNGYNFEDAVIM----SERVVM 301

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
            + R  + H  +       +ER   +    D   E   +       L     +  G     
Sbjct: 302  EDRFTSVHIDE-----YVIERRSTKQGNEDVTRELPNVSEAAKKYLDSDGIVAIGTEVKV 356

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   +     F  +   V+ N   +    +     +      K 
Sbjct: 357  GDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGDGIVQAI------KR 410

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 G D+P  VL ++KV++  KR IQ GDKM+GRHGNKG++SRILP EDMP L+DGTP
Sbjct: 411  FSAADGFDLPADVLEIIKVYIVQKRKIQEGDKMSGRHGNKGVISRILPIEDMPHLEDGTP 470

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDI+LNP G+PSRMN+GQI E HLG A   LG K+ + + +     ++  +         
Sbjct: 471  VDIMLNPQGIPSRMNIGQILELHLGMAAKKLGIKVATPVFEGVNAKELDEIMKEAGMTNF 530

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                                  GQ    
Sbjct: 531  GKVKLI-----------------------------------------------DGQ---- 539

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
               TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 540  ---TGEAMDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQSGGQRFG 594


>gi|116563536|gb|ABJ99784.1| RpoB [Bacillus amyloliquefaciens]
 gi|116563624|gb|ABJ99828.1| RpoB [Bacillus amyloliquefaciens]
 gi|116563626|gb|ABJ99829.1| RpoB [Bacillus amyloliquefaciens]
 gi|116563628|gb|ABJ99830.1| RpoB [Bacillus amyloliquefaciens]
          Length = 212

 Score =  350 bits (898), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL 212


>gi|116563604|gb|ABJ99818.1| RpoB [Bacillus subtilis subsp. spizizenii]
 gi|116563610|gb|ABJ99821.1| RpoB [Bacillus subtilis subsp. spizizenii]
          Length = 212

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLVGENEYLRNTLDKDNTENSDKALL 212


>gi|290751456|emb|CAQ16389.1| RNA polymerase beta subunit [Pseudomonas sp. R-26428]
          Length = 362

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 214/357 (59%), Positives = 275/357 (77%)

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH
Sbjct: 6   PDQRQPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVH 65

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
           PTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+D+V+LSA+EE
Sbjct: 66  PTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDDIVFLSAIEE 125

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            +  IAQA++++DE     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFL
Sbjct: 126 ADHVIAQASATMDEKKHLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFL 185

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA R
Sbjct: 186 EHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASR 245

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           IV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+
Sbjct: 246 IVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVQRSDIMADGPSTDM 305

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPE
Sbjct: 306 GELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPE 362


>gi|183584771|gb|ACC63828.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584777|gb|ACC63831.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584779|gb|ACC63832.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584781|gb|ACC63833.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584789|gb|ACC63837.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584791|gb|ACC63838.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584805|gb|ACC63845.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584807|gb|ACC63846.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584809|gb|ACC63847.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584811|gb|ACC63848.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584813|gb|ACC63849.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584815|gb|ACC63850.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584817|gb|ACC63851.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584823|gb|ACC63854.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
 gi|183584845|gb|ACC63865.1| RNA polymerase subunit B [Acinetobacter beijerinckii]
          Length = 286

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 134/289 (46%), Positives = 187/289 (64%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   +
Sbjct: 2    KIFEEAARERIVRLLTGQESNGGGTT-KRGDKLSVDVLSGLELVDLLEIQPNDEAIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   TQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP    G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ +
Sbjct: 121  NKGVVSNILPVEDMPHDIHGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LRSFL+K+    G   E++    D  +L ++   ++GVP++TPVFDGA
Sbjct: 181  LKEQRT---VIELRSFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +AD+  +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKDLLELADISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 286


>gi|116563546|gb|ABJ99789.1| RpoB [Bacillus licheniformis]
 gi|116563550|gb|ABJ99791.1| RpoB [Bacillus licheniformis]
 gi|116563552|gb|ABJ99792.1| RpoB [Bacillus licheniformis]
 gi|116563558|gb|ABJ99795.1| RpoB [Bacillus licheniformis]
 gi|116563560|gb|ABJ99796.1| RpoB [Bacillus licheniformis]
 gi|116563562|gb|ABJ99797.1| RpoB [Bacillus licheniformis]
 gi|116563566|gb|ABJ99799.1| RpoB [Bacillus licheniformis]
 gi|116563568|gb|ABJ99800.1| RpoB [Bacillus licheniformis]
 gi|116563570|gb|ABJ99801.1| RpoB [Bacillus licheniformis]
 gi|116563572|gb|ABJ99802.1| RpoB [Bacillus licheniformis]
 gi|116563574|gb|ABJ99803.1| RpoB [Bacillus licheniformis]
 gi|116563580|gb|ABJ99806.1| RpoB [Bacillus licheniformis]
 gi|116563588|gb|ABJ99810.1| RpoB [Bacillus licheniformis]
 gi|116563590|gb|ABJ99811.1| RpoB [Bacillus licheniformis]
 gi|116563592|gb|ABJ99812.1| RpoB [Bacillus licheniformis]
 gi|116563594|gb|ABJ99813.1| RpoB [Bacillus licheniformis]
 gi|116563596|gb|ABJ99814.1| RpoB [Bacillus licheniformis]
 gi|116563598|gb|ABJ99815.1| RpoB [Bacillus licheniformis]
 gi|116563600|gb|ABJ99816.1| RpoB [Bacillus licheniformis]
 gi|116563602|gb|ABJ99817.1| RpoB [Bacillus licheniformis]
 gi|116563614|gb|ABJ99823.1| RpoB [Bacillus licheniformis]
 gi|116563616|gb|ABJ99824.1| RpoB [Bacillus licheniformis]
 gi|116563618|gb|ABJ99825.1| RpoB [Bacillus licheniformis]
 gi|116563620|gb|ABJ99826.1| RpoB [Bacillus licheniformis]
 gi|116563632|gb|ABJ99832.1| RpoB [Bacillus licheniformis]
          Length = 212

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EI+             D      +   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGENEYLRNTLDKDNTENTDKALL 212


>gi|212373979|emb|CAP09916.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35715]
          Length = 352

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 210/351 (59%), Positives = 275/351 (78%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E++  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEEVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 302 LALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 352


>gi|83699925|gb|ABC40939.1| RNA polymerase beta subunit [Mesoplasma seiffertii]
          Length = 599

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 219/417 (52%), Positives = 312/417 (74%), Gaps = 9/417 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDV-VYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGFI TPYRKV DG + N++  YL+A EE N  IAQ+N   DE G   +E+V 
Sbjct: 61  TYAKVNEYGFITTPYRKVVDGVIQNNIVEYLTADEERNFIIAQSNVQQDETGKILDEVVV 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G++ +   E++D+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+  
Sbjct: 121 SRYKGDDYMARLEELDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLINP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E+P VGTG+E   A+ SG+A+VA  +GIV+ VD+  I +         + +G+  Y L  
Sbjct: 181 ESPIVGTGIEFEAARDSGSAVVATESGIVKYVDSKIITV--------EAKTGIKTYTLSD 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           ++RSN  + +   P+VK GD+V++ +IIADGPS + G+LA+G+N++VAF  ++GYNFED+
Sbjct: 233 WERSNNGSALVHFPIVKAGDKVKKGEIIADGPSMEKGELAIGQNVVVAFSTYNGYNFEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V ED FTS+H++E+ +  R+TK G EE+TR+IPN+SE+  K +D  GI+ +G 
Sbjct: 293 IIMSERVVMEDRFTSVHVDEYTIEVRNTKQGEEEVTREIPNISEQAKKFLDLDGIVAIGT 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           EV  GDILVGK+TPKG++ ++PE+KLL AIFGEK+ +V+D SL+VP+G  G V  ++
Sbjct: 353 EVKVGDILVGKVTPKGQAQLSPEDKLLHAIFGEKSRNVKDNSLKVPNGGEGIVQAIK 409



 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 178/420 (42%), Gaps = 72/420 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V  G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 247  IVKAGDKVKKGEIIADGPS-MEKGELAIGQNVVVAFSTYNGYNFEDAIIMSERVVMEDRF 305

Query: 941  DVRIFNRHGIDKNERSISVER-----EQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+        E        I   A+   D   I+      ++ +IL G+  
Sbjct: 306  TSVHVDEYTIEVRNTKQGEEEVTREIPNISEQAKKFLDLDGIVAIGTEVKVGDILVGKVT 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R           KV    E +    +        RFK 
Sbjct: 366  PKGQAQLSPEDKLLHAIFGEKSR----NVKDNSLKVPNGGEGIVQAIK--------RFKA 413

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      G ++P  V+ V+KV++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+DG
Sbjct: 414  KSPLNPDGIELPADVMEVIKVYIVQKRKIQEGDKMSGRHGNKGIISRILPIEDMPHLEDG 473

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNP GVPSRMN+GQI E HLG A   LG KI + + +     ++  + +     
Sbjct: 474  TPVDIMLNPQGVPSRMNIGQILEIHLGMAAKKLGAKIATPVFEGLNETELDEIMAEAGMD 533

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                                    GQ  
Sbjct: 534  NYGKVKLI-----------------------------------------------DGQ-- 544

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGE  D+P+ VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR G
Sbjct: 545  -----TGEAIDKPIAVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRFG 599


>gi|67810650|gb|AAY82001.1| RNA polymerase II second largest subunit [Sphagnum sp. JL-2005]
          Length = 704

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 140/755 (18%), Positives = 241/755 (31%), Gaps = 148/755 (19%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   A +     +      + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMAYITVGSAVNPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +   ++ +  +GS+             +   R ++   D + +  V     L       
Sbjct: 54   AVIPNSTKIFVNGSWVGIHRDPELLVRTLRQLRRQV---DVNTEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+K              A  SG                 +  I
Sbjct: 111  DYGRCSRPLFIVEKQRLLIKKSDVRALQ---QKEATESGW-----------YDLVSKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              V+ + + +T        +   R+N     +                    PS  LG  
Sbjct: 157  EYVDTEEEETTMISMTIADLVNARNNPEASFS-----------VTYTHCEIHPSMILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCGSIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        IF R   D+ +R  ++ +E+ E   R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSIFYRSYRDEEKRQGTLIKEEFERPNRENTTGMRHGSYDELDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T L                  QD+   +     K    T 
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTTPL-----------------PQDDNASQAQRYTKRDQSTC 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK+ V   R  Q GDK + RHG K  V     
Sbjct: 392  LRHSESGMIDQVLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKCTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ ++G   DI++NP  +PSRM +GQ+ E  +G     +GK+              
Sbjct: 447  QEDMPWTQEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------ 494

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F  A  + I+  L  
Sbjct: 495  -----------------------------------------ATP-FTDATVDNISKALHK 512

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G  ++Y+G TG      + +G  Y  +L HM+ DK+++R  G   ++T+QP  G
Sbjct: 513  CGYQMRGFEVMYNGHTGRRLSAHIFLGPTYYQRLKHMMDDKIHSRGRGPVQILTRQPAEG 572

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 573  RSRVGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 607



 Score = 65.9 bits (159), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 54/331 (16%), Positives = 104/331 (31%), Gaps = 36/331 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  ++   +  ++  S    + I+   + ++   F   S + 
Sbjct: 11  EGQACGLVKNLALMAYITVGSAVNPILEFLEEWSTENFEEISPAVIPNSTKIFVNGSWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 71  IHRDPELLVRTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 129

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      V A    E       D      + Y+   EEE   I+              
Sbjct: 130 KKS-----DVRALQQKEATESGWYDLVSKGFIEYVDTEEEETTMISM----------TIA 174

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E            +  P  ++ +  S+IPF +++ S R      M +QA+ 
Sbjct: 175 DLVNARNNPEASF--SVTYTHCEIHPSMILGVCGSIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 233 IYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 292

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              +  +D        YR  + +   Q T +
Sbjct: 293 IMNQSSIDRGFFRSIFYRSYRDEEKRQGTLI 323


>gi|281429790|gb|ADA70034.1| RpoB [Bacillus sp. NK-2]
          Length = 193

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 82/215 (38%), Positives = 132/215 (61%), Gaps = 22/215 (10%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ +
Sbjct: 1   GQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDI 50

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K  
Sbjct: 51  SPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKET 101

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +  
Sbjct: 102 GEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTA 158

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 159 TVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 193


>gi|212373973|emb|CAP09913.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35712]
          Length = 361

 Score =  350 bits (897), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 212/357 (59%), Positives = 277/357 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 5   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 64

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 65  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 124

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 125 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 184

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 185 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 244

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 245 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 304

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 305 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 361


>gi|242061214|ref|XP_002451896.1| hypothetical protein SORBIDRAFT_04g009491 [Sorghum bicolor]
 gi|241931727|gb|EES04872.1| hypothetical protein SORBIDRAFT_04g009491 [Sorghum bicolor]
          Length = 289

 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 111/267 (41%), Positives = 157/267 (58%), Gaps = 39/267 (14%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGV SRMN
Sbjct: 6    MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVSSRMN 65

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 66   VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 118

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 119  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 146

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ +G A++LQ
Sbjct: 147  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEGFGVAHILQ 206

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTF 1339
            E+LT KSD ++ R  +  + + G    
Sbjct: 207  EILTYKSDHLIARQEILNATIWGKRGP 233


>gi|116563514|gb|ABJ99773.1| RpoB [Bacillus sp. 3EC2A3]
 gi|116563608|gb|ABJ99820.1| RpoB [Bacillus sp. 3EC5B1]
          Length = 212

 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 85/227 (37%), Positives = 132/227 (58%), Gaps = 23/227 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V +   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVAESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           +VRIDR RK+PVT  L ALG  S+ EIL             +     
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFSSDQEILDLIGENEYLRNTLEKDNTE 205


>gi|289190486|gb|ADC93348.1| RNA polymerase beta subunit [Rhizobium etli]
          Length = 197

 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 134/197 (68%), Positives = 162/197 (82%)

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G++I  LI 
Sbjct: 1    GVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMGRQIGELIE 60

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             YKANG+I PLR  +  V+G G   E++ ++DD+SVLR+A+QWK GV ++TPVFDGA+E 
Sbjct: 61   AYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDESVLRLADQWKRGVSIATPVFDGANEG 120

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++ARS G YSL
Sbjct: 121  DVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHARSIGPYSL 180

Query: 1278 VTQQPLGGKSNRGGQRL 1294
            VTQQPLGGK+  GGQR 
Sbjct: 181  VTQQPLGGKAQFGGQRF 197


>gi|289190488|gb|ADC93349.1| RNA polymerase beta subunit [Rhizobium etli]
          Length = 197

 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 135/197 (68%), Positives = 162/197 (82%)

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+VSRI+P EDMPFL+DGT VD+VLNPLGVPSRMNVGQI ETHLGWAC G+G++I  LI 
Sbjct: 1    GVVSRIVPVEDMPFLEDGTHVDVVLNPLGVPSRMNVGQILETHLGWACAGMGRQIGELIE 60

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             YKANG+I PLR  +  V+G G   E++ ++DDDSVLR+A+QWK GV ++TPVFDGA+E 
Sbjct: 61   AYKANGNIEPLRKTIGDVVGAGPKAEQVHEFDDDSVLRLADQWKRGVSIATPVFDGANEG 120

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +N MLR+A L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++ARS G YSL
Sbjct: 121  DVNDMLRLAGLKDTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHARSIGPYSL 180

Query: 1278 VTQQPLGGKSNRGGQRL 1294
            VTQQPLGGK+  GGQR 
Sbjct: 181  VTQQPLGGKAQFGGQRF 197


>gi|212373941|emb|CAP09897.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35716]
          Length = 352

 Score =  349 bits (896), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 210/351 (59%), Positives = 272/351 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 302 LALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 352


>gi|156181154|gb|ABU54856.1| RpoB [Bacillus licheniformis]
          Length = 195

 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 81/215 (37%), Positives = 132/215 (61%), Gaps = 22/215 (10%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
             +V  G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ +
Sbjct: 3   GQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDI 52

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            P+  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K  
Sbjct: 53  SPVEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKET 103

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +  
Sbjct: 104 GEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTA 160

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 161 TVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 195


>gi|290489614|gb|ADD31191.1| RNA polymerase beta subunit protein [Lonicera japonica]
          Length = 1067

 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 227/605 (37%), Positives = 344/605 (56%), Gaps = 18/605 (2%)

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDS 403
           +  V          N     K   +++A+L+ Y+      GD              FF  
Sbjct: 195 LENVCYPEIFLSFLNAKEKKKIGSKENAILEFYQQFACVGGDPVFSESLSKELQKKFF-Q 253

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            K +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G G +DD+++L N+R
Sbjct: 254 QKCELGRIGRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGMKFGMGPLDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQ 521
           +RSV ++L++Q+ L L R+E  I+  IS      +   PQ+L+ + P+ +    FF    
Sbjct: 314 IRSVADLLQDQFGLALSRLENVIRGTISGALRHKLIPTPQNLVTSTPLTTTYESFFSLHP 373

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP++YGRICP +TSEG N+G
Sbjct: 374 LSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSYYGRICPIDTSEGINVG 433

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L+ SL   AR+  +G +E+P+ ++ +      ++YLS   +E   +A  NS         
Sbjct: 434 LIGSLAIHARIGRWGSLESPFYEISEKPKGARMLYLSPGRDEYSMVAAGNSLALNQSIQE 493

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++V  R   E + V  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAV
Sbjct: 494 EQVVPARYRQEFLTVAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAV 553

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL ++E   VGTG+E   A  SGA  +AK  G +  +D  +I++ S    L     G   
Sbjct: 554 PLSRSEKCIVGTGLERQAALDSGALAIAKHEGKISYIDTDKILLSSNRDTLSIMGRG--- 610

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
                   SN+ TC++Q+P V+    +++  I+  G +T  G+LALG+N+LVA+MPW GY
Sbjct: 611 --------SNKKTCMHQKPQVRRVKCIKKGQILGYGAATVGGELALGKNVLVAYMPWEGY 662

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N ED++LISER+V ED++TS HI ++E     T  GPE +T +IP++    L+N+D+ GI
Sbjct: 663 NSEDAVLISERLVYEDIYTSFHIRKYETKICVTSQGPERVTNEIPHLEAHLLRNLDKRGI 722

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GDILVGK+TPK     +  PE +LLRAI G +A   ++T L++P G  G V
Sbjct: 723 VMLGSWVEAGDILVGKLTPKIVKESSSAPEARLLRAILGIQAATSKETCLKLPIGGRGRV 782

Query: 940 VDVRI 944
           +DVR 
Sbjct: 783 IDVRW 787



 Score =  327 bits (838), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 122/410 (29%), Positives = 189/410 (46%), Gaps = 77/410 (18%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +   ++ G    +G     K T       S  P ++  +  +  +        LK+  
Sbjct: 717  LDKRGIVMLGSWVEAGDILVGKLTPKIVKESSSAPEARLLRAILGIQAATSKETCLKLPI 776

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +++ R+  +       +++       + V +  KR I+ GDK+AGRHGNKGI+S+
Sbjct: 777  GGRGRVIDVRWIQQ-------NEVSGSNPERICVSILQKREIKVGDKVAGRHGNKGIISK 829

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            ILP +DMP+L+DG PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +  
Sbjct: 830  ILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGDLLNRHYRIAPFDERYE 889

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             + S    F E    +                               VF+          
Sbjct: 890  QEASRKLVFSELYEASKQTANPW------------------------VFE---------- 915

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  +  G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y++VTQQ 
Sbjct: 916  -----PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGQYAVVTQQ- 969

Query: 1283 LGGKSNRGGQRLG--------------EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
                                       EMEVW ++ +G A++LQEMLT KSD +  R  +
Sbjct: 970  -------------AVRGRSRGGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHMRARQGI 1016

Query: 1329 YESIVAGNDTFET-GTPESFNVLVKEMQALGLSID--LENSRTKNSAKME 1375
              + + G       G PESF +LV+E+++L L ++  L + +     + E
Sbjct: 1017 LGTTLIGGTIPNPEGAPESFRLLVRELRSLALELNHFLVSEKNFQIHREE 1066



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDP 83
           IP L ++Q   +  F+          ++GL         I      A   L   +Y+F  
Sbjct: 12  IPGLNQIQFEGFCRFI----------DQGLMEELSKFPKIEDTDQKAEFQLFMETYQFVE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D +++ LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GT
Sbjct: 62  PLIKERDAVYKLLTYSSELYVSAGLIW---------KTRRDMQEQTIFIGNIPLMNSLGT 112

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++KGI RIV++Q+ +SPGI++  +      +G   Y   II D G    +E D K  I 
Sbjct: 113 SIVKGIYRIVINQILQSPGIYYRSELD---HNGIEAYTGTIISDWGGRSGLEIDRKARIW 169

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
            R+ R++K+ +     A+G +  EIL    YP+I  S         + + +
Sbjct: 170 ARVSRKQKISILVLSSAMGSNLREILENVCYPEIFLSFLNAKEKKKIGSKE 220


>gi|212373989|emb|CAP09921.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35720]
          Length = 356

 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 211/355 (59%), Positives = 275/355 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 302 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 356


>gi|239949585|gb|ACS36589.1| RNA polymerase subunit B [Acinetobacter baylyi]
          Length = 286

 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 131/289 (45%), Positives = 182/289 (62%), Gaps = 5/289 (1%)

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I +     R++ +L GQ +  G    K+   LS D++S             DE +   +
Sbjct: 2    KIFEEAARERIVRLLNGQESNGGGTT-KRGDKLSDDVLSGLELVDLLDIQPTDEGIAERL 60

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG
Sbjct: 61   SQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHG 120

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG KI  +
Sbjct: 121  NKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDKM 180

Query: 1156 INDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            + + +    +  LR FL+K+    G   E +    D+ +L ++   + GVP++TPVFDGA
Sbjct: 181  MKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPVFDGA 237

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 238  EESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|318603127|emb|CBJ04601.1| RNA polymerase beta subunit [Pseudomonas sp. R-38773]
          Length = 359

 Score =  349 bits (895), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 213/359 (59%), Positives = 281/359 (78%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N Y
Sbjct: 61  THKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +
Sbjct: 121 GFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTV 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGM
Sbjct: 181 KAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC
Sbjct: 241 ERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTC 300

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           +NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V
Sbjct: 301 INQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVV 359


>gi|212373957|emb|CAP09905.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35704]
          Length = 355

 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 211/354 (59%), Positives = 274/354 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI
Sbjct: 302 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHI 355


>gi|212373951|emb|CAP09902.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35701]
          Length = 348

 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 208/348 (59%), Positives = 270/348 (77%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYG
Sbjct: 1   PVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  I
Sbjct: 61  RVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVI 120

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 AQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 180

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R 
Sbjct: 181 NRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRV 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LAL
Sbjct: 241 ADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELAL 300

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           G+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E   +ARDTK
Sbjct: 301 GQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQELTCVARDTK 348


>gi|116563510|gb|ABJ99771.1| RpoB [Bacillus licheniformis]
 gi|116563516|gb|ABJ99774.1| RpoB [Bacillus licheniformis]
 gi|116563518|gb|ABJ99775.1| RpoB [Bacillus licheniformis]
 gi|116563520|gb|ABJ99776.1| RpoB [Bacillus licheniformis]
 gi|116563522|gb|ABJ99777.1| RpoB [Bacillus licheniformis]
 gi|116563524|gb|ABJ99778.1| RpoB [Bacillus licheniformis]
 gi|116563528|gb|ABJ99780.1| RpoB [Bacillus licheniformis]
 gi|116563530|gb|ABJ99781.1| RpoB [Bacillus licheniformis]
 gi|116563532|gb|ABJ99782.1| RpoB [Bacillus licheniformis]
 gi|116563542|gb|ABJ99787.1| RpoB [Bacillus licheniformis]
 gi|116563544|gb|ABJ99788.1| RpoB [Bacillus licheniformis]
          Length = 212

 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 136/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EI+             D      +   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEIIDLVGENEYLRNTLDKDNTENTDKALL 212


>gi|28190295|gb|AAO33041.1| RNA polymerase beta subunit [Buchnera aphidicola (Diuraphis noxia)]
          Length = 325

 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 138/328 (42%), Positives = 204/328 (62%), Gaps = 3/328 (0%)

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           LMT++GTF+I G +R+VVSQLHRSPG+ FD DKG+   SGK+LY  RIIP +G W+D EF
Sbjct: 1   LMTENGTFIINGTERVVVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEF 60

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
           D KD + VRIDRRRK+PVT  L AL  ++EEIL  F+ K ++    +     L    L  
Sbjct: 61  DPKDNLFVRIDRRRKLPVTVILRALNYNTEEILDIFFEKNIFKIETNKIELTLVPERL-R 119

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
           G   S ++     G+  +E G+++T+  ++ LK   +  + +  + + G  V+++ ++ +
Sbjct: 120 GETASFNIE--KDGKIYVEKGRRITARHIQDLKNNKITSITVPIEYILGRIVSKNYMDKK 177

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           TGE  I A   I  + LE++  S    I  L+ + +++  YI  TL  D   DR  AL++
Sbjct: 178 TGETIIFANTEISLEILEKLKKSNFDIIETLFTNDLDHGPYISETLKIDSANDRASALIE 237

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           IYRVMRPG+  T    E++F  LFF  D+YDLS+VGR+K N  L     +    + K+DI
Sbjct: 238 IYRVMRPGEPPTKEATENLFENLFFSEDRYDLSSVGRMKFNRSLLRKEIEGSGTLNKKDI 297

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           I +IK ++++RNGKG +DDID+LGNRR+
Sbjct: 298 IDVIKKIINIRNGKGEVDDIDHLGNRRI 325


>gi|212373963|emb|CAP09908.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35707]
          Length = 357

 Score =  348 bits (894), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 210/357 (58%), Positives = 276/357 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF S QLSQ  +  N  S ITH RR+SALG GG
Sbjct: 1   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSXQLSQFMDQNNPXSEITHKRRVSALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 121 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 357


>gi|67810558|gb|AAY81998.1| RNA polymerase II second largest subunit [Spirogyra sp. UWCC FW670]
          Length = 670

 Score =  348 bits (892), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 113/592 (19%), Positives = 192/592 (32%), Gaps = 100/592 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
              +  +T +           A       +      I   ++     + I   +     R+
Sbjct: 154  TMEEETTMIAMTINDVVSARANPETAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRN 213

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T             V+   L+      +  +        +    +       +      +
Sbjct: 214  TYQSAMGKQAMGIYVTNYQLRM---DTLAYILYYPQKPLVTTRAMEHLHFRELPAGINAI 270

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +        IF R   D+ ++  ++ +E+ E   RD   
Sbjct: 271  VAIACYSGYNQEDSVIMNQSSIDRG-FHRSIFYRSYRDEEKKQGTLTKEEFEKPNRDITS 329

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +          G           K+  L  D                D   Q 
Sbjct: 330  GMRHGSYDKLDSDGIAPPGTRVAGEDVIIGKTMPLPQD----------------DSGTQA 373

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               + + Q  T +          I  I           R VK+ V   R  Q GDK A R
Sbjct: 374  QRFTKRDQSTTLRHSESGMIDQVILTIN------NDGFRFVKIRVRSIRIPQIGDKFASR 427

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF ++G   D+V+NP  +PSRM +G + E  +G     +GK+  
Sbjct: 428  HGQKGTIGMTYTQEDMPFSQEGISPDLVVNPHAIPSRMTIGHLIECLMGKVAALMGKEGD 487

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                 +TP F  
Sbjct: 488  -----------------------------------------------------ATP-FTD 493

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
               ++I+  L        G  ++Y+G TG      + +G  Y  +L HMV DK+++R  G
Sbjct: 494  VTVDSISRALHSCGYQMRGFEVMYNGHTGRKLQAHIFLGPTYYQRLKHMVDDKIHSRGRG 553

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE--- 1330
               ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD    R  V E   
Sbjct: 554  PVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD--AYRVHVCEHCG 611

Query: 1331 -----SIVAG----------NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                 ++              D  +   P +  +L +E+ ++ ++  +    
Sbjct: 612  LIANANLKKSFFECRGCKNKTDIVQVHIPYACKLLFQELMSMAIAPRMMTRD 663



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 50/323 (15%), Positives = 103/323 (31%), Gaps = 36/323 (11%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  S    +  ++  ++   + I+   + +A   F     +    +  
Sbjct: 10  LVKNLALMTYITVGSSANPILDFLEEWTMENLEEISPALIPTATKIFVNGCWVGVHRDPE 69

Query: 530 NSLSRITHTRRL-SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR  +   +  + R     E+R ++  +     P    +   + +      
Sbjct: 70  MLIRTLRKLRRQLNVKSEVSMVRDVRLNELR-LYTDYGRCSRPLFIVKNQRLLIKKE--- 125

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
              ++A    E              + Y+  MEEE   IA              ++V  R
Sbjct: 126 --DIDALQQKEITGVGWHQLIAKGIIEYVDTMEEETTMIAM----------TINDVVSAR 173

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP------ 702
              E      +     +  P  ++ + AS+IPF +++ S R      M +QA+       
Sbjct: 174 ANPET--AYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 231

Query: 703 ----------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                     L   + P V T  ME +  +   A I A  A            +   +  
Sbjct: 232 QLRMDTLAYILYYPQKPLVTTRAMEHLHFRELPAGINAIVAIACYSGYNQEDSVIMNQSS 291

Query: 752 LDPSTSGVDIYRLMKFQRSNQNT 774
           +D        YR  + +   Q T
Sbjct: 292 IDRGFHRSIFYRSYRDEEKKQGT 314


>gi|226689|prf||1603356P RNA polymerase beta
          Length = 1000

 Score =  348 bits (892), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 232/699 (33%), Positives = 382/699 (54%), Gaps = 28/699 (4%)

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           E   K + I +  +   +     +  +  E          + S+  +  +   ++  +  
Sbjct: 135 ELDHKGISIYTGTIISDWGGRSELAIDKKERIWARVSRKQKISILVLSSAMGSNLKEILD 194

Query: 350 DSVNNNAYIR--NTLVTDKNKDRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDK 405
           +      ++   N     + + ++ A+L+ Y+      GD+             FF   K
Sbjct: 195 NVSYPEIFLSFPNAKEKKRIESKEKAILEFYQQFACVGGDLVFSESLCEELQKKFF-QQK 253

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID--NLGNRR 463
            +L  +GR  MN RLNLD P +   +   D++A    L+ ++   G +DD D  +L N+R
Sbjct: 254 CELGRIGRRNMNRRLNLDIPQNSTFLLPRDVLAATDHLIGMKFETGILDDDDMNHLKNKR 313

Query: 464 VRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKP----VVSAVCEFF 517
           +RSV ++L++Q+ L L R++ +++   R   +      PQ L+        +++    FF
Sbjct: 314 IRSVADLLQDQFGLALGRLQHAVQKTIRRVFIRQSKPTPQTLVTPTSTSILLITTYETFF 373

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  LSQ+ +  N L++  H R++S LG GG+    A    RD+HP+HYGRICP +TSEG
Sbjct: 374 GTYPLSQVFDQTNPLTQTVHGRKVSCLGPGGLTGRTASFRSRDIHPSHYGRICPIDTSEG 433

Query: 578 HNIGLVSSLTSFARVN-AYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSS 633
            N+GL  SL   AR++  +G +E+P+ ++ +         VVYLS   +E   IA  NS 
Sbjct: 434 INVGLTGSLAIHARIDHWWGSVESPFYEISEKAKKKKERQVVYLSPNRDEYYMIAAGNSL 493

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
               G   E++V  R   E + +  E+I      P Q  SI  SLIPF+E++D+NR LM 
Sbjct: 494 SLNRGIQEEQVVPARYRQEFLTIAWEQIHVRSIFPFQYFSIGGSLIPFIEHNDANRALMS 553

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPL ++E   VGTG+E   A  S  +++A+R G +   ++ +I++        
Sbjct: 554 SNMQRQAVPLSRSEKCIVGTGLERQTALDSRVSVIAEREGKIISTNSHKILL-------- 605

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S+       L+  +RSN+NTC++Q+P V  G  +++  I+A+G +T  G+LALG+N+LV
Sbjct: 606 SSSGKTISIPLVTHRRSNKNTCMHQKPRVPRGKSIKKGQILAEGAATVGGELALGKNVLV 665

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEG 872
           A+MPW GYNFED++LISER+V ED++TS HI ++E+    T  G  E+IT++IP++ E  
Sbjct: 666 AYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTDTTSQGSAEKITKEIPHLEEHL 725

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLR 930
           L+N+D  G++ +G+ V  GDILVGK+TP+  S  +   E  LLRAIFG +    ++TSL+
Sbjct: 726 LRNLDRNGVVKLGSWVETGDILVGKLTPQIASESSYIAEAGLLRAIFGLEVSTSKETSLK 785

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +P G  G V+DV+   R  +D   R   +++ +I++  +
Sbjct: 786 LPIGGRGRVIDVKWIQRDPLDIMVRVYILQKREIKVGDK 824



 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 100/232 (43%), Positives = 137/232 (59%), Gaps = 39/232 (16%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V NPLGVPSRMN
Sbjct: 808  MVRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVFNPLGVPSRMN 867

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQIFE+ LG A   L K  +    D +   + S    F E    +              
Sbjct: 868  VGQIFESSLGLAGDLLKKHYRIAPFDERYEQEASRKLVFSELYEASKQTKNPW------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                             VF+                +  G+S ++DG TG+PF++PV +G
Sbjct: 921  -----------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVLIG 948

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
              Y+LKL H V +K++ RSTG YSLVTQQP+ G++ +GGQR+GEMEVW ++ 
Sbjct: 949  KSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRAKQGGQRIGEMEVWALEG 1000



 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 105/234 (44%), Gaps = 27/234 (11%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I         +     Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHEISFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+I +G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTISIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMV 256
            R+ R++K+ +     A+G + +EIL    YP+I  S         + + +  +
Sbjct: 168 ARVSRKQKISILVLSSAMGSNLKEILDNVSYPEIFLSFPNAKEKKRIESKEKAI 221


>gi|296495882|gb|ADH29833.1| RNA polymerase beta subunit [Spiroplasma sp. YY0801]
          Length = 565

 Score =  348 bits (892), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 224/427 (52%), Positives = 308/427 (72%), Gaps = 9/427 (2%)

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG+E+RDVH +HYGRICP ET +G NIGL+++LT++A++N+YGFIETPY
Sbjct: 1   ALGPGGLSRERAGLEVRDVHYSHYGRICPIETPQGPNIGLINNLTTYAKINSYGFIETPY 60

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V   KVT +  YL+A EE+N  +AQAN  L + G   +E V  R  GE I+  R  +D
Sbjct: 61  RLVIGCKVTMENDYLTADEEKNYVVAQANIRLSDKGEILDEQVVARFQGENIIAGRNDVD 120

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQ+VSIA S IPFLENDD+NR LMG  MQRQA+PL+   +P+VGTG+E   A+ 
Sbjct: 121 YVDVSPKQIVSIATSCIPFLENDDANRALMGAKMQRQAIPLIAPNSPYVGTGVEYAAARD 180

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG AIV++  GIV+ VDA RIV+++ E        G+  Y L  F RSNQ T +   PLV
Sbjct: 181 SGLAIVSQYDGIVDFVDATRIVLKTKE--------GLKNYNLDTFVRSNQGTSLTHVPLV 232

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           + G +V +  ++ADGPS D G+ ALG+N++VAF  W+GYN+ED++++SER+VSEDVFTSI
Sbjct: 233 RQGQKVEKGQVLADGPSIDKGE-ALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVFTSI 291

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           HIEE+ +  R TK GPEEITR+IPN+SE   K +D+ G++ +G EV PGDILVGK+TPKG
Sbjct: 292 HIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGLVIIGTEVKPGDILVGKVTPKG 351

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
           ++ ++PE+KLL+AIFGEK+ +V+D SLRVP+G  G +  ++ F R   + +   + V + 
Sbjct: 352 QTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYELSADVLEVIKL 411

Query: 963 QIELLAR 969
            I    +
Sbjct: 412 YIVQKRK 418



 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 117/404 (28%), Positives = 179/404 (44%), Gaps = 69/404 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L     P  +      + ++ A       +  D  +     VS  V 
Sbjct: 231  LVRQGQKVEKGQVLAD--GPSIDKGEALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 288

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 289  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 342

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 343  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 400

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTPVDI
Sbjct: 401  -----LSADVLEVIKLYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPVDI 455

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +            
Sbjct: 456  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGMTNEELIEIMD---------- 505

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                    + ++        + +L DG 
Sbjct: 506  ---------------------------------------KAGMKNFG-----KEVLIDGR 521

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
            TGE FD PV+VG +YMLKL+HMV DK++AR+ GSYSL+TQ P G
Sbjct: 522  TGEKFDNPVSVGVMYMLKLSHMVDDKLHARNVGSYSLITQLPSG 565


>gi|207081362|gb|ACI22949.1| RNA polymerase subunit B [Pseudomonas fuscovaginae]
          Length = 368

 Score =  348 bits (892), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 214/357 (59%), Positives = 277/357 (77%)

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +MPQ+LI A+PV +AV EFF SSQLS   +  N LS ITH RR+SALG GG+ R RAG E
Sbjct: 12  LMPQNLIVAEPVAAAVKEFFGSSQLSHFMDQNNPLSEITHKRRVSALGPGGLTRERAGFE 71

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+D+V+L
Sbjct: 72  VRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDDIVFL 131

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 132 SAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 191

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ 
Sbjct: 192 LIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDS 251

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADG
Sbjct: 252 VDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADG 311

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           PSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT IHI+E   +ARDT
Sbjct: 312 PSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTPIHIQELPCVARDT 368


>gi|68300814|gb|AAY89348.1| RNA polymerase II second largest subunit [Antirrhinum majus]
          Length = 1200

 Score =  348 bits (892), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 115/599 (19%), Positives = 197/599 (32%), Gaps = 111/599 (18%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDT 854
              T    L+   N   A+   +       S+++     ++            ++      
Sbjct: 688  SMTINDLLSAKVNPTEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 747

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G          V+    +      +  V        +    +       +      + 
Sbjct: 748  AMG--------IYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 796

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R     
Sbjct: 797  AIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMG 855

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T +S                  D+   + 
Sbjct: 856  MRHGSYDKLDDDGLAPPGTRCSGEDVIIGKTTPISP-----------------DDAQGQA 898

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K  + TS    E    +++      D +     R VKV V   R  Q GDK + RH
Sbjct: 899  ARYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRH 953

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+   
Sbjct: 954  GQKGTVGMTYTQEDMPWTVEGISPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD- 1012

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP F   
Sbjct: 1013 ----------------------------------------------------ATP-FTDV 1019

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              + I+  L        G   +Y+G TG      + +G  Y  +L HMV DK+++R  G 
Sbjct: 1020 TVDNISKALHKCGYQMRGFETMYNGHTGRRLSSMIFLGPTYYQRLKHMVDDKIHSRGRGP 1079

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE---- 1330
              ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD    R  V E    
Sbjct: 1080 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD--AYRIHVCEQCGL 1137

Query: 1331 -SIV---------AG----NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
             +I           G     D  +   P +  +L +E+ ++ ++  +     K S +  
Sbjct: 1138 IAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMSMAIAPRMLTKDIKQSKEQR 1196



 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 132/995 (13%), Positives = 279/995 (28%), Gaps = 207/995 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGA-AML 74
           L+  Q  S+D F+   +          Q        I               F+     +
Sbjct: 47  LVRQQLDSFDEFIQNTM----------QEIVDESADIEIRPESQHNPGQQPDFAETIYKI 96

Query: 75  EFVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITL--RLIVFDVDEFTGAKSI 122
            F       P     D             R+LTY+ PL + +  R+I    D     ++ 
Sbjct: 97  SFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVSKRVIKKGHDGEEVTETQ 156

Query: 123 KDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH 158
              K   +++G +P+M +                         G F+I G ++++++Q  
Sbjct: 157 DFTK---VFIGKVPIMLRSSYCTLYQNSEKDLTELGECPLDQGGYFIINGSEKVLIAQEK 213

Query: 159 RSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR-------- 208
            S   ++      +     K  Y   +        + +      + VR+  R        
Sbjct: 214 MSTNHVY----VFKKRQPNKYAYVAEVR----SMAEAQNRPPSTMFVRMLSRTSAKGGSS 265

Query: 209 -----------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                      R ++P+     ALG  ++ +IL         +Q  +     L  A ++ 
Sbjct: 266 GQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICFNSSDTQMMELLRPSLEEAFVIQ 325

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             +V+   +        +   K++     + L+++ +  +G+   C          +   
Sbjct: 326 NQQVALDYIGKRGSTVGVTKEKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH- 383

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              + + A     E   +   +  +    P+L          +   + +   K   +   
Sbjct: 384 --RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKD 441

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKE 434
              +        T  +  S+    +  ++           +N      T   +R +    
Sbjct: 442 VNLQFXIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLBSPI 501

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N +  +         +      ++KN   +  + +  +    +  ++
Sbjct: 502 GREGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLE 558

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARAR 553
                  + I+   +  A   F     +         +S +   RR   +  + GV R  
Sbjct: 559 EWGTENFEEISPAVIPQATKIFVNGLWVGIHRNPDMLVSTLRRLRRRVDVNTEVGVVRDI 618

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSS----LTSFARVNAYGFIETPYRKVCDGK 609
              E+R ++  +     P    E   + +       L      +  G+ E          
Sbjct: 619 RLKELR-IYTDYGRCSRPLFIVEKQRLLIKKKDVQALQQRESPDDGGWHELV-------- 669

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               + Y+   EEE   I+   + L                        +     +  P 
Sbjct: 670 AKGFIEYIDTEEEETTMISMTINDLLS------------AKVNPTEAYSDTYTHCEIHPS 717

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +      F                   
Sbjct: 718 LILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF------------------- 758

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            R   +  V                                       Q+PLV       
Sbjct: 759 -RMDTLAYV-----------------------------------LYYPQKPLV------- 775

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                          L  G N +VA   + GYN EDS+++++  +    F S+    +  
Sbjct: 776 ---TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRD 832

Query: 850 MARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +      +E        +   +       +D+ G+   G   +  D+++GK TP    
Sbjct: 833 EEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRCSGEDVIIGKTTPISPD 892

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                     A         RD S  +    +G V
Sbjct: 893 D---------AQGQAARYTKRDHSTSLRHSETGMV 918


>gi|183584763|gb|ACC63824.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949549|gb|ACS36571.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949557|gb|ACS36575.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949561|gb|ACS36577.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949563|gb|ACS36578.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949565|gb|ACS36579.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949571|gb|ACS36582.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949577|gb|ACS36585.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949589|gb|ACS36591.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949593|gb|ACS36593.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949597|gb|ACS36595.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949599|gb|ACS36596.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949601|gb|ACS36597.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949605|gb|ACS36599.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949607|gb|ACS36600.1| RNA polymerase subunit B [Acinetobacter berezinae]
 gi|239949609|gb|ACS36601.1| RNA polymerase subunit B [Acinetobacter berezinae]
          Length = 286

 Score =  347 bits (891), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 130/290 (44%), Positives = 182/290 (62%), Gaps = 5/290 (1%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I +     R++ +L GQ +  G    K+   L+ D++S        +    DE +   
Sbjct: 1    FKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLTEDVLSNLELVDLLEVQPADEGIAER 59

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRH
Sbjct: 60   LTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRH 119

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG KI  
Sbjct: 120  GNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDK 179

Query: 1155 LINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            ++ + +    +  LR FL+K+    G   E +    D+ +L ++   + GVP++TPVFDG
Sbjct: 180  MMKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPVFDG 236

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            A+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 237  AEEGQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|297582233|ref|ZP_06944149.1| DNA-directed RNA polymerase [Vibrio cholerae RC385]
 gi|297533534|gb|EFH72379.1| DNA-directed RNA polymerase [Vibrio cholerae RC385]
          Length = 303

 Score =  347 bits (891), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 130/253 (51%), Positives = 177/253 (69%), Gaps = 5/253 (1%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              +    R +W +  +++E++Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGV
Sbjct: 1    AKLGSIERKKWLEQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGV 60

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L++VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PVDIVLNPLGVPSR
Sbjct: 61   LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSR 120

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--GTGSHTEKISDY 1188
            MN+GQI E HLG A  G+G KI  +I   K   +++ LR FL+KV   G       IS+ 
Sbjct: 121  MNIGQILEVHLGLAAKGIGDKINQMI---KEQQELAKLREFLQKVYDLGDTRQRVDISEL 177

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
             D+ V  +A   ++G+PV+TPVFDGA E +I +ML +ADL  SGQ  L+DG TG+ F+RP
Sbjct: 178  SDEDVRTLAHNLRAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERP 237

Query: 1249 VTVGYIYMLKLNH 1261
            VTVGY+YMLKLNH
Sbjct: 238  VTVGYMYMLKLNH 250


>gi|302703655|gb|ADL62674.1| RNA polymerase beta subunit [Ureaplasma canigenitalium]
          Length = 773

 Score =  347 bits (891), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 227/553 (41%), Positives = 331/553 (59%), Gaps = 42/553 (7%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI------------ 504
           D+LGN+R++ + E+L+ +    + R+E+ I E+++  D  S    +              
Sbjct: 1   DHLGNKRLKLIHELLRARVATSMSRIEKFIAEKLAISDGSSNNITNTNDKNIDPELDREL 60

Query: 505 --------------------NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                               N K   + + +FF S QL Q  +  N L+ +T+ RR+SA+
Sbjct: 61  EESDLTEEEKKKKISVKSVINTKQFQALIKDFFNSHQLIQFIDQQNPLAELTNKRRISAM 120

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG++R    +++RDVH +HY RICP ET EG NIGL+ SL S A+++  GFI  PY  
Sbjct: 121 GPGGISREDPNLDIRDVHHSHYSRICPIETPEGMNIGLIMSLASLAKIDENGFIVAPYYV 180

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT++ VYL+A E++N  I+++   LDE+     + V CR  G   L    ++DFI
Sbjct: 181 VKDGIVTDEFVYLTAHEDDNYIISESTVELDENNRIKGDSVICRYRGSTGLFKPSEVDFI 240

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D  P+QVVSIAAS IPF+ENDD  R LMG NMQRQA PL++  AP V TG E  +A  SG
Sbjct: 241 DIVPRQVVSIAASSIPFVENDDGARALMGSNMQRQATPLIRPYAPIVATGTEFKIAHDSG 300

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            A+ A+  GIV  VD   I +   +      T   +  +L+K+++SNQ+TC NQ P+V V
Sbjct: 301 MAVTARDNGIVTHVDGRSITVEYED------TKKPEKVKLVKYRKSNQDTCNNQTPIVDV 354

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            + V +   +ADGP+   G+LALGRN+LV +  W GYNFED+++ISER+V+ DVFTSIHI
Sbjct: 355 NEHVTKGQTLADGPAMQNGELALGRNVLVGYTTWRGYNFEDAIVISERLVTSDVFTSIHI 414

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           +E  +    TK G EEITRD+PN S+   + +D+ GI+ VGAEV+ GD+LVGK TP+G  
Sbjct: 415 DEHVIQCMKTKNGDEEITRDVPNTSDNSRRFLDQNGIVIVGAEVHEGDVLVGKTTPRGNV 474

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
              PE+KLL+ IFG+KA  V+D+SL+V  G  G V  V+  +     K++ +  +  + +
Sbjct: 475 DTIPEDKLLQTIFGDKAKTVKDSSLKVKHGQEGIVAAVKRIS----SKDDNASDLPDDVL 530

Query: 965 ELLARDKDDEQVI 977
           E++      ++ I
Sbjct: 531 EIVKVYIVQKRKI 543



 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 151/517 (29%), Positives = 230/517 (44%), Gaps = 32/517 (6%)

Query: 800  TDLGDLALGRNMLVAFMP--WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                       ++  + P    G  F+ +      + + D     H++   +        
Sbjct: 268  MGSNMQRQATPLIRPYAPIVATGTEFKIAHDSGMAVTARDNGIVTHVDGRSITVEYEDTK 327

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              E  + +           ++  I+ V   V  G  L           +     +L    
Sbjct: 328  KPEKVKLVKYRKSNQDTCNNQTPIVDVNEHVTKGQTLADGP-AMQNGELALGRNVLVGYT 386

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  +  D  +     V+  V      + H I   + + + + E    +    D+ +  
Sbjct: 387  TWRGYNFEDAIVISERLVTSDVFTSIHIDEHVIQCMK-TKNGDEEITRDVPNTSDNSRRF 445

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD+N       ++ G     G     K+T   +  +   P  +  Q    D+   + V+ 
Sbjct: 446  LDQN-----GIVIVGAEVHEGDVLVGKTTPRGN--VDTIPEDKLLQTIFGDK--AKTVKD 496

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
              ++ +  +  +    K    K     D+P  VL +VKV++  KR IQ GDKMAGRHGNK
Sbjct: 497  SSLKVKHGQEGIVAAVKRISSKDDNASDLPDDVLEIVKVYIVQKRKIQVGDKMAGRHGNK 556

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK------ 1151
            GIVS+++P +DMPFLKDGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +GKK      
Sbjct: 557  GIVSKVVPIQDMPFLKDGTPLDILLNPLGVPSRMNIGQILELHLGYAAHEIGKKELVRVA 616

Query: 1152 -------IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS-- 1202
                       +     N      +   + V    +   +  D  D  ++  +       
Sbjct: 617  LEGKGFEEYVNLFGLHENIASRLYKKMTDLVKEKNATKVEDIDLIDKLIILNSLGLSMDD 676

Query: 1203 -GVPVSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              + V++PVFDGA +E I  ML  AD+D +    +  LYDG TGE FD  ++VG  YMLK
Sbjct: 677  IAIKVASPVFDGATKEDIVKMLDEADIDTNEKRAKQTLYDGRTGEAFDGLISVGVSYMLK 736

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L+HMV DK+++RS G YS +TQQPLGGKS  GGQR G
Sbjct: 737  LDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFG 773


>gi|83699929|gb|ABC40941.1| RNA polymerase beta subunit [Mesoplasma photuris]
          Length = 599

 Score =  347 bits (891), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 223/452 (49%), Positives = 320/452 (70%), Gaps = 13/452 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+
Sbjct: 1   QINPLSELTNKRRLTALGPGGLSRERAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGS---FTEE 643
           ++A VN YGFI TPYRKV +G +  +++V+L+A EE++  IAQAN   D D       E 
Sbjct: 61  TYAAVNEYGFITTPYRKVENGLILNDEIVHLTADEEKDFIIAQANVEKDGDKILIPHGEM 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R  G++ +    +ID+ID SPKQ+VS+A S IPFLE+DD+NR LMG NMQRQAVPL
Sbjct: 121 GIVSRYKGDDYIAAINEIDYIDVSPKQIVSVATSAIPFLEHDDANRALMGANMQRQAVPL 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +  E+P VGTG+E   A+ SG+A+VA   G+V+ VD+ RI +         S +G   Y 
Sbjct: 181 INPESPIVGTGIEFEAARDSGSAVVALEDGVVKYVDSTRITV--------ESKNGSKTYT 232

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  ++RSN  + + Q  +VKVGD+V+  +IIADGPS D G+LA+G+N++VAF  ++GYNF
Sbjct: 233 LSNWERSNNGSAIVQSSIVKVGDKVKAGEIIADGPSMDKGELAIGQNVVVAFSTYNGYNF 292

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED++++SER+V ED FTS+HI+E+ +  R+TK G EE+T +IPNVSE+  K +DE GI+ 
Sbjct: 293 EDAIIMSERVVMEDRFTSVHIDEYTIEIRNTKQGAEEVTSEIPNVSEQAKKFLDEDGIVR 352

Query: 884 VGAEVNPGDILVGKITPKGE-SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           +G EV  GDILVGK+TPKG+   ++PE+KLL+AIFG+K+  V+D+SL+VP+G  G V  V
Sbjct: 353 IGTEVKVGDILVGKVTPKGQAQQLSPEDKLLQAIFGDKSKHVKDSSLKVPNGGEGIVQAV 412

Query: 943 RIFNRHGIDKNERSISVEREQIELLARDKDDE 974
           + F       +  +  +E+  + ++ + K  E
Sbjct: 413 KRFKAEDGYDDLGADVIEKVIVYIVQKRKIQE 444



 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 126/421 (29%), Positives = 180/421 (42%), Gaps = 77/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +V  G+I+    +   +  +   + ++ A       +  D  +     V     
Sbjct: 250  IVKVGDKVKAGEIIADGPS-MDKGELAIGQNVVVAFSTYNGYNFEDAIIMSERVVMEDRF 308

Query: 941  DVRIFNRHGIDKNERSISVEREQIE-----LLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                 + + I+        E    E       A+   DE  I+      ++ +IL G+  
Sbjct: 309  TSVHIDEYTIEIRNTKQGAEEVTSEIPNVSEQAKKFLDEDGIVRIGTEVKVGDILVGKVT 368

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
               PKG  +       L+      +         KV    E +                 
Sbjct: 369  ---PKGQAQQLSPEDKLLQAIFGDKSKHVKDSSLKVPNGGEGIVQAV------------- 412

Query: 1056 KIEKIQWG-DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            K  K + G DD+   V+  V V++  KR IQ GDKM+GRHGNKGI+SRILP EDMP L+D
Sbjct: 413  KRFKAEDGYDDLGADVIEKVIVYIVQKRKIQEGDKMSGRHGNKGIISRILPIEDMPHLED 472

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNP GVPSRMN+GQI E HLG A   LG KI + + +     ++  + +    
Sbjct: 473  GTPVDIMLNPQGVPSRMNIGQILEIHLGMAAQKLGLKINTPVFEGLNEEELKEIMAEAGM 532

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                  +                                                  GQ+
Sbjct: 533  TNFGKVNLI-----------------------------------------------DGQT 545

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   GE  D+P++VG +YMLKL+HMV DK++AR+ G YSL+TQQPLGGK+  GGQR 
Sbjct: 546  -------GEMIDKPISVGVMYMLKLSHMVDDKLHARNVGPYSLITQQPLGGKAQNGGQRF 598

Query: 1295 G 1295
            G
Sbjct: 599  G 599


>gi|68300810|gb|AAY89346.1| RNA polymerase II second largest subunit [Nicotiana sylvestris]
          Length = 1087

 Score =  347 bits (891), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 115/608 (18%), Positives = 194/608 (31%), Gaps = 104/608 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                   +      I   ++     +
Sbjct: 560  HDLVAKGYIEYIDTEEEETTMISMTINDLXQARLNPEEAYSDTYTHCEIHPSLILGVCAS 619

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 620  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 676

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI         D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 677  LHFRQLPAGINAIVAISCYSGYSQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 735

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T +S           
Sbjct: 736  KEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ---------- 785

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+   +     +  + TS    E    +++      D +     R VKV V  
Sbjct: 786  -------DDAQGQASRYTRKDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 833

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 834  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 893

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 894  MGKVAAHMGKEGD----------------------------------------------- 906

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L 
Sbjct: 907  ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRLK 959

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 960  HMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 1019

Query: 1321 ----DVVGR----------TRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSID 1362
                 V  R             +E    G     D  +   P +  +L +E+ A+ ++  
Sbjct: 1020 AYRVHVCERCGLIAIANLKKSSFEC--RGCKNKTDIVQVHIPYACKLLFQELMAMAIAPR 1077

Query: 1363 LENSRTKN 1370
            +     K 
Sbjct: 1078 MLTKDVKQ 1085



 Score =  208 bits (529), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 117/911 (12%), Positives = 256/911 (28%), Gaps = 171/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 14  PKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTK--VFIGKVPIMLRSSYCTL 71

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  + 
Sbjct: 72  YQNSEKDLTELGECPLDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAFV 127

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 128 AEVR----SMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 183

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 184 GFVADKDILEHICYDFNDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTREKRI 243

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                K + +K +       +                  + + A     E   +   +  
Sbjct: 244 --KYAKEILQKEMLPHVGIGEYCETKKAYYFGYIIHR--LLLCALGRRAEDDRDHYGNKR 299

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 300 LDLAGPLLGGXFRMLFRKLTRDVRAYVQKXVDNGKDVNLQFAIKAKTITSGLKYSLATGN 359

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N +  +     
Sbjct: 360 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAE 419

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++       + I+   +  A   F  
Sbjct: 420 TPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVN 476

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            + +    +    +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 477 GTWVGIHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEK 535

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L         G+         D      + Y+   EEE   I+     
Sbjct: 536 QRLLIKKKDIQTLQQRESPEEGGW--------HDLVAKGYIEYIDTEEEETTMISM---- 583

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +L   R   E      +     +  P  ++ + AS+IPF +++ S R    
Sbjct: 584 ------TINDLXQARLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 635

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +      F                    R   +  V               
Sbjct: 636 SAMGKQAMGIYVTNYQF--------------------RMDTLAYV--------------- 660

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 661 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 690

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A   + GY+ EDS+++++  +    F S+    +    +      +E            +
Sbjct: 691 AISCYSGYSQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGM 750

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           A         +D S
Sbjct: 751 RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRKDHS 801

Query: 929 LRVPSGVSGTV 939
             +    +G V
Sbjct: 802 TSLRHSETGMV 812


>gi|302703653|gb|ADL62673.1| RNA polymerase beta subunit [Ureaplasma cati]
          Length = 777

 Score =  347 bits (890), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 220/490 (44%), Positives = 312/490 (63%), Gaps = 9/490 (1%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +E    ++       ++  + +IN K   S V EFF S QL Q  +  N L+ +T+ RR+
Sbjct: 57  VESEEYQQKEEDKKRAISVKSVINTKQFQSLVKEFFNSHQLIQFIDQQNPLAELTNKRRI 116

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SA+G GG++R    +++RDVH +HY RICP ET EG NIGL+ SL S A+V+  GFI  P
Sbjct: 117 SAMGPGGISREDPNLDIRDVHHSHYSRICPIETPEGMNIGLIMSLASLAKVDENGFITAP 176

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           Y  V +G +T+++V+L+A E+++  I+++   +DE+       V  R  G       E++
Sbjct: 177 YYAVKNGVITDEIVHLTAHEDDDYIISESEVQVDENNKIISNEVIARYRGTTSSFKPEEV 236

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           DFID  P+QVVSIAAS IPF+ENDD  R LMG NMQRQA PL+K  AP VGTG E  +A 
Sbjct: 237 DFIDIVPRQVVSIAASAIPFIENDDGARALMGSNMQRQATPLIKPYAPIVGTGAEFKIAH 296

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG AIVAK  G + +VD   IV+ + E   +        Y+L+K+++SNQ+TC NQ P+
Sbjct: 297 DSGMAIVAKSDGKITKVDGREIVVTNSENKKES-------YKLIKYRKSNQDTCNNQVPI 349

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V +G+EV+ +  IADGP+   G+LALGRN+LVA+  W GYNFED+++ISER+V +DVFTS
Sbjct: 350 VALGEEVKASQTIADGPAMRNGELALGRNVLVAYTTWRGYNFEDAIVISERLVDQDVFTS 409

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHI+E  +    TK G EEITRD PNVSE   + +D+ GI+ VGAEV+ GD+LVGK TP+
Sbjct: 410 IHIDEHTIQCMKTKNGDEEITRDTPNVSEHARRFLDQDGIVLVGAEVHEGDVLVGKTTPR 469

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR--IFNRHGIDKNERSISV 959
                 PE++L++ IFG+KA  V+D+SL+V  G  G V  V+       G +  +  + +
Sbjct: 470 ANVDTVPEDRLIQTIFGDKAKTVKDSSLKVKHGQEGIVAAVKRITSTDEGNELPDDVLEI 529

Query: 960 EREQIELLAR 969
            +  I    +
Sbjct: 530 IKIYIVQKRK 539



 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 148/468 (31%), Positives = 221/468 (47%), Gaps = 38/468 (8%)

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                 +E  + I           ++  I+ +G EV     +           +     +L
Sbjct: 322  NSENKKESYKLIKYRKSNQDTCNNQVPIVALGEEVKASQTIADGP-AMRNGELALGRNVL 380

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A    +  +  D  +     +S  +VD  +F    ID++       +   E + RD  +
Sbjct: 381  VAYTTWRGYNFEDAIV-----ISERLVDQDVFTSIHIDEHTIQCMKTKNGDEEITRDTPN 435

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                  R    +   +L G     G     K+T      +   P  +  Q    D+    
Sbjct: 436  VSEHARR-FLDQDGIVLVGAEVHEGDVLVGKTTP--RANVDTVPEDRLIQTIFGDKAKTV 492

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               SLK                +I     G+++P  VL ++K+++  KR IQ GDKMAGR
Sbjct: 493  KDSSLK---VKHGQEGIVAAVKRITSTDEGNELPDDVLEIIKIYIVQKRKIQVGDKMAGR 549

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK-- 1151
            HGNKGIVS+++P +DMPFL DGTPVDI+LNPLGVPSRMN+GQI E HLG+A   +GKK  
Sbjct: 550  HGNKGIVSKVVPIQDMPFLADGTPVDIMLNPLGVPSRMNIGQILELHLGYAATEIGKKQL 609

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY-------------DDDSVLRVAE 1198
            +  +I D     +++  + +++         + + +              +D  ++ +  
Sbjct: 610  VNIVIEDLNNPNNVNGYQRYVDLFGIDEVTAQTLYNKVKNLVVSKNATKPNDIDLIDMTI 669

Query: 1199 QWKS--------GVPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDR 1247
              K         G+ VSTPVF GA  E I + +  A++D   + G+  LYDG TGE FD 
Sbjct: 670  ILKEIGLSFDDIGIKVSTPVFAGARHEDIVAAMDEAEIDTKIKKGKQKLYDGRTGEAFDG 729

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
             ++VG  YMLKL+HMV DK+++RS G YS +TQQPLGGKS  GGQR G
Sbjct: 730  LISVGISYMLKLDHMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFG 777


>gi|305663643|ref|YP_003859931.1| DNA-directed RNA polymerase subunit B [Ignisphaera aggregans DSM
            17230]
 gi|304378212|gb|ADM28051.1| DNA-directed RNA polymerase subunit B [Ignisphaera aggregans DSM
            17230]
          Length = 1150

 Score =  347 bits (890), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 121/604 (20%), Positives = 215/604 (35%), Gaps = 98/604 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G     + +       +L D     N LVA  P         + I    +     ++
Sbjct: 622  VKKGMMTFEDLVKKG--YIELLDPEEEENALVAINPEDIGKETTHVEIWPPAMMGVAAST 679

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R+              ++   L+         +        +    ++  
Sbjct: 680  IPYAEHNQSPRNAYQSAMAKQALGFYMANFILR---TDTRAHILHYPQIPLVQTRALSII 736

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G +     + ++ A+      ++ D  +   S V   +     F  +  ++ + +   E 
Sbjct: 737  GYNDRPSGQNMVVAVMSYTGYNMEDALIMNKSSVDRGLARSNFFRLYSTEELKYAGGQE- 795

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
                       D   I D  +     +    +    G    +        LI +    ++
Sbjct: 796  -----------DRIEIPDPKVLGYRGKESYTKLDEDGIAKVEVQVKGGEALIGKTSPPRF 844

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    +  +    L  + + S   +       ++ +     +     R++KV V   
Sbjct: 845  V-------EEYKGYGILAQRRKDSSVTVRHGEIGWVDAVFITSSLEGH--RLIKVRVRDL 895

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  ++P  DMP+  DG   D+++NP  +PSRM +GQ+ E+  
Sbjct: 896  RIPEIGDKFASRHGQKGVIGALIPQYDMPYTPDGITPDLIINPHALPSRMTLGQLMESIA 955

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      GK +                                                 
Sbjct: 956  GKVAALRGKNVDG----------------------------------------------- 968

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F+  + + +   L M      G   +YDG TGE    P+ +G +Y  KL+H
Sbjct: 969  ------TPFFE-ENIDELKRQLLMFGYPMDGTEPMYDGRTGELIGNPIFIGIVYYQKLHH 1021

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MVSDK++ARS G   L+T+QP  G++  GG R GEME   I  +GAA +L+E   ++S D
Sbjct: 1022 MVSDKMHARSKGPVQLLTRQPTEGRAREGGLRFGEMERDAIIGHGAAALLRER-MVESSD 1080

Query: 1322 --------VVG------RTR-VYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLE 1364
                    + G      R + +YE  + G+         P +F +L++E+ ++G+   L 
Sbjct: 1081 KTIVYVCELCGFIGWYNRKKEIYECPIHGDKGVLHPIVIPYAFKLLLQELMSMGIKPRLL 1140

Query: 1365 NSRT 1368
                
Sbjct: 1141 LGDK 1144



 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 120/629 (19%), Positives = 220/629 (34%), Gaps = 70/629 (11%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            D V  N  + + +        +DAL  I   +  G         S      +  DKY L
Sbjct: 269 FDPVIQNELLPSFVQASDIATVEDALDYIGSRIAIGQARE-----SRIERAKYVLDKYFL 323

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             +G              + R  +   +  +   L++   G   +DD D+  N+R++  G
Sbjct: 324 PHLGSK-----------PEDRLRKALFLGQMACKLIEFVLGYRPVDDKDHYANKRIKLAG 372

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD---------LINAKPVVSAVCEFFCS 519
           EML   +R+      R ++ ++    I                    K  ++        
Sbjct: 373 EMLALLFRVAFKAFLRDLRYQLERAKIKERRLNIALYIRSDVITERIKHAMATGTWIGGR 432

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           + +SQ+ +  N +S I+H RR  +     ++R++   E RD+H T +GR+CP ET EG N
Sbjct: 433 TGVSQILDRTNWISSISHMRRTLS----PLSRSQPHFEARDLHGTQFGRLCPFETPEGPN 488

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV---------YLSAMEEENRYIAQA 630
            GLV +L   A ++  G  E    K+   K T  ++          LS  + +       
Sbjct: 489 CGLVKNLALMATIS-VGEDEHLVEKILYDKGTIPILVLFEKVRNGELSYEDIKTWSKVYL 547

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKI------DFIDASPKQVVSIAASLIPFLEN 684
           N +L       +ELV      +       ++                      L P +  
Sbjct: 548 NGTLIGYHPNGKELVEKLRDMKHRGELSYEVGIAYYRTKYINEVYVNTDSGRILRPLMVV 607

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD----- 739
           ++    +    + +    ++  E       +E +  +    A+VA     + +       
Sbjct: 608 ENGKLKITKEVIDKVKKGMMTFEDLVKKGYIELLDPEEEENALVAINPEDIGKETTHVEI 667

Query: 740 ---AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDEVRRNDII 794
              A+  V  S     + + S  + Y+    +++      N   R   +          +
Sbjct: 668 WPPAMMGVAASTIPYAEHNQSPRNAYQSAMAKQALGFYMANFILRTDTRAHILHYPQIPL 727

Query: 795 ADGPS---TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
               +       D   G+NM+VA M + GYN ED++++++  V   +  S     +    
Sbjct: 728 VQTRALSIIGYNDRPSGQNMVVAVMSYTGYNMEDALIMNKSSVDRGLARSNFFRLYSTEE 787

Query: 852 RDTKLGPEEI-TRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                G E+      P V     +E    +DE GI  V  +V  G+ L+GK +P      
Sbjct: 788 LKYAGGQEDRIEIPDPKVLGYRGKESYTKLDEDGIAKVEVQVKGGEALIGKTSPPRFVEE 847

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                +L       A   +D+S+ V  G 
Sbjct: 848 YKGYGIL-------AQRRKDSSVTVRHGE 869



 Score =  137 bits (344), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 103/731 (14%), Positives = 211/731 (28%), Gaps = 121/731 (16%)

Query: 32  VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK------ 85
               SY+ F+             L         I        +    +    P+      
Sbjct: 50  HHIDSYNAFIEKI----------LGEIIMEEPVIETSIPGFKVVIKGWRVGEPQVKEIDG 99

Query: 86  -----FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
                    +C  RD+TY+VP+ IT  L+ ++ D               + +G++PLM K
Sbjct: 100 SINRNITPMECRHRDITYSVPIYIT--LVPYENDVPGNPV--------EVLIGEIPLMVK 149

Query: 141 D------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHD-KGRA 172
                                    G F+I G +RI+V+Q   +     + +  +     
Sbjct: 150 SSKDPLSKMTSEELIKIGEDPKDPGGYFIIDGTERIIVAQEDLASNRVIVDYGQEGLNIT 209

Query: 173 SL----SGKLLYACRIIPDQGLWMDIEFDSKD-IIHVRIDRRR-KVPVTSFLMALGMDSE 226
                 S  + Y   +I D+          KD  +HV       K+P    + ALG++ +
Sbjct: 210 HTAKVISSTIGYRVPVIMDR---------HKDGTLHVSFPAVPGKIPFVVLMRALGLERD 260

Query: 227 -EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +I        V              A  +   + +   +       + ++ +       
Sbjct: 261 FDIAIAVSFDPVIQNE---LLPSFVQASDIATVEDALDYIGSRIA--IGQARESRIERAK 315

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-LEEIFHSEIRDI 344
             L +  +  LG   +      +    +  +  E  +    V D+     +        +
Sbjct: 316 YVLDKYFLPHLGSKPEDRLRKALFLGQMACKLIEFVLGYRPVDDKDHYANKRIKLAGEML 375

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +L+   V   A++R+     +    K+  L+I   +R  DV T  +  +M    +    
Sbjct: 376 ALLF--RVAFKAFLRDLRYQLERAKIKERRLNIALYIR-SDVITERIKHAMATGTWIGGR 432

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNRR 463
                 + R      ++         + +       + L   + G+    +  +      
Sbjct: 433 TGVSQILDRTNWISSISHMRRTLSP-LSRSQPHFEARDLHGTQFGRLCPFETPEGPNCGL 491

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVD---IDSVMPQDLINAKPVVSAVCEFFCSS 520
           V+++  M           +E+ + ++ +       + V   +L        +      + 
Sbjct: 492 VKNLALMATISVGEDEHLVEKILYDKGTIPILVLFEKVRNGELSYEDIKTWSKVYLNGTL 551

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-CPAETSEGHN 579
                              R     + G+A  R          T  GRI  P    E   
Sbjct: 552 IGYHPNGKELVEKLRDMKHRGELSYEVGIAYYRTKYINEVYVNTDSGRILRPLMVVENGK 611

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           + +   +    +     F         D      +  L   EEEN  +A     + +   
Sbjct: 612 LKITKEVIDKVKKGMMTF--------EDLVKKGYIELLDPEEEENALVAINPEDIGK--- 660

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                               +   ++  P  ++ +AAS IP+ E++ S R      M +Q
Sbjct: 661 --------------------ETTHVEIWPPAMMGVAASTIPYAEHNQSPRNAYQSAMAKQ 700

Query: 700 AVPLLKAEAPF 710
           A+    A    
Sbjct: 701 ALGFYMANFIL 711


>gi|68300812|gb|AAY89347.1| RNA polymerase II second largest subunit [Petunia x hybrida]
          Length = 1195

 Score =  347 bits (890), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 111/574 (19%), Positives = 189/574 (32%), Gaps = 100/574 (17%)

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
              +      I   ++     + I   +     R+T             V+    +     
Sbjct: 700  YSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---D 756

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  V        +    +       +      + AI      +  D+ +   S +    
Sbjct: 757  TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGF 816

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D+ ++  ++ +E      R           +          G       
Sbjct: 817  F-RSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGED 875

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T +S                  D+   +     +  + TS    E    +++  
Sbjct: 876  VIIGKTTPISQ-----------------DDAQGQASRYTRKDHSTSLRHSETGMVDQVLL 918

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   D
Sbjct: 919  TTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPD 973

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +GQ+ E  +G     +GK+                            
Sbjct: 974  IIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------- 1007

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     + I+  L        G   +Y+G
Sbjct: 1008 ---------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNG 1039

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME 
Sbjct: 1040 HTGRRLPAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMER 1099

Query: 1300 WCIQAYGAAYVLQEMLTIKSD----DVVGR----------TRVYESIVAG----NDTFET 1341
             C+ A+GAA+ L+E L  +SD     V  R             +E    G     D  + 
Sbjct: 1100 DCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIAIANLKKNSFEC--RGCKNKTDIVQV 1157

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
              P +  +L +E+ A+ ++  +     K +   +
Sbjct: 1158 HIPYACKLLFQELMAMAIAPRMLTKDVKQARDQK 1191



 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 132/989 (13%), Positives = 278/989 (28%), Gaps = 195/989 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 42  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIN 92

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 93  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 152

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 153 FTK--VFIGKVPIMLRSSYCTLYQNSEKDLTELGECPLDQGGYFIINGSEKVLIAQEKMS 210

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR---------- 208
              ++      +     K  +   +        + +      + VR+  R          
Sbjct: 211 TNHVY----VFKKRQPNKYAFVAEVR----SMAESQNRPPSTMFVRMLSRTSAKGGSSGQ 262

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 263 YIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFNDTQMMELLRPSLEEAFVIQNQ 322

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +V+   +        +   K++     + L+++ +  +G+   C          +     
Sbjct: 323 QVALDYIGKRGATVGVTKEKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH--- 378

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   + +   K   +     
Sbjct: 379 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVN 438

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 439 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 498

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +   + + L     + +      I E +     +
Sbjct: 499 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEXGTE 558

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           +                 +   +      +  +   +     RR+    + GV R     
Sbjct: 559 NFEEISPAVIPQATKIFVB--GTWMGIHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRLK 616

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR-KVCDGKVTNDVV 615
           E+R ++  +     P    E   + +         +      ETP      D      + 
Sbjct: 617 ELR-IYTDYGRCSRPLFIVEKQKLLIKKK-----DIQQLQQRETPEEGGWHDLVAKGYIE 670

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE   I+              +LV      E      +     +  P  ++ + 
Sbjct: 671 YIDTEEEETTMISM----------TINDLVQASINPE--DAYSDTYTHCEIHPSLILGVC 718

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +      F                    R   +
Sbjct: 719 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------RMDTL 758

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             V                                       Q+PLV             
Sbjct: 759 AYV-----------------------------------LYYPQKPLV----------TTR 773

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    L  G N +VA   + GYN EDS+++++  +    F S+    +    +   
Sbjct: 774 AMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 833

Query: 856 LGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +E            +       +D+ G+   G  V+  D+++GK TP  +       
Sbjct: 834 TLVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD----- 888

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               A         +D S  +    +G V
Sbjct: 889 ----AQGQASRYTRKDHSTSLRHSETGMV 913


>gi|116563540|gb|ABJ99786.1| RpoB [Bacillus licheniformis]
          Length = 212

 Score =  347 bits (890), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 135/234 (57%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EI              D      +   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEIXDLVGENEYLRNTLDKDNTENTDKALL 212


>gi|253745453|gb|EET01374.1| DNA-directed RNA polymerase RPB2 [Giardia intestinalis ATCC 50581]
          Length = 1293

 Score =  347 bits (889), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 198/1359 (14%), Positives = 424/1359 (31%), Gaps = 230/1359 (16%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAA-----MLEFVSYEFD 82
            L  +Q  SY+HF+   +          +    S  PI    +        +L F   + +
Sbjct: 26   LAAMQIDSYNHFVKHTM----------KNIIASFPPIQVTRTENFCCYNHILSFSDPQLE 75

Query: 83   PPK-FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS--IYMGDLPLMT 139
            P      +DC  +  +Y   +K+ +   +           ++++  +   I     P+M 
Sbjct: 76   PNVHIKPNDCRIQSSSYMAAIKVKISYTIQQYSFSNNEGLVQEVTYEPKLIDFCLFPVMV 135

Query: 140  ------------------------------KDGTFVIKGIQRIVVSQ-------LHRSPG 162
                                          + G F+I+G ++ V++Q       L   PG
Sbjct: 136  NSCLCYLNTNRVLGSDIKAHRIINDECPYDEGGYFIIRGAEKAVIAQEGNRPNRLLILPG 195

Query: 163  IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
                          K+ Y  ++I           +    +H +I                
Sbjct: 196  ----------DPGSKIPYTAQLIS---------TNPAKNLHSKI---------------- 220

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
                 +L  +          D     ++     +   +   L+ +   +  + + + L S
Sbjct: 221  -----VLKYWSTNKWGRTIQDINQPQITFTMQGIRDDLPLFLLILALWQDNVYAARDLLS 275

Query: 283  GLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             ++    +  +    + S  L         +  +    G + +       +   + +   
Sbjct: 276  IVIPDESDTELIEHLLPSYNLFCSTPQSSKDKCIEFLAGRLIVGEQMDSAKAKYDRLMS- 334

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                  +L    V   +++          +    LL      R  D       + +    
Sbjct: 335  -HLSTRLLPHIGVTPESHLDKAFFIGYMTNL---LLQTVIGRRSPDDRDHWGGKRLQLTG 390

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
               +DK+            RL     D    ++  + I ++   ++  +         + 
Sbjct: 391  SLLADKFRFEY---ELFLRRLARKLHDTGSILKVREDINMVSPNIEGSSFIPQSKYDPHG 447

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +     +L         R++ +    IS     ++        + V +        
Sbjct: 448  KVPGLEDPRRLLD--------RIKVAATSYISKNITSALSTGTWKTNEVVGNT------K 493

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S +SQ    ++  S ++  RR S+     V      +  R +H T +G +CPAET EG  
Sbjct: 494  SGVSQSLVRLSYTSALSQIRRSSS----SVEETSKAIGPRLLHTTQFGYMCPAETPEGAK 549

Query: 580  IGLVSSLTSFARVNAYGFI-ETPYRKVC-DGKVTNDVVYLSAMEEE----NRYIAQANSS 633
            +GL+ + +  A V       E   RK+  + +V      +S ++      N     ++  
Sbjct: 550  VGLIKNFSLMANVTLDNPKDEQDLRKLLTEYRVQTQHGPISVLKSFHTVTNAKKLVSDVK 609

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +GS+   +           + R + +        +  +A      + +D+       
Sbjct: 610  IFLNGSWLGFIDRAYVQRLIADLKRWRFEGKINREVSIAYLAHKQEITINSDEGRVTRPV 669

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +  P LK          E  V   +      +   I+  +   + ++  ++   +
Sbjct: 670  FVVLTEIHPTLKLVTNLSLAITEEDVETLATIPQPEQWNSILAGLGTGKCMVEFLD--PN 727

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG-----DEVRRNDIIADGPSTDLG-DLAL 807
                 +    +  F+   Q     +  ++  G     D +R +++      T L    ++
Sbjct: 728  EEEMALICMDIYHFREEIQKAHAIRDIILTYGEENAIDYIRAHNVPLAHNYTHLEIHPSM 787

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLGPEEITRDI 865
              + + + +P+  +N     L    M  +   ++   +++ F+    +    P+      
Sbjct: 788  VLSAITSLIPFPDHNQSPRNLYQASMGKQAVGIYALNYLKRFDTSGINVMHYPQLPLVTT 847

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPG----DILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             ++     + +     + +   V  G    D L+   +      M              A
Sbjct: 848  RSMPHVKFRYLPAGQNVIIAIAVYSGFNQEDSLIMSQSAVDRGLMRATYYHTYEEMISSA 907

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
                +   R+         +++     G                            L+ +
Sbjct: 908  ASSINAPDRIEKFCRPIGPNIKGVKDPGCA------------------------SYLEAD 943

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
               R+   +  Q  + G     K T+ S              +  QD  ++  +E    +
Sbjct: 944  GLPRVGNAVNSQRLIIGKIRPNKRTMNSRA---------VSTYDFQDVSLKVKMEE-TGR 993

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             ++     + R ++ + +    +        + KV V   R  Q GDK + RHG KG V 
Sbjct: 994  VDSVIIAPDLREQSFLSEGVDSNATGAEGSLLAKVRVRSSRVPQLGDKFSSRHGQKGTVG 1053

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             +L  ED+PF  DG   DI++NP  +PSRM +GQ+ E+         G ++     +   
Sbjct: 1054 MLLRHEDLPFTLDGITPDIIMNPHAIPSRMTIGQLMESVASKLGALSGHEVDGTAFNAPP 1113

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                  + + L                                                 
Sbjct: 1114 GSTDKQIAADL------------------------------------------------- 1124

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                    +     + +G+TGE  +  + +G  +  +L HMV DK+ +R+TG    +T+Q
Sbjct: 1125 --HARGYQKHNYEAMMNGMTGEMMNYRIFIGPTFYQRLKHMVLDKISSRNTGPIVTLTRQ 1182

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P  G+SN GG R+GEME     A+GA  +L++ L   SD
Sbjct: 1183 PNEGRSNYGGMRIGEMEKDAFIAHGATAILRDRLLFSSD 1221


>gi|116563496|gb|ABJ99764.1| RpoB [Bacillus halodurans]
          Length = 212

 Score =  347 bits (889), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 90/234 (38%), Positives = 137/234 (58%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q ASY  FL          +EGL+  F+ + PI  F+G  +LEF+ Y   
Sbjct: 1   VLELPNLIEIQTASYQWFL----------DEGLREMFQDISPIQDFTGNLVLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ VD+   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT  G
Sbjct: 51  EPKYPVDESKERDVTYAAPLRVKVRLI---------NKETGEVKEQEVFMGDFPLMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP +++     +   +GK  Y   +IP++G W+++E D+KDI+
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYYSEKIDK---NGKKGYTATVIPNRGAWLELETDAKDIV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EI+             +      +   L+
Sbjct: 159 YVRIDRTRKIPVTVLLRALGFGSDQEIIDLLGEDEYLRNTLEKDNTDSAEKALL 212


>gi|116563500|gb|ABJ99766.1| RpoB [Bacillus atrophaeus]
 gi|116563636|gb|ABJ99834.1| RpoB [Bacillus atrophaeus]
 gi|116563638|gb|ABJ99835.1| RpoB [Bacillus atrophaeus]
 gi|116563640|gb|ABJ99836.1| RpoB [Bacillus atrophaeus]
 gi|116563642|gb|ABJ99837.1| RpoB [Bacillus atrophaeus]
 gi|116563644|gb|ABJ99838.1| RpoB [Bacillus atrophaeus]
 gi|116563646|gb|ABJ99839.1| RpoB [Bacillus atrophaeus]
 gi|116563648|gb|ABJ99840.1| RpoB [Bacillus atrophaeus]
          Length = 212

 Score =  347 bits (889), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 135/234 (57%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EI              D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEITDLIGENEYLRNTLDKDNTENSDKALL 212


>gi|183584765|gb|ACC63825.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949547|gb|ACS36570.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949551|gb|ACS36572.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949553|gb|ACS36573.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949555|gb|ACS36574.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949559|gb|ACS36576.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949567|gb|ACS36580.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949569|gb|ACS36581.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949573|gb|ACS36583.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949575|gb|ACS36584.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949579|gb|ACS36586.1| RNA polymerase subunit B [Acinetobacter baylyi]
 gi|239949587|gb|ACS36590.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949591|gb|ACS36592.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949595|gb|ACS36594.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949603|gb|ACS36598.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949611|gb|ACS36602.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949613|gb|ACS36603.1| RNA polymerase subunit B [Acinetobacter guillouiae]
 gi|239949615|gb|ACS36604.1| RNA polymerase subunit B [Acinetobacter guillouiae]
          Length = 286

 Score =  346 bits (888), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 131/290 (45%), Positives = 182/290 (62%), Gaps = 5/290 (1%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I +     R++ +L GQ +  G    K+   LS D++S        +    DE +   
Sbjct: 1    FKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEVQPTDEGIAER 59

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRH
Sbjct: 60   LTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRH 119

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG KI  
Sbjct: 120  GNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDK 179

Query: 1155 LINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            ++ + +    +  LR FL+K+    G   E +    D+ +L ++   + GVP++TPVFDG
Sbjct: 180  MMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPVFDG 236

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            A+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 237  AEESQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLV 286


>gi|318602976|emb|CBJ04570.1| RNA polymerase beta subunit [Pseudomonas sp. R-37123]
 gi|318603025|emb|CBJ04582.1| RNA polymerase beta subunit [Pseudomonas sp. R-37323]
 gi|318603122|emb|CBJ04600.1| RNA polymerase beta subunit [Pseudomonas sp. R-38757]
          Length = 356

 Score =  346 bits (887), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 210/356 (58%), Positives = 277/356 (77%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V 
Sbjct: 301 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQ 356


>gi|318603002|emb|CBJ04577.1| RNA polymerase beta subunit [Pseudomonas sp. R-37257]
          Length = 355

 Score =  345 bits (886), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 210/355 (59%), Positives = 278/355 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDQKVLVDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVV 355


>gi|309385707|gb|ADO66704.1| RNA polymerase beta subunit [Ureaplasma sp. CSL7743-GEN]
          Length = 764

 Score =  345 bits (886), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 227/540 (42%), Positives = 334/540 (61%), Gaps = 37/540 (6%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD------------------------- 494
           GN+R++ + E+L+ +    + R+E+ I E+++  D                         
Sbjct: 1   GNKRLKLIHELLRARVATSMSRIEKFISEKLAISDGSNANIANYTDNANLDEDEKNELEE 60

Query: 495 --IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
               +V  + ++N K   + + +FF S QL Q  +  N L+ +T+ RR+SA+G GG++R 
Sbjct: 61  EKKRAVTVKSIVNTKQFQTLIKDFFNSHQLIQFIDQQNPLAELTNKRRISAMGPGGISRE 120

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
              +++RDVH +HY RICP ET EG NIGL+ SL S A+V+  GFI  PY KV +G VT 
Sbjct: 121 DPNLDIRDVHHSHYSRICPIETPEGMNIGLIMSLASLAKVDENGFIVAPYFKVNNGVVTQ 180

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           + VYL+A E++N  I+++  +LDE+   T + V CR  G   L   E++D+ID  P+QVV
Sbjct: 181 EHVYLTAHEDDNFIISESAVNLDENYRITNDQVVCRYRGSTGLFKPEQVDYIDIVPRQVV 240

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           SIAAS IPF+ENDD  R LMG NMQRQ+VPL+K  AP VGTG E  +A  SG A+++K +
Sbjct: 241 SIAASAIPFIENDDGARALMGSNMQRQSVPLIKPYAPIVGTGTEYKIAHDSGMAVISKTS 300

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           G +  VDA +IV+                Y L+K+++SNQ+TC NQ P+V +  +V  N+
Sbjct: 301 GTISYVDAQKIVVTDENETD-------HTYELIKYRKSNQDTCNNQTPIVSLNQKVSANE 353

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
            IADGP+   G+LALGRN+LV +  W GYNFED+++ISER+VS DVFTSIHI+E  +   
Sbjct: 354 TIADGPAMQNGELALGRNVLVGYTTWSGYNFEDAIIISERLVSMDVFTSIHIDELTLQCV 413

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            TK G EEITRD+PNVS+   + +D+ GI+ VGAEV+ GD+LVGK TP+G   + PE+KL
Sbjct: 414 KTKNGDEEITRDMPNVSDHAKRFLDKDGIVFVGAEVHEGDVLVGKTTPRGNIDVNPEDKL 473

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGT---VVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           L+ IFG+K+  V+D+S++V  G  G    V  ++    +  +  +  + + +  I    +
Sbjct: 474 LQTIFGDKSKSVKDSSMKVKHGQEGIVAAVKRIKATEANNNELPDDVLEIVKIYIVQKRK 533



 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 124/335 (37%), Positives = 183/335 (54%), Gaps = 23/335 (6%)

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            +    +   +  G     G     K+T   +  I   P  +  Q    D+       S+K
Sbjct: 434  KRFLDKDGIVFVGAEVHEGDVLVGKTTPRGN--IDVNPEDKLLQTIFGDKSKSVKDSSMK 491

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V++      +    K         +++P  VL +VK+++  KR IQ GDKMAGRHGNKGI
Sbjct: 492  VKHGQ--EGIVAAVKRIKATEANNNELPDDVLEIVKIYIVQKRKIQVGDKMAGRHGNKGI 549

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK-IKSLIND 1158
            VS+++P +DMPFL DGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +GKK + ++  +
Sbjct: 550  VSKVVPIQDMPFLADGTPLDIMLNPLGVPSRMNIGQILELHLGYAASEIGKKELINIPFN 609

Query: 1159 YKANGDISPLRSF----LEKVIGTGSHTEKISDYDDDSVLRVAEQW-----------KSG 1203
             +       L        E++ G      +     D   + V +Q               
Sbjct: 610  NQGYEKYVSLFGLTDIVAERLYGKMRDFIENKKITDPKQIDVLDQLIILNSLGLSFDDVA 669

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + V+TPVFDG   + + +++  A++D   + G+ +LYDG TG+ FD  +++G+ YMLKL+
Sbjct: 670  IKVATPVFDGVKTDDLVAIMNEAEIDIKEKKGKQVLYDGRTGDAFDGLISIGHTYMLKLD 729

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            HMV DK+++RS G YS +TQQPLGGKS  GGQR G
Sbjct: 730  HMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFG 764


>gi|306410411|gb|ADM85827.1| DNA-directed RNA polymerase beta chain [Frankia alni]
 gi|306410413|gb|ADM85828.1| DNA-directed RNA polymerase beta chain [Frankia alni]
 gi|306410415|gb|ADM85829.1| DNA-directed RNA polymerase beta chain [Frankia alni]
 gi|306410417|gb|ADM85830.1| DNA-directed RNA polymerase beta chain [Frankia alni]
 gi|306410421|gb|ADM85832.1| DNA-directed RNA polymerase beta chain [Frankia sp. CpI1]
          Length = 217

 Score =  345 bits (886), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 117/246 (47%), Positives = 151/246 (61%), Gaps = 38/246 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   + GD++PPGV  +V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPFL+DG
Sbjct: 2    RVFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRHGNKGVIAKILPQEDMPFLEDG 61

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDIVLNP GVP RMN+GQI ETHLGW     G ++ +   D+K               
Sbjct: 62   TPVDIVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDAGTEDWKERLRGIG-------- 112

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                                 A+    G  V+TPVFDGA EE I  +L     +      
Sbjct: 113  ---------------------ADSSTPGTNVATPVFDGAREEEITGLLDSTLPNRDGVQL 151

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G++ L+DG TGEP+  PV VGYIY+LKL H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 152  IGSSGKATLFDGRTGEPYPYPVAVGYIYILKLLHLVDDKIHARSTGPYSMITQQPLGGKA 211

Query: 1288 NRGGQR 1293
              GGQR
Sbjct: 212  QFGGQR 217


>gi|55975962|gb|AAQ72384.2| RpoB [Klebsiella variicola]
 gi|55975970|gb|AAQ72382.2| RpoB [Klebsiella variicola]
 gi|55975972|gb|AAQ72379.2| RpoB [Klebsiella variicola]
          Length = 347

 Score =  345 bits (886), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 219/347 (63%), Positives = 275/347 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R++
Sbjct: 121 PYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+
Sbjct: 301 CVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 347


>gi|289190490|gb|ADC93350.1| RNA polymerase beta subunit [Rhizobium tropici]
          Length = 197

 Score =  345 bits (886), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 134/197 (68%), Positives = 160/197 (81%)

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+VSRI+P EDMPFL+DGT VDIVLNPLGVPSRMNVGQI ETHLGWAC G+G++I  LI 
Sbjct: 1    GVVSRIVPVEDMPFLEDGTHVDIVLNPLGVPSRMNVGQILETHLGWACAGMGRQIGELIE 60

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             YKA+G+I PLR  ++ V+G G  ++ + +YDD SVLR+A+QWK GV ++TPVFDGA E 
Sbjct: 61   AYKASGNIEPLRQTIDMVVGDGPKSDDVHEYDDASVLRLADQWKRGVSIATPVFDGAGEV 120

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +N ML MA L ++GQS LYDG TGE FDR VTVGYIYMLKLNH+V DK++ARS G YSL
Sbjct: 121  DVNEMLAMAGLKQTGQSTLYDGRTGEQFDRQVTVGYIYMLKLNHLVDDKIHARSIGPYSL 180

Query: 1278 VTQQPLGGKSNRGGQRL 1294
            VTQQPLGGK+  GGQR 
Sbjct: 181  VTQQPLGGKAQFGGQRF 197


>gi|290751448|emb|CAQ16385.1| RNA polymerase beta subunit [Pseudomonas sp. R-27204]
          Length = 354

 Score =  345 bits (885), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 208/350 (59%), Positives = 271/350 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 2   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 61

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  
Sbjct: 62  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHV 121

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 122 IAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAASLIPFLEHDD 181

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 182 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 241

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 242 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 301

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKL
Sbjct: 302 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKL 351


>gi|165918911|ref|ZP_02218997.1| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii RSA 334]
 gi|165917381|gb|EDR35985.1| DNA-directed RNA polymerase, beta subunit [Coxiella burnetii RSA 334]
          Length = 217

 Score =  345 bits (885), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 110/193 (56%), Positives = 140/193 (72%), Gaps = 1/193 (0%)

Query: 1160 KANGDISPLRSFLEKVIGTGSHTE-KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +   D   LR  L+ +          +   +D  ++ +A+  + GVP+S+PVFDGA EE 
Sbjct: 8    EKGADAKELRKSLKPIYDLSKTQRFDLEALEDPEIVTLAKNLRKGVPISSPVFDGATEEE 67

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I  +L+MADL  SGQ+ LYDG TG+ FDR VTVGY+YMLKLNH+V DK++ARSTGSYSLV
Sbjct: 68   IKQLLKMADLPTSGQAALYDGRTGKKFDRSVTVGYMYMLKLNHLVDDKMHARSTGSYSLV 127

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQEMLT+KSDDV GRTR+Y++IV G+  
Sbjct: 128  TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTRMYKNIVDGDHR 187

Query: 1339 FETGTPESFNVLV 1351
             + G PESF  L+
Sbjct: 188  MDAGMPESFGRLI 200


>gi|15679063|ref|NP_276180.1| DNA-directed RNA polymerase subunit B' [Methanothermobacter
            thermautotrophicus str. Delta H]
 gi|3122768|sp|O27124|RPOB1_METTH RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|2622149|gb|AAB85541.1| DNA-dependent RNA polymerase, subunit B' [Methanothermobacter
            thermautotrophicus str. Delta H]
          Length = 603

 Score =  345 bits (885), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 122/585 (20%), Positives = 198/585 (33%), Gaps = 95/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A  P    +    + I    +       I         R+T     
Sbjct: 97   IEYLDAEEEENAYIAMSPDEINDEHTHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S   L+         +        +    I   G       +  + A+   
Sbjct: 157  TKQALGLYASNYDLR---TDTRAHLLHHPQVPIVKTRIIDVTGYDERPSGQNFVVAVMSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +   +     F R       R    + ++ E+  +        + 
Sbjct: 214  EGYNMEDALILNKASLERGLARSSFF-RSYEAAERRYPGGQEDRFEIPEKG-------VR 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                      L     ++         VL           +  +F    E+ +    ++ 
Sbjct: 266  GYRSESDYRHLDEDGIINPEAEVSSGDVLIGKTSPPRFLEEIDEFGTVAERRRETSVTV- 324

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                        R   K               R+ K+ V  +R  + GDK A RHG KG+
Sbjct: 325  ------------RHGEKGIVDAVLLTETVEGSRLAKIRVREQRQPELGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  I+  EDMPF +DG   D+++NP  +PSRM+VGQ+ E   G A    G+++       
Sbjct: 373  VGLIVSQEDMPFTEDGIVPDLIVNPHAIPSRMSVGQVLEMLAGKAACMEGRRVDG----- 427

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                            TP F G DE+ I
Sbjct: 428  ------------------------------------------------TP-FTGEDEDDI 438

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               LR    + +G   LY+G+TGE  +  + +G  Y  KL+HM +DKVYARS G   ++T
Sbjct: 439  KEALRANGFETAGVESLYNGITGERIEAEIFIGVAYYQKLHHMTTDKVYARSRGPVQVLT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVGRTRVYES 1331
            +QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD        D  G   VY+ 
Sbjct: 499  RQPTEGRAREGGLRFGEMERDCLIAHGAALALKERLLDESDKYEALVCAD-CGMIAVYDK 557

Query: 1332 IVAGNDTF--------ETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            I                     +F +L+ E+++L +   L     
Sbjct: 558  IRDKKYCPICEDSESFPVEVSYAFKLLLDELKSLCIFPKLILEDK 602



 Score = 51.6 bits (122), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 52/184 (28%), Gaps = 31/184 (16%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
                +  +   RR   +                +         P    E     L    
Sbjct: 18  NPEEFVEEMRKKRRSGEVSPEMNITHYPENHEIYIFTDPGRARRPLIIVEDGEPLLTEEH 77

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                      +ET      D      + YL A EEEN YIA +   ++           
Sbjct: 78  LE--------KLETGEMSWDDLIAAGIIEYLDAEEEENAYIAMSPDEIN----------- 118

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                       ++   ++  P  ++ I A +IPF  ++ S R  M   M +QA+ L  +
Sbjct: 119 ------------DEHTHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGMTKQALGLYAS 166

Query: 707 EAPF 710
               
Sbjct: 167 NYDL 170


>gi|309322098|ref|YP_003933914.1| RNA polymerase beta subunit [Erodium texanum]
 gi|300069191|gb|ADJ66313.1| RNA polymerase beta subunit [Erodium texanum]
          Length = 1064

 Score =  345 bits (884), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 216/605 (35%), Positives = 352/605 (58%), Gaps = 13/605 (2%)

Query: 369 DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            +++A+L+ Y+      GD              FF   + +L  +GR  +N RLNL    
Sbjct: 272 SKENAILEFYQQFVCVGGDPVFSDSLCKELQNQFF-RQRCELGRIGRRNINRRLNLAISQ 330

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSVG++L++Q RL L+R+E+ +
Sbjct: 331 NNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIRSVGDLLQDQLRLALIRLEKVV 390

Query: 487 KE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           K   R +        PQ+ + + P+ +    FF    LSQ+ +  N L++I H R+ S L
Sbjct: 391 KRAIREAMKGKLIPTPQNFVTSTPLKTTYESFFGLHPLSQVLDETNPLTQIVHGRKWSFL 450

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+    A    RD+HP++YGRIC  +TSEG N+GL+ SL   AR+  +G +E+P+ +
Sbjct: 451 GPGGLTGQTASFRRRDIHPSYYGRICTIDTSEGINVGLIGSLAIHARIGDFGSLESPFYE 510

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + +      ++YLS+  +E   I   NS    +    E++V  R   E + +  E++   
Sbjct: 511 ISEKSKRARILYLSSRRDEYCMIGIGNSLALNESFQEEQIVPARYRQEFLTIAWEQVHLR 570

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              P Q +SI  SLIPF+E++D+ R LM  NMQRQAV L ++E   VGTG+E  VA  SG
Sbjct: 571 SIFPFQYISIGVSLIPFIEHNDATRALMSSNMQRQAVALSRSEKCIVGTGLEGQVALDSG 630

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            +++ + AG +  +          +  L           L+++QRSN+NTC++Q+P V+ 
Sbjct: 631 VSLITEHAGKIISIH--------TDKILLSGNGNTLSIPLVRYQRSNKNTCIHQQPQVRW 682

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G  +++  I+ADG ST  G+LALG+N+LVA+MPW GYNFED++LISER+V ED+ TS HI
Sbjct: 683 GKCIKKGQILADGASTVGGELALGKNLLVAYMPWEGYNFEDAVLISERLVYEDILTSFHI 742

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            ++E+    T  GPE++T  IP+++   L+N+ + G++ +G+ V  GDILVGK+ P+   
Sbjct: 743 RKYEIQIHVTNQGPEKVTNKIPHLAPHLLRNLGKNGVVILGSWVEAGDILVGKLRPRLAQ 802

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            ++PE++ + A+ G +    R T L+VP G  G V+DVR    +   ++ +  S ER ++
Sbjct: 803 DVSPEDRFVDALLGTQIATSRPTCLKVPRGGRGRVIDVRWIRSNPERESRKRKSRERIRV 862

Query: 965 ELLAR 969
            +  +
Sbjct: 863 YISQK 867



 Score =  263 bits (673), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 87/220 (39%), Positives = 122/220 (55%), Gaps = 39/220 (17%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG P+D+V NPLGVPSRM
Sbjct: 858  ERIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGKPIDMVFNPLGVPSRM 917

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQIFE  LG A   L +  +    D +   + S    F E    +             
Sbjct: 918  NVGQIFECSLGLAGALLDRHYRVAPFDERYEQEASRKLVFSELHEASKQTGNPW------ 971

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                              VF+                +  G+S ++DG TG+PF++PV V
Sbjct: 972  ------------------VFE---------------PEYPGKSRIFDGRTGDPFEQPVIV 998

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G  Y+LKL H V DK++ RSTG Y+ +TQQP+ G++  GG
Sbjct: 999  GQPYILKLIHQVDDKIHGRSTGHYTPLTQQPVKGRAKGGG 1038



 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 69/379 (18%), Positives = 136/379 (35%), Gaps = 63/379 (16%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-------FVS 78
           IP L ++Q   +  F+   +  +      ++   K    I  F   A LE       F+ 
Sbjct: 12  IPGLNQIQFEGFCRFVDQGLREELSKFPTVEGLIKDFLDIEDFLDMANLEDLEDLEDFLD 71

Query: 79  Y--------------------------------------EFDPPKFDVDDCLWRDLTYAV 100
                                                  +   P     D ++  LTY+ 
Sbjct: 72  AVGQDLEKEVDEGIDIDEDVDEDVEKDVDVCFQLFAETSKLVEPLIKERDAVYESLTYSS 131

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
            L ++  LI      +        +++Q+I +G++PLM   G F++ G+ R+VV+Q+ +S
Sbjct: 132 ELYVSAGLIWKRKGYY--------MQKQTILIGNIPLMNSWGVFIVNGMYRMVVNQILQS 183

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
           PGI++  +       G L+Y   II D G  +++E D K  I  R+ R++K+ +     A
Sbjct: 184 PGIYYRSELDHK---GILVYTGTIISDWGGRLELEIDRKGRIWARVSRKQKISILVLSSA 240

Query: 221 LGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           +G +  EIL    YP+++ +   D     + + +  +       +             K+
Sbjct: 241 MGSNLSEILENVCYPELLLAFLYDKENATIGSKENAILEFYQQFVCVGGDPVFSDSLCKE 300

Query: 280 LTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           L +   +   E G       +  L         ++    +   T  +      +     +
Sbjct: 301 LQNQFFRQRCELGRIGRRNINRRLNLAISQNNTFLLPRDILAATDHLIGMKFGMGTLDDM 360

Query: 334 EEIFHSEIRDIPILYVDSV 352
             + +  IR +  L  D +
Sbjct: 361 NHLKNKRIRSVGDLLQDQL 379


>gi|52694149|emb|CAG30604.1| DNA-directed RNA polymerase beta chain [Pseudomonas asplenii]
          Length = 354

 Score =  345 bits (884), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 213/354 (60%), Positives = 278/354 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           LV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V
Sbjct: 301 LVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVV 354


>gi|146263054|gb|ABQ15297.1| RpoB [Yersinia enterocolitica subsp. enterocolitica]
 gi|146263056|gb|ABQ15298.1| RpoB [Yersinia enterocolitica subsp. enterocolitica]
 gi|146263058|gb|ABQ15299.1| RpoB [Yersinia enterocolitica]
 gi|146263060|gb|ABQ15300.1| RpoB [Yersinia enterocolitica]
 gi|146263074|gb|ABQ15307.1| RpoB [Yersinia rohdei]
 gi|146263076|gb|ABQ15308.1| RpoB [Yersinia intermedia]
 gi|146263078|gb|ABQ15309.1| RpoB [Yersinia mollaretii]
 gi|146263080|gb|ABQ15310.1| RpoB [Yersinia frederiksenii]
 gi|146263082|gb|ABQ15311.1| RpoB [Yersinia bercovieri]
          Length = 349

 Score =  344 bits (883), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 220/349 (63%), Positives = 277/349 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+
Sbjct: 301 CVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 349


>gi|111054571|gb|ABH04343.1| RNA polymerase beta subunit [Proteus mirabilis]
          Length = 346

 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 214/346 (61%), Positives = 267/346 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +  VT+++ YLSA+EE N  IAQANS LD+DG F EELV CR  GE  L  R++
Sbjct: 121 PYRVVENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDGHFVEELVTCRHKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           + ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA
Sbjct: 181 VQYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDETYAGEAGIDIYSLTKYTRSNQNTCINQTP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            V +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN+EDS
Sbjct: 301 CVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNYEDS 346


>gi|146263066|gb|ABQ15303.1| RpoB [Yersinia ruckeri]
 gi|146263068|gb|ABQ15304.1| RpoB [Yersinia massiliensis]
 gi|146263070|gb|ABQ15305.1| RpoB [Yersinia massiliensis]
          Length = 349

 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 220/349 (63%), Positives = 277/349 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+
Sbjct: 301 CVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 349


>gi|309385709|gb|ADO66705.1| RNA polymerase beta subunit [Ureaplasma sp. CSL7644-GEN]
 gi|313799155|gb|ADR82158.1| RNA polymerase beta subunit [Ureaplasma sp. CSL7590-GEN]
          Length = 761

 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 218/494 (44%), Positives = 315/494 (63%), Gaps = 10/494 (2%)

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
              ++   K  +      +V  + ++N K   + + +FF S QL Q  +  N L+ +T+ 
Sbjct: 44  NANLDEDEKNELEEEKKRAVTVKSIVNTKQFQTLIKDFFNSHQLIQFIDQQNPLAELTNK 103

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SA+G GG++R    +++RDVH +HY RICP ET EG NIGL+ SL S A+V+  GFI
Sbjct: 104 RRISAMGPGGISREDPNLDIRDVHHSHYSRICPIETPEGMNIGLIMSLASLAKVDENGFI 163

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
             PY KV +G VT + VYL+A E++N  I+++  +LDE+   T + V CR  G   L   
Sbjct: 164 VAPYFKVNNGVVTQEHVYLTAHEDDNFIISESAVNLDENYRITNDQVVCRYRGSTGLFKP 223

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           E++D+ID  P+QVVSIAAS IPF+ENDD  R LMG NMQRQ+VPL+K  AP VGTG E  
Sbjct: 224 EQVDYIDIVPRQVVSIAASAIPFIENDDGARALMGSNMQRQSVPLIKPYAPIVGTGTEYK 283

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
           +A  SG A+++K +G +  VDA +IV+                Y L+K+++SNQ+TC NQ
Sbjct: 284 IAHDSGMAVISKTSGTISYVDAQKIVVTDENETD-------HTYELIKYRKSNQDTCNNQ 336

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            P+V +  +V  N+ IADGP+   G+LALGRN+LV +  W GYNFED+++ISER+VS DV
Sbjct: 337 TPIVSLNQKVSANETIADGPAMQNGELALGRNVLVGYTTWSGYNFEDAIIISERLVSMDV 396

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           FTSIHI+E  +    TK G EEITRD+PNVS+   + +D+ GI+ VGAEV+ GD+LVGK 
Sbjct: 397 FTSIHIDELTLQCVKTKNGDEEITRDMPNVSDHAKRFLDKDGIVFVGAEVHEGDVLVGKT 456

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT---VVDVRIFNRHGIDKNER 955
           TP+G   + PE+KLL+ IFG+K+  V+D+S++V  G  G    V  ++    +  +  + 
Sbjct: 457 TPRGNIDVNPEDKLLQTIFGDKSKSVKDSSMKVKHGQEGIVAAVKRIKATEANNNELPDD 516

Query: 956 SISVEREQIELLAR 969
            + + +  I    +
Sbjct: 517 VLEIVKIYIVQKRK 530



 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 124/335 (37%), Positives = 183/335 (54%), Gaps = 23/335 (6%)

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            +    +   +  G     G     K+T   +  I   P  +  Q    D+       S+K
Sbjct: 431  KRFLDKDGIVFVGAEVHEGDVLVGKTTPRGN--IDVNPEDKLLQTIFGDKSKSVKDSSMK 488

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V++      +    K         +++P  VL +VK+++  KR IQ GDKMAGRHGNKGI
Sbjct: 489  VKHGQ--EGIVAAVKRIKATEANNNELPDDVLEIVKIYIVQKRKIQVGDKMAGRHGNKGI 546

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK-IKSLIND 1158
            VS+++P +DMPFL DGTP+DI+LNPLGVPSRMN+GQI E HLG+A   +GKK + ++  +
Sbjct: 547  VSKVVPIQDMPFLADGTPLDIMLNPLGVPSRMNIGQILELHLGYAASEIGKKELINIPFN 606

Query: 1159 YKANGDISPLRSF----LEKVIGTGSHTEKISDYDDDSVLRVAEQW-----------KSG 1203
             +       L        E++ G      +     D   + V +Q               
Sbjct: 607  NQGYEKYVSLFGLTDIVAERLYGKMRDFIENKKITDPKQIDVLDQLIILNSLGLSFDDVA 666

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLD---ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            + V+TPVFDG   + + +++  A++D   + G+ +LYDG TG+ FD  +++G+ YMLKL+
Sbjct: 667  IKVATPVFDGVKTDDLVAIMNEAEIDIKEKKGKQVLYDGRTGDAFDGLISIGHTYMLKLD 726

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            HMV DK+++RS G YS +TQQPLGGKS  GGQR G
Sbjct: 727  HMVDDKIHSRSVGPYSKITQQPLGGKSQNGGQRFG 761


>gi|307178142|gb|EFN66950.1| DNA-directed RNA polymerase III subunit RPC2 [Camponotus floridanus]
          Length = 1120

 Score =  344 bits (883), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 184/1117 (16%), Positives = 353/1117 (31%), Gaps = 205/1117 (18%)

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE----- 340
            + + E+  K +  + +        +  + G+ G+ YI      D+  +  +F +      
Sbjct: 171  RIIVEEDGKEIIASCNSFTHEKKTKTSIVGKAGKYYIRNNMFQDDILITVVFKAMGIVSD 230

Query: 341  IRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA-ESMFN 397
            I  I ++       + +I              K AL  +    R    +    A  S+ +
Sbjct: 231  IDIIQMIGEKEKYLDKFIACIENCQELGIFSEKQALKYLNNKRRQTRSAQSYAAKFSVID 290

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             +        LS V  +  N R            +   +  +I+ ++D ++ +  ID+ D
Sbjct: 291  EMKDLLAANVLSHVPVIDFNFRT-----------KALHLALMIRRVIDAQSDRNLIDNKD 339

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS----VMPQDLINAKPVVSAV 513
              GN+R+   G +L   +     R    +K                    I    + + +
Sbjct: 340  YYGNKRLELAGSLLALMFEDLFKRFNWELKMIADKNIPKVKAAPFDITKYIRKDTITNGL 399

Query: 514  CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTH 565
                 S   +     +          RLS +   G+         + R     R +H + 
Sbjct: 400  AFAISSGNWTIKRFRMERHGVTQVLSRLSYISALGMMTRVHSQFEKTRKISGPRALHGSQ 459

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CP +T EG   GLV +L   A +      E P+ K+        +      E   +
Sbjct: 460  WGMLCPNDTPEGEACGLVKNLALMAHITTE-MPEGPFIKLMRNLGVQIIYTCVGGELIKK 518

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             I     + +  G   E LV        +L     ID         +S+         + 
Sbjct: 519  DIYVVFVNGNMAGIIKESLVLQLVHQFRLLRRMGYIDCF-----VSISVQRRHKCVQVSC 573

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R+     + +   PL++ E       M                      V A  I  
Sbjct: 574  DGGRLCRPLIIVKDGKPLIE-EKHMNYLEMNLWTFND--------------FVHAGLIEY 618

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              V  + D   +              ++  + Q   +++ +           P  +    
Sbjct: 619  LDVNEENDSLIA------------CKESEIIAQTTHLEIAEFTILGVCAGLIPYPNHNQS 666

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                     +    G     ++  ++R   + +  ++                    R I
Sbjct: 667  P-----RNTYQCAMGKQAIGAIGYNQRNRIDTLMYNLVY----------------PQRPI 705

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                +  L N D+                           +   E  L A+      D+ 
Sbjct: 706  VKTRQIELINFDK---------------------------LPAGENALVAVMSFSGYDIE 738

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +   + +        ++          S  + +     +        VIL +++ + 
Sbjct: 739  DALILNKASIDRGYGRCLVY--------RNSKCIIKNHPNQVMD------VILGQSLDAI 784

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
              + +   + +          ++ +    +   ++       +    R+       Y ++
Sbjct: 785  TKKPIPKHDILENDGIAAAGVMVENK---KVMVNKAVSTRSGNLGPSRSDNFQSQDYRSA 841

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
            +   +      IEK+    +       ++K+ +   R  + GDK + RHG KG+V  I+ 
Sbjct: 842  EVSYKGSVPAYIEKVMVSSNAENAF--LIKLLLRQTRRPEIGDKFSSRHGQKGVVGLIVD 899

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             ED+PF   G   D+++NP G PSRM VG++ E   G A +  GK               
Sbjct: 900  QEDLPFNDYGICPDVIMNPHGFPSRMTVGKLIEVLAGKAGIVNGKF-------------- 945

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +T  F+GA  E +   L  
Sbjct: 946  ---------------------------------------HDAT-AFEGAKVEDLCEELAQ 965

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
               +  G+ + Y G+ G+P    +  G +Y  KL HMV DK++ R+ G   ++T+QP  G
Sbjct: 966  HGYNYLGKDLFYSGMNGQPITGYLFFGPVYYQKLKHMVQDKIHVRAKGPKVILTRQPTEG 1025

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAGND---- 1337
            +S  GG RLGEME  C+  YGA+ +L E L + SD    D+       +  + G +    
Sbjct: 1026 RSKDGGLRLGEMERDCLIGYGASMLLIERLMLSSDSFQVDICN-----KCGLMGYNGWCQ 1080

Query: 1338 -------TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                         P +  +L +E+Q + +   L    
Sbjct: 1081 RCSSSSSISTITMPYACKLLFQELQCMNILPRLTLKD 1117



 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 119/969 (12%), Positives = 268/969 (27%), Gaps = 218/969 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    SY++F+   I    + NE       S            +++++     P    
Sbjct: 22  LVKQHIDSYNYFINKEIKNIVKANE---KVLSS----EDA--HFYIKYLNIRVGLPDIDD 72

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDL Y+ P+ + +  I          ++ + I+  ++ +G +P+M
Sbjct: 73  GSNVMKSTTPHECRLRDLNYSAPIIVDIEHI----------RNNQRIRNTNMVIGRMPVM 122

Query: 139 T------------------------KDGTFVIKGIQRIVVS--QLHR------------- 159
                                      G FVI G +++++   Q+ R             
Sbjct: 123 LRSSNCVLTNKSHYELAKLNECPHDPGGYFVINGQEKVILIQEQMVRNRIIVEEDGKEII 182

Query: 160 -SPGIHFDHDKGRASLSGKL-LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            S        K + S+ GK   Y  R                + +      +  + +T  
Sbjct: 183 ASCNSFTHEKKTKTSIVGKAGKYYIR----------------NNMF-----QDDILITVV 221

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
             A+G+ S+ +I+     K  Y    D +   +     +       +L  ++   +   S
Sbjct: 222 FKAMGIVSDIDIIQMIGEKEKY---LDKFIACIENCQELGIFSEKQALKYLNNKRRQTRS 278

Query: 277 GKKLTSGL-----LKSLKEKG-VKFLGITSDCLCGLYVA-----EDIVNGETGEIYIEAG 325
            +   +       +K L     +  + +         +        +++ ++    I+  
Sbjct: 279 AQSYAAKFSVIDEMKDLLAANVLSHVPVIDFNFRTKALHLALMIRRVIDAQSDRNLIDNK 338

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D    K LE            L+         I +  +       K A  DI + +R  D
Sbjct: 339 DYYGNKRLELAGSLLALMFEDLFKRFNWELKMIADKNIPKV----KAAPFDITKYIRK-D 393

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
             T  +A +  +   +   ++ +   G  ++  RL+  +   +            KI   
Sbjct: 394 TITNGLAFA-ISSGNWTIKRFRMERHGVTQVLSRLSYISALGMMTRVHSQFEKTRKISGP 452

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
                       +     +    +  + +    +  +           +   +     + 
Sbjct: 453 ---------RALHGSQWGMLCPNDTPEGEACGLVKNLALMAHITTEMPEGPFIKLMRNLG 503

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE-MRDVHPT 564
            + + + V        +  +  + N    I  +  L  + Q  + R    ++    +   
Sbjct: 504 VQIIYTCVGGELIKKDIYVVFVNGNMAGIIKESLVLQLVHQFRLLRRMGYIDCFVSISVQ 563

Query: 565 HYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
              +        G     +  +             ++E       D      + YL   E
Sbjct: 564 RRHKCVQVSCDGGRLCRPLIIVKDGKPLIEEKHMNYLEMNLWTFNDFVHAGLIEYLDVNE 623

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E +  IA   S +                         +   ++ +   ++ + A LIP+
Sbjct: 624 ENDSLIACKESEIIA-----------------------QTTHLEIAEFTILGVCAGLIPY 660

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             ++ S R    C M +QA+  +         G                           
Sbjct: 661 PNHNQSPRNTYQCAMGKQAIGAI---------GYNQRNRID------------------- 692

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                                          N    QRP+VK                 +
Sbjct: 693 ---------------------------TLMYNLVYPQRPIVK----------TRQIELIN 715

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
              L  G N LVA M + GY+ ED++++++  +       +     + + ++      ++
Sbjct: 716 FDKLPAGENALVAVMSFSGYDIEDALILNKASIDRGYGRCLVYRNSKCIIKNHPNQVMDV 775

Query: 862 T-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                   I          ++  GI   G  V    ++V K        + P        
Sbjct: 776 ILGQSLDAITKKPIPKHDILENDGIAAAGVMVENKKVMVNKAVSTRSGNLGPSRSDNFQS 835

Query: 917 FGEKAVDVR 925
              ++ +V 
Sbjct: 836 QDYRSAEVS 844


>gi|40388703|gb|AAR85529.1| RNA polymerase II [Botryotinia fuckeliana]
          Length = 952

 Score =  344 bits (882), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 163/984 (16%), Positives = 309/984 (31%), Gaps = 157/984 (15%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +       S+        
Sbjct: 97   VSDEDILNHICYDRNDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGNGTSL---TRDKR 153

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             KY    + +  +      +  +  +      +  ++  L+    G+   DD D+ G +R
Sbjct: 154  IKYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHKLLQCALGRRETDDRDHFGKKR 210

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    R+   +    +    +         + +  + + +     +  
Sbjct: 211  LDLAGPLLAKLFRNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGN 270

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 271  WGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 326

Query: 569  ICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L    +  V         +    + +V  +   L A      +
Sbjct: 327  VCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVF 386

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN- 684
            +      +  D +   + V        I      I +  D   K          P L   
Sbjct: 387  VNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVID 446

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA--AIVAKRAGIVEQVDAIR 742
            +D +    G  +  +       +   +   M+      +G          G+VE +DA  
Sbjct: 447  NDPDSANKGNLVLNKDHIRRLEDDQLLPANMDKDEKVRNGYYGFQGLINDGVVEYLDAEE 506

Query: 743  I---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                +I     DLD S      Y++    R +++  +N+R    +             PS
Sbjct: 507  EETVMITMTPEDLDISRQLQAGYQI----RPDESGDLNKRVKAPINPTAHVWTHCEIHPS 562

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N                        ++       +G  
Sbjct: 563  MILG-------ICASIIPFPDHNQSPRNC------------------YQSAMGKQAMGVF 597

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D+               +  +             +       +   +  + AI   
Sbjct: 598  LTNFDVRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCY 646

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L 
Sbjct: 647  SGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLK 702

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +  Y +L +   +  G           K+  ++ D                +E  QR   
Sbjct: 703  QGTYDKLDDDGIVAPGVRVTGADIIIGKTAPIAPD---------------SEEMGQRTKA 747

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +K    T     E    +++             LR VKV +   +  Q GDK A RHG 
Sbjct: 748  HVKRDASTPLRSTESGLVDQVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQ 802

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      +DMPF ++G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 803  KGTIGITYMQQDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATP 862

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L                         LR       G  +          
Sbjct: 863  FTEVTVDSVSKL-------------------------LRAHGYHSRGFEIM--------- 888

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G +    G         V +G  Y  +L HMV DK++AR+ G   
Sbjct: 889  -------------YHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDKIHARARGPVQ 928

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVW 1300
            ++T+QP+ G++  GG R GEME  
Sbjct: 929  ILTRQPVEGRARDGGLRFGEMERD 952



 Score =  132 bits (333), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 112/862 (12%), Positives = 233/862 (27%), Gaps = 146/862 (16%)

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
            G F+I G ++++++Q  RS          +   +  + Y   I    ++G  +      
Sbjct: 1   GGYFIINGSEKVLIAQE-RSAANI--VQVFKKPANSAVSYLAEIRSALEKGSRLISSLQI 57

Query: 199 KDIIHVRIDRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQR 241
           K  ++ + D  R                 +P+     ALG +  E+IL+        +Q 
Sbjct: 58  K--LYDKGDSNRGGFGKTVKSTLPYIKADIPIAIVFRALGVVSDEDILNHICYDRNDTQM 115

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            +     +  A ++   +V+   +        +   K++     + + +K +        
Sbjct: 116 LEMLKPCIEEAFVIQDREVALDFIGKRGNGTSLTRDKRI--KYARDIMQKEL-------- 165

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
                      ++ + G    +A  +              R+                  
Sbjct: 166 --------LPHISQKEGSETRKAFFLGYMVHKLLQCALGRRETDDRDHFGKKRLDLAGPL 217

Query: 362 LVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           L        +    D+YR + R  + +               +        G      + 
Sbjct: 218 LAKLFRNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKA 277

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
              T    + + +    + +  L        R+GK       +  +  +    E  + Q 
Sbjct: 278 ASSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 337

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEE 527
              +  +       + +     V      N + +         +A   F     +    +
Sbjct: 338 CGLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVGIHRD 397

Query: 528 HVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHN 579
             + +  +   RR   +  +  + R     E        R   P       P   ++G+ 
Sbjct: 398 PAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNDPDSANKGNL 457

Query: 580 IGLVSSL-------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           +     +          A ++    +   Y           V YL A EEE   I     
Sbjct: 458 VLNKDHIRRLEDDQLLPANMDKDEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPE 517

Query: 633 SLDEDG--------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            LD              E     +     I          +  P  ++ I AS+IPF ++
Sbjct: 518 DLDISRQLQAGYQIRPDESGDLNKRVKAPINPTAHVWTHCEIHPSMILGICASIIPFPDH 577

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           + S R      M +QA+ +               V   + A I+      +    ++  +
Sbjct: 578 NQSPRNCYQSAMGKQAMGVFLT---------NFDVRMDTMANILYYPQKPLATTRSMEFL 628

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                     +   +  Y              NQ                    S  +  
Sbjct: 629 KFRELPAGQNAIVAIMCYSG-----------YNQE------------------DSVIMNQ 659

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            ++ R +  +       + E  + ++     E  + S                      D
Sbjct: 660 SSIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPYRS----------------------D 697

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              + +     +D+ GI+  G  V   DI++GK  P         ++        KA   
Sbjct: 698 TLKLKQGTYDKLDDDGIVAPGVRVTGADIIIGKTAPIAPDSEEMGQRT-------KAHVK 750

Query: 925 RDTSLRVPSGVSGTVVDVRIFN 946
           RD S  + S  SG V  V I  
Sbjct: 751 RDASTPLRSTESGLVDQVLITT 772


>gi|260159598|gb|ACX32467.1| RNA polymerase subunit B [Acinetobacter sp. Du6]
          Length = 276

 Score =  344 bits (882), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 132/280 (47%), Positives = 182/280 (65%), Gaps = 5/280 (1%)

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     R++ +L GQ +  G  G K+   LS D++S        +    DE +   +  +
Sbjct: 1    EEAARERIVRLLSGQESNGG-GGTKRGDKLSEDMLSGLELVDLLEIQPSDEAIAERLTQI 59

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG
Sbjct: 60   QVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKG 119

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++  
Sbjct: 120  VVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKML-- 177

Query: 1159 YKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA+E 
Sbjct: 178  -KQQREIAELRVFLDKIYNKVGGQQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGAEES 236

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             I  +L +A++  SGQ++LYDG TGE FDRPVTVGY+YML
Sbjct: 237  QIKELLELAEIPRSGQTVLYDGRTGERFDRPVTVGYMYML 276


>gi|52694207|emb|CAG30633.1| DNA-directed RNA polymerase beta chain [Pseudomonas oleovorans]
          Length = 345

 Score =  343 bits (881), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 208/344 (60%), Positives = 267/344 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV   V EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAVEVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 122 KVTDEIVFLSAIEEADHVIAQASATLNDKGELVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 242 ARRGGVIDSVDASRIVVRVNDNEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            R DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SER
Sbjct: 302 SRGDIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSER 345


>gi|55975968|gb|AAR13020.2| RNA polymerase beta subunit [Klebsiella variicola]
          Length = 346

 Score =  343 bits (881), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 218/346 (63%), Positives = 274/346 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++
Sbjct: 121 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 181 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 241 DSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPC 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+
Sbjct: 301 VSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 346


>gi|52694305|emb|CAG37992.1| RNA polymerase beta subunit [Pseudomonas pertucinogena]
          Length = 350

 Score =  343 bits (881), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 215/351 (61%), Positives = 271/351 (77%), Gaps = 1/351 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNEYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           +V D  VT+++V+LSA+EE +  IAQA++ +  DG   EELV  R   E  +   E++  
Sbjct: 121 RVKDTVVTDEIVFLSAIEEADHVIAQASAEV-RDGKLVEELVAVRHMNEFSVKAPEEVTL 179

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SP+QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  S
Sbjct: 180 MDVSPRQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVALDS 239

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  + A+R G+V+ VDA RIVIR  + +++   +GVDIY L+K+ RSNQNTC+NQRPLVK
Sbjct: 240 GVCVTARRGGVVDSVDASRIVIRVNDDEVEAGEAGVDIYTLIKYTRSNQNTCINQRPLVK 299

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            GD V   DI+ADG S D+G+LALG+NM VAFMPW+GYNFEDS+LISER+V
Sbjct: 300 KGDVVAVKDILADGSSVDMGELALGQNMRVAFMPWNGYNFEDSILISERVV 350


>gi|124028419|ref|YP_001013739.1| DNA-directed RNA polymerase subunit B [Hyperthermus butylicus DSM
            5456]
 gi|123979113|gb|ABM81394.1| DNA-directed RNA polymerase subunit B [Hyperthermus butylicus DSM
            5456]
          Length = 1138

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 117/586 (19%), Positives = 205/586 (34%), Gaps = 94/586 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     N  +A  P         M I    +     ++I   E     R+T      
Sbjct: 628  EFLDAEEEENTYIALNPEDLTPEHTHMEIWPAGIFGVTASTIPYAEHNQSPRNTYQAAMA 687

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                    +   ++         +        +    +   G +     + ++ A+    
Sbjct: 688  KQALGLYAANFQIRV---DTRSHLLHYPEKPLVQTRALELMGYNDRPAGQNMVVAVMSFT 744

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +   S +    +    F R    +  R      ++IE+   +       ++ 
Sbjct: 745  GYNIEDAVIMNKSSIDRG-LARSTFFRLYATEERRYPGGLSDKIEIPEAN-------VEG 796

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +    + + L     +S     K   VL           ++ +F               V
Sbjct: 797  SKPPEMYKKLDADGIISPEVEVKGGEVLIGKTSPPRFMEEYREF-------------GTV 843

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                  + +  R   K               ++VKV V  +R  + GDK A RHG KG++
Sbjct: 844  TVRKRDTSVTMRHGEKGVVDTVIITENIEGYKLVKVRVRDQRIPELGDKFASRHGQKGVI 903

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              ++P  DMPF +DG   D+++NP   PSRM +GQ+FET  G       + +        
Sbjct: 904  GMLIPQYDMPFTEDGITPDLIINPHAFPSRMTLGQLFETIAGKYAAIYARFVDG------ 957

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                           TP F     E + 
Sbjct: 958  -----------------------------------------------TP-FAKESIENLR 969

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L        G  I+YDG TGE    P+ +G +Y  KL+HMV+DK++AR+ G   ++T+
Sbjct: 970  IELLKTGYAPDGTEIMYDGRTGEMIRTPILIGLVYYQKLHHMVADKIHARARGPVQVLTR 1029

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------RTR 1327
            QP  G++  GG R GEME  C+  +GAA +L+E +   SD       ++ G      R +
Sbjct: 1030 QPTEGRAREGGLRFGEMERDCLVGHGAAMLLRERMLESSDRYVLYVCELCGHIAWFDRNK 1089

Query: 1328 -VYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
              Y   V G+         P +F +L++E+ ++ +   L+ +    
Sbjct: 1090 RGYICPVHGDKGKIAAVIVPYAFKLLLQELMSMCIMPRLKLASKHE 1135



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 113/738 (15%), Positives = 219/738 (29%), Gaps = 118/738 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY+ F+             L+   K    I+       +  V  E   P    
Sbjct: 25  LVKQHIDSYNRFIEKE----------LKEIVKEFGTISTPRREYEVRIVDVELGEPIVIE 74

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTYA P+K  + ++   ++             + I +G LP+M
Sbjct: 75  SDGSEHPVTPMECRIRDLTYAAPIKAKVVIVENGIEREA----------EEIILGFLPVM 124

Query: 139 T---------------------------------KDGTFVIKGIQRIVVSQ----LHRSP 161
                                               G F+I G +R++V Q    L+R  
Sbjct: 125 LRSKADPLARCMYEGKSWKECEQKLIEAGEDPRDPGGYFIINGSERVIVIQEDQALNR-- 182

Query: 162 GIHFDHDKGRASLSGKLLYACRIIP-DQGLWMDIEFD-SKD-IIHVRIDRR-RKVPVTSF 217
            I     +   + +   LY  ++I    G+   +  D  KD  +HV + R   K+P    
Sbjct: 183 -ILVGKARAGTASA---LYTAKVISAHAGVRYQVILDYHKDGTLHVSMSRALSKIPFVIL 238

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
           + ALG++S+ +I+    P     Q        L  A  +   + +   V     E + + 
Sbjct: 239 MRALGLESDRDIVLAVSPDPQIQQM---LIPSLEQARAINTVEDALDYVGSRFREGLAKP 295

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--E 334
            ++      + L       +G +        +    +  +  E         D+     +
Sbjct: 296 REQRIRVAERILDTILFPHIGTSPKDRIRKALFLGQMAAKLLEYVAGRRKEDDKDHYANK 355

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
            +  +      +  +        IR  L   + + R  +L  I R     D+ T  + E+
Sbjct: 356 RVLLAGDLIAMVFRIAMRALAYDIRQQLEKLRARGRHISLRMIIR----SDIITNRLREA 411

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI- 453
           +    +          + R      L+      V  + +       + +   + G+    
Sbjct: 412 LATGNWPGQRTGVSQILDRTNWLSMLSHLRRV-VSQLSRTQPHFEARDVHGTQWGRICPF 470

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSA 512
           +  +      V+++  M      +    +E+ +        ++     +      P    
Sbjct: 471 ETPEGPNCGLVKNLALMAYVSAGVDDKDVEKLLYSMGVRDAVELFEEVRKQGYYPPEYIK 530

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
             + F + +L         L+      R S    G +    +    R             
Sbjct: 531 WSKVFLNGRLIGYHPDGEKLAEELRKLRRS----GKLHYEVSVSVYRTETINEVYINTDP 586

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                    + S    + R      +     +  D      V +L A EEEN YIA    
Sbjct: 587 GRIMRPVFVVESGKLLY-RPEHAEKLRKGEWRFSDLVRNGIVEFLDAEEEENTYIALNPE 645

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L  +                          ++  P  +  + AS IP+ E++ S R   
Sbjct: 646 DLTPEH-----------------------THMEIWPAGIFGVTASTIPYAEHNQSPRNTY 682

Query: 693 GCNMQRQAVPLLKAEAPF 710
              M +QA+ L  A    
Sbjct: 683 QAAMAKQALGLYAANFQI 700



 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 115/591 (19%), Positives = 211/591 (35%), Gaps = 54/591 (9%)

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           ++ T    R  +   +  +   L++   G+   DD D+  N+RV   G+++   +R+ + 
Sbjct: 314 HIGTSPKDRIRKALFLGQMAAKLLEYVAGRRKEDDKDHYANKRVLLAGDLIAMVFRIAMR 373

Query: 481 RMERSIKERISSVDIDSVMPQ---------DLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +   I++++  +                      +  ++        + +SQ+ +  N 
Sbjct: 374 ALAYDIRQQLEKLRARGRHISLRMIIRSDIITNRLREALATGNWPGQRTGVSQILDRTNW 433

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS ++H RR+ +     ++R +   E RDVH T +GRICP ET EG N GLV +L   A 
Sbjct: 434 LSMLSHLRRVVS----QLSRTQPHFEARDVHGTQWGRICPFETPEGPNCGLVKNLALMAY 489

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYL--------SAMEEENRYIAQANSSLDEDG----S 639
           V+A    +   + +    V + V              E         N  L         
Sbjct: 490 VSAGVDDKDVEKLLYSMGVRDAVELFEEVRKQGYYPPEYIKWSKVFLNGRLIGYHPDGEK 549

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE-NDDSNRVLMGCNMQR 698
             EEL   R +G+        +   +   +  ++     I       +S ++L       
Sbjct: 550 LAEELRKLRRSGKLHYEVSVSVYRTETINEVYINTDPGRIMRPVFVVESGKLLYRPEHAE 609

Query: 699 QAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------KRAGIVEQVDAIRIVIRSVE 749
           +        +  V  G+ E + A+      +A        +   +      I  V  S  
Sbjct: 610 KLRKGEWRFSDLVRNGIVEFLDAEEEENTYIALNPEDLTPEHTHMEIWPAGIFGVTASTI 669

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG----DEVRRNDIIADG-PSTDLGD 804
              + + S  + Y+    +++      N +  V           +  +           D
Sbjct: 670 PYAEHNQSPRNTYQAAMAKQALGLYAANFQIRVDTRSHLLHYPEKPLVQTRALELMGYND 729

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
              G+NM+VA M + GYN ED++++++  +   +  S     +    R    G  +   +
Sbjct: 730 RPAGQNMVVAVMSFTGYNIEDAVIMNKSSIDRGLARSTFFRLYATEERRYPGGLSD-KIE 788

Query: 865 IPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           IP          E  K +D  GII    EV  G++L+GK +P        E        G
Sbjct: 789 IPEANVEGSKPPEMYKKLDADGIISPEVEVKGGEVLIGKTSPPRFMEEYREF-------G 841

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              V  RDTS+ +  G  G V  V I       K  +    ++   EL  +
Sbjct: 842 TVTVRKRDTSVTMRHGEKGVVDTVIITENIEGYKLVKVRVRDQRIPELGDK 892


>gi|116563534|gb|ABJ99783.1| RpoB [Bacillus amyloliquefaciens]
          Length = 212

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 135/234 (57%), Gaps = 23/234 (9%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +S   FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSXXWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           +VRIDR RK+PVT  L ALG  S+ EIL             D      S   L+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL 212


>gi|257438254|ref|ZP_05614009.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium
           prausnitzii A2-165]
 gi|257199331|gb|EEU97615.1| DNA-directed RNA polymerase, beta subunit [Faecalibacterium
           prausnitzii A2-165]
          Length = 292

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 91/251 (36%), Positives = 134/251 (53%), Gaps = 24/251 (9%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG 70
              R  F    E+I +P+LIEVQK SY  FL          +EGL+  F  +  I  ++G
Sbjct: 11  KTERMSFSHIDEVISMPNLIEVQKNSYQWFL----------DEGLKEVFHDIGTIEDYTG 60

Query: 71  AAMLEFVSYEFD-PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              L FV +  D  PK+ + +C  RD+TYA PL++T RL+          K   ++K+Q 
Sbjct: 61  NLALSFVDFRLDKEPKYSIKECKERDVTYAAPLRVTARLL---------NKETGEVKDQE 111

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           I+MGD PLMT  GTFVI G +R +VSQL RSPG+ +   K +    G  LY+  + P++G
Sbjct: 112 IFMGDFPLMTDAGTFVINGAERAIVSQLVRSPGVFYGDAKDKV---GNDLYSATMNPNRG 168

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
            W++ E D+ ++ +VRID+ RK+PVT    ALG+ S+ EIL+ F          +     
Sbjct: 169 AWLEYETDAANVFYVRIDKNRKLPVTVLCRALGLSSDEEILNFFGEDERILATLEKDTTK 228

Query: 249 LSAADLMVGAK 259
                L+   +
Sbjct: 229 NQDEGLLEVYR 239


>gi|126339649|ref|XP_001365927.1| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Monodelphis domestica]
          Length = 1133

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 105/505 (20%), Positives = 175/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSSVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM VG++ E   G                                        
Sbjct: 930  NPHGFPSRMTVGKLIELLAGK--------------------------------------- 950

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A          T  F G+  + +   L     +  G+  +  G+TG
Sbjct: 951  --------------AGVLDGKFHYGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 114/947 (12%), Positives = 272/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    +I    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNIAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  +E  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKMEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 584 SSLTSF---ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
             +              +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTEKHMDELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSSVPQQPQYKDVP 855


>gi|146263072|gb|ABQ15306.1| RpoB [Yersinia aldovae]
          Length = 349

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 217/349 (62%), Positives = 277/349 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFLEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+L+
Sbjct: 301 CVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 349


>gi|67937436|gb|AAY83285.1| RNA polymerase beta subunit [Mycoplasma imitans]
          Length = 670

 Score =  343 bits (880), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 217/451 (48%), Positives = 307/451 (68%), Gaps = 15/451 (3%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +T+ RR+SA+G GG++R    +++RDVH +HYGRICP ET EG NIGL+ SL  
Sbjct: 1   QNPLSELTNKRRISAMGPGGISREDPNLDIRDVHYSHYGRICPIETPEGMNIGLIMSLAF 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS--SLDEDGSFTEELVF 646
           +A ++  GF+ TPY KV +GK+T+ V +L+A+ E+   IA+A+S  ++ +DG+   E + 
Sbjct: 61  YATIDKNGFLMTPYLKVENGKITDKVEHLTALREDEYIIAEASSYMNVAKDGTIQNEKII 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R    + L   +++D+ID SPKQVVS+AASLIPFLENDDS+R LMG NMQRQA PLLK 
Sbjct: 121 ARYRSSQDLYDPKQVDYIDVSPKQVVSVAASLIPFLENDDSSRALMGANMQRQATPLLKP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            +P VGTG+E  +A+ SG  + AK+ G V  VDA +I I+  +            Y L+K
Sbjct: 181 YSPLVGTGVEYKIAQDSGMLVTAKKPGTVTYVDASKITIKDEDNKKTD-------YNLLK 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F +SN+NTC NQ P+V VGD+V  N  +ADGPS   G++ALG+N+LV F  W GYN+ED+
Sbjct: 234 FVKSNKNTCYNQSPIVAVGDKVDANQALADGPSMKNGEIALGQNVLVGFTTWSGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++IS+R+  EDV++SIHI+E+ +    TK G EEITRDIPN+SE   + +DE G+I VGA
Sbjct: 294 VIISDRLFKEDVYSSIHIDEYTIECLRTKNGDEEITRDIPNISESAKRYLDEEGVIMVGA 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVGK +PKG+  ++PEEKL++AI G+K   VR++SL+VP+G  G V  ++ F+
Sbjct: 354 EVKEGDILVGKTSPKGQVELSPEEKLIQAILGDKVKGVRESSLKVPNGGDGIVAGIKRFS 413

Query: 947 RHGIDKNERSISVEREQIELLARDKDDEQVI 977
               D       +E + +EL+      ++ I
Sbjct: 414 IANGD------ELEDDVLELVKVYVVQKRKI 438



 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 143/520 (27%), Positives = 224/520 (43%), Gaps = 41/520 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLI-SERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                       +L  + P  G   E  +   S  +V+     ++   +   +    +   
Sbjct: 166  MGANMQRQATPLLKPYSPLVGTGVEYKIAQDSGMLVTAKKPGTVTYVDASKITIKDEDNK 225

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +     +  V        ++  I+ VG +V+    L    + K    +   + +L     
Sbjct: 226  KTDYNLLKFVKSNKNTCYNQSPIVAVGDKVDANQALADGPSMKN-GEIALGQNVLVGFTT 284

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA-RDKDDEQVI 977
                +  D  +              I +R   +    SI ++   IE L  ++ D+E   
Sbjct: 285  WSGYNYEDAVI--------------ISDRLFKEDVYSSIHIDEYTIECLRTKNGDEEITR 330

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               NI       L  +  +      K+  +L      +       +  +    +   V+ 
Sbjct: 331  DIPNISESAKRYLDEEGVIMVGAEVKEGDILVGKTSPKGQVELSPEEKLIQAILGDKVKG 390

Query: 1038 LKVQYETSKSILEDRFK-NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
            ++       +  +      K   I  GD++   VL +VKV+V  KR IQ GDK+AGRHGN
Sbjct: 391  VRESSLKVPNGGDGIVAGIKRFSIANGDELEDDVLELVKVYVVQKRKIQIGDKVAGRHGN 450

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KGI+S+I+  EDMP L+DGTP+DI+LNPLGVPSRMN+GQIFE HLG+A   L  K     
Sbjct: 451  KGIISKIVAQEDMPHLEDGTPLDILLNPLGVPSRMNIGQIFELHLGYAARELANKRLIEA 510

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV--AEQWKSGVP--------- 1205
                           L+K          +       V  +  A+     +          
Sbjct: 511  CFDDKLAAELNTIFGLDKSKTDSLIKNLVQHMKSIGVTNLNQAKNLVRTIHIDIVLKQLG 570

Query: 1206 ---------VSTPVFDGADEEAINSMLRMADLDES---GQSILYDGLTGEPFDRPVTVGY 1253
                     ++TPVF+G + + + S++  A +D     G+  L DG TGEPF++P++VG 
Sbjct: 571  LTYDDLAFKIATPVFEGVNMDDLKSIMSEAGIDPDKTEGKFKLIDGRTGEPFEKPISVGI 630

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +YMLKL+HMV DK++AR+ G YS +TQQPLGGKS  GGQR
Sbjct: 631  MYMLKLDHMVDDKIHARAVGPYSKITQQPLGGKSQNGGQR 670


>gi|304315185|ref|YP_003850332.1| DNA-directed RNA polymerase, subunit B' [Methanothermobacter
            marburgensis str. Marburg]
 gi|302588644|gb|ADL59019.1| DNA-directed RNA polymerase, subunit B' [Methanothermobacter
            marburgensis str. Marburg]
          Length = 603

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 124/616 (20%), Positives = 206/616 (33%), Gaps = 106/616 (17%)

Query: 781  LVKVGDEVRRNDIIADGPS-------------TDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            +VK G+ + + + +    S              +  D     N  +A  P    +    +
Sbjct: 65   IVKDGEPLLKEEHLEKLESGEMEWDDLINEGIIEYLDAEEEENAYIAMSPEDLTDEHTHL 124

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
             I    +       I         R+T              S   L+         +   
Sbjct: 125  EIDPSTMLGICAGIIPFANHNSSPRNTMEAGMTKQALGLYASNYDLR---TDTRAHLLHH 181

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                 +    I   G       +  + A+   +  ++ D  +   + +   +     F R
Sbjct: 182  PQVPIVKTRIIDVTGYDERPSGQNFVVAVMSYEGYNMEDALILNKASLERGLARSSFF-R 240

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
                   R    + ++ E+  +        +           L     ++         V
Sbjct: 241  SYEAAERRYPGGQEDRFEIPEKG-------VRGYRSESDYRHLDEDGIINPEAVVSSGDV 293

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L           +  +F    E+ +    ++             R   K           
Sbjct: 294  LIGKTSPPRFLEEIDEFGTVAERRRETSVTV-------------RHGEKGIVDAVLLTET 340

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                R+ K+ V  +R  + GDK A RHG KG+V  I+  EDMPF +DG   D+++NP  +
Sbjct: 341  VEGSRLAKIRVREQRQPELGDKFASRHGQKGVVGLIVSQEDMPFTEDGVVPDLIVNPHAI 400

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM+VGQ+ E   G A    G+++                                   
Sbjct: 401  PSRMSVGQVLEMLAGKAACMEGRRVDG--------------------------------- 427

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  I   LR    + +G   LY+G+TGE  + 
Sbjct: 428  --------------------TP-FTGEDERDIKKALRANGFESAGVESLYNGITGERIEA 466

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G  Y  KL+HM +DKVYARS G   ++T+QP  G++  GG R GEME  C+ A+GA
Sbjct: 467  EIFIGVAYYQKLHHMTTDKVYARSRGPVQVLTRQPTEGRAREGGLRFGEMERDCLIAHGA 526

Query: 1308 AYVLQEMLTIKSDDV-------VGRTRVYESIVAGNDTF--------ETGTPESFNVLVK 1352
            A  L+E L  +SD          G   +Y+ I                     +F +L+ 
Sbjct: 527  ALALKERLLDESDKYEALVCTECGMIAIYDKIRDKKYCPICEDSESFPVEISYAFKLLLD 586

Query: 1353 EMQALGLSIDLENSRT 1368
            E+++L +   L     
Sbjct: 587  ELKSLCIFPKLILEDK 602



 Score = 52.4 bits (124), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/113 (23%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E+   +  D      + YL A EEEN YIA +   L                       
Sbjct: 81  LESGEMEWDDLINEGIIEYLDAEEEENAYIAMSPEDLT---------------------- 118

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            ++   ++  P  ++ I A +IPF  ++ S R  M   M +QA+ L  +    
Sbjct: 119 -DEHTHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGMTKQALGLYASNYDL 170


>gi|55975958|gb|AAQ72383.2| RpoB [Klebsiella variicola]
 gi|55975960|gb|AAQ72385.2| RpoB [Klebsiella pneumoniae]
 gi|55975964|gb|AAQ72381.2| RpoB [Klebsiella variicola]
          Length = 345

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 218/345 (63%), Positives = 273/345 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++
Sbjct: 121 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 181 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 241 DSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPC 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS
Sbjct: 301 VSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDS 345


>gi|52694299|emb|CAG37989.1| RNA polymerase beta subunit [Pseudomonas asplenii]
          Length = 353

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 212/353 (60%), Positives = 276/353 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E + 
Sbjct: 121 RVVKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V 
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQ 353


>gi|67810752|gb|AAY82003.1| RNA polymerase II second largest subunit [Psilotum nudum]
          Length = 614

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 138/755 (18%), Positives = 237/755 (31%), Gaps = 148/755 (19%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   + +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMSYITVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +  +G +             +   R ++   D + +  V     L       
Sbjct: 54   AVIPQATKIFVNGCWVGIHRDPELLVRTLRQLRRQV---DVNTEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +      L+K          ES  +  +   +VAK  G +E VD      
Sbjct: 111  DYGRCSRPLFIVENQRLLIKKSHIRALQQKESTXS--AWYDLVAK--GFIEYVDTEEEET 166

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +  +     +  D                                     PS  LG  
Sbjct: 167  TMISMNXSDXEAARDHPEEA---------------------YSDTYTHCEIHPSMILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLFYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        IF R   D+  +  ++ +E+ E   R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSIFYRSYRDEEXKQGTLVKEEFERPNRETXTNMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T LS                  D+   +     K    T 
Sbjct: 349  DGLTPPGTRVSGEDVIIGKTTPLSQ-----------------DDTGNQAQRYSKRDQSTC 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK+ V   R  Q GDK + RHG KG V     
Sbjct: 392  LRXSESGMIDQVLLTTNADGL-----RFVKIRVRSIRVPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ ++G   DI++NP  +PSRM +GQ+ E  +G     +G++              
Sbjct: 447  QEDMPWTQEGISPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGREGD------------ 494

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++I+  L  
Sbjct: 495  -----------------------------------------ATP-FTDVTVDSISKALHK 512

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G   +Y+G T    +  + +G  Y  +L HMV DK+++R  G   ++T+QP  G
Sbjct: 513  CGYQMRGFETMYNGHTXRRLNAMIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEG 572

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 573  RSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 607



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 53/329 (16%), Positives = 101/329 (30%), Gaps = 36/329 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 11  EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 71  IHRDPELLVRTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVENQRLLI 129

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S    A           Y  V  G     + Y+   EEE   I+   S  +      E
Sbjct: 130 KKS-HIRALQQKESTXSAWYDLVAKGF----IEYVDTEEEETTMISMNXSDXEAARDHPE 184

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E               +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 185 E------------AYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 703 LL----------------KAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           +                   + P V T  ME +  +   A I A  A            +
Sbjct: 233 IYVTNYQLRMDTLAYVLFYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 292

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 293 IMNQSSIDRGFFRSIFYRSYRDEEXKQGT 321


>gi|70794966|gb|AAZ08457.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum]
          Length = 1191

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 113/603 (18%), Positives = 192/603 (31%), Gaps = 104/603 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 657  HDLVAKGFIEYIDTEEEETTMISMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 716

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 717  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTVAYVLYYPQKPLVTTRAMEH 773

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 774  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 832

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T ++           
Sbjct: 833  KEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVVIGKTTPIAQ---------- 882

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE         +  + TS    E    +++      D +     R VKV V  
Sbjct: 883  -------DEAQGPAARYTRRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 930

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 931  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECI 990

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 991  MGKVAAHMGKEGD----------------------------------------------- 1003

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L 
Sbjct: 1004 ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQRLK 1056

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 1057 HMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 1116

Query: 1321 ----DVVGR----------TRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSID 1362
                 V  R             +E    G     D  +   P +  +L +E+ ++ ++  
Sbjct: 1117 AYRIHVCERCGLIAIANLKKNSFEC--RGCKNKTDIVQVHIPYACKLLFQELMSMAIAPR 1174

Query: 1363 LEN 1365
            +  
Sbjct: 1175 MLT 1177



 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 138/989 (13%), Positives = 284/989 (28%), Gaps = 195/989 (19%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 38  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 88

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 89  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 148

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             +  +++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 149 FTK--VFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMS 206

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR---------- 208
              ++      +     K  Y   +        + +      + VR+  R          
Sbjct: 207 TNHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPPSTMFVRMLSRTSAKGGSSGQ 258

Query: 209 ---------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                    R ++P+     ALG  ++ +IL         +Q  +     L  A ++   
Sbjct: 259 YIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQ 318

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +V+   +        +   K++     + L+++ +  +G+   C          +     
Sbjct: 319 QVALDYIGKRGATVGVTKEKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH--- 374

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A     E   +   +  +    P+L          +   +     K   +     
Sbjct: 375 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVN 434

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDI 436
            +        T  +  S+    +  ++           +N      T   +R +      
Sbjct: 435 LQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGR 494

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
              +     L N +  +         +      ++KN   +  + +  +    +  ++  
Sbjct: 495 EGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEW 551

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
                + I+   +  A   F     +    +    +  +   RR   +  + GV R    
Sbjct: 552 GTENFEEISPAVIPQATKIFVNGCWVGIHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRL 611

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+R ++  +     P    E   + L+      A        +       D      + 
Sbjct: 612 KELR-IYTDYGRCSRPLFIVEKQRL-LIKRKDIQALQQRETPEDGG---WHDLVAKGFIE 666

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+   EEE   I+              +LV  R   E      E     +  P  ++ + 
Sbjct: 667 YIDTEEEETTMISM----------TINDLVSARLNPE--EAYSETYTHCEIHPSLILGVC 714

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +      F                    R   V
Sbjct: 715 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF--------------------RMDTV 754

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             V                                       Q+PLV             
Sbjct: 755 AYV-----------------------------------LYYPQKPLV----------TTR 769

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    L  G N +VA   + GYN EDS+++++  +    F S+    +    +   
Sbjct: 770 AMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 829

Query: 856 LGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +E        +   +       +D+ G+   G  V+  D+++GK TP  +       
Sbjct: 830 TLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVVIGKTTPIAQDE----- 884

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               A         RD S  +    +G V
Sbjct: 885 ----AQGPAARYTRRDHSTSLRHSETGMV 909


>gi|146263062|gb|ABQ15301.1| RpoB [Yersinia kristensenii]
 gi|146263064|gb|ABQ15302.1| RpoB [Yersinia kristensenii]
          Length = 349

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 219/349 (62%), Positives = 276/349 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LDEDG F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTSVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            V +G+ + R D++ADGPSTDLG+LALG+NM VA MPW+GYNFEDS+L+
Sbjct: 301 CVNLGEPIERGDVLADGPSTDLGELALGQNMRVASMPWNGYNFEDSILV 349


>gi|82749760|gb|ABB89764.1| RNA polymerase beta subunit [Acholeplasma vituli]
          Length = 631

 Score =  342 bits (878), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 238/455 (52%), Positives = 312/455 (68%), Gaps = 33/455 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGRICP ET EG +IGL+SSL S+
Sbjct: 2   NPLAELTQKRRVSALGTGGLARDRAGVEVRDVHESHYGRICPIETPEGPSIGLISSLASY 61

Query: 590 ARVNAYGFIETPYRKVCD-----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TPY KV         VT++ VY +A EEE+  IA A+S  DE+G F  E 
Sbjct: 62  AKVDQYGFIQTPYLKVDKSNPDKPFVTSEYVYFTAGEEEHHIIASADSQTDENGYFKTET 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE      +K+DF+D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 VIGRFMGETKTYSSKKVDFMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
             ++P VGTG+E   AK SG+AIVA   G+V   DA +IVI         +T G      
Sbjct: 182 VPDSPIVGTGIEYRSAKDSGSAIVAHVDGVVTYADARKIVIAVKPEASIKTTRGKLVYDK 241

Query: 759 ----------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                                  + Y L +F RSNQ+T + Q+P+V++G+++ R D+IAD
Sbjct: 242 DTEFNWEAYDQIRQAKMTDLLRFETYELTQFLRSNQDTSILQKPIVQIGEKIDRGDVIAD 301

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GPS + G+LALGRN++VAFM W GYN+ED++++SE +V  DV+TSIHI+E +V +RDTKL
Sbjct: 302 GPSINKGELALGRNVVVAFMTWEGYNYEDAVIMSEDLVKNDVYTSIHIDEHQVESRDTKL 361

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           G EEITR+IPNVS + LK +D+ G++  G EV  GDILVGKITPKG++  TPEEKLL+AI
Sbjct: 362 GKEEITREIPNVSPDALKFLDDRGVVIPGTEVKEGDILVGKITPKGQTEPTPEEKLLQAI 421

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           F EKA +VRDTSL+VP G  G V  ++ F++   D
Sbjct: 422 FNEKAREVRDTSLKVPHGGGGIVHSIQYFSKSNGD 456



 Score =  285 bits (728), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 122/449 (27%), Positives = 193/449 (42%), Gaps = 77/449 (17%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
             A+ T L   E       +      +I +  I+ +G +++ GD++    +   +  +   
Sbjct: 255  QAKMTDLLRFETYELTQFLRSNQDTSILQKPIVQIGEKIDRGDVIADGPS-INKGELALG 313

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELL 967
              ++ A    +  +  D  +     V   V      + H ++  +  +  E    +I  +
Sbjct: 314  RNVVVAFMTWEGYNYEDAVIMSEDLVKNDVYTSIHIDEHQVESRDTKLGKEEITREIPNV 373

Query: 968  ARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            + D     D++ ++      +  +IL G+    G         L   + +E  R      
Sbjct: 374  SPDALKFLDDRGVVIPGTEVKEGDILVGKITPKGQTEPTPEEKLLQAIFNEKAR------ 427

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          ++            GD++ PGV  V++V++  KR I
Sbjct: 428  -----EVRDTSLKVPHGGGGIVHSIQY------FSKSNGDELGPGVNEVIRVYIVKKRKI 476

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG++S+ILP EDMP++ DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 477  SEGDKMAGRHGNKGVISKILPREDMPYMADGTPIDIMLNPLGVPSRMNIGQVLEIHLGMA 536

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG KI + + D     D+  + S                                  
Sbjct: 537  AKKLGIKIATPVFDGLTQEDLKEIMSEAGMSNDGKQVL---------------------- 574

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                       G        TGEP++  V+VG +YM+KL+HMV 
Sbjct: 575  -------------------------YDG-------RTGEPYENRVSVGVMYMIKLSHMVD 602

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            DK++ARS G Y+LVTQQP+GGK+  GGQR
Sbjct: 603  DKLHARSVGPYTLVTQQPMGGKAQNGGQR 631


>gi|325182727|emb|CCA17182.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B isoform
            2 putative [Albugo laibachii Nc14]
          Length = 1177

 Score =  342 bits (877), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 96/342 (28%), Positives = 139/342 (40%), Gaps = 67/342 (19%)

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             Y  S +  +    + ++K+            +VKV +   R  + GDK + RHG KG+ 
Sbjct: 889  SYGPSPTCYKGAVPSIVDKVLITSSETYQTSLLVKVLLRQTRRPEIGDKFSSRHGQKGVC 948

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I   EDMPF   G   D+++NP G PSRM VG++ E   G A V  G++        K
Sbjct: 949  GTICSQEDMPFNDQGICPDLIMNPHGFPSRMTVGKMIELVAGKAGVLHGRRAYGTAFGEK 1008

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                   L                                                   +
Sbjct: 1009 YGTADRVL-------------------------------------------------ECS 1019

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L  A  + +G+  L  G+TGEP    + +G IY  KL HMV DK++AR+ G  +++T+
Sbjct: 1020 RDLVKAGFNYAGKDYLTSGITGEPLLCYIFMGPIYYQKLKHMVMDKMHARARGPRAVLTR 1079

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--RTRVYESIVA 1334
            QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV    R   YE    
Sbjct: 1080 QPTEGRSRDGGLRLGEMERDCLIGYGASMLLMERLMISSDGFKADVCQGCRMLGYE---- 1135

Query: 1335 G--------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            G        +       P +  +L +E+Q + +   L    T
Sbjct: 1136 GWCPSCNSPDKVASIRIPYACKLLFQELQGMNIVPRLTLKET 1177



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 119/977 (12%), Positives = 251/977 (25%), Gaps = 238/977 (24%)

Query: 26  IPDLIEV------QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
           +P  +++         S+D+F    +              +S            L++   
Sbjct: 41  LPYFLQLRGLVKQHIDSFDYFTATELKKIVHAKA--NNVVRS-----DADPKFFLQYTDI 93

Query: 80  EFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           +   P                C  RD TYA P+ ++++            +  K +    
Sbjct: 94  QIGNPSIEEDAFVSSTVTPHQCRLRDRTYAAPVYVSVKY----------RRGPKIVTNNK 143

Query: 130 IYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHF 165
           + +G +P+M                           G F++KG++++V+  +H       
Sbjct: 144 VLIGRIPIMLRSANCVLTGKNHTQLAALKECPYDPGGYFIVKGVEKVVL--IH------- 194

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR---RK----------- 211
                +           R+I        +E D K  I   I      RK           
Sbjct: 195 -EQLSKN----------RVI--------LELDPKQNICASITSSTHERKSRTNIFLKGGR 235

Query: 212 -----------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                      +P+ + L  +GM+ + EI+     +             +S   L    +
Sbjct: 236 IYLKSNSFGSDIPIIAILRGMGMEHDQEIIDLIGSEPNIMDALLASFEQVSELKLFTQLQ 295

Query: 260 VSSSL----VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--DCLCGLYVAEDIV 313
               +         G+    +G       +       +  L +      +    +    +
Sbjct: 296 ALEYIGSKMTSQSRGKANSRNGGASQPTNIAETARAALANLVLNHVPCEIDQFRLKCVYI 355

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIR----DIPILYVDSVNNNAYIRNTLVTDKNKD 369
                 I     D       +   +  +      + +L+ D                   
Sbjct: 356 AHIVRRIIFTDRDRTRLDDKDYYGNKRLELAGQLLSLLFEDLFKRFNSDLKRQADMILSK 415

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
              A +         D  T     ++     +   ++ +   G   +  RL+  +   + 
Sbjct: 416 PNRASMFDIVKCIRTDTITQGFIHAL-ATGNWTLKRFRMDRAGVTHVLSRLSYMSALGMM 474

Query: 430 HIRKEDIIAIIKILVDLR---NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
                      K+        +  G +   D         V  +    +       +   
Sbjct: 475 TRISSQFEKTRKVSGPRSLQPSQWGMLCPADTPEGEACGLVKNLALLCHVTSDEESDPIR 534

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +        D  +             +        +    +    ++++   RR   +G+
Sbjct: 535 RLCFDLGVTDVCLCSGEALNHRSNYLIM--LNGIIIGTHGDPRMFVTKLRRIRRAGLIGE 592

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                      +  +  +  GR+C                +   R      ++   R + 
Sbjct: 593 FVSVMIHDVQRVVYI-ASDGGRVCRPLLLIDPKTHRPKLSSRQMR-----ELQAHVRTLH 646

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
              V   V Y+   EE N  IA     L ED                      +   ++ 
Sbjct: 647 SLIVEGCVEYVDVNEENNCLIA-----LHEDDITV------------------RTTHLEI 683

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + ++LIP+  ++ S R    C M +QA+                         
Sbjct: 684 DPVTILGVVSALIPYPHHNQSPRNTYQCAMGKQAIGT----------------------- 720

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                             I   + +   +     +Y  M   +S     VN        D
Sbjct: 721 ------------------IAMNQFERIDTLLYTLVYPHMPMVKSRVLDLVNF-------D 755

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V                     N +VA M + GY+ ED++++++  +           +
Sbjct: 756 HVPAGQ-----------------NAIVAVMSYSGYDIEDAIVLNKASLDRGFGRCTVFRK 798

Query: 847 FEVMARDTKLGPEEITRDIPN-----------------VSEEGLKNIDECGIICVGAEVN 889
            + M +    G  +     P+                        ++D  GI  VG  V+
Sbjct: 799 LQAMVKKYPNGTFDRIVGPPDFESVLSTATGGTAAALGFRNARYASLDADGIARVGGIVH 858

Query: 890 PGDILVGKITPKGESPM 906
            G IL+ K  P     M
Sbjct: 859 HGAILINKEQPSNAHSM 875


>gi|55925640|gb|AAQ72386.2| RpoB [Klebsiella pneumoniae]
          Length = 343

 Score =  342 bits (877), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 216/343 (62%), Positives = 271/343 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++
Sbjct: 121 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 181 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P 
Sbjct: 241 DSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPC 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           V +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFE
Sbjct: 301 VSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 343


>gi|318603021|emb|CBJ04581.1| RNA polymerase beta subunit [Pseudomonas sp. R-37283]
          Length = 347

 Score =  342 bits (876), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 207/347 (59%), Positives = 269/347 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 121 IVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI
Sbjct: 241 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDI 300

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 MADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 347


>gi|296412297|ref|XP_002835861.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629657|emb|CAZ80018.1| unnamed protein product [Tuber melanosporum]
          Length = 436

 Score =  342 bits (876), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 96/513 (18%), Positives = 175/513 (34%), Gaps = 108/513 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R  +D+ +R      E+ E   R+   +      +       I  G        
Sbjct: 61   -RSLFYRSYMDQEKRIGMQIVEEFEKPTRNNTLKLKHGTYDKLDDDGLIAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D+     R ++         ++     +  Q                   
Sbjct: 120  IIGKTAPIAPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML---------------- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 164  ----TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++++LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSTLLRQNGYQSRGFEVMYNGY 285

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG      V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  
Sbjct: 286  TGRKLVAQVFLGPTYYQRLRHMVDDKIHARARGPVQILTRQPVEGRARDGGLRFGEMERD 345

Query: 1301 CIQAYGAAYVLQEMLTIKSD-------DVVG------------------RTRVYESIVAG 1335
            C+ A+GA+  L+E L   SD       D+ G                  R +        
Sbjct: 346  CMIAHGASAFLKERLFEVSDAFRVHICDICGLMTPIANLKKNLFECRPCRNKT------- 398

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                +   P +  +L +E+ ++ ++  + + R+
Sbjct: 399  -KISQIHLPYAAKLLFQELASMNIAARMYHKRS 430



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +D+ G+I  G  V+
Sbjct: 56  DRGLFRSLFYRSYMDQEKRIGMQIVEEFEKPTRNNTLKLKHGTYDKLDDDGLIAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIAPDVDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 168

Query: 950 IDK 952
             K
Sbjct: 169 GLK 171


>gi|55975954|gb|AAQ72387.2| RpoB [Raoultella planticola]
          Length = 345

 Score =  342 bits (876), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 217/345 (62%), Positives = 273/345 (79%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D
Sbjct: 121 RKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 181 YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V
Sbjct: 241 SGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+
Sbjct: 301 SLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 345


>gi|195431078|ref|XP_002063575.1| GK21338 [Drosophila willistoni]
 gi|194159660|gb|EDW74561.1| GK21338 [Drosophila willistoni]
          Length = 999

 Score =  342 bits (876), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 155/967 (16%), Positives = 293/967 (30%), Gaps = 196/967 (20%)

Query: 431  IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
            ++   +  +++ ++     K   DD D  GN+R+   G ++   +     RM   +K   
Sbjct: 198  MKAIYVALMVRRVMAAELDKTLFDDRDYYGNKRLELAGSLISLMFEDLFKRMNWELKMIA 257

Query: 491  SSVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
                      Q      + A  + + +     S   +     +          RLS +  
Sbjct: 258  DKNIPKVKAAQFDVVKHMRAAQITAGLESAISSGNWTIKRFKMERGGVTQVLSRLSYISA 317

Query: 547  GGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
             G+         ++R     R + P+ +G +CP++T EG   GLV +L     +      
Sbjct: 318  LGMMTRVNSQFEKSRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVD- 376

Query: 599  ETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDEDGSFTEELVFCRCAGEEILV 656
            E P   +       D+  +S     N ++     N ++       + LV           
Sbjct: 377  EHPVMILAYNAGVEDIREVSGNPINNPHVFLVFINGNVLGLTLNHKHLVKNMRYMRRKGR 436

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                +    +  ++ V +         + D  R+     +  +  PL+            
Sbjct: 437  IGSFVSIHTSYSQRCVFV---------HTDGGRLCRPYIIVEKCRPLV------------ 475

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                          R      +D +   +   E     + S +  Y       +      
Sbjct: 476  --KQHHLDELQRGIRKFDDFLLDGLIEYLDVNEE----NDSFIACYEENINPTTTHLEI- 528

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                                       +      +    +P+  +N          M  +
Sbjct: 529  ---------------------------EPFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQ 561

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +     +  +    R   L    +    P V  +                         
Sbjct: 562  AMG----MIGYNQKNRIDSLMYNLVYPQAPMVKSKT------------------------ 593

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             I       +   +    A+      D+ D  +   + +        ++        +R 
Sbjct: 594  -IELTNFDKVPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTV-KRY 651

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
             +   ++I    +D    +VI   ++      +  G+   +      K     +      
Sbjct: 652  ANQTFDRIMGPVKDALTNKVIFKHDVLDTDGIVSPGEQVQNKQIMINKEMPAVT------ 705

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                      Q  +V          Y       +    + +E++    +       ++K+
Sbjct: 706  ---SINPLEGQSPQVP---------YTAVPISYKGSEPSYVERVMVSANAEEDF--LIKI 751

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++NP G PSRM V   
Sbjct: 752  LLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPFNDFGICPDMIMNPHGFPSRMTV--- 808

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
                 G     LG K   L   +                                     
Sbjct: 809  -----GKTLELLGGKAGVLEGKFHYGT--------------------------------- 830

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                          F G+  + I + L     +  G+   Y G+TG P +  +  G +Y 
Sbjct: 831  -------------AFGGSKVQDIQAELVRHGFNYMGKDFFYSGITGAPLEAYIYSGPVYY 877

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+ ++ E L 
Sbjct: 878  QKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGASMLIMERLM 937

Query: 1317 IKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
            I SD    DV    GR   Y          +        +   P +  +L +E+ ++ + 
Sbjct: 938  ISSDAFEVDVCRICGRL-AYCSWCHFCQSSA-----HVSKISMPYACKLLFQELTSMNVV 991

Query: 1361 IDLENSR 1367
              L    
Sbjct: 992  PKLILED 998



 Score =  131 bits (330), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 103/895 (11%), Positives = 243/895 (27%), Gaps = 167/895 (18%)

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDH 167
           +G +PLM                           G FV++G +++++ Q   S       
Sbjct: 3   IGRMPLMLRSSNCVLSGKTEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTE 62

Query: 168 DKG-----RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMAL 221
           D       + + S     +  ++                 +++ +     +P+     AL
Sbjct: 63  DFNGVVQCQVTSSTHEKKSRTLV----------LSKHGRYYLKHNSMTDDIPIVVIFKAL 112

Query: 222 GM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G+   +EI+S          R            +    +    +      ++   +  K 
Sbjct: 113 GIVSDQEIMSHIGVDPQSQNRFGASLLEAFNLKIFTQQRALDYMGSKLVVKRFQSATTKT 172

Query: 281 TSGLLKSLKEKGV------KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
                + L    +               +    +   ++  E  +   +  D    K LE
Sbjct: 173 PPEEARDLLMTTILAHVPVDNFNFQMKAIYVALMVRRVMAAELDKTLFDDRDYYGNKRLE 232

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                       L+         I +  +       K A  D+ + MR   ++  +  ES
Sbjct: 233 LAGSLISLMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLES 286

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             +   +   ++ +   G  ++  RL+  +   +            K+            
Sbjct: 287 AISSGNWTIKRFKMERGGVTQVLSRLSYISALGMMTRVNSQFEKSRKVSGPRSLQ----- 341

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
                    +    +  + +    +  +           +   ++       + +     
Sbjct: 342 ----PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEHPVMILAYNAGVEDIREVSG 397

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
               +  +  +  + N L    +  +        + R         +H ++  R     T
Sbjct: 398 NPINNPHVFLVFINGNVLGLTLNH-KHLVKNMRYMRRKGRIGSFVSIHTSYSQRCVFVHT 456

Query: 575 SEGHNIGLVSSLTSFARVNAYGF---IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             G        +     +        ++   RK  D  +   + YL   EE + +IA   
Sbjct: 457 DGGRLCRPYIIVEKCRPLVKQHHLDELQRGIRKFDDFLLDGLIEYLDVNEENDSFIACYE 516

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +++                            ++  P  ++ + A L+P+  ++ S R  
Sbjct: 517 ENINP-----------------------TTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNT 553

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             C M +QA+ ++         G        S                            
Sbjct: 554 YQCAMGKQAMGMI---------GYNQKNRIDS---------------------------- 576

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                                N    Q P+VK                T+   +  G+N 
Sbjct: 577 ------------------LMYNLVYPQAPMVKS----------KTIELTNFDKVPAGQNA 608

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----P 866
            VA M + GY+ ED++++++  +       +  +  +   +       +           
Sbjct: 609 TVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALT 668

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFG 918
           N        +D  GI+  G +V    I++ K  P        +G+SP  P   +  +  G
Sbjct: 669 NKVIFKHDVLDTDGIVSPGEQVQNKQIMINKEMPAVTSINPLEGQSPQVPYTAVPISYKG 728

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            +   V    +   +     +  +    R     ++ S    ++ +  L  D++D
Sbjct: 729 SEPSYVERVMVSANAEEDFLIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQED 783


>gi|55975966|gb|AAQ72380.2| RpoB [Klebsiella variicola]
          Length = 344

 Score =  342 bits (876), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 217/344 (63%), Positives = 272/344 (79%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D+
Sbjct: 121 KVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDY 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 181 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V 
Sbjct: 241 GVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+
Sbjct: 301 LGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 344


>gi|87242632|gb|ABD33840.1| RNA polymerase beta subunit [Acholeplasma morum]
          Length = 631

 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 236/455 (51%), Positives = 306/455 (67%), Gaps = 33/455 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGRICP ET EG +IGL+SSL S+
Sbjct: 2   NPLAELTQKRRVSALGTGGLARDRAGVEVRDVHESHYGRICPIETPEGPSIGLISSLASY 61

Query: 590 ARVNAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           ARV+ YGFI+TPY +V         VT++ VYL+A EEE   IA A+  LDEDG F  E 
Sbjct: 62  ARVDEYGFIQTPYLRVDKSNPKRHVVTDEFVYLTAGEEEQFVIASADIQLDEDGGFQTET 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE    P  ++DF D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 IIGRFMGETKAFPSSRVDFQDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
             ++P VGTG+E   AK SG+AIV+   GIV   D+  I I         +  G      
Sbjct: 182 IPDSPIVGTGIEHRAAKDSGSAIVSGVEGIVVYADSRIIKIAIKPEASLKTPRGKVVYDK 241

Query: 759 ----------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                                 V+ Y L +F RSNQ+T + Q+P+V +G+ V++ D+IAD
Sbjct: 242 DQAFNWEAYDQIRQAKMTDLLKVEAYPLTQFLRSNQDTAILQKPIVSIGEYVQKGDVIAD 301

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GPS    +LALGRN++VAFM W GYN+ED++++SE +V +DV+TSIHI+E ++  RDTKL
Sbjct: 302 GPSISKAELALGRNVVVAFMTWEGYNYEDAVIMSENLVRDDVYTSIHIDEHQIECRDTKL 361

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           G EEITR+IPN S + LK +D+ GI+ +G EV  GDILVGKITPKG++  TPEEKLL+AI
Sbjct: 362 GKEEITREIPNASADALKYLDDRGIVVLGTEVKEGDILVGKITPKGQTEPTPEEKLLQAI 421

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           F EKA +VRDTSLRVP G  G V  ++ F++   D
Sbjct: 422 FNEKAREVRDTSLRVPHGGGGIVQSIQYFSKSNGD 456



 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 124/449 (27%), Positives = 192/449 (42%), Gaps = 77/449 (17%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
             A+ T L   E       +       I +  I+ +G  V  GD++    +   ++ +   
Sbjct: 255  QAKMTDLLKVEAYPLTQFLRSNQDTAILQKPIVSIGEYVQKGDVIADGPS-ISKAELALG 313

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELL 967
              ++ A    +  +  D  +   + V   V      + H I+  +  +  E    +I   
Sbjct: 314  RNVVVAFMTWEGYNYEDAVIMSENLVRDDVYTSIHIDEHQIECRDTKLGKEEITREIPNA 373

Query: 968  ARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            + D     D++ I+      +  +IL G+    G         L   + +E  R      
Sbjct: 374  SADALKYLDDRGIVVLGTEVKEGDILVGKITPKGQTEPTPEEKLLQAIFNEKARE-VRDT 432

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +++       +      +  S                 GD++ PGV  V++V++  KR I
Sbjct: 433  SLRVPHGGGGIVQSIQYFSKS----------------NGDELGPGVNEVIRVYIVKKRKI 476

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG++S+ILP EDMP++ DGTP+DI+LNPLGVPSRMN+GQI E HLG A
Sbjct: 477  SEGDKMAGRHGNKGVISKILPREDMPYMADGTPIDIMLNPLGVPSRMNIGQILEIHLGMA 536

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG K+ + + D     D++ + +                                  
Sbjct: 537  AKKLGVKVATPVFDGLTQADLADIMAEAGMAPDGKQTL---------------------- 574

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                       G        TGEP++  V+VG +YM+KL+HMV 
Sbjct: 575  -------------------------YDG-------RTGEPYENRVSVGVMYMIKLSHMVD 602

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            DK++ARS G Y+LVTQQP+GGK+  GGQR
Sbjct: 603  DKLHARSVGPYTLVTQQPMGGKAQNGGQR 631


>gi|224077112|ref|XP_002305137.1| predicted protein [Populus trichocarpa]
 gi|222848101|gb|EEE85648.1| predicted protein [Populus trichocarpa]
          Length = 421

 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 104/492 (21%), Positives = 166/492 (33%), Gaps = 97/492 (19%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +      + AI      +  D+ +   S +        +F R   D+ ++  ++ +
Sbjct: 5    HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVK 63

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E      R           +          G           K+T +             
Sbjct: 64   EDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPI------------- 110

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                      Q   +    +Y      +  R        Q         LR VKV V   
Sbjct: 111  ---------AQEEAQGQSARYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSV 161

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +
Sbjct: 162  RIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIM 221

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     +GK+                                                  
Sbjct: 222  GKVAAHMGKEGD------------------------------------------------ 233

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L H
Sbjct: 234  -----ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRLKH 287

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD 
Sbjct: 288  MVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDA 347

Query: 1321 ---DVVGR----------TRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                V  R             +E    G     D  +   P +  +L +E+ A+ ++  +
Sbjct: 348  YRVHVCERCGLIAIANLKKNSFEC--RGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRM 405

Query: 1364 ENSRTKNSAKME 1375
                 K +   +
Sbjct: 406  LTKDIKQAKSQK 417



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/144 (20%), Positives = 54/144 (37%), Gaps = 14/144 (9%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
               L  G N +VA   + GYN EDS+++++  +    F S+    +    +      +E
Sbjct: 5   HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKE 64

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   +   +       +D+ G+   G  V+  D+++GK TP  +           A
Sbjct: 65  DFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQEE---------A 115

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
                    RD S+ +    +G V
Sbjct: 116 QGQSARYTRRDHSISLRHSETGMV 139


>gi|212373959|emb|CAP09906.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35705]
          Length = 339

 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 203/339 (59%), Positives = 264/339 (77%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYG
Sbjct: 1   PVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  I
Sbjct: 61  RVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVI 120

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 AQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 180

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R 
Sbjct: 181 NRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRV 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LAL
Sbjct: 241 ADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELAL 300

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           G+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+E
Sbjct: 301 GQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQE 339


>gi|90902244|gb|ABE01890.1| RNA polymerase beta subunit [Acholeplasma hippikon]
          Length = 639

 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 226/459 (49%), Positives = 305/459 (66%), Gaps = 31/459 (6%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  + +N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+
Sbjct: 1   QFMDQINPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGK-----VTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           SSL ++A+V+ YGFI+TP+ KV   +     VT++VVYL+A +E +  IA A S ++ DG
Sbjct: 61  SSLATYAKVDDYGFIKTPFLKVVKNEEGHPLVTDEVVYLTADQEGDEVIASAASPVNADG 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           +F E  V  R  GE  ++  + + ++D SPKQ+VS+A++ IPFLE+DD++R LMG NMQR
Sbjct: 121 TFKENKVIARANGETTILDSQSVTYMDVSPKQLVSVASASIPFLEHDDASRALMGANMQR 180

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLLK  +P VGTG+E   AK SGA +VA  AG V  VDA +++I     +     + 
Sbjct: 181 QAVPLLKPTSPIVGTGIEHKAAKDSGAVVVAHHAGYVTYVDAKKVIITREPKEDVKVGNK 240

Query: 759 V------------------------DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V                        D Y  ++F RSNQ+T V Q P+V  G+ V   D+I
Sbjct: 241 VIYKVGGDFNYAIAKQLYDYKLAETDTYEFIQFFRSNQDTLVLQSPIVFQGEYVEAGDVI 300

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
            DGPST+ G+LALGRN+ VAFM W GYN+ED++++ E +V  DV+TSIHI+E+E+  RD 
Sbjct: 301 GDGPSTEKGELALGRNVTVAFMTWEGYNYEDAVIMCEDLVKNDVYTSIHIDEYEIETRDL 360

Query: 855 K--LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           K   G EEITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL
Sbjct: 361 KQSNGKEEITREIPNVGQEAVKYLDERGIIIPGSEVKEGDILVGKITPKGVFEPTPSEKL 420

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + A+ G+KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 421 IHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 459



 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 127/418 (30%), Positives = 189/418 (45%), Gaps = 65/418 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD ++G      +  +     +  A    +  +  D  +     V   V 
Sbjct: 287  IVFQGEYVEAGD-VIGDGPSTEKGELALGRNVTVAFMTWEGYNYEDAVIMCEDLVKNDVY 345

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   S  +E+I     +   E V            I+ G     G  
Sbjct: 346  TSIHIDEYEIETRDLKQSNGKEEITREIPNVGQEAV----KYLDERGIIIPGSEVKEGDI 401

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 402  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 457

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGT VDI
Sbjct: 458  --GDQLPAGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYMADGTYVDI 515

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ + + D  ++ D+  + +          
Sbjct: 516  MLNPLGVPSRMNIGQILEIHLGISAKKLGIKVATPVFDGVSDQDLKEIMAE--------- 566

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +    DG                      LYDG 
Sbjct: 567  --------------------------AGIAPDGKTV-------------------LYDGR 581

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            TGEPF   ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR GEME
Sbjct: 582  TGEPFQNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQRFGEME 639


>gi|116563650|gb|ABJ99841.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563654|gb|ABJ99843.1| RpoB [Bacillus subtilis subsp. subtilis]
 gi|116563656|gb|ABJ99844.1| RpoB [Bacillus subtilis subsp. spizizenii]
 gi|116563662|gb|ABJ99847.1| RpoB [Bacillus mojavensis]
 gi|116563664|gb|ABJ99848.1| RpoB [Bacillus mojavensis]
 gi|116563676|gb|ABJ99854.1| RpoB [Bacillus licheniformis]
 gi|284154640|gb|ADB78421.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154642|gb|ADB78422.1| RNA polymerase beta-subunit [Bacillus sp. B-51132]
 gi|284154644|gb|ADB78423.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154646|gb|ADB78424.1| RNA polymerase beta-subunit [Bacillus sp. B-51134]
 gi|284154648|gb|ADB78425.1| RNA polymerase beta-subunit [Bacillus sp. B-51135]
 gi|284154650|gb|ADB78426.1| RNA polymerase beta-subunit [Bacillus sp. B-51136]
 gi|284154652|gb|ADB78427.1| RNA polymerase beta-subunit [Bacillus sp. B-51137]
 gi|284154654|gb|ADB78428.1| RNA polymerase beta-subunit [Bacillus sp. B-51138]
 gi|284154656|gb|ADB78429.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154658|gb|ADB78430.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154660|gb|ADB78431.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154664|gb|ADB78433.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154666|gb|ADB78434.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154668|gb|ADB78435.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154670|gb|ADB78436.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154672|gb|ADB78437.1| RNA polymerase beta-subunit [Bacillus sp. B-51148]
 gi|284154674|gb|ADB78438.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154676|gb|ADB78439.1| RNA polymerase beta-subunit [Bacillus sp. B-51150]
 gi|284154678|gb|ADB78440.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154680|gb|ADB78441.1| RNA polymerase beta-subunit [Bacillus sp. B-51152]
 gi|284154682|gb|ADB78442.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154684|gb|ADB78443.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154686|gb|ADB78444.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154688|gb|ADB78445.1| RNA polymerase beta-subunit [Bacillus sp. B-51157]
 gi|284154690|gb|ADB78446.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154692|gb|ADB78447.1| RNA polymerase beta-subunit [Bacillus sp. B-51159]
 gi|284154694|gb|ADB78448.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154696|gb|ADB78449.1| RNA polymerase beta-subunit [Bacillus sp. B-51161]
 gi|284154698|gb|ADB78450.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154700|gb|ADB78451.1| RNA polymerase beta-subunit [Bacillus sp. B-51164]
 gi|284154702|gb|ADB78452.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154704|gb|ADB78453.1| RNA polymerase beta-subunit [Bacillus sp. B-51169]
 gi|284154706|gb|ADB78454.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154708|gb|ADB78455.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154710|gb|ADB78456.1| RNA polymerase beta-subunit [Bacillus sp. B-51172]
 gi|284154712|gb|ADB78457.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154714|gb|ADB78458.1| RNA polymerase beta-subunit [Bacillus sp. B-51174]
 gi|284154716|gb|ADB78459.1| RNA polymerase beta-subunit [Bacillus sp. B-51175]
 gi|284154718|gb|ADB78460.1| RNA polymerase beta-subunit [Bacillus sp. B-51176]
 gi|284154720|gb|ADB78461.1| RNA polymerase beta-subunit [Bacillus sp. B-51177]
 gi|284154722|gb|ADB78462.1| RNA polymerase beta-subunit [Bacillus sp. B-51178]
 gi|284154724|gb|ADB78463.1| RNA polymerase beta-subunit [Bacillus sp. B-51179]
 gi|284154726|gb|ADB78464.1| RNA polymerase beta-subunit [Bacillus sp. B-51180]
 gi|284154728|gb|ADB78465.1| RNA polymerase beta-subunit [Bacillus sp. B-51181]
 gi|284154730|gb|ADB78466.1| RNA polymerase beta-subunit [Bacillus sp. B-51182]
 gi|284154732|gb|ADB78467.1| RNA polymerase beta-subunit [Bacillus sp. B-51183]
 gi|284154734|gb|ADB78468.1| RNA polymerase beta-subunit [Bacillus mojavensis]
 gi|284154736|gb|ADB78469.1| RNA polymerase beta-subunit [Bacillus sp. B-51185]
 gi|284154738|gb|ADB78470.1| RNA polymerase beta-subunit [Bacillus sp. B-51186]
 gi|284154740|gb|ADB78471.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154742|gb|ADB78472.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154744|gb|ADB78473.1| RNA polymerase beta-subunit [Bacillus sp. B-51190]
 gi|284154746|gb|ADB78474.1| RNA polymerase beta-subunit [Bacillus licheniformis]
 gi|284154748|gb|ADB78475.1| RNA polymerase beta-subunit [Bacillus sp. B-51192]
 gi|284154750|gb|ADB78476.1| RNA polymerase beta-subunit [Bacillus sp. B-51193]
 gi|284154754|gb|ADB78478.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154756|gb|ADB78479.1| RNA polymerase beta-subunit [Bacillus mojavensis]
 gi|284154758|gb|ADB78480.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154760|gb|ADB78481.1| RNA polymerase beta-subunit [Bacillus sp. B-51199]
 gi|284154762|gb|ADB78482.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154764|gb|ADB78483.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154766|gb|ADB78484.1| RNA polymerase beta-subunit [Bacillus sp. B-51202]
 gi|284154768|gb|ADB78485.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154770|gb|ADB78486.1| RNA polymerase beta-subunit [Bacillus mojavensis]
 gi|284154772|gb|ADB78487.1| RNA polymerase beta-subunit [Bacillus sp. B-51205]
 gi|284154774|gb|ADB78488.1| RNA polymerase beta-subunit [Bacillus sp. B-51206]
 gi|284154776|gb|ADB78489.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154778|gb|ADB78490.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154780|gb|ADB78491.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154782|gb|ADB78492.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154784|gb|ADB78493.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154786|gb|ADB78494.1| RNA polymerase beta-subunit [Bacillus sp. B-51212]
 gi|284154788|gb|ADB78495.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154790|gb|ADB78496.1| RNA polymerase beta-subunit [Bacillus sp. B-51214]
 gi|284154792|gb|ADB78497.1| RNA polymerase beta-subunit [Bacillus sp. B-51215]
 gi|284154794|gb|ADB78498.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154796|gb|ADB78499.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154798|gb|ADB78500.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154800|gb|ADB78501.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154802|gb|ADB78502.1| RNA polymerase beta-subunit [Bacillus sp. B-51220]
 gi|284154804|gb|ADB78503.1| RNA polymerase beta-subunit [Bacillus sp. B-51222]
 gi|284154806|gb|ADB78504.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154808|gb|ADB78505.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154810|gb|ADB78506.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154812|gb|ADB78507.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154814|gb|ADB78508.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154816|gb|ADB78509.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154818|gb|ADB78510.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154822|gb|ADB78512.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154824|gb|ADB78513.1| RNA polymerase beta-subunit [Bacillus sp. B-51232]
 gi|284154826|gb|ADB78514.1| RNA polymerase beta-subunit [Bacillus mojavensis]
 gi|284154828|gb|ADB78515.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154830|gb|ADB78516.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154832|gb|ADB78517.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154834|gb|ADB78518.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154836|gb|ADB78519.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154838|gb|ADB78520.1| RNA polymerase beta-subunit [Bacillus sp. B-51240]
 gi|284154840|gb|ADB78521.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154842|gb|ADB78522.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154844|gb|ADB78523.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154846|gb|ADB78524.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154848|gb|ADB78525.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154850|gb|ADB78526.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154852|gb|ADB78527.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154854|gb|ADB78528.1| RNA polymerase beta-subunit [Bacillus sp. B-51249]
 gi|284154856|gb|ADB78529.1| RNA polymerase beta-subunit [Bacillus sp. B-51250]
 gi|284154858|gb|ADB78530.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154860|gb|ADB78531.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154862|gb|ADB78532.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154864|gb|ADB78533.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154866|gb|ADB78534.1| RNA polymerase beta-subunit [Bacillus sp. B-51256]
 gi|284154868|gb|ADB78535.1| RNA polymerase beta-subunit [Bacillus sp. B-51257]
 gi|284154870|gb|ADB78536.1| RNA polymerase beta-subunit [Bacillus sp. B-51258]
 gi|284154872|gb|ADB78537.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154874|gb|ADB78538.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154880|gb|ADB78541.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154884|gb|ADB78543.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154886|gb|ADB78544.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. inaquosorum]
 gi|284154894|gb|ADB78548.1| RNA polymerase beta-subunit [Bacillus mojavensis]
 gi|284154896|gb|ADB78549.1| RNA polymerase beta-subunit [Bacillus mojavensis]
          Length = 182

 Score =  341 bits (875), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 129/204 (63%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|52694391|emb|CAG38035.1| RNA polymerase beta subunit [Pseudomonas marginalis]
          Length = 346

 Score =  341 bits (875), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 203/346 (58%), Positives = 265/346 (76%), Gaps = 1/346 (0%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           E F SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 1   ELFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 60

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++
Sbjct: 61  PEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATM 120

Query: 635 DEDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ++     + ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 121 NDKKVIGSTELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 180

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++
Sbjct: 181 SNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVE 240

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
              +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPST++G+LALG+NM +
Sbjct: 241 TGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTNMGELALGQNMRI 300

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           AFM W+G+NFEDS+ +SER+V E  F+ IHI+E   +ARDTKLGPE
Sbjct: 301 AFMAWNGFNFEDSICLSERVVQEGRFSRIHIQELTCVARDTKLGPE 346


>gi|284154876|gb|ADB78539.1| RNA polymerase beta-subunit [Bacillus altitudinis]
          Length = 182

 Score =  341 bits (875), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 128/204 (62%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V +   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVAESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFSSD 182


>gi|318603015|emb|CBJ04580.1| RNA polymerase beta subunit [Pseudomonas sp. R-37267]
          Length = 351

 Score =  341 bits (874), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 207/351 (58%), Positives = 274/351 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDQKVLVDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 351


>gi|285310168|emb|CBH41065.1| DNA-directed RNA polymerase beta subunit [Pseudomonas
           nitroreducens]
          Length = 334

 Score =  341 bits (874), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 203/334 (60%), Positives = 263/334 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++D+V+LSA+EE +  IAQA
Sbjct: 61  PIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGLVSDDIVFLSAIEEADHVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           +++L+E G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR 
Sbjct: 121 SATLNEKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRA 180

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + 
Sbjct: 181 LMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVNDD 240

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R+DI+ADGPSTD+G+LALG+N
Sbjct: 241 EVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDQVSRSDILADGPSTDMGELALGQN 300

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           M VAFMPW+G+NFEDS+ +SER+V ED FT+IHI
Sbjct: 301 MRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHI 334


>gi|301110510|ref|XP_002904335.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide
            [Phytophthora infestans T30-4]
 gi|262096461|gb|EEY54513.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide
            [Phytophthora infestans T30-4]
          Length = 1166

 Score =  341 bits (874), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 127/627 (20%), Positives = 212/627 (33%), Gaps = 83/627 (13%)

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            S  G     L+        T + QR L ++   VR    +      +  D+    N LVA
Sbjct: 608  SDGGRVCRPLLLIDPVTHRTRLTQRHLDELRAGVRDLSSLIVEGCVEYVDVNEENNCLVA 667

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
                   +    + I    +   V   I         R+T        + I  ++    +
Sbjct: 668  LHESEIGDRTTHLEIDPVTILGVVSGLIPYPHHNQSPRNTYQCAM-GKQAIGTIAMNQFE 726

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             ID   ++          +    +       +   +  + A+      D+ D  +   + 
Sbjct: 727  RIDT--LLYTMVYPQMPMVKTRVLDLVNFDRVPAGQNAIVAVMSYSGYDIEDAIVLNKAS 784

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +        +F ++     + +       +     D             +     L    
Sbjct: 785  LDRGFGRCMVFKKYQTMIKKYANGSYDRIVGPPDFDSLAAAGGAGMGFRNAKFSSLDADG 844

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                    +   ++ +            Q    ++ V    + L V Y  S +  +    
Sbjct: 845  ISRVGGIVQNGAIMINKE----------QPTQFNDSVDGR-DPLDVTYSPSPTTYKGPIP 893

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
              ++K+            +VKV +   R  + GDK + RHG KG+   I   EDMPF   
Sbjct: 894  AYVDKVLLTSSEANHF--LVKVLIRQTRRPEIGDKFSSRHGQKGVCGTIRNQEDMPFNDQ 951

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G PSRM VG++ E   G A V  G++        K              
Sbjct: 952  GICPDLIMNPHGFPSRMTVGKMIELIAGKAGVLTGRRAYGTAFGEKYGS----------- 1000

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +  V D + E      L     + +G+ 
Sbjct: 1001 --------------------------------ADHVLDCSRE------LVKNGFNYAGKD 1022

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L  G+TGE  +  + +G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RL
Sbjct: 1023 YLTSGITGEAIECYIFMGPIYYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRL 1082

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--RTRVYESIVAG--------NDTFE 1340
            GEME  C+  YGA+ +L E L + SD    DV    R   YE    G             
Sbjct: 1083 GEMERDCLIGYGASMLLMERLMLSSDAFSADVCQGCRMLGYE----GWCQHCKSEEKVVS 1138

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSR 1367
               P +  +L +E+QA+ +   L    
Sbjct: 1139 IRIPYACKLLFQELQAMNIVPRLTLKE 1165



 Score =  169 bits (427), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 110/960 (11%), Positives = 262/960 (27%), Gaps = 177/960 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S+D+F  +++    R         +S            L++   +   P    
Sbjct: 44  LVKQHIDSFDYFTSVDMRNIVRAQA--NNVVRS-----DADPKFFLQYTDIQLGAPSIDE 96

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  RD TYA P+ +++R          G K + + K   + +G +P+M
Sbjct: 97  EAFVSASVTPHQCRLRDRTYAAPVYVSVRY-------RRGNKIVTNNK---VLIGRIPIM 146

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRAS 173
                                      G F+++G++++V+     S   +  + D     
Sbjct: 147 LRSSRCVLAGKSEAALAKLKECPYDPGGYFIVRGVEKVVLIHEQLSKNRVIIEED----- 201

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEIL 229
             GK      I      +    +I F +K  ++++ +     +P+      +G++S++ +
Sbjct: 202 --GKHNVCASITSSTHERKSRTNI-FLNKGRVYLKSNSFGSDIPIVIVFRGMGVESDQEI 258

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            +               F  ++   +   + +   +                        
Sbjct: 259 VSLVGSESDICDALSASFEEASDLKVFTQQQALEYIGSKMNALTKIGAMGGRHRGGAGRP 318

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEI--YIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           +     +      L  L +     +     +     A  V      ++            
Sbjct: 319 QNDRNLVDAARSALANLVLNHVPCDNFNFRLKSIYVAHIVRRILFTDKDRTRLDDKDYYG 378

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                     +         +   D       V+   + ++                 Y 
Sbjct: 379 NKRLELAGQLLSLLFEDLFKRFNSDLKRQADMVLSKPNRASVFDILKCVRTDTITQGFYH 438

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNGKGTIDDIDNLGNRRV 464
             + G   +  R  +D       + +   ++ + ++  +         +    +L   + 
Sbjct: 439 ALSTGNWTL-KRFRMDRAGVTHVLSRLSYMSALGMMTRISSQFEKTRKVSGPRSLQPSQW 497

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             +      +     L    ++   ++S +  + + +   +      ++      +  S 
Sbjct: 498 GMLCPADTPEGEACGLVKNLALLCHVTSDEEPAPIKRLCFDLGVTDVSLSSGEEINHASN 557

Query: 525 LEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
               +N +   TH   R        + RA    E   V      R+    +  G     +
Sbjct: 558 YLVMLNGVIIGTHVNPRAFVTRLRRIRRAGLIGEFVSVMIHDVQRVVYIASDGGRVCRPL 617

Query: 584 SSLTSFARVN-----AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             +                +    R +    V   V Y+   EE N  +A   S +    
Sbjct: 618 LLIDPVTHRTRLTQRHLDELRAGVRDLSSLIVEGCVEYVDVNEENNCLVALHESEIG--- 674

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                               ++   ++  P  ++ + + LIP+  ++ S R    C M +
Sbjct: 675 --------------------DRTTHLEIDPVTILGVVSGLIPYPHHNQSPRNTYQCAMGK 714

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+                                           I   + +   +   
Sbjct: 715 QAIGT-----------------------------------------IAMNQFERIDTLLY 733

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +Y               Q P+VK                 +   +  G+N +VA M +
Sbjct: 734 TMVYP--------------QMPMVK----------TRVLDLVNFDRVPAGQNAIVAVMSY 769

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP------------ 866
            GY+ ED++++++  +       +  ++++ M +    G  +     P            
Sbjct: 770 SGYDIEDAIVLNKASLDRGFGRCMVFKKYQTMIKKYANGSYDRIVGPPDFDSLAAAGGAG 829

Query: 867 -NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    ++D  GI  VG  V  G I++ K  P   +        L   +       +
Sbjct: 830 MGFRNAKFSSLDADGISRVGGIVQNGAIMINKEQPTQFNDSVDGRDPLDVTYSPSPTTYK 889


>gi|306410419|gb|ADM85831.1| DNA-directed RNA polymerase beta chain [Frankia sp. CcI3]
 gi|306410423|gb|ADM85833.1| DNA-directed RNA polymerase beta chain [Frankia sp. Cj1-82]
          Length = 217

 Score =  341 bits (874), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 117/246 (47%), Positives = 152/246 (61%), Gaps = 38/246 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   + GD++PPGV  +V+V+VA KR I  GDK+AGRHGNKG++++ILP EDMPFL+DG
Sbjct: 2    RVFSREDGDELPPGVNELVRVYVAQKRKITDGDKLAGRHGNKGVIAKILPAEDMPFLEDG 61

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD+VLNP GVP RMN+GQI ETHLGW     G ++ S   D+K               
Sbjct: 62   TPVDVVLNPHGVPRRMNIGQILETHLGWVAK-TGWQVDSGTEDWKERLRGIG-------- 112

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                                 A+   +G  V+TPVFDGA EE I  +L     +      
Sbjct: 113  ---------------------ADAASAGTNVATPVFDGAREEEITGLLDSTLPNRDGIQL 151

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G++ L+DG TGEP+  PV VGYIY+LKL H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 152  IGSSGKAKLFDGRTGEPYPYPVAVGYIYILKLLHLVDDKIHARSTGPYSMITQQPLGGKA 211

Query: 1288 NRGGQR 1293
              GGQR
Sbjct: 212  QFGGQR 217


>gi|331225399|ref|XP_003325370.1| DNA-directed RNA polymerase III subunit RPC2 [Puccinia graminis f.
            sp. tritici CRL 75-36-700-3]
 gi|309304360|gb|EFP80951.1| DNA-directed RNA polymerase III subunit RPC2 [Puccinia graminis f.
            sp. tritici CRL 75-36-700-3]
          Length = 1272

 Score =  341 bits (874), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 162/962 (16%), Positives = 302/962 (31%), Gaps = 199/962 (20%)

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK-------ERIS 491
            + + +V        +DD D +GN+R+   G++L   +     +    +K       ++ +
Sbjct: 474  MARRVVQAMANPKLVDDRDYVGNKRLELAGQLLSLLFEDLFKKFNTDLKLNIDKVLKKPN 533

Query: 492  SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA- 550
                   + Q  ++A  + +       +   S     +          RLS +   G+  
Sbjct: 534  RTTEFDAINQFRMHADHISNGFIRAISTGNWSIKRFKMERAGITHVLSRLSYISALGMMT 593

Query: 551  -------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                   + R     R + P+ +G +CP++T EG   GLV +L     +      E P  
Sbjct: 594  RISSQFEKTRKVSGPRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDTD-EEPIW 652

Query: 604  KVCDGKVTNDVVYLSAMEEE--NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             V       D+  ++  E      YI   N ++       E  V             E +
Sbjct: 653  NVAYTIGCEDISSVTGTELYLPRHYIVFINGNILGLTRSPERFVEVFRQFRRAGKISEFV 712

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
                 + +Q V+IA          D  R         + + ++      V T     +  
Sbjct: 713  SIYMNADQQTVNIAT---------DGGR-------ICRPMIIVTNGDSMVKTHHIEKLKA 756

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +       G++E +D         +  +      +D Y                   
Sbjct: 757  GELSFDDFLSQGLIEYLDCNE----ENDSFIALYEEDIDSYT------------------ 794

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                        +   P T LG +A         +P+  +N          M  + +   
Sbjct: 795  ----------THLEIEPFTLLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGVI 837

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
             + +   +                               ++ +    +   +    I   
Sbjct: 838  AYNQLHRIDT-----------------------------LLYLMVYPHHPMVRTKTIELV 868

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G   +   +    A+      D+ D  +   + +       ++F R      +R  +   
Sbjct: 869  GYDKLPAGQNATVAVMSYSGYDIEDALILNKASLDRGFGRCQVF-RKATAMIKRYPNGTY 927

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++I        D     +  +  +      G  A  G K +  +  ++            
Sbjct: 928  DRIA-------DPPRDPEGQVLEKWKPCDDGGVADVGMKVYNGNVYINKQ---------- 970

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
               +  ++       +    +  +         + I+K+   D        +VKV +   
Sbjct: 971  -SPSNANDNSVGAGAATVTSWANTPMTYRGTVPSYIDKVMVTD--TESDQTLVKVLLRQT 1027

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK + RHG KG+   I+  EDMPF   GT  DI+         MN         
Sbjct: 1028 RRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDRGTCPDII---------MN--------- 1069

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                                                 G  +        + +   A   +
Sbjct: 1070 -----------------------------------PHGFPSRMTVGKMLELLSGKAGVLR 1094

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              V   T  F G+    ++ +L        G+  L  G+TG+P +  V +G IY  KL H
Sbjct: 1095 GTVEYGT-AFGGSKAVEMSKILIEHGYSYLGKDYLTSGITGQPLEHYVFMGPIYYQKLKH 1153

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ A+GA+ +L E L + SD 
Sbjct: 1154 MVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAHGASQLLLERLMLSSDS 1213

Query: 1321 ---DVVG------------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
               DV              R +       GN   +   P +  +L +E+ A+ ++  L  
Sbjct: 1214 FELDVCQDCGFMGYNGWCVRCK------NGNSVTKITIPYACKLLFQELMAMNIAPRLVL 1267

Query: 1366 SR 1367
              
Sbjct: 1268 ED 1269



 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 117/945 (12%), Positives = 266/945 (28%), Gaps = 202/945 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP-ITAFSGAAMLEFVSYEFDPP--- 84
           L +     +++F           +  LQ+  ++    I+       L ++      P   
Sbjct: 171 LGKQHLDLFNYF----------GDVDLQSILRANATVISDVDPNFHLSYLDINVGEPSRL 220

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TY+ P+ +T++            K  K +  + I +G +P
Sbjct: 221 DTGSATNKRITPHECRLRDITYSAPISVTIQYT----------KGNKRVLSKGIPIGRIP 270

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M                           G FV+KG +++++ Q   S   I  + D  +
Sbjct: 271 IMLRSNKCVLTGKSDAELAKMTECPLDPGGYFVVKGTEKVILVQEQLSKNRILIETDSRK 330

Query: 172 ----------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMA 220
                             Y                     ++++ +  + ++P+   L A
Sbjct: 331 GTIMASVTSSTHERKSKTYVVT--------------KNSKVYLKHNSIQEEIPIAIALKA 376

Query: 221 LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID----TGEQVIE 275
            G+ S+ E++          +     C        +   K + + +           V  
Sbjct: 377 YGITSDREVVQIVCGNNDDYRAAFSICMEHCHEAGVFTQKQALAYIGKSVKMVKKGPVAG 436

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             + LT   L+ L    +    + +D L     A  +       +   A    + K +++
Sbjct: 437 PKRPLTEEALEVLSTVVLAH--VPADNLNLQPKAIYLAVMARRVVQAMA----NPKLVDD 490

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
             +   + + +           +         K   D  L+I +V++  + +T   A + 
Sbjct: 491 RDYVGNKRLEL-------AGQLLSLLFEDLFKKFNTDLKLNIDKVLKKPNRTTEFDAINQ 543

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKG 451
           F           +  +     +++        + H    +     + ++  +        
Sbjct: 544 FRMHADHISNGFIRAISTGNWSIKRFKMERAGITHVLSRLSYISALGMMTRISSQFEKTR 603

Query: 452 TIDDIDNLGNRRVR--SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            +     L   +       +  + +    +  +         + +         I  + +
Sbjct: 604 KVSGPRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDTDEEPIWNVAYTIGCEDI 663

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            S         +   +  + N L       R   +      RA    E   ++     + 
Sbjct: 664 SSVTGTELYLPRHYIVFINGNILGLTRSPERFVEVF-RQFRRAGKISEFVSIYMNADQQT 722

Query: 570 CPAETSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
               T  G        V++  S  + +    ++       D      + YL   EE + +
Sbjct: 723 VNIATDGGRICRPMIIVTNGDSMVKTHHIEKLKAGELSFDDFLSQGLIEYLDCNEENDSF 782

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IA     +D                            ++  P  ++   A LIP+  ++ 
Sbjct: 783 IALYEEDID-----------------------SYTTHLEIEPFTLLGAVAGLIPYPHHNQ 819

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           S R    C M +QA+                                          VI 
Sbjct: 820 SPRNTYQCAMGKQAIG-----------------------------------------VIA 838

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +     +   + +Y      R+                                  L 
Sbjct: 839 YNQLHRIDTLLYLMVYPHHPMVRTK------------------------TIELVGYDKLP 874

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            G+N  VA M + GY+ ED++++++  +           +   M +    G  +   D P
Sbjct: 875 AGQNATVAVMSYSGYDIEDALILNKASLDRGFGRCQVFRKATAMIKRYPNGTYDRIADPP 934

Query: 867 NVSEEG-LKNI---DECGIICVGAEVNPGDILVGKITPKGESPMT 907
              E   L+     D+ G+  VG +V  G++ + K +P   +  +
Sbjct: 935 RDPEGQVLEKWKPCDDGGVADVGMKVYNGNVYINKQSPSNANDNS 979


>gi|312374784|gb|EFR22267.1| hypothetical protein AND_15508 [Anopheles darlingi]
          Length = 1134

 Score =  340 bits (873), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 163/961 (16%), Positives = 292/961 (30%), Gaps = 182/961 (18%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  +I+ ++     +  +DD D  GN+R+   G +L   +   L R    +K    
Sbjct: 330  KAIYVALMIRRVMAAELDRSAVDDRDYYGNKRLELAGSLLSLMFEDLLKRFNWELKMIAD 389

Query: 492  SVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                     Q      +    + S +     +   +     +          RLS +   
Sbjct: 390  KNIPKIKAAQFDVGKHMREALITSGLETAISTGNWTIKRFKMERAGVTQVLSRLSYISAL 449

Query: 548  GVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            G+         + R     R + P+ +G +CP++T EG   GLV +L     +      E
Sbjct: 450  GMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEE 509

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVP 657
               R   +  V  D+  +      N  +     N ++         LV          + 
Sbjct: 510  PVIRLAYNAGV-EDIRLIGGETINNPKVFMVFINGNILGVTIAYRRLVEVFRMMRRRGLI 568

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
               +    +  ++ V I         + D  R              L      V  G+  
Sbjct: 569  GAFVSIHTSFTQRCVYI---------HTDGGR--------------LCRPYIIVQAGLPL 605

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V+ +      +  R       D +   +   E +          Y+              
Sbjct: 606  VLQEHIEQLKLGLRKFDDFLHDGLIEYLDVNEEND-----SFIAYQERDID--------- 651

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
                        +   +   P T LG       +    +P+  +N          M  + 
Sbjct: 652  ----------PEKTTHLEIEPFTLLG-------VCAGLVPYPHHNQSPRNTYQCAMGKQA 694

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +     I  +    R   L    +    P V                             
Sbjct: 695  MG----IIGYNQKNRIDTLMYNIVYPQTPMVRSRT------------------------- 725

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            I       +   +    A+      D+ D  +   + +        ++        +R  
Sbjct: 726  IELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTI-KRYS 784

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
            +   ++I    +D    +VI           +  G+  V       K             
Sbjct: 785  NQTFDRIMGPMKDSLTGKVIARHECLDTDGIVSPGERLVCKQTMVNKEMPA--------- 835

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      +   Q+      + Y       +    +  E++    +       +VK+ 
Sbjct: 836  ------VKSNNPIEQKESGQQPIAYSAVPITYKGTEPSYAERVLVSTNNEEEF--LVKIL 887

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   R  + GDK + RHG KG+   I+  ED+PF   G   D+V+NP G PSRM V    
Sbjct: 888  LRQTRRPEIGDKFSSRHGQKGVTGLIVDQEDLPFNDYGMAPDMVMNPHGFPSRMTV---- 943

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
                G     LG K   L   +                                      
Sbjct: 944  ----GKTLELLGSKAGVLEGKFHYGT---------------------------------- 965

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                         F G+  + +   L     +  G+ + Y G+TGEP +  +  G +Y  
Sbjct: 966  ------------AFGGSKCQDLQDELFQNGFNYLGKDVFYSGITGEPLEVYIYSGPVYYQ 1013

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+ ++ E L I
Sbjct: 1014 KLKHMVQDKMHARARGPRAVLTRQPTQGRSREGGLRLGEMERDCLISYGASMLIMERLMI 1073

Query: 1318 KSD-------DVVGRTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             SD       +V GR   Y S            +   P +  +L +E+ ++ +   L+  
Sbjct: 1074 SSDAFDVDVCNVCGRL-AYSSWCHNCRSSASVSKISMPYACKLLFQELTSMNIVPRLKLQ 1132

Query: 1367 R 1367
             
Sbjct: 1133 N 1133



 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 120/962 (12%), Positives = 276/962 (28%), Gaps = 194/962 (20%)

Query: 15  KFFGKNPEIID-----IPDLIEV------QKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
           K + K    ++     +P  ++V         ++++F+ ++I    + N   Q   KS  
Sbjct: 13  KGYKKVKRALEEKWKLVPAFLQVKGLVKQHIDAFNYFINVDIKKIVQAN---QEV-KS-- 66

Query: 64  PITAFSGAAMLEFVSYEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDV 113
                     L++++     P               +C  RD+TY+ P+ + +       
Sbjct: 67  ---DADPCFYLKYLNVHVGKPDVEEGFNNTKSTTPHECRLRDMTYSAPITVDVEYT---- 119

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGI 149
                 +  + +    + +G +P+M                           G F+I+G 
Sbjct: 120 ------RGTQRVVRNGLLIGRMPIMLRSSNCILNGKSDYELSQVNECPMDPGGYFIIRGT 173

Query: 150 QRIVVSQLHRSPGIHFDHDKG-----RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           +++++ Q   S       D       + + S     +  I+          +      ++
Sbjct: 174 EKVILIQEQLSWNKMITEDYNGLIQCQVTSSTHEKKSRTIL----------YSKHGRYYL 223

Query: 205 RIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           + +    ++PV   L A+G+ S++ +         +Q+        +A   +   + +  
Sbjct: 224 KHNSMTEEIPVAIILKAMGVASDQEIMQLVGIDQETQKRFAPSLLEAAKHKVYTQQRALE 283

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +           G KL +    +   K         D L    +A   V     ++   
Sbjct: 284 YM-----------GSKLIAKRFTTAATKYRTTADEARDLLATTILAHVPVRSFNFQVKAI 332

Query: 324 AGDVIDEK-SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
              ++  +    E+  S + D        +     + + +  D  K     L  I     
Sbjct: 333 YVALMIRRVMAAELDRSAVDDRDYYGNKRLELAGSLLSLMFEDLLKRFNWELKMIADKNI 392

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
           P   +               S      + G   +  R  ++     + + +   I+ + +
Sbjct: 393 PKIKAAQFDVGKHMREALITSGLETAISTGNWTI-KRFKMERAGVTQVLSRLSYISALGM 451

Query: 443 LVDLRNGKGTIDDIDNLG-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           +  + +       +            +    +  + +    +  +           +   
Sbjct: 452 MTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEEPV 511

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +        + +     E   + ++  +  + N L      RRL  + +  + R      
Sbjct: 512 IRLAYNAGVEDIRLIGGETINNPKVFMVFINGNILGVTIAYRRLVEVFRM-MRRRGLIGA 570

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDV 614
              +H +   R     T  G        + +   +     IE      RK  D      +
Sbjct: 571 FVSIHTSFTQRCVYIHTDGGRLCRPYIIVQAGLPLVLQEHIEQLKLGLRKFDDFLHDGLI 630

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   EE + +IA                       +E  +  EK   ++  P  ++ +
Sbjct: 631 EYLDVNEENDSFIA----------------------YQERDIDPEKTTHLEIEPFTLLGV 668

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A L+P+  ++ S R    C M +QA+ ++         G                    
Sbjct: 669 CAGLVPYPHHNQSPRNTYQCAMGKQAMGII---------GYNQKNRID------------ 707

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                 N    Q P+V+           
Sbjct: 708 ----------------------------------TLMYNIVYPQTPMVRS---------- 723

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T+   L  G+N  VA M + GY+ ED++++++  +       +  +  +   +  
Sbjct: 724 RTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTIKRY 783

Query: 855 KLGPEEITRDIPNVS-----EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                +        S         + +D  GI+  G  +     +V K  P  +S    E
Sbjct: 784 SNQTFDRIMGPMKDSLTGKVIARHECLDTDGIVSPGERLVCKQTMVNKEMPAVKSNNPIE 843

Query: 910 EK 911
           +K
Sbjct: 844 QK 845


>gi|212373945|emb|CAP09899.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35698]
          Length = 341

 Score =  340 bits (873), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 203/340 (59%), Positives = 264/340 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 2   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 61

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 62  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 121

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 122 IAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 181

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 182 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 241

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 242 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 301

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E
Sbjct: 302 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQE 341


>gi|116753353|ref|YP_842471.1| DNA-directed RNA polymerase subunit B' [Methanosaeta thermophila PT]
 gi|116664804|gb|ABK13831.1| DNA-directed RNA polymerase, subunit B' [Methanosaeta thermophila PT]
          Length = 604

 Score =  340 bits (873), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 121/584 (20%), Positives = 191/584 (32%), Gaps = 94/584 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A            + +   ++       +   E     R+T     
Sbjct: 97   IEYLDAEEEENAYIAIWENDLTEEHTHLEVDPSLILGICTALVPYPEHNASPRNTMGAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                    ++   L+  D  G            +        G       +  + A+   
Sbjct: 157  IKQCLGFPMANIRLRP-DTRG--HYLHYPQQPIVSTRTAKAIGFDKRPAGQNFVVAVLAY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   S V   +     F     ++ +     E            D+  I D
Sbjct: 214  EGYNIEDALVMNKSAVERGLARSHFFRVSEAEERKYPGGQE------------DKFEIPD 261

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              +         GQ    G                  P             ++   E   
Sbjct: 262  LEVRGARGSETYGQLDADGLVNPNA---------DVGPNDVLIGKTSPPRFLEEPTEFGI 312

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
               +  ++ +  R   K               R+ KV    +R  + GDK A RHG KG+
Sbjct: 313  SPQQRRETSVTMRSNEKGVVDLVILTESQNGNRLAKVKTRDQRIPELGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  +LP EDMPF + G   D++LNP  +PSRM VG + E   G      G+ I       
Sbjct: 373  VGLLLPQEDMPFSESGMVPDLLLNPHAIPSRMTVGHVLEMIGGKVGSLEGRFID------ 426

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                           +T  F G  E  +
Sbjct: 427  -----------------------------------------------AT-AFLGEKEWDL 438

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
             S L       +G+ +LYDG TGE     + VG I   KL HMV+ K++ARS G   ++T
Sbjct: 439  RSALTRLGFAHTGKEVLYDGATGERIQADIFVGVILYQKLYHMVTGKMHARSRGPVQVLT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG-------R 1325
            +QP  G++  GG R GEME   + A+GAA  L+E L  +SD V        G       R
Sbjct: 499  RQPTEGRAREGGLRFGEMERDVLIAHGAALALKERLVEESDKVTELVCSKCGVIAIHDRR 558

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              +    V G   D +      +F +L+ E+++LG++  L    
Sbjct: 559  RNMDLCPVCGTDTDIYPVEMSYAFKLLLDEIKSLGVAPRLMLED 602



 Score = 95.9 bits (237), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 75/454 (16%), Positives = 133/454 (29%), Gaps = 110/454 (24%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    E    ++ I   RR   +                ++        P    E     
Sbjct: 13  VGHHPEPEKLVAEIRRLRRAGVISNQINVAYYDRTNEIVINTDSGRARRPLIIVENG--- 69

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
                           +E       D      + YL A EEEN YIA   + L       
Sbjct: 70  -----QPLVTEEDIRRLERGEATFDDLVREGKIEYLDAEEEENAYIAIWENDLT------ 118

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            E+   ++  P  ++ I  +L+P+ E++ S R  MG  M +Q +
Sbjct: 119 -----------------EEHTHLEVDPSLILGICTALVPYPEHNASPRNTMGAGMIKQCL 161

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
               A                                                +      
Sbjct: 162 GFPMANIRL-----------------------------------------RPDTRGHYLH 180

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q+P+V                +        G+N +VA + + GY
Sbjct: 181 YP--------------QQPIVS----------TRTAKAIGFDKRPAGQNFVVAVLAYEGY 216

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV------SEEGLKN 875
           N ED++++++  V   +  S      E   R    G E+   +IP++        E    
Sbjct: 217 NIEDALVMNKSAVERGLARSHFFRVSEAEERKYPGGQEDKF-EIPDLEVRGARGSETYGQ 275

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  G++   A+V P D+L+GK +P        E        G      R+TS+ + S  
Sbjct: 276 LDADGLVNPNADVGPNDVLIGKTSPPRFLEEPTEF-------GISPQQRRETSVTMRSNE 328

Query: 936 SGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            G V  V +      ++  +  + ++   EL  +
Sbjct: 329 KGVVDLVILTESQNGNRLAKVKTRDQRIPELGDK 362


>gi|318603046|emb|CBJ04586.1| RNA polymerase beta subunit [Pseudomonas sp. R-37908]
          Length = 339

 Score =  340 bits (873), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 203/339 (59%), Positives = 264/339 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           LG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 LGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIHIQ 339


>gi|212373975|emb|CAP09914.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35713]
          Length = 342

 Score =  340 bits (872), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 204/341 (59%), Positives = 265/341 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 302 LALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 342


>gi|87242634|gb|ABD33841.1| RNA polymerase beta subunit [Acholeplasma morum]
          Length = 631

 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 235/455 (51%), Positives = 305/455 (67%), Gaps = 33/455 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGRICP ET EG +IGL+SSL S+
Sbjct: 2   NPLAELTQKRRVSALGTGGLARDRAGVEVRDVHESHYGRICPIETPEGPSIGLISSLASY 61

Query: 590 ARVNAYGFIETPYRKV-----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           ARV+ YGFI+TPY +V         VT++ VYL+A EEE   IA A+  LDEDG F  E 
Sbjct: 62  ARVDEYGFIQTPYLRVDKSNPKRHVVTDEFVYLTAGEEEQFVIASADIQLDEDGGFQTET 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R  GE    P  ++DF D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 IIGRFMGETKAFPSSRVDFQDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
             ++P VGTG+E   AK SG+AIV+   GIV   D+  I I         +  G      
Sbjct: 182 IPDSPIVGTGIEHRAAKDSGSAIVSGVEGIVVYADSRIIKIAIKPEASLKTPRGKVVYDK 241

Query: 759 ----------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                                 V+ Y L +F RSNQ+T + Q+P+V +G+ V++ D+IAD
Sbjct: 242 DQAFNWEAYDQIRQAKMTDLLKVEAYPLTQFLRSNQDTAILQKPIVSIGEYVQKGDVIAD 301

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GPS    +LALGRN++VAFM W GYN+ED++++SE +V +DV+TSIHI+E ++   DTKL
Sbjct: 302 GPSISKAELALGRNVVVAFMTWEGYNYEDAVIMSENLVRDDVYTSIHIDEHQIECCDTKL 361

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           G EEITR+IPN S + LK +D+ GI+ +G EV  GDILVGKITPKG++  TPEEKLL+AI
Sbjct: 362 GKEEITREIPNASADALKYLDDRGIVVLGTEVKEGDILVGKITPKGQTEPTPEEKLLQAI 421

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           F EKA +VRDTSLRVP G  G V  ++ F++   D
Sbjct: 422 FNEKAREVRDTSLRVPHGGGGIVQSIQYFSKSNGD 456



 Score =  296 bits (757), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 125/449 (27%), Positives = 192/449 (42%), Gaps = 77/449 (17%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
             A+ T L   E       +       I +  I+ +G  V  GD++    +   ++ +   
Sbjct: 255  QAKMTDLLKVEAYPLTQFLRSNQDTAILQKPIVSIGEYVQKGDVIADGPS-ISKAELALG 313

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELL 967
              ++ A    +  +  D  +   + V   V      + H I+  +  +  E    +I   
Sbjct: 314  RNVVVAFMTWEGYNYEDAVIMSENLVRDDVYTSIHIDEHQIECCDTKLGKEEITREIPNA 373

Query: 968  ARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            + D     D++ I+      +  +IL G+    G         L   + +E  R      
Sbjct: 374  SADALKYLDDRGIVVLGTEVKEGDILVGKITPKGQTEPTPEEKLLQAIFNEKARE-VRDT 432

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +++       +      +  S                 GD++ PGV  V++V++  KR I
Sbjct: 433  SLRVPHGGGGIVQSIQYFSKS----------------NGDELGPGVNEVIRVYIVKKRKI 476

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG++S+ILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQI E HLG A
Sbjct: 477  SEGDKMAGRHGNKGVISKILPREDMPYMADGTPVDIMLNPLGVPSRMNIGQILEIHLGMA 536

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG K+ + + D     D++ + +                                  
Sbjct: 537  AKKLGVKVATPVFDGLTQADLADIMAEAGMAPDGKQTL---------------------- 574

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                       G        TGEP++  V+VG +YM+KL+HMV 
Sbjct: 575  -------------------------YDG-------RTGEPYENRVSVGVMYMIKLSHMVD 602

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            DK++ARS G Y+LVTQQP+GGK+  GGQR
Sbjct: 603  DKLHARSVGPYTLVTQQPMGGKAQNGGQR 631


>gi|116563660|gb|ABJ99846.1| RpoB [Bacillus atrophaeus]
 gi|116563666|gb|ABJ99849.1| RpoB [Bacillus amyloliquefaciens]
 gi|116563668|gb|ABJ99850.1| RpoB [Bacillus vallismortis]
 gi|284154638|gb|ADB78420.1| RNA polymerase beta-subunit [Bacillus vallismortis]
 gi|284154752|gb|ADB78477.1| RNA polymerase beta-subunit [Bacillus vallismortis]
 gi|284154820|gb|ADB78511.1| RNA polymerase beta-subunit [Bacillus vallismortis]
 gi|284154882|gb|ADB78542.1| RNA polymerase beta-subunit [Bacillus subtilis subsp. spizizenii]
 gi|284154888|gb|ADB78545.1| RNA polymerase beta-subunit [Bacillus amyloliquefaciens]
 gi|284154890|gb|ADB78546.1| RNA polymerase beta-subunit [Bacillus amyloliquefaciens]
 gi|284154892|gb|ADB78547.1| RNA polymerase beta-subunit [Bacillus tequilensis]
          Length = 182

 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 129/204 (63%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|55583704|gb|AAV53371.1| RNA polymerase II second largest subunit [Strobilomyces floccopus]
          Length = 908

 Score =  340 bits (872), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 159/1035 (15%), Positives = 314/1035 (30%), Gaps = 172/1035 (16%)

Query: 286  KSLKEKGVKFLGITSDCLCGLY----VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G      +    V+     ++   G + D   LE I +   
Sbjct: 26   KTISQFQVKMFHRNQERTLGNIMKATIPYIRVDIPIWVVFRALGVISDRDILEHICYDMQ 85

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I                +       
Sbjct: 86   DSQMLEMLKPCIDDGFV--------IQDREVALDFI------------GNRGTTTGLSRE 125

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G 
Sbjct: 126  RRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGK 182

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 183  KRLDLAGPLLANLFRMLFKKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLAT 242

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 243  GNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 298

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN +
Sbjct: 299  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAH 350

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 351  SSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 407

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +       L+ +   ++  G      +      + K  GI+E +DA     
Sbjct: 408  AGRVCRPLFIVENQQLALQKKHIKWLNQGFRDDDGEEFKWEQLVK-TGIIELLDAEEEET 466

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +       +    ++ +     R  +K G            PS  LG  
Sbjct: 467  VMISMTPEDLENSRLQSAGINPHENDGDFDPAAR--LKAGINAHTWTHCEIHPSMILG-- 522

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       +
Sbjct: 523  -----VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLV 559

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 560  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 608

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D  +   S +   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 609  DFVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLED 667

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G N         K+  +  D      R++          ++     +  Q    
Sbjct: 668  DGLIAPGTNVKGEDIIIGKTAPIPPDSEELGQRTRTHNRRDVSTPLKSTENGIVDQVLI- 726

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q GDK A RHG KG +     
Sbjct: 727  -------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYR 767

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +          +
Sbjct: 768  QEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESV 827

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S      +K   +                                            L +
Sbjct: 828  STFLR--QKGYQSRG------------------------------------------LEV 843

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 +G+               + +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 844  MYHGHTGK----------KLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 893

Query: 1286 KSNRGGQRLGEMEVW 1300
            +S  GG R GEME  
Sbjct: 894  RSRDGGLRFGEMERD 908



 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 97/772 (12%), Positives = 216/772 (27%), Gaps = 113/772 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R+D    +P+     ALG+ S+ +IL      +  SQ  +     +    ++   +V+
Sbjct: 54  YIRVD----IPIWVVFRALGVISDRDILEHICYDMQDSQMLEMLKPCIDDGFVIQDREVA 109

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   +++     + L+++ +  + +            G  +   ++  
Sbjct: 110 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 168

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 169 LERRELDDRDHFGKKRLDLAGPLLANLFRMLFKKLTKDVYRYLQKCVETHKEFNLSLAV- 227

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 228 -------KHQTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 280

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       I  +
Sbjct: 281 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMACISVGSYSAPVIEFL 337

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +      NA         F     +    +  N +  I   RR   +         
Sbjct: 338 EEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 396

Query: 554 AGVEMRDVHPTHYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
                  ++        P    E          +    +       E    K      T 
Sbjct: 397 IRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGFRDDDGEE--FKWEQLVKTG 454

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFID 665
            +  L A EEE   I+     L+     +  +      G+          +        +
Sbjct: 455 IIELLDAEEEETVMISMTPEDLENSRLQSAGINPHENDGDFDPAARLKAGINAHTWTHCE 514

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ + AS+IPF +++ S R      M +QA+ +                      
Sbjct: 515 IHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV--------------- 559

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + +  Y       +     +  R      
Sbjct: 560 --------------------------RMDTMANILYYPQKPLATTRSMEYLKFR------ 587

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N +VA + + GYN ED +++++  +   +F SI+  
Sbjct: 588 ------------------ELPAGQNAIVAILCYSGYNQEDFVIMNQSSIDRGLFRSIYYR 629

Query: 846 EFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +  + + + +   E            +       +++ G+I  G  V   DI++GK  P
Sbjct: 630 SYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNVKGEDIIIGKTAP 689

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    ++        +  + RD S  + S  +G V  V I       K
Sbjct: 690 IPPDSEELGQRT-------RTHNRRDVSTPLKSTENGIVDQVLITTNSEGQK 734


>gi|116563672|gb|ABJ99852.1| RpoB [Bacillus sonorensis]
          Length = 182

 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 81/204 (39%), Positives = 129/204 (63%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP +++    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYYS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|147718|gb|AAA24579.1| RNA-polymerase beta subunit [Escherichia coli]
 gi|223239|prf||0611204A polymerase beta N term,RNA
          Length = 188

 Score =  340 bits (871), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 91/194 (46%), Positives = 133/194 (68%), Gaps = 6/194 (3%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL++++ +   G  ++
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEG--TV 114

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           KDIKEQ +YMG++PLMT +GTFVI G +R++VSQLHRSPG+ FD DKG+   SGK+LY  
Sbjct: 115 KDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNA 174

Query: 183 RIIPDQGLWMDIEF 196
           RIIP +G W+D EF
Sbjct: 175 RIIPYRGSWLDFEF 188


>gi|303390954|ref|XP_003073707.1| DNA-directed RNA polymerase subunit beta [Encephalitozoon
            intestinalis ATCC 50506]
 gi|303302855|gb|ADM12347.1| DNA-directed RNA polymerase subunit beta [Encephalitozoon
            intestinalis ATCC 50506]
          Length = 1140

 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 107/596 (17%), Positives = 186/596 (31%), Gaps = 118/596 (19%)

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMAR 852
                + +   L   +      + +       +++  I    +            ++    
Sbjct: 640  MSMIAMNTKALEESKKASDVKISYTHCEIHPALILGICASTIPFPDHNQSPRNTYQSAMG 699

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G                  +    +  +        +    +       +   +  
Sbjct: 700  KQAMGIYATNFL-----------LRMDTLSNILFYPQKPLVTTKSMEYLRFKELPSGQNA 748

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L AI      +  D+ +   S +   +     F R   D+   S     E+    +R   
Sbjct: 749  LVAIACYSGYNQEDSIIMNQSAIDRGLF-RSFFYRTYTDQESMSRPGVNEEFCKPSRGTV 807

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                 L+ N       I  G           K T +                    +  +
Sbjct: 808  LRMKNLNYNKLDEDGLISPGTRVTGDDVLIGKITPIL-------------------DPER 848

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               E+    Y+ S + +       ++ +           +  K+ V   R  Q GDK A 
Sbjct: 849  STKEAPVYVYKDSSTAMRRTETGIVDTVIV---TNKDGYKFSKIKVRSGRIPQMGDKFAS 905

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RH  KG +   L  EDMPF  DG   DI++NP  +PSRM +G + E  LG      G++ 
Sbjct: 906  RHAQKGTIGITLRQEDMPFTSDGIVPDIIINPHAIPSRMTIGHLIECLLGKVSAMSGEEG 965

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 966  D-----------------------------------------------------ATP-FS 971

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                  I++ L+     + G  ++Y+G+TG      V  G  Y  +L HMV DK++AR+ 
Sbjct: 972  DMTVNEISAKLKSYGFQQRGLEVMYNGMTGRKLRAQVFFGPTYYQRLKHMVDDKIHARAR 1031

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESI 1332
            G   ++T+QP+ G+S  GG R GEME  CI ++GA+  L+E L   SD        Y   
Sbjct: 1032 GPLQILTRQPVEGRSRDGGLRFGEMERDCIISHGASAFLKERLMDVSD-------AYSCF 1084

Query: 1333 V-----------------AG----NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            V                  G     +      P +F +LV+E+  + ++  +    
Sbjct: 1085 VCNFCGLLAMGGSKVNECKGCNNTTNVSMIEIPYAFKLLVQELMGMNIAPRIRFEE 1140



 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 137/992 (13%), Positives = 282/992 (28%), Gaps = 187/992 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------AFSGAAMLEFVSY 79
           L+  Q  S+D F+   +          Q        I                 + F   
Sbjct: 23  LVRQQLDSFDQFVKTKM----------QEVIDESPAIIVQSAPTAGIETQKRITVRFGQI 72

Query: 80  EFDPPK-FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
               P  +            ++   RDLTYA PL I +       +  +    +   K  
Sbjct: 73  YVSKPPIYTESDGRTITVFPNEARIRDLTYASPLFIDVT-----KETISELGVVDKHKYS 127

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR--SPG 162
            +  G LP+M +                         G F++ G ++++V+Q  R  S  
Sbjct: 128 RVPFGSLPVMLRSSYCVLYGLSDKDLIDLGECPYDQGGYFIVNGSEKVIVAQE-RMASNT 186

Query: 163 IHFDHDKGRASLSGKLLYACRI--IPDQGLWMDIEFDSK-----DIIHVRIDR-RRKVPV 214
           ++      + +      +   I  +P++          K      +I V +   ++ +P+
Sbjct: 187 VY----VFKKAQPATYTHYAEIRSVPEKSSRNPSTLSMKLCRSPGVIRVSLPLVKQDIPL 242

Query: 215 TSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
                ALG    +EI+     +    +  +     +    ++    V+   +   +    
Sbjct: 243 FVLYRALGFLSDKEIIDHILYEDD-DEMFELLKESIEEGMVVQDQNVALDYIGKRSAPVG 301

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
               K++   + K L  K V     T +              +   + + A    +    
Sbjct: 302 TPQEKRII--IAKDLLAKEVLPHIGTQEFCETKKAYFIGYIVQR--LLLVALGRKNPDDR 357

Query: 334 EEIFHSEIR-DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           +      +    P+L          +         K  ++       +     + T    
Sbjct: 358 DHYGKKRMDLSGPLLASLFRTLFKKLCADTTRHMQKCIENGREFNIALGLKASIITQGFR 417

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGK 450
            ++    + D  K   +  G  ++  R N  +      R     +    +     L N  
Sbjct: 418 YALATGNWGDQAKAMQTRAGVAQVLNRYNFVSTLSHLRRVNTPIEKEGKLAAPRQLHNTH 477

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +         +      ++KN   +  + +  S    +  ++   V   + I+   + 
Sbjct: 478 WGMVCPAETPEGQACG---LVKNLSLMAYISVGSSSGPLVEFLEECGVESLEEISTPQLN 534

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +A   F     +    + V  +  +   RR        +   +    +RD+         
Sbjct: 535 AATKIFVNGIWVGIHSDPVYLIKSLKLLRR-------SLEMDKEVSIVRDIREKEIRIQS 587

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            A       + + ++            ++    K  +      + +L   EEE   IA  
Sbjct: 588 DAGRPCRPLLVVKNN-ELVITPEDIKRLKRGEIKWDNLISEGFIEFLDVEEEEMSMIAMN 646

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
             +L+E    ++  +                   +  P  ++ I AS IPF +++ S R 
Sbjct: 647 TKALEESKKASDVKISY--------------THCEIHPALILGICASTIPFPDHNQSPRN 692

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                                               
Sbjct: 693 TYQSAMGKQAMGIYATNFLL---------------------------------------- 712

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               + S +  Y               Q+PLV                     +L  G+N
Sbjct: 713 -RMDTLSNILFYP--------------QKPLV----------TTKSMEYLRFKELPSGQN 747

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----I 865
            LVA   + GYN EDS+++++  +   +F S     +      ++ G  E         +
Sbjct: 748 ALVAIACYSGYNQEDSIIMNQSAIDRGLFRSFFYRTYTDQESMSRPGVNEEFCKPSRGTV 807

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +DE G+I  G  V   D+L+GKITP  +   + +E  +          V 
Sbjct: 808 LRMKNLNYNKLDEDGLISPGTRVTGDDVLIGKITPILDPERSTKEAPVY---------VY 858

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
             S          +VD  I       K  +  
Sbjct: 859 KDSSTAMRRTETGIVDTVIVTNKDGYKFSKIK 890


>gi|159041032|ref|YP_001540284.1| DNA-directed RNA polymerase subunit B [Caldivirga maquilingensis
            IC-167]
 gi|157919867|gb|ABW01294.1| RNA polymerase Rpb2 domain 6 [Caldivirga maquilingensis IC-167]
          Length = 1131

 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 96/321 (29%), Positives = 144/321 (44%), Gaps = 78/321 (24%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 +++KV V   R  + GDK A RHG KG+V  I+P EDMPF ++G   D+V+NP  
Sbjct: 866  SSEGFKLIKVKVRELRIPELGDKFASRHGQKGVVGMIVPMEDMPFTENGITPDVVINPHA 925

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +GQ+ E   G      G  +                                  
Sbjct: 926  LPSRMTIGQLLEAIAGKTAALYGTLVD--------------------------------- 952

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F+G  E  I SML  A    SG+  +Y GL G   D
Sbjct: 953  --------------------ATP-FEGVPEGTIRSMLMKAGYRWSGRETMYSGLMGTRLD 991

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G +Y  KL+HMV+DK++AR+TG   ++T+QP  G+S  GG RLGEME   + A+G
Sbjct: 992  ADIFIGVVYYQKLHHMVADKIHARATGPMQILTRQPTEGRSREGGLRLGEMERDVLIAHG 1051

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYE------------------SIVAGND--TFETGTPES 1346
            AA +L E   ++S D   +  +Y                     + G+     +   P +
Sbjct: 1052 AAALLHER-MVESSD---KYVMYVCEDCGMMAWWDDFKKRPICPIHGDKGRIAKVIVPYA 1107

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
            F +L++E+ +LG+   L+ S 
Sbjct: 1108 FKLLLQELISLGIYPKLKLSE 1128



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 122/659 (18%), Positives = 231/659 (35%), Gaps = 61/659 (9%)

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +   D +         +         +A   I R +  G      +  ++        
Sbjct: 258 LAVSDNDEIQRELLASFEMAIQIAPTVDEARDYIGRRIVLGHPREIRIQRAL-----EYL 312

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           DKY L  +G             D VR  +  ++   +  +++L  G    DD D++ N+R
Sbjct: 313 DKYFLPHLGTT---------PDDKVRLSKAIELGQAVAGVIELYKGWRQPDDKDHMSNKR 363

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ---------DLINAKPVVSAVC 514
           VR VG++L   +R    +  + ++ ++        +P+              K  +S   
Sbjct: 364 VRLVGDLLAQLFRSIFAQFVQDLRNQLEKQYSRGKIPELRTIVRADIISDRLKHALSTGN 423

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                + ++Q+ +  N +S I+H RR+ +     ++R +   E RD+HPT +GR+C  ET
Sbjct: 424 WVGGKTGVTQMLDRTNYVSTISHLRRVVS----SLSRTQPHFEARDLHPTQWGRLCAIET 479

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG N GLV ++   A V   G  E     +       +V+     E +   +   N  L
Sbjct: 480 PEGQNCGLVKNMALMATVT-VGVDEASVEAMLREMGVINVLDARRNEIKGANVLL-NGRL 537

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA---SLIPFLENDDSNRVL 691
                  + LV              +++         V +      L   L    + ++ 
Sbjct: 538 IGIHRDPQALVNAIREARRRGDINGEVNVGYIEKLNEVRVNCDGGRLRRPLLIISNGKLR 597

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGM-------ESVVAK----SSGAAIVAKRAGIVEQVDA 740
           +      +           V  G+       E   A      +    ++K   +      
Sbjct: 598 LTKEHIEKLRSGEWTWDDLVKNGIVEYLDADEEENAMVTIGDTKDVDLSKYTHMEIIPSI 657

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGD---EVRRNDIIAD 796
           +   +  +    + + S  +IY     ++S      N R  +   G       R  +   
Sbjct: 658 MLGAVAHIIPYSEHNQSPRNIYEAAMAKQSLGFPYSNYRYRIDSRGHLLLYPERPLVTTR 717

Query: 797 G-PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           G           G+N ++A + + GY+ ED+++I++  +   +F SI    +E  A    
Sbjct: 718 GLELIGYSMRPSGQNAVLALVSFMGYSIEDAVMINKAAIERGMFRSIFYRSYETEAMRYP 777

Query: 856 LGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +G  +     P         E   ++DE GI+     V+  ++L+GKI+P        E 
Sbjct: 778 MGENDRITIPPPTVRDYRGAEAYAHLDEDGIVPPEVFVSSKEVLIGKISPPRFYSALAES 837

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +L        A + +D S+ V  G  G V  V I       K  +    E    EL  +
Sbjct: 838 QL--------AGEWKDNSITVRRGEKGIVDQVLITESSEGFKLIKVKVRELRIPELGDK 888



 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 107/734 (14%), Positives = 239/734 (32%), Gaps = 133/734 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L+  Q  S++ F+             L+   +  F I    G   ++F+  E   P+F  
Sbjct: 45  LVRHQIDSFNDFVDRK----------LKEIVQE-FNID--LGDVKVKFIDVEVGKPRFKE 91

Query: 88  ---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R++TYA P+++ + L +   +             +++ +GDLP+M
Sbjct: 92  PTGVENVIYPMEARLRNITYAAPMRLKVMLYINGEEYT-----------ETVPLGDLPIM 140

Query: 139 TKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGRA 172
            K                         G F+I G +R+VVSQ  L  +  I+   ++G  
Sbjct: 141 VKSKYCNLYGLKPQAIVKKLEDPNDPGGYFIINGSERVVVSQEDLALNKPIYDYDERGAT 200

Query: 173 SLSGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDR--RRKVPVTSFLMALGMDSE 226
            +        +II      +   + +E+    +I+V+I +   R +P    + ALG++ +
Sbjct: 201 RIPR-----AKIISMGPGYR-TTVVVEYHKDGVIYVQIPKIPTR-MPFPVVMRALGLEKD 253

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI--ESGKKLTSGL 284
           + ++        S   +     L++ ++ +    +        G +++     +      
Sbjct: 254 QDIAL-----AVSDNDEIQRELLASFEMAIQIAPTVDEARDYIGRRIVLGHPREIRIQRA 308

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI-------EAGDVIDEKSLEEIF 337
           L+ L +  +  LG T D    L  A ++     G I +       +  D +  K +  + 
Sbjct: 309 LEYLDKYFLPHLGTTPDDKVRLSKAIELGQAVAGVIELYKGWRQPDDKDHMSNKRVRLVG 368

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
               +    ++   V +   +RN L    ++ +   L  I R     D+ +  +  ++  
Sbjct: 369 DLLAQLFRSIFAQFVQD---LRNQLEKQYSRGKIPELRTIVR----ADIISDRLKHALST 421

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDI 456
             +          + R      ++      V  + +       + L   + G+   I+  
Sbjct: 422 GNWVGGKTGVTQMLDRTNYVSTISHLRRV-VSSLSRTQPHFEARDLHPTQWGRLCAIETP 480

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           +      V+++  M      +    +E  ++E      +D+         +  +      
Sbjct: 481 EGQNCGLVKNMALMATVTVGVDEASVEAMLREMGVINVLDA--------RRNEIKGANVL 532

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                +    +    ++ I   RR   +           +    V+        P     
Sbjct: 533 LNGRLIGIHRDPQALVNAIREARRRGDINGEVNVGYIEKLNEVRVNCDGGRLRRPLLIIS 592

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              + L        R   + +         D      V YL A EEEN  +   ++    
Sbjct: 593 NGKLRLTKEHIEKLRSGEWTW--------DDLVKNGIVEYLDADEEENAMVTIGDTK--- 641

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                              V   K   ++  P  ++   A +IP+ E++ S R +    M
Sbjct: 642 ------------------DVDLSKYTHMEIIPSIMLGAVAHIIPYSEHNQSPRNIYEAAM 683

Query: 697 QRQAVPLLKAEAPF 710
            +Q++    +   +
Sbjct: 684 AKQSLGFPYSNYRY 697


>gi|52694181|emb|CAG30620.1| DNA-directed RNA polymerase beta chain [Pseudomonas nitroreducens]
          Length = 350

 Score =  339 bits (870), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 205/339 (60%), Positives = 267/339 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 12  ESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 71

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++D
Sbjct: 72  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGLVSDD 131

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 132 IVFLSAIEEADHVIAQASATLNEKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 191

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 192 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 251

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R+DI
Sbjct: 252 VIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDQVSRSDI 311

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           +ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ ++ER
Sbjct: 312 LADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLNER 350


>gi|19074634|ref|NP_586140.1| DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST SUBUNIT
            [Encephalitozoon cuniculi GB-M1]
 gi|51702025|sp|Q8SR75|RPB2_ENCCU RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA
            polymerase II subunit 2; Short=RNA polymerase II subunit
            B2
 gi|19069276|emb|CAD25744.1| DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST SUBUNIT
            [Encephalitozoon cuniculi GB-M1]
          Length = 1141

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 112/590 (18%), Positives = 193/590 (32%), Gaps = 105/590 (17%)

Query: 795  ADGPSTDLGDLA-LGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMA 851
                + +   LA   RN     + +       +++  I    +            ++   
Sbjct: 640  MSMIAMNTKILADESRNSSDVSVSYTHCEIHPALILGICASTIPFPDHNQSPRNTYQSAM 699

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                +G                  +    +  +        +    +       +   + 
Sbjct: 700  GKQAMGIYATNFL-----------LRMDTLSNILFYPQKPLVTTKSMEYLRFKELPSGQN 748

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             L AI      +  D+ +   S +   +     F R   D+   S     E+    +R  
Sbjct: 749  ALVAIACYSGYNQEDSIIMNQSAIDRGLF-RSFFYRTYTDQESMSRPGVNEEFCKPSRGA 807

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                  L+ N       I  G           K T +                    +  
Sbjct: 808  VLRMKNLNYNKLDDDGLISPGTRVTGDDVLIGKITPIL-------------------DPE 848

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +   E+    Y+ S + +       ++ +           +  KV V   R  Q GDK A
Sbjct: 849  RSTKEAPVYVYKDSSTAMRRTETGIVDTVIV---TNKDGYKFSKVKVRSGRIPQMGDKFA 905

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RH  KG +   L  EDMPF  +G   DI++NP  +PSRM +G + E  LG      G++
Sbjct: 906  SRHAQKGTIGITLRQEDMPFTSEGIVPDIIINPHAIPSRMTIGHLIECLLGKVSAMSGEE 965

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                                   +TP F
Sbjct: 966  GD-----------------------------------------------------ATP-F 971

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             G   + I+S L+     + G  ++Y+G+TG      +  G  Y  +L HMV DK++AR+
Sbjct: 972  SGVTVDGISSRLKSYGFQQRGLEVMYNGMTGRKLRAQMFFGPTYYQRLKHMVDDKIHARA 1031

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG 1324
             G   ++T+QP+ G+S  GG R GEME  CI ++GA+  L+E L   SD       D  G
Sbjct: 1032 RGPLQILTRQPVEGRSRDGGLRFGEMERDCIISHGASAFLKERLMDVSDAYSCYVCDFCG 1091

Query: 1325 RTRVYESIV---AG----NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +  S V    G     +      P +F +L++E+  + ++  +    
Sbjct: 1092 LLAMGGSKVNECKGCNNTTNVSMVEIPYAFKLLIQELMGMNIAPRIRFEE 1141



 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 140/993 (14%), Positives = 279/993 (28%), Gaps = 188/993 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------AFSGAAMLEFVSY 79
           L+  Q  S+D F+   +          Q        I                 + F   
Sbjct: 23  LVRQQLDSFDQFVKTKM----------QEVINESPVIIVQSAPTAGIETQKRIAVRFGQI 72

Query: 80  EFDPP-KFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
               P  +            ++   RDLTYA PL I +       +  +    +   K  
Sbjct: 73  YVSKPPVYTESDGRTITVFPNEARIRDLTYASPLFIDVT-----KETLSELGVVDKHKYS 127

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR--SPG 162
            +  G LP+M +                         G F++ G ++++V+Q  R  S  
Sbjct: 128 RVPFGSLPVMLRSSYCVLYGLGDKDLIDLGECPYDQGGYFIVNGSEKVIVAQE-RMASNT 186

Query: 163 IHFDHDKGRASLSGKLLYACRI--IPDQGLWMDIEFDSK-----DIIHVRIDR-RRKVPV 214
           ++      + +      +   I  +P++          K      +I V +   ++ VP+
Sbjct: 187 VY----VFKKAQPATYTHYAEIRSVPEKSSRNPSTLSMKLCRSPGVIRVSLPLVKQDVPL 242

Query: 215 TSFLMALGM-DSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
                ALG    +EI+    Y                    ++    V+   +   +   
Sbjct: 243 FVLYRALGFLSDKEIIDHILYEDDEEMFELLKESIEEGT--VVQDQNVALDYIGKRSAPI 300

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
                K++   + K L  K V     T +              +   + + A    +   
Sbjct: 301 GTPQEKRI--VMAKDLLAKEVLPHIGTQEFCETKKAYFIGYIVQR--LLLVALGRRNPDD 356

Query: 333 LEEIFHSEIR-DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            +      +    P+L          +         K  ++       +     + T   
Sbjct: 357 RDHYGKKRMDLSGPLLASLFRTLFKKLCVDTTRHMQKCIENGREFNIALGLKASIITQGF 416

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNG 449
             ++    + D  K   +  G  ++  R N  +      R     +    +     L N 
Sbjct: 417 RYALATGNWGDQAKAMQTRAGVAQVLNRYNFVSTLSHLRRVNTPIEKEGKLAAPRQLHNT 476

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +         +      ++KN   +  + +  S    +  ++   V   + I+   +
Sbjct: 477 HWGMVCPAETPEGQACG---LVKNLSLMAYISVGSSSGPLVEFLEECGVESLEEISTSQL 533

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +A   F     +    + V  +  +   RR        +   +    +RD+        
Sbjct: 534 DAATKIFVNGVWVGIHSDPVGLIKSLKLLRR-------SLEMDKEVSIVRDIREKEIRVQ 586

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
             A       + +  +       +    ++    K  +   +  + +L   EEE   IA 
Sbjct: 587 SDAGRPCRPLLVVKDNKLVITAEDIR-KLKRGEIKWDNLVTSGFIEFLDVEEEEMSMIAM 645

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            N+ +  D S     V                   +  P  ++ I AS IPF +++ S R
Sbjct: 646 -NTKILADESRNSSDVSVSY------------THCEIHPALILGICASTIPFPDHNQSPR 692

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                 M +QA+ +                                              
Sbjct: 693 NTYQSAMGKQAMGIYATNFLL--------------------------------------- 713

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                + S +  Y               Q+PLV                     +L  G+
Sbjct: 714 --RMDTLSNILFYP--------------QKPLV----------TTKSMEYLRFKELPSGQ 747

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD----- 864
           N LVA   + GYN EDS+++++  +   +F S     +      ++ G  E         
Sbjct: 748 NALVAIACYSGYNQEDSIIMNQSAIDRGLFRSFFYRTYTDQESMSRPGVNEEFCKPSRGA 807

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           +  +       +D+ G+I  G  V   D+L+GKITP  +   + +E  +          V
Sbjct: 808 VLRMKNLNYNKLDDDGLISPGTRVTGDDVLIGKITPILDPERSTKEAPVY---------V 858

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
              S          +VD  I       K  +  
Sbjct: 859 YKDSSTAMRRTETGIVDTVIVTNKDGYKFSKVK 891


>gi|133460|sp|P09845|RPOB1_METTW RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|809726|emb|CAA30837.1| unnamed protein product [Methanothermobacter thermautotrophicus]
          Length = 604

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 115/585 (19%), Positives = 198/585 (33%), Gaps = 94/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A  P         + I    +       I         R+T     
Sbjct: 97   IEYLDAEEEENTYIAMSPEEVTEEHTHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S   L+         +        +    I   G       +  + A+   
Sbjct: 157  TKQALGLYASNYNLR---TDTRAHLLHHPQVPIVKTRIIDVTGYDERPSGQNFVVAVMSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +   +     F R       R    + ++ E+  +        + 
Sbjct: 214  EGYNMEDALILNKASLERGLARSSFF-RSYEATERRYPGGQEDRFEIPEKG-------VR 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                 R    L     ++         VL           +  +F    E+ +    +++
Sbjct: 266  GYRSERDYRHLDEDGIINPETEVSSGDVLIGKTSPPRFLEEIDEFGTVAERRRETSVTVR 325

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ-SGDKMAGRHGNKG 1098
               E     +                      R+ K+ V  +R  +  GDK A RHG KG
Sbjct: 326  HGEEGIVDAVLL-------------TETVEGSRLAKIRVREQRQPEFIGDKFASRHGQKG 372

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +V  I+  EDMPF +DG   D+++NP  +PSRM+VGQ+ E   G A    G+++      
Sbjct: 373  VVGLIVSQEDMPFTEDGVVPDLIVNPHAIPSRMSVGQVLEMLAGKAACMEGRRVDG---- 428

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                             TP F G +E+ 
Sbjct: 429  -------------------------------------------------TP-FTGEEEKD 438

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L+    + +G   LY+G+TGE  +  + +G  Y  KL+HM +D++YARS G   ++
Sbjct: 439  LKEALKANGFESAGVETLYNGITGERIEAEIFIGVAYYQKLHHMTTDRIYARSRGPVQVL 498

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYES 1331
            T+QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD          G   +Y+ 
Sbjct: 499  TRQPTEGRAREGGLRFGEMERDCLIAHGAALALKERLLDESDKYEALVCAECGMIAIYDK 558

Query: 1332 IVAGNDTF--------ETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            I                     +F +L+ E+++L +   L     
Sbjct: 559  IRDKKYCPICEDSESFPVEISYAFKLLLDELKSLCIFPKLVLEDK 603



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 42/113 (37%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           + +   +  D      + YL A EEEN YIA +   +                       
Sbjct: 81  LSSGEMEWDDLISQGIIEYLDAEEEENTYIAMSPEEVT---------------------- 118

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E+   ++  P  ++ I A +IPF  ++ S R  M   M +QA+ L  +    
Sbjct: 119 -EEHTHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGMTKQALGLYASNYNL 170


>gi|66876485|gb|AAY58031.1| RpoB [Cuscuta japonica]
          Length = 456

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 133/464 (28%), Positives = 204/464 (43%), Gaps = 61/464 (13%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL        E  +   + +L A    +  +  D  L         + +
Sbjct: 50   VRRGQFIKKGQILAD-GAATVEGELALGKSVLVAYMPWEGYNSEDAVL---------ISE 99

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY---SRLMEILCGQNAVSG 998
              ++       + R   ++            +E   L+ +      +   +L G     G
Sbjct: 100  CLVYEDIFTSFHIRKYEIQTHVTTQGPEKVTNEIPHLEAHFIRNLDKNGIVLQGSWVEPG 159

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T       S  P  +  +  +  +        LKV       +++ R+  K  
Sbjct: 160  DVLVGKLTPQVVKESSYAPEDRLLRALLGIQVSASKETCLKVPIGGRGRVIDVRWIQKKG 219

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                G    P     ++V++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG  V
Sbjct: 220  ----GYGYNP---EKIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRSV 272

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S  +    ++   
Sbjct: 273  DLVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASR-KIVFSELYEA 331

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
               T     ++ +                                        G+S ++D
Sbjct: 332  SKQTANPWAFEPE--------------------------------------YPGKSRIFD 353

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG  F+ PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEME
Sbjct: 354  GRTGNTFEHPVLIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRAKQGGQRVGEME 413

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-SIVAGNDTFET 1341
            VW ++ +G A++LQEMLT KSD +  R  V   ++V G      
Sbjct: 414  VWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTLVXGT-IPNP 456



 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 91/234 (38%), Positives = 147/234 (62%), Gaps = 6/234 (2%)

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           R+     E  L           L+ +QRSN+NTC+ Q+P V+ G  +++  I+ADG +T 
Sbjct: 10  RVFYTDTEKILVSGDGKTINIPLVMYQRSNKNTCIYQKPRVRRGQFIKKGQILADGAATV 69

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+++LVA+MPW GYN ED++LISE +V ED+FTS HI ++E+    T  GPE++
Sbjct: 70  EGELALGKSVLVAYMPWEGYNSEDAVLISECLVYEDIFTSFHIRKYEIQTHVTTQGPEKV 129

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGE 919
           T +IP++    ++N+D+ GI+  G+ V PGD+LVGK+TP+     +  PE++LLRA+ G 
Sbjct: 130 TNEIPHLEAHFIRNLDKNGIVLQGSWVEPGDVLVGKLTPQVVKESSYAPEDRLLRALLGI 189

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHG----IDKNERSISVEREQIELLAR 969
           +    ++T L+VP G  G V+DVR   + G      +  R   +++ +I++  +
Sbjct: 190 QVSASKETCLKVPIGGRGRVIDVRWIQKKGGYGYNPEKIRVYILQKREIKVGDK 243


>gi|78714195|gb|ABB51080.1| RNA polymerase beta subunit [Acholeplasma laidlawii]
 gi|78714197|gb|ABB51081.1| RNA polymerase beta subunit [Acholeplasma laidlawii]
          Length = 628

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 230/452 (50%), Positives = 301/452 (66%), Gaps = 30/452 (6%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 2   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 61

Query: 590 ARVNAYGFIETPYRKVC----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           A+V+ YGFI+TP+ KV     +  VT +V+YL+A EE +  IA A + +DE G F E  V
Sbjct: 62  AKVDEYGFIKTPFLKVVQNGNETSVTKEVIYLTADEESDHVIASAATPMDEHGLFIESRV 121

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  +    +I  +D SPKQVVS+A S IPFLE+DD++R LMG NMQRQAVPLL+
Sbjct: 122 IARRNGETGIYDANEITAMDVSPKQVVSVATSSIPFLEHDDASRALMGANMQRQAVPLLQ 181

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV------ 759
             +P VGTG+E   AK SGA ++AK +G V  VD  +I+I     D   S S        
Sbjct: 182 PTSPIVGTGVEYRAAKDSGAVVIAKNSGYVTYVDGKKIIITPEPTDTIKSGSKTLYKVGG 241

Query: 760 ------------------DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                             D Y L++F RSNQ+T + Q+P+V  G+ V   D+IADGPST+
Sbjct: 242 EFDYGIAKKLYETKSVQNDQYDLVQFFRSNQDTLILQKPIVMQGEYVDAGDVIADGPSTE 301

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LGPE 859
            G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G E
Sbjct: 302 NGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQANGKE 361

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ G+
Sbjct: 362 EITREIPNVGQEAIKFLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVIGD 421

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 422 KAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 453



 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 124/413 (30%), Positives = 189/413 (45%), Gaps = 65/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V+ GD++    + +    +     +  A    +  +  D  +     V   V 
Sbjct: 281  IVMQGEYVDAGDVIADGPSTEN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 339

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   +  +E+I     +   E +            I+ G     G  
Sbjct: 340  TSIHIDEYEIETRDLKQANGKEEITREIPNVGQEAI----KFLDERGIIVPGSEVKEGDI 395

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 396  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 451

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP+L DGT VDI
Sbjct: 452  --GDQLPTGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYLADGTYVDI 509

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ S + D   N ++               
Sbjct: 510  MLNPLGVPSRMNIGQILEIHLGISAQKLGIKVASPVFDGVTNDEL--------------- 554

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                            GA  E        A +   G++ LYDG 
Sbjct: 555  --------------------------------GAIMEE-------AGIAPDGKTTLYDGR 575

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEP++  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 576  TGEPYNNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 628


>gi|260159596|gb|ACX32466.1| RNA polymerase subunit B [Acinetobacter sp. JB15]
          Length = 274

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 130/278 (46%), Positives = 180/278 (64%), Gaps = 5/278 (1%)

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            +     R++ +L GQ +  G  G K+   LS D++S        +    DE +   +  +
Sbjct: 1    EEAARERIVRLLSGQESNGG-GGTKRGDKLSEDMLSGLELVDLLEIQPSDEAIAERLTQI 59

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG
Sbjct: 60   QVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKG 119

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++  
Sbjct: 120  VVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKML-- 177

Query: 1159 YKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA+E 
Sbjct: 178  -KQQREIAELRVFLDKIYNKVGGQQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGAEES 236

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
             I  +L +A++  SGQ++LYDG TGE FDRPVTVGY+Y
Sbjct: 237  QIKELLELAEIPRSGQTVLYDGRTGERFDRPVTVGYMY 274


>gi|55975974|gb|AAQ72388.2| RpoB [Raoultella terrigena]
          Length = 343

 Score =  339 bits (869), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 215/343 (62%), Positives = 271/343 (79%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D+
Sbjct: 121 KVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDY 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 181 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G   VAKR G V+ VDA RIVI+  + ++ P  +G+DIY L K+ RSNQNTC+NQ P V 
Sbjct: 241 GVTAVAKRGGTVQYVDASRIVIKVNDDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS
Sbjct: 301 LGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDS 343


>gi|159119582|ref|XP_001710009.1| DNA-directed RNA polymerase subunit B' [Giardia lamblia ATCC 50803]
 gi|157438127|gb|EDO82335.1| DNA-directed RNA polymerase subunit B [Giardia lamblia ATCC 50803]
          Length = 1238

 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 154/977 (15%), Positives = 310/977 (31%), Gaps = 196/977 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM-ERSIKERI 490
            +   +  +I+  +    G    D  D +GN+++ + G++L+  +      +    +++  
Sbjct: 417  KAVYLATMIRRAILFDFGVIKGDSKDFVGNKKIETAGDLLELIFDDAFKTLLAHMVRKVD 476

Query: 491  SSVDIDSVMPQDLINAKPVV----SAVCEFFCSS----------------QLSQLEEHVN 530
            S +  D     DL N   V     S +   F S+                 +SQ+   ++
Sbjct: 477  SVLRSDRNRGTDLTNYDIVSLVDPSIITRAFNSAISTGNWKIEKIGVDRVGVSQILSRLS 536

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             +S +    RLS+       +A      R ++ +  G  CP++T EG ++G+V +L+  A
Sbjct: 537  YISALGQVTRLSST----FDKAMKSSGPRMLNFSQMGIFCPSDTPEGESVGIVKNLSIMA 592

Query: 591  RVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            R             +   + T+ +    +S   E+       ++     G         +
Sbjct: 593  R-------------ISKDESTDSISKLLMSIGVEDLASCWSGDTFSLGYGYMVFLNGTIK 639

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                + ++    I       +  +S   S     E+             R  + +   + 
Sbjct: 640  GVIAKDMLKGFIITLRTFRRRGYISYLTSFHFNDEHQAVYINCDSGRACRPLLIVENGKL 699

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                + +E +V       +     G VE +D        +  D    T            
Sbjct: 700  MLTRSDIELLVDNQ-KCFVDLIYEGKVEYLDVNEAKNAYIAMDTKDLTP----------- 747

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                     Q    ++        ++   P                +    G     ++ 
Sbjct: 748  ---------QHTHCEIESYTLLGYVVGLIPYPHHNQSP-----RNCYQCSMGKQASGAIA 793

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
             ++                                      E  +  +D           
Sbjct: 794  FNQ----------------------------------LERFETAMFLLD---------YP 810

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     +   G   +   +     +    + D+ D  +   + +        I+   
Sbjct: 811  QQPLTSTKILKLTGYERLPAGQNATVCVMSYSSFDIEDALILNRNAIDRGFGRCSIYRSV 870

Query: 949  GIDKNE---RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
              + N    +S+   ++ +    +D   +           L  +  G +  +G     K 
Sbjct: 871  STELNSIGSKSVDGIKDILLGPPKDHLKQYEGYHAIEDDGLCAV--GAHLKTGDIVINKG 928

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
              +++                  E ++  +E++              + +K+     GD 
Sbjct: 929  RHITNIPGLSDGTEATASLIKAPESLKSPLETIT-------------YVDKVLVTTNGD- 974

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   ++KV     R  + GDK + RHG KG+   I+P  D+PF   G   D+++NP 
Sbjct: 975  ----GNMLIKVLTREPRRPEVGDKFSSRHGQKGVCGLIVPQSDLPFTSQGIVPDLIMNPH 1030

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V ++ E     +    G++        K +                       
Sbjct: 1031 GYPSRMTVAKLLELLSNKSGCFRGEQTDGTCFRTKTDETFL------------------- 1071

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                             +   LR+A    SG+ +LY GLTG+  
Sbjct: 1072 -------------------------------AELYDSLRVAGFSYSGKDVLYSGLTGDVI 1100

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               +  G IY  KL HMV DK+++R TG  +++T+QP  G+   GG R+GEME  C  +Y
Sbjct: 1101 PVYIFNGPIYYQKLKHMVKDKIHSRGTGPITMLTRQPTEGRRVHGGLRMGEMERDCAISY 1160

Query: 1306 GAAYVLQEMLTIKSDD-------VVG-----RTRVYESIVA--GNDTFETGTPESFNVLV 1351
            GA+ +L E   + SDD         G     +  V        G D  +   P +  +++
Sbjct: 1161 GASALLLERFMLSSDDFLAYVCETCGLFSYEKNGVLWCPTCQSGKDVVKIRIPYAAKLMI 1220

Query: 1352 KEMQALGLSIDLENSRT 1368
            +E+ ++G+ + ++   +
Sbjct: 1221 QELISMGVLVRMQLEDS 1237



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 29/214 (13%), Positives = 72/214 (33%), Gaps = 53/214 (24%)

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT------- 139
              +C  R++TYA P+ I +R       + +   S++  KE  I +G +P+M        
Sbjct: 99  TPHECRQRNMTYAAPITIDVR------CKASNKSSVQYYKE--ICIGYIPIMLRSNRCIL 150

Query: 140 -----------------KDGTFVIKGIQRIVV-------SQLHRSPGIHFDHDKGRASLS 175
                              G F+++G ++ ++       +++    G + D +      S
Sbjct: 151 TNKSRKQQAFLQECPDDPGGYFIVRGAEKSILLAEQMTMNRIVL--GRNADGNVEVTVAS 208

Query: 176 GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR--RRKVPVTSFLMALGMDSE-EILSTF 232
                       +   +          ++  ++  ++ +P+ +   A+G  ++  +LS  
Sbjct: 209 NTTERKS-----RCAVLY----KNKKFYLIHNKFNKKPIPIVTVFKAMGFVNDVTVLSLI 259

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               ++           S   +    +    L D
Sbjct: 260 GTDQLFLDYMSLSVQECSNDKIYTQEQALKYLAD 293



 Score = 44.3 bits (103), Expect = 0.16,   Method: Composition-based stats.
 Identities = 60/443 (13%), Positives = 126/443 (28%), Gaps = 48/443 (10%)

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
             TG   I S   LT+    +   K V    +    +            + G I  ++ D
Sbjct: 393 ASTGASTIGSAASLTNTARFNWLPKAVYLATMIRRAIL----------FDFGVIKGDSKD 442

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNA-YIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
            +  K +E             +   + +    + + L +D+N+       DI  ++ P  
Sbjct: 443 FVGNKKIETAGDLLELIFDDAFKTLLAHMVRKVDSVLRSDRNRGTDLTNYDIVSLVDPSI 502

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--L 443
           ++    +    +   +  +K  +  VG  ++  RL+  +               +K    
Sbjct: 503 ITRAFNSA--ISTGNWKIEKIGVDRVGVSQILSRLSYISALGQVTRLSSTFDKAMKSSGP 560

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
             L   +  I    +        + + L    R+       SI + + S+ ++ +     
Sbjct: 561 RMLNFSQMGIFCPSDTPEGESVGIVKNLSIMARISKDESTDSISKLLMSIGVEDLASCWS 620

Query: 504 INAKPVVSAVCEFFCSS--QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            +   +      F   +   +   +     +  +   RR   +            +   +
Sbjct: 621 GDTFSLGYGYMVFLNGTIKGVIAKDMLKGFIITLRTFRRRGYISYLTSFHFNDEHQAVYI 680

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           +        P    E   + L  S       N   F++  Y           V YL   E
Sbjct: 681 NCDSGRACRPLLIVENGKLMLTRSDIELLVDNQKCFVDLIYE--------GKVEYLDVNE 732

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            +N YIA     L                              +     ++     LIP+
Sbjct: 733 AKNAYIAMDTKDLTPQH-----------------------THCEIESYTLLGYVVGLIPY 769

Query: 682 LENDDSNRVLMGCNMQRQAVPLL 704
             ++ S R    C+M +QA   +
Sbjct: 770 PHHNQSPRNCYQCSMGKQASGAI 792


>gi|318603097|emb|CBJ04595.1| RNA polymerase beta subunit [Pseudomonas sp. R-38253]
          Length = 337

 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 202/337 (59%), Positives = 262/337 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           LG+NM +AFM W+GYNFEDS+ +SER+V ED FT+IH
Sbjct: 301 LGQNMRIAFMAWNGYNFEDSICLSERVVQEDRFTTIH 337


>gi|52694235|emb|CAG30647.1| DNA-directed RNA polymerase beta chain [Pseudomonas alcaligenes]
          Length = 339

 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 205/339 (60%), Positives = 263/339 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +GKVT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGKVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA+++L+  G   +ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DEIVFLSAIEEADHVIAQASATLNAKGELIDELVNVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R 
Sbjct: 241 GGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVSRG 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           DI+ADGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +S
Sbjct: 301 DIMADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLS 339


>gi|318603033|emb|CBJ04584.1| RNA polymerase beta subunit [Pseudomonas sp. R-37904]
 gi|318603064|emb|CBJ04589.1| RNA polymerase beta subunit [Pseudomonas sp. R-37987]
          Length = 340

 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 202/339 (59%), Positives = 263/339 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 2   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 61

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 62  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 121

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 122 IAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 181

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 182 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 241

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 242 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 301

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 302 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 340


>gi|55975956|gb|AAQ72389.2| RpoB [Klebsiella oxytoca]
          Length = 343

 Score =  338 bits (868), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 215/343 (62%), Positives = 272/343 (79%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++
Sbjct: 121 VTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVAKRGGLVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSL 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           G+ + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS+
Sbjct: 301 GEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 343


>gi|56541770|emb|CAI30267.1| hypothetical protein [Pongo abelii]
          Length = 1116

 Score =  338 bits (867), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 105/499 (21%), Positives = 177/499 (35%), Gaps = 85/499 (17%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 692  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 751

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 752  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 810

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 811  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 853

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK-GIVSRILPCEDMPFLKDGTPVDIV 1121
              +       ++K+ +   R  + GDK + RHG K G+   I+P EDMPF   G   DI+
Sbjct: 854  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKKGVCGLIVPQEDMPFCDSGICPDII 911

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP G PSRM VG++ E   G                                       
Sbjct: 912  MNPHGFPSRMTVGKLIELLAGK-------------------------------------- 933

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                           A          T  F G+  + +   L     +  G+  +  G+T
Sbjct: 934  ---------------AGVLDGRFHYGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGIT 977

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C
Sbjct: 978  GEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDC 1037

Query: 1302 IQAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLV 1351
            +  YGA+ +L E L I SD    DV G+  +            +        P +  +L 
Sbjct: 1038 LIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLF 1097

Query: 1352 KEMQALGLSIDLENSRTKN 1370
            +E+Q++ +   L+ S+   
Sbjct: 1098 QELQSMNIIPRLKLSKYNE 1116



 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 122/947 (12%), Positives = 275/947 (29%), Gaps = 201/947 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNRVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    V    V    G+  ++  D    K LE         
Sbjct: 316 TI--LTHVPVKEFNFRAKCIY-TAVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSLL 372

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
              L+    +    I + ++  +   + D +    +   P                + ++
Sbjct: 373 FGDLFKKFNSEMKKIADQVIPKQRAAQFDVVNTCAKTRSP--------------MAWVNA 418

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
                 ++ R KM+ ++N       + + +   I+ + ++  + +       +       
Sbjct: 419 ISTGNWSLKRFKMDRQVN-------QVLYRLLYISALGMMTRISSQFEKTRKVSVPEGEA 471

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
              V  +                       D   V     +  + V     E      + 
Sbjct: 472 CGLVKNLAL------------MTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 519

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 520 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 578

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 579 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 627

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 628 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 675

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 676 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 695

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 696 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 730

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 731 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 790

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 791 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 837


>gi|302348973|ref|YP_003816611.1| DNA-directed RNA polymerase subunit B [Acidilobus saccharovorans
            345-15]
 gi|302329385|gb|ADL19580.1| DNA-directed RNA polymerase subunit B [Acidilobus saccharovorans
            345-15]
          Length = 1179

 Score =  338 bits (867), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 91/318 (28%), Positives = 139/318 (43%), Gaps = 70/318 (22%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  +VKV V   R  + GDK A RHG KG+V  + P  DMP+ +DG   DI++NP G
Sbjct: 880  TTDRNLLVKVKVRDLRIPELGDKFASRHGQKGVVGMLYPKYDMPYTEDGIVPDIIINPHG 939

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM VGQI E   G A     + +                                  
Sbjct: 940  IPSRMTVGQILELITGKAAAMEARYVDG-------------------------------- 967

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 TP F   D +    +L        G  ++YDG TG+  +
Sbjct: 968  ---------------------TP-FYKDDVDQYKIILIKHGYSPDGTEVMYDGRTGQLLE 1005

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
             P+++G ++  +L HMV+DK++AR+TG   L+T+QP  GK+ +GG R GEME  C+  +G
Sbjct: 1006 TPISIGVVFYQRLYHMVADKMHARATGKVQLLTRQPTEGKARQGGLRFGEMERDCLVGHG 1065

Query: 1307 AAYVLQEMLTIKSD-----------DV---VGRTRVYESIVAGND--TFETGTPESFNVL 1350
            A  +L++ +   SD            V     R  VYE  + G +        P +F + 
Sbjct: 1066 ATMLLRDRMLDGSDAYTMYVCTLCGHVAWYNSRKNVYECPIHGENGDIKPVKVPYAFKLF 1125

Query: 1351 VKEMQALGLSIDLENSRT 1368
            ++E+ ++G+   +E S  
Sbjct: 1126 LQEIMSMGIKPRIEVSDR 1143



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 145/999 (14%), Positives = 303/999 (30%), Gaps = 208/999 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF------PITAFSGAAMLEFVSYEFD 82
           L      SY+ F+   +         ++  +K V       P        +L        
Sbjct: 27  LARQHLDSYNAFVTERMQEIVDSFGEIRPLYKQVSRRREAAPEEGPDIKIVL--GKIRIG 84

Query: 83  PPKF------------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            P+                +   R+ TY+ PL + ++L+              ++    +
Sbjct: 85  EPQVKEADGNLRRKDVTPLEARLRNFTYSAPLFLQMKLVENGT----------EVYSDEV 134

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFD 166
            +GD P+M K                         G F+I G +R+VV+Q   +      
Sbjct: 135 KVGDFPIMVKSVIDPLSKASYRELLEAGEDPNDPGGYFIINGSERVVVAQEDLAVNRIIV 194

Query: 167 HDKGRASLSGKLLYACR-----------IIPDQ---GLWMDIEFDSKDIIHVRIDRRRKV 212
                 + + K+ ++ +           +I D+   G  +++          R++ R  +
Sbjct: 195 --GVSTANTAKITHSAKTVSTILGLRRQVIVDRMSDGS-LEVSMS-------RLNYR--I 242

Query: 213 PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
           P    + ALG++ + EI +   P     +        +SAA       +      I TG+
Sbjct: 243 PFIVMMKALGLEKDAEIAAAVSPDPDVQRELLPSFEKVSAAIRTKEDALEFLGNRIATGQ 302

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
                 +       + +  + +  +G+T             +     ++Y+      D+ 
Sbjct: 303 P----REIRIQRAEEFIDTQFLPHIGLTPADRLAKAYFLGEMANRVLQLYLGKRQEDDKD 358

Query: 332 SL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            L  + +  +      I           I + L    ++ RK  + D+  ++RP D+ T 
Sbjct: 359 HLANKRLRLAGDLIAEIFRDAFQQLATLIASELEEYISQHRK--VRDLRSLVRP-DIITE 415

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            V  ++    +  +       + R      L+       R I             DL   
Sbjct: 416 RVRAALATGNWTGNRTGVSQALDRTNWMSLLSHLR----RVISPLSRGESNFEARDLHGT 471

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
                            + + L     + +   E+ +K  + S+D+  +       A   
Sbjct: 472 HWGRLCPFETPEGINCGLVKNLAMTAYISVGVNEQHVKNILMSMDLIPLDDAIKEIASGE 531

Query: 510 VSAVCEF-------FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--RARAGVEMRD 560
             A+ ++            +  +++      ++   RR  +L          + G++   
Sbjct: 532 PEAIEKYTNMAKVFLNGKPIGYVQDGAELRRKLIAMRRSGSLSYEVSVAYIEQGGIKEVY 591

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           ++      + P    E     L         V      E  +  +    V   + +L   
Sbjct: 592 INTDEGRLMRPVIVVENGKPKLTKE-----MVEKVKRGEMSFWDLVRNGV---IEFLDPD 643

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEEN Y+A++   +  +                          ++     + S+  S+ P
Sbjct: 644 EEENAYVAESPEEVTPEH-----------------------THLEMWTPGIFSVVTSITP 680

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++ S R      M +QA+ L           +       S A               
Sbjct: 681 FLEHNQSPRNTYQAAMAKQALGLY---------ALNYQYRMDSHA--------------- 716

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                                Q+P+V+                 
Sbjct: 717 -------------------------------YLLHYPQKPIVQ----------TRSLEEI 735

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              D   G+N +VA MP+ GYN ED++++++  V   +  +     + VM      G ++
Sbjct: 736 GYNDRPSGQNFIVAIMPYMGYNMEDAIIMNKTSVDYGLGRAHFFRVYTVMENTYAGGLKD 795

Query: 861 I-----TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                  +   +  ++    +   GII    EV+ GD+LVG+ +P         E+ + +
Sbjct: 796 TITVPSPKLYDHKGDQYYTKLGPDGIIEPEVEVDGGDVLVGRESPPRFL----GEERVMS 851

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           +      D          GV  TV+  +  +R+ + K +
Sbjct: 852 LGTLTKRDTSVQLRYGEHGVVDTVLITQTTDRNLLVKVK 890


>gi|56405813|gb|AAV87310.1| RNA polymerase beta subunit [Klebsiella variicola]
          Length = 339

 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 214/339 (63%), Positives = 267/339 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           + + R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFE
Sbjct: 301 EPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 339


>gi|126465702|ref|YP_001040811.1| DNA-directed RNA polymerase subunit B [Staphylothermus marinus F1]
 gi|126014525|gb|ABN69903.1| DNA-directed RNA polymerase, subunit B' / DNA-directed RNA
            polymerase, subunit B' [Staphylothermus marinus F1]
          Length = 1156

 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 89/333 (26%), Positives = 142/333 (42%), Gaps = 72/333 (21%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            R   K               R+VKV V   R  + GDK A RHG KG++  ++P +DMPF
Sbjct: 874  RHGEKGIVDVVMVTTDIDGNRLVKVRVRDLRIPELGDKFASRHGQKGVIGLLVPQQDMPF 933

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             ++G   D+++NP   PSRM VGQ+ E+  G A    G+ + +     +   ++      
Sbjct: 934  TEEGIVPDLIINPHAFPSRMTVGQLIESIAGKAAALEGRFVDATPFHKEPIDNLMITLK- 992

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                         + G P+                        S
Sbjct: 993  -----------------------------RHGYPM------------------------S 999

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G   +YDG TGE    P+ +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG
Sbjct: 1000 GYETMYDGRTGEILKTPIFIGIVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAKEGG 1059

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESI----------VA 1334
             R GEMEV C+  +GA+ +L+E +  KSD       ++ G    Y+ I            
Sbjct: 1060 LRFGEMEVDCLVGHGASLLLKEQMLDKSDKTTIYVCELCGHIGYYDRIRGKYMCPIHKDK 1119

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            G          +F +LV+E+ ++ +   L+   
Sbjct: 1120 GKLKP-VEVSYAFKLLVQELMSMCIMPRLKLED 1151



 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 157/1008 (15%), Positives = 302/1008 (29%), Gaps = 223/1008 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-PPKF- 86
           L+     SY+ F+          +  L         IT  SG   L    Y     PK  
Sbjct: 26  LVRQHLDSYNRFI----------DHLLPEIISEHKEIT-ISGNRKLLIKGYRIGSEPKIR 74

Query: 87  ---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  R+ TYAVP+ + + L                 KEQ I + DLP+
Sbjct: 75  TIEGFERTVTPLECRLRNFTYAVPIYLKVALQD----------ETGIYKEQEIKLMDLPV 124

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKG 170
           M K                         G F+I G ++++V+Q   +     + +  +  
Sbjct: 125 MLKSKIDPLSKMTAEELVAIGEDPKDPGGYFIINGSEKVLVAQEDLASNNILVDYASEGS 184

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EI- 228
            A+   K++   +    +   + IE     I +  +   R +PV   + ALG+ SE EI 
Sbjct: 185 SATHIAKVISVAK---GRRSQLVIERRKDGIFYANLHGHR-IPVVILMTALGLASELEIT 240

Query: 229 --------LSTF-----------YPKIVYSQRGDFWCFP-LSAADLMVGAKVSSSLVDID 268
                   L T+           +P++   +         +         + +   +   
Sbjct: 241 YAVSLDPDLQTYLLPSIMQAQSVFPRLEIPENASPEEQKRIEEEHRRKTIETALDYIGAR 300

Query: 269 TG------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
                   E++  + + L   LL  +  +    +        G  V + I      E+ +
Sbjct: 301 IAIGRPREERIRRAQRALDEYLLPHIGTEPTPEVRRKKAYFIGQMVNKLI------ELIV 354

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +     D+            D+    V       +IR    + +    K   LD+  V++
Sbjct: 355 DRRKPDDKDHYRNKRLKLAGDLLAQLVRHNLVTYFIREVKSSIERSYSKYGRLDLKLVIK 414

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL-----------DTPDDVRHI 431
           PG + T  +  +M    +          + R  +   L+                + R +
Sbjct: 415 PGML-TDRILHAMATGNWPGGKTGVSQLLDRTNLMSTLSHLRRVVSPLKRTQPHFEAREL 473

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--LGLLRMERSIKER 489
                  +           G + ++  + +  V    E ++      LG+  ++  I+E 
Sbjct: 474 HPTQWGRMCPFETPEGANIGLVKNLALMAHVSVGVPEEHIEPILYRKLGVKNLDEIIEEI 533

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
             ++  +     D  +   V      +     +    +       I + RR        +
Sbjct: 534 KKAITGEVEEYPDYTSWSRV------YLNGRLIGYHPDGKKLAQEIRNLRRRG-----KI 582

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
           +       +RD H         A       + + +      +      +++   K  D  
Sbjct: 583 SVEVNVAHIRDEHLNEVYINTDAGRIRRPLLVVENGKLKL-KPEHIAKLKSGEWKFSDLV 641

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               + YL A EEE  YIA     +  +                          ++    
Sbjct: 642 KRGIIEYLDADEEEEAYIALTPDQITPEH-----------------------THMEIWTP 678

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IP+ E++ S R      M +Q++ L  A                       
Sbjct: 679 AIMGITASIIPYAEHNQSPRNSYEAAMAKQSLGLYSANFQ-------------------- 718

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    +   +  Y               Q+PLV+      
Sbjct: 719 ---------------------QRMDTRGHLLHYP--------------QKPLVQTRAMEV 743

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +   G+NM+VA M + GYN ED++++++  V   +  S     +  
Sbjct: 744 NG----------YNERPAGQNMVVAVMSFTGYNIEDALIMNKSSVDRGLARSTFFRLYTT 793

Query: 850 MARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           +      G E+     P         +  + +DE GI+     V  GD+L+GKI+P    
Sbjct: 794 VEYRYPGGQEDRIMIPPSNVRGYRGPKAYEKLDEDGIVSPETPVKGGDVLIGKISP---- 849

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              P     +       +  +D S+    G  G V  V +      ++
Sbjct: 850 ---PRFMTAQEYTVGAGITRQDASVVTRHGEKGIVDVVMVTTDIDGNR 894


>gi|318603028|emb|CBJ04583.1| RNA polymerase beta subunit [Pseudomonas sp. R-37902]
          Length = 339

 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 201/339 (59%), Positives = 263/339 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           +PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   QPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+
Sbjct: 301 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQ 339


>gi|284154662|gb|ADB78432.1| RNA polymerase beta-subunit [Bacillus mojavensis]
          Length = 182

 Score =  338 bits (866), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 82/204 (40%), Positives = 128/204 (62%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q + MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVVMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|159471568|ref|XP_001693928.1| DNA-directed RNA polymerase III, subunit 2 [Chlamydomonas
            reinhardtii]
 gi|158277095|gb|EDP02864.1| DNA-directed RNA polymerase III, subunit 2 [Chlamydomonas
            reinhardtii]
          Length = 1161

 Score =  338 bits (866), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 91/310 (29%), Positives = 133/310 (42%), Gaps = 65/310 (20%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            +KV +   R  + GDK + RHG KG+V  I+  ED PF + G   D+++NP G PSRM V
Sbjct: 900  IKVLIRHTRRPELGDKFSSRHGQKGVVGNIVRQEDFPFSERGVCPDLIMNPHGFPSRMTV 959

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G++ E     A V  G+                                           
Sbjct: 960  GKMIELLGSKAAVSCGRFH----------------------------------------- 978

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                     G     P       E I++ L       SG+  L  G+TGEP +  + +G 
Sbjct: 979  --------YGTAFGEPSNLADKVEDISATLVRHGFSYSGKDFLTSGITGEPLEAYIFMGP 1030

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +Y  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E
Sbjct: 1031 VYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLLLE 1090

Query: 1314 MLTIKSD--DVVGRTRV------------YESIVA--GNDTFETGTPESFNVLVKEMQAL 1357
             L I SD  +V  R  V              S V    ++      P +  +L +E+Q++
Sbjct: 1091 RLMISSDQFEVRARVCVGLLGWWDAHRNCPVSPVDRTSDNMATIKIPYACKLLFQELQSM 1150

Query: 1358 GLSIDLENSR 1367
             +   L  + 
Sbjct: 1151 NIIPRLRLAD 1160



 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 121/976 (12%), Positives = 262/976 (26%), Gaps = 189/976 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L++    S+++ L             L+    +   +T        L++ +     P   
Sbjct: 44  LVKQHLDSFNYLLNSE----------LRKIVAANEKVTCDTDPNFYLKYTNIYVGGPSVD 93

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIV-FDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       C  RD TY+ P+ + +      ++    G   +       + +G +PL
Sbjct: 94  EDMVQVGTTPQQCRLRDATYSAPITVDIEYTRGKEIVVKRGRGGVGA-----VSIGRMPL 148

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD---- 168
           M                           G F+++G +++++ Q   S   I  D D    
Sbjct: 149 MLRCDRCVLYNKNEAQLAQLGECPLDPGGYFIVRGTEKVILIQEQLSKNRIIIDTDSHNE 208

Query: 169 -KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE 226
                + S     +   I            SK  I+++ +  +  V +   L A+G +S+
Sbjct: 209 VMASVTSSTHERKSKTNIVF----------SKGKIYLKHNAFQDDVNIFVVLKAMGCESD 258

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +           +              +    +    L            G +       
Sbjct: 259 QEAVQAVGAAALAALLVPSVQEAKGLGVFTQMQALDYLGGKLKASPKFGGGDQKRRKSKV 318

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                 +  + +    +     A+ I       +      V+D   +++  +   + + +
Sbjct: 319 DEARDVLAHVVLCHVPVPRYQFAQKIAYVAVM-VRRMLYAVLDPACIDDRDYYGNKRLEL 377

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +         +   D       V+   + +T                  
Sbjct: 378 -------AGGLLSLLFEDLFKRLNSDIKRQADAVLSKANRATQFDVAKAIRTDTITYGLE 430

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-----NLGN 461
              + G   +  R  ++     + + +   IA + ++  + +       +      +   
Sbjct: 431 SALSSGNWII-RRFRMERKGVTQVLSRLSFIAAMGMMTRMTSQFEKTRKVSGPRALHPSQ 489

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA-VCEFFCSS 520
             +    +  + +    +  +           +   +    ++  +P+ +    E     
Sbjct: 490 WGMLCPADTPEGESCGLVKNLALMTHVTTDEEEGPLIRLLVMLGTEPITAIAPAEMHGHG 549

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
                    N      H R    + +   + RA    E   VH    G  C      G  
Sbjct: 550 GALVFL---NGTLVGVHRRPHRLVREARELRRAGHLGEFVHVHLQ--GDACYISCDGGRV 604

Query: 580 IGLVSS------LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
              +              +      E       D      + YL   EE    IA     
Sbjct: 605 CRPLIICDAGVPRVRQEHITKLRSGERCEWGFPDFLARGLLEYLDVNEENVSLIA----- 659

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           L E                      +    ++  P  ++ + + LIPF  ++ S R    
Sbjct: 660 LYEKDCN------------------KLTTHLEIEPFTIMGVVSGLIPFPHHNQSPRNTYQ 701

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+                                           I   +    
Sbjct: 702 CAMGKQAMGN-----------------------------------------IAYNQMSRM 720

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S   + +Y               QRPL+                      L  G+N  V
Sbjct: 721 DSLLYLLVYP--------------QRPLL----------TSRTIELVGFDKLGAGQNASV 756

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT-KLGPEEITRDIPNVSEEG 872
           A M + GY+ ED++++++  +       I ++++    R       + I   +P   ++ 
Sbjct: 757 AVMSYSGYDIEDAIVMNKYSLDRGFGRCIVLKKYGASLRKYANRASDRIVAPLPLPGQKA 816

Query: 873 ----LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                + +D  GI CVG  + PGD+ +    P       P   +  A +    +  +  S
Sbjct: 817 VAPRFRLLDRDGIACVGDYILPGDVYINMQRPSNTRDPLPAANMPDAFYRPSPMSWK--S 874

Query: 929 LRVPSGVSGTVVDVRI 944
               +G    V  V+I
Sbjct: 875 TPAMAGERCIVDKVQI 890


>gi|318602984|emb|CBJ04572.1| RNA polymerase beta subunit [Pseudomonas sp. R-37154]
          Length = 344

 Score =  337 bits (865), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 204/343 (59%), Positives = 266/343 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   ESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 122 IVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 182 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 241

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI
Sbjct: 242 VIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDI 301

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           +ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V E
Sbjct: 302 MADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQE 344


>gi|111054611|gb|ABH04363.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 343

 Score =  337 bits (865), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 213/343 (62%), Positives = 269/343 (78%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V DG VT+++ YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE++
Sbjct: 121 YRLVRDGLVTDEIHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           +++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA 
Sbjct: 181 EYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAV 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG   VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P 
Sbjct: 241 DSGVTAVARRGGSVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPC 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           V +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFE
Sbjct: 301 VSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 343


>gi|52694317|emb|CAG37998.1| RNA polymerase beta subunit [Pseudomonas fuscovaginae]
          Length = 348

 Score =  337 bits (865), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 209/348 (60%), Positives = 272/348 (78%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +G VT+D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +
Sbjct: 121 VKEGVVTDDIVFLSAIEEADHVIAQASATMNEQKVLVDELVAVRHLNEFTVKAPEDVTLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 181 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  
Sbjct: 241 VCVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER
Sbjct: 301 GDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSER 348


>gi|52694379|emb|CAG38029.1| RNA polymerase beta subunit [Pseudomonas alcaligenes]
          Length = 337

 Score =  337 bits (864), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 203/336 (60%), Positives = 261/336 (77%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D +VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTQVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA+++++  G   +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNAKGQLVDELVDVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+A
Sbjct: 241 DSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVSRGDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           DGPSTD+G+LALG+NM VAFMPW+G+NFEDS+ +SE
Sbjct: 301 DGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSE 336


>gi|308158713|gb|EFO61279.1| DNA-directed RNA polymerase RPB2 [Giardia lamblia P15]
          Length = 1293

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 191/1361 (14%), Positives = 425/1361 (31%), Gaps = 234/1361 (17%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAA-----MLEFVSYEFD 82
            L  +Q  SY+HF+   +          +    S  PI    +        +L F   + +
Sbjct: 26   LAAMQIDSYNHFVKHTM----------KNIMASFPPIQVTRTENFCCYNHILSFSDPQLE 75

Query: 83   PPK-FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS--IYMGDLPLMT 139
            P      +DC  +  +Y   +K+ +   +           ++++  +   I     P+M 
Sbjct: 76   PNVHIKPNDCRIQSSSYMAAIKVKISYTIQQYSFSNNEGLVQEVTYEPKLIDFCLFPVMV 135

Query: 140  ------------------------------KDGTFVIKGIQRIVVSQ-------LHRSPG 162
                                          + G F+I+G ++ V++Q       L   PG
Sbjct: 136  NSCLCYLNTNKVAGSDIKAHRIINDECPYDEGGYFIIRGAEKAVIAQEGNRPNRLLILPG 195

Query: 163  IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
                          K+ Y  +++           +    +H ++                
Sbjct: 196  ----------DPGSKIPYTAQLVS---------TNPAKNLHSKV---------------- 220

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
                 +L  +          D     ++     +   +   L+ +   +  + + + L S
Sbjct: 221  -----VLKYWSTNKWGRTIQDINQPQITFTMQGIRDDLPLFLLILALWQDNVYAARDLLS 275

Query: 283  GLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             ++    +  +    + S  L         +  +    G + +           + +  S
Sbjct: 276  IVVPDESDTELIEHLLPSYNLFCSTPQSSKDKCIEFLAGRLIVGEQMDSARAKYDRLM-S 334

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             +    + ++         +   +          LL      R  D       + +    
Sbjct: 335  HLSTRLLPHIGVTPEFHLDKAFFIGYMTNL----LLQTVVGRRSPDDRDHWGGKRLQLTG 390

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
               +DK+            RL     D    ++ ++ I+++   ++  +    +    + 
Sbjct: 391  SLLADKFRFEY---ELFLRRLARKLHDTGSILKVKEDISMVSPNIEGSSFIPQLKYDPHG 447

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +     +L         R++ +    IS     ++        + V +        
Sbjct: 448  KVPGLEDPRRLLD--------RIKVAATSYISKNITSALSTGTWKTNEVVGNT------K 493

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S +SQ    ++  S ++  RR S+     V      +  R +H T +G +CPAET EG  
Sbjct: 494  SGVSQSLVRLSYTSALSQIRRSSS----SVEETSKAIGPRLLHTTQFGYMCPAETPEGAK 549

Query: 580  IGLVSSLTSFARVNAYGF--------IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            +GL+ + +  A V             + T YR       T+ +     +    + +  ++
Sbjct: 550  VGLIKNFSLMANVTLDNPKDEYDLRKLLTEYRVQAPHGPTSVLKPFHTVTNAKKLV--SD 607

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              +  +GS+   +           + R + +        +  +A      + +D+     
Sbjct: 608  VKIFLNGSWLGFIDREYVQRLITDLKRWRFEGKINREVSISYLAHKQEISINSDEGRVTR 667

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                +     P LK          E  V   +    + +   ++  +   + +I  ++  
Sbjct: 668  PVFVVITDIHPTLKLVTNLSLAITEEDVETLATIPQMEQWNSLLSGLGTGKCMIEFLD-- 725

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD-----EVRRNDIIADGPSTDLG-DL 805
             +     +    +  F+   +     +  ++  G+      ++ ++I      T L    
Sbjct: 726  PNEEEMALICMDIYHFKEEIRKAHTIRDIILTYGEDNAINYIKTHNIPLASNYTHLEIHP 785

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLGPEEITR 863
            ++  + + + +P+  +N     L    M  +   ++   +++ F+    +    P+    
Sbjct: 786  SMVLSAITSLIPFPDHNQSPRNLYQASMGKQAVGIYALNYLKRFDTSGINVMHYPQLPLV 845

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPG----DILVGKITPKGESPMTPEEKLLRAIFGE 919
               ++     + +     + +   V  G    D L+   +      M             
Sbjct: 846  TTRSMPHVKFRYLPAGQNVIIAIAVYSGFNQEDSLIMSQSAVDRGFMRATYYHTYEEMIS 905

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
             A    +   R+         +++     G                            L+
Sbjct: 906  SAASSINAPDRIEKFCRPIGPNIKGVKDPGCA------------------------SYLE 941

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +   R+   +  Q  + G     K ++ S              +  QD  ++  +E   
Sbjct: 942  ADGLPRVGNAVNSQRLIIGKIRPNKRSMNSRA---------VSTYDFQDVSLKVKMEE-T 991

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             + ++     + R ++ + +    +        + KV V   R  Q GDK + RHG KG 
Sbjct: 992  GRVDSVIIAPDLREQSFLSEGVDSNTTGAEGSLLAKVRVRSSRVPQLGDKFSSRHGQKGT 1051

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  +L  ED+PF  DG   DI++NP  +PSRM +GQ+ E+         G ++     + 
Sbjct: 1052 VGMLLRHEDLPFTLDGITPDIIMNPHAIPSRMTIGQLMESVASKLGALSGHEVDGTAFNA 1111

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                                    ++ I
Sbjct: 1112 PPGS---------------------------------------------------TDKQI 1120

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
             + L      +     + +G+TGE     + +G  +  +L HMV DK+ +R+TG    +T
Sbjct: 1121 AADLHARGYQKHNYEAMMNGMTGEMMTYRIFIGPTFYQRLKHMVLDKISSRNTGPIVTLT 1180

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +QP  G+SN GG R+GEME     A+GA  +L++ L   SD
Sbjct: 1181 RQPNEGRSNYGGMRIGEMEKDAFIAHGATAILRDRLLFSSD 1221


>gi|270265481|emb|CBI68358.1| DNA-directed RNA polymerase beta chain [Pseudomonas fulva]
          Length = 344

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 197/332 (59%), Positives = 257/332 (77%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
            FF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 13  RFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 72

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL ++AR N YGF+E+PYR V +G V++D+V+LSA+EE +  IAQA++++
Sbjct: 73  PEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVSDDIVFLSAIEEADHVIAQASAAM 132

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           ++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG 
Sbjct: 133 NDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGS 192

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++ 
Sbjct: 193 NMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVET 252

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R DI+ADGPSTD+G+LALG+NM +A
Sbjct: 253 GEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDMVQRGDIMADGPSTDMGELALGQNMRIA 312

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
           FM W+G+NFEDS+ +SER+V ED FT+IHI+E
Sbjct: 313 FMAWNGFNFEDSICLSERVVQEDRFTTIHIQE 344


>gi|226897626|gb|ACO90262.1| RNA polymerase beta subunit gene [Bacillus badius]
          Length = 388

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 228/372 (61%), Positives = 288/372 (77%), Gaps = 3/372 (0%)

Query: 583 VSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           ++SL+++A+VN +GFIETPYRKV    G+VT+ + YL+A EE+N  +AQAN  L+EDGSF
Sbjct: 1   INSLSTYAKVNRFGFIETPYRKVDPDTGRVTDRIDYLTADEEDNYVVAQANVRLNEDGSF 60

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E V  R   E  +V RE++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQA
Sbjct: 61  ADEEVVARFRSENTVVKRERVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQA 120

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGV 759
           VPL++ EAP VGTGME V  K SGAA++ KRAGIVE V+A  I +R VE          +
Sbjct: 121 VPLMQPEAPIVGTGMEYVSGKDSGAAVICKRAGIVEHVEAREIWVRRVEEVDGKEIKGDL 180

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D YRL+KF RSNQ TC NQRP+V VGD V + +I+ADGPS + G+LALGRN++V FM W 
Sbjct: 181 DKYRLLKFIRSNQGTCYNQRPIVSVGDRVTKGEILADGPSMEKGELALGRNVMVGFMTWD 240

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE 
Sbjct: 241 GYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDER 300

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V
Sbjct: 301 GIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV 360

Query: 940 VDVRIFNRHGID 951
           +DV++FNR   D
Sbjct: 361 LDVKVFNREDGD 372


>gi|90079569|dbj|BAE89464.1| unnamed protein product [Macaca fascicularis]
          Length = 501

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 105/569 (18%), Positives = 177/569 (31%), Gaps = 107/569 (18%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       SM+  +   ++            ++       +G                 
Sbjct: 19   TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITN-----------F 67

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            ++    +  V        +    +       +      + AI      +  D+ +   S 
Sbjct: 68   HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA 127

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V        +F R   ++  +    + E  E   R+          +       I  G  
Sbjct: 128  VDRGFF-RSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVR 186

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L                     + +  +ES   +Y         R  
Sbjct: 187  VSGDDVIIGKTVTL--------------------PENEDELESTNRRYTKRDCSTFLRTS 226

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  Q    +     +  K+ V   R  Q GDK A RHG KG        EDMPF  +
Sbjct: 227  ETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCE 286

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  +PSRM +G + E   G      G+                        
Sbjct: 287  GITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--------------------- 325

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP  D  + + I+++L        G  
Sbjct: 326  --------------------------------ATPFNDAVNVQKISNLLSDYGYHLRGNE 353

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LY+G TG      + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R 
Sbjct: 354  VLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRF 413

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAG----N 1336
            GEME  C  A+GAA  L+E L   SD     V            RT  YE    G     
Sbjct: 414  GEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKT 471

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                   P +  +L +E+ ++ ++  + +
Sbjct: 472  QISLVRMPYACKLLFQELMSMSIAPRMMS 500



 Score = 90.5 bits (223), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 79/242 (32%), Gaps = 23/242 (9%)

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM-KFQRSNQNTC 775
               +   + I+   A I+   D  +    + +  +     GV I     +         
Sbjct: 20  YTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLY 79

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+PLV                     +L  G N +VA   + GYN EDS++++   V 
Sbjct: 80  YPQKPLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVD 129

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNP 890
              F S+    ++          EE+           +       +D+ G+I  G  V+ 
Sbjct: 130 RGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSG 189

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            D+++GK     E+    E          +    RD S  + +  +G V  V +      
Sbjct: 190 DDVIIGKTVTLPENEDELEST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEG 242

Query: 951 DK 952
            K
Sbjct: 243 YK 244


>gi|52694155|emb|CAG30607.1| DNA-directed RNA polymerase beta chain [Pseudomonas mandelii]
          Length = 344

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 204/344 (59%), Positives = 268/344 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 61  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 121 PYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPED 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 241 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           LV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFE
Sbjct: 301 LVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFE 344


>gi|111054619|gb|ABH04367.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 342

 Score =  337 bits (864), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 213/342 (62%), Positives = 268/342 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V DG VT+++ YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++
Sbjct: 121 RLVRDGLVTDEIHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVE 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  
Sbjct: 181 YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG   VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V
Sbjct: 241 SGVTAVARRGGSVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFE
Sbjct: 301 SLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 342


>gi|6606101|gb|AAF19063.1|AF107791_1 DNA-dependent RNA polymerase II RPB140 [Chaetomium elatum]
          Length = 934

 Score =  337 bits (864), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 170/1042 (16%), Positives = 311/1042 (29%), Gaps = 165/1042 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  KG    G  ++ +  + +     +   G ++   G V DE  L
Sbjct: 37   LEKGSRLISSLQMKLHSKGSPEKGRLANTVS-VTLPYVREDVSLGIVFRALGIVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A+          +DR+ AL  I +              
Sbjct: 96   NHICYDRTDTQMLEALRPCIEEAF--------CIQDREIALDFIGKR---------GNGN 138

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +  N +       DL     ++  M  ++   +     +   +  ++  L+    G+   
Sbjct: 139  AGQNRMNRVRAAKDL-----LQKEMLPHISQTEGCETRKAFFLGYMVHRLLQCALGRRDP 193

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R  + RM + +    +       +      I    + +
Sbjct: 194  DDRDHFGKKRLDLAGPLLAKLFRNVIRRMTQDLMSYMKRCIDTNKNFSLALGIKHSTLTN 253

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 254  GLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKP 309

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPA+T EG   GLV +L+    V+     +    +      +V  +   
Sbjct: 310  RQLHNTHWGLVCPADTPEGQACGLVKNLSLMCYVSVGTPADPIVEFMIARGMEVLEEYEP 369

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L        ++      + +D      LV        I      + D  D   K      
Sbjct: 370  LRYPNATKVFVNGTWVGVHQDPKHLVTLVQGLRRKNVISFEVSLVRDIRDREFKIFSDAG 429

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
              + P    +       G       +         + T                 ++G +
Sbjct: 430  RVMRPLFTVEQEPNGESGAEKGALILNKEHIGKLKLDTEY-GKYHPDYWGWQGLLKSGAI 488

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E +DA       +              +  +F++ N     N R   K            
Sbjct: 489  EYLDAEEEETVMICMTPQDLDQFRA-RKQGRFEQDNSGL-GNNRIKTKPNPITHMYTHCE 546

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N          M  + +     +  +        
Sbjct: 547  IHPSMLLG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---- 593

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 594  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 630

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D  +R      EQ E    ++ D  
Sbjct: 631  IACYSGYNQEDSVIMNQSSIDRGIF-RSLFFRSYTDCEKRVGINIVEQFEKP--NRSDTL 687

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
              L  + Y +L     +  G           K+  ++ D      RS             
Sbjct: 688  R-LKHSTYDKLDADGIVAPGIRVSGEDIIIGKTCPINPDNAELGQRSN------------ 734

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               + +K    T     E    +++      D      +R VKV V   +  Q GDK A 
Sbjct: 735  ---QHVKRDASTPLRSTESGIIDQVVVTTNQD-----GMRYVKVRVRTTKVPQIGDKFAS 786

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G + 
Sbjct: 787  RHGQKGTIGVTYRQEDMPFTAEGITPDIIINPHAIPSRMTIAHLIECLLSKVSTLKGMEG 846

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +                              ++      +LR       G  +      
Sbjct: 847  DATPFT-------------------------DVTVDSVSDLLREHGYQSRGFEIM----- 876

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                               G +    G         V  G  Y  +L HMV DK++AR+ 
Sbjct: 877  -----------------YHGHT----GR---KLRSQVFFGPTYYQRLRHMVDDKIHARAR 912

Query: 1273 GSYSLVTQQPLGGKSNRGGQRL 1294
            G   ++T+QP+ G++  GG R 
Sbjct: 913  GPLQIMTRQPVEGRARDGGLRF 934



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 83/609 (13%), Positives = 178/609 (29%), Gaps = 67/609 (11%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK------- 199
            ++++++Q  RS          +    G + Y   I    ++G  +      K       
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKPPGGSVSYQAEIRSALEKGSRLISSLQMKLHSKGSP 57

Query: 200 ------DII-----HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
                 + +     +VR D    V +     ALG+   E+IL+        +Q  +    
Sbjct: 58  EKGRLANTVSVTLPYVRED----VSLGIVFRALGIVSDEDILNHICYDRTDTQMLEALRP 113

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV-------KFLGITS 300
            +  A  +   +++   +    G       +       K L +K +       +      
Sbjct: 114 CIEEAFCIQDREIALDFIGKR-GNGNAGQNRMNRVRAAKDLLQKEMLPHISQTEGCETRK 172

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
               G  V   ++    G    +  D   +K L+       +    +      +      
Sbjct: 173 AFFLGYMV-HRLLQCALGRRDPDDRDHFGKKRLDLAGPLLAKLFRNVIRRMTQDLMSYMK 231

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             + D NK+   AL   +  +  G      +  S+    + D  K   ST G  ++  R 
Sbjct: 232 RCI-DTNKNFSLALGIKHSTLTNG------LKYSLATGNWGDQKKAASSTAGVSQVLNRY 284

Query: 421 NLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
              +      R          +     L N    +    +    +   + + L     + 
Sbjct: 285 TFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPADTPEGQACGLVKNLSLMCYVS 344

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           +      I E + +  ++ +   + +               + +   ++  + ++ +   
Sbjct: 345 VGTPADPIVEFMIARGMEVLEEYEPLRYPNATKVF---VNGTWVGVHQDPKHLVTLVQGL 401

Query: 539 RRLSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           RR + +  +  + R     E        R + P       P   S      L+ +     
Sbjct: 402 RRKNVISFEVSLVRDIRDREFKIFSDAGRVMRPLFTVEQEPNGESGAEKGALILNKEHIG 461

Query: 591 RV---NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL-----DEDGSFTE 642
           ++     YG     Y        +  + YL A EEE   I      L      + G F +
Sbjct: 462 KLKLDTEYGKYHPDYWGWQGLLKSGAIEYLDAEEEETVMICMTPQDLDQFRARKQGRFEQ 521

Query: 643 ELVFCRCAGEEILVPR--EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           +         +             +  P  ++ I AS+IPF +++ S R      M +QA
Sbjct: 522 DNSGLGNNRIKTKPNPITHMYTHCEIHPSMLLGICASIIPFPDHNQSPRNTYQSAMGKQA 581

Query: 701 VPLLKAEAP 709
           +        
Sbjct: 582 MGFFLTNYS 590


>gi|116563658|gb|ABJ99845.1| RpoB [Bacillus subtilis subsp. spizizenii]
          Length = 182

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 81/204 (39%), Positives = 128/204 (62%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L AL   S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALXFGSD 182


>gi|226897624|gb|ACO90261.1| RNA polymerase beta subunit gene [Bacillus badius]
          Length = 393

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 228/372 (61%), Positives = 288/372 (77%), Gaps = 3/372 (0%)

Query: 583 VSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           ++SL+++A+VN +GFIETPYRKV    G+VT+ + YL+A EE+N  +AQAN  L+EDGSF
Sbjct: 1   INSLSTYAKVNRFGFIETPYRKVDPDTGRVTDRIDYLTADEEDNYVVAQANVRLNEDGSF 60

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E V  R   E  +V RE++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQA
Sbjct: 61  ADEEVVARFRSENTVVKRERVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQA 120

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS-TSGV 759
           VPL++ EAP VGTGME V  K SGAA++ KRAGIVE V+A  I +R VE          +
Sbjct: 121 VPLMQPEAPIVGTGMEYVSGKDSGAAVICKRAGIVEHVEAREIWVRRVEEVDGKEIKGDL 180

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D YRL+KF RSNQ TC NQRP+V VGD V + +I+ADGPS + G+LALGRN++V FM W 
Sbjct: 181 DKYRLLKFIRSNQGTCYNQRPIVSVGDRVTKGEILADGPSMEKGELALGRNVMVGFMTWD 240

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE 
Sbjct: 241 GYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDER 300

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V
Sbjct: 301 GIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIV 360

Query: 940 VDVRIFNRHGID 951
           +DV++FNR   D
Sbjct: 361 LDVKVFNREDGD 372



 Score = 45.8 bits (107), Expect = 0.051,   Method: Composition-based stats.
 Identities = 42/275 (15%), Positives = 87/275 (31%), Gaps = 25/275 (9%)

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNVSEEGL 873
            M +       + +I +R    +   +  I    V   D K   G  +  R +  +     
Sbjct: 135  MEYVSGKDSGAAVICKRAGIVEHVEAREIWVRRVEEVDGKEIKGDLDKYRLLKFIRSNQG 194

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG  V  G+IL    +   +  +     ++         +  D  +    
Sbjct: 195  TCYNQRPIVSVGDRVTKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMSER 253

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      +  +
Sbjct: 254  LVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVKDGD 313

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L G+    G         L   +  E  R      +++       +             
Sbjct: 314  LLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI------------- 359

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                   K+   + GD++PPGV ++V+V++  KR 
Sbjct: 360  ---VLDVKVFNREDGDELPPGVNQLVRVYIVQKRK 391


>gi|78714185|gb|ABB51075.1| RNA polymerase beta subunit [Acholeplasma brassicae]
          Length = 631

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 229/455 (50%), Positives = 301/455 (66%), Gaps = 33/455 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGRICP ET EG +IGL+SSL S+
Sbjct: 2   NPLAELTQKRRVSALGTGGLARDRAGVEVRDVHESHYGRICPIETPEGPSIGLISSLASY 61

Query: 590 ARVNAYGFIETPYRKVC-----DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TPY  V      +  V+N+ +YL+A EEE   IA ANS LDE G F  + 
Sbjct: 62  AKVDRYGFIQTPYLTVDFTDPNNPTVSNEYIYLTAGEEEKFVIASANSPLDEQGHFINDT 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  G         + ++D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 VIGRLNGATNEFKITDVHYMDVSPKQIVSVATSTIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
             ++P VGTG+E   AK SG+A+V+   G+V   D  +I+I         +  G  +Y  
Sbjct: 182 VPDSPIVGTGVEYRAAKDSGSALVSSVDGVVTYADGKKIIIAVKPEASIKTPRGKVVYDH 241

Query: 765 MK----------------------------FQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +                            F RSNQ+T + Q+P+V++G+ +++ D+IAD
Sbjct: 242 NEEFNWEAYDLLRQAKMTDLLVFKNYELTQFLRSNQDTAILQKPIVEIGENIKKGDVIAD 301

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           GPS   G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E +V +RDTKL
Sbjct: 302 GPSISNGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKYDVYTSIHIDEHQVESRDTKL 361

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           G EEITR+IPN S + LK +D+ GII  G EV  GDILVGKITPKG S  TPEEKLL+AI
Sbjct: 362 GKEEITREIPNASLDALKYLDDRGIIIPGTEVKEGDILVGKITPKGLSEPTPEEKLLQAI 421

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           F EKA +VRDTSL+VP G  G V  ++ F++   D
Sbjct: 422 FNEKAREVRDTSLKVPHGGGGIVHSIQYFSKSNGD 456



 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 117/419 (27%), Positives = 183/419 (43%), Gaps = 79/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGE-----SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            I+ +G  +  GD++    +           +T           E AV + +  ++     
Sbjct: 286  IVEIGENIKKGDVIADGPSISNGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKYDVYT 345

Query: 936  SGTVVDVRIFNRH-GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            S  + + ++ +R   + K E +  +    ++ L     D++ I+      +  +IL G+ 
Sbjct: 346  SIHIDEHQVESRDTKLGKEEITREIPNASLDALK--YLDDRGIIIPGTEVKEGDILVGKI 403

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L   + +E  R           +V+     +          ++    
Sbjct: 404  TPKGLSEPTPEEKLLQAIFNEKAR-----------EVRDTSLKVPHGGGGIVHSIQY--- 449

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                    GD++ PGV  V++V++  KR I  GDKMAGRHGNKG++S+ILP EDMP++ D
Sbjct: 450  ---FSKSNGDELAPGVNEVIRVYIVKKRKINEGDKMAGRHGNKGVISKILPREDMPYMAD 506

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG K+ + + D     D++ +      
Sbjct: 507  GTPVDIMLNPLGVPSRMNIGQVLEIHLGMAAKKLGLKVATPVFDGLEQNDLNDILKEAGM 566

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                     G  
Sbjct: 567  APDGKQVL-----------------------------------------------YDG-- 577

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                  TGEP++  ++VG +YM+KL+HMV DK++ARS G Y+LVTQQP+GGK+  GGQR
Sbjct: 578  -----RTGEPYENRISVGIMYMIKLSHMVDDKLHARSVGPYTLVTQQPMGGKAQNGGQR 631


>gi|156334831|ref|XP_001619534.1| hypothetical protein NEMVEDRAFT_v1g151047 [Nematostella vectensis]
 gi|156202955|gb|EDO27434.1| predicted protein [Nematostella vectensis]
          Length = 382

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 197/382 (51%), Positives = 268/382 (70%), Gaps = 5/382 (1%)

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           ++  D +   P DLINAK + S +  FF ++QLSQ  +  N L+ ITH RRLSALG GG+
Sbjct: 1   MNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGL 60

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD-- 607
           +R RAG E+RDVH THYGR+CP ET EG NIGL+SSL  +A+VN  GFIETPYRKV D  
Sbjct: 61  SRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLGVYAKVNGMGFIETPYRKVTDGV 120

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             + ++ +YLSA EEE + I+QAN  +DE+G    + V  R  G+  +V   KID+ D +
Sbjct: 121 IDIHSEPIYLSAEEEEGKLISQANIEIDENGKILPDNVIAREEGDFPVVEPSKIDYADVA 180

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P Q+ SI+ASLIPFLE+DD+NR LMG NM RQAVPLL+ EAP VGTG+E  VA  S   I
Sbjct: 181 PNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPEAPIVGTGLERQVASDSRVLI 240

Query: 728 VAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            A+  G+V  VD+ +I I+     +  L         Y+L+KF+++NQ+TC+N +P+V+ 
Sbjct: 241 NAEGDGVVAYVDSNKITIKYDRTEDERLVSFDDDDKTYQLIKFRKTNQSTCINLKPIVRK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD V +  ++ +G +T  G+LA+GRN+ VAFMPW GYNFED+++ISE++V +D+FTSIHI
Sbjct: 301 GDRVTKGQVLCEGYATQNGELAIGRNLKVAFMPWKGYNFEDAIVISEKVVRDDIFTSIHI 360

Query: 845 EEFEVMARDTKLGPEEITRDIP 866
           +++ +  RDTKLG EE+T DIP
Sbjct: 361 DDYSLEVRDTKLGNEELTNDIP 382


>gi|52694323|emb|CAG38001.1| RNA polymerase beta subunit [Pseudomonas chlororaphis]
          Length = 345

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 206/345 (59%), Positives = 270/345 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            +G VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D
Sbjct: 121 KEGLVTDEIVFLSAIEEADHVIAQASATMNDKGQLIDELVAVRHLNEFTVKAPEDVTLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG 
Sbjct: 181 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  G
Sbjct: 241 CVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           D V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 301 DRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 345


>gi|3005758|gb|AAC09367.1| RNA polymerase II 140 kDa subunit [Homo sapiens]
          Length = 476

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 102/509 (20%), Positives = 166/509 (32%), Gaps = 94/509 (18%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            ++    +  V        +    +       +      + AI      +  D+ +   S 
Sbjct: 43   HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA 102

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V        +F R   ++  +    + E  E   R+          +       I  G  
Sbjct: 103  VDRGFF-RSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVR 161

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L                     + +  +ES   +Y         R  
Sbjct: 162  VSGDDVIIGKTVTL--------------------PENEDELESTNRRYTKRDCSTFLRTS 201

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  Q    +     +  K+ V   R  Q GDK A RHG KG        EDMPF  +
Sbjct: 202  ETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCE 261

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  +PSRM +G + E   G      G+                        
Sbjct: 262  GITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--------------------- 300

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP  D  + + I+++L        G  
Sbjct: 301  --------------------------------ATPFNDAVNVQKISNLLSDYGYHLRGNE 328

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +LY+G TG      + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R 
Sbjct: 329  VLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRF 388

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAG----N 1336
            GEME  C  A+GAA  L+E L   SD     V            RT  YE    G     
Sbjct: 389  GEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC--RGCRNKT 446

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                   P +  +L +E+ ++ ++  + +
Sbjct: 447  QISLVRMPYACKLLFQELMSMSIAPRMMS 475



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 78/236 (33%), Gaps = 23/236 (9%)

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM-KFQRSNQNTCVNQRPL 781
             + I+   A I+   D  +    + +  +     GV I     +           Q+PL
Sbjct: 1   HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPL 60

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V                     +L  G N +VA   + GYN EDS++++   V    F S
Sbjct: 61  V----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRS 110

Query: 842 IHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    ++          EE+           +       +D+ G+I  G  V+  D+++G
Sbjct: 111 VFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIG 170

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K     E+    E          +    RD S  + +  +G V  V +       K
Sbjct: 171 KTVTLPENEDELEST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 219


>gi|318603037|emb|CBJ04585.1| RNA polymerase beta subunit [Pseudomonas sp. R-37907]
 gi|318603102|emb|CBJ04596.1| RNA polymerase beta subunit [Pseudomonas sp. R-38255]
          Length = 337

 Score =  337 bits (863), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 201/337 (59%), Positives = 261/337 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIH 337


>gi|81171095|gb|ABB58774.1| RNA polymerase beta subunit [Mycoplasma fermentans]
          Length = 598

 Score =  336 bits (862), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 211/453 (46%), Positives = 310/453 (68%), Gaps = 10/453 (2%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  + +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+
Sbjct: 2   QFMDQINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +  ++A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+    +
Sbjct: 62  LNFATYAQVNKYGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVD 121

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           + +  R     I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVP
Sbjct: 122 KQLTMRHNYNYIIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVP 181

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL  EAPFV TG+ES +AK S    VAK  G+VE VD  +I +R+ +G LD        Y
Sbjct: 182 LLIPEAPFVATGIESDIAKYSSGNFVAKNDGLVEYVDGKKIKVRNQKGTLD-------TY 234

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L  FQRSNQ+T V+QRPLVK G E+++ D++ DG S   G+LALG+N++VAF  + GYN
Sbjct: 235 YLKNFQRSNQDTVVHQRPLVKEGQEIKKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYN 294

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED+++++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+
Sbjct: 295 YEDAVILNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDEHGIV 354

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +G+EV PGD+LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G +GTV+ V
Sbjct: 355 RIGSEVVPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQLNVKDTSLKVKNGHNGTVIGV 414

Query: 943 RIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            + +R     +     +E+     +A  +  + 
Sbjct: 415 DVLSRENG--DALEDGIEKIVKVSIAIKRKIKV 445



 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 141/527 (26%), Positives = 221/527 (41%), Gaps = 86/527 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L+   P+     E  +   +     
Sbjct: 148  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIESDIA--KYSSGN 205

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + E+ V  +  K+  ++ T D   +      N D    +  ++  G E+  GD
Sbjct: 206  FVAKNDGLVEY-VDGKKIKVRNQKGTLDTYYLKNFQRSNQDTVVHQRPLVKEGQEIKKGD 264

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K    +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 265  LLVDGSSFKN-GELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQF 323

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++++   +   A    DE  I+         ++L G+ +  G     +  
Sbjct: 324  RTSKAGDDE-LTLDIPNVSKYATRHLDEHGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEE 382

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++                  QR +       +             +   + GD +
Sbjct: 383  KLLSAVLQ-----------------QRQLNVKDTSLKVKNGHNGTVIGVDVLSRENGDAL 425

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 426  EDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 485

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG K  +   D     +I  +                  
Sbjct: 486  VPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFDGVKKEEIQDV------------------ 527

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                          ++G+P+                        SG+  L D +TG   D
Sbjct: 528  ------------TLEAGLPL------------------------SGKQWLIDPITGNKLD 551

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 552  KPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 598


>gi|212373985|emb|CAP09919.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35718]
          Length = 337

 Score =  336 bits (862), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 201/337 (59%), Positives = 263/337 (78%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E++  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDQKVLIDELVAVRHLNEFTVKAPEEVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IH
Sbjct: 301 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIH 337


>gi|260159594|gb|ACX32465.1| RNA polymerase subunit B [Acinetobacter sp. JB10]
          Length = 269

 Score =  336 bits (862), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 130/273 (47%), Positives = 179/273 (65%), Gaps = 5/273 (1%)

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             R++ +L GQ +  G  G K+   LS D++S        +    DE +   +  ++V  +
Sbjct: 1    ERIVRLLSGQESNGG-GGTKRGDKLSEDMLSGLELVDLLEIQPSDEAIAERLTQIQVFLK 59

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                 ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS I
Sbjct: 60   EKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNI 119

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            LP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   K   
Sbjct: 120  LPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGEQIDKML---KQQR 176

Query: 1164 DISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++TPVFDGA+E  I  +
Sbjct: 177  EIAELRVFLDKIYNKVGGQQEDLDSLTDDEILVLAGNLRAGVPLATPVFDGAEESQIKEL 236

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            L +A++  SGQ++LYDG TGE FDRPVTVGY+Y
Sbjct: 237  LELAEIPRSGQTVLYDGRTGERFDRPVTVGYMY 269


>gi|116563674|gb|ABJ99853.1| RpoB [Bacillus sonorensis]
          Length = 182

 Score =  336 bits (862), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 80/204 (39%), Positives = 128/204 (62%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP +++    G+   +GK  +   + P++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYYS---GKVDKNGKKGFTATVXPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|6606121|gb|AAF19073.1|AF107801_1 DNA-dependent RNA polymerase II RPB140 [Stagonosporopsis
            cucurbitacearum]
          Length = 940

 Score =  336 bits (862), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 162/1048 (15%), Positives = 314/1048 (29%), Gaps = 170/1048 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S       E  +              +     +     ++   G V DE+ L
Sbjct: 36   VEKGTRLISSFNIKWAENSLASGKRMPGPFAYATLPYIKADVPMAIVFRSLGIVSDEEIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +        +         +DR+ AL  I R       +T    +
Sbjct: 96   GHIVYDRTDTQMLELLKPSIEEGSV--------VQDRESALDFIARRG-----ATQGTKD 142

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                F      +  L  +              +     +      +I  ++    G+   
Sbjct: 143  RRLKFARDIMQREFLPHI-----------SQREGQDTRKAYFFGYMIHRMLQCVLGRRDE 191

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  + A  + +
Sbjct: 192  DDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYLQRCVENNSDFNVQMAVKASIITN 251

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      V R     + 
Sbjct: 252  GLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKP 307

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVY 616
            R +H +H+G +CPAET EG   GLV +L+    V+          +    + ++  +   
Sbjct: 308  RQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDATPIADFMGKRNMQLLEEYDQ 367

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                +    ++      +  +       V        +      I D  D   K      
Sbjct: 368  NQNPDATKVFVNGVWVGVHNNAQQLVSTVQELRRNGTLSYEMSLIRDIRDREFKIFTDAG 427

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGT---GMESVVAKSSGAAIVAK 730
              + P     +        ++   +     L  E     T   G E   A + G      
Sbjct: 428  RVMRPLFVVQNDVTKDDRNHLVFNQDHYNKLVQEQQAQATAGIGEEEKTALTYG-WKGLI 486

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            + G++E +DA       +    +      D    + +  R+ Q      R   K    + 
Sbjct: 487  QDGVIEYLDAEEEETAMIVMSPEDLGEWRDMKQGIPQDARNPQGKDRLARIKPKPDPRIH 546

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    P+  LG       +  + +P+  +N          M  + +  ++      +
Sbjct: 547  AYTHCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRM 599

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                              V             +       +   
Sbjct: 600  ETMMN-----------------------------VLYYPQKPLATTRSMEYLKFRELPAG 630

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   +
Sbjct: 631  QNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEK 686

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                + + L    Y +L +   +  G           K+  +++D      ++       
Sbjct: 687  PTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAQEMGQKTSLHTKRD 746

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                ++     +  Q                             LR VKV     +  Q 
Sbjct: 747  VSTPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRTTKVPQI 786

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF +DG   D+V+NP  +PSRM +  + E  L     
Sbjct: 787  GDKFASRHGQKGTIGITYRHEDMPFTRDGVTPDLVINPHAIPSRMTIAHLVECLLSKVGA 846

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G++  +          IS                          +L  A   K G  +
Sbjct: 847  ITGREGDATPFTDVTVDQIS-------------------------ELLEDAGYQKRGFEI 881

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                         +Y+G TG+     + +G  Y  +L HMV DK
Sbjct: 882  -----------------------------MYNGHTGKKMRTQIFLGPTYYQRLRHMVDDK 912

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 913  IHARARGPLQILTRQPVEGRARDGGLRF 940



 Score =  129 bits (323), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 109/836 (13%), Positives = 249/836 (29%), Gaps = 108/836 (12%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK---DII- 202
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K   + + 
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFNIKWAENSLA 56

Query: 203 ---------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWC 246
                          +++ D    VP+     +LG+   EEIL         +Q  +   
Sbjct: 57  SGKRMPGPFAYATLPYIKAD----VPMAIVFRSLGIVSDEEILGHIVYDRTDTQMLELLK 112

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------S 300
             +    ++   + +   +      Q  +  +   +  +  ++ + +  +          
Sbjct: 113 PSIEEGSVVQDRESALDFIARRGATQGTKDRRLKFARDI--MQREFLPHISQREGQDTRK 170

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIR 359
               G  +   ++    G    +  D   +K L+           IL++  + +   Y++
Sbjct: 171 AYFFGYMI-HRMLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYLQ 229

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             +  + + + + A+           + T  +  S+    + D  K   +  G  ++  R
Sbjct: 230 RCVENNSDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLNR 281

Query: 420 LNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
               +      R          +     L N    +         +   + + L     +
Sbjct: 282 YTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYV 341

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +      I + +   ++  +   D                   +         +S +  
Sbjct: 342 SVGSDATPIADFMGKRNMQLLEEYDQNQNPDATKVF---VNGVWVGVHNNAQQLVSTVQE 398

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR   L             +RD+    +     A         + + +T   R N   F
Sbjct: 399 LRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVQNDVTKDDR-NHLVF 450

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +  Y K+   +                  AQA + + E+        +     + +   
Sbjct: 451 NQDHYNKLVQEQQ-----------------AQATAGIGEEEKTALTYGWKGLIQDGV--- 490

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME- 716
              I+++DA  ++   I  S     E  D  + +       Q    L    P     +  
Sbjct: 491 ---IEYLDAEEEETAMIVMSPEDLGEWRDMKQGIPQDARNPQGKDRLARIKPKPDPRIHA 547

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DIYRLMKFQRSNQNTC 775
               +   A I+   A I+   D  +    + +  +     GV      ++ +       
Sbjct: 548 YTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRMETMMNVLY 607

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+PL                      +L  G+N +VA   + GYN EDS+++++  + 
Sbjct: 608 YPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 657

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNP 890
             +F S+    +    +   +   E        D   +       +D+ G++  G  V+ 
Sbjct: 658 RGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSG 717

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            DI++GK  P         +K             RD S  + S  +G V  V    
Sbjct: 718 DDIIIGKTAPIAADAQEMGQKT-------SLHTKRDVSTPLRSTENGIVDQVLFTT 766


>gi|52694395|emb|CAG38037.1| RNA polymerase beta subunit [Pseudomonas syncyanea]
          Length = 348

 Score =  336 bits (862), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 205/348 (58%), Positives = 271/348 (77%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V +G V++D+V+LSA+EE +  IAQA++++ +     +ELV  R   E  +   E +
Sbjct: 121 YRVVKEGVVSDDIVFLSAIEEADHVIAQASAAMSDKKQLIDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           V  GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +
Sbjct: 301 VSKGDKVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICL 348


>gi|111054581|gb|ABH04348.1| RNA polymerase beta subunit [Proteus hauseri]
          Length = 338

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 258/338 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVE 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ ++D 
Sbjct: 121 NNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHRGESSLFSRDQVQYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN+E
Sbjct: 301 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNYE 338


>gi|111054585|gb|ABH04350.1| RNA polymerase beta subunit [Proteus penneri]
          Length = 340

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 208/340 (61%), Positives = 261/340 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ ++
Sbjct: 121 VENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VAKR G+V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVAKRGGVVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSL 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN+E
Sbjct: 301 GEPVDRGDVLADGPSTDLGELALGQNMRVAFMPWNGYNYE 340


>gi|20090128|ref|NP_616203.1| DNA-directed RNA polymerase subunit B' [Methanosarcina acetivorans
            C2A]
 gi|19915108|gb|AAM04683.1| DNA-directed RNA polymerase, subunit B [Methanosarcina acetivorans
            C2A]
          Length = 604

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 116/585 (19%), Positives = 191/585 (32%), Gaps = 94/585 (16%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              +  D     N  +A       +    M I   ++       +   E     R+T    
Sbjct: 96   CVEYLDAEEEENAYIALYESDITSRHTHMEIDPELMLGICTGMVPYPEHNASPRNTMGAA 155

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
              + +    VS    + +       V                 G       +  + AI  
Sbjct: 156  --MIKQCIGVSTAN-QKLRPDTRAHVLHYPQRALTRTRTSEAIGFDDRPAGQNFVVAILS 212

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  ++ D  +     +    +    F R    +  R    + ++ E+   +        
Sbjct: 213  YEGYNIEDALIFNKGSIERG-LGRSHFLRTFEGEERRYPGGQEDKFEIPDSEY--RGARS 269

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                 +  ++ L       GP             + E                   VE  
Sbjct: 270  AEAYANLDVDGLVNPETPVGPNDVLIGKTSPPRFLEEPSDFGI------------AVEQR 317

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T +S         I              R+ KV V  +R    GDK A RHG KG
Sbjct: 318  RESSVTMRSNETGIVDTVIL------TESINGTRLAKVKVRDERIPDIGDKFASRHGQKG 371

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++   +P  DMPF + G   D+++NP  +PSRM VG + E   G      G+++      
Sbjct: 372  VIGLKVPIADMPFTESGLTPDLMINPHAIPSRMTVGHVLEMIGGKVGSMEGRRVN----- 426

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +T  F G +E+ 
Sbjct: 427  ------------------------------------------------AT-AFSGENEDD 437

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L+      +G+ I YDG TG      V VG I   KL+HMV+ K++ARS G   ++
Sbjct: 438  LREALKKHGFAHTGKEIFYDGATGRMIPADVFVGVILYQKLHHMVTSKMHARSRGPVQVL 497

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE- 1330
            T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G    Y+ 
Sbjct: 498  TRQPTEGRAREGGLRFGEMERDVLVGHGAAMSLKERLLDESDKVVELVCSHCGMIATYDK 557

Query: 1331 ------SIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                      G   D +      +F +L+ E+++LG++  L    
Sbjct: 558  QRNVAFCSACGADTDIYPVEMSYAFKLLLDEIKSLGVAPRLNLED 602



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/335 (16%), Positives = 113/335 (33%), Gaps = 37/335 (11%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI----AASLIPFLENDD 686
           N  L        EL              ++++       + V I      +  P +  ++
Sbjct: 9   NGELVGTHDNPAELAEELRKMRRQGFISKQVNIALNDNTREVIINSDMGRARRPLVVVEN 68

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                   ++Q+     +  +       +E + A+    A +A        + +    + 
Sbjct: 69  GVLRATEEHVQKLKSKEITFDDLVKEGCVEYLDAEEEENAYIA---LYESDITSRHTHME 125

Query: 747 SVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQRPLVKVGDEVRRNDIIAD-------- 796
                +    +G+  Y       + +     + Q   V   ++  R D  A         
Sbjct: 126 IDPELMLGICTGMVPYPEHNASPRNTMGAAMIKQCIGVSTANQKLRPDTRAHVLHYPQRA 185

Query: 797 ------GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   +    D   G+N +VA + + GYN ED+++ ++  +   +  S  +  FE  
Sbjct: 186 LTRTRTSEAIGFDDRPAGQNFVVAILSYEGYNIEDALIFNKGSIERGLGRSHFLRTFEGE 245

Query: 851 ARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            R    G E+   +IP+       S E   N+D  G++     V P D+L+GK +P    
Sbjct: 246 ERRYPGGQEDKF-EIPDSEYRGARSAEAYANLDVDGLVNPETPVGPNDVLIGKTSPPRFL 304

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                     + FG      R++S+ + S  +G V
Sbjct: 305 EEP-------SDFGIAVEQRRESSVTMRSNETGIV 332



 Score = 52.0 bits (123), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 62/194 (31%), Gaps = 30/194 (15%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F + +L    ++   L+      R        V  A        +  +  GR        
Sbjct: 7   FINGELVGTHDNPAELAEELRKMRRQGFISKQVNIALNDNTREVIINSDMGRAR------ 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              + +V +    A       +++      D      V YL A EEEN YIA   S +  
Sbjct: 61  -RPLVVVENGVLRATEEHVQKLKSKEITFDDLVKEGCVEYLDAEEEENAYIALYESDIT- 118

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                  +   ++  P+ ++ I   ++P+ E++ S R  MG  M
Sbjct: 119 ----------------------SRHTHMEIDPELMLGICTGMVPYPEHNASPRNTMGAAM 156

Query: 697 QRQAVPLLKAEAPF 710
            +Q + +  A    
Sbjct: 157 IKQCIGVSTANQKL 170


>gi|325960116|ref|YP_004291582.1| DNA-directed RNA polymerase subunit B [Methanobacterium sp. AL-21]
 gi|325331548|gb|ADZ10610.1| DNA-directed RNA polymerase subunit B [Methanobacterium sp. AL-21]
          Length = 603

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 119/585 (20%), Positives = 203/585 (34%), Gaps = 95/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  +A  P         + I    +       I         R+T     
Sbjct: 97   IEYMDAEEEENSYIAMFPEDITENHSHLEIDPSTMLGICAGIIPFANHNSSPRNTMEAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                    VS   ++         +        +    +           +  + A+   
Sbjct: 157  TKQALGLYVSNYNMR---TDTRAHLLHHPQVPLVKTKSMDATKYDKRPSGQNFVVAVMSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +   +     F R       R    + ++ E+          I+ 
Sbjct: 214  EGYNMEDALILNKASIERGLARSSFF-RSYEASERRYPGGQEDKFEVPE-------NIVR 265

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                  +   L     V+     K   VL           +  +F    E+ +    +++
Sbjct: 266  GYRSEEVYRHLDEDGIVNPEVEVKSGDVLIGKTSPPRFLEEIDEFGTVAERRRETSVTVR 325

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                     +                      ++ K+ V  +R  + GDK A RHG KG+
Sbjct: 326  HGEHGVVDAVLL-------------TETVEGSKLAKIRVRDQRQPEFGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  I+  E+MPF + G   D+++NP  +PSRM+VGQ+ E   G A    GK++       
Sbjct: 373  VGLIVSQENMPFTEVGVVPDLIINPHAIPSRMSVGQVIEMLAGKAGTMEGKRMDG----- 427

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                            TP F G  E  I
Sbjct: 428  ------------------------------------------------TP-FGGKQEAEI 438

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L+    + +G+  LY+G+TGE  +  + VG  +  KL+HM +DKVYARS G   ++T
Sbjct: 439  MELLKQNGFETAGRESLYNGITGERIEAEIFVGVAFYQKLHHMTADKVYARSRGPVQVLT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVGRTRVYES 1331
            +QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD        D  G   +Y+ 
Sbjct: 499  RQPTEGRAREGGLRFGEMERDCLIAHGAALALKERLLDESDKYEALVCQD-CGMIAIYDR 557

Query: 1332 I-------VAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            I       + G  +TF      +F +L+ E+++L +   L     
Sbjct: 558  IRDKKYCAICGESETFPVEISYAFKLLLDELKSLCIFPKLVLEDK 602



 Score = 98.6 bits (244), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 96/291 (32%), Gaps = 27/291 (9%)

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           +      M    +  +   +  E      + +E   +   G                   
Sbjct: 93  NQGIIEYMDAEEEENSYIAMFPEDITENHSHLEIDPSTMLGICAGIIPFANHNSSPRNT- 151

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                 G    +         M+           Q PLVK               +T   
Sbjct: 152 ---MEAGMTKQALGLYVSNYNMRTDTRAHLLHHPQVPLVK----------TKSMDATKYD 198

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE---E 860
               G+N +VA M + GYN ED++++++  +   +  S     +E   R    G E   E
Sbjct: 199 KRPSGQNFVVAVMSYEGYNMEDALILNKASIERGLARSSFFRSYEASERRYPGGQEDKFE 258

Query: 861 ITRDIP--NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           +  +I     SEE  +++DE GI+    EV  GD+L+GK +P        E        G
Sbjct: 259 VPENIVRGYRSEEVYRHLDEDGIVNPEVEVKSGDVLIGKTSPPRFLEEIDEF-------G 311

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
             A   R+TS+ V  G  G V  V +       K  +    ++ Q E   +
Sbjct: 312 TVAERRRETSVTVRHGEHGVVDAVLLTETVEGSKLAKIRVRDQRQPEFGDK 362



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 51/184 (27%), Gaps = 31/184 (16%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  + +  +   RR   +            +   +         P    E     L    
Sbjct: 18  DPEDFVRSMREKRRTGEVSPEMNITYYKETDEIFLFTDPGRTRRPLIVVENGESKLTEET 77

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                      IE              + Y+ A EEEN YIA     + E+ S       
Sbjct: 78  IQL--------IEDGELDWEGLINQGIIEYMDAEEEENSYIAMFPEDITENHSHL----- 124

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                             +  P  ++ I A +IPF  ++ S R  M   M +QA+ L  +
Sbjct: 125 ------------------EIDPSTMLGICAGIIPFANHNSSPRNTMEAGMTKQALGLYVS 166

Query: 707 EAPF 710
               
Sbjct: 167 NYNM 170


>gi|242392298|dbj|BAH80342.1| RNA polymerase subunit B' [Halobiforma lacisalsi]
          Length = 609

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 127/596 (21%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDILVAVDEDDLTADHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSLEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + SG+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELREGLEEAGFESSGKETMYSGITGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICAQCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.0 bits (97), Expect = 0.74,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +           +I   RR+  + +      +       ++        P    
Sbjct: 11  YVNGSLVGTHPNPHELAEQIREARRIGDVSEMVNVSVKERTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  N  G +E       D      V ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISDEEIEALRN--GDLE-----FEDLVDHGYVEFIDAEEEEDILVAVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 ADH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|52694339|emb|CAG38009.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. III]
          Length = 343

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 202/342 (59%), Positives = 264/342 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           +R+DI+ADGPSTD+G+L LG+NM +AFM W+GYNFEDS+ +S
Sbjct: 302 QRSDIMADGPSTDMGELPLGQNMRIAFMAWNGYNFEDSICLS 343


>gi|315259442|gb|ADT91920.1| DNA-directed RNA polymerase beta subunit [Vagococcus fluvialis]
          Length = 392

 Score =  336 bits (861), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 140/449 (31%), Positives = 192/449 (42%), Gaps = 79/449 (17%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                G  +    I         + ++  I+ +G  V  GD L    +   +  M   + +
Sbjct: 17   RRNNGALDKYNVIKFHRSNAGTSYNQRPIVSLGEIVEAGDTLADGSS-MEQGEMALGQNV 75

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA---- 968
            L A    +  +  D  +     V   V        +  +  +  +  E    EL      
Sbjct: 76   LVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITRELPNVGDD 135

Query: 969  --RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +D  DE  I+      +  ++L G+    G         L   +  E  R        
Sbjct: 136  ALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR-------- 186

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
               +V+     +          +      KI   + GD++ PGV  +V+V++  KR I  
Sbjct: 187  ---EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELAPGVNMLVRVYIVQKRKINE 237

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A  
Sbjct: 238  GDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAR 297

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
             LG  + + + D     D+                                         
Sbjct: 298  SLGIHVATPVFDGADEDDVW---------------------------------------- 317

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                   A           ADL    ++ILYDG TGEPFD  ++VG +YMLKL HMV DK
Sbjct: 318  -------ATVAE-------ADLARDAKTILYDGRTGEPFDNRISVGVMYMLKLAHMVDDK 363

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            ++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 364  LHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 126/222 (56%), Positives = 163/222 (73%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y ++KF RSN  T  NQRP+V +G+ V 
Sbjct: 1   KHDGVVEYVDAKEIRVRRNNGALDK-------YNVIKFHRSNAGTSYNQRPIVSLGEIVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
             D +ADG S + G++ALG+N+LVAFM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  AGDTLADGSSMEQGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR++PNV ++ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITRELPNVGDDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|34493988|emb|CAD66137.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  335 bits (860), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGEFSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|318603145|emb|CBJ04604.1| RNA polymerase beta subunit [Pseudomonas sp. R-39443]
          Length = 340

 Score =  335 bits (860), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 202/340 (59%), Positives = 263/340 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+
Sbjct: 241 GGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRS 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           DI+ADGPSTD+G+LALG+NM +AFM W+GYNFEDS+ +SE
Sbjct: 301 DIMADGPSTDMGELALGQNMRIAFMAWNGYNFEDSICLSE 340


>gi|242392296|dbj|BAH80341.1| RNA polymerase subunit B' [Halobiforma haloterrestris]
          Length = 609

 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 127/596 (21%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDILVAVDEDDLSEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSLEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + SG+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELREGLEEAGFESSGKETMYSGITGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICGQCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 43.1 bits (100), Expect = 0.38,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +           +I   RR+  + +      +       ++        P    
Sbjct: 11  YVNGSLVGTHPNPHELAEQIREARRIGDVSEMVNVSVKERTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  N  G +E       D      V ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISDEEIEALRN--GDLE-----FEDLVDHGYVEFIDAEEEEDILVAVDEDDLS 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|111054583|gb|ABH04349.1| RNA polymerase beta subunit [Proteus penneri]
          Length = 339

 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 208/339 (61%), Positives = 260/339 (76%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ +
Sbjct: 121 VVENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQY 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  S
Sbjct: 181 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G   VAKR G+V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V 
Sbjct: 241 GVTAVAKRGGVVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 301 LGEPVDRGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 339


>gi|111054569|gb|ABH04342.1| RNA polymerase beta subunit [Proteus mirabilis]
          Length = 338

 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 259/338 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +  VT+++ YLSA+EE N  IAQANS LD+DG F EELV CR  GE  L  R+++ ++
Sbjct: 121 VENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDGHFVEELVTCRHKGESSLFSRDQVQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVAKRGGTVQYVDASRIVIKVNEDETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSL 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 301 GEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 338


>gi|6606131|gb|AAF19078.1|AF107806_1 DNA-dependent RNA polymerase II RPB140 [Microglossum viride]
          Length = 938

 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 162/1047 (15%), Positives = 315/1047 (30%), Gaps = 171/1047 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  KG    G +        +     +   G ++   G V DE  L
Sbjct: 37   LEKGSRLISSLTIKLHSKGDNQRG-SFGSTVKSTLPYIKADIPIGIVFRALGVVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A++         +DR+ AL  I +              
Sbjct: 96   NHICYDRNDTQMLEMLKPCIEEAFV--------IQDREVALDYIGKR------------G 135

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +          KY    + +  +      +  +  +      +  ++  L+    G+   
Sbjct: 136  NAMGLTRDKRIKYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHKLLQCALGRRET 192

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + +    +    +     P   I +  + +
Sbjct: 193  DDRDHFGKKRLDLAGPLLAKLFRNLFKKLTQDLFKYTQRCVENRKEFNPALGIKSTTLTA 252

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 253  GLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 308

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V         +      +V  +   
Sbjct: 309  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRSMEVLEEYEP 368

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L +      ++      +  D +   + V        I      I D  D   K      
Sbjct: 369  LRSPNATKVFVNGVWVGVHRDPAHLVQTVRDLRRSHHISYEVSLIRDIRDREFKIFTDAG 428

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                P F+ ++D +    G  +  +       +   +  G++    +  G        G 
Sbjct: 429  RVCRPLFVIDNDVSSKNKGNLVLNKGHIKRLEDDATLPLGLDLEEKQERGY------FGF 482

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD---EVRRN 791
               +D    V+  V+ + + +   V     ++  R  Q     Q      G+    V+  
Sbjct: 483  QGLID--EGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYQIQE--DNSGELNRRVKAP 538

Query: 792  DIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                    T      ++   +  + +P+  +N                        ++  
Sbjct: 539  MKPTAHIWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSA 580

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                 +G      D                +  +             +       +   +
Sbjct: 581  MGKQAMGVFLTNFDQRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQ 629

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   + 
Sbjct: 630  NAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYTDQEKR---IGMNVVEQFEKP 685

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
              ++ + L    Y +L +   +  G           K+  ++ D      R++       
Sbjct: 686  FRNDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDNEELGQRTKAHSKRDA 745

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +  Q                             LR VKV +   +  Q G
Sbjct: 746  STPLRSTENGIVDQVLI--------------------TTNAEGLRFVKVRMRTTKIPQIG 785

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +  I   EDMPF ++G   D+++NP  +PSRM +  + E  L      
Sbjct: 786  DKFASRHGQKGTIGIIYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVASL 845

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +         ++S L                                       
Sbjct: 846  SGYEGDATPFTDVTVDNVSKLLREHGYQSRGFEIM------------------------- 880

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G +    G         V +G  Y  +L HMV DK+
Sbjct: 881  ----------------------YHGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 911

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +AR+ G   ++T+QP+ G++  GG R 
Sbjct: 912  HARARGPVQILTRQPVEGRARDGGLRF 938



 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 112/854 (13%), Positives = 239/854 (27%), Gaps = 146/854 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          +        +   I    ++G  +      K  +H + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKPPPSPTPFVAEIRSALEKGSRLISSLTIK--LHSKG 55

Query: 207 DRRR----------------KVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           D +R                 +P+     ALG+   E+IL+        +Q  +     +
Sbjct: 56  DNQRGSFGSTVKSTLPYIKADIPIGIVFRALGVVSDEDILNHICYDRNDTQMLEMLKPCI 115

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD-------C 302
             A ++   +V+   +        +   K++     + + +K +       +        
Sbjct: 116 EEAFVIQDREVALDYIGKRGNAMGLTRDKRI--KYARDIMQKELLPHISQKEGSETRKAF 173

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
             G  V + ++    G    +  D   +K L+       +    L+         +   L
Sbjct: 174 FLGYMVHK-LLQCALGRRETDDRDHFGKKRLDLAGPLLAKLFRNLFKK-------LTQDL 225

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                +  ++       +       T  +  S+    + D  K   ST G  ++  R   
Sbjct: 226 FKYTQRCVENRKEFNPALGIKSTTLTAGLKYSLATGNWGDQKKAASSTAGVSQVLNRYTF 285

Query: 423 DTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +      R          I     L N    +         +   + + L     + + 
Sbjct: 286 ASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVG 345

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
                I E +    ++ +   + + +               +    +  + +  +   RR
Sbjct: 346 TPSDPIVEFMIQRSMEVLEEYEPLRSPNATKVF---VNGVWVGVHRDPAHLVQTVRDLRR 402

Query: 541 LSALG-QGGVARARAGVEM----------RDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              +  +  + R     E           R +           + +   N G +  L   
Sbjct: 403 SHHISYEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDVSSKNKGNLVLNKGHIKRLEDD 462

Query: 590 AR----VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           A     ++     E  Y           V Y+ A EEE   I      L+          
Sbjct: 463 ATLPLGLDLEEKQERGYFGFQGLIDEGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYQ 522

Query: 646 F--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                     R     +          +  P  ++ I AS+IPF +++ S R      M 
Sbjct: 523 IQEDNSGELNRRVKAPMKPTAHIWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 582

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 583 KQAMGVFLTNF-----------------------------------------DQRMDTMA 601

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y       +     +  R                        +L  G+N +VA + 
Sbjct: 602 NILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILC 637

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    +    +   +   E        D   +    
Sbjct: 638 YSGYNQEDSVIMNQSSIDRGLFRSLFFRSYTDQEKRIGMNVVEQFEKPFRNDTLKLKHGT 697

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G++  G  V+  DI++GK  P         ++        KA   RD S  + 
Sbjct: 698 YDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDNEELGQRT-------KAHSKRDASTPLR 750

Query: 933 SGVSGTVVDVRIFN 946
           S  +G V  V I  
Sbjct: 751 STENGIVDQVLITT 764


>gi|302676710|ref|XP_003028038.1| hypothetical protein SCHCODRAFT_83253 [Schizophyllum commune H4-8]
 gi|300101726|gb|EFI93135.1| hypothetical protein SCHCODRAFT_83253 [Schizophyllum commune H4-8]
          Length = 1142

 Score =  335 bits (860), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 171/969 (17%), Positives = 296/969 (30%), Gaps = 200/969 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---- 487
            +   +  + + ++   + +  +DD D +GN+R+   G++L   +         ++K    
Sbjct: 340  KAIFVATMTRRVLMAMHDEKMVDDRDYVGNKRLELAGQLLALLFEDLFKTYCSNLKAAID 399

Query: 488  ---ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               ++ S           +     + +       +   S     +          RLS +
Sbjct: 400  KVLKKPSRTTEFDAYNTMMFQGDHITAGFVRAISTGNWSLKRFRMERAGVTHVLSRLSFI 459

Query: 545  GQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
               G+         + R     R + P+ +G +CP++T EG   GLV +L     +    
Sbjct: 460  SALGMMTRISSQFEKTRKVSGPRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDV 519

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
              E   R          + YL  +E+    IA A+ S           V     G     
Sbjct: 520  DEEPIIR----------LAYLLGVED----IALASGSEIYGTHAFIVSVNGNIIGLTKYP 565

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             R   +F      + +S   S+     +        G  + R  +         V  G  
Sbjct: 566  ARFVTNFRKMRRARRISEFVSIYINHHHRTVQIATDGGRICRPMI--------IVEKGRS 617

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             V ++     I   + G     D +R  +       + + + + +Y              
Sbjct: 618  RVHSEH----IALLKKGAATFDDFLRKGLVEYLDVNEENDAYIALYEA------------ 661

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                     D V     +   P T LG +A         +P+  +N          M  +
Sbjct: 662  ---------DIVPTTTHLEIEPFTLLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQ 705

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +                                  L  ID   ++ +        +   
Sbjct: 706  AIGAIGF---------------------------NQLNRIDT--LLYLSVYPQQPMVKTK 736

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             I   G   +   +    A+      D+ D  +   + +       ++  ++     +  
Sbjct: 737  TIELIGYDKLPAGQNATVAVMSYSGYDIEDALILNKASLDRGYGRCQVLRKNATLVRKYP 796

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEI---LCGQNAVSGPKGFKKSTVLSSDLI 1013
                                      Y RL +      G  A               + +
Sbjct: 797  -----------------------NGTYDRLADAPVDENGNIAKKYDIIQADGLAGVGERV 833

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                     Q          N ++  V Y+ +    +      I+K+   D     +  +
Sbjct: 834  DPGDVYVNKQSPTNATDNTFNGQAAAVPYKNTPLTYKSPVAGNIDKVLISDTENDQL--L 891

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  + GDK + RHG KG+   I+  EDMPF   G   D ++NP G PSRM V
Sbjct: 892  VKVLIRQTRRPELGDKFSSRHGQKGVCGLIVNQEDMPFNDQGINPDTIMNPHGFPSRMTV 951

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
                    G     L  K   L    +                                 
Sbjct: 952  --------GKMIELLAGKAGVLTGKLQYGT------------------------------ 973

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                             F G+  E ++ +L       +G+ +L  G+TGEP +  V  G 
Sbjct: 974  ----------------AFGGSKVEDMSRILIENGFSYAGKDMLTSGITGEPMEAYVYFGP 1017

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG RLGEME  C+  YGA  +L E
Sbjct: 1018 IYYQKLKHMVMDKMHARARGPRATLTRQPTEGRSREGGLRLGEMERDCLIGYGATQLLLE 1077

Query: 1314 MLTIKSD----DVVGRTRVYESIVAG-----------NDTFETGTPESFNVLVKEMQALG 1358
             L I SD    D        E  + G               +   P +  +L +E+ A+ 
Sbjct: 1078 RLMISSDKFEVDACQ-----ECGLMGYNGWCTYCKSSKKMAQLTIPYAAKLLFQELMAMN 1132

Query: 1359 LSIDLENSR 1367
            +   L    
Sbjct: 1133 VVPRLVLDD 1141



 Score =  135 bits (339), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 89/734 (12%), Positives = 199/734 (27%), Gaps = 127/734 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    S++HF+  +I    + N  +          +       ++F+  E        
Sbjct: 46  LVKQHIDSFNHFVDADIKNIVKANNKIT---------SDVDPRFWIKFMDIEVGFPDRNE 96

Query: 84  PK------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
           P+          +C  RD+TY+ P+ +T +                        +G LP+
Sbjct: 97  PEAHDKKSITPHECRLRDITYSAPITVTFQYTRGRSIVQRRQT-----------IGRLPI 145

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR- 171
           M                           G FV+KG +++++ Q   S   I  + D  + 
Sbjct: 146 MLRSNKCVLTGRTEAQLARMTECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVETDPVKG 205

Query: 172 ---------ASLSGK-LLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMA 220
                         K   Y                  K  I++R +     VP+   L  
Sbjct: 206 IVQASCTSSTHGGVKSKAYVVT--------------KKGRIYLRHNSIHEDVPIVIALKG 251

Query: 221 LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG+ S+ EI+          +         +A   +   + +   +           G +
Sbjct: 252 LGIQSDKEIMLLTAGNTEAYKIAFSANLEDAAKMGVFTQQQALEWLGARVRVNRRPMGPR 311

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             +          +    +  D L     A   V   T  + +   D       + + + 
Sbjct: 312 RPAYEEALEALATLLLAHVRMDGLDFRPKAI-FVATMTRRVLMAMHDEKMVDDRDYVGNK 370

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            +                +             +    I +V++    +T   A +   F 
Sbjct: 371 RLEL----------AGQLLALLFEDLFKTYCSNLKAAIDKVLKKPSRTTEFDAYNTMMFQ 420

Query: 400 FFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                   +  +     +  R  ++       + +   I+ + ++  + +       +  
Sbjct: 421 GDHITAGFVRAISTGNWSLKRFRMERAGVTHVLSRLSFISALGMMTRISSQFEKTRKVSG 480

Query: 459 LG-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                     +    +  + +    +  +           +   +    L+  + +  A 
Sbjct: 481 PRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDVDEEPIIRLAYLLGVEDIALAS 540

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                 +    +  + N +    +  R        + RAR   E   ++  H+ R     
Sbjct: 541 GSEIYGTHAFIVSVNGNIIGLTKYPARFVT-NFRKMRRARRISEFVSIYINHHHRTVQIA 599

Query: 574 TSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T  G     +  +              ++       D      V YL   EE + YIA  
Sbjct: 600 TDGGRICRPMIIVEKGRSRVHSEHIALLKKGAATFDDFLRKGLVEYLDVNEENDAYIALY 659

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            + +                             ++  P  ++   A LIP+  ++ S R 
Sbjct: 660 EADIVP-----------------------TTTHLEIEPFTLLGAVAGLIPYPHHNQSPRN 696

Query: 691 LMGCNMQRQAVPLL 704
              C M +QA+  +
Sbjct: 697 TYQCAMGKQAIGAI 710


>gi|115454339|ref|NP_001050770.1| Os03g0646800 [Oryza sativa Japonica Group]
 gi|113549241|dbj|BAF12684.1| Os03g0646800 [Oryza sativa Japonica Group]
          Length = 368

 Score =  335 bits (859), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 130/322 (40%), Gaps = 74/322 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 95   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPH 154

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 155  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 182

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 183  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKL 220

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 221  TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 280

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYE-----SIV---------AG----NDTFETGTPESF 1347
            GAA+ L+E L  +SD    R  V E     +I           G     D  +   P + 
Sbjct: 281  GAAFFLKERLFDQSD--AYRVHVCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYAC 338

Query: 1348 NVLVKEMQALGLSIDLENSRTK 1369
             +L +E+ A+ ++  +     K
Sbjct: 339  KLLFQELMAMAIAPRMLTQDNK 360



 Score = 45.8 bits (107), Expect = 0.049,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 10/96 (10%)

Query: 844 IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           I+ +E      + G      +   +       +D+ G+   G  V+  D+++GK +P  +
Sbjct: 3   IQSYEKRTCKEEFGR-PNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQ 61

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                      A         RD S  +    SG V
Sbjct: 62  DD---------AQGQATRYTKRDHSTSLRHSESGMV 88


>gi|52694327|emb|CAG38003.1| RNA polymerase beta subunit [Pseudomonas corrugata]
          Length = 345

 Score =  335 bits (859), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 205/345 (59%), Positives = 268/345 (77%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D
Sbjct: 121 KDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG 
Sbjct: 181 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  G
Sbjct: 241 CVVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           D V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 301 DRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 345


>gi|90902242|gb|ABE01889.1| RNA polymerase beta subunit [Acholeplasma parvum]
          Length = 636

 Score =  335 bits (859), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 221/457 (48%), Positives = 300/457 (65%), Gaps = 30/457 (6%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+S
Sbjct: 1   FMDQINPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLIS 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGK----VTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           SL+++AR + YGFI+TP+ KV        VT+ +VYL+A +E    IA A S ++ D  F
Sbjct: 61  SLSTYARADEYGFIQTPFLKVVHENGVAKVTDKIVYLTADQEVGEVIASAASPVNADNQF 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            EE +  R  GE  +  + +I F+D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQA
Sbjct: 121 VEERIIARSGGETAIYEQHQITFMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQA 180

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV------------ 748
           VPL++ E+P VGTG+E   AK SG  I++K AG V   DA +IV+               
Sbjct: 181 VPLIQPESPIVGTGIEYRAAKDSGCLIISKTAGYVTYADAKKIVVTEEPSELVSIGGRII 240

Query: 749 ------------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                       +   D   +    Y L +F RSNQ+T V Q+P+V  G+ V   D++AD
Sbjct: 241 YEPGKEFNYLIAKELHDYGLTTETEYELTQFFRSNQDTLVLQKPIVVAGEYVEAGDVLAD 300

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR--DT 854
           GPST+ G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  R   T
Sbjct: 301 GPSTEKGELALGRNVTVAFMTWEGYNYEDAIIMSEDLVKNDVYTSIHIDEYEIEIRELKT 360

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             G EEITR+IP+V  + +KN+DE GII  G+EV  GDILVGKITPKG    +P EKL+ 
Sbjct: 361 GTGKEEITREIPHVGADAIKNLDEMGIITPGSEVKEGDILVGKITPKGIFEPSPAEKLIH 420

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           A+ GEK+ + RD+SLR+P G  G V  +R F++   D
Sbjct: 421 AVIGEKSREYRDSSLRIPHGGGGVVQSIRYFSKKNGD 457



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 128/424 (30%), Positives = 189/424 (44%), Gaps = 79/424 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR----VPSGVS 936
            I+  G  V  GD+L    + + +  +     +  A    +  +  D  +     V + V 
Sbjct: 285  IVVAGEYVEAGDVLADGPSTE-KGELALGRNVTVAFMTWEGYNYEDAIIMSEDLVKNDVY 343

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD---DEQVILDRNIYSRLMEILCGQ 993
             ++            K          +I  +  D     DE  I+      +  +IL G+
Sbjct: 344  TSIHIDEYEIEIRELKTGTGKEEITREIPHVGADAIKNLDEMGIITPGSEVKEGDILVGK 403

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G      +  L   +I E  R    ++     ++      +             R+
Sbjct: 404  ITPKGIFEPSPAEKLIHAVIGEKSR----EYRDSSLRIPHGGGGVVQSI---------RY 450

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K      GD +P GV  VV+V+VA KR I  GDKMAGRHGNKG++S+ILP EDMP+++
Sbjct: 451  FSKKN----GDILPSGVNEVVRVYVAKKRKISEGDKMAGRHGNKGVISKILPREDMPYME 506

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT VDI+LNPLGVPSRMN+GQI E HLG +   LG K+ + + D  ++ D+  + +   
Sbjct: 507  DGTHVDIMLNPLGVPSRMNIGQILEIHLGISAKRLGIKVATPVFDGVSDNDLREIMAESG 566

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 567  VEPDGK----------------------------TVLYDG-------------------- 578

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEPFD  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 579  ------RTGEPFDNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 632

Query: 1294 LGEM 1297
             GEM
Sbjct: 633  FGEM 636


>gi|52694343|emb|CAG38011.1| RNA polymerase beta subunit [Pseudomonas chlororaphis]
          Length = 343

 Score =  335 bits (859), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 204/342 (59%), Positives = 267/342 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 343


>gi|318602991|emb|CBJ04574.1| RNA polymerase beta subunit [Pseudomonas sp. R-37184]
          Length = 344

 Score =  335 bits (859), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 203/344 (59%), Positives = 269/344 (78%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 121 SPYRVVKEGVVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 241 ARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 300

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           PLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NF
Sbjct: 301 PLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNF 344


>gi|83415473|gb|ABC17944.1| RNA polymerase II second largest subunit [Conidiobolus coronatus]
          Length = 727

 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 139/854 (16%), Positives = 259/854 (30%), Gaps = 149/854 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +++   +  + +    +              +    + + +     +
Sbjct: 2    KRMDLAGPLLTQLFKVLFAKFNKDLAKYLQKCIDSNREFNMNMAVKPNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+  A V+     +    Y      +      +   +    
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLLAHVSVGSPADGINSYLNDYYTESLEQSQHFRDIRGTK 177

Query: 625  RYIAQANSSLDEDG-SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             ++      +  DG    + L   RC  +         D  D              P   
Sbjct: 178  IFLNGDWIGMHNDGPRLVKILKALRCRVDLSPEISVVRDIRDREVHIFTDAGRVCRPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+   +L   +++   +           T M     +        K    ++ + A   
Sbjct: 238  VDECKLLLTKRHIELLKLQEKLDSFDDQKTSMSVQDRE--------KIKNQMQYIGADEE 289

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +        +   +  R    T  + R  + +G    +       PS  LG
Sbjct: 290  ETCLICMSYEDLLDAKYFFDHHQP-RPKNITDFSARVTMDMGVYSTKWTHCEIHPSMILG 348

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +                         
Sbjct: 349  -------ICASIIPFPDHNQSPRNTYQSAMGKQAMG------------------------ 377

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                +S   L+      +  +        +    +       +   +  + AI      +
Sbjct: 378  --IYLSNYQLRM---DTLANILYYPQKPLVATRSMEYLRFRELPAGQNAIVAILCYSGYN 432

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +     +  +   +      V  +++E+  +   +  + L    Y
Sbjct: 433  QEDSVIMNQSSIDRGLFRSMFYRTYMDQE----KQVGSKKLEIFEKPTRESTLRLKHGTY 488

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  +  D                DE++ +     K 
Sbjct: 489  EKLEDDGLIAPGIRVSGDDIIIGKTVPIPDD----------------DEELGQRTNHTKR 532

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E    +++      D +     + VKV V   R  Q GDK A RHG KG +
Sbjct: 533  DASTPLRSTETGIVDQVMLTTNNDGL-----KFVKVRVRSTRVPQMGDKFASRHGQKGTI 587

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  DG   D+++NP  +PSRM +G + E  LG     LG +  +      
Sbjct: 588  GVTYRQEDMPFTADGLTPDLIINPHAIPSRMTIGHLVECLLGKVGTMLGAEGDATPFTDV 647

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                IS                           L +    K G  V              
Sbjct: 648  TVDSISKQ-------------------------LELRGYQKRGFEV-------------- 668

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                           +Y+G TG      V  G  Y  +L HMV DK+++R+ G   ++T+
Sbjct: 669  ---------------MYNGHTGRKLTAQVYFGPTYYQRLKHMVDDKIHSRARGPVQILTR 713

Query: 1281 QPLGGKSNRGGQRL 1294
            QP+ G+S  GG R 
Sbjct: 714  QPVEGRSRDGGLRF 727


>gi|52694219|emb|CAG30639.1| DNA-directed RNA polymerase beta chain [Pseudomonas tolaasii]
          Length = 344

 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 202/343 (58%), Positives = 264/343 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLIN KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINFKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SE
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSE 344


>gi|66876507|gb|AAY58045.1| RpoB [Cuscuta europaea]
          Length = 403

 Score =  335 bits (858), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 135/439 (30%), Positives = 205/439 (46%), Gaps = 52/439 (11%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E  +   + LL A    +  +  D  L     +S  +V   I+    I K E    V  +
Sbjct: 17   EGELALGKTLLVAYMPWEGYNFEDAVL-----ISERLVYEEIYTSLHIRKFEIQTHVTSQ 71

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E + ++    +  L RN+      I+ G     G     K T       S  P  +  
Sbjct: 72   GPEQVTKEIPHLEAHLIRNL-DINGIIMQGSWVQPGDVLVGKLTPHVVKESSYAPEDRLL 130

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +  +  +        LKV       +++ R+  K         +       ++V+V  KR
Sbjct: 131  RAILGIQVSTSKETCLKVPIGGRGRVIDVRWIQKK-------GVYNSNPEKIQVYVLQKR 183

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I+ GDK+AGRHGNKGI+S+IL  +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG
Sbjct: 184  EIKVGDKIAGRHGNKGIISKILSRQDMPYLQDGRAVDLVFNPLGVPSRMNVGQIFECSLG 243

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   L +  +    D +                   +  + +     ++  + A  W  
Sbjct: 244  LAGSLLNRHYRIAPFDER---------------YEQEASRKIVFSQLHEASKKTAHPW-- 286

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                    F+                +  G+S ++DG TG PF++P+ +G  Y+LKL H 
Sbjct: 287  -------AFE---------------PEYPGKSRIFDGRTGNPFEQPILIGKAYILKLIHQ 324

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            V DK++ RS+G Y+LVTQQPL G++ +GGQR+GEMEVW ++ +G A++L EMLT KSD +
Sbjct: 325  VDDKLHGRSSGHYALVTQQPLRGRAKQGGQRVGEMEVWALEGFGVAHILHEMLTYKSDHI 384

Query: 1323 VGRTRVYESIVAGNDTFET 1341
              R +V  + + G      
Sbjct: 385  RARQQVLGTTILGGTIPHP 403



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 78/190 (41%), Positives = 127/190 (66%), Gaps = 6/190 (3%)

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
             +++  ++A+G +T  G+LALG+ +LVA+MPW GYNFED++LISER+V E+++TS+HI 
Sbjct: 1   QFIKKGQVLAEGAATVEGELALGKTLLVAYMPWEGYNFEDAVLISERLVYEEIYTSLHIR 60

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP--KGE 903
           +FE+    T  GPE++T++IP++    ++N+D  GII  G+ V PGD+LVGK+TP    E
Sbjct: 61  KFEIQTHVTSQGPEQVTKEIPHLEAHLIRNLDINGIIMQGSWVQPGDVLVGKLTPHVVKE 120

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI----SV 959
           S   PE++LLRAI G +    ++T L+VP G  G V+DVR   + G+  +         +
Sbjct: 121 SSYAPEDRLLRAILGIQVSTSKETCLKVPIGGRGRVIDVRWIQKKGVYNSNPEKIQVYVL 180

Query: 960 EREQIELLAR 969
           ++ +I++  +
Sbjct: 181 QKREIKVGDK 190


>gi|226897632|gb|ACO90265.1| RNA polymerase beta subunit gene [Bacillus cereus]
          Length = 402

 Score =  335 bits (858), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 231/378 (61%), Positives = 290/378 (76%), Gaps = 3/378 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           G NIGL++SL+SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L
Sbjct: 1   GPNIGLINSLSSFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKL 60

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            ++G F  E +  R  GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG 
Sbjct: 61  SDEGEFLSEDIVARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGA 120

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLD 753
           NMQRQAVPL+  E+P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D  
Sbjct: 121 NMQRQAVPLMNPESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQ 180

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                +D Y++ KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV
Sbjct: 181 TVKGDLDRYKMQKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLV 240

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L
Sbjct: 241 GFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDAL 300

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP 
Sbjct: 301 RNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPH 360

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G ++DV++FNR   D
Sbjct: 361 GGGGIILDVKVFNREDGD 378



 Score = 51.6 bits (122), Expect = 0.001,   Method: Composition-based stats.
 Identities = 46/275 (16%), Positives = 92/275 (33%), Gaps = 15/275 (5%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 141  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 200

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 201  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 255

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 256  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 313

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 314  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 367

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              K+   + GD++PPGV ++V+ ++  KR I  GD
Sbjct: 368  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGD 402


>gi|288561072|ref|YP_003424558.1| DNA-directed RNA polymerase subunit B' RpoB1 [Methanobrevibacter
            ruminantium M1]
 gi|288543782|gb|ADC47666.1| DNA-directed RNA polymerase subunit B' RpoB1 [Methanobrevibacter
            ruminantium M1]
          Length = 603

 Score =  335 bits (858), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 128/658 (19%), Positives = 221/658 (33%), Gaps = 97/658 (14%)

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            + A+R       +               +  G     L+  ++            +  G+
Sbjct: 26   MRARRRSGEIHNEMNITYYDENHEIYIFTDPGRARRPLILVEKGEPLLKDEHIEAITKGE 85

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
               + D + +    +  D     N  +A            + I    +       I   +
Sbjct: 86   L--KWDNLFELGLLEYLDAEEEENSYIAMNLSQLNEDHTHLEIDPSTMLGICAGIIPFSD 143

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                 R+T             VS   L+  D  G   +        +    I        
Sbjct: 144  HNSSPRNTMEAGMTKQALGLYVSNYALRT-DTRG--HLLHHPQTPLVKTRIIDAINYDDR 200

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
               + L+ A+   +  ++ D  +   S +    +    F R       R    + ++ E 
Sbjct: 201  PSGQNLVVALMSYEGYNMEDAMILNKSSLERG-MGRSSFFRSYEASERRYPGGQEDKFER 259

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              +        +         + L     V+     +   VL           +  +F  
Sbjct: 260  PEKG-------VKGYRSEEAYKNLDEDGIVNPESHVESGDVLIGKTSPPRFLGEIDEFGT 312

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
              EK +    +++   +     +      +  K+              K+ V   R  + 
Sbjct: 313  VAEKRRETSVTVRHGEKGIVDAVLLTETVEGSKLT-------------KIRVRDTRQPEF 359

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG+V  IL  +D+PF +DG   DI++NP  +PSRM+VGQ+ E   G A  
Sbjct: 360  GDKFASRHGQKGVVGLILSQDDIPFTEDGVVPDIIVNPHAIPSRMSVGQVLEMVAGKAGC 419

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G ++                                                      
Sbjct: 420  MEGHRMDG---------------------------------------------------- 427

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             TP F+   E  I   L     + +G   LY+G+TGE  +  + VG  Y  KL+HM +DK
Sbjct: 428  -TP-FNDNVEGEIKRALHDNGFESAGCESLYNGVTGERIEAEIFVGVAYYQKLHHMTTDK 485

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG-- 1324
            VYARSTG   ++T+QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD      
Sbjct: 486  VYARSTGPVQVLTRQPTEGRAREGGLRFGEMERDCLIAHGAALALKERLLDESDKYEAVV 545

Query: 1325 -------------RTRVYESIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                         + ++Y   + G+ +T+      +F +L+ E+++L +   L     
Sbjct: 546  CNECGMLAVYDKNKNKMY-CPICGDSETYPVEISYAFKLLLDELKSLCIFPKLILGDK 602



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           I     K  +      + YL A EEEN YIA   S L+ED                    
Sbjct: 81  ITKGELKWDNLFELGLLEYLDAEEEENSYIAMNLSQLNEDH------------------- 121

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P  ++ I A +IPF +++ S R  M   M +QA+ L  +    
Sbjct: 122 ----THLEIDPSTMLGICAGIIPFSDHNSSPRNTMEAGMTKQALGLYVSNYAL 170


>gi|111054599|gb|ABH04357.1| RNA polymerase beta subunit [Providencia alcalifaciens]
          Length = 340

 Score =  334 bits (857), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 210/340 (61%), Positives = 264/340 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N  GF+ETPYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEXGFLETPYRL 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT+++ YLSA+EE N  IAQAN+ L +DG F EELV CR  GE  L  RE+++++
Sbjct: 121 VRDGIVTDEIHYLSAIEEGNFIIAQANTVLSDDGRFIEELVTCRNKGESSLFSREQVEYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQA P L+A+ P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAXPTLRADKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VA+R G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVARRGGLVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSL 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFE
Sbjct: 301 GEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 340


>gi|313611127|gb|EFR85969.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes FSL
            F2-208]
          Length = 178

 Score =  334 bits (857), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 87/155 (56%), Positives = 113/155 (72%)

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A +    ++ILYDG +GE FD  ++VG +YM+KL HMV DK++ARSTG YSLVTQQPLG
Sbjct: 1    EAGMARDAKTILYDGRSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLG 60

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G P
Sbjct: 61   GKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVP 120

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            ESF VL+KE+Q+LG+ + + ++  +     +   D
Sbjct: 121  ESFKVLIKELQSLGMDVKMLSADEEEIEMRDMDDD 155


>gi|34494014|emb|CAD66150.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 210/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ AS IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASXIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|52694371|emb|CAG38025.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 335

 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 203/336 (60%), Positives = 259/336 (77%), Gaps = 1/336 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDL NAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLFNAKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA R+V+R  +G+++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDASRVVVRVHDGEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVERGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           DGPSTD+G LALG+NM V FMPW+GYNFEDS+L+SE
Sbjct: 300 DGPSTDMGQLALGQNMRVEFMPWNGYNFEDSILLSE 335


>gi|81171073|gb|ABB58763.1| RNA polymerase beta subunit [Acholeplasma pleciae]
          Length = 628

 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 231/452 (51%), Positives = 304/452 (67%), Gaps = 30/452 (6%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 2   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 61

Query: 590 ARVNAYGFIETPYRKV----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           A+V+ YGFI+TP+ KV     + KVT +V+YL+A EE +  IA A + +D+ G FTE  V
Sbjct: 62  AKVDEYGFIKTPFLKVIHNGDESKVTQEVIYLTADEEADHVIASAATPMDDQGVFTETRV 121

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R +GE  +    +I  +D SPKQVVS+A S IPFLE+DD++R LMG NMQRQAVPLL+
Sbjct: 122 IARRSGETAIFDANEITAMDVSPKQVVSVATSSIPFLEHDDASRALMGANMQRQAVPLLQ 181

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV------ 759
             +P VGTG+E   AK SGA ++AK +G V  VDA +I+I +   +     S        
Sbjct: 182 PTSPIVGTGIEYRAAKDSGAVVIAKASGYVTYVDAKKIIITNEPTEHVKVGSKTIYKVGG 241

Query: 760 ------------------DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                             D Y L++F RSNQ+T V Q+P+V  G+ V    +IADGPSTD
Sbjct: 242 EFDYGIAKKLYDLKLADNDQYDLIQFFRSNQDTLVLQKPIVFQGEYVNEGHVIADGPSTD 301

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LGPE 859
            G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G E
Sbjct: 302 NGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQANGKE 361

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ G+
Sbjct: 362 EITREIPNVGQEAIKFLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVIGD 421

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 422 KAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 453



 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 118/413 (28%), Positives = 182/413 (44%), Gaps = 65/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  VN G ++    +      +     +  A    +  +  D  +     V   V 
Sbjct: 281  IVFQGEYVNEGHVIADGPSTDN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 339

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   +  +E+I     +   E +            I+ G     G  
Sbjct: 340  TSIHIDEYEIETRDLKQANGKEEITREIPNVGQEAI----KFLDERGIIVPGSEVKEGDI 395

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 396  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 451

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V+VA KR I  GDKMAGRHGNKG++S+ILP EDMP+L+DGT VDI
Sbjct: 452  --GDQLPSGVNEQIRVYVAKKRKITEGDKMAGRHGNKGVISKILPREDMPYLEDGTYVDI 509

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ S + D   N +++ +            
Sbjct: 510  MLNPLGVPSRMNIGQILEIHLGISAQKLGIKVASPVFDGVTNDELAAIMEEAGVAPDGK- 568

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T ++DG                           
Sbjct: 569  ---------------------------TTLYDG--------------------------R 575

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE ++  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 576  TGEAYNNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 628


>gi|34494354|emb|CAD98752.1| RNA polymerase beta subunit [Enterobacter nimipressuralis]
 gi|34494356|emb|CAD98753.1| RNA polymerase beta subunit [Enterobacter amnigenus]
 gi|34494368|emb|CAD98759.1| RNA polymerase beta subunit [Enterobacter nimipressuralis]
          Length = 336

 Score =  334 bits (857), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 208/336 (61%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L   +++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34493892|emb|CAD66089.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493894|emb|CAD66090.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493896|emb|CAD66091.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493898|emb|CAD66092.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493902|emb|CAD66094.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493904|emb|CAD66095.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493906|emb|CAD66096.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493908|emb|CAD66097.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493910|emb|CAD66098.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493912|emb|CAD66099.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493916|emb|CAD66101.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493918|emb|CAD66102.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493922|emb|CAD66104.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493924|emb|CAD66105.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493926|emb|CAD66106.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493928|emb|CAD66107.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493930|emb|CAD66108.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493932|emb|CAD66109.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493934|emb|CAD66110.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493936|emb|CAD66111.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493938|emb|CAD66112.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493940|emb|CAD66113.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493942|emb|CAD66114.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493944|emb|CAD66115.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493946|emb|CAD66116.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493948|emb|CAD66117.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493950|emb|CAD66118.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493952|emb|CAD66119.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493954|emb|CAD66120.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493956|emb|CAD66121.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493962|emb|CAD66124.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493964|emb|CAD66125.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493966|emb|CAD66126.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493968|emb|CAD66127.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493970|emb|CAD66128.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493972|emb|CAD66129.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493976|emb|CAD66131.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493978|emb|CAD66132.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493980|emb|CAD66133.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493984|emb|CAD66135.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493986|emb|CAD66136.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493990|emb|CAD66138.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493992|emb|CAD66139.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493994|emb|CAD66140.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34493998|emb|CAD66142.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494000|emb|CAD66143.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494004|emb|CAD66145.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494008|emb|CAD66147.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494010|emb|CAD66148.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494012|emb|CAD66149.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494016|emb|CAD66151.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494018|emb|CAD66152.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494020|emb|CAD66153.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494024|emb|CAD66155.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494026|emb|CAD66156.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494028|emb|CAD66157.1| RNA polymerase beta subunit [Enterobacter hormaechei]
 gi|34494030|emb|CAD66158.1| RNA polymerase beta subunit [Enterobacter cloacae subsp.
           dissolvens]
 gi|34494032|emb|CAD66159.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|34494034|emb|CAD66160.1| RNA polymerase beta subunit [Enterobacter asburiae]
 gi|34494366|emb|CAD98758.1| RNA polymerase beta subunit [Enterobacter kobei]
          Length = 336

 Score =  334 bits (856), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|318603119|emb|CBJ04599.1| RNA polymerase beta subunit [Pseudomonas sp. R-38666]
          Length = 345

 Score =  334 bits (856), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 203/338 (60%), Positives = 265/338 (78%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+
Sbjct: 1   MPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LS
Sbjct: 61  RDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASL
Sbjct: 121 AIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ V
Sbjct: 181 IPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSV 240

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGP
Sbjct: 241 DASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGP 300

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           STD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V +
Sbjct: 301 STDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQK 338


>gi|34493920|emb|CAD66103.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  334 bits (856), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERMSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34493960|emb|CAD66123.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  334 bits (856), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVALG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34494022|emb|CAD66154.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  334 bits (856), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 211/335 (62%), Positives = 263/335 (78%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 2   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 61

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 62  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D 
Sbjct: 122 DGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 182 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 242 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 301

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 302 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34493982|emb|CAD66134.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  334 bits (856), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 211/335 (62%), Positives = 263/335 (78%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 2   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 61

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 62  GGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D 
Sbjct: 122 DGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 182 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 242 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 301

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 302 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|111054573|gb|ABH04344.1| RNA polymerase beta subunit [Proteus vulgaris]
          Length = 338

 Score =  333 bits (855), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 207/338 (61%), Positives = 258/338 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ ++
Sbjct: 121 VENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VAKR G V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVAKRGGXVQYVDASRIVIKVNEDETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSL 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           G+ V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 301 GEPVDRGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 338


>gi|111054603|gb|ABH04359.1| RNA polymerase beta subunit [Providencia stuartii]
          Length = 336

 Score =  333 bits (855), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 262/336 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVR 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQAN+ L EDGSF EEL+ CR  GE  L  R++++++D 
Sbjct: 121 DGIVTDEIHYLSAIEEGNFIIAQANTVLAEDGSFVEELITCRNRGESSLFSRDQVEYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 301 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 336


>gi|34493958|emb|CAD66122.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  333 bits (855), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD +G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDNEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|73697695|gb|AAZ81464.1| RNA polymerase beta subunit [Mycoplasma meleagridis]
          Length = 595

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 212/422 (50%), Positives = 300/422 (71%), Gaps = 8/422 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L 
Sbjct: 1   QINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A++N YGF++TPY KV +G V  + V YL+A EE N YIAQ+   +D++     + + 
Sbjct: 61  TYAKINEYGFLQTPYFKVENGIVQYDKVEYLTATEEINFYIAQSTVKVDKNNRIIGDQIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     +L   E ID+I+ +  Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ 
Sbjct: 121 MRHNYTYVLEKPEIIDYIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQT 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFV TG+ES +AK S A   AK +G+VE VD  +I +R+ +  LD        Y L  
Sbjct: 181 EAPFVATGLESAIAKYSSANFTAKHSGVVEYVDGSKIKVRNNKNTLD-------TYSLKN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQ+T V+QRPLVKVG EV + D++ DG S   G+L+LG+N++VAF  + GYN+ED+
Sbjct: 234 FQRSNQDTVVHQRPLVKVGQEVNKGDLLVDGSSFKNGELSLGKNLVVAFTTYKGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++ER+V +DV TSIHIEE  +  R +++G +E+T DIPNVS+  ++N+DE GI+ VG+
Sbjct: 294 IILNERLVKDDVLTSIHIEEHTIQFRTSRMGDDELTVDIPNVSKASIRNLDENGIVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGD+LVG+++PKG+   + EEKLL A+ G++  +V+DTSL+V +G  GTV+ V + N
Sbjct: 354 EVIPGDVLVGRVSPKGDENPSQEEKLLSAVLGQRLSNVKDTSLKVKNGHGGTVIAVEVLN 413

Query: 947 RH 948
           R 
Sbjct: 414 RD 415



 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 148/521 (28%), Positives = 215/521 (41%), Gaps = 72/521 (13%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E ++   +   + 
Sbjct: 143  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQTEAPFVATGLESAIA--KYSSAN 200

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
                   + E+   ++  K+   + T D  ++      N D    +  ++ VG EVN GD
Sbjct: 201  FTAKHSGVVEYVDGSK-IKVRNNKNTLDTYSLKNFQRSNQDTVVHQRPLVKVGQEVNKGD 259

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +LV   + K    ++  + L+ A    K  +  D  +     V   V+       H I  
Sbjct: 260  LLVDGSSFKN-GELSLGKNLVVAFTTYKGYNYEDAIILNERLVKDDVLTSIHIEEHTIQF 318

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               S   + E    +          LD N   R+   +   + + G    K     S + 
Sbjct: 319  -RTSRMGDDELTVDIPNVSKASIRNLDENGIVRVGSEVIPGDVLVGRVSPKGDENPSQE- 376

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   +   Q     +     V++       +  +L     +             GV +
Sbjct: 377  -EKLLSAVLGQRLSNVKDTSLKVKNGHGGTVIAVEVLNRDSDSNA-------QFEDGVDK 428

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP+L+DGTPVD++LNP GVPSRMN
Sbjct: 429  IIKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPYLEDGTPVDVMLNPQGVPSRMN 488

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLG A   L  K  +   D     DI                           
Sbjct: 489  IGQVLEIHLGMAAKSLQCKFVTPTFDGIKKEDI--------------------------- 521

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                              F+   E           L ESG+  L D +TG+ FD PV+VG
Sbjct: 522  ------------------FELIKEAK---------LPESGKQFLIDPITGQKFDNPVSVG 554

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 555  VMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 595


>gi|297527625|ref|YP_003669649.1| DNA-directed RNA polymerase subunit B [Staphylothermus hellenicus DSM
            12710]
 gi|297256541|gb|ADI32750.1| DNA-directed RNA polymerase subunit B [Staphylothermus hellenicus DSM
            12710]
          Length = 1156

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 88/333 (26%), Positives = 141/333 (42%), Gaps = 72/333 (21%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            R   K               R+VK  V   R  + GDK A RHG KG++  ++P +DMPF
Sbjct: 874  RHGEKGIVDLVMVTTDIDGNRLVKARVRDLRIPELGDKFASRHGQKGVIGLLVPQQDMPF 933

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             ++G   D+++NP   PSRM VGQ+ E+  G A    G+ + +     +   ++      
Sbjct: 934  TEEGIVPDLIINPHAFPSRMTVGQLIESIAGKAAALEGRFVDATPFHKEPIENLMITLK- 992

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                         + G P+                        S
Sbjct: 993  -----------------------------RHGYPM------------------------S 999

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G   +YDG TGE    P+ +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG
Sbjct: 1000 GYETMYDGRTGEILKTPIFIGIVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAKEGG 1059

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESI----------VA 1334
             R GEMEV C+  +GA+ +L+E +  KSD       ++ G    Y+ I            
Sbjct: 1060 LRFGEMEVDCLVGHGASLLLKEQMLDKSDKTTIYVCELCGHIGYYDRIRGKYVCPIHKDK 1119

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            G          +F +LV+E+ ++ +   L+   
Sbjct: 1120 GKLKP-VKVSYAFKLLVQELMSMCIMPRLKLED 1151



 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 158/1026 (15%), Positives = 302/1026 (29%), Gaps = 225/1026 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-PPKF- 86
           L+     SY+ F+          +  L         I   SG+  L    Y     PK  
Sbjct: 26  LVRQHLDSYNRFI----------DHLLPEIISEHKEIK-ISGSRKLLIKGYRIGNEPKIR 74

Query: 87  ---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  R+ TYAVP+ + + L                 KEQ I + DLP+
Sbjct: 75  TIEGFERTVTPLECRLRNFTYAVPVYLRVALQD----------ETGIYKEQEIKLMDLPV 124

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHR-SPGIHFDHDKGRA 172
           M K                         G F+I G ++++V+Q    S  I  D+    +
Sbjct: 125 MLKSKIDPLSKMTAEELIAIGEDPKDPGGYFIINGSEKVLVAQEDLASNNILIDYASEGS 184

Query: 173 SLSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
           S +    +  ++I     +   + IE     I +  +   R +PV   + ALG+ SE  +
Sbjct: 185 SAT----HIAKVISVAKGRRSQLVIERRKDGIFYANLHGHR-IPVVILMTALGLASELEI 239

Query: 230 ----------------------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
                                 S F    +           +         +++   +  
Sbjct: 240 THAVSLDPDLQTYLLPSIMQAQSIFPKLEIPENASSEEQKRIEEEHRRKTIEIALDYIGA 299

Query: 268 DTG------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
                    E++  + + L   LL  +  +    +        G  V + I      E+ 
Sbjct: 300 RIAIGRPREERIRRAQRALDEYLLPHIGTEPTPEVRRKKAYFIGQMVNKLI------ELI 353

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +      D+            D+    +       +IR    + +    K   LD+  V+
Sbjct: 354 VGRRKPDDKDHYRNKRLKLAGDLLAQLIRHNLVTYFIREVKSSIERSYSKYGKLDLKLVI 413

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL-----------DTPDDVRH 430
           +PG + T  +  +M    +          + R  +   L+                + R 
Sbjct: 414 KPGML-TDRILHAMATGNWPGGKTGVSQLLDRTNLMSTLSHLRRVVSPLKRTQPHFEARE 472

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--LGLLRMERSIKE 488
           +       +           G + ++  + +  V    E ++      LG+  +E  I E
Sbjct: 473 LHPTQWGRMCPFETPEGANIGLVKNLALMAHVSVGVPEEHIEPILYEKLGVKSIEEIIGE 532

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
              +V  +     D  +   V      +     +    +       I + RR        
Sbjct: 533 VKKAVTGELEEYPDYTSWSRV------YLNGRLIGYYPDGKKLAEEIRNMRRRG-----K 581

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++       ++D H         A       + + +      +      +++   K  D 
Sbjct: 582 ISIEVNVAHIQDEHLNEVYINTDAGRIRRPLLVVENGKLKL-KPEHIAKLKSGEWKFSDL 640

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                + YL A EEE  YIA     +  +                          ++   
Sbjct: 641 VKKGIIEYLDADEEEEAYIALTPDQITPEH-----------------------THMEIWT 677

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ I AS+IP+ E++ S R      M +Q++ L  A                      
Sbjct: 678 PAIMGITASIIPYAEHNQSPRNSYEAAMAKQSLGLYSANFQ------------------- 718

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                                     +   +  Y               Q+PLV+     
Sbjct: 719 ----------------------RRMDTHGHLLHYP--------------QKPLVQTRAME 742

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          +   G+NM+VA M + GYN ED++++++  V   +  S     + 
Sbjct: 743 VNG----------YNERPAGQNMVVAVMSFTGYNIEDALIMNKSSVDRGLARSTFFRLYT 792

Query: 849 VMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            +      G E+     P         +  + +DE GI+     V  GD+L+GKI+P   
Sbjct: 793 TVEYRYPGGQEDKITIPPSNVRGYRGPKAYEKLDEDGIVSPETPVKGGDVLIGKISP--- 849

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
               P     +       +  +D S+    G  G V  V +      ++  ++   +   
Sbjct: 850 ----PRFMTAQEYTVGAGITRQDASVVTRHGEKGIVDLVMVTTDIDGNRLVKARVRDLRI 905

Query: 964 IELLAR 969
            EL  +
Sbjct: 906 PELGDK 911


>gi|80978859|gb|ABB54678.1| RNA polymerase beta subunit [Mycoplasma gallinarum]
          Length = 593

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 213/423 (50%), Positives = 305/423 (72%), Gaps = 7/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLSEISNERRITSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY +V +G V  + V YL+A++E   YIAQ+   +D+D   T+E +  R
Sbjct: 62  AKVNQYGFLQTPYYRVKNGVVQYDKVDYLTAVDEVGFYIAQSTVKVDKDNRITDEQITMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   E +D+I+ +  Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 122 HNYTFIMGGPEDVDYIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+ES +AK S A ++AK+ GIVE VD  +I IR+ EG        +D Y L  FQ
Sbjct: 182 PFVATGIESAIAKYSSANLIAKKDGIVEYVDGKKIKIRTAEGKS------LDTYHLKNFQ 235

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T V+QRP+V+VG ++++ D++ DG S   G+L+LG+N++VAF    GYN+ED+++
Sbjct: 236 RSNQDTVVHQRPIVEVGQQIKKGDLLVDGSSFKNGELSLGKNLVVAFSTMKGYNYEDAII 295

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V EDV TS+HIEE  +  R+++ G +E+T DIPNVS+  L+++DE GI+ VG+EV
Sbjct: 296 LNERLVKEDVLTSVHIEELVIQFRNSRAGNDELTNDIPNVSKHSLRHLDENGIVRVGSEV 355

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL AI  ++  +V+DTSL+V +G SGTV+ V + +R 
Sbjct: 356 TPGDVLVGRVSPKGDDNPSQEEKLLSAILAQRQQNVKDTSLKVKNGHSGTVIGVELLSRE 415

Query: 949 GID 951
             D
Sbjct: 416 NND 418



 Score =  310 bits (795), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 146/521 (28%), Positives = 211/521 (40%), Gaps = 73/521 (14%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L A  P+     E ++   +   + 
Sbjct: 142  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQAEAPFVATGIESAIA--KYSSAN 199

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             +     I E+    +      E  + D  ++      N D    +  I+ VG ++  GD
Sbjct: 200  LIAKKDGIVEYVDGKKIKIRTAEGKSLDTYHLKNFQRSNQDTVVHQRPIVEVGQQIKKGD 259

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +LV   + K    ++  + L+ A    K  +  D  +     V   V+   +     + +
Sbjct: 260  LLVDGSSFKN-GELSLGKNLVVAFSTMKGYNYEDAIILNERLVKEDVL-TSVHIEELVIQ 317

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               S +   E    +          LD N   R+   +   + + G    K     S + 
Sbjct: 318  FRNSRAGNDELTNDIPNVSKHSLRHLDENGIVRVGSEVTPGDVLVGRVSPKGDDNPSQE- 376

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   +   Q     +     V++          +L           +  D    GV +
Sbjct: 377  -EKLLSAILAQRQQNVKDTSLKVKNGHSGTVIGVELLSR---------ENNDQFEDGVDK 426

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP+L+DGTPVD++LNP GVPSRMN
Sbjct: 427  LVKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPYLEDGTPVDVILNPQGVPSRMN 486

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E  LG A   L  K  +   D     DI                           
Sbjct: 487  IGQVLEIQLGLAAKSLQTKFVTPAFDGIKRDDIMA------------------------- 521

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                   EE        A L  SG+  L D +TG  FD PV+VG
Sbjct: 522  ---------------------VTEE--------AGLPVSGKQFLIDPITGRRFDNPVSVG 552

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 553  VMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 593


>gi|318603108|emb|CBJ04597.1| RNA polymerase beta subunit [Pseudomonas sp. R-38645]
          Length = 333

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 199/333 (59%), Positives = 258/333 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           LG+NM +AFM W+GYNFEDS+ +SER+V ED F
Sbjct: 301 LGQNMRIAFMAWNGYNFEDSICLSERVVQEDRF 333


>gi|226897634|gb|ACO90266.1| RNA polymerase beta subunit gene [Bacillus firmus]
          Length = 368

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 226/367 (61%), Positives = 287/367 (78%), Gaps = 3/367 (0%)

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQA 630
           ET EG NIGL++SL+SFA+VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQA
Sbjct: 1   ETPEGPNIGLINSLSSFAKVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQA 60

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           N+ L +DGSF +E V  R  GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR 
Sbjct: 61  NALLGDDGSFLDEEVVARFKGENTVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRA 120

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPL++ EAP VGTGME V  K SGAA++ K  GIVE V+A  + +R ++ 
Sbjct: 121 LMGANMQRQAVPLMQPEAPRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIKN 180

Query: 751 -DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            D       +D YR++KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGR
Sbjct: 181 VDGQEVKGDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGR 240

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVAFM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV 
Sbjct: 241 NVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVG 300

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ L+N+DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSL
Sbjct: 301 EDALRNLDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 360

Query: 930 RVPSGVS 936
           RVP G S
Sbjct: 361 RVPHGGS 367


>gi|34493974|emb|CAD66130.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 210/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +A  EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAGKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|52694335|emb|CAG38007.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. III]
          Length = 344

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 204/344 (59%), Positives = 266/344 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D 
Sbjct: 121 DALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 344


>gi|228481105|gb|ACQ42251.1| RNA polymerase beta subunit [Mycoplasma microti]
          Length = 661

 Score =  333 bits (855), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 138/510 (27%), Positives = 228/510 (44%), Gaps = 63/510 (12%)

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG--------- 880
            +E  ++ D   ++   E +        G +   ++   V +  L   ++           
Sbjct: 171  NEYKIAHDSGMAVVYNEEKDGEVVYVDGSKIKIKNQQGVKDYDLLKFNKSNQNTCNNQTP 230

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            ++ +G +V  GD +           +   +  L A       +  D  +           
Sbjct: 231  LVSLGDKVKKGDTIADGP-AMCNGELALGQNALVAFTTWSGYNYEDAIILSKRLFTEDVF 289

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  +V+  I      + +E          E   R  DDE  I+      +  ++L G+ 
Sbjct: 290  TSIHIVEYSIECLRTKNGDEEITRDIPNVSESSKRYLDDE-GIIMIGAEVKEGDVLVGKI 348

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G         L   +  +  ++            +     +    E + +++     
Sbjct: 349  SPKGQVELSSEEKLLQAIFGDKSKNH-----------KETSLKVPHGGEGTVALV----- 392

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K+Q   ++   V+  +KV+V  KR IQ GDKMAGRHGNKGI+S+I+P EDMP L+D
Sbjct: 393  -KRFKVQDDYELDADVIEQIKVYVVQKRKIQIGDKMAGRHGNKGIISKIVPVEDMPHLED 451

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL-----------GKKIKSLINDYKANG 1163
            GTP+DI+LNP+GVPSRMN+GQI E HLG+A   +             K+   +  +  N 
Sbjct: 452  GTPIDIMLNPVGVPSRMNIGQILELHLGFAMKKITLIKFLELVFENAKLDEYVQWFGLNE 511

Query: 1164 DISPLRSF-------LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV--PVSTPVFDGA 1214
            +++             +++       ++ S++D    L  A   +  +   V+TPVF+G 
Sbjct: 512  NLAKALVKNVKKLLDDKEIKSFEQAKKEFSEFDFVIALTRAGISRDQIVYKVATPVFEGV 571

Query: 1215 DEEAINSMLRMADLDE---------SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +   ++  ++ A +D          SG+  L DG TGE FD  ++VG +YMLKL+HMV D
Sbjct: 572  NRNDLSEAMKEAGIDPITSEEGKGKSGKFKLIDGRTGEYFDGAISVGVMYMLKLDHMVDD 631

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            K+++R+ G YS +TQQPLGGKS  GGQR G
Sbjct: 632  KIHSRAVGPYSKITQQPLGGKSQNGGQRFG 661



 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 208/428 (48%), Positives = 293/428 (68%), Gaps = 12/428 (2%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           +G GG++R    +++RDVH +HYG+ICP ET EG NIGL+ SL S+A  +  GF+ TPYR
Sbjct: 1   MGPGGISREDPNLDIRDVHYSHYGKICPIETPEGMNIGLIMSLASYAGTDENGFLVTPYR 60

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V  G +T+++ +L+A+ E+   IA +N  + ++  F ++ V CR          EK+D+
Sbjct: 61  VVKKGIITDEIAWLTALREDEYIIACSNLDI-KNNKFKDKKVLCRYRSSWEFFDIEKVDY 119

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVSIAAS IPFLENDD+NR LMG NMQRQA PL++  AP VGTG E  +A  S
Sbjct: 120 LDISPKQVVSIAASSIPFLENDDANRALMGANMQRQATPLVRPIAPIVGTGNEYKIAHDS 179

Query: 724 GAAI--VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
           G A+    ++ G V  VD  +I I++ +G  D        Y L+KF +SNQNTC NQ PL
Sbjct: 180 GMAVVYNEEKDGEVVYVDGSKIKIKNQQGVKD--------YDLLKFNKSNQNTCNNQTPL 231

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V +GD+V++ D IADGP+   G+LALG+N LVAF  W GYN+ED++++S+R+ +EDVFTS
Sbjct: 232 VSLGDKVKKGDTIADGPAMCNGELALGQNALVAFTTWSGYNYEDAIILSKRLFTEDVFTS 291

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHI E+ +    TK G EEITRDIPNVSE   + +D+ GII +GAEV  GD+LVGKI+PK
Sbjct: 292 IHIVEYSIECLRTKNGDEEITRDIPNVSESSKRYLDDEGIIMIGAEVKEGDVLVGKISPK 351

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
           G+  ++ EEKLL+AIFG+K+ + ++TSL+VP G  GTV  V+ F +   D    +  +E+
Sbjct: 352 GQVELSSEEKLLQAIFGDKSKNHKETSLKVPHGGEGTVALVKRF-KVQDDYELDADVIEQ 410

Query: 962 EQIELLAR 969
            ++ ++ +
Sbjct: 411 IKVYVVQK 418


>gi|34494358|emb|CAD98754.1| rpoB [Enterobacter cancerogenus]
          Length = 336

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 209/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           + +R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VNDRLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34494360|emb|CAD98755.1| RNA polymerase beta subunit [Enterobacter cowanii]
          Length = 336

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 208/336 (61%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +K+R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKDRLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQAN++LDE+G F E+LV CR  GE  L   +++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFAEDLVTCRSKGESSLFSADQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVYLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + + R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|269912560|emb|CAY86060.1| RNA polymerase beta subunit [Gluconacetobacter diazotrophicus]
          Length = 325

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 158/328 (48%), Positives = 212/328 (64%), Gaps = 28/328 (8%)

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+
Sbjct: 1   FIINGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIY 60

Query: 204 VRIDRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVY 238
           VRIDR+RK+PVT+ L AL                         GMD++EIL  FY ++V+
Sbjct: 61  VRIDRKRKLPVTTLLYALEGASSAAARAAKVAEGGDVDALEIRGMDADEILGYFYNQVVF 120

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           ++    W  P  A     G K+   LVD  +GE V E+  KLT+ +++ + E   K + +
Sbjct: 121 TKGPKGWARPFDAE-SFRGLKLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLV 178

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
               L G YVA D+VN ETGEIY EAG+ + E  LE +  + +  +P L VD+ N   +I
Sbjct: 179 GPAGLIGRYVAHDLVNMETGEIYAEAGEELTEARLEALEEAGVDQLPTLAVDASN-GPWI 237

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           RNTL  DKN  R+DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNM
Sbjct: 238 RNTLTVDKNTSREDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNM 297

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDL 446
           RL LD PD +R +RKEDI+  +KI+ +L
Sbjct: 298 RLGLDAPDTIRVLRKEDILRTVKIMCEL 325


>gi|242392356|dbj|BAH80391.1| RNA polymerase subunit B' [Natrialba aegyptia]
          Length = 609

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 122/591 (20%), Positives = 209/591 (35%), Gaps = 95/591 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDLNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEVPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEDAYAHLDEDGLVNPETDVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+++NP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTENGVVPDLIVNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELRDGLEDAGFNSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    +V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINVCGQCGMS 557

Query: 1325 ------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY     G   D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVY-CPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 45.5 bits (106), Expect = 0.067,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 45/113 (39%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           ++    +  D      + ++ A EEE+ Y+A     L+ED                    
Sbjct: 85  LQNDELEFEDLVDHGYIEFIDAEEEEDIYVAVDEDDLNEDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMVKQSLGLPSANYRI 174


>gi|256073421|ref|XP_002573029.1| DNA-directed rna polymerase II subunit [Schistosoma mansoni]
 gi|238658199|emb|CAZ29261.1| DNA-directed rna polymerase II subunit, putative [Schistosoma
            mansoni]
          Length = 1304

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 97/497 (19%), Positives = 168/497 (33%), Gaps = 98/497 (19%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +       V   +    +     +++     R     
Sbjct: 874  NVLYYPQKPLVATRSMEYLRFRELPAGINAIVAIATYTGYNQEDSVIINESAIQRGFF-- 931

Query: 953  NERSISVEREQIELLARDKDDEQVI-LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
                    R +     +D++    + L+        +   G       K      +    
Sbjct: 932  --------RSEFYRTYKDQETRHGMDLEEVFEKPNPQNCQGMRHAIYDKLDDDGLIAPGT 983

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
             +S           +   + +  +E  + +Y    + +  R        Q          
Sbjct: 984  RVSGDDVLIGKTITL--PENEDEMEGGQRRYTKRDASVFMRRSEYGIVDQVMVTWNNEGN 1041

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            +  KV V   +  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM
Sbjct: 1042 KFCKVRVRTTKAPQVGDKFASRHGQKGTCGIRYRQEDMPFTCEGITPDIIINPHAIPSRM 1101

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E   G      G+                                         
Sbjct: 1102 TIGHLIECLQGKVSANKGEIGD-------------------------------------- 1123

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP  D  +   I+ +L+      +G  I+Y+G TG   +  + +
Sbjct: 1124 ---------------ATPFNDAVNVRKISLLLQEYGYQHTGNEIMYNGFTGRKLNSQIFL 1168

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y  +L HMV DK+++RS G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L
Sbjct: 1169 GPTYYQRLKHMVDDKIHSRSRGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFL 1228

Query: 1312 QEMLTIKSD-------DVVG-------RTRVYE----------SIVAGNDTFETGTPESF 1347
            +E L   SD       ++ G       R + YE          S+V          P + 
Sbjct: 1229 RERLFFASDPYQVYVCNLCGLIAIAHQRNKTYECRSCKNTTQISLVK--------LPYAC 1280

Query: 1348 NVLVKEMQALGLSIDLE 1364
             +L +E+ ++ ++  + 
Sbjct: 1281 KLLFQELMSMSIAPRMM 1297



 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 141/908 (15%), Positives = 278/908 (30%), Gaps = 135/908 (14%)

Query: 29   LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
            L+  Q  S+D F+  +I    ++ P   LQA  +    I        L+F          
Sbjct: 165  LVRQQLDSFDEFIQTSIQKIVEDSPIIELQAEAQHSGGILETPVQYRLKFEQIYLSKATH 224

Query: 87   ----------DVDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                        +D   R+LTYA PL + + + I+ D  E       K       ++G +
Sbjct: 225  WEKDGSSVPMTPNDARLRNLTYAAPLYVDVMKKIIRDEIEEEKPLEKK-------FIGKI 277

Query: 136  PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
            P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 278  PIMLRSTYCLLSVMSDRDLAELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFKQKD 337

Query: 171  RASLSGKLLYACRIIPDQ-GLWMDIEFDS---KD-----IIHVRIDR-----RRKVPVTS 216
                    + +C     +    + I   +   KD      I  RI       ++++PV  
Sbjct: 338  SKYAYKTEIRSCLEHSSRPASTLWINMMARGGKDGSKRATIGQRIVAILPYIKQEIPVLI 397

Query: 217  FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
               ALG  ++ +IL         ++  +     L  A ++   KV+ + +        + 
Sbjct: 398  VFRALGFVADRDILEHIIYDFDDTEMREMIKPSLDDAFVIQEQKVALNFIGSRGARPGVT 457

Query: 276  SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
              K++     + L+++ +  +G++  C          +      + + A    D    + 
Sbjct: 458  KEKRIKYAK-EILQKETLPHVGVSDFCETRKAYFLGYMVH---RLLLAALKRRDVDDRDH 513

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
              +  +                +            K+  L   + +  G    F++  ++
Sbjct: 514  YGNKRLDL----------AGPLLAFLFRGLFRNLTKEIRLYAQKFIDKG--KDFNLELAI 561

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGK 450
             + +  D  KY L   G      + N   P   + + +    + +  L  L     R+GK
Sbjct: 562  RSQIITDGLKYSL-ATGNWGDQKKANQARPGVSQVLNRLTFASTLSHLRRLNSPIGRDGK 620

Query: 451  GTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
                   +     +    E        ++KN   +  + +       +  ++  S+   +
Sbjct: 621  LARPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLE 680

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
             I    +      F     +       + +  +   RR   +    V+  R   +     
Sbjct: 681  EIAPSAIGKTCKIFVNGCWVGIHSSPDHLMGTLRKLRRQVDVIVSEVSMIRDYRDQEIRI 740

Query: 563  PTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
             T  GRIC P    E   + L  S     +  AY           D  ++  V Y+  +E
Sbjct: 741  YTDAGRICRPLVIVEKGKLLLKRSHIELLKDKAYNR-----YSWQDLVLSGVVEYIDTLE 795

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EE   IA   + +                    +   +     +  P  ++ I AS+IPF
Sbjct: 796  EETVMIAMGPAEMQA-----------------AVNYCKTHTHCEIHPSMILGICASIIPF 838

Query: 682  LENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKSSG 724
             +++ S R      M +QA+                 L   + P V T  ME +  +   
Sbjct: 839  PDHNQSPRNTYQSAMGKQAMGVYISNFHTRMDTLANVLYYPQKPLVATRSMEYLRFRELP 898

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV-----NQR 779
            A I A  A            +   E  +       + YR  K Q +     +        
Sbjct: 899  AGINAIVAIATYTGYNQEDSVIINESAIQRGFFRSEFYRTYKDQETRHGMDLEEVFEKPN 958

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P    G      D + D      G    G ++L+        N ++      R    D  
Sbjct: 959  PQNCQGMRHAIYDKLDDDGLIAPGTRVSGDDVLIGKTITLPENEDEMEGGQRRYTKRDAS 1018

Query: 840  TSIHIEEF 847
              +   E+
Sbjct: 1019 VFMRRSEY 1026



 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 102/683 (14%), Positives = 219/683 (32%), Gaps = 65/683 (9%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  +     I ++    I    +  +    +       +    +         DA +  
Sbjct: 379  GQRIVAILPYIKQEIPVLIVFRALGFVADRDILEHIIYDFDDTEMREMIKPSLDDAFVIQ 438

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 439  EQKVALNFIGSRGARPGV---TKEKRIKYAKEILQKETLPHVGVSDFCETRK---AYFLG 492

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDI 495
             ++  L+     +  +DD D+ GN+R+   G +L   +R     + + I+   +      
Sbjct: 493  YMVHRLLLAALKRRDVDDRDHYGNKRLDLAGPLLAFLFRGLFRNLTKEIRLYAQKFIDKG 552

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I ++ +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 553  KDFNLELAIRSQIITDGLKYSLATGNWGDQKKANQARPGVSQVLNRLTFASTLSHLRRLN 612

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R       R +H T +G ICPAET EGH +GLV +L   A ++         
Sbjct: 613  S----PIGRDGKLARPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 668

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI- 661
              + +  + N      +   +   I      +    S    +   R    ++ V   ++ 
Sbjct: 669  EFLEEWSMENLEEIAPSAIGKTCKIFVNGCWVGIHSSPDHLMGTLRKLRRQVDVIVSEVS 728

Query: 662  ---DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGM- 715
               D+ D   +          P +  +    +L   +++  +       +    V +G+ 
Sbjct: 729  MIRDYRDQEIRIYTDAGRICRPLVIVEKGKLLLKRSHIELLKDKAYNRYSWQDLVLSGVV 788

Query: 716  ESVVAKSSGAAI----VAKRAGIVEQV-DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            E +        +     A+    V          I         ++           + +
Sbjct: 789  EYIDTLEEETVMIAMGPAEMQAAVNYCKTHTHCEIHPSMILGICASIIPFPDHNQSPRNT 848

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIA--------------DGPSTDLGDLALGRNMLVAFM 816
             Q+    Q   V + +   R D +A                      +L  G N +VA  
Sbjct: 849  YQSAMGKQAMGVYISNFHTRMDTLANVLYYPQKPLVATRSMEYLRFRELPAGINAIVAIA 908

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEE 871
             + GYN EDS++I+E  +    F S     ++       +  EE       ++   +   
Sbjct: 909  TYTGYNQEDSVIINESAIQRGFFRSEFYRTYKDQETRHGMDLEEVFEKPNPQNCQGMRHA 968

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                +D+ G+I  G  V+  D+L+GK     E+    E        G++    RD S+ +
Sbjct: 969  IYDKLDDDGLIAPGTRVSGDDVLIGKTITLPENEDEMEG-------GQRRYTKRDASVFM 1021

Query: 932  PSGVSGTVVDVRIFNRHGIDKNE 954
                 G V   ++      + N+
Sbjct: 1022 RRSEYGIV--DQVMVTWNNEGNK 1042


>gi|73697669|gb|AAZ81451.1| RNA polymerase beta subunit [Acholeplasma granularum]
 gi|77543236|gb|ABA87042.1| RNA polymerase beta subunit [Acholeplasma granularum]
 gi|77543238|gb|ABA87043.1| RNA polymerase beta subunit [Acholeplasma granularum]
 gi|77543240|gb|ABA87044.1| RNA polymerase beta subunit [Acholeplasma granularum]
          Length = 628

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 226/453 (49%), Positives = 303/453 (66%), Gaps = 31/453 (6%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 1   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 60

Query: 590 ARVNAYGFIETPYRKVCDG-----KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TP+ KV        +VT +V+YL+A EE    IA A + +++ G F+E  
Sbjct: 61  AKVDEYGFIKTPFLKVVQDDNGQTRVTKEVIYLTADEESEHIIASAATPMNDSGIFSETR 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE  +   E I  +D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 121 VIARQNGETGIFDAEFITAMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---------------- 748
           +  +P VGTG+E   AK SGA ++A+ +G V  VDA +IVI                   
Sbjct: 181 QPTSPIVGTGIEYRAAKDSGAVVIAQNSGYVTYVDARKIVITKEPTEDVKLGSKVIYKAG 240

Query: 749 --------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +   D + +  D Y L++F RSNQ+T + Q+P+V  G+ V + D+I DGPST
Sbjct: 241 GDFNYAIAKKLYDSNLADTDNYDLIQFFRSNQDTLILQKPIVFQGEFVDKGDVIGDGPST 300

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LGP 858
           D G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G 
Sbjct: 301 DKGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQANGK 360

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNV ++ +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ G
Sbjct: 361 EEITREIPNVGQDAVKYLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVIG 420

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 421 DKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 453



 Score =  283 bits (724), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 122/420 (29%), Positives = 184/420 (43%), Gaps = 79/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR----VPSGVS 936
            I+  G  V+ GD ++G      +  +     +  A    +  +  D  +     V   V 
Sbjct: 281  IVFQGEFVDKGD-VIGDGPSTDKGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 339

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARD---KDDEQVILDRNIYSRLMEILCGQ 993
             ++            K          +I  + +D     DE+ I+      +  +IL G+
Sbjct: 340  TSIHIDEYEIETRDLKQANGKEEITREIPNVGQDAVKYLDERGIIVPGSEVKEGDILVGK 399

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G             +    P  +     + D+  +    SL+V +     +   ++
Sbjct: 400  ITPKG-------------VFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQY 446

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K      GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP+L 
Sbjct: 447  FSKKN----GDQLPSGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYLA 502

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT VDI+LNPLGVPSRMN+GQI E HLG A   L  K+ S + D   N ++  +     
Sbjct: 503  DGTYVDIMLNPLGVPSRMNIGQILEIHLGIAAKKLNIKVASPVFDGVTNDELGDIMQEAG 562

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                              T ++DG                    
Sbjct: 563  IAPDGK----------------------------TTLYDG-------------------- 574

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   TGEP++  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 575  ------RTGEPYNNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 628


>gi|15920466|ref|NP_376135.1| DNA-directed RNA polymerase subunit B [Sulfolobus tokodaii str. 7]
 gi|15621249|dbj|BAB65244.1| 1126aa long hypothetical DNA-directed RNA polymerase subunit B
            [Sulfolobus tokodaii str. 7]
          Length = 1126

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 122/614 (19%), Positives = 209/614 (34%), Gaps = 104/614 (16%)

Query: 779  RPLVKVGD--EVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +PLV   D  ++R+ +I  D        +  D     N  +A  P         + I   
Sbjct: 584  KPLVSEDDIEKLRKGEITFDDLVKQGKIEFLDAEEEENAYIALNPQDLTKDHTHLEIWPP 643

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
             +     + I   E     R+T              +   L+         +        
Sbjct: 644  AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLR---TDTRAHLLHYPQKPL 700

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    +   G +        + A+      ++ D  +   S V   +     F       
Sbjct: 701  VGTKILDIIGYNDRPAGNNAILAVMSYTGYNMEDAIIMNKSSVERGMYRSTFF------- 753

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIY-SRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              R  S E  +      DK  +     +    +    +L     VS     K   VL   
Sbjct: 754  --RLYSTEELKYPGGQEDKIMKPEPGTKGYKGNEYYRLLEDNGIVSPEVEVKGGDVLIGK 811

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +       ++ + + +  K   ++  +    E     L    +                 
Sbjct: 812  VSPPRFLQEFKELSPEQSKRDTSI--VTRHGEMGIVDLVLVTE------------SSEGN 857

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++VKV V   R  + GDK A RHG KG++  ++   DMP+   G   DI+LNP  +PSRM
Sbjct: 858  KLVKVRVRDLRIPEIGDKFATRHGQKGVIGMLIDQADMPYTVKGVVPDIILNPHALPSRM 917

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +GQI E   G      GK +                                       
Sbjct: 918  TIGQIMEALAGKYVALTGKPVD-------------------------------------- 939

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP  +    E I   +R + L   G  ++YDG TG+     +  
Sbjct: 940  ---------------ATPFIESPPLEEIRKGIRESGLLPDGTEVVYDGRTGQKLKGRILF 984

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+  +G A ++
Sbjct: 985  GIVYYQKLHHMVADKMHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLI 1044

Query: 1312 QEMLTIKSD-------DVVG--------RTRVYESIVAGN--DTFETGTPESFNVLVKEM 1354
            ++ L   SD       D  G        R + Y   + G   + +      +F +L++E+
Sbjct: 1045 KDRLLDNSDKATIYVCDKCGYIGWYDRARNK-YVCPIHGENANLYPVTVSYAFKLLLQEL 1103

Query: 1355 QALGLSIDLENSRT 1368
             ++ +S  L     
Sbjct: 1104 MSMVISPRLVLGDK 1117



 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 168/1164 (14%), Positives = 330/1164 (28%), Gaps = 256/1164 (21%)

Query: 3    KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
              +  N    + K F K         L+     S++ FL             LQ      
Sbjct: 1    MSLTVNERWEIVKSFFKLRG------LVRQHLDSFNDFLRNK----------LQQIIDEQ 44

Query: 63   FPITAFSGAAMLEFVSYEFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVF 111
              I        ++     +D P           +    +   R+LTYAVPL +T+  I  
Sbjct: 45   GEIITEIPGLKIKLGKIRYDRPGIRETDKGPPKELTPLEARLRNLTYAVPLYLTMIPIEN 104

Query: 112  DVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIK 147
            +++               +Y+GDLP+M K                         G F++ 
Sbjct: 105  NIEGEPI----------EVYIGDLPIMLKSIADPTSNMTYDELIKIGEDPKDPGGYFIVN 154

Query: 148  GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP----DQGLWMDIEFDSKDIIH 203
            G ++++V+Q   +       D G++  +  + +  +I       +             + 
Sbjct: 155  GTEKVIVAQEDLATNRVLV-DYGKSGSN--ITHVAKITSAAAGYR-------------VQ 198

Query: 204  VRIDRRR-------------KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
            V I+R +             K+P    + ALG  ++         IVY+   D       
Sbjct: 199  VVIERLKDSSIQVSFATVPGKIPFVIMMRALGFTTD-------KDIVYAVSLDPEIQNEL 251

Query: 251  AADLMV---GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
               L        V  +L  I     + +  +       + + +  +  +G + +      
Sbjct: 252  LPSLEQASSITTVEDALDFIGNRIAIGQKRENRIQRAEQIIDKYFLPHIGTSPEDRKKKG 311

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
                    +  E+Y+      D+       +            + +   V +  Y     
Sbjct: 312  YYLAAAVNKLLELYLGRRQPDDKDHYANKRVRLAGDLFTSLFRVAFKAFVKDLVYQLEKA 371

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                 +    AL+         D+ T  V  ++    +          + R      L+ 
Sbjct: 372  KVRGRRLSLTALVR-------ADIITERVRHALATGNWVGGRTGVSQLLDRTNWLSMLSH 424

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR 481
                 V  + +       + L   + G+    +  +   +  V+++  + +    +    
Sbjct: 425  LRRV-VSSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALLAQVSVGINESS 483

Query: 482  MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            +E+ I E+      + +                + + + +L         L+      R 
Sbjct: 484  IEKVIYEQGVISQEELIDRLSAEEDINKYLNWSKVYLNGRLLGYYPDGKELAEKIRELRR 543

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            S      V  A    E    +       C         I +          +    +   
Sbjct: 544  SGKISDEVNVAHIVTE----YINEVHINCDGGRVRRPLIIVKDGKP-LVSEDDIEKLRKG 598

Query: 602  YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                 D      + +L A EEEN YIA     L +D                        
Sbjct: 599  EITFDDLVKQGKIEFLDAEEEENAYIALNPQDLTKDH----------------------- 635

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              ++  P  ++ I AS+IP+ E++ S R      M +QA+ L  A               
Sbjct: 636  THLEIWPPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQL----------- 684

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                             + + +  Y               Q+PL
Sbjct: 685  ------------------------------RTDTRAHLLHYP--------------QKPL 700

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V           I D       D   G N ++A M + GYN ED++++++  V   ++ S
Sbjct: 701  V--------GTKILDI--IGYNDRPAGNNAILAVMSYTGYNMEDAIIMNKSSVERGMYRS 750

Query: 842  IHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                 +         G E+               E  + +++ GI+    EV  GD+L+G
Sbjct: 751  TFFRLYSTEELKYPGGQEDKIMKPEPGTKGYKGNEYYRLLEDNGIVSPEVEVKGGDVLIG 810

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K++P        E    ++         RDTS+    G  G V              +  
Sbjct: 811  KVSPPRFLQEFKELSPEQSK--------RDTSIVTRHGEMGIV--------------DLV 848

Query: 957  ISVEREQIELLARDKDDEQVILD--RNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +  E  +   L + +  +  I +      +R   + + G         +    V+   ++
Sbjct: 849  LVTESSEGNKLVKVRVRDLRIPEIGDKFATRHGQKGVIGMLIDQADMPYTVKGVVPDIIL 908

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
            + +            E +     +L  +   +   +E     +I K      + P    V
Sbjct: 909  NPHALPSRMTIGQIMEALAGKYVALTGKPVDATPFIESPPLEEIRKGIRESGLLPDGTEV 968

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNK 1097
            V             D   GR G K
Sbjct: 969  V------------YD---GRTGQK 977


>gi|169837727|ref|ZP_02870915.1| DNA-directed RNA polymerase beta chain [candidate division TM7
           single-cell isolate TM7a]
          Length = 487

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 220/518 (42%), Positives = 319/518 (61%), Gaps = 48/518 (9%)

Query: 216 SFLMALGM--DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            FL A+     +EEI++ F+          +  +  +  +                    
Sbjct: 3   VFLKAVDFFHTNEEIMNEFFELKEVELSEFYSKYKDTELEE------------------- 43

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
                                   I    L G +V ED+++ ETGE   EA ++ID   +
Sbjct: 44  ------------------------ILRSRLEGSFVREDVLDEETGEFVAEAEEIIDIPVI 79

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
           ++I  +++  + I  V   +    I N LV D  K+  +A+++++R +RPGD+ T   A 
Sbjct: 80  QKIIDAKVEKLSIWEVKPEDR--IIANALVHDSTKNSDEAVIEVFRKLRPGDLVTVDSAR 137

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+   +FF+  +YDL+ VGR K+N RL LD P DV  + KED++  I+ + +L +G+G  
Sbjct: 138 SLVKQMFFNPQRYDLADVGRYKVNKRLKLDVPADVIVLTKEDVLQTIEYVKNLVSGEGFT 197

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDIDNL NRRVR VGE+L  Q + G+L+M + ++E+++  DI ++ PQ L+N KP+ + +
Sbjct: 198 DDIDNLSNRRVRGVGELLSIQIKGGMLKMSKMVREKMTIQDITTLTPQSLLNTKPLNALI 257

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF S QLSQ  +  N LS +TH RR+SALG GG++R RAG E+RDVH +HYGRICP E
Sbjct: 258 LEFFGSGQLSQFMDQSNPLSELTHKRRISALGPGGLSRDRAGFEVRDVHNSHYGRICPIE 317

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANS 632
           T EG NIGL++SL+++ +VN YGFIETP+ K+ DGK   ND+ YL+A EEE  +IAQA++
Sbjct: 318 TPEGPNIGLIASLSTYGKVNKYGFIETPFVKINDGKADFNDIRYLAADEEEGLFIAQADT 377

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +D+DG+F  + V CR   E + + + K+D +D SPKQ+VS++A LIPFLE+DD+NR LM
Sbjct: 378 PIDKDGNFLTDEVVCRYGDEIVHIDKSKVDILDVSPKQLVSVSAGLIPFLEHDDANRALM 437

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           G NMQRQAVPLLK EAP+VGTG+E  VA  SGA I +K
Sbjct: 438 GSNMQRQAVPLLKTEAPYVGTGLERKVAVDSGAVITSK 475


>gi|34493914|emb|CAD66100.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 210/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           + ER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VIERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|222445207|ref|ZP_03607722.1| hypothetical protein METSMIALI_00830 [Methanobrevibacter smithii DSM
            2375]
 gi|222434772|gb|EEE41937.1| hypothetical protein METSMIALI_00830 [Methanobrevibacter smithii DSM
            2375]
          Length = 603

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 123/609 (20%), Positives = 205/609 (33%), Gaps = 109/609 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  G+   + D + D    +  D     N  +A            + I    +       
Sbjct: 81   VAKGEL--KWDDLIDNGFIEYLDAEEEENSYIAMSIADLNEDHTHLEIDPATMLGICAGI 138

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   +     R+T             VS   L+         +        +    I   
Sbjct: 139  IPFSDHNSSPRNTMEAGMTKQALGLYVSNYALR---TDTRAHLLHHPQTPIVKTRIIDST 195

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  +     +   +     F R      +R    + 
Sbjct: 196  NYDKRPSGQNFVVALMSYEGYNMEDAMVINKGSLERGLARSSFF-RAYDTAEKRYPGGQE 254

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  ++       +           L     V+     +   VL           + 
Sbjct: 255  DKFEVPDKN-------IKGYRSEDAYRHLDDDGVVNPESYVESGDVLIGKTSPPRFLEEI 307

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +F    EK +    ++             R   K               R+ K+ V   
Sbjct: 308  DEFGTVAEKRRETSVTV-------------RHGEKGIVDAVLLTETVEGSRLAKIRVRDT 354

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  IL  ED+PF + G   D+++NP  +PSRM+VGQ+ E   
Sbjct: 355  RQPEFGDKFASRHGQKGVLGLILSPEDVPFTESGVVPDLIVNPHAIPSRMSVGQVLEMVA 414

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A    G+++                                                 
Sbjct: 415  GKAGCLEGERVDG----------------------------------------------- 427

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F+   E+ I   L+    + +G   LY+G+TGE  +  + VG  Y  KL+H
Sbjct: 428  ------TP-FNTELEKEIKQQLKNHGFESAGCESLYNGVTGERIEAEIFVGVAYYQKLHH 480

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            M +DKVYARS G   ++T+QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD 
Sbjct: 481  MTTDKVYARSRGPVQVLTRQPTEGRAREGGLRFGEMERDCLIAHGAALTLKERLLDESD- 539

Query: 1322 VVGRTRVYESIV-----------AGND-----------TFETGTPESFNVLVKEMQALGL 1359
                   YE+IV              +           T+      +F +L+ E+++L +
Sbjct: 540  ------KYEAIVCENCGMLAVYDKNKNKKYCPICGDVETYPIEISYAFKLLLDELKSLCI 593

Query: 1360 SIDLENSRT 1368
               L     
Sbjct: 594  FPKLVLGDK 602



 Score = 53.5 bits (127), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 61/196 (31%), Gaps = 33/196 (16%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +     L   ++  +  + +   RR   +                +         P    
Sbjct: 7   YINGELLGYCKDPESFTNEMREKRRNGEVSHEMNITYYDKNNEIYIFNDPGRARRPLIIV 66

Query: 576 E-GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           + G  +     L   A+            K  D      + YL A EEEN YIA + + L
Sbjct: 67  KDGKPVLTDKHLEKVAK---------GELKWDDLIDNGFIEYLDAEEEENSYIAMSIADL 117

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +ED                          ++  P  ++ I A +IPF +++ S R  M  
Sbjct: 118 NEDH-----------------------THLEIDPATMLGICAGIIPFSDHNSSPRNTMEA 154

Query: 695 NMQRQAVPLLKAEAPF 710
            M +QA+ L  +    
Sbjct: 155 GMTKQALGLYVSNYAL 170


>gi|300122083|emb|CBK22657.2| unnamed protein product [Blastocystis hominis]
          Length = 1194

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 161/1015 (15%), Positives = 312/1015 (30%), Gaps = 222/1015 (21%)

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            S + +  M   +N+D   +    +   +  ++  L++    +   +D D++ N+R+   G
Sbjct: 302  SRLLQKIMLPHINVDFGPNSNCKKAFYLGYMVHKLLNCSLNRNEQEDRDHISNKRMDLAG 361

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDS-----VMPQDLINAKPVVSAVCEFFCSSQ-- 521
             M+   +   L R  + ++  +  V         +       +  +   +   F +    
Sbjct: 362  PMIGRLFHGLLYRFTKELRSHMKKVVNSRKGSSFINIMTNAKSSIISDGLKYSFATGNWG 421

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ    +   S ++  RRL +     +       + R +H T +G +C
Sbjct: 422  DRSRGMPTTTGVSQSLNRLTYASSLSSLRRLKS----PIDTTSKVTKPRLLHSTQWGMMC 477

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYG----------FIETPYRKVCDGKVTNDVVYLSAM 620
            PAET EG + G+V +L     ++              +E  YR + +  V  ++  +++ 
Sbjct: 478  PAETPEGQSCGIVKNLALMCYISVGNPVGAAGARDWQVEKIYRLLENNGV-EELETIASS 536

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                      N      G   +  V      +         D  +   +          P
Sbjct: 537  LIPKTTKVFVNGVWV--GIHRDPKVILDHREDFDTDVSMVYDIQERELRITADAGRCCRP 594

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D   + +    +++  +  L+ E  F    +                  ++E V A
Sbjct: 595  LYVVDPITQRV---KIRKYHLRNLQPETMFSDLVLNR----------------LIEYVSA 635

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +  DL    + V+      +                              PS 
Sbjct: 636  EEEEYCMIGMDLKTMRACVENRSCTTY------------------------THCEIHPSM 671

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N       S R   +       +  +    R        
Sbjct: 672  ILG-------VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYVSNYRQRM----- 713

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                   V +      +    +T      +      + AI    
Sbjct: 714  ------------------DTTAHVLSYPQQPLVTTKAMTYLRFKELPAGCNCVVAICCYS 755

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER-------SISVEREQIELLARDKDD 973
              +  D+ +   S +   +     +  +   +  R       S+S      E   R   +
Sbjct: 756  GYNQEDSLILNQSAIERGLFRSIFYRTYQDTEVRRDTTTSSLSLSNPSMGNERFCRPLSE 815

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            +  +       R          +      K  + ++ D I     +   +  V      +
Sbjct: 816  QCSMTKDEGLYR---------NLDEDGLVKPGSRVTGDSILIGKATPTGELNVHGRSNLK 866

Query: 1034 NVESLKVQYET-SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            +  +     E+     +      K  +          V              Q GDK++ 
Sbjct: 867  DNSTGLRHAESGIVDEVMLTTNEKGFRFVKVKVRSVRV-------------PQIGDKLSS 913

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   DI++NP  +PSRM +GQ+ E         LGK  
Sbjct: 914  RHGQKGTIGMTYRQEDMPFTENGIVPDIIMNPHAIPSRMTIGQLIE-------CLLGK-- 964

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                        A Q + G   +   F 
Sbjct: 965  ------------------------------------------VAALQAREGDGTA---FS 979

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                E I++ L      + G  +LY+G TG   +  V +G  +  +L H+V DK++AR+ 
Sbjct: 980  DVTVEDISNKLHNEGYQKRGYEVLYNGHTGRRMEARVFMGPTFYQRLKHLVDDKIHARAR 1039

Query: 1273 G----SYSLV--TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------ 1320
            G       ++  T+QPL G+S  GG R+GEME   + AYGA+ +++E     SD      
Sbjct: 1040 GMNTKPGRILHPTRQPLEGRSRDGGLRMGEMERDVLIAYGASQLVRERFFYSSDAYVVTI 1099

Query: 1321 -DVVGRT-----RVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             D  G         Y  I           +   P +  +L +E+ ++ ++  +  
Sbjct: 1100 CDDCGLICTMIDNTY--ICKNCDNKTRFSKVEIPYACKLLFQELMSMNIAPRIHT 1152



 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 131/908 (14%), Positives = 265/908 (29%), Gaps = 178/908 (19%)

Query: 88  VDDCLWRDLTYAVPLKITLRLI-VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD----- 141
             +   R+LTYA  + + +    V      +     K +    I +  +P+M +      
Sbjct: 65  PREARLRNLTYAASIYVGMTQTSVHIKGNESDDAVSKSM---DIRLCTIPVMLRSEACNL 121

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
                              G F+I G ++ +++Q  ++    +  +K       K  +  
Sbjct: 122 YGLDDERRASIGECIYDQGGYFIINGSEKAIIAQERQTTNKVYVFEK---KQPSKYSWTA 178

Query: 183 RI--IPDQGLWM--------------DIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDS 225
            I  +P+ G  +                +  +K  I  ++     ++PV     ALG ++
Sbjct: 179 EIRSVPE-GSSVPAQTLMLCMYAHSSKSQIKNKYCIWAKLPTLSDEIPVCILFRALGCEN 237

Query: 226 E-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           +  I+          +  + +   L  A      +V+ + +     + + E+G +  S  
Sbjct: 238 DRSIIQHICYNFDDVEMMERFRPSLVEASECRTREVALNFIATRHPKMIDENGTRPRSER 297

Query: 285 LKSLKEKGVKFLGITSDCLCG------LYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIF 337
           +K       K +    +   G             +  +     +   +  D   +  +  
Sbjct: 298 VKFASRLLQKIMLPHINVDFGPNSNCKKAFYLGYMVHKLLNCSLNRNEQEDRDHISNKRM 357

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                 I  L+   +        + +      RK +            + +  +  S   
Sbjct: 358 DLAGPMIGRLFHGLLYRFTKELRSHMKKVVNSRKGSSFINIMTNAKSSIISDGLKYSFAT 417

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDD 455
             + D  +   +T G  +   RL   +      R     D  + +     L + +  +  
Sbjct: 418 GNWGDRSRGMPTTTGVSQSLNRLTYASSLSSLRRLKSPIDTTSKVTKPRLLHSTQWGMMC 477

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRME-------RSIKERISSVDIDSVMPQDLINAKP 508
                  +   + + L     + +             +++    ++ + V   + I +  
Sbjct: 478 PAETPEGQSCGIVKNLALMCYISVGNPVGAAGARDWQVEKIYRLLENNGVEELETIASSL 537

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT-HYG 567
           +      F     +    +       + H                  ++ R++  T   G
Sbjct: 538 IPKTTKVFVNGVWVGIHRDPKVI---LDHRE-----DFDTDVSMVYDIQERELRITADAG 589

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R C            V       R       ET +    D  +   + Y+SA EEE   I
Sbjct: 590 RCCRPLYVVDPITQRVKIRKYHLR---NLQPETMF---SDLVLNRLIEYVSAEEEEYCMI 643

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                          +L   R   E            +  P  ++ + AS+IPF +++ S
Sbjct: 644 GM-------------DLKTMRACVENR--SCTTYTHCEIHPSMILGVCASIIPFPDHNQS 688

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +  +                                         
Sbjct: 689 PRNTYQSAMGKQAMGVYVSNYR-------------------------------------- 710

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  +T+ V  Y               Q+PLV                     +L  
Sbjct: 711 ---QRMDTTAHVLSYP--------------QQPLV----------TTKAMTYLRFKELPA 743

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA--RDT----------K 855
           G N +VA   + GYN EDS+++++  +   +F SI    ++     RDT           
Sbjct: 744 GCNCVVAICCYSGYNQEDSLILNQSAIERGLFRSIFYRTYQDTEVRRDTTTSSLSLSNPS 803

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +G E   R           E   +N+DE G++  G+ V    IL+GK TP GE  +    
Sbjct: 804 MGNERFCRPLSEQCSMTKDEGLYRNLDEDGLVKPGSRVTGDSILIGKATPTGELNVHGRS 863

Query: 911 KLLRAIFG 918
            L     G
Sbjct: 864 NLKDNSTG 871


>gi|311255211|ref|XP_003126132.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like, partial
            [Sus scrofa]
          Length = 438

 Score =  333 bits (854), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 15   YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 74

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 75   LVYKNAKCTL-KRYTNQTFDKVMGPVLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 133

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 134  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 176

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 177  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 234

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 235  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 267

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 268  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 300

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 301  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 360

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 361  IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 420

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 421  ELQSMNIIPRLKLSKYNE 438



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 55/165 (33%), Gaps = 15/165 (9%)

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +  +           Q+P+VK                 +   L  G+N  VA M + GY+
Sbjct: 6   QRNRIDTLMYLLAYPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSGYD 55

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----ID 877
            ED++++++  +       +  +  +    R T    +++   + + +          +D
Sbjct: 56  IEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPVLDAATRKPIWRHEILD 115

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             GI   G +V    +LV K  P           + +    +   
Sbjct: 116 ADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 160


>gi|148642970|ref|YP_001273483.1| DNA-directed RNA polymerase subunit B' [Methanobrevibacter smithii
            ATCC 35061]
 gi|261350231|ref|ZP_05975648.1| DNA-directed RNA polymerase subunit B [Methanobrevibacter smithii DSM
            2374]
 gi|148551987|gb|ABQ87115.1| DNA-dependent RNA polymerase, subunit B', RpoB [Methanobrevibacter
            smithii ATCC 35061]
 gi|288861017|gb|EFC93315.1| DNA-directed RNA polymerase subunit B [Methanobrevibacter smithii DSM
            2374]
          Length = 603

 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 123/609 (20%), Positives = 205/609 (33%), Gaps = 109/609 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V  G+   + D + D    +  D     N  +A            + I    +       
Sbjct: 81   VAKGEL--KWDDLIDNGFIEYLDAEEEENSYIAMSIADLNEEHTHLEIDPATMLGICAGI 138

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   +     R+T             VS   L+         +        +    I   
Sbjct: 139  IPFSDHNSSPRNTMEAGMTKQALGLYVSNYALR---TDTRAHLLHHPQTPIVKTRIIDST 195

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  +     +   +     F R      +R    + 
Sbjct: 196  NYDKRPSGQNFVVALMSYEGYNMEDAMVINKGSLERGLARSSFF-RAYDTAEKRYPGGQE 254

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  ++       +           L     V+     +   VL           + 
Sbjct: 255  DKFEVPDKN-------IKGYRSEDAYRHLDDDGVVNPESYVESGDVLIGKTSPPRFLEEI 307

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +F    EK +    ++             R   K               R+ K+ V   
Sbjct: 308  DEFGTVAEKRRETSVTV-------------RHGEKGIVDAVLLTETVEGSRLAKIRVRDT 354

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  IL  ED+PF + G   D+++NP  +PSRM+VGQ+ E   
Sbjct: 355  RQPEFGDKFASRHGQKGVLGLILSPEDVPFTESGVVPDLIVNPHAIPSRMSVGQVLEMVA 414

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A    G+++                                                 
Sbjct: 415  GKAGCLEGERVDG----------------------------------------------- 427

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F+   E+ I   L+    + +G   LY+G+TGE  +  + VG  Y  KL+H
Sbjct: 428  ------TP-FNTELEKEIKQQLKNHGFESAGCESLYNGVTGERIEAEIFVGVAYYQKLHH 480

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            M +DKVYARS G   ++T+QP  G++  GG R GEME  C+ A+GAA  L+E L  +SD 
Sbjct: 481  MTTDKVYARSRGPVQVLTRQPTEGRAREGGLRFGEMERDCLIAHGAALTLKERLLDESD- 539

Query: 1322 VVGRTRVYESIV-----------AGND-----------TFETGTPESFNVLVKEMQALGL 1359
                   YE+IV              +           T+      +F +L+ E+++L +
Sbjct: 540  ------KYEAIVCENCGMLAVYDKNKNKKYCPICGDVETYPIEISYAFKLLLDELKSLCI 593

Query: 1360 SIDLENSRT 1368
               L     
Sbjct: 594  FPKLVLGDK 602



 Score = 52.4 bits (124), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 61/196 (31%), Gaps = 33/196 (16%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +     L   ++  +  + +   RR   +                +         P    
Sbjct: 7   YINGELLGYCKDPESFTNEMREKRRNGEVSHEMNITYYDKNNEIYIFNDPGRARRPLIIV 66

Query: 576 E-GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           + G  +     L   A+            K  D      + YL A EEEN YIA + + L
Sbjct: 67  KDGKPVLSDKHLEKVAK---------GELKWDDLIDNGFIEYLDAEEEENSYIAMSIADL 117

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +                       E+   ++  P  ++ I A +IPF +++ S R  M  
Sbjct: 118 N-----------------------EEHTHLEIDPATMLGICAGIIPFSDHNSSPRNTMEA 154

Query: 695 NMQRQAVPLLKAEAPF 710
            M +QA+ L  +    
Sbjct: 155 GMTKQALGLYVSNYAL 170


>gi|34493900|emb|CAD66093.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 211/335 (62%), Positives = 263/335 (78%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 2   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 61

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 62  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D 
Sbjct: 122 DGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 182 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 242 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 301

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 302 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|323472374|gb|ADX77915.1| DNA-directed RNA polymerase beta chain [Erwinia sp. DSM 22678]
          Length = 340

 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 209/340 (61%), Positives = 268/340 (78%)

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH
Sbjct: 1   GLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITH 60

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF
Sbjct: 61  KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGF 120

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYR+V +G VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L  
Sbjct: 121 LETPYRRVREGLVTDEIHYLSAIEEGNYVIAQANTNLDEEGHFVDDLVTCRSKGESSLFN 180

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME 
Sbjct: 181 RDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMER 240

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+N
Sbjct: 241 AVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCIN 300

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           Q P V +G+ + R D++ADGPSTDLG+LALG+NM VAFMP
Sbjct: 301 QMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMP 340


>gi|226897640|gb|ACO90269.1| RNA polymerase beta subunit gene [Bacillus firmus]
          Length = 391

 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 229/376 (60%), Positives = 293/376 (77%), Gaps = 3/376 (0%)

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           NIGL++SL+SFA+VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQAN+ L +
Sbjct: 1   NIGLINSLSSFAKVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQANALLGD 60

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           DGSF +E V  R  GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 61  DGSFLDEEVVARFKGENKVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 120

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPS 755
           QRQAVPL++ EAP VGTGME V  K SGAA++ K  GIVE V+A  + +R ++  D    
Sbjct: 121 QRQAVPLMQPEAPRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIQNVDGQEV 180

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +D YR++KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAF
Sbjct: 181 KGDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAF 240

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N
Sbjct: 241 MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 300

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G 
Sbjct: 301 LDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGG 360

Query: 936 SGTVVDVRIFNRHGID 951
            G V+DV++FNR   D
Sbjct: 361 GGIVLDVKVFNREDGD 376


>gi|31873396|emb|CAD97689.1| hypothetical protein [Homo sapiens]
          Length = 1133

 Score =  333 bits (853), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 105/505 (20%), Positives = 174/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EPF+  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPFEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|116563652|gb|ABJ99842.1| RpoB [Bacillus subtilis subsp. subtilis]
          Length = 182

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 81/203 (39%), Positives = 127/203 (62%), Gaps = 22/203 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G  ++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAXLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDS 225
           +VRIDR RK+PVT  L ALG  S
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGS 181


>gi|209881586|ref|XP_002142231.1| DNA-directed RNA polymerase, beta subunit family protein
            [Cryptosporidium muris RN66]
 gi|209557837|gb|EEA07882.1| DNA-directed RNA polymerase, beta subunit family protein
            [Cryptosporidium muris RN66]
          Length = 1341

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 211/1453 (14%), Positives = 405/1453 (27%), Gaps = 274/1453 (18%)

Query: 33   QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--------FSGAAMLEFVSYEFDPP 84
               S++ FL+  ++        +     S + I                ++    +   P
Sbjct: 54   HIESFNCFLLTGLSNIVINLPSIY--IDSDYVIDDCELNVGYIPREYLRIKVTCIKVGKP 111

Query: 85   KFDVDD--------CLWRD--LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
             F   +        C  R+  L+Y+ PL I                S K     +++ G 
Sbjct: 112  IFGSTESSNTKMYPCSARNGHLSYSAPLWIEF---------ECYNSSSKSSVRHNLFAGS 162

Query: 135  LPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
            +P+M +                         G F+I G +                    
Sbjct: 163  IPIMVRSLACHLYSLSPNELVANGEDPNEVGGYFIINGNE-------------------- 202

Query: 171  RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR------IDRRRKVPVTSFLMALGMD 224
                        R+I               +I  R      + R R              
Sbjct: 203  ------------RVIRY-------------VIQQRCNYPVGLKRSR------------FT 225

Query: 225  SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG-----EQVIESGKK 279
            S +I  T Y  ++ S R D                V   L++           ++  G  
Sbjct: 226  SRDIFGTEYAILLRSLRNDGTSTANYLYGTTDNQCVYRILLNRQEWLLPFWNVLLAVGSI 285

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
              +   K+L+ K +++   T D    LY    ++N  T E  ++    ++   +   +  
Sbjct: 286  YDA---KTLRNKILQYCCNTRDEYDPLY---GVINMLTIEWGLDNSSGVENSVIPPSYDG 339

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKD---RKDALLDIYRVMRPGDVSTFSVAESMF 396
               DI I+    ++N   +    V          +DA   I        +  ++      
Sbjct: 340  AFGDIEIIENRHLHNLGKLVWEGVVFYLPPGSLYQDAGRFIIDNHILVHLPEWNAKLECL 399

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              +F    K     +    ++     +              AI   L  +R    T    
Sbjct: 400  ILMFIKLLKLQYGQIREESIDSFAYQEILSSGNLYASVLKDAIFSFLQKIRMIYITEIRN 459

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
             N       +  E+        L  +      + S +   S++P+ +       +     
Sbjct: 460  RNSSKSEKEASDELPLPYSSAALDLLRDDSFFKTSLIRNISMIPKRIQYFMATGNIKTTQ 519

Query: 517  FCSSQLSQLE---EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                QLS      + +N    ++H R   A+ +G         ++R +    +G +CP  
Sbjct: 520  LDLQQLSGWTVVADRLNFNRFLSHFR---AVHRGQFFTTMKTTDVRKLMGETWGFLCPVH 576

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV-----------TNDVVYLSAMEE 622
            T +G   GL+  L+          I++  + + D  V           T  + + S   +
Sbjct: 577  TPDGEPCGLLLHLSQDTIPVTQFEIQSTLKNLRDYLVGQNIPCDDGLGTLSIQWGSLNLD 636

Query: 623  ENRY-IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            +        +  +  DG         +            + +        V    + IP 
Sbjct: 637  DIYVPDLSKSVPVMLDGRVMFH--IPKLKFTFWQEKLRNLKWSKTPSILPVHTEIACIPP 694

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                    V  G  M      L++         ++ +          A+    +   +  
Sbjct: 695  D-----CGVFSGIFMFTAPGRLVRPVLHLKSNKIDWIGPL-------AQPWMDIGVTEEE 742

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +               +     +  N   NQ     + + ++++  +   P   
Sbjct: 743  TQKSIKLYNLQMKLFGLYRNDNITSDIETTDNMDKNQ-----IEEMIKKDYTLGCNPVMY 797

Query: 802  LGD---LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                   +   ++  + +P+  +N     +   +M+ + + T  +   +    R      
Sbjct: 798  THQELHPSTILSITASLIPYAHHNQSPRNMYQCQMLKQTMGTPCYSYPYRTDNRMY---- 853

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  II     +             G S        + A+  
Sbjct: 854  ---------------------RIITPQNPLVITKGYASY----GFSEYPTGTNAIVAVIS 888

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                D+ D  +   +     +       +  I     +  +++   E            +
Sbjct: 889  HSGYDMEDAMVLNKASYERGIFHA-CVYKTKILFAAPNSVIKKSDAESYR------FHNI 941

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +    + E+      + G K  K S +   + +               +  +  VE +
Sbjct: 942  GPDGKLVIKELGADGLPMIGQKLVKGSPMCRVEKLGSGGVISNAIVQTYHDDEEAYVEKI 1001

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                    +               G +   G    + + + + R    GDK A RHG KG
Sbjct: 1002 NRVGSGLSTESHSDSTLGGSGGPGGSEYSSGYGEKISLKLRIVRNPMVGDKFASRHGQKG 1061

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S + P E+MPF + G   DI+ NP G PSRM VG + E   G A    G         
Sbjct: 1062 ILSMLWPHENMPFGESGIVPDILFNPHGFPSRMTVGMLIECMAGKAACLHGASALDATPF 1121

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            ++   D   +    E  I     +                                  + 
Sbjct: 1122 HRNITDKQTILEDKEMGIDLSKQS--------------------------------TVDY 1149

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L        G   L++G+TG      + +G IY  +L HMV+DK   RSTG    +
Sbjct: 1150 FGKALLKTGFQYFGCEPLFNGMTGTEMPCHIFMGVIYYQRLRHMVADKAQVRSTGPIDAL 1209

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--- 1335
            T+QP+ G+   GG R GEME   + +YG + ++ + L   SD+     + Y     G   
Sbjct: 1210 TRQPVKGRKRHGGIRFGEMERDSLISYGVSSIIADRLLKCSDE----HKAYVCPYCGLIF 1265

Query: 1336 ----------------NDTFETGT-------------PESFNVLVKEMQALGLSIDLENS 1366
                                                 P  F  L  E+  + + I LE  
Sbjct: 1266 SAILPRKTTNFQNRLATTLPHVAICKVCKTPCRLITLPYVFRYLCNELATMNIVIRLELE 1325

Query: 1367 RTKNSAKMEEIPD 1379
            +      +  I D
Sbjct: 1326 QEDVPISIRSIKD 1338


>gi|111054607|gb|ABH04361.1| RNA polymerase beta subunit [Providencia stuartii]
          Length = 340

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 213/340 (62%), Positives = 264/340 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVR 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQAN+ L EDGSF EEL+ CR  GE  L  R++++++D 
Sbjct: 121 DGIVTDEIHYLSAIEEGNFIIAQANTVLAEDGSFVEELITCRNRGESSLFSRDQVEYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+ R LMG NMQRQAVP L+A+ P VGTGME  VA   G  
Sbjct: 181 STQQVVSVGASLIPFLEHDDAXRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDXGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GYNFEDS
Sbjct: 301 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDS 340


>gi|66351048|emb|CAI13209.1| RNA polymerase beta subunit [Pseudomonas putida]
          Length = 343

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 203/343 (59%), Positives = 268/343 (78%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETXEGPNIGLINSLAAYARTNQYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +
Sbjct: 121 YRVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           V  GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFE
Sbjct: 301 VSKGDKVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFE 343


>gi|312183601|gb|ADQ42370.1| DNA-directed RNA polymerase subunit B' [Methanosaeta harundinacea]
          Length = 607

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 117/602 (19%), Positives = 205/602 (34%), Gaps = 98/602 (16%)

Query: 786  DEVRRNDIIADGPS----TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            ++VRR +I  D        +  D     N LVA            M +   +V       
Sbjct: 82   EKVRRGEITFDDLVREGLVEYLDAEEEENALVAIEEMEITPDHTHMEVDPSLVLGICTGL 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   E     R+T             ++   L+  D  G                     
Sbjct: 142  VPYPEHNASPRNTMGAGMIKQCLGTPLANTKLRP-DTRG--HYLHYPQRALCRSRTADAV 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     +    +    F R    +  +    + 
Sbjct: 199  GFDERPAGQNFVVAVLVYEGYNIEDALILNRGSIERG-LGRSHFFRVSEAEERKYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +     +     L     V+       + VL           + 
Sbjct: 258  DKFEIPDME-------VRGARGTEAYSQLDDDGLVNPNAVVAPNDVLIGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +F +  ++ +    +++   +     +                      R+ KV    +
Sbjct: 311  TEFGITPQQRRETSVTMRSNEKGVVDTVIL-------------TESSNGNRLAKVKTRDQ 357

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  I+P  DMPF + G   D+++NP  +PSRM VG + E   
Sbjct: 358  RVPELGDKFASRHGQKGVIGLIVPPADMPFTEAGQVPDLIVNPHAIPSRMTVGHVLEMIG 417

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+ +                                                 
Sbjct: 418  GKMGSLEGRFVD------------------------------------------------ 429

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +T  F G +E  + + L       +G+ ++Y+G+ GE     V VG I   KL H
Sbjct: 430  -----AT-AFLGEEETDMRAALTKFGFSHTGREVMYNGINGEQIMADVFVGVILYQKLYH 483

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA  L+E L  +SD 
Sbjct: 484  MVAGKMHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIAHGAALALKERLVDESDK 543

Query: 1322 V-------VG-------RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V        G       R  V    V G   + +      +F +L+ E+++LG++  L  
Sbjct: 544  VTELVCSRCGMIAIHDKRRNVDYCSVCGSDTEIYPVEMSYAFKLLLDEIKSLGVAPRLVL 603

Query: 1366 SR 1367
              
Sbjct: 604  ED 605



 Score = 48.5 bits (114), Expect = 0.009,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 52/184 (28%), Gaps = 31/184 (16%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + ++    +   RR   +         A      ++        P    EG +  +    
Sbjct: 21  DPISLAKEMRRLRRGGKISNQINVSYFARTNEILINTDSGRARRPLIVVEGGSALVTEEH 80

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
               R     F         D      V YL A EEEN  +A     +  D         
Sbjct: 81  VEKVRRGEITF--------DDLVREGLVEYLDAEEEENALVAIEEMEITPDH-------- 124

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                            ++  P  V+ I   L+P+ E++ S R  MG  M +Q +    A
Sbjct: 125 ---------------THMEVDPSLVLGICTGLVPYPEHNASPRNTMGAGMIKQCLGTPLA 169

Query: 707 EAPF 710
               
Sbjct: 170 NTKL 173


>gi|116743386|emb|CAJ28865.2| DNA-directed RNA polymerase beta chain [Enterobacter
           nickellidurans]
          Length = 332

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 207/332 (62%), Positives = 260/332 (78%)

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+
Sbjct: 1   MSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGL 60

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG 
Sbjct: 61  TRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGV 120

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT+++ YLSA+EE N  IAQAN++LD++G F E+LV CR  GE  L  R+++D++D S +
Sbjct: 121 VTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQ 180

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA
Sbjct: 181 QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVA 240

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           KR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V 
Sbjct: 241 KRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVE 300

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 RGDVLADGPSTDLGELALGQNMRVAFMPWNGY 332


>gi|242392384|dbj|BAH80405.1| RNA polymerase subunit B' [Natronococcus occultus SP4]
          Length = 609

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 124/595 (20%), Positives = 207/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVEHGYIEFIDAEEEEDIYVAVDEDDLEEEHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYTHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELREGLEEAGFDSAGKETMYSGITGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 43.5 bits (101), Expect = 0.24,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A     G +E       D      + ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-PRISEQELEAL--QDGDLE-----FEDLVEHGYIEFIDAEEEEDIYVAVDEDDLE 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EEHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|52694377|emb|CAG38028.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 335

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 204/336 (60%), Positives = 261/336 (77%), Gaps = 1/336 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA R+V+R  +G+++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDASRVVVRVHDGEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVERGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           DGPSTD+G+LALG+NM V  MPW+GYNFEDS+L+SE
Sbjct: 300 DGPSTDMGELALGQNMRVELMPWNGYNFEDSILLSE 335


>gi|242392314|dbj|BAH80330.1| RNA polymerase subunit B' [Halalkalicoccus tibetensis]
          Length = 608

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 129/593 (21%), Positives = 210/593 (35%), Gaps = 95/593 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D + +    +  D     ++ VA       +    + I   ++       I   E     
Sbjct: 92   DSLVEHGYIEFIDAEEEEDIYVAVDREEVNDEHTHLEIDPSLIFGIGAGMIPYPEHNASP 151

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R T      + +    +     +   +     +        +        G       + 
Sbjct: 152  RITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQN 208

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + A+   +  ++ D  L +  G     +    F R    +  R    + ++ E+   D 
Sbjct: 209  FVVAVMSYEGFNIEDA-LVMNGGSVDRALARSHFFRTYEGEERRYPGGQEDRFEIPGED- 266

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                  +           L     V+      +S+VL           +         + 
Sbjct: 267  ------VRGARGEESYTHLDDDGLVNPETDVDESSVLLGKTSPPRFLEEPDDMGGLSPQK 320

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +R         E+         + +               ++ KV V  +R  + GDK A
Sbjct: 321  RRETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVKVRDERIPELGDKFA 368

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG++  I P EDMPF ++G   D+VLNP  +PSRM VG + E   G      G++
Sbjct: 369  SRHGQKGVIGHIAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGSLEGRR 428

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +                                                       TP F
Sbjct: 429  VDG-----------------------------------------------------TP-F 434

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             G DEE +   L       SG+ ++Y G++GE  +  + VG I+  KL HMVS+K++ARS
Sbjct: 435  SGEDEEELRDALEERGFKSSGKEVMYSGVSGEKIEAEIFVGTIFYHKLYHMVSNKLHARS 494

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--- 1324
             G   ++T+QP  G++  GG R+GEME   +  +GAA VL+E L   SD    DV G   
Sbjct: 495  RGPVQVLTRQPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDREYIDVCGNCG 554

Query: 1325 --------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                    + RVY     G   D  E     +FN+L+ EM+ALG++  LE S 
Sbjct: 555  MTAVENVQQQRVY-CPNCGEETDIHEIEMSYAFNLLLDEMKALGIAPRLELSD 606



 Score = 42.4 bits (98), Expect = 0.62,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + ++ A EEE+ Y+A     ++                       ++   ++  P  +  
Sbjct: 100 IEFIDAEEEEDIYVAVDREEVN-----------------------DEHTHLEIDPSLIFG 136

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 137 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 173


>gi|318603006|emb|CBJ04578.1| RNA polymerase beta subunit [Pseudomonas sp. R-37260]
          Length = 342

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 202/342 (59%), Positives = 267/342 (78%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +
Sbjct: 121 YRVVKEGVVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+
Sbjct: 181 TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL
Sbjct: 241 DSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPL 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           V+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NF
Sbjct: 301 VRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNF 342


>gi|226897630|gb|ACO90264.1| RNA polymerase beta subunit gene [Bacillus cereus]
          Length = 401

 Score =  333 bits (853), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 230/377 (61%), Positives = 289/377 (76%), Gaps = 3/377 (0%)

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            NIGL++SL+SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L 
Sbjct: 1   PNIGLINSLSSFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLS 60

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ++G F  E +  R  GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG N
Sbjct: 61  DEGEFLSEDIVARFRGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDP 754
           MQRQAVPL+  E+P VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D   
Sbjct: 121 MQRQAVPLMNPESPIVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQT 180

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
               +D Y++ KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV 
Sbjct: 181 VKGDLDRYKMQKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVG 240

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+
Sbjct: 241 FMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALR 300

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G
Sbjct: 301 NLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHG 360

Query: 935 VSGTVVDVRIFNRHGID 951
             G ++DV++FNR   D
Sbjct: 361 GGGIILDVKVFNREDGD 377



 Score = 51.6 bits (122), Expect = 0.001,   Method: Composition-based stats.
 Identities = 46/275 (16%), Positives = 92/275 (33%), Gaps = 15/275 (5%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 140  MEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 199

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 200  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 254

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 255  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 312

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 313  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 366

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              K+   + GD++PPGV ++V+ ++  KR I  GD
Sbjct: 367  DVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGD 401


>gi|193787264|dbj|BAG52470.1| unnamed protein product [Homo sapiens]
          Length = 838

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 415  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 474

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 475  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 533

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 534  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 576

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 577  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 634

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 635  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 667

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 668  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 700

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 701  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 760

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 761  IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 820

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 821  ELQSMNIIPRLKLSKYNE 838



 Score =  128 bits (321), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 82/562 (14%), Positives = 175/562 (31%), Gaps = 39/562 (6%)

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                  K  +     +  +  L      +     K    A++   V L  G   +DD D
Sbjct: 1   MWGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRD 60

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSAV 513
             GN+R+   G++L   +     +    +K+    V       Q      +    + + +
Sbjct: 61  YYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGM 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTH 565
                +   S     ++         RLS +   G+         + R     R + P+ 
Sbjct: 121 VNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQ 180

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           +G +CP++T EG   GLV +L     +      + P  K+       DV  L   EE + 
Sbjct: 181 WGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIVKLASNLGVEDVNLL-CGEELSY 238

Query: 626 ---YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----L 678
              ++   N ++       ++LV             E +        + V I++      
Sbjct: 239 PNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLC 298

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            P++        +   +M+  A      E     + +E +         +A     + + 
Sbjct: 299 RPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKD 358

Query: 739 DAIRI--------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV-- 788
                        V   +      + S  + Y+    +++      NQR  +     +  
Sbjct: 359 TTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLA 418

Query: 789 ---RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +           +   L  G+N  VA M + GY+ ED++++++  +       +  +
Sbjct: 419 YPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYK 478

Query: 846 EFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITP 900
             +    R T    +++   + + +          +D  GI   G +V    +LV K  P
Sbjct: 479 NAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKSMP 538

Query: 901 KGESPMTPEEKLLRAIFGEKAV 922
                      + +    +   
Sbjct: 539 TVTQIPLEGSNVPQQPQYKDVP 560


>gi|52694177|emb|CAG30618.1| DNA-directed RNA polymerase beta chain [Pseudomonas migulae]
          Length = 341

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 202/341 (59%), Positives = 265/341 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  
Sbjct: 121 VVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVR 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFE
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFE 341


>gi|242392378|dbj|BAH80402.1| RNA polymerase subunit B' [Natronobacterium gregoryi SP2]
          Length = 609

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 127/596 (21%), Positives = 209/596 (35%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++LVA            + I  +++       I   E     R 
Sbjct: 95   LVEHGYVEFIDAEEEEDILVAVDEDDITESHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DEE +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEEDLRDGLEEAGFDAAGKETMYSGITGEKVEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICGQCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 41.6 bits (96), Expect = 0.90,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 60/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +        R    G +E       D      V ++ A EEE+  +A     + 
Sbjct: 71  EDGEPRISDEEIEALR---DGSLE-----FEDLVEHGYVEFIDAEEEEDILVAVDEDDIT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E                           ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 ESH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|116563670|gb|ABJ99851.1| RpoB [Bacillus vallismortis]
          Length = 182

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 81/203 (39%), Positives = 127/203 (62%), Gaps = 22/203 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  DPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDS 225
           +VRIDR RK+P T  L ALG  S
Sbjct: 159 YVRIDRTRKLPXTXLLRALGFXS 181


>gi|80978847|gb|ABB54672.1| RNA polymerase beta subunit [Mycoplasma spermatophilum]
          Length = 592

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 214/423 (50%), Positives = 299/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEIANKRRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY KV DG V  ++V YL+A EE    IAQ+  S+DE+   T++ +  R
Sbjct: 62  AKVNEYGFLQTPYFKVEDGVVDYSEVHYLTAFEEIGYNIAQSTISIDENNRLTDKNITMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   + ID+I+ +P+Q+VS+AA  +PFLENDD+NR LM  NMQRQAVPLL+ EA
Sbjct: 122 QNYTYIMGTPKDIDYIEVAPRQMVSVAAGCVPFLENDDANRALMASNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S A   AK  GIVE VD  +I IR+ +  LD        Y L  FQ
Sbjct: 182 PFVATGIEADIAKYSSANFTAKNDGIVEYVDGEKIKIRNTKKTLD-------TYNLQNFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+TC+ Q+P+V  G EV + D++ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTCITQKPIVHEGQEVHKGDLLVDGSSFKDGELALGKNVLVAFTTYKGYNYEDAVV 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E+TRDIPNVS++ ++ +DE GI+ VG+EV
Sbjct: 295 LNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTRDIPNVSKQAIRFLDEHGIVRVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+  ++ + V+DTSL+V +G SGTV+ V + NR 
Sbjct: 355 VPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQLAVKDTSLKVKNGHSGTVIGVEVLNRE 414

Query: 949 GID 951
             D
Sbjct: 415 NGD 417



 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 125/413 (30%), Positives = 181/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G EV+ GD+LV   + K +  +   + +L A    K  +  D  +     V   V 
Sbjct: 247  IVHEGQEVHKGDLLVDGSSFK-DGELALGKNVLVAFTTYKGYNYEDAVVLNERLVKDDVF 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E    +          LD +   R+   +   + + G  
Sbjct: 306  -TSIHIEEQTIQFRTSKAGDDELTRDIPNVSKQAIRFLDEHGIVRVGSEVVPGDVLVGRV 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +        Q  Q AV+D              +            ++   
Sbjct: 365  SPKGDDNPSQEEKLLSAVLQQRQLAVKD-----------TSLKVKNGHSGTVIGVEVLNR 413

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD+
Sbjct: 414  ENGDQLEDGIDKIVKVSIATKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDV 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  + + D      I+ + S          
Sbjct: 474  MLNPQGVPSRMNIGQVLELHLGMAARNLKCKFVTPVFDGIKKEAIADVMS---------- 523

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                      ++ L +  +     P++   FD                            
Sbjct: 524  ----------EANLSLTGKQTLIDPITGRKFD---------------------------- 545

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                   PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 546  ------HPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 592


>gi|242392366|dbj|BAH80396.1| RNA polymerase subunit B' [Natrialba taiwanensis]
          Length = 609

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 121/591 (20%), Positives = 209/591 (35%), Gaps = 95/591 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDLNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEVPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEDAYAHLDEDGLVNPETDVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+++NP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTENGVVPDLIVNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELRDGLEDAGFNSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    ++ G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINICGQCGMS 557

Query: 1325 ------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY     G   D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVY-CPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 45.5 bits (106), Expect = 0.067,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 45/113 (39%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           ++    +  D      + ++ A EEE+ Y+A     L+ED                    
Sbjct: 85  LQNDELEFEDLVDHGYIEFIDAEEEEDIYVAVDEDDLNEDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMVKQSLGLPSANYRI 174


>gi|120561247|gb|ABM27008.1| RNA polymerase II second largest subunit [Furculomyces boomerangus]
          Length = 906

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 160/995 (16%), Positives = 286/995 (28%), Gaps = 174/995 (17%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V  +  LE I +       +         A++         
Sbjct: 67   IPYIRSDIPVVVVFRALGMVAVKDILEHICYDGNDHQMLEKFKPSIEEAFV--------I 118

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +D+  AL  I +       +     +    +      K  L  VG    N          
Sbjct: 119  QDKDVALDFIGKR----GTAVGVSKDKRIKYGAEILQKEFLPHVGTQAHN---------- 164

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI- 486
                +      ++  L+     +   DD D+ G +R+   G +L   +R    ++ + + 
Sbjct: 165  -ETRKSFFFGYMVHRLLLCALERREQDDRDHYGKKRMDLAGPLLAMLFRNLFRKVTKDMT 223

Query: 487  -KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSL 532
               +              I +  + + +     +               +SQ+       
Sbjct: 224  RYLQKCIDSKREFNLTMAIKSNTITAGLKYSLATGNWGDQKKSMQSRTGVSQVLNRYTFA 283

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L   A +
Sbjct: 284  STLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMAHI 339

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF----CR 648
               G    P     +     ++  L+A    +      N            LV      R
Sbjct: 340  T-IGAESGPLLLFLEEWAMENLEELTASNIPDATKIFVNGVWVGIHRDANRLVSTLLQMR 398

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               +         D  +   +          P    ++  R+ +  ++ R        + 
Sbjct: 399  RRLDLSYELSIVRDVREKELRLFTDAGRVSRPLFVVNN-LRLNLTKDIVRAIEARDVNDP 457

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              V                     GIVE +DA       +             +      
Sbjct: 458  EAVR-------------WHDLMVEGIVEYLDAEEEETAMICMTSAELKESRMFHEHGIEP 504

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            ++  +     R   +   ++         PS  LG       +  + +P+  +N      
Sbjct: 505  QAEDDLASRIRS--RRNVQIHTWTHCEIHPSMILG-------ICASIVPFPDHNQSPRNT 555

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
                M  + +                             ++   L+      +  +    
Sbjct: 556  YQSAMGKQAMG--------------------------IMLTSYQLRM---DTLSNILYYP 586

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     +     S +   +  + AI      +  D+ +   S +   +    +F R 
Sbjct: 587  QKPLATTHSMEYIKFSDLPAGQNAVVAILCYSGYNQEDSVIMNQSSIDRGLF-RSMFYRT 645

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              D+ +R         E   R+                  I  G           K+T +
Sbjct: 646  YQDEEDRQGMKTMGTFERPTRETTLRLKHGTYEKLEDDGLIAPGTRVTGDDIIIGKTTPI 705

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              D I               E  QR V   K+         E    +++     GD    
Sbjct: 706  PIDSI---------------ELGQRTVTHTKLDASKPLRSTETGIVDQVMLTTNGD---- 746

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +P
Sbjct: 747  -GFKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRTEDMPFTSEGVVPDLIINPHAIP 805

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +G + E  L      +G                                       
Sbjct: 806  SRMTIGHLVECLLSKLATLIGTTAD----------------------------------- 830

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                              +TP F     EAI+  L        G  ++Y+G TG      
Sbjct: 831  ------------------ATP-FTDVTVEAISRELFSLGYQSRGFEVMYNGHTGRKLQAQ 871

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            V +G  Y  +L HMV DK+++R+ G   ++T QP+
Sbjct: 872  VFLGPTYYQRLKHMVDDKIHSRARGPVQILTSQPV 906



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 109/762 (14%), Positives = 224/762 (29%), Gaps = 93/762 (12%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +PV     ALGM + ++IL          Q  + +   +  A ++    V+
Sbjct: 69  YIRSD----IPVVVVFRALGMVAVKDILEHICYDGNDHQMLEKFKPSIEEAFVIQDKDVA 124

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   K++  G  + L+++ +  +G  +            +      + 
Sbjct: 125 LDFIGKRGTAVGVSKDKRIKYG-AEILQKEFLPHVGTQAHNETRKSFFFGYMVH---RLL 180

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  ++   +      +    P+L +   N    +   +     K           +
Sbjct: 181 LCALERREQDDRDHYGKKRMDLAGPLLAMLFRNLFRKVTKDMTRYLQKCIDSKREFNLTM 240

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   S  G  ++  R    +      R         
Sbjct: 241 AIKSNTITAGLKYSLATGNWGDQKKSMQSRTGVSQVLNRYTFASTLSHLRRCNTPIGRDG 300

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +      ++KN   +  + +       +  ++  ++
Sbjct: 301 KIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLALMAHITIGAESGPLLLFLEEWAM 357

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVE 557
              + + A  +  A   F     +    +    +S +   RR   L  +  + R     E
Sbjct: 358 ENLEELTASNIPDATKIFVNGVWVGIHRDANRLVSTLLQMRRRLDLSYELSIVRDVREKE 417

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R +         P        + L   +            E    +  D  V   V YL
Sbjct: 418 LR-LFTDAGRVSRPLFVVNNLRLNLTKDIVRAIEARDVNDPEAV--RWHDLMVEGIVEYL 474

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPKQ 670
            A EEE   I   ++ L E   F E  +  +              V        +  P  
Sbjct: 475 DAEEEETAMICMTSAELKESRMFHEHGIEPQAEDDLASRIRSRRNVQIHTWTHCEIHPSM 534

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS++PF +++ S R      M +QA+ ++                  + + I+  
Sbjct: 535 ILGICASIVPFPDHNQSPRNTYQSAMGKQAMGIMLTSYQL---------RMDTLSNILYY 585

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
               +    ++  +  S       +   +  Y              NQ            
Sbjct: 586 PQKPLATTHSMEYIKFSDLPAGQNAVVAILCYSG-----------YNQ-----------E 623

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
           + +I +  S D G            M +  Y  E           ED      +  FE  
Sbjct: 624 DSVIMNQSSIDRGLFRS--------MFYRTYQDE-----------EDRQGMKTMGTFERP 664

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            R+T             +     + +++ G+I  G  V   DI++GK TP     +   +
Sbjct: 665 TRET----------TLRLKHGTYEKLEDDGLIAPGTRVTGDDIIIGKTTPIPIDSIELGQ 714

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           + +            D S  + S  +G V  V +       K
Sbjct: 715 RTV-------THTKLDASKPLRSTETGIVDQVMLTTNGDGFK 749


>gi|242392390|dbj|BAH80408.1| RNA polymerase subunit B' [Natronorubrum aibiense]
          Length = 609

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 125/595 (21%), Positives = 208/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDVSEEHTHLEIDPSLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDDDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTQDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELRGGLEDAGFNSAGKEVMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 43.1 bits (100), Expect = 0.36,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +        R    G +E       D      + ++ A EEE+ Y+A     + 
Sbjct: 71  EDGEPRISDQEIEALR---QGDLE-----FEDLVDHGYIEFIDAEEEEDIYVAVDEDDV- 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P  +  I A +IP+ E++ S R+ MG  
Sbjct: 122 ----------------------SEEHTHLEIDPSLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|6606133|gb|AAF19079.1|AF107807_1 DNA-dependent RNA polymerase II RPB140 [Leotia viscosa]
          Length = 938

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 162/1047 (15%), Positives = 314/1047 (29%), Gaps = 171/1047 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  KG    G     +    +     +   G ++   G V DE  L
Sbjct: 37   LEKGSRLISSLTIKLHSKGDNQRGSFGATIKST-LPYIKADIPMGIVFRALGVVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A++         +DR+ AL  I +              
Sbjct: 96   NHICYDRNDTQMLEMLKPCIEEAFV--------IQDREVALDYIGKR------------G 135

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +          KY    + +  +      +  +  +      +  ++  L+    G+   
Sbjct: 136  NAMGLTRDKRIKYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHKLLQCALGRRET 192

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + +    +    +     P   I +  + +
Sbjct: 193  DDRDHFGKKRLDLAGPLLAKLFRNLFKKLTQDLFKYTQRCVENRKEFNPALGIKSTTLTA 252

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 253  GLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 308

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V         +      +V  +   
Sbjct: 309  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRSMEVLEEYEP 368

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L +      ++      +  D +   + V        I      I D  D   K      
Sbjct: 369  LRSPNATKVFVNGVWVGVHRDPAHLVQTVRDLRRSHHISYEVSLIRDIRDREFKIFTDAG 428

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                P F+ ++D N    G  +  +       +   +  G++    +  G        G 
Sbjct: 429  RVCRPLFVIDNDVNSKNKGNLVLNKGHIKRLEDDTTLPLGLDLEEKQERGY------FGF 482

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD---EVRRN 791
               +D    V+  V+ + + +   V     ++  R  Q     Q      G+    V+  
Sbjct: 483  QGLID--EGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYQIQE--DNSGELNRRVKAP 538

Query: 792  DIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                    T      ++   +  + +P+  +N                        ++  
Sbjct: 539  MKPTAHIWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSA 580

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                 +G      D                +  +             +       +   +
Sbjct: 581  MGKQAMGVFLTNFDQRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQ 629

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   + 
Sbjct: 630  NAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYTDQEKR---IGMNVVEQFEKP 685

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
              ++ + L    Y +L +   +  G           K+  ++ D      R++       
Sbjct: 686  FRNDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDNEELGQRTKAHSKRDA 745

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +  Q                             LR VKV +   +  Q G
Sbjct: 746  STPLRSTENGIVDQVLI--------------------TTNAEGLRFVKVRMRTTKVPQIG 785

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L      
Sbjct: 786  DKFASRHGQKGTIGITYKQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVASL 845

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +         ++S L                                       
Sbjct: 846  SGYEGDATPFTDVTVDNVSKLLREHGYQSRGFEIM------------------------- 880

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                    G +    G         V +G  Y  +L HMV DK+
Sbjct: 881  ----------------------YHGHT----GR---KLTAQVFLGPTYYQRLRHMVDDKI 911

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +AR+ G   ++T+QP+ G++  GG R 
Sbjct: 912  HARARGPVQILTRQPVEGRARDGGLRF 938



 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 114/854 (13%), Positives = 240/854 (28%), Gaps = 146/854 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          +        Y   I    ++G  +      K  +H + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKPPPSPTPYVAEIRSALEKGSRLISSLTIK--LHSKG 55

Query: 207 DRRR----------------KVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           D +R                 +P+     ALG+   E+IL+        +Q  +     +
Sbjct: 56  DNQRGSFGATIKSTLPYIKADIPMGIVFRALGVVSDEDILNHICYDRNDTQMLEMLKPCI 115

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD-------C 302
             A ++   +V+   +        +   K++     + + +K +       +        
Sbjct: 116 EEAFVIQDREVALDYIGKRGNAMGLTRDKRI--KYARDIMQKELLPHISQKEGSETRKAF 173

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
             G  V + ++    G    +  D   +K L+       +    L+         +   L
Sbjct: 174 FLGYMVHK-LLQCALGRRETDDRDHFGKKRLDLAGPLLAKLFRNLFKK-------LTQDL 225

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                +  ++       +       T  +  S+    + D  K   ST G  ++  R   
Sbjct: 226 FKYTQRCVENRKEFNPALGIKSTTLTAGLKYSLATGNWGDQKKAASSTAGVSQVLNRYTF 285

Query: 423 DTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            +      R          I     L N    +         +   + + L     + + 
Sbjct: 286 ASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVG 345

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
                I E +    ++ +   + + +               +    +  + +  +   RR
Sbjct: 346 TPSDPIVEFMIQRSMEVLEEYEPLRSPNATKVF---VNGVWVGVHRDPAHLVQTVRDLRR 402

Query: 541 LSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVSSLTSF 589
              +  +  + R     E        R   P           ++G+   N G +  L   
Sbjct: 403 SHHISYEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDVNSKNKGNLVLNKGHIKRLEDD 462

Query: 590 AR----VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
                 ++     E  Y           V Y+ A EEE   I      L+          
Sbjct: 463 TTLPLGLDLEEKQERGYFGFQGLIDEGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYQ 522

Query: 646 F--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                     R     +          +  P  ++ I AS+IPF +++ S R      M 
Sbjct: 523 IQEDNSGELNRRVKAPMKPTAHIWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 582

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 583 KQAMGVFLTNF-----------------------------------------DQRMDTMA 601

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y       +     +  R                        +L  G+N +VA + 
Sbjct: 602 NILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILC 637

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    +    +   +   E        D   +    
Sbjct: 638 YSGYNQEDSVIMNQSSIDRGLFRSLFFRSYTDQEKRIGMNVVEQFEKPFRNDTLKLKHGT 697

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G++  G  V+  DI++GK  P         ++        KA   RD S  + 
Sbjct: 698 YDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDNEELGQRT-------KAHSKRDASTPLR 750

Query: 933 SGVSGTVVDVRIFN 946
           S  +G V  V I  
Sbjct: 751 STENGIVDQVLITT 764


>gi|242392358|dbj|BAH80392.1| RNA polymerase subunit B' [Natrialba asiatica]
          Length = 609

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 121/591 (20%), Positives = 209/591 (35%), Gaps = 95/591 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDLNEEHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEVPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEDAYAHLDEDGLVNPETDVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+++NP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTENGVVPDLIVNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELRDGLEDAGFNSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    ++ G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINICGQCGMS 557

Query: 1325 ------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY     G   D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVY-CPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 44.7 bits (104), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           ++    +  D      + ++ A EEE+ Y+A     L+                      
Sbjct: 85  LQNDELEFEDLVDHGYIEFIDAEEEEDIYVAVDEDDLN---------------------- 122

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E+   ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 123 -EEHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMVKQSLGLPSANYRI 174


>gi|320165828|gb|EFW42727.1| polymerase III polypeptide B [Capsaspora owczarzaki ATCC 30864]
          Length = 1138

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 105/494 (21%), Positives = 182/494 (36%), Gaps = 93/494 (18%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    I       M   +    A+      D+ D  +   + +        ++ 
Sbjct: 722  YPQRPMVQTRTIELIDFHNMPAGQNACVAVMSYSGYDIEDALILNQASLDRGFGRCMVY- 780

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R      +   ++  ++I    R++DD   +   ++  +      G+   +G     K T
Sbjct: 781  RKQTVSIKTYPNMLVDRIVAPTRNRDDSSRLAKFDVLDQEGICRPGERVENGSTLVLKET 840

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +++                      ++  +  VQY+ +    +   +  ++K+      
Sbjct: 841  PVNT------------------SNPIQDPHNAAVQYKPAYVSYKGPCEGVVDKVLL--TN 880

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   DI++NP G
Sbjct: 881  NSEDNHLIKILLRTTRRPEVGDKFSSRHGQKGVCGLIVRQEDMPFSDIGICPDIIMNPHG 940

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++ E   G                                            
Sbjct: 941  FPSRMTVGKLMEFLSGK------------------------------------------- 957

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                      A          T  F G     ++ +L     + +G+  +  G+TGEP  
Sbjct: 958  ----------AGALIGKFHYGT-AFGGDKVVDMSKILVEHGFNYAGKDFVTSGITGEPLS 1006

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  YG
Sbjct: 1007 AYIFFGPVYYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1066

Query: 1307 AAYVLQEMLTIKSD--DVV--------GRTRVYES---IVAGNDTFET-GTPESFNVLVK 1352
            A+ +L E L I SD  DV         G    YES       + +      P +  +L +
Sbjct: 1067 ASMLLLERLMISSDKFDVHVCRACGLLG----YESWCQYCKASSSMSILSIPYASKLLFQ 1122

Query: 1353 EMQALGLSIDLENS 1366
            E+Q++ +   L   
Sbjct: 1123 ELQSMNIVPRLRLE 1136



 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 96/734 (13%), Positives = 221/734 (30%), Gaps = 122/734 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           L++    S+++FL +           ++   ++   IT        L + + +   P   
Sbjct: 44  LVKQHIDSFNYFLNVE----------IRKIVQANDRITSDADPTFYLRYTNIQVGAPTAE 93

Query: 86  --FD--------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
             +            C  RD+TYA P+ + +  +          +  + I   ++++G +
Sbjct: 94  EYYSYATSPPIAPQQCRLRDMTYAAPITVNVEYM----------RGSQKIVRDNLFIGRM 143

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           P+M                           G F+IKG++++++ Q   S       +  +
Sbjct: 144 PIMLRSSNCILHGKSRAELTKLGECPNDPGGYFIIKGVEKVILIQEQLSKNRMIIENDRK 203

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EIL 229
                 +  + +   ++    ++   +    +++ +     + V     ALG++++ EI+
Sbjct: 204 GIPGASVTSSTQ---ERKSRTNVVCKA-GRFYLKHNTLSEDINVVILFKALGVETDQEIM 259

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
                + +Y Q          A  +  G    +  +D       + S  +L        +
Sbjct: 260 QMIGFEDMYQQ----AIAATFAESIEHGITTQNQALD------FVGSRVRLAKRAWGGAR 309

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           +  V         +   +V     N     +Y+        + +  +  +   D    Y 
Sbjct: 310 KSKVDEARELLASIILAHVPVHKYNFRPKSLYLALMV---RRVILALNEALPVDDKDYYG 366

Query: 350 D-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +  +     +   L  D  K     L  +  +  P   +T       F            
Sbjct: 367 NKRLELAGQLLALLFEDVFKKFNTELKKVTDLTIPKQRATQYDVVKKFRPQIISDGLTHA 426

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNGKGTIDDIDNLGNRRVR 465
            + G   +  R  +D     + + +   I+ + ++  +         +    +L   +  
Sbjct: 427 ISTGNWTV-KRFKMDRGGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWG 485

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            +      +     L    ++   I++ D +S + +   N         E         L
Sbjct: 486 MLCPSDTPEGEACGLVKNLALMTHITTDDEESNIARLAFNFGV------EDINVLSAEDL 539

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP--------AETSEG 577
               + L  +        +    + RA   +  RD   +H+  ICP          +  G
Sbjct: 540 TRDESYLVFLNGLLLGVTIHPTILVRAFRMLR-RDGRLSHFLSICPNDRQRCVYIASDGG 598

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKV---CDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   +           +E   +KV    D      + YL   EE    IA   S +
Sbjct: 599 RVCRPYIIVDKNGPKVTNTHLERLAQKVLRFDDFLKLGLIEYLDVNEENGANIAMYESEI 658

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                        ++  P  ++ + A +IP+  ++ S R    C
Sbjct: 659 KPY-----------------------TTHLEIEPFTILGVCAGIIPYPHHNQSPRNTYQC 695

Query: 695 NMQRQAVPLLKAEA 708
            M +QA+  + A  
Sbjct: 696 AMGKQAIGTIAANQ 709



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 82/491 (16%), Positives = 162/491 (32%), Gaps = 37/491 (7%)

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAK 507
            +DD D  GN+R+   G++L   +     +    +K+            Q         +
Sbjct: 358 PVDDKDYYGNKRLELAGQLLALLFEDVFKKFNTELKKVTDLTIPKQRATQYDVVKKFRPQ 417

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMR 559
            +   +     +   +     ++         RLS +   G+         + R     R
Sbjct: 418 IISDGLTHAISTGNWTVKRFKMDRGGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPR 477

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            + P+ +G +CP++T EG   GLV +L     +          R   +  V  D+  LSA
Sbjct: 478 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDDEESNIARLAFNFGV-EDINVLSA 536

Query: 620 ME--EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            +   +  Y+   N  L         LV               +       ++ V IA+ 
Sbjct: 537 EDLTRDESYLVFLNGLLLGVTIHPTILVRAFRMLRRDGRLSHFLSICPNDRQRCVYIASD 596

Query: 678 ----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS-GAAIVAKRA 732
                 P++  D +   +   +++R A  +L+ +       +E +      GA I    +
Sbjct: 597 GGRVCRPYIIVDKNGPKVTNTHLERLAQKVLRFDDFLKLGLIEYLDVNEENGANIAMYES 656

Query: 733 GIVEQVDAIRI-------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR----PL 781
            I      + I       V   +      + S  + Y+    +++      NQ      L
Sbjct: 657 EIKPYTTHLEIEPFTILGVCAGIIPYPHHNQSPRNTYQCAMGKQAIGTIAANQYVRFDTL 716

Query: 782 VKVGDEVRRNDIIADG-PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +      +R  +        D  ++  G+N  VA M + GY+ ED++++++  +      
Sbjct: 717 LYTLLYPQRPMVQTRTIELIDFHNMPAGQNACVAVMSYSGYDIEDALILNQASLDRGFGR 776

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEG-----LKNIDECGIICVGAEVNPGDILV 895
            +   +  V  +       +         ++         +D+ GI   G  V  G  LV
Sbjct: 777 CMVYRKQTVSIKTYPNMLVDRIVAPTRNRDDSSRLAKFDVLDQEGICRPGERVENGSTLV 836

Query: 896 GKITPKGESPM 906
            K TP   S  
Sbjct: 837 LKETPVNTSNP 847


>gi|226897648|gb|ACO90273.1| RNA polymerase beta subunit gene [Bacillus litoralis]
          Length = 397

 Score =  332 bits (852), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 223/375 (59%), Positives = 288/375 (76%), Gaps = 3/375 (0%)

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
           IGL++SL+S+A+VN +GFIETPYR+V    GKVT  + YL+A EE+N  +AQAN+ L +D
Sbjct: 1   IGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTARIDYLTADEEDNYVVAQANARLADD 60

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           GSF +  +  R  GE  ++ R++ID++D SPKQVVS A + IPFLENDDSNR LMG NMQ
Sbjct: 61  GSFIDTDIVARFRGENTVINRDRIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQ 120

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPST 756
           RQAVPL+  EAP VGTGME V  K SGAA++ K  GIVE+V+A  + +R   + +     
Sbjct: 121 RQAVPLMNPEAPLVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVYVRRYEDVNGQKVK 180

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +D Y ++KF RSNQ TC NQRP+V  GDEV + +I+ADGPS + G+LALGRN++VAFM
Sbjct: 181 GNLDKYSMLKFIRSNQGTCYNQRPIVSEGDEVVKGEILADGPSMEQGELALGRNVMVAFM 240

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+
Sbjct: 241 TWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNL 300

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  
Sbjct: 301 DERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGG 360

Query: 937 GTVVDVRIFNRHGID 951
           G ++DV++FNR   D
Sbjct: 361 GIILDVKVFNREDGD 375



 Score = 52.4 bits (124), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 40/278 (14%), Positives = 90/278 (32%), Gaps = 25/278 (8%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V      ++++  +E +      G  +    +  +     
Sbjct: 138  MEYVSGKDSGAAVICKHPGIVERVEAKNVYVRRYEDVNGQKVKGNLDKYSMLKFIRSNQG 197

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+  G EV  G+IL    +   +  +     ++ A       +  D  +    
Sbjct: 198  TCYNQRPIVSEGDEVVKGEILADGPS-MEQGELALGRNVMVAFMTWDGYNYEDAIIMSER 256

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLME 988
             V   V        +  +  +  +  E     I  +  D     DE+ I+      +  +
Sbjct: 257  LVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAEVKDGD 316

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L G+    G         L   +  E  R      +++       +             
Sbjct: 317  LLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI------------- 362

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                   K+   + GD++PPGV ++V+V++  KR I  
Sbjct: 363  ---ILDVKVFNREDGDELPPGVNQLVRVYIVQKRKISE 397


>gi|189396503|gb|ACD93405.1| RNA polymerase beta subunit [Mycoplasma hyorhinis]
          Length = 598

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 209/447 (46%), Positives = 298/447 (66%), Gaps = 11/447 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + 
Sbjct: 1   DQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQNIGLILNF 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             +A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE+    E 
Sbjct: 61  AVYAKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDENNKIIEP 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NMQRQAVPL
Sbjct: 121 EIIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNMQRQAVPL 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +  EAP+V TG+E+ VAK S   I A   G V  VD+  I I++ +G        +  Y 
Sbjct: 181 ITTEAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG-------NIKTYH 233

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 234 LRYFERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFSTWYGYNY 293

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++DE GI+ 
Sbjct: 294 EDAIIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVR 353

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           +G+EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  GTV+DV+
Sbjct: 354 IGSEVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQ 413

Query: 944 IFNRHGID-KNERSISVEREQIELLAR 969
           I +R   D   +    + +  I    +
Sbjct: 414 ILSRTREDNLEDGVEKIIKVFIAQKRK 440



 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/415 (31%), Positives = 186/415 (44%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD++    +   +  +   + +L A       +  D  +     V   V 
Sbjct: 251  IVEVGQFVKQGDLICDGPST-DQGELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 309

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    +   S +   +    +       +  LD N   R+   +   + + G  
Sbjct: 310  -TSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGSEVSAGDILVGRT 368

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W + A   +     V+           IL    +      
Sbjct: 369  SPKGEDNPTPE--EKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILSRTRE------ 420

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
               D++  GV +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMPFL+DGTP+DI
Sbjct: 421  ---DNLEDGVEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPFLEDGTPIDI 477

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP G+PSRMN+GQI E HLG     L  K    + D      +  L +          
Sbjct: 478  LLNPQGIPSRMNIGQILEMHLGMVAKKLDIKFVCPVFDGVKLDKMKELFN---------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 528  --------------------QAGIP------------------------ESGKFTLYDGI 543

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD  V++GY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 544  TGQPFDNDVSIGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFG 598


>gi|34494364|emb|CAD98757.1| RNA polymerase beta subunit [Kluyvera intermedia]
          Length = 336

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 209/336 (62%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +K+R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKDRLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + + R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|284163647|ref|YP_003401926.1| DNA-directed RNA polymerase subunit B [Haloterrigena turkmenica DSM
            5511]
 gi|284013302|gb|ADB59253.1| DNA-directed RNA polymerase subunit B [Haloterrigena turkmenica DSM
            5511]
          Length = 609

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 128/598 (21%), Positives = 210/598 (35%), Gaps = 105/598 (17%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D + D    +  D     ++LVA    H       + I   ++       I   E     
Sbjct: 93   DDLVDHGYVEFIDAEEEEDILVAVDEEHLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASP 152

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R T      + +    +     +   +     +        +        G       + 
Sbjct: 153  RITMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQN 209

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D 
Sbjct: 210  FVVAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD- 267

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                  +           L     V+      +++VL           +         + 
Sbjct: 268  ------VRGARGEDAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQK 321

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +R         E+         + +               ++ KV V  +R  + GDK A
Sbjct: 322  RRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFA 369

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G++
Sbjct: 370  SRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRR 429

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +                                                       TP F
Sbjct: 430  VDG-----------------------------------------------------TP-F 435

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             G DE+ +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS
Sbjct: 436  LGEDEDELRDGLEDAGFDSAGKETMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARS 495

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------- 1320
             G   ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD           
Sbjct: 496  RGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICANCG 555

Query: 1321 -----DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                 +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 556  MSAVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.0 bits (97), Expect = 0.67,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A     G +E       D      V ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISQQEIEAL--QDGDLE-----FDDLVDHGYVEFIDAEEEEDILVAVDEEHLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|226897638|gb|ACO90268.1| RNA polymerase beta subunit gene [Bacillus firmus]
          Length = 367

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 224/364 (61%), Positives = 285/364 (78%), Gaps = 3/364 (0%)

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQAN 631
           T EG NIGL++SL+SFA+VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQAN
Sbjct: 1   TPEGPNIGLINSLSSFAKVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQAN 60

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + L +DGSF +E V  R  GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR L
Sbjct: 61  ALLGDDGSFLDEEVVARFKGENTVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRAL 120

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG- 750
           MG NMQRQAVPL++ EAP VGTGME V  K SGAA++ K  GIVE V+A  + +R ++  
Sbjct: 121 MGANMQRQAVPLMQPEAPRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIKNV 180

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           D       +D YR++KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN
Sbjct: 181 DGQEVKGDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRN 240

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVAFM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E
Sbjct: 241 VLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGE 300

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           + L+N+DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR
Sbjct: 301 DALRNLDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLR 360

Query: 931 VPSG 934
           VP G
Sbjct: 361 VPHG 364


>gi|34494362|emb|CAD98756.1| RNA polymerase beta subunit [Enterobacter gergoviae]
          Length = 336

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 208/336 (61%), Positives = 264/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+L ++G F ++LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNFVIAQANSNLSDEGRFVDDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TSVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + + R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|318603082|emb|CBJ04593.1| RNA polymerase beta subunit [Pseudomonas sp. R-38242]
          Length = 336

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 199/335 (59%), Positives = 259/335 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 2   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 61

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 62  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 121

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 122 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 181

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 182 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 241

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 242 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 301

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+
Sbjct: 302 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTT 336


>gi|318603078|emb|CBJ04592.1| RNA polymerase beta subunit [Pseudomonas sp. R-38235]
          Length = 336

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 200/335 (59%), Positives = 258/335 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 2   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 61

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 62  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 121

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++ E     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 122 IAQASATMSEQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 181

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 182 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 241

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 242 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 301

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT+
Sbjct: 302 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTT 336


>gi|52694263|emb|CAG30661.1| DNA-directed RNA polymerase beta chain [Marinobacterium georgiense]
          Length = 343

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 206/343 (60%), Positives = 271/343 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER+++ER+S  + D++MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVRERLSMAESDNLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRV 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVFARTNDYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG+VT+++ YLSA+EE    IAQA++++D++G  T++LV  R   E  ++P E+I
Sbjct: 121 YRRVLDGQVTDEIDYLSAIEENKYVIAQASAAMDDNGRLTDDLVAVRHLNEFTVMPPERI 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            ++D SP+QVVS+AA+LIPFLE+DD+NR LMG NMQRQAVP L AE P VGTG+E  VA+
Sbjct: 181 QYMDVSPRQVVSVAAALIPFLEHDDANRALMGSNMQRQAVPTLLAEKPLVGTGIERNVAQ 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG  +VA+R G++E VDA R+V+R  + ++    +GVDIY L K+ RSNQNTC+NQR +
Sbjct: 241 DSGVCVVARRGGVIESVDAARVVVRVHDDEVQAGDAGVDIYNLTKYVRSNQNTCINQRSI 300

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           V+ G+ V+R DI+ADGPS DLG+LALG+NM +AFMPW+GYNFE
Sbjct: 301 VRPGEVVQRGDIMADGPSVDLGELALGQNMRIAFMPWNGYNFE 343


>gi|242392394|dbj|BAH80410.1| RNA polymerase subunit B' [Natronorubrum sulfidifaciens]
          Length = 609

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 125/595 (21%), Positives = 209/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDLNEKHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYTHLDDDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTQDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELREGLEDAGFNSAGKEVMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 45.5 bits (106), Expect = 0.073,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      ++     A       +E    +  D      + ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-PRITDQEIDA-------LEQGDLEFEDLVDHGYIEFIDAEEEEDIYVAVDEDDLN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|73697639|gb|AAZ81436.1| RNA polymerase beta subunit [Mycoplasma cavipharyngis]
          Length = 668

 Score =  332 bits (851), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 150/519 (28%), Positives = 240/519 (46%), Gaps = 38/519 (7%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLG 857
                       +L  + P  G   E ++       +V++   T + ++   +  R    G
Sbjct: 163  MGANMQRQATPLLKPYAPTVGTGLEYAIARDSGMALVAKADGTVVAVDGDSLSIRYDHAG 222

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +              +  +  I+ VG +V    ILV          +   + +L A  
Sbjct: 223  VNKRYHLTKFKRSNQDTSNSQTPIVRVGEKVFKDQILVDGP-AMQNGELALGQNVLIAFT 281

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D  +     V   +      + H I+   R+ + + E    +    DD +  
Sbjct: 282  TWSGYNYEDAIVLSSRLVEDDIFTSIHIDEHTIEC-LRTKNGDEEITRQIPNVSDDAKRY 340

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            LD +       I+ G     G     K++  +    +   +     FA +  +V+ +   
Sbjct: 341  LDED-----GIIMVGAEVYEGDILVGKTSPKAQVEQTSEEKLLQAIFAEKVRQVKDSSLK 395

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +    E   + +      K   +Q G+D+   V+ ++K+F+A KR IQ GDKMAGRHGNK
Sbjct: 396  VPHGGEGVVAAV------KRFSVQSGNDLNDDVIEIIKIFIAQKRKIQMGDKMAGRHGNK 449

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG---------- 1147
            GIVSRI+P EDMP L+DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A             
Sbjct: 450  GIVSRIVPIEDMPHLEDGTPIDILLNPLGVPSRMNIGQVLEMHLGLAARKLVLKELIKAH 509

Query: 1148 ---LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               L   + S +   + +     +++F E +      T++ ++   +++  V    KSG+
Sbjct: 510  FTNLDHSVISQMFGVRESSIKLLMKNFKEHLATLKIDTQEKANKKLNNLNLVIILQKSGL 569

Query: 1205 -------PVSTPVFDGADEEAINSMLRMADLDE---SGQSILYDGLTGEPFDRPVTVGYI 1254
                    + TPVF G +++ +  +++ A +D     G+  LYDG TGE F+ P+ VG  
Sbjct: 570  TIEDLNYKICTPVFSGVNQKDLVEIMQEAGIDPIKTKGKFDLYDGRTGEKFEHPIAVGIS 629

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            YMLKL+HMV DK++ARS G YS +TQQPLGGKS  GGQ+
Sbjct: 630  YMLKLDHMVDDKIHARSVGPYSKITQQPLGGKSQNGGQK 668



 Score =  327 bits (838), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 207/442 (46%), Positives = 293/442 (66%), Gaps = 8/442 (1%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +T+ RR+SA+G GG+ R    +++RDVH ++YGRICP ET EG NIGL+ SL +
Sbjct: 1   QNPLSELTNKRRISAMGPGGINRDDPNLDIRDVHYSNYGRICPIETPEGMNIGLIMSLAT 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++R++  GFI +PY KV +G++T+++ +L+A+ E+   I +A S+ +E        V  R
Sbjct: 61  YSRIDELGFITSPYYKVKNGQITDEITWLTALREDEYVITEAISARNEKNELLSP-VNAR 119

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                     + +D+ID +P QVVSI+ + IPFLENDD+NR LMG NMQRQA PLLK  A
Sbjct: 120 YRSFIESFDAKDVDYIDVNPSQVVSISTASIPFLENDDANRALMGANMQRQATPLLKPYA 179

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  +A+ SG A+VAK  G V  VD   + IR     ++        Y L KF+
Sbjct: 180 PTVGTGLEYAIARDSGMALVAKADGTVVAVDGDSLSIRYDHAGVN------KRYHLTKFK 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T  +Q P+V+VG++V ++ I+ DGP+   G+LALG+N+L+AF  W GYN+ED+++
Sbjct: 234 RSNQDTSNSQTPIVRVGEKVFKDQILVDGPAMQNGELALGQNVLIAFTTWSGYNYEDAIV 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +S R+V +D+FTSIHI+E  +    TK G EEITR IPNVS++  + +DE GII VGAEV
Sbjct: 294 LSSRLVEDDIFTSIHIDEHTIECLRTKNGDEEITRQIPNVSDDAKRYLDEDGIIMVGAEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN-R 947
             GDILVGK +PK +   T EEKLL+AIF EK   V+D+SL+VP G  G V  V+ F+ +
Sbjct: 354 YEGDILVGKTSPKAQVEQTSEEKLLQAIFAEKVRQVKDSSLKVPHGGEGVVAAVKRFSVQ 413

Query: 948 HGIDKNERSISVEREQIELLAR 969
            G D N+  I + +  I    +
Sbjct: 414 SGNDLNDDVIEIIKIFIAQKRK 435


>gi|146302818|ref|YP_001190134.1| DNA-directed RNA polymerase subunit B [Metallosphaera sedula DSM
            5348]
 gi|145701068|gb|ABP94210.1| DNA-directed RNA polymerase, subunit B' / DNA-directed RNA
            polymerase, subunit B' [Metallosphaera sedula DSM 5348]
          Length = 1124

 Score =  332 bits (850), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 121/612 (19%), Positives = 204/612 (33%), Gaps = 101/612 (16%)

Query: 779  RPLVKVGDE--VRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +PLV   D   +++  I  D        +  D     N  +A  P         + I   
Sbjct: 583  KPLVTKEDIENLKKGKITFDTLVKEGKIEFLDAEEEENAYIALEPKDVTKDHTHLEIWAP 642

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
             +     + I   E     R+T              +   ++         +        
Sbjct: 643  AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQIR---TDTRAHLLHYPQKPI 699

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    +   G +        + A+      ++ D  +   S V   +     F  +  ++
Sbjct: 700  VQTRALEAIGYTERPAGNNAIFALMSYTGYNMEDAVIMNKSSVDRGMFRSTFFRLYSAEE 759

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             +     E E +      +  +              +L     VS     K   VL   +
Sbjct: 760  IKYPGGQEDEILLPEPGVRGYKGKD--------YYRLLESNGIVSPEVDVKGGDVLIGKV 811

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                   ++ + +    K   ++  +    E     L    +                 +
Sbjct: 812  SPPRFLQEFKELSPDQAKRDTSI--ITRHGERGTVDLVLVTE------------TSEGNK 857

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV V   R  + GDK A RHG KG++  ++P  DMP+   G   DI+LNP  +PSRM 
Sbjct: 858  LVKVRVRDLRIPEIGDKFATRHGQKGVIGMLIPQVDMPYTTSGLVPDIILNPHALPSRMT 917

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQI E   G      G  I                                        
Sbjct: 918  VGQIMEAIAGKFVAATGNPID--------------------------------------- 938

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP F     E I   L        G  ++YDG TGE     +  G
Sbjct: 939  --------------ATP-FYNTPIEEIQRKLLEHGYLSDGSEVVYDGRTGEKLKGRILFG 983

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  KL+HMV+DK++ R  G   ++T+QP  G++  GG R GEME  C+  YGAA +++
Sbjct: 984  IVYYQKLHHMVADKMHGRGRGPVQILTRQPTEGRAREGGLRFGEMERDCLIGYGAAMLIK 1043

Query: 1313 EMLTIKSD-------DVVG------RTR-VYESIVAGNDT--FETGTPESFNVLVKEMQA 1356
            + L   SD       +  G      RT+  Y   + G+ T  +      +F +L++E+ +
Sbjct: 1044 DRLLDNSDRATVYVCEQCGYVGWYDRTKNKYICPIHGDKTTLYPVVISYAFKLLLQELMS 1103

Query: 1357 LGLSIDLENSRT 1368
            + ++  L     
Sbjct: 1104 MVIAPKLVLGDK 1115



 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 145/980 (14%), Positives = 296/980 (30%), Gaps = 198/980 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+     S++ F+             LQ        I        +         P+   
Sbjct: 20  LVRQHLDSFNDFIKNK----------LQEIIDEQGEIITEIPGLKIRLGKIRVGKPRVRE 69

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R+LTYA P+ +T+  +  +++               +++GD+P+M
Sbjct: 70  ADKGDKEITPMEARLRNLTYAAPIFLTMTPVENNIEGDPT----------EVHIGDIPIM 119

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++V+Q   +       D G+A  
Sbjct: 120 LKSIADPTSEFSQDKLVEIGEDPKDPGGYFIINGSERVIVTQEDLATNRVLT-DVGKAGS 178

Query: 175 SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
           +  + +  +II      + + + IE      IHV       ++P    + ALG++++E  
Sbjct: 179 N--VTHTAKIISSTSGYR-VPITIERLKDSTIHVSFPSAPGRIPFAILMRALGVETDE-- 233

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                 I  +   D          L   + +SS    +D     +  G+K    + K   
Sbjct: 234 -----DITLAVSLDPQIQNELLPSLEQASSISSKEDALDFIGNRVAIGQKREMRIQKAEQ 288

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
            L +  +  +G                  +  E+Y+   +  D+       L+       
Sbjct: 289 ILDKYFLPHIGTNPSDRVAKAYYLAFAVSKLIELYLGRREPDDKDHYANKRLKLAGDLFA 348

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
               + +   V +  +          +   +AL+      RP D+ +  +  ++    + 
Sbjct: 349 SLFRVAFKAFVKDLVFQLEKSKVRGRRLAINALV------RP-DIISERIRHALATGNWV 401

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                    + R      L+      V  + +       + L   + G+    +  +   
Sbjct: 402 GGRTGVSQLLDRTNWLSMLSHLRRV-VSSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 460

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE--FFC 518
           +  V+++  + +    +    +ER++         D++        +             
Sbjct: 461 SGLVKNIALLAQISVGINEKSLERTLYNLGVVPIDDAIKKVKSEEGQSENYQTWSKVILN 520

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PTHYGRICPAETSEG 577
              +    +      +I  +RR   L               +V+  +  GR+        
Sbjct: 521 GRLIGYYPDGRELAEKIRESRREGELSDEVNVSYNITETFNEVYINSDSGRVR------- 573

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + +V              ++              + +L A EEEN YIA     + +D
Sbjct: 574 RPLIVVKHGKPLVTKEDIENLKKGKITFDTLVKEGKIEFLDAEEEENAYIALEPKDVTKD 633

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                                     ++     ++ I AS+IP+ E++ S R      M 
Sbjct: 634 H-----------------------THLEIWAPAILGITASIIPYPEHNQSPRNTYQSAMA 670

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ L  A                                                + +
Sbjct: 671 KQALGLYAANYQI-----------------------------------------RTDTRA 689

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y               Q+P+V+               +    +   G N + A M 
Sbjct: 690 HLLHYP--------------QKPIVQ----------TRALEAIGYTERPAGNNAIFALMS 725

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNV----SEEG 872
           + GYN ED++++++  V   +F S     +         G E EI    P V     ++ 
Sbjct: 726 YTGYNMEDAVIMNKSSVDRGMFRSTFFRLYSAEEIKYPGGQEDEILLPEPGVRGYKGKDY 785

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + ++  GI+    +V  GD+L+GK++P        E    +A         RDTS+   
Sbjct: 786 YRLLESNGIVSPEVDVKGGDVLIGKVSPPRFLQEFKELSPDQAK--------RDTSIITR 837

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
            G  GTV  V +      +K
Sbjct: 838 HGERGTVDLVLVTETSEGNK 857


>gi|224095387|ref|XP_002196633.1| PREDICTED: hypothetical protein [Taeniopygia guttata]
          Length = 1280

 Score =  332 bits (850), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 103/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 857  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 916

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 917  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 975

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 976  NKSMP------------TVTQTPLEGSSVPQQ-----PQYKDVPVTYKGATDSYIEKVMI 1018

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 1019 SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDTGICPDIIM 1076

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 1077 NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 1109

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 1110 ---------------------------AFGGSKVKDVCEDLIRHGYNYLGKDYVTSGITG 1142

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1143 EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1202

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 1203 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1262

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ ++   
Sbjct: 1263 ELQSMNIIPRLKLAKYNE 1280



 Score =  203 bits (517), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 129/955 (13%), Positives = 279/955 (29%), Gaps = 200/955 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
            L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 187  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGTPDVEE 237

Query: 85   ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 238  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 287

Query: 139  T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                       G F++KG++++++ Q   S          R   
Sbjct: 288  LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEA-DRKGT 346

Query: 175  SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMALGMD 224
             G  + +               + K   ++ + + R           +P+     A+G++
Sbjct: 347  VGASVTSST------------HEKKSRTNMVVKQGRFYLRHNTLSEDIPIAIIFKAMGVE 394

Query: 225  SE-EILSTFYPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
            S+ EI+     +            +      F    A   +G KV    +     +  +E
Sbjct: 395  SDQEIVQMIGTEEHVMAAFAPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGPKKTKME 454

Query: 276  SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
              ++L +  +  L    VK     + C+    V    V    GE  ++  D    K LE 
Sbjct: 455  EARELLASTI--LTHVLVKEFNFRAKCIY-TAVMVRRVILAQGENKVDDRDYYGNKRLEL 511

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                       L+    +    I + ++  +      A  D+ + MR   ++   V    
Sbjct: 512  AGQLLSLLFEDLFKKFNSELKKIADQVIPKQR----AAQFDVVKHMRQDQITNGMVNA-- 565

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
             +   +   ++ +   G  ++  RL+  +   +            K+             
Sbjct: 566  ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ------ 619

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                    +    +  + +    +  +           D   +     +  + V     E
Sbjct: 620  ---PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLASNLGVEDVNLLCGE 676

Query: 516  FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +  +  + N L  I   ++L    +  + RA    E   +      R     + 
Sbjct: 677  ELSYPNVFLVFLNGNILGVIRDHQKLVNTFRI-LRRAGYINEFVSISTNLSDRCVYISSD 735

Query: 576  EGHNIGL--VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             G       +      A  N     +   YR   D      V YL   EE +  IA   +
Sbjct: 736  GGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHEGLVEYLDVNEENDCNIALYEN 795

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            ++++D                          ++  P  ++ + A LIP+  ++ S R   
Sbjct: 796  TINKD-----------------------TTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 832

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             C M +QA+  +         G        +   ++A                       
Sbjct: 833  QCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----------------------- 860

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                     Q+P+VK                 D   L  G+N  
Sbjct: 861  -----------------------YPQKPMVK----------TKTIELIDFEKLPAGQNAT 887

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEE 871
            VA M + GY+ ED++++++  +       +  +  +    R T    +++   + + +  
Sbjct: 888  VAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATR 947

Query: 872  GLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                    +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 948  KPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQTPLEGSSVPQQPQYKDVP 1002


>gi|224031673|gb|ACN34912.1| unknown [Zea mays]
          Length = 362

 Score =  332 bits (850), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 131/322 (40%), Gaps = 74/322 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 89   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPH 148

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 149  AIPSRMTIGQLIECIMGKVAAQMGKEGD-------------------------------- 176

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L   +    G   +Y+G TG   
Sbjct: 177  ---------------------ATP-FTDVTVDNISKALHKCNYQMRGFETMYNGHTGRKL 214

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 215  TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 274

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYE-----SIV---------AG----NDTFETGTPESF 1347
            GAA+ L+E L  +SD    R  V E     +I           G     D  +   P + 
Sbjct: 275  GAAFFLKERLFDQSD--AYRVHVCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYAC 332

Query: 1348 NVLVKEMQALGLSIDLENSRTK 1369
             +L +E+ A+ ++  +     K
Sbjct: 333  KLLFQELMAMAIAPRMLTHDMK 354



 Score = 42.4 bits (98), Expect = 0.59,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 9/76 (11%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK +P  +           A        
Sbjct: 16  NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDD---------AQGQASRYS 66

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 67  KRDHSTALRHSESGMV 82


>gi|318603059|emb|CBJ04588.1| RNA polymerase beta subunit [Pseudomonas sp. R-37948]
          Length = 334

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 199/334 (59%), Positives = 258/334 (77%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHY
Sbjct: 1   KPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  
Sbjct: 61  GRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 IAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDD 180

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R
Sbjct: 181 ANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVR 240

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LA
Sbjct: 241 VADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELA 300

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           LG+NM +AFM W+G+NFEDS+ +SER+V ED FT
Sbjct: 301 LGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFT 334


>gi|158602609|gb|ABW74628.1| RpoB [Bacillus subtilis subsp. subtilis]
          Length = 183

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 78/205 (38%), Positives = 126/205 (61%), Gaps = 22/205 (10%)

Query: 7   FNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT 66
             G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI 
Sbjct: 1   QYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIE 50

Query: 67  AFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
            F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K
Sbjct: 51  DFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVK 101

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           +Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP
Sbjct: 102 DQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIP 158

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRK 211
           ++G W++ E D+KD+++VRIDR RK
Sbjct: 159 NRGAWLEYETDAKDVVYVRIDRTRK 183


>gi|34494006|emb|CAD66146.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 208/336 (61%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           + ER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VIERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GZ  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGZSSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP ++A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPSVRADXPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|189396505|gb|ACD93406.1| RNA polymerase beta subunit [Mycoplasma hyorhinis]
          Length = 598

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 210/447 (46%), Positives = 299/447 (66%), Gaps = 11/447 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + 
Sbjct: 1   DQINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQNIGLILNF 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             +A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE+    E 
Sbjct: 61  AVYAKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDENNKIIEP 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NMQRQAVPL
Sbjct: 121 EIIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNMQRQAVPL 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +  EAP+V TG+E+ VAK S   I A   G V  VD+  I I++ +G        + IY 
Sbjct: 181 ITTEAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG-------NIKIYH 233

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF  W+GYN+
Sbjct: 234 LRYFERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFSTWYGYNY 293

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++DE GI+ 
Sbjct: 294 EDAIIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVR 353

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           +G+EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  GTV+DV+
Sbjct: 354 IGSEVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQ 413

Query: 944 IFNRHGID-KNERSISVEREQIELLAR 969
           I +R   D   +    + +  I    +
Sbjct: 414 ILSRTREDNLEDGVEKIIKVFIAQKRK 440



 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 129/415 (31%), Positives = 186/415 (44%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD++    +   +  +   + +L A       +  D  +     V   V 
Sbjct: 251  IVEVGQFVKQGDLICDGPST-DQGELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 309

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    +   S +   +    +       +  LD N   R+   +   + + G  
Sbjct: 310  -TSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGSEVSAGDILVGRT 368

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W + A   +     V+           IL    +      
Sbjct: 369  SPKGEDNPTPE--EKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILSRTRE------ 420

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
               D++  GV +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMPFL+DGTP+DI
Sbjct: 421  ---DNLEDGVEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPFLEDGTPIDI 477

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP G+PSRMN+GQI E HLG     L  K    + D      +  L +          
Sbjct: 478  LLNPQGIPSRMNIGQILEMHLGMVAKKLDIKFVCPVFDGVKLDKMKELFN---------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 528  --------------------QAGIP------------------------ESGKFTLYDGI 543

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD  V++GY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 544  TGQPFDNDVSIGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFG 598


>gi|325294355|ref|YP_004280869.1| DNA-directed RNA polymerase subunit beta [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325064803|gb|ADY72810.1| DNA-directed RNA polymerase subunit beta [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 1446

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 139/463 (30%), Positives = 219/463 (47%), Gaps = 76/463 (16%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           RK F K  E   IPDL++    SY+ FL +N APD+R N GL++AF+  FPI   S    
Sbjct: 21  RKSFAKRKETFPIPDLLQFPFESYERFLQLNKAPDKRENVGLESAFRQAFPIVDESSGVE 80

Query: 74  LEFVSYEFD----------------------------PPKFDVDDCLWRDLTYAVPLKIT 105
           + +  YE                               PK+  D+C  R + Y+ PL++ 
Sbjct: 81  IHYKGYEIGDWYCKCGKFQGLGGKGVVCPKCGMEVVFRPKYSPDECKERGIDYSAPLRVL 140

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
             L ++  D  TG K    IKE  +Y G++PLMT+ GTF+I G +++VVSQLHRSPG+ F
Sbjct: 141 FELHIWQKDPKTGEKIAPIIKENKMYFGEIPLMTERGTFIINGTEKVVVSQLHRSPGLFF 200

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-D 224
             +  + +   +++    IIP  G W++ E    +I++ +IDR+R+   T  L A G+  
Sbjct: 201 KSEVSKTTQVARIIDIASIIPAMGSWLEFEIPYNEILYAKIDRKRRFIGTYLLRAFGIRT 260

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
            EEIL+ FY                   +  V    +  +V+I TGE   +         
Sbjct: 261 DEEILNLFYGD---------AIETFKVENGEVVKVENGEVVNIKTGEIKTQ--------- 302

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
                           + L G Y+  D+++ ETGEI  EA + +   S +    +E + I
Sbjct: 303 ----------------EELTGYYLVSDVIDPETGEIVQEAYEELSTSSRKLPEGAEFKAI 346

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKD--------ALLDIYRVMRPGDVSTFSVAESMF 396
              +  +    A I NTL  +K    ++        A ++I+R +RPGD +T   A+ +F
Sbjct: 347 ---HSKATPYGAVIVNTLRKEKRDRVREKIDDPLIAAYVEIFRKVRPGDTATVEGAKKLF 403

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +FF +  YDLS VGR K+N ++     + +  + KED+ +I
Sbjct: 404 ESMFFSTKNYDLSRVGRAKINEKVYPK--EKLSKLTKEDLKSI 444


>gi|38677884|emb|CAE30282.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 182

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 78/204 (38%), Positives = 127/204 (62%), Gaps = 22/204 (10%)

Query: 9   GLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
           G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F
Sbjct: 1   GRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDF 50

Query: 69  SGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           +G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q
Sbjct: 51  TGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQ 101

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
            ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++
Sbjct: 102 DVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNR 158

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKV 212
           G W++ E D+KD+++VRIDR RK+
Sbjct: 159 GAWLEYETDAKDVVYVRIDRTRKL 182


>gi|193735380|gb|ACF20192.1| RNA polymerase beta subunit [Mycoplasma columbinum]
          Length = 596

 Score =  332 bits (850), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 210/422 (49%), Positives = 304/422 (72%), Gaps = 8/422 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGF++TPY KV +G V  + V YL+A+EE   YIAQ+   +DE+    ++ + 
Sbjct: 61  TYAKVNEYGFLQTPYYKVDNGIVNYDQVEYLTAIEEIGFYIAQSTVKVDENNKIVDDQIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     +L   ++ID+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ 
Sbjct: 121 MRHNYTYVLGKADQIDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLET 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFV TG+ES +AK S   I AK +G+VE VD  +I +R+ +  LD        Y L  
Sbjct: 181 EAPFVATGLESAIAKYSSTNITAKNSGVVEYVDGSKIKVRNEKNTLD-------TYMLKN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQ+T V+QRPLVKVG  + + D++ DG S   G+LALG+N++VAF  + GYN+ED+
Sbjct: 234 FQRSNQDTVVHQRPLVKVGQSIEKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++ER+V +DVFTSIHIEE  ++ R +++G +E+T DIPNVS+   +++DE GI+ VG+
Sbjct: 294 VILNERLVKDDVFTSIHIEEQTILFRTSRVGDDELTADIPNVSKFATRHLDENGIVKVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGD+LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G SGTV++V + +
Sbjct: 354 EVLPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQINVKDTSLKVKNGHSGTVINVEVLS 413

Query: 947 RH 948
           R 
Sbjct: 414 RD 415



 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 138/453 (30%), Positives = 202/453 (44%), Gaps = 82/453 (18%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              K+  E+ T D   +      N D    +  ++ VG  +  GD+LV   + K    +  
Sbjct: 216  KIKVRNEKNTLDTYMLKNFQRSNQDTVVHQRPLVKVGQSIEKGDLLVDGSSFKN-GELAL 274

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVERE 962
             + ++ A    K  +  D  +            S  + +  I  R     ++  ++ +  
Sbjct: 275  GKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTILFRTSRVGDDE-LTADIP 333

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +   A    DE  I+         ++L G+ +  G     +   L S ++      Q  
Sbjct: 334  NVSKFATRHLDENGIVKVGSEVLPGDVLVGRVSPKGDDNPSQEEKLLSAVL------QQR 387

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q  V+D  +   V++       +  +L         + +       GV ++VKV +A+KR
Sbjct: 388  QINVKDTSL--KVKNGHSGTVINVEVL--------SRDENNVQFEDGVEKIVKVSIAVKR 437

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP GVPSRMN+GQ+ E HLG
Sbjct: 438  KIRVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLG 497

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG K  +   D     +I                                     
Sbjct: 498  MAARELGVKFVTPAFDGIKKEEI------------------------------------- 520

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                    F+   E  +          ESG+  L D +TG  FD PV+VG +YMLKLNHM
Sbjct: 521  --------FNLIKEAKL---------PESGKQYLIDPITGRRFDNPVSVGVMYMLKLNHM 563

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            V DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 564  VDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|73697703|gb|AAZ81468.1| RNA polymerase beta subunit [Acholeplasma oculi]
 gi|77543232|gb|ABA87040.1| RNA polymerase beta subunit [Acholeplasma oculi]
          Length = 629

 Score =  331 bits (849), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 228/454 (50%), Positives = 303/454 (66%), Gaps = 32/454 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 1   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 60

Query: 590 ARVNAYGFIETPYRKVCD-----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TP+ KV        KV+ +V+YL+A +E++  IA A + +D+DG+FT+  
Sbjct: 61  AKVDDYGFIKTPFLKVTKTASGTPKVSEEVIYLTADQEQDEVIASAATPMDKDGNFTDTR 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE  +     +  +D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 121 VIARKNGETGIYDASDVTCMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
           +  +P VGTG+E   AK SGA +VA  AG V  VDA +IVI           +       
Sbjct: 181 QPTSPIVGTGIEYRAAKDSGAVVVALNAGYVTYVDARKIVIVKEPTTDVKVGNKTIYKTG 240

Query: 759 -------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                               + Y L++F RSNQ+T V Q+P+V  G+ V + D+IADGPS
Sbjct: 241 GDFNYAIAKQLYDHKQLDLFETYELIQFFRSNQDTLVLQKPIVFQGEYVEKGDVIADGPS 300

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LG 857
           TD G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G
Sbjct: 301 TDNGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQSNG 360

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ 
Sbjct: 361 KEEITREIPNVGQEAVKYLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVI 420

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           G+KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 421 GDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 454



 Score =  284 bits (727), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 118/413 (28%), Positives = 180/413 (43%), Gaps = 65/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD++    +      +     +  A    +  +  D  +     V   V 
Sbjct: 282  IVFQGEYVEKGDVIADGPSTDN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 340

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   S  +E+I     +   E V            I+ G     G  
Sbjct: 341  TSIHIDEYEIETRDLKQSNGKEEITREIPNVGQEAV----KYLDERGIIVPGSEVKEGDI 396

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 397  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 452

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGT VDI
Sbjct: 453  --GDQLPVGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYMADGTYVDI 510

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ + + D   + D+  + S          
Sbjct: 511  MLNPLGVPSRMNIGQILEIHLGISAKKLGIKVATPVFDGVTDEDLKEIMSDAGIAPDGK- 569

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T ++DG                           
Sbjct: 570  ---------------------------TYLYDG--------------------------R 576

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE +   ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 577  TGEAYKNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 629


>gi|242392346|dbj|BAH80386.1| RNA polymerase subunit B' [Haloterrigena thermotolerans]
 gi|242392348|dbj|BAH80387.1| RNA polymerase subunit B' [Haloterrigena turkmenica]
          Length = 609

 Score =  331 bits (849), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 124/596 (20%), Positives = 207/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVGVDEDDLTENHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             D++ +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDKDELREGLEEAGFDSAGKETMYSGITGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 41.2 bits (95), Expect = 1.4,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A       ++    +  D      + ++ A EEE+  +      L 
Sbjct: 71  EDGE-PRISEQEIEA-------LQEGDLEFEDLVDHGYIEFIDAEEEEDILVGVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+                          ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 ENH-----------------------THLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|80978861|gb|ABB54679.1| RNA polymerase beta subunit [Mycoplasma equigenitalium]
          Length = 598

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 216/442 (48%), Positives = 303/442 (68%), Gaps = 3/442 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ ++  RRL++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S 
Sbjct: 2   NPLAELSSKRRLTSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASH 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN  GF+ETPY +V DG V  NDV YLSA EE      Q+++ ++E+    ++ V  R
Sbjct: 62  ARVNELGFLETPYFRVNDGVVDYNDVCYLSAAEETGHIFIQSSTKVNENNEIADDFVVAR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ I VP+ +++FID   KQ+ S+AAS IPFLENDD+NR LMG NMQRQAVPLL +EA
Sbjct: 122 YNGDYIQVPKTEVEFIDVDSKQMTSLAASAIPFLENDDANRALMGSNMQRQAVPLLISEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E+ +AK S + +V +RAG V  VD  RI I++ E   +     VD Y L  F+
Sbjct: 182 PLVGTGIEADIAKFSYSNVVCERAGEVVYVDGNRIEIKTEEDKKNK-KGHVDKYYLRVFE 240

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ + ++Q+P+VK+GD V   +IIADG S   G+L+LG+N++VAF   +GYN+ED+++
Sbjct: 241 RSNQASLIHQKPVVKLGDFVEEGEIIADGSSCSEGELSLGKNVIVAFSTLNGYNYEDAVI 300

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE  +  R++K G + +T DIPN S    +++D  GI+ +G+EV
Sbjct: 301 LSERLVKDDVYTSIHIEEQTIQFRNSKAGNDILTTDIPNTSTASKRHLDANGIVTIGSEV 360

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVG+++PK +   TPEEKLL A+F +K  + RDTSL+V +G SGT++D  + +R 
Sbjct: 361 QPGDILVGRVSPKADDNPTPEEKLLSALFSKKQANTRDTSLKVKNGHSGTIIDTEVLSRE 420

Query: 949 GIDK-NERSISVEREQIELLAR 969
             D   +    + +  I    +
Sbjct: 421 NGDVLEDGVEKIVKVWIAQKRK 442



 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 135/506 (26%), Positives = 204/506 (40%), Gaps = 84/506 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSM-------LISERMVSEDVFTSIHIEEFEVMAR 852
                       +L++  P  G   E  +       ++ ER           IE      +
Sbjct: 165  MGSNMQRQAVPLLISEAPLVGTGIEADIAKFSYSNVVCERAGEVVYVDGNRIEIKTEEDK 224

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              K G  +               I +  ++ +G  V  G+ ++   +   E  ++  + +
Sbjct: 225  KNKKGHVDKYYLRVFERSNQASLIHQKPVVKLGDFVEEGE-IIADGSSCSEGELSLGKNV 283

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTV-----VDVRIFNRHGIDKNERSISVEREQIELL 967
            + A       +  D  +     V   V     ++ +             ++ +       
Sbjct: 284  IVAFSTLNGYNYEDAVILSERLVKDDVYTSIHIEEQTIQFRNSKAGNDILTTDIPNTSTA 343

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            ++   D   I+      +  +IL G+ +            L S L S+            
Sbjct: 344  SKRHLDANGIVTIGSEVQPGDILVGRVSPKADDNPTPEEKLLSALFSK------------ 391

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                 +   +     +            ++   + GD +  GV ++VKV++A KR I+ G
Sbjct: 392  -----KQANTRDTSLKVKNGHSGTIIDTEVLSRENGDVLEDGVEKIVKVWIAQKRKIKVG 446

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG++S +LP EDMP++ DGTPVDIVLNP GVPSRMN+GQ+ E HLG A   
Sbjct: 447  DKMAGRHGNKGVISIVLPVEDMPYMADGTPVDIVLNPQGVPSRMNIGQVLELHLGLAAKK 506

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG K  + + D      I                                          
Sbjct: 507  LGVKFATPVFDGINKDQI------------------------------------------ 524

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
               F    E           L E+G+  LYDG+TGEPFD+ ++VG +YMLKL+HMV DK+
Sbjct: 525  ---FAALKEA---------GLPENGKMTLYDGVTGEPFDKQISVGIMYMLKLSHMVDDKM 572

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 573  HARSIGPYSLITQQPLGGKSQNGGQR 598


>gi|73697693|gb|AAZ81463.1| RNA polymerase beta subunit [Mycoplasma elephantis]
          Length = 597

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 209/442 (47%), Positives = 299/442 (67%), Gaps = 3/442 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ ++  RRL++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S 
Sbjct: 1   NPLAELSSKRRLTSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLASH 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN  GF+ETPY +V +G V  +DV YLSA EE      Q+++ +++     ++ V  R
Sbjct: 61  ARVNELGFLETPYFRVNEGVVDYDDVCYLSAAEETGHVFIQSSTRVNDKNEIVDDYVVAR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             G+ +   + +++FID   KQ+ S+AAS IPFLENDD+NR LMG NMQRQAVPLL +EA
Sbjct: 121 YNGDYVQTHKSEVEFIDVDSKQMTSLAASAIPFLENDDANRALMGSNMQRQAVPLLVSEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E+ +AK S + IV + AG V  VDA RI I++ E   +     VD Y L  F+
Sbjct: 181 PLVATGIEADIAKFSFSNIVCEHAGEVVYVDANRIEIKTEEDSRNK-KGHVDKYYLRVFE 239

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ + ++QRP+VK+G+ V    IIADG S   G+L+LG+N++VAF   +GYN+ED+++
Sbjct: 240 RSNQASLIHQRPVVKLGEYVETGQIIADGSSCCDGELSLGKNVIVAFSTLNGYNYEDAVI 299

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE  +  R++K G + +T +IPN S    +++D  GI+ +G+EV
Sbjct: 300 LSERLVKDDVYTSIHIEEQTIQFRNSKAGNDILTTEIPNTSTASKRHLDVNGIVTIGSEV 359

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVG+++PK +   TPEEKLL A+F +K  +VRDTS++V +G SGT++D  + +R 
Sbjct: 360 QPGDILVGRVSPKADDNPTPEEKLLSALFSKKQANVRDTSIKVKNGHSGTIIDTEVLSRE 419

Query: 949 GID-KNERSISVEREQIELLAR 969
             D   +    + +  I    +
Sbjct: 420 NGDILEDGVEKIVKVWIAQKRK 441



 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 108/240 (45%), Positives = 139/240 (57%), Gaps = 54/240 (22%)

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              ++   + GD +  GV ++VKV++A KR I+ GDKMAGRHGNKG++S +LP EDMP++ 
Sbjct: 412  DTEVLSRENGDILEDGVEKIVKVWIAQKRKIKVGDKMAGRHGNKGVISVVLPIEDMPYMA 471

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDIVLNP GVPSRMN+GQ+ E HLG A   LG K  + + D      I        
Sbjct: 472  DGTPVDIVLNPQGVPSRMNIGQVLELHLGLAAKKLGVKFATPVFDGINKEQI-------- 523

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                 F+   E         A L E+G+
Sbjct: 524  -------------------------------------FEAFKE---------AGLPENGK 537

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             +LYDG+TGEPFD+ ++VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 538  MVLYDGVTGEPFDKEISVGIMYMLKLSHMVDDKMHARSIGPYSLITQQPLGGKSQNGGQR 597


>gi|242392396|dbj|BAH80411.1| RNA polymerase subunit B' [Natronorubrum tibetense]
          Length = 609

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 123/595 (20%), Positives = 209/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVEHGYIEFIDAEEEEDILVAVDEDDLSEKHTHLEIDPSLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  + +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRGGLEDAGFNSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     + G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAAQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG    +        +    G +E       D      + ++ A EEE+  +A     L 
Sbjct: 71  EGGEPRISDQEIEALQ---DGDLE-----FEDLVEHGYIEFIDAEEEEDILVAVDEDDL- 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  +  I A +IP+ E++ S R+ MG  
Sbjct: 122 ----------------------SEKHTHLEIDPSLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|242392374|dbj|BAH80400.1| RNA polymerase subunit B' [Natrinema pellirubrum DSM 15624]
          Length = 609

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 124/596 (20%), Positives = 207/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVGVDEDDLTENHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             D++ +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDKDELREGLEEAGFDSAGKETMYSGITGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 41.2 bits (95), Expect = 1.5,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A       ++    +  D      + ++ A EEE+  +      L 
Sbjct: 71  EDGE-PRISEQEIEA-------LQEGDLEFEDLVDHGYIEFIDAEEEEDILVGVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+                          ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 ENH-----------------------THLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|77543234|gb|ABA87041.1| RNA polymerase beta subunit [Acholeplasma oculi]
          Length = 629

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 228/454 (50%), Positives = 303/454 (66%), Gaps = 32/454 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 1   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 60

Query: 590 ARVNAYGFIETPYRKVCDG-----KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TP+ KV        KV+ +V+YL+A +E++  IA A + +D+DG+FT+  
Sbjct: 61  AKVDDYGFIKTPFLKVTKNALGTPKVSEEVIYLTADQEQDEVIASAATPMDKDGNFTDTR 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE  +     +  +D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 121 VIARKNGETGIYDASDVTCMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
           +  +P VGTG+E   AK SGA +VA  AG V  VDA +IVI           +       
Sbjct: 181 QPTSPIVGTGIEYRAAKDSGAVVVALNAGYVTYVDARKIVIVKEPTTDVKVGNKTIYKTG 240

Query: 759 -------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                               + Y L++F RSNQ+T V Q+P+V  G+ V + D+IADGPS
Sbjct: 241 GDFNYAIAKQLYDHKQLDLFETYELIQFFRSNQDTLVLQKPIVFQGEYVEKGDVIADGPS 300

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LG 857
           TD G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G
Sbjct: 301 TDNGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQSNG 360

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ 
Sbjct: 361 KEEITREIPNVGQEAVKYLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVI 420

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           G+KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 421 GDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 454



 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 118/413 (28%), Positives = 180/413 (43%), Gaps = 65/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD++    +      +     +  A    +  +  D  +     V   V 
Sbjct: 282  IVFQGEYVEKGDVIADGPSTDN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 340

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   S  +E+I     +   E V            I+ G     G  
Sbjct: 341  TSIHIDEYEIETRDLKQSNGKEEITREIPNVGQEAV----KYLDERGIIVPGSEVKEGDI 396

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 397  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 452

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGT VDI
Sbjct: 453  --GDQLPVGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYMADGTYVDI 510

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ + + D   + D+  + S          
Sbjct: 511  MLNPLGVPSRMNIGQILEIHLGISAKKLGIKVATPVFDGVTDEDLKEIMSDAGIAPDGK- 569

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T ++DG                           
Sbjct: 570  ---------------------------TYLYDG--------------------------R 576

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE +   ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 577  TGEAYKNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 629


>gi|194270600|gb|ACF36846.1| RNA polymerase beta subunit [Mycoplasma iners]
          Length = 595

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 210/422 (49%), Positives = 298/422 (70%), Gaps = 8/422 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGF++TPY KV +G V    V YL+A EE   YIAQ+   +DE+    ++ V 
Sbjct: 61  TYAKVNEYGFLQTPYYKVENGVVNYEKVEYLTATEEIGFYIAQSTVKVDENNRIIDKQVT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     +L    +ID+I+ +  Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ 
Sbjct: 121 MRHNYTYVLGEPTQIDYIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQT 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFV TG+ES +AK S A  VAK  G+VE VD  +I IR+  G  D        Y L  
Sbjct: 181 EAPFVATGLESAIAKYSSANFVAKNDGVVEYVDGSKIKIRNNNGKSDS-------YSLRN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQ+T V+QRPLVK+G EV++ D++ DG S   G+L+LG+N++VAF  + GYN+ED+
Sbjct: 234 FQRSNQDTVVHQRPLVKIGQEVKKGDLLVDGSSFKNGELSLGKNLVVAFTTYKGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++ER+V EDV TSIHIEE  +  R +++G +E+T +IPNVS+  ++++DE G++ VG+
Sbjct: 294 IILNERLVKEDVLTSIHIEEHTIQFRTSRMGDDELTAEIPNVSKYSIRHLDENGVVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGD+LVG+++PKG+   + EEKLL +I G++  +V+DTSL+V +G  GTV+ V + +
Sbjct: 354 EVMPGDVLVGRVSPKGDDNPSQEEKLLSSILGQRLTNVKDTSLKVKNGHGGTVIGVEVLS 413

Query: 947 RH 948
           R 
Sbjct: 414 RD 415



 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 147/524 (28%), Positives = 213/524 (40%), Gaps = 76/524 (14%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L    P+     E ++   +   + 
Sbjct: 143  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLQTEAPFVATGLESAIA--KYSSAN 200

Query: 837  DVFTSIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
             V  +  + E+   ++       G  +               + +  ++ +G EV  GD+
Sbjct: 201  FVAKNDGVVEYVDGSKIKIRNNNGKSDSYSLRNFQRSNQDTVVHQRPLVKIGQEVKKGDL 260

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LV   + K    ++  + L+ A    K  +  D  +     V   V+       H I   
Sbjct: 261  LVDGSSFKN-GELSLGKNLVVAFTTYKGYNYEDAIILNERLVKEDVLTSIHIEEHTIQF- 318

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD-- 1011
              S   + E    +          LD N   R+   +   + + G    K     S +  
Sbjct: 319  RTSRMGDDELTAEIPNVSKYSIRHLDENGVVRVGSEVMPGDVLVGRVSPKGDDNPSQEEK 378

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            L+S     +         KV+       +  E        +F++ I+KI           
Sbjct: 379  LLSSILGQRLTNVKDTSLKVKNGHGGTVIGVEVLSRDSNAQFEDGIDKI----------- 427

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
              VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP+L+DGTPVD++LNP GVPSRM
Sbjct: 428  --VKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPYLEDGTPVDVMLNPQGVPSRM 485

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            N+GQ+ E HLG A   L  K  +   D     +I                          
Sbjct: 486  NIGQVLEIHLGMAARSLNCKFVTPTFDGIKKEEI-------------------------- 519

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                               F+   E  +          ESG+  L D +TG+ FD PV+V
Sbjct: 520  -------------------FNLIKEAKL---------PESGKQYLIDPITGKRFDNPVSV 551

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            G +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 552  GVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|45545301|gb|AAS67498.1| DNA-dependent RNA polymerase II second largest subunit [Amanita
            phalloides]
          Length = 917

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 160/1032 (15%), Positives = 307/1032 (29%), Gaps = 179/1032 (17%)

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDI----VNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G  +   I    V+     ++   G + D   LE I +   
Sbjct: 42   KTISQFQVKMFHRNQERSLGNVIKATIPYIKVDVPIWVVFRALGVISDRDILEHICYDMQ 101

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I         +T    E    +   
Sbjct: 102  DAQMLEMLKPCIDDGFV--------IQDREVALDFIGNR----GTTTGLSRERRIRYAQE 149

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               K  L  V              +     +      +I  L+     +  +DD D+ G 
Sbjct: 150  ILQKEMLPHV-----------SMSEGSESKKAYFFGYMIHRLLVAALERRELDDRDHFGK 198

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +   +S              +  + + + +     +
Sbjct: 199  KRLDLAGPLLANLFRMLFRKLTKDVYRYLSKCVETHKEFNLALAVKHQTITNGLKYSLAT 258

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 259  GNWGDQKKSMSTKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 314

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN +
Sbjct: 315  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAH 366

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             A   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 367  SAVPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 423

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQV---DAIR 742
            + RV     +       L+ +   ++G G     +   G     +       V   DA  
Sbjct: 424  AGRVCRPLFIVENHQLALQKKHVRWLGNG-----SNDDGDVFRWEHLVKGGIVELLDAEE 478

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   +       +    ++     +    +K G            PS  L
Sbjct: 479  EETVMISMTPEDLETSRLQQSGVDPNVNDGE--YDPAVRLKAGTSAHTWTHCEIHPSMIL 536

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 537  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 571

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 572  FLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 620

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          + 
Sbjct: 621  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDK 679

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G N         K+  +  D      R++          ++     +  Q 
Sbjct: 680  LEDDGLIAPGTNVTGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQV 739

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 740  LI--------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGI 779

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 780  TYRQEDMPFTAEGITPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTV 839

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S      +K   +                                            
Sbjct: 840  ESVSTFLR--QKGYHSRGLEVM-------------------------------------- 859

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                     G +       G      + +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 860  -------YHGHT-------GRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 905

Query: 1283 LGGKSNRGGQRL 1294
            + G+S  GG R 
Sbjct: 906  VEGRSRDGGLRF 917



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 100/775 (12%), Positives = 218/775 (28%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    VP+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 70  YIKVD----VPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 125

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + ++             +      + 
Sbjct: 126 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMSEGSESKKAYFFGYMIH---RLL 181

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 182 VAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLSKCV 231

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 232 ETH--KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSTKAGVSQVLNRYTYASTLS 288

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 289 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAP 348

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA   V     F     +    +  N +  I   RR   +     
Sbjct: 349 VIEFLEEWGLESLEENAHSAVPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVS 408

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                      ++        P    E H + L      +  +      +    +     
Sbjct: 409 VVRDIRERELRLYTDAGRVCRPLFIVENHQLALQKKHVRW--LGNGSNDDGDVFRWEHLV 466

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               V  L A EEE   I+     L+        +      GE                 
Sbjct: 467 KGGIVELLDAEEEETVMISMTPEDLETSRLQQSGVDPNVNDGEYDPAVRLKAGTSAHTWT 526

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 527 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI------------ 574

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 575 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 602

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 603 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 641

Query: 843 HIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E            +       +++ G+I  G  V   DI++GK
Sbjct: 642 YYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNVTGEDIIIGK 701

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 702 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 749


>gi|73697681|gb|AAZ81457.1| RNA polymerase beta subunit [Mycoplasma molare]
          Length = 592

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 218/448 (48%), Positives = 313/448 (69%), Gaps = 14/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L S+
Sbjct: 1   NPLAEIANKRRVTSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGQNIGLILNLASY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++V+ YGFI+TPY  V DG V  + V +++A++E     AQ++ ++D+D    +E +  R
Sbjct: 61  SKVDDYGFIQTPYYAVEDGIVNYDKVHWMTAVQEYGFKFAQSSITVDDDNRIIDETITVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E ++V  E++D+I+ S KQ+ SIA+S IPFLENDD+NR LMG NMQRQAVPL+++E+
Sbjct: 121 KDHEFLIVKPEEVDYIEVSSKQMTSIASSTIPFLENDDANRALMGANMQRQAVPLIESES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFVGTG E  VAK +   + AK++G V  VD+ +I I+S +       + +  Y L  F+
Sbjct: 181 PFVGTGSEYDVAKYAATNLRAKKSGEVIFVDSQQIKIKSED------KNEIITYNLRIFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T +NQ+P+VK+G++V +  +I DGPST  G+LALG+N+LVAF  W GYNFED+++
Sbjct: 235 RSNQGTVINQKPIVKLGEKVYQGQLICDGPSTKNGELALGKNILVAFTTWQGYNFEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DVFTSIHIEE  +  R +K G + +T DIPN S    +++DE GI+ +G+EV
Sbjct: 295 ISEKLVKDDVFTSIHIEEQTIQFRASKAGDDILTTDIPNASARSKRHLDENGIVRIGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
           N GDILVG+ +PKGE   TPEEKL+ AIFG KA + +DTSL+V +G  GTV+DV+I +R 
Sbjct: 355 NTGDILVGRTSPKGEDNPTPEEKLMNAIFGNKASNQKDTSLKVKNGEGGTVIDVQILSRS 414

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 415 QGDSLEDGIDKIVKVFIAQKRKIKVGDK 442



 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 129/503 (25%), Positives = 191/503 (37%), Gaps = 81/503 (16%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L  +          Y+       + R         I ++  ++  +    
Sbjct: 165  GANMQRQAVPLIESESPFVGTGSEYDVAKYAATNLRAKKSG--EVIFVDSQQIKIKSEDK 222

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                               I++  I+ +G +V  G ++    + K    +   + +L A 
Sbjct: 223  NEIITYNLRIFERSNQGTVINQKPIVKLGEKVYQGQLICDGPSTKN-GELALGKNILVAF 281

Query: 917  FGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
               +  +  D  +            S  + +  I  R     ++   +          R 
Sbjct: 282  TTWQGYNFEDAIIISEKLVKDDVFTSIHIEEQTIQFRASKAGDDILTTDIPNASARSKR- 340

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+         +IL G+ +  G         L + +      +Q          
Sbjct: 341  HLDENGIVRIGSEVNTGDILVGRTSPKGEDNPTPEEKLMNAIFGNKASNQKDT------- 393

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                        +            +I     GD +  G+ ++VKVF+A KR I+ GDKM
Sbjct: 394  ----------SLKVKNGEGGTVIDVQILSRSQGDSLEDGIDKIVKVFIAQKRKIKVGDKM 443

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++S +LP EDMP+L+DGTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  
Sbjct: 444  AGRHGNKGVISLVLPVEDMPYLEDGTPIDILLNPQGVPSRMNIGQVLELHLGMAAKKLNV 503

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            K  + + D   N DI+ +                                          
Sbjct: 504  KFVTPVFDGVKNKDITAVLEEAGLPTSGKFKL---------------------------- 535

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            FD                          G+TG PFD  V+VG +YMLKL HMV DK+ AR
Sbjct: 536  FD--------------------------GITGLPFDNEVSVGVMYMLKLQHMVDDKINAR 569

Query: 1271 STGSYSLVTQQPLGGKSNRGGQR 1293
            S G YSL+TQQPLGGKS  GGQR
Sbjct: 570  SVGPYSLITQQPLGGKSQNGGQR 592


>gi|81171087|gb|ABB58770.1| RNA polymerase beta subunit [Acholeplasma oculi]
          Length = 630

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 228/454 (50%), Positives = 303/454 (66%), Gaps = 32/454 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 2   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 61

Query: 590 ARVNAYGFIETPYRKVCD-----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI+TP+ KV        KV+ +V+YL+A +E++  IA A + +D+DG+FT+  
Sbjct: 62  AKVDDYGFIKTPFLKVTKTASGTPKVSEEVIYLTADQEQDEVIASAATPMDKDGNFTDTR 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE  +     +  +D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 VIARKNGETGIYDASDVTCMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG------ 758
           +  +P VGTG+E   AK SGA +VA  AG V  VDA +IVI           +       
Sbjct: 182 QPTSPIVGTGIEYRAAKDSGAVVVALNAGYVTYVDARKIVIVKEPTTDVKVGNKTIYKTG 241

Query: 759 -------------------VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                               + Y L++F RSNQ+T V Q+P+V  G+ V + D+IADGPS
Sbjct: 242 GDFNYAIAKQLYDHKQLDLFETYELIQFFRSNQDTLVLQKPIVFQGEYVEKGDVIADGPS 301

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LG 857
           TD G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  RD K   G
Sbjct: 302 TDNGELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVYTSIHIDEYEIETRDLKQSNG 361

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
            EEITR+IPNV +E +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ 
Sbjct: 362 KEEITREIPNVGQEAVKYLDERGIIVPGSEVKEGDILVGKITPKGVFEPTPSEKLIHAVI 421

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           G+KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 422 GDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 455



 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 118/413 (28%), Positives = 180/413 (43%), Gaps = 65/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD++    +      +     +  A    +  +  D  +     V   V 
Sbjct: 283  IVFQGEYVEKGDVIADGPSTDN-GELALGRNVTVAFMTWEGYNYEDAVIMSEDLVKHDVY 341

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                 + + I+  +   S  +E+I     +   E V            I+ G     G  
Sbjct: 342  TSIHIDEYEIETRDLKQSNGKEEITREIPNVGQEAV----KYLDERGIIVPGSEVKEGDI 397

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                  +    +    P  +     + D+  +    SL+V +     +   ++ +K    
Sbjct: 398  LV--GKITPKGVFEPTPSEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQYFSKKN-- 453

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP++ DGT VDI
Sbjct: 454  --GDQLPVGVNEQIRVYIAKKRKITEGDKMAGRHGNKGVISKILPREDMPYMADGTYVDI 511

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNPLGVPSRMN+GQI E HLG +   LG K+ + + D   + D+  + S          
Sbjct: 512  MLNPLGVPSRMNIGQILEIHLGISAKKLGIKVATPVFDGVTDEDLKEIMSDAGIAPDGK- 570

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T ++DG                           
Sbjct: 571  ---------------------------TYLYDG--------------------------R 577

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE +   ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 578  TGEAYKNRISVGVMYMIKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 630


>gi|111378453|gb|ABH09238.1| RpoB [Klebsiella singaporensis]
          Length = 336

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 210/336 (62%), Positives = 264/336 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R++
Sbjct: 121 PYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFM
Sbjct: 301 CVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFM 336


>gi|242392370|dbj|BAH80398.1| RNA polymerase subunit B' [Natrinema ejinorense]
          Length = 609

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVDEDDLTENHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  + +G+  +Y G++GE  D  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRQGLEDAGFNSAGKETMYSGISGEKIDAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.8 bits (99), Expect = 0.45,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 23/106 (21%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + ++ A EEE+  +A     L E+                          +
Sbjct: 92  FEDLVDHGYIEFIDAEEEEDILVAVDEDDLTENH-----------------------THL 128

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  P  + SI A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 129 EIDPSLIFSIGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 174


>gi|7022389|dbj|BAA91581.1| unnamed protein product [Homo sapiens]
          Length = 343

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 93/375 (24%), Positives = 148/375 (39%), Gaps = 71/375 (18%)

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             V +  ++         Q  ++   V +       QY+      +    + IEK+    +
Sbjct: 30   KVENKQVLVNKSMPTVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMISSN 84

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++NP 
Sbjct: 85   AEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPH 142

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     L  K   L   +                          
Sbjct: 143  GFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT---------------------- 172

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G+  + +   L     +  G+  +  G+TGEP 
Sbjct: 173  ------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPL 208

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  Y
Sbjct: 209  EAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGY 268

Query: 1306 GAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVKEMQ 1355
            GA+ +L E L I SD    DV G+  +            +        P +  +L +E+Q
Sbjct: 269  GASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQ 328

Query: 1356 ALGLSIDLENSRTKN 1370
            ++ +   L+ S+   
Sbjct: 329  SMNIIPRLKLSKYNE 343


>gi|4867858|emb|CAB43085.1| RNA polymerase II [Stephanotis floribunda]
          Length = 261

 Score =  331 bits (849), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTAEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|242392372|dbj|BAH80399.1| RNA polymerase subunit B' [Natrinema pallidum]
          Length = 609

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVEEDDLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  D +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRQGLEDAGFDSAGKETMYSGISGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.4 bits (98), Expect = 0.63,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A       ++    +  D      + ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISQQEVEA-------LQEGDLEFEDLVDHGYIEFIDAEEEEDILVAVEEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|52694175|emb|CAG30617.1| DNA-directed RNA polymerase beta chain [Pseudomonas veronii]
          Length = 339

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 201/339 (59%), Positives = 263/339 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D  VT+++V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  
Sbjct: 121 VVKDALVTDEIVFLSAIEEADHVIAQASATMNEKKVLVDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVR 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFN 339


>gi|24429617|gb|AAM18214.1| RNA polymerase III subunit RPC2 [Homo sapiens]
          Length = 1133

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 1056 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1115

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 1116 ELQSMNIIPRLKLSKYNE 1133



 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 273/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
                            +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTAEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|281338612|gb|EFB14196.1| hypothetical protein PANDA_017492 [Ailuropoda melanoleuca]
          Length = 1058

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 635  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 694

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 695  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 753

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 754  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 796

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 797  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 854

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 855  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 887

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 888  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 920

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 921  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 980

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 981  IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1040

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 1041 ELQSMNIIPRLKLSKYNE 1058



 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 109/888 (12%), Positives = 254/888 (28%), Gaps = 165/888 (18%)

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
           S+    P     +C  RD+TY+ P+ + +             +  + I   ++ +G +P+
Sbjct: 15  SFNVTRPV-SPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPI 63

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++KG++++++ Q   S          R  
Sbjct: 64  MLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIVEA-DRKG 122

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILST 231
             G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+  
Sbjct: 123 AVGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQM 179

Query: 232 FYPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
              +              +       + A   +        +      +  IE  ++L +
Sbjct: 180 IGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLA 239

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
             +  L    VK     + C+    +   ++  +      +     +++          +
Sbjct: 240 STI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQ 292

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            + +L+ D           +       ++ A  D+ + MR   ++   V     +   + 
Sbjct: 293 LLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWS 350

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             ++ +   G  ++  RL+  +   +            K+                    
Sbjct: 351 LKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQW 401

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            +    +  + +    +  +           D   V     +  + V     E      +
Sbjct: 402 GMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNV 461

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
             +  + N L  I   ++L    +  + RA    E   +      R     +  G     
Sbjct: 462 FLVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRP 520

Query: 583 --VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             +      A  N     +   YR   D    + V YL   EE +  IA           
Sbjct: 521 YIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL---------- 570

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                              +    ++  P  ++ + A LIP+  ++ S R    C M +Q
Sbjct: 571 -------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQ 617

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           A+  +         G        +   ++A                              
Sbjct: 618 AMGTI---------GYNQRNRIDTLMYLLA------------------------------ 638

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                             Q+P+VK                 +   L  G+N  VA M + 
Sbjct: 639 ----------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYS 672

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN--- 875
           GY+ ED++++++  +       +  +  +    R T    +++   + + +         
Sbjct: 673 GYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHE 732

Query: 876 -IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 733 ILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 780


>gi|242392342|dbj|BAH80384.1| RNA polymerase subunit B' [Haloterrigena longa]
          Length = 609

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVDEDDLTENHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  + +G+  +Y G++GE  D  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRQGLEDAGFNSAGKETMYSGISGEKIDAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.8 bits (99), Expect = 0.47,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 23/106 (21%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + ++ A EEE+  +A     L E+                          +
Sbjct: 92  FEDLVDHGYIEFIDAEEEEDILVAVDEDDLTENH-----------------------THL 128

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  P  + SI A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 129 EIDPSLIFSIGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 174


>gi|226897656|gb|ACO90277.1| RNA polymerase beta subunit gene [Bacillus sp. UST2006-BC008]
          Length = 389

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 225/370 (60%), Positives = 286/370 (77%), Gaps = 3/370 (0%)

Query: 585 SLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           SL+SFA+VN +GFIETPYR+V    GKVTN + YL+A EE+N  +AQAN+ L +DGSF +
Sbjct: 2   SLSSFAKVNRFGFIETPYRRVDPDTGKVTNRMDYLTADEEDNYVVAQANARLSDDGSFLD 61

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           + V  R  GE  +V RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVP
Sbjct: 62  DEVIARFRGENTVVKRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVP 121

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDI 761
           L+  E+P VGTGME V AK SGAA++ K  G+VE+V+A ++ +R ++  D       +D 
Sbjct: 122 LMNPESPIVGTGMEHVSAKDSGAAVICKHEGLVERVEAKQVWVRQIKEIDGQEVKGDLDK 181

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           YR+ KF RSNQ TC NQRP+V  GD V + +I+ADGPS + G+LALGRN++V FM W GY
Sbjct: 182 YRMQKFIRSNQGTCYNQRPIVSEGDRVTKGEILADGPSMEKGELALGRNVMVGFMTWDGY 241

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GI
Sbjct: 242 NYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGI 301

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+D
Sbjct: 302 IRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLD 361

Query: 942 VRIFNRHGID 951
           V++FNR   D
Sbjct: 362 VKVFNREDGD 371



 Score = 38.5 bits (88), Expect = 8.6,   Method: Composition-based stats.
 Identities = 33/231 (14%), Positives = 71/231 (30%), Gaps = 23/231 (9%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R    +        ++  I+  G  V  G+IL    +   +  +     ++   
Sbjct: 177  GDLDKYRMQKFIRSNQGTCYNQRPIVSEGDRVTKGEILADGPS-MEKGELALGRNVMVGF 235

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 236  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 295

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R      +++    
Sbjct: 296  LDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHG 354

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               +                    K+   + GD++PPGV ++V+ ++  KR
Sbjct: 355  GGGI----------------VLDVKVFNREDGDELPPGVNQLVRAYIVQKR 389


>gi|238908505|ref|NP_001154180.1| DNA-directed RNA polymerase III subunit RPC2 isoform 2 [Homo sapiens]
 gi|114646705|ref|XP_509335.2| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B isoform
            4 [Pan troglodytes]
          Length = 1075

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 652  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 711

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 712  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 770

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 771  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 813

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 814  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 871

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 872  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 904

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 905  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 937

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 938  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 997

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 998  IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1057

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 1058 ELQSMNIIPRLKLSKYNE 1075



 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 109/910 (11%), Positives = 258/910 (28%), Gaps = 174/910 (19%)

Query: 66  TAFSGAAMLEFVSYEFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDE 115
           +       L++++     P               +C  RD+TY+ P+ + +         
Sbjct: 9   SDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYT------ 62

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQR 151
               +  + I   ++ +G +P+M                           G F++KG+++
Sbjct: 63  ----RGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEK 118

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RR 210
           +++ Q   S          R    G  + +     ++    ++    +   ++R +    
Sbjct: 119 VILIQEQLSKNRIIVEA-DRKGAVGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSE 174

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVY---------SQRGDFWCFPLSAADLMVGAKV 260
            +P+     A+G++S+ EI+     +              +       + A   +     
Sbjct: 175 DIPIVIIFKAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVR 234

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
              +      +  IE  ++L +  +  L    VK     + C+    +   ++  +    
Sbjct: 235 RQRMWGGGPKKTKIEEARELLASTI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNK 292

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             +     +++          + + +L+ D           +       ++ A  D+ + 
Sbjct: 293 VDDRDYYGNKRL-----ELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKH 347

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           MR   ++   V     +   +   ++ +   G  ++  RL+  +   +            
Sbjct: 348 MRQDQITNGMVNA--ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTR 405

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           K+                     +    +  + +    +  +           D   V  
Sbjct: 406 KVSGPRSLQ---------PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKL 456

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
              +  + V     E      +  +  + N L  I   ++L    +  + RA    E   
Sbjct: 457 ASNLGVEDVNLLCGEELSYPNVFLVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVS 515

Query: 561 VHPTHYGRICPAETSEGHNIGL--VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYL 617
           +      R     +  G       +      A  N     +   YR   D    + V YL
Sbjct: 516 ISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYL 575

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EE +  IA                              +    ++  P  ++ + A 
Sbjct: 576 DVNEENDCNIAL-----------------------YEHTINKDTTHLEIEPFTLLGVCAG 612

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIP+  ++ S R    C M +QA+  +         G        +   ++A        
Sbjct: 613 LIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLMYLLA-------- 655

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                                                   Q+P+VK              
Sbjct: 656 --------------------------------------YPQKPMVK----------TKTI 667

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKL 856
              +   L  G+N  VA M + GY+ ED++++++  +       +  +  +    R T  
Sbjct: 668 ELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQ 727

Query: 857 GPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             +++   + + +          +D  GI   G +V    +LV K  P           +
Sbjct: 728 TFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNV 787

Query: 913 LRAIFGEKAV 922
            +    +   
Sbjct: 788 PQQPQYKDVP 797


>gi|114646701|ref|XP_001161529.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B isoform
            2 [Pan troglodytes]
          Length = 1133

 Score =  331 bits (848), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 92/737 (12%), Positives = 220/737 (29%), Gaps = 114/737 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPL-LKAEAPFVGTGME 716
           + + L      + T M 
Sbjct: 694 MGVHLANMRNRIDTLMY 710



 Score =  128 bits (321), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 83/564 (14%), Positives = 174/564 (30%), Gaps = 41/564 (7%)

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                   K  +     +  +  L      +     K    A++   V L  G   +DD 
Sbjct: 295 RMWGGGPKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDR 354

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DLINAKPVVSA 512
           D  GN+R+   G++L   +     +    +K+    V       Q      +    + + 
Sbjct: 355 DYYGNKRLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNG 414

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPT 564
           +     +   S     ++         RLS +   G+         + R     R + P+
Sbjct: 415 MVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPS 474

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP++T EG   GLV +L     +      + P  K+       DV  L   EE +
Sbjct: 475 QWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDGPIVKLASNLGVEDVNLL-CGEELS 532

Query: 625 R---YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS---- 677
               ++   N ++       ++LV             E +        + V I++     
Sbjct: 533 YPNVFLVFLNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRL 592

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P++        +   +M+  A      E     + +E +         +A     + +
Sbjct: 593 CRPYIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINK 652

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD- 796
            D   + I         +      +     + + Q     Q   V + +   R D +   
Sbjct: 653 -DTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGVHLANMRNRIDTLMYL 711

Query: 797 -------------GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                            +   L  G+N  VA M + GY+ ED++++++  +       + 
Sbjct: 712 LAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLV 771

Query: 844 IEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKI 898
            +  +    R T    +++   + + +          +D  GI   G +V    +LV K 
Sbjct: 772 YKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKS 831

Query: 899 TPKGESPMTPEEKLLRAIFGEKAV 922
            P           + +    +   
Sbjct: 832 MPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|318603052|emb|CBJ04587.1| RNA polymerase beta subunit [Pseudomonas sp. R-37923]
          Length = 333

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 197/333 (59%), Positives = 257/333 (77%)

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           V +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR
Sbjct: 1   VAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGR 60

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IA
Sbjct: 61  VCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIA 120

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+N
Sbjct: 121 QASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDAN 180

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  
Sbjct: 181 RALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVA 240

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG
Sbjct: 241 DDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALG 300

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           +NM +AFM W+G+NFEDS+ +SER+V ED FT+
Sbjct: 301 QNMRIAFMAWNGFNFEDSICLSERVVQEDRFTT 333


>gi|111054575|gb|ABH04345.1| RNA polymerase beta subunit [Proteus vulgaris]
          Length = 335

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 206/335 (61%), Positives = 256/335 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVE 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ ++D 
Sbjct: 121 NNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G+V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGVVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 PVDRGDVLADGPSTDLGELALGQNMRVAFMPWNGY 335


>gi|300795995|ref|NP_001179718.1| DNA-directed RNA polymerase III subunit RPC2 [Bos taurus]
 gi|297474988|ref|XP_002687706.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B [Bos
            taurus]
 gi|296487427|gb|DAA29540.1| polymerase (RNA) III (DNA directed) polypeptide B [Bos taurus]
          Length = 1133

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHFCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|193784141|dbj|BAG53685.1| unnamed protein product [Homo sapiens]
          Length = 1075

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 652  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 711

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 712  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 770

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 771  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 813

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 814  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 871

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 872  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 904

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 905  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 937

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 938  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 997

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 998  IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1050

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1051 ACKLLFQELQSMNIIPRLKLSKYNE 1075



 Score =  180 bits (457), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 109/910 (11%), Positives = 259/910 (28%), Gaps = 174/910 (19%)

Query: 66  TAFSGAAMLEFVSYEFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDE 115
           +       L++++     P               +C  RD+TY+ P+ + +         
Sbjct: 9   SDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYT------ 62

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQR 151
               +  + I   ++ +G +P+M                           G F++KG+++
Sbjct: 63  ----RGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEK 118

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RR 210
           +++ Q   S          R    G  + +     ++    ++    +   ++R +    
Sbjct: 119 VILIQEQLSKNRIIVEA-DRKGAVGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSE 174

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVY---------SQRGDFWCFPLSAADLMVGAKV 260
            +P+     A+G++S+ EI+     +              +       + A   +     
Sbjct: 175 DIPIVIIFKAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVR 234

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
              +      +  IE  ++L +  +  L    VK     + C+    +   ++  +    
Sbjct: 235 RQRMWGGGPKKTKIEEARELLASTI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNK 292

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
             +     +++          + + +L+ D           +       ++ A  D+ + 
Sbjct: 293 VDDRDYYGNKRL-----ELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKH 347

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           MR   ++   V     +   +   ++ +   G  ++  RL+  +   +            
Sbjct: 348 MRQDQITNGMVNA--ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTR 405

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
           K+                     +    +  + +    +  +           D   V  
Sbjct: 406 KVSGPRSLQ---------PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKL 456

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
              +  + V     E      +  +  + N L  I   ++L    +  + RA    E   
Sbjct: 457 ASNLGVEDVNLLCGEELSYPNVFLVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVS 515

Query: 561 VHPTHYGRICPAETSEGHNIGL--VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYL 617
           +      R     +  G       +      A +N     +   YR   D    + V YL
Sbjct: 516 ISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAVINKHMEELAQGYRNFEDFLHESLVEYL 575

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EE +  IA                              +    ++  P  ++ + A 
Sbjct: 576 DVNEENDCNIAL-----------------------YEHTINKDTTHLEIEPFTLLGVCAG 612

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIP+  ++ S R    C M +QA+  +         G        +   ++A        
Sbjct: 613 LIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLMYLLA-------- 655

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                                                   Q+P+VK              
Sbjct: 656 --------------------------------------YPQKPMVK----------TKTI 667

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKL 856
              +   L  G+N  VA M + GY+ ED++++++  +       +  +  +    R T  
Sbjct: 668 ELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQ 727

Query: 857 GPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             +++   + + +          +D  GI   G +V    +LV K  P           +
Sbjct: 728 TFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNV 787

Query: 913 LRAIFGEKAV 922
            +    +   
Sbjct: 788 PQQPQYKDVP 797


>gi|149742988|ref|XP_001499030.1| PREDICTED: similar to DNA-directed RNA polymerase III subunit RPC2
            (RNA polymerase III subunit C2) (DNA-directed RNA
            polymerase III subunit B) (DNA-directed RNA polymerase
            III 127.6 kDa polypeptide) (C128) [Equus caballus]
          Length = 1133

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|238908503|ref|NP_060552.4| DNA-directed RNA polymerase III subunit RPC2 isoform 1 [Homo sapiens]
 gi|109098552|ref|XP_001099515.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 isoform 2
            [Macaca mulatta]
 gi|114646699|ref|XP_001161567.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B isoform
            3 [Pan troglodytes]
 gi|301784547|ref|XP_002927687.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like
            [Ailuropoda melanoleuca]
 gi|29428029|sp|Q9NW08|RPC2_HUMAN RecName: Full=DNA-directed RNA polymerase III subunit RPC2; Short=RNA
            polymerase III subunit C2; AltName: Full=C128; AltName:
            Full=DNA-directed RNA polymerase III 127.6 kDa
            polypeptide; AltName: Full=DNA-directed RNA polymerase
            III subunit B
 gi|28277230|gb|AAH46238.1| Polymerase (RNA) III (DNA directed) polypeptide B [Homo sapiens]
 gi|119618186|gb|EAW97780.1| polymerase (RNA) III (DNA directed) polypeptide B, isoform CRA_a
            [Homo sapiens]
 gi|158256702|dbj|BAF84324.1| unnamed protein product [Homo sapiens]
          Length = 1133

 Score =  331 bits (848), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|34494002|emb|CAD66144.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  330 bits (847), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 211/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMYQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|34494036|emb|CAD66161.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  330 bits (847), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 209/336 (62%), Positives = 262/336 (77%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           + ER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VIERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPS DLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSPDLGELALGQNMRVAFMPWNGY 336


>gi|293348540|ref|XP_002726935.1| PREDICTED: DNA-directed RNA polymerase III B-like [Rattus norvegicus]
          Length = 1098

 Score =  330 bits (847), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 103/498 (20%), Positives = 175/498 (35%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 675  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 734

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 735  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 793

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 794  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 836

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 837  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 894

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 895  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 927

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 928  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 960

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 961  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1020

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 1021 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1080

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ ++   
Sbjct: 1081 ELQSMNIIPRLKLAKYNE 1098



 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 119/937 (12%), Positives = 272/937 (29%), Gaps = 198/937 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFY 233
            G  + +     ++    ++    +   ++R +     +P+     A+G++S++ +    
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEI---- 251

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
                                 V    +   V    G  + E  K      +++LK  G 
Sbjct: 252 ----------------------VQMIGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGN 289

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
           K   +    + G    +  +  E  E+   A  ++    +       +  + +L+ D   
Sbjct: 290 K---VRRQRMWGGGPKKTKI-EEARELL--ASTILTHVPVSNCQIRIMFLLSLLFEDLFK 343

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                   +       ++ A  D+ + MR   ++   V     +   +   ++ +   G 
Sbjct: 344 KFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSLKRFKMDRQGV 401

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            ++  RL+  +   +            K+                     +    +  + 
Sbjct: 402 TQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWGMLCPSDTPEG 452

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           +    +  +           D   +     +  + V     E      +  +  + N L 
Sbjct: 453 EACGLVKNLALMTHITTDMEDGPIIKLAGNLGVEDVNLLCGEELSYPNVFLVFLNGNILG 512

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL--VSSLTSFAR 591
            I   ++L +  +  + RA    E   +      R     +  G       +      A 
Sbjct: 513 VIRDHKKLVSTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQKPAV 571

Query: 592 VN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            N     +   YR   D    + V YL   EE +  IA                      
Sbjct: 572 TNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL--------------------- 610

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   +    ++  P  ++ + A LIP+  ++ S R    C M +QA+  +      
Sbjct: 611 --YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI------ 662

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
              G        +   ++A                                         
Sbjct: 663 ---GYNQRNRIDTLMYLLA----------------------------------------- 678

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q+P+VK                 D   L  G+N  VA M + GY+ ED+++++
Sbjct: 679 -----YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLN 723

Query: 831 ERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVG 885
           +  +       +  +  +    R T    +++   + + +          +D  GI   G
Sbjct: 724 KASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPG 783

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +V    +LV K  P           + +    +   
Sbjct: 784 EKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 820


>gi|193735378|gb|ACF20191.1| RNA polymerase beta subunit [Mycoplasma hyorhinis]
 gi|194591919|gb|ACF76535.1| RNA polymerase beta subunit [Mycoplasma hyorhinis]
          Length = 597

 Score =  330 bits (847), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 209/446 (46%), Positives = 297/446 (66%), Gaps = 11/446 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE+    E  
Sbjct: 61  VYAKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDENNKIIEPE 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           +  R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NMQRQAVPL+
Sbjct: 121 IIVRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNMQRQAVPLI 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
             EAP+V TG+E+ VAK S   I A   G V  VD+  I I++ +G        +  Y L
Sbjct: 181 TTEAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG-------NIKTYHL 233

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF  W+GYN+E
Sbjct: 234 RYFERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFSTWYGYNYE 293

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D+++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++DE GI+ +
Sbjct: 294 DAIIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRI 353

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  GTV+DV+I
Sbjct: 354 GSEVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQI 413

Query: 945 FNRHGID-KNERSISVEREQIELLAR 969
            +R   D   +    + +  I    +
Sbjct: 414 LSRTREDNLEDGVEKIIKVFIAQKRK 439



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/415 (31%), Positives = 186/415 (44%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD++    +   +  +   + +L A       +  D  +     V   V 
Sbjct: 250  IVEVGQFVKQGDLICDGPST-DQGELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 308

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    +   S +   +    +       +  LD N   R+   +   + + G  
Sbjct: 309  -TSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGSEVSAGDILVGRT 367

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W + A   +     V+           IL    +      
Sbjct: 368  SPKGEDNPTPE--EKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILSRTRE------ 419

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
               D++  GV +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMPFL+DGTP+DI
Sbjct: 420  ---DNLEDGVEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPFLEDGTPIDI 476

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP G+PSRMN+GQI E HLG     L  K    + D      +  L +          
Sbjct: 477  LLNPQGIPSRMNIGQILEMHLGMVAKKLDIKFVCPVFDGVKLDKMKELFN---------- 526

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 527  --------------------QAGIP------------------------ESGKFTLYDGI 542

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD  V++GY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 543  TGQPFDNDVSIGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFG 597


>gi|83415471|gb|ABC17943.1| RNA polymerase II second largest subunit [Entomophthora muscae]
          Length = 726

 Score =  330 bits (847), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 135/858 (15%), Positives = 257/858 (29%), Gaps = 156/858 (18%)

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFC 518
             +R+   G ++   +R+   ++ + +   +               + +  + + +     
Sbjct: 1    QKRLDLAGPLMAGLFRMLFQKLTKDVTRYLQKCIEAKREFNMSLAVKSTIISNGLRYSLA 60

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+       S ++H RR +      + R     + R +H TH
Sbjct: 61   TGNWGDQQKAMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTH 116

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE--- 622
            +G +CPAET EG   GLV +L   + +   G    P     +  + +   +  A  E   
Sbjct: 117  WGLVCPAETPEGQACGLVKNLALMSYIT-VGTDPQPLVNYLEEYMNDPAKHGDAEAEAAD 175

Query: 623  -ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
              +      +  +         L++                  D SP+  +     +   
Sbjct: 176  ITDHTRVFIDGVMMGQERDPLTLIYNLRRLRRN---------FDISPEISIVRDIRVREI 226

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     + R    LL                          +   ++ +   
Sbjct: 227  RLYTDAGRVTRPLFVVRDNKILL--------------------------KKHHIQYIKDG 260

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPS 799
                    G  +   +G+  Y     +      C++   L  V++G   R  ++      
Sbjct: 261  YSPSHPNYGFSNLIENGLLEYLGA-HEEECSLICMSLEELEEVRLG---RLGNLPEANAV 316

Query: 800  TDLGDLALGRNMLVAF-MPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKL 856
             D    A  +N LV +   W       SM+  I   +V            ++       +
Sbjct: 317  VD--MTATIKNSLVGYSYHWTHCEVHPSMVLGICATIVPFPDHNQSPRNTYQSAMGKQAM 374

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G                  +    +  +        +    +       +   +  + AI
Sbjct: 375  GVYLTN-----------YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAI 423

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    I+ R  +D+ +++  VE E  E           
Sbjct: 424  CCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRTYLDQEKKAGLVEMETFEKPTSATTLRLR 482

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                        I  G           K+  +  D      R            ++    
Sbjct: 483  HGTYEKLEDDGLIAPGTRVSGDDIIIGKTAPVPPDSEELGQRRHGQTKRDVSTPLKSTET 542

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  +   + +                       +R  KV V   R  Q GDK A RHG 
Sbjct: 543  GIVDRVMLTINQ--------------------EGMRFAKVRVRSTRVPQIGDKFASRHGQ 582

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      E MPF  +G   D+V+NP  +PSRM +G + E  +G      G +     
Sbjct: 583  KGTIGMTYRNEGMPFSAEGIVPDLVINPHAIPSRMTIGHMVECLVGKVGTLDGSEGD--- 639

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                              +TP F     
Sbjct: 640  --------------------------------------------------ATP-FTNVTV 648

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            + I+ +L      + G  ++Y+G TG+     +  G  Y  +L HMV DK+++R+ G   
Sbjct: 649  DGISGLLEKFGYQKRGFEVMYNGHTGKKLTAQIYFGPTYYQRLKHMVDDKIHSRARGPVQ 708

Query: 1277 LVTQQPLGGKSNRGGQRL 1294
            ++T+QP+ G+S  GG R 
Sbjct: 709  ILTRQPVEGRSRDGGLRF 726



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 59/411 (14%), Positives = 113/411 (27%), Gaps = 30/411 (7%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
              + +  +  S+    + D  K   +  G  ++  R    +      R          I
Sbjct: 47  KSTIISNGLRYSLATGNWGDQQKAMQAKAGVSQVLNRYTFASTLSHLRRCNTPIGRDGKI 106

Query: 441 KILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
                L N   G +   +    +    V  +    Y       +  +      ++  +  
Sbjct: 107 AKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYITVGTDPQPLVNYLEEYMNDPAKH 166

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
                 A  +      F     + Q  + +  +  +   RR   +           V   
Sbjct: 167 GDAEAEAADITDHTRVFIDGVMMGQERDPLTLIYNLRRLRRNFDISPEISIVRDIRVREI 226

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            ++        P      + I L      + + + Y      Y    +      + YL A
Sbjct: 227 RLYTDAGRVTRPLFVVRDNKILLKKHHIQYIK-DGYSPSHPNY-GFSNLIENGLLEYLGA 284

Query: 620 MEEENRYIAQANSSLDE-------DGSFTEELVFCRCAGEEILVPRE-KIDFIDASPKQV 671
            EEE   I  +   L+E       +      +V      +  LV         +  P  V
Sbjct: 285 HEEECSLICMSLEELEEVRLGRLGNLPEANAVVDMTATIKNSLVGYSYHWTHCEVHPSMV 344

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-G 714
           + I A+++PF +++ S R      M +QA+                 L   + P V T G
Sbjct: 345 LGICATIVPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQLRMDTLANILYYPQKPLVATRG 404

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           ME +  +   A   A  A            +   +  +D        YR  
Sbjct: 405 MEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRGLFRSIYYRTY 455


>gi|34493996|emb|CAD66141.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 336

 Score =  330 bits (847), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 210/336 (62%), Positives = 263/336 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+E  N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEXGNYLIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|85083820|ref|XP_957195.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Neurospora
            crassa OR74A]
 gi|7800864|emb|CAB91222.1| probable DNA-directed RNA polymerase III second-largest chain
            [Neurospora crassa]
 gi|28918282|gb|EAA27959.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Neurospora
            crassa OR74A]
          Length = 1155

 Score =  330 bits (847), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 114/494 (23%), Positives = 189/494 (38%), Gaps = 86/494 (17%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   + +       ++F 
Sbjct: 733  YPQRPMVITKTIQLIHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASLDRGFGRCQVFR 792

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            ++  +    + +  R+++  + +D+DD+  I+   I         G    SG    KK T
Sbjct: 793  KYTAELQGYT-NGRRDRVGGIMKDEDDKP-IVKHAILDADGLAQVGSKVESGQTMIKKET 850

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L                 +  ++   +       Y  S   +       I+K+     +
Sbjct: 851  PLDQ-----------ISTGIAGDRGSDDYRDASTNYRISDPAI-------IDKVMI--SV 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 +++KV     R  + GDK + RHG KG+V  I+  EDMPF   G   DI++NP G
Sbjct: 891  NERENKLIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVNEEDMPFSDKGLRPDIIMNPHG 950

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++FE   G A V  G                       EK  G G       
Sbjct: 951  FPSRMTVGKLFECLTGKASVIAG-----------------------EKDYGFGD------ 981

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     E++   L        G+     G+TGEP +
Sbjct: 982  -----------------------AFRSHPVESMGQALIDHGFSWEGKDYFTSGITGEPME 1018

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G I+  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1019 AYIYNGPIFYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYG 1078

Query: 1307 AAYVLQEMLTIKSD----DVV------GRTRVYESIVAGN-DTFETGTPESFNVLVKEMQ 1355
            A+ +L E L I SD    DV       G  + Y +      +  +   P +  +LV+E+ 
Sbjct: 1079 ASQLLLERLMISSDGTELDVCQECGLFG-YKGYCNACKSTRNVTQMTMPYACKLLVQELI 1137

Query: 1356 ALGLSIDLENSRTK 1369
            ++ + + L+     
Sbjct: 1138 SMNVGVKLKLEDEF 1151



 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 131/1003 (13%), Positives = 273/1003 (27%), Gaps = 201/1003 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+   I    R N       +S            LEF       P    
Sbjct: 44  LVKQHIDSYNYFVNEEIKDIVRAN----RVVRS-----DQDPNFWLEFRDIRVGMPTRTE 94

Query: 86  ----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                         +C  RDLTYA P+++ +             +    I  ++I +  +
Sbjct: 95  DGEQVQSRNPVTPMECRLRDLTYAAPVEVDI----------AYTRDKNVIVRKNIPLCRI 144

Query: 136 PLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           P+M K                         G FVI G +++++ Q   S          +
Sbjct: 145 PVMLKSAKCYLNGATNAQMEVFNECPLDPGGYFVIGGTEKVILIQEQLSKNRIIVEADEK 204

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL 221
                  + +               + K   +V + + R           +P+   L A 
Sbjct: 205 TGGVMASVTSST------------HERKSKTYVVLKKDRIVLQHNTLSEPIPIVIVLKAF 252

Query: 222 -GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
            G+   +I+         ++  D +      A          +L  +    ++  +  K 
Sbjct: 253 GGLSDNDIIELVCGGD--ARYQDDFLINFDEAGRAGVYTQQQALEYVGARVKMGGNRPKF 310

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV------IDEKSLE 334
            +   ++  E+G+  L      L   +V  + ++     +YI            + K ++
Sbjct: 311 GAAPRRNHAEEGLDALA----NLVIAHVTVEGLDFYPKAVYIAMMVRRVLMAAQNPKLVD 366

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           +      + + +           +    ++D   +  +      R               
Sbjct: 367 DRDFVGNKRLELAGQLISLLFEDLFKKFISDVKYNIDNFFKKPNRTSTYDPHGAIMANGH 426

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             +     + +    TV R  MN          + +I    ++  I    +         
Sbjct: 427 YISHGLNRAIQSGNWTVKRFNMNRAGITHVLSRLSYIAALGMMTRISSQFEKTRKVSGPR 486

Query: 455 DIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
            +       + +           +  L +   I   +    +  ++     +  P+    
Sbjct: 487 ALQPSQWGMLCTSDTPEGEACGLVKNLALMTHITTNVPEEPVKKMIFAADESVGPIREYT 546

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                S     +  +    +     +R +A  +  + R         +H   +       
Sbjct: 547 GTEMHSKGSYIIHLNGTPFAVTREPKRFAARFRT-LRRRGWVSPFVSIHINEHFSAVHIA 605

Query: 574 TSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T EG        V +  S  +      ++           +  V YL   EE +  +A  
Sbjct: 606 TDEGRICRPYIIVKNGKSMLKAEHLKMLQLGQATFDTFLTSGVVEYLDVNEENDTLVALQ 665

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +                             ++  P  ++   A LIPF  ++ S R 
Sbjct: 666 EDQIT-----------------------NSTTHMEIEPFTILGAVAGLIPFPHHNQSPRN 702

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+                                           I   + 
Sbjct: 703 TYQCAMGKQAIGA-----------------------------------------IAYNQF 721

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +   +     +Y               QRP+V          I           L  G+N
Sbjct: 722 NRIDTLLYTLVYP--------------QRPMV----------ITKTIQLIHYDKLPAGQN 757

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             V  M + GY+ ED++++++  +           ++    +    G  +    I    +
Sbjct: 758 ATVVVMSYSGYDIEDALVLNKASLDRGFGRCQVFRKYTAELQGYTNGRRDRVGGIMKDED 817

Query: 871 E----GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           +        +D  G+  VG++V  G  ++ K TP  +                 + D RD
Sbjct: 818 DKPIVKHAILDADGLAQVGSKVESGQTMIKKETPLDQIS-------TGIAGDRGSDDYRD 870

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            S          + D  I ++  I  NER   + + Q     R
Sbjct: 871 ASTNYR------ISDPAIIDKVMISVNERENKLIKVQTRQTRR 907


>gi|242392300|dbj|BAH80343.1| RNA polymerase subunit B' [Halobiforma nitratireducens]
          Length = 609

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 124/596 (20%), Positives = 209/596 (35%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++LVA       +    + I  +++       I   E     R 
Sbjct: 95   LVEHGYVEFIDAEEEEDILVAVDEDDVTDDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVIGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSLEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DEE +   L  A  + SG+  +Y G+TGE  +  +  G I+  KL HMVS+K++ARS G
Sbjct: 438  EDEEDLRKGLEEAGFEPSGKETMYSGITGEKIEAEIFSGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICGQCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 43.1 bits (100), Expect = 0.31,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  N  G +E       D      V ++ A EEE+  +A     + 
Sbjct: 71  EDGE-PRISDEEIEALRN--GDLE-----FEDLVEHGYVEFIDAEEEEDILVAVDEDDVT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 DDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|242392368|dbj|BAH80397.1| RNA polymerase subunit B' [Natrinema altunense]
          Length = 609

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVDEDDLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  D +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRQGLEDAGFDSAGKETMYSGISGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.8 bits (99), Expect = 0.41,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A     G +E       D      + ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISQQEVEAL--QDGDLE-----FEDLVDHGYIEFIDAEEEEDILVAVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|46195739|ref|NP_081699.1| DNA-directed RNA polymerase III subunit RPC2 [Mus musculus]
 gi|51704303|sp|P59470|RPC2_MOUSE RecName: Full=DNA-directed RNA polymerase III subunit RPC2; Short=RNA
            polymerase III subunit C2; AltName: Full=C128; AltName:
            Full=DNA-directed RNA polymerase III 127.6 kDa
            polypeptide; AltName: Full=DNA-directed RNA polymerase
            III subunit B
 gi|45829714|gb|AAH68143.1| Polymerase (RNA) III (DNA directed) polypeptide B [Mus musculus]
          Length = 1133

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 103/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ ++   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLAKYNE 1133



 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 275/947 (29%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   +     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLAGNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L +  +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVSTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 D   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|326429748|gb|EGD75318.1| RNA polymerase II [Salpingoeca sp. ATCC 50818]
          Length = 1139

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 85/313 (27%), Positives = 132/313 (42%), Gaps = 76/313 (24%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++K+ V   R  + GDK + RHG KG+   I+  EDMPF   G   D+++NP G
Sbjct: 879  SSENYMIIKIRVRSTRIPELGDKFSSRHGQKGVCGLIVNQEDMPFNDQGVCPDMIMNPHG 938

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++ E   G A V                                        
Sbjct: 939  FPSRMTVGKLMELVGGKAAV---------------------------------------- 958

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                     ++  +  G       F G   E +   L     +  G+  L  G+TGEP +
Sbjct: 959  ---------LSGNFNYGT-----AFGGTPLEEMCETLVDHGYNYHGKEFLTSGITGEPLE 1004

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G +Y  KL HMV DK++AR+TG  +L+T+QP  G+S +GG RLGEME  C+  +G
Sbjct: 1005 AYIFFGPVYYQKLKHMVMDKMHARATGPITLLTRQPTEGRSRQGGLRLGEMERDCLIGHG 1064

Query: 1307 AAYVLQEMLTIKSD--DVVGRTRVYESIVAG--------------NDTFETGTPESFNVL 1350
             + +L E L + SD  +V   ++       G               +  +   P +  +L
Sbjct: 1065 TSMLLLERLMVSSDAFEVTACSK------CGLLGYAGWCQYCKSSANVCKLELPYACKLL 1118

Query: 1351 VKEMQALGLSIDL 1363
             +E+Q++ +   L
Sbjct: 1119 FQELQSMNIVPRL 1131



 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 112/723 (15%), Positives = 214/723 (29%), Gaps = 110/723 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S++HF+ ++I    + N         V P         LE+ S     P    
Sbjct: 51  LVRQHVDSFNHFVEIDIHNIVKANS---KIVSDVNP------RVYLEYTSIRVGEPVIQN 101

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK------------ 126
                      +C  R+ TYA P+ + +RL +           I  +             
Sbjct: 102 GPFDDHDVTPMECRLRNTTYAAPMHVNVRLSLSGEVRNYNDILIGRLPIMLRSKKCRLFK 161

Query: 127 ---EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYAC 182
              EQ   MG+ PL    G F+I G +++++ Q   S   I  + D+     +     + 
Sbjct: 162 ANDEQMAKMGECPL-DPGGYFIIGGTEKVILMQEQLSKNRIIVERDRHGEMSASVTSSSA 220

Query: 183 -----RIIPD-QGL-WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP 234
                 II   +G   + +   ++D+           P+   L A+GM S+ EIL     
Sbjct: 221 ERKTKTIINMKRGNFMLKVNMLAEDV-----------PLVVVLKAMGMTSDQEILQFIGA 269

Query: 235 KI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE-SGKKLTSGLL 285
                        Q  +   F    A   +G KV     +     +  E   + + + ++
Sbjct: 270 DEQSMELFGPSLQQCAELEVFTQDQALRYLGTKVRIPRREYGPSRRTKEDEARSILASVV 329

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
             L    V+   +   C+    +A  ++     +   +  D    K LE           
Sbjct: 330 --LSHIEVRNFDMRPKCIYLCVMARRMIAAIRNKSGGDDRDYYGNKRLELAGSLMALLFE 387

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
             +          R     D    R  A       +   +  T ++  +  +   ++  +
Sbjct: 388 DSFKTLNG-----RIKRELDHTFVRVTARAFDPAQIIRANPITQAINYA-ISSGNWNLKR 441

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---NGKGTIDDIDNLGNR 462
           + +   G   +  RL+      +            K+        +  G +   D     
Sbjct: 442 FRMERAGVTSVLSRLSFIAALGMMTRITSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGE 501

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
               V  +    Y    +  E  +     ++ ++ +   +        + V     +  L
Sbjct: 502 TCGLVKNLALMSYVTVDVD-EAPLIRLAYNLGVEGLNLVNGEEFSHEDTYVVFVNGTM-L 559

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHNIG 581
                  + +  +   RR   + +   A   A    R VH  +  GR+C       H   
Sbjct: 560 GVTRSPHHLVRAVRLLRRAGRINEFVSAYISA--STRTVHIASDAGRVCRPYIIVEHGQP 617

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           LV+             +        D      V YL   E  +  IA             
Sbjct: 618 LVTPQQLR-------DLALGILHFDDFIRLGVVEYLDVNELNDSLIAL------------ 658

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            E+   ++  P  V+   A LIP+  ++ S R    C M +QA+
Sbjct: 659 -----------YEKDMCEETTHLEIEPFTVLGACAGLIPYPHHNQSPRNTYQCAMGKQAM 707

Query: 702 PLL 704
            ++
Sbjct: 708 GVI 710



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 79/625 (12%), Positives = 184/625 (29%), Gaps = 86/625 (13%)

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           +   G      +          V        +      S ++ T  ++   +   +  + 
Sbjct: 181 FIIGGTEKVILMQEQLSKNRIIVERDRHGEMSASVTSSSAERKTKTIINMKRGNFMLKVN 240

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY 357
           + ++ +                + ++A  +  ++ + +   ++ + + +           
Sbjct: 241 MLAEDV-------------PLVVVLKAMGMTSDQEILQFIGADEQSMELF--------GP 279

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                   +   +  AL  +   +R        +    +       +    S +  V ++
Sbjct: 280 SLQQCAELEVFTQDQALRYLGTKVR--------IPRREYGPSRRTKEDEARSILASVVLS 331

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                +     + I    +  + + ++     K   DD D  GN+R+   G ++   +  
Sbjct: 332 HIEVRNFDMRPKCI---YLCVMARRMIAAIRNKSGGDDRDYYGNKRLELAGSLMALLFED 388

Query: 478 GLL----RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
                  R++R +      V   +  P  +I A P+  A+     S   +     +    
Sbjct: 389 SFKTLNGRIKRELDHTFVRVTARAFDPAQIIRANPITQAINYAISSGNWNLKRFRMERAG 448

Query: 534 RITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
             +   RLS +   G+         + R     R + P+ +G +CP++T EG   GLV +
Sbjct: 449 VTSVLSRLSFIAALGMMTRITSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGETCGLVKN 508

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE---ENRYIAQANSSLDEDGSFTE 642
           L   + V          R   +  V  + + L   EE   E+ Y+   N ++        
Sbjct: 509 LALMSYVTVDVDEAPLIRLAYNLGV--EGLNLVNGEEFSHEDTYVVFVNGTMLGVTRSPH 566

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQR 698
            LV             E +    ++  + V IA+       P++  +    ++    ++ 
Sbjct: 567 HLVRAVRLLRRAGRINEFVSAYISASTRTVHIASDAGRVCRPYIIVEHGQPLVTPQQLRD 626

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV----------------------E 736
            A+ +L  +       +E +       +++A     +                       
Sbjct: 627 LALGILHFDDFIRLGVVEYLDVNELNDSLIALYEKDMCEETTHLEIEPFTVLGACAGLIP 686

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                +    + +  +     GV  Y   +            QRPLVK            
Sbjct: 687 YPHHNQSPRNTYQCAMGKQAMGVIAYNYQRRIDTLLYALMYPQRPLVK----------TK 736

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHG 820
                D   L  G+    A +   G
Sbjct: 737 TIELIDFEKLPAGQVSCEARVCASG 761


>gi|300798312|ref|NP_001178807.1| DNA-directed RNA polymerase III subunit RPC2 [Rattus norvegicus]
          Length = 1133

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 103/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ ++   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLAKYNE 1133



 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 275/947 (29%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   +     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLAGNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L +  +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVSTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 D   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|226897652|gb|ACO90275.1| RNA polymerase beta subunit gene [Bacillus vietnamensis]
          Length = 376

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 223/372 (59%), Positives = 287/372 (77%), Gaps = 3/372 (0%)

Query: 583 VSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           V+SL+SFA+VN  GFIETPYR+V    GKVT+ + YL+A EE+N  +AQAN+ L +DG+F
Sbjct: 1   VNSLSSFAKVNNSGFIETPYRRVDPDTGKVTDRIDYLTADEEDNYVVAQANARLGDDGAF 60

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E V  R  GE  ++ RE++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQA
Sbjct: 61  LDEEVISRFRGENTVIKRERLDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQA 120

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGV 759
           VPL+  E+P VGTGME V AK SGAA++ K  GIVE+V+A ++ +R V+  D       +
Sbjct: 121 VPLMNPESPIVGTGMEHVSAKDSGAAVICKYEGIVEKVEAKQVWVRRVKEIDGQEVKGDL 180

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D YR+ KF RSNQ TC NQRP+V  GD V + +I+ADGPS + G+LALGRN++V FM W 
Sbjct: 181 DKYRMQKFIRSNQGTCYNQRPIVSEGDRVVKGEILADGPSMEKGELALGRNVMVGFMTWD 240

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE 
Sbjct: 241 GYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDER 300

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G +
Sbjct: 301 GIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII 360

Query: 940 VDVRIFNRHGID 951
           +DV++FNR   D
Sbjct: 361 LDVKVFNREDGD 372


>gi|284154878|gb|ADB78540.1| RNA polymerase beta-subunit [Bacillus amyloliquefaciens]
          Length = 182

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 80/204 (39%), Positives = 126/204 (61%), Gaps = 22/204 (10%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+ IE+Q   Y  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNXIEIQTXXYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE 226
           +VRIDR RK+PVT  L ALG  S+
Sbjct: 159 YVRIDRTRKLPVTVLLRALGFGSD 182


>gi|7022241|dbj|BAA91527.1| unnamed protein product [Homo sapiens]
          Length = 343

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 93/375 (24%), Positives = 148/375 (39%), Gaps = 71/375 (18%)

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             V +  ++         Q  ++   V +       QY+      +    + IEK+    +
Sbjct: 30   KVENKQVLVNKSMPTVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMISSN 84

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++NP 
Sbjct: 85   AEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPH 142

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     L  K   L   +                          
Sbjct: 143  GFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT---------------------- 172

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G+  + +   L     +  G+  +  G+TGEP 
Sbjct: 173  ------------------------AFGGSKVKDVCEDLVCHGYNYLGKDYVTSGITGEPL 208

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  Y
Sbjct: 209  EAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGY 268

Query: 1306 GAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVKEMQ 1355
            GA+ +L E L I SD    DV G+  +            +        P +  +L +E+Q
Sbjct: 269  GASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQ 328

Query: 1356 ALGLSIDLENSRTKN 1370
            ++ +   L+ S+   
Sbjct: 329  SMNIIPRLKLSKYNE 343


>gi|12545412|ref|NP_074962.1| RNA polymerase beta subunit [Euglena longa]
 gi|14286166|sp|P27059|RPOB_ASTLO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|12329876|emb|CAC24573.1| RNA polymerase subunit [Euglena longa]
          Length = 1076

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 112/388 (28%), Positives = 194/388 (50%), Gaps = 41/388 (10%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +  EI      +        +      + S+    +     ++   +   VE +    
Sbjct: 723  KEKKEEITKNIPDIKLKNVKNLNNNGIIKIGSKINGKEILIGIIKKRLINYEVELIYEIL 782

Query: 1043 ETSKSILEDRFKNK--IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               +         K  +  +             +++++  K+ IQ GDK++GRHGNKG++
Sbjct: 783  SEYERKNISVLSPKNLVGIVTNTKIHKIKNCYQIEIYITEKKKIQIGDKLSGRHGNKGVI 842

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            S+I+P  DMP+L DGTP+DI+LNPLG+PSRMNVGQI+E  L  + + L ++ K    D  
Sbjct: 843  SKIIPIVDMPYLPDGTPIDIILNPLGIPSRMNVGQIYECLLNLSAINLKERYKIQPFDEY 902

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               + S +  + +                                               
Sbjct: 903  QYKNNSEILIYKKLNQSRKKTK-------------------------------------K 925

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L   + +  G++IL++G  G+PF + ++ GY Y+LKL H+  +K++A++  +YS + +
Sbjct: 926  EWL--FNPNNPGKTILFNGKNGKPFKQTISFGYSYILKLMHIAEEKIHAKTISNYSSIIK 983

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFE 1340
            QP+ GKS  GGQR GEMEVW I+ +GAA++LQE+LTIKSDD+  ++++ ++++ G    +
Sbjct: 984  QPVKGKSKNGGQRFGEMEVWAIEGFGAAFLLQELLTIKSDDLHNKSQILKNLMNGLSMSK 1043

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSRT 1368
               PESF +L+ E+Q+LGL+I++   + 
Sbjct: 1044 PNVPESFKLLILELQSLGLNINIFTKKK 1071



 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 187/642 (29%), Positives = 329/642 (51%), Gaps = 51/642 (7%)

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
               F +SD Y+L   GR K+N ++   +   + + +  ED + I   ++ ++N     +
Sbjct: 228 LYNRFLNSDNYNLGDTGRFKINKKIYKTEFFTNKKILMPEDFLGIFNYMIKIKNINIKSN 287

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD------------ 502
            ID+L N+ V SVGE+++N++   +  +   I E+I+  +      +             
Sbjct: 288 KIDDLKNKIVLSVGELMQNKFNNIIKDIYTKIIEKINKFEQKKKQEEKYNKEKKEEKIKI 347

Query: 503 ----LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                IN+K +   + +F  ++ LSQL   +N LS +TH R++S LG GG+ + +A  ++
Sbjct: 348 NKTYFINSKNLTDNIKKFITTNPLSQLLNDLNPLSELTHKRKISTLGIGGIEKNKASTKI 407

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVY 616
           R++H +HYGRICP ETSEG N GLV SL    R+N +GFIE+P+ KV  G +  +  + +
Sbjct: 408 REIHNSHYGRICPIETSEGKNAGLVLSLAKDIRINKHGFIESPFYKVIKGNIKKNKGIFF 467

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +S+  E+N  IA  +           +    +   E      + I+FI  S  Q  SI  
Sbjct: 468 ISSENEKNIKIAPCDIL---KNFKLNKNYGVKNKNEFYYDSYKSINFISTSTDQFNSIGT 524

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            +IPFLE++D+NRVLMG  MQ+QA+ L   E   + TG E ++ + S + I+AK +G V 
Sbjct: 525 GIIPFLEHNDANRVLMGATMQKQALILKNKEPSLIETGREILINRDSKSTIIAKESGTVI 584

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVD--------------------IYRLMKFQRSNQNTCV 776
              + +I+I+            +                     IY L   +++N N   
Sbjct: 585 YSSSKKIIIQKKSKKSKFKNINLFKKYFKKKLKKNKKIKKHKHTIYLLNIDEKNNSNIYQ 644

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            +  +VK  D +++  IIA+G  +  G+L LG+N+LV ++ W GYNFED+++ISER+ +E
Sbjct: 645 TRTSIVKKNDWIKKGQIIAEGIGSLNGNLCLGKNILVGYLSWEGYNFEDAIIISERLRNE 704

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           D+ TSIH+++ +    + K   EEIT++IP++  + +KN++  GII +G+++N  +IL+G
Sbjct: 705 DILTSIHVKKCKSFLINHKEKKEEITKNIPDIKLKNVKNLNNNGIIKIGSKINGKEILIG 764

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            I    +  +  E +L+  I  E   + ++ S+  P  + G V + +I       KN   
Sbjct: 765 II---KKRLINYEVELIYEILSE--YERKNISVLSPKNLVGIVTNTKIH----KIKNCYQ 815

Query: 957 ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
           I +   + + +           ++ + S+++ I+       G
Sbjct: 816 IEIYITEKKKIQIGDKLSGRHGNKGVISKIIPIVDMPYLPDG 857



 Score =  140 bits (353), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 73/442 (16%), Positives = 164/442 (37%), Gaps = 47/442 (10%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +L+ +Q  S+ +FL + I  + +    +Q    S F I        +  + Y+   PK  
Sbjct: 10  NLLNIQSKSFKNFLKIGIINELKK---IQKIIHSNFEI-----NFHINALKYK--KPKLS 59

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
            + CL ++ TY + +KI + +       F         K++ I    +P MT+ GTF+  
Sbjct: 60  SESCLIKNETYNIDIKIPMEIKYEGKIIF---------KKKYISFCKIPFMTEKGTFICN 110

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G  RI+++QL RSPGI+    K              +IP  G W+ I+ + K    ++ID
Sbjct: 111 GNTRIIINQLIRSPGIYIKKKKNCLL--------ATLIPKTGSWITIKRNKKKENFIKID 162

Query: 208 R-RRKVPVTSFLMALGMDSEEI-LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           +    +P+ +FL  LG+  ++I LS        + +             +      +++ 
Sbjct: 163 KINNSIPLFTFLNILGLSKKKITLSLNKNNYSKNFKISKKKKIEIPTINLTQLSKENNIK 222

Query: 266 DIDTGE----------QVIESGKKLTSGLLKSLKEKGVKFLGITSDC--LCGLYVAEDIV 313
            I               + ++G+   +  +   +    K + +  D   +    +    +
Sbjct: 223 TIRNNLYNRFLNSDNYNLGDTGRFKINKKIYKTEFFTNKKILMPEDFLGIFNYMIKIKNI 282

Query: 314 NGETGEI--YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           N ++ +I        +   + ++  F++ I+DI    ++ +N     +        + ++
Sbjct: 283 NIKSNKIDDLKNKIVLSVGELMQNKFNNIIKDIYTKIIEKINKFEQKKKQEEKYNKEKKE 342

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           + +             T ++               DL+ +  +    +++      +  I
Sbjct: 343 EKIKINKTYFINSKNLTDNIK-KFITTNPLSQLLNDLNPLSELTHKRKIS---TLGIGGI 398

Query: 432 RKEDIIAIIKILVDLRNGKGTI 453
            K      I+ + +   G+   
Sbjct: 399 EKNKASTKIREIHNSHYGRICP 420


>gi|313237761|emb|CBY12898.1| unnamed protein product [Oikopleura dioica]
          Length = 1139

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 160/976 (16%), Positives = 299/976 (30%), Gaps = 207/976 (21%)

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +  +R   +   +V +     ++  +      R G    DD D  GN+R++  G+++   
Sbjct: 299  RFQVRTPRNREQEVHNWLVSTLLVNVPYCYK-RRGMIKADDRDYYGNKRIQLAGDLISLL 357

Query: 475  YRLGLLRMERSIKERISSVDIDSV--------MPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +          ++  I                  + L N   +         +  L + +
Sbjct: 358  FEEHFKNFNDELRRTIGKKLEKKTAQVVDVISSMKSLQNKITLAMEAAIQTGNWNLKRFK 417

Query: 527  EHVNSLSRITHTRRLSALGQGG--------VARARAGVEMRDVHPTHYGRICPAETSEGH 578
                 ++ I +     ++   G          +       R +  + +G +CP++T EG 
Sbjct: 418  MDRKGITEILNRMSFISIILVGTMTRIKGHFEKTMKVTGPRALQGSQWGMLCPSDTPEGA 477

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV ++   + V  +   +  +R + +  V  +   LS        +  AN  +  +G
Sbjct: 478  QCGLVKNMALLSHVTTFEDDKPIHRLLINLGV-EETSTLS-----GYDLHGANYLVFLNG 531

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            +        +     + + R      +      V ++          D  R+   C +  
Sbjct: 532  ALVGATRNPKSLTRTVQLIRRAGRLPE---FVSVYVSEEHRAVYLASDGGRLTRPCIIVE 588

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
               P +  +                   I A   G V+  D ++  +       + +++ 
Sbjct: 589  NGRPKVTQKH------------------INALLEGRVKFPDFVKNGLIEYLDVNEENSAL 630

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            +D      F++   N  +  R L +    +    +      +   +      +    +P+
Sbjct: 631  IDTTFFNYFRKIFFNQNLINRWLKRA--YLNFKKVNNFLNCSKEIEPFALLGVCAGLIPY 688

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N          M  + + T                    I  +     +  L N+  
Sbjct: 689  PDHNQSPRNTYQCAMGKQAMGT--------------------IAMNQRERIDSCLYNL-- 726

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
                          +    I   G   +   +    A+      D+ D  +   + V   
Sbjct: 727  -------VYPQRPLVKTRTIELIGFEQLPAGQNATVAVMSYSGYDIEDALVLNKASVDRG 779

Query: 939  VVDVRIFNRHGIDKNERSISVE--REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                 ++         R   VE   E+I+  A D    + I           +  G+   
Sbjct: 780  YGRCLVYRNEKTQLQRRGTLVETIEERIDGPALDAKSGEKIRADECLDMDGIVAPGERVK 839

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   KS  +  + +     + W                                   
Sbjct: 840  DRAPTMAKSQPIHIERVMISEDATW----------------------------------- 864

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                           R+VK+     R  + GDK + RHG KG+   I+P E+MPF + G 
Sbjct: 865  ---------------RMVKLSYRQTRRPELGDKFSSRHGQKGVTGLIVPQENMPFNEIGM 909

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP G PSRM VG++ E                                      
Sbjct: 910  CPDVIMNPHGYPSRMTVGKLMECIGSK--------------------------------- 936

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                A          T  F G   E +   +     +  G+ +L
Sbjct: 937  --------------------AGALSGKFHYGT-AFGGNTTEEMAQTMLDYGFNYYGKDLL 975

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
              G TGEP +  + +G IY  KL HMV DK++AR+TG    +T+QPL G++  GG RLGE
Sbjct: 976  MSGETGEPLEAYIFMGPIYYQKLRHMVMDKMHARATGKVHNLTRQPLEGRAKDGGLRLGE 1035

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------------RTRVYESIVAGNDT 1338
            ME   + AYGA+ +L E     SD    ++ G              RT        G   
Sbjct: 1036 MERDALLAYGASNLLNERFFYSSDKYSVEICGNCGLHGYSGWCRVCRT--------GEHM 1087

Query: 1339 FETGTPESFNVLVKEM 1354
                 P +  +L++E+
Sbjct: 1088 ASINMPYACKLLLQEL 1103



 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 125/960 (13%), Positives = 258/960 (26%), Gaps = 195/960 (20%)

Query: 17  FGKNPEIID----IPDLIEV-----Q---KASYDHFLMMNIAPDERPNEGLQAAFKSVFP 64
           +    E+ +    +P  +E      Q     S+++ L           +GLQ   K+   
Sbjct: 10  YESISEVQEKWKLVPAFLETRGLVKQHLDLDSFNYLLT----------QGLQKIIKANAR 59

Query: 65  ITAFSGAAMLEFVSYEFDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDE 115
            T         +     DPP              +C  RD+TY+ P+K+ +  +  +   
Sbjct: 60  -TDVDQNFFWNYDHIYVDPPDVEYGMRSEAITPHECRLRDMTYSAPIKVDVTYVRDNQIR 118

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQR 151
                           +G +P+M                           G FV+KG ++
Sbjct: 119 KARGLV----------IGRMPIMLRSARCVLANMSQEQFFKAKECPLDPGGYFVVKGAEK 168

Query: 152 IVVSQLH----R------SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           +++ Q      R        G+     K ++  +                      SK+ 
Sbjct: 169 VLLMQEQAVSNRILVEKDKTGMFCAVVKSKSDTANTQTNL--------------IQSKNK 214

Query: 202 IHVRIDRRRK-VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           I+V+ ++ R+ V V     ALG++ + EI      +           F     ++    +
Sbjct: 215 IYVKQNKLREPVNVVVLFKALGIERDQEIAELIATEDSTLALLAPSLFECQQLEIFSQNQ 274

Query: 260 VSSSLVD--IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
               L    +     ++   +  +   +++ + +  +        L    V         
Sbjct: 275 AMKYLEKTIMRIQNPIVSRSQMQSRFQVRTPRNREQEVHNWLVSTLL---VNVPYCYKRR 331

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G I  +  D    K ++         I +L+ +   N        +  K + +   ++D+
Sbjct: 332 GMIKADDRDYYGNKRIQLAGDL----ISLLFEEHFKNFNDELRRTIGKKLEKKTAQVVDV 387

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
              M+          E+      ++          R KM+ +   +  + +  I    + 
Sbjct: 388 ISSMKSLQNKITLAMEAAIQTGNWNLK--------RFKMDRKGITEILNRMSFISIILVG 439

Query: 438 AIIKILVDLRNGKGTIDDIDNLG-NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            + +I                 G    +    +  +      +  M           D  
Sbjct: 440 TMTRIKGHFEKTMKVTGPRALQGSQWGMLCPSDTPEGAQCGLVKNMALLSHVTTFEDDKP 499

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
                  +  +   +        +            +          +    + RA    
Sbjct: 500 IHRLLINLGVEETSTLSGYDLHGANYLVFLNGALVGATRNPKSLTRTVQL--IRRAGRLP 557

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR---KVCDGKVTND 613
           E   V+ +   R     +  G        + +         I        K  D      
Sbjct: 558 EFVSVYVSEEHRAVYLASDGGRLTRPCIIVENGRPKVTQKHINALLEGRVKFPDFVKNGL 617

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI-----DASP 668
           + YL   EE +  I    +  +                +   +  +K++       +  P
Sbjct: 618 IEYLDVNEENSALI--DTTFFNYFRKIFFNQNLINRWLKRAYLNFKKVNNFLNCSKEIEP 675

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ + A LIP+ +++ S R    C M +QA+  +          M       S     
Sbjct: 676 FALLGVCAGLIPYPDHNQSPRNTYQCAMGKQAMGTI---------AMNQRERIDS----- 721

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                                                       N    QRPLVK     
Sbjct: 722 -----------------------------------------CLYNLVYPQRPLVK----- 735

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                           L  G+N  VA M + GY+ ED++++++  V       +     +
Sbjct: 736 -----TRTIELIGFEQLPAGQNATVAVMSYSGYDIEDALVLNKASVDRGYGRCLVYRNEK 790

Query: 849 VMARDTKLGPE--EITRDIPNV------SEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
              +      E  E   D P +           + +D  GI+  G  V      + K  P
Sbjct: 791 TQLQRRGTLVETIEERIDGPALDAKSGEKIRADECLDMDGIVAPGERVKDRAPTMAKSQP 850


>gi|242392350|dbj|BAH80388.1| RNA polymerase subunit B' [Haloterrigena sp. GSL-11]
          Length = 609

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVDEDDLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  D +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRQGLEDAGFDSAGKETMYSGISGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.8 bits (99), Expect = 0.41,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A     G +E       D      + ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISQQEVEAL--QDGDLE-----FEDLVDHGYIEFIDAEEEEDILVAVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|3746594|gb|AAC64012.1| RNA polymerase II subunit 2 [Periploca graeca]
          Length = 260

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 111/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF ++G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTQEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHRCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|291389954|ref|XP_002711473.1| PREDICTED: DNA-directed RNA polymerase III B [Oryctolagus cuniculus]
          Length = 1133

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 174/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+  +
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYND 1133



 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 115/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + +   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRVIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPSVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|73697701|gb|AAZ81467.1| RNA polymerase beta subunit [Mycoplasma columbinum]
          Length = 592

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 210/420 (50%), Positives = 303/420 (72%), Gaps = 8/420 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY KV +G V  + V YL+A+EE   YIAQ+   +DE+    ++ +  R
Sbjct: 61  AKVNEYGFLQTPYYKVDNGIVNYDQVEYLTAIEEIGFYIAQSTVKVDENNKIVDDQITMR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +L   ++ID+I+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 HNYTYVLGKADQIDYIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+ES +AK S   I AK +G+VE VD  +I +R+ +  LD        Y L  FQ
Sbjct: 181 PFVATGLESAIAKYSSTNITAKNSGVVEYVDGSKIKVRNEKNTLD-------TYMLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T V+QRPLVKVG  + + D++ DG S   G+LALG+N++VAF  + GYN+ED+++
Sbjct: 234 RSNQDTVVHQRPLVKVGQSIEKGDLLVDGSSFKNGELALGKNVVVAFTTYKGYNYEDAVI 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  ++ R +++G +E+T DIPNVS+   +++DE GI+ VG+EV
Sbjct: 294 LNERLVKDDVFTSIHIEEQTILFRTSRVGDDELTADIPNVSKFATRHLDENGIVKVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+  ++ ++V+DTSL+V +G SGTV++V + +R 
Sbjct: 354 LPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQINVKDTSLKVKNGHSGTVINVEVLSRD 413



 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 137/451 (30%), Positives = 201/451 (44%), Gaps = 82/451 (18%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              K+  E+ T D   +      N D    +  ++ VG  +  GD+LV   + K    +  
Sbjct: 214  KIKVRNEKNTLDTYMLKNFQRSNQDTVVHQRPLVKVGQSIEKGDLLVDGSSFKN-GELAL 272

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVERE 962
             + ++ A    K  +  D  +            S  + +  I  R     ++  ++ +  
Sbjct: 273  GKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTILFRTSRVGDDE-LTADIP 331

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
             +   A    DE  I+         ++L G+ +  G     +   L S ++      Q  
Sbjct: 332  NVSKFATRHLDENGIVKVGSEVLPGDVLVGRVSPKGDDNPSQEEKLLSAVL------QQR 385

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q  V+D  +   V++       +  +L         + +       GV ++VKV +A+KR
Sbjct: 386  QINVKDTSL--KVKNGHSGTVINVEVL--------SRDENNVQFEDGVEKIVKVSIAVKR 435

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP GVPSRMN+GQ+ E HLG
Sbjct: 436  KIRVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLG 495

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A   LG K  +   D     +I                                     
Sbjct: 496  MAARELGVKFVTPAFDGIKKEEI------------------------------------- 518

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                    F+   E  +          ESG+  L D +TG  FD PV+VG +YMLKLNHM
Sbjct: 519  --------FNLIKEAKL---------PESGKQYLIDPITGRRFDNPVSVGVMYMLKLNHM 561

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            V DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 562  VDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|52694179|emb|CAG30619.1| DNA-directed RNA polymerase beta chain [Pseudomonas jessenii]
          Length = 340

 Score =  330 bits (846), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 201/340 (59%), Positives = 264/340 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  
Sbjct: 121 VVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEPYVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVR 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NF
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNF 340


>gi|111378455|gb|ABH09239.1| RpoB [Enterobacter aerogenes]
          Length = 336

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 209/336 (62%), Positives = 264/336 (78%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R++
Sbjct: 121 PYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            V +G+ + R D++ADGPSTDLG+LALG+NM VAFM
Sbjct: 301 CVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFM 336


>gi|46370579|gb|AAS90117.1| RpoB [Enterobacteriaceae bacterium Smarlab 3301641]
          Length = 333

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 207/332 (62%), Positives = 260/332 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ +
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPI 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            R D++ADGPSTDLG+LALG+NM VAFMPW+G
Sbjct: 302 ERGDVLADGPSTDLGELALGQNMRVAFMPWNG 333


>gi|73697671|gb|AAZ81452.1| RNA polymerase beta subunit [Mycoplasma columbinasale]
          Length = 592

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 217/452 (48%), Positives = 313/452 (69%), Gaps = 11/452 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDV  THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRVTSLGPGGLNRDTAQFEVRDVRATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY KV DG V  + V YL+A EE   YIAQ+  ++DE+    +  +  R
Sbjct: 61  AKVNEYGFLQTPYFKVVDGYVHYDKVEYLTATEELGFYIAQSTVAVDENNKIVDPQITMR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +L   E++D+I+A+P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 HNYTYVLGKPEEVDYIEAAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+ES +A+ S A I A++AGIVE VD  +I +R  +G L+        Y L  FQ
Sbjct: 181 PFVATGLESAIARFSSANITARQAGIVEYVDGAKIKVRDDKGKLE-------TYTLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T V+QRPLVK+G  V + D++ DG S   G+LALG+N++VAF  ++GYN+ED+++
Sbjct: 234 RSNQDTVVHQRPLVKMGQRVEKGDLLVDGSSFKDGELALGKNVVVAFTTFNGYNYEDAVI 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +++G +E+T DIPNVS+   +N+DE GI+ VG+EV
Sbjct: 294 LNERLVKDDVFTSIHIEEQTIQFRSSRVGDDELTADIPNVSKWATRNLDERGIVKVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   T EEKLL A+  ++ ++V+DTSL+V +G +GTV+DV +    
Sbjct: 354 LPGDVLVGRVSPKGDDNPTQEEKLLSAVLNQRQMNVKDTSLKVKNGHNGTVIDVEVL--- 410

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILDR 980
              K++       E I  ++     +  + D+
Sbjct: 411 DQKKDDVQFEDGIETIVKVSIAVKRKIRVGDK 442



 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 137/551 (24%), Positives = 211/551 (38%), Gaps = 80/551 (14%)

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCV-NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            D   +      Y L K +  +      NQ   V  G      +  A+             
Sbjct: 114  DPQITMRHNYTYVLGKPEEVDYIEAAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAV 173

Query: 810  NMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
             +L    P+     E ++    S  + +       +++  ++  RD K G  E       
Sbjct: 174  PLLETEAPFVATGLESAIARFSSANITARQAGIVEYVDGAKIKVRDDK-GKLETYTLKNF 232

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE-----EKLLRAIFGEKAV 922
                    + +  ++ +G  V  GD+LV   + K       +              E AV
Sbjct: 233  QRSNQDTVVHQRPLVKMGQRVEKGDLLVDGSSFKDGELALGKNVVVAFTTFNGYNYEDAV 292

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
             + +  ++     S  + +  I  R     ++   +      +   R+  DE+ I+    
Sbjct: 293  ILNERLVKDDVFTSIHIEEQTIQFRSSRVGDDELTADIPNVSKWATRNL-DERGIVKVGS 351

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                 ++L G+ +  G     +   L S ++         Q  +  +     V++     
Sbjct: 352  EVLPGDVLVGRVSPKGDDNPTQEEKLLSAVL--------NQRQMNVKDTSLKVKNGHNGT 403

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +L+ +  +             G+  +VKV +A+KR I+ GDKM+GRHGNKG+VS 
Sbjct: 404  VIDVEVLDQKKDDVQF--------EDGIETIVKVSIAVKRKIRVGDKMSGRHGNKGVVSI 455

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            +LP EDMP+L+DGTPVD++LNP GVPSRMN+GQ+ E HLG A   L  K  +   D    
Sbjct: 456  VLPEEDMPYLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAARSLNIKFVTPAFDGIKK 515

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             +I  L            +                                         
Sbjct: 516  EEIFNLIREANLPESGKQYLINPIT----------------------------------- 540

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                            G     FD PV+VG +YMLKLNHMV DK++ARS G YSL+TQQP
Sbjct: 541  ----------------GR---KFDNPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQP 581

Query: 1283 LGGKSNRGGQR 1293
            LGGKS  GGQR
Sbjct: 582  LGGKSQNGGQR 592


>gi|296212778|ref|XP_002752985.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 [Callithrix
            jacchus]
          Length = 1133

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 105/500 (21%), Positives = 176/500 (35%), Gaps = 88/500 (17%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSRVKDVCEDLVRHGYNYLGKDYVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVL 1350
              YGA+ +L E L I SD    DV G+  +     +G                P +  +L
Sbjct: 1056 IGYGASMLLLERLMISSDAFEVDVCGKCGLLGY--SGWCHFCKSSRQVSSLRIPYACKLL 1113

Query: 1351 VKEMQALGLSIDLENSRTKN 1370
             +E+Q++ +   L+ S+   
Sbjct: 1114 FQELQSMNIIPRLKLSKYNE 1133



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVPSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|73969955|ref|XP_531760.2| PREDICTED: similar to DNA-directed RNA polymerase III subunit 127.6
            kDa polypeptide (RNA polymerase III subunit 2) (RPC2)
            [Canis familiaris]
          Length = 1133

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 104/505 (20%), Positives = 173/505 (34%), Gaps = 98/505 (19%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 930  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 962

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 963  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDFVTSGITG 995

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 996  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1055

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPE 1345
              YGA+ +L E L I SD        +E  V G                         P 
Sbjct: 1056 IGYGASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPY 1108

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKN 1370
            +  +L +E+Q++ +   L+ S+   
Sbjct: 1109 ACKLLFQELQSMNIIPRLKLSKYNE 1133



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855


>gi|284504063|ref|YP_003406778.1| DNA-directed RNA polymerase subunit beta [Marseillevirus]
 gi|282935501|gb|ADB03816.1| DNA-directed RNA polymerase subunit beta [Marseillevirus]
          Length = 1277

 Score =  330 bits (845), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 166/1005 (16%), Positives = 334/1005 (33%), Gaps = 110/1005 (10%)

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
            T+ +             D +      ++A     + ++ G    +D D+  N+RV  V  
Sbjct: 335  TLSKELCEKLFPCYREADKKVWFMCYMLA---RALKVKTGDRQPEDRDHYTNKRVDCVDS 391

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
            +L N +     +  + IK+     +  +  P   I +K +   +     +   S      
Sbjct: 392  LLNNLFYSMWNQTTKFIKDSCKGKE-RTADPLKPIRSKSITKKIRTAMSTGNWSSFNTKS 450

Query: 530  NSLSRITHTRRLSALGQGGVARA--------RAGVEMRDVHPTHYGRICPAETSEGH-NI 580
                   +  R + +      R             + R VH + YG ICP +T E     
Sbjct: 451  KKQGTSQNYERYNIVASCSNLRKVHAAIGTEGNMTKPRRVHESSYGFICPPDTPESKDKT 510

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GL   L   A ++    +E  +  +        + Y S       ++      +    S 
Sbjct: 511  GLSKVLALSATMSLGCTVEECFEILSA------LEYFSQDFGLETFVFLNGVIMGSTDSP 564

Query: 641  TEELVFCRCAGEEILVPREKIDFID-ASPKQVVSIAASL-IPFLENDDSNRVLMGCNMQR 698
             E +              +     D    +  V+  A   I  L   +  ++  G     
Sbjct: 565  KELIGELSVLKRAGDFFWDCCFVFDEKHNEVRVNCDAGRLIRPLMVVEGGKLRFGPEHYE 624

Query: 699  QAVPLLKAEAPFVGTGM----ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            + +        F+G G+    ++   + S     A++ G  E  +     I  +      
Sbjct: 625  RLMKGTITWQEFIGLGIVEILDAEQQEHSLICPSAEQLGQSESKEWTHCEIHPLLVYGVC 684

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQR---PLVKVGDEVRRNDIIAD----------GPSTD 801
            ++           + S   +        P +  G       ++                 
Sbjct: 685  ASIIPYSANNPSPRLSYFASMAKSSVAVPRLDFGIAPFDQHVLHYPQKPLTSTKASRLLG 744

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            +    + +N++VA   + G+  ED+++  +         S H++ +  +    K      
Sbjct: 745  MNKSPICQNLVVAVCSYDGFGQEDAIVACKAFTQRGGMVSDHVQNYVAIIDHEKEQISPS 804

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                   S    +   +      G +V        K+ P+  S   P     + I   K 
Sbjct: 805  RCSDVEFSSSCQRFWCKN----CGKKV--------KLCPECGSEYVPSFSGHKGIVCRKK 852

Query: 922  VDVRDTSLRVPSGVSGTVVDVR--IFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
             D                +D +   +NR+ I++ +R + V+ E+     ++ D+++  L 
Sbjct: 853  ED-----------ERRAFIDRQTVFWNRNPINRIKRKVVVDGEE-----KEVDNQKKFLG 896

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            +  +  L E                  V     +         +     E     +    
Sbjct: 897  KKKWDCLCE-----------------EVEELPRLDHLDPEGVVEVGEVVEDGDILIAVAG 939

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMP-PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            V     K       K+K  ++        P     ++V VA  R  ++GDK    H  KG
Sbjct: 940  VSGAKRKDESIYFGKDKRGRVTSVSYFQNPNGYLCIRVAVASTRIPETGDKATSFHSQKG 999

Query: 1099 IVSRILPCEDMPFLKDG---TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            + S  +  +DMPF  D    T  D ++NPL  PSRM +GQ  E++ G       +++   
Sbjct: 1000 VFSLFVEEQDMPFTSDAFSATHPDFLINPLAFPSRMTIGQPKESNTGKMTASAYRELPDS 1059

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
             + ++       L + ++K +       K  +  +      +  +    P ++      +
Sbjct: 1060 -HRFEYENLYRTLSARIQKEVPEAEEAAKELEKRNPKTKGYSGSYTDCTPFTS------N 1112

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + +   L+       G+    DG TG+  +  + VG +   +L HMV DK++AR+TG  
Sbjct: 1113 YQVVEDELKRRGYAPGGKEFFIDGRTGKKMEVSLFVGLVPYNRLKHMVIDKIHARATGKI 1172

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD-------------V 1322
              +T+QP  G+S  GG + G ME   +   GA + L++ L +  D              V
Sbjct: 1173 QSLTRQPTEGRSRNGGLKTGIMERDSLVGNGAVFCLRDRLFLSCDKFEVWVCESCGLIAV 1232

Query: 1323 VGRTRVYESIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              + + Y     G  +  +   P +  +  +E+ A+G++  +   
Sbjct: 1233 ESKEKKYCRACHGKSNVVKLAVPYATKLSFQELMAMGITPRILVK 1277


>gi|242392340|dbj|BAH80383.1| RNA polymerase subunit B' [Haloterrigena limicola]
          Length = 609

 Score =  330 bits (845), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 125/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVAVDEDDLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             D++ +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDKDELREGLEDAGFDSAGKETMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.8 bits (99), Expect = 0.44,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  +  G +E       D      + ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISEQEIEALKD--GDLE-----FEDLVDHGYIEFIDAEEEEDILVAVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|86451161|gb|ABC96803.1| RNA polymerase II [Ixora parviflora]
          Length = 214

 Score =  330 bits (845), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 81/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  KSD
Sbjct: 199  GAAHFLKERLFAKSD 213


>gi|52694161|emb|CAG30610.1| DNA-directed RNA polymerase beta chain [Pseudomonas gessardii]
          Length = 339

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 200/339 (58%), Positives = 262/339 (77%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+S
Sbjct: 1   ERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           R V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E + 
Sbjct: 121 RVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVT 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ 
Sbjct: 181 LMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV
Sbjct: 241 SGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLV 300

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 301 SKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGF 339


>gi|111054615|gb|ABH04365.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 332

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 205/329 (62%), Positives = 257/329 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 4   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 64  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDE 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++++D S +QVVS
Sbjct: 124 IHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVEYMDVSTQQVVS 183

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 184 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 243

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V +G+ V R D+
Sbjct: 244 SVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLGEPVERGDV 303

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 304 LADGPSTDLGELALGQNMRVAFMPWNGYN 332


>gi|318603087|emb|CBJ04594.1| RNA polymerase beta subunit [Pseudomonas sp. R-38247]
          Length = 334

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 199/334 (59%), Positives = 257/334 (76%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 1   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 60

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 61  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 120

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++ E     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 121 HVIAQASATMSEQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 180

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 181 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 240

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 241 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 300

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           LALG+NM +AFM W+G+NFEDS+ +SER+V E+ 
Sbjct: 301 LALGQNMRIAFMAWNGFNFEDSICLSERVVQENR 334


>gi|92090451|gb|ABE73083.1| RNA polymerase beta subunit [Mycoplasma edwardii]
          Length = 601

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 215/456 (47%), Positives = 305/456 (66%), Gaps = 14/456 (3%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 1   FMDQINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLIL 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +  ++A+V+  GF++TPY KV +G V  NDV YL+A EE    IAQ++  +DE+   T+E
Sbjct: 61  NFATYAKVDDKGFLKTPYYKVNNGVVDYNDVQYLTASEEFGYSIAQSSVHVDENNKITDE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +  R          E +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPL
Sbjct: 121 FLTIRRNYTYENGRSEDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQAVPL 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           L+ EAP + TG+E+ +AK S   +VAK AG V  VD  RI +   E  +       D Y 
Sbjct: 181 LQTEAPLIATGIEADIAKYSSYNLVAKNAGTVTYVDGSRIHVTRNESTV------TDKYT 234

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           L  F+RSNQ T + QRPLV++GD+V   DI+ DG S   G+L+LG+N+LV F  W+GYNF
Sbjct: 235 LRNFERSNQGTLIQQRPLVRIGDKVEVGDILTDGSSFKDGELSLGKNVLVGFTTWNGYNF 294

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
           ED+++I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+DIPN S+  L+N+DE GI+ 
Sbjct: 295 EDAVIINERLVKNDVYTSIHIEEQTIQFRTSRAGNDELTKDIPNASKYSLRNLDEFGIVK 354

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           VG+EV PGD+LVG+++PKGE   + EEK+L AI G+++   +DTSL+V +G SGT++ V 
Sbjct: 355 VGSEVYPGDVLVGRVSPKGEENPSQEEKMLYAILGQRSPSTKDTSLKVKNGHSGTIIHVE 414

Query: 944 IFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           I +R   D       V  E IE + +    ++  + 
Sbjct: 415 ILSREKGD-------VLEEGIEKIVKVSIAQKRKIK 443



 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 130/423 (30%), Positives = 188/423 (44%), Gaps = 79/423 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD------TSLRVPSG 934
            ++ +G +V  GDIL    + K +  ++  + +L         +  D        ++    
Sbjct: 252  LVRIGDKVEVGDILTDGSSFK-DGELSLGKNVLVGFTTWNGYNFEDAVIINERLVKNDVY 310

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     N+          +   R+  DE  I+         ++L G+ 
Sbjct: 311  TSIHIEEQTIQFRTSRAGNDELTKDIPNASKYSLRNL-DEFGIVKVGSEVYPGDVLVGRV 369

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G +   +   +   ++ +   S            +     +K  +  +   +E   +
Sbjct: 370  SPKGEENPSQEEKMLYAILGQRSPS-----------TKDTSLKVKNGHSGTIIHVEILSR 418

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K      GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 419  EK------GDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 472

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQI E HLG A   LG K  S   D     DI         
Sbjct: 473  GTPLDIMLNPQGVPSRMNIGQILELHLGMAARKLGVKFVSPSFDGVKKPDIEAALEEAG- 531

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                            L         + 
Sbjct: 532  ------------------------------------------------LDKTG-----KQ 538

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +L D +TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 539  VLIDPITGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 598

Query: 1295 GEM 1297
            GEM
Sbjct: 599  GEM 601


>gi|52694369|emb|CAG38024.1| RNA polymerase beta subunit [Pseudomonas syringae]
          Length = 368

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 213/371 (57%), Positives = 279/371 (75%), Gaps = 8/371 (2%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 1   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 60

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 61  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASPKQVVS 673
           V+LSA+EE +  IAQA++++++     +ELV  R         R+  +  +D SPKQVVS
Sbjct: 121 VFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLKRNSPSRRQADVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES----VVAKSSGAAIVA 729
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P    G        VA+ SG  +VA
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPA---GRYWPWSANVARDSGVCVVA 237

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           +R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+
Sbjct: 238 RRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQ 297

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           R+DI+ADGPST++G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E   
Sbjct: 298 RSDIMADGPSTNMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQELTC 357

Query: 850 MARDTKLGPEE 860
           +ARDTKLGP+E
Sbjct: 358 VARDTKLGPKE 368


>gi|89888190|gb|ABD78639.1| DNA-directed RNA polymerase beta subunit [Bordetella trematum]
          Length = 184

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 94/186 (50%), Positives = 126/186 (67%), Gaps = 2/186 (1%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           K F K  ++ ++P L+  Q  SY  FL       ER NEGLQAAF S+FPI + +G A L
Sbjct: 1   KSFAKREDVQNVPFLLATQLQSYLTFLQAETISAERLNEGLQAAFTSIFPIVSHNGMARL 60

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFVSY    P FDV +C  R LTYA PL+  +RL++ D        +IK++KEQ +YMG+
Sbjct: 61  EFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLMDR--EVSKPTIKEVKEQEVYMGE 118

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ R+IP +G W+D 
Sbjct: 119 IPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARVIPYRGSWLDF 178

Query: 195 EFDSKD 200
           EFD KD
Sbjct: 179 EFDPKD 184


>gi|318603068|emb|CBJ04590.1| RNA polymerase beta subunit [Pseudomonas sp. R-38083]
          Length = 333

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 195/329 (59%), Positives = 254/329 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA
Sbjct: 61  PIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           ++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR 
Sbjct: 121 SATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRA 180

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + 
Sbjct: 181 LMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADD 240

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+N
Sbjct: 241 EVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQN 300

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           M +AFM W+G+NFEDS+ +SER+V ED F
Sbjct: 301 MRIAFMAWNGFNFEDSICLSERVVQEDRF 329


>gi|242392392|dbj|BAH80409.1| RNA polymerase subunit B' [Natronorubrum bangense]
          Length = 609

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 124/591 (20%), Positives = 204/591 (34%), Gaps = 95/591 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDVTEKHTHLEIDPSLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF +DG   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTQDGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  D +G+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESELRGGLEDAGFDSAGKEVMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLVDESDREEVYISAETGMI 557

Query: 1321 ---DVVGRTRVYESIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               DV  R RVY+ +     D        +F +L+ EM ALG+   L    
Sbjct: 558  AVQDVNQR-RVYDQLTGDESDIHRVEISYAFKLLLDEMMALGIRPRLNLKD 607



 Score = 42.4 bits (98), Expect = 0.52,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 23/106 (21%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + ++ A EEE+ Y+A     +                        EK   +
Sbjct: 92  FEDLVDHGYIEFIDAEEEEDIYVAVDEDDVT-----------------------EKHTHL 128

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  P  +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 129 EIDPSLIFGIGAGMIPYPEHNASPRITMGAGMVKQSLGLPSANYRI 174


>gi|318602956|emb|CBJ04567.1| RNA polymerase beta subunit [Pseudomonas sp. R-37096]
          Length = 334

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 198/332 (59%), Positives = 257/332 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 3   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 62

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 63  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 122

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 123 HVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 182

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 183 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 242

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 243 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 302

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
           LALG+NM +AFM W+G+NFEDS+ +SER+V E
Sbjct: 303 LALGQNMRIAFMAWNGFNFEDSICLSERVVQE 334


>gi|226897620|gb|ACO90259.1| RNA polymerase beta subunit gene [Bacillus anthracis]
          Length = 393

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 228/373 (61%), Positives = 287/373 (76%), Gaps = 3/373 (0%)

Query: 582 LVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L++SL+SFA+VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L E+G 
Sbjct: 1   LITSLSSFAKVNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSEEGE 60

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F +E +  R  GE I+  +E+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 61  FLDEDIVARFRGENIVTNKERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 120

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSG 758
           AVPL+  E+P VGTGME V AK SGAA++ K  GIVE+V+A  + +R  VE D       
Sbjct: 121 AVPLMNPESPIVGTGMEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGD 180

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +D Y++ KF RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W
Sbjct: 181 LDRYKMQKFIRSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTW 240

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE
Sbjct: 241 DGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDE 300

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G 
Sbjct: 301 RGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGI 360

Query: 939 VVDVRIFNRHGID 951
           ++DV++FNR   D
Sbjct: 361 ILDVKVFNREDGD 373



 Score = 43.1 bits (100), Expect = 0.33,   Method: Composition-based stats.
 Identities = 43/270 (15%), Positives = 89/270 (32%), Gaps = 15/270 (5%)

Query: 816  MPWHGYNFEDSMLISE--RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M +       + +I +   +V       + +  +  +   T  G  +  +    +     
Sbjct: 136  MEYVSAKDSGAAVICKHPGIVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFIRSNQG 195

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG EV  G+IL    +      +     +L         +  D  +    
Sbjct: 196  TCYNQRPIVSVGNEVVKGEILADGPS-MELGELALGRNVLVGFMTWDGYNYEDAII---- 250

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +S  +V   ++    I++ E      +   E + RD  +      RN+  R   I  G 
Sbjct: 251  -MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDER-GIIRVGA 308

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G     K T      ++   R     F  +  +V+     +               
Sbjct: 309  EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGII------L 362

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
              K+   + GD++PPGV ++V+ ++  KR 
Sbjct: 363  DVKVFNREDGDELPPGVNQLVRAYIVQKRK 392


>gi|145512048|ref|XP_001441946.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124409207|emb|CAK74549.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1214

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 156/1035 (15%), Positives = 318/1035 (30%), Gaps = 206/1035 (19%)

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +   +      D +         +  N+  ++    + R  +   +  I+  L++   G
Sbjct: 336  WIGNKIKKAENQDPETLIQEAKKLINKNILPHIGVSTESRDRKAYFLGYIVHRLLNASLG 395

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI---DSVMPQDLINA 506
            K   DD D+ G +R+   G M+   ++    + +++ K+ +             Q  I  
Sbjct: 396  KTDQDDRDHYGKKRLDMAGAMMMGVFKTSFEQFKQNSKKALEKYINGGRRGRGQQTKIEN 455

Query: 507  KPVVSAVCEFFCSSQLSQLEEH---------------------------VNSLSRITHTR 539
                  +  FF   Q+S+  ++                            +  + ++H R
Sbjct: 456  MRQPDDIKSFFDGEQISKDIDNALATGNWGRSKEGQVVKTGVAQTLKRETSLFATLSHLR 515

Query: 540  RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            R++A     +       + R +H TH+G ICPAET EG  IG+V +L+    V+      
Sbjct: 516  RMNA----PINPQMKLSKPRQLHNTHFGFICPAETPEGQKIGIVKNLSLMTTVSND---- 567

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
                +  D +    ++ +S   + +  + Q +    +    T+ LV     G      + 
Sbjct: 568  ---LQSKDKETLLKLIMVSQQNDFDFILLQGDFQAQDIPRMTKVLVDGNWIGFTRNPEQF 624

Query: 660  KIDFIDA-SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
              +F +  S ++        I F   +   R+        + + +++     +  G+ + 
Sbjct: 625  IHEFKNLRSAEESYIPIEVSINFDYVNKEIRIYTDAGRCMRPLFIVQNNKLKLMKGVLNQ 684

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
            +       +  K   +++  +    +I      +   T     Y                
Sbjct: 685  I-NDWEELLKNKCVELLDVEEEEGSLIAMDIDIMMRGTQNFKRY---------------- 727

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               P    G       +  + +P+  +N      +   M  + +
Sbjct: 728  -------------THCEIHPCMMFG-------VCASVIPFANHNQGPRNTLQSAMGKQAM 767

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
                                                NI    ++ +             +
Sbjct: 768  GL-----------------------------NSTNFNIRFDTLVHILHYPQKPLASSRAV 798

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                 + +      + +I      +  D+ +     +         +  +   +++   +
Sbjct: 799  DFITVNEVPIGINCVTSIACFTGYNQEDSIIINQYAIDRGFFRSVFYRTYKESEDKDPDN 858

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
                +I             +  N   +L   L     V       +   +    +     
Sbjct: 859  FTETKITKP----------IGDNFAGKLFIKLDSDGIVPPGTKVDEEEPIIGKELI---- 904

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                            + +   Q  T +  L  R   +               ++VKV V
Sbjct: 905  -----------IDNIMLNTANGQKNTKECSLLTRRAERGVVDSVLISENQKGYKLVKVKV 953

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK   RHG KG        ED+P+   G   D+ +NP  +PSRM +G + E
Sbjct: 954  RSLRIPQIGDKFCSRHGQKGTCGMTYRQEDLPYTLVGISPDLTINPHCIPSRMTIGHLIE 1013

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
                      G+                                                
Sbjct: 1014 CLSSKLASIKGQFND--------------------------------------------- 1028

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F       I + L      + G  ++ +  TG  F  P+ VG  Y  +
Sbjct: 1029 --------ATP-FAQILVNDIANELHKVGWQKWGNEVMTNPYTGNMFSIPIFVGPTYYQR 1079

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L H+V DK+YARS G  + +T+QP  G+S +GG R GEME  CI ++G A  L+E     
Sbjct: 1080 LRHLVDDKMYARSRGPVTGITRQPTHGRSRKGGLRFGEMERDCIISHGTAKFLKERTYDV 1139

Query: 1319 SD----DVVGRTRV-----------YESIVAGND----TFETGTPESFNVLVKEMQALGL 1359
            SD     V  +  +           Y ++    +     ++   P +   L++E+ ++ +
Sbjct: 1140 SDAFRVHVCSKCGMFAVANLENQEFYCNLCKNQNNQNKIYQVQMPYAAKTLIQELISMNI 1199

Query: 1360 SIDLENSRTKNSAKM 1374
            +  L+  ++K   ++
Sbjct: 1200 APRLKFDQSKMKHEI 1214



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 106/780 (13%), Positives = 231/780 (29%), Gaps = 147/780 (18%)

Query: 29  LIEVQKASYDHFLMMNIA-------------PDERPNEGLQAAFKSV---FPIT-AFSGA 71
           L+  Q  SY+ F+   I                +   E  Q A+      F IT  F G 
Sbjct: 46  LVSQQIGSYESFVENVIKFVRGHEGTFVVRVKPQYKEEERQEAYLEYLYQFQITRCFMGK 105

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             +  V  +F+   F       RDLTY+  LKI L + +   ++  G    K  K+Q  +
Sbjct: 106 KNIH-VD-KFEEEIF-PMIARLRDLTYSRQLKIDLEVTMQQRNKRDGTIEEKS-KQQ--F 159

Query: 132 MG----DLPLMTKD-----------------------------GTFVIKGIQRIVVSQLH 158
            G     LP+M +                              G F+++G ++++V+Q  
Sbjct: 160 KGLPFFKLPIMVRSRFCSLQKDPKDAELIQLRIQNGECGFDQGGYFILRGSEKVIVAQE- 218

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRII-----PDQGLWMDIEFDSKDIIHV--------- 204
                       R + +  L++  +I+      +     D+ F + ++  V         
Sbjct: 219 ------------RIANNVVLVFKSKIVNKPWVAEIRSQPDL-FSNPNVFKVELRYIQNTP 265

Query: 205 -------RIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                  + +  + +P+ +   ALG+ S+ EIL      +     G      L  +    
Sbjct: 266 VIRCSVKQFNSTQGIPLFTLFRALGISSDQEILERIVYNLEDEFMGPMLEM-LYGSLQEG 324

Query: 257 GAKVSSSLVDIDTGEQVIES----GKKLTSGLLKSLKEKGVKFLGITSD------CLCGL 306
           G      L     G ++ ++     + L     K + +  +  +G++++         G 
Sbjct: 325 GEYEDEELCLRWIGNKIKKAENQDPETLIQEAKKLINKNILPHIGVSTESRDRKAYFLG- 383

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT-- 364
           Y+   ++N   G+   +  D   +K L+      +      +     N+       +   
Sbjct: 384 YIVHRLLNASLGKTDQDDRDHYGKKRLDMAGAMMMGVFKTSFEQFKQNSKKALEKYINGG 443

Query: 365 -----DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                 + K       D  +    G+  +  +  ++    +  S +  +   G  +   R
Sbjct: 444 RRGRGQQTKIENMRQPDDIKSFFDGEQISKDIDNALATGNWGRSKEGQVVKTGVAQTLKR 503

Query: 420 LNLDTPDDVRH------IRKEDIIAIIKILVDLRNGKGTIDDI---DNLGNRRVRSVGEM 470
                            I  +  ++  + L +   G     +      +G  +  S+   
Sbjct: 504 ETSLFATLSHLRRMNAPINPQMKLSKPRQLHNTHFGFICPAETPEGQKIGIVKNLSLMTT 563

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           + N  +         +       D D ++ Q    A+ +          + +        
Sbjct: 564 VSNDLQSKDKETLLKLIMVSQQNDFDFILLQGDFQAQDIPRMTKVLVDGNWIGFTRNPEQ 623

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +    + R          A          ++  +  +     T  G             
Sbjct: 624 FIHEFKNLR---------SAEESYIPIEVSINFDYVNKEIRIYTDAG----RCMRPLFIV 670

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           + N    ++    ++ D             E       +     +E+GS     +     
Sbjct: 671 QNNKLKLMKGVLNQINDW-----------EELLKNKCVELLDVEEEEGSLIAMDIDIMMR 719

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   ++    +  P  +  + AS+IPF  ++   R  +   M +QA+ L       
Sbjct: 720 ---GTQNFKRYTHCEIHPCMMFGVCASVIPFANHNQGPRNTLQSAMGKQAMGLNSTNFNI 776


>gi|6606135|gb|AAF19080.1|AF107808_1 DNA-dependent RNA polymerase II RPB140 [Sclerotinia sclerotiorum]
          Length = 938

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 159/978 (16%), Positives = 304/978 (31%), Gaps = 157/978 (16%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +       S+        
Sbjct: 89   VSDEDILNHICYDRNDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGNGTSL---TRDKR 145

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             KY    + +  +      +  +  +      +  ++  L+    G+   DD D+ G +R
Sbjct: 146  IKYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHKLLQCALGRRETDDRDHFGKKR 202

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    R+   +    +    +         + +  + + +     +  
Sbjct: 203  LDLAGPLLAKLFRNLFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGN 262

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 263  WGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 318

Query: 569  ICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L    +  V         +    + +V  +   L A      +
Sbjct: 319  VCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVF 378

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN- 684
            +      +  D +   + V        I      I +  D   K          P L   
Sbjct: 379  VNGVWVGVHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVID 438

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA--AIVAKRAGIVEQVDAIR 742
            +D +    G  +  +       +   + + M+       G          G+VE +DA  
Sbjct: 439  NDPDSPNKGNLVLNKDHIRRLEDDQSLPSNMDKDEKVHHGYYGFQGLINDGVVEYLDAEE 498

Query: 743  I---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                +I     DLD S      Y++    R + +  +N+R    +             PS
Sbjct: 499  EETVMITMTPEDLDISRQLQAGYQI----RPDDSGDLNKRVKAPINPTAHVWTHCEIHPS 554

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N                        ++       +G  
Sbjct: 555  MILG-------ICASIIPFPDHNQSPRNC------------------YQSAMGKQAMGVF 589

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D+               +  +             +       +   +  + AI   
Sbjct: 590  LTNFDVRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCY 638

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L 
Sbjct: 639  SGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLK 694

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +  Y +L +   +  G           K+  ++ D                +E  QR   
Sbjct: 695  QGTYEKLDDDGIVAPGVRVTGADIIIGKTAPIAPD---------------SEEMGQRTKA 739

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +K    T     E    +++             LR VKV +   +  Q GDK A RHG 
Sbjct: 740  HVKRDASTPLRSTESGLVDQVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQ 794

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      +DMPF ++G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 795  KGTIGITYMQQDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGLEGDATP 854

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L                         LR       G  +          
Sbjct: 855  FTEVTVDSVSKL-------------------------LRAHGYHSRGFEIM--------- 880

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G +    G         V +G  Y  +L HMV DK++AR+ G   
Sbjct: 881  -------------YHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDKIHARARGPVQ 920

Query: 1277 LVTQQPLGGKSNRGGQRL 1294
            ++T+QP+ G++  GG R 
Sbjct: 921  ILTRQPVEGRARDGGLRF 938



 Score =  107 bits (267), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 104/847 (12%), Positives = 228/847 (26%), Gaps = 146/847 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          +   +  + Y   I    ++G  +      K  ++ + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKPANQAVSYLAEIRSALEKGSRLISSLQIK--LYDKG 55

Query: 207 DRRR----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPL 249
           D  R                 +P+     ALG +  E+IL+        +Q  +     +
Sbjct: 56  DSGRGGFGKTVKSTLPYIKQDIPIAIVFRALGVVSDEDILNHICYDRNDTQMLEMLKPCI 115

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A ++   +V+   +        +   K++     + + +K +                
Sbjct: 116 EEAFVIQDREVALDFIGKRGNGTSLTRDKRI--KYARDIMQKEL---------------- 157

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
              ++ + G    +A  +              R+                  L       
Sbjct: 158 LPHISQKEGSETRKAFFLGYMVHKLLQCALGRRETDDRDHFGKKRLDLAGPLLAKLFRNL 217

Query: 370 RKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            +    D+YR + R  + +               +        G      +    T    
Sbjct: 218 FRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAASSTAGVS 277

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R+GK       +  +  +    E  + Q    +  + 
Sbjct: 278 QVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 337

Query: 484 RSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRI 535
                 + +     V      N + +         +A   F     +    +  + +  +
Sbjct: 338 LMCYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVGVHRDPAHLVKCV 397

Query: 536 THTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSL- 586
              RR   +  +  + R     E        R   P       P   ++G+ +     + 
Sbjct: 398 QDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNDPDSPNKGNLVLNKDHIR 457

Query: 587 ------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-- 638
                 +  + ++    +   Y           V YL A EEE   I      LD     
Sbjct: 458 RLEDDQSLPSNMDKDEKVHHGYYGFQGLINDGVVEYLDAEEEETVMITMTPEDLDISRQL 517

Query: 639 ------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                    +     +     I          +  P  ++ I AS+IPF +++ S R   
Sbjct: 518 QAGYQIRPDDSGDLNKRVKAPINPTAHVWTHCEIHPSMILGICASIIPFPDHNQSPRNCY 577

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              M +QA+ +               V   + A I+      +    ++  +        
Sbjct: 578 QSAMGKQAMGVFLT---------NFDVRMDTMANILYYPQKPLATTRSMEFLKFRELPAG 628

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             +   +  Y              NQ                    S  +   ++ R + 
Sbjct: 629 QNAIVAIMCYSG-----------YNQE------------------DSVIMNQSSIDRGLF 659

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            +       + E  + ++     E  + S                      D   + +  
Sbjct: 660 RSLFYRAYTDQEKRIGMNVVEQFEKPYRS----------------------DTLKLKQGT 697

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + +D+ GI+  G  V   DI++GK  P         ++        KA   RD S  + 
Sbjct: 698 YEKLDDDGIVAPGVRVTGADIIIGKTAPIAPDSEEMGQRT-------KAHVKRDASTPLR 750

Query: 933 SGVSGTV 939
           S  SG V
Sbjct: 751 STESGLV 757


>gi|242392364|dbj|BAH80395.1| RNA polymerase subunit B' [Natrialba magadii]
          Length = 609

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 125/595 (21%), Positives = 210/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDIYVAVEEADLTADHTHLEIDPQLIFSIGSGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTITLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE A+   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESALRDGLEEAGFDSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    +V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCEEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 43.5 bits (101), Expect = 0.24,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 65/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  +  G +E       D      V ++ A EEE+ Y+A   + L 
Sbjct: 71  EDGE-PRISEQEIEALRD--GDLE-----FEDLVDHGYVEFIDAEEEEDIYVAVEEADLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ + SI + +IP+ E++ S R+ MG  
Sbjct: 123 ADH-----------------------THLEIDPQLIFSIGSGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|40644996|emb|CAD88981.1| DNA-directed RNA polymerase subunit B [Vicia sativa]
          Length = 260

 Score =  329 bits (844), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 116/289 (40%), Gaps = 54/289 (18%)

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q   +    +Y      +  R        Q         LR VKV V   R  Q GDK +
Sbjct: 6    QEEAQGQAARYSKRDHSISLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFS 65

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+
Sbjct: 66   SRHGQKGTVGMTYTQEDMPWTAEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE 125

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                                   +TP F
Sbjct: 126  GD-----------------------------------------------------ATP-F 131

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                 + I+  L        G   +Y+G TG      + +G  Y  +L HMV DK+++R 
Sbjct: 132  TDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRG 191

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 192  RGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 240


>gi|147921535|ref|YP_684649.1| DNA-directed RNA polymerase, subunit B2 [uncultured methanogenic
            archaeon RC-I]
 gi|110620045|emb|CAJ35323.1| DNA-directed RNA polymerase, subunit B2 [uncultured methanogenic
            archaeon RC-I]
          Length = 605

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 121/603 (20%), Positives = 203/603 (33%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDIIAD----GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            D++RR +I  D        +  D     N  +A            + ++  ++       
Sbjct: 79   DQLRRGEITFDDLVKRGLIEYIDAEEEENTFIAIDESQLTPEHTHLELNPSLILGIAAGM 138

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +S    + +                +        
Sbjct: 139  IPYPEHNASPRVTMGAG--MIKQCLGMSTAN-QKLRPDTRGHFLHYPQRAIVNTQTAEAV 195

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
              +     +  + A+   +  ++ D  +     +    +    F R    +  R    + 
Sbjct: 196  NFNERPAGQNFVVAVLSFEGYNIEDALVFNRGSIERG-LGRSHFFRTTEGEERRYPGGQE 254

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEI-LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +  E+   +    +   +   YS+L E  L     V GP             + E   + 
Sbjct: 255  DTFEVPDAEV---RGAREAEFYSQLDEDGLVNPETVVGPNDVLIGKTSPPRFLEE--PTD 309

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                                  +  ++ +  R   K               R+ KV    
Sbjct: 310  LGGITP---------------LKRRETSVTMRSNEKGIVDTVILTATQNGSRLAKVRTRD 354

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            +R  + GDK A RHG KG++  I   EDMPF ++G   D+++NP  +PSRM +G + E  
Sbjct: 355  QRIPELGDKFASRHGQKGVIGLIAQQEDMPFAENGLVPDLIINPHAIPSRMTIGHVLEMI 414

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G+ +                                                
Sbjct: 415  GGKMGSLEGRFVDG---------------------------------------------- 428

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                   TP F+  DE  + + L+      SG+ + Y G TGE     V VG I   KL 
Sbjct: 429  -------TP-FNNEDELNMRATLKKFGFSHSGKEVFYSGTTGERIVADVFVGVILYQKLY 480

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVS K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD
Sbjct: 481  HMVSSKMHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLDESD 540

Query: 1321 DV-------VGRT-------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             V        G         +V      G   + ++     +F +L+ EM+ALG++  LE
Sbjct: 541  KVFEYVCNNCGMVATEDKKRKVIYCPNCGADTNIYKIEMSYAFKLLLDEMKALGIAPRLE 600

Query: 1365 NSR 1367
               
Sbjct: 601  LED 603



 Score = 88.6 bits (218), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 75/460 (16%), Positives = 136/460 (29%), Gaps = 106/460 (23%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
             F +  L  + ++   L      +R   L    +  A   +    +  T  GR      
Sbjct: 5   RVFVNGALVGMHDNPTELVESIREKRRQGLVSNQINIAHHKLTNEVIINTDMGRAR---- 60

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                + +V              +        D      + Y+ A EEEN +IA   S L
Sbjct: 61  ---RPLIIVKDGKPMITAEETDQLRRGEITFDDLVKRGLIEYIDAEEEENTFIAIDESQL 117

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +                          ++ +P  ++ IAA +IP+ E++ S RV MG 
Sbjct: 118 TPEH-----------------------THLELNPSLILGIAAGMIPYPEHNASPRVTMGA 154

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +Q + +  A                                                
Sbjct: 155 GMIKQCLGMSTANQKL-----------------------------------------RPD 173

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           +      Y               QR +V                + +  +   G+N +VA
Sbjct: 174 TRGHFLHYP--------------QRAIVN----------TQTAEAVNFNERPAGQNFVVA 209

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVS 869
            + + GYN ED+++ +   +   +  S      E   R    G E+              
Sbjct: 210 VLSFEGYNIEDALVFNRGSIERGLGRSHFFRTTEGEERRYPGGQEDTFEVPDAEVRGARE 269

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
            E    +DE G++     V P D+L+GK +P               + G   +  R+TS+
Sbjct: 270 AEFYSQLDEDGLVNPETVVGPNDVLIGKTSPPRFLEEPT------DLGGITPLKRRETSV 323

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + S   G V  V +       +  +  + ++   EL  +
Sbjct: 324 TMRSNEKGIVDTVILTATQNGSRLAKVRTRDQRIPELGDK 363


>gi|98991112|gb|ABF60574.1| RNA polymerase beta subunit [Mycoplasma subdolum]
          Length = 595

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 203/446 (45%), Positives = 298/446 (66%), Gaps = 9/446 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L 
Sbjct: 1   QCNPLAEMSNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ +GF+++PY +V +  V  ++ +YL+A+EE      Q+   +D+ G  T++ V 
Sbjct: 61  SFAKIDRFGFLQSPYFRVKNRHVDFSEPIYLTAIEEIGYTFTQSTIHIDKKGYITDDFVM 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E + V  E +D++ AS +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  
Sbjct: 121 ARKNNEYMEVKAEDVDYVAASNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLSP 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ VAK S   I A   GIV  +D+ +I ++         +S  + Y L  
Sbjct: 181 EAPLVATGVEADVAKYSSTNIRALHDGIVTYIDSQKIKVQ------ISGSSKTETYFLRT 234

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T ++Q P+VK+G E++  D++ DGPS   G++ALG+N+LV F  W+GYN+ED+
Sbjct: 235 FERSNQGTLIHQTPIVKIGQEIKAGDLLVDGPSMKDGEMALGKNVLVGFTTWNGYNYEDA 294

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TSIHIEE  +  R +K G + +T DIPN S    + +DE GI+ +G+
Sbjct: 295 VILSERLVKDDVYTSIHIEEQTIQFRHSKAGEDWLTDDIPNASNYSKRFLDENGIVRIGS 354

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVVDV I +
Sbjct: 355 EVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTSSRKDTSLKVRHGHNGTVVDVEILS 414

Query: 947 RHGIDKNERSISVEREQIELLARDKD 972
           R     ++    +E+     +A+ + 
Sbjct: 415 RDTG--DQLEDGIEKIVKVSIAQKRK 438



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 90/414 (21%), Positives = 145/414 (35%), Gaps = 67/414 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G E+  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 249  IVKIGQEIKAGDLLVDGPS-MKDGEMALGKNVLVGFTTWNGYNYEDAVILSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E    + +    +  +  LD N   R+   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRHSKAGEDWLTDDIPNASNYSKRFLDENGIVRIGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V            IL           
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTSSRKDTSLKVRHGHNGTVVDVEILSRD-------- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A                 K    R +   D            
Sbjct: 417  -TGDQLEDGIEKIVKVSIA----------------QK----RKIRVGD------------ 443

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
                                        G K    I             + L+ ++    
Sbjct: 444  ----------------------KMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDILLNPQG 481

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
               +++      +   +     G   +TP+FDG   + +  +L  A LD SG++ +Y G 
Sbjct: 482  VPSRMNIGQVLELALGSAAKVLGTKFATPIFDGITHKQVQEILEEAKLDPSGKAYVYSGQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            TGE FD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 542  TGEKFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 595


>gi|52538143|emb|CAH19173.1| RNA polymerase beta-subunit [Pseudomonas mandelii]
          Length = 336

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 200/336 (59%), Positives = 260/336 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDS 336


>gi|56675686|emb|CAB43081.2| RNA polymerase II [Potalia resinifera]
          Length = 250

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTSEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|19114602|ref|NP_593690.1| DNA-directed RNA polymerase III complex subunit Rpc2
            [Schizosaccharomyces pombe 972h-]
 gi|1710663|sp|Q10233|RPC2_SCHPO RecName: Full=DNA-directed RNA polymerase III subunit RPC2; Short=RNA
            polymerase III subunit 2; Short=RNA polymerase III
            subunit C2; AltName: Full=C128; AltName:
            Full=DNA-directed RNA polymerase III 130 kDa polypeptide;
            AltName: Full=RPC130
 gi|1204209|emb|CAA93558.1| DNA-directed RNA polymerase III complex subunit Rpc2
            [Schizosaccharomyces pombe]
 gi|76782167|gb|ABA54854.1| RNA polymerase III large subunit Rpc2 [Schizosaccharomyces pombe]
          Length = 1165

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 109/504 (21%), Positives = 186/504 (36%), Gaps = 86/504 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    AI      D+ D  +   S +   
Sbjct: 735  DTLLYLMVYPQQPMVKTKTIELIGYDKLPAGQNATVAIMSYSGYDIEDALVLNKSSIDRG 794

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++F++H +   +   +   ++I    RD +  +V+    +         G     G
Sbjct: 795  FGRCQVFHKHSVIVRK-YPNGTHDRIGDPQRDPETGEVVWKHGVVEDDGLAGVGCRVQPG 853

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T  +               A+ +     + ++++  Y+ +    +      I+
Sbjct: 854  QIYVNKQTPTN---------------ALDNSITLGHTQTVESGYKATPMTYKAPEPGYID 898

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+            ++KV +   R  + GDK + RHG KG+   I+  EDMPF   G   
Sbjct: 899  KVML--TTTDSDQTLIKVLMRQTRRPELGDKFSSRHGQKGVCGVIVQQEDMPFNDQGICP 956

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP G PSRM V        G     L  K+  L    +                  
Sbjct: 957  DIIMNPHGFPSRMTV--------GKMIELLSGKVGVLRGTLEYGTC-------------- 994

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                            F G   E  + +L     + SG+ +L  
Sbjct: 995  --------------------------------FGGTKVEDASRILVEHGYNYSGKDMLTS 1022

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE  +  + +G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME
Sbjct: 1023 GITGETLEAYIFMGPIYYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEME 1082

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPES 1346
              C+ AYGA+ +L E L I SD    DV G+  +      G         +  +   P +
Sbjct: 1083 RDCLIAYGASQLLLERLMISSDACDVDVCGQCGLLGY--KGWCNSCQSTREVVKMTIPYA 1140

Query: 1347 FNVLVKEMQALGLSIDLENSRTKN 1370
              +L +E+ ++ +   L       
Sbjct: 1141 AKLLFQELLSMNIVPRLALEDEFK 1164



 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 113/937 (12%), Positives = 258/937 (27%), Gaps = 188/937 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ +++    + NE        V P         L+++      P    
Sbjct: 63  LVKQHLDSYNYFVDVDLKKIVQANE---KVTSDVEP------WFYLKYLDIRVGAPVRTD 113

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY   + + +             +  + ++ +++ +G +P+M
Sbjct: 114 ADAIQASISPHECRLRDLTYGANIYVDIEYT----------RGKQVVRRRNVPIGRMPVM 163

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG +++++ Q   S        + +   
Sbjct: 164 LRSNKCVLSGKNEMEMAALNECPLDPGGYFIVKGTEKVILVQEQLSKNRIIVEAEPK--- 220

Query: 175 SGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGM-DSEEIL 229
             K L+   +      +             ++++ +     +P+   L A+G+   +EI 
Sbjct: 221 --KGLWQASVTSSTHERKSK-TYVITKNGKLYLKHNSVADDIPIVVVLKAMGLQSDQEIF 277

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
                     Q          A   +  A+ +   +                   +K  +
Sbjct: 278 ELVAGAEASYQDLFAPSIEECAKLNIYTAQQALEYIGAR----------------VKVNR 321

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
             G   L    +    +  A  + +     +      V        +  + +  + +   
Sbjct: 322 RAGANRLP-PHEEALEVLAAVVLAHINVFNLEFRPKAVYIGIMARRVLMAMVDPLQVDDR 380

Query: 350 DSVNN------NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           D V N         +         K   D  L+I +V++    +    A +         
Sbjct: 381 DYVGNKRLELAGQLLALLFEDLFKKFNSDLKLNIDKVLKKPHRTQEFDAYNQLTVHSDHI 440

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +  +  +     +++        V H    +     + ++  +         +    +L
Sbjct: 441 TQGMVRALSTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRITSQFEKTRKVSGPRSL 500

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +   +      +     L    ++   I++ + +  + +           V      
Sbjct: 501 QASQFGMLCTSDTPEGEACGLVKNLALMTHITTDEEEEPIIKLAYAFGIEDIHVISGREL 560

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                   ++N             +     + R+        +    + R     T  G 
Sbjct: 561 HSHGTYLVYLNGAILGISRYPSLFVASFRKLRRSGKISPFIGIFINTHQRAVFISTDGGR 620

Query: 579 NIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               +  + +            ++       D      V Y+   EE +  I+     + 
Sbjct: 621 ICRPLIIVQNGLPKVESKHIRLLKEGKWGFEDFLKQGLVEYVDVNEENDSLISVYERDIT 680

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P  ++   A LIP+  ++ S R    C 
Sbjct: 681 PD-----------------------TTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCA 717

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+                                           I   +     +
Sbjct: 718 MGKQAIGA-----------------------------------------IAYNQLQRIDT 736

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              + +Y               Q+P+VK                     L  G+N  VA 
Sbjct: 737 LLYLMVYP--------------QQPMVK----------TKTIELIGYDKLPAGQNATVAI 772

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI---PNVSEEG 872
           M + GY+ ED++++++  +           +  V+ R    G  +   D    P   E  
Sbjct: 773 MSYSGYDIEDALVLNKSSIDRGFGRCQVFHKHSVIVRKYPNGTHDRIGDPQRDPETGEVV 832

Query: 873 LKN--IDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            K+  +++ G+  VG  V PG I V K TP      +
Sbjct: 833 WKHGVVEDDGLAGVGCRVQPGQIYVNKQTPTNALDNS 869


>gi|193786878|dbj|BAG52201.1| unnamed protein product [Homo sapiens]
          Length = 523

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 104/498 (20%), Positives = 174/498 (34%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 100  YLLAYPQKPMVKTKTIELIEFEKLPAGQNAAVAVMSYSGYDIEDALVLNKASLDRGFGRC 159

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 160  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 218

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 219  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 261

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 262  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 319

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     L  K   L   +                       
Sbjct: 320  NPHGFPSRMTV--------GKLIELLAGKAGVLDGRFHYGT------------------- 352

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+  + +   L     +  G+  +  G+TG
Sbjct: 353  ---------------------------AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITG 385

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 386  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 445

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA  +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 446  IGYGANMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 505

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 506  ELQSMNIIPRLKLSKYNE 523



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/330 (14%), Positives = 94/330 (28%), Gaps = 93/330 (28%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +   YR   D    + V YL   EE +  IA                             
Sbjct: 4   LAQGYRNFEDFLHESLVEYLDVNEENDCNIAL-----------------------YEHTI 40

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            +    ++  P  ++ + A LIP+  ++ S R    C M +QA+  +         G   
Sbjct: 41  NKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQ 91

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                +   ++A                                                
Sbjct: 92  RNRIDTLMYLLA----------------------------------------------YP 105

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P+VK                 +   L  G+N  VA M + GY+ ED++++++  +   
Sbjct: 106 QKPMVK----------TKTIELIEFEKLPAGQNAAVAVMSYSGYDIEDALVLNKASLDRG 155

Query: 838 VFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGD 892
               +  +  +    R T    +++   + + +          +D  GI   G +V    
Sbjct: 156 FGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQ 215

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +LV K  P           + +    +   
Sbjct: 216 VLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 245


>gi|242392388|dbj|BAH80407.1| RNA polymerase subunit B' [Natronolimnobius innermongolicus]
          Length = 609

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 124/595 (20%), Positives = 210/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LVA    H       + I   ++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDILVAVDEEHLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVIGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L  A  + +G+ ++Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESKLRDGLEDAGFNSAGKEVMYSGISGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 42.8 bits (99), Expect = 0.47,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHKLAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A       +E    +  D      V ++ A EEE+  +A     L 
Sbjct: 71  EDGE-PRISQQELEA-------VEDGDLEFEDLVDHGYVEFIDAEEEEDILVAVDEEHLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|4867872|emb|CAB43073.1| RNA polymerase II [Mussaenda erythrophylla]
          Length = 261

 Score =  329 bits (843), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|78714203|gb|ABB51084.1| RNA polymerase beta subunit [Mycoplasma hyorhinis ATCC 17981]
          Length = 594

 Score =  329 bits (843), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 209/444 (47%), Positives = 296/444 (66%), Gaps = 11/444 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +   +
Sbjct: 2   NPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHVTHYGRICPVETPEGQNIGLILNFAVY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           A+ N YGFI+TPY  V +G V     ++V+L+A EE     AQ++  +DE+    E  + 
Sbjct: 62  AKTNPYGFIQTPYFPVENGVVNYDPQNIVWLTAAEEFGYTFAQSSLLVDENNKIIEPEII 121

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     + V  E++DFI  S KQ+ S++AS +PFLEN+D+NR LMG NMQRQAVPL+  
Sbjct: 122 VRKNYTYLTVKPEQVDFIAVSSKQMTSLSASAVPFLENNDANRALMGSNMQRQAVPLITT 181

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP+V TG+E+ VAK S   I A   G V  VD+  I I++ +G        +  Y L  
Sbjct: 182 EAPYVATGIEADVAKFSSTNIRASEDGEVVFVDSKSIQIKNEQG-------NIKTYHLRY 234

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + QRP+V+VG  V++ D+I DGPSTD G+LALG+N+LVAF  W+GYN+ED+
Sbjct: 235 FERSNQETLILQRPIVEVGQFVKQGDLICDGPSTDQGELALGKNVLVAFSTWYGYNYEDA 294

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++ISE++V +DVFTSIHI+E  +  R +K G +++TR+IPN S+   +++DE GI+ +G+
Sbjct: 295 IIISEKLVKDDVFTSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGS 354

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+ GDILVG+ +PKGE   TPEEKL+ AI+G+KA   +DTSL+V  G  GTV+DV+I +
Sbjct: 355 EVSAGDILVGRTSPKGEDNPTPEEKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILS 414

Query: 947 RHGID-KNERSISVEREQIELLAR 969
           R   D   +    + +  I    +
Sbjct: 415 RTREDNLEDGVEKIIKVFIAQKRK 438



 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 128/413 (30%), Positives = 185/413 (44%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD++    +   +  +   + +L A       +  D  +     V   V 
Sbjct: 249  IVEVGQFVKQGDLICDGPST-DQGELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 307

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    +   S +   +    +       +  LD N   R+   +   + + G  
Sbjct: 308  -TSIHIQEQTIQFRSSKAGNDDLTREIPNASQRSKRHLDENGIVRIGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W + A   +     V+           IL    +      
Sbjct: 367  SPKGEDNPTPE--EKLMNAIWGKKASSQKDTSLKVKHGDGGTVIDVQILSRTRE------ 418

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
               D++  GV +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMPFL+DGTP+DI
Sbjct: 419  ---DNLEDGVEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPFLEDGTPIDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP G+PSRMN+GQI E HLG     L  K    + D      +  L +          
Sbjct: 476  LLNPQGIPSRMNIGQILEMHLGMVAKKLDIKFVCPVFDGVKLDKMKELFN---------- 525

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 526  --------------------QAGIP------------------------ESGKFTLYDGI 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TG+PFD  V++GY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR
Sbjct: 542  TGQPFDNDVSIGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQR 594


>gi|242392250|dbj|BAH80362.1| RNA polymerase subunit B' [Halopiger xanaduensis SH-6]
          Length = 609

 Score =  329 bits (843), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 125/593 (21%), Positives = 205/593 (34%), Gaps = 105/593 (17%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                +  D     ++LVA            + I   ++       I   E     R T  
Sbjct: 98   HGYIEFIDAEEEEDILVAVDEDDLTEKHTHLEIDPSLMFSIGAGMIPYPEHNASPRITMG 157

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                + +    +     +   +     +        +        G       +  + A+
Sbjct: 158  AG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFVVAV 214

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D      
Sbjct: 215  MSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD------ 267

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             +           L     V+      +++VL           +         + +R   
Sbjct: 268  -VRGARGEDAYAHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRRETS 326

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                  E+         + +               ++ KV V  +R  + GDK A RHG 
Sbjct: 327  VTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASRHGQ 374

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V  + P EDMPF + G   D+VLNP  +PSRM VG I E   G      G+++    
Sbjct: 375  KGVVGHLAPQEDMPFTESGLVPDLVLNPHALPSRMTVGHILEMIGGKLGSLEGRRVDG-- 432

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                               TP F G DE
Sbjct: 433  ---------------------------------------------------TP-FLGEDE 440

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            + +   L  A  + SG+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   
Sbjct: 441  DKLREGLEEAGFESSGKETMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRGPVQ 500

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---------------- 1320
            ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD                
Sbjct: 501  VLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYIPICANCGMSAVE 560

Query: 1321 DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 561  NVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 42.4 bits (98), Expect = 0.63,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + ++ A EEE+  +A     L                        EK   ++  P  + S
Sbjct: 101 IEFIDAEEEEDILVAVDEDDLT-----------------------EKHTHLEIDPSLMFS 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 174


>gi|52694209|emb|CAG30634.1| DNA-directed RNA polymerase beta chain [Pseudomonas amygdali]
          Length = 344

 Score =  329 bits (843), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 201/343 (58%), Positives = 263/343 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ + E
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLFE 344


>gi|156084478|ref|XP_001609722.1| DNA-directed RNA polymerase, beta subunit [Babesia bovis T2Bo]
 gi|154796974|gb|EDO06154.1| DNA-directed RNA polymerase, beta subunit, putative [Babesia bovis]
          Length = 1283

 Score =  329 bits (843), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 191/1280 (14%), Positives = 394/1280 (30%), Gaps = 217/1280 (16%)

Query: 88   VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
                     TY   L +   L +              +  + + +G +P+M K       
Sbjct: 99   PRHAKIAHTTYESSLIVKFGLKI---------PGTSKVLTKELTVGYIPIMVKSKRCNLD 149

Query: 142  ------------------GTFVIKGIQRIVVSQLH--RSPGIHFDHDKGRASLSGKLLYA 181
                              G FV++G +R +V QL   RS   +    K   + +  +L+ 
Sbjct: 150  GISPEEMVEQGEDIDEPGGYFVVRGNER-IVRQLIVLRS--NYPLAIKSGNNRTKHVLFT 206

Query: 182  CRIIPDQGLWMDIEFDSKDIIHVRIDRR-----------RKVPVTSFLMA-LGMDSEEIL 229
               I  +    D      +++++ +++R           + +P    L A + + S+E L
Sbjct: 207  DYSIMMRSQCHDDGCSVNNVLYLTVNKRCMFRTIVKGSVQLIPFGVLLRATMPLMSDEEL 266

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
                 K++    GD           +   +    + DID  E          +  L  L 
Sbjct: 267  K---QKLLQDTLGDEALTVYYQRFFLDLVEREPDICDIDLKE----------NRHLYRLG 313

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                             Y+       E G  ++    ++  K+  E F + +     L  
Sbjct: 314  SACWSQ--------VNQYLHPGATYEECGAYFLRHYVLLQAKTNAEKFETLLYMFKKL-- 363

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
                    I+ +    + ++          ++ PG + +  + ES++             
Sbjct: 364  --------IKVSRGEIQTENYDSFAFQ--ELLLPGQIYSCILKESLY------------- 400

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             V  +K+    + +  +  ++I  +      + L+D+        D+ +   + +     
Sbjct: 401  -VALLKIRSIYHAELLELCKNISGDATRHSKRRLIDV--------DLQSHEQKELLEKLL 451

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                 +   + ++   I +++             +      +   E   SS L+ + E +
Sbjct: 452  EKPELFSYAVEKVASDIPKKL----------HSFLATGNATNMHFELTQSSGLTVVAERI 501

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N    ++H R   +L +G +       E+R +    +G ICP  T +G   GL+  L  +
Sbjct: 502  NYHRFMSHFR---SLHRGSLFAKMRSTEVRKLLGETWGFICPVHTPDGAPCGLLLHLAQY 558

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDV-VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A        E     V     T+   V  +  E    ++      +       + +  C 
Sbjct: 559  AVPVTATDCEGAAEAVKSLLRTHGYSVDFTGHETVTDFVTHDAQHIKRIHVIVDGVPMCT 618

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                E     ++I       K  +     ++   +       +M   +      +++   
Sbjct: 619  LPINEAPKLYDEIKLAKRYGKFGLKEHYEIVASPDVKGEYTSIM---ILTYPGRVIRPVI 675

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                  +E +   +   + +A           +       +         +         
Sbjct: 676  CLTSGEIEWIGPITQLWSTIAVSEEEARISHQMVASNAEGKCKTLSIDEALMHDNSSDHA 735

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
             S     ++  P+     EV  + I++               +  A  P+  +N     +
Sbjct: 736  VSPVKKVIDNVPVKYDYMEVSPSAILS---------------VTAALTPFSNHNQSPRNM 780

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
               +M+ + +    H E+F    +                     + +            
Sbjct: 781  YQCQMLKQSMGVPYHCEQFRSDVK-------------------AYRLL----------FP 811

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIF 945
                +   +               + A+      D+ D  +   S +          +  
Sbjct: 812  QKPLVTTTEFRQMNYEDYPTGMNAVVAVIAHTGFDMEDAMIINKSSLDRGAFHGCIYKSK 871

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
                +  N RS               +        ++ S+++  L      +     KK 
Sbjct: 872  VIDAMPANGRSRG-------------NQHYFANTNHLGSKIIASLDKDGLPNVGARVKKG 918

Query: 1006 TVLS-----SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            T +        +      S   +    ++ +   V  +    + S + + +    K  + 
Sbjct: 919  TPICRIESHEKVGGSKQISDRVEKYHDEDAIVDQVTIIGCN-DASVAEMPNASNIKGTRA 977

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                           +   + R    GDK A RHG KGI+S   P E+MPFL+ G   DI
Sbjct: 978  T--------------IKFRIVRNPIVGDKFASRHGQKGILSMAWPAENMPFLESGIIPDI 1023

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            + NP G+PSRM +G++ E   G +    G    +           +  +      +    
Sbjct: 1024 IFNPHGLPSRMTIGKLIECMAGKSAAIHGAFQDATCFRKYPKQMATGNKWIDHGGLKGWE 1083

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                     ++ + +  +                  +     L  A  D  G   +Y G 
Sbjct: 1084 ERGFRYMSKEEELSKTEDDV---------------IDYFGKTLLQAGYDYYGTESMYCGS 1128

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
             G      + +G I+  +L HMVSDK   R+TG    +T+QP+ G+ NRGG R GEME  
Sbjct: 1129 LGTEIRTHIFIGCIFYQRLRHMVSDKAQVRATGPVDAITKQPVKGRKNRGGIRFGEMERD 1188

Query: 1301 CIQAYGAAYVLQEMLTIKSD 1320
             + A+GA+ +LQ+ L   SD
Sbjct: 1189 SLIAHGASALLQDRLIHCSD 1208


>gi|168006293|ref|XP_001755844.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162693163|gb|EDQ79517.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1135

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 117/673 (17%), Positives = 212/673 (31%), Gaps = 91/673 (13%)

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+     + +      +RAG + +  ++ +  +        S  G     L+   +    
Sbjct: 534  GVHRRPNRFAEVLRKLRRAGKIGEFVSVHVNPKHQRNIQIASDGGRVCRPLVIADKGVSR 593

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               +    +K G      D        +  D+    N L+A            + I    
Sbjct: 594  VKEHHMKELKDGFRTF--DDFLREGLVEYLDVNEENNSLIALYEGDATPDTTHIEIEPFT 651

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI-DECGIICVGAEVNPGD 892
            +       I         R+T     +       +       +     ++ +        
Sbjct: 652  ILGVCAGLIPYPHHNQSPRNT----YQCAMGKQAMGNIAYNQLQRMDTLLYLLVYPQRPL 707

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    I   G   +   +    A+      D+ D  +   S +        +  +  +  
Sbjct: 708  LSTKSIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVIKKSVVPM 767

Query: 953  NERS-ISVEREQIELLARDKDDEQVIL-DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
             + +  + +R     L         ++  + +         G+    G     K + + +
Sbjct: 768  KKYANRTADRIMAPELQSSAKGGVQVVARQQLQDHDGIAAVGEMIRPGDIYVNKQSPIDT 827

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
                                V   +      Y+ +    +          +         
Sbjct: 828  -----------------RNNVNNPMALPDSAYKRTPQTYKGAAGETAVVDKVLLTSNDEN 870

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              VVK  +   R  + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSR
Sbjct: 871  HFVVKCLIRQTRRPEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 930

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M VG++ E   G A +  GK          +                             
Sbjct: 931  MTVGKMIELLGGKAGLHNGKFHYGSAFGEPSGHAD------------------------- 965

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                        I++ L       SG+  +Y G+TG P    + 
Sbjct: 966  ------------------------KVSTISATLVKHGFSYSGKDFIYSGITGSPLQAYIF 1001

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G IY  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C+ AYGA+ +
Sbjct: 1002 MGPIYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRSREGGLRLGEMERDCLIAYGASMM 1061

Query: 1311 LQEMLTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNVLVKEM 1354
            + E L I SD          G    Y   +          G++      P +  +L +E+
Sbjct: 1062 ILERLMISSDQFQIQVCTKCGMIGYYHHKLKICLCSTCKSGDNIATMKLPYACKLLFQEL 1121

Query: 1355 QALGLSIDLENSR 1367
            Q++ +   L  + 
Sbjct: 1122 QSMNIVPRLTLAE 1134



 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 141/994 (14%), Positives = 286/994 (28%), Gaps = 210/994 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S+++F+   I       +G +     V           L+++      P    
Sbjct: 38  LVKQHIDSFNYFINCEIKKIIHA-QGNEKVTSDV------DANFYLKYLDIFVGEPCVEQ 90

Query: 86  ------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                      C  RD+TY+ P+ + +           G + +  I      +G +P+M 
Sbjct: 91  DYIYEPITPQQCRLRDMTYSAPISVDVEYTR-------GKEVVGSIN-----IGRMPIML 138

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                     G FV+KG +++++ Q   S     +        S
Sbjct: 139 RSSRCILAGKNEAQLAKVGECPLDPGGYFVVKGTEKVILIQEQLSK----NRIIITTDSS 194

Query: 176 GKLLYACRIIPDQGLWMDIEFDSKDIIHV---RIDRRRK-----VPVTSFLMALGMDSE- 226
           G +  A  +          E  SK  + V   RI  R       +P+   + A+GM+S+ 
Sbjct: 195 GSV--AASVTSS-----THERKSKTNMVVKHERIYLRHNTFGDDIPIVVVMRAMGMESDQ 247

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI+        Y+   +      +A  +    +    L      +  ++  + + + ++ 
Sbjct: 248 EIVQMVGRDPKYAGILNPSLQECAALKIYTSHQALEYL----GSKVRVDEARDILATVV- 302

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE--IYIEAGDVIDEKSLEEIFHSEIRDI 344
                 +  + +         +   ++  +  E  +  EA D +D    + +  +     
Sbjct: 303 ------LAHVPVHQFDFRAKCIYLAVIIRKMLEAMLNREAVDDMDYVGNKRLELAGQLLS 356

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +        NA ++ ++    +K  +    DI +++RP  ++               + 
Sbjct: 357 LLFEDLFKRMNAELKKSMDATLSKANRSTQFDIIKLIRPDTLT----------NGLEHAI 406

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
                 V R KM+ +        V  +     +  +  +         +     L   + 
Sbjct: 407 SSGNWAVKRFKMDRKGVTQV---VSRLSFIAALGHMTRISSQFEKTRKVSGPRALQPSQW 463

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             +      +     L    S+   +++ + ++ + +          ++           
Sbjct: 464 GMLCPCDTPEGEACGLVKNLSLMTHVTTDEEEAPLIELCTTLGVEDLSLLSGEELHSPKT 523

Query: 525 LEEHVNSLSRITHTRRLS-ALGQGGVARARAGVEMRDVHPT-HYGRICPAETSEGHNIGL 582
                N      H R    A     + RA    E   VH    + R     +  G     
Sbjct: 524 YLVFFNGTILGVHRRPNRFAEVLRKLRRAGKIGEFVSVHVNPKHQRNIQIASDGGRVCRP 583

Query: 583 VSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           +          + +    ++  +R   D      V YL   EE N  IA        D  
Sbjct: 584 LVIADKGVSRVKEHHMKELKDGFRTFDDFLREGLVEYLDVNEENNSLIALYEGDATPD-- 641

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                   I+  P  ++ + A LIP+  ++ S R    C M +Q
Sbjct: 642 ---------------------TTHIEIEPFTILGVCAGLIPYPHHNQSPRNTYQCAMGKQ 680

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           A+                                           I   +     +   +
Sbjct: 681 AMGN-----------------------------------------IAYNQLQRMDTLLYL 699

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            +Y               QRPL+                      L  G+N  VA M + 
Sbjct: 700 LVYP--------------QRPLLS----------TKSIELVGYDKLGAGQNATVAVMSYS 735

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG------- 872
           GY+ ED++++++  +       I I++  V  +       +        S          
Sbjct: 736 GYDIEDAIVMNKSSLDRGFGRCIVIKKSVVPMKKYANRTADRIMAPELQSSAKGGVQVVA 795

Query: 873 -LKNIDECGIICVGAEVNPGDILVGKITPKGES---------PMTPEEKLLRAIFGEKAV 922
             +  D  GI  VG  + PGDI V K +P             P +  ++  +   G    
Sbjct: 796 RQQLQDHDGIAAVGEMIRPGDIYVNKQSPIDTRNNVNNPMALPDSAYKRTPQTYKGAAGE 855

Query: 923 D-VRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNE 954
             V D  L   +  +  VV   I   R     ++
Sbjct: 856 TAVVDKVLLTSNDENHFVVKCLIRQTRRPEVGDK 889


>gi|52694157|emb|CAG30608.1| DNA-directed RNA polymerase beta chain [Pseudomonas brassicacearum]
          Length = 344

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 199/337 (59%), Positives = 259/337 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 8   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 67

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 68  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 127

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 128 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 187

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 188 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 247

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 248 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 307

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +R+DI+ DGPSTD+G+LALG+NM +AFM W+G+NFED
Sbjct: 308 QRSDIMPDGPSTDMGELALGQNMRIAFMAWNGFNFED 344


>gi|315259460|gb|ADT91929.1| DNA-directed RNA polymerase beta subunit [Enterococcus thailandicus]
 gi|315259466|gb|ADT91932.1| DNA-directed RNA polymerase beta subunit [Enterococcus thailandicus]
          Length = 392

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 135/425 (31%), Positives = 184/425 (43%), Gaps = 87/425 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I  +G  V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 45   IALLGERVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 95

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 96   --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 147

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 148  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 206

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 207  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 261

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+     
Sbjct: 262  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGATDEDVW---- 317

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                       A           A +  
Sbjct: 318  -------------------------------------------ATVRE-------AGMAS 327

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
              +++LYDG TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 328  DAKTVLYDGRTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 387

Query: 1291 GQRLG 1295
            GQR G
Sbjct: 388  GQRFG 392



 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 127/222 (57%), Positives = 163/222 (73%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+  +G+ V 
Sbjct: 1   KHDGVVEYVDASEIRVRRDNGALDK-------YVVTKFRRSNSGTSYNQRPIALLGERVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|73697685|gb|AAZ81459.1| RNA polymerase beta subunit [Mycoplasma bovis]
 gi|73697687|gb|AAZ81460.1| RNA polymerase beta subunit [Mycoplasma bovis]
          Length = 591

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 210/423 (49%), Positives = 300/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N+L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++
Sbjct: 1   NALAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +  V  ++VVYL+A +E    IAQ+ +++D++    +E +  R
Sbjct: 61  ASVNEYGFLQTPYFKVENSVVDYDNVVYLTAADEFGYNIAQSTATVDDNNRLIDETLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 KNYTYILGKPSDVDLIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            FV TG E+ +AK S A   A++ G VE VD  +I IR+ +G LD        Y L  FQ
Sbjct: 181 AFVATGNEADIAKFSAANFRARQEGKVEYVDGAKIKIRNNKGTLD-------TYNLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+P++KVG EV + D++ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 234 RSNQDTVIHQKPIIKVGQEVAKGDLLVDGSSFKDGELALGKNLLVAFSTYKGYNYEDAIV 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+  +DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV
Sbjct: 294 LNERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R 
Sbjct: 354 IPGDVLVGRVSPKGDDNPSREEKLLAAILGQRQLNVKDTSLKVKNGHNGTVIGVEILSRE 413

Query: 949 GID 951
             D
Sbjct: 414 NKD 416



 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 124/502 (24%), Positives = 186/502 (37%), Gaps = 80/502 (15%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L           +  +       + R   E     +   + ++       
Sbjct: 165  GSNMQRQAVPLLETEAAFVATGNEADIAKFSAANFRARQEGKVEYVDGAKIKI---RNNK 221

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +               I +  II VG EV  GD+LV   + K +  +   + LL A 
Sbjct: 222  GTLDTYNLKNFQRSNQDTVIHQKPIIKVGQEVAKGDLLVDGSSFK-DGELALGKNLLVAF 280

Query: 917  FGEKAVDVRDTS-LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ----IELLARDK 971
               K  +  D   L         +  + I  +    +  ++ + E  +    +   A   
Sbjct: 281  STYKGYNYEDAIVLNERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRH 340

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE  I+         ++L G+ +  G     +   L + ++                  
Sbjct: 341  LDEHGIVLVGSEVIPGDVLVGRVSPKGDDNPSREEKLLAAILG----------------- 383

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR +       +            +I   +  D +  G+  +VKV +A+KR I+ GDKM+
Sbjct: 384  QRQLNVKDTSLKVKNGHNGTVIGVEILSRENKDLLEDGIDMIVKVSIAVKRKIRVGDKMS 443

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GRHGNKG+VS ILP EDM              P             E          G  
Sbjct: 444  GRHGNKGVVSVILPEEDM--------------PH-----------LE---------DGTP 469

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I  ++                           +++      V         G    TPVF
Sbjct: 470  IDVML--------------------NPQGVPSRMNIGQVLEVHLGMAARSLGCKFVTPVF 509

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG  +EAI  ++  A L  SG+  L D +TGE FD PV+VG +YM KLNHMV DK++ARS
Sbjct: 510  DGVKKEAIQDVISEAGLPLSGKQTLIDPITGEKFDNPVSVGVMYMFKLNHMVDDKMHARS 569

Query: 1272 TGSYSLVTQQPLGGKSNRGGQR 1293
             G YSL+TQQPLGGKS  GGQR
Sbjct: 570  VGPYSLITQQPLGGKSQNGGQR 591


>gi|4867878|emb|CAB43080.1| RNA polymerase II [Pinckneya pubescens]
          Length = 263

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 43   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 102

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 103  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 130

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 131  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 168

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 169  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 228

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 229  GAAHFLKERLFDQSD 243


>gi|40644720|emb|CAD92662.1| RNA polymerase II [Solanum lycopersicum]
          Length = 396

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 96/442 (21%), Positives = 154/442 (34%), Gaps = 77/442 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 6    DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 66   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGE 124

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T +S                  D+   +     +  + TS    E    +++ 
Sbjct: 125  DVIIGKTTPISQ-----------------DDAQGQASRYTRKDHSTSLRHSETGMVDQVL 167

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 168  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 222

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 223  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------- 257

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+  L        G   +Y+
Sbjct: 258  ----------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYN 288

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME
Sbjct: 289  GHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEME 348

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD 1320
              C+ A+GAA+ L+E L  +SD
Sbjct: 349  RDCMIAHGAAHFLKERLFDQSD 370



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 58/182 (31%), Gaps = 24/182 (13%)

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
              +           Q+PLV                      L  G N +VA   + GYN
Sbjct: 1   YQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSGYN 50

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E            +       +D
Sbjct: 51  QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYDKLD 110

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           A         +D S  +    +G
Sbjct: 111 DDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRKDHSTSLRHSETG 161

Query: 938 TV 939
            V
Sbjct: 162 MV 163


>gi|212373947|emb|CAP09900.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35699]
          Length = 327

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 194/326 (59%), Positives = 251/326 (76%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++
Sbjct: 62  ETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASA 121

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           ++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 122 TMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 181

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 182 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEV 241

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM 
Sbjct: 242 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMR 301

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDV 838
           +AFM W+GYNFEDS+ +SER+V ED 
Sbjct: 302 IAFMAWNGYNFEDSICLSERVVQEDR 327


>gi|67550155|gb|AAY68424.1| RNA polymerase subunit B [Lysinibacillus sphaericus]
          Length = 546

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 220/376 (58%), Positives = 286/376 (76%), Gaps = 8/376 (2%)

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            NIGL++SL +FA+VN YGFIETPYR++   + + TND+VY++A EE+   IA+++  +D
Sbjct: 1   PNIGLINSLATFAKVNEYGFIETPYRRIDPKNKRATNDIVYMTADEEDLYVIARSDEPID 60

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E G F ++ V  R   E ++VP  +++++D SP+Q+VS+A ++IPFLENDD++R LMG N
Sbjct: 61  EKGYFLDDKVTVRAKEEVLVVPVSEVEYMDISPRQLVSVATAMIPFLENDDASRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLLK +AP VGTG+E   A  SG    AK AG V  V A  I +R        S
Sbjct: 121 MQRQAVPLLKPQAPIVGTGIEYKAATDSGVLPKAKNAGTVVYVSADEIRVRRD------S 174

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             G+D Y+L+KF+RSNQ TC+NQRP+V   + V +  ++ADGPSTDLG++ALG+N+L+ F
Sbjct: 175 DGGIDKYKLLKFKRSNQGTCINQRPIVSKDEVVAKETLLADGPSTDLGEIALGKNILMGF 234

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + W GYN+ED+MLISE++V EDVFTSIHIEE+E  ARDTKLGPEEITRDIPNV EE LK+
Sbjct: 235 ITWEGYNYEDAMLISEQLVKEDVFTSIHIEEYEAEARDTKLGPEEITRDIPNVGEEALKD 294

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           IDE GII +GAEV  GDILVGK+TPKGE+ +T EE+LLRAIFGEKA +VRDTSLRVP G 
Sbjct: 295 IDERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGE 354

Query: 936 SGTVVDVRIFNRHGID 951
           +G +VDV+IF R   D
Sbjct: 355 AGIIVDVKIFTRENGD 370



 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 126/330 (38%), Gaps = 72/330 (21%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE+ I+      R  +IL G+    G         L   +  E  R      
Sbjct: 289  EEALKDI-DERGIIRIGAEVRSGDILVGKVTPKGETELTAEERLLRAIFGEKAR------ 341

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   KI   + GD++PPGV ++V+ ++A     
Sbjct: 342  -----------EVRDTSLRVPHGEAGIIVDVKIFTRENGDELPPGVNKLVRCYIA----- 385

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
                        K  +S                               VG          
Sbjct: 386  -----------QKRKIS-------------------------------VG-------DKM 396

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G K        + +    P    L+  +       +++      V       K G 
Sbjct: 397  AGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGLAASKLGW 456

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             ++TPVFDGA E  I   LR A   E G+++LYDG TGEPFD  VTVGY+Y+LKL H+V 
Sbjct: 457  HIATPVFDGAIESDIVDCLRKAGYSEDGKTVLYDGRTGEPFDNRVTVGYMYILKLAHLVD 516

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 517  DKIHARSTGPYSLVTQQPLGGKAQFGGQRF 546


>gi|111054591|gb|ABH04353.1| RNA polymerase beta subunit [Morganella morganii]
          Length = 334

 Score =  328 bits (842), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 205/334 (61%), Positives = 257/334 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDNLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVR 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ CR  GE  L  R+++ ++D 
Sbjct: 121 DDVVTDEIHYLSAIEEGNFIIAQANTVLDDDGHFVDELITCRNKGESSLFSRDQVQYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            V R D++ADGPSTDLG+LALG+NM VAFMPW+G
Sbjct: 301 PVERGDVLADGPSTDLGELALGQNMRVAFMPWNG 334


>gi|242392328|dbj|BAH80345.1| RNA polymerase subunit B' [Halococcus hamelinensis]
          Length = 613

 Score =  328 bits (842), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 121/594 (20%), Positives = 204/594 (34%), Gaps = 97/594 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D + +G   +  D     ++LV             + I  +++       I   E     
Sbjct: 97   DDLVEGGYIEFIDAEEEEDILVGVDEDDLTPDHTHLEIDPQLMFGIGAGMIPYPEHNASP 156

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R T      + +    +     +   +     +        +        G       + 
Sbjct: 157  RITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQN 213

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + A+   +  ++ D  L +  G     +    F R    +  R    + ++ E+   D 
Sbjct: 214  FVVAVMSYEGFNIEDA-LVLNGGSIDRALGRSHFFRTYEGEERRYPGGQEDRFEIPDDD- 271

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                  +           L     V+      +S VL           +         + 
Sbjct: 272  ------VRGARGEEAYTHLDEDGLVNPETEVSESAVLLGKTSPPRFLEEPNDMGGLSPQK 325

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +R         E          + +               ++ KV V  +R  + GDK A
Sbjct: 326  RRETSVTMRSGEAGVVDTVTLMQGE------------DGSKLSKVSVRDERIPELGDKFA 373

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG++  I P EDMPF ++G   D+++NP  +PSRM VG + E   G      G++
Sbjct: 374  SRHGQKGVIGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHVLEMLGGKVGSLEGRR 433

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +       +   ++                                              
Sbjct: 434  VDGTAFTGEEEEELR--------------------------------------------- 448

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             GA E+           D SG+  +Y G+TGE  D  + VG I+  KL HMVS+K++ARS
Sbjct: 449  -GALED--------HGFDSSGKERMYSGVTGEKIDAEIFVGTIFYQKLYHMVSNKIHARS 499

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------- 1320
             G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD           
Sbjct: 500  RGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDREFIYVCGNCG 559

Query: 1321 -----DVVGRTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                 +V  R RVY     G   D  E     +F +L+ EM+ALG++  L+   
Sbjct: 560  MSAVENVEQR-RVY-CPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLDLID 611



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 66/430 (15%), Positives = 124/430 (28%), Gaps = 109/430 (25%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   +        + G     ++        P    
Sbjct: 15  YVNGSLVGTHADPEGLAHQVREARRRGDVASTVNVSVKDGTNEVIINADAGRARRPLIVV 74

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L+S     + V+             D      + ++ A EEE+  +      L 
Sbjct: 75  ENGE-PLISEAEVESVVDGESD-------FDDLVEGGYIEFIDAEEEEDILVGVDEDDLT 126

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 127 PDH-----------------------THLEIDPQLMFGIGAGMIPYPEHNASPRITMG-- 161

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
                                      SG    +                          
Sbjct: 162 ---------------------------SGMIKQSLGLPSANY------------------ 176

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    ++           Q  +VK                    D    +N +VA 
Sbjct: 177 --------RIRPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAV 218

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VS 869
           M + G+N ED+++++   +   +  S     +E   R    G E+   +IP+        
Sbjct: 219 MSYEGFNIEDALVLNGGSIDRALGRSHFFRTYEGEERRYPGGQEDRF-EIPDDDVRGARG 277

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE   ++DE G++    EV+   +L+GK +P               + G      R+TS+
Sbjct: 278 EEAYTHLDEDGLVNPETEVSESAVLLGKTSPPRFLEEP------NDMGGLSPQKRRETSV 331

Query: 930 RVPSGVSGTV 939
            + SG +G V
Sbjct: 332 TMRSGEAGVV 341


>gi|89888211|gb|ABD78648.1| DNA-directed RNA polymerase beta subunit [Bordetella hinzii]
          Length = 183

 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 94/185 (50%), Positives = 126/185 (68%), Gaps = 2/185 (1%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           K F K  ++ ++P L+  Q  SY  FL    A  ER NEGLQAAF S+FPI + +G A L
Sbjct: 1   KSFAKREDVQNVPFLLATQLQSYLTFLQAETATAERVNEGLQAAFSSIFPIVSHNGMARL 60

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFVSY    P FDV +C  R LTYA PL+  +RL++ D        +IK++KEQ +YMG+
Sbjct: 61  EFVSYALGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTIKEVKEQEVYMGE 118

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ R+IP +G W+D 
Sbjct: 119 IPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARVIPYRGSWLDF 178

Query: 195 EFDSK 199
           EFD K
Sbjct: 179 EFDPK 183


>gi|8489819|gb|AAF75766.1|AF265351_1 DNA-directed RNA polymerase II polypeptide B [Sus scrofa]
          Length = 381

 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 97/440 (22%), Positives = 154/440 (35%), Gaps = 79/440 (17%)

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            I NR  +D+        R   E  ++   D++ + ++           G       K   
Sbjct: 2    IMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRE----TCQGMRHAIYDKLDD 57

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               +     +S           V   + +  +E    +Y         R        Q  
Sbjct: 58   DGLIAPGVRVSG--DDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVM 115

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
              +     +  K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++N
Sbjct: 116  VTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 175

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +G + E   G      G+                                 
Sbjct: 176  PHAIPSRMTIGHLIECLQGKVSANKGEIGD------------------------------ 205

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP  D  + + I+++L        G  +LY+G TG 
Sbjct: 206  -----------------------ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGR 242

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
                 + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S  GG R GEME  C  
Sbjct: 243  KITSQIFIGPTYYQRLKHMVDDKIHSRTRGPIQILNRQPMEGRSRDGGLRFGEMERDCQI 302

Query: 1304 AYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPE 1345
            A+GAA  L+E L   SD     V            RT  YE    G            P 
Sbjct: 303  AHGAAQFLRERLFEASDPYQAHVCNLCGIMAIANTRTHTYEC--RGCRNKTQISLVRMPY 360

Query: 1346 SFNVLVKEMQALGLSIDLEN 1365
            +  +L +E+ ++ ++  + +
Sbjct: 361  ACKLLFQELMSMSIAPRMMS 380



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/131 (16%), Positives = 44/131 (33%), Gaps = 12/131 (9%)

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGI 881
           ++++   V    F S+    ++          EE+           +       +D+ G+
Sbjct: 1   VIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGL 60

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           I  G  V+  D+++GK     E+    E          +    RD S  + +  +G V  
Sbjct: 61  IAPGVRVSGDDVIIGKTVTLPENEDELEGT-------NRRYTKRDCSTFLRTSETGIVDQ 113

Query: 942 VRIFNRHGIDK 952
           V +       K
Sbjct: 114 VMVTLNQEGYK 124


>gi|89888197|gb|ABD78642.1| DNA-directed RNA polymerase beta subunit [Bordetella petrii]
          Length = 182

 Score =  328 bits (841), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 92/184 (50%), Positives = 126/184 (68%), Gaps = 2/184 (1%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            F K  ++ D+P L+  Q  SY  FL  +  P +R +EGLQAAF S+FPI + +G A LE
Sbjct: 1   SFAKREDVQDVPFLLATQLQSYLTFLQADTPPSDRASEGLQAAFSSIFPIVSHNGMARLE 60

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           FVSY    P FDV +C  R LTYA PL+  +RL++ D        +IK++KEQ +YMG++
Sbjct: 61  FVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTIKEVKEQEVYMGEI 118

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ R+IP +G W+D E
Sbjct: 119 PLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARVIPYRGSWLDFE 178

Query: 196 FDSK 199
           FD K
Sbjct: 179 FDPK 182


>gi|242392362|dbj|BAH80394.1| RNA polymerase subunit B' [Natrialba hulunbeirensis]
          Length = 609

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 125/595 (21%), Positives = 210/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDIYVAVEEDDLTADHTHLEIDPQLIFSIGSGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTITLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE A+   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESALREGLEEAGFDSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    +V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCEEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 42.8 bits (99), Expect = 0.47,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  +  G +E       D      V ++ A EEE+ Y+A     L 
Sbjct: 71  EDGE-PRISEQEIEALRD--GDLE-----FEDLVDHGYVEFIDAEEEEDIYVAVEEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ + SI + +IP+ E++ S R+ MG  
Sbjct: 123 ADH-----------------------THLEIDPQLIFSIGSGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|76800711|ref|YP_325719.1| DNA-directed RNA polymerase subunit B' [Natronomonas pharaonis DSM
            2160]
 gi|76556576|emb|CAI48147.1| DNA-directed RNA polymerase subunit B' [Natronomonas pharaonis DSM
            2160]
          Length = 610

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 138/320 (43%), Gaps = 78/320 (24%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D++LNP  +
Sbjct: 347  EDGSKLSKVKVRDERVPELGDKFASRHGQKGVVGHLAPQEDMPFTQDGVVPDLILNPHAL 406

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 407  PSRMTVGHILEMLGGKVGSLEGRRVDG--------------------------------- 433

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L       +G+ ++Y G+TGE  + 
Sbjct: 434  --------------------TP-FQGEDEDELRESLIDRGFKSNGKEVMYSGITGEKIEA 472

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 473  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 532

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAG--------------------NDTFETGTPESF 1347
            A  L+E L  +SD    R  +Y     G                     D  E     +F
Sbjct: 533  AMTLKERLLDESD----REDIYVCGQCGMSAVENVEQRRVYCPNCDEETDVHEVEMSYAF 588

Query: 1348 NVLVKEMQALGLSIDLENSR 1367
             +L+ EM+ALG++  +E   
Sbjct: 589  KLLLDEMKALGIAPRIELED 608



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 58/358 (16%), Positives = 117/358 (32%), Gaps = 28/358 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +      ++   R  GE   +    +               +  P +  +D   +L
Sbjct: 19  GTHPDPHKLANDIREARRRGEVDEMVNVSVRDRTDEVIVNADAGRARRPLIVVEDGEPLL 78

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               ++      L+ E       +E + A+      VA     + + D   + +      
Sbjct: 79  GDAEIEALEDGELEFEDLVDRGYVEFIDAEEEEDIYVAVDEDDLSE-DHTHLEVDPQLMF 137

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPST 800
              +            + +  +  + Q           RP  +          I    +T
Sbjct: 138 GIGAGMIPYPEHNASPRITMGSGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSIVKTQTT 197

Query: 801 D---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +     D    +N +VA M + G+N ED++++++  +   +  S     +E   R    G
Sbjct: 198 EQIGYDDRPAAQNFVVAVMSYEGFNIEDALVMNKASIERALARSHFFRTYEGEERRYPGG 257

Query: 858 PEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            E+   +IP+        EE   ++DE G++     V   D+L+GK +P           
Sbjct: 258 QED-HFEIPDDEVRGARGEEAYSHLDEDGLVNPETHVGENDVLLGKTSPPRFLEEP---- 312

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
               + G      R+TS+ + SG SG V  V +       K  +    +    EL  +
Sbjct: 313 --DDMGGLSPQKRRETSVTMRSGESGIVDTVTLMEGEDGSKLSKVKVRDERVPELGDK 368



 Score = 45.1 bits (105), Expect = 0.096,   Method: Composition-based stats.
 Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+ Y+A     L ED                    
Sbjct: 86  LEDGELEFEDLVDRGYVEFIDAEEEEDIYVAVDEDDLSEDH------------------- 126

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 127 ----THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSGMIKQSLGLPSANYRI 175


>gi|4867899|emb|CAB43088.1| RNA polymerase II [Usteria guineensis]
          Length = 268

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 41   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 100

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 101  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 128

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 129  ---------------------ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPL 166

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 167  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 226

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 227  GAAHFLKERLFDQSD 241


>gi|111054627|gb|ABH04371.1| RNA polymerase beta subunit [Providencia rustigianii]
          Length = 329

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 203/327 (62%), Positives = 254/327 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L +DG F EEL+ CR  GE  L  RE+++++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVEYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 243 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHG 820
           +ADGPSTDLG+LALG+NM VAFMPW+G
Sbjct: 303 LADGPSTDLGELALGQNMRVAFMPWNG 329


>gi|3746592|gb|AAC64011.1| RNA polymerase II subunit 2 [Mostuea brunonis]
          Length = 261

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 36   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTGEGITPDIIVNPH 95

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 96   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 123

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 124  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 161

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 162  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 221

Query: 1306 GAAYVLQEMLTIKSD 1320
            GA++ L+E L  +SD
Sbjct: 222  GASHFLKERLFDQSD 236


>gi|318602948|emb|CBJ04566.1| RNA polymerase beta subunit [Pseudomonas sp. R-37095]
 gi|318602971|emb|CBJ04569.1| RNA polymerase beta subunit [Pseudomonas sp. R-37116]
          Length = 330

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 197/330 (59%), Positives = 256/330 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 1   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 60

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 61  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 120

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 121 HVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 180

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 181 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 240

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 241 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 300

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           LALG+NM +AFM W+G+NFEDS+ +SER+V
Sbjct: 301 LALGQNMRIAFMAWNGFNFEDSICLSERVV 330


>gi|4867880|emb|CAB43083.1| RNA polymerase II [Rondeletia odorata]
          Length = 261

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 41   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 100

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 101  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 128

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 129  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 166

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 167  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 226

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 227  GAAHFLKERLFDQSD 241


>gi|296809049|ref|XP_002844863.1| DNA-directed RNA polymerase III subunit RPC2 [Arthroderma otae CBS
            113480]
 gi|238844346|gb|EEQ34008.1| DNA-directed RNA polymerase III subunit RPC2 [Arthroderma otae CBS
            113480]
          Length = 1211

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 106/518 (20%), Positives = 177/518 (34%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +  + A+      D+ D  +  
Sbjct: 773  NNQFLRIDSLLYAMVYPQKPMVKTRTIELTNYDKLPAGQNAMVAVMSYSGYDIEDALVLN 832

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V       ++F ++  +    S   +   +              +  +  R   +L 
Sbjct: 833  KGSVDRGFGRCQVFRKYSANLKSYSNGTKDRLVGPTR----------ENGVSIRKHGLLD 882

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
                 +  +      V  +    +   S        D  +          Y     + + 
Sbjct: 883  NDGLAAVGEKVSPGEVYINKETPDNALSS--GITGSDAGLPVKYNPTPQTY----KLPDY 936

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
             + +K+           G  +++KV     R  + GDK + RHG KG+V  I    DMPF
Sbjct: 937  SYIDKV-----MISTTEGESQLIKVQTRQTRRPEVGDKFSSRHGQKGVVGIIAEQADMPF 991

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
               G   DI++NP G PSRM VG++ E   G A +  G+                     
Sbjct: 992  TDTGLVPDIIMNPHGFPSRMTVGKMLELVAGKAGIISGQFGYG----------------- 1034

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                                TP F G+  E ++++L        
Sbjct: 1035 ------------------------------------TP-FGGSPVEEMSAILVDHGFSYG 1057

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGEP    V  G IY  KL HMV DK+++R+ G  + +T+QP  G+S  GG
Sbjct: 1058 GKDYLTSGITGEPLTYYVFTGPIYYQKLKHMVQDKMHSRARGPRATLTRQPTEGRSRDGG 1117

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1118 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCEGCGFMGYSGWCQRCKTSAGVVK- 1176

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +   L         +
Sbjct: 1177 -----MVIPYAAKLLVQELFSMNVVARLRLQDEFPEDR 1209



 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 96/749 (12%), Positives = 215/749 (28%), Gaps = 139/749 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P+  
Sbjct: 101 LVKQHIDSYNYFVEVQ----------LKKIVQSSAEIRSDIDPKFYIKFHDIYLGTPRRT 150

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 151 DEEQSGIKVDSTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 200

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 201 RMPVMLRSSKCVLSNKSAREMYTLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 260

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K  I++R +     +P+   L A
Sbjct: 261 SKKEIVQASVTSSSHERKSKSYII-----------MKKGRIYLRHNVLNDDIPIVILLKA 309

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESG-- 277
           +G+ S++ +      +    + DF      A  L +   + +   +          SG  
Sbjct: 310 MGIQSDKEMLLLVAGVDLEYQEDFAINFEEAIKLGIFTQQQALEYLGARIKINRKASGFG 369

Query: 278 ---KKLTSGLLKSLKEKGVKFLGITS-----DCLCGLYVAEDIVNGETGEIYIEAGDVID 329
              +   +  ++++    +  + +         L   Y+A  ++  +     ++  D + 
Sbjct: 370 PARRNYVAEAIEAISSVIISHVQVQDMNFRPKALYVTYMARRVLMAKLDPSLVDDRDYVG 429

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            K LE            L+                   K   D  ++I +V++    +  
Sbjct: 430 NKRLELAGQLLALLFEDLF------------------KKFCFDIKMNIDKVLKKPVRTEA 471

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
             A  +         +     +     +  R  ++       + +   IA + ++  + +
Sbjct: 472 FDAYPVVAIHGNHITQGMNRAIATGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISS 531

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAK 507
                  +      +    G +  +    G    + +++         D   P   +   
Sbjct: 532 QFEKTRKVSGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTNDEEEPVQKLVFT 591

Query: 508 PVVSAVCEFFCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPT 564
                +          Q      +N        R    L     + R     E   V   
Sbjct: 592 LGAEDIQTVGGRECFGQGAYIVFMNGSPIALTRRPKYFLNAFRRLRRMGRISEFVSVFIN 651

Query: 565 HYGRICPAETSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAME 621
           H  +     T +G     L+      ++V       + +      D      V Y+   E
Sbjct: 652 HNQKSVHVSTDDGRICRPLIIVEKKRSKVTARHLSALRSGTMDFDDFLSNGLVEYVDVNE 711

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E +  IA     +D +                          ++  P  V+   A LIP+
Sbjct: 712 ENDANIAVYEREIDAN-----------------------TTHLEIEPFTVLGAVAGLIPY 748

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             ++ S R    C M +QA+  +      
Sbjct: 749 PHHNQSPRNTYQCAMGKQAIGAIANNQFL 777


>gi|4867807|emb|CAB43064.1| RNA polymerase II [Chiococca alba]
          Length = 267

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGINPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|89888204|gb|ABD78645.1| DNA-directed RNA polymerase beta subunit [Achromobacter
           xylosoxidans]
          Length = 184

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 92/186 (49%), Positives = 128/186 (68%), Gaps = 2/186 (1%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           K F K  ++ ++P L+  Q  SY  FL  + AP +R  +GLQAAF S+FPI + +G A L
Sbjct: 1   KSFAKREDVQNVPFLLATQLQSYLTFLQADTAPSDRVADGLQAAFSSIFPIVSHNGMARL 60

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFVSY    P FDV +C  R LTYA PL+  +RL++ D        ++K++KEQ +YMG+
Sbjct: 61  EFVSYVLGEPVFDVKECQQRGLTYASPLRAKVRLVLLDR--EVSKPTVKEVKEQEVYMGE 118

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           +PLMT  G+FVI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ R+IP +G W+D 
Sbjct: 119 IPLMTGTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARVIPYRGSWLDF 178

Query: 195 EFDSKD 200
           EFD KD
Sbjct: 179 EFDPKD 184


>gi|100913649|gb|ABF69723.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913653|gb|ABF69725.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 596

 Score =  328 bits (840), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 214/451 (47%), Positives = 303/451 (67%), Gaps = 15/451 (3%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L
Sbjct: 1   DQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            SFA+++ YGFI++PY  V +  V  ++  YL+A+EE     AQ+   + +D    ++ V
Sbjct: 61  ASFAKIDKYGFIQSPYFPVKNRIVDFSEPKYLTAIEEAGYTFAQSTIKI-DDNYIVDDKV 119

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L 
Sbjct: 120 IVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLF 179

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E+ VAK S   I+AKR G+V+ VDA  I +           S +D+Y L 
Sbjct: 180 PESPLVATGVEADVAKFSSTNILAKREGVVKYVDASVIKVLPT------GHSKLDVYHLR 233

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q PLVKVGD V+  D++ DGPS   G+LALG+N+LV F  WHGYN+ED
Sbjct: 234 TFERSNQGTLIHQTPLVKVGDIVKEGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYED 293

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE GI+ VG
Sbjct: 294 AVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVG 353

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + I 
Sbjct: 354 SEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDIL 413

Query: 946 NR-------HGIDKNERSISVEREQIELLAR 969
           +R        GI+K  +    ++ +I++  +
Sbjct: 414 SRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 444



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 129/415 (31%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 249  LVKVGDIVKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 416  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +            
Sbjct: 476  VLNPQGVPSRMNIGQILELHLGSAAKNLNTKFVTPIFDGITHNQIREILDEA-------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                K  V   T V+D                          G 
Sbjct: 528  --------------------KMDVTGKTVVYD--------------------------GQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  TGEPFDSPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|73697653|gb|AAZ81443.1| RNA polymerase beta subunit [Mycoplasma falconis]
          Length = 592

 Score =  328 bits (840), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 212/448 (47%), Positives = 300/448 (66%), Gaps = 10/448 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA ++ YGFI++PY +V + KV  ++ VYL+A+EE +   AQ+   + +D    ++ V  
Sbjct: 61  FAHIDKYGFIQSPYFRVKNRKVDFSEPVYLTAIEEADYAFAQSTCHIKDD-MIVDDYVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V  E++DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRNNEFVEVKAEEVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   + A RAG V  VDA  I I+  EG        VD+Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNLRANRAGEVVYVDAEMIKIKPEEGKK------VDVYNLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q P+VKVG  +   D++ DGPS   G++ALG+N+LV F  WHGYN+ED++
Sbjct: 234 ERSNQGTVIHQVPIVKVGQRIEAGDLLVDGPSMKNGEMALGKNVLVGFTTWHGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G +E+T +IPN S    + +DE GI+ +G+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGDDELTAEIPNASNFSKRFLDERGIVRIGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K  + +DTSL+V  G +GTVV V + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTANCKDTSLKVKHGHNGTVVAVEVLSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQ 975
                ++    +E+     +A+ +  + 
Sbjct: 414 ENG--DQLEDGIEKIVKVSIAQKRKIKV 439



 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 128/413 (30%), Positives = 182/413 (44%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  IVKVGQRIEAGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E    +    +  +  LD     R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGDDELTAEIPNASNFSKRFLDERGIVRIGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTANCKDTSLKVKHGHNGTVVAVEVLSR--------- 413

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 414  ENGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
             LNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 474  CLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILE---------- 523

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               E  I         D SG+  +YDG 
Sbjct: 524  -----------------------------------EADI---------DPSGKMKIYDGR 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEPFDKPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|100913651|gb|ABF69724.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 596

 Score =  328 bits (840), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 215/451 (47%), Positives = 304/451 (67%), Gaps = 15/451 (3%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L
Sbjct: 1   DQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            SFA+++ YGFI++PY  V +  V  ++  YL+A+EE     AQ+   + +D    ++ V
Sbjct: 61  ASFAKIDKYGFIQSPYFPVKNRIVDFSEPKYLTAIEEAGYTFAQSTIKI-DDNYIVDDKV 119

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L 
Sbjct: 120 IVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLF 179

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E+ VAK S   I+AKR G+V+ VDA  I +      L    S +D+Y L 
Sbjct: 180 PESPLVATGVEADVAKFSSTNILAKREGVVKYVDASVIKV------LPAGHSKLDVYHLR 233

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q PLVKVGD V+  D++ DGPS   G+LALG+N+LV F  WHGYN+ED
Sbjct: 234 TFERSNQGTLIHQTPLVKVGDIVKEGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYED 293

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE GI+ VG
Sbjct: 294 AVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVG 353

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + I 
Sbjct: 354 SEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDIL 413

Query: 946 NR-------HGIDKNERSISVEREQIELLAR 969
           +R        GI+K  +    ++ +I++  +
Sbjct: 414 SRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 444



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 129/415 (31%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG  V  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 249  LVKVGDIVKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 416  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +            
Sbjct: 476  VLNPQGVPSRMNIGQILELHLGSAAKNLNTKFVTPIFDGITHNQIREILDEA-------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                K  V   T V+D                          G 
Sbjct: 528  --------------------KMDVTGKTVVYD--------------------------GQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  TGEPFDSPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|242392376|dbj|BAH80401.1| RNA polymerase subunit B' [Natrinema versiforme]
          Length = 609

 Score =  328 bits (840), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 124/596 (20%), Positives = 207/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVGVDEDDLTEKHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETTVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF + G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVIGHLAPQEDMPFTEGGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ + S L  +  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRSGLEDSGFDSAGKETMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 40.4 bits (93), Expect = 2.1,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E        S      +N  G +E       D      + ++ A EEE+  +      L 
Sbjct: 71  EDGE--PRISDQEMEALNE-GDLE-----FEDLVDHGYIEFIDAEEEEDILVGVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------EKHTHLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|81171083|gb|ABB58768.1| RNA polymerase beta subunit [Mycoplasma agalactiae]
          Length = 592

 Score =  328 bits (840), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 210/423 (49%), Positives = 299/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N+L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++
Sbjct: 2   NALAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +  V  +DVVYL+A +E    IAQ+ +++D++    +E +  R
Sbjct: 62  ASVNEYGFLQTPYFKVNNSVVDYDDVVYLTAADEFGYNIAQSTATVDDENRLVDETLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 KNYTYILGKPSDVDLIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            FV TG E+ +AK S A   A+  G VE VD  +I IR+ +G LD        Y L  FQ
Sbjct: 182 AFVATGNEADIAKFSAANFRARNEGKVEYVDGAKIKIRNNKGTLD-------TYSLKNFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+P++KVG +V + D++ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVIHQKPIIKVGQDVAKGDLLVDGSSFKDGELALGKNLLVAFSTYKGYNYEDAIV 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+  +DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV
Sbjct: 295 LNERLAKKDVLTSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R 
Sbjct: 355 IPGDVLVGRVSPKGDDNPSREEKLLAAILGQRQLNVKDTSLKVKNGHNGTVIGVEILSRE 414

Query: 949 GID 951
             D
Sbjct: 415 NKD 417



 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 117/418 (27%), Positives = 169/418 (40%), Gaps = 77/418 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS-LRVPSGVSGTV 939
            II VG +V  GD+LV   + K +  +   + LL A    K  +  D   L         +
Sbjct: 247  IIKVGQDVAKGDLLVDGSSFK-DGELALGKNLLVAFSTYKGYNYEDAIVLNERLAKKDVL 305

Query: 940  VDVRIFNRHGIDKNERSISVEREQ----IELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
              + I  +    +  ++ + E  +    +   A    DE  I+         ++L G+ +
Sbjct: 306  TSIHIEEQTIQFRTSKAGADELTRDIPNVSKYAIRHLDEHGIVLVGSEVIPGDVLVGRVS 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G     +   L + ++                  QR +       +            
Sbjct: 366  PKGDDNPSREEKLLAAILG-----------------QRQLNVKDTSLKVKNGHNGTVIGV 408

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +I   +  D +  G+  +VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM      
Sbjct: 409  EILSRENKDLLEDGIDMIVKVSIAVKRKIRVGDKMSGRHGNKGVVSVILPEEDM------ 462

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                    P             E          G  I  ++                   
Sbjct: 463  --------PH-----------LE---------DGTPIDVML------------------- 475

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                    +++      V         G    TPVFDG  +EAI  ++  A L  SG+  
Sbjct: 476  -NPQGVPSRMNIGQVLEVHLGMAARSLGCKFVTPVFDGVKKEAIQDVISEAGLPLSGKQT 534

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            L D +TGE FD PV+VG +YM KLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 535  LIDPITGEKFDNPVSVGVMYMFKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|4867793|emb|CAB43061.1| RNA polymerase II [Buddleja asiatica]
          Length = 260

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 78/255 (30%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+ ++G   DI++NP 
Sbjct: 38   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGICPDIIVNPH 97

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 98   AIPSRMTIGQLIECVMGKVAAHMGKEGD-------------------------------- 125

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 126  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGYETMYNGHTGRRL 163

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 164  PAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 223

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 224  GAAHFLKERLFDQSD 238


>gi|6606117|gb|AAF19071.1|AF107799_1 DNA-dependent RNA polymerase II RPB140 [Aureobasidium pullulans]
          Length = 936

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 165/1042 (15%), Positives = 314/1042 (30%), Gaps = 164/1042 (15%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            E G +L S +   L +KG +  G          +     +     ++   G V D + L+
Sbjct: 37   EKGTRLLSSMQLKLYQKGEQKKGGILTGTIKATLPYIKADIPIVIVFRALGIVSDMQILD 96

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
             I +          +      A++         +DR++AL  I +               
Sbjct: 97   CICYDANDTQLREMIKPCLEEAFV--------VQDRENALDFIGKRGNQV---------- 138

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
                      +Y    + +  +      +  +  +      +  +I  +  +  G+   D
Sbjct: 139  ---GGKEKRIRYARDILQKEFLPHISQREGSETRK---AFFLGYMINRMCQVMLGRCDED 192

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSA 512
            D D+ G +R+   G ++   +RL   ++ R ++  +S              + +  + S 
Sbjct: 193  DRDHFGKKRLDLSGPLMAQVFRLKFTQLVRDMRVYLSRCIEQGRDFNLTLAVKSNILTSG 252

Query: 513  VCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            +     +               +SQ+       S ++H RR +      + R     + R
Sbjct: 253  LRYCLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKPR 308

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYL 617
             +H TH+G +CPAET EG   GLV +L+    V+     E    +    + ++  +    
Sbjct: 309  QLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVEFMNQRNMELLEEYEPK 368

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAA 676
            +  +    ++      +  D S   ++V        I      I D  +   K       
Sbjct: 369  NNPDATKVFVNGVWVGVHRDPSQLVKVVQSLRRNGTISFEISLIRDVREREFKIFTDAGR 428

Query: 677  SLIP-FLENDDSNRVLMGCNMQRQAVP---LLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
             + P F+ N+D      G     ++     L   E   +G   E       G        
Sbjct: 429  VMRPLFVVNNDPASPTKGQLTLNRSHISQLLNARETDTIGLSEEERDGTIYG-WKNLISD 487

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE +DA    +  +    +       +   + ++    +     +   +    VR   
Sbjct: 488  GVVEYLDAEEEEVAMMVMSPEDLDEHRQMRAGLVYEEPVTDPHRRIKS--RPNANVRTWT 545

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 P+  LG       +  + +P+  +N          M  + +  ++          
Sbjct: 546  HCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGITL---------- 588

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                  N+    +  V             +       +   +  
Sbjct: 589  -------------------TNYNVRMDTMANVLYYPQKPLGTTRSMEYLKFRELPAGQNA 629

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R  +D+ +R      EQ E   R   
Sbjct: 630  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYMDQEKRVGMSVVEQFEKPTRGDT 688

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       I  G           K+  ++ D      R+++         ++
Sbjct: 689  MRMKHGTYDKLDDDGIIAPGTRVSGEDIIIGKTAPMAPDAEELGQRTKFHIKRDVSTPLR 748

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 L  Q                             L+ VKV     +  Q GDK A 
Sbjct: 749  STESGLIDQVLL--------------------TTNVEGLKFVKVRTRTTKIPQIGDKFAS 788

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  DG   DI++NP  +PSRM +  + E  L       G++ 
Sbjct: 789  RHGQKGTIGITYRQEDMPFTADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGSLRGQEG 848

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          IS L                                            
Sbjct: 849  DATPFTDVTVTQISDLLRQHGFQQRGFEVM------------------------------ 878

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                              +G +    G      +  V +G  Y  +L HMV DK++AR+ 
Sbjct: 879  -----------------YNGHT----GR---KMNAQVFLGPTYYQRLRHMVDDKIHARAR 914

Query: 1273 GSYSLVTQQPLGGKSNRGGQRL 1294
            G   ++T+QP+ G++  GG R 
Sbjct: 915  GPTQILTRQPVEGRARDGGLRF 936



 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 103/768 (13%), Positives = 219/768 (28%), Gaps = 110/768 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+ S+ +IL         +Q  +     L  A ++   + +
Sbjct: 72  YIKAD----IPIVIVFRALGIVSDMQILDCICYDANDTQLREMIKPCLEEAFVVQDRENA 127

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +     +   +  +   +  +  L+++ +  +                +     ++ 
Sbjct: 128 LDFIGKRGNQVGGKEKRIRYARDI--LQKEFLPHISQREGSETRKAFFLGYMINRMCQVM 185

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +   D  D     +         P++          +   +    ++  +        + 
Sbjct: 186 LGRCDEDDRDHFGK--KRLDLSGPLMAQVFRLKFTQLVRDMRVYLSRCIEQGRDFNLTLA 243

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
              ++ T  +   +    + D  K   +  G  ++  R    +      R          
Sbjct: 244 VKSNILTSGLRYCLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGK 303

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I     L N    +         +   + + L     + +      I E ++  +++ + 
Sbjct: 304 IAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVEFMNQRNMELLE 363

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM 558
             +  N                +    +    +  +   RR   +  +  + R     E 
Sbjct: 364 EYEPKNNPDATKVF---VNGVWVGVHRDPSQLVKVVQSLRRNGTISFEISLIRDVREREF 420

Query: 559 -------RDVHPTHYGRICPAETSEGH---NIGLVSSLTSFARVNAYGFIETP----YRK 604
                  R + P       PA  ++G    N   +S L +    +  G  E         
Sbjct: 421 KIFTDAGRVMRPLFVVNNDPASPTKGQLTLNRSHISQLLNARETDTIGLSEEERDGTIYG 480

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV-------FCRCAGEEILVP 657
             +      V YL A EEE   +  +   LDE       LV         R         
Sbjct: 481 WKNLISDGVVEYLDAEEEEVAMMVMSPEDLDEHRQMRAGLVYEEPVTDPHRRIKSRPNAN 540

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++ S R      M +QA+ +              
Sbjct: 541 VRTWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGI-------------- 586

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                        +       + + V  Y       +     + 
Sbjct: 587 ---------------------------TLTNYNVRMDTMANVLYYPQKPLGTTRSMEYLK 619

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            R                        +L  G+N +VA   + GYN EDS+++++  +   
Sbjct: 620 FR------------------------ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 655

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +   +   E        D   +       +D+ GII  G  V+  D
Sbjct: 656 LFRSLFYRAYMDQEKRVGMSVVEQFEKPTRGDTMRMKHGTYDKLDDDGIIAPGTRVSGED 715

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I++GK  P         E+L +        DV        SG+   V+
Sbjct: 716 IIIGKTAPMAPDA----EELGQRTKFHIKRDVSTPLRSTESGLIDQVL 759


>gi|40644994|emb|CAD88980.1| DNA-directed RNA polymerase subunit B [Vicia sativa]
          Length = 401

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 97/442 (21%), Positives = 148/442 (33%), Gaps = 77/442 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R                      G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYEKLDDDGLAPPGTRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T LS                      Q   +    +Y      +  R      
Sbjct: 137  DVIIGKTTPLS----------------------QEEAQGQAARYSKRDHSISLRHSENGI 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              Q         LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 175  VDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 234

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 235  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------- 269

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+  L        G   +Y+
Sbjct: 270  ----------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYN 300

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME
Sbjct: 301  GHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEME 360

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD 1320
              C+ A+GAA+ L+E L  +SD
Sbjct: 361  RDCMIAHGAAHFLKERLFDQSD 382



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 60/184 (32%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E            +     + 
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYEK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           A         RD S+ +    
Sbjct: 121 LDDDGLAPPGTRVSGEDVIIGKTTPLSQEE---------AQGQAARYSKRDHSISLRHSE 171

Query: 936 SGTV 939
           +G V
Sbjct: 172 NGIV 175


>gi|307103979|gb|EFN52235.1| hypothetical protein CHLNCDRAFT_56318 [Chlorella variabilis]
          Length = 1155

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 90/318 (28%), Positives = 131/318 (41%), Gaps = 68/318 (21%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  VVKV V   R  + GDK + RHG KG+V  I    DMPF + G   D+++NP G
Sbjct: 888  NDDCSCVVKVLVRHTRRPELGDKFSSRHGQKGVVGSIWSQSDMPFSERGLVPDLIMNPHG 947

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++ E     A V  G+                                    
Sbjct: 948  FPSRMTVGKMIELLGSKAAVCTGRFH---------------------------------- 973

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                            G     P       E+I+  L  A    SG+  L+ G+TGE  +
Sbjct: 974  ---------------YGTAFGEPAGLADKVESISQELVEAGYSYSGKDFLHSGITGEALE 1018

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G +Y  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C+  YG
Sbjct: 1019 AHIFMGPVYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1078

Query: 1307 AAYVLQEMLTIKSDDVVGRTRV--------YES--------IVAG-NDTFETGTPESFNV 1349
            A+ +L E L I SD      +V        Y+         ++           P +  +
Sbjct: 1079 ASMLLLERLMISSDQFE--VQVCTHCGLMGYKRHDGLAVCPLLRSPEHIASLRIPYAAKL 1136

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L +E+Q++ +   L  + 
Sbjct: 1137 LFQELQSMNIVPKLLLAE 1154



 Score =  141 bits (355), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 124/987 (12%), Positives = 273/987 (27%), Gaps = 188/987 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           LI    +S++HF+  ++    +  +G +                 L + +     P    
Sbjct: 25  LIRQHVSSFNHFIASDLLKIIKA-KGNERVT------CDADPNFYLRYTNIYVGRPSLEE 77

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                +   + C  RD TY+ P+ + +             KS        I +G +P+M 
Sbjct: 78  DYIQTELTPNQCRLRDQTYSAPISVDVEYTRGKEVVIRKGKSGAGA----ILIGRMPIML 133

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                     G FV+KG +++++ Q   S       D G  +L+
Sbjct: 134 RSDRCVLTGKSEEELAWVGECPLDPGGYFVVKGTEKVILIQEQLSKNRIII-DTGTPALA 192

Query: 176 GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR--------RRKVPVTSFLMALGMDSEE 227
            +  +   +          E  SK  I  + +R           V +   + A+G++S+E
Sbjct: 193 ARHSHGAVVASVTSS--THERKSKTNIVSKHNRLMLKHNAFTEDVNIVIVMRAMGVESDE 250

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID---TGEQVIESGKKLTSGL 284
            +                       + +   + +   +      +G     +G    +  
Sbjct: 251 EVLQLVGTEGPFASLLTPTLQHCKEEGVYTRQQALDYLAGKVKGSGRPASPAGGGGFTRR 310

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG--DVIDEKSLEEIFHSEIR 342
            +S  ++    L     C   +   +         + +       +D   +++  +   +
Sbjct: 311 TRSRVDEARDILANVVLCHVPVVQFDYQQKVTYIAVMVRRMLYAKLDPSFIDDRDYYGNK 370

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL--------LDIYRVMRPGDVSTFSVAES 394
            + +           +   +  D  +    +L         DI + +R  D  TF +  +
Sbjct: 371 RLELAGGLLALLFEDLFKRMNADLKRQADSSLSKANRATQFDIAKCIR-TDTITFGLEHA 429

Query: 395 MFNFLFFDSD-KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           + +  +     + +   V +V   +          R   + +    +     L+  +  +
Sbjct: 430 ISSGNWTIKRFRMERKGVTQVLSRLSFISAVGMMTRITSQFEKTRKVSGPRALQPSQWGM 489

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
               +        + + L     +     E  I      + ++     +    +    A+
Sbjct: 490 LCPADTPEGESCGLVKNLALMTHVTTDEEEAPIARLAHIMGVEPASLVNQSELRERGCAL 549

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                +  L         +      RR   +G+      +          +  GR+C   
Sbjct: 550 VFLNGNI-LGVHRRPKYFVRSFREMRRRGRVGEFVSVYMQHDTVQ---IASDGGRVCRPL 605

Query: 574 TSEGHNIGLVS----SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
                 +  V      L    + N   F+ +             + YL   EE N  +A 
Sbjct: 606 IICDRGVPRVKDEHLQLLRMGKWNFNSFLHSGL-----------LEYLDVNEENNSLVAL 654

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
             +                           ++  ++  P  ++ + A LIPF  ++ S R
Sbjct: 655 YEADCGP-----------------------RVTHLEIEPFTILGVVAGLIPFPHHNQSPR 691

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+                                           +   +
Sbjct: 692 NTYQCAMGKQAMGN-----------------------------------------VAFNQ 710

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            +   +   +  Y               QRPL+                      L  G+
Sbjct: 711 LNRMDTLLYLLCYP--------------QRPLL----------TTKTIELVGFDRLGAGQ 746

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT------- 862
           N  VA M + GY+ ED+++++   +       I + ++    +      ++         
Sbjct: 747 NATVAVMSYSGYDIEDAIVMNRASLDRGFGRCIVLRKYGTSLKKYANRTQDRIVLPAAAV 806

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                      + +D  GI   G  +  G+ILV K  P            +   F   A 
Sbjct: 807 GPASAPRPAKFRVLDRDGIAAAGEVLTQGEILVNKQMPTNTRDPVSNPAAMPDTFYRNAP 866

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                S +  +G    VVD  +   + 
Sbjct: 867 ----VSWKGYTGGEKCVVDKVLLTSND 889


>gi|242392382|dbj|BAH80404.1| RNA polymerase subunit B' [Natronococcus jeotgali]
          Length = 609

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 122/595 (20%), Positives = 207/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDIYVAVDEDDLNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYTHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L     + +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELREGLERNGFNSAGKETMYSGVSGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 45.1 bits (105), Expect = 0.083,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKERTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E                     ++    +  D      + ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE--------PRISEQEMSALQDGDLEFEDLVDHGYIEFIDAEEEEDIYVAVDEDDLN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|242392344|dbj|BAH80385.1| RNA polymerase subunit B' [Haloterrigena saccharevitans]
          Length = 609

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 123/596 (20%), Positives = 207/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I   ++       I   E     R 
Sbjct: 95   LVDHGYIEFIDAEEEEDILVGVDEDDLTENHTHLEIDPSLIFSIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGIVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             D++ +   L  A  D +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDKDELREGLEEAGFDSAGKETMYSGISGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHVCANCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A     G +E       D      + ++ A EEE+  +      L 
Sbjct: 71  EDGE-PRISEQEIEAL--REGDLE-----FEDLVDHGYIEFIDAEEEEDILVGVDEDDLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+                          ++  P  + SI A +IP+ E++ S R+ MG  
Sbjct: 123 ENH-----------------------THLEIDPSLIFSIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|21425513|emb|CAD33798.1| DNA-directed RNA polymerase beta subunit [Cuscuta reflexa]
          Length = 727

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 195/567 (34%), Positives = 316/567 (55%), Gaps = 26/567 (4%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +   A      + LE + + EI    +   +                   +++A+L+ Y+
Sbjct: 181 VLSSAMGSNLREILENVCYPEILLFFLRDKEKKKIG-------------SKENAILEFYK 227

Query: 380 VMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                 GD              FF   + +L  +GR  MN RL+LD P +   +   DI+
Sbjct: 228 KFACVGGDPLFSESLCKELQNKFF-QQRCELGRIGRRNMNRRLHLDIPHNNTFLLPRDIL 286

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS--SVDI 495
                L+ L+ G GT+DD+++L N+R+RSV ++L++Q+ L L+R+E +++  +       
Sbjct: 287 EATDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQFGLALVRLENAVQGTLCGAIRHK 346

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
               PQ+L+ +  + +    FF    LSQ+ +  N L++I H R++S+LG GG+    A 
Sbjct: 347 RIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDGTNPLTQIVHARKVSSLGPGGLTGRTAS 406

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
             +RD+HP+HYGRICP +TSEG N+GL+ SL    R+  +G +E+P+ ++ D      V+
Sbjct: 407 FRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHVRIGNWGSLESPFYEISDRLTGVRVL 466

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LS   +E   +A  NS         +++V  R   E + +  E+++     P Q  SI 
Sbjct: 467 HLSPGRDEYYMVAAGNSLALNQDIQEDQVVPARYRQEFLTIAWEQVNLRSIFPFQYFSIG 526

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPF+E++D+NR LM  NMQRQAVPL  +E   VGTGME   A  SG+  +A+R G V
Sbjct: 527 ASLIPFIEHNDANRALMSSNMQRQAVPLTWSEKCIVGTGMERQAALDSGSLAIAEREGRV 586

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D  +I++                  L+ +QRSN+NTC+ Q+P V+ G  +++  I+A
Sbjct: 587 IYTDTEKILV--------SGDGKTINIPLVMYQRSNKNTCMYQQPQVRRGQFIKKGQILA 638

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
            G +T  G+LALG+++LVA+MPW GYN ED++LISE +V ED+FTS HI+++E+    T 
Sbjct: 639 GGAATVEGELALGKSVLVAYMPWEGYNSEDAVLISECLVYEDIFTSFHIKKYEIQIHMTT 698

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGII 882
            GPE++T +IP++    ++N+D+ GI+
Sbjct: 699 QGPEKVTNEIPHLEAHLIRNLDKNGIV 725



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 72/335 (21%), Positives = 132/335 (39%), Gaps = 31/335 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDP 83
           IP L ++Q   +  F+          ++GL         I         + FV  Y+   
Sbjct: 11  IPGLNQIQLEGFCRFI----------DQGLMEELSKFQKIEDIDQEIEFQLFVETYQLVE 60

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++  LI          K+ KD++EQ+I++G LP+M   GT
Sbjct: 61  PLIKERDAVYDSLTYSSELYVSAGLI---------RKASKDMQEQTIFIGSLPIMNSLGT 111

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
            ++ GI RIV++Q+ +SPGI++  +      +G  +Y   II D G   ++E D K  + 
Sbjct: 112 SIVNGIYRIVINQILQSPGIYYRSELD---QNGISVYTGTIISDWGGRSELEIDRKPRVW 168

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
            R+ R++K+ +     A+G +  EIL    YP+I+     D     + + +  +      
Sbjct: 169 ARVSRKQKISILVLSSAMGSNLREILENVCYPEILLFFLRDKEKKKIGSKENAILEFYKK 228

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL------CGLYVAEDIVNGE 316
                          K+L +   +   E G       +  L         ++    +   
Sbjct: 229 FACVGGDPLFSESLCKELQNKFFQQRCELGRIGRRNMNRRLHLDIPHNNTFLLPRDILEA 288

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           T  +      +     +  + +  IR +  L  D 
Sbjct: 289 TDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQ 323


>gi|66351046|emb|CAI13208.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 336

 Score =  327 bits (839), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 201/335 (60%), Positives = 258/335 (77%), Gaps = 1/335 (0%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 3   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 62

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET  G NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 63  GGLTRERAGFEVRDVHPTHYGRVCPIETPXGPNIGLINSLAAYARTNQYGFLESPYRVVK 122

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D 
Sbjct: 123 EGEVTDEIVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  
Sbjct: 182 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVC 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA R+V+R  +G+++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD
Sbjct: 242 VVARRGGVIDSVDASRVVVRVHDGEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGD 301

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            V R DI+ADGPSTD+G+LALG+NM VAFMPW+GY
Sbjct: 302 VVERGDIMADGPSTDMGELALGQNMRVAFMPWNGY 336


>gi|226480014|emb|CAX73303.1| putative DNA-directed RNA polymerase II 140 kDa polypeptide (RNA
            polymerase II subunit 2) (RPB2) [Schistosoma japonicum]
          Length = 1196

 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 96/497 (19%), Positives = 168/497 (33%), Gaps = 98/497 (19%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +       V   +    +     +++     R     
Sbjct: 766  NVLYYPQKPLVATRSMEYLRFRELPAGINAIVAIATYTGYNQEDSVIINESAIQRGFF-- 823

Query: 953  NERSISVEREQIELLARDKDDEQVI-LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
                    R +     +D++    + L+        +   G       K      +    
Sbjct: 824  --------RSEFYRTYKDQETRHGMDLEEVFEKPNPQNCQGMRHAIYDKLDDDGLIAPGT 875

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
             +S           +   + +  +E  + +Y    + +  R        Q          
Sbjct: 876  RVSGDDVLIGKTITL--PENEDEMEGGQRRYTKRDASVFMRRSEYGIVDQVMVTWNNEGN 933

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            +  KV V   +  Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM
Sbjct: 934  KFCKVRVRTTKAPQVGDKFASRHGQKGTCGIRYRQEDMPFTCEGITPDIIINPHAIPSRM 993

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E   G      G+                                         
Sbjct: 994  TIGHLIECLQGKVSANKGEIGD-------------------------------------- 1015

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                           +TP  D  +   I+ +L+      +G  I+Y+G TG   +  + +
Sbjct: 1016 ---------------ATPFNDAVNVRKISLLLQEYGYQHTGNEIMYNGFTGRKLNSQIFL 1060

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  Y  +L HMV DK++++S G   ++ +QP+ G+S  GG R GEME  C  A+GAA  L
Sbjct: 1061 GPTYYQRLKHMVDDKIHSQSRGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFL 1120

Query: 1312 QEMLTIKSD-------DVVG-------RTRVYE----------SIVAGNDTFETGTPESF 1347
            +E L   SD       ++ G       R + YE          S+V          P + 
Sbjct: 1121 RERLFFASDPYQVYVCNLCGLIAIAHQRNKTYECRSCKNTTQISLVK--------LPYAC 1172

Query: 1348 NVLVKEMQALGLSIDLE 1364
             +L +E+ ++ ++  + 
Sbjct: 1173 KLLFQELMSMSIAPRMM 1189



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 141/908 (15%), Positives = 278/908 (30%), Gaps = 135/908 (14%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           L+  Q  S+D F+  +I    ++ P   LQA  +    I        L+F          
Sbjct: 57  LVRQQLDSFDEFIQTSIQKIVEDSPIIELQAEAQHSGGILENPVQYRLKFEQIYLSKATH 116

Query: 87  ----------DVDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                       +D   R+LTYA PL + + + I+ D  E       K       ++G +
Sbjct: 117 WEKDGSSVPMTPNDARLRNLTYAAPLYVDVMKKIIRDETEEEKPLEKK-------FIGKI 169

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 170 PIMLRSTYCLLSVMSDRDLAELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFKQKD 229

Query: 171 RASLSGKLLYACRIIPDQ-GLWMDIEFDS---KD-----IIHVRIDR-----RRKVPVTS 216
                   + +C     +    + I   +   KD      I  RI       ++++PV  
Sbjct: 230 SKYAYKTEIRSCLEHSSRPASTLWINMMARGGKDGSKRATIGQRIVAILPYIKQEIPVLI 289

Query: 217 FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
              ALG  ++ +IL         ++  +     L  A ++   KV+ + +        + 
Sbjct: 290 VFRALGFVADRDILEHIIYDFDDTEMREMIKPSLDDAFVIQEQKVALNFIGSRGARPGVT 349

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             K++     + L+++ +  +G++  C          +      + + A    D    + 
Sbjct: 350 KEKRIKYAK-EILQKETLPHVGVSDFCETRKAYFLGYMVH---RLLLAALKRRDVDDRDH 405

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
             +  +                +            K+  L   + +  G    F++  ++
Sbjct: 406 YGNKRLDL----------AGPLLAFLFRGLFRNLTKEIRLYAQKFIDKG--KDFNLELAI 453

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGK 450
            + +  D  KY L   G      + N   P   + + +    + +  L  L     R+GK
Sbjct: 454 RSQIITDGLKYSL-ATGNWGDQKKANQARPGVSQVLNRLTFASTLSHLRRLNSPIGRDGK 512

Query: 451 GTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
                  +     +    E        ++KN   +  + +       +  ++  S+   +
Sbjct: 513 LARPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLE 572

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            I    +      F     +       + +  +   RR   +    V+  R   +     
Sbjct: 573 EIAPSAIGKTCKIFVNGCWVGIHSSPDHLMGTLRKLRRQVDVIVSEVSMIRDYRDQEIRI 632

Query: 563 PTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            T  GRIC P    E   + L  S     +  AY           D  ++  V Y+  +E
Sbjct: 633 YTDAGRICRPLVIVEKGKLLLKRSHIELLKDKAYNR-----YSWQDLVLSGVVEYIDTLE 687

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           EE   IA   + +                    +   +     +  P  ++ I AS+IPF
Sbjct: 688 EETVMIAMGPAEMQA-----------------AVNYCKTHTHCEIHPSMILGICASIIPF 730

Query: 682 LENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKSSG 724
            +++ S R      M +QA+                 L   + P V T  ME +  +   
Sbjct: 731 PDHNQSPRNTYQSAMGKQAMGVYISNFHTRMDTLANVLYYPQKPLVATRSMEYLRFRELP 790

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV-----NQR 779
           A I A  A            +   E  +       + YR  K Q +     +        
Sbjct: 791 AGINAIVAIATYTGYNQEDSVIINESAIQRGFFRSEFYRTYKDQETRHGMDLEEVFEKPN 850

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P    G      D + D      G    G ++L+        N ++      R    D  
Sbjct: 851 PQNCQGMRHAIYDKLDDDGLIAPGTRVSGDDVLIGKTITLPENEDEMEGGQRRYTKRDAS 910

Query: 840 TSIHIEEF 847
             +   E+
Sbjct: 911 VFMRRSEY 918



 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 102/683 (14%), Positives = 219/683 (32%), Gaps = 65/683 (9%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G+  +     I ++    I    +  +    +       +    +         DA +  
Sbjct: 271 GQRIVAILPYIKQEIPVLIVFRALGFVADRDILEHIIYDFDDTEMREMIKPSLDDAFVIQ 330

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 331 EQKVALNFIGSRGARPGV---TKEKRIKYAKEILQKETLPHVGVSDFCETRK---AYFLG 384

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDI 495
            ++  L+     +  +DD D+ GN+R+   G +L   +R     + + I+   +      
Sbjct: 385 YMVHRLLLAALKRRDVDDRDHYGNKRLDLAGPLLAFLFRGLFRNLTKEIRLYAQKFIDKG 444

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                +  I ++ +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 445 KDFNLELAIRSQIITDGLKYSLATGNWGDQKKANQARPGVSQVLNRLTFASTLSHLRRLN 504

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           +     + R       R +H T +G ICPAET EGH +GLV +L   A ++         
Sbjct: 505 S----PIGRDGKLARPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPIL 560

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI- 661
             + +  + N      +   +   I      +    S    +   R    ++ V   ++ 
Sbjct: 561 EFLEEWSMENLEEIAPSAIGKTCKIFVNGCWVGIHSSPDHLMGTLRKLRRQVDVIVSEVS 620

Query: 662 ---DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGM- 715
              D+ D   +          P +  +    +L   +++  +       +    V +G+ 
Sbjct: 621 MIRDYRDQEIRIYTDAGRICRPLVIVEKGKLLLKRSHIELLKDKAYNRYSWQDLVLSGVV 680

Query: 716 ESVVAKSSGAAI----VAKRAGIVEQV-DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           E +        +     A+    V          I         ++           + +
Sbjct: 681 EYIDTLEEETVMIAMGPAEMQAAVNYCKTHTHCEIHPSMILGICASIIPFPDHNQSPRNT 740

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIA--------------DGPSTDLGDLALGRNMLVAFM 816
            Q+    Q   V + +   R D +A                      +L  G N +VA  
Sbjct: 741 YQSAMGKQAMGVYISNFHTRMDTLANVLYYPQKPLVATRSMEYLRFRELPAGINAIVAIA 800

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEE 871
            + GYN EDS++I+E  +    F S     ++       +  EE       ++   +   
Sbjct: 801 TYTGYNQEDSVIINESAIQRGFFRSEFYRTYKDQETRHGMDLEEVFEKPNPQNCQGMRHA 860

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G+I  G  V+  D+L+GK     E+    E        G++    RD S+ +
Sbjct: 861 IYDKLDDDGLIAPGTRVSGDDVLIGKTITLPENEDEMEG-------GQRRYTKRDASVFM 913

Query: 932 PSGVSGTVVDVRIFNRHGIDKNE 954
                G V   ++      + N+
Sbjct: 914 RRSEYGIV--DQVMVTWNNEGNK 934


>gi|40643994|emb|CAD90166.1| DNA-directed RNA polymerase II largest subunit [Gardenia sp. Oxelman
            2319]
          Length = 627

 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 132/748 (17%), Positives = 230/748 (30%), Gaps = 147/748 (19%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L     +            + +    N        EE +  +    +
Sbjct: 2    ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQAT 54

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +G +             +   R ++   D + +  V     L       D  R   
Sbjct: 55   KIFVNGCWVGIHRNPDLLVRTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSR 111

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  +   L+K +        E          +              +  I  V+ + 
Sbjct: 112  PLFIVEKQRLLIKKKDILALQQREYTDEFGWHDLVA-------------KGYIEYVDTEE 158

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N +   +                    PS  LG       + 
Sbjct: 159  EETTMISMTINDLMNSRLNPDEAYS-----------ETYTHCEIHPSLILG-------VC 200

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   ++I  ++                        
Sbjct: 201  ASIIPFPDHNQSPRNTYQSAMGKQAMG--MYITNYQ------------------------ 234

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 235  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQ 291

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        IF R   D+ ++  ++ +E+     R+          +          G
Sbjct: 292  SSIDRGFF-RSIFFRSYRDEEKKMGTLVKEEFGSPNRENTMGMRHGSYDKLDADGFAPPG 350

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T L                  QDE   +     +  + TS    E  
Sbjct: 351  TRVSGEDVIIGKTTSL-----------------PQDEAQGQASRYTRRDHSTSLRHSESG 393

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 394  IVDQVALTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 448

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 449  IEGISPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 489

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 490  ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 514

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG 
Sbjct: 515  FERVYNGHTGRIMGDLIFMGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGL 574

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 575  RFGEMERDCMIAHGAAHFLKERLFDQSD 602



 Score =  112 bits (281), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 73/486 (15%), Positives = 137/486 (28%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 5   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 64

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
                   +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 65  IHRNPDLLVRTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 123

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L      + +G+         D      + Y+   EEE   I+   + L    
Sbjct: 124 KKKDILALQQREYTDEFGWH--------DLVAKGYIEYVDTEEEETTMISMTINDLMNSR 175

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +E               E     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 176 LNPDE------------AYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 223

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +                           R   +  V                    
Sbjct: 224 QAMGMYITNYQL--------------------RMDTLAYV-------------------- 243

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 244 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAVVAIACY 278

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS+++++  +    F SI    +    +      +E        +   +     
Sbjct: 279 SGYNQEDSVIMNQSSIDRGFFRSIFFRSYRDEEKKMGTLVKEEFGSPNRENTMGMRHGSY 338

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D  G    G  V+  D+++GK T   +           A         RD S  +  
Sbjct: 339 DKLDADGFAPPGTRVSGEDVIIGKTTSLPQDE---------AQGQASRYTRRDHSTSLRH 389

Query: 934 GVSGTV 939
             SG V
Sbjct: 390 SESGIV 395


>gi|242392380|dbj|BAH80403.1| RNA polymerase subunit B' [Natronococcus amylolyticus]
          Length = 609

 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 121/595 (20%), Positives = 207/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVEHGYIEFIDAEEEEDIYVAVDEDDLNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYTHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L     D +G+  +Y G++GE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELREGLEQNGFDSAGKETMYSGISGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD     + G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFIHICGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 43.9 bits (102), Expect = 0.19,   Method: Composition-based stats.
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 23/106 (21%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + ++ A EEE+ Y+A     L+ED                          +
Sbjct: 92  FEDLVEHGYIEFIDAEEEEDIYVAVDEDDLNEDH-----------------------THL 128

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 129 EIDPQLIFGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 174


>gi|111054587|gb|ABH04351.1| RNA polymerase beta subunit [Proteus penneri]
          Length = 331

 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 201/329 (61%), Positives = 250/329 (75%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+ ALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRIYALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V +  VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVENNAVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS LD+D  F EELV CR  GE  L  R+++ ++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA   G   VAKR G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDXGVTAVAKRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +V+ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 243 VVQYVDASRIVIKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGEPVDRGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 303 LADGPSTDLGELALGQNMRVAFMPWNGYN 331


>gi|6606099|gb|AAF19062.1|AF107790_1 DNA-dependent RNA polymerase II RPB140 [Podospora anserina]
          Length = 934

 Score =  327 bits (839), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 168/1038 (16%), Positives = 301/1038 (28%), Gaps = 157/1038 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  K     G  ++ +  + +     +     ++   G V DE  L
Sbjct: 37   LEKGSRLISSLQMKLHTKASNEKGRLANTVS-VTLPYVREDVSLAIVFRALGIVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A+          +DR+ AL  I +    G+ +      
Sbjct: 96   NHICYDRKDTQMLEALRPCIEEAF--------CIQDREIALDFIGKR---GNGNMGQNRM 144

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +          K  L  +              +     +   +  ++  L+    G+   
Sbjct: 145  NRIRAAKDLLQKEMLPHI-----------SQTEGCETRKAFFLGYMVNKLLQCALGRRDT 193

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R  + RM + +    +              I A  + +
Sbjct: 194  DDRDHFGKKRLDLAGPLLAKLFRGVVRRMTQDLMGYMKRCLDTNKHFTLALGIKANTLTN 253

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            A+     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 254  ALKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKP 309

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    V+     +    +       V  +   
Sbjct: 310  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPADPIVDFMTARGMDVLEEYEP 369

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            L A      ++      +  D      LV        I      +  I     ++ S A 
Sbjct: 370  LRAPNATKVFVNGTWVGVHNDPKQLVTLVQDLRRKNVISFEVSLVRDIREREFKIFSDAG 429

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             ++  L   +          + Q +      A                      ++G +E
Sbjct: 430  RVMRPLFTVEQEEKGNHGVEKGQLILNKDHIARLQRDKELGKYHPDYWGWQGLLKSGAIE 489

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA       +                + F     +   N R   KV            
Sbjct: 490  YLDAEEEETTMICMTPQDLDDFRMT--KLGFHIETTSGQGNNRIRTKVNKTTHMYTHCEI 547

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             P+  LG       +  + +P+  +N          M  + +     +  +         
Sbjct: 548  HPAMLLG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM----- 593

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 594  ----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 631

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D  +R      E  E   R       
Sbjct: 632  LCYSGYNQEDSVVMNQSSIDRGIF-RSLFFRSYTDCEKRVGINIVEMFEKPTRGDTLRLK 690

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +       I  G           K++ ++ D                 E  QR  +
Sbjct: 691  HGTYDKLDADGIIAPGIRVSGEDIIIGKTSPINPD---------------NAELGQRQQQ 735

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +K    T     E    + +      D      +R VKV V   +  Q GDK A RHG 
Sbjct: 736  HVKRDASTPLRSTESGIVDSVVLTTNQD-----GMRYVKVRVRTTKIPQIGDKFASRHGQ 790

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G +  +  
Sbjct: 791  KGTIGLTYRMEDMPFTAEGITPDIIINPHAIPSRMTIAHLVECLLSKVATLKGLEGDATP 850

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E+   +                                      
Sbjct: 851  FTDVTVDSVSDLLR--EQGYQSRGF----------------------------------- 873

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                 +L        G +    G            G  Y  +L HMV DK++AR+ G   
Sbjct: 874  ----EIL------YHGHT----GR---KLRAQCFFGPTYYQRLRHMVDDKIHARARGPVQ 916

Query: 1277 LVTQQPLGGKSNRGGQRL 1294
            ++T+QP+ G++  GG R 
Sbjct: 917  IMTRQPVEGRARDGGLRF 934


>gi|326523005|dbj|BAJ88548.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 263

 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 84/312 (26%), Positives = 126/312 (40%), Gaps = 74/312 (23%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ
Sbjct: 1    VRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTIGQ 60

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  +G     +GK+                                            
Sbjct: 61   LIECIMGKVAAHMGKEGD------------------------------------------ 78

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP F     + I+  L        G   +Y+G TG      + +G  Y
Sbjct: 79   -----------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTY 126

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L
Sbjct: 127  YQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAFFLKERL 186

Query: 1316 TIKSDDVVGRTRVYE-----SIV---------AG----NDTFETGTPESFNVLVKEMQAL 1357
              +SD    R  V E     +I           G     D  +   P +  +L +E+ A+
Sbjct: 187  FDQSD--AYRVHVCEKCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAM 244

Query: 1358 GLSIDLENSRTK 1369
             ++  +     K
Sbjct: 245  AIAPRMLTHEVK 256


>gi|253778912|emb|CAY90191.1| RNA polymerase subunit B [Acinetobacter sp. D10]
          Length = 280

 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 126/283 (44%), Positives = 176/283 (62%), Gaps = 5/283 (1%)

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            R++ +L GQ +  G    K+   L+ D++S        +    DE +   +  ++V  + 
Sbjct: 1    RIVRLLKGQESNGGGTT-KRGDKLTEDVLSNLELVDLLEVQPADEGIAERLTQIQVFLKE 59

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHG       IL
Sbjct: 60   KSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGKXXXXXNIL 119

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG KI  ++ + +    
Sbjct: 120  PVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIDKMMKEQRT--- 176

Query: 1165 ISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            +  LR FL+K+    G   E +    D+ +L ++   + GVP++TPVFDGA+E  I  +L
Sbjct: 177  VLELREFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPVFDGAEEGQIKELL 236

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             +  +  +GQ++LYDG TGE FDRPVTVGY+YMLKLNH+V DK
Sbjct: 237  ELGGISRTGQTVLYDGRTGERFDRPVTVGYMYMLKLNHLVDDK 279


>gi|70606496|ref|YP_255366.1| DNA-directed RNA polymerase subunit B [Sulfolobus acidocaldarius DSM
            639]
 gi|73920765|sp|P11513|RPOB_SULAC RecName: Full=DNA-directed RNA polymerase subunit B
 gi|68567144|gb|AAY80073.1| DNA directed RNA polymerase subunit B [Sulfolobus acidocaldarius DSM
            639]
          Length = 1126

 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 121/619 (19%), Positives = 206/619 (33%), Gaps = 102/619 (16%)

Query: 777  NQRPLVKVGD--EVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            N  PLV   D  +++  +I  D        +  D     N  VA  P         + I 
Sbjct: 582  NGTPLVDTEDIKKLKNGEITFDDLVKQGKIEFIDAEEEENAYVALNPQDLTPDHTHLEIW 641

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
               +   + + I   E     R+T              S   ++         +      
Sbjct: 642  PSAILGIIASIIPYPEHNQSPRNTYQSAMAKQSLGLYASNYQIR---TDTRAHLLHYPQM 698

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
              +    +   G +        + AI      ++ D+ +   S +   +     F     
Sbjct: 699  PLVQTRMLGVIGYNDRPAGANAILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFF----- 753

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSR-LMEILCGQNAVSGPKGFKKSTVLS 1009
                R  S E  +      DK        +    +    +L     VS     K   VL 
Sbjct: 754  ----RLYSTEEVKYPGGQEDKIVTPEAGVKGYKGKDYYRLLEDNGVVSPEVEVKGGDVLI 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              +       ++ + + +  K   ++  +    E     L    +               
Sbjct: 810  GKVSPPRFLQEFKELSPEQAKRDTSI--VTRHGENGIVDLVLITE------------TLE 855

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
              ++VKV V   R  + GDK A RHG KG+V  ++   DMP+   G   DI+LNP  +PS
Sbjct: 856  GNKLVKVRVRDLRIPEIGDKFATRHGQKGVVGILIDQVDMPYTAKGIVPDIILNPHALPS 915

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +GQI E   G      GK +                                     
Sbjct: 916  RMTIGQIMEAIGGKYAALSGKPVD------------------------------------ 939

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP  +    + +   +           ++YDG TG+     +
Sbjct: 940  -----------------ATPFLETPKLQEMQKEILKLGHLPDSTEVVYDGRTGQKLKSRI 982

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
              G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+  +G A 
Sbjct: 983  LFGIVYYQKLHHMVADKMHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAM 1042

Query: 1310 VLQEMLTIKSD-------DVVG------RTR-VYESIVAGND--TFETGTPESFNVLVKE 1353
            ++++ L   SD       D  G      R++  Y   V G+           +F +L++E
Sbjct: 1043 LIKDRLLDNSDKAVVYICDQCGYVGWYDRSKNRYVCPVHGDKSVLHPVTVSYAFKLLIQE 1102

Query: 1354 MQALGLSIDLENSRTKNSA 1372
            + ++ +S  L      N  
Sbjct: 1103 LMSMVISPRLILGEKVNLG 1121



 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 141/991 (14%), Positives = 294/991 (29%), Gaps = 219/991 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+     S++ FL             LQ        I        ++     ++ P    
Sbjct: 20  LVRQHLDSFNDFLRNK----------LQQVIYEQGEIVTEVPGLKIKLGKIRYEKPSIRE 69

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  +    +   R+LTY+ P+ +++  +  +++               IY+GDLP+
Sbjct: 70  TDKGPMREITPMEARLRNLTYSSPIFLSMIPVENNIEGEPI----------EIYIGDLPI 119

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKG 170
           M K                         G F++ G ++++++Q   +     + +     
Sbjct: 120 MLKSVADPTSNLPIDKLIEIGEDPKDPGGYFIVNGSEKVIIAQEDLATNRVLVDYGKSGS 179

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-------------KVPVTSF 217
             +   K+  +      +             + V I+R +             ++P    
Sbjct: 180 NITHVAKVTSSAAG--YR-------------VQVMIERLKDSTIQISFATVPGRIPFAII 224

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           + ALG  ++         IVY+   D          L   + ++S+   +D     +  G
Sbjct: 225 MRALGFVTD-------RDIVYAVSLDPQIQNELLPSLEQASSITSAEEALDFIGNRVAIG 277

Query: 278 KKLTSGLLK---SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-- 332
           +K  + + K    + +  +  LG + +              +  E+Y+   +  D+    
Sbjct: 278 QKRENRIQKAEQVIDKYFLPHLGTSPEDRKKKGYYLASAVNKILELYLGRREPDDKDHYA 337

Query: 333 ---LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              +            + +   V +  Y          +    AL+         D+ T 
Sbjct: 338 NKRVRLAGDLFTSLFRVAFKAFVKDLVYQLEKSKVRGRRLSLTALVR-------ADIITE 390

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            +  ++    +          + R      L+      V  + +       + L   + G
Sbjct: 391 RIRHALATGNWVGGRTGVSQLLDRTNWLSMLSHLRRV-VSSLARGQPNFEARDLHGTQWG 449

Query: 450 K-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +    +  +   +  V+++  + +    +    +ER   E       D +      N   
Sbjct: 450 RMCPFETPEGPNSGLVKNLALLAQVSVGINESVVERVAYELGVVSVEDVIRRISEQNEDV 509

Query: 509 VVSAVCE--FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                    +     L   E+      +I  +RR   L         A   + +VH    
Sbjct: 510 EKYMSWSKVYLNGRLLGYYEDGKELAKKIRESRRQGKLSDEVNVAYIATDYLNEVHIN-- 567

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
              C A       I +V++ T          ++       D      + ++ A EEEN Y
Sbjct: 568 ---CDAGRVRRPLI-IVNNGTPLVDTEDIKKLKNGEITFDDLVKQGKIEFIDAEEEENAY 623

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +A     L  D                          ++  P  ++ I AS+IP+ E++ 
Sbjct: 624 VALNPQDLTPDH-----------------------THLEIWPSAILGIIASIIPYPEHNQ 660

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           S R      M +Q++ L  +                                        
Sbjct: 661 SPRNTYQSAMAKQSLGLYASNYQI------------------------------------ 684

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                   + + +  Y               Q PLV+                    D  
Sbjct: 685 -----RTDTRAHLLHYP--------------QMPLVQTRMLGVIG----------YNDRP 715

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            G N ++A M + GYN EDS+++++  +   ++ S     +         G E+      
Sbjct: 716 AGANAILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFFRLYSTEEVKYPGGQEDKIVTPE 775

Query: 867 -----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                   ++  + +++ G++    EV  GD+L+GK++P        E    +A      
Sbjct: 776 AGVKGYKGKDYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK----- 830

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              RDTS+    G +G V  V I      +K
Sbjct: 831 ---RDTSIVTRHGENGIVDLVLITETLEGNK 858


>gi|318603073|emb|CBJ04591.1| RNA polymerase beta subunit [Pseudomonas sp. R-38101]
          Length = 327

 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 193/326 (59%), Positives = 251/326 (76%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++
Sbjct: 62  ETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASA 121

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           ++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 122 TMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 181

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 182 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEV 241

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM 
Sbjct: 242 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMR 301

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDV 838
           +AFM W+G+NFEDS+ +SER+V ED 
Sbjct: 302 IAFMAWNGFNFEDSICLSERVVQEDR 327


>gi|4867862|emb|CAB43072.1| RNA polymerase II [Logania vaginalis]
          Length = 262

 Score =  327 bits (839), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTGEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|296109332|ref|YP_003616281.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus infernus
            ME]
 gi|295434146|gb|ADG13317.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus infernus
            ME]
          Length = 629

 Score =  327 bits (838), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 107/500 (21%), Positives = 181/500 (36%), Gaps = 97/500 (19%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + AI   +  ++ D  +   S V    +    F R       R    + 
Sbjct: 195  GFDERPAGQNFVVAIMSYEGFNMEDAIIFNKSAVDRG-LGRSTFFRTYEACERRYPGGQM 253

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++IE+ +++       +  N    L + L     VS     K   VL           ++
Sbjct: 254  DKIEIPSKE-------VRGNKPDELYKNLEEDGIVSVESFVKSGEVLVGKTSPPRFLEEY 306

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                     +   ++  +          E+ + +K+   +          ++VKV V   
Sbjct: 307  --------DITIQIKPQRRDSSVCVRHGEEGYVDKVMITE-----TKEGNKLVKVKVRDL 353

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  ++  EDMPF + G   DI++NP G+PSRM VGQ+ E   
Sbjct: 354  RVPELGDKFASRHGQKGVIGLLVNQEDMPFTESGIVPDIIINPHGIPSRMTVGQLLEMIG 413

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++I   I + +    +      L                             
Sbjct: 414  GKVGSLEGRRIDGTIFNGEEEMSLREALEKLGFKHHGREVM------------------- 454

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+       TG+  +  + +G IY  KL+H
Sbjct: 455  ----------------------------YDGK-------TGKKLEVEIYIGVIYYQKLHH 479

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA +L+E L  +SD 
Sbjct: 480  MVAGKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDP 539

Query: 1321 -DV-----VG-------RTRVYESIVAGN--------DTFETGTPESFNVLVKEMQALGL 1359
             DV      G       R ++    V G            +   P +F +LV E++++ +
Sbjct: 540  YDVYICSNCGDFAIFDFRRKIKYCPVCGEVESPFVDRKMAKIRIPYAFKLLVDELKSMCI 599

Query: 1360 SIDLENSRTKNSAKMEEIPD 1379
            S               E  +
Sbjct: 600  SPKFRVKDKVELEDFPEFIE 619



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 80/423 (18%), Positives = 139/423 (32%), Gaps = 112/423 (26%)

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI---ETPY 602
                +       + + P +       E ++ H       +     V   G     E   
Sbjct: 18  PEEFVKQIREARRKGLIPKYTTVAYHEENNDIHINTDAGRIVRPLIVVENGKPKLTEEHI 77

Query: 603 RKVCDGKVT-------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            K+  G++T         + YL A EEEN YIA +   L+                    
Sbjct: 78  EKLKKGEITFDDLVKEGVIEYLDAEEEENAYIAVSEEELN-------------------- 117

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              EK   ++ +P  ++ I A + P+ E++ + R+ M   M +Q++    +   +     
Sbjct: 118 ---EKHTHLEINPLTILGIGAGIAPYPEHNSAPRITMAAAMGKQSLGFPMSNIKW----- 169

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                                  +      Y             
Sbjct: 170 ------------------------------------RMDTRGHYLHYP------------ 181

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q P+VK     +  DI+         +   G+N +VA M + G+N ED+++ ++  V 
Sbjct: 182 --QVPIVKT----KHQDIL------GFDERPAGQNFVVAIMSYEGFNMEDAIIFNKSAVD 229

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIP------NVSEEGLKNIDECGIICVGAEVN 889
             +  S     +E   R    G  +   +IP      N  +E  KN++E GI+ V + V 
Sbjct: 230 RGLGRSTFFRTYEACERRYPGGQMD-KIEIPSKEVRGNKPDELYKNLEEDGIVSVESFVK 288

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            G++LVGK +P               I  +     RD+S+ V  G  G V  V I     
Sbjct: 289 SGEVLVGKTSPPRFLEE-------YDITIQIKPQRRDSSVCVRHGEEGYVDKVMITETKE 341

Query: 950 IDK 952
            +K
Sbjct: 342 GNK 344


>gi|190341737|gb|ACE74945.1| RNA polymerase beta subunit [Enterobacter asburiae]
 gi|190341739|gb|ACE74946.1| RNA polymerase beta subunit [Enterobacter asburiae]
 gi|190341741|gb|ACE74947.1| RNA polymerase beta subunit [Enterobacter sp. R11-2]
 gi|256861703|gb|ACV32535.1| RNA polymerase beta subunit [Enterobacter mori]
 gi|256861705|gb|ACV32536.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 332

 Score =  327 bits (838), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 208/332 (62%), Positives = 260/332 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           + V R D++ADGPSTDLG+LALG+NM VAFMP
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMP 332


>gi|111054621|gb|ABH04368.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 336

 Score =  327 bits (838), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 205/336 (61%), Positives = 259/336 (77%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+E PYR V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLEXPYRLV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++++D
Sbjct: 121 RDGLVTDEIHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVEYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAV  L+A+   VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVXTLRADKXLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VA+R G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V +G
Sbjct: 241 TAVARRGGSVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + V R D++ADGPSTDLG+LALG+NM VAFMPW+GY
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 336


>gi|67550157|gb|AAY68425.1| RNA polymerase subunit B [Clostridium sporogenes]
          Length = 553

 Score =  327 bits (838), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 228/377 (60%), Positives = 289/377 (76%), Gaps = 3/377 (0%)

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLD 635
            NIGL++SL+SFA+VN +GFIETPYR++     +VT  + YL+A EE+N Y+AQANS L+
Sbjct: 1   PNIGLINSLSSFAKVNKFGFIETPYRRIDHETGRVTEQIDYLTADEEDNYYVAQANSPLN 60

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            DG+F  + V  R  G+  +  + ++D++D SPKQVVS A + IPFLENDDSNR LMG N
Sbjct: 61  PDGTFVNDEVVGRFRGDNTVFNKAQMDYMDVSPKQVVSAATACIPFLENDDSNRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPLL  EAPFVGTGME V A+ SGAA+VAK  GIVE V+A  I +R +E      
Sbjct: 121 MQRQAVPLLNPEAPFVGTGMEHVDARDSGAAVVAKYDGIVEHVEARSIHVRRIEVVDGKE 180

Query: 756 TSGVDI-YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             G    Y+L KF RSNQ T  NQRPLVKVG+ V+  DI+ADGPS + G+LALGRN+LVA
Sbjct: 181 VKGDLTKYKLQKFIRSNQGTSYNQRPLVKVGERVKPRDILADGPSMEKGELALGRNVLVA 240

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           FM W+G+N+ED++++SER+V +DV+TS+HIEE+E  +RDTKLGPEEITRDIPNV E+ L+
Sbjct: 241 FMTWNGFNYEDAVIMSERLVKDDVYTSVHIEEYESESRDTKLGPEEITRDIPNVGEDALR 300

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           N+DE GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G
Sbjct: 301 NLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHG 360

Query: 935 VSGTVVDVRIFNRHGID 951
             G ++DV++FNR   D
Sbjct: 361 AGGIILDVKVFNREDGD 377



 Score =  326 bits (836), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 140/467 (29%), Positives = 201/467 (43%), Gaps = 77/467 (16%)

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V      SIH+   EV+      G     +    +      + ++  ++ VG  V P D
Sbjct: 159  IVEHVEARSIHVRRIEVVDGKEVKGDLTKYKLQKFIRSNQGTSYNQRPLVKVGERVKPRD 218

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            IL    +   +  +     +L A       +  D  +     V   V        +  + 
Sbjct: 219  ILADGPS-MEKGELALGRNVLVAFMTWNGFNYEDAVIMSERLVKDDVYTSVHIEEYESES 277

Query: 953  NERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
             +  +  E     I  +  D     DE+ I+      R  +IL G+    G         
Sbjct: 278  RDTKLGPEEITRDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEER 337

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L   +  E  R      +++       +                    K+   + GD++P
Sbjct: 338  LLHAIFGEKARE-VRDTSLRVPHGAGGI----------------ILDVKVFNREDGDELP 380

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGV
Sbjct: 381  PGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGV 440

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRMN+GQ+ E HLG A   LG  + + + D     D+                      
Sbjct: 441  PSRMNIGQVLELHLGMASRYLGVHMATPVFDGANEEDVW--------------------- 479

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  +  A   + G                             ++ILYDG +GEPFD 
Sbjct: 480  ----ETMEEAGMNRDG-----------------------------KTILYDGRSGEPFDN 506

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             V+VG +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR 
Sbjct: 507  RVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRF 553


>gi|4867866|emb|CAB43074.1| RNA polymerase II [Mitreola petiolata]
          Length = 261

 Score =  327 bits (838), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 41   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTGEGITPDIIVNPH 100

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 101  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 128

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 129  ---------------------ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPL 166

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 167  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 226

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 227  GAAHFLKERLFDQSD 241


>gi|6606125|gb|AAF19075.1|AF107803_1 DNA-dependent RNA polymerase II RPB140 [Curvularia brachyspora]
          Length = 942

 Score =  327 bits (838), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 157/1054 (14%), Positives = 320/1054 (30%), Gaps = 180/1054 (17%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY----VAEDIVNGETGEIYIEAGDVID 329
            +E G +L S       E  +         + G +    +     +     ++   G V D
Sbjct: 36   VEKGTRLISSFNIKWAENSLAG---PGKRIPGPFAYATLPYIKADVPMAIVFRALGIVSD 92

Query: 330  EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            E+ L  I +       +  +        +         +DR+ AL  I +          
Sbjct: 93   EEILSHIVYDRTDTQMLELLKPSIEEGSV--------VQDRETALDFIAKRGANSGTKDR 144

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +  +          +  L  + +            +     +      +I  L+    G
Sbjct: 145  RLKFA-----RDIMQREFLPHISQK-----------EGQDTRKAYFFGYMIHRLLQCVLG 188

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAK 507
            +   DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  + A 
Sbjct: 189  RRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYLQRCVENNQDFNVQMAVKAS 248

Query: 508  PVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             + + +     +               +SQ+       S ++H RR +      V R   
Sbjct: 249  IITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGK 304

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTN 612
              + R +H +H+G +CPAET EG   GLV +L+    V+          +    + ++  
Sbjct: 305  LAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLE 364

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQV 671
            +       +    ++      +  +      +V        +      I D  D   K  
Sbjct: 365  EYDQNQNPDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIF 424

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
                  + P    ++  R     ++   ++    LKAE     T       +   A    
Sbjct: 425  TDAGRVMRPLFVVENDIRKPNRNHLIFTKEISNKLKAEQSETSTRQGWSQEEVEQATYGW 484

Query: 730  K---RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI---YRLMKFQRSNQNTCVNQRPLVK 783
            +   + G+VE +DA       +    +      ++       +     ++     +PL  
Sbjct: 485  RGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMKMGLPAAERSTEGKDRLRRLKPL-- 542

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                +         P+  LG       +  + +P+  +N          M  + +  ++ 
Sbjct: 543  PDPRIHSYTHCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALT 595

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
                 +                                  V             +     
Sbjct: 596  NFALRMETMMN-----------------------------VLYYPQKPLATTRSMEYLKF 626

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              +   +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    
Sbjct: 627  RELPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNV 682

Query: 964  IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E   +    + + L    Y +L +   +  G           K+  +++D      ++ 
Sbjct: 683  LEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAQELGQKTT 742

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                      ++     +  Q                             LR VKV    
Sbjct: 743  MHTKRDVSTPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRT 782

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  
Sbjct: 783  TKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVTPDLIINPHAIPSRMTIAHLVECL 842

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            L       G++  +          IS                          +L  A   
Sbjct: 843  LSKVGAITGQEGDATPFTDVTVDQIS-------------------------QLLEDAGYQ 877

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            K G  +                             +Y+G TG+     + +G  Y  +L 
Sbjct: 878  KRGFEI-----------------------------MYNGHTGKKLRTQIFLGPTYYQRLR 908

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            HMV DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 909  HMVDDKIHARARGPLQILTRQPVEGRARDGGLRF 942



 Score =  128 bits (322), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 106/838 (12%), Positives = 248/838 (29%), Gaps = 110/838 (13%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK---DII- 202
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K   + + 
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFNIKWAENSLA 56

Query: 203 ----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFW 245
                           +++ D    VP+     ALG+   EEILS        +Q  +  
Sbjct: 57  GPGKRIPGPFAYATLPYIKAD----VPMAIVFRALGIVSDEEILSHIVYDRTDTQMLELL 112

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------ 299
              +    ++   + +   +         +  +   +  +  ++ + +  +         
Sbjct: 113 KPSIEEGSVVQDRETALDFIAKRGANSGTKDRRLKFARDI--MQREFLPHISQKEGQDTR 170

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYI 358
                G  +   ++    G    +  D   +K L+           IL++  + +   Y+
Sbjct: 171 KAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYL 229

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           +  +  +++ + + A+           + T  +  S+    + D  K   +  G  ++  
Sbjct: 230 QRCVENNQDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLN 281

Query: 419 RLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           R    +      R          +     L N    +         +   + + L     
Sbjct: 282 RYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCY 341

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           + +      I + ++  ++  +   D                   +         ++ + 
Sbjct: 342 VSVGSDASPIIDFMTQRNMQLLEEYDQNQNPDATKVF---VNGVWVGVHSNAQQLVTVVQ 398

Query: 537 HTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
             RR   L  +  + R     E + +       + P    E        +   F +    
Sbjct: 399 ELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVVENDIRKPNRNHLIFTK---- 453

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                                    E  N+  A+ + +    G   EE+          L
Sbjct: 454 -------------------------EISNKLKAEQSETSTRQGWSQEEVEQATYGWR-GL 487

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +    ++++DA  ++   I  S     E  +    L       +    L+   P     +
Sbjct: 488 IQDGVVEYLDAEEEETAMITFSPEDLEEWREMKMGLPAAERSTEGKDRLRRLKPLPDPRI 547

Query: 716 E-SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DIYRLMKFQRSNQN 773
                 +   A I+   A I+   D  +    + +  +     GV      ++ +     
Sbjct: 548 HSYTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNFALRMETMMNV 607

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q+PL                      +L  G+N +VA   + GYN EDS+++++  
Sbjct: 608 LYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIMNQSS 657

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEV 888
           +   +F S+    +    +   +   E        D   +       +D+ G++  G  V
Sbjct: 658 IDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRV 717

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           +  DI++GK  P         +K             RD S  + S  +G V  V    
Sbjct: 718 SGDDIIIGKTAPIAADAQELGQKT-------TMHTKRDVSTPLRSTENGIVDQVLFTT 768


>gi|4867870|emb|CAB43084.1| RNA polymerase II [Spigelia anthelmia]
          Length = 260

 Score =  327 bits (838), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTXEGVTPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 128  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 226  GAAHFLKERLFDQSD 240


>gi|86451157|gb|ABC96801.1| RNA polymerase II [Calycophyllum candidissimum]
          Length = 214

 Score =  327 bits (838), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 199  GAAHFLKERLFDQSD 213


>gi|73697667|gb|AAZ81450.1| RNA polymerase beta subunit [Mycoplasma caviae]
          Length = 591

 Score =  327 bits (838), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 211/423 (49%), Positives = 297/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNKRRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE     +  +  R
Sbjct: 61  AQVNKYGFLQTPYFKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDEKNRLVDNQLTMR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   E++DFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL  EA
Sbjct: 121 HNYSYIIGKPEEVDFIEVAPNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S    VAK  G+VE VD  +I +R+ +G LD        Y L  FQ
Sbjct: 181 PFVATGIEADIAKYSSGNFVAKNDGVVEFVDGKKIKVRNQKGALD-------TYYLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T V+QRPLVK G EV++ D++ DG S   G+LALG+N++VAF  + GYN+ED+++
Sbjct: 234 RSNQDTVVHQRPLVKEGQEVKKGDLLVDGSSFKDGELALGKNVVVAFTTYKGYNYEDAVI 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ +G+EV
Sbjct: 294 LNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTLDIPNVSKYATRHLDEYGIVRIGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+  ++  +V+DTSL+V +G +GTV+ V + +R 
Sbjct: 354 VPGDVLVGRVSPKGDDNPSQEEKLLSAVLQQRQQNVKDTSLKVKNGHNGTVIGVDVLSRD 413

Query: 949 GID 951
             D
Sbjct: 414 NGD 416



 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 140/527 (26%), Positives = 226/527 (42%), Gaps = 86/527 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L+   P+     E  +   +     
Sbjct: 141  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLIPEAPFVATGIEADIA--KYSSGN 198

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + EF V  +  K+  ++   D   +      N D    +  ++  G EV  GD
Sbjct: 199  FVAKNDGVVEF-VDGKKIKVRNQKGALDTYYLKNFQRSNQDTVVHQRPLVKEGQEVKKGD 257

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   + K +  +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 258  LLVDGSSFK-DGELALGKNVVVAFTTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQF 316

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++++   +   A    DE  I+         ++L G+ +  G     +  
Sbjct: 317  RTSKAGDDE-LTLDIPNVSKYATRHLDEYGIVRIGSEVVPGDVLVGRVSPKGDDNPSQEE 375

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++ +  ++           V+     +K  +  +   ++   ++       GD +
Sbjct: 376  KLLSAVLQQRQQN-----------VKDTSLKVKNGHNGTVIGVDVLSRD------NGDTL 418

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 419  EDGIEKIVKVSIAIKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 478

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   LG K  +   D                    G   E+I 
Sbjct: 479  VPSRMNIGQVLEIHLGMAAKKLGCKFVTPTFD--------------------GVKKEEIH 518

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
            D   ++ L ++ +     P++   FD                                  
Sbjct: 519  DVTMEAGLPLSGKQWLIDPITGNKFD---------------------------------- 544

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 545  KPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 591


>gi|242392360|dbj|BAH80393.1| RNA polymerase subunit B' [Natrialba chahannaoensis]
          Length = 609

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 124/595 (20%), Positives = 210/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDIYVAVEEDDLNEDHTHLEIDPQLIFSIGSGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + +    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASIE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTITLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE A+   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESALRDGLEEAGFDSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    +V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFINVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCEEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 43.5 bits (101), Expect = 0.25,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 66/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  +  G +E       D      V ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-PRISQQEIEALRD--GDLE-----FEDLVDHGYVEFIDAEEEEDIYVAVEEDDLN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ + SI + +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFSIGSGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|52538157|emb|CAH19180.1| RNA polymerase beta-subunit [Pseudomonas veronii]
 gi|52538159|emb|CAH19181.1| RNA polymerase beta-subunit [Pseudomonas veronii]
          Length = 332

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 197/332 (59%), Positives = 256/332 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNEKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFN 332


>gi|242392386|dbj|BAH80406.1| RNA polymerase subunit B' [Natronolimnobius baerhuensis]
          Length = 609

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 122/596 (20%), Positives = 208/596 (34%), Gaps = 105/596 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++ VA       +    + I  +++       I   E     R 
Sbjct: 95   LVEHGYIEFIDAEEEEDIYVAVDEDDLNDDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYNHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L     + +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDEDELRDGLEDNGFNSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD             
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREYINICAQCGMS 557

Query: 1321 ---DVVGRTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY      E      D  E     +F +L+ EM+ALG++  LE   
Sbjct: 558  AVENVEQR-RVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELED 607



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 65/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I  +RR+  +        R       ++        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIRESRRIGDVSDMVNVSVRDRTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      ++     A  +  G +E       D      + ++ A EEE+ Y+A     L+
Sbjct: 71  ENGE-PRITDEEIQALKD--GDLE-----FEDLVEHGYIEFIDAEEEEDIYVAVDEDDLN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 DDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|52694405|emb|CAG38042.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 325

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 198/326 (60%), Positives = 253/326 (77%), Gaps = 1/326 (0%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 179

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 180 ASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVI 239

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA R+V+R  +G+++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+A
Sbjct: 240 DSVDASRVVVRVHDGEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVVERGDIMA 299

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGY 821
           DGPSTD+G+LALG+NM VAFMPW+GY
Sbjct: 300 DGPSTDMGELALGQNMRVAFMPWNGY 325


>gi|284174418|ref|ZP_06388387.1| DNA-directed RNA polymerase subunit B [Sulfolobus solfataricus 98/2]
 gi|167744883|pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|167744894|pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|239782145|pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|239782158|pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|261601839|gb|ACX91442.1| DNA-directed RNA polymerase subunit B [Sulfolobus solfataricus 98/2]
          Length = 1124

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 114/587 (19%), Positives = 193/587 (32%), Gaps = 99/587 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 613  IEYLDAEEEENAYVALEPNDLTPDHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 672

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 673  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVMSF 729

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 730  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEAGV 780

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 781  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 838

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 839  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRIPTIGDKFASRHGQKG 886

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   DI+LNP  +PSRM +GQI E   G                
Sbjct: 887  VIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAA------------ 934

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 935  -----------------------------------------LSGNIVDATP-FYKTPIEQ 952

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           ++YDG TG+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 953  LQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHARARGPVQIL 1012

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------- 1324
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD       D  G       
Sbjct: 1013 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTMIYVCDQCGYIGWYDK 1072

Query: 1325 -RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             + + Y   + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1073 NKNK-YVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLVLEDK 1118



 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 176/1161 (15%), Positives = 347/1161 (29%), Gaps = 234/1161 (20%)

Query: 1    MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
            MA  +  +   RV + + K+        L+     SY+ F+             LQ    
Sbjct: 1    MASNLTIDERWRVIEAYFKSKG------LVRQHLDSYNDFVRNK----------LQEIID 44

Query: 61   SVFPITAFSGAAMLEFVSYEFDPPK----------FDVDDCLWRDLTYAVPLKITLRLIV 110
                I        +         P+              +   R+LTYA PL +T+  + 
Sbjct: 45   EQGEIPTEIPGLKVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVE 104

Query: 111  FDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVI 146
             +++             + +Y+GDLP+M K                         G F++
Sbjct: 105  NNIEAEP----------EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIV 154

Query: 147  KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP----DQGLWMDIEFDSKDII 202
             G +R++V+Q   +P      D G+   +  + +  +II      + + + IE       
Sbjct: 155  NGSERVIVTQEDLAPNRVLV-DTGKTGSN--ITHTAKIISSTAGYR-VPVTIERLKDGTF 210

Query: 203  HVRIDRRR-KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            HV       K+P    + ALG+ ++         IVY+   D          L   + ++
Sbjct: 211  HVSFPAVPGKIPFVILMRALGILTD-------RDIVYAVSLDPEVQNELFPSLEQASSIA 263

Query: 262  SSLVDIDTGEQVIESGKKLTSGLLK---SLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
            +    +D     +  G+K  + + K    + +  +  LG +++              +  
Sbjct: 264  NVDDALDFIGSRVAIGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVI 323

Query: 319  EIYIEAGDVIDEKS-----LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
            E+Y+   +  D+       L            + +   V +  Y          K    A
Sbjct: 324  ELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKA 383

Query: 374  LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L+      RP D+ T  +  ++    +          + R      L+      +  + +
Sbjct: 384  LV------RP-DIVTERIRHALATGNWVGGRTGVSQLLDRTNWLSMLSHLRRV-ISSLAR 435

Query: 434  EDIIAIIKILVDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                   + L   + G+    +  +   +  V+++  M +    +    +E+++ E    
Sbjct: 436  GQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGVV 495

Query: 493  VDIDSV-MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
               + +    +    +       +   + +L    +    L+     RR        V  
Sbjct: 496  PVEEVIRRVTEGGEDQNEYLKWSKVILNGRLIGYYQDGGELANKIRERRRKGEISDEVNV 555

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 +            C +       I + +       +     +E+      D    
Sbjct: 556  GHIVTD----FINEVHVNCDSGRVRRPLIIVSNG-NPLVTIEDIEKLESGAITFDDLVRQ 610

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
              + YL A EEEN Y+A   + L  D                          ++     +
Sbjct: 611  GKIEYLDAEEEENAYVALEPNDLTPDH-----------------------THLEIWSPAI 647

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
            + I AS+IP+ E++ S R      M +QA+ L  A                         
Sbjct: 648  LGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQL--------------------- 686

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                   + + +  Y               QRPLV    + R  
Sbjct: 687  --------------------RTDTRAHLLHYP--------------QRPLV----QTRAL 708

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            DII             G N ++A M + GYN EDS++++   V   ++ S     +    
Sbjct: 709  DIIGYTN------RPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEE 762

Query: 852  RDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                 G E+              +E  + +++ G++    EV  GD+L+GK++P      
Sbjct: 763  VKYPGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQE 822

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
              E    +A         RDTS+    G  G V              +  +  E  +   
Sbjct: 823  FKELSPEQAK--------RDTSIVTRHGEMGIV--------------DLVLITETAEGNK 860

Query: 967  LARDKDDEQVI--LDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            L + +  +  I  +     SR   + + G         +    V+   +++ +       
Sbjct: 861  LVKVRVRDLRIPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMT 920

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                 E +     +L      +    +   +    +I     +P                
Sbjct: 921  LGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILRYGYLPDATE------------ 968

Query: 1084 IQSGDKMAGRHGNKGIVSRIL 1104
                D   GR G K I SRI 
Sbjct: 969  -VVYD---GRTGQK-IKSRIY 984


>gi|4867795|emb|CAB43060.1| RNA polymerase II [Alstonia scholaris]
          Length = 258

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG +      EDMPF  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPFTAEGITPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 128  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGFRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 226  GAAHFLKERLFDQSD 240


>gi|330833900|ref|YP_004408628.1| DNA-directed RNA polymerase subunit B [Metallosphaera cuprina Ar-4]
 gi|329566039|gb|AEB94144.1| DNA-directed RNA polymerase subunit B [Metallosphaera cuprina Ar-4]
          Length = 1124

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 120/612 (19%), Positives = 204/612 (33%), Gaps = 101/612 (16%)

Query: 779  RPLVKVGDE--VRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +PLV   D   +++  I  D        +  D     N  +A  P         + I   
Sbjct: 583  KPLVTKEDIENLKKGKITFDTLIREGKIEFLDAEEEENAYIALEPKDVTKDHTHLEIWTP 642

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
             +     + I   E     R+T              +   ++         +        
Sbjct: 643  AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQIR---TDTRAHLLHYPQKPI 699

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    +   G +        + A+      ++ D  +   S +   +     F  +  ++
Sbjct: 700  VQTRALEAIGYTERPAGNNAIFALMSYTGYNMEDAVIMNKSSIERGMFRSTFFRLYSAEE 759

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             +     E E +      +  +              +L     VS     K   VL   +
Sbjct: 760  IKYPGGQEDEILLPEPGVRGYKGKD--------YYRLLESNGIVSPEVDVKGGDVLIGKV 811

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                   ++ + +    K   ++  +    E     L    +                 +
Sbjct: 812  SPPRFLQEFKELSPDQAKRDTSI--ITRHGERGTVDLVLVTE------------TSEGNK 857

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV V   R  + GDK A RHG KG+V  I+P  DMP+   G   DI+LNP  +PSRM 
Sbjct: 858  LVKVRVRDLRIPEIGDKFATRHGQKGVVGMIIPQVDMPYTTSGLTPDIILNPHALPSRMT 917

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VGQI E   G      G+ I                                        
Sbjct: 918  VGQIMEALSGKFVAATGESID--------------------------------------- 938

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP F     E I   L  +     G  ++YDG TGE     +  G
Sbjct: 939  --------------ATP-FYNIPIEEIQKKLLNSGYLGDGSEVVYDGRTGEKLKGRILFG 983

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  KL+HMV+DK++ R  G   ++T+QP  G++  GG R GEME  C+  YGAA +++
Sbjct: 984  IVYYQKLHHMVADKMHGRGRGPVQILTRQPTEGRAREGGLRFGEMERDCLIGYGAAMLIK 1043

Query: 1313 EMLTIKSDDV-------VG------RTR-VYESIVAGND--TFETGTPESFNVLVKEMQA 1356
            + L   SD          G      R++  Y   + G+    +      +F +L++E+ +
Sbjct: 1044 DRLLDNSDKATVYVCEQCGYVGWYDRSKNKYICPIHGDKSTLYPVAVSYAFKLLLQELMS 1103

Query: 1357 LGLSIDLENSRT 1368
            + ++  L     
Sbjct: 1104 MVIAPKLVLGER 1115



 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 137/976 (14%), Positives = 291/976 (29%), Gaps = 190/976 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+     S++ F+             LQ        IT       +         P+   
Sbjct: 20  LVRQHLDSFNDFIKNK----------LQEIIDEQAEITTEIPGLKIRLGKIRVGKPRVRE 69

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R+LTYA P+ + +  I  +++               +Y+GD+P+M
Sbjct: 70  ADKGDKEITPMEARLRNLTYAAPVYLEMTPIENNIEGDLT----------EVYIGDIPIM 119

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F++ G +R++V+Q   +       D G+   
Sbjct: 120 LKSIADPTSEFTSEKLVEIGEDPKDPGGYFIVNGSERVIVTQEDLATNRVLT-DVGKTGS 178

Query: 175 SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
           +  + +  +II      + + + IE      IHV       K+P    + ALG++++E +
Sbjct: 179 N--ITHTAKIISSTSGYR-VPITIEKLKDSTIHVSFPAVPGKIPFAILMRALGIETDEEI 235

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-L 288
                 +  S   D     L + +           +D       I   +++     +  L
Sbjct: 236 -----TLAVSLDPDIQNELLPSIEQASSIISKDDALDFIGNRIAIGQKREMRIQKAEQVL 290

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIRD 343
            +  +  +G  +               +  E+Y+   +  D+       L+         
Sbjct: 291 DKYFLPHIGTNASDRTAKAYYLAFAVSKLIELYLGRREPDDKDHYANKRLKLAGDLFASL 350

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
             + +   V +  +          +   +AL+         D+ +  +  ++    +   
Sbjct: 351 FRVAFKAFVKDLVFQLEKSKVRGRRLAVNALVR-------QDIISERIRHALATGNWVGG 403

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNR 462
                  + R      L+      V  + +       + L   + G+    +  +   + 
Sbjct: 404 RTGVSQLLDRTNWLSMLSHLRRV-VSSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSG 462

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE-FFCSSQ 521
            V+++  + +    +    +ER +         + +        K            + +
Sbjct: 463 LVKNLALLGQISVGVNEKSVERLLYNLGVIPIEEVIKKYRSQEEKSEDYENWSKVILNGR 522

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L     + + L+     +R     +G ++        R            +       I 
Sbjct: 523 LIGYYPNGSELAEKIREKRR----EGELSDEVNVNYTRTETYNEVYINSDSGRVRRPLIV 578

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           +        + +    ++              + +L A EEEN YIA     + +D    
Sbjct: 579 VRHGKPLVTKEDIE-NLKKGKITFDTLIREGKIEFLDAEEEENAYIALEPKDVTKDH--- 634

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                                 ++     ++ I AS+IP+ E++ S R      M +QA+
Sbjct: 635 --------------------THLEIWTPAILGITASIIPYPEHNQSPRNTYQSAMAKQAL 674

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            L  A                                                + + +  
Sbjct: 675 GLYAANYQI-----------------------------------------RTDTRAHLLH 693

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q+P+V+               +    +   G N + A M + GY
Sbjct: 694 YP--------------QKPIVQ----------TRALEAIGYTERPAGNNAIFALMSYTGY 729

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNV----SEEGLKNI 876
           N ED++++++  +   +F S     +         G E EI    P V     ++  + +
Sbjct: 730 NMEDAVIMNKSSIERGMFRSTFFRLYSAEEIKYPGGQEDEILLPEPGVRGYKGKDYYRLL 789

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           +  GI+    +V  GD+L+GK++P        E    +A         RDTS+    G  
Sbjct: 790 ESNGIVSPEVDVKGGDVLIGKVSPPRFLQEFKELSPDQAK--------RDTSIITRHGER 841

Query: 937 GTVVDVRIFNRHGIDK 952
           GTV  V +      +K
Sbjct: 842 GTVDLVLVTETSEGNK 857


>gi|78714199|gb|ABB51082.1| RNA polymerase beta subunit [Acholeplasma palmae]
          Length = 628

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 227/452 (50%), Positives = 296/452 (65%), Gaps = 30/452 (6%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 2   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGK----VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           AR + YGFI+TP+ +V        V++ + YL+A +E    IA A S L+ D SF EE +
Sbjct: 62  ARTDEYGFIQTPFLQVIHENGISKVSDKITYLTADQEAGEVIASAASPLNPDNSFKEERI 121

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  GE  +  + +I F+D SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL 
Sbjct: 122 IARSNGETGMYEQHEITFMDVSPKQIVSVATSSIPFLEHDDASRALMGANMQRQAVPLLA 181

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV----------------- 748
            E+P VGTG+E   AK SG  IV K AG V   DA +I+I                    
Sbjct: 182 PESPIVGTGIEYRAAKDSGCVIVTKNAGYVTYADAKKIIITEEPTDVVSIGGRIIYEPNK 241

Query: 749 -------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +   D   +    Y L++F RSNQ+T V Q+P+V  G+ V   DIIADGPSTD
Sbjct: 242 EFNYMIAKELHDYGMAPESEYELIQFFRSNQDTLVLQKPIVVAGEYVEAGDIIADGPSTD 301

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR--DTKLGPE 859
            G+LALGRN+ VAFM W GYN+ED++++SE +V  DV+TSIHI+E+E+  R   T  G E
Sbjct: 302 QGELALGRNVTVAFMTWEGYNYEDAIIMSEELVKNDVYTSIHIDEYEIETRELKTGTGKE 361

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITR+IPNV  + +KN+DE GII  G+EV  GDILVGKITPKG    +P EKL+ A+ GE
Sbjct: 362 EITREIPNVGPDAIKNLDEKGIIIPGSEVKEGDILVGKITPKGIFEPSPSEKLIHAVIGE 421

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           K+ + RD+SLRVP G  G V  +R F++   D
Sbjct: 422 KSREYRDSSLRVPHGGGGVVQSIRYFSKKNGD 453



 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 131/478 (27%), Positives = 198/478 (41%), Gaps = 79/478 (16%)

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
             E + ++S                      D  + PE     I          + +  I+
Sbjct: 223  EEPTDVVSIGGRIIYEPNKEFNYMIAKELHDYGMAPESEYELIQFFRSNQDTLVLQKPIV 282

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
              G  V  GDI+    +   +  +     +  A    +  +  D  +     V   V   
Sbjct: 283  VAGEYVEAGDIIADGPST-DQGELALGRNVTVAFMTWEGYNYEDAIIMSEELVKNDVYTS 341

Query: 943  RIFNRHGIDKNERSISVEREQIELL-------ARDKDDEQVILDRNIYSRLMEILCGQNA 995
               + + I+  E      +E+I          A    DE+ I+      +  +IL G+  
Sbjct: 342  IHIDEYEIETRELKTGTGKEEITREIPNVGPDAIKNLDEKGIIIPGSEVKEGDILVGKIT 401

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G      S  L   +I E  R    ++     +V      +             R+ +
Sbjct: 402  PKGIFEPSPSEKLIHAVIGEKSR----EYRDSSLRVPHGGGGVVQSI---------RYFS 448

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      GD +P GV   ++V++A KR I  GDKMAGRHGNKG++S+ILP EDMP+++DG
Sbjct: 449  KKN----GDILPSGVNETIRVYIAKKRKISEGDKMAGRHGNKGVISKILPKEDMPYMEDG 504

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            T VDI+LNPLGVPSRMN+GQI E HLG +   LG K+ + + D   + D+  + +     
Sbjct: 505  TTVDIMLNPLGVPSRMNIGQILEIHLGISAKRLGIKVATPVFDGVEDKDLKDIMAEAGLE 564

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 565  PDGK----------------------------TTLYDG---------------------- 574

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                 TGEP++  ++VG +YM+KL+HMV DK++ARS G Y+LVTQQP+GGK+  GGQR
Sbjct: 575  ----RTGEPYENRISVGVMYMIKLSHMVDDKLHARSVGPYTLVTQQPMGGKAQNGGQR 628


>gi|224587859|gb|ACN58727.1| DNA-directed RNA polymerase III subunit RPC2 [Salmo salar]
          Length = 814

 Score =  327 bits (837), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 89/340 (26%), Positives = 138/340 (40%), Gaps = 66/340 (19%)

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            QY       +    + IEK+    +       ++K+ +   R  + GDK + RHG KG+ 
Sbjct: 531  QYRDVPVSYKGSTDSYIEKVMISSNADDAF--LIKILLRQTRRPEIGDKFSSRHGQKGVC 588

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I+P EDMPF   G   DI++NP G PSRM V        G     L  K   +   + 
Sbjct: 589  GLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTV--------GKLIELLAGKAGVMDGRFH 640

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G+  + + 
Sbjct: 641  YGT----------------------------------------------AFGGSKVKDVC 654

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L     +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++T+
Sbjct: 655  EDLIRYGYNYQGKDYVTSGITGEPIEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTR 714

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----S 1331
            QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G+  +        
Sbjct: 715  QPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCH 774

Query: 1332 IVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                +        P +  +L +E+Q++ +   L+ +R   
Sbjct: 775  YCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLARYNE 814



 Score =  125 bits (314), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 79/534 (14%), Positives = 165/534 (30%), Gaps = 39/534 (7%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           K   +A++   V L  G+  +DD D  GN+R+   G++L   +     +    +K+    
Sbjct: 12  KCIYLAVMVRRVILAQGENKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKISDQ 71

Query: 493 VDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           +       Q      +    + + +     +   S     ++         RLS +   G
Sbjct: 72  IIPKQRAAQFDIVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSFISALG 131

Query: 549 VA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +         + R     R + P+ +G +CP++T EG   GLV +L     +      + 
Sbjct: 132 MMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTD-MEDG 190

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENR---YIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           P  K+       DV  L   EE +    ++   N ++       + LV+           
Sbjct: 191 PIVKLAFNLGVEDVNLL-CGEELSYPSVFLVFLNGNILGVIRDHQRLVYTFRLMRRAGFI 249

Query: 658 REKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            E +        + V +++       P++       ++   +++         E     +
Sbjct: 250 NEFVSISTNLTDRCVYVSSDGGRLCRPYIIVKKGQPMVKNKHIEELTQGYRTFEDFLHES 309

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRI--------VIRSVEGDLDPSTSGVDIYRLM 765
            +E +         +A    ++ +              V   +      + S  + Y+  
Sbjct: 310 LVEYLDVNEENDCQIALYEHMINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCA 369

Query: 766 KFQRSNQNTCVNQRPLVKV-----GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             +++      NQR  +       G   +           D   L  G+N  VA M + G
Sbjct: 370 MGKQAMGTIGYNQRNRIDTLMYLLGYPQKPMVKTRTIELIDFEKLPAGQNATVAVMSYSG 429

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKN 875
           Y+ ED++++++  +       +  +  +   R       +                    
Sbjct: 430 YDIEDALILNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAATRKPIWRHSI 489

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           +D  GI C G +V    +LV K  P                           S 
Sbjct: 490 LDADGICCPGEKVENKQVLVNKSMPTVTQTPLEGSAQPGQPQYRDVPVSYKGST 543


>gi|86451151|gb|ABC96798.1| RNA polymerase II [Coptosapelta diffusa]
          Length = 214

 Score =  326 bits (836), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGLTYTQEDMPFTVEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHACGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 199  GAAHFLKERLFDQSD 213


>gi|52538147|emb|CAH19175.1| RNA polymerase beta-subunit [Pseudomonas migulae]
          Length = 332

 Score =  326 bits (836), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 196/332 (59%), Positives = 256/332 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFN 332


>gi|194591895|gb|ACF76528.1| RNA polymerase beta subunit [Mycoplasma equirhinis]
          Length = 600

 Score =  326 bits (836), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 212/455 (46%), Positives = 298/455 (65%), Gaps = 16/455 (3%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+
Sbjct: 1   QFMDQSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +L SF++++ YGFI++PY KV + KV  ++ +YL+A+EE     AQ+ + + ++    +
Sbjct: 61  LNLASFSKIDKYGFIQSPYFKVTNRKVDFSEPIYLTAIEEVGYTFAQSTTHI-KNNVIVD 119

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E V  R   E + V  +++D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP
Sbjct: 120 EKVMARRDNEFVEVSADEVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVP 179

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +L  E P V TG+E+ +AK S   I A RAG+V  VDA  I I           S  D+Y
Sbjct: 180 VLFPEKPLVATGVEADIAKYSSTNICATRAGVVSYVDAEIIKIIPD------GLSKPDVY 233

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L  F+RSNQ T ++Q P+VK+   +   D++ DGPS   G+LALG+N+LV F  WHGYN
Sbjct: 234 HLRTFERSNQGTLIHQIPIVKLNQRIEAGDLLVDGPSMQDGELALGKNVLVGFTTWHGYN 293

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNVSEEGLKNIDECGI 881
           +ED++++SER+V +DV+TSIHIEE  +  R +K G +     DIPNVS    + +DE GI
Sbjct: 294 YEDAVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGDDLLTADDIPNVSNFSKRFLDENGI 353

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV 
Sbjct: 354 VKVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTTSRKDTSLKVKHGHNGTVVA 413

Query: 942 VRIFNR-------HGIDKNERSISVEREQIELLAR 969
           V I +R        GIDK  +    ++ +I++  +
Sbjct: 414 VDILSRETGDQLEDGIDKIVKVSIAQKRKIKVGDK 448



 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 123/421 (29%), Positives = 185/421 (43%), Gaps = 78/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD------TSLRVPSG 934
            I+ +   +  GD+LV   +   +  +   + +L         +  D        ++    
Sbjct: 252  IVKLNQRIEAGDLLVDGPS-MQDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDVY 310

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  RH    ++   + +   +   ++   DE  I+         +IL G+ 
Sbjct: 311  TSIHIEEQTIQFRHSKAGDDLLTADDIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 370

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G +       L + +  +   S+           +     +K  +  +   ++    
Sbjct: 371  SPKGEENPTPEEKLMAAIFGQKTTSR-----------KDTSLKVKHGHNGTVVAVD---- 415

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
              I   + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+D
Sbjct: 416  --ILSRETGDQLEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLED 473

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DIVLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +    + 
Sbjct: 474  GTPLDIVLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIREILEEAKI 533

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                               V+DG                     
Sbjct: 534  DPSGKMV----------------------------VYDG--------------------- 544

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                  TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 545  -----RTGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 599

Query: 1295 G 1295
            G
Sbjct: 600  G 600


>gi|81171081|gb|ABB58767.1| RNA polymerase beta subunit [Mycoplasma auris]
          Length = 592

 Score =  326 bits (836), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 213/424 (50%), Positives = 292/424 (68%), Gaps = 8/424 (1%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRVTSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA ++ YGFI+TPY +V + KV  ++V YL+A+EE     AQ+  S+ +D    +  V  
Sbjct: 61  FADIDKYGFIKTPYFRVKNKKVDFSNVQYLTAIEEAGYTFAQSTVSIKDD-LIVDTNVIA 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + + VP  ++D+ID S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNQYLEVPASEVDYIDVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P V TG+E+ +AK S   I AK  GIV  VDA  I ++  E      +S VD Y L  F
Sbjct: 180 VPLVATGVEADIAKFSSTNITAKYDGIVSYVDANVIRVKRNE------SSKVDSYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q PLVK+  E++  D++ DGPS   G+++LG+N+LV F  WHG+N+ED++
Sbjct: 234 ERSNQGTLIHQVPLVKLNQEIKAGDLLVDGPSMKNGEMSLGKNVLVGFTTWHGFNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    +++DE GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNFSKRHLDENGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDVLSR 413

Query: 948 HGID 951
              D
Sbjct: 414 KMGD 417



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 123/413 (29%), Positives = 178/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  E+  GD+LV   + K    M+  + +L         +  D  +     V   V 
Sbjct: 247  LVKLNQEIKAGDLLVDGPSMKN-GEMSLGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNFSKRHLDENGIVRVGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L  +        
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDVLSRKM------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 416  --GDALEDGIEQIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILEEANIAPSGKL 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DG                           
Sbjct: 534  T----------------------------VYDG--------------------------R 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|23006310|ref|ZP_00048687.1| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 299

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 163/283 (57%), Positives = 207/283 (73%), Gaps = 1/283 (0%)

Query: 153 VVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV 212
           +VSQ+HRSPG+ FDHDKG+   SGKLL+A RIIP +G W+D+EFD+KDI+HVRIDR+RK+
Sbjct: 18  IVSQMHRSPGVFFDHDKGKTHSSGKLLFAARIIPYRGSWLDVEFDAKDIVHVRIDRKRKL 77

Query: 213 PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
           PVTS L ALG+D EEILSTFY ++ Y + G  W  P  A  L  G K S  L+D D+GE 
Sbjct: 78  PVTSLLFALGLDGEEILSTFYNRVTYERDGADWRVPFDAERL-KGFKASVDLIDADSGEV 136

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           V+E+GKKL +   + + EKG KFL  T + L G Y+AED+VN +TGEI+ EAGD I EK 
Sbjct: 137 VLEAGKKLNARNARLIGEKGTKFLKATDEDLVGQYIAEDLVNVQTGEIWAEAGDEISEKL 196

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +    + +IP+L +D VN   YIRNTL  DKN  R+ AL DIYRVMRPG+  T   A
Sbjct: 197 LKSLDEVGVTEIPVLDIDHVNVGPYIRNTLAVDKNSGREGALFDIYRVMRPGEPPTLDTA 256

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           E+MF+ LFFD+++YDLS VGRVKMNMRL+LD  D VR +R+ED
Sbjct: 257 EAMFHSLFFDAERYDLSAVGRVKMNMRLDLDAADTVRTLRRED 299


>gi|212373965|emb|CAP09909.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35708]
          Length = 322

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 190/322 (59%), Positives = 248/322 (77%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++
Sbjct: 61  GPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMND 120

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NM
Sbjct: 121 KKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNM 180

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   
Sbjct: 181 QRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGE 240

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 241 AGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFM 300

Query: 817 PWHGYNFEDSMLISERMVSEDV 838
            W+G+NFEDS+ +SER+V ED 
Sbjct: 301 AWNGFNFEDSICLSERVVQEDR 322


>gi|4867897|emb|CAB43086.1| RNA polymerase II [Strychnos potatorum]
          Length = 263

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GA++ L+E L  +SD
Sbjct: 228  GASHFLKERLFDQSD 242


>gi|80978853|gb|ABB54675.1| RNA polymerase beta subunit [Mycoplasma lipofaciens]
          Length = 592

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 207/424 (48%), Positives = 297/424 (70%), Gaps = 8/424 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN +GF++TPY KV +G V   +V YL+A EE +  IAQ+  ++DE+     + +  R
Sbjct: 62  AKVNKFGFLQTPYYKVENGIVDYENVHYLTASEELDSNIAQSTVNVDENNRIIGDQITMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   E I++I+ +  Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 RNYHYIMGSPEDIEYIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+ES +AK S    +AK  G+VE VD ++I IR ++   D        Y L  FQ
Sbjct: 182 PLVATGLESQIAKYSSGNFLAKNDGVVEYVDGLKIKIRDLKDRTD-------TYLLKNFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+P+VK G  V++ D++ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVIHQKPIVKEGQHVKKGDLLVDGSSFKDGELALGKNVLVAFTTYKGYNYEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+  ++++DE GI+ VG+EV
Sbjct: 295 LNERLVKDDVFTSIHIEEQTIQFRTSKAGNDELTSDIPNVSKHSIRHLDEHGIVRVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PKG+   + EEKLL+++  +K+  VRDTSL+V +G SGT++ V I +R 
Sbjct: 355 TPGDVLVGRTSPKGDDNPSQEEKLLQSVLQQKSQQVRDTSLKVKNGHSGTIIGVEILSRA 414

Query: 949 GIDK 952
             DK
Sbjct: 415 NGDK 418



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 129/413 (31%), Positives = 180/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+LV   + K +  +   + +L A    K  +  D  +     V   V 
Sbjct: 247  IVKEGQHVKKGDLLVDGSSFK-DGELALGKNVLVAFTTYKGYNYEDAIILNERLVKDDVF 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S +   E    +          LD +   R+   +   + + G  
Sbjct: 306  -TSIHIEEQTIQFRTSKAGNDELTSDIPNVSKHSIRHLDEHGIVRVGSEVTPGDVLVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +  +S   Q + Q       V++          IL           
Sbjct: 365  SPKGDDNPSQE--EKLLQSVLQQKSQQVRDTSLKVKNGHSGTIIGVEILSRA-------- 414

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV VA+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTP+D+
Sbjct: 415  -NGDKLEDGIEQIVKVSVAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPIDV 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  +   D     DI+ +            
Sbjct: 474  MLNPQGVPSRMNIGQVLEIHLGMAARELNCKFVTPTFDGVKKEDINEVIKEAN------- 526

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      +  L D +
Sbjct: 527  ------------------------------------------LPESG-----KQFLIDPI 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD PV+VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEKFDNPVSVGVMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 592


>gi|52694187|emb|CAG30623.1| DNA-directed RNA polymerase beta chain [Pseudomonas fluorescens]
          Length = 337

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 198/337 (58%), Positives = 260/337 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +
Sbjct: 121 VKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 181 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  
Sbjct: 241 VCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSK 300

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 301 GDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGF 337


>gi|190341743|gb|ACE74948.1| RNA polymerase beta subunit [Enterobacter mori LMG 25706]
          Length = 332

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 207/332 (62%), Positives = 259/332 (78%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLG 300

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           + V R D++ADGPSTDLG+LALG+NM V FMP
Sbjct: 301 EPVERGDVLADGPSTDLGELALGQNMRVPFMP 332


>gi|52538155|emb|CAH19179.1| RNA polymerase beta-subunit [Pseudomonas migulae]
          Length = 332

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 195/332 (58%), Positives = 255/332 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +DI+ DGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 SDIMPDGPSTDMGELALGQNMRIAFMAWNGFN 332


>gi|100913643|gb|ABF69720.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913645|gb|ABF69721.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913647|gb|ABF69722.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 596

 Score =  326 bits (836), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 213/451 (47%), Positives = 303/451 (67%), Gaps = 15/451 (3%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L
Sbjct: 1   DQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            SFA+++ YGFI++PY  V +  V  ++  YL+A+EE     AQ+   + +D    ++ V
Sbjct: 61  ASFAKIDRYGFIQSPYFPVKNRIVDFSEPKYLTAIEEAGYTFAQSTVKI-KDNYIIDDKV 119

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L 
Sbjct: 120 IVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLF 179

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E+ VAK S   I AKR G+V+ VDA  I +           + +D+Y L 
Sbjct: 180 PESPLVATGVEADVAKFSSTNISAKRDGVVKYVDASVIKVMPT------GLNKLDVYHLR 233

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q PLVKVGDE++  D++ DGPS   G+LALG+N+LV F  WHGYN+ED
Sbjct: 234 TFERSNQGTLIHQIPLVKVGDEIKEGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYED 293

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE GI+ VG
Sbjct: 294 AVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVG 353

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + I 
Sbjct: 354 SEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDIL 413

Query: 946 NR-------HGIDKNERSISVEREQIELLAR 969
           +R        GI+K  +    ++ +I++  +
Sbjct: 414 SRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 444



 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 249  LVKVGDEIKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 416  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +    +       
Sbjct: 476  VLNPQGVPSRMNIGQILELHLGSAAKNLNTKFVTPIFDGITHNQIRDILEEAKMDTTGK- 534

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 535  ---------------------------TVVYD--------------------------GQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|296087814|emb|CBI35070.3| unnamed protein product [Vitis vinifera]
          Length = 461

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 99/505 (19%), Positives = 175/505 (34%), Gaps = 86/505 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    A+      D+ D  +   S +   
Sbjct: 26   DSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRG 85

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +  +     N+R  +   ++I    +   D + +          +IL      + 
Sbjct: 86   FGRCIVMKKF-SAVNQRYENNASDRIVRPLKVGHDAERM----------QILDDDGLAAP 134

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
             +  K + +  +       +          +            Y+ S+   +        
Sbjct: 135  GEIIKPNDIYINKESPIITKGPLISPVGLPDSA----------YKPSRQTFKGPEGEASV 184

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              +            +K  +   R  + GDK + RHG KG+   I+  ED PF + G   
Sbjct: 185  VDRVALCSDKNSNLCIKFLIRHTRRPEVGDKFSSRHGQKGVCGTIIQQEDFPFSERGICP 244

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM VG++ E   G A V  G+          +                 
Sbjct: 245  DLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHAD------------- 291

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  E I+  L       SG+  +Y 
Sbjct: 292  ------------------------------------KVETISKTLVKHGFSYSGKDFIYS 315

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TG P    + +G IY  KL HMV DK++AR +G   ++T+QP  G++  GG R+GEME
Sbjct: 316  GITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGLRVGEME 375

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDD-------VVGRTRVYESIVA---------GNDTFETG 1342
              C+ AYGA+ ++ E L + SD        V G    Y   +          G++     
Sbjct: 376  RDCLIAYGASMLIFERLMVSSDPFEVQVCRVCGLLGYYNHKLKIGICSTCKNGDNISTMK 435

Query: 1343 TPESFNVLVKEMQALGLSIDLENSR 1367
             P +  +L +E+QA+ +   L+ + 
Sbjct: 436  LPYACKLLFQELQAMNVVPRLKLTE 460



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/151 (17%), Positives = 57/151 (37%), Gaps = 12/151 (7%)

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            + I +L +           QRPL+                      L  G+N  VA M 
Sbjct: 16  NILILQLCRMDSLLYLLVYPQRPLL----------TTRTIELVGYDKLGAGQNATVAVMS 65

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG--LKN 875
           + GY+ ED++++++  +       I +++F  + +  +    +       V  +   ++ 
Sbjct: 66  YSGYDIEDAIVMNKSSLDRGFGRCIVMKKFSAVNQRYENNASDRIVRPLKVGHDAERMQI 125

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +D+ G+   G  + P DI + K +P      
Sbjct: 126 LDDDGLAAPGEIIKPNDIYINKESPIITKGP 156


>gi|289581816|ref|YP_003480282.1| DNA-directed RNA polymerase subunit B [Natrialba magadii ATCC 43099]
 gi|289531369|gb|ADD05720.1| DNA-directed RNA polymerase subunit B [Natrialba magadii ATCC 43099]
          Length = 609

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 125/595 (21%), Positives = 210/595 (35%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 95   LVDHGYVEFIDAEEEEDIYVAVEEADLTADHTHLEIDPQLIFSIGSGMIPYPEHNASPRI 154

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 155  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 211

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 212  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 267

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 268  ----VRGARGEEAYAHLDEDGLVNPETEVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 323

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 324  ETSVTMRSGESGVVDTITLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 371

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+VLNP  +PSRM VG I E   G      G+++ 
Sbjct: 372  HGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHALPSRMTVGHILEMIGGKLGAMEGRRVD 431

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 432  G-----------------------------------------------------TP-FLG 437

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE A+   L  A  D +G+  +Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 438  EDESALRDGLEEAGFDSAGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVSNKLHARSRG 497

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    +V G     
Sbjct: 498  PVQVLTRQPTEGRAREGGLRIGEMESDVFIGHGAAMTLKERLLDESDREFINVCGQCGMS 557

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      D  E     +F +L+ EM+ALG++  LE + 
Sbjct: 558  AVENVEQRRVYCPNCEEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRLELAD 607



 Score = 43.9 bits (102), Expect = 0.22,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 65/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHELAEQIREARRIGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      +S     A  +  G +E       D      V ++ A EEE+ Y+A   + L 
Sbjct: 71  EDGE-PRISEQEIEALRD--GDLE-----FEDLVDHGYVEFIDAEEEEDIYVAVEEADLT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ + SI + +IP+ E++ S R+ MG  
Sbjct: 123 ADH-----------------------THLEIDPQLIFSIGSGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MIKQSLGLPSANYRI 174


>gi|40644726|emb|CAD92665.1| RNA polymerase II [Mimulus guttatus]
          Length = 629

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 102/501 (20%), Positives = 167/501 (33%), Gaps = 79/501 (15%)

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
              +      I   ++     + I   +     R+T             V+    +     
Sbjct: 181  YSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---D 237

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  V        +    +       +      + AI      +  D+ +   S +    
Sbjct: 238  TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGF 297

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R    + ++  ++ +E      R           +          G       
Sbjct: 298  F-RSLFFRSYRAEXKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGED 356

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T ++ D                  + Q N    K  + TS    E    +++  
Sbjct: 357  VIIGKTTPITPDE----------------AQGQANARYTKRDHSTSLRHSETGMVDQVLL 400

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   D
Sbjct: 401  TTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGINPD 455

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +GQ+ E  +G     +GK+                            
Sbjct: 456  IIVNPHAIPSRMTIGQLIECVMGKVAAHMGKEGD-------------------------- 489

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     + I+  L        G   +Y+G
Sbjct: 490  ---------------------------ATP-FTDVTVDNISKALHKCGYQMRGYETMYNG 521

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME 
Sbjct: 522  HTGRKLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMER 581

Query: 1300 WCIQAYGAAYVLQEMLTIKSD 1320
             C+ A+GAA+ L+E L  +SD
Sbjct: 582  DCMIAHGAAHFLKERLFDQSD 602



 Score =  105 bits (263), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 72/486 (14%), Positives = 138/486 (28%), Gaps = 104/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
                   +S +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 64  IHRNPDMLVSTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L      +  G+         D      + Y+   EEE   I+          
Sbjct: 123 KKKDIQALQQRESPDDGGWH--------DLVAKGFIEYIDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R          +     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLVSARLNP--GEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRAEXKKMGTLVKEDFGRPDRANTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP                        RD S  +  
Sbjct: 338 DKLDDDGLAPPGTRVSGEDVIIGKTTPITPDE--------AQGQANARYTKRDHSTSLRH 389

Query: 934 GVSGTV 939
             +G V
Sbjct: 390 SETGMV 395


>gi|225464023|ref|XP_002265454.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 1142

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 111/599 (18%), Positives = 196/599 (32%), Gaps = 91/599 (15%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D VR  D        +  D+    N L+A            + I    +       I   
Sbjct: 617  DGVRTFDDFLRDGLIEYLDVNEENNALIALYEADAKPETTHIEIEPFTILGVCAGLIPFP 676

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNID-ECGIICVGAEVNPGDILVGKITPKGES 904
                  R+T     +       +       +     ++ +        +    I   G  
Sbjct: 677  HHNQSPRNT----YQCAMGKQAMGNIAYNQLCRMDSLLYLLVYPQRPLLTTRTIELVGYD 732

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +    A+      D+ D  +   S +        +  +     N+R  +   ++I
Sbjct: 733  KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVMKKF-SAVNQRYENNASDRI 791

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                +   D + +          +IL      +  +  K + +  +       +      
Sbjct: 792  VRPLKVGHDAERM----------QILDDDGLAAPGEIIKPNDIYINKESPIITKGPLISP 841

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                +            Y+ S+   +          +            +K  +   R  
Sbjct: 842  VGLPDSA----------YKPSRQTFKGPEGEASVVDRVALCSDKNSNLCIKFLIRHTRRP 891

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSRM VG++ E   G A
Sbjct: 892  EVGDKFSSRHGQKGVCGTIIQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKA 951

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
             V  G+          +                                           
Sbjct: 952  GVSCGRFHYGSAFGEPSGHAD--------------------------------------- 972

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                        E I+  L       SG+  +Y G+TG P    + +G IY  KL HMV 
Sbjct: 973  ----------KVETISKTLVKHGFSYSGKDFIYSGITGCPLQAYIFMGPIYYQKLKHMVL 1022

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD--- 1321
            DK++AR +G   ++T+QP  G++  GG R+GEME  C+ AYGA+ ++ E L + SD    
Sbjct: 1023 DKMHARGSGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMVSSDPFEV 1082

Query: 1322 ----VVGRTRVYESIVA---------GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                V G    Y   +          G++      P +  +L +E+QA+ +   L+ + 
Sbjct: 1083 QVCRVCGLLGYYNHKLKIGICSTCKNGDNISTMKLPYACKLLFQELQAMNVVPRLKLTE 1141



 Score =  164 bits (416), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 93/723 (12%), Positives = 210/723 (29%), Gaps = 105/723 (14%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+  +I    R N+       SV P      +  L F       P    
Sbjct: 34  LVKQHLDSFNYFVKTDIKKIVRAND---RIVSSVDP------SIYLRFKDVRIGEPSITV 84

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K +   C   D+TYA P+ + +  I     + T       +++  + +G +P+M 
Sbjct: 85  DGISEKLNPHTCRLSDMTYAAPILVNIEYITGSHVQKTR------VEKNDVVIGRMPIML 138

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDK----- 169
                                     G FV+KG +++++ Q   S   I  D DK     
Sbjct: 139 RSCCCVLYKKDEAELARLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIIDTDKKGNIN 198

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-E 227
              + S +   +  +I             K+ I +++++   K+P+   + A+GM+S+ E
Sbjct: 199 ASVTSSTESTKSKTVI----------VMEKEKIWLQLNQFTSKIPIMIVMKAMGMESDQE 248

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           ++        YS          ++  +    +    L              +     +  
Sbjct: 249 VVQMVGRNPRYSALLLPSMEECASHGIYTQQQALEFLERKVKKLPFYNPSLEKEGRGMAI 308

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           L++  +  + +  +      +   ++      +      ++++ ++++  +   + + + 
Sbjct: 309 LRDTFIANVPVRQNNFRPKCLYVAVM------LRRMMDAILNKDAMDDKDYVGNKRLELS 362

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                     +  T++++  K     L    R  R      FS                 
Sbjct: 363 GQLISLLFEDLFKTMISEVKKTIDAILAKPSRSSRF----DFSQCLRFIVRDSITVGLER 418

Query: 408 LSTVGRVKMNMRLNLDTPDDVRH--IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             + G   +                +     +  +  +         +     L   +  
Sbjct: 419 TLSTGNWDVKRFRMHRKGMSQVVARLSYIGSLGHMTKISPQFEKSRKVSGPRALQPSQWG 478

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            +      +     L    ++   +++ + +S +     +       +         +  
Sbjct: 479 MLCPCDTPEGEACGLVKNLALMTHVTTDEEESPLISLCYSLGVEDLELLSGEELHTPNSF 538

Query: 526 EEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
               N L    H R          + RA    E   V            +  G     V 
Sbjct: 539 LIIFNGLILGKHRRPQRFANALRKLRRAGKIGEFVSVFVNEKQHCVYIASDGGRVCRPVV 598

Query: 585 SLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
                    + +    +    R   D      + YL   EE N  IA   +         
Sbjct: 599 IADKGKSRIKEHHMKELIDGVRTFDDFLRDGLIEYLDVNEENNALIALYEADAKP----- 653

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                             +   I+  P  ++ + A LIPF  ++ S R    C M +QA+
Sbjct: 654 ------------------ETTHIEIEPFTILGVCAGLIPFPHHNQSPRNTYQCAMGKQAM 695

Query: 702 PLL 704
             +
Sbjct: 696 GNI 698


>gi|190682997|gb|ACE81780.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 327

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 204/324 (62%), Positives = 254/324 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 4   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 64  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 124 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 183

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 184 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 243

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 244 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 303

Query: 794 IADGPSTDLGDLALGRNMLVAFMP 817
           +ADGPSTDLG+LALG+NM VAFMP
Sbjct: 304 LADGPSTDLGELALGQNMRVAFMP 327


>gi|120561261|gb|ABM27015.1| RNA polymerase II second largest subunit [Allomyces macrogynus]
          Length = 896

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 161/1000 (16%), Positives = 303/1000 (30%), Gaps = 184/1000 (18%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V D   LE I +    D  +  +    +NA+          
Sbjct: 61   LPYIQQDIPIMVLFRALGLVADRDILERICYDFSDDQMLEMLKPSIDNAFTIQEREV--- 117

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 AL  I +  R                      +Y    + R  +           
Sbjct: 118  -----ALDFIGKRGRN------------IGLTRDKRIRYAHDLLERELLPHI---GITPG 157

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +  +   I  ++  L+    G+  +DD D+ G +R+   G +L + +R    ++ + + 
Sbjct: 158  CQTRKSYFIGYMVHRLLLAALGRRQVDDRDHFGKKRLDLAGPLLASLFRTFFQKLTKDVS 217

Query: 488  ERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSL 532
               +              IN+  + + +     +               +SQ+       
Sbjct: 218  RYFTVCIERGREFNLNMAINSNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFA 277

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ++H RRL+      + R     + R +H TH+G +CPAET EG   GLV +L   A +
Sbjct: 278  STLSHLRRLNT----PIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAYI 333

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----FCR 648
            +  G    P  +  +   T ++  ++A    +      N S        + LV      R
Sbjct: 334  S-VGSASGPILEFLEEWTTENLEEITASAIGSNTKVFVNGSWVGIHRQPDSLVQTLISLR 392

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             +G+ +       D  D   +          P    ++  ++++  +   +         
Sbjct: 393  RSGDIMPEVSVVRDVRDNELRIYTDAGRICRPLFIVNEQQQLVLRRDHVARLEVGEWGWE 452

Query: 709  PFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              +  G+ E +  +     ++                +   +          D  +L K 
Sbjct: 453  ELLANGIVEYLDTEEEETTMIC---------------MTPDDLAESRGDPIPDKSKLDKT 497

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             R             K GD  ++       PS  LG       +  + +P+  +N     
Sbjct: 498  ARLKSR---------KAGDVCKQWSHCEIHPSMILG-------ICASIIPFPDHNQ---- 537

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
              S R   +       +  +    +                       +    +  +   
Sbjct: 538  --SPRNTYQSAMGKQAMGLYLTNFQ-----------------------LRMDTLANILYY 572

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                 +    +       +   +  + AI      +  D+ +   S +   +    I+ R
Sbjct: 573  PQKPLVATRSMKYLRFRELPAGQNAVVAIAVYSGYNQEDSIIMNQSSIDRGLF-RSIYYR 631

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +D+ ++S   + E  E  AR+   +      +       +  G           K+  
Sbjct: 632  AYMDQEKKSGFSDVETFEKPARETTLKLRHGSYDKIEEDGLVAPGTRVTGDDIIIGKTAP 691

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L  D      R+                   K    TS    E    + +      D   
Sbjct: 692  LPPDTSEMGARTT----------------QTKKDVSTSLKSTEQGIVDHVMLTTNND--- 732

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                + VKV V   R  Q GDK A RHG KG V      EDMPF  DG   D+++NP  +
Sbjct: 733  --GYKFVKVRVRSTRVPQMGDKFASRHGQKGTVGMTYRQEDMPFSADGVTPDLIVNPHAI 790

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E  L       G +  +         +I+                     
Sbjct: 791  PSRMTIGHLVECLLSKVGSLTGTEGDATPFTDITVQEIA--------------------- 829

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  LR     + G  +                        +G +       G+    
Sbjct: 830  ----DRLRSCGYQQRGFEIM----------------------YNGHT-------GKKLAA 856

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
             V  G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S
Sbjct: 857  QVFFGPTYYQRLKHMVDDKIHSRARGPLQILTRQPVEGRS 896



 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 105/749 (14%), Positives = 218/749 (29%), Gaps = 110/749 (14%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG+ ++ +IL          Q  +     +  A  +   +V+   +     
Sbjct: 68  IPIMVLFRALGLVADRDILERICYDFSDDQMLEMLKPSIDNAFTIQEREVALDFIGKRGR 127

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEA 324
              +   K++       L+ + +  +GIT           G  V   ++    G   ++ 
Sbjct: 128 NIGLTRDKRIRYAH-DLLERELLPHIGITPGCQTRKSYFIGYMVHRLLL-AALGRRQVDD 185

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            D   +K L+             +   + + + Y    +   +  +   A+         
Sbjct: 186 RDHFGKKRLDLAGPLLASLFRTFFQKLTKDVSRYFTVCIERGREFNLNMAI--------N 237

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVG-RVKMNMRLNLDTPDDVRHI-RKEDIIAIIK 441
            +  T  +  ++    + D  K+  +  G    +N      T   +R +         + 
Sbjct: 238 SNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFASTLSHLRRLNTPIGREGKLA 297

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +         +      ++KN   +  + +  +    +  ++  +    
Sbjct: 298 KPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMAYISVGSASGPILEFLEEWTTENL 354

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           + I A  + S    F   S +    +  + +  +   RR   +             +RDV
Sbjct: 355 EEITASAIGSNTKVFVNGSWVGIHRQPDSLVQTLISLRRSGDIMP-------EVSVVRDV 407

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                     A         +        R +    +E       +      V YL   E
Sbjct: 408 RDNELRIYTDAGRICRPLFIVNEQQQLVLRRDHVARLEVGEWGWEELLANGIVEYLDTEE 467

Query: 622 EENRYIAQANSSLDEDGSFTEELVF-----CRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           EE   I      L E                R    +     ++    +  P  ++ I A
Sbjct: 468 EETTMICMTPDDLAESRGDPIPDKSKLDKTARLKSRKAGDVCKQWSHCEIHPSMILGICA 527

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ L                                 
Sbjct: 528 SIIPFPDHNQSPRNTYQSAMGKQAMGLYLTNFQL-------------------------- 561

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y               Q+PLV              
Sbjct: 562 ---------------RMDTLANILYYP--------------QKPLVA----------TRS 582

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA   + GYN EDS+++++  +   +F SI+   +    + +  
Sbjct: 583 MKYLRFRELPAGQNAVVAIAVYSGYNQEDSIIMNQSSIDRGLFRSIYYRAYMDQEKKSGF 642

Query: 857 GPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E            +       I+E G++  G  V   DI++GK  P     + P+  
Sbjct: 643 SDVETFEKPARETTLKLRHGSYDKIEEDGLVAPGTRVTGDDIIIGKTAP-----LPPDTS 697

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            + A   +   DV  +      G+   V+
Sbjct: 698 EMGARTTQTKKDVSTSLKSTEQGIVDHVM 726


>gi|100913633|gb|ABF69715.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913635|gb|ABF69716.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913637|gb|ABF69717.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913639|gb|ABF69718.1| RNA polymerase beta subunit [Mycoplasma phocidae]
 gi|100913641|gb|ABF69719.1| RNA polymerase beta subunit [Mycoplasma phocidae]
          Length = 596

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 215/451 (47%), Positives = 304/451 (67%), Gaps = 15/451 (3%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L
Sbjct: 1   DQCNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            SFA+++ YGFI++PY  V +  V  ++  YL+A+EE     AQ+   + +D   T++ V
Sbjct: 61  ASFAKIDRYGFIQSPYFPVKNRVVDFSEPKYLTAIEEAGYTFAQSTVKI-KDNYITDDKV 119

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E + V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L 
Sbjct: 120 IVRRDNEYVEVDAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLF 179

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E+ VAK S   I AKR GIV+ VDA  I +           + +D+Y L 
Sbjct: 180 PESPLVATGVEADVAKFSSTNISAKRDGIVKYVDASVIKVMPT------GLNKLDVYHLR 233

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q PLVKVGDE++  D++ DGPS   G+LALG+N+LV F  WHGYN+ED
Sbjct: 234 TFERSNQGTLIHQIPLVKVGDEIKEGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYED 293

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE  +  R +K G +++T +IPNVS    + +DE GI+ VG
Sbjct: 294 AVVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVG 353

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + I 
Sbjct: 354 SEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDIL 413

Query: 946 NR-------HGIDKNERSISVEREQIELLAR 969
           +R        GI+K  +    ++ +I++  +
Sbjct: 414 SRETGDQLEDGIEKIVKVSIAQKRKIKVGDK 444



 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 249  LVKVGDEIKEGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E +    +    +  +  LD N   ++   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRHSKAGEDQLTNEIPNVSNFSKRFLDENGIVKVGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL           
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIDILSR--------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS ILP E+MP+L+DGTP+DI
Sbjct: 416  ETGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPVEEMPYLEDGTPLDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   L  K  + I D   +  I  +    +       
Sbjct: 476  VLNPQGVPSRMNIGQILELHLGSAAKNLNTKFVTPIFDGITHNQIREILEEAKMDTTGK- 534

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 535  ---------------------------TIVYD--------------------------GQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|52538165|emb|CAH19184.1| RNA polymerase beta-subunit [Pseudomonas rhodesiae]
          Length = 332

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 196/332 (59%), Positives = 255/332 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGFN 332


>gi|105969653|gb|ABF81663.1| RNA polymerase beta subunit [Mycoplasma orale]
          Length = 594

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 213/443 (48%), Positives = 301/443 (67%), Gaps = 9/443 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA+++ YGFI+TPY +V + KV  +  VYL+A+EE N  IAQ+  ++ ++G   +++V  
Sbjct: 61  FAKIDKYGFIQTPYFRVKNRKVDFSQPVYLTAIEELNVVIAQSTINV-KNGIIIDDVVMA 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E I    E +++I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++KAE
Sbjct: 120 RKDNEYIQAKTEDVNYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVIKAE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   + +   G V  VDA +I I +            D+Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNLRSNTTGKVTYVDANQIKILAD------GAKKADVYNLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q P+VKVGDE++  D++ DGPS   G++ALG+N+LV F  W+GYN+ED++
Sbjct: 234 ERSNQGTLIHQIPIVKVGDEIKEGDLLVDGPSMKNGEMALGKNVLVGFSTWNGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + ++E GI+ +G+E
Sbjct: 294 ILSERLVKDDVYTSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG+ +PKGE   TPEEKL+ AIFG+K+ + +DTSL+V  G +GTVVDV I +R
Sbjct: 354 VTAGDILVGRTSPKGEENPTPEEKLMAAIFGQKSSNRKDTSLKVKHGHNGTVVDVEIISR 413

Query: 948 HGIDK-NERSISVEREQIELLAR 969
              D+  E    + +  I    +
Sbjct: 414 EDGDQLEEGVEKIIKVSIAQKRK 436



 Score =  293 bits (750), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 123/420 (29%), Positives = 187/420 (44%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ VG E+  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  IVKVGDEIKEGDLLVDGPSMKN-GEMALGKNVLVGFSTWNGYNYEDAVILSERLVKDDVY 305

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +          E  ++ +   +   ++   +E  I+         +IL G+ +
Sbjct: 306  TSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSEVTAGDILVGRTS 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +       L + +  +   ++           +     +K  +  +   +E     
Sbjct: 366  PKGEENPTPEEKLMAAIFGQKSSNR-----------KDTSLKVKHGHNGTVVDVE----- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I   + GD +  GV +++KV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DG
Sbjct: 410  -IISREDGDQLEEGVEKIIKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDG 468

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQ+ E HLG A   LG+K  + + D   +  I  +    +  
Sbjct: 469  TPLDMLLNPQGVPSRMNIGQVLELHLGQAAKNLGEKFVTPVFDGITHNQIKDILEEAKVN 528

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T V+ G                      
Sbjct: 529  PTGK----------------------------TVVYSGLT-------------------- 540

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 541  ------GEPFDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 594


>gi|4867799|emb|CAB43059.1| RNA polymerase II [Antonia ovata]
          Length = 262

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEXD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FXDVTVDNISRALHXCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|83415499|gb|ABC17957.1| RNA polymerase II second largest subunit [Synchytrium macrosporum]
          Length = 710

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 137/853 (16%), Positives = 252/853 (29%), Gaps = 164/853 (19%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI----NAKPVVSAVCEFF 517
            +R+   G +L   +RL   ++ + + + ++            I     +  + + +    
Sbjct: 2    KRLDLAGPLLAGLFRLYFQKVNKDLSKHLTKTLDSKQTVNVRIVAGVRSSTMTNGLKYAL 61

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+      +S ++H RRL++     + R       R +H T
Sbjct: 62   ATGNWGDQTKAMQARAGVSQVLNRYTYVSTLSHLRRLNS----PIGRDGKLARPRQLHNT 117

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L+  A ++     +     + +  +       ++  E+ 
Sbjct: 118  HWGMVCPAETPEGQACGLVKNLSLMATISVGSPHDHLIEFLDEEAMERFTEVSASQIEDA 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS---LIPF 681
              I    S +         + + R       +PRE     D   K++   A +     P 
Sbjct: 178  CKIFINGSWIGIHRDPAMIVQYLRELRRGSSIPREMSIVWDVRDKEIRIFADAGRIQRPL 237

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               DD  + L               +  F     E       G   +         + A+
Sbjct: 238  FIVDDQEQRLKWSLKPEVVQDFHANQHNF-----EWDEFVDRGVIELLDTEEEETVMIAM 292

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                 SV           ++                          + R       PS  
Sbjct: 293  TPHDLSVHRSHMAEDYEGEVN-------------------------IHRYTHCEIHPSMI 327

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +                       
Sbjct: 328  LG-------VCASIIPFPDHNQPPRNTYQSAMGKQAMGV--------------------- 359

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                  +S   L+      ++ +             +     S +   +  +  I     
Sbjct: 360  -----FLSNYQLRM---DTMMNILFYPQKPLGATRAMQYLKFSELPAGQNAIVCIACYSG 411

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +     +  +   + +   S   E IE  AR+          +
Sbjct: 412  YNQEDSLIMNQSSIDRGLFRSMFYRTYMDQEKKVGRSAMSETIEKPARENTARMKHGSYS 471

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G+  +       K+  LS D                  +  + +   K  
Sbjct: 472  KLDEDGLIAVGETVIGDDILVGKTMPLSQD---------------DQGQGGQRILQTKRD 516

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                    E+   +++              + VKV V   R  Q GDK A RHG KG V 
Sbjct: 517  ISKPLRSAENGVVDQVLI-----STNQSGYKFVKVRVRSMRIPQIGDKFASRHGQKGTVG 571

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF + G   D+V+NP  +PSRM +G + E  L       G++  +       
Sbjct: 572  MTYRHEDMPFTEQGIAPDLVINPHAIPSRMTIGHLVECLLSKVAALRGREGDATPFTELT 631

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              +IS                                                       
Sbjct: 632  VAEISRELEEYG------------------------------------------------ 643

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
              +          +LY G TG   +  V  G  +  +L HMV DK+++R+ G  + +T+Q
Sbjct: 644  -FQKRGF-----EVLYHGHTGRKLEAQVFTGPTFYQRLKHMVDDKIHSRARGPVTNLTRQ 697

Query: 1282 PLGGKSNRGGQRL 1294
            P  G++  GG R 
Sbjct: 698  PTEGRARDGGLRF 710


>gi|73697691|gb|AAZ81462.1| RNA polymerase beta subunit [Mycoplasma lagogenitalium]
          Length = 592

 Score =  326 bits (835), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 214/448 (47%), Positives = 307/448 (68%), Gaps = 14/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L S+
Sbjct: 1   NPLAEIANKRRVTSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGQNIGLILNLASY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++V+ +GFI+ PY  V DG +  + V +L+A++E     AQ++  +DE+     +L+  R
Sbjct: 61  SKVDKHGFIQAPYYPVEDGIINYDKVEWLTAVQEYGFTFAQSSIEVDENNKIIGDLITVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + ++V   ++D+ID + KQ+ SIA+S IPFLENDD+NR LMG NMQRQAVPL+ +EA
Sbjct: 121 KDHQYLMVKPTEVDYIDVASKQMTSIASSAIPFLENDDANRALMGANMQRQAVPLIDSEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  VAK +   + AK+AG V  VD+ +I I+  E         +  Y L  F+
Sbjct: 181 PLVGTGVEYDVAKYAATNLRAKKAGKVIFVDSQQIKIQEQE------KGEITNYNLRIFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+P+VKVGD V   D+I DGPST  G+LALG+N+LVAF  W+G+N+ED+++
Sbjct: 235 RSNQGTVITQKPIVKVGDVVEAGDLICDGPSTKDGELALGKNVLVAFTTWNGFNYEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DV+TSIHIEE  +  R +K G + +T DIPN S    +++DE GI+ +G+EV
Sbjct: 295 ISEKLVKDDVYTSIHIEEQTIQFRASKAGDDILTYDIPNASTRSKRHLDENGIVRIGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
           + GDILVG+ +PKGE   TPEEKL+ AIFG KA + +DTSL+V +G SGTV+DV+I +R 
Sbjct: 355 STGDILVGRTSPKGEDNPTPEEKLMNAIFGNKASNQKDTSLKVKNGDSGTVIDVQILSRA 414

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 415 QGDVLEDGIDKIIKVFIAQKRKIKVGDK 442



 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 129/503 (25%), Positives = 194/503 (38%), Gaps = 81/503 (16%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L  +          Y+       + R         I ++  ++  ++ + 
Sbjct: 165  GANMQRQAVPLIDSEAPLVGTGVEYDVAKYAATNLRAKKAG--KVIFVDSQQIKIQEQEK 222

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G                  I +  I+ VG  V  GD++    + K +  +   + +L A 
Sbjct: 223  GEITNYNLRIFERSNQGTVITQKPIVKVGDVVEAGDLICDGPSTK-DGELALGKNVLVAF 281

Query: 917  FGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
                  +  D  +            S  + +  I  R     ++  ++ +       ++ 
Sbjct: 282  TTWNGFNYEDAIIISEKLVKDDVYTSIHIEEQTIQFRASKAGDD-ILTYDIPNASTRSKR 340

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
              DE  I+         +IL G+ +  G         L + +      +Q          
Sbjct: 341  HLDENGIVRIGSEVSTGDILVGRTSPKGEDNPTPEEKLMNAIFGNKASNQKDT------- 393

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                        +            +I     GD +  G+ +++KVF+A KR I+ GDKM
Sbjct: 394  ----------SLKVKNGDSGTVIDVQILSRAQGDVLEDGIDKIIKVFIAQKRKIKVGDKM 443

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            AGRHGNKG++S +LP EDMP+L+DGTPVDI+LNP GVPSRMN+GQ+ E HLG A   L  
Sbjct: 444  AGRHGNKGVISLVLPVEDMPYLEDGTPVDILLNPQGVPSRMNIGQVLELHLGMAAKKLNV 503

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            K  S + D   N +I+ +                                          
Sbjct: 504  KFVSPVFDGVKNNNITSVLKEANLPTSGKFKL---------------------------- 535

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                                 G       +TG PFD  V+VG +YMLKL HMV DK+ AR
Sbjct: 536  -------------------YDG-------MTGIPFDNEVSVGVMYMLKLQHMVDDKMNAR 569

Query: 1271 STGSYSLVTQQPLGGKSNRGGQR 1293
            S G YSL+TQQPLGGKS  GGQR
Sbjct: 570  SVGPYSLITQQPLGGKSQNGGQR 592


>gi|194591891|gb|ACF76526.1| RNA polymerase beta subunit [Mycoplasma orale]
          Length = 595

 Score =  325 bits (834), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 213/444 (47%), Positives = 301/444 (67%), Gaps = 9/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ YGFI+TPY +V + KV  +  VYL+A+EE N  IAQ+  ++ ++G   +++V 
Sbjct: 61  SFAKIDKYGFIQTPYFRVKNRKVDFSQPVYLTAIEELNVVIAQSTINV-KNGIIIDDVVM 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E I    E +++I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++KA
Sbjct: 120 ARKDNEYIQAKAEDVNYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVIKA 179

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ +AK S   + +   G V  VDA +I I +            D+Y L  
Sbjct: 180 EAPLVATGVEADIAKYSSTNLRSNTTGKVTYVDANQIKILAD------GAKKADVYNLRT 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T ++Q P+VKVGDE++  D++ DGPS   G++ALG+N+LV F  W+GYN+ED+
Sbjct: 234 FERSNQGTLIHQIPIVKVGDEIKEGDLLVDGPSMKDGEMALGKNVLVGFSTWNGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + ++E GI+ +G+
Sbjct: 294 VILSERLVKDDVYTSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVG+ +PKGE   TPEEKL+ AIFG+K+ + +DTSL+V  G +GTVVDV I +
Sbjct: 354 EVTAGDILVGRTSPKGEENPTPEEKLMAAIFGQKSSNRKDTSLKVKHGHNGTVVDVEIIS 413

Query: 947 RHGIDK-NERSISVEREQIELLAR 969
           R   D+  E    + +  I    +
Sbjct: 414 REDGDQLEEGVEKIIKVSIAQKRK 437



 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 122/420 (29%), Positives = 187/420 (44%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ VG E+  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 248  IVKVGDEIKEGDLLVDGPS-MKDGEMALGKNVLVGFSTWNGYNYEDAVILSERLVKDDVY 306

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +          E  ++ +   +   ++   +E  I+         +IL G+ +
Sbjct: 307  TSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSEVTAGDILVGRTS 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +       L + +  +   ++           +     +K  +  +   +E     
Sbjct: 367  PKGEENPTPEEKLMAAIFGQKSSNR-----------KDTSLKVKHGHNGTVVDVE----- 410

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I   + GD +  GV +++KV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DG
Sbjct: 411  -IISREDGDQLEEGVEKIIKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQ+ E HLG A   LG+K  + + D   +  I  +    +  
Sbjct: 470  TPLDMLLNPQGVPSRMNIGQVLELHLGQAAKNLGEKFVTPVFDGITHNQIKDILEEAKVN 529

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T V+ G                      
Sbjct: 530  PSGK----------------------------TVVYSGLT-------------------- 541

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                  GEPFD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  ------GEPFDNPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|4867856|emb|CAB43079.1| RNA polymerase II [Peltanthera floribunda]
          Length = 260

 Score =  325 bits (834), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 78/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 128  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 226  GAAHFLKERLFDQSD 240


>gi|86451163|gb|ABC96804.1| RNA polymerase II [Guettarda uruguensis]
          Length = 213

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 110/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 199  GAAHFLKERLFDQSD 213


>gi|73697651|gb|AAZ81442.1| RNA polymerase beta subunit [Mycoplasma gypis]
          Length = 593

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 230/588 (39%), Positives = 341/588 (57%), Gaps = 43/588 (7%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++ S+
Sbjct: 2    NPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNMASY 61

Query: 590  ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A+++ YGFI+TPY KV +G V  N+V YL+A+EE N   AQ++ ++ +DG   ++ V  R
Sbjct: 62   AKIDEYGFIQTPYFKVNNGVVDFNNVKYLTAIEEINYTFAQSSINISDDGQILDDRVVVR 121

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               + I V +E++D++  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVPL+K EA
Sbjct: 122  KNNDYIEVNKEEVDYLGVSSRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPLIKPEA 181

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            PFV TG+E+ +A+ S A I + +AG V  VDA +I+I+  +            ++L  F+
Sbjct: 182  PFVATGVEADIARYSAANITSDKAGEVVYVDASKILIKGEK------DKKPHEFKLKTFE 235

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            +SNQ T ++QRP+VKVG ++   D++ DGPS + G+LALG+N+LV F  W+GYN+ED+++
Sbjct: 236  KSNQGTVIHQRPIVKVGQKIEVGDLLTDGPSMNNGELALGKNVLVGFTTWNGYNYEDAVI 295

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            ++ER+V +D++TSIHIEE  ++ R +K G + +T DIPNVS    + + E GI+ VG+EV
Sbjct: 296  LNERLVKDDIYTSIHIEEQTILFRRSKAGDDILTSDIPNVSNRSKRFLTEQGIVRVGSEV 355

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            + GDILVG+I+PK E   +PEEKL+ AIFG+KA   +DTSL+V  G +GTVV V + +R 
Sbjct: 356  SAGDILVGRISPKAEENPSPEEKLMAAIFGQKASTHKDTSLKVKHGHAGTVVAVDVLSRE 415

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              D  E       + IE + +    ++  +      ++ + + G++   G          
Sbjct: 416  NGDTLE-------DGIERIVKVSIAQKRKI------KVGDKMAGRHGNKGVVSIVLPEEE 462

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQR-NVESLKVQYETSK---SILEDRFKNKIEKIQWGD 1064
               L    P            ++    V  L +     K     +   F     K     
Sbjct: 463  MPYLEDGTPLDILLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVSPVFDGISYKQIQEI 522

Query: 1065 DMPPGVLRVVK--VFVAMK-----RPIQSG------------DKMAGR 1093
                G+ +  K  V+ A        PI  G            DKM  R
Sbjct: 523  QEEAGLDKSGKMTVYSAQTGEPFDNPISVGIMYYLKLYHMVDDKMHAR 570



 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 120/413 (29%), Positives = 176/413 (42%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG ++  GD+L    +      +   + +L         +  D  +     V    +
Sbjct: 248  IVKVGQKIEVGDLLTDGPS-MNNGELALGKNVLVGFTTWNGYNYEDAVILNERLVKD-DI 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I          RS + +      +    +  +  L      R+   +   + + G  
Sbjct: 306  YTSIHIEEQTILFRRSKAGDDILTSDIPNVSNRSKRFLTEQGIVRVGSEVSAGDILVGRI 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q A   +     V+        +  +L           
Sbjct: 366  SPKAEENPSPE--EKLMAAIFGQKASTHKDTSLKVKHGHAGTVVAVDVLSR--------- 414

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ R+VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 415  ENGDTLEDGIERIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPEEEMPYLEDGTPLDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  S + D  +   I  ++           
Sbjct: 475  LLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVSPVFDGISYKQIQEIQEEAG------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      +  +Y   
Sbjct: 528  ------------------------------------------LDKSG-----KMTVYSAQ 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 541  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 593


>gi|226897650|gb|ACO90274.1| RNA polymerase beta subunit gene [Bacillus sporothermodurans]
          Length = 357

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 220/357 (61%), Positives = 275/357 (77%), Gaps = 3/357 (0%)

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQAN 631
           T EG NIGL++SL+S+A+VN YGFIETPYR+V    GK+T+ + YL+A EE+N  +AQAN
Sbjct: 1   TPEGPNIGLINSLSSYAKVNPYGFIETPYRRVDPETGKLTDQIDYLTADEEDNYVVAQAN 60

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           S + EDGSF +E V  R  GE     R++ID++D SPKQVVS A + IPFLENDDSNR L
Sbjct: 61  SRIAEDGSFADEEVIARFRGENTAFKRDRIDYMDVSPKQVVSAATACIPFLENDDSNRAL 120

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG- 750
           MG NMQRQAVPL++ EAP VGTGME V AK SGAA++ K  GIVE V+A  I +R V+  
Sbjct: 121 MGANMQRQAVPLMQPEAPIVGTGMEHVSAKDSGAAVICKHDGIVEHVEAREIWVRQVKNI 180

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           D       ++ YRL KF RSNQ TC NQRP+V VGD V + +++ DGPS +  +LALGRN
Sbjct: 181 DGQEVKGDLNKYRLQKFIRSNQGTCYNQRPIVSVGDRVVKGEVLGDGPSMEKAELALGRN 240

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +LVAFM W GYN+ED++++SER+V +DV+TSIHIEE+E  ARDTKLGPEE+TRDIPNV E
Sbjct: 241 VLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEMTRDIPNVGE 300

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           + L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDT
Sbjct: 301 DALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 357


>gi|310831213|ref|YP_003969856.1| putative DNA-directed RNA polymerase subunit Rpb2 precursor
            [Cafeteria roenbergensis virus BV-PW1]
 gi|309386397|gb|ADO67257.1| putative DNA-directed RNA polymerase subunit Rpb2 precursor
            [Cafeteria roenbergensis virus BV-PW1]
          Length = 1331

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 223/1458 (15%), Positives = 463/1458 (31%), Gaps = 249/1458 (17%)

Query: 3    KGVVFNGLGRVRK--------FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG 54
               +      +RK        +F   P+++    L     +SY  F+   I         
Sbjct: 1    MSEIITNKKDLRKGIDSLIDLYFS-QPKVL-YSHL----FSSYHQFVEEMIPYS------ 48

Query: 55   LQAAFKSVFPITAFSGAAML---EFVSYEFDPPKFD-------VDDCLWRDLTYAVPLKI 104
            L+    + F     + A  L   +F   +  PP  +               L Y   +  
Sbjct: 49   LEEE-TNYFYDNVTNDAIYLYGFKFEDTKILPPVRERDNEIIFPQMARKNFLNYFANINT 107

Query: 105  TLRLIVFDVDEFTGAKSIKDI--KEQSIYMGDLPLMTKD--------------------- 141
             +      V+  TG  + ++I   E+ + +  +P+M K                      
Sbjct: 108  KVTQFQEKVNLHTGEITRRNIGDPEEMV-VASIPVMVKSKYCATSLKPETSKYECKYDPG 166

Query: 142  GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD------IE 195
            G F++ G +++VVS             K  +S     +Y  +I   +  W +      I 
Sbjct: 167  GYFIVGGQEKVVVSIEKMIDNKILVFSKSDSSFPKGKMYTSQINSRKHDWSENLQIIAIR 226

Query: 196  FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL--------STFYPKIVYSQRGDFWCF 247
             +  D + +   +  ++P+   L ALG++++  L               +     +    
Sbjct: 227  NNKDDSLIITTSQLVEIPIMVLLRALGIENDRELIARITNNLDDIPMVNLLRNSLENSVD 286

Query: 248  PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--DCLCG 305
                        ++  +  +  G ++ +S +++     K L EK +    +      + G
Sbjct: 287  DNGNLIKTREEAINFLMTKMKAGRRISQSDEQVAQAQKKLLLEKIITKDLLPHLGADIPG 346

Query: 306  LYVAEDIVNGETGEIYIEAGDVIDEKSLE-EIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
                  ++  +   + +      D  + E +   +    +  L+  + N        L  
Sbjct: 347  KASFICLMVKKILLVMLGRKQEDDRDAFENKRVETPGVLLGQLFRQNFNKMLKEIGKLFR 406

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
             KN   +  +  + ++             +   +    +      ++ R+     ++   
Sbjct: 407  RKNNSDETPINMVSQITPTTIEQGIKSGLATGIWGVSKTKAGAAQSLSRLTWLQTISYLR 466

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               ++    +   + I  +  + N +            +   + + L     +   R+E 
Sbjct: 467  --RIKSPNMDTSTSKITSIRQINNVQAFFVCNVETPEGQPIGLAKSLSMMATITP-RLES 523

Query: 485  SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
              +     ++    M          ++ + + F +     + +     S   + ++    
Sbjct: 524  QTELINKLIEEHPKMYHPFAVNPEDINNMIKIFHNGSWKGVLDIKEGYSFFENLKK---- 579

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R     +   +   ++ +     T  G  I                       K
Sbjct: 580  ----MRRNSKINKFVTITLDYFEKDLYIYTEAGRLIRP-------------------LLK 616

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            V D +                 I    + + +               + +L   + +D+ 
Sbjct: 617  VDDNE-----------------IKLTKTIVADIKKHLTGDKKSSGWNQILLKYPDLVDYE 659

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D    + +  A  +   LEN  ++   +    +               T  E   +   G
Sbjct: 660  DIESSRHLMFAMDMQMLLENKANSLRDINTKEEIIKPNRYGKFRYVNYTHSEFHPSMMLG 719

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              +       V  ++        +         G+           +      Q PLV  
Sbjct: 720  TIV-----STVPFINHNPSPRGIIFFSQAKQAIGIYSTAYKDRMDISNILYHPQVPLV-- 772

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            G +  + +           D+  G N++VA M + GYN EDS++I++  +   +F +  +
Sbjct: 773  GTKASKYN--------RFDDIPSGENIIVAIMSYKGYNVEDSIMINQTSLDRGLFRADSL 824

Query: 845  EEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             ++           ++     P+      ++    + ++E G I     V   DIL+GK+
Sbjct: 825  RKYSSKIEKNPSSSQDDIFMKPDRNKVTGMTRGNYEKLNEKGYIPEETPVTSNDILIGKV 884

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDT--------------SLRVPSGVSGTVVDVRI 944
            +P   +      K    +F      V D               S+RV       ++  + 
Sbjct: 885  SPIQPTSDNKVYKDKSELFKSNVDGVVDRVHKDIFNNDGYEMISMRVRM-ERPPIIGDKF 943

Query: 945  FNRHGIDKNERSISVEREQIELLARD---KDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++          ++  +I++        D    I+     S+      G         
Sbjct: 944  CQKYDTLVLTHLGWIKLGEIDITIHKVATLDKHDNIIYVYPTSKFEFDYDGDFYEHKNNS 1003

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEK-----VQRNVESLKVQYETSKSILEDRFKNK 1056
                  ++  L  +Y  S  +     D+      + +N+E+  +  + SK  + + +K K
Sbjct: 1004 IDIECTINHKLYCKYNLSSSFTLIPADKVYGNKVIMKNMENEVIWTDPSKEQIHN-YKGK 1062

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQ----SGDKMAGRHGNKGIVSRILPCEDMPFL 1112
            +  I+  D           ++      I      G+  + +HG KG V   LP  DMPF 
Sbjct: 1063 VYCIEVPDS---------HIYYMKTSSITPPVWIGN--STKHGQKGTVGITLPQRDMPFT 1111

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   D++ NP G+P+RM +GQ+ ET    A   +G+                      
Sbjct: 1112 SEGMTPDLIFNPHGMPTRMTMGQLAETLASKAAANIGELFDG------------------ 1153

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               TP F   D   I  +L+   +DE G
Sbjct: 1154 -----------------------------------TP-FSDYDVTEIPKVLKELGMDEYG 1177

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               +Y G+TG      + +G ++ L+L HMV DKV++RS G    +T+QP+ G+S  GG 
Sbjct: 1178 TEEMYCGMTGRKMKARIFIGPMFYLRLKHMVLDKVHSRSMGPRQAITRQPMEGRSKDGGL 1237

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGR--TRVY--ESIVAGN----- 1336
            ++GEME   + A+G    L+E +   SD       D  G   T+V   E  V  N     
Sbjct: 1238 KIGEMEKDAMVAHGIGQFLKERMMENSDITTIMVCDKCGTFATKVMDKEYYVCNNCNNHT 1297

Query: 1337 DTFETGTPESFNVLVKEM 1354
            D      P +F ++V+E+
Sbjct: 1298 DFSNVAMPYAFKLMVQEL 1315


>gi|256811203|ref|YP_003128572.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus fervens
            AG86]
 gi|256794403|gb|ACV25072.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus fervens
            AG86]
          Length = 633

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 102/501 (20%), Positives = 179/501 (35%), Gaps = 100/501 (19%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + AI   +  ++ D  +   S +    +    F R       R    + 
Sbjct: 198  GFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSAIDRG-LGRSTFFRTYDACERRYPGGQM 256

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +         + L      S     K   V+           + 
Sbjct: 257  DRFEVPDKG-------VRGYRSEEAYKHLEEDGIASVEAHVKGGDVIVGKTSPPRFLEEH 309

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    ++   V+  +          E+ + +K+   +          R+VKV V   
Sbjct: 310  --------EITIQVKPQRRDSSVVVRHGEEGYIDKVILTE-----TKEGNRLVKVKVRDL 356

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++   +P ED+PF + G   DI++NP  +PSRM VGQ+ E   
Sbjct: 357  RVPELGDKFASRHGQKGVIGLTVPQEDLPFTESGIVPDIIINPHAIPSRMTVGQLLEMLG 416

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++I   I   +   D+      L                             
Sbjct: 417  GKVGALEGRRIDGTIFSGEKEWDLRKALEALGFKNHGKEVM------------------- 457

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+       TG+ F+  + +G  Y  KL+H
Sbjct: 458  ----------------------------YDGK-------TGKKFEVEIYIGIAYYQKLHH 482

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA +L+E L  +SD 
Sbjct: 483  LVAGKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLMDESDP 542

Query: 1321 -DVV-------------GRTRVY-------ESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
             D+               R   Y       E++           P +F +L+ E++++ +
Sbjct: 543  YDICICSKCGDFAILDYKRNLKYCPICGEIENLYNSKKIPFVRLPYAFKLLLDELKSMCI 602

Query: 1360 SIDLENSRTKNSAKMEEIPDF 1380
               L   + K+  ++E+  DF
Sbjct: 603  ---LPKIKVKDKVELEDFEDF 620



 Score = 92.1 bits (227), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 62/331 (18%), Positives = 107/331 (32%), Gaps = 100/331 (30%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YL A EEEN YIA +   L                        EK   ++  P  ++ 
Sbjct: 99  IEYLDAEEEENAYIALSEEELT-----------------------EKHTHLEIDPLTILG 135

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I A + P+ E++ + R+ M   M +Q++ +  +   +                       
Sbjct: 136 IGAGVAPYPEHNSAPRITMAAAMGKQSLGIPMSNIKW----------------------- 172

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                +      Y               Q P+V+   +      
Sbjct: 173 ------------------RLDTRGHYLHYP--------------QVPIVRTKHQ------ 194

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                         G+N +VA M + GYN ED+++ ++  +   +  S     ++   R 
Sbjct: 195 ----EILGFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSAIDRGLGRSTFFRTYDACERR 250

Query: 854 TKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              G  +             SEE  K+++E GI  V A V  GD++VGK +P        
Sbjct: 251 YPGGQMDRFEVPDKGVRGYRSEEAYKHLEEDGIASVEAHVKGGDVIVGKTSPPRFLEE-- 308

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  I  +     RD+S+ V  G  G +
Sbjct: 309 -----HEITIQVKPQRRDSSVVVRHGEEGYI 334


>gi|56675684|emb|CAB43058.2| RNA polymerase II [Anthocleista grandiflora]
          Length = 257

 Score =  325 bits (834), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 107/250 (42%), Gaps = 54/250 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 38   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTSEGITPDIIVNPH 97

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 98   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 125

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 126  ---------------------ATP-FTDVTVDNISKALHRCGYQMRGFERMYNGHTGRPL 163

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 164  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 223

Query: 1306 GAAYVLQEML 1315
            GAA+ L+E L
Sbjct: 224  GAAHFLKERL 233


>gi|91773159|ref|YP_565851.1| DNA-directed RNA polymerase subunit B' [Methanococcoides burtonii DSM
            6242]
 gi|91712174|gb|ABE52101.1| DNA-directed RNA polymerase subunit B' [Methanococcoides burtonii DSM
            6242]
          Length = 604

 Score =  325 bits (833), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 111/602 (18%), Positives = 194/602 (32%), Gaps = 96/602 (15%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ G+   R+  + D    +  D     N  +             + I   ++       
Sbjct: 81   VRDGEISFRD--LLDMGYVEYLDAEEEENAFIGLYEEDLTPNHTHLEIDPSLMLGICTGM 138

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   E     R+T      + +    VS   L  +       V                 
Sbjct: 139  VPYPEHNASPRNTMGAA--MIKQCIGVSSSNL-KLRPDTRAHVLHYPQKAMTRTQTCDAI 195

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  +    G     +    F R    +  R    + 
Sbjct: 196  HFDERPAGQNFVVAVMSYEGHNIEDALVFNK-GSIQRGLGRSHFLRTFEGEERRYPGGQE 254

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +             +  ++ L     V GP             + E      
Sbjct: 255  DKFEIPDSEF--RGARSADAYANLDIDGLVNPETVVGPNDVLIGKTSPPRFLEEQSD--- 309

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   ++               +  +S +  R   K               R+ KV +  +
Sbjct: 310  FGITIE---------------QRRESAITMRSNEKGIVDTVILTESINGTRLAKVKIRDE 354

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  I+P  DMPF + G   D+V+NP  +PSRM V  + E   
Sbjct: 355  RIPEIGDKFASRHGQKGVIGLIVPYHDMPFTELGMVPDLVINPHAIPSRMTVAHVLEMIG 414

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++             I                                    
Sbjct: 415  GKLGSLEGQRKWGTAFSGDMEDGIR----------------------------------- 439

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                      DG                 +G+ +  DG+TG+     V VG I   KL+H
Sbjct: 440  ----------DGLKNR---------GFSHTGKEVFCDGVTGKKIQADVFVGVILYQKLHH 480

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD 
Sbjct: 481  MVASKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMTLKERLLDESDK 540

Query: 1322 V-------VGRTRVYE---SIVAGND------TFETGTPESFNVLVKEMQALGLSIDLEN 1365
            V        G    ++   +I   ++              +F +L+ E+++LG++  L  
Sbjct: 541  VVELVCAQCGMVATFDRTRNIRYCSNCGAETDIHPVEMSYAFKLLLDEIKSLGVAPRLRL 600

Query: 1366 SR 1367
              
Sbjct: 601  DD 602



 Score = 90.5 bits (223), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 71/457 (15%), Positives = 138/457 (30%), Gaps = 110/457 (24%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F   +L         L      +R S +    +           +  +  GR        
Sbjct: 7   FLDGELIGTHNDPVELVESIRGQRRSGMLPHQLNVTLYEDIHEVILSSDIGRARRPAIVV 66

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            + +  +++      V      E  +R + D      V YL A EEEN +I      L  
Sbjct: 67  ENGVPSITAEY----VEKVRDGEISFRDLLDMGY---VEYLDAEEEENAFIGLYEEDLTP 119

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +                          ++  P  ++ I   ++P+ E++ S R  MG  M
Sbjct: 120 NH-----------------------THLEIDPSLMLGICTGMVPYPEHNASPRNTMGAAM 156

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +Q + +  +                                                + 
Sbjct: 157 IKQCIGVSSSNLKL-----------------------------------------RPDTR 175

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           + V  Y      R+     +                           +   G+N +VA M
Sbjct: 176 AHVLHYPQKAMTRTQTCDAI------------------------HFDERPAGQNFVVAVM 211

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSE 870
            + G+N ED+++ ++  +   +  S  +  FE   R    G E+   +IP+       S 
Sbjct: 212 SYEGHNIEDALVFNKGSIQRGLGRSHFLRTFEGEERRYPGGQEDKF-EIPDSEFRGARSA 270

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           +   N+D  G++     V P D+L+GK +P             ++ FG      R++++ 
Sbjct: 271 DAYANLDIDGLVNPETVVGPNDVLIGKTSPPRFLEE-------QSDFGITIEQRRESAIT 323

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
           + S     +VD  I            + +  E+I  +
Sbjct: 324 MRSNEK-GIVDTVILTESINGTRLAKVKIRDERIPEI 359


>gi|226897642|gb|ACO90270.1| RNA polymerase beta subunit gene [Bacillus firmus]
          Length = 387

 Score =  325 bits (833), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 222/366 (60%), Positives = 283/366 (77%), Gaps = 3/366 (0%)

Query: 589 FARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           FA+VN +GFIETPYR++    GKVT+ + YL+A EE+N  +AQAN+ L +DGSF +E V 
Sbjct: 2   FAKVNRFGFIETPYRRIDPETGKVTSRIDYLTADEEDNYVVAQANALLGDDGSFLDEEVV 61

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  GE  +V R+++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ 
Sbjct: 62  ARFKGENTVVKRDRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQP 121

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLM 765
           EAP VGTGME V  K SGAA++ K  GIVE V+A  + +R ++  D       +D YR++
Sbjct: 122 EAPRVGTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRIKNVDGQEVKGDLDKYRML 181

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAFM W GYN+ED
Sbjct: 182 KFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAFMTWDGYNYED 241

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII  G
Sbjct: 242 AIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGIIRTG 301

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           AEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++F
Sbjct: 302 AEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVF 361

Query: 946 NRHGID 951
           NR   D
Sbjct: 362 NREDGD 367



 Score = 46.2 bits (108), Expect = 0.043,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 72/233 (30%), Gaps = 23/233 (9%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  +        ++  I+ VG  V  G+IL    +      +     +L A 
Sbjct: 173  GDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPS-MELGELALGRNVLVAF 231

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 232  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 291

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 292  LDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR------------- 338

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                E                   K+   + GD++PPGV ++V+V++  KR +
Sbjct: 339  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRNL 387


>gi|52694255|emb|CAG30657.1| DNA-directed RNA polymerase beta chain [Pseudomonas putida]
          Length = 327

 Score =  325 bits (833), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 194/327 (59%), Positives = 254/327 (77%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLIN+KPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINSKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 FLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVA 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G++
Sbjct: 181 ASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERYVARDSGVCVVARRGGVI 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+A
Sbjct: 241 DSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMA 300

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYN 822
           DGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 DGPSTDMGELALGQNMRIAFMAWNGFN 327


>gi|6606103|gb|AAF19064.1|AF107792_1 DNA-dependent RNA polymerase II RPB140 [Microascus trigonosporus]
          Length = 937

 Score =  325 bits (833), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 166/1047 (15%), Positives = 309/1047 (29%), Gaps = 172/1047 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L  KG +    +S  +    +           I+   G V DE  L
Sbjct: 37   LEKGSRLISQLALRLYSKGGRGAS-SSGAIVHATLPYVREETPIALIFRAYGVVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      +++         +DR+ AL  I +  + G  +     +
Sbjct: 96   NHICYDRNDSQMLEMLKPCIEESFV--------VQDREVALDHIGKRGQQGGFA--LTRD 145

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                       K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 146  KRIRTAKEILQKETLPHI-----------SQAEGSETRKAFFLGYMVHKLLQCALGRRDV 194

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R  + RM   +    ++   +  +      I    + +
Sbjct: 195  DDRDHFGKKRLDLAGPLLSKLFRNIMRRMNTELTSYMKMCIQNNRNFQISQGIRITTLTN 254

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 255  GMKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKP 310

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    V+     +    +    + ++  +   
Sbjct: 311  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTPTDPIEEFMIDREMEIVEEYEP 370

Query: 617  LSAMEEENRYIAQANSSLD-EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            L        ++  A   +  E     EE++  R             D  D   K      
Sbjct: 371  LRFPNATKVFVNGAWVGVHQEPQRLMEEMIKARRVNSFPAEVSLVRDIRDREFKVFSDAG 430

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK--RAG 733
              + P    +   R        ++   +L  E     T  E  +             R+G
Sbjct: 431  RVMRPVFVVN---RENNEYEGVQKGTLVLSKEQVAQLTE-ERDLPTEQRKLKWEDLVRSG 486

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             VE +DA       +    +             +    N N   N+R    +        
Sbjct: 487  AVEYLDAEEEETAMICMTPEDLELFRQTKVEGHQVPPPNINDEPNRRLKTDLNPTTYTYT 546

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVM 850
                 PS  LG       +  + +P+  +N          M  +    F + ++      
Sbjct: 547  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYMRR---- 595

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                          +  +             +       +   +
Sbjct: 596  ---------------------------MDTMANILYYPQKPLATTMAMEHLKFRELPAGQ 628

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D  +R        +E   + 
Sbjct: 629  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYTDCEKRVGI---NLLEQFEKP 684

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               E + L    Y +L E   +  G           K++ LS +      R+        
Sbjct: 685  FRSETLRLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTSPLSPESQELGQRTTQHTQRDA 744

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +                                ++ VKV V   +  Q G
Sbjct: 745  STPLRSTESGIVDS--------------------VVFTTNADGMKYVKVRVRTTKVPQIG 784

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L      
Sbjct: 785  DKFASRHGQKGTIGVTYRQEDMPFTREGITPDIIINPHAIPSRMTIAHLIECLLSKVATL 844

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +          +S L     +   +       +                     
Sbjct: 845  KGLEGDATPFTDVTVDSVSALLRA--EGYHSRGFEIMYNG-------------------- 882

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                   +G+               V  G  Y  +L HMV DK+
Sbjct: 883  ----------------------HTGK----------KLRAQVFFGPTYYQRLRHMVDDKI 910

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +AR+ G   ++T+QP+ G++  GG R 
Sbjct: 911  HARARGPVQIMTRQPVEGRARDGGLRF 937



 Score =  155 bits (391), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 122/854 (14%), Positives = 244/854 (28%), Gaps = 135/854 (15%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEF---------- 196
            ++++++Q  RS          + +      Y   I    ++G  +  +           
Sbjct: 1   SEKVIIAQE-RSAANI--VQVFKKAQPSPYSYTAEIRSALEKGSRLISQLALRLYSKGGR 57

Query: 197 ---DSKDIIHVRIDRRRK-VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSA 251
               S  I+H  +   R+  P+     A G+   E+IL+        SQ  +     +  
Sbjct: 58  GASSSGAIVHATLPYVREETPIALIFRAYGVVSDEDILNHICYDRNDSQMLEMLKPCIEE 117

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGIT------SDCLC 304
           + ++   +V+   +     +      +       K  L+++ +  +              
Sbjct: 118 SFVVQDREVALDHIGKRGQQGGFALTRDKRIRTAKEILQKETLPHISQAEGSETRKAFFL 177

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G  V + ++    G   ++  D   +K L+       +    +               + 
Sbjct: 178 GYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLSKLFRNIMRRMNTELTSYMKMCIQ 236

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           +    +    + I  +       T  +  S+    + D  K   ST G  ++  R    +
Sbjct: 237 NNRNFQISQGIRITTL-------TNGMKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFAS 289

Query: 425 PDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                 R          +     L N    +         +   + + L     + +   
Sbjct: 290 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTP 349

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
              I+E +   D +  + ++    +   +       +      E        I   R  S
Sbjct: 350 TDPIEEFMI--DREMEIVEEYEPLRFPNATKVFVNGAWVGVHQEPQRLMEEMIKARRVNS 407

Query: 543 ALGQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
              +  + R     E        R + P         E        LV S    A++   
Sbjct: 408 FPAEVSLVRDIRDREFKVFSDAGRVMRPVFVVNRENNEYEGVQKGTLVLSKEQVAQLTEE 467

Query: 596 GFIETPYRK--VCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVF----- 646
             + T  RK    D   +  V YL A EEE   I     +  L          V      
Sbjct: 468 RDLPTEQRKLKWEDLVRSGAVEYLDAEEEETAMICMTPEDLELFRQTKVEGHQVPPPNIN 527

Query: 647 ---CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R    ++          +  P  ++ I AS+IPF +++ S R      M +QA+  
Sbjct: 528 DEPNRRLKTDLNPTTYTYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGF 587

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                              + + +  Y 
Sbjct: 588 FLTNYM-----------------------------------------RRMDTMANILYYP 606

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                 +     +  R                        +L  G+N +VA   + GYN 
Sbjct: 607 QKPLATTMAMEHLKFR------------------------ELPAGQNAIVAIACYSGYNQ 642

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDE 878
           EDS+++++  +   +F S+    +    +   +   E        +   +       +DE
Sbjct: 643 EDSVIMNQSSIDRGLFRSLFFRSYTDCEKRVGINLLEQFEKPFRSETLRLKHGTYDKLDE 702

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GI+  G  V+  DI++GK +P     ++PE + L     +     RD S  + S  SG 
Sbjct: 703 DGIVAPGVRVSGEDIIIGKTSP-----LSPESQELGQRTTQHTQ--RDASTPLRSTESGI 755

Query: 939 VVDVRIFNRHGIDK 952
           V  V         K
Sbjct: 756 VDSVVFTTNADGMK 769


>gi|83415503|gb|ABC17959.1| RNA polymerase II second largest subunit [Glomus intraradices]
          Length = 764

 Score =  325 bits (833), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 142/866 (16%), Positives = 261/866 (30%), Gaps = 136/866 (15%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R+   ++ + +   +               I A+ + + +     +
Sbjct: 2    KRMDLAGPLLASLFRMLFKKLTKDVSAYLRKCIDGNREFNLNLAIKAQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CP+ET EG   GLV +L+  + ++     +             +   ++  ++ +  
Sbjct: 118  GMVCPSETPEGQACGLVKNLSLMSYISVGSASKPI------IDFLEEYGMINLNQQFDPA 171

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              + N+ +  +G +             +   R  +   D SP+  V             D
Sbjct: 172  NIRDNAKVFVNGKWVGISSSPEQLSYTLKGLRRTV---DVSPEVSVVRDIREKELRIYTD 228

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + RV     +   A   +         G+   + K+  A  V +    +   D       
Sbjct: 229  AGRVCRPLFIVESARLKITK-------GLIQKLDKNRQAGQVEESDDDLFDDDENIDDDM 281

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              E   +P        +  K     Q    N      V + +   +           DLA
Sbjct: 282  EEEDIDNPEQPSRRRRKKKKSSFGWQELISN-----SVVEYIDAEEEETVMICMTPEDLA 336

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
              R              E  +      V  D    I+      +     LG        P
Sbjct: 337  SSRVFHETGEVKQEKAHERDIA---ARVKTDTNLKIYTWTHCEIHPSMILGICASIIPFP 393

Query: 867  NVSEE-GLKNIDECGIICVGAEVNPGDILVG-----------------KITPKGESPMTP 908
            + ++          G   +G  V    + +                   +       +  
Sbjct: 394  DHNQSPRNTYQSAMGKQAMGIYVTNHQLRMDTLANILYYPQKPVVTTRAMEFLRFRELPA 453

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    IF R  +D+ ++   +  E+ E   
Sbjct: 454  GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIFYRSYMDQEKKVGMLTIEEFEKPT 512

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            ++                  I  G           K T +S++ +    R          
Sbjct: 513  KETTLRLKHGTYEKLEDDGLIAPGTRVSGDDIIIGKVTPISNETLELGQRQTTHTQRDAS 572

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +  Q                             ++ VKV V   R  Q GD
Sbjct: 573  TPMRSTETGIVDQ--------------------VMVTTNAEGMKFVKVRVRSTRVPQMGD 612

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  +G   D+V+NP  +PSRM +G + E  LG      
Sbjct: 613  KFASRHGQKGTIGITYRQEDMPFTAEGIAPDLVINPHAIPSRMTIGHLVECLLGKVSTLT 672

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G++  +          IS                           LR+      G  V  
Sbjct: 673  GQEGDATPFTDVTVEAIS-------------------------QSLRLQGYQSRGFEVM- 706

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                  +G +       G      V +G  Y  +L HMV DK++
Sbjct: 707  ---------------------YNGHT-------GRKLAAQVFLGPTYYQRLKHMVDDKIH 738

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +R+ G   ++T+QP+ G+S  GG R 
Sbjct: 739  SRARGPVQILTRQPVEGRSRDGGLRF 764


>gi|4867874|emb|CAB43077.1| RNA polymerase II [Oldenlandia corymbosa]
          Length = 262

 Score =  325 bits (833), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 79/254 (31%), Positives = 109/254 (42%), Gaps = 54/254 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 42   TNADGLRFVKVRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKS 1319
            GAA+ L+E L  +S
Sbjct: 228  GAAHFLKERLFDQS 241


>gi|255569145|ref|XP_002525541.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis]
 gi|223535120|gb|EEF36800.1| DNA-directed RNA polymerase III subunit, putative [Ricinus communis]
          Length = 1139

 Score =  325 bits (832), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 118/599 (19%), Positives = 200/599 (33%), Gaps = 94/599 (15%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D VR  D        +  D+    N LVA            + I    +       I   
Sbjct: 617  DGVRTFDDFLRDGLIEYLDVNEENNALVALYEGEATPETTHIEIEPFTILGVCAGLIPFP 676

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNI-DECGIICVGAEVNPGDILVGKITPKGES 904
                  R+T     +       +       +     ++ +        +    I   G  
Sbjct: 677  HHNQSPRNT----YQCAMGKQAMGNIAYNQLFRMDSLLYLLVYPQRPLLTTRTIELVGYD 732

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +    A+      D+ D  +   + +        +  ++            R++ 
Sbjct: 733  KLGAGQNATVAVMSYSGYDIEDAIVMNKASLDRGFGRCIVMKKYPA---------IRQKY 783

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E  A D      IL  +       +L      +  +  K S +                 
Sbjct: 784  ENGASD-----RILRPDRTVERERVLDYDGLAAPGEIIKPSDIYVKKECPI--------D 830

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             +   K    +E++K  Y  S    +          +            +KV +   R  
Sbjct: 831  TMGPVKSSAALENIK--YRPSPLSYKGPEGESPVIDRVALSSDRNNNLCIKVMIRHTRRP 888

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSRM VG++ E   G A
Sbjct: 889  EVGDKFSSRHGQKGVCGTIIQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKA 948

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
             V  G+          +                                           
Sbjct: 949  GVSCGRFHYGSAFGEPSGHAD--------------------------------------- 969

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                        EAI+  L       +G+ I+Y G+TG P    + +G IY  KL HMV 
Sbjct: 970  ----------TVEAISETLVNRGFSYNGKDIIYSGITGCPLQAYIFMGPIYYQKLKHMVL 1019

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD--- 1321
            DK++AR  G   ++T+QP  G++  GG R+GEME  C+ AYGA+ ++ E L I SD    
Sbjct: 1020 DKMHARGNGPRVMLTRQPTEGRARNGGLRVGEMERDCLIAYGASMLIFERLMISSDPFEV 1079

Query: 1322 ----VVG---------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                V G         R  +  +   G++      P +  +L++E+Q++ +   L+ + 
Sbjct: 1080 QVCRVCGLLGYFNQKLRAGICSTCKNGDNISTMKLPYACKLLIQELQSMNIVPRLKLAE 1138



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 141/970 (14%), Positives = 290/970 (29%), Gaps = 191/970 (19%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAAMLE 75
           F   PE + +  L++    S+++F+          N G++   ++   I +       L 
Sbjct: 38  FQLLPEFLKVRGLVKQHLDSFNYFV----------NIGIKKIVRANDRIVSTVDPGIYLR 87

Query: 76  FVSYEFDPPK---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           F       P               C   D TYA P+ + +  I    D+ T       ++
Sbjct: 88  FKDVRIGTPSDIMDGVSEQLSPHMCRLSDKTYAAPILVNVEYIYGSHDQKTR------VE 141

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
           +  + +G +P+M                           G FVIKG +++++ Q   S  
Sbjct: 142 KNDVVIGRMPIMLRSRSCVLYGKDEAELARLGECPLDPGGYFVIKGTEKVILIQEQLSKN 201

Query: 163 -IHFDHDK-----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVT 215
            I  D DK        + S +   +  II             K+ +++ +++  +K+P+ 
Sbjct: 202 RIIIDTDKKGNINASVTSSTEATKSKTII----------QMEKEKMYLCLNQFVKKIPIM 251

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             + A+GM+S+ E++        YS          +   +    K    L   +      
Sbjct: 252 VVIKAMGMESDQEVVQMVGRDPRYSALLLPSIEECAGLSIYTQQKALEYLDGKEN----- 306

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL- 333
                     L  L++  +  + +  +      +   ++     E  +    + D+  + 
Sbjct: 307 --------RALTILRDVFLANVPVHKNNFRPKCLYVAVMLRRMMEAMLNKDAMDDKDYVG 358

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            +      + I +L+ D       +  T++T+  +     L    R  R  D++ + V +
Sbjct: 359 NKRLELSGQLISLLFED-------LFKTMITEVQRTIDTVLTKQNRSSR-FDLAQYIVRD 410

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++ N L       +   V R KM+ +           +     + ++  +         +
Sbjct: 411 NITNGLERTLSTGNFD-VKRFKMHRKGMTQVLVR---LSYIASLGMMTRVSPQFEKSRKV 466

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                L   +   +      +     L    ++   +++ D +  +             +
Sbjct: 467 SGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDDEEGPLISLCYCLGVEDLEL 526

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPA 572
                    +      N L    H R    +     + RA    E   V      R    
Sbjct: 527 LSGEELHTPNSFLVIFNGLILGKHRRPQYFVNSMRKLRRAGKIGEFVSVFVNEKQRAVYL 586

Query: 573 ETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            +  G     +          + +    +    R   D      + YL   EE N  +A 
Sbjct: 587 ASDGGRVCRPLVIADRGVSRIKEHHMKELRDGVRTFDDFLRDGLIEYLDVNEENNALVAL 646

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                                         +   I+  P  ++ + A LIPF  ++ S R
Sbjct: 647 YEGEATP-----------------------ETTHIEIEPFTILGVCAGLIPFPHHNQSPR 683

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+                                           I   +
Sbjct: 684 NTYQCAMGKQAMGN-----------------------------------------IAYNQ 702

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                S   + +Y               QRPL+                      L  G+
Sbjct: 703 LFRMDSLLYLLVYP--------------QRPLL----------TTRTIELVGYDKLGAGQ 738

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N  VA M + GY+ ED++++++  +       I ++++  + +  + G  +     P+ +
Sbjct: 739 NATVAVMSYSGYDIEDAIVMNKASLDRGFGRCIVMKKYPAIRQKYENGASDRILR-PDRT 797

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
            E  + +D  G+   G  + P DI V K  P            L  I    +      S 
Sbjct: 798 VERERVLDYDGLAAPGEIIKPSDIYVKKECPIDTMGPVKSSAALENIKYRPSP----LSY 853

Query: 930 RVPSGVSGTV 939
           + P G S  +
Sbjct: 854 KGPEGESPVI 863


>gi|82749748|gb|ABB89758.1| RNA polymerase beta subunit [Mycoplasma alkalescens]
          Length = 592

 Score =  325 bits (832), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 217/443 (48%), Positives = 297/443 (67%), Gaps = 9/443 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRVTSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA ++ YGFI++PY +V + KV  +   YL+A+EE     AQ+  ++ E+    ++LV  
Sbjct: 61  FADIDKYGFIKSPYFRVKNKKVDFSQPHYLTAIEEAGYAFAQSTVNI-ENDEIVDDLVIV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + VP  ++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNEYLEVPASEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I+AK  GIV  VDA  I I+         +S +D Y L  F
Sbjct: 180 APLVATGVEADIAKFSSTNIIAKYDGIVTYVDANIIKIQRE------GSSKIDTYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q PLVK+G EVR  D++ DGPS   G++ALG+N+LV F  WHG+N+ED++
Sbjct: 234 ERSNQGTLIHQVPLVKLGQEVRVGDLLVDGPSMKNGEMALGKNVLVGFTTWHGFNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +DE GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDENGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTTSRKDTSLKVKHGHNGTVVAVDILSR 413

Query: 948 H-GIDKNERSISVEREQIELLAR 969
             G    +    + +  I    +
Sbjct: 414 KLGDTLEDGIEQIVKVSIAQKRK 436



 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 127/413 (30%), Positives = 179/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  LVKLGQEVRVGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDENGIVRVGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL  +        
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTTSRKDTSLKVKHGHNGTVVAVDILSRKL------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 416  --GDTLEDGIEQIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILEEANIDSSGKL 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DGA                          
Sbjct: 534  T----------------------------VYDGA-------------------------- 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|302832249|ref|XP_002947689.1| hypothetical protein VOLCADRAFT_103593 [Volvox carteri f.
            nagariensis]
 gi|300267037|gb|EFJ51222.1| hypothetical protein VOLCADRAFT_103593 [Volvox carteri f.
            nagariensis]
          Length = 1206

 Score =  325 bits (832), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 104/596 (17%), Positives = 185/596 (31%), Gaps = 135/596 (22%)

Query: 816  MPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
              +       +M+  +   ++            ++       +G                
Sbjct: 698  TTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGMYATNYQTRM------ 751

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               D  G +          +    +       +      + AI      +  D SL +  
Sbjct: 752  ---DTQGFVL--YYPQKPLVCTRAMDYLKFRELPAGINAIVAIMCYSGYNQED-SLMLNG 805

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
                      IF R   ++ +++ S+ RE+IE        +      +          G 
Sbjct: 806  SSIDRGFHRSIFYRAYKEEEKKAGSLSREEIEAPDPVVTAKMKHGTYDKLDADGLCPPGT 865

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L  D     P     +F  +D  +                 L    
Sbjct: 866  RVSGEDIICGKTVTLPDD-----PTGAVQRFTKKDASL----------------ALRGHE 904

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
               I+++           + VK+ V      Q GDK A RHG KG        EDMPF  
Sbjct: 905  AGVIDQVML--TTNDEGQKFVKIRVRTICIPQVGDKFASRHGQKGTCGITYTMEDMPFSA 962

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +G + E  +      +G +                      
Sbjct: 963  EGIVPDIIVNPHAIPSRMTIGHLVEALMSKVAALMGSEGD-------------------- 1002

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + ++ ML        G 
Sbjct: 1003 ---------------------------------ATP-FTKVTVDNVSQMLHDLGYQRRGW 1028

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             ++Y+G TG      + +   Y  +L HMV  K+++R  G   ++T+QP  G++  GG R
Sbjct: 1029 EVMYNGHTGRQLRAQIFLNPTYYQRLKHMVDFKIHSRGRGPVQVLTRQPAEGRARDGGLR 1088

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR---------------TRVYESIVA 1334
             GEME  CI ++GAA  L+E L  +SD     V  R               + +Y+    
Sbjct: 1089 FGEMERDCIISHGAAAFLKERLFDQSDAYRVHVCERSGLIAVANLKKQQFTSTIYK---D 1145

Query: 1335 GNDTFETG----------------------TPESFNVLVKEMQALGLSIDLENSRT 1368
            G++ ++                         P +  +L +E+ A+ ++  ++  R 
Sbjct: 1146 GSNIYQASYRRNPRWAAGGGYKRMWNKDVYVPYACKLLFQELMAMCIAPRMQFERD 1201



 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 138/1004 (13%), Positives = 271/1004 (26%), Gaps = 206/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------------TAFSGA-AMLE 75
           L+  Q  S++ F+ +           +Q        I             A      +++
Sbjct: 39  LVRQQLDSFNEFVNVT----------IQEIIDETPEIVIKPESQHLPGVEAHEEKEYIIK 88

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P+              +   R+LTY  PL + +    +        +  ++ 
Sbjct: 89  FGQVYLSRPQITEQDGESVVLFPKEARLRNLTYCAPLYVDVTKTEYTRQADDTVEEKQET 148

Query: 126 KEQSIYMGDLPLMTKD-------------------------GTFVIKGIQRIVVSQLHRS 160
               +++G +P+M K                          G FVI G ++++++Q  R 
Sbjct: 149 LSH-VHLGKVPIMLKSERCNLHEAATEQEATNLGECPYDQGGYFVINGSEKVLIAQE-RM 206

Query: 161 PG--IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS-----------------KDI 201
               ++      + S   K  +   I       ++    S                   +
Sbjct: 207 ANNHVY----VFKKSQPSKYTFCAEIR----SVVEGSTRSASSMSIMMLAKGKKAGAAGV 258

Query: 202 IHVRIDRRR-KVPVTSFLMALGMDSE-EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGA 258
           I  +I   R + P+     ALG  S+ +IL    Y         +     +  A  +   
Sbjct: 259 IRAQIPYIRAEFPIFILFRALGFVSDRDILEHIVYDLDSDPAMLEALRASVEEAQEVQTQ 318

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG---LLKSLKEKGVKFLGIT--SDCLCGLYVAEDIV 313
           + + + +             ++      L+K L         +        G  V   ++
Sbjct: 319 EEALNYLGKRGTVTGASKADRIQYARNLLIKELLPHLGTEEFMETRKGYFVGYMVHRLML 378

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
               G    +  D    K L+           +L+             +V        DA
Sbjct: 379 -VALGRRPEDDRDHYANKRLDLGGPLMAGLFRLLFRKLCKELRMHAQRMV--------DA 429

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHI 431
             +I  +    +       +       +          G  ++  RL   +      R  
Sbjct: 430 GKEINVLSAINEKIITRGLKYSLATGNWGEQGKQGIRAGVSQVLARLTYASTLSHLRRVN 489

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +       ++
Sbjct: 490 SPIGREGKLAKPRQLHNSLWGMFCPAETPEGQAVG---LVKNMALMCYITVGTPSLPVVA 546

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            ++  +    D +    + +A   F     L    +    +  +   RR  A        
Sbjct: 547 HLEEFNTEALDEVTPADIAAATKVFINGVWLGIQRDPTALIKNLRAMRRQVAFSTEVSII 606

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
               ++   +   +     P    E + + +  +             E            
Sbjct: 607 YDGPLKELRIFTDYGRTSRPLYIVEDNRLLVTKNHIRRLISPLPDEEEYA---WPQLVQD 663

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V Y+ A EEE   IA   + L             R A E            +  P  +
Sbjct: 664 GLVEYIDAEEEETTMIAMTIADL-------------RNAREAGSATGTTYTHCEIHPAMI 710

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+                              
Sbjct: 711 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMG----------------------------- 741

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                       +  +       +   V  Y               Q+PLV         
Sbjct: 742 ------------MYATNYQTRMDTQGFVLYYP--------------QKPLV--------- 766

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA M + GYN EDS++++   +      SI    ++   
Sbjct: 767 -CTRAMDYLKFRELPAGINAIVAIMCYSGYNQEDSLMLNGSSIDRGFHRSIFYRAYKEEE 825

Query: 852 RDTK-LGPEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +    L  EEI    P V           +D  G+   G  V+  DI+ GK     + P 
Sbjct: 826 KKAGSLSREEIEAPDPVVTAKMKHGTYDKLDADGLCPPGTRVSGEDIICGKTVTLPDDPT 885

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
              ++             +D SL +  G    V+D  +   +  
Sbjct: 886 GAVQRF----------TKKDASLALR-GHEAGVIDQVMLTTNDE 918


>gi|157695032|gb|ABV66105.1| DNA dependent RNA polymerase beta chain [Rickettsiella melolonthae]
          Length = 190

 Score =  325 bits (832), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 110/190 (57%), Positives = 139/190 (73%)

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +S I+P EDMP+++DGTPVDIVLNPLGVPSRMNVGQ+ ETHLGWA  GLG KI  +++  
Sbjct: 1    ISTIIPVEDMPYMEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAKGLGIKIAGMLDAQ 60

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            K   +I      +       +    +    D+SV+ +A+  ++GVP++TPVFDG  E  I
Sbjct: 61   KNIKEIKNFLGSIYNDTKETAQKVDLDKLSDESVVELAQNLRNGVPMATPVFDGVTEAEI 120

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              ML +ADL ESGQ+ LYDG TGE F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVT
Sbjct: 121  KRMLSLADLPESGQTTLYDGRTGERFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVT 180

Query: 1280 QQPLGGKSNR 1289
            QQPLGGK+  
Sbjct: 181  QQPLGGKAQF 190


>gi|52694333|emb|CAG38006.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. IV]
          Length = 334

 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 198/334 (59%), Positives = 257/334 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D 
Sbjct: 121 DALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFMAWNG 334


>gi|219116230|ref|XP_002178910.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409677|gb|EEC49608.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 1211

 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 103/511 (20%), Positives = 174/511 (34%), Gaps = 89/511 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             G+I          +    +       +        A+      D+ D  +   + V   
Sbjct: 769  DGLIYTLIYPQKPMVKSRTLDLVNFDNIPGGHNACIAVMSYSGYDIEDAIILNKAAVDRG 828

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLAR----DKDDEQVILDRNIYSRLMEILCGQN 994
                 +  +H       +                 D +D++         +      G+ 
Sbjct: 829  FGRCMVLRKHQTSVRRYANGTMDRTCAPPDPGSFPDGEDDKRFARYMAIDKDGICRVGEK 888

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G     K          E P       A  D      +    + Y+ S         
Sbjct: 889  IENGSVMVNK----------ESPADTTSNMAGVDFGFNSGMSMAHLNYKPSGVSYRGSAS 938

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
              ++K+            ++KV +   R  + GDK A RHG KG+   I+P ED+PF + 
Sbjct: 939  TYVDKVLI--TSNENEQFLIKVMLRQVRRPEIGDKFASRHGQKGVCGLIVPEEDLPFNEF 996

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G PSRM VG++ E  +G A +  G++  S     +     +   +    
Sbjct: 997  GHVPDLIMNPHGFPSRMTVGKLLELLVGKAGLYEGRQGYSSAFGEEFGSADTAQSA---- 1052

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                         +  L    L+ +G+ 
Sbjct: 1053 ---------------------------------------------SEALLRNGLNYTGKD 1067

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ILY G  GEP D  +  G ++  KL HMV DK +AR+ G  +++T+QP  G+S  GG RL
Sbjct: 1068 ILYSGTNGEPLDAYIFSGPVFYQKLKHMVLDKAHARARGPRAVLTRQPTEGRSRDGGLRL 1127

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA-----------------GND 1337
            GEME  C+ AYG + ++ E L   SD        + + V                  G  
Sbjct: 1128 GEMERDCLIAYGVSNLIMERLMHSSD-------AFSANVCLTCGLLQYEGWCQYCRSGEK 1180

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
              +   P +  +L +E+Q++ +   L     
Sbjct: 1181 VADIRLPYACKLLFQELQSMNVLPRLRLQDK 1211



 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 135/1017 (13%), Positives = 288/1017 (28%), Gaps = 207/1017 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSGAAMLEFVSYEFDPPKF- 86
           L+     S+DHF+ + +    +          S   I +       L + +     P   
Sbjct: 80  LLRQHIDSFDHFVDVEMQQIVQSP--------SACEIRSEHDPKFYLRYEACWVGEPSVE 131

Query: 87  ---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                        C  RD TY+ P+ + +R            +  + + ++ + +G +P+
Sbjct: 132 EDSYSVKSATPFQCRLRDCTYSAPIYVNVRYT----------RGRQIVVKRKVMIGRMPI 181

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRA 172
           M                           G FVIKG++++++ Q   S   +  + D    
Sbjct: 182 MLRSKKCLLRDRSEDDLAGMKECPYDPGGYFVIKGVEKVILIQEQLSKNRVILEEDNKGI 241

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR---K-------VPVTSFLMALG 222
             S   + +               + K   ++ I   R   K       +PV   L A+G
Sbjct: 242 MAS---ITSST------------HERKSKAYILIKNGRVYLKNNTLGDDIPVAVVLKAMG 286

Query: 223 MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
           ++S+  L                     +   +     +   +      +   SG   + 
Sbjct: 287 IESDLELVQLVGSESPIINALALSLEEPSRLGIHTQAQALRFIGAKIRGRSGPSGPSSSY 346

Query: 283 GLLKSLKEKG-------------VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
               S +++              V         L   ++   ++    G++ ++  D   
Sbjct: 347 RKNVSPEDEAREVLANVVLSHVPVTHFDFREKALYIGHIVRRVLLVHLGKMPLDDKDYYG 406

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            K LE   +        L+     +     + +++  N+ +     D+ + +RP  ++  
Sbjct: 407 NKRLELAGNLLSLLFEDLFKIFNKDLKRQADLVLSKPNRTQA---FDVVKTIRPDTITNG 463

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            +             + D + V +V                +     + ++  +      
Sbjct: 464 MINAIATGNWVLKRFRMDRAGVTQVLSR-------------LSYMSALGMMTRINSQFEK 510

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +    +L   +   +      +     L    ++   I++ + D+   + +     V
Sbjct: 511 TRKVSGPRSLQPSQWGMLCPADTPEGEACGLVKNLALLGHITTDEADTRPIERICRDLGV 570

Query: 510 VSAVCEFFCSSQLSQ-LEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYG 567
                         Q     +N L    HTR R        + R     E   V+     
Sbjct: 571 EDVKRMTGHEINSHQAFLVFLNGLILGVHTRPRELVRNLRKMRRRGLAGEFVSVYLHDEQ 630

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN-----DVVYLSAMEE 622
                 T  G     +  +     +     I      +    +T+      V Y+   EE
Sbjct: 631 CAVHIATDGGRVCRPLLIVDEETGLPKLQQIHMESLALGTMDITDLMRQGIVEYVDCNEE 690

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            N  IA     L+         V      E   +   +   ++  P  ++ +   +IPF 
Sbjct: 691 NNTLIAVTERDLE---------VAILHGLETRKM---RYTHLEVDPFTILGVVGGIIPFP 738

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            ++ S R      M +QA+                                         
Sbjct: 739 HHNQSPRNTYTVAMAKQAMGS--------------------------------------- 759

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             +   + +         IY               Q+P+VK                 + 
Sbjct: 760 --VSMNQYERMDGLIYTLIYP--------------QKPMVKS----------RTLDLVNF 793

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            ++  G N  +A M + GY+ ED++++++  V       + + + +   R    G  + T
Sbjct: 794 DNIPGGHNACIAVMSYSGYDIEDAIILNKAAVDRGFGRCMVLRKHQTSVRRYANGTMDRT 853

Query: 863 RDIPNVSE----------EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              P+                  ID+ GI  VG ++  G ++V K +P   +        
Sbjct: 854 CAPPDPGSFPDGEDDKRFARYMAIDKDGICRVGEKIENGSVMVNKESPADTTSNMAGVDF 913

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                G  +          PSGVS         ++  I  NE    + +  +  + R
Sbjct: 914 -----GFNSGMSMAHLNYKPSGVSYRGSASTYVDKVLITSNENEQFLIKVMLRQVRR 965


>gi|86451155|gb|ABC96800.1| RNA polymerase II [Rubia tinctorum]
          Length = 214

 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 111/255 (43%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VK+ V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     ++I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDSISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 199  GAAHFLKERLFDQSD 213


>gi|71026390|ref|XP_762870.1| DNA-directed RNA polymerase III subunit [Theileria parva strain
            Muguga]
 gi|68349822|gb|EAN30587.1| DNA-directed RNA polymerase III subunit, putative [Theileria parva]
          Length = 1244

 Score =  325 bits (832), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 106/577 (18%), Positives = 195/577 (33%), Gaps = 79/577 (13%)

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            D+    N+L+        N    + IS   +   V   I         R+T        +
Sbjct: 733  DVNEENNLLIVMREKDITNLTTHLEISPMSILGVVAGLIPFPNHNQSPRNTYQCAM-GKQ 791

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I ++     +  D   ++ +        +    I       +   +  + A+   +  +
Sbjct: 792  SIGSIGYNQFQRCDT--VVHLMNYTQQPLVTTKTIQLVNFDKLPAGQNAIVAVMSYQGYE 849

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            + D  +   + +           R   +               +           + +  
Sbjct: 850  IEDAIILNKASIDRGFARCYTLRRLTCE---------------ITSGNATSLNGFNPSKS 894

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                     +  +   +      VL S        +       +     +   +      
Sbjct: 895  QNKDSDSNNEFVIGVGEQVSPGQVLISTKAPPTDFTTNGSMNGKGTDKNQKTGNDDKYIV 954

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
               ++      +++   +  +       ++ K+ V   RP + GDK + RHG KG+V  I
Sbjct: 955  NKYNLNTGGCIDRVILTENYN-----GNKMYKIMVRQSRPPEIGDKFSSRHGQKGVVGLI 1009

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF + G   D+++NP G PSRM VG++ E     + V  G  + S       + 
Sbjct: 1010 AEHEDMPFTESGIVPDLIMNPHGFPSRMTVGKLLELVASKSSVFSGNFVDSTPFSNSYSD 1069

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            ++    +                                                I  +L
Sbjct: 1070 NLCNDLNNSGSN---------------------------------------KMSDICDIL 1090

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                    G+ ILY G++G P +  + +G IY  +L HMV+DK++AR  G    +T+QP 
Sbjct: 1091 IKNGFHPKGKEILYSGISGNPINTLIFIGPIYYQRLKHMVTDKIHARGRGPRQPITRQPT 1150

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV------GRTRVYESIV 1333
             G+S  GG RLGEME  C+ AYG++ +L E L + SD    +V       G    Y +  
Sbjct: 1151 EGRSRDGGLRLGEMERDCLIAYGSSNLLVERLMLSSDVFNIEVCSSCGFMG----YNNFC 1206

Query: 1334 A---GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                 N   +   P +  +L +E+QA+ +   L   +
Sbjct: 1207 KFCQNNSLAQVSLPYACKLLFQELQAMNIRPSLIVKK 1243



 Score =  138 bits (347), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 131/1035 (12%), Positives = 287/1035 (27%), Gaps = 227/1035 (21%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP-------- 84
              SY++F++  I              +     T    +  LEFV  +   P        
Sbjct: 51  HINSYNNFVLHEIKDIINAPS--NKVLR-----TDLYPSLSLEFVDIKIGKPFFTDHSKH 103

Query: 85  --KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG--------- 133
             K     C  RD TY+ P+ +T   I +  D     K   +I    + +          
Sbjct: 104 VFKLTPQLCRIRDFTYSAPILVT---IDYFRDYTFTRKENLEIGRIPVMLRSCICFLSSD 160

Query: 134 --------------------------DLP--------------LMT------KDGTFVIK 147
                                     D+P               M         G F+IK
Sbjct: 161 SESNSDHDSSGLPEYNSSKKSMKNNFDIPDGLSKEDRESFYKSYMLDECPYDPGGYFIIK 220

Query: 148 GIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
           G++++++ Q   S   I  + D  +   +            +   +         +++RI
Sbjct: 221 GVEKVILMQEQLSKSRIIVEMDVKKNICATVTSATAES-KSRTAVVY----KNSQLYLRI 275

Query: 207 DR-RRKVPVTSFLMALGMDSE-EILSTFYPK-IVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           +     VP+   L A+G++++ EI+         +    +      +  + +      + 
Sbjct: 276 NSFTDDVPLCIVLKAMGIETDHEIIQLISNSPTTFKNSNNLTTPSSNLPNGLDYITFLND 335

Query: 264 LVDIDTGEQ---VIESGKKLTSGLLKSLKEKGVKF-------------LGITSDCLCGLY 307
           L + D   +   ++  GKK+   +L        K                I S  L    
Sbjct: 336 LYNEDINSRLDALMYIGKKIRPRVLGKGFFSSNKDRAPKSKQMILEDTHDILSRVLLSHI 395

Query: 308 VAEDIVNGETGEIYIEAGDV------IDEKSLEEIFHSEIR-------DIPILYVDSVNN 354
             +D  +       +            + + L++  H   +        I IL+ D    
Sbjct: 396 PMKDCRDFSGKIKTLSLMAHRVLNVVNNVEPLDDKDHYGNKRLELAGQMISILFEDFYKK 455

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYR----------VMRPGDVSTFSVAESMFNFLFFDSD 404
                   +        +A  +  +           + P D+ T  +  +      ++  
Sbjct: 456 FLSNMKKSIESILVKYLEANPNPAKGENSNFPDIFGLMPTDIITNGMQNA-IATGNWNIK 514

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIR-----KEDIIAIIKILVDLRNGKGTIDDIDNL 459
           ++ +   G  ++  RL+  +   +         K   ++  + L   + G     D    
Sbjct: 515 RFRMEKSGVSQVLSRLSYISSIGMMTKTDSQFEKGRKVSGPRALQPSQFGILCPCDTPEG 574

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +  +     ++ +        +  ++   +    ID++   D+ N     S  C+   +
Sbjct: 575 ESCGLVKNLSLMTHVTSDVPTPVLETLLFTLGVEPIDTLSSHDMFNPWKGTSEKCDNLLN 634

Query: 520 SQLSQLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++L      +N +    H   +        + R         V+           +  G 
Sbjct: 635 ARLVL----LNGILLGIHRNAKFLVNSIIKLRRRGLINMFVSVYENSQQNQVHISSDGGR 690

Query: 579 NIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               +  + +            +     K+        + ++   EE N  I      + 
Sbjct: 691 LCRPLIVVQNSVPRLTDELVQQLVENKIKMEYLFNNGILEWIDVNEENNLLIVMREKDIT 750

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                       ++ SP  ++ + A LIPF  ++ S R    C 
Sbjct: 751 -----------------------NLTTHLEISPMSILGVVAGLIPFPNHNQSPRNTYQCA 787

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +Q++                                           I   +     +
Sbjct: 788 MGKQSIGS-----------------------------------------IGYNQFQRCDT 806

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +  Y               Q+PLV                  +   L  G+N +VA 
Sbjct: 807 VVHLMNY--------------TQQPLV----------TTKTIQLVNFDKLPAGQNAIVAV 842

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M + GY  ED++++++  +         +         T      +    P+ S+    +
Sbjct: 843 MSYQGYEIEDAIILNKASIDRGFARCYTLRRLTCEI--TSGNATSLNGFNPSKSQNKDSD 900

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +   +I VG +V+PG +L+    P  +               +K  +     +   +  
Sbjct: 901 SNNEFVIGVGEQVSPGQVLISTKAPPTDFTTNGSMNGKGTDKNQKTGNDDKYIVNKYNLN 960

Query: 936 SGTVVDVRIFNRHGI 950
           +G  +D  I   +  
Sbjct: 961 TGGCIDRVILTENYN 975


>gi|85001437|ref|XP_955436.1| DNA-directed RNA polymerase iii [Theileria annulata strain Ankara]
 gi|65303582|emb|CAI75960.1| DNA-directed RNA polymerase iii, putative [Theileria annulata]
          Length = 1244

 Score =  324 bits (831), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 113/576 (19%), Positives = 202/576 (35%), Gaps = 76/576 (13%)

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            D+    N+L+        N    + IS   +   V   I         R+T        +
Sbjct: 732  DVNEENNLLIVMRERDITNLTTHLEISPMSILGVVAGLIPFPNHNQSPRNTYQCAM-GKQ 790

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I ++    L+  D   ++ +        +    I       +   +  + A+   +  +
Sbjct: 791  SIGSIGYNQLQRCDT--VVHLMNYTQQPLVTTKTIQLVNFDKLPAGQNAIVAVMSYQGYE 848

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQIELLARDKDDEQVILDRNI 982
            + D  +   + +           R   +     + S+             D         
Sbjct: 849  IEDAIILNKASIDRGFARCYTLRRLTCEITPGNATSINGYNPNKSQNKDSD--------- 899

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                      +  +   +  K   VL S        +       ++ +  ++  + + +Y
Sbjct: 900  -------STNEYVIGVGEPVKPGQVLISTKAPPTDFTTNGSMNGKNGESNQSSGTNEDKY 952

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
              +K  L          +            + K+ V   RP + GDK + RHG KG+V  
Sbjct: 953  IVNKYDLNTGGYIDRLILTE----NFNGNTMYKIMVRQSRPPEIGDKFSSRHGQKGVVGL 1008

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I   EDMPF + G   D+++NP G PSRM VG++ E     + V  G  + S       +
Sbjct: 1009 IAEHEDMPFTESGIVPDLIMNPHGFPSRMTVGKLLELVASKSSVFSGNFVDSTPFSNSYS 1068

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             ++    +  +                                         +   I ++
Sbjct: 1069 DNLCNDLNNTKT---------------------------------------DNMSDICNI 1089

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L        G+ ILY G++G P +  + +G IY  +L HMV+DK++AR  G    +T+QP
Sbjct: 1090 LIKNGFHPKGKEILYSGISGNPINTLIFIGPIYYQRLKHMVTDKIHARGRGPRQPITRQP 1149

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV--------VGRTRVYESIVA 1334
              G+S  GG RLGEME  C+ AYG++ +L E L + SD V         G    Y +   
Sbjct: 1150 TEGRSRDGGLRLGEMERDCLIAYGSSNLLIERLMLSSD-VFNIEICTSCG-FMGYNNFCK 1207

Query: 1335 ---GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                N   +   P +  +L +E+QA+ +   L   +
Sbjct: 1208 FCQNNSLAQVSLPYACKLLFQELQAMNIRPSLIVKK 1243



 Score =  137 bits (346), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 121/996 (12%), Positives = 271/996 (27%), Gaps = 186/996 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPP------- 84
              SY++F++  I              +  ++P      +  LEFV  +   P       
Sbjct: 51  HINSYNNFVLHEIKDIINAPS--NKVLRTELYP------SLSLEFVDIKIGKPFFTDHSK 102

Query: 85  ---KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI----------- 130
              K     C  RD TY+ P+ +T   I +  D     K   +I    +           
Sbjct: 103 HVFKLTPQLCRIRDFTYSAPILVT---IDYFRDYTFTRKENLEIGRIPVMLRSCICFLSS 159

Query: 131 ---------YMG---------------DLP--------------LMT------KDGTFVI 146
                     +G               D+P               M         G F+I
Sbjct: 160 DSESQSDEDSLGSSEYNHPKKSTKNNFDIPDGLSKEDRESFYKSYMLDECPYDPGGYFII 219

Query: 147 KGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           KG++++++ Q   S   I  + D  +   +            +   +         +++R
Sbjct: 220 KGVEKVILMQEQLSKSRIIVEMDVKKNICATVTSATAES-KSRTAVVY----KNSQLYLR 274

Query: 206 IDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           I+     VP+     A+G++++ EI+          ++        +  +        + 
Sbjct: 275 INSFTDDVPLCIVFKAMGIETDHEIIQLISNSSTNFKKSKKSNQSSNLPNGFDYITFLND 334

Query: 264 LVDIDTGEQ---VIESGKKLTSGLL--------KSLKEKGVKFLGITSDCLCGLYVAEDI 312
           L + +   +   ++  GKK+   +L        K    K  + +   +  +    +   I
Sbjct: 335 LYNENINTRLDALMYIGKKIRPRILGKGFFSSNKDRAPKSKQMIIEDTHDILSRVLLSHI 394

Query: 313 VNGE----TGEI----YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
              +    +G+I     +    +    ++E +   +      L +     +    +    
Sbjct: 395 PMRDCRDFSGKIKTLSLMAHRVLNVVNNVEPLDDKDHYGNKRLELAGQMISILFEDFYKK 454

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM--NMRLNL 422
             N  +K     I + +      T     +  +           + +       N  +  
Sbjct: 455 FLNNMKKSIESIIVKYLESNPNPTKGENSNFPDIFGLMPTDIITNGMQNAIATGNWNIKR 514

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
              +     +    ++ I  +  +       +    +   R     +             
Sbjct: 515 FRMEKTGVSQVLSRLSYISSIGMMTKTDSQFEKGRKVSGPRALQPSQFGILCPCDTPEGE 574

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
              + + +S +   +      +    + +   E   +     +       S  +  RR S
Sbjct: 575 SCGLVKNLSLMTHVTSDVPTPVLETLLFTLGVEPIDTLSSHDMFNPWKGTSGKSDNRRNS 634

Query: 543 ALGQGGVARARAGVEMRDVH--PTHYGRICPAETSEGHNIGLVSSLTSFARVNAY-GFIE 599
            L    +         R+ +   +   ++              +S  +   +++  G + 
Sbjct: 635 RL---VLLNGILLGIHRNANFLISSIIKLRRKGLINMFVSVYENSQQNQVHISSDGGRLC 691

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
            P   V +         +  + E    I      L  +G      V        ++  R+
Sbjct: 692 RPLIVVQNSVPKLTDELVQQLVENKIKI----DYLFNNGILEWIDVNEENNLLIVMRERD 747

Query: 660 K---IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                  ++ SP  ++ + A LIPF  ++ S R    C M +Q++  +         G  
Sbjct: 748 ITNLTTHLEISPMSILGVVAGLIPFPNHNQSPRNTYQCAMGKQSIGSI---------GYN 798

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
            +                                                          
Sbjct: 799 QLQRCD----------------------------------------------TVVHLMNY 812

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PLV                  +   L  G+N +VA M + GY  ED++++++  +  
Sbjct: 813 TQQPLV----------TTKTIQLVNFDKLPAGQNAIVAVMSYQGYEIEDAIILNKASIDR 862

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                  +         T      I    PN S+    +     +I VG  V PG +L+ 
Sbjct: 863 GFARCYTLRRLTCEI--TPGNATSINGYNPNKSQNKDSDSTNEYVIGVGEPVKPGQVLIS 920

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              P  +               + +    D  +   
Sbjct: 921 TKAPPTDFTTNGSMNGKNGESNQSSGTNEDKYIVNK 956


>gi|37784146|gb|AAO83543.1| DNA-directed RNA polymerase beta subunit [Hydrogenothermus marinus]
          Length = 430

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 220/430 (51%), Positives = 292/430 (67%), Gaps = 12/430 (2%)

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            F E+DD+NR LMG NMQRQAVPLLK E P  GTG+E +VAK+SG+ +VAKR G+VE V  
Sbjct: 1    FFEHDDANRALMGSNMQRQAVPLLKTEYPLAGTGIERIVAKNSGSVVVAKRGGVVEYVSG 60

Query: 741  IRIVIRSVEGD---LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
             +IVI+  + +    DP   G+DIY+L KF+ SNQ TC+NQRPLV+ GD V +  IIADG
Sbjct: 61   DKIVIKVNQDEINENDPLDIGMDIYKLKKFRGSNQATCINQRPLVRKGDIVEKGAIIADG 120

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             ST  G+LALG+N+LVAFMPW GYNFED+++ISER+V +DVFTSIHIEE EV AR+T LG
Sbjct: 121  TSTYKGELALGKNVLVAFMPWRGYNFEDAIVISERLVKDDVFTSIHIEELEVEARETNLG 180

Query: 858  PEEITRDIPNVSEEGLKNIDEC-GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             EEITRDIP VSE  L N     GI+ +G+ V PGDILVGKITPKGE+P TPEEK++   
Sbjct: 181  SEEITRDIPGVSERALANFGWSLGIVRIGSFVKPGDILVGKITPKGETPATPEEKIITCY 240

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQ 975
            FGEKA DV+DTSLRVP+GV G VVDV++F R  G  KN     +  E+IE L ++ +D++
Sbjct: 241  FGEKASDVKDTSLRVPTGVEGIVVDVQVFARKKGNKKNAYLEKLLNEEIEKLEKELEDKK 300

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA-------VQD 1028
              +     S+L E++ G       K   K+ + +   I+E       +F        ++D
Sbjct: 301  DFIQNRRDSQLKEVIIGSKVSKDVKIAGKTILKAGKEITEENFDSVVKFIAVNPAGFLKD 360

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            ++V    + +  + +    + E  + +KI++++ G D+ PGV  +VKV++A KR IQ GD
Sbjct: 361  KEVTEKAKEIIDKAKLQIQLWEKIYSSKIKEVEKGADLKPGVNELVKVYIAQKRKIQVGD 420

Query: 1089 KMAGRHGNKG 1098
            KMAGRHGNKG
Sbjct: 421  KMAGRHGNKG 430


>gi|194303502|gb|ACF41174.1| RNA polymerase beta subunit [Mycoplasma moatsii]
 gi|194303504|gb|ACF41175.1| RNA polymerase beta subunit [Mycoplasma moatsii]
          Length = 596

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 216/510 (42%), Positives = 324/510 (63%), Gaps = 24/510 (4%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             +N LS I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1    QINPLSEISNKRRITSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588  SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             +AR+N YGF+ETPY +V  G V  +  +YL A EE     AQ+  +++E    T +LV 
Sbjct: 61   VYARINEYGFLETPYYRVNKGVVDYSKPIYLIASEEYGFTFAQSTVTVNEKNKITNKLVT 120

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
             R   + I+V  E++DFID + +Q+ SIAAS IPFLENDD+NR LMG NMQRQAV LL  
Sbjct: 121  VRKNHDFIIVKPEEVDFIDVASRQMTSIAASCIPFLENDDANRALMGSNMQRQAVSLLNP 180

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            EAP VGTG+E+ +A  S   + AK++G V  VD+ +I I++ + D       V +Y L +
Sbjct: 181  EAPIVGTGIEASIASFSAGNLKAKKSGRVVFVDSTKIKIKTEDSD------EVIVYNLKQ 234

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
            F++SNQ T ++QRPLVK+ D+V ++D++ DG S   G++ALG+N+LVAF  W+GYN+ED+
Sbjct: 235  FEKSNQGTLIHQRPLVKLNDKVEKDDLLTDGSSFKDGEMALGKNLLVAFSTWNGYNYEDA 294

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            ++I+E++V +DV TSIHIEE  +  R +K G +++T +IPN S    + +DE GI+ VG+
Sbjct: 295  IIINEKLVKDDVLTSIHIEEQTIQFRTSKTGNDQLTAEIPNTSTYSKRFLDENGIVVVGS 354

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            EV+ GDILVG+++PKGE   TPEEKL+ AIFG +  +++DTSL+V  G +GTV++V + +
Sbjct: 355  EVSAGDILVGRVSPKGEHNPTPEEKLMAAIFGSRDSNLQDTSLKVKHGQAGTVINVEVLS 414

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D       V  + I+ + +    ++  +      ++ + L G++   G        
Sbjct: 415  REQGD-------VLEDGIDKIVKVYIAQKRKI------KVGDKLAGRHGNKGVISV---- 457

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            +L  + +            +  + V   + 
Sbjct: 458  ILPEEDMPHLEDGTPVDICLNPQGVPSRMN 487



 Score =  301 bits (772), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 129/420 (30%), Positives = 182/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            ++ +  +V   D+L    + K +  M   + LL A       +  D  +     V   V 
Sbjct: 249  LVKLNDKVEKDDLLTDGSSFK-DGEMALGKNLLVAFSTWNGYNYEDAIIINEKLVKDDVL 307

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +             ++ E       ++   DE  I+         +IL G+ +
Sbjct: 308  TSIHIEEQTIQFRTSKTGNDQLTAEIPNTSTYSKRFLDENGIVVVGSEVSAGDILVGRVS 367

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L + +              +D  +Q     +K     +   +E     
Sbjct: 368  PKGEHNPTPEEKLMAAIFGS-----------RDSNLQDTSLKVKHGQAGTVINVE----- 411

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             +   + GD +  G+ ++VKV++A KR I+ GDK+AGRHGNKG++S ILP EDMP L+DG
Sbjct: 412  -VLSREQGDVLEDGIDKIVKVYIAQKRKIKVGDKLAGRHGNKGVISVILPEEDMPHLEDG 470

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI LNP GVPSRMN+GQI E HLG+A   LG K      D     DI  +    +  
Sbjct: 471  TPVDICLNPQGVPSRMNLGQILELHLGYAGKKLGVKFACPSFDGVKTEDIKNVLKEAKL- 529

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                             PV                    SG+  
Sbjct: 530  ---------------------------------PV--------------------SGKQK 536

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LY+ +TGE  D  V VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 537  LYNPVTGEVVDNDVAVGVMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|52694243|emb|CAG30651.1| DNA-directed RNA polymerase beta chain [Pseudomonas resinovorans]
          Length = 334

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 197/331 (59%), Positives = 255/331 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + DS++PQDLI AKPV +A+ EFF SSQLSQ  +  N LS ITH R +SALG GG+ R R
Sbjct: 2   EGDSLLPQDLIIAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRGVSALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V   +VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNQYGFLESPYRVVNGTQVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +V+LSA+EE +  IAQA+++++E G   +ELV  R   E  +   E +  +D SPKQVVS
Sbjct: 122 IVFLSAIEEADHVIAQASATMNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVS 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G
Sbjct: 182 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGG 241

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI
Sbjct: 242 VIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDVVARADI 301

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           +ADGPSTD+G+LALG+NM V FMPW+G+NFE
Sbjct: 302 LADGPSTDMGELALGQNMRVEFMPWNGFNFE 332


>gi|52694203|emb|CAG30631.1| DNA-directed RNA polymerase beta chain [Pseudomonas stutzeri]
          Length = 332

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 198/332 (59%), Positives = 254/332 (76%), Gaps = 1/332 (0%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPHDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SP
Sbjct: 122 EVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAPEDVTLMDVSP 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +V
Sbjct: 181 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 241 ARRGGVIDSVDASRIVVRVRDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDVV 300

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            R DI+ADGPSTD+G+LALG+NM VAFMPW+G
Sbjct: 301 ARGDIMADGPSTDMGELALGQNMRVAFMPWNG 332


>gi|4867854|emb|CAB43082.1| RNA polymerase II [Retzia capensis]
          Length = 256

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 78/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQXGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECVMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 128  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 226  GAAHFLKERLFDQSD 240


>gi|261403646|ref|YP_003247870.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus vulcanius
            M7]
 gi|261370639|gb|ACX73388.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus vulcanius
            M7]
          Length = 643

 Score =  324 bits (831), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 112/621 (18%), Positives = 204/621 (32%), Gaps = 107/621 (17%)

Query: 786  DEVRRNDIIADGPS----TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +++++ +I           +  D     N  +A            + I    +       
Sbjct: 84   EKLKKGEITFSDLVKEGVIEYLDAEEEENAYIALSEEELTEKHTHLEIDPLTILGIGAGV 143

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                E     R T             +S    + +D  G            +        
Sbjct: 144  APYPEHNSAPRITMAAAMGKQSLGIPMSNIKWR-LDTRG--HYLHYPQVPIVRTKHQEIL 200

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + AI   +  ++ D  +   S +    +    F R       R    + 
Sbjct: 201  GFDKRPAGQNFVVAIMSYEGYNMEDAIIFNKSAIDRG-LGRSTFFRTYDTCERRYPGGQM 259

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +           L     V+     K   V+           + 
Sbjct: 260  DRFEVPDKG-------VRGYRSEECYRHLEEDGIVAVESHVKGGDVIVGKTSPPRFLEEH 312

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    ++   V+  +          E+ + +K+   +          R+VKV V   
Sbjct: 313  --------EITIQVKPQRRDSSIVVRHGEEGYVDKVILTE-----TKEGNRLVKVKVRDL 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++   +P ED+PF + G   DI++NP  +PSRM VGQ+ E   
Sbjct: 360  RVPELGDKFASRHGQKGVIGLTVPQEDLPFTESGIVPDIIINPHAIPSRMTVGQLLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++I   I   +   D+      L                             
Sbjct: 420  GKVGSLEGRRIDGTIFTGETEWDLRKALEALGFESHGKEVM------------------- 460

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+       TG+ F+  + +G  Y  KL+H
Sbjct: 461  ----------------------------YDGK-------TGKKFEVEIYIGVAYYQKLHH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA +L+E L  +SD 
Sbjct: 486  LVAGKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLMDESDP 545

Query: 1321 -DV-----VGRTRVY---------------ESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
             D+      G   +                E++           P +F +L+ E++++ +
Sbjct: 546  YDICICSKCGDFAILDYRRGLKYCPICGEIENLYNSKKIPFVRIPYAFKLLLDELKSMCI 605

Query: 1360 SIDLENSRTKNSAKMEEIPDF 1380
               L   + K+  ++E+  DF
Sbjct: 606  ---LPRMKVKDKVELEDFEDF 623



 Score = 94.8 bits (234), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 61/331 (18%), Positives = 108/331 (32%), Gaps = 100/331 (30%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YL A EEEN YIA +   L                        EK   ++  P  ++ 
Sbjct: 102 IEYLDAEEEENAYIALSEEELT-----------------------EKHTHLEIDPLTILG 138

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I A + P+ E++ + R+ M   M +Q++ +  +   +                       
Sbjct: 139 IGAGVAPYPEHNSAPRITMAAAMGKQSLGIPMSNIKW----------------------- 175

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                +      Y               Q P+V+   +      
Sbjct: 176 ------------------RLDTRGHYLHYP--------------QVPIVRTKHQ------ 197

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                         G+N +VA M + GYN ED+++ ++  +   +  S     ++   R 
Sbjct: 198 ----EILGFDKRPAGQNFVVAIMSYEGYNMEDAIIFNKSAIDRGLGRSTFFRTYDTCERR 253

Query: 854 TKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              G  +             SEE  ++++E GI+ V + V  GD++VGK +P        
Sbjct: 254 YPGGQMDRFEVPDKGVRGYRSEECYRHLEEDGIVAVESHVKGGDVIVGKTSPPRFLEE-- 311

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  I  +     RD+S+ V  G  G V
Sbjct: 312 -----HEITIQVKPQRRDSSIVVRHGEEGYV 337


>gi|52694197|emb|CAG30628.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           plecoglossicida]
          Length = 334

 Score =  324 bits (830), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 199/334 (59%), Positives = 259/334 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNEYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G V++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D 
Sbjct: 121 EGVVSDDIVFLSAIEEADHVIAQASAAMNEKKQLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G
Sbjct: 301 KVQRSDIMADGPSTDMGELALGQNMRIAFMAWNG 334


>gi|145525932|ref|XP_001448777.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124416343|emb|CAK81380.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1203

 Score =  324 bits (830), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 157/1019 (15%), Positives = 309/1019 (30%), Gaps = 195/1019 (19%)

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +   +      D +         +  N+  ++    + R  +   I  I+  L++   G
Sbjct: 336  WIGNKIKKAENQDPETLIQEAKKLINKNILPHIGVSSESRDRKAYFIGYIVHRLLNASLG 395

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ-----DLI 504
            K   DD D+ G +R+   G M+   ++      +++ K+ +        M Q        
Sbjct: 396  KTDQDDRDHYGKKRLDMAGAMMMGVFKTSFESFKQNAKKALEKYINGENMRQPDDIKSFF 455

Query: 505  NAKPVVSAVCEFFCSSQLSQLEE--------------HVNSLSRITHTRRLSALGQGGVA 550
            + + +   +     +    + +E                +  + ++H RR++A     + 
Sbjct: 456  DGEQISKDIDNALATGNWGRSKEGQVVKTGVAQTLKRETSLFATLSHLRRMNA----PIN 511

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
                  + R +H TH+G ICPAET EG  IG+V +L+    V+     +     +    V
Sbjct: 512  PQMKLSKPRQLHNTHFGFICPAETPEGQKIGIVKNLSLMTAVSNDLQQKDKETLLKLIMV 571

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA-SPK 669
                V+       +  + Q +    +    T+ LV     G      +   +F +  S +
Sbjct: 572  LKQDVF-------DFQLLQGDFQAQDIPKMTKVLVDGNWIGFTRNPEQFIQEFKNLRSAE 624

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            +        I F   +   R+        + + +++     +          +S      
Sbjct: 625  ESFIPIEVSINFDYVNKEIRIYTDAGRCMRPLFIVQDNKLKLK-----KNQLNS----FT 675

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                +++      + +   EG L      +       F+R                    
Sbjct: 676  DWEQLLQNKCVELLDVEEEEGSLIAMDLNIMTRGTQNFKRYTH----------------- 718

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    P    G       +  + +P+  +N      +   M  + +           
Sbjct: 719  ----CEIHPCMMFG-------VCASVIPFANHNQGPRNTLQSAMGKQAMGL--------- 758

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                     NI    ++ +             +     + +   
Sbjct: 759  --------------------NSTNFNIRFDTLVHILHYPQKPLASSKAVDFITVNEVPIG 798

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
               + +I      +  D+ +     +         +  +   +++   +    +I     
Sbjct: 799  INCVTSIACFTGYNQEDSIIINQYAIDRGFFRSVFYRTYKESEDKDPDNFTETKITKP-- 856

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
                    L  N   +L   L     V       +   +    +                
Sbjct: 857  --------LGDNYAGKLFIKLDSDGIVPPGTKVDEEEPIIGKELI--------------- 893

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                 + +   Q  T +  L  R   +               ++VKV V   R  Q GDK
Sbjct: 894  IDNIMLNTANGQKNTKECSLLTRRAERGVVDSVLISENQKGYKLVKVKVRSLRIPQIGDK 953

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
               RHG KG        ED+PF   G   D+ +NP  +PSRM +G + E          G
Sbjct: 954  FCSRHGQKGTCGMTYRQEDLPFTLVGISPDLTINPHCIPSRMTIGHLIECLSSKLASIKG 1013

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +                                                        +TP
Sbjct: 1014 QFND-----------------------------------------------------ATP 1020

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F       I + L      + G  ++ +  +G  F  P+ VG  Y  +L H+V DK+YA
Sbjct: 1021 -FAQISVNDIANKLHEVGWQKWGNEVMTNPYSGNMFQIPIFVGPTYYQRLRHLVDDKMYA 1079

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR 1325
            RS G  + +T+QP  G+S +GG R GEME  CI ++G A  L+E     SD     V  +
Sbjct: 1080 RSRGPVTGITRQPTHGRSRKGGLRFGEMERDCIISHGTAKFLKERTYDVSDAFRVHVCSK 1139

Query: 1326 -----------TRVYESIVAGND----TFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
                          Y +I    +     ++   P +   L++E+ ++ ++  L+  ++K
Sbjct: 1140 CGLFAVANLENQEFYCNICKNTNQQNQIYQVLMPYAAKTLIQELISMNIAPRLKFDQSK 1198



 Score = 92.8 bits (229), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 93/765 (12%), Positives = 226/765 (29%), Gaps = 128/765 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG---------------------------LQAAFKS 61
           L+  Q  SY+ F+  NI    R +EG                           +Q  F  
Sbjct: 46  LVSQQINSYESFVE-NIIKYVRGHEGTFVVRVKPQYKEEERMDAQTEYLYQFQIQRCFMG 104

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       ++    +F+   F       RDLTY+  LKI L + +   ++  G+  
Sbjct: 105 -------KKNIHID----KFEEEIF-PMIARLRDLTYSRQLKIDLEVTMQQRNKRDGSIE 152

Query: 122 IKDIKE-QSIYMGDLPLMTKD-----------------------------GTFVIKGIQR 151
            K  +  + +    LP+M +                              G F+++G ++
Sbjct: 153 EKSKQTFKGLPFFKLPIMVRSRFCSLPKDPKDPEQIQQRIQSGECGFDQGGYFILRGSEK 212

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII-----PDQGLWMDIEFDSKDI-IHVR 205
           ++V+Q              R + +  L++  +I+      +     D+  +  +  + +R
Sbjct: 213 VIVAQE-------------RIANNVVLVFKSKIVNKPWVAEIRSQPDLWSNPNNFKVELR 259

Query: 206 --------------IDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
                          +  + +P+ +   ALG+ S+ EIL      +   Q G      L 
Sbjct: 260 YIQNTPVIRCSVKQFNSTQGIPLFTLFRALGISSDQEILERIVYNLEDEQMGPMLEM-LY 318

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIES----GKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
            +    G      L     G ++ ++     + L     K + +  +  +G++S+     
Sbjct: 319 GSLQEGGEYEDEELCLRWIGNKIKKAENQDPETLIQEAKKLINKNILPHIGVSSES---R 375

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
                 +      +   +    D+   +      +              A +     T  
Sbjct: 376 DRKAYFIGYIVHRLLNASLGKTDQDDRDHYGKKRLDM----------AGAMMMGVFKTSF 425

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
              +++A   + + +   ++      +S F+      D  +    G    +    +    
Sbjct: 426 ESFKQNAKKALEKYINGENMRQPDDIKSFFDGEQISKDIDNALATGNWGRSKEGQVVKTG 485

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             + +++E  +      +   N         +   +   +    +         ++    
Sbjct: 486 VAQTLKRETSLFATLSHLRRMNAPINPQMKLSKPRQLHNTHFGFICPAETPEGQKIGIVK 545

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
              + +   + +  +D      ++  + +     QL Q +     + ++T          
Sbjct: 546 NLSLMTAVSNDLQQKDKETLLKLIMVLKQDVFDFQLLQGDFQAQDIPKMTKVLVDGNWIG 605

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                 +   E +++       I    +     +     + + A     G    P   V 
Sbjct: 606 FTRNPEQFIQEFKNLRSAEESFIPIEVSINFDYVNKEIRIYTDA-----GRCMRPLFIVQ 660

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV-PREKIDFID 665
           D K+      L++  +  + +      L +       L+              ++    +
Sbjct: 661 DNKLKLKKNQLNSFTDWEQLLQNKCVELLDVEEEEGSLIAMDLNIMTRGTQNFKRYTHCE 720

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             P  +  + AS+IPF  ++   R  +   M +QA+ L       
Sbjct: 721 IHPCMMFGVCASVIPFANHNQGPRNTLQSAMGKQAMGLNSTNFNI 765


>gi|80978845|gb|ABB54671.1| RNA polymerase beta subunit [Mycoplasma spumans]
          Length = 592

 Score =  324 bits (830), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 207/448 (46%), Positives = 296/448 (66%), Gaps = 10/448 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ +++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEMSNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA+++ YGFI++PY +V D  V  +  +YL+A+EE     AQ+   +  +    +E V  
Sbjct: 61  FAQIDKYGFIQSPYFRVKDKVVDFSKPIYLTAIEEAGYTFAQSTLHIH-NNKIIDEKVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E I V  E++DF+  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNEYIEVNAEEVDFVGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +A+ S + I A R G+V  VDA  + I           +  DIY L  F
Sbjct: 180 APLVATGVEADIARYSSSNIRASRDGVVNYVDAEVVKITPT------GATKSDIYNLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           ++SNQ T ++Q P+VKVG E++  D++ DGPS   G++ALG+N+LV F  WHGYN+ED++
Sbjct: 234 EKSNQGTLIHQVPIVKVGQEIKAGDLLVDGPSMKDGEMALGKNVLVGFTTWHGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +D+ GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTTDIPNVSNASKRFLDDNGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMGAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQ 975
                ++    +E+     +A+ +  + 
Sbjct: 414 EQG--DQLEDGIEKIVKVSIAQKRKIKV 439



 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 127/413 (30%), Positives = 185/413 (44%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG E+  GD+LV   +   +  M   + +L         +  D  +     V   V 
Sbjct: 247  IVKVGQEIKAGDLLVDGPS-MKDGEMALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDILTTDIPNVSNASKRFLDDNGIVRVGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L           
Sbjct: 365  SPKGEENPTPE--EKLMGAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSR--------- 413

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 414  EQGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +            
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKSLKTKFVTPIFDGITHNQIKEILE---------- 523

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               E  +N          +G++++Y+G 
Sbjct: 524  -----------------------------------EADLN---------TTGKTVIYNGQ 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEPFDNPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|194270604|gb|ACF36848.1| RNA polymerase beta subunit [Mycoplasma buteonis]
          Length = 595

 Score =  324 bits (830), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 215/450 (47%), Positives = 304/450 (67%), Gaps = 15/450 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +FA+V+  GF++TPY KV DG V  NDV YL+A +E     AQ++  +D+        + 
Sbjct: 61  TFAKVDDLGFLKTPYYKVNDGIVDYNDVRYLTAADEIGYSFAQSSVLVDDTNRIVSPTLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     I+   E +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+A
Sbjct: 121 VRRDYNYIIAKPEDVDFIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLLQA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP+V TG+ES +AK S   I AK+ G V  VD  RI I++ +G  D        Y L  
Sbjct: 181 EAPYVATGIESDIAKYSSYNITAKKPGEVVYVDGSRIHIKNDKGVTDK-------YSLRN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + QRP+V+VG  V + D++ DG S   G++ALG+N+LV F  W+GYNFED+
Sbjct: 234 FERSNQGTLIQQRPIVQVGQFVEKGDLLVDGSSFKDGEMALGKNLLVGFTTWNGYNFEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I+ER+V +DVFTSIHIEE  +  R ++ G +E+T DIPNVS+  L+++DE GI+ VG+
Sbjct: 294 VIINERLVKDDVFTSIHIEEQTIQFRSSRAGDDELTNDIPNVSKFALRHLDENGIVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVG+ +PKGE   + EEKLL AI  +++ + +DTSL+V +G +GTV+ V + +
Sbjct: 354 EVVPGDILVGRTSPKGEENPSQEEKLLMAILQQRSSNKKDTSLKVKNGHNGTVIHVEVLS 413

Query: 947 RH-------GIDKNERSISVEREQIELLAR 969
           R        GIDK  +    ++ +I++  +
Sbjct: 414 RDKGDVLEEGIDKIVKVSIAQKRKIKVGDK 443



 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 127/415 (30%), Positives = 179/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  V  GD+LV   + K +  M   + LL         +  D  +     V   V 
Sbjct: 248  IVQVGQFVEKGDLLVDGSSFK-DGEMALGKNLLVGFTTWNGYNFEDAVIINERLVKDDVF 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E    +          LD N   R+   +   + + G  
Sbjct: 307  -TSIHIEEQTIQFRSSRAGDDELTNDIPNVSKFALRHLDENGIVRVGSEVVPGDILVGRT 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++          +L           
Sbjct: 366  SPKGEENPSQE--EKLLMAILQQRSSNKKDTSLKVKNGHNGTVIHVEVLSRD-------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDK+AGRHGNKG++S +LP EDMP+L+DGTP+D+
Sbjct: 416  -KGDVLEEGIDKIVKVSIAQKRKIKVGDKVAGRHGNKGVISIVLPEEDMPYLEDGTPLDV 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG +   LG K  +   D     DI               
Sbjct: 475  MLNPQGVPSRMNIGQILELHLGMSARKLGVKFVTPSFDGVKKTDIEAALEEAG------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L  +      + +L D +
Sbjct: 528  ------------------------------------------LNKSG-----KQVLIDPI 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 541  TGRKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|170097637|ref|XP_001880038.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164645441|gb|EDR09689.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 1142

 Score =  324 bits (830), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 95/339 (28%), Positives = 141/339 (41%), Gaps = 72/339 (21%)

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y+ +    +      I+K+   D        ++KV +   R  + GDK + RHG KG+  
Sbjct: 862  YKNTPLTYKSPVAGNIDKVMISDTEND--QTLIKVLIRQTRRPELGDKFSSRHGQKGVCG 919

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             I+  EDMPF  DG   D ++NP G PSRM VG++ E   G A V               
Sbjct: 920  LIVNQEDMPFNDDGINPDTIMNPHGFPSRMTVGKMIELLAGKAGV--------------- 964

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                              +A + + G       F G+  E ++ 
Sbjct: 965  ----------------------------------LAGKLQYGT-----AFGGSKVEDMSR 985

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L       +G+ +L  G+TGEP +  V  G IY  KL HMV DK++AR+ G  + +T+Q
Sbjct: 986  ILIDHGFSYAGKDMLTSGITGEPLEAYVYFGPIYYQKLKHMVMDKMHARARGPRATLTRQ 1045

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DVVGRTR----------VY 1329
            P  G+S  GG RLGEME  C+  YGA  +L E L I SD  +V                Y
Sbjct: 1046 PTEGRSREGGLRLGEMERDCLIGYGATQLLLERLMISSDKFEVNACEECGLMGYNGWCTY 1105

Query: 1330 -ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             +S        +   P +  +L +E+ A+ +   L    
Sbjct: 1106 CKS---SKKMAQLTIPYAAKLLFQELMAMNVVPRLILDD 1141



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 129/960 (13%), Positives = 277/960 (28%), Gaps = 195/960 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ ++I    R N         V P         L++       P    
Sbjct: 47  LVKQHIDSFNYFVDIDIKNIVRAN---NKVTSDVDP------RFWLKYTDINVGFPDRNE 97

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 +    +C  RD+TY  P+ +T++               K I ++++ +G LP+M
Sbjct: 98  LEAIDKRVTPHECRLRDITYGAPIVVTIQYTRG-----------KSIVQRNVNIGRLPIM 146

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRS-----------PGI 163
                                      G FV+KG +++++ Q   S            G+
Sbjct: 147 LRSSKCVLTGRTEAQLARMTECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVETDTVKGV 206

Query: 164 HFDHDKGRASLSGK-LLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMAL 221
                        K   Y                  K  I++R +     VP+   L AL
Sbjct: 207 VQASCTSSTHGGLKSKTYVAT--------------KKGRIYLRHNSIHEDVPIVIALKAL 252

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+ S++ +         + +  F      AA L V  +            + I S  K+ 
Sbjct: 253 GIQSDKEILLLTAGTTEAYKNTFSANLEDAAKLGVYTRQQ--------ALEYIGSRVKIN 304

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             ++   +    + L   +  +   +V  + ++  +  I++    +     +     + +
Sbjct: 305 RRVMGPRRPAWEEALEALA-TIVLAHVPVNGLDFRSKAIFVA--TMTRRVLMAMQDENMV 361

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-LDIYRVMRPGDVSTFSVAESMFNFLF 400
            D   +    +     +   L  D  K     L + I +V++    ++   A +      
Sbjct: 362 DDRDYVGNKRLELAGQLLALLFEDLFKTYNSNLKIAIDKVLKKPSRTSEFDAYNTMQMQG 421

Query: 401 FDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                  +  +     +  R  ++       + +   I+ + ++  + +       +   
Sbjct: 422 DHLTSGFVRAISTGNWSLKRFKMERAGVTHVLSRLSFISALGMMTRISSQFEKTRKVSGP 481

Query: 460 G-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
                    V    +  + +    +  +           +        ++  + +     
Sbjct: 482 RALQPSQWGVLCPSDTPEGEACGLVKNLALMTHITTDVEEEPITRLAFMLGIEDINLTTG 541

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                  +  +  +   +    +  R  A     + RAR   E   V+  H+       +
Sbjct: 542 TEIYGPGVFVVNVNGTIIGVTRYPARFVA-QFRSLRRARRFSEFVSVYINHHHHAVHIAS 600

Query: 575 SEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             G        + +            ++       D      V YL   EE + YIA   
Sbjct: 601 DGGRICRPAIIVENGRPKVASEHMMHLKKGNVTFDDFLRKGLVEYLDVNEENDTYIALYE 660

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           S +                             ++  P  ++   A LIP+  ++ S R  
Sbjct: 661 SDIVP-----------------------ATTHLEIEPFTILGAVAGLIPYPHHNQSPRNT 697

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             C M +QA+                                           I   + +
Sbjct: 698 YQCAMGKQAIGA-----------------------------------------IGYNQMN 716

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              +   + +Y               Q+P+VK                     L  G+N 
Sbjct: 717 RIDTLLYLSVYP--------------QQPMVK----------TKTIELIGYDRLPAGQNA 752

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            VA M + GY+ ED++++++  +         + +   + R    G  +   D P     
Sbjct: 753 TVAVMSYSGYDIEDALILNKASLDRGYGRCQVLRKNATLIRKYPNGTFDRLADAPLDENG 812

Query: 872 GL-KNID---ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            L K  D     G+  VG  V+PGD+ V K +P   +  T   +     +    +  +  
Sbjct: 813 QLNKKYDIIQSDGLAGVGERVDPGDVYVNKQSPTNATDNTFTGQAASVPYKNTPLTYKSP 872


>gi|81171089|gb|ABB58771.1| RNA polymerase beta subunit [Mycoplasma felifaucium]
 gi|81171091|gb|ABB58772.1| RNA polymerase beta subunit [Mycoplasma felifaucium]
          Length = 592

 Score =  324 bits (830), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 210/423 (49%), Positives = 297/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L  +
Sbjct: 2   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNLAIY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +G V  N V +L+A +E    I Q+  ++DE+    +E V  R
Sbjct: 62  ANVNEYGFLQTPYFKVKNGVVDYNKVDWLTAADEFGFNIVQSTVNVDENNRLVDEQVTMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   E +D+I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 KNYTYIMGKPEDVDYIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG E+ +AK S A   AK  G VE VD  +I IR+ +G  +        Y L  FQ
Sbjct: 182 PFVATGNEADIAKYSSANFRAKSDGKVEYVDGAKIKIRTEKGTAE-------TYYLKTFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++QRPLVK GD +++ D++ DG S   G+L+LG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVIHQRPLVKEGDIIQKGDLLVDGSSFKNGELSLGKNLLVAFTTYKGYNYEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V  DV TSIHIEE  +  R +K G +E+TR+IPNVS+  ++++DE GI+ VG+EV
Sbjct: 295 LNERLVKNDVLTSIHIEEQIIQFRTSKAGSDELTREIPNVSKHSIRHLDEHGIVLVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+ G+++++V+DTSL+V +G +GTV+ V I +R 
Sbjct: 355 TPGDVLVGRVSPKGDDNPSQEEKLLAAVLGQRSLNVKDTSLKVKNGHNGTVIGVEILSRE 414

Query: 949 GID 951
             D
Sbjct: 415 NND 417



 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 136/479 (28%), Positives = 210/479 (43%), Gaps = 80/479 (16%)

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKLGPEEITRDIPNVSEEGLKNIDEC 879
              +   I++   +     S    E+   A+    T+ G  E               I + 
Sbjct: 186  TGNEADIAKYSSANFRAKSDGKVEYVDGAKIKIRTEKGTAETYYLKTFQRSNQDTVIHQR 245

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             ++  G  +  GD+LV   + K    ++  + LL A    K  +  D  +     V   V
Sbjct: 246  PLVKEGDIIQKGDLLVDGSSFKN-GELSLGKNLLVAFTTYKGYNYEDAVILNERLVKNDV 304

Query: 940  V-DVRIFNRHGIDKNERSISVE-REQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
            +  + I  +    +  ++ S E   +I  +++      DE  I+         ++L G+ 
Sbjct: 305  LTSIHIEEQIIQFRTSKAGSDELTREIPNVSKHSIRHLDEHGIVLVGSEVTPGDVLVGRV 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L + ++                  QR++       +           
Sbjct: 365  SPKGDDNPSQEEKLLAAVLG-----------------QRSLNVKDTSLKVKNGHNGTVIG 407

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +I   +  D +  G+ +++KV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP L+D
Sbjct: 408  VEILSRENNDQLEDGIDKIIKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPHLED 467

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD++LNP GVPSRMN+GQ+ E HLG A   L  K  + + D     +I  +      
Sbjct: 468  GTPVDVMLNPQGVPSRMNIGQVLEIHLGMAAKTLQCKFVTPVFDGVKKEEIQDVIQ---- 523

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                      ++G+P+                        +G+ 
Sbjct: 524  --------------------------EAGLPI------------------------TGKQ 533

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             L D +TGE FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 534  TLIDPITGEKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|52694341|emb|CAG38010.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. V]
          Length = 333

 Score =  324 bits (830), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 196/332 (59%), Positives = 255/332 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +R+DI+ADGPSTD+G+LALG+NM +AFM W+G
Sbjct: 302 QRSDIMADGPSTDMGELALGQNMRIAFMAWNG 333


>gi|183584850|gb|ACC63893.1| RNA polymerase beta subunit [Mycoplasma sp. 1220]
          Length = 594

 Score =  324 bits (830), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 213/450 (47%), Positives = 310/450 (68%), Gaps = 15/450 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN  GF++TPY KV +G +  NDV YL+A EE     +Q++ ++DE+    +EL+ 
Sbjct: 61  TYAKVNEMGFLQTPYFKVNNGVIDYNDVRYLTASEEIGYKFSQSSVTVDENNRIVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     ++    ++DFI+ S KQ+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+A
Sbjct: 121 IRHNYNYVIDKPSEVDFIEVSSKQMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP+V TG+E  +AK S   +VAK AG V  VD+ +I I++ +G  D        Y L  
Sbjct: 181 EAPYVATGIEGDIAKYSAYNLVAKNAGEVVYVDSQKIHIKNDKGTTDK-------YVLRN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T +NQ P+VK+GD+V   ++I DG S   G+LALG+N+LVAF  W+GYN+ED+
Sbjct: 234 FERSNQGTVINQIPIVKLGDKVEEGELIVDGSSFKNGELALGKNVLVAFTTWNGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++E++V +DV+TSIHIEE  +  R++K G +++T  IPNVS+  L+N+DE GI+ VG+
Sbjct: 294 IILNEKLVKDDVYTSIHIEEQTIQFRNSKAGDDKLTASIPNVSKYSLRNLDENGIVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGD+LVG+++PKGE   T EEKLL AI  ++    RDTSL+V +G +GTV+ V + +
Sbjct: 354 EVVPGDVLVGRVSPKGEENPTQEEKLLMAILQQRPSSDRDTSLKVKNGHNGTVIGVEVLS 413

Query: 947 R-------HGIDKNERSISVEREQIELLAR 969
           R        GIDK  +    ++ +I++  +
Sbjct: 414 RELGDVLEDGIDKIVKVSIAQKRKIKVGDK 443



 Score =  301 bits (771), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 142/525 (27%), Positives = 224/525 (42%), Gaps = 82/525 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMVS 835
            Q   V  G      +  A+              +L A  P+     E  +    +  +V+
Sbjct: 144  QMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQAEAPYVATGIEGDIAKYSAYNLVA 203

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    ++++  ++  ++ K   ++        S +G   I++  I+ +G +V  G+++V
Sbjct: 204  KNAGEVVYVDSQKIHIKNDKGTTDKYVLRNFERSNQGTV-INQIPIVKLGDKVEEGELIV 262

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHG 949
               + K    +   + +L A       +  D  +            S  + +  I  R+ 
Sbjct: 263  DGSSFKN-GELALGKNVLVAFTTWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNS 321

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
               +++  +      +   R+  DE  I+         ++L G+ +  G +   +   L 
Sbjct: 322  KAGDDKLTASIPNVSKYSLRNL-DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLL 380

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              ++ + P S        D      V++          +L             GD +  G
Sbjct: 381  MAILQQRPSS--------DRDTSLKVKNGHNGTVIGVEVLSREL---------GDVLEDG 423

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP L+DGTPVDI+LNP GVPS
Sbjct: 424  IDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPHLEDGTPVDIMLNPQGVPS 483

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG A   LG K  +   D     DI                        
Sbjct: 484  RMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKQDI------------------------ 519

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
             ++ L  A   K+G  +                             L D +TGE FD PV
Sbjct: 520  -ENALEEAGLPKTGKQI-----------------------------LIDPVTGEKFDNPV 549

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +VG +YMLKLNHM+ DK++ RS G YSL+TQQPLGGKS  GGQR 
Sbjct: 550  SVGVMYMLKLNHMIDDKMHGRSVGPYSLITQQPLGGKSQNGGQRF 594


>gi|52538161|emb|CAH19182.1| RNA polymerase beta-subunit [Pseudomonas grimontii]
          Length = 330

 Score =  323 bits (829), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 195/330 (59%), Positives = 254/330 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +DI+ADGPSTD+G+LALG+NM +AFM W+G
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNG 330


>gi|237823479|pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
 gi|237823491|pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
 gi|237823507|pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
 gi|323462789|pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
            P21 Space Group
 gi|323462805|pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
            P21 Space Group
 gi|219814433|gb|ACL36490.1| RNA polymerase subunit 2 [Sulfolobus shibatae B12]
          Length = 1131

 Score =  323 bits (829), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 113/587 (19%), Positives = 192/587 (32%), Gaps = 99/587 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 616  IEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 675

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 676  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 733  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEPGV 783

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 784  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 841

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 842  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRIPSIGDKFASRHGQKG 889

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   D++LNP  +PSRM +GQI E   G                
Sbjct: 890  VIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAA------------ 937

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 938  -----------------------------------------LSGNIVDATP-FYKTPIEQ 955

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           + YDG TG+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 956  LQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------- 1324
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD       D  G       
Sbjct: 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDK 1075

Query: 1325 -RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             + + Y   + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1076 NKNK-YVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILEDR 1121



 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 171/1133 (15%), Positives = 338/1133 (29%), Gaps = 228/1133 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L+     SY+ F+             LQ        I        +         P+   
Sbjct: 26   LVRQHLDSYNDFVRNK----------LQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRE 75

Query: 86   -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +   R+LTYA PL +T+  +  +++             + +Y+GDLP+M
Sbjct: 76   SDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEP----------EEVYIGDLPIM 125

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F++ G +R++V+Q   +P      D G+   
Sbjct: 126  LKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV-DTGKTGS 184

Query: 175  SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
            +  + +  +II      + + + IE       HV       K+P    + ALG+ ++   
Sbjct: 185  N--ITHTAKIISSTAGYR-VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTD--- 238

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                  IVY+   D          L   + +++    +D     +  G+K  + + K   
Sbjct: 239  ----RDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQ 294

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
             + +  +  LG ++D              +  E+Y+   +  D+       L        
Sbjct: 295  IIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFA 354

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                + +   V +  Y          K    AL+      RP D+ T  +  ++    + 
Sbjct: 355  SLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALV------RP-DIVTERIRHALATGNWV 407

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                     + R      L+      +  + +       + L   + G+    +  +   
Sbjct: 408  GGRTGVSQLLDRTNWLSMLSHLRRV-ISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSAVCEFFCS 519
            +  V+++  M +    +    +E+++ E       + +    +    +       +   +
Sbjct: 467  SGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILN 526

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +L         L++    RR        V       +            C +       
Sbjct: 527  GRLVGYYRDGEELAKKIRERRRKGEISDEVNVGHIVTD----FINEVHVNCDSGRVRRPL 582

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            I + +      R +    +++      D      + YL A EEEN Y+A   S L  +  
Sbjct: 583  IIVSNGNPLVTREDIE-KLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEH- 640

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                    ++     ++ I AS+IP+ E++ S R      M +Q
Sbjct: 641  ----------------------THLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQ 678

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            A+ L  A                                                + + +
Sbjct: 679  ALGLYAANYQL-----------------------------------------RTDTRAHL 697

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y               QRPLV    + R  DII             G N ++A + + 
Sbjct: 698  LHYP--------------QRPLV----QTRALDIIGYTN------RPAGNNAILAVISFT 733

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLK 874
            GYN EDS++++   V   ++ S     +         G E+              +E  +
Sbjct: 734  GYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYR 793

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++ G++    EV  GD+L+GK++P        E    +A         RDTS+    G
Sbjct: 794  LLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK--------RDTSIVTRHG 845

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI--LDRNIYSRLM-EILC 991
              G V              +  +  E  +   L + +  +  I  +     SR   + + 
Sbjct: 846  EMGIV--------------DLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVI 891

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G         +    V+   +++ +            E +     +L      +    + 
Sbjct: 892  GMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKT 951

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
              +    +I     +P                    D   GR G K I SRI 
Sbjct: 952  PIEQLQNEILKYGYLPDATEVT-------------YD---GRTGQK-IKSRIY 987


>gi|52538153|emb|CAH19178.1| RNA polymerase beta-subunit [Pseudomonas gessardii]
          Length = 331

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 195/331 (58%), Positives = 254/331 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           +DI+ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFMAWNGF 331


>gi|15897172|ref|NP_341777.1| DNA-directed RNA polymerase subunit B' [Sulfolobus solfataricus P2]
 gi|13813361|gb|AAK40567.1| DNA-directed RNA polymerase, subunit B' (rpoB1) [Sulfolobus
            solfataricus P2]
          Length = 649

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 114/587 (19%), Positives = 193/587 (32%), Gaps = 99/587 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 138  IEYLDAEEEENAYVALEPNDLTPDHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 197

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 198  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVMSF 254

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 255  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEAGV 305

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 306  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 363

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 364  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRIPTIGDKFASRHGQKG 411

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   DI+LNP  +PSRM +GQI E   G                
Sbjct: 412  VIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAA------------ 459

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 460  -----------------------------------------LSGNIVDATP-FYKTPIEQ 477

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           ++YDG TG+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 478  LQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHARARGPVQIL 537

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------- 1324
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD       D  G       
Sbjct: 538  TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTMIYVCDQCGYIGWYDK 597

Query: 1325 -RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             + + Y   + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 598  NKNK-YVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLVLEDK 643



 Score = 94.8 bits (234), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 91/551 (16%), Positives = 160/551 (29%), Gaps = 136/551 (24%)

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                    C +       I + +       +     +E+      D      + YL A E
Sbjct: 87   FINEVHVNCDSGRVRRPLIIVSNG-NPLVTIEDIEKLESGAITFDDLVRQGKIEYLDAEE 145

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN Y+A   + L  D                          ++     ++ I AS+IP+
Sbjct: 146  EENAYVALEPNDLTPDH-----------------------THLEIWSPAILGITASIIPY 182

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             E++ S R      M +QA+ L  A                                   
Sbjct: 183  PEHNQSPRNTYQSAMAKQALGLYAANYQL------------------------------- 211

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                         + + +  Y               QRPLV    + R  DII       
Sbjct: 212  ----------RTDTRAHLLHYP--------------QRPLV----QTRALDIIGYTN--- 240

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                  G N ++A M + GYN EDS++++   V   ++ S     +         G E+ 
Sbjct: 241  ---RPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDK 297

Query: 862  TRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                         +E  + +++ G++    EV  GD+L+GK++P        E    +A 
Sbjct: 298  IVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK 357

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                    RDTS+    G  G V              +  +  E  +   L + +  +  
Sbjct: 358  --------RDTSIVTRHGEMGIV--------------DLVLITETAEGNKLVKVRVRDLR 395

Query: 977  I--LDRNIYSRLM-EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            I  +     SR   + + G         +    V+   +++ +            E +  
Sbjct: 396  IPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAG 455

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               +L      +    +   +    +I     +P                    D   GR
Sbjct: 456  KYAALSGNIVDATPFYKTPIEQLQNEILRYGYLPDATE-------------VVYD---GR 499

Query: 1094 HGNKGIVSRIL 1104
             G K I SRI 
Sbjct: 500  TGQK-IKSRIY 509


>gi|193735376|gb|ACF20190.1| RNA polymerase beta subunit [Mycoplasma salivarium]
          Length = 595

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 214/446 (47%), Positives = 298/446 (66%), Gaps = 10/446 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ YGFI+TPY KV + KV  +   YL+A+EE    IAQ+   + E+    +++V 
Sbjct: 61  SFAQIDKYGFIQTPYFKVNNRKVDFSKPHYLTAIEEMGMVIAQSTVKI-ENNIIIDDVVM 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E +    + ID+I  S +Q++SIAAS IPFLENDD+NR LMG NMQRQAVP++K 
Sbjct: 120 ARKNNEYVEANADDIDYIGVSNRQMISIAASAIPFLENDDANRALMGANMQRQAVPVIKP 179

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ +AK S   I +   GIV  VDA +I I   EG         D Y L  
Sbjct: 180 EAPLVATGVEADIAKFSSTNIRSNTDGIVTYVDATQIKIMPFEGKKA------DTYYLRT 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T ++Q PLVKVG E+++ D++ DGPS   G++ALGRN+LV F  WHGYN+ED+
Sbjct: 234 FERSNQGTLIHQIPLVKVGQEIKKGDLLVDGPSMKDGEMALGRNVLVGFSTWHGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TSIHIEE  +  R +K G + +T DIPN S    + ++E GI+ +G+
Sbjct: 294 VVLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTSDIPNASNYSKRFLNEDGIVRIGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVG+ +PKGE   TPEEKL+ AIFG+K+V+ +DTSL+V  G +GTVV V +  
Sbjct: 354 EVTAGDILVGRTSPKGEDNPTPEEKLMAAIFGQKSVNRKDTSLKVKHGHNGTVVAVEVLT 413

Query: 947 RHGIDKNERSISVEREQIELLARDKD 972
           R     ++    +E+     +A+ + 
Sbjct: 414 REFG--DQLEDGIEKIVKVSIAQKRK 437



 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 126/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  M     +L         +  D  +     V   V 
Sbjct: 248  LVKVGQEIKKGDLLVDGPS-MKDGEMALGRNVLVGFSTWHGYNYEDAVVLSERLVKDDV- 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L+ +   R+   +   + + G  
Sbjct: 306  YTSIHIEEQTIQFRHSKAGEDILTSDIPNASNYSKRFLNEDGIVRIGSEVTAGDILVGRT 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q +V  +     V+        +  +L   F       
Sbjct: 366  SPKGEDNPTPE--EKLMAAIFGQKSVNRKDTSLKVKHGHNGTVVAVEVLTREF------- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 417  --GDQLEDGIEKIVKVSIAQKRKIRVGDKMAGRHGNKGVVSIVLPVEDMPYLEDGTPLDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   LG K  + + D   +  I  +    +       
Sbjct: 475  VLNPQGVPSRMNIGQILELHLGLAAKKLGVKFVTPVFDGITHNQIKEILEEAKVDTSGK- 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 534  ---------------------------TYVYD--------------------------GQ 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD P++VG +Y LKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 541  TGEKFDHPISVGIMYYLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|78714205|gb|ABB51085.1| RNA polymerase beta subunit [Mycoplasma opalescens]
          Length = 592

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 205/423 (48%), Positives = 300/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEIANKRRITSLGPGGLNRETAQFEVRDVHATHYGRICPIETPEGPNIGLILNYATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN +GF++TPY +V +G V  ++VVYL+A +E    IAQ+ + +DE+    +E +  R
Sbjct: 62  AKVNDHGFLQTPYYRVENGIVDYSEVVYLTAADEIGYRIAQSIAHIDENNKIVDERLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++    +IDFI+ +  Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPL++ +A
Sbjct: 122 YNYNYVVGTPAEIDFIEVASNQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLIETQA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+V TG+ES +A+ S A + AK  G+VE VD  +I +R+ +G+LD        Y L  ++
Sbjct: 182 PYVATGLESAIARYSSANLTAKNDGVVEYVDGKKIKVRNQKGNLD-------TYHLRNYE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T V+QRPLVK G E+ + DI+ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVVHQRPLVKEGQEISKGDILVDGSSFKNGELALGKNVLVAFTTYKGYNYEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E++ DIP+VS+  L+N+DE GI+ +G+EV
Sbjct: 295 LNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELSSDIPSVSKYSLRNLDENGIVRIGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVG+++PKG+   T EEKLL A+  ++  ++RDTSL+V +G +GTV+ V + +R 
Sbjct: 355 VAGDILVGRLSPKGDDNPTQEEKLLSAVLQQRQGNMRDTSLKVKNGHNGTVIGVEVLSRA 414

Query: 949 GID 951
             D
Sbjct: 415 FGD 417



 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 144/527 (27%), Positives = 210/527 (39%), Gaps = 86/527 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              ++    P+     E ++       + 
Sbjct: 142  NQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLIETQAPYVATGLESAIA--RYSSAN 199

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
                +  + E+ V  +  K+  ++   D  ++      N D    +  ++  G E++ GD
Sbjct: 200  LTAKNDGVVEY-VDGKKIKVRNQKGNLDTYHLRNYERSNQDTVVHQRPLVKEGQEISKGD 258

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            ILV   + K    +   + +L A    K  +  D  +            S  + +  I  
Sbjct: 259  ILVDGSSFKN-GELALGKNVLVAFTTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQF 317

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++   S      +   R+  DE  I+         +IL G+ +  G     +  
Sbjct: 318  RTSKAGDDELSSDIPSVSKYSLRNL-DENGIVRIGSEVVAGDILVGRLSPKGDDNPTQEE 376

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L S ++         Q           V++          +L   F         GD +
Sbjct: 377  KLLSAVLQ--------QRQGNMRDTSLKVKNGHNGTVIGVEVLSRAF---------GDQL 419

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP L+DGTPVD++LNP G
Sbjct: 420  EDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPHLEDGTPVDVMLNPQG 479

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+FE HLG A   LG    +   D      I          +          
Sbjct: 480  VPSRMNIGQVFEVHLGMAARTLGCHFVTPTFDGVKKNHIYEAMDEANLPLSG-------- 531

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                               ML              D +TG  FD
Sbjct: 532  ---------------------------------KQML-------------IDPITGRHFD 545

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PVTVG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 546  NPVTVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|242392338|dbj|BAH80382.1| RNA polymerase subunit B' [Halostagnicola larsenii XH-48]
          Length = 609

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 127/604 (21%), Positives = 214/604 (35%), Gaps = 104/604 (17%)

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
             DE+   D++A G   +  D     ++ VA            + I  +++       I  
Sbjct: 87   NDELEFEDLVAHG-YIEFIDAEEEEDIYVAVDEDDLNERHTHLEIDPQLIFGIGAGMIPY 145

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             E     R T      + +    +     +   +     +        +        G  
Sbjct: 146  PEHNASPRITMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFD 202

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
                 +  + A+   +  ++ D  +   + V    +    F R    +  R    + ++ 
Sbjct: 203  DRPAAQNFVVAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRF 261

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E+ ++D       +           L     V+      +++VL           +    
Sbjct: 262  EIPSQD-------VRGARGEEAYTHLDEDGLVNPETDVDENSVLLGKTSPPRFLEEPDDM 314

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 + +R         E+         + +               ++ KV V  +R  
Sbjct: 315  GGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIP 362

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK A RHG KG+V  + P EDMPF + G   D+V+NP  +PSRM VG I E   G  
Sbjct: 363  ELGDKFASRHGQKGVVGHLAPQEDMPFTEAGVVPDLVINPHALPSRMTVGHILEMIGGKL 422

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G+++                                                    
Sbjct: 423  GAMEGRRVDG-------------------------------------------------- 432

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP F G DE+ +   L  +  + SG+  +Y G+TGE  +  + VG I+  KL HMVS
Sbjct: 433  ---TP-FLGEDEDELRGGLEESGFESSGKETMYSGVTGEKIEAEIFVGIIFYQKLYHMVS 488

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            +K++ARS G   ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD    
Sbjct: 489  NKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDREFI 548

Query: 1321 DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +V G           + RVY      E      D  E     +F +L+ EM+ALG++  L
Sbjct: 549  NVCGQCGMSAVENVEQRRVYCPNCDEE-----TDIHEIEMSYAFKLLLDEMKALGIAPRL 603

Query: 1364 ENSR 1367
            E   
Sbjct: 604  ELVD 607



 Score = 45.1 bits (105), Expect = 0.092,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +   ++      +I   RRL  + +      +       ++        P    
Sbjct: 11  YVNGSLVGTHDDPHELAEQIREARRLGDVSEMVNVSVKDRTREVIINADAGRARRPLLVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E      ++     A  N          +  D      + ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-PRITDEEIEALRNDE-------LEFEDLVAHGYIEFIDAEEEEDIYVAVDEDDLN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 -----------------------ERHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MVKQSLGLPSANYRI 174


>gi|116563498|gb|ABJ99765.1| RpoB [Bacillus licheniformis]
          Length = 204

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 81/226 (35%), Positives = 126/226 (55%), Gaps = 23/226 (10%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E Q +S   FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EXQTSSXQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
           R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR R
Sbjct: 102 RVIVSQLVRSPSVYFS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTR 158

Query: 211 KVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLM 255
           K+PVT  L ALG  S++ I+             D      +   L+
Sbjct: 159 KLPVTVLLRALGFGSDQXIIDLVGEXEYLRNSLDKDNTENTDKALL 204


>gi|81171085|gb|ABB58769.1| RNA polymerase beta subunit [Mycoplasma adleri]
          Length = 592

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 211/423 (49%), Positives = 296/423 (69%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L  +
Sbjct: 2   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLALY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +G V  N V +L+A +E    I Q+  ++D+D    +E V  R
Sbjct: 62  ANVNEYGFLQTPYFKVNNGVVDYNQVDWLTAADEFGFNIVQSTVNVDKDNKIVDEQVTMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   E +D+I+ S +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 KNYTYIMGKPEDVDYIEVSSRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG E+ +AK S A   AK  G VE VD  +I IR+ +G  D        Y L  FQ
Sbjct: 182 PFVATGTEADIAKYSSANFRAKNDGKVEYVDGSKIKIRTEKGTAD-------TYTLKTFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+PLV+ GD V++ D++ DG S   G+LALG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVIHQKPLVREGDIVKKGDLLVDGSSFKDGELALGKNLLVAFTTYKGYNYEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++E++   DV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VGAEV
Sbjct: 295 LNEKLAKNDVLTSIHIEEQVIQFRTSKAGADELTRDIPNVSKHSIRHLDEFGIVLVGAEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+ G+++++V+DTSL+V +G +GTV+ V I +R 
Sbjct: 355 TPGDVLVGRVSPKGDDNPSQEEKLLAAVLGQRSLNVKDTSLKVKNGHNGTVIGVEILSRE 414

Query: 949 GID 951
             D
Sbjct: 415 NND 417



 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 116/423 (27%), Positives = 172/423 (40%), Gaps = 87/423 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------- 933
            ++  G  V  GD+LV   + K +  +   + LL A    K  +  D  +           
Sbjct: 247  LVREGDIVKKGDLLVDGSSFK-DGELALGKNLLVAFTTYKGYNYEDAVILNEKLAKNDVL 305

Query: 934  ---GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
                +   V+  R       +      +V +  I  L     DE  I+         ++L
Sbjct: 306  TSIHIEEQVIQFRTSKAGADELTRDIPNVSKHSIRHL-----DEFGIVLVGAEVTPGDVL 360

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G+ +  G     +   L + ++                  QR++       +       
Sbjct: 361  VGRVSPKGDDNPSQEEKLLAAVLG-----------------QRSLNVKDTSLKVKNGHNG 403

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 +I   +  D +  G+ +++KV +A+KR I+ GDKM+GRHGNKG+VS ILP EDM 
Sbjct: 404  TVIGVEILSRENNDQLEDGIDKIIKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDM- 462

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
                         P             E                   D   N    P R 
Sbjct: 463  -------------PH-----------LE--------------DGTPVDVMLNPQGVPSRM 484

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
             + +V+                +         G    TPVF G  +EAI + +  A+L +
Sbjct: 485  NIGQVL---------------EIHLGMAARSLGCKFVTPVFGGVKKEAIQAAMEEANLPK 529

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
            +G+ IL D +TGE FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  G
Sbjct: 530  TGKQILIDPITGEKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNG 589

Query: 1291 GQR 1293
            GQR
Sbjct: 590  GQR 592


>gi|4867876|emb|CAB43078.1| RNA polymerase II [Ophiorrhiza mungos]
          Length = 263

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 43   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPH 102

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 103  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 130

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 131  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 168

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++   G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 169  TATIFLGPTYYQRLKHMVDDKIHSXGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 228

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 229  GAAHFLKERLFDQSD 243


>gi|80978867|gb|ABB54682.1| RNA polymerase beta subunit [Mycoplasma collis]
          Length = 594

 Score =  323 bits (829), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 213/448 (47%), Positives = 304/448 (67%), Gaps = 13/448 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS + + RR+++LG GG+ R  A  E+RDVH T+YGRICP ET EG NIGL+ +L ++
Sbjct: 2   NPLSELANKRRITSLGPGGLNRETAQFEVRDVHSTYYGRICPIETPEGQNIGLILNLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++ + +GFI+TPY  V +G V  +++ +L+A++E     AQ++ ++D++    +E V  R
Sbjct: 62  SKTDDFGFIQTPYFPVVNGYVNYDEIKWLTAVDEYGYTFAQSSLTIDDNNKIIDEFVTVR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + ++V   ++D+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQAVPLL+++A
Sbjct: 122 KDYQYLIVKANEVDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQAVPLLESQA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E  +AK +   I A  +G V  VDA  I I+  +         +DIY L  FQ
Sbjct: 182 PLIATGVEHDIAKFAATNIRANNSGKVIYVDAKTIKIKPDDE-----DLAIDIYHLRNFQ 236

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T +NQ P VKV D + + D+I DGPST  G+LALG+N+LVAF  W+GYNFED+++
Sbjct: 237 KSNQGTTINQIPTVKVDDYIEKGDLICDGPSTKDGELALGKNVLVAFTTWNGYNFEDAII 296

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DVFTSIHIEE  +  R +K G + +T DIPN S    +++DE GI+ VG+EV
Sbjct: 297 ISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTNDIPNASIRSKRHLDENGIVRVGSEV 356

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G  GTV+DV+I +R 
Sbjct: 357 TTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGTNQKDTSLKVKHGDEGTVIDVQIISRA 416

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 417 NGDVLEDGIDKIVKVFIAQKRKIKVGDK 444



 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 131/445 (29%), Positives = 196/445 (44%), Gaps = 71/445 (15%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              K   E++  DI ++      N    I++   + V   +  GD++    + K +  +  
Sbjct: 217  KIKPDDEDLAIDIYHLRNFQKSNQGTTINQIPTVKVDDYIEKGDLICDGPSTK-DGELAL 275

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             + +L A       +  D  +     V   V    I       +   S + +      + 
Sbjct: 276  GKNVLVAFTTWNGYNFEDAIIISEKLVKDDVF-TSIHIEEQTIQFRTSKAGDDTLTNDIP 334

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                  +  LD N   R+   +   + + G    K     + +        +       +
Sbjct: 335  NASIRSKRHLDENGIVRVGSEVTTGDILVGRISPKGEDNPTPE-------EKLLNAIFGN 387

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            +   +   SLKV++    ++++     +I     GD +  G+ ++VKVF+A KR I+ GD
Sbjct: 388  KGTNQKDTSLKVKHGDEGTVID----VQIISRANGDVLEDGIDKIVKVFIAQKRKIKVGD 443

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG++S +LP EDMP+L+DGTPVDI+LNP GV SRMN+GQ+ E HLG A   L
Sbjct: 444  KMAGRHGNKGVISLVLPVEDMPYLEDGTPVDILLNPQGVASRMNIGQVLELHLGMAAKKL 503

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
              K  S + D   N D+  +                                        
Sbjct: 504  NVKFISPVFDGIKNEDLDSIL--------------------------------------- 524

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                   E           L  SG+  L+DG+TG+ FD  V+VG +YMLKL HMV DK+ 
Sbjct: 525  ------KEAD---------LPTSGRFKLFDGITGKEFDSKVSVGIMYMLKLQHMVDDKIN 569

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQR 1293
            ARS G YSL++QQPLGGKS  GGQR
Sbjct: 570  ARSVGPYSLISQQPLGGKSQNGGQR 594


>gi|86451149|gb|ABC96797.1| RNA polymerase II [Alstonia scholaris]
          Length = 210

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 107/250 (42%), Gaps = 54/250 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG +      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPFTAEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEML 1315
            GAA+ L+E L
Sbjct: 199  GAAHFLKERL 208


>gi|110589450|gb|ABG77234.1| DNA-directed RNA polymerase beta subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 176

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 87/171 (50%), Positives = 117/171 (68%)

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              P FDV +C  R  TYA PL++ +RL+++D +   G+  +KDI+EQ +YMG++PLMT 
Sbjct: 1   LGEPVFDVRECQLRGTTYAAPLRVLVRLVIYDKEAPAGSNVVKDIREQEVYMGEMPLMTD 60

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLL++ R+IP +G W+D EFD KD
Sbjct: 61  TGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFSARVIPYRGSWLDFEFDPKD 120

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
            + VRIDRRRK+P T  L ALG D+E+IL  F+    +S         L A
Sbjct: 121 NVFVRIDRRRKLPATVLLRALGYDTEQILGMFFETDTFSLTKRTVKVNLGA 171


>gi|189396507|gb|ACD93407.1| RNA polymerase beta subunit [Mycoplasma sp. CSL7503-lung]
          Length = 597

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 229/578 (39%), Positives = 345/578 (59%), Gaps = 17/578 (2%)

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
            + +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ + 
Sbjct: 1    DQINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHATHYGRICPIETPEGLNIGLILNY 60

Query: 587  TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
             +FA+V+  GF++TPY KV DG V   DV YL+A EE     AQ+   +D++     E +
Sbjct: 61   ATFAQVDDLGFLKTPYFKVNDGVVDYEDVRYLTAAEEIGYSFAQSLVKIDDNNKIVSESL 120

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R     ++   + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+
Sbjct: 121  TIRRDYNYLIGTPKDVDFIEVSSKQMVSVAAAGIPFLENDDANRALMGSNMQRQAVPLLQ 180

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             EAP + TG+ES +AK S   + AK AG+V  VD+ +I I+  E      T   D Y L 
Sbjct: 181  TEAPLIATGIESDIAKYSSYNLTAKNAGVVTFVDSSKIHIKRDE------TGVTDKYMLR 234

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
             F+RSNQ T ++Q+P+VK+ D V   D++ DG S   G+L+LG+N+LV F  W+GYNFED
Sbjct: 235  TFERSNQGTIIHQKPIVKLNDRVEVGDLLTDGSSFKDGELSLGKNVLVGFTTWNGYNFED 294

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
            +++I+ER+V EDV+TSIHIEE  +  R+++ G +E+T +IPNVS+  ++N+DE GI+ +G
Sbjct: 295  AIIINERLVKEDVYTSIHIEEHIIQFRNSRAGKDELTPNIPNVSKYAIRNLDEYGIVKLG 354

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            ++VNPGD+LVG+ +PKGE   + EEKLL AI G K++  +DTSL+V +G  GTV+D+++ 
Sbjct: 355  SDVNPGDVLVGRTSPKGEENPSQEEKLLNAILGTKSLAYKDTSLKVKNGHGGTVIDIQVL 414

Query: 946  NRHGIDK-NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            ++   D   E    + +  I    + K  +++         +  IL  ++      G   
Sbjct: 415  SKENNDVLEEGVEKIVKVSIAQKRKLKPGDKMAGRHGNKGVVSIILPVEDMPYLEDGTPL 474

Query: 1005 STVLSSDLISE-YPRSQWWQFAVQDEKVQRNVESLKVQYETSKS-----ILEDRFKNKIE 1058
              +L+   +       Q  +  +     + NV+ +   ++  K       LE+   +K  
Sbjct: 475  DIMLNPQGVPSRMNIGQILELHLGMAARKLNVKFVTPSFDGVKKPDIEAALEEAGLDKSG 534

Query: 1059 KIQWGDDMPP-GVLRVVKVFVAMKRPIQ--SGDKMAGR 1093
            K    D +      + V V V     +     DKM GR
Sbjct: 535  KQTLIDPITGRKFDKPVSVGVMYMLKLNHMVDDKMHGR 572



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 132/491 (26%), Positives = 200/491 (40%), Gaps = 81/491 (16%)

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              A +   G   + +   S  + +++      ++  ++  +  + G  +           
Sbjct: 181  TEAPLIATGIESDIAKYSSYNLTAKNAGVVTFVDSSKIHIKRDETGVTDKYMLRTFERSN 240

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                I +  I+ +   V  GD+L    + K +  ++  + +L         +  D  +  
Sbjct: 241  QGTIIHQKPIVKLNDRVEVGDLLTDGSSFK-DGELSLGKNVLVGFTTWNGYNFEDAIIIN 299

Query: 932  PSGVSGTVVDVRIFNRHGID-------KNERSISVEREQIELLARDKDDEQVILDRNIYS 984
               V   V        H I        K+E + ++    +   A    DE  I+      
Sbjct: 300  ERLVKEDVYTSIHIEEHIIQFRNSRAGKDELTPNI--PNVSKYAIRNLDEYGIVKLGSDV 357

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
               ++L G+ +  G +   +   L + ++           A +D  ++          + 
Sbjct: 358  NPGDVLVGRTSPKGEENPSQEEKLLNAILGTKS------LAYKDTSLKVKNGHGGTVIDI 411

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E+            D +  GV ++VKV +A KR ++ GDKMAGRHGNKG+VS IL
Sbjct: 412  QVLSKENN-----------DVLEEGVEKIVKVSIAQKRKLKPGDKMAGRHGNKGVVSIIL 460

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+L+DGTP+DI+LNP GVPSRMN+GQI E HLG A   L  K  +   D     D
Sbjct: 461  PVEDMPYLEDGTPLDIMLNPQGVPSRMNIGQILELHLGMAARKLNVKFVTPSFDGVKKPD 520

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            I                                                         L 
Sbjct: 521  IEAALEEAG-------------------------------------------------LD 531

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             +      +  L D +TG  FD+PV+VG +YMLKLNHMV DK++ RS G YSL+TQQPLG
Sbjct: 532  KSG-----KQTLIDPITGRKFDKPVSVGVMYMLKLNHMVDDKMHGRSVGPYSLITQQPLG 586

Query: 1285 GKSNRGGQRLG 1295
            GKS  GGQR G
Sbjct: 587  GKSQNGGQRFG 597


>gi|4867895|emb|CAB43089.1| RNA polymerase II [Wrightia arborea]
          Length = 249

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 29   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTAEGITPDIIVNPH 88

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 89   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 116

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 117  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 154

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 155  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 214

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+  L  +SD
Sbjct: 215  GAAHFLKXRLFDQSD 229


>gi|78714187|gb|ABB51076.1| RNA polymerase beta subunit [Acholeplasma cavigenitalium]
 gi|78714189|gb|ABB51077.1| RNA polymerase beta subunit [Acholeplasma cavigenitalium]
          Length = 636

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 224/460 (48%), Positives = 305/460 (66%), Gaps = 38/460 (8%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T  RR+SALG GG+AR RAGVE+RDVH THYGRICP ET EG +IGL+SSLT++
Sbjct: 2   NPLSELTQKRRVSALGTGGLARDRAGVEVRDVHTTHYGRICPIETPEGPSIGLISSLTTY 61

Query: 590 ARVNAYGFIETPYRKVCDGKV----------TNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            +V+ YGFI+TPY K+   K+           N++ YL+A EEE R IA A + ++EDG 
Sbjct: 62  GQVDKYGFIQTPYFKLDRSKIDENGRPVPRLVNEIEYLTADEEEERIIASAATPVNEDGY 121

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F E  V  R  GE  +   ++I  +D SPKQ+VS++ + IPFLE+DD+ R LMG NMQRQ
Sbjct: 122 FVENRVIARHMGETNIFYADEITHMDVSPKQIVSVSTATIPFLEHDDATRALMGANMQRQ 181

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST--- 756
           AVPL+KAE+P VGTG+E   AK SG+ +V+K AGIV  VDA +IVI     +        
Sbjct: 182 AVPLIKAESPIVGTGIEYRAAKDSGSVVVSKVAGIVSYVDAEKIVITEKPEETIKMGTTT 241

Query: 757 ---------------------SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                                     Y L  F+RSNQ+T + Q+P+V++G+ +   D+IA
Sbjct: 242 LYNPADPFTLEVAQRISGYGLGNSTTYELETFRRSNQDTLILQKPIVELGETIEVGDVIA 301

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DG STD G+LALGRN+ VAFM W GYN+ED++++SE +V +DV+TS+H++++E+  R+ K
Sbjct: 302 DGASTDKGELALGRNVTVAFMTWDGYNYEDAIIMSEDLVKDDVYTSVHLDKYEIDTREIK 361

Query: 856 ----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                  EEITR++PN S + LKN+D  GII VG+EV  GDILVGKITPKG +  TP EK
Sbjct: 362 AAGANYQEEITREVPNASADALKNLDANGIIVVGSEVKEGDILVGKITPKGVNEPTPAEK 421

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           L+++I G+K+ + RD+SLRVP G  G V  V+ +++   D
Sbjct: 422 LIQSILGDKSREYRDSSLRVPHGGGGVVQKVQYYSKENGD 461



 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 125/418 (29%), Positives = 199/418 (47%), Gaps = 73/418 (17%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G  +  GD++    +   +  +     +  A       +  D  +     +S  +V
Sbjct: 287  IVELGETIEVGDVIADGAST-DKGELALGRNVTVAFMTWDGYNYEDAII-----MSEDLV 340

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               ++    +DK E    ++  +I+    +  +E      N  +  ++ L     +    
Sbjct: 341  KDDVYTSVHLDKYE----IDTREIKAAGANYQEEITREVPNASADALKNLDANGIIVVGS 396

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K+  +L              +    ++ +Q  +     +Y  S   +       ++K+
Sbjct: 397  EVKEGDILVGK----ITPKGVNEPTPAEKLIQSILGDKSREYRDSSLRVPHGGGGVVQKV 452

Query: 1061 Q-----WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            Q      GD +PPGV +V++VFV+ KR I  GDKMAGRHGNKG++S+ILP EDMP+++DG
Sbjct: 453  QYYSKENGDILPPGVTQVIRVFVSQKRKISEGDKMAGRHGNKGVISKILPREDMPYMEDG 512

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG KI + + D  ++ ++  +       
Sbjct: 513  TPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKLGIKIATPVFDGVSDQELRDIM------ 566

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                    E  I+           G++ 
Sbjct: 567  ---------------------------------------KEAGISE---------DGKTT 578

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            LYDG TGEPFD  ++VG +YM+KL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 579  LYDGRTGEPFDSRISVGVMYMIKLSHMVDDKLHARAVGPYTLVTQQPMGGKAQNGGQR 636


>gi|73697707|gb|AAZ81470.1| RNA polymerase beta subunit [Mycoplasma edwardii]
          Length = 592

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 215/451 (47%), Positives = 303/451 (67%), Gaps = 14/451 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+  GF++TPY KV +G V  NDV YL+A EE    IAQ++  +DE+   T+E +  R
Sbjct: 61  AKVDDKGFLKTPYYKVNNGVVDYNDVQYLTASEEFGYSIAQSSVHVDENNKITDEFLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                     E +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 RNYTYENGRSEDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQAVPLLQTEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E+ +AK S   +VAK AG V  VD  RI +   E  +       D Y L  F+
Sbjct: 181 PLIATGIEADIAKYSSYNLVAKNAGTVTYVDGSRIHVTRNESTV------TDKYTLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + QRPLV++GD+V   DI+ DG S   G+L+LG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTLIQQRPLVRIGDKVEVGDILTDGSSFKDGELSLGKNVLVGFTTWNGYNFEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+DIPN S+  L+N+DE GI+ VG+EV
Sbjct: 295 INERLVKNDVYTSIHIEEQTIQFRTSRAGNDELTKDIPNASKYSLRNLDEFGIVKVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKGE   + EEK+L AI G+++   +DTSL+V +G SGT++ V I +R 
Sbjct: 355 YPGDVLVGRVSPKGEENPSQEEKMLYAILGQRSPSTKDTSLKVKNGHSGTIIHVEILSRE 414

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       V  E IE + +    ++  + 
Sbjct: 415 KGD-------VLEEGIEKIVKVSIAQKRKIK 438



 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 127/419 (30%), Positives = 185/419 (44%), Gaps = 79/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL------RVPSG 934
            ++ +G +V  GDIL    + K +  ++  + +L         +  D  +      +    
Sbjct: 247  LVRIGDKVEVGDILTDGSSFK-DGELSLGKNVLVGFTTWNGYNFEDAVIINERLVKNDVY 305

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     N+          +   R+  DE  I+         ++L G+ 
Sbjct: 306  TSIHIEEQTIQFRTSRAGNDELTKDIPNASKYSLRNL-DEFGIVKVGSEVYPGDVLVGRV 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G +   +   +   ++ +   S            +     +K  +  +   +E   +
Sbjct: 365  SPKGEENPSQEEKMLYAILGQRSPS-----------TKDTSLKVKNGHSGTIIHVEILSR 413

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K      GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 414  EK------GDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 467

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQI E HLG A   LG K  S   D     DI         
Sbjct: 468  GTPLDIMLNPQGVPSRMNIGQILELHLGMAARKLGVKFVSPSFDGVKKPDIEAALEEAG- 526

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                            L         + 
Sbjct: 527  ------------------------------------------------LDKTG-----KQ 533

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +L D +TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 534  VLIDPITGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|78714191|gb|ABB51078.1| RNA polymerase beta subunit [Acholeplasma equifetale]
 gi|78714193|gb|ABB51079.1| RNA polymerase beta subunit [Acholeplasma equifetale]
          Length = 629

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 225/453 (49%), Positives = 296/453 (65%), Gaps = 31/453 (6%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +T  RR+SALG GG+AR RAGVE+RDVH +HYGR+CP ET EG +IGL+SSL ++
Sbjct: 2   NPLAELTQKRRVSALGTGGIARDRAGVEVRDVHNSHYGRLCPIETPEGPSIGLISSLATY 61

Query: 590 ARVNAYGFIETPYRKVCD-----GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           A+V+ YGFI TP+ KV        +V N+ VYL+A +E N  IA A S ++++G F E  
Sbjct: 62  AKVDEYGFIMTPFLKVVKDEEGKPRVINETVYLTADQEINEVIASAASPVNDEGYFMESR 121

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R  GE  +     + +ID SPKQ+VS+A S IPFLE+DD++R LMG NMQRQAVPLL
Sbjct: 122 VIARSNGETAIFEANDVTYIDVSPKQLVSVATSCIPFLEHDDASRALMGANMQRQAVPLL 181

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-------GDLDPSTS 757
           + E+P VGTG+E   AK SGA +V+   G V  VDA +I+I           G+      
Sbjct: 182 QTESPIVGTGIEHRAAKDSGAVVVSNVTGYVVYVDARKILILEEPTEDIIIRGETLYKVG 241

Query: 758 GVDIYRLMK-----------------FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           G   Y + K                 F RSNQ+T + Q+P+V  G+ V + D+IADGPST
Sbjct: 242 GDFNYGIAKRLYDLKIVEPKVFELIQFNRSNQDTLILQKPIVVQGEYVEKGDVIADGPST 301

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--LGP 858
             G+LALGRN+ VAFM W GYN+ED++++ E +V  DV+TSIHI+E+E+  RD K   G 
Sbjct: 302 SKGELALGRNVTVAFMTWEGYNYEDAIIMCEDLVKNDVYTSIHIDEYEIETRDLKQANGK 361

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNV  + +K +DE GII  G+EV  GDILVGKITPKG    TP EKL+ A+ G
Sbjct: 362 EEITREIPNVGPDAVKFLDERGIIIPGSEVKEGDILVGKITPKGVFEPTPAEKLIHAVIG 421

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +KA + RD+SLRVP G  G V  V+ F++   D
Sbjct: 422 DKAKEYRDSSLRVPHGGGGVVQSVQYFSKKNGD 454



 Score =  300 bits (769), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 130/420 (30%), Positives = 190/420 (45%), Gaps = 79/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD++    +   +  +     +  A    +  +  D  +     V   V 
Sbjct: 282  IVVQGEYVEKGDVIADGPST-SKGELALGRNVTVAFMTWEGYNYEDAIIMCEDLVKNDVY 340

Query: 941  DVRIFNRHGIDKNERSISVEREQIELL-------ARDKDDEQVILDRNIYSRLMEILCGQ 993
                 + + I+  +   +  +E+I          A    DE+ I+      +  +IL G+
Sbjct: 341  TSIHIDEYEIETRDLKQANGKEEITREIPNVGPDAVKFLDERGIIIPGSEVKEGDILVGK 400

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                G             +    P  +     + D+  +    SL+V +     +   ++
Sbjct: 401  ITPKG-------------VFEPTPAEKLIHAVIGDKAKEYRDSSLRVPHGGGGVVQSVQY 447

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K      GD + PGV   ++VF+A KR I  GDKMAGRHGNKG++SRILP EDMP+L 
Sbjct: 448  FSKKN----GDQLMPGVNEQIRVFIAKKRKITEGDKMAGRHGNKGVISRILPREDMPYLA 503

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTPVDI+LNPLGVPSRMN+GQI E HLG +   LG KI + + D  ++ D+  + +   
Sbjct: 504  DGTPVDIMLNPLGVPSRMNIGQILEIHLGISAKKLGIKIATPVFDGVSDEDLRNIMAEAG 563

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                  DG                    
Sbjct: 564  MEP-----------------------------------DGKTV----------------- 571

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LYDG TGEPF   ++VG +YMLKL+HMV DK++AR+ G Y+LVTQQP+GGK+  GGQR
Sbjct: 572  --LYDGRTGEPFQNRISVGVMYMLKLSHMVDDKLHARNVGPYTLVTQQPMGGKAQNGGQR 629


>gi|319790545|ref|YP_004152178.1| DNA-directed RNA polymerase, beta subunit [Thermovibrio
           ammonificans HB-1]
 gi|317115047|gb|ADU97537.1| DNA-directed RNA polymerase, beta subunit [Thermovibrio
           ammonificans HB-1]
          Length = 1449

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 133/463 (28%), Positives = 213/463 (46%), Gaps = 84/463 (18%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           RK F K  E   IPDL++ Q  SY+ F+ +N AP ER N GL++AF+  FPI   +    
Sbjct: 21  RKSFAKRKETYPIPDLLQFQFESYERFIQLNKAPHERENVGLESAFRQAFPIIDETTGVE 80

Query: 74  LEFVSYEFD----------------------------PPKFDVDDCLWRDLTYAVPLKIT 105
           + +  YE                               P++  D+C  R + Y+ PL++ 
Sbjct: 81  IHYKGYEIGDWYCKCGKFQGLGGKGVVCPKCGMEVVFRPRYTPDECKERGIDYSAPLRVL 140

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
             L V+  D  TG K    IKE  +Y G++PLMT+ GTF+I G +++VVSQLHRSPG+ F
Sbjct: 141 FELHVWQKDPKTGEKIAPVIKENKMYFGEIPLMTERGTFIINGTEKVVVSQLHRSPGLFF 200

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-D 224
            ++  + +   +++    IIP  G W++ E    DI++ +IDR+R+   T  L A G+  
Sbjct: 201 KNEISKTTQVARVIDIASIIPAMGSWLEFEIPYNDILYAKIDRKRRFIGTYLLRAFGLRT 260

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
            EEIL  FY  ++ + +                  V+  LVD +TGE             
Sbjct: 261 DEEILKVFYGDVIETLK-----------------VVNGELVDAETGEV----------KK 293

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            + L +  +    +  +               TGE+  EA + +   S +    +   + 
Sbjct: 294 PEELNDYYLVSDVVDPE---------------TGEVIQEAYEELSTSSRKLPEGA---EF 335

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKD--------ALLDIYRVMRPGDVSTFSVAESMF 396
            ++        A I NTL  +K    ++        A ++I+R +RPGD +T   A  +F
Sbjct: 336 KVINKKKTPYGAVIVNTLRKEKRDRVREKIEDPLIAAYVEIFRKVRPGDTATVEGARKLF 395

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +FF +  YDLS VGR K+N ++     + +  + KED+  I
Sbjct: 396 EAMFFSTRNYDLSRVGRAKVNEKIYPK--EKLERLTKEDLKEI 436


>gi|111054617|gb|ABH04366.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 328

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 202/326 (61%), Positives = 254/326 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVEYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V +G+ V R D+
Sbjct: 243 SVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWH 819
           +ADGPSTDLG+LALG+NM VAFMPW+
Sbjct: 303 LADGPSTDLGELALGQNMRVAFMPWN 328


>gi|296421976|ref|XP_002840539.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636757|emb|CAZ84730.1| unnamed protein product [Tuber melanosporum]
          Length = 434

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 93/352 (26%), Positives = 146/352 (41%), Gaps = 82/352 (23%)

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              + + +V Y+ +    +      I+K+            ++KV     R  + GDK + 
Sbjct: 138  EKISAGEVYYKDAPMTYKLHDHAYIDKVLV--STSESEQTLIKVLTRQTRRPELGDKFSS 195

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG+   I   EDMPF   G   DI++NP G PSRM VG++ E   G A V      
Sbjct: 196  RHGQKGVCGIIARQEDMPFSDTGIIPDIIMNPHGFPSRMTVGKMIELLAGKAGV------ 249

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                       +A + + G       F 
Sbjct: 250  -------------------------------------------LAGKLQYGT-----AFG 261

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G+  + +  +L       SG+  +  G+TGE  +  +  G IY  KL HMV DK+++R+ 
Sbjct: 262  GSKVDDMAKILVDNGFSYSGKDFVTSGITGESLEAYIFFGPIYYQKLKHMVQDKMHSRAR 321

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-- 1330
            G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD       V+E  
Sbjct: 322  GPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGASQLLLERLMLSSD-------VHEID 374

Query: 1331 -SIVAG--------------NDTFETGTPESFNVLVKEMQALGL--SIDLEN 1365
               V G                  +   P +  +L++E+ ++ +   I LE+
Sbjct: 375  LCEVCGLMGHSNWCTTCQSSKGVVKMKIPYAAKLLIQELLSMNVLARIRLED 426


>gi|56675685|emb|CAB43065.2| RNA polymerase II [Fagraea sp. Bremer 900109]
          Length = 258

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 107/250 (42%), Gaps = 54/250 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTSEGITPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 128  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEML 1315
            GAA+ L+E L
Sbjct: 226  GAAHFLKERL 235


>gi|83763771|emb|CAJ00219.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio
            proteolyticus]
          Length = 355

 Score =  323 bits (828), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 188/368 (51%), Positives = 260/368 (70%), Gaps = 13/368 (3%)

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+E  +A  SG   VAKR GI++ VDA RIV++  + +L P  +G+DIY L K+ RS
Sbjct: 1    VGTGIERNIAVDSGVTAVAKRGGIIQSVDASRIVVKVNDEELVPGEAGIDIYNLTKYTRS 60

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRP V  G+ V+R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+S
Sbjct: 61   NQNTCINQRPCVMPGEPVQRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVS 120

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  
Sbjct: 121  ERVVQEDRFTTIHIQELSCVARDTKLGAEEITADIPNVGESALSKLDESGIVYIGAEVKG 180

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G+
Sbjct: 181  GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGV 240

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                    
Sbjct: 241  EKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLIEGGHA-------------E 287

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              +    R +W +  ++D+ +Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PGV
Sbjct: 288  AKLDSVDRKKWLEMTLEDDALQTQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPGV 347

Query: 1071 LRVVKVFV 1078
            L++VKV+ 
Sbjct: 348  LKIVKVYW 355


>gi|20094124|ref|NP_613971.1| DNA-directed RNA polymerase subunit B' [Methanopyrus kandleri AV19]
 gi|19887125|gb|AAM01901.1| DNA-directed RNA polymerase second-largest subunit, the N-terminal
            part [Methanopyrus kandleri AV19]
          Length = 640

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 88/320 (27%), Positives = 131/320 (40%), Gaps = 80/320 (25%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +  +R  + GDK + RHG KG++  I+P EDMPF +DG   D++LNP  
Sbjct: 366  TSDGHKLVKVRIRDERVPELGDKFSSRHGQKGVIGMIVPEEDMPFTEDGITPDLILNPHA 425

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSR  +  I ET  G A    GK+I                                  
Sbjct: 426  LPSRETMAHILETLAGKAAALSGKRIDGSAFTSNPKEAY--------------------- 464

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                          E I  MLR    + +G+ ++YDG TG+  +
Sbjct: 465  ------------------------------EEIKKMLRELGFEPTGKEVMYDGRTGQKLE 494

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G     KL HMV DK +ARS G   ++T+QP  G++  GG R GEME   + A+G
Sbjct: 495  AEVFIGVCLYRKLYHMVKDKYHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDDLVAWG 554

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVA-------------GNDT-FETG--------TP 1344
            A+  L+E L  +SD        YE+ +              G       G          
Sbjct: 555  ASLFLKERLLDESD-------KYEAYICPNCGELCYVHAATGKTICPICGEVRADRVEMS 607

Query: 1345 ESFNVLVKEMQALGLSIDLE 1364
             +F +L+ E+++  +   LE
Sbjct: 608  YAFKILLDELKSFCMDAVLE 627



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 62/369 (16%), Positives = 116/369 (31%), Gaps = 21/369 (5%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G++E P   V   +       L        +       ++ D       +     GE  L
Sbjct: 33  GYVEDPEEFVEKVRELRREGVLHPRVNAAYHEDLNEVHVNCDRGRVVRPLLVVEDGEVKL 92

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                    +            +I FL+ ++    L+  +++      +  E     T +
Sbjct: 93  TEEHLEKLREGEISWKDLEEEGVIEFLDAEEEENALIAQSLEEFYS--MPKEERKKYTHV 150

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A   G                  +           +         ++ +       
Sbjct: 151 ELDPAAIFGTCCSCIPWPESNSAPRNTMG----TNMTRQALGFYAANHPIRMESRGHLLY 206

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              RPLVK               + D  +   G+NM+VA + + GYN ED+++++E  + 
Sbjct: 207 YPHRPLVK----------TRGTEAFDYDERPAGQNMIVAVLTYEGYNMEDAIIMNESAIE 256

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNP 890
             +  S   + FE  AR    G ++             SE+  K++ E G+  VG  V  
Sbjct: 257 RGLARSFFFKTFEDEARTYPGGMKDKFCIPEKEVRGYRSEDAYKHLGEDGLAEVGERVEG 316

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            D+++GK +P         E+L      E +  +R T   +   V  T            
Sbjct: 317 RDVIIGKTSPPRFLEEFRPEELPAEERRESSTAIRHTDSGIVDSVIITETSDGHKLVKVR 376

Query: 951 DKNERSISV 959
            ++ER   +
Sbjct: 377 IRDERVPEL 385


>gi|318602961|emb|CBJ04568.1| RNA polymerase beta subunit [Pseudomonas sp. R-37102]
          Length = 325

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 196/325 (60%), Positives = 254/325 (78%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+
Sbjct: 1   MPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LS
Sbjct: 61  RDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASL
Sbjct: 121 AIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ V
Sbjct: 181 IPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSV 240

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGP
Sbjct: 241 DASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGP 300

Query: 799 STDLGDLALGRNMLVAFMPWHGYNF 823
           STD+G+LALG+NM +AFM W+G+NF
Sbjct: 301 STDMGELALGQNMRIAFMAWNGFNF 325


>gi|120561243|gb|ABM27006.1| RNA polymerase II second largest subunit [Smittium culisetae]
          Length = 899

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 143/919 (15%), Positives = 263/919 (28%), Gaps = 165/919 (17%)

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                  KY    + +  +         +  +      +  ++  L+     +   DD D+
Sbjct: 123  NREKRIKYAREILQKEFLPHVGTQPHNETRKT---YFLGYMVHRLLQCVLERRDQDDRDH 179

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R    +M R +    +              + +  + + +   
Sbjct: 180  YGRKRLDLAGPLLAMLFRNLFKKMTRDMTRYLQKCIESRREFNLSMALKSNTITAGLKYS 239

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               ++Q+       S ++H RR +      + R     + R +H 
Sbjct: 240  LATGNWGDQKKAMQSRTGVAQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHN 295

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A +       +    + +  + N    +     +
Sbjct: 296  THWGLVCPAETPEGQACGLVKNLALMAHITVGSDSGSILMFLEEWAMENLEELVGDSLAD 355

Query: 624  NRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            +  I      +            L   R   E         D  +   + +        P
Sbjct: 356  STKIFVNGVWVGIHKEAVRLAATLKQLRRRLEFSYELSIVHDVREREIRILTDAGRVCRP 415

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                +     L               +          +  + +         GIVE +DA
Sbjct: 416  LFVVNHMRLAL--------------TKPVVAAIEARRLGERDAVRWHDLLSEGIVEYLDA 461

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +                                 V  G    ++D        
Sbjct: 462  EEEETAMIVMSPHELDESRRF--------------------VHTGQLPPKDD-------- 493

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              G +   RN  +    W       SM+  I   +V            ++       +G 
Sbjct: 494  --GRIRSRRN--IGITTWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGKQAMGI 549

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                     V  + L N+                     +     S +   +  + AI  
Sbjct: 550  LLTNYQ---VRMDTLANL--------LYYPQKPLATTHAMEYIKFSELPAGQNAIVAILC 598

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +     F  +  ++++  +      +    +      + L
Sbjct: 599  YTGYNQEDSLIMNQSSIDRGLFRSIFFRSYMDEEDKLGM----RTMGRFEKPSRASTLRL 654

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                Y +L +   I  G           K+T +    +               E  QR +
Sbjct: 655  KIGTYEKLDDDGLIAPGTRVTGDDIIIGKTTPIPIASL---------------ELGQRTL 699

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K+         E    +++     GD       + VKV V   R  Q GDK A RHG
Sbjct: 700  AHTKLDASKPLRATESGIVDQVLLTTNGD-----GFKFVKVRVRSTRVPQIGDKFASRHG 754

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +  +   EDMPF  DG   D+++NP  +PSRM +G + E  L      +G    + 
Sbjct: 755  QKGTIGIVYTSEDMPFTADGIVPDLIINPHAIPSRMTIGHLIECLLSKLATLVGTAADAS 814

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     IS       ++   G H+  +                              
Sbjct: 815  PFTDVTVDAISA------ELFSLGYHSRGLEVM--------------------------- 841

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                           +G      G         V  G  Y  +L HMV DK+++R+ G  
Sbjct: 842  --------------YNGH----SGR---KLYSQVFFGPTYYQRLKHMVDDKIHSRARGPL 880

Query: 1276 SLVTQQPLGGKSNRGGQRL 1294
             ++T+QP+ G+S  GG R 
Sbjct: 881  QILTRQPVEGRSRDGGLRF 899



 Score = 98.6 bits (244), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 76/506 (15%), Positives = 154/506 (30%), Gaps = 15/506 (2%)

Query: 212 VPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           VPV     ALG + +++IL         S+  + +   +  A ++   +VS   +     
Sbjct: 59  VPVVVVFRALGTVAAKDILEHICYDSNDSEMVEEFKASIEEAFVIQDREVSLDFIGKRGT 118

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
              +   K++     + L+++ +  +G               +     +  +E  D  D 
Sbjct: 119 TVGVNREKRIKYAR-EILQKEFLPHVGTQPHNETRKTYFLGYMVHRLLQCVLERRDQDDR 177

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
                         P+L +   N    +   +     K  +        +    +  T  
Sbjct: 178 DHYGR--KRLDLAGPLLAMLFRNLFKKMTRDMTRYLQKCIESRREFNLSMALKSNTITAG 235

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           +  S+    + D  K   S  G  ++  R    +      R          I     L N
Sbjct: 236 LKYSLATGNWGDQKKAMQSRTGVAQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHN 295

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +         +      ++KN   +  + +       +  ++  ++   + +    
Sbjct: 296 THWGLVCPAETPEGQACG---LVKNLALMAHITVGSDSGSILMFLEEWAMENLEELVGDS 352

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           +  +   F     +   +E V   + +   RR        ++      E      T  GR
Sbjct: 353 LADSTKIFVNGVWVGIHKEAVRLAATLKQLRR-RLEFSYELSIVHDVREREIRILTDAGR 411

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +C       +++ L  +    A + A    E    +  D      V YL A EEE   I 
Sbjct: 412 VCRPLFV-VNHMRLALTKPVVAAIEARRLGERDAVRWHDLLSEGIVEYLDAEEEETAMIV 470

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREK----IDFIDASPKQVVSIAASLIPFLEN 684
            +   LDE   F             I   R          +  P  ++ I AS++PF ++
Sbjct: 471 MSPHELDESRRFVHTGQLPPKDDGRIRSRRNIGITTWTHCEIHPSMILGICASIVPFPDH 530

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPF 710
           + S R      M +QA+ +L      
Sbjct: 531 NQSPRNTYQSAMGKQAMGILLTNYQV 556


>gi|83415483|gb|ABC17949.1| RNA polymerase II second largest subunit [Mortierella verticillata]
          Length = 721

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 134/852 (15%), Positives = 247/852 (28%), Gaps = 151/852 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +++   ++ + + +  R         +    + +  + + +     +
Sbjct: 2    KRMDLAGPLLGGLFKMLFTKLTKDVSKYLRKCIDSNKDFVLSVAVKSNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQLKAMQSRAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++  G    P  +  +G    ++  L+A    +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSAIS-VGSPSAPIIEFLEGWGMENLEELTANNILDAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFL 682
                N            LV         +    ++    D  +   +        L P  
Sbjct: 177  KVFVNGVWAGVHRDPGSLVNTLKRLRRNMDINSEVSIVKDIREKELRMYTDAGRCLRPLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D   +L   ++          +    G  ME        +       GIVE VDA  
Sbjct: 237  IVEDQALLLRKEHIDELTRAPYYED----GKAMEPWGWNDLLS------NGIVEFVDAEE 286

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D       +  +       Q     QR        +         PS  L
Sbjct: 287  EETIMICMTPDDLAESRQVDHVQ------QPKDAAQRVKGTSSTSLHTWTHCEIHPSMIL 340

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +   I++  ++V             
Sbjct: 341  G-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQVRM----------- 380

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 381  ----------------DTLANILYYPQKPLATTRSMEYLRFRELPAGQNAVVAILCYSGY 424

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D+ ++      E+ E   R+            
Sbjct: 425  NQEDSVIMNQSSIDRGLF-RSVYFRTYMDQEKKIGMTTMEEFEKPTREHVLRLRHGTYEK 483

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R+           ++     +  Q 
Sbjct: 484  LDDDGLIAPGTRVSGDDIIIGKTKPIPVDSTEMGQRTGSHSKLDASTPLRSTETGIVDQV 543

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        ++ VKV V   R  Q GDK A RHG KG +  
Sbjct: 544  ML--------------------TTNHEGVKFVKVRVRSTRVPQMGDKFASRHGQKGTIGI 583

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L       G +  +        
Sbjct: 584  TYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLVECLLSKVSTLEGSEGDATPFTDVTV 643

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS                                                        
Sbjct: 644  EAISEALKKHNYQQRGFEVM---------------------------------------- 663

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    +G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 664  -------YNGHT----GR---KLAAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 709

Query: 1283 LGGKSNRGGQRL 1294
            + G+S  GG R 
Sbjct: 710  VEGRSRDGGLRF 721


>gi|242392334|dbj|BAH80348.1| RNA polymerase subunit B' [Halococcus saccharolyticus]
          Length = 608

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 119/597 (19%), Positives = 199/597 (33%), Gaps = 107/597 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I  +++       I   E     R 
Sbjct: 94   LVDRGYIEFIDAEEEEDILVGVDEGDLTKDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 153

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 154  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 210

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  L +  G     +    F R    +  R    + ++ E+   D   
Sbjct: 211  VAVMSYEGFNIEDA-LVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRFEMPDDD--- 266

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +S VL           +         + +R
Sbjct: 267  ----VRGARGEEAYTHLDEDGLVNPETTVDESAVLLGKTSPPRFLEEPDDMGGLSPQKRR 322

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 323  ETSVTMRSGESGVVDTVTLMQGE------------DGSKLSKVSVRDQRIPELGDKFASR 370

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG + E   G      G+++ 
Sbjct: 371  HGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHVLEMLGGKVGSLEGRRVD 430

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                  +   ++                                             FD 
Sbjct: 431  GTAFTGEDEEELRGSLEEHG-------------------------------------FD- 452

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                             SG+ I+Y G+TGE  D  + VG I+  KL HMVS+K++ARS G
Sbjct: 453  ----------------SSGKEIMYSGVTGEKIDAEIFVGTIFYQKLYHMVSNKIHARSRG 496

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
               ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD    R  VY   V
Sbjct: 497  PVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESD----REFVY---V 549

Query: 1334 AGN-----------------------DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             G                        +  E     +F +L+ EM+ALG++  LE   
Sbjct: 550  CGECGMSAVENVEQRRVYCPNCGEETEIHEIEMSYAFKLLLDEMKALGIAPRLELED 606



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 55/317 (17%), Positives = 102/317 (32%), Gaps = 36/317 (11%)

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                ++ D       +     GE ++   E     D   +    +    I F++ ++  
Sbjct: 50  TNEVIINADAGRARRPLIVVEEGEPLITEEEVETLTDGDTEFEDLVDRGYIEFIDAEEEE 109

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI-RIVIRS 747
            +L+G +                 T +E          I    AG++   +      I  
Sbjct: 110 DILVGVDEGDLTKD---------HTHLEIDPQ-----LIFGIGAGMIPYPEHNASPRITM 155

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             G +  S         ++           Q  +VK                    D   
Sbjct: 156 GAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPA 205

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            +N +VA M + G+N ED+++++E  V   +  S     +E   R    G E+      +
Sbjct: 206 AQNFVVAVMSYEGFNIEDALVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRFEMPDD 265

Query: 868 -----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                  EE   ++DE G++     V+   +L+GK +P               + G    
Sbjct: 266 DVRGARGEEAYTHLDEDGLVNPETTVDESAVLLGKTSPPRFLEEP------DDMGGLSPQ 319

Query: 923 DVRDTSLRVPSGVSGTV 939
             R+TS+ + SG SG V
Sbjct: 320 KRRETSVTMRSGESGVV 336



 Score = 41.2 bits (95), Expect = 1.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + ++ A EEE+  +      L +D                          ++  P+ +  
Sbjct: 100 IEFIDAEEEEDILVGVDEGDLTKDH-----------------------THLEIDPQLIFG 136

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 137 IGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 173


>gi|289193124|ref|YP_003459065.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus sp.
            FS406-22]
 gi|288939574|gb|ADC70329.1| DNA-directed RNA polymerase subunit B [Methanocaldococcus sp.
            FS406-22]
          Length = 633

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 110/621 (17%), Positives = 204/621 (32%), Gaps = 107/621 (17%)

Query: 786  DEVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +++++ +I           +  D     N  +A            + I    +       
Sbjct: 81   EKLKKGEITFSDLVKEGIIEYLDAEEEENAYIALSEEELTEKHTHLEIDPLTILGIGAGV 140

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                E     R T             +S    + +D  G            +        
Sbjct: 141  APYPEHNSAPRITMAAAMGKQSLGIPMSNIKWR-LDTRG--HYLHYPQVPIVRTKHQEIL 197

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + AI   +  ++ D  +   S +    +    F R       R    + 
Sbjct: 198  GFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSAIDRG-LGRSTFFRTYDACERRYPGGQM 256

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +         + L      +     K   V+           + 
Sbjct: 257  DRFEIPDKG-------VRGYRSEEAYKYLEEDGIAAVEAHVKGGDVIVGKTSPPRFLEEH 309

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    ++   V+  +          E+ + +K+   +          R+VKV V   
Sbjct: 310  --------EITIQVKPQRRDSSVVVRHGEEGYIDKVILTE-----TKEGNRLVKVKVRDL 356

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++   +P ED+PF + G   DI++NP  +PSRM VGQ+ E   
Sbjct: 357  RIPELGDKFASRHGQKGVIGLTVPQEDLPFTESGIVPDIIINPHAIPSRMTVGQLLEMLG 416

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++I   I   +   D+      L                             
Sbjct: 417  GKVGALEGRRIDGTIFSGEKEWDLRKALEALGFKHHGKEVM------------------- 457

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+       TG+ F+  + +G  Y  KL+H
Sbjct: 458  ----------------------------YDGK-------TGKKFEVEIYIGIAYYQKLHH 482

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA +L+E L  +SD 
Sbjct: 483  LVAGKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLMDESDP 542

Query: 1321 -DV-----VGRTRVY---------------ESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
             D+      G   +                E++           P +F +L+ E++++ +
Sbjct: 543  YDICICSKCGDFAILDYKRGIKYCPICGEIENLYNSKKIPFVRIPYAFKLLLDELKSMCI 602

Query: 1360 SIDLENSRTKNSAKMEEIPDF 1380
               L   + ++  ++E+  DF
Sbjct: 603  ---LPRIKVRDKVELEDFKDF 620



 Score = 91.3 bits (225), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 71/411 (17%), Positives = 120/411 (29%), Gaps = 108/411 (26%)

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            I   RR   L Q              ++      + P    E     L           
Sbjct: 27  FIKEARRKGELPQYTTVAYHEESNDIHINTDAGRIVRPLIVVENGKPKLTKEHIE----- 81

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
               ++       D      + YL A EEEN YIA +   L                   
Sbjct: 82  ---KLKKGEITFSDLVKEGIIEYLDAEEEENAYIALSEEELT------------------ 120

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                EK   ++  P  ++ I A + P+ E++ + R+ M   M +Q++ +  +   +   
Sbjct: 121 -----EKHTHLEIDPLTILGIGAGVAPYPEHNSAPRITMAAAMGKQSLGIPMSNIKW--- 172

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    +      Y           
Sbjct: 173 --------------------------------------RLDTRGHYLHYP---------- 184

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q P+V+   +                    G+N +VA M + GYN ED+++ ++  
Sbjct: 185 ----QVPIVRTKHQ----------EILGFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSA 230

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEV 888
           +   +  S     ++   R    G  +             SEE  K ++E GI  V A V
Sbjct: 231 IDRGLGRSTFFRTYDACERRYPGGQMDRFEIPDKGVRGYRSEEAYKYLEEDGIAAVEAHV 290

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             GD++VGK +P               I  +     RD+S+ V  G  G +
Sbjct: 291 KGGDVIVGKTSPPRFLEE-------HEITIQVKPQRRDSSVVVRHGEEGYI 334


>gi|194591899|gb|ACF76530.1| RNA polymerase beta subunit [Mycoplasma corogypsi]
          Length = 595

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 204/450 (45%), Positives = 299/450 (66%), Gaps = 15/450 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGQNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +FA+V+  GF++TPY KV +G V  NDV YL+A EE     AQ++  ++E+      ++ 
Sbjct: 61  TFAKVDDLGFLKTPYFKVNNGVVDYNDVRYLTASEEIGYSFAQSSVEVNEENRIVSPVLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R      +     IDFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPL+++
Sbjct: 121 IRRNYNYTIGTPNDIDFIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLIQS 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ +AK S   + AK  G V  VD  +I I       +     +D Y L  
Sbjct: 181 EAPLVATGIEADIAKFSSYNLTAKNEGTVVFVDGTKIKI-------EKPNGKIDQYSLRN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + QRP+V+ GD V+  D++ DG S   G++ALG+N+LV F  + GYNFED+
Sbjct: 234 FERSNQGTLIQQRPIVRAGDYVKEGDLLVDGTSFKDGEMALGKNVLVGFTTYKGYNFEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I+ER+V +DVFTSIHIEE  +  R+++ G +E+T DIP++S    +++DE GI+ VG+
Sbjct: 294 VIINERLVKDDVFTSIHIEEHSIQFRNSRAGNDELTADIPHLSRAAGRHLDENGIVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+PGD+LVG+ +PKGE   T EEKLL AI G++ ++V+DTSL+V +G  GT++   I +
Sbjct: 354 EVSPGDVLVGRTSPKGEENPTQEEKLLAAILGQRPLNVKDTSLKVKNGHGGTIIHTEILS 413

Query: 947 RH-------GIDKNERSISVEREQIELLAR 969
           R        G+DK  +    ++ +I++  +
Sbjct: 414 RDQGDVLEEGVDKIVKVSVAQKRKIKVGDK 443



 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 131/420 (31%), Positives = 184/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G  V  GD+LV   + K +  M   + +L      K  +  D  +     V   V 
Sbjct: 248  IVRAGDYVKEGDLLVDGTSFK-DGEMALGKNVLVGFTTYKGYNFEDAVIINERLVKDDVF 306

Query: 941  DVRIFNRHGID-KNERSISVERE----QIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                   H I  +N R+ + E       +   A    DE  I+         ++L G+ +
Sbjct: 307  TSIHIEEHSIQFRNSRAGNDELTADIPHLSRAAGRHLDENGIVRVGSEVSPGDVLVGRTS 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +   +   L + ++ + P +                       +            
Sbjct: 367  PKGEENPTQEEKLLAAILGQRPLNVKDT-----------------SLKVKNGHGGTIIHT 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            +I     GD +  GV ++VKV VA KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DG
Sbjct: 410  EILSRDQGDVLEEGVDKIVKVSVAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNP GVPSRMN+GQ+ E HLG A   LG K  +   D     DI          
Sbjct: 470  TPLDIMLNPQGVPSRMNIGQVLELHLGMAAKKLGVKFVTPSFDGVKKNDIEDAL------ 523

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                       + + L         + +
Sbjct: 524  -------------------------------------------VEAGLDKTG-----KQV 535

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            + D +TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 536  IIDPITGRKFDKPISVGVMYMLKLNHMVDDKMHARSIGPYSLITQQPLGGKSQNGGQRFG 595


>gi|227828173|ref|YP_002829953.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus M.14.25]
 gi|229585402|ref|YP_002843904.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus M.16.27]
 gi|238620363|ref|YP_002915189.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus M.16.4]
 gi|227459969|gb|ACP38655.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus M.14.25]
 gi|228020452|gb|ACP55859.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus M.16.27]
 gi|238381433|gb|ACR42521.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus M.16.4]
 gi|323475226|gb|ADX85832.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus REY15A]
 gi|323477958|gb|ADX83196.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus HVE10/4]
          Length = 1131

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 113/590 (19%), Positives = 191/590 (32%), Gaps = 105/590 (17%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 616  IEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 675

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 676  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 733  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEPGV 783

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 784  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 841

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 842  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRIPSIGDKFASRHGQKG 889

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   D++LNP  +PSRM +GQI E   G                
Sbjct: 890  VIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAA------------ 937

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 938  -----------------------------------------LSGNIVDATP-FYKTPIEQ 955

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           + YDG TG+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 956  LQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-------- 1330
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD    RT +Y         
Sbjct: 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSD----RTTIYVCDQCGYIG 1071

Query: 1331 ----------SIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                        + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1072 WYDKNKNKYICPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILEDR 1121



 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 171/1133 (15%), Positives = 339/1133 (29%), Gaps = 228/1133 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L+     SY+ F+             LQ        I        +         P+   
Sbjct: 26   LVRQHLDSYNDFVRNK----------LQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRE 75

Query: 86   -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +   R+LTYA PL +T+  +  +++             + +Y+GDLP+M
Sbjct: 76   SDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEP----------EEVYIGDLPIM 125

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F++ G +R++V+Q   +P      D G+   
Sbjct: 126  LKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV-DTGKTGS 184

Query: 175  SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
            +  + +  +II      + + + IE       HV       K+P    + ALG+ ++   
Sbjct: 185  N--ITHTAKIISSTAGYR-VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTD--- 238

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                  IVY+   D          L   + +++    +D     +  G+K  + + K   
Sbjct: 239  ----RDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQ 294

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
             + +  +  LG ++D              +  E+Y+   +  D+       L        
Sbjct: 295  IIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFA 354

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                + +   V +  Y          K    AL+      RP D+ T  +  ++    + 
Sbjct: 355  SLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALV------RP-DIVTERIRHALATGNWV 407

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                     + R      L+      +  + +       + L   + G+    +  +   
Sbjct: 408  GGRTGVSQLLDRTNWLSMLSHLRRV-ISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSAVCEFFCS 519
            +  V+++  M +    +    +E+++ E       + +    +    +       +   +
Sbjct: 467  SGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILN 526

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +L         L++    RR +      V       +            C +       
Sbjct: 527  GRLVGYYRDGEELAKKIRERRRNGEISDEVNVGHIVTD----FINEVHVNCDSGRVRRPL 582

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            I + +      R +    +++      D      + YL A EEEN Y+A   S L  +  
Sbjct: 583  IIVSNGNPLVTREDIE-KLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEH- 640

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                    ++     ++ I AS+IP+ E++ S R      M +Q
Sbjct: 641  ----------------------THLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQ 678

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            A+ L  A                                                + + +
Sbjct: 679  ALGLYAANYQL-----------------------------------------RTDTRAHL 697

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y               QRPLV    + R  DII             G N ++A + + 
Sbjct: 698  LHYP--------------QRPLV----QTRALDIIGYTN------RPAGNNAILAVISFT 733

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLK 874
            GYN EDS++++   V   ++ S     +         G E+              +E  +
Sbjct: 734  GYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYR 793

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++ G++    EV  GD+L+GK++P        E    +A         RDTS+    G
Sbjct: 794  LLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK--------RDTSIVTRHG 845

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI--LDRNIYSRLM-EILC 991
              G V              +  +  E  +   L + +  +  I  +     SR   + + 
Sbjct: 846  EMGIV--------------DLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVI 891

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G         +    V+   +++ +            E +     +L      +    + 
Sbjct: 892  GMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKT 951

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
              +    +I     +P                    D   GR G K I SRI 
Sbjct: 952  PIEQLQNEILKYGYLPDATEVT-------------YD---GRTGQK-IKSRIY 987


>gi|112382383|gb|ABI17423.1| RNA polymerase II second largest subunit [Sympodiomycopsis
            paphiopedili]
          Length = 746

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 145/864 (16%), Positives = 261/864 (30%), Gaps = 143/864 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ R I         +         + +  + + + 
Sbjct: 1    DHFGKKRLDLGGPLLAGLFRMLFRKLTRDIYRHLERCVEESREFHLTTAVKSSTITNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--- 618
            H TH+G +CPAET EG   GLV +L+  + ++  G    P     D    +++V +S   
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMSLIS-VGSPSAPLHHFLDEFGLDNLVDMSISS 175

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            A   +         +  E  S  E L   R   +         D  +   +        L
Sbjct: 176  AKATKVFVNGVWAGTHSEPSSLVETLRDLRRKDDITTEVSVVHDVREKELRLYTDSGRVL 235

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM---ESVVAKSSGAAIVAKRAGIV 735
             P    D  +  L+      Q +   +        GM   E    +   + +VA+  G++
Sbjct: 236  RPLFIVDPKSMRLLVTREHVQWLNAEEKPGTIDDLGMDADEDDKERFRWSQLVAE--GVI 293

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP---LVKVGDE-VRRN 791
            E +DA       +            + R                P   LV          
Sbjct: 294  EYLDADEEETVMICMSPQDLAKSRKLNRHGILTGETAGLDGLPDPSARLVSARTYEPSTW 353

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  P+  LG       +  + +P+  +N       S R   +       +  +    
Sbjct: 354  THCEIHPAMILG-------VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYLTNY 400

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            +                            +  +             +       +   + 
Sbjct: 401  QMRM-----------------------DTMANILYYPQKPLATTRAMEHLNFRELPAGQN 437

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    ++ R   D  ++     +E+ E   R+ 
Sbjct: 438  AIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTYTDFEKKVGFTLQEEFEKPTREX 496

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                     +       +  G           K+  L  D      RS+          +
Sbjct: 497  SIRLKHGTYDKIDADGLVAPGTRVSGEDIIIGKTAPLPPDSEELGLRSKTHTKRDVSTPL 556

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +  Q   S                          + VKV V   R  Q+GDK A
Sbjct: 557  KSTESGIVDQVLVS--------------------TNQEGSKFVKVRVRSTRVPQTGDKFA 596

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++
Sbjct: 597  SRHGQKGTIGITYRQEDMPFTIEGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQE 656

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S + + L                            K G+ V     
Sbjct: 657  GDATPFTDLTVEAVSSILAKL-------------------------GYQKRGLEVM---- 687

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                               +G +       G      V +G  Y  +L HMV DK+++R+
Sbjct: 688  ------------------YNGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRA 722

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLG 1295
             G   ++T+QP+ G+S  GG R G
Sbjct: 723  RGPVQILTRQPVEGRSRDGGLRFG 746



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 85/622 (13%), Positives = 172/622 (27%), Gaps = 118/622 (18%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR +     +   F +  ++ +    +  +Y L   G      +         + + +
Sbjct: 29  DIYRHLERCVEESREFHLTTAVKSSTITNGLRYSL-ATGNWGDQKKFMQAKAGVSQVLNR 87

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 88  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSLI 147

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCE-------FFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S         D      +V            F          E  + +  +   RR 
Sbjct: 148 SVGSPSAPLHHFLDEFGLDNLVDMSISSAKATKVFVNGVWAGTHSEPSSLVETLRDLRRK 207

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSE---------GHNIGLVSSLTSFARV 592
             +            +   ++      + P    +           ++  +++      +
Sbjct: 208 DDITTEVSVVHDVREKELRLYTDSGRVLRPLFIVDPKSMRLLVTREHVQWLNAEEKPGTI 267

Query: 593 NAYGFI----ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV--- 645
           +  G      +    +         + YL A EEE   I  +   L +        +   
Sbjct: 268 DDLGMDADEDDKERFRWSQLVAEGVIEYLDADEEETVMICMSPQDLAKSRKLNRHGILTG 327

Query: 646 ----------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                        +  P  ++ + AS+IPF +++ S R      
Sbjct: 328 ETAGLDGLPDPSARLVSARTYEPSTWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSA 387

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 388 MGKQAMGVYLTNYQM-----------------------------------------RMDT 406

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +N R                        +L  G+N +VA 
Sbjct: 407 MANILYYPQKPLATTRAMEHLNFR------------------------ELPAGQNAIVAI 442

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG-PEEITRDI----PNVSE 870
           + + GYN EDS+++++  +   +F S++   +    +       EE  +        +  
Sbjct: 443 LCYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDFEKKVGFTLQEEFEKPTREXSIRLKH 502

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                ID  G++  G  V+  DI++GK  P    P   EE  LR+    K    RD S  
Sbjct: 503 GTYDKIDADGLVAPGTRVSGEDIIIGKTAP---LPPDSEELGLRS----KTHTKRDVSTP 555

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V +       K
Sbjct: 556 LKSTESGIVDQVLVSTNQEGSK 577


>gi|6606123|gb|AAF19074.1|AF107802_1 DNA-dependent RNA polymerase II RPB140 [Botryosphaeria rhodina]
          Length = 942

 Score =  323 bits (827), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 151/974 (15%), Positives = 300/974 (30%), Gaps = 149/974 (15%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            V++   I +      +    +A+       V+    VS         +       K +  
Sbjct: 87   VSDEDIISHICFDKNDTQLMEAIRPSIEESVLIQDRVSALDFIGRRGSNPSTGGTKRERV 146

Query: 410  TVGRVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + R  +           +     +   +  +I  L+    G+   DD D+ G +R+   
Sbjct: 147  KLARDIIQKEFLPHISQAEGSETKKAFFLGYMIYRLLQCHLGRRDEDDRDHFGKKRLDLA 206

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R   L++ R +   +            Q  +    + + +     +      
Sbjct: 207  GPLLANLFRSLFLKLTRDVFSYLKKCVEAGRPFSLQSAVKQGTITNGLKYSLATGNWGDQ 266

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 267  KKAASAKAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPA 322

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L+    V     +     +    + ++  +     +      +I   
Sbjct: 323  ETPEGQACGLVKNLSLMCNVTVGSDVTPIQDFMTQRNMELLEEYEPNVSPHATKIFINGV 382

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +    +V        +      I D  D   K          P    DD   
Sbjct: 383  WVGVHRDPTQLVSVVKKLRRDGTLSPEMSLIRDVRDREFKIFTDAGRVCRPLFIIDDDPF 442

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIR 746
                 N+   R+ +  L+A+     +G+     +           +G+VE +DA    + 
Sbjct: 443  SPNKGNLALTREHIDKLEADQEIDVSGLSDEERQEKRYGWQGLLHSGVVEYMDAEEEEVA 502

Query: 747  SVEGDLDPSTSGVDIYR---LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +    D   +     +       + + +N   ++R +      V++       PS  LG
Sbjct: 503  MIVMTPDDLRAHHRARQGIIDEDDEETKRNRDPHERVVPPPNPSVKQYTHCEIHPSMILG 562

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   +   E                 
Sbjct: 563  -------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVCLTNYE----------------- 598

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                        +    ++ V             +       +   +  + AI      +
Sbjct: 599  ------------LRMDTMVNVLYYPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYN 646

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +     +  +   + +  ++V    +E   +    + + L    Y
Sbjct: 647  QEDSVIMNQSSIDRGLFRSLFYRSYTDQEKKVGMAV----VEQFEKPMRSDTMRLKHGTY 702

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   +  G           K+  ++ D                +E  QR    +K 
Sbjct: 703  DKLDDDGVVAPGVRVSGEDIIIGKTAPIAPD---------------AEELGQRTKMHIKR 747

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   + +      D +     + VKV     +  Q GDK A RHG KG +
Sbjct: 748  DVSTPLRSTENGIVDSVLLTTNSDGL-----KFVKVRTRTTKIPQIGDKFASRHGQKGTI 802

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 803  GITYRHEDMPFTREGLTPDLIINPHAIPSRMTIAHLIECLLSKVGALRGXEGDATPFTDV 862

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L                           +     +G  ++  VF         
Sbjct: 863  TVXQVSSLLR---------------EHGYQSRGFEIMYNGHTGKKLTAQVF--------- 898

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                                          +G  Y  +L HMV DK++AR+ G   ++T+
Sbjct: 899  ------------------------------LGPTYYQRLRHMVDDKIHARARGPVQILTR 928

Query: 1281 QPLGGKSNRGGQRL 1294
            QP+ G++  GG R 
Sbjct: 929  QPVEGRARDGGLRF 942



 Score = 95.9 bits (237), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 67/546 (12%), Positives = 154/546 (28%), Gaps = 54/546 (9%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +V+ D    VP+     ALG+   E+I+S        +Q  +     +  + L+     +
Sbjct: 70  YVKAD----VPIPIVFRALGIVSDEDIISHICFDKNDTQLMEAIRPSIEESVLIQDRVSA 125

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGI------TSDCLCGLYVAEDIVN 314
              +            K+    L +  ++++ +  +              G  +   ++ 
Sbjct: 126 LDFIGRRGSNPSTGGTKRERVKLARDIIQKEFLPHISQAEGSETKKAFFLGYMIYR-LLQ 184

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDA 373
              G    +  D   +K L+            L++  + +  +Y++  +   +    + A
Sbjct: 185 CHLGRRDEDDRDHFGKKRLDLAGPLLANLFRSLFLKLTRDVFSYLKKCVEAGRPFSLQSA 244

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHI 431
           +             T  +  S+    + D  K   +  G  ++  R    +      R  
Sbjct: 245 VKQ--------GTITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYSSTLSHLRRTN 296

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +   +     
Sbjct: 297 TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMCNVTVGSDVTPIQD 353

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVA 550
            +   ++   +         A   F     +    +    +S +   RR   L     + 
Sbjct: 354 FMTQRNMELLEEYEPNVSPHATKIFINGVWVGVHRDPTQLVSVVKKLRRDGTLSPEMSLI 413

Query: 551 RARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSF-----ARVNAYGFI 598
           R     E        R   P       P   ++G+       +          V+     
Sbjct: 414 RDVRDREFKIFTDAGRVCRPLFIIDDDPFSPNKGNLALTREHIDKLEADQEIDVSGLSDE 473

Query: 599 ETPYRK--VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----------- 645
           E   ++        +  V Y+ A EEE   I      L       + ++           
Sbjct: 474 ERQEKRYGWQGLLHSGVVEYMDAEEEEVAMIVMTPDDLRAHHRARQGIIDEDDEETKRNR 533

Query: 646 -FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                         ++    +  P  ++ I AS+IPF +++ S R      M +QA+ + 
Sbjct: 534 DPHERVVPPPNPSVKQYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVC 593

Query: 705 KAEAPF 710
                 
Sbjct: 594 LTNYEL 599


>gi|194303498|gb|ACF41172.1| RNA polymerase beta subunit [Mycoplasma sualvi]
          Length = 596

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 215/453 (47%), Positives = 307/453 (67%), Gaps = 14/453 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QINPLSEISNKRRITSLGPGGLNRETAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            +AR+N YGF+ETPY +V  G V  ++ VYL A EE     AQ+  ++D++     E V 
Sbjct: 61  VYARINEYGFLETPYFRVNKGVVDYSEPVYLIASEEFGFTFAQSTVTIDDNNRIVNEEVT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   + I+V  E++DFID S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAV LL A
Sbjct: 121 VRKNHDFIIVKPEEVDFIDVSSRQMTSIAASAIPFLENDDANRALMGSNMQRQAVSLLNA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP VGTG+ES +A  S   + AK++G V  VD+ +I I+S       ++  + +Y L +
Sbjct: 181 EAPIVGTGIESAIANFSAGNLKAKKSGEVVFVDSTKIKIKSD------NSDEIIVYNLKQ 234

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F++SNQ T ++Q P+VK+ D V  ND++ DG S   G++ALG+N+LVAF  W+GYNFED+
Sbjct: 235 FEKSNQGTLIHQIPIVKLNDHVNENDLLTDGSSFKDGEMALGKNLLVAFSTWNGYNFEDA 294

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I+ER+V +DV TSIHIEE  +  R +K G +++T +IPNVS    + +DE GI+ +G+
Sbjct: 295 IIINERLVKDDVLTSIHIEEQTIQFRSSKTGNDKLTAEIPNVSTASKRFLDENGIVIIGS 354

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+ GDILVG+++PKGE   TPEEKL+ AIFG +  +++DTSL+V  G +GTV++V I +
Sbjct: 355 EVSAGDILVGRVSPKGEHNPTPEEKLMAAIFGSRDSNLQDTSLKVKHGQAGTVINVEILS 414

Query: 947 RHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           R   D       +  + IE + +    ++  + 
Sbjct: 415 RDHGD-------ILEDGIEKIVKVYIAQKRKIK 440



 Score =  284 bits (727), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 123/420 (29%), Positives = 175/420 (41%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ +   VN  D+L    + K +  M   + LL A       +  D  +     V   V 
Sbjct: 249  IVKLNDHVNENDLLTDGSSFK-DGEMALGKNLLVAFSTWNGYNFEDAIIINERLVKDDVL 307

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +             ++ E   +   ++   DE  I+         +IL G+ +
Sbjct: 308  TSIHIEEQTIQFRSSKTGNDKLTAEIPNVSTASKRFLDENGIVIIGSEVSAGDILVGRVS 367

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L + +              +D  +Q     +K     +   +E   ++
Sbjct: 368  PKGEHNPTPEEKLMAAIFGS-----------RDSNLQDTSLKVKHGQAGTVINVEILSRD 416

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                   GD +  G+ ++VKV++A KR I+ GDK+AGRHGNKG++S ILP EDMP+L+DG
Sbjct: 417  ------HGDILEDGIEKIVKVYIAQKRKIKVGDKLAGRHGNKGVISVILPEEDMPYLEDG 470

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI LNP GVPSRMN+GQI E HLG+A   L  K      D     DI  +    +  
Sbjct: 471  TPIDICLNPQGVPSRMNLGQILELHLGYAGKKLNVKFACPSFDGIKINDIQNVLKEAKLP 530

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            I                                                           
Sbjct: 531  ISGKQKLYNP-------------------------------------------------- 540

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
              +G   E  D  V VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 541  -ING---EVIDNDVAVGVMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|45545335|gb|AAS67515.1| DNA-dependent RNA polymerase II second largest subunit
            [Mycosphaerella punctiformis]
          Length = 935

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 148/960 (15%), Positives = 286/960 (29%), Gaps = 143/960 (14%)

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I N   T   +  K  L + + V    +   F               +Y    + +  + 
Sbjct: 96   IVNKEDTQMLEMLKPCLEEAFVVQDRDNALDFIGRRGQQTGTKDRRIRYARDIMQKEFLP 155

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                 +  +  +      +  ++  ++    G+   DD D+ G +R+   G ++   +RL
Sbjct: 156  HISQEEGSETKK---AFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRL 212

Query: 478  GLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ-------------L 522
              +++ + +K  +               I    + S +     +               +
Sbjct: 213  KFVQLVKEMKMYLHRCVEGGRDFNITLAIKTNILTSGLRYCLATGNWGDQKKASSAKAGV 272

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   GL
Sbjct: 273  SQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGL 328

Query: 583  VSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            V +L+   +  V   G   T + +     +  +   +   +    +I      + ++   
Sbjct: 329  VKNLSLMCYVTVGTPGEPLTDFMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNAGQ 388

Query: 641  TEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD----SNRVLMGCN 695
              E +        +      I D  +   +          P    D+    + R  +   
Sbjct: 389  LTETLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNKPDAAERGSLVLR 448

Query: 696  MQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
              + A      E      G+ E   A  S   +     G+VE +DA       +    + 
Sbjct: 449  QDQVAKLQQDQENAASLRGISEEDKALHSYGWMGLVNEGVVEYLDAEEEETAMIIMTPED 508

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +    ++     +     +P  K   +V         P+  LG       +  +
Sbjct: 509  LDEHRALRSGAEYDDPKSDPHRRIKP--KPNMQVHTWTHCEIHPAMILG-------ICAS 559

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +  ++                                
Sbjct: 560  IIPFPDHNQSPRNTYQSAMGKQAMGVTL-----------------------------TNY 590

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            N+    +  V             +       +   +  + AI      +  D+ +   S 
Sbjct: 591  NVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIASYSGYNQEDSVIMNQSS 650

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    +F R  +D+ +R      E  E   R    +      +       +  G  
Sbjct: 651  IDRGLF-RSLFYRAYMDQEKRVGMSVVESFERPERAATMKMKHGSYDKLDDDGIVSPGCR 709

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G     K+  ++ D      R++          ++     +  Q             
Sbjct: 710  VSGGDMLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLL---------- 759

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            LR  KV   + +  Q GDK A RHG KG +      EDMPF  D
Sbjct: 760  ----------TTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAD 809

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  +PSRM +  + E  L       G++  +          IS + +    
Sbjct: 810  GLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILA---- 865

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                 V     +G  ++  VF                       
Sbjct: 866  -----------DHGFQQRGFEVMYNGHTGKKLNAQVF----------------------- 891

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                            +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 892  ----------------LGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 89/694 (12%), Positives = 198/694 (28%), Gaps = 101/694 (14%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK--------- 199
            ++++++Q  RS   +      +   +  ++   R   ++G  +      K         
Sbjct: 1   SEKVLIAQE-RSA-ANIVQVFKKKGTNTPVMAELRSAVERGTRLISSTTVKLYNQAVNAN 58

Query: 200 --------DIIHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLS 250
                    + +++ D    +P+     ALG +  E+IL+    K   +Q  +     L 
Sbjct: 59  NPGQTIKGSLPYIKTD----IPIAIIFRALGVVSDEDILNHIVNKED-TQMLEMLKPCLE 113

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A ++     +   +    G+Q     +++       ++++ +  +        G    +
Sbjct: 114 EAFVVQDRDNALDFIGRR-GQQTGTKDRRIRYAR-DIMQKEFLPHISQEE----GSETKK 167

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
               G      ++      E+   + F  +  D+             +         +  
Sbjct: 168 AFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDL---------AGPLMAQVFRLKFVQLV 218

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           K+  + ++R +  G    F++  ++   +     +Y L   G      + +       + 
Sbjct: 219 KEMKMYLHRCVEGGR--DFNITLAIKTNILTSGLRYCL-ATGNWGDQKKASSAKAGVSQV 275

Query: 431 IRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           + +    + +  L        R+GK       +  +  +    E  + Q    +  +   
Sbjct: 276 LNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 335

Query: 486 IKER--------ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
                          +    +   +  +      +   F   + +   +        +  
Sbjct: 336 CYVTVGTPGEPLTDFMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNAGQLTETLRS 395

Query: 538 TRRLSALG-QGGVARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFA 590
            RR   L  +  + R     E+R    T  GR+C        +        LV      A
Sbjct: 396 LRRKGLLSFEVTIIRDVREREIRV--FTDAGRVCRPLFVVDNKPDAAERGSLVLRQDQVA 453

Query: 591 RVNAYGFIETPYRKVCDGK------------VTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           ++          R + +                  V YL A EEE   I      LDE  
Sbjct: 454 KLQQDQENAASLRGISEEDKALHSYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDLDEHR 513

Query: 639 -------SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                      +    R    +  +        +  P  ++ I AS+IPF +++ S R  
Sbjct: 514 ALRSGAEYDDPKSDPHRRIKPKPNMQVHTWTHCEIHPAMILGICASIIPFPDHNQSPRNT 573

Query: 692 MGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGI 734
               M +QA+                 L   + P   T  ME +  +   A   A  A  
Sbjct: 574 YQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIA 633

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                     +   +  +D        YR    Q
Sbjct: 634 SYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQ 667


>gi|242392352|dbj|BAH80389.1| RNA polymerase subunit B' [Halovivax asiaticus]
          Length = 610

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 121/595 (20%), Positives = 208/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +    S +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 96   LVAHGSIEFIDAEEEEDIFVAVDEDDLTEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 155

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 156  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 212

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 213  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 268

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 269  ----VRGARGEDAYTHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 324

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 325  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 372

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG I E   G      G+++ 
Sbjct: 373  HGQKGVVGHLAPQEDMPFTQEGVVPDLVVNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 432

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 433  G-----------------------------------------------------TP-FLG 438

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  + +G+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 439  EDEDELRGGLEDAGFNSAGKEVMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 498

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+G ME      +GAA  L+E L  +SD     V G     
Sbjct: 499  PVQVLTRQPTEGRAREGGLRIGTMERDVFIGHGAALTLKERLLDESDREYIHVCGNCGMS 558

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      +  E     +F +L+ EM+ALG++  LE   
Sbjct: 559  AVENVEQRRVYCPNCDEE-----TEIHEIEMSYAFKLLLDEMKALGIAPRLELED 608



 Score = 44.3 bits (103), Expect = 0.15,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR+  + +      +       V+        P    
Sbjct: 12  YVNGSLVGTHPDPNELAEQIREARRVGDVSEMVNVSVKDRTREVIVNADAGRARRPLIVV 71

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +      ++     A  +  G +E       D      + ++ A EEE+ ++A     L 
Sbjct: 72  DDGE-PRITEAEIEALND--GDLE-----FEDLVAHGSIEFIDAEEEEDIFVAVDEDDLT 123

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 124 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 160

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 161 MVKQSLGLPSANYRI 175


>gi|242392354|dbj|BAH80390.1| RNA polymerase subunit B' [Halovivax ruber XH-70]
          Length = 610

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 121/595 (20%), Positives = 208/595 (34%), Gaps = 103/595 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            +    S +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 96   LVAHGSIEFIDAEEEEDIFVAVDEDDLTEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 155

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 156  TMGAG--MVKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 212

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +   + V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 213  VAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 268

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 269  ----VRGARGEDAYTHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 324

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 325  ETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 372

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG I E   G      G+++ 
Sbjct: 373  HGQKGVVGHLAPQEDMPFTQEGVVPDLVVNPHALPSRMTVGHILEMIGGKLGSMEGRRVD 432

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 433  G-----------------------------------------------------TP-FLG 438

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE+ +   L  A  + +G+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G
Sbjct: 439  EDEDELRGGLEDAGFNSAGKEVMYSGVTGEKIEAEIFVGVIFYQKLYHMVSNKLHARSRG 498

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----- 1324
               ++T+QP  G++  GG R+G ME      +GAA  L+E L  +SD     V G     
Sbjct: 499  PVQVLTRQPTEGRAREGGLRIGTMERDVFIGHGAALTLKERLLDESDREYIHVCGNCGMS 558

Query: 1325 ------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  + RVY      E      +  E     +F +L+ EM+ALG++  LE   
Sbjct: 559  AVENVEQRRVYCPNCDEE-----TEIHEIEMSYAFKLLLDEMKALGIAPRLELED 608



 Score = 44.3 bits (103), Expect = 0.15,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 23/106 (21%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + ++ A EEE+ ++A     L ED                          +
Sbjct: 93  FEDLVAHGSIEFIDAEEEEDIFVAVDEDDLTEDH-----------------------THL 129

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 130 EIDPQLIFGIGAGMIPYPEHNASPRITMGAGMVKQSLGLPSANYRI 175


>gi|288931147|ref|YP_003435207.1| DNA-directed RNA polymerase subunit B [Ferroglobus placidus DSM
            10642]
 gi|288893395|gb|ADC64932.1| DNA-directed RNA polymerase subunit B [Ferroglobus placidus DSM
            10642]
          Length = 604

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 87/319 (27%), Positives = 139/319 (43%), Gaps = 70/319 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +     ++ KV V  +R  + GDK A RHG KG++  I+P EDMPF + G   D+++NP 
Sbjct: 339  LSENGAKLAKVRVRDQRIPELGDKFASRHGQKGVIGLIVPEEDMPFTESGIVPDMIINPH 398

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM V        G     +G KI ++                              
Sbjct: 399  AIPSRMTV--------GHVLEMIGGKIGAIEARRVDGT---------------------- 428

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                    +F G  EE +   L+      +G+ ++YDG+TG+ F
Sbjct: 429  ------------------------IFHGEKEEDLREALKKYGFSYTGKEVMYDGITGKRF 464

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + VG IY  KL HMVS K++ARS G   ++T+QP  G+S +GG R GEME   +  +
Sbjct: 465  VAEIFVGVIYYEKLYHMVSSKIHARSRGPVQILTRQPTEGRSRKGGLRFGEMERDVLIGH 524

Query: 1306 GAAYVLQEMLTIKSDDV-------VGRTRVYE-------SIVAGN--DTFETGTPESFNV 1349
            GAA +L++ L  +SD V        G    Y+         V  +  +  +     +F +
Sbjct: 525  GAALLLKDRLLEESDKVEVWVCGNCGHVATYDYKRNTAYCKVCDDESNVHKIEMSYAFKL 584

Query: 1350 LVKEMQALGLSIDLENSRT 1368
            L+ E++++ ++  L     
Sbjct: 585  LLDELKSMLIAPRLILGDK 603



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 71/411 (17%), Positives = 126/411 (30%), Gaps = 100/411 (24%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           ++  RI          + +V +            ++       D      + +L A EEE
Sbjct: 47  SNEVRINTDAGRARRPLIVVKNGKPLVTEKHIEKLKKGEITFEDLVRQGRIEFLDAEEEE 106

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N YIA     L E+ +  E                         P  +V I    IP+ E
Sbjct: 107 NAYIAVNEEELTEEHTHLEL-----------------------DPSLIVGICTGSIPYPE 143

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R  MG  M +Q++ +  A  P                                  
Sbjct: 144 HNASPRNTMGAAMIKQSLGIPYANLPL--------------------------------- 170

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      +   +  Y               Q P+V    ++               
Sbjct: 171 --------RADTRGHLLHYP--------------QIPIVTTDTQLE----------IKYD 198

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +   G+N +VA + + GYN ED+++ ++  +   +  S     +E        G E+   
Sbjct: 199 ERPAGQNFVVAVVSYEGYNIEDALIFNKASIERGLGRSHFYRTYEAEEIRYPGGQEDKFE 258

Query: 864 DIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             P         E   ++DE G++    EV P D+L+GK +P          ++      
Sbjct: 259 IPPSDVNGYRGAEAYIHLDEDGLVVPETEVGPDDVLIGKTSPPRFLEEPTRLEV------ 312

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                 R+TS+ + S  SG V  V +       K  +    ++   EL  +
Sbjct: 313 -SPQKRRETSVTMRSNESGIVDAVFLTLSENGAKLAKVRVRDQRIPELGDK 362


>gi|194270602|gb|ACF36847.1| RNA polymerase beta subunit [Mycoplasma iguanae]
          Length = 595

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 213/444 (47%), Positives = 298/444 (67%), Gaps = 9/444 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS I + RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +  
Sbjct: 1   QNNPLSEIANKRRITSLGPGGLNRETAQFEVRDVHPTHYGRICPIETPEGQNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           S+++++ YGFI+ PY KV +G V  + VV+L+A++E     AQ+   +D      EE V 
Sbjct: 61  SYSKIDEYGFIQAPYFKVNNGVVDYSKVVWLTAIQEIGYTFAQSTVEIDSKNRIIEENVT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     ++V  + ID+ID S K++ SIAAS IPFLENDD+NR LMG NMQRQAVPLLKA
Sbjct: 121 VRKNHNYLIVEPKDIDYIDVSSKEMTSIAASAIPFLENDDANRALMGSNMQRQAVPLLKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG E+ +AK +   +VAK  G V  VD+ +I I+        +      Y L  
Sbjct: 181 EAPLVATGSEADIAKYATTNLVAKVDGEVVFVDSEKIKIK-------DAEGATKTYNLRL 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F++SNQ T ++QRP+VK+GD+V+  D+I DGPS+D G+LALG+N+LVAF  W+GYN+ED+
Sbjct: 234 FEKSNQGTLISQRPIVKIGDKVKAGDLIVDGPSSDKGELALGKNVLVAFTTWNGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++ISE++V  D FTSIHIEE  +  R++K G + +T DIPNVS    +++D  GI+ VG+
Sbjct: 294 IIISEKLVKNDAFTSIHIEEQTIPFRNSKAGDDILTADIPNVSNYAKRSLDANGIVTVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+ GD+LVG+ +PK E  +TPEEKL+ AIF +K  + +DTSL+V  G  GTV+DV+I +
Sbjct: 354 EVSAGDVLVGRTSPKVEDNLTPEEKLMNAIFSQKISNRKDTSLKVKHGHGGTVIDVQILS 413

Query: 947 RH-GIDKNERSISVEREQIELLAR 969
           R  G +  +    + +  I    +
Sbjct: 414 RDAGDNLEDGIEKIIKVFIAQKRK 437



 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 120/421 (28%), Positives = 173/421 (41%), Gaps = 79/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL------RVPSG 934
            I+ +G +V  GD++V   +   +  +   + +L A       +  D  +      +  + 
Sbjct: 248  IVKIGDKVKAGDLIVDGPS-SDKGELALGKNVLVAFTTWNGYNYEDAIIISEKLVKNDAF 306

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R+    ++   +          R  D    I+         ++L G+ 
Sbjct: 307  TSIHIEEQTIPFRNSKAGDDILTADIPNVSNYAKRSLDAN-GIVTVGSEVSAGDVLVGRT 365

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +            L + + S+   ++                      +           
Sbjct: 366  SPKVEDNLTPEEKLMNAIFSQKISNRKDT-----------------SLKVKHGHGGTVID 408

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +I     GD++  G+ +++KVF+A KR I+ GDKMAGRHGNKG++S +LP EDMP L+D
Sbjct: 409  VQILSRDAGDNLEDGIEKIIKVFIAQKRKIKVGDKMAGRHGNKGVISLVLPVEDMPHLED 468

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMNVGQ+ E HLG A   L  K  S + D      I  L      
Sbjct: 469  GTPIDILLNPQGVPSRMNVGQVLELHLGMAAKTLDVKFVSPVFDGVKYDQIQELLEETGL 528

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                 DG                     
Sbjct: 529  PKNGKVTLI----------------------------DGIT------------------- 541

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   G+ FD  V+VG +YMLKL HMV DKV+ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 542  -------GDHFDNEVSVGVMYMLKLYHMVDDKVHARSVGPYSLITQQPLGGKSQNGGQRF 594

Query: 1295 G 1295
            G
Sbjct: 595  G 595


>gi|120561275|gb|ABM27022.1| RNA polymerase II second largest subunit [Neocallimastix frontalis]
          Length = 915

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 160/1047 (15%), Positives = 303/1047 (28%), Gaps = 194/1047 (18%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVID 329
            +ESG +  S L   +     K     +  + G      +     +     ++   G V D
Sbjct: 37   VESGSRHASTLYIKMLA---KASTRANSEIVGQSIKATLPYVRQDIPIVIVFRALGVVPD 93

Query: 330  EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
               LE I +       +  +     +A++         +D++ AL  I +          
Sbjct: 94   RDILEHICYDFRDYQMLEMLKPCIEDAFV--------IQDKEIALDFIGKR--------- 136

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
                +          +Y    + +  +         +  +         +I  L+     
Sbjct: 137  ---GTTVGVTKEKRIRYAAEILQKELLPHIGTRAHTETKK---AYFFGYMIHRLLLAALE 190

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAK 507
            +   DD D+ G +R+   G +L + +R+   ++ + + +  ++             I   
Sbjct: 191  RRECDDRDHFGKKRLDLAGPLLGSLFRMLFRKLTKDVSKTLQMCIDRNREFNLNSAIRPN 250

Query: 508  PVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             +   +     +               +SQ+       S ++H RRL+      + R   
Sbjct: 251  TISDGLKYSLATGNWGAQSKFMQSRAGVSQVLNRYTFASTLSHLRRLNT----PIGRDGK 306

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TN 612
              + R +H TH+G +CPAET EG   GLV +L   + V+           + +  +    
Sbjct: 307  LAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSYVSVGSSSAPIVEFLEEWTMENME 366

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQV 671
            +V     ++    ++      +  D     + +      + +      + D  +   K  
Sbjct: 367  EVHVSHIIDATKIFVNGVWVGIHRDPDHLVKTLRDLRRSQNVNAEISIVRDIREKELKIY 426

Query: 672  VSIAASLIPFLENDDSNRVLMGCNM----QRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
                    P    ++    L   ++    +R            +  G+           I
Sbjct: 427  TDAGRICRPLFIVENQKLKLKKSHIAMIQERNETGQGWGWDDLIENGIIE--------FI 478

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+              +   + D       +  Y   K  +S      N          
Sbjct: 479  DAEEEETTLIC------MSHEDLDPKDGEMNIQDYGTSKRLKSRSVYSRN---------- 522

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                      PS  LG       +  + +P+  +N       S R   +       +  +
Sbjct: 523  ---WTHCEIHPSMILG-------ICASIVPFPDHNQ------SPRNTYQSAMGKQAMGIY 566

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                +                       +    +  +        +    +       + 
Sbjct: 567  LTNFQ-----------------------LRMDTMANILYYPQKPLVTTRAMEYLRFRDLP 603

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
              +  + AI      +  D+ +   S +   +    +F R  +D+ ++      E  E  
Sbjct: 604  AGQNAIVAIACYSGYNQEDSIIMNQSSIDRGLF-RSLFYRSYMDQEKKVGMFNVENFEKP 662

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
             R+                  I  G           K+  LS D                
Sbjct: 663  TRETCLRLRHGTYEKLEDDGLIAPGIRVTGDDIIIGKTIPLSQD---------------S 707

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             E  QR     K    T     E    +++      D      ++ VKV V   R  Q G
Sbjct: 708  QELGQRTEHHTKRDASTPLRSTETGIVDRVLVTNNQD-----GMKFVKVRVRSTRIPQMG 762

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG V      EDMPF  +G   DI++NP  +PSRM +G + E  LG     
Sbjct: 763  DKFASRHGQKGTVGMTYRTEDMPFTFNGITPDIIINPHAIPSRMTIGHLVECLLGKVSTL 822

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +          IS L                                       
Sbjct: 823  TGDEGDATPFTDVTVEAISKLLRENGFQSRGFEVM------------------------- 857

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
               F+G                 +G+               + +G  Y  +L HMV DK+
Sbjct: 858  ---FNG----------------HTGK----------KLQAQIFLGPTYYQRLKHMVDDKI 888

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++R+ G   ++T+QP+ G+S  GG R 
Sbjct: 889  HSRARGPVQILTRQPVEGRSRDGGLRF 915



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 89/675 (13%), Positives = 201/675 (29%), Gaps = 83/675 (12%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLW----MDIEFDSK--- 199
            ++++++Q   +  I +     +   S    Y   I    + G      + I+  +K   
Sbjct: 1   SEKVLIAQERMASNIIYV--FAKTPPS-PYSYTAEIRSAVESGSRHASTLYIKMLAKAST 57

Query: 200 ----DII---------HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
               +I+         +VR D    +P+     ALG+  + +IL          Q  +  
Sbjct: 58  RANSEIVGQSIKATLPYVRQD----IPIVIVFRALGVVPDRDILEHICYDFRDYQMLEML 113

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +  A ++   +++   +        +   K++     + L+++ +  +G  +     
Sbjct: 114 KPCIEDAFVIQDKEIALDFIGKRGTTVGVTKEKRIRYA-AEILQKELLPHIGTRAHTETK 172

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
                  +      + + A +  +    +            L +      +  R      
Sbjct: 173 KAYFFGYMIH---RLLLAALERRECDDRDHFGKKR------LDLAGPLLGSLFRMLFRKL 223

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                K   + I R         F++  ++      D  KY L   G      +      
Sbjct: 224 TKDVSKTLQMCIDRN------REFNLNSAIRPNTISDGLKYSL-ATGNWGAQSKFMQSRA 276

Query: 426 DDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE--------MLK 472
              + + +    + +  L  L     R+GK       +  +  +    E        ++K
Sbjct: 277 GVSQVLNRYTFASTLSHLRRLNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVK 336

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           N   +  + +  S    +  ++  ++   + ++   ++ A   F     +    +  + +
Sbjct: 337 NLALMSYVSVGSSSAPIVEFLEEWTMENMEEVHVSHIIDATKIFVNGVWVGIHRDPDHLV 396

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR- 591
             +   RR   +            +   ++        P    E   + L  S  +  + 
Sbjct: 397 KTLRDLRRSQNVNAEISIVRDIREKELKIYTDAGRICRPLFIVENQKLKLKKSHIAMIQE 456

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL-DEDGSFTEELVFCRCA 650
            N  G          D      + ++ A EEE   I  ++  L  +DG    +       
Sbjct: 457 RNETGQG----WGWDDLIENGIIEFIDAEEEETTLICMSHEDLDPKDGEMNIQDYGTSKR 512

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP-------- 702
            +   V        +  P  ++ I AS++PF +++ S R      M +QA+         
Sbjct: 513 LKSRSVYSRNWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGKQAMGIYLTNFQL 572

Query: 703 --------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                   L   + P V T  ME +  +   A   A  A            I   +  +D
Sbjct: 573 RMDTMANILYYPQKPLVTTRAMEYLRFRDLPAGQNAIVAIACYSGYNQEDSIIMNQSSID 632

Query: 754 PSTSGVDIYRLMKFQ 768
                   YR    Q
Sbjct: 633 RGLFRSLFYRSYMDQ 647


>gi|226897628|gb|ACO90263.1| RNA polymerase beta subunit gene [Bacillus cereus]
          Length = 378

 Score =  322 bits (826), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 221/363 (60%), Positives = 276/363 (76%), Gaps = 3/363 (0%)

Query: 592 VNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           VN +GFIETPYR+V    G VT  V YL+A EE+N  +AQAN  L ++G F  E +  R 
Sbjct: 1   VNEFGFIETPYRRVDPETGLVTGHVDYLTADEEDNYVVAQANMKLSDEGEFLSEDIVARF 60

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            GE I+  RE+ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+P
Sbjct: 61  RGENIVTNRERIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESP 120

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQ 768
            VGTGME V AK SGAA++ K  G+VE+V+A  + +R  VE D       +D Y++ KF 
Sbjct: 121 IVGTGMEYVSAKDSGAAVICKHPGVVERVEAREVWVRRYVEVDGQTVKGDLDRYKMQKFI 180

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ TC NQRP+V VG+EV + +I+ADGPS +LG+LALGRN+LV FM W GYN+ED+++
Sbjct: 181 RSNQGTCYNQRPIVSVGNEVVKGEILADGPSMELGELALGRNVLVGFMTWDGYNYEDAII 240

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SER+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII VGAEV
Sbjct: 241 MSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRVGAEV 300

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G ++DV++FNR 
Sbjct: 301 KDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIILDVKVFNRE 360

Query: 949 GID 951
             D
Sbjct: 361 DGD 363


>gi|55584698|gb|AAV53580.1| RNA polymerase II second largest subunit [Rhodocollybia maculata]
          Length = 721

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 137/849 (16%), Positives = 258/849 (30%), Gaps = 145/849 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYMQKCVETHKEFNLALAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +         L ++EE    
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWG-------LESLEENAHS 170

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                 + +  +G +       R     +   R+     D SP+  V             D
Sbjct: 171  TTPTMTKVFVNGVWMG---VHREPANLVKTIRKLRRKDDISPEVSVVRDIRERELRLYTD 227

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +      +L+ +   ++  G     A          ++GI+E +DA     
Sbjct: 228  AGRVCRPLFIVEDQQLVLQKKHVRWLQNGHNDDSADFKWE--HLVKSGIIELLDAEEEET 285

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +     + +    ++       R  +K G            PS  LG  
Sbjct: 286  VMISMTPEDLENSRLQQQGIDPHENDGEFDPAAR--LKSGITAHTWTHCEIHPSMILG-- 341

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 342  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLI 378

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 379  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGHNQE 427

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 428  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTYDKLED 486

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G   +       K+  +  D      R++          ++     +  Q    
Sbjct: 487  DGLIAPGTGVLGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI- 545

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VK+ V   R  Q GDK A RHG KG +     
Sbjct: 546  -------------------TTNSEGRKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYR 586

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 587  QEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 639

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++     + LR       G+ V    F G            
Sbjct: 640  ------------------DLTVESVSTFLRDRGYQSRGLEVM---FHGHT---------- 668

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                         G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 669  -------------GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 712

Query: 1286 KSNRGGQRL 1294
            +S  GG R 
Sbjct: 713  RSRDGGLRF 721



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 61/449 (13%), Positives = 123/449 (27%), Gaps = 42/449 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYMQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 --------MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                   ++KN   +  + +       I  ++   +   +        +    F     
Sbjct: 125 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSTTPTMTKVFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    E  N +  I   RR   +                ++        P    E   + 
Sbjct: 185 MGVHREPANLVKTIRKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVEDQQLV 244

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L      + + N +      + K      +  +  L A EEE   I+     L+      
Sbjct: 245 LQKKHVRWLQ-NGHNDDSADF-KWEHLVKSGIIELLDAEEEETVMISMTPEDLENSRLQQ 302

Query: 642 EELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           + +      GE          +        +  P  ++ I AS+IPF +++ S R     
Sbjct: 303 QGIDPHENDGEFDPAARLKSGITAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 362

Query: 695 NMQRQAVP----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
            M +QA+                 L   + P   T  ME +  +   A   A  A +   
Sbjct: 363 AMGKQAMGIFLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 422

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                  +   +  +D        YR   
Sbjct: 423 GHNQEDSVIMNQSSIDRGLFRSIYYRSYM 451


>gi|45545315|gb|AAS67505.1| DNA-dependent RNA polymerase II second largest subunit [Cenococcum
            geophilum]
          Length = 935

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 163/1046 (15%), Positives = 316/1046 (30%), Gaps = 171/1046 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S       E  +              +     +     ++   G V DE  L
Sbjct: 36   VEKGSRLISTFNIKWAESSLIAKRAPGPFAY-AILPYIRADVPMSVVFRALGVVSDEDIL 94

Query: 334  EEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              I +       + L   S+   + I+         DR++AL  I +           + 
Sbjct: 95   NHIVYDRNDTQMLELLKPSIEEGSMIQ---------DRENALDWIAKRGSSTGTKDKRL- 144

Query: 393  ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
                        KY    + R  +         +     +   +  +I  L+    G+  
Sbjct: 145  ------------KYARDIMQREFLPHISQK---EGQDTRKAFFLGYMIHRLLQCVLGRRD 189

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVV 510
             DD D+ G +R+   G ++ N +R+  +++ R + +  +    +      Q  + A  + 
Sbjct: 190  EDDRDHFGKKRLDLAGPLIANLFRILFIKLTRDVYKYLQKCVENNQEFSIQMAVKASLIT 249

Query: 511  SAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + +     +               +SQ+       S ++H RR +      V R     +
Sbjct: 250  NGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAK 305

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVV 615
             R +H TH+G +CPAET EG   GLV +L+    V+        T +    + ++  +  
Sbjct: 306  PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMELLEEYD 365

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSI 674
             +        ++      +    S    +V        +      I D  D   K     
Sbjct: 366  PVVNPSATKVFVNGVWVGVHSQPSQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDA 425

Query: 675  AASLIPF--LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-R 731
               + P   +EN+ +        + +  +  L  +     +G+    A+ +         
Sbjct: 426  GRVMRPLFVIENNPTKTNRGSLVLNKTHIEKLHEDKEIDVSGLNDEDAEKAKFGWKGLLH 485

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +G+VE +DA       +    +       +           +     +P  K    V+  
Sbjct: 486  SGVVEYLDAEEEETAMIIMTPEDLEDHHRVSAGTMIYDDGGDPHKRIKP--KPNPTVKTF 543

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  PS  LG       +  + +P+  +N          M  + +  ++      +  
Sbjct: 544  THCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRMET 596

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                                            V             +       +   + 
Sbjct: 597  MMN-----------------------------VLYYPQKPLATTRSMEYLKFRELPAGQN 627

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   +  
Sbjct: 628  AIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTEQEKR---IGVNVLEQFEKPT 683

Query: 972  DDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              + + +    Y +L +   +  G           K+  +  D                 
Sbjct: 684  RSDTLRMKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPPD---------------AK 728

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
            E  Q+ +   K    T     E+   +++             LR VKV     +  Q GD
Sbjct: 729  ELGQKTIMHTKRDVSTPLRSTENGIVDQVLF-----TTNTEGLRFVKVRTRTTKVPQIGD 783

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       
Sbjct: 784  KFASRHGQKGTIGVTYRQEDMPFTREGLTPDLIINPHAIPSRMTIAHLIECLLSKVGSLR 843

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +          +S L                           V     +G  +  
Sbjct: 844  GCEGDATPFTDVTVESVSKLLR---------------EHGYQSRGFEVMYNGHTGKKMVA 888

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             VF                                       +G  Y  +L HMV DK++
Sbjct: 889  QVF---------------------------------------LGPTYYQRLRHMVDDKIH 909

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            AR+ G   ++T+QP+ G++  GG R 
Sbjct: 910  ARARGPLQILTRQPVEGRARDGGLRF 935



 Score =  102 bits (254), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 83/619 (13%), Positives = 189/619 (30%), Gaps = 74/619 (11%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK------- 199
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K       
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWTAEIRSAVEKGSRLISTFNIKWAESSLI 56

Query: 200 ----------DII-HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
                      I+ ++R D    VP++    ALG+   E+IL+        +Q  +    
Sbjct: 57  AKRAPGPFAYAILPYIRAD----VPMSVVFRALGVVSDEDILNHIVYDRNDTQMLELLKP 112

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SD 301
            +    ++   + +   +    G       K+L       ++ + +  +           
Sbjct: 113 SIEEGSMIQDRENALDWI-AKRGSSTGTKDKRLKYAR-DIMQREFLPHISQKEGQDTRKA 170

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRN 360
              G  +   ++    G    +  D   +K L+           IL++  + +   Y++ 
Sbjct: 171 FFLGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFIKLTRDVYKYLQK 229

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +  ++    + A+           + T  +  S+    + D  K   S  G  ++  R 
Sbjct: 230 CVENNQEFSIQMAV--------KASLITNGLKYSLATGNWGDQKKAASSKAGVSQVLNRY 281

Query: 421 NLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
              +      R          +     L N    +         +   + + L     + 
Sbjct: 282 TYASTLSHLRRTNTPVGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 341

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           +      I + +S  +++ +   D +                 +    +    ++ +   
Sbjct: 342 VGSESTPITDFMSQRNMELLEEYDPVVNPSATKVF---VNGVWVGVHSQPSQLVTVVQEL 398

Query: 539 RRLSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVSSLT 587
           RR   L  +  + R     E        R + P       P +T+ G    N   +  L 
Sbjct: 399 RRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVIENNPTKTNRGSLVLNKTHIEKLH 458

Query: 588 SFARVNAYGFIETPYRKVCDGK----VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
               ++  G  +    K   G      +  V YL A EEE   I      L++    +  
Sbjct: 459 EDKEIDVSGLNDEDAEKAKFGWKGLLHSGVVEYLDAEEEETAMIIMTPEDLEDHHRVSAG 518

Query: 644 LV-------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +         +    +     +     +  P  ++ I AS+IPF +++ S R      M
Sbjct: 519 TMIYDDGGDPHKRIKPKPNPTVKTFTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 578

Query: 697 QRQAVPLLKAEAPFVGTGM 715
            +QA+ +           M
Sbjct: 579 GKQAMGVALTNYALRMETM 597


>gi|322227637|gb|ADW95283.1| DNA-directed RNA polymerase subunit beta [Enterobacter sp. 247 BMC]
          Length = 326

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 202/322 (62%), Positives = 252/322 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 304

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 305 LADGPSTDLGELALGQNMRVAF 326


>gi|82749752|gb|ABB89760.1| RNA polymerase beta subunit [Mycoplasma phocicerebrale]
          Length = 592

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 211/445 (47%), Positives = 298/445 (66%), Gaps = 10/445 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           F+ ++ YGFI+TPY +V + KV  +   YL+A+EE     AQ+  ++ E+    +ELV  
Sbjct: 61  FSDIDKYGFIKTPYFRVKNKKVDFSKPEYLTAIEENGYTFAQSTVNI-ENDVIVDELVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + VP  ++D++  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNEYLEVPASEVDYVGVSSRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   IVAK  G+V  VDA  + ++         +  +D Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIVAKYDGVVTYVDAAVVKVKRE------GSKTIDSYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q PLVK+G E++  D++ DGPS   G++ALG+N+LV F  WHGYN+ED++
Sbjct: 234 ERSNQGTLIHQVPLVKLGQEIKVGDLLVDGPSMKNGEMALGKNVLVGFTTWHGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T +IPNVS    + +DE GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTTEIPNVSNYSKRFLDENGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVVDV + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVDVEVLSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKD 972
                +     +E+     +A+ + 
Sbjct: 414 EFG--DALEDGIEKIVKVSIAQKRK 436



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 91/413 (22%), Positives = 147/413 (35%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G E+  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  LVKLGQEIKVGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDILTTEIPNVSNYSKRFLDENGIVRVGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+           +L   F       
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVDVEVLSREF------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A                 K    R +   D            
Sbjct: 416  --GDALEDGIEKIVKVSIA----------------QK----RKIRVGD------------ 441

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
                                        G K    I             + L+ ++    
Sbjct: 442  ----------------------KMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDILLNPQG 479

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
               +++      +       K      TP+FDG     I  +L  A++D SG++++YDG 
Sbjct: 480  VPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILEEANIDSSGKTVVYDGR 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGERFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|100913631|gb|ABF69714.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 599

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 213/429 (49%), Positives = 296/429 (68%), Gaps = 8/429 (1%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++
Sbjct: 1   DQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNM 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-GSFTEEL 644
            S+A+++ YGFI+TPY KV DG V  ND+ YL+A+EE N   AQ++ ++DE+ G   +E 
Sbjct: 61  ASYAKIDDYGFIQTPYFKVNDGVVDFNDIRYLTAIEEINFTFAQSSINIDEETGEILDER 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E I + +++ID+I  + +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVPL+
Sbjct: 121 VMSRKNNEYIELDKKEIDYIGVTSRQMTSISASAIPFLENDDANRALMGSNMQRQAVPLI 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           K EAP V TG+E+ +A+ S + + A + GIV  VDA  I I+S +           IY L
Sbjct: 181 KPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSDDEKKPS------IYFL 234

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             F+RSNQ T ++Q+PLVKVG E++  D++ DGPS + G+LALG+N+LV F  W GYN+E
Sbjct: 235 RTFERSNQGTVIHQKPLVKVGQEIKAGDLLTDGPSMENGELALGKNVLVGFSTWFGYNYE 294

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D+++++E++V EDV+TSIHIEE  +  R +K G + +T DIPN S    + + E GI+ +
Sbjct: 295 DAVILNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVII 354

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GTVV V +
Sbjct: 355 GSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDV 414

Query: 945 FNRHGIDKN 953
             R   D N
Sbjct: 415 LRRDTDDTN 423



 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 127/499 (25%), Positives = 194/499 (38%), Gaps = 68/499 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +            +       + R   + + T +   E  + + D K 
Sbjct: 169  GSNMQRQAVPLIKPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSDDEKK 228

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                  R     ++  + +     ++ VG E+  GD+L    +      +   + +L   
Sbjct: 229  PSIYFLRTFERSNQGTVIHQKP--LVKVGQEIKAGDLLTDGPS-MENGELALGKNVLVGF 285

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       +  RS + +      +    +  + 
Sbjct: 286  STWFGYNYEDAVILNEKLVKEDV-YTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKR 344

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             L  +    +   +   + + G    K     S +   +   + + Q     +     V+
Sbjct: 345  FLGEDGIVIIGSEVGPGDILVGRISPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVK 402

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                    +  +L     +         ++  G+  +VKV +A KR I+ GDKMAGRHGN
Sbjct: 403  HGHGGTVVAVDVLRRDTDD--------TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGN 454

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+VS ILP EDMP+L DGTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  S +
Sbjct: 455  KGVVSIILPEEDMPYLADGTPLDILLNPQGVPSRMNIGQVLELHLGLAARKLNCKFVSPV 514

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +   I  ++                                               
Sbjct: 515  FDGISYKQIQEIQKEAGIDPSGKMTV---------------------------------- 540

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                          SG+       TGEPFD P++VG +Y LKL HMV DK++ARS G YS
Sbjct: 541  -------------YSGK-------TGEPFDNPISVGVMYYLKLYHMVDDKMHARSVGPYS 580

Query: 1277 LVTQQPLGGKSNRGGQRLG 1295
            L+TQQPLGGKS  GGQR G
Sbjct: 581  LITQQPLGGKSQNGGQRFG 599


>gi|194591901|gb|ACF76531.1| RNA polymerase beta subunit [Mycoplasma glycophilum]
          Length = 601

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 207/444 (46%), Positives = 300/444 (67%), Gaps = 3/444 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG+ R  A  E+RDVH TH GRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHIGRICPIETPEGPNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +FA+V+  GF++TPY KV +G V  NDV YL+A EE     AQ++  +D++   T   + 
Sbjct: 61  TFAKVDDLGFLKTPYFKVNNGVVDYNDVRYLTAAEEIGYSFAQSSVKVDDNNKITVPTLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     I+    ++DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+A
Sbjct: 121 VRRDYNYIIASPSEVDFIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLLQA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ +AK S   IVAK +G V  VD  +I I+      +P     D Y L  
Sbjct: 181 EAPLVATGIEADIAKYSSYNIVAKNSGEVTFVDGSKIHIKY-PSPKEPDKFITDKYTLRN 239

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + QRP+V+VG +V + D++ DG S   G++ALG+N+L+ F  W+GYN+ED+
Sbjct: 240 FERSNQGTLIQQRPIVEVGQKVEKGDLLVDGSSFKDGEMALGKNLLIGFSTWNGYNYEDA 299

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I+ER+V +DVFTSIHIEE  +  R ++ G +++T +IPNVS+  L+++DE GI+ VG+
Sbjct: 300 VIINERLVKDDVFTSIHIEEQTIQFRSSRAGDDKLTPNIPNVSKYALRHLDEQGIVRVGS 359

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGD+LVG+ +PKGE   + EEKLL AI  +K+ + +DTSL+V +G +GTV+ V + +
Sbjct: 360 EVVPGDVLVGRTSPKGEENPSQEEKLLMAILQQKSSNEKDTSLKVKNGHNGTVIHVEVLS 419

Query: 947 RHGIDK-NERSISVEREQIELLAR 969
           R   D  +E    + +  I    +
Sbjct: 420 RDKGDVLDEGIDKIVKVSIAQKRK 443



 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 129/421 (30%), Positives = 189/421 (44%), Gaps = 79/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ VG +V  GD+LV   + K +  M   + LL         +  D  +           
Sbjct: 254  IVEVGQKVEKGDLLVDGSSFK-DGEMALGKNLLIGFSTWNGYNYEDAVIINERLVKDDVF 312

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     +++        +   A    DEQ I+         ++L G+ 
Sbjct: 313  TSIHIEEQTIQFRSSRAGDDKLTPNI-PNVSKYALRHLDEQGIVRVGSEVVPGDVLVGRT 371

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G +   +   L   ++ +   ++           +     +K  +  +   +E   +
Sbjct: 372  SPKGEENPSQEEKLLMAILQQKSSNE-----------KDTSLKVKNGHNGTVIHVEVLSR 420

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K      GD +  G+ ++VKV +A KR I+ GDK+AGRHGNKG++S +LP EDMP+L+D
Sbjct: 421  DK------GDVLDEGIDKIVKVSIAQKRKIKVGDKVAGRHGNKGVISIVLPEEDMPYLED 474

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+D++LNP GVPSRMN+GQI E HLG A   LG K  +   D     DI         
Sbjct: 475  GTPLDVMLNPQGVPSRMNIGQILELHLGMAARKLGVKFVTPSFDGVKKPDIEAALEEAG- 533

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                            L  +      + 
Sbjct: 534  ------------------------------------------------LDKSG-----KQ 540

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            IL D +TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 541  ILIDPITGRKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 600

Query: 1295 G 1295
            G
Sbjct: 601  G 601


>gi|45545321|gb|AAS67508.1| DNA-dependent RNA polymerase II second largest subunit [Cryphonectria
            parasitica]
          Length = 941

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 135/894 (15%), Positives = 263/894 (29%), Gaps = 143/894 (15%)

Query: 426  DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +     +   +  +   L+    G+   DD D+ G +R+   G +L   +R  + ++   
Sbjct: 166  EGCETRKAYFLGYMTHKLLQCALGRRDTDDRDHFGKKRLDLAGPLLAKLFRNIVKKLTGD 225

Query: 486  IK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVN 530
            +    +    +         I    + + +     +               +SQ+     
Sbjct: 226  MMAYMKRCVSEGKHFDLALGIRHSTLTNGLKYSLATGNWGEQKKAMSSTAGVSQVLNRYT 285

Query: 531  SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+   
Sbjct: 286  FASTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC 341

Query: 591  RVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             V+     E    +    + +V  +    ++ +    +I      +    +    LV   
Sbjct: 342  YVSVGSPAEPIKDFMVQRNMEVLEEYEPGASPDATKIFINGTWVGVHSQPAHLVTLVQEL 401

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                 I      + D  D   K        + P    +  +                   
Sbjct: 402  RRRCIISHEVSLVRDIRDREFKIFSDAGRVMRPLFVVNTPDNENRSRRRDLALTKEHAGV 461

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               +         +        + +G++E +DA       +    +            K 
Sbjct: 462  LRMMPKYSRKKDDEDYFGWDGLQNSGVIEYLDAEEEETAMICMTPEDLEDFRQRKLRGKD 521

Query: 768  QR----SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             +     ++   +N R   ++  ++         P+  LG       +  + +P+  +N 
Sbjct: 522  GKDEEPEDEGRSLNARVKTRINPDIHMYTHCEIHPAMLLG-------ICASIIPFPDHNQ 574

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +     +  +                                 +  
Sbjct: 575  SPRNTYQSAMGKQAMG--FFLTNYSRRM---------------------------DTMAN 605

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 606  ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 664

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R   D  +R        +E   +    + + L    Y +L +   I  G        
Sbjct: 665  LFFRSYTDSEKRVGI---NVVESFEKPFRSDTLRLKHGTYDKLDDDGIIAPGVRVSGEDI 721

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K++ +++D                     + +     Q+    +    R        
Sbjct: 722  IIGKTSPINAD--------------------NQELGQRTEQHVKRDASTPLRSTESGIID 761

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      LR VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 762  SVIVTTNQDGLRYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGITPDI 821

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  +       G +  +          IS              
Sbjct: 822  IINPHAIPSRMTIAHLIECLMSKLATLKGMEGDATPFTEVTVDSIS-------------- 867

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                        +LR       G  V                        +G +    G 
Sbjct: 868  -----------ELLRQHGYQSRGFEVM----------------------YNGHT----GR 890

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                    V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 891  ---KLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRF 941



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 115/858 (13%), Positives = 232/858 (27%), Gaps = 145/858 (16%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK------- 199
            ++++++Q  RS          + +     LY   I    ++G  +      K       
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKAQPSPDLYQAEIRSALEKGSRLISSTTLKLKAKGET 57

Query: 200 ------DIIHVRIDRRRK-VPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
                   I   +   +K +P+     ALG +  E+IL+        +Q  +     +  
Sbjct: 58  ARGGFGQTIQATLPYVKKEIPIAIVFRALGVISDEDILNAVCYDRQDTQMMEMLRPCIEE 117

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCG 305
           A  +   +V+   +   +      S  +      + L+++ +  +  T           G
Sbjct: 118 AFAIQEREVALDYIAKRSNSGHSASKIQRMKNAKEILQKELLPHIAQTEGCETRKAYFLG 177

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
            Y+   ++    G    +  D   +K L+       +    +      +        V+ 
Sbjct: 178 -YMTHKLLQCALGRRDTDDRDHFGKKRLDLAGPLLAKLFRNIVKKLTGDMMAYMKRCVS- 235

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           + K    AL   +  +  G      +  S+    + +  K   ST G  ++  R    + 
Sbjct: 236 EGKHFDLALGIRHSTLTNG------LKYSLATGNWGEQKKAMSSTAGVSQVLNRYTFAST 289

Query: 426 DDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                R          +     L N   G +   +    +    V  +    Y       
Sbjct: 290 LSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPA 349

Query: 483 E--RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           E  +    + +   ++   P    +A  +          SQ + L             RR
Sbjct: 350 EPIKDFMVQRNMEVLEEYEPGASPDATKIFINGTWVGVHSQPAHL-----VTLVQELRRR 404

Query: 541 LSALGQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHN--IGLVSSLTSFAR 591
                +  + R     E        R + P         E                    
Sbjct: 405 CIISHEVSLVRDIRDREFKIFSDAGRVMRPLFVVNTPDNENRSRRRDLALTKEHAGVLRM 464

Query: 592 VNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL--------------- 634
           +  Y   +    Y      + +  + YL A EEE   I      L               
Sbjct: 465 MPKYSRKKDDEDYFGWDGLQNSGVIEYLDAEEEETAMICMTPEDLEDFRQRKLRGKDGKD 524

Query: 635 ---DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              +++G      V  R   +            +  P  ++ I AS+IPF +++ S R  
Sbjct: 525 EEPEDEGRSLNARVKTRINPDI-----HMYTHCEIHPAMLLGICASIIPFPDHNQSPRNT 579

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +QA+                     + A I+      +    ++  +       
Sbjct: 580 YQSAMGKQAMGFFLTNYS---------RRMDTMANILYYPQKPLATTRSMEFLKFRELPA 630

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              +   +  Y              NQ                    S  +   ++ R +
Sbjct: 631 GQNAIVAIACYSG-----------YNQE------------------DSVIMNQSSIDRGL 661

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
             +       + E  + I+     E  F S                      D   +   
Sbjct: 662 FRSLFFRSYTDSEKRVGINVVESFEKPFRS----------------------DTLRLKHG 699

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ GII  G  V+  DI++GK +P         ++  + +        RD S  +
Sbjct: 700 TYDKLDDDGIIAPGVRVSGEDIIIGKTSPINADNQELGQRTEQHVK-------RDASTPL 752

Query: 932 PSGVSGTVVDVRIFNRHG 949
            S  SG +  V +     
Sbjct: 753 RSTESGIIDSVIVTTNQD 770


>gi|4867813|emb|CAB43067.1| RNA polymerase II [Gelsemium sempervirens]
          Length = 236

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 80/255 (31%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI +NP 
Sbjct: 25   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIXVNPH 84

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 85   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 112

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 113  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 150

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 151  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 210

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 211  GAAHFLKERLFDQSD 225


>gi|73697699|gb|AAZ81466.1| RNA polymerase beta subunit [Mycoplasma bovoculi M165/69]
          Length = 591

 Score =  322 bits (825), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 203/423 (47%), Positives = 284/423 (67%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  +   RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + + F
Sbjct: 1   NPLGEMASKRRVTSLGPGGLNRETAQFEVRDVHATHYGRICPVETPEGQNIGLILNYSVF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+ N YGFI TPY KV +  V  +   +L+A EE     AQ++  ++E      + V  R
Sbjct: 61  AKTNPYGFILTPYFKVNNRVVDYSQPHWLTAAEEFGLTFAQSSLPINEKNEIIADKVTVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+V   +ID+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL+KAE+
Sbjct: 121 KNQTFIVVDANEIDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLIKAES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+ES VA  S   I ++  G+V  VD+ +I++   E +          Y L  F+
Sbjct: 181 PFVATGIESDVALYSSTNIRSETDGVVTFVDSKKIIVTDEEDNE-------HTYYLRHFE 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T + Q+P+V +G +V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+ED+++
Sbjct: 234 KSNQETLILQKPIVSLGQQVKKGQLICDGPSTDKGELALGKNVLVAFTTWNGYNYEDAII 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V +DVFTSIHI+E  +  R TK G + +T ++PN S +   ++D  GI+ VG+EV
Sbjct: 294 ISERLVKDDVFTSIHIQEQTIKFRSTKAGTDILTAEVPNTSAKSRSHLDANGIVRVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           N GDILVG+ +PKGE   TPE++L+  I+G+KA+  +DTSLRV  G  GTV+DV++ +R 
Sbjct: 354 NTGDILVGRTSPKGEDNPTPEDRLIVTIWGKKALAQKDTSLRVKHGEGGTVIDVQVLSRE 413

Query: 949 GID 951
             D
Sbjct: 414 NGD 416



 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 125/413 (30%), Positives = 181/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  G ++    +   +  +   + +L A       +  D  +     V   V 
Sbjct: 246  IVSLGQQVKKGQLICDGPST-DKGELALGKNVLVAFTTWNGYNYEDAIIISERLVKDDVF 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    K   + +        +       +  LD N   R+   +   + + G  
Sbjct: 305  -TSIHIQEQTIKFRSTKAGTDILTAEVPNTSAKSRSHLDANGIVRVGSEVNTGDILVGRT 363

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +       + W + A+  +     V+  +                ++   
Sbjct: 364  SPKGEDNPTPE--DRLIVTIWGKKALAQKDTSLRVKHGEGG---------TVIDVQVLSR 412

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  GV  +VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMPFL+DGTPVDI
Sbjct: 413  ENGDTLEDGVGMLVKVLIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEDMPFLEDGTPVDI 472

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG     L  +  + + D      +  L            
Sbjct: 473  LLNPQGVPSRMNIGQVLELHLGMVAKNLNTRFVTPVFDGIKPDTMKSL------------ 520

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                          F  A             + ESG+  LYDG+
Sbjct: 521  ------------------------------FQEAS------------MPESGKFKLYDGI 538

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TG+ FD+ V+VGY+YMLKL HMV DK++AR+ G YSL TQQPLGGKS  GGQR
Sbjct: 539  TGKAFDKEVSVGYMYMLKLQHMVDDKMHARAVGPYSLTTQQPLGGKSQNGGQR 591


>gi|82749750|gb|ABB89759.1| RNA polymerase beta subunit [Mycoplasma indiense]
          Length = 592

 Score =  322 bits (824), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 209/443 (47%), Positives = 299/443 (67%), Gaps = 9/443 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           F++++ YGFI+TPY KV D KV  +  +YL+A+EE N  IAQ+  ++ +D    +++V  
Sbjct: 61  FSKIDKYGFIQTPYFKVKDRKVDFSQPIYLTAIEELNAVIAQSTINI-KDNIILDDIVMA 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   + I    E +D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++K E
Sbjct: 120 RKDNDYIQAKAEDVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVIKPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   + +   G+V  VDA +I I++            + Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNLRSNIDGVVVYVDAKQIKIQAE------GAKRPETYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q P+VK+G E+++ D++ DGPS   G++ALG+N+LV F  W+GYN+ED++
Sbjct: 234 ERSNQGTLIHQVPIVKLGQEIKKGDLLVDGPSMKNGEMALGKNVLVGFSTWNGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + ++E GI+ +G+E
Sbjct: 294 ILSERLVKDDVYTSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG+ +PKGE   TPEEKL+ AIFG+K+ + +DTSL+V  G +GTVVDV I +R
Sbjct: 354 VTAGDILVGRTSPKGEENPTPEEKLMAAIFGQKSSNRKDTSLKVKHGHNGTVVDVEIISR 413

Query: 948 H-GIDKNERSISVEREQIELLAR 969
             G    E    + +  I    +
Sbjct: 414 ETGDQLEEGVEKIIKVSIAQKRK 436



 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 123/418 (29%), Positives = 187/418 (44%), Gaps = 77/418 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ +G E+  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  IVKLGQEIKKGDLLVDGPSMKN-GEMALGKNVLVGFSTWNGYNYEDAVILSERLVKDDVY 305

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +          E  ++ +   +   ++   +E  I+         +IL G+ +
Sbjct: 306  TSIHIEEQTIQFRQSKAGEDYLTTDIPNVSNYSKRFLNEDGIVRIGSEVTAGDILVGRTS 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +       L + +  +   ++           +     +K  +  +   +E     
Sbjct: 366  PKGEENPTPEEKLMAAIFGQKSSNR-----------KDTSLKVKHGHNGTVVDVE----- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I   + GD +  GV +++KV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DG
Sbjct: 410  -IISRETGDQLEEGVEKIIKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDG 468

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQI E HLG A   LG+K  + + D   +  I  +    +  
Sbjct: 469  TPLDMLLNPQGVPSRMNIGQILELHLGLAAKKLGEKFVTPVFDGITHNQIKDILEEAKVN 528

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                +                                                  SGQ  
Sbjct: 529  PSGKTMI-----------------------------------------------YSGQ-- 539

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                 TGEPFD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  -----TGEPFDHPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 592


>gi|281207896|gb|EFA82075.1| RNA polymerase III [Polysphondylium pallidum PN500]
          Length = 1139

 Score =  322 bits (824), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 101/504 (20%), Positives = 175/504 (34%), Gaps = 97/504 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +             +       +        A+      D+ D  +   + +   
Sbjct: 717  DTLLYLLVYPQRPMCQTRTLELVNYVKLPAGHNATVAVMSYSGYDIEDALVMNKASLDRG 776

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIE-LLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
                 +F +      + +       I       +  +  +LD +  ++      G+ A  
Sbjct: 777  FGRCIVFKKQVSAVKKYANQTADRIIPPNAETSRQPKFALLDEDGIAK-----PGELAQK 831

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K + +++                  +K+  +       Y++S +  +      +
Sbjct: 832  GQILINKYSPINT-----------VDIVANSDKIPDS------GYKSSYTAYKYENPAFV 874

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+            ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G  
Sbjct: 875  DKVML--TTGDDDQLLIKLLMRSTRRPELGDKFSSRHGQKGVCGIIVKQEDMPFTDLGIC 932

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             DI++NP G PSRM +G++ E   G                                   
Sbjct: 933  PDIIMNPHGFPSRMTIGKMIELLAGK---------------------------------- 958

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                               A   + G    T  F G   E I+ +L        G+  + 
Sbjct: 959  -------------------AGVLRGGFGYGT-CFGGDKVEDISKVLISKGFSYGGKDYVT 998

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
             G+TGEP    +  G I+  KL HMV DK++AR+ G    +T+QP  G++  GG RLGEM
Sbjct: 999  SGVTGEPLQCFIFFGPIFYQKLKHMVMDKMHARARGPTVTLTRQPTEGRARGGGLRLGEM 1058

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------------NDTFETGT 1343
            E  C+  YGA+ ++ E L I SD    R  VY     G                      
Sbjct: 1059 ERDCLIGYGASALIMERLMISSD----RFTVYACKKCGFLGYEGWCQYCKSTLQVSTLQI 1114

Query: 1344 PESFNVLVKEMQALGLSIDLENSR 1367
            P +  +L +E+QA+ +   L+   
Sbjct: 1115 PYACKLLFQELQAMNIVPKLKLED 1138



 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 113/961 (11%), Positives = 258/961 (26%), Gaps = 161/961 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S++ F+ + +    + NE L      V P      A   +F   +   P    
Sbjct: 48  LVKQHIDSFNFFINVEMKKIVKANEKLT---TEVDP------AFYAKFTEIQVGMPALTE 98

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK------------ 126
                       C  RD+TY+ P+ + L  +            I  I             
Sbjct: 99  ENYESVSMTPQKCRLRDMTYSAPITVNLEYVRGKQIVGRKNVVIGRIPIMLRSSNCVLTN 158

Query: 127 ---EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
              EQ   +G+ PL    G F+++G ++++++    S          +      +  +  
Sbjct: 159 KSHEQLANLGECPL-DPGGYFIVRGNEKVILNHEQLSKNRIIIETDAKGVPCSTVTSSTH 217

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRG 242
               +   +         ++++ +     +PV  FL  +G+++++ +             
Sbjct: 218 ERKSRTSII----MKHGKLYLKHNTFAEDIPVVIFLKGMGVETDQEVVQLVGSEEIFLDA 273

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG--KKLTSGLLKSLKEKGVKFLGITS 300
                       +     +   +           G  KK  S   K +   GV    +  
Sbjct: 274 IASSLEECNKCKVHTQTQALDYLGARIKSIRKPWGMSKKSKSEEAKDIL-AGVVLNHVPV 332

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR----DIPILYVDSVNNNA 356
                  +    V      I I   D       +   +  +      I +L+ D      
Sbjct: 333 RR-YNFRLKVIYVALMIRRIIIATKDRSTLDDKDYYGNKRLELSGQLISLLFEDLFKKFL 391

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
                           A++  +  +   +  T     +  +   ++  ++ +   G  ++
Sbjct: 392 AELKKATDQAILKPNRAMVFDFASIIRTETLTNGFVHA-ISSGQWNLKRFKMERSGVTQV 450

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             R           +     + ++  +         I    +L   +   +      +  
Sbjct: 451 LSR-----------LSFISALGMMTRIQSQFEKTRKISGPRSLQPSQWGMLCPSDTPEGE 499

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
              L    +    +++ + +  + +   N       +      +  +     +N      
Sbjct: 500 ACGLVKNFAQMTHVTTDEPEGPLLRLAYNLGVQDILLITGEELNSRTAFLVFLNGQIIGI 559

Query: 537 HTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           H      +     + RA    E   +      +        G     +  + +       
Sbjct: 560 HNSPTLFVNTLRKMRRAGRIREFISICKNEAHKTVSIACDGGRLCRPMIIVENGRPRVQQ 619

Query: 596 GFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             IE      R   D      + YL   EE + ++A   S++++                
Sbjct: 620 FHIEELKDGLRTFDDFIREGLIEYLDVNEENDSFLAWNESAVNK---------------- 663

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                      ++  P  ++   ++LIP+  ++ S R    C M +QA+           
Sbjct: 664 -------TTTHMEIEPFTLLGCVSALIPYPHHNQSPRNTYQCAMGKQAIGA--------- 707

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                                           I   +     +   + +Y          
Sbjct: 708 --------------------------------IAYNQLSRIDTLLYLLVYP--------- 726

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                QRP+ +                 +   L  G N  VA M + GY+ ED++++++ 
Sbjct: 727 -----QRPMCQ----------TRTLELVNYVKLPAGHNATVAVMSYSGYDIEDALVMNKA 771

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP--NVSEEGLKNIDECGIICVGAEVNP 890
            +       I  ++     +       +           +     +DE GI   G     
Sbjct: 772 SLDRGFGRCIVFKKQVSAVKKYANQTADRIIPPNAETSRQPKFALLDEDGIAKPGELAQK 831

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           G IL+ K +P            + A   +       +S       +   VD  +      
Sbjct: 832 GQILINKYSPINTVD-------IVANSDKIPDSGYKSSYTAYKYENPAFVDKVMLTTGDD 884

Query: 951 D 951
           D
Sbjct: 885 D 885


>gi|169806505|ref|XP_001827997.1| DNA-directed RNA polymerase [Enterocytozoon bieneusi H348]
 gi|161779137|gb|EDQ31162.1| DNA-directed RNA polymerase [Enterocytozoon bieneusi H348]
          Length = 1138

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 101/504 (20%), Positives = 167/504 (33%), Gaps = 97/504 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   + +   
Sbjct: 717  DTLSNILCYPQKPLVSTKSMEYIKFKELPSGQNCIVAIACYSGYNQEDSIIMNQASIDRG 776

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +       R   D+ +   +   E+I  + R         + +I      +  G      
Sbjct: 777  LF-RSFLFRTYSDQEKMKYTGVNEKICKIERSVIFRPKKNNYDILGNDGIVCPGTQVYGD 835

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T +                   ++    N   L     T     E    +K+ 
Sbjct: 836  DVIIGKMTPILD----------------VEKSTPGNPFYLFKDTSTLIRKTEQGNIDKVI 879

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         +  KV V   R  Q GDK A RH  KG+V   L  EDMPF  DG   
Sbjct: 880  VTTK------DGYKFTKVKVRSMRIPQMGDKFASRHAQKGVVGITLKQEDMPFTSDGLIP 933

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G +FE  LG      G +  +     K                  
Sbjct: 934  DVIINPHAIPSRMTIGHLFEALLGKLTTLNGIEGDATPFANKPQ---------------- 977

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  + I+  L      + G  I++ 
Sbjct: 978  ------------------------------------TIDEISKELAKYGYQKRGFEIMHS 1001

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G TG      + +G  Y  +L HMV DK++AR+ G   ++T+QP+ G+S  GG R GEME
Sbjct: 1002 GATGYKLKSQIFIGPTYYQRLKHMVDDKLHARARGPLQIMTRQPVEGRSREGGLRFGEME 1061

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN---------------DTFETGT 1343
              CI ++GA+  L+E L   SD       VY   V  N                      
Sbjct: 1062 RDCIISHGASAFLKERLMDVSD-------VYTCGVCDNCGLICNNNCTGCNNSTISNINI 1114

Query: 1344 PESFNVLVKEMQALGLSIDLENSR 1367
            P +F +L++E+Q + + + ++   
Sbjct: 1115 PYAFKLLIQELQGMNIFMRIQTQE 1138



 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 140/999 (14%), Positives = 284/999 (28%), Gaps = 223/999 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------AFSGAAMLEFVSY 79
           L+  Q  S++ F+ + +          Q        I+         +      L F   
Sbjct: 34  LVRQQLDSFNQFVKIKM----------QEIIDENSIISVKSIPTAGNSIEREIKLYFGQI 83

Query: 80  E-FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
               PP              ++   RDLTY V + I ++   ++         +   K  
Sbjct: 84  SILGPPINTEIDGTSSKILPNEARLRDLTYWVNMFIDVKKAYYENGIE-----VDVSKTI 138

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL------- 157
            +  G LP+M K                         G F+I G ++++V+Q        
Sbjct: 139 RVPFGSLPVMVKSELCALKELNDKDNIRLGECPYDQGGYFIITGGEKVIVAQERIATNMV 198

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDR------R 209
           H    I       + S      Y   I    + G  +   F  K + ++R+ R      +
Sbjct: 199 H----IF------KKSQPAPYTYFAEIRSVAEIGSKLPSIFSLKVVKNLRVIRASINLVK 248

Query: 210 RKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           + +PV     ALG +S+ EILS         +  ++    L  A  +     +   +   
Sbjct: 249 QDIPVLIIFRALGFNSDKEILSYIQY-DNDKELNEYLLNSLEEASCIQDQLSALDFIGKR 307

Query: 269 TGEQVIESGKKLTSGLLKSLKE----KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
           +        K++       +KE     G +    T       Y+   I+   TG+  ++ 
Sbjct: 308 SAPIGSPKSKRIDFAKQILIKEFLPHIGQQEFCETKKAYFLGYMINKILLVITGKRDVDD 367

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
            D   +K ++           +L+   +          V +  +      L         
Sbjct: 368 RDHYGKKRMDLSGPLLANLFKVLFKKLLTETTKYLQKCVENNREFNLTIGL-------KS 420

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKI 442
            + T     ++    +   +K   +  G  ++  R N  +      R     +    +  
Sbjct: 421 SIITQGFKYALATGNWGHQEKAMSTRAGVAQVLSRYNFLSTLSHLRRVNTPIEKEGKLAA 480

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              L N    +             + + L     + + +    I E +  + ++ +   +
Sbjct: 481 PRQLHNTHWGMICPIETPEGHACGLVKNLSLMAYISVGKSSNQIIEILEELGVERLEEIE 540

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            I    ++        +S      + V  +  +   RR   +                  
Sbjct: 541 YIYGTKILVNGAWIGVTS------DPVRIVQILKKFRRHGEID----------------- 577

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            +    I   + +E               +     +E     V                E
Sbjct: 578 -SEISIIFDIKENEIKINSDAGRPCRPLFI-----VENNELLVNKQ-----------DIE 620

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCR------CAGEEILVPREKIDFIDASPKQVVSIAA 676
           + + I      L ++G      +             ++    ++    +  P  ++ I A
Sbjct: 621 DLKNIKIKWDDLIKNGKIELLDIEEEEVSLIAMGLNDLKDTNKQYTHCEIHPAIILGITA 680

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF  ++ S R      M +QA+ +                                 
Sbjct: 681 SVIPFPTHNPSPRNTYQSAMGKQAMGIYSTNFF--------------------------- 713

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + S +  Y               Q+PLV              
Sbjct: 714 --------------KRMDTLSNILCYP--------------QKPLVS----------TKS 735

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA   + GYN EDS+++++  +   +F S     +    +    
Sbjct: 736 MEYIKFKELPSGQNCIVAIACYSGYNQEDSIIMNQASIDRGLFRSFLFRTYSDQEKMKYT 795

Query: 857 GPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           G  E    I         +     +   GI+C G +V   D+++GK+TP  +   +    
Sbjct: 796 GVNEKICKIERSVIFRPKKNNYDILGNDGIVCPGTQVYGDDVIIGKMTPILDVEKST--- 852

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                 G      +DTS  +     G +  V +  + G 
Sbjct: 853 -----PGNPFYLFKDTSTLIRKTEQGNIDKVIVTTKDGY 886


>gi|242392336|dbj|BAH80349.1| RNA polymerase subunit B' [Halococcus salifodinae]
          Length = 608

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 93/323 (28%), Positives = 136/323 (42%), Gaps = 84/323 (26%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 345  EDGSKLSKVSVRDQRIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 404

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 405  PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEDEEELRGSLEEHG-------------- 450

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I+Y G+TGE  D 
Sbjct: 451  -----------------------FD-----------------SSGKEIMYSGVTGEKIDA 470

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 471  EIFVGTIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 530

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------------DTFETGTP 1344
            A  L+E L  +SD    R  VY   V G                        +  E    
Sbjct: 531  AMALKERLLDESD----REFVY---VCGECGMSAVENVEQRRVYCPNCGEETEIHEIEMS 583

Query: 1345 ESFNVLVKEMQALGLSIDLENSR 1367
             +F +L+ EM+ALG++  LE   
Sbjct: 584  YAFKLLLDEMKALGIAPRLELED 606



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/317 (15%), Positives = 99/317 (31%), Gaps = 26/317 (8%)

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            ++   R  G+        +               +  P +  ++ + ++    +     
Sbjct: 27  HQIREARRRGDVAETVNVSVKGRTNEVIVNADAGRARRPLIVVEEGDPLITEEEIGALED 86

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
              + E       +E + A+     I+          D   + I         +      
Sbjct: 87  GESEFEDLVEQGYIEFIDAEEEED-ILVGVDEDDLSEDHTHLEIDPQLIFGIGAGMIPYP 145

Query: 762 YRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPSTD---LGDLAL 807
                 + +     + Q           RP  +          +    +T+     D   
Sbjct: 146 EHNASPRITMGAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGYDDRPA 205

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            +N +VA M + G+N ED+++++E  V   +  S     +E   R    G E+      +
Sbjct: 206 AQNFVVAVMSYEGFNIEDALVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRFEMPDD 265

Query: 868 -----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                  EE   ++DE G++     V+   +L+GK +P               + G    
Sbjct: 266 DVRGARGEEAYTHLDEDGLVNPETTVDESAVLLGKTSPPRFLEEP------DDMGGLSPQ 319

Query: 923 DVRDTSLRVPSGVSGTV 939
             R+TS+ + SG SG V
Sbjct: 320 KRRETSVTMRSGESGVV 336



 Score = 43.9 bits (102), Expect = 0.19,   Method: Composition-based stats.
 Identities = 24/115 (20%), Positives = 43/115 (37%), Gaps = 23/115 (20%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G +E    +  D      + ++ A EEE+  +      L ED                  
Sbjct: 82  GALEDGESEFEDLVEQGYIEFIDAEEEEDILVGVDEDDLSEDH----------------- 124

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 125 ------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPSANYRI 173


>gi|300712257|ref|YP_003738071.1| DNA-directed RNA polymerase subunit B' [Halalkalicoccus jeotgali B3]
 gi|242392312|dbj|BAH80329.1| RNA polymerase subunit B' [Halalkalicoccus jeotgali B3]
 gi|299125940|gb|ADJ16279.1| DNA-directed RNA polymerase subunit B' [Halalkalicoccus jeotgali B3]
          Length = 608

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 127/595 (21%), Positives = 212/595 (35%), Gaps = 99/595 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            + + +    +  D     ++ VA            + I  +++       I   E     
Sbjct: 92   ETLVEHGYVEFIDAEEEEDVYVAVDREEVSEDHTHLEIDPQLIFGIGAGMIPYPEHNASP 151

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R T      + +    +     +   +     +        +        G       + 
Sbjct: 152  RITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQN 208

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + A+   +  ++ D  L +  G     +    F R    +  R    + ++ E+     
Sbjct: 209  FVVAVMSYEGFNIEDA-LVMNGGSVDRGLARSHFFRTYEGEERRYPGGQEDRFEIP---- 263

Query: 972  DDEQV--ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            +DE      +        + L       G              + E P         +  
Sbjct: 264  NDEVRGGRGEEAYTHLDEDGLVNPETNVGENSVLLGKTSPPKFLEE-PDDMGGMGVQKRR 322

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +    + S +     + +++E    +K+                 KV V  +R  + GDK
Sbjct: 323  ETSVTMRSGESGIVDTVTLMEGEDGSKLS----------------KVKVRDERIPELGDK 366

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   G      G
Sbjct: 367  FASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVINPHALPSRMTVGHVLEMLGGKVGALEG 426

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            +++                                                       TP
Sbjct: 427  QRVDG-----------------------------------------------------TP 433

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F G DE+ +   L       SG+ ++Y G++GE  +  + VG I   KL HMVS+K++A
Sbjct: 434  -FSGRDEDELRDSLEERGFMSSGKEVMYSGVSGEKIEAEIFVGTILYHKLYHMVSNKLHA 492

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG- 1324
            RS G   ++T+QP  G++  GG R+GEME   +  +GAA VL+E L   SD    DV G 
Sbjct: 493  RSRGPVQVLTRQPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDREYIDVCGN 552

Query: 1325 ----------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                      + RVY     G   D  E     +FN+L+ EM+ALG++  LE S 
Sbjct: 553  CGMTAVENVQQQRVY-CPNCGEETDIHEIEMSYAFNLLLDEMKALGIAPRLELSE 606



 Score = 43.5 bits (101), Expect = 0.29,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + +      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVREARRRGEVSEMVNVSVKDRTREVVINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V A    E  +  + +      V ++ A EEE+ Y+A     + 
Sbjct: 70  EDGE-----PLITDEAVEALESGEIEFETLVEHGY---VEFIDAEEEEDVYVAVDREEVS 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPSANYRI 173


>gi|83415481|gb|ABC17948.1| RNA polymerase II second largest subunit [Coemansia reversa]
          Length = 722

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 142/856 (16%), Positives = 256/856 (29%), Gaps = 158/856 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    R+ + I    +              + +  + S +     +
Sbjct: 2    KRMDLGGPLLAMLFRTLFRRLTKDIGMYLQKCIESNRDFNMTLAVKSNIITSGLRYALAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKAMQARAGVSQVLNRYTFASTLSHMRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A V   G   +P R+  +     ++  + A    N  
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMAHVT-VGVDSSPIREFLNEWSMENLAEVQAKSIANAT 176

Query: 627  IAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                N          +ELV C    R   +         D  +   +          P L
Sbjct: 177  KVFLNGDWVGIHRKPDELVECMLDARRKADITFETSIVRDIRERELRIHTDSGRVCRPLL 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D S R+ +             AE                 A ++A         +   
Sbjct: 237  IVDSSLRLRLKKAHIDAIERYDVAEDDAYK-----------WADLLADGVIEYLDAEEEE 285

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ-NTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            + +  +       +        +    ++Q +   +QR +      +         PS  
Sbjct: 286  LAMICMTPQELAESHAYRTTGALPPVETDQASRVRSQRNI-----YINTWTHCEIHPSMI 340

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +                       
Sbjct: 341  LG-------ICASIVPFPDHNQSPRNTYQSAMGKQAMG---------------------- 371

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                  ++   L+      +  V             +       +   +  + AI     
Sbjct: 372  ----IMLTNYQLRM---DTLANVLYYPQKPLATTRAMDYLKFRDLPAGQNAIVAIMCYGG 424

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +     F  +  ++++    +  +++    +   D  + L   
Sbjct: 425  YNQEDSVIMNQSSIERGLFRSLYFRTYHDEEDK----LGSKELGTFEKPTPDTTLRLKHG 480

Query: 982  IYSRLM---EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L     I  G           K+T +  D +               E  QR     
Sbjct: 481  TYEKLEGDGLIAPGTRVTGDDIIIGKTTAIPPDSL---------------ELGQRTKSHS 525

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+    +    E    +++     GD       + VKV +   R  Q GDK A RHG KG
Sbjct: 526  KIDASKALRSTECGIVDQVMMTTNGD-----GFKFVKVRIRSTRVPQMGDKFASRHGQKG 580

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   DI++NP  +PSRM VG + E  L      +  +  +    
Sbjct: 581  TIGITYRTEDMPFSAEGIVPDIIINPHAIPSRMTVGHLVECLLSKLSTLMASEGDATPFT 640

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  IS  R  L                                              
Sbjct: 641  DVTVEAIS--RELLGHGYQPRGFEVM---------------------------------- 664

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                        +G +    G         V +G  Y  +L HMV DK+++R+ G   ++
Sbjct: 665  -----------YNGHT----GR---KLAAQVFLGPTYYQRLKHMVDDKIHSRARGPLQIL 706

Query: 1279 TQQPLGGKSNRGGQRL 1294
            T+QP+ G++  GG R 
Sbjct: 707  TRQPVEGRARDGGLRF 722



 Score =  118 bits (295), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 86/585 (14%), Positives = 170/585 (29%), Gaps = 92/585 (15%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +  ++    + +  K   +  G  ++  R    +      R          I
Sbjct: 47  KSNIITSGLRYALATGNWGEQKKAMQARAGVSQVLNRYTFASTLSHMRRCNTPIGRDGKI 106

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +         +      ++KN   +  + +          ++  S+  
Sbjct: 107 AKPRQLHNTHWGLVCPAETPEGQACG---LVKNLALMAHVTVGVDSSPIREFLNEWSMEN 163

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMR 559
              + AK + +A   F     +    +    +  +   RR + +  +  + R     E+R
Sbjct: 164 LAEVQAKSIANATKVFLNGDWVGIHRKPDELVECMLDARRKADITFETSIVRDIRERELR 223

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            +H        P    +      +      A +  Y   E    K  D      + YL A
Sbjct: 224 -IHTDSGRVCRPLLIVDSSLRLRLKKAHIDA-IERYDVAEDDAYKWADLLADGVIEYLDA 281

Query: 620 MEEENRYIAQANSSLDEDGSFTE-------ELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            EEE   I      L E  ++         E         +  +        +  P  ++
Sbjct: 282 EEEELAMICMTPQELAESHAYRTTGALPPVETDQASRVRSQRNIYINTWTHCEIHPSMIL 341

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            I AS++PF +++ S R      M +QA+ ++                            
Sbjct: 342 GICASIVPFPDHNQSPRNTYQSAMGKQAMGIMLTNYQL---------------------- 379

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                 + + V  Y       +     +  R             
Sbjct: 380 -------------------RMDTLANVLYYPQKPLATTRAMDYLKFR------------- 407

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                      DL  G+N +VA M + GYN EDS+++++  +   +F S++   +     
Sbjct: 408 -----------DLPAGQNAIVAIMCYGGYNQEDSVIMNQSSIERGLFRSLYFRTYHDEED 456

Query: 853 DTK---LGPEEITRD--IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 LG  E         +     + ++  G+I  G  V   DI++GK T      + 
Sbjct: 457 KLGSKELGTFEKPTPDTTLRLKHGTYEKLEGDGLIAPGTRVTGDDIIIGKTTAIPPDSLE 516

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        K+    D S  + S   G V  V +       K
Sbjct: 517 LGQRT-------KSHSKIDASKALRSTECGIVDQVMMTTNGDGFK 554


>gi|40644555|emb|CAD89596.1| RNA polymerase II, second largest subunit [Myoporum insulare]
          Length = 350

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 78/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 190  AIPSRMTIGQLIECVMGKVAAHMGKEGD-------------------------------- 217

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 218  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 255

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 256  TAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 315

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 316  GAAHFLKERLFDQSD 330



 Score = 72.4 bits (176), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/132 (19%), Positives = 48/132 (36%), Gaps = 14/132 (10%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPN 867
           VA   + GYN EDS+++++  +    F S+    +    +      +E        +   
Sbjct: 1   VAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMG 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP              A         RD 
Sbjct: 61  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPINPED---------AQGQAARYTKRDH 111

Query: 928 SLRVPSGVSGTV 939
           S  +    +G V
Sbjct: 112 STSLRHSETGIV 123


>gi|100913629|gb|ABF69713.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 599

 Score =  322 bits (824), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 213/429 (49%), Positives = 296/429 (68%), Gaps = 8/429 (1%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++
Sbjct: 1   DQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNM 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-GSFTEEL 644
            S+A+++ YGFI+TPY KV DG V  ND+ YL+A+EE N   AQ++ ++DE+ G   +E 
Sbjct: 61  ASYAKIDDYGFIQTPYFKVNDGVVDFNDIRYLTAIEEINFTFAQSSINIDEETGEILDER 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E I + +++ID+I  + +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVPL+
Sbjct: 121 VMSRKNNEYIELDKKEIDYIGVTSRQMTSISASAIPFLENDDANRALMGSNMQRQAVPLI 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           K EAP V TG+E+ +A+ S + + A + GIV  VDA  I I+S +           IY L
Sbjct: 181 KPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSEDEKKPS------IYFL 234

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             F+RSNQ T ++Q+PLVKVG E++  D++ DGPS + G+LALG+N+LV F  W GYN+E
Sbjct: 235 RTFERSNQGTVIHQKPLVKVGQEIKAGDLLTDGPSMENGELALGKNVLVGFSTWFGYNYE 294

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D+++++E++V EDV+TSIHIEE  +  R +K G + +T DIPN S    + + E GI+ +
Sbjct: 295 DAVILNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVII 354

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GTVV V +
Sbjct: 355 GSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDV 414

Query: 945 FNRHGIDKN 953
             R   D N
Sbjct: 415 LRRDTDDTN 423



 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 127/499 (25%), Positives = 194/499 (38%), Gaps = 68/499 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +            +       + R   + + T +   E  + + D K 
Sbjct: 169  GSNMQRQAVPLIKPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSEDEKK 228

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                  R     ++  + +     ++ VG E+  GD+L    +      +   + +L   
Sbjct: 229  PSIYFLRTFERSNQGTVIHQKP--LVKVGQEIKAGDLLTDGPS-MENGELALGKNVLVGF 285

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       +  RS + +      +    +  + 
Sbjct: 286  STWFGYNYEDAVILNEKLVKEDV-YTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKR 344

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             L  +    +   +   + + G    K     S +   +   + + Q     +     V+
Sbjct: 345  FLGEDGIVIIGSEVGPGDILVGRISPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVK 402

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                    +  +L     +         ++  G+  +VKV +A KR I+ GDKMAGRHGN
Sbjct: 403  HGHGGTVVAVDVLRRDTDD--------TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGN 454

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+VS ILP EDMP+L DGTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  S +
Sbjct: 455  KGVVSIILPEEDMPYLADGTPLDILLNPQGVPSRMNIGQVLELHLGLAARKLNCKFVSPV 514

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +   I  ++                                               
Sbjct: 515  FDGISYKQIQEIQKEAGIDPSGKMTV---------------------------------- 540

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                          SG+       TGEPFD P++VG +Y LKL HMV DK++ARS G YS
Sbjct: 541  -------------YSGK-------TGEPFDNPISVGVMYYLKLYHMVDDKMHARSVGPYS 580

Query: 1277 LVTQQPLGGKSNRGGQRLG 1295
            L+TQQPLGGKS  GGQR G
Sbjct: 581  LITQQPLGGKSQNGGQRFG 599


>gi|73697665|gb|AAZ81449.1| RNA polymerase beta subunit [Mycoplasma anatis]
          Length = 591

 Score =  321 bits (823), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 211/448 (47%), Positives = 308/448 (68%), Gaps = 15/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN  GF++TPY KV +G +  NDV YL+A EE     +Q++ ++DE+    +EL+  R
Sbjct: 61  AKVNEMGFLQTPYFKVNNGVIDYNDVRYLTASEEIGYKFSQSSVTVDENNKIVDELITIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++    ++DFI+ S KQ+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 HNYNYVIDKPSEVDFIEVSSKQMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQTEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+V TG+E  +AK S   +VAK AG V  VD+ +I I++ +G  D        Y L  F+
Sbjct: 181 PYVATGIEGDIAKYSAYNLVAKNAGEVIYVDSQKIHIKNDKGTTDK-------YVLRNFE 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T +NQ P+VK+GD+V   ++I DG S   G+LALG+N+LVAF  W+GYN+ED+++
Sbjct: 234 RSNQGTVINQIPIVKLGDKVEEGELIVDGSSFKNGELALGKNVLVAFTTWNGYNYEDAII 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++E++V +DV+TSIHIEE  +  R++K G +++T  IPNVS+  ++N+DE GI+ VG+EV
Sbjct: 294 LNEKLVKDDVYTSIHIEEQTIQFRNSKAGDDKLTASIPNVSKYSIRNLDENGIVRVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
            PGD+LVG+++PKGE   T EEKLL AI  ++    RDTSL+V +G +GTV+ V + +R 
Sbjct: 354 VPGDVLVGRVSPKGEENPTQEEKLLMAILQQRPSSDRDTSLKVKNGHNGTVIGVEVLSRE 413

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 414 LGDVLEDGIDKIVKVSIAQKRKIKVGDK 441



 Score =  300 bits (767), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 143/524 (27%), Positives = 223/524 (42%), Gaps = 82/524 (15%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMVS 835
            Q   V  G      +  A+              +L    P+     E  +    +  +V+
Sbjct: 142  QMVSVAAGAIPFLENDDANRALMGSNMQRQAVPLLQTEAPYVATGIEGDIAKYSAYNLVA 201

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ++    I+++  ++  ++ K   ++        S +G   I++  I+ +G +V  G+++V
Sbjct: 202  KNAGEVIYVDSQKIHIKNDKGTTDKYVLRNFERSNQGTV-INQIPIVKLGDKVEEGELIV 260

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRHG 949
               + K    +   + +L A       +  D  +            S  + +  I  R+ 
Sbjct: 261  DGSSFKN-GELALGKNVLVAFTTWNGYNYEDAIILNEKLVKDDVYTSIHIEEQTIQFRNS 319

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
               +++  +      +   R+  DE  I+         ++L G+ +  G +   +   L 
Sbjct: 320  KAGDDKLTASIPNVSKYSIRNL-DENGIVRVGSEVVPGDVLVGRVSPKGEENPTQEEKLL 378

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              ++ + P S        D      V++          +L             GD +  G
Sbjct: 379  MAILQQRPSS--------DRDTSLKVKNGHNGTVIGVEVLSREL---------GDVLEDG 421

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
            + ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP L+DGTPVDI+LNP GVPS
Sbjct: 422  IDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPHLEDGTPVDIMLNPQGVPS 481

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG A   LG K  +   D     DI                        
Sbjct: 482  RMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKQDI------------------------ 517

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
             ++ L  A   K+G  +                             L D +TGE FD PV
Sbjct: 518  -ENALEEAGLPKTGKQI-----------------------------LIDPVTGEKFDNPV 547

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +VG +YMLKLNHMV DK++ RS G YSL+TQQPLGGKS  GGQR
Sbjct: 548  SVGVMYMLKLNHMVDDKMHGRSVGPYSLITQQPLGGKSQNGGQR 591


>gi|52694241|emb|CAG30650.1| DNA-directed RNA polymerase beta chain [Pseudomonas chlororaphis]
          Length = 326

 Score =  321 bits (823), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 194/325 (59%), Positives = 252/325 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DEIVFLSAIEEADHVIAQASATMNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+
Sbjct: 241 GGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRS 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAFM 816
           DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 301 DIMADGPSTDMGELALGQNMRIAFM 325


>gi|6606091|gb|AAF19058.1|AF107786_1 DNA-dependent RNA polymerase II RPB140 [Neolecta vitellina]
          Length = 930

 Score =  321 bits (823), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 149/1043 (14%), Positives = 306/1043 (29%), Gaps = 171/1043 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S L   L     K   +++  L    +     + +   ++   G + D + L
Sbjct: 37   VEKGSRLISSLQIKLLRNPQKT-SVSNGRLIKATLPYIKDDIDIVIVFRALGVLADREIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E I         +  +      A++         +++  AL  I +       +T    +
Sbjct: 96   EHICFDPNDHQMLELLKPCIEEAFV--------IQEKDLALDYIGKR----GQTTGLSRD 143

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                       K  L  V              +     +   +  ++  L+ +   +   
Sbjct: 144  RRIRHAREIMQKELLPHV-----------SQTEGYESRKAFFLGYMVHRLLLVALERREQ 192

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + +    +    +         + A  +  
Sbjct: 193  DDRDHFGKKRLDLAGPLLANLFRMLFKKLYKDVYRYMQKCVENNREFNLTLAVKAPTITQ 252

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 253  GLKYSLATGNWGEQKKAAQAKVGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 308

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H +H+G +CPAET EG   GLV +L   + ++  G        + +  + +   Y  
Sbjct: 309  RQLHNSHWGLVCPAETPEGQACGLVKNLALMSYISVGGPSAPLIEFLEEWGMESLEDYSP 368

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            +       I      L         +   R     + +  E     D   +++     + 
Sbjct: 369  SSTPNTTKIFVNGVWLGVHRDAGSLVNTVRNLRRRVDISPEITIVRDIRERELRLFTDAG 428

Query: 679  I----PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                  F+ ++D +       M ++       E          +              GI
Sbjct: 429  RVMRPLFIVDNDEHSPRKNFLMLQRQHVETINEHK----DNPEIPDHERWNFSKLIENGI 484

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +E +DA       +        S   +    + +         + P       +      
Sbjct: 485  IEYIDAEEEETAMIAMTRKDLESWRKMKEGFQIEEEFDPASRVEPP---PNPNIAMYTHC 541

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               PS  LG       +  + +P+  +N          M  + +   + +  ++      
Sbjct: 542  EIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQ------ 586

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                                 +    +  +             +       +   +  + 
Sbjct: 587  ---------------------LRMDTMANILYYPQKPLATTRSMEYLKFRDLPAGQNAIV 625

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +     +  +   + +    +  + +E   +     
Sbjct: 626  AILCYSGYNQEDSVIMNQSSIDRGLFRSMFYRCYNDQEKK----IGMQVMEEFEKPTRQT 681

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + L    Y +L E   I  G           K+  +S D      R+           +
Sbjct: 682  TLRLKHGTYEKLEEDGLIAPGIRVSGEDIIIGKTAPISPDTQELGQRTSHHTKRDVSTPL 741

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +                                L+ VKV +   R  Q GDK A
Sbjct: 742  RSTENGIVDH--------------------VVVTTNQEGLKFVKVRMRSTRVPQIGDKFA 781

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF   G   D+++NP  +PSRM V  + E  L       G +
Sbjct: 782  SRHGQKGTIGITYRHEDMPFSAQGVVPDLIINPHAIPSRMTVAHLIECQLSKVSAMGGYE 841

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S      +++   G  +       +                     
Sbjct: 842  GDATPFTEVTVEQVS------QQLRNQGFQSRGFEVMYNG-------------------- 875

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                               +G+ ++            V +G  Y  +L HMV DK++AR+
Sbjct: 876  ------------------HTGKKLM----------AQVFLGPTYYQRLKHMVDDKIHARA 907

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRL 1294
             G   ++T+QP+ G+S  GG R 
Sbjct: 908  RGPVQILTRQPVEGRSRDGGLRF 930



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 97/848 (11%), Positives = 234/848 (27%), Gaps = 130/848 (15%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK------- 199
            ++++++Q  RS   +      +++ S  L +   +    ++G  +      K       
Sbjct: 1   SEKVIIAQE-RSA-ANTVQVFTKSAPS-PLSHVAEVRSAVEKGSRLISSLQIKLLRNPQK 57

Query: 200 -----DII------HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
                  +      +++ D    + +     ALG+ ++ EIL          Q  +    
Sbjct: 58  TSVSNGRLIKATLPYIKDD----IDIVIVFRALGVLADREILEHICFDPNDHQMLELLKP 113

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            +  A ++    ++   +        +   +++     + + +K +      ++      
Sbjct: 114 CIEEAFVIQEKDLALDYIGKRGQTTGLSRDRRI--RHAREIMQKELLPHVSQTEGYESRK 171

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDK 366
                +      + + A +  ++   +      +    P+L          +   +    
Sbjct: 172 AF--FLGYMVHRLLLVALERREQDDRDHFGKKRLDLAGPLLANLFRMLFKKLYKDVYRYM 229

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            K  ++       +       T  +  S+    + +  K   + VG  ++  R    +  
Sbjct: 230 QKCVENNREFNLTLAVKAPTITQGLKYSLATGNWGEQKKAAQAKVGVSQVLNRYTFASTL 289

Query: 427 DV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
               R          I     L N    +         +      ++KN   +  + +  
Sbjct: 290 SHLRRTNTPIGRDGKIAKPRQLHNSHWGLVCPAETPEGQACG---LVKNLALMSYISVGG 346

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                I  ++   +   +  +     +    F     L    +  + ++ + + RR   +
Sbjct: 347 PSAPLIEFLEEWGMESLEDYSPSSTPNTTKIFVNGVWLGVHRDAGSLVNTVRNLRRRVDI 406

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF---------ARVNAY 595
                           +       + P    +        +                +  
Sbjct: 407 SPEITIVRDIRERELRLFTDAGRVMRPLFIVDNDEHSPRKNFLMLQRQHVETINEHKDNP 466

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
              +              + Y+ A EEE   IA     L+      E             
Sbjct: 467 EIPDHERWNFSKLIENGIIEYIDAEEEETAMIAMTRKDLESWRKMKEGFQIEEEFDPASR 526

Query: 656 VPR------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           V              +  P  ++ + AS+IPF +++ S R      M +QA+ +      
Sbjct: 527 VEPPPNPNIAMYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQ 586

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                                                        + + +  Y       
Sbjct: 587 L-----------------------------------------RMDTMANILYYPQKPLAT 605

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +     +  R                        DL  G+N +VA + + GYN EDS+++
Sbjct: 606 TRSMEYLKFR------------------------DLPAGQNAIVAILCYSGYNQEDSVIM 641

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E            +     + ++E G+I  
Sbjct: 642 NQSSIDRGLFRSMFYRCYNDQEKKIGMQVMEEFEKPTRQTTLRLKHGTYEKLEEDGLIAP 701

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  DI++GK  P      +P+ + L           RD S  + S  +G V  V +
Sbjct: 702 GIRVSGEDIIIGKTAPI-----SPDTQELGQRTSHH--TKRDVSTPLRSTENGIVDHVVV 754

Query: 945 FNRHGIDK 952
                  K
Sbjct: 755 TTNQEGLK 762


>gi|111054589|gb|ABH04352.1| RNA polymerase beta subunit [Proteus myxofaciens]
          Length = 326

 Score =  321 bits (823), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 201/322 (62%), Positives = 252/322 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGEXSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 305 LADGPSTDLGELALGQNMRVAF 326


>gi|166064926|gb|ABY79072.1| RNA polymerase beta subunit [Enterobacter oryzae]
          Length = 329

 Score =  321 bits (823), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 205/329 (62%), Positives = 258/329 (78%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D 
Sbjct: 121 DGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G+V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+
Sbjct: 241 AVAKRGGMVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + R D++ADGPSTDLG+LALG+NM VAF
Sbjct: 301 PIERGDVLADGPSTDLGELALGQNMRVAF 329


>gi|82749756|gb|ABB89762.1| RNA polymerase beta subunit [Mycoplasma anseris]
          Length = 592

 Score =  321 bits (823), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 204/448 (45%), Positives = 295/448 (65%), Gaps = 10/448 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTH+GRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHFGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA+++ YGFI+TPY KV + KV  +  +YL+A+EE     AQ+   +  D    +E V  
Sbjct: 61  FAQIDKYGFIQTPYFKVNNKKVDFSAPIYLTAIEEIGYTFAQSTVHIKND-EIIDEYVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V  E++D++  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++  E
Sbjct: 120 RRDNEYVQVKAEEVDYLGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVITPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I A++ G+V  VD+  + I   +      ++    Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIRAQKDGVVTYVDSNMVKIMPHD------SNKAQTYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  T ++Q P+VKVG E++  D++ DGPS   G+LALG+N+LV F  WHGYN+ED++
Sbjct: 234 ERSNAGTLIHQVPIVKVGQEIKNGDLLVDGPSMKNGELALGKNVLVGFSTWHGYNYEDAI 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPN S    + +DE GI+ +G+E
Sbjct: 294 ILSERLVKDDVYTSIHIEEQTIQFRHSKAGEDWLTNDIPNASNFSKRFLDENGIVRIGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIEVLSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQ 975
                ++    +E+     +A+ +  + 
Sbjct: 414 EFG--DQLEDGIEKIVKVSIAQKRKIKV 439



 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 124/413 (30%), Positives = 178/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG E+  GD+LV   + K    +   + +L         +  D  +     V   V 
Sbjct: 247  IVKVGQEIKNGDLLVDGPSMKN-GELALGKNVLVGFSTWHGYNYEDAIILSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDWLTNDIPNASNFSKRFLDENGIVRIGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L   F       
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIEVLSREF------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+D+
Sbjct: 416  --GDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDM 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  + + D   +  I  +    +      +
Sbjct: 474  MLNPQGVPSRMNIGQILELHLGLAAKKLNTKFVTPVFDGITHNQIKEILEEAKIDPSAKT 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SGQ       
Sbjct: 534  TV-----------------------------------------------YSGQ------- 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD P++VG +YMLKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEKFDHPISVGVMYMLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|193735374|gb|ACF20189.1| RNA polymerase beta subunit [Mycoplasma salivarium]
          Length = 595

 Score =  321 bits (823), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 213/446 (47%), Positives = 297/446 (66%), Gaps = 10/446 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ YGFI+TPY KV + KV  +   YL+A+EE    IAQ+   + E+    +++V 
Sbjct: 61  SFAQIDKYGFIQTPYFKVNNRKVDFSKPHYLTAIEEMGMVIAQSTVKI-ENNMIIDDVVM 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E +    + ID+I  S +Q++SIAAS IPFLENDD+NR LMG NMQRQAVP++K 
Sbjct: 120 ARKNNEYVEANADDIDYIGVSNRQMISIAASAIPFLENDDANRALMGANMQRQAVPVIKP 179

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+E+ +AK S   I +   GIV  VDA +I I   EG         D Y L  
Sbjct: 180 EAPLVATGVEADIAKFSSTNIRSNTDGIVTYVDATQIKIMPFEGKKA------DTYYLRT 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T ++Q PLVKVG E+++ D++ DGPS   G++ALGRN+LV F  WHGYN+ED+
Sbjct: 234 FERSNQGTLIHQIPLVKVGQEIKKGDLLVDGPSMKDGEMALGRNVLVGFSTWHGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +++SER+V +DV+TSIHIEE  +    +K G + +T DIPN S    + ++E GI+ +G+
Sbjct: 294 VVLSERLVKDDVYTSIHIEEQTIQFIHSKAGEDILTSDIPNASNYSKRFLNEDGIVRIGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV  GDILVG+ +PKGE   TPEEKL+ AIFG+K+V+ +DTSL+V  G +GTVV V +  
Sbjct: 354 EVTAGDILVGRTSPKGEDNPTPEEKLMAAIFGQKSVNRKDTSLKVKHGHNGTVVAVEVLT 413

Query: 947 RHGIDKNERSISVEREQIELLARDKD 972
           R     ++    +E+     +A+ + 
Sbjct: 414 REFG--DQLEDGIEKIVKVSIAQKRK 437



 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 126/415 (30%), Positives = 181/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   +   +  M     +L         +  D  +     V   V 
Sbjct: 248  LVKVGQEIKKGDLLVDGPS-MKDGEMALGRNVLVGFSTWHGYNYEDAVVLSERLVKDDV- 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L+ +   R+   +   + + G  
Sbjct: 306  YTSIHIEEQTIQFIHSKAGEDILTSDIPNASNYSKRFLNEDGIVRIGSEVTAGDILVGRT 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q +V  +     V+        +  +L   F       
Sbjct: 366  SPKGEDNPTPE--EKLMAAIFGQKSVNRKDTSLKVKHGHNGTVVAVEVLTREF------- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 417  --GDQLEDGIEKIVKVSIAQKRKIRVGDKMAGRHGNKGVVSIVLPVEDMPYLEDGTPLDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQI E HLG A   LG K  + + D   +  I  +    +       
Sbjct: 475  VLNPQGVPSRMNIGQILELHLGLAAKKLGVKFVTPVFDGITHNQIKEILEEAKVDTSGK- 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                       T V+D                          G 
Sbjct: 534  ---------------------------TYVYD--------------------------GQ 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE FD P++VG +Y LKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 541  TGEKFDHPISVGIMYYLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|52538133|emb|CAH19170.1| RNA polymerase beta-subunit [Pseudomonas libanensis]
          Length = 336

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 195/336 (58%), Positives = 258/336 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQ+TC+NQRPLV+ G  V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQHTCINQRPLVRKGYRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +DI+ DGPS+D+G+LALG+NM +AFM W+G+NFEDS
Sbjct: 301 SDIMPDGPSSDMGELALGQNMRIAFMAWNGFNFEDS 336


>gi|242392290|dbj|BAH80338.1| RNA polymerase subunit B' [Halobacterium jilantaiense]
          Length = 608

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 123/583 (21%), Positives = 199/583 (34%), Gaps = 93/583 (15%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LV        +    + I  +++       I   E     R T      
Sbjct: 101  EFIDAEEEEDILVGVDEEELTDNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 159  MMKQSLGLPAANYRIRPDTR-QHLLHYPQKAMVNTQTTKQIGYDDRPAGQNFVVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+   D       +  
Sbjct: 218  GFNIEDALVMNKGSVE-RALSRSHFFRTYEGEERRYPGGQEDRFEIPGDD-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+       S+VL           +         + +R       
Sbjct: 270  ARGEDAYTHLDDDGLVNPETKVDDSSVLLGKTSPPRFLEEPEDMGGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E          + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 330  SGEDGVVDTVTLMEGE------------DGSKLAKVSVRDERIPELGDKFASRHGQKGVV 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF ++G   D+VLNP  +PSRM VG + E   G A    G+ +        
Sbjct: 378  GHLAPHEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKAGSLDGRSVDG------ 431

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                           TP F G DE+ I 
Sbjct: 432  -----------------------------------------------TP-FTGEDEDEIR 443

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L       SG+ +LY G++GE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 444  GTLEDRGFKSSGKEVLYSGVSGEKIEAEIFVGTIFYHKLYHMVSNKIHARSKGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR-----TRVYE- 1330
            QP  G++  GG R+GEME   +  +GAA VL+E L   SD     V G         YE 
Sbjct: 504  QPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDREEVHVCGNCGMTAVENYEQ 563

Query: 1331 ------SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  +     D        +F +L+ EM+ALG++  LE   
Sbjct: 564  RRVYCPNCEEETDVHSIEMSYAFKLLLDEMKALGIAPRLELED 606



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 60/370 (16%), Positives = 126/370 (34%), Gaps = 35/370 (9%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +S   E   Y+  +     E+     E +   R  GE   +    +              
Sbjct: 1   MSTEREAKVYVNGSLVGTHENPEQLAEQIREARRRGEVSEMVNVSVKDRTGEVIVNADAG 60

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            +  P L  +D   V+    ++      ++ E       +E + A+     +V       
Sbjct: 61  RARRPLLVVEDGEPVVTQQEVEALESGDIEFEDLVREGKVEFIDAEEEEDILV---GVDE 117

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQ-----------RPLV 782
           E++      +      +    +G+  Y       + +     + Q           RP  
Sbjct: 118 EELTDNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDT 177

Query: 783 KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           +          + +  +T      D   G+N +VA M + G+N ED++++++  V   + 
Sbjct: 178 RQHLLHYPQKAMVNTQTTKQIGYDDRPAGQNFVVAVMSYEGFNIEDALVMNKGSVERALS 237

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIP------NVSEEGLKNIDECGIICVGAEVNPGDI 893
            S     +E   R    G E+   +IP         E+   ++D+ G++    +V+   +
Sbjct: 238 RSHFFRTYEGEERRYPGGQEDRF-EIPGDDVRGARGEDAYTHLDDDGLVNPETKVDDSSV 296

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           L+GK +P               + G      R+TS+ + SG  G V    +    G D +
Sbjct: 297 LLGKTSPPRFLEEP------EDMGGLSPQKRRETSVTMRSGEDGVV--DTVTLMEGEDGS 348

Query: 954 ERSISVEREQ 963
           + +    R++
Sbjct: 349 KLAKVSVRDE 358



 Score = 42.8 bits (99), Expect = 0.42,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E+   +  D      V ++ A EEE+  +      L ++                    
Sbjct: 84  LESGDIEFEDLVREGKVEFIDAEEEEDILVGVDEEELTDNH------------------- 124

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 125 ----THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 173


>gi|194591905|gb|ACF76533.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
 gi|194591907|gb|ACF76534.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
          Length = 597

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 215/453 (47%), Positives = 309/453 (68%), Gaps = 13/453 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS + + RR+++LG GG+ R  A  E+RDVH T+YGRICP ET EG NIGL+ +L 
Sbjct: 1   QINPLSELANKRRITSLGPGGLNRETAQFEVRDVHSTYYGRICPIETPEGQNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++++ + +GFI+TPY  V +G V   +V +L+A++E     AQ++ ++DE+    +E + 
Sbjct: 61  TYSKTDDFGFIQTPYFPVKNGVVNYGEVKWLTAVDEYGYTFAQSSVTIDENNKIIDEFIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   + ++V  E+ID+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQAVPL++A
Sbjct: 121 VRKDYQYLIVKPEEIDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQAVPLIEA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP +GTG+E  +AK +   I A  +GIV  VDA  I I+  + +L+      DIY L  
Sbjct: 181 EAPLIGTGVEHDIAKYAATNIRAFNSGIVTYVDAKTIKIKPFDENLEE-----DIYYLKS 235

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQ+SNQ T +NQ P V+VG+ + +  ++ DGPST  G+LALG+N+LVAF  WHGYNFED+
Sbjct: 236 FQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTKDGELALGKNVLVAFTTWHGYNFEDA 295

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++ISE++V +DVFTSIHIEE  +  R +K G + +T +IPN S    +++DE GI+ VG+
Sbjct: 296 IIISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDENGIVRVGS 355

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EVN GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G +GTV+DV+I +
Sbjct: 356 EVNTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGSNQKDTSLKVKHGDAGTVIDVQIIS 415

Query: 947 RHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           R   D       +  + I+ + +    ++  + 
Sbjct: 416 RANGD-------ILEDGIDKIVKVFIAQKRKIK 441



 Score =  300 bits (769), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 136/500 (27%), Positives = 206/500 (41%), Gaps = 72/500 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ A  P  G   E  +            + I     +      K   E
Sbjct: 166  MGANMQRQAVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYV-DAKTIKIKPFDE 224

Query: 860  EITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             +  DI  +      N    I++   + VG  +  G ++    + K +  +   + +L A
Sbjct: 225  NLEEDIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTK-DGELALGKNVLVA 283

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                   +  D  +     V   V    I       +   S + +      +       +
Sbjct: 284  FTTWHGYNFEDAIIISEKLVKDDVF-TSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSK 342

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD N   R+   +   + + G    K     + +        +       ++   +  
Sbjct: 343  RHLDENGIVRVGSEVNTGDILVGRISPKGEDNPTPE-------EKLLNAIFGNKGSNQKD 395

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLKV++  + ++++     +I     GD +  G+ ++VKVF+A KR I+ GDKMAGRHG
Sbjct: 396  TSLKVKHGDAGTVID----VQIISRANGDILEDGIDKIVKVFIAQKRKIKVGDKMAGRHG 451

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S +LP EDMP+L+DGTP+DI+LNP GV SRMN+GQ+ E HLG A   L  K  S 
Sbjct: 452  NKGVISLVLPVEDMPYLEDGTPIDILLNPQGVASRMNIGQVLELHLGMAAKKLNVKFVSP 511

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D   N  +  +                                               
Sbjct: 512  VFDGIKNESLDSIL---------------------------------------------K 526

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E           L ESG+  LYDG+TG+ +D  V+VG +YMLKL HMV DK+ ARS G Y
Sbjct: 527  EAD---------LPESGRFTLYDGITGKQYDSKVSVGVMYMLKLQHMVDDKINARSVGPY 577

Query: 1276 SLVTQQPLGGKSNRGGQRLG 1295
            SL++QQPLGGKS  GGQR G
Sbjct: 578  SLISQQPLGGKSQNGGQRFG 597


>gi|6606139|gb|AAF19082.1|AF107810_1 DNA-dependent RNA polymerase II RPB140 [Morchella elata]
          Length = 927

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 147/975 (15%), Positives = 292/975 (29%), Gaps = 161/975 (16%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +     ++ +        
Sbjct: 88   VSDEDILNHVCYDRNDTQMLEMMKPCIEEAFVIQDREVALDFIGKRGSSQGI---NKEKR 144

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +Y    + +  +         +     +   +  ++  ++     +  +DD D+ G +R
Sbjct: 145  IRYARDIMQKELLPHISQ---SEGSETRKAFFLGYMVHRMLQCALERREVDDRDHFGKKR 201

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    ++ + + + +               + +  + + +     +  
Sbjct: 202  LDLAGPLLAGLFRTLWKKLTKDVYKYLEKCVETGKDFNLTLAVKSNTITNGLKYSLATGN 261

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 262  WGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 317

Query: 569  ICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L+  + +     G+    +    D ++  +     +      +
Sbjct: 318  VCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPNATKVF 377

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
            +         D     ++V        +      I D  D   K          P    D
Sbjct: 378  VNGVWVGTHRDPLMLHKVVQDVRRQGVVNHEVSIIRDIRDREFKIFTDAGRVCRPLFVID 437

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI-- 743
            +  R      +  Q   + K E         ++  +           G VE +DA     
Sbjct: 438  NDPRSERRGQLVLQKEHIEKLEDD------HALPMEDRFGWEGLLFGGTVEYLDAEEEET 491

Query: 744  -VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             +I     DLD S      Y   K + S +       P                 PS  L
Sbjct: 492  VMIVMTPEDLDMSRQMQLGYEEPKDEFSAKRVKAPINP-----HTAHTWTHCEIHPSMIL 546

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +   + +  F               
Sbjct: 547  G-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM----------- 586

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 587  ----------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 630

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R  +D+ +R   +  + +E   +      + L    
Sbjct: 631  NQEDSVIMNQSSIDRGLF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGT 686

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L E   +  G           K+  ++ D+     R ++         ++     + 
Sbjct: 687  YDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIV 746

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                             L+ VKV +   +  Q GDK A RHG KG 
Sbjct: 747  DQVML--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGT 786

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +     
Sbjct: 787  VGITYRQEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTD 846

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 +S L    +    +       + Y                               
Sbjct: 847  VTVESVSTLLR--QNGYQSRGFEVMYNGYT------------------------------ 874

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                               G         V +G  Y  +L HMV DK++AR+ G   ++T
Sbjct: 875  -------------------GR---KLVCQVFLGPTYYQRLRHMVDDKIHARARGPVQILT 912

Query: 1280 QQPLGGKSNRGGQRL 1294
            +QP+ G++  GG R 
Sbjct: 913  RQPVEGRARDGGLRF 927



 Score =  151 bits (381), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 115/857 (13%), Positives = 238/857 (27%), Gaps = 151/857 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIH--- 203
            ++++++Q  RS          + +L     Y   I    ++G  +      K  ++   
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKALPSPTPYVAEIRSAVEKGSRLISSMQIK--LYSKG 55

Query: 204 -------VRIDR-----RRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLS 250
                    I       +  +P+     ALG+   E+IL+        +Q  +     + 
Sbjct: 56  EARGGYNATIKSTLPYIKSDIPIVIVFRALGVVSDEDILNHVCYDRNDTQMLEMMKPCIE 115

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A ++   +V+   +      Q I   K++     + + +K +                 
Sbjct: 116 EAFVIQDREVALDFIGKRGSSQGINKEKRI--RYARDIMQKEL----------------L 157

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             ++   G    +A  +            E R++                 L        
Sbjct: 158 PHISQSEGSETRKAFFLGYMVHRMLQCALERREVDDRDHFGKKRLDLAGPLLAGLFRTLW 217

Query: 371 KDALLDIYRVMRPGDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
           K    D+Y+ +         F++  ++ +    +  KY L   G      +         
Sbjct: 218 KKLTKDVYKYLEKCVETGKDFNLTLAVKSNTITNGLKYSL-ATGNWGEQKKAASSKAGVS 276

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R+GK       +  +  +    E  + Q    +  + 
Sbjct: 277 QVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS 336

Query: 484 RSIKERISSV--------DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
                 I +           + +   +    +   +A   F     +    + +     +
Sbjct: 337 LMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPNATKVFVNGVWVGTHRDPLMLHKVV 396

Query: 536 THTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              RR   +  +  + R     E        R   P       P     G  +     + 
Sbjct: 397 QDVRRQGVVNHEVSIIRDIRDREFKIFTDAGRVCRPLFVIDNDPRSERRGQLVLQKEHIE 456

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF------- 640
                + +                  V YL A EEE   I      LD            
Sbjct: 457 KLE--DDHALPMEDRFGWEGLLFGGTVEYLDAEEEETVMIVMTPEDLDMSRQMQLGYEEP 514

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E    R                +  P  ++ I AS+IPF +++ S R      M +QA
Sbjct: 515 KDEFSAKRVKAPINPHTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQA 574

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                         A+R   +  +                      
Sbjct: 575 MGVFLTN--------------------FAERMDTMANI---------------------- 592

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+PL                      +L  G+N +VA + + G
Sbjct: 593 -------------LYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 629

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +   +       
Sbjct: 630 YNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDK 689

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G++  G  V+  DI++GK  P         ++       +K    RD S  + S  
Sbjct: 690 LDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTE 742

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 743 NGIVDQVMLTTNAEGLK 759


>gi|194591897|gb|ACF76529.1| RNA polymerase beta subunit [Mycoplasma conjunctivae HRC/581]
          Length = 595

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 136/415 (32%), Positives = 188/415 (45%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +N GD++    +      +   + +L A       +  D  +     V   V 
Sbjct: 248  IVKVGQTINKGDLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I  +    K   S +        L    +  +  LD N   R+   +   + + G  
Sbjct: 307  -TSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDANGIVRIGSEVNTGDILVGRT 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + W +  +Q +     V+  +        I+           
Sbjct: 366  SPKGEDNPTPE--DKLMSAIWGKKTLQQKDTSLRVKHGEGGTVIDVQIISRDL------- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD++  GV  +VKV VA KR I+ GDKMAGRHGNKG+VS +LP EDMPFL+DGTPVDI
Sbjct: 417  --GDNLEDGVGMIVKVLVAQKRKIKVGDKMAGRHGNKGVVSIVLPVEDMPFLEDGTPVDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG+A   L  K  + + D      +  L            
Sbjct: 475  LLNPQGVPSRMNIGQVLELHLGFAAKKLNTKFVTPVFDGIKLETMQELFR---------- 524

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                ++G+P                        ESG+  LYDG+
Sbjct: 525  --------------------EAGIP------------------------ESGKFTLYDGI 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG+PFD  V+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 541  TGQPFDNKVSVGYMYMLKLQHMVDDKMHARSVGPYSLTTQQPLGGKSQNGGQRFG 595



 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 206/425 (48%), Positives = 283/425 (66%), Gaps = 8/425 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + +
Sbjct: 1   QINPLGEMANKRRVTSLGPGGLNRETAQFEVRDVHATHYGRICPVETPEGQNIGLILNFS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            FA+ N YGFI TPY KV +  V  +   +L+A EE     AQ++ +++E      + V 
Sbjct: 61  VFAKTNPYGFILTPYYKVTNKVVDYSKPHWLTAAEEFGLAFAQSSIAINEKNEIIADKVT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     ++V   ++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPLLK+
Sbjct: 121 VRKNQTYLVVDASQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLLKS 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+ES VA  S   I ++  G+V  VDA +IVI   E            Y L  
Sbjct: 181 EAPLVATGIESDVALYSSTNIRSEVDGVVSFVDAKKIVITDYEDKQ-------HTYFLRY 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F++SNQ T + Q P+VKVG  + + D+I DGPSTD G+LALG+N+LVAF  W+GYN+ED+
Sbjct: 234 FEKSNQETLIIQHPIVKVGQTINKGDLICDGPSTDNGELALGKNVLVAFSTWYGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++ISE++V +DVFTSIHI+E  +  R +K G + +T D+PN S     ++D  GI+ +G+
Sbjct: 294 IIISEKLVKDDVFTSIHIQEQTIKFRSSKAGNDILTADLPNSSNRSKAHLDANGIVRIGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EVN GDILVG+ +PKGE   TPE+KL+ AI+G+K +  +DTSLRV  G  GTV+DV+I +
Sbjct: 354 EVNTGDILVGRTSPKGEDNPTPEDKLMSAIWGKKTLQQKDTSLRVKHGEGGTVIDVQIIS 413

Query: 947 RHGID 951
           R   D
Sbjct: 414 RDLGD 418


>gi|83763755|emb|CAJ00211.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12D10]
          Length = 358

 Score =  321 bits (822), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 188/368 (51%), Positives = 258/368 (70%), Gaps = 13/368 (3%)

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
              GTG+E  +A  SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ R
Sbjct: 2    LYGTGIERNIAVDSGVTAVAKRGGQVQSVDASRIVVKVNEDELIPGEAGIDIYNLTKYTR 61

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFE+S+L+
Sbjct: 62   SNQNTCINQRPTVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEESILV 121

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 122  SERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVK 181

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G
Sbjct: 182  GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDG 241

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S
Sbjct: 242  VEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLARVRAVLINGG-------------YS 288

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
               +    R QW +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PG
Sbjct: 289  EAKLDAIGRKQWLELTIEDDALQSQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPG 348

Query: 1070 VLRVVKVF 1077
            VL++VKV+
Sbjct: 349  VLKIVKVY 356


>gi|284998387|ref|YP_003420155.1| hypothetical protein LD85_2132 [Sulfolobus islandicus L.D.8.5]
 gi|284446283|gb|ADB87785.1| conserved hypothetical protein [Sulfolobus islandicus L.D.8.5]
          Length = 1131

 Score =  321 bits (822), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 113/590 (19%), Positives = 191/590 (32%), Gaps = 105/590 (17%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 616  IEYLDAEEEENGYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 675

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 676  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 733  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEPGV 783

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 784  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 841

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 842  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRVPSIGDKFASRHGQKG 889

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   DI+LNP  +PSRM +GQI E   G                
Sbjct: 890  VIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAA------------ 937

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 938  -----------------------------------------LSGNIVDATP-FYKTPIEQ 955

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           + YDG +G+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 956  LQNEILKYGYLPDATEVTYDGRSGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-------- 1330
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD    RT +Y         
Sbjct: 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSD----RTTIYVCDQCGYIG 1071

Query: 1331 ----------SIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                        + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1072 WYDKNKNKYICPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILEDR 1121



 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 170/1133 (15%), Positives = 338/1133 (29%), Gaps = 228/1133 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L+     SY+ F+             LQ        I        +         P+   
Sbjct: 26   LVRQHLDSYNDFVRNK----------LQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRE 75

Query: 86   -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +   R+LTYA PL +T+  +  +++             + +Y+GDLP+M
Sbjct: 76   SDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEP----------EEVYIGDLPIM 125

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F++ G +R++V+Q   +P      D G+   
Sbjct: 126  LKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV-DTGKTGS 184

Query: 175  SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
            +  + +  +II      + + + IE       HV       K+P    + ALG+ ++   
Sbjct: 185  N--ITHTAKIISSTAGYR-VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTD--- 238

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                  IVY+   D          L   + +++    +D     +  G+K  + + K   
Sbjct: 239  ----RDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQ 294

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
             + +  +  LG ++D              +  E+Y+   +  D+       L        
Sbjct: 295  IIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFA 354

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                + +   V +  Y          K    AL+      RP D+ T  +  ++    + 
Sbjct: 355  SLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALV------RP-DIVTERIRHALATGNWV 407

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                     + R      L+      +  + +       + L   + G+    +  +   
Sbjct: 408  GGRTGVSQLLDRTNWLSMLSHLRRV-ISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSAVCEFFCS 519
            +  V+++  M +    +    +E+++ E       + +    +    +       +   +
Sbjct: 467  SGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILN 526

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +L         L++    RR +      V       +            C +       
Sbjct: 527  GRLVGYYRDGEELAKKIRERRRNGEISDEVNVGHIVTD----FINEVHVNCDSGRVRRPL 582

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            I + +      R +    +++      D      + YL A EEEN Y+A   S L  +  
Sbjct: 583  IIVSNGNPLVTREDIE-KLDSGSITFDDLVRQGKIEYLDAEEEENGYVALEPSDLTPEH- 640

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                    ++     ++ I AS+IP+ E++ S R      M +Q
Sbjct: 641  ----------------------THLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQ 678

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            A+ L  A                                                + + +
Sbjct: 679  ALGLYAANYQL-----------------------------------------RTDTRAHL 697

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y               QRPLV    + R  DII             G N ++A + + 
Sbjct: 698  LHYP--------------QRPLV----QTRALDIIGYTN------RPAGNNAILAVISFT 733

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLK 874
            GYN EDS++++   V   ++ S     +         G E+              +E  +
Sbjct: 734  GYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYR 793

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++ G++    EV  GD+L+GK++P        E    +A         RDTS+    G
Sbjct: 794  LLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK--------RDTSIVTRHG 845

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV---ILDRNIYSRLMEILC 991
              G V              +  +  E  +   L + +  +     I D+       + + 
Sbjct: 846  EMGIV--------------DLVLITETAEGNKLVKVRVRDLRVPSIGDKFASRHGQKGVI 891

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G         +    V+   +++ +            E +     +L      +    + 
Sbjct: 892  GMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKT 951

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
              +    +I     +P                    D   GR G K I SRI 
Sbjct: 952  PIEQLQNEILKYGYLPDATEVT-------------YD---GRSGQK-IKSRIY 987


>gi|46669|emb|CAA32924.1| RNA polymerase subunit B (AA 1-1126) [Sulfolobus acidocaldarius]
          Length = 1126

 Score =  321 bits (822), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 120/619 (19%), Positives = 205/619 (33%), Gaps = 102/619 (16%)

Query: 777  NQRPLVKVGD--EVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            N  PLV   D  +++  +I  D        +  D     N  VA  P         + I 
Sbjct: 582  NGTPLVDTEDIKKLKNGEITFDDLVKQGKIEFIDAEEEENAYVALNPQDLTPDHTHLEIW 641

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
               +   + + I   E     R+T              S   ++         +      
Sbjct: 642  PSAILGIIASIIPYPEHNQSPRNTYQSAMAKQSLGLYASNYQIR---TDTRAHLLHYPQM 698

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
              +    +   G +        + AI      ++ D+ +   S +   +     F     
Sbjct: 699  PLVQTRMLGVIGYNDRPAGANAILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFF----- 753

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSR-LMEILCGQNAVSGPKGFKKSTVLS 1009
                R  S E  +      DK        +    +    +L     VS     K   VL 
Sbjct: 754  ----RLYSTEEVKYPGGQEDKIVTPEAGVKGYKGKDYYRLLEDNGVVSPEVEVKGGDVLI 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
              +       ++ + + +  K   ++  +    E     L    +               
Sbjct: 810  GKVSPPRFLQEFKELSPEQAKRDTSI--VTRHGENGIVDLVLITE------------TLE 855

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
              ++VKV V   R  + GDK A RHG KG+V  ++   DMP+   G   DI+LNP  +PS
Sbjct: 856  GNKLVKVRVRDLRIPEIGDKFATRHGQKGVVGILIDQVDMPYTAKGIVPDIILNPHALPS 915

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +GQI E   G      GK +                                     
Sbjct: 916  RMTIGQIMEAIGGKYAALSGKPVD------------------------------------ 939

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP  +    + +   +           ++YDG TG+     +
Sbjct: 940  -----------------ATPFLETPKLQEMQKEILKLGHLPDSTEVVYDGRTGQKLKSRI 982

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
              G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+  +G A 
Sbjct: 983  LFGIVYYQKLHHMVADKMHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAM 1042

Query: 1310 VLQEMLTIKSD-------DVVG------RTR-VYESIVAGND--TFETGTPESFNVLVKE 1353
            ++++ L   S        D  G      R++  Y   V G+           +F +L++E
Sbjct: 1043 LIKDRLLDNSYKAVVYICDQCGYVGWYDRSKNRYVCPVHGDKSVLHPVTVSYAFKLLIQE 1102

Query: 1354 MQALGLSIDLENSRTKNSA 1372
            + ++ +S  L      N  
Sbjct: 1103 LMSMVISPRLILGEKVNLG 1121



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 141/991 (14%), Positives = 294/991 (29%), Gaps = 219/991 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+     S++ FL             LQ        I        ++     ++ P    
Sbjct: 20  LVRQHLDSFNDFLRNK----------LQQVIYEQGEIVTEVPGLKIKLGKIRYEKPSIRE 69

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  +    +   R+LTY+ P+ +++  +  +++               IY+GDLP+
Sbjct: 70  TDKGPMREITPMEARLRNLTYSSPIFLSMIPVENNIEGEPI----------EIYIGDLPI 119

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKG 170
           M K                         G F++ G ++++++Q   +     + +     
Sbjct: 120 MLKSVADPTSNLPIDKLIEIGEDPKDPGGYFIVNGSEKMIIAQEDLATNRVLVDYGKSGS 179

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-------------KVPVTSF 217
             +   K+  +      +             + V I+R +             ++P    
Sbjct: 180 NITHVAKVTSSAAG--YR-------------VQVMIERLKDSTIQISFATVPGRIPFAII 224

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           + ALG  ++         IVY+   D          L   + ++S+   +D     +  G
Sbjct: 225 MRALGFVTD-------RDIVYAVSLDPQIQNELLPSLEQASSITSAEEALDFIGNRVAIG 277

Query: 278 KKLTSGLLK---SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-- 332
           +K  + + K    + +  +  LG + +              +  E+Y+   +  D+    
Sbjct: 278 QKRENRIQKAEQVIDKYFLPHLGTSPEDRKKKGYYLASAVNKILELYLGRREPDDKDHYA 337

Query: 333 ---LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              +            + +   V +  Y          +    AL+         D+ T 
Sbjct: 338 NKRVRLAGDLFTSLFRVAFKAFVKDLVYQLEKSKVRGRRLSLTALVR-------ADIITE 390

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            +  ++    +          + R      L+      V  + +       + L   + G
Sbjct: 391 RIRHALATGNWVGGRTGVSQLLDRTNWLSMLSHLRRV-VSSLARGQPNFEARDLHGTQWG 449

Query: 450 K-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           +    +  +   +  V+++  + +    +    +ER   E       D +      N   
Sbjct: 450 RMCPFETPEGPNSGLVKNLALLAQVSVGINESVVERVAYELGVVSVEDVIRRISEQNEDV 509

Query: 509 VVSAVCE--FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                    +     L   E+      +I  +RR   L         A   + +VH    
Sbjct: 510 EKYMSWSKVYLNGRLLGYYEDGKELAKKIRESRRQGKLSDEVNVAYIATDYLNEVHIN-- 567

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
              C A       I +V++ T          ++       D      + ++ A EEEN Y
Sbjct: 568 ---CDAGRVRRPLI-IVNNGTPLVDTEDIKKLKNGEITFDDLVKQGKIEFIDAEEEENAY 623

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +A     L  D                          ++  P  ++ I AS+IP+ E++ 
Sbjct: 624 VALNPQDLTPDH-----------------------THLEIWPSAILGIIASIIPYPEHNQ 660

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           S R      M +Q++ L  +                                        
Sbjct: 661 SPRNTYQSAMAKQSLGLYASNYQI------------------------------------ 684

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                   + + +  Y               Q PLV+                    D  
Sbjct: 685 -----RTDTRAHLLHYP--------------QMPLVQTRMLGVIG----------YNDRP 715

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            G N ++A M + GYN EDS+++++  +   ++ S     +         G E+      
Sbjct: 716 AGANAILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFFRLYSTEEVKYPGGQEDKIVTPE 775

Query: 867 -----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                   ++  + +++ G++    EV  GD+L+GK++P        E    +A      
Sbjct: 776 AGVKGYKGKDYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK----- 830

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              RDTS+    G +G V  V I      +K
Sbjct: 831 ---RDTSIVTRHGENGIVDLVLITETLEGNK 858


>gi|207093298|ref|ZP_03241085.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 262

 Score =  321 bits (822), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 107/270 (39%), Positives = 170/270 (62%), Gaps = 9/270 (3%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVS 78
           K P  +++P+L+ +Q+ SYD FL       +    G++  FKS+FPI        LE+  
Sbjct: 1   KTPTDLEVPNLLLLQRDSYDSFL----YSKDGKESGIEKVFKSIFPIQDEHNRITLEYAG 56

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSIYMGDLPL 137
            EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K SIKDIKEQSI++ ++PL
Sbjct: 57  CEFGKSKYTVREVMERGITYSIPLKIKVRLILWEKDTKSGEKNSIKDIKEQSIFIREIPL 116

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT+  +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+G W+  E+D
Sbjct: 117 MTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDRGSWLYFEYD 175

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           SKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D +  P ++ D    
Sbjct: 176 SKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLD--AN 233

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            ++   L D   G+ ++ +GKKLTS  +K 
Sbjct: 234 QRMEFDLKDSQ-GKIILLAGKKLTSRKIKE 262


>gi|83763741|emb|CAJ00204.1| putative DNA-directed rna polymerase, beta subunit [Vibrio sp. 14A09]
          Length = 355

 Score =  320 bits (821), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 193/368 (52%), Positives = 258/368 (70%), Gaps = 13/368 (3%)

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            F GTG+E  VA  SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ R
Sbjct: 1    FSGTGIERNVAVDSGVTAVAKRGGLVQSVDASRIVIKVNEEELVPGEAGIDIYNLTKYTR 60

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+
Sbjct: 61   SNQNTCINQRPTVLPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILV 120

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 121  SERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVK 180

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R G
Sbjct: 181  GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRDG 240

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S
Sbjct: 241  VEKDKRALEIEQMQLKEAKKDITEEFQILEGGLLARVRTLLLAAG-------------TS 287

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
               +    R QW +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ PG
Sbjct: 288  EVKLDAMDRKQWLEITLDDESQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAPG 347

Query: 1070 VLRVVKVF 1077
            VL++VKV+
Sbjct: 348  VLKIVKVY 355


>gi|194303500|gb|ACF41173.1| RNA polymerase beta subunit [Mycoplasma canimucosale]
          Length = 595

 Score =  320 bits (821), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 206/435 (47%), Positives = 304/435 (69%), Gaps = 10/435 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN +GF+ETPY +V +G V  ++ VYL+A +E    IAQ+   +D++    +  + 
Sbjct: 61  TYAKVNEFGFLETPYYRVENGLVDYSEPVYLTAADEMGYKIAQSTVKVDKNNQIIDNNIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R      +   ++IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+A
Sbjct: 121 IRHNYTYQIGNADEIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLEA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP+V TG+ES +AK S    VAK  G+VE VD  +I +R+++G       G+D Y L  
Sbjct: 181 EAPYVATGIESEIAKYSSGNFVAKADGLVEFVDGRKIKVRNLKG-------GLDTYNLKN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQ+T ++Q+PLVK G E+++  ++ DG S   G+LALG+N+LVAF  + GYN+ED+
Sbjct: 234 FQRSNQDTVIHQKPLVKEGQEIKKGQLLVDGSSFQNGELALGKNVLVAFSTYKGYNYEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ VG+
Sbjct: 294 VILNERLVKDDVFTSIHIEEQTIQFRSSKAGDDELTSDIPNVSKYSTRHLDELGIVRVGS 353

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           +V PGD+LVG+++PKG+   + EEKLL A+  ++   V+DTSL+V +G  GTV+ V I +
Sbjct: 354 DVVPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQTPVKDTSLKVKNGHGGTVIGVEILS 413

Query: 947 RHGIDKNERSISVER 961
           R    K++    +++
Sbjct: 414 REN--KDQLEDGIDK 426



 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 131/527 (24%), Positives = 200/527 (37%), Gaps = 82/527 (15%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW--HGYNFEDSMLISERMV 834
            NQ   V  G      +  A+              +L A  P+   G   E +   S   V
Sbjct: 143  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLEAEAPYVATGIESEIAKYSSGNFV 202

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ++       ++  ++  R+ K G +         S +    I +  ++  G E+  G +L
Sbjct: 203  AKADGLVEFVDGRKIKVRNLKGGLDTYNLKNFQRSNQDTV-IHQKPLVKEGQEIKKGQLL 261

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRH 948
            V   + +    +   + +L A    K  +  D  +            S  + +  I  R 
Sbjct: 262  VDGSSFQN-GELALGKNVLVAFSTYKGYNYEDAVILNERLVKDDVFTSIHIEEQTIQFRS 320

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                ++   S     +   +    DE  I+         ++L G+ +  G     +   L
Sbjct: 321  SKAGDDELTSDI-PNVSKYSTRHLDELGIVRVGSDVVPGDVLVGRVSPKGDDNPSQEEKL 379

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
               ++         Q     +     V++          IL    K         D +  
Sbjct: 380  LLAVLQ--------QRQTPVKDTSLKVKNGHGGTVIGVEILSRENK---------DQLED 422

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDM              P    
Sbjct: 423  GIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDM--------------PH--- 465

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
                     E                   D   N    P R  + +V+            
Sbjct: 466  --------LE--------------DGTPVDVMLNPQGVPSRMNIGQVL------------ 491

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                +              T  FDG  +EAI  +++ A+L  SG+ IL D +TGE FD P
Sbjct: 492  ---EIHLGMAARSLNTKFVTRAFDGIKKEAIYDVIKEANLPVSGKQILIDPITGEKFDNP 548

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            V+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 549  VSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 595


>gi|167950500|ref|ZP_02537574.1| DNA-directed RNA polymerase, beta subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 176

 Score =  320 bits (821), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 87/170 (51%), Positives = 117/170 (68%)

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             P FDV +C  R  TYA PL++ +RL+++D +   G+  +KDI+EQ +YMG++PLMT  
Sbjct: 2   GEPVFDVRECQLRGTTYAAPLRVLVRLVIYDKEAPAGSNVVKDIREQEVYMGEMPLMTDT 61

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI 201
           GTFVI G +R++VSQLHRSPG+ FDHDKG+   SGKLL++ R+IP +G W+D EFD KD 
Sbjct: 62  GTFVINGTERVIVSQLHRSPGVFFDHDKGKTHSSGKLLFSARVIPYRGSWLDFEFDPKDN 121

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
           + VRIDRRRK+P T  L ALG D+E+IL  F+    +S         L A
Sbjct: 122 VFVRIDRRRKLPATVLLRALGYDTEQILGMFFETDTFSLTKRTVKVNLGA 171


>gi|39978199|ref|XP_370487.1| hypothetical protein MGG_06984 [Magnaporthe oryzae 70-15]
 gi|145013440|gb|EDJ98081.1| hypothetical protein MGG_06984 [Magnaporthe oryzae 70-15]
          Length = 1158

 Score =  320 bits (821), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 110/499 (22%), Positives = 183/499 (36%), Gaps = 95/499 (19%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   +         ++F 
Sbjct: 735  YPQRPMVITKTIELIHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVFR 794

Query: 947  RHGIDK----NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
            +H  +     N +S  +   +I+       ++   +D +  +R+     G    SG    
Sbjct: 795  KHTAELQTYANNKSEKISGPEIDERTGKPAEKYAAIDSDGLARV-----GYRIHSGEVML 849

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            +K T          P  Q       D       E+      ++ S ++    ++ EK   
Sbjct: 850  RKLT----------PIDQGSTGIGNDVGSNDYRETSLSYRVSNPSYIDKVMVSQTEKEHI 899

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                      + KV     R  + GDK + RHG KG+V  I+  EDMPF   G   DI++
Sbjct: 900  ----------LAKVQTRQTRRPELGDKFSSRHGQKGVVGIIVEQEDMPFADSGLVPDIIM 949

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM VG++FE   G A +  G                                 
Sbjct: 950  NPHGFPSRMTVGKLFECLTGKASIVEG--------------------------------- 976

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                              + G   +   F     E +   L        G+     G+TG
Sbjct: 977  ----------------NRRYGYGDA---FRSHPVEEMGKALIERGFSWEGKDYFTSGITG 1017

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G IY  +L HMV DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1018 EPLEAYLFNGPIYYQRLKHMVQDKMHSRAKGPRAILTRQPTEGRSRDGGLRLGEMERDCL 1077

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVL 1350
             AYGA+ +L E L + SD    D+  R  ++     G         +  E   P +  +L
Sbjct: 1078 IAYGASQLLLERLMLSSDATKIDICQRCGLFGY--KGYCQTCKSTKEVTEMTMPYAAKLL 1135

Query: 1351 VKEMQALGLSIDLENSRTK 1369
            V+E+ ++ + + L      
Sbjct: 1136 VQELISMNVGVRLVLEDEF 1154



 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 121/939 (12%), Positives = 249/939 (26%), Gaps = 188/939 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S++ F+   I    + N       +S            LEF       P    
Sbjct: 45  LVKQHIDSFNFFINTEIKEIVKAN----RIVRS-----DVESGFFLEFTDIRVGKPNRAE 95

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TYA P+K+ +             +  K +  +++ +G +P
Sbjct: 96  YSDIKAQNEVSPMECRLRDMTYAAPIKVDI----------AYFRDKKKVLRKNVTLGRMP 145

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 146 IMLKSSNCWLSGANNAEMEDMNECPLDPGGYFIINGTEKVILIQEQLSKNRVIVEADEKN 205

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL- 221
           ++    + +               + K   +V + + R           +P+   L AL 
Sbjct: 206 NVISASVTSST------------HERKSKTYVTLKKERITLAHNTLVEPIPIAIILKALG 253

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+   EI+     +    Q      F  +A   +   + S   +        + S +  T
Sbjct: 254 GLPDHEIIQLVAGEDARYQDDFAVNFDDAARAGVFTQQQSLEYIGSR---VKMGSNRFKT 310

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            G     +    + L   ++ + G +V    ++      Y+ A  V              
Sbjct: 311 PGGQAPRRNNAEEGLEALANMIIG-HVPILDLDFYPKACYV-AMMVRRVLMAAHDHKLVD 368

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG------DVSTFSVAES- 394
               +           +         K   D   +I +V+R        D      A S 
Sbjct: 369 DRDFVGNKRLELAGQMLSLLFEDLFKKFLVDLRFNIDKVLRKSNRGVAFDPLNSITATSG 428

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
                   +      TV R  MN          + +I    ++  I    +         
Sbjct: 429 HITAGMNRAISSGNWTVKRFNMNRAGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPR 488

Query: 455 DIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
            +       + +           +  L +   I        +   +      A+ + +  
Sbjct: 489 ALQPSQWGMLCTSDTPEGEACGLVKNLALMTHITTHFEEDPVKEWILAMDSGAEALSNFS 548

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                +     +  +    +   +             R         +   ++       
Sbjct: 549 GSEMHTPGTFVITVNGTPFALTWNPEEF-CKKFRDTRRKGELSAFVSISINYHFATVNIA 607

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK---VTNDVVYLSAMEEENRYIAQA 630
           T EG        + +  +      +E+  +   D         V YL   EE++  +A  
Sbjct: 608 TDEGRICRPYIIIENGVQRIKEEHLESLRQGDKDFDYFLNNGIVEYLDVNEEQDTLVALY 667

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +                             ++  P  ++   A LIPF  ++ S R 
Sbjct: 668 EKDVTPAH-----------------------THLEIEPFTILGAVAGLIPFPHHNQSPRN 704

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+                                           I   + 
Sbjct: 705 TYQCAMGKQAIGA-----------------------------------------IAYNQF 723

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +   +     +Y               QRP+V          I           L  G+N
Sbjct: 724 NRIDTLLYTLVYP--------------QRPMV----------ITKTIELIHYDKLPAGQN 759

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN--- 867
             V  M + GY+ ED++++++              +     +       E          
Sbjct: 760 ATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVFRKHTAELQTYANNKSEKISGPEIDER 819

Query: 868 --VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                E    ID  G+  VG  ++ G++++ K+TP  + 
Sbjct: 820 TGKPAEKYAAIDSDGLARVGYRIHSGEVMLRKLTPIDQG 858


>gi|78714201|gb|ABB51083.1| RNA polymerase beta subunit [Mycoplasma primatum]
          Length = 592

 Score =  320 bits (821), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 209/423 (49%), Positives = 299/423 (70%), Gaps = 8/423 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++
Sbjct: 2   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY +V +  V  NDVVYL+A +E    IAQ+  ++DE+    ++ +  R
Sbjct: 62  ANVNEYGFLQTPYFRVNNAVVDYNDVVYLTAADEFGFNIAQSTITVDENNRIVDDTLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+     +DFI+ + +Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 KNYSYIIGKASDVDFIEVASRQMVSVAAGCIPFLENDDANRALMGSNMQRQAVPLLETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG E+ +AK S A   AK  G VE VD  +I IR+++  LD        Y L  FQ
Sbjct: 182 PFVATGTEADIAKYSAANFRAKNDGKVEYVDGSKIKIRNLKETLD-------TYNLKNFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T  +Q+PLVKVGD++ + D++ DG S   G+L+LG+N+LVAF  + GYN+ED+++
Sbjct: 235 RSNQDTVTHQKPLVKVGDQISKGDLLVDGSSFKDGELSLGKNLLVAFTTYKGYNYEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+  +DV TSIHIEE  +  R +K G +E+TR+IPNVS+  ++++DE GI+ +G+EV
Sbjct: 295 LNERLAKKDVLTSIHIEEQTIQFRTSKAGTDELTREIPNVSKYSIRHLDEHGIVLIGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL AI G++ ++V+DTSL+V +G +GTV+ V I +R 
Sbjct: 355 VPGDVLVGRVSPKGDDNPSREEKLLAAILGQRQMNVKDTSLKVKNGHNGTVIGVEILSRE 414

Query: 949 GID 951
             D
Sbjct: 415 NKD 417



 Score =  296 bits (757), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 127/420 (30%), Positives = 188/420 (44%), Gaps = 81/420 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG------ 934
            ++ VG +++ GD+LV   + K +  ++  + LL A    K  +  D  +           
Sbjct: 247  LVKVGDQISKGDLLVDGSSFK-DGELSLGKNLLVAFTTYKGYNYEDAIILNERLAKKDVL 305

Query: 935  VSGTVVDVRIFNRHGID-KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             S  + +  I  R      +E +  +    +   +    DE  I+         ++L G+
Sbjct: 306  TSIHIEEQTIQFRTSKAGTDELTREI--PNVSKYSIRHLDEHGIVLIGSEVVPGDVLVGR 363

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             +  G     +   L + ++                  QR +       +          
Sbjct: 364  VSPKGDDNPSREEKLLAAILG-----------------QRQMNVKDTSLKVKNGHNGTVI 406

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              +I   +  D +  G+  +VKV +A+KR I+ GDKM+GRHGNKG+VS ILP EDMP L+
Sbjct: 407  GVEILSRENKDQLEDGIDMIVKVSIAVKRKIRVGDKMSGRHGNKGVVSIILPEEDMPHLE 466

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGTP+D+++NP GVPSRMN+GQ+ E HLG A   LG K  + + D      I  +     
Sbjct: 467  DGTPIDVMVNPQGVPSRMNIGQVLEVHLGMAARKLGCKFVTPVFDGVTKEQIQDV----- 521

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                       ++G+PV                        SG+
Sbjct: 522  -------------------------TLEAGLPV------------------------SGK 532

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L D +TGE  D PV+VG +YM KLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 533  YTLIDPITGEKMDNPVSVGIMYMFKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|29788820|gb|AAP03366.1| putative RNA polymerase III [Oryza sativa Japonica Group]
          Length = 1174

 Score =  320 bits (821), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 104/506 (20%), Positives = 175/506 (34%), Gaps = 85/506 (16%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    A+      D+ D  +   S +   
Sbjct: 738  DSLLYLLVYAQRPLLTTKTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRG 797

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                    ++ + K +       ++I    RDKD   +  +            G    + 
Sbjct: 798  FGRCIAMKKYTVTKEK-YEGGYSDRIVKPQRDKDGALLKQNMRALDEDGFAAPGLIIRNH 856

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T  ++   S    +                      Y+ S ++ +        
Sbjct: 857  DIYVNKQTPRNTKRDSGAHLTD-------------------RDYKDSPAVYKGVDGETTV 897

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              +           ++K  +   R  + GDK + RHG KG+   I+  ED PF + G   
Sbjct: 898  VDRVMLCSDTDEKLIIKCIIRHTRRPEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICP 957

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM +G++ E   G A V  G+          +                 
Sbjct: 958  DLIMNPHGFPSRMTIGKMIELLGGKAGVSCGQFHYGSAFGEPSGNAD------------- 1004

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  E I+  L       +G+ +LY 
Sbjct: 1005 ------------------------------------KVEDISRTLVKHGFSYNGKDLLYS 1028

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+ G P    V +G IY  KL HMV DK++AR++G   L+T+QP  G+S  GG RLGEME
Sbjct: 1029 GILGHPCQAYVFMGPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEME 1088

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYESIVA---------GNDTFETG 1342
              C+ AYGA+ ++ E L I SD          G    Y   +          G +  +  
Sbjct: 1089 RDCLIAYGASMLIFERLLISSDPYQVQVCRKCGLLGYYNHKLKASYCSMCKNGENMAKMR 1148

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRT 1368
             P +  +L +E+QA+ +   L+ +  
Sbjct: 1149 MPYACKLLFQELQAMNVVPRLKLTEG 1174



 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 105/725 (14%), Positives = 221/725 (30%), Gaps = 113/725 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLEFVSYEFDPP--- 84
           L++    S+++F+           +G++   K+   I A +  +  L + S     P   
Sbjct: 69  LVKEHIDSFNYFIT----------KGIRNIVKANNRIEARNNPSIFLRYNSVRVGVPSVQ 118

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 K     C   D TY+ P+   +   V    E     +          +G LP+M
Sbjct: 119 VQYIAEKITPHFCRLTDRTYSAPVLADIEYTVGKQYELKRKPNFI--------IGYLPIM 170

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDHDKGR- 171
                                      G F++KG +++++ Q   S    I     KGR 
Sbjct: 171 LRSHACVLNGKDEAELARYGECPLDPGGYFIVKGTEKVILIQEQLSKNRIIIDTDSKGRV 230

Query: 172 ---ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEE 227
               + S   + +  +I          F  K+ I++++++  + +P+   + A+GM+S++
Sbjct: 231 IASVTSSTHEIKSKTVI----------FMEKEKIYLQLNQFTKPIPIIVVMKAMGMESDQ 280

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            ++    +        +      A + +   K +   +D         +G +        
Sbjct: 281 EVAQMVGRDPRYGDLLYPSIQECAFERIYTQKQALQYMDDKVMYP--GAGNQKEGRSKSI 338

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK-----SLEEIFHSEIR 342
           L++  V  + + S       +   ++     +  + A    D+       LE        
Sbjct: 339 LRDVFVAHVPVESGNFRPKCIYTAVMLRRMMDAILNADTFDDKDYVGNKRLELSGQLISL 398

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
               L+    +N   + N      +    D  L I       +       E   +   +D
Sbjct: 399 LFEDLFKTMNSNAVELMNKTSEKIHSSPLDLSLHI------KENIITHGLERAISTGNWD 452

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G  ++  RL+                   K      L+  +  +    +  
Sbjct: 453 IKRFRMHRKGVSQVLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTP 512

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +   + E  +     S+ ++ +            S +   F   
Sbjct: 513 EGEACGLTKNLALLTHVTTDQEEGPLMNLCYSLGVEDLSLLSGEEIHASGSFLV-MFNGL 571

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHN 579
            L +  +     + +   RR   +G+          +   +H  +  GR+C         
Sbjct: 572 ILGKHRQPQRFANAMRKLRRSGIIGE--FVSIFVNEKQHCIHIASDGGRVCRPLIIADKG 629

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I  V              +    R   D      + YL   EE N  IA           
Sbjct: 630 IPRVKEHH-------MKQLRDGIRSFDDFLRDGLIEYLDVNEENNALIA----------- 671

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                       ++  V R  I  I+  P  ++ + A LIP+  ++ S R    C M +Q
Sbjct: 672 -------LYEHEDQDDVQRSSITHIEIEPLTILGVVAGLIPYPHHNQSPRNTYQCAMGKQ 724

Query: 700 AVPLL 704
           A+  +
Sbjct: 725 AMGNI 729


>gi|105969655|gb|ABF81664.1| RNA polymerase beta subunit [Mycoplasma hominis]
          Length = 594

 Score =  320 bits (821), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 213/448 (47%), Positives = 294/448 (65%), Gaps = 10/448 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA+++ YGFI++PY +V    V  ++ VY++A+EE     AQ+   + E     +E V  
Sbjct: 61  FAKIDKYGFIQSPYFRVNKKVVDFSEPVYITAIEETGYTFAQSTVHI-EGNVIVDEKVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V  E +DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNEYLEVNAEDVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I A R+G+V  VDA  I +         ++S  D+Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIRATRSGVVNYVDANVIKVTPE------NSSKSDVYHLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q PLVKVG ++   D++ DGPS   G+LALG+N+LV F  WHGYN+ED++
Sbjct: 234 ERSNQGTLIHQVPLVKVGQQINAGDLLVDGPSMKDGELALGKNVLVGFTTWHGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + + E GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V I +R
Sbjct: 354 VTAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQ 975
                ++    +E+     +A+ +  + 
Sbjct: 414 EFG--DQLEDGIEKIVKVSIAQKRKIQV 439



 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 128/415 (30%), Positives = 180/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG ++N GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 247  LVKVGQQINAGDLLVDGPS-MKDGELALGKNVLVGFTTWHGYNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L  N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQSIQFRHSKAGEDILTADIPNVSNYSKRFLGENGIVRVGSEVTAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVDILSREF------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP E+MP+L DGTP+DI
Sbjct: 416  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSIVLPVEEMPYLADGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D  ++  I  +       +   S
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGISHNQIRDILEEANIDVTGKS 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DGA                          
Sbjct: 534  I----------------------------VYDGA-------------------------- 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK+ ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 540  TGEPFDHPISVGIMYYLKLYHMVDDKMQARSVGPYSLITQQPLGGKSQNGGQRFG 594


>gi|52694315|emb|CAG37997.1| RNA polymerase beta subunit [Pseudomonas fluorescens bv. V]
          Length = 338

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 198/338 (58%), Positives = 260/338 (76%), Gaps = 1/338 (0%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR 
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRV 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-TEELVFCRCAGEEILVPREKIDF 663
           V D  VT+++V+LSA+EE +  IAQA++++++     + ELV  R   E  +   E +  
Sbjct: 121 VKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVIGSTELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 301 KGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGF 338


>gi|323514497|gb|ADX89818.1| RNA polymerase beta subunit [Enterobacter sp. KN/03/21]
          Length = 323

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 201/321 (62%), Positives = 251/321 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 123 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 243 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVA 814
           +ADGPSTDLG+LALG+NM VA
Sbjct: 303 LADGPSTDLGELALGQNMRVA 323


>gi|52694403|emb|CAG38041.1| RNA polymerase beta subunit [Pseudomonas fulva]
          Length = 328

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 194/327 (59%), Positives = 249/327 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  +   +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESQGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVQEGVV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR  MG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRAFMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDVVAR 301

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMP 817
            DI+ADGPSTD+G+LALG+NM VA MP
Sbjct: 302 GDIMADGPSTDMGELALGQNMRVALMP 328


>gi|194591903|gb|ACF76532.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 598

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 212/428 (49%), Positives = 295/428 (68%), Gaps = 8/428 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++ 
Sbjct: 1   QINPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNMA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-GSFTEELV 645
           S+A+++ YGFI+TPY KV DG V  ND+ YL+A+EE N   AQ++ ++DE+ G   +E V
Sbjct: 61  SYAKIDDYGFIQTPYFKVNDGVVDFNDIRYLTAIEEINFTFAQSSINIDEETGEILDERV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I + +++ID+I  + +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 121 MSRKNNEYIELDKKEIDYIGVTSRQMTSISASAIPFLENDDANRALMGSNMQRQAVPLIK 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            EAP V TG+E+ +A+ S + + A + GIV  VDA  I I+S +           IY L 
Sbjct: 181 PEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSDDEKKPS------IYFLR 234

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q+PLVKVG E++  D++ DGPS + G+LALG+N+LV F  W GYN+ED
Sbjct: 235 TFERSNQGTVIHQKPLVKVGQEIKAGDLLTDGPSMENGELALGKNVLVGFSTWFGYNYED 294

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++E++V EDV+TSIHIEE  +  R +K G + +T DIPN S    + + E GI+ +G
Sbjct: 295 AVILNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVIIG 354

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GTVV V + 
Sbjct: 355 SEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVL 414

Query: 946 NRHGIDKN 953
            R   D N
Sbjct: 415 RRDTDDTN 422



 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 127/499 (25%), Positives = 194/499 (38%), Gaps = 68/499 (13%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G +     + L +            +       + R   + + T +   E  + + D K 
Sbjct: 168  GSNMQRQAVPLIKPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSDDEKK 227

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                  R     ++  + +     ++ VG E+  GD+L    +      +   + +L   
Sbjct: 228  PSIYFLRTFERSNQGTVIHQKP--LVKVGQEIKAGDLLTDGPS-MENGELALGKNVLVGF 284

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       +  RS + +      +    +  + 
Sbjct: 285  STWFGYNYEDAVILNEKLVKEDV-YTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKR 343

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
             L  +    +   +   + + G    K     S +   +   + + Q     +     V+
Sbjct: 344  FLGEDGIVIIGSEVGPGDILVGRISPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVK 401

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                    +  +L     +         ++  G+  +VKV +A KR I+ GDKMAGRHGN
Sbjct: 402  HGHGGTVVAVDVLRRDTDD--------TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGN 453

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+VS ILP EDMP+L DGTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  S +
Sbjct: 454  KGVVSIILPEEDMPYLADGTPLDILLNPQGVPSRMNIGQVLELHLGLAARKLNCKFVSPV 513

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             D  +   I  ++                                               
Sbjct: 514  FDGISYKQIQEIQKEAGIDPSGKMTV---------------------------------- 539

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                          SG+       TGEPFD P++VG +Y LKL HMV DK++ARS G YS
Sbjct: 540  -------------YSGK-------TGEPFDNPISVGVMYYLKLYHMVDDKMHARSVGPYS 579

Query: 1277 LVTQQPLGGKSNRGGQRLG 1295
            L+TQQPLGGKS  GGQR G
Sbjct: 580  LITQQPLGGKSQNGGQRFG 598


>gi|115453445|ref|NP_001050323.1| Os03g0403100 [Oryza sativa Japonica Group]
 gi|108708688|gb|ABF96483.1| DNA-directed RNA polymerase III 130 kDa polypeptide, putative,
            expressed [Oryza sativa Japonica Group]
 gi|113548794|dbj|BAF12237.1| Os03g0403100 [Oryza sativa Japonica Group]
          Length = 1155

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 104/506 (20%), Positives = 175/506 (34%), Gaps = 85/506 (16%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    A+      D+ D  +   S +   
Sbjct: 719  DSLLYLLVYAQRPLLTTKTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRG 778

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                    ++ + K +       ++I    RDKD   +  +            G    + 
Sbjct: 779  FGRCIAMKKYTVTKEK-YEGGYSDRIVKPQRDKDGALLKQNMRALDEDGFAAPGLIIRNH 837

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T  ++   S    +                      Y+ S ++ +        
Sbjct: 838  DIYVNKQTPRNTKRDSGAHLTD-------------------RDYKDSPAVYKGVDGETTV 878

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              +           ++K  +   R  + GDK + RHG KG+   I+  ED PF + G   
Sbjct: 879  VDRVMLCSDTDEKLIIKCIIRHTRRPEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICP 938

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM +G++ E   G A V  G+          +                 
Sbjct: 939  DLIMNPHGFPSRMTIGKMIELLGGKAGVSCGQFHYGSAFGEPSGNAD------------- 985

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  E I+  L       +G+ +LY 
Sbjct: 986  ------------------------------------KVEDISRTLVKHGFSYNGKDLLYS 1009

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+ G P    V +G IY  KL HMV DK++AR++G   L+T+QP  G+S  GG RLGEME
Sbjct: 1010 GILGHPCQAYVFMGPIYYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEME 1069

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYESIVA---------GNDTFETG 1342
              C+ AYGA+ ++ E L I SD          G    Y   +          G +  +  
Sbjct: 1070 RDCLIAYGASMLIFERLLISSDPYQVQVCRKCGLLGYYNHKLKASYCSMCKNGENMAKMR 1129

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRT 1368
             P +  +L +E+QA+ +   L+ +  
Sbjct: 1130 MPYACKLLFQELQAMNVVPRLKLTEG 1155



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 105/725 (14%), Positives = 221/725 (30%), Gaps = 113/725 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLEFVSYEFDPP--- 84
           L++    S+++F+           +G++   K+   I A +  +  L + S     P   
Sbjct: 50  LVKEHIDSFNYFIT----------KGIRNIVKANNRIEARNNPSIFLRYNSVRVGVPSVQ 99

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 K     C   D TY+ P+   +   V    E     +          +G LP+M
Sbjct: 100 VQYIAEKITPHFCRLTDRTYSAPVLADIEYTVGKQYELKRKPNFI--------IGYLPIM 151

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDHDKGR- 171
                                      G F++KG +++++ Q   S    I     KGR 
Sbjct: 152 LRSHACVLNGKDEAELARYGECPLDPGGYFIVKGTEKVILIQEQLSKNRIIIDTDSKGRV 211

Query: 172 ---ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEE 227
               + S   + +  +I          F  K+ I++++++  + +P+   + A+GM+S++
Sbjct: 212 IASVTSSTHEIKSKTVI----------FMEKEKIYLQLNQFTKPIPIIVVMKAMGMESDQ 261

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            ++    +        +      A + +   K +   +D         +G +        
Sbjct: 262 EVAQMVGRDPRYGDLLYPSIQECAFERIYTQKQALQYMDDKVMYP--GAGNQKEGRSKSI 319

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK-----SLEEIFHSEIR 342
           L++  V  + + S       +   ++     +  + A    D+       LE        
Sbjct: 320 LRDVFVAHVPVESGNFRPKCIYTAVMLRRMMDAILNADTFDDKDYVGNKRLELSGQLISL 379

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
               L+    +N   + N      +    D  L I       +       E   +   +D
Sbjct: 380 LFEDLFKTMNSNAVELMNKTSEKIHSSPLDLSLHI------KENIITHGLERAISTGNWD 433

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G  ++  RL+                   K      L+  +  +    +  
Sbjct: 434 IKRFRMHRKGVSQVLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTP 493

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +   + E  +     S+ ++ +            S +   F   
Sbjct: 494 EGEACGLTKNLALLTHVTTDQEEGPLMNLCYSLGVEDLSLLSGEEIHASGSFLV-MFNGL 552

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHN 579
            L +  +     + +   RR   +G+          +   +H  +  GR+C         
Sbjct: 553 ILGKHRQPQRFANAMRKLRRSGIIGE--FVSIFVNEKQHCIHIASDGGRVCRPLIIADKG 610

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I  V              +    R   D      + YL   EE N  IA           
Sbjct: 611 IPRVKEHH-------MKQLRDGIRSFDDFLRDGLIEYLDVNEENNALIA----------- 652

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                       ++  V R  I  I+  P  ++ + A LIP+  ++ S R    C M +Q
Sbjct: 653 -------LYEHEDQDDVQRSSITHIEIEPLTILGVVAGLIPYPHHNQSPRNTYQCAMGKQ 705

Query: 700 AVPLL 704
           A+  +
Sbjct: 706 AMGNI 710


>gi|242392292|dbj|BAH80339.1| RNA polymerase subunit B' [Halobacterium salinarum]
          Length = 608

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 124/602 (20%), Positives = 204/602 (33%), Gaps = 97/602 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + V+  DI    + +    +  D     ++LV             + I  +++       
Sbjct: 82   EAVKNGDIDFEDLVEAGKVEFIDAEEEEDILVGVEEEELTADHTHLEIDPQLIFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLLHYPQKAMVNTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     V    +    F R    +  R    + 
Sbjct: 199  GYDDRPAGQNFVVAVMSYEGFNIEDALVMNKGSVE-RALSRSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   D       +           L     V+       S+VL           + 
Sbjct: 258  DRFEIPGDD-------VRGARGEDAYTHLDDDGLVNPETKVDDSSVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E          + +               ++ KV V  +
Sbjct: 311  EDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGE------------DGSKLAKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG + E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A    G+ +                                                 
Sbjct: 419  GKAGSLDGRSVDG----------------------------------------------- 431

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G  E+ I   L       SG+ ++Y G++GE  +  + VG I+  KL H
Sbjct: 432  ------TP-FTGEGEDEIRGTLEDRGFKSSGKEVMYSGVSGEKIEAEIFVGTIFYHKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA VL+E L   SD 
Sbjct: 485  MVSNKLHARSKGPVQVLTRQPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDR 544

Query: 1321 ---DVVGR-----TRVYE-------SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                V G         YE       +     D        +F +L+ EM+ALG++  LE 
Sbjct: 545  EEIHVCGNCGMTAVENYEQRRVYCPNCEEETDVHSIEMSYAFKLLLDEMKALGIAPRLEL 604

Query: 1366 SR 1367
              
Sbjct: 605  EE 606



 Score = 41.6 bits (96), Expect = 0.97,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 59/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +   E       +I   RR   + +      R       V+        P    
Sbjct: 10  YVNGSLVGTHENPEELAEQIREARRRGEVSEMVNVSVRDRTGEVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +V+     A  N     E       D      V ++ A EEE+  +      L 
Sbjct: 70  ENGE-PVVTQEEVEAVKNGDIDFE-------DLVEAGKVEFIDAEEEEDILVGVEEEELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 ADH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPAANYRI 173


>gi|323447819|gb|EGB03728.1| hypothetical protein AURANDRAFT_39265 [Aureococcus anophagefferens]
          Length = 1222

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 133/322 (41%), Gaps = 80/322 (24%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VKV V   R  + GDK A RHG KG+   I+  EDMPF   G   D+++NP G PSRM 
Sbjct: 918  LVKVMVRQCRRPEVGDKFASRHGQKGVCGAIVSQEDMPFSDTGVCPDVIMNPHGFPSRMT 977

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VG+I E   G   V  G++        K                                
Sbjct: 978  VGKIIELVAGKCGVCSGRQAYGTAFGEKTGSA---------------------------- 1009

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                               D A E   +  L        G+ +LY G++GEP    V +G
Sbjct: 1010 -------------------DCASEA--SCTLLKHGFSYIGKDMLYSGISGEPLRVYVFMG 1048

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             ++  KL HMV DK++AR+ G  + +T+QP  G+S  GG RLGEME  C+ +YGAA ++ 
Sbjct: 1049 PVFYQKLKHMVMDKMHARARGPRAQLTRQPTEGRSRDGGLRLGEMERDCLISYGAANLIT 1108

Query: 1313 EMLTIKSD--DVV--------GRTRVY------ESIV-----------AGNDTFETGTPE 1345
            E L I SD  DV         G    Y      E I            +         P 
Sbjct: 1109 ERLMISSDQFDVHVCEGCGLLG----YSTAQNTERIDSTFTSWCQNCRSNEQMARICIPY 1164

Query: 1346 SFNVLVKEMQALGLSIDLENSR 1367
            +  +L +E+Q++ ++  L+   
Sbjct: 1165 ACKLLFQELQSMNVTPRLKLED 1186



 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 138/1046 (13%), Positives = 272/1046 (26%), Gaps = 266/1046 (25%)

Query: 26  IPDLIEV---QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           +P  + +     AS+D+F+   I                V P         L +      
Sbjct: 22  LPHFLRLMNQHIASFDYFIETEIKKVVAAEPN-HTVRSEVDP------NFYLSYTDVYVG 74

Query: 83  PPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            P               +C  RD TY+ P+ + +R            +  + +  + + +
Sbjct: 75  VPSIEEDAFTSTAATPFECRLRDCTYSAPIFVDVRY----------RRGPQIVTTKRVPI 124

Query: 133 GDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHD 168
           G +P+M                           G FV+KG++++++ Q   S        
Sbjct: 125 GRIPIMLRSSQCVLHNKSWSQLEALKECPHDPGGYFVVKGVEKVILMQEQLSKN------ 178

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR---RK-------------- 211
                         R+I        IE D+K  +   I      RK              
Sbjct: 179 --------------RMI--------IELDAKGFVCATITSSTHERKSRCSIVVKPTTHGH 216

Query: 212 ------------VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSA-----ADL 254
                       +PV   L A+GM+S++ ++             F               
Sbjct: 217 RVYLKHNTLGDDIPVVVILKAMGMESDQEIAELVSSADLKIADIFVNSMEEPCAAHVKTQ 276

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED--- 311
               +     +      Q ++  +       +       +   + +  +      ED   
Sbjct: 277 KQALEYVGQAIRAKQKAQSVDGSRSQYLPHSRRPVSIEDEAREVLAHVVLSHVPVEDYDF 336

Query: 312 -----IVNGETGEIYIEAGDVIDEKSLEEIFHSEIR----DIPILYVDSVNN-NAYIRNT 361
                 +   T  +   + D       +   +  +      + +L+ D     NA ++ +
Sbjct: 337 VAKRTYIGHVTRRVLAASLDNSLLDDKDYYGNKRLELAGQLLSLLFEDLFKRFNADLKRS 396

Query: 362 LVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                 K  + A+ DI +  V R   +S   V             K D + V +V   + 
Sbjct: 397 ADLVLQKQNRTAVFDIVKSTVWRTDTISQGFVHAISTGNWVLKRFKMDRAGVTQVLSRLS 456

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNG-KGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                    R   + +          L+    G +   D         V  +    +   
Sbjct: 457 YVSAIGMMTRVNSQFEKTRKTSGPRALQLSQWGMLCPADTPEGETCGLVKNLALLAHVTT 516

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
              +E++ +                       + +        +            +   
Sbjct: 517 DAEVEKTKRSCFDLGVEQLGYLNGAELNSHPGAYLVFLNGLV-IGACRRPHKLARGLRCM 575

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRIC--------------------------PA 572
           RR   +G+              V     GR+C                          P 
Sbjct: 576 RRSKRIGEFVSVYTHTVHRAIYV-ACDGGRVCRPLIIATHGHSRLTAAQLATAFAKTYPN 634

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             S+  N G  + L S A   + G +               + Y+   EE N +IA    
Sbjct: 635 SNSQSKNDGDPNRLQSHASTQSVGTL-------DHLTTVGIIEYVDVNEENNCFIALDER 687

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L                         +   ++  P  ++ I + L+ F  ++ S R   
Sbjct: 688 ELTP-----------------------RHTHVEIDPVTILGIVSGLVAFPHHNQSPRNTY 724

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+         V T     +     + +                         
Sbjct: 725 QCAMGKQAMGS-------VATNQYERMDSLLYSLV------------------------- 752

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    Q+P+VK                     L  G N  
Sbjct: 753 -----------------------YPQKPMVKS----------RVLDLVHFDALPGGCNAT 779

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS--- 869
           +A M + GY+ ED+++++   +       + I+  +V  R    G  + T   P++    
Sbjct: 780 LAVMSYSGYDIEDAIVLNRASLDRGFMRCLVIKRHQVSIRRYANGACDRTTGPPSIELFL 839

Query: 870 ---EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                    +D  GI  VG +++   I++ +  P  +       +L  A+ G  +  V  
Sbjct: 840 QGYVFRYSALDNDGICRVGEKLHDQSIMINREMPVEDRD-----ELTPALPGRVSAFVVL 894

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   V   V+         + K
Sbjct: 895 HYKSPAPSVVDRVLLTANETDQFLVK 920


>gi|15791389|ref|NP_281213.1| DNA-directed RNA polymerase subunit B' [Halobacterium sp. NRC-1]
 gi|169237150|ref|YP_001690350.1| DNA-directed RNA polymerase subunit B' [Halobacterium salinarum R1]
 gi|1350834|sp|P15351|RPOB1_HALSA RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|43541|emb|CAA40425.1| RNA polymerase subunit B' [Halobacterium salinarum]
 gi|10582044|gb|AAG20693.1| DNA-directed RNA polymerase subunit B' [Halobacterium sp. NRC-1]
 gi|167728216|emb|CAP15004.1| DNA-directed RNA polymerase subunit B' [Halobacterium salinarum R1]
          Length = 608

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 124/602 (20%), Positives = 204/602 (33%), Gaps = 97/602 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + V+  DI    + +    +  D     ++LV             + I  +++       
Sbjct: 82   EAVKNGDIDFEDLVEAGKVEFIDAEEEEDILVGVEEEELTTDHTHLEIDPQLIFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLLHYPQKAMVNTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     V    +    F R    +  R    + 
Sbjct: 199  GYDDRPAGQNFVVAVMSYEGFNIEDALVMNKGSVE-RALSRSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   D       +           L     V+       S+VL           + 
Sbjct: 258  DRFEIPGDD-------VRGARGEDAYTHLDDDGLVNPETKVDDSSVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E          + +               ++ KV V  +
Sbjct: 311  EDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGE------------DGSKLAKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG + E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A    G+ +                                                 
Sbjct: 419  GKAGSLDGRSVDG----------------------------------------------- 431

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G  E+ I   L       SG+ ++Y G++GE  +  + VG I+  KL H
Sbjct: 432  ------TP-FTGEGEDEIRGTLEDRGFKSSGKEVMYSGVSGEKIEAEIFVGTIFYHKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA VL+E L   SD 
Sbjct: 485  MVSNKLHARSKGPVQVLTRQPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDR 544

Query: 1321 ---DVVGR-----TRVYE-------SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                V G         YE       +     D        +F +L+ EM+ALG++  LE 
Sbjct: 545  EEIHVCGNCGMTAVENYEQRRVYCPNCEEETDVHSIEMSYAFKLLLDEMKALGIAPRLEL 604

Query: 1366 SR 1367
              
Sbjct: 605  EE 606



 Score = 41.6 bits (96), Expect = 0.96,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 59/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +   E       +I   RR   + +      R       V+        P    
Sbjct: 10  YVNGSLVGTHENPEELAEQIREARRRGEVSEMVNVSVRDRTGEVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +V+     A  N     E       D      V ++ A EEE+  +      L 
Sbjct: 70  ENGE-PVVTQEEVEAVKNGDIDFE-------DLVEAGKVEFIDAEEEEDILVGVEEEELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 TDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPAANYRI 173


>gi|269913263|emb|CAY86058.1| RNA polymerase beta subunit [Gluconacetobacter diazotrophicus]
          Length = 316

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 153/318 (48%), Positives = 203/318 (63%), Gaps = 28/318 (8%)

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRI
Sbjct: 1   NGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRI 60

Query: 207 DRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQR 241
           DR+RK+PVT+ L AL                         GMD++EIL  FY ++V+++ 
Sbjct: 61  DRKRKLPVTTLLYALEGASSAAARAAKVAEGGDVDALEIRGMDADEILGYFYNQVVFTKG 120

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
              W  P  A     G K+   LVD  +GE V E+  KLT+ +++ + E   K + +   
Sbjct: 121 PKGWARPFDAE-SFRGLKLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLVGPA 178

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            L G YVA D+VN ETGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNT
Sbjct: 179 GLIGRYVAHDLVNMETGEIYAEAGEELTEVRLEALEEAGVDQLPTLAVDASN-GPWIRNT 237

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  DKN  R+DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL 
Sbjct: 238 LTVDKNTSREDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLG 297

Query: 422 LDTPDDVRHIRKEDIIAI 439
           LD PD +R +RKEDI+  
Sbjct: 298 LDAPDTIRVLRKEDILRT 315


>gi|209876614|ref|XP_002139749.1| DNA-directed RNA polymerase, beta subunit family protein
            [Cryptosporidium muris RN66]
 gi|209555355|gb|EEA05400.1| DNA-directed RNA polymerase, beta subunit family protein
            [Cryptosporidium muris RN66]
          Length = 1219

 Score =  320 bits (820), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 155/989 (15%), Positives = 295/989 (29%), Gaps = 163/989 (16%)

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
            L T+ RV ++    +      + +    +  + + ++D    +  +DD D  GN+R+   
Sbjct: 364  LETLNRVVLSHVGTIYGDLRPKAL---ILCLMARRVIDASENQSLLDDKDYYGNKRIELA 420

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            G+++   +     R     K++I                             + +   + 
Sbjct: 421  GQLISILFEDLFKRFASLTKKQIDQ---------------------------TLVRYFQT 453

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              NS    +     ++            +  R +           +       G+   L+
Sbjct: 454  KDNSSKVTSGKEDTNSNYPDCFRNLPTDIITRGMQTALSTGNWSIKRFRMERSGMTQVLS 513

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
             ++ ++A G +    R     +    V    A++     I        E  S        
Sbjct: 514  RYSYISALGIMT---RVDSQFEKARKVSGPRALQPSQWGIL-CPCDTPEGESCGLVKNLA 569

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                       + +  +  S       +AS   + ++       +  +        +   
Sbjct: 570  LTTHITTDHNPQYLIGLLFSLGVQDIASASWFEWKQHSQDGNTSLREHNLSGNAYFIFIN 629

Query: 708  APFVGTGME-SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
               +G       +A +               +                +  G     L+ 
Sbjct: 630  GALLGIHYNPETLASNLRDLRRKGYISQFVSIFCNHSQYS----VQIATDGGRLCRPLII 685

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG-----RNMLVAFMPWHGY 821
                 Q        + K   E   N  I      + G L         N+L+A    +  
Sbjct: 686  VDNGKQR-------IQKEHIENLENKQITFNDLINKGILEWIDVNEENNLLIALKEENIT 738

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
                 + I    +   V   I         R+T                + L+      I
Sbjct: 739  EETTHVEIDPLAILGVVSGLIPYPNHNQSPRNTYQCAMGKQVMGVVGLNQFLRC---DSI 795

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +             I       +   +    AI      D+ D  +   + +      
Sbjct: 796  LYLLVYPQKPLCKTRTIEMINFEQLPAGQNSSVAIMSYTGYDIEDAIIMNKASIDRGFAR 855

Query: 942  VRIFNRHGIDKNERSISVEREQI-------ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
              +  R  ++  +    +    I           +  +    +L+ +   R+ E++    
Sbjct: 856  CFVIKRQTVELQKLPNGLAECVIGPNKLLDNSSTKVYNSNWNVLEEDGICRVGEMV---- 911

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            A       K S + + + + +  +    ++ +         + +   Y     + E+   
Sbjct: 912  AEDDIIVNKVSPINTREYVGDPSQVNLSEYRL----TPIKYKGIAPSYIDRVLLTEN--- 964

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                              + K+     R  + GDK + RHG KG+V  I+  ED PF + 
Sbjct: 965  -------------SEGSHIYKIITRQTRLPELGDKFSSRHGQKGVVGLIVSQEDFPFSES 1011

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G PSRM VG++ E     A V  G                         
Sbjct: 1012 GWCPDLIMNPHGFPSRMTVGKLMELISSKASVLDG------------------------- 1046

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                     ++ G       F G   E     L       SG+ 
Sbjct: 1047 ------------------------NYRYGT-----AFGGTPVEDAAKCLIQNGFHYSGKE 1077

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L  G+TGE  +  + VG I+  KL HMV DK++AR  G   ++T+QP  G+S  GG RL
Sbjct: 1078 YLTSGITGEAIETYIFVGPIFYQKLRHMVLDKMHARGRGPRQILTRQPTEGRSKDGGLRL 1137

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG-----------------ND 1337
            GEME  C+ AYGA+ +L E L + SD       V+E+ V                   +D
Sbjct: 1138 GEMERDCLVAYGASNLLIERLMLNSD-------VFETYVCNKCGLFGYNNYCHYCRNSDD 1190

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENS 1366
                  P +  +L +E+QA+ +   ++  
Sbjct: 1191 ISIIRLPYACKLLFQELQAMNVCPRIKTK 1219



 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 140/1008 (13%), Positives = 300/1008 (29%), Gaps = 174/1008 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    SY++F+ ++I    R +        + F  +    +  +EF+      PK   
Sbjct: 56  LVKHHIESYNYFVTVDIRNIIRAHS-------NRFIKSDVDPSFFIEFLDARVGMPKLEE 108

Query: 87  -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                      C  RD+TYA P+ + +  +          +    ++++++ +G +P+M 
Sbjct: 109 NMVTIDLTPMMCRMRDITYAAPIYVDVDYV----------RGNNVVRKKNVEIGRIPVML 158

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                     G FV+KG +++++ Q   S       ++    L 
Sbjct: 159 RSKVCILYGKTPLEMINLSECPHDPGGYFVVKGTEKVILMQEQLS------KNRIIVELD 212

Query: 176 GKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILS 230
            K  Y   +       +   + +       +++R +     +P+   L A+G+++E+ L 
Sbjct: 213 NKHNYCATVTSTTAESKSRTLVVY--KNGKLYLRHNSFTDDIPLCIVLKAMGIETEQELF 270

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
                  Y   G          + ++  + +   +      +V  S         +    
Sbjct: 271 QVIGNKSYHYEGIITSLQDVHIEKIITQRQALQFMSKRMKSKVRMSFGFTGGRPNRHNPT 330

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                   + + L       D +N    +  +       E  LE +    +  +  +Y D
Sbjct: 331 Y--TEQNRSEEAL-------DRMNTSNADNTLVRQVNGIEDVLETLNRVVLSHVGTIYGD 381

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  +        +     +LLD         +    +A  + + LF D  K   S 
Sbjct: 382 LRPKALILCLMARRVIDASENQSLLDDKDYYGNKRI---ELAGQLISILFEDLFKRFASL 438

Query: 411 VGRVKMNMRL-NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +      +    T D+   +               RN    I                
Sbjct: 439 TKKQIDQTLVRYFQTKDNSSKVTSGKEDTNSNYPDCFRNLPTDIITRGMQTA-------- 490

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +    + +   RMER                                   S ++Q+    
Sbjct: 491 LSTGNWSIKRFRMER-----------------------------------SGMTQVLSRY 515

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           + +S +    R+ +       +AR     R + P+ +G +CP +T EG + GLV +L   
Sbjct: 516 SYISALGIMTRVDS----QFEKARKVSGPRALQPSQWGILCPCDTPEGESCGLVKNLALT 571

Query: 590 ARVNAYGFIETPYRKVCDGKVTND-----VVYL-------SAMEEEN-----RYIAQANS 632
             +      +     +    V +        +        +++ E N      +I    +
Sbjct: 572 THITTDHNPQYLIGLLFSLGVQDIASASWFEWKQHSQDGNTSLREHNLSGNAYFIFINGA 631

Query: 633 SLDEDGSF---TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            L    +       L   R  G          +    S +          P +  D+  +
Sbjct: 632 LLGIHYNPETLASNLRDLRRKGYISQFVSIFCNHSQYSVQIATDGGRLCRPLIIVDNGKQ 691

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD--------AI 741
            +   +++      +          +E +        ++A +   + +          AI
Sbjct: 692 RIQKEHIENLENKQITFNDLINKGILEWIDVNEENNLLIALKEENITEETTHVEIDPLAI 751

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADG-- 797
             V+  +    + + S  + Y+    ++      +NQ       +   V     +     
Sbjct: 752 LGVVSGLIPYPNHNQSPRNTYQCAMGKQVMGVVGLNQFLRCDSILYLLVYPQKPLCKTRT 811

Query: 798 -PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
               +   L  G+N  VA M + GY+ ED++++++  +         I+   V  +    
Sbjct: 812 IEMINFEQLPAGQNSSVAIMSYTGYDIEDAIIMNKASIDRGFARCFVIKRQTVELQKLPN 871

Query: 857 GPEEI--------TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM-- 906
           G  E               V       ++E GI  VG  V   DI+V K++P        
Sbjct: 872 GLAECVIGPNKLLDNSSTKVYNSNWNVLEEDGICRVGEMVAEDDIIVNKVSPINTREYVG 931

Query: 907 ------TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                   E +L    +   A    D  L   +     +   +I  R 
Sbjct: 932 DPSQVNLSEYRLTPIKYKGIAPSYIDRVLLTENSEGSHI--YKIITRQ 977


>gi|100913627|gb|ABF69712.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 599

 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 214/429 (49%), Positives = 296/429 (68%), Gaps = 8/429 (1%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + VN L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++
Sbjct: 1   DQVNPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNM 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-GSFTEEL 644
            S+A+++ YGFI+TPY KV DG V  ND+ YL+A+EE N   AQ++ ++DE+ G   +E 
Sbjct: 61  ASYAKIDDYGFIQTPYFKVNDGIVDFNDIRYLTAIEEINFTFAQSSINIDEETGEILDER 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E I + +++ID+I  + +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVPL+
Sbjct: 121 VMSRKNNEYIELDKKEIDYIGVTSRQMTSISASAIPFLENDDANRALMGSNMQRQAVPLI 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           K EAP V TG+E+ +A+ S + + A + GIV  VDA  I I+S      P      IY L
Sbjct: 181 KPEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQS------PDEKKPSIYFL 234

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             F+RSNQ T ++Q+PLVKVG E++  D++ DGPS + G+LALG+N+LV F  W GYN+E
Sbjct: 235 RTFERSNQGTVIHQKPLVKVGQEIKTGDLLTDGPSMENGELALGKNVLVGFSTWFGYNYE 294

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D+++++E++V EDV+TSIHIEE  +  R +K G + +T DIPN S    + + E GI+ +
Sbjct: 295 DAVILNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVII 354

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G+EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GTVV V +
Sbjct: 355 GSEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDV 414

Query: 945 FNRHGIDKN 953
             R   D N
Sbjct: 415 LRRDTDDTN 423



 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 119/415 (28%), Positives = 172/415 (41%), Gaps = 66/415 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+L    +      +   + +L         +  D  +     V   V 
Sbjct: 251  LVKVGQEIKTGDLLTDGPS-MENGELALGKNVLVGFSTWFGYNYEDAVILNEKLVKEDV- 308

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  RS + +      +    +  +  L  +    +   +   + + G  
Sbjct: 309  YTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVIIGSEVGPGDILVGRI 368

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V+        +  +L     +     
Sbjct: 369  SPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVLRRDTDD----- 421

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                ++  G+  +VKV +A KR I+ GDKMAGRHGNKG+VS ILP EDMP+L DGTP+DI
Sbjct: 422  ---TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPEEDMPYLADGTPLDI 478

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  S + D  +   I  ++           
Sbjct: 479  LLNPQGVPSRMNIGQVLELHLGLAARKLNCKFVSPVFDGISYKQIQEIQKEAGIDPSGKM 538

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SG+       
Sbjct: 539  TV-----------------------------------------------YSGK------- 544

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 545  TGEPFDNPISVGVMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 599


>gi|318602999|emb|CBJ04576.1| RNA polymerase beta subunit [Pseudomonas sp. R-37245]
          Length = 323

 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 190/323 (58%), Positives = 249/323 (77%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYG
Sbjct: 1   PVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  I
Sbjct: 61  RVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVI 120

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 AQASATMNDQKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 180

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R 
Sbjct: 181 NRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRV 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+AD PSTD+G+LAL
Sbjct: 241 ADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADDPSTDMGELAL 300

Query: 808 GRNMLVAFMPWHGYNFEDSMLIS 830
           G+NM +AFM W+G+NFEDS+ +S
Sbjct: 301 GQNMRIAFMAWNGFNFEDSICLS 323


>gi|52694367|emb|CAG38023.1| RNA polymerase beta subunit [Pseudomonas viridiflava]
          Length = 328

 Score =  320 bits (819), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 193/328 (58%), Positives = 253/328 (77%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 1   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 60

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++
Sbjct: 61  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEI 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IA+A++++++     +ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 121 VFLSAIEEADHVIARASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 180

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 181 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 240

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 241 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 300

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           ADGPSTD+G+LALG+NM +AFM W+G+N
Sbjct: 301 ADGPSTDMGELALGQNMRIAFMAWNGFN 328


>gi|229579766|ref|YP_002838165.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus
            Y.G.57.14]
 gi|229581565|ref|YP_002839964.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus
            Y.N.15.51]
 gi|228010481|gb|ACP46243.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus Y.G.57.14]
 gi|228012281|gb|ACP48042.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus Y.N.15.51]
          Length = 1131

 Score =  320 bits (819), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 112/590 (18%), Positives = 191/590 (32%), Gaps = 105/590 (17%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 616  IEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 675

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 676  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 733  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEPGV 783

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 784  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 841

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 842  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRVPSIGDKFASRHGQKG 889

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   D++LNP  +PSRM +GQI E   G                
Sbjct: 890  VIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAA------------ 937

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP F     E 
Sbjct: 938  -----------------------------------------LSGNIVDATP-FYKTPIEQ 955

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            + + +           + YDG +G+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 956  LQNEILKYGYLPDATEVTYDGRSGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-------- 1330
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD    RT +Y         
Sbjct: 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSD----RTTIYVCDQCGYIG 1071

Query: 1331 ----------SIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                        + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1072 WYDKNKNKYICPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILEDR 1121



 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 170/1133 (15%), Positives = 338/1133 (29%), Gaps = 228/1133 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L+     SY+ F+             LQ        I        +         P+   
Sbjct: 26   LVRQHLDSYNDFVRNK----------LQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRE 75

Query: 86   -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +   R+LTYA PL +T+  +  +++             + +Y+GDLP+M
Sbjct: 76   SDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEP----------EEVYIGDLPIM 125

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F++ G +R++V+Q   +P      D G+   
Sbjct: 126  LKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV-DTGKTGS 184

Query: 175  SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
            +  + +  +II      + + + IE       HV       K+P    + ALG+ ++   
Sbjct: 185  N--ITHTAKIISSTAGYR-VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTD--- 238

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                  IVY+   D          L   + +++    +D     +  G+K  + + K   
Sbjct: 239  ----RDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQ 294

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
             + +  +  LG ++D              +  E+Y+   +  D+       L        
Sbjct: 295  IIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFA 354

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                + +   V +  Y          K    AL+      RP D+ T  +  ++    + 
Sbjct: 355  SLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALV------RP-DIVTERIRHALATGNWV 407

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                     + R      L+      +  + +       + L   + G+    +  +   
Sbjct: 408  GGRTGVSQLLDRTNWLSMLSHLRRV-ISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSAVCEFFCS 519
            +  V+++  M +    +    +E+++ E       + +    +    +       +   +
Sbjct: 467  SGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILN 526

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +L         L++    RR +      V       +            C +       
Sbjct: 527  GRLVGYYRDGEELAKKIRERRRNGEISDEVNVGHIVTD----FINEVHVNCDSGRVRRPL 582

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            I + +      R +    +++      D      + YL A EEEN Y+A   S L  +  
Sbjct: 583  IIVSNGNPLVTREDIE-KLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEH- 640

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                    ++     ++ I AS+IP+ E++ S R      M +Q
Sbjct: 641  ----------------------THLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQ 678

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            A+ L  A                                                + + +
Sbjct: 679  ALGLYAANYQL-----------------------------------------RTDTRAHL 697

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y               QRPLV    + R  DII             G N ++A + + 
Sbjct: 698  LHYP--------------QRPLV----QTRALDIIGYTN------RPAGNNAILAVISFT 733

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLK 874
            GYN EDS++++   V   ++ S     +         G E+              +E  +
Sbjct: 734  GYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYR 793

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++ G++    EV  GD+L+GK++P        E    +A         RDTS+    G
Sbjct: 794  LLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK--------RDTSIVTRHG 845

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV---ILDRNIYSRLMEILC 991
              G V              +  +  E  +   L + +  +     I D+       + + 
Sbjct: 846  EMGIV--------------DLVLITETAEGNKLVKVRVRDLRVPSIGDKFASRHGQKGVI 891

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G         +    V+   +++ +            E +     +L      +    + 
Sbjct: 892  GMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKT 951

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
              +    +I     +P                    D   GR G K I SRI 
Sbjct: 952  PIEQLQNEILKYGYLPDATEVT-------------YD---GRSGQK-IKSRIY 987


>gi|52694361|emb|CAG38020.1| RNA polymerase beta subunit [Pseudomonas coronafaciens]
          Length = 329

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 193/327 (59%), Positives = 251/327 (76%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 3   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 62

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 63  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 122

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 123 VFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 182

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 183 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 242

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 243 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 302

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGY 821
           ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 303 ADGPSTDMGELALGQNMRIAFMAWNGF 329


>gi|86451165|gb|ABC96805.1| RNA polymerase II [Cephalanthus occidentalis]
          Length = 214

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L  MV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKXMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 199  GAAHFLKERLFDQSD 213


>gi|73697675|gb|AAZ81454.1| RNA polymerase beta subunit [Mycoplasma simbae]
          Length = 591

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 207/433 (47%), Positives = 299/433 (69%), Gaps = 10/433 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN +GF+ETPY +V  G V  ++ VYL+A +E    IAQ+   +DE+    +E +  R
Sbjct: 61  AKVNEFGFLETPYYRVEKGVVDYSEPVYLTAADEMGYKIAQSTVKVDENNKIIDEQLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                 +   E IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 HNYTYQMGSAEDIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E  +AK S    VAK  G+VE VD  +I IR+ +        GVD Y L  FQ
Sbjct: 181 PFVATGIEGEIAKYSSGNFVAKNDGVVEFVDGKKIKIRNNKN-------GVDTYYLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+PLV+   E+++ D++ DG S + G+LALG+N++VAF  + GYN+ED+++
Sbjct: 234 RSNQDTVIHQKPLVRENQEIKKGDLLVDGSSFNNGELALGKNVVVAFSTYKGYNYEDAII 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ VG++V
Sbjct: 294 LNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTADIPNVSKFSTRHLDEFGIVRVGSDV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+  ++   V+DTSL+V +G  GTV+ V I +R 
Sbjct: 354 TPGDVLVGRVSPKGDDNPSQEEKLLLAVLQQRQQAVKDTSLKVKNGHGGTVIGVEILSRA 413

Query: 949 GIDKNERSISVER 961
              K++    +++
Sbjct: 414 N--KDQLEDGIDK 424



 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 129/527 (24%), Positives = 202/527 (38%), Gaps = 86/527 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM--LISERMV 834
            NQ   V  G      +  A+              +L    P+     E  +    S   V
Sbjct: 141  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLETEAPFVATGIEGEIAKYSSGNFV 200

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            +++      ++  ++  R+ K G +         S +    I +  ++    E+  GD+L
Sbjct: 201  AKNDGVVEFVDGKKIKIRNNKNGVDTYYLKNFQRSNQDTV-IHQKPLVRENQEIKKGDLL 259

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFNRH 948
            V   +      +   + ++ A    K  +  D  +            S  + +  I  R 
Sbjct: 260  VDGSSF-NNGELALGKNVVVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQFRT 318

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                ++  ++ +   +   +    DE  I+         ++L G+ +  G     +   L
Sbjct: 319  SKAGDDE-LTADIPNVSKFSTRHLDEFGIVRVGSDVTPGDVLVGRVSPKGDDNPSQEEKL 377

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW--GDDM 1066
               ++                   +  +                    +E +     D +
Sbjct: 378  LLAVL-------------------QQRQQAVKDTSLKVKNGHGGTVIGVEILSRANKDQL 418

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP L+DGTPVD++LNP G
Sbjct: 419  EDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPHLEDGTPVDVMLNPQG 478

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   L  K  + + D      I  +       I          
Sbjct: 479  VPSRMNIGQVLEIHLGMAARSLNTKFVTRVFDGIKKEAIYDVIEEANLPITGKQILID-- 536

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                              P++   FD                                  
Sbjct: 537  ------------------PITGERFD---------------------------------- 544

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 545  NPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 591


>gi|73697705|gb|AAZ81469.1| RNA polymerase beta subunit [Mycoplasma phocirhinis]
          Length = 591

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 206/433 (47%), Positives = 301/433 (69%), Gaps = 10/433 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF+ETPY +V +G V   + VYL+A +E    IAQ+  ++D+D    +  +  R
Sbjct: 61  AKVNKYGFLETPYYRVENGVVDYTEPVYLTAADEMGYKIAQSTVNVDQDNKIIDSQLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                 +   E IDFI+ +P Q+VS+AA  IPFLENDD+NR LMG NMQRQAVPLL+AE+
Sbjct: 121 HNYTYQIGTAEDIDFIEVAPNQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLEAES 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S A  VA+  G+VE VD  +I IR+ +         VD Y L  FQ
Sbjct: 181 PFVATGIEAEIAKYSSANFVARNEGVVEFVDGKKIKIRNHKNT-------VDTYNLKNFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++Q+PLV  G EV++ D++ DG S + G+LALG+N++VAF  + GYN+ED+++
Sbjct: 234 RSNQDTVIHQKPLVVEGQEVKKGDLLVDGASFNNGELALGKNVVVAFSTYKGYNYEDAII 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R +K G +E+T DIPNVS+   +++DE GI+ +G++V
Sbjct: 294 LNERLVKDDVFTSIHIEEQTIQFRTSKAGDDELTPDIPNVSKFSTRHLDEFGIVRIGSDV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKL+ A+  ++   V+DTSL+V +G  GTV+ V I +R 
Sbjct: 354 TPGDVLVGRVSPKGDENPSQEEKLMLAVLQQRQQPVKDTSLKVKNGHGGTVIGVEILSRA 413

Query: 949 GIDKNERSISVER 961
              K++    +++
Sbjct: 414 N--KDQLEDGIDK 424



 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 137/527 (25%), Positives = 212/527 (40%), Gaps = 86/527 (16%)

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            NQ   V  G      +  A+              +L A  P+     E  +   +   + 
Sbjct: 141  NQMVSVAAGCIPFLENDDANRALMGANMQRQAVPLLEAESPFVATGIEAEIA--KYSSAN 198

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID----ECGIICVGAEVNPGD 892
             V  +  + EF V  +  K+   + T D  N+      N D    +  ++  G EV  GD
Sbjct: 199  FVARNEGVVEF-VDGKKIKIRNHKNTVDTYNLKNFQRSNQDTVIHQKPLVVEGQEVKKGD 257

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------GVSGTVVDVRIFN 946
            +LV   +      +   + ++ A    K  +  D  +            S  + +  I  
Sbjct: 258  LLVDGASF-NNGELALGKNVVVAFSTYKGYNYEDAIILNERLVKDDVFTSIHIEEQTIQF 316

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R     ++  ++ +   +   +    DE  I+         ++L G+ +  G +   +  
Sbjct: 317  RTSKAGDDE-LTPDIPNVSKFSTRHLDEFGIVRIGSDVTPGDVLVGRVSPKGDENPSQEE 375

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L   ++ +  +          +     V++          IL    K         D +
Sbjct: 376  KLMLAVLQQRQQPV--------KDTSLKVKNGHGGTVIGVEILSRANK---------DQL 418

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
              G+ ++VKV +A+KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+DGTPVD++LNP G
Sbjct: 419  EDGIDKIVKVSIAVKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLEDGTPVDVMLNPQG 478

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            VPSRMN+GQ+ E HLG A   L  K  + + D      I  + +          +     
Sbjct: 479  VPSRMNIGQVLEIHLGMAARSLNTKFVTRVFDGIKKEAIYDVIAEAGLPTTGKQYLID-- 536

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                              P++   FD                                  
Sbjct: 537  ------------------PITGEKFD---------------------------------- 544

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 545  NPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 591


>gi|52694359|emb|CAG38019.1| RNA polymerase beta subunit [Pseudomonas chlororaphis]
          Length = 327

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 193/327 (59%), Positives = 252/327 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V+
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVS 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R+
Sbjct: 241 GGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQRS 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPW 818
           DI+ADGPSTD+G+LALG+NM +AFM W
Sbjct: 301 DIMADGPSTDMGELALGQNMRIAFMAW 327


>gi|227830880|ref|YP_002832660.1| DNA-directed RNA polymerase subunit B [Sulfolobus islandicus
            L.S.2.15]
 gi|227457328|gb|ACP36015.1| RNA polymerase Rpb2 domain 6 [Sulfolobus islandicus L.S.2.15]
          Length = 1131

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 114/590 (19%), Positives = 194/590 (32%), Gaps = 105/590 (17%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P         + I    +     + I   E     R+T     
Sbjct: 616  IEYLDAEEEENAYVALEPSDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAM 675

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+         +        +    +   G +        + A+   
Sbjct: 676  AKQALGLYAANYQLR---TDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D+ +   S V   +     F         R  S E  +      DK        
Sbjct: 733  TGYNMEDSIIMNRSSVERGMYRSTFF---------RLYSTEEVKYPGGQEDKIVMPEPGV 783

Query: 980  RNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            R    +    +L     VS     K   VL   +       ++ + + +  K   ++  +
Sbjct: 784  RGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSI--V 841

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E     L    +                 ++VKV V   R    GDK A RHG KG
Sbjct: 842  TRHGEMGIVDLVLITE------------TAEGNKLVKVRVRDLRVPSIGDKFASRHGQKG 889

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  ++P  DMP+   G   DI+LNP  +PSRM +GQI E   G                
Sbjct: 890  VIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAA------------ 937

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                         +  +TP++    E+ 
Sbjct: 938  -----------------------------------------LSGNIVDATPIYKTPIEQL 956

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
             N +L+          + YDG +G+     +  G +Y  KL+HMV+DK++AR+ G   ++
Sbjct: 957  QNEILK-YGYLPDATEVTYDGRSGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYE-------- 1330
            T+QP  G++  GG R GEME  C+  +G A +L++ L   SD    RT +Y         
Sbjct: 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSD----RTTIYVCDQCGYIG 1071

Query: 1331 ----------SIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                        + G+  + F      +F +L++E+ ++ +S  L     
Sbjct: 1072 WYDKNKNKYICPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILEDR 1121



 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 171/1133 (15%), Positives = 339/1133 (29%), Gaps = 228/1133 (20%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
            L+     SY+ F+             LQ        I        +         P+   
Sbjct: 26   LVRQHLDSYNDFVRNK----------LQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRE 75

Query: 86   -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       +   R+LTYA PL +T+  +  +++             + +Y+GDLP+M
Sbjct: 76   SDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEP----------EEVYIGDLPIM 125

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F++ G +R++V+Q   +P      D G+   
Sbjct: 126  LKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLV-DTGKTGS 184

Query: 175  SGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL 229
            +  + +  +II      + + + IE       HV       K+P    + ALG+ ++   
Sbjct: 185  N--ITHTAKIISSTAGYR-VPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTD--- 238

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK--- 286
                  IVY+   D          L   + +++    +D     +  G+K  + + K   
Sbjct: 239  ----RDIVYAVSLDPEIQNELFPSLEQASSIANVDDALDFIGSRVAIGQKRENRIEKAQQ 294

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEI 341
             + +  +  LG ++D              +  E+Y+   +  D+       L        
Sbjct: 295  IIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFA 354

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                + +   V +  Y          K    AL+      RP D+ T  +  ++    + 
Sbjct: 355  SLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALV------RP-DIVTERIRHALATGNWV 407

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
                     + R      L+      +  + +       + L   + G+    +  +   
Sbjct: 408  GGRTGVSQLLDRTNWLSMLSHLRRV-ISSLARGQPNFEARDLHGTQWGRMCPFETPEGPN 466

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV-MPQDLINAKPVVSAVCEFFCS 519
            +  V+++  M +    +    +E+++ E       + +    +    +       +   +
Sbjct: 467  SGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILN 526

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +L         L++    RR +      V       +            C +       
Sbjct: 527  GRLVGYYRDGEELAKKIRERRRNGEISDEVNVGHIVTD----FINEVHVNCDSGRVRRPL 582

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
            I + +      R +    +++      D      + YL A EEEN Y+A   S L  +  
Sbjct: 583  IIVSNGNPLVTREDIE-KLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEH- 640

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                    ++     ++ I AS+IP+ E++ S R      M +Q
Sbjct: 641  ----------------------THLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQ 678

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
            A+ L  A                                                + + +
Sbjct: 679  ALGLYAANYQL-----------------------------------------RTDTRAHL 697

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              Y               QRPLV    + R  DII             G N ++A + + 
Sbjct: 698  LHYP--------------QRPLV----QTRALDIIGYTN------RPAGNNAILAVISFT 733

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLK 874
            GYN EDS++++   V   ++ S     +         G E+              +E  +
Sbjct: 734  GYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYR 793

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +++ G++    EV  GD+L+GK++P        E    +A         RDTS+    G
Sbjct: 794  LLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAK--------RDTSIVTRHG 845

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV---ILDRNIYSRLMEILC 991
              G V              +  +  E  +   L + +  +     I D+       + + 
Sbjct: 846  EMGIV--------------DLVLITETAEGNKLVKVRVRDLRVPSIGDKFASRHGQKGVI 891

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G         +    V+   +++ +            E +     +L      +  I + 
Sbjct: 892  GMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPIYKT 951

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
              +    +I     +P                    D   GR G K I SRI 
Sbjct: 952  PIEQLQNEILKYGYLPDATEVT-------------YD---GRSGQK-IKSRIY 987


>gi|82749746|gb|ABB89757.1| RNA polymerase beta subunit [Mycoplasma arginini]
          Length = 592

 Score =  319 bits (818), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 210/449 (46%), Positives = 299/449 (66%), Gaps = 15/449 (3%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA ++ YGFI++PY +V + KV  +   YL+A+EE     AQ+   + E+    ++ V  
Sbjct: 61  FADIDKYGFIKSPYFRVVNKKVDFSKPYYLTAIEEAGYSFAQSTVKI-ENDEIVDDFVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + VP  ++DF+  S +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVP+L  E
Sbjct: 120 RRDNEYLEVPANEVDFVGVSNRQMTSISASAIPFLENDDANRALMGSNMQRQAVPVLFPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I+AK  G+V  VDA  I+++         ++  D Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIIAKFDGVVTYVDANVIIVKRE------GSNKKDHYYLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q PLVK+  EV+  D++ DGPS   G++ALG+N+LV F  WHG+N+ED++
Sbjct: 234 ERSNQGTLIHQVPLVKLNQEVKAGDLLVDGPSMKNGEMALGKNVLVGFTTWHGFNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G + +T DIPNVS    + +DE GI+ VG+E
Sbjct: 294 VLSERLVKDDVYTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDENGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V + +R
Sbjct: 354 VSAGDILVGRTSPKGEENPTPEEKLMGAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSR 413

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   GI+K  +    ++ +I++  +
Sbjct: 414 EFGDTLEDGIEKIVKVSIAQKRKIKVGDK 442



 Score =  299 bits (765), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 126/413 (30%), Positives = 178/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  EV  GD+LV   + K    M   + +L         +  D  +     V   V 
Sbjct: 247  LVKLNQEVKAGDLLVDGPSMKN-GEMALGKNVLVGFTTWHGFNYEDAVVLSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGEDILTADIPNVSNYSKRYLDENGIVRVGSEVSAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L   F       
Sbjct: 365  SPKGEENPTPE--EKLMGAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSREF------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+DI
Sbjct: 416  --GDTLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDI 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   L  K  + I D   +  I  +           S
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKKLNTKFVTPIFDGITHNQIKEILEEANINSSGKS 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                         V+DG                           
Sbjct: 534  V----------------------------VYDG--------------------------R 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGEPFD+P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEPFDQPISVGIMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|111054625|gb|ABH04370.1| RNA polymerase beta subunit [Providencia rustigianii]
          Length = 324

 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 199/322 (61%), Positives = 249/322 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L +DG F EEL+ CR  GE  L  RE+++++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVEYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 243 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 303 LADGPSTDLGELALGQNMRVAF 324


>gi|83763739|emb|CAJ00203.1| putative DNA-directed rna polymerase, beta subunit [Vibrio sp. 12F02]
          Length = 356

 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 193/368 (52%), Positives = 257/368 (69%), Gaps = 13/368 (3%)

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             F GTG+E  VA  SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ 
Sbjct: 1    SFSGTGIERNVAVDSGVTAVAKRGGVVQSVDASRIVIKVNEEELVPGEAGIDIYNLTKYT 60

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            RSNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L
Sbjct: 61   RSNQNTCINQRPTVLPGEPVTRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSIL 120

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV
Sbjct: 121  VSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEV 180

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+D+SLRVP+ VSGT++DV++F R 
Sbjct: 181  KGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTIIDVQVFTRD 240

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
            G++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  
Sbjct: 241  GVEKDKRALEIEQMQLKEAKKDITEEFQILEGGLLARVRTLLVAAGV------------- 287

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            S   +    R QW +  + DE  Q  +E L  QY+  K+  + +F+ K  KI  GDD+ P
Sbjct: 288  SEVKLDAMDRKQWLEITLDDEAQQNQLEQLAEQYDELKAEFDKKFETKRRKITQGDDLAP 347

Query: 1069 GVLRVVKV 1076
            GVL++VKV
Sbjct: 348  GVLKIVKV 355


>gi|242398379|ref|YP_002993803.1| DNA-directed RNA polymerase subunit B [Thermococcus sibiricus MM 739]
 gi|242264772|gb|ACS89454.1| DNA-directed RNA polymerase subunit B [Thermococcus sibiricus MM 739]
          Length = 1118

 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 111/586 (18%), Positives = 201/586 (34%), Gaps = 95/586 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  PW        + I    +     + +   E     R+T     
Sbjct: 610  IEYLDAEEEENAYVATWPWEVTEEHTHLEIMPATILGLPASLVPYPEHNAAPRNTYGAGM 669

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++ +D  G   +        +    +   G       +  + A+   
Sbjct: 670  AKQSLGLGWANFRIR-VDTRG--HLMHYPQVPLVNSRIMEAVGFEQRPAGQNFIVAVLSY 726

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D  +   + +   +     F  +              + +     + D+  I D
Sbjct: 727  SGYNMEDAVIMNKASIERGLARSTFFRTY------------EAEEKKYMGGQTDKFEIPD 774

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              +   L E         G    +        L++     ++ +       +   +   +
Sbjct: 775  PTVRGFLGEKYYRNLDEDGIAFPESKVQGKDVLVARTSPPRFLEEQTS---LGAGILQGR 831

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +   +    E+   +KI   + GD       ++VKV V   R  + GDK A RHG KG+
Sbjct: 832  RETSITMRPGEEGIIDKIIITETGD-----GTKLVKVTVRDLRIPEFGDKFASRHGQKGV 886

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMP+ ++G   D+++NP G+PSRM VGQ+ E   G      G++I       
Sbjct: 887  IGLIVPQEDMPWTENGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRIDGTAFIG 946

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +    +      L                                      +DG      
Sbjct: 947  EPEEKLRKELEELGFKHSGREVM----------------------------YDGIT---- 974

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                  G  F+  + VG IY  +L+HMV+DK++ARS G   ++T
Sbjct: 975  ----------------------GRKFEADIFVGVIYYQRLHHMVADKLHARSRGPVQVLT 1012

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG--------------- 1324
            +QP  G++  GG R GEME   +  +GA+ +L E L  +SD                   
Sbjct: 1013 KQPTEGRAREGGLRFGEMERDVLIGHGASMLLVERLLEESDKTEAWICESCGHLAVEDKR 1072

Query: 1325 RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R ++Y   V G   +  +     +F +L+ E++A+G+   L+    
Sbjct: 1073 RDKIY-CPVCGEEENISKVEMSYAFKLLLDEIKAMGIRPSLKLKER 1117



 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 143/982 (14%), Positives = 294/982 (29%), Gaps = 207/982 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            G+Q        +        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------EHGMQEVISEFEGVKPDIPDFEVKFGRVRLGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ P+ + +  +V  +++              + +G+LP+M
Sbjct: 77  AHGQRKPLYPIDARIRNLTYSAPVFLGMIPVVKGIEQEPV----------EVRIGELPVM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKGR 171
            K                         G F+I G +R++VS    +P    +  D  + R
Sbjct: 127 LKSKICRLYNLSDEELIAHGEDPKDPGGYFIINGSERVIVSIEDLAPNRTLVEIDERQNR 186

Query: 172 ASLSGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPVTS----FLMALGMD 224
                   Y  +    +      + +E     +++V I     VP        + ALG++
Sbjct: 187 --------YIAKCFSYRHGYRALITVERRKDGLLYVSI---PNVPGVLKFVHIMRALGLE 235

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           S+ EI+          Q            +     +     +D      +    K+    
Sbjct: 236 SDKEIVDAVGNNPEVQQ------VLFDNLEDASDVQTQEEALDYIGKRAMPGQPKEYRLR 289

Query: 284 LLKSLKEKG-VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIF 337
              S+ +   +  +G++ +          ++  +  E+ +   +  D+       L+   
Sbjct: 290 RAHSIIDNNLLPHMGVSPEDRIRKAYYLGMMALKVTELSLGLREEDDKDHYASKRLKLAG 349

Query: 338 HSEIRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                   + +   V +  Y   +      +    +D    +   +RP DV T  +  ++
Sbjct: 350 DLLKDLFRVAFGQLVKDMQYQLTKTYQRKGEKYTFQDIQRFVRNSVRP-DVLTERIEHAL 408

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
               +          + R      L+         + +E      + L       G I  
Sbjct: 409 ATGAWPGGRTGVSQLLDRTNYMSTLSHLRRVTSP-LSREQPHFEARDLHGTH--WGRICP 465

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +         V  +        + ++  +I E      ++S+    +   +P       
Sbjct: 466 TETPEGPNCGLVKNLS------LMSQITTAIPEEEVFAYLESLGIVHIEERRPEPDDWRV 519

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +     +   ++ V  +++I   RR   + +         V    ++        P    
Sbjct: 520 YLNGVLVGTYKDGVELINKIKTDRREGRISEVINVAYYEDVREIYINSDEGRVRRPLIIV 579

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L          +    I+    K  D      + YL A EEEN Y+A       
Sbjct: 580 ENGVPKLTK--------DHVEAIKKGTLKWSDLIRIGVIEYLDAEEEENAYVAT------ 625

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P  ++ + ASL+P+ E++ + R   G  
Sbjct: 626 -----------------WPWEVTEEHTHLEIMPATILGLPASLVPYPEHNAAPRNTYGAG 668

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +Q++ L  A                                                +
Sbjct: 669 MAKQSLGLGWANFRI-----------------------------------------RVDT 687

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +  Y               Q PLV                +        G+N +VA 
Sbjct: 688 RGHLMHYP--------------QVPLVNS----------RIMEAVGFEQRPAGQNFIVAV 723

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SE 870
           + + GYN ED++++++  +   +  S     +E   +    G  ++     P V     E
Sbjct: 724 LSYSGYNMEDAVIMNKASIERGLARSTFFRTYEAEEKKYMGGQTDKFEIPDPTVRGFLGE 783

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           +  +N+DE GI    ++V   D+LV + +P        E+  L A   +     R+TS+ 
Sbjct: 784 KYYRNLDEDGIAFPESKVQGKDVLVARTSPPRFLE---EQTSLGAGILQ---GRRETSIT 837

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           +  G  G +  + I       K
Sbjct: 838 MRPGEEGIIDKIIITETGDGTK 859


>gi|296243132|ref|YP_003650619.1| DNA-directed RNA polymerase subunit B' [Thermosphaera aggregans DSM
            11486]
 gi|296095716|gb|ADG91667.1| DNA-directed RNA polymerase, subunit B' ;DNA-directed RNA polymerase,
            subunit B' [Thermosphaera aggregans DSM 11486]
          Length = 1163

 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 93/338 (27%), Positives = 144/338 (42%), Gaps = 72/338 (21%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            R + K               ++VKV V   R  + GDK A RHG KG++  ++P  DMPF
Sbjct: 881  RHEEKGIVDTVLITTDNEGNKLVKVRVRDLRIPELGDKFASRHGQKGVLGLLVPQYDMPF 940

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +DG   D+V+NP   PSRM VGQ+ E+  G                             
Sbjct: 941  TEDGVVPDLVINPHAFPSRMTVGQLIESIAGKVAA------------------------- 975

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                         +  V  +TP F     + +  +L+      S
Sbjct: 976  ----------------------------LEGRVVDATP-FHKTPVKDLEIVLKRHRYLPS 1006

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+ ++YDG TGE    PV +G +Y  KL+HMVSDKV+AR+ G   ++T+QP  G+S  GG
Sbjct: 1007 GEEVMYDGRTGEMISSPVFIGIVYYQKLHHMVSDKVHARARGPVQILTRQPTEGRSRAGG 1066

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG------RTR-VYESIV---A 1334
             R GEMEV C+  +G + +L+E +  +SD       ++ G      R +  Y   +    
Sbjct: 1067 LRWGEMEVDCLVGHGTSLLLRETILDRSDITRVYVCEICGHIGWYDRNKGKYLCPIHKEK 1126

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            G+         +F +L++E+ + G+   L     +   
Sbjct: 1127 GSLKP-VEISYAFKLLLQELMSFGVKPRLVVKDVRKEV 1163



 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 157/1008 (15%), Positives = 294/1008 (29%), Gaps = 213/1008 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SYD F+   +             FK + PIT       +  V Y  + PK+  
Sbjct: 23  LVRQHLDSYDRFIRELLPEML-------KEFKEI-PIT---EDVKITIVDYRIEEPKWIT 71

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  R+LTYA P+ + ++ +                KEQ + + DLP+M
Sbjct: 72  LEGIPERKTPMECRLRNLTYAAPVMVKIKYVD----------ESGRSKEQELKLMDLPVM 121

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G ++++V+Q   +       D      
Sbjct: 122 LKSSIDPLSKMTPEELTSIGEDPKDPGGYFIINGSEKVLVAQEDLASNNIIT-DVAPEGS 180

Query: 175 SGKLLYACRIIP-DQG--LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSEEIL- 229
           S   L   +II   +G    + IE       +    +  K+PV   + ALG+   +EIL 
Sbjct: 181 SYTHL--AKIISVSKGKRSQLVIERRKDGTFYANF-QGHKIPVIVLMKALGLVGEDEILY 237

Query: 230 --------------------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                                 F  + +           +         + +   +    
Sbjct: 238 AVSLNSDIQLHMFPSIQEVSKIFPREPLPEGLSPEEEERVLRERREKEVEEALDYIGSRI 297

Query: 270 G------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
                  E++  + + L   LL  +         I      G  ++  I+    G    +
Sbjct: 298 AIGRPREERIRRALRALDENLLPHIGTDPSPETRIKKAVFIGQMISR-IIELHLGFREPD 356

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D    K L+         +    +      A+ R+   + +    K+  LD+  V++P
Sbjct: 357 DKDHYRNKRLKLAGDLLSVLLRTALL------AFTRDLKESAEKYLAKNRKLDLKMVVKP 410

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
             V T  +  +M    +          + R  M   L+         + +       + L
Sbjct: 411 S-VITDRILHAMATGNWPGGKTGVSQLLDRTNMLSTLSHLRRVVSP-LSRGQPHFEAREL 468

Query: 444 VDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              + G+    +  +      V+++  M+     +    +E  + +      I       
Sbjct: 469 HGTQWGRMCPFETPEGANIGLVKNLALMVNVSVGVPESEIEPILYKHQVKPLITITDRAT 528

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR--LSALGQGGVARARAGVEMRD 560
               K ++  V E           E+        + R       G+  V   R       
Sbjct: 529 GKTVKGILDEVKEAVRKYGGELPSEYEGWSKVYLNGRLIGYHPNGEELVKELRKMRRQGK 588

Query: 561 VHP--------THYGRICPAETSEGHNIGLVSSL---TSFARVNAYGFIETPYRKVCDGK 609
           + P        T Y       T  G     +  +              +        D  
Sbjct: 589 LSPEVNIAHIKTEYLDEVYVNTDPGRIRRPLLVVEKGEIKLTRTHLEKLRKGEISFEDLV 648

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               + YL   EEEN YIA +  ++                         +    +    
Sbjct: 649 HKGIIEYLDPDEEENAYIALSIDNIT-----------------------SEHTHAEIWIP 685

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IP+ E++ S R +    M +Q++ L  A                       
Sbjct: 686 AILGITASIIPYPEHNQSPRNMYQAAMAKQSLGLYSANFQ-------------------- 725

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    +      Y               Q+PLV+      
Sbjct: 726 ---------------------KRMDTRGHFLHYP--------------QKPLVQ------ 744

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +   G+NM+VA + + GYN ED++++++      +  S     +  
Sbjct: 745 ----TRSMEVIGYNERPAGQNMVVAVLTFTGYNIEDALIMNKSSADRGLARSTFFRLYST 800

Query: 850 MARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           +      G ++     P            + ++E GI+    +V  GD+LVGKI+P    
Sbjct: 801 VEYKYMGGQQDEIVIPPTNIRGYRGLRAYEKLEEDGIVAPETQVAGGDVLVGKISP---- 856

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              P     +       +  +DTS+ +     G V  V I   +  +K
Sbjct: 857 ---PRFLGAQEYMLGAGLTKQDTSVVMRHEEKGIVDTVLITTDNEGNK 901


>gi|111054605|gb|ABH04360.1| RNA polymerase beta subunit [Providencia stuartii]
          Length = 324

 Score =  319 bits (817), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 200/322 (62%), Positives = 250/322 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQ++INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQEMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L EDGSF EEL+ CR  GE  L  R++++++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLAEDGSFVEELITCRNRGESSLFSRDQVEYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 243 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 303 LADGPSTDLGELALGQNMRVAF 324


>gi|6606137|gb|AAF19081.1|AF107809_1 DNA-dependent RNA polymerase II RPB140 [Peziza quelepidotia]
          Length = 927

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 141/974 (14%), Positives = 293/974 (30%), Gaps = 159/974 (16%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            I   D +N+  Y RN   ++       ++A +   R +    +     +  +        
Sbjct: 88   IPDEDILNHVCYDRNDVQMLDMLKPCLEEAFVIQKREIALDFIGRRGSSSGVAKDKRV-- 145

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +Y    + +  +      +  +  +      +  ++  ++     +   DD D+ G +R
Sbjct: 146  -RYAREILQKEFLPHISQKEGSETRK---AFFLGYMVHQMLLCALERKEPDDRDHFGKKR 201

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    ++ + + +  +              + +  + + +     +  
Sbjct: 202  LDLAGPLLAGLFRTLFKKLTKDVYKYLQKCVESSREFNLTLAVKSTTITNGLKYSLATGN 261

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H R  +      + R     + R +H TH+G 
Sbjct: 262  WGEQKKAASARAGVSQVLNRYTFASTLSHLRGTNT----PIGRDGKIAKPRQLHNTHWGL 317

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L   + V+     +    +    + +V  +     +      +
Sbjct: 318  VCPAETPEGQACGLVKNLALMSYVSVGSPADPIIDFMLQRNMEVLEEYEPSRSPNATKIF 377

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLE 683
            +      +  D  F    +        I      I  I     ++ + A      +  ++
Sbjct: 378  VNGVWVGIHRDPGFIVRTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVD 437

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            ND ++       +Q+  +  L+ +     T  E                G+VE +DA   
Sbjct: 438  NDPASPRRGELVLQKHHIEKLEDDKDI--TDDEQRYG-----WQGLISDGVVEYIDAEEE 490

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +    +   + Q+        QR    V             PS  LG
Sbjct: 491  ETVMIVMTPEDLETSRQFHAGYEIQQEIDPA---QRVKAAVNKYAHTWTHCEIHPSMILG 547

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N       S R   +       +  F    R+          
Sbjct: 548  -------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM-------- 586

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             +  +             +       +   +  + AI      +
Sbjct: 587  ---------------DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYN 631

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R  +D+ +R   +    +E   +      + L    Y
Sbjct: 632  QEDSVIMNQSSIDRGLF-RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTY 687

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   +  G           K+  ++ +      R+++         ++     +  
Sbjct: 688  DKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVD 747

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                             L+ VKV +   +  Q GDK A RHG KG +
Sbjct: 748  Q--------------------VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTI 787

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 788  GITYRNEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDV 847

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L                                                    
Sbjct: 848  TVDSVSKLLREHGYQSRGFEIM-------------------------------------- 869

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      +G +    G         V +G  Y  +L HMV DK++AR+ G   ++T+
Sbjct: 870  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIHARARGPVQILTR 913

Query: 1281 QPLGGKSNRGGQRL 1294
            QP+ G++  GG R 
Sbjct: 914  QPVEGRARDGGLRF 927



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 104/838 (12%), Positives = 225/838 (26%), Gaps = 113/838 (13%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          + +      +   I    ++G  +      K  +  ++
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKAPPSPTPFVAEIRSAVEKGSRLISSMQIK--MFGKM 55

Query: 207 DRRR---------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLS 250
           D R                 +PV     ALG +  E+IL+         Q  D     L 
Sbjct: 56  DSRGGYGQTIKSTLPYIKSDIPVAIVFRALGVIPDEDILNHVCYDRNDVQMLDMLKPCLE 115

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A ++   +++   +        +   K++     + L+++ +  +              
Sbjct: 116 EAFVIQKREIALDFIGRRGSSSGVAKDKRVRYAR-EILQKEFLPHISQKEGSETRKAFFL 174

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +  +     +E  +  D     +         P+L          +   +     K  
Sbjct: 175 GYMVHQMLLCALERKEPDDRDHFGK--KRLDLAGPLLAGLFRTLFKKLTKDVYKYLQKCV 232

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-- 428
           + +      +       T  +  S+    + +  K   +  G  ++  R    +      
Sbjct: 233 ESSREFNLTLAVKSTTITNGLKYSLATGNWGEQKKAASARAGVSQVLNRYTFASTLSHLR 292

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
                      I     L N    +         +   + + L     + +      I +
Sbjct: 293 GTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVSVGSPADPIID 352

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QG 547
            +   +++ +   +   +               +    +    +  I   RR + +G + 
Sbjct: 353 FMLQRNMEVLEEYEPSRSPNATKIF---VNGVWVGIHRDPGFIVRTIQKLRRQNHIGHEV 409

Query: 548 GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            + +     E        R   P       PA    G  +     +            E 
Sbjct: 410 SLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKDITDDEQ 469

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAGEEI 654
            Y           V Y+ A EEE   I      L+    F       +E+   +     +
Sbjct: 470 RY-GWQGLISDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEIDPAQRVKAAV 528

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                     +  P  ++ I AS+IPF +++ S R      M +QA+ +           
Sbjct: 529 NKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT-------- 580

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                   + A I+                                    +KF+      
Sbjct: 581 -NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFRELPAGQ 618

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
                 L   G             S  +   ++ R +  +       + E  + +S    
Sbjct: 619 NAIVAILCYSG--------YNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMS---- 666

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                    +EEFE   R           +   +       +D+ G++  G  V+  DI+
Sbjct: 667 --------VVEEFEKPTR----------GNTLRLKHGTYDKLDDDGLVAPGVRVSGEDII 708

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P   +     ++        K    RD S  + S  +G V  V +       K
Sbjct: 709 IGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 759


>gi|73697641|gb|AAZ81437.1| RNA polymerase beta subunit [Mycoplasma cloacale]
          Length = 594

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 201/443 (45%), Positives = 287/443 (64%), Gaps = 7/443 (1%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVH TH+GRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHSTHFGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           F++++ YGFI+TPY KV +  V  +  VYL+A+EE     AQ+   + E+    +E V  
Sbjct: 61  FSQIDKYGFIQTPYFKVKNKVVDFSQPVYLTAIEEIGYTFAQSTVHI-ENDVIVDEYVMV 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V  ++++++  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++  E
Sbjct: 120 RRDNEYVQVKADEVNYLGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVIAPE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I A + G+V  VD+  I I       +       +Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIRATKDGVVTYVDSTMIKIAPNGSKKEKEQ----VYNLRTF 235

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSN  T ++Q P+V VG  ++  D++ DGPS   G+LALG+N+LV F  WHGYN+ED++
Sbjct: 236 ERSNAGTVIHQVPIVNVGQNIKAGDLLVDGPSMKNGELALGKNVLVGFTTWHGYNYEDAV 295

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +M R +K G + +T DIPN S    + +DE GI+ +G+E
Sbjct: 296 ILSERLVKDDVYTSIHIEEQTLMFRHSKAGEDWLTNDIPNASNYSKRFLDENGIVRIGSE 355

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV + I +R
Sbjct: 356 VSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIEILSR 415

Query: 948 -HGIDKNERSISVEREQIELLAR 969
             G    +    + +  I    +
Sbjct: 416 EFGDQLEDGVEKIVKVSIAQKRK 438



 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 128/413 (30%), Positives = 180/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG  +  GD+LV   + K    +   + +L         +  D  +     V   V 
Sbjct: 249  IVNVGQNIKAGDLLVDGPSMKN-GELALGKNVLVGFTTWHGYNYEDAVILSERLVKDDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I           S + E      +    +  +  LD N   R+   +   + + G  
Sbjct: 307  YTSIHIEEQTLMFRHSKAGEDWLTNDIPNASNYSKRFLDENGIVRIGSEVSAGDILVGRT 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  IL   F       
Sbjct: 367  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAIEILSREF------- 417

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  GV ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+D+
Sbjct: 418  --GDQLEDGVEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDM 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  + + D   +  I  +            
Sbjct: 476  MLNPQGVPSRMNIGQILELHLGMAAKKLNTKFVTPVFDGITHNQIKEILE---------- 525

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                               E  I         D S ++ +Y G 
Sbjct: 526  -----------------------------------EAEI---------DPSAKTTVYSGQ 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD P++VG +YMLKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 542  TGEKFDHPISVGVMYMLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 594


>gi|242392320|dbj|BAH80333.1| RNA polymerase subunit B' [Haloarcula californiae]
          Length = 608

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 207/607 (34%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV        +    + +  +++       
Sbjct: 84   VKTGEL--EFEELVERGLVEFIDAEEEEDILVGVDEGELTDNHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEDELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 42.0 bits (97), Expect = 0.73,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 58/195 (29%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +        +     F E   R          V ++ A EEE+  +      L 
Sbjct: 70  EDGEPLMTDEEVEQVKTGELEFEELVER--------GLVEFIDAEEEEDILVGVDEGELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ++                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DNH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|111054595|gb|ABH04355.1| RNA polymerase beta subunit [Morganella morganii]
          Length = 323

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 197/322 (61%), Positives = 247/322 (76%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   DLDNLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V D  VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDDVVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ LD+DG F +EL+ CR  GE  L  R+++ ++D S +QVVS
Sbjct: 122 IHYLSAIEEGNFIIAQANTVLDDDGHFVDELITCRNKGESSLFSRDQVQYMDVSTQQVVS 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 182 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 241

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 242 TVQYVDASRIVIKVNEDEMYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGEPVERGDV 301

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 302 LADGPSTDLGELALGQNMRVAF 323


>gi|310798473|gb|EFQ33366.1| RNA polymerase Rpb2 [Glomerella graminicola M1.001]
          Length = 1151

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 109/494 (22%), Positives = 179/494 (36%), Gaps = 87/494 (17%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   +         ++F 
Sbjct: 730  YPQRPMVISKTIQLVNYDKLPAGQNATVIVMSYSGYDIEDALVLNKASCDRGFGRCQVFR 789

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            ++  +  +   +  RE+I     D++                 + G    SG    KK T
Sbjct: 790  KYTAELQK-YPNGRRERIGDPVNDEN--GRTTKHEALDDDGLAIVGYKVNSGEVMIKKET 846

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L +               +  ++         + Y  +    +  + +K+         
Sbjct: 847  PLDT-----------GSTGIGMDRGPSEFRDSSISYRIA----DPAYIDKV-----MVSH 886

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  VVKV     R  + GDK + RHG KG+V  I+  ED+PF   G   DI++NP G
Sbjct: 887  TERETMVVKVQTRQTRRPELGDKFSSRHGQKGVVGIIVDQEDLPFSDTGLVPDIIMNPHG 946

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++ E   G A V  G                        K  G G       
Sbjct: 947  FPSRMTVGKLLECLTGKASVLDG-----------------------RKDYGFGD------ 977

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     E +++ L        G+     G+TGEP +
Sbjct: 978  -----------------------AFRSHPLEQMSAALVDHGFSWEGKDYFTSGITGEPLE 1014

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1015 AYIFNGPIYYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYG 1074

Query: 1307 AAYVLQEMLTIKSD----DVV------GRTRVYESIVAGN-DTFETGTPESFNVLVKEMQ 1355
            A+ +L E L I SD    D+       G  + Y        +  +   P +  +LV+E+ 
Sbjct: 1075 ASQLLLERLMISSDGTQIDICQQCGLFG-YKGYCHTCKSTREVTQMTMPYAAKLLVQELI 1133

Query: 1356 ALGLSIDLENSRTK 1369
            ++ + + L+     
Sbjct: 1134 SMNVGVRLQLEDEF 1147



 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 138/999 (13%), Positives = 275/999 (27%), Gaps = 219/999 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY+ F+   I    R N       +S       + +  LEF     + P    
Sbjct: 42  LVKQHIDSYNFFVENEIKEIVRAN----RIIRS-----DVNSSFWLEFTDIRVERPSRVD 92

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TYA P+ + +  I          +    I  +++ +G LP
Sbjct: 93  FNDIRAQNEVTPMECRLRDMTYAAPIMVDIAYI----------RDKSKIVRKNVPLGRLP 142

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 143 VMLKSSICRLGGANNAEMSRMNECPLDPGGYFIINGTEKVILIQEQLSKNRVIVEADEKN 202

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMALG 222
           S+    + +               + K   +V + + R           +P+   L ALG
Sbjct: 203 SVITASVTSST------------HERKSKTYVTLKKDRILLTANILVEGIPIVIILKALG 250

Query: 223 MDSEEILSTFYPKIVYSQRGDFWCFPLSAAD---LMVGAKVSSSLVDIDTGEQVIESGKK 279
             ++  +           + +F      A           +      +  G+  +    +
Sbjct: 251 GLTDYEIMQLVAGDNGKYQDEFLVQFEEATKAGVYTQQQALEYIGARVKMGKSRVPFAAQ 310

Query: 280 LTSGLLKSLKEK---------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           +    ++   +           ++ L      +   ++   ++  +     ++  D +  
Sbjct: 311 VRRNHVEEALDALANLIIAHVPIEGLDFYPKAIYVAFMTRRVLMAQNDPSLVDDRDFVGN 370

Query: 331 KSLEEIFHSEIRDIPILYVDSV-NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           K LE            L+     N  + I   L  D      DA+  I            
Sbjct: 371 KRLELAGQLLSLLFEDLFKQFCGNVKSSIDKVLKKDNRAVPLDAVNMI------------ 418

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           S   +M       + +    TV R  MN          + +I    ++  I    +    
Sbjct: 419 SNHANMIGQGINRAIQTGNWTVKRFNMNRAGVTHVLSRLSYISALGMMTRISSQFEKTRK 478

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
                 +       + +          L    ++        + +++    +  +     
Sbjct: 479 VSGPRALQPSQWGMLCTSDTPEGEACGL----VKNLALMTHITTNVEEAPVKRWVFTLDA 534

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLS----RITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                  F   ++ +   +V  ++     +T   +  A     + R         +H  +
Sbjct: 535 GVEPIRNFSGGEMHRETSYVIHINGTPFALTRYPKRFAGKFRTMRRRGWISPFVSIHINN 594

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV-------CDGKVTNDVVYLS 618
           +       T EG             R       E   R +        D      V YL 
Sbjct: 595 HFNAVHIATDEGRICRP----YIIVRNGKPKLKEEHLRLLQLGRATFDDFLTHGIVEYLD 650

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EE +  +A     +                             ++  P  V+   A L
Sbjct: 651 VNEENDTLVALYEKDVTP-----------------------LTTHMEIEPFTVLGAVAGL 687

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF  ++ S R    C M +QA+                                     
Sbjct: 688 IPFPHHNQSPRNTYQCAMGKQAIGA----------------------------------- 712

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 I   + +   +     +Y               QRP+V          I     
Sbjct: 713 ------IAYNQFNRIDTLLYTLVYP--------------QRPMV----------ISKTIQ 742

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
             +   L  G+N  V  M + GY+ ED++++++              ++    +    G 
Sbjct: 743 LVNYDKLPAGQNATVIVMSYSGYDIEDALVLNKASCDRGFGRCQVFRKYTAELQKYPNGR 802

Query: 859 EEITRDIPNVSEEGLKN---IDECGIICVGAEVNPGDILVGKITPKGES------PMTPE 909
            E   D  N           +D+ G+  VG +VN G++++ K TP             P 
Sbjct: 803 RERIGDPVNDENGRTTKHEALDDDGLAIVGYKVNSGEVMIKKETPLDTGSTGIGMDRGPS 862

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           E    +I    A       + V      T+V V++  R 
Sbjct: 863 EFRDSSISYRIADPAYIDKVMVSHTERETMV-VKVQTRQ 900


>gi|196051461|gb|ACG68884.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 598

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 211/428 (49%), Positives = 294/428 (68%), Gaps = 8/428 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L  I++ RR+++LG  G+ R  A  E+RDVH THYGRICP ET EG NIGL+ ++ 
Sbjct: 1   QINPLGEISNKRRVTSLGPRGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNMA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-GSFTEELV 645
           S+A+++ YGFI+TPY KV DG V  ND+ YL+A+EE N   AQ++ ++DE+ G   +E V
Sbjct: 61  SYAKIDDYGFIQTPYFKVNDGIVDFNDIRYLTAIEEINFTFAQSSINIDEETGEILDERV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R   E I + +++ID+I  + +Q+ SI+AS IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 121 MSRKNNEYIELDKKEIDYIGVTSRQMTSISASAIPFLENDDANRALMGSNMQRQAVPLIK 180

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            EAP V TG+E+ +A+ S + + A + GIV  VDA  I I+S +           IY L 
Sbjct: 181 PEAPLVATGVEADIARFSASNVRATKDGIVTYVDANEIRIQSSDEKKPS------IYFLR 234

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSNQ T ++Q+PLVK G E++  D++ DGPS + G+LALG+N+LV F  W GYN+ED
Sbjct: 235 TFERSNQGTVIHQKPLVKAGQEIKAGDLLTDGPSMENGELALGKNVLVGFSTWFGYNYED 294

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++++E++V EDV+TSIHIEE  +  R +K G + +T DIPN S    + + E GI+ +G
Sbjct: 295 AVILNEKLVKEDVYTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVIIG 354

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV PGDILVG+I+PK E   +PEEKL+ AIFG+K    +DTSL+V  G  GTVV V + 
Sbjct: 355 SEVGPGDILVGRISPKAEENPSPEEKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVL 414

Query: 946 NRHGIDKN 953
            R   D N
Sbjct: 415 RRDTDDTN 422



 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 118/415 (28%), Positives = 172/415 (41%), Gaps = 66/415 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G E+  GD+L    +      +   + +L         +  D  +     V   V 
Sbjct: 250  LVKAGQEIKAGDLLTDGPS-MENGELALGKNVLVGFSTWFGYNYEDAVILNEKLVKEDV- 307

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +  RS + +      +    +  +  L  +    +   +   + + G  
Sbjct: 308  YTSIHIEEQTIQFRRSKAGDDILTSDIPNASNRSKRFLGEDGIVIIGSEVGPGDILVGRI 367

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   + + Q     +     V+        +  +L     +     
Sbjct: 368  SPKAEENPSPE--EKLMAAIFGQKTSTHKDTSLKVKHGHGGTVVAVDVLRRDTDD----- 420

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                ++  G+  +VKV +A KR I+ GDKMAGRHGNKG+VS ILP EDMP+L DGTP+DI
Sbjct: 421  ---TNLEDGIEMIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIILPEEDMPYLADGTPLDI 477

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   L  K  S + D  ++  I  ++           
Sbjct: 478  LLNPQGVPSRMNIGQVLELHLGLAARKLNCKFVSPVFDGISHKQIQEIQKEAGIDPSGKM 537

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SG+       
Sbjct: 538  TV-----------------------------------------------YSGK------- 543

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGEPFD P++VG +Y LKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 544  TGEPFDNPISVGVMYYLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 598


>gi|86451147|gb|ABC96796.1| RNA polymerase II [Gentiana lutea]
          Length = 206

 Score =  319 bits (817), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 76/248 (30%), Positives = 105/248 (42%), Gaps = 54/248 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTAEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRSL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  SATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVLQE 1313
            GAA+ L+E
Sbjct: 199  GAAHFLKE 206


>gi|3746590|gb|AAC64010.1| RNA polymerase II subunit 2 [Kopsia fruticosa]
          Length = 269

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 77/255 (30%), Positives = 108/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + +HG KG +      EDMP   +G   DI +NP 
Sbjct: 42   TNADGLRFVKVRVRSVRIPQIGDKFSSKHGQKGTIGMTYTQEDMPSTAEGITPDISVNPH 101

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 102  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 129

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 130  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 167

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 168  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 227

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 228  GAAHFLKERLFDQSD 242


>gi|6606109|gb|AAF19067.1|AF107795_1 DNA-dependent RNA polymerase II RPB140 [Trichophyton rubrum]
          Length = 1109

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 163/1045 (15%), Positives = 322/1045 (30%), Gaps = 167/1045 (15%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 208  VEKGSRILSQLSIKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 266

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G        E
Sbjct: 267  NHICYDRNDTSMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSPMSMNQE 315

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 316  KRVRYARDIIQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRYV 364

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+  +R+ + + +  +        +     + A  +  
Sbjct: 365  DDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLTG 424

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 425  GLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKP 480

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 481  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNREVLEEFEP 540

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 541  QVSPNSTKVFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAG 600

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D      G   + ++ +  L+A+         E    +  G   + K +
Sbjct: 601  RVCRPLFVVDNDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-S 659

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G++E VDA       +    +   +    Y+          T  N+R    +  +     
Sbjct: 660  GVIEYVDAEEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWT 718

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   +   E  +   
Sbjct: 719  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFEQRMET- 770

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +     +
Sbjct: 771  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGRNV 802

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +    +    +E   +   
Sbjct: 803  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMR 858

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + +    Y ++ +   +  G           K++ L+ +                +E
Sbjct: 859  SDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEE 903

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  +  K+   T     E    +++      DD+     + VKV +   +  Q GDK
Sbjct: 904  LGQRTKQHTKLDVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDK 958

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 959  FASRHGQKGTIGITYRHEDMPFTREGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 1018

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L    E    +                               
Sbjct: 1019 YEGDATPFTDVTVDSVSSLLR--EHGYQSRGFEVM------------------------- 1051

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                 +G +    G         V +G  Y  +L HMV DK++A
Sbjct: 1052 --------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIHA 1084

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRL 1294
            R+ G   ++T+QP+ G++  GG R 
Sbjct: 1085 RARGPTQILTRQPVEGRARDGGLRF 1109



 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 138/1003 (13%), Positives = 286/1003 (28%), Gaps = 212/1003 (21%)

Query: 71  AAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDE----- 115
              L+F +     P               +   R+LTYA PL + +   + +  E     
Sbjct: 30  RYELKFGTVMLARPSMTEGDGATSIMLPQEARLRNLTYASPLYLGISKKIMEGRERLLSE 89

Query: 116 -------------------------FTGAKSIKDIKEQSIYMGDLPLMTKD--------- 141
                                            + +E++I++G +P+M K          
Sbjct: 90  RDEEEEEIEEKGDEERRNRGTYLHWERKPTMEDEAEEENIFIGKMPIMLKSKYCILKDLG 149

Query: 142 ---------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
                          G FVI G ++++++Q  RS G        + +      Y   I  
Sbjct: 150 EQALYNWNECPYDSGGYFVINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPYVAEIRS 206

Query: 187 --DQGLWMDIEFDSKDIIHVRIDR----------------RRKVPVTSFLMALG-MDSEE 227
             ++G  +  +   K  +  + D                 +  +P+     ALG +  E+
Sbjct: 207 AVEKGSRILSQLSIK--LFSKGDSAKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDED 264

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           IL+        +   +     +    ++   +V+   +       +  + +K        
Sbjct: 265 ILNHICYDRNDTSMLEMLKPCIEEGFVIQDREVALDFISKRGSSPMSMNQEKRVRYARDI 324

Query: 288 LKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           ++++ +  +  +           G  V   ++    G  Y++  D   +K L+       
Sbjct: 325 IQKEFLPHISQSEGSETRKAFFLGYMV-HRLLQCALGRRYVDDRDHFGKKRLDLAGPLLA 383

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
               +L++    +        V    +   +  +    +       T  +  ++    + 
Sbjct: 384 NLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTL-------TGGLKYALATGNWG 436

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDN 458
           +  K   S  G  ++  R    +      R          I     L N   G +   + 
Sbjct: 437 EQKKAASSKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAET 496

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEF 516
              +    V  +            E  I    + +   ++   PQ   N+  V      F
Sbjct: 497 PEGQACGLVKNLALMCCITVGTPSEPIIDFMIQRNREVLEEFEPQVSPNSTKV------F 550

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGR 568
                +    +  + +  +   RR + +                      R   P     
Sbjct: 551 VNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFVVD 610

Query: 569 ICPAETSEGHNIGLVSSLTSF-ARVNAYGFIETPYRK-----VCDGKVTNDVVYLSAMEE 622
             P   + G  + +   +    A       ++   R+           +  + Y+ A EE
Sbjct: 611 NDPKSENSGSLVLVKEHIHKLEADKELPPDLDPEERRERHFGWDGLVKSGVIEYVDAEEE 670

Query: 623 ENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           E   I      L+    +         +     R     +          +  P  ++ I
Sbjct: 671 ETIMIVMTPEDLEASKQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSMILGI 730

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +         T  E  +   +           
Sbjct: 731 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFL-------TNFEQRMETMANIL-------- 775

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                      Q+PL             
Sbjct: 776 ----------------------------------------YYPQKPL----------ATT 785

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  GRN++VA   + GYN EDS+++++  +   +F S+    +    +  
Sbjct: 786 RSMEFLKFRELPAGRNVIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMI 845

Query: 855 KLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            L   E     +  D   +       +D+ GI+  G  V+  DI++GK +P     + PE
Sbjct: 846 GLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGKTSP-----LAPE 900

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            + L     +      D S  + S  SG V  V +   +   K
Sbjct: 901 AEELGQRTKQH--TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 941


>gi|212373971|emb|CAP09912.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35711]
          Length = 320

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 188/320 (58%), Positives = 247/320 (77%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF S  LSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 1   VKEFFGSXXLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 60

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++
Sbjct: 61  ETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLSAIEEADHVIAQASA 120

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           ++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 121 TMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 180

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 181 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEV 240

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+NM 
Sbjct: 241 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQNMR 300

Query: 813 VAFMPWHGYNFEDSMLISER 832
           +AFM W+G+NFEDS+ +SER
Sbjct: 301 IAFMAWNGFNFEDSICLSER 320


>gi|83415489|gb|ABC17952.1| RNA polymerase II second largest subunit [Umbelopsis ramanniana]
          Length = 717

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 129/849 (15%), Positives = 248/849 (29%), Gaps = 149/849 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ + +R+   ++ + +    +              + +  + + +     +
Sbjct: 2    KRMDLAGPLMASLFRMLFKKLTKDVAKYLQKCIESSREFNLTLAVKSSTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQSKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
              +CPAET EG   GLV +L   + ++  G    P     +     ++  LSA    +  
Sbjct: 118  DMVCPAETPEGQACGLVKNLALMSYIS-VGSAAAPLILFLEEWAMENLEELSASNIPDAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N           EL+         +         D SP+  +             D
Sbjct: 177  KIFVNGVWVGIHRDPGELITSLKQMRRSV---------DISPEVSIVRDIREKELRMYTD 227

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA-AIVAKRAGIVEQVDAIRIVI 745
            + R      +       L  +   +      +    S          GI+E +DA     
Sbjct: 228  AGRCCRPLFIVEDQQLKLTKDHVAL------LQDPDSNYRWQDLISDGIIEYIDAEEEET 281

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +            K  +S+++     +   +              PS  LG  
Sbjct: 282  AMICMTPEDLAESRYSAEYGKPLQSDRDVASRLKT--QQSGYSHTWTHCEIHPSMILG-- 337

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   +++  ++V                
Sbjct: 338  -----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYLTNYQVRM-------------- 376

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 377  -------------DTLANILYYPQKPLTTTRSMEFLRFRELPAGQNAIVAILCYSGYNQE 423

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R  +D  +++  +  E+ E   RD               
Sbjct: 424  DSVIMNQSSIDRGLF-RSLFLRTYMDAEKKAGMMFMEEFEKPTRDNTLRLKHGTYEKLEE 482

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  + +D      R++          ++     +  Q    
Sbjct: 483  DGLIAPGTRVSGDDIIIGKTAPIPADSEELGQRTKGHNKRDASTPLRSTETGIVDQ---- 538

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV V   R  Q GDK A RHG KG +     
Sbjct: 539  ----------------VMVTTNQDGLKFVKVRVRSTRVPQMGDKFASRHGQKGTIGITYR 582

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             ED+PF  +G   DI++NP  +PSRM +G + E  LG      G +  +          +
Sbjct: 583  HEDLPFSGEGVTPDIIINPHAIPSRMTIGHLVECLLGKVPTLTGNEGDATPFTDVTVEAV 642

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S      E+                                                   
Sbjct: 643  SQAL--AEQGYQQRGFEVM----------------------------------------- 659

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 +G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 660  ----YNGHT----GR---KLAAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 708

Query: 1286 KSNRGGQRL 1294
            +S  GG R 
Sbjct: 709  RSRDGGLRF 717


>gi|242392280|dbj|BAH80377.1| RNA polymerase subunit B' [Halorubrum tibetense]
          Length = 609

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 133/603 (22%), Positives = 211/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            D + R D+    + D    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   DALERGDVEFEDLVDRGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDERPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ A+D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPAQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE + S L       SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRSGLEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 42.4 bits (98), Expect = 0.54,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+  +A     + +D                    
Sbjct: 85  LERGDVEFEDLVDRGYVEFIDAEEEEDILVAVDEEDVTDDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ V  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|82749754|gb|ABB89761.1| RNA polymerase beta subunit [Mycoplasma neurolyticum]
          Length = 594

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 214/451 (47%), Positives = 308/451 (68%), Gaps = 13/451 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS + + RR+++LG GG+ R  A  E+R VH T+YGRICP ET EG NIGL+ +L ++
Sbjct: 2   NPLSELANKRRITSLGPGGLNRETAQFEVRVVHSTYYGRICPIETPEGQNIGLILNLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++++ +GFI+TPY  V +G V   +V +L+A++E     AQ++ ++DE+    +E +  R
Sbjct: 62  SKIDDFGFIQTPYFPVKNGVVNYGEVKWLTAVDEYGYTFAQSSVTIDENNKIIDEFITVR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              + ++V  E+ID+I  + KQ+ SIA+S IPFLENDDSNRVLMG NMQRQAVPL++AEA
Sbjct: 122 KDYQYLIVKPEEIDYIAVASKQMTSIASSAIPFLENDDSNRVLMGANMQRQAVPLIEAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P +GTG+E  +AK +   I A  +GIV  VDA  I I+  + +L+      DIY L  FQ
Sbjct: 182 PLIGTGVEHDIAKYAATNIRAFNSGIVTYVDAKTIKIKPFDENLEE-----DIYYLKSFQ 236

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T +NQ P V+VG+ + +  ++ DGPST  G+LALG+N+LVAF  WHGYNFED+++
Sbjct: 237 KSNQGTTINQIPTVEVGETIEKGQLVCDGPSTKDGELALGKNVLVAFTTWHGYNFEDAII 296

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DVFTSIHIEE  +  R +K G + +T +IPN S    +++DE GI+ VG+EV
Sbjct: 297 ISEKLVKDDVFTSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSKRHLDENGIVRVGSEV 356

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           N GDILVG+I+PKGE   TPEEKLL AIFG K  + +DTSL+V  G +GTV+DV+I +R 
Sbjct: 357 NTGDILVGRISPKGEDNPTPEEKLLNAIFGNKGSNQKDTSLKVKHGDAGTVIDVQIISRA 416

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       +  + I+ + +    ++  + 
Sbjct: 417 NGD-------ILEDGIDKIVKVFIAQKRKIK 440



 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 135/498 (27%), Positives = 205/498 (41%), Gaps = 72/498 (14%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                       ++ A  P  G   E  +            + I     +      K   E
Sbjct: 165  MGANMQRQAVPLIEAEAPLIGTGVEHDIAKYAATNIRAFNSGIVTYV-DAKTIKIKPFDE 223

Query: 860  EITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             +  DI  +      N    I++   + VG  +  G ++    + K +  +   + +L A
Sbjct: 224  NLEEDIYYLKSFQKSNQGTTINQIPTVEVGETIEKGQLVCDGPSTK-DGELALGKNVLVA 282

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                   +  D  +     V   V    I       +   S + +      +       +
Sbjct: 283  FTTWHGYNFEDAIIISEKLVKDDVF-TSIHIEEQTIQFRTSKAGDDTLTSEIPNASTRSK 341

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              LD N   R+   +   + + G    K     + +        +       ++   +  
Sbjct: 342  RHLDENGIVRVGSEVNTGDILVGRISPKGEDNPTPE-------EKLLNAIFGNKGSNQKD 394

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             SLKV++  + ++++     +I     GD +  G+ ++VKVF+A KR I+ GDKMAGRHG
Sbjct: 395  TSLKVKHGDAGTVID----VQIISRANGDILEDGIDKIVKVFIAQKRKIKVGDKMAGRHG 450

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            NKG++S +LP EDMP+L+DGTP+DI+LNP GV SRMN+GQ+ E HLG A   L  K  S 
Sbjct: 451  NKGVISLVLPVEDMPYLEDGTPIDILLNPQGVASRMNIGQVLELHLGMAAKKLNVKFVSP 510

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            + D   N  +  +                                               
Sbjct: 511  VFDGIKNESLDSIL---------------------------------------------K 525

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E           L ESG+  LYDG+TG+ +D  V+VG +YMLKL HMV DK+ ARS G Y
Sbjct: 526  EAD---------LPESGRFTLYDGITGKQYDSKVSVGVMYMLKLQHMVDDKINARSVGPY 576

Query: 1276 SLVTQQPLGGKSNRGGQR 1293
            SL++QQPLGGKS  GGQR
Sbjct: 577  SLISQQPLGGKSQNGGQR 594


>gi|52694123|emb|CAG30591.1| DNA-directed RNA polymerase beta chain [Pseudomonas fulva]
          Length = 390

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 194/348 (55%), Positives = 254/348 (72%), Gaps = 2/348 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 3   RVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 62

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+
Sbjct: 63  VSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLES 122

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E 
Sbjct: 123 PYRVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPED 182

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 183 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 242

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 243 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 302

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           LV  GD+V+R DI+ADGPSTD+G+    R    A   W G        
Sbjct: 303 LVSKGDKVQRGDIMADGPSTDMGERRWVR--TCASRSWRGTASTSKTP 348


>gi|4867864|emb|CAB43075.1| RNA polymerase II [Mitrasacme pilosa]
          Length = 242

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 79/255 (30%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 40   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGICPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 128  ---------------------ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPL 165

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 166  TSTIFLGPXYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGXRFGEMERDCMIAH 225

Query: 1306 GAAYVLQEMLTIKSD 1320
             AA+ L+E L  +SD
Sbjct: 226  XAAHFLKERLLDQSD 240


>gi|83415475|gb|ABC17945.1| RNA polymerase II second largest subunit [Scutellospora heterogama]
          Length = 761

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 130/862 (15%), Positives = 253/862 (29%), Gaps = 131/862 (15%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R+   ++ + I    R              I A+ + + +     +
Sbjct: 2    KRMDLAGPLLASLFRMLFKKLTKDISIYLRKCIDTSREFNLHLAIKAQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + ++     +             +   ++  ++ +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMSYISVGSSSKPI------VDFLEEYGMINLNQQFDPA 171

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
              + N+ +  +G +             +   R  +   D SP+  V             D
Sbjct: 172  NIRDNTKVFVNGKWAGISTAPEQLANTLRGLRRSV---DVSPEVSVVRDIREKELRIYTD 228

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + RV     +      ++  E   +   ++     S               VD   I   
Sbjct: 229  AGRVCRPLFIVEDQCLVISKE---LINNLDQKGRTSGQVYDDEYPDEDNRHVDGEEIQGE 285

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            + +           +Y       +     ++      V   +   D+ A       G   
Sbjct: 286  NAQEQSQKRRQDRQVYVWHDLISNGAIEYIDAEEEETVMICMTPEDLAASMHFYQTGIAR 345

Query: 807  LGRNM------------LVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMAR 852
              +               ++   W       SM+  I   ++            ++    
Sbjct: 346  TSKTHEKDVAARVKSESNLSIHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 405

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G          V+   L+      +  +        +    +       +   +  
Sbjct: 406  KQAMG--------IYVTNYQLRM---DTLANILYYPQKPLVTTRAMEFLRFRELPAGQNA 454

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  ++ +   S +   +    IF R  +D+ ++   +  E+ +   R+  
Sbjct: 455  IVAILCYSGYNQENSVIMNQSSIDRGLF-RSIFYRSYMDQEKKVGILSIEEFDKPTRETT 513

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                            I  G           K T +    I    R            ++
Sbjct: 514  LRLKHGTYEKLEEDGLIAPGTRVSGDDIIIGKVTPIPEHTIELGQRKNTHTHRDASTPMR 573

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             ++ VKV V   R  Q GDK A 
Sbjct: 574  STENGIVDQ--------------------VMVTTNAEGMKFVKVRVRSTRIPQMGDKFAS 613

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +G + E  LG      G++ 
Sbjct: 614  RHGQKGTIGITYRQEDMPFTSEGITPDLIINPHAIPSRMTIGHLVECLLGKVSTLTGQEG 673

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          IS      +    +                                  
Sbjct: 674  DATPFTDVTVEAISHSLR--QNGYHSRGFEVM---------------------------- 703

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                              +G +    G         V +G  Y  +L HMV DK+++R+ 
Sbjct: 704  -----------------YNGHT----GR---KLAAQVFLGPTYYQRLKHMVDDKIHSRAR 739

Query: 1273 GSYSLVTQQPLGGKSNRGGQRL 1294
            G   ++T+QP+ G+S  GG R 
Sbjct: 740  GPVQILTRQPVEGRSRDGGLRF 761


>gi|194270594|gb|ACF36843.1| RNA polymerase beta subunit [Mycoplasma columborale]
 gi|194270596|gb|ACF36844.1| RNA polymerase beta subunit [Mycoplasma columborale]
 gi|194270598|gb|ACF36845.1| RNA polymerase beta subunit [Mycoplasma columborale]
          Length = 596

 Score =  318 bits (816), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 210/451 (46%), Positives = 307/451 (68%), Gaps = 16/451 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N LS +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLSEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +FA+VN  GF++TPY +V DG V  ++VVYL+A EE     AQ++  +DE+       + 
Sbjct: 61  TFAKVNDLGFLQTPYFRVKDGVVNYDEVVYLTAAEEIGYAFAQSSVKVDENNRIVSPSLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     I+    ++DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+A
Sbjct: 121 IRKDYNYIIGSPLEVDFIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLLQA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP+V TG+E+ +AK S   + AK +G V  VD  RI +++ +G  D        Y L  
Sbjct: 181 EAPYVATGIEADIAKYSSYNLTAKNSGEVVFVDGSRIHVKNDKGVTDK-------YFLRN 233

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + Q+P+V++G  V + D++ DG S   G++ALG+N+LV F  W+GYNFED+
Sbjct: 234 FERSNQGTLIQQKPIVEIGQMVEKGDLLVDGSSFKDGEMALGKNVLVGFTTWNGYNFEDA 293

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVG 885
           ++I+ER+V +DV+TSIHIEE  +  R ++ G +++TR DIPNVS+  ++++DE GI+ VG
Sbjct: 294 VIINERLVKDDVYTSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKYSIRHLDEQGIVRVG 353

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +EV  GD+LVG+I+PKGE   T EEKLL AI  ++  +V+DTSL+V +G +GTV+ V + 
Sbjct: 354 SEVVAGDVLVGRISPKGEDNPTQEEKLLMAILQQRPQNVKDTSLKVKNGHNGTVIHVEVL 413

Query: 946 NR-------HGIDKNERSISVEREQIELLAR 969
           +R        GIDK  +    ++ +I++  +
Sbjct: 414 SRDKGDVLEDGIDKIVKVSIAQKRKIKVGDK 444



 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 128/421 (30%), Positives = 190/421 (45%), Gaps = 78/421 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ +G  V  GD+LV   + K +  M   + +L         +  D  +           
Sbjct: 248  IVEIGQMVEKGDLLVDGSSFK-DGEMALGKNVLVGFTTWNGYNFEDAVIINERLVKDDVY 306

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R      ++    +   +   +    DEQ I+         ++L G+ 
Sbjct: 307  TSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKYSIRHLDEQGIVRVGSEVVAGDVLVGRI 366

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L   ++ + P++           V+     +K  +  +   +E   +
Sbjct: 367  SPKGEDNPTQEEKLLMAILQQRPQN-----------VKDTSLKVKNGHNGTVIHVEVLSR 415

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K      GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 416  DK------GDVLEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 469

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQ+ E HLG A   LG K  +   D     DI         
Sbjct: 470  GTPLDIMLNPQGVPSRMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKKDIEDAL----- 524

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                        + + L  +      + 
Sbjct: 525  --------------------------------------------VEAGLDRSG-----KQ 535

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             L D +TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 536  TLIDPITGRKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 595

Query: 1295 G 1295
            G
Sbjct: 596  G 596


>gi|52694355|emb|CAG38017.1| RNA polymerase beta subunit [Pseudomonas putida]
          Length = 327

 Score =  318 bits (816), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 193/326 (59%), Positives = 252/326 (77%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 SDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R
Sbjct: 241 RGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFM 816
           +DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 301 SDIMADGPSTDMGELALGQNMRIAFM 326


>gi|21228374|ref|NP_634296.1| DNA-directed RNA polymerase subunit B' [Methanosarcina mazei Go1]
 gi|20906844|gb|AAM31968.1| DNA-directed RNA polymerase beta chain [Methanosarcina mazei Go1]
          Length = 604

 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 116/585 (19%), Positives = 187/585 (31%), Gaps = 94/585 (16%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              +  D     N  +A       +    M I   M+       +   E     R+T    
Sbjct: 96   CVEYLDAEEEENAYIALYESDITDRHTHMEIDPEMMLGICTGMVPYPEHNASPRNTMGAA 155

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
              + +    VS    + +       V                 G       +  + AI  
Sbjct: 156  --MIKQCIGVSTAN-QKLRPDTRAHVLHYPQRALTRTRTSEAIGFDDRPAGQNFVVAILS 212

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  ++ D  +    G     +    F R    +  R    + ++ E+   +        
Sbjct: 213  YEGYNIEDALIFNR-GSIDRGLGRSHFLRTFEGEERRYPGGQEDKFEIPDSEY--RGARS 269

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                 +  ++ L       GP             + E                   VE  
Sbjct: 270  AEAYANLDVDGLVNPETPVGPNDVLIGKTSPPRFLEEPSDFGI------------AVEQR 317

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T +S         I              R+ KV V  +R    GDK A RHG KG
Sbjct: 318  RESSVTMRSNETGIVDTVIL------TESINGTRLAKVKVRDERIPDIGDKFASRHGQKG 371

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++   +P  DMPF + G   D+++NP  +PSRM V        G     +G K+ S+   
Sbjct: 372  VIGLKVPIADMPFTESGLTPDLMINPHAIPSRMTV--------GHVLEMIGGKVGSMEGR 423

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                                F G  E+ 
Sbjct: 424  RVNAT----------------------------------------------AFSGEKEDD 437

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L+      +G+ + YDG TG      V VG I   KL+HMV+ K++ARS G   ++
Sbjct: 438  LREALKKHGFAHTGKEVFYDGATGRMIPADVFVGVILYQKLHHMVTSKMHARSRGPVQVL 497

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE- 1330
            T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G    Y+ 
Sbjct: 498  TRQPTEGRAREGGLRFGEMERDVLVGHGAAMSLKERLLDESDKVVELVCSHCGMVATYDK 557

Query: 1331 ------SIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                      G   D +      +F +L+ E+++LG++  L    
Sbjct: 558  QRNVAFCSACGADTDIYPVEMSYAFKLLLDEIKSLGVAPRLNLED 602



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 58/335 (17%), Positives = 113/335 (33%), Gaps = 37/335 (11%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI----AASLIPFLENDD 686
           N  L        ELV              +++       + V I      +  P L  ++
Sbjct: 9   NGELVGTHDNPAELVEELRKMRRQGFISRQVNIALNDSTREVIINSDMGRARRPLLVVEN 68

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            +  +   ++Q+     +  +       +E + A+    A +A        +      + 
Sbjct: 69  GSPKVTEEHVQKLKNKEISFDDLVKEGCVEYLDAEEEENAYIA---LYESDITDRHTHME 125

Query: 747 SVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQRPLVKVGDEVRRNDIIAD-------- 796
                +    +G+  Y       + +     + Q   V   ++  R D  A         
Sbjct: 126 IDPEMMLGICTGMVPYPEHNASPRNTMGAAMIKQCIGVSTANQKLRPDTRAHVLHYPQRA 185

Query: 797 ------GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   +    D   G+N +VA + + GYN ED+++ +   +   +  S  +  FE  
Sbjct: 186 LTRTRTSEAIGFDDRPAGQNFVVAILSYEGYNIEDALIFNRGSIDRGLGRSHFLRTFEGE 245

Query: 851 ARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            R    G E+   +IP+       S E   N+D  G++     V P D+L+GK +P    
Sbjct: 246 ERRYPGGQEDKF-EIPDSEYRGARSAEAYANLDVDGLVNPETPVGPNDVLIGKTSPPRFL 304

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                     + FG      R++S+ + S  +G V
Sbjct: 305 EEP-------SDFGIAVEQRRESSVTMRSNETGIV 332



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 33/194 (17%), Positives = 61/194 (31%), Gaps = 30/194 (15%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F + +L    ++   L       R        V  A        +  +  GR        
Sbjct: 7   FINGELVGTHDNPAELVEELRKMRRQGFISRQVNIALNDSTREVIINSDMGRAR------ 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              + +V + +          ++       D      V YL A EEEN YIA   S +  
Sbjct: 61  -RPLLVVENGSPKVTEEHVQKLKNKEISFDDLVKEGCVEYLDAEEEENAYIALYESDIT- 118

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                 ++   ++  P+ ++ I   ++P+ E++ S R  MG  M
Sbjct: 119 ----------------------DRHTHMEIDPEMMLGICTGMVPYPEHNASPRNTMGAAM 156

Query: 697 QRQAVPLLKAEAPF 710
            +Q + +  A    
Sbjct: 157 IKQCIGVSTANQKL 170


>gi|198423468|ref|XP_002121670.1| PREDICTED: similar to polymerase (RNA) III (DNA directed) polypeptide
            B [Ciona intestinalis]
          Length = 1141

 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 117/559 (20%), Positives = 200/559 (35%), Gaps = 76/559 (13%)

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE-GLKNIDECGIICVGAEV 888
            ++  V+ D     H      +   T LG        P+ ++          G   +G   
Sbjct: 641  NDCFVALDESYITHKSTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 700

Query: 889  NPGDILVGKITPKGESPMTP--EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +  +      P  P  + + +  I  EK    ++  + V S     + D  + N
Sbjct: 701  YNQQQRIDTLMYLLVYPQAPLVKSRTIELINFEKLPAGQNAIIAVMSYSGYDIEDALVLN 760

Query: 947  RHGIDKNERSISVEREQ---IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            R  +D+      V R Q   ++  A    D+ +    N  +R            G     
Sbjct: 761  RASVDRGYGRCLVYRNQKCILKRYANQTFDKVMGPALNAETREPIWRHQGLDADGIIMPG 820

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    ++                     ++     Y+ +         + IEK+   
Sbjct: 821  VKVESKQKIMCXLYXXXXXXXXXXXXXXXXXLQGPSTSYQETPISYRGPVGSTIEKVMVS 880

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
             +       ++K+ +   R  + GDK + RHG KG+   I+   DMPF +DG   D+++N
Sbjct: 881  SNNEES--SLIKILLRQTRRPELGDKFSSRHGQKGVTGLIVQQADMPFNQDGICPDVIMN 938

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P G PSRM VG++ E         LG K  ++   +                        
Sbjct: 939  PHGYPSRMTVGKLME--------LLGSKAGAIGGKFHYGT-------------------- 970

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                       F G   E ++ +L     +  G+  L  G+TGE
Sbjct: 971  --------------------------AFGGDKVEDLSQVLTDNGYNYVGKDCLTSGITGE 1004

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F+  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S+ GG RLGEME  C+ 
Sbjct: 1005 SFEAYIYQGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSHDGGLRLGEMERDCLI 1064

Query: 1304 AYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVLV 1351
             YGA+ +L E L I SD    DV G+  +      G         +      P +  +L 
Sbjct: 1065 GYGASMLLLERLMISSDQFEVDVCGKCGLLGY--DGWCQFCKSSKNVATLKIPYACKLLF 1122

Query: 1352 KEMQALGLSIDLENSRTKN 1370
            +E+ ++ +   L+      
Sbjct: 1123 QELTSMNIIPRLKLKPYNE 1141



 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 122/931 (13%), Positives = 275/931 (29%), Gaps = 186/931 (19%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
            PE + +  L++    S+++F+ ++I    + N+            +       LE++  
Sbjct: 31  LPEFLKVKGLVKQHIDSFNYFVNVDIKNIVKANK---RVL------SDADPNWYLEYLDI 81

Query: 80  EFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               P               +C  RD+TY+  + + +             +  + I  ++
Sbjct: 82  HVGVPDVEESFNVTRAVTPHECRLRDMTYSASITVDIEYT----------RGQQRIIRKA 131

Query: 130 IYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHF 165
           + +G +P+M                           G FV KG++++++ Q   S     
Sbjct: 132 LPIGRMPIMLRSSNCVLTGKNGVELAKMNECPYDPGGYFVCKGVEKVILIQEQMS----- 186

Query: 166 DHDKGRASLSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMAL 221
             ++       K   +C +      +   +++    K   +++ +     +P+     A+
Sbjct: 187 -KNRMIVERDRKGFCSCSVHSSTHEKKTRVNV-LQKKGHFYLQQNALNEDMPICVIFKAM 244

Query: 222 GMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV-DIDTGEQVIESGKK 279
           G++SE+ I+     +                 ++    + S  +   I     V  + ++
Sbjct: 245 GVESEQSIMQLIGTEENVMSMFSPSLEDCHKLEVFTQLQASKYISGKIRRQRPVWGAARQ 304

Query: 280 LTSGLLKSLKEKGV------KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
             +   +      +            +  +    +   I+  + G + ++  D    K +
Sbjct: 305 SKTDETRDWLNTTLLAHIPVTDWNYHAKAVYLALMIRRIILTQLGYLEVDDRDYYGNKRM 364

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
           E         I +L+ D           +        + A  D+ R MR   ++T  V  
Sbjct: 365 ELAGGL----ISLLFEDLFKRFNSELKKIADLTIPKPRAAQFDVVRHMRQDLITTSLVIA 420

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---NGK 450
              +   +   ++ +   G  ++  RL+  +   +            K+        +  
Sbjct: 421 --ISSGNWIVKRFKMERKGVTQVLTRLSYISALGMMTRIASQFEKTRKVSGPRSLQPSQW 478

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           G +   D         V  +    +    +  E + +   +    D  M         + 
Sbjct: 479 GMLCPSDTPEGEACGLVKNLALMTHITVDVEEEPTARLLFNLGVEDVYMLSGEEIHSQLS 538

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PTHYGRI 569
             V  F     L  + + V+ ++ +   RR   L              R V+  +  GR+
Sbjct: 539 YIV--FLNGLVLGVVRDPVHLVTTLRLMRRHGYLN--DFISVSTNRAHRTVYVSSDGGRL 594

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           C           LV+S            ++   R   D   +  V YL   EE + ++A 
Sbjct: 595 CRPYIIVSKGKPLVTSHHIE-------ELKRGLRSFEDFLRSGLVEYLDVSEENDCFVAL 647

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
             S +                         K   ++  P  ++ + A LIP+  ++ S R
Sbjct: 648 DESYIT-----------------------HKSTHLEIEPFTLLGVCAGLIPYPHHNQSPR 684

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+                                           I   +
Sbjct: 685 NTYQCAMGKQAMGT-----------------------------------------IGYNQ 703

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                +   + +Y               Q PLVK                 +   L  G+
Sbjct: 704 QQRIDTLMYLLVYP--------------QAPLVKS----------RTIELINFEKLPAGQ 739

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N ++A M + GY+ ED+++++   V       +     + + +       +         
Sbjct: 740 NAIIAVMSYSGYDIEDALVLNRASVDRGYGRCLVYRNQKCILKRYANQTFDKVMGPALNA 799

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                    + +D  GII  G +V     ++
Sbjct: 800 ETREPIWRHQGLDADGIIMPGVKVESKQKIM 830


>gi|73697655|gb|AAZ81444.1| RNA polymerase beta subunit [Mycoplasma faucium]
          Length = 592

 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 208/448 (46%), Positives = 299/448 (66%), Gaps = 10/448 (2%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           FA+++ YGFI+TPY KV + KV  +  +YL+A+EE    I Q+   +  D    +E V  
Sbjct: 61  FAKIDQYGFIQTPYFKVKNKKVDFSTPIYLTAIEEMGATITQSTVKIVND-EIIDEYVMA 119

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E + V   ++D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++K E
Sbjct: 120 RRDNEYVEVLASEVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPVIKTE 179

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AP V TG+E+ +AK S   I +   G V  VDA +I +  + G        V+ Y L  F
Sbjct: 180 APLVATGVEADIAKYSSTNIRSNIDGTVTYVDANQIKVMPLTGKK------VETYNLRTF 233

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +RSNQ T ++Q+PLV +GDE+++ D++ DGPS + G+LALG+N+LV F  W+GYN+ED++
Sbjct: 234 ERSNQGTLIHQKPLVNIGDEIKKGDLLVDGPSMNNGELALGKNILVGFSTWNGYNYEDAV 293

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +DV+TSIHIEE  +  R +K G +E+T +IPN S    + ++E GI+ +G+E
Sbjct: 294 ILSERLVKDDVYTSIHIEEQTIQFRHSKAGDDELTANIPNASNFSKRFLNENGIVRIGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GDILVG+ +PKGE   TPEEKL+ AIFG+K+   +DTSL+V  G +GTVV V + +R
Sbjct: 354 VAAGDILVGRTSPKGEENPTPEEKLMAAIFGQKSSSSKDTSLKVKHGHNGTVVAVEVLSR 413

Query: 948 HGIDKNERSISVEREQIELLARDKDDEQ 975
                ++    +E+     +A+ +  + 
Sbjct: 414 EQG--DQLEDGIEKIVKVSIAQKRKIKV 439



 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 122/413 (29%), Positives = 180/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G E+  GD+LV   +      +   + +L         +  D  +     V   V 
Sbjct: 247  LVNIGDEIKKGDLLVDGPS-MNNGELALGKNILVGFSTWNGYNYEDAVILSERLVKDDV- 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E    +    +  +  L+ N   R+   +   + + G  
Sbjct: 305  YTSIHIEEQTIQFRHSKAGDDELTANIPNASNFSKRFLNENGIVRIGSEVAAGDILVGRT 364

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q +   +     V+        +  +L           
Sbjct: 365  SPKGEENPTPE--EKLMAAIFGQKSSSSKDTSLKVKHGHNGTVVAVEVLSR--------- 413

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+D+
Sbjct: 414  EQGDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEDMPYLEDGTPLDM 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + + D   +  I  +    +      S
Sbjct: 474  VLNPQGVPSRMNIGQVLELHLGLAAKKLGVKFVTPVFDGITHNQIKEILQEAKIDPSGKS 533

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              SGQ       
Sbjct: 534  VV-----------------------------------------------YSGQ------- 539

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD P++VG +YMLKL HMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  TGEKFDHPISVGIMYMLKLYHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|55379096|ref|YP_136946.1| DNA-directed RNA polymerase subunit B' [Haloarcula marismortui ATCC
            43049]
 gi|55231821|gb|AAV47240.1| DNA-directed RNA polymerase beta subunit [Haloarcula marismortui ATCC
            43049]
 gi|242392410|dbj|BAH80412.1| RNA polymerase subunit B' [Haloarcula sinaiiensis ATCC 33800]
          Length = 608

 Score =  318 bits (815), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 207/607 (34%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV        +    + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEGELTDNHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEDELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 41.6 bits (96), Expect = 0.89,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEGELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ++                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DNH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|46019148|emb|CAE52316.1| DNA-directed RNA polymerase beta chain [Bacillus subtilis subsp.
           subtilis]
          Length = 174

 Score =  318 bits (815), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 75/196 (38%), Positives = 122/196 (62%), Gaps = 22/196 (11%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
            + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LE
Sbjct: 1   SYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLE 50

Query: 76  FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD 
Sbjct: 51  FIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDF 101

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E
Sbjct: 102 PIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYE 158

Query: 196 FDSKDIIHVRIDRRRK 211
            D+KD+++VRIDR RK
Sbjct: 159 TDAKDVVYVRIDRTRK 174


>gi|199612849|gb|ACH91612.1| RNA polymerase subunit B [Bacillus subtilis]
          Length = 174

 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 76/196 (38%), Positives = 123/196 (62%), Gaps = 22/196 (11%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV 77
            +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+
Sbjct: 1   ARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFI 50

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+
Sbjct: 51  DYSLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPI 101

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD 197
           MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D
Sbjct: 102 MTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETD 158

Query: 198 SKDIIHVRIDRRRKVP 213
           +KD+++VRIDR RK+P
Sbjct: 159 AKDVVYVRIDRTRKLP 174


>gi|194591893|gb|ACF76527.1| RNA polymerase beta subunit [Mycoplasma cynos]
          Length = 596

 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 214/453 (47%), Positives = 301/453 (66%), Gaps = 14/453 (3%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+V+  GF++TPY KV DG V  NDV YL+A EE    IAQ++  +DE+   T+E + 
Sbjct: 61  TYAKVDEKGFLKTPYYKVNDGVVDYNDVRYLTAAEEFGYSIAQSSVHVDENNRITDENLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R     I      +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+ 
Sbjct: 121 IRRNYTYINGKNSDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQAVPLLET 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP + TG+ES +AK S   +VAK  G V  VD  RI I+  E  +       D Y L  
Sbjct: 181 EAPLIATGIESYIAKYSSYNLVAKNPGTVTFVDGSRIHIQRKESTV------TDKYTLRN 234

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F+RSNQ T + QRPLV+ GD V   DI+ DG S   G+LALG+N+LV F  W+GYNFED+
Sbjct: 235 FERSNQGTIIQQRPLVRTGDIVEAGDILTDGSSFKDGELALGKNVLVGFTTWNGYNFEDA 294

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+D+PN S+  L+N+D+ GI+ +G+
Sbjct: 295 VIINERLVKNDVYTSIHIEEQTIQFRSSRAGDDELTKDVPNASKYSLRNLDDNGIVKIGS 354

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV PGDILVG+++PKGE   + E+KLL A+ G+++   +DTSL+V +G +GT+  V I +
Sbjct: 355 EVYPGDILVGRVSPKGEENPSQEDKLLYAVLGQRSPSTKDTSLKVKNGHNGTITHVEILS 414

Query: 947 RHGIDKNERSISVEREQIELLARDKDDEQVILD 979
           R   D       V  E IE + +    ++  + 
Sbjct: 415 REKGD-------VLEEGIEKIVKVSIAQKRKIK 440



 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 131/415 (31%), Positives = 182/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V  GDIL    + K +  +   + +L         +  D  +     V   V 
Sbjct: 249  LVRTGDIVEAGDILTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAVIINERLVKNDV- 306

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E  + +          LD N   ++   +   + + G  
Sbjct: 307  YTSIHIEEQTIQFRSSRAGDDELTKDVPNASKYSLRNLDDNGIVKIGSEVYPGDILVGRV 366

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++      T   IL           
Sbjct: 367  SPKGEENPSQE--DKLLYAVLGQRSPSTKDTSLKVKNGHNGTITHVEILSR--------- 415

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 416  EKGDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 475

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  S   D     DI               
Sbjct: 476  MLNPQGVPSRMNIGQILELHLGMAAKKLNVKFVSPSFDGVKKPDIEEALIEAG------- 528

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                          FD                 ++G+ IL D +
Sbjct: 529  ------------------------------FD-----------------KTGKQILIDPI 541

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR G
Sbjct: 542  TGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRFG 596


>gi|243010756|gb|ACS94455.1| RpoB [Mycobacterium arosiense]
          Length = 248

 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 142/240 (59%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGTPDWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEDLRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.5 bits (106), Expect = 0.077,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|257051868|ref|YP_003129701.1| DNA-directed RNA polymerase subunit B' [Halorhabdus utahensis DSM
            12940]
 gi|242392254|dbj|BAH80364.1| RNA polymerase subunit B' [Halorhabdus utahensis]
 gi|256690631|gb|ACV10968.1| RNA polymerase Rpb2 domain 6 [Halorhabdus utahensis DSM 12940]
          Length = 608

 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 95/321 (29%), Positives = 136/321 (42%), Gaps = 80/321 (24%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KGIV  I P EDMPF + G   D+++NP  +
Sbjct: 345  EDGSKLSKVKVRDERIPELGDKFASRHGQKGIVGHIAPQEDMPFTEQGVVPDLIINPHAL 404

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   D+                      
Sbjct: 405  PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEDLRDSLEDHG-------------- 450

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ ++Y G+TGE  + 
Sbjct: 451  -----------------------FD-----------------SSGKEVMYSGITGEKVEA 470

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 471  EIFVGNIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 530

Query: 1308 AYVLQEMLTIKSD----DVVG-----------RTRVY------ESIVAGNDTFETGTPES 1346
            A  L+E L  +SD     V G           + RVY      E      D  E     +
Sbjct: 531  ALTLKERLLDESDQEWIHVCGQCGMTAVENVDQRRVYCPNCDEE-----TDVHEVEMSYA 585

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
            F +L+ EM+ALG++  +E   
Sbjct: 586  FKLLLDEMKALGIAPRIELED 606



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 65/381 (17%), Positives = 115/381 (30%), Gaps = 101/381 (26%)

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           Y  IE       +      V ++ A EEE+  +A     L E+                 
Sbjct: 81  YAAIENGELTFEELVERGFVEFIDAEEEEDILVAVDTDELTENH---------------- 124

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                    ++  P+ +  I A +IP+ E++ S R+ MG                     
Sbjct: 125 -------THLEVDPQLIFGIGAGMIPYPEHNASPRITMG--------------------- 156

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                   SG    +                                   ++        
Sbjct: 157 --------SGMIKQSLGLPSANY--------------------------RVRPDTRQHLL 182

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q  +VK                    D    +N  VA M + G+N ED++++++  V
Sbjct: 183 HYPQLSMVK----------TQTTEQIGYDDRPAAQNFTVAVMSYEGFNIEDALVMNKGSV 232

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEV 888
              +  S     +E   R    G E+   +IP+        E+   ++DE G++    +V
Sbjct: 233 ERALARSHFFRTYEGEERRYPGGQEDRF-EIPDDEVRGARGEDAYTHLDEDGLVNPETKV 291

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
               +L+GK +P               + G      R+TS+ + SG SG V  V +    
Sbjct: 292 GENAVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE 345

Query: 949 GIDKNERSISVEREQIELLAR 969
              K  +    +    EL  +
Sbjct: 346 DGSKLSKVKVRDERIPELGDK 366


>gi|52694265|emb|CAG30662.1| DNA-directed RNA polymerase beta chain [Marinobacterium stanieri]
          Length = 324

 Score =  318 bits (814), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 191/324 (58%), Positives = 251/324 (77%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + D++MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R
Sbjct: 1   MAESDNLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  FAR N YGF+ETPYR+V DG+VT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVFARTNDYGFLETPYRRVVDGQVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D+ YLSA+EE    IAQA+++++++G  T++LV  R   E  ++P E++ ++D S +QV
Sbjct: 121 DDIDYLSAIEENKYVIAQASATMNDNGRLTDDLVTVRHLNETTVMPPERVQYMDVSARQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTG+E  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGIERNVAQDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G++E VDA RIV+R  + ++    +GVDIY L K+ RSNQNTC+NQR +V  G+ V+R 
Sbjct: 241 GGVIESVDAARIVVRVHDDEVQAGEAGVDIYNLTKYVRSNQNTCINQRSIVNPGETVQRG 300

Query: 792 DIIADGPSTDLGDLALGRNMLVAF 815
           D++ADGPS DLG+LALG+NM +AF
Sbjct: 301 DVMADGPSVDLGELALGQNMRIAF 324


>gi|120561277|gb|ABM27023.1| RNA polymerase II second largest subunit [Neocallimastix frontalis]
          Length = 915

 Score =  318 bits (814), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 153/1040 (14%), Positives = 299/1040 (28%), Gaps = 192/1040 (18%)

Query: 282  SGLLKSLKEKGV-KFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
            S    +L  K + K     +  + G      +     +     ++   G V D   LE I
Sbjct: 41   SRHASTLYIKMLAKASARANSEIVGQSIKATLPYIRQDIPIVIVFRALGIVPDRDILEHI 100

Query: 337  FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
             +       +  +     +A++         +D++ AL  I +              +  
Sbjct: 101  CYDFNDTQMLEMLKPCIEDAFV--------IQDKEIALDFIGKR------------GTTV 140

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                    +Y    + +  +         +  +         +I  L+     +   DD 
Sbjct: 141  GVTKEKRMRYAAEILQKELLPHIGTKAHTETKK---AYFFGYMIHRLLLAALERRECDDR 197

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L + +R+   ++   + +  +              I    +   + 
Sbjct: 198  DHFGKKRLDLAGPLLGSLFRMLFRKLTSDVSKSLQKCIDRNREFNLNVAIRPNTITDGLK 257

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RRL+      + R     + R +
Sbjct: 258  YSLATGNWGAQSKFMQSRAGVSQVLNRYTFASTLSHLRRLNT----PIGRDGKLAKPRQL 313

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L   + V+           + +  +    +V     
Sbjct: 314  HNTHWGMVCPAETPEGQACGLVKNLALMSYVSVGSSSAPIIEFLEEWSMENMEEVHVSHI 373

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
            +     ++      +  D     + +     G+ +      + D  +   +         
Sbjct: 374  LNATKIFVNGVWVGVHRDPEHLVKTLRDLRRGQNVNAEISIVRDIRERELRIYTDAGRIC 433

Query: 679  IPFLENDDSNRVLMGCNM----QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             P    ++    L   ++    ++            +  G+           I A+    
Sbjct: 434  RPLFIVENQKLKLKKSHIALIQEKNETGEGWGWDDLIENGIIE--------FIDAEEEET 485

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                      +   + D   +   +  Y + K  +S      N                 
Sbjct: 486  TLIC------MSHEDLDPKDTEMDIQDYGISKRLKSRSVYSRN-------------WTHC 526

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               PS  LG       +  + +P+  +N       S R   +       +  +    +  
Sbjct: 527  EIHPSMILG-------ICASIVPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQ-- 571

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                                 +    +  +        +    +       +   +  + 
Sbjct: 572  ---------------------LRMDTMANILYYPQKPLVTTRAMEYLRFRDLPAGQNAIV 610

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R  +D+ ++      E  E   R+    
Sbjct: 611  AIACYSGYNQEDSIIMNQSSIDRGLF-RSLFYRSYMDQEKKVGMFNVENFEKPTRETCLR 669

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                          I  G           K+  LS D      R++          ++  
Sbjct: 670  LRHGTYEKLEDDGLIAPGIRVTGDDIIIGKTIPLSQDSEELGQRTEHHTKRDASTPLRST 729

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  +                             +R VKV V   R  Q GDK A RH
Sbjct: 730  ETGIVDR--------------------VLVTNNQDGMRFVKVRVRSTRIPQMGDKFASRH 769

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMPF  +G   DI++NP  +PSRM +G + E  LG      G +  +
Sbjct: 770  GQKGTVGMTYRTEDMPFTVNGITPDIIINPHAIPSRMTIGHLVECLLGKVSTLTGDEGDA 829

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      IS L    E    +                                F+G 
Sbjct: 830  TPFTDVTVEAISKLLR--ENGYQSRGFEVM--------------------------FNG- 860

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                            +G+               + +G  Y  +L HMV DK+++R+ G 
Sbjct: 861  ---------------HTGK----------KLQAQIFLGPTYYQRLKHMVDDKIHSRARGP 895

Query: 1275 YSLVTQQPLGGKSNRGGQRL 1294
              ++T+QP+ G+S  GG R 
Sbjct: 896  VQILTRQPVEGRSRDGGLRF 915



 Score =  106 bits (265), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 92/676 (13%), Positives = 208/676 (30%), Gaps = 85/676 (12%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLW----MDIEFDSK--- 199
            ++++++Q   +  + +   K   S      Y   I    + G      + I+  +K   
Sbjct: 1   SEKVLIAQERMASNVIYVFAKSPPSP---YSYTAEIRSAVETGSRHASTLYIKMLAKASA 57

Query: 200 ----DII---------HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFW 245
               +I+         ++R D    +P+     ALG+  + +IL         +Q  +  
Sbjct: 58  RANSEIVGQSIKATLPYIRQD----IPIVIVFRALGIVPDRDILEHICYDFNDTQMLEML 113

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
              +  A ++   +++   +        +   K++     + L+++ +  +G  +     
Sbjct: 114 KPCIEDAFVIQDKEIALDFIGKRGTTVGVTKEKRMRYA-AEILQKELLPHIGTKAHTETK 172

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
                  +      + + A +  +    +            L +      +  R      
Sbjct: 173 KAYFFGYMIH---RLLLAALERRECDDRDHFGKKR------LDLAGPLLGSLFRMLFRKL 223

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            +   K     I R         F++  ++      D  KY L   G      +      
Sbjct: 224 TSDVSKSLQKCIDRN------REFNLNVAIRPNTITDGLKYSL-ATGNWGAQSKFMQSRA 276

Query: 426 DDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE--------MLK 472
              + + +    + +  L  L     R+GK       +  +  +    E        ++K
Sbjct: 277 GVSQVLNRYTFASTLSHLRRLNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVK 336

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           N   +  + +  S    I  ++  S+   + ++   +++A   F     +    +  + +
Sbjct: 337 NLALMSYVSVGSSSAPIIEFLEEWSMENMEEVHVSHILNATKIFVNGVWVGVHRDPEHLV 396

Query: 533 SRITHTRR-LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
             +   RR  +   +  + R     E+R ++        P    E   + L  S  +  +
Sbjct: 397 KTLRDLRRGQNVNAEISIVRDIRERELR-IYTDAGRICRPLFIVENQKLKLKKSHIALIQ 455

Query: 592 -VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
             N  G          D      + ++ A EEE   I  ++  LD   +  +   +    
Sbjct: 456 EKNETGEG----WGWDDLIENGIIEFIDAEEEETTLICMSHEDLDPKDTEMDIQDYGISK 511

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP------- 702
             +   V        +  P  ++ I AS++PF +++ S R      M +QA+        
Sbjct: 512 RLKSRSVYSRNWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGKQAMGIYLTNFQ 571

Query: 703 ---------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
                    L   + P V T  ME +  +   A   A  A            I   +  +
Sbjct: 572 LRMDTMANILYYPQKPLVTTRAMEYLRFRDLPAGQNAIVAIACYSGYNQEDSIIMNQSSI 631

Query: 753 DPSTSGVDIYRLMKFQ 768
           D        YR    Q
Sbjct: 632 DRGLFRSLFYRSYMDQ 647


>gi|117912927|gb|ABG77311.2| RNA polymerase beta subunit [Enterobacter helveticus]
          Length = 322

 Score =  318 bits (814), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 196/321 (61%), Positives = 247/321 (76%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGVVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S +QVVS
Sbjct: 122 IHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQVVS 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 182 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 241

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V + + V R D+
Sbjct: 242 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLNEPVERGDV 301

Query: 794 IADGPSTDLGDLALGRNMLVA 814
           +ADGPSTDLG+LALG+NM VA
Sbjct: 302 LADGPSTDLGELALGQNMRVA 322


>gi|243010760|gb|ACS94457.1| RpoB [Mycobacterium malmoense]
          Length = 251

 Score =  318 bits (814), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 106/240 (44%), Positives = 141/240 (58%), Gaps = 37/240 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G K+           ++       E  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKVDVAGGTPDWAANLPEDLLHAE-- 157

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 158  --------------------------PDAIVSTPVFDGAKEEELQGLLSSTLPNRDGEVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 192  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 251



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|195054746|ref|XP_001994284.1| GH25170 [Drosophila grimshawi]
 gi|193896154|gb|EDV95020.1| GH25170 [Drosophila grimshawi]
          Length = 267

 Score =  318 bits (814), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 123/317 (38%), Gaps = 73/317 (23%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +     +  K+ V   R  Q GDK A RHG KG        EDM F  +G   DI++NP 
Sbjct: 4    LNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPH 63

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +G + E   G      G+                                   
Sbjct: 64   AIPSRMTIGHLIECLQGKLGSNKGEIGD-------------------------------- 91

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP  D  + + I++ L+       G  ++Y+G TG   
Sbjct: 92   ---------------------ATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKI 130

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V +G  Y  +L HMV DK+++R+ G   ++ +QP+ G++  GG R GEME  C  ++
Sbjct: 131  NAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISH 190

Query: 1306 GAAYVLQEMLTIKSD----DVVG----------RTRVYESIVAG----NDTFETGTPESF 1347
            GAA  L+E L   SD     +            R   +E    G        +   P + 
Sbjct: 191  GAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRNNTFEC--KGCKNKTQISQVRLPYAA 248

Query: 1348 NVLVKEMQALGLSIDLE 1364
             +L +E+ ++ ++  L 
Sbjct: 249  KLLFQELMSMNIAPRLM 265


>gi|242392318|dbj|BAH80332.1| RNA polymerase subunit B' [Haloarcula argentinensis]
          Length = 608

 Score =  318 bits (814), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 206/607 (33%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV             + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEGELTENHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEDELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 42.0 bits (97), Expect = 0.71,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEGELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 ENH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|318602945|emb|CBJ04565.1| RNA polymerase beta subunit [Pseudomonas sp. R-37093]
          Length = 320

 Score =  317 bits (813), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 190/319 (59%), Positives = 246/319 (77%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAD 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 122 HVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV
Sbjct: 182 DDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           +R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 242 VRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 301

Query: 805 LALGRNMLVAFMPWHGYNF 823
           LALG+NM +AFM W+G+NF
Sbjct: 302 LALGQNMRIAFMAWNGFNF 320


>gi|269912656|emb|CAY86108.1| RNA polymerase beta subunit [Granulibacter bethesdensis]
          Length = 311

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 148/313 (47%), Positives = 197/313 (62%), Gaps = 25/313 (7%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+++VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLVYVRIDR 60

Query: 209 RRKVPVTSFLMAL----------------------GMDSEEILSTFYPKIVYSQRGDFWC 246
           RRK+PVT+ L AL                      GM +EEILS FY ++V++     W 
Sbjct: 61  RRKLPVTTLLYALEGQRTEAAIASGTDPQDLPEIHGMTAEEILSYFYTQVVFTSTPKGWA 120

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
            P        G  ++ +L+D DTG  V E+G KLT+   + + E+  K + +    L G 
Sbjct: 121 RPFDPE-AFRGITLAEALIDADTGTVVAEAGTKLTARSARKIAEQA-KTVLVGRADLLGR 178

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
           Y+AED+VN +TGEIY EAG+ + E  L  +    +  +P L VD      +IRNTL  DK
Sbjct: 179 YMAEDLVNDQTGEIYAEAGEELTEARLAALETLGVTSLPTLAVDQ-TTGPWIRNTLAIDK 237

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
           N  R DAL+DIYRVMRPG+  T   AE++F  LFFD D+YDLS+VGRVKMNMRL +D PD
Sbjct: 238 NSTRDDALIDIYRVMRPGEPPTPETAEALFRGLFFDMDRYDLSSVGRVKMNMRLGVDAPD 297

Query: 427 DVRHIRKEDIIAI 439
            VR +RKEDI+  
Sbjct: 298 TVRTLRKEDILRT 310


>gi|242392286|dbj|BAH80380.1| RNA polymerase subunit B' [Halorubrum xinjiangense]
          Length = 609

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 129/603 (21%), Positives = 210/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L     + SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRDQLEEHGFESSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 117/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEVEALERGDVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTDDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 42.4 bits (98), Expect = 0.64,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + +D                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTDDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|45545343|gb|AAS67519.1| DNA-dependent RNA polymerase II second largest subunit [Phragmidium
            sp. MB]
          Length = 931

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 134/891 (15%), Positives = 275/891 (30%), Gaps = 136/891 (15%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +  +  +      ++  L+     +  +DD D+ G +R+   G +L + +R+   
Sbjct: 160  HISMSEGQQGKKAYFFGYMVHRLLLAALDRRDLDDRDHFGKKRLDLAGPLLASLFRILFR 219

Query: 481  RMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ + +   +               + +  + + +     +               +SQ+
Sbjct: 220  KLTKDVYRHLQKCVEMQKPFNLNAAVKSNTITNGLKYSLATGNWGDQKKAMQAKAGVSQV 279

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H +H+G +CPAET EG   GLV +
Sbjct: 280  LNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKN 335

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEE 643
            L   + ++           + +  + +   Y S M    +                  + 
Sbjct: 336  LALMSYISVGSPSAPIVEFLEEWGMESLDEYSSDMASGTKVFVNGVWQGVHRSPADLLDT 395

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            +   R  G+         D  +   +          P    ++   +L   +++  +   
Sbjct: 396  IKRLRRCGDIEPEVSVMRDVRERELRVFTDGGRVCRPLFIVENQQLLLKKEHVEWLSNGC 455

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            + A         E        + +VA+  GIVE +DA       +    +      +   
Sbjct: 456  ISASDDPNAEIPEDEGQPFGWSQLVAR--GIVEYLDAEEEETVMICMTPEELEQSREYQL 513

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              +  R   +     +  V +             P+  LG       +  + +P+  +N 
Sbjct: 514  TGQVPREQFDPAARLKGNVSM--YSHTWTHCEIHPAMILG-------ICASIIPFPDHNQ 564

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                  S R   +       +  +    R                            +  
Sbjct: 565  ------SPRNTYQSAMGKQAMGVYLTNFRMRM-----------------------DTMAN 595

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 596  ILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RS 654

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             + R  +D+ +++ ++  E+ E  +R+          +       I  G           
Sbjct: 655  FYYRSYMDQEKKAGALSMEEFEKPSRETTLRLKQGTYDKLDEDGIINPGTRVSGDDIIIG 714

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +                   +E  QR+    K          E+   +++      
Sbjct: 715  KTASIPE---------------GSEEMGQRDKSHTKRDVSMPLKSTENGIIDQVLITTNS 759

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D++     + VKV +   R  ++GDK A RHG KG V  +   EDMPF  +G   DI++N
Sbjct: 760  DNL-----KFVKVRIRSTRIPETGDKFASRHGQKGTVGILYRQEDMPFTSEGVCPDIIIN 814

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +G + E  L       G +  +          IS L    E    +     
Sbjct: 815  PHAIPSRMTIGHLVECLLSKVSTITGNEGDATPFSEVTVEAISSLLK--ENGYHSRGLEI 872

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                       F+G                         G    
Sbjct: 873  M--------------------------FNGHT-----------------------GR--- 880

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   +G  Y  +L HMV+DK+++R+ G   ++T+QP+ G+S  GG R 
Sbjct: 881  KLRAQCYLGPTYYQRLKHMVNDKIHSRARGPVQILTRQPVEGRSRDGGLRF 931



 Score =  140 bits (352), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 108/781 (13%), Positives = 216/781 (27%), Gaps = 120/781 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    VP+     ALG+  + EIL             +     L  +  +   +V+
Sbjct: 72  YIRND----VPIVVVFRALGIIPDKEILDHICYDRNDIGMLEMLKPCLEDSFPIQEQEVA 127

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              +    G     S ++      + L+++ +  + ++           G  V   ++  
Sbjct: 128 LDFIGRR-GTSTGLSRERRLQYAEEILQKEMLPHISMSEGQQGKKAYFFGYMVHRLLLAA 186

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      +K L+           IL+     +        V  +     +A +
Sbjct: 187 LDRRDLDDRDHFG-KKRLDLAGPLLASLFRILFRKLTKDVYRHLQKCVEMQKPFNLNAAV 245

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                    +  T  +  S+    + D  K   +  G  ++  R    +      R    
Sbjct: 246 -------KSNTITNGLKYSLATGNWGDQKKAMQAKAGVSQVLNRYTFASTLSHLRRCNTP 298

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       +  +
Sbjct: 299 IGRDGKIAKPRQLHNSHWGMVCPAETPEGQACG---LVKNLALMSYISVGSPSAPIVEFL 355

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +   D  ++              Q        + L  I   RR   +         
Sbjct: 356 EEWGMESLDEYSSDMASGTKVFVNGVWQ-GVHRSPADLLDTIKRLRRCGDIEPEVSVMRD 414

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL-------TSFARVNAYGFIETPYRKVC 606
                  V         P    E   + L              A  +    I     +  
Sbjct: 415 VRERELRVFTDGGRVCRPLFIVENQQLLLKKEHVEWLSNGCISASDDPNAEIPEDEGQPF 474

Query: 607 DGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFT-------EELVFCRCAGEEILV 656
                     V YL A EEE   I      L++   +        E+          + +
Sbjct: 475 GWSQLVARGIVEYLDAEEEETVMICMTPEELEQSREYQLTGQVPREQFDPAARLKGNVSM 534

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ I AS+IPF +++ S R      M +QA+ +             
Sbjct: 535 YSHTWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNFRM------ 588

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                                                 + + +  Y       +     +
Sbjct: 589 -----------------------------------RMDTMANILYYPQKPLATTRSMEYL 613

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             R                        +L  G+N +VA + + GYN EDS+++++  +  
Sbjct: 614 RFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 649

Query: 837 DVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S +   +    +    L  EE  +        + +     +DE GII  G  V+  
Sbjct: 650 GLFRSFYYRSYMDQEKKAGALSMEEFEKPSRETTLRLKQGTYDKLDEDGIINPGTRVSGD 709

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK     E      ++       +K+   RD S+ + S  +G +  V I       
Sbjct: 710 DIIIGKTASIPEGSEEMGQR-------DKSHTKRDVSMPLKSTENGIIDQVLITTNSDNL 762

Query: 952 K 952
           K
Sbjct: 763 K 763


>gi|6606089|gb|AAF19057.1|AF107785_1 DNA-dependent RNA polymerase II RPB140 [Agaricus bisporus]
          Length = 914

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 141/911 (15%), Positives = 279/911 (30%), Gaps = 149/911 (16%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 137  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 193

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 194  GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 253

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 254  ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 309

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 310  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 361

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 362  AHSTSPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIY 418

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      LL      ++ +G +    +     +   + G++E +DA   
Sbjct: 419  TDAGRVCRPLFIVENQQLLLGKRHIRWLNSGSDDEGNEYKWEQL--IKGGVIELLDAEEE 476

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +       +    ++ +     R  +K G            PS  LG
Sbjct: 477  ETVMISMTPEDLENSRLQAAGVDPHANDGDFDPAAR--LKAGTHAHTWTHCEIHPSMILG 534

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 535  -------ICASIIPFPDHNQSPRN------------------TYQSAMAKQAMGIYLTNF 569

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 570  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 618

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 619  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKL 677

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          V   ++S ++   
Sbjct: 678  EDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTR----THTRRDVSTPLKSTEIGIV 733

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                I                       + VKV V   R  Q GDK A  HG KG V   
Sbjct: 734  DQVLI----------------TTNSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGIT 777

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 778  YRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 832

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 833  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 856

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                    G +       G      + +G  Y  +L HMV DK+++R+ G   ++T+QP+
Sbjct: 857  ------YHGHT-------GRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 903

Query: 1284 GGKSNRGGQRL 1294
             G+S  GG R 
Sbjct: 904  EGRSRDGGLRF 914



 Score =  141 bits (355), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 96/775 (12%), Positives = 216/775 (27%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+      LG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 67  YIKVD----IPIWVVFRGLGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 122

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + +              +      + 
Sbjct: 123 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 179 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLQKCV 228

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 229 --ETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 285

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 286 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAP 345

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 346 VIEFLEEWGLESLEENAHSTSPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVS 405

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                  +   ++        P    E   + L      +  +N+    E    K     
Sbjct: 406 VVRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRW--LNSGSDDEGNEYKWEQLI 463

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               +  L A EEE   I+     L+        +      G+                 
Sbjct: 464 KGGVIELLDAEEEETVMISMTPEDLENSRLQAAGVDPHANDGDFDPAARLKAGTHAHTWT 523

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 524 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLI------------ 571

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 572 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 599

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 600 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 638

Query: 843 HIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E            +       +++ G+I  G  V   DI++GK
Sbjct: 639 YYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGK 698

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S   G V  V I       K
Sbjct: 699 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTEIGIVDQVLITTNSEGQK 746


>gi|81171079|gb|ABB58766.1| RNA polymerase beta subunit [Mycoplasma canis]
          Length = 593

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 213/451 (47%), Positives = 301/451 (66%), Gaps = 14/451 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+  GF++TPY KV +G V   DV YL+A EE    IAQ++  +DE+    +E +  R
Sbjct: 62  AKVDDKGFLKTPYYKVNNGVVDYEDVRYLTASEEFGYSIAQSSVRVDENNKIIDEFLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                     + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 122 RNYTYENGRSDDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMGANMQRQAVPLLQTEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E+ +AK S   +VAK AG V  VD  RI I+  E  +       D Y L  F+
Sbjct: 182 PLIATGIEADIAKYSSYNLVAKNAGKVTFVDGSRIHIQRKESTV------TDKYTLRNFE 235

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + QRPLV++GDEV   DI+ DG S   G+LALG+N+LV F  W+GYNFED+++
Sbjct: 236 RSNQGTLIQQRPLVRIGDEVEVGDILTDGSSFKDGELALGKNVLVGFTTWNGYNFEDAVI 295

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V  DV+TSIHIEE  +  R ++ G +E+T+++PN S+  L+N+D+ GI+ VG+EV
Sbjct: 296 INERLVKNDVYTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDDGIVKVGSEV 355

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVG+++PKGE   + EEK+L AI G+++   +DTSL+V +G SGT+  V I +R 
Sbjct: 356 YPGDILVGRVSPKGEENPSQEEKMLYAILGQRSPSTKDTSLKVKNGHSGTITHVEILSRE 415

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       V  E IE + +    ++  + 
Sbjct: 416 KGD-------VLEEGIEKIVKVSIAQKRKIK 439



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 127/413 (30%), Positives = 179/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G EV  GDIL    + K +  +   + +L         +  D  +     V   V 
Sbjct: 248  LVRIGDEVEVGDILTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAVIINERLVKNDV- 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + + E  + +          LD +   ++   +   + + G  
Sbjct: 306  YTSIHIEEQTIQFRTSRAGDDELTKEVPNASKYSLRNLDDDGIVKVGSEVYPGDILVGRV 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +   +   Q +   +     V++      T   IL           
Sbjct: 366  SPKGEENPSQE--EKMLYAILGQRSPSTKDTSLKVKNGHSGTITHVEILSR--------- 414

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 415  EKGDVLEEGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   L  K  S   D     DI               
Sbjct: 475  MLNPQGVPSRMNIGQILELHLGMAARKLNVKFVSPSFDGVKKPDIEAALEEAG------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                      L         + +L D +
Sbjct: 528  ------------------------------------------LDKTG-----KQVLIDPI 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TG  FD+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 541  TGRKFDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 593


>gi|258571555|ref|XP_002544581.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Uncinocarpus
            reesii 1704]
 gi|237904851|gb|EEP79252.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Uncinocarpus
            reesii 1704]
          Length = 1202

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 111/518 (21%), Positives = 183/518 (35%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +    A+      D+ D  +  
Sbjct: 764  NNQFLRIDSLLYTMVYPQKPMVKTRTIELVKYDRLPAGQSATVAVMSYSGYDIEDALVLN 823

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
             + V       ++F ++  +    S   +     LL  D+++   I    +         
Sbjct: 824  KASVDRGFGRCQVFRKYSANLKSYSNGTKDR---LLGPDRENGAPIRKHALLDSDGLAAV 880

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G+   SG     K T    + +S             D           + Y  S    + 
Sbjct: 881  GEKVSSGEVYINKVTP--ENALSS-------GITGSD-------AGGPIAYIPSPQTYKL 924

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               + I+K+        G  +++KV     R  + GDK + RHG KG+V  I    DMPF
Sbjct: 925  PDPSYIDKVMI--STTEGENQLLKVQTRQTRRPEVGDKFSSRHGQKGVVGIIAEQADMPF 982

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
               G   DI++NP G PSRM VG++                                   
Sbjct: 983  TDQGIVPDIIMNPHGFPSRMTVGKML---------------------------------- 1008

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                               + V+  A          TP F G+  E ++++L        
Sbjct: 1009 -------------------ELVVGKAGVLSGQFGYGTP-FGGSPVEEMSAILVSKGFSYG 1048

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGEP    V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG
Sbjct: 1049 GKDYLTSGITGEPLPAYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGG 1108

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1109 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK- 1167

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +    + +      +
Sbjct: 1168 -----MAIPYAAKLLVQELFSMNVVARFKLADEFPEER 1200



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 89/742 (11%), Positives = 216/742 (29%), Gaps = 122/742 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 89  LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGSPRRAD 139

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                            ++C  RD+TYA P+ +    +          +  + +K     
Sbjct: 140 EEQSEDTRFKVESTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTA 189

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   +  +
Sbjct: 190 IGRMPVMLRSSKCVLSKKSPGEMYQLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVE 249

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      II             KD I++R +     VP+   L
Sbjct: 250 TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDRIYLRHNVLSDDVPIVIIL 298

Query: 219 MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ S+ E+L          Q      F  S    +   + +   +        I+  
Sbjct: 299 KAMGIQSDKEMLLLVAGVDSVYQEDFAINFEESIKLGIYTQQQALEYLGSH-----IKIM 353

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           +K  S     ++   ++        +   +V  + +N     +Y+ A         +   
Sbjct: 354 RKPNS--FGGVRRNYIQEAVEAIASVIISHVQVENMNFRPKALYV-AHMARRVLMAKHDP 410

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V++    +    A S+  
Sbjct: 411 SLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAFSVVA 470

Query: 398 FLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                  +     +     +  R  ++       + +   I+ + ++  + +       +
Sbjct: 471 IHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYISALGMMTRISSQFEKTRKV 530

Query: 457 DNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
                 +    G +      + +    +  +        +  +         + A+ V +
Sbjct: 531 SGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEEPVRKLVYALGAEDVQA 590

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                F       +  + + ++ +T   +        + R     E   ++  H+     
Sbjct: 591 VGGREFYGQGAYIIFLNGSPIA-LTRRPKFFLNSFRRLRRMGRVSEFVSIYINHHQSAMH 649

Query: 572 AETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             T +G     +  +         +    + +   +  D      V YL   EE + YI+
Sbjct: 650 IATDDGRICRPLIIVEKQKSRVTADHLSQLRSGEMEFDDFLAQGLVEYLDVNEENDSYIS 709

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                ++E+                          ++  P  ++   A LIP+  ++ S 
Sbjct: 710 VYEREINEN-----------------------TTHLEIEPFTILGAVAGLIPYPHHNQSP 746

Query: 689 RVLMGCNMQRQAVPLLKAEAPF 710
           R    C M +QA+  +      
Sbjct: 747 RNTYQCAMGKQAIGAIANNQFL 768


>gi|73697657|gb|AAZ81445.1| RNA polymerase beta subunit [Mycoplasma lipophilum]
          Length = 591

 Score =  317 bits (813), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 204/451 (45%), Positives = 306/451 (67%), Gaps = 15/451 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGQNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +VN YG ++TPY KV +G V   +V YL+A +E    IAQ+ + +DE+    ++ +  R
Sbjct: 61  TKVNKYGLLQTPYYKVNNGVVDYENVQYLTAAQEIGFNIAQSTTKIDENNRIIDDKLTVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++   + +D+I+ + KQ+ SIAA  IPFLENDD+NR LMG NMQRQAVPL++ EA
Sbjct: 121 HDYNYVVALSKDVDYIEVASKQMTSIAAGAIPFLENDDANRALMGANMQRQAVPLIQTEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S + +VA+ AG+VE VD  +I IR            V  Y+L  FQ
Sbjct: 181 PFVATGIEADIAKYSSSNLVAETAGVVEYVDGSKIKIRKDNDV-------VSTYKLRIFQ 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T ++Q+P+VKVG  V + D++ DGPS   G+LALG+N+LVAF  +HGYN+ED+++
Sbjct: 234 RSNQGTVISQKPIVKVGQRVEKGDLLVDGPSFKDGELALGKNVLVAFTTYHGYNYEDAVI 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R ++ G +++T DIPNVS+  ++N+DE GI+ +G+EV
Sbjct: 294 LNERLVKDDVFTSIHIEEQIIQFRTSRAGDDKLTADIPNVSKYAIRNLDEHGIVKIGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PKG+   + EEKLL AI  ++ ++V+DTSL+V +G +GTV+++ I +R 
Sbjct: 354 VPGDVLVGRTSPKGDDNPSQEEKLLSAILQQRPMNVKDTSLKVKNGHNGTVINIEILDRK 413

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D          + I+ + +    ++  + 
Sbjct: 414 NGD-------ALEDDIDKIVKVFIAQKRKIK 437



 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 123/419 (29%), Positives = 181/419 (43%), Gaps = 79/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ VG  V  GD+LV   + K +  +   + +L A       +  D  +           
Sbjct: 246  IVKVGQRVEKGDLLVDGPSFK-DGELALGKNVLVAFTTYHGYNYEDAVILNERLVKDDVF 304

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     +++  +      +   R+  DE  I+         ++L G+ 
Sbjct: 305  TSIHIEEQIIQFRTSRAGDDKLTADIPNVSKYAIRNL-DEHGIVKIGSEVVPGDVLVGRT 363

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L S ++ + P        +  +     V++       +  IL+ +  
Sbjct: 364  SPKGDDNPSQEEKLLSAILQQRP--------MNVKDTSLKVKNGHNGTVINIEILDRK-- 413

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                    GD +   + ++VKVF+A KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+D
Sbjct: 414  -------NGDALEDDIDKIVKVFIAQKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLED 466

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD++LNP GVPSRMN+GQI E HLG A   L  K  + + D     +I+        
Sbjct: 467  GTPVDVMLNPQGVPSRMNIGQILELHLGMAAKKLNCKYVTPVFDGVKKEEIADALEEAGI 526

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                  +                                                     
Sbjct: 527  NPTGKQYLIDPIT----------------------------------------------- 539

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                G      D+PV+VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 540  ----GR---KIDKPVSVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 591


>gi|3746598|gb|AAC64014.1| RNA polymerase II subunit 2 [Kopsia fruticosa]
          Length = 259

 Score =  317 bits (813), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 109/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG +      EDMP+  +G   DI++NP 
Sbjct: 39   TNADGLRFVKVRMRSVRLPQIGDKFSSRHGQKGTIGMTYTQEDMPWTLEGVTPDIIVNPH 98

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 99   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 126

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 127  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRIM 164

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 165  GDMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 224

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 225  GAAHFLKERLFDQSD 239


>gi|242392284|dbj|BAH80379.1| RNA polymerase subunit B' [Halorubrum vacuolatum]
          Length = 609

 Score =  317 bits (813), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 128/602 (21%), Positives = 208/602 (34%), Gaps = 101/602 (16%)

Query: 788  VRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            + R D+    + +    +  D     ++LVA            + I  ++V       I 
Sbjct: 85   LERGDVGFEGLVERGYVEFIDAEEEEDILVAVDEEDITEEHTHLEIDPQLVFGIGAGMIP 144

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              E     R T      + +    +     +   +     +        +          
Sbjct: 145  YPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLMHYPQLAMVKTQTTEQINF 201

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
                  +  + A+   +  ++ D  L +  G     +    F R    +  R    + ++
Sbjct: 202  DERPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQEDR 260

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E+ ++D       +           L     V+      +S+VL           +   
Sbjct: 261  FEIPSQD-------VRGARGEDAYTHLDEDGLVNPETVVDESSVLLGKTSPPRFLEEPDD 313

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                  + +R         E+         + +               ++ KV V  +R 
Sbjct: 314  MGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQRV 361

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   G 
Sbjct: 362  PELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVVNPHALPSRMTVGHVLEMLGGK 421

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                                                                     +  
Sbjct: 422  V-----------------------------------------------------GSLRGS 428

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                TP F G DE  +   L     + SG+ ++Y G+TGE  D  + VG I+  KL HMV
Sbjct: 429  RVDGTP-FQGEDEAELREGLEEFGFNSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMV 487

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
            S+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD   
Sbjct: 488  SNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLQSSDAER 547

Query: 1321 -------------DVVGRTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                         D   R RVY+  V G  +D  E     +F +L+ EM ALG+   LE 
Sbjct: 548  VYVSAETGLVAVEDREQR-RVYD-PVTGNEDDIHELEVSYAFKLLLDEMIALGIRPKLEL 605

Query: 1366 SR 1367
              
Sbjct: 606  ED 607



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/350 (16%), Positives = 117/350 (33%), Gaps = 32/350 (9%)

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           E++   R  G+   +    +               +  P +  ++   +L    +     
Sbjct: 28  EQIREARRRGDVSEMVNVSVKERTREVIVNADAGRARRPLIVVENGEPLLGDEEIAALER 87

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
             +  E       +E + A+     +VA      E +      +      +    +G+  
Sbjct: 88  GDVGFEGLVERGYVEFIDAEEEEDILVA---VDEEDITEEHTHLEIDPQLVFGIGAGMIP 144

Query: 762 YRLM-----------KFQRSNQNTCVNQR--PLVKVGDEVRRNDIIADGPST---DLGDL 805
           Y                ++S      N R  P  +          +    +T   +  + 
Sbjct: 145 YPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHLMHYPQLAMVKTQTTEQINFDER 204

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
              +N +VA M + G+N ED++++++  V   +  S     +E   R    G E+   +I
Sbjct: 205 PAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALARSHFFRTYEGEERRYPGGQEDRF-EI 263

Query: 866 PN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           P+        E+   ++DE G++     V+   +L+GK +P               + G 
Sbjct: 264 PSQDVRGARGEDAYTHLDEDGLVNPETVVDESSVLLGKTSPPRFLEEP------DDMGGL 317

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                R+TS+ + SG SG V  V +       K  +    ++   EL  +
Sbjct: 318 SPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKVKVRDQRVPELGDK 367



 Score = 43.1 bits (100), Expect = 0.33,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 61/198 (30%), Gaps = 37/198 (18%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR   + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPTALAEQIREARRRGDVSEMVNVSVKERTREVIVNADAGRARRPLIVV 70

Query: 576 EGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           E     L     +      V   G +E  Y           V ++ A EEE+  +A    
Sbjct: 71  ENGEPLLGDEEIAALERGDVGFEGLVERGY-----------VEFIDAEEEEDILVAVDEE 119

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +                        E+   ++  P+ V  I A +IP+ E++ S R+ M
Sbjct: 120 DIT-----------------------EEHTHLEIDPQLVFGIGAGMIPYPEHNASPRITM 156

Query: 693 GCNMQRQAVPLLKAEAPF 710
           G  M +Q++ L  A    
Sbjct: 157 GAGMMKQSLGLPSANYRI 174


>gi|294950795|ref|XP_002786777.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Perkinsus marinus ATCC 50983]
 gi|239901131|gb|EER18573.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Perkinsus marinus ATCC 50983]
          Length = 1140

 Score =  317 bits (812), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 89/307 (28%), Positives = 131/307 (42%), Gaps = 67/307 (21%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ K      R  + GDK + RHG KG+V  I+  EDMPF + G   D+++NP G PSRM
Sbjct: 887  KIFKCITRQTRRPELGDKFSSRHGQKGVVGLIVNQEDMPFGEKGWCPDLIMNPHGFPSRM 946

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             VG++ E   G A V  G++             ++                         
Sbjct: 947  TVGKLLECVSGKAGVLDGERSYGTAFGGTTKEHMTQSL---------------------- 984

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                     + G   S      A E                   +  G+TGE  +  + V
Sbjct: 985  --------IRHGFHPS------AKE------------------YITSGVTGEALECYIFV 1012

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IY  KL HMV DK++ARSTG  + +T+QP  G++  GG RLGEME  C+ AYGA+ +L
Sbjct: 1013 GPIYYQKLKHMVMDKIHARSTGPVNQLTRQPTEGRAKDGGLRLGEMERDCLVAYGASNLL 1072

Query: 1312 QEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVLVKEMQALGL 1359
             E L + SD     V  R  +  S   G         +  +   P +  +L +E+QA+ +
Sbjct: 1073 LERLMLSSDVFTASVCRRCGLL-SYQNGTCKLCGTSENIVDIRMPYACKLLFQELQAMNV 1131

Query: 1360 SIDLENS 1366
               L+  
Sbjct: 1132 CPRLKVE 1138



 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 94/745 (12%), Positives = 196/745 (26%), Gaps = 148/745 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L++    S+++F+   I               S   IT        LE+       P + 
Sbjct: 45  LVKQHIDSFNYFVTTEIKDIVLAE--------SNRRITSDVDPNWFLEYHDVRVGAPSYR 96

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  RD+TYA  + + +  +          +  + +++  + +G LP+M
Sbjct: 97  GVLQHVQTTPMMCRIRDMTYASDILVDISYV----------RGREVVRKNGVCVGRLPIM 146

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+IKG +++++ Q   S              
Sbjct: 147 LRSKLCRLHDATTEQMERMQECPHDPGGYFIIKGTEKVLLMQEQLS-------------- 192

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI------DRRRK----------------- 211
                   RII        +E D K ++   +      ++ R                  
Sbjct: 193 ------NNRII--------VEMDPKKLVQAVVTSSTADNKSRTVVCFKSELSGLFVKHSA 238

Query: 212 ----VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
               +P    L A+GM+S++ +             D     L  A          +L  +
Sbjct: 239 FTELIPAVIMLRAMGMESDQEIVQMVGTEKCHV--DGMILSLQDAHATGVFSQQQALEYL 296

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               ++        S      K    K L  +  C     +    ++  +    ++  D 
Sbjct: 297 GNKLKIRMYADGSFSSAFDQDKGGATKPLDFSGKCRFLCLMMRRALDARSDSTLLDDRDY 356

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
              K LE            L+           +  +T   +    A      V       
Sbjct: 357 YGNKRLELAGQLIALLFEDLFKSMNTEIKKSVDMRLTKFFQQTSSARAGRSTVGLDSGYP 416

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVD 445
                  +      +  ++ +   G  ++  R +           K       K+     
Sbjct: 417 D------VLLRATGNIKRFRIDRSGVSQVLSRFSFIAALGAMTRVKSQFEKSRKLAGPRA 470

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L+  +  +    +        + + L     +     E  I+    S+ ++         
Sbjct: 471 LQPSQWGMLCPSDTPEGEQCGLIKALSLLAHVTTPDEEGPIRRLCYSLGVEDAAGLTGEE 530

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                  +  F   + L         +S +   RR   +G+              +  T 
Sbjct: 531 LHSAG-TITVFLNGALLGVHRRPQTFMSDMRTLRRRGKIGEFVSIYEHEAQRA-IIIATD 588

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            GR+C         I +               + +   +  D      + ++   EE N 
Sbjct: 589 GGRLC------RPLIVVKKGKPMLKPEVHLRKLRSGELRFTDFLRLGIIEWVDVNEENNS 642

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           YIA     +                         +   ++  P  ++   A L+P+  ++
Sbjct: 643 YIAINPEDVTM-----------------------ESTHLEIEPLTLLGAVAGLVPYPHHN 679

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPF 710
            S R    C M +QA+  +      
Sbjct: 680 QSPRNTYQCAMGKQAMGNIACNQHL 704


>gi|80978855|gb|ABB54676.1| RNA polymerase beta subunit [Mycoplasma hyopharyngis]
 gi|80978857|gb|ABB54677.1| RNA polymerase beta subunit [Mycoplasma hyopharyngis]
          Length = 592

 Score =  317 bits (812), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 207/451 (45%), Positives = 303/451 (67%), Gaps = 15/451 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGQNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +VN YG ++TPY KV  G V   DV YL+A EE    IAQ+ + +D++    +E +  R
Sbjct: 62  TKVNKYGLLQTPYYKVNKGVVDYEDVRYLTAAEEIGFNIAQSTARVDKNNKIIDEKLTVR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++   + +D+I+ + KQ+ SIAA  IPFLENDD+NR LMG NMQRQAVPL+  EA
Sbjct: 122 QNYNYVVAFSKDVDYIEVASKQMTSIAAGAIPFLENDDANRALMGANMQRQAVPLITTEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S A I A+ AG+VE VD  +I IR            V  Y+L  FQ
Sbjct: 182 PFVATGIEADIAKYSSANISAETAGVVEYVDGQKIKIRKENDV-------VTTYKLRIFQ 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T ++Q+P+VKVG  V + D++ DGPS   G+LALG+N+LVAF  +HGYN+ED+++
Sbjct: 235 RSNQGTVISQKPIVKVGQRVEKGDLLVDGPSFKDGELALGKNVLVAFTTYHGYNYEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DVFTSIHIEE  +  R ++ G +++T DIPNVS+  ++N+DE GI+ +G+EV
Sbjct: 295 LNERLVKDDVFTSIHIEEQIIQFRTSRAGDDKLTADIPNVSKYAIRNLDEHGIVRIGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PKG+   + EEKLL AI  ++ ++ +DTSL+V +G +GTV+++ I +R 
Sbjct: 355 VPGDVLVGRTSPKGDENPSQEEKLLSAILQQRPMNAKDTSLKVKNGHNGTVINIEILSRE 414

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       V  + I+ + +    ++  + 
Sbjct: 415 NGD-------VLEDDIDKIVKVFIAQKRKIK 438



 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 121/419 (28%), Positives = 178/419 (42%), Gaps = 79/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ VG  V  GD+LV   + K +  +   + +L A       +  D  +           
Sbjct: 247  IVKVGQRVEKGDLLVDGPSFK-DGELALGKNVLVAFTTYHGYNYEDAVILNERLVKDDVF 305

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     +++  +      +   R+  DE  I+         ++L G+ 
Sbjct: 306  TSIHIEEQIIQFRTSRAGDDKLTADIPNVSKYAIRNL-DEHGIVRIGSEVVPGDVLVGRT 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G +   +   L S ++ + P +                       +           
Sbjct: 365  SPKGDENPSQEEKLLSAILQQRPMNAKDT-----------------SLKVKNGHNGTVIN 407

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             +I   + GD +   + ++VKVF+A KR I+ GDKM+GRHGNKG+VS +LP EDMP+L+D
Sbjct: 408  IEILSRENGDVLEDDIDKIVKVFIAQKRKIKVGDKMSGRHGNKGVVSIVLPEEDMPYLED 467

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVD++LNP GVPSRMN+GQI E HLG A   L  K  + + D     +I+        
Sbjct: 468  GTPVDVMLNPQGVPSRMNIGQILELHLGMAAKKLNCKYVTPVFDGVKKEEIADALQEAGI 527

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                  +                                                     
Sbjct: 528  DPSGKQYLIDPIT----------------------------------------------- 540

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                G     FD+PV++G +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 541  ----GR---KFDKPVSIGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|15669230|ref|NP_248035.1| DNA-directed RNA polymerase subunit B' [Methanocaldococcus jannaschii
            DSM 2661]
 gi|2500640|sp|Q60181|RPOB1_METJA RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|1591694|gb|AAB99044.1| DNA-directed RNA polymerase, subunit B' (rpoB1) [Methanocaldococcus
            jannaschii DSM 2661]
          Length = 636

 Score =  317 bits (812), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 110/625 (17%), Positives = 202/625 (32%), Gaps = 104/625 (16%)

Query: 786  DEVRRNDIIADGPS----TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +++++ +I           +  D     N  +A            + I    +       
Sbjct: 84   EKLKKGEITFSDLVKEGVIEYLDAEEEENAYIALSEEELTEKHTHLEIDPLTILGIGAGV 143

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                E     R T             +S    + +D  G            +        
Sbjct: 144  APYPEHNSAPRITMAAAMGKQSLGIPMSNIKWR-LDTRG--HYLHYPQVPIVRTKHQEIL 200

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + AI   +  ++ D  +   S +    +    F R       R    + 
Sbjct: 201  GFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSAIDRG-LGRSTFFRTYDACERRYPGGQM 259

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +           L     V+     K   V+           + 
Sbjct: 260  DRFEIPDKG-------VRGYRSEECYRYLEEDGIVAVESHVKGGDVIVGKTSPPRFLEEH 312

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    ++   V+  +          E+ + +K+   +          R+VKV V   
Sbjct: 313  --------EITIQVKPQRRDSSVVVRHGEEGYIDKVILTE-----TKEGNRLVKVKVRDL 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++   +P ED+PF + G   DI++NP  +PSRM VGQ+ E   
Sbjct: 360  RIPELGDKFASRHGQKGVMGLTVPQEDLPFTESGIVPDIIINPHAIPSRMTVGQLLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++I   I   +   D+      L                             
Sbjct: 420  GKVGALEGRRIDGTIFSGEKEWDLRKALEALGFKHHGKEVM------------------- 460

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+       TG+ F+  + +G  Y  KL+H
Sbjct: 461  ----------------------------YDGK-------TGKKFEVEIYIGIAYYQKLHH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA +L+E L  +SD 
Sbjct: 486  LVAGKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLMDESDP 545

Query: 1321 -DV-----VGRTRVY---------------ESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
             D+      G   +                E++ +         P +F +L+ E++++ +
Sbjct: 546  YDICICSKCGDFAILDYKRGLKYCPICGEIENLYSSKKIPFVRIPYAFKLLLDELKSMCI 605

Query: 1360 SIDLENSRTKNSAKMEEIPDFNKCE 1384
               ++          EE  +  + E
Sbjct: 606  LPRIKVRDKVELEDFEEFVEKLEKE 630



 Score = 92.1 bits (227), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 69/411 (16%), Positives = 121/411 (29%), Gaps = 108/411 (26%)

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            I   RR   L Q              ++      + P    E     L           
Sbjct: 30  FIREKRRKGELPQYTTVAYNEESNDIHINTDAGRIVRPLIVVENGKPKLTKEHIE----- 84

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
               ++       D      + YL A EEEN YIA +   L                   
Sbjct: 85  ---KLKKGEITFSDLVKEGVIEYLDAEEEENAYIALSEEELT------------------ 123

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                EK   ++  P  ++ I A + P+ E++ + R+ M   M +Q++ +  +   +   
Sbjct: 124 -----EKHTHLEIDPLTILGIGAGVAPYPEHNSAPRITMAAAMGKQSLGIPMSNIKW--- 175

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    +      Y           
Sbjct: 176 --------------------------------------RLDTRGHYLHYP---------- 187

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q P+V+   +                    G+N +VA M + GYN ED+++ ++  
Sbjct: 188 ----QVPIVRTKHQ----------EILGFDKRPAGQNFVVAIMSYEGYNMEDAIVFNKSA 233

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEV 888
           +   +  S     ++   R    G  +             SEE  + ++E GI+ V + V
Sbjct: 234 IDRGLGRSTFFRTYDACERRYPGGQMDRFEIPDKGVRGYRSEECYRYLEEDGIVAVESHV 293

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             GD++VGK +P               I  +     RD+S+ V  G  G +
Sbjct: 294 KGGDVIVGKTSPPRFLEE-------HEITIQVKPQRRDSSVVVRHGEEGYI 337


>gi|243010744|gb|ACS94449.1| RpoB [Mycobacterium avium subsp. avium ATCC 25291]
          Length = 248

 Score =  317 bits (812), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 140/240 (58%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.1 bits (105), Expect = 0.081,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|111054613|gb|ABH04364.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 324

 Score =  317 bits (812), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 199/322 (61%), Positives = 250/322 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++++D S +QVVS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVEYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V +G+ V R D+
Sbjct: 243 SVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLGEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 303 LADGPSTDLGELALGQNMRVAF 324


>gi|313192584|emb|CBY17538.1| RNA polymerase subunit B [Halonotius pteroides]
          Length = 608

 Score =  317 bits (812), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 123/592 (20%), Positives = 203/592 (34%), Gaps = 97/592 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + D    +  D     ++LV             + I   ++       I   E     R 
Sbjct: 94   LVDRGYVEFIDAEEEEDILVGVDEDDLTERHTHLEIDPSLIFGIGAGMIPYPEHNASPRI 153

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 154  TMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 210

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +     V   ++    F R    +  R    + ++ E+  +D   
Sbjct: 211  VAVMSYEGFNIEDALVLNKGSVERALMRSHFF-RTYEGEERRYPGGQEDRFEIPDQD--- 266

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 267  ----VRGARGEDAYTHLDEDGLVNPETPVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 322

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E          +N     + G  +        KV V  +R  + GDK A R
Sbjct: 323  ETSVTMRSGEDGVVDTVTVMEN-----EDGSMLS-------KVKVRDERIPELGDKFASR 370

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG++  + P EDMPF ++G   D+V+NP  +PSRM VG + E   G      G+++ 
Sbjct: 371  HGQKGVIGHLAPQEDMPFTEEGLVPDLVMNPHALPSRMTVGHVLEMLGGKVGALEGRRVD 430

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                  TP F G
Sbjct: 431  G-----------------------------------------------------TP-FQG 436

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
             DE  +   L       SG+ ++Y G++GE  D  + VG I+  KL HMVS+K++ARS G
Sbjct: 437  EDEAELRGALEEHGFKSSGKEVMYSGVSGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRG 496

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD             
Sbjct: 497  PVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDKETVYVSEDTGMI 556

Query: 1321 ---DVVGRTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               D   R RVY+    G  ++  E     +F +L+ EM ALG+   LE   
Sbjct: 557  AVEDREQR-RVYD-PATGSEDNIHELDVSYAFKLLLDEMMALGIRPTLELED 606



 Score = 38.9 bits (89), Expect = 6.9,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +      L                        E+   ++  P  +  
Sbjct: 100 VEFIDAEEEEDILVGVDEDDLT-----------------------ERHTHLEIDPSLIFG 136

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 137 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 173


>gi|89274902|gb|ABD65892.1| RNA polymerase II second largest subunit [Sparassis crispa]
          Length = 900

 Score =  317 bits (812), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 143/905 (15%), Positives = 273/905 (30%), Gaps = 153/905 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 129  RYAQEILQKEMLPHISMAEGSESKK---AYFFGYMIHRLLLAALERRDLDDRDHFGKKRL 185

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              + +  + + +     +   
Sbjct: 186  DLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLNLAVKSNTITNGLKYSLATGNW 245

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 246  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 301

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  A ++           + +  + +         EEN + A 
Sbjct: 302  CPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLEEWGLESL--------EENAHSAT 353

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 354  PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGR 410

Query: 690  VLMGCNMQRQAVPLLKAEA--PFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIR 746
            V     +      LL  +       +  E      SG       ++G++E +DA      
Sbjct: 411  VCRPLFIVENQQLLLTKKHIDLLNRSAEEEKALPGSGYKWDNLIKSGVIELLDAEEEETV 470

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +    +   +                       L   G +   ND   D  +     L 
Sbjct: 471  MICMTPEDLDNSR---------------------LQSSGVDPHANDEDFDPAA----RLK 505

Query: 807  LGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
               N       W       SM+  +   ++            ++       +G       
Sbjct: 506  AVTNAH----TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFL 561

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +               +  +             +       +   +  + AI      + 
Sbjct: 562  VRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQ 610

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    ++ R  +D  ++S   + E+ E   RD          +   
Sbjct: 611  EDSVIMNQSSIDRGLF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLE 669

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  +  D                +E  QR     K    T
Sbjct: 670  DDGLIAPGTGVNGEDIIIGKTAPIPPD---------------SEELGQRTRAHTKRDVST 714

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E    +++      D       + VK+ V   R  Q GDK A RHG KG +    
Sbjct: 715  PLKSTESGIIDQVLITTNAD-----GQKFVKIRVRSTRVPQIGDKFASRHGQKGTIGITY 769

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +          
Sbjct: 770  RQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTELTVES 829

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S +    +K   +                                              
Sbjct: 830  VSQVLR--QKGYQSRGLEVM---------------------------------------- 847

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ 
Sbjct: 848  -----YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVE 895

Query: 1285 GKSNR 1289
            G+S  
Sbjct: 896  GRSRD 900



 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 101/774 (13%), Positives = 227/774 (29%), Gaps = 114/774 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 54  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 109

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  +   ++  
Sbjct: 110 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMIHRLLL-A 167

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDAL 374
                 ++  D   +K L+           +L+   + +   Y++  + + K  +   A+
Sbjct: 168 ALERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLNLAV 227

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
                     +  T  +  S+    + D  K   S  G  ++  R    +      R   
Sbjct: 228 --------KSNTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT 279

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  I     L N    +         +   + + L     + +  +   + E +  
Sbjct: 280 PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLEE 339

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++S+      NA         F     +    +  N +  I   RR   +        
Sbjct: 340 WGLESL----EENAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVR 395

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKV 610
                   ++        P    E   + L          +      +     K  +   
Sbjct: 396 DIRERELRLYTDAGRVCRPLFIVENQQLLLTKKHIDLLNRSAEEEKALPGSGYKWDNLIK 455

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDF 663
           +  +  L A EEE   I      LD     +  +       +     R            
Sbjct: 456 SGVIELLDAEEEETVMICMTPEDLDNSRLQSSGVDPHANDEDFDPAARLKAVTNAHTWTH 515

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
            +  P  ++ + AS+IPF +++ S R      M +QA+ +                    
Sbjct: 516 CEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------- 562

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                          + + +  Y       +     +  R    
Sbjct: 563 ----------------------------RMDTMANILYYPQKPLATTRSMEYLRFR---- 590

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +L  G+N +VA + + GYN EDS+++++  +   +F S++
Sbjct: 591 --------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMY 630

Query: 844 IEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  + + + +   E            +       +++ G+I  G  VN  DI++GK 
Sbjct: 631 YRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKT 690

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P         ++        +A   RD S  + S  SG +  V I       K
Sbjct: 691 APIPPDSEELGQRT-------RAHTKRDVSTPLKSTESGIIDQVLITTNADGQK 737


>gi|269912626|emb|CAY86093.1| RNA polymerase beta subunit [Gluconobacter cerinus]
          Length = 322

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 148/322 (45%), Positives = 205/322 (63%), Gaps = 28/322 (8%)

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRI
Sbjct: 1   NGTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRI 60

Query: 207 DRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQR 241
           DR+RK+PVT+ L AL                         GMD +EILS FY  + +++ 
Sbjct: 61  DRKRKLPVTTLLYALEGANYIAQREEKIAEGGDVEGLDIRGMDQDEILSYFYDMVTFTRM 120

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
           GD W  P    D   G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +   
Sbjct: 121 GDGWARPFEP-DAFRGQKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRL 178

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            + G Y+A D++N  TGEIY EAG+ + E  L  +    I ++P L +D  ++  +IRNT
Sbjct: 179 DVLGCYLAHDLINENTGEIYGEAGEELTEDRLAALEELGITELPTLSIDG-SHGPWIRNT 237

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS+VGRVKMNMRL+
Sbjct: 238 LSVDKNTSRDEALIDIYRIMRPGEPPTKETAEAMFRGLFFDQDRYDLSSVGRVKMNMRLD 297

Query: 422 LDTPDDVRHIRKEDIIAIIKIL 443
           +  PD +R +RKEDI+  I+  
Sbjct: 298 VXAPDTLRVLRKEDILRTIRSC 319


>gi|243010746|gb|ACS94450.1| RpoB [Mycobacterium intracellulare ATCC 13950]
 gi|243010750|gb|ACS94452.1| RpoB [Mycobacterium chimaera]
          Length = 248

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 108/240 (45%), Positives = 142/240 (59%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.1 bits (105), Expect = 0.082,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|189332910|dbj|BAG41982.1| RNA polymerase subunit B' [Haloarcula japonica]
 gi|242392324|dbj|BAH80335.1| RNA polymerase subunit B' [Haloarcula japonica]
          Length = 608

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 115/588 (19%), Positives = 200/588 (34%), Gaps = 103/588 (17%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LV        +    + +  +++       I   E     R T      
Sbjct: 101  EFIDAEEEEDILVGVDEDELTDNHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 159  MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFVVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  L +  G     +    F R    +  R    + ++ E+   +       +  
Sbjct: 218  GFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQEDRFEIPDDE-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      ++ VL           +         + +R       
Sbjct: 270  ARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEPDDMGGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 330  SGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASRHGQKGVV 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I P EDMPF ++G   D+++NP  +PSRM VG I E   G      G+++       +
Sbjct: 378  GHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIGGKVGALEGRRVDGTAFTGE 437

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                                             FD        
Sbjct: 438  DEEELRGSLEDHG-------------------------------------FD-------- 452

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      SG+  +Y G+TGE  D  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 453  ---------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYHMVSNKLHARSRGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG-----------R 1325
            QP  G++  GG R+GEME   +  +GAA  L+E L  +SD    +V G           +
Sbjct: 504  QPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDREWINVCGQCGMTAVENVEQ 563

Query: 1326 TRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y      E      D  E     +F +L+ EM+ALG++  +E   
Sbjct: 564  RRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIAPRIELED 606



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 61/376 (16%), Positives = 126/376 (33%), Gaps = 33/376 (8%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +S   E   Y+  +      D     E V   R  G+   +    +              
Sbjct: 1   MSQGREAKVYVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAG 60

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            +  P L  +D   ++    +++     L+ E       +E + A+     +V       
Sbjct: 61  RARRPLLVVEDGEPLMTDEEVEQVKNGELEFEELVERGLVEFIDAEEEEDILV---GVDE 117

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQ-----------RPLV 782
           +++      +      +    +G+  Y       + +  +  + Q           RP  
Sbjct: 118 DELTDNHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSGMIKQSLGLPSANYRIRPDT 177

Query: 783 KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           +          +    +T+     D    +N +VA M + G+N ED++++++  V   + 
Sbjct: 178 RQHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALA 237

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDI 893
            S     +E   R    G E+   +IP+        EE   ++D+ G++    +V    +
Sbjct: 238 RSHFFRTYEGEERRYPGGQEDRF-EIPDDEVRGARGEEAYTHLDDDGLVNPETKVGENAV 296

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           L+GK +P               + G      R+TS+ + SG SG V  V +       K 
Sbjct: 297 LLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKL 350

Query: 954 ERSISVEREQIELLAR 969
            +    +    EL  +
Sbjct: 351 SKVSVRDERIPELGDK 366



 Score = 41.6 bits (96), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKNGELEFEELVER---GLVEFIDAEEEEDILVGVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ++                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DNH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|243010748|gb|ACS94451.1| RpoB [Mycobacterium colombiense]
          Length = 248

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 106/240 (44%), Positives = 141/240 (58%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.1 bits (105), Expect = 0.081,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|242392224|dbj|BAH80337.1| RNA polymerase subunit B' [Haloarcula vallismortis ATCC 29715]
          Length = 608

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 206/607 (33%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV             + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEDELTENHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEEELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 41.6 bits (96), Expect = 0.96,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 ENH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|298712018|emb|CBJ32957.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 451

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 80/312 (25%), Positives = 123/312 (39%), Gaps = 73/312 (23%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   D+++NP G PSRM 
Sbjct: 195  LIKILLRQTRRPEVGDKFSSRHGQKGVCGIIVPQEDMPFADSGICPDLIMNPHGFPSRMT 254

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VG++ E   G A V  G +        +                                
Sbjct: 255  VGKMVELVAGKAGVLHGHQAYGTAFGEEHGSADRVHLC---------------------- 292

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                          L        G+ +L  G  GEP    +  G
Sbjct: 293  ---------------------------CQALVERGYSYVGKDMLTSGTGGEPLMNYIFAG 325

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             ++  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  YGA+ ++ 
Sbjct: 326  PVFYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASALIM 385

Query: 1313 EMLTIKSDDVVGRTRVYESIVA-G----------------NDTFETGTPESFNVLVKEMQ 1355
            E L I SD        + + V  G                    +   P +  +L +E+Q
Sbjct: 386  ERLMISSD-------AFTANVCQGCGLLGYSGWCQNCRSPEKMADIRLPYACKLLFQELQ 438

Query: 1356 ALGLSIDLENSR 1367
            ++ +   L+   
Sbjct: 439  SMNIVPRLKLQD 450



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/155 (20%), Positives = 55/155 (35%), Gaps = 20/155 (12%)

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             +           Q+P+V                      +  G+N  +A M + GY+ 
Sbjct: 17  HERMDGLLYALVHPQKPMV----------TTRVLDLVHFDQVPGGQNASIAVMSYSGYDI 66

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE----------EITRDIPNVSEEGL 873
           ED+++++   +       +   + +   R    G +          E  R   +      
Sbjct: 67  EDAIVLNRGSLDRGFGRCMVFRKHQAPIRKYPNGTQDKIVGKVRASEFPRGEDDPRWPRY 126

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
           K +DE GI  VGA ++PG I+V K +P   S   P
Sbjct: 127 KALDEDGICRVGARLDPGTIMVNKHSPASTSGSGP 161


>gi|242392260|dbj|BAH80367.1| RNA polymerase subunit B' [Halorubrum arcis]
          Length = 609

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 129/603 (21%), Positives = 210/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDERPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L     + SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGQLEEYGFESSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 42.4 bits (98), Expect = 0.65,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + +D                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTDDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|313192586|emb|CBY17539.1| RNA polymerase subunit B [Halogranum gelatinilyticum]
          Length = 608

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 115/592 (19%), Positives = 206/592 (34%), Gaps = 93/592 (15%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
            D + +    +  D     ++ VA            + I  +++       I   E     
Sbjct: 92   DDLVERGYVEFIDAEEEEDIYVAVDEDEVSEDHTHLEIDPQLIFGIGAGMIPYPEHNASP 151

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            R T      + +    +     +   +     +        +        G       + 
Sbjct: 152  RITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQN 208

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + A+   +  ++ D  +     V    +    F R    +  R    + ++ E+ ++D 
Sbjct: 209  FVVAVMSYEGFNIEDALVMNKGSVE-RAMARSHFFRTYEGEERRYPGGQEDRFEIPSQD- 266

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                  +           L     V+      +S+VL           +         + 
Sbjct: 267  ------VRGARGEDAYTHLDEDGLVNPETVVDESSVLLGKTSPPRFLEEPDDMGGLSPQK 320

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +R         E          + +               ++ KV V  +R  + GDK A
Sbjct: 321  RRETSVTMRSGEDGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFA 368

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG+V  + P EDMPF + G   D+V+NP  +PSRM VG + E   G      G++
Sbjct: 369  SRHGQKGVVGHLAPQEDMPFTEQGVVPDLVINPHALPSRMTVGHVLEMLGGKVGALEGRR 428

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            +       ++  ++                                              
Sbjct: 429  VDGTAFQGESEDELR--------------------------------------------- 443

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
             GA EE           + +G+ ++Y G+TGE  +  + +G I+  KL HMVS+K++ARS
Sbjct: 444  -GALEE--------HGFNSAGKEVMYSGVTGEKIEAQIFLGIIFYHKLYHMVSNKLHARS 494

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----VVGRT- 1326
             G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L   SD     V G T 
Sbjct: 495  RGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREEVYVSGDTG 554

Query: 1327 ----------RVYESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                      R+Y+ I    ++  +     +F +L+ EM+ALG+   +E   
Sbjct: 555  MVAVEDREQRRIYDPITGDEDNIHKIEVSYAFKLLLDEMKALGIRPKIELED 606



 Score = 43.5 bits (101), Expect = 0.26,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 64/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       V+        P    
Sbjct: 10  YVNGSLVGTHPDPHQLAAQIREARRRGDVSQMVNVSVKDRTREVIVNADAGRARRPLIVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L+      A  N  G +E       D      V ++ A EEE+ Y+A     + 
Sbjct: 70  ENGE-PLLGDEEIEAVEN--GDLE-----FDDLVERGYVEFIDAEEEEDIYVAVDEDEVS 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPSANYRI 173


>gi|223994131|ref|XP_002286749.1| DNA directed RNA polymerase III, second largest subunit
            [Thalassiosira pseudonana CCMP1335]
 gi|220978064|gb|EED96390.1| DNA directed RNA polymerase III, second largest subunit
            [Thalassiosira pseudonana CCMP1335]
          Length = 1108

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 87/312 (27%), Positives = 133/312 (42%), Gaps = 73/312 (23%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +   R  + GDK A RHG KG+   I+P  DMPF + G P D+++NP G PSRM 
Sbjct: 852  LIKVMLRQVRRPELGDKFASRHGQKGVCGLIVPQVDMPFNEQGFPPDLIMNPHGFPSRMT 911

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VG++ E  +G A V  G++  +     +     +   + L                    
Sbjct: 912  VGKLIELLVGKAGVFEGRQAYASAFGEEFGSTDTVQSAEL-------------------- 951

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                          L    L+ +G+ I Y G+ G P D  +  G
Sbjct: 952  -----------------------------ALIRNGLNYTGKDIFYSGVNGAPLDAYIFSG 982

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             ++  KL HMV DK++ARS G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ ++ 
Sbjct: 983  PVFYQKLKHMVLDKMHARSRGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASNLIM 1042

Query: 1313 EMLTIKSDDVVGRTRVYESIVA-----------------GNDTFETGTPESFNVLVKEMQ 1355
            E L   SD        + + V                  G    +   P +  +L +E+Q
Sbjct: 1043 ERLMHSSD-------AFSASVCMTCGLLQYQNWCQYCRSGEKVSDIRLPYACKLLFQELQ 1095

Query: 1356 ALGLSIDLENSR 1367
            A+ +   L    
Sbjct: 1096 AMNVLPRLRLKD 1107



 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 125/959 (13%), Positives = 270/959 (28%), Gaps = 197/959 (20%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVD--- 89
              S+DHF+ + +    + +       +S      +     L +       P  D D   
Sbjct: 4   HIDSFDHFVNVEMRQIVQVSRW--QLIRS-----DYDPKFYLRYTDCWVGEPSIDEDSYA 56

Query: 90  -------DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT--- 139
                   C  RD TY+ P+ + +R            +  + + ++ + +G +P+M    
Sbjct: 57  TTQATPFQCRLRDCTYSAPIYVNVRYT----------RGRQIVVKKKVMIGRMPIMLRSS 106

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G FVIKG++++++ Q   S       +  +       
Sbjct: 107 KCLLRDKSERELAQMKECPYDPGGYFVIKGVEKVILIQEQLSKNRVIIEEDSKTGCVSAS 166

Query: 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV----------PVTSFLMALGMDSEEI 228
           + +               + K   ++ I   R            P+   + A+G++S+  
Sbjct: 167 ITSST------------RERKSKAYIFIKNGRLFLKHNTLAEDVPICVAMKAMGVESD-- 212

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           L          +  D     L     +       +L  I          K+   G  + L
Sbjct: 213 LEFVQSVGSEPEVIDALALSLEEPSKLGIVTQRHALKYIGNK----MRAKRGAFGSTRKL 268

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEI--YIEA--GDVIDEKSLEEIFHSEIRDI 344
             +        +  L  + V     + +T  I   +       + + SL++  +   + +
Sbjct: 269 SPEDEARDVFANVVLSHVPVVNFDFHAKTIYIGHIVRRLVMVQLGKSSLDDKDYYGNKRL 328

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDAL--------LDIYRVMRPGDVSTFSVAESMF 396
            +           +     TD  K     L         D+ + +RP  ++   ++    
Sbjct: 329 ELAGSLLSLLFEDLFKHFNTDLKKQTDMVLSKPNRAQAFDVIKTIRPDSIAYGMMSAISS 388

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                   + D + V +V   +          R   + +    +     L+  +  +   
Sbjct: 389 GNWVLKRFRMDRAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCP 448

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            +        + + L     +       +I+       ++ V            + +   
Sbjct: 449 ADTPEGEACGLVKNLALLAHITTDEESEAIERLCRDCGVEDVTLLSGHEIHSRNAFLV-L 507

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                +      +  +  +   RR   +G+        G +   +  T  GR+C      
Sbjct: 508 LNGLIVGVHTRPLWLVKSLRSLRRQGQMGEFVSLYLHDGQKAVHI-ATDGGRVCRPLIIV 566

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                L           A G I      + D      V Y+   EE N  IA     L  
Sbjct: 567 DEKTALPRLKQVHIEGLALGTIH-----IKDLLRQGVVEYVDVNEENNCLIAVTEREL-- 619

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                      ++  P  ++ + A LIP   ++ S R      M
Sbjct: 620 --------------------EWMAYTHLEIDPMTLLGVVAGLIPNPHHNQSPRNTYQSAM 659

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                           +   +       
Sbjct: 660 GKQAIGT-----------------------------------------VAINQYSRFDGM 678

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               +Y      ++     +N                          ++  G+N  +A M
Sbjct: 679 LYTMVYPHKPMVKTRTLDLIN------------------------FDNIPAGQNACIAVM 714

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS------- 869
            + GY+ ED++++++  V       + +++ +   R  + G  + T   P+ S       
Sbjct: 715 SYSGYDIEDAVVLNKASVDRGFGRCMVLKKSQASVRRYQNGTMDRTCGAPDPSAFPSGEE 774

Query: 870 ---EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                  + ID+ G+  VG  +  G ++V K +P   S  TP E+L +  +    +  R
Sbjct: 775 DKRYARYRGIDKDGLCMVGELMENGTVMVNKESPTDTS--TPVERLAQVSYKYSGMSYR 831


>gi|82749758|gb|ABB89763.1| RNA polymerase beta subunit [Mycoplasma sturni]
          Length = 593

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 219/449 (48%), Positives = 309/449 (68%), Gaps = 16/449 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  +F
Sbjct: 2   NPLSEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN  GF++TPY KV DGKV  ++VVYL+A EE     AQ++  +DE  +     +  R
Sbjct: 62  AKVNELGFLQTPYFKVIDGKVHYDEVVYLTAAEEIGYSFAQSSVRVDESNNIVSPTLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 122 KDYNYIIGTPKDVDFIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLLQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +AK S   + AK AG+V  VD  RI I++ +G  D        Y L  F+
Sbjct: 182 PFVATGIEADIAKYSSYNLTAKHAGVVTFVDGGRIHIKNEKGVTDK-------YFLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+P+V+VG EV + D++ DG S   G++ALG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTIIQQKPIVEVGQEVAKGDLLVDGSSFKDGEMALGKNVLVGFTTWNGYNFEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-IPNVSEEGLKNIDECGIICVGAE 887
           I+ER+V +DVFTSIHIEE  +  R +K G +E+TRD IPNVS+  ++++D+ GI+ VG+E
Sbjct: 295 INERLVKDDVFTSIHIEEQTIQFRSSKAGEDELTRDKIPNVSKHSIRHLDDRGIVRVGSE 354

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVG+I+PKGE   T EEKLL AI  ++  +++DTSL+V +G +GTV+ V I +R
Sbjct: 355 VVAGDVLVGRISPKGEENPTQEEKLLLAILQQRPQNIKDTSLKVKNGHNGTVIHVEILSR 414

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   GIDK  +    ++ +I++  +
Sbjct: 415 DKGDMLEDGIDKIVKVSIAQKRKIKVGDK 443



 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 126/413 (30%), Positives = 180/413 (43%), Gaps = 66/413 (15%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG EV  GD+LV   + K +  M   + +L         +  D  +     V   V 
Sbjct: 247  IVEVGQEVAKGDLLVDGSSFK-DGEMALGKNVLVGFTTWNGYNFEDAVIINERLVKDDVF 305

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                     I         +    + +          LD     R+   +   + + G  
Sbjct: 306  TSIHIEEQTIQFRSSKAGEDELTRDKIPNVSKHSIRHLDDRGIVRVGSEVVAGDVLVGRI 365

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +        Q     ++D  +      +K  +  +   +E   ++K    
Sbjct: 366  SPKGEENPTQEEKLLLAILQQRPQNIKDTSL-----KVKNGHNGTVIHVEILSRDK---- 416

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 417  --GDMLEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 474

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQ+ E HLG A   LG K  +   D     DI               
Sbjct: 475  MLNPQGVPSRMNIGQVLELHLGMAARQLGVKFVTPSFDGVKKNDIEDAL----------- 523

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                  + + L  +      +  L D +
Sbjct: 524  --------------------------------------VEAGLDKSG-----KQTLIDPI 540

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 541  TGRKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 593


>gi|242392326|dbj|BAH80336.1| RNA polymerase subunit B' [Haloarcula quadrata]
          Length = 608

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 206/607 (33%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV             + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEDELTEKHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEDELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 40.8 bits (94), Expect = 1.5,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 -----------------------EKHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|242392316|dbj|BAH80331.1| RNA polymerase subunit B' [Haloarcula amylolytica]
          Length = 608

 Score =  317 bits (811), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 206/607 (33%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV             + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEDELTEKHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEEELRGSLEEHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 40.8 bits (94), Expect = 1.5,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 -----------------------EKHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|242392256|dbj|BAH80365.1| RNA polymerase subunit B' [Halorubrum aidingense]
          Length = 609

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 132/603 (21%), Positives = 207/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + V R DI    + D    +  D     ++LVA            + I  ++V       
Sbjct: 83   EAVERGDIEFEDLVDRGYVEFIDAEEEEDILVAVDEEDVSEDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDERPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALMRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E          + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGENGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEDLRGGLEDHGFKSSGKEVMYSGVTGEKVDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 42.8 bits (99), Expect = 0.49,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + ED                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVSEDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|242392226|dbj|BAH80350.1| RNA polymerase subunit B' [Halococcus thailandensis]
          Length = 611

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/318 (29%), Positives = 138/318 (43%), Gaps = 74/318 (23%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 348  EDGSKLSKVSVRDQRVPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIVNPHAL 407

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 408  PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEEEEELRDSLEEHG-------------- 453

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I++ G+TGE  D 
Sbjct: 454  -----------------------FD-----------------SSGKEIMHSGVTGEKIDA 473

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 474  EIFVGTIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 533

Query: 1308 AYVLQEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFNV 1349
            A  L+E L  +SD                +V  R RVY     G   D  E     +F +
Sbjct: 534  AMALKERLLDESDREFIYVCGECGMSAVENVEQR-RVY-CPNCGEETDIHEIEMSYAFKL 591

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L+ EM+ALG++  LE   
Sbjct: 592  LLDEMKALGIAPRLELLD 609



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/343 (16%), Positives = 111/343 (32%), Gaps = 28/343 (8%)

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+        +               +  P +  +D   ++    ++       + 
Sbjct: 35  ARRRGDIGRTVNVSVKDTTNEVIINADAGRARRPLIIVEDGEPLITESEVESLTDGDTEF 94

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E       +E + A+     +V      + + D   + I         +           
Sbjct: 95  EELVERGYIEFIDAEEEEDILVGVDEEDLTE-DHTHLEIDPQLIFGIGAGMIPYPEHNAS 153

Query: 767 FQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNML 812
            + +     + Q           RP  +          +    +T+     D    +N +
Sbjct: 154 PRITMGAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 213

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
           VA M + G+N ED+++++E  V   +  S     +E   R    G E+   +IP+     
Sbjct: 214 VAVMSYEGFNIEDALVLNEGSVDRALARSHFFRTYEGEERRYPGGQED-HFEIPDDDVRG 272

Query: 868 -VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
              EE   ++DE G++    +V    +L+GK +P               + G      R+
Sbjct: 273 AHGEEAYTHLDEDGLVNPETKVGESAVLLGKTSPPRFLEEP------DDMGGLSPQKRRE 326

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           TS+ + SG SG V  V +       K  +    ++   EL  +
Sbjct: 327 TSVTMRSGESGIVDTVTLMQGEDGSKLSKVSVRDQRVPELGDK 369



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     +++   RR   +G+      +       ++        P    
Sbjct: 13  YVNGSLVGTHADPEQLATQVRQARRRGDIGRTVNVSVKDTTNEVIINADAGRARRPLIIV 72

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L++     +  +     E    +         + ++ A EEE+  +      L 
Sbjct: 73  EDGE-PLITESEVESLTDGDTEFEELVER-------GYIEFIDAEEEEDILVGVDEEDLT 124

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 125 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 161

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 162 MIKQSLGLPSANYRI 176


>gi|73697679|gb|AAZ81456.1| RNA polymerase beta subunit [Mycoplasma ovipneumoniae ATCC 29419]
          Length = 590

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 203/423 (47%), Positives = 283/423 (66%), Gaps = 9/423 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L    + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + + F
Sbjct: 1   NPLGETANKRRVTSLGPGGLNRDTAQFEVRDVHATHYGRICPVETPEGQNIGLILNFSVF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +R N YGFI TPY KV +  V  + V +L+A EE     AQ++  +DE+     + +  R
Sbjct: 61  SRTNKYGFIMTPYYKVTNRVVDFSKVHWLTAAEEFGLSFAQSSIEIDENNKIIADKLTVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +++   ++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL+K EA
Sbjct: 121 KNQTYLVLDANQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLIKPEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E+ +A+ S   I A   G V  VDA +IV+         S +    Y L  F+
Sbjct: 181 PLVATGIEADIARFSATNIRALEDGKVIFVDAKKIVVN--------SENSTKTYFLRAFE 232

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T + Q+P VKVGD V++  +I DGPST+ G+LALG+N+LVAF  W+GYN+ED+++
Sbjct: 233 KSNQETLILQKPTVKVGDFVKKGQLICDGPSTENGELALGKNVLVAFSTWYGYNYEDAII 292

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISE++V +DVFTSIHI+E  +  R +K G + +T ++PN S     ++D  GI+ VG+EV
Sbjct: 293 ISEKLVKDDVFTSIHIQEQTIKFRSSKAGNDILTAEVPNASARSRAHLDANGIVIVGSEV 352

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+I +R 
Sbjct: 353 DTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQILSRD 412

Query: 949 GID 951
             D
Sbjct: 413 QGD 415



 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 129/412 (31%), Positives = 185/412 (44%), Gaps = 67/412 (16%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG  V  G ++    + +    +   + +L A       +  D  +     V   V  
Sbjct: 246  VKVGDFVKKGQLICDGPSTEN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 303

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   S +        +       +  LD N    +   +   + + G   
Sbjct: 304  TSIHIQEQTIKFRSSKAGNDILTAEVPNASARSRAHLDANGIVIVGSEVDTGDILVGRTS 363

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 364  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 412

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  +VK+ +A KR I+ GDKMAGRHGNKG+VS +LP EDMPFL+DGTP+DIV
Sbjct: 413  QGDNLEEGVGMLVKILIAQKRKIKVGDKMAGRHGNKGVVSVVLPVEDMPFLEDGTPIDIV 472

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG A   L  K  + + D                       
Sbjct: 473  LNPQGVPSRMNIGQVLELHLGMAAKKLDTKFVTPVFD----------------------- 509

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                 G+ + T + D   E  I          +SG+  L DG+T
Sbjct: 510  ---------------------GIKIDT-IQDLFKEANI---------PQSGKFKLIDGIT 538

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            G+PF+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR
Sbjct: 539  GQPFENPVSVGYMYMLKLQHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQR 590


>gi|242392322|dbj|BAH80334.1| RNA polymerase subunit B' [Haloarcula hispanica ATCC 33960]
          Length = 608

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 118/607 (19%), Positives = 206/607 (33%), Gaps = 105/607 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+     + + +    +  D     ++LV             + +  +++       
Sbjct: 84   VKEGEL--EFEELVERGLVEFIDAEEEEDILVGVDEDELTEKHTHLEVDPQLMFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GYDDRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +       +           L     V+      ++ VL           + 
Sbjct: 258  DRFEIPDDE-------VRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG I E   
Sbjct: 359  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHALPSRMTVGHILEMIG 418

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 419  GKVGALEGRRVDGTAFTGEDEEELRGSLEDHG---------------------------- 450

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     FD                  SG+  +Y G+TGE  D  + VG I+  KL H
Sbjct: 451  ---------FD-----------------SSGKETMYSGVTGEKIDAEIFVGDIFYQKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 544

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + R+Y      E      D  E     +F +L+ EM+ALG++
Sbjct: 545  EWINVCGQCGMTAVENVEQRRIYCPNCEEE-----TDIHEVEMSYAFKLLLDEMKALGIA 599

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 600  PRIELED 606



 Score = 40.8 bits (94), Expect = 1.5,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      ++   RR   + Q      +       ++        P    
Sbjct: 10  YVNGSLVGTHPDPEQLAEQVRQARRRGDVSQMVNVSVKNRTGEVIINADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L +   V      E  + ++ +      V ++ A EEE+  +      L 
Sbjct: 70  EDGE-----PLMTDEEVEQVKEGELEFEELVER---GLVEFIDAEEEEDILVGVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  EK   ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 -----------------------EKHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MIKQSLGLPSANYRI 173


>gi|242392332|dbj|BAH80347.1| RNA polymerase subunit B' [Halococcus qingdaonensis]
          Length = 611

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 94/318 (29%), Positives = 138/318 (43%), Gaps = 74/318 (23%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 348  EDGSKLSKVSVRDQRVPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIVNPHAL 407

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 408  PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEEEEELRDSLEEHG-------------- 453

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I++ G+TGE  D 
Sbjct: 454  -----------------------FD-----------------SSGKEIMHSGVTGEKIDA 473

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 474  EIFVGTIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 533

Query: 1308 AYVLQEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFNV 1349
            A  L+E L  +SD                +V  R RVY     G   D  E     +F +
Sbjct: 534  AMALKERLLDESDREFIYVCGECGMSAVENVEQR-RVY-CPNCGEETDIHEIEMSYAFKL 591

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L+ EM+ALG++  LE   
Sbjct: 592  LLDEMKALGIAPRLELLD 609



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 55/343 (16%), Positives = 111/343 (32%), Gaps = 28/343 (8%)

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+        +               +  P +  +D   ++    ++       + 
Sbjct: 35  ARRRGDIGRTVNVSVKDTTNEVIINADAGRARRPLIIVEDGEPLITESEVESLTEGDTEF 94

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E       +E + A+     +V      + + D   + I         +           
Sbjct: 95  EELVERGYIEFIDAEEEEDILVGVDEEDLTE-DHTHLEIDPQLIFGIGAGMIPYPEHNAS 153

Query: 767 FQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNML 812
            + +     + Q           RP  +          +    +T+     D    +N +
Sbjct: 154 PRITMGAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 213

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
           VA M + G+N ED+++++E  V   +  S     +E   R    G E+   +IP+     
Sbjct: 214 VAVMSYEGFNIEDALVLNEGSVDRALARSHFFRTYEGEERRYPGGQED-HFEIPDDDVRG 272

Query: 868 -VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
              EE   ++DE G++    +V    +L+GK +P               + G      R+
Sbjct: 273 AHGEEAYTHLDEDGLVNPETKVGESAVLLGKTSPPRFLEEP------DDMGGLSPQKRRE 326

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           TS+ + SG SG V  V +       K  +    ++   EL  +
Sbjct: 327 TSVTMRSGESGIVDTVTLMQGEDGSKLSKVSVRDQRVPELGDK 369



 Score = 44.3 bits (103), Expect = 0.15,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 66/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     +++   RR   +G+      +       ++        P    
Sbjct: 13  YVNGSLVGTHADPEQLATQVRQARRRGDIGRTVNVSVKDTTNEVIINADAGRARRPLIIV 72

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L + + V +    +T + ++ +      + ++ A EEE+  +      L 
Sbjct: 73  EDGE-----PLITESEVESLTEGDTEFEELVERGY---IEFIDAEEEEDILVGVDEEDLT 124

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 125 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 161

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 162 MIKQSLGLPSANYRI 176


>gi|111054631|gb|ABH04373.1| RNA polymerase beta subunit [Providencia heimbachae]
          Length = 324

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 198/322 (61%), Positives = 249/322 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDALMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN+ L EDGSF EEL+ CR  GE  L  RE+++++D S +Q+VS
Sbjct: 123 IHYLSAIEEGNFIIAQANTVLGEDGSFVEELITCRNRGESSLFSREQVEYMDVSTQQIVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V + + V R D+
Sbjct: 243 SVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLNEPVERGDV 302

Query: 794 IADGPSTDLGDLALGRNMLVAF 815
           +ADGPSTDLG+LALG+NM VAF
Sbjct: 303 LADGPSTDLGELALGQNMRVAF 324


>gi|243010758|gb|ACS94456.1| RpoB [Mycobacterium simiae]
          Length = 248

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 105/240 (43%), Positives = 142/240 (59%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +  +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPDWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +       +    VSTPVFDGA EE +  +L     +      
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGLLGSTLPNRDGDVM 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDADGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|58271124|ref|XP_572718.1| DNA-directed RNA polymerase [Cryptococcus neoformans var. neoformans
            JEC21]
 gi|134114572|ref|XP_773994.1| hypothetical protein CNBH0410 [Cryptococcus neoformans var.
            neoformans B-3501A]
 gi|50256624|gb|EAL19347.1| hypothetical protein CNBH0410 [Cryptococcus neoformans var.
            neoformans B-3501A]
 gi|57228977|gb|AAW45411.1| DNA-directed RNA polymerase, putative [Cryptococcus neoformans var.
            neoformans JEC21]
          Length = 1129

 Score =  316 bits (810), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 129/313 (41%), Gaps = 78/313 (24%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++K+     R  + GDK + RHG KG+   I+P  DMPF   G   DI++NP G PSRM 
Sbjct: 877  LIKILTRQTRRPELGDKFSSRHGQKGVCGLIVPQADMPFNDQGIVPDIIMNPHGFPSRMT 936

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VG++ E   G A V                                              
Sbjct: 937  VGKMIELLSGKAGV---------------------------------------------- 950

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
               VA + + G       F G+    ++ +L        G+ +L  G+TG+P +  V  G
Sbjct: 951  ---VAGKLQYGT-----AFGGSKVVDMSQILIDNGFSYGGKDMLTSGITGQPMEAYVYFG 1002

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR TG  + +T+QP  G+S  GG RLGEME  C+  YGA  +L 
Sbjct: 1003 PIYYQKLKHMVMDKMHARPTGPRANLTRQPTEGRSKDGGLRLGEMERDCLIGYGATQLLL 1062

Query: 1313 EMLTIKSDDVVGRTRVYESIVA-----------------GNDTFETGTPESFNVLVKEMQ 1355
            E L I SD        +E+ V                  G        P +  +L++E+ 
Sbjct: 1063 ERLMISSD-------AFETQVCESCGMLGYNNWCPKCKSGKGVVGLTIPYAAKLLIQELM 1115

Query: 1356 ALGLSIDLENSRT 1368
             + +   L    T
Sbjct: 1116 GMNIMPKLCLEDT 1128



 Score =  194 bits (494), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 117/923 (12%), Positives = 268/923 (29%), Gaps = 166/923 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S+++F+ ++I      N         + P         + +       P    
Sbjct: 37  LVKQHLDSFNYFVNVDIKAILAANS---LVISDINP------KYYIRYTDIRVGRPARHD 87

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI---------------K 123
                      +C   D TY+ P+ + +  +  +         I                
Sbjct: 88  ANQVASALSPMECRLTDSTYSAPIYVDVEYMGEEKRSKQRGVQIGMLPVMLRSDLCNLKG 147

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC- 182
             + +   MG+ P M   G FV+KG +++++ Q   S        K +       + +  
Sbjct: 148 KNEAELARMGECP-MDPGGYFVVKGTEKVILVQEQLSKNRILVM-KDKKDEVMAEVTSST 205

Query: 183 --RIIPDQGLWMDIEFDSKDIIHVRIDRRRK-VPVTSFLMALGMDSE-EILSTFYPKIVY 238
             R++              + +++R +  ++ +P+   L A+G+ ++ EIL         
Sbjct: 206 HDRVVKT------YVVSKANRLYLRHNSFKEFIPIVIALKAMGLTADKEILQLICGSDER 259

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDID-----------TGEQVIESGKKLTSGLLKS 287
            Q         +A +     + +   +              + +++  S     +     
Sbjct: 260 YQEAFGVSLEEAAKEKTFTRRQALEWIGARVSPNQAKDDSGSNQKLTPSDIAQQALAAMV 319

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           L    V+ +     C+    +A  ++     +  ++  D +  K LE             
Sbjct: 320 LGHVPVRNMNFRPKCIYLATMARRVLMAMIDDHMVDDRDYVGNKRLELAGQLLSLLFEDS 379

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           +    +    ++  +     K  +    D   ++R G            +   +   ++ 
Sbjct: 380 FKTFNSE---LKKRMDKILEKPNRAGPFDAGTLIRQGGDPITQAFVRSISTGNWSLKRFH 436

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +   G   +  R           +     + ++  +         +     L   +   +
Sbjct: 437 VERAGVTHVLSR-----------LSFIAALGMMTRISSQFEKTRKVSGPRALQPSQWGML 485

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
                 +     L    ++   I++   ++ + +          ++       +      
Sbjct: 486 CPSDTPEGEACGLVKNLALMTHITTDVPETPLVKMAFMLGVEDISLVTGNELYRPGVHMV 545

Query: 528 HVN-SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
            VN +L  +T+  +        + RA    E   +   H+ +I    +  G     +  +
Sbjct: 546 QVNGTLIGVTNMAKRFVRQFRKLRRAGRMSEFVSIFINHHHKIIYIASDGGRICRPMIIV 605

Query: 587 TS-FARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
               +RV           KV          V YL   EE + +IA   + ++E       
Sbjct: 606 EKGRSRVTTEHVRLLKEGKVTFDHFLRAGLVEYLDVNEENDSFIACYENEIEEG------ 659

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                               ++  P  ++   A LIP+  ++ S R    C M +QA+  
Sbjct: 660 -----------------TTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA 702

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                    I   + +   +   +  Y 
Sbjct: 703 -----------------------------------------IAYNQLNRIDTLLYLMTYP 721

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+P+VK                     L  G+N  VA M + GY+ 
Sbjct: 722 --------------QQPMVK----------TKTIELIGYNKLPAGQNATVAVMSYSGYDI 757

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDE-CGI 881
           ED+++++   V         +++     R    G  E T    P    +    +D+  G+
Sbjct: 758 EDALILNRASVDRGFGRCHVLKKVTTPMRTFHNGSHERTAYPDPPPRPDAYTFVDKADGM 817

Query: 882 ICVGAEVNPGDILVGKITPKGES 904
              GA +N  D+++ + TP    
Sbjct: 818 TAPGATINQYDVMIHRETPVDTR 840


>gi|243010742|gb|ACS94448.1| RpoB [Mycobacterium scrofulaceum]
          Length = 251

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 105/240 (43%), Positives = 140/240 (58%), Gaps = 37/240 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I           ++       +  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNINVAEGVPPWAANLPEDLLHAQPN 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                                          VSTPVFDGA E  +  +L            
Sbjct: 160  A----------------------------IVSTPVFDGAREAELQGLLSCTLPNRDNEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 192  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 251



 Score = 45.8 bits (107), Expect = 0.058,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|311977620|ref|YP_003986740.1| DNA-directed RNA polymerase subunit 2 [Acanthamoeba polyphaga
            mimivirus]
 gi|311788809|gb|ADO18079.2| DNA-directed RNA polymerase subunit 2 [Acanthamoeba polyphaga
            mimivirus]
          Length = 1193

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 184/1112 (16%), Positives = 341/1112 (30%), Gaps = 185/1112 (16%)

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              V+   I +    G      +       I +      +      I    I     +   
Sbjct: 209  YYVRVQSIPASQFVGNPQLFTVKMKRDNSIILSIPHFKEVSIFTFIRALGIETDEDIVDS 268

Query: 351  SVNNNA--------YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
             ++            I        +  +++AL  +   ++     T +  E         
Sbjct: 269  ILDVKKEKDLLNLLSICMNSSNTPSVTKEEALEIMANQIKSTKTFTDTNPEVKAEQRRRY 328

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGKGT--IDDIDN 458
             DK     V     +   + +        +I       +   L   R  +     DD D+
Sbjct: 329  LDKIMTQFVLPHITSGTGDPEIDKIYKAHYICYMIHKLLKCYLRGAREVEEYRGCDDRDS 388

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD---LINAKPVVSAVCE 515
            + N+R+   G +L   ++    +M     +   + +ID   P +    I    +   + +
Sbjct: 389  MVNKRIDLTGRLLGGLFKQFYDKMLNDCNKIFRTKNIDDKKPPNIIPHIKPNSIEQGLRQ 448

Query: 516  FFCSSQ--------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
               +          LSQ+   +N L  +++ RR+  +     A        R +H T YG
Sbjct: 449  ALSTGNFGSQSRKGLSQMLNRMNHLHSLSYMRRV--ITPTVDASTMKMTSPRHLHNTQYG 506

Query: 568  RICPAETSEGHNIGLVSSLTSF--ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
             +CP E+ EG   GLV ++       +N    I                        E+ 
Sbjct: 507  SMCPLESPEGPKTGLVKNMAMMEGITINMNSQIPII---------------------ESY 545

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID-FIDASPKQVVSIAASLIPFLEN 684
             I +  +    +     + V     G  + V R  I    D    +     + ++  + N
Sbjct: 546  LIGKITTLESANKKRLHQYVKVFLNGNWLGVTRNIIKIHNDLRAMRFRGELSRMVGLVLN 605

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
              +    +  +  R   P L      +    E +   +S    +AK   ++E VD     
Sbjct: 606  YKTAEFHIYTDGGRLIRPYLTVTDNKLNFKPEMLDEVNSWEEFLAKFPEVIEYVDKEEEQ 665

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG- 803
               +            I         +Q   +N            R D       T    
Sbjct: 666  NIMLAVFPQYIQDANRIMSKKPINSRDQLNKIN---------RTNRYDDNVYVRYTHCEI 716

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
               +   ++ + +P+  +N       S R + +       +  +    R+          
Sbjct: 717  HPCMILGLISSNIPFPDHNQ------SPRGIFQYNQARQAMGLYISDYRERTD------- 763

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             I  +        +        G       E  + AI      +
Sbjct: 764  -----------------ISYILYHPQIPLVTSRASKYTGTHIFPAGENSIVAIASYTGYN 806

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +    +  +   ++     +   S +        R+K D         Y
Sbjct: 807  QEDSLVINDSAIQKGYMRAQALKKYMEIIKKNPASSQTSIFMKPDRNKVDNLR---DANY 863

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +L E           +G+ K   +  D             A +DE           QY+
Sbjct: 864  DKLSE-----------EGYAKVETVIRDGDVVIGVVNPKPTAREDE----------KQYK 902

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             + SI +      ++K+    ++      ++K+ +  +R    GDK + R G KG +   
Sbjct: 903  DASSIYKSLIPGAVDKVIT--EVNNDGYPIIKMRIRSERIPNVGDKFSSRAGQKGTIGYK 960

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
                DM F K G   DI++NP  +P RM +GQ+ E  LG  C   G              
Sbjct: 961  AHRADMLFSKSGLIPDIIINPNCMPKRMTIGQLIECLLGKLCAVKGVYGD---------- 1010

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F   D  AIN  L
Sbjct: 1011 -------------------------------------------ATP-FTSVDLNAINDEL 1026

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
              A  +E G   +Y+G+ G+     + +G  Y  +L  MV DK ++R+ G   L+T+Q  
Sbjct: 1027 VAAGYEEWGNETMYNGMNGKKLPVKIFIGPTYYQRLKQMVGDKAHSRARGPTQLLTRQAP 1086

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRT------RVYE 1330
             G+S  GG R+GEME   + A+G A  L+E     SD       D  G+       + Y 
Sbjct: 1087 EGRSRDGGLRIGEMERDALCAHGVAQFLKEKTVDNSDIYTCHVCDSCGQFAHKVPEKKYY 1146

Query: 1331 SIVAGND---TFETGTPESFNVLVKEMQALGL 1359
            +     +     +   P +F +L++E+ ++ +
Sbjct: 1147 TCTGCRNTTSISKIVIPYAFKLLLQELASINI 1178


>gi|110631327|gb|ABG81009.1| RNA polymerase beta subunit [Candidatus Nicolleia massiliensis]
          Length = 197

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 111/197 (56%), Positives = 139/197 (70%), Gaps = 5/197 (2%)

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            VS+I+P EDMPFL+DGTPVD+VLNPLGVPSRMNVGQI ETHLGWA   LGK+I  +++  
Sbjct: 1    VSKIVPVEDMPFLEDGTPVDMVLNPLGVPSRMNVGQILETHLGWASANLGKQIGKMLDTV 60

Query: 1160 KANGDISPLRSFLEKVIG-----TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
              NG+ + LR+ L +V            E I+   +     +A+  K G+P +TPVFDG 
Sbjct: 61   VVNGEANNLRNALCEVYDSNRSSDKQARELIASLSEKEAKDLAKNLKKGIPFATPVFDGV 120

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
             EE +N +L  A LD SGQ  L DG TGE F+R VTVGYIYM+KL+H+V +K++ARS G 
Sbjct: 121  KEEELNKLLTKAGLDTSGQVRLIDGRTGEYFERKVTVGYIYMMKLDHLVDNKIHARSIGP 180

Query: 1275 YSLVTQQPLGGKSNRGG 1291
            YSLVTQQPLGGKS+ GG
Sbjct: 181  YSLVTQQPLGGKSHFGG 197


>gi|323541231|gb|ADX96003.1| RNA polymerase beta subunit [Enterobacter sp. KN/03/24]
          Length = 319

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 197/316 (62%), Positives = 247/316 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 4   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 64  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 124 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 183

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 184 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 243

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 244 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 303

Query: 794 IADGPSTDLGDLALGR 809
           +ADGPSTDLG+LALG+
Sbjct: 304 LADGPSTDLGELALGQ 319


>gi|150401219|ref|YP_001324985.1| DNA-directed RNA polymerase subunit B' [Methanococcus aeolicus
            Nankai-3]
 gi|150013922|gb|ABR56373.1| RNA polymerase Rpb2 domain 6 [Methanococcus aeolicus Nankai-3]
          Length = 611

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 135/322 (41%), Gaps = 76/322 (23%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ K+ V   R  + GDK A RHG KG++  I+P EDMPF ++G   D+++NP  +P
Sbjct: 343  EGNRLAKIRVRDLRIPELGDKFASRHGQKGVLGLIVPQEDMPFTENGVVPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +        G     +G K+ S+                                 
Sbjct: 403  SRMTI--------GQVLEMIGGKVGSMNCKRIDGT------------------------- 429

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                 +F G  E  + S +       +G+ +++DG TG+  +  
Sbjct: 430  ---------------------IFSGDPEWELRSSMEKCGYKHNGKEVMFDGKTGKKLECE 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +G A
Sbjct: 469  IFVGIAYYQKLHHLVAGKMHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLIGHGTA 528

Query: 1309 YVLQEMLTIKSD----DV---VGRTRVY---------------ESIVAGNDTFETGTPES 1346
             +L+E L  +SD     +    G   +Y               E +           P +
Sbjct: 529  LLLKERLFDESDPYECHICSNCGEVAIYDHKRGMKRCQACGETEDVQNNRKIPSVRLPYA 588

Query: 1347 FNVLVKEMQALGLSIDLENSRT 1368
            F +L+ E++++G++  LE    
Sbjct: 589  FKLLLDELRSMGINPKLELKDR 610



 Score = 90.1 bits (222), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 71/409 (17%), Positives = 125/409 (30%), Gaps = 114/409 (27%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHY--GRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           RR   +            E  D+H +      + P    E     L   L          
Sbjct: 31  RRNGQISP--FTSISYNEESSDIHISTDAGRAVRPLIVVENGVSKLNEELIK-------- 80

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            +E              + YL A EEEN YIA     L ++                   
Sbjct: 81  KVEQGELNFSGLVKMGVIEYLDAEEEENAYIANYEKDLTKNH------------------ 122

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                  ++  P  ++ I A + P+ E++ + R+ M   M +Q++               
Sbjct: 123 -----THLEIDPLSILGIGAGVAPYPEHNSAPRITMAAAMGKQSLG-------------- 163

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                                      +  +       + + +  Y              
Sbjct: 164 ---------------------------MPLANMKLRMDTKAHLLHYP------------- 183

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q P+V+   +                    G+N +VA M + GYN ED+ +I++  +  
Sbjct: 184 -QVPIVRTKHQ----------EILGFDRRPAGQNFVVAVMSYEGYNMEDAFIINKASIER 232

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS------EEGLKNIDECGIICVGAEVNP 890
            +  S     +E   +    G  +   +IP         EE  +N+ + GI+ V +EV  
Sbjct: 233 GLARSSFFRSYEGFEKRHPGGQVDRF-EIPEQGVRGYRAEEAYRNLGDDGIVEVESEVKS 291

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GD+++GK +P             + I        RDTS+ +  G  G V
Sbjct: 292 GDVIIGKTSPPRFLEE-------QDISLRSKSQRRDTSITIRHGEGGIV 333


>gi|73671121|ref|YP_307136.1| DNA-directed RNA polymerase subunit B' [Methanosarcina barkeri str.
            Fusaro]
 gi|72398283|gb|AAZ72556.1| DNA-directed RNA polymerase, subunit B' [Methanosarcina barkeri str.
            Fusaro]
          Length = 604

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 114/585 (19%), Positives = 190/585 (32%), Gaps = 94/585 (16%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              +  D     N  +A       +    M I   ++       +   E     R+T    
Sbjct: 96   CIEYLDAEEEENAYIALYEADLNSKHTHMEIDPELILGISTGMVPYPEHNASPRNTMGAA 155

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
              + +    V+    + +       V                 G       +  + AI  
Sbjct: 156  --MIKQCIGVATAN-QKLRPDTRAHVLHYPQRAMTRTRTSEAIGFDDRPAGQNFVVAILS 212

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  ++ D  +     +    +    F R    +  R    + ++ E+   +        
Sbjct: 213  YEGYNIEDALIFNKGSIERG-LGRSHFLRTFEGEERRYPGGQEDKFEIPDSEY--RGARS 269

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                 +   + L       GP             + E                  +VE  
Sbjct: 270  AEAYANLDTDGLVNPETPVGPNDVLIGKTSPPRFLEEPSDFGI------------SVEQR 317

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T +S         I              R+ KV V  +R    GDK A RHG KG
Sbjct: 318  RESSITMRSNETGIVDTVIL------TESINGTRLAKVKVRDERIPDIGDKFASRHGQKG 371

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++   +P  DMPF + G   D+++NP  +PSRM V        G     +G K+ S+   
Sbjct: 372  VIGLKVPIADMPFTESGLTPDLMINPHAIPSRMTV--------GHVLEMIGGKVGSMEGR 423

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                                F G +EE 
Sbjct: 424  RVNAT----------------------------------------------AFSGENEED 437

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L+      +G+ + YDG TG+     V VG I   KL+HMV+ K++ARS G   ++
Sbjct: 438  LREALKRHGFAHTGKEVFYDGATGKMIPADVFVGVILYQKLHHMVTSKMHARSRGPVQVL 497

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE- 1330
            T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G    Y+ 
Sbjct: 498  TRQPTEGRAREGGLRFGEMERDVLVGHGAAMSLKERLLDESDKVVELVCSHCGMIATYDK 557

Query: 1331 ------SIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                      G   D +      +F +L+ E+++LG++  L+   
Sbjct: 558  QRNVAFCSTCGADTDIYPVEMSYAFKLLLDEIKSLGVAPRLKLED 602



 Score = 96.7 bits (239), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 73/406 (17%), Positives = 133/406 (32%), Gaps = 113/406 (27%)

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
             + R        +V      R     +  G     +  + + A        E    K+ 
Sbjct: 27  RKMRRQGFISRQVNVALNSNTREVIINSDMGRARRPLIVVENGA----PRVTEEHVEKIK 82

Query: 607 DGKVTND-------VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           + ++T D       + YL A EEEN YIA   + L+                        
Sbjct: 83  NKEITFDDLVKEGCIEYLDAEEEENAYIALYEADLN-----------------------S 119

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           K   ++  P+ ++ I+  ++P+ E++ S R  MG  M +Q +         V T      
Sbjct: 120 KHTHMEIDPELILGISTGMVPYPEHNASPRNTMGAAMIKQCIG--------VAT------ 165

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                      + +     + + V  Y      R+  +      
Sbjct: 166 ---------------------------ANQKLRPDTRAHVLHYPQRAMTRTRTS------ 192

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                              +    D   G+N +VA + + GYN ED+++ ++  +   + 
Sbjct: 193 ------------------EAIGFDDRPAGQNFVVAILSYEGYNIEDALIFNKGSIERGLG 234

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDI 893
            S  +  FE   R    G E+   +IP+       S E   N+D  G++     V P D+
Sbjct: 235 RSHFLRTFEGEERRYPGGQEDKF-EIPDSEYRGARSAEAYANLDTDGLVNPETPVGPNDV 293

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           L+GK +P              + FG      R++S+ + S  +G V
Sbjct: 294 LIGKTSPPRFLEEP-------SDFGISVEQRRESSITMRSNETGIV 332


>gi|83415479|gb|ABC17947.1| RNA polymerase II second largest subunit [Smittium culisetae]
          Length = 718

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 136/857 (15%), Positives = 245/857 (28%), Gaps = 162/857 (18%)

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             +R+   G +L   +R    +M R +    +              + +  + + +     
Sbjct: 1    RKRLDLAGPLLAMLFRNLFKKMTRDMTRYLQKCIESRREFNLSMALKSNTITAGLKYSLA 60

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               ++Q+       S ++H RR +      + R     + R +H TH
Sbjct: 61   TGNWGDQKKAMQSRTGVAQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTH 116

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   A +       +    + +  + N    +     ++ 
Sbjct: 117  WGLVCPAETPEGQACGLVKNLALMAHITVGSDSGSILMFLEEWAMENLEELVGDSLADST 176

Query: 626  YIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             I      +            L   R   E         D  +   + +        P  
Sbjct: 177  KIFVNGVWVGIHKEAVRLAATLKQLRRRLEFSYELSIVHDVREREIRILTDAGRVCRPLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +     L               +          +  + +         GIVE +DA  
Sbjct: 237  VVNHMRLAL--------------TKPVVAAIEARRLGERDAVRWHDLLSEGIVEYLDAEE 282

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +                                 V  G    ++D          
Sbjct: 283  EETAMIVMSPHELDESRRF--------------------VHTGQLPPKDD---------- 312

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            G +   RN  +    W       SM+  I   +V            ++       +G   
Sbjct: 313  GRIRSRRN--IGITTWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGKQAMGILL 370

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                   V  + L N+                     +     S +   +  + AI    
Sbjct: 371  TNYQ---VRMDTLANL--------LYYPQKPLATTHAMEYIKFSELPAGQNAIVAILCYT 419

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +     F  +  ++++  +      +    +      + L  
Sbjct: 420  GYNQEDSLIMNQSSIDRGLFRSIFFRSYMDEEDKLGM----RTMGRFEKPSRASTLRLKI 475

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   I  G           K+T +    +               E  QR +  
Sbjct: 476  GTYEKLDDDGLIAPGTRVTGDDIIIGKTTPIPIASL---------------ELGQRTLAH 520

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             K+         E    +++     GD       + VKV V   R  Q GDK A RHG K
Sbjct: 521  TKLDASKPLRATESGIVDQVLLXTNGD-----GFKFVKVRVRSTRVPQIGDKFASRHGQK 575

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +  +   EDMPF  DG   D+++NP  +PSRM +G + E  L      +G    +   
Sbjct: 576  GTIGIVYTSEDMPFTADGIVPDLIINPHAIPSRMTIGHLIECLLSKLATLVGTAADASPF 635

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   IS       ++   G H+  +                                
Sbjct: 636  TDVTVDAISA------ELFSLGYHSRGLEVM----------------------------- 660

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                         +G      G         V  G  Y  +L HMV DK+++R+ G   +
Sbjct: 661  ------------YNGH----SGR---KLYSQVFFGPTYYQRLKHMVDDKIHSRARGPLQI 701

Query: 1278 VTQQPLGGKSNRGGQRL 1294
            +T+QP+ G+S  GG R 
Sbjct: 702  LTRQPVEGRSRDGGLRF 718



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 112/372 (30%), Gaps = 11/372 (2%)

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           P+L +   N    +   +     K  +        +    +  T  +  S+    + D  
Sbjct: 9   PLLAMLFRNLFKKMTRDMTRYLQKCIESRREFNLSMALKSNTITAGLKYSLATGNWGDQK 68

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           K   S  G  ++  R    +      R          I     L N    +         
Sbjct: 69  KAMQSRTGVAQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEG 128

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +      ++KN   +  + +       +  ++  ++   + +    +  +   F     +
Sbjct: 129 QACG---LVKNLALMAHITVGSDSGSILMFLEEWAMENLEELVGDSLADSTKIFVNGVWV 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +E V   + +   RR        ++      E      T  GR+C       +++ L
Sbjct: 186 GIHKEAVRLAATLKQLRR-RLEFSYELSIVHDVREREIRILTDAGRVCRPLFV-VNHMRL 243

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             +    A + A    E    +  D      V YL A EEE   I  +   LDE   F  
Sbjct: 244 ALTKPVVAAIEARRLGERDAVRWHDLLSEGIVEYLDAEEEETAMIVMSPHELDESRRFVH 303

Query: 643 ELVFCRCAGEEILVPREK----IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                      I   R          +  P  ++ I AS++PF +++ S R      M +
Sbjct: 304 TGQLPPKDDGRIRSRRNIGITTWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGK 363

Query: 699 QAVPLLKAEAPF 710
           QA+ +L      
Sbjct: 364 QAMGILLTNYQV 375


>gi|6606127|gb|AAF19076.1|AF107804_1 DNA-dependent RNA polymerase II RPB140 [Pleospora tarda]
          Length = 942

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 157/1052 (14%), Positives = 315/1052 (29%), Gaps = 176/1052 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGV----KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +E G +L S       E  +    K +           +     +     ++   G V D
Sbjct: 36   VEKGTRLISSFNIKWAENSLAGHGKRIPGPFAYA---TLPYIKADVPMAIVFRALGIVSD 92

Query: 330  EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            E+ L  I +       +  +        +         +DR+ AL  I +          
Sbjct: 93   EEILSHIVYDRTDTQMLELLKPSIEEGSV--------VQDRETALDFIAKRGANSGTKDR 144

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
             +  +          +  L  + +            +     +      +I  L+    G
Sbjct: 145  RLKFA-----RDIMQREFLPHISQK-----------EGQDTRKAYFFGYMIHRLLQCVLG 188

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAK 507
            +   DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  + A 
Sbjct: 189  RRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYLQRCVENNQDFNVQMAVKAS 248

Query: 508  PVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             + + +     +               +SQ+       S ++H RR +      V R   
Sbjct: 249  IITNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGK 304

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTN 612
              + R +H +H+G +CPAET EG   GLV +L+    V+          +    + ++  
Sbjct: 305  LAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLE 364

Query: 613  DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQV 671
            +       +    ++      +  +      +V        +      I D  D   K  
Sbjct: 365  EYDQNQNPDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIF 424

Query: 672  VSIAASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
                  + P    ++  R      +   +     LKAE     T       +   A    
Sbjct: 425  TDAGRVMRPLFVVENDFRRENRNQLVFTKAISNKLKAEQQETSTRQGWSQEEVENATYGW 484

Query: 730  K---RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVG 785
            +   + G+VE +DA       +    +      +    L   +RS +     +R      
Sbjct: 485  RGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMKMGLPAVERSTEGKDRLRRLKPAPD 544

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              +         P+  LG       +  + +P+  +N          M  + +  ++   
Sbjct: 545  PRIHAYTHCEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNF 597

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
               +                                  V             +       
Sbjct: 598  ALRMETMMN-----------------------------VLYYPQKPLATTRSMEYLKFRE 628

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E
Sbjct: 629  LPAGQNAIVAIATYGGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLE 684

Query: 966  LLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
               +    + + L    Y +L +   +  G           K+  +++D      ++   
Sbjct: 685  QFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIATDAQELGQKTTLH 744

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    ++     +  Q                             LR VKV     +
Sbjct: 745  TKRDVSTPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRTTK 784

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L 
Sbjct: 785  VPQIGDKFASRHGQKGTIGITYRQEDMPFSKEGLTPDLIINPHAIPSRMTIAHLVECLLS 844

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G++  +          +S                          +L  A   K 
Sbjct: 845  KVGAITGQEGDATPFTDVTVDQVS-------------------------QLLEDAGYQKR 879

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G  +                        +G +       G+     + +G  Y  +L HM
Sbjct: 880  GFEIM----------------------YNGHT-------GKKMRTQIFLGPTYYQRLRHM 910

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            V DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 911  VDDKIHARARGPLQILTRQPVEGRARDGGLRF 942



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 110/854 (12%), Positives = 239/854 (27%), Gaps = 142/854 (16%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK---DII- 202
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K   + + 
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWIAEIRSAVEKGTRLISSFNIKWAENSLA 56

Query: 203 ----------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFW 245
                           +++ D    VP+     ALG+   EEILS        +Q  +  
Sbjct: 57  GHGKRIPGPFAYATLPYIKAD----VPMAIVFRALGIVSDEEILSHIVYDRTDTQMLELL 112

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------ 299
              +    ++   + +   +         +  +   +  +  ++ + +  +         
Sbjct: 113 KPSIEEGSVVQDRETALDFIAKRGANSGTKDRRLKFARDI--MQREFLPHISQKEGQDTR 170

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYI 358
                G  +   ++    G    +  D   +K L+           IL++  + +   Y+
Sbjct: 171 KAYFFGYMI-HRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVYKYL 229

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           +  +  +++ + + A+           + T  +  S+    + D  K   +  G  ++  
Sbjct: 230 QRCVENNQDFNVQMAV--------KASIITNGLKYSLATGNWGDQKKAASAKAGVSQVLN 281

Query: 419 RLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           R    +      R          +     L N    +         +   + + L     
Sbjct: 282 RYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCY 341

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           + +      I + ++  ++  +   D                   +         ++ + 
Sbjct: 342 VSVGSDASPIIDFMTQRNMQLLEEYDQNQNPDATKVF---VNGVWVGVHSNAQQLVTVVQ 398

Query: 537 HTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG-------------HNIGL 582
             RR   L  +  + R     E + +       + P    E                I  
Sbjct: 399 ELRRNGTLSYEMSLIRDIRDREFK-IFTDAGRVMRPLFVVENDFRRENRNQLVFTKAISN 457

Query: 583 VSSLTSFARVNAYGF----IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
                        G+    +E              V YL A EEE   I  +   L+E  
Sbjct: 458 KLKAEQQETSTRQGWSQEEVENATYGWRGLIQDGVVEYLDAEEEETAMITFSPEDLEEWR 517

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                L     + E                                        G +  R
Sbjct: 518 EMKMGLPAVERSTE----------------------------------------GKDRLR 537

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           +  P          T  E   A   G       A I+   D  +    + +  +     G
Sbjct: 538 RLKPAPDPRIH-AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRNTYQSAMGKQAMG 591

Query: 759 V-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           V      ++ +         Q+PL                      +L  G+N +VA   
Sbjct: 592 VALTNFALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIAT 641

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    +    +   +   E        D   +    
Sbjct: 642 YGGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGT 701

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G++  G  V+  DI++GK  P         +K             RD S  + 
Sbjct: 702 YDKLDDDGVVAPGVRVSGDDIIIGKTAPIATDAQELGQKT-------TLHTKRDVSTPLR 754

Query: 933 SGVSGTVVDVRIFN 946
           S  +G V  V    
Sbjct: 755 STENGIVDQVLFTT 768


>gi|243010754|gb|ACS94454.1| RpoB [Mycobacterium triplex]
          Length = 248

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 105/240 (43%), Positives = 140/240 (58%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEGLRHAQPDQTVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.5 bits (106), Expect = 0.071,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|52694389|emb|CAG38034.1| RNA polymerase beta subunit [Pseudomonas putida bv. A]
          Length = 319

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 192/319 (60%), Positives = 249/319 (78%)

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E
Sbjct: 1   LMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFE 60

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++D+V+L
Sbjct: 61  VRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVSDDIVFL 120

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           SA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 SAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 180

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ 
Sbjct: 181 LIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDS 240

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R+DI+ADG
Sbjct: 241 VDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQRSDIMADG 300

Query: 798 PSTDLGDLALGRNMLVAFM 816
           PSTD+G+LALG+NM +AFM
Sbjct: 301 PSTDMGELALGQNMRIAFM 319


>gi|52538135|emb|CAH19171.1| RNA polymerase beta-subunit [Pseudomonas libanensis]
          Length = 330

 Score =  316 bits (809), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 190/330 (57%), Positives = 252/330 (76%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQ+TC+NQRPLV+ G  V+R
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQHTCINQRPLVRKGYRVQR 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +DI+ DGPS+D+G+LALG+NM +AFM W+G
Sbjct: 301 SDIMPDGPSSDMGELALGQNMRIAFMAWNG 330


>gi|269913257|emb|CAY86055.1| RNA polymerase beta subunit [Gluconacetobacter azotocaptans]
          Length = 309

 Score =  315 bits (808), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 152/312 (48%), Positives = 202/312 (64%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD++EIL+ FY K+V+ +   
Sbjct: 61  KRKLPVTTLLYALEGEASAAARAAKVAEGGDVDSLDIQGMDADEILNYFYGKVVFVKTSK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P  A     G K+   L+D ++GE V E+  KLT+ +++ + EK  K + + +  L
Sbjct: 121 GWARPFDAE-SFRGLKLLEPLIDAESGEVVAEADAKLTARMVRKIAEK-TKDVLVGAAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G YVA D+VN +TGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL 
Sbjct: 179 IGRYVAYDLVNQDTGEIYAEAGEELTEARLEALEEAGLDRLPTLAVDASN-GPWIRNTLT 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD
Sbjct: 238 VDKNTTRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLD 297

Query: 424 TPDDVRHIRKED 435
            PD VR +RKED
Sbjct: 298 APDTVRVLRKED 309


>gi|83763753|emb|CAJ00210.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12C03]
          Length = 353

 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 187/365 (51%), Positives = 256/365 (70%), Gaps = 13/365 (3%)

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SG   VAKR G+V+ VDA RIV++  E +L P  +G+DIY L K+ RSN
Sbjct: 1    GTGIERNVAVDSGVTAVAKRGGMVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSN 60

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SE
Sbjct: 61   QNTCINQRPTVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSE 120

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  G
Sbjct: 121  RVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGG 180

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++
Sbjct: 181  DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVE 240

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++R++ +E  Q++   +D  +E  I +  +  R+  +L                  S  
Sbjct: 241  KDKRALEIEHMQLKEAKKDLTEEFQIFEGGLLVRVKAVLLNGG-------------YSEA 287

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
             +    R +W +  ++++++Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL
Sbjct: 288  KLDSIDRKKWLEQTLENDELQSQLEQLAEQWDELKADFDKKFEAKRRKITQGDDLAPGVL 347

Query: 1072 RVVKV 1076
            ++VKV
Sbjct: 348  KIVKV 352


>gi|321261728|ref|XP_003195583.1| DNA-directed RNA polymerase [Cryptococcus gattii WM276]
 gi|317462057|gb|ADV23796.1| DNA-directed RNA polymerase, putative [Cryptococcus gattii WM276]
          Length = 1129

 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 130/313 (41%), Gaps = 78/313 (24%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++K+     R  + GDK + RHG KG+   I+P  DMPF   G   DI++NP G PSRM 
Sbjct: 877  LIKILTRQTRRPELGDKFSSRHGQKGVCGLIVPQADMPFNDQGIVPDIIMNPHGFPSRMT 936

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            VG++ E   G A V                                              
Sbjct: 937  VGKMIELLSGKAGV---------------------------------------------- 950

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
               +A + + G       F G+    ++ +L        G+ +L  G+TG+P +  V  G
Sbjct: 951  ---IAGKLQYGT-----AFGGSKVVDMSQILIDNGFSYGGKDMLTSGITGQPMEAYVYFG 1002

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR TG  + +T+QP  G+S  GG RLGEME  C+  YGA  +L 
Sbjct: 1003 PIYYQKLKHMVMDKMHARPTGPRANLTRQPTEGRSKDGGLRLGEMERDCLIGYGATQLLL 1062

Query: 1313 EMLTIKSDDVVGRTRVYESIVA-----------------GNDTFETGTPESFNVLVKEMQ 1355
            E L I SD        +E+ V                  GN       P +  +L++E+ 
Sbjct: 1063 ERLMISSD-------AFETQVCESCGMLGYNNWCPKCKSGNGVVGLTIPYAAKLLIQELM 1115

Query: 1356 ALGLSIDLENSRT 1368
             + +   L    T
Sbjct: 1116 GMNIMPKLCLEDT 1128



 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 121/917 (13%), Positives = 275/917 (29%), Gaps = 154/917 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S+++F+ ++I      N         + P         + +       P    
Sbjct: 37  LVKQHLDSFNYFVNVDIKAILAANS---LVISDINP------KYYIRYTDIRVGRPARHD 87

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI---------------K 123
                      +C   D TY+ P+ + +  +  +         I                
Sbjct: 88  ANQVASALSPMECRLTDSTYSAPIYVDVEYMGEEKRSKQRGVQIGMLPVMLRSDLCNLKG 147

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC- 182
             + +   MG+ P M   G FV+KG +++++ Q   S        K +       + +  
Sbjct: 148 KNEAELARMGECP-MDPGGYFVVKGTEKVILVQEQLSKNRILVM-KDKKDEVMAEVTSST 205

Query: 183 --RIIPDQGLWMDIEFDSKDIIHVRIDRRRK-VPVTSFLMALGMDSE-EILSTFYPKIVY 238
             R++              + +++R +  ++ +P+   L A+G+ ++ EIL         
Sbjct: 206 HDRVVKT------YVVSKANRLYLRHNSFKEFIPIVIALKAMGLTADKEILQLICGSDER 259

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            Q         +A +     + +   +    G +V  +  K  SG  + L    +    +
Sbjct: 260 YQEAFGVSLEEAAKEKTFTRRQALEWI----GARVSPNQAKDDSGSNQKLTPSDIAQQAL 315

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
            +  L   +V    +N     IY+    +     +  I    + D   +    +     +
Sbjct: 316 AAMVLG--HVPVRNMNFRPKCIYLA--TMTRRVLMAMIDDHMVDDRDYVGNKRLELAGQL 371

Query: 359 RNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            + L  D  K    +    + +++   + +    A ++         +  + ++     +
Sbjct: 372 LSLLFEDSFKTFNSELKKRMDKILEKPNRAGPFDAGTLIRQGGDPITQAFVRSISTGNWS 431

Query: 418 MRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           ++        V H    +     + ++  +         +     L   +   +      
Sbjct: 432 LKRFHVERAGVTHVLSRLSFIAALGMMTRISSQFEKTRKVSGPRALQPSQWGMLCPSDTP 491

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN-SL 532
           +     L    ++   I++   ++ + +          ++       +       VN +L
Sbjct: 492 EGEACGLVKNLALMTHITTDVPEAPLVKMAFMLGVEDISLVTGNELYRPGVHMVQVNGTL 551

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS-FAR 591
             +T+  +        + RA    E   +   H+ +I    +  G     +  +    +R
Sbjct: 552 IGVTNMAKKFVRQFRKLRRAGRMSEFVSIFINHHHKIIYIASDGGRICRPMIIVEKGRSR 611

Query: 592 VNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           V           KV          V YL   EE + +IA   + ++E             
Sbjct: 612 VTTEHVRLLKEGKVTFDHFLRAGLVEYLDVNEENDAFIACYENEIEEG------------ 659

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
                         ++  P  ++   A LIP+  ++ S R    C M +QA+        
Sbjct: 660 -----------TTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA------ 702

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                                              I   + +   +   +  Y       
Sbjct: 703 -----------------------------------IAYNQLNRIDTLLYLMTYP------ 721

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+P+VK                     L  G+N  VA M + GY+ ED++++
Sbjct: 722 --------QQPMVK----------TKTIELIGYNKLPAGQNATVAVMSYSGYDIEDALIL 763

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDE-CGIICVGAE 887
           +   V         +++     R    G  E T    P    +    +D+  G+   GA 
Sbjct: 764 NRASVDRGFGRCHVLKKVTTPMRTFHNGSHERTAYPDPPPRPDAYTFVDKADGMTAPGAT 823

Query: 888 VNPGDILVGKITPKGES 904
           +N  D+++ + TP    
Sbjct: 824 INQYDVMIHRETPIDTR 840


>gi|89274894|gb|ABD65888.1| RNA polymerase II second largest subunit [Laetiporus sulphureus]
          Length = 897

 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 133/905 (14%), Positives = 262/905 (28%), Gaps = 155/905 (17%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 129  RYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAAMERRDLDDRDHFGKKRL 185

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +    + + +     +   
Sbjct: 186  DLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVKHNTITNGLKYSLATGNW 245

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 246  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 301

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  + ++           + +  + +         EEN + A 
Sbjct: 302  CPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSAT 353

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 354  PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGR 410

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            V     +      LL                +        +             VI  ++
Sbjct: 411  VCRPLFIVENQQLLLAK-----------KHIQYLNDGQDEEGKPYKWDSLVKGGVIELLD 459

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG- 808
             + + +         ++  R   NT  +                       + G+     
Sbjct: 460  AEEEETVMICMTPEDLENSRMQSNTIDSH---------------------MNDGEFDPAA 498

Query: 809  -RNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                      W       SM+  +   ++            ++       +G       +
Sbjct: 499  RLKATTNTHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV 558

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 559  RM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQE 607

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +    
Sbjct: 608  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKLED 666

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 667  DGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRTRAHTRRDVSTPLKSTESGIIDQVLI- 725

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VK+ V   R  Q GDK A RHG KG +     
Sbjct: 726  -------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYR 766

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +           
Sbjct: 767  QEDMPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 819

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++       LR       G+ V                   
Sbjct: 820  ------------------DLTVESVSQFLRQKGYQSRGLEVM------------------ 843

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 844  ----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 892

Query: 1286 KSNRG 1290
            +S  G
Sbjct: 893  RSRDG 897



 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 102/771 (13%), Positives = 221/771 (28%), Gaps = 112/771 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +   Q  +     +    ++   +V+
Sbjct: 54  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDVQMLEMLKPCIDDGFVIQDREVA 109

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  +   ++  
Sbjct: 110 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 168

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 169 MERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVK 228

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 229 HNT--------ITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 280

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + E +   
Sbjct: 281 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEW 340

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++S+      NA         F     +    +  N +  I   RR   +         
Sbjct: 341 GLESL----EENAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 396

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L      +  +N     E    K         
Sbjct: 397 IRERELRLYTDAGRVCRPLFIVENQQLLLAKKHIQY--LNDGQDEEGKPYKWDSLVKGGV 454

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDA 666
           +  L A EEE   I      L+     +  +      GE     R             + 
Sbjct: 455 IELLDAEEEETVMICMTPEDLENSRMQSNTIDSHMNDGEFDPAARLKATTNTHTWTHCEI 514

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 515 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 558

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 559 -------------------------RMDTMANILYYPQKPLATTRSMEYLRFR------- 586

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F SI+   
Sbjct: 587 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRS 629

Query: 847 FEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E        +   +       +++ G+I  G  VN  DI++GK  P 
Sbjct: 630 YMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPI 689

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++        +A   RD S  + S  SG +  V I       K
Sbjct: 690 PPDSEELGQRT-------RAHTRRDVSTPLKSTESGIIDQVLITTNAEGQK 733


>gi|83763743|emb|CAJ00205.1| putative DNA-directed rna polymerase, beta subunit [Vibrio sp. 12G06]
          Length = 357

 Score =  315 bits (808), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 188/364 (51%), Positives = 256/364 (70%), Gaps = 13/364 (3%)

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            TG+E  +A  SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQ
Sbjct: 6    TGIERNIAVDSGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQ 65

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            NTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER
Sbjct: 66   NTCINQRPTVLPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSER 125

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GD
Sbjct: 126  VVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGD 185

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K
Sbjct: 186  ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEK 245

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            ++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S   
Sbjct: 246  DKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAK 292

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +    R QW +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL+
Sbjct: 293  LDTSVRKQWLEQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLK 352

Query: 1073 VVKV 1076
            +VKV
Sbjct: 353  IVKV 356


>gi|73697683|gb|AAZ81458.1| RNA polymerase beta subunit [Mycoplasma leopharyngis]
          Length = 591

 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 210/433 (48%), Positives = 307/433 (70%), Gaps = 10/433 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L  +
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLAIY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +G V  ++V YL+A +E    I Q+   +DED   T+E +  R
Sbjct: 61  AGVNEYGFLQTPYFKVNNGVVDYSNVEYLTAADEFGFNIGQSTVHVDEDNKITDEFLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   + ID+I+ + +Q+VS+AA  IPFLENDD+NR LMG NMQRQ+VPL++ EA
Sbjct: 121 KNYNYIIGAPKDIDYIEVASRQMVSVAAGCIPFLENDDANRALMGSNMQRQSVPLIETEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG E+ +AK S A   AK+ G+VE  D  +I IR+ +G LD        Y L  F+
Sbjct: 181 PFVATGTEADIAKYSAANFRAKQDGVVEFADGSKIKIRNKKGTLD-------TYNLKNFK 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ+T ++QRPLVKVG EV+++D++ DG S   G+L+LG+N+LVAF  + G+N+ED+++
Sbjct: 234 RSNQDTVIHQRPLVKVGQEVKKDDLLVDGSSFKNGELSLGKNLLVAFTTYKGFNYEDAVI 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V EDV TSIHIEE  +  R +K G +E+TRDIPNVS+  ++++DE GI+ VG+EV
Sbjct: 294 LNERLVKEDVLTSIHIEEQTIQFRTSKAGVDELTRDIPNVSKHSIRHLDERGIVLVGSEV 353

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKG+   + EEKLL A+ G++ ++V+DTSL+V +G +GT++ V I +R 
Sbjct: 354 TPGDVLVGRVSPKGDDNPSQEEKLLSAVLGQRQMNVKDTSLKVKNGHNGTIIGVEILSRE 413

Query: 949 GIDKNERSISVER 961
              K++    +++
Sbjct: 414 N--KDQLEDGIDK 424



 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 139/446 (31%), Positives = 193/446 (43%), Gaps = 77/446 (17%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              K G  +               I +  ++ VG EV   D+LV   + K    ++  + L
Sbjct: 218  RNKKGTLDTYNLKNFKRSNQDTVIHQRPLVKVGQEVKKDDLLVDGSSFKN-GELSLGKNL 276

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLAR- 969
            L A    K  +  D  +     V   V+         I        V+     I  +++ 
Sbjct: 277  LVAFTTYKGFNYEDAVILNERLVKEDVLTSIHIEEQTIQFRTSKAGVDELTRDIPNVSKH 336

Query: 970  --DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 DE+ I+         ++L G+ +  G     +   L S ++              
Sbjct: 337  SIRHLDERGIVLVGSEVTPGDVLVGRVSPKGDDNPSQEEKLLSAVLG------------- 383

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                QR +       +            +I   +  D +  G+ ++VKV +A+KR I+ G
Sbjct: 384  ----QRQMNVKDTSLKVKNGHNGTIIGVEILSRENKDQLEDGIDKIVKVSIAVKRKIRVG 439

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKM+GRHGNKG+VS ILP EDMP L+DGTPVD++LNP GVPSRMN+GQ+ E HLG A   
Sbjct: 440  DKMSGRHGNKGVVSVILPEEDMPHLEDGTPVDVMLNPQGVPSRMNIGQVLEIHLGMAARK 499

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
            LG K  + + D     DI                                          
Sbjct: 500  LGCKFVTPVFDGIKKEDIQ----------------------------------------- 518

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                      AI      A+L  SG+ IL D +TGE  D+PV+VG +YMLKLNHMV DK+
Sbjct: 519  ---------AAIKE----ANLPISGKQILIDPITGEKIDKPVSVGVMYMLKLNHMVDDKM 565

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 566  HARSVGPYSLITQQPLGGKSQNGGQR 591


>gi|269912578|emb|CAY86069.1| RNA polymerase beta subunit [Gluconacetobacter intermedius]
          Length = 318

 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 152/321 (47%), Positives = 200/321 (62%), Gaps = 28/321 (8%)

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRI
Sbjct: 1   NGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRI 60

Query: 207 DRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQR 241
           DR+RK+PVT+ L AL                         GM  +EILS FY K+ +++ 
Sbjct: 61  DRKRKLPVTTLLYALEGAESEAARAAKAAEGGDVESMEIQGMSPDEILSYFYGKVEFAKT 120

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
              W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +   
Sbjct: 121 EKGWARRFDA-DAFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPA 178

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            L G ++A DIVN  TGEIY EAGD + E+ LEE+    +  +  L VD+ N   +IRNT
Sbjct: 179 GLIGRFIASDIVNEHTGEIYAEAGDELTEQKLEELEEVGLTTLSTLAVDAAN-GPWIRNT 237

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           L  DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL 
Sbjct: 238 LAVDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLG 297

Query: 422 LDTPDDVRHIRKEDIIAIIKI 442
           +D PD VR +RKEDI+  +KI
Sbjct: 298 VDVPDTVRVLRKEDILRTVKI 318


>gi|163930841|dbj|BAF96015.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 323

 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 197/323 (60%), Positives = 251/323 (77%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N Y
Sbjct: 61  THKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L
Sbjct: 121 GFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSL 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
             R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGM
Sbjct: 181 FSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E  VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC
Sbjct: 241 ERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTC 300

Query: 776 VNQRPLVKVGDEVRRNDIIADGP 798
           +NQ P V +G+   R D++ADGP
Sbjct: 301 INQMPCVSLGEPXERGDVLADGP 323


>gi|6606129|gb|AAF19077.1|AF107805_1 DNA-dependent RNA polymerase II RPB140 [Preussia minima]
          Length = 937

 Score =  315 bits (807), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 164/1048 (15%), Positives = 311/1048 (29%), Gaps = 173/1048 (16%)

Query: 274  IESGKKLTSGLLKSLKEKG--VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
            +E G +L S       +    VK             +     +     ++   G V DE 
Sbjct: 36   VEKGTRLISSFNIKWTDNSMIVKRQPGPFAYAV---LPYIKADVPMAIVFRALGIVSDED 92

Query: 332  SLEEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             L  I +       + L   S+   A I+           + AL  I R           
Sbjct: 93   ILNHIVYDRNDTQMLELLKPSIEEGAMIQER---------ETALDWIARRGNQTGTKDKR 143

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
            +  +          +  L  + +            +     +      +I  L+    G+
Sbjct: 144  LKFA-----REIMQREFLPHISQK-----------EGQDTRKAFFFGYMIHRLLQCVLGR 187

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKP 508
               DD D+ G +R+   G ++ N +R+  L++ + +    R              + A  
Sbjct: 188  RDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDMFNYLRKCVDAEQEFNATLALKASI 247

Query: 509  VVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            V + +     +               +SQ+       S ++H RR +      V R    
Sbjct: 248  VTNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKL 303

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTND 613
             + R +H TH+G +CPAET EG   GLV +L+    V+          +    +  +  +
Sbjct: 304  AKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGNESAPIIDFMSQRNMDLLEE 363

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVV 672
               +        ++      +  + S    +V        +      I D  D   K   
Sbjct: 364  YDPIQNPTATKVFVNGTWVGVHSNPSQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFT 423

Query: 673  SIAASLIPFL--ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA- 729
                 + P    E + +        + +  +  L+A+     +GM               
Sbjct: 424  DAGRVMRPLFVVETNYNKPNRGSLVLTKAHIEKLQADKEIDTSGMNDEDTAERKYGWFGL 483

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               G+VE +DA       +    +      D+ +  + Q   ++   ++R   K    ++
Sbjct: 484  IHDGVVEYLDAEEEEGAMIIMSPEDLDEHRDLMQGTQTQEDKEDNDRHKRIKPKPNPSIK 543

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    PS  LG       +  + +P+  +N          M  + +  ++      +
Sbjct: 544  TYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRM 596

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                              V             +       +   
Sbjct: 597  ETMMN-----------------------------VLYYPQKPLATTRSMEYLRFRELPAG 627

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   +
Sbjct: 628  QNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEK 683

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                + + L    Y +L +   +  G           K+  +  D               
Sbjct: 684  PTRQDTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPGD--------------- 728

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
              E  Q+     K    T     E+   +++             LR VKV     +  Q 
Sbjct: 729  AQELGQKTQNHTKRDVSTPLRSTENGIVDQVLF-----TTNTEGLRFVKVRTRTTKVPQI 783

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L     
Sbjct: 784  GDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHAIPSRMTIAHLVECLLSKVGS 843

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +          +S L                +          V     +G  +
Sbjct: 844  LKGAEGDATPFTDVTVESVSKLL---------------VEHGYQQRGFEVMYNGHTGKKL 888

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
               VF                                       +G  Y  +L HMV DK
Sbjct: 889  RAQVF---------------------------------------LGPTYYQRLRHMVDDK 909

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            ++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 910  IHARARGPLQILTRQPVEGRARDGGLRF 937



 Score =  139 bits (350), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 105/827 (12%), Positives = 246/827 (29%), Gaps = 102/827 (12%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK---DII- 202
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K   + + 
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWTAEIRSAVEKGTRLISSFNIKWTDNSMI 56

Query: 203 --------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
                         +++ D    VP+     ALG+   E+IL+        +Q  +    
Sbjct: 57  VKRQPGPFAYAVLPYIKAD----VPMAIVFRALGIVSDEDILNHIVYDRNDTQMLELLKP 112

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            +    ++   + +   +    G Q     K+L     + ++ + +  +           
Sbjct: 113 SIEEGAMIQERETALDWI-ARRGNQTGTKDKRLKFAR-EIMQREFLPHISQKEGQDTRKA 170

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIRDIPILYVD-SVNNNAYIRNT 361
                +     +  +   D  D        L+           IL++  + +   Y+R  
Sbjct: 171 FFFGYMIHRLLQCVLGRRDEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDMFNYLRKC 230

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +  ++  +   AL           + T  +  S+    + D  K   +  G  ++  R  
Sbjct: 231 VDAEQEFNATLAL--------KASIVTNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 282

Query: 422 LDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
             +      R          +     L N    +         +   + + L     + +
Sbjct: 283 YASTLSHLRRTNTPVGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSV 342

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
                 I + +S  ++D +   D I               + +         +S +   R
Sbjct: 343 GNESAPIIDFMSQRNMDLLEEYDPIQNPTATKVF---VNGTWVGVHSNPSQLVSVVQELR 399

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R   L             +RD+    +     A         + ++     R +      
Sbjct: 400 RNGTLSY-------EMSLIRDIRDREFKIFTDAGRVMRPLFVVETNYNKPNRGS------ 446

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
                V        +              QA+  +D  G   E+    +      L+   
Sbjct: 447 ----LVLTKAHIEKL--------------QADKEIDTSGMNDEDTAERKYGW-FGLIHDG 487

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            ++++DA  ++   I  S     E+ D  +       +       + +     +      
Sbjct: 488 VVEYLDAEEEEGAMIIMSPEDLDEHRDLMQGTQTQEDKEDNDRHKRIKPKPNPSIKTYTH 547

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DIYRLMKFQRSNQNTCVNQ 778
            +   + I+   A I+   D  +    + +  +     GV      ++ +         Q
Sbjct: 548 CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRMETMMNVLYYPQ 607

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +PL                      +L  G+N +VA   + GYN EDS+++++  +   +
Sbjct: 608 KPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 657

Query: 839 FTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           F S+    +    +   +   E        D   +       +D+ G++  G  V+  DI
Sbjct: 658 FRSLFYRAYTEQEKRIGVNVLEQFEKPTRQDTLRLKGGTYDKLDDDGVVAPGVRVSGDDI 717

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++GK  P         ++L +        DV        +G+   V+
Sbjct: 718 IIGKTAPIPGDA----QELGQKTQNHTKRDVSTPLRSTENGIVDQVL 760


>gi|224132576|ref|XP_002321356.1| predicted protein [Populus trichocarpa]
 gi|222868352|gb|EEF05483.1| predicted protein [Populus trichocarpa]
          Length = 1141

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 109/588 (18%), Positives = 204/588 (34%), Gaps = 94/588 (15%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D+    N L+A   W        + I    +   V   I         R+T     
Sbjct: 627  IEYLDVNEENNALIALYEWEATPETTHIEIEPFTILGVVAGLIPYPHHNQSPRNT----Y 682

Query: 860  EITRDIPNVSEEGLKN-IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            +       +             ++ +        +    I   G   +   +    A+  
Sbjct: 683  QCAMGKQAMGNIAYNQASRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMS 742

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                D+ D  +   + +        +  ++    N++  +   ++I    ++++ E+V+ 
Sbjct: 743  YSGYDIEDAIVMNKASLDRGFGRCIVLKKYTCT-NQKYENGASDRILRPRKNEERERVLD 801

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFK-KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            D  + +    I  G   ++     + +  + S+  +++       Q     E     V+ 
Sbjct: 802  DDGLAAPGEIIRHGDIYINKESPIETRGPLKSAAALADVKYRPCAQIFKGTEGESCVVDR 861

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +                +K                 +K  +   R  + GDK + RHG K
Sbjct: 862  V------------ALCSDK------------NNNLCIKYKIRHTRRPEVGDKFSSRHGQK 897

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+   I+  ED PF + G   D+++NP G PSRM VG++ E   G A V  G+       
Sbjct: 898  GVCGTIIQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRFHYGSAF 957

Query: 1158 DYKAN--GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
               +     +  +R FL  +                                        
Sbjct: 958  GEPSGHADRVEAIRHFLSLI---------------------------------------- 977

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   L       +G+  +Y G+TG P    + +G IY  KL HMV DK++AR +G  
Sbjct: 978  -----ETLVKHGFSYNGKDFIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPR 1032

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRV 1328
             ++T+QP  G++  GG R+GEME  C+ AYG + +L E L + SD          G    
Sbjct: 1033 VMLTRQPTDGRARNGGLRVGEMEKDCLVAYGTSMLLYERLMVSSDQFEAQVCRACGLLGY 1092

Query: 1329 YESIVA---------GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            Y   +          G+       P +  +L++E+Q++ +   L+ + 
Sbjct: 1093 YNQKLKAAMCTTCKNGDKVSTMKLPYACKLLIQELQSMNIVPRLKLAE 1140



 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 127/938 (13%), Positives = 277/938 (29%), Gaps = 174/938 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAAMLEFVSYEFDPPK-- 85
           L++    S+++F+          N G++   ++   I +    +  L F   +   P   
Sbjct: 33  LVKQHLDSFNYFI----------NIGIKKIVRANDRIVSTVDPSLYLRFTDVKIGKPSMV 82

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C   D TYA P+ + +  I             + + +  + +G +P+M
Sbjct: 83  VDAISEQITPHMCRLSDTTYAAPILVNIEYISGSHGRK------EKMIKNDVVIGRMPIM 136

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDK---- 169
                                      G FV+KG +++++ Q   S   I  D+DK    
Sbjct: 137 LRSCCCVLYGKNEAELARLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIIDNDKKGNI 196

Query: 170 -GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE- 226
               + S +   +  +I             K+ +++ +++  +K+P+   + A+GM+S+ 
Sbjct: 197 NASVTSSTEATKSKTVI----------LMEKEKMYLCLNQFAKKIPIMVVMKAMGMESDQ 246

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           E++        YS          ++  +    +    L  +        S  +  +  L 
Sbjct: 247 EVVQMVGRDPRYSALLLPSIEECASHGVYTQQQALEYLEAMVKRSTYSSSSTEKENRALA 306

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFHSEIRDIP 345
            L++  +  + +  +      +   ++     E  +    + D+  +  +      + I 
Sbjct: 307 ILRDVFIANVPVRKNNFRPKCIYVAVMLRRMMEALLNKDAMDDKDYVGNKRLELSGQLIS 366

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L+ D       +  T++T+  K     L+   R  R     +  +           +  
Sbjct: 367 LLFED-------LFKTMITEVQKTADTLLVKQNRSSRFDF--SQYIVRDSITNGLERALS 417

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
                V R +MN +           +     +  +  +         +     L   +  
Sbjct: 418 TGNWDVKRFRMNRKGVTQVLVR---LSYMASLGHMTRISPQFEKSRKVSGPRALQPSQWG 474

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            +      +     L    ++   +++ + +S +             +         +  
Sbjct: 475 MLCPCDTPEGEACGLVKNLALMTHVTTDEEESPLISLCKCLGVEDLELLSGEELHTPNSF 534

Query: 526 EEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
               N L    H R +  A     + RA    E   V      R     +  G     + 
Sbjct: 535 LVIFNGLILGKHRRPQQFANAMRKLRRAGKIGEFVSVFVNEKQRAVYIASDGGRVCRPLV 594

Query: 585 SLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
                    + +    +    R   D      + YL   EE N  IA             
Sbjct: 595 IADKGVSRIKEHHMRELMDGARTFDDFLHEGLIEYLDVNEENNALIAL------------ 642

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                             +   I+  P  ++ + A LIP+  ++ S R    C M +QA+
Sbjct: 643 -----------YEWEATPETTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAM 691

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
                                                      I   +     S   + +
Sbjct: 692 GN-----------------------------------------IAYNQASRMDSLLYLLV 710

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               QRPL+                      L  G+N  VA M + GY
Sbjct: 711 YP--------------QRPLL----------TTRTIELVGYDKLGAGQNATVAVMSYSGY 746

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           + ED++++++  +       I ++++    +  + G  +     P  +EE  + +D+ G+
Sbjct: 747 DIEDAIVMNKASLDRGFGRCIVLKKYTCTNQKYENGASDRILR-PRKNEERERVLDDDGL 805

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
              G  +  GDI + K +P            L  +   
Sbjct: 806 AAPGEIIRHGDIYINKESPIETRGPLKSAAALADVKYR 843


>gi|242392274|dbj|BAH80374.1| RNA polymerase subunit B' [Halorubrum sodomense]
          Length = 609

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/601 (21%), Positives = 207/601 (34%), Gaps = 99/601 (16%)

Query: 788  VRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
            V R ++    + +    +  D     ++LVA            + I  ++V       I 
Sbjct: 85   VERGEVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTEDHTHLEIDPQLVFGIGAGMIP 144

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              E     R T      + +    +     +   +     +        +          
Sbjct: 145  YPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQISF 201

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
                  +  + A+   +  ++ D  L +  G     +    F R    +  R    + ++
Sbjct: 202  DKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQEDR 260

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E+  +D       +           L     V+      +S+VL           +   
Sbjct: 261  FEIPEQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEPDD 313

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                  + +R         E+         + +               ++ KV V  +R 
Sbjct: 314  MGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQRV 361

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   G 
Sbjct: 362  PELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLGGK 421

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                                                                     +  
Sbjct: 422  V-----------------------------------------------------GSLRGS 428

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                TP F G DEE +   L       SG+ ++Y G+TGE  D  + VG I+  KL HMV
Sbjct: 429  RVDGTP-FQGEDEEELRDGLEDHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMV 487

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
            S+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD   
Sbjct: 488  SNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDAET 547

Query: 1321 -DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE  
Sbjct: 548  VHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLELE 606

Query: 1367 R 1367
             
Sbjct: 607  D 607



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 59/374 (15%), Positives = 119/374 (31%), Gaps = 33/374 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    +       ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEIAAVERGEVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTEDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILV 895
                +E   R    G E+   +IP         E+   ++DE G++    +V+   +L+
Sbjct: 241 HFFRTYEGEERRYPGGQEDRF-EIPEQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLL 299

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           GK +P               + G      R+TS+ + SG SG V  V +       K  +
Sbjct: 300 GKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSK 353

Query: 956 SISVEREQIELLAR 969
               ++   EL  +
Sbjct: 354 VKVRDQRVPELGDK 367



 Score = 43.1 bits (100), Expect = 0.32,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+  +A     + ED                    
Sbjct: 85  VERGEVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTEDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ V  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|6606119|gb|AAF19072.1|AF107800_1 DNA-dependent RNA polymerase II RPB140 [Dothidea insculpta]
 gi|82706467|gb|ABB89611.1| RNA polymerase II second largest subunit [Dothidea insculpta]
          Length = 936

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 154/975 (15%), Positives = 294/975 (30%), Gaps = 147/975 (15%)

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            + D+ IL     + N    + +        ++A +   R     +V+   + +       
Sbjct: 88   VSDMQILDCICYDAND---SQMREMIKPCLEEAFVIQDR-----EVALDFIGKRGQQMGT 139

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
             +        V + +    ++     + R  +   +  +I  L+    G+   DD D+ G
Sbjct: 140  REXRIRYARDVMQKEFLPHISQKEGSETR--KAFFLGYMINRLLQCALGRVEEDDRDHFG 197

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFC 518
             +R+   G ++   +RL   ++ R  +  +S              + A  + S +     
Sbjct: 198  KKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLA 257

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+       S ++H RR +      + R     + R +H TH
Sbjct: 258  TGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTH 313

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEE 623
            +G +CPAET EG   GLV +L+    V+     E    +    + ++  +    +  +  
Sbjct: 314  WGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPIIEFMNQRNMELLEEYEPKNNPDAT 373

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL 682
              ++      +  D +   ++V        I      I D  D   K        + P  
Sbjct: 374  KVFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISLIRDVRDREFKIFTDAGRVMRPLF 433

Query: 683  ENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVD 739
              D+        ++   R  +  L+ +     TG+ E     +          GI+E +D
Sbjct: 434  VVDNEPTSERRGHLVLARSNIERLQTDREMDLTGLSEEQRDSNIYGWKGLIGDGIIEYLD 493

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A       +    +       +               ++R   K    VR        P+
Sbjct: 494  AEEEEAAMITMSPEDLDEHRQVRAGAPVYDDVGLD-PHRRFKAKPNQSVRMWTHCEIHPA 552

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N          M  + +  ++                 
Sbjct: 553  MILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVTL----------------- 588

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                           N+    +  V             +       +   +  + AI   
Sbjct: 589  ------------TNYNVRMDTMANVLYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACY 636

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R  +D+ +R      EQ E   R          
Sbjct: 637  GGYNQEDSVIMNQSSIDRGLF-RSLFYRAYMDQEKRVGMSVVEQFEKPTRADTLRMKHGT 695

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G           K+  ++ D      R++                 +K
Sbjct: 696  YDKLDDDGIISPGSRVSGEDIIIGKTAPMAPDAEELGQRTKL---------------HVK 740

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                T     E    +++      D       + VKV     +  Q GDK A RHG KG 
Sbjct: 741  RDVSTPLRSTESGIIDQVLLTTNID-----GHKFVKVRTRTTKIPQIGDKFASRHGQKGT 795

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  DG   D+++NP  +PSRM +  + E  L       G++  +     
Sbjct: 796  IGVTYRQEDMPFTADGLVPDLIINPHAIPSRMTIAHLIECLLSKVGALRGQEGDATPFTD 855

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 +S L                 +         +     +G      VF G      
Sbjct: 856  VTITQVSDLLR---------------AHGFQQRGFEIMYNGHTGKKQVAQVFLG------ 894

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                               Y  +L HMV DK++AR+ G   ++T
Sbjct: 895  ---------------------------------PTYYQRLRHMVDDKIHARARGPXQILT 921

Query: 1280 QQPLGGKSNRGGQRL 1294
            +QP+ G++  GG R 
Sbjct: 922  RQPVEGRARDGGLRF 936



 Score =  141 bits (356), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 108/787 (13%), Positives = 227/787 (28%), Gaps = 126/787 (16%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+ S+ +IL         SQ  +     L  A ++   +V+
Sbjct: 71  YIKSD----IPIAIVFRALGVVSDMQILDCICYDANDSQMREMIKPCLEEAFVIQDREVA 126

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              +     +      +   +  +  ++++ +  +              G  +   ++  
Sbjct: 127 LDFIGKRGQQMGTREXRIRYARDV--MQKEFLPHISQKEGSETRKAFFLGYMI-NRLLQC 183

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
             G +  +  D   +K L+       +   + +   + +     +  V    +      +
Sbjct: 184 ALGRVEEDDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAV 243

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                    ++ +  +   +    + D  K   +  G  ++  R    +      R    
Sbjct: 244 -------KANILSSGLRYCLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNTP 296

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +      I E ++  
Sbjct: 297 IGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPIIEFMNQR 356

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +++ +   +  N                +    +    +  +   RR   +  +  + R 
Sbjct: 357 NMELLEEYEPKNNPDATKVF---VNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISLIRD 413

Query: 553 RAGVEM-------RDVHPTHYGRICPAETSEGHNIGL---VSSLTSFARVNAYGFIETP- 601
               E        R + P       P     GH +     +  L +   ++  G  E   
Sbjct: 414 VRDREFKIFTDAGRVMRPLFVVDNEPTSERRGHLVLARSNIERLQTDREMDLTGLSEEQR 473

Query: 602 ---YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS--------FTEELVFCRCA 650
                          + YL A EEE   I  +   LDE               L   R  
Sbjct: 474 DSNIYGWKGLIGDGIIEYLDAEEEEAAMITMSPEDLDEHRQVRAGAPVYDDVGLDPHRRF 533

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +           +  P  ++ I AS+IPF +++ S R      M +QA+         
Sbjct: 534 KAKPNQSVRMWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG-------- 585

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                                            V  +       + + V  Y       +
Sbjct: 586 ---------------------------------VTLTNYNVRMDTMANVLYYPQKPLGTT 612

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                +  R                        +L  G+N +VA   + GYN EDS++++
Sbjct: 613 RSMEYLKFR------------------------ELPAGQNAIVAIACYGGYNQEDSVIMN 648

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVG 885
           +  +   +F S+    +    +   +   E        D   +       +D+ GII  G
Sbjct: 649 QSSIDRGLFRSLFYRAYMDQEKRVGMSVVEQFEKPTRADTLRMKHGTYDKLDDDGIISPG 708

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           + V+  DI++GK  P     M P+ + L           RD S  + S  SG +  V + 
Sbjct: 709 SRVSGEDIIIGKTAP-----MAPDAEELGQRTKLHVK--RDVSTPLRSTESGIIDQVLLT 761

Query: 946 NRHGIDK 952
                 K
Sbjct: 762 TNIDGHK 768


>gi|242392302|dbj|BAH80344.1| RNA polymerase subunit B' [Halococcus dombrowskii]
 gi|242392330|dbj|BAH80346.1| RNA polymerase subunit B' [Halococcus morrhuae DSM 1307]
          Length = 611

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 119/592 (20%), Positives = 201/592 (33%), Gaps = 97/592 (16%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++LV             + I  +++       I   E     R 
Sbjct: 97   LVERGYIEFIDAEEEEDILVGVDEEDLTEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 156

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 157  TMGAG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 213

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  L +  G     +    F R    +  R    + ++ E+   D   
Sbjct: 214  VAVMSYEGFNIEDA-LVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRFEIPDDD--- 269

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +S VL           +         + +R
Sbjct: 270  ----VRGAHGEEAYTHLDEDGLVNPETKVGESAVLLGKTSPPRFLEEPDDMGGLSPQKRR 325

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E+         + +               ++ KV V  +R  + GDK A R
Sbjct: 326  ETSVTMRSGESGIVDTVTLMQGE------------DGSKLSKVSVRDQRVPELGDKFASR 373

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG + E   G      G+++ 
Sbjct: 374  HGQKGVVGHIAPQEDMPFTEEGVVPDLIVNPHALPSRMTVGHVLEMLGGKVGSLEGRRVD 433

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                  +   ++                                             FD 
Sbjct: 434  GTAFTGEEEEELRSSLEEHG-------------------------------------FD- 455

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                             SG+ I++ G+TGE  D  + VG I+  KL HMVS+K++ARS G
Sbjct: 456  ----------------SSGKEIMHSGVTGEKIDAEIFVGTIFYQKLYHMVSNKIHARSRG 499

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------------- 1320
               ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD             
Sbjct: 500  PVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDREFIYVCGECGMS 559

Query: 1321 ---DVVGRTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               +V  R RVY     G   D  E     +F +L+ EM+ALG++  LE   
Sbjct: 560  AVENVEQR-RVY-CPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLELLD 609



 Score = 82.0 bits (201), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/343 (16%), Positives = 111/343 (32%), Gaps = 28/343 (8%)

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R  G+        +               +  P +  +D   ++    ++       + 
Sbjct: 35  ARRRGDVGRTVNVSVKDTTNEVIINADAGRARRPLIIVEDGEPLITESEVESLTEGDTEF 94

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E       +E + A+     +V      + + D   + I         +           
Sbjct: 95  EELVERGYIEFIDAEEEEDILVGVDEEDLTE-DHTHLEIDPQLIFGIGAGMIPYPEHNAS 153

Query: 767 FQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNML 812
            + +     + Q           RP  +          +    +T+     D    +N +
Sbjct: 154 PRITMGAGMIKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFV 213

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
           VA M + G+N ED+++++E  V   +  S     +E   R    G E+   +IP+     
Sbjct: 214 VAVMSYEGFNIEDALVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRF-EIPDDDVRG 272

Query: 868 -VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
              EE   ++DE G++    +V    +L+GK +P               + G      R+
Sbjct: 273 AHGEEAYTHLDEDGLVNPETKVGESAVLLGKTSPPRFLEEP------DDMGGLSPQKRRE 326

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           TS+ + SG SG V  V +       K  +    ++   EL  +
Sbjct: 327 TSVTMRSGESGIVDTVTLMQGEDGSKLSKVSVRDQRVPELGDK 369



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 66/195 (33%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     +++   RR   +G+      +       ++        P    
Sbjct: 13  YVNGSLVGTHADPEQLATQVRQARRRGDVGRTVNVSVKDTTNEVIINADAGRARRPLIIV 72

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L + + V +    +T + ++ +      + ++ A EEE+  +      L 
Sbjct: 73  EDGE-----PLITESEVESLTEGDTEFEELVERGY---IEFIDAEEEEDILVGVDEEDLT 124

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 125 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 161

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 162 MIKQSLGLPSANYRI 176


>gi|242392282|dbj|BAH80378.1| RNA polymerase subunit B' [Halorubrum trapanicum]
          Length = 609

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/603 (21%), Positives = 209/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRDGLEDHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 117/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEIEALERGDVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTDDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 42.4 bits (98), Expect = 0.66,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + +D                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTDDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|4867893|emb|CAB43087.1| RNA polymerase II [Sanango racemosum]
          Length = 259

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 77/255 (30%), Positives = 108/255 (42%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GD  + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 38   TNADGLRFVKVRVRSVRIPQIGDXFSSRHGQKGTVGMTYTQEDMPWTVEGISPDIIVNPX 97

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 98   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 125

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 126  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 163

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 164  TSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 223

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 224  GAAHFLKERLFDQSD 238


>gi|221125321|ref|XP_002155784.1| PREDICTED: similar to DNA-directed RNA polymerase II subunit RPB2
            [Hydra magnipapillata]
          Length = 484

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 75/254 (29%), Positives = 106/254 (41%), Gaps = 53/254 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 +  K+ V   R  Q GDK A RHG KG        EDMPF  +G   DI++NP  
Sbjct: 73   NEEGYKFCKIKVRSVRIPQIGDKFASRHGQKGTCGITYRQEDMPFTCEGISPDIIINPHA 132

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +G + E   G      G+                                    
Sbjct: 133  IPSRMTIGHLIECLQGKVSANKGEIGD--------------------------------- 159

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP  D  + + ++S+L+       G  +LY+G TG   +
Sbjct: 160  --------------------ATPFNDAVNVQLVSSLLQEYGYHLRGNEVLYNGFTGRKLN 199

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S  GG R GEME  C  A+G
Sbjct: 200  AQVFLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPMEGRSRDGGLRFGEMERDCQIAHG 259

Query: 1307 AAYVLQEMLTIKSD 1320
            AA  L E L   SD
Sbjct: 260  AAQFLNERLFEASD 273


>gi|89274922|gb|ABD65902.1| RNA polymerase II second largest subunit [Tremellodendron pallidum]
          Length = 716

 Score =  315 bits (807), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 136/861 (15%), Positives = 252/861 (29%), Gaps = 170/861 (19%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK--PVVSAVCEF 516
             G +R+   G +L   +RL   ++ +     +        +       K   + + +   
Sbjct: 1    FGKKRLDLAGPLLTGLFRLLFRKVSKDCYRYMQKCAETGRLFDVSRAIKVATISNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQQHAMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         EE
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVGEFLDEWGLESL--------EE 168

Query: 624  NRYIAQANSSLDEDGSF----------TEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            N   A   + +  +G +             L   R   +         D  +   +    
Sbjct: 169  NAQAATPCTKVFVNGVWMGVHRDPAALVRTLKKLRRNEDLNPEVSVVRDIREKELRIYTD 228

Query: 674  IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                  P    +D   ++   ++ + A     A +  +  G+  ++       ++     
Sbjct: 229  SGRVCRPLFVVNDGKLLIQKEHVLKIAEKQGYAWSDLIHDGVIELLDAEEEETVM----- 283

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                             +   +      QR  VK   +      
Sbjct: 284  ---------------ICMSPEDLEAARTQADTTYHTESAAPDPAQR--VKTVIKAHAWSH 326

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +  S+           
Sbjct: 327  CEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGISL----------- 368

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                  +    +  +             +       +   +  +
Sbjct: 369  ------------------SNFLLRMDTMANILYYPQKPLATTRALEYLKFRELPAGQNAI 410

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +        I+ +  +D  + +  V  E+ E  +R+   
Sbjct: 411  VAILCYSGYNQEDSVIMNQSSIDRGXF-RSIYYKSYMDVEKTTGQVILEEFEKPSRENTX 469

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                 + +       I  G N +       K+  L                   +E  QR
Sbjct: 470  RMKHGNYDKLDDDGIIAPGTNVIGEDILIGKTAPLPE---------------GSEELGQR 514

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                 +    T     E    + +        +     R VK+ V   R  Q GDK A R
Sbjct: 515  KSTHTRRDVSTPLKSTESGIVDHVIV-----SLNADGHRFVKIRVRSTRVPQIGDKFASR 569

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  DG   D+V+NP  +PSRM +G + E  L      LG+   
Sbjct: 570  HGQKGTIGVTYRQEDMPFTADGITPDLVINPHAIPSRMTIGHLVECLLSKVATLLGQDGD 629

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +                              ++     +VL+       G+ V       
Sbjct: 630  ATPFT-------------------------DLTVEGVSAVLKERGFQSRGLEVM------ 658

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                              G +    G         V +G  Y  +L HMV DK+++R+ G
Sbjct: 659  ----------------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVEDKIHSRARG 695

Query: 1274 SYSLVTQQPLGGKSNRGGQRL 1294
               ++T+QP+ G+S  GG R 
Sbjct: 696  PVQILTRQPVEGRSRDGGLRF 716


>gi|242392264|dbj|BAH80369.1| RNA polymerase subunit B' [Halorubrum distributum]
 gi|242392270|dbj|BAH80372.1| RNA polymerase subunit B' [Halorubrum litoreum]
 gi|242392278|dbj|BAH80376.1| RNA polymerase subunit B' [Halorubrum terrestre]
          Length = 609

 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/603 (21%), Positives = 209/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA            + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTEDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L     + SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGQLEEYGFESSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 117/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEIEALERGDVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTEDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 42.4 bits (98), Expect = 0.53,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + ED                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTEDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|52694193|emb|CAG30626.1| DNA-directed RNA polymerase beta chain [Pseudomonas libanensis]
          Length = 331

 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 193/330 (58%), Positives = 254/330 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAGKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D 
Sbjct: 121 EGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQ+TC+NQRPLV+ G 
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQHTCINQRPLVRKGY 300

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            V+R+DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 301 RVQRSDIMADGPSTDMGELALGQNMRIAFM 330


>gi|300719173|gb|ADK32529.1| RNA polymerase B [Bacillus amyloliquefaciens]
          Length = 173

 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 77/195 (39%), Positives = 123/195 (63%), Gaps = 22/195 (11%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
             E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y
Sbjct: 1   MSEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDY 50

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT
Sbjct: 51  SLGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMT 101

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
             GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+K
Sbjct: 102 DTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAK 158

Query: 200 DIIHVRIDRRRKVPV 214
           D+++VRIDR RK+PV
Sbjct: 159 DVVYVRIDRTRKLPV 173


>gi|242392276|dbj|BAH80375.1| RNA polymerase subunit B' [Halorubrum tebenquichense]
          Length = 609

 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/603 (21%), Positives = 209/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVSDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRDGLEDHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 56/371 (15%), Positives = 114/371 (30%), Gaps = 27/371 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA     V  
Sbjct: 64  RRPLIVVENGEPLLGDEEIEALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDV-S 122

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR---PLVKVGDEVRRNDII 794
            D   + I         +            + +     + Q    P             +
Sbjct: 123 DDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHL 182

Query: 795 ADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              P                     +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 LHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +E   R    G E+              E+   ++DE G++    +V+   +L+GK 
Sbjct: 243 FRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKT 302

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
           +P               + G      R+TS+ + SG SG V  V +       K  +   
Sbjct: 303 SPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKVKV 356

Query: 959 VEREQIELLAR 969
            ++   EL  +
Sbjct: 357 RDQRVPELGDK 367



 Score = 42.0 bits (97), Expect = 0.68,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + +D                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVSDDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|157367326|gb|ABV45531.1| RNA polymerase beta subunit [Pantoea agglomerans]
          Length = 321

 Score =  315 bits (806), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 192/319 (60%), Positives = 247/319 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 3   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 62

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 63  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 122

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 123 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 182

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 183 QQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 242

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ V
Sbjct: 243 AKRGGTVQYVDASRIVIKVNEDEMHAGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPV 302

Query: 789 RRNDIIADGPSTDLGDLAL 807
            R D++ADGPSTDLG+LAL
Sbjct: 303 ERGDVLADGPSTDLGELAL 321


>gi|273067686|gb|ACZ97541.1| DNA-directed RNA polymerase beta chain [Klebsiella oxytoca]
          Length = 328

 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 197/320 (61%), Positives = 249/320 (77%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 9   RAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 68

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 69  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 128

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D+
Sbjct: 129 KVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDY 188

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 189 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 248

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V 
Sbjct: 249 GVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVS 308

Query: 784 VGDEVRRNDIIADGPSTDLG 803
           +G+ + R D++ADGPSTDLG
Sbjct: 309 LGEPIERGDVLADGPSTDLG 328


>gi|159487647|ref|XP_001701834.1| DNA-directed RNA polymerase II, 135 kDa polypeptide [Chlamydomonas
            reinhardtii]
 gi|158281053|gb|EDP06809.1| DNA-directed RNA polymerase II, 135 kDa polypeptide [Chlamydomonas
            reinhardtii]
          Length = 1634

 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 148/959 (15%), Positives = 290/959 (30%), Gaps = 169/959 (17%)

Query: 358  IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            I            +D L  I   +        ++  S+       + +  L+ +G+    
Sbjct: 311  IFILFRALGFVSDRDILEHIVYDLDADPAMLEALRSSVEEAQEVQTQEEALNYLGKRGTV 370

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
               + +  +  +      +  ++  L+ +  G+   DD D+  N+R+   G ++   +RL
Sbjct: 371  TGASKEFMETRK---GYFVGYMVHRLMLVALGRRPEDDRDHYANKRLDLGGPLMAGLFRL 427

Query: 478  GLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ------------LS 523
               ++ + ++ +   +      +     IN K +   +     +              +S
Sbjct: 428  LFRKLCKELRMQAQRMVDAGKEINVISAINDKVITRGLKYSLATGNWGEQGKQGIRAGVS 487

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+   +   S ++H RR+++     + R     + R +H + +G  CPAET EG  +GLV
Sbjct: 488  QVLARLTYASTLSHLRRVNS----PIGREGKLAKPRQLHNSLWGIFCPAETPEGQAVGLV 543

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             ++     +            + +           A++E       A++ +  +G +   
Sbjct: 544  KNMALMCYITVGTPSLPVVAHLEEFNTE-------ALDEVTPADIAASTKVFINGVWLGI 596

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                    + +   R ++ F              L  F +   ++R L  C   R  V  
Sbjct: 597  QRDPTALIKNLRAMRRQVAFSTEVAIIYDGPLKELRIFTDYGRASRPLYICEDNRLLVS- 655

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                   +   +  +  +   A     + G+VE +DA            + +T       
Sbjct: 656  ----KHHIRRLISPLPDEDEYAWPQLVQDGLVEYIDAEE----------EETTMIAMTIA 701

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             ++  R                            P+  LG       +  + +P+  +N 
Sbjct: 702  DLRNAREAGAATGT------------TYTHCEIHPAMILG-------VCASIIPFPDHNQ 742

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                                   ++       +G                   D  G + 
Sbjct: 743  SPRN------------------TYQSAMGKQAMGMYATNYQTRM---------DTQGFVL 775

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                     +    +       +      + AI      +  D SL +            
Sbjct: 776  --YYPQKPLVCTRAMDYLKFRELPAGINAIVAIMCYSGYNQED-SLMLNGSSIDRGFHRS 832

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            IF R   ++ +++ S+ RE+IE        +      +          G           
Sbjct: 833  IFYRAYKEEEKKAGSMAREEIEAPDPSVTSKMKHGTYDKLDADGLCPPGTRVSGEDIICG 892

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L  D     P     +F  +D  +                 L       I+++   
Sbjct: 893  KTVTLPDD-----PTGAVQRFTKKDASL----------------ALRGHEAGVIDQVML- 930

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+ V      Q GDK A RHG KG        EDMPF  +G   DI++N
Sbjct: 931  -TTNDEGQKFVKIRVRTICIPQVGDKFASRHGQKGTCGITYTMEDMPFTAEGIVPDIIVN 989

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +G + E  +      +G +  +         ++S +   L           
Sbjct: 990  PHAIPSRMTIGHLVEALMSKVASLMGSEGDATPFTKVTVDNVSQMLHDL----------- 1038

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                             + G  V                        SG +       G 
Sbjct: 1039 --------------GYQRRGWEVM----------------------YSGHT-------GR 1055

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                 + +   Y  +L HMV  K+++R  G   ++T+QP  G++  GG R GEME  C+
Sbjct: 1056 QLRAQIFLNPTYYQRLKHMVDFKIHSRGRGPVQVLTRQPAEGRARDGGLRFGEMERDCL 1114



 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 117/839 (13%), Positives = 227/839 (27%), Gaps = 159/839 (18%)

Query: 141 DGTFVIKGIQRIVVSQLHRSPG--IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
            G FVI G ++++++Q  R     ++      + S   K  +   I       ++    S
Sbjct: 227 GGYFVINGSEKVLIAQE-RMANNHVY----VFKKSQPSKYTFCAEIR----SVVEGSTRS 277

Query: 199 -----------------KDIIHVRIDRRR-KVPVTSFLMALGMDSE-EILSTF-YPKIVY 238
                              +I  +I   R + P+     ALG  S+ +IL    Y     
Sbjct: 278 ASSMSIMMLAKGKKAGAAGVIRAQIPYIRAEFPIFILFRALGFVSDRDILEHIVYDLDAD 337

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
               +     +  A  +   + + + +    G     S + + +                
Sbjct: 338 PAMLEALRSSVEEAQEVQTQEEALNYLGKR-GTVTGASKEFMETR--------------- 381

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                 G  V   ++    G    +  D    K L+           +L+          
Sbjct: 382 -KGYFVGYMVHRLML-VALGRRPEDDRDHYANKRLDLGGPLMAGLFRLLFRKLCKE---- 435

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
               +  + +   DA  +I  +    D       +       +          G  ++  
Sbjct: 436 ----LRMQAQRMVDAGKEINVISAINDKVITRGLKYSLATGNWGEQGKQGIRAGVSQVLA 491

Query: 419 RLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           RL   +      R          +     L N    I         +      ++KN   
Sbjct: 492 RLTYASTLSHLRRVNSPIGREGKLAKPRQLHNSLWGIFCPAETPEGQAVG---LVKNMAL 548

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +  + +       ++ ++  +    D +    + ++   F     L    +    +  + 
Sbjct: 549 MCYITVGTPSLPVVAHLEEFNTEALDEVTPADIAASTKVFINGVWLGIQRDPTALIKNLR 608

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             RR  A            ++   +   +     P    E + + +              
Sbjct: 609 AMRRQVAFSTEVAIIYDGPLKELRIFTDYGRASRPLYICEDNRLLVSKHHIRRLISPLPD 668

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             E              V Y+ A EEE   IA   + L             R A E    
Sbjct: 669 EDEYA---WPQLVQDGLVEYIDAEEEETTMIAMTIADL-------------RNAREAGAA 712

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ + AS+IPF +++ S R      M +QA+               
Sbjct: 713 TGTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG-------------- 758

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                                      +  +       +   V  Y              
Sbjct: 759 ---------------------------MYATNYQTRMDTQGFVLYYP------------- 778

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PLV                     +L  G N +VA M + GYN EDS++++   +  
Sbjct: 779 -QKPLV----------CTRAMDYLKFRELPAGINAIVAIMCYSGYNQEDSLMLNGSSIDR 827

Query: 837 DVFTSIHIEEFEVMARDTKLG-PEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPG 891
               SI    ++   +       EEI    P+V           +D  G+   G  V+  
Sbjct: 828 GFHRSIFYRAYKEEEKKAGSMAREEIEAPDPSVTSKMKHGTYDKLDADGLCPPGTRVSGE 887

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           DI+ GK     + P    ++             +D SL +  G    V+D  +   +  
Sbjct: 888 DIICGKTVTLPDDPTGAVQRF----------TKKDASLALR-GHEAGVIDQVMLTTNDE 935



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 19/136 (13%), Positives = 41/136 (30%), Gaps = 34/136 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+ +           +Q        I              A     +++
Sbjct: 38  LVRQQLDSFNEFVNVT----------IQEIIDETPEIVIKPESQHLPGVEAAEEKEYIIK 87

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P+              +   R+LTY  PL + +    +        +   + 
Sbjct: 88  FGQVYLSRPQITEQDGESVVLFPKEARLRNLTYCAPLYVDVTKTEYTRVGENEVEEKTET 147

Query: 126 KEQSIYMGDLPLMTKD 141
               +++G +P+M K 
Sbjct: 148 FSH-VHLGKVPIMLKS 162



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 22/87 (25%)

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVVGRT---------------RVYESIVAGNDTFET 1341
            CI ++GAA  L+E L  +SD     V  R+                +Y+    G++ ++ 
Sbjct: 1544 CIISHGAAAFLKERLFDQSDAYRIHVCERSGLIAVANLKKQQFTSTIYK---DGSNIYQV 1600

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  ++  R 
Sbjct: 1601 YIPYACKLLFQELMAMCIAPRMQFERD 1627


>gi|257386582|ref|YP_003176355.1| DNA-directed RNA polymerase subunit B' [Halomicrobium mukohataei DSM
            12286]
 gi|242392248|dbj|BAH80361.1| RNA polymerase subunit B' [Halomicrobium mukohataei DSM 12286]
 gi|257168889|gb|ACV46648.1| RNA polymerase Rpb2 domain 6 [Halomicrobium mukohataei DSM 12286]
          Length = 608

 Score =  315 bits (806), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 117/589 (19%), Positives = 203/589 (34%), Gaps = 105/589 (17%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LVA       +    + +  +++       I   E     R T      
Sbjct: 101  EFIDAEEEEDILVAVSEEDVTDDHTHLEVDPQLMFGIGAGMIPYPEHNASPRITMGSG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +    A+   +
Sbjct: 159  MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGYDDRPAAQNFTVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  L +  G     +    F R    +  R    + ++ E+   +       +  
Sbjct: 218  GFNIEDA-LVMNEGSVERALARSHFFRTYEGEERRYPGGQEDRFEIPDDE-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+     K++ VL           +         + +R       
Sbjct: 270  ARGEEAYTHLDEDGLVNPETNVKENEVLLGKTSPPRFLEEPDDMGGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 330  SGESGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASRHGQKGVV 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF + G   D++LNP  +PSRM VG + E   G      G+++       +
Sbjct: 378  GHLAPQEDMPFTEAGVVPDLILNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFTGE 437

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++                                               GA E+   
Sbjct: 438  DEAELR----------------------------------------------GALED--- 448

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 449  -----RGFKSSGKEVMYSGVTGEKVEAEIFVGTIFYQKLYHMVSNKLHARSRGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------------DVVG 1324
            QP  G++  GG R+G ME   +  +GAA VL+E L  +SD                +V  
Sbjct: 504  QPTEGRAREGGLRVGHMERDVLIGHGAAMVLKERLLDESDREWIKICGECGMTAVENVEQ 563

Query: 1325 RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            R R+Y      E      D  E   P +F +L+ EM+ALG++  +E   
Sbjct: 564  R-RIYCPNCEEE-----TDIHEVEMPYAFKLLLDEMKALGIAPRIELED 606



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 76/460 (16%), Positives = 136/460 (29%), Gaps = 109/460 (23%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR   + +      +   +   V+        P    
Sbjct: 10  YVNGSLVGTHPDPEQLADQIRQARRRGDVSEMVNVSVKDRTDEVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +  S     +    GF E   R V        V ++ A EEE+  +A +   + 
Sbjct: 70  EDGEPLITESEVQQVKDGELGFEELVERGV--------VEFIDAEEEEDILVAVSEEDVT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DDH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMG-- 156

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
                                      SG    +                          
Sbjct: 157 ---------------------------SGMIKQSLGLPSANY------------------ 171

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    ++           Q  +VK                    D    +N  VA 
Sbjct: 172 --------RIRPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFTVAV 213

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VS 869
           M + G+N ED+++++E  V   +  S     +E   R    G E+   +IP+        
Sbjct: 214 MSYEGFNIEDALVMNEGSVERALARSHFFRTYEGEERRYPGGQEDRF-EIPDDEVRGARG 272

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE   ++DE G++     V   ++L+GK +P               + G      R+TS+
Sbjct: 273 EEAYTHLDEDGLVNPETNVKENEVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSV 326

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + SG SG V  V +       K  +    +    EL  +
Sbjct: 327 TMRSGESGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 366


>gi|83415467|gb|ABC17941.1| RNA polymerase II second largest subunit [Endogone pisiformis]
          Length = 720

 Score =  314 bits (805), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 135/850 (15%), Positives = 244/850 (28%), Gaps = 148/850 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R+   ++ + + +  +              + +  + + +     +
Sbjct: 2    KRMDLAGPLLASLFRMLFKKLTKDVSKYLQKCIESSREFNLTLAVKSNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQSKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++  G    P  +        ++  LSA    +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSYIS-VGSAAAPIIEFLGEWTMENLEELSASNIPDAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N           ELV             E    +D SP+  V             D
Sbjct: 177  KIFVNGVWVGIHRDPAELVRTLK---------ELRRCVDISPEVSVVRDIREKELRLYTD 227

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + R      +  +   L+K +               S         G+VE +DA      
Sbjct: 228  AGRCCRPLFIVEKQKLLIKKD-HITKLAESREDDTQSYGWQDLVSGGLVEYIDAEEEETA 286

Query: 747  SVEGDLDP--STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             +    +    +  +        +R   +   +Q                   PS  LG 
Sbjct: 287  MICMTPEDLSESREMAETGFAPKERDVASRVKSQNSG-----YAHTWTHCEIHPSMILG- 340

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                   I++  ++V               
Sbjct: 341  ------ICASIIPFPDHNQSPRNTYQSAXXX--XXXXIYLTNYQVRM------------- 379

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                            +  +        +    +       +   +  + AI      + 
Sbjct: 380  --------------DTLANILYYPQKPLVTTRSMEYLRFRELPAGQNAIVAILCYSGYNQ 425

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    +F R  +D  ++   +  E+ E   RD              
Sbjct: 426  EDSVIMNQSSIDRGLF-RSLFFRSYMDAEKKVGMMVMEEFEKPTRDTTLRLKHGTYEKLE 484

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  +  D      R+           ++     +  Q   
Sbjct: 485  EDGLIAPGTRVSGEDIIIGKTAPIPPDSEELGQRTGTHSKRDASTPLRSTETGIVDQ--- 541

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      L+ VKV V   R  Q GDK A RHG KG +    
Sbjct: 542  -----------------VMVTTNQEGLKFVKVRVRSTRVPQMGDKFASRHGQKGTIGITY 584

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +G + E  LG      G +  +          
Sbjct: 585  RQEDMPFSAEGVTPDLIINPHAIPSRMTIGHLVECLLGKVSTLTGNEGDATPFTDVTVEA 644

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            IS                                                          
Sbjct: 645  ISQALKAQNYQQRGFEVM------------------------------------------ 662

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                  +G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ 
Sbjct: 663  -----YNGHT----GR---KLAAQVYLGPTYYQRLKHMVDDKIHSRARGPLQILTRQPVE 710

Query: 1285 GKSNRGGQRL 1294
            G+S  GG R 
Sbjct: 711  GRSRDGGLRF 720



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 56/418 (13%), Positives = 109/418 (26%), Gaps = 30/418 (7%)

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           P+L          +   +     K  + +      +    +  T  +  S+    + D  
Sbjct: 9   PLLASLFRMLFKKLTKDVSKYLQKCIESSREFNLTLAVKSNTITNGLKYSLATGNWGDQK 68

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           K   S  G  ++  R    +      R          I     L N    +         
Sbjct: 69  KAMQSKAGVSQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEG 128

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +   + + L     + +      I E +    ++++      N   +  A   F     +
Sbjct: 129 QACGLVKNLALMSYISVGSAAAPIIEFLGEWTMENLEELSASN---IPDATKIFVNGVWV 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +    +  +   RR   +            +   ++        P    E   + +
Sbjct: 186 GIHRDPAELVRTLKELRRCVDISPEVSVVRDIREKELRLYTDAGRCCRPLFIVEKQKLLI 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED----- 637
                +    +     ++      D      V Y+ A EEE   I      L E      
Sbjct: 246 KKDHITKLAESREDDTQS--YGWQDLVSGGLVEYIDAEEEETAMICMTPEDLSESREMAE 303

Query: 638 -GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC-- 694
            G   +E         +           +  P  ++ I AS+IPF +++ S R       
Sbjct: 304 TGFAPKERDVASRVKSQNSGYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAX 363

Query: 695 --------------NMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
                          M   A  L   + P V T  ME +  +   A   A  A +   
Sbjct: 364 XXXXXXIYLTNYQVRMDTLANILYYPQKPLVTTRSMEYLRFRELPAGQNAIVAILCYS 421


>gi|157367328|gb|ABV45532.1| RNA polymerase beta subunit [Pantoea agglomerans]
          Length = 319

 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 192/318 (60%), Positives = 246/318 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ V
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMHAGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPV 301

Query: 789 RRNDIIADGPSTDLGDLA 806
            R D++ADGPSTDLG+LA
Sbjct: 302 ERGDVLADGPSTDLGELA 319


>gi|163930843|dbj|BAF96016.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 322

 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 196/322 (60%), Positives = 251/322 (77%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   VGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YG
Sbjct: 61  HKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           F+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L 
Sbjct: 121 FLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLF 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME
Sbjct: 181 SRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+
Sbjct: 241 RAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCI 300

Query: 777 NQRPLVKVGDEVRRNDIIADGP 798
           NQ P V +G+ + R D++ADGP
Sbjct: 301 NQMPCVSLGEPIERGDVLADGP 322


>gi|327401233|ref|YP_004342072.1| DNA-directed RNA polymerase subunit B [Archaeoglobus veneficus SNP6]
 gi|327316741|gb|AEA47357.1| DNA-directed RNA polymerase subunit B [Archaeoglobus veneficus SNP6]
          Length = 604

 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 108/588 (18%), Positives = 197/588 (33%), Gaps = 100/588 (17%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA            + +   ++      SI   E     R+T     
Sbjct: 97   IEFLDAEEEENAYVAVSEEELTPEHTHLELCPSLIVGICTGSIPYPEHNASPRNTMGAA- 155

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE---SPMTPEEKLLRAI 916
             + +    +    L    +      G  ++   I +     + E         +  + A+
Sbjct: 156  -MIKQSLGLPYANLAWRTDTR----GHLLHYPQIPIVTTDTQLEIKFDERPAGQNFVVAV 210

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
               +  ++ D  +    G     +    F R    +  R    + ++ E+   D      
Sbjct: 211  ISYEGYNIEDALIFNK-GSIDRGLGRSHFFRTYETEEMRYPGGQEDRFEIPGAD------ 263

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                         + G           +  ++  +     P             ++   E
Sbjct: 264  -------------ISGFRGAEAYAHLDEDGLVFPET-EVGPDDVLIGKTSPPRFLEEPTE 309

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                  +  ++ +  R   K               ++ KV V   R  + GDK A RHG 
Sbjct: 310  LGISPQKRRETSITMRSNEKGIVDAVFLMQSESGSKLAKVRVRDLRIPELGDKFASRHGQ 369

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++  I+P EDMPF + G   D+++NP  +PSRM VG + E   G      G++I + +
Sbjct: 370  KGVIGLIVPEEDMPFTESGIVPDMIVNPHAIPSRMTVGHVLEMIGGKVGSLEGRRIDATV 429

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
               +   D+  +     K  G     +++                               
Sbjct: 430  FYGEKEKDLREIL----KAYGFSHTGKEVM------------------------------ 455

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                           G       +TG+ F   + VG IY  KL HMVS K++ARS G   
Sbjct: 456  -------------YDG-------ITGKRFTVDIFVGVIYYQKLYHMVSSKIHARSRGPVQ 495

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVY 1329
            ++T+QP  G++ +GG R GEME   +  +GAA +L++ L  +SD V        G    Y
Sbjct: 496  VLTRQPTEGRARKGGLRFGEMERDVLIGHGAALLLKDRLLEESDKVEVYVCGNCGHVATY 555

Query: 1330 E---SIVAGN------DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            +   +I          +        +F +L+ E++++ ++  L     
Sbjct: 556  DYRRNIAYCKICDDDSNIHRVEMSYAFKLLLDELKSMMIAPRLILGDK 603



 Score = 96.3 bits (238), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 65/354 (18%), Positives = 111/354 (31%), Gaps = 102/354 (28%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + +L A EEEN Y+A +   L  +                          +
Sbjct: 88  FDDLVKQGLIEFLDAEEEENAYVAVSEEELTPEH-----------------------THL 124

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  +V I    IP+ E++ S R  MG  M +Q++ L  A   +              
Sbjct: 125 ELCPSLIVGICTGSIPYPEHNASPRNTMGAAMIKQSLGLPYANLAW-------------- 170

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         +   +  Y               Q P+V  
Sbjct: 171 ---------------------------RTDTRGHLLHYP--------------QIPIVTT 189

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
             ++               +   G+N +VA + + GYN ED+++ ++  +   +  S   
Sbjct: 190 DTQLE----------IKFDERPAGQNFVVAVISYEGYNIEDALIFNKGSIDRGLGRSHFF 239

Query: 845 EEFEVMARDTKLGPEEITRDIP------NVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             +E        G E+   +IP          E   ++DE G++    EV P D+L+GK 
Sbjct: 240 RTYETEEMRYPGGQEDRF-EIPGADISGFRGAEAYAHLDEDGLVFPETEVGPDDVLIGKT 298

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +P        E        G      R+TS+ + S   G V  V +       K
Sbjct: 299 SPPRFLEEPTE-------LGISPQKRRETSITMRSNEKGIVDAVFLMQSESGSK 345


>gi|269912588|emb|CAY86074.1| RNA polymerase beta subunit [Gluconacetobacter liquefaciens]
 gi|269912592|emb|CAY86076.1| RNA polymerase beta subunit [Gluconacetobacter liquefaciens]
          Length = 311

 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 153/314 (48%), Positives = 202/314 (64%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD++EIL  FY K+V+++   
Sbjct: 61  KRKLPVTTLLYALEGEASAAARAAKTAEGGDVDAMEIRGMDADEILGYFYNKVVFTKGPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P  A     G K+   LVD  +GE V E+  KLT+ +++ + E   K + + +  L
Sbjct: 121 GWARPFDAE-SFRGMKLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLVGAAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G YVA D+VN ETGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL 
Sbjct: 179 VGRYVAHDLVNPETGEIYAEAGEELTEARLEALEEAGVDCLPTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD
Sbjct: 238 VDKNGSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLD 297

Query: 424 TPDDVRHIRKEDII 437
            PD +R +RKEDI+
Sbjct: 298 APDTMRVLRKEDIL 311


>gi|111054593|gb|ABH04354.1| RNA polymerase beta subunit [Morganella morganii]
          Length = 319

 Score =  314 bits (805), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 192/319 (60%), Positives = 243/319 (76%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           D++MP+D+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   DNLMPEDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V D  VT+++ 
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDDVVTDEIH 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLSA+EE N  IAQAN+ LB+DG F +EL+ CR  GE  L  R+++ ++D S +QVVS+ 
Sbjct: 121 YLSAIEEGNFIIAQANTVLBDDGHFVDELITCRNKGESSLFSRDQVQYMDVSTQQVVSVG 180

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V
Sbjct: 181 ASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTV 240

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++A
Sbjct: 241 QYVDASRIVIKVNEDEMYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGEPVERGDVLA 300

Query: 796 DGPSTDLGDLALGRNMLVA 814
           D PSTDLG+LALG+NM VA
Sbjct: 301 DVPSTDLGELALGQNMRVA 319


>gi|242092386|ref|XP_002436683.1| hypothetical protein SORBIDRAFT_10g006995 [Sorghum bicolor]
 gi|241914906|gb|EER88050.1| hypothetical protein SORBIDRAFT_10g006995 [Sorghum bicolor]
          Length = 1137

 Score =  314 bits (804), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 120/609 (19%), Positives = 208/609 (34%), Gaps = 95/609 (15%)

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED-----SMLISERMVS 835
            + K+ D     D    G   +  D+    N L+A       +  +      + I    + 
Sbjct: 601  MTKLRDGTYDFDDFLSGGLIEYLDVNEENNALIALYEHMDQDDVERSSITHIEIEPLSIL 660

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI-DECGIICVGAEVNPGDIL 894
              V   I         R+T     +       +       +     ++ +        + 
Sbjct: 661  GVVSGLIPYPHHNQSPRNT----YQCAMGKQAMGNIAYNQLFRADSLLYLLVYAQRPLLT 716

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               I   G   +   +    A+ G    D+ D  +   S +           ++ + K+ 
Sbjct: 717  TKTIELVGYDKLGAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDN 776

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                V  ++I    RDKD   +  +         +  GQ   +      K T +++    
Sbjct: 777  YVDGV-SDRIVKPQRDKDGVLMKQNMRALDDDGIVAPGQIIRNHDIYVNKQTPMNTSKGI 835

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
              P +                      Y+ S +I +          +            +
Sbjct: 836  GRPLTD-------------------SCYKDSPAIYKGVDGETTVVDRVMLCSDTNDKLSI 876

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            K  +   R  + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSRM +G
Sbjct: 877  KCIIRHTRRPEVGDKFSSRHGQKGVCGTIIQQEDFPFSERGICPDLIMNPHGFPSRMTIG 936

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            ++ E   G A V  G+                                            
Sbjct: 937  KMIELLGGKAGVSCGRFH------------------------------------------ 954

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                    G     P  +  +   I+S L       +G+  LY G+ G+P +  + +G I
Sbjct: 955  -------YGSAFGEPSGNADNVADISSTLIKHGFSYNGKDFLYSGILGQPLEAYIFMGPI 1007

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  KL HMV DK++AR++G   L+T+QP  G+S  GG RLGEME  C+ AYGA+ ++ E 
Sbjct: 1008 YYQKLKHMVLDKMHARASGPRVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFER 1067

Query: 1315 LTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNVLVKEMQALG 1358
            L + SD          G    Y   +          G +  +   P +  +L +E+ A+ 
Sbjct: 1068 LMLSSDPYQVQVCRKCGLLGYYNHKLKTSYCSMCKNGENMAKMRLPYACKLLFQELHAMN 1127

Query: 1359 LSIDLENSR 1367
            +   L+ + 
Sbjct: 1128 VVPRLKLTE 1136



 Score =  151 bits (381), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 95/717 (13%), Positives = 225/717 (31%), Gaps = 97/717 (13%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLEFVSYEFDPPKF- 86
           L++    S+++F+          ++G++   ++   I A +  +  L ++      P   
Sbjct: 32  LVKEHIDSFNYFI----------DKGIKKIVEANNRIEARNDPSIYLRYLDVRVGMPSIY 81

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C   D TY+ P+++ ++  V    +    +  K I      +G +P+M
Sbjct: 82  ENCNVESITPHLCRLTDRTYSAPIEVDIQYTVGK--QHVVKRRNKFI------IGYMPIM 133

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+KG +++++ Q   S          +  +
Sbjct: 134 LRSSACILNEMDEDELAKYGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIVDTDSKGRV 193

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFY 233
              +  +   I  + + +      K  I++++++  + +P+   + A+GM+S++      
Sbjct: 194 IASVTSSTHAIKSKTVVL----MDKGKIYLQLNQFTKPIPIIVVMKAMGMESDQEAVQMV 249

Query: 234 PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID---TGEQVIESGKKLTSGLLKSLKE 290
            +        F      A++ +   + +   +D      G    + G+  +      +  
Sbjct: 250 GRDPRYGDLLFPSIQECASERIYTRQQALQYMDEKVMYPGATNNKEGRSNSILHDVFIAH 309

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             VK   +   C+    +   +++        +  D +  K  E            L+  
Sbjct: 310 VPVKDGNLRPKCIYTAVMLRRMLDAILNSDTFDDKDYVGNKRFELSGQLISLLFEDLFKT 369

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
             +      N           D    I +     D  TF +  +  +   +D  ++ +  
Sbjct: 370 MNSQAVERMNKNSDKTRSSPLDFSQLIMQ-----DTITFGLERA-ISTGNWDIKRFRMHR 423

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLGNRRVRSVG 468
            G  ++  RL+                   K      L+  +  +    +        + 
Sbjct: 424 KGVSQVLSRLSYMATLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLT 483

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           + L     +   + E  + +   S+ ++ ++           S +        L + ++ 
Sbjct: 484 KNLALLSHITTDQEEGPLIDLCHSLGVEDLLFLSSEEIHAPGSFLV-MLNGLILGKHKDP 542

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHNIGLVSSLT 587
              +  + + RR + +G+          + R VH  +  GR+C         I  +    
Sbjct: 543 QRLVIHLRNLRRSNVIGE--FVSIFINEKQRCVHIASDGGRVCRPLIIADMGISRIDE-- 598

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                     +        D      + YL   EE N  IA                   
Sbjct: 599 -----THMTKLRDGTYDFDDFLSGGLIEYLDVNEENNALIA------------------L 635

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
               ++  V R  I  I+  P  ++ + + LIP+  ++ S R    C M +QA+  +
Sbjct: 636 YEHMDQDDVERSSITHIEIEPLSILGVVSGLIPYPHHNQSPRNTYQCAMGKQAMGNI 692



 Score =  129 bits (325), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 104/651 (15%), Positives = 214/651 (32%), Gaps = 60/651 (9%)

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           IV+ ++    I +          +      +    L ++       I   +     +  +
Sbjct: 184 IVDTDSKGRVIASVTSSTHAIKSKTVVLMDKGKIYLQLNQFTKPIPIIVVMKAMGMESDQ 243

Query: 372 DALLDIYRVMRPGDV--STFSVAESMFNFLFFDSDKYDLSTV------------GRVKMN 417
           +A+  + R  R GD+   +     S   +    + +Y    V                ++
Sbjct: 244 EAVQMVGRDPRYGDLLFPSIQECASERIYTRQQALQYMDEKVMYPGATNNKEGRSNSILH 303

Query: 418 MRLNLDTPDDVRHIRK--EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                  P    ++R        +++ ++D      T DD D +GN+R    G+++   +
Sbjct: 304 DVFIAHVPVKDGNLRPKCIYTAVMLRRMLDAILNSDTFDDKDYVGNKRFELSGQLISLLF 363

Query: 476 RLGLLRMERSIKERISSVDIDS----VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
                 M     ER++     +    +    LI    +   +     +         ++ 
Sbjct: 364 EDLFKTMNSQAVERMNKNSDKTRSSPLDFSQLIMQDTITFGLERAISTGNWDIKRFRMHR 423

Query: 532 LSRITHTRRLSALGQGG--------VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
                   RLS +   G          + R     R + P+ +G +CP +T EG   GL 
Sbjct: 424 KGVSQVLSRLSYMATLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTPEGEACGLT 483

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE--NRYIAQANSSLDEDGSFT 641
            +L   + +      E P   +C      D+++LS+ E      ++   N  +       
Sbjct: 484 KNLALLSHITTD-QEEGPLIDLCHSLGVEDLLFLSSEEIHAPGSFLVMLNGLILGKHKDP 542

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQ 697
           + LV          V  E +       ++ V IA+       P +  D     +   +M 
Sbjct: 543 QRLVIHLRNLRRSNVIGEFVSIFINEKQRCVHIASDGGRVCRPLIIADMGISRIDETHMT 602

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-------- 749
           +        +    G  +E +       A++A     ++Q D  R  I  +E        
Sbjct: 603 KLRDGTYDFDDFLSGGLIEYLDVNEENNALIAL-YEHMDQDDVERSSITHIEIEPLSILG 661

Query: 750 ------GDLDPSTSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDEVRRNDIIADGPSTD 801
                      + S  + Y+    +++  N   NQ  R    +   V     +    + +
Sbjct: 662 VVSGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLFRADSLLYLLVYAQRPLLTTKTIE 721

Query: 802 ---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                 L  G+N  VA M + GY+ ED++++++  +       I ++++ V+  +   G 
Sbjct: 722 LVGYDKLGAGQNATVAVMGYSGYDIEDAIVMNKSSLDRGFGRCIALKKYTVLKDNYVDGV 781

Query: 859 EEITRDIPNVSEEGLKN-----IDECGIICVGAEVNPGDILVGKITPKGES 904
            +         +  L       +D+ GI+  G  +   DI V K TP   S
Sbjct: 782 SDRIVKPQRDKDGVLMKQNMRALDDDGIVAPGQIIRNHDIYVNKQTPMNTS 832


>gi|269912590|emb|CAY86075.1| RNA polymerase beta subunit [Gluconacetobacter liquefaciens]
          Length = 310

 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 152/312 (48%), Positives = 200/312 (64%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD++EIL  FY K+V+++   
Sbjct: 61  KRKLPVTTLLYALEGEASAAARAAKTAEGGDVDAMEIRGMDADEILGYFYNKVVFTKGPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P  A     G K+   LVD  +GE V E+  KLT+ +++ + E   K + + +  L
Sbjct: 121 GWARPFDAE-SFRGMKLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLVGAAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G YVA D+VN ETGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL 
Sbjct: 179 VGRYVAHDLVNPETGEIYAEAGEELTEARLEALEEAGVDCLPTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD
Sbjct: 238 VDKNGSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLD 297

Query: 424 TPDDVRHIRKED 435
            PD +R +RKED
Sbjct: 298 APDTMRVLRKED 309


>gi|111378459|gb|ABH09241.1| RpoB [Cronobacter sakazakii]
          Length = 321

 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 196/320 (61%), Positives = 247/320 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR GIV+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V + + V
Sbjct: 242 AKRGGIVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLNEPV 301

Query: 789 RRNDIIADGPSTDLGDLALG 808
            R D++ADGPSTDLG+LALG
Sbjct: 302 ERGDVLADGPSTDLGELALG 321


>gi|157367330|gb|ABV45533.1| RNA polymerase beta subunit [Pantoea ananatis]
          Length = 320

 Score =  314 bits (804), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 193/316 (61%), Positives = 247/316 (78%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG V+++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDGVVSDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDV 304

Query: 794 IADGPSTDLGDLALGR 809
           +ADGPSTDLG+LALG+
Sbjct: 305 LADGPSTDLGELALGQ 320


>gi|55583692|gb|AAV53365.1| RNA polymerase II second largest subunit [Hygrophoropsis aurantiaca]
          Length = 863

 Score =  314 bits (804), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 137/907 (15%), Positives = 271/907 (29%), Gaps = 148/907 (16%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 89   RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 145

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ R +    +              +  + + + +    
Sbjct: 146  GKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL 205

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 206  ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 261

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 262  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 313

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 314  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 370

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      +L+ +   ++  G      +      + K   I         
Sbjct: 371  TDAGRVCRPLFIVENQQLMLQKKHVKWLNQGYREEDGEEYKWEQLIKGGIIELLDAEEEE 430

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +       D   S +   +       + +   +    +K G            PS  LG
Sbjct: 431  TVMISMTPEDLENSRL---QSAGIDPQSNDVDYDPAARLKAGINAHTWTHCEIHPSMILG 487

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 488  -------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 522

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 523  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 571

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 572  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKI 630

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 631  EDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 690

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q+GDK A RHG KG +   
Sbjct: 691  I--------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGIT 730

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 731  YRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 785

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 786  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 809

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                    G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+
Sbjct: 810  ------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 856

Query: 1284 GGKSNRG 1290
             G+S  G
Sbjct: 857  EGRSRDG 863



 Score =  139 bits (350), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 94/759 (12%), Positives = 214/759 (28%), Gaps = 108/759 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R+D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 19  YIRVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 74

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   +++     + L+++ +  + +            G  +   ++  
Sbjct: 75  LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 133

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 134 LERRELDDRDHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAV- 192

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 193 -------KHQTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 245

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       I  +
Sbjct: 246 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSCISVGSYSAPVIEFL 302

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +      NA         F     +    +  N +  I   RR   +         
Sbjct: 303 EEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 361

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L      +     Y   +    K         
Sbjct: 362 IRERELRLYTDAGRVCRPLFIVENQQLMLQKKHVKWLN-QGYREEDGEEYKWEQLIKGGI 420

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDA 666
           +  L A EEE   I+     L+     +  +       +          +        + 
Sbjct: 421 IELLDAEEEETVMISMTPEDLENSRLQSAGIDPQSNDVDYDPAARLKAGINAHTWTHCEI 480

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 481 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 524

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 525 -------------------------RMDTMANILYYPQKPLATTRSMEYLKFR------- 552

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F SI+   
Sbjct: 553 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRS 595

Query: 847 FEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E            +       I++ G+I  G  V+  DI++GK  P 
Sbjct: 596 YMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI 655

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   E+L +        DV        +G+   V+
Sbjct: 656 ----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 690


>gi|123481595|ref|XP_001323594.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
 gi|121906462|gb|EAY11371.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
          Length = 1177

 Score =  314 bits (804), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 81/312 (25%), Positives = 129/312 (41%), Gaps = 74/312 (23%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L++ +V     R  + GDK   RHG KG+       EDMPF +DG   DI++NP  +PSR
Sbjct: 916  LQLARVRTRQMRRPEIGDKFCSRHGQKGVCGMTYRQEDMPFTRDGMVPDIIMNPHALPSR 975

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G + E  LG       +                                        
Sbjct: 976  MTIGHLIECLLGKCTAIDPQNADEGD---------------------------------- 1001

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                            +TP F G   +AI   L+ A  ++ G   LY+G +G+     + 
Sbjct: 1002 ----------------ATP-FCGVTVDAIAKRLQDAGFEKYGNETLYNGRSGKRLKAKIY 1044

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
             G  Y  +L HMV DK +AR+ G  SL+ +QP+ G++  GG R GEME  C+ A+G + +
Sbjct: 1045 FGPTYYQRLKHMVGDKAHARALGRKSLILRQPVDGRARNGGLRFGEMERDCLIAHGVSAM 1104

Query: 1311 LQEMLTIKSDDVVGRTRV-------YESIVAGNDTFET------------GTPESFNVLV 1351
            +++ L   SD    R  V         +I   + T E               P +F +++
Sbjct: 1105 MRDRLLENSD----RYFVPVCKTCGLIAIEKTDGTMECPACQDEGRLAKVEMPYAFKLVI 1160

Query: 1352 KEMQALGLSIDL 1363
            +E+ ++ ++  L
Sbjct: 1161 QELMSMCIAPRL 1172



 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 108/760 (14%), Positives = 223/760 (29%), Gaps = 124/760 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG-------------LQAAFKSVFPITAFSGAAMLE 75
           L++ Q  SY+ F+   +      ++G             ++  F S            + 
Sbjct: 34  LVKQQLKSYNSFINNCVDSVL-DDKGHITLQSDQLLANKIKMDFNSNDDDEDQGKTIHIS 92

Query: 76  FVSYEFDPPK------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           F +     P               R L+Y++ L+  +R++V D       K++K +    
Sbjct: 93  FGTSTVLRPTTPEGKQLTPMISRLRSLSYSLILRSDIRVVVMD-----SNKNMKQLDVDG 147

Query: 130 IYMGDLPLM--------------------------TKDGTFVIKGIQRIVVSQLHR---S 160
           + +  +P+M                             G F++ G +++++ Q H     
Sbjct: 148 VEIAKVPVMIRSEYCHLSNHRDDRAINDNLNECDYDPGGYFIVNGSEKVIIGQEHMVINK 207

Query: 161 PGIHFDHDKGRASLSGKLLYACRII------------------PDQGLWMDIEFDSKDII 202
           P  +      +  L+ ++    ++                   P++             I
Sbjct: 208 PICYAQKSMVKYDLATEIRSQPKVFGRLSQPFNLFLLAPTAKQPERP------------I 255

Query: 203 HVRIDRRRK-VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           H ++ +  K +P+     AL     +EIL         S+  D     +  +   +  + 
Sbjct: 256 HAKLSKTEKTIPLFILFRALKFKGDKEILDLICYDPEDSEFIDVLRPSIEESSSFLDDRA 315

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL-----YVAEDIVNG 315
               V         E  ++L     + L E  +  LG              Y+A +++N 
Sbjct: 316 CLDFVGKRCSIAAEEKSQRLRKAQ-RLLNEYLLPHLGEKESDTTSKAFFIGYMAHNLINV 374

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK---D 372
             G    +  D    K L+       +   +L+   + +        + D N D+     
Sbjct: 375 VLGRRDQDDRDHYSNKRLDLAGPLIGQLFALLFEKMIKSLTQHLEKRLKDGNIDQMAKSA 434

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           A L    V+    +++                    + V ++   +       +  R   
Sbjct: 435 ADLTRQGVLNFKSITSGLEYSIGTGNWSVQRQAGSKAGVSQMLNRLTFLSTLSNLRRTNT 494

Query: 433 KEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                  +     L N   G I  ++    +    +  +           +E        
Sbjct: 495 PIGRDGKLTGPRHLHNTHWGYICPVETPEGQSCGLIKNLALMSIVTVNRELEAGDAITRI 554

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             D  ++ P   I    +  +   F   +      +  + +  +   RR S      V+ 
Sbjct: 555 LEDTGTI-PIQQITPDQIKDSTKIFLNGAWYGIHTDAYDLMETLLSERR-SLKIPSDVSF 612

Query: 552 ARAGVEMRDVHPTHYGRI-CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
                +      T  GRI  P       ++ L  S+      N          KV   K 
Sbjct: 613 VHHIRDQEIFIWTDGGRITRPVLIVNDMHLTLKKSVLYDENTNW---------KVLRYKG 663

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              V YL   EEE + IA + + L+E+                     +     +  P  
Sbjct: 664 M--VEYLDIDEEETKLIALSPADLEEN--------------RNSPTGVKTYTHCEIHPSL 707

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +  +  ++IPF +++ S R    C M +QA+ L       
Sbjct: 708 IFGVCGTIIPFPDHNQSPRNTYQCAMGKQAIGLYTTNYMI 747



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 111/673 (16%), Positives = 223/673 (33%), Gaps = 107/673 (15%)

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD--IPILYVDSVNNNAYI 358
           +      +++         ++       D++ L+ I +       I +L      +++++
Sbjct: 252 ERPIHAKLSKTEKTIPLFILFRALKFKGDKEILDLICYDPEDSEFIDVLRPSIEESSSFL 311

Query: 359 RNTLVTDKN-KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
            +    D   K    A  +  + +R                     ++Y L  +G     
Sbjct: 312 DDRACLDFVGKRCSIAAEEKSQRLRKAQ---------------RLLNEYLLPHLGEK--- 353

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                   +     +   I  +   L+++  G+   DD D+  N+R+   G ++   + L
Sbjct: 354 --------ESDTTSKAFFIGYMAHNLINVVLGRRDQDDRDHYSNKRLDLAGPLIGQLFAL 405

Query: 478 GLLRMERSIKERISSVDID-----------SVMPQDLINAKPVVSAVCEFFCSSQ----- 521
              +M +S+ + +     D            +  Q ++N K + S +     +       
Sbjct: 406 LFEKMIKSLTQHLEKRLKDGNIDQMAKSAADLTRQGVLNFKSITSGLEYSIGTGNWSVQR 465

Query: 522 -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                  +SQ+   +  LS +++ RR +      + R       R +H TH+G ICP ET
Sbjct: 466 QAGSKAGVSQMLNRLTFLSTLSNLRRTNT----PIGRDGKLTGPRHLHNTHWGYICPVET 521

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            EG + GL+ +L   + V     +E      ++ +   T  +  ++  + ++      N 
Sbjct: 522 PEGQSCGLIKNLALMSIVTVNRELEAGDAITRILEDTGTIPIQQITPDQIKDSTKIFLNG 581

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI----AASLIPFLENDDS- 687
           +     +   +L+    +    L     + F+     Q + I         P L  +D  
Sbjct: 582 AWYGIHTDAYDLMETLLSERRSLKIPSDVSFVHHIRDQEIFIWTDGGRITRPVLIVNDMH 641

Query: 688 --------------NRVLMGCNMQRQAV------------PLLKAEAPFVGTGM-ESVVA 720
                          +VL    M                 P    E     TG+      
Sbjct: 642 LTLKKSVLYDENTNWKVLRYKGMVEYLDIDEEETKLIALSPADLEENRNSPTGVKTYTHC 701

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM-KFQRSNQNTCVNQR 779
           +   + I      I+   D  +    + +  +     G+     M +   S+      Q+
Sbjct: 702 EIHPSLIFGVCGTIIPFPDHNQSPRNTYQCAMGKQAIGLYTTNYMIRMDSSSHVLWYPQK 761

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV   +              +   L  G N+ VA   + GYN EDS++++   +   +F
Sbjct: 762 PLVATRN----------MRYLNFNKLPAGINVTVAICCYTGYNQEDSLMLNASAIDRGLF 811

Query: 840 TSIHIEEF-EVMARDTKLGPEE--ITRDIPNVSEEGLK---NIDECGIICVGAEVNPGDI 893
            S     + E    D   G  E     D   V    L     ID  G+   GA V+  D+
Sbjct: 812 RSYFFRTYKETAEGDGTEGASEVFTFPDPQTVKGIKLHDSSKIDADGLAIPGAVVSAQDV 871

Query: 894 LVGKITPKGESPM 906
           ++GKI+P   + +
Sbjct: 872 IIGKISPDSPTEL 884


>gi|86451153|gb|ABC96799.1| RNA polymerase II [Bouvardia ternifolia]
          Length = 204

 Score =  314 bits (804), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 76/246 (30%), Positives = 104/246 (42%), Gaps = 54/246 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GAAYVL 1311
            GAA+ L
Sbjct: 199  GAAHFL 204


>gi|120561245|gb|ABM27007.1| RNA polymerase II second largest subunit [Capniomyces stellatus]
          Length = 924

 Score =  314 bits (804), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 141/923 (15%), Positives = 264/923 (28%), Gaps = 182/923 (19%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            KY    + +  +         +  +         +I  L+     +   DD D+ G +R+
Sbjct: 151  KYAREILQKEFLPHVGTQAHNETRKT---YFFGYMIHRLLLCGLERREQDDRDHYGKKRM 207

Query: 465  RSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R    ++ + +    +              + +  + + +     +   
Sbjct: 208  DLAGPLLAMLFRNLFRKVTKDMTRYLQKCIDSKREFNLTMAMKSNTITAGLKYSLATGNW 267

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 268  GDQKKAMQSRTGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGLV 323

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   A +   G    P     +     ++  L+     +     
Sbjct: 324  CPAETPEGQACGLVKNLALMAHIT-VGTDSGPILLFLEEWAMENLEELAGSSINDSTKIF 382

Query: 630  ANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             N            LV      R   E         D  +   + +        P    +
Sbjct: 383  VNGVWVGIHKEPIRLVSTLKQLRRRLEFSYEVSIVRDVREKELRILTDSGRVCRPLFVVN 442

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +S   +                                   I A  A  V  V+A+R   
Sbjct: 443  NSRLNINK-------------------------------DVIKAIEAREVSDVEAVRWHD 471

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               EG ++   +  +   ++                          ++       + G +
Sbjct: 472  LLSEGIIEYLDAEEEETAMIIMT---------------------PQELTESRLYVENGIV 510

Query: 806  ALGRNML---------VAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
                  L         +    W       SM+  I   +V            ++      
Sbjct: 511  PAVELDLASRVKSKRNIGISTWTHCEIHPSMILGICASIVPFPDHNQSPRNTYQSAMGKQ 570

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G    +             +    +  +             +     S +   +  + 
Sbjct: 571  AMGIMLTS-----------YQLRMDTLSNILYYPQKPLATTHSMEYLKFSDLPAGQNAIV 619

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   + +   +     F  +  ++++  +      +    +   + 
Sbjct: 620  AILCYSGYNQEDSLIMSQTSIDRGLFRSIFFRSYQDEEDKLGM----RTMGKFEKPTRET 675

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + L    Y +L E   I  G           K+T +  D +               E  
Sbjct: 676  TLRLKHGTYEKLEEDGLIAPGTRVTGDDIIIGKTTPIPVDSL---------------ELG 720

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR V   K+         E    +++     GD       + VKV +   R  Q GDK A
Sbjct: 721  QRTVTHTKLDASKPLRSTETGIVDQVMLTTNGD-----GFKFVKVRMRSTRIPQIGDKFA 775

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF   G   D+++NP  +PSRM +G + E  L      +G  
Sbjct: 776  SRHGQKGTIGMTYRSEDMPFTSQGLVPDLIINPHAIPSRMTIGHLVECLLSKLATLMGTT 835

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          IS       ++   G  +                             
Sbjct: 836  ADATPFTDVTVDAIS------HELFNLGYQSRGFEVM----------------------- 866

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                               +G +    G         V  G  Y  +L HMV DK+++R+
Sbjct: 867  ------------------YNGHT----GR---KLYTQVFFGPTYYQRLKHMVDDKIHSRA 901

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRL 1294
             G   ++T+QP+ G+S  GG R 
Sbjct: 902  RGPLQILTRQPVEGRSRDGGLRF 924



 Score =  109 bits (271), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 103/762 (13%), Positives = 225/762 (29%), Gaps = 93/762 (12%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDS-EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +PV     ALGM + ++IL         ++  + +   +    ++   +VS
Sbjct: 76  YIRSD----IPVVVVFRALGMVAAKDILEHICYDGNDNELLEEFKGSIEEGFVIQDKEVS 131

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   K++     + L+++ +  +G  +            +        
Sbjct: 132 LDFIGKRGTTVGVSKEKRVKYAR-EILQKEFLPHVGTQAHNETRKTYFFGYMIHRLLLCG 190

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +E  +  D     +         P+L +   N    +   +     K           + 
Sbjct: 191 LERREQDDRDHYGK--KRMDLAGPLLAMLFRNLFRKVTKDMTRYLQKCIDSKREFNLTMA 248

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
              +  T  +  S+    + D  K   S  G  ++  R    +      R          
Sbjct: 249 MKSNTITAGLKYSLATGNWGDQKKAMQSRTGVSQVLNRYTFASTLSHLRRCNTPIGRDGK 308

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I     L N    +         +      ++KN   +  + +       +  ++  ++ 
Sbjct: 309 IAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLALMAHITVGTDSGPILLFLEEWAME 365

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM 558
             + +    +  +   F     +   +E +  +S +   RR      +  + R     E+
Sbjct: 366 NLEELAGSSINDSTKIFVNGVWVGIHKEPIRLVSTLKQLRRRLEFSYEVSIVRDVREKEL 425

Query: 559 RDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           R +  T  GR+C P        + +   +           +E    +  D      + YL
Sbjct: 426 RIL--TDSGRVCRPLFVVNNSRLNINKDVIKAIEAREVSDVEAV--RWHDLLSEGIIEYL 481

Query: 618 SAMEEENRYIAQANSSLDEDGSFTE-------ELVFCRCAGEEILVPREKIDFIDASPKQ 670
            A EEE   I      L E   + E       EL        +  +        +  P  
Sbjct: 482 DAEEEETAMIIMTPQELTESRLYVENGIVPAVELDLASRVKSKRNIGISTWTHCEIHPSM 541

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS++PF +++ S R      M +QA+ ++                  + + I+  
Sbjct: 542 ILGICASIVPFPDHNQSPRNTYQSAMGKQAMGIMLTSYQL---------RMDTLSNILYY 592

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
               +    ++  +  S       +   +  Y              NQ            
Sbjct: 593 PQKPLATTHSMEYLKFSDLPAGQNAIVAILCYSG-----------YNQE----------- 630

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   S  +   ++ R +  +       + ED + +              + +FE  
Sbjct: 631 -------DSLIMSQTSIDRGLFRSIFFRSYQDEEDKLGMR------------TMGKFEKP 671

Query: 851 ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            R+T             +     + ++E G+I  G  V   DI++GK TP     +   +
Sbjct: 672 TRET----------TLRLKHGTYEKLEEDGLIAPGTRVTGDDIIIGKTTPIPVDSLELGQ 721

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           + +            D S  + S  +G V  V +       K
Sbjct: 722 RTV-------THTKLDASKPLRSTETGIVDQVMLTTNGDGFK 756


>gi|51035519|emb|CAH10895.1| RNA polymerase B subunit [Halobiforma haloterrestris]
          Length = 435

 Score =  313 bits (803), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 85/253 (33%), Positives = 117/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSLEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  +   L  A  + SG+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESELREGLEEAGFESSGKETMYSGITGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|269913239|emb|CAY86046.1| RNA polymerase beta subunit [Asaia bogorensis]
 gi|269913245|emb|CAY86049.1| RNA polymerase beta subunit [Asaia krungthepensis]
          Length = 312

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 146/315 (46%), Positives = 201/315 (63%), Gaps = 28/315 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EIL+ FY  + +++  
Sbjct: 61  RKRKLPVTTLLYALEGEHSIAARAAKAAEGGDVEALGIRGMDQDEILAYFYGTVPFTRMP 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
             W  P        G K+   L D DTGE V E+  KLT+ + + + E   K + +    
Sbjct: 121 KGWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMCRKIAET-TKDVLVGRAD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G ++A+D+VN  TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL
Sbjct: 179 LLGRFIAQDLVNENTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +
Sbjct: 238 AVDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEV 297

Query: 423 DTPDDVRHIRKEDII 437
           D PD +R +RKEDI+
Sbjct: 298 DAPDTMRVLRKEDIL 312


>gi|268373734|gb|ACZ04320.1| RpoB [Mycobacterium parascrofulaceum]
 gi|299013529|gb|ADJ00328.1| RNA polymerase subunit B [Mycobacterium parascrofulaceum]
          Length = 251

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 104/240 (43%), Positives = 139/240 (57%), Gaps = 37/240 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I           ++       +  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNINVAEGVPPWAANLPEDLLHAQPN 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                                          VSTPVFDGA E  +  +L            
Sbjct: 160  A----------------------------IVSTPVFDGAREAELQGLLSATLPNRDNEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 192  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 251



 Score = 45.8 bits (107), Expect = 0.056,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|282163887|ref|YP_003356272.1| DNA-directed RNA polymerase subunit B' [Methanocella paludicola
            SANAE]
 gi|282156201|dbj|BAI61289.1| DNA-directed RNA polymerase subunit B' [Methanocella paludicola
            SANAE]
          Length = 604

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 118/604 (19%), Positives = 195/604 (32%), Gaps = 99/604 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ G+     D +      +  D     N  +A            M +   ++       
Sbjct: 80   VRKGEASF--DDMVKRGFIEYIDAEEEENTFIAIDESQLTKDHTHMELDSSLILGIAAGM 137

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T            + S + L+  D  G          G +        
Sbjct: 138  IPYPEHNASPRVTMGAGMVKQSLGVSTSNQKLRP-DTRG--HFLHYPQEGIVSTQTARSI 194

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  +     +    +    F R    +  R    + 
Sbjct: 195  NFDQRPSGQNFVVAVLSYEGYNIEDALVFNKGSIERG-LGRSHFFRTTEGEERRYPGGQE 253

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEI-LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +  E+   +    +   +   YS L E  L       GP             + E   + 
Sbjct: 254  DTFEVPDAEV---RGARESEFYSMLDEDGLVNPETEVGPNDVLIGKTSPPRFLEE--PTD 308

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                                  +  ++ +  R   K               R+ KV    
Sbjct: 309  LGGITP---------------LKRRETSVTMRSNEKGIVDTVILTETQNGSRLAKVRTRD 353

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            +R  + GDK A RHG KG++  I   EDMPF ++G   D+++NP  +PSRM +G + ET 
Sbjct: 354  QRVPELGDKFASRHGQKGVIGLIAQQEDMPFTENGMVPDLIINPHAIPSRMTIGHVLETI 413

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G      G+ +     + +   ++                                   
Sbjct: 414  GGKIGSLEGRFVDGTAFNNETEDELRKEFKKFGFSHTGKE-------------------- 453

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                     VF                         YDG+TG+     + VG I   KL 
Sbjct: 454  ---------VF-------------------------YDGITGQRITADIFVGVILYQKLY 479

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVS K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD
Sbjct: 480  HMVSSKMHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLDESD 539

Query: 1321 DV-------VG--------RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDL 1363
             V        G        R  VY     G   + ++     +F +L+ EM+ALG++  L
Sbjct: 540  KVFEYVCNNCGMVATEDKKRRLVY-CPNCGADTNIYKVEMSYAFKLLLDEMKALGIAPRL 598

Query: 1364 ENSR 1367
            +   
Sbjct: 599  DLED 602



 Score = 46.2 bits (108), Expect = 0.039,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 62/196 (31%), Gaps = 30/196 (15%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
             F +  L    ++          +R   +    +  A   +    +  T  GR      
Sbjct: 4   RIFVNGALIGSHDNPLEFVENIREKRRQGIISNQINIAYHKLTNEVIINTDMGRAR---- 59

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                I + +        +    +        D      + Y+ A EEEN +IA   S L
Sbjct: 60  --RPLIIVKNGKPV-ITNDDIEQVRKGEASFDDMVKRGFIEYIDAEEEENTFIAIDESQL 116

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +D                          ++     ++ IAA +IP+ E++ S RV MG 
Sbjct: 117 TKDH-----------------------THMELDSSLILGIAAGMIPYPEHNASPRVTMGA 153

Query: 695 NMQRQAVPLLKAEAPF 710
            M +Q++ +  +    
Sbjct: 154 GMVKQSLGVSTSNQKL 169


>gi|52694267|emb|CAG30663.1| DNA-directed RNA polymerase beta chain [Oceanimonas doudoroffii]
          Length = 317

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 186/313 (59%), Positives = 241/313 (76%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL  ++R N YGF+ETPYR+V DG++T++
Sbjct: 65  AGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLACYSRTNEYGFLETPYRRVVDGQITDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YLSA+EE +  IAQAN+++DE+G   +ELV  R  GE   +  +++ ++D SP+Q+VS
Sbjct: 125 VDYLSAIEEGHFVIAQANAAIDEEGRLLDELVPSRHKGEATYMNADQVQYMDVSPQQIVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG+E  VA  SG   VAKR G
Sbjct: 185 VAASLIPFLEHDDANRALMGSNMQRQAVPTLKADKPLVGTGIERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +V+ VDA RIV++  E ++ P  +G+DIY L K+ R NQNTC+NQRP V  G+ V   D+
Sbjct: 245 VVDYVDASRIVVKVNEEEMLPGEAGIDIYNLTKYTRYNQNTCINQRPCVMPGERVISGDV 304

Query: 794 IADGPSTDLGDLA 806
           +ADGPSTDLG+LA
Sbjct: 305 LADGPSTDLGELA 317


>gi|52694205|emb|CAG30632.1| DNA-directed RNA polymerase beta chain [Pseudomonas citronellolis]
          Length = 321

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 188/320 (58%), Positives = 243/320 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++V+LSA+EE +  IAQA+++LD  G   +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVSDEIVFLSAIEEADHVIAQASATLDAKGRLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD +
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVI 301

Query: 789 RRNDIIADGPSTDLGDLALG 808
            R DI+ADGPSTD+G+LAL 
Sbjct: 302 ARGDILADGPSTDMGELALA 321


>gi|110589620|gb|ABG77312.1| RNA polymerase beta subunit [Enterobacter turicensis]
          Length = 322

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 194/322 (60%), Positives = 247/322 (76%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D
Sbjct: 121 RDGVVTDEIHYLSAIEEGNFVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQIVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V + 
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLN 300

Query: 786 DEVRRNDIIADGPSTDLGDLAL 807
           + V R D++ADGPSTDLG+LAL
Sbjct: 301 EPVERGDVLADGPSTDLGELAL 322


>gi|269913241|emb|CAY86047.1| RNA polymerase beta subunit [Asaia krungthepensis]
          Length = 313

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 146/315 (46%), Positives = 201/315 (63%), Gaps = 28/315 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EIL+ FY  + +++  
Sbjct: 61  RKRKLPVTTLLYALEGEHSIAARAAKAAEGGDVEALGIRGMDQDEILAYFYGTVPFTRMP 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
             W  P        G K+   L D DTGE V E+  KLT+ + + + E   K + +    
Sbjct: 121 KGWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMCRKIAET-TKDVLVGRAD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G ++A+D+VN  TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL
Sbjct: 179 LLGRFIAQDLVNENTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +
Sbjct: 238 AVDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEV 297

Query: 423 DTPDDVRHIRKEDII 437
           D PD +R +RKEDI+
Sbjct: 298 DAPDTMRVLRKEDIL 312


>gi|401018|sp|P31814|RPOB_THECE RecName: Full=DNA-directed RNA polymerase subunit B
 gi|48140|emb|CAA47722.1| Subunit B of DNA-dependent RNA polymerase [Thermococcus celer]
          Length = 1122

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 113/577 (19%), Positives = 198/577 (34%), Gaps = 95/577 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N LVA  PW        + +    +     + +   E     R+T     
Sbjct: 614  IEYLDAEEEENALVATWPWEVTEEHTHLELMPAAILGIPASLVPYPEHNARPRNTYGAGM 673

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++ +D  G   +        +    +   G       +  + A+   
Sbjct: 674  AKQSLGLGWANFRIR-VDTRG--HLMHYPQVPLVNSRIMKAVGFEERPAGQNFVVAVLSY 730

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D  +   + +    +    F R    + +R +  +            D   I D
Sbjct: 731  AGYNMEDAIIMNKASIERG-LARSTFFRTYEAEEKRYLGGQ-----------TDRFEIPD 778

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              I   L E         G    +        L+      ++ +   +   +   +   +
Sbjct: 779  PTIQGYLGERYYRHLDEDGIIFPESKVNGKDVLVGRTSPPRFLE---EQSGLGGIILQER 835

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +   +    E    +K+   + GD       ++VKV     R  + GDK A RHG KG+
Sbjct: 836  RETSLTVRPSETGVVDKVIITETGD-----GTKLVKVTTRDLRIPEFGDKFASRHGQKGV 890

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMP+ + G   D+++NP G+PSRM VGQ+ E   G      G+++       
Sbjct: 891  IGLIVPQEDMPWTESGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRVDGTAFIG 950

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +    +      L                                      +DG      
Sbjct: 951  EPEEKLRKELEELGFKHSGREVM----------------------------YDGIT---- 978

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                  G   +  V VG IY  +L+HMV+DK++ARS G   ++T
Sbjct: 979  ----------------------GRRLEADVFVGVIYYQRLHHMVADKMHARSRGPVQVLT 1016

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG-------- 1324
            +QP  G++  GG R GEME   +  +GAA +L E L  +SD          G        
Sbjct: 1017 KQPTEGRAREGGLRFGEMERDVLIGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKR 1076

Query: 1325 RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGL 1359
            R +VY   V G +    +     +F +L+ E++A+G+
Sbjct: 1077 RGKVY-CPVCGEEERISKVEMSYAFKLLLDELKAMGI 1112



 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 164/975 (16%), Positives = 313/975 (32%), Gaps = 191/975 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L+     SY+ F+          + G+Q        +        ++F       P+F  
Sbjct: 29  LVRQHLDSYNAFI----------DHGMQEVIDEFGGVKPDIPDFEVKFGKVRLGEPEF-- 76

Query: 89  DDCL-WRDLTYAVPLK-ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVI 146
            +    R      PL  +  R+                     IY+  +P        V+
Sbjct: 77  QEAQGQRK-----PLYPMDARIRNLTYSAP-------------IYLELIP--------VV 110

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G     VSQ                                             + VRI
Sbjct: 111 NG-----VSQE-------------------------------------------AVEVRI 122

Query: 207 DRRRKVPVTSFLMA---LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
               ++P+     A    G+  EE++            G+    P     +    +V  S
Sbjct: 123 ---GELPIMLKSKACRLYGLSDEELIKL----------GEDPKDPGGYFIVNGSERVIVS 169

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           + D+   + ++E  ++    + K    +      IT +      +   + N      ++ 
Sbjct: 170 IEDLAPNKTLVERDERQNRIIAKCFSYRHGYRALITVERRKDGILYVKLPNVPRPVKFVY 229

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
               +   S  EI  +   D  I +V          N         +++AL  I ++  P
Sbjct: 230 VMRALGLLSDREIVEAVSDDPRIQHV-------LFDNLEDASDVTTQEEALDYIGKLSLP 282

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-NLDTPDDVRHIRKEDIIAIIKI 442
           G                    +Y L     +  N  L ++   +  R  +   +  +   
Sbjct: 283 GQP-----------------KEYRLRRAQNIIDNNLLPHMGVEEKDRKAKAYYLGMMALR 325

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           +++L  G    DD D+  N+R++  G++L + +R+   ++ + ++ +++           
Sbjct: 326 VLELSLGLRGEDDKDHYANKRLKLAGDLLMDLFRVAFGQLVKDMQYQMTKTYQRKGERYT 385

Query: 503 LINAK-----------------PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
             N +                   ++        + +SQL +  N +S ++H RR+++  
Sbjct: 386 FENIQRFVRNSIRPDVLSERIEHALATGSWPGGRTGVSQLLDRTNYISTLSHLRRVTS-- 443

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              ++R +   E RD+H TH+GRICP ET EG N GLV +L   +++      E     +
Sbjct: 444 --PLSREQPHFEARDLHGTHWGRICPTETPEGPNCGLVKNLALMSQITTGVPEEEVREYL 501

Query: 606 CDGKVTNDVVYLSAMEEENRY----IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
               V         +EE            N  L       E  V             + I
Sbjct: 502 ERLGVV-------PIEERRPNPDLWRLYLNGVLVGTVEDGEGFVNRIRTDRRSGKISDII 554

Query: 662 DF-----IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-M 715
           +       D     V S    +   L   ++ R  +               +  V  G +
Sbjct: 555 NVALYQDEDVKEIYVNSDDGRVRRPLIIVENGRPKLTREHVEAIKNGSLTWSDLVKMGVI 614

Query: 716 ESVVAKSSGAAIVA--------KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           E + A+    A+VA        +   +     AI  +  S+    + +    + Y     
Sbjct: 615 EYLDAEEEENALVATWPWEVTEEHTHLELMPAAILGIPASLVPYPEHNARPRNTYGAGMA 674

Query: 768 QRSNQNTCVNQRPLVKV-GDEVRRNDII----ADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           ++S      N R  V   G  +    +         +    +   G+N +VA + + GYN
Sbjct: 675 KQSLGLGWANFRIRVDTRGHLMHYPQVPLVNSRIMKAVGFEERPAGQNFVVAVLSYAGYN 734

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE---EITRDIP--NVSEEGLKNID 877
            ED++++++  +   +  S     +E   +    G     EI        + E   +++D
Sbjct: 735 MEDAIIMNKASIERGLARSTFFRTYEAEEKRYLGGQTDRFEIPDPTIQGYLGERYYRHLD 794

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E GII   ++VN  D+LVG+ +P               + G    + R+TSL V    +G
Sbjct: 795 EDGIIFPESKVNGKDVLVGRTSPPRFLEEQSG------LGGIILQERRETSLTVRPSETG 848

Query: 938 TVVDVRIFNRHGIDK 952
            V  V I       K
Sbjct: 849 VVDKVIITETGDGTK 863


>gi|73697637|gb|AAZ81435.1| RNA polymerase beta subunit [Mycoplasma alligatoris A21JP2]
          Length = 592

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 135/486 (27%), Positives = 210/486 (43%), Gaps = 79/486 (16%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G   + ++  +    +++     +++ +++  +    G ++             
Sbjct: 180  APLVATGIEKDIALYSAYNFRAKNDGEVTYVDSYKIHIKTNDKGTKDKYYLKNFERSNQG 239

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              I +  I+ VG +V  GD+LV   + K +  +   + +L A       +  D  +    
Sbjct: 240  TIISQKAIVKVGDQVKKGDLLVDGSSFK-DGELALGKNVLVAFSTYNGYNYEDAVILNER 298

Query: 934  ------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + +  +  R     ++R  +      +   R+  DE  I+         
Sbjct: 299  LVKDDVYTSVHIEEQTVLFRSSKAGDDRLTADIPNTSKFSLRNL-DEMGIVRVGSEVVPG 357

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +IL G+ +  G +   +   L   ++ + P        + D+     V++          
Sbjct: 358  DILVGRVSPKGEENPSQEEKLLMAVLQQRP--------LNDKDTSLRVKNGHNGTVIGIE 409

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            IL           Q GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP E
Sbjct: 410  ILSR---------QTGDILEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEE 460

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L+DGTPVDI+LNP GVPSRMN+GQI E HLG A   L  K  +   D     DI  
Sbjct: 461  DMPYLEDGTPVDIMLNPQGVPSRMNIGQILELHLGIAAKKLNTKFVTPSFDGVKKTDIED 520

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                                      L  + 
Sbjct: 521  VLEEAG-------------------------------------------------LDKSG 531

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L D +TG+ FD PV+VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS
Sbjct: 532  -----KAYLIDPITGKKFDNPVSVGIMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKS 586

Query: 1288 NRGGQR 1293
              GGQR
Sbjct: 587  QNGGQR 592



 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 206/448 (45%), Positives = 304/448 (67%), Gaps = 14/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN  GF++TPY KV +G +   D+ YL+A EE     AQ++  +D+D    +E +  R
Sbjct: 61  AKVNELGFLQTPYFKVNEGVIDYEDLRYLTAAEETGLAFAQSSVRVDQDNKIIDESLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+    +IDFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQ+VPLL+AEA
Sbjct: 121 KDYNYIIGKPTEIDFIEVSSKQMVSVAAAAIPFLENDDANRALMGANMQRQSVPLLEAEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E  +A  S     AK  G V  VD+ +I I++ +          D Y L  F+
Sbjct: 181 PLVATGIEKDIALYSAYNFRAKNDGEVTYVDSYKIHIKTND------KGTKDKYYLKNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T ++Q+ +VKVGD+V++ D++ DG S   G+LALG+N+LVAF  ++GYN+ED+++
Sbjct: 235 RSNQGTIISQKAIVKVGDQVKKGDLLVDGSSFKDGELALGKNVLVAFSTYNGYNYEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DV+TS+HIEE  V+ R +K G + +T DIPN S+  L+N+DE GI+ VG+EV
Sbjct: 295 LNERLVKDDVYTSVHIEEQTVLFRSSKAGDDRLTADIPNTSKFSLRNLDEMGIVRVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGDILVG+++PKGE   + EEKLL A+  ++ ++ +DTSLRV +G +GTV+ + I +R 
Sbjct: 355 VPGDILVGRVSPKGEENPSQEEKLLMAVLQQRPLNDKDTSLRVKNGHNGTVIGIEILSRQ 414

Query: 949 -------GIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 415 TGDILEDGIDKIVKVSIAQKRKIKVGDK 442


>gi|4867819|emb|CAB43068.1| RNA polymerase II [Gardenia thunbergia]
          Length = 269

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 103/237 (43%), Gaps = 54/237 (22%)

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             Q GDK + RHG KG V      EDMPF  +G   DI++NP  +PSRM +GQ+ E  +G 
Sbjct: 61   PQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPHAIPSRMTIGQLIECIMGK 120

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                +GK+                                                    
Sbjct: 121  VAAHMGKEGD-------------------------------------------------- 130

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +TP F     + I+  L        G   +Y+G TG P    + +G  Y  +L HMV
Sbjct: 131  ---ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPLTATIFLGPTYYQRLKHMV 186

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 187  DDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 243


>gi|318603011|emb|CBJ04579.1| RNA polymerase beta subunit [Pseudomonas sp. R-37265]
          Length = 311

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 181/311 (58%), Positives = 240/311 (77%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +EL
Sbjct: 61  SLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDQKVLVDEL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L
Sbjct: 121 VAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTL 180

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           +A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L
Sbjct: 181 RADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNL 240

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFE
Sbjct: 241 TKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFE 300

Query: 825 DSMLISERMVS 835
           DS+ +SER+V 
Sbjct: 301 DSICLSERVVQ 311


>gi|81171077|gb|ABB58765.1| RNA polymerase beta subunit [Mycoplasma bovirhinis]
          Length = 593

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 204/451 (45%), Positives = 300/451 (66%), Gaps = 14/451 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLSEVSNKRRVTSLGPGGLSRDTAQFEVRDVHATHYGRICPIETPEGLNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+++  GF++TPY KV +G +  +DV YL+A +E    IAQ++  +DE+    ++ +  R
Sbjct: 62  AQIDDKGFLKTPYYKVNNGVIDYSDVRYLNATQELGYSIAQSSVKVDENNKIIDDNLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                      +IDF++ S KQ++S+AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 122 RNYTYTNGTSSEIDFVEVSSKQILSVAAAGIPFLENDDANRALMGSNMQRQAVPLLQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E+ +AK S   +VAK  G V  VD   I I+  E      T   D Y L  F+
Sbjct: 182 PLIATGIEADIAKYSSYNLVAKNPGTVTYVDGSHIHIQRHE------TGITDKYSLRNFE 235

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q PLV++GD V   DI+ DG S   G++ALG+N+LV F  W+GYNFED+++
Sbjct: 236 RSNQGTIIQQIPLVRIGDVVEAGDILTDGSSFKDGEMALGKNVLVGFTTWNGYNFEDAVI 295

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DVFTSIHIEE  +  R ++ G +E+T+DIPN+S+  ++++D+ GI+ VG+EV
Sbjct: 296 INERLVKDDVFTSIHIEEQIIQFRSSRAGDDELTKDIPNISKHSIRHLDDTGIVKVGSEV 355

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+++PKGE   + EEK+L AI G++   ++DTSL+V  G +GT+  V I +R 
Sbjct: 356 YPGDVLVGRVSPKGEENPSQEEKMLFAILGQRPPSIKDTSLKVKHGHNGTITHVEILSRD 415

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       +  E IE + +    ++  + 
Sbjct: 416 KGD-------ILEEGIEKIVKVSIAQKRKIK 439



 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 118/418 (28%), Positives = 181/418 (43%), Gaps = 77/418 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G  V  GDIL    + K +  M   + +L         +  D  +     V   V 
Sbjct: 248  LVRIGDVVEAGDILTDGSSFK-DGEMALGKNVLVGFTTWNGYNFEDAVIINERLVKDDVF 306

Query: 941  -DVRIFNRHGIDKNERSISVEREQ----IELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
              + I  +    ++ R+   E  +    I   +    D+  I+         ++L G+ +
Sbjct: 307  TSIHIEEQIIQFRSSRAGDDELTKDIPNISKHSIRHLDDTGIVKVGSEVYPGDVLVGRVS 366

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +   +   +   ++ + P S           ++     +K  +  + + +E   ++
Sbjct: 367  PKGEENPSQEEKMLFAILGQRPPS-----------IKDTSLKVKHGHNGTITHVEILSRD 415

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K      GD +  G+ ++VKV +A KR I+ GDK+AGRHGNKG+VS +LP EDMP+L+DG
Sbjct: 416  K------GDILEEGIEKIVKVSIAQKRKIKVGDKVAGRHGNKGVVSIVLPEEDMPYLEDG 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNP GVPSRMN+GQI E HLG A   L  K  S   D     DI          
Sbjct: 470  TPLDVMLNPQGVPSRMNIGQILELHLGMAARKLNVKFVSPSFDGVKKPDIEAALEEAG-- 527

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          + +  ++     +G     P+  G                     +
Sbjct: 528  -------------LNKTGKQIIIDPITGRKFDKPISVG---------------------V 553

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +Y                  MLKLNHMV DK++ RS G YSL+TQQPLGGKS  GGQR
Sbjct: 554  MY------------------MLKLNHMVDDKMHVRSVGPYSLITQQPLGGKSQNGGQR 593


>gi|83763757|emb|CAJ00212.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12G02]
          Length = 352

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 187/365 (51%), Positives = 257/365 (70%), Gaps = 13/365 (3%)

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
             GTG+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RS
Sbjct: 1    CGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRS 60

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+S
Sbjct: 61   NQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVS 120

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  
Sbjct: 121  ERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKG 180

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G+
Sbjct: 181  GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGV 240

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            +K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S 
Sbjct: 241  EKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLIEGG-------------YSE 287

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              +    R +W +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGV
Sbjct: 288  AKLDTTDRKKWLELTLEDDALQTPLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGV 347

Query: 1071 LRVVK 1075
            L++VK
Sbjct: 348  LKIVK 352


>gi|303244445|ref|ZP_07330780.1| DNA-directed RNA polymerase subunit B [Methanothermococcus
            okinawensis IH1]
 gi|302485143|gb|EFL48072.1| DNA-directed RNA polymerase subunit B [Methanothermococcus
            okinawensis IH1]
          Length = 611

 Score =  313 bits (803), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 128/322 (39%), Gaps = 76/322 (23%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ K+ V   R  + GDK A RHG KG++  I+P EDMPF ++G   D+++NP  +P
Sbjct: 343  EGNRLAKIRVRDVRIPELGDKFASRHGQKGVIGLIVPQEDMPFTENGVFPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +GQ+ E   G       +++   I   +   D+                       
Sbjct: 403  SRMTIGQVLEMIGGKVGALECRRVDGTIFSGEKEWDLRETLEKYGFKHHGKEVM------ 456

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                                       G+       TG+  +  
Sbjct: 457  -----------------------------------------YDGK-------TGKKLECE 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA
Sbjct: 469  IFVGIAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAA 528

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYE-------SIVAGN--------DTFETGTPES 1346
             +L+E L  +SD          G   +Y+         V G                P +
Sbjct: 529  LLLKERLFDESDPYECYICSKCGEIAIYDHKRGIKYCPVCGETEDIQSNRKIPPVNLPYA 588

Query: 1347 FNVLVKEMQALGLSIDLENSRT 1368
            F +L+ E++++G++  +E    
Sbjct: 589  FKLLLDELRSMGINPKMELKDR 610



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 72/418 (17%), Positives = 120/418 (28%), Gaps = 108/418 (25%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
                +  +   RR   L                +       I P    E     L    
Sbjct: 19  NPEEFVKYLREKRREGELSPYTSISYNEESNDIHISTDAGRAIRPLIVVENGKPKLTKEH 78

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
               R     F         D      + YL A EEEN YIA     LD           
Sbjct: 79  IEKLRNGEITF--------SDLVNEGIIEYLDAEEEENAYIAVYEKELD----------- 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                       EK   ++  P  ++ I A + P+ E++ + R+ M   M +Q++ +  +
Sbjct: 120 ------------EKHTHLEIDPMSILGIGAGVAPYPEHNSAPRITMAAAMGKQSLGIPMS 167

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                                                           +   +  Y    
Sbjct: 168 NLKL-----------------------------------------RMDTKGHLLHYP--- 183

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q P+V+   +                    G+N +VA M + GYN ED+
Sbjct: 184 -----------QVPIVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNMEDA 222

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGI 881
            + ++  +   +  S     +E   +    G  +             +EE  +N+ + GI
Sbjct: 223 FIFNKASIERGLGRSSFFRSYEGFEKRYPGGQLDRFEVPEQGVRGYRAEEAYRNLGDDGI 282

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + V +EV  GD+++GK +P             + I        RDTS+ V  G  G V
Sbjct: 283 VEVESEVKSGDVIIGKTSPPRFLEE-------QDISLRTKSQRRDTSVTVRHGEGGIV 333


>gi|68300857|gb|AAY89365.1| RNA polymerase IV second largest subunit precursor [Chlamydomonas
            reinhardtii]
          Length = 1607

 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 158/998 (15%), Positives = 301/998 (30%), Gaps = 189/998 (18%)

Query: 320  IYIEA-GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            I   A G V D   LE I       +  L  D     A   +     + + +++AL  + 
Sbjct: 264  ILFRALGFVSDRDILEHI-------VYDLDADPAMLEALRSSVEEAQEVQTQEEALNYLG 316

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            +        T +       +      K  L  +G           T + +   +   +  
Sbjct: 317  KR----GTVTGASKADRIQYARNLLIKELLPHLG-----------TEEFMETRKGYFVGY 361

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--D 496
            ++  L+ +  G+   DD D+  N+R+   G ++   +RL   ++ + ++ +   +     
Sbjct: 362  MVHRLMLVALGRRPEDDRDHYANKRLDLGGPLMAGLFRLLFRKLCKELRMQAQRMVDAGK 421

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSAL 544
             +     IN K +   +     +              +SQ+   +   S ++H RR+++ 
Sbjct: 422  EINVISAINDKVITRGLKYSLATGNWGEQGKQGIRAGVSQVLARLTYASTLSHLRRVNS- 480

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R     + R +H + +G  CPAET EG  +GLV ++     +            
Sbjct: 481  ---PIGREGKLAKPRQLHNSLWGIFCPAETPEGQAVGLVKNMALMCYITVGTPSLPVVAH 537

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            + +           A++E       A++ +  +G +           + +   R ++ F 
Sbjct: 538  LEEFNTE-------ALDEVTPADIAASTKVFINGVWLGIQRDPTALIKNLRAMRRQVAFS 590

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
                         L  F +   ++R L  C   R  V         +   +  +  +   
Sbjct: 591  TEVAIIYDGPLKELRIFTDYGRASRPLYICEDNRLLVS-----KHHIRRLISPLPDEDEY 645

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            A     + G+VE +DA            + +T        ++  R               
Sbjct: 646  AWPQLVQDGLVEYIDAEE----------EETTMIAMTIADLRNAREAGAATGT------- 688

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                         P+  LG       +  + +P+  +N                      
Sbjct: 689  -----TYTHCEIHPAMILG-------VCASIIPFPDHNQSPRN----------------- 719

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              ++       +G                   D  G +          +    +      
Sbjct: 720  -TYQSAMGKQAMGMYATNYQTRM---------DTQGFVL--YYPQKPLVCTRAMDYLMFR 767

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +      + AI      +  D SL +            I  R   ++ +++ S+ RE+I
Sbjct: 768  ELPAGINAIVAIMCYSGYNQED-SLMLNGSSIDRGFHRSILYRAYKEEEKKAGSMAREEI 826

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E        +      +          G           K+  L  D     P     +F
Sbjct: 827  EAPDPSVTSKMKHGTYDKLDADGLCPPGTRVSGEDIICGKTVTLPDD-----PTGAVQRF 881

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
              +D  +                 L       I+++           + VK+ V      
Sbjct: 882  TKKDASL----------------ALRGHEAGVIDQVML--TTNDEGQKFVKIRVRTICIP 923

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDK A RHG KG        EDMPF  +G   DI++NP  +PSRM +G + E  +   
Sbjct: 924  QVGDKFASRHGQKGTCGITYTMEDMPFTAEGIVPDIIVNPHAIPSRMTIGHLVEALMSKV 983

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               +G +  +         ++S +   L                            + G 
Sbjct: 984  ASLMGSEGDATPFTKVTVDNVSQMLHDL-------------------------GYQRRGW 1018

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
             V                        SG +       G      + +   Y  +L HMV 
Sbjct: 1019 EVM----------------------YSGHT-------GRQLRAQIFLNPTYYQRLKHMVD 1049

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             K+++R  G   ++T+QP  G++  GG R GEME  C+
Sbjct: 1050 FKIHSRGRGPVQVLTRQPAEGRARDGGLRFGEMERDCL 1087



 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 138/1004 (13%), Positives = 271/1004 (26%), Gaps = 207/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+ +           +Q        I              A     +++
Sbjct: 30  LVRQQLDSFNEFVNVT----------IQEIIDETPEIVIKPESQHLPGVEAAEEKEYIIK 79

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P+              +   R+LTY  PL + +    +        +   D+
Sbjct: 80  FGQVYLSRPQITEQDGESVVLFPKEARLRNLTYCAPLYVDVTKTEYTRVGENEVEEKTDL 139

Query: 126 KEQSIYMGDLPLMTKD-------------------------GTFVIKGIQRIVVSQLHRS 160
               +++G +P+M K                          G FVI G ++++++Q  R 
Sbjct: 140 --SHVHLGKVPIMLKSERCNLHEASTEQEATNLGECPYDQGGYFVINGSEKVLIAQE-RM 196

Query: 161 PG--IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS-----------------KDI 201
               ++      + S   K  +   I       ++    S                   +
Sbjct: 197 ANNHVY----VFKKSQPSKYTFCAEIR----SVVEGSTRSASSMSIMMLAKGKKAGAAGV 248

Query: 202 IHVRIDRRR-KVPVTSFLMALGMDSE-EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGA 258
           I  +I   R + P+     ALG  S+ +IL    Y         +     +  A  +   
Sbjct: 249 IRAQIPYIRAEFPIFILFRALGFVSDRDILEHIVYDLDADPAMLEALRSSVEEAQEVQTQ 308

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSG---LLKSLKEKGVKFLGIT--SDCLCGLYVAEDIV 313
           + + + +             ++      L+K L         +        G  V   ++
Sbjct: 309 EEALNYLGKRGTVTGASKADRIQYARNLLIKELLPHLGTEEFMETRKGYFVGYMVHRLML 368

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
               G    +  D    K L+           +L+              +  + +   DA
Sbjct: 369 -VALGRRPEDDRDHYANKRLDLGGPLMAGLFRLLFRKLCKE--------LRMQAQRMVDA 419

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHI 431
             +I  +    D       +       +          G  ++  RL   +      R  
Sbjct: 420 GKEINVISAINDKVITRGLKYSLATGNWGEQGKQGIRAGVSQVLARLTYASTLSHLRRVN 479

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    I         +      ++KN   +  + +       ++
Sbjct: 480 SPIGREGKLAKPRQLHNSLWGIFCPAETPEGQAVG---LVKNMALMCYITVGTPSLPVVA 536

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            ++  +    D +    + ++   F     L    +    +  +   RR  A        
Sbjct: 537 HLEEFNTEALDEVTPADIAASTKVFINGVWLGIQRDPTALIKNLRAMRRQVAFSTEVAII 596

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
               ++   +   +     P    E + + +                E            
Sbjct: 597 YDGPLKELRIFTDYGRASRPLYICEDNRLLVSKHHIRRLISPLPDEDEYA---WPQLVQD 653

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V Y+ A EEE   IA   + L             R A E            +  P  +
Sbjct: 654 GLVEYIDAEEEETTMIAMTIADL-------------RNAREAGAATGTTYTHCEIHPAMI 700

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+                              
Sbjct: 701 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMG----------------------------- 731

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                       +  +       +   V  Y               Q+PLV         
Sbjct: 732 ------------MYATNYQTRMDTQGFVLYYP--------------QKPLV--------- 756

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G N +VA M + GYN EDS++++   +      SI    ++   
Sbjct: 757 -CTRAMDYLMFRELPAGINAIVAIMCYSGYNQEDSLMLNGSSIDRGFHRSILYRAYKEEE 815

Query: 852 RDTKLG-PEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +       EEI    P+V           +D  G+   G  V+  DI+ GK     + P 
Sbjct: 816 KKAGSMAREEIEAPDPSVTSKMKHGTYDKLDADGLCPPGTRVSGEDIICGKTVTLPDDPT 875

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
              ++             +D SL +  G    V+D  +   +  
Sbjct: 876 GAVQRF----------TKKDASLALR-GHEAGVIDQVMLTTNDE 908



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 22/87 (25%)

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVVGRT---------------RVYESIVAGNDTFET 1341
            CI ++GAA  L+E L  +SD     V  R+                +Y+    G++ ++ 
Sbjct: 1517 CIISHGAAAFLKERLFDQSDAYRIHVCERSGLIAVANLKKQQFTSTIYK---DGSNIYQV 1573

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSRT 1368
              P +  +L +E+ A+ ++  ++  R 
Sbjct: 1574 YIPYACKLLFQELMAMCIAPRMQFERD 1600


>gi|253741841|gb|EES98701.1| DNA-directed RNA polymerase subunit B' [Giardia intestinalis ATCC
            50581]
          Length = 1239

 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 93/485 (19%), Positives = 174/485 (35%), Gaps = 87/485 (17%)

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE---RSI 957
             G   +   +     +    + D+ D  +   S +        I+     + N    +S+
Sbjct: 824  TGYERLPAGQNATVCVMSYSSFDIEDALILNRSAIDRGFGRCSIYRSVSAELNSTGSKSV 883

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
               ++ +    +D   +           L  +  G +  +G     K   +++       
Sbjct: 884  DGTKDVLLGPPKDHLKQYESYHAVEDDGLCAV--GAHLKTGDIVINKGRHVTNIPGLSDG 941

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       E ++  +E++              + +K+      D        ++KV 
Sbjct: 942  PEAAETLIKSPESLKSPLETIT-------------YIDKVLVTTNND-----GNLLIKVL 983

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                R  + GDK + RHG KG+   I+   D+PF   G   D+++NP G PSRM V ++ 
Sbjct: 984  TREPRRPEVGDKFSSRHGQKGVCGLIVSQSDLPFTSQGIVPDLIMNPHGYPSRMTVAKLL 1043

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E     +    G++                                      D+  +   
Sbjct: 1044 ELLSNKSSCFRGEQTDGTCF----------------------------RTKTDEEFI--- 1072

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                                 +   LR A    SG+ +LY GLTG+     +  G IY  
Sbjct: 1073 -------------------AELYDSLRAAGFSYSGKDVLYSGLTGDVIPVYIFNGPIYYQ 1113

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            KL HMV DK+++R TG  +++T+QP  G+   GG R+GEME  C  +YGA+ +L E   +
Sbjct: 1114 KLKHMVKDKIHSRGTGPITMLTRQPTEGRRVHGGLRMGEMERDCAISYGASALLLERFML 1173

Query: 1318 KSDDVVG------------RTRVYESIVA--GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             SD+ +             R           G D  +   P +  ++++E+ ++G+ + +
Sbjct: 1174 SSDEFLAYVCEACGLFSYERNGALWCPTCQSGKDVVKIRIPYAAKLMIQELISMGVLVRM 1233

Query: 1364 ENSRT 1368
            +   +
Sbjct: 1234 QLEDS 1238



 Score =  126 bits (316), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 133/981 (13%), Positives = 284/981 (28%), Gaps = 202/981 (20%)

Query: 31  EVQKASYDHFLMMNIAPDERPNE------------GLQAA-FKSVF------PITAFSGA 71
           +    S++H L + I    + N              ++    K V       P ++  G 
Sbjct: 36  KHHLDSFNHLLDVTIPAIIKENPLLVVAKHPHFYLRIEKVDVKQVSHGSSKSPGSSTGGN 95

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             L               +C  R++TYA P+ I +R    +       K         I 
Sbjct: 96  VGL------------TPHECRQRNMTYAAPITIDVRCRASNKSSVQYYK--------DIC 135

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVV-------SQLHRS 160
           +G +P+M                           G F+++G ++ ++       +++   
Sbjct: 136 IGYIPIMLRSNRCILANKSRKQQAFFQECPDDPGGYFIVRGAEKSILLAEQITMNRIVL- 194

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR--RRKVPVTSFL 218
            G + D +      S            +   +          ++  ++  ++ +P+ +  
Sbjct: 195 -GRNTDGNIEVTVASNTTERKS-----RCAVLY----KNKKFYLIHNKFNKKPIPIVTIF 244

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G                    D     L   D +    +S S+ +    +       
Sbjct: 245 KAMGF-----------------VNDVTVLSLIGTDQLFLDYMSLSVQECSNDKIYT---- 283

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI--YIEAGDVIDEKSLEEI 336
                     +E+ +K+L    D +     A   VN  T  +    +A        L   
Sbjct: 284 ----------QEQALKYLA---DRIVVRTYANTNVNFPTSPVAMTAKASIESARDCLAHF 330

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
             S I  +  L +  V  N   + +  T  N                G  +T    +S  
Sbjct: 331 VLSHIPVVERLNLQQVAQNIQPQTSASTASNTSVSTHT---------GTTATSVGGKSGS 381

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII-KILVDLRNGKGTIDD 455
                       ++V                   + K   +A + +  +    G    D 
Sbjct: 382 VSAMAKPAIGSGASVVASNTGSTAPPVNMARFNWLPKAVYLATMVRRAILFDFGVIKGDS 441

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLR-MERSIKERISSVDIDSVMPQDLINAKPVV---- 510
            D +GN+++ + G++L+  +       +    ++    +  D     DL N   V     
Sbjct: 442 KDFVGNKKIETAGDLLELIFDDAFKTLLAHMARKVDVILRSDKNRGTDLTNYDVVSLVDP 501

Query: 511 SAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           S +   F S+                 +SQ+   ++ +S +    RLS+       +A  
Sbjct: 502 SIITRAFNSAISTGNWKIERIGVDRVGVSQVLSRLSYISTLGQVTRLSST----FDKAMK 557

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
               R ++ +  G  CP++T EG ++G+V +L+  AR++     ++  + +    V +  
Sbjct: 558 SSGPRMLNFSQMGIFCPSDTPEGESVGIVKNLSIMARISKDENADSISKLLMSIGVEDLA 617

Query: 615 VYLSAME---EENRYIAQANSSLDED-----GSFTEELVFCRCAGEEILVPREKIDFIDA 666
              S           +    +            F   L   R  G    +     +    
Sbjct: 618 SCWSGDTFSLGYGYMVFLNGTIKGVIAKDMLKGFIITLRTFRRKGYISYLTSFHFNDEHQ 677

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           +         +  P L  ++    L   +++                 +E +    +  A
Sbjct: 678 AVYINCDSGRACRPLLIVENGKLKLTLNDIELLVNNQKCFVDFIYEGKVEYLDVNEAKNA 737

Query: 727 IVAKRAGI----------------------VEQVDAIRIVIRSVEGDLDPSTSG-VDIYR 763
            +A                           +      +      +  +    SG +   +
Sbjct: 738 YIAMDTKDLTPQHTHCEIESYTLLGYVVGLIPYPHHNQSPRNCYQCSMGKQASGAIAFNQ 797

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             +F+ +       QRPL                  T    L  G+N  V  M +  ++ 
Sbjct: 798 FERFETAMFLLDYPQRPLTS----------TKILKLTGYERLPAGQNATVCVMSYSSFDI 847

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE-------EGLKNI 876
           ED+++++   +                   T     + T+D+            E    +
Sbjct: 848 EDALILNRSAIDRGFGRCSIYRSVSAELNSTGSKSVDGTKDVLLGPPKDHLKQYESYHAV 907

Query: 877 DECGIICVGAEVNPGDILVGK 897
           ++ G+  VGA +  GDI++ K
Sbjct: 908 EDDGLCAVGAHLKTGDIVINK 928


>gi|243010730|gb|ACS94442.1| RpoB [Mycobacterium paraffinicum]
 gi|243010732|gb|ACS94443.1| RpoB [Mycobacterium paraffinicum]
 gi|243010734|gb|ACS94444.1| RpoB [Mycobacterium paraffinicum]
 gi|243010736|gb|ACS94445.1| RpoB [Mycobacterium paraffinicum]
 gi|243010738|gb|ACS94446.1| RpoB [Mycobacterium paraffinicum]
 gi|243010740|gb|ACS94447.1| RpoB [Mycobacterium paraffinicum]
          Length = 248

 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 144/240 (60%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +   +              
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAAS-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             + +  +  +    VSTPVFDGA E  +  +L            
Sbjct: 146  -----------------LPKELQSAEPNAIVSTPVFDGAREAELQGLLSCTLPNRDNEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            ++  G+++L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.5 bits (106), Expect = 0.061,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|110669269|ref|YP_659080.1| DNA-directed RNA polymerase subunit B' [Haloquadratum walsbyi DSM
            16790]
 gi|109627016|emb|CAJ53492.1| DNA-directed RNA polymerase subunit B' [Haloquadratum walsbyi DSM
            16790]
          Length = 611

 Score =  313 bits (802), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 131/603 (21%), Positives = 212/603 (35%), Gaps = 97/603 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK GD    +  + +    +  D     ++ VA            + I  +++       
Sbjct: 87   VKSGDLSFED--LVNRGYIEFIDAEEEEDIYVAVDEDELEEAHTHLEIDPQLIFGIGAGM 144

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 145  IPYPEHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLLHYPQLSMVKTQTTEQI 201

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 202  GFDERPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRAMARSHFFRTYEGEERRYPGGQE 260

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 261  DRFEIPSQD-------VRGARGENAYTHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEP 313

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 314  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLAKVSVRDQ 361

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM V        
Sbjct: 362  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTV-------- 413

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG K+ SL                                              
Sbjct: 414  GHVLEMLGGKVGSLQGRRVDGT-------------------------------------- 435

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     F G DEE +   L     + SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 436  --------AFQGEDEEDLREGLEEYGFNSSGKEVMYSGITGEKIDAEIFVGTIFYHKLYH 487

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD 
Sbjct: 488  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDK 547

Query: 1321 -------DV-------VGRTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                   D         G+ R+Y+  V G  +D  E     +F +L+ EM ALG+   L+
Sbjct: 548  EEVYVSADTGMVAVEDRGQRRIYD-PVTGDEDDIHEIEISYAFKLLLDEMIALGIRPRLD 606

Query: 1365 NSR 1367
               
Sbjct: 607  LQD 609



 Score = 42.4 bits (98), Expect = 0.61,   Method: Composition-based stats.
 Identities = 24/118 (20%), Positives = 45/118 (38%), Gaps = 23/118 (19%)

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N    +++      D      + ++ A EEE+ Y+A     L+E                
Sbjct: 82  NEIDAVKSGDLSFEDLVNRGYIEFIDAEEEEDIYVAVDEDELEEAH-------------- 127

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                      ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 128 ---------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 176


>gi|13542013|ref|NP_111701.1| DNA-directed RNA polymerase subunit B [Thermoplasma volcanium GSS1]
 gi|14325446|dbj|BAB60350.1| DNA-directed RNA polymerase B [Thermoplasma volcanium GSS1]
          Length = 1195

 Score =  313 bits (802), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 214/1337 (16%), Positives = 416/1337 (31%), Gaps = 272/1337 (20%)

Query: 79   YEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                 P+             ++   RDL Y  P  +TL+L + +     G+++IK     
Sbjct: 85   IFVGKPEIKEASGASNQITPNEARLRDLNYMAP--VTLKLRIVEDGIEKGSETIK----- 137

Query: 129  SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
               +GD+P+M                    RS        K      G            
Sbjct: 138  ---VGDIPVM-------------------VRS--------KICTLAEGN----------- 156

Query: 189  GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIV----YSQRGDF 244
               +D   +  +            P+       G+   E L            Y   G  
Sbjct: 157  ---LDQYIEKNNG-----------PI-------GLSRREKLQYVGEDPDDPGGYFIIGGS 195

Query: 245  WCFPLSAADLMVGAKVSSSLVDIDTGEQVIES-GKKLTSGLLKSLKEKGVKFLGITSDCL 303
                +S  DL     +       ++  +V +   ++     L S+++     + ++   +
Sbjct: 196  ERVIVSLEDLAPNKIMVEWEDRYESKVEVAKVFSQRGGFRALTSMEKGSDGTINVSIPSV 255

Query: 304  CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
             G              I ++A  +  +  + +   S     PI+Y +  ++       L 
Sbjct: 256  AGTVPL---------VILMKALGLERDVDVHDAIASVPEMEPIIYANIEDSKN--PKILP 304

Query: 364  TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
             +     +DA+  + +    G    F                 D      +  ++  +L 
Sbjct: 305  PNGVNTTEDAISYLEKRFAAGQAKEFR----------------DKKISQMLDHSLLPHLG 348

Query: 424  TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                 R  +   +  + + L++L  G    DD D+L N+R++  G+++   +R     + 
Sbjct: 349  DSASDRIRKAIYLGRMARSLLELSLGIRKEDDKDHLANKRIKLAGDLMDELFRSAFQSVM 408

Query: 484  RSIKERISSVDIDSVMPQDLI---------NAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            + +K ++          +                 +S        + +SQL + V++LS 
Sbjct: 409  KDLKYQLEKTYNRKRGIKIRPAVRQDLLTQRILHAMSTGNWIGGRTGVSQLLDRVSNLST 468

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            I+H RR+ +     + R +   E RD+HPT +GRICP ET EG N GLV +      V  
Sbjct: 469  ISHLRRIIS----PLTRTQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNAALLINVTQ 524

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
                ET    +    V   +      E  N+     N            LV         
Sbjct: 525  GIDSETVMEILKGMDVKEVLE-----ESPNKGRVYLNGDFVGYHDDPRYLVRRLREERRA 579

Query: 655  LVPREKID--FIDASPKQVVSIAASLIPFLE-NDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                ++I+  + D + + +V+     +          R ++  +M  +      +    V
Sbjct: 580  GRISDEINVRYDDNTNEVIVNCDRGRLRRPLLVLKDGRTVITEDMIEKLRKDEYSFEDLV 639

Query: 712  GTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
              G +E + A+                               +   + V +Y     ++ 
Sbjct: 640  KVGALEWLDAE-------------------------------EEEDAYVAVYAYNIPEKC 668

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
               +    R +V   +    N I+  G   +  ++                     + I 
Sbjct: 669  PHCSSYLYRSMVDWSNPGSNNIILECGFCYNKFEVPSLITP-----------EHTHLEID 717

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              M+   V + I   E     R T              S   ++  D  G   +      
Sbjct: 718  PAMILGVVASIIPYPEHNSSPRITIASAMAKQSLGFAQSNVRIRP-DTRG--HLLHYPQV 774

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
              +    +           +  + A+   +  +++D  +   + +    +    F R   
Sbjct: 775  PLVRTRVMEYTHYDRRPAGQNFVVAVLSYEGYNIQDALVINKAAIDRG-LGRSTFFRTYS 833

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
             +  R    + ++ E+   D                   + G  A    K   +S ++  
Sbjct: 834  AEERRYPGGQEDKFEIPTHD-------------------VIGARAEEYYKNLDESGIIYP 874

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            +       S          +     E         +S +  R             +    
Sbjct: 875  EAY--VEGSDVLIGKTSPPRFLEEGEERLGPQRRRESSVTMRPNESGYVDNVFLTVSESN 932

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             RVVK+ V  +R  +         G+K                               SR
Sbjct: 933  SRVVKIKVRSERIPEL--------GDK-----------------------------FASR 955

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
                              G+K    +   + +   +      + +    S   +++    
Sbjct: 956  -----------------HGQKGVIGLVVPQEDMPFTEEGIIPDLIFNPHSIPSRMTVGHI 998

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
              ++      ++G  +   +F G  E+++   L      +SG  ++YDG+TG  F   + 
Sbjct: 999  LEMIGGKIASRTGKFIDGTIFSGEPEKSLRDELVKYGFRKSGTEVMYDGITGRKFRADIF 1058

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG IY  KL+HMV+ K +ARS G   ++T+QP  G+S +GG R GEME   + A+GAA V
Sbjct: 1059 VGVIYYQKLHHMVAGKFHARSRGPVQILTRQPTEGRSRQGGLRFGEMERDTLIAHGAAMV 1118

Query: 1311 LQEMLTIKSDD----VVG------------RTRVYESIVAGN--DTFETGTPESFNVLVK 1352
            +++ L  +SD     V G            R       V GN  + +   T  +F ++  
Sbjct: 1119 IKDRLLDQSDGTVLYVCGNPSCGHIAIYDRRKGTLRCPVCGNTGNIYPIETSYAFKLMRD 1178

Query: 1353 EMQALGLSIDLENSRTK 1369
            E+ +LG+ + L     K
Sbjct: 1179 ELISLGVVMRLMLGDMK 1195


>gi|156087649|ref|XP_001611231.1| DNA-directed RNA polymerase, beta subunit [Babesia bovis T2Bo]
 gi|154798485|gb|EDO07663.1| DNA-directed RNA polymerase, beta subunit, putative [Babesia bovis]
          Length = 1171

 Score =  313 bits (802), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 120/583 (20%), Positives = 206/583 (35%), Gaps = 99/583 (16%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G + L +      + W   N E++ LI  R               E          E   
Sbjct: 668  GQIPLSKLFASGVLEWIDVNEENNTLIVMR---------------ESDITPKTTHLEISP 712

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              +  V    +   +         +   G   +G I     +       L+         
Sbjct: 713  MSMLGVVAGLIPFPNHNQSPRNTYQCAMGKQSIGSIGYNQLNRCDTILHLMVYPQRPLVT 772

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
                  +      +G  V V + +  G +  +  +  +       +R     +V ++   
Sbjct: 773  TKAIQLVNFDKLPAGQNVIVAVMSYQGYEIEDAVVINKASSERGFSRCYSLRRVTVE--- 829

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
              +L         ++        T +  D ++        Q   +D+ + + +       
Sbjct: 830  IEKLNHAAERPGGLNNRPQITNVTPV--DDLTGDSVIGVGQKVKKDDTLLKKLTQTSTG- 886

Query: 1043 ETSKSILEDRFKN--KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            +   + ++ +F     ++++     +   V  + K+ +   R  + GDK + RHG KG+V
Sbjct: 887  QIKVTDIKYQFNQPAYVDRVMCITTIAESV--MYKIMLRQVRLPEIGDKYSSRHGQKGVV 944

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I   E++PF + G   D+++NP G PSRM VG++ E     A V  G           
Sbjct: 945  GLIESQENLPFSEHGWVPDLIMNPHGFPSRMTVGKMLELVAAKAAVLNGIFEDG------ 998

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                           TP F+     AI 
Sbjct: 999  -----------------------------------------------TP-FEADSLPAIE 1010

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L       +G+ ILY G+TGEP +  +  G +Y  KL HMVSDK++AR+ G    +T+
Sbjct: 1011 RSLIKKGFHPAGKEILYSGITGEPLETLIFTGPMYYQKLKHMVSDKIHARAVGPRQSLTR 1070

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV------GRTRVYE 1330
            QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD    DV       G    Y+
Sbjct: 1071 QPTEGRSKDGGLRLGEMERDCLIAYGASGLLVERLMLSSDVFQMDVCHQCGFIG----YD 1126

Query: 1331 -----SIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                     G  T     P +  +L +E+QA+ +  ++    +
Sbjct: 1127 GWCAYCKQRGQ-TATVAIPYACKLLFQELQAMNIRPNVILKES 1168



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 126/1000 (12%), Positives = 275/1000 (27%), Gaps = 202/1000 (20%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF------ 86
              SY++F++  I              KS            +EF+      P        
Sbjct: 56  HINSYNNFVLREIKEIVNAPS--NKMLKS-----DACKKFYIEFIDINVGEPTMSENNNK 108

Query: 87  ----DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT--- 139
                   C  RD+TY+ P+ + +     +            +  + + +G LP+M    
Sbjct: 109 PILLTPQLCRMRDITYSAPMYVDVEYYNGEG-----------VASKRVEIGRLPVMLRSC 157

Query: 140 -----------------------------KDGTFVIKGIQRIVVSQLHRSP-GIHFDHDK 169
                                          G F+IKG++++++ Q   S   +  + D 
Sbjct: 158 VCALSGGMRANGNVDNFELSSRLGECPYDPGGYFIIKGVEKVILMQEQLSKCRVIVETDV 217

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            +   +            +   +         ++VR +     VP+   L A+G+ ++E 
Sbjct: 218 KKNICATVTSATAES-KSRTAVVY----KNQKLYVRHNSFTDDVPLCIILKAMGVTTDEE 272

Query: 229 LSTF----YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID--------------TG 270
           ++        +      GD+        +  +  ++ + L                  + 
Sbjct: 273 IAQLIGTAGAREYLPTGGDYILSIEDLYNEGINTRMDALLYVGRKVRPRPLAKGFFTSSK 332

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC-GLY-----VAEDIVNGETGEIYIEA 324
           E++ ++ + L       L    +  + + +     G       +A  +++  +G+  ++ 
Sbjct: 333 ERLPKTNQNLIEDTHDILTRVLLSHIPMRNCRDFSGKIKSLCLMARRVLSVASGKEPMDD 392

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYV------DSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            D    K LE            L+           +    R+  +       + A     
Sbjct: 393 KDHYGNKRLELAGQLISILFEDLFKAFLGQLKKQIDATLTRHYEIVSNCHGGEQAKYPDC 452

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
            V  P D+ T    ++  +   ++  ++ +   G  ++  RL+  +   +          
Sbjct: 453 LVSLPTDIIT-RGMQATISTGNWNIKRFRIERSGVSQILSRLSYISCLGMMTKTNSQFEK 511

Query: 439 IIKILVDLRNGK---GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
             K+           G I   D         V  +    +      +ER ++       +
Sbjct: 512 GRKVSKPRALQPSQLGLICPCDTPEGESCGLVKNLSLMNHVTTDGDIERLVELLYWLG-V 570

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           +S       +       V  F     +   +     +  +   RR   +           
Sbjct: 571 ESADALSARDCFDDDRNVTVFLNGIIIGVHQNGKQLIKDVVALRRRGKISA--FVSVFEN 628

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            + R+VH +  G            I + +             +E     +     +  + 
Sbjct: 629 YQQREVHISSDG-----GRLCRPLIVVENGKPLLTPKVLSQLVEGQI-PLSKLFASGVLE 682

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           ++   EE N  I    S +                         K   ++ SP  ++ + 
Sbjct: 683 WIDVNEENNTLIVMRESDITP-----------------------KTTHLEISPMSMLGVV 719

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           A LIPF  ++ S R    C M +Q++  +         G   +                 
Sbjct: 720 AGLIPFPNHNQSPRNTYQCAMGKQSIGSI---------GYNQLNRCD------------- 757

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                                                     QRPLV             
Sbjct: 758 ---------------------------------TILHLMVYPQRPLV----------TTK 774

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                +   L  G+N++VA M + GY  ED+++I++            +    V      
Sbjct: 775 AIQLVNFDKLPAGQNVIVAVMSYQGYEIEDAVVINKASSERGFSRCYSLRRVTVEIEKLN 834

Query: 856 LGPEEI---TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
              E            +   + ++    +I VG +V   D L+ K+T +  +       +
Sbjct: 835 HAAERPGGLNNRPQITNVTPVDDLTGDSVIGVGQKVKKDDTLLKKLT-QTSTGQIKVTDI 893

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    VD       +   V   ++  ++      DK
Sbjct: 894 KYQFNQPAYVDRVMCITTIAESVMYKIMLRQVRLPEIGDK 933


>gi|83763751|emb|CAJ00209.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 14C08]
          Length = 351

 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 185/364 (50%), Positives = 255/364 (70%), Gaps = 13/364 (3%)

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+E  VA  SG   VAKR G+V+ VDA RIV++  E +L    +G+DIY L K+ RSNQN
Sbjct: 1    GIERNVAVDSGVTAVAKRGGMVQSVDASRIVVKVNEDELVSGEAGIDIYYLTKYTRSNQN 60

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+
Sbjct: 61   TCINQRPTVLPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERV 120

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDI
Sbjct: 121  VQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDI 180

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT+ DV++F R G++K+
Sbjct: 181  LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTISDVQVFPRDGVEKD 240

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +R++ +E  Q++   +D  +E  IL+  + +R+  +L                  S   +
Sbjct: 241  KRALEIEHMQLKEAKKDLTEEFQILEGGLLARVKAVLINGG-------------YSEAKL 287

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                R +W +  ++++++Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++
Sbjct: 288  DAIDRKKWLEQTLENDELQSQLEQLAEQWDELKADFDKKFEAKRRKITQGDDLAPGVLKI 347

Query: 1074 VKVF 1077
            VKV+
Sbjct: 348  VKVY 351


>gi|66362272|ref|XP_628100.1| RNA polymerase 1 beta subunit [Cryptosporidium parvum Iowa II]
 gi|46227419|gb|EAK88354.1| RNA polymerase 1 beta subunit [Cryptosporidium parvum Iowa II]
          Length = 1281

 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 174/1213 (14%), Positives = 354/1213 (29%), Gaps = 174/1213 (14%)

Query: 175  SGKLLYACRIIPDQGLWMDIE-------FDSKDIIHVRIDRRRKVPVTS------FLMAL 221
            +G + Y+  +      W++ E         SK  I+        +P+             
Sbjct: 92   NGHISYSAPL------WLEFEGYNSSLDTVSKHSIYA-----GTIPIMVKSSSCHLF--- 137

Query: 222  GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
            G+ ++E++                         ++  + +  +          +S     
Sbjct: 138  GLGTKELVEK-GEDPNEVGGYFIINGNERVIRYVIQQRCNYPIGLKRPRFATFDSFGSEY 196

Query: 282  SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            + L++SL++ G               +   ++N +  E  I    ++    +  I+ S +
Sbjct: 197  AVLMRSLRDDGTSTANYLYGTSDHQCIYRVLLNRQ--EWLIPFWPLLMA--VGSIYDSNV 252

Query: 342  RDIPIL------YVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAES 394
                IL        +  N    +      D +     +     +    PGD         
Sbjct: 253  LRSKILQYCNPKDENLFNTINMLTLEWGLDNSVGVDAEFNSVSFGNKGPGDTDILENRYL 312

Query: 395  MFNFL-------FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                        F       L   GR  ++  + +   +    +    ++ I   L+ L+
Sbjct: 313  HQIGRLVWEGVAFHLPPGSLLQEAGRFLIDNYVLVHLEEWNAKLECLILMFI--KLIKLQ 370

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER------------------ 489
              +   + ID+   + + S G +    ++  +    + I+                    
Sbjct: 371  LNEIREESIDSFAYQELLSPGNLYSALFKDAIFSFLQKIRSTYLIEIRSKSGEKNKESKN 430

Query: 490  --ISSVDIDSVMPQDLINAKPVVSAVCEFFCS-------------SQLSQLEEHVNSLSR 534
                  D          N   +   +  F  +             S  + + + +N    
Sbjct: 431  GVNLLRDTAYFKSVLSKNISMIPKRLQYFMATGNVKTTQLDLQQLSGWTVVADRLNFNRF 490

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ++H R   A+ +G         ++R +    +G +CP  T +G   GL+  L+       
Sbjct: 491  LSHFR---AVHRGQFFTTMKTTDVRKLTGETWGFLCPVHTPDGEPCGLLLHLSQDCIPVT 547

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
                +   R++ +  +++ +                        S  + L          
Sbjct: 548  QWDSQETLRRLRNYLISHGI------------------------SCDDGLGSLSSTWGIE 583

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
               R+ +   D +    V +   ++  +  +D           +                
Sbjct: 584  SSSRDDLYSPDLTKSIPVMLDGRVLFHIPREDFMVWENKLRTLKWQTNPSVLPVHAEIAC 643

Query: 715  MESVVAKSSGAAIV-AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            +       SG  I  A    +   +      +  +     P  +           R +  
Sbjct: 644  VPPDSGMFSGIYIFTAPGRLVRPIMHLETAQVDWIGPLGQPWMNIGVTEEE---TRKSTK 700

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--E 831
                Q+ L+ + D      +  D  +         R +    + +       S ++S   
Sbjct: 701  LLEIQKRLIGISDTESEEQLKNDLKALKKLIKDNDRVLSSVPVNYTHMELHPSTILSVTA 760

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             ++            ++       +G      + P  ++  +  +               
Sbjct: 761  SLIPYAHHNQSPRNMYQCQMLKQTMGT--PCLNHPYRTDNKMYRL---------LTPQEP 809

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             I+    +  G S        + A+      D+ D  +   S     +    ++      
Sbjct: 810  TIITKGYSSFGFSEYPTGTNAIVAVMSYSGYDMEDAMILNKSSYDRGMFHACVYKTK--- 866

Query: 952  KNERSISVEREQIELLARDKDDEQVILDR---NIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                   +         +  D E         +    + E+        G +  K S + 
Sbjct: 867  -------IISAAPPSATKKSDAESYFFHNIGPDGELVVKELSADGLPNIGQRLTKGSPIC 919

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              + I               +     VE +          L+    +       G     
Sbjct: 920  RVERIGSGGGPSNATIQTYHDDEVAFVEKINRIASGISIELQQ--DSLSGGGGDGASSSS 977

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G    V + + + R    GDK A RHG KGI+S + P E+MPF + G   DI+ NP G P
Sbjct: 978  GYGEKVSIKLRIVRNPMVGDKFASRHGQKGILSMLWPQENMPFSESGMVPDILFNPHGFP 1037

Query: 1129 SRMNVGQIFETHLGWACVGLGKK-IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            SRM +G + E+  G A    G + + +   +   + D+S                     
Sbjct: 1038 SRMTIGMLLESMGGKAACIHGARSLDATPFNINISDDLSRS------------------- 1078

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                      E  K+G             +     L  A     G   LY+G+TG     
Sbjct: 1079 ------EENCEDDKAGEKT--------TVDYFGKALERAGFQYYGCEPLYNGMTGVELPC 1124

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G IY  +L HMV+DK   R+TG    +T+QP+ G+   GG R GEME   + +YG 
Sbjct: 1125 HIFMGVIYYQRLRHMVADKAQVRATGPIDALTRQPVKGRKRHGGIRFGEMERDSLISYGV 1184

Query: 1308 AYVLQEMLTIKSD 1320
            + +L + L I SD
Sbjct: 1185 SSILVDRLLICSD 1197



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 117/823 (14%), Positives = 235/823 (28%), Gaps = 189/823 (22%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG----AAML-------EFVSY-- 79
              S++ FL +          GL+   K++  I   SG       L       E++    
Sbjct: 16  HIESFNTFLSV----------GLKNIVKNLPKIYVDSGFIQDDCELNAAYSPAEYLRIGV 65

Query: 80  ---EFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
              +   P          K          ++Y+ PL +                S+  + 
Sbjct: 66  TSAKIGKPIFGNSESSGTKLTPQHARNGHISYSAPLWLEF---------EGYNSSLDTVS 116

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV--VSQ---- 156
           + SIY G +P+M K                         G F+I G +R++  V Q    
Sbjct: 117 KHSIYAGTIPIMVKSSSCHLFGLGTKELVEKGEDPNEVGGYFIINGNERVIRYVIQQRCN 176

Query: 157 ----LHR-------SPG----IHFDHDKGRASLSGKLLYAC-------RIIPDQGLWMDI 194
               L R       S G    +     +   + +   LY         R++ ++  W+  
Sbjct: 177 YPIGLKRPRFATFDSFGSEYAVLMRSLRDDGTSTANYLYGTSDHQCIYRVLLNRQEWL-- 234

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSE----EILSTFYPKIVYSQRGDFWCFP 248
                            +P    LMA+G   DS     +IL    PK             
Sbjct: 235 -----------------IPFWPLLMAVGSIYDSNVLRSKILQYCNPKDENLFNTINMLTL 277

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE---KGVKFLGITSDCL-- 303
               D  VG     + V              L +  L  +     +GV F       L  
Sbjct: 278 EWGLDNSVGVDAEFNSVSFGNKGP--GDTDILENRYLHQIGRLVWEGVAFHLPPGSLLQE 335

Query: 304 CGLYVAEDIVNGETGEIYIE------AGDVIDEKSLEEIFHSEIRDIPI--LYVDSVNNN 355
            G ++ ++ V     E   +          + +  L EI    I       L       +
Sbjct: 336 AGRFLIDNYVLVHLEEWNAKLECLILMFIKLIKLQLNEIREESIDSFAYQELLSPGNLYS 395

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF-----------DSD 404
           A  ++ + +   K R   L++I       +  + +    + +  +F              
Sbjct: 396 ALFKDAIFSFLQKIRSTYLIEIRSKSGEKNKESKNGVNLLRDTAYFKSVLSKNISMIPKR 455

Query: 405 KYDLSTVGRVKMN---------MRLNLDTPDDVRHIRKEDIIAIIKILVDLR-------- 447
                  G VK             +  D  +  R +     +   +    ++        
Sbjct: 456 LQYFMATGNVKTTQLDLQQLSGWTVVADRLNFNRFLSHFRAVHRGQFFTTMKTTDVRKLT 515

Query: 448 -NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G +  +          +  + ++   +     + +++   + +    +   D + +
Sbjct: 516 GETWGFLCPVHTPDGEPCGLLLHLSQDCIPVTQWDSQETLRRLRNYLISHGISCDDGLGS 575

Query: 507 KPVVSAV----CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
                 +     +   S  L++    +     + H  R   +      R         V 
Sbjct: 576 LSSTWGIESSSRDDLYSPDLTKSIPVMLDGRVLFHIPREDFMVWENKLRTLKWQTNPSVL 635

Query: 563 PTHYGRIC-----------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           P H    C              T+ G  +  +  L + A+V+  G +  P+    +  VT
Sbjct: 636 PVHAEIACVPPDSGMFSGIYIFTAPGRLVRPIMHLET-AQVDWIGPLGQPWM---NIGVT 691

Query: 612 NDVVYLSA--MEEENRYIAQANSSLDE--DGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            +    S   +E + R I  +++  +E             +     +         ++  
Sbjct: 692 EEETRKSTKLLEIQKRLIGISDTESEEQLKNDLKALKKLIKDNDRVLSSVPVNYTHMELH 751

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           P  ++S+ ASLIP+  ++ S R +  C M +Q +       P+
Sbjct: 752 PSTILSVTASLIPYAHHNQSPRNMYQCQMLKQTMGTPCLNHPY 794


>gi|242392272|dbj|BAH80373.1| RNA polymerase subunit B' [Halorubrum saccharovorum]
          Length = 609

 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 126/586 (21%), Positives = 201/586 (34%), Gaps = 95/586 (16%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              +  D     ++LVA            + I  ++V       I   E     R T    
Sbjct: 100  YVEFIDAEEEEDILVAVDEEDVTEDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAG 159

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
              + +    +     +   +     +        +                +  + A+  
Sbjct: 160  --MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMS 216

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  ++ D  L +  G     +    F R    +  R    + ++ E+  +D       +
Sbjct: 217  YEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQEDRFEIPDQD-------V 268

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                       L     V+      +S+VL           +         + +R     
Sbjct: 269  RGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEPDDMGGLSPQKRRETSVT 328

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                E+         + +               ++ KV V  +R  + GDK A RHG KG
Sbjct: 329  MRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQRVPELGDKFASRHGQKG 376

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   G                
Sbjct: 377  VVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLGGKV-------------- 422

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                      +      TP F G DEE 
Sbjct: 423  ---------------------------------------GSLRGSRVDGTP-FQGEDEEE 442

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++
Sbjct: 443  LRGGLEDHGFKSSGKEVMYSGVTGEKIEAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVL 502

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRT-------- 1326
            T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD     V   T        
Sbjct: 503  TRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDAETVHVSAETGLVAVEDR 562

Query: 1327 ---RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               RVY+  V G  +D  E     +F +L+ EM ALG+   LE   
Sbjct: 563  EQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLELED 607



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 116/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHPDPEALAEQIREARRRGDVSDMVNVSVKDRTQEVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEVEALERGEVEFEDLIERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTEDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 43.9 bits (102), Expect = 0.22,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+  +A     + ED                    
Sbjct: 85  LERGEVEFEDLIERGYVEFIDAEEEEDILVAVDEEDVTEDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ V  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|313760297|emb|CAY86059.3| RNA polymerase beta subunit [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 310

 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 151/312 (48%), Positives = 200/312 (64%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD++EIL  FY ++V+++   
Sbjct: 61  KRKLPVTTLLYALEGASSAAARAAKVAEGGDVDALEIRGMDADEILGYFYNQVVFTKGPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P  A     G K+   LVD  +GE V E+  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARPFDAE-SFRGLKLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G YVA D+VN ETGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL 
Sbjct: 179 IGRYVAHDLVNMETGEIYAEAGEELTEVRLEALEEAGVDQLPTLAVDASN-GPWIRNTLT 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R+DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD
Sbjct: 238 VDKNTSREDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLD 297

Query: 424 TPDDVRHIRKED 435
            PD +R +RKED
Sbjct: 298 APDTIRVLRKED 309


>gi|81171097|gb|ABB58775.1| RNA polymerase beta subunit [Mycoplasma felis]
          Length = 597

 Score =  313 bits (801), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 199/451 (44%), Positives = 292/451 (64%), Gaps = 10/451 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  +F
Sbjct: 2   NPLAEISNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNYATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+  GF++TPY KV +G +   D+ YL+A EE     AQ++  +DE        +  R
Sbjct: 62  AQVDKLGFLKTPYYKVNNGVIDYEDLRYLTASEEIGYSFAQSSVEVDESNRIVSPSLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                ++   E +DF++ S +Q+VS+AA+ IPFLENDD+NR LMG NMQRQAVPL++ EA
Sbjct: 122 RDYNYLIGSPEDVDFLEVSSRQMVSLAAAGIPFLENDDANRALMGSNMQRQAVPLIETEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E+ +A+ S   +VAK +G+V  VD  +  I       D      D Y L  F+
Sbjct: 182 PLIATGIENDIARYSSYNLVAKNSGVVTYVDGSK--IHIERPGSDNLKGITDKYSLRNFE 239

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T V QRP+VK G +V   D++ DG S   G+LALG+N+LV F  W+GYNFED+++
Sbjct: 240 RSNQGTIVQQRPIVKKGQKVEAGDLLTDGSSFKDGELALGKNVLVGFTTWNGYNFEDAII 299

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DVFTSIHIEE  +  R ++ G + +TRDIP VS+  ++++D+ GI+ VG+EV
Sbjct: 300 INERLVKDDVFTSIHIEEQIIQFRSSRAGNDTLTRDIPQVSKYSIRHLDDHGIVRVGSEV 359

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PK E   + EEKLL+ I   ++ + +DTSL+V +G  GTV+ V + +R 
Sbjct: 360 LPGDVLVGRTSPKAEENPSQEEKLLQNILNVRSSNTKDTSLKVKNGHGGTVIHVEVLSRD 419

Query: 949 GIDKNERSISVEREQIELLARDKDDEQVILD 979
             D       +  E IE + +    ++  + 
Sbjct: 420 NND-------LLDEGIEKIVKVSVAQKRKIK 443



 Score =  293 bits (750), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 124/413 (30%), Positives = 179/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+  G +V  GD+L    + K +  +   + +L         +  D  +     V   V 
Sbjct: 252  IVKKGQKVEAGDLLTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAIIINERLVKDDVF 310

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I     I +   S +        + +        LD +   R+   +   + + G  
Sbjct: 311  -TSIHIEEQIIQFRSSRAGNDTLTRDIPQVSKYSIRHLDDHGIVRVGSEVLPGDVLVGRT 369

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     S +   +  ++     +   +     V++          +L           
Sbjct: 370  SPKAEENPSQE--EKLLQNILNVRSSNTKDTSLKVKNGHGGTVIHVEVLSRDNN------ 421

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
               D +  G+ ++VKV VA KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DGTP+DI
Sbjct: 422  ---DLLDEGIEKIVKVSVAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDGTPLDI 478

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            +LNP GVPSRMN+GQI E HLG A   LG+K  +   D     DI               
Sbjct: 479  MLNPQGVPSRMNIGQILELHLGMAAKKLGEKFVTPSFDGVKKTDIESAL----------- 527

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                  I + L       SG+ ++ D +
Sbjct: 528  --------------------------------------IEAGLDK-----SGKQVVIDPI 544

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TG  FD+P++VG +YMLKLNHMV DK++ RS G YSL+TQQPLGGKS  GGQR
Sbjct: 545  TGNKFDKPISVGIMYMLKLNHMVDDKMHGRSVGPYSLITQQPLGGKSQNGGQR 597


>gi|269912725|emb|CAZ65633.1| RNA polymerase beta subunit [Acetobacter aceti NBRC 14818]
          Length = 309

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 143/311 (45%), Positives = 193/311 (62%), Gaps = 28/311 (9%)

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R++VSQ+HRSPG+ FDHDKG+   SGK L++ R+IP +G W+D EFD+KD+I+VRIDR+
Sbjct: 1   ERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFSARVIPYRGSWLDFEFDAKDLIYVRIDRK 60

Query: 210 RKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDF 244
           RK+P T+ L AL                         GMDS+EIL  FY K+++ +    
Sbjct: 61  RKLPATTLLYALEGANSEAARKKKAEEGGDVASMDIGGMDSDEILDYFYGKVIFQKTAKG 120

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
           W           G K+ S L+D D+GE V E+  KLT+  ++ + E   K + +T   L 
Sbjct: 121 WARAFDPE-AFKGQKLLSDLIDADSGEVVAEADTKLTARAVRKIAET-TKEVLVTEADLL 178

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G ++A DIVN  TGEIY E G+ + E  L  +  + I ++P L VD  N   +IRNT+  
Sbjct: 179 GRFIAHDIVNPNTGEIYGEGGEELTEARLLALEEAGITELPTLAVDQAN-GPWIRNTMTV 237

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           DKN  R +AL+DIYRVMRPG+  T   AE+MF  LFFD D+YDLS+VGRVKMNMRL L+ 
Sbjct: 238 DKNNSRDEALIDIYRVMRPGEPPTAETAEAMFRSLFFDPDRYDLSSVGRVKMNMRLGLEC 297

Query: 425 PDDVRHIRKED 435
           PD VR +RKE 
Sbjct: 298 PDTVRVLRKET 308


>gi|291088180|dbj|BAI82371.1| RNA polymerase subunit B' [Halarchaeum acidiphilum]
          Length = 608

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 119/584 (20%), Positives = 199/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LVA       +    + I  +++       +   E     R T      
Sbjct: 101  EYIDAEEEEDILVAVDEDELTDDHTHLEIDPQLIFGIGAGMVPYPEHNASPRITMGAG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +    A+   +
Sbjct: 159  MMKQSLGLPAANYRIRPDTR-QHIMHYPQAAMVNTQTTEQIGYDDRPAGQNFTVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+   D       +  
Sbjct: 218  GFNIEDALVMNKGSVE-RALGRSHFFRTYEGEERRYPGGQEDRFEVPGED-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +        L     V+      +++VL           +    A    + +R       
Sbjct: 270  SRGEDAYTHLDEDGMVNPETQVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E          + +               ++ KV V  +R  + GDK A RHG KG++
Sbjct: 330  SGEDGVVDTVTVMEGE------------DGSKLAKVSVRDERVPELGDKFASRHGQKGVI 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF ++G   D+++NP  +PSRM VG + E   G A    G+ +       +
Sbjct: 378  GHLAPHEDMPFTEEGVVPDLIVNPHALPSRMTVGHVLEMLGGKAGALDGRSVDGTAFTGE 437

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               +I                                             FD        
Sbjct: 438  DEEEIRGTLEAHG-------------------------------------FD-------- 452

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      SG+  LY G++GE  +  + VG I+  KL HMVS+KV+ARS G   ++T+
Sbjct: 453  ---------SSGKEQLYSGVSGEKIEAQIFVGNIFYHKLYHMVSNKVHARSKGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG---------R-- 1325
            QP  G++  GG RLGEME   +  +GAA VL+E L   SD     + G         R  
Sbjct: 504  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLKERLLESSDQEYVHICGNCGMTAVENREQ 563

Query: 1326 TRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             RVY     G   D        +F +L+ EM+ALG++  LE   
Sbjct: 564  RRVY-CPNCGEETDVHNIEMSYAFKLLLDEMKALGIAPRLELKD 606



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 53/357 (14%), Positives = 114/357 (31%), Gaps = 26/357 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +     +++   R  G+   +    +               +  P L  +D   + 
Sbjct: 17  GTHPDPYELADQIRESRRRGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVVEDGETIA 76

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
              +++      ++ E       +E + A+     +VA     +   D   + I      
Sbjct: 77  DESDVEAVQNGEMEFEDLVEEGKVEYIDAEEEEDILVAVDEDELTD-DHTHLEIDPQLIF 135

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPST 800
              +            + +     + Q           RP  +          + +  +T
Sbjct: 136 GIGAGMVPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHIMHYPQAAMVNTQTT 195

Query: 801 D---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +     D   G+N  VA M + G+N ED++++++  V   +  S     +E   R    G
Sbjct: 196 EQIGYDDRPAGQNFTVAVMSYEGFNIEDALVMNKGSVERALGRSHFFRTYEGEERRYPGG 255

Query: 858 PEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            E+              E+   ++DE G++    +V+   +L+GK +P            
Sbjct: 256 QEDRFEVPGEDVRGSRGEDAYTHLDEDGMVNPETQVDENSVLLGKTSPPRFLEEP----- 310

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              + G      R+TS+ + SG  G V  V +       K  +    +    EL  +
Sbjct: 311 -DDMAGLSPQKRRETSVTMRSGEDGVVDTVTVMEGEDGSKLAKVSVRDERVPELGDK 366



 Score = 48.5 bits (114), Expect = 0.009,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I  +RR   + +      +       V+        P    
Sbjct: 10  YVNGSLVGTHPDPYELADQIRESRRRGDVSEMVNVSVKDRTREVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E           + A  +    ++    +  D      V Y+ A EEE+  +A     L 
Sbjct: 70  EDGE--------TIADESDVEAVQNGEMEFEDLVEEGKVEYIDAEEEEDILVAVDEDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                          ++  P+ +  I A ++P+ E++ S R+ MG  
Sbjct: 122 DDH-----------------------THLEIDPQLIFGIGAGMVPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPAANYRI 173


>gi|89274904|gb|ABD65893.1| RNA polymerase II second largest subunit [Spongipellis pachyodon]
          Length = 901

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 140/906 (15%), Positives = 272/906 (30%), Gaps = 153/906 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 133  RYAQEILQKEMLPHISMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGKKRL 189

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +    + + +     +   
Sbjct: 190  DLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKYSLATGNW 249

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H  H+G +
Sbjct: 250  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNHHWGMV 305

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  + ++   F       + +  + +         EEN +   
Sbjct: 306  CPAETPEGQACGLVKNLSLMSCISVGSFSGPVIEFLEEWGLESL--------EENVHSPT 357

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 358  PTTKVFVNGVWMG---VHRDPVNLVKTIKKLRRKDDISPEVSVVRDTRERELRIYTDAGR 414

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG-AAIVAKRAGIVEQVDAIRIVIRSV 748
            V     +       +K +       +  +  K S  A     + GI+E +DA       +
Sbjct: 415  VCRPLFIVEDEQLAIKKK------HIRMLEDKDSNFAWDDMIKKGIIELLDAEEEETAMI 468

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +   +           + +++     + L   G  +         PS  LG     
Sbjct: 469  CMTPEDLEASRL--AGAGMDQEDESEFDPSKRLRTTGSSIHTWTHCEIHPSMILG----- 521

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N       S R   +       +  +                     
Sbjct: 522  --VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFLSRM------------- 560

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 561  ----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 610

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    I+ R  +D  ++S   + E+ E   RD          +       
Sbjct: 611  IMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGL 669

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G N         K+  +  D      R++          ++     +  Q       
Sbjct: 670  IAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI---- 725

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   + VK+ V   R  Q G K A RHG KG +      ED
Sbjct: 726  ----------------TTNAEGQKFVKIGVRSTRVPQIGGKFASRHGQKGTIGITYRQED 769

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DIV+NP  +PSRM +G + E  L       G++  +          +S  
Sbjct: 770  MPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKLATLTGQEGDATPFTELTVESVSQY 829

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                +K   +                                                  
Sbjct: 830  LR--QKGYQSRGLEVM-------------------------------------------- 843

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S 
Sbjct: 844  -YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSR 895

Query: 1289 RGGQRL 1294
             GG R 
Sbjct: 896  DGGLRF 901



 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 102/772 (13%), Positives = 218/772 (28%), Gaps = 118/772 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 58  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDNQMLEMLKPCIDDGFVIQDREVA 113

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  +   ++  
Sbjct: 114 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMIHRLLL-A 171

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDAL 374
                 ++  D   +K L+           +L+   + +   Y++  + T K  +   A+
Sbjct: 172 ALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAV 231

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
                        T  +  S+    + D  K   S  G  ++  R    +      R   
Sbjct: 232 KHNT--------ITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT 283

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  I     L N    +         +   + + L     + +      + E +  
Sbjct: 284 PLGREGKIAKPRQLHNHHWGMVCPAETPEGQACGLVKNLSLMSCISVGSFSGPVIEFLEE 343

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++S+      N          F     +    + VN +  I   RR   +        
Sbjct: 344 WGLESL----EENVHSPTPTTKVFVNGVWMGVHRDPVNLVKTIKKLRRKDDISPEVSVVR 399

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
                   ++        P    E   + +              F         D     
Sbjct: 400 DTRERELRIYTDAGRVCRPLFIVEDEQLAIKKKHIRMLEDKDSNFA------WDDMIKKG 453

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDG-------SFTEELVFCRCAGEEILVPREKIDFID 665
            +  L A EEE   I      L+             E                      +
Sbjct: 454 IIELLDAEEEETAMICMTPEDLEASRLAGAGMDQEDESEFDPSKRLRTTGSSIHTWTHCE 513

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ + AS+IPF +++ S R      M +QA+ +                      
Sbjct: 514 IHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFL---------------- 557

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + +  Y       +     +  R      
Sbjct: 558 -------------------------SRMDTMANILYYPQKPLATTRSMEYLKFR------ 586

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N +VA + + GYN EDS+++++  +   +F SI+  
Sbjct: 587 ------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYR 628

Query: 846 EFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +  + + + +   E            +       +++ G+I  G  VN  DI++GK  P
Sbjct: 629 SYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNVNGEDIIIGKTAP 688

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    ++        +    RD S  + S  SG V  V I       K
Sbjct: 689 IPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNAEGQK 733


>gi|57641018|ref|YP_183496.1| DNA-directed RNA polymerase subunit beta [Thermococcus kodakarensis
            KOD1]
 gi|57159342|dbj|BAD85272.1| DNA-directed RNA polymerase, subunit B [Thermococcus kodakarensis
            KOD1]
          Length = 1123

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 111/586 (18%), Positives = 203/586 (34%), Gaps = 95/586 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  PW        + +    +     + +   E     R+T     
Sbjct: 615  IEYLDAEEEENAYVATWPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGM 674

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++ +D  G   +        +    +   G       +  + A+   
Sbjct: 675  AKQSLGLGWANFRIR-VDTRG--HLMHYPQVPLVNSRIMKAVGFEDRPAGQNFVVAVLSY 731

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D  +   + +    +    F R    + +R +  +++  E+ + +       + 
Sbjct: 732  HGYNMEDAVIINKASIERG-LARSTFFRTYEAEEKRYLGGQKDNFEVPSPN-------IQ 783

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              +  +    L     +      +   VL         R+   +F  +   +   V   +
Sbjct: 784  GYLGEKYYRHLDEDGLIFPESKVEGKDVL-------VGRTSPPRFIEEQSSLGSMVLQGR 836

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +   +    E    +K+   + GD       ++VKV V   R  + GDK A RHG KG+
Sbjct: 837  RETSVTVRPSEKGVVDKVIVTETGD-----GTKLVKVTVRDLRIPELGDKFASRHGQKGV 891

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMP+ + G   D+++NP G+PSRM VGQ+ E   G      G+++       
Sbjct: 892  IGLIVPQEDMPWTESGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLTGRRVDGTAFIG 951

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +    +      L                                      +DG      
Sbjct: 952  EPEEKLRKELEELGFKHSGREIM----------------------------YDGIT---- 979

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                                  G   +  + +G IY  +L+HMV+DK++ARS G   ++T
Sbjct: 980  ----------------------GRRLEADIFIGVIYYQRLHHMVADKMHARSRGPVQVLT 1017

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG-------- 1324
            +QP  G++  GG R GEME   +  +GAA +L E L  +SD          G        
Sbjct: 1018 KQPTEGRAREGGLRFGEMERDVLIGHGAAMLLIERLLEESDKTEVWVCESCGHLALEDKR 1077

Query: 1325 RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R +VY   V G D    +     +F +L+ E++A+ +   L     
Sbjct: 1078 RGKVY-CPVCGEDERISKVEMSYAFKLLLDELKAMVIRPSLRLKDR 1122



 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 152/982 (15%), Positives = 298/982 (30%), Gaps = 205/982 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
            +     SY+ F+          + GLQ        +        ++F       P+F  
Sbjct: 30  FVRQHLDSYNAFI----------DHGLQDVVNEFGEVVPDIPNFKVKFGKIRIGQPEFQE 79

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + +  +V  +++              + +G+LP+M
Sbjct: 80  AQGQRRPLYPMDARIRNLTYSAPLYLEMIPVVNGIEQEPV----------EVRIGELPIM 129

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKGR 171
            K                         G F+I G +R++VS    +P    +  D  + +
Sbjct: 130 LKSKACRLYGLSDEELIKLGEDPKDPGGYFIINGSERVIVSIEDLAPNKTLVERDERQNK 189

Query: 172 ASLSGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPV--TSFLMALGMDSE 226
                      ++   +      + +E     I++V I    K PV     + ALG+ ++
Sbjct: 190 V--------VAKVFSYRHGYRALITVERKKDGILYVTIPNVPK-PVKFVYVMRALGLLTD 240

Query: 227 -EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            EI+          Q         +  D    +    +L  I       +  +       
Sbjct: 241 KEIVEAVSDDPRIQQ-----VLFDNLEDASDISTQEEALDYIGRLALPGQPKEYRLRRAE 295

Query: 286 KSLKEKGVKFLGITSD------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             +    +  +G+  +         G+  A  ++    G    +  D    K L+     
Sbjct: 296 HIIDNNLLPHMGVDPENRRAKAYYLGMM-ALKVLELSLGLRGEDDKDHYANKRLKLAGDL 354

Query: 340 EIRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                 + +   V +  Y   +      +    ++    +   +RP DV +  +  ++  
Sbjct: 355 LKDLFRVAFGQLVKDMQYQMTKTYQRKGERYTFENIQRFVRNSIRP-DVLSERIEHALAT 413

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             +          + R      L+         + ++      + L       G I   +
Sbjct: 414 GSWPGGRTGVSQLLDRTNYMSTLSHLRRVTSP-LSRDQPHFEARDLHGTH--WGRICPTE 470

Query: 458 NLGNRRVRSVGEM-LKNQYRLG-LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                    V  + L +Q   G   R  R    ++  V I+   P               
Sbjct: 471 TPEGPNCGLVKNLALMSQITTGIPEREVREYLMKMGVVPIEERRP--------APGLYRV 522

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +     +  +E+    + RI   RR   +            E+++V+             
Sbjct: 523 YLNGVLIGTVEDGRKLVERIRADRRAGKISDVINVALYEDEEVKEVYINS-----DDGRV 577

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               I + +      R +  G I+       D      + YL A EEEN Y+A       
Sbjct: 578 RRPLIVVENGKPKLTREHVEG-IKNGTLTWSDLIRMGVIEYLDAEEEENAYVAT------ 630

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                  E+   ++  P  ++ I ASL+P+ E++ + R   G  
Sbjct: 631 -----------------WPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAG 673

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +Q++ L  A                                                +
Sbjct: 674 MAKQSLGLGWANFRI-----------------------------------------RVDT 692

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +  Y               Q PLV                +    D   G+N +VA 
Sbjct: 693 RGHLMHYP--------------QVPLVNS----------RIMKAVGFEDRPAGQNFVVAV 728

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP----EEITRDIP-NVSE 870
           + +HGYN ED+++I++  +   +  S     +E   +    G     E  + +I   + E
Sbjct: 729 LSYHGYNMEDAVIINKASIERGLARSTFFRTYEAEEKRYLGGQKDNFEVPSPNIQGYLGE 788

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           +  +++DE G+I   ++V   D+LVG+ +P        E+  L ++  +     R+TS+ 
Sbjct: 789 KYYRHLDEDGLIFPESKVEGKDVLVGRTSPPRFIE---EQSSLGSMVLQ---GRRETSVT 842

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           V     G V  V +       K
Sbjct: 843 VRPSEKGVVDKVIVTETGDGTK 864


>gi|297184061|gb|ADI20180.1| hypothetical protein [uncultured Sphingobacterium sp. EB080_L08E11]
          Length = 241

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 121/238 (50%), Gaps = 9/238 (3%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
            R  F         PD +++Q  S+  F  +   P ER  EGL   F   FPI+      
Sbjct: 10  ERINFSSTAIKTAFPDFLDIQLKSFMDFFQIETKPSERSEEGLYRVFAENFPISDSRNNF 69

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           +LEF+ Y  DPP++   +C+ R LT+ VPLK  L+L   D +       +     Q +Y+
Sbjct: 70  VLEFLDYFVDPPRYSERECIERGLTFCVPLKARLKLYCTDPEHEDFETIV-----QDVYL 124

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           G +P M+  GTF++ G +RI+VSQLHRSPG+ F         +G  LY+ RIIP +G W+
Sbjct: 125 GTIPYMSPRGTFIVNGAERIIVSQLHRSPGVFFGQS---YHANGTKLYSARIIPFKGSWI 181

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPL 249
           +   D   +++  IDR++K+PVT+ L ++G + + +IL  F                +
Sbjct: 182 EFATDINQVMYAYIDRKKKLPVTTLLRSIGFERDKDILEIFDLAEEVKVSKASLKRSI 239


>gi|226897644|gb|ACO90271.1| RNA polymerase beta subunit gene [Bacillus halmapalus]
          Length = 365

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 207/342 (60%), Positives = 262/342 (76%), Gaps = 1/342 (0%)

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T  + YL+A EE+N  +AQAN+ L EDG+F ++ V  R  GE  +V  E+ID++D SPKQ
Sbjct: 1   TGQIDYLTADEEDNYVVAQANARLGEDGTFLDQNVVARFRGENTVVISERIDYMDVSPKQ 60

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS A + IPFLENDDSNR LMG NMQRQAVPL++ E+P VGTGME V A+ SGAA++ K
Sbjct: 61  VVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPESPIVGTGMEHVSARDSGAAVICK 120

Query: 731 RAGIVEQVDAIRIVIR-SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
             G+VE+V+A  + +R   E D       +D YR+ KF RSNQ TC NQRP+V VGD+V 
Sbjct: 121 YPGVVERVEAREVWVRRMEEVDGQQIKGNLDKYRMQKFIRSNQGTCYNQRPIVSVGDQVT 180

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + +I+ADGPS + G+LALGRN++V FM W GYN+ED++++SER+V +DV+TSIHIEE+E 
Sbjct: 181 KGEILADGPSMEKGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYES 240

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITRDIPNV EE LKN+D+ GII VGAEV  GD+LVGK+TPKG + +T E
Sbjct: 241 EARDTKLGPEEITRDIPNVGEEALKNLDDRGIIRVGAEVKDGDLLVGKVTPKGVTELTAE 300

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 301 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKVFNREDGD 342



 Score = 46.2 bits (108), Expect = 0.045,   Method: Composition-based stats.
 Identities = 45/280 (16%), Positives = 93/280 (33%), Gaps = 27/280 (9%)

Query: 816  MPWHGYNFEDSMLISER--MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            M         + +I +   +V       + +   E +      G  +  R    +     
Sbjct: 105  MEHVSARDSGAAVICKYPGVVERVEAREVWVRRMEEVDGQQIKGNLDKYRMQKFIRSNQG 164

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
               ++  I+ VG +V  G+IL    +   +  +     ++         +  D  +    
Sbjct: 165  TCYNQRPIVSVGDQVTKGEILADGPS-MEKGELALGRNVMVGFMTWDGYNYEDAIIMS-- 221

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
                            + K++   S+  E+ E  ARD       + R+I +   E L   
Sbjct: 222  --------------ERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEEALKNL 267

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED 1051
            +     +      V   DL+      +       +E++   +  E  +   +TS  +   
Sbjct: 268  DDRGIIRVGA--EVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHG 325

Query: 1052 ----RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                    K+   + GD++PPGV +VV+ ++  KR I  G
Sbjct: 326  GGGIVLDVKVFNREDGDELPPGVNQVVRAYIVQKRKISEG 365


>gi|83415469|gb|ABC17942.1| RNA polymerase II second largest subunit [Basidiobolus ranarum]
          Length = 720

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 136/852 (15%), Positives = 255/852 (29%), Gaps = 152/852 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              + +  + + +     +
Sbjct: 2    KRMDPAGPLLAMLFRMLXRKLTKDVGRYLQKCIDSNREFNLTLAVKSNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++  G    P  +V        +   SA    +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSYIS-VGNPSAPVVEVLADWAMESLEQFSANNIADAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N            L+                  +D SP+  +             D
Sbjct: 177  KIFVNGVWVGIHRDPGNLIETMRRFR---------RRVDISPEVSIVRDIRDKEIRFYTD 227

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + RV     +       L+ E        E          +V    GIVE +DA    + 
Sbjct: 228  AGRVCRPLYVVENQRITLRKEHVVALQMREYDGEPFGWQDLV--VNGIVEYLDAEEEEVS 285

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DL 805
             +    +   +   +Y  + +    +    +          V+ +  +     T      
Sbjct: 286  MICMTPEDL-AESRMYSKLGYIPEREADIAS---------RVKSSAALITHTWTHCEIHP 335

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ++      + +P+  +N          M  + +   I++  ++                 
Sbjct: 336  SMILGTCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 376

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  +             +       +   +  + AI      +  
Sbjct: 377  ----------LRMDTMANILYYPQKPLCTTRAMEYLRFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   + +   +    IF R  +D+ ++   +  E+ E   R+       L R  Y +
Sbjct: 427  DSLIMNQTSIDRGLF-RSIFYRSYMDQEKKVGMMVMEEFEKPTRESTLR---LKRGTYEK 482

Query: 986  LM---EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L     I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 483  LEGDGLIAPGTRVSGDDIIIGKTAPIPPDSEELGQRTKTHNKRDASTPLRSTENGIVDQV 542

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        L+ VKV V   R  Q GDK A RHG KG +  
Sbjct: 543  ML--------------------TTNQEGLKFVKVRVRSTRVPQMGDKFASRHGQKGTIGV 582

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF ++G   D+++NP  +PSRM +G + E  L       G +  +        
Sbjct: 583  TYRQEDMPFNREGIVPDLIINPHAIPSRMTIGHMVECLLSKVSTLSGNEGDATPFTEVTV 642

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS                                  K G  V   +F+G         
Sbjct: 643  EAISHALQE-------------------------HGYQKRGFEV---LFNGHT------- 667

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                            G         +  G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 668  ----------------GR---KLTAQIYFGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 708

Query: 1283 LGGKSNRGGQRL 1294
            + G+S  GG R 
Sbjct: 709  VEGRSRDGGLRF 720


>gi|269913251|emb|CAY86052.1| RNA polymerase beta subunit [Asaia siamensis]
          Length = 311

 Score =  312 bits (800), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 145/313 (46%), Positives = 200/313 (63%), Gaps = 28/313 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EIL+ FY  + +++  
Sbjct: 61  RKRKLPVTTLLYALEGEHSIAARAAKAAEGGDVESMAIRGMDQDEILAYFYGTVPFTRMP 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
             W  P        G K+   L D DTGE V E+  KLT+ +++ + E   K + +    
Sbjct: 121 KGWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMVRKIAET-TKDVLVGRAD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           L G ++A+D+VN ETGEIY EAG+ + E  LE +    + ++P+L VDS ++  +IRNTL
Sbjct: 179 LLGRFMAQDLVNEETGEIYAEAGEELTEARLEALEELGVTELPMLAVDS-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +
Sbjct: 238 AVDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEV 297

Query: 423 DTPDDVRHIRKED 435
           D PD +R +RKED
Sbjct: 298 DAPDTMRVLRKED 310


>gi|4867817|emb|CAB43066.1| RNA polymerase II [Gardneria angustifolia]
          Length = 261

 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 103/237 (43%), Gaps = 54/237 (22%)

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             Q GDK + RHG KG V      EDMPF  +G   DI++NP  +PSRM +GQ+ E  +G 
Sbjct: 59   PQIGDKFSSRHGQKGTVGMTYTQEDMPFTVEGITPDIIVNPHAIPSRMTIGQLIECIMGK 118

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                +GK+                                                    
Sbjct: 119  VAAHMGKEGD-------------------------------------------------- 128

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +TP F     + I+  L        G   +Y+G TG P    + +G  Y  +L HMV
Sbjct: 129  ---ATP-FTDVTVDNISRALHKCGYQMRGFERMYNGHTGRPLTATIFLGPTYYQRLKHMV 184

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 185  DDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 241


>gi|581388|emb|CAA51727.1| DNA-directed RNA polymerase [Methanococcus vannielii]
          Length = 614

 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 133/325 (40%), Gaps = 82/325 (25%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ KV V   R  + GDK A RHG KG++  ++P ED+PF +DG   D+++NP  +P
Sbjct: 346  EGNRLGKVRVRDLRVPEFGDKFASRHGQKGVIGLVVPQEDLPFTEDGVIPDLIINPHAIP 405

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +        G     +G K+ SL                                 
Sbjct: 406  SRMTI--------GQVLEMIGGKVGSLECRRVDGT------------------------- 432

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                 +F G  E A+   L       SG+  +YDG TG   +  
Sbjct: 433  ---------------------IFSGEGEWALRHALENYGFTHSGKETMYDGKTGRKLECE 471

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA
Sbjct: 472  IFVGVAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAA 531

Query: 1309 YVLQEMLTIKSD---D----------------------VVGRTRVYESIVAGNDTFETGT 1343
             +L+E L  +SD   D                      V G +   E I           
Sbjct: 532  LLLKERLLDESDPHEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKI 588

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
              +F +L+ E++++G+   L+    
Sbjct: 589  AYAFKLLLDELKSMGIDPKLKLKDR 613



 Score = 93.2 bits (230), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 74/420 (17%), Positives = 131/420 (31%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +  N +  +   RR   L            E  D+H +  G   + P    E     L +
Sbjct: 22  DPENLVKSLRIQRRSGKLSPN--TSISFNEESNDIHISTDGGRAVRPLVVVENGFSKLTN 79

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            L      N      T    V     T  + +L A EEEN  IA  N  +  +       
Sbjct: 80  ELLEKVNNNEL----TFEYLVK----TGVIEFLDAEEEENARIAMYNDEITFEN------ 125

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              ++  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 126 -----------------THVEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMGKQSLGIP 168

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 169 MANIKW-----------------------------------------RMDTRGHLLHYP- 186

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 187 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 223

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +EE  +N+ + 
Sbjct: 224 DAFVINKASLERGLGRSTFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEEAYRNLGDD 283

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + +EV  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 284 GLIDLESEVRSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGVV 336


>gi|254485755|ref|ZP_05098960.1| DNA-directed RNA polymerase, beta subunit [Roseobacter sp. GAI101]
 gi|214042624|gb|EEB83262.1| DNA-directed RNA polymerase, beta subunit [Roseobacter sp. GAI101]
          Length = 309

 Score =  312 bits (800), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 152/230 (66%), Gaps = 3/230 (1%)

Query: 104 ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGI 163
           +  R I           ++KDIKEQ ++MGD+PLMT +GTFV+ G +R++VSQ+HRSPG+
Sbjct: 37  VRWRAIKSRFTREVRRVAVKDIKEQDVFMGDMPLMTPNGTFVVNGTERVIVSQMHRSPGV 96

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM 223
            FDHDKG+   SGKLL+ACRIIP +G W+D EFD+KDI+  RIDRRRK+PVT+ L ALG+
Sbjct: 97  FFDHDKGKTHSSGKLLFACRIIPYRGSWLDFEFDAKDIVFARIDRRRKLPVTTLLYALGL 156

Query: 224 DSEEILSTFYPKIVYSQR-GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
           D E I+  +Y  + Y+ + G+ W  P    D + G + +  L+D  TGE + E GKK+T 
Sbjct: 157 DQEAIMDAYYDTVTYTLKAGEGWVAPFYP-DRVRGTRPTYDLIDAATGEVLFEKGKKVTP 215

Query: 283 GLLKSLKEKG-VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
             +K L ++G V  L +  + + G + A DI+N ETG IY+E GD +  +
Sbjct: 216 RAVKQLVDEGKVSELVLPFEHIVGKFAARDIINEETGAIYVEPGDEMTLE 265


>gi|315301211|ref|ZP_07872462.1| DNA-directed RNA polymerase, beta subunit [Listeria ivanovii FSL
           F6-596]
 gi|313630420|gb|EFR98302.1| DNA-directed RNA polymerase, beta subunit [Listeria ivanovii FSL
           F6-596]
          Length = 182

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 77/200 (38%), Positives = 121/200 (60%), Gaps = 22/200 (11%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWMDIEFDSKDI 201
             +IP++G W++ E D+KD+
Sbjct: 163 STVIPNRGAWLEYETDAKDV 182


>gi|298674728|ref|YP_003726478.1| DNA-directed RNA polymerase subunit B [Methanohalobium evestigatum
            Z-7303]
 gi|298287716|gb|ADI73682.1| DNA-directed RNA polymerase subunit B [Methanohalobium evestigatum
            Z-7303]
          Length = 604

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 107/583 (18%), Positives = 186/583 (31%), Gaps = 94/583 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     N  +A            + I   M+       +   E     R+T      
Sbjct: 98   EYLDAEEEENAYIALYASDLTPEHTHLEIDPSMILGICTGMVPYPEHNAAPRNTMGAA-- 155

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +S    + +       V                         +  + A+   +
Sbjct: 156  MVKQCVGMSTSN-QKLRPDTRAHVLHYPQKALTKTQPADSIHFDERPAGQNFVVAVMSYE 214

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     +    +    F R    +  R    + ++ E+   D          
Sbjct: 215  GYNIEDALVFNKGSIERG-LARSHFLRTFEGEERRYAGGQEDKFEIPDSDY--RGARGAE 271

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
               +   + L     V+ P             + E                   VE  + 
Sbjct: 272  AYANLDEDGLVNPETVAAPNDVLIGKTSPPRFLEEQSDFGL------------AVEQRRE 319

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T +S  +    N I              R+ KV V  +R  + GDK A RHG KG++
Sbjct: 320  SAITMRSNEKGIVDNVIL------TESINGTRLAKVKVRDQRVPEIGDKFASRHGQKGVI 373

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I+P +DMPF +DG   D+++NP  +PSRM VG + E   G      G+++ +     +
Sbjct: 374  GLIVPYQDMPFTEDGLVPDLIVNPHAIPSRMTVGHVLEMIGGKVGSMEGRRVDATAFSGE 433

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            +  ++                                            VF         
Sbjct: 434  SEEELRNGLRDYGFSHTGKE-----------------------------VFT-------- 456

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                             DG+TG+        G I   KL+HMV+ K++ARS G   ++T+
Sbjct: 457  -----------------DGVTGKKIQADTFSGVILYQKLHHMVASKMHARSRGPVQVLTR 499

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYESIV 1333
            QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G    Y+   
Sbjct: 500  QPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLMDESDKVVQLVCSNCGMIATYDRKQ 559

Query: 1334 A---------GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                        D +      +F +L+ E+++LG++  +    
Sbjct: 560  KMAFCSNCESETDIYPVEMSYAFKLLLDEIKSLGVTPRMGLED 602



 Score = 49.7 bits (117), Expect = 0.004,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 55/195 (28%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           F     +      V  +  I   RR   + Q         +    ++        P    
Sbjct: 7   FLNGELVGTHNNPVELVEDIREQRRNGLISQQVNVALYEDINEIIINSDIGRARRPLIIV 66

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +     +        + N             D      V YL A EEEN YIA   S L 
Sbjct: 67  KDGKPLVTDEQIEQLKNNEITS--------EDLVKQGFVEYLDAEEEENAYIALYASDLT 118

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +                          ++  P  ++ I   ++P+ E++ + R  MG  
Sbjct: 119 PEH-----------------------THLEIDPSMILGICTGMVPYPEHNAAPRNTMGAA 155

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q V +  +    
Sbjct: 156 MVKQCVGMSTSNQKL 170


>gi|73697697|gb|AAZ81465.1| RNA polymerase beta subunit [Mycoplasma buccale]
          Length = 598

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 213/453 (47%), Positives = 291/453 (64%), Gaps = 14/453 (3%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L S
Sbjct: 1   CNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAS 60

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDED-----GSFTE 642
           FA+++ YGFI+TPY KV    V     VYL+A+EE     AQ+   +D D        T+
Sbjct: 61  FAQIDKYGFIQTPYFKVNKSIVDFTKPVYLTAIEETGYSFAQSTVHIDYDKQNKEYKITD 120

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             V  R   E I V   ++DFI  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP
Sbjct: 121 PNVMVRRDNEYIEVSVNEVDFIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVP 180

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           ++  EAP V TG+E+ +AK S   I A + GIV  VD+  I I          +S  +IY
Sbjct: 181 VIYPEAPLVATGVEADIAKYSSTNIRANKDGIVTYVDSSMIKILPT------GSSKTEIY 234

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L  F+RSNQ T ++Q PLV VG E++  D++ DGPS   G+LALG+N+LV F  WHGYN
Sbjct: 235 YLRTFERSNQGTLIHQIPLVNVGQEIKAGDLLVDGPSMKNGELALGKNVLVGFSTWHGYN 294

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++++SER+V +D++TSIHIEE  +  R +K G + +T DIPN S    + + E GI+
Sbjct: 295 YEDAVILSERLVKDDIYTSIHIEEQTIQFRHSKAGEDILTDDIPNASNYSKRFLGENGIV 354

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            VG+EV+ GDILVG+ +PKGE   TPEEKL+ AIFG+K    +DTSL+V  G +GTVV V
Sbjct: 355 RVGSEVSAGDILVGRTSPKGEENPTPEEKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAV 414

Query: 943 RIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            + +R     ++    +E+     +A+ +  + 
Sbjct: 415 EVLSREYG--DQLEDGIEKIVKVSIAQKRKIKV 445



 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 119/413 (28%), Positives = 179/413 (43%), Gaps = 67/413 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG E+  GD+LV   + K    +   + +L         +  D  +     V    +
Sbjct: 253  LVNVGQEIKAGDLLVDGPSMKN-GELALGKNVLVGFSTWHGYNYEDAVILSERLVKD-DI 310

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E    + +    +  +  L  N   R+   +   + + G  
Sbjct: 311  YTSIHIEEQTIQFRHSKAGEDILTDDIPNASNYSKRFLGENGIVRVGSEVSAGDILVGRT 370

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q     +     V+        +  +L   +       
Sbjct: 371  SPKGEENPTPE--EKLMAAIFGQKTASRKDTSLKVKHGHNGTVVAVEVLSREY------- 421

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG+VS +LP E+MP+L+DGTP+D+
Sbjct: 422  --GDQLEDGIEKIVKVSIAQKRKIKVGDKMAGRHGNKGVVSIVLPVEEMPYLEDGTPLDM 479

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   +G K  + + D   +  I  +    +   G   
Sbjct: 480  VLNPQGVPSRMNIGQVLELHLGLAAKKMGIKFVTPVFDGITHNQIKDILEEADLPSGGKQ 539

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
            +                                                  GQ       
Sbjct: 540  YV-----------------------------------------------YDGQ------- 545

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            TGE FD P++VG +YMLKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 546  TGEKFDHPISVGVMYMLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 598


>gi|150399423|ref|YP_001323190.1| DNA-directed RNA polymerase subunit B' [Methanococcus vannielii SB]
 gi|160370008|sp|P41557|RPOB1_METVS RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|150012126|gb|ABR54578.1| RNA polymerase Rpb2 domain 6 [Methanococcus vannielii SB]
          Length = 611

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 133/325 (40%), Gaps = 82/325 (25%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ KV V   R  + GDK A RHG KG++  ++P ED+PF +DG   D+++NP  +P
Sbjct: 343  EGNRLGKVRVRDLRVPEFGDKFASRHGQKGVIGLVVPQEDLPFTEDGVIPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +        G     +G K+ SL                                 
Sbjct: 403  SRMTI--------GQVLEMIGGKVGSLECRRVDGT------------------------- 429

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                 +F G  E A+   L       SG+  +YDG TG   +  
Sbjct: 430  ---------------------IFSGEGEWALRHALENYGFTHSGKETMYDGKTGRKLECE 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA
Sbjct: 469  IFVGVAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAA 528

Query: 1309 YVLQEMLTIKSD---D----------------------VVGRTRVYESIVAGNDTFETGT 1343
             +L+E L  +SD   D                      V G +   E I           
Sbjct: 529  LLLKERLLDESDPHEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKI 585

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
              +F +L+ E++++G+   L+    
Sbjct: 586  AYAFKLLLDELKSMGIDPKLKLKDR 610



 Score = 93.2 bits (230), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 74/420 (17%), Positives = 131/420 (31%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +  N +  +   RR   L            E  D+H +  G   + P    E     L +
Sbjct: 19  DPENLVKSLRIQRRSGKLSPN--TSISFNEESNDIHISTDGGRAVRPLVVVENGFSKLTN 76

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            L      N      T    V     T  + +L A EEEN  IA  N  +  +       
Sbjct: 77  ELLEKVNNNEL----TFEYLVK----TGVIEFLDAEEEENARIAMYNDEITFEN------ 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              ++  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 123 -----------------THVEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMGKQSLGIP 165

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 166 MANIKW-----------------------------------------RMDTRGHLLHYP- 183

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 184 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 220

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +EE  +N+ + 
Sbjct: 221 DAFVINKASLERGLGRSTFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEEAYRNLGDD 280

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + +EV  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 281 GLIDLESEVRSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGVV 333


>gi|52694411|emb|CAG38045.1| RNA polymerase beta subunit [Pseudomonas luteola]
          Length = 335

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 186/314 (59%), Positives = 240/314 (76%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
               LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 22  RTTRLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 81

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D   ++++V+LSA+EE N  IAQA+++LDE+    +ELV  
Sbjct: 82  TYARTNQYGFLESPYRVVKDAVASDEIVFLSAIEEANHVIAQASAALDENNRLVDELVAV 141

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++
Sbjct: 142 RHQNEFTVKSPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSD 201

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R    +++   +GVDIY L K+
Sbjct: 202 KPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVANAEVETGEAGVDIYNLTKY 261

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQNTC+NQRPLV  GD + R DI+ADGPSTD+G+LALG+NM VAFM W+G+NFEDS+
Sbjct: 262 TRSNQNTCINQRPLVNKGDVIARGDILADGPSTDMGELALGQNMRVAFMTWNGFNFEDSI 321

Query: 828 LISERMVSEDVFTS 841
           L+SER+V ED FT+
Sbjct: 322 LLSERVVQEDRFTT 335


>gi|195485554|ref|XP_002091138.1| GE12399 [Drosophila yakuba]
 gi|194177239|gb|EDW90850.1| GE12399 [Drosophila yakuba]
          Length = 1137

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 113/621 (18%), Positives = 206/621 (33%), Gaps = 122/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 608  NRRPLVKQHHLNELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 667

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 668  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 716

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 717  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 776

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 777  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 835

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + +E++  
Sbjct: 836  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYVERVMV 877

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 878  SANSEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 935

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 936  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 956

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 957  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1002 TPLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1061

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1062 ISYGASMLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----NVSKISMPYA 1115

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1116 CKLLFQELTSMNVVPKMILEN 1136



 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 122/993 (12%), Positives = 277/993 (27%), Gaps = 204/993 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDE 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 LSTF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           + +           +   +             A + M    V        T     E+ +
Sbjct: 258 IQSLIGIDSKSQNRFGASLLDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEARE 317

Query: 279 -KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             LT+ L     +     +      L    V    ++        +  D    K LE   
Sbjct: 318 LLLTTILAHVPVDNFNLQMKAIYVSLMVRRVMAAELDKT----LFDDRDYYGNKRLELAG 373

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+         I +  +       K A  D+ + MR   ++  +  ES  +
Sbjct: 374 SLLSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAIS 427

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+  +   +            K+               
Sbjct: 428 SGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ-------- 479

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +    +  + +    +  +           +   ++       + +        
Sbjct: 480 -PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIREVSGNPI 538

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  +  +  + N L    +  +        + R         VH ++  R     T  G
Sbjct: 539 NNPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGG 597

Query: 578 HNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   + +   +     +       RK  D  +   + YL   EE + +IA      
Sbjct: 598 RLCRPYVIVENRRPLVKQHHLNELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------ 651

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                + E+ +  R               ++  P  ++ + A L+P+  ++ S R    C
Sbjct: 652 -----WNEDQIEDR------------TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQC 694

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 695 AMGKQAMGMI---------GYNQKNRIDS------------------------------- 714

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N      P+VK                T+   L  G+N  VA
Sbjct: 715 ---------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVA 749

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEG 872
            M + GY+ ED++++++  +       +  +  +   +          +      ++ + 
Sbjct: 750 VMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKV 809

Query: 873 LKN---IDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKA 921
           +     +D  GI+  G +V    I++ K  P        +G+S   P   +  +  G + 
Sbjct: 810 IFKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPYTAVPISYKGPEP 869

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
             V    +   S     +  +    R     ++
Sbjct: 870 SYVERVMVSANSEEDFLIKILLRQTRIPEIGDK 902


>gi|67624195|ref|XP_668380.1| DNA-directed RNA polymerase I polypeptide 2 (RNA polymerase I subunit
            2) [Cryptosporidium hominis TU502]
 gi|54659575|gb|EAL38145.1| DNA-directed RNA polymerase I polypeptide 2 (RNA polymerase I subunit
            2) [Cryptosporidium hominis]
          Length = 1281

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 175/1213 (14%), Positives = 353/1213 (29%), Gaps = 174/1213 (14%)

Query: 175  SGKLLYACRIIPDQGLWMDIE-------FDSKDIIHVRIDRRRKVPVTS------FLMAL 221
            +G + Y+  +      W++ E         SK  I+        +P+             
Sbjct: 92   NGHISYSAPL------WLEFEGYNSSLDTVSKHSIYA-----GTIPIMVKSSNCHLF--- 137

Query: 222  GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
            G+ ++E++                         ++  + +  +          +S     
Sbjct: 138  GLGTKELVEK-GEDPNEVGGYFIINGNERVIRYVIQQRCNYPIGLKRPRFATFDSFGSEY 196

Query: 282  SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            + L++SL++ G               +   ++N +  E  I    ++    +  I+ S +
Sbjct: 197  AVLMRSLRDDGTSTANYLYGTSDHQCIYRVLLNRQ--EWLIPFWPLLMA--VGSIYDSNV 252

Query: 342  RDIPIL------YVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAES 394
                IL        +  N    +      D +     +     +    PGD         
Sbjct: 253  LRSKILQYCNPKDENLFNTINMLTLEWGLDNSVGVDAEFNSVSFGNKGPGDTDILENRYL 312

Query: 395  MFNFL-------FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                        F       L   GR  ++  + +   +    +    ++ I   L+ L+
Sbjct: 313  HQIGRLVWEGVAFHLPPGSLLQEAGRFLIDNYVLVHLEEWNAKLECLILMFI--KLIKLQ 370

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER------------------ 489
              +   + ID+   + + S G +    ++  +    + I+                    
Sbjct: 371  LNEIREESIDSFAYQELLSPGNLYSALFKDAIFSFLQKIRSTYLIEIRSKSGEKNKESKN 430

Query: 490  --ISSVDIDSVMPQDLINAKPVVSAVCEFFCS-------------SQLSQLEEHVNSLSR 534
                  D          N   +   +  F  +             S  + + + +N    
Sbjct: 431  GANLLRDTAYFKSVLSKNISMIPKRLQYFMATGNVKTTQLDLQQLSGWTVVADRLNFNRF 490

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ++H R   A+ +G         ++R +    +G +CP  T +G   GL+  L+       
Sbjct: 491  LSHFR---AVHRGQFFTTMKTTDVRKLTGETWGFLCPVHTPDGEPCGLLLHLSQDCIPVT 547

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
                +   R++ +  +++ +                        S  + L          
Sbjct: 548  QWDSQETLRRLRNYLISHGI------------------------SCDDGLGSLSSTWGIE 583

Query: 655  LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
               R+ +   D +    V +   ++  +  +D           +                
Sbjct: 584  SSSRDDLYSPDLTKSIPVMLDGRVLFHIPREDFMIWENKLRTLKWQTNPSVLPVHAEIAC 643

Query: 715  MESVVAKSSGAAIV-AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            +       SG  I  A    +   +      +  +     P  +           R +  
Sbjct: 644  VPPDSGMFSGIYIFTAPGRLVRPIMHLETAQVDWIGPLGQPWMNIGVTEEE---TRKSTK 700

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS--E 831
                Q+ L+ + D      +  D  +         R +    + +       S ++S   
Sbjct: 701  LLEIQKRLIGISDTESEEQLKNDLKALKKLIKDNDRVLSSVPVNYTHMELHPSTILSVTA 760

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             ++            ++       +G        P +         +  +  +     P 
Sbjct: 761  SLIPYAHHNQSPRNMYQCQMLKQTMG-------TPCL---NYPYRTDNKMYRLLTPQEPT 810

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             I  G  +  G S        + A+      D+ D  +   S     +    ++      
Sbjct: 811  IITKGYSSF-GFSEYPTGTNAIVAVMSYSGYDMEDAMILNKSSYDRGMFHACVYKTK--- 866

Query: 952  KNERSISVEREQIELLARDKDDEQVILDR---NIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                   +         +  D E         +    + E+        G +  K S + 
Sbjct: 867  -------IISAAPPSATKKSDAESYFFHNIGPDGELVVKELSADGLPNIGQRLTKGSPIC 919

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +                 +     VE +          L+    +       G     
Sbjct: 920  RVERTGSGGGPSNATIQTYHDDEVAFVEKINRIASGISIELQQ--DSLSGGGGDGASSSS 977

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G    V + + + R    GDK A RHG KGI+S + P E+MPF + G   DI+ NP G P
Sbjct: 978  GYGEKVSIKLRIVRNPMVGDKFASRHGQKGILSMLWPQENMPFSESGMVPDILFNPHGFP 1037

Query: 1129 SRMNVGQIFETHLGWACVGLGKK-IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            SRM +G + E+  G A    G + + +   +   + D+S                     
Sbjct: 1038 SRMTIGMLLESMGGKAACIHGARSLDATPFNINISDDLSRS------------------- 1078

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                      E  K+G             +     L  A     G   LY+G+TG     
Sbjct: 1079 ------EENCEDDKAGEKT--------TVDYFGKALERAGFQYYGCEPLYNGMTGVELPC 1124

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G IY  +L HMV+DK   R+TG    +T+QP+ G+   GG R GEME   + +YG 
Sbjct: 1125 HIFMGVIYYQRLRHMVADKAQVRATGPIDALTRQPVKGRKRHGGIRFGEMERDSLISYGV 1184

Query: 1308 AYVLQEMLTIKSD 1320
            + +L + L I SD
Sbjct: 1185 SSILVDRLLICSD 1197



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 118/823 (14%), Positives = 236/823 (28%), Gaps = 189/823 (22%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG----AAML-------EFVSY-- 79
              S++ FL +          GL+   K++  I   SG       L       E++    
Sbjct: 16  HIESFNTFLSV----------GLKNIVKNLPKIYVDSGFIQDDCELNAAYSPAEYLRIGV 65

Query: 80  ---EFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
              +   P          K          ++Y+ PL +                S+  + 
Sbjct: 66  TSAKIGKPIFGYSESSGTKLTPQHARNGHISYSAPLWLEF---------EGYNSSLDTVS 116

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV--VSQ---- 156
           + SIY G +P+M K                         G F+I G +R++  V Q    
Sbjct: 117 KHSIYAGTIPIMVKSSNCHLFGLGTKELVEKGEDPNEVGGYFIINGNERVIRYVIQQRCN 176

Query: 157 ----LHR-------SPG----IHFDHDKGRASLSGKLLYAC-------RIIPDQGLWMDI 194
               L R       S G    +     +   + +   LY         R++ ++  W+  
Sbjct: 177 YPIGLKRPRFATFDSFGSEYAVLMRSLRDDGTSTANYLYGTSDHQCIYRVLLNRQEWL-- 234

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALG--MDSE----EILSTFYPKIVYSQRGDFWCFP 248
                            +P    LMA+G   DS     +IL    PK             
Sbjct: 235 -----------------IPFWPLLMAVGSIYDSNVLRSKILQYCNPKDENLFNTINMLTL 277

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE---KGVKFLGITSDCL-- 303
               D  VG     + V              L +  L  +     +GV F       L  
Sbjct: 278 EWGLDNSVGVDAEFNSVSFGNKGP--GDTDILENRYLHQIGRLVWEGVAFHLPPGSLLQE 335

Query: 304 CGLYVAEDIVNGETGEIYIE------AGDVIDEKSLEEIFHSEIRDIPI--LYVDSVNNN 355
            G ++ ++ V     E   +          + +  L EI    I       L       +
Sbjct: 336 AGRFLIDNYVLVHLEEWNAKLECLILMFIKLIKLQLNEIREESIDSFAYQELLSPGNLYS 395

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF-----------DSD 404
           A  ++ + +   K R   L++I       +  + + A  + +  +F              
Sbjct: 396 ALFKDAIFSFLQKIRSTYLIEIRSKSGEKNKESKNGANLLRDTAYFKSVLSKNISMIPKR 455

Query: 405 KYDLSTVGRVKMN---------MRLNLDTPDDVRHIRKEDIIAIIKILVDLR-------- 447
                  G VK             +  D  +  R +     +   +    ++        
Sbjct: 456 LQYFMATGNVKTTQLDLQQLSGWTVVADRLNFNRFLSHFRAVHRGQFFTTMKTTDVRKLT 515

Query: 448 -NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
               G +  +          +  + ++   +     + +++   + +    +   D + +
Sbjct: 516 GETWGFLCPVHTPDGEPCGLLLHLSQDCIPVTQWDSQETLRRLRNYLISHGISCDDGLGS 575

Query: 507 KPVVSAV----CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
                 +     +   S  L++    +     + H  R   +      R         V 
Sbjct: 576 LSSTWGIESSSRDDLYSPDLTKSIPVMLDGRVLFHIPREDFMIWENKLRTLKWQTNPSVL 635

Query: 563 PTHYGRIC-----------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           P H    C              T+ G  +  +  L + A+V+  G +  P+    +  VT
Sbjct: 636 PVHAEIACVPPDSGMFSGIYIFTAPGRLVRPIMHLET-AQVDWIGPLGQPWM---NIGVT 691

Query: 612 NDVVYLSA--MEEENRYIAQANSSLDE--DGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            +    S   +E + R I  +++  +E             +     +         ++  
Sbjct: 692 EEETRKSTKLLEIQKRLIGISDTESEEQLKNDLKALKKLIKDNDRVLSSVPVNYTHMELH 751

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           P  ++S+ ASLIP+  ++ S R +  C M +Q +       P+
Sbjct: 752 PSTILSVTASLIPYAHHNQSPRNMYQCQMLKQTMGTPCLNYPY 794


>gi|79529842|ref|NP_199327.4| NRPC2; DNA binding / DNA-directed RNA polymerase/ ribonucleoside
            binding [Arabidopsis thaliana]
 gi|332007826|gb|AED95209.1| DNA-directed RNA polymerase III subunit C2 [Arabidopsis thaliana]
          Length = 1161

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 91/370 (24%), Positives = 147/370 (39%), Gaps = 75/370 (20%)

Query: 1024 FAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDD---------MPPGVLRV 1073
                D  + + V      ++ ++ S  + R   +  K   G+                  
Sbjct: 840  IRPNDIYINKQVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQVVDRVALCSDKKGQLC 899

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            +K  +   R  + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSRM V
Sbjct: 900  IKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTV 959

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G++ E     A V  G+         ++                                
Sbjct: 960  GKMIELLGSKAGVSCGRFHYGSAFGERSGHAD---------------------------- 991

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                   E I++ L       SG+ +LY G++GEP +  + +G 
Sbjct: 992  ---------------------KVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGP 1030

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IY  KL HMV DK++AR +G   ++T+QP  GKS  GG R+GEME  C+ AYGA+ ++ E
Sbjct: 1031 IYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYE 1090

Query: 1314 MLTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNVLVKEMQAL 1357
             L I SD          G    Y   +          G++      P +  +L +E+Q++
Sbjct: 1091 RLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTCKNGDNIATMKLPYACKLLFQELQSM 1150

Query: 1358 GLSIDLENSR 1367
             +   L+ + 
Sbjct: 1151 NVVPRLKLTE 1160



 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 129/940 (13%), Positives = 285/940 (30%), Gaps = 170/940 (18%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAAMLE 75
           F   PE + +  L++    S+++F+          N G+    K+   IT+    +  L 
Sbjct: 33  FQLVPEFLKVRGLVKQHLDSFNYFI----------NVGIHKIVKANSRITSTVDPSIYLR 82

Query: 76  FVSYEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           F       P           +   C   D+TYA P+ + +  +         AKS KD  
Sbjct: 83  FKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFVNIEYVHG--SHGNKAKSAKD-- 138

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
             ++ +G +P+M                           G F+IKG +++++ Q   S  
Sbjct: 139 --NVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 196

Query: 163 -IHFDHDK-----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVT 215
            I  D DK        + S ++  +  +I             K+ I++ + R  +K+P+ 
Sbjct: 197 RIIIDSDKKGNINASVTSSTEMTKSKTVI----------QMEKEKIYLFLHRFVKKIPII 246

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             L A+GM+S+ EI+        +S            ++ +   K +   ++    +   
Sbjct: 247 IVLKAMGMESDQEIVQMVGRDPRFSASLLP-SIEECVSEGVNTQKQALDYLEAKVKKISY 305

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            +  +     L  L++  +  + +  +          ++     E  +      ++ +++
Sbjct: 306 GTPPEKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRMIEAML------NKDAMD 359

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           +  +   + + +       +   I             +A+ ++  ++     ++      
Sbjct: 360 DKDYVGNKRLEL-------SGQLISLLFEDLFKTMLSEAIKNVDHILNKPIRASRFDFSQ 412

Query: 395 MFNFLFFDSDKYDLSTVGRV--KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNG 449
             N     S    L            R  +      + + +   I  +  +  +      
Sbjct: 413 CLNKDSRYSISLGLERTLSTGNFDIKRFRMHRKGMTQVLTRLSFIGSMGFITKISPQFEK 472

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +    +L   +   +      +     L    ++   +++ + +  +          
Sbjct: 473 SRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGVT 532

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGR 568
              V               +N L    H+R          + RA    E   V       
Sbjct: 533 DLEVLSAEELHTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQH 592

Query: 569 ICPAETSEGHNIGLVSSLTS-FARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENR 625
                +  G     +       +RV  +    ++   R   D      + YL   EE N 
Sbjct: 593 CVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNA 652

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA      + DG+   +        E     +     I+  P  ++ + A LIP+  ++
Sbjct: 653 LIA----LYESDGTTELD--------EGAEAAKADTTHIEIEPFTILGVVAGLIPYPHHN 700

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R    C M +QA+                                           I
Sbjct: 701 QSPRNTYQCAMGKQAMGN-----------------------------------------I 719

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              + +   +   + +Y               QRPL+                      L
Sbjct: 720 AYNQLNRMDTLLYLLVYP--------------QRPLL----------TTRTIELVGYDKL 755

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             G+N  VA M + GY+ ED++++++  +       I +++   M++       +     
Sbjct: 756 GAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIP 815

Query: 866 PNVSEEG--LKNIDECGIICVGAEVNPGDILVGKITPKGE 903
                +   ++ +D+ G+   G  + P DI + K  P   
Sbjct: 816 QRTGPDAEKMQILDDDGLATPGEIIRPNDIYINKQVPVDT 855


>gi|83415485|gb|ABC17950.1| RNA polymerase II second largest subunit [Rhopalomyces elegans]
          Length = 723

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 127/849 (14%), Positives = 248/849 (29%), Gaps = 143/849 (16%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++   +R+   ++ + +    +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLIAGLFRMLFRKLTKDVGKYLQRVIDENRDFNLTLAVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV-YLSAMEEENR 625
            G +CPAET EG   GLV +L     ++           + +  + N    Y +   +  +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMTHISVGAPSRPVIEFLEEWAMVNLDEMYKTGTADATK 177

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                 N       +   +LV              ++ F + S    +      +      
Sbjct: 178  VFV--NGVWVGVHNEPTQLVSVFRNFRRHETAATRV-FQEVSCVSDIRERELWMF----S 230

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+ R      +  Q    +  +   V    +    + SG        G++E +D      
Sbjct: 231  DAGRCCRPLYVVEQNRLKITKQQVRVLDERDEEGKRVSG-WNRLISEGVIEFIDTEEEET 289

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +      + Y     +  +++        +               PS  LG  
Sbjct: 290  AMICMSPEDLAEAREYYETGVPRPPSRDPAA----RISTTIYSHTWTHCEIHPSMILG-- 343

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N       S R   +       +  +                  
Sbjct: 344  -----ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYLTN--------------- 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  +        +    +       +   +    AI      +  
Sbjct: 378  --------YQLRMDTLANIIYYPQKPLVTTRAMEYLKFRDLPAGQNATVAILCYSGYNQE 429

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R  +D+ +++     E+ E   RD          +    
Sbjct: 430  DSVIMNQSSIDRGLF-RSLFYRCYMDQEKKAGVKVMEEFEKPTRDATLRMKHGTYDKLED 488

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  L  +      R++          ++     +  Q    
Sbjct: 489  DGLIAPGVRVSGEDIIIGKTAPLPEESAELGQRTRSHTRRDISTPLRSTETGIVDQVML- 547

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     ++ VKV V   R  Q GDK A RHG KG +     
Sbjct: 548  -------------------TTNQEGVKFVKVRVRSTRIPQMGDKFASRHGQKGTIGITYR 588

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  DG   D+++NP  +PSRM +G + E  L       G +  +          I
Sbjct: 589  QEDMPFSADGIVPDLIINPHAIPSRMTIGHMVECLLSKVSTLTGSEGDATPFTDVTVDAI 648

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S                                        +   F     E I      
Sbjct: 649  SKAL-------------------------------------AVHGFHQRGFEVI------ 665

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 +G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 666  ----YNGHT----GR---KLTAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 714

Query: 1286 KSNRGGQRL 1294
            +S  GG R 
Sbjct: 715  RSRDGGLRF 723



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 88/621 (14%), Positives = 186/621 (29%), Gaps = 96/621 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              I         K  KD    + RV+   +   F++  ++ +    +  KY L   G  
Sbjct: 8   GPLIAGLFRMLFRKLTKDVGKYLQRVI--DENRDFNLTLAVKSTTLTNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 --------MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                   ++KN   +  + +    +  I  ++  +++  D +       A   F     
Sbjct: 125 TPEGQACGLVKNLALMTHISVGAPSRPVIEFLEEWAMVNLDEMYKTGTADATKVFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY---GRICPAETSEGH 578
           +    E    +S   + RR                ++R+     +   GR C        
Sbjct: 185 VGVHNEPTQLVSVFRNFRRHETAATRVFQEVSCVSDIRERELWMFSDAGRCCRPLYVVEQ 244

Query: 579 NIGLVSSLTSFA--RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           N   ++          +  G   + + ++    V   + ++   EEE   I  +   L E
Sbjct: 245 NRLKITKQQVRVLDERDEEGKRVSGWNRLISEGV---IEFIDTEEEETAMICMSPEDLAE 301

Query: 637 DGSFTEELVFCRCAGEE-----ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              + E  V    + +        +        +  P  ++ I AS+IPF +++ S R  
Sbjct: 302 AREYYETGVPRPPSRDPAARISTTIYSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNT 361

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +QA+ +                                 ++D +  +I   +  
Sbjct: 362 YQSAMGKQAMGVYLTNYQL--------------------------RMDTLANIIYYPQKP 395

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           L  + +       +KF+            L   G   + + +I +  S D G        
Sbjct: 396 LVTTRA----MEYLKFRDLPAGQNATVAILCYSG-YNQEDSVIMNQSSIDRGLFRS---- 446

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            + +  +     +  + +              +EEFE   RD              +   
Sbjct: 447 -LFYRCYMDQEKKAGVKV--------------MEEFEKPTRD----------ATLRMKHG 481

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +++ G+I  G  V+  DI++GK  P  E      ++        ++   RD S  +
Sbjct: 482 TYDKLEDDGLIAPGVRVSGEDIIIGKTAPLPEESAELGQRT-------RSHTRRDISTPL 534

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            S  +G V  V +       K
Sbjct: 535 RSTETGIVDQVMLTTNQEGVK 555


>gi|297595161|gb|ADI48097.1| RNA polymerase beta subunit [Erwinia sp. DAPP-PG 531]
 gi|297595848|gb|ADI48233.1| RNA polymerase beta subunit [Erwinia sp. DAPP-PG 672]
          Length = 319

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 190/319 (59%), Positives = 247/319 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V +G VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R++
Sbjct: 121 PYRRVREGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYAGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDEVRRNDIIADGPS 799
            V +G+ + R D++ADGPS
Sbjct: 301 CVNLGEPIERGDVLADGPS 319


>gi|269912632|emb|CAY86096.1| RNA polymerase beta subunit [Gluconobacter cerinus]
          Length = 311

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 147/313 (46%), Positives = 202/313 (64%), Gaps = 28/313 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EILS FY  + +++ G
Sbjct: 61  RKRKLPVTTLLYALEGANYIAQREEKIAEGGDVEGLDIRGMDQDEILSYFYDMVTFTRMG 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           D W  P    D   G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +    
Sbjct: 121 DGWARPFEP-DAFRGQKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G Y+A D++N  TGEIY EAG+ + E  L  +    I ++P L +D  ++  +IRNTL
Sbjct: 179 VLGCYLAHDLINENTGEIYGEAGEELTEDRLAALEELGITELPTLSIDG-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS+VGRVKMNMRL++
Sbjct: 238 SVDKNTSRDEALIDIYRIMRPGEPPTKETAEAMFRGLFFDQDRYDLSSVGRVKMNMRLDV 297

Query: 423 DTPDDVRHIRKED 435
           D PD +R +RKED
Sbjct: 298 DAPDTLRVLRKED 310


>gi|81171093|gb|ABB58773.1| RNA polymerase beta subunit [Mycoplasma feliminutum]
          Length = 637

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 210/487 (43%), Positives = 304/487 (62%), Gaps = 37/487 (7%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T  RR+SALG GG++R RAG+E+RDVHP+HYGRICP ET EG +IGL+SSLTS+
Sbjct: 2   NPLSELTQKRRISALGAGGISRDRAGIEVRDVHPSHYGRICPIETPEGQSIGLISSLTSY 61

Query: 590 ARVNAYGFIETPYRKVC----------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           A +N YGFI+TPY              + +VT+ +  L+A +E +  +A ++S L+EDG+
Sbjct: 62  AEINEYGFIQTPYLVCDTTNLDENGEVNPRVTDKIEKLTADQEYDFVVASSSSELNEDGT 121

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F  + +     GE  +  R  + +++ SPKQ+VS+AAS IPFLE+++++R LMG NMQRQ
Sbjct: 122 FKHKTIVASYKGETGIFDRSLVRYMNLSPKQIVSVAASTIPFLEHNEASRCLMGANMQRQ 181

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVP+++  +P VGTG+E   AK SGA +V++  G V   DA +I +     +     + V
Sbjct: 182 AVPVIRPVSPIVGTGVELKAAKDSGAVVVSQHDGYVVFSDANKIEVLPKPNEKITFGNEV 241

Query: 760 ------------------------DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                                     Y L+ F+RSNQ+TC+ QRP+V  G+ + + D+IA
Sbjct: 242 LFEVGKEWSFEQALKIYSYGLMESYTYPLITFERSNQDTCLLQRPIVFRGEYIEKGDVIA 301

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           DGPSTD G+LALG+N+ VAFM W GYN+ED++++SE MV  DV+TSIHIEE+ V AR  K
Sbjct: 302 DGPSTDKGELALGQNVFVAFMTWDGYNYEDAVIMSEDMVQNDVYTSIHIEEYSVEARKIK 361

Query: 856 LGP--EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                E+ T +IP+   E  + +D+ GII +G EVN  DILVGKITPK  + + PEE L 
Sbjct: 362 ENKVDEQFTSEIPHAKNELKRKLDKNGIILIGTEVNEEDILVGKITPKTSNEVRPEEALT 421

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
            AI GEKA D +D+SL+VP G  G V  +  F++   + ++ ++     ++  +   K  
Sbjct: 422 LAIIGEKAKDFKDSSLKVPHGGGGIVQKIIKFSKQNKE-DKDALPDGVNELVKVFVAKKR 480

Query: 974 EQVILDR 980
           +    D+
Sbjct: 481 KIREGDK 487



 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 118/452 (26%), Positives = 193/452 (42%), Gaps = 66/452 (14%)

Query: 845  EEFEVMARDTKLGPEE--ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
              FE   +    G  E      I          + +  I+  G  +  GD++    +   
Sbjct: 249  WSFEQALKIYSYGLMESYTYPLITFERSNQDTCLLQRPIVFRGEYIEKGDVIADGPST-D 307

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            +  +   + +  A       +  D  +         V +    + H  + +  +  ++  
Sbjct: 308  KGELALGQNVFVAFMTWDGYNYEDAVIM----SEDMVQNDVYTSIHIEEYSVEARKIKEN 363

Query: 963  QI-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E    +    +  L R +  +   IL G           K   ++    +E    + 
Sbjct: 364  KVDEQFTSEIPHAKNELKRKL-DKNGIILIGTEVNEEDILVGK---ITPKTSNEVRPEEA 419

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
               A+  EK +   +S          I++   K   +  +  D +P GV  +VKVFVA K
Sbjct: 420  LTLAIIGEKAKDFKDSSLKVPHGGGGIVQKIIKFSKQNKEDKDALPDGVNELVKVFVAKK 479

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R I+ GDK+AGRHGNKG++S+ILP EDMP+++DGTP+DI+L+PLGVP RMN+GQI E HL
Sbjct: 480  RKIREGDKIAGRHGNKGVISKILPREDMPYMQDGTPIDIMLSPLGVPKRMNIGQILEIHL 539

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G A   LG K+ + + +   + D+  + +                               
Sbjct: 540  GHAAKKLGVKVATPVFEGVNDQDLLDIMNEANI--------------------------- 572

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                          +    ++L        G        TGE F   ++VG +YM+KL+H
Sbjct: 573  --------------DTDGKAIL------YDG-------RTGEAFKERISVGVMYMIKLSH 605

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            MV DK++ R+ G Y+L+TQQP+GGK+  GGQR
Sbjct: 606  MVDDKLHTRNVGKYTLITQQPMGGKAQNGGQR 637


>gi|83415463|gb|ABC17939.1| RNA polymerase II second largest subunit [Cladochytrium replicatum]
          Length = 725

 Score =  312 bits (799), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 128/858 (14%), Positives = 263/858 (30%), Gaps = 157/858 (18%)

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL--INAKPVVSAVCEFFC 518
             +R+   G ++   +R    +M + I   +      ++       +    + + +     
Sbjct: 1    MKRLDLAGALMGGLFRQLFKKMTKEINNYMRKCVDTNLTFDLKWAVKGNIIKNGLQFSLA 60

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+       S ++H R L+      + R     + R +H TH
Sbjct: 61   TGNWGDQKKLNAARAGVSQVLNRYTYASTLSHLRHLNT----PIGREGKLAKPRQLHNTH 116

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            +G +CPAET EG   GLV +L+  A V+  +       + +V +    +++         
Sbjct: 117  WGMVCPAETPEGQACGLVKNLSLMACVSVASPSRPVLEFLEVLNLNNLDEIRPSQISHST 176

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP--- 680
              ++      +  + +  E +   R    ++ V  E     D   K++     +      
Sbjct: 177  RVFLNGDWVGIVGESAVEEMVTELRNLRRKVEVSPELSIVRDVREKELWIYTDAGRIYRP 236

Query: 681  -FLENDDSNRVLMGCNMQRQAVP-LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
             F+ ++ ++   +      Q     L  +   V   +E +        ++A     + Q 
Sbjct: 237  LFIVDEKTHHTFIQRRHVTQIHNRELNFDDLLVEGLVEYIDTLEEETIMIA-----MSQS 291

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            D  +     ++         ++ +          +T    +P    G   ++       P
Sbjct: 292  DLTQTRTYLLQQADPDIELPLNPH--------ANDTSYRLKP--NAGAYSQQWTHCEIHP 341

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKL 856
            +  LG       +  + +P+  +N          M  +    F + ++  ++ M      
Sbjct: 342  AMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGTFLTNYLLRYDTMM----- 389

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                       +             +       +   +    AI
Sbjct: 390  --------------------------NILFYPQKPLGTTRSMEYLRFRELPAGQNACVAI 423

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    ++ R  +D+ ++   ++ E  E   R+      
Sbjct: 424  ACYSGYNQEDSIIMNXSSIDRGLF-RSMYYRVYMDQEKKVGMLQTETFEKPTRETTLRLR 482

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                        I  G           K+  L ++                 +++ +   
Sbjct: 483  HGTYEKLEDDGLIAPGMRVSGDDIIIGKTVPLQTE----------------SDELGQRQA 526

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
              K    T     E    + +      D       + +KV V   R  Q GDK A RHG 
Sbjct: 527  QTKRDASTPLKSTEQGIVDSVLVTTNSD-----GYKFIKVRVRSVRIPQMGDKFASRHGQ 581

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG V      EDMPF  +G   D+++NP  +PSRM +G + E  L       G++  +  
Sbjct: 582  KGTVGMTYRQEDMPFTAEGISPDLIVNPHAIPSRMTIGHLVECLLSKVATLTGREGDATP 641

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L          G                                     
Sbjct: 642  FTDLTVHQVSDLL------YEHGHQQRGFEVL---------------------------- 667

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                          +G +       G+     + +G  Y  +L HMV DK+++R+ G   
Sbjct: 668  -------------YNGHT-------GKKLRAQLFMGPTYYQRLKHMVDDKIHSRARGPVQ 707

Query: 1277 LVTQQPLGGKSNRGGQRL 1294
            ++T+QP+ G+S  GG R 
Sbjct: 708  ILTRQPVEGRSRDGGLRF 725


>gi|315259448|gb|ADT91923.1| DNA-directed RNA polymerase beta subunit [Enterococcus faecalis]
          Length = 392

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 131/420 (31%), Positives = 182/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L A    +  +  D  +     V   V 
Sbjct: 45   IVHLGEKVEKGDTLADGPS-MEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R      +++       +                    
Sbjct: 164  PKGVTELSAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI----------------VHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 267  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 312  -------------TDEDVWETVREAGMASDAKTVLYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 128/222 (57%), Positives = 166/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEFVDAKEIRVRRDNGALDK-------YMVTKFRRSNSGTSYNQRPIVHLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LVAFM W GYN+ED++++S R+V +DV+TS+HIEE+E 
Sbjct: 54  KGDTLADGPSMEEGEMALGQNVLVAFMTWEGYNYEDAIIMSRRLVKDDVYTSVHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|226897646|gb|ACO90272.1| RNA polymerase beta subunit gene [Bacillus hwajinpoensis]
          Length = 375

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 218/360 (60%), Positives = 270/360 (75%), Gaps = 3/360 (0%)

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           +GFIETPYR+V    GKVT  + YL+A E++N  +AQAN+ L EDGSF +E +  R   E
Sbjct: 1   FGFIETPYRRVDPETGKVTEYIDYLTADEQDNYVVAQANAKLHEDGSFQDEDIVARFRDE 60

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            I++ REKID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAP VG
Sbjct: 61  NIIIAREKIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMVPEAPIVG 120

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSN 771
           TGME V  K SGAA++ K  G+VE   A  I +R +   D       +D Y+L+KF RSN
Sbjct: 121 TGMEHVNGKDSGAAVICKHDGLVEFASAAEIHVRRISVIDGQEVKGDLDRYKLLKFIRSN 180

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC NQ+P+V  GD V + +I+ DGPS + G++ALGRN+LV FM W GYN+ED++++SE
Sbjct: 181 QGTCYNQKPIVSEGDRVVKGEILGDGPSMEKGEMALGRNVLVGFMTWEGYNYEDAIIMSE 240

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE+E  ARDTKLGPEEITRDIPNV E+ L+N+DE GII +GAEV  G
Sbjct: 241 RLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDERGIIRMGAEVKDG 300

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DVRIFNR   D
Sbjct: 301 DILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIVLDVRIFNREDGD 360


>gi|224812769|gb|ACN65018.1| RpoB [Cronobacter turicensis z3032]
          Length = 317

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 193/317 (60%), Positives = 243/317 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D 
Sbjct: 121 DGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V + +
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLNE 300

Query: 787 EVRRNDIIADGPSTDLG 803
            V R D++ADGPSTDLG
Sbjct: 301 PVERGDVLADGPSTDLG 317


>gi|212223363|ref|YP_002306599.1| DNA-directed RNA polymerase subunit B [Thermococcus onnurineus NA1]
 gi|212008320|gb|ACJ15702.1| Subunit B of DNA-dependent RNA polymerase [Thermococcus onnurineus
            NA1]
          Length = 1120

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 87/327 (26%), Positives = 135/327 (41%), Gaps = 77/327 (23%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E    +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDM
Sbjct: 844  EKGIVDKVIITETGD-----GTKLVKVTVRDLRIPEFGDKFASRHGQKGVIGLIVPQEDM 898

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P+ + G   D+++NP G+PSRM VGQ+ E   G      G+++       +    +    
Sbjct: 899  PWTESGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRVDGTAFIGEPEERLRKEL 958

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L                                      +DG                
Sbjct: 959  EELGFKHSGREVM----------------------------YDGIT-------------- 976

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
                        G   +  + VG IY  +L+HMV+DK++ARS G   ++T+QP  G++  
Sbjct: 977  ------------GRRLEADIFVGVIYYQRLHHMVADKMHARSRGPVQVLTKQPTEGRARE 1024

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG--------RTRVYESIVA 1334
            GG R GEME   +  +GAA +L E L  +SD          G        R +VY   V 
Sbjct: 1025 GGLRFGEMERDVLIGHGAAMLLIERLLEESDKTEVWACESCGHLALEDKRRGKVY-CPVC 1083

Query: 1335 GND--TFETGTPESFNVLVKEMQALGL 1359
            G +    +     +F +L+ E++A+G+
Sbjct: 1084 GEEEKISKVEMSYAFKLLLDELKAMGI 1110



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 151/979 (15%), Positives = 290/979 (29%), Gaps = 199/979 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+          + G+Q        I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------DYGMQQVINEFGGIKPDIPDFEVKFGKIRLGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + L  +V  + +              + +G+LP+M
Sbjct: 77  AQGQRKPLYPMDARIRNLTYSAPLYLELIPVVNGIAQEPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R + 
Sbjct: 127 LKSKACRLYGLSDEELIKLGEDPKDPGGYFIINGSERVIVSIEDLAPNKTLVERDERQNR 186

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI---DRRRKVPVTSFLMALGMDSE-EILS 230
                ++ R    +   + +E     I++V I    R  K      + ALG++S+ EI+ 
Sbjct: 187 IIAKCFSYR-HGYR-ALITVERRKDGILYVNIPNVPRPVKF--VYVMRALGLESDKEIVE 242

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
                    Q            +           +D      +    K+      + + +
Sbjct: 243 AVSDDPRIQQ------VLFDNLEDASDIMSREEALDYIGKLALPGQPKEYRLRRAEHIID 296

Query: 291 KGV-------KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             +       +          G+  A  ++    G    +  D    K L+         
Sbjct: 297 NNLLPHMGVEEKDRRAKAYYLGMM-ALKVLELSLGLRGEDDKDHYANKRLKLAGDLLRDL 355

Query: 344 IPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             + +   V +  Y   +      +    ++    +   +RP DV +  +  ++    + 
Sbjct: 356 FRVAFGQLVKDMQYQMTKTYQRKGERYTFENIQRFVRNSIRP-DVLSERIEHALATGAWP 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                    + R      L+         + ++      + L       G I   +    
Sbjct: 415 GGRTGVSQLLDRTNYMSTLSHLRRVTSP-LSRDQPHFEARDLHGTH--WGRICPTETPEG 471

Query: 462 RRVRSVGEM-LKNQYRLGLLRME-RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                V  + L  Q   G+   E R    R+  V I+   P               +   
Sbjct: 472 PNCGLVKNLALMAQITTGIPEEEVRDYLNRLGVVPIEEKRPSL--------ELWRVYLNG 523

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PTHYGRICPAETSEGH 578
             +  +E+    + RI   RR   +            E+++++  +  GR+         
Sbjct: 524 VLIGTVEDGERLVKRIRADRRSGRISDVINVAIYQDEEVKEIYVNSDDGRVR------RP 577

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            I + +      R +  G I+       D      + YL A EEEN Y+A          
Sbjct: 578 LIIVENGQPKLTREHVEG-IKNGTLTWSDLIKMGVIEYLDAEEEENAYVAT--------- 627

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                +   ++  P  ++ I ASL+P+ E++ + R   G  M +
Sbjct: 628 --------------WPWEVTAEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGMAK 673

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           Q++ L  A                                                +   
Sbjct: 674 QSLGLGWANFRI-----------------------------------------RVDTRGH 692

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
              Y               Q PLV                +    +   G+N +VA + +
Sbjct: 693 FMHYP--------------QVPLVNS----------RIMKAVGFEERPAGQNFVVAVLSY 728

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE---EITRDIP--NVSEEGL 873
            GYN ED++++++  +   +  S     +E   +    G     E+        + E+  
Sbjct: 729 QGYNMEDAIIMNKASIERGLARSTFFRTYEAEEKRYLGGQTDRFEVPDPTIQGYLGEKYY 788

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +++DE GII   ++V   D+LVG+ +P               + G    + R+TS+ V  
Sbjct: 789 RHLDEDGIIFPESKVEGKDVLVGRTSPPRFLEEQSG------LGGIILQERRETSVAVRP 842

Query: 934 GVSGTVVDVRIFNRHGIDK 952
              G V  V I       K
Sbjct: 843 SEKGIVDKVIITETGDGTK 861


>gi|17647877|ref|NP_523706.1| RNA polymerase III 128kD subunit [Drosophila melanogaster]
 gi|78099797|sp|P25167|RPC2_DROME RecName: Full=DNA-directed RNA polymerase III subunit RPC2; Short=RNA
            polymerase III subunit C2; AltName: Full=DNA-directed RNA
            polymerase III 128 kDa polypeptide; Short=C128
 gi|7303535|gb|AAF58590.1| RNA polymerase III 128kD subunit [Drosophila melanogaster]
 gi|220943532|gb|ACL84309.1| RpIII128-PA [synthetic construct]
          Length = 1137

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 114/621 (18%), Positives = 206/621 (33%), Gaps = 122/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 608  NRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 667

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 668  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 716

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 717  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 776

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 777  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 835

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + IE++  
Sbjct: 836  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYIERVMV 877

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 878  SANAEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 935

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 936  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 956

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 957  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1002 TPLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1061

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1062 ISYGASMLIMERLMISSDAFEVDVCRTCGR-MAYCSWCHFCQSSA-----NVSKISMPYA 1115

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1116 CKLLFQELTSMNVVPKMILEN 1136



 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 119/992 (11%), Positives = 280/992 (28%), Gaps = 202/992 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 LSTF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           + +           +   +             A + M    V        T     E+ +
Sbjct: 258 IQSLIGIDSKSQNRFGASLIDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEARE 317

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            L + +   L    V    +    +    +   ++  E  +   +  D    K LE    
Sbjct: 318 LLLTTI---LAHVPVDNFNLQMKAIYVSMMVRRVMAAELDKTLFDDRDYYGNKRLELAGS 374

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                   L+         I +  +       K A  D+ + MR   ++  +  ES  + 
Sbjct: 375 LLSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAISS 428

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             +   ++ +   G  ++  RL+  +   +            K+                
Sbjct: 429 GNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ--------- 479

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                +    +  + +    +  +           +   ++       + +         
Sbjct: 480 PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIREVSGNPIN 539

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  +  +  + N L    +  +        + R         VH ++  R     T  G 
Sbjct: 540 NPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGGR 598

Query: 579 NIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                  + +   +     ++      RK  D  +   + YL   EE + +IA       
Sbjct: 599 LCRPYVIVENRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------- 651

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
               + E+ +  R               ++  P  ++ + A L+P+  ++ S R    C 
Sbjct: 652 ----WNEDQIEDR------------TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCA 695

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ ++         G        S                                
Sbjct: 696 MGKQAMGMI---------GYNQKNRIDS-------------------------------- 714

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                            N      P+VK                T+   L  G+N  VA 
Sbjct: 715 --------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVAV 750

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEGL 873
           M + GY+ ED++++++  +       +  +  +   +          +      ++ + +
Sbjct: 751 MSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKVI 810

Query: 874 KN---IDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKAV 922
                +D  GI+  G +V    I++ K  P        +G+S   P   +  +  G +  
Sbjct: 811 FKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPYTAVPISYKGPEPS 870

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +    +   +     +  +    R     ++
Sbjct: 871 YIERVMVSANAEEDFLIKILLRQTRIPEIGDK 902


>gi|52538179|emb|CAH19191.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 15]
          Length = 316

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 192/313 (61%), Positives = 242/313 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R R
Sbjct: 4   DLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRER 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D  VT++
Sbjct: 64  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVKDALVTDE 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLSA+EE N  IAQANS+LDEDG F EELV CR  GE  L  ++++D++D   +QVVS
Sbjct: 124 IMYLSAIEEGNYVIAQANSNLDEDGHFEEELVTCRSKGESSLFSKDQVDYMDVFAQQVVS 183

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  +VAKR G
Sbjct: 184 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTVVAKRGG 243

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            ++ VDA RIVI+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D+
Sbjct: 244 EIQYVDASRIVIKVNEDETYSGEAGIDIYNLTKYTRSNQNTCINQSPHVSLGEPVERGDV 303

Query: 794 IADGPSTDLGDLA 806
           +ADGPSTDLG+LA
Sbjct: 304 LADGPSTDLGELA 316


>gi|311901492|gb|ADQ13238.1| RNA polymerase subunit B [Mycobacterium conceptionense]
          Length = 237

 Score =  312 bits (798), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 105/236 (44%), Positives = 138/236 (58%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 144  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 182  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPL 237


>gi|3746596|gb|AAC64013.1| RNA polymerase II subunit 2 [Chironia linoides]
          Length = 256

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 104/237 (43%), Gaps = 54/237 (22%)

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             Q GDK + RHG KG V      EDMPF  +G   DI++NP  +PSRM +GQ+ E  +G 
Sbjct: 34   PQIGDKFSSRHGQKGTVGMTYTQEDMPFTSEGITPDIIVNPHAIPSRMTIGQLIECIMGK 93

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                +GK+                                                    
Sbjct: 94   VAAHMGKEGD-------------------------------------------------- 103

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +TP F     + I+  L        G   +++G TG PF   + +G  Y  +L HMV
Sbjct: 104  ---ATP-FTDVTVDNISRALPKCGYQMRGFERMFNGHTGRPFTATIFLGPTYYQRLKHMV 159

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD
Sbjct: 160  DDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSD 216


>gi|260826766|ref|XP_002608336.1| hypothetical protein BRAFLDRAFT_126222 [Branchiostoma floridae]
 gi|229293687|gb|EEN64346.1| hypothetical protein BRAFLDRAFT_126222 [Branchiostoma floridae]
          Length = 1104

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 144/913 (15%), Positives = 281/913 (30%), Gaps = 172/913 (18%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY    + +  +      D  +  +      +  I+  L+    G+  +DD D+ GN+
Sbjct: 337  RIKYAREILQKEMLPHVGISDYCETKK---AYFLGYIVHRLLLAALGRRELDDRDHYGNK 393

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R     + + ++               +  I  + +   +     + 
Sbjct: 394  RLDLAGPLLAYLFRGLFKNLTKEVRIYAQKFIDRGKDFNLELAIKTRIITDGLKYSLATG 453

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+   +   S ++H RRL++     + R     + R +H + +G
Sbjct: 454  NWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNS----PIGRDGKLAKPRQLHNSLWG 509

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             ICPAET EG  +GLV +L   A ++           V +  +               YI
Sbjct: 510  MICPAETPEGQAVGLVKNLALMAYISMVHDNGQAVGLVKNLALM-------------AYI 556

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            +  +                    E  +   E++     +    + +    +    + D 
Sbjct: 557  SVGSQPSP----------ILEFLEEWSMENLEEVAPSAIANATKIFVNGCWVG--VHRDP 604

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI---------VEQV 738
             +++      R+ + ++ +E   V    E  +   + A  + +   I            V
Sbjct: 605  EQLMNTLKKLRRQMDIIVSEVSMVRDIREREIRIFTDAGRICRPLLIVEKQKLLLKKHHV 664

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            D ++    +     D    GV  Y     + +            K              P
Sbjct: 665  DMLKEREYNNYSWQDLVAGGVVEYIDTLEEETVMLAMTPDDLQDKGVAYCSTYTHCEIHP 724

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  + +   ++I  F           
Sbjct: 725  SMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNF----------- 764

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                            ++    +  V        +    +       +      + AI  
Sbjct: 765  ----------------HVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINAIVAIAS 808

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +     +  +   ++++ +  E    E+  +   DE   +
Sbjct: 809  YTGYNQEDSVIMNASAIDRGLFRSVFYRSYKESESKKGLDQE----EIFEKPTRDEVTGM 864

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
               IY +L +   I  G           K+  L                     + +  +
Sbjct: 865  RNAIYDKLDDDGIIAPGVRVSGEDVIIGKTVTL--------------------PENEDEL 904

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            ES   ++    S    R        Q    +     +  KV V   R  Q GDK A RHG
Sbjct: 905  ESTTKRFTKRDSSTFLRSSETGIVDQVMVSINQEGYKFCKVRVRSVRIPQIGDKFASRHG 964

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG        EDMPF  +G   DI++NP  VPSRM +G + E   G      G+   + 
Sbjct: 965  QKGTCGITYRQEDMPFTAEGISPDIIINPHAVPSRMTIGHLIECLQGKVSANKGEIGDAT 1024

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
              +                                                     D  +
Sbjct: 1025 PFN-----------------------------------------------------DAVN 1031

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + I+++L        G  ++Y+G TG      + +G  Y  +L HMV DK+++R+ G  
Sbjct: 1032 VQKISNLLHEYGYHLRGNEVVYNGFTGRKLSTQLFIGPTYYQRLKHMVDDKIHSRARGPV 1091

Query: 1276 SLVTQQPLGGKSN 1288
              + +QP+ G+S 
Sbjct: 1092 QNLNRQPMEGRSR 1104



 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 151/1021 (14%), Positives = 296/1021 (28%), Gaps = 217/1021 (21%)

Query: 29  LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFK------SVFPITAFSGAAMLEFVSYE 80
           L+  Q  S+D F+ M++    ++ P   LQA  +       V P        +L F    
Sbjct: 41  LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHLTMEAEVPP------RYLLNFEQIY 94

Query: 81  FDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              P              ++   R+LTY+ PL + +   +    E        + + Q  
Sbjct: 95  LSKPTHWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTIVKDGEERI-----ETQHQKT 149

Query: 131 YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
           ++G +P+M                           G F+I G ++++++Q   +   ++ 
Sbjct: 150 FIGKIPIMLRSTYCLLSGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNSVYV 209

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK--------- 211
              K       K  +   I       ++        + V +  R     RK         
Sbjct: 210 FAKKDS-----KYAFTGEIR----SCLEHSSRPTSTLWVHMLARGGTGQRKSAIGQRIVA 260

Query: 212 --------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
                   +P+     ALG  S+ +IL          +  +     L  A ++    V+ 
Sbjct: 261 VLPYIRQEIPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMLKPSLDEAFVIQEQNVAL 320

Query: 263 SLVDIDTGEQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           + +     +  +   K++         + L   G+     T       Y+   ++    G
Sbjct: 321 NFIGARGAKPGVTKDKRIKYAREILQKEMLPHVGISDYCETKKAYFLGYIVHRLLLAALG 380

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
              ++  D    K L+            L+ +            +        +      
Sbjct: 381 RRELDDRDHYGNKRLDLAGPLLAYLFRGLFKNLTKEVRIYAQKFIDRGKDFNLE------ 434

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDI 436
            +     + T  +  S+    + D  K   +  G  ++  RL   +      R       
Sbjct: 435 -LAIKTRIITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGR 493

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE-------------------MLKNQYRL 477
              +     L N    +         +   + +                   ++KN   +
Sbjct: 494 DGKLAKPRQLHNSLWGMICPAETPEGQAVGLVKNLALMAYISMVHDNGQAVGLVKNLALM 553

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             + +       +  ++  S+   + +    + +A   F     +    +    ++ +  
Sbjct: 554 AYISVGSQPSPILEFLEEWSMENLEEVAPSAIANATKIFVNGCWVGVHRDPEQLMNTLKK 613

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYG 596
            RR   +    V+  R   E      T  GRIC P    E   + L         V+   
Sbjct: 614 LRRQMDIIVSEVSMVRDIREREIRIFTDAGRICRPLLIVEKQKLLLKKH-----HVDMLK 668

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             E       D      V Y+  +EEE   +A     L + G                + 
Sbjct: 669 EREYNNYSWQDLVAGGVVEYIDTLEEETVMLAMTPDDLQDKG----------------VA 712

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ + AS+IPF +++ S R      M +QA+ +             
Sbjct: 713 YCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------ 766

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                                                 + + V  Y              
Sbjct: 767 -----------------------------------RMDTLAHVLYYP------------- 778

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PLV                     +L  G N +VA   + GYN EDS++++   +  
Sbjct: 779 -QKPLV----------TTRSMEYLRFRELPAGINAIVAIASYTGYNQEDSVIMNASAIDR 827

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    ++       L  EEI       ++  +       +D+ GII  G  V+  
Sbjct: 828 GLFRSVFYRSYKESESKKGLDQEEIFEKPTRDEVTGMRNAIYDKLDDDGIIAPGVRVSGE 887

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           D+++GK     E+    E          K    RD+S  + S  +G V  V +       
Sbjct: 888 DVIIGKTVTLPENEDELESTT-------KRFTKRDSSTFLRSSETGIVDQVMVSINQEGY 940

Query: 952 K 952
           K
Sbjct: 941 K 941


>gi|332157775|ref|YP_004423054.1| DNA-directed RNA polymerase subunit B [Pyrococcus sp. NA2]
 gi|331033238|gb|AEC51050.1| DNA-directed RNA polymerase subunit B [Pyrococcus sp. NA2]
          Length = 1117

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 87/336 (25%), Positives = 138/336 (41%), Gaps = 77/336 (22%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E    +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDM
Sbjct: 841  EKGIVDKVIITETGD-----GTKLVKVTVRDLRIPEIGDKFASRHGQKGVIGLIVPQEDM 895

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P+ + G   D+++NP G+PSRM VGQ+ E   G      G+++       +    +    
Sbjct: 896  PWTESGIVPDLIVNPHGIPSRMTVGQLLEAIGGKVAALKGRRVDGTAFIGEPEEKLRKEL 955

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L                                      +DG                
Sbjct: 956  EELGFKHTGREIM----------------------------YDGIT-------------- 973

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G+           F+  + +G IY  +L+HMV+DK++ARS G   ++T+QP  G++  
Sbjct: 974  --GK----------RFEADIFIGVIYYQRLHHMVADKIHARSRGPVQVLTKQPTEGRARE 1021

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG--------RTRVYESIVA 1334
            GG R GEME   +  +GAA +L E L  +SD          G        R +VY   V 
Sbjct: 1022 GGLRFGEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKRRHKVY-CPVC 1080

Query: 1335 GND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            G +    +     +F +L+ E++A+ +   L  +  
Sbjct: 1081 GEEERISKVEMSYAFKLLLDELKAMCIRPKLNLTER 1116



 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 146/976 (14%), Positives = 292/976 (29%), Gaps = 196/976 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            GLQ     V  I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------ERGLQEVVDEVGGIKPDIPDFEVKFGKIRVGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + +  ++  V++              + +G+LP+M
Sbjct: 77  PHGQRKPLYPMDARIRNLTYSAPLYLEMIPVIRGVEQDPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R   
Sbjct: 127 LKSKVCRLYGLSDEELIKLGEDPKDPGGYFIINGSERVIVSIEDIAPNRTLVEKDERQ-- 184

Query: 175 SGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRI---DRRRKVPVTSFLMALGMDSE-E 227
                Y  ++   +      + +E     I++V I    R  K      + ALG++ + +
Sbjct: 185 ---ERYIAKVFSYRHGYRALVTVERKKDGILYVGIPNVPRPVKF--VYVMRALGLERDKD 239

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I+          Q         +  D         +L  I       ++ +         
Sbjct: 240 IVDAVGNDPEVQQ-----ILFDNLEDASDITTQQEALEYIGKLVAPGQAREYRLKRAEYV 294

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIRDIP 345
           +    +  +G+  +          ++  +  E+ +      D+     + +  +      
Sbjct: 295 IDNNLLPHMGVNPEDRIRKAYYLGMMALKVIELSLGKRGEDDKDHYANKRLRLAGDLLKD 354

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALL-DIYRVMRPG---DVSTFSVAESMFNFLFF 401
           +  V        I+  +     +  +  +  +I+R +R     DV T  +  ++    + 
Sbjct: 355 LFRVAFNQLVKDIQYQMTKTYQRRGEKYVFGNIHRFIRNSIRPDVLTERIEHALATGAWP 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                    + R      ++         + +E      + L       G I   +    
Sbjct: 415 GGRTGVSQLLDRTNYVSTMSHLRRVTSP-LDREQPHFEARDLHGTH--WGRICPTETPEG 471

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                V  +        + ++  ++ E      + S+    +   +P       +     
Sbjct: 472 PNCGLVKNLA------LMAQITTAVPEEEVREYLMSLGIVPIEVRRPSPELWRVYLNGVL 525

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +  +E+    + +I   RR   +           V+   V+        P    E     
Sbjct: 526 IGTVEDGKALVEKIRSDRRSGKISDIINVAYYEDVKEVYVNSDDGRVRRPLIIVENGKPK 585

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L               I+    K  D      + YL A EEEN Y+A             
Sbjct: 586 LTKEHVQ--------AIKEGRLKWSDLIKMGVIEYLDAEEEENAYVAM------------ 625

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            ++   ++  P  ++ + ASLIP+ E++ + R   G  M +Q++
Sbjct: 626 -----------WPWEVTKEHTHLELMPAAILGLPASLIPYPEHNAAPRNTYGAGMAKQSL 674

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            +  A                                                +   +  
Sbjct: 675 GIGWANFRI-----------------------------------------RVDTRGHLLH 693

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q PLV                +    D   G+N +VA + + GY
Sbjct: 694 YP--------------QIPLVNS----------RIMKAVGYEDRPAGQNFVVAVLAYQGY 729

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNI 876
           N ED+++I++  +   +  S     +E   +    G  ++     P V     E+  +++
Sbjct: 730 NMEDAIIINKASIERGLARSTFFRTYEAEEKKYLGGQTDKFEIPSPTVRGYRGEKYYRHL 789

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE G+I   ++V   D+L+G+ +P        EE+ L A+      + R+TS+ V     
Sbjct: 790 DEDGLIFPESKVEGKDVLIGRTSPPRFL----EERGLGAV---SLQERRETSVAVRPSEK 842

Query: 937 GTVVDVRIFNRHGIDK 952
           G V  V I       K
Sbjct: 843 GIVDKVIITETGDGTK 858


>gi|83763761|emb|CAJ00214.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12D02]
          Length = 351

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 186/364 (51%), Positives = 256/364 (70%), Gaps = 13/364 (3%)

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            G+G+E  +A  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSN
Sbjct: 1    GSGIERNIAVDSGVTAVAKRGGMIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSN 60

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRP V  G+ V R D+IADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SE
Sbjct: 61   QNTCINQRPCVMPGELVARGDVIADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSE 120

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  G
Sbjct: 121  RVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGG 180

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT +DV++F R G++
Sbjct: 181  DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTSIDVQVFPRDGVE 240

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S  
Sbjct: 241  KDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVRAVLIDGG-------------YSEA 287

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
             +    R +W +  ++D+ +Q  +E L  QY+  ++  + +F+ K  KI  GDD+ PGVL
Sbjct: 288  KLDTTDRKKWLELTLEDDALQTQLEQLAEQYDELRADFDKKFETKRRKITQGDDLAPGVL 347

Query: 1072 RVVK 1075
            ++VK
Sbjct: 348  KIVK 351


>gi|213876739|gb|ACJ54366.1| RNA polymerase subunit B [Mycobacterium porcinum]
          Length = 244

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 105/236 (44%), Positives = 138/236 (58%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 151  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 189  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPL 244



 Score = 42.8 bits (99), Expect = 0.44,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|21464338|gb|AAM51972.1| LD14594p [Drosophila melanogaster]
          Length = 1146

 Score =  311 bits (797), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 114/621 (18%), Positives = 206/621 (33%), Gaps = 122/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 617  NRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 676

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 677  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 725

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 726  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 785

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 786  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 844

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + IE++  
Sbjct: 845  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYIERVMV 886

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 887  SANAEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 944

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 945  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 965

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 966  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 1010

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1011 TPLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1070

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1071 ISYGASMLIMERLMISSDAFEVDVCRTCGR-MAYCSWCHFCQSSA-----NVSKISMPYA 1124

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1125 CKLLFQELTSMNVVPKMILEN 1145



 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 119/992 (11%), Positives = 280/992 (28%), Gaps = 202/992 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 56  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 106

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 107 GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 156

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 157 LRCSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 216

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 217 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 266

Query: 229 LSTF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           + +           +   +             A + M    V        T     E+ +
Sbjct: 267 IQSLIGIDSKSQNRFGASLIDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEARE 326

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            L + +   L    V    +    +    +   ++  E  +   +  D    K LE    
Sbjct: 327 LLLTTI---LAHVPVDNFNLQMKAIYVSMMVRRVMAAELDKTLFDDRDYYGNKRLELAGS 383

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                   L+         I +  +       K A  D+ + MR   ++  +  ES  + 
Sbjct: 384 LLSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAISS 437

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             +   ++ +   G  ++  RL+  +   +            K+                
Sbjct: 438 GNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ--------- 488

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                +    +  + +    +  +           +   ++       + +         
Sbjct: 489 PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIREVSGNPIN 548

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  +  +  + N L    +  +        + R         VH ++  R     T  G 
Sbjct: 549 NPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGGR 607

Query: 579 NIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                  + +   +     ++      RK  D  +   + YL   EE + +IA       
Sbjct: 608 LCRPYVIVENRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------- 660

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
               + E+ +  R               ++  P  ++ + A L+P+  ++ S R    C 
Sbjct: 661 ----WNEDQIEDR------------TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCA 704

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ ++         G        S                                
Sbjct: 705 MGKQAMGMI---------GYNQKNRIDS-------------------------------- 723

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                            N      P+VK                T+   L  G+N  VA 
Sbjct: 724 --------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVAV 759

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEGL 873
           M + GY+ ED++++++  +       +  +  +   +          +      ++ + +
Sbjct: 760 MSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKVI 819

Query: 874 KN---IDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKAV 922
                +D  GI+  G +V    I++ K  P        +G+S   P   +  +  G +  
Sbjct: 820 FKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPYTAVPISYKGPEPS 879

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +    +   +     +  +    R     ++
Sbjct: 880 YIERVMVSANAEEDFLIKILLRQTRIPEIGDK 911


>gi|307353876|ref|YP_003894927.1| DNA-directed RNA polymerase subunit B [Methanoplanus petrolearius DSM
            11571]
 gi|307157109|gb|ADN36489.1| DNA-directed RNA polymerase subunit B [Methanoplanus petrolearius DSM
            11571]
          Length = 609

 Score =  311 bits (797), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 115/597 (19%), Positives = 196/597 (32%), Gaps = 118/597 (19%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     ++ +A            + I   ++       +   E     R T     
Sbjct: 102  IEFIDAEEEEDLFIAIREEDLTPEHTHLEIDPSLILGIGAAHVPFPEHNASPRVTMGAGM 161

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S   L+  D  G   +   V    +        G       + L+ A+   
Sbjct: 162  IKQALGFGASNMKLRP-DTRG--HLLHYVQKPIVHTQTSKVIGSDDRAAGQNLVVAVLSY 218

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD------- 972
            +  ++ D  +   + +   V     F R    +  R    + ++IE+   +         
Sbjct: 219  EGFNIEDALIFNKASIERGV-GRSHFFRTYDGEERRYPGGQIDKIEVPDEEVSGSHGAES 277

Query: 973  ----DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
                D   I++     R  ++L G+ +           ++S +               + 
Sbjct: 278  YQNLDSDGIINPETVVREKDVLIGKTSPPRFLEEPSGELISVE---------------KR 322

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                  + S +     +  + E    +                R+VKV     R  + GD
Sbjct: 323  RDTSVTMRSNERGIVDTVILTEGENSS----------------RLVKVRTRDIRVPEVGD 366

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG+V  I+P E+MPF + G   D+V+NP  +PSRM VG + E   G      
Sbjct: 367  KFASRHGQKGVVGLIIPQENMPFTEAGIAPDLVVNPHAIPSRMTVGHMLEMLGGKVGSLE 426

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G++I++     +    +      L                                    
Sbjct: 427  GRRIEATAFSGEEEDTLRDSLQALGFAHNGREVM-------------------------- 460

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                   G       +TG+ F   + VG IY  KL HMVS K++
Sbjct: 461  ---------------------YDG-------ITGKQFKADIYVGVIYYQKLYHMVSSKMH 492

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV------ 1322
            ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V      
Sbjct: 493  ARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMALKERLLDESDKVQQYVCA 552

Query: 1323 ---------VGRTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                       R      +  GN  D +      +F +L+ EM+++G++  L     
Sbjct: 553  KCGMIAFLDHNRNVT-RCLACGNETDIYSVEMSYAFKLLLDEMKSMGIAPRLHLEDQ 608



 Score = 79.7 bits (195), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 57/349 (16%), Positives = 111/349 (31%), Gaps = 35/349 (10%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G  E P   V + +       LS     +      +  +  D       +     G  ++
Sbjct: 19  GLCEDPTALVQNVRKMRRRGELSTEINISYKEFNGDIIVHTDRGRARRPLIVVENGRPLI 78

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +         +    I++ LI F++ ++   + +    +               T +
Sbjct: 79  TNDDIRKLETNDIEFPDLISSGLIEFIDAEEEEDLFIAIREEDLTPE---------HTHL 129

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   +   G  I A      E   + R+ + +  G +  +         ++         
Sbjct: 130 EIDPSLILG--IGAAHVPFPEHNASPRVTMGA--GMIKQALGFGASNMKLRPDTRGHLLH 185

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+P+V                     D A G+N++VA + + G+N ED+++ ++  + 
Sbjct: 186 YVQKPIVH----------TQTSKVIGSDDRAAGQNLVVAVLSYEGFNIEDALIFNKASIE 235

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNP 890
             V  S     ++   R    G  +               E  +N+D  GII     V  
Sbjct: 236 RGVGRSHFFRTYDGEERRYPGGQIDKIEVPDEEVSGSHGAESYQNLDSDGIINPETVVRE 295

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            D+L+GK +P         E +            RDTS+ + S   G V
Sbjct: 296 KDVLIGKTSPPRFLEEPSGELI-------SVEKRRDTSVTMRSNERGIV 337


>gi|57337348|emb|CAH69682.1| RNA polymerase, beta subunit [uncultured bacterium]
          Length = 313

 Score =  311 bits (797), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 185/308 (60%), Positives = 237/308 (76%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++
Sbjct: 65  AGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YLSA+EE    IAQAN++  EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS
Sbjct: 125 VDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AA+LIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  +VAKR G
Sbjct: 185 VAAALIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERAVAVDSGVTVVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +++ VDA RIVI+  E +L P  +G+DIY L K+ RSNQNTC+NQRP V +G+ V   D+
Sbjct: 245 MIDYVDASRIVIKVNEDELLPGEAGIDIYSLTKYTRSNQNTCINQRPCVMLGEPVMAGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|83763747|emb|CAJ00207.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 14D05]
          Length = 351

 Score =  311 bits (796), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 186/362 (51%), Positives = 254/362 (70%), Gaps = 13/362 (3%)

Query: 715  MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            +E  +A  SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNT
Sbjct: 1    LERNIAVDSGVTAVAKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNT 60

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            C+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V
Sbjct: 61   CINQRPTVLPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVV 120

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDIL
Sbjct: 121  QEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDIL 180

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            VGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++
Sbjct: 181  VGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDK 240

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S   + 
Sbjct: 241  RALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLD 287

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R QW +  ++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++V
Sbjct: 288  TIGRKQWLEQVLEDDALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIV 347

Query: 1075 KV 1076
            KV
Sbjct: 348  KV 349


>gi|58618681|gb|AAW80835.1| RNA polymerase II second largest subunit [Cotylidia sp. MB5]
          Length = 892

 Score =  311 bits (796), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 138/900 (15%), Positives = 273/900 (30%), Gaps = 148/900 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 124  RYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERPELDDRDHFGKKRL 180

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   ++ + +   +        +      +    + + +     +   
Sbjct: 181  DLAGPLLAGLFRMLFRKLTKDVYRYLQKCVEGHKAFNISLAVKHNTITNGLKYSLATGNW 240

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 241  GDQKKSMTTKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 296

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   A ++           + +         L ++EE     A 
Sbjct: 297  CPAETPEGQACGLVKNLALMATISVGSLSAPVIEFLEEWG-------LESLEEN----AH 345

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            +   L +       +   R     +   ++     D SP+  V             D+ R
Sbjct: 346  SPIPLTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGR 405

Query: 690  VLMGCNMQRQAVPLLKAEAP--FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            V     +       L+ +          +   A+         + G++E +DA       
Sbjct: 406  VCRPLFIVENQQLALQKKHVKWLNQGYRDDDPAQDPYKWDSLVKGGVIEYLDAEEEETVM 465

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +    +   +     + +    ++ +     R  +K              PS  LG    
Sbjct: 466  ICMTPEDLENSRLQQQGIDPHANDGDFDPAAR--LKSVQNAHTWTHCEIHPSMILG---- 519

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N                        ++       +G       +  
Sbjct: 520  ---ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM 558

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 559  -----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDS 607

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    ++ R  +D  ++S   + E+ E   R+          +      
Sbjct: 608  VIMNQSSIDRGLF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDG 666

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K+  +  D                +E  QR     +    T   
Sbjct: 667  LIAPGTGVSGEDIIIGKTAPIPPD---------------SEELGQRTRTHTRRDVSTPLK 711

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +++      D       + VKV V   R  Q GDK A RHG KG +      E
Sbjct: 712  STENGIVDQVLITTNSD-----GQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQE 766

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +             
Sbjct: 767  DMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--------- 817

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                             ++     + LR       G+ V                     
Sbjct: 818  ----------------DLTVESVSTFLRQKGYQSRGLEVM-------------------- 841

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G+S
Sbjct: 842  --YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRS 892



 Score =  138 bits (347), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 96/767 (12%), Positives = 217/767 (28%), Gaps = 101/767 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 49  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREIA 104

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G     S ++      + L+++ +  + +              +      + 
Sbjct: 105 LDFIGNR-GTATGLSRERRLRYAQEILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 160

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  +    +      +    P+L          +   +     K  +        +
Sbjct: 161 LAALERPELDDRDHFGKKRLDLAGPLLAGLFRMLFRKLTKDVYRYLQKCVEGHKAFNISL 220

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   +  G  ++  R    +      R         
Sbjct: 221 AVKHNTITNGLKYSLATGNWGDQKKSMTTKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 280

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +  +   + E +    ++S+
Sbjct: 281 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMATISVGSLSAPVIEFLEEWGLESL 340

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 NA   +     F     +    +  N +  I   RR   +            + 
Sbjct: 341 ----EENAHSPIPLTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKE 396

Query: 559 RDVHPTHYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
             ++        P    E          +    +            K         + YL
Sbjct: 397 LRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNQGYRDDDPAQDPYKWDSLVKGGVIEYL 456

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQ 670
            A EEE   I      L+      + +      G+     R             +  P  
Sbjct: 457 DAEEEETVMICMTPEDLENSRLQQQGIDPHANDGDFDPAARLKSVQNAHTWTHCEIHPSM 516

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS+IPF +++ S R      M +QA+ +                           
Sbjct: 517 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV-------------------- 556

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + +  Y       +     +  R           
Sbjct: 557 ---------------------RMDTMANILYYPQKPLATTRSMEYLKFR----------- 584

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G+N +VA + + GYN EDS+++++  +   +F S++   +  +
Sbjct: 585 -------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDL 631

Query: 851 ARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            + + +   E            +       I++ G+I  G  V+  DI++GK  P     
Sbjct: 632 EKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDS 691

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               ++        +    RD S  + S  +G V  V I       K
Sbjct: 692 EELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITTNSDGQK 731


>gi|51035545|emb|CAH10908.1| RNA polymerase B subunit [Natronobacterium gregoryi]
 gi|51035547|emb|CAH10909.1| RNA polymerase B subunit [Natronobacterium sp. SSL-6]
          Length = 435

 Score =  311 bits (796), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 86/253 (33%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DEE +   L  A  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDEEDLRDGLEEAGFDAAGKETMYSGITGEKVEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    +V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETKVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|89274900|gb|ABD65891.1| RNA polymerase II second largest subunit [Pycnoporus sp. ZW02.30]
          Length = 896

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 152/1025 (14%), Positives = 298/1025 (29%), Gaps = 166/1025 (16%)

Query: 285  LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            ++S  EKG K +      L        + N     I     D+        +       I
Sbjct: 18   IRSAVEKGGKTISQFQVKLYHRSQERSLGNVMKATIPYIKVDIPIWVVFRALG-----VI 72

Query: 345  PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
                +          N ++        +  +   R +    +        +         
Sbjct: 73   SDRDILEHICYDMQDNQMLEMLKPCIDEGFVIQDREIALDYIGNRGTTTGL---NRERRL 129

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 130  RYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRDLDDRDHFGKKRL 186

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +    + + +     +   
Sbjct: 187  DLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKYSLATGNW 246

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 247  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 302

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  + ++           + +  + +         EEN + + 
Sbjct: 303  CPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSST 354

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D  R
Sbjct: 355  PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDPGR 411

Query: 690  VLMGCNMQRQAVPLLKAEA--PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            V     +      LL+       V    +          I      +++  +   ++I  
Sbjct: 412  VCRPLFIVENQQLLLQKRHIENLVRGKEDPEFEYKWDNLIKDGVIELLDAEEEETVMICM 471

Query: 748  VEGDLDPST---SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               DL+ S    +G+D +   +F  S           +K              PS  LG 
Sbjct: 472  TPEDLENSRLQAAGIDPHADAEFDPSA---------RLKAPTNAHTWTHCEIHPSMILG- 521

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                        ++       +G       
Sbjct: 522  ------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFL 557

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +               +  +             +       +   +  + AI      + 
Sbjct: 558  VRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQ 606

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +   
Sbjct: 607  EDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLE 665

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G N         K+  +  D      R++          ++     +  Q   
Sbjct: 666  EDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRTHTKRDVSTPLKSTESGIVDQVLI 725

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       + VK+ V   R  Q GDK A RHG KG +    
Sbjct: 726  --------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITY 765

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +          
Sbjct: 766  RQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------ 819

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                ++       LR       G+ V                  
Sbjct: 820  -------------------DLTVESVSQFLRQKGYQSRGLEVM----------------- 843

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ 
Sbjct: 844  -----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVE 891

Query: 1285 GKSNR 1289
            G+S  
Sbjct: 892  GRSRD 896



 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 102/771 (13%), Positives = 218/771 (28%), Gaps = 113/771 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 55  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDNQMLEMLKPCIDEGFVIQDREIA 110

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  +   ++  
Sbjct: 111 LDYIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 169

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 170 LERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVK 229

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 230 HNT--------ITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTP 281

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + E +   
Sbjct: 282 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEW 341

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++S+      NA         F     +    +  N +  I   RR   +         
Sbjct: 342 GLESL----EENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 397

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L         V      E  Y K  +      
Sbjct: 398 IRERELRLYTDPGRVCRPLFIVENQQLLLQKR-HIENLVRGKEDPEFEY-KWDNLIKDGV 455

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDA 666
           +  L A EEE   I      L E+       +      E                   + 
Sbjct: 456 IELLDAEEEETVMICMTPEDL-ENSRLQAAGIDPHADAEFDPSARLKAPTNAHTWTHCEI 514

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 515 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 558

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 559 -------------------------RMDTMANILYYPQKPLATTRSMEYLRFR------- 586

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F SI+   
Sbjct: 587 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRS 629

Query: 847 FEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E            +       ++E G+I  G  VN  DI++GK  P 
Sbjct: 630 YMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEEDGLIAPGTNVNGEDIIIGKTAPI 689

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++        +    RD S  + S  SG V  V I       K
Sbjct: 690 PPDSEELGQRT-------RTHTKRDVSTPLKSTESGIVDQVLITTNAEGQK 733


>gi|195333588|ref|XP_002033472.1| GM21328 [Drosophila sechellia]
 gi|195582601|ref|XP_002081115.1| GD10835 [Drosophila simulans]
 gi|194125442|gb|EDW47485.1| GM21328 [Drosophila sechellia]
 gi|194193124|gb|EDX06700.1| GD10835 [Drosophila simulans]
          Length = 1137

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 114/621 (18%), Positives = 206/621 (33%), Gaps = 122/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 608  NRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 667

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 668  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 716

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 717  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 776

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 777  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 835

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + IE++  
Sbjct: 836  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYIERVMV 877

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 878  SANAEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 935

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 936  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 956

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 957  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1002 SPLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1061

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1062 ISYGASMLIMERLMISSDAFEVDVCRTCGR-MAYCSWCHFCQSSA-----NVSKISMPYA 1115

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1116 CKLLFQELTSMNVVPKMILEN 1136



 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 119/992 (11%), Positives = 280/992 (28%), Gaps = 202/992 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 LSTF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           + +           +   +             A + M    V        T     E+ +
Sbjct: 258 IQSLIGLDSKSQNRFGASLIDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEARE 317

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            L + +   L    V    +    +    +   ++  E  +   +  D    K LE    
Sbjct: 318 LLLTTI---LAHVPVDNFNLQMKAIYVSMMVRRVMAAELDKTLFDDRDYYGNKRLELAGS 374

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                   L+         I +  +       K A  D+ + MR   ++  +  ES  + 
Sbjct: 375 LLSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAISS 428

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             +   ++ +   G  ++  RL+  +   +            K+                
Sbjct: 429 GNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ--------- 479

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                +    +  + +    +  +           +   ++       + +         
Sbjct: 480 PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIREVSGNPIN 539

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +  +  +  + N L    +  +        + R         VH ++  R     T  G 
Sbjct: 540 NPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGGR 598

Query: 579 NIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                  + +   +     ++      RK  D  +   + YL   EE + +IA       
Sbjct: 599 LCRPYVIVENRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------- 651

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
               + E+ +  R               ++  P  ++ + A L+P+  ++ S R    C 
Sbjct: 652 ----WNEDQIEDR------------TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCA 695

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ ++         G        S                                
Sbjct: 696 MGKQAMGMI---------GYNQKNRIDS-------------------------------- 714

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                            N      P+VK                T+   L  G+N  VA 
Sbjct: 715 --------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVAV 750

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEGL 873
           M + GY+ ED++++++  +       +  +  +   +          +      ++ + +
Sbjct: 751 MSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKVI 810

Query: 874 KN---IDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKAV 922
                +D  GI+  G +V    I++ K  P        +G+S   P   +  +  G +  
Sbjct: 811 FKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPYTAVPISYKGPEPS 870

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +    +   +     +  +    R     ++
Sbjct: 871 YIERVMVSANAEEDFLIKILLRQTRIPEIGDK 902


>gi|126722445|dbj|BAF48636.1| DNA-dependent RNA polymerase subunit B' [Natronococcus occultus]
          Length = 434

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 101/427 (23%), Positives = 161/427 (37%), Gaps = 78/427 (18%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +   + V    +    F R    +  R    + 
Sbjct: 51   GFDERPAAQNFVVAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQE 109

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 110  DRFEIPSQD-------VRGARGEEAYTHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEP 162

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 163  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 210

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   
Sbjct: 211  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIG 270

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++                                                 
Sbjct: 271  GKLGAMEGRRVDG----------------------------------------------- 283

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DE  +   L  A  D +G+  +Y G+TGE  +  + VG I+  KL H
Sbjct: 284  ------TP-FLGEDESELREGLEEAGFDSAGKETMYSGITGEKIEAEIFVGIIFYQKLYH 336

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD 
Sbjct: 337  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDR 396

Query: 1321 ---DVVG 1324
                V G
Sbjct: 397  EFIHVCG 403



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYTHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    +V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETKVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|194883820|ref|XP_001975995.1| GG20240 [Drosophila erecta]
 gi|190659182|gb|EDV56395.1| GG20240 [Drosophila erecta]
          Length = 1137

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 113/621 (18%), Positives = 206/621 (33%), Gaps = 122/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 608  NRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 667

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 668  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 716

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 717  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 776

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 777  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 835

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + +E++  
Sbjct: 836  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYVERVMV 877

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 878  SANAEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 935

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 936  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 956

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 957  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1002 APLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1061

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1062 ISYGASMLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----NVSKISMPYA 1115

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1116 CKLLFQELTSMNVVPKMILEN 1136



 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 121/993 (12%), Positives = 278/993 (27%), Gaps = 204/993 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDE 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 LSTF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           + +           +   +             A + M    V        T     E+ +
Sbjct: 258 IQSLIGIDSKSQNRFGASLLDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEARE 317

Query: 279 -KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             LT+ L     +     +      L    V    ++        +  D    K LE   
Sbjct: 318 LLLTTILAHVPVDNFNLQMKAIYVSLMVRRVMAAELDKT----LFDDRDYYGNKRLELAG 373

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+         I +  +       K A  D+ + MR   ++  +  ES  +
Sbjct: 374 SLLSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAIS 427

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+  +   +            K+               
Sbjct: 428 SGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ-------- 479

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +    +  + +    +  +           +   ++       + +        
Sbjct: 480 -PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIREVSGNPI 538

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  +  +  + N L    +  +        + R         VH ++  R     T  G
Sbjct: 539 NNPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGG 597

Query: 578 HNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   + +   +     ++      RK  D  +   + YL   EE + +IA      
Sbjct: 598 RLCRPYVIVENRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------ 651

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                + E+ +  R               ++  P  ++ + A L+P+  ++ S R    C
Sbjct: 652 -----WNEDQIEDR------------TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQC 694

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 695 AMGKQAMGMI---------GYNQKNRIDS------------------------------- 714

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N      P+VK                T+   L  G+N  VA
Sbjct: 715 ---------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVA 749

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEG 872
            M + GY+ ED++++++  +       +  +  +   +          +      ++ + 
Sbjct: 750 VMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKV 809

Query: 873 LKN---IDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKA 921
           +     +D  GI+  G +V    I++ K  P        +G+S   P   +  +  G + 
Sbjct: 810 IFKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPYTAVPISYKGPEP 869

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
             V    +   +     +  +    R     ++
Sbjct: 870 SYVERVMVSANAEEDFLIKILLRQTRIPEIGDK 902


>gi|52694213|emb|CAG30636.1| DNA-directed RNA polymerase beta chain [Pseudomonas psychrophila]
          Length = 319

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 187/318 (58%), Positives = 244/318 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLA 806
           +R+DI+ADGPSTD+G+LA
Sbjct: 302 QRSDIVADGPSTDMGELA 319


>gi|242392240|dbj|BAH80357.1| RNA polymerase subunit B' [Haloferax prahovense]
          Length = 609

 Score =  311 bits (796), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 204/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEQVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIDISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNNDLDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 43.9 bits (102), Expect = 0.18,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+ Y+A     L+ED                          ++  P+ +  
Sbjct: 101 VEFIDAEEEEDIYVAVDEDELNEDH-----------------------THLEIDPQLIFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 174


>gi|255083755|ref|XP_002508452.1| predicted protein [Micromonas sp. RCC299]
 gi|226523729|gb|ACO69710.1| predicted protein [Micromonas sp. RCC299]
          Length = 1159

 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 125/319 (39%), Gaps = 72/319 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                    VK  V   R  + GDK + RHG KG+   I+   D+PF + G   D+++NP 
Sbjct: 895  TSDEGQFNVKCLVRHTRRPEVGDKFSSRHGQKGVCGTIVEQSDLPFSERGICPDLIMNPH 954

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     LG K       +K                         
Sbjct: 955  GFPSRMTV--------GKMIELLGGKAGLQDGKFKYGT---------------------- 984

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G    +++ +L       +G+ +++ G+TGEP 
Sbjct: 985  ------------------------AFGGDTVTSLSEVLVEHGFSYNGKDLMHCGITGEPL 1020

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  KL HMV DK++AR+ G   ++T+QP  G++  GG RLGEME  C+  Y
Sbjct: 1021 VAYIFMGPVYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRARDGGLRLGEMERDCLIGY 1080

Query: 1306 GAAYVLQEMLTIKSD-----------------DVVGRTRVYESIVAGNDTFETGTPESFN 1348
            GAA ++ E L I SD                    GR    +    G        P +  
Sbjct: 1081 GAAMLILERLMISSDQFEAQVCTNCGLLGYKHHGTGRNLCQQC-ADGGTVSALKLPYACK 1139

Query: 1349 VLVKEMQALGLSIDLENSR 1367
            +L +E+Q++ +   L  S 
Sbjct: 1140 LLFQELQSMNICPRLTLSD 1158



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 130/986 (13%), Positives = 284/986 (28%), Gaps = 204/986 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFPIT-AFSGAAMLEFVSYEFDPP- 84
           L+     S+++ +          NE ++     K+   +T        L++ + +   P 
Sbjct: 53  LVRQHIDSFNYLI----------NEEIKKIIAAKANEKVTCDTDPNFYLKYTNIQVGKPS 102

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIV-FDVDEFTGAKSIKDIKEQSIYMGDL 135
                   +     C  RD+TYA P+ + +      ++   T    +       + +G +
Sbjct: 103 VEEDFIVEEITPQQCRLRDMTYAAPVTVDVEYTRGKEIVTNTSKNGVG-----GVTIGRI 157

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDK- 169
           PLM                           G FV+KG +++++ Q   S   I  D D  
Sbjct: 158 PLMLRSSRCILTGKSEEELARLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIIIDIDNK 217

Query: 170 ----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMD 224
                  + S     +   I  +             +++R +    ++P+   L A+G +
Sbjct: 218 GEVGASVTSSTHERKSKTNIVVK----------HGKLYLRHNTFTDEIPIMVALKAMGCE 267

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA----------KVSSSLVDIDTGEQV 273
           S+ E++    P   Y+          SA  +              ++++ ++        
Sbjct: 268 SDQEVVQMVGPDTAYASLLLPSLLECSALAIFTQQQALEYCGGKVRMATRMMYSRNKRSK 327

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           ++  + + +G++       +  + + +       V   I+        ++   V D+   
Sbjct: 328 VDEARDILAGVV-------LAHVPVPAYDFRQKCVYVAIMIRRILHAMVDPTQVDDKDYY 380

Query: 334 --EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             + +  +      +        NA ++       +K  +    DI + +R         
Sbjct: 381 GNKRLELAGQLLALLFEDCFKRLNADLKRQADAVLSKSNRATQFDIIKCIR--------- 431

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            +   +     +      TV R +M  +        +  I     + ++  +        
Sbjct: 432 -QDTLSNGLEHAISSGNWTVKRFRMERKGVTQVLSRLSFISA---LGMMTRITSQFEKTR 487

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +     L   +   +      +     L    ++   +++ D +  +            
Sbjct: 488 KVSGPRALQPSQWGMLCPSDTPEGESCGLVKNLALMTHVTTDDEEEPLRSLAHVLGVEPL 547

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRIC 570
            +               +N      H            + R     E   VH T      
Sbjct: 548 LLLVGQELHSPGSALVFLNGHILGVHQDPARFASDFRLLRRRGRVGEFVSVHTTTG--NV 605

Query: 571 PAETSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              +  G        V +     +      ++       D      V YL   EE N YI
Sbjct: 606 YIASDGGRVCRPLLIVENGELLVKQVHLDALKAGRWTFNDFLTQGFVEYLDVNEENNSYI 665

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A   S +                         +   ++  P  ++ + A +IP+  ++ S
Sbjct: 666 ALYESEITP-----------------------ETTHLEIEPFTLLGVCAGIIPYPHHNQS 702

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R    C M +QA+                                           I  
Sbjct: 703 PRNTYQCAMGKQAMGN-----------------------------------------IAF 721

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            + +   +   + +Y               Q+P+VK                     L  
Sbjct: 722 NQLNRMDTLMYLLVYP--------------QKPIVK----------TKTIELIGYDRLGA 757

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-GPEEITRDIP 866
           G+N  VA M + GY+ ED+++++   +       I + ++    +       + I    P
Sbjct: 758 GQNATVAVMSYSGYDIEDAIVMNRASLDRGFGRCIVLRKYGCTIKKYSNRTQDRIVPPTP 817

Query: 867 NV--SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                    + +D+ GI  VG +++PGD+ + K +P       P  + +   F       
Sbjct: 818 AQTGPNGRHRLLDKDGIAAVGEKISPGDVYINKQSPGNTRDPLPNPQAMPDSFYRPTA-- 875

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGI 950
              S + P G S  VVD  +      
Sbjct: 876 --QSYKGPQGES-CVVDKVMLTTSDE 898


>gi|315259444|gb|ADT91921.1| DNA-directed RNA polymerase beta subunit [Enterococcus caccae]
          Length = 392

 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 131/420 (31%), Positives = 182/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L      +  +  D  +     V   V 
Sbjct: 45   IVLLGEKVEKGDTLADGPS-MEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R      +++       +                    
Sbjct: 164  PKGVTELSAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI----------------VHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKINEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D                 
Sbjct: 267  TPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHIATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                         +DD V     +        T ++DG                      
Sbjct: 312  -------------NDDDVWETVREAGMASDAKTVLYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 127/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  + +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEYVDASEVRVRRDNGALDK-------YMVTKFRRSNSGTSYNQRPIVLLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|148243057|ref|YP_001228214.1| hypothetical protein SynRCC307_1958 [Synechococcus sp. RCC307]
 gi|147851367|emb|CAK28861.1| Hypothetical protein SynRCC307_1958 [Synechococcus sp. RCC307]
          Length = 165

 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 83/142 (58%), Positives = 106/142 (74%)

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            + DG +GEPFD+PVTVG  Y+LKL H+V DK++ARSTG YSLVTQQPLGGK+ +GGQRLG
Sbjct: 1    MIDGRSGEPFDQPVTVGRAYILKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLG 60

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGAAY LQE+LT+KSDD+ GR     +IV G      GTPESF VL++E+Q
Sbjct: 61   EMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQ 120

Query: 1356 ALGLSIDLENSRTKNSAKMEEI 1377
            +LGL I +          M+++
Sbjct: 121  SLGLDIAVYTDEGAEVDLMQDV 142


>gi|243010752|gb|ACS94453.1| RpoB [Mycobacterium nebraskense]
          Length = 248

 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 142/240 (59%), Gaps = 40/240 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAA--------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             + +  +  +    VSTPVFDGA E  +  +L            
Sbjct: 145  ----------------GLPKELQSAEPNAIVSTPVFDGAREAELQGLLSCTLPNRDNEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +D  G+++L+DG +G+PF  PVTVG++Y++KL+H+V DK++ARSTG YS++TQQPLGGK+
Sbjct: 189  VDGDGKAVLFDGRSGDPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKA 248



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|242392262|dbj|BAH80368.1| RNA polymerase subunit B' [Halorubrum coriense]
          Length = 609

 Score =  310 bits (795), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 128/603 (21%), Positives = 208/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA            + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEGDVTEDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L     + SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGQLEEYGFESSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++AR  G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARLRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 56/373 (15%), Positives = 116/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +     E+     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHENPDELAEQIREARRRGDVSEMVNVSVKDRTREVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA        
Sbjct: 64  RRPLIVVENGEPLLGDEEVEALERGDVEFEDLVERGYVEFIDAEEEEDILVA---VDEGD 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTEDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 42.8 bits (99), Expect = 0.45,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + ED                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEGDVTEDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|52694215|emb|CAG30637.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           frederiksbergensis]
          Length = 318

 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 186/317 (58%), Positives = 243/317 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRV 301

Query: 789 RRNDIIADGPSTDLGDL 805
           +R+DI+ADGPSTD+G+L
Sbjct: 302 QRSDIMADGPSTDMGEL 318


>gi|269913237|emb|CAY86045.1| RNA polymerase beta subunit [Asaia bogorensis]
          Length = 309

 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 144/312 (46%), Positives = 198/312 (63%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL+ FY  + +++   
Sbjct: 61  KRKLPVTTLLYALEGEHSIAARAAKAAEGGDVEALGIRGMDQDEILAYFYGTVPFTRMPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+   L D DTGE V E+  KLT+ + + + E   K + +    L
Sbjct: 121 GWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMCRKIAET-TKDVLVGRADL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A+D+VN  TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL 
Sbjct: 179 LGRFIAQDLVNENTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVD 297

Query: 424 TPDDVRHIRKED 435
            PD +R +RKED
Sbjct: 298 APDTMRVLRKED 309


>gi|315259456|gb|ADT91927.1| DNA-directed RNA polymerase beta subunit [Enterococcus moraviensis]
 gi|315259464|gb|ADT91931.1| DNA-directed RNA polymerase beta subunit [Enterococcus termitis]
          Length = 392

 Score =  310 bits (795), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 132/420 (31%), Positives = 179/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L      +  +  D  +     V   V 
Sbjct: 45   IVLLGEKVEKGDTLADGPS-MEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E                   
Sbjct: 164  PKGVTELSAEERLLHAIFGEKAR-----------------EVRDTSLRVPHGGGGIVHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D                 
Sbjct: 267  TPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHIATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                         +DD V     +        T ++DG                      
Sbjct: 312  -------------NDDDVWETVREAGMASDAKTVLYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 127/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  + +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEYVDASEVRVRRDNGALDK-------YMVTKFRRSNSGTSYNQRPIVLLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|291196474|emb|CBG27594.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           thermotolerans]
          Length = 305

 Score =  310 bits (795), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 188/305 (61%), Positives = 236/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DGKVT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDGKVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++LDE+G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLDEEGRLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLVK GD V R DI+AD
Sbjct: 241 SVDASRIVVRVQDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVKKGDVVARGDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|313127541|ref|YP_004037811.1| DNA-directed RNA polymerase, subunit b' [Halogeometricum borinquense
            DSM 11551]
 gi|242392246|dbj|BAH80360.1| RNA polymerase subunit B' [Halogeometricum borinquense DSM 11551]
 gi|312293906|gb|ADQ68366.1| DNA-directed RNA polymerase, subunit B' [Halogeometricum borinquense
            DSM 11551]
          Length = 610

 Score =  310 bits (795), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 129/601 (21%), Positives = 206/601 (34%), Gaps = 96/601 (15%)

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              DE+   D+I  G   +  D     ++ VA            + I  +++       I 
Sbjct: 87   KNDEIDFEDLIDRG-YIEFIDAEEEEDIYVAVDEDDLNEDHTHLEIDPQLIFGIGAGMIP 145

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              E     R T      + +    +     +   +     +        +        G 
Sbjct: 146  YPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGF 202

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
                  +    A+   +  ++ D  L +  G     +    F R    +  R    + ++
Sbjct: 203  DERPAAQNFTVAVMSYEGFNIEDA-LVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEDR 261

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
             E+ ++D       +           L     V+      +++VL           +   
Sbjct: 262  FEVPSQD-------VRGARGEDAYNHLDDDGLVNPETVVDENSVLLGKTSPPRFLEEPDD 314

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                  + +R         E          + +               ++ KV V  +R 
Sbjct: 315  MGGLSPQKRRETSVTMRSGENGVVDTVTLMEGE------------DGSKLAKVSVRDQRI 362

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             + GDK A RHG KG+V  + P EDMPF  DG   D+V+NP  +PSRM V        G 
Sbjct: 363  PELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVINPHALPSRMTV--------GH 414

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                LG K+ +L                                                
Sbjct: 415  VLEMLGGKVGALEGRRVDGT---------------------------------------- 434

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                   F G DE  +   L       SG+ ++Y G+TGE  +  + VG I+  KL HMV
Sbjct: 435  ------AFQGEDESELRGALEEHGFKSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMV 488

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
            S+K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD   
Sbjct: 489  SNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEE 548

Query: 1321 -----D-----VVGR--TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                 D     V  R   R+Y+  V G  ++  E     +F +L+ EM ALG+   L   
Sbjct: 549  VYVSADTGMVAVEDRDQRRIYD-PVTGDEDNIHEIEISYAFKLLLDEMIALGIRPRLNLE 607

Query: 1367 R 1367
             
Sbjct: 608  D 608



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + ++ A EEE+ Y+A     L+ED                          ++  P+ +  
Sbjct: 102 IEFIDAEEEEDIYVAVDEDDLNEDH-----------------------THLEIDPQLIFG 138

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 139 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 175


>gi|315259446|gb|ADT91922.1| DNA-directed RNA polymerase beta subunit [Enterococcus durans]
          Length = 392

 Score =  310 bits (795), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 129/420 (30%), Positives = 181/420 (43%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +     V   V 
Sbjct: 45   IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R      +++       +                    
Sbjct: 164  PKGVTELSAEERLLHAIFGEKARE-VRDTSLRVPHGGGGI----------------VHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 267  TPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 312  -------------SDEDVWETVREAGMASDAKTVLYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  191 bits (486), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 128/222 (57%), Positives = 166/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA +I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEFVDASQIRVRRDNGALDK-------YDITKFRRSNSGTSYNQRPIVHLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|269913243|emb|CAY86048.1| RNA polymerase beta subunit [Asaia krungthepensis]
          Length = 312

 Score =  310 bits (795), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 145/314 (46%), Positives = 200/314 (63%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL+ FY  + +++   
Sbjct: 61  KRKLPVTTLLYALEGEHSIAARAAKAAEGGDVEALGIRGMDQDEILAYFYGTVPFTRMPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+   L D DTGE V E+  KLT+ + + + E   K + +    L
Sbjct: 121 GWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMCRKIAET-TKDVLVGRADL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A+D+VN  TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL 
Sbjct: 179 LGRFIAQDLVNENTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD +R +RKEDI+
Sbjct: 298 APDTMRVLRKEDIL 311


>gi|60416616|emb|CAI43377.1| RNA polymerase, beta subunit [Klebsiella pneumoniae subsp.
           pneumoniae]
 gi|82655104|emb|CAJ19621.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655106|emb|CAJ19622.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655108|emb|CAJ19623.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655110|emb|CAJ19624.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655112|emb|CAJ19625.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655114|emb|CAJ19626.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655116|emb|CAJ19627.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655118|emb|CAJ19628.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655120|emb|CAJ19629.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655122|emb|CAJ19630.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655124|emb|CAJ19631.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655126|emb|CAJ19632.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655128|emb|CAJ19633.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655130|emb|CAJ19634.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655132|emb|CAJ19635.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655134|emb|CAJ19636.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655138|emb|CAJ19638.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655140|emb|CAJ19639.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655142|emb|CAJ19640.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655144|emb|CAJ19641.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655146|emb|CAJ19642.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655148|emb|CAJ19643.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655150|emb|CAJ19644.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|82655152|emb|CAJ19645.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 313

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 191/308 (62%), Positives = 239/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|289620352|emb|CBI53210.1| unnamed protein product [Sordaria macrospora]
          Length = 1117

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 107/441 (24%), Positives = 168/441 (38%), Gaps = 78/441 (17%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   + +       ++F 
Sbjct: 728  YPQRPMVITKTIQLIHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASLDRGFGRCQVFR 787

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            ++  +    + +  R+++  + +D+DD+  I    I         G    SG    KK T
Sbjct: 788  KYTAELQGYT-NGRRDRVGGIMKDEDDKP-IAKHAILDADGLAQVGSKVESGQTMIKKET 845

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L                 +  ++   +       Y  S   +       I+K+     +
Sbjct: 846  PLDQ-----------ISTGIAGDRGSDDYRDASTNYRISDPAI-------IDKVMI--SV 885

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 +++KV     R  + GDK + RHG KG+V  I+  EDMPF   G   DI++NP G
Sbjct: 886  NERENKLIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVNEEDMPFSDKGLRPDIIMNPHG 945

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++FE   G A V  G                       EK  G G       
Sbjct: 946  FPSRMTVGKLFECLTGKASVIAG-----------------------EKDYGFGD------ 976

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     E++   L        G+     G+TGEP +
Sbjct: 977  -----------------------AFRSHPVESMGQALIDHGFSWEGKDYFTSGITGEPME 1013

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G I+  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1014 AYIYNGPIFYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYG 1073

Query: 1307 AAYVLQEMLTIKSD----DVV 1323
            A+ +L E L I SD    DV 
Sbjct: 1074 ASQLLLERLMISSDGTELDVC 1094



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 134/998 (13%), Positives = 278/998 (27%), Gaps = 196/998 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L++    SY++F+   I    + N       +S            LEF       P    
Sbjct: 44  LVKQHIDSYNYFVNEEIKDIVKAN----RVVRS-----DQDPNFWLEFRDIRVGMPTRTE 94

Query: 89  D-D-------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
           D +       C  RDLTYA P+++ +         +T  KS+  I  ++I +  +P+M K
Sbjct: 95  DGEQVQSRNPCRLRDLTYAAPVEVDI--------AYTRDKSV--IVRKNIPLCRIPVMLK 144

Query: 141 D------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G FVI G +++++ Q   S          +     
Sbjct: 145 SAKCYLNGATNAQMEVFNECPLDPGGYFVIGGTEKVILIQEQLSKNRIIVEADEKTGGVM 204

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL-GMDS 225
             + +               + K   +V + + R           +P+   L A  G+  
Sbjct: 205 ASVTSST------------HERKSKTYVVLKKDRIVLQHNTLSEPIPIVIVLKAFGGLSD 252

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +I+         ++  D +      A          +L  +    ++  +  K  +   
Sbjct: 253 NDIIELVCGGD--ARYQDDFLINFDEAGRAGVYTQQQALEYVGARVKMGGNRPKFGAAPR 310

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV------IDEKSLEEIFHS 339
           ++  E+G+  L      L   +V  + ++     +YI            + K +++    
Sbjct: 311 RNHAEEGLDALA----NLVIAHVTVEGLDFYPKAVYIAMMVRRVLMAAQNPKLVDDRDFV 366

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             + + +           +    ++D   +  +      R                 +  
Sbjct: 367 GNKRLELAGQLISLLFEDLFKKFISDVKYNIDNFFKKPNRTSTYDPHGAIMANGHYISHG 426

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              + +    TV R  MN          + +I    ++  I    +          +   
Sbjct: 427 LNRAIQSGNWTVKRFNMNRAGITHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPS 486

Query: 460 GNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               + +           +  L +   I   +    +  ++     +  P+         
Sbjct: 487 QWGMLCTSDTPEGEACGLVKNLALMTHITTNVPEEPVKKMIFAADESVGPIREYTGTEMH 546

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S     +  +    +     +R +A  +  + R         +H   +       T EG 
Sbjct: 547 SKGSYIIHLNGTPFAVTREPKRFAARFRT-LRRRGWVSPFVSIHINEHFSAVHIATDEGR 605

Query: 579 NIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                  V +  S  +      ++           +  V YL   EE +  +A     + 
Sbjct: 606 ICRPYIIVKNGKSMLKAEHLKMLQLGQATFDTFLTSGVVEYLDVNEENDTLVALQEDQIT 665

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                       ++  P  ++   A LIPF  ++ S R    C 
Sbjct: 666 -----------------------NSTTHMEIEPFTILGAVAGLIPFPHHNQSPRNTYQCA 702

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+                                           I   + +   +
Sbjct: 703 MGKQAIGA-----------------------------------------IAYNQFNRIDT 721

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                +Y               QRP+V          I           L  G+N  V  
Sbjct: 722 LLYTLVYP--------------QRPMV----------ITKTIQLIHYDKLPAGQNATVVV 757

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI----TRDIPNVSEE 871
           M + GY+ ED++++++  +           ++    +    G  +      +D  +    
Sbjct: 758 MSYSGYDIEDALVLNKASLDRGFGRCQVFRKYTAELQGYTNGRRDRVGGIMKDEDDKPIA 817

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D  G+  VG++V  G  ++ K TP  +                 + D RD S   
Sbjct: 818 KHAILDADGLAQVGSKVESGQTMIKKETPLDQIS-------TGIAGDRGSDDYRDASTNY 870

Query: 932 PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                  + D  I ++  I  NER   + + Q     R
Sbjct: 871 R------ISDPAIIDKVMISVNERENKLIKVQTRQTRR 902


>gi|269913249|emb|CAY86051.1| RNA polymerase beta subunit [Asaia siamensis]
          Length = 311

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 146/314 (46%), Positives = 202/314 (64%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL+ FY  + +++   
Sbjct: 61  KRKLPVTTLLYALEGEHSIAARAAKAAEGGDVESMAIRGMDQDEILAYFYGTVPFTRMPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+   L D DTGE V E+  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMVRKIAET-TKDVLVGRADL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A+D+VN ETGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL 
Sbjct: 179 LGRFMAQDLVNEETGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD +R +RKEDI+
Sbjct: 298 APDTMRVLRKEDIL 311


>gi|242392232|dbj|BAH80353.1| RNA polymerase subunit B' [Haloferax gibbonsii]
          Length = 609

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 204/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEKVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNNDLDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 43.9 bits (102), Expect = 0.18,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+ Y+A     L+ED                          ++  P+ +  
Sbjct: 101 VEFIDAEEEEDIYVAVDEDELNEDH-----------------------THLEIDPQLIFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 174


>gi|242392230|dbj|BAH80352.1| RNA polymerase subunit B' [Haloferax denitrificans ATCC 35960]
          Length = 609

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 204/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEKVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNDDLDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 43.9 bits (102), Expect = 0.18,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+ Y+A     L+ED                          ++  P+ +  
Sbjct: 101 VEFIDAEEEEDIYVAVDEDELNEDH-----------------------THLEIDPQLIFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 174


>gi|52694217|emb|CAG30638.1| DNA-directed RNA polymerase beta chain [Pseudomonas lini]
          Length = 324

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 189/323 (58%), Positives = 247/323 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPSTDLGDLALGRNM 811
           +R+DI+ADGPSTD+G+LALG++M
Sbjct: 302 QRSDIMADGPSTDMGELALGQDM 324


>gi|57337370|emb|CAH69693.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
          Length = 313

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 189/308 (61%), Positives = 238/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INA P+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAXPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV +G VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|297791275|ref|XP_002863522.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp.
            lyrata]
 gi|297309357|gb|EFH39781.1| hypothetical protein ARALYDRAFT_917015 [Arabidopsis lyrata subsp.
            lyrata]
          Length = 1165

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 96/402 (23%), Positives = 150/402 (37%), Gaps = 66/402 (16%)

Query: 979  DRNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            +     R LM    G +A               ++I       + Q  V   + +     
Sbjct: 808  ENGTVDRILMPQRTGPDAEKMQILDDDGIASPGEIIRPNDVYIYKQIPVCTTRDKITSPL 867

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
               QY  ++   +          +            +K  +   R  + GDK + RHG K
Sbjct: 868  SDSQYRPAREFFKGPEGETQVVDRVALCSDKSGSLCIKYIIRHTRRPELGDKFSSRHGQK 927

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+   I+  ED PF + G   D+++NP G PSRM VG++ E     A V  G+       
Sbjct: 928  GVCGTIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAF 987

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              ++                                                       E
Sbjct: 988  GERSGHAD-------------------------------------------------KVE 998

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I+  L       SG+ +LY GL+GEP +  + +G IY  KL HMV DK++AR +G   +
Sbjct: 999  TISKTLVDKGFSYSGKDLLYSGLSGEPLEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVM 1058

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE 1330
            +T+QP  GKS  GG R+GEME  C+ AYGA+ ++ E L I SD          G    Y 
Sbjct: 1059 MTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYN 1118

Query: 1331 SIVA---------GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
              +          G++      P +  +L +E+Q++ +   L
Sbjct: 1119 YKLKKAVCSTCKNGDNIATMKLPYACKLLFQELQSMNVVPRL 1160



 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 133/999 (13%), Positives = 297/999 (29%), Gaps = 173/999 (17%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSGAAMLE 75
           F   PE + +  L++    S+++F+          N G++    +   I +    +  L 
Sbjct: 33  FQLVPEFLKVRGLVKQHLDSFNYFI----------NVGIKKIVHANCRIASVTDPSIYLR 82

Query: 76  FVSYEFDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           F +     P         + +   C   D+TYA P+ + +  +     +   +     I 
Sbjct: 83  FKNVRVGEPSIMNINISEEINPHMCRLADMTYAAPIYVNIEYVHGSHGKKATSVKNDFI- 141

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
                +G +P+M                           G FVIKG +++++ Q   S  
Sbjct: 142 -----IGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFVIKGTEKVLLIQEQLSKN 196

Query: 163 -IHFDHDK-----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVT 215
            I  D DK        + S ++  +  +I             K+ I++ + +  +K+P+ 
Sbjct: 197 RIIIDSDKKGNINASVTSSTEMTKSKTVI----------QMEKEKIYLFLHQFVKKIPIV 246

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             L A+GM+S+ EI+        +S            ++ +   K +   ++    +   
Sbjct: 247 IVLKAMGMESDQEIVQMVGRDPRFSASLLP-SIEECVSEGVNTQKQALDYLEAKVKKTSY 305

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
               +     L  L++  +  + +  +          ++     E  +      ++ S++
Sbjct: 306 GPPPEKDGRALYILRDLFLAHVPVRDNNFRQKCFYVGVMLRRMIEAML------NKDSMD 359

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVA 392
           +  +   + + +           +  T++++  K     L    R          T   +
Sbjct: 360 DKDYVGNKRLELSGQLMSLLFEDLFKTMLSEAIKKVDAILSKPSRASRFDFSQYLTTGDS 419

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           ++  +     +       + R +M+ +        +  +     +  I  +         
Sbjct: 420 QNTISVGLERTLSTGNFDIKRFRMHRKGMTQV---LTRLSFIGSLGFITKISPQFEKSRK 476

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +    +L   +   +      +     L    ++   +++ + +  +             
Sbjct: 477 VSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGVTDLE 536

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICP 571
           V               +N L    H R          + RA    E   V          
Sbjct: 537 VLSAEELHTPDSFLVILNGLILGKHRRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVY 596

Query: 572 AETSEGHNIGLVSSLTS-FARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             +  G     +       +RV  +    ++   R   D      + YL   EE N  IA
Sbjct: 597 VASDGGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNALIA 656

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              S    +     E              +     I+  P  ++ + A LIP+  ++ S 
Sbjct: 657 LYESEATTELDEGAE----------AAKIKADTTHIEIEPFTILGVVAGLIPYPHHNQSP 706

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R    C M +QA+                                           I   
Sbjct: 707 RNTYQCAMGKQAMGN-----------------------------------------IAYN 725

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           + +   +   + +Y               QRPL+                      L  G
Sbjct: 726 QLNRMDTLLYLLVYP--------------QRPLL----------TTRTIELVGYDKLGAG 761

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           +N  VA M   GY+ ED++++++  +       I +++     +  + G  +        
Sbjct: 762 QNATVAVMSNSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVATCQKYENGTVDRILMPQRT 821

Query: 869 SEEG--LKNIDECGIICVGAEVNPGDILVGK-----------ITPKGESPMTPEEKLLRA 915
             +   ++ +D+ GI   G  + P D+ + K            +P  +S   P  +  + 
Sbjct: 822 GPDAEKMQILDDDGIASPGEIIRPNDVYIYKQIPVCTTRDKITSPLSDSQYRPAREFFKG 881

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
             GE  V V   +L      S  +  +    R     ++
Sbjct: 882 PEGETQV-VDRVALCSDKSGSLCIKYIIRHTRRPELGDK 919


>gi|302820918|ref|XP_002992124.1| hypothetical protein SELMODRAFT_430375 [Selaginella moellendorffii]
 gi|300140050|gb|EFJ06779.1| hypothetical protein SELMODRAFT_430375 [Selaginella moellendorffii]
          Length = 1440

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 88/318 (27%), Positives = 132/318 (41%), Gaps = 65/318 (20%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   V+K  V   R  + GDK + RHG KG+   I+  +D PF + G   D+++NP 
Sbjct: 1171 TNESQQMVIKCQVRHTRRPELGDKFSSRHGQKGVCGTIVEQQDFPFTERGVCPDLIMNPH 1230

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM VG++ E   G A V  GK                                   
Sbjct: 1231 GFPSRMTVGKMIELLGGKAGVQSGK----------------------------------- 1255

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                          +  G     P       EAI++ L        G+ ++Y G+TG P 
Sbjct: 1256 --------------YHYGSAFGEPSGHADTVEAISATLVKHGFSYCGKDLIYSGITGCPL 1301

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G IY  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C+ AY
Sbjct: 1302 QAYIYMGPIYYQKLKHMVLDKMHARAQGPRVVLTRQPTEGRSREGGLRLGEMERDCLVAY 1361

Query: 1306 GAAYVLQEMLTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNV 1349
            G++ ++ E L I SD          G    Y   +          G +      P +  +
Sbjct: 1362 GSSMLILERLMISSDQFQVQVCTNCGLLGYYSHKLKMNFCSYCKNGENMAAMKLPYACKL 1421

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L +E+Q++ +   L+ + 
Sbjct: 1422 LFQELQSMNIVPRLQLAE 1439



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 131/926 (14%), Positives = 265/926 (28%), Gaps = 179/926 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP---IT-------AFSGAAMLEFVS 78
            L++    SY++F+   I       +G +     V P   I         +    +  F+ 
Sbjct: 333  LVKQHLDSYNYFVNCEIKKIIHA-KGNEKITSDVDPNFYIKYACDTFFQYFTNILFRFLD 391

Query: 79   YEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 P               C  RD+TY+ P+ + +        +    +  KD +   
Sbjct: 392  IFVGTPSIEQDYIRQDITPQQCRLRDMTYSAPISVDIEYT---RGKDIITRKGKDGQGAQ 448

Query: 130  IYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IH 164
            + +G +P+M                           G FV+KG +++++ Q   S   I 
Sbjct: 449  V-IGRMPVMLRSSRCILTGKSDAELAKLGECPLDPGGYFVVKGTEKVILIQEQLSKNRII 507

Query: 165  FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
             D D      +G L  A      +G            ++V  D    VP+   + A+GM+
Sbjct: 508  IDSD-----STGSLSLAVH---MRG-----------KLNVFSD---DVPIVVVMKAMGME 545

Query: 225  SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL-VDIDTGEQVIESGKKLTS 282
            S+ EI+        ++          ++  +    +    L   +    Q      K   
Sbjct: 546  SDQEIIQMVGTDPKFAGILAPSMQECASLGVYTTHQALEYLGTKVRVNRQWGSKQTKSKV 605

Query: 283  GLLKS-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFHSE 340
               +  L    +  + +         +   ++     E  ++   V D   +  +     
Sbjct: 606  DEARDILLNVFLAHVAVHKYDFRPKCIYVALMLRRMLEAILDKECVDDRDYVGNKRLELA 665

Query: 341  IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
             + + +L+ D    +     + V         A           D+ T  +  ++ +  +
Sbjct: 666  GQLLALLFEDLFKRSCSELKSNVDRTLSKMNRASQYDVSKSLKPDMLTSGLENAISSGNW 725

Query: 401  FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                     TV R +M+ +        V  +     +  +  +         +    +L 
Sbjct: 726  ---------TVKRFRMDKKGVTQV---VSRLSYIAALGHMTRVASQFEKSRKVSGPRSLQ 773

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              +   +      +     L    ++   I++ D ++ +     N       +       
Sbjct: 774  PSQWGMLCPCDTPEGEGCGLTKNLALMTHITTDDEEAPLIDLCTNLGVEDINLLSGEEFH 833

Query: 521  QLSQLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +      N      H R +  A     + RA    E   +      R     +  G  
Sbjct: 834  SKNAFLVMFNGTILGIHRRPQQFATLMRKLRRAGKIGEFVSIFVNEKQRCIYIASDGGRV 893

Query: 580  IGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
               V          + +    ++  +R   D      V YL   EE N  IA        
Sbjct: 894  CRPVVIADHGVSRIKEHHMKELKDGFRTFDDFLREGLVEYLDVNEENNALIAL------- 946

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                       I+  P  ++ + A LIP+  ++ S R    C M
Sbjct: 947  ----------------YEKEADSTTTHIEIEPFTILGVCAGLIPYPHHNQSPRNTYQCAM 990

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
             +QA+                                           I   +     + 
Sbjct: 991  GKQAMGN-----------------------------------------IAYNQLQRIDTL 1009

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
              + +Y               QRPL+                  +   L  G+N  VA M
Sbjct: 1010 LYLLVYP--------------QRPLL----------TTKSIELVNYDKLGAGQNASVAVM 1045

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
             + GY+ ED++++++  +       I +++F  + R  +    +             + +
Sbjct: 1046 SYSGYDIEDAIVMNKASLDRGFGRCIVLKKFSCLVRKYENRTMDRIVAPRQHGHATSQLL 1105

Query: 877  DECGIICVGAEVNPGDILVGKITPKG 902
            D+ GI  VG  +   DI V K +PK 
Sbjct: 1106 DQDGIASVGERIYDKDIFVNKESPKD 1131


>gi|269913253|emb|CAY86053.1| RNA polymerase beta subunit [Asaia siamensis]
          Length = 312

 Score =  310 bits (794), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 146/314 (46%), Positives = 202/314 (64%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL+ FY  + +++   
Sbjct: 61  KRKLPVTTLLYALEGEHSIAARAAKAAEGGDVESMAIRGMDQDEILAYFYGTVPFTRMPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+   L D DTGE V E+  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMVRKIAET-TKDVLVGRADL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A+D+VN ETGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL 
Sbjct: 179 LGRFMAQDLVNEETGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD +R +RKEDI+
Sbjct: 298 APDTMRVLRKEDIL 311


>gi|315259454|gb|ADT91926.1| DNA-directed RNA polymerase beta subunit [Enterococcus hirae]
          Length = 392

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 133/425 (31%), Positives = 182/425 (42%), Gaps = 87/425 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 45   IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 95

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 96   --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 147

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 148  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 206

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 207  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 261

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 262  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 311

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 312  ------------------SDEDVWETVREAGMASDAKTILYDG----------------- 336

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 337  ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 387

Query: 1291 GQRLG 1295
            GQR G
Sbjct: 388  GQRFG 392



 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 128/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEFVDASEIRVRRDNGALDK-------YAVTKFRRSNSGTSYNQRPIVHLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|269912602|emb|CAY86081.1| RNA polymerase beta subunit [Gluconacetobacter oboediens]
          Length = 311

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 149/314 (47%), Positives = 197/314 (62%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAESEAARAAKAAEGGDVESMEIQGMSPDEILSYFYGKVEFAKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DAFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEIY EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNESTGEIYAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD VR +RKEDI+
Sbjct: 298 VPDTVRVLRKEDIL 311


>gi|315259458|gb|ADT91928.1| DNA-directed RNA polymerase beta subunit [Enterococcus mundtii]
          Length = 392

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 133/425 (31%), Positives = 182/425 (42%), Gaps = 87/425 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 45   IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 95

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 96   --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 147

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 148  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 206

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 207  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 261

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 262  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 311

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 312  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 336

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 337  ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 387

Query: 1291 GQRLG 1295
            GQR G
Sbjct: 388  GQRFG 392



 Score =  191 bits (486), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 128/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEFVDASEIRVRRDNGALDK-------YSVTKFRRSNSGTSYNQRPIVHLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|80978843|gb|ABB54670.1| RNA polymerase beta subunit [Mycoplasma verecundum]
          Length = 592

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 204/448 (45%), Positives = 305/448 (68%), Gaps = 15/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNYATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+  GF++TPY KV +G V  +   YL+A EE     AQ++  +D+     +  +  R
Sbjct: 62  AKVDDLGFLKTPYFKVNNGVVDYSTTHYLTAAEEIGFSFAQSSVKVDDTNKIIDPYLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+   ++ID+I+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 122 RDYNYIIGTPDEIDYIEVSSKQIVSVAAAAIPFLENDDANRALMGSNMQRQAVPLLQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PFV TG+E+ +A+ S   +VAK AG+V  VD  +I+I++ +G+ D        Y L  F+
Sbjct: 182 PFVATGIEADIARYSSYNLVAKNAGVVTFVDGSKIMIKNEKGNTD-------RYSLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + QRP+V VG EV++ D++ DG S   G++ALG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTLIQQRPIVFVGQEVKKGDLLVDGSSFKNGEMALGKNVLVGFTTWNGYNFEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE  +  R ++ G + +T +I NVS+  L+N+D+ GI+ VG+EV
Sbjct: 295 INERLVKDDVYTSIHIEEQTIQFRTSRAGDDILTNEIQNVSKFALRNLDDRGIVKVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
            PGD+LVG+++PKGE   + EEKLL AI  ++    +DTSL+V +G +GTV+ V + +R 
Sbjct: 355 LPGDVLVGRLSPKGEDNPSQEEKLLMAILQQRPQTTKDTSLKVKNGHAGTVIHVEVLSRE 414

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  G+DK  +    ++ +I++  +
Sbjct: 415 QGDALEEGVDKIVKVSIAQKRKIKVGDK 442



 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 127/419 (30%), Positives = 186/419 (44%), Gaps = 79/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS------G 934
            I+ VG EV  GD+LV   + K    M   + +L         +  D  +           
Sbjct: 247  IVFVGQEVKKGDLLVDGSSFKN-GEMALGKNVLVGFTTWNGYNFEDAVIINERLVKDDVY 305

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
             S  + +  I  R     ++   +  +   +   R+ DD   I+         ++L G+ 
Sbjct: 306  TSIHIEEQTIQFRTSRAGDDILTNEIQNVSKFALRNLDDR-GIVKVGSEVLPGDVLVGRL 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L   ++ + P++         +     V++          +L     
Sbjct: 365  SPKGEDNPSQEEKLLMAILQQRPQTT--------KDTSLKVKNGHAGTVIHVEVLSR--- 413

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                  + GD +  GV ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 414  ------EQGDALEEGVDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 467

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQ+ E HLG A   LG K  +   D     DI         
Sbjct: 468  GTPLDIMLNPQGVPSRMNIGQVLELHLGMAARKLGVKFVTPSFDGVKKTDIENAL----- 522

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                        + + L  +      + 
Sbjct: 523  --------------------------------------------VEAGLDKSG-----KQ 533

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             L D +TG  FD+P+++G +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR
Sbjct: 534  TLIDPITGRKFDKPISIGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQR 592


>gi|67937438|gb|AAY83286.1| RNA polymerase beta subunit [Mycoplasma oxoniensis]
          Length = 592

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 208/449 (46%), Positives = 305/449 (67%), Gaps = 16/449 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  +F
Sbjct: 1   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN  GF++TPY KV  G +  + V+YL+A EE     AQ++ ++DE+       +  R
Sbjct: 61  AKVNDLGFLQTPYFKVNQGVIDYSQVIYLTATEEIGYSFAQSSINVDENNKIVSPTLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+     +DFI+ S KQ+ S+AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 121 RDYNYIIGTPLDVDFIEVSSKQIASVAAAAIPFLENDDANRALMGSNMQRQAVPLLEAEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+V TGME+ +AK S   +VAK  G V  VD  +I I++         +  D Y L  F+
Sbjct: 181 PYVATGMEADIAKYSSYNLVAKNDGEVTFVDGSKIYIKNE-------RTVTDKYSLRNFE 233

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+P+VK+GD+V++ D++ DG S   G+++LG+N+LV F  W+GYNFED+++
Sbjct: 234 RSNQGTLIQQKPIVKIGDKVKKGDLLVDGSSFKDGEMSLGKNVLVGFTTWNGYNFEDAII 293

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVGAE 887
           I+ER+V +DV+TSIHIEE  +  R ++ G +++TR DIPNVS+  ++++DE GI+ VG+E
Sbjct: 294 INERLVKDDVYTSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKHSIRHLDEQGIVRVGSE 353

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVG+++PKGE   + EEKLL AI  +K  +V+DTSL+V +G +GTV+ V I +R
Sbjct: 354 VVAGDVLVGRVSPKGEDNPSQEEKLLMAILQQKPQNVKDTSLKVKNGHNGTVIHVEILSR 413

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   GIDK  +    ++ +I++  +
Sbjct: 414 DKGDVLEDGIDKIVKVSIAQKRKIKVGDK 442



 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 126/419 (30%), Positives = 191/419 (45%), Gaps = 78/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ +G +V  GD+LV   + K +  M+  + +L         +  D  +     V   V 
Sbjct: 246  IVKIGDKVKKGDLLVDGSSFK-DGEMSLGKNVLVGFTTWNGYNFEDAIIINERLVKDDVY 304

Query: 940  --VDVRIFNRHGIDKNERSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
              + +                + R+ I  +++      DEQ I+         ++L G+ 
Sbjct: 305  TSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKHSIRHLDEQGIVRVGSEVVAGDVLVGRV 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L   ++ + P++           V+     +K  +  +   +E   +
Sbjct: 365  SPKGEDNPSQEEKLLMAILQQKPQN-----------VKDTSLKVKNGHNGTVIHVEILSR 413

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K      GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 414  DK------GDVLEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 467

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  +   D     DI         
Sbjct: 468  GTPLDIMLNPQGVPSRMNIGQVLELHLGMAAKKLNTKFVTPSFDGVKKEDIEDAL----- 522

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                        + + L         + 
Sbjct: 523  --------------------------------------------VEAGLSKTG-----KQ 533

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            I+ D +TG  FD+P++VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 534  IVIDPITGRQFDKPISVGIMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 592


>gi|195123595|ref|XP_002006289.1| GI20961 [Drosophila mojavensis]
 gi|193911357|gb|EDW10224.1| GI20961 [Drosophila mojavensis]
          Length = 1136

 Score =  310 bits (793), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 112/621 (18%), Positives = 199/621 (32%), Gaps = 123/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            NQRPLV+          VR+ D        +  D+    +  +A+           + I 
Sbjct: 608  NQRPLVQQRHLDELMRGVRKFDDFLHDGLIEYLDVNEENDSFIAWNEEQLEPHTTHLEIE 667

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                +      ++
Sbjct: 668  PFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLM 716

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 717  YNLVYPQAPMVKSRTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 776

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 777  LVYKNSKCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 835

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     +                    +       +V Y       +    + IE++  
Sbjct: 836  NKEMPAVT-------------------SINPLEGQSQVPYTAVPISYKGPEPSYIERVMV 876

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 877  SANAEEDF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPFNDFGICPDMIM 934

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K   L   +                       
Sbjct: 935  NPHGFPSRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------- 967

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G+    + + L     +  G+   Y G+TG
Sbjct: 968  ---------------------------AFGGSKAADVQAELVRHGFNYMGKDFFYSGITG 1000

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1001 APLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1060

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +        +   P +
Sbjct: 1061 ISYGASMLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----HVSKISMPYA 1114

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   L    
Sbjct: 1115 CKLLFQELTSMNVVPKLILEN 1135



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 122/943 (12%), Positives = 260/943 (27%), Gaps = 198/943 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVRAN----EIVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPISVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 L-----------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           +           + F   ++ +     +     A D M    V        T     E+ 
Sbjct: 258 IMAHIGLDARSQNRFGASLLEAFNLKIF-TQQRALDYMGSKLVVKRFQSATTKTPSEEAR 316

Query: 278 K-KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           +  LT+ L     +     +      L    V    ++        +  D    K LE  
Sbjct: 317 ELLLTTILAHVPVDNFNFQMKAIYVSLMVRRVMAAELDKT----LFDDRDYYGNKRLELA 372

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                     L+         I +  +       K A  D+ + MR   ++  +  ES  
Sbjct: 373 GSLISLMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAI 426

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           +   +   ++ +   G  ++  RL+  +   +            K+              
Sbjct: 427 SSGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ------- 479

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                  +    +  + +    +  +           +   +        + +       
Sbjct: 480 --PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDERPVMTLAYNAGVEDIREVSGNP 537

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             +  +  +  + N L    + +R        + R         +H ++  R     T  
Sbjct: 538 INNPHVFLVFINGNVLGLTIN-QRHLVRNLRYMRRKGRMGSFVSIHTSYTQRCIFIHTDG 596

Query: 577 GHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           G        V +     +      +    RK  D      + YL   EE + +IA     
Sbjct: 597 GRLCRPYIIVENQRPLVQQRHLDELMRGVRKFDDFLHDGLIEYLDVNEENDSFIAWNEEQ 656

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           L+                            ++  P  ++ + A L+P+  ++ S R    
Sbjct: 657 LEP-----------------------HTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQ 693

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+ ++         G        S                              
Sbjct: 694 CAMGKQAMGMI---------GYNQKNRIDS------------------------------ 714

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                              N    Q P+VK                T+   L  G+N  V
Sbjct: 715 ----------------LMYNLVYPQAPMVKS----------RTIELTNFDKLPAGQNATV 748

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNV 868
           A M + GY+ ED++++++  +       +  +  +   +       +           N 
Sbjct: 749 AVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNK 808

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                  +D  GI+  G +V    I++ K  P   S    E +
Sbjct: 809 VIFKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSINPLEGQ 851


>gi|315426560|dbj|BAJ48190.1| DNA-directed RNA polymerase subunit B [Candidatus Caldiarchaeum
            subterraneum]
          Length = 1117

 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 120/588 (20%), Positives = 207/588 (35%), Gaps = 98/588 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  P    N    + IS   +     + I   E     R+      
Sbjct: 609  IEYLDAEEEENAYVAISPDKVTNEHTHLEISSFAMLGVTASLIPYAEHNQSPRNVYEAAM 668

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     S   L+         +        +        G       + ++ AI   
Sbjct: 669  AKQALGVFASNYALR---TDSRSHLLVYPQRPIVTTRTADLIGIDKRPLGQNMVVAILTG 725

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            K  ++ D  +   S V   +         G+  + R   VE  Q     RD   +  I +
Sbjct: 726  KGYNMEDAVVLNRSSVERGL---------GLSLSWRIYEVEARQTPGGQRD---KFGIPE 773

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             ++     E         G    +      + ++      ++        +  + V + +
Sbjct: 774  PSVRGYRGEQFYRVLDKDGFAHIESDVSGGTVIVGMMSPPRFL-------EEYQRVPTRE 826

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            + +  S   ++      +E I     +      +VK  V      + GDK + RHG KG+
Sbjct: 827  MVWRDSSETVQPSETGNVENIFI--TINAEGNLLVKAKVRSTCFTEIGDKFSSRHGQKGV 884

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  ++P EDMP+ KDG   D+++NP   PSRM +GQ+ E+        LG          
Sbjct: 885  VGMLIPQEDMPYTKDGIVPDLLINPHAFPSRMTIGQLIESL----AGKLG---------- 930

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                     K+ +   TP F G   E +
Sbjct: 931  ---------------------------------------SIKAEIVDGTP-FLGKSLEEL 950

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
             + L       SG+ +LY+G TG+  +  V +G +Y  +L+H+V DK++AR+ G   ++T
Sbjct: 951  RAELEALGFKSSGRELLYNGATGKILEAEVFIGVVYYQRLHHLVRDKIHARARGQVQMLT 1010

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------------DVV 1323
            +QP  G+S  GG + GEME  C+ AYGA+Y+L + L  +SD                D+ 
Sbjct: 1011 RQPTEGRSRGGGLKFGEMERDCLIAYGASYLLLDRLLEQSDKYTAYFCEKCGMPCYYDLK 1070

Query: 1324 GRTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
                 +   V G D          +F +L+ EM ++ +   +     +
Sbjct: 1071 --QERFVCPVDGKDVRVKAVSMSYAFYLLLNEMMSMCIHPRILLEEPE 1116



 Score =  181 bits (460), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 141/980 (14%), Positives = 296/980 (30%), Gaps = 221/980 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF--PITAFSGAAMLEFVSYEFDPPKF 86
           L++    S+++F+            GLQ    S+    I    G  +++F     D P  
Sbjct: 23  LVQHHLRSFNYFV----------KTGLQQLVNSMSDYEIKTKHGTVVVKFGQVTIDIPTK 72

Query: 87  ------DVD-----DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                 +       +   R+LTY  P+ I + +                   +++++G++
Sbjct: 73  REIDAPNPQPLYPWEARLRNLTYEAPIYIKMSIYFDGKPIAPP---------ENVWVGNI 123

Query: 136 PLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           P+M K                         G F+I G +R++V     +P         +
Sbjct: 124 PVMVKSDICPLSKMTHDELLAHGEDPQDPGGYFIINGSERVIVGIEDLAPNRII---VTK 180

Query: 172 ASLSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDRRRK-VPVTSFLMALGMDSEE 227
                K  Y+  I+     + + +++ +     + V   R  K VP    L ALG+  ++
Sbjct: 181 KEGDSKPQYSAVILSAAHGRQVRVEVSYRKDSPVKVYFSRIYKGVPAIIMLRALGLTKDQ 240

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            ++         +  +        A+ +   + +   +         E  +   +  +  
Sbjct: 241 EIANL--ISPLKEVQELLEPSFREAEGVETVEQALDYIGSRIAFGYAEEYRLEKAEQIVD 298

Query: 288 --------LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                     +       +    + G  +   +   E  +    A   +  +S       
Sbjct: 299 TMFMLHLGTTKAARMKKAVHLCEMIGRVLETSLGLREPDDRDHYANKRLKLESALLTELY 358

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            +  + +L          I                + I   +R G VS        F   
Sbjct: 359 RMAFVKLLRDLRYQLERIIPTRQP-----------ISISTYVRHGIVSE-------FVKH 400

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-N 458
              +  +    VG  ++  R N                 + ++   L  G+   +  D +
Sbjct: 401 AMATGNWPGGRVGVTQLLNRTNYLATLSH----------LRRVQSPLSRGQPHFEARDLH 450

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             +       E  +      +  +  S +    +   + +     +N  P+   + +   
Sbjct: 451 GTHWGRLCPCETPEGSNAGLVKNLALSAEVSFQANKKELLDRLFQLNVIPLNEIIAKRRP 510

Query: 519 SSQLSQLEE------HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI--C 570
              +    +      H N +  +   RR        + R     +  +V    YG +   
Sbjct: 511 PPNVKVFVDGVLEGYHSNGVMLVNELRR--------LRREGIISQNINVALYTYGHVQEV 562

Query: 571 PAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              T EG     +  + +     +      I+    K  D      + YL A EEEN Y+
Sbjct: 563 VINTDEGRIRRPLIVVQNGQPLLQRQHVELIKRKTSKFRDLVSLGIIEYLDAEEEENAYV 622

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A +   +                         +   ++ S   ++ + ASLIP+ E++ S
Sbjct: 623 AISPDKVT-----------------------NEHTHLEISSFAMLGVTASLIPYAEHNQS 659

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R +    M +QA+ +  +                S +                      
Sbjct: 660 PRNVYEAAMAKQALGVFASNYAL---------RTDSRS---------------------- 688

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         QRP+V                   +    L
Sbjct: 689 ------------------------HLLVYPQRPIV----------TTRTADLIGIDKRPL 714

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG-PEEITRDIP 866
           G+NM+VA +   GYN ED+++++   V   +  S+    +EV AR T  G  ++     P
Sbjct: 715 GQNMVVAILTGKGYNMEDAVVLNRSSVERGLGLSLSWRIYEVEARQTPGGQRDKFGIPEP 774

Query: 867 NV----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +V     E+  + +D+ G   + ++V+ G ++VG ++P                   + +
Sbjct: 775 SVRGYRGEQFYRVLDKDGFAHIESDVSGGTVIVGMMSPPRFLEE-------YQRVPTREM 827

Query: 923 DVRDTSLRVPSGVSGTVVDV 942
             RD+S  V    +G V ++
Sbjct: 828 VWRDSSETVQPSETGNVENI 847


>gi|57337368|emb|CAH69692.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
          Length = 313

 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 190/308 (61%), Positives = 238/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INA P+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAXPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|269912658|emb|CAY86109.1| RNA polymerase beta subunit [Kozakia baliensis]
          Length = 307

 Score =  310 bits (793), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 143/310 (46%), Positives = 195/310 (62%), Gaps = 28/310 (9%)

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+
Sbjct: 1   ERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRK 60

Query: 210 RKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDF 244
           RK+PVT+ L AL                         GMD +EILS FY  + +++    
Sbjct: 61  RKLPVTTLLYALEGEHSIAARAAKAAEGGDVDALDVRGMDQDEILSYFYEAVPFTRMPKG 120

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
           W  P    D   G K+   L D DTGE V E+  KLT+ +++ + E   + + +    L 
Sbjct: 121 WARPFDP-DAFRGLKLLEPLYDADTGEVVAEAEAKLTARMVRKIAE-NTRVVLVGRADLL 178

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G +VA D+VN  TGEIY EAG+ + E  L  +  + + ++P+L VD   +  +IRNTL  
Sbjct: 179 GRFVAHDLVNENTGEIYAEAGEELTEARLAALEEAGVTELPVLSVDGA-HGPWIRNTLAV 237

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           DKN +R DAL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS VGRVKMNMRL +D 
Sbjct: 238 DKNNNRDDALIDIYRIMRPGEPPTPETAEAMFRGLFFDPDRYDLSAVGRVKMNMRLEVDA 297

Query: 425 PDDVRHIRKE 434
           PD +R +RKE
Sbjct: 298 PDTLRVLRKE 307


>gi|302790720|ref|XP_002977127.1| hypothetical protein SELMODRAFT_443461 [Selaginella moellendorffii]
 gi|300155103|gb|EFJ21736.1| hypothetical protein SELMODRAFT_443461 [Selaginella moellendorffii]
          Length = 1386

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 130/318 (40%), Gaps = 65/318 (20%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   V+K  V   R  + GDK + RHG KG+   I+  +D PF + G   D+++NP 
Sbjct: 1117 TNESQQMVIKCQVRHTRRPELGDKFSSRHGQKGVCGTIVEQQDFPFTERGVCPDLIMNPH 1176

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM VG++ E   G A V  GK          +                        
Sbjct: 1177 GFPSRMTVGKMIELLGGKAGVQSGKYHYGSAFGEPSGHAD-------------------- 1216

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                           EAI++ L        G+ ++Y G+TG P 
Sbjct: 1217 -----------------------------TVEAISATLVKHGFSYCGKDLIYSGITGCPL 1247

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G IY  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C+ AY
Sbjct: 1248 QAYIYMGPIYYQKLKHMVLDKMHARAQGPRVVLTRQPTEGRSREGGLRLGEMERDCLVAY 1307

Query: 1306 GAAYVLQEMLTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNV 1349
            G++ ++ E L I SD          G    Y   +          G +      P +  +
Sbjct: 1308 GSSMLILERLMISSDQFQVQVCTNCGLLGYYSHKLKMNFCSYCKNGENMAAMKLPYACKL 1367

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L +E+Q++ +   L+ + 
Sbjct: 1368 LFQELQSMNIVPRLQLAE 1385



 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 127/931 (13%), Positives = 262/931 (28%), Gaps = 183/931 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP---IT------AFSGAAMLEFVSY 79
            L++    SY++F+   I       +G +     V P   I        +    +  F+  
Sbjct: 273  LVKQHLDSYNYFVNCEIKKIIHA-KGNEKITSDVDPNFYIKYACDTFQYFTNILFRFLDI 331

Query: 80   EFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
                P               C  RD+TY+ P+ + +        +    +  KD +   +
Sbjct: 332  FVGTPSIEQDYIRQDITPQQCRLRDMTYSAPISVDIEYT---RGKDIITRKGKDGQGAQV 388

Query: 131  YMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHF 165
             +G +P+M                           G FV+KG +++++ Q   S   I  
Sbjct: 389  -IGRMPVMLRSSRCILTGKSDAELAKLGECPLDPGGYFVVKGTEKVILIQEQLSKNRIII 447

Query: 166  DHD-----KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLM 219
            D D         + S     +   I              + I+V+++     VP+   + 
Sbjct: 448  DSDSTGSVTASVTSSTHERKSKTNI----------IIKHEKIYVKLNVFSDDVPIVVVMK 497

Query: 220  ALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL-VDIDTGEQVIESG 277
            A+GM+S+ EI+        ++          ++  +    +    L   +    Q     
Sbjct: 498  AMGMESDQEIIQMVGTDPKFAGILAPSMQECASLGVYTTHQALEYLGTKVRVNRQWGSKQ 557

Query: 278  KKLTSGLLKS-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EE 335
             K      +  L    +  + +         +   ++     E  ++   V D   +  +
Sbjct: 558  TKSKVDEARDILLNVFLAHVAVHRYDFRPKCIYVALMLRRMLEAILDKECVDDRDYVGNK 617

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                  + + +L+ D    +     + V         A           D+ T  +  ++
Sbjct: 618  RLELAGQLLALLFEDLFKRSCSELKSNVDRTLSKMNRASQYDVSKSLKPDMLTSGLENAI 677

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
             +  +         TV R +M+ +                 ++ +  +  L +       
Sbjct: 678  SSGNW---------TVKRFRMDKKGVTQV------------VSRLSYIAALGHMTRVASQ 716

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             +      +    +  + +       +           +   +     +  + +     E
Sbjct: 717  FEKSRKWGMLCPCDTPEGEGCGLTKNLALMTHITTDDEEAPLIDLCTNLGVEDINLLSGE 776

Query: 516  FFCSSQLSQLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
             F S          N      H R +  A     + RA    E   +      R     +
Sbjct: 777  EFHSKN--AFLVMFNGTILGIHRRPQQFATLMRKLRRAGKIGEFVSIFVNEKQRCIYIAS 834

Query: 575  SEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
              G     V          + +    ++  +R   D      V YL   EE N  IA   
Sbjct: 835  DGGRVCRPVVIADHGVSRIKEHHMKELKDGFRTFDDFLREGLVEYLDVNEENNALIAL-- 892

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                                            I+  P  ++ + A LIP+  ++ S R  
Sbjct: 893  ---------------------YEKEADSTTTHIEIEPFTILGVCAGLIPYPHHNQSPRNT 931

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
              C M +QA+                                           I   +  
Sbjct: 932  YQCAMGKQAMGN-----------------------------------------IAYNQLQ 950

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
               +   + +Y               QRPL+                  +   L  G+N 
Sbjct: 951  RIDTLLYLLVYP--------------QRPLL----------TTKSIELVNYDKLGAGQNA 986

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
             VA M + GY+ ED++++++  +       I +++F  + R  +    +           
Sbjct: 987  SVAVMSYSGYDIEDAIVMNKASLDRGFGRCIVLKKFSCLVRKYENRTMDRIVAPRQHGHA 1046

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKG 902
              + +D+ GI  VG  +   DI V K +PK 
Sbjct: 1047 TSQLLDQDGIASVGERIYDKDIFVNKESPKD 1077


>gi|273067674|gb|ACZ97537.1| DNA-directed RNA polymerase beta chain [Enterobacter ludwigii]
 gi|273067677|gb|ACZ97538.1| DNA-directed RNA polymerase beta chain [Enterobacter ludwigii]
          Length = 312

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 192/312 (61%), Positives = 241/312 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 1   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 60

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 61  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 120

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S 
Sbjct: 121 VVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVST 180

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 181 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 240

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V
Sbjct: 241 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPV 300

Query: 789 RRNDIIADGPST 800
            R D++ADGPST
Sbjct: 301 ERGDVLADGPST 312


>gi|269912598|emb|CAY86079.1| RNA polymerase beta subunit [Gluconacetobacter oboediens]
          Length = 311

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 149/314 (47%), Positives = 197/314 (62%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAESEAARAAKAAEGGDVESMEIQGMSPDEILSYFYGKVEFAKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DAFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEIY EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNENTGEIYAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD VR +RKEDI+
Sbjct: 298 VPDTVRVLRKEDIL 311


>gi|55583696|gb|AAV53367.1| RNA polymerase II second largest subunit [Phyllotopsis sp. MB35]
          Length = 889

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 140/907 (15%), Positives = 272/907 (29%), Gaps = 155/907 (17%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 119  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 175

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 176  GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 235

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 236  ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 291

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 292  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 343

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 344  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 400

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV---DA 740
             D+ RV     +   Q + L K    ++ +G         G A   +       +   DA
Sbjct: 401  TDAGRVCRPLFIVENQQLALQKKHVKWLNSGFN-----DEGEAFKWEHLVKNGIIELLDA 455

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +       +    ++ +     R  +K G            PS 
Sbjct: 456  EEEETVMISMTPEDLENSRLQQSGLDPHANDGDFDPAAR--LKAGINAHTWTHCEIHPSM 513

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 514  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 548

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 549  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 597

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 598  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPMRDNTLRMKHGTY 656

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 657  DKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVD 716

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 717  QVLI--------------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTI 756

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 757  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 814

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V    F G       
Sbjct: 815  -----------------------DLTVESVSTFLRQKGYQSRGLEVM---FHGHT----- 843

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                              G         V +G  Y  +L HMV DK+++R+ G   ++T+
Sbjct: 844  ------------------GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTR 882

Query: 1281 QPLGGKS 1287
            QP+ G+S
Sbjct: 883  QPVEGRS 889



 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 98/775 (12%), Positives = 220/775 (28%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+      LG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 49  YIKVD----IPIWVVFRGLGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 104

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + +              +      + 
Sbjct: 105 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 160

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 161 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLQKCV 210

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 211 ETH--KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 267

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 268 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAP 327

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 328 VIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVS 387

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                  +   ++        P    E   + L      +  +N+    E    K     
Sbjct: 388 VVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVKW--LNSGFNDEGEAFKWEHLV 445

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               +  L A EEE   I+     L+        L      G+          +      
Sbjct: 446 KNGIIELLDAEEEETVMISMTPEDLENSRLQQSGLDPHANDGDFDPAARLKAGINAHTWT 505

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 506 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI------------ 553

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 554 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 581

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 582 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 620

Query: 843 HIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E     +  +   +       +++ G+I  G  V   DI++GK
Sbjct: 621 YYRSYMDLEKKSGIQQLEEFEKPMRDNTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGK 680

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 681 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 728


>gi|292654526|ref|YP_003534423.1| DNA-directed RNA polymerase subunit B [Haloferax volcanii DS2]
 gi|242392228|dbj|BAH80351.1| RNA polymerase subunit B' [Haloferax alexandrinus]
 gi|242392242|dbj|BAH80358.1| RNA polymerase subunit B' [Haloferax sulfurifontis ATCC BAA-897]
 gi|291370551|gb|ADE02778.1| DNA-directed RNA polymerase subunit B [Haloferax volcanii DS2]
          Length = 609

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 204/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEKVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNDELDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 45.1 bits (105), Expect = 0.098,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L     V A    E  +    D      V ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-----PLLDDDHVEALDNDELDF---DDLVERGLVEFIDAEEEEDIYVAVDEDELN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|73697689|gb|AAZ81461.1| RNA polymerase beta subunit [Mycoplasma leonicaptivi]
          Length = 592

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 207/442 (46%), Positives = 298/442 (67%), Gaps = 8/442 (1%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLSEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+  GF++TPY KV +G V  NDV YL+A EE    IAQ++  LD++   T+E++  +
Sbjct: 61  AQVDERGFLKTPYFKVNNGVVDYNDVRYLTASEELGYSIAQSSVHLDDNNKITDEVLTIK 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +     ++DFI+ + KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPLL+ EA
Sbjct: 121 RDYTYVTGTSSEVDFIEVASKQIVSVAAAGIPFLENDDANRALMGANMQRQAVPLLQTEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           PF+ TG+E+ +AK S   +VAK AG+V  V+  +I +   E      +   D Y L  F+
Sbjct: 181 PFIATGIETEIAKYSSYNLVAKNAGVVSHVEGSKIHVVRHE------SGVTDKYTLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+PLV+VGD V   D++ DG S   G+LALG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTIIQQKPLVRVGDVVEAGDLLTDGSSFSNGELALGKNVLVGFTTWNGYNFEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+E++V  DVFTSIHIEE  +  R ++ G +E+T +IPN S+  L+++DE GI+ VG+EV
Sbjct: 295 INEKLVKGDVFTSIHIEEQIIQFRTSRAGNDELTAEIPNASKYSLRHLDENGIVKVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PKGE   + EEK+L +I G ++   +DTSL+V +G  GT+  V I +R 
Sbjct: 355 LPGDVLVGRTSPKGEENPSQEEKMLYSILGTRSSTNKDTSLKVKNGHGGTITHVEILSRE 414

Query: 949 GIDKNERSI-SVEREQIELLAR 969
             D  E  I  + +  I    +
Sbjct: 415 KGDVMEEGIDKIIKVSIAQKRK 436



 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 137/482 (28%), Positives = 196/482 (40%), Gaps = 67/482 (13%)

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              A     G   E +   S  +V+++     H+E  ++     + G  +           
Sbjct: 178  TEAPFIATGIETEIAKYSSYNLVAKNAGVVSHVEGSKIHVVRHESGVTDKYTLRNFERSN 237

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                I +  ++ VG  V  GD+L    +      +   + +L         +  D  +  
Sbjct: 238  QGTIIQQKPLVRVGDVVEAGDLLTDGSSFSN-GELALGKNVLVGFTTWNGYNFEDAVIIN 296

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V G V    I     I +   S +   E    +          LD N   ++   + 
Sbjct: 297  EKLVKGDVF-TSIHIEEQIIQFRTSRAGNDELTAEIPNASKYSLRHLDENGIVKVGSEVL 355

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
              + + G    K     S +   +   S     +  ++     V++      T   IL  
Sbjct: 356  PGDVLVGRTSPKGEENPSQE--EKMLYSILGTRSSTNKDTSLKVKNGHGGTITHVEILSR 413

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                     + GD M  G+ +++KV +A KR I+ GDKMAGRHGNKG++S +LP EDMP 
Sbjct: 414  ---------EKGDVMEEGIDKIIKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPH 464

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L+DGTP+DI+LNP GVPSRMN+GQI E HLG A   LG K  +   D     DI      
Sbjct: 465  LEDGTPLDIMLNPQGVPSRMNIGQILELHLGMAAKKLGVKFVAPSFDGVKKPDIEAALEE 524

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                                               L        
Sbjct: 525  AG-------------------------------------------------LDKTG---- 531

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             + IL D +TG  FD+P++VG +YMLKLNHMV DK++ARS G YSL+TQQPLGGKS  GG
Sbjct: 532  -KQILIDPITGNKFDKPISVGVMYMLKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGG 590

Query: 1292 QR 1293
            QR
Sbjct: 591  QR 592


>gi|52694225|emb|CAG30642.1| DNA-directed RNA polymerase beta chain [Pseudomonas oryzihabitans]
          Length = 319

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 185/315 (58%), Positives = 238/315 (75%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGLGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++ +     EELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATMSDKRQLVEELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R
Sbjct: 242 RGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVER 301

Query: 791 NDIIADGPSTDLGDL 805
           +DI+ADGPSTD+G+ 
Sbjct: 302 SDILADGPSTDMGER 316


>gi|73697647|gb|AAZ81440.1| RNA polymerase beta subunit [Mycoplasma dispar]
          Length = 591

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 199/423 (47%), Positives = 286/423 (67%), Gaps = 9/423 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + + F
Sbjct: 1   NPLGEMANKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPVETPEGQNIGLILNFSVF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +++N YGFI TPY KV +  V    V +L+A EE     AQ++  +D+      + +  R
Sbjct: 61  SKINKYGFIITPYYKVTNRVVDFKQVHWLTAAEEYGLSFAQSSIEIDKKNRIVADKLTVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +++  E++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL+K+EA
Sbjct: 121 KNQTYLVLDSEQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLIKSEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+ES +A+ S   + A  +G V  VD+ +++I               I+ L  F+
Sbjct: 181 PLVATGIESDIARFSATNLRATVSGKVVFVDSKKVIIND--------GESQKIHYLRAFE 232

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +SNQ T + Q+P VKVGD V++  +I DGPSTD G+LALG+N+LVAF  W+GYN+ED+++
Sbjct: 233 KSNQETLILQKPTVKVGDVVKKGQLICDGPSTDNGELALGKNVLVAFSTWYGYNYEDAII 292

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +SE++V +DVFTSIHI+E  +  R +K G + +T ++PN S +   ++D  GI+ VG+EV
Sbjct: 293 LSEKLVKDDVFTSIHIQEQTIKFRSSKAGNDVLTAEVPNASTKSRAHLDANGIVIVGSEV 352

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           + GDILVG+ +PKGE   T EEKL+ AI+G+KA+  +DTSLRV +G  GTV+DV+I +R 
Sbjct: 353 DTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKALAQKDTSLRVKNGEGGTVIDVQILSRD 412

Query: 949 GID 951
             D
Sbjct: 413 QGD 415



 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 126/413 (30%), Positives = 180/413 (43%), Gaps = 67/413 (16%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + VG  V  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 246  VKVGDVVKKGQLICDGPSTDN-GELALGKNVLVAFSTWYGYNYEDAIILSEKLVKDDVF- 303

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   S +        +       +  LD N    +   +   + + G   
Sbjct: 304  TSIHIQEQTIKFRSSKAGNDVLTAEVPNASTKSRAHLDANGIVIVGSEVDTGDILVGRTS 363

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W + A+  +     V++ +                +I    
Sbjct: 364  PKGEDNPTAE--EKLMAAIWGKKALAQKDTSLRVKNGEGG---------TVIDVQILSRD 412

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  +VK+ +A KR ++ GDKMAGRHGNKG+VS +LP EDMPFL+DGTPVD+V
Sbjct: 413  QGDNLEEGVGMLVKILIAQKRKVKVGDKMAGRHGNKGVVSIVLPVEDMPFLEDGTPVDVV 472

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG A   L  K  + + D      I  L             
Sbjct: 473  LNPQGVPSRMNIGQVLELHLGMAAKRLNTKFVTPVFDGIKIDTIKSL------------- 519

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         F  A+               SG+  L+DG+T
Sbjct: 520  -----------------------------FAEANIPE------------SGKFKLFDGIT 538

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            G+ F+ PV+VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR 
Sbjct: 539  GQAFENPVSVGYMYMLKLQHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRF 591


>gi|269912640|emb|CAY86100.1| RNA polymerase beta subunit [Gluconobacter oxydans]
 gi|269912642|emb|CAY86101.1| RNA polymerase beta subunit [Gluconobacter oxydans]
          Length = 312

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 147/315 (46%), Positives = 203/315 (64%), Gaps = 28/315 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EILS FY  + +++ G
Sbjct: 61  RKRKLPVTTLLYALEGANYLAQREQKIAEGGDVEGLDIRGMDQDEILSYFYEAVPFTRLG 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
             W  P    D   G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +    
Sbjct: 121 GEWARPFDP-DAFRGLKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G ++A D+VN  TGEIY EAG+ + E  L  +    I ++P+L VD  ++  +IRNTL
Sbjct: 179 ILGRFLAYDLVNENTGEIYGEAGEELTEDRLAALEEMGITELPLLSVDG-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF+ LFFD  +YDLS VGRVKMNMRL++
Sbjct: 238 AADKNSCRDEALIDIYRIMRPGEPPTKETAEAMFHGLFFDQGRYDLSAVGRVKMNMRLDV 297

Query: 423 DTPDDVRHIRKEDII 437
           D PD +R +RKEDI+
Sbjct: 298 DAPDTLRVLRKEDIL 312


>gi|82655136|emb|CAJ19637.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 313

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 190/308 (61%), Positives = 238/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA R G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAXRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|213876741|gb|ACJ54367.1| RNA polymerase subunit B [Mycobacterium fortuitum]
          Length = 246

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 137/236 (58%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 152

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 153  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 190

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 191  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 246



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 48


>gi|242392236|dbj|BAH80355.1| RNA polymerase subunit B' [Haloferax lucentense]
          Length = 609

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 203/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + +  E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDHFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEKVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNDELDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQED-HFEIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 45.1 bits (105), Expect = 0.097,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L     V A    E  +    D      V ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-----PLLDDDHVEALDNDELDF---DDLVERGLVEFIDAEEEEDIYVAVDEDELN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|89888218|gb|ABD78651.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888225|gb|ABD78654.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888232|gb|ABD78657.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888239|gb|ABD78660.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888246|gb|ABD78663.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888253|gb|ABD78666.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888260|gb|ABD78669.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
          Length = 172

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 88/174 (50%), Positives = 120/174 (68%), Gaps = 2/174 (1%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P L+  Q  SY  FL    A  +R NEGLQAAF S+FPI + +G A LEFVSY    P
Sbjct: 1   NVPFLLATQLQSYLTFLQAETATADRVNEGLQAAFSSIFPIVSHNGMARLEFVSYVLGEP 60

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
            FDV +C  R LT+A PL+  +RL++ D        +IK++KEQ +YMG++PLMT  G+F
Sbjct: 61  VFDVKECQQRGLTFASPLRAKVRLVLLDR--EVSKPTIKEVKEQEVYMGEIPLMTSTGSF 118

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
           VI G +R++VSQLHRSPG+ F+HD+G+   SGKLL++ R+IP +G W+D EFD 
Sbjct: 119 VINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSARVIPYRGSWLDFEFDP 172


>gi|315259450|gb|ADT91924.1| DNA-directed RNA polymerase beta subunit [Enterococcus faecium]
          Length = 392

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 133/425 (31%), Positives = 182/425 (42%), Gaps = 87/425 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   +  M   + +L      +  +  D  +           
Sbjct: 45   IVHLGEKVEKGDTLADGPS-MEQGEMALGQNVLVGFMTWEGYNYEDAIIMSR-------- 95

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI----------YSRLMEIL 990
                     + K++   S+  E+ E  ARD       + R I             +  I 
Sbjct: 96   --------RLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIR 147

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G     G     K T      +S   R     F  +  +V+     +          + 
Sbjct: 148  IGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDV- 206

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                 KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP
Sbjct: 207  -----KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMP 261

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            FL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D            
Sbjct: 262  FLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA---------- 311

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                               D+ V     +        T ++DG                 
Sbjct: 312  ------------------SDEDVWETVREAGMASDAKTVLYDG----------------- 336

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                      TGEPFD  V+VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  G
Sbjct: 337  ---------RTGEPFDGRVSVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 387

Query: 1291 GQRLG 1295
            GQR G
Sbjct: 388  GQRFG 392



 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 128/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  I +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEYVDASEIRVRRDNGALDK-------YDVTKFRRSNSGTSYNQRPIVHLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEQGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|45545303|gb|AAS67499.1| DNA-dependent RNA polymerase II second largest subunit [Aspergillus
            fumigatus]
          Length = 936

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 152/901 (16%), Positives = 283/901 (31%), Gaps = 152/901 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L N +R+   
Sbjct: 161  HISQSEGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFT 220

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ R ++   +        +     I A  +   +     +               +SQ+
Sbjct: 221  RVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKKAASSKAGVSQV 280

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 281  LSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 336

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-TE 642
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 337  LALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGVHRDPAHLVN 396

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ-RQA 700
             ++  R             D  +   K          P F+ ++D      G  +  +  
Sbjct: 397  TMLSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKDH 456

Query: 701  VPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPST 756
            +  L+ +         E    +  G   + K +G+VE VDA      +I     DL+ S 
Sbjct: 457  IRKLEQDKELPADLDPEDRRERYFGWDGLVK-SGVVEYVDAEEEETIMIVMTPEDLEISK 515

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                 Y         +    N+R    +  +          PS  LG       +  + +
Sbjct: 516  QLQAGYA------LPEEDDPNKRVRSVLSQKAHTWTHCEIHPSMILG-------VCASII 562

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +                     E   +I    ++ L   
Sbjct: 563  PFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLA-- 610

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                                 +       +   +  + AI      +  D+ +   S + 
Sbjct: 611  -----------------TTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 653

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R   D  +         +E   +    + + + +  Y +L E   I  G 
Sbjct: 654  RGLF-RSLFYRTYTDSEKMVGL---TVVERFEKPMRSDTIGMRKGTYDKLDEDGIIAPGV 709

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L+ +                +E  QR     K+   T     E+  
Sbjct: 710  RVSGEDIIIGKTAPLAPE---------------AEELGQRTKAHTKLDVSTPLRSTENGI 754

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF +
Sbjct: 755  VDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTR 809

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +  +          IS L    E
Sbjct: 810  EGVSPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTDVTVDSISRLLR--E 867

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +                                                    +G 
Sbjct: 868  HGYQSRGFEVM---------------------------------------------YNGH 882

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +    G         V +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R
Sbjct: 883  T----GR---KLVAQVFLGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLR 935

Query: 1294 L 1294
             
Sbjct: 936  F 936



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 117/854 (13%), Positives = 243/854 (28%), Gaps = 136/854 (15%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      Y   I    ++G  +  +   K  +  + 
Sbjct: 1   SEKVLIAQE-RSAGN--TVQVFKKAPPSPTPYVAEIRSAVEKGSRLLSQLSLK--LFAKG 55

Query: 207 DR----------------RRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           D                 +  +P+     ALG+   E+IL+        +   +     +
Sbjct: 56  DSAKGGFGPTIRSTLPYVKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCI 115

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCL 303
               ++   +V+   +      Q   + ++      + ++++ +  +  +          
Sbjct: 116 EEGFVIQDREVALDFIAKRGSSQSSMNHERRVRYAREIMQKELLPHISQSEGSETRKAFF 175

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G  V   ++    G   ++  D   +K L+           +L+     +        V
Sbjct: 176 LGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFTRVTRD----LQRYV 230

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
               +  ++  L+I          T  +  ++    + +  K   S  G  ++  R    
Sbjct: 231 QRCVETNREIYLNIG---IKASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLSRYTYA 287

Query: 424 TPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +      R          I     L N   G +   +    +    V  +    Y     
Sbjct: 288 STLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGT 347

Query: 481 RMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
             E  I    + +   ++   PQ   NA  V      F     +    +  + ++ +   
Sbjct: 348 PSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGVHRDPAHLVNTMLSL 401

Query: 539 RRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           RR + +  +  + R     E        R   P       P   + G  +     +    
Sbjct: 402 RRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNDPKSENCGSLVLNKDHIRKLE 461

Query: 591 RVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT--- 641
           +                Y        +  V Y+ A EEE   I      L+         
Sbjct: 462 QDKELPADLDPEDRRERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQLQAGY 521

Query: 642 ---EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              EE    +     +          +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 522 ALPEEDDPNKRVRSVLSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGK 581

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +                   + A I+      +    ++  +          +   
Sbjct: 582 QAMGVFLT---------NFDQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVA 632

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +  Y              NQ            + +I +  S D G         + +  +
Sbjct: 633 IACYSG-----------YNQ-----------EDSVIMNQSSIDRGLFRS-----LFYRTY 665

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
                   + + ER              FE   R   +G            +     +DE
Sbjct: 666 TDSEKMVGLTVVER--------------FEKPMRSDTIGM----------RKGTYDKLDE 701

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII  G  V+  DI++GK  P     + PE + L      KA    D S  + S  +G 
Sbjct: 702 DGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVSTPLRSTENGI 754

Query: 939 VVDVRIFNRHGIDK 952
           V  V +   +   K
Sbjct: 755 VDQVLVSTSNDDLK 768


>gi|269912630|emb|CAY86095.1| RNA polymerase beta subunit [Gluconobacter cerinus]
          Length = 309

 Score =  309 bits (792), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 146/312 (46%), Positives = 201/312 (64%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY  + +++ GD
Sbjct: 61  KRKLPVTTLLYALEGANYIAQREEKIAEGGDVEGLDIRGMDQDEILSYFYDMVTFTRMGD 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P    D   G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +    +
Sbjct: 121 GWARPFEP-DAFRGQKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDV 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G Y+A D++N  TGEIY EAG+ + E  L  +    I ++P L +D  ++  +IRNTL 
Sbjct: 179 LGCYLAHDLINENTGEIYGEAGEELTEDRLAALEELGITELPTLSIDG-SHGPWIRNTLS 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS+VGRVKMNMRL++D
Sbjct: 238 VDKNTSRDEALIDIYRIMRPGEPPTKETAEAMFRGLFFDQDRYDLSSVGRVKMNMRLDVD 297

Query: 424 TPDDVRHIRKED 435
            PD +R +RKED
Sbjct: 298 APDTLRVLRKED 309


>gi|269912566|emb|CAY86063.1| RNA polymerase beta subunit [Gluconacetobacter europaeus]
          Length = 314

 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 149/316 (47%), Positives = 198/316 (62%), Gaps = 28/316 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIRGMDPDEILSYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DSFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEI+ EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNEHTGEIFAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKEDIIAI 439
            PD VR +RKEDI+  
Sbjct: 298 VPDTVRVLRKEDILRT 313


>gi|45545333|gb|AAS67514.1| DNA-dependent RNA polymerase II second largest subunit [Melanomma
            radicans]
          Length = 936

 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 160/1052 (15%), Positives = 310/1052 (29%), Gaps = 182/1052 (17%)

Query: 274  IESGKKLTSGLLKSLKEKGV--KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
            +E G +L S       +  +  K             +     +     ++   G V DE 
Sbjct: 36   VEKGTRLISSFNIKWTDNSLILKRTPGPFAYAL---LPYIKADVPMAIVFRALGIVSDED 92

Query: 332  SLEEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             L  I +       + L   S+   + I+         DR++AL  I R        T  
Sbjct: 93   ILNHIVYDREDTQMLELLKPSIEEGSMIQ---------DRENALDWIARRGN-----TTG 138

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
              E    F      +  L  +              +     +      +I  L+    G+
Sbjct: 139  TKERRLKFAKEIMQREFLPHI-----------SQREGADTRKAFFFGYMIHRLLQCVLGR 187

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKP 508
               DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  +    
Sbjct: 188  REEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVFKYLQKCVENNQEFNVQMAVKGSV 247

Query: 509  VVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            + + +     +               +SQ+       S ++H RR +      V R    
Sbjct: 248  LTNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKL 303

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY--GFIETPYRKVCDGKVTND 613
             + R +H TH+G +CPAET EG   GLV +L+    V+        T Y      ++  +
Sbjct: 304  AKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTESTPITDYMSQRQMELLEE 363

Query: 614  VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVV 672
               +        ++         + +     V        +      I D  D   K   
Sbjct: 364  YDPVVNPSAIKVFVNGVWVGTHNNPTQLVNNVQELRRNGTLSYEMSLIRDIRDREFKIFT 423

Query: 673  SIAASLIPFLENDDSNR--VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
                 + P    ++      +    + +  V  L  +     +GM     + + +     
Sbjct: 424  DAGRVMRPLFVVENRLNQANVGQLVLNKGHVQKLLDDREIDTSGM---SDEDAASVKFGW 480

Query: 731  RAGIV----EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVG 785
            R  +     E +DA       +    +      ++   +      +++     +P  K  
Sbjct: 481  RGLLHSGVIEYLDAEEEETAMIVMTPEDLEEHRELQLGVTAPAVPDEDRHRRIKP--KPN 538

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
              VR        PS  LG       +  + +P+  +N          M  + +  ++   
Sbjct: 539  PSVRFYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNY 591

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
               +                                  V             +       
Sbjct: 592  ALRMETMMN-----------------------------VLYYPQKPLATTRSMEYLKFRE 622

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   +  + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E
Sbjct: 623  LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLE 678

Query: 966  LLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
               +    + + L    Y +L +   +  G           K+  + +D      ++   
Sbjct: 679  RFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPTDAKELGQKTTMH 738

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    ++     +  Q                             LR VKV     +
Sbjct: 739  TKRDVSTPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRTTK 778

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L 
Sbjct: 779  VPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHAIPSRMTIAHLVECLLS 838

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G +  +          +S L +                         V     +
Sbjct: 839  KVGSLKGNEGDATPFTDVTVDGVSNLLA---------------QHGYQQRGFEVMYNGHT 883

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G  +   VF                                       +G  Y  +L HM
Sbjct: 884  GKKLRAQVF---------------------------------------LGPTYYQRLRHM 904

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            V DK++AR+ G   ++T+QP+ G++  GG R 
Sbjct: 905  VDDKIHARARGPLQILTRQPVEGRARDGGLRF 936



 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 114/855 (13%), Positives = 248/855 (29%), Gaps = 150/855 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSK---DII- 202
            ++++++Q  RS        + +    G + +   I    ++G  +   F+ K   + + 
Sbjct: 1   SEKVLIAQE-RSAANIVQVFRKKQ---GPIPWTAEIRSAVEKGTRLISSFNIKWTDNSLI 56

Query: 203 --------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
                         +++ D    VP+     ALG+   E+IL+        +Q  +    
Sbjct: 57  LKRTPGPFAYALLPYIKAD----VPMAIVFRALGIVSDEDILNHIVYDREDTQMLELLKP 112

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
            +    ++   + +   +         +  +   +  +  ++ + +  +           
Sbjct: 113 SIEEGSMIQDRENALDWIARRGNTTGTKERRLKFAKEI--MQREFLPHISQREGADTRKA 170

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIRDIPILYVD-SVNNNAYIRNT 361
                +     +  +   +  D        L+           IL++  + +   Y++  
Sbjct: 171 FFFGYMIHRLLQCVLGRREEDDRDHFGKKRLDLAGPLIANLFRILFLKLTKDVFKYLQKC 230

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +  ++  + + A+         G V T  +  S+    + D  K   +  G  ++  R  
Sbjct: 231 VENNQEFNVQMAV--------KGSVLTNGLKYSLATGNWGDQKKAASAKAGVSQVLNRYT 282

Query: 422 LDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
             +      R          +     L N    +         +   + + L     + +
Sbjct: 283 YASTLSHLRRTNTPVGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSV 342

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
                 I + +S   ++ +   D +      SA+  F     +         ++ +   R
Sbjct: 343 GTESTPITDYMSQRQMELLEEYDPV---VNPSAIKVFVNGVWVGTHNNPTQLVNNVQELR 399

Query: 540 RLSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVSSLTS 588
           R   L  +  + R     E        R + P         + + G    N G V  L  
Sbjct: 400 RNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENRLNQANVGQLVLNKGHVQKLLD 459

Query: 589 FARVNAYGFIETPYRKVCDGK----VTNDVVYLSAMEEENRYIAQANSSLDEDGS----- 639
              ++  G  +     V  G      +  + YL A EEE   I      L+E        
Sbjct: 460 DREIDTSGMSDEDAASVKFGWRGLLHSGVIEYLDAEEEETAMIVMTPEDLEEHRELQLGV 519

Query: 640 ---FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                 +    R    +           +  P  ++ I AS+IPF +++ S R      M
Sbjct: 520 TAPAVPDEDRHRRIKPKPNPSVRFYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 579

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                                                   + 
Sbjct: 580 GKQAMGVALTNYAL-----------------------------------------RMETM 598

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             V  Y       +     +  R                        +L  G+N +VA  
Sbjct: 599 MNVLYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAIA 634

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
            + GYN EDS+++++  +   +F S+    +    +   +   E        D   +   
Sbjct: 635 CYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLERFEKPTRADTLRLKGG 694

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G++  G  V+  DI++GK  P         +K             RD S  +
Sbjct: 695 TYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPTDAKELGQKT-------TMHTKRDVSTPL 747

Query: 932 PSGVSGTVVDVRIFN 946
            S  +G V  V    
Sbjct: 748 RSTENGIVDQVLFTT 762


>gi|163930845|dbj|BAF96017.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 320

 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 194/320 (60%), Positives = 248/320 (77%)

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH
Sbjct: 1   GLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITH 60

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF
Sbjct: 61  KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGF 120

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  
Sbjct: 121 LETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFS 180

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME 
Sbjct: 181 RDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMER 240

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+N
Sbjct: 241 AVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCIN 300

Query: 778 QRPLVKVGDEVRRNDIIADG 797
             P V +G+ + R D++ADG
Sbjct: 301 XMPCVSLGEPIERGDVLADG 320


>gi|294495209|ref|YP_003541702.1| DNA-directed RNA polymerase, subunit B' [Methanohalophilus mahii DSM
            5219]
 gi|292666208|gb|ADE36057.1| DNA-directed RNA polymerase, subunit B' [Methanohalophilus mahii DSM
            5219]
          Length = 604

 Score =  309 bits (791), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 115/610 (18%), Positives = 193/610 (31%), Gaps = 114/610 (18%)

Query: 786  DEVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            D+++  D+ ++        +  D     N  VA            + I   ++       
Sbjct: 79   DKLKSGDLTSEDLIRQGRIEYLDAEEEENSYVALYEEDITPKHTHLEIDPSLILGICAGM 138

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            +   E     R T      + +    VS   L  +       V                 
Sbjct: 139  VPYPEHNASPRITMGAA--MLKQCIGVSTSNL-KLRPDTRAHVLHYPQKALTRTQTCDSI 195

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  +     +    +    F R    +  R    + 
Sbjct: 196  HFDERPAGQNFVVAVMSYEGYNIEDALVFNKGSIERG-LGRSHFVRTFEGEERRYPGGQE 254

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+   +             +  ++ L       GP             + E      
Sbjct: 255  DKFEIPDSEY--RGARSAEAYANLDVDGLVNPETTVGPNSVLIGKTSPPRFLEEQTD--- 309

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +   V+               +  +S +  R   K               R+ KV V  +
Sbjct: 310  FGITVE---------------QRRESAITMRSNEKGVVDTVLLTESINGTRLTKVKVRDQ 354

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  I+P +DMPF + G   D+VLNP  +PSRM VG + E   
Sbjct: 355  RIPEIGDKFASRHGQKGVIGLIVPYQDMPFTESGMVPDLVLNPHAIPSRMTVGHVLEMIG 414

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G++IK+     +   D+                                    
Sbjct: 415  GKVGSIEGRRIKATAFSGENEDDLRAGLQNHGFSHTGKE--------------------- 453

Query: 1202 SGVPVSTPVF-DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                    VF DG                            G+     + VG I   KL+
Sbjct: 454  --------VFYDGVT--------------------------GKKVQADIFVGVILYQKLH 479

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+ K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD
Sbjct: 480  HMVASKMHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVMIGHGAAMTLKERLLDESD 539

Query: 1321 DVVGRTRVYESIVAGN-----------------------DTFETGTPESFNVLVKEMQAL 1357
             V       E +V GN                       D        +F +L+ E+++L
Sbjct: 540  KV-------EELVCGNCGMIATFDRRRNVRYCSNCGSETDIHRVEMSYAFKLLLDEIKSL 592

Query: 1358 GLSIDLENSR 1367
            G++  L    
Sbjct: 593  GVAPRLRLDD 602



 Score = 47.8 bits (112), Expect = 0.015,   Method: Composition-based stats.
 Identities = 30/184 (16%), Positives = 60/184 (32%), Gaps = 31/184 (16%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + VN +  I   RR        ++R        D+H            +    + + + L
Sbjct: 18  DPVNLVEDIRKQRRAGM-----LSRQVNVALYEDIH--EVIINSDIGRARRALVVVENGL 70

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                 +    +++      D      + YL A EEEN Y+A     +            
Sbjct: 71  P-LVTEDHIDKLKSGDLTSEDLIRQGRIEYLDAEEEENSYVALYEEDITPKH-------- 121

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                            ++  P  ++ I A ++P+ E++ S R+ MG  M +Q + +  +
Sbjct: 122 ---------------THLEIDPSLILGICAGMVPYPEHNASPRITMGAAMLKQCIGVSTS 166

Query: 707 EAPF 710
               
Sbjct: 167 NLKL 170


>gi|57337364|emb|CAH69690.1| RNA polymerase, beta subunit [Raoultella planticola]
 gi|60416580|emb|CAI43359.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416582|emb|CAI43360.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416588|emb|CAI43363.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416590|emb|CAI43364.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416592|emb|CAI43365.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416594|emb|CAI43366.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416596|emb|CAI43367.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416598|emb|CAI43368.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416600|emb|CAI43369.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416602|emb|CAI43370.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416604|emb|CAI43371.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416606|emb|CAI43372.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416608|emb|CAI43373.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416610|emb|CAI43374.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416614|emb|CAI43376.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 313

 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 190/308 (61%), Positives = 239/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|269912564|emb|CAY86062.1| RNA polymerase beta subunit [Gluconacetobacter europaeus]
          Length = 308

 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 147/311 (47%), Positives = 195/311 (62%), Gaps = 28/311 (9%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIRGMDPDEILSYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DSFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEI+ EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNEHTGEIFAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKE 434
            PD VR +RKE
Sbjct: 298 VPDTVRVLRKE 308


>gi|315259452|gb|ADT91925.1| DNA-directed RNA polymerase beta subunit [Enterococcus
            haemoperoxidus]
          Length = 392

 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 131/420 (31%), Positives = 179/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ +G +V  GD L    +   E  M   + +L      +  +  D  +     V   V 
Sbjct: 45   IVLLGEKVEKGDTLADGPS-MEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSIHIEEYESEARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E                   
Sbjct: 164  PKGVTELSAEERLLHAIFGEKAR-----------------EVRDTSLRVPHGGGGIVHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKINEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+D++LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D                 
Sbjct: 267  TPIDVMLNPLGVPSRMNIGQVLELHLGMAARQLGIHIATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                         +DD V     +        T ++DG                      
Sbjct: 312  -------------NDDDVWETVREAGMARDAKTVLYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 TGEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 127/222 (57%), Positives = 165/222 (74%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  G+VE VDA  + +R   G LD        Y + KF+RSN  T  NQRP+V +G++V 
Sbjct: 1   KHDGVVEYVDASEVRVRRDNGALDK-------YMVTKFRRSNSGTSYNQRPIVLLGEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           + D +ADGPS + G++ALG+N+LV FM W GYN+ED++++S R+V +DV+TSIHIEE+E 
Sbjct: 54  KGDTLADGPSMEEGEMALGQNVLVGFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGD 215


>gi|219852749|ref|YP_002467181.1| DNA-directed RNA polymerase subunit B' [Methanosphaerula palustris
            E1-9c]
 gi|219547008|gb|ACL17458.1| RNA polymerase Rpb2 domain 6 [Methanosphaerula palustris E1-9c]
          Length = 604

 Score =  309 bits (791), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 112/584 (19%), Positives = 191/584 (32%), Gaps = 94/584 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             ++ D     ++ +A            + +   ++       +   E     R T     
Sbjct: 97   IEMIDAEEEEDLYIAINEDQVTPEHTHLEVDPSLILGIGAAHVPFPEHNASPRVTMGAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                            +       +   V             G       +  + AI   
Sbjct: 157  VKQALGFC---SANMKLRPDTRGHLLHYVQKSLTRTQTSELIGSDDRPAGQNFVVAILSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +    +    F R    +  R    + ++IE           I D
Sbjct: 214  EGFNIEDALIFNRASIDRG-LGRSHFLRTYEGEERRYPGGQVDRIE-----------IPD 261

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              +     E         G    + +      LI +    ++ +    D           
Sbjct: 262  TEVTGAHGEEYYKNLDDDGIINPETTVSEKDVLIGKTSPPRFLEEPSSDLITVEKRRDTS 321

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V   +++  + D        I  G++      R+VKV     R  + GDK A RHG KG+
Sbjct: 322  VTMRSNEHGIVDT-----VIITEGENSS----RLVKVRTRDPRIPEIGDKFASRHGQKGV 372

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I P EDMPF + G   DIV+NP  +PSRM +G + E   G      G++I       
Sbjct: 373  IGLIAPQEDMPFTESGMVPDIVINPHAIPSRMTIGHMLEMIGGKVGSLEGRRINGTAFSG 432

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +   D+                                             F     E +
Sbjct: 433  ELEADLRSSLKKFG-------------------------------------FSPTGREVM 455

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L       +G+           F   + VG IY  KL HMVS K++ARS G   ++T
Sbjct: 456  YDGL-------TGK----------RFTADIYVGVIYYQKLYHMVSSKMHARSRGPVQVLT 498

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE-- 1330
            +QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G   + +  
Sbjct: 499  RQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLDESDKVQQYVCAKCGMVAMLDRK 558

Query: 1331 -----SIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  +V G   D +      +F +L+ EM+++G++  +    
Sbjct: 559  RNTTRCLVCGSETDIYYVEMSYAFKLLLDEMKSMGIAPRMILED 602



 Score = 68.9 bits (167), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 36/152 (23%), Positives = 62/152 (40%), Gaps = 14/152 (9%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     D   G+N +VA + + G+N ED+++ +   +   +  S  +  +E   R 
Sbjct: 189 TQTSELIGSDDRPAGQNFVVAILSYEGFNIEDALIFNRASIDRGLGRSHFLRTYEGEERR 248

Query: 854 TKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              G  +   +IP+        EE  KN+D+ GII     V+  D+L+GK +P       
Sbjct: 249 YPGGQVD-RIEIPDTEVTGAHGEEYYKNLDDDGIINPETTVSEKDVLIGKTSPPRFLEEP 307

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             + +            RDTS+ + S   G V
Sbjct: 308 SSDLI-------TVEKRRDTSVTMRSNEHGIV 332



 Score = 42.8 bits (99), Expect = 0.41,   Method: Composition-based stats.
 Identities = 29/184 (15%), Positives = 55/184 (29%), Gaps = 31/184 (16%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +    ++ I   RR   +     A  +       +H        P    +     + +  
Sbjct: 18  DPEALIADIRKMRRSGTVSTEVNASYKQYNGDVIIHTDRGRARRPLIVLQNGKPLISNE- 76

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                      ++       D      +  + A EEE+ YIA     +  +         
Sbjct: 77  -------DLERLKKKEITFQDLVTRGLIEMIDAEEEEDLYIAINEDQVTPEH-------- 121

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                            ++  P  ++ I A+ +PF E++ S RV MG  M +QA+    A
Sbjct: 122 ---------------THLEVDPSLILGIGAAHVPFPEHNASPRVTMGAGMVKQALGFCSA 166

Query: 707 EAPF 710
               
Sbjct: 167 NMKL 170


>gi|242392244|dbj|BAH80359.1| RNA polymerase subunit B' [Haloferax volcanii]
          Length = 609

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 204/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDELNEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DDSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G +EE + 
Sbjct: 431  DGT----------------------------------------------AFQGENEEELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKEKVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLDDDHVEALDNDELDFDDLVERGLVEFIDAEEEEDIYVAVDEDELNE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDDSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 45.1 bits (105), Expect = 0.100,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L     V A    E  +    D      V ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-----PLLDDDHVEALDNDELDF---DDLVERGLVEFIDAEEEEDIYVAVDEDELN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|73697645|gb|AAZ81439.1| RNA polymerase beta subunit [Mycoplasma crocodyli MP145]
          Length = 593

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 131/487 (26%), Positives = 210/487 (43%), Gaps = 79/487 (16%)

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            A +   G   + ++  +    +++     +++ F++  +    G ++             
Sbjct: 180  APLVATGIEKDIALYSAYNFRAKNDGVVSYVDSFKIYVKTHDKGTQDKYYLKNFERSNQG 239

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              I +  I+ VG EV  GD+LV   + K +  +   + +L A       +  D  +    
Sbjct: 240  TVICQKSIVKVGDEVKKGDLLVDGSSFK-DGELALGKNVLVAFTTYNGYNYEDAVILNER 298

Query: 934  ------GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
                    S  + +  +  R     +++  +      +   R+  DE  I+         
Sbjct: 299  LVKDDVYTSIHIEEQTVLFRSSKAGDDKLTADIPNTSKFSTRNL-DEYGIVRVGSEVIAG 357

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            ++L G+ +  G +   +   L   ++ + P        + D+     V++          
Sbjct: 358  DVLVGRVSPKGEENPSQEEKLLMAILQQRP--------LNDKDTSLRVKNGHNGTVIGIE 409

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
            +L           + GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP E
Sbjct: 410  VLSR---------ETGDILEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISVVLPEE 460

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+L+DGTPVDI+LNP GVPSRMN+GQ+ E HLG A   L  K  +   D     DI  
Sbjct: 461  DMPYLEDGTPVDIMLNPQGVPSRMNIGQVLELHLGMAARKLNTKFVTPSFDGVKKSDIED 520

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            +                                                      L  + 
Sbjct: 521  VLEEAG-------------------------------------------------LDKSG 531

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 ++ L D +TG+  D+PV+VG +YMLKL+HMV DK++ARS G YSL+TQQPLGGKS
Sbjct: 532  -----KAYLIDPITGKKLDKPVSVGVMYMLKLSHMVDDKMHARSVGPYSLITQQPLGGKS 586

Query: 1288 NRGGQRL 1294
              GGQR 
Sbjct: 587  QNGGQRF 593



 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 202/448 (45%), Positives = 303/448 (67%), Gaps = 14/448 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN +GF++TPY KV +G +   D+ YL+A EE     AQ++  +D+     E+ +  R
Sbjct: 61  AKVNEHGFLQTPYFKVNNGVIDYEDLRYLTASEETGLAFAQSSVRVDDTNKIIEKTLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+    +IDFI+ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQ+VPL++AEA
Sbjct: 121 KDYNYIIGKPSEIDFIEVSSKQMVSVAAAAIPFLENDDANRALMGANMQRQSVPLIEAEA 180

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P V TG+E  +A  S     AK  G+V  VD+ +I +++ +          D Y L  F+
Sbjct: 181 PLVATGIEKDIALYSAYNFRAKNDGVVSYVDSFKIYVKTHD------KGTQDKYYLKNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+ +VKVGDEV++ D++ DG S   G+LALG+N+LVAF  ++GYN+ED+++
Sbjct: 235 RSNQGTVICQKSIVKVGDEVKKGDLLVDGSSFKDGELALGKNVLVAFTTYNGYNYEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ++ER+V +DV+TSIHIEE  V+ R +K G +++T DIPN S+   +N+DE GI+ VG+EV
Sbjct: 295 LNERLVKDDVYTSIHIEEQTVLFRSSKAGDDKLTADIPNTSKFSTRNLDEYGIVRVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR- 947
             GD+LVG+++PKGE   + EEKLL AI  ++ ++ +DTSLRV +G +GTV+ + + +R 
Sbjct: 355 IAGDVLVGRVSPKGEENPSQEEKLLMAILQQRPLNDKDTSLRVKNGHNGTVIGIEVLSRE 414

Query: 948 ------HGIDKNERSISVEREQIELLAR 969
                  GIDK  +    ++ +I++  +
Sbjct: 415 TGDILEDGIDKIVKVSIAQKRKIKVGDK 442


>gi|269912622|emb|CAY86091.1| RNA polymerase beta subunit [Gluconobacter albidus]
 gi|269912624|emb|CAY86092.1| RNA polymerase beta subunit [Gluconobacter albidus]
          Length = 312

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 147/315 (46%), Positives = 203/315 (64%), Gaps = 28/315 (8%)

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRID
Sbjct: 1   GTERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRID 60

Query: 208 RRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRG 242
           R+RK+PVT+ L AL                         GMD +EILS FY  + +++ G
Sbjct: 61  RKRKLPVTTLLYALEGANYLAQRERKIADGGDVDGLDIRGMDQDEILSYFYQTVPFTRLG 120

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
             W  P    D   G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +    
Sbjct: 121 GEWARPFDP-DAFRGLKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLD 178

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
           + G ++A D+VN  TGEIY EAG+ + E  L  +    I ++P+L VD  ++  +IRNTL
Sbjct: 179 ILGRFLAYDLVNENTGEIYGEAGEELTEDRLATLEEMGITELPLLSVDG-SHGPWIRNTL 237

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             DKN  R +AL+DIYR+MRPG+  T   AE+MF+ LFFD  +YDLS VGRVKMNMRL++
Sbjct: 238 AADKNSSRDEALIDIYRIMRPGEPPTKETAEAMFHGLFFDQGRYDLSAVGRVKMNMRLDV 297

Query: 423 DTPDDVRHIRKEDII 437
           D PD +R +RKEDI+
Sbjct: 298 DAPDTLRVLRKEDIL 312


>gi|83415501|gb|ABC17958.1| RNA polymerase II second largest subunit [Boothiomyces macroporosum]
          Length = 714

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 141/852 (16%), Positives = 252/852 (29%), Gaps = 158/852 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + I +  + S            + +  + + +     +
Sbjct: 2    KRLDLAGPLLGGLFRMLFKKLTKDISKYVQKSMELGKEFNLSLAVKSGIITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RRL+      + R     + R +H TH+
Sbjct: 62   GNWGDQKKFMQARAGVSQVLNRYTFASTLSHLRRLNT----PIGRDGKLAKPRQLHDTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  A +   G    P  +  D      +  ++  +  +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMAYIT-VGSASRPVLEFLDEWTMESLEDINPGQIPSAT 176

Query: 627  IAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                N +      + +ELV      R + +         D  D   +             
Sbjct: 177  KVFLNGAWVGVHRYPDELVNNLRTLRRSLDISPEVSVVHDVRDKELRIYTDPGRICRSLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
                  R+L+   +              +  G+                   VE +D   
Sbjct: 237  IVSPEQRLLLTKPIVEALNSKEMTWNDLLANGI-------------------VEYIDTEE 277

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +         +    Q + Q      +  V   +           PS  L
Sbjct: 278  EETIMIVMSPEDLMDARLAVQGQ--QITQQEGHQRLKSAVYARNY----THCEIHPSMIL 331

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N     +    M  + +     I       R   +G     
Sbjct: 332  G-------ICASIIPFPDHNQSPRNVYQSAMGKQAMG----IFLTNFQMRMDTMGNILFY 380

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
               P                               +       +   + ++ AI      
Sbjct: 381  PQKPL-------------------------ATTQAMRYMNFGELPAGQNVVVAIACYTGY 415

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D+ ++S  +E E IE   RD            
Sbjct: 416  NQEDSLIMNQSSIDRGMF-RSLYYRVYMDQEKKSGLLESECIEKPTRDTTLRM---KHGS 471

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            Y +L +                   +S + I               E  QR V   K   
Sbjct: 472  YDKLED----------DGLIAPGVRVSGEDIDIIIGKTVPIPENSVELGQRTVNHTKRDA 521

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             T     E+   + +      D       + VKV +   R  Q GDK A RHG KG V  
Sbjct: 522  STPLKSTENGIVDNVMVTTNQD-----GFKFVKVRIRSIRIPQMGDKFASRHGQKGTVGI 576

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  DG   D+++NP  +PSRM +G + E  L       G +  +        
Sbjct: 577  TYRTEDMPFTADGITPDLIINPHAIPSRMTIGHLVECLLSKVSTFTGNEGDATPFTDVTV 636

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS   +                                                    
Sbjct: 637  EAISQALAAQGYQRRGFEVL---------------------------------------- 656

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    +G +    G      +  +  G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 657  -------YNGHT----GR---KLNAQIYTGPTYYQRLKHMVDDKIHSRARGPLQILTRQP 702

Query: 1283 LGGKSNRGGQRL 1294
            + G+S  GG R 
Sbjct: 703  VEGRSRDGGLRF 714


>gi|242392234|dbj|BAH80354.1| RNA polymerase subunit B' [Haloferax larsenii]
          Length = 609

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 125/600 (20%), Positives = 206/600 (34%), Gaps = 102/600 (17%)

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
             D V R  +       +  D     ++ V             + I  +++       I  
Sbjct: 93   NDMVERGLV-------EFIDAEEEEDIYVGVDEDELTEDHTHLEIDPQLIFGIGAGMIPY 145

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             E     R T      + +    +     +   +     +        +        G  
Sbjct: 146  PEHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFD 202

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
                 +  + A+   +  ++ D  +     V    +    F R    +  R    + ++ 
Sbjct: 203  ERPAAQNFVVAVMSYEGFNIEDALVMNKGSVE-RALSRSHFFRTYEGEERRYPGGQEDRF 261

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E+ ++D       +           L     V+      +++VL           +    
Sbjct: 262  EIPSQD-------VRGARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDM 314

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            A    + +R         E+         + +               ++ KV V  +R  
Sbjct: 315  AGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVP 362

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK A RHG KG+V  + P EDMPF  DG   D+++NP  +PSRM V        G  
Sbjct: 363  ELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLIINPHALPSRMTV--------GHV 414

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG K+ +L                                                 
Sbjct: 415  LEMLGGKVGALEGRRVDGT----------------------------------------- 433

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                  F G  E+ + S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS
Sbjct: 434  -----AFQGESEDELRSALEERGYMSSGKEVMYSGVTGEKVEAEIFVGIIFYHKLYHMVS 488

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            +K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD    
Sbjct: 489  NKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKESV 548

Query: 1321 ----D-----VVGR--TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                D     V  R   R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 549  YISADTGMVAVEDRDQRRIYD-PVTGDEDNIHEIDISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 43.5 bits (101), Expect = 0.28,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 59/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPEQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L               +E       D      V ++ A EEE+ Y+      L 
Sbjct: 71  EDGEPLLGDEHVE--------ALENNELDFNDMVERGLVEFIDAEEEEDIYVGVDEDELT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|126722431|dbj|BAF48629.1| DNA-dependent RNA polymerase subunit B' [Natronorubrum tibetense]
          Length = 435

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 84/261 (32%), Positives = 120/261 (45%), Gaps = 58/261 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L  A  + +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRGGLEDAGFNSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD----DVVG 1324
            A  L+E L  +SD     + G
Sbjct: 383  AMTLKERLLDESDREFIHICG 403



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|291196424|emb|CBG27569.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas jinjuensis]
          Length = 305

 Score =  308 bits (790), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 185/305 (60%), Positives = 237/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGQVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++LDE G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLDEQGRLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R+DI+AD
Sbjct: 241 SVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDKVSRSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|205277600|gb|ACI02067.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
 gi|205277602|gb|ACI02068.1| RNA polymerase subunit B [Acinetobacter genomosp. 13TU]
          Length = 255

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 117/254 (46%), Positives = 164/254 (64%), Gaps = 4/254 (1%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G    K+   LS DL+S        +    DE +   +  ++V  +   + ++++F  
Sbjct: 5    SNGGGSTKRGDKLSEDLLSGLELVDLLEIQPTDEAIAERLTQIQVFLKEKSAEIDEKFAE 64

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G
Sbjct: 65   KKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANG 124

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ ++ + +    +  LR FL+K+
Sbjct: 125  VPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT---VLELREFLDKI 181

Query: 1176 IGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                G   E +    DD +L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ+
Sbjct: 182  YNKVGGEQEDLDSLTDDEILALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQT 241

Query: 1235 ILYDGLTGEPFDRP 1248
            +L+DG TGE FDRP
Sbjct: 242  VLFDGRTGEQFDRP 255


>gi|57337360|emb|CAH69688.1| RNA polymerase, beta subunit [Raoultella terrigena]
 gi|57337366|emb|CAH69691.1| RNA polymerase, beta subunit [Raoultella terrigena]
          Length = 313

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 189/308 (61%), Positives = 239/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  + ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNDDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|57337362|emb|CAH69689.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416584|emb|CAI43361.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|60416586|emb|CAI43362.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
 gi|257136314|gb|ACV44457.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|257136316|gb|ACV44458.1| RNA polymerase beta subunit [Klebsiella oxytoca]
          Length = 313

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 190/308 (61%), Positives = 240/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 LVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|300521500|gb|ADK25961.1| RNA polymerase B [Candidatus Nitrososphaera gargensis]
          Length = 1116

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 83/315 (26%), Positives = 125/315 (39%), Gaps = 74/315 (23%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ K+ V   R  + GDK A RHG KG+V  ++  ED+P+ +DG   DI++NP   PSRM
Sbjct: 857  KMYKIRVRDMRIPEIGDKFASRHGQKGVVGMLVNQEDVPYTEDGVVPDIMINPHAFPSRM 916

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             VGQ  E+  G A    G+ +       +   DI                          
Sbjct: 917  TVGQFMESLGGKAASLRGRIVDGSAFLGEKGDDIKTAMEQYGFKYTGKETM--------- 967

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                    G        TG  F   V +
Sbjct: 968  --------------------------------------YDG-------RTGRKFPADVYI 982

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  KL+HMV+DK+++R+ G   ++T+QP  G++  GG R GEME  C+ AYGA+ +L
Sbjct: 983  GVVYYQKLHHMVADKIHSRARGQVQMLTKQPTEGRARGGGLRFGEMERDCLIAYGASMML 1042

Query: 1312 QEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFNVLVKE 1353
            ++ L  +SD                DV  R   Y   V G            +F +L++E
Sbjct: 1043 KDRLLEESDKAEVNVCERCGLLAYYDVKQRR--YICRVCGEKAKISSVVIAYAFKLLLQE 1100

Query: 1354 MQALGLSIDLENSRT 1368
            M +L ++  L     
Sbjct: 1101 MMSLNVAPRLLVKEK 1115



 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 123/640 (19%), Positives = 232/640 (36%), Gaps = 66/640 (10%)

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
            S+      + ++    +    +          +DA++ I + + PG +  F +  +   
Sbjct: 233 ESDKDIADSVSLNETIQDELEPSFEKAGDVNTSRDAIVYISKRIAPGMLEEFQIKRAETL 292

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             +       L  +G+             D RH +   +      L++L+ G    DD D
Sbjct: 293 LDWGL-----LPHIGK-----------NPDNRHEKALFLGEAASKLIELKLGWIDADDKD 336

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP---------QDLINAKP 508
           + GN+ ++  G+ML + +R     + R +K ++        +                  
Sbjct: 337 HYGNKVIKFAGQMLADLFRTAFRNLIRDMKYQLERSGQKRGINAVAAAVRPGIVSDKLNN 396

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            ++          ++QL +  N +S I+H RR+    Q  ++R++   E RD+H TH+GR
Sbjct: 397 AIATGNWGRGRVGVTQLLDRTNYMSTISHLRRI----QSPLSRSQPNFEARDLHATHFGR 452

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           ICPAET EG N GLV +L   A ++          K+ +  V N V        E+    
Sbjct: 453 ICPAETPEGSNCGLVKNLALSAIISVNVQSAEVTEKLYELGVQN-VEDAREDLRESGTRV 511

Query: 629 QANSSLD---EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL------I 679
             +  L    E G    + +       +I        +   +      +  S        
Sbjct: 512 FVDGRLIGYVEKGEHLSDTLRSMRRSGKIHPHVGIYLYSSQNENATKRLYISCNAGRVLR 571

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA--------KR 731
           P +   D   ++    +++ +   L          +E V A       VA        K 
Sbjct: 572 PLVVLRDGKPLVTNEVIEKVSKKFLSWNDLLYMGVIELVDANEEENCYVAIDPKKLEPKH 631

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS--NQNTCVNQRPLVKVGDEVR 789
             +     AI  V  S+    + + S  + Y     ++S       +N    V+    + 
Sbjct: 632 THLEIFPSAILGVGASIIPYPEHNQSPRNTYESAMAKQSLGFSTPLMNASTYVRQHFMLY 691

Query: 790 RNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
               +    + +   L D   G+N +VA +P+ GYN ED+++ ++  V   +  +     
Sbjct: 692 PQTPVVSTKAINLLGLEDRPTGQNAVVAVLPFEGYNIEDAVVFNKSSVDRGLGRTFFYRI 751

Query: 847 FEVMARDTKLGPEEITRDIP-------NVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           +E  A+    G ++                E+  + +++ G I   A VN GDIL+G+ +
Sbjct: 752 YEAEAKQYPGGMKDNFELPQPDANIRGYRGEKAYRLLEQDGAIMHEAVVNGGDILIGRTS 811

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           P        E ++       K    RDTS+ V    +G V
Sbjct: 812 PPRFMEEYKEFEV-------KGPYRRDTSVGVRPSENGVV 844



 Score =  132 bits (333), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 99/725 (13%), Positives = 211/725 (29%), Gaps = 124/725 (17%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA--MLEFVSYEFDPPKF---- 86
              SY+ F+            GLQ+    V  I   +      ++    +   P+     
Sbjct: 25  HLNSYNEFM----------ERGLQSIIDEVGEIEIETAEYPYKIKLGKIKLQQPRIMELD 74

Query: 87  ------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
                    +   R+LTYA P  + L   V +  +   ++         I++GD+P+M K
Sbjct: 75  GSITHVAPMEARLRNLTYASP--VMLECSVVEDGKILESRF--------IHIGDMPVMVK 124

Query: 141 D------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F+I G +R++V     S   +          +G
Sbjct: 125 SNTCILHNLPESKLIEFGEDPRDPGGYFIINGSERVIVGLEDLS---YNKIIVDAEEATG 181

Query: 177 KLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSE-EILS 230
            LLY  ++       +   +++       I  +I      +P+ + + ALG++S+ +I  
Sbjct: 182 TLLYKAKVYSSIVGYR-AKLELVMRPDGSIVTKIPGSPVDIPLITLIRALGLESDKDIAD 240

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL-- 288
           +           D        A  +  ++ +   +       ++E  +   +  L     
Sbjct: 241 SVSLNETI---QDELEPSFEKAGDVNTSRDAIVYISKRIAPGMLEEFQIKRAETLLDWGL 297

Query: 289 -KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
               G          L     A  ++  + G I  +  D    K ++             
Sbjct: 298 LPHIGKNPDNRHEKALFLGEAASKLIELKLGWIDADDKDHYGNKVIKFAGQMLADLFRTA 357

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALL---DIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           + + + +  Y        +  +   A +    +   +     +       +      D  
Sbjct: 358 FRNLIRDMKYQLERSGQKRGINAVAAAVRPGIVSDKLNNAIATGNWGRGRVGVTQLLDRT 417

Query: 405 KYDLSTVGRVKMNMRLNLDTPD-DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            Y  +     ++   L+   P+ + R +       I        +  G + ++       
Sbjct: 418 NYMSTISHLRRIQSPLSRSQPNFEARDLHATHFGRICPAETPEGSNCGLVKNLALSAIIS 477

Query: 464 VRS-VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           V     E+ +  Y LG+  +E +        D+     +  ++ + +         S  L
Sbjct: 478 VNVQSAEVTEKLYELGVQNVEDA------REDLRESGTRVFVDGRLIGYVEKGEHLSDTL 531

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR-ICPAETSEGHNIG 581
             +         +      S           +    R + P    R   P  T+E     
Sbjct: 532 RSMRRSGKIHPHVGIYLYSSQNENATKRLYISCNAGRVLRPLVVLRDGKPLVTNEVIEKV 591

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               L          + +  Y  V        +  + A EEEN Y+A     L+      
Sbjct: 592 SKKFL---------SWNDLLYMGV--------IELVDANEEENCYVAIDPKKLEPKH--- 631

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                                 ++  P  ++ + AS+IP+ E++ S R      M +Q++
Sbjct: 632 --------------------THLEIFPSAILGVGASIIPYPEHNQSPRNTYESAMAKQSL 671

Query: 702 PLLKA 706
                
Sbjct: 672 GFSTP 676


>gi|269912568|emb|CAY86064.1| RNA polymerase beta subunit [Gluconacetobacter europaeus LMG 18494]
          Length = 310

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 148/312 (47%), Positives = 196/312 (62%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIRGMDPDEILSYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DSFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEI+ EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNEHTGEIFAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKED 435
            PD VR +RKED
Sbjct: 298 VPDTVRVLRKED 309


>gi|51035541|emb|CAH10906.1| RNA polymerase B subunit [Natrialba asiatica]
          Length = 435

 Score =  308 bits (790), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 81/253 (32%), Positives = 117/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+++NP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTENGVVPDLIVNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  +   L  A  + +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESELRDGLEDAGFNSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 73/209 (34%), Gaps = 21/209 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECG 880
           ++++++  V   +  S     +E   R    G E+              E+   ++DE G
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRFEVPSQDVRGARGEDAYAHLDEDG 135

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++    +V+   +L+GK +P               + G      R+TS+ + SG SG V 
Sbjct: 136 LVNPETDVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVD 189

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLAR 969
            V +       K  +    +    EL  +
Sbjct: 190 TVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|194591887|gb|ACF76524.1| RNA polymerase beta subunit [Mycoplasma hyosynoviae]
 gi|194591889|gb|ACF76525.1| RNA polymerase beta subunit [Mycoplasma hyosynoviae]
          Length = 606

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 203/454 (44%), Positives = 297/454 (65%), Gaps = 9/454 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ YGFI+TPY KV D K+  ++  YL+A+EE    IAQ+   + ++    +E V 
Sbjct: 61  SFAKIDKYGFIQTPYFKVKDRKIDFSEPKYLTAIEEMGAIIAQSTVRI-KNNMIIDEYVM 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E I V   K+D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++K 
Sbjct: 120 ARKDSEFIEVEASKVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPIIKP 179

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-----GDLDPSTSGVDI 761
           EAP V TG+E+ +A+ S   + +   G V  +DA +I I   +           +   ++
Sbjct: 180 EAPLVATGVEADIARYSSTNLRSTIDGTVTYIDADKIEITPDDFAETSTKSTKKSKRPEV 239

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + L  F+RSNQ T ++Q PLVK+G ++++ D++ DGPS   G+LALG+N+LV F  WHGY
Sbjct: 240 FYLRTFERSNQGTLIHQIPLVKLGQKIQKGDLLVDGPSMKDGELALGKNVLVGFSTWHGY 299

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++SE++V +DV+TSIHIEE  +  R +K G + +T DIPN S    + +++ GI
Sbjct: 300 NYEDAVILSEKLVKDDVYTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKRFLNDQGI 359

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + VG+EV  GDILVG+ +PKGE   TPEEKL+ AIF +K+   +DTSL+V  G +GTVV 
Sbjct: 360 VRVGSEVIAGDILVGRTSPKGEENPTPEEKLMAAIFSQKSSQRKDTSLKVKHGHNGTVVA 419

Query: 942 VRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
           V + +R     ++    +E+     +A+ +  + 
Sbjct: 420 VEVLSREFG--DQLEDGIEKIVKVSIAQKRKIQV 451



 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 121/415 (29%), Positives = 179/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G ++  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 259  LVKLGQKIQKGDLLVDGPS-MKDGELALGKNVLVGFSTWHGYNYEDAVILSEKLVKDDV- 316

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L+     R+   +   + + G  
Sbjct: 317  YTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKRFLNDQGIVRVGSEVIAGDILVGRT 376

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q + Q +     V+        +  +L   F       
Sbjct: 377  SPKGEENPTPE--EKLMAAIFSQKSSQRKDTSLKVKHGHNGTVVAVEVLSREF------- 427

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 428  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSVVLPVEDMPYLEDGTPLDI 485

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + + D   +  I  +    +      S
Sbjct: 486  VLNPQGVPSRMNIGQVLELHLGLAAKKLGVKFVTPVFDGITHNQIKDILQEAKIDPSGKS 545

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +GQ       
Sbjct: 546  VV-----------------------------------------------YNGQ------- 551

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE  D P++VG +Y LKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 552  TGEKLDAPISVGIMYYLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 606


>gi|303287030|ref|XP_003062804.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455440|gb|EEH52743.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 1197

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 128/324 (39%), Gaps = 83/324 (25%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            M    +  VK  V   R  + GDK + RHG KG++  ILP  D PF + G   D+++NP 
Sbjct: 934  MTDEGVFNVKCLVRHTRRPEVGDKFSSRHGQKGVIGTILPQRDFPFSERGITPDLIMNPH 993

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     +G K  +    +                          
Sbjct: 994  GFPSRMTV--------GKMLELVGGKAGAQDGRFHDGT---------------------- 1023

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G   E I + L       +G+ +L+ G+TGEP 
Sbjct: 1024 ------------------------AFAGDTAEDIGATLVNHGFSYNGKDLLHCGITGEPL 1059

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  KL HMV DK++AR+ G   ++T+QP  G++  GG RLGEME  C+  Y
Sbjct: 1060 VAYIFMGPVYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRARDGGLRLGEMERDCLIGY 1119

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGN----------------------DTFETGT 1343
            GA+ ++ E L I SD        +E+ V                         D      
Sbjct: 1120 GASALILERLMISSD-------QFEAQVCNKCGLLAYRHHGTGKDACAQCEDADVSALKL 1172

Query: 1344 PESFNVLVKEMQALGLSIDLENSR 1367
            P +  +L +E+Q++ +   L  S 
Sbjct: 1173 PYACKLLFQELQSMNICPRLTLSD 1196



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 137/1005 (13%), Positives = 282/1005 (28%), Gaps = 237/1005 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           L+     S+++ +   I    R         K+   +T     +  L + +     P   
Sbjct: 87  LVRQHIDSFNYLINEEIRKIIRA--------KANERVTCDTDPSFYLRYTNIHVGKPCVE 138

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  RD+TYA P+ +          +    +   +     I +G +PLM
Sbjct: 139 EDYIVEDITPQQCRLRDMTYAAPVTVDAEYT---RGKEIVTRKTNEQGVGGITIGRIPLM 195

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+KG++++V+ Q   S              
Sbjct: 196 LRSSRCVLTGKSEDELARLGECPLDPGGYFVVKGVEKVVLIQEQLSKN------------ 243

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-----DRRRK------------------ 211
                   RII        I+ D+K  I   +     +R+ K                  
Sbjct: 244 --------RII--------IDVDAKGEIGASVTSSTHERKSKTNIVVKHGKLYLRHNTFV 287

Query: 212 --VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS----- 263
             VP+   L A+G +S+ E++    P   Y+          SA  +    +         
Sbjct: 288 EDVPILVALKAMGTESDQEVVQLVGPDPAYANLLIPSLQECSALAIFTQQQALEYCGAKV 347

Query: 264 --------LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
                             ++  + + +G++       +  + + +    G      ++  
Sbjct: 348 RTQSRMGGYQYGRNRRNRVDEARDILAGVV-------LAHVPVVAYDFRGKCAYVAVMIR 400

Query: 316 ETGEIYIEAGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                 I+   + D+     + +  +      +        NA ++       +K  +  
Sbjct: 401 RILHAMIDRTQIDDKDYYGNKRLELAGQLLALLFEDCFKRLNADLKRQADAVLSKSNRAT 460

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             DI + +R          +   +     +      TV R +M  +        +  I  
Sbjct: 461 QFDIIKCIR----------QDTLSNGLEHAISSGNWTVKRFRMERKGVTQVLSRLSFISA 510

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
              + ++  +         +     L   +   +      +     L    ++   +++ 
Sbjct: 511 ---LGMMTRITSQFEKTRKVSGPRALQPSQWGMLCPSDTPEGESCGLVKNLALMTHVTTD 567

Query: 494 DIDSVMPQDLIN--AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           D +  + +       +P+         +   + +  + + L   +   R  A     + R
Sbjct: 568 DEEEPLRKLAFTLGTQPLSLICGAELHAPGGAIVFLNGSILGVHSAPDRF-ARDMRYLRR 626

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDG 608
                E   VH T  GR+    +  G     +  +      A       ++       D 
Sbjct: 627 IGKVGEFVSVHTTQGGRL-YIASDGGRVCRPLLIVADGEPLATREHLDELKAGRWGFNDF 685

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V YL   EE   YIA   + +  D                          ++  P
Sbjct: 686 LKRGLVEYLDVNEENISYIALYENEITRDH-----------------------THLEIEP 722

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ + A +IP+  ++ S R    C M +QA+                           
Sbjct: 723 FTMLGVCAGIIPYPHHNQSPRNTYQCAMGKQAMGN------------------------- 757

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                           I   + +   +   + +Y               Q+P+VK     
Sbjct: 758 ----------------IAFNQLNRMDTLMYLLVYP--------------QKPIVK----- 782

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                           L  G+N  VA M + GY+ ED++++++  +       I + ++ 
Sbjct: 783 -----TKTIELIGYDRLGAGQNATVAVMSYSGYDIEDAIVMNKASLDRGFGRCIVLRKYA 837

Query: 849 VMARDTKLGPEEI---TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
              +       +      +         + +D  GI  VG  +NPGD+ V K +P     
Sbjct: 838 TQVKKYSNRTMDRIVAPTESQAGPTGRHRLLDRDGIASVGTLINPGDVYVNKQSPSNTRD 897

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
             P    +   F          S + P G S  VVD  +      
Sbjct: 898 PLPNPHAMPDTFYRPTP----QSYKGPQGES-CVVDKVMLTMTDE 937


>gi|194303506|gb|ACF41176.1| RNA polymerase beta subunit [Mycoplasma flocculare ATCC 27399]
          Length = 594

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 202/425 (47%), Positives = 285/425 (67%), Gaps = 9/425 (2%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L  + + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ + +
Sbjct: 1   QINPLGEMANKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPVETPEGQNIGLILNFS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            ++RVN YGFI TPY KV +G V  N V +L+A EE     AQ +  +D++     E + 
Sbjct: 61  VYSRVNKYGFIITPYYKVKNGVVDFNQVHWLTAAEEFGLSFAQYSIEIDKNNKIVPEKLI 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R      ++  +++D+ID S  Q+ SI+AS IPFLEN+D+NR LMG NMQRQAVPL+KA
Sbjct: 121 VRKNQSYFVLDSKQVDYIDVSSMQMTSISASAIPFLENNDANRALMGSNMQRQAVPLIKA 180

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAP V TG+ES +A+ S   + A   G V  VDA +I+I               ++ L  
Sbjct: 181 EAPLVATGIESDIARFSATNLRASMDGEVSFVDAKKIII--------TDGEVEKVHYLRA 232

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F++SNQ T + Q+P VK+GD++++  +I DGPST  G+LALG+N+LVAF  W+GYN+ED+
Sbjct: 233 FEKSNQETLILQKPTVKLGDKIKKGQLICDGPSTYNGELALGKNVLVAFSTWYGYNYEDA 292

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++ISE++V +DVFTSIHI+E  +  R +K G + +T +IPN S +   ++D  GI+ VG+
Sbjct: 293 IIISEKLVKDDVFTSIHIQEQTIKFRSSKAGDDVLTAEIPNASAKSRIHLDANGIVIVGS 352

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EV+ GDILVG+ +PKGE   T EEKL+ AI+G+K    +DTSLRV +G  GTV+DV+I +
Sbjct: 353 EVDTGDILVGRTSPKGEDNPTAEEKLMAAIWGKKVFAQKDTSLRVKNGEGGTVIDVQILS 412

Query: 947 RHGID 951
           R   D
Sbjct: 413 RDQGD 417



 Score =  291 bits (746), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 120/414 (28%), Positives = 174/414 (42%), Gaps = 67/414 (16%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            + +G ++  G ++    +      +   + +L A       +  D  +     V   V  
Sbjct: 248  VKLGDKIKKGQLICDGPSTYN-GELALGKNVLVAFSTWYGYNYEDAIIISEKLVKDDVF- 305

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I  +    K   S + +      +       ++ LD N    +   +   + + G   
Sbjct: 306  TSIHIQEQTIKFRSSKAGDDVLTAEIPNASAKSRIHLDANGIVIVGSEVDTGDILVGRTS 365

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K     +++   +   + W +     +     V++ +                +I    
Sbjct: 366  PKGEDNPTAE--EKLMAAIWGKKVFAQKDTSLRVKNGEGG---------TVIDVQILSRD 414

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  ++K+ +A KR ++ GDKMAGRHGNKG+VS ILP EDMPFL+DGTPVDIV
Sbjct: 415  QGDNLEDGVGMLIKILIAQKRKVKVGDKMAGRHGNKGVVSVILPVEDMPFLEDGTPVDIV 474

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNP GVPSRMN+GQ+ E HLG     L  K  + + D      I  L +           
Sbjct: 475  LNPQGVPSRMNIGQVLELHLGMVAKKLKTKFVTPVFDGIKIDTIKSLFAEANIPKSGKFK 534

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         FD                          G+T
Sbjct: 535  L----------------------------FD--------------------------GIT 540

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            G+ FD P +VGY+YMLKL HMV DK++ARS G YSL TQQPLGGKS  GGQR G
Sbjct: 541  GQAFDNPTSVGYMYMLKLQHMVDDKMHARSIGPYSLTTQQPLGGKSQNGGQRFG 594


>gi|126722421|dbj|BAF48624.1| DNA-dependent RNA polymerase subunit B' [Natrinema pellirubrum]
          Length = 435

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G D++ +   L  A  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDKDELREGLEEAGFDSAGKETMYSGITGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|281204919|gb|EFA79113.1| RNA polymerase II core subunit [Polysphondylium pallidum PN500]
          Length = 1965

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 126/655 (19%), Positives = 222/655 (33%), Gaps = 119/655 (18%)

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
               + L   +   V  G E  +   +  A      G+    D+I + I +    +     
Sbjct: 884  EDLIQLGLGDCKLVKNGSEFNIVHQATDAAATLFIGLGAFSDSIPLWIMNGSRLVQSQYL 943

Query: 758  GVDIYRLMKFQRSNQNTCVN-----------QRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                ++  +    +Q+               Q   +  G ++  N I     ST  G L 
Sbjct: 944  SSLQFKTTQISTKSQSFIYTAPTTSQVSKLEQMVELYKGLDIETNGIYRSSSST--GILI 1001

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEEITRDI 865
              +N           N+ + + ++     +    S    E+    AR  +LG   +    
Sbjct: 1002 SLKNQQNLV------NYHERIGVNYNQRKQREIAST--AEYIRYQARQRELGSTTVKSQA 1053

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT---PEEKLLRAIFGEKAV 922
               S   LK   +   + + + V+  + ++G IT + E+          +  +  G++A+
Sbjct: 1054 QWQSR--LKAHGDALYVPIESVVDCANCIIGDITTESENHSFVGGQGFFIHNSAMGKQAM 1111

Query: 923  DVRDTSLRVPSGVSGTVV----DVRIFNRHGIDKNERSISVEREQ---IELLARDKDDEQ 975
             V  T+ ++       V+       +  R     + R +   +     I   +    ++ 
Sbjct: 1112 GVYITNYQLRMDTMAHVLFYPQKPLVTTRSMEYLHFRELPAGQNVCVAIACYSGYNQEDS 1171

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV-QDEKVQRN 1034
            +IL+++   R   +       S     KK T +  +   +  R           EK+  +
Sbjct: 1172 LILNQSAIDR--GLFRSMFYRSYKDEQKKQTSMMEETFEKPDRDTCVGMRHGSYEKIDED 1229

Query: 1035 --------------VESLKVQYETSKSIL--EDRFKNKIEKIQWGDDMPPGVLRVV---- 1074
                          +             L  + R ++K +          G++  V    
Sbjct: 1230 GLVAPGVRVTGDDIIIGKTTPLPPQDEDLGPKTRRQSKRDSSTAMRSSENGIVDSVILTT 1289

Query: 1075 --------KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                    KV V   R  Q GDK + RHG KG        ED+P+  +G   DIV+NP  
Sbjct: 1290 SGDGLKFTKVRVRSMRTPQIGDKFSSRHGQKGTCGMTYRQEDLPWTVEGIVPDIVVNPHA 1349

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +GQ+ E  LG      G +                                   
Sbjct: 1350 IPSRMTIGQLIECLLGKVSSMTGDEGD--------------------------------- 1376

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     EAI+  L       +G  ++Y+G TG   D
Sbjct: 1377 --------------------ATP-FTDVTVEAISKALHGIGYQMTGHEVMYNGHTGRRMD 1415

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
              + +G  Y  +L HMV DK+++RS G   ++T+QP+ G+S  GG R GEME  C
Sbjct: 1416 AQIFIGPTYYQRLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLRFGEMERDC 1470



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 89/737 (12%), Positives = 214/737 (29%), Gaps = 150/737 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---------------AFSGAAM 73
           L+  Q  S+D F+   +          Q       PIT                FS    
Sbjct: 35  LVRQQLDSFDEFIQNTM----------QEIIDESPPITLRPEAQHHPGQQQVHNFS-TFS 83

Query: 74  LEFVSYEFDPPK---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           ++F       P             +    R+LTY+ PL + +       D          
Sbjct: 84  IKFGQIYLSKPTSEIDGMTQPVTPNQARIRNLTYSAPLYVDITKTQVTKDRRDEEPL--- 140

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
              + I++G +P+M +                         G F+I G ++++++Q   S
Sbjct: 141 ---EKIFIGKVPIMLRSKYCMLDETSDVDLPMMGECPYDQGGYFIINGSEKVLIAQEKMS 197

Query: 161 PG-IHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDR--------- 208
              ++      + +   K  Y   I    + G            ++V++ +         
Sbjct: 198 HNHVY----VFKKTPPSKYSYVAEIRSCQETGSR------PTSTMYVKMLQNSNKGPIGI 247

Query: 209 -------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
                  ++ VP+     ALG  ++ +IL          Q  D     L  + ++   ++
Sbjct: 248 KATIPYIKQDVPIVVVFRALGFVADKDILEHICYDFSDQQMMDLMRPSLEESFVIQNQEI 307

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +   +            +   +   + L+++ +  + +              +      +
Sbjct: 308 ALDYLGKRGSTVGTREQRIKFAR--EVLQKEMLPHVSVAEYFETKKAYYFGYIVH---RL 362

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + A +       +   +  +    P+L          +   + +   +        I  
Sbjct: 363 LLAALERRPLDDRDHFANKRLDLAGPLLGTLFRQLFKKLTKDVRSHLQRCIDKGREFIPS 422

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                   T  +  S+    +  ++    + V                 + + +    + 
Sbjct: 423 QAIKSKTITSGLKYSLATGNWGAANTGARAGV----------------AQVLNRLTFAST 466

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID-SV 498
           +  L  L    G          R       ++KN   +  + +  + +  +  ++   + 
Sbjct: 467 LSHLRRLNTPIG----------REEGQACGLVKNLAMMAYISVGSASQPILEFLEEWSTE 516

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVE 557
             +++ ++  +++A   F     +    +  + L  +   RR   +  +  + R     E
Sbjct: 517 NLEEITDSSTILNATKIFVNGMWVGIHHQPDHLLKTLRVLRRCGDVSVEVSIVRDIREKE 576

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +R ++        P    +  +  L    +   ++++      P  K  D      V Y+
Sbjct: 577 LR-LYTDSGRCCRPLFVVDDKDYKLTIKKSHIRQLDSD-----PEYKWLDLITDGLVEYI 630

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EEE   IA   + L                     +        +  P  ++ I  S
Sbjct: 631 DTEEEETVMIAMTPADLI---------------PSTTEIVTHNYTHCEIHPSMILGICCS 675

Query: 678 LIPFLENDDSNRVLMGC 694
           +IPF +++ S R    C
Sbjct: 676 IIPFPDHNQSPRNTYQC 692



 Score = 48.1 bits (113), Expect = 0.010,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 18/82 (21%)

Query: 1301 CIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-------YESIVAGND---TFETGT 1343
            C+ ++GAA  L+E L  +SD       D+ G   +       YE      +     +   
Sbjct: 1885 CMISHGAAQFLKERLFDQSDSYRVHVCDICGLIAIANLKKNHYECR-RCKNKTQISQVKM 1943

Query: 1344 PESFNVLVKEMQALGLSIDLEN 1365
            P +  +L +E+ A+ ++  +  
Sbjct: 1944 PYAAKLLFQELMAMSIAPRMFT 1965


>gi|52694237|emb|CAG30648.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           cremoricolorata]
          Length = 315

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 183/315 (58%), Positives = 239/315 (75%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V+
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVS 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           +D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQV
Sbjct: 121 DDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQV 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R
Sbjct: 181 VSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 240

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R 
Sbjct: 241 GGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQRG 300

Query: 792 DIIADGPSTDLGDLA 806
           DI+ADGPSTD+G+  
Sbjct: 301 DIMADGPSTDMGERR 315


>gi|273067683|gb|ACZ97540.1| DNA-directed RNA polymerase beta chain [Raoultella terrigena]
          Length = 311

 Score =  308 bits (789), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 189/308 (61%), Positives = 239/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 3   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 63  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 123 IHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 183 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 242

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  + ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 243 TVQYVDASRIVIKVNDDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 302

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 303 LADGPSTD 310


>gi|14520830|ref|NP_126305.1| DNA-directed RNA polymerase subunit B [Pyrococcus abyssi GE5]
 gi|5458046|emb|CAB49536.1| rpoB DNA-directed RNA polymerase, subunit B (EC 2.7.7.6) [Pyrococcus
            abyssi GE5]
          Length = 1117

 Score =  308 bits (789), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 137/331 (41%), Gaps = 77/331 (23%)

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDMP+ + 
Sbjct: 846  DKVIITETGD-----GTKLVKVTVRDLRIPEIGDKFASRHGQKGVIGLIVPQEDMPWTES 900

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G+PSRM VGQ+ E   G      G+++       +    +      L  
Sbjct: 901  GIVPDLIVNPHGIPSRMTVGQLLEAIGGKVAALKGRRVDGTAFIGEPEEKLRKELEELGF 960

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                +DG                  G+ 
Sbjct: 961  KHTGREIM----------------------------YDGIT----------------GK- 975

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                      F+  + VG IY  +L+HMV+DK++ARS G   ++T+QP  G++  GG R 
Sbjct: 976  ---------RFEADIFVGVIYYQRLHHMVADKIHARSRGPVQVLTKQPTEGRAREGGLRF 1026

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG--------RTRVYESIVAGND-- 1337
            GEME   +  +GAA +L E L  +SD          G        R +VY   V G +  
Sbjct: 1027 GEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKRRHKVY-CPVCGEEER 1085

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
              +     +F +L+ E++A+ +   L  +  
Sbjct: 1086 ISKVEMSYAFKLLLDELKAMVIRPKLNLTER 1116



 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 151/975 (15%), Positives = 295/975 (30%), Gaps = 194/975 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+          + GLQ        I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------DRGLQEVVDEFGGIKPDIPDFEVKFGKIRVGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + +  ++  +++              + +G+LP+M
Sbjct: 77  PHGQRKPLYPMDARIRNLTYSAPLYLEMIPVIRGIEQEPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R   
Sbjct: 127 LKSKVCRLYGLSDDELRQLGEDPKDPGGYFIINGSERVIVSIEDIAPNRTLVEKDERQEK 186

Query: 175 SGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPV--TSFLMALGMDSE-EI 228
                Y  ++   +      + +E     I++V I    K PV     + ALG++ + +I
Sbjct: 187 -----YIAKVFSYRHGYRALVTVERKKDGILYVGIPNVPK-PVKFVYVMRALGLERDKDI 240

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +          Q         +  D         +L  I       ++ +         +
Sbjct: 241 VDAVGNDPEVQQ-----ILFDNLEDASDITTQQEALEYIGKLVAPGQAREYRLKRAEYVI 295

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIRDIPI 346
               +  +G++ +          ++  +  E+ +   D  D+     + +  +      +
Sbjct: 296 DNNLLPHIGVSPEDRIRKAYYLGMMALKVIELSLGKRDEDDKDHYANKRLRLAGDLLKDL 355

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALL-DIYRVMRPG---DVSTFSVAESMFNFLFFD 402
             V        I+  +     +  +  +  +I+R +R     DV T  +  ++    +  
Sbjct: 356 FRVAFSQLVKDIQYQMTKTYQRRGEKYVFGNIHRFIRNSIRPDVLTERIEHALATGAWPG 415

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
                   + R      L+         + +E      + L       G I   +     
Sbjct: 416 GRTGVSQLLDRTNYVSTLSHLRRVTSP-LDREQPHFEARDLHGTH--WGRICPTETPEGP 472

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
               V  +        + ++  ++ E      + S+    +   +P       +     +
Sbjct: 473 NCGLVKNLA------LMAQITTAVPEEEVKEYLMSLGIVPIEVRRPSPELWRVYLNGVII 526

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
             +E+    + RI   RR   +           V    V+        P    E     L
Sbjct: 527 GTIEDGKALVERIKKDRRSGKISDIINVAYYEDVREVYVNSDDGRVRRPLIIVENGKPKL 586

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                          I+    K  D      + YL A EEEN Y+A              
Sbjct: 587 TKEHVQ--------AIKEGRLKWSDLVRMGVIEYLDAEEEENAYVAM------------- 625

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                           E+   ++  P  ++ + ASLIP+ E++ + R   G  M +Q++ 
Sbjct: 626 ----------WPWEVTEEHTHLELMPAAILGLPASLIPYPEHNAAPRNTYGAGMAKQSLG 675

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L  A                                                +   +  Y
Sbjct: 676 LGWANFRI-----------------------------------------RVDTRGHLLHY 694

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q PLV                +    D   G+N +VA + +HGYN
Sbjct: 695 P--------------QIPLVNS----------RIMKAVGYEDRPAGQNFVVAVLAYHGYN 730

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNID 877
            ED+++I++  +   +  S     +E   +    G  ++     P V     E+  +++D
Sbjct: 731 MEDAIIINKASIERGLARSTFFRTYEAEEKKYLGGQTDKFEIPSPTVRGYRGEKYYRHLD 790

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           E G+I   ++V   D+L+G+ +P        EE+ L A+      + R+TS+ V     G
Sbjct: 791 EDGLIFPESKVEGKDVLIGRTSPPRFL----EERGLGAV---SLQERRETSVAVRPSERG 843

Query: 938 TVVDVRIFNRHGIDK 952
            V  V I       K
Sbjct: 844 VVDKVIITETGDGTK 858


>gi|105969657|gb|ABF81665.1| RNA polymerase beta subunit [Mycoplasma cricetuli]
          Length = 593

 Score =  308 bits (789), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 206/449 (45%), Positives = 303/449 (67%), Gaps = 16/449 (3%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  +F
Sbjct: 2   NPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN  GF++TPY KV  G +  + V YL+A EE     AQ++  +DE+       +  R
Sbjct: 62  AKVNELGFLQTPYFKVNQGVIDYSKVFYLTASEEIGYSFAQSSIHVDENNKIISPTLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I+     +DFI+ S KQ+ S+AA+ IPFLENDD+NR LMG NMQRQAVPLL+AEA
Sbjct: 122 RDYNYIIGTPLDVDFIEVSSKQIASVAAAAIPFLENDDANRALMGSNMQRQAVPLLQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P+V TGME+ +AK S   +  K AG V  VD  +I +++ +G  D        Y L  F+
Sbjct: 182 PYVATGMEADIAKYSSYNLTTKNAGEVVFVDGSKIYVKNEKGVTDK-------YSLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T + Q+P+VK+GD+V++ D++ DG S   G+++LG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTLIQQKPIVKIGDKVQKGDLLVDGSSFKDGEMSLGKNVLVGFTTWNGYNFEDAII 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVGAE 887
           I+ER+V +DV+TSIHIEE  +  R ++ G +++TR DIPNVS+  ++++DE GI+ VG+E
Sbjct: 295 INERLVKDDVYTSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKHSIRHLDEHGIVRVGSE 354

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V  GD+LVG+I+PKGE   + EEKLL AI  +K  +V+DTSL+V +G +GTV+ + + +R
Sbjct: 355 VVAGDVLVGRISPKGEDNPSQEEKLLMAILQQKPQNVKDTSLKVKNGHNGTVIHIEVLSR 414

Query: 948 -------HGIDKNERSISVEREQIELLAR 969
                   GIDK  +    ++ +I++  +
Sbjct: 415 DKGDVLEDGIDKIVKVSIAQKRKIKVGDK 443



 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 126/419 (30%), Positives = 191/419 (45%), Gaps = 78/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+ +G +V  GD+LV   + K +  M+  + +L         +  D  +     V   V 
Sbjct: 247  IVKIGDKVQKGDLLVDGSSFK-DGEMSLGKNVLVGFTTWNGYNFEDAIIINERLVKDDVY 305

Query: 940  --VDVRIFNRHGIDKNERSISVEREQIELLAR---DKDDEQVILDRNIYSRLMEILCGQN 994
              + +                + R+ I  +++      DE  I+         ++L G+ 
Sbjct: 306  TSIHIEEQTIQFRSSRAGEDQLTRDDIPNVSKHSIRHLDEHGIVRVGSEVVAGDVLVGRI 365

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
            +  G     +   L   ++ + P++           V+     +K  +  +   +E   +
Sbjct: 366  SPKGEDNPSQEEKLLMAILQQKPQN-----------VKDTSLKVKNGHNGTVIHIEVLSR 414

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K      GD +  G+ ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+D
Sbjct: 415  DK------GDVLEDGIDKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLED 468

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTP+DI+LNP GVPSRMN+GQ+ E HLG A   L  K  +   D    GDI         
Sbjct: 469  GTPLDIMLNPQGVPSRMNIGQVLELHLGMAAKKLNTKFVTPSFDGVKKGDIEDAL----- 523

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                        + + L         + 
Sbjct: 524  --------------------------------------------VEAGLDKTG-----KQ 534

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            I+ D +TG  FD+P++VG +YMLKLNHMV DK+++RS G YSL+TQQPLGGKS  GGQR
Sbjct: 535  IVIDPITGRKFDKPISVGIMYMLKLNHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQR 593


>gi|51035549|emb|CAH10910.1| RNA polymerase B subunit [Natronomonas pharaonis DSM 2160]
          Length = 435

 Score =  308 bits (789), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 86/269 (31%), Positives = 122/269 (45%), Gaps = 61/269 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D++LNP  +
Sbjct: 197  EDGSKLSKVKVRDERVPELGDKFASRHGQKGVVGHLAPQEDMPFTQDGVVPDLILNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMLGGKVGSLEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L       +G+ ++Y G+TGE  + 
Sbjct: 284  --------------------TP-FQGEDEDELRESLIDRGFKSNGKEVMYSGITGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            A  L+E L  +SD    R  +Y   V G 
Sbjct: 383  AMTLKERLLDESD----REDIY---VCGQ 404



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSIVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  +   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASIERALARSHFFRTYEGEERRYPGGQED-HFEIPDDEVRGARGEEAYSHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V   D+L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETHVGENDVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVKVRDERVPELGDK 218


>gi|313221111|emb|CBY31939.1| unnamed protein product [Oikopleura dioica]
          Length = 1110

 Score =  308 bits (788), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 84/315 (26%), Positives = 126/315 (40%), Gaps = 80/315 (25%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 R+VK+     R  + GDK + RHG KG+   I+P E+MPF + G   D+++NP G
Sbjct: 852  EDATWRMVKLSYRQTRRPELGDKFSSRHGQKGVTGLIVPQENMPFNEIGMCPDVIMNPHG 911

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG++ E                                                
Sbjct: 912  YPSRMTVGKLMECIGSK------------------------------------------- 928

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                      A          T  F G   E +   +     +  G+ +L  G TGEP +
Sbjct: 929  ----------AGALSGKFHYGT-AFGGNTTEEMAQTMLDYGFNYYGKDLLMSGETGEPLE 977

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G IY  KL HMV DK++AR+TG    +T+QPL G++  GG RLGEME   + AYG
Sbjct: 978  AYIFMGPIYYQKLRHMVMDKMHARATGKVHNLTRQPLEGRAKDGGLRLGEMERDALLAYG 1037

Query: 1307 AAYVLQEMLTIKSD----DVVG--------------RTRVYESIVAGNDTFETGTPESFN 1348
            A+ +L E     SD    ++ G              RT        G        P +  
Sbjct: 1038 ASNLLNERFFYSSDKYSVEICGNCGLHGYSGWCRVCRT--------GEHMASINMPYACK 1089

Query: 1349 VLVKEMQALGLSIDL 1363
            +L++E+ ++ +   +
Sbjct: 1090 LLLQELFSMNIMPRI 1104



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 124/954 (12%), Positives = 253/954 (26%), Gaps = 209/954 (21%)

Query: 16  FFGKNPEIID----IPDLIEV------QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
            +    E+ +    +P  +E          S+++ L           +GLQ   K+    
Sbjct: 27  SYESISEVQEKWKLVPAFLETRGLVKQHLDSFNYLLT----------QGLQKIIKANAR- 75

Query: 66  TAFSGAAMLEFVSYEFDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
           T         +     DPP              +C  RD+TY+ P+K+ +  +  +    
Sbjct: 76  TDVDQNFFWNYDHIYVDPPDVEYGMRSEAITPHECRLRDMTYSAPIKVDVTYVRDNQIRK 135

Query: 117 TGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRI 152
                          +G +P+M                           G FV+KG +++
Sbjct: 136 ARGLV----------IGRMPIMLRSARCVLANMSQEQFFKAKECPLDPGGYFVVKGAEKV 185

Query: 153 VVSQLH----R------SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           ++ Q      R        G+     K ++  +                      SK+ I
Sbjct: 186 LLMQEQAVSNRILVEKDKTGMFCAVVKSKSDTANTQTNL--------------IQSKNKI 231

Query: 203 HVRIDRRRK-VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
           +V+ ++ R+ V V     ALG++ + EI      +           F     ++    + 
Sbjct: 232 YVKQNKLREPVNVVVLFKALGIERDQEIAELIATEDSTLALLAPSLFECQQLEIFSQNQA 291

Query: 261 SSSLVD--IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
              L    +     ++   +  +   +++ + +  +        L    V         G
Sbjct: 292 MKYLEKTIMRIQNPIVSRSQMQSRFQVRTPRNREQEVHNWLVSTLL---VNVPYCYKRRG 348

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            I  +  D    K ++         I +L+ +   N        +  K + +   ++D+ 
Sbjct: 349 MIKADDRDYYGNKRIQLAGDL----ISLLFEEHFKNFNDELRRTIGKKLEKKTAQVVDVI 404

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
             M+          E+      ++          R KM+ +   +  + +  I    +  
Sbjct: 405 SSMKSLQNKITLAMEAAIQTGNWNLK--------RFKMDRKGITEILNRMSFISIILVGT 456

Query: 439 IIKILVDLRNGKGTIDDIDNLG-NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           + +I                 G    +    +  +      +  M           D   
Sbjct: 457 MTRIKGHFEKTMKVTGPRALQGSQWGMLCPSDTPEGAQCGLVKNMALLSHVTTFEDDKPI 516

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                 +  +   +        +            +          +    + RA    E
Sbjct: 517 HRLLINLGVEETSTLSGYDLHGANYLVFLNGALVGATRNPKSLTRTVQL--IRRAGRLPE 574

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR---KVCDGKVTNDV 614
              V+ +   R     +  G        + +         I        K  D      +
Sbjct: 575 FVSVYVSEEHRAVYLASDGGRLTRPCIIVENGRPKVTQKHINALLEGRVKFPDFVKNGLI 634

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   EE +  IA     + +                           ++  P  ++ +
Sbjct: 635 EYLDVNEENSALIAVYERDITKKH-----------------------THLEIEPFALLGV 671

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A LIP+ +++ S R    C M +QA+  +          M       S           
Sbjct: 672 CAGLIPYPDHNQSPRNTYQCAMGKQAMGTI---------AMNQRERIDS----------- 711

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                 N    QRPLVK           
Sbjct: 712 -----------------------------------CLYNLVYPQRPLVK----------T 726

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                     L  G+N  VA M + GY+ ED++++++  V       +     +   +  
Sbjct: 727 RTIELIGFEQLPAGQNATVAVMSYSGYDIEDALVLNKASVDRGYGRCLVYRNEKTQLQRR 786

Query: 855 KLGPE--EITRDIPNV------SEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
               E  E   D P +           + +D  GI+  G  V      + K  P
Sbjct: 787 GTLVETIEERIDGPALDAKSGEKIRADECLDMDGIVAPGERVKDRAPTMAKSQP 840


>gi|150402531|ref|YP_001329825.1| DNA-directed RNA polymerase subunit B' [Methanococcus maripaludis C7]
 gi|150033561|gb|ABR65674.1| RNA polymerase Rpb2 domain 6 [Methanococcus maripaludis C7]
          Length = 611

 Score =  308 bits (788), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 128/325 (39%), Gaps = 82/325 (25%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ KV V   R  + GDK A RHG KG++  I+P ED+P+ +DG   D+++NP  +P
Sbjct: 343  EGNRLGKVRVRDLRIPEFGDKFASRHGQKGVIGLIVPQEDLPYTEDGVIPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +GQ+ E   G       ++I   I   ++   +                       
Sbjct: 403  SRMTIGQVLEMIGGKVGSLECRRIDGTIFSGESEWKLREGLEKYGFKHHA---------- 452

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                               + A  D         G +G   +  
Sbjct: 453  -----------------------------------KEAMYD---------GKSGRKLECD 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA
Sbjct: 469  IFVGVAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAA 528

Query: 1309 YVLQEMLTIKSD---D----------------------VVGRTRVYESIVAGNDTFETGT 1343
             +L+E L  +SD   D                      V G +   E I           
Sbjct: 529  MLLKERLLDESDPHEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKI 585

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
              +F +L+ E++++G+   LE    
Sbjct: 586  AYAFKLLLDELKSMGIDPKLELKDR 610



 Score = 88.6 bits (218), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 74/420 (17%), Positives = 129/420 (30%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +    +  +   RR   L            E  DVH +  G   + P   +E     L  
Sbjct: 19  DPETLVKNLRDNRRSGKLSPS--TSISFNEESNDVHISTDGGRAVRPLVVAENGASKLTE 76

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            L          F E     V        + YL A EEEN  IA     + E+       
Sbjct: 77  ELLEKVDAQELTFHELVESGV--------IEYLDAEEEENARIAMYADEVTEEN------ 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              ++  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 123 -----------------THVEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMSKQSLGIP 165

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 166 MANIKW-----------------------------------------RMDTRGHLLHYP- 183

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 184 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 220

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +EE  +N+ + 
Sbjct: 221 DAFIINKASLERGLGRSTFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEEAYRNLGDD 280

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + +EV  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 281 GLIDLESEVRSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGIV 333


>gi|269912572|emb|CAY86066.1| RNA polymerase beta subunit [Gluconacetobacter hansenii ATCC 23769]
          Length = 313

 Score =  308 bits (788), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 146/316 (46%), Positives = 194/316 (61%), Gaps = 28/316 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EIL  FY ++ + + G 
Sbjct: 61  KRKLPVTTLLYALEGEESRAAREAKAAEGGDVDSMEIQGMSPDEILGYFYGQVEFIKSGK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W       D   G K+   LVD DTGE V +   KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDP-DAFRGQKLLEPLVDADTGEIVAQVDTKLTARMVRKIAET-TKDVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A D+VN +TGEI+ EAGD + E  LE +    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIAFDMVNPDTGEIFAEAGDELTETRLEALEADGVTKLVTLAIDATN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 IDKNTSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKEDIIAI 439
            PD VR +RKEDI+  
Sbjct: 298 VPDTVRVLRKEDILRT 313


>gi|45358925|ref|NP_988482.1| DNA-directed RNA polymerase subunit B' [Methanococcus maripaludis S2]
 gi|45047791|emb|CAF30918.1| Glycoside hydrolase, family 1:DNA-directed RNA polymerase, beta
            subunit:ATP/GTP-binding site motif A (P-loop)
            [Methanococcus maripaludis S2]
          Length = 611

 Score =  308 bits (788), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 96/492 (19%), Positives = 169/492 (34%), Gaps = 103/492 (20%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +   + +   +     F R      +R    + 
Sbjct: 197  GFDKRPAGQNFVVAVMSYEGYNMEDAFIINKASLERGLGRSSFF-RSYESFEKRYPGGQL 255

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +           L     +      K   V+           + 
Sbjct: 256  DKFEVPEKG-------VRGYRAEEAYRNLGDDGLIDLESSVKSGDVILGKTSPPRFLEE- 307

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             +  +Q +  +R+        E     L    + K               R+ KV V   
Sbjct: 308  QEITLQTKSQRRDTSVTIRHGEEGIVDLVILSETK------------EGNRLGKVRVRDL 355

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  I+P ED+P+ +DG   D+++NP  +PSRM +GQ+ E   
Sbjct: 356  RIPEFGDKFASRHGQKGVIGLIVPQEDLPYTEDGVIPDLIINPHAIPSRMTIGQVLEMIG 415

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G       ++I   I   ++   +                                    
Sbjct: 416  GKVGSLECRRIDGTIFSGESEWKLREGLEKYGFEHHA----------------------- 452

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                  + A  D         G +G   +  + VG  Y  KL+H
Sbjct: 453  ----------------------KEAMYD---------GKSGRKLECDIFVGVAYYQKLHH 481

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA +L+E L  +SD 
Sbjct: 482  LVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAAMLLKERLLDESDP 541

Query: 1321 --D----------------------VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
              D                      V G +   E I             +F +L+ E+++
Sbjct: 542  HEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKIAYAFKLLLDELKS 598

Query: 1357 LGLSIDLENSRT 1368
            +G+   LE    
Sbjct: 599  MGIDPKLELKDR 610



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 70/420 (16%), Positives = 129/420 (30%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +    +  +   RR   L            E  DVH +  G   + P    E     +  
Sbjct: 19  DPETLVKNLRENRRSGKLSPS--TSISFNEESNDVHISTDGGRAVRPLIVVENGASKVTE 76

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +           +E+      D   +  + YL A EEEN  IA     + E+       
Sbjct: 77  EILE--------KMESKELTFLDLVNSGIIEYLDAEEEENARIAMYEDEITEEN------ 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              ++  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 123 -----------------THVEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMSKQSLGIP 165

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 166 MANIKW-----------------------------------------RMDTRGHLLHYP- 183

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 184 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 220

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +EE  +N+ + 
Sbjct: 221 DAFIINKASLERGLGRSSFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEEAYRNLGDD 280

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + + V  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 281 GLIDLESSVKSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGIV 333


>gi|273067680|gb|ACZ97539.1| DNA-directed RNA polymerase beta chain [Raoultella terrigena]
          Length = 309

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 189/308 (61%), Positives = 239/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 1   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 60

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 61  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 120

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 121 IHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 181 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 240

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  + ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 241 TVQYVDASRIVIKVNDDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 300

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 301 LADGPSTD 308


>gi|299013527|gb|ADJ00327.1| RNA polymerase subunit B [Mycobacterium monacense]
          Length = 237

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 139/236 (58%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +        ++
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAAGTPDWAEKLPE------EL 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                S +                       V+TPVFDGA E  ++ +L            
Sbjct: 144  YSAPSDSI----------------------VATPVFDGARENELSGLLASTLPNRDGDVM 181

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            ++E G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 182  VNEDGKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 237


>gi|53789473|emb|CAH10911.1| RNA polymerase B subunit [Natronorubrum sp. Tenzan-10]
          Length = 435

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 85/261 (32%), Positives = 120/261 (45%), Gaps = 58/261 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQDGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  +   L  A  + +G+ ++Y G++GE  + 
Sbjct: 284  --------------------TP-FLGEDESELRGGLEDAGFNSAGKEVMYSGISGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD----DVVG 1324
            A  L+E L  +SD     V G
Sbjct: 383  AMTLKERLLDESDREFIHVCG 403



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETRVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|301599271|emb|CBW31645.1| RNA polymerase subunit B [Haloferax elongans]
          Length = 609

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 125/599 (20%), Positives = 206/599 (34%), Gaps = 102/599 (17%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V R  +       +  D     ++ V             + I  +++       I   
Sbjct: 94   DMVERGLV-------EFIDAEEEEDIYVGVDEDELTEDHTHLEIDPQLIFGIGAGMIPYP 146

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E     R T      + +    +     +   +     +        +        G   
Sbjct: 147  EHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDE 203

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
                +  + A+   +  ++ D  +     V    +    F R    +  R    + ++ E
Sbjct: 204  RPAAQNFVVAVMSYEGFNIEDALVMNKGSVE-RALSRSHFFRTYEGEERRYPGGQEDRFE 262

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            + ++D       +           L     V+      +++VL           +    A
Sbjct: 263  IPSQD-------VRGARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMA 315

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                + +R         E+         + +               ++ KV V  +R  +
Sbjct: 316  GLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPE 363

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG+V  + P EDMPF  DG   D+++NP  +PSRM V        G   
Sbjct: 364  LGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLIINPHALPSRMTV--------GHVL 415

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              LG K+ +L                                                  
Sbjct: 416  EMLGGKVGALEGRRVDGT------------------------------------------ 433

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                 F G  E+ + S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+
Sbjct: 434  ----AFQGESEDELRSALEERGYMSSGKEVMYSGVTGEKVEAEIFVGIIFYHKLYHMVSN 489

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----- 1320
            K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD     
Sbjct: 490  KLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKESVY 549

Query: 1321 ---D-----VVGR--TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               D     V  R   R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 550  ISADTGMVAVEDRDQRRIYD-PVTGDEDNIHEIDISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 57/372 (15%), Positives = 117/372 (31%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D       +   R  G+   +    +               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPEQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+     I          
Sbjct: 64  RRPLIVVEDGEPLLGDEHVEALENNELDFDDMVERGLVEFIDAEEEED-IYVGVDEDELT 122

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 123 EDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 LHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALSRSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 43.9 bits (102), Expect = 0.21,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 59/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPEQLAAQIREARRRGDVSQMVNVSVKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L               +E       D      V ++ A EEE+ Y+      L 
Sbjct: 71  EDGEPLLGDEHVE--------ALENNELDFDDMVERGLVEFIDAEEEEDIYVGVDEDELT 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|269912570|emb|CAY86065.1| RNA polymerase beta subunit [Gluconacetobacter europaeus LMG 18890]
          Length = 306

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 145/309 (46%), Positives = 193/309 (62%), Gaps = 28/309 (9%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIRGMDPDEILSYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DSFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEI+ EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNEHTGEIFAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIR 432
            PD VR +R
Sbjct: 298 VPDTVRVLR 306


>gi|291196444|emb|CBG27579.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas otitidis]
          Length = 305

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 235/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V   +VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNQYGFLESPYRVVKGTQVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLNEQGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R+DI+AD
Sbjct: 241 SVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDKVSRSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|38677882|emb|CAE30281.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 170

 Score =  308 bits (788), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 70/192 (36%), Positives = 118/192 (61%), Gaps = 22/192 (11%)

Query: 12  RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G 
Sbjct: 1   RQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGN 50

Query: 72  AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
             LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++
Sbjct: 51  LSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVF 101

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W
Sbjct: 102 MGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAW 158

Query: 192 MDIEFDSKDIIH 203
           ++ E D+KD+++
Sbjct: 159 LEYETDAKDVVY 170


>gi|242392238|dbj|BAH80356.1| RNA polymerase subunit B' [Haloferax mediterranei]
          Length = 609

 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 126/584 (21%), Positives = 203/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDEINEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  DG   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G DE  + 
Sbjct: 431  DGT----------------------------------------------AFQGEDEHELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKESVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 120/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    I               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSIKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +    +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEGGEPLLGDEHVEALENNDLDFDDLVERGLVEFIDAEEEEDIYVAVDEDEINE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 46.6 bits (109), Expect = 0.028,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSIKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG    L          N   F +   R          V ++ A EEE+ Y+A     ++
Sbjct: 71  EGGEPLLGDEHVEALENNDLDFDDLVER--------GLVEFIDAEEEEDIYVAVDEDEIN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|315230005|ref|YP_004070441.1| DNA-directed RNA polymerase subunit B [Thermococcus barophilus MP]
 gi|315183033|gb|ADT83218.1| DNA-directed RNA polymerase subunit B [Thermococcus barophilus MP]
          Length = 1118

 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 85/320 (26%), Positives = 132/320 (41%), Gaps = 77/320 (24%)

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDMP+ + 
Sbjct: 847  DKVIITETGD-----GTKLVKVTVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPWTES 901

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G+PSRM VGQ+ E   G      G++I       +    +      L  
Sbjct: 902  GIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRIDGTAFIGEPEEKLRKELEELGF 961

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                +DG                     
Sbjct: 962  KHSGREIM----------------------------YDGIT------------------- 974

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                   G   +  + +G IY  +L+HMV+DK++ARS G   ++T+QP  G++  GG R 
Sbjct: 975  -------GRRLEADIFIGVIYYQRLHHMVADKMHARSRGPVQVLTKQPTEGRAREGGLRF 1027

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG--------RTRVYESIVAG--ND 1337
            GEME   +  +GAA +L E L  +SD       +  G        R +VY   V G    
Sbjct: 1028 GEMERDVLIGHGAAMLLVERLLEESDKTEVWVCETCGHLALEDKRRGQVY-CPVCGETEK 1086

Query: 1338 TFETGTPESFNVLVKEMQAL 1357
              +     +F +L+ E++A+
Sbjct: 1087 ISKVEMSYAFKLLLDELKAM 1106



 Score =  208 bits (529), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 141/976 (14%), Positives = 289/976 (29%), Gaps = 195/976 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+          + G+Q        I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------DHGMQEVINEFGGIKPDIPNFEVKFGKIRLGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTYA P+ + +  +V  +++              + +G+LP+M
Sbjct: 77  AQGQRKPLYPMDARIRNLTYAAPIYLEMIPVVNGIEQEPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R   
Sbjct: 127 LKSKACRLYGKSEEELIKLGEDPKDPGGYFIINGSERVIVSIEDLAPNRTLVEKDERQDK 186

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTS----FLMALGMDSE-EIL 229
                ++ R    +   + +E     +++V I     VP        + ALG++S+ EI+
Sbjct: 187 VVAKCFSYR-HGYR-ALIAVERRKDGLLYVSI---PNVPGVVKFVYVMRALGLESDKEIV 241

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
                     Q            +     +     +D    + +    ++      +S+ 
Sbjct: 242 DAISDDPRIQQ------VLFDNLEDASDIQTQEEALDYIGKKALPGQPREYRLRRAESII 295

Query: 290 EKG-VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIRD 343
           +   +  +G+  +          ++  +  E+ +      D+       L          
Sbjct: 296 DNNLLPHMGVRPEDRIKKAYYLGMMALKVLELSLGLRGEDDKDHYANKRLRLAGDLLRDL 355

Query: 344 IPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             + +   V +  Y   +      +    ++    +   +RP DV T  +  ++    + 
Sbjct: 356 FRVAFGQLVKDMQYQLTKTYQRKGEKYVFENVQRFVRNSVRP-DVLTERIEHALATGAWP 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                    + R      L+         + ++      + L       G I   +    
Sbjct: 415 GGRTGVSQLLDRTNYMSTLSHLRRVTSP-LSRDQPHFEARDLHGTH--WGRICPTETPEG 471

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                V  +        + ++  +I E      +  +    +   +P       +     
Sbjct: 472 PNCGLVKNLA------LMAQITTAIPEEEVLKYLRKLGIVSIEERRPNPHVWRVYLNGVL 525

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +  +E+ +  ++RI   RR   +           V    ++        P    E     
Sbjct: 526 IGTVEDGIALVNRIKADRRAGKISDVINVAYYDDVREVYINSDDGRVRRPLIVVENGVPK 585

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L        +     +         D      + YL A EEEN Y+A             
Sbjct: 586 LTKEHVEGIKNGTLTW--------SDLIKMGVIEYLDAEEEENAYVAT------------ 625

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            ++   ++  P  ++ I ASL+P+ E++ + R   G  M +Q++
Sbjct: 626 -----------WPWEVTKEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGMAKQSL 674

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            L  A                                                +   +  
Sbjct: 675 GLGWANFRI-----------------------------------------RVDTRGHLLH 693

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q PLV                +    +   G+N +VA + + GY
Sbjct: 694 YP--------------QIPLVNS----------RIMKAVGFEERPAGQNFVVAVLSYQGY 729

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNI 876
           N ED+++I++  +   +  S     +E   +    G  ++     P V     E+  +++
Sbjct: 730 NMEDAIVINKASIERGLARSTFFRTYEAEEKKYLGGQTDKFEIPDPTVRGYRGEKYYRHL 789

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII   ++V+  D+LVG+ +P               + G    + R+TS+ V     
Sbjct: 790 DEDGIIFPESKVSGKDVLVGRTSPPRFLEEQSG------LGGIILQERRETSIAVRPSEK 843

Query: 937 GTVVDVRIFNRHGIDK 952
           G V  V I       K
Sbjct: 844 GVVDKVIITETGDGTK 859


>gi|253746328|gb|EET01680.1| DNA-directed RNA polymerase subunit B [Giardia intestinalis ATCC
            50581]
          Length = 1235

 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 168/1018 (16%), Positives = 313/1018 (30%), Gaps = 205/1018 (20%)

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG--RVKMNMRLNLDTPDDV 428
            +  L D ++       +   +    F  +    D+YDL+ +    +     L ++ P + 
Sbjct: 292  EAMLRDFHKYRIFSHKACKQLLGGKFRMILSLLDRYDLTDMDCCDLLFERNLLINIPKED 351

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               +   +  + +  + L  G    D+ D L ++   + G   K +    L++  R I  
Sbjct: 352  TRAKFNMMCLMARKCLLLFGGFIKSDNPDLLSSQEAITPGAFFKAEIASTLIKTMRLISR 411

Query: 489  RISSV--DIDSVMPQDLINAKPVVSAVCEFFCS----------------------SQLSQ 524
              +S        +    I+       +     S                      S LS 
Sbjct: 412  NATSTGAIGSYELSNSWISHYIASPKLWRSLTSGLRSLTGPGVMRAYRGHDYSNMSGLSV 471

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            L + +N +  + H R    + +G          +R ++P  YG  C   T +G   G+++
Sbjct: 472  LADRINYVRFLAHFR---CINRGNAFAGHKITSIRKLYPESYGFQCAVHTPDGAPCGILT 528

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
             L   A V +                       +A +  N ++  +   L    S    L
Sbjct: 529  HLCYKAAVLSSTP--------------------TADQTANLFMLLSQFGLSPSLSEVYTL 568

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-----FLENDDSNRVLMGCNMQRQ 699
                       +   +      +  +   I A++ P     F+E D+ +R+  G  M   
Sbjct: 569  AVVLNGTVLGFIDTNEHAAKLVACIRAAKIQAAIFPSTEVVFIERDNKDRLFPGVYMNTS 628

Query: 700  AVPLLKAEAPFVGTGMESV-----------------------VAKSSGAAIVAKRAGIVE 736
                 +     +    E +                         + +  ++++    +V 
Sbjct: 629  MGRFYRPVHSLISNSQEYITPLEQIFLQIAIYGDDVRPGVTTHQEITPTSLLSILGLLVP 688

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D  +      E  +   T  +       ++   +      QRP+V+            
Sbjct: 689  FSDHNQSPRNMYECQMLKQTMAIPCRNLSYRYDTKSYLLTTPQRPIVRNAIIHDLG---- 744

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                        G N++VA   +  Y+ ED+ LI++  +   +F        ++  R+ K
Sbjct: 745  -----GFDTHPTGTNLVVAVSAYTSYDMEDAALINKASLERGLFHGTVYSVHDIDCRNDK 799

Query: 856  LG-------------PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +                     I ++ E     +DE G+  VG+ ++ G +      P  
Sbjct: 800  MMSFVLTVAEVFPHLRRSPDYIITHMDENYDTELDEDGLPPVGSYLSHGSVFYQTYDPPK 859

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            +                              G    V+ +      G             
Sbjct: 860  QR-------------------YTTHLYHHEPGFVEKVIVIHKTTAKGEY----------- 889

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
                  +D   E    D    +R        +A SG +                  SQ  
Sbjct: 890  ---WTDKDAPVEMRE-DPQPRTRSSSTSNFNDAASGDEI----------------DSQSA 929

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
              +  DE  Q      +      +     +   ++EK           ++ V++ +   R
Sbjct: 930  DSSALDEDQQTATSRSRANKAEQRPTRRSQAYARVEKASLC------FIQRVRIVIRHDR 983

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
                GDK+A RHG KGI+       DMPF   G   D+++NP   PSRM VG + E+   
Sbjct: 984  TPVVGDKVASRHGQKGIMGIRWRQTDMPFTSSGIVPDLIINPHAFPSRMTVGMLIESLAS 1043

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
               V     + S    +                                           
Sbjct: 1044 KIGVHYADFVDSSPFQWSDERR-------------------------------------- 1065

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                +  VF          +L+    +  G  ++Y  +TG+P    + +G +Y  +L HM
Sbjct: 1066 ----AVDVFG-------EQLLKTGQFNRYGSEVMYSAMTGDPMPADIFIGVVYYQRLRHM 1114

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            V+DK   R+ G    VT+QP+ G+   GG R GEME   + A+GA   L+  L  +SD
Sbjct: 1115 VTDKYQVRAEGPSDKVTKQPIKGRKRGGGLRFGEMERDALLAHGAMASLRGRLCTESD 1172



 Score = 42.0 bits (97), Expect = 0.74,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 38/147 (25%), Gaps = 48/147 (32%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---AFSGAAMLEFVSYEFDPPKFDVD 89
              S++ F+                  K    IT     S A  +E  +   + P F   
Sbjct: 57  HVNSFNDFIDSLNTT----------ILKHAPSITINLNTSKAIKVELANLSLNAPPFTPA 106

Query: 90  DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-------- 141
                   Y   L +T+++    +            K   I  GD+P+M           
Sbjct: 107 FARETHANYCGTLNVTIKVSDGPMS-----------KTAVINAGDVPIMVGSKLCLLYGK 155

Query: 142 ----------------GTFVIKGIQRI 152
                           G F+  G  ++
Sbjct: 156 TREERIRLREDERDAGGYFISNGQDKV 182


>gi|269912576|emb|CAY86068.1| RNA polymerase beta subunit [Gluconacetobacter hansenii]
          Length = 312

 Score =  307 bits (787), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 146/314 (46%), Positives = 194/314 (61%), Gaps = 28/314 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EIL  FY ++ + + G 
Sbjct: 61  KRKLPVTTLLYALEGEESRAAREAKAAEGGDVDSMEIQGMSPDEILGYFYGQVEFIKSGK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W       D   G K+   LVD DTGE V +   KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDP-DAFRGQKLLEPLVDADTGEIVAQVDTKLTARMVRKIAET-TKDVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A D+VN +TGEI+ EAGD + E  LE +    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIAFDMVNPDTGEIFAEAGDELTETRLEALEADGVTKLVTLAIDATN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 IDKNTSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKEDII 437
            PD VR +RKEDI+
Sbjct: 298 VPDTVRVLRKEDIL 311


>gi|329765755|ref|ZP_08257324.1| DNA-directed RNA polymerase subunit beta [Candidatus Nitrosoarchaeum
            limnia SFB1]
 gi|329137821|gb|EGG42088.1| DNA-directed RNA polymerase subunit beta [Candidatus Nitrosoarchaeum
            limnia SFB1]
          Length = 1115

 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 81/320 (25%), Positives = 126/320 (39%), Gaps = 74/320 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ K+ V   R  + GDK A RHG KG++  +   ED+P+  DG   D+++NP  
Sbjct: 851  SNEGGKMYKIRVRDMRIPEIGDKFASRHGQKGVLGILAKAEDLPYTADGISPDVLINPHA 910

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG   E+  G A    G +        +   ++ P+                  
Sbjct: 911  FPSRMTVGMFMESICGKAAALRGSQFDGSAFVGEKMEEVKPVMDAAGFKYSGKETM---- 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                         G        TG+ F 
Sbjct: 967  -------------------------------------------YDG-------RTGKSFP 976

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+ AYG
Sbjct: 977  VEVFIGVVYYQKLHHMVADKIHARARGQVQMLTKQPTEGRARGGGLRFGEMERDCLIAYG 1036

Query: 1307 AAYVLQEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFN 1348
            A+ +L++ L  +SD                DV  R   Y   V G+           +F 
Sbjct: 1037 ASMILKDRLLDESDKSDIFVCERCGLVAYHDVKQRK--YVCRVCGDKAKVSSVSVAYAFK 1094

Query: 1349 VLVKEMQALGLSIDLENSRT 1368
            +L++EMQ+L ++  L     
Sbjct: 1095 LLLQEMQSLNVAPRLLIKEK 1114



 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 122/639 (19%), Positives = 232/639 (36%), Gaps = 72/639 (11%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             KDA++ I + + PG +  F +  +     +       L  +G+   N +         
Sbjct: 264 TAKDAIVYISKRIAPGMLEEFQIKRAETLLDWGL-----LPHLGKHPENRKE-------- 310

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              + + +      L++L+ G  + DD D+ GN+ ++  G+ML + +R     + R +K 
Sbjct: 311 ---KAQFLGEAACKLLELKLGWISPDDKDHYGNKVIKFAGQMLADLFRTAFRNLVRDMKY 367

Query: 489 RISSVDIDSVMP---------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           ++        +                   ++          ++QL +  N LS I+H R
Sbjct: 368 QLERSGQKRGINAVSAAIRPGIITDKLNNAIATGNWGRGRVGVTQLLDRTNYLSTISHLR 427

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+    Q  ++R +   E RD+H TH+GRICP+ET EG N GLV +L     ++     E
Sbjct: 428 RI----QSPLSRTQPNFEARDLHATHFGRICPSETPEGSNCGLVKNLALSGIISVNVPSE 483

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-----------ELVFCR 648
                V        + +  A E+  +  A+        G + +                 
Sbjct: 484 ---EIVEKLYDLGTIHFFDAKEDVKKDGARIFVDGRLIGYYKDGAQLAESLRDLRRNSKI 540

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                I   + +I+          +    L P +   D+  +L    + + +  LL    
Sbjct: 541 HPHVGISFHKSEIEGSTKRLYVNCNAGRVLRPLIIIKDNKPLLTQDLLDKISKKLLSWTD 600

Query: 709 PFVGTGMESVVAKSSGAAIVA-------KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
                 +E + A       +        K   +     AI     S+    + + S  + 
Sbjct: 601 LLRMGVLEMIDANEEENCYITLDEKDTKKHTHLEVFPPAILGAGASIIPYPEHNQSPRNT 660

Query: 762 YRLMKFQRS--NQNTCVNQRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFM 816
           Y     ++S       +N    V+    +     I +  +     L D   G+N +VA +
Sbjct: 661 YESAMAKQSLGFSTPMMNTSTYVRQHLMLYPQTPIVNTKAMKLLGLEDRPAGQNCVVAVL 720

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP--------NV 868
           P+ GYN ED++++S   V   +  +     ++  A+    G  +   +IP          
Sbjct: 721 PFDGYNIEDAIVLSRASVDRGLGRTFFFRIYDAEAKQYPGGMRDTF-EIPNAEDNIRGYK 779

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            E+  + ++E G++   + V+ GDIL+GK +P        E +             RDTS
Sbjct: 780 GEKAYRLLEEDGVVASESPVHGGDILIGKTSPPRFMEEYREFE-------SSGPYRRDTS 832

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
           + V    +  VVD  +  +         I V   +I  +
Sbjct: 833 IGVRPSET-GVVDTVVMTQSNEGGKMYKIRVRDMRIPEI 870



 Score =  130 bits (328), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 98/733 (13%), Positives = 214/733 (29%), Gaps = 139/733 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA--MLEFVSYEFDPPK----- 85
              S+D FL            GLQ+    V  I   +      ++    +   P+     
Sbjct: 25  HLNSFDEFL----------ERGLQSIINEVGQIEIENAEYPYKIQLGKVKLQQPRMMELD 74

Query: 86  -----FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-- 138
                    +   R+++Y+ P  + +   V +  +   ++         +++GD+P+M  
Sbjct: 75  GSITHITPAEARLRNVSYSAP--VMMEASVVEDGKILESRF--------VHIGDVPVMAK 124

Query: 139 ----------------------TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F+I G +R++V     S   +      R S+ G
Sbjct: 125 SNACILHNFSTQKLIEHGEDPNDPGGYFIINGSERVIVGLEDLS---YNKIIVDRESVGG 181

Query: 177 KLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSE-EI-- 228
             ++  ++       +   +++   +  +I  RI      +PV +   ALG++S+ EI  
Sbjct: 182 NTVFKAKVYSSIVGYR-AKLELVMKNDGLIVARIPGSPVDIPVVTLTRALGLESDREIAA 240

Query: 229 ----LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKLT 281
               +     ++  S            A + +  +++        I   E +++ G  L 
Sbjct: 241 AVSLVDEIQNELEGSFEKAGDVPTAKDAIVYISKRIAPGMLEEFQIKRAETLLDWG--LL 298

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             L K  + +  K   +          A  ++  + G I  +  D    K ++       
Sbjct: 299 PHLGKHPENRKEKAQFLGE-------AACKLLELKLGWISPDDKDHYGNKVIKFAGQMLA 351

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL---DIYRVMRPGDVSTFSVAESMFNF 398
                 + + V +  Y        +  +   A +    I   +     +       +   
Sbjct: 352 DLFRTAFRNLVRDMKYQLERSGQKRGINAVSAAIRPGIITDKLNNAIATGNWGRGRVGVT 411

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPD-DVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              D   Y  +     ++   L+   P+ + R +       I        +  G + ++ 
Sbjct: 412 QLLDRTNYLSTISHLRRIQSPLSRTQPNFEARDLHATHFGRICPSETPEGSNCGLVKNLA 471

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
             G   V    E +  +               I   D    + +D          +  + 
Sbjct: 472 LSGIISVNVPSEEIVEKLYD---------LGTIHFFDAKEDVKKDGARIFVDGRLIGYYK 522

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQG---GVARARAGVEMRDVHPTHYGRICPAET 574
             +QL            +   RR S +         ++      + ++       C A  
Sbjct: 523 DGAQL---------AESLRDLRRNSKIHPHVGISFHKSEIEGSTKRLYVN-----CNAGR 568

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                I +  +     + +    I        D      +  + A EEEN YI       
Sbjct: 569 VLRPLIIIKDNKPLLTQ-DLLDKISKKLLSWTDLLRMGVLEMIDANEEENCYIT------ 621

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                   +K   ++  P  ++   AS+IP+ E++ S R     
Sbjct: 622 ------------------LDEKDTKKHTHLEVFPPAILGAGASIIPYPEHNQSPRNTYES 663

Query: 695 NMQRQAVPLLKAE 707
            M +Q++      
Sbjct: 664 AMAKQSLGFSTPM 676


>gi|134045261|ref|YP_001096747.1| DNA-directed RNA polymerase subunit B' [Methanococcus maripaludis C5]
 gi|132662886|gb|ABO34532.1| DNA-directed RNA polymerase, subunit B' [Methanococcus maripaludis
            C5]
          Length = 611

 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 128/325 (39%), Gaps = 82/325 (25%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ KV V   R  + GDK A RHG KG++  I+P ED+P+ +DG   D+++NP  +P
Sbjct: 343  EGNRLGKVRVRDLRIPEFGDKFASRHGQKGVIGLIVPQEDLPYTEDGVIPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +GQ+ E   G       ++I   I   ++   +                       
Sbjct: 403  SRMTIGQVLEMIGGKVGSLECRRIDGTIFSGESEWKLREGLEKYGFEHHA---------- 452

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                               + A  D         G +G   +  
Sbjct: 453  -----------------------------------KEAMYD---------GKSGRKLECD 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA
Sbjct: 469  IFVGVAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAA 528

Query: 1309 YVLQEMLTIKSD---D----------------------VVGRTRVYESIVAGNDTFETGT 1343
             +L+E L  +SD   D                      V G +   E I           
Sbjct: 529  MLLKERLLDESDPHEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKI 585

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
              +F +L+ E++++G+   LE    
Sbjct: 586  AYAFKLLLDELKSMGIDPKLELKDR 610



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 73/420 (17%), Positives = 130/420 (30%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +    +  +   RR   L            E  DVH +  G   + P    E     L  
Sbjct: 19  DPETLVKNLRENRRSGKLSPS--TSISFNEESNDVHISTDGGRAVRPLVVVENGASKLTQ 76

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            L            E  + ++ D  V   + YL A EEEN  IA     + E+       
Sbjct: 77  ELLEKVDAQ-----ELTFHELVDSGV---IEYLDAEEEENARIAMYEDEITEEN------ 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              I+  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 123 -----------------THIEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMSKQSLGIP 165

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 166 MANIKW-----------------------------------------RMDTRGHLLHYP- 183

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 184 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 220

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +E+  +N+ + 
Sbjct: 221 DAFIINKASLERGLGRSTFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEDAYRNLGDD 280

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + + V  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 281 GLIDLESNVRSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGIV 333


>gi|269912586|emb|CAY86073.1| RNA polymerase beta subunit [Gluconacetobacter kombuchae]
          Length = 310

 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 145/312 (46%), Positives = 192/312 (61%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EIL  FY ++ + + G 
Sbjct: 61  KRKLPVTTLLYALEGEESRAAREAKAAEGGDVDSMEIQGMSPDEILGYFYGQVEFIKSGK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W       D   G K+   LVD DTGE V +   KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDP-DAFRGQKLLEPLVDADTGEIVAQVDTKLTARMVRKIAET-TKDVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A D+VN +TGEI+ EAGD + E  LE +    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIAFDMVNPDTGEIFAEAGDELTETRLEALEADGVTKLVTLAIDATN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 IDKNTSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKED 435
            PD VR +RKED
Sbjct: 298 VPDTVRVLRKED 309


>gi|111054609|gb|ABH04362.1| RNA polymerase beta subunit [Providencia rettgeri]
          Length = 312

 Score =  307 bits (787), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 192/311 (61%), Positives = 239/311 (76%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQAN+ L +DGSF EEL+ CR  GE  L  RE+++++D S +QVVS+ ASLIPFLE+
Sbjct: 122 FIIAQANTVLGDDGSFVEELITCRNKGESSLFSREQVEYMDVSTQQVVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGGSVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V +G+ V R D++ADGPSTDLG+
Sbjct: 242 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLGEPVERGDVLADGPSTDLGE 301

Query: 805 LALGRNMLVAF 815
           LALG+NM VAF
Sbjct: 302 LALGQNMRVAF 312


>gi|213876743|gb|ACJ54368.1| RNA polymerase subunit B [Mycobacterium chelonae]
          Length = 243

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 136/236 (57%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 145  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 187

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 188  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 243



 Score = 44.7 bits (104), Expect = 0.13,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 48


>gi|126722437|dbj|BAF48632.1| DNA-dependent RNA polymerase subunit B' [Natrialba chahannaoensis]
          Length = 429

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 84/253 (33%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG++  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE A+   L  A  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESALRDGLEEAGFDSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVKA----------QTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  +   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASIERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    EV+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETEVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             + +       K  +    +    EL  +
Sbjct: 189 DTITLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|125808948|ref|XP_001360931.1| GA21006 [Drosophila pseudoobscura pseudoobscura]
 gi|54636103|gb|EAL25506.1| GA21006 [Drosophila pseudoobscura pseudoobscura]
          Length = 1137

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 97/555 (17%), Positives = 182/555 (32%), Gaps = 108/555 (19%)

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +   +V            ++       +G                +      ++      
Sbjct: 674  VCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLMYNLVYP 722

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                +    I       +   +    A+      D+ D  +   + +        ++   
Sbjct: 723  QAPMVKTKTIELTNFDKLPAGQNATVAVMSFSGYDIEDALILNKASIDRGYGRCLVYKNS 782

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +R  +   ++I    +D    +VI   ++               G +   K  ++
Sbjct: 783  KCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLD------TDGIVAPGEQILNKQIMI 835

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + ++ +    +     + Q       +              +    + +E++    +   
Sbjct: 836  NKEMPAVTSLNPLEGQSTQVPYTAVPIS------------YKGPEPSYVERVMVSANSEE 883

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K+ +   R  + GDK + RHG KG+   I+  EDMP+   G   D+++NP G P
Sbjct: 884  DF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPYNDSGICPDMIMNPHGFP 941

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM V        G     LG K   L   +                             
Sbjct: 942  SRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F G+    I + L     +  G+   Y G+TG P    
Sbjct: 969  ---------------------AFGGSKVGDIQAELERHGFNYMGKDFFYSGITGAPLQAY 1007

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+
Sbjct: 1008 IYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGAS 1067

Query: 1309 YVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPESFNVLVK 1352
             ++ E L I SD    DV    GR   Y          +        +   P +  +L +
Sbjct: 1068 MLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----HVSKISMPYACKLLFQ 1121

Query: 1353 EMQALGLSIDLENSR 1367
            E+ ++ +   +    
Sbjct: 1122 ELTSMNVVPKMILED 1136



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 128/1008 (12%), Positives = 282/1008 (27%), Gaps = 196/1008 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVRQHIDSFNHFINVDIKKIVRAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GYNITKATTPHECRLRDTTYSSPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGRYYLKHNSMTDDIPIVVIFKALGIVSDQE 257

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG----- 283
           +         SQ         +    +   + +   +      +  +S    T       
Sbjct: 258 IMAHIGIDTKSQNRFGASLLEAFNLKVFTQQRALDYMGSKLVVKRFQSATTKTPAEEARD 317

Query: 284 --LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             L   L    V         +    +   +++ E  +   +  D    K LE       
Sbjct: 318 LLLTTILAHVPVDNFNFQMKAIYVSMMVRRVMSAELDKTLFDDRDYYGNKRLELAGSLIS 377

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L+         I +  +       K A  D+ + MR   ++  +  ES  +   +
Sbjct: 378 LMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAISSGNW 431

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
              ++ +   G  ++  RL+  +   +            K+                   
Sbjct: 432 TIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ---------PSQ 482

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             +    +  + +    +  +           +   ++       + +         +  
Sbjct: 483 WGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMILAFNAGVEDIREVSGNPINNPN 542

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +  +  + N L    +  +        + R         VH ++  R     T  G    
Sbjct: 543 VFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSFVSVHTSYTQRCIYIHTDGGRLCR 601

Query: 582 LVSSLTSFARVNAYGF---IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               +              +E   RK  D  +   + YL   EE + +IA  N    E+G
Sbjct: 602 PYIIVEKRRPRVKQFHLDELERGVRKFDDFLLDGLIEYLDVNEENDSFIA-WNEEHIEEG 660

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           +                        ++  P  ++ + A L+P+  ++ S R    C M +
Sbjct: 661 T----------------------THLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCAMGK 698

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ ++         G        S                                   
Sbjct: 699 QAMGMI---------GYNQKNRIDS----------------------------------- 714

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                         N    Q P+VK                T+   L  G+N  VA M +
Sbjct: 715 -----------LMYNLVYPQAPMVK----------TKTIELTNFDKLPAGQNATVAVMSF 753

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVSEEGL 873
            GY+ ED++++++  +       +  +  +   +       +           N      
Sbjct: 754 SGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNKVIFKH 813

Query: 874 KNIDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKAVDVR 925
             +D  GI+  G ++    I++ K  P        +G+S   P   +  +  G +   V 
Sbjct: 814 DVLDTDGIVAPGEQILNKQIMINKEMPAVTSLNPLEGQSTQVPYTAVPISYKGPEPSYVE 873

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
              +   S     +  +    R     ++ S    ++ +  L  D++D
Sbjct: 874 RVMVSANSEEDFLIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQED 921


>gi|195153847|ref|XP_002017835.1| GL17093 [Drosophila persimilis]
 gi|194113631|gb|EDW35674.1| GL17093 [Drosophila persimilis]
          Length = 1137

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 97/555 (17%), Positives = 182/555 (32%), Gaps = 108/555 (19%)

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +   +V            ++       +G                +      ++      
Sbjct: 674  VCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLMYNLVYP 722

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                +    I       +   +    A+      D+ D  +   + +        ++   
Sbjct: 723  QAPMVKTKTIELTNFDKLPAGQNATVAVMSFSGYDIEDALILNKASIDRGYGRCLVYKNS 782

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +R  +   ++I    +D    +VI   ++               G +   K  ++
Sbjct: 783  KCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLD------TDGIVAPGEQILNKQIMI 835

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + ++ +    +     + Q       +              +    + +E++    +   
Sbjct: 836  NKEMPAVTSLNPLEGQSTQVPYTAVPIS------------YKGPEPSYVERVMVSANSEE 883

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K+ +   R  + GDK + RHG KG+   I+  EDMP+   G   D+++NP G P
Sbjct: 884  DF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPYNDSGICPDMIMNPHGFP 941

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM V        G     LG K   L   +                             
Sbjct: 942  SRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F G+    I + L     +  G+   Y G+TG P    
Sbjct: 969  ---------------------AFGGSKVGDIQAELERHGFNYMGKDFFYSGITGAPLQAY 1007

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+
Sbjct: 1008 IYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGAS 1067

Query: 1309 YVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPESFNVLVK 1352
             ++ E L I SD    DV    GR   Y          +        +   P +  +L +
Sbjct: 1068 MLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----HVSKISMPYACKLLFQ 1121

Query: 1353 EMQALGLSIDLENSR 1367
            E+ ++ +   +    
Sbjct: 1122 ELTSMNVVPKMILED 1136



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 131/1012 (12%), Positives = 287/1012 (28%), Gaps = 204/1012 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVRQHIDSFNHFINVDIKKIVRAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GYNITKATTPHECRLRDTTYSSPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGRYYLKHNSMTDDIPIVVIFKALGIVSDQE 257

Query: 229 L-----------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           +           + F   ++ +     +     A D M    V        T     E+ 
Sbjct: 258 IMAHIGIDTKSQNRFGASLLEAFNLKVF-TQQRALDYMGSKLVVKRFQSATTKTPAEEAR 316

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           + L + +   L    V         +    +   +++ E  +   +  D    K LE   
Sbjct: 317 ELLLTTI---LAHVPVDNFNFQMKAIYVSMMVRRVMSAELDKTLFDDRDYYGNKRLELAG 373

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+         I +  +       K A  D+ + MR   ++  +  ES  +
Sbjct: 374 SLISLMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAIS 427

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+  +   +            K+               
Sbjct: 428 SGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ-------- 479

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +    +  + +    +  +           +   ++       + +        
Sbjct: 480 -PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEERPVMILAFNAGVEDIREVSGNPI 538

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  +  +  + N L    +  +        + R         VH ++  R     T  G
Sbjct: 539 NNPNVFLVFINGNVLGLTLNH-KHLVRNLRYMRRKGRMGSFVSVHTSYTQRCIYIHTDGG 597

Query: 578 HNIGLVSSLTSFARVNAYGF---IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   +              +E   RK  D  +   + YL   EE + +IA  N   
Sbjct: 598 RLCRPYIIVEKRRPRVKQFHLDELERGVRKFDDFLLDGLIEYLDVNEENDSFIA-WNEEH 656

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            E+G+                        ++  P  ++ + A L+P+  ++ S R    C
Sbjct: 657 IEEGT----------------------THLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQC 694

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 695 AMGKQAMGMI---------GYNQKNRIDS------------------------------- 714

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N    Q P+VK                T+   L  G+N  VA
Sbjct: 715 ---------------LMYNLVYPQAPMVK----------TKTIELTNFDKLPAGQNATVA 749

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVS 869
            M + GY+ ED++++++  +       +  +  +   +       +           N  
Sbjct: 750 VMSFSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNKV 809

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKA 921
                 +D  GI+  G ++    I++ K  P        +G+S   P   +  +  G + 
Sbjct: 810 IFKHDVLDTDGIVAPGEQILNKQIMINKEMPAVTSLNPLEGQSTQVPYTAVPISYKGPEP 869

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             V    +   S     +  +    R     ++ S    ++ +  L  D++D
Sbjct: 870 SYVERVMVSANSEEDFLIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQED 921


>gi|302417061|ref|XP_003006362.1| DNA-directed RNA polymerase II subunit RPB2 [Verticillium albo-atrum
            VaMs.102]
 gi|261355778|gb|EEY18206.1| DNA-directed RNA polymerase II subunit RPB2 [Verticillium albo-atrum
            VaMs.102]
          Length = 1260

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 193/1233 (15%), Positives = 371/1233 (30%), Gaps = 222/1233 (18%)

Query: 197  DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
            D KD+I   I R   +P+        +  E     F        +G ++    S   L+ 
Sbjct: 184  DMKDMIF--IGR---MPIMVKSKICHLSRESENDLFMLNECPYDQGGYFVINGSEKVLIA 238

Query: 257  GAKVSSSLVDIDTG------------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
              + ++++V +                  +E G +L S L+  L  K     G+      
Sbjct: 239  QERSAANIVQVFKKAQPSPFSYTAEIRSALEKGSRLISSLMLKLHSKSPAKGGVGQT--I 296

Query: 305  GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
               +    V+   G ++   G V DE  L  I +       +  +      A+I      
Sbjct: 297  HCTLPYVKVDIPIGIVFRAFGIVSDEDILNHICYDRNDTQMLEMLRPCIEEAFIVQDRNV 356

Query: 365  DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
                    AL  I +    G+ +     E           K  L  +             
Sbjct: 357  --------ALDWIGKR---GNSNHTMTREKRVRSAKEILQKETLPHI-----------SQ 394

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  +   L+    G+  IDD D+ G +R+   G +L   +R  + RM +
Sbjct: 395  SEGSETRKAFFLGYMTHKLLQCALGRRDIDDRDHFGKKRLDLAGPLLAKLFRTIVRRMNQ 454

Query: 485  SIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             +                   +  + + + +     +               +SQ+    
Sbjct: 455  ELSGHLKRCVESNRQFSLTLGVKPQTLSNGLKYSLATGNWGDQKKAASSTAGVSQVLNRY 514

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 515  TFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 570

Query: 590  ARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              V+     E    Y      +V  +   L        ++      + +D       V  
Sbjct: 571  CYVSVGTPAEPIIDYMIQRGMEVLEEYEPLRYPNATKVFLNGVWVGVHQDPRVLVPDVQG 630

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSN-------RVLMGCNMQRQ 699
                  I      + D  D   K        + P    + S+        +++  ++  +
Sbjct: 631  TRRRNVISHEVSLVRDIRDREFKIFSDAGRVMRPVFVVEQSHHGAVPQGSLVLQKDLVNE 690

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                 +         +       SG         I+E +DA       +    +      
Sbjct: 691  MRDQQENPPDNPEDKITWQTLAHSG---------IIEYLDAEEEETSMICMTPEDLELYR 741

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                  + +    +   N+R   K+             PS  LG       +  + +P+ 
Sbjct: 742  LRKAGHEVEEDI-SEGPNRRLRTKIAKTTHMYTHCEIHPSMILG-------ICASIIPFP 793

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     +  +                                
Sbjct: 794  DHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------------------------D 824

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 825  TMANILYYPQKPLATTRSMEFLKFRELPAGQNAVVAIACYSGYNQEDSVIMNQSSIDRGL 884

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAV 996
                +F R   D  +R        +E   +   ++ + L    Y +L +   +  G    
Sbjct: 885  F-RSLFFRSYTDCEKRVGI---NLVEQFEKPFRNDTLRLKHGTYDKLDDDGIVAPGVRVS 940

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K++ ++ D                 E  QR ++ +K    T     E+   + 
Sbjct: 941  GEDIIIGKTSPINPD---------------NQELGQRTMQHVKRDASTPLRSTENGIIDS 985

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     R VKV V   +  Q GDK A                         
Sbjct: 986  VILTTNQDGL-----RYVKVRVRTTKIPQIGDKFA------------------------- 1015

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
                        SR         H     +G+  + + +    +              + 
Sbjct: 1016 ------------SR---------HGQKGTIGVTYRQEDMPFTSEGITPDI-------IIN 1047

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                 +     +  + +L      K     +TP F     ++++ +LR       G  ++
Sbjct: 1048 PHAIPSRMTIAHLIECLLSKVSTLKGMEGDATP-FTDVTVDSVSQLLRDQGYQSRGFEVM 1106

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y+G TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GE
Sbjct: 1107 YNGHTGKKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRFGE 1166

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------------------- 1335
            ME  C+ A+GAA  L+E L   SD    R  V E  + G                     
Sbjct: 1167 MERDCMIAHGAASFLKERLFEVSD--AFRVHVCE--ICGLMTPIANLSKQSFECRPCKNK 1222

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                +   P +  +L +E+Q++ ++  +   R+
Sbjct: 1223 TKIAQIHIPYAAKLLFQELQSMNIAARMFTDRS 1255



 Score =  202 bits (513), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 131/1038 (12%), Positives = 283/1038 (27%), Gaps = 220/1038 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT--------AFSG-----AAMLE 75
           L+  Q  S+D F    +          Q        IT                    ++
Sbjct: 39  LVSQQVDSFDEFTTSTV----------QELIDEYSHITLDQPNPASDSDRAIALRRYEVK 88

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIV--------------- 110
           F +     P               +C  R+LTYA PL + +   V               
Sbjct: 89  FGTVMVSRPSITEADGKVSTLLPYECRDRNLTYASPLYVRITKKVSIAVENQIPLNELDD 148

Query: 111 -----------------FDVDEFTGAKSIKDIKEQS----IYMGDLPLMTKD-------- 141
                            ++ +E          K +     I++G +P+M K         
Sbjct: 149 EQHDEMGRTGEHPTRLEWEEEESGDDPGADKDKPEDMKDMIFIGRMPIMVKSKICHLSRE 208

Query: 142 ----------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
                           G FVI G ++++++Q  RS          + +      Y   I 
Sbjct: 209 SENDLFMLNECPYDQGGYFVINGSEKVLIAQE-RSAANI--VQVFKKAQPSPFSYTAEIR 265

Query: 186 P--DQGLWMDIEFD--------SKDII---------HVRIDRRRKVPVTSFLMALGM-DS 225
              ++G  +             +K  +         +V++D    +P+     A G+   
Sbjct: 266 SALEKGSRLISSLMLKLHSKSPAKGGVGQTIHCTLPYVKVD----IPIGIVFRAFGIVSD 321

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           E+IL+        +Q  +     +  A ++    V+   +          + +K      
Sbjct: 322 EDILNHICYDRNDTQMLEMLRPCIEEAFIVQDRNVALDWIGKRGNSNHTMTREKRVRSAK 381

Query: 286 KSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           + L+++ +  +  +           G Y+   ++    G   I+  D   +K L+     
Sbjct: 382 EILQKETLPHISQSEGSETRKAFFLG-YMTHKLLQCALGRRDIDDRDHFGKKRLDLAGPL 440

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             +    +        +      V    +      +            +  +  S+    
Sbjct: 441 LAKLFRTIVRRMNQELSGHLKRCVESNRQFSLTLGV-------KPQTLSNGLKYSLATGN 493

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDID 457
           + D  K   ST G  ++  R    +      R          I     L N    +    
Sbjct: 494 WGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPA 553

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                +   + + L     + +      I + +    ++ +   + +             
Sbjct: 554 ETPEGQACGLVKNLSLMCYVSVGTPAEPIIDYMIQRGMEVLEEYEPLRYPNATKVF---L 610

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRI 569
               +   ++    +  +  TRR + +  +  + R     E        R + P      
Sbjct: 611 NGVWVGVHQDPRVLVPDVQGTRRRNVISHEVSLVRDIRDREFKIFSDAGRVMRPVFVVEQ 670

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYI 627
                    ++ L   L +  R       + P  K+       +  + YL A EEE   I
Sbjct: 671 SHHGAVPQGSLVLQKDLVNEMRDQQENPPDNPEDKITWQTLAHSGIIEYLDAEEEETSMI 730

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                                       +  E ++             A      +  + 
Sbjct: 731 C---------------------------MTPEDLELYRLRK-------AGHEVEEDISEG 756

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               +   + +                      +   + I+   A I+   D  +    +
Sbjct: 757 PNRRLRTKIAKTTHM--------------YTHCEIHPSMILGICASIIPFPDHNQSPRNT 802

Query: 748 VEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +  +     G        +           Q+PL                      +L 
Sbjct: 803 YQSAMGKQAMGFFLTNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELP 852

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT---- 862
            G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E      
Sbjct: 853 AGQNAVVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYTDCEKRVGINLVEQFEKPF 912

Query: 863 -RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             D   +       +D+ GI+  G  V+  DI++GK +P         ++ ++ +     
Sbjct: 913 RNDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTSPINPDNQELGQRTMQHVK---- 968

Query: 922 VDVRDTSLRVPSGVSGTV 939
              RD S  + S  +G +
Sbjct: 969 ---RDASTPLRSTENGII 983


>gi|254172599|ref|ZP_04879274.1| DNA-directed RNA polymerase, beta subunit, putative [Thermococcus sp.
            AM4]
 gi|214033528|gb|EEB74355.1| DNA-directed RNA polymerase, beta subunit, putative [Thermococcus sp.
            AM4]
          Length = 1122

 Score =  307 bits (786), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 113/586 (19%), Positives = 205/586 (34%), Gaps = 95/586 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  PW        + +    +     + +   E     R+T     
Sbjct: 614  IEYLDAEEEENAYVATWPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGM 673

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++ +D  G   +        +    +   G       +  + A+   
Sbjct: 674  AKQSLGLGWANFRIR-VDTRG--HLMHYPQVPLVNSRIMKAVGFEERPAGQNFVVAVLSY 730

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +    +    F R    + +R +  + ++ E    D   +  + D
Sbjct: 731  QGYNMEDAIIINKASIERG-LARSTFFRTYEAEEKRYLGGQMDRFEKP--DPTIKGYLGD 787

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            R   +   + +    +    K            + E  +S     A+Q+          +
Sbjct: 788  RYYRNLDEDGIIFPESKVEGKDVLVGRTSPPRFLEE--QSGLGGIALQE----------R 835

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +   +    E    +K+   + GD       ++VKV V   R  + GDK A RHG KG+
Sbjct: 836  RETSVAVRPSEKGIVDKVIITETGD-----GTKLVKVTVRDLRIPELGDKFASRHGQKGV 890

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMP+ ++G   D+++NP G+PSRM VGQ+ E   G      G+++       
Sbjct: 891  IGLIVPQEDMPWTENGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRVDGTAFIG 950

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +    +      L                                      +DG      
Sbjct: 951  EPEERLRKELEELGFKHTGREVM----------------------------YDGIT---- 978

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                               G      +  + VG IY  +L+HMV+DK++ARS G   ++T
Sbjct: 979  -------------------GR---RLEADIFVGVIYYQRLHHMVADKMHARSRGPVQVLT 1016

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG-------- 1324
            +QP  G++  GG R GEME   +  +GAA +L E L  +SD          G        
Sbjct: 1017 KQPTEGRAREGGLRFGEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKR 1076

Query: 1325 RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R +VY   V G +    +     +F +L+ E++A+ +   L     
Sbjct: 1077 RGKVY-CPVCGEEERISKVEMSYAFKLLLDELKAMVIRPSLRLKDR 1121



 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 153/984 (15%), Positives = 296/984 (30%), Gaps = 209/984 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            GLQ        +        ++F       P F  
Sbjct: 29  LVRQHLDSYNAFI----------EHGLQEVINEFGGVKPDIPNFEVKFGKIRLGEPIFQE 78

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + L  +V  +++              + +G+LPLM
Sbjct: 79  AQGQRRPLYPMDARIRNLTYSAPLFLELIPVVNGIEQEPV----------EVRIGELPLM 128

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPG---IHFDHDKGR 171
            K                         G F+I G +R++VS    +P    +  D  + +
Sbjct: 129 LKSKACRLYGLSDEELIELGEDPKDPGGYFIINGSERVIVSIEDLAPNKTLVERDERQNK 188

Query: 172 ASLSGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPV--TSFLMALG-MDS 225
                      ++   +      + +E     I++V I    K PV     + ALG +  
Sbjct: 189 V--------VAKVFSYRHGYRALITVESRKDGILYVSIPNVPK-PVKFVYVMRALGLLSD 239

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           +EI+          Q         +  +     +     +D      +    K+      
Sbjct: 240 KEIVEAISEDPRIQQ------VLFNNLEDASDIRTQEEALDFIGRLSLPGQPKEYRLRRA 293

Query: 286 KSLKEKG-VKFLGITSD------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           + + +   +  +G+  +         G+  A  ++    G    +  D    K L+    
Sbjct: 294 EHIIDNNLLPHMGVEPENRKAKAYYLGMM-ALKVLELALGLRGEDDKDHYANKRLKLAGD 352

Query: 339 SEIRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                  + +   V +  Y   +      +    ++    +   +RP DV +  +  ++ 
Sbjct: 353 LLKDLFRVAFGQLVKDMQYQMTKTYQRKGERYTFENIQRFVRNSVRP-DVLSERIEHALA 411

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              +          + R      L+         + ++      + L       G I   
Sbjct: 412 TGSWPGGRTGVSQLLDRTNYISTLSHLRRVTSP-LSRDQPHFEARDLHGTH--WGRICPT 468

Query: 457 DNLGNRRVRSVGEM-LKNQYRLGLLRME-RSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           +         V  + L  Q   G+   E R    ++  V I+   P              
Sbjct: 469 ETPEGPNCGLVKNLALMAQITTGIPEEEVREYLLKLGVVPIEERRPS--------PGLYR 520

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PTHYGRICPAE 573
            +     +  +E+    +  I   RR   +            ++R+++  +  GR+    
Sbjct: 521 VYLNGVLIGTIEDGKALVQTIRSDRRAGKISDVINVAIYEEEDVREIYVNSDDGRVRRPL 580

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
               +    ++     A  N  G +E       D      + YL A EEEN Y+A     
Sbjct: 581 IIVENGKPKLTREHVEAIKN--GQLE-----WSDLIRMGVIEYLDAEEEENAYVAT---- 629

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                                    E+   ++  P  ++ I ASL+P+ E++ + R   G
Sbjct: 630 -------------------WPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYG 670

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +Q++ L  A                                               
Sbjct: 671 AGMAKQSLGLGWANFRI-----------------------------------------RV 689

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +   +  Y               Q PLV                +    +   G+N +V
Sbjct: 690 DTRGHLMHYP--------------QVPLVNS----------RIMKAVGFEERPAGQNFVV 725

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NV 868
           A + + GYN ED+++I++  +   +  S     +E   +    G  +            +
Sbjct: 726 AVLSYQGYNMEDAIIINKASIERGLARSTFFRTYEAEEKRYLGGQMDRFEKPDPTIKGYL 785

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            +   +N+DE GII   ++V   D+LVG+ +P        E+  L  I  +   + R+TS
Sbjct: 786 GDRYYRNLDEDGIIFPESKVEGKDVLVGRTSPPRFLE---EQSGLGGIALQ---ERRETS 839

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
           + V     G V  V I       K
Sbjct: 840 VAVRPSEKGIVDKVIITETGDGTK 863


>gi|269913235|emb|CAY86044.1| RNA polymerase beta subunit [Asaia bogorensis]
          Length = 309

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 145/312 (46%), Positives = 199/312 (63%), Gaps = 28/312 (8%)

Query: 151 RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
           R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+R
Sbjct: 1   RVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKR 60

Query: 211 KVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFW 245
           K+PVT+ L AL                         GMD +EIL+ FY  + +++    W
Sbjct: 61  KLPVTTLLYALEGEHSIAARAAKAAEGGDVEALGIRGMDQDEILAYFYGTVPFTRMPKGW 120

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG 305
             P        G K+   L D DTGE V E+  KLT+ + + + E   K + +    L G
Sbjct: 121 ARPFDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMCRKIAEA-TKDVLVGRADLLG 178

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
            ++A+D+VN  TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL  D
Sbjct: 179 RFIAQDLVNENTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLAVD 237

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
           KN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D P
Sbjct: 238 KNNRRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVDAP 297

Query: 426 DDVRHIRKEDII 437
           D +R +RKEDI+
Sbjct: 298 DTMRVLRKEDIL 309


>gi|291196422|emb|CBG27568.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas guineae]
          Length = 305

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI+AD
Sbjct: 241 SVDASRVVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVERSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|89274898|gb|ABD65890.1| RNA polymerase II second largest subunit [Polyporus squamosus]
          Length = 898

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 148/1026 (14%), Positives = 305/1026 (29%), Gaps = 175/1026 (17%)

Query: 286  KSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK    + +   G      +    V+     ++   G + D   LE I +   
Sbjct: 27   KTISQFQVKLYHRSKERSLGNVMKATIPYIKVDIPIWVVFRALGVISDRDILEHICYDLQ 86

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             +  +  +    +  ++         +DR+ AL  I                +       
Sbjct: 87   DNQMLEMLKPCIDEGFV--------IQDREIALDFI------------GNRGTTIGLNRE 126

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G 
Sbjct: 127  RRLRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRDLDDRDHFGK 183

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +   +               +    + + +     +
Sbjct: 184  KRLDLAGPLLANLFRMLFRKLTKDVYRHLQKCVEMNKEFNLSLAVKHNTITNGLKYSLAT 243

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 244  GNWGDQKKSMSAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 299

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + ++           + +  + +         EEN +
Sbjct: 300  GMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL--------EENTH 351

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   R      D + +  V             D
Sbjct: 352  ASTPCTKVFVNGVWMG---VHRDPAGLVRTLRRLRRKDDINCEVSVVRDIRERELRLYTD 408

Query: 687  SNRVLMGCNMQRQAVPLLKAEA--PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
            + RV     +  +   L++ +     V +  +     +    I   + G++E +DA    
Sbjct: 409  AGRVCRPLFIVEEQQLLVQKKHIENLVRSKEDPSYEYNWDNMI---KEGVIELLDAEEEE 465

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +    +   +     +            V+    +K              PS  LG 
Sbjct: 466  TVMICMTPEDLENSRL--QAAGIDPHADEEHVDPSARLKAPTFSHTWTHCEIHPSMILG- 522

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                        ++       +G       
Sbjct: 523  ------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFL 558

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +               +  +             +       +   +  + AI      + 
Sbjct: 559  VRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQ 607

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +   
Sbjct: 608  EDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLE 666

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G N         K+  +  D      R++          ++   + +  Q   
Sbjct: 667  NDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRTHTKRDVSTPLKSTEQGIVDQVLI 726

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       + VK+ V   R  Q GDK A RHG KG +    
Sbjct: 727  --------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITY 766

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +          
Sbjct: 767  RQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNEGDATPFTNLTVET 826

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S      +K   +                                              
Sbjct: 827  VSTFLR--QKGYQSRGLEVM---------------------------------------- 844

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ 
Sbjct: 845  -----YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVE 892

Query: 1285 GKSNRG 1290
            G+S  G
Sbjct: 893  GRSRDG 898



 Score =  129 bits (325), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 98/768 (12%), Positives = 214/768 (27%), Gaps = 106/768 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 55  YIKVD----IPIWVVFRALGVISDRDILEHICYDLQDNQMLEMLKPCIDEGFVIQDREIA 110

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   ++L     + L+++ +  + +              +      + 
Sbjct: 111 LDFIGNRGTTIGLNRERRLRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 166

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  D    +      +    P+L          +   +     K  +        +
Sbjct: 167 LAALERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRHLQKCVEMNKEFNLSL 226

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   +  G  ++  R    +      R         
Sbjct: 227 AVKHNTITNGLKYSLATGNWGDQKKSMSAKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 286

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +  +   + E      ++  
Sbjct: 287 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEF-----LEEW 341

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             + L       +   + F +     +      L R     R        V+  R   E 
Sbjct: 342 GLESLEENTHASTPCTKVFVNGVWMGVHRDPAGLVRTLRRLRRKDDINCEVSVVRDIRER 401

Query: 559 RDVHPTHYGRICP--AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
                T  GR+C       E   +     + +  R       E       +      +  
Sbjct: 402 ELRLYTDAGRVCRPLFIVEEQQLLVQKKHIENLVRSKEDPSYEYN---WDNMIKEGVIEL 458

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPK 669
           L A EEE   I      L+        +             R             +  P 
Sbjct: 459 LDAEEEETVMICMTPEDLENSRLQAAGIDPHADEEHVDPSARLKAPTFSHTWTHCEIHPS 518

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +                          
Sbjct: 519 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------------- 559

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 560 ----------------------RMDTMANILYYPQKPLATTRSMEYLRFR---------- 587

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  
Sbjct: 588 --------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMD 633

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + + + +   E            +       ++  G+I  G  VN  DI++GK  P    
Sbjct: 634 LEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLENDGLIAPGTNVNGEDIIIGKTAPIPPD 693

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                ++        +    RD S  + S   G V  V I       K
Sbjct: 694 SEELGQRT-------RTHTKRDVSTPLKSTEQGIVDQVLITTNAEGQK 734


>gi|159905694|ref|YP_001549356.1| DNA-directed RNA polymerase subunit B' [Methanococcus maripaludis C6]
 gi|159887187|gb|ABX02124.1| RNA polymerase Rpb2 domain 6 [Methanococcus maripaludis C6]
          Length = 611

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 128/325 (39%), Gaps = 82/325 (25%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               R+ KV V   R  + GDK A RHG KG++  I+P ED+P+ +DG   D+++NP  +P
Sbjct: 343  EGNRLGKVRVRDLRIPEFGDKFASRHGQKGVIGLIVPQEDLPYTEDGVIPDLIINPHAIP 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +GQ+ E   G       ++I   I   ++   +                       
Sbjct: 403  SRMTIGQVLEMIGGKVGSLECRRIDGTIFSGESEWKLREGLEKYGFEHHA---------- 452

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                               + A  D         G +G   +  
Sbjct: 453  -----------------------------------KEAMYD---------GKSGRKLECD 468

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG  Y  KL+H+V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA
Sbjct: 469  IFVGIAYYQKLHHLVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAA 528

Query: 1309 YVLQEMLTIKSD---D----------------------VVGRTRVYESIVAGNDTFETGT 1343
             +L+E L  +SD   D                      V G +   E I           
Sbjct: 529  MLLKERLLDESDPHEDYVCAKCGEIAIFDYKRGMKFCPVCGES---EDIQDNRKIPPVKI 585

Query: 1344 PESFNVLVKEMQALGLSIDLENSRT 1368
              +F +L+ E++++G+   LE    
Sbjct: 586  AYAFKLLLDELKSMGIDPKLELKDR 610



 Score = 88.2 bits (217), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 73/420 (17%), Positives = 131/420 (31%), Gaps = 112/420 (26%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR--ICPAETSEGHNIGLVS 584
           +    +  +   RR   L            E  DVH +  G   + P    E     L  
Sbjct: 19  DPETLVKNLRENRRSGKLSPS--TSISFNEESNDVHISTDGGRAVRPLVVVENGASKLTQ 76

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            L            E  + ++ +  V   + YL A EEEN  IA     + E+       
Sbjct: 77  ELLEKVDAQ-----ELTFHELVNSGV---IEYLDAEEEENARIAMYEDEVTEEN------ 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              ++  P  ++ I A + P+ E++ + R+ M   M +Q++ + 
Sbjct: 123 -----------------THVEIDPLVILGIGAGVAPYPEHNSAPRITMAAAMSKQSLGIP 165

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            A   +                                            +   +  Y  
Sbjct: 166 MANIKW-----------------------------------------RMDTRGHLLHYP- 183

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q PLV+   +                    G+N +VA M + GYN E
Sbjct: 184 -------------QVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNME 220

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDEC 879
           D+ +I++  +   +  S     +E   +    G  +             +EE  +N+ + 
Sbjct: 221 DAFIINKASLERGLGRSTFFRSYESFEKRYPGGQLDKFEVPEKGVRGYRAEEAYRNLGDD 280

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+I + +EV  GD+++GK +P             + I  +     RDTS+ +  G  G V
Sbjct: 281 GLIDLESEVRSGDVILGKTSPPRFLEE-------QEITLQTKSQRRDTSVTIRHGEEGIV 333


>gi|213876735|gb|ACJ54364.1| RNA polymerase subunit B [Mycobacterium sp. FI-03099]
          Length = 244

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 133/236 (56%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +          
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPDWAAKLPEDLYSAP-- 154

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                                          VSTPVFDGA E  +  +L            
Sbjct: 155  --------------------------RDSIVSTPVFDGAQEGELQGLLGSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 189  VDADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 244



 Score = 42.8 bits (99), Expect = 0.43,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|185179194|gb|ACC77610.1| RpoB [Mycobacterium kansasii]
          Length = 215

 Score =  307 bits (786), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 101/236 (42%), Positives = 136/236 (57%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 12   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 71

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 72   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 130  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 159

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPL
Sbjct: 160  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPL 215


>gi|186660236|gb|ACC85971.1| RpoB [Mycobacterium insubricum]
          Length = 251

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 102/236 (43%), Positives = 136/236 (57%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 48   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 107

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  ++                      
Sbjct: 108  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNVEGSPEWAAN-------------- 152

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +   V+TPVFDGA EE +  +L            
Sbjct: 153  -----------------LPEDLLHAPADSIVATPVFDGAREEELQGLLSSTLPNRDGEVM 195

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 196  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 251



 Score = 52.8 bits (125), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/56 (64%), Positives = 46/56 (82%)

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            K+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   AKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 56


>gi|86451159|gb|ABC96802.1| RNA polymerase II [Coffea arabica]
          Length = 200

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 101/242 (41%), Gaps = 54/242 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMPF  +G   DI++NP 
Sbjct: 13   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPH 72

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 73   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 100

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG P 
Sbjct: 101  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPL 138

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 139  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 198

Query: 1306 GA 1307
            GA
Sbjct: 199  GA 200


>gi|52694183|emb|CAG30621.1| DNA-directed RNA polymerase beta chain [Pseudomonas mediterranea]
          Length = 318

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 185/314 (58%), Positives = 240/314 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 5   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 64

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D 
Sbjct: 65  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDA 124

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 125 LVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSP 184

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 185 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 244

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 245 ARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 304

Query: 789 RRNDIIADGPSTDL 802
           +R+DI+ADGPSTD+
Sbjct: 305 QRSDIMADGPSTDM 318


>gi|295291779|gb|ABH04346.2| RNA polymerase beta subunit [Proteus vulgaris]
          Length = 310

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 188/309 (60%), Positives = 232/309 (75%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVENNAVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQANS LD+D  F EELV CR  GE  L  R+++ ++D S +QVVS+ ASLIPFLE+
Sbjct: 122 FIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYMDVSTQQVVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG   VAKR G+V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+
Sbjct: 242 IKVNEEETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGEPVDRGDVLADGPSTDLGE 301

Query: 805 LALGRNMLV 813
           LALG+NM V
Sbjct: 302 LALGQNMRV 310


>gi|72388214|ref|XP_844531.1| DNA-directed RNA polymerase II subunit 2 [Trypanosoma brucei TREU927]
 gi|62359772|gb|AAX80202.1| DNA-directed RNA polymerase II subunit 2, putative [Trypanosoma
            brucei]
 gi|70801064|gb|AAZ10972.1| DNA-directed RNA polymerase II subunit 2, putative [Trypanosoma
            brucei brucei strain 927/4 GUTat10.1]
          Length = 1190

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 103/576 (17%), Positives = 175/576 (30%), Gaps = 110/576 (19%)

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                    F      +    + I   ++            ++       +G      ++ 
Sbjct: 701  PSEVGKNYFYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASNFNMR 760

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                             V        +    ++    + +      + AI      +  D
Sbjct: 761  M-----------DTTAHVLFYPQKPLVRTKAMSYMRSNDLPAGHNAIVAIACYSGYNQED 809

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S V         +  +   + ++    E  +I       D +   + R  Y++L
Sbjct: 810  SIIMSRSAVERGFFRSVFWRSYKASEEKKREGREMFEIP------DRKVCHVKRADYTKL 863

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G   + G     K+  +   L  E P S   +   +D  +            
Sbjct: 864  DTDGLIKPGMPVIGGDIIVGKTIPVPKTLSEESPVSD-TRILKRDCSISSRAA------- 915

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                        +   +           R  KV +   +    GDK   RHG KG     
Sbjct: 916  ------------EKGVVDRVMLTENKGNRFTKVRIRTIKIPNIGDKFCSRHGQKGTNGIQ 963

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  DG   D+++NP  +PSRM V  + ET  G                     
Sbjct: 964  FRQEDMPFNHDGISPDLIINPHAIPSRMTVAHLIETLAGKVAC----------------- 1006

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                +K G   +TP F     E     L
Sbjct: 1007 ------------------------------------YKGGEVYATP-FCSVVVEDFGKAL 1029

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                L+  G   LY+G TG P D  +  G  Y  +L H+ SDK++AR  G    + +QP 
Sbjct: 1030 TQLKLNRYGNERLYNGHTGLPLDHLIFFGPTYYQRLKHLSSDKIHARPRGPLQPLVRQPT 1089

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR------TRVYESIV 1333
             G+++ GG R GEME  C+ +YGA+  L+E L   SD     V             +++ 
Sbjct: 1090 EGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYSVHVCNMCGTICAADTDQNLY 1149

Query: 1334 AGN------DTFETGTPESFNVLVKEMQALGLSIDL 1363
                        +   P +  +L +E+ ++ +   L
Sbjct: 1150 KCQGCDNDSHISQVLMPYACKLLFQELMSMAILPRL 1185



 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 154/1007 (15%), Positives = 301/1007 (29%), Gaps = 195/1007 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVF-P---ITAFSGAAMLEFVSYEF 81
           L+  Q  SY+ FL + I    R    L          F P   + +      L       
Sbjct: 56  LVHQQVDSYNDFL-LRIPRMARS---LLEIVPRQDDQFDPGVHVESEPDQYRLSLEDVVV 111

Query: 82  DPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             P  +              ++C  RDLTY    ++TL + V+   E    ++     E 
Sbjct: 112 GNPSHEMSGFSRTEMHPLFPNECRLRDLTYDAVAQVTLAIRVYRSREEQPYRTFLQNME- 170

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-I 163
              +G +P+M K                         G F++ G ++++++Q  ++   +
Sbjct: 171 ---LGRIPIMLKSMRCNLLNKDEEELPRLNECPHDQGGYFIVNGTEKVLIAQERQAANHV 227

Query: 164 H-FDHDKG-----RASLSG--KLLYACRII-PDQ--GLWMDIEFDSKDIIH--VRIDRRR 210
           + F   KG     ++ + G        +I+ P +  G     E    +++    ++D   
Sbjct: 228 YAFTRPKGLLCEIKSIVEGSLNKPRTLQILMPYKKSGPGHGYE----NLLCRVAQMDEL- 282

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            +P+     AL M S+ EIL T  P +      +     +  A  +       +L  I  
Sbjct: 283 -IPLFVLFRALDMGSDKEILQTVVPDLKDVAMLEMLRGSMEDASTLEIFTRDEALWFIGK 341

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
                +S + L       L    +  +G+      G  +    +      + +   +  D
Sbjct: 342 RLGKQDSRENLQREAQDLLMRDLLPHMGVDCAADRGKCLFIGYMVHRLLLLALGRREDTD 401

Query: 330 EKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
              L  + I  +       L    V     +  T+            +  +  +    + 
Sbjct: 402 RDFLGHKRIDVAGSLLTFQLNQFLVQVRREMAQTVHDYSTNRGG---VVSFGRILHNRLI 458

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA--IIKILVD 445
           T  +   +    F D    ++ T     +N      +  ++R I+     +    +    
Sbjct: 459 TDGMRRCLATGNFGDLKSGNIKTGVSQTLNRLTYSSSLSNLRRIQNPISASSKATRPRNL 518

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQY------RLGLLRMERSIKERISSVD----I 495
                G I  ++      +  +  +             G+++  +S      S+      
Sbjct: 519 HCTQWGYICPVETPEGGSIGLLKNLALMCLVSRGSDHTGVVQAVQSRITGFHSIALSDLA 578

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           D  + +  +N   +            L          + ++  R +        +     
Sbjct: 579 DVRVARVFVNGTLIGVHGDPERLLRDLRARRRGGELSNEVSIVRDIRDREIRVFSDGGRC 638

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
           +  R +      RI   +   G  +   ++L     ++    ++  Y           V 
Sbjct: 639 L--RPLFVVEKSRIKLQKAGIGELLEPSTTLGGRREISWNKVMKKGY-----------VE 685

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            +   EE++  IA   S + ++  +                        +  P  ++ I 
Sbjct: 686 LIDCEEEDSLLIAMVPSEVGKNYFY---------------------SHCEMDPSMILGIC 724

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IP+  ++ S R      M +QA+ +                                
Sbjct: 725 ASIIPYPNHNQSPRNTYQSAMGKQAMGIY------------------------------- 753

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                      S       +T+ V  Y               Q+PLV+            
Sbjct: 754 ----------ASNFNMRMDTTAHVLFYP--------------QKPLVR----------TK 779

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   DL  G N +VA   + GYN EDS+++S   V    F S+    ++      +
Sbjct: 780 AMSYMRSNDLPAGHNAIVAIACYSGYNQEDSIIMSRSAVERGFFRSVFWRSYKASEEKKR 839

Query: 856 LGP---EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            G    E   R + +V       +D  G+I  G  V  GDI+VGK  P    P T  E+ 
Sbjct: 840 EGREMFEIPDRKVCHVKRADYTKLDTDGLIKPGMPVIGGDIIVGKTIPV---PKTLSEES 896

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
             +       D   +S     GV   V+              R+I +
Sbjct: 897 PVSDTRILKRDCSISSRAAEKGVVDRVMLTENKGNRFTKVRIRTIKI 943


>gi|28881404|emb|CAD70445.1| DNA-dependent RNA polymerase II RPB140 (RPB2) [Neurospora crassa]
          Length = 1287

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 193/1210 (15%), Positives = 368/1210 (30%), Gaps = 196/1210 (16%)

Query: 211  KVPVTSFLMA--LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
            K+P+        L M+ +E  S F        +G ++    S   L+   + ++++V + 
Sbjct: 217  KIPIMVKSKICHLYMEDDE--SLFTLNECPYDQGGYFIINGSEKVLIAQERSAANIVQVF 274

Query: 269  TG------------EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
                             +E G +L S L   L  K  +  G  ++ +  + +        
Sbjct: 275  KKPPGGSVSYQAEIRSALEKGSRLISSLQMRLHTKADQNKGRLANTVS-VTLPYVKEEVS 333

Query: 317  TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
               ++   G V DE  L  I +       +  +      A+          +DR+ AL  
Sbjct: 334  LAIVFRALGVVSDEDILNHICYDRRDSQMLEALRPCIEEAF--------CIQDREVALDY 385

Query: 377  IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            I +    G+ ST                K  L  +              +     +   +
Sbjct: 386  IGKR---GNGSTGINRNGRIKAAKEMLQKELLPHI-----------SQAEGCETRKAFFL 431

Query: 437  IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVD 494
              ++  L+    G+   DD D+ G +R+   G +L   +R  + R+ + +    +     
Sbjct: 432  GYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVRRLTQDLMGYMKRCVDT 491

Query: 495  IDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRL 541
                     I A  + + +     +               +SQ+       S ++H RR 
Sbjct: 492  NKHFSLALGIKASTLTNGLKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFSSTLSHLRRT 551

Query: 542  SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET- 600
            +      + R     + R +H TH+G +CPAET EG   GLV +L+    V+     +  
Sbjct: 552  NT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTLADPI 607

Query: 601  -PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
              +    + +V  +   L        ++      + +D      LV        I     
Sbjct: 608  IEFMIARNMEVLEEYEPLRYPNATKVFVNGTWVGVHQDPKHLVTLVQNLRRKNIISFEVS 667

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +  I     ++ S A  ++  L   +          + Q +   +              
Sbjct: 668  LVRDIRDREFKIFSDAGRVMRPLFVVEQEDNSESGVEKGQLILTKEHIRRLEQDKELGKY 727

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ----RSNQNTC 775
             +          +G +E +DA       +    +     +D YR  KF+      +    
Sbjct: 728  HEDYFGWQGLLESGAIEYLDAEEEETAMICMTPED----LDTYRQHKFKGREFEDDAANR 783

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             N R   K              PS  LG       +  + +P+  +N          M  
Sbjct: 784  GNSRIKTKFNPTTHMYTHCEIHPSMLLG-------ICASIIPFPDHNQSPRNTYQSAMGK 836

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +     +  +                                 +  +           
Sbjct: 837  QAMG--FFLTNYSRRM---------------------------DTMANILYYPQKPLATT 867

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +   +  + AI      +  D+ +   S +   +    +F R   D  +R
Sbjct: 868  RSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGIF-RSLFFRSYTDCEKR 926

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                  EQ E   R           +       I  G           K++ ++ D    
Sbjct: 927  VGINIVEQFEKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPD---- 982

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                         E  QR  + +K    T     E    + +      D +     R VK
Sbjct: 983  -----------NQELGQRTAQHVKRDASTPLRSTESGIVDSVAFTTNQDGL-----RYVK 1026

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V V   +  Q GDK A                                     SR     
Sbjct: 1027 VRVRTTKIPQIGDKFA-------------------------------------SR----- 1044

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                H     +G+  + + +    +              +      +     +  + +L 
Sbjct: 1045 ----HGQKGTIGVTYRQEDMPFTAEGITPDI-------IINPHAIPSRMTIAHLIECLLS 1093

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                 K     +TP F     ++++++LR       G  I+Y G TG+     V  G  Y
Sbjct: 1094 KVGALKGMEGDATP-FTDVTVDSVSNLLREHGYQSRGFEIMYHGHTGKKLRAQVFFGPTY 1152

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L
Sbjct: 1153 YQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRFGEMERDCMIAHGAAAFLKERL 1212

Query: 1316 TIKSD-------DVVGRTRVYESIVA-------GND---TFETGTPESFNVLVKEMQALG 1358
               SD       ++ G      ++           +     +   P +  +L +E+ ++ 
Sbjct: 1213 FEVSDAFRVHICEICGLMTPIANLTKQSFECRPCKNKTKIAQVHMPYAAKLLFQELMSMN 1272

Query: 1359 LSIDLENSRT 1368
            ++  L  SR+
Sbjct: 1273 IASRLFTSRS 1282



 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 140/1065 (13%), Positives = 285/1065 (26%), Gaps = 231/1065 (21%)

Query: 20   NPEIIDIPDLIEVQKASYDHFLMMNI-------------APDERPNEGLQAAFKSVFPIT 66
                 D+  L+  Q  S++ F    +              P    +EG +   +      
Sbjct: 52   ISSYFDLKGLVSQQIDSFNEFTTDTVQSLIDEYADLTLDHPSPGDDEGREIILR------ 105

Query: 67   AFSGAAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITL---------- 106
                   + F       P               +C  R+LTY+ P+   +          
Sbjct: 106  ----RYDVHFGEIIISRPTLTEATGETISLLPYECRDRNLTYSAPIYCKVTKRARIAVSE 161

Query: 107  -----RLIVFDVDEFTGAKS--------------IKDIKEQSI---------YMGDLPLM 138
                 +L   + D                      +  K+  I         ++G +P+M
Sbjct: 162  KKPLNQLTDDEHDHMARTGEHPTALRWIEEESAPPEPPKDDKINPENLKGYLFLGKIPIM 221

Query: 139  TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             K                         G F+I G ++++++Q  RS          +   
Sbjct: 222  VKSKICHLYMEDDESLFTLNECPYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKPP 278

Query: 175  SGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDRRR-----KVPVT-----------S 216
             G + Y   I    ++G  +         +H + D+ +      V VT            
Sbjct: 279  GGSVSYQAEIRSALEKGSRLISSLQM--RLHTKADQNKGRLANTVSVTLPYVKEEVSLAI 336

Query: 217  FLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
               ALG +  E+IL+        SQ  +     +  A  +   +V+   +          
Sbjct: 337  VFRALGVVSDEDILNHICYDRRDSQMLEALRPCIEEAFCIQDREVALDYIGKRGNGSTGI 396

Query: 276  SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-- 333
            +         + L+++ +  +     C          +  +  +  +   D  D      
Sbjct: 397  NRNGRIKAAKEMLQKELLPHISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDHFGK 456

Query: 334  EEIFHSEIRDIPIL--YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            + +  +      +    V  +  +         D NK    AL      +  G      +
Sbjct: 457  KRLDLAGPLLAKLFRGIVRRLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNG------L 510

Query: 392  AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNG 449
              S+    + D  K   ST G  ++  R    +      R          +     L N 
Sbjct: 511  KYSLATGNWGDQKKAMSSTAGVSQVLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNT 570

Query: 450  KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
               +         +   + + L     + +  +   I E + + +++ +   + +     
Sbjct: 571  HWGLVCPAETPEGQACGLVKNLSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLRYPNA 630

Query: 510  VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                      + +   ++  + ++ + + RR + +                +       +
Sbjct: 631  TKVF---VNGTWVGVHQDPKHLVTLVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVM 687

Query: 570  CPAETSE-----------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             P    E           G  I     +    +    G     Y        +  + YL 
Sbjct: 688  RPLFVVEQEDNSESGVEKGQLILTKEHIRRLEQDKELGKYHEDYFGWQGLLESGAIEYLD 747

Query: 619  AMEEENRYIAQANSSLDE------DGSFTEELVFCRCAGEEILVPR---EKIDFIDASPK 669
            A EEE   I      LD        G   E+    R                   +  P 
Sbjct: 748  AEEEETAMICMTPEDLDTYRQHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPS 807

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
             ++ I AS+IPF +++ S R      M +QA+                            
Sbjct: 808  MLLGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYS-------------------- 847

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                     + + +  Y       +     +  R          
Sbjct: 848  ---------------------RRMDTMANILYYPQKPLATTRSMEYLKFR---------- 876

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                          +L  G+N +VA   + GYN EDS+++++  +   +F S+    +  
Sbjct: 877  --------------ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGIFRSLFFRSYTD 922

Query: 850  MARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              +   +   E        +           ++  GII  G  V   DI++GK +P    
Sbjct: 923  CEKRVGINIVEQFEKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPD 982

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                 ++  + +        RD S  + S  SG V  V       
Sbjct: 983  NQELGQRTAQHVK-------RDASTPLRSTESGIVDSVAFTTNQD 1020


>gi|213876753|gb|ACJ54373.1| RNA polymerase subunit B [Mycobacterium murale]
          Length = 246

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 100/236 (42%), Positives = 133/236 (56%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +   ++          
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIDVAQGVPEWASNLPEALYSAPAD 158

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
              T                            +TPVFDG  E  +  +L     +      
Sbjct: 159  TNT----------------------------ATPVFDGTRENELTGLLGSTLPNRDGDVM 190

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 191  VDGDGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 246



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 48


>gi|308159405|gb|EFO61937.1| DNA-directed RNA polymerase subunit B [Giardia lamblia P15]
          Length = 1236

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 158/1011 (15%), Positives = 313/1011 (30%), Gaps = 190/1011 (18%)

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG--RVKMNMRLNLDTPDDV 428
            +  L D ++       +   +    F  +    D+YDL+ +    +     L ++ P + 
Sbjct: 292  EAMLRDFHKYRIFSHKACKQLLGGKFRMILSLLDRYDLTDIECCDLLFEQYLLINIPKED 351

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               +   +  + +  + L  G    D  D L ++   + G + K +    L+++ R I  
Sbjct: 352  TRAKFNMMCLMARKCLLLFGGFIQSDSPDMLSSQEALTPGALFKAEIASTLIKIMRLISR 411

Query: 489  RISSV--DIDSVMPQDLINAKPVVSAVCEFFCS----------------------SQLSQ 524
              +S        +    I+       +     S                      S +S 
Sbjct: 412  NATSTGAIGSYELSNSWISHYLASPKLWRPLSSGLRSLAGPGVMRAYKGHDYSNMSGISV 471

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            L + +N +  + H R    + +G          +R ++P  YG  C   T +G   G+++
Sbjct: 472  LADRINYVRFLAHFR---CINRGNAFATHKITSIRKLYPESYGFQCAVHTPDGAPCGILT 528

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL---------SAMEEENRYIAQA-NSSL 634
             L   A V            +     T+ +  L         S    +   +    N ++
Sbjct: 529  HLCYKATV------------LSSTPTTDQIANLFILLSQFGLSPSLSDTYTLGVVLNGTI 576

Query: 635  ---DEDGSFTEELVFCRC--------AGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
                +      +LV                 ++  EK +     P   ++ +        
Sbjct: 577  LGFMDTNKRASQLVASIRAAKIESTIFPYTEIIFIEKGNKDHLFPGIYMNTSMGRFYRPV 636

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +   N  L       Q    +      V +G+     + +  ++++    +V   D  + 
Sbjct: 637  HSLINNSLEYITPLEQIFLQIAIYGDDVRSGVT-THQEVTPTSLLSILGLLVPFSDHNQS 695

Query: 744  VIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 E  +   T  +       ++   +      Q+P+V+                   
Sbjct: 696  PRNMYECQMLKQTMAIPCRNLTYRYDAKSYLLTTPQKPIVRNAIIHDIG---------GF 746

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-- 860
                 G N++VA   +  Y+ ED+ LI++  +   +F        ++   D KL      
Sbjct: 747  DTHPTGTNLVVAVSAYTSYDMEDAALINKASLERGLFHGTVYSVHDIDCYDDKLMRYMRS 806

Query: 861  -----------ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                           + ++ E     +DE G+  +GA ++ G +      P  +   T  
Sbjct: 807  MTTAVPYLKRSPDYSVTHMDENYDTELDEDGLPPIGAYLSHGSVFYQTYDPTKQCYST-- 864

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                               L  P  V   +V  +   +     +      ++ +      
Sbjct: 865  ----------------KLYLHEPGFVEKIIVIHKSAAKGEYWTDSDVGPKKKRE------ 902

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
                                            F      SS+  S     +         
Sbjct: 903  ------------------------------PSFHDGESSSSNFDSNTSDDEINNQPSDGS 932

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +   +   +      +    ++  K +++     +      ++ V++ +   R    GDK
Sbjct: 933  ESNED-RQIATSRSHTDKAEKNSSKKQLQVHARMEKSSLCFIQRVRIVIRHDRTPVVGDK 991

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +A RHG KGI+       DMPF   G   D+++NP   PSRM VG + E+      V   
Sbjct: 992  VASRHGQKGIMGIRWRQTDMPFTSSGIVPDLIINPHAFPSRMTVGMLIESLASKIGVHYA 1051

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
              + S    +                                               +  
Sbjct: 1052 DFVDSSPFQWSDERR------------------------------------------AVD 1069

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            VF          +L+    ++ G  ++Y  +TG+P    + +G +Y  +L HMVSDK   
Sbjct: 1070 VFG-------EQLLKTGRFNKYGSEVMYSAITGDPMPADIFIGVVYYQRLRHMVSDKYQV 1122

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            R+ G    +T+QP+ G+   GG R GEME   + A+GA   L+  L  +SD
Sbjct: 1123 RAEGPSDKITKQPIKGRKRGGGLRFGEMERDALLAHGAMASLRGRLCTESD 1173



 Score = 52.0 bits (123), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/148 (17%), Positives = 40/148 (27%), Gaps = 48/148 (32%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---AFSGAAMLEFVSYEFDPPKFDVD 89
              S++ F+                  K    I      S A  +E V+    PP F   
Sbjct: 57  HVNSFNDFIDSLNTT----------ILKHAPAIVVNLNTSKAIKVEIVNLTIKPPSFTPA 106

Query: 90  DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-------- 141
                   Y  PL +TL++     D       +       I  GD+P+M           
Sbjct: 107 FARETCANYCGPLHVTLKV----SDGPMSKTIV-------INAGDVPIMVGSKLCLLHGK 155

Query: 142 ----------------GTFVIKGIQRIV 153
                           G F+  G  ++V
Sbjct: 156 TREEKIRLREDERDAGGYFISNGQDKVV 183


>gi|126722429|dbj|BAF48628.1| DNA-dependent RNA polymerase subunit B' [Natronorubrum bangense]
          Length = 433

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 85/261 (32%), Positives = 120/261 (45%), Gaps = 58/261 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P E+MPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEEMPFTQDGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  +   L  A  + +G+ ++Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESELRGGLEDAGFNSAGKEVMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD----DVVG 1324
            A  L+E L  +SD     V G
Sbjct: 383  AMTLKERLLDESDREFIHVCG 403



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETRVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|126722439|dbj|BAF48633.1| DNA-dependent RNA polymerase subunit B' [Natrialba hulunbeirensis]
          Length = 433

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 84/253 (33%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG++  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE A+   L  A  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESALREGLEEAGFDSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    EV+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETEVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             + +       K  +    +    EL  +
Sbjct: 189 DTITLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|261327712|emb|CBH10689.1| DNA-directed RNA polymerase II subunit 2,putative [Trypanosoma brucei
            gambiense DAL972]
          Length = 1189

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 102/576 (17%), Positives = 174/576 (30%), Gaps = 110/576 (19%)

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                    F      +    + I   ++            ++       +G      ++ 
Sbjct: 700  PSEVGKNYFYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASNFNMR 759

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                             V        +    ++    + +      + AI      +  D
Sbjct: 760  M-----------DTTAHVLFYPQKPLVRTKAMSYMRSNDLPAGHNAIVAIACYSGYNQED 808

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S V         +  +   + ++    E  +I       D +   + R  Y++L
Sbjct: 809  SIIMSRSAVERGFFRSVFWRSYKASEEKKREGREMFEIP------DRKVCHVKRADYTKL 862

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G   + G     K T+     +SE       +   +D  +            
Sbjct: 863  DTDGLIKPGMPVIGGDIIVGK-TIPVPKTLSEGSPVSDTRILKRDCSISSRAA------- 914

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                        +   +           R  KV +   +    GDK   RHG KG     
Sbjct: 915  ------------EKGVVDRVMLTENKGNRFTKVRIRTIKIPNIGDKFCSRHGQKGTNGIQ 962

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  DG   D+++NP  +PSRM V  + ET  G                     
Sbjct: 963  FRQEDMPFNHDGISPDLIINPHAIPSRMTVAHLIETLAGKVAC----------------- 1005

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                +K G   +TP F     E     L
Sbjct: 1006 ------------------------------------YKGGEVYATP-FCSVVVEDFGKAL 1028

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                L+  G   LY+G TG P D  +  G  Y  +L H+ SDK++AR  G    + +QP 
Sbjct: 1029 TQLKLNRYGNERLYNGHTGLPLDHLIFFGPTYYQRLKHLSSDKIHARPRGPLQPLVRQPT 1088

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR------TRVYESIV 1333
             G+++ GG R GEME  C+ +YGA+  L+E L   SD     V             +++ 
Sbjct: 1089 EGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYSVHVCNMCGTICAADTDQNLY 1148

Query: 1334 AGN------DTFETGTPESFNVLVKEMQALGLSIDL 1363
                        +   P +  +L +E+ ++ +   L
Sbjct: 1149 KCQGCDNDSHISQVLMPYACKLLFQELMSMAILPRL 1184



 Score =  186 bits (471), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 152/1005 (15%), Positives = 298/1005 (29%), Gaps = 191/1005 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVF-P---ITAFSGAAMLEFVSYEF 81
           L+  Q  SY+ FL + I    R    L          F P   + +      L       
Sbjct: 55  LVHQQVDSYNDFL-LRIPRMARS---LLEIVPRQDDQFDPGVHVESEPDQYRLSLEDVVV 110

Query: 82  DPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
             P  +              ++C  RDLTY    ++TL + V+   E    ++     E 
Sbjct: 111 GNPSHEMSGFSRTEMHPLFPNECRLRDLTYDAVAQVTLAIRVYRSREEQPYRTFLQNME- 169

Query: 129 SIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-I 163
              +G +P+M K                         G F++ G ++++++Q  ++   +
Sbjct: 170 ---LGRIPIMLKSMRCNLLNKDEEELPRLNECPHDQGGYFIVNGTEKVLIAQERQAANHV 226

Query: 164 H-FDHDKG-----RASLSG--KLLYACRII-PDQ--GLWMDIEFDSKDIIH--VRIDRRR 210
           + F   KG     ++ + G        +I+ P +  G     E    +++    ++D   
Sbjct: 227 YAFTRPKGLLCEIKSIVEGSLNKPRTLQILMPYKKSGPGHGYE----NLLCRVAQMDEL- 281

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            +P+     AL M S+ EIL T  P +      +     +  A  +       +L  I  
Sbjct: 282 -IPLFVLFRALDMGSDKEILQTVVPDLKDVAMLEMLRGSMEDASTLEIFTRDEALWFIGK 340

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
                +S + L       L    +  +G+      G  +    +      + +   +  D
Sbjct: 341 RLGKQDSRENLQREAQDLLMRDLLPHMGVDCAADRGKCLFIGYMVHRLLLLALGRREDTD 400

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              L          +    ++        R    T  +       +  +  +    + T 
Sbjct: 401 RDFLGHKRIDVAGSLLTFQLNQFLV-QVRREMAQTVHDYSTNRGGVVSFGRILHNRLITD 459

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA--IIKILVDLR 447
            +   +    F D    ++ T     +N      +  ++R I+     +    +      
Sbjct: 460 GMRRCLATGNFGDLKSGNIKTGVSQTLNRLTYSSSLSNLRRIQNPISASSKATRPRNLHC 519

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQY------RLGLLRMERSIKERISSVD----IDS 497
              G I  ++      +  +  +             G+++  +S      S+      D 
Sbjct: 520 TQWGYICPVETPEGGSIGLLKNLALMCLVSRGSDHTGVVQAVQSRITGFHSIALSDLADV 579

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + +  +N   +            L          + ++  R +        +     + 
Sbjct: 580 RVARVFVNGTLIGVHGDPERLLRDLRARRRGGELSNEVSIVRDIRDREIRVFSDGGRCL- 638

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            R +      RI   +   G  +   ++L     ++    ++  Y           V  +
Sbjct: 639 -RPLFVVEKSRIKLQKAGIGELLEPSTTLGGRREISWNKVMKKGY-----------VELI 686

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EE++  IA   S + ++  +                        +  P  ++ I AS
Sbjct: 687 DCEEEDSLLIAMVPSEVGKNYFY---------------------SHCEMDPSMILGICAS 725

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IP+  ++ S R      M +QA+ +                                  
Sbjct: 726 IIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------------- 752

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                    S       +T+ V  Y               Q+PLV+              
Sbjct: 753 --------ASNFNMRMDTTAHVLFYP--------------QKPLVR----------TKAM 780

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 DL  G N +VA   + GYN EDS+++S   V    F S+    ++      + G
Sbjct: 781 SYMRSNDLPAGHNAIVAIACYSGYNQEDSIIMSRSAVERGFFRSVFWRSYKASEEKKREG 840

Query: 858 P---EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
               E   R + +V       +D  G+I  G  V  GDI+VGK  P    P T  E    
Sbjct: 841 REMFEIPDRKVCHVKRADYTKLDTDGLIKPGMPVIGGDIIVGKTIPV---PKTLSEGSPV 897

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           +       D   +S     GV   V+              R+I +
Sbjct: 898 SDTRILKRDCSISSRAAEKGVVDRVMLTENKGNRFTKVRIRTIKI 942


>gi|154151473|ref|YP_001405091.1| DNA-directed RNA polymerase subunit B' [Candidatus Methanoregula
            boonei 6A8]
 gi|154000025|gb|ABS56448.1| DNA-directed RNA polymerase [Methanoregula boonei 6A8]
          Length = 604

 Score =  307 bits (785), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 113/585 (19%), Positives = 194/585 (33%), Gaps = 96/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     ++L+A  P         + I   ++       +   E     R T     
Sbjct: 97   IEFVDAEEEEDLLIAMNPADITPAHTHLEIDPSLILGIGAAHVPFPEHNASPRVTMGAGM 156

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   L+  D  G   +   V             G       +  + AI   
Sbjct: 157  VKQALGFAAANMKLRP-DTRG--HMLHYVQKPLTHTQTSELIGSDDRPAGQNFVVAILSY 213

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
            +  ++ D  +   + +    +    F R    +  R    + ++IE+   D         
Sbjct: 214  EGYNIEDALIFNKASIDRG-LGRSHFFRTYEGEERRYPGGQIDRIEVPDED--------- 263

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                      + G +     K   +  V++ + I                +         
Sbjct: 264  ----------VSGAHGAESYKNLDEDGVINPETI--VAEKDVLIGKTSPPRFLEEPSGEL 311

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMP-PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +  E  +        N+   +            R+VKV     R  + GDK A RHG KG
Sbjct: 312  IAVEKRRDTSVTMRSNEHGIVDTVIITEGENSSRLVKVRTRDLRVPEIGDKFASRHGQKG 371

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  I+  EDMPF + G   D+V+NP  +PSRM +G + E   G      G++I +    
Sbjct: 372  VIGLIVNQEDMPFTESGLSPDLVINPHAIPSRMTIGHMLEMIGGKVGSLEGRRINATAFG 431

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             ++  D+      L                                      +DG     
Sbjct: 432  GESEADLRASLRKLGYSHTGREVM----------------------------YDG----- 458

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                        +G+S          F   + +G IY  KL HMVS K++ARS G   ++
Sbjct: 459  -----------YTGKS----------FKADIYIGVIYYQKLYHMVSSKMHARSRGPVQVL 497

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYE- 1330
            T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G   + + 
Sbjct: 498  TRQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLDESDKVQEYVCAHCGMVAMLDR 557

Query: 1331 ------SIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                   +  GN  D +      +F +L+ EM+++G++  L    
Sbjct: 558  KRNMTRCLACGNETDIYPVEMSYAFKLLLDEMKSMGIAPRLRLED 602



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 57/341 (16%), Positives = 108/341 (31%), Gaps = 35/341 (10%)

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V + +       +S+    +      +  L  D       +     G+ ++   +    
Sbjct: 22  LVENIRSMRRQGAISSEVNVSFKEFNGDVILLTDRGRARRPLIVLKDGKSLISEDDIKKL 81

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
                     +   LI F++ ++   +L+  N          A+     T +E   +   
Sbjct: 82  AKREIDFSSFVQRGLIEFVDAEEEEDLLIAMN---------PADITPAHTHLEIDPSLIL 132

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  I A      E   + R+ + +  G +  +         ++           Q+PL  
Sbjct: 133 G--IGAAHVPFPEHNASPRVTMGA--GMVKQALGFAAANMKLRPDTRGHMLHYVQKPL-- 186

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               D   G+N +VA + + GYN ED+++ ++  +   +  S  
Sbjct: 187 --------THTQTSELIGSDDRPAGQNFVVAILSYEGYNIEDALIFNKASIDRGLGRSHF 238

Query: 844 IEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +E   R    G  +               E  KN+DE G+I     V   D+L+GK 
Sbjct: 239 FRTYEGEERRYPGGQIDRIEVPDEDVSGAHGAESYKNLDEDGVINPETIVAEKDVLIGKT 298

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           +P         E +            RDTS+ + S   G V
Sbjct: 299 SPPRFLEEPSGELI-------AVEKRRDTSVTMRSNEHGIV 332


>gi|14591329|ref|NP_143407.1| DNA-directed RNA polymerase subunit beta [Pyrococcus horikoshii OT3]
 gi|3257974|dbj|BAA30657.1| 1117aa long hypothetical DNA-directed RNA polymerase subunit B
            [Pyrococcus horikoshii OT3]
          Length = 1117

 Score =  306 bits (784), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 87/336 (25%), Positives = 138/336 (41%), Gaps = 77/336 (22%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E    +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDM
Sbjct: 841  EKGIVDKVIITETGD-----GTKLVKVTVRDLRIPEIGDKFASRHGQKGVIGLIVPQEDM 895

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P+ + G   D+++NP G+PSRM VGQ+ E   G      G+++       +    +    
Sbjct: 896  PWTESGIVPDLIVNPHGIPSRMTVGQLLEAIGGKVAALKGRRVDGTAFIGEPEEKLRKEL 955

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
              L                                      +DG                
Sbjct: 956  EELGFKHTGREIM----------------------------YDGIT-------------- 973

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G+           F+  + +G IY  +L+HMV+DK++ARS G   ++T+QP  G++  
Sbjct: 974  --GK----------RFEADIFIGIIYYQRLHHMVADKIHARSRGPVQVLTKQPTEGRARE 1021

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG--------RTRVYESIVA 1334
            GG R GEME   +  +GAA +L E L  +SD          G        R +VY   V 
Sbjct: 1022 GGLRFGEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIAIEDKRRHKVY-CPVC 1080

Query: 1335 GND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            G +    +     +F +L+ E++A+ +   L  +  
Sbjct: 1081 GEEERISKVEMSYAFKLLLDELKAMVIRPKLNLTER 1116



 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 150/977 (15%), Positives = 294/977 (30%), Gaps = 198/977 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            GLQ        I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------ERGLQEVVDEFGGIKPDIPDFEVKFGKIRVGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + +  ++  +++              + +G+LP+M
Sbjct: 77  PHGQRKPLYPMDARIRNLTYSAPLYLEMIPVIRGIEQDPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R   
Sbjct: 127 LKSKACRLYGLSDEELIKLGEDPKDPGGYFIINGSERVIVSIEDIAPNRTLVEKDERQEK 186

Query: 175 SGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRI---DRRRKVPVTSFLMALGMDSE-E 227
                Y  ++   +      + +E     I++V I    R  K      + ALG++ + +
Sbjct: 187 -----YIAKVFSYRHGYRALVTVERKKDGILYVGIPNVPRPVKF--VYVMRALGLERDKD 239

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I+          Q         +  D         +L  I       ++ +         
Sbjct: 240 IVDAVGNDPEVQQ-----ILFDNLEDASDITTQQEALEYIGKLVAPGQAREYRLKRAEYV 294

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIRDIP 345
           +    +  +G+T +          ++  +  E+ +   D  D+     + +  +      
Sbjct: 295 IDNNLLPHMGVTPEDRIRKAYYLGMMALKVIELSLGKRDEDDKDHYANKRLRLAGDLLKD 354

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALL-DIYRVMRPG---DVSTFSVAESMFNFLFF 401
           +  V        I+  +     +  +  +  +I+R +R     DV T  +  ++    + 
Sbjct: 355 LFRVAFSQLIKDIQYQMTKTYQRRGEKYVFSNIHRFIRNSIRPDVLTERIEHALATGAWP 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                    + R      L+         + +E      + L       G I   +    
Sbjct: 415 GGRTGVSQLLDRTNYVSTLSHLRRVTSP-LDREQPHFEARDLHGTH--WGRICPTETPEG 471

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                V  +        + ++  ++ E      + S+    +   +P       +     
Sbjct: 472 PNCGLVKNLA------LMAQITTAVPEEEVREYLMSLGIVPIEVRRPSPELWRVYLNGVL 525

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +  +E+    + RI   RR   +           V+   V+        P    E     
Sbjct: 526 IGTVEDGKALVERIKKDRRSGKISDIINVAYYEDVKEVYVNSDDGRVRRPLIIVENGVPK 585

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L               I+    K  D      + YL A EEEN Y+A             
Sbjct: 586 LTKEHVQ--------AIKEGRLKWSDLVRMGVIEYLDAEEEENAYVAM------------ 625

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            ++   ++  P  ++ + ASLIP+ E++ + R   G  M +Q++
Sbjct: 626 -----------WPWEVTKEHTHLELMPAAILGLPASLIPYPEHNAAPRNTYGAGMAKQSL 674

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            L  A                                                +   +  
Sbjct: 675 GLGWANFRI-----------------------------------------RVDTRGHLLH 693

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q PLV                +    D   G+N +VA + +HGY
Sbjct: 694 YP--------------QIPLVNS----------RIMKAVGYEDRPAGQNFVVAVLAYHGY 729

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP------NVSEEGLKN 875
           N ED+++I++  +   +  S     +E   +    G  +   +IP         E+  ++
Sbjct: 730 NMEDAIIINKASIERGLARSTFFRTYEAEEKKYLGGQTDRF-EIPAPTVRGYRGEKYYRH 788

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G+I   ++V   D+L+G+ +P        EE+ L A+      + R+TS+ V    
Sbjct: 789 LDEDGLIFPESKVEGKDVLIGRTSPPRFL----EERGLGAV---SLQERRETSVAVRPSE 841

Query: 936 SGTVVDVRIFNRHGIDK 952
            G V  V I       K
Sbjct: 842 KGIVDKVIITETGDGTK 858


>gi|291196454|emb|CBG27584.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas peli]
          Length = 305

 Score =  306 bits (784), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++++  G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNNKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI+AD
Sbjct: 241 SVDASRVVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVERSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|291196460|emb|CBG27587.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           psychrotolerans]
          Length = 305

 Score =  306 bits (784), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 232/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DG  T+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRMVKDGVATDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE N  IAQA++ LDE+    +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEANHVIAQASAGLDENNRLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V + DI+AD
Sbjct: 241 SVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVAKFDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|242392258|dbj|BAH80366.1| RNA polymerase subunit B' [Halorubrum alkaliphilum]
          Length = 609

 Score =  306 bits (784), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 131/603 (21%), Positives = 207/603 (34%), Gaps = 102/603 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+  D V R  +       +  D     ++LVA            + I  ++V       
Sbjct: 90   VEFNDLVDRGYV-------EFIDAEEEEDILVAVDEEDVTEDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPEQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  D  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGGLEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 42.8 bits (99), Expect = 0.39,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + ED                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTEDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|295291785|gb|ABH04369.2| RNA polymerase beta subunit [Providencia rustigianii]
          Length = 310

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 190/309 (61%), Positives = 236/309 (76%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQAN+ L +DG F EEL+ CR  GE  L  RE+++++D S +QVVS+ ASLIPFLE+
Sbjct: 122 FIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVEYMDVSTQQVVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGGTVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+
Sbjct: 242 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGE 301

Query: 805 LALGRNMLV 813
           LALG+NM V
Sbjct: 302 LALGQNMRV 310


>gi|291196470|emb|CBG27592.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas straminea]
          Length = 305

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 235/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGQVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDVVARGDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|52694229|emb|CAG30644.1| DNA-directed RNA polymerase beta chain [Pseudomonas kilonensis]
          Length = 317

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 184/316 (58%), Positives = 240/316 (75%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 122 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 181

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 182 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 241

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPL   GD V+R
Sbjct: 242 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLGSKGDRVQR 301

Query: 791 NDIIADGPSTDLGDLA 806
           +D++ADGPSTD+G+LA
Sbjct: 302 SDVMADGPSTDMGELA 317


>gi|71028652|ref|XP_763969.1| DNA-directed RNA polymerase subunit beta [Theileria parva strain
            Muguga]
 gi|68350923|gb|EAN31686.1| DNA-directed RNA polymerase, beta subunit, putative [Theileria parva]
          Length = 1235

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 157/908 (17%), Positives = 301/908 (33%), Gaps = 133/908 (14%)

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
              L       +  IR    + I   L  L+  +G   +   +G +      ++ +   R 
Sbjct: 381  CILKESLYLSLTRIRTVYNLEINNFLNHLKGKRGFKRNYAGVG-KLENLDQDLEEEMVRK 439

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             +  +              +      ++     +   E   ++  + + + +N     +H
Sbjct: 440  FMNSVNLFNFAINKVAPEITKKVHHFLSTGNAFNTHYELNQNTGFALVLDRINYHRFSSH 499

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             R   ++ +G +       ++R +    +G ICP  T +G   GL+  L+ +A+      
Sbjct: 500  LR---SVHRGNIFMKMRSTQVRKLLGETWGFICPVHTPDGAPCGLLLHLSQYAKPVT-TP 555

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
             +  Y       + +  +++S            +++    G+    LV          +P
Sbjct: 556  NKPSYLNSIKSFLKSQPLHIS-----------GSTNKVNGGNDRIPLV-------VDGIP 597

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
               ++  D               F +   +++ L    M R        +   V + +  
Sbjct: 598  ISYVNLEDVEE------------FYDKLKTSKNLEKFGMCRHFETCAIRDKFGVFSSIY- 644

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             +    G  +   R     Q++ I  + +               +  +   ++N +    
Sbjct: 645  -IMTFPGRLVRPVRNIKDNQIELIGPITQLWSTIAINEYELNKSHNKLLDLQANPSAMNK 703

Query: 778  -QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             Q P      +    D           D+    ++  +  P+  +N     +   +M+ +
Sbjct: 704  VQVPKPLKSLKDNELDNCPVLYEYVELDMCCILSLSASLTPFSNHNQSPRNMYQCQMLKQ 763

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             V    H + +    +   L   +     P V+ +  +                      
Sbjct: 764  SVGIPFHSQFYRSEVKTYVLTSLQR----PLVATKEYEK--------------------- 798

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                 G          + AI      D+ D  +   + V   + +  I+    ID N ++
Sbjct: 799  ----MGFQDYPTGVNCVVAIIAHSGFDMEDAMILNKASVDRGLFNSFIYKSKVIDLNSQA 854

Query: 957  ISVERE--QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             S +     +E       D ++I+ +  +  L  +        G K  K S         
Sbjct: 855  SSTKERGGTVEYFNNMDKDSKLIVKKLDFDGLPRL--------GEKLTKNSPF------- 899

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR-- 1072
                     + +++      V    V+Y    +I++        +I  GD +    L+  
Sbjct: 900  ---------YRIEERGKNNIVNDKVVKYTEEPAIVDQITLVGKSEITVGDKISCPGLKHD 950

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
               + + + R    GDK A RHG KGI+S + P EDMPFL++G   D++ NP G+PSRM 
Sbjct: 951  RAIIKLRVLRSPIVGDKFASRHGQKGILSAVWPTEDMPFLENGIVPDVIFNPHGLPSRMT 1010

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G++ E   G      GK   S       + +       +E+V                 
Sbjct: 1011 IGKLIEGMAGKVASIYGKPQDSTCFQAYYSENPENGDEEMEEVDV--------------- 1055

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                    +     L  +  +  G   +Y G  G      + VG
Sbjct: 1056 -----------------------VDYFGKSLIKSGYEYYGTESMYCGTLGTEIQTHIFVG 1092

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  +L HMVSDK   RSTG    +T+QP+ G+ N GG R GEME   + A+G A +LQ
Sbjct: 1093 LIYYQRLRHMVSDKAQVRSTGPVDTITKQPVKGRKNLGGIRFGEMERDALIAHGTANLLQ 1152

Query: 1313 EMLTIKSD 1320
            + L   SD
Sbjct: 1153 DRLLHCSD 1160



 Score = 53.5 bits (127), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/132 (18%), Positives = 43/132 (32%), Gaps = 42/132 (31%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----- 139
           K           TY  PL +T  +  F+ +          I  + + +G +P+M      
Sbjct: 84  KMYPRHAKISHTTYEAPLVVTFGIKFFESES---------IITKEVPVGHIPIMVRSNRC 134

Query: 140 -------------------KDGTFVIKGIQRIVVSQLH--RS--PGIHFDHDKGRASLSG 176
                                G F+IKG ++++  QL   RS  P       K  ++   
Sbjct: 135 NLKGLSGEEMIKQGEDADEPGGYFIIKGNEKML-RQLIVPRSNYPIAF----KSDSNSQK 189

Query: 177 KLLYACRIIPDQ 188
            +L+    I  +
Sbjct: 190 NVLFTEYSIFMR 201


>gi|167525657|ref|XP_001747163.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774458|gb|EDQ88087.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1097

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 89/347 (25%), Positives = 139/347 (40%), Gaps = 72/347 (20%)

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL----RVVKVFVAMKRPIQSGD 1088
                 +K   E   +  + R+K  + K  + D +          ++K+ V   R  + GD
Sbjct: 800  NKQTPIKRGTEIDYASTQVRYKGTVGKDAYCDQVMVSSNNEDSMLIKIRVRSTRIPELGD 859

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+   I+  EDMPF   G   D ++NP G PSRM V        G      
Sbjct: 860  KFSSRHGQKGVCGLIVNQEDMPFNDAGVCPDKIMNPHGFPSRMTV--------GKLMEFC 911

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G K   L  +Y                                                 
Sbjct: 912  GAKAGVLNGNYNYGT--------------------------------------------- 926

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
              F G     + + L     +  G+  L  G+TGEP +  + +G ++  KL HMV DK++
Sbjct: 927  -AFGGTTIPEMCNTLLKHGYNYHGKDYLTSGITGEPLESYIFMGPVFYQKLKHMVMDKMH 985

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DVVGRT 1326
            ARS G  +L+T+QP  G++  GG RLGEME  C+  +G++ +L E L I SD  +V   +
Sbjct: 986  ARSQGPMTLLTRQPTEGRAREGGLRLGEMERDCLIGHGSSMLLLERLMISSDAFEVHACS 1045

Query: 1327 R----------VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +           Y     G    +   P +  +L +E+Q++ +   L
Sbjct: 1046 QCGLLGSAGWCQYCKSSRG--ISKLQLPYACKLLFQELQSMNIVPRL 1090



 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 127/976 (13%), Positives = 259/976 (26%), Gaps = 195/976 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S++HF+ ++I      N           P         + ++     PP    
Sbjct: 23  LVRQHIESFNHFIEVDIKKILAANA---KVTSDNDP------NFYVRYLDIRVLPPSINE 73

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  R  TYA  + + L    +     T       I       G +P+M
Sbjct: 74  GFKTNNTVTPMQCRLRSATYAGDIVVDLE---YRRGHETLRVENTRI-------GRMPIM 123

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDK----- 169
                                      G FV+ G +++++ Q   S       +      
Sbjct: 124 LRSNLCVLNGASHAKQAKYGECPHDPGGYFVVSGTEKVILIQEQLSKNRIIVEEFKGDLT 183

Query: 170 -GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALG-MDSE 226
               S S        II              D  ++ ++     VP+   L A+G +  +
Sbjct: 184 ASVTSSSADRKTKTTII--------F---KNDQFYMLVNTLSEAVPLVVVLKAMGVISDQ 232

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI+     +              +  ++    +             +   G K+     K
Sbjct: 233 EIMQLIGAEEEAMLVLGPSVERCANLNIFTQNQA------------LAYLGSKI-----K 275

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD--VIDEKSLEEIFHSEIRDI 344
            L+  G               V    V  E  +   +A    ++  + +  +      D 
Sbjct: 276 LLRTYGGARTKEDMGRDLLSSVVLAHVPCENFDFRAKAVFLSLMVRRVIISMGDKMTDDR 335

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
             L    +     + + L  D  K+    L     V    +      A +        + 
Sbjct: 336 DYLGNKRLELAGSLMSLLFEDTFKNFNAQLKRQADVNLSKNRVAAFDATNFMREDIITNS 395

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA---IIKILVDLRNGKGTIDDIDNLGN 461
             +  + G   +  R  ++       + +   IA   ++  +         +    +L  
Sbjct: 396 LRNAISSGNWIL-KRFKMERHGVTSVLSRLSFIASLGMMTRITSQFEKTRKVSGPRSLQP 454

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC--EFFCS 519
            +   +      +     L    ++   +++ D +  + +   N       +   E F  
Sbjct: 455 SQWGMLCPADTPEGEACGLVKNLALMTHVTNDDEEEPLVKLAYNLGVESLHLINGEEFGR 514

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S    +  +   L  +T   R+       + R+        +      R     +  G  
Sbjct: 515 SSTFLVFINGLMLG-VTRRPRIMVRNFRLLRRSGRISPFVSISLNKKHRCVYIASDAGRT 573

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKV---CDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                 + +         +E     +    D  +   V YL   EE +  +A   ++++ 
Sbjct: 574 CRPYIIVENGKSKVRPHHLEELNMGITTFDDFVINGLVEYLDVNEENDSLLALYENNIEA 633

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           D                          ++  P  ++   A LIP+  ++ S R    C M
Sbjct: 634 D-----------------------TTHLEIEPFTILGACAGLIPYPNHNQSPRNTYQCAM 670

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                          VI         + 
Sbjct: 671 GKQAMG-----------------------------------------VIALNYQQRIDTL 689

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               +Y +              RP+VK                 D   L  G+N +VA M
Sbjct: 690 LYSLVYPM--------------RPVVK----------TRTIELIDFEKLPAGQNPIVAVM 725

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            + GY+ ED+ +++           +   + +   +       +I R  P          
Sbjct: 726 SFSGYDIEDATVMNRASFDRGYGRCVVYSKMQTSLKKYNGNLTDIIRPAPRDEAGN---- 781

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR-DTSLRVPSGV 935
              GI+ VG  +   D+LV K TP                 G    D   D  +   +  
Sbjct: 782 -AKGIVAVGQPMYNRDVLVNKQTPIKRGTEIDYASTQVRYKGTVGKDAYCDQVMVSSNNE 840

Query: 936 SGTVVDVRIFNRHGID 951
              ++ +R+ +    +
Sbjct: 841 DSMLIKIRVRSTRIPE 856


>gi|51035537|emb|CAH10904.1| RNA polymerase B subunit [Haloterrigena sp. GSL-11]
          Length = 435

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L  A  D +G+  +Y G++GE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRQGLEDAGFDSAGKETMYSGISGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|225348569|gb|ACN87266.1| RNA polymerase beta subunit [Mycobacterium simulans]
          Length = 254

 Score =  306 bits (784), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 102/236 (43%), Positives = 136/236 (57%), Gaps = 37/236 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 48   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 107

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G K+ +          +       E  
Sbjct: 108  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKVDAGNGVPDWAARLPDDLLHAEPN 166

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 167  A----------------------------IVSTPVFDGAQEAELQGLLSATLPNRDGEVL 198

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPL
Sbjct: 199  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPL 254



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 56


>gi|194591885|gb|ACF76523.1| RNA polymerase beta subunit [Mycoplasma hyosynoviae]
          Length = 606

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 202/454 (44%), Positives = 296/454 (65%), Gaps = 9/454 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ I++ RR+++LG  G+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L 
Sbjct: 1   QSNPLAEISNKRRITSLGPRGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           SFA+++ YGFI+TPY KV D K+  ++  YL+A+EE    IAQ+   + ++    +E   
Sbjct: 61  SFAKIDKYGFIQTPYFKVKDRKIDFSEPKYLTAIEEMGAIIAQSTVRI-KNNMIIDEYAM 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
            R   E I V   K+D+I  S +Q+ SIAAS IPFLENDD+NR LMG NMQRQAVP++K 
Sbjct: 120 ARKDSEFIEVEASKVDYIGVSNRQMTSIAASAIPFLENDDANRALMGSNMQRQAVPIIKP 179

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE-----GDLDPSTSGVDI 761
           EAP V TG+E+ +A+ S   + +   G V  +DA +I I   +           +   ++
Sbjct: 180 EAPLVATGVEADIARYSSTNLRSTIDGTVTYIDADKIEITPDDFAETSTKSTKKSKRPEV 239

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           + L  F+RSNQ T ++Q PLVK+G ++++ D++ DGPS   G+LALG+N+LV F  WHGY
Sbjct: 240 FYLRTFERSNQGTLIHQIPLVKLGQKIQKGDLLVDGPSMKDGELALGKNVLVGFSTWHGY 299

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           N+ED++++SE++V +DV+TSIHIEE  +  R +K G + +T DIPN S    + +++ GI
Sbjct: 300 NYEDAVILSEKLVKDDVYTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKRFLNDQGI 359

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           + VG+EV  GDILVG+ +PKGE   TPEEKL+ AIF +K+   +DTSL+V  G +GTVV 
Sbjct: 360 VRVGSEVIAGDILVGRTSPKGEENPTPEEKLMAAIFSQKSSQRKDTSLKVKHGHNGTVVA 419

Query: 942 VRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
           V + +R     ++    +E+     +A+ +  + 
Sbjct: 420 VEVLSREFG--DQLEDGIEKIVKVSIAQKRKIQV 451



 Score =  298 bits (764), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 121/415 (29%), Positives = 179/415 (43%), Gaps = 67/415 (16%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +G ++  GD+LV   +   +  +   + +L         +  D  +     V   V 
Sbjct: 259  LVKLGQKIQKGDLLVDGPS-MKDGELALGKNVLVGFSTWHGYNYEDAVILSEKLVKDDV- 316

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I       +   S + E      +    +  +  L+     R+   +   + + G  
Sbjct: 317  YTSIHIEEQTIQFRHSKAGEDYLTADIPNASNFSKRFLNDQGIVRVGSEVIAGDILVGRT 376

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K     + +   +   + + Q + Q +     V+        +  +L   F       
Sbjct: 377  SPKGEENPTPE--EKLMAAIFSQKSSQRKDTSLKVKHGHNGTVVAVEVLSREF------- 427

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD +  G+ ++VKV +A KR IQ GDKMAGRHGNKG+VS +LP EDMP+L+DGTP+DI
Sbjct: 428  --GDQLEDGIEKIVKVSIAQKRKIQVGDKMAGRHGNKGVVSVVLPVEDMPYLEDGTPLDI 485

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            VLNP GVPSRMN+GQ+ E HLG A   LG K  + + D   +  I  +    +      S
Sbjct: 486  VLNPQGVPSRMNIGQVLELHLGLAAKKLGVKFVTPVFDGITHNQIKDILQEAKIDPSGKS 545

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +GQ       
Sbjct: 546  VV-----------------------------------------------YNGQ------- 551

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            TGE  D P++VG +Y LKL HMV DK+++RS G YSL+TQQPLGGKS  GGQR G
Sbjct: 552  TGEKLDAPISVGIMYYLKLYHMVDDKMHSRSVGPYSLITQQPLGGKSQNGGQRFG 606


>gi|126722419|dbj|BAF48623.1| DNA-dependent RNA polymerase subunit B' [Natrinema sp. XA3-1]
          Length = 435

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L  A  D +G+  +Y G++GE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRQGLEDAGFDSAGKETMYSGISGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|51035543|emb|CAH10907.1| RNA polymerase B subunit [Natrinema pallidum]
          Length = 435

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L  A  D +G+  +Y G++GE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRQGLEDAGFDSAGKETMYSGISGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|291196432|emb|CBG27573.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas marincola]
          Length = 305

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI+AD
Sbjct: 241 SVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVARSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|269912608|emb|CAY86084.1| RNA polymerase beta subunit [Gluconacetobacter saccharivorans]
          Length = 309

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 144/312 (46%), Positives = 195/312 (62%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL  FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGATSAAARAAKAAEGGDVEAMEIQGMDPDEILGYFYGKVEFNKTPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A     G K+   L+D  TGE+V  +  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDAE-AFRGQKLLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A D+VN  TGEIY EAG+ + E+ LEE+    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIASDMVNENTGEIYAEAGEELTEQKLEELDAEGLTTLTTLAIDATN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R++AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNASREEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKED 435
            PD VR +RKED
Sbjct: 298 VPDTVRVLRKED 309


>gi|213876733|gb|ACJ54363.1| RNA polymerase subunit B [Mycobacterium simiae]
          Length = 243

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 102/236 (43%), Positives = 137/236 (58%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPDWASN-------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +       +    VSTPVFDGA EE +  +L     +      
Sbjct: 145  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGLLGSTLPNRDGDVM 187

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQPL
Sbjct: 188  VDADGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPL 243



 Score = 44.3 bits (103), Expect = 0.14,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 48


>gi|126722447|dbj|BAF48637.1| DNA-dependent RNA polymerase subunit B' [Natronolimnobius
            innermongolicus]
          Length = 433

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 117/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L     + +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRDGLEDNGFNSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETRVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|308799767|ref|XP_003074664.1| RNA polymerase III subunit RPC2 (ISS) [Ostreococcus tauri]
 gi|116000835|emb|CAL50515.1| RNA polymerase III subunit RPC2 (ISS) [Ostreococcus tauri]
          Length = 2569

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 129/327 (39%), Gaps = 82/327 (25%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            M       +K  V   R  + GDK + RHG KG+   IL  ED PF + G   D+++NP 
Sbjct: 912  MTDEGQFNIKTLVRQTRRPEVGDKFSSRHGQKGVCGVILDQEDFPFSERGITPDLIMNPH 971

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     LG K       +                          
Sbjct: 972  GFPSRMTV--------GKMIELLGGKAGLENGRFHDGT---------------------- 1001

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G   EAI   L  A     G+ +L+ G+TGE  
Sbjct: 1002 ------------------------AFAGDSVEAIQQTLVEAGFSHKGKDMLHCGITGEAL 1037

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V +G +Y  KL HMV DK++AR+ G   ++T+QP  G++  GG RLGEME  C+  Y
Sbjct: 1038 EVNVFMGPVYYQKLKHMVQDKMHARARGPRVVLTRQPTEGRARDGGLRLGEMERDCLIGY 1097

Query: 1306 GAAYVLQEMLTIKSD-----------------DVVGRT-----RVYESIVAGNDTFETGT 1343
            GA+ ++ E L I SD                  + G+      +  E+     +      
Sbjct: 1098 GASQLILERLMISSDQFEAQVCTKCGLLGFQHHITGKNACTLCKT-EA-----EVATLKL 1151

Query: 1344 PESFNVLVKEMQALGLSIDLENSRTKN 1370
            P +  +L +E+Q+  ++  +  +  +N
Sbjct: 1152 PYAAKLLFQELQSCNIAPRINLAEARN 1178



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 121/966 (12%), Positives = 265/966 (27%), Gaps = 177/966 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPP--- 84
           L+     S+++ +   I    R         K+   +T        L++ +     P   
Sbjct: 62  LVRQHIDSFNYLVNEEIKKIVRA--------KANERVTCDSDPNFYLKYTNIHVGRPSVE 113

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIV-FDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                 +     C  RD+TYA P+ + +      ++        +  I      +G +PL
Sbjct: 114 EDYVVEEITPQQCRLRDMTYAAPITVDVEYTRGKEIVTRQQKNGVGGIV-----IGRIPL 168

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++KG++++++ Q   S       D     
Sbjct: 169 MLRSSRCVLTGKNEEELARLGECPLDPGGYFIVKGVEKVILIQEQLSKNRIII-DVDNKG 227

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-----DRRRKVPVTSFLMALGMDSEEI 228
             G  + +     ++    +I       +++R      D    + +   L A+GM+S++ 
Sbjct: 228 EIGASVTSST--HERKSKTNIVV-KHGKLYLRHNTCADD----IAIMIVLKAMGMESDQE 280

Query: 229 -LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            +        Y+        P        G       ++    +  +   +   +  +  
Sbjct: 281 AVHMIGSDPTYA----MLLAPTLQECHASGIFTMQQALEYCASKVRVVKMQSPRTQ-IGG 335

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            +  G   +    D L G+ +A   V             ++  + L  +      D    
Sbjct: 336 ARTYGRSRIDEARDILAGVVLAHVPVVAYDFRQKCAYISIMVRRILNALLDPTQVDDKDY 395

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           Y +     A     L+ +    R +A L      V+   + +T              +  
Sbjct: 396 YGNKRLELAGQLIALLFEDCFKRLNADLKRQADAVLSKANRATQFDILKCIRQDTLSNGL 455

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG----- 460
               + G   +  R  ++     + + +   I+ + ++  + +       +         
Sbjct: 456 EHAISSGNWTV-KRFRMERKGVTQVLSRLSFISALGMMTRITSQFEKTRKVSGPRALQPS 514

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              +    +  + +    +  +           +         +  +P+         S 
Sbjct: 515 QWGMLCPSDTPEGESCGLVKNLALMTHVTTDDEEEPLRRLAHALGVEPLTWLNAGEMHSP 574

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           Q + +  + + L          A     + RA    E   V+           +  G   
Sbjct: 575 QGAHVLMNGSLLGVHAQPEAF-AHAFRKLRRAGRVGEFVSVYAADG--CVYISSDGGRVC 631

Query: 581 GLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             +  +              ++  +R   D      V YL   EE + YIA         
Sbjct: 632 RPLIIIERGEPLLTQEHLEELKDGHRTFTDFLREGLVEYLDVNEENDSYIAL-------- 683

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                                E+   ++  P  ++ + A +IP+  ++ S R    C M 
Sbjct: 684 ---------------YEDEMNEETTHLEIEPFTLLGVCAGIIPYPHHNQSPRNTYQCAMG 728

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+                                           I   + +   +  
Sbjct: 729 KQAMGN-----------------------------------------IAFNQLNRMDTLM 747

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            + +Y               Q+P+VK                     L  G+N  +A M 
Sbjct: 748 YLLVYP--------------QKPIVK----------TKTIELIGYDRLGAGQNATIAVMS 783

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGL 873
           + GY+ ED+++++   +         + ++    +       +       D         
Sbjct: 784 YSGYDIEDAIVMNRASLDRGFGRCTVLRKYSTQVKKYSNRTMDRIIGPKEDQRANENGRY 843

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D  GI  VG  + PGDI V K +P            +              S + P 
Sbjct: 844 HLLDGDGIAAVGGRIKPGDIYVNKQSPINTRDPMANPHGMPDTMYRSNP----LSYKGPP 899

Query: 934 GVSGTV 939
           G +  V
Sbjct: 900 GETAIV 905


>gi|126722449|dbj|BAF48638.1| DNA-dependent RNA polymerase subunit B' [Natronolimnobius
            baerhuensis]
          Length = 435

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 117/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ +   L     + +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRDGLEDNGFNSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 74/210 (35%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +V  M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVTVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G+      V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLANPETRVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|297747842|gb|ADI52589.1| RNA polymerase beta-subunit [Yersinia massiliensis]
 gi|297747846|gb|ADI52591.1| RNA polymerase beta-subunit [Yersinia massiliensis]
 gi|297747848|gb|ADI52592.1| RNA polymerase beta-subunit [Yersinia massiliensis]
          Length = 305

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 191/304 (62%), Positives = 235/304 (77%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS
Sbjct: 62  ETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANS 121

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           +LDEDG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LM
Sbjct: 122 NLDEDGRFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALM 181

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA RIVI+  E ++
Sbjct: 182 GANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTSVAKRGGTVQYVDASRIVIKVNEDEM 241

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D++ADGPSTDLG+LALG+NM 
Sbjct: 242 YPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMR 301

Query: 813 VAFM 816
           VAFM
Sbjct: 302 VAFM 305


>gi|111054597|gb|ABH04356.1| RNA polymerase beta subunit [Providencia alcalifaciens DSM 30120]
 gi|295291783|gb|ABH04358.2| RNA polymerase beta subunit [Providencia alcalifaciens]
          Length = 310

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 190/309 (61%), Positives = 236/309 (76%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQAN+ L +DG F EEL+ CR  GE  L  RE+++++D S +QVVS+ ASLIPFLE+
Sbjct: 122 FIIAQANTVLSDDGRFIEELITCRNKGESSLFSREQVEYMDVSTQQVVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGGSVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+
Sbjct: 242 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGE 301

Query: 805 LALGRNMLV 813
           LALG+NM V
Sbjct: 302 LALGQNMRV 310


>gi|194753345|ref|XP_001958974.1| GF12287 [Drosophila ananassae]
 gi|190620272|gb|EDV35796.1| GF12287 [Drosophila ananassae]
          Length = 1137

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 98/557 (17%), Positives = 185/557 (33%), Gaps = 112/557 (20%)

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +   +V            ++       +G                +      ++      
Sbjct: 674  VCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLMYNLVYP 722

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                +    I       +   +    A+      D+ D  +   + +        ++   
Sbjct: 723  QAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNS 782

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +R  +   ++I    +D    +VI   ++      +  G+          K  ++
Sbjct: 783  KCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLDTDGIVAPGEMVQ------NKQIMI 835

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + ++ +    +     + Q       +              +    + IE++    +   
Sbjct: 836  NKEMPAVTSMNPLDGQSPQVPYTAVPIS------------YKGPEPSYIERVMVSANAEE 883

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K+ +   R  + GDK + RHG KG+   I+  EDMP+   G   D+++NP G P
Sbjct: 884  DF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVEQEDMPYNDLGICPDMIMNPHGFP 941

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM V        G     LG K   L   +                             
Sbjct: 942  SRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F G+  + I + L     +  G+   Y G+TG P +  
Sbjct: 969  ---------------------AFGGSKVQDIQAELERHGFNYMGKDFFYSGITGAPLEAY 1007

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+
Sbjct: 1008 IYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGAS 1067

Query: 1309 YVLQEMLTIKSD----DV---VGR-----------TRVYESIVAGNDTFETGTPESFNVL 1350
             ++ E L I SD    DV    GR           +  Y          +   P +  +L
Sbjct: 1068 MLIMERLMISSDAFEVDVCRTCGRLAYCSWCHFCQSSAY--------VSKISMPYACKLL 1119

Query: 1351 VKEMQALGLSIDLENSR 1367
             +E+ ++ +   +    
Sbjct: 1120 FQELTSMNVVPKMILED 1136



 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 129/993 (12%), Positives = 277/993 (27%), Gaps = 204/993 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVRAN----EMVTS-----GADPLFYLKYLDVRVGKPDIDE 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACR-IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI 228
            + + S     +   +I   G           +          +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLVISKHG---KYYLKHNSM-------TDDIPIVVIFKALGVVSDQE 257

Query: 229 L-----------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           +           + F   ++ +     +     A D M    V        T     E+ 
Sbjct: 258 IMAHIGIDSKSQNRFGASLLEAFNLKVF-TQQRALDYMGSKLVVKRFQSATTKTPAEEAR 316

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           + L + +   L    V         +    +   ++  E  +   +  D    K LE   
Sbjct: 317 ELLLTTI---LAHVPVDNFNFQMKAIYVSMMVRRVMAAELDKTLFDDRDYYGNKRLELAG 373

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+         I +  +       K A  D+ + MR   ++  +  ES  +
Sbjct: 374 SLISLMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAIS 427

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+  +   +            K+               
Sbjct: 428 SGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ-------- 479

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +    +  + +    +  +           +   ++       + +        
Sbjct: 480 -PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVEEKPVMVLAFNAGVEDIREVSGNPI 538

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  +  +  + N L    +  R        + R         VH ++  R     T  G
Sbjct: 539 NNPNVFLVFINGNVLGLTLNH-RHLVKNLRYMRRKGRMGSYVSVHTSYTQRCIYIHTDGG 597

Query: 578 HNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   +     +     ++      RK  D  +   + YL   EE + +IA      
Sbjct: 598 RLCRPYIIVEKCRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------ 651

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                + EE +             E+   ++  P  ++ + A L+P+  ++ S R    C
Sbjct: 652 -----WNEEHIE------------ERTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQC 694

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 695 AMGKQAMGMI---------GYNQKNRIDS------------------------------- 714

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N    Q P+VK                T+   L  G+N  VA
Sbjct: 715 ---------------LMYNLVYPQAPMVKS----------KTIELTNFDKLPAGQNATVA 749

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVS 869
            M + GY+ ED++++++  +       +  +  +   +       +           N  
Sbjct: 750 VMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNKV 809

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEKA 921
                 +D  GI+  G  V    I++ K  P         G+SP  P   +  +  G + 
Sbjct: 810 IFKHDVLDTDGIVAPGEMVQNKQIMINKEMPAVTSMNPLDGQSPQVPYTAVPISYKGPEP 869

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
             +    +   +     +  +    R     ++
Sbjct: 870 SYIERVMVSANAEEDFLIKILLRQTRIPEIGDK 902


>gi|81990385|sp|Q7T6X7|RPO2_MIMIV RecName: Full=DNA-directed RNA polymerase subunit 2
 gi|55664869|gb|AAQ09583.2| DNA directed RNA polymerase subunit 2 [Acanthamoeba polyphaga
            mimivirus]
          Length = 1196

 Score =  306 bits (783), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 179/1114 (16%), Positives = 343/1114 (30%), Gaps = 186/1114 (16%)

Query: 291  KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
              V+   I +    G      +       I +      +      I    I     +   
Sbjct: 209  YYVRVQSIPASQFVGNPQLFTVKMKRDNSIILSIPHFKEVSIFTFIRALGIETDEDIVDS 268

Query: 351  SVNNNA--------YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
             ++            I        +  +++AL  +   ++     T +  E         
Sbjct: 269  ILDVKKEKDLLNLLSICMNSSNTPSVTKEEALEIMANQIKSTKTFTDTNPEVKAEQRRRY 328

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPD--DVRHIRKEDIIAIIKILVDLRNGKGT--IDDIDN 458
             DK     V     +   + +        +I       +   L   R  +     DD D+
Sbjct: 329  LDKIMTQFVLPHITSGTGDPEIDKIYKAHYICYMIHKLLKCYLRGAREVEEYRGCDDRDS 388

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD---LINAKPVVSAVCE 515
            + N+R+   G +L   ++    +M     +   + +ID   P +    I    +   + +
Sbjct: 389  MVNKRIDLTGRLLGGLFKQFYDKMLNDCNKIFRTKNIDDKKPPNIIPHIKPNSIEQGLRQ 448

Query: 516  FFCSSQ--------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
               +          LSQ+   +N L  +++ RR+  +     A        R +H T YG
Sbjct: 449  ALSTGNFGSQSRKGLSQMLNRMNHLHSLSYMRRV--ITPTVDASTMKMTSPRHLHNTQYG 506

Query: 568  RICPAETSEG-HNIGLVSSLTSF--ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +CP E+ EG    GLV ++       +N    I                        E+
Sbjct: 507  SMCPLESPEGKPKTGLVKNMAMMEGITINMNSQIPII---------------------ES 545

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID-FIDASPKQVVSIAASLIPFLE 683
              I +  +    +     + V     G  + V R  I    D    +     + ++  + 
Sbjct: 546  YLIGKITTLESANKKRLHQYVKVFLNGNWLGVTRNIIKIHNDLRAMRFRGELSRMVGLVL 605

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            N  +    +  +  R   P L      +    E +   +S    +AK   ++E VD    
Sbjct: 606  NYKTAEFHIYTDGGRLIRPYLTVTDNKLNFKPEMLDEVNSWEEFLAKFPEVIEYVDKEEE 665

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +            I         +Q   +N            R D       T   
Sbjct: 666  QNIMLAVFPQYIQDANRIMSKKPINSRDQLNKIN---------RTNRYDDNVYVRYTHCE 716

Query: 804  -DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                +   ++ + +P+  +N       S R + +       +  +    R+         
Sbjct: 717  IHPCMILGLISSNIPFPDHNQ------SPRGIFQYNQARQAMGLYISDYRERTDI----- 765

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                                          IL     P   S  +          GE ++
Sbjct: 766  ----------------------------SYILYHPQIPLVTSRASKYTGTHIFPAGENSI 797

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
                +   + +     V++     +  +    R+ ++++    +       +  I  +  
Sbjct: 798  VAIASYTGLMNQEDSLVINDSAIQKGYM----RAQALKKYMEIIKKNPASSQTSIFMKPD 853

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
             +++  +          +G+ K   +  D             A +DE           QY
Sbjct: 854  RNKVDNLRDANYDKLSEEGYAKVETVIRDGDVVIGVVNPKPTAREDE----------KQY 903

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            + + SI +      ++K+    ++      ++K+ +  +R    GDK + R G KG +  
Sbjct: 904  KDASSIYKSLIPGAVDKVIT--EVNNDGYPIIKMRIRSERIPNVGDKFSSRAGQKGTIGY 961

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                 DM F K G   DI++NP  +P RM +GQ+ E  LG  C   G             
Sbjct: 962  KAHRADMLFSKSGLIPDIIINPNCMPKRMTIGQLIECLLGKLCAVKGVYGD--------- 1012

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F   D  AIN  
Sbjct: 1013 --------------------------------------------ATP-FTSVDLNAINDE 1027

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L  A  +E G   +Y+G+ G+     + +G  Y  +L  MV DK ++R+ G   L+T+Q 
Sbjct: 1028 LVAAGYEEWGNETMYNGMNGKKLPVKIFIGPTYYQRLKQMVGDKAHSRARGPTQLLTRQA 1087

Query: 1283 LGGKSNRGGQRLG-EMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRT------RV 1328
              G+S  GG R+G EME   + A+G A  L+E     SD       D  G+       + 
Sbjct: 1088 PEGRSRDGGLRIGFEMERDALCAHGVAQFLKEKTVDNSDIYTCHVCDSCGQFAHKVPEKK 1147

Query: 1329 YESIVAGND---TFETGTPESFNVLVKEMQALGL 1359
            Y +     +     +   P +F +L++E+ ++ +
Sbjct: 1148 YYTCTGCRNTTSISKIVIPYAFKLLLQELASINI 1181



 Score =  128 bits (322), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 109/770 (14%), Positives = 225/770 (29%), Gaps = 112/770 (14%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPD-ERPNEGLQAAFKSVFPITAFSGAAML 74
           FF K+ ++     L++    S++ F+   I    +  +  +         I        L
Sbjct: 27  FFEKDKQV-----LVKHHIDSFNQFIEEIIPNILQGGDNVISEKATENKII-----RYRL 76

Query: 75  EFVSYEFDPPKFDVDD-------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI-- 125
            F      PP  + ++        + + ++Y+     T+      VD  T     + I  
Sbjct: 77  TFNDLGIKPPTLENEENLLYPLDAIRKQISYSAKYTATVTQWQDIVDIDTKKTETRIIGS 136

Query: 126 KEQSIYMGDLPLMT---------------------KDGTFVIKGIQRIVV---SQLHRSP 161
            E+ + +  +P+M                        G F++ G +++V+   S + R P
Sbjct: 137 PEKDVPIAKIPIMVLSKYCNLTLRPDIAGKHCKYDAGGYFIVNGSEKVVLSVESMIPRKP 196

Query: 162 GIHFDHDKGRASLSGKLLYACRI--IP---DQGLWMDIEFDSK--DIIHVRIDRRRKVPV 214
            +    D+        LLY  R+  IP     G         K  + I + I   ++V +
Sbjct: 197 VVFTQRDQNS------LLYYVRVQSIPASQFVGNPQLFTVKMKRDNSIILSIPHFKEVSI 250

Query: 215 TSFLMALGMDSEE-----ILSTFYPKIVYSQ-------RGDFWCFPLSAADLMVGAKVSS 262
            +F+ ALG++++E     IL     K + +                  A ++M     S+
Sbjct: 251 FTFIRALGIETDEDIVDSILDVKKEKDLLNLLSICMNSSNTPSVTKEEALEIMANQIKST 310

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSL-----------KEKGVKFLGITSDCLCGLYVAED 311
                   E   E  ++    ++               E    +       +    +   
Sbjct: 311 KTFTDTNPEVKAEQRRRYLDKIMTQFVLPHITSGTGDPEIDKIYKAHYICYMIHKLLKCY 370

Query: 312 IVNGETGEIYIEAGDVIDE--KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
           +      E Y    D      K ++             Y   +N+   I  T   D  K 
Sbjct: 371 LRGAREVEEYRGCDDRDSMVNKRIDLTGRLLGGLFKQFYDKMLNDCNKIFRTKNIDDKKP 430

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
                  I   ++P  +                S K     + R+     L+       R
Sbjct: 431 PN-----IIPHIKPNSIEQGLRQALSTGNFGSQSRKGLSQMLNRMNHLHSLSYMR----R 481

Query: 430 HIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            I      + +K+     L N +            + ++             + M   I 
Sbjct: 482 VITPTVDASTMKMTSPRHLHNTQYGSMCPLESPEGKPKTGLVKNMAMMEGITINMNSQIP 541

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
              S +       +   N K +   V  F   + L      +   + +   R    L + 
Sbjct: 542 IIESYLIGKITTLES-ANKKRLHQYVKVFLNGNWLGVTRNIIKIHNDLRAMRFRGELSRM 600

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                        ++      I P  T   + +     +     VN++      + +V  
Sbjct: 601 VGLVLNYKTAEFHIYTDGGRLIRPYLTVTDNKLNFKPEM--LDEVNSWEEFLAKFPEV-- 656

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPRE 659
                 + Y+   EE+N  +A     + +             ++L               
Sbjct: 657 ------IEYVDKEEEQNIMLAVFPQYIQDANRIMSKKPINSRDQLNKINRTNRYDDNVYV 710

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           +    +  P  ++ + +S IPF +++ S R +   N  RQA+ L  ++  
Sbjct: 711 RYTHCEIHPCMILGLISSNIPFPDHNQSPRGIFQYNQARQAMGLYISDYR 760


>gi|301599273|emb|CBW31646.1| RNA polymerase subunit B [Haloferax mucosum ATCC BAA-1512]
          Length = 609

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 124/584 (21%), Positives = 203/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++ VA            + I  +++       I   E     R T      
Sbjct: 102  EFIDAEEEEDIYVAVDEDEINEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 159

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 160  MMKQSLGLPAANYRIRPDTR-QHLMHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYE 218

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+ ++D       +  
Sbjct: 219  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRG 270

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+      +++VL           +    A    + +R       
Sbjct: 271  ARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMR 330

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E+         + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 331  SGESGVVDTVTLMEGE------------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVV 378

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF  +G   D+VLNP  +PSRM V        G     LG K+ +L     
Sbjct: 379  GHLAPQEDMPFTAEGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVGALEGRRV 430

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                              F G  E+ + 
Sbjct: 431  DGT----------------------------------------------AFQGESEQELR 444

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            S L       SG+ ++Y G+TGE  +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 445  SALEDRGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTR 504

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------D-----VVGR-- 1325
            QP  G++  GG RLGEME   +  +GAA VLQE L   SD        D     V  R  
Sbjct: 505  QPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSDKESVYISADTGMVAVEDRDQ 564

Query: 1326 TRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R+Y+  V G  ++  E     +F +L+ EM ALG+   +E   
Sbjct: 565  RRIYD-PVTGDEDNIHEIEISYAFKLLLDEMVALGVRPRIELKD 607



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 121/372 (32%), Gaps = 29/372 (7%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D +     +   R  G+   +    I               +
Sbjct: 4   AQREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSIKERTREVIINADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  +D   +L   +++      L  +       +E + A+      VA     + +
Sbjct: 64  RRPLIVVEDGEPLLGDEHVEALDNDELDFDDLVERGLVEFIDAEEEEDIYVAVDEDEINE 123

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGD 786
            D   + I         +            + +     + Q           RP  +   
Sbjct: 124 -DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHL 182

Query: 787 EVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                  +    +T+     +    +N +VA M + G+N ED++++++  V   +  S  
Sbjct: 183 MHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERALARSHF 242

Query: 844 IEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+GK
Sbjct: 243 FRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDEDGLVNPETVVDENSVLLGK 301

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +P               + G      R+TS+ + SG SG V  V +       K  +  
Sbjct: 302 TSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLAKVS 355

Query: 958 SVEREQIELLAR 969
             ++   EL  +
Sbjct: 356 VRDQRVPELGDK 367



 Score = 44.3 bits (103), Expect = 0.14,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 63/195 (32%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       ++        P    
Sbjct: 11  YVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSIKERTREVIINADAGRARRPLIVV 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E         L     V A    E  +    D      V ++ A EEE+ Y+A     ++
Sbjct: 71  EDGE-----PLLGDEHVEALDNDELDF---DDLVERGLVEFIDAEEEEDIYVAVDEDEIN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 159

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 160 MMKQSLGLPAANYRI 174


>gi|209489360|gb|ACI49130.1| hypothetical protein Cbre_JD16.002 [Caenorhabditis brenneri]
          Length = 1152

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 103/504 (20%), Positives = 172/504 (34%), Gaps = 81/504 (16%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              I+ +        +    I       +      + A+      D+ D  +   + +   
Sbjct: 718  DSIMYLLCYPQRPLVKSKTIELINFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRG 777

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 ++ +H      +  +   +++   A D   ++ I+      +   +  G   +  
Sbjct: 778  YGRCLVY-KHVKGTARKYPNQTFDRLLGPALDPITKKPIMKHKNLDKEGIVFAGARILPK 836

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K   + S   +    S               +   +V Y+      +    +  E
Sbjct: 837  QTIINKHMPVVSGDNNPASASA----------NTIGIAGRQVDYKDVSVTYKTPTPSYAE 886

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++    +       + KV +   R  + GDK + RHG KG+   I   EDMPF   G   
Sbjct: 887  RVLLTYNEEEA--HLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVP 944

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM VG++ E   G A V  G              D+    +        
Sbjct: 945  DMIMNPHGYPSRMTVGKLMELLSGKAGVMNGTYHYGTAFGGDQVKDVCEELAARGYNYMG 1004

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                       ML               
Sbjct: 1005 -----------------------------------------KDMLT-------------S 1010

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TG+P    +  G IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG RLGEME
Sbjct: 1011 GITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEME 1070

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPES 1346
              C+ AYGA+ +L E L + SD    DV     V  S   G                P +
Sbjct: 1071 RDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGS--KGWCQKCRSSKSMANIKIPYA 1128

Query: 1347 FNVLVKEMQALGLSIDLENSRTKN 1370
              +L +E+Q++ +   L+ +R   
Sbjct: 1129 CKLLFQELQSMNIVPRLDLARYTE 1152



 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 133/973 (13%), Positives = 289/973 (29%), Gaps = 203/973 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+DHF+   I      N+ +          +  +    L+++      P    
Sbjct: 40  LVKQHLVSFDHFVNEEIRNIMLSNQKIT---------SDANPNFYLKYLDIRVGTPSSEE 90

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  RD+TY+ P+ + +             +  + + ++ + +G +P+
Sbjct: 91  GLNMTHDKITPQECRLRDMTYSAPISVDIEYT----------RGNQRVLKKDLIIGRMPI 140

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G FV+KG +++++ Q   S       ++    
Sbjct: 141 MLRSSKCILRDLAEEGLARVQECPYDPGGYFVVKGSEKVILIQEQLS------KNRIMVG 194

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EI 228
            +      C ++     +          K    VR ++    VPV+    A+G++S+ +I
Sbjct: 195 RNSSKELQCEVLSSTSERKSK-TYVTVKKGKYLVRHNQLTDDVPVSIIFKAMGIESDYDI 253

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +ST   +  Y             A +    +  + +       +    G    + +    
Sbjct: 254 VSTIGHEEKYVSAFAQTIEECINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLT 313

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG------DVIDEKSLEEIFHSEIR 342
             K  + +   S+ +   ++A    N +   IY+           + E  L++      +
Sbjct: 314 PPKEHEAVDFLSNSMI-THIACPDGNFKMKAIYLGQMTRRLIQTELGENELDDRDFYGNK 372

Query: 343 DIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
            +        +L+ D           +  +       A LDI + MR  D+ T ++  +M
Sbjct: 373 RLELAGSLLALLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQ-DMITNTIVNAM 431

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +   +   ++ +  +G  ++  R           +     + ++  +         +  
Sbjct: 432 -STGNWIIKRFRMERLGVTQVLSR-----------LSYISALGMMTRINSTFEKTRKVSG 479

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             +L   +   +      +     L    ++   I++   +  + + L+N+        E
Sbjct: 480 PRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGV------E 533

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              +   S + +  N+L  +      +A+    V RA   +    +              
Sbjct: 534 DLNNVHFSHINKPENTLIFLNGVLIGTAVDPERVVRAVRDLRRSGLLSEFVSVSRSITNR 593

Query: 576 EGHNIGLVSSLTSFARVNAYG----------FIETPYRKVCDGKVTNDVVYLSAMEEENR 625
                     L     +   G           ++   R   D      V YL   E  + 
Sbjct: 594 SVFISSDGGRLCRPYIIVKDGKPMLTQENVTELKEGKRIFEDFVDDGIVEYLDVNEMNDA 653

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA   + +                         +   ++  P  ++ + A LIP+  ++
Sbjct: 654 LIAVYENEIGL-----------------------ETTHLEIEPFTLLGVCAGLIPYPHHN 690

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R    C M +QA+  +                  S                      
Sbjct: 691 QSPRNTYQCAMGKQAMGTI---------AYNQQKRIDS---------------------- 719

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                                        C  QRPLVK                 +   L
Sbjct: 720 ------------------------IMYLLCYPQRPLVKS----------KTIELINFEKL 745

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI---- 861
             G N ++A M + GY+ ED++++++  +       +  +  +  AR       +     
Sbjct: 746 PAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTARKYPNQTFDRLLGP 805

Query: 862 -TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI-FGE 919
               I        KN+D+ GI+  GA + P   ++ K  P       P       I    
Sbjct: 806 ALDPITKKPIMKHKNLDKEGIVFAGARILPKQTIINKHMPVVSGDNNPASASANTIGIAG 865

Query: 920 KAVDVRDTSLRVP 932
           + VD +D S+   
Sbjct: 866 RQVDYKDVSVTYK 878


>gi|60416612|emb|CAI43375.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 313

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 189/308 (61%), Positives = 238/308 (77%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SS LSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 5   DLDTLMPQDMINAKPISAAVKEFFGSSLLSQFMDQNNPLSEITHKRRISALGPGGLTRER 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 65  AGFEVRDVHPTHYGRVCPIETPEGPNIGLLNSLSVYAQTNEYGFLETPYRKVTDGIVTDE 124

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 125 IHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 184

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G
Sbjct: 185 VGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG 244

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D+
Sbjct: 245 TVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDV 304

Query: 794 IADGPSTD 801
           +ADGPSTD
Sbjct: 305 LADGPSTD 312


>gi|213876747|gb|ACJ54370.1| RNA polymerase subunit B [Mycobacterium bolletii]
          Length = 242

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 136/236 (57%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 144  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 187  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 242



 Score = 43.5 bits (101), Expect = 0.25,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 47


>gi|169264489|gb|ACA52271.1| rpoB [Mycobacterium arosiense]
          Length = 248

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 103/235 (43%), Positives = 137/235 (58%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 46   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 105

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 106  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGTPDWAAN-------------- 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 151  -----------------LPEDLRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 193

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQP
Sbjct: 194  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQP 248



 Score = 50.8 bits (120), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/54 (64%), Positives = 45/54 (83%)

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   VTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 54


>gi|291196452|emb|CBG27583.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas panipatensis]
          Length = 305

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGLVSDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++LDE G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLDEQGRLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD + R DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVIARGDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|315259462|gb|ADT91930.1| DNA-directed RNA polymerase beta subunit [Enterococcus sulfureus]
          Length = 392

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 128/420 (30%), Positives = 177/420 (42%), Gaps = 77/420 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +  +V  GD L    +      M   + +L A    +  +  D  +     V   V 
Sbjct: 45   LVSLNEKVEAGDTLADGPS-MENGEMALGQNVLVAFMTWEGYNYEDAVIMSRRLVKDDVY 103

Query: 941  DVRIFNRHGIDKNERSISVER--EQIELLARDKD---DEQVILDRNIYSRLMEILCGQNA 995
                   +  +  +  +  E    +I  +  D     DE  I+      +  ++L G+  
Sbjct: 104  TSVHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVT 163

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G         L   +  E  R                 E                   
Sbjct: 164  PKGVTELSAEERLLHAIFGEKAR-----------------EVRDTSLRVPHGGGGIIHDV 206

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 207  KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 266

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D                 
Sbjct: 267  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA--------------- 311

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          D+ V     +        T ++DG                      
Sbjct: 312  -------------SDEDVWETVREAGMARDAKTILYDG---------------------- 336

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
                 +GEPFD  ++VG +YM+KL HMV DK++ARS G YSLVTQQPLGGK+  GGQR G
Sbjct: 337  ----RSGEPFDGRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 129/222 (58%), Positives = 164/222 (73%), Gaps = 7/222 (3%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K  GIVE VDA  I +R   G LD        Y + KF+RSN  T  NQRPLV + ++V 
Sbjct: 1   KHDGIVEYVDAKEIRVRRDNGTLD-------TYTVTKFRRSNSGTSYNQRPLVSLNEKVE 53

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
             D +ADGPS + G++ALG+N+LVAFM W GYN+ED++++S R+V +DV+TS+HIEE+E 
Sbjct: 54  AGDTLADGPSMENGEMALGQNVLVAFMTWEGYNYEDAVIMSRRLVKDDVYTSVHIEEYES 113

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            ARDTKLGPEEITR+IPNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ E
Sbjct: 114 EARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAE 173

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+LL AIFGEKA +VRDTSLRVP G  G + DV+IF R   D
Sbjct: 174 ERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKIFTREAGD 215


>gi|240103983|ref|YP_002960292.1| DNA-directed RNA polymerase subunit B [Thermococcus gammatolerans
            EJ3]
 gi|239911537|gb|ACS34428.1| DNA-directed RNA polymerase subunit B (rpoB) [Thermococcus
            gammatolerans EJ3]
          Length = 1122

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 112/586 (19%), Positives = 205/586 (34%), Gaps = 95/586 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N  VA  PW        + +    +     + +   E     R+T     
Sbjct: 614  IEYLDAEEEENAYVATWPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGM 673

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++ +D  G   +        +    +   G       +  + A+   
Sbjct: 674  AKQSLGLGWANFRIR-VDTRG--HLMHYPQVPLVNSRIMKAVGFEERPAGQNFVVAVLSY 730

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               ++ D  +   + +    +    F R    + +R +  + ++ E    D   +  + D
Sbjct: 731  GGYNMEDAIVINKASIERG-LARSTFFRTYEAEEKRYLGGQMDRFEKP--DPTIKGYLGD 787

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            R   +   + +    +    K            + E  +S     A+Q+          +
Sbjct: 788  RYYRNLDEDGIIFPESKVEGKDVLVGRTSPPRFLEE--QSGLGGIALQE----------R 835

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +   +    E    +K+   + GD       ++VKV V   R  + GDK A RHG KG+
Sbjct: 836  RETSVAVRPSEKGIVDKVIITETGD-----GTKLVKVTVRDLRIPELGDKFASRHGQKGV 890

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +  I+P EDMP+ ++G   D+++NP G+PSRM VGQ+ E   G      G+++       
Sbjct: 891  IGLIVPQEDMPWTENGIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRVDGTAFIG 950

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            +    +      L                                      +DG      
Sbjct: 951  EPEEKLRKELEELGFKHTGREVM----------------------------YDGIT---- 978

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                               G      +  + +G IY  +L+HMV+DK++ARS G   ++T
Sbjct: 979  -------------------GR---RLEADIFIGVIYYQRLHHMVADKMHARSRGPVQVLT 1016

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG-------- 1324
            +QP  G++  GG R GEME   +  +GAA +L E L  +SD          G        
Sbjct: 1017 KQPTEGRAREGGLRFGEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKR 1076

Query: 1325 RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            R +VY   V G +    +     +F +L+ E++A+ +   L+    
Sbjct: 1077 RGKVY-CPVCGEEERISKVEMSYAFKLLLDELKAMVIRPSLKLKDR 1121



 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 147/979 (15%), Positives = 289/979 (29%), Gaps = 199/979 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            GLQ        +        ++F       P F  
Sbjct: 29  LVRQHLDSYNAFI----------EHGLQEVINEFGGVKPDIPNFEVKFGKIRLGEPIFQE 78

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTY+ PL + L  +V  +++              + +G+LPLM
Sbjct: 79  AQGQRRPLYPMDARIRNLTYSAPLFLELIPVVNGIEQEPV----------EVRIGELPLM 128

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P    +        
Sbjct: 129 LKSKACRLYGLSDEELIELGEDPKDPGGYFIINGSERVIVSIEDLAP----NKTLVEKDE 184

Query: 175 SGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPV--TSFLMALG-MDSEEI 228
             K +   ++   +      + +E     I++V I    K PV     + ALG +  +EI
Sbjct: 185 RQKKV-VAKVFSYRHGYRALITVESRKDGILYVSIPNVPK-PVKFVYVMRALGLLSDKEI 242

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +          Q         +  +     +     +D      +    K+      + +
Sbjct: 243 VEAISEDPRIQQ------VLFNNLEDASDIRTQEEALDFIGRLSLPGQPKEYRLRRAEHI 296

Query: 289 KEKG-VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-----LEEIFHSEIR 342
            +   +  +G+  +          ++  +  E+ +      D+       L+        
Sbjct: 297 IDNNLLPHMGVEPENRKAKAYYLGMMALKVLELSLGLRGEDDKDHYANKRLKLAGDLLKD 356

Query: 343 DIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
              + +   V +  Y   +      +    ++    +   +RP DV +  +  ++    +
Sbjct: 357 LFRVAFGQLVKDMQYQMTKTYQRKGERYTFENIQRFVRNSVRP-DVLSERIEHALATGSW 415

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                     + R      L+         + +E      + L       G I   +   
Sbjct: 416 PGGRTGVSQLLDRTNYISTLSHLRRVTSP-LSREQPHFEARDLHGTH--WGRICPTETPE 472

Query: 461 NRRVRSVGEM-LKNQYRLGLLRME-RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                 V  + L +Q   G+   E +    ++  V I+   P               +  
Sbjct: 473 GPNCGLVKNLALMSQITTGIPEEEVKEYILKLGVVPIEERRPS--------PGLYRVYLN 524

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
              +  +E+    +  I   RR   +            ++R+++                
Sbjct: 525 GVLIGTIEDGKALVQTIRSDRRAGKISDVINVALYEEGDVREIYINS-----DDGRVRRP 579

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            I + +      R      I+       D      + YL A EEEN Y+A          
Sbjct: 580 LIIVENGRPKLTR-EHVEAIKNGTLTWSDLIRMGVIEYLDAEEEENAYVAT--------- 629

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                               E+   ++  P  ++ I ASL+P+ E++ + R   G  M +
Sbjct: 630 --------------WPWEVTEEHTHLELMPAAILGIPASLVPYPEHNAAPRNTYGAGMAK 675

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           Q++ L  A                                                +   
Sbjct: 676 QSLGLGWANFRI-----------------------------------------RVDTRGH 694

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           +  Y               Q PLV                +    +   G+N +VA + +
Sbjct: 695 LMHYP--------------QVPLVNS----------RIMKAVGFEERPAGQNFVVAVLSY 730

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGL 873
            GYN ED+++I++  +   +  S     +E   +    G  +            + +   
Sbjct: 731 GGYNMEDAIVINKASIERGLARSTFFRTYEAEEKRYLGGQMDRFEKPDPTIKGYLGDRYY 790

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +N+DE GII   ++V   D+LVG+ +P        E+  L  I  +   + R+TS+ V  
Sbjct: 791 RNLDEDGIIFPESKVEGKDVLVGRTSPPRFLE---EQSGLGGIALQ---ERRETSVAVRP 844

Query: 934 GVSGTVVDVRIFNRHGIDK 952
              G V  V I       K
Sbjct: 845 SEKGIVDKVIITETGDGTK 863


>gi|302824457|ref|XP_002993871.1| hypothetical protein SELMODRAFT_236845 [Selaginella moellendorffii]
 gi|300138238|gb|EFJ05012.1| hypothetical protein SELMODRAFT_236845 [Selaginella moellendorffii]
          Length = 1069

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 209/616 (33%), Positives = 323/616 (52%), Gaps = 20/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDR--KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D ++N  Y  N      N     + A+ + +++    D  T        +       +++
Sbjct: 185 DILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSDIFEESRQKSPQPRFE 244

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              +GR   N + + + P +   +  +D++A    L+ +  G GT+DDID+L NRR+R+V
Sbjct: 245 TGEIGRTNSNKKPDPEVPKNEIFLLPKDVLAATDYLIGIGIGIGTLDDIDHLKNRRIRTV 304

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLSQL 525
            ++L++Q RL L R+  S++  +S       +P    ++N+  +++ + EFF S  LSQ 
Sbjct: 305 ADLLQDQLRLALERLADSMRGGVSRAARRKNVPTMRSVVNSSLLLTTLKEFFGSHPLSQS 364

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N L+++ H R+LS+LG GG  R  A  ++RD+HP+HYGR  P ETSEG N GL+SS
Sbjct: 365 LDQTNPLTQMVHKRKLSSLGPGGPTRRTASYQVRDIHPSHYGRARPIETSEGTNAGLISS 424

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEE 643
           L   A VN +G++ +P+ ++         V  Y+SA +E    I     S        E+
Sbjct: 425 LALHAGVNHWGYLTSPFHRISGVLSGGGEVAAYVSAEDE-GYRITTGTCSYVYRKDRGEQ 483

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R   E + +  ++I     SP Q  S+ ASLIPFLEN+D+NR L G N QRQA PL
Sbjct: 484 ATAARYRQEFVTLAWDQIHLRSISPLQNFSVGASLIPFLENNDANRTLTGSNTQRQAAPL 543

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           L+ E   VGTG+E  +A       +A R G ++ +D  R         ++  +       
Sbjct: 544 LRTEQRIVGTGLEGQIASDPWDTAIAVRGGKIDYIDCERTTSVDDGETIETES------- 596

Query: 764 LMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            + +Q  N NT V+Q+P  +   G    +  I AD  +   G+LA GRN+ +A+MPW GY
Sbjct: 597 -VMYQSPNNNTRVHQKPAGRFGKGGFPMKGQIAADTGAAKGGELASGRNISMAYMPWEGY 655

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECG 880
           N EDS+  SER   E ++TSIHIE++E+ AR T  G  E ITR IP+  +   ++ DE G
Sbjct: 656 NSEDSVPTSERPTFEGIYTSIHIEKYEMEARVTLQGTAEIITRKIPHSDDYFPRHSDESG 715

Query: 881 IICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            +  G+ V  GD+LVGK TP+   ESP  PE    +AI G      R+T  +VP+G  G 
Sbjct: 716 PVSPGSRVETGDVLVGKPTPRNPEESPKAPESNSPQAIPGIDVTTARETCPKVPTGGRGR 775

Query: 939 VVDVRIFNRHGIDKNE 954
           ++DVR        + +
Sbjct: 776 IIDVRWIYPEDTSRYK 791



 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 113/296 (38%), Positives = 154/296 (52%), Gaps = 43/296 (14%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            RVV V+V   R +Q GDK AGRHGNKGI+ +I P +DMP+L+DGT +D++ +PLGVP RM
Sbjct: 793  RVVHVYVLQVREMQVGDKAAGRHGNKGIIPKIAPRQDMPYLQDGTSIDMIPSPLGVPPRM 852

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI E   G A   L    + +  D +   +    +S   +       T     ++  
Sbjct: 853  NVGQISERVPGPAGYNLETHHRIIPFDERYEREAPR-KSVYPETYEASEQTANPRSFE-- 909

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                LD  G+S   DG TGE  ++PVT 
Sbjct: 910  ------------------------------------LDNPGKSQPIDGRTGEASEQPVTA 933

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  +M K  H   DK++ARS+G +  VTQQPL GKS +GGQR+GEMEV   + YG +++L
Sbjct: 934  GKAHMPKSVHQADDKIHARSSGPHPRVTQQPLKGKSKQGGQRVGEMEVRASEGYGVSHIL 993

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTF----ETGTPESFNVLVKEMQALGLSIDL 1363
            QEM T+K D V  R +V  ++VAG   +    E  TPES    V+E + L   +DL
Sbjct: 994  QEMPTMKPDHVRARRKVVGTLVAGEPVYDGPAEATTPESPRSPVREPRRLAPDLDL 1049



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/326 (18%), Positives = 122/326 (37%), Gaps = 34/326 (10%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            ++  F+      +   + G++   + + P   F G        Y    P  D  D ++ 
Sbjct: 13  EAFYRFINWGSMEEPNDSPGIEDTDREMGP-RPFGGR-------YYVIEPLSDKRDAVYE 64

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
            + Y     + ++         +  K     +EQ +Y G  P  +  GT V+ GI R+ +
Sbjct: 65  PIAYPSESYVPVQ---------STRKGEAWAEEQIVYTGSTPSTSPQGTLVVNGIDRVTI 115

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           +Q+ RSPG    H K     +G  +Y    IP++G    +E D K+ I VR+ ++RK P+
Sbjct: 116 NQISRSPG---THHKMERGPNGNPVYTGTTIPNRGGKPKLEPDGKNRIWVRVRKKRKTPI 172

Query: 215 TSFLMALGMDSEEILSTFYPKIVYSQRGDF--WCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
               +A+G  +++IL        Y ++ D   W    +  +    +  +    ++     
Sbjct: 173 QPPSLAMGPSTKDILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSD--- 229

Query: 273 VIESGKKLTSGLLKSLKEKGVK------FLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           + E  ++ +        E G           +  + +    +    V   T  +      
Sbjct: 230 IFEESRQKSPQPRFETGEIGRTNSNKKPDPEVPKNEIF---LLPKDVLAATDYLIGIGIG 286

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSV 352
           +     ++ + +  IR +  L  D +
Sbjct: 287 IGTLDDIDHLKNRRIRTVADLLQDQL 312


>gi|255961294|ref|YP_003097476.1| RNA polymerase beta chain [Selaginella moellendorffii]
 gi|254941466|gb|ACT88981.1| RNA polymerase beta chain [Selaginella moellendorffii]
          Length = 1077

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 209/616 (33%), Positives = 323/616 (52%), Gaps = 20/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDR--KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D ++N  Y  N      N     + A+ + +++    D  T        +       +++
Sbjct: 193 DILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSDIFEESRQKSPQPRFE 252

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              +GR   N + + + P +   +  +D++A    L+ +  G GT+DDID+L NRR+R+V
Sbjct: 253 TGEIGRTNSNKKPDPEVPKNEIFLLPKDVLAATDYLIGIGIGIGTLDDIDHLKNRRIRTV 312

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLSQL 525
            ++L++Q RL L R+  S++  +S       +P    ++N+  +++ + EFF S  LSQ 
Sbjct: 313 ADLLQDQLRLALERLADSMRGGVSRAARRKNVPTMRSVVNSSLLLTTLKEFFGSHPLSQS 372

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N L+++ H R+LS+LG GG  R  A  ++RD+HP+HYGR  P ETSEG N GL+SS
Sbjct: 373 LDQTNPLTQMVHKRKLSSLGPGGPTRRTASYQVRDIHPSHYGRARPIETSEGTNAGLISS 432

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEE 643
           L   A VN +G++ +P+ ++         V  Y+SA +E    I     S        E+
Sbjct: 433 LALHAGVNHWGYLTSPFHRISGVLSGGGEVAAYVSAEDE-GYRITTGTCSYVYRKDRGEQ 491

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R   E + +  ++I     SP Q  S+ ASLIPFLEN+D+NR L G N QRQA PL
Sbjct: 492 ATAARYRQEFVTLAWDQIHLRSISPLQNFSVGASLIPFLENNDANRTLTGSNTQRQAAPL 551

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           L+ E   VGTG+E  +A       +A R G ++ +D  R         ++  +       
Sbjct: 552 LRTEQRIVGTGLEGQIASDPWDTAIAVRGGKIDYIDCERTTSVDDGETIETES------- 604

Query: 764 LMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            + +Q  N NT V+Q+P  +   G    +  I AD  +   G+LA GRN+ +A+MPW GY
Sbjct: 605 -VMYQSPNNNTRVHQKPAGRFGKGGFPMKGQIAADTGAAKGGELASGRNISMAYMPWEGY 663

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECG 880
           N EDS+  SER   E ++TSIHIE++E+ AR T  G  E ITR IP+  +   ++ DE G
Sbjct: 664 NSEDSVPTSERPTFEGIYTSIHIEKYEMEARVTLQGTAEIITRKIPHSDDYFPRHSDESG 723

Query: 881 IICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            +  G+ V  GD+LVGK TP+   ESP  PE    +AI G      R+T  +VP+G  G 
Sbjct: 724 PVSPGSRVETGDVLVGKPTPRNPEESPKAPESNSPQAIPGIDVTTARETCPKVPTGGRGR 783

Query: 939 VVDVRIFNRHGIDKNE 954
           ++DVR        + +
Sbjct: 784 IIDVRWIYPEDTSRYK 799



 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 113/296 (38%), Positives = 154/296 (52%), Gaps = 43/296 (14%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            RVV V+V   R +Q GDK AGRHGNKGI+ +I P +DMP+L+DGT +D++ +PLGVP RM
Sbjct: 801  RVVHVYVLQVREMQVGDKAAGRHGNKGIIPKIAPRQDMPYLQDGTSIDMIPSPLGVPPRM 860

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI E   G A   L    + +  D +   +    +S   +       T     ++  
Sbjct: 861  NVGQISERVPGPAGYNLETHHRIIPFDERYEREAPR-KSVYPETYEASEQTANPRSFE-- 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                LD  G+S   DG TGE  ++PVT 
Sbjct: 918  ------------------------------------LDNPGKSQPIDGRTGEASEQPVTA 941

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  +M K  H   DK++ARS+G +  VTQQPL GKS +GGQR+GEMEV   + YG +++L
Sbjct: 942  GKAHMPKSVHQADDKIHARSSGPHPRVTQQPLKGKSKQGGQRVGEMEVRASEGYGVSHIL 1001

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTF----ETGTPESFNVLVKEMQALGLSIDL 1363
            QEM T+K D V  R +V  ++VAG   +    E  TPES    V+E + L   +DL
Sbjct: 1002 QEMPTMKPDHVRARRKVVGTLVAGEPVYDGPAEATTPESPRSPVREPRRLAPDLDL 1057



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/326 (18%), Positives = 122/326 (37%), Gaps = 34/326 (10%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            ++  F+      +   + G++   + + P   F G        Y    P  D  D ++ 
Sbjct: 21  EAFYRFINWGSMEEPNDSPGIEDTDREMGP-RPFGGR-------YYVIEPLSDKRDAVYE 72

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
            + Y     + ++         +  K     +EQ +Y G  P  +  GT V+ GI R+ +
Sbjct: 73  PIAYPSESYVPVQ---------STRKGEAWAEEQIVYTGSTPSTSPQGTLVVNGIDRVTI 123

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           +Q+ RSPG    H K     +G  +Y    IP++G    +E D K+ I VR+ ++RK P+
Sbjct: 124 NQISRSPG---THHKMERGPNGNPVYTGTTIPNRGGKPKLEPDGKNRIWVRVRKKRKTPI 180

Query: 215 TSFLMALGMDSEEILSTFYPKIVYSQRGDF--WCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
               +A+G  +++IL        Y ++ D   W    +  +    +  +    ++     
Sbjct: 181 QPPSLAMGPSTKDILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSD--- 237

Query: 273 VIESGKKLTSGLLKSLKEKGVK------FLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           + E  ++ +        E G           +  + +    +    V   T  +      
Sbjct: 238 IFEESRQKSPQPRFETGEIGRTNSNKKPDPEVPKNEIF---LLPKDVLAATDYLIGIGIG 294

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSV 352
           +     ++ + +  IR +  L  D +
Sbjct: 295 IGTLDDIDHLKNRRIRTVADLLQDQL 320


>gi|195381659|ref|XP_002049565.1| GJ20682 [Drosophila virilis]
 gi|194144362|gb|EDW60758.1| GJ20682 [Drosophila virilis]
          Length = 1137

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 99/555 (17%), Positives = 184/555 (33%), Gaps = 108/555 (19%)

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +   +V            ++       +G                +      ++      
Sbjct: 674  VCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLMYNLVYP 722

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                +    I       +   +    A+      D+ D  +   + +        ++   
Sbjct: 723  QAPMVKSRTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNS 782

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +R  +   ++I    +D    +VI   ++               G +   K  ++
Sbjct: 783  KCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLD------TDGIVAPGEQVLNKQIMI 835

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + ++ +    +     + Q       +              +    + IE++    +   
Sbjct: 836  NKEMPAVTSINPLEGQSAQVPYTAVPIS------------YKGPEPSYIERVMVSANAEE 883

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++NP G P
Sbjct: 884  DF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPFNDFGICPDMIMNPHGFP 941

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM V        G     LG K   L   +                             
Sbjct: 942  SRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F G+    + + L     +  G+ + Y G+TG P +  
Sbjct: 969  ---------------------AFGGSKAADVQAELVRHGFNYMGKDLFYSGITGAPLEAY 1007

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+
Sbjct: 1008 IYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGAS 1067

Query: 1309 YVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPESFNVLVK 1352
             ++ E L I SD    DV    GR   Y          +        +   P +  +L +
Sbjct: 1068 MLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----HVSKISMPYACKLLFQ 1121

Query: 1353 EMQALGLSIDLENSR 1367
            E+ ++ +   L    
Sbjct: 1122 ELTSMNVVPKLILEN 1136



 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 122/948 (12%), Positives = 256/948 (27%), Gaps = 196/948 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVRAN----EIVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPISVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALG-MDSEE 227
            + + S     +  ++                 +++ +     +P+     ALG +  +E
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 228 ILSTF---------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           I+S           +   +             A D M    V              E+ +
Sbjct: 258 IMSHIGLDARSQNRFGASLLEAFNLKVFTQQRALDYMGSKLVVKRFQSATNKTPSEEARE 317

Query: 279 -KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
             LT+ L     +     +      L    V    ++        +  D    K LE   
Sbjct: 318 LLLTTILAHVPVDNFNFQMKAIYVSLMVRRVMAAELDKT----LFDDRDYYGNKRLELAG 373

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+         I +  +       K A  D+ + MR   ++     ES  +
Sbjct: 374 SLISLMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--VGLESAIS 427

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+  +   +            K+               
Sbjct: 428 SGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ-------- 479

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +    +  + +    +  +           +   +        + +        
Sbjct: 480 -PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDERPVMTLAYNAGVEDIREVSGNPI 538

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +  +  +  + N L    + R L       + R         +H ++  R     T  G
Sbjct: 539 NNPHVFLVFINGNVLGLTINHRHLVHNL-RYMRRKGRMGSFVSIHTSYTQRCIFIHTDGG 597

Query: 578 HNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   +       +      +    RK  D      + YL   EE + +IA      
Sbjct: 598 RLCRPYIIVEKSRPLVQQRHLDELLRGVRKFDDFLHDGLIEYLDVNEENDSFIA------ 651

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                             E  +       ++  P  ++ + A L+P+  ++ S R    C
Sbjct: 652 ----------------WNEEHIEPH-TTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQC 694

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 695 AMGKQAMGMI---------GYNQKNRIDS------------------------------- 714

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N    Q P+VK                T+   L  G+N  VA
Sbjct: 715 ---------------LMYNLVYPQAPMVKS----------RTIELTNFDKLPAGQNATVA 749

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVS 869
            M + GY+ ED++++++  +       +  +  +   +       +           N  
Sbjct: 750 VMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNKV 809

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                 +D  GI+  G +V    I++ K  P   S    E +  +  +
Sbjct: 810 IFKHDVLDTDGIVAPGEQVLNKQIMINKEMPAVTSINPLEGQSAQVPY 857


>gi|169264485|gb|ACA52269.1| rpoB [Mycobacterium mucogenicum]
          Length = 242

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 101/235 (42%), Positives = 132/235 (56%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 38   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 143  -----------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVM 185

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQP
Sbjct: 186  VDADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQP 240



 Score = 42.4 bits (98), Expect = 0.53,   Method: Composition-based stats.
 Identities = 31/46 (67%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 46


>gi|145341844|ref|XP_001416013.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576236|gb|ABO94305.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 1146

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 85/320 (26%), Positives = 126/320 (39%), Gaps = 82/320 (25%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            M       +K  V   R  + GDK + RHG KG+   IL  ED PF + G   D+++NP 
Sbjct: 882  MTDEGQFNIKTLVRQTRRPEVGDKFSSRHGQKGVCGIILDQEDFPFSERGITPDLIMNPH 941

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     LG K       +                          
Sbjct: 942  GFPSRMTV--------GKMIELLGGKAGLESGRFHDGT---------------------- 971

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F G   EAI   L  +     G+ +L+ G+TGE  
Sbjct: 972  ------------------------AFGGDTVEAIQQTLVESGYSYKGKDMLHCGITGEAL 1007

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V +G +Y  KL HMV DK++AR+ G   ++T+QP  G++  GG RLGEME  C+  Y
Sbjct: 1008 EVNVFMGPVYYQKLKHMVQDKMHARARGPRVVLTRQPTEGRARDGGLRLGEMERDCLIGY 1067

Query: 1306 GAAYVLQEMLTIKSD-----------------DVVGRT-----RVYESIVAGNDTFETGT 1343
            GA+ ++ E L I SD                  +  R      +  E+     +      
Sbjct: 1068 GASQLILERLMISSDQFEAQVCTKCGLLGFQHHITRRNACTLCKT-EA-----EVATLKL 1121

Query: 1344 PESFNVLVKEMQALGLSIDL 1363
            P +  +L +E+Q++ ++  L
Sbjct: 1122 PYACKLLFQELQSMNIAPRL 1141



 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 137/991 (13%), Positives = 279/991 (28%), Gaps = 229/991 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFPIT-AFSGAAMLEFVSYEFDPP- 84
           L+     S+++ +          NE ++     K+   +T        L++ +     P 
Sbjct: 34  LVRQHIDSFNYLV----------NEEIKKIIHAKANERVTCDSDPNFYLKYTNIHVGRPS 83

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +     C  RD+TYA P+ + +            AK+        + +G +P
Sbjct: 84  VEEDYVVEEITPQQCRLRDMTYAAPITVDVEYTRGKEIVTRQAKNGVG----GVVIGRIP 139

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           LM                           G F++KG++++++ Q   S            
Sbjct: 140 LMLRSSRCVLTGKNEDELARLGECPLDPGGYFIVKGVEKVILIQEQLSKN---------- 189

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-----DRRRK---------------- 211
                     RII        IE D+K  I   +     +R+ K                
Sbjct: 190 ----------RII--------IEVDAKGEIGASVTSSTHERKSKTNIVVKHGKFYLRHNT 231

Query: 212 ----VPVTSFLMALGMDSEEI-----------LSTFYPKIVYSQRGDFWCFPLSAADLMV 256
               +P+   L A+G++S++                 P +   Q    +    +      
Sbjct: 232 FADDIPIMIVLKAMGLESDQEAVQMIGSEPAYAMLLGPTLQECQAAGVFTTQQALEYCAN 291

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             +V  + +    G +     +   +  +  L    +  + +TS           I+   
Sbjct: 292 KVRVVKTHMTNRPGVRNFGRSRVDEARDI--LAGVVLAHVPVTSYDFRQKCAYISIMVRR 349

Query: 317 TGEIYIEAGDVIDEKSL-EEIFHSEIRDIPILYVDSVNN-NAYIRNTLVTDKNKDRKDAL 374
                ++   + D+     +      + I +L+ D     NA ++       +K  +   
Sbjct: 350 ILNAMLDPTQIDDKDYYGNKRLELAGQLIALLFEDCFKRLNADLKRQADAVLSKANRATQ 409

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            DI + +R   +S                 + +   V +V   +          R   + 
Sbjct: 410 FDILKCIRQDTLSNGLEHAISSGNWTVKRFRMERKGVTQVLSRLSFISALGMMTRITSQF 469

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           +    +     L+  +  +    +        + + L     +     E  ++    ++ 
Sbjct: 470 EKTRKVSGPRALQPSQWGMLCPSDTPEGESCGLVKNLALMTHVTTDDEEEPLRRLAHAL- 528

Query: 495 IDSVMPQDLINAKPVVSAV--CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
              V P   +NA  + S          S L    +           RR   +G+      
Sbjct: 529 --GVEPLTWLNAGEMHSPSGAHVLMNGSLLGVHAQPEAFSHAFRKLRRAGRIGEFVSVYT 586

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
             G        +  GR+C           L++             ++  +R   D     
Sbjct: 587 ADGCVYIS---SDGGRVCRPLIIIERGEPLLTQEHLD-------ELKDGHRTFNDFLREG 636

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V YL   EE N YIA     ++                       ++   ++  P  ++
Sbjct: 637 LVEYLDVNEENNSYIALYEDEVN-----------------------DETTHLEIEPFTLL 673

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + A +IP+  ++ S R    C M +QA+                               
Sbjct: 674 GVCAGIIPYPHHNQSPRNTYQCAMGKQAMGN----------------------------- 704

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                       I   + +   +   + +Y               Q+P+VK         
Sbjct: 705 ------------IAFNQLNRMDTLMYLLVYP--------------QKPIVK--------- 729

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G+N  +A M + GY+ ED+++++   +         + ++    +
Sbjct: 730 -TKTIELIGYDRLGAGQNATIAVMSYSGYDIEDAIVMNRASLDRGFGRCTVLRKYSAQVK 788

Query: 853 DTKLGPEE----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                  +       D           +D+ GI  VG  + PGDI V K TP        
Sbjct: 789 KYSNRTMDRIVGPKDDHRANQNSRHHLLDDDGIAAVGGRIKPGDIYVNKQTPVNTRDPMA 848

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
               +              S + P+G S  V
Sbjct: 849 NPHAMPDTMYRSNP----LSYKGPAGESAIV 875


>gi|70990294|ref|XP_749996.1| DNA-directed RNA polymerase III, beta subunit [Aspergillus fumigatus
            Af293]
 gi|66847628|gb|EAL87958.1| DNA-directed RNA polymerase III, beta subunit, putative [Aspergillus
            fumigatus Af293]
 gi|159130477|gb|EDP55590.1| DNA-directed RNA polymerase III, beta subunit, putative [Aspergillus
            fumigatus A1163]
          Length = 1200

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 106/514 (20%), Positives = 175/514 (34%), Gaps = 98/514 (19%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +   +  + A+      D+ D  +    
Sbjct: 765  QFLRIDSILYLMVYPQKPMVKSRTIELVKYDQLPAGQNAMVAVMSYSGYDIEDALVLNKG 824

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F R  +   +   +  ++++       ++   I    +         G+
Sbjct: 825  SVDRGFGRCQVF-RKYVTNLKSYSNGTKDRLNPPT--YENGAPIRKHALLEADGLAAVGE 881

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST          P          D           + Y     + +  +
Sbjct: 882  QVNAGEVYINKST----------PEQSNLSGIGSDAGRPVQYTPTPMTY----KLHDPAY 927

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+        +     ++VKV V   R  + GDK + RHG KG+V  I    DMPF  
Sbjct: 928  IDKV-----MYSVQENENQLVKVLVRQTRRPEVGDKFSSRHGQKGVVGIIADQVDMPFTD 982

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI++NP G PSRM VG++ E   G A V  G              + S +     
Sbjct: 983  SGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLAGHHGYGTCFGGTPVEEASRVLIDHG 1042

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   +                               G   EA+              
Sbjct: 1043 FSYGGKDYLTS----------------------------GITGEAL-------------- 1060

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                      PF   V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1061 ----------PF--YVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1108

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1109 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1165

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1166 ---MTIPYAAKLLIQELMSMNVTARLKLDDEFPE 1196



 Score =  202 bits (514), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 115/938 (12%), Positives = 264/938 (28%), Gaps = 192/938 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P   
Sbjct: 92  LVKQHIDSYNYFIEVQ----------LKKIVESSSTIRSDIDHTFYIKFTDIYVGSPCRA 141

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+ +    I          +  + +  + + 
Sbjct: 142 DEPQDVTPDATPSDVSPHECRLRDTTYAAPILVNFEYI----------RGRQRVTRKGVS 191

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 192 IGRMPIMLRSSKCVLANKTPSEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 251

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      II             KD ++V+ +     +P+   L
Sbjct: 252 TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDKLYVKHNVLSEDIPIVILL 300

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +E+ +      +    + DF      +  L  G       +D       I   +
Sbjct: 301 RAMGIHTEQEMLLLVAGVDSLYQDDFAINFEESIKL--GIYTQQQALDWIGARIKINRKQ 358

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
                       + +  + I+   +  +      V          A         +    
Sbjct: 359 SSYRRTHIQEAVEAIASVIISHIEVKNMNFRPKAVYV--------AHMARRVLMAKNDPS 410

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +           +         K   D  ++I +V+   + +    A ++ + 
Sbjct: 411 LVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRAEQFDAWTVMSM 470

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 471 HSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 530

Query: 458 NLGNRRVRSVGEML-KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +   +        + +++         D   P   +        +   
Sbjct: 531 GPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPIKNLVFMLGAEDIM-A 589

Query: 517 FCSSQLSQ---LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPA 572
               QL         +N        R    L     + R     E   ++  H+      
Sbjct: 590 LGGKQLYIPGSYTISINGTPIALTRRPKYFLNAFRRLRRMGRISEFVSIYINHHQCAVHI 649

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            T +G     +  + +   +     +E       +  D      V YL   EE +  IA 
Sbjct: 650 ATDDGRICRPLIVVENGRSLVKDHHLEKLRDGTMQFDDFLAQGLVEYLDVNEENDSLIAL 709

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +                        +    ++  P  V+   A LIP+  ++ S R
Sbjct: 710 YEKDIT-----------------------DTTTHLEIEPFTVLGAVAGLIPYPHHNQSPR 746

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+  + +                              ++D+I  ++    
Sbjct: 747 NTYQCAMGKQAIGAIASNQFL--------------------------RIDSILYLMVY-- 778

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                                 Q   V  R +    + V+ + + A   +          
Sbjct: 779 ---------------------PQKPMVKSRTI----ELVKYDQLPAGQNAM--------- 804

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
              VA M + GY+ ED++++++  V           ++    +    G ++        +
Sbjct: 805 ---VAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTNLKSYSNGTKDRLNPPTYEN 861

Query: 870 EEGLKN---IDECGIICVGAEVNPGDILVGKITPKGES 904
              ++    ++  G+  VG +VN G++ + K TP+  +
Sbjct: 862 GAPIRKHALLEADGLAAVGEQVNAGEVYINKSTPEQSN 899


>gi|80978851|gb|ABB54674.1| RNA polymerase beta subunit [Mycoplasma mustelae]
          Length = 593

 Score =  305 bits (782), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 203/442 (45%), Positives = 295/442 (66%), Gaps = 9/442 (2%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ +  +F
Sbjct: 2   NPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLILNFATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+V+ +GF++TPY KV +G V  N V YL+A EE+    AQ++  +DE+       +  R
Sbjct: 62  AQVDEFGFLKTPYYKVKNGIVDYNTVDYLTAAEEKGLSFAQSSVQVDENNRIITPSLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                 L   E++D+++ S KQ+VS+AA+ IPFLENDD+NR LMG NMQRQAVPL++AEA
Sbjct: 122 SDYTYRLGKPEEVDYLEVSSKQMVSVAAAGIPFLENDDANRALMGSNMQRQAVPLIQAEA 181

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P + TG+E+ +AK S   ++AK AGIV  VD  +I I+   G  D        Y L  F+
Sbjct: 182 PLIATGIEADIAKYSSYNLIAKNAGIVTAVDGSKITIKRENGVSDK-------YSLRNFE 234

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQ T V Q+P+V  G EV++ D++ DG S   G+LALG+N+LV F  W+GYNFED+++
Sbjct: 235 RSNQGTLVQQKPIVVKGQEVKQGDLLTDGSSFKDGELALGKNVLVGFTTWNGYNFEDAVI 294

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I+ER+V +DV+TSIHIEE  +  R ++ G + +T DIP +S+  ++++DE GI+ VG+EV
Sbjct: 295 INERLVKDDVYTSIHIEEQIIQFRSSRSGNDVLTVDIPQISKYSIRHLDEHGIVKVGSEV 354

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            PGD+LVG+ +PKGE     EEKLL+AI G ++   +DTSL+V +G  GTV+ V + ++ 
Sbjct: 355 LPGDVLVGRTSPKGEENPAQEEKLLQAILGSRSNGTKDTSLKVKNGHGGTVIHVEVLSKD 414

Query: 949 GID-KNERSISVEREQIELLAR 969
             D   E    + +  I    +
Sbjct: 415 NNDLLEEGVEKIVKVSIAQKRK 436



 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 122/419 (29%), Positives = 182/419 (43%), Gaps = 77/419 (18%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV- 939
            I+  G EV  GD+L    + K +  +   + +L         +  D  +     V   V 
Sbjct: 247  IVVKGQEVKQGDLLTDGSSFK-DGELALGKNVLVGFTTWNGYNFEDAVIINERLVKDDVY 305

Query: 940  ----VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
                ++ +I            ++V+  QI   +    DE  I+         ++L G+ +
Sbjct: 306  TSIHIEEQIIQFRSSRSGNDVLTVDIPQISKYSIRHLDEHGIVKVGSEVLPGDVLVGRTS 365

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G +   +   L   ++               +     V++          +L      
Sbjct: 366  PKGEENPAQEEKLLQAILGSRSNGT--------KDTSLKVKNGHGGTVIHVEVLSKDNN- 416

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                    D +  GV ++VKV +A KR I+ GDKMAGRHGNKG++S +LP EDMP+L+DG
Sbjct: 417  --------DLLEEGVEKIVKVSIAQKRKIKVGDKMAGRHGNKGVISIVLPEEDMPYLEDG 468

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TP+DI+LNP GVPSRMN+GQI E HLG A + L +K  S   D     DI          
Sbjct: 469  TPLDIMLNPQGVPSRMNIGQILELHLGMAALKLNEKFVSPSFDGVKKQDIEAAL------ 522

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                          +++ L  +E+     P++   FD                       
Sbjct: 523  --------------EEAGLDRSEKQVVIDPITGNKFD----------------------- 545

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                       +P++VG +Y++KLNHMV DK++ARS G YSL+TQQPLGGKS  GGQR 
Sbjct: 546  -----------KPISVGVMYIMKLNHMVDDKMHARSVGPYSLITQQPLGGKSQNGGQRF 593


>gi|84996561|ref|XP_953002.1| DNA-directed RNA polymerase I, second largest subunit [Theileria
            annulata strain Ankara]
 gi|65303998|emb|CAI76377.1| DNA-directed RNA polymerase I, second largest subunit, putative
            [Theileria annulata]
          Length = 1218

 Score =  305 bits (781), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 157/897 (17%), Positives = 298/897 (33%), Gaps = 133/897 (14%)

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
              IR    + I   L  L+  +G   +   +G   +    ++ +   R  +  +      
Sbjct: 401  TRIRTVYNLEINNFLSHLKGKRGFKRNFTGVGKPEI-LDQDLEEEMIRKFMNSVNLFNFA 459

Query: 489  RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
                    +      ++     +   E   S+  + + + +N     +H R   ++ +G 
Sbjct: 460  INKVAPEVTKKIHHFLSTGNAFNTHYELNQSTGFAIVLDRINYHRFSSHLR---SIHRGN 516

Query: 549  VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
            +       ++R +    +G ICP  T +G   GL+  L+ +A                  
Sbjct: 517  IFMKMRSTQVRKLLGETWGFICPVHTPDGAPCGLLLHLSQYA---------------KAV 561

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
               N   YL++++   +     +  L   GS     V        ++V    + ++D   
Sbjct: 562  TTPNKPSYLNSIKSFLK-----SQRLHNTGST--NKVNGGNDRIPLVVDGIPVAYVDVEE 614

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             +          F +   + + L    M +        +   V + +   +    G  + 
Sbjct: 615  VEE---------FYDKLRTAKNLEKFGMCKHFETCAMRDKFGVFSSIY--IMTFPGRLVR 663

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN-QRPLVKVGDE 787
              R     Q++ I  + +               +  +   +SN +     Q P V    +
Sbjct: 664  PVRNIKDNQIELIGPITQLWSTIAINEYELNKSHNKLLSLQSNPSAMNKVQVPKVVKSLK 723

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                D           D+    ++  +  P+  +N     +   +M+ + V    H + +
Sbjct: 724  DNELDNCPVLYEYVELDMCCILSLSASLTPFSNHNQSPRNMYQCQMLKQSVGIPFHSQFY 783

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                +   L   +     P V+ +  +                           G     
Sbjct: 784  RSEVKTYVLTSLQR----PLVATKEYEK-------------------------MGFQDYP 814

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE--QIE 965
                 + AI      D+ D  +   + V   + +  I+    +D N +  S +     +E
Sbjct: 815  TGVNCVVAIIAHSGFDMEDAMILNKASVDRGLFNSFIYKSKVVDLNSQYSSNKERGGTVE 874

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
                   D ++I+ +  +  L  +        G K  K S                  + 
Sbjct: 875  YFNNMDKDSKLIVKKLDFDGLPRL--------GEKLTKNSPF----------------YR 910

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR--VVKVFVAMKRP 1083
            ++++     +    V+Y    +I++         +  GD +    L+     + + + R 
Sbjct: 911  IEEKGKNNIMNDRVVKYTDEPAIVDQITLVGKSDLTVGDKISCPGLKHDRAIIKLRVLRS 970

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
               GDK A RHG KGI+S + P EDMPFL++G   D++ NP G+PSRM +G++ E   G 
Sbjct: 971  PIVGDKFASRHGQKGILSAVWPTEDMPFLENGIVPDVIFNPHGLPSRMTIGKLIEGMAGK 1030

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                 GK   S       + +       +E+V                            
Sbjct: 1031 VASIYGKPQDSTCFQTYYSENNDKGNEEMEEVDV-------------------------- 1064

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                         +     L  A  +  G   +Y G  G      + VG IY  +L HMV
Sbjct: 1065 ------------VDYFGKSLISAGYEYYGTESMYCGTLGTEIQTHIFVGLIYYQRLRHMV 1112

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            SDK   R+TG    +T+QP+ G+ N GG R GEME   + A+G A +LQ+ L   SD
Sbjct: 1113 SDKAQVRATGPVDTITKQPVKGRKNLGGIRFGEMERDALIAHGTANLLQDRLLHCSD 1169



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 98/875 (11%), Positives = 235/875 (26%), Gaps = 113/875 (12%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----- 139
           K           TY  PL +T  +  F+ +          I  + + +G +P+M      
Sbjct: 84  KMYPRHAKTTHTTYEAPLIVTFGVKFFESES---------IITKEVPVGHIPIMVRSNRC 134

Query: 140 ----------------------------KDGTFVIKGIQRIVVSQLH--RS--PGIHFDH 167
                                         G F+I+G ++++  QL   RS  P      
Sbjct: 135 NLKVKFVDKKFTGLSGEEMIKQGEDLDEPGGYFIIRGNEKMI-RQLIVPRSNYPIAF--- 190

Query: 168 DKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDS- 225
            K  ++    +L+    I  +    +D      + +H+ I++R           +  +S 
Sbjct: 191 -KSESNSQKNVLFTEYSIFMRCQSDLD-GTCVSNYLHLTINKR------CMFRVIVRNSV 242

Query: 226 -EEILSTFYPKIVYSQRGDFWCFPLSA---ADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
               L      ++     D +   L      +  +        +D+   + V+     + 
Sbjct: 243 VLVPLFLLLRALLPLISEDEFKRKLLENCSNNQEMTILYHRIFLDMAQCDPVLSDIDFIQ 302

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           +  L  L +       ++     G    E   +     + I A   +D+        +++
Sbjct: 303 NRYLYRLGKACWN--QVSQYLHPGSTFEECAQHLIKYFVIIHAKSNLDKFRTLLFMFNKL 360

Query: 342 RDIPILYVDSVNNNAY----------IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            ++    + S + +++            + ++ +        +  +Y +     +S    
Sbjct: 361 VNLSNGNIQSESYDSFAFQEIMLAGQSYSCILKESLYLCLTRIRTVYNLEINNFLSHLKG 420

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
                           L      +M  +           I K       KI   L  G  
Sbjct: 421 KRGFKRNFTGVGKPEILDQDLEEEMIRKFMNSVNLFNFAINKVAPEVTKKIHHFLSTGNA 480

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
                +   +     V + +        LR        +                  +  
Sbjct: 481 FNTHYELNQSTGFAIVLDRINYHRFSSHLRSIHRGNIFMKMRSTQVRKL-LGETWGFICP 539

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                     L              +           +   ++ ++ + +H T       
Sbjct: 540 VHTPDGAPCGLLLHLSQYAKAVTTPNK-------PSYLNSIKSFLKSQRLHNT-GSTNKV 591

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV----VYLSAMEEENRYI 627
              ++   + +     ++  V     +E  Y K+   K          + +    +   +
Sbjct: 592 NGGNDRIPLVVDGIPVAYVDVE---EVEEFYDKLRTAKNLEKFGMCKHFETCAMRDKFGV 648

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
             ++  +          V      +  L+                 +  S    L    +
Sbjct: 649 -FSSIYIMTFPGRLVRPVRNIKDNQIELIGP-ITQLWSTIAINEYELNKSHNKLLSLQSN 706

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
              +    + +    L   E        E V        I++  A +    +  +     
Sbjct: 707 PSAMNKVQVPKVVKSLKDNELDNCPVLYEYVELDMC--CILSLSASLTPFSNHNQSPRNM 764

Query: 748 VEGDLDPSTSGVDIY-RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +  +   + G+  + +  + +         QRPLV   +                 D  
Sbjct: 765 YQCQMLKQSVGIPFHSQFYRSEVKTYVLTSLQRPLVATKEY----------EKMGFQDYP 814

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA------RDTKLGPEE 860
            G N +VA +   G++ ED+M++++  V   +F S   +   V           + G  E
Sbjct: 815 TGVNCVVAIIAHSGFDMEDAMILNKASVDRGLFNSFIYKSKVVDLNSQYSSNKERGGTVE 874

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
              ++   S+  +K +D  G+  +G ++       
Sbjct: 875 YFNNMDKDSKLIVKKLDFDGLPRLGEKLTKNSPFY 909


>gi|296399256|gb|ADH10431.1| RNA polymerase beta subunit [Selaginella moellendorffii]
          Length = 1077

 Score =  305 bits (781), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 209/616 (33%), Positives = 323/616 (52%), Gaps = 20/616 (3%)

Query: 350 DSVNNNAYIRNTLVTDKNKDR--KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D ++N  Y  N      N     + A+ + +++    D  T        +       +++
Sbjct: 193 DILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSDIFEESRQKSPQPRFE 252

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              +GR   N + + + P +   +  +D++A    L+ +  G GT+DDID+L NRR+R+V
Sbjct: 253 TGEIGRTNSNKKPDPEVPKNEIFLLPKDVLAATDYLIGIGIGIGTLDDIDHLKNRRIRTV 312

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ--DLINAKPVVSAVCEFFCSSQLSQL 525
            ++L++Q RL L R+  S++  +S       +P    ++N+  +++ + EFF S  LSQ 
Sbjct: 313 ADLLQDQLRLALERLADSMRGGVSRAARRKNVPTMRSVVNSSLLLTTLKEFFGSHPLSQS 372

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N L+++ H R+LS+LG GG  R  A  ++RD+HP+HYGR  P ETSEG N GL+SS
Sbjct: 373 LDQTNPLTQMVHKRKLSSLGPGGPTRRTASYQVRDIHPSHYGRARPIETSEGTNAGLISS 432

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVV--YLSAMEEENRYIAQANSSLDEDGSFTEE 643
           L   A VN +G++ +P+ ++         V  Y+SA +E    I     S        E+
Sbjct: 433 LALHAGVNHWGYLTSPFHRISGVLSGGGEVAAYVSAEDE-GYRITTGTCSYVYRKDRGEQ 491

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R   E + +  ++I     SP Q  S+ ASLIPFLEN+D+NR L G N QRQA PL
Sbjct: 492 ATAARYRQEFVTLAWDQIHLRSISPLQNFSVGASLIPFLENNDANRTLTGSNTQRQAAPL 551

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           L+ E   VGTG+E  +A       +A R G ++ +D  R         ++  +       
Sbjct: 552 LRTEQRIVGTGLEGQIASDPWDTAIAVRGGKIDYIDCERTTSVDDGETIETES------- 604

Query: 764 LMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            + +Q  N NT V+Q+P  +   G    +  I AD  +   G+LA GRN+ +A+MPW GY
Sbjct: 605 -VMYQSPNNNTRVHQKPAGRFGKGGFPMKGQIAADTGAAKGGELASGRNISMAYMPWEGY 663

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNIDECG 880
           N EDS+  SER   E ++TSIHIE++E+ AR T  G  E ITR IP+  +   ++ DE G
Sbjct: 664 NSEDSVPTSERPTFEGIYTSIHIEKYEMEARVTLQGTAEIITRKIPHSDDYFPRHSDESG 723

Query: 881 IICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            +  G+ V  GD+LVGK TP+   ESP  PE    +AI G      R+T  +VP+G  G 
Sbjct: 724 PVSPGSRVETGDVLVGKPTPRNPEESPKAPESNSPQAIPGIDVTTARETCPKVPTGGRGR 783

Query: 939 VVDVRIFNRHGIDKNE 954
           ++DVR        + +
Sbjct: 784 IIDVRWIYPEDTSRYK 799



 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 113/296 (38%), Positives = 154/296 (52%), Gaps = 43/296 (14%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            RVV V+V   R +Q GDK AGRHGNKGI+ +I P +DMP+L+DGT +D++ +PLGVP RM
Sbjct: 801  RVVHVYVLQVREMQVGDKAAGRHGNKGIIPKIAPRQDMPYLQDGTSIDMIPSPLGVPPRM 860

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
            NVGQI E   G A   L    + +  D +   +    +S   +       T     ++  
Sbjct: 861  NVGQISERVPGPAGYNLETHHRIIPFDERYEREAPR-KSVYPETYEASEQTANPRSFE-- 917

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                LD  G+S   DG TGE  ++PVT 
Sbjct: 918  ------------------------------------LDNPGKSQPIDGRTGEASEQPVTA 941

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G  +M K  H   DK++ARS+G +  VTQQPL GKS +GGQR+GEMEV   + YG +++L
Sbjct: 942  GKAHMPKSVHQADDKIHARSSGPHPRVTQQPLKGKSKQGGQRVGEMEVRASEGYGVSHIL 1001

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTF----ETGTPESFNVLVKEMQALGLSIDL 1363
            QEM T+K D V  R +V  ++VAG   +    E  TPES    V+E + L   +DL
Sbjct: 1002 QEMPTMKPDHVRARRKVVGTLVAGEPVYDGPAEATTPESPRSPVREPRRLAPDLDL 1057



 Score =  120 bits (301), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/326 (18%), Positives = 122/326 (37%), Gaps = 34/326 (10%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
            ++  F+      +   + G++   + + P   F G        Y    P  D  D ++ 
Sbjct: 21  EAFYRFINWGSMEEPNDSPGIEDTDREMGP-RPFGGR-------YYVIEPLSDKRDAVYE 72

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
            + Y     + ++         +  K     +EQ +Y G  P  +  GT V+ GI R+ +
Sbjct: 73  PIAYPSESYVPVQ---------STRKGEAWAEEQIVYTGSTPSTSPQGTLVVNGIDRVTI 123

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           +Q+ RSPG    H K     +G  +Y    IP++G    +E D K+ I VR+ ++RK P+
Sbjct: 124 NQISRSPG---THHKMERGPNGNPVYTGTTIPNRGGKPKLEPDGKNRIWVRVRKKRKTPI 180

Query: 215 TSFLMALGMDSEEILSTFYPKIVYSQRGDF--WCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
               +A+G  +++IL        Y ++ D   W    +  +    +  +    ++     
Sbjct: 181 QPPSLAMGPSTKDILDNVCYPDNYWEKKDNNVWSREHAVPESHKLSYGTDEYTELSD--- 237

Query: 273 VIESGKKLTSGLLKSLKEKGVK------FLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           + E  ++ +        E G           +  + +    +    V   T  +      
Sbjct: 238 IFEESRQKSPQPRFETGEIGRTNSNKKPDPEVPKNEIF---LLPKDVLAATDYLIGIGIG 294

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSV 352
           +     ++ + +  IR +  L  D +
Sbjct: 295 IGTLDDIDHLKNRRIRTVADLLQDQL 320


>gi|291196426|emb|CBG27570.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas knackmussii]
          Length = 305

 Score =  305 bits (781), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 184/305 (60%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+V++D+V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKEGQVSDDIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++LDE G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATLDEQGRLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD + R DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVIARGDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|322823745|gb|EFZ29414.1| DNA-directed RNA polymerase III subunit, putative [Trypanosoma cruzi]
          Length = 1186

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 100/580 (17%), Positives = 175/580 (30%), Gaps = 114/580 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            + +       +      +    + I   ++            ++       +G      +
Sbjct: 695  MTMTEVSKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASNFN 754

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +                  V        +    ++    + +      + AI      + 
Sbjct: 755  MRM-----------DTTAHVLFYPQKPLVRTKAMSYMRSNDLPAGHNAVVAIACYSGYNQ 803

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S V         + R      ER     ++ +     + D +   + R  Y+
Sbjct: 804  EDSIIMSRSAVERGFFRSAFW-RSYKATEER-----KKDVRETFENPDRKICRVKRADYT 857

Query: 985  RL---MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L     I  G   + G     K+  +S   +                            
Sbjct: 858  KLDADGLIKPGMPVIGGDILVGKTIPISEAKLENAALDDTRLL----------------- 900

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                +        ++   ++          R  KV +   +    GDK   RHG KG   
Sbjct: 901  ---KRDCSIASRTSEKGVVERVMLTENSGNRFTKVKIRTIKIPNIGDKFCSRHGQKGTNG 957

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF +DG   D+++NP  +PSRM V  + ET  G                   
Sbjct: 958  IQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVAC--------------- 1002

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                  +K     +TP F     E    
Sbjct: 1003 --------------------------------------YKGSEVYATP-FCSVVVEDFGK 1023

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L        G   LY+G TG P D  +  G  Y  +L H+  DK++AR  G    + +Q
Sbjct: 1024 ALHQLKFQRYGNECLYNGHTGSPLDHLIFFGPTYYQRLKHLSGDKIHARPRGPLQPLVRQ 1083

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTR 1327
            P  G+++ GG R GEME  C+ +YGA+  L+E L   SD       ++ G          
Sbjct: 1084 PTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYSVHVCNICGTICAADTEQN 1143

Query: 1328 VYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
            VY+    G        +T  P +  +L +E+ ++ +   L
Sbjct: 1144 VYKC--QGCDNDTRISQTLMPYACKLLFQELMSMAILPRL 1181



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 156/1011 (15%), Positives = 294/1011 (29%), Gaps = 203/1011 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS-----------GAAMLEFV 77
           L+  Q  SY+ FL + I    R           V P                    L   
Sbjct: 52  LVHQQIDSYNDFL-LRIPRMARS-------LLEVVPRQDEQFEPGTQTETEPDQYRLSLE 103

Query: 78  SYEFDPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                 P  +              ++C  RDLTY    ++TL + V+   E    ++   
Sbjct: 104 DVVIGNPSHEVSGFSRHEMHPLFPNECRLRDLTYDANAQVTLGIRVYRSREEQPYRTFLQ 163

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRS 160
             E    +G +P+M K                         G FVI G ++++++Q  ++
Sbjct: 164 NME----LGRIPIMLKSMRCNLQNKDEDELPRLNECPHDQGGYFVISGTEKVLIAQERQA 219

Query: 161 PG-IH-FDHDKG-----RASLSG--KLLYACRII-PD--QGLWMDIEFDSKDIIH--VRI 206
              ++ F   KG     ++ + G        +I+ P   +G     E    +++    ++
Sbjct: 220 ANHVYAFSRQKGLLCEIKSIVEGSLNKPRTLQILMPYKKKGPGHGYE----NLLCRVAQM 275

Query: 207 DRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           D    +P+     AL M S+ EIL T  P +  +   +     +  A  +       +L 
Sbjct: 276 DEL--IPLFVLFRALDMGSDKEILQTVVPDLKDAAMLEMLRGSMEDASTLQIFTRDEALW 333

Query: 266 DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
            I       +S + L       L    +  +G+         +    +      + +   
Sbjct: 334 FIGKRLGKQDSRENLQRDAQGLLMRDLLPHMGVDCAADRSKCLFIGYMVHRLLLLALGRR 393

Query: 326 DVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           +  D   L  + I  +       L    V     +  T+            +  +  +  
Sbjct: 394 EDTDRDFLGHKRIDVAGALLTFQLNQFLVQVRKEMVKTVHDYSTNRGG---VVSFGRILH 450

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA--IIK 441
             + T  +   +    F D    ++ T     +N      +  ++R I+     +    K
Sbjct: 451 SRLITDGLRRCLATGNFGDMKSGNIKTGVAQTLNRLTYSSSLSNLRRIQNPISASSKATK 510

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY------RLGLLRMERSIKERISSVD- 494
                    G I  ++      +  +  +             G+++  ++      S+D 
Sbjct: 511 PRNLHCTQWGYICPVETPEGGSIGLLKNLALMCLISRGSDHTGVVQAVQARITGFHSIDL 570

Query: 495 ---IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
               D  + +  +N   +           +L          + ++  R +        + 
Sbjct: 571 PGLADVRVARVFVNGTLIGVHRDPERLLRELRARRRGGELSNEVSIVRDIRDREIRVFSD 630

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
               +  R +      RI   +T  G  +    +L     ++    I+  Y         
Sbjct: 631 GGRCL--RPLFVVERSRIKLQKTGIGELLEPSKTLGGKREISWNRIIKKGY--------- 679

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  +   EE++  IA   + + ++  +                        +  P  +
Sbjct: 680 --VELIDCEEEDSLLIAMTMTEVSKNYYY---------------------SHCEMDPSMI 716

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IP+  ++ S R      M +QA+ +                            
Sbjct: 717 LGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------- 749

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                          S       +T+ V  Y               Q+PLV+        
Sbjct: 750 --------------ASNFNMRMDTTAHVLFYP--------------QKPLVR-------- 773

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       DL  G N +VA   + GYN EDS+++S   V    F S     ++   
Sbjct: 774 --TKAMSYMRSNDLPAGHNAVVAIACYSGYNQEDSIIMSRSAVERGFFRSAFWRSYKATE 831

Query: 852 RDTKLGPEEITRD---IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
              K   E        I  V       +D  G+I  G  V  GDILVGK  P  E+ +  
Sbjct: 832 ERKKDVRETFENPDRKICRVKRADYTKLDADGLIKPGMPVIGGDILVGKTIPISEAKL-- 889

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            E            D    S     GV   V+              R+I +
Sbjct: 890 -ENAALDDTRLLKRDCSIASRTSEKGVVERVMLTENSGNRFTKVKIRTIKI 939


>gi|299013525|gb|ADJ00326.1| RNA polymerase subunit B [Mycobacterium elephantis]
          Length = 234

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 107/236 (45%), Positives = 141/236 (59%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G K++                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWAA-HSGWKVEGKP------------------- 130

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                    + +    D +L           VSTPVFDGA  E +  +L            
Sbjct: 131  --------EWASQLPDDLLEAEPN----TIVSTPVFDGATGEELQGLLGSTLPNRDGEKL 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +D  G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQPL
Sbjct: 179  VDSDGKAMLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQPL 234


>gi|159117422|ref|XP_001708931.1| DNA-directed RNA polymerase subunit B [Giardia lamblia ATCC 50803]
 gi|157437045|gb|EDO81257.1| DNA-directed RNA polymerase subunit B [Giardia lamblia ATCC 50803]
          Length = 1235

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 156/997 (15%), Positives = 291/997 (29%), Gaps = 163/997 (16%)

Query: 371  KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG--RVKMNMRLNLDTPDDV 428
            +  L D ++       +   +    F  +    D+YDL+ V    +     L ++ P + 
Sbjct: 292  EAMLRDFHKYRIFSHKACKQLLGGKFRMILSLLDRYDLTDVDCCDLLFEQYLLINIPKED 351

Query: 429  RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               +   +  + +  + L       D  D L ++   + G   K +    L+++ R +  
Sbjct: 352  TRAKFNMMCLMARKCLLLFGSFIKPDSPDLLSSQEALTPGAFFKAEVTSTLIKIMRLVSR 411

Query: 489  RISSV--DIDSVMPQDLINAKPVVSAVCEFFCS----------------------SQLSQ 524
              +S        +    I+       +     S                      S LS 
Sbjct: 412  NATSTGAIGSYELSNSWISHYIASPKLWRPLSSGLRSLAGPGVMRAYKGHDYSNMSGLSV 471

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            L + +N +  + H R    + +G          +R ++P  YG  C   T +G   G+++
Sbjct: 472  LADRINYVRFLAHFR---CINRGNAFATHKITSIRKLYPESYGFQCAVHTPDGAPCGILT 528

Query: 585  SLTSFARV--------------------NAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             L   A V                         +   Y        T  + YL   E   
Sbjct: 529  HLCYKATVLSSTPTTDQIANLFILLAQFGLSPSLSDIYSLCVVLNGT-ILGYLDTNERAI 587

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            + +A                V         +V  EK +     P   ++ +        +
Sbjct: 588  QLVA----------CIRAAKVKSIIFPYTEVVFIEKGNKDHLFPGIYMNTSMGRFYRPVH 637

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
              +N          Q    +      V  G+     + +  ++++    +V   D  +  
Sbjct: 638  SLTNNSPEYITPLEQIFLQIAIYGDDVRLGVT-THQEITPTSLLSILGLLVPFSDHNQSP 696

Query: 745  IRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                E  +   T G+       K+   +      Q+PLV+                    
Sbjct: 697  RNMYECQMLKQTMGIPCRNLAYKYDTKSYLLTTPQKPLVRNAIIHDIG---------GFD 747

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                G N++VA   +  Y+ ED+ LI++  +   +F        ++   D KL     T 
Sbjct: 748  THPTGTNLVVAVSAYTSYDMEDAALINKASLERGLFHGTVYSVHDIDCYDDKLMRYMRTV 807

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             I+         D  + +              +    +      
Sbjct: 808  ATAV----PYLKRSPDYIVT--HMDENYDTELDEDGLPPVGAYLSHGSVFYQTYDPTKQC 861

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
                      G    V+                                    I      
Sbjct: 862  YSTKLYHHEPGFVEKVIV-----------------------------------IHKSAAK 886

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                              F      SS+L ++    +         +   + ++   +  
Sbjct: 887  GEYWTDNDIATKKKRDSSFPAGDSNSSNLDNDASDDEISNQPGSGSESNEDNQTATPRSH 946

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             SK+  +   + +         +    ++ V++ +   R    GDK+A RHG KGI+   
Sbjct: 947  ASKAERKSSRQLQTRARTESSSL--HFIQRVRIVIRHDRTPVVGDKVASRHGQKGIMGIR 1004

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
                DMPF   G   D+++NP   PSRM VG + E+      V     + S    +    
Sbjct: 1005 WRQTDMPFTSSGIVPDLIINPHAFPSRMTVGMLIESLASKIGVHYADFVDSSPFQWSDER 1064

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +  VF          +L
Sbjct: 1065 R------------------------------------------AIDVFG-------EQLL 1075

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +    +  G  ++Y  +TG+P    + +G +Y  +L HMVSDK   R+ G    +T+QP+
Sbjct: 1076 KTGQFNRYGSEVMYSAITGDPMPADIFIGVVYYQRLRHMVSDKYQVRAEGPSDKITKQPI 1135

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G+   GG R GEME   + A+GA   L+  L  +SD
Sbjct: 1136 KGRKRGGGLRFGEMERDALLAHGAMASLRGRLCTESD 1172



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 40/145 (27%), Gaps = 42/145 (28%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCL 92
              S++ F+        +    +           + S A  +E V+    PP F      
Sbjct: 57  HVNSFNDFIDSLNTTIIKHAPAI--VIN-----LSTSKAIKVEIVNLTIKPPSFTPAFAR 109

Query: 93  WRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD----------- 141
                Y  PL +TL++        +    I          GD+P+M              
Sbjct: 110 ETRANYCGPLHVTLKVS---DGPMSKTVVINA--------GDVPVMVGSKLCLLHGKTRE 158

Query: 142 -------------GTFVIKGIQRIV 153
                        G F+  G  ++V
Sbjct: 159 ERIRLREDERDAGGYFISNGQDKVV 183


>gi|126722443|dbj|BAF48635.1| DNA-dependent RNA polymerase subunit B' [Natronococcus amylolyticus]
          Length = 435

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 98/427 (22%), Positives = 161/427 (37%), Gaps = 78/427 (18%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +   + V    +    F R    +  R    + 
Sbjct: 51   GFDERPAAQNFVVAVMSYEGFNIEDALVMNKASVE-RALARSHFFRTYEGEERRYPGGQE 109

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 110  DRFEIPSQD-------VRGARGEEAYTHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEP 162

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 163  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 210

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM VG I E   
Sbjct: 211  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHALPSRMTVGHILEMIG 270

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++                                                 
Sbjct: 271  GKLGAMEGRRVDG----------------------------------------------- 283

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DE+ +   L     D +G+  +Y G++GE  +  + VG I+  KL H
Sbjct: 284  ------TP-FLGEDEDELREGLEQNGFDSAGKETMYSGISGEKIEAEIFVGIIFYQKLYH 336

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GAA  L+E L  +SD 
Sbjct: 337  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGAAMTLKERLLDESDR 396

Query: 1321 ---DVVG 1324
                + G
Sbjct: 397  EFIHICG 403



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYTHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    +V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETKVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|110589624|gb|ABG77314.1| RNA polymerase beta subunit [Enterobacter turicensis]
          Length = 308

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 184/306 (60%), Positives = 233/306 (76%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 2   DTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAG 61

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ 
Sbjct: 62  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGVVTDEIH 121

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S +Q+VS+ 
Sbjct: 122 YLSAIEEGNFVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQIVSVG 181

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V
Sbjct: 182 ASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTV 241

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
           + VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V + + V R D++A
Sbjct: 242 QYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLNEPVERGDVLA 301

Query: 796 DGPSTD 801
           DGPSTD
Sbjct: 302 DGPSTD 307


>gi|83763763|emb|CAJ00215.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 7A03]
          Length = 347

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 181/360 (50%), Positives = 250/360 (69%), Gaps = 13/360 (3%)

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E  +A  SG   VAKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC
Sbjct: 1    ERNIAVDSGVTAVAKRGGSVQSVDASRIVVKVNENELVPGEAGIDIYNLTKYTRSNQNTC 60

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +NQRP V  G+ V + D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V 
Sbjct: 61   INQRPTVLPGEPVAKGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQ 120

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE G++ +GAEV  GDILV
Sbjct: 121  EDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGVVYIGAEVKGGDILV 180

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++  R G++K++R
Sbjct: 181  GKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVLPRDGVEKDKR 240

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
            ++ +E+ Q++   +D  +E  IL+  + +R+  +L       G              +  
Sbjct: 241  ALEIEQMQLKEAKKDLTEEFQILEGGLLNRVRAVLIAGGYSEG-------------KLDS 287

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
              R +W +  ++D+ +Q  +E L  Q +  K+  + +F+ K  KI  GDD+ PGVL++VK
Sbjct: 288  IERKKWLELTLEDDALQSQLEQLAEQNDELKADFDKKFETKRRKITQGDDLAPGVLKIVK 347


>gi|269912604|emb|CAY86082.1| RNA polymerase beta subunit [Gluconacetobacter rhaeticus]
          Length = 309

 Score =  305 bits (781), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 144/312 (46%), Positives = 196/312 (62%), Gaps = 28/312 (8%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL  FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIRGMDPDEILGYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A     G K+   L+D  TGE+V  +  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDAE-AFRGQKLLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A+D+VN  TGEIY EAG+ + E+ LEE+    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIAQDMVNEHTGEIYAEAGEELTEQKLEELEGEGLTTLTTLAIDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
            DKN  R++AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D
Sbjct: 238 VDKNAAREEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVD 297

Query: 424 TPDDVRHIRKED 435
            PD VR +RKED
Sbjct: 298 VPDTVRVLRKED 309


>gi|269912614|emb|CAY86087.1| RNA polymerase beta subunit [Gluconacetobacter swingsii]
          Length = 297

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 140/299 (46%), Positives = 186/299 (62%), Gaps = 28/299 (9%)

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI 206
            G +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRI
Sbjct: 1   NGTERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRI 60

Query: 207 DRRRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQR 241
           DR+RK+PVT+ L AL                         GMD +EILS FY K+ +++ 
Sbjct: 61  DRKRKLPVTTLLYALEGEASEAARAAKAAEGGDVESMEIRGMDPDEILSYFYGKVEFTKT 120

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
              W     A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +   
Sbjct: 121 EKGWARRFDA-DSFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPA 178

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            L G ++A DIVN  TGEI+ EAGD + E+ LEE+  + +  +  L VD+ N   +IRNT
Sbjct: 179 GLIGRFIASDIVNEHTGEIFAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNT 237

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
           L  DKN  R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL
Sbjct: 238 LAVDKNASRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRL 296


>gi|55583688|gb|AAV53363.1| RNA polymerase II second largest subunit [Grifola frondosa]
          Length = 719

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 136/852 (15%), Positives = 254/852 (29%), Gaps = 151/852 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + +    +              +    + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L+  + ++           + +  + +      
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL----- 171

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
               EEN + A   + +  +G +       R     +   ++     D SP+  V      
Sbjct: 172  ---EENAHSATPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRE 225

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLL---KAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
                   D+ RV     +      LL     E    G   E              + G++
Sbjct: 226  RELRLYTDAGRVCRPLFIVENQQLLLQKKHIEKLVKGKDDELGYKWD-----NLIKDGVI 280

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E +DA       +    D   +       +    +        R  +K            
Sbjct: 281  ELLDAEEEETVMICMTPDDLENSRLQASGVDPHANEGEFDPGAR--LKAPTNAHTWTHCE 338

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N                        ++       
Sbjct: 339  IHPSMILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQA 373

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G       +               +  +             +       +   +  + A
Sbjct: 374  MGIYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVA 422

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    ++ R  +D  ++S   + E+ E   RD     
Sbjct: 423  ILCYSGYNQEDSVIMNQSSIDRGLF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRM 481

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +       I  G           K+  +  D      R++          ++   
Sbjct: 482  KHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTE 541

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +  Q                              + VK+ V   R  Q GDK A RHG
Sbjct: 542  SGIIDQVLI--------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHG 581

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  + 
Sbjct: 582  QKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDAT 641

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                         ++     +VLR       G+ V         
Sbjct: 642  PFT-------------------------DVTVESVSAVLRQRGYQSRGLEVM-------- 668

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                            G +    G         V +G  Y  +L HMV DK+++R+ G  
Sbjct: 669  --------------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPV 707

Query: 1276 SLVTQQPLGGKS 1287
             ++T+QP+ G+S
Sbjct: 708  QILTRQPVEGRS 719



 Score =  120 bits (300), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 83/622 (13%), Positives = 168/622 (27%), Gaps = 102/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHNTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 192 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 251

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                        G  +    K  +      +  L A EEE   I      L+       
Sbjct: 252 QKKHIEKL---VKGKDDELGYKWDNLIKDGVIELLDAEEEETVMICMTPDDLENSRLQAS 308

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE                   +  P  ++ + AS+IPF +++ S R      
Sbjct: 309 GVDPHANEGEFDPGARLKAPTNAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLV-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLRFR------------------------ELPAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F S++   +  + + + +   E            +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  VN  DI++GK  P         ++        +    RD S  
Sbjct: 484 GTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 536

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG +  V I       K
Sbjct: 537 LKSTESGIIDQVLITTNAEGQK 558


>gi|163930839|dbj|BAF96014.1| RNA polymerase, beta subunit [Klebsiella oxytoca]
          Length = 314

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 191/314 (60%), Positives = 244/314 (77%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   VGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YG
Sbjct: 61  HKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           F+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L 
Sbjct: 121 FLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLF 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME
Sbjct: 181 SRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+
Sbjct: 241 RAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCI 300

Query: 777 NQRPLVKVGDEVRR 790
           NQ P V +G+ + R
Sbjct: 301 NQMPCVSLGEPIER 314


>gi|126178250|ref|YP_001046215.1| DNA-directed RNA polymerase subunit B' [Methanoculleus marisnigri
            JR1]
 gi|126178263|ref|YP_001046228.1| DNA-directed RNA polymerase subunit B' [Methanoculleus marisnigri
            JR1]
 gi|125861044|gb|ABN56233.1| DNA-directed RNA polymerase [Methanoculleus marisnigri JR1]
 gi|125861057|gb|ABN56246.1| DNA-directed RNA polymerase, subunit B' [Methanoculleus marisnigri
            JR1]
          Length = 604

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 83/312 (26%), Positives = 122/312 (39%), Gaps = 70/312 (22%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R+VKV     R  + GDK A RHG KG++  I P  DMPF + G   D+++NP  VPSRM
Sbjct: 345  RLVKVRTRDLRVPEVGDKFASRHGQKGVIGLIQPSADMPFTESGMTPDLIINPHAVPSRM 404

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E   G      G +I +     +    +      L                   
Sbjct: 405  TIGHMLEMLGGKVGSLEGHRINATAFRGERETALRSSLKELGFSHNGREVM--------- 455

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                                    G       +TG  F   + +
Sbjct: 456  --------------------------------------YDG-------ITGRQFAADIYI 470

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IY  KL HMVS K++ARS G   ++T+QP  G++  GG R GEME   +  +GAA  L
Sbjct: 471  GVIYYQKLYHMVSSKMHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVMIGHGAAMAL 530

Query: 1312 QEMLTIKSDDV-------VGRT-------RVYESIVAG--NDTFETGTPESFNVLVKEMQ 1355
            +E L  +SD V        G         +V   +  G   D +      +F +L+ EM+
Sbjct: 531  KERLLDESDKVTQWVCAKCGMVAMVDRKRKVTRCLACGGETDIYPVEMSYAFKLLLDEMK 590

Query: 1356 ALGLSIDLENSR 1367
            ++G++  L    
Sbjct: 591  SMGIAPRLRLDD 602



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 54/350 (15%), Positives = 108/350 (30%), Gaps = 37/350 (10%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G ++ P   V   +       +S+    +      +  +  D       +     G   +
Sbjct: 14  GLVDDPRELVERMREMRRHGEISSEVNVSYKDFNNDVIIHTDRGRARRPLIVVKGGVPQV 73

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +     +             I F++ ++   + +  N                 T +
Sbjct: 74  TDDDIERLRNGETIFEDVARKGAIEFVDAEEEEDLFIAINEADLTPE---------HTHL 124

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   +   G  I A      E   + R+ + +  G +  +         ++         
Sbjct: 125 EIDPSLILG--IGAAHVPFPEHNASPRVTMGA--GMVKQALGFAASNMKLRPDTRGHMLH 180

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+PL                      D   G+N +VA + + G+N ED+++I++  + 
Sbjct: 181 YGQKPL----------TFTQTSDVIGSDDRPAGQNFVVAIISYEGFNIEDALIINKASID 230

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVN 889
             +  S     ++   R    G  +   +IP+         E   N+D  G+I     V 
Sbjct: 231 RGLGRSHFFRTYDGEERRYPGGQVD-RIEIPDEEVSGAHGAEFYANLDIDGVINPETVVR 289

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+L+GK +P         E +            RDTS+ + S   G V
Sbjct: 290 EKDVLIGKTSPPRFLEEPTSELI-------AVEKRRDTSVTMRSNEHGIV 332



 Score = 47.0 bits (110), Expect = 0.024,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 58/176 (32%), Gaps = 31/176 (17%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +    + R+   RR   +        +       +H        P    +G  +  V+  
Sbjct: 18  DPRELVERMREMRRHGEISSEVNVSYKDFNNDVIIHTDRGRARRPLIVVKGG-VPQVTDD 76

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                 N     E   RK         + ++ A EEE+ +IA   + L  +         
Sbjct: 77  DIERLRNGETIFEDVARK-------GAIEFVDAEEEEDLFIAINEADLTPEH-------- 121

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                            ++  P  ++ I A+ +PF E++ S RV MG  M +QA+ 
Sbjct: 122 ---------------THLEIDPSLILGIGAAHVPFPEHNASPRVTMGAGMVKQALG 162


>gi|291196414|emb|CBG27564.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas borbori]
          Length = 305

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 232/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVNDTLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRCDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R    +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI+AD
Sbjct: 241 SVDASRIVVRVNNDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVERSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|297747844|gb|ADI52590.1| RNA polymerase beta-subunit [Yersinia massiliensis]
          Length = 305

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 190/304 (62%), Positives = 234/304 (76%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EF  SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFLGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS
Sbjct: 62  ETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEGNFVIAQANS 121

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           +LDEDG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LM
Sbjct: 122 NLDEDGRFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALM 181

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA RIVI+  E ++
Sbjct: 182 GANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTSVAKRGGTVQYVDASRIVIKVNEDEM 241

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R D++ADGPSTDLG+LALG+NM 
Sbjct: 242 YPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMR 301

Query: 813 VAFM 816
           VAFM
Sbjct: 302 VAFM 305


>gi|126722423|dbj|BAF48625.1| DNA-dependent RNA polymerase subunit B' [Natrinema versiforme]
          Length = 435

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 118/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG++  + P EDMPF + G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVIGHLAPQEDMPFTEGGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE+ + S L  +  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDEDELRSGLEDSGFDSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYNHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGIV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|55583706|gb|AAV53372.1| RNA polymerase II second largest subunit [Suillus pictus]
          Length = 899

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 136/899 (15%), Positives = 263/899 (29%), Gaps = 148/899 (16%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 133  RERRIRYAQEILQKEMLPHVSMSEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 189

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ R +    +              +  + + + +    
Sbjct: 190  GKKRLDLAGPLLAGLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL 249

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 250  ATGNWGDQKKAMSSKAGVSQVLNRYTYASTLSHLRRTNT----PLGREGKIAKPRQLHNT 305

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 306  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 357

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 358  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 414

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +       L+ +   ++  G      +      + K   I         
Sbjct: 415  TDAGRVCRPLFIVENQQLALQKKHIKWLNQGYREDDGEEFKWEQLVKNGIIELLDAEEEE 474

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +       D   S +    +   Q        +    +K G            PS  LG
Sbjct: 475  TVMICMTPEDLENSRLQSAGIDPHQNDGD---YDPAARLKAGINSHTWTHCEIHPSMILG 531

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 532  -------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 566

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 567  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 615

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 616  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKI 674

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 675  EDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 734

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 735  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 774

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +         
Sbjct: 775  YRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 829

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 830  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 853

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    G +       G+     V +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 854  ------YHGHT-------GKKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 899



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 96/766 (12%), Positives = 217/766 (28%), Gaps = 122/766 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R+D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 63  YIRVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              +        +   +++     + L+++ +  + ++           G  +   ++  
Sbjct: 119 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMSEGSESKKAYFFGYMIHRLLLAA 177

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 178 LERRELDDRDHFGKKRLDLAGPLLAGLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAV- 236

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 237 -------KHQTITNGLKYSLATGNWGDQKKAMSSKAGVSQVLNRYTYASTLSHLRRTNTP 289

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       I  +
Sbjct: 290 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMACISVGSYSAPVIEFL 346

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +      NA         F     +    +  N +  I   RR   +         
Sbjct: 347 EEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR-------KVC 606
                  ++        P    E   + L              ++   YR       K  
Sbjct: 406 IRERELRLYTDAGRVCRPLFIVENQQLALQKK--------HIKWLNQGYREDDGEEFKWE 457

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPRE 659
                  +  L A EEE   I      L+     +  +   +  G+          +   
Sbjct: 458 QLVKNGIIELLDAEEEETVMICMTPEDLENSRLQSAGIDPHQNDGDYDPAARLKAGINSH 517

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                +  P  ++ + AS+IPF +++ S R      M +QA+ +                
Sbjct: 518 TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV--------- 568

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                              + + +  Y       +     +  R
Sbjct: 569 --------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR 596

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                                   +L  G+N +VA + + GYN EDS+++++  +   +F
Sbjct: 597 ------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 632

Query: 840 TSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            SI+   +  + + + +   E            +       I++ G+I  G  V+  DI+
Sbjct: 633 RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDII 692

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +GK  P         E+L +        DV        +G+   V+
Sbjct: 693 IGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 734


>gi|111054629|gb|ABH04372.1| RNA polymerase beta subunit [Providencia heimbachae]
          Length = 311

 Score =  305 bits (780), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 190/310 (61%), Positives = 237/310 (76%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGLVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQAN+ L EDGSF EEL+ CR  GE  L  RE+++++D S +Q+VS+ ASLIPFLE+
Sbjct: 122 FIIAQANTVLGEDGSFVEELITCRNRGESSLFSREQVEYMDVSTQQIVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+R G V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVARRGGSVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E ++ P  +G+DIY L K+ RSNQNTC++Q P V + + V R D++ADGPSTDLG+
Sbjct: 242 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCISQMPCVSLNEPVERGDVLADGPSTDLGE 301

Query: 805 LALGRNMLVA 814
           LALG+NM VA
Sbjct: 302 LALGQNMRVA 311


>gi|281494512|gb|ADA72012.1| RNA polymerase subunit B [Acinetobacter sp. UA4]
          Length = 255

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 114/254 (44%), Positives = 161/254 (63%), Gaps = 4/254 (1%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G    K+   L+ D++S        +    DE +   +  ++V  +     ++++F  
Sbjct: 5    SNGGGSTKRGDKLTEDVLSGLELVDLLEIQPNDEAIAERLTQIQVFLKEKSYEIDEKFAE 64

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G
Sbjct: 65   KKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANG 124

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ ++   K    +  LR FL+K+
Sbjct: 125  VPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKML---KEQRTVIELREFLDKI 181

Query: 1176 IGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                G   E++    D  +L ++   ++GVP++TPVFDGA+E  I  +L +AD+  +GQ+
Sbjct: 182  YNKVGGEQEELDSLTDAEILALSGNLRAGVPLATPVFDGAEESQIKDLLELADISRTGQT 241

Query: 1235 ILYDGLTGEPFDRP 1248
            +L+DG TGE  DRP
Sbjct: 242  VLFDGRTGERLDRP 255


>gi|291196406|emb|CBG27560.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           anguilliseptica]
          Length = 305

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGLGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDTLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++ + G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMSDKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R+DI+AD
Sbjct: 241 SVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVERSDILAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|169264487|gb|ACA52270.1| rpoB [Mycobacterium massiliense]
          Length = 236

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 102/235 (43%), Positives = 135/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 33   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 92

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 93   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 137

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 138  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 180

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQP
Sbjct: 181  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQP 235


>gi|195024375|ref|XP_001985862.1| GH20856 [Drosophila grimshawi]
 gi|193901862|gb|EDW00729.1| GH20856 [Drosophila grimshawi]
          Length = 1137

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 101/555 (18%), Positives = 180/555 (32%), Gaps = 108/555 (19%)

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
            +   +V            ++       +G                +      ++      
Sbjct: 674  VCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNQKNRIDSLMYNLVYP 722

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                +    I       +   +    A+      D+ D  +   + +        ++   
Sbjct: 723  QAPMVKSRTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNS 782

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +R  +   ++I    +D    +VI   ++      +  G+   +      K    
Sbjct: 783  KCTV-KRYANQTFDRIMGPVKDALTNKVIFKHDVLDTDGIVAPGEMVQNKQIMINKEMPA 841

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
             +                Q  +V          Y       +    + IE++    +   
Sbjct: 842  VT---------SINPLEGQSPQVP---------YTAVPISYKGPEPSYIERVMVSANSEE 883

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++NP G P
Sbjct: 884  DF--LIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQEDMPFNDYGICPDMIMNPHGFP 941

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM V        G     LG K   L   +                             
Sbjct: 942  SRMTV--------GKTLELLGGKAGVLEGKFHYGT------------------------- 968

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                  F G+    + + L     +  G+   Y G+TG P +  
Sbjct: 969  ---------------------AFGGSKAADVQAELVRHGFNYMGKDFFYSGITGGPLEAY 1007

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+
Sbjct: 1008 IYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCLISYGAS 1067

Query: 1309 YVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPESFNVLVK 1352
             ++ E L I SD    DV    GR   Y          +        +   P +  +L +
Sbjct: 1068 MLIMERLMISSDAFEVDVCRTCGRL-AYCSWCHFCQSSA-----HVSKISMPYACKLLFQ 1121

Query: 1353 EMQALGLSIDLENSR 1367
            E+ ++ +   L    
Sbjct: 1122 ELTSMNVVPKLILEN 1136



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 128/1013 (12%), Positives = 282/1013 (27%), Gaps = 206/1013 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    R N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVRAN----EIVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPISVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG---- 170
                                      G FV++G +++++ Q   S       D      
Sbjct: 148 LRCSNCVLTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQ 207

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
            + + S     +  ++                 +++ +     +P+     ALG+ S++ 
Sbjct: 208 CQVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQE 257

Query: 229 L-----------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           +           + F   ++ +     +     A D M    V              E+ 
Sbjct: 258 IMTHIGLDARSQNRFGASLLEAFNLKVF-TQQRALDYMGSKLVVKRFQSATNKTPSEEAR 316

Query: 278 K-KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
           +  LT+ L     +     +      L    V    ++        +  D    K LE  
Sbjct: 317 ELLLTTILAHVPVDNFNFQMKAIYVSLMVRRVMAAELDKT----LFDDRDYYGNKRLELA 372

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
                     L+         I +  +       K A  D+ + MR   ++     ES  
Sbjct: 373 GSLMSLMFEDLFKRMNWELKMIADKNIPKV----KAAQFDVVKHMRAAQIT--VGLESAI 426

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           +   +   ++ +   G  ++  RL+  +   +            K+              
Sbjct: 427 SSGNWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQ------- 479

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                  +    +  + +    +  +           +   +        + +       
Sbjct: 480 --PSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDERPVMTLAYNAGVEDIREVSGNP 537

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             +  +  +  + N L    + ++        + R         +H ++  R     T  
Sbjct: 538 MNNPHVFLVFINGNVLGLTIN-QKHLVRNLRYMRRKGRMGSFVSIHTSYTQRCIFIHTDG 596

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           G        + +   +     ++      RK  D      + YL   EE + +IA     
Sbjct: 597 GRLCRPYIIVDNMRPLVEQRHLDELLRGIRKFDDFLHDGLIEYLDVNEENDSFIA----- 651

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                              E  +       ++  P  ++ + A L+P+  ++ S R    
Sbjct: 652 -----------------WNEEHIEP-LTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQ 693

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+ ++         G        S                              
Sbjct: 694 CAMGKQAMGMI---------GYNQKNRIDS------------------------------ 714

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                              N    Q P+VK                T+   L  G+N  V
Sbjct: 715 ----------------LMYNLVYPQAPMVKS----------RTIELTNFDKLPAGQNATV 748

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNV 868
           A M + GY+ ED++++++  +       +  +  +   +       +           N 
Sbjct: 749 AVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPVKDALTNK 808

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITP--------KGESPMTPEEKLLRAIFGEK 920
                  +D  GI+  G  V    I++ K  P        +G+SP  P   +  +  G +
Sbjct: 809 VIFKHDVLDTDGIVAPGEMVQNKQIMINKEMPAVTSINPLEGQSPQVPYTAVPISYKGPE 868

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
              +    +   S     +  +    R     ++ S    ++ +  L  D++D
Sbjct: 869 PSYIERVMVSANSEEDFLIKILLRQTRIPEIGDKFSSRHGQKGVTGLIVDQED 921


>gi|323449030|gb|EGB04921.1| hypothetical protein AURANDRAFT_38738 [Aureococcus anophagefferens]
          Length = 1147

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 105/255 (41%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 ++  KV     R  Q GDK A RHG KG +      EDMP+ +DG   DIV+NP 
Sbjct: 860  TNQEGMKFTKVRTRTIRIPQIGDKFASRHGQKGTIGMTYSQEDMPWTRDGVSPDIVVNPH 919

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +G + E          GK+                                  
Sbjct: 920  AIPSRMTIGHLVECLQSKVGALTGKEGD-------------------------------- 947

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I  +L        G  ++Y G TG   
Sbjct: 948  ---------------------ATP-FTDVSVDQIAGVLHELGYHRHGNEVMYSGHTGRMI 985

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               V +G  +  +L H+V DK++ARS G  +++T+QP+ G++  GG R+GEME  C+ ++
Sbjct: 986  HAKVFLGPTFYQRLKHLVDDKIHARSRGPVTMLTRQPMEGRARDGGLRMGEMERDCLVSH 1045

Query: 1306 GAAYVLQEMLTIKSD 1320
            G +  L++ +   SD
Sbjct: 1046 GVSSFLRDRMFANSD 1060



 Score =  187 bits (476), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 154/972 (15%), Positives = 287/972 (29%), Gaps = 209/972 (21%)

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRL----IVFDVDEFTGAKS 121
           F       P               +   R++TY+ P+ + + +     +  + E      
Sbjct: 35  FNQVYVSKPTATERDGTTSNMFPHEARLRNMTYSSPMYVDISVNSACRIRMLAEDGSTHR 94

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQL 157
           I   KE   ++G +P+M +                         G FVI G +++VV+Q 
Sbjct: 95  IDSPKE---FLGYVPIMLRSRFCVLADKSDKELCELGECIYDQGGYFVINGSEKVVVAQE 151

Query: 158 HRSPG-IHFDHDKGRASLS------GKLLYACRIIPDQGLWMDIEFDSK--------DII 202
             S   ++    K     S        + +  R  P     + ++  +K        + I
Sbjct: 152 RMSNNHVYCFRKKQPHKYSWVVECRSHVEHGAR--PT--STIYMQMYNKAGRGQSQGNQI 207

Query: 203 -----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                ++R+D    VPV     ALG  ++ +IL         ++  +     L  A ++ 
Sbjct: 208 RMTLPYIRVD----VPVIIVFRALGFVADRDILEHVVYDFSDTEMMEQLRPSLDEAFVVQ 263

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
              ++   +        I   K++     K L +K V     T +               
Sbjct: 264 NQTIALDFIGRRGSATNIGRSKRVQY--AKELLQKEVLPHVGTEEQSDTKKAFFV----- 316

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            G I  +      E+  E+      +    L          +         K  KD L  
Sbjct: 317 -GYIVHKLLMCSLERIDEDDRDHYGKKRLDL------AGPLLGGLFRMLFRKLTKDVLAY 369

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
           + + +  G    F++A ++ + +  D  +Y L+T        R +       + + +   
Sbjct: 370 LQKCIDEGR--DFNLASAIKSRVITDGLRYSLATG---NWGDRKDASRAGVSQVLNRLTY 424

Query: 437 IAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRME 483
            + +  L  L     R GK       +  +       E        ++KN   +  + + 
Sbjct: 425 ASTLSHLRRLNTPLGREGKQAKPRQLHNTHWGFICPAETPEGQAVGLVKNLALMSYVSVG 484

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCE--FFCSSQLSQLEEHVNSLSRITHTRRL 541
                 +  ++  S+   + I+ + +        F   S +    +     S +   RR 
Sbjct: 485 SPQSPILEFLEEWSMENLEEISPQTIADPGTTKIFVNGSWVGVHRDPSTLESTLRSLRRQ 544

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +    V+  R   E      T  GR+C         I   S      R +    +   
Sbjct: 545 IDIDPE-VSVVRDIKEKELRIYTDAGRVC----RPLLIISKFSRQELRLRKSHIQKLVNG 599

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                   V   V  +   EEE   IA   S L+E                         
Sbjct: 600 ELGWTQLLVKGLVELVDTEEEETTMIAMVPSDLNE-------------------TYSSTY 640

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +  P  ++ I  S+IPF +++ S R      M +QA+ +  +               
Sbjct: 641 THCEIHPSMILGICGSIIPFPDHNQSPRNTYQSAMGKQAMGIYASNFQ------------ 688

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                            + S V  Y       +     ++ R  
Sbjct: 689 -----------------------------QRMDTLSHVLHYPQKPLATTRAMEHLHFR-- 717

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                 +L  G N +VA M + GYN EDS+++++  +   +F S
Sbjct: 718 ----------------------ELPSGVNAIVAIMCYTGYNQEDSLIMNQAAIDRGLFRS 755

Query: 842 IHIEEFEVMARDTKLGP------EEITRD-IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                +        LG       E  TRD    +       +D  G++  G  V+  DIL
Sbjct: 756 TFYRTYVDQESIRGLGEAFHETFERPTRDQCTAMRHGSYDKVDCDGLVAPGLRVSGADIL 815

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK-- 952
           +GK  P            +           +D+S  +    SG V  V +       K  
Sbjct: 816 IGKTAPTTPL-------GMDGNLNHCQFTKQDSSTAMRPNESGLVDQVMLSTNQEGMKFT 868

Query: 953 NERSISVEREQI 964
             R+ ++   QI
Sbjct: 869 KVRTRTIRIPQI 880


>gi|10963|emb|CAA41631.1| DNA-directed RNA polymerase [Drosophila melanogaster]
          Length = 1135

 Score =  304 bits (779), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 115/621 (18%), Positives = 206/621 (33%), Gaps = 123/621 (19%)

Query: 777  NQRPLVKVGDE------VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI- 829
            N+RPLVK          +R+ D        +  D+    +  +A+      +    + I 
Sbjct: 607  NRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIAWNEDQIEDRTTHLEIE 666

Query: 830  -------SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      +V            ++       +G                 N     ++
Sbjct: 667  TFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGM-----------IGYNHNNRIDSLM 715

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +    A+      D+ D  +   + +       
Sbjct: 716  YNLVYPHAPMVKSKTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRC 775

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   ++I    +D    +VI   ++      +  G+   +     
Sbjct: 776  LVYKNSKCTV-KRYANQTFDRIMGPMKDALTNKVIFKHDVLDTDGIVAPGEQVQNKQIMI 834

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K     + +                       +S +V Y       +    + IE++  
Sbjct: 835  NKEMPAVTSM------------------NPLQGQSAQVPYTAVPISYKGPEPSYIERVMV 876

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D+++
Sbjct: 877  SANAEEDF--LIKILLRQTRIPR-GDKFSSRHGQKGVTGLIVEQEDMPFNDFGICPDMIM 933

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM V        G     LG K                               
Sbjct: 934  NPHGFPSRMTV--------GKTLELLGGK------------------------------- 954

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   +      T  F G+  E I + L     +  G+   Y G+TG
Sbjct: 955  --------------AGLLEGKFHYGT-AFGGSKVEDIQAELERHGFNYVGKDFFYSGITG 999

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
             P +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1000 TPLEAYIYSGPVYYQKLKHMVQDKMHARARGPKAVLTRQPTQGRSREGGLRLGEMERDCL 1059

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VGRTRVY---------ESIVAGNDTFETGTPES 1346
             +YGA+ ++ E L I SD    DV    GR   Y          +     +  +   P +
Sbjct: 1060 ISYGASMLIMERLMISSDAFEVDVCRTCGR-MAYCSWCHFCQSSA-----NVSKISMPYA 1113

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ +   +    
Sbjct: 1114 CKLLFQELTSMNVVPKMILEN 1134



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 122/948 (12%), Positives = 276/948 (29%), Gaps = 197/948 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S++HF+ ++I    + N        S            L+++      P    
Sbjct: 47  LVKQHIDSFNHFINVDIKKIVKAN----ELVTS-----GADPLFYLKYLDVRVGKPDIDD 97

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD TY+ P+ + +             +  + IK  ++ +G +PLM
Sbjct: 98  GFNITKATTPHECRLRDTTYSAPITVDIEYT----------RGTQRIKRNNLLIGRMPLM 147

Query: 139 T-----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG----- 170
                                     G FV++G +++++ Q   S       D       
Sbjct: 148 LRSNCALTGKSEFELSKLNECPLDPGGYFVVRGQEKVILIQEQLSWNKMLTEDFNGVVQC 207

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEIL 229
           + + S     +  ++                 +++ +     +P+     ALG+ S++ +
Sbjct: 208 QVTSSTHEKKSRTLV----------LSKHGKYYLKHNSMTDDIPIVVIFKALGVVSDQEI 257

Query: 230 STF----------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
            +           +   +             A + M    V        T     E+ + 
Sbjct: 258 QSLIGIDSKSQNRFGASLIDAYNLKVFTQQRALEYMGSKLVVKRFQSATTKTPSEEAREL 317

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           L + +   L    V    +    +    +   ++  E  +   +  D    K LE     
Sbjct: 318 LLTTI---LAHVPVDNFNLQMKAIYVSMMVRRVMAAELDKTLFDDRDYYGNKRLELAGSL 374

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                  L+         I +  +       K A  D+ + MR   ++  +  ES  +  
Sbjct: 375 LSMMFEDLFKRMNWELKTIADKNIPKV----KAAQFDVVKHMRAAQIT--AGLESAISSG 428

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDID 457
            +   ++ +   G  ++  RL+  +   +            K+     L+  +  +    
Sbjct: 429 NWTIKRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPS 488

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                    + + L     +     ER +     +  ++ +  +   N     +    F 
Sbjct: 489 YTPEGEACGLVKNLALMTHITTEVEERPVMIVAFNAGVEDIR-EVSGNPINNPNVFLVFI 547

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             + L     H + +  + + RR   +G               VH ++  R     T  G
Sbjct: 548 NGNVLGLTLNHKHLVRNLRYMRRKGRMGS-----------YVSVHTSYTQRCIYIHTDGG 596

Query: 578 HNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   + +   +     ++      RK  D  +   + YL   EE + +IA      
Sbjct: 597 RLCRPYVIVENRRPLVKQHHLDELNRGIRKFDDFLLDGLIEYLDVNEENDSFIA------ 650

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                + E+ +  R               ++     ++ + A L+P+  ++ S R    C
Sbjct: 651 -----WNEDQIEDR------------TTHLEIETFTLLGVCAGLVPYPHHNQSPRNTYQC 693

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ ++         G        S                               
Sbjct: 694 AMGKQAMGMI---------GYNHNNRIDS------------------------------- 713

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             N      P+VK                T+   L  G+N  VA
Sbjct: 714 ---------------LMYNLVYPHAPMVKS----------KTIELTNFDKLPAGQNATVA 748

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP--EEITRDIPNVSEEG 872
            M + GY+ ED++++++  +       +  +  +   +          +      ++ + 
Sbjct: 749 VMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTVKRYANQTFDRIMGPMKDALTNKV 808

Query: 873 LKN---IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           +     +D  GI+  G +V    I++ K  P   S    + +  +  +
Sbjct: 809 IFKHDVLDTDGIVAPGEQVQNKQIMINKEMPAVTSMNPLQGQSAQVPY 856


>gi|238583448|ref|XP_002390243.1| hypothetical protein MPER_10509 [Moniliophthora perniciosa FA553]
 gi|215453438|gb|EEB91173.1| hypothetical protein MPER_10509 [Moniliophthora perniciosa FA553]
          Length = 250

 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 121/298 (40%), Gaps = 74/298 (24%)

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +G + E  L    
Sbjct: 1    IGDKFASRHGQKGTIGITYRQEDMPFTNEGIVPDLIINPHAIPSRMTIGHLVECLLSKVA 60

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +G +                                                      
Sbjct: 61   TLIGNEGD---------------------------------------------------- 68

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
             +TP F     E+++  LR       G  ++Y G TG      V +G  Y  +L HMV D
Sbjct: 69   -ATP-FTDLTVESVSMFLRQKGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKHMVDD 126

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----- 1320
            K+++R+ G   ++T+QP+ G+S  GG R GEME  C+ ++G A  L+E L   SD     
Sbjct: 127  KIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCMISHGIAGFLKERLFEASDAYRLH 186

Query: 1321 --DVVGRTRVYESIVAGND-----------TFETGTPESFNVLVKEMQALGLSIDLEN 1365
              D+ G T +  + +   +             +   P +  +L +E+Q++ ++  L  
Sbjct: 187  VCDICGLTAI--ANLKKQNFECRACKNKTAISQLYIPYAAKLLFQELQSMNIAARLYT 242


>gi|119497281|ref|XP_001265400.1| DNA-directed rna polymerase III subunit [Neosartorya fischeri NRRL
            181]
 gi|119413562|gb|EAW23503.1| DNA-directed rna polymerase III subunit [Neosartorya fischeri NRRL
            181]
          Length = 1200

 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 106/514 (20%), Positives = 175/514 (34%), Gaps = 98/514 (19%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +   +  + A+      D+ D  +    
Sbjct: 765  QFLRIDSILYLMVYPQKPMVKSRTIELVKYDQLPAGQNAMVAVMSYSGYDIEDALVLNKG 824

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F R  +   +   +  ++++       ++   I    +         G+
Sbjct: 825  SVDRGFGRCQVF-RKYVTNLKSYSNGTKDRLNPPT--YENGAPIRKHALLEADGLAAVGE 881

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST          P          D           + Y     + +  +
Sbjct: 882  QVNAGEVYINKST----------PEQSNLSGIGSDAGRPVQYTPTPMTY----KLHDPAY 927

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+        +     ++VKV V   R  + GDK + RHG KG+V  I    DMPF  
Sbjct: 928  IDKV-----MYSVQENENQLVKVLVRQTRRPEVGDKFSSRHGQKGVVGIIADQADMPFTD 982

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI++NP G PSRM VG++ E   G A V  G              + S +     
Sbjct: 983  AGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLAGHHGYGTCFGGTPVEEASRILIDHG 1042

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   +                               G   EA+              
Sbjct: 1043 FSYGGKDYLTS----------------------------GITGEAL-------------- 1060

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                      PF   V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1061 ----------PF--YVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1108

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1109 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1165

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1166 ---MTIPYAAKLLIQELMSMNVTARLKLDDEFPE 1196



 Score =  201 bits (510), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 114/938 (12%), Positives = 262/938 (27%), Gaps = 192/938 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P   
Sbjct: 92  LVKQHIDSYNYFIEVQ----------LKKIVESSSTIRSDIDHTFYIKFTDIYVGSPCRA 141

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+ +    I          +  + +  + + 
Sbjct: 142 DEPQDVTPDATPSDVSPHECRLRDTTYAAPILVNFEYI----------RGRQRVTRKGVS 191

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 192 IGRMPIMLRSSKCVLANKTPSEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 251

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      II             KD ++V+ +     +P+   L
Sbjct: 252 TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDKLYVKHNVLSEDIPIVILL 300

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +E+ +      +    + DF      +  L  G       +D       I   +
Sbjct: 301 RAMGIHTEQEMLLLVAGVDSLYQDDFAINFEESIKL--GIYTQQQALDWIGARIKINRKQ 358

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
                       + +  + I+   +  +      V          A         +    
Sbjct: 359 SSYRRTHIQEAVEAIASVIISHIEVKNMNFRPKAVYV--------AHMARRVLMAKNDPS 410

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +           +         K   D  ++I +V+   + +    A ++ + 
Sbjct: 411 LVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRAEQFDAWTVMSM 470

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 471 HSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 530

Query: 458 NLGNRRVRSVGEML-KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G +   +        + +++         D   P   +        +   
Sbjct: 531 GPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPIKNLVFMLGAEDIM-A 589

Query: 517 FCSSQLSQ---LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPA 572
               QL         +N        R    L     + R     E   ++  H+      
Sbjct: 590 LGGKQLYTPGSYTISINGTPIALTRRPKYFLNAFRRLRRMGRISEFVSIYINHHQCAVHI 649

Query: 573 ETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            T +G     +  + +            +     +  D      V YL   EE +  IA 
Sbjct: 650 ATDDGRICRPLIVVENGRSLVTARHLDKLRDGTMQFDDFLAQGLVEYLDVNEENDSLIAL 709

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +                        +    ++  P  V+   A LIP+  ++ S R
Sbjct: 710 YEKDIT-----------------------DTTTHLEIEPFTVLGAVAGLIPYPHHNQSPR 746

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+  + +                              ++D+I  ++    
Sbjct: 747 NTYQCAMGKQAIGAIASNQFL--------------------------RIDSILYLMVY-- 778

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                                 Q   V  R +    + V+ + + A   +          
Sbjct: 779 ---------------------PQKPMVKSRTI----ELVKYDQLPAGQNAM--------- 804

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
              VA M + GY+ ED++++++  V           ++    +    G ++        +
Sbjct: 805 ---VAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTNLKSYSNGTKDRLNPPTYEN 861

Query: 870 EEGLKN---IDECGIICVGAEVNPGDILVGKITPKGES 904
              ++    ++  G+  VG +VN G++ + K TP+  +
Sbjct: 862 GAPIRKHALLEADGLAAVGEQVNAGEVYINKSTPEQSN 899


>gi|242392252|dbj|BAH80363.1| RNA polymerase subunit B' [Haloplanus natans]
          Length = 608

 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 128/604 (21%), Positives = 208/604 (34%), Gaps = 99/604 (16%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ GD       + +    +  D     ++ VA            + I  +++       
Sbjct: 84   VEEGDLSFEQ--LVERGYIEFIDAEEEEDIYVAVDEDELNERHTHLEIDPQLIFGIGAGM 141

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 142  IPYPEHNASPRITMGAG--MMKQSLGLPAANYRIRPDTR-QHLMHYPQLAMVKTQTTEQI 198

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 199  GFDERPAAQNFVVAVMSYEGFNIEDA-LVMNKGSVDRALARSHFFRTYEGEERRYPGGQE 257

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 258  DRFEVPSQD-------VRGARGEDAYTHLDEDGLVNPETQVDENSVLLGKTSPPRFLEEP 310

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E          + +               ++ KV V  +
Sbjct: 311  DDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGE------------DGSKLSKVSVRDE 358

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +PSRM V        
Sbjct: 359  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTV-------- 410

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG K+ SL                                              
Sbjct: 411  GHVLEMLGGKVGSLEGRRVDGT-------------------------------------- 432

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     F G DE  +   L     + SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 433  --------AFQGEDESELRDALEDHGFESSGKEVMYSGVTGEKIEAEIFVGTIFYHKLYH 484

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L   SD 
Sbjct: 485  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDR 544

Query: 1321 ---------------DVVGRTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                           DV  R RVY+  V G  +D  E     +F +L+ EM ALG+   L
Sbjct: 545  ENVYISAETGMVAVEDVEQR-RVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPRL 602

Query: 1364 ENSR 1367
            E   
Sbjct: 603  ELED 606



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 53/357 (14%), Positives = 112/357 (31%), Gaps = 26/357 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +     E++   R  G+   +    I               +  P +  +D + +L
Sbjct: 17  GTHPDPEQLAEQIREARRRGDVSDMVNVSIKERTREVIINADAGRARRPLIVVEDGDPLL 76

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               ++      L  E       +E + A+      VA     + +     + I      
Sbjct: 77  TDEEIEAVEEGDLSFEQLVERGYIEFIDAEEEEDIYVAVDEDELNE-RHTHLEIDPQLIF 135

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPST 800
              +            + +     + Q           RP  +          +    +T
Sbjct: 136 GIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHLMHYPQLAMVKTQTT 195

Query: 801 D---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +     +    +N +VA M + G+N ED++++++  V   +  S     +E   R    G
Sbjct: 196 EQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRALARSHFFRTYEGEERRYPGG 255

Query: 858 PEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            E+              E+   ++DE G++    +V+   +L+GK +P            
Sbjct: 256 QEDRFEVPSQDVRGARGEDAYTHLDEDGLVNPETQVDENSVLLGKTSPPRFLEEP----- 310

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
              + G      R+TS+ + SG  G V  V +       K  +    +    EL  +
Sbjct: 311 -DDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 366



 Score = 43.1 bits (100), Expect = 0.39,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + ++ A EEE+ Y+A     L+                       E+   ++  P+ +  
Sbjct: 100 IEFIDAEEEEDIYVAVDEDELN-----------------------ERHTHLEIDPQLIFG 136

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 137 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRI 173


>gi|297619553|ref|YP_003707658.1| DNA-directed RNA polymerase subunit B [Methanococcus voltae A3]
 gi|297378530|gb|ADI36685.1| DNA-directed RNA polymerase subunit B [Methanococcus voltae A3]
          Length = 611

 Score =  304 bits (779), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 95/489 (19%), Positives = 169/489 (34%), Gaps = 97/489 (19%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +   + +   +     F R      +R    + 
Sbjct: 197  GFDKRPAGQNFVVAVMSYEGYNMEDAFIINKASIERGLGRSSFF-RSYESFEKRYPGGQL 255

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +        +           L G   +          V+           + 
Sbjct: 256  DRFEVPEKG-------VRGYRAEGAYRNLGGDGLIELESEVSSGDVIIGKTSPPRFLEE- 307

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + ++Q +  +R+        E     L    + K               R+ KV V   
Sbjct: 308  NEISLQQKSQRRDTSVTIRHGEEGTVDLVILSETK------------EGNRLSKVRVRDS 355

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG++  ++P ED+PF +DG   D+++NP  VPSRM +GQ+ E   
Sbjct: 356  RIPELGDKFASRHGQKGVIGLVVPQEDLPFTEDGVIPDLIINPHAVPSRMTIGQVLEMIG 415

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G       ++I   I   +    +                                    
Sbjct: 416  GKVGSLDCRRIDGTIFSGEGEWSLRDALEAHGFKHNGKETV------------------- 456

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                          G+S       G+  +  V VG  Y  KL+H
Sbjct: 457  ----------------------------YEGKS-------GKKLECEVFVGVAYYQKLHH 481

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            +V+ K++ARS G   ++T+QP  G++  GG R GEME   + A+GAA +L+E L  +SD 
Sbjct: 482  LVAGKIHARSRGPIQVLTRQPTEGRAREGGLRFGEMERDVLVAHGAALLLKERLLDESDP 541

Query: 1321 --DV----VGRTRVYE-------SIVAGN--------DTFETGTPESFNVLVKEMQALGL 1359
              D      G   +Y+         + G                  +F +L+ E++++G+
Sbjct: 542  HEDYVCAKCGEIAIYDFKRGIKYCPICGEVEDVQDNRKIPSVKIAYAFKLLLDELKSMGI 601

Query: 1360 SIDLENSRT 1368
               L+    
Sbjct: 602  DPKLKLKDR 610



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 62/356 (17%), Positives = 119/356 (33%), Gaps = 44/356 (12%)

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAM---EEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++     E   R + + +    +   +++   EE N      +  +  DG      +   
Sbjct: 14  IDTVDNPEELVRNLRESRRNARISPYTSISFNEESN------DVHISTDGGRAVRPLVVV 67

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             GE  +         +   K    +   L+ +L+ ++              + + + + 
Sbjct: 68  ENGELKITQEHLELVKEGELKFSDLVERGLVEYLDAEEEENA---------YIAIYEKDI 118

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
               T ME       G  I A  A   E   A RI + +            +I    +  
Sbjct: 119 NENTTHMEIDPISILG--IGAGVAPYPEHNSAPRITMAAAMSKQSLGVPMANI--KWRMD 174

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q PLV+   +                    G+N +VA M + GYN ED+ +
Sbjct: 175 TRGHLLHYPQVPLVRTKHQ----------EILGFDKRPAGQNFVVAVMSYEGYNMEDAFI 224

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIIC 883
           I++  +   +  S     +E   +    G  +             +E   +N+   G+I 
Sbjct: 225 INKASIERGLGRSSFFRSYESFEKRYPGGQLDRFEVPEKGVRGYRAEGAYRNLGGDGLIE 284

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +EV+ GD+++GK +P               I  ++    RDTS+ +  G  GTV
Sbjct: 285 LESEVSSGDVIIGKTSPPRFLEE-------NEISLQQKSQRRDTSVTIRHGEEGTV 333


>gi|242392268|dbj|BAH80371.1| RNA polymerase subunit B' [Halorubrum lipolyticum]
          Length = 609

 Score =  304 bits (778), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 128/603 (21%), Positives = 209/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + V R ++    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EAVERGEVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGGLEEHGFKSSGKEVMYSGVTGEKIEAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 116/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHPDPEALAEQIREARRRGDVSEMVNVSVKDRTQEVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEVEAVERGEVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTDDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 43.1 bits (100), Expect = 0.34,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+  +A     + +D                    
Sbjct: 85  VERGEVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDH------------------- 125

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P+ V  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 126 ----THLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|154342160|ref|XP_001567028.1| DNA-directed RNA polymerase II subunit 2 [Leishmania braziliensis
            MHOM/BR/75/M2904]
 gi|134064357|emb|CAM42447.1| putative DNA-directed RNA polymerase II subunit 2 [Leishmania
            braziliensis MHOM/BR/75/M2904]
          Length = 1185

 Score =  304 bits (778), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 107/580 (18%), Positives = 180/580 (31%), Gaps = 113/580 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            +         +      +    + I   ++            ++       +G      +
Sbjct: 693  MTPSEVEKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASNFN 752

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +                  V        +    +T    + +      + AI      + 
Sbjct: 753  MRM-----------DTTAHVLFYPQKPLVRTKAMTYMHSNDLPAGHNAVVAISCYSGYNQ 801

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S V         + R    K ER     R+ +E    + + E   + R  YS
Sbjct: 802  EDSIIMSRSAVERGFFRSAFW-RSFKAKEERQK---RDALETFE-NPNREVCRVKRADYS 856

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L     I  G   + G     K+  L    + +       +   +D  +          
Sbjct: 857  KLDTDGLIKPGMRVLGGDVVVGKTIPLPEADLDKLTTGN-TKITKRDASITSRTTE---- 911

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                        K  +EK+           R  KV +   +    GDK   RHG KG   
Sbjct: 912  ------------KGVVEKVM---LTMNSSDRFAKVKIRTIKIPNIGDKFCSRHGQKGTNG 956

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF +DG   D+++NP  +PSRM V  + ET  G                   
Sbjct: 957  IQFRQEDMPFNRDGVVPDLIINPHAIPSRMTVAHLIETLAGKVAC--------------- 1001

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                  +K G   +TP F     +    
Sbjct: 1002 --------------------------------------YKGGEVYATP-FCSVVVDDFGK 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L        G   LY+G TG P D  +  G  +  +L H+  DK++AR  G    + +Q
Sbjct: 1023 ALHALGSQRYGNECLYNGHTGLPLDHLIFFGPTFYQRLKHLSGDKIHARPRGPLQPLVRQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------GRTRV- 1328
            P  G+++ GG R GEME  C+ +YGA+  L+E L   SD     V           T++ 
Sbjct: 1083 PTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYTVHVCNHCGTICVADTKLN 1142

Query: 1329 -YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
             Y+    G        +   P +  +L +E+ ++ +   L
Sbjct: 1143 RYQC--KGCENDTRISQVLMPYACKLLFQELMSMTILPRL 1180



 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 152/995 (15%), Positives = 301/995 (30%), Gaps = 214/995 (21%)

Query: 29  LIEVQKASYDHFLMMNIA----------PDERPNEG--LQA-------AFKSVFPITAFS 69
           L+  Q  SY+ FLM               D++ + G  ++          + V  I   S
Sbjct: 51  LVHQQLDSYNDFLMRIPKMIESMAVIPRQDDQYDPGVTMEEQRDQPRLVLQDVV-IGNPS 109

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 F      PP F  ++C  RD+TY    ++TL + ++     T      D   ++
Sbjct: 110 HQTHSYFAGGPL-PPLF-PNECRLRDMTYDAQAQVTLGVELYHPHADTP----HDTFLRN 163

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
           + +G +P+M K                         G FVI G ++++++Q  ++   ++
Sbjct: 164 VELGRIPIMLKSMRCNLSGKDEDELPRLNECPHDQGGYFVINGTEKVLIAQERQAANHVY 223

Query: 165 -FDHDKG-----RASLSG--KLLYACRII-PDQ----GLWMDIEFDSKDIIHVRI---DR 208
            F   KG     ++ + G        +II P +    G   +        +  R+   D 
Sbjct: 224 TFSRQKGLLCEVKSIVEGSLNKPRTLQIIMPYRNRGPGSGFE-------SLMCRVAQMDE 276

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +P+     A+ M ++ EIL T  P +  +   +     +S A  +       +L  I
Sbjct: 277 T--IPLFVLFRAMDMVADKEILQTVVPDLKDTAMLELLRGSMSDASTLQIFTREEALGYI 334

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                  ++   L       L    +  +G          +    +  +   + +   + 
Sbjct: 335 GRRLGKQDAMANLQREAESLLMRDLLPHMGTDPSANRTKCLYMGYMVHKLLLVALGRHEE 394

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-----LDIYRVMR 382
            D   L        + I +               +  +  K  +D       +  +  + 
Sbjct: 395 TDRDFL------GHKRIDVAGTLLTVQLQTFLAQVRKEMIKTLQDHAANPRGVFSFGRVI 448

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR----KEDIIA 438
              + T  +   +    F D    ++ T     +N      +  ++R I+          
Sbjct: 449 HSRLVTDGLRRCLATGNFGDLKTGNIKTGVAQTLNRLTYSSSLSNLRRIQNPIAASSKAT 508

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDI-- 495
             + L   + G     +    G+  +     ++    R      + ++++ RI       
Sbjct: 509 RPRNLHCTQWGYICPVETPEGGSIGLLKNVALMCLMSRGTDHAEVVQAVQARIDGFRTIG 568

Query: 496 -----DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
                D  + +  +N   +            L     +    + ++  R +        +
Sbjct: 569 LEDTADVRVARVFVNGTMIGVDRNPERLLHDLRTRRRNGELSNEVSIVRDIRDREIRVFS 628

Query: 551 RARAGVEMRDVHPTHYGRICPAE--TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                   R + P      C  +   S   ++ +         ++    ++  Y      
Sbjct: 629 DGG-----RCLRPLFVVENCHLKLRKSSMRDLLVSEKAGGKKSISWNTVLKKGY------ 677

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V  +   EE++  +A   S ++++  +                        +  P
Sbjct: 678 -----VELIDCEEEDSLLVAMTPSEVEKNYYY---------------------SHCEMDP 711

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ I AS+IP+  ++ S R      M +QA+ +                         
Sbjct: 712 SMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY------------------------ 747

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                             S       +T+ V  Y               Q+PLV+     
Sbjct: 748 -----------------ASNFNMRMDTTAHVLFYP--------------QKPLVR----- 771

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          DL  G N +VA   + GYN EDS+++S   V    F S     F+
Sbjct: 772 -----TKAMTYMHSNDLPAGHNAVVAISCYSGYNQEDSIIMSRSAVERGFFRSAFWRSFK 826

Query: 849 VMARDTK----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                 K       E   R++  V       +D  G+I  G  V  GD++VGK  P    
Sbjct: 827 AKEERQKRDALETFENPNREVCRVKRADYSKLDTDGLIKPGMRVLGGDVVVGKTIP---- 882

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
              PE  L +   G   +  RD S+   +   G V
Sbjct: 883 --LPEADLDKLTTGNTKITKRDASITSRTTEKGVV 915


>gi|156767165|gb|ABU95097.1| ribosomal polymerase B subunit [Acinetobacter tandoii]
          Length = 266

 Score =  304 bits (778), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 119/270 (44%), Positives = 169/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G  G K+   LS D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLSGQESNGG-GGTKRGDKLSEDMLSGLELVDLLEIQPSDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   K   +I+ LR FL+K+    G   E +    DD +L +A   ++GVP++T
Sbjct: 180  EQIDKML---KQQREIAELRVFLDKIYNKVGGQQEDLDSLTDDEILVLAGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A++  SGQ++LYD
Sbjct: 237  PVFDGAEESQIKELLELAEIPRSGQTVLYD 266


>gi|183579275|gb|ACC63215.1| RpoB [Mycobacterium abscessus]
          Length = 233

 Score =  304 bits (778), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 102/235 (43%), Positives = 135/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQP
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQP 233


>gi|226897658|gb|ACO90278.1| RNA polymerase beta subunit gene [Bacillus sp. UST991130-010]
          Length = 378

 Score =  303 bits (777), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 217/360 (60%), Positives = 268/360 (74%), Gaps = 3/360 (0%)

Query: 595 YGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           YGFIETPYR+V    GK+T+ + YL+A EE+N  +AQANS + EDGSF +E V  R  GE
Sbjct: 1   YGFIETPYRRVDPETGKLTDQIDYLTADEEDNYVVAQANSRIAEDGSFADEEVIARFRGE 60

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                R++ID++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL++ EAP VG
Sbjct: 61  NTAFKRDRIDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPIVG 120

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGVDIYRLMKFQRSN 771
           TGME V AK SGAA++ K  GIVE V+A  I +R V   D       ++ YRL KF RSN
Sbjct: 121 TGMEHVSAKDSGAAVICKHDGIVEHVEAREIWVRQVSNIDGQEVKGDLNKYRLQKFIRSN 180

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           Q TC NQR L   G +V + +++ DGPS +L  LALGR +LVA M W GYN+ED++++SE
Sbjct: 181 QGTCYNQRQLQSKGSDVLKGEVLVDGPSMELAVLALGRIVLVALMTWDGYNYEDAIIMSE 240

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +DV+TSIHIEE+E  ARDTKLGPEE+TRDIPNV E+ L+N+DE GII VGAEV  G
Sbjct: 241 RLVKDDVYTSIHIEEYESEARDTKLGPEEMTRDIPNVGEDALRNLDERGIIRVGAEVKDG 300

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 301 DLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGEGIVLDVKVFNREDGD 360



 Score = 41.6 bits (96), Expect = 0.98,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 50/135 (37%), Gaps = 4/135 (2%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  ARD       + R+I +   + L   +     +     K   +L
Sbjct: 244  KDDVYTSIHIEEYESEARDTKLGPEEMTRDIPNVGEDALRNLDERGIIRVGAEVKDGDLL 303

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          E      K+   + GD++P
Sbjct: 304  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGEGIVLDVKVFNREDGDELP 363

Query: 1068 PGVLRVVKVFVAMKR 1082
            PGV ++V+V++  KR
Sbjct: 364  PGVNQLVRVYIVQKR 378


>gi|310877109|gb|ADP36916.1| RNA polymerase subunit B [Mycobacterium sp. M05]
          Length = 236

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 103/236 (43%), Positives = 135/236 (57%), Gaps = 38/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I        A      + S     
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAATPEWAAKLPEQMLSAPPDS 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
            I                             V+TPVFDGA E  +  +L     +      
Sbjct: 150  I-----------------------------VATPVFDGAQEGELQGLLGATLPNRDGETM 180

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQ PL
Sbjct: 181  VNADGKAVLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQPPL 236


>gi|291196430|emb|CBG27572.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas lutea]
          Length = 305

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 235/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAAMNDKGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|291196412|emb|CBG27563.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas azotifigens]
          Length = 304

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 184/305 (60%), Positives = 233/305 (76%), Gaps = 1/305 (0%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V DG+VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDGEVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAKL-EGRKLVDELVAVRHQNEFTVKAPEDVTLMDVSPKQVVSVAA 179

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 180 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 239

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  G++V R DI+AD
Sbjct: 240 SVDASRIVVRVNDDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGEQVARGDIMAD 299

Query: 797 GPSTD 801
           GPSTD
Sbjct: 300 GPSTD 304


>gi|11121238|emb|CAC14804.1| RNA polymerase beta subunit [Neisseria meningitidis]
 gi|11121244|emb|CAC14807.1| RNA polymerase beta subunit [Neisseria meningitidis]
 gi|11121246|emb|CAC14808.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 193/341 (56%), Positives = 248/341 (72%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N             +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+
Sbjct: 1   LNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQF 60

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +
Sbjct: 61  RSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEV 120

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N Y
Sbjct: 121 THKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDY 180

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+
Sbjct: 181 GFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIM 240

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+
Sbjct: 241 ATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGI 300

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           E  VA  S  AIVA+R G+VE VDA R+VIR  + +     
Sbjct: 301 ERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|76556191|emb|CAI91182.1| RNA polymerase beta subunit [Pseudomonas avellanae]
          Length = 313

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 237/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPXDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE++D+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHNDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDATRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|126722441|dbj|BAF48634.1| DNA-dependent RNA polymerase subunit B' [Natrialba magadii]
          Length = 433

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 117/253 (46%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++  V V  +R  + GDK A RHG KG++  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSXVSVRDERIPELGDKFASRHGQKGVLGHLAPQEDMPFTENGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGAMEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE A+   L  A  D +G+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESALRDGLEEAGFDSAGKETMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGIIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/193 (21%), Positives = 72/193 (37%), Gaps = 23/193 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    EV+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETEVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDK 952
             + +       K
Sbjct: 189 DTITLMEGEDGSK 201


>gi|222478545|ref|YP_002564782.1| RNA polymerase Rpb2 domain 6 [Halorubrum lacusprofundi ATCC 49239]
 gi|222451447|gb|ACM55712.1| RNA polymerase Rpb2 domain 6 [Halorubrum lacusprofundi ATCC 49239]
 gi|242392266|dbj|BAH80370.1| RNA polymerase subunit B' [Halorubrum lacusprofundi ATCC 49239]
          Length = 609

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 128/603 (21%), Positives = 209/603 (34%), Gaps = 99/603 (16%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + + R D+    + +    +  D     ++LVA       +    + I  ++V       
Sbjct: 83   EALERGDVEFEDLVERGYVEFIDAEEEEDILVAVDEEDVTDDHTHLEIDPQLVFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLAMVKTQTSDQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                    +  + A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 200  SFDKRPAAQNFVVAVMSYEGFNIEDA-LVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+  +D       +           L     V+      +S+VL           + 
Sbjct: 259  DRFEIPDQD-------VRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVKVRDQ 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +PSRM VG + E   
Sbjct: 360  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHALPSRMTVGHVLEMLG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G                                                          +
Sbjct: 420  GKV-----------------------------------------------------GSLR 426

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  TP F G DEE +   L       SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 427  GSRVDGTP-FQGEDEEELRGGLEEHGFKSSGKEVMYSGVTGEKIEAEIFVGTIFYHKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA+ VL E L   SD 
Sbjct: 486  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGASMVLNERLLESSDA 545

Query: 1321 ---DVVGRT-----------RVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V   T           RVY+  V G  +D  E     +F +L+ EM ALG+   LE
Sbjct: 546  ETVHVSAETGLVAVEDREQRRVYD-PVTGDEDDIHELEVSYAFKLLLDEMIALGIRPKLE 604

Query: 1365 NSR 1367
               
Sbjct: 605  LED 607



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 116/373 (31%), Gaps = 31/373 (8%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A  E   Y+  +      D     E +   R  G+   +    +               +
Sbjct: 4   AEREAKVYVNGSLVGTHPDPEALAEQIREARRRGDVSEMVNVSVKDRTQEVIVNADAGRA 63

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P +  ++   +L    ++      ++ E       +E + A+     +VA      E 
Sbjct: 64  RRPLIVVENGEPLLGDEEIEALERGDVEFEDLVERGYVEFIDAEEEEDILVA---VDEED 120

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQR---PLVKVGDEVRRND 792
           V      +      +    +G+  Y       + +     + Q    P            
Sbjct: 121 VTDDHTHLEIDPQLVFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQ 180

Query: 793 IIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +   P                     +N +VA M + G+N ED++++++  V   +  S
Sbjct: 181 HLLHYPQLAMVKTQTSDQISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRS 240

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +E   R    G E+              E+   ++DE G++    +V+   +L+G
Sbjct: 241 HFFRTYEGEERRYPGGQEDRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLG 300

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           K +P               + G      R+TS+ + SG SG V  V +       K  + 
Sbjct: 301 KTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKV 354

Query: 957 ISVEREQIELLAR 969
              ++   EL  +
Sbjct: 355 KVRDQRVPELGDK 367



 Score = 42.4 bits (98), Expect = 0.55,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 23/97 (23%)

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V ++ A EEE+  +A     + +D                          ++  P+ V  
Sbjct: 101 VEFIDAEEEEDILVAVDEEDVTDDH-----------------------THLEIDPQLVFG 137

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 138 IGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|55273987|gb|AAV48864.1| RNA polymerase II second largest subunit [Albatrellus higanensis]
          Length = 913

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 128/899 (14%), Positives = 264/899 (29%), Gaps = 132/899 (14%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 129  RYAQEILQKEMLPHVSMNEGSESKK---AYFFGYMIHRLLLAALERRDLDDRDHFGKKRL 185

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +    + + +     +   
Sbjct: 186  DLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKYSLATGNW 245

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 246  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 301

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  + ++           + +  + +         EEN + + 
Sbjct: 302  CPAETPEGQACGLVKNLSLMSVISVGSLSAPVIEFLEEWGLESL--------EENAHSST 353

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 354  PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGR 410

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV-AKRAGIVEQVDAIRIVIRSV 748
            V     +      +++ +   + T       +        A R       D  +    + 
Sbjct: 411  VCRPLFIVENQQLVIQKKHIKMLTEAADKSKQDEEEEREKAARGEPPMDPDGEKKPEYTW 470

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +  +      +            +   +   P               +       D A  
Sbjct: 471  DHLVRGGLIELL------DAEEEETVMICMTPEDLYNSRTDEAQSDPNEEF----DPATR 520

Query: 809  RNMLVAFMPWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                     W       SM++     ++            ++       +G       + 
Sbjct: 521  LKARTNAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVR 580

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 581  M-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAVVAILCYSGYNQED 629

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    ++ R  +D  ++S   + E+ E   R+          +     
Sbjct: 630  SVIMNQSSIDRGLF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKHGTYDKLEDD 688

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G N         K+  +  D      R++          V   ++S +       
Sbjct: 689  GLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTK----THSRRDVSTPLKSTESGIIDQV 744

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
             +                       + VK+ V   R  Q GDK A RHG KG +      
Sbjct: 745  LL----------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGIAYRQ 788

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF  +G   D+++NP  +PSRM +G + E  L      LG++  +            
Sbjct: 789  EDMPFTAEGITPDLIINPHAIPSRMTIGHLVECLLSKVATLLGQEGDATPFT-------- 840

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                              ++       LR       G+ +                    
Sbjct: 841  -----------------DLTVESVSHFLREKGYQSRGLEIM------------------- 864

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 865  ---YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 913



 Score =  134 bits (337), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 95/786 (12%), Positives = 216/786 (27%), Gaps = 121/786 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 54  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 109

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   ++L     + L+++ +  + +              +      + 
Sbjct: 110 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHVSMNEGSESKKAYFFGYMIH---RLL 165

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  D    +      +    P+L          +   +     K  +        +
Sbjct: 166 LAALERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSL 225

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   S  G  ++  R    +      R         
Sbjct: 226 AVKHNTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 285

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +  +   + E +    ++S+
Sbjct: 286 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSVISVGSLSAPVIEFLEEWGLESL 345

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 NA         F     +    +  N +  I   RR   +            + 
Sbjct: 346 ----EENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKE 401

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR-----------------------VNAY 595
             ++        P    E   + +                                ++  
Sbjct: 402 LRLYTDAGRVCRPLFIVENQQLVIQKKHIKMLTEAADKSKQDEEEEREKAARGEPPMDPD 461

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G  +  Y           +  L A EEE   I      L    +   +            
Sbjct: 462 GEKKPEY-TWDHLVRGGLIELLDAEEEETVMICMTPEDLYNSRTDEAQSDPNEEFDPATR 520

Query: 656 ----VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                        +  P  ++ + AS+IPF +++ S R      M +QA+ +        
Sbjct: 521 LKARTNAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV- 579

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                                                      + + +  Y       + 
Sbjct: 580 ----------------------------------------RMDTMANILYYPQKPLATTR 599

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
               +  R                        +L  G+N +VA + + GYN EDS+++++
Sbjct: 600 SMEYLRFR------------------------ELPAGQNAVVAILCYSGYNQEDSVIMNQ 635

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S++   +  + + + +   E        +   +       +++ G+I  G 
Sbjct: 636 SSIDRGLFRSMYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKHGTYDKLEDDGLIAPGT 695

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            VN  DI++GK  P         ++        K    RD S  + S  SG +  V +  
Sbjct: 696 NVNGEDIIIGKTAPIPPDSEELGQRT-------KTHSRRDVSTPLKSTESGIIDQVLLTT 748

Query: 947 RHGIDK 952
                K
Sbjct: 749 NAEGQK 754


>gi|118576748|ref|YP_876491.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Cenarchaeum
            symbiosum A]
 gi|118195269|gb|ABK78187.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [Cenarchaeum
            symbiosum A]
          Length = 1115

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 125/320 (39%), Gaps = 74/320 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ K+ V   R  + GDK A RHG KG++  +   ED+P+  +G   D+++NP  
Sbjct: 851  SNEGGKMYKIRVRDMRVPEIGDKFAARHGQKGVLGILAKNEDLPYTAEGVTPDVLINPHA 910

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG   E+  G A    G +        +   ++  +                  
Sbjct: 911  FPSRMTVGMFMESITGKAAALRGTQFDGSAFVGEKMEEVREVMDTAGFKYSGKEIM---- 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                         G        TG+ F 
Sbjct: 967  -------------------------------------------YDG-------RTGKAFP 976

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+ AYG
Sbjct: 977  VEVFIGVVYYQKLHHMVADKIHARARGQVQMLTKQPTEGRARGGGLRFGEMERDCLIAYG 1036

Query: 1307 AAYVLQEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFN 1348
            A+ +L++ L  +SD                DV  R   Y   V G+           +F 
Sbjct: 1037 ASMILKDRLLDESDKSDIYVCERCGLVAYHDVKQRK--YVCRVCGDKAKVSSVSVAYAFK 1094

Query: 1349 VLVKEMQALGLSIDLENSRT 1368
            +L++EMQ+L ++  L     
Sbjct: 1095 LLLQEMQSLNVAPRLLIKEK 1114



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 133/987 (13%), Positives = 278/987 (28%), Gaps = 227/987 (22%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA--MLEFVSYEFDPPK----- 85
              S+D FL            GLQ+       I   +      ++    +   P+     
Sbjct: 25  HLNSFDEFL----------ERGLQSIIDEQGQIEIENAEYPYKIQLGKVKLQKPRMMELD 74

Query: 86  -----FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-- 138
                    +   R+++Y+ P  + +   V +  +   +K         +++GD+P M  
Sbjct: 75  GSITYITPAEGRLRNVSYSAP--VMMEASVVEDGKTLESKF--------VHIGDIPTMIK 124

Query: 139 ----------------------TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F+I G +R+VV     S   +      + ++ G
Sbjct: 125 SSACVLHNLPDQKLIEQGEDPNDPGGYFIINGSERVVVGLEDLS---YNKIIVDKETVGG 181

Query: 177 KLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILST 231
             +Y  ++       +   +++   +  +I VRI      +PV + + ALG++S+  +++
Sbjct: 182 NPVYKAKVYSSIVGYR-AKLELIMKNDGLIVVRIPGSPVDIPVVTLMKALGLESDREIAS 240

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
                  S   D       + +     K S           ++   K++  G+L+  + K
Sbjct: 241 -----SASLNDDIQNELEGSFEKAGEVKTSKDA--------IVYISKRIAPGMLEEFQIK 287

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI-LYVD 350
                   ++ L    +             +       ++  + +  +  + + + L   
Sbjct: 288 R-------AETLLDWSLLPH----------LGKHPENRKEKAQFLGEATCKLLELKLVWI 330

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVM---------RPGDVSTFSVAESMFNFLFF 401
             ++  +  N ++    +   D     +R +         R G         +       
Sbjct: 331 PADDKDHYGNKVIKFAGQMLADLFRTAFRNLVRDMKYQLERSGQKRGIHAVAAAIRPGIV 390

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
                +    G             D   ++     +  +   L   +      D      
Sbjct: 391 TDKLNNAIATGNWGRGRVGVTQLLDRTNYLSTISHLRRVQSPLSRTQPNFEARDLHATHF 450

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS- 519
            R   S      N   +  L +   I   + S +I   +                   + 
Sbjct: 451 GRICPSETPEGSNCGLVKNLALSAIISVHVPSQEITEKLFDMGTVHFTDAKEDARATGTR 510

Query: 520 -----SQLSQLEEHVNSLSRITHTRRLSALGQG---GVARARAGVEMRDVHPTHYGRICP 571
                  +   ++       +   RR S +         R       R ++       C 
Sbjct: 511 IFVDGRLIGYYKDGGGLADSLRDLRRSSKIHPHVSISFNRPAEDGATRRLYVN-----CS 565

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
           A       I +        + +    I +      D      +  + A EEEN Y+    
Sbjct: 566 AGRVLRPMIIIKDGKPLLTQ-DLLDKISSKLLSWNDLLRMGVIELIDANEEENCYVT--- 621

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                                      +    ++  P  ++   AS+IP+ E++ S R  
Sbjct: 622 ---------------------LDEKEAKGHTHLEIFPSAILGAGASIIPYPEHNQSPRNT 660

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               M +Q++                                                  
Sbjct: 661 YESAMAKQSLGFSTPM-------------------------------------------- 676

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                     Y    F          Q P+V                   L D   G+N 
Sbjct: 677 -----MNTSTYVRQHFM------LYPQTPIVN----------TRAMGLLGLEDRPAGQNC 715

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP----- 866
           +VA +P+ GYN ED++++S+  V   +  +     ++  A+    G  +   +IP     
Sbjct: 716 VVAVLPFDGYNIEDAIVLSKSSVDRGLARTFFYRIYDAEAKQYPGGMRDNF-EIPGAEDN 774

Query: 867 ---NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                 E+  + +++ G+I   + V  GDIL+GK +P        E +            
Sbjct: 775 IRGYKGEKSYRLLEDDGVIASESTVLGGDILIGKTSPPRFMEEYKEFE-------PSGPY 827

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            RDTS+ V    +  VVD  +  +   
Sbjct: 828 RRDTSIGVRPSET-GVVDTVVMTQSNE 853


>gi|260505169|gb|ACX42076.1| RNA polymerase beta subunit [Leclercia sp. 1185/07]
          Length = 309

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 186/309 (60%), Positives = 237/309 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L   +++D++
Sbjct: 121 VTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +
Sbjct: 241 VTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSL 300

Query: 785 GDEVRRNDI 793
           G+ V R D+
Sbjct: 301 GEPVERGDV 309


>gi|283551242|emb|CBI83139.1| RNA polymerase subunit B [Haloferax sp. B-1]
 gi|283551244|emb|CBI83140.1| RNA polymerase subunit B [Haloferax sp. B-3]
 gi|283551246|emb|CBI83141.1| RNA polymerase subunit B [Haloferax sp. B-4]
 gi|283551248|emb|CBI83142.1| RNA polymerase subunit B [Halogranum rubrum]
          Length = 608

 Score =  303 bits (777), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 114/594 (19%), Positives = 200/594 (33%), Gaps = 101/594 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 94   LVERGYVEFIDAEEEEDIYVAVDEDEVSEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 153

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 154  TMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 210

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +     V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 211  VAVMSYEGFNIEDALVMNKGSVE-RAMARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 266

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 267  ----VRGARGEDAYTHLDDDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 322

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E          + +               ++ KV V  +R  + GDK A R
Sbjct: 323  ETSVTMRSGEDGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 370

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF + G   D+V+NP  +PSRM V        G     LG K+ 
Sbjct: 371  HGQKGVVGHLAPQEDMPFTEQGVVPDLVINPHALPSRMTV--------GHVLEMLGGKVG 422

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +L                                                       F G
Sbjct: 423  ALEGRRVDGT----------------------------------------------AFQG 436

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
              EE +   L     + +G+ ++Y G+TGE  +  + +G I+  KL HMVS+K++ARS G
Sbjct: 437  ESEEELRGALEEHGFNSAGKEVMYSGVTGEKVEAQIFLGIIFYHKLYHMVSNKLHARSRG 496

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES-- 1331
               ++T+QP  G++  GG R+GEME   +  +GAA  L+E L   SD    R  VY S  
Sbjct: 497  PVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSD----REEVYVSAD 552

Query: 1332 ----------------IVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                             + G  ++  +     +F +L+ EM+ALG+   +E   
Sbjct: 553  TGMVAVEDREQRRIYDPITGDEDNIHKIEVSYAFKLLLDEMKALGIRPKIELED 606



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 52/358 (14%), Positives = 113/358 (31%), Gaps = 28/358 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +      ++   R  G+   +    +               +  P +  ++   +L
Sbjct: 17  GTHPDPHQLAAQIREARRRGDVSQMVNVSVKDRTREVIVNADAGRARRPLIVVENGEPLL 76

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               ++      L+ E       +E + A+      VA         D   + I      
Sbjct: 77  GDEEIEAVDNDELEFEDLVERGYVEFIDAEEEEDIYVA-VDEDEVSEDHTHLEIDPQLIF 135

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPST 800
              +            + +     + Q           RP  +          +    +T
Sbjct: 136 GIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTT 195

Query: 801 D---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +     +    +N +VA M + G+N ED++++++  V   +  S     +E   R    G
Sbjct: 196 EQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERAMARSHFFRTYEGEERRYPGG 255

Query: 858 PEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            E+   +IP+        E+   ++D+ G++     V+   +L+GK +P           
Sbjct: 256 QEDRF-EIPSQDVRGARGEDAYTHLDDDGLVNPETVVDENSVLLGKTSPPRFLEEP---- 310

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
               + G      R+TS+ + SG  G V  V +       K  +    +    EL  +
Sbjct: 311 --DDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 366



 Score = 44.3 bits (103), Expect = 0.15,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       V+        P    
Sbjct: 10  YVNGSLVGTHPDPHQLAAQIREARRRGDVSQMVNVSVKDRTREVIVNADAGRARRPLIVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     L+      A  N     E    +         V ++ A EEE+ Y+A     + 
Sbjct: 70  ENGE-PLLGDEEIEAVDNDELEFEDLVER-------GYVEFIDAEEEEDIYVAVDEDEVS 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPSANYRI 173


>gi|255762382|gb|ACU33028.1| RNA polymerase subunit B [Mycobacterium bolletii]
          Length = 241

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 102/235 (43%), Positives = 135/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 144  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQQP
Sbjct: 187  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQQP 241



 Score = 43.5 bits (101), Expect = 0.25,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 47


>gi|159116724|ref|XP_001708583.1| DNA-directed RNA polymerase RPB2 [Giardia lamblia ATCC 50803]
 gi|21842205|gb|AAM77733.1|AF510641_1 RNA polymerase II subunit Rpb2 [Giardia intestinalis]
 gi|157436695|gb|EDO80909.1| DNA-directed RNA polymerase RPB2 [Giardia lamblia ATCC 50803]
          Length = 1293

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 161/1011 (15%), Positives = 329/1011 (32%), Gaps = 178/1011 (17%)

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLR 447
              +A  +      DS K     +        L         H+ K   I  +  +L+   
Sbjct: 310  EFLAGRLVVGEQMDSAKAKYDRLMSHLSTRLLPHIGVTPEFHLDKAFFIGYMTNLLLQTV 369

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRL-----------------GLLRMERSIKERI 490
             G+ + DD D+ G +R++  G +L +++R                   +L+++  I    
Sbjct: 370  VGRRSPDDRDHWGGKRLQLTGSLLADKFRFEYELFLRRLARKLHDTGSILKVKEDISMVS 429

Query: 491  SSVDIDSVMPQDLINAK----------------------PVVSAVCEFFCS--------- 519
             +++  S +PQ   +                         +   +     +         
Sbjct: 430  PNIEGSSFIPQSKYDTHGKVPGLEDPRRLLDRIKVAATSYISKNITSALSTGTWKTNEVV 489

Query: 520  ----SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                S +SQ    ++  S ++  RR S+     V      +  R +H T +G +CPAET 
Sbjct: 490  GNTKSGVSQSLVRLSYTSALSQIRRSSS----SVEETSKAIGPRLLHTTQFGYMCPAETP 545

Query: 576  EGHNIGLVSSLTSFARVNAYGF--------IETPYRKVCDGKVTNDVVYLSA------ME 621
            EG  +GL+ + +  A V             + T YR        + +           + 
Sbjct: 546  EGAKVGLIKNFSLMANVTLDNPKDEHDLRKLLTEYRVQASHGPISVLKSFHTVTNAKKLV 605

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
             + +     +     D  + + L+              ++     + KQ +SI++     
Sbjct: 606  SDVKIFLNGSWLGFIDREYVQRLITDLKRWRFEGKINREVSISYLAHKQEISISS----- 660

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               D+         +     P LK          E  V   +    + +   ++  +   
Sbjct: 661  ---DEGRVTRPVFVVITDIHPTLKLVTNLSLAITEEDVETLATIPQMEQWNSLLSGLGTG 717

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD-----EVRRNDIIAD 796
            + +I  ++   +     +    +  F+   Q     +  ++  G+      ++ ++I   
Sbjct: 718  KCMIEFLD--PNEEEMALICMDIYHFKEEIQKAHTIRDIILAHGEDNAINYIKAHNIPLA 775

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARD 853
               T L    ++  + + + +P+  +N     L    M  +   ++   +++ F+    +
Sbjct: 776  NNYTHLEIHPSMVLSAITSLIPFPDHNQSPRNLYQASMGKQAVGIYALNYLKRFDTSGIN 835

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG----DILVGKITPKGESPMTPE 909
                P+       ++     + +     + +   V  G    D L+   +      M   
Sbjct: 836  VMHYPQLPLVTTRSMPHVKFRYLPAGQNVIIAIAVYSGFNQEDSLIMSQSAVDRGFMRAT 895

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                       A    +   R+         +++     G                    
Sbjct: 896  YYHTYEEMISSAASSINAPDRIEKFCRPIGPNIKGIKDPGCA------------------ 937

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
                    L+ +   R+   +  Q  + G     K ++ S              +  QD 
Sbjct: 938  ------SYLEADGLPRVGNAVNSQRLIIGKIRPNKRSMNSRA---------VSTYDFQDV 982

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++  +E    + ++     + R ++ + +    +        + KV V   R  Q GDK
Sbjct: 983  SLKVKMEE-TGRVDSVIIAPDLREQSFLSEGVDSNTTGAEGSLLAKVRVRSSRVPQLGDK 1041

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             + RHG KG V  +L  ED+PF  DG   DI++NP  +PSRM +GQ+ E+         G
Sbjct: 1042 FSSRHGQKGTVGMLLRHEDLPFTLDGITPDIIMNPHAIPSRMTIGQLMESVASKLGALSG 1101

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             ++     +                                                   
Sbjct: 1102 HEVDGTAFNAPPGS---------------------------------------------- 1115

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                  ++ I + L      +     + +G+TGE     + +G  +  +L HMV DK+ +
Sbjct: 1116 -----TDKQIAADLHARGYQKHNYEAMMNGMTGEMMTYRIFIGPTFYQRLKHMVLDKISS 1170

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            R+TG    +T+QP  G+SN GG R+GEME     A+GA  +L++ L   SD
Sbjct: 1171 RNTGPIVTLTRQPNEGRSNYGGMRIGEMEKDAFIAHGATAILRDRLLFSSD 1221



 Score =  100 bits (250), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 144/1089 (13%), Positives = 313/1089 (28%), Gaps = 234/1089 (21%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAA-----MLEFVSYEFD 82
            L  +Q  SY+HF+   +          +    S  PI    +        +L F   + +
Sbjct: 26   LAAMQIDSYNHFVKHTM----------KNIMASFPPIQVTRTENFCCYNHILSFSDPQLE 75

Query: 83   PPK-FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ--SIYMGDLPLMT 139
            P      +DC  +  +Y   +K+ +   +           ++++  +   I     P+M 
Sbjct: 76   PNVHIKPNDCRIQSSSYMAAIKVKISYTIQQYSFSNNEGLVQEVTYEPKLIDFCLFPVMV 135

Query: 140  ------------------------------KDGTFVIKGIQRIVVSQ-------LHRSPG 162
                                          + G F+I+G ++ V++Q       L   PG
Sbjct: 136  NSCLCYLNTNKVAGSDIKAHRIINDECPYDEGGYFIIRGAEKAVIAQEGNRPNRLLILPG 195

Query: 163  IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
                          K+ Y  +++           +S   +H ++                
Sbjct: 196  ----------DPGSKIPYTAQLVS---------TNSTKNLHSKV---------------- 220

Query: 223  MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
                 +L  +          D     ++     +   +   L+ +   +  + + + L S
Sbjct: 221  -----VLKYWSTNKWGRTIQDINQPQITFTMQGIRDDLPLFLLILALWQDNVYAARDLLS 275

Query: 283  GLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             ++    +  +    + S  L         +  +    G + +       +   + +  S
Sbjct: 276  IVVPDESDTELIEHLLPSYNLFCSTPQSSKDKCIEFLAGRLVVGEQMDSAKAKYDRLM-S 334

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             +    + ++         +   +          LL      R  D       + +    
Sbjct: 335  HLSTRLLPHIGVTPEFHLDKAFFIGYMTNL----LLQTVVGRRSPDDRDHWGGKRLQLTG 390

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
               +DK+            RL     D    ++ ++ I+++   ++  +         + 
Sbjct: 391  SLLADKFRFEY---ELFLRRLARKLHDTGSILKVKEDISMVSPNIEGSSFIPQSKYDTHG 447

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +     +L         R++ +    IS     ++        + V +        
Sbjct: 448  KVPGLEDPRRLLD--------RIKVAATSYISKNITSALSTGTWKTNEVVGNT------K 493

Query: 520  SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            S +SQ    ++  S ++  RR S+     V      +  R +H T +G +CPAET EG  
Sbjct: 494  SGVSQSLVRLSYTSALSQIRRSSS----SVEETSKAIGPRLLHTTQFGYMCPAETPEGAK 549

Query: 580  IGLVSSLTSFARVNAYGF--------IETPYRKVCDGKVTNDVVYLSA------MEEENR 625
            +GL+ + +  A V             + T YR        + +           +  + +
Sbjct: 550  VGLIKNFSLMANVTLDNPKDEHDLRKLLTEYRVQASHGPISVLKSFHTVTNAKKLVSDVK 609

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-----LIP 680
                 +     D  + + L+              ++     + KQ +SI++         
Sbjct: 610  IFLNGSWLGFIDREYVQRLITDLKRWRFEGKINREVSISYLAHKQEISISSDEGRVTRPV 669

Query: 681  FLENDDSNRVL-----------------------------------MGCNMQRQAVPLLK 705
            F+   D +  L                                    G  M     P  +
Sbjct: 670  FVVITDIHPTLKLVTNLSLAITEEDVETLATIPQMEQWNSLLSGLGTGKCMIEFLDPNEE 729

Query: 706  AEAPFVGTGMESVV----AKSSGAAIVA----------KRAGIVEQVDAIRIVIRSVEGD 751
              A               A +    I+A          K   I    +   + I      
Sbjct: 730  EMALICMDIYHFKEEIQKAHTIRDIILAHGEDNAINYIKAHNIPLANNYTHLEIHPSMVL 789

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND------------IIADGPS 799
               ++           +   Q +   Q   +   + ++R D             +    S
Sbjct: 790  SAITSLIPFPDHNQSPRNLYQASMGKQAVGIYALNYLKRFDTSGINVMHYPQLPLVTTRS 849

Query: 800  TDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA----- 851
                    L  G+N+++A   + G+N EDS+++S+  V      + +   +E M      
Sbjct: 850  MPHVKFRYLPAGQNVIIAIAVYSGFNQEDSLIMSQSAVDRGFMRATYYHTYEEMISSAAS 909

Query: 852  -RDTKLGPEEITRDI-PNVS----EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
              +     E+  R I PN+           ++  G+  VG  VN   +++GKI P   S 
Sbjct: 910  SINAPDRIEKFCRPIGPNIKGIKDPGCASYLEADGLPRVGNAVNSQRLIIGKIRPNKRSM 969

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV------DVRIFNRHGIDKNERSISV 959
             +               D +D SL+V    +G V       D+R  +      +  +   
Sbjct: 970  NS---------RAVSTYDFQDVSLKVKMEETGRVDSVIIAPDLREQSFLSEGVDSNTTGA 1020

Query: 960  EREQIELLA 968
            E   +  + 
Sbjct: 1021 EGSLLAKVR 1029


>gi|295291781|gb|ABH04347.2| RNA polymerase beta subunit [Proteus vulgaris]
          Length = 310

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 186/309 (60%), Positives = 229/309 (74%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V +  VT+++ YL A+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVENNAVTDEIHYLXAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQANS LD+D  F EELV CR  GE  L  R+++ ++D S +QV S+ ASLIPFLE+
Sbjct: 122 FIIAQANSVLDDDNHFVEELVTCRHKGESSLFSRDQVQYMDVSTQQVDSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG   VAKR G V+ VDA RIV
Sbjct: 182 DDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSGVTAVAKRGGAVQYVDASRIV 241

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I+  E +     +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTDLG+
Sbjct: 242 IKVNEDETYAGEAGIDIYSLTKYTRSNQNTCINQTPCVSLGEPVDRGDVLADGPSTDLGE 301

Query: 805 LALGRNMLV 813
           LALG+NM V
Sbjct: 302 LALGQNMRV 310


>gi|291196408|emb|CBG27561.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas antarctica]
          Length = 305

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|156767169|gb|ABU95099.1| ribosomal polymerase B subunit [Acinetobacter towneri]
          Length = 266

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDMLSGLALVDLLEIQPSDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++   +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQTFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   K   +I+ LR+FL+K+    G   E +    DD +L +A   ++GVP++T
Sbjct: 180  EQIDKML---KQQREIAELRAFLDKIYNKVGGEQEDLDSLTDDEILVLAGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  SGQ++LYD
Sbjct: 237  PVFDGAEEGQIKELLELAELPRSGQTVLYD 266


>gi|11121240|emb|CAC14805.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  303 bits (776), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 193/341 (56%), Positives = 248/341 (72%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N             +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+
Sbjct: 1   LNETFAGAAEKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQF 60

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +
Sbjct: 61  RSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEV 120

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N Y
Sbjct: 121 THKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDY 180

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+
Sbjct: 181 GFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIM 240

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+
Sbjct: 241 ATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGI 300

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           E  VA  S  AIVA+R G+VE VDA R+VIR  + +     
Sbjct: 301 ERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|269913255|emb|CAY86054.1| RNA polymerase beta subunit [Gluconacetobacter azotocaptans]
          Length = 303

 Score =  303 bits (776), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 197/306 (64%), Gaps = 28/306 (9%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GMD++EIL+ FY K+V+ +    W  P
Sbjct: 61  VTTLLYALEGEASAAARAAKVAEGGDVDSLDIQGMDADEILNYFYGKVVFVKTSKGWARP 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             A     G K+   L+D ++GE V E+  KLT+ +++ + EK  K + + +  L G YV
Sbjct: 121 FDAE-SFRGLKLLEPLIDAESGEVVAEADAKLTARMVRKIAEK-TKDVLVGAAGLIGRYV 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A D+VN +TGEIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL  DKN 
Sbjct: 179 AYDLVNQDTGEIYAEAGEELTEARLEALEEAGLDRLPTLAVDASN-GPWIRNTLTVDKNT 237

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R DAL DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD PD V
Sbjct: 238 TRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLDAPDTV 297

Query: 429 RHIRKE 434
           R +RKE
Sbjct: 298 RVLRKE 303


>gi|55584694|gb|AAV53578.1| RNA polymerase II second largest subunit [Boletellus projectellus]
          Length = 899

 Score =  303 bits (776), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 147/1017 (14%), Positives = 300/1017 (29%), Gaps = 172/1017 (16%)

Query: 286  KSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G      +    V+     ++   G + D   LE I +   
Sbjct: 35   KTISQFQVKMFHRNQERSLGNVMKATIPYIRVDIPIWVVFRALGVISDRDILEHICYDMQ 94

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I                +       
Sbjct: 95   DSQMLEVLKPCIDDGFV--------IQDREVALDFI------------GNRGTTTGLSRE 134

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G 
Sbjct: 135  RRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGK 191

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 192  KRLDLAGPLLANLFRMLFKKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLAT 251

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 252  GNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 307

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN +
Sbjct: 308  GMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAH 359

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 360  SSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 416

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +       L+ +   ++  G      +      + K   I          +
Sbjct: 417  AGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEEFKWEQLVKSGIIELLDAEEEETV 476

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                   D   S +    +      + +   +    +K G            PS  LG  
Sbjct: 477  MISMTPEDLENSRLQSAGINP---QDHDADHDPAARLKAGITAHTWTHCEIHPSMILG-- 531

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       +
Sbjct: 532  -----VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLV 568

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 569  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 617

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 618  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIED 676

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G N         K+  +  D      R++          ++     +  Q    
Sbjct: 677  DGLIAPGTNVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI- 735

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q GDK A RHG KG +     
Sbjct: 736  -------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYR 776

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 777  QEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 829

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++     + LR       G+ V                   
Sbjct: 830  ------------------DLTVESVSTFLRQKGYQSRGLEVM------------------ 853

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  G +       G+     + +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 854  ----YHGHT-------GKKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 899



 Score =  140 bits (353), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 96/766 (12%), Positives = 216/766 (28%), Gaps = 122/766 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R+D    +P+     ALG+ S+ +IL      +  SQ  +     +    ++   +V+
Sbjct: 63  YIRVD----IPIWVVFRALGVISDRDILEHICYDMQDSQMLEVLKPCIDDGFVIQDREVA 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   +++     + L+++ +  + +            G  +   ++  
Sbjct: 119 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 177

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 178 LERRELDDRDHFGKKRLDLAGPLLANLFRMLFKKLTKDVYRYLQKCVETHKEFNLSLAV- 236

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 237 -------KHQTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 289

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       I  +
Sbjct: 290 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSCISVGSYSAPVIEFL 346

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +      NA         F     +    +  N +  I   RR   +         
Sbjct: 347 EEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 405

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR-------KVC 606
                  ++        P    E   + L              ++   YR       K  
Sbjct: 406 IRERELRLYTDAGRVCRPLFIVENQQLALQKK--------HIKWLNQGYRDDDGEEFKWE 457

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE-------EILVPRE 659
               +  +  L A EEE   I+     L+     +  +       +       +  +   
Sbjct: 458 QLVKSGIIELLDAEEEETVMISMTPEDLENSRLQSAGINPQDHDADHDPAARLKAGITAH 517

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                +  P  ++ + AS+IPF +++ S R      M +QA+ +                
Sbjct: 518 TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV--------- 568

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                              + + +  Y       +     +  R
Sbjct: 569 --------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR 596

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                                   +L  G+N +VA + + GYN EDS+++++  +   +F
Sbjct: 597 ------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 632

Query: 840 TSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            SI+   +  + + + +   E            +       I++ G+I  G  V   DI+
Sbjct: 633 RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTNVRGEDII 692

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +GK  P         E+L +        DV        +G+   V+
Sbjct: 693 IGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 734


>gi|317139935|ref|XP_001817863.2| DNA-directed RNA polymerase III subunit RET1 [Aspergillus oryzae
            RIB40]
          Length = 1218

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 105/514 (20%), Positives = 175/514 (34%), Gaps = 97/514 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +      + A+      D+ D  +    
Sbjct: 782  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGHNAMVAVMSYSGYDIEDALVLNKG 841

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F +   +    S   +   +     + D++  I    +         G+
Sbjct: 842  SVDRGFGRCQVFKKSVANLKSYSNGTKDILMPP---EYDNDAPIRKHALLESDGLAAVGE 898

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST           +S    F   D           + Y     + +  +
Sbjct: 899  QVNAGEVYINKSTP---------DQSLASGFPGSDMGRPVKYTPTPMTY----KLHDPAY 945

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++              +++KV     R  + GDK + RHG KG+V  I    DMPF  
Sbjct: 946  IDQVLV-----STTENENQLIKVLTRQTRRPEVGDKFSSRHGQKGVVGIIADQADMPFTD 1000

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI++NP G PSRM VG++ E   G A V  G+             ++S +     
Sbjct: 1001 QGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLAGQHGYGTCFGGSPVEEMSQILIDKG 1060

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   +                               G   EA+              
Sbjct: 1061 FSYGGKDYLTS----------------------------GITGEAL-------------- 1078

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                      PF   V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1079 ----------PF--YVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1126

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1127 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1183

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1184 ---MAIPYAAKLLIQELMSMNVTARLKLEDEFPE 1214



 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 120/936 (12%), Positives = 273/936 (29%), Gaps = 189/936 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 108 LVKQHIDSYNYLVEVQ----------LKKIVESSSIIRSDIDHNFYIKFTDIYLGAPRRA 157

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    I          +  + +K+    
Sbjct: 158 DEQQDVGPGFTGSTVSPHECRLRDTTYAAPIQVDFEYI----------RGRQRVKKTGCS 207

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 208 IGRMPVMLRSSKCVLSDKTPAEMTVLDECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 267

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 268 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLSEDIPIVILL 316

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +++ +      I    + DF      A  L  G       +D       I  GK
Sbjct: 317 KAMGIHTDKEMLLLVAGIDKVYQEDFAINFEEAIKL--GIYTQQQALDWIGSRIKINRGK 374

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           +      ++  ++ V+ +      +   ++    +N     +Y+ A         +    
Sbjct: 375 QNNYR--RTHVQEAVEAIA----SVIISHIEVKDMNFRPKAVYV-AHMARRVLMAKNDPS 427

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +           +         K   D  +++ +V+   + +    A ++ + 
Sbjct: 428 LVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNVDKVLNKRNRAEAFDAWTVMSM 487

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 488 HSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 547

Query: 458 NLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G + L +        + +++         D   P   +        +   
Sbjct: 548 GPRALQPSQFGMLCLADTPEGEACGLVKNLALMTHITTNDEEGPIRNLIFMLGAEDISTL 607

Query: 517 FCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                         +N        R  S L     + R     E   ++  H+ R     
Sbjct: 608 GGKELYGPGCYTISINGTPMALTRRPKSFLNAFRRLRRMGRISEFVSIYINHHQRAVHVA 667

Query: 574 TSEGHNIG---LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G       +V +  +  R +    +        D      V YL   EE +  IA  
Sbjct: 668 TDDGRICRPLIVVENGKNRVRSHHLKKLREGTMSFDDFLAQGLVEYLDVNEENDSLIAIY 727

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +                        E    ++  P  V+   A LIP+  ++ S R 
Sbjct: 728 EKDIT-----------------------EATTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 764

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+  + +                              ++D+I  ++     
Sbjct: 765 TYQCAMGKQAIGAIASNQFL--------------------------RIDSILYLMVY--- 795

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                                Q   V  R +    +  + + + A   +           
Sbjct: 796 --------------------PQKPMVKSRTI----ELTKYDQLPAGHNAM---------- 821

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             VA M + GY+ ED++++++  V          ++     +    G ++I       ++
Sbjct: 822 --VAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFKKSVANLKSYSNGTKDILMPPEYDND 879

Query: 871 EGLKN---IDECGIICVGAEVNPGDILVGKITPKGE 903
             ++    ++  G+  VG +VN G++ + K TP   
Sbjct: 880 APIRKHALLESDGLAAVGEQVNAGEVYINKSTPDQS 915


>gi|126722425|dbj|BAF48626.1| DNA-dependent RNA polymerase subunit B' [Halobiforma nitratireducens]
          Length = 435

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 116/253 (45%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG++  + P EDMPF ++G   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVIGHLAPQEDMPFTEEGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSLEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DEE +   L  A  + SG+  +Y G+ GE  + 
Sbjct: 284  --------------------TP-FLGEDEEDLRKGLEEAGFEPSGKETMYSGIAGEKVEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFSGVIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N++VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNLVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|291196434|emb|CBG27574.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas meridiana]
 gi|291196436|emb|CBG27575.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas mohnii]
 gi|291196438|emb|CBG27576.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas moorei]
 gi|291196450|emb|CBG27582.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas panacis]
 gi|291196462|emb|CBG27588.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas reinekei]
 gi|291196480|emb|CBG27597.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas umsongensis]
          Length = 305

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|291196428|emb|CBG27571.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas koreensis]
          Length = 305

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 236/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E++  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEEVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|321172108|gb|ADW77119.1| RNA polymerase beta subunit [Mycobacterium kansasii ATCC 12478]
          Length = 250

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 100/235 (42%), Positives = 135/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 48   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 107

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 108  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 165

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 166  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 195

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQQP
Sbjct: 196  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQP 250



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 56


>gi|186885867|gb|ACC93341.1| RNA polymerase beta subunit [Gerbera serrata]
          Length = 1028

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 100/268 (37%), Positives = 145/268 (54%), Gaps = 42/268 (15%)

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    
Sbjct: 799  YLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLV 858

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
            F E    +                               VF+                + 
Sbjct: 859  FSELYEASKQTANPW------------------------VFE---------------PEY 879

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+L+TQQPL G++ +G
Sbjct: 880  PGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALLTQQPLKGRAKQG 939

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNV 1349
            GQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  + + G         PESF +
Sbjct: 940  GQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTTIIGGTIPTPEDAPESFRL 999

Query: 1350 LVKEMQALGLSID--LENSRTKNSAKME 1375
            LV+E+++L L ++  L + +T    + E
Sbjct: 1000 LVRELRSLALELNHFLVSEKTFQINRKE 1027



 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 145/440 (32%), Positives = 226/440 (51%), Gaps = 6/440 (1%)

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            I++          L  +    +    IL  V          N     K   +++A+L+ 
Sbjct: 125 RIWVRVSRKQKLSILVLLSAMGLNLKEILENVCYPEIFLSFLNDKEKKKIGSKENAILEF 184

Query: 378 YRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           Y+      GD        +     FF   + +L  +GR  +N RLNLD P +   +   D
Sbjct: 185 YQQFACVGGDPVFSESLCNDLQKKFF-QQRCELGGIGRRNINRRLNLDIPQNNTFLLPRD 243

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--V 493
           I+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q+ L L+R+E   +  I     
Sbjct: 244 ILAAADHLIGIKFGMGTLDDMNHLKNKRIRSVADLLQEQFGLALVRLENMARGNICVALK 303

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                 PQ L+N+ P+      FF    LSQ+ +  N L++I H R+LS LG GG+    
Sbjct: 304 HKWIPTPQKLVNSTPLTGTYEVFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRT 363

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+  +G +E+P+ ++ +      
Sbjct: 364 ANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARIGRWGSLESPFYEIYERSKGAR 423

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           ++YLS   +E   +A  NS     G   E++V  R   E + +  E++        Q  S
Sbjct: 424 MLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 483

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E   A  SGA  +A+  G
Sbjct: 484 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLERQAALDSGALAIAEHEG 543

Query: 734 IVEQVDAIRIVIRSVEGDLD 753
            +   D  +I++      L+
Sbjct: 544 KIIYTDTDKILLSGNGDTLN 563



 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 97/184 (52%), Gaps = 11/184 (5%)

Query: 71  AAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
              L    Y+   P     D ++  LTY+  L ++ RLI             ++I+EQ+I
Sbjct: 5   DFQLFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWK-------TSRRRNIQEQTI 57

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MG +PLM   GTF++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D G 
Sbjct: 58  FMGKIPLMNSLGTFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGG 114

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPL 249
            +++E D K  I VR+ R++K+ +   L A+G++ +EIL    YP+I  S   D     +
Sbjct: 115 RLELEIDRKARIWVRVSRKQKLSILVLLSAMGLNLKEILENVCYPEIFLSFLNDKEKKKI 174

Query: 250 SAAD 253
            + +
Sbjct: 175 GSKE 178


>gi|313192588|emb|CBY17540.1| RNA polymerase subunit B [Halogranum amylolyticum]
          Length = 608

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 115/594 (19%), Positives = 200/594 (33%), Gaps = 101/594 (17%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
            + +    +  D     ++ VA            + I  +++       I   E     R 
Sbjct: 94   LVERGYVEFIDAEEEEDIYVAVDEEEVSEDHTHLEIDPQLIFGIGAGMIPYPEHNASPRI 153

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            T      + +    +     +   +     +        +        G       +  +
Sbjct: 154  TMGAG--MMKQSLGLPSANYRIRPDTR-QHLLHYPQLSMVKTQTTEQIGFDERPAAQNFV 210

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             A+   +  ++ D  +     V    +    F R    +  R    + ++ E+ ++D   
Sbjct: 211  VAVMSYEGFNIEDALVMNKGSVE-RAMARSHFFRTYEGEERRYPGGQEDRFEIPSQD--- 266

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                +           L     V+      +++VL           +         + +R
Sbjct: 267  ----VRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMGGLSPQKRR 322

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                     E          + +               ++ KV V  +R  + GDK A R
Sbjct: 323  ETSVTMRSGEDGVVDTVTLMEGE------------DGSKLSKVSVRDERIPELGDKFASR 370

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+V  + P EDMPF + G   D+VLNP  +PSRM V        G     LG K+ 
Sbjct: 371  HGQKGVVGHLAPQEDMPFTEQGVVPDLVLNPHALPSRMTV--------GHVLEMLGGKVG 422

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +L                                                       F G
Sbjct: 423  ALEGRRVDGT----------------------------------------------AFQG 436

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
              EE +   L     + +G+ ++Y G+TGE  +  + +G I+  KL HMVS+K++ARS G
Sbjct: 437  ESEEELRGALEDHGFNSAGKEVMYSGVTGEKVEAQIFLGIIFYHKLYHMVSNKLHARSRG 496

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES-- 1331
               ++T+QP  G++  GG R+GEME   +  +GAA  L+E L   SD    R  VY S  
Sbjct: 497  PVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSD----REEVYVSAD 552

Query: 1332 ----------------IVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                             + G  ++  +     +F +L+ EM+ALG+   +E   
Sbjct: 553  TGMVAVEDREQRRIYDPITGDEDNIHKIEVSYAFKLLLDEMKALGIRPKIELED 606



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/358 (15%), Positives = 115/358 (32%), Gaps = 28/358 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +      ++   R  G+   +    +               +  P +  ++   +L
Sbjct: 17  GTHPDPNELAAQIREARRRGDVSQMVNVSVKERTREVIVNADAGRARRPLIVVEEGQPLL 76

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               ++      L+ E       +E + A+      VA     V + D   + I      
Sbjct: 77  GDDEIEAVENGELEFEDLVERGYVEFIDAEEEEDIYVAVDEEEVSE-DHTHLEIDPQLIF 135

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKVGDEVRRNDIIADGPST 800
              +            + +     + Q           RP  +          +    +T
Sbjct: 136 GIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQTT 195

Query: 801 D---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +     +    +N +VA M + G+N ED++++++  V   +  S     +E   R    G
Sbjct: 196 EQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVERAMARSHFFRTYEGEERRYPGG 255

Query: 858 PEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            E+   +IP+        E+   ++DE G++     V+   +L+GK +P           
Sbjct: 256 QEDRF-EIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEP---- 310

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
               + G      R+TS+ + SG  G V  V +       K  +    +    EL  +
Sbjct: 311 --DDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 366



 Score = 44.7 bits (104), Expect = 0.13,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 61/195 (31%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +     ++I   RR   + Q      +       V+        P    
Sbjct: 10  YVNGSLVGTHPDPNELAAQIREARRRGDVSQMVNVSVKERTREVIVNADAGRARRPLIVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E                +    +E    +  D      V ++ A EEE+ Y+A     + 
Sbjct: 70  EEG--------QPLLGDDEIEAVENGELEFEDLVERGYVEFIDAEEEEDIYVAVDEEEVS 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 EDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPSANYRI 173


>gi|291196410|emb|CBG27562.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           argentinensis]
          Length = 305

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +GKVT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVQEGKVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V R DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDVVARGDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|18977936|ref|NP_579293.1| DNA-directed RNA polymerase subunit beta [Pyrococcus furiosus DSM
            3638]
 gi|18893706|gb|AAL81688.1| DNA-directed RNA polymerase subunit b [Pyrococcus furiosus DSM 3638]
          Length = 1117

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 136/331 (41%), Gaps = 77/331 (23%)

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+   + GD       ++VKV V   R  + GDK A RHG KG++  I+P EDMP+ + 
Sbjct: 846  DKVIITETGD-----GTKLVKVTVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPWTES 900

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP G+PSRM VGQ+ E   G      G+++       +    +      L  
Sbjct: 901  GIVPDLIVNPHGIPSRMTVGQLIEAIGGKVASLKGRRVDGTAFIGEPEEKLRKELEELGF 960

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                +DG                  G+ 
Sbjct: 961  KHTGREIM----------------------------YDGIT----------------GK- 975

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                       +  + +G IY  +L+HMV+DK++ARS G   ++T+QP  G++  GG R 
Sbjct: 976  ---------RLEADIFIGVIYYQRLHHMVADKIHARSRGPVQVLTKQPTEGRAREGGLRF 1026

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG--------RTRVYESIVAGND-- 1337
            GEME   +  +GAA +L E L  +SD          G        R RVY   V G +  
Sbjct: 1027 GEMERDVLVGHGAAMLLIERLLEESDKTEVWVCENCGHIALEDKRRRRVY-CPVCGEEER 1085

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
              +     +F +L+ E++A+ +   L  S  
Sbjct: 1086 ISKVEMSYAFKLLLDELKAMVIRPKLNLSER 1116



 Score =  204 bits (520), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 154/976 (15%), Positives = 290/976 (29%), Gaps = 196/976 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY+ F+            GLQ        I        ++F       P+F  
Sbjct: 27  LVRQHLDSYNAFI----------ERGLQEVVNEFGGIKPDIPDFEVKFGKIRVGEPEFQE 76

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      D   R+LTYA PL + +  ++  V++              + +G+LP+M
Sbjct: 77  PHGQRKPLYPMDARIRNLTYAAPLYLEMIPVIKGVEQDPV----------EVRIGELPIM 126

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F+I G +R++VS    +P         R   
Sbjct: 127 LKSKVCRLYGLSDEELIKLGEDPKDPGGYFIINGSERVIVSIEDIAPNRTLVEKDERQEK 186

Query: 175 SGKLLYACRIIPDQ---GLWMDIEFDSKDIIHVRIDRRRKVPV--TSFLMALGMDSE-EI 228
                Y  ++   +      + +E     I++V I    K PV     + ALG++ + +I
Sbjct: 187 -----YIAKVFSYRHGYRALVAVERRKDGILYVDIPNVPK-PVKFVYVMRALGLERDKDI 240

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +          Q         +  D         +L  I       ++ +         +
Sbjct: 241 VEAVGNDPEVQQ-----IMFDNLEDASDITTQQEALEFIGKLVAPGQAREYRLKRAEYVI 295

Query: 289 KEKGVKFLGITSDCLCGL-----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
               +  +G++ +           +A  ++    G    +  D    K L          
Sbjct: 296 DNNLLPHMGVSPEDRIKKAYYLGMMALKVIELSLGRRPEDDKDHYANKRLRLAGDLLKDL 355

Query: 344 IPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             + +   V +  Y   +            +    I   +RP DV T  +  ++    + 
Sbjct: 356 FRVAFSQLVKDIQYQMTKTYQRKGDKYTFGNIHRFIRNSIRP-DVLTERIEHALATGAWP 414

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                    + R      L+         + +E      + L       G I   +    
Sbjct: 415 GGRTGVSQLLDRTNYMSTLSHLRRVTSP-LDREQPHFEARDLHGTH--WGRICPTETPEG 471

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                V  +        + ++  ++ E      + S+    +   +P  +    +     
Sbjct: 472 PNCGLVKNLA------LMAQITTAVPEEEIREYLMSLGIVPIEVRRPDPTLWRVYLNGVL 525

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +  +E+    + RI   RR   +           V+   V+        P    E    G
Sbjct: 526 IGTIEDGKALVQRIRQDRRSGKISDVINVAYYEDVKEVYVNSDDGRVRRPLIIVEN---G 582

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           +        +    G +     K  D      + YL A EEEN Y+A             
Sbjct: 583 VPKLTKEHVQAVKEGRL-----KWSDLIKMGIIEYLDAEEEENAYVAM------------ 625

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            E+   ++  P  ++ + ASL+P+ E++ + R   G  M +Q++
Sbjct: 626 -----------WPWEVTEEHTHLELMPAAILGLPASLVPYPEHNAAPRNTYGAGMAKQSL 674

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            L  A                                                +   +  
Sbjct: 675 GLGWANFRI-----------------------------------------RVDTRGHLLH 693

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               Q PLV                +    D   G+N +VA + + GY
Sbjct: 694 YP--------------QIPLVNS----------RIMKAVGYEDRPAGQNFVVAVLAYQGY 729

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNI 876
           N ED+++I++  +   +  S     +E   +    G  ++     P V     E+  +N+
Sbjct: 730 NMEDAIIINKASIERGLARSTFFRTYEAEEKKYLGGQTDKFEIPDPTVRGYRGEKYYRNL 789

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE G+I   ++V   D+LVG+ +P        EE+ L  +      + R+TS+ V     
Sbjct: 790 DEDGLIFPESKVEGKDVLVGRTSPPRFL----EERGLGTV---SLQERRETSVAVRPSEK 842

Query: 937 GTVVDVRIFNRHGIDK 952
           G V  V I       K
Sbjct: 843 GVVDKVIITETGDGTK 858


>gi|89274896|gb|ABD65889.1| RNA polymerase II second largest subunit [Phaeolus schweinitzii]
          Length = 887

 Score =  303 bits (775), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 126/910 (13%), Positives = 262/910 (28%), Gaps = 173/910 (19%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         ++  L+     +  +DD D+ G +R+
Sbjct: 124  RYAQEILQKEMLPHISMAEGSESKK---AYFFGYMVHRLLLAAMEREDLDDRDHFGKKRL 180

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +    + + +     +   
Sbjct: 181  DLAGPLLSNLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVKHNTITNGLKYSLATGNW 240

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 241  GDQKRTMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 296

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR---- 625
            CPAET EG   GLV +L+  + +            + +         L ++EE       
Sbjct: 297  CPAETPEGQACGLVKNLSLMSCITVGTLSAPVIEFLEEWG-------LESLEENAHSTIP 349

Query: 626  ----YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +   + +      ++I      + D  +   +          P
Sbjct: 350  CTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDINAEVSVVRDIRERELRVYTDAGRVSRP 409

Query: 681  FLENDDSNRVLMGCN---MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                ++   +    +   M           +  V TG+  ++       ++       E 
Sbjct: 410  LFIVENQQLLFTKKHINLMLSTDEEKKLKWSALVKTGLIEMLDAEEEETVMI--CMTPED 467

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            ++  R+    V+   +                            +K              
Sbjct: 468  LENSRLQSMGVDPHANDGDFDPAA-------------------RLKANPNAHTWTHCEIH 508

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 509  PSMILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 543

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   +               +  +             +       +   +  + AI 
Sbjct: 544  IYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAIL 592

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    ++ R  +D  ++S   + E+ E   R+       
Sbjct: 593  CYSGYNQEDSVIMNQSAIDRGLF-RSMYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKH 651

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G N         K+  +  D      R++          ++     
Sbjct: 652  GTYDKLEDDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRAHTRRDVSTPLKSTESG 711

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VK+ V   R  Q GDK A RHG K
Sbjct: 712  IIDQVLI--------------------TTNAEGQKFVKIRVRSTRVPQIGDKFASRHGQK 751

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +   
Sbjct: 752  GTIGITYRQEDMPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKVATIIGNEGDATPF 811

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S +    +K   +                                       
Sbjct: 812  TELTVEGVSDVLR--QKGYHSRGLEIM--------------------------------- 836

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                          G +       G      V +G  Y  +L HMV DK+++R+ G   +
Sbjct: 837  ------------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQI 877

Query: 1278 VTQQPLGGKS 1287
            +T+QP+ G+S
Sbjct: 878  LTRQPVEGRS 887



 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 101/771 (13%), Positives = 222/771 (28%), Gaps = 114/771 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 49  YIKVD----IPIWVLFRALGVISDRDILEHICYDMQDAQMLELLKPCIDDGFVIQDREVA 104

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  V   ++  
Sbjct: 105 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMVHRLLLAA 163

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
              E   +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 164 MEREDLDDRDHFGKKRLDLAGPLLSNLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVK 223

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  +   S  G  ++  R    +      R    
Sbjct: 224 HNT--------ITNGLKYSLATGNWGDQKRTMASKAGVSQVLNRYTYASTLSHLRRCNTP 275

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + E +   
Sbjct: 276 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCITVGTLSAPVIEFLEEW 335

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++S+      NA   +     F     +    +  N +  I   RR   +         
Sbjct: 336 GLESL----EENAHSTIPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDINAEVSVVRD 391

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  V+        P    E   +       +          E    K      T  
Sbjct: 392 IRERELRVYTDAGRVSRPLFIVENQQLLFTKKHINL----MLSTDEEKKLKWSALVKTGL 447

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDA 666
           +  L A EEE   I      L+     +  +      G+     R             + 
Sbjct: 448 IEMLDAEEEETVMICMTPEDLENSRLQSMGVDPHANDGDFDPAARLKANPNAHTWTHCEI 507

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 508 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 551

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 552 -------------------------RMDTMANILYYPQKPLATTRSMEYLRFR------- 579

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F S++   
Sbjct: 580 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSAIDRGLFRSMYYRS 622

Query: 847 FEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E        +   +       +++ G+I  G  VN  DI++GK  P 
Sbjct: 623 YMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKLEDDGLIAPGTNVNGEDIIIGKTAPI 682

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++        +A   RD S  + S  SG +  V I       K
Sbjct: 683 PPDSEELGQRT-------RAHTRRDVSTPLKSTESGIIDQVLITTNAEGQK 726


>gi|291196456|emb|CBG27585.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas poae]
 gi|291196478|emb|CBG27596.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas trivialis]
          Length = 305

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 235/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++    T+ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKVLTDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|291196440|emb|CBG27577.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas moraviensis]
          Length = 305

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 235/305 (77%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNEQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|3746600|gb|AAC64015.1| RNA polymerase II subunit 2 [Mostuea brunonis]
          Length = 255

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 107/255 (41%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 L+ VK+ +   R  Q G+K   R G KG +      EDMP+  +G   DI++NP 
Sbjct: 36   TNADGLKFVKIRMKSVRIPQIGNKFTSRPGQKGTIGMTYTPEDMPWTLEGITPDIIVNPH 95

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 96   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 123

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 124  ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRLM 161

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+
Sbjct: 162  GDVIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAH 221

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L  +SD
Sbjct: 222  GAAHFLKERLFDQSD 236


>gi|291196442|emb|CBG27578.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas mosselii]
          Length = 305

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 183/305 (60%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++D+V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVSDDIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAAMNEKKQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V+R DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKVQRGDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|213876737|gb|ACJ54365.1| RNA polymerase subunit B [Mycobacterium sp. FI-06114]
          Length = 251

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 100/236 (42%), Positives = 140/236 (59%), Gaps = 40/236 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 48   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 107

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +   +              
Sbjct: 108  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAAS-------------- 152

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             + +  +  +    VSTPVFDGA E  +  +L            
Sbjct: 153  -----------------LPKELQSAEPNAIVSTPVFDGAREAELQGLLSCTLPNRDNEVM 195

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            ++  G+++L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARSTG YS++TQQPL
Sbjct: 196  VNGDGKAVLFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYSMITQQPL 251



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GK+TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 56


>gi|291196446|emb|CBG27580.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           pachastrellae]
          Length = 304

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 232/305 (76%), Gaps = 1/305 (0%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR+V D +VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNQYGFLESPYRRVKDAEVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++ + EDG   ++LV  R   E  +   E +  +D SP+QVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAKV-EDGKLVDDLVAVRHMNEFTVKAPEDVTLMDVSPRQVVSVAA 179

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA+ SG  + A+R G+++
Sbjct: 180 SLIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERNVARDSGVCVTARRGGVID 239

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L+K+ RSNQNTC+NQRPLVK GD V R DI+AD
Sbjct: 240 SVDASRIVVRVNDDEVEAGEAGVDIYTLIKYTRSNQNTCINQRPLVKKGDVVSRKDILAD 299

Query: 797 GPSTD 801
           G S D
Sbjct: 300 GSSVD 304


>gi|55273999|gb|AAV48870.1| RNA polymerase II second largest subunit [Climacodon septentrionalis]
          Length = 886

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 148/1021 (14%), Positives = 301/1021 (29%), Gaps = 179/1021 (17%)

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDI----VNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G  +   I    V+     ++   G + D   LE I +   
Sbjct: 25   KTISQFQVKLYHRNQERSMGNVLKATIPYIKVDIPIWVVFRALGVISDRDILEHICYDMQ 84

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I                +       
Sbjct: 85   DAQMLEMLKPCIDDGFV--------IQDREIALDFI------------GNRGTTTGLNRE 124

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + +  +      +  +  +          I  L+     +  +DD D+ G 
Sbjct: 125  RRLRYAQEILQKEMLPHISMAEGSESKK---AYFFGYRIHRLLLAALERRDLDDRDHFGK 181

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +    + + +     +
Sbjct: 182  KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKYSLAT 241

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 242  GNWGDQKKMMSAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 297

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + ++           + +  + +         EEN +
Sbjct: 298  GMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL--------EENAH 349

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             A   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 350  SATPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 406

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA-AIVAKRAGIVEQVDAIRIVI 745
            + RV     +       +  +       +  +  K SG       + G++E +DA     
Sbjct: 407  AGRVCRPLFIVENQQLTITKK------HISQLSDKESGYKWDDLIKGGVIELLDAEEEET 460

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +      +    +          ++    +K      +       PS  LG  
Sbjct: 461  VMICMTPEDLELARNGIDPL----QQDAADIDMSVRLKTAQTAHKFTHCEIHPSMILG-- 514

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       +
Sbjct: 515  -----VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLV 551

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 552  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 600

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+     R+          +    
Sbjct: 601  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFGKPTRETTLRMKHGTYDKIED 659

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 660  DGLIAPGTGVNGEDIIIGKTAPIPPDSEKLGQRTRQHTRRDVSTPLKSTESGIIDQVLI- 718

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VK+ V   R  Q GDK A RHG KG +     
Sbjct: 719  -------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYR 759

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 760  QEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 812

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++       LR       G+ V                   
Sbjct: 813  ------------------DLTVESVSQFLRKEGYQSRGLEVM------------------ 836

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G +    G         V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 837  ----YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 885

Query: 1286 K 1286
            +
Sbjct: 886  R 886



 Score =  140 bits (354), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 103/758 (13%), Positives = 225/758 (29%), Gaps = 113/758 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 53  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREIA 108

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   ++L     + L+++ +  + +            G  +   ++  
Sbjct: 109 LDFIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYRIHRLLL-A 166

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDAL 374
                 ++  D   +K L+           +L+   + +   Y++  + T K  +   A+
Sbjct: 167 ALERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAV 226

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
                        T  +  S+    + D  K   +  G  ++  R    +      R   
Sbjct: 227 KHNT--------ITNGLKYSLATGNWGDQKKMMSAKAGVSQVLNRYTYASTLSHLRRCNT 278

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  I     L N    +         +   + + L     + +  +   + E +  
Sbjct: 279 PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEE 338

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             ++S+      NA         F     +    +  N +  I   RR   +        
Sbjct: 339 WGLESL----EENAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVR 394

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
                   ++        P    E   + +         ++     E+ Y K  D     
Sbjct: 395 DIRERELRLYTDAGRVCRPLFIVENQQLTITKK-----HISQLSDKESGY-KWDDLIKGG 448

Query: 613 DVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPR---EKIDFIDAS 667
            +  L A EEE   I     +  L  +G    +           L       K    +  
Sbjct: 449 VIELLDAEEEETVMICMTPEDLELARNGIDPLQQDAADIDMSVRLKTAQTAHKFTHCEIH 508

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ + AS+IPF +++ S R      M +QA+ +                        
Sbjct: 509 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV----------------- 551

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + +  Y       +     +  R        
Sbjct: 552 ------------------------RMDTMANILYYPQKPLATTRSMEYLKFR-------- 579

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +
Sbjct: 580 ----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSY 623

Query: 848 EVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             + + + +   E            +       I++ G+I  G  VN  DI++GK  P  
Sbjct: 624 MDLEKKSGVQQLEEFGKPTRETTLRMKHGTYDKIEDDGLIAPGTGVNGEDIIIGKTAPI- 682

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                  EKL +        DV        SG+   V+
Sbjct: 683 ---PPDSEKLGQRTRQHTRRDVSTPLKSTESGIIDQVL 717


>gi|320593507|gb|EFX05916.1| DNA-directed RNA polymerase beta [Grosmannia clavigera kw1407]
          Length = 1165

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 171/1159 (14%), Positives = 356/1159 (30%), Gaps = 201/1159 (17%)

Query: 242  GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
            G ++    +   +++  ++S + V +++ E+       +TS    + + K   ++ +  +
Sbjct: 173  GGYFIVNGTEKVILIQEQLSKNRVIVESEEKNGVISASVTSS---THERKSKTYVTLKKE 229

Query: 302  CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
             +   +    +V+     I ++A   + +  + ++       +        ++ A   + 
Sbjct: 230  RIALQH--NVLVDNIPIVIVLKAFGGLTDYEIMQL-------VAGSDGRYQDDFAINFDE 280

Query: 362  LVTDKNKDRKDALLDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
                    ++ AL  +   ++ G  +             +   + + ++        N+ 
Sbjct: 281  AAKMGVFTQQQALEYVGARVKMGTRNGGGPGGGPGGMRPMGPPTKRNNVEEGLDALANII 340

Query: 420  LNLDTPDDVRHIRKEDIIAII-KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            +     D +    K   +A++ + ++   +    +DD D +GN+R+   G++L   +   
Sbjct: 341  IAHVPIDGLDFFPKAVYVAMMARRVLMAMHNPQLVDDRDFVGNKRLELAGQLLSLLFEDL 400

Query: 479  LLRMERSIKERI-------SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
              + +  ++  I               +         +   +     +   S     +N 
Sbjct: 401  FKKFQSDLRFNIDKFFKKPHQGVAFDPLTSISATGHHISQGMNRAIQTGNWSVKRFGMNR 460

Query: 532  LSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
                    RLS +   G+         + R     R + P+ +G +CP++T EG   GLV
Sbjct: 461  GGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPRALQPSQWGMLCPSDTPEGEACGLV 520

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             +L     +  +         V    + + V  L        + A           +   
Sbjct: 521  KNLALMTHITTHVEEGPVRAWV--FSLDDSVEPLRNFSGAEMHRAGWYVVHVNGTPYALT 578

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                R       + R        SP   ++I +                           
Sbjct: 579  PNPRRFCARFRTMRRRGW----ISPFVSININSHF--------------ASVHIATDEGR 620

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +      V  G   + A+        +    V   D +R  +       +   + V +Y 
Sbjct: 621  ICRPYIIVKNGQSRLRAEHLRLLQQGR----VTFDDFLRRGVIEYLDVNEEQDALVALYE 676

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                                  D    +  +   P T LG +A         +P+  +N 
Sbjct: 677  A---------------------DCTAASTHMEIEPFTILGAVA-------GLIPFPHHNQ 708

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +    + +   +                               ++ 
Sbjct: 709  SPRNTYQCAMGKQAIGAIAYNQFHRIDT-----------------------------LLY 739

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                     +    I       +   +     +      D+ D  +   + +       +
Sbjct: 740  TLVYPQRPMVATKTIELVHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASIDRGYGRCQ 799

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  + + +R  +   E++    RDKD E+ I              G     G    K
Sbjct: 800  VF-RKYVAEMQRFPNGRTERVGGPERDKDGEK-ISKHAAIDNDGLAAVGWRVQHGDVMIK 857

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI-EKIQW 1062
            K + +                 +  ++         + Y  +    +  + +K+      
Sbjct: 858  KESPV-----------DLTTTGIGADRGSNEYRDSSLTYRIN----DPSYVDKVMVSQTE 902

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
             D +      + KV     R  + GDK + RHG KG+V  I+  EDMPF   G   DI+ 
Sbjct: 903  KDTL------IFKVQTRQTRRPEIGDKFSSRHGQKGVVGIIVEQEDMPFADSGLVPDII- 955

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                             +    
Sbjct: 956  --------MN----------------------------------------PHGYPSRMTV 967

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
             K+ +        VA +   G   +   F     EA+   L       +G+     G TG
Sbjct: 968  GKLFECLTGKASVVAGRRDYGYGDA---FRSHPVEAMGEELVRHGFSWAGKDCFTSGTTG 1024

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G IY  +L HMV DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1025 EPMEAHIFNGPIYYQRLKHMVQDKMHSRAKGPRAILTRQPTEGRSRDGGLRLGEMERDCL 1084

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVL 1350
             AYGA+ +L E L   SD    D+     ++     G         D  +   P +  +L
Sbjct: 1085 IAYGASQLLLERLMFSSDATSLDLCQHCGLFGY--KGYCQTCRSTRDVTQMTMPYAAKLL 1142

Query: 1351 VKEMQALGLSIDLENSRTK 1369
            V+E+ ++ + + L+     
Sbjct: 1143 VQELISMNVGVRLQLEDEF 1161



 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 123/1007 (12%), Positives = 271/1007 (26%), Gaps = 199/1007 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY+ F+   I      N  ++         +       LEF       P    
Sbjct: 44  LVKQHIDSYNFFVEQEIKDIVTANRTIR---------SDVQSGFYLEFTDIRVGRPTRTD 94

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TYA P+ + +             +  K I  ++I +G +P
Sbjct: 95  FSDIKSQNEVTPMECRLRDMTYAAPIVVDI----------AYTRDKKRIIRRNITLGRMP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F++ G +++++ Q   S        + + 
Sbjct: 145 VMLKSSKCCLSGATNSQMEVMNECPLDPGGYFIVNGTEKVILIQEQLSKNRVIVESEEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL- 221
            +    + +               + K   +V + + R           +P+   L A  
Sbjct: 205 GVISASVTSST------------HERKSKTYVTLKKERIALQHNVLVDNIPIVIVLKAFG 252

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+   EI+          Q      F  +A   +   + +   V           G    
Sbjct: 253 GLTDYEIMQLVAGSDGRYQDDFAINFDEAAKMGVFTQQQALEYVGARVKMGTRNGGGPGG 312

Query: 282 SGLLKSLKEKGVKFLGITS-----DCLCGLYVAEDIVNGETGEIYIEAGDVI------DE 330
                       K   +         +   +V  D ++     +Y+            + 
Sbjct: 313 GPGGMRPMGPPTKRNNVEEGLDALANIIIAHVPIDGLDFFPKAVYVAMMARRVLMAMHNP 372

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
           + +++      + + +           +     +D   +        ++ +    +++ S
Sbjct: 373 QLVDDRDFVGNKRLELAGQLLSLLFEDLFKKFQSDLRFNIDKFFKKPHQGVAFDPLTSIS 432

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
                 +     + +    +V R  MN          + +I    ++  I    +     
Sbjct: 433 ATGHHISQGMNRAIQTGNWSVKRFGMNRGGVTHVLSRLSYISALGMMTRISSQFEKTRKV 492

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
                +       +             +  L +   I   +    + + +     + +P+
Sbjct: 493 SGPRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTHVEEGPVRAWVFSLDDSVEPL 552

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +        +    +  +    +   + RR  A  +  + R         ++   +   
Sbjct: 553 RNFSGAEMHRAGWYVVHVNGTPYALTPNPRRFCARFRT-MRRRGWISPFVSININSHFAS 611

Query: 570 CPAETSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
               T EG        V +  S  R      ++       D      + YL   EE++  
Sbjct: 612 VHIATDEGRICRPYIIVKNGQSRLRAEHLRLLQQGRVTFDDFLRRGVIEYLDVNEEQDAL 671

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +A   +                               ++  P  ++   A LIPF  ++ 
Sbjct: 672 VALYEADCTAAS-----------------------THMEIEPFTILGAVAGLIPFPHHNQ 708

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           S R    C M +QA+                                           I 
Sbjct: 709 SPRNTYQCAMGKQAIGA-----------------------------------------IA 727

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +     +     +Y               QRP+V                      L 
Sbjct: 728 YNQFHRIDTLLYTLVYP--------------QRPMVA----------TKTIELVHYDKLP 763

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----IT 862
            G+N  V  M + GY+ ED++++++  +           ++    +    G  E      
Sbjct: 764 AGQNATVVVMSYSGYDIEDALVLNKASIDRGYGRCQVFRKYVAEMQRFPNGRTERVGGPE 823

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RD           ID  G+  VG  V  GD+++ K +P   +                + 
Sbjct: 824 RDKDGEKISKHAAIDNDGLAAVGWRVQHGDVMIKKESPVDLT-------TTGIGADRGSN 876

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           + RD+SL         + D    ++  + + E+   + + Q     R
Sbjct: 877 EYRDSSLTYR------INDPSYVDKVMVSQTEKDTLIFKVQTRQTRR 917


>gi|76556256|emb|CAJ00148.1| RNA polymerase beta subunit [Pseudomonas syringae pv. primulae]
 gi|76556270|emb|CAJ00155.1| RNA polymerase beta subunit [Pseudomonas cannabina]
 gi|76556278|emb|CAJ00159.1| RNA polymerase beta subunit [Pseudomonas syringae pv. delphinii]
 gi|76556280|emb|CAJ00160.1| RNA polymerase beta subunit [Pseudomonas syringae pv. garcae]
 gi|76556282|emb|CAJ00161.1| RNA polymerase beta subunit [Pseudomonas syringae pv. lachrymans]
 gi|76556290|emb|CAJ00165.1| RNA polymerase beta subunit [Pseudomonas syringae pv. persicae]
 gi|76556298|emb|CAJ00169.1| RNA polymerase beta subunit [Pseudomonas syringae pv. tomato]
 gi|76556300|emb|CAJ00170.1| RNA polymerase beta subunit [Pseudomonas syringae pv. apii]
 gi|76556306|emb|CAJ00173.1| RNA polymerase beta subunit [Pseudomonas syringae pv. antirrhini]
 gi|76556308|emb|CAJ00174.1| RNA polymerase beta subunit [Pseudomonas syringae pv. theae]
 gi|76556318|emb|CAJ00179.1| RNA polymerase beta subunit [Pseudomonas syringae pv. philadelphi]
          Length = 313

 Score =  302 bits (774), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 182/312 (58%), Positives = 237/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|291196468|emb|CBG27591.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas simiae]
          Length = 305

 Score =  302 bits (774), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|291196418|emb|CBG27566.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas costantinii]
 gi|291196420|emb|CBG27567.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           extremorientalis]
 gi|291196458|emb|CBG27586.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas proteolytica]
 gi|291196466|emb|CBG27590.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas salomonii]
          Length = 305

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|238483555|ref|XP_002373016.1| DNA-directed RNA polymerase III, beta subunit, putative [Aspergillus
            flavus NRRL3357]
 gi|220701066|gb|EED57404.1| DNA-directed RNA polymerase III, beta subunit, putative [Aspergillus
            flavus NRRL3357]
          Length = 1218

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 105/514 (20%), Positives = 175/514 (34%), Gaps = 97/514 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +      + A+      D+ D  +    
Sbjct: 782  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGHNAMVAVMSYSGYDIEDALVLNKG 841

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F +   +    S   +   +     + D++  I    +         G+
Sbjct: 842  SVDRGFGRCQVFKKSVANLKSYSNGTKDILMPP---EYDNDAPIRKHALLESDGLAAVGE 898

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST           +S    F   D           + Y     + +  +
Sbjct: 899  QVNAGEVYINKSTP---------DQSLASGFPGSDMGRPVKYTPTPMTY----KLHDPAY 945

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++              +++KV     R  + GDK + RHG KG+V  I    DMPF  
Sbjct: 946  IDQVLV-----STTENENQLIKVLTRQTRRPEVGDKFSSRHGQKGVVGIIADQADMPFTD 1000

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI++NP G PSRM VG++ E   G A V  G+             ++S +     
Sbjct: 1001 QGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLAGQHGYGTCFGGSPVEEMSQILIDKG 1060

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   +                               G   EA+              
Sbjct: 1061 FSYGGKDYLTS----------------------------GITGEAL-------------- 1078

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                      PF   V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1079 ----------PF--YVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1126

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1127 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1183

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1184 ---MAIPYAAKLLIQELMSMNVTARLKLEDEFPE 1214



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 120/936 (12%), Positives = 273/936 (29%), Gaps = 189/936 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 108 LVKQHIDSYNYLVEVQ----------LKKIVESSSIIRSDIDHNFYIKFTDIYLGAPRRA 157

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    I          +  + +K+    
Sbjct: 158 DEQQDVGPGFTGSTVSPHECRLRDTTYAAPIQVDFEYI----------RGRQRVKKTGCS 207

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 208 IGRMPVMLRSSKCVLSDKTPAEMTVLDECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 267

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 268 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLSEDIPIVILL 316

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +++ +      I    + DF      A  L  G       +D       I  GK
Sbjct: 317 KAMGIHTDKEMLLLVAGIDKVYQEDFAINFEEAIKL--GIYTQQQALDWIGSRIKINRGK 374

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           +      ++  ++ V+ +      +   ++    +N     +Y+ A         +    
Sbjct: 375 QNNYR--RTHVQEAVEAIA----SVIISHIEVKDMNFRPKAVYV-AHMARRVLMAKNDPS 427

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +           +         K   D  +++ +V+   + +    A ++ + 
Sbjct: 428 LVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNVDKVLNKRNRAEAFDAWTVMSM 487

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 488 HSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 547

Query: 458 NLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G + L +        + +++         D   P   +        +   
Sbjct: 548 GPRALQPSQFGMLCLADTPEGEACGLVKNLALMTHITTNDEEGPIRNLIFMLGAEDISTL 607

Query: 517 FCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                         +N        R  S L     + R     E   ++  H+ R     
Sbjct: 608 GGKELYGPGCYTISINGTPMALTRRPKSFLNAFRRLRRMGRISEFVSIYINHHQRAVHVA 667

Query: 574 TSEGHNIG---LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G       +V +  +  R +    +        D      V YL   EE +  IA  
Sbjct: 668 TDDGRICRPLIVVENGKNRVRSHHLKKLREGTMSFDDFLAQGLVEYLDVNEENDSLIAIY 727

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +                        E    ++  P  V+   A LIP+  ++ S R 
Sbjct: 728 EKDIT-----------------------EATTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 764

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+  + +                              ++D+I  ++     
Sbjct: 765 TYQCAMGKQAIGAIASNQFL--------------------------RIDSILYLMVY--- 795

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                                Q   V  R +    +  + + + A   +           
Sbjct: 796 --------------------PQKPMVKSRTI----ELTKYDQLPAGHNAM---------- 821

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             VA M + GY+ ED++++++  V          ++     +    G ++I       ++
Sbjct: 822 --VAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFKKSVANLKSYSNGTKDILMPPEYDND 879

Query: 871 EGLKN---IDECGIICVGAEVNPGDILVGKITPKGE 903
             ++    ++  G+  VG +VN G++ + K TP   
Sbjct: 880 APIRKHALLESDGLAAVGEQVNAGEVYINKSTPDQS 915


>gi|76556334|emb|CAJ00187.1| RNA polymerase beta subunit [Pseudomonas syringae pv. mellea]
          Length = 313

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 182/312 (58%), Positives = 235/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
            R+DI+ADGPST
Sbjct: 302 HRSDIMADGPST 313


>gi|291196448|emb|CBG27581.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas palleroniana]
          Length = 305

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 232/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++ +     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMSDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|330507364|ref|YP_004383792.1| DNA-directed RNA polymerase subunit B' [Methanosaeta concilii GP-6]
 gi|328928172|gb|AEB67974.1| DNA-directed RNA polymerase subunit B' [Methanosaeta concilii GP-6]
          Length = 597

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 111/586 (18%), Positives = 189/586 (32%), Gaps = 100/586 (17%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     N L+A            + +   M+       +   E     R+T      
Sbjct: 91   EYLDAEEEENSLIAIWEEDITPEHTHLELDPSMILGIAAGLVPYPEHNASPRNTMGAG-- 148

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP---KGESPMTPEEKLLRAIF 917
            + +    +S   ++   +      G  +N     + +       G       +  + A+ 
Sbjct: 149  MVKQCLGMSTANMRLRPDTR----GHYLNSPQKAIVRTKTSKAIGFDERPAGQNFVVAVL 204

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
              +  ++ D  +    G     +    F R    +  +    + ++ E+   D +     
Sbjct: 205  AYEGYNIEDALVMNR-GSIQRGLARSHFFRVSEAEERKYPGGQEDKFEIP--DVEVRGAR 261

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
                      + L   NA  GP             + E                      
Sbjct: 262  GSEAYDQLDSDGLVNPNAYVGPNDVLIGKTSPPRFLEEPSEFGLTPQ------------- 308

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                 +  ++ +  R   K               R+ KV    +R  + GDK A RHG K
Sbjct: 309  -----QRRETSVTMRSNEKGVVDMVILTESSNGNRLAKVKSRDQRIPELGDKFASRHGQK 363

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+V  I+P EDMPF + G   D++LNP  +PSRM VG + E   G      G+ I +   
Sbjct: 364  GVVGLIVPQEDMPFTESGIVPDLLLNPHAIPSRMTVGHVLEMIGGKVGSLDGRFIDATAF 423

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              +   ++    +                                        ++GA  E
Sbjct: 424  LGENEPELRTALTKFGFSHTGREIL----------------------------YNGATGE 455

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I + L                           VG I   KL HMV+ K++ARS G   +
Sbjct: 456  QIMADL--------------------------FVGVILYQKLYHMVTGKMHARSRGPVQV 489

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG------ 1324
            +T+QP  G++  GG R GEME   + A+GAA  L+E L  +SD V        G      
Sbjct: 490  LTRQPTEGRAREGGLRFGEMERDVLIAHGAALALKERLVDESDKVTELVCSHCGMIAIHD 549

Query: 1325 -RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R         G   + +      +F +L+ E+++LG++  L    
Sbjct: 550  RRRNADFCPTCGADTEIYPVEMSYAFKLLLDEIKSLGVAPRLILED 595



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 33/146 (22%), Positives = 48/146 (32%), Gaps = 25/146 (17%)

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           G I     S      L+      A V       I+    K  D      V YL A EEEN
Sbjct: 41  GEIFMNTDSGRARRPLIVVEDGRALVTDEHVTRIQKGEMKFDDLVAEGLVEYLDAEEEEN 100

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA     +  +                          ++  P  ++ IAA L+P+ E+
Sbjct: 101 SLIAIWEEDITPEH-----------------------THLELDPSMILGIAAGLVPYPEH 137

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPF 710
           + S R  MG  M +Q + +  A    
Sbjct: 138 NASPRNTMGAGMVKQCLGMSTANMRL 163


>gi|308234647|ref|ZP_07665384.1| DNA-directed RNA polymerase subunit beta [Gardnerella vaginalis
           ATCC 14018]
          Length = 461

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 92/305 (30%), Positives = 142/305 (46%), Gaps = 27/305 (8%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPN------------EGLQAAFKS 61
           R  FG   E ID+P L+ VQ  S+D  +                        GL+  F+ 
Sbjct: 30  RVNFGSICEPIDVPYLLGVQTDSFDWLIGSERWKKRVEEDEANGTHTVPHVSGLEEVFQE 89

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+    L F    F+ P+  V +C  +D TY+ PL +                 
Sbjct: 90  ISPIENFAETMSLTFSDPYFEEPRHTVLECKEKDYTYSAPLYVNA---------EFENGE 140

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             +IK Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++ 
Sbjct: 141 TGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRTQDRT--SDKDVFG 198

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYS 239
            +IIP +G W++ E D +D++ VR+DR+R      FLMA+GM   EI   F  YP ++ +
Sbjct: 199 AKIIPSRGAWLEFEIDKRDVLGVRVDRKRTQSAIVFLMAIGMTKPEIAEAFQGYPLVLDA 258

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLG 297
              +       A   +      +     D G  ++ES    T    L +  + K  + LG
Sbjct: 259 LEKEPIDTQNDALTDLYRKIRPADTATPDAGRNLLESFYFNTKRYDLARVGRYKINRKLG 318

Query: 298 ITSDC 302
           + +D 
Sbjct: 319 LEADY 323



 Score =  132 bits (331), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 85/210 (40%), Positives = 130/210 (61%), Gaps = 15/210 (7%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + + L  +    + DAL D+YR +RP D +T     ++    +F++ +YDL+ VGR 
Sbjct: 252 YPLVLDALEKEPIDTQNDALTDLYRKIRPADTATPDAGRNLLESFYFNTKRYDLARVGRY 311

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L L+   + R + +EDIIA IK LV L +G+                 +DDID+ 
Sbjct: 312 KINRKLGLEADYNDRSLNREDIIATIKYLVTLHSGEKTFPGKRDGEDVQLRVDVDDIDHF 371

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF +
Sbjct: 372 GNRRIRQVGELVQNQIRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFFGT 431

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           SQLSQ  +  N L+ +T+ RRLSALG GG+
Sbjct: 432 SQLSQFMDQNNPLAGVTNKRRLSALGPGGL 461


>gi|76556294|emb|CAJ00167.1| RNA polymerase beta subunit [Pseudomonas syringae pv. maculicola]
          Length = 313

 Score =  302 bits (773), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 237/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI++DGPST
Sbjct: 302 QRSDIMSDGPST 313


>gi|186885807|gb|ACC93311.1| RNA polymerase beta subunit [Baccharis neglecta]
          Length = 1024

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 100/268 (37%), Positives = 144/268 (53%), Gaps = 42/268 (15%)

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +L+DG PVD+V NPLGVPSRMNVGQIFE+ LG A   L +  +    D +   + S    
Sbjct: 795  YLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGDLLDRHYRIAPFDERYEQEASRKLV 854

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
            F E    +                               VF+                + 
Sbjct: 855  FSELYEASKQTANPW------------------------VFE---------------PES 875

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
             G+S ++DG TG+PF++PV +G  Y+LKL H V DK++ RS+G YS +TQQPL G++ +G
Sbjct: 876  PGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKG 935

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPESFNV 1349
            GQR+GEMEVW ++ +G AY+LQEMLT KSD +  R  V  +I+ G         PESF +
Sbjct: 936  GQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEDAPESFRL 995

Query: 1350 LVKEMQALGLSID--LENSRTKNSAKME 1375
             V+E+++L L ++  L + +T    + E
Sbjct: 996  FVRELRSLALELNHFLVSEKTFQLNRKE 1023



 Score =  229 bits (583), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 142/456 (31%), Positives = 236/456 (51%), Gaps = 3/456 (0%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   +I  +  +     
Sbjct: 101 ISVYTGTIISDWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGD-VSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            ++       K   +++A+L+ Y+     +    FS + S      F   + +L  +GR 
Sbjct: 161 LFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRR 220

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            MN RLNLD P +   +   DI+A    L+ ++ G GT+DD+++L N+R+RSV ++L+ Q
Sbjct: 221 NMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQ 280

Query: 475 YRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           + L L+R+E   +     +     +  PQ+L+N+ P+      FF    LSQ+ +  N L
Sbjct: 281 FGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKAFFRLHPLSQVLDRTNPL 340

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           ++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   AR+
Sbjct: 341 TQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARI 400

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
             +G +E+P+ K+ +      ++YLS   +E   +A  NS     G   E++V  R   E
Sbjct: 401 GRWGSLESPFYKIYEKSKGARMLYLSPGTDEYYMVAAGNSLALNRGIQEEQVVPARYRQE 460

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL ++E   VG
Sbjct: 461 FLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVG 520

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           TG+E   A  SGA  +A+R G +   D  +I++   
Sbjct: 521 TGLEGQAALDSGALAIAEREGKIFYTDTDKILLSGN 556



 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 57/182 (31%), Positives = 94/182 (51%), Gaps = 13/182 (7%)

Query: 69  SGAAMLEF--VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           +     EF    Y+   P     D ++  LTY+  L ++ RLI  +          + I+
Sbjct: 1   NQEIYFEFFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRR-------RIIQ 53

Query: 127 EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP 186
           EQ+I +G +PLMT  G F++ GI RIV++Q+ +SPGI++  +      +G  +Y   II 
Sbjct: 54  EQTILIGKIPLMTSLGAFIVNGIYRIVINQILQSPGIYYQSELN---DNGISVYTGTIIS 110

Query: 187 DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFW 245
           D G  +++E D K  I VR+ R++K+ +   L A+G++  EIL    YP++  S   D  
Sbjct: 111 DWGGRLELEIDRKARIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLNDKK 170

Query: 246 CF 247
             
Sbjct: 171 KI 172


>gi|76556258|emb|CAJ00149.1| RNA polymerase beta subunit [Pseudomonas syringae pv. oryzae]
 gi|76556268|emb|CAJ00154.1| RNA polymerase beta subunit [Pseudomonas syringae pv. atropurpurea]
 gi|76556284|emb|CAJ00162.1| RNA polymerase beta subunit [Pseudomonas syringae pv. atrofaciens]
 gi|76556296|emb|CAJ00168.1| RNA polymerase beta subunit [Pseudomonas syringae pv. dysoxyli]
 gi|76556304|emb|CAJ00172.1| RNA polymerase beta subunit [Pseudomonas syringae pv. ulmi]
 gi|76556314|emb|CAJ00177.1| RNA polymerase beta subunit [Pseudomonas syringae pv. tabaci]
 gi|76556316|emb|CAJ00178.1| RNA polymerase beta subunit [Pseudomonas syringae pv. hibisci]
 gi|76556320|emb|CAJ00180.1| RNA polymerase beta subunit [Pseudomonas syringae pv. ciccaronei]
 gi|76556322|emb|CAJ00181.1| RNA polymerase beta subunit [Pseudomonas syringae pv. aceris]
 gi|76556324|emb|CAJ00182.1| RNA polymerase beta subunit [Pseudomonas syringae pv. berberidis]
 gi|76556326|emb|CAJ00183.1| RNA polymerase beta subunit [Pseudomonas syringae pv. panici]
 gi|76556328|emb|CAJ00184.1| RNA polymerase beta subunit [Pseudomonas syringae pv. photiniae]
 gi|76556330|emb|CAJ00185.1| RNA polymerase beta subunit [Pseudomonas syringae pv. myricae]
 gi|76556336|emb|CAJ00188.1| RNA polymerase beta subunit [Pseudomonas syringae pv. pisi]
 gi|76556340|emb|CAJ00190.1| RNA polymerase beta subunit [Pseudomonas syringae pv.
           dendropanacis]
 gi|76556342|emb|CAJ00191.1| RNA polymerase beta subunit [Pseudomonas syringae pv. tagetis]
 gi|76556344|emb|CAJ00192.1| RNA polymerase beta subunit [Pseudomonas syringae pv. lachrymans]
 gi|76556346|emb|CAJ00193.1| RNA polymerase beta subunit [Pseudomonas syringae pv. helianthi]
 gi|76556348|emb|CAJ00194.1| RNA polymerase beta subunit [Pseudomonas syringae pv. phaseolicola]
 gi|76556350|emb|CAJ00195.1| RNA polymerase beta subunit [Pseudomonas syringae pv. sesami]
 gi|76556352|emb|CAJ00196.1| RNA polymerase beta subunit [Pseudomonas syringae pv. lapsa]
 gi|76556354|emb|CAJ00197.1| RNA polymerase beta subunit [Pseudomonas syringae pv. aptata]
 gi|76556356|emb|CAJ00198.1| RNA polymerase beta subunit [Pseudomonas syringae pv. glycinea]
          Length = 313

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 182/312 (58%), Positives = 236/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|189418945|gb|ACD93718.1| RNA polymerase beta subunit [Mangrovibacter plantisponsor]
          Length = 306

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 187/305 (61%), Positives = 234/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           ++MPQD+INAKP+ +AV EFF SSQLSQ  +  + LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   TLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNDPLSEITHKRRISALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ Y
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHY 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+E  N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D++D S +QVVS+ A
Sbjct: 121 LSAIEGGNFVIAQANSNLDDDGHFVEDLVTCRNKGESSLFSRDQVDYMDVSTQQVVSVGA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG   VAKR G V+
Sbjct: 181 SLIPFLEHDDANRALMGANMQRQAVPTLRFDKPLVGTGMERAVAVDSGVTAVAKRGGTVQ 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++AD
Sbjct: 241 YVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|76556266|emb|CAJ00153.1| RNA polymerase beta subunit [Pseudomonas syringae pv. striafaciens]
          Length = 313

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 182/312 (58%), Positives = 236/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAARHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|291196464|emb|CBG27589.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas
           rhizosphaerae]
          Length = 305

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 182/305 (59%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVNKGDVVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|83765718|dbj|BAE55861.1| unnamed protein product [Aspergillus oryzae]
          Length = 1180

 Score =  301 bits (772), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 105/514 (20%), Positives = 175/514 (34%), Gaps = 97/514 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +      + A+      D+ D  +    
Sbjct: 744  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGHNAMVAVMSYSGYDIEDALVLNKG 803

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F +   +    S   +   +     + D++  I    +         G+
Sbjct: 804  SVDRGFGRCQVFKKSVANLKSYSNGTKDILMPP---EYDNDAPIRKHALLESDGLAAVGE 860

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST           +S    F   D           + Y     + +  +
Sbjct: 861  QVNAGEVYINKSTP---------DQSLASGFPGSDMGRPVKYTPTPMTY----KLHDPAY 907

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++              +++KV     R  + GDK + RHG KG+V  I    DMPF  
Sbjct: 908  IDQVLV-----STTENENQLIKVLTRQTRRPEVGDKFSSRHGQKGVVGIIADQADMPFTD 962

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI++NP G PSRM VG++ E   G A V  G+             ++S +     
Sbjct: 963  QGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLAGQHGYGTCFGGSPVEEMSQILIDKG 1022

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G   +                               G   EA+              
Sbjct: 1023 FSYGGKDYLTS----------------------------GITGEAL-------------- 1040

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                      PF   V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1041 ----------PF--YVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1088

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1089 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1145

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1146 ---MAIPYAAKLLIQELMSMNVTARLKLEDEFPE 1176



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 120/936 (12%), Positives = 273/936 (29%), Gaps = 189/936 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 70  LVKQHIDSYNYLVEVQ----------LKKIVESSSIIRSDIDHNFYIKFTDIYLGAPRRA 119

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    I          +  + +K+    
Sbjct: 120 DEQQDVGPGFTGSTVSPHECRLRDTTYAAPIQVDFEYI----------RGRQRVKKTGCS 169

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 170 IGRMPVMLRSSKCVLSDKTPAEMTVLDECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 229

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 230 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLSEDIPIVILL 278

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +++ +      I    + DF      A  L  G       +D       I  GK
Sbjct: 279 KAMGIHTDKEMLLLVAGIDKVYQEDFAINFEEAIKL--GIYTQQQALDWIGSRIKINRGK 336

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           +      ++  ++ V+ +      +   ++    +N     +Y+ A         +    
Sbjct: 337 QNNYR--RTHVQEAVEAIA----SVIISHIEVKDMNFRPKAVYV-AHMARRVLMAKNDPS 389

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +           +         K   D  +++ +V+   + +    A ++ + 
Sbjct: 390 LVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNVDKVLNKRNRAEAFDAWTVMSM 449

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 +     +     +  R  ++       + +   IA + ++  + +       + 
Sbjct: 450 HSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVS 509

Query: 458 NLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +    G + L +        + +++         D   P   +        +   
Sbjct: 510 GPRALQPSQFGMLCLADTPEGEACGLVKNLALMTHITTNDEEGPIRNLIFMLGAEDISTL 569

Query: 517 FCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
                         +N        R  S L     + R     E   ++  H+ R     
Sbjct: 570 GGKELYGPGCYTISINGTPMALTRRPKSFLNAFRRLRRMGRISEFVSIYINHHQRAVHVA 629

Query: 574 TSEGHNIG---LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T +G       +V +  +  R +    +        D      V YL   EE +  IA  
Sbjct: 630 TDDGRICRPLIVVENGKNRVRSHHLKKLREGTMSFDDFLAQGLVEYLDVNEENDSLIAIY 689

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +                        E    ++  P  V+   A LIP+  ++ S R 
Sbjct: 690 EKDIT-----------------------EATTHLEIEPFTVLGAVAGLIPYPHHNQSPRN 726

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+  + +                              ++D+I  ++     
Sbjct: 727 TYQCAMGKQAIGAIASNQFL--------------------------RIDSILYLMVY--- 757

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                                Q   V  R +    +  + + + A   +           
Sbjct: 758 --------------------PQKPMVKSRTI----ELTKYDQLPAGHNAM---------- 783

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             VA M + GY+ ED++++++  V          ++     +    G ++I       ++
Sbjct: 784 --VAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFKKSVANLKSYSNGTKDILMPPEYDND 841

Query: 871 EGLKN---IDECGIICVGAEVNPGDILVGKITPKGE 903
             ++    ++  G+  VG +VN G++ + K TP   
Sbjct: 842 APIRKHALLESDGLAAVGEQVNAGEVYINKSTPDQS 877


>gi|52694121|emb|CAG30590.1| DNA-directed RNA polymerase beta chain [Pseudomonas cichorii]
          Length = 396

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 197/398 (49%), Positives = 267/398 (67%), Gaps = 12/398 (3%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 62  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +    
Sbjct: 122 SPYRVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPA 181

Query: 660 KIDFIDASPKQVVSIAASL---IPFLENDDSNRVLMGCNMQRQAVPLL----KAEAPFVG 712
            +  +D    Q  S   S    +P                 R   P +     +   +  
Sbjct: 182 DVTLMDGRFAQAGSFGRSFPDSVPRARRRQPCVDGFRTCSVRLYQPCVPTSRWSVPAWSA 241

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           T +    A +S   +    A +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQ
Sbjct: 242 T-LPVTPAFASWLVV----AVLIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQ 296

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER
Sbjct: 297 NTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSER 356

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +V ED FT+IHI+E   +ARDTKLGPEEIT DIPNV E
Sbjct: 357 VVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGE 394


>gi|76556302|emb|CAJ00171.1| RNA polymerase beta subunit [Pseudomonas syringae pv. aesculi]
          Length = 313

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 235/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPHDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|260809401|ref|XP_002599494.1| hypothetical protein BRAFLDRAFT_223894 [Branchiostoma floridae]
 gi|229284773|gb|EEN55506.1| hypothetical protein BRAFLDRAFT_223894 [Branchiostoma floridae]
          Length = 1140

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 118/600 (19%), Positives = 194/600 (32%), Gaps = 105/600 (17%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +T    +   RN+    +   G   +  M I  R        + H               
Sbjct: 614  TTPARMMRPVRNLFTGTVEMIGSFEQVYMNICVRPEEAHPGVTTH--------------Q 659

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E     I +V+       D         +   G   +G            +   ++    
Sbjct: 660  ELRETSILSVAASFTPFSDFNQSPRNMYQCQMGKQTMGTPLHAFGHRTDNKLYRIQNPQS 719

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL---ARDKDDEQ 975
                        +     GT   V + +  G D  E ++ + +  +E           E 
Sbjct: 720  PTVRPYAYDHYHMDDYPLGTNAVVAVISYTGYDM-EDAMILNKSSLERGFGHGTIYKTEI 778

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + L     S    +        G K  +    L  D +                  ++  
Sbjct: 779  ISLRDLAQSARGPVTLVFGCAEGDKRVEG--RLDDDGLPPIGSKLETGDPFYSYVDKQTG 836

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E+  V Y+  +  + D       K+   D     + + V + + + R    GDK + RHG
Sbjct: 837  EARVVLYKNQEKAIVDNI-----KVLGNDQGTSDMNK-VAIVMRINRNPIIGDKFSSRHG 890

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG+ S+  P EDMPF + G   DI+ NP G PSRM +G + E+  G +    G    + 
Sbjct: 891  QKGVCSQQWPVEDMPFTEGGMTPDIIFNPHGFPSRMTIGMMIESMAGKSAAQHGLCHDAT 950

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
               +                                                    D + 
Sbjct: 951  PFTFSE--------------------------------------------------DNSA 960

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             +    ML  A  +  G   +Y G+TG  F+  + +G +Y  +L HMV+DK   R+TG  
Sbjct: 961  IDYYGRMLIEAGYNYYGHERMYSGVTGVEFEADIFIGVVYYQRLRHMVADKFQVRTTGPI 1020

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT--------- 1326
             +VT QP+ G+   GG R GEME   + A+GA ++LQ+ L   SD    R          
Sbjct: 1021 DIVTHQPIKGRKRAGGIRFGEMERDSLLAHGATFLLQDRLFNCSDKSTCRVCTQCGSILS 1080

Query: 1327 ---------------RVYESIVAGNDTFET-----GTPESFNVLVKEMQALGLSIDLENS 1366
                           RV+ ++   N  F         P  F  LV E+ A+ + + +E  
Sbjct: 1081 PLLDKPLLFCSVPQCRVFCTLCCSNSVFSPPPQLIAVPYVFRYLVAELAAMNIKVTMETK 1140



 Score = 99.0 bits (245), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 114/786 (14%), Positives = 217/786 (27%), Gaps = 159/786 (20%)

Query: 17  FGKNPEIIDIP--DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS----G 70
           +G+  +    P  DL+     S++ FL           EGL  A +++ P   FS     
Sbjct: 20  YGRPEKTQHRPLQDLVRPHVESFNWFLR----------EGLSLAVQAI-PKLDFSLSNGR 68

Query: 71  AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
              L +V      P            K    +C  R  TY   L+  +   V  V++ + 
Sbjct: 69  RISLSYVDASVGVPTVAQGNTFSRTLKVYPAECRERGTTYRAGLQARIAWSVDGVNQGSV 128

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV- 153
            +           +G++PLM K                         G F+  GI+++V 
Sbjct: 129 ERM----------LGEIPLMVKSAHCNITKLTPAELIQRHEEAEEMGGYFINNGIEKVVR 178

Query: 154 --V-------SQLHRSP-----GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFD-- 197
             V         + R P     G  +           K   A  I+      +    +  
Sbjct: 179 MLVMPRRNYPMAIVR-PSWKGRGKLYTEYGVSMRCVTKDQTAATIV------LHYLTNGT 231

Query: 198 -------SKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
                   K+   V        P+   L AL   +++     Y +++  +  + +     
Sbjct: 232 VTLCFVYKKEQFFV--------PLIIILKALVETTDQ---HIYSELIKGKEDNSFFKGCV 280

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
           A+ L                      G    +G+LK + E+    L +            
Sbjct: 281 ASMLRQAQN----------------EGLMTQAGILKYIGERFRVKLPVPD---------- 314

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
              + E G+  +     I   S  + F++ +     L+  +        +    D    +
Sbjct: 315 WYTDEEVGQFLLRQCVCIHLDSDWDKFNTLVLMTQKLFALAKGE----CSVENQDSPMMQ 370

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK---YDLSTVGRVKMNMRLNLDTPDD 427
           +  L     +    D     + +  +       DK   Y L TV  +   MRL  D    
Sbjct: 371 EMLLAGHLYLTILKDKLELWLTQLRYGIDKRSQDKGPSYKLDTV-EMMSAMRLCSDVTRG 429

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           + H      + + K  + L    G     D L   R   +              M R+  
Sbjct: 430 MEHFMATGSV-VSKSNLGLMQTAGLTVVADKLNFMR--YLSHFRCVHRGAFFAEM-RTTS 485

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            R    +    +             +     S +   L+     + ++  +  ++ L   
Sbjct: 486 VRKLLPEAWGFLCPVHTPDGAPCGLLNHMTASCEAVTLQPTTVHIPKLLCSLGMAPLDSP 545

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV-- 605
             A             T             +    ++      +V   G I      V  
Sbjct: 546 APAPPVDCY-------TVLLDGRVVGRVAANMAPDMARKLRMLKVTREGKIPVMTEIVLV 598

Query: 606 ----CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                  +     ++ +              +++  GSF  E V+               
Sbjct: 599 PKTGKASQFPGLFLFTTPARMMRPVRNLFTGTVEMIGSF--EQVYMNICVRPEEAHPGVT 656

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMESVVA 720
              +     ++S+AAS  PF + + S R +  C M +Q +   L A        +  +  
Sbjct: 657 THQELRETSILSVAASFTPFSDFNQSPRNMYQCQMGKQTMGTPLHAFGHRTDNKLYRIQN 716

Query: 721 KSSGAA 726
             S   
Sbjct: 717 PQSPTV 722


>gi|52694257|emb|CAG30658.1| DNA-directed RNA polymerase beta chain [Pseudomonas meliae]
          Length = 310

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 181/310 (58%), Positives = 236/310 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R++++AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSNVMAD 300

Query: 797 GPSTDLGDLA 806
           GPSTD+G+LA
Sbjct: 301 GPSTDMGELA 310


>gi|207744568|ref|YP_002260960.1| dna-directed rna polymerase beta chain (partial sequence) protein
           [Ralstonia solanacearum IPO1609]
 gi|206595974|emb|CAQ62901.1| dna-directed rna polymerase beta chain (partial sequence) protein
           [Ralstonia solanacearum IPO1609]
          Length = 182

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 86/184 (46%), Positives = 119/184 (64%), Gaps = 3/184 (1%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               F    R+RK F K   +  +P L+  Q  SY  FL  +++  +R  EGLQAAF ++
Sbjct: 1   MAYSFTEKKRIRKSFAKRATVHQVPFLLATQIQSYAQFLQEHVSVAQRKTEGLQAAFNAI 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G A +EFVSY    P FDV +C  R LT+   L+  +RLI+ D +  T    +
Sbjct: 61  FPIVSHNGLARMEFVSYHLSHPPFDVKECQQRGLTFHSALRAKVRLIINDRENPT---KV 117

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           K+IKEQ +YMG++PLMT  G+FVI G +R++VSQLHRSPG+ F+HDKG+   SGKLL++ 
Sbjct: 118 KEIKEQEVYMGEIPLMTSTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHSSGKLLFSA 177

Query: 183 RIIP 186
           RIIP
Sbjct: 178 RIIP 181


>gi|83763745|emb|CAJ00206.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12A10]
          Length = 339

 Score =  301 bits (771), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 181/348 (52%), Positives = 247/348 (70%), Gaps = 13/348 (3%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AKR G V+ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V  G+ V
Sbjct: 4    AKRGGQVQSVDASRIVVKVNEDELVPGEAGIDIYNLTKYTRSNQNTCINQRPTVLPGEPV 63

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IHI+E  
Sbjct: 64   ARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELS 123

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TP
Sbjct: 124  CVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTP 183

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ Q++   
Sbjct: 184  EEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKEAK 243

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D  +E  IL+  + +R+  +L                  S   +    R QW +  ++D
Sbjct: 244  KDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDTIGRKQWLEQVLED 290

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
            + +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VKV
Sbjct: 291  DALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVKV 338


>gi|28268686|dbj|BAC56866.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268688|dbj|BAC56867.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268690|dbj|BAC56868.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268692|dbj|BAC56869.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268694|dbj|BAC56870.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268696|dbj|BAC56871.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268698|dbj|BAC56872.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268700|dbj|BAC56873.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268702|dbj|BAC56874.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268704|dbj|BAC56875.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268706|dbj|BAC56876.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268708|dbj|BAC56877.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268710|dbj|BAC56878.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268712|dbj|BAC56879.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268714|dbj|BAC56880.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268716|dbj|BAC56881.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268718|dbj|BAC56882.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268720|dbj|BAC56883.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268722|dbj|BAC56884.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268724|dbj|BAC56885.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|28268726|dbj|BAC56886.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 166

 Score =  301 bits (771), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 69/188 (36%), Positives = 116/188 (61%), Gaps = 22/188 (11%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           +MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYET 158

Query: 197 DSKDIIHV 204
           D+KD+++V
Sbjct: 159 DAKDVVYV 166


>gi|76556264|emb|CAJ00152.1| RNA polymerase beta subunit [Pseudomonas syringae pv. striafaciens]
          Length = 313

 Score =  301 bits (771), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 182/312 (58%), Positives = 236/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAARHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIVADGPST 313


>gi|194293711|gb|ACF39951.1| RNA polymerase B subunit [Mycobacterium vulneris]
          Length = 242

 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 101/235 (42%), Positives = 134/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGSPEWAVN-------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 143  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 185

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQ P
Sbjct: 186  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQAP 240



 Score = 42.4 bits (98), Expect = 0.54,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|11121226|emb|CAC14798.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  301 bits (770), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 192/341 (56%), Positives = 247/341 (72%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N             +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+
Sbjct: 1   LNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQF 60

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ     N LS +
Sbjct: 61  RSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMVQTNPLSEV 120

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+R+VHPTHYGR+CP ET EG NIGL++SL+ +AR N Y
Sbjct: 121 THKRRVSALGPGGLTRERAGFEVRNVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDY 180

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+
Sbjct: 181 GFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIM 240

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+
Sbjct: 241 ATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGI 300

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           E  VA  S  AIVA+R G+VE VDA R+VIR  + +     
Sbjct: 301 ERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|146094444|ref|XP_001467277.1| DNA-directed RNA polymerase II subunit 2 [Leishmania infantum JPCM5]
 gi|134071642|emb|CAM70332.1| putative DNA-directed RNA polymerase II subunit 2 [Leishmania
            infantum JPCM5]
 gi|322501339|emb|CBZ36417.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 1181

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 111/582 (19%), Positives = 183/582 (31%), Gaps = 115/582 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +A+  N +     +     + SM+  I   ++            ++       +G     
Sbjct: 687  IAMTPNEVEKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASN 746

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             ++                  V        +    +T    + +      + AI      
Sbjct: 747  FNMRM-----------DTTAHVLFYPQKPLVRTKAMTYMHSNDLPAGHNAVVAISCYSGY 795

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S V         + R    K ER      E  E   R    E   + R  
Sbjct: 796  NQEDSIIMSRSAVERGFFRSAFW-RSFKAKEERQKRDALETFENPDR----ELCRVKRAD 850

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            YS+L     I  G   + G     K+  L    + +       +   +D  +        
Sbjct: 851  YSKLDTDGLIKPGMRVLGGDVVVGKTIPLPEADLEKLTTGN-TKITKRDASITSRTTE-- 907

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                          K  ++K+           R  KV +   +    GDK   RHG KG 
Sbjct: 908  --------------KGVVDKVM---LTMNNNDRFTKVKIRTIKIPNIGDKFCSRHGQKGT 950

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                   EDMPF +DG   D+++NP  +PSRM V  + ET  G                 
Sbjct: 951  NGIQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVAC------------- 997

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                    +K G   +TP F     +  
Sbjct: 998  ----------------------------------------YKGGEVYATP-FCSVVVDDF 1016

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L        G   LY+G TG P D  +  G  +  +L H+  DK++AR  G    + 
Sbjct: 1017 GKALHALRSQRYGNECLYNGHTGLPLDHLIFFGPTFYQRLKHLSGDKIHARPRGPLQPLV 1076

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------GRTR 1327
            +QP  G+++ GG R GEME  C+ +YGA+  L+E L   SD     V           T+
Sbjct: 1077 RQPTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYTVHVCNMCGTICVADTK 1136

Query: 1328 V--YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +  Y+    G        +   P +  +L +E+ ++ +   L
Sbjct: 1137 LNRYQC--KGCENDTRISQVLMPYACKLLFQELMSMTILPRL 1176



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 155/1010 (15%), Positives = 310/1010 (30%), Gaps = 209/1010 (20%)

Query: 29  LIEVQKASYDHFLMMNIA----------PDERPNEG--LQA-------AFKSVFPITAFS 69
           L+  Q  SY+ FLM               D++ + G  ++          + V  I   S
Sbjct: 47  LVHQQLDSYNDFLMRIPKMIESMAVIPRQDDQYDPGVTMEEQRDQPRLVLQDVV-IGNPS 105

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 F      PP F  ++C  RD+TY    ++TL + ++     T      D   ++
Sbjct: 106 HQTHSYFAGGPL-PPLF-PNECRLRDMTYDAQAQVTLGVELYHPHADTP----HDTFLRN 159

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
           + +G +P+M K                         G FVI G ++++++Q  ++   ++
Sbjct: 160 VELGRIPIMLKSMRCNLSGKDEDELPRLNECPHDQGGYFVINGTEKVLIAQERQAANHVY 219

Query: 165 -FDHDKG-----RASLSG--KLLYACRII---PDQGLWMDIEFDSKDIIH--VRIDRRRK 211
            F   KG     ++ + G        +II    ++G     E    +++    ++D    
Sbjct: 220 TFSRQKGLLCEVKSIVEGSLNKPRTLQIIMQYKNKGPGSGFE----NLMCRVAQMDET-- 273

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     A+ M ++ EIL T  P +  +   +     +S A  +       +L  I   
Sbjct: 274 IPLFVLFRAMDMVADKEILQTVVPDLKDTAMLELLRGSMSDASTLQIFTREEALGYIGRR 333

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
               ++   L       L    +  +G          +    +  +   + +   +  D 
Sbjct: 334 LGKQDAMANLQREAESLLMRDLLPHMGTDPSANRTKCLYMGYMVHKLLLVALGRHEETDR 393

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-----LDIYRVMRPGD 385
             L        + I +               +  +  K  +D       +  +  +    
Sbjct: 394 DFL------GHKRIDVAGTLLTVQLQTFLAQVRKEMIKTLQDHAANPRGVFSFGRVIHSK 447

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR----KEDIIAIIK 441
           + T  +   +    F D    ++ T     +N      +  ++R I+            +
Sbjct: 448 LITDGLRRCLATGNFGDLKTGNIKTGVAQTLNRLTYSSSLSNLRRIQNPIAASSKATRPR 507

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDI----- 495
            L   + G     +    G+  +     ++    R      + ++++ RI          
Sbjct: 508 NLHCTQWGYICPVETPEGGSIGLLKNVALMCLMSRGTDHAEVVQAVQARIDGFRTIGLED 567

Query: 496 --DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             D  + +  +N   +            L     +    + ++  R +        + A 
Sbjct: 568 TADVRVARVFVNGTMIGVDRNPERLLHDLRTRRRNGELSNEVSIVRDIRDREIRVFSDAG 627

Query: 554 AGVEMRDVHPTHYGRICPAE--TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                R + P      C  +   S   N+ +         ++    ++  Y         
Sbjct: 628 -----RCLRPLFVAENCHLKLRKSGMRNLLVSEKAGGKKSISWNTALKKGY--------- 673

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  +   EE++  IA   + ++++  +                        +  P  +
Sbjct: 674 --VELIDCEEEDSLLIAMTPNEVEKNYYY---------------------SHCEMDPSMI 710

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IP+  ++ S R      M +QA+ +                            
Sbjct: 711 LGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------- 743

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                          S       +T+ V  Y               Q+PLV+        
Sbjct: 744 --------------ASNFNMRMDTTAHVLFYP--------------QKPLVR-------- 767

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       DL  G N +VA   + GYN EDS+++S   V    F S     F+   
Sbjct: 768 --TKAMTYMHSNDLPAGHNAVVAISCYSGYNQEDSIIMSRSAVERGFFRSAFWRSFKAKE 825

Query: 852 RDTK----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              K       E   R++  V       +D  G+I  G  V  GD++VGK  P       
Sbjct: 826 ERQKRDALETFENPDRELCRVKRADYSKLDTDGLIKPGMRVLGGDVVVGKTIP------L 879

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
           PE  L +   G   +  RD S+   +     VVD  +   +  D+  +  
Sbjct: 880 PEADLEKLTTGNTKITKRDASITSRT-TEKGVVDKVMLTMNNNDRFTKVK 928


>gi|83763765|emb|CAJ00216.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12F04]
          Length = 357

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 176/358 (49%), Positives = 249/358 (69%), Gaps = 13/358 (3%)

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
               +G+E  VA  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ R
Sbjct: 1    LSWSGIERNVAVDSGVTAVAKRGGMIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTR 60

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+
Sbjct: 61   SNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILV 120

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V +D FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 121  SERVVQDDRFTTIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVK 180

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ V+GTV+DV++F R G
Sbjct: 181  GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDG 240

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S
Sbjct: 241  VEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLARVRSLLITGG-------------YS 287

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
               +    R +W +  ++++++Q  +E +  QY+  ++  + +F+ K  KI  GDD+ 
Sbjct: 288  EAKLDAIDRKKWLEQTLENDELQTQLEQMAEQYDELRAEFDKKFETKRRKITQGDDLH 345


>gi|310831534|ref|YP_003970177.1| putative DNA-directed RNA polymerase subunit Rpb2 [Cafeteria
            roenbergensis virus BV-PW1]
          Length = 1185

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 181/1080 (16%), Positives = 343/1080 (31%), Gaps = 203/1080 (18%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            +    G   D + +  I ++      +  + +   N+   N  +    K R++A+  +  
Sbjct: 248  LLRALGIENDRELIARITNNLDDIPMVNLLRNSLENSVDDNGNLI---KTREEAINFLMT 304

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             M+ G   + S        +     K  L  +    +   L  D P     I       +
Sbjct: 305  KMKAGRRISQSD-----EQVAQAQKKLLLEKIITKDLLPHLGADIPGKASFIC-----LM 354

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI---KERISSVDID 496
            +K ++ +  G+   DD D   N+RV + G +L   +R    +M + I     R ++ D  
Sbjct: 355  VKKILLVMLGRKQEDDRDAFENKRVETPGVLLGQLFRQNFNKMLKEIGKLFRRKNNSDET 414

Query: 497  SVMPQDLINAKPVVSAVCEFFCSS---------QLSQLEEHVNSLSRITHTRRLSALGQG 547
             +     I    +   +     +            +Q    +  L  I++ RR+ +    
Sbjct: 415  PINMVSQITPTTIEQGIKSGLATGIWGVSKTKAGAAQSLSRLTWLQTISYLRRIKS--PN 472

Query: 548  GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA--YGFIETPYRKV 605
                      +R ++      +C  ET EG  IGL  SL+  A +        E   + +
Sbjct: 473  MDTSTSKITSIRQINNVQAFFVCNVETPEGQPIGLAKSLSMMATITPRLESQTELINKLI 532

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANS------SLDEDGSFTEELVFCRCAGEEILVPRE 659
             +         ++  +  N      N        + E  SF E L   R   +       
Sbjct: 533  EEHPKMYHPFAVNPEDINNMIKIFHNGSWKGVLDIKEGYSFFENLKKMRRNSKINKFVTI 592

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG----- 714
             +D+ +            + P L+  D N + +   +       L  +    G       
Sbjct: 593  TLDYFEKDLYIYTEAGRLIRPLLKV-DDNEIKLTKTIVADIKKHLTGDKKSSGWNQILLK 651

Query: 715  ----MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                ++    +SS   + A    ++ +  A  +     + +        + Y   ++   
Sbjct: 652  YPDLVDYEDIESSRHLMFAMDMQMLLENKANSLR----DINTKEEIIKPNRYGKFRYVNY 707

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
              +       L           I++  P  +                            S
Sbjct: 708  THSEFHPSMML---------GTIVSTVPFINHNP-------------------------S 733

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
             R +         I  +    +D       +                   +  VG +   
Sbjct: 734  PRGIIFFSQAKQAIGIYSTAYKDRMDISNILYHP---------------QVPLVGTK--- 775

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                           +   E ++ AI   K  +V D+ +   + +   +       ++  
Sbjct: 776  ------ASKYNRFDDIPSGENIIVAIMSYKGYNVEDSIMINQTSLDRGLFRADSLRKYSS 829

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
               +   S + +      R+K                  + G    +  K  +K  +   
Sbjct: 830  KIEKNPSSSQDDIFMKPDRNK------------------VTGMTRGNYEKLNEKGYIPEE 871

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
              ++           +  +       S    Y+    + +      ++++   D      
Sbjct: 872  TPVTS-------NDILIGKVSPIQPTSDNKVYKDKSELFKSNVDGVVDRVHK-DIFNNDG 923

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
              ++ + V M+RP   GDK + +HG KG V   LP  DMPF  +G   D++ NP G+P+R
Sbjct: 924  YEMISMRVRMERPPIIGDKFSTKHGQKGTVGITLPQRDMPFTSEGMTPDLIFNPHGMPTR 983

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +GQ+ ET    A   +G+                                        
Sbjct: 984  MTMGQLAETLASKAAANIGELFDG------------------------------------ 1007

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP F   D   I  +L+   +DE G   +Y G+TG      + 
Sbjct: 1008 -----------------TP-FSDYDVTEIPKVLKELGMDEYGTEEMYCGMTGRKMKARIF 1049

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++ L+L HMV DKV++RS G    +T+QP+ G+S  GG ++GEME   + A+G    
Sbjct: 1050 IGPMFYLRLKHMVLDKVHSRSMGPRQAITRQPMEGRSKDGGLKIGEMEKDAMVAHGIGQF 1109

Query: 1311 LQEMLTIKSD-------DVVGR--TRVY--ESIVAGN-----DTFETGTPESFNVLVKEM 1354
            L+E +   SD       D  G   T+V   E  V  N     D      P +F ++V+E+
Sbjct: 1110 LKERMMENSDITTIMVCDKCGTFATKVMDKEYYVCNNCNNHTDFSNVAMPYAFKLMVQEL 1169



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 126/1018 (12%), Positives = 298/1018 (29%), Gaps = 142/1018 (13%)

Query: 3   KGVVFNGLGRVRK--------FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEG 54
              +      +RK        +F   P+++    L     +SY  F+   I         
Sbjct: 1   MSEIITNKKDLRKGIDSLIDLYFS-QPKVL-YSHL----FSSYHQFVEEMIPYS------ 48

Query: 55  LQAAFKSVFPITAFSGAAML---EFVSYEFDPPKFD-------VDDCLWRDLTYAVPLKI 104
           L+    + F     + A  L   +F   +  PP  +               L Y   +  
Sbjct: 49  LEEE-TNYFYDNVTNDAIYLYGFKFEDTKILPPVRERDNEIIFPQMARKNFLNYFANINT 107

Query: 105 TLRLIVFDVDEFTGAKSIKDI--KEQSIYMGDLPLMTKD--------------------- 141
            +      V+  TG  + ++I   E+ + +  +P+M K                      
Sbjct: 108 KVTQFQEKVNLHTGEITRRNIGDPEEMV-VASIPVMVKSKYCATSLKPETSKYECKYDPG 166

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD------IE 195
           G F++ G +++VVS             K  +S     +Y  +I   +  W +      I 
Sbjct: 167 GYFIVGGQEKVVVSIEKMIDNKILVFSKSDSSFPKGKMYTSQINSRKHDWSENLQIIAIR 226

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI--------LSTFYPKIVYSQRGDFWCF 247
            +  D + +   +  ++P+   L ALG++++          L       +     +    
Sbjct: 227 NNKDDSLIITTSQLVEIPIMVLLRALGIENDRELIARITNNLDDIPMVNLLRNSLENSVD 286

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--DCLCG 305
                       ++  +  +  G ++ +S +++     K L EK +    +      + G
Sbjct: 287 DNGNLIKTREEAINFLMTKMKAGRRISQSDEQVAQAQKKLLLEKIITKDLLPHLGADIPG 346

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLE-EIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
                 ++  +   + +      D  + E +   +    +  L+  + N        L  
Sbjct: 347 KASFICLMVKKILLVMLGRKQEDDRDAFENKRVETPGVLLGQLFRQNFNKMLKEIGKLFR 406

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            KN   +  +  + ++             +   +    +      ++ R+     ++   
Sbjct: 407 RKNNSDETPINMVSQITPTTIEQGIKSGLATGIWGVSKTKAGAAQSLSRLTWLQTISYLR 466

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
              ++    +   + I  +  + N +            +   + + L     +   R+E 
Sbjct: 467 --RIKSPNMDTSTSKITSIRQINNVQAFFVCNVETPEGQPIGLAKSLSMMATITP-RLES 523

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
             +     ++    M          ++ + + F +     + +     S   + ++    
Sbjct: 524 QTELINKLIEEHPKMYHPFAVNPEDINNMIKIFHNGSWKGVLDIKEGYSFFENLKK---- 579

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
               + R     +   +   ++ +     T  G  I                       K
Sbjct: 580 ----MRRNSKINKFVTITLDYFEKDLYIYTEAGRLIRP-------------------LLK 616

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D +                 I    + + +               + +L   + +D+ 
Sbjct: 617 VDDNE-----------------IKLTKTIVADIKKHLTGDKKSSGWNQILLKYPDLVDYE 659

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D    + +  A  +   LEN  ++   +    +               T  E   +   G
Sbjct: 660 DIESSRHLMFAMDMQMLLENKANSLRDINTKEEIIKPNRYGKFRYVNYTHSEFHPSMMLG 719

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
             +       V  ++        +         G+           +      Q PLV  
Sbjct: 720 TIV-----STVPFINHNPSPRGIIFFSQAKQAIGIYSTAYKDRMDISNILYHPQVPLV-- 772

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           G +  + +   D PS        G N++VA M + GYN EDS++I++  +   +F +  +
Sbjct: 773 GTKASKYNRFDDIPS--------GENIIVAIMSYKGYNVEDSIMINQTSLDRGLFRADSL 824

Query: 845 EEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            ++           ++     P+      ++    + ++E G I     V   DIL+GK+
Sbjct: 825 RKYSSKIEKNPSSSQDDIFMKPDRNKVTGMTRGNYEKLNEKGYIPEETPVTSNDILIGKV 884

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           +P   +      K    +F      V D        +     +       R  I  ++
Sbjct: 885 SPIQPTSDNKVYKDKSELFKSNVDGVVDRVHKDIFNNDGYEMISMRVRMERPPIIGDK 942


>gi|88601370|ref|YP_501548.1| DNA-directed RNA polymerase subunit B' [Methanospirillum hungatei
            JF-1]
 gi|88186832|gb|ABD39829.1| DNA-directed RNA polymerase, subunit B' [Methanospirillum hungatei
            JF-1]
          Length = 606

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 110/587 (18%), Positives = 185/587 (31%), Gaps = 98/587 (16%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              +L D     ++ +A  P +       + +   ++       +   E     R T    
Sbjct: 98   YIELIDAEEEEDLNIAIKPENITPEHTHLEVDPSLILGIGAAHVPFPEHNASPRVTMGAG 157

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                      +   L+  D  G   +   V    +        G       +  + AI  
Sbjct: 158  MVKQALGFGCANMKLRP-DTRG--HLLHYVQKPLVYTQTSDVIGSDDRAAGQNFVVAILS 214

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             +  ++ D  +   + +   V     F R    +  R    + ++IE+   D       +
Sbjct: 215  YEGYNIEDALIFNKASIDRGV-GRSHFFRTYEGEERRYPGGQIDRIEVPDED-------V 266

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                 S     L     ++     K+  V+                    E     +   
Sbjct: 267  TGAHGSDYYANLDDDGIINPETIVKEKDVIIGKTSPPRFLE---------EPTSELITV- 316

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL--RVVKVFVAMKRPIQSGDKMAGRHGN 1096
                   +       ++    I     +  G    ++VKV     R  + GDK A RHG 
Sbjct: 317  -----EKRRDTSVTMRSNEHGIVDTVILTEGENNSKLVKVRTRDLRIPEVGDKFASRHGQ 371

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V  I P  DMPF   G   D+V+NP  +PSRM +G + E   G      G++I    
Sbjct: 372  KGVVGLITPSVDMPFTAGGLTPDLVINPHAIPSRMTIGHMLEMLGGKVGSLEGRRIAGTA 431

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
               +   D+                                              DG   
Sbjct: 432  FSGEREEDLRASLKKFGFSHTGREAMW----------------------------DGIT- 462

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                                     G  F   + VG IY  KL HMVS K++ARS G   
Sbjct: 463  -------------------------GRRFLADIYVGVIYYQKLYHMVSSKMHARSRGPVQ 497

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVY 1329
            ++T+QP  G++  GG R GEME   +  +GAA  L+E L  +SD V        G   + 
Sbjct: 498  VLTRQPTEGRAREGGLRFGEMERDVMIGHGAAMALKERLLEESDKVTEYVCARCGMVAML 557

Query: 1330 E---SIVAGND------TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            +   +I    +       +      +F +L+ EM+++ ++  L    
Sbjct: 558  DRKQNITRCLNCGSETDIYPVEMSYAFKLLLDEMKSMTIAPRLNLED 604



 Score = 87.4 bits (215), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 69/418 (16%), Positives = 121/418 (28%), Gaps = 108/418 (25%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +    +++I   RR   +        +       +H        P    E    G+ +  
Sbjct: 20  DPKALVTQIRALRRQGVISTEVNCSYKEFNGDIIIHTDRGRARRPLIVLEN---GVPTIP 76

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
               +      IE       D      +  + A EEE+  IA    ++  +         
Sbjct: 77  EEEIQKLKNKEIE-----FVDLIKKGYIELIDAEEEEDLNIAIKPENITPEH-------- 123

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                            ++  P  ++ I A+ +PF E++ S RV MG  M +QA+     
Sbjct: 124 ---------------THLEVDPSLILGIGAAHVPFPEHNASPRVTMGAGMVKQALGFGC- 167

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                                                   +       +   +  Y    
Sbjct: 168 ----------------------------------------ANMKLRPDTRGHLLHYV--- 184

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PLV                     D A G+N +VA + + GYN ED+
Sbjct: 185 -----------QKPLVY----------TQTSDVIGSDDRAAGQNFVVAILSYEGYNIEDA 223

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGI 881
           ++ ++  +   V  S     +E   R    G  +               +   N+D+ GI
Sbjct: 224 LIFNKASIDRGVGRSHFFRTYEGEERRYPGGQIDRIEVPDEDVTGAHGSDYYANLDDDGI 283

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           I     V   D+++GK +P         E +            RDTS+ + S   G V
Sbjct: 284 INPETIVKEKDVIIGKTSPPRFLEEPTSELI-------TVEKRRDTSVTMRSNEHGIV 334


>gi|83763749|emb|CAJ00208.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12F11]
          Length = 353

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 182/356 (51%), Positives = 248/356 (69%), Gaps = 13/356 (3%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A  SG   VAKR G+++ VDA RIV++  E  L P  +G+DIY L K+ RSNQNTC+NQR
Sbjct: 6    AVDSGVTAVAKRGGMIQSVDASRIVVKVNEDGLVPGEAGIDIYNLTKYTRSNQNTCINQR 65

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P V   + V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS  ISER+V ED F
Sbjct: 66   PTVLPVEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSNFISERVVQEDRF 125

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            T+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+T
Sbjct: 126  TTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVT 185

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +
Sbjct: 186  PKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFPRDGVEKDKRALEI 245

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            E+ Q++   +D  +E  IL+  + +R+  +L                  S   +    R 
Sbjct: 246  EQMQLKEAKKDLTEEFQILEGGLLNRVKAVLLSGG-------------YSEAKLDAIGRK 292

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
            +W + A++D+ +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++VK
Sbjct: 293  KWLEQALEDDALQSQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIVK 348


>gi|51035521|emb|CAH10896.1| RNA polymerase B subunit [Halococcus saccharolyticus]
          Length = 435

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 83/269 (30%), Positives = 119/269 (44%), Gaps = 61/269 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 197  EDGSKLSKVSVRDQRIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 257  PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEDEEELRGSLEEHG-------------- 302

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I+Y G+TGE  D 
Sbjct: 303  -----------------------FD-----------------SSGKEIMYSGVTGEKIDA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 323  EIFVGTIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 382

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGN 1336
            A  L+E L  +SD    R  VY   V G 
Sbjct: 383  AMALKERLLDESD----REFVY---VCGE 404



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/179 (21%), Positives = 65/179 (36%), Gaps = 21/179 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECG 880
           +++++E  V   +  S     +E   R    G E+      +       EE   ++DE G
Sbjct: 76  ALVLNEGSVDRALARSHFFRTYEGEERRYPGGQEDRFEMPDDDVRGARGEEAYTHLDEDG 135

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           ++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 136 LVNPETTVDESAVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188


>gi|291196484|emb|CBG27599.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas xanthomarina]
          Length = 304

 Score =  301 bits (770), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 181/305 (59%), Positives = 231/305 (75%), Gaps = 1/305 (0%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGEVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++ L +     +ELV  R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAKL-DGRKLVDELVAVRHQNEFTVKAPEDVTLMDVSPKQVVSVAA 179

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 180 SLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNVARDSGVCVVARRGGVID 239

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V R DI+AD
Sbjct: 240 SVDASRVVVRVHDAEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVERGDIMAD 299

Query: 797 GPSTD 801
           GPSTD
Sbjct: 300 GPSTD 304


>gi|322493781|emb|CBZ29070.1| DNA-directed RNA polymerase II subunit 2,putative [Leishmania
            mexicana MHOM/GT/2001/U1103]
          Length = 1185

 Score =  300 bits (769), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 107/580 (18%), Positives = 177/580 (30%), Gaps = 113/580 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            +         +      +    + I   ++            ++       +G      +
Sbjct: 693  MTPSEVEKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASNFN 752

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            +                  V        +    +T    + +      + AI      + 
Sbjct: 753  MRM-----------DTTAHVLFYPQKPLVRTKAMTYMHSNDLPAGHNAVVAISCYSGYNQ 801

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S V         + R    K ER      E  E   R    E   + R  YS
Sbjct: 802  EDSIIMSRSAVERGFFRSAFW-RSFKAKEERQKRDALETFENPDR----EVCRVKRADYS 856

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L     I  G   + G     K+  L    + +       +   +D  +          
Sbjct: 857  KLDTDGLIKPGMRVLGGDVVVGKTIPLPEADLEKLTTGN-TKITKRDASITSRATE---- 911

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                        K  ++K+           R  KV +   +    GDK   RHG KG   
Sbjct: 912  ------------KGVVDKVM---LTMNNNDRFTKVKIRTIKIPNIGDKFCSRHGQKGTNG 956

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF +DG   D+++NP  +PSRM V  + ET  G                   
Sbjct: 957  IQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVAC--------------- 1001

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                  +K G   +TP F     +    
Sbjct: 1002 --------------------------------------YKGGEVYATP-FCSVVVDDFGK 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L        G   LY+G TG P D  +  G  +  +L H+  DK++AR  G    + +Q
Sbjct: 1023 ALHALRSQRYGNECLYNGHTGLPLDHLIFFGPTFYQRLKHLSGDKIHARPRGPLQPLVRQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------GRTRV- 1328
            P  G+++ GG R GEME  C+ +YGA+  L+E L   SD     V           T++ 
Sbjct: 1083 PTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYTVHVCNMCGTICVADTKLN 1142

Query: 1329 -YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
             Y+    G        +   P +  +L +E+ ++ +   L
Sbjct: 1143 RYQC--KGCENDTRISQVLMPYACKLLFQELMSMTILPRL 1180



 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 155/1010 (15%), Positives = 310/1010 (30%), Gaps = 209/1010 (20%)

Query: 29  LIEVQKASYDHFLMMNIA----------PDERPNEG--LQA-------AFKSVFPITAFS 69
           L+  Q  SY+ FLM               D++ + G  ++          + V  I   S
Sbjct: 51  LVHQQLDSYNDFLMRIPKMIESMAVIPRQDDQYDPGVTMEEQRDQPRLVLQDVV-IGNPS 109

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 F      PP F  ++C  RD+TY    ++TL + ++     T      D   ++
Sbjct: 110 HQTQSYFAGGSL-PPLF-PNECRLRDMTYDAQAQVTLGVELYHPHADTP----HDTFLRN 163

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
           + +G +P+M K                         G FVI G ++++++Q  ++   ++
Sbjct: 164 VELGRIPIMLKSMRCNLSGKDEDELPRLNECPHDQGGYFVINGTEKVLIAQERQAANHVY 223

Query: 165 -FDHDKG-----RASLSG--KLLYACRII---PDQGLWMDIEFDSKDIIH--VRIDRRRK 211
            F   KG     ++ + G        +II    ++G     E    +++    ++D    
Sbjct: 224 TFSRQKGLLCEVKSIVEGSLNKPRTLQIIMQYKNKGPGSGFE----NLMCRVAQMDET-- 277

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     A+ M ++ EIL T  P +  +   +     +S A  +       +L  I   
Sbjct: 278 IPLFVLFRAMDMVADKEILQTVVPDLKDTAMLELLRGSMSDASTLQIFTREEALGYIGRR 337

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
               ++   L       L    +  +G          +    +  +   + +   +  D 
Sbjct: 338 LGKQDAMANLQREAESLLMRDLLPHMGTDPSANRTKCLYMGYMVHKLLLVALGRHEETDR 397

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-----LDIYRVMRPGD 385
             L        + I +               +  +  K  +D       +  +  +    
Sbjct: 398 DFL------GHKRIDVAGTLLTVQLQTFLAQVRKEMIKTLQDHAANPRGVFSFGRVIHSK 451

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR----KEDIIAIIK 441
           + T  +   +    F D    ++ T     +N      +  ++R I+            +
Sbjct: 452 LITDGLRRCLATGNFGDLKTGNIKTGVAQTLNRLTYSSSLSNLRRIQNPIAASSKATRPR 511

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDI----- 495
            L   + G     +    G+  +     ++    R      + ++++ RI          
Sbjct: 512 NLHCTQWGYICPVETPEGGSIGLLKNVALMCLMSRGTDHAEVVQAVQARIDGFRTIGLED 571

Query: 496 --DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             D  + +  +N   +            L     +    + ++  R +        + A 
Sbjct: 572 TADVRVARVFVNGTMIGVDRNPERLLHDLRTRRRNGELSNEVSIVRDIRDREIRVFSDAG 631

Query: 554 AGVEMRDVHPTHYGRICPAE--TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                R + P      C  +   S   ++ +         ++    ++  Y         
Sbjct: 632 -----RCLRPLFVAENCHLKLRKSGMRDLLVSEKAGGKKSISWSTALKKGY--------- 677

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  +   EE++  IA   S ++++  +                        +  P  +
Sbjct: 678 --VELIDCEEEDSLLIAMTPSEVEKNYYY---------------------SHCEMDPSMI 714

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IP+  ++ S R      M +QA+ +                            
Sbjct: 715 LGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------- 747

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                          S       +T+ V  Y               Q+PLV+        
Sbjct: 748 --------------ASNFNMRMDTTAHVLFYP--------------QKPLVR-------- 771

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       DL  G N +VA   + GYN EDS+++S   V    F S     F+   
Sbjct: 772 --TKAMTYMHSNDLPAGHNAVVAISCYSGYNQEDSIIMSRSAVERGFFRSAFWRSFKAKE 829

Query: 852 RDTK----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              K       E   R++  V       +D  G+I  G  V  GD++VGK  P       
Sbjct: 830 ERQKRDALETFENPDREVCRVKRADYSKLDTDGLIKPGMRVLGGDVVVGKTIP------L 883

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
           PE  L +   G   +  RD S+   +     VVD  +   +  D+  +  
Sbjct: 884 PEADLEKLTTGNTKITKRDASITSRA-TEKGVVDKVMLTMNNNDRFTKVK 932


>gi|11121234|emb|CAC14802.1| RNA polymerase beta subunit [Neisseria meningitidis]
 gi|11121236|emb|CAC14803.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 192/341 (56%), Positives = 248/341 (72%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N             +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+
Sbjct: 1   LNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQF 60

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +
Sbjct: 61  RSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEV 120

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           T+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N Y
Sbjct: 121 TYKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDY 180

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+
Sbjct: 181 GFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIM 240

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+
Sbjct: 241 ATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGI 300

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           E  VA  S  AIVA+R G+VE VDA R+VIR  + +     
Sbjct: 301 ERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|11121228|emb|CAC14799.1| RNA polymerase beta subunit [Neisseria meningitidis]
 gi|11121230|emb|CAC14800.1| RNA polymerase beta subunit [Neisseria meningitidis]
 gi|11121232|emb|CAC14801.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 192/341 (56%), Positives = 246/341 (72%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           +N             +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+ +NQ+
Sbjct: 1   LNETFAGAADKGGYVLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQF 60

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ     N LS +
Sbjct: 61  RSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMVQTNPLSEV 120

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N Y
Sbjct: 121 THKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDY 180

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+
Sbjct: 181 GFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIM 240

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
              +++ ++D +  QVVS+A SLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+
Sbjct: 241 ATPDRVQYMDVATGQVVSVAVSLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGI 300

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           E  VA  S  AIVA+R G+VE VDA R+VIR  + +     
Sbjct: 301 ERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|11121242|emb|CAC14806.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 342

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 191/327 (58%), Positives = 247/327 (75%)

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +  EDI+A I  LV+LRNG G +DDID+LGNRRVRSVGE+++NQ+R GL R+ER++KER
Sbjct: 15  VLSVEDIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELIENQFRSGLARVERAVKER 74

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           ++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +T+ RR+SALG GG+
Sbjct: 75  LNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEVTNKRRVSALGPGGL 134

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPYR+V DGK
Sbjct: 135 TRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPYRRVIDGK 194

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+   +++ ++D +  
Sbjct: 195 VTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIMATPDRVQYMDVATG 254

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  S  AIVA
Sbjct: 255 QVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGIERSVAVDSATAIVA 314

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPST 756
           +R G+VE VDA R+VIR  + +     
Sbjct: 315 RRGGVVEYVDANRVVIRVHDDEATAGE 341


>gi|157872958|ref|XP_001685000.1| DNA-directed RNA polymerase II subunit 2 [Leishmania major strain
            Friedlin]
          Length = 1185

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 111/582 (19%), Positives = 183/582 (31%), Gaps = 115/582 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +A+  N +     +     + SM+  I   ++            ++       +G     
Sbjct: 691  IAMTPNEVEKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASN 750

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             ++                  V        +    +T    + +      + AI      
Sbjct: 751  FNMRM-----------DTTAHVLFYPQKPLVRTKAMTYMHSNDLPAGHNAVVAISCYSGY 799

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S V         + R    K ER      E  E   R    E   + R  
Sbjct: 800  NQEDSIIMSRSAVERGFFRSAFW-RSFKAKEERQKRDALETFENPDR----ELCRVKRAD 854

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            YS+L     I  G   + G     K+  L    + +       +   +D  +        
Sbjct: 855  YSKLDTDGLIKPGMRVLGGDVVVGKTIPLPEADLEKLTTGN-TKITKRDASITSRTTE-- 911

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                          K  ++K+           R  KV +   +    GDK   RHG KG 
Sbjct: 912  --------------KGVVDKVM---LTMNNNDRFTKVKIRTIKIPNIGDKFCSRHGQKGT 954

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                   EDMPF +DG   D+++NP  +PSRM V  + ET  G                 
Sbjct: 955  NGIQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVAC------------- 1001

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                    +K G   +TP F     +  
Sbjct: 1002 ----------------------------------------YKGGEVYATP-FCSVVVDDF 1020

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L        G   LY+G TG P D  +  G  +  +L H+  DK++AR  G    + 
Sbjct: 1021 GKALHALRSQRYGNECLYNGHTGLPLDHLIFFGPTFYQRLKHLSGDKIHARPRGPLQPLV 1080

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------GRTR 1327
            +QP  G+++ GG R GEME  C+ +YGA+  L+E L   SD     V           T+
Sbjct: 1081 RQPTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYTVHVCNMCGTICVADTK 1140

Query: 1328 V--YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +  Y+    G        +   P +  +L +E+ ++ +   L
Sbjct: 1141 LNRYQC--KGCENDTRISQVLMPYACKLLFQELMSMTILPRL 1180



 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 154/1010 (15%), Positives = 310/1010 (30%), Gaps = 209/1010 (20%)

Query: 29  LIEVQKASYDHFLMMNIA----------PDERPNEG--LQA-------AFKSVFPITAFS 69
           L+  Q  SY+ FLM               D++ + G  ++          + V  I   S
Sbjct: 51  LVHQQLDSYNDFLMRIPKMIESMAVIPRQDDQYDPGVTMEEQRDQPRLVLQDVV-IGNPS 109

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 F      PP F  ++C  RD+TY    ++TL + ++     T      D   ++
Sbjct: 110 HQTHSYFTGGPL-PPLF-PNECRLRDMTYDAQAQVTLGVELYHPHADTP----HDTFLRN 163

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
           + +G +P+M K                         G FVI G ++++++Q  ++   ++
Sbjct: 164 VELGRIPIMLKSMRCNLSGKDEDELPRLNECPHDQGGYFVINGTEKVLIAQERQAANHVY 223

Query: 165 -FDHDKG-----RASLSG--KLLYACRIIP---DQGLWMDIEFDSKDIIH--VRIDRRRK 211
            F   KG     ++ + G        +II    ++G     E    +++    ++D    
Sbjct: 224 TFSRQKGLLCEVKSIVEGSLNKPRTLQIIMQYRNKGPGSGFE----NLMCRVAQMDET-- 277

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     A+ M ++ EIL T  P +  +   +     +S A  +       +L  I   
Sbjct: 278 IPLFVLFRAMDMVADKEILQTVVPDLKDTAMLELLRGSMSDASTLQIFTREEALGYIGRR 337

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
               ++   L       L    +  +G          +    +  +   + +   +  D 
Sbjct: 338 LGKQDAMANLQREAESLLMRDLLPHMGTDPSANRTKCLYMGYMVHKLLLVALGRHEETDR 397

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-----LDIYRVMRPGD 385
             L        + I +               +  +  K  +D       +  +  +    
Sbjct: 398 DFL------GHKRIDVAGTLLTVQLQTFLAQVRKEMIKTLQDHAANPRGVFSFGRVIHSK 451

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR----KEDIIAIIK 441
           + T  +   +    F D    ++ T     +N      +  ++R I+            +
Sbjct: 452 LITDGLRRCLATGNFGDLKTGNIKTGVAQTLNRLTYSSSLSNLRRIQNPIAASSKATRPR 511

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDI----- 495
            L   + G     +    G+  +     ++    R      + ++++ RI          
Sbjct: 512 NLHCTQWGYICPVETPEGGSIGLLKNVALMCLMSRGTDHAEVVQAVQARIDGFRTIGLED 571

Query: 496 --DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             D  + +  +N   +            L     +    + ++  R +        + A 
Sbjct: 572 TADVRVARVFVNGTMIGVDRNPERLLHDLRTRRRNGELSNEVSIVRDIRDREIRVFSDAG 631

Query: 554 AGVEMRDVHPTHYGRICPAE--TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                R + P      C  +   S   ++ +         ++    ++  Y         
Sbjct: 632 -----RCLRPLFVAENCRLKLRKSGMRDLLVSEKAGGKKSISWKTALKKGY--------- 677

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  +   EE++  IA   + ++++  +                        +  P  +
Sbjct: 678 --VELIDCEEEDSLLIAMTPNEVEKNYYY---------------------SHCEMDPSMI 714

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IP+  ++ S R      M +QA+ +                            
Sbjct: 715 LGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------- 747

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                          S       +T+ V  Y               Q+PLV+        
Sbjct: 748 --------------ASNFNMRMDTTAHVLFYP--------------QKPLVR-------- 771

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       DL  G N +VA   + GYN EDS+++S   V    F S     F+   
Sbjct: 772 --TKAMTYMHSNDLPAGHNAVVAISCYSGYNQEDSIIMSRSAVERGFFRSAFWRSFKAKE 829

Query: 852 RDTK----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              K       E   R++  V       +D  G+I  G  V  GD++VGK  P       
Sbjct: 830 ERQKRDALETFENPDRELCRVKRADYSKLDTDGLIKPGMRVLGGDVVVGKTIP------L 883

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
           PE  L +   G   +  RD S+   +     VVD  +   +  D+  +  
Sbjct: 884 PEADLEKLTTGNTKITKRDASITSRT-TEKGVVDKVMLTMNNNDRFTKVK 932


>gi|52694251|emb|CAG30655.1| DNA-directed RNA polymerase beta chain [Pseudomonas viridiflava]
          Length = 312

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 180/312 (57%), Positives = 238/312 (76%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + ++P+DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 1   SEGLLPKDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 60

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++
Sbjct: 61  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEI 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IA+A++++++     +ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 121 VFLSAIEEADHVIARASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 180

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 181 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 240

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   + VDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 241 IDSVDASRIVVRVADDEVETGETSVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 300

Query: 795 ADGPSTDLGDLA 806
           ADGPSTD+G+LA
Sbjct: 301 ADGPSTDMGELA 312


>gi|321399803|emb|CAJ08180.2| putative DNA-directed RNA polymerase II subunit 2 [Leishmania major
            strain Friedlin]
          Length = 1185

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 111/582 (19%), Positives = 183/582 (31%), Gaps = 115/582 (19%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +A+  N +     +     + SM+  I   ++            ++       +G     
Sbjct: 691  IAMTPNEVEKNYYYSHCEMDPSMILGICASIIPYPNHNQSPRNTYQSAMGKQAMGIYASN 750

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             ++                  V        +    +T    + +      + AI      
Sbjct: 751  FNMRM-----------DTTAHVLFYPQKPLVRTKAMTYMHSNDLPAGHNAVVAISCYSGY 799

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S V         + R    K ER      E  E   R    E   + R  
Sbjct: 800  NQEDSIIMSRSAVERGFFRSAFW-RSFKAKEERQKRDALETFENPDR----ELCRVKRAD 854

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            YS+L     I  G   + G     K+  L    + +       +   +D  +        
Sbjct: 855  YSKLDTDGLIKPGMRVLGGDVVVGKTIPLPEADLEKLTTGN-TKITKRDASITSRTTE-- 911

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                          K  ++K+           R  KV +   +    GDK   RHG KG 
Sbjct: 912  --------------KGVVDKVM---LTMNNNDRFTKVKIRTIKIPNIGDKFCSRHGQKGT 954

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                   EDMPF +DG   D+++NP  +PSRM V  + ET  G                 
Sbjct: 955  NGIQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVAC------------- 1001

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                    +K G   +TP F     +  
Sbjct: 1002 ----------------------------------------YKGGEVYATP-FCSVVVDDF 1020

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L        G   LY+G TG P D  +  G  +  +L H+  DK++AR  G    + 
Sbjct: 1021 GKALHALRSQRYGNECLYNGHTGLPLDHLIFFGPTFYQRLKHLSGDKIHARPRGPLQPLV 1080

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------GRTR 1327
            +QP  G+++ GG R GEME  C+ +YGA+  L+E L   SD     V           T+
Sbjct: 1081 RQPTEGRAHEGGLRFGEMERDCMLSYGASQWLRERLFRVSDYYTVHVCNMCGTICVADTK 1140

Query: 1328 V--YESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +  Y+    G        +   P +  +L +E+ ++ +   L
Sbjct: 1141 LNRYQC--KGCENDTRISQVLMPYACKLLFQELMSMTILPRL 1180



 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 154/1010 (15%), Positives = 310/1010 (30%), Gaps = 209/1010 (20%)

Query: 29  LIEVQKASYDHFLMMNIA----------PDERPNEG--LQA-------AFKSVFPITAFS 69
           L+  Q  SY+ FLM               D++ + G  ++          + V  I   S
Sbjct: 51  LVHQQLDSYNDFLMRIPKMIESMAVIPRQDDQYDPGVTMEEQRDQPRLVLQDVV-IGNPS 109

Query: 70  GAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
                 F      PP F  ++C  RD+TY    ++TL + ++     T      D   ++
Sbjct: 110 HQTHSYFTGGPL-PPLF-PNECRLRDMTYDAQAQVTLGVELYHPHADTP----HDTFLRN 163

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IH 164
           + +G +P+M K                         G FVI G ++++++Q  ++   ++
Sbjct: 164 VELGRIPIMLKSMRCNLSGKDEDELPRLNECPHDQGGYFVINGTEKVLIAQERQAANHVY 223

Query: 165 -FDHDKG-----RASLSG--KLLYACRIIP---DQGLWMDIEFDSKDIIH--VRIDRRRK 211
            F   KG     ++ + G        +II    ++G     E    +++    ++D    
Sbjct: 224 TFSRQKGLLCEVKSIVEGSLNKPRTLQIIMQYRNKGPGSGFE----NLMCRVAQMDET-- 277

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     A+ M ++ EIL T  P +  +   +     +S A  +       +L  I   
Sbjct: 278 IPLFVLFRAMDMVADKEILQTVVPDLKDTAMLELLRGSMSDASTLQIFTREEALGYIGRR 337

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
               ++   L       L    +  +G          +    +  +   + +   +  D 
Sbjct: 338 LGKQDAMANLQREAESLLMRDLLPHMGTDPSANRTKCLYMGYMVHKLLLVALGRHEETDR 397

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-----LDIYRVMRPGD 385
             L        + I +               +  +  K  +D       +  +  +    
Sbjct: 398 DFL------GHKRIDVAGTLLTVQLQTFLAQVRKEMIKTLQDHAANPRGVFSFGRVIHSK 451

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR----KEDIIAIIK 441
           + T  +   +    F D    ++ T     +N      +  ++R I+            +
Sbjct: 452 LITDGLRRCLATGNFGDLKTGNIKTGVAQTLNRLTYSSSLSNLRRIQNPIAASSKATRPR 511

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR-LGLLRMERSIKERISSVDI----- 495
            L   + G     +    G+  +     ++    R      + ++++ RI          
Sbjct: 512 NLHCTQWGYICPVETPEGGSIGLLKNVALMCLMSRGTDHAEVVQAVQARIDGFRTIGLED 571

Query: 496 --DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
             D  + +  +N   +            L     +    + ++  R +        + A 
Sbjct: 572 TADVRVARVFVNGTMIGVDRNPERLLHDLRTRRRNGELSNEVSIVRDIRDREIRVFSDAG 631

Query: 554 AGVEMRDVHPTHYGRICPAE--TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                R + P      C  +   S   ++ +         ++    ++  Y         
Sbjct: 632 -----RCLRPLFVAENCRLKLRKSGMRDLLVSEKAGGKKSISWKTALKKGY--------- 677

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V  +   EE++  IA   + ++++  +                        +  P  +
Sbjct: 678 --VELIDCEEEDSLLIAMTPNEVEKNYYY---------------------SHCEMDPSMI 714

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IP+  ++ S R      M +QA+ +                            
Sbjct: 715 LGICASIIPYPNHNQSPRNTYQSAMGKQAMGIY--------------------------- 747

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                          S       +T+ V  Y               Q+PLV+        
Sbjct: 748 --------------ASNFNMRMDTTAHVLFYP--------------QKPLVR-------- 771

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       DL  G N +VA   + GYN EDS+++S   V    F S     F+   
Sbjct: 772 --TKAMTYMHSNDLPAGHNAVVAISCYSGYNQEDSIIMSRSAVERGFFRSAFWRSFKAKE 829

Query: 852 RDTK----LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              K       E   R++  V       +D  G+I  G  V  GD++VGK  P       
Sbjct: 830 ERQKRDALETFENPDRELCRVKRADYSKLDTDGLIKPGMRVLGGDVVVGKTIP------L 883

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
           PE  L +   G   +  RD S+   +     VVD  +   +  D+  +  
Sbjct: 884 PEADLEKLTTGNTKITKRDASITSRT-TEKGVVDKVMLTMNNNDRFTKVK 932


>gi|156767125|gb|ABU95077.1| ribosomal polymerase B subunit [Acinetobacter septicus]
 gi|156767171|gb|ABU95100.1| ribosomal polymerase B subunit [Acinetobacter ursingii DSM 16037]
          Length = 266

 Score =  300 bits (769), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ++  G    K+   L+ DL+S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQDSNGGGTT-KRGDKLTEDLLSGLELVDLLEIQPSDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   GIAERLSQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   +    I+ LR FL+K+    G   E ++   DD VL +A   + GVP++T
Sbjct: 180  EQIDKMLQQQRT---IAELRIFLDKIYNKVGGEQEDLNSLTDDEVLVLAGNLRKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  +GQ IL+D
Sbjct: 237  PVFDGAEESQIKELLELAELPRTGQQILFD 266


>gi|68076215|ref|XP_680027.1| DNA-directed RNA polymerase, beta subunit [Plasmodium berghei strain
            ANKA]
 gi|56500894|emb|CAH97643.1| DNA-directed RNA polymerase, beta subunit, putative [Plasmodium
            berghei]
          Length = 1451

 Score =  300 bits (769), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 164/1120 (14%), Positives = 345/1120 (30%), Gaps = 37/1120 (3%)

Query: 212  VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
            +P    +  L +   +  S  Y KI    + +     +   + +    + +++ + +  E
Sbjct: 273  IPFNVLI--LCLSPIKKKSYIYNKIKLGIKNENAIKYI--ENYINSIFLKNNINEKEIFE 328

Query: 272  QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY-VAEDIVNGETGEIYIEAGDVIDE 330
            +         + + +++              +     +     N E  E        +  
Sbjct: 329  KYNLKYIGKYANVSRTIFRYYEGNNHKKGKSVINYCVLPHLQTNSEKFETICLMFKQLVL 388

Query: 331  KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
               + I       +    V + ++   + + ++ ++       +  +Y       +    
Sbjct: 389  SKFKLITTVNKDSLEYHSVTTCSS---LLSNILKERILSCFYRMQMLYSRSLHKFLEKKY 445

Query: 391  VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
                +     +   K  +          ++ L+   D     +E       +   + + K
Sbjct: 446  EVFKLNVKQIYLRYKEMILHELSEDHFNQILLNNNADKLENNEELTSENDHMNSKMDSTK 505

Query: 451  GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                   N   +   S    L+  +        R   E   +    S     L     + 
Sbjct: 506  NLRLMFMNEKEKLFASADGYLREMFSDA-----RVFIENSRTFGAASFSISYLFKTGNIA 560

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
            S    +   S    L + +N+L  +T+ R   ++ +G   +    +  R +    +G IC
Sbjct: 561  SDYIHYQQKSGWVILADEINNLRLLTNFR---SIHRGSFFQDVKVLSPRKLLGESWGFIC 617

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P  T +G   GL++ L+ +  +      E+    +        +            I + 
Sbjct: 618  PVHTPDGSPCGLLNHLSQYCCIYNVASNESHKFNIKMYLKKIGININLDETSGIHTIYEN 677

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
             +      S     +        +   +   +    + K    I A L      D     
Sbjct: 678  QTIPIIVDSVPITYISETEFKRTVYKLKYAKNHNLYNLKSHFEILAYLNEQSMMDSIIIN 737

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGM-----ESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                 + R  + L      F+  G       +V         +A++    ++      + 
Sbjct: 738  TCTGRIIRPILNLKMKCIEFISPGYQPYVSIAVNYDDILKNNLARKILKKKENIVNLNMN 797

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             +              Y   K     +    N+  +V+  +  + +       +      
Sbjct: 798  NTKNTKKMTLKEQYHFYTNKKHNIEKEAKNYNESEIVRK-ENKKASKSKNKVLNILENKK 856

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISE----RMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                N              +S   S+         D   +++I+ +E + +  +    + 
Sbjct: 857  QYQFNEDEYISSSDYETSSESDKYSDDNMSSTTYIDSDENLNIDIYEQIPQKFEYMELKQ 916

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            T  +  ++       D         +       +G  +       T +   +        
Sbjct: 917  TSFLSFLAS-LTPFSDHNQSPRNIYQCQMLKQTMGIQSLNMFYTFTNKIYRIITPQFPLV 975

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
            V        V +  SGT   V I    G D  +  I  +      + R    +  ++D  
Sbjct: 976  VTRDYEFYGVDNFPSGTNAVVAILAYTGYDMEDALIINKASSDRGMFRTHIYKTEVIDLY 1035

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
              +   + + G N             +         +        +  +       +  +
Sbjct: 1036 KKTNSPDFVLGNNIRYNANSLSSKNNIREHKGKFLNKDGLPCINQKILENNPLYSYINKK 1095

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             E +   +     +                ++  + +   RP   GDK A RHG KG++S
Sbjct: 1096 NELTTYEIFKTHGDYYVDC----VSNSQNNQIAIIRLRTTRPPLVGDKFASRHGQKGVIS 1151

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R+ P EDMPF + G   D++ NP G+PSRM +G + E+  G A    GK+I +       
Sbjct: 1152 RLFPHEDMPFSESGIVPDVIFNPHGIPSRMTIGMLIESICGKAASIYGKRIDATPFR--- 1208

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDD-SVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +  +SF    I        ++  D++    +   +  +G   +T +      +   
Sbjct: 1209 --KYTKQKSFNNPWIDGCGVKGFLNKLDENADEKKTTIKGSTGNSDTTEISYDEKIDFFA 1266

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +L     D  G  +LY G+ G P    +  G IY  +L HM  DK   R TG    +T 
Sbjct: 1267 KLLLNKGYDYYGTELLYSGIYGVPLQAHIFFGVIYYQRLRHMAYDKAQVRRTGPVCHLTH 1326

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            QPL GK   GG RLGEME   + ++G ++++ E   + SD
Sbjct: 1327 QPLKGKKKHGGIRLGEMERDGLISHGCSFIINERFLMNSD 1366


>gi|161527855|ref|YP_001581681.1| DNA-directed RNA polymerase subunit B [Nitrosopumilus maritimus SCM1]
 gi|160339156|gb|ABX12243.1| RNA polymerase Rpb2 domain 6 [Nitrosopumilus maritimus SCM1]
          Length = 1115

 Score =  300 bits (769), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 125/320 (39%), Gaps = 74/320 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ K+     R  + GDK A RHG KG++  +   ED+P+   G   D+++NP  
Sbjct: 851  SNEGGKMYKIRARDMRIPEIGDKFASRHGQKGVLGILAKAEDLPYTASGMSPDVLINPHA 910

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG + E+  G +    GK+        +   ++  +                  
Sbjct: 911  FPSRMTVGMMMESICGKSAALRGKRFDGSAFVGEKMDEVREVMDAHGFEYSGKEIM---- 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                         G        TG+ F 
Sbjct: 967  -------------------------------------------YDG-------RTGKSFP 976

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  C+ AYG
Sbjct: 977  VEVFIGVVYYQKLHHMVADKIHARARGQVQMLTKQPTEGRARGGGLRFGEMERDCLIAYG 1036

Query: 1307 AAYVLQEMLTIKSD----------------DVVGRTRVYESIVAGN--DTFETGTPESFN 1348
            A+ +L++ L  +SD                DV  R   Y   V G+           +F 
Sbjct: 1037 ASMILKDRLLDESDKSDIFVCERCGLVAYHDVKQRK--YVCRVCGDKAKVSSVSVAYAFK 1094

Query: 1349 VLVKEMQALGLSIDLENSRT 1368
            +L++EMQ+L ++  L     
Sbjct: 1095 LLLQEMQSLNVAPRLLIKEK 1114



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 141/1001 (14%), Positives = 290/1001 (28%), Gaps = 221/1001 (22%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI--TAFSGAAMLEFVSYEFDPPK----- 85
              S+D FL            GLQ+    V  I          ++    +   P+     
Sbjct: 25  HLNSFDEFL----------ERGLQSIINEVGQIDIENAEYPYKIQLGKVKLQQPRMMELD 74

Query: 86  -----FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-- 138
                    +   R+++Y+ P  + +   V +  +   ++         +++GD+P+M  
Sbjct: 75  GSITHITPAEARLRNVSYSAP--VMMEASVVEDGKILESRF--------VHIGDVPVMAK 124

Query: 139 ----------------------TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F+I G +R++V     S   +      R ++ G
Sbjct: 125 SNACILHNFSTQKLVEHGEDPNDPGGYFIINGSERVIVGLEDLS---YNKIIVDRETVGG 181

Query: 177 KLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSE-EI-- 228
            +++  ++       +   +++   +  +I  RI      +PV + + ALG++S+ EI  
Sbjct: 182 NIVHKAKVYSSIVGYR-AKLELVMKNDGLIVARIPGSPVDIPVVTLMRALGLESDREIAA 240

Query: 229 ----LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKLT 281
               +     ++  S            A + +  +++        I   E +++ G    
Sbjct: 241 AVSLVDELQDELEASFEKAGDVPTAKDAIVYISKRIAPGMLEEFQIKRAETLLDWGLLPH 300

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            G     +++  +FLG  +  L  L +     + +         D    K ++       
Sbjct: 301 LGKHPENRKEKAQFLGEAACKLLELKLDWIRPDDK---------DHYGNKVIKFAGQMLA 351

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL---DIYRVMRPGDVSTFSVAESMFNF 398
                 + + V +  Y        +  +   A +    I   +     +       +   
Sbjct: 352 DLFRTAFRNLVRDMKYQLERSGQKRGINAVAAAIRPGIITDKLNNAIATGNWGRGRVGVT 411

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPD-DVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              D   Y  +     ++   L+   P+ + R +       I        +  G + ++ 
Sbjct: 412 QLLDRTNYLSTISHLRRIQSPLSRTQPNFEARDLHATHFGRICPSETPEGSNCGLVKNLA 471

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
             G   V    E +  +               +   D    + +D          +  + 
Sbjct: 472 LSGIISVNVPSEEIVEKLYD---------LGTVHFFDAKEDLKKDGTRIFVDGRLIGYYK 522

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQG---GVARARAGVEMRDVHPTHYGRICPAET 574
              QL            +   RR S +         ++      R ++       C A  
Sbjct: 523 DGEQL---------AESLRDLRRNSKIHPHVGVSFHKSEIEGSTRRLYVN-----CNAGR 568

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                I +  +       +    I        D      +  + A EEEN Y+       
Sbjct: 569 VLRPLIIIKDNKPLL-TADLLDKISKKLISWTDLLRMGVLEMIDANEEENCYVT------ 621

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                   +K   ++  P  ++   AS+IP+ E++ S R     
Sbjct: 622 ------------------LDEKDTKKHTHLEVFPPAILGAGASIIPYPEHNQSPRNTYES 663

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +Q++                                                     
Sbjct: 664 AMAKQSLGFSTPM----------------------------------------------- 676

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y    F          Q P+V                   L D   G+N +VA
Sbjct: 677 --MNTSTYVRQHFM------LYPQVPIVN----------TKAMKLLGLEDRPAGQNCVVA 718

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-------- 866
            +P+ GYN ED++++S+  V   +  +     ++  A+    G  +   +IP        
Sbjct: 719 VLPFDGYNIEDAIVLSKASVDRGLGRTFFFRIYDAEAKQYPGGMRDAF-EIPNAEDNIRG 777

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
              E   + ++E G++   A V  GDIL+GK +P        E +             RD
Sbjct: 778 YKGERAYRLLEEDGVVATEAPVKGGDILIGKTSPPRFMEEYREFE-------SSGPYRRD 830

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
           TS+ V    +  VVD  +  +         I     +I  +
Sbjct: 831 TSIGVRPSET-GVVDTVVMTQSNEGGKMYKIRARDMRIPEI 870


>gi|221504639|gb|EEE30312.1| DNA-directed RNA polymerase I, beta subunit, putative [Toxoplasma
            gondii VEG]
          Length = 1388

 Score =  300 bits (769), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 99/511 (19%), Positives = 167/511 (32%), Gaps = 67/511 (13%)

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             +  P+  +N     +   +M+ + + T  H     +  R        IT   P V  E 
Sbjct: 845  ASLTPYSHHNQSPRNIYQCQMLKQTMGTPFH----SIPFRHDNKAYRLITPQRPLVRTED 900

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +  D                                   + A+      D+ D  +   
Sbjct: 901  YRRFDFD-------------------------DYPSGVNAVVAVMCYTGFDMEDAMILNK 935

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +        ++         +S  ++       A                + +  L G
Sbjct: 936  GSMERGAFHGCVY---------KSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDG 986

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL--- 1049
                +     +K             ++     +     +Q   +  +  Y    + +   
Sbjct: 987  DGFPAIGAKIEKGNTYCR------VQTSSSSSSFASNGIQHAYKDGETAYVDGVTFISPP 1040

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +   +   +    G            + +   R    GDK A RHG KGI+S + P EDM
Sbjct: 1041 DAAHERLAKSGLKG--------CRASLRLRCVRKPVIGDKFASRHGQKGILSMLWPHEDM 1092

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G A    G    +               
Sbjct: 1093 PFTESGLVPDILFNPHGFPSRMTIGMLIESMAGKAAAVHGAYQDATPFREFPPQSADGKN 1152

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
             ++++    G           +   +  ++ +      TPV      +     L  A   
Sbjct: 1153 KWVDQGGYHGWVKRGERYRTPEEERQAQDEPE------TPV------DYFGKALMRAGYQ 1200

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY G+ G P    +  G IY  +L HMV+DK   R+TG    +T QP+ G+   
Sbjct: 1201 YYGTEELYSGVYGVPLTAHIFTGLIYYQRLRHMVTDKHQVRATGPVDALTHQPVKGRKRH 1260

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + ++GAA +LQ+ L   SD
Sbjct: 1261 GGVRFGEMERDALISHGAAALLQDRLLHCSD 1291



 Score = 58.9 bits (141), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 50/184 (27%), Gaps = 82/184 (44%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSV----------------FPITAFSGAAMLEFVSY 79
           S+D FL +           LQ   K +                 P  + +    L   S 
Sbjct: 66  SFDSFLEVY----------LQEMVKDLPVVYVDPSYDPDKHEANPYYSPTDYIKLAISSV 115

Query: 80  EFDPP-KFD--------------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
               P +FD                       C    +TY  PLK+    +  D  +   
Sbjct: 116 SIGAPVRFDAAGARLQPGVGGSGDDQLLLPKHCREAHITYGAPLKV--SFVRSDRRDGAA 173

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV- 153
            K       + + +G  PLM +                         G F+I G +R++ 
Sbjct: 174 LK-------KEVVVGMAPLMVRSKLCSTRGMSPAELQRAGEDVDDGGGYFIINGNERVIR 226

Query: 154 -VSQ 156
            V Q
Sbjct: 227 FVVQ 230



 Score = 56.2 bits (134), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 66/206 (32%), Gaps = 21/206 (10%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVK 783
            +A ++  A +       +      +  +   T G   +    +           QRPLV+
Sbjct: 838  SAFLSIAASLTPYSHHNQSPRNIYQCQMLKQTMGTPFHSIPFRHDNKAYRLITPQRPLVR 897

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              D              D  D   G N +VA M + G++ ED+M++++  +    F   H
Sbjct: 898  TEDY----------RRFDFDDYPSGVNAVVAVMCYTGFDMEDAMILNKGSMERGAF---H 944

Query: 844  IEEFEVMARDTKLG-------PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               ++    D            +    ++     + +  +D  G   +GA++  G+    
Sbjct: 945  GCVYKSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDGDGFPAIGAKIEKGNTYCR 1004

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAV 922
              T    S             GE A 
Sbjct: 1005 VQTSSSSSSFASNGIQHAYKDGETAY 1030


>gi|221481595|gb|EEE19977.1| DNA-directed RNA polymerase I, beta subunit, putative [Toxoplasma
            gondii GT1]
          Length = 1385

 Score =  300 bits (769), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 99/511 (19%), Positives = 167/511 (32%), Gaps = 67/511 (13%)

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             +  P+  +N     +   +M+ + + T  H     +  R        IT   P V  E 
Sbjct: 842  ASLTPYSHHNQSPRNIYQCQMLKQTMGTPFH----SIPFRHDNKAYRLITPQRPLVRTED 897

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +  D                                   + A+      D+ D  +   
Sbjct: 898  YRRFDFD-------------------------DYPSGVNAVVAVMCYTGFDMEDAMILNK 932

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +        ++         +S  ++       A                + +  L G
Sbjct: 933  GSMERGAFHGCVY---------KSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDG 983

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL--- 1049
                +     +K             ++     +     +Q   +  +  Y    + +   
Sbjct: 984  DGFPAIGAKIEKGNTYCR------VQTSSSSSSFASNGIQHAYKDGETAYVDGVTFISPP 1037

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +   +   +    G            + +   R    GDK A RHG KGI+S + P EDM
Sbjct: 1038 DAAHERLAKSGLKG--------CRASLRLRCVRKPVIGDKFASRHGQKGILSMLWPHEDM 1089

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G A    G    +               
Sbjct: 1090 PFTESGLVPDILFNPHGFPSRMTIGMLIESMAGKAAAVHGAYQDATPFREFPPQSADGKN 1149

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
             ++++    G           +   +  ++ +      TPV      +     L  A   
Sbjct: 1150 KWVDQGGYHGWVKRGERYRTPEEERQAQDEPE------TPV------DYFGKALMRAGYQ 1197

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY G+ G P    +  G IY  +L HMV+DK   R+TG    +T QP+ G+   
Sbjct: 1198 YYGTEELYSGVYGVPLTAHIFTGLIYYQRLRHMVTDKHQVRATGPVDALTHQPVKGRKRH 1257

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + ++GAA +LQ+ L   SD
Sbjct: 1258 GGVRFGEMERDALISHGAAALLQDRLLHCSD 1288



 Score = 58.9 bits (141), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 50/184 (27%), Gaps = 82/184 (44%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSV----------------FPITAFSGAAMLEFVSY 79
           S+D FL +           LQ   K +                 P  + +    L   S 
Sbjct: 66  SFDSFLEVY----------LQEMVKDLPVVYVDPSYDPDKHEANPYYSPTDYIKLAISSV 115

Query: 80  EFDPP-KFD--------------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
               P +FD                       C    +TY  PLK+    +  D  +   
Sbjct: 116 SIGAPVRFDAAGARLQPGVGGSGDDQLLLPKHCREAHITYGAPLKV--SFVRSDRRDGAA 173

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV- 153
            K       + + +G  PLM +                         G F+I G +R++ 
Sbjct: 174 LK-------KEVVVGMAPLMVRSKLCSTRGMSPAELQRAGEDVDDGGGYFIINGNERVIR 226

Query: 154 -VSQ 156
            V Q
Sbjct: 227 FVVQ 230



 Score = 56.2 bits (134), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 66/206 (32%), Gaps = 21/206 (10%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVK 783
            +A ++  A +       +      +  +   T G   +    +           QRPLV+
Sbjct: 835  SAFLSIAASLTPYSHHNQSPRNIYQCQMLKQTMGTPFHSIPFRHDNKAYRLITPQRPLVR 894

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              D              D  D   G N +VA M + G++ ED+M++++  +    F   H
Sbjct: 895  TEDY----------RRFDFDDYPSGVNAVVAVMCYTGFDMEDAMILNKGSMERGAF---H 941

Query: 844  IEEFEVMARDTKLG-------PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               ++    D            +    ++     + +  +D  G   +GA++  G+    
Sbjct: 942  GCVYKSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDGDGFPAIGAKIEKGNTYCR 1001

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAV 922
              T    S             GE A 
Sbjct: 1002 VQTSSSSSSFASNGIQHAYKDGETAY 1027


>gi|237843771|ref|XP_002371183.1| DNA-directed RNA polymerase I subunit RPA2, putative [Toxoplasma
            gondii ME49]
 gi|211968847|gb|EEB04043.1| DNA-directed RNA polymerase I subunit RPA2, putative [Toxoplasma
            gondii ME49]
          Length = 1388

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 99/511 (19%), Positives = 167/511 (32%), Gaps = 67/511 (13%)

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             +  P+  +N     +   +M+ + + T  H     +  R        IT   P V  E 
Sbjct: 845  ASLTPYSHHNQSPRNIYQCQMLKQTMGTPFH----SIPFRHDNKAYRLITPQRPLVRTED 900

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +  D                                   + A+      D+ D  +   
Sbjct: 901  YRRFDFD-------------------------DYPSGVNAVVAVMCYTGFDMEDAMILNK 935

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
              +        ++         +S  ++       A                + +  L G
Sbjct: 936  GSMERGAFHGCVY---------KSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDG 986

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL--- 1049
                +     +K             ++     +     +Q   +  +  Y    + +   
Sbjct: 987  DGFPAIGAKIEKGNTYCR------VQTSSSSSSFASNGIQHAYKDGETAYVDGVTFISPP 1040

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +   +   +    G            + +   R    GDK A RHG KGI+S + P EDM
Sbjct: 1041 DAAHERLAKSGLKG--------CRASLRLRCVRKPVIGDKFASRHGQKGILSMLWPHEDM 1092

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G A    G    +               
Sbjct: 1093 PFTESGLVPDILFNPHGFPSRMTIGMLIESMAGKAAAVHGAYQDATPFREFPPQSADGKN 1152

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
             ++++    G           +   +  ++ +      TPV      +     L  A   
Sbjct: 1153 KWVDQGGYHGWVKRGERYRTPEEERQAQDEPE------TPV------DYFGKALMRAGYQ 1200

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY G+ G P    +  G IY  +L HMV+DK   R+TG    +T QP+ G+   
Sbjct: 1201 YYGTEELYSGVYGVPLTAHIFTGLIYYQRLRHMVTDKHQVRATGPVDALTHQPVKGRKRH 1260

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + ++GAA +LQ+ L   SD
Sbjct: 1261 GGVRFGEMERDALISHGAAALLQDRLLHCSD 1291



 Score = 60.1 bits (144), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 50/184 (27%), Gaps = 82/184 (44%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSV----------------FPITAFSGAAMLEFVSY 79
           S+D FL +           LQ   K +                 P  + +    L   S 
Sbjct: 66  SFDSFLEVY----------LQEMVKDLPVVYVDPSYDPDKHEANPFYSPTDYIKLAISSV 115

Query: 80  EFDPP-KFD--------------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
               P +FD                       C    +TY  PLK+    +  D  +   
Sbjct: 116 SIGAPVRFDAAGARLQPGVGGSGDDQLLLPKHCREAHITYGAPLKV--SFVRSDRRDGAA 173

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV- 153
            K       + + +G  PLM +                         G F+I G +R++ 
Sbjct: 174 LK-------KEVVVGMAPLMVRSKLCSTRGMSPAELQRAGEDVDDGGGYFIINGNERVIR 226

Query: 154 -VSQ 156
            V Q
Sbjct: 227 FVVQ 230



 Score = 56.2 bits (134), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 66/206 (32%), Gaps = 21/206 (10%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVK 783
            +A ++  A +       +      +  +   T G   +    +           QRPLV+
Sbjct: 838  SAFLSIAASLTPYSHHNQSPRNIYQCQMLKQTMGTPFHSIPFRHDNKAYRLITPQRPLVR 897

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              D              D  D   G N +VA M + G++ ED+M++++  +    F   H
Sbjct: 898  TEDY----------RRFDFDDYPSGVNAVVAVMCYTGFDMEDAMILNKGSMERGAF---H 944

Query: 844  IEEFEVMARDTKLG-------PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               ++    D            +    ++     + +  +D  G   +GA++  G+    
Sbjct: 945  GCVYKSKVIDAAPASARAGAASQYTFGNVNEFGRKHIATLDGDGFPAIGAKIEKGNTYCR 1004

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAV 922
              T    S             GE A 
Sbjct: 1005 VQTSSSSSSFASNGIQHAYKDGETAY 1030


>gi|156767145|gb|ABU95087.1| ribosomal polymerase B subunit [Acinetobacter johnsonii]
          Length = 266

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS+D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLTGQESNGGGTT-KRGDKLSADVLSGLELVDLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   KA   +  LR FL+K+    G   E +    DD +L ++   ++GVP++T
Sbjct: 180  EEIDKML---KAQRTVLELRGFLDKIYNKVGGEQEDLDSLTDDEILVLSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A++  +GQ++LYD
Sbjct: 237  PVFDGAEESQIKDLLELANISRTGQTVLYD 266


>gi|76556262|emb|CAJ00151.1| RNA polymerase beta subunit [Pseudomonas syringae pv. zizaniae]
          Length = 313

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 235/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+D +ADGPST
Sbjct: 302 QRSDSMADGPST 313


>gi|156767149|gb|ABU95089.1| ribosomal polymerase B subunit [Acinetobacter lwoffii]
 gi|156767155|gb|ABU95092.1| ribosomal polymerase B subunit [Acinetobacter lwoffii]
          Length = 266

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 114/270 (42%), Positives = 167/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEFKIFEEAARERVIRLLNGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEIQPVDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSFEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             +I  ++ + +    +  LR FL+K+    G   E +    D+ +L+++   ++GVP++T
Sbjct: 180  DQIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEILKLSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L++A L  +GQ++LYD
Sbjct: 237  PVFDGAEEGQIKELLQLAGLSSTGQTVLYD 266


>gi|46107920|ref|XP_381019.1| hypothetical protein FG00843.1 [Gibberella zeae PH-1]
          Length = 1157

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 151/973 (15%), Positives = 287/973 (29%), Gaps = 197/973 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  + + ++   +    +DD D +GN+R+   G++L   +     +   +++  I 
Sbjct: 343  KAIYVAMMTRRVLIAAHNPKLVDDRDFVGNKRLELAGQLLSLLFEDLFKQFTTNVRMSID 402

Query: 492  SV--DIDSVMPQDLINA-----KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                  +  +P D +N        +   +     +   +    ++N         RLS +
Sbjct: 403  KFLKKNNRAVPLDAVNMISNHANNIGYGINRAIQTGNWNVKRFNMNRAGVTHVLSRLSYI 462

Query: 545  GQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
               G+         + R     R + P+ +G +C ++T EG   GLV +L     +    
Sbjct: 463  AALGMMTRISSQFEKTRKVSGPRALQPSQWGMLCTSDTPEGEACGLVKNLALMTHITTNV 522

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-----EELVFCRCAG 651
              E     V     T     L A  E       + + +  +GS+            R   
Sbjct: 523  DEEP----VKRWIFT-----LDAGVE--PIRNFSGAEMHREGSYIIHVNGTPFALTRYPK 571

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                  R        SP   ++I          +  +       + R  + +   +    
Sbjct: 572  RFAQKFRTMRRRGWISPFVGININT------HFNAVHIATDEGRICRPYIIVKNGKQKLK 625

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               +  +              G     D +   I       + + + + IY     Q + 
Sbjct: 626  PEHLRLLQ------------MGKATFDDFLNRGIVEYLDVNEENDALITIYEHQVTQSTT 673

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                     L           +    P                +    G     ++  ++
Sbjct: 674  HLEIEPFTVL---------GAVAGLIPFPHHNQSP-----RNTYQCAMGKQAIGAIAYNQ 719

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                + +  ++                                                 
Sbjct: 720  FNRIDTLLYTLVYP-------------------------------------------QRP 736

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
             ++   I   G   +   +     +      D+ D  +   + V       ++F ++  +
Sbjct: 737  MVISKTIQLIGYDKLPAGQNATVVVMSYSGYDIEDALVLNKASVDRGFGRCQVFRKYTTE 796

Query: 952  KNE----RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +    R   +   ++E   +    ++ I            + G    SG    KK T 
Sbjct: 797  LQKYPNGRRERIGDPEMEGEGKS---KRRITKHEALDDDGLAIVGYKVHSGEAMVKKETP 853

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L                          ++    ++  S           I+K+       
Sbjct: 854  LDQT------------------STGIGLDRGPGEFRDSSVSYRIADPAYIDKVMI--SQT 893

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                 V+KV     R  + GDK + RHG KG+V  I+  ED+PF   G   DI+      
Sbjct: 894  EKDTTVIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVEQEDLPFSDSGLSPDII------ 947

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
               MN                G   +  +                    G G        
Sbjct: 948  ---MNP--------------HGFPSRMTVGKLLECLTGKASIIHGRPDYGFGD------- 983

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   F     E ++ +L        G+     G+TGEP + 
Sbjct: 984  ----------------------AFRSHPLEEMSQVLVDHGFSWEGKDYFTSGITGEPLEA 1021

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V  G IY  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AYGA
Sbjct: 1022 YVFNGPIYYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGA 1081

Query: 1308 AYVLQEMLTIKSD----DVV------GRTRVYESIVAGN-DTFETGTPESFNVLVKEMQA 1356
            + +L E L I SD    D+       G  + Y        +  +   P +  +LV+E+ +
Sbjct: 1082 SQLLLERLMISSDGTEIDICQQCGLFG-YKGYCHTCKSTREVTKMTMPYAAKLLVQELIS 1140

Query: 1357 LGLSIDLENSRTK 1369
            + + + L+     
Sbjct: 1141 MNVGVRLQMDDEF 1153



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 127/935 (13%), Positives = 269/935 (28%), Gaps = 180/935 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY+ F+   I    R N  +++   S            LEF     D P+   
Sbjct: 44  LVKQHIDSYNFFVEHEIKDIVRANRTIRSEVDS---------NFWLEFTDIRVDKPRRQD 94

Query: 86  ---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RD+TYA P+ + ++ I          +  + I  +++ +G +P
Sbjct: 95  WQDAKSHTEVTPMECRLRDMTYAAPISVDIQYI----------RDKQRIVRKNVPLGRMP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 145 VMLKSSICRLGGANNTKMEEMNECPLDPGGYFIIGGTEKVILIQEQLSKNRIIVEADEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-----VPVTSFLMAL-GMDSE 226
           ++    + +     ++          KD    RI          +P+   L AL G+   
Sbjct: 205 NIISASVTSST--HERKSK-TYVTLKKD----RILLTHNVLVEGIPIVIILKALGGLSDM 257

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI+          +  D +      A  +       +L  I T  ++          + +
Sbjct: 258 EIMQLVAGSDG--RYQDEFLVNFDEATKVGVFTQHQALEYIGTRVKMAPRRGIFGPQVRR 315

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           +  E+G+  L      L   +V  + ++     IY+ A                     +
Sbjct: 316 NHVEEGLDALA----NLVIAHVPIEGLDFYPKAIYV-AMMTRRVLIAAHNPKLVDDRDFV 370

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +         +   +  + I + ++  + +    A +M +    +    
Sbjct: 371 GNKRLELAGQLLSLLFEDLFKQFTTNVRMSIDKFLKKNNRAVPLDAVNMISNHANNIGYG 430

Query: 407 DLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
               +     N  R N++       + +   IA + ++  + +       +      +  
Sbjct: 431 INRAIQTGNWNVKRFNMNRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPS 490

Query: 466 SVGEMLKN--QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
             G +  +          ++        + ++D    +  I            F  +++ 
Sbjct: 491 QWGMLCTSDTPEGEACGLVKNLALMTHITTNVDEEPVKRWIFTLDAGVEPIRNFSGAEMH 550

Query: 524 QLEEHVNSLS----RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +   ++  ++     +T   +  A     + R         ++   +       T EG  
Sbjct: 551 REGSYIIHVNGTPFALTRYPKRFAQKFRTMRRRGWISPFVGININTHFNAVHIATDEGRI 610

Query: 580 IGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                 V +     +      ++       D      V YL   EE +  I      + +
Sbjct: 611 CRPYIIVKNGKQKLKPEHLRLLQMGKATFDDFLNRGIVEYLDVNEENDALITIYEHQVTQ 670

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                      ++  P  V+   A LIPF  ++ S R    C M
Sbjct: 671 S-----------------------TTHLEIEPFTVLGAVAGLIPFPHHNQSPRNTYQCAM 707

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                           I   + +   + 
Sbjct: 708 GKQAIGA-----------------------------------------IAYNQFNRIDTL 726

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               +Y               QRP+V          I           L  G+N  V  M
Sbjct: 727 LYTLVYP--------------QRPMV----------ISKTIQLIGYDKLPAGQNATVVVM 762

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN- 875
            + GY+ ED++++++  V           ++    +    G  E   D     E   K  
Sbjct: 763 SYSGYDIEDALVLNKASVDRGFGRCQVFRKYTTELQKYPNGRRERIGDPEMEGEGKSKRR 822

Query: 876 ------IDECGIICVGAEVNPGDILVGKITPKGES 904
                 +D+ G+  VG +V+ G+ +V K TP  ++
Sbjct: 823 ITKHEALDDDGLAIVGYKVHSGEAMVKKETPLDQT 857


>gi|213876745|gb|ACJ54369.1| RNA polymerase subunit B [Mycobacterium duvalii]
          Length = 245

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 102/233 (43%), Positives = 138/233 (59%), Gaps = 35/233 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  +                      V
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNLN---------------------V 137

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
             GT    +      ++     A+       V+TPVFDGA E  ++ +L     +      
Sbjct: 138  AGTEGVPDWAEKLPEELHSAPADSL-----VATPVFDGAQEGELSGLLGSTLPNRDGETM 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQ
Sbjct: 193  VDADGKAVLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQ 245



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 48


>gi|268308301|gb|ACY95380.1| RNA polymerase beta subunit [Spiroplasma diminutum]
          Length = 339

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 187/347 (53%), Positives = 257/347 (74%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV + KV + +  YL+A +E++  +AQAN +L  DG+  +E V  
Sbjct: 1   YAKINEYGFIETPYRKVKNTKVISGEYEYLTADKEKDYVVAQANINLGADGTILDEQVVA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+V  + +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMVSPQDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG AIVA   GIV+ VD+ +I+I   +        G+  Y L  F
Sbjct: 121 SPIVGTGVEHEAARDSGDAIVATADGIVKYVDSKKIIIEQKD--------GIKTYDLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VK+GD+V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 SRSNNGTAITHLPIVKLGDKVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEE+TRDIPN+SE   K +DE GI+ +GAE
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEVTRDIPNISEASKKYLDEDGIVAIGAE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|76556276|emb|CAJ00158.1| RNA polymerase beta subunit [Pseudomonas syringae pv. viburni]
          Length = 313

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 237/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFVSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI++DGPST
Sbjct: 302 QRSDIMSDGPST 313


>gi|76556310|emb|CAJ00175.1| RNA polymerase beta subunit [Pseudomonas syringae pv. eriobotryae]
 gi|76556332|emb|CAJ00186.1| RNA polymerase beta subunit [Pseudomonas syringae pv. papulans]
          Length = 313

 Score =  300 bits (768), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 181/311 (58%), Positives = 235/311 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPS 799
           +R+DI+ADGPS
Sbjct: 302 QRSDIMADGPS 312


>gi|76556254|emb|CAJ00147.1| RNA polymerase beta subunit [Pseudomonas syringae pv. ribicola]
          Length = 313

 Score =  300 bits (767), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 237/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IA+A++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIARASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|86559347|gb|ABD04081.1| RNA polymerase II second largest subunit [Coniophora arida]
          Length = 711

 Score =  300 bits (767), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 130/839 (15%), Positives = 249/839 (29%), Gaps = 144/839 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ R +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   F       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSSTVCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      LL+ +   ++  G                + G++E +DA   
Sbjct: 226  TDAGRVCRPLFIVENQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEEE 285

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +     +         +   +    +K G            PS  LG
Sbjct: 286  ETVMISMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILG 343

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 344  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 378

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 379  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 427

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 428  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKI 486

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 487  EDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 546

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 547  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 586

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 587  YRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 641

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 642  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 665

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 666  ------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 711



 Score =  118 bits (295), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 166/610 (27%), Gaps = 96/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNISLAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESLEENAHSSTVCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +          T   K         +  L A EEE   I+     L+     + 
Sbjct: 246 QKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEEEETVMISMTPEDLENSRLQSA 305

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +   +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 306 GIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 365

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 366 MGKQAMGIYLTNFLV-----------------------------------------RMDT 384

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 385 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 420

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 421 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKH 480

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 481 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 536

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 537 TENGIVDQVL 546


>gi|9759599|dbj|BAB11387.1| DNA-directed RNA polymerase subunit [Arabidopsis thaliana]
          Length = 1194

 Score =  300 bits (767), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 92/378 (24%), Positives = 149/378 (39%), Gaps = 76/378 (20%)

Query: 1024 FAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDD---------MPPGVLRV 1073
                D  + + V      ++ ++ S  + R   +  K   G+                  
Sbjct: 850  IRPNDIYINKQVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQVVDRVALCSDKKGQLC 909

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            +K  +   R  + GDK + RHG KG+   I+  ED PF + G   D+++NP G PSRM V
Sbjct: 910  IKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTV 969

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G++ E     A V  G+         ++                                
Sbjct: 970  GKMIELLGSKAGVSCGRFHYGSAFGERSGHAD---------------------------- 1001

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                   E I++ L       SG+ +LY G++GEP +  + +G 
Sbjct: 1002 ---------------------KVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGP 1040

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            IY  KL HMV DK++AR +G   ++T+QP  GKS  GG R+GEME  C+ AYGA+ ++ E
Sbjct: 1041 IYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYE 1100

Query: 1314 MLTIKSDDV-------VGRTRVYESIVA---------GNDTFETGTPESFNVLVKEMQAL 1357
             L I SD          G    Y   +          G++      P +  +L + ++ +
Sbjct: 1101 RLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTCKNGDNIATMKLPYACKLLFQ-VKTI 1159

Query: 1358 GLSIDLENSRTKNSAKME 1375
            GL   L+ S + +    +
Sbjct: 1160 GLFFKLKLSTSSHLENDK 1177



 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 124/940 (13%), Positives = 278/940 (29%), Gaps = 181/940 (19%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF-SGAAMLE 75
           F   PE + +  L++    S+++F+          N G+    K+   IT+    +  L 
Sbjct: 54  FQLVPEFLKVRGLVKQHLDSFNYFI----------NVGIHKIVKANSRITSTVDPSIYLR 103

Query: 76  FVSYEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           F       P           +   C   D+TYA P+ + +  +         AKS KD  
Sbjct: 104 FKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFVNIEYVHG--SHGNKAKSAKD-- 159

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
             ++ +G +P+M                           G F+IKG +++++ Q   S  
Sbjct: 160 --NVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 217

Query: 163 -IHFDHDK-----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVT 215
            I  D DK        + S ++  +  +I             K+ I++ + R  +K+P+ 
Sbjct: 218 RIIIDSDKKGNINASVTSSTEMTKSKTVI----------QMEKEKIYLFLHRFVKKIPII 267

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             L A+GM+S+ EI+        +S            ++ +   K +   ++    +   
Sbjct: 268 IVLKAMGMESDQEIVQMVGRDPRFSASLLP-SIEECVSEGVNTQKQALDYLEAKVKKISY 326

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            +  +     L  L++  +  + +  +          ++     E  +      ++ +++
Sbjct: 327 GTPPEKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRMIEAML------NKDAMD 380

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
           +  +   + + +       +   I             +A+ ++  ++     ++      
Sbjct: 381 DKDYVGNKRLEL-------SGQLISLLFEDLFKTMLSEAIKNVDHILNKPIRASRFDFSQ 433

Query: 395 MFNFLFFDSDKYDLSTVGRV--KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNG 449
             N     S    L            R  +      + + +   I  +  +  +      
Sbjct: 434 CLNKDSRYSISLGLERTLSTGNFDIKRFRMHRKGMTQVLTRLSFIGSMGFITKISPQFEK 493

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +    +L   +   +      +     L    ++   +++ + +  +          
Sbjct: 494 SRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGVT 553

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGR 568
              V               +N L    H+R          + RA    E   V       
Sbjct: 554 DLEVLSAEELHTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQH 613

Query: 569 ICPAETSEGHNIGLVSSLTS-FARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENR 625
                +  G     +       +RV  +    ++   R   D      + YL   EE N 
Sbjct: 614 CVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNA 673

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +                              +     I+  P  ++ + A LIP+  ++
Sbjct: 674 LV-----------------------CLRAEAAKADTTHIEIEPFTILGVVAGLIPYPHHN 710

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R    C M +QA+                                           I
Sbjct: 711 QSPRNTYQCAMGKQAMGN-----------------------------------------I 729

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              + +   +   + +Y               QRPL+                      L
Sbjct: 730 AYNQLNRMDTLLYLLVYP--------------QRPLL----------TTRTIELVGYDKL 765

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             G+N  VA M + GY+ ED++++++  +       I +++   M++       +     
Sbjct: 766 GAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIP 825

Query: 866 PNVSEEG--LKNIDECGIICVGAEVNPGDILVGKITPKGE 903
                +   ++ +D+ G+   G  + P DI + K  P   
Sbjct: 826 QRTGPDAEKMQILDDDGLATPGEIIRPNDIYINKQVPVDT 865


>gi|253778914|emb|CAY90192.1| RNA polymerase subunit B [Acinetobacter sp. F5]
          Length = 282

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 118/286 (41%), Positives = 170/286 (59%), Gaps = 5/286 (1%)

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             +E  I +     R++ +L GQ +  G    K+   L+ D++S        +    DE +
Sbjct: 1    KEEFKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLTEDVLSNLELVDLLEVQPADEGI 59

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
               +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ      
Sbjct: 60   AERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQXXXXXX 119

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
              HGNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG K
Sbjct: 120  XXHGNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLGDK 179

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            I  ++ + +    +  LR FL+K+    G   E +    D+ +L ++   + GVP++TPV
Sbjct: 180  IDKMMKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLATPV 236

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            FDGA+E  I  +L +  +  +GQ++LYDG TGE FDRPVTVGY+YM
Sbjct: 237  FDGAEEGQIKELLELGGISRTGQTVLYDGRTGERFDRPVTVGYMYM 282


>gi|6606115|gb|AAF19070.1|AF107798_1 DNA-dependent RNA polymerase II RPB140 [Capronia pilosella]
          Length = 937

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 147/917 (16%), Positives = 277/917 (30%), Gaps = 147/917 (16%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +   + + + +    +        R  +   +  ++  L+    G+   DD D+LG 
Sbjct: 144  HERQKHATDILQKEFLPHIGQGPDATAR--KAFFLGYMVNRLLKCALGRAEPDDRDHLGK 201

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP--VVSAVCEFFCS 519
            +R+   G ++ N +RL   +  +     +      +     +   K   + S +     +
Sbjct: 202  KRLDLAGPLMTNLFRLQFDKATKDFYRYMQKRVESNQPINIMAGFKHPIITSGLKYSLAT 261

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +A     + R     + R +H TH+
Sbjct: 262  GNWGDQKKLDKAKAGVSQVLSRYTFASTLSHLRRTNA----PIGREGKIAKPRQLHNTHW 317

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+  + V           Y      +   D       +   
Sbjct: 318  GYVCPAETPEGQACGLVKNLSLMSMVTNTYETGPLLNYILTKHVEALEDWEPRLNPQATK 377

Query: 625  RYI--AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             ++        L +     ++L   R  G          D  D   K        + P  
Sbjct: 378  VFVDGVWFAVVLRDPKRLVDDLRKLRRKGVFDSQVSLVWDIRDKEFKISGDSGRIVRPLF 437

Query: 683  --ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
              E D ++  L    + +  +  L   A     G +               +G+VE +DA
Sbjct: 438  IVETDRASENLGNLVLNKDHISKLDQTAYLKEGGFQWTDEIRPYGWNDLLESGVVEYLDA 497

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +  +     +  M+ +  +     N  PL+               PS 
Sbjct: 498  EEEETAMIIMTPEALSDSKAKWLGMEIENEDDPLRRN-DPLLNPHSHTF--THCEIHPSM 554

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +                     E
Sbjct: 555  ILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRME 597

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               +I    ++ L                        +       +   +  + AI    
Sbjct: 598  TMANILYYPQKPLAR-------------------TMAMDYLKFRELPAGQNAIVAIACYS 638

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +     +  +     +   SV    +E   +    + + L  
Sbjct: 639  GYNQEDSVIMNQSSIDRGLFRSLFYRTYQ----DSEKSVGHSVMEQFEKPTRTDTLRLKH 694

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y ++ E   +  G           K+  ++ D                +E  QR  + 
Sbjct: 695  GTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPD---------------AEELGQRQKQH 739

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +K    T     E    +++      D       R  KV V   +  Q GDK A RHG K
Sbjct: 740  IKRDVSTPLRSTESGIVDQVMLTTTND-----GHRFAKVRVRTTKTPQIGDKFASRHGQK 794

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 795  GTIGITYRTEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPF 854

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L   +                                             
Sbjct: 855  TKVTVTQVSDLLRRMGYQSRGFEVM----------------------------------- 879

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                         +G +    G         V +G  Y  +L HMV DK+++R+ G   +
Sbjct: 880  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIHSRARGPTQI 920

Query: 1278 VTQQPLGGKSNRGGQRL 1294
            +T+QP+ G++  GG R 
Sbjct: 921  LTRQPVEGRARDGGLRF 937



 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 111/861 (12%), Positives = 233/861 (27%), Gaps = 155/861 (18%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      +   I    D+G  M  +   K  +  R+
Sbjct: 1   SEKVLIAQE-RSAGNI--VQVFQKAAPAPFTHLAEIRSVIDRGARMMSQCTVK--LFRRV 55

Query: 207 D-----------R------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           D           R      ++ +P+     AL + S+ +IL          +  D     
Sbjct: 56  DGPDGTKIDNPIRVQLPYVKQDIPLVIVFRALDIVSDADILEKICFDQSDKEMMDMLMGS 115

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           L     + GA ++   +        ++S ++        L+++ +  +G   D       
Sbjct: 116 LQEGQAIQGADLARDFIARRGNVPTLKSHER-QKHATDILQKEFLPHIGQGPDATARKAF 174

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               +      +   A    +    + +    +                + N      +K
Sbjct: 175 F---LGYMVNRLLKCALGRAEPDDRDHLGKKRLDL----------AGPLMTNLFRLQFDK 221

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             KD    + + +              F      S        G      +L+       
Sbjct: 222 ATKDFYRYMQKRVESNQPINIMAG---FKHPIITSGLKYSLATGNWGDQKKLDKAKAGVS 278

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R GK       +  +       E  + Q   GL++  
Sbjct: 279 QVLSRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC-GLVKNL 337

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL----------EEHVNSLS 533
             +    ++ +   ++   L      +                          +    + 
Sbjct: 338 SLMSMVTNTYETGPLLNYILTKHVEALEDWEPRLNPQATKVFVDGVWFAVVLRDPKRLVD 397

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +   RR                +   +       + P    E              + +
Sbjct: 398 DLRKLRRKGVFDSQVSLVWDIRDKEFKISGDSGRIVRPLFIVETDRASENLGNLVLNKDH 457

Query: 594 AYGFIETPYRKVCDGKVTNDV--------------VYLSAMEEENRYIAQANSSLDEDG- 638
                +T Y K    + T+++               YL A EEE   I     +L +   
Sbjct: 458 ISKLDQTAYLKEGGFQWTDEIRPYGWNDLLESGVVEYLDAEEEETAMIIMTPEALSDSKA 517

Query: 639 -----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    E    R     +          +  P  ++ + AS+IPF +++ S R    
Sbjct: 518 KWLGMEIENEDDPLRRNDPLLNPHSHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQ 577

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                                                  
Sbjct: 578 SAMGKQAMGVFLTNF-----------------------------------------DQRM 596

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            + + +  Y      R+     +                           +L  G+N +V
Sbjct: 597 ETMANILYYPQKPLARTMAMDYL------------------------KFRELPAGQNAIV 632

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A   + GYN EDS+++++  +   +F S+    ++   +       E        D   +
Sbjct: 633 AIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDSEKSVGHSVMEQFEKPTRTDTLRL 692

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  IDE GI+  G  V+  DI++GK  P         ++       +K    RD S
Sbjct: 693 KHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPDAEELGQR-------QKQHIKRDVS 745

Query: 929 LRVPSGVSGTVVDVRIFNRHG 949
             + S  SG V  V +   + 
Sbjct: 746 TPLRSTESGIVDQVMLTTTND 766


>gi|241068592|ref|XP_002408479.1| RNA polymerase II second largest subunit (RPB2), putative [Ixodes
            scapularis]
 gi|215492467|gb|EEC02108.1| RNA polymerase II second largest subunit (RPB2), putative [Ixodes
            scapularis]
          Length = 194

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 105/253 (41%), Positives = 131/253 (51%), Gaps = 59/253 (23%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+VVKVF+A K  +Q GDKMAGRHGNK                            GV SR
Sbjct: 1    LKVVKVFIATKHKLQPGDKMAGRHGNK----------------------------GVISR 32

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            +                       +  +     +   +   +   +G  S        + 
Sbjct: 33   I-----------------------VPEEDMPFLENGTVIDIVLNPLGLPSRMNIGQILE- 68

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                        GV  +TPVFDGA  + +  ML++A  D SGQ  L DG TGE FDR VT
Sbjct: 69   -------THLGKGVHFATPVFDGAKVQDVKDMLKLAGQDPSGQVKLIDGRTGEYFDRLVT 121

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG  Y+LKL+H+V +K+++RS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY 
Sbjct: 122  VGQKYLLKLHHLVDNKIHSRSIGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYT 181

Query: 1311 LQEMLTIKSDDVV 1323
            LQEMLT+KSDDV 
Sbjct: 182  LQEMLTVKSDDVN 194


>gi|76556338|emb|CAJ00189.1| RNA polymerase beta subunit [Pseudomonas syringae pv. japonica]
          Length = 313

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 180/312 (57%), Positives = 234/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKP  +A  EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPGAAADKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|76556312|emb|CAJ00176.1| RNA polymerase beta subunit [Pseudomonas tremae]
          Length = 313

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 235/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+ I+ADGPST
Sbjct: 302 QRSYIMADGPST 313


>gi|158297007|ref|XP_317312.4| AGAP008151-PA [Anopheles gambiae str. PEST]
 gi|157014987|gb|EAA12689.4| AGAP008151-PA [Anopheles gambiae str. PEST]
          Length = 1089

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 85/306 (27%), Positives = 127/306 (41%), Gaps = 66/306 (21%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +VK+ +   R  + GDK + RHG KG+   I+  ED+PF   G   D+V+NP G PSRM 
Sbjct: 838  LVKILLRQTRRPEIGDKFSSRHGQKGVTGLIVEQEDLPFNDYGMSPDMVMNPHGFPSRMT 897

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            V        G     LG K   L   +                                 
Sbjct: 898  V--------GKTLELLGSKAGVLEGKFHYGT----------------------------- 920

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                              F G+    +   L     +  G+ + Y G+TGEP +  +  G
Sbjct: 921  -----------------AFGGSKCSDLQDELFNHGFNYLGKDVFYSGITGEPLEVYIYSG 963

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ +YGA+ ++ 
Sbjct: 964  PVYYQKLKHMVQDKMHARARGPRAVLTRQPTQGRSREGGLRLGEMERDCLISYGASMLIM 1023

Query: 1313 EMLTIKSD-------DVVGRTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSI 1361
            E L I SD       +V GR   Y S                P +  +L +E+ ++ +  
Sbjct: 1024 ERLMISSDAFDVDVCNVCGRL-AYSSWCHNCRSSASVSTISMPYACKLLFQELTSMNIVP 1082

Query: 1362 DLENSR 1367
             L+   
Sbjct: 1083 RLKLQN 1088



 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 90/741 (12%), Positives = 215/741 (29%), Gaps = 134/741 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF------ 86
              S+++F+ ++I    + N   Q   KS            L++++     P        
Sbjct: 37  HIDSFNYFINVDIKKIVQAN---QEV-KS-----DADPCFYLKYLNVHVGKPDVEEGFNN 87

Query: 87  ----DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT--- 139
                  +C  RD+TY+ P+ + +             +  + +    + +G +P+M    
Sbjct: 88  TKSTTPHECRLRDMTYSAPITVDIEYT----------RGTQRVVRNGLLIGRMPIMLRSS 137

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG-----RAS 173
                                  G F+I+G +++++ Q   S       D       + +
Sbjct: 138 NCVLTGKSDYQLSKVNECPMDPGGYFIIRGTEKVILIQEQLSWNKMITEDYNGVIQCQVT 197

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTF 232
            S     +  I+                 +++ +    ++PV   L A+G+ S++ +   
Sbjct: 198 SSTHEKKSRTIL----------LTKHGRYYLKHNSMTEEIPVAIILKAMGIASDQEIMQL 247

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
                 +Q+        +A   +   + +   +           G KL +    +   K 
Sbjct: 248 VGIDPETQKRFAPSLLEAANHKVFTQQRALEYM-----------GSKLIAKRFTTAATKY 296

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK-SLEEIFHSEIRDIPILYVDS 351
                   D L    +A   V     ++      ++  +    E+  S + D        
Sbjct: 297 KTTADEARDLLATTILAHVPVPSFNFQVKAIYVALMIRRVMAAELDRSAVDDRDYYGNKR 356

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +     + + +  D  K     L  I     P   +               +      + 
Sbjct: 357 LELAGSLLSLMFEDLFKRFNWELKMIADKNIPKIKAAQFDVGKHMREALITAGLETAIST 416

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG-----NRRVRS 466
           G   +  R  ++     + + +   I+ + ++  + +       +            +  
Sbjct: 417 GNWTI-KRFKMERAGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLC 475

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
             +  + +    +  +           +   +        + +     E   + ++  + 
Sbjct: 476 PSDTPEGEACGLVKNLALMTHITTEVDEEPVIRLAYNAGVEDIRLLGGETINNPKVFMVF 535

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
            + N L      RRL  + +  + R         +H +   R     T  G         
Sbjct: 536 INGNILGVTIAYRRLVEVFRM-MRRRGLIGAFVSIHTSFTQRCVYIHTDGGRLCRP---- 590

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                          Y  V         +YL   EE + +IA                  
Sbjct: 591 ---------------YIIV----QAGRPLYLDVNEENDSFIA------------------ 613

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL-K 705
                +E  +  EK   ++  P  ++ + A L+P+  ++ S R    C M +QA+ ++  
Sbjct: 614 ----YQERDIDPEKTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCAMGKQAMGIIGY 669

Query: 706 AEAPFVGTGMESVVAKSSGAA 726
            +   + T M ++V   S   
Sbjct: 670 NQKNRIDTLMYNIVYPQSPMV 690



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 79/549 (14%), Positives = 166/549 (30%), Gaps = 45/549 (8%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
           +   +  +I+ ++     +  +DD D  GN+R+   G +L   +     R    +K    
Sbjct: 325 KAIYVALMIRRVMAAELDRSAVDDRDYYGNKRLELAGSLLSLMFEDLFKRFNWELKMIAD 384

Query: 492 SVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                    Q      +    + + +     +   +     +          RLS +   
Sbjct: 385 KNIPKIKAAQFDVGKHMREALITAGLETAISTGNWTIKRFKMERAGVTQVLSRLSYISAL 444

Query: 548 GVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           G+         + R     R + P+ +G +CP++T EG   GLV +L     +      E
Sbjct: 445 GMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEE 504

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVP 657
              R   +  V  D+  L      N  +     N ++         LV          + 
Sbjct: 505 PVIRLAYNAGV-EDIRLLGGETINNPKVFMVFINGNILGVTIAYRRLVEVFRMMRRRGLI 563

Query: 658 REKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLK--AEAPFV 711
              +    +  ++ V I         P++       + +  N +  +    +     P  
Sbjct: 564 GAFVSIHTSFTQRCVYIHTDGGRLCRPYIIVQAGRPLYLDVNEENDSFIAYQERDIDPEK 623

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL-MKFQRS 770
            T +E       G       AG+V      +    + +  +     G+  Y    +    
Sbjct: 624 TTHLEIEPFTLLGVC-----AGLVPYPHHNQSPRNTYQCAMGKQAMGIIGYNQKNRIDTL 678

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
             N    Q P+V+                T+   L  G+N  VA M + GY+ ED+++++
Sbjct: 679 MYNIVYPQSPMVRS----------RTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILN 728

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS-----EEGLKNIDECGIICVG 885
           +  +       +  +  +   +       +                  + +D  GI+  G
Sbjct: 729 KASIDRGYGRCLVYKNSKCTIKRYSNQTFDRIMGPMKDGVTGKIIAKHECLDTDGIVSPG 788

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             +     +V K  P  +S    E+K         +  V    +   +     V  +   
Sbjct: 789 ERLTCKQTMVNKEMPAVKSNNPIEQKESGQQPIAYSARV---LVSTNNEEEFLVKILLRQ 845

Query: 946 NRHGIDKNE 954
            R     ++
Sbjct: 846 TRRPEIGDK 854


>gi|52694309|emb|CAG37994.1| RNA polymerase beta subunit [Pseudomonas sp. LMG 13964]
          Length = 382

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 207/385 (53%), Positives = 266/385 (69%), Gaps = 9/385 (2%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL-----TSFARVNAYGFI 598
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL         R+      
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLGGLRPHQPVRLPGKPVP 120

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
               R+          V +      +R+         ++    +ELV  R   E  +   
Sbjct: 121 RGEGRRCQRRHR----VPVGNRRGGSRHRTGFGRDERQESQLIDELVAVRHLNEFTVKAP 176

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  
Sbjct: 177 EDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERN 236

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
           VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQ
Sbjct: 237 VARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQ 296

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPLV  GD+V+R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED 
Sbjct: 297 RPLVSKGDKVQRGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDR 356

Query: 839 FTSIHIEEFEVMARDTKLGPEEITR 863
           FT+IHI+E   +ARDTKLGPEEI  
Sbjct: 357 FTTIHIQELTCVARDTKLGPEEIYC 381


>gi|76556274|emb|CAJ00157.1| RNA polymerase beta subunit [Pseudomonas syringae pv. morsprunorum]
          Length = 313

 Score =  300 bits (767), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 180/311 (57%), Positives = 234/311 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPHDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPS 799
           +R+DI+ADGPS
Sbjct: 302 QRSDIMADGPS 312


>gi|325114622|emb|CBZ50178.1| DNA-directed RNA polymerase,related [Neospora caninum Liverpool]
          Length = 1365

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 108/244 (44%), Gaps = 12/244 (4%)

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK A RHG KGI+S + P EDMPF + G   DI+ NP G PSRM +G +
Sbjct: 1061 RLRCVRKPVIGDKFASRHGQKGILSMLWPHEDMPFTESGLVPDILFNPHGFPSRMTIGML 1120

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E+  G A    G    +                ++++    G           +   + 
Sbjct: 1121 IESMAGKAAAVHGAYQDATPFREFPPQTADGKNKWVDQGGYHGWVKRGERYRTPEEERQA 1180

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
             ++ +      TPV      +     L  A     G   LY G+ G P    +  G IY 
Sbjct: 1181 EDEPE------TPV------DYFGKALMRAGYQYYGTEELYSGVYGVPLTAHIFTGLIYY 1228

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV+DK   R+TG    +T QP+ G+   GG R GEME   + ++GAA +LQ+ L 
Sbjct: 1229 QRLRHMVTDKHQVRATGPVDALTHQPVKGRKRHGGVRFGEMERDALISHGAAALLQDRLL 1288

Query: 1317 IKSD 1320
              SD
Sbjct: 1289 HCSD 1292



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 74/245 (30%), Gaps = 23/245 (9%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVK 783
            +A ++  A +       +      +  +   T G   +    +           QRPLV+
Sbjct: 839  SAFLSIAASLTPYSHHNQSPRNIYQCQMLKQTMGTPFHSVPYRHDNKAYRLITPQRPLVR 898

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              D              D  D   G N +VA M + G++ ED+M++++  +    F   H
Sbjct: 899  TEDY----------RRFDFDDYPSGVNAVVAVMCYTGFDMEDAMILNKGSMERGAF---H 945

Query: 844  IEEFEVMARDTKLG-------PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               ++    D            +    ++     +    +D  G   +GA+++ G     
Sbjct: 946  GCVYKTKVVDAAPASARAGAASQYTFSNVNEFGRKHNATLDADGFPAIGAKIDKGSTYCR 1005

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAV--DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
              T    S             GE A    V   S    +      + ++        +  
Sbjct: 1006 VQTSSSSSSFANNGIQHAYKDGETAYVDGVTYISPPDSAHERLAKLGLKGCRASLRLRCV 1065

Query: 955  RSISV 959
            R   +
Sbjct: 1066 RKPVI 1070



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 36/145 (24%), Gaps = 57/145 (39%)

Query: 60  KSVFPITAFSGAAMLEFVSYEFDPP-KFD---------------------VDDCLWRDLT 97
               P  + +    L   S     P +FD                        C    +T
Sbjct: 95  HEANPYYSPTDYIKLAISSVSLGTPVRFDTAGAAPKLGESRDACADQLLLPRHCREAHIT 154

Query: 98  YAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD---------------- 141
           Y  PLK+                       + + +G  PLM +                 
Sbjct: 155 YGAPLKVAF---------VRSNNRDGSAVRKDVVVGMAPLMVRSKLCSTRGMSPEELQRA 205

Query: 142 --------GTFVIKGIQRIV--VSQ 156
                   G F+I G +R++  V Q
Sbjct: 206 GEDVDDGGGYFIINGNERVIRFVVQ 230


>gi|291196416|emb|CBG27565.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas congelans]
 gi|291196472|emb|CBG27593.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas syringae]
 gi|291196476|emb|CBG27595.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas tremae]
          Length = 305

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 181/305 (59%), Positives = 232/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|76556288|emb|CAJ00164.1| RNA polymerase beta subunit [Pseudomonas syringae pv. theae]
          Length = 313

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 181/312 (58%), Positives = 235/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  G  V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGARV 301

Query: 789 RRNDIIADGPST 800
           +R DI+ADGPST
Sbjct: 302 QRTDIMADGPST 313


>gi|6606111|gb|AAF19068.1|AF107796_1 DNA-dependent RNA polymerase II RPB140 [Exophiala jeanselmei]
          Length = 937

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 157/902 (17%), Positives = 284/902 (31%), Gaps = 165/902 (18%)

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
            DV   +   +  ++  L+    G+   DD D+LG +R+   G ++ N +RL   +  +  
Sbjct: 167  DVATKKAFFLGYMVNRLLKAALGRAEPDDRDHLGKKRLDLAGPLMTNLFRLQFDKATKDF 226

Query: 487  --KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNS 531
                +        +          + S +     +               +SQ+      
Sbjct: 227  FRYMQKRVEAGQPISIHAGFKHPIITSGLKYSLATGNWGDQKKLDKAKAGVSQVLSRYTF 286

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
             S ++H RR +A     + R     + R +H TH+G +CPAET EG   GLV +L+  + 
Sbjct: 287  ASTLSHLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLSLMSM 342

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-------TEEL 644
            V      E     V +  V        A+EE    +    + +  DG +        + L
Sbjct: 343  VTNSYETEPLRAYVLNKHV-------DAIEEWEPRLNPQATKIFIDGVWFAVVLRDPKRL 395

Query: 645  VFCRCAGEEILVPREKIDF-IDASPKQVVSIAAS-----LIPFLENDDSNRVLMGCNMQR 698
            V              ++    D   K+      S      +  +E D ++  +    + +
Sbjct: 396  VDDLRRLRRQGTFDAQVSLVWDIREKEFRISGDSGRIIRPLFVVETDKASENVGNLVLNK 455

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPS 755
            + +  L        +G +     S+       +AG+VE +DA      +I      L  S
Sbjct: 456  EHINKLDQTNYLKESGYQFNDEVSAYGWDDLLKAGVVEYLDAEEEETAMIVMTPEVLADS 515

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             +      +  F            PL+               PS  LG       +  + 
Sbjct: 516  KARWLGIEIENFDDPLGRN----EPLLTPNSHSF--THCEIHPSMILG-------VCASI 562

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N          M  + +                     E   +I    ++ L  
Sbjct: 563  IPFPDHNQSPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLAR 612

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                                  +       +   +  + AI      +  D+ +   S +
Sbjct: 613  -------------------TMAMDYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 653

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    +F R   D+ +   SV    IE   +    + + L    Y ++ E   +  G
Sbjct: 654  DRGLF-RSLFYRAYQDQEK---SVGHAVIESFEKPTRADTLRLKHGTYDKIDEDGIVAPG 709

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  ++ D                +E  QR  + +K    T     E  
Sbjct: 710  VRVSGEDIIMGKTAPMAPD---------------AEELGQRQKQHVKRDVSTPLRSTESG 754

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D       R  KV V   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 755  IVDQVMLTTTND-----GHRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFT 809

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   D+++NP  +PSRM +  + E  L       G++  +          IS +   +
Sbjct: 810  REGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGEEGDATPFTKVTVTQISDILRKM 869

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                   V     +G  +   VF                     
Sbjct: 870  GY---------------QSRGFEVMYNGHTGKKLVAQVF--------------------- 893

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
                              +G  Y  +L HMV DK+++R+ G   ++T+QP+ G++  GG 
Sbjct: 894  ------------------LGPTYYQRLRHMVDDKIHSRARGPTQILTRQPVEGRARDGGL 935

Query: 1293 RL 1294
            R 
Sbjct: 936  RF 937



 Score =  137 bits (345), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 121/832 (14%), Positives = 248/832 (29%), Gaps = 97/832 (11%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      +   I    D+G  M  +   K  +  R+
Sbjct: 1   SEKVLIAQE-RSAGNI--VQVFQKAAPAPFTHLAEIRSVIDRGARMMSQCTVK--LFRRV 55

Query: 207 D-----------R------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           D           R      ++ +P+     AL + S+ +IL          +  D     
Sbjct: 56  DGPDGTKIDNPIRVQLPYVKQDIPLVIVFRALDIVSDADILEKICFDQSDKEMLDMLMGS 115

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           L     +  A ++   +        ++S ++     +  L+++ +  +G   D       
Sbjct: 116 LQEGQPIQSADLARDFIARRGNIPTLKSHER-QKHAIDILQKEFLPHIGQGPDVATKKAF 174

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               +      +   A    +    + +    +                + N      +K
Sbjct: 175 FLGYM---VNRLLKAALGRAEPDDRDHLGKKRLDL----------AGPLMTNLFRLQFDK 221

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             KD    + + +  G   +       F      S        G      +L+       
Sbjct: 222 ATKDFFRYMQKRVEAGQPISIHAG---FKHPIITSGLKYSLATGNWGDQKKLDKAKAGVS 278

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R GK       +  +       E  + Q   GL++  
Sbjct: 279 QVLSRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC-GLVKNL 337

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
             +    +S + + +    L      +                + V     +   +RL  
Sbjct: 338 SLMSMVTNSYETEPLRAYVLNKHVDAIEEWEPRLNPQATKIFIDGVWFAVVLRDPKRLV- 396

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                + R R            +          G +                G I  P  
Sbjct: 397 ---DDLRRLRRQGTFDAQVSLVWDIREKEFRISGDS----------------GRIIRPLF 437

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V   K + +V  L   +E    + Q N  L E G    + V      + +      +++
Sbjct: 438 VVETDKASENVGNLVLNKEHINKLDQTN-YLKESGYQFNDEVSAYGWDDLLKAGV--VEY 494

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +DA  ++   I    +      DS    +G  ++    PL + E             +  
Sbjct: 495 LDAEEEETAMIV---MTPEVLADSKARWLGIEIENFDDPLGRNEPLLTPNSHSFTHCEIH 551

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLV 782
            + I+   A I+   D  +    + +  +     GV       + +         Q+PL 
Sbjct: 552 PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFDQRMETMANILYYPQKPLA 611

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           +                    +L  G+N +VA   + GYN EDS+++++  +   +F S+
Sbjct: 612 R----------TMAMDYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 661

Query: 843 HIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               ++   +       E        D   +       IDE GI+  G  V+  DI++GK
Sbjct: 662 FYRAYQDQEKSVGHAVIESFEKPTRADTLRLKHGTYDKIDEDGIVAPGVRVSGEDIIMGK 721

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             P     M P+ + L     +     RD S  + S  SG V  V +   + 
Sbjct: 722 TAP-----MAPDAEELGQRQKQHVK--RDVSTPLRSTESGIVDQVMLTTTND 766


>gi|315425379|dbj|BAJ47045.1| DNA-directed RNA polymerase subunit beta [Candidatus Caldiarchaeum
            subterraneum]
          Length = 250

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 131/301 (43%), Gaps = 70/301 (23%)

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+V  ++P EDMP+ KDG   D+++NP   PSRM +GQ+ E+     
Sbjct: 3    EIGDKFSSRHGQKGVVGMLIPQEDMPYTKDGIVPDLLINPHAFPSRMTIGQLIESL---- 58

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG                                                   K+ +
Sbjct: 59   AGKLG-------------------------------------------------SIKAEI 69

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP F G   E + + L       SG+ +LY+G TG+  +  V +G +Y  +L+H+V 
Sbjct: 70   VDGTP-FLGKSLEELRAELEALGFKSSGRELLYNGATGKILEAEVFIGVVYYQRLHHLVR 128

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++AR+ G   ++T+QP  G+S  GG + GEME  C+ AYGA+Y+L + L  +SD    
Sbjct: 129  DKIHARARGQVQMLTRQPTEGRSRGGGLKFGEMERDCLIAYGASYLLLDRLLEQSDKYTA 188

Query: 1325 --------------RTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                          +   +   V G D          +F +L+ EM ++ +   +     
Sbjct: 189  YFCEKCGMPCYYDLKQERFVCPVDGKDVRVKAVSMSYAFYLLLNEMMSMCIHPRILLEEP 248

Query: 1369 K 1369
            +
Sbjct: 249  E 249


>gi|22086505|gb|AAM90663.1|AF401093_1 RNA polymerase beta subunit [Ehrlichia muris]
          Length = 371

 Score =  299 bits (766), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 202/358 (56%), Positives = 258/358 (72%), Gaps = 1/358 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
              ++TH RRLSALG GG+ R R   E+RDVHPTHYGRICP ET EG NIGL+SSL  +A
Sbjct: 13  HYLKVTHKRRLSALGPGGLTRERGWFEVRDVHPTHYGRICPIETPEGQNIGLISSLAIYA 72

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R+N +GFIE+PYRKV +G VT+ V YL AM+E N YIA A+++LDE+  F +++++CR  
Sbjct: 73  RINKHGFIESPYRKVDNGVVTDKVEYLLAMQESNYYIADASATLDENNRFVDDMLYCRHD 132

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G  ++V RE++D+ID SPKQ+VS+AASLIPFLEN+D+NR LMG NMQRQAVPLLKA+AP 
Sbjct: 133 GNFVMVKREQVDYIDVSPKQIVSVAASLIPFLENNDANRALMGSNMQRQAVPLLKADAPL 192

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGMES+VA  SG  ++AKR+GIV     +                 VDIY L KFQRS
Sbjct: 193 VGTGMESIVAAGSGTVVLAKRSGIVPSCGWVIYSYSCDLNQEKNEYLRVDIYNLRKFQRS 252

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N NTC+NQRPL+ +    ++  + ADG + D G+LAL  N+LVAFM W GYNFEDS++IS
Sbjct: 253 NHNTCINQRPLLNLEIMYKQMMLYADGSAIDQGELALVYNVLVAFMSWQGYNFEDSIVIS 312

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL-KNIDECGIICVGAE 887
             +V +DVFTSIHIEE  V  RDT LGPE+I R +P+++E       D+ GI+ VGA 
Sbjct: 313 SEVVKKDVFTSIHIEELNVYFRDTTLGPEKIMRSVPDINERLFVSFWDDVGIVNVGAN 370


>gi|270161063|gb|ACZ63409.1| RpoB [Rahnella sp. 10-Salad]
 gi|270161065|gb|ACZ63410.1| RpoB [Rahnella sp. 120-Carrot]
 gi|270161067|gb|ACZ63411.1| RpoB [Rahnella sp. 121-Celery]
 gi|270161069|gb|ACZ63412.1| RpoB [Rahnella sp. 136-Carrot]
 gi|270161071|gb|ACZ63413.1| RpoB [Rahnella sp. 142-Salad]
 gi|270161073|gb|ACZ63414.1| RpoB [Rahnella sp. 147-Tomato]
 gi|270161075|gb|ACZ63415.1| RpoB [Rahnella sp. 153-Carrot]
 gi|270161077|gb|ACZ63416.1| RpoB [Rahnella sp. 16-Salad]
 gi|270161079|gb|ACZ63417.1| RpoB [Rahnella sp. 171-Carrot]
 gi|270161081|gb|ACZ63418.1| RpoB [Rahnella sp. 17-Carrott]
 gi|270161083|gb|ACZ63419.1| RpoB [Rahnella sp. 186-Peach]
 gi|270161085|gb|ACZ63420.1| RpoB [Rahnella sp. 193-Celery]
 gi|270161087|gb|ACZ63421.1| RpoB [Rahnella sp. 207-Apple]
 gi|270161089|gb|ACZ63422.1| RpoB [Rahnella sp. 214-Radish]
 gi|270161091|gb|ACZ63423.1| RpoB [Rahnella sp. 285-Celery]
 gi|270161093|gb|ACZ63424.1| RpoB [Rahnella sp. 296-Salad]
 gi|270161095|gb|ACZ63425.1| RpoB [Rahnella sp. 305-Carrot]
 gi|270161097|gb|ACZ63426.1| RpoB [Rahnella sp. 309-Salad]
 gi|270161099|gb|ACZ63427.1| RpoB [Rahnella sp. 311-Carrot]
 gi|270161101|gb|ACZ63428.1| RpoB [Rahnella sp. 320-Radish]
 gi|270161103|gb|ACZ63429.1| RpoB [Rahnella sp. 326-Celery]
 gi|270161105|gb|ACZ63430.1| RpoB [Rahnella sp. 330-Salad]
 gi|270161107|gb|ACZ63431.1| RpoB [Rahnella sp. 336-Pear]
 gi|270161109|gb|ACZ63432.1| RpoB [Rahnella sp. 339-Carrot]
 gi|270161111|gb|ACZ63433.1| RpoB [Rahnella sp. 344-Salad]
 gi|270161113|gb|ACZ63434.1| RpoB [Rahnella sp. 346-Carrot]
 gi|270161115|gb|ACZ63435.1| RpoB [Rahnella sp. 348-Celery]
 gi|270161117|gb|ACZ63436.1| RpoB [Rahnella sp. 34-Carrot]
 gi|270161119|gb|ACZ63437.1| RpoB [Rahnella sp. 362-Apple]
 gi|270161121|gb|ACZ63438.1| RpoB [Rahnella sp. 366-Carrot]
 gi|270161123|gb|ACZ63439.1| RpoB [Rahnella sp. 36-Radish]
 gi|270161125|gb|ACZ63440.1| RpoB [Rahnella sp. 370-Salad]
 gi|270161127|gb|ACZ63441.1| RpoB [Rahnella sp. 371-Carrot]
 gi|270161129|gb|ACZ63442.1| RpoB [Rahnella sp. 376-Carrot]
 gi|270161131|gb|ACZ63443.1| RpoB [Rahnella sp. 377-Radish]
 gi|270161135|gb|ACZ63445.1| RpoB [Rahnella sp. 387-Salad]
 gi|270161137|gb|ACZ63446.1| RpoB [Rahnella sp. 390-Radish]
 gi|270161139|gb|ACZ63447.1| RpoB [Rahnella sp. 39-Strawberry]
 gi|270161141|gb|ACZ63448.1| RpoB [Rahnella sp. 401-Salad]
 gi|270161143|gb|ACZ63449.1| RpoB [Rahnella sp. 42-Carrot]
 gi|270161145|gb|ACZ63450.1| RpoB [Rahnella sp. 51-Carrot]
 gi|270161147|gb|ACZ63451.1| RpoB [Rahnella sp. 55-Salad]
 gi|270161149|gb|ACZ63452.1| RpoB [Rahnella sp. 56-Salad]
 gi|270161151|gb|ACZ63453.1| RpoB [Rahnella sp. 57-Carrot]
 gi|270161153|gb|ACZ63454.1| RpoB [Rahnella sp. 59-Radish]
 gi|270161155|gb|ACZ63455.1| RpoB [Rahnella sp. 71-Salad]
 gi|270161157|gb|ACZ63456.1| RpoB [Rahnella sp. 73-Celery]
 gi|270161159|gb|ACZ63457.1| RpoB [Rahnella sp. 75-Radish]
 gi|270161161|gb|ACZ63458.1| RpoB [Rahnella sp. 91-Salad]
 gi|270161163|gb|ACZ63459.1| RpoB [Rahnella sp. 9-Pear]
 gi|270161165|gb|ACZ63460.1| RpoB [Rahnella aquatilis]
 gi|270161167|gb|ACZ63461.1| RpoB [Rahnella genomosp. 1]
 gi|270161169|gb|ACZ63462.1| RpoB [Rahnella genomosp. 2]
 gi|270161171|gb|ACZ63463.1| RpoB [Rahnella aquatilis]
          Length = 307

 Score =  299 bits (765), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 190/307 (61%), Positives = 239/307 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDEEGRFIEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR GIV+ VDA RIVIR  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDE 787
            V +G+ 
Sbjct: 301 CVNLGEP 307


>gi|156767147|gb|ABU95088.1| ribosomal polymerase B subunit [Acinetobacter johnsonii]
          Length = 266

 Score =  299 bits (765), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGEKLSEDMLSGLELVDLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   K    I+ LRSFL+K+    G   E++    D+ + ++A   ++GVP++T
Sbjct: 180  EQIDKML---KQQRTIAELRSFLDKIYNKVGGEQEQLDTLTDEEIFKLAGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  SGQ IL+D
Sbjct: 237  PVFDGAEESQIKELLELAELPRSGQQILFD 266


>gi|317032172|ref|XP_001394181.2| DNA-directed RNA polymerase I subunit RPA135 [Aspergillus niger CBS
            513.88]
          Length = 1236

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 96/480 (20%), Positives = 166/480 (34%), Gaps = 69/480 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E    +I ++        D+        +       +G      +     +   L+ 
Sbjct: 696  THIEFTPTNILSIVANMTPFSDQNQSPRNMYQCQMSKQTMGTPGTAIQYRTDNKLYRLQT 755

Query: 916  ---IFGEKAVDVRDTSLRVPSGVSGTV----------VDVRIFNRHGIDKNERSISVERE 962
                     +         P+G +  V           D  I N+   ++     ++ + 
Sbjct: 756  GQTPIVRPPLYNAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGYGTIYKT 815

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQ 1020
            +I  L  D+ D +    R   ++L     G    +       +         + E     
Sbjct: 816  KIHSL--DEKDSRRGKSRREVTKLFGFAPGGEIRADWRATLDEDGLPHIGARVKEGSLVA 873

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W     D      V    + +       E+ + + +  +     + PG    VK  +  
Sbjct: 874  AWHTVRYDAASDSYVNVDGITHFVKYKDAEEGYIDSVRILGAESGVEPGQALSVKYRI-- 931

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+ 
Sbjct: 932  PRKPIIGDKFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESM 991

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +      +                                  
Sbjct: 992  AGKAGALHGHPQDSTPFQFSEENTAA---------------------------------- 1017

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     LR A  +  G   LY G+TG+ F   + +G ++  +L 
Sbjct: 1018 ----------------DYFGHQLRKAGYNYFGNEPLYSGITGKEFAADIFIGVVHYQRLR 1061

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1062 HMVNDKFQVRTTGPVNQLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAHILQDRLMNCSD 1121



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 58/411 (14%), Positives = 127/411 (30%), Gaps = 56/411 (13%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G  CP  T +G 
Sbjct: 493 PSGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFFCPVHTPDGS 549

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L     +            V    +   +V L     ++      + ++  DG
Sbjct: 550 PCGLLNHLAHKCLIATSD--------VDTTHIPKALVQLGV-RSDSSVSVTESVTVQLDG 600

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQ------------------VVSIAASLIP 680
                    + +     + R K+   D  P++                  + S AA +  
Sbjct: 601 RIIGYCSPKQASAIANTLRRWKVMGSDKIPRELEIGYIPNTNGGQYPGIYMFSQAARMYR 660

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPF---VGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            +++   +++      ++  + +          V T +E                    Q
Sbjct: 661 PVKHLGLDKLDYVGPFEQPFMEIACLPQDLISGVSTHIEFTPTNILSIVANMTPFSDQNQ 720

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                   +  +  +    + +      K  R        Q P+V+              
Sbjct: 721 SPRNMYQCQMSKQTMGTPGTAIQYRTDNKLYRLQTG----QTPIVRP----------PLY 766

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE--FEVMARDTK 855
            +  L +   G N +VA + + GY+ +D+M+I++             +     +  +D++
Sbjct: 767 NAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIHSLDEKDSR 826

Query: 856 LGPEEITRDIPN-------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            G                 +  +    +DE G+  +GA V  G ++    T
Sbjct: 827 RGKSRREVTKLFGFAPGGEIRADWRATLDEDGLPHIGARVKEGSLVAAWHT 877



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 97/703 (13%), Positives = 193/703 (27%), Gaps = 144/703 (20%)

Query: 78  SYEFDPP------KFD-------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
               + P      KF          +C  R  TY   L+  +   V + D     +    
Sbjct: 102 EVFLEKPALPPSNKFTTRNRNIYPSECRERHATYRGKLRARIEWRVNNGDWMESVRE--- 158

Query: 125 IKEQSIYMGDLPLMTK------------------------DGTFVIKGIQRIVVSQLHRS 160
                  +G +P+M +                         G F++ G ++     L R 
Sbjct: 159 -------LGQVPIMLRTNRCHLEKATPSELVEHKEESEELGGYFIVNGNEK-----LIRM 206

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLW---------------------------MD 193
             +            GK  Y   II  +G +                           + 
Sbjct: 207 LVV------------GKRNYPMAII--RGSFVRRGHTYTKYGVQIRSVRPDQTSQTNVLH 252

Query: 194 IEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
              D    +  R   R+    VPV   L AL +++ +     +  IV S   +       
Sbjct: 253 YLTDGN--LTFRFSWRKAEYLVPVMMILKAL-VETND--REIFEGIVGSASSEGIKNTFV 307

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +  +V  +             G+K    L                       V  
Sbjct: 308 TDRVELLLRVYKAYNTHSRAACRAYLGEKFRPVL----------------------GVPA 345

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK--NK 368
           D+ N + G  ++    +    +     + +     ++        A +      D     
Sbjct: 346 DMSNEDAGTEFLRKVVLPHLGNQNVTENQDYDKFKMILFMIRKLYALVAGDCAPDNPDAV 405

Query: 369 DRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             ++ LL   +Y ++    +  +                +     G    +     D   
Sbjct: 406 SNQEILLGGFLYGMILKERLEEW------VRSFQPILRDWSNRNGGAKFTDPAFERDFLA 459

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER-- 484
            V     E++   ++  +   N   +   +D         + E +     +   RM    
Sbjct: 460 KVVKRSNENLGGALEYFLSTGN-LVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMIHRG 518

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSA 543
           S   ++ +  +  ++P+      PV +         + L+       S    TH  +  A
Sbjct: 519 SFFAQLKTTTVRKLLPESWGFFCPVHTPDGSPCGLLNHLAHKCLIATSDVDTTHIPK--A 576

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSE--GHNIGLVSSLTSFARVNAYGFIETP 601
           L Q GV    +      V     GRI    + +        +              +E  
Sbjct: 577 LVQLGVRSDSSVSVTESVTVQLDGRIIGYCSPKQASAIANTLRRWKVMGSDKIPRELEIG 636

Query: 602 YRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           Y    +G     +   S A              LD  G F +  +   C  ++++     
Sbjct: 637 YIPNTNGGQYPGIYMFSQAARMYRPVKHLGLDKLDYVGPFEQPFMEIACLPQDLISGVS- 695

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
              I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 696 -THIEFTPTNILSIVANMTPFSDQNQSPRNMYQCQMSKQTMGT 737


>gi|156767127|gb|ABU95078.1| ribosomal polymerase B subunit [Acinetobacter baumannii]
 gi|156767129|gb|ABU95079.1| ribosomal polymerase B subunit [Acinetobacter baumannii]
          Length = 266

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS DL+S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERVIRLLKGQESNGG-GSTKRGDKLSEDLLSGLELVDLLEIQPADE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI+ ++ + +    +  LR FL+K+    G   E +    D+ +L +A   ++GVP++T
Sbjct: 180  DKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 237  PVFDGAEESQIKDLLELADISRTGQTVLFD 266


>gi|45545359|gb|AAS67527.1| DNA-dependent RNA polymerase II second largest subunit [Aureobasidium
            pullulans]
          Length = 937

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 147/891 (16%), Positives = 268/891 (30%), Gaps = 153/891 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  ++  L+    G+   DD D+LG +R+   G ++ N +RL   +  +      +
Sbjct: 172  KAFFLGYMVNRLLKCALGRAEPDDRDHLGKKRLDLAGPLMTNLFRLQFDKATKDFFRYMQ 231

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
                   ++          V S +     +               +SQ+       S ++
Sbjct: 232  KRVEAGQAINIHAGFKHPIVTSGLKYSLATGNWGDQKKLDKAKAGVSQVLSRYTFASTLS 291

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +A     + R     + R +H TH+G +CPAET EG   GLV +L+  + V    
Sbjct: 292  HLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLSLMSMVTNSY 347

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF-------TEELVFCRC 649
                    V    V        A+E+    +    + +  DG +        + LV    
Sbjct: 348  ETLPLMNYVLTKHVE-------ALEDWEPRLNPQATKVFVDGVWFAVVLRDPKRLVDDLR 400

Query: 650  AGEEILVPREKIDF-IDASPKQVVSIAAS-----LIPFLENDDSNRVLMGCNMQRQAVPL 703
                  V   ++    D   K+      S      +  +E D ++  L    + +  +  
Sbjct: 401  KLRRKGVFDSQVSLVWDIREKEFKISGDSGRIVRPLFVVETDRASENLGNLVLNKDHITK 460

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +        +G                 +G+VE +DA       +    +        + 
Sbjct: 461  IDQTNYLKESGFNFTDEFKPYGWQDLLESGVVEYLDAEEEETAMLVMTPEALADSKARWL 520

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
             M+ +  +     N  PL+               PS  LG       +  + +P+  +N 
Sbjct: 521  GMEIESEDDPLSRN-DPLLNPHSHTF--THCEIHPSMILG-------VCASIIPFPDHNQ 570

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +                     E   +I    ++ L          
Sbjct: 571  SPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLAR-------- 612

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                          +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 613  -----------TMAMDYLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLF-RS 660

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ +       EQ E   R           +       +  G           
Sbjct: 661  LFYRAYQDQEKSVGHSVVEQFERPTRADTLRLKHGTYDKIDEDGIVAPGVRVSGEDIIMG 720

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D                +E  QR  + +K    T     E    +++      
Sbjct: 721  KTAPMAPD---------------AEELGQRQKQHVKRDVSTPLRSTESGIVDQVMLTTTS 765

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D       R  KV V   +  Q GDK A RHG KG +      EDMPF + G   D+++N
Sbjct: 766  D-----GHRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTRGGIVPDLIIN 820

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +  +          +S L   +           
Sbjct: 821  PHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQVSDLLRKMGYQSRGFEVM- 879

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                           +G +    G    
Sbjct: 880  ----------------------------------------------YNGHT----GR--- 886

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                 V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G++  GG R 
Sbjct: 887  KLVAQVFLGPTYYQRLRHMVDDKIHSRARGPTQILTRQPVEGRARDGGLRF 937



 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 115/861 (13%), Positives = 234/861 (27%), Gaps = 155/861 (18%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      +   I    D+G  M  +   K  +  R+
Sbjct: 1   SEKVLIAQE-RSAGNI--VQVFQKAAPAPFTHLAEIRSVIDRGARMMSQCTVK--LFRRV 55

Query: 207 D-----------R------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           D           R      ++ +P+     AL + S+ +IL          +  D     
Sbjct: 56  DGPDGTKIDNPIRVQLPYVKQDIPLVIVFRALDIVSDADILEKICFDQSDKEMLDMLMGS 115

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           L     + GA ++   +        ++S ++     +  L+++ +  +G   D       
Sbjct: 116 LQEGQPIQGADLARDFIARRGNIPTLKSHER-QKHAMDILQKEFLPHIGQGPDVAARKAF 174

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               +      +   A    +    + +    +                + N      +K
Sbjct: 175 FLGYM---VNRLLKCALGRAEPDDRDHLGKKRLDL----------AGPLMTNLFRLQFDK 221

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             KD    + + +  G           F      S        G      +L+       
Sbjct: 222 ATKDFFRYMQKRVEAGQAINIHAG---FKHPIVTSGLKYSLATGNWGDQKKLDKAKAGVS 278

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R GK       +  +       E  + Q   GL++  
Sbjct: 279 QVLSRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC-GLVKNL 337

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL----------EEHVNSLS 533
             +    +S +   +M   L      +                          +    + 
Sbjct: 338 SLMSMVTNSYETLPLMNYVLTKHVEALEDWEPRLNPQATKVFVDGVWFAVVLRDPKRLVD 397

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +   RR                +   +       + P    E              + +
Sbjct: 398 DLRKLRRKGVFDSQVSLVWDIREKEFKISGDSGRIVRPLFVVETDRASENLGNLVLNKDH 457

Query: 594 AYGFIETPYRKVCDGKVTND--------------VVYLSAMEEENRYIAQANSSLDEDG- 638
                +T Y K      T++              V YL A EEE   +     +L +   
Sbjct: 458 ITKIDQTNYLKESGFNFTDEFKPYGWQDLLESGVVEYLDAEEEETAMLVMTPEALADSKA 517

Query: 639 -----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    E          +          +  P  ++ + AS+IPF +++ S R    
Sbjct: 518 RWLGMEIESEDDPLSRNDPLLNPHSHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQ 577

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                                                  
Sbjct: 578 SAMGKQAMGVFLTNF-----------------------------------------DQRM 596

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            + + +  Y      R+     +                           +L  G+N +V
Sbjct: 597 ETMANILYYPQKPLARTMAMDYL------------------------KFRELPAGQNAIV 632

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A   + GYN EDS+++++  +   +F S+    ++   +       E        D   +
Sbjct: 633 AIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYQDQEKSVGHSVVEQFERPTRADTLRL 692

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  IDE GI+  G  V+  DI++GK  P     M P+ + L     +     RD S
Sbjct: 693 KHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAP-----MAPDAEELGQRQKQHVK--RDVS 745

Query: 929 LRVPSGVSGTVVDVRIFNRHG 949
             + S  SG V  V +     
Sbjct: 746 TPLRSTESGIVDQVMLTTTSD 766


>gi|164428317|ref|XP_957106.2| DNA-directed RNA polymerase II 140 kDa polypeptide [Neurospora crassa
            OR74A]
 gi|157072100|gb|EAA27870.2| DNA-directed RNA polymerase II 140 kDa polypeptide [Neurospora crassa
            OR74A]
          Length = 1005

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 150/921 (16%), Positives = 279/921 (30%), Gaps = 140/921 (15%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+   DD D+ G +R+   G +L   +R  + 
Sbjct: 180  HISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVR 239

Query: 481  RMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ + +    +              I A  + + +     +               +SQ+
Sbjct: 240  RLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNGLKYSLATGNWGDQKKAMSSTAGVSQV 299

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 300  LNRYTFSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKN 355

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L+    V+     +    +    + +V  +   L        ++      + +D      
Sbjct: 356  LSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLRYPNATKVFVNGTWVGVHQDPKHLVT 415

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV        I      +  I     ++ S A  ++  L   +          + Q +  
Sbjct: 416  LVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVMRPLFVVEQEDNSESGVEKGQLILT 475

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             +               +          +G +E +DA       +    +     +D YR
Sbjct: 476  KEHIRRLEQDKELGKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTPED----LDTYR 531

Query: 764  LMKFQ----RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              KF+      +     N R   K              PS  LG       +  + +P+ 
Sbjct: 532  QHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPSMLLG-------ICASIIPFP 584

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     +  +                                
Sbjct: 585  DHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------------------------D 615

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 616  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGI 675

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D  +R      EQ E   R           +       I  G       
Sbjct: 676  F-RSLFFRSYTDCEKRVGINIVEQFEKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDD 734

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K++ ++ D                 E  QR  + +K    T     E    + +  
Sbjct: 735  IIIGKTSPINPD---------------NQELGQRTAQHVKRDASTPLRSTESGIVDSVAF 779

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV V   +  Q GDK A                            
Sbjct: 780  TTNQDGL-----RYVKVRVRTTKIPQIGDKFA---------------------------- 806

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                     SR         H     +G+  + + +    +              +    
Sbjct: 807  ---------SR---------HGQKGTIGVTYRQEDMPFTAEGITPDI-------IINPHA 841

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
              +     +  + +L      K     +TP F     ++++++LR       G  I+Y G
Sbjct: 842  IPSRMTIAHLIECLLSKVGALKGMEGDATP-FTDVTVDSVSNLLREHGYQSRGFEIMYHG 900

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG+     V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME 
Sbjct: 901  HTGKKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRFGEMER 960

Query: 1300 WCIQAYGAAYVLQEMLTIKSD 1320
             C+ A+GAA  L+E L   SD
Sbjct: 961  DCMIAHGAAAFLKERLFEVSD 981



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 117/866 (13%), Positives = 242/866 (27%), Gaps = 137/866 (15%)

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLW 191
           + P   + G F+I G ++++++Q  RS          +    G + Y   I    ++G  
Sbjct: 6   ECPY-DQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKPPGGSVSYQAEIRSALEKGSR 61

Query: 192 MDIEFDSKDIIHVRIDRRR-----KVPVT-----------SFLMALG-MDSEEILSTFYP 234
           +         +H + D+ +      V VT               ALG +  E+IL+    
Sbjct: 62  LISSLQM--RLHTKADQNKGRLANTVSVTLPYVKEEVSLAIVFRALGVVSDEDILNHICY 119

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
               SQ  +     +  A  +   +V+   +          +         + L+++ + 
Sbjct: 120 DRRDSQMLEALRPCIEEAFCIQDREVALDYIGKRGNGSTGINRNGRIKAAKEMLQKELLP 179

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIRDIPIL--YVD 350
            +     C          +  +  +  +   D  D      + +  +      +    V 
Sbjct: 180 HISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVR 239

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +  +         D NK    AL      +  G      +  S+    + D  K   ST
Sbjct: 240 RLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNG------LKYSLATGNWGDQKKAMSST 293

Query: 411 VGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            G  ++  R    +      R          +     L N    +         +   + 
Sbjct: 294 AGVSQVLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLV 353

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           + L     + +  +   I E + + +++ +   + +               + +   ++ 
Sbjct: 354 KNLSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLRYPNATKVF---VNGTWVGVHQDP 410

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE-----------G 577
            + ++ + + RR + +                +       + P    E           G
Sbjct: 411 KHLVTLVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVMRPLFVVEQEDNSESGVEKG 470

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE- 636
             I     +    +    G     Y        +  + YL A EEE   I      LD  
Sbjct: 471 QLILTKEHIRRLEQDKELGKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTPEDLDTY 530

Query: 637 -----DGSFTEELVFCRCAGEEILVPR---EKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                 G   E+    R                   +  P  ++ I AS+IPF +++ S 
Sbjct: 531 RQHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPSMLLGICASIIPFPDHNQSP 590

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+                                               
Sbjct: 591 RNTYQSAMGKQAMGFFLTNYS--------------------------------------- 611

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 612 --RRMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAG 645

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----R 863
           +N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        
Sbjct: 646 QNAIVAIACYSGYNQEDSVIMNQSSIDRGIFRSLFFRSYTDCEKRVGINIVEQFEKPDRS 705

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +           ++  GII  G  V   DI++GK +P         ++  + +       
Sbjct: 706 NTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPDNQELGQRTAQHVK------ 759

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHG 949
            RD S  + S  SG V  V       
Sbjct: 760 -RDASTPLRSTESGIVDSVAFTTNQD 784


>gi|189230055|ref|NP_001121521.1| polymerase (RNA) III (DNA directed) polypeptide B [Xenopus (Silurana)
            tropicalis]
 gi|183986364|gb|AAI66377.1| LOC100158643 protein [Xenopus (Silurana) tropicalis]
          Length = 1134

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 96/503 (19%), Positives = 170/503 (33%), Gaps = 94/503 (18%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 711  YLLAYPQRPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 770

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D +  + I    I         G+   +     
Sbjct: 771  LVYKNAKCTL-KRYSNQTFDKVMGPMLDANTRKQIWRHEILDADGICSPGEKVENKQVLV 829

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K                  Q  ++   V +       QY+      +    + IEK+  
Sbjct: 830  NKYMP------------TVTQTPLEGSSVPQQ-----PQYKDVPITYKGPTDSYIEKVMI 872

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF + G   DI+ 
Sbjct: 873  SSNAEDAF--LIKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCETGICPDII- 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                              G  +
Sbjct: 930  --------MN--------------------------------------------PHGYPS 937

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                    + +   A          T  F G+  + +   L     +  G+  +  G+TG
Sbjct: 938  RMTVGKLIELLAGKAGVLDGRFHYGT-AFGGSKVKDVCEDLIRYGYNYLGKDYVTSGITG 996

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 997  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1056

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAGN-----------DTFETGTPESF 1347
              YGA+ +L E L I SD    DV G     +  + G                   P + 
Sbjct: 1057 IGYGASMLLLERLMISSDAFEVDVCG-----KCGLLGYSGWCHFCKSSCHVSSLRIPYAC 1111

Query: 1348 NVLVKEMQALGLSIDLENSRTKN 1370
             +L +E+Q++ +   L+ ++   
Sbjct: 1112 KLLFQELQSMNIIPRLKLAKYNE 1134



 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 120/955 (12%), Positives = 275/955 (28%), Gaps = 198/955 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+   I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINDEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR--------RRKVPVTSFLMALGMDSE 226
            G  + +             E  S+  + V+  R           +P+     A+G++S+
Sbjct: 199 VGASVTSST----------HEKKSRTNLVVKQGRFYLKHNTLTEDIPIAIIFKAMGVESD 248

Query: 227 -EILSTFYPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG--EQVIE 275
            EI+     +            +      F    A   +G KV    +   +G  +  I+
Sbjct: 249 QEIVQMIGTEEHVIAAFAPSLEECQKAQIFTQMQALKFIGNKVRRQRMWGSSGPKKSKID 308

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             ++L +  +  L    VK     + C+    +   ++  +      +     +++    
Sbjct: 309 EARELLASTI--LTHVPVKEFHFRTKCIYIAVMVRRVILAQGANKVDDRDYYGNKRL--- 363

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                 + + +L+ D           +       ++ A  D+ + MR   ++   V    
Sbjct: 364 --ELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA-- 419

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +   +   ++ +   G  ++  RL+      +            K+             
Sbjct: 420 ISSGNWSLKRFKMDRQGVTQVLSRLSYIAALGMMTRISSQFEKTRKVSGPRSLQ------ 473

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                   +    +  + +    +  +           D   +     +  + V     E
Sbjct: 474 ---PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLAANLGVEDVNLLCGE 530

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
               + +  +  + N L  I   ++L    +  + RA    E   +      R     + 
Sbjct: 531 ELSYANVFLVFLNGNILGVIRDHQKLVNTFRL-MRRAGYINEFVSISTNISDRCVYISSD 589

Query: 576 EGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            G        V +  S         +   YR   D    + V YL   EE +  +A    
Sbjct: 590 GGRLCRPYIIVKNQRSAVTNKHIQELSQGYRSFEDFLHESLVEYLDVNEENDCNVAL--- 646

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                                     +    ++  P  ++ + A LIP+  ++ S R   
Sbjct: 647 --------------------YEHTITKHTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 686

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +         G        +   ++A                       
Sbjct: 687 QCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----------------------- 714

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    QRP+VK                 +   L  G+N  
Sbjct: 715 -----------------------YPQRPMVK----------TKTIELIEFEKLPAGQNAT 741

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT-KLGPEEITRDIPNVSEE 871
           VA M + GY+ ED++++++  +       +  +  +   +       +++   + + +  
Sbjct: 742 VAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYSNQTFDKVMGPMLDANTR 801

Query: 872 GLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                   +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 802 KQIWRHEILDADGICSPGEKVENKQVLVNKYMPTVTQTPLEGSSVPQQPQYKDVP 856


>gi|254573076|ref|XP_002493647.1| Second-largest subunit of RNA polymerase III [Pichia pastoris GS115]
 gi|238033446|emb|CAY71468.1| Second-largest subunit of RNA polymerase III [Pichia pastoris GS115]
 gi|328354525|emb|CCA40922.1| DNA-directed RNA polymerase II subunit B [Pichia pastoris CBS 7435]
          Length = 1158

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 120/583 (20%), Positives = 197/583 (33%), Gaps = 97/583 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D+    + L+A       N+   + I    V   V   I         R+T      
Sbjct: 655  EYLDVNEENDSLIALYEKDIKNYTTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAM- 713

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              + I  +       ID   ++ +        +    I   G   +   +    A+    
Sbjct: 714  GKQAIGAIGYNQFNRIDT--LLYLMVYPQQPMVKTKTIELIGYDKLPAGQNATVAVMSYS 771

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              D+ D  +   + +       ++F R      +R  +  ++ +  ++ +   E  I   
Sbjct: 772  GYDIEDALVLNKASIDRGFGRCQVF-RKNTTLLKRYPNHTKDILGGMSVNDQGEP-IFQH 829

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                       G    SG     K   ++S+                D          K 
Sbjct: 830  RSLGPDGLGEVGLPLESGQVYVNKFVPINSE-------ESIIGQTPDD-------SQRKE 875

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q+  +  +      + I+++     +      +VK  +   R  + GDK + RHG KG+ 
Sbjct: 876  QHRETPMVYRGPEPSYIDQMMM--SLGENDQVLVKALLRQTRRPELGDKFSSRHGQKGVC 933

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              I+  ED+PF  DG   DI++NP G PSRM VG++ E   G A V  G           
Sbjct: 934  GIIVQQEDLPFNDDGISPDIIMNPHGFPSRMTVGKMIELISGKAGVLDGSLQYGTCFGGS 993

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               ++S +                                                    
Sbjct: 994  DLKEMSQILIDKGFSYSGKDQL-------------------------------------- 1015

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      SG       +TGE     +  G IY  KL HMV DK++ARS G  +++T+
Sbjct: 1016 ---------YSG-------ITGECLQAYIFFGPIYYQKLKHMVLDKMHARSRGPRAVLTR 1059

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV------GRT---- 1326
            QP  G+S  GG RLGEME  C+ AYGA+ +L E L I SD    DV       G      
Sbjct: 1060 QPTEGRSRDGGLRLGEMERDCVVAYGASQLLLERLMISSDAFEVDVCNTCGLMGYNGWCP 1119

Query: 1327 --RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              +  E I+          P +  +L +E+ ++ ++  LE   
Sbjct: 1120 TCKSSEFIIK------MTIPYAAKLLFQELVSMNIAPRLELGD 1156



 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 111/966 (11%), Positives = 278/966 (28%), Gaps = 172/966 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
           L++    S+++F+  ++    + NE        V P         L+++           
Sbjct: 57  LVKQHLDSFNYFVDKDLKKIIKANE---KVLSDVDP------EFYLKYLDIRVGYKSTED 107

Query: 83  --PPKFD---VDDCLWRDLTYAVPLKITL-----RLIVFDVDEFTG--------AKSIKD 124
               K +      C   D TY+ P+ + +     R I+   D   G         K I +
Sbjct: 108 LQKVKRNMIPPHQCRLSDTTYSAPIYVDVEYTRGRKIIMHRDLEIGKMPIMLRSNKCILE 167

Query: 125 IKE--QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
            K+  Q   + + PL    G F++ G +++++ Q   S          +     K +   
Sbjct: 168 SKDESQMASLCECPL-DPGGYFIVNGTEKVILVQEQLSKNRIIVEADDK-----KQIVQA 221

Query: 183 RIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIV 237
            +      +     +     + I+++ +    +VP+   L A G+ S+ EI+        
Sbjct: 222 SVTSSTHERKSKTYVVT-KNNKIYLKHNSISEEVPIVLVLKAAGIVSDLEIMQLVCGDDS 280

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE----KGV 293
             Q      F  +A   +   + +   +        +++ ++L +  L   +E       
Sbjct: 281 TYQDLFTINFEEAAKLDIHTQRDALEYIGKR-----VKTMRRLGAPKLSIYQEGVEAIAN 335

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
             +   S            +   T  + +      +   +++  +   + + +       
Sbjct: 336 TIVAHISVEDLNFREKAIYLAIMTRRVVMAMH---NPTMIDDRDYVGNKRLEL------- 385

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
               +         K   D   +I ++++  + ++   A    N    +        +  
Sbjct: 386 AGQLMSLLFEDLFKKFNSDFKANIDKILKKPNRASEFDALLSINVHSNNITTGINRAIST 445

Query: 414 VKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
              +++        V H    +     + ++  +         +     L   +   +  
Sbjct: 446 GNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCT 505

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
               +     L    ++   I++ D +  + +           + +    S  S    ++
Sbjct: 506 SDTPEGEACGLVKNLALMTHITTDDEEEPVRKICYLLGAEDIKIVDSSVISSRSNFGVYL 565

Query: 530 NSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
           N    I   R  +        + R+        ++   + +        G     +  + 
Sbjct: 566 NGT-MIGVIRYPTVFVTKFRKLRRSGKVSAFISIYINSHHKAVHLAADGGRICRPLIIVE 624

Query: 588 SFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           +         ++       +         V YL   EE +  IA     +          
Sbjct: 625 NGVSKVEAHHLQKLKDGEWQFDSFLTNGLVEYLDVNEENDSLIALYEKDI---------- 674

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                        +     ++  P  V+   A LIP+  ++ S R    C M +QA+   
Sbjct: 675 -------------KNYTTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA- 720

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                                                   I   + +   +   + +Y  
Sbjct: 721 ----------------------------------------IGYNQFNRIDTLLYLMVYP- 739

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q+P+VK                     L  G+N  VA M + GY+ E
Sbjct: 740 -------------QQPMVK----------TKTIELIGYDKLPAGQNATVAVMSYSGYDIE 776

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDECG 880
           D++++++  +           +   + +      ++    ++ +         +++   G
Sbjct: 777 DALVLNKASIDRGFGRCQVFRKNTTLLKRYPNHTKDILGGMSVNDQGEPIFQHRSLGPDG 836

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +  VG  +  G + V K  P      + E  + +     +  +    +  V  G   + +
Sbjct: 837 LGEVGLPLESGQVYVNKFVPIN----SEESIIGQTPDDSQRKEQHRETPMVYRGPEPSYI 892

Query: 941 DVRIFN 946
           D  + +
Sbjct: 893 DQMMMS 898


>gi|89274890|gb|ABD65886.1| RNA polymerase II second largest subunit [Ganoderma tsugae]
          Length = 883

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 144/1021 (14%), Positives = 292/1021 (28%), Gaps = 182/1021 (17%)

Query: 286  KSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK    + +   G      +    ++     ++   G + D   LE I +   
Sbjct: 21   KTISQFQVKLYHRSKERSLGNVMKATIPYIKIDIPIWVVFRALGVISDRDILEHICYDMQ 80

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             +  +  +    +  ++         +DR+ AL  I                +       
Sbjct: 81   DNQMLEMLKPCIDEGFV--------IQDREIALDYI------------GNRGTTTGLNRE 120

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G 
Sbjct: 121  RRLRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRDLDDRDHFGK 177

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +    + + +     +
Sbjct: 178  KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNISLAVKHNTITNGLKYSLAT 237

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 238  GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 293

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + ++  G +  P  +  +      +   +A       
Sbjct: 294  GMVCPAETPEGQACGLVKNLSLMSCIS-VGTLSAPVIEFLEEWGLESLE-ENAHASTPCT 351

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N           +LV                   D + +  V             D
Sbjct: 352  KVFVNGVWMGVHRDPVKLVSTLRKLRRKD---------DINCEVSVVRDIRERELRLYTD 402

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA---IRI 743
            + RV     +      L++               K   + + AK    +           
Sbjct: 403  AGRVCRPLFIVENQQLLIQK--------------KHIESLVRAKEDPTLSYNWDSLLKDG 448

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            VI  ++ + + +         ++  R                          D  + +  
Sbjct: 449  VIELLDAEEEETVMICMTPEDLENSRLQAAGI--------------------DPHADEEN 488

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            D +       +   W       SM++     ++            ++       +G    
Sbjct: 489  DPSARLKAPTSAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLT 548

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 549  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSG 597

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 598  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYD 656

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G N         K+  +  D      R++          ++   + +  Q
Sbjct: 657  KLEDDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRTHTKRDVSTPLKSTEQGIVDQ 716

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VK+ V   R  Q GDK A RHG KG + 
Sbjct: 717  VLI--------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIG 756

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +       
Sbjct: 757  ITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNEGDATPFT--- 813

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                   ++       LR       G+ +               
Sbjct: 814  ----------------------DLTVESVSQFLRQKGYQSRGLEIM-------------- 837

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
                      G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+Q
Sbjct: 838  --------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQ 882

Query: 1282 P 1282
            P
Sbjct: 883  P 883



 Score =  137 bits (344), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 106/766 (13%), Positives = 222/766 (28%), Gaps = 103/766 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ID    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 49  YIKID----IPIWVVFRALGVISDRDILEHICYDMQDNQMLEMLKPCIDEGFVIQDREIA 104

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   ++L     + L+++ +  + +              +      + 
Sbjct: 105 LDYIGNRGTTTGLNRERRLRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 160

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  D    +      +    P+L          +   +     K  +        +
Sbjct: 161 LAALERRDLDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNISL 220

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   S  G  ++  R    +      R         
Sbjct: 221 AVKHNTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 280

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +  +   + E +    ++S+
Sbjct: 281 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGTLSAPVIEFLEEWGLESL 340

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 NA         F     +    + V  +S +   RR   +    V+  R   E 
Sbjct: 341 ----EENAHASTPCTKVFVNGVWMGVHRDPVKLVSTLRKLRRKDDIN-CEVSVVRDIRER 395

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
                T  GR+C       +   L+      + V A       Y           +  L 
Sbjct: 396 ELRLYTDAGRVCRPLFIVENQQLLIQKKHIESLVRAKEDPTLSY-NWDSLLKDGVIELLD 454

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQV 671
           A EEE   I      L E+       +      E     R             +  P  +
Sbjct: 455 AEEEETVMICMTPEDL-ENSRLQAAGIDPHADEENDPSARLKAPTSAHTWTHCEIHPSMI 513

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                            
Sbjct: 514 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI--------------------- 552

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                                  + + +  Y       +     +  R            
Sbjct: 553 --------------------RMDTMANILYYPQKPLATTRSMEYLRFR------------ 580

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                       +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + 
Sbjct: 581 ------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLE 628

Query: 852 RDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           + + +   E            +       +++ G+I  G  VN  DI++GK  P      
Sbjct: 629 KKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNVNGEDIIIGKTAPIPPDSE 688

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              ++        +    RD S  + S   G V  V I       K
Sbjct: 689 ELGQRT-------RTHTKRDVSTPLKSTEQGIVDQVLITTNAEGQK 727


>gi|45545317|gb|AAS67506.1| DNA-dependent RNA polymerase II second largest subunit [Ceramothyrium
            linnaeae]
          Length = 936

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 142/886 (16%), Positives = 268/886 (30%), Gaps = 144/886 (16%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  ++  ++    G+   DD D+LG +R+   G ++ N +R+ L +  +     + 
Sbjct: 172  KAFFLGYMVNRMLKCALGRTEPDDRDHLGKKRLDLSGPLMANLFRMQLDKATKDFFRYMQ 231

Query: 492  SVDIDSVMPQDLINAKP--VVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
                           KP  V + +     +               +SQ+       S ++
Sbjct: 232  KRVESGQTIAIKAGWKPNIVTNGLKYSLATGNWGDQKKLDKAKAGVSQVLSRYTFASTLS 291

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY- 595
            H RR +A     + R     + R +H TH+G +CPAET EG   GLV +L   + V  + 
Sbjct: 292  HLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLALMSMVTNHY 347

Query: 596  -GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGE 652
                   Y    + +   D       +    ++        L +     +     R  G 
Sbjct: 348  DTAPLQSYILEKNVEALEDWEPHLNPQATKVFVNGVWFAVILKDPKFLVDHFRMLRRRGT 407

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                     D  D   K        + P F+   D +    G  +  +       E  + 
Sbjct: 408  IDTEVSLVWDIRDKEFKISGDSGRIIRPLFIVETDRSSDNHGNLVLNKEHIAKLDETAY- 466

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
               ME  + +       A        + A   VI  ++ + + +   V     +   R+ 
Sbjct: 467  --HMEQEMGE------PADGYYRWLDLLAD-GVIEYLDAEEEETVMIVMSPEALLDSRNA 517

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            Q            G     +D                 N           +    + +  
Sbjct: 518  QM-----------GQPPEPDDDPLRRND-------PLLNPHAHTFTHCEIHPSMILGVCA 559

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             ++            ++       +G      D    +           +  +       
Sbjct: 560  SIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFDQRMET-----------MANILYYPQKP 608

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
                  +       +   +  + AI      +  D+ +   S +   +    +F R   D
Sbjct: 609  LARTMAMEYLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYQD 667

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVL 1008
            + +    +    +E   +    + + L    Y +L +   +  G           K+  +
Sbjct: 668  QEK---MIGHAVVEQFEKPTRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIMGKTAPM 724

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + D                +E  QR  + +K    T     E    +++     GD    
Sbjct: 725  APD---------------AEELGQRMKQHIKRDVSTPLRSTESGVIDQVLLTTTGD---- 765

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
               +  KV V   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +P
Sbjct: 766  -GCKFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGIVPDLIINPHAIP 824

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +  + E  L       G +  +          IS                      
Sbjct: 825  SRMTIAHLIECLLSKVGALRGDEGDATPFTKVTVTQISS--------------------- 863

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                +L      + G  V                        +G +    G         
Sbjct: 864  ----ILENMGYQRRGFEVM----------------------YNGHT----GR---KLVAQ 890

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G++  GG R 
Sbjct: 891  VFLGPTYYQRLRHMVDDKIHSRARGPTQILTRQPVEGRARDGGLRF 936



 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 114/848 (13%), Positives = 243/848 (28%), Gaps = 145/848 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            ++++++Q  RS G      +  A      L   R + ++G  M  +  +K  ++ R+D 
Sbjct: 1   SEKVLIAQE-RSAGNIVQIFQKAAPAPFTHLAEIRSVIEKGARMMSQCTAK--LYRRVDG 57

Query: 209 -----------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
                            ++ +P+     AL + S+ +IL          +  D     L 
Sbjct: 58  PDGSKIENPIRVQLPYVKQDIPLAIVFRALDIVSDTDILEKICFDQRDQEMMDMLMGSLQ 117

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
               + GA ++   +        ++S ++     +  L ++ +  +G TSD         
Sbjct: 118 EGQPIQGADLARDYIARRGNVPSLKSHER-QKHAIDILTKEFLPHIGQTSDATARKAFFL 176

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +     +  +   +  D   L        + + +       +   + N      +K  
Sbjct: 177 GYMVNRMLKCALGRTEPDDRDHL------GKKRLDL-------SGPLMANLFRMQLDKAT 223

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           KD    + + +  G              +  +  KY L   G      +L+       + 
Sbjct: 224 KDFFRYMQKRVESGQTIAIKAGWK--PNIVTNGLKYSL-ATGNWGDQKKLDKAKAGVSQV 280

Query: 431 IRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           + +    + +  L        R GK       +  +       E  + Q    +  +   
Sbjct: 281 LSRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLALM 340

Query: 486 IKERISSV---------DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
                            + +    +D        +             L++    +    
Sbjct: 341 SMVTNHYDTAPLQSYILEKNVEALEDWEPHLNPQATKVFVNGVWFAVILKDPKFLVDHFR 400

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE-----GHNIGLVSSLTSFAR 591
             RR   +            +   +       I P    E      ++  LV +    A+
Sbjct: 401 MLRRRGTIDTEVSLVWDIRDKEFKISGDSGRIIRPLFIVETDRSSDNHGNLVLNKEHIAK 460

Query: 592 VNA--------YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS---- 639
           ++          G     Y +  D      + YL A EEE   I  +  +L +  +    
Sbjct: 461 LDETAYHMEQEMGEPADGYYRWLDLLADGVIEYLDAEEEETVMIVMSPEALLDSRNAQMG 520

Query: 640 --FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +    R     +          +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 521 QPPEPDDDPLRRNDPLLNPHAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMG 580

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 581 KQAMGIFLTNF-----------------------------------------DQRMETMA 599

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y      R+     +                           +L  G+N +VA   
Sbjct: 600 NILYYPQKPLARTMAMEYL------------------------KFRELPAGQNAIVAIAT 635

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    ++   +       E        D   +    
Sbjct: 636 YSGYNQEDSVIMNQSSIDRGLFRSLFYRAYQDQEKMIGHAVVEQFEKPTRSDTLRLKHGT 695

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ GI+  G  V+  DI++GK  P         E+L + +      DV        
Sbjct: 696 YDKLDDDGIVAPGVRVSGEDIIMGKTAPMAPDA----EELGQRMKQHIKRDVSTPLRSTE 751

Query: 933 SGVSGTVV 940
           SGV   V+
Sbjct: 752 SGVIDQVL 759


>gi|270161133|gb|ACZ63444.1| RpoB [Rahnella sp. 381-Salad]
          Length = 307

 Score =  299 bits (765), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 189/307 (61%), Positives = 239/307 (77%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGLVTDEINYLSAIEEGNFVIAQANSNLDDEGRFIEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR GIV+ VDA RIVIR  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGIVQYVDASRIVIRVNEEEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVKVGDE 787
            V +G+ 
Sbjct: 301 CVNLGEP 307


>gi|156767139|gb|ABU95084.1| ribosomal polymerase B subunit [Acinetobacter junii]
          Length = 266

 Score =  298 bits (764), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 169/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGEKLSEDMLSGLELVDLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   K    I+ LRSFL+K+    G   E++    D+ +L+++   ++GVP++T
Sbjct: 180  EQIDKML---KQQRTIAELRSFLDKIYNKVGGEQEQLDTLTDEEILKLSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  SGQ IL+D
Sbjct: 237  PVFDGAEESQIKELLELAELPRSGQQILFD 266


>gi|156767141|gb|ABU95085.1| ribosomal polymerase B subunit [Acinetobacter haemolyticus]
 gi|156767143|gb|ABU95086.1| ribosomal polymerase B subunit [Acinetobacter haemolyticus]
          Length = 266

 Score =  298 bits (764), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 168/270 (62%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEIQPADE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSIEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP    G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDIHGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   +    I+ LR+FL+K+    G   E +    D+ VL++A   ++GVP++T
Sbjct: 180  EQIDKMLQQQRT---IAELRAFLDKIYNKVGGEQEDLDSLTDEEVLKLAGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  +GQ++L+D
Sbjct: 237  PVFDGAEESQIKELLELAELPRTGQTVLFD 266


>gi|134078852|emb|CAK45911.1| unnamed protein product [Aspergillus niger]
          Length = 1213

 Score =  298 bits (764), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 96/480 (20%), Positives = 166/480 (34%), Gaps = 69/480 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E    +I ++        D+        +       +G      +     +   L+ 
Sbjct: 696  THIEFTPTNILSIVANMTPFSDQNQSPRNMYQCQMSKQTMGTPGTAIQYRTDNKLYRLQT 755

Query: 916  ---IFGEKAVDVRDTSLRVPSGVSGTV----------VDVRIFNRHGIDKNERSISVERE 962
                     +         P+G +  V           D  I N+   ++     ++ + 
Sbjct: 756  GQTPIVRPPLYNAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGYGTIYKT 815

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQ 1020
            +I  L  D+ D +    R   ++L     G    +       +         + E     
Sbjct: 816  KIHSL--DEKDSRRGKSRREVTKLFGFAPGGEIRADWRATLDEDGLPHIGARVKEGSLVA 873

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W     D      V    + +       E+ + + +  +     + PG    VK  +  
Sbjct: 874  AWHTVRYDAASDSYVNVDGITHFVKYKDAEEGYIDSVRILGAESGVEPGQALSVKYRI-- 931

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+ 
Sbjct: 932  PRKPIIGDKFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESM 991

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +      +                                  
Sbjct: 992  AGKAGALHGHPQDSTPFQFSEENTAA---------------------------------- 1017

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     LR A  +  G   LY G+TG+ F   + +G ++  +L 
Sbjct: 1018 ----------------DYFGHQLRKAGYNYFGNEPLYSGITGKEFAADIFIGVVHYQRLR 1061

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1062 HMVNDKFQVRTTGPVNQLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAHILQDRLMNCSD 1121



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 58/411 (14%), Positives = 127/411 (30%), Gaps = 56/411 (13%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G  CP  T +G 
Sbjct: 493 PSGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFFCPVHTPDGS 549

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L     +            V    +   +V L     ++      + ++  DG
Sbjct: 550 PCGLLNHLAHKCLIATSD--------VDTTHIPKALVQLGV-RSDSSVSVTESVTVQLDG 600

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQ------------------VVSIAASLIP 680
                    + +     + R K+   D  P++                  + S AA +  
Sbjct: 601 RIIGYCSPKQASAIANTLRRWKVMGSDKIPRELEIGYIPNTNGGQYPGIYMFSQAARMYR 660

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPF---VGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            +++   +++      ++  + +          V T +E                    Q
Sbjct: 661 PVKHLGLDKLDYVGPFEQPFMEIACLPQDLISGVSTHIEFTPTNILSIVANMTPFSDQNQ 720

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                   +  +  +    + +      K  R        Q P+V+              
Sbjct: 721 SPRNMYQCQMSKQTMGTPGTAIQYRTDNKLYRLQTG----QTPIVRP----------PLY 766

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE--FEVMARDTK 855
            +  L +   G N +VA + + GY+ +D+M+I++             +     +  +D++
Sbjct: 767 NAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIHSLDEKDSR 826

Query: 856 LGPEEITRDIPN-------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            G                 +  +    +DE G+  +GA V  G ++    T
Sbjct: 827 RGKSRREVTKLFGFAPGGEIRADWRATLDEDGLPHIGARVKEGSLVAAWHT 877



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 97/703 (13%), Positives = 193/703 (27%), Gaps = 144/703 (20%)

Query: 78  SYEFDPP------KFD-------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
               + P      KF          +C  R  TY   L+  +   V + D     +    
Sbjct: 102 EVFLEKPALPPSNKFTTRNRNIYPSECRERHATYRGKLRARIEWRVNNGDWMESVRE--- 158

Query: 125 IKEQSIYMGDLPLMTK------------------------DGTFVIKGIQRIVVSQLHRS 160
                  +G +P+M +                         G F++ G ++     L R 
Sbjct: 159 -------LGQVPIMLRTNRCHLEKATPSELVEHKEESEELGGYFIVNGNEK-----LIRM 206

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLW---------------------------MD 193
             +            GK  Y   II  +G +                           + 
Sbjct: 207 LVV------------GKRNYPMAII--RGSFVRRGHTYTKYGVQIRSVRPDQTSQTNVLH 252

Query: 194 IEFDSKDIIHVRIDRRR---KVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
              D    +  R   R+    VPV   L AL +++ +     +  IV S   +       
Sbjct: 253 YLTDGN--LTFRFSWRKAEYLVPVMMILKAL-VETND--REIFEGIVGSASSEGIKNTFV 307

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              + +  +V  +             G+K    L                       V  
Sbjct: 308 TDRVELLLRVYKAYNTHSRAACRAYLGEKFRPVL----------------------GVPA 345

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK--NK 368
           D+ N + G  ++    +    +     + +     ++        A +      D     
Sbjct: 346 DMSNEDAGTEFLRKVVLPHLGNQNVTENQDYDKFKMILFMIRKLYALVAGDCAPDNPDAV 405

Query: 369 DRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
             ++ LL   +Y ++    +  +                +     G    +     D   
Sbjct: 406 SNQEILLGGFLYGMILKERLEEW------VRSFQPILRDWSNRNGGAKFTDPAFERDFLA 459

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER-- 484
            V     E++   ++  +   N   +   +D         + E +     +   RM    
Sbjct: 460 KVVKRSNENLGGALEYFLSTGN-LVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMIHRG 518

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSA 543
           S   ++ +  +  ++P+      PV +         + L+       S    TH  +  A
Sbjct: 519 SFFAQLKTTTVRKLLPESWGFFCPVHTPDGSPCGLLNHLAHKCLIATSDVDTTHIPK--A 576

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSE--GHNIGLVSSLTSFARVNAYGFIETP 601
           L Q GV    +      V     GRI    + +        +              +E  
Sbjct: 577 LVQLGVRSDSSVSVTESVTVQLDGRIIGYCSPKQASAIANTLRRWKVMGSDKIPRELEIG 636

Query: 602 YRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           Y    +G     +   S A              LD  G F +  +   C  ++++     
Sbjct: 637 YIPNTNGGQYPGIYMFSQAARMYRPVKHLGLDKLDYVGPFEQPFMEIACLPQDLISGVS- 695

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
              I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 696 -THIEFTPTNILSIVANMTPFSDQNQSPRNMYQCQMSKQTMGT 737


>gi|299741189|ref|XP_001834288.2| DNA-directed RNA polymerase [Coprinopsis cinerea okayama7#130]
 gi|298404597|gb|EAU87529.2| DNA-directed RNA polymerase [Coprinopsis cinerea okayama7#130]
          Length = 1149

 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 107/510 (20%), Positives = 170/510 (33%), Gaps = 99/510 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    AI      D+ D  +   + +   
Sbjct: 717  DTLLYLSVYPQQPMVKTRTIELIGYDRLPAGQNATVAIMSYSGYDIEDALILNKASLDRG 776

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++  ++     +          + LA    DE   + R       + L G      
Sbjct: 777  YGRCQVLRKNATLLRKYPNG----TFDRLADAPLDENGQIQRRYDIVQADGLPGVGERVD 832

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
            P     +    ++        Q                     Y+ +    +      I+
Sbjct: 833  PGDIYVNKQSPTNATDNTFTGQAASVP----------------YKNAPLSYKSPVCGMID 876

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+   D        ++KV +   R  + GDK + RHG KG+   I+  ED+PF +DG   
Sbjct: 877  KVMISD--TDNDQTLIKVLIRQTRRPELGDKFSSRHGQKGVCGLIVNQEDLPFNEDGIVP 934

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D ++NP G PSRM V        G     L  K   L    +                  
Sbjct: 935  DTIMNPHGFPSRMTV--------GKMIELLAGKAGVLTGKLQYGT--------------- 971

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                            F G+  E ++ +L        G+ +L  
Sbjct: 972  -------------------------------AFGGSKVEDMSRILIEHGFSYGGKDMLTS 1000

Query: 1239 GLTGEPFDRPVTVGYIYMLK---------LNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
            G+TGEP +  V  G IY  K         L HMV DK++AR+ G  + +T+QP  G+S  
Sbjct: 1001 GITGEPLEAYVYFGPIYYQKAILTVYFQKLKHMVMDKMHARARGPRATLTRQPTEGRSRE 1060

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-VGRTRVYESIVAG-----------ND 1337
            GG RLGEME  C+  YGA  +L E L I SD   VG  +  E  + G             
Sbjct: 1061 GGLRLGEMERDCLIGYGATQLLLERLMISSDKFEVGACQ--ECGLMGYNGWCTYCKSSKK 1118

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                  P +  +L +E+ A+ +   L    
Sbjct: 1119 MATLTIPYAAKLLFQELMAMNVVPRLVLDD 1148



 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 123/937 (13%), Positives = 274/937 (29%), Gaps = 189/937 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ ++I    + N         V P         L++       P    
Sbjct: 45  LVKQHIDSFNYFVDVDIKNIVKAN---NKVTSDVDP------RFWLKYTDINVGFPDRNE 95

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 +    +C  RD TY+ P+ +T++               K I ++++ +G LP+M
Sbjct: 96  MEAIDKRVTPHECRLRDTTYSAPIIVTIQYTRG-----------KSIVQRNVNIGRLPIM 144

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR-- 171
                                      G FV+KG +++++ Q   S   I  + D  +  
Sbjct: 145 LRSNKCVLTGKTEAQLARMTECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVETDNVKGI 204

Query: 172 -----ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDS 225
                 S +   L +                 K  I++R +     VP+   L ALG+ S
Sbjct: 205 VQASCTSSTHGGLKSKT----------YVITKKGRIYLRHNSIHEDVPIVIALKALGIQS 254

Query: 226 E-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           + EIL          +         +A   +     +   +        ++  +K+    
Sbjct: 255 DKEILLLTAGNTEEYKTIFSANIEDAAKLGIFTRHQALEYIGAR-----VKVNRKVMGPR 309

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
             + +E            +   +V    ++     I++         ++++   S + D 
Sbjct: 310 RPAWEEALEA-----LATIVLAHVPVQGLDFRAKAIFVATMTRRVLMAMDD--ESMVDDR 362

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALL-DIYRVMRPGDVSTFSVAESMFNFLFFDS 403
             +    +     +   L  D  K     L   I +V++    ++   A +         
Sbjct: 363 DYVGNKRLELAGQLLALLFEDLFKTYNSNLKSAIDKVLKKPSRTSEFDAFNTMQMQGDHL 422

Query: 404 DKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG-- 460
               +  +     +  R  ++       + +   I+ + ++  + +       +      
Sbjct: 423 TSGFVRAISTGNWSLKRFKMERAGVTHVLSRLSFISALGMMTRISSQFEKTRKVSGPRAL 482

Query: 461 ---NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 V    +  + +    +  +           +   +    ++  + +        
Sbjct: 483 QPSQWGVLCPSDTPEGEACGLVKNLALMTHITTDVEEGPIIRLAFMLGVEDISLTTGTEI 542

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                  +  +   +       +  +     + RAR   E   V+  H+ R     +  G
Sbjct: 543 YGPNSYVVYINGTIIGVTRTPTKFVS-QFRKLRRARRFSEFVSVYINHHHRAVHIASDGG 601

Query: 578 HNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                +  +         +    ++       D      V YL   EE + +IA      
Sbjct: 602 RICRPMIIVEKGRSRVTSDHIVQLKKGNVTFDDFLRKGLVEYLDVNEENDTFIAL----- 656

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                   ++V                  ++  P  ++   A LIP+  ++ S R    C
Sbjct: 657 -----HEHDIVPT-------------TTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQC 698

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+                                           I   + +   
Sbjct: 699 AMGKQAIGA-----------------------------------------IAYNQMNRID 717

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           +   + +Y               Q+P+VK                     L  G+N  VA
Sbjct: 718 TLLYLSVYP--------------QQPMVK----------TRTIELIGYDRLPAGQNATVA 753

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            M + GY+ ED++++++  +         + +   + R    G  +   D P      ++
Sbjct: 754 IMSYSGYDIEDALILNKASLDRGYGRCQVLRKNATLLRKYPNGTFDRLADAPLDENGQIQ 813

Query: 875 NIDE----CGIICVGAEVNPGDILVGKITPKGESPMT 907
              +     G+  VG  V+PGDI V K +P   +  T
Sbjct: 814 RRYDIVQADGLPGVGERVDPGDIYVNKQSPTNATDNT 850


>gi|126722427|dbj|BAF48627.1| DNA-dependent RNA polymerase subunit B' [Halobiforma lacisalsi]
          Length = 435

 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 84/253 (33%), Positives = 115/253 (45%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + G K A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGGKFASRHGQKGVVGHLAPQEDMPFTEDGVVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++                                   
Sbjct: 257  PSRMTVGHILEMIGGKLGSLEGRRVDG--------------------------------- 283

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                TP F G DE  +   L  A  + SG+  +Y G+TGE  + 
Sbjct: 284  --------------------TP-FLGEDESELREGLEEAGFESSGKETMYSGITGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K+YA S G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 323  EIFVGVIFYQKLYHMVSNKLYAHSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMTLKERLLDESD 395



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/180 (21%), Positives = 68/180 (37%), Gaps = 23/180 (12%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKASVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEEAYAHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETTVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188


>gi|327272386|ref|XP_003220966.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2-like [Anolis
            carolinensis]
          Length = 1132

 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 96/498 (19%), Positives = 171/498 (34%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 709  YLLAYPQRPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 768

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 769  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATHKPIWRHEILDADGICSPGEKVENKQVLV 827

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 828  NKSMP------------TVTQTPLEGSSVPQQ-----PQYKDVPVTYKGATDSYIEKVMI 870

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI+ 
Sbjct: 871  SSNAEDAF--LIKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDII- 927

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                             +    
Sbjct: 928  --------MN----------------------------------------PHGYPSRMTV 939

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
             K+ +        +  ++  G       F G+  + +   L     +  G+  +  G+TG
Sbjct: 940  GKLIELLAGKAGVLDGRFHYGT-----AFGGSKVKDVCEDLIRYGYNYLGKDYVTSGITG 994

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 995  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1054

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 1055 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1114

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ S+   
Sbjct: 1115 ELQSMNIIPRLKLSKYNE 1132



 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 119/955 (12%), Positives = 275/955 (28%), Gaps = 200/955 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE +          +       L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANEKIT---------SDADPMWYLKYLNIYVGTPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPVGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGT 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR---K-------VPVTSFLMALGMD 224
            G  + +               + K   ++ + + R   K       +P+     A+G++
Sbjct: 199 VGASVTSST------------HEKKSRTNITVKQGRFYLKHNTLSEDIPIAIIFKAMGVE 246

Query: 225 SE-EILSTFYPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S+ EI+     +            +      F    A   +G KV    +     +  +E
Sbjct: 247 SDQEIVQMIGTEEHVMAAFAPSLEECQKAQIFTQMQALKYLGNKVRRQRMWGGPKKTKME 306

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             ++L +  +  L    VK     S C+    +   ++  +      +     +++    
Sbjct: 307 EARELLATTI--LAHVPVKEFNFRSKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL--- 361

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                 + + +L+ D           +       ++ A  D+ + MR   ++   V    
Sbjct: 362 --ELAGQLLSLLFEDLFKKFNSELKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA-- 417

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +   +   ++ +   G  ++  RL+  +   +            K+             
Sbjct: 418 ISTGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ------ 471

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                   +    +  + +    +  +           D   +     +  + V     E
Sbjct: 472 ---PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLAGNLGVEDVNLLCGE 528

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                 +  +  + N L  I   ++L    +  + RA    E   +      R     + 
Sbjct: 529 ELSYPNVFLVFLNGNILGVIRDHQKLVYTFRL-MRRAGYINEFVSISTNLTDRCVYISSD 587

Query: 576 EGHNIGLVSSLTSFARVNAYGFIET---PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            G        +           +E     YR   D    + V YL   EE +  IA    
Sbjct: 588 GGRLCRPYIIVKKQTPAVTEKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEQ 647

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           ++++D                          ++  P  ++ + A LIP+  ++ S R   
Sbjct: 648 TINKD-----------------------TTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 684

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +         G        +   ++A                       
Sbjct: 685 QCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----------------------- 712

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    QRP+VK                 +   L  G+N  
Sbjct: 713 -----------------------YPQRPMVK----------TKTIELIEFEKLPAGQNAT 739

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----N 867
           VA M + GY+ ED++++++  +       +  +  +   +       +           +
Sbjct: 740 VAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATH 799

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                 + +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 800 KPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQTPLEGSSVPQQPQYKDVP 854


>gi|149346308|gb|ABR23664.1| RNA polymerase beta subunit [Enterobacter pulveris]
 gi|149346328|gb|ABR23665.1| RNA polymerase beta subunit [Enterobacter pulveris]
 gi|149346347|gb|ABR23666.1| RNA polymerase beta subunit [Enterobacter pulveris]
          Length = 304

 Score =  298 bits (763), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 183/303 (60%), Positives = 232/303 (76%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   ++
Sbjct: 121 PYRLVRDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P
Sbjct: 241 VDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMP 300

Query: 781 LVK 783
            V 
Sbjct: 301 CVS 303


>gi|269912662|emb|CAY86111.1| RNA polymerase beta subunit [Swaminathania salitolerans]
          Length = 306

 Score =  298 bits (763), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 144/309 (46%), Positives = 197/309 (63%), Gaps = 28/309 (9%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GMD +EIL+ FY  + +++    W  P
Sbjct: 61  VTTLLYALEGEHSIAARAAKAAEGGDVESMTVRGMDQDEILAYFYGTVPFTRMPKGWARP 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                   G K+   L D DTGE V E+  KLT+ + + + E   K + +    L G ++
Sbjct: 121 FDPE-AFRGLKLLEPLYDADTGEVVAEADAKLTARMCRKIAET-TKDVLVGRADLLGRFI 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A+D+VN +TGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL  DKN 
Sbjct: 179 AQDLVNEDTGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLAVDKNN 237

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R +AL+DIYR+MRPG+  T   AE+MF  LFFD+D+YDLS VGRVKMNMRL +D PD +
Sbjct: 238 RRDEALIDIYRIMRPGEPPTPETAEAMFQGLFFDADRYDLSAVGRVKMNMRLEVDAPDTM 297

Query: 429 RHIRKEDII 437
           R +RKEDI+
Sbjct: 298 RVLRKEDIL 306


>gi|212373977|emb|CAP09915.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35714]
          Length = 297

 Score =  298 bits (763), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 173/296 (58%), Positives = 227/296 (76%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 2   PSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 61

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++  
Sbjct: 62  NIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDQK 121

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQR
Sbjct: 122 VLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 181

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +G
Sbjct: 182 QAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAG 241

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           VDIY L K+ RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+NM +A
Sbjct: 242 VDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQNMRIA 297


>gi|307343498|emb|CBJ18666.1| RNA polymerase B subunit [Micromonospora sp. CR38]
          Length = 232

 Score =  298 bits (763), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 106/229 (46%), Positives = 141/229 (61%), Gaps = 38/229 (16%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 34   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 93

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 94   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 142

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L  +  +        
Sbjct: 143  -------------------AHESEGDTNVATPVFDGAREEEISGLLESSLPNRDGKQLIG 183

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V DK++ARSTG YS++
Sbjct: 184  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVDDKIHARSTGPYSMI 232


>gi|76556286|emb|CAJ00163.1| RNA polymerase beta subunit [Pseudomonas syringae pv. theae]
          Length = 313

 Score =  298 bits (762), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 180/312 (57%), Positives = 236/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+   + +++   +GVDIY L K+ RSNQNTC+N+RPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVSVADDEVETGEAGVDIYNLTKYTRSNQNTCINKRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+DI+ADGPST
Sbjct: 302 QRSDIMADGPST 313


>gi|213876749|gb|ACJ54371.1| RNA polymerase subunit B [Mycobacterium bolletii]
          Length = 239

 Score =  298 bits (762), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 101/235 (42%), Positives = 134/235 (57%), Gaps = 40/235 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T QP
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITPQP 238



 Score = 41.2 bits (95), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|76556260|emb|CAJ00150.1| RNA polymerase beta subunit [Pseudomonas syringae pv. porri]
          Length = 313

 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 180/312 (57%), Positives = 234/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R+D +ADGPST
Sbjct: 302 QRSDNMADGPST 313


>gi|51035529|emb|CAH10900.1| RNA polymerase B subunit [Halorhabdus utahensis]
          Length = 433

 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 81/261 (31%), Positives = 114/261 (43%), Gaps = 58/261 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KGIV  I P EDMPF + G   D+++NP  +
Sbjct: 195  EDGSKLSKVKVRDERIPELGDKFASRHGQKGIVGHIAPQEDMPFTEQGVVPDLIINPHAL 254

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   D+                      
Sbjct: 255  PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEDLRDSLEDHG-------------- 300

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ ++Y G+TGE  + 
Sbjct: 301  -----------------------FD-----------------SSGKEVMYSGITGEKVEA 320

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME      +GA
Sbjct: 321  EIFVGNIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRIGEMERDVFIGHGA 380

Query: 1308 AYVLQEMLTIKSD----DVVG 1324
            A  L+E L  +SD     V G
Sbjct: 381  ALTLKERLLDESDQEWIHVCG 401



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 75/210 (35%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N  VA M + G+N ED
Sbjct: 24  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFTVAVMSYEGFNIED 73

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        E+   ++DE 
Sbjct: 74  ALVMNKGSVERALARSHFFRTYEGEERRYPGGQEDRF-EIPDDEVRGARGEDAYTHLDED 132

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    +V    +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 133 GLVNPETKVGENAVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 186

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 187 DTVTLMEGEDGSKLSKVKVRDERIPELGDK 216


>gi|76556272|emb|CAJ00156.1| RNA polymerase beta subunit [Pseudomonas syringae pv. mori]
          Length = 310

 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 179/309 (57%), Positives = 233/309 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADG 797
           +R+DI+ADG
Sbjct: 302 QRSDIMADG 310


>gi|83415465|gb|ABC17940.1| RNA polymerase II second largest subunit [Dimargaris bacillispora]
          Length = 723

 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 131/855 (15%), Positives = 253/855 (29%), Gaps = 155/855 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++   +++ LL+M + I    +              + A  + + +     +
Sbjct: 2    KRMDMAGPLMAQLFKMLLLKMSKEIGRYLQKCIDAGRDFNLTLAVKANTMTAGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S  +H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQSKFMQTRAGVSQVLNRYTFASTXSHLRRCNT----PIGRDGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+  + ++     +     + +  V    +V   S  +   
Sbjct: 118  GIVCPAETPEGQACGLVKNLSLMSHISIGVTEKKLVELLDETAVENLEEVAPSSIAQATK 177

Query: 625  RYIAQANSSLDE-DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL 682
             +I      +   +G    E        +  LV    + D  +   + +        P  
Sbjct: 178  VFINGRWVGIYSGNGHELYERYRVLRQTQVELVDITVVYDPREREVRTLSDAGRVCRPLF 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
               +   +L   ++      + + +                   +     G+++ +DA  
Sbjct: 238  VVRNQRILLNRGHISALHNRVDRGDGK----------PFDFNTLV---NFGVIDYMDAEE 284

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +        Y       ++Q+     R        +         PS  L
Sbjct: 285  EETAMICMSSEDLADSRMFYEHGY--VNDQDRDSTARVKGTSALYIHSWTHCEIHPSMIL 342

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +   I +  ++              
Sbjct: 343  G-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTSYQSRM----------- 382

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 383  ----------------DTLANILYYPQKLLATTRSMEYLRFRELPAGQNAIVAILCYSGY 426

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+ +R   +    +E   +   +  V L    
Sbjct: 427  NQEDSLIMNQSSIDRGLF-RSLFYRSYQDQEKR---LGMTVMESFDKPTRETTVRLKHGT 482

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L +   I  G           K+  L  D      R         ++ V   + S +
Sbjct: 483  YEKLEDDGLIAPGIRVSGDDIIIGKTAPLPDDTTELGQRV----VTHANKDVSTPLRSTE 538

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                    +                      L+ VKV +   R  Q GDK A RHG KG 
Sbjct: 539  TGIVDQVML----------------TTNQDGLKFVKVRIRSTRVPQMGDKFASRHGQKGT 582

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF ++G   D+++NP  +PSRM +G + E  L       G +  +     
Sbjct: 583  IGITYRTEDMPFSREGITPDLIINPHAIPSRMTIGHLVECLLSKLSTLTGSEGDATPFTD 642

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 IS   +                                                 
Sbjct: 643  VTVEAISEALAANGYQQRGFEVL------------------------------------- 665

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                       +G +    G         V  G  Y  +L HMV DK+++R+ G   ++T
Sbjct: 666  ----------YNGHT----GR---KLTAQVFFGPTYYQRLKHMVDDKIHSRARGPVQILT 708

Query: 1280 QQPLGGKSNRGGQRL 1294
            +QP+ G+S  GG R 
Sbjct: 709  RQPVEGRSRDGGLRF 723



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/328 (14%), Positives = 100/328 (30%), Gaps = 18/328 (5%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K+  +  G  ++  R    +      R          +     
Sbjct: 52  TAGLKYSLATGNWGDQSKFMQTRAGVSQVLNRYTFASTXSHLRRCNTPIGRDGKLAKPRQ 111

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    I         +   + + L     + +   E+ +   +  +D  +V   + + 
Sbjct: 112 LHNTHWGIVCPAETPEGQACGLVKNLSLMSHISIGVTEKKL---VELLDETAVENLEEVA 168

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +  A   F     +     + + L       R + +    +       E      + 
Sbjct: 169 PSSIAQATKVFINGRWVGIYSGNGHELYERYRVLRQTQVELVDITVVYDPREREVRTLSD 228

Query: 566 YGRICP---AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            GR+C       ++   +          RV+        +  + +  V   + Y+ A EE
Sbjct: 229 AGRVCRPLFVVRNQRILLNRGHISALHNRVDRGDGKPFDFNTLVNFGV---IDYMDAEEE 285

Query: 623 ENRYIAQANSSLDEDGSFTE-------ELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           E   I  ++  L +   F E       +            +        +  P  ++ I 
Sbjct: 286 ETAMICMSSEDLADSRMFYEHGYVNDQDRDSTARVKGTSALYIHSWTHCEIHPSMILGIC 345

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           AS+IPF +++ S R      M +QA+ +
Sbjct: 346 ASIIPFPDHNQSPRNTYQSAMGKQAMGI 373


>gi|109289335|gb|ABG29161.1| RNA polymerase II largest subunit [Asterotremella humicola]
          Length = 706

 Score =  298 bits (762), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 129/833 (15%), Positives = 247/833 (29%), Gaps = 148/833 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +   +             + I    + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRILFKKLTRDVYRHLQKCVETHKEFTLVNAIKPGIITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQAKAMQARAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +   Y +A  
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSYISVGSYSAPVMEFLEEWGLEDQTEYSNAPS 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D     + +     G ++      + D  +   +          P
Sbjct: 177  ATKVFVNGVWMGIHRDAVTLHQNLLSMRRGGQLKHEVSIVRDIRERELRLYTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQRQA----VPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIV 735
                ++   +++  +   +         KA    + TG+ E V A+     ++A     +
Sbjct: 237  LFIVNEDQTLMLQRSHIERIDELEEEEGKAWEEMLSTGIVEYVDAEEEETILIAMVQEDL 296

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E                                                           
Sbjct: 297  ENARKFHTREEVNRDHAAXXXXXXXXXXXXXXXXXXXXXXXTH---------------CE 341

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N       S R   +       +  +        
Sbjct: 342  IHPSMILG-------VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTN----- 383

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                +    +  +             +     S +   +  + A
Sbjct: 384  ------------------YQLRMDTMANILYYPQSPLATTQSMKYLKFSELPAGQNAIVA 425

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    ++ R   D  +     + E  E   RD+    
Sbjct: 426  ILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRAYTDTEKMVGMQKVEAFEKPNRDETLRM 484

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 + Y++    L G   ++         ++        P S+        E  QR+ 
Sbjct: 485  KHGPSDRYAK----LDGDGLITPATNVNGDDIIIGKTAPIPPGSE--------ELGQRSA 532

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K    T     E    +++      D +     + VK+ +   R  Q GDK A RHG
Sbjct: 533  THTKRDVSTPMKSTEQGVVDQVMITTNADGL-----KFVKIRIRSTRVPQIGDKFASRHG 587

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++    
Sbjct: 588  QKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLTGREGD-- 645

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP F    
Sbjct: 646  ---------------------------------------------------ATP-FTDLT 653

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             E+++ +LR       G  ++Y G TG+     V  G  Y  +L HMV DK+ 
Sbjct: 654  VESVSKLLRERGYQSRGLEVMYHGHTGKKLRAQVYFGPTYYQRLKHMVDDKIQ 706



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 87/604 (14%), Positives = 158/604 (26%), Gaps = 95/604 (15%)

Query: 376 DIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           D+YR + +  +        +        +        G      +         + + + 
Sbjct: 29  DVYRHLQKCVETHKEFTLVNAIKPGIITNGLKYSLATGNWGDQAKAMQARAGVSQVLNRY 88

Query: 435 DIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
              + +  L        R+GK       +  +  +    E  + Q    +  +       
Sbjct: 89  TFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSYIS 148

Query: 490 ISSVDI------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           + S         +    +D        SA   F     +    + V     +   RR   
Sbjct: 149 VGSYSAPVMEFLEEWGLEDQTEYSNAPSATKVFVNGVWMGIHRDAVTLHQNLLSMRRGGQ 208

Query: 544 L-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           L  +  + R     E+R    T  GR+C        +  L+   +   R++     E   
Sbjct: 209 LKHEVSIVRDIRERELR--LYTDAGRVCRPLFIVNEDQTLMLQRSHIERIDELEEEEGK- 265

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA------------ 650
               +   T  V Y+ A EEE   IA     L+    F       R              
Sbjct: 266 -AWEEMLSTGIVEYVDAEEEETILIAMVQEDLENARKFHTREEVNRDHAAXXXXXXXXXX 324

Query: 651 --GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                           +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 325 XXXXXXXXXXXXXTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNY 384

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                              +A      +   A    ++                  +KF 
Sbjct: 385 QL-------------RMDTMANILYYPQSPLATTQSMKY-----------------LKFS 414

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                       L   G   + + +I +  S D G                  + E  + 
Sbjct: 415 ELPAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLYY-------RAYTDTEKMVG 466

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           + +                  +    K   +E  R   +   +    +D  G+I     V
Sbjct: 467 MQK------------------VEAFEKPNRDETLRM-KHGPSDRYAKLDGDGLITPATNV 507

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           N  DI++GK  P       P  + L           RD S  + S   G V  V I    
Sbjct: 508 NGDDIIIGKTAPI-----PPGSEELGQRSATH--TKRDVSTPMKSTEQGVVDQVMITTNA 560

Query: 949 GIDK 952
              K
Sbjct: 561 DGLK 564


>gi|269856492|gb|ACZ51473.1| RNA polymerase beta subunit [Ensifer adhaerens]
          Length = 204

 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 158/204 (77%), Gaps = 1/204 (0%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD+PLMT +GTF++ G +R++VSQ+HRSPG+ FDHDKG++  SGKLL+A R+IP +G W+
Sbjct: 1   GDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKSHSSGKLLFAARVIPYRGSWL 60

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
           DIEFD+KDI+H RIDRRRK+PVTS LMALGMD EEIL TFY K +Y + G+ W  P    
Sbjct: 61  DIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGEEILDTFYTKSLYQRDGEGWRVPFQP- 119

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           D + G K  + +VD DTGE V+E+GKKLT  LL+ L+EKG+K L  T+D L G Y+AED+
Sbjct: 120 DALKGQKAITEMVDADTGEVVVEAGKKLTPRLLRQLQEKGLKALKATNDDLYGNYLAEDV 179

Query: 313 VNGETGEIYIEAGDVIDEKSLEEI 336
           VN  TGEIY+EAGD IDEK+L  I
Sbjct: 180 VNYSTGEIYLEAGDEIDEKTLPVI 203


>gi|291196482|emb|CBG27598.1| DNA-directed RNA polymerase beta-subunit [Pseudomonas viridiflava]
          Length = 305

 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 180/305 (59%), Positives = 233/305 (76%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG 
Sbjct: 1   GLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGF 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+
Sbjct: 61  EVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTDEIVF 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LSA+EE +  IA+A++++++     +ELV  R   E  +     +  +D SPKQVVS+AA
Sbjct: 121 LSAIEEADHVIARASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSVAA 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++
Sbjct: 181 SLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVID 240

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+AD
Sbjct: 241 SVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMAD 300

Query: 797 GPSTD 801
           GPSTD
Sbjct: 301 GPSTD 305


>gi|269308440|gb|ACZ34216.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5353]
 gi|269308458|gb|ACZ34225.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5382]
 gi|269308464|gb|ACZ34228.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5443]
 gi|269308470|gb|ACZ34231.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5405]
 gi|269308472|gb|ACZ34232.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5358]
 gi|269308476|gb|ACZ34234.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5861]
 gi|269308480|gb|ACZ34236.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5865]
 gi|269308484|gb|ACZ34238.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5853]
          Length = 339

 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 188/347 (54%), Positives = 255/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV + KV  +   YL+A +E+   +AQAN  + EDG+  ++ V  
Sbjct: 1   YAKINEYGFIETPYRKVKNKKVILDQYEYLTADKEKEYVVAQANIKIAEDGTIIDDQVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMVNSSDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLIDPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG AIVA   G+V+ VD+ RIV+           +G+  Y L  F
Sbjct: 121 SPVVGTGVEFEAARDSGDAIVATEGGVVKYVDSKRIVV--------EQKNGIKNYDLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+V++ DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 NRSNNGTAITHIPIVKVGDKVKKRDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK G EEITRDIPNVSE   KN+DE GI+ +G+E
Sbjct: 233 IVSERVVIDDRFTSIHIDEYTIERRQTKQGQEEITRDIPNVSEAIKKNLDEDGIVAIGSE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|322696543|gb|EFY88334.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Metarhizium
            acridum CQMa 102]
          Length = 1157

 Score =  297 bits (761), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 104/500 (20%), Positives = 172/500 (34%), Gaps = 95/500 (19%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   + +       ++F 
Sbjct: 732  YPQRPMVITKTIQLVHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASIDRGFGRCQVFR 791

Query: 947  RHGIDKNE----RSISVER--EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            ++  +  +    R   +     Q+      ++++   LD +          G    SG  
Sbjct: 792  KYTTELQKYPNGRRERIGDPVNQVNGGTTRREEKYEALDDD-----GLATVGYRVKSGEV 846

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              KK T L                          ++    +Y  S           I+K+
Sbjct: 847  MVKKETPLDLTT------------------TGIGLDRGPSEYRDSAISYRIPDPAYIDKV 888

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                        V+KV     R  + GDK + RHG KG+V  I+  EDMPF  +G   DI
Sbjct: 889  MI--SQTEKDTTVIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVDQEDMPFADNGLCPDI 946

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP G PSRM V        G     L  K   +                         
Sbjct: 947  IMNPHGFPSRMTV--------GKLLECLTGKASIIDGRPDYGFGD--------------- 983

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                          F     + ++ +L        G+     GL
Sbjct: 984  -----------------------------AFRSHPVKDMSQVLLDYGFSWEGKDYFTSGL 1014

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP +  +  G IY  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  
Sbjct: 1015 TGEPLEAYIFNGPIYYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERD 1074

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVV----------GRTRVYESIVAGN-DTFETGTPESFNV 1349
            C+ AYGA+ +L E L + SD V           G  + Y +         +   P +  +
Sbjct: 1075 CLIAYGASQLLLERLMLSSDGVTLDICQQCGLFG-YKGYCNTCKSTRQVTQMQMPYAAKL 1133

Query: 1350 LVKEMQALGLSIDLENSRTK 1369
            LV+E+ ++ + + L+     
Sbjct: 1134 LVQELISMNVGVRLQLEDEF 1153



 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 128/969 (13%), Positives = 269/969 (27%), Gaps = 197/969 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY+ F+   I    R N  ++         +       LEF     D P+   
Sbjct: 44  LVKQHIDSYNFFVEQEIKDIVRANRTIR---------SDVDSNFWLEFTDIRVDRPRRQD 94

Query: 86  ---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RD+TYA P+ + +  I          +  + I  +++ +G +P
Sbjct: 95  HNDAKSRSEVTPMECRLRDMTYAAPIVVDIAYI----------RDKQRIIRRNVPLGRMP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G FVI G +++++ Q   S          + 
Sbjct: 145 VMLKSSRCRLSGANNAQMEAMNECPLDPGGYFVINGTEKVILIQEQLSKNRVIVEADEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL- 221
           ++    + +               + K   +V + + R           +P+   L AL 
Sbjct: 205 NIISASVTSST------------HERKSKTYVTLKKDRIVMTHNVLVEGIPIVIILKALG 252

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+   EI+          +  D +      A          +L  I    ++        
Sbjct: 253 GLSDYEIMQLVAGSDG--RYQDEFVINFDEATRAGVFTQHQALEYIGARVKMGSRKAMFG 310

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             + ++  E+G+  L      L   +V  + ++     IY+ A          +      
Sbjct: 311 PQVRRNNVEEGLDALA----NLIIAHVPIEGLDFYPKAIYV-AMMTRRVLMASQDSKLVD 365

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
               +           +         +   +  + I + ++  + +    A  M +    
Sbjct: 366 DRDFVGNKRLELAGQLLSLLFEDLFKRFMGEVKMSIDKFLKKNNRAVPLDAVHMISNHAN 425

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDID 457
           +        +     +++        V H    +     + ++  +         +    
Sbjct: 426 NIGMGINRAIQTGNWSVKRFNMNRAGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPR 485

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            L   +   +      +     L ++        + ++D    +  I            F
Sbjct: 486 ALQPSQWGMLCPSDTPEGEACGL-VKNLALMTHITTNVDEAPVKRWIFTLDTGVEPIRNF 544

Query: 518 CSSQLSQ---LEEHVNSLSR-ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
             +++ +      HVN     +T   +  A     + R         ++   +       
Sbjct: 545 SGAEMHREGSWVIHVNGTPFALTRYPKRFASRFRAMRRRGWISPFVSINLNSHFNAVHIA 604

Query: 574 TSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T EG        V +     +      +        D      V YL   EE++  +   
Sbjct: 605 TDEGRICRPYIIVKNGKQKLKDEHLKLLHLGKVTFDDFLTRGIVEYLDVNEEQDALVTIY 664

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            + + +                           ++  P  ++   A LIPF  ++ S R 
Sbjct: 665 ENQITQS-----------------------TTHLEIEPFTLLGAVAGLIPFPHHNQSPRN 701

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+                                           I   + 
Sbjct: 702 TYQCAMGKQAIGA-----------------------------------------IAYNQF 720

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +   +     +Y               QRP+V          I           L  G+N
Sbjct: 721 NRIDTLLYTLVYP--------------QRPMV----------ITKTIQLVHYDKLPAGQN 756

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN--- 867
             V  M + GY+ ED++++++  +           ++    +    G  E   D  N   
Sbjct: 757 ATVVVMSYSGYDIEDALVLNKASIDRGFGRCQVFRKYTTELQKYPNGRRERIGDPVNQVN 816

Query: 868 ----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                 EE  + +D+ G+  VG  V  G+++V K TP   +        +    G     
Sbjct: 817 GGTTRREEKYEALDDDGLATVGYRVKSGEVMVKKETPLDLTT-----TGIGLDRGPSEYR 871

Query: 924 VRDTSLRVP 932
               S R+P
Sbjct: 872 DSAISYRIP 880


>gi|52694117|emb|CAG30588.1| DNA-directed RNA polymerase beta chain [Pseudomonas abietaniphila]
          Length = 322

 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 181/317 (57%), Positives = 232/317 (73%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           K         + MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KSVCRWQKAKACMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVK 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +G VT+++ +LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E +  +D 
Sbjct: 121 EGLVTDEIFFLSAIEEADHVIAQASATMNDKGHLIDELVAVRHLNEFTVKAPEDVTLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DDSNR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 181 SPKQVVSVAASLIPFLEHDDSNRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++P  +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 241 VVARRGGVIDSVDASRIVVRVADDEVEPGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 300

Query: 787 EVRRNDIIADGPSTDLG 803
            V+R+DI+AD      G
Sbjct: 301 RVQRSDIMADRSVHRHG 317


>gi|51035513|emb|CAH10892.1| RNA polymerase B subunit [Haloarcula aidinensis]
          Length = 435

 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 78/253 (30%), Positives = 113/253 (44%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 257  PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEELRGSLEEHG-------------- 302

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+  +Y G+TGE  D 
Sbjct: 303  -----------------------FD-----------------SSGKETMYSGVTGEKIDA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 323  EIFVGDIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMALKERLLDESD 395



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 71/182 (39%), Gaps = 13/182 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     D    +N +VA M + G+N ED++++++  V   +  S     +E   R 
Sbjct: 44  TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALARSHFFRTYEGEERR 103

Query: 854 TKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
              G E+   +IP+        EE   ++D+ G++    +V    +L+GK +P       
Sbjct: 104 YPGGQEDRF-EIPDDEVRGARGEEAYTHLDDDGLVNPETKVGENAVLLGKTSPPRFLEEP 162

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
                   + G      R+TS+ + SG SG V  V +       K  +    +    EL 
Sbjct: 163 ------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKVSVRDERIPELG 216

Query: 968 AR 969
            +
Sbjct: 217 DK 218


>gi|269912600|emb|CAY86080.1| RNA polymerase beta subunit [Gluconacetobacter oboediens]
          Length = 309

 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 148/311 (47%), Positives = 193/311 (62%), Gaps = 28/311 (9%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GM  +EILS FY K+ +++    W   
Sbjct: 61  VTTLLYALEGAESEAARAAKAAEGGDVESMEIQGMSPDEILSYFYGKVEFAKTEKGWARR 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             A D   G K+   L+D  TGE+V     KLT+ +++ + E   K + +    L G ++
Sbjct: 121 FDA-DAFRGMKLLEPLIDAQTGEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGLIGRFI 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A DIVN  TGEIY EAGD + E+ LEE+  + +  +  L VD+ N   +IRNTL  DKN 
Sbjct: 179 ASDIVNESTGEIYAEAGDELTEQKLEELEEAGLTTLSTLAVDAAN-GPWIRNTLAVDKNA 237

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R +AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D PD V
Sbjct: 238 SRDEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVDVPDTV 297

Query: 429 RHIRKEDIIAI 439
           R +RKEDI+  
Sbjct: 298 RVLRKEDILRT 308


>gi|156767137|gb|ABU95083.1| ribosomal polymerase B subunit [Acinetobacter gerneri]
          Length = 266

 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 115/270 (42%), Positives = 167/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS +L+S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSEELLSGLELVDLLEIQPSDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   GIAERLTQIQVFLKEKSHEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDINGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++ + +    I+ LR FL+K+    G   E +    D+ +L ++   + GVP++T
Sbjct: 180  EQIDKMLKEQRT---IAELRVFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  SGQ++LYD
Sbjct: 237  PVFDGAEEGQIKELLELAELPRSGQTVLYD 266


>gi|76556292|emb|CAJ00166.1| RNA polymerase beta subunit [Pseudomonas syringae pv. passiflorae]
          Length = 313

 Score =  297 bits (761), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 180/311 (57%), Positives = 236/311 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+N+RPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINKRPLVSKGDRV 301

Query: 789 RRNDIIADGPS 799
           +R+DI+ADGPS
Sbjct: 302 QRSDIMADGPS 312


>gi|268308299|gb|ACY95379.1| RNA polymerase beta subunit [Spiroplasma corruscae]
          Length = 339

 Score =  297 bits (761), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 186/347 (53%), Positives = 253/347 (72%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV + KV  +   YL+A  E+   +AQAN  + EDG+  ++ V  
Sbjct: 1   YAKINEYGFIETPYRKVKNKKVFLDQYEYLTADREKEYVVAQANIKMAEDGTILDDQVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMVNASDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLIDPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG AIVA  +G+V+ VD+ RIV+           +G+  Y L  F
Sbjct: 121 SPVVGTGVEFEAARDSGDAIVATESGVVKYVDSKRIVV--------EQKNGIKSYDLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+V+VGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 NRSNNGTAITHIPIVRVGDKIQERDILADGPSMENGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK G EEITRDIPNVSE   KN+D  GI+ +GAE
Sbjct: 233 IVSERVVIDDRFTSIHIDEYTIERRQTKQGQEEITRDIPNVSETVKKNLDADGIVAIGAE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|4867868|emb|CAB43076.1| RNA polymerase II [Neuburgia corynocarpum]
          Length = 258

 Score =  297 bits (761), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 75/255 (29%), Positives = 107/255 (41%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR+VKV V   R  Q GD+ + RHG KG V      EDMPF  +G   D+++NP 
Sbjct: 32   TNADGLRLVKVRVRSVRIPQIGDRFSSRHGQKGTVGMTYTQEDMPFTIEGITPDVIVNPH 91

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +      +GK+                                  
Sbjct: 92   AIPSRMTIGQLIECIMHKVAAQMGKEGD-------------------------------- 119

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     E I+  L        G   +Y+G TG P 
Sbjct: 120  ---------------------ATP-FTDVTVENISRALHKCSYQMRGFERMYNGHTGRPL 157

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S   G + GE E  C+ A+
Sbjct: 158  TATIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDDGLQFGERERDCMIAH 217

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA+ L+E L   SD
Sbjct: 218  GAAHFLKERLFDXSD 232


>gi|326432519|gb|EGD78089.1| RNA polymerase [Salpingoeca sp. ATCC 50818]
          Length = 1130

 Score =  297 bits (760), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 119/557 (21%), Positives = 200/557 (35%), Gaps = 92/557 (16%)

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV--NPGDILVGKITPKGESPMTPE 909
            R+     E++  DI     E  +N ++ GI     E+  +    +V   TP  +   +P 
Sbjct: 624  RELISSLEQVYLDIGVDIAECHRNHEKFGINYTHMEISKHGMLSVVSSFTPFSDFNQSPR 683

Query: 910  EKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
                         I  +      D  L V +     VV  R +N + +D      +    
Sbjct: 684  NMYQCQMGKQTMGIPSQAIPYRADNKLYVLNSGQTPVVHPRAYNEYNLDDYPLGNNAVVC 743

Query: 963  QIELLARDKDDEQVILD----------RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             I     D +D  +I            R + + +++++             +    +SD 
Sbjct: 744  VIAYTGYDMEDAMIINKGSIDRGFMHARVLKTEIVDLVDRSGVSKAFGLLPRHRAENSDF 803

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + +    +      + +     V+  +  +         R ++ +  +   D      ++
Sbjct: 804  LDDDGLPRVGIMVEKGDPFYAVVDEEQSNHIHRYKGEPARIES-VRLLLASDTSTKREVQ 862

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             + + V++ R    GDK A RHG KGI+S++LP EDMPF + G   DI+ NP G PSRM 
Sbjct: 863  RIAITVSVNRNPIIGDKFASRHGQKGILSQMLPSEDMPFTESGITPDIIFNPHGFPSRMT 922

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G A     +   S    +                                 
Sbjct: 923  IGMLIESMAGKAGCLHERFYDSTPFQFDE------------------------------- 951

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                               D    E     LR A  +  G   +Y G+TGE  +  V +G
Sbjct: 952  -------------------DDTAVEFFGEELRKAGYNYFGHERMYSGITGEELEVDVFIG 992

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             ++  +L HMVSDK   R+TG     T+QP+ G+   GG R GEME   + A+G A++LQ
Sbjct: 993  NVFYQRLRHMVSDKYQVRATGPVDSRTRQPIKGRKRHGGVRFGEMERDALIAHGTAFLLQ 1052

Query: 1313 EMLTIKSDD-------VVGRTRVYESIV---------------AGNDTFETGTPESFNVL 1350
            + L   SDD         G      SI                  +   +   P  F  L
Sbjct: 1053 DRLLRCSDDSEATVCKSCGGVLSTTSIAQSAASRIRKDVCLSCKDSKVVKVRLPYVFRYL 1112

Query: 1351 VKEMQALGLSIDLENSR 1367
              E+  + +++ L+ S 
Sbjct: 1113 GAELAGMNINMSLDVSE 1129



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/173 (15%), Positives = 47/173 (27%), Gaps = 58/173 (33%)

Query: 19  KNPEIIDIPDLIEV---QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE 75
           K  E + I DL ++      S++ F+  N+       E L+     V             
Sbjct: 16  KMKEKMQI-DLRDITRAHVESFNEFISHNLPLAV---EDLEPVMFDVN-----DQTVTTR 66

Query: 76  FVSYEFDPPK-----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            V      P                +C    ++Y   +  TL + +      T       
Sbjct: 67  IVGCSIGAPSLNSRVVSAQTDITPAECRQCHVSYKGNI--TLEIEINVNGHVTTVPR--- 121

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
                 Y+G  P+M                           G F+I G ++++
Sbjct: 122 ------YVGQAPIMVMSDKCILSKLTTAQKIAKQEEAREFGGYFIINGNEKVI 168


>gi|82594366|ref|XP_725394.1| DNA-directed RNA polymerase subunit beta [Plasmodium yoelii yoelii
            str. 17XNL]
 gi|23480386|gb|EAA16959.1| DNA-directed RNA polymerase, beta subunit [Plasmodium yoelii yoelii]
          Length = 1470

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 168/1118 (15%), Positives = 361/1118 (32%), Gaps = 72/1118 (6%)

Query: 230  STFYPKIVYSQRGD---FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
            S  Y KI    + +    +      +  +        + D    + + +     TS  + 
Sbjct: 313  SYIYNKIKLGIKNENAIKYIENYINSIFLKNDINEKEVFDKYNLKYLGKYAN--TSRTIF 370

Query: 287  SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
               +      G   + +    +     N E  E              +++  S+ + I  
Sbjct: 371  RYYDGNNYKKG--KNVVKYCVLPHLQSNSEKFETICLMF--------KQLVLSKFKLINT 420

Query: 347  LYVDSVNNNAY-----IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
            +  DS+  ++      + + ++ ++       +  +Y       +        +     +
Sbjct: 421  VNKDSLEYHSVTTCSGLLSNILKERILSCFYRMQMLYSRSLHRFLEKKYEGFKLNVKQIY 480

Query: 402  DSDKYD-LSTVGRVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
               K   L  +     N  L  +T   ++   +  E+   I K           +++ + 
Sbjct: 481  LRYKEMILHELSEDHFNQILLNNTDKLENNEELTSENDNMISKRDSTKNLRLMFMNEKEK 540

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L       + E+  +          R   E   +  + S     L     + S    +  
Sbjct: 541  LFTNVDGYLREIFSDS---------RLFIENTRTFGVASFAISYLFKTGNISSDYIHYQQ 591

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             S    L + +N+L  +T+ R   A+ +G   +    +  R +    +G ICP  T +G 
Sbjct: 592  KSGWVILADEINNLRLLTNFR---AIHRGSFFQDVKVLSPRKLLGESWGFICPVHTPDGS 648

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GL++ L+ +  ++     E     +    +    + ++  E    +    N ++    
Sbjct: 649  PCGLLNHLSQYCCIHNVASNEPHKFNIK-MYLKKIGINVNLDETSGIHTVYENQTIP--- 704

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                + V      E     +  +  +  +    +    S    + + +   ++    +  
Sbjct: 705  -IIVDSVPITYISENDF--KRTVYKLKYAKNHNLYNLKSHFEIIAHLNEQSLMDSITIHT 761

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD------- 751
                +++         +E +         +A     + + +  R +++  E         
Sbjct: 762  CTGRIIRPILNLKMKCIEFISPGYQPYVSIAVNYDDILKNNLARKILKKKENMVNLNSIN 821

Query: 752  ------LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                            Y   K     +    N+  +V+  ++ +  +++ +       + 
Sbjct: 822  NTKNTKKMTLKEQYHFYTNKKHNIEKEAENYNESEIVRKKNKNKILNMLENKKQYQFNED 881

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                +             +D+M         D   +++I+ +E + +  +    + T  +
Sbjct: 882  EYISSSDYETSSESDKYSDDNM---SSTTYIDSDENLNIDIYEQIPQKFEYMELKQTSFL 938

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
              ++       D         +       +G  +       T +   +        V   
Sbjct: 939  SFLAS-LTPFSDHNQSPRNIYQCQMLKQTMGIQSLNMFYTFTNKIYRIITPQFPLVVTRD 997

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD-EQVILDRNIYS 984
                 V +  SGT   V I    G D  +  I      I   + D+      I    +  
Sbjct: 998  YEFYGVDNFPSGTNAVVAILAYTGYDMEDALI------INKASSDRGMFRTHIYKTEVID 1051

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
               +      A+     +  +++ + +   EY      +  +     +    +    Y  
Sbjct: 1052 LYKKTNSPDFALGNNVRYTINSLPTKNNPREYKGRFLNKDGLPCINQKILENNPLYSYIN 1111

Query: 1045 SKSIL--EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             K+ L   + FK   +             +V  + +   RP   GDK A RHG KG+VSR
Sbjct: 1112 KKNELTTYEVFKTHGDYYVDCVSNSQSNNQVAIIRLRTTRPPLVGDKFASRHGQKGVVSR 1171

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            + P EDMPF + G   D++ NP G+PSRM +G + E+  G A    GK+I +        
Sbjct: 1172 LFPHEDMPFSESGIVPDVIFNPHGIPSRMTIGMLIESICGKAASIYGKRIDATPFRKYTK 1231

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                              + +  +  +  + ++ + +       +T +      +    +
Sbjct: 1232 QKSFNNPWIDGCGAKGFLNKQDENADEKKTTIKSSTENSD----TTEISYDEKIDFFAKL 1287

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L     D  G  +LY G+ G P    +  G IY  +L HM  DK   R TG    +T QP
Sbjct: 1288 LLNKGYDYYGTELLYSGIYGVPLQAHIFFGVIYYQRLRHMAYDKAQVRRTGPVCHLTHQP 1347

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            L GK   GG RLGEME   + ++G ++++ E   + SD
Sbjct: 1348 LKGKKKHGGIRLGEMERDGLISHGCSFIINERFLMNSD 1385


>gi|156767133|gb|ABU95081.1| ribosomal polymerase B subunit [Acinetobacter bouvetii]
          Length = 266

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 113/270 (41%), Positives = 165/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS +++S    +   +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGGGTT-KRGDKLSEEVLSGLELADLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   GIAERLTQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI  ++   K    +  LR FL+K+    G   E +    DD +L ++   ++GVP++T
Sbjct: 180  DKIDKMM---KEQRTVLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +  +  +GQ++LYD
Sbjct: 237  PVFDGAEESQIKELLELGGISRTGQTVLYD 266


>gi|318603140|emb|CBJ04603.1| RNA polymerase beta subunit [Pseudomonas sp. R-39396]
          Length = 297

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 174/297 (58%), Positives = 226/297 (76%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYG
Sbjct: 1   PVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  I
Sbjct: 61  RVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVI 120

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 AQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 180

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R 
Sbjct: 181 NRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRV 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD+G+
Sbjct: 241 ADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTDMGE 297


>gi|322710723|gb|EFZ02297.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Metarhizium
            anisopliae ARSEF 23]
          Length = 1157

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 102/495 (20%), Positives = 167/495 (33%), Gaps = 85/495 (17%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   + +       ++F 
Sbjct: 732  YPQRPMVITKTIQLVHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASIDRGFGRCQVFR 791

Query: 947  RHGIDKNERSISV-EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            ++  +  +      ER    +   +    +  +             G    SG    KK 
Sbjct: 792  KYTTELQKYPNGRRERIGDPVNQVNGGTTRREVKYEALDDDGLATVGYRVKSGEVMVKKE 851

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            T L                          ++    +Y  S           I+K+     
Sbjct: 852  TPLDLTT------------------TGIGLDRGPSEYRDSAISYRIPDPAYIDKVMI--S 891

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   V+KV     R  + GDK + RHG KG+V  I+  EDMPF  +G   DI++NP 
Sbjct: 892  QTEKDTTVIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVDQEDMPFADNGLCPDIIMNPH 951

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM V        G     L  K   +                              
Sbjct: 952  GFPSRMTV--------GKLLECLTGKASIIDGRPDYGFGD-------------------- 983

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                     F     + ++ +L        G+     GLTGEP 
Sbjct: 984  ------------------------AFRSHPVKDMSQVLLDYGFSWEGKDYFTSGLTGEPL 1019

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  +  G IY  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AY
Sbjct: 1020 EAYIFNGPIYYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAY 1079

Query: 1306 GAAYVLQEMLTIKSDDVV----------GRTRVYESIVAGN-DTFETGTPESFNVLVKEM 1354
            GA+ +L E L + SD V           G  + Y +         +   P +  +LV+E+
Sbjct: 1080 GASQLLLERLMLSSDGVTLDICQQCGLFG-YKGYCNTCKSTRQVTQMQMPYAAKLLVQEL 1138

Query: 1355 QALGLSIDLENSRTK 1369
             ++ + + L+     
Sbjct: 1139 ISMNVGVRLQLEDEF 1153



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 129/969 (13%), Positives = 268/969 (27%), Gaps = 197/969 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY+ F+   I    R N  ++         +       LEF     D P+   
Sbjct: 44  LVKQHIDSYNFFVEQEIKDIVRANRTIR---------SDVDSNFWLEFTDIRVDRPRRQD 94

Query: 86  ---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RD+TYA P+ + +  I          +  + I  +++ +G +P
Sbjct: 95  HNDAKSRTEVTPMECRLRDMTYAAPIVVDIAYI----------RDKQRIIRRNVPLGRMP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G FVI G +++++ Q   S          + 
Sbjct: 145 VMLKSSRCRLSGANNAQMEAMNECPLDPGGYFVINGTEKVILIQEQLSKNRVIVEADEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL- 221
           ++    + +               + K   +V + + R           +P+   L AL 
Sbjct: 205 NIISASVTSST------------HERKSKTYVTLKKDRIVMTHNVLVEGIPIVIILKALG 252

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+   EI+          +  D +      A          +L  I    ++        
Sbjct: 253 GLSDYEIMQLVAGSDG--RYQDEFVINFDEATRAGVFTQHQALEYIGARVKMGSRKAMFG 310

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
             + ++  E+G+  L      L   +V  + ++     IY+ A          +      
Sbjct: 311 PQVRRNNVEEGLDALA----NLIIAHVPIEGLDFYPKAIYV-AMMTRRVLMASQDSKLVD 365

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
               +           +         +   +  + I + ++  + +    A  M +    
Sbjct: 366 DRDFVGNKRLELAGQLLSLLFEDLFKRFMGEVKMSIDKFLKKNNRAVPLDAVHMISNHAN 425

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDID 457
           +        +     +++        V H    +     + ++  +         +    
Sbjct: 426 NIGMGINRAIQTGNWSVKRFNMNRAGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPR 485

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            L   +   +      +     L ++        + ++D    +  I            F
Sbjct: 486 ALQPSQWGMLCPSDTPEGEACGL-VKNLALMTHITTNVDEAPVKRWIFTLDTGVEPIRNF 544

Query: 518 CSSQLSQ---LEEHVNSLSR-ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
             +++ +      HVN     +T   +  A     + R         ++   +       
Sbjct: 545 SGAEMHREGSWVIHVNGTPFALTRYPKRFASRFRTMRRRGWISPFVSINLNSHFNAVHIA 604

Query: 574 TSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           T EG        V +     R      +        D      V YL   EE++  I   
Sbjct: 605 TDEGRICRPYIIVKNGKQKLRHEHLKLLHLGKVTFDDFLTKGIVEYLDVNEEQDALITLY 664

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            + + +                           ++  P  ++   A LIPF  ++ S R 
Sbjct: 665 ENQITQS-----------------------TTHLEIEPFTLLGAVAGLIPFPHHNQSPRN 701

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              C M +QA+                                           I   + 
Sbjct: 702 TYQCAMGKQAIGA-----------------------------------------IAYNQF 720

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +   +     +Y               QRP+V          I           L  G+N
Sbjct: 721 NRIDTLLYTLVYP--------------QRPMV----------ITKTIQLVHYDKLPAGQN 756

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN--- 867
             V  M + GY+ ED++++++  +           ++    +    G  E   D  N   
Sbjct: 757 ATVVVMSYSGYDIEDALVLNKASIDRGFGRCQVFRKYTTELQKYPNGRRERIGDPVNQVN 816

Query: 868 ----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                 E   + +D+ G+  VG  V  G+++V K TP   +        +    G     
Sbjct: 817 GGTTRREVKYEALDDDGLATVGYRVKSGEVMVKKETPLDLTT-----TGIGLDRGPSEYR 871

Query: 924 VRDTSLRVP 932
               S R+P
Sbjct: 872 DSAISYRIP 880


>gi|209395027|gb|ACI45317.1| RNA polymerase subunit B [uncultured Verminephrobacter sp.]
          Length = 234

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 98/188 (52%), Positives = 125/188 (66%), Gaps = 13/188 (6%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQ+ E HLGWA  G+G++I  ++   +     S LR FLEKV      T
Sbjct: 1    NPLGVPSRMNIGQVLEVHLGWAGKGIGQRIGDML---QQQVKASELRKFLEKVYNARGRT 57

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD----ESG------ 1232
            E ++   D+ +  +A     GVP +TPVFDGA EE I  ML++A  D      G      
Sbjct: 58   EDLAQLSDEELRVMATHLTQGVPYATPVFDGASEEEIKDMLKIAYPDDVAGRKGLTATRT 117

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            Q+ LYDG TGE F+RP T+G+++ LKL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQ
Sbjct: 118  QAFLYDGRTGERFERPTTIGHMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQ 177

Query: 1293 RLGEMEVW 1300
            R GEMEVW
Sbjct: 178  RFGEMEVW 185


>gi|328853924|gb|EGG03059.1| hypothetical protein MELLADRAFT_49581 [Melampsora larici-populina
            98AG31]
          Length = 1135

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 101/505 (20%), Positives = 174/505 (34%), Gaps = 97/505 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +    +   +    I   G   +   +    A+      D+ D  +   + +   
Sbjct: 709  DTLLYLMVYPHHPMVRTKTIELVGYDKLPAGQNATVAVMSYSGYDIEDALILNKASLDRG 768

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++F R      +R  +   ++I        D     D  I  +      G  A  G
Sbjct: 769  FGRCQVF-RKATAMIKRYPNGTYDRIA-------DPPRDTDGQILEKWKPCDEGGVADVG 820

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
             K F  +  ++               +  ++       +    +  +         + I+
Sbjct: 821  MKVFSGNVYVNKQ-----------TPSNANDNSVAGGAATVTAWNNTPMTYRGTIPSYID 869

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+   D        +VKV +   R  + GDK + RHG KG+   I+  EDMPF   G+  
Sbjct: 870  KVLVTD--TESDQTLVKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFNDHGSCP 927

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI+         MN                                              
Sbjct: 928  DII---------MN--------------------------------------------PH 934

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
            G  +        + +   A   +  V   T  F G+    ++ +L        G+  L  
Sbjct: 935  GFPSRMTVGKMLELLSGKAGVLRGTVEYGT-AFGGSKAVEMSKILIEHGYSYLGKDYLTS 993

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TG+  +  V +G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME
Sbjct: 994  GITGQALEHYVFMGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEME 1053

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVG------------RTRVYESIVAGNDTFETG 1342
              C+ A+GA+ +L E L I SD    DV              R +       G    +  
Sbjct: 1054 RDCLIAHGASQLLLERLMISSDAFELDVCQDCGFMGYSGWCVRCK------NGKSVTKIT 1107

Query: 1343 TPESFNVLVKEMQALGLSIDLENSR 1367
             P +  +L +E+ A+ ++  L    
Sbjct: 1108 IPYACKLLFQELMAMNIAPRLVLEN 1132



 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 114/944 (12%), Positives = 264/944 (27%), Gaps = 200/944 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + +    R N         V P         L ++      P    
Sbjct: 34  LVKQHIDSFNYFVDVELKAILRANA---TVVSDVDP------NFHLTYLDINVGEPCRLD 84

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  +    +C  RD+TY+ P+ +T++            K  K +  + I +G +P+
Sbjct: 85  TGSATNKRITPHECRLRDITYSAPISVTIQYT----------KGNKRVLSKGIPIGRMPI 134

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR- 171
           M                           G FV+KG +++++ Q   S   I  + D  + 
Sbjct: 135 MLRSNKCVLTNKSDAELAKMTECPLDPGGYFVVKGTEKVILVQEQLSKNRILIETDSRKG 194

Query: 172 ---------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMAL 221
                            Y                     ++++ +  + ++PV   L A 
Sbjct: 195 TIMASVTSSTHERKSKTYVVT--------------KNSKVYLKHNSIQEEIPVVIALKAY 240

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID----TGEQVIES 276
           G+ S+ E++          +     C        +   K +   +           ++  
Sbjct: 241 GITSDNEVVQLVCGNNDDYRSTFSICIEQCHEAGIYTQKQALEYIGKSVKVMKKGPMVTV 300

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
            + L+   L+ L    +    + ++ +     A  +       I   A    + K +++ 
Sbjct: 301 KRPLSEEALEVLSTVVLAH--VPAENMNLQPKALYLAVMARRVIQAMA----NPKLVDDR 354

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            +   + + +           +         K   D  ++I ++++  + +T   A + F
Sbjct: 355 DYVGNKRLEL-------AGQLLSLLFEDLFKKFNTDLKMNIDKILKKPNRTTEFDAINQF 407

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGT 452
                      +  +     +++        + H    +     + ++  +         
Sbjct: 408 RMHGDHISHGFIRAISTGNWSIKRFKMERAGITHVLSRLSYISALGMMTRISSQFEKTRK 467

Query: 453 IDDIDNLGNRRVR--SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           +     L   +       +  + +    +  +           +         I  + + 
Sbjct: 468 VSGPRALQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDVDEEPIWNVAYTIGCEDIS 527

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           S         +   +  + N L       R   +      RA    E   ++     +  
Sbjct: 528 SVTGTELYLPRHYIVFINGNILGLSRSPERFVKVF-RQFRRAGQVSEFVSIYMNSDQQTV 586

Query: 571 PAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              T  G     +  +         +    ++       D      + YL   EE + +I
Sbjct: 587 NIATDGGRICRPMIIVDHGVPRVTSSHIQLLKENKMCFDDFLTAGLIEYLDCNEENDSFI 646

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +D+                           ++  P  ++   A LIP+  ++ S
Sbjct: 647 ALYEEDVDQ-----------------------FTTHLEIEPFTLLGAVAGLIPYPHHNQS 683

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R    C M +QA+                                           I  
Sbjct: 684 PRNTYQCAMGKQAIGA-----------------------------------------IAY 702

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +     +   + +Y      R+                                  L  
Sbjct: 703 NQLHRIDTLLYLMVYPHHPMVRTK------------------------TIELVGYDKLPA 738

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N  VA M + GY+ ED++++++  +           +   M +    G  +   D P 
Sbjct: 739 GQNATVAVMSYSGYDIEDALILNKASLDRGFGRCQVFRKATAMIKRYPNGTYDRIADPPR 798

Query: 868 VSEEGL----KNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            ++  +    K  DE G+  VG +V  G++ V K TP   +  +
Sbjct: 799 DTDGQILEKWKPCDEGGVADVGMKVFSGNVYVNKQTPSNANDNS 842


>gi|156767167|gb|ABU95098.1| ribosomal polymerase B subunit [Acinetobacter tjernbergiae]
          Length = 266

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 167/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS+D++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLTGQESNGG-GSTKRGDKLSADVLSGLELVDLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI+ ++   K    +  LR FL+K+    G   E++    D  VL ++   ++GVP++T
Sbjct: 180  DKIEKML---KEQRTVIELREFLDKIYNKVGGEQEELDSLTDAEVLALSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 237  PVFDGAEESQIKDLLELADISRTGQTVLFD 266


>gi|302412759|ref|XP_003004212.1| DNA-directed RNA polymerase III subunit RPC2 [Verticillium albo-atrum
            VaMs.102]
 gi|261356788|gb|EEY19216.1| DNA-directed RNA polymerase III subunit RPC2 [Verticillium albo-atrum
            VaMs.102]
          Length = 1105

 Score =  297 bits (760), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 84/320 (26%), Positives = 127/320 (39%), Gaps = 66/320 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  V+KV     R  + GDK + RHG KG+V  I+  ED+PF   G   DI++NP G
Sbjct: 840  SEKDNMVIKVQTRQTRRPELGDKFSSRHGQKGVVGIIVEQEDLPFSDKGLVPDIIMNPHG 899

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V        G     L  K   L                               
Sbjct: 900  FPSRMTV--------GKLLECLTGKASVLDGRPDYGFGD--------------------- 930

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     + ++  L        G+     G+TGEP +
Sbjct: 931  -----------------------AFRSHPLKQMSEALVDHGFSWEGKDYFTSGITGEPLE 967

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  +L HMV DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 968  AYIFNGPIYYQRLKHMVQDKMHSRARGPRAILTRQPTEGRSREGGLRLGEMERDCLIAYG 1027

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVLVKEM 1354
            A+ +L E L I SD    D+  +  ++     G         +  +   P +  +LV+E+
Sbjct: 1028 ASQLLLERLMISSDGTEIDICQQCGLFGY--KGYCHTCRSTKEVTKMTMPYAAKLLVQEL 1085

Query: 1355 QALGLSIDLENSRTKNSAKM 1374
             ++ + + L+        K 
Sbjct: 1086 ISMNVGVRLQMEDEFPHPKE 1105



 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 107/856 (12%), Positives = 234/856 (27%), Gaps = 180/856 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY+ F+   I    R N  ++         +  + +  LEF     + P    
Sbjct: 44  LVKQHIDSYNFFVDHEIKDIVRANRTIR---------SDVNSSFWLEFTDIRVESPSRLD 94

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TY  P+ + +  I          +    I  +++ +G LP
Sbjct: 95  FNDARAHSEVTPMECRLRDMTYGAPIFVDIAYI----------RDKSKIVRRNVPLGRLP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 145 VMLKSAKCRLNGASNKEMALMNECPLDPGGYFIINGTEKVILIQEQLSKNRVIVEADEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV--------PVTSFLMAL-GM 223
           ++    + +             E  +K  I ++ DR   V        P+   L AL G+
Sbjct: 205 NIITASVTSST----------HERKTKTNITLKKDRISLVHNVLVEPAPIVIVLKALGGL 254

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
              EI+          Q      F  +    +   + +   +        ++ G +    
Sbjct: 255 SDLEIMQLVAGDDGRYQDEFTVNFDEATKQGVYTQQQALEWIGSR-----VKMGGRGRFQ 309

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                ++  ++        L   ++  + ++     IY+ A         +         
Sbjct: 310 PNSQARKNNIEEGMDALSNLIIAHIPVEGLDFYPKAIYV-AFMTRRVLMAQANMSLVDDR 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
             +           +         K   D    I +V++  + +    A +M +    + 
Sbjct: 369 DFVGNKRLELAGQLLSLLFEDLFKKFCGDVKASIDKVLKKDNRAVAMDAVTMISNHANNI 428

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +     +      ++        V H    +     + ++  +         +     L
Sbjct: 429 GQGINRAIQTGNWTVKRFNMNRAGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPRAL 488

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS----VMPQDLINAKPVVSAVCE 515
              +   +      +     L    ++   I++   +      +     N +P+ +    
Sbjct: 489 QPSQWGMLCPSDTPEGEACGLVKNLALMTHITTNAEEEPVKRWVFTVDDNVEPIRNFSGS 548

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                    +  +    +     +R +   +  + R         VH  ++       T 
Sbjct: 549 EMHREGSYIIHINGTPFALTKFPKRFTNRFRT-MRRRGWISPFVGVHINNHFNAVHIATD 607

Query: 576 EGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           EG        V +     +      ++       D      V YL   EE +  +A   +
Sbjct: 608 EGRICRPYIIVKNGKPKLKAEHLKLLQLGKATFDDFLTNGVVEYLDVNEENDTLVALYET 667

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +++                           ++  P  ++   A LIPF  ++ S R   
Sbjct: 668 DVNQS-----------------------TTHMEIEPFTILGAVAGLIPFPHHNQSPRNTY 704

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+                                           I   + + 
Sbjct: 705 QCAMGKQAIGA-----------------------------------------IAYNQFNR 723

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             +     +Y               QRP+V          I           L  G+N  
Sbjct: 724 IDTLLYTLVYP--------------QRPMV----------ISKTIQLIHYDKLPAGQNAT 759

Query: 813 VAFMPWHGYNFEDSML 828
           V  M + GY+ ED++L
Sbjct: 760 VVVMSYSGYDIEDALL 775


>gi|156767163|gb|ABU95096.1| ribosomal polymerase B subunit [Acinetobacter schindleri]
          Length = 266

 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 114/270 (42%), Positives = 162/270 (60%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S             DE
Sbjct: 1    DLKEEYKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLDIQPVDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSLEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI  ++ + +    +  LR FL+K+    G   E +    DD +L ++   + GVP++T
Sbjct: 180  DKIDKMLQEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +  +  +GQ++LYD
Sbjct: 237  PVFDGAEESQIKELLELGGISRTGQTVLYD 266


>gi|261885865|ref|ZP_06009904.1| DNA-directed RNA polymerase subunit beta [Campylobacter fetus subsp.
            venerealis str. Azul-94]
          Length = 147

 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 78/147 (53%), Positives = 105/147 (71%)

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
            MA +D  G++ LYDG TG      V VG +YMLKL+H+V +KV+ARSTG YSLVTQQP+G
Sbjct: 1    MAKIDMDGKTELYDGRTGSKMAERVNVGCMYMLKLHHLVDEKVHARSTGPYSLVTQQPVG 60

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTP 1344
            GK+  GGQR GEMEVW ++AYGAA+ L+EMLT+KSDDV GR   Y+++  G +   TG P
Sbjct: 61   GKALSGGQRFGEMEVWALEAYGAAHTLREMLTVKSDDVEGRLAAYKALTRGENVPSTGIP 120

Query: 1345 ESFNVLVKEMQALGLSIDLENSRTKNS 1371
            E+F VL  E+++L L +++ +    N 
Sbjct: 121  ETFFVLTNELKSLALDVEIYDEEENNE 147


>gi|125843259|ref|XP_690811.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 isoform 2
            [Danio rerio]
 gi|122891099|emb|CAM12989.1| novel protein similar to vertebrate polymerase (RNA) III (DNA
            directed) polypeptide B (POLR3B) [Danio rerio]
          Length = 1130

 Score =  296 bits (759), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 97/498 (19%), Positives = 170/498 (34%), Gaps = 84/498 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 707  YLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 766

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++         R  +   +++     D +  + I   +I         G+   +     
Sbjct: 767  LVYKNAKCTL-RRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLV 825

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                    V    ++ + +  + QY       +    + IEK+  
Sbjct: 826  NKSMP-----------------TVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI 868

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       +VK+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI+ 
Sbjct: 869  SSNAEDAF--LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDII- 925

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                              G  +
Sbjct: 926  --------MN--------------------------------------------PHGYPS 933

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                    + +   A          T  F G+  + +   L     +  G+  +  G+TG
Sbjct: 934  RMTVGKLIELLAGKAGVLDGRFHYGT-AFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITG 992

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 993  EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1052

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYE-----SIVAGN-DTFETGTPESFNVLVK 1352
              YGA+ +L E L I SD    DV G+  +            +        P +  +L +
Sbjct: 1053 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQ 1112

Query: 1353 EMQALGLSIDLENSRTKN 1370
            E+Q++ +   L+ +R   
Sbjct: 1113 ELQSMNIIPRLKLARYNE 1130



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 130/952 (13%), Positives = 275/952 (28%), Gaps = 200/952 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE +          +       L++++     P    
Sbjct: 37  LVKQHIDSFNYFINVEIKKIMKANEKIT---------SDADPMWYLKYLNIYVGMPDVEE 87

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 88  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 137

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG +++++ Q   S       D+ R   
Sbjct: 138 LRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIV-DQDRKGT 196

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR---KV-------PVTSFLMALGMD 224
            G  + +               + K   ++ + + R   K        P+     A+G++
Sbjct: 197 VGASVTSST------------HEKKSRTNMIVKQGRFYLKHNTLSEDAPIAIIFKAMGVE 244

Query: 225 SE-EILSTFYPKI--------VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
           S+ EI+     +            +      F  + A   +G KV    +     +  +E
Sbjct: 245 SDQEIVQMIGTEEHVMAAFAPSLEECQKAQIFTQTQALRYIGNKVRRQRMWGGPKKTKME 304

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
             ++L +  +  L    VK     + C+  L V    V    G+  ++  D    K LE 
Sbjct: 305 EARELLASTI--LTHVPVKEFNFRAKCIY-LAVMVRRVILAQGDNKVDDRDYYGNKRLEL 361

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                      L+    +    I + ++  +      A  D+ + MR   ++   V    
Sbjct: 362 AGQLLSLLFEDLFKKFNSELKKIADQIIPKQR----AAQFDVVKHMRQDQITNGMVNA-- 415

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +   +   ++ +   G  ++  RL+  +   +            K+             
Sbjct: 416 ISTGNWSLKRFKMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQ------ 469

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                   +    +  + +    +  +           D   +     +  + V     E
Sbjct: 470 ---PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIIKLAFNLGVEDVNLLCGE 526

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                 +  +  + N L  I   ++L    +  + RA    E   +      R     + 
Sbjct: 527 ELSYPTVFLVFLNGNILGVIRDHQKLVYTFRL-MRRAGFINEFVSISTNLTDRCVYISSD 585

Query: 576 EGHNIGL--VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            G       +      A  N     +   YR   D    + V YL   EE +  IA    
Sbjct: 586 GGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIAL--- 642

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                                  +  +    ++  P  ++ + A LIP+  ++ S R   
Sbjct: 643 --------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 682

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +         G        +   ++A                       
Sbjct: 683 QCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----------------------- 710

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    QRP+VK                 D   L  G+N  
Sbjct: 711 -----------------------YPQRPMVK----------TKTIELIDFEKLPAGQNAT 737

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGPEEITRDIPNVSEE 871
           VA M + GY+ ED++++++  +       +  +  +   R  T    +++   + +    
Sbjct: 738 VAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETR 797

Query: 872 GLKN----IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                   +D  GI   G +V    +LV K  P                   
Sbjct: 798 KPIWRHSILDADGICSPGEKVENKQVLVNKSMPTVTQTPLEGSAQPGQPQYR 849


>gi|260594187|gb|ACX46388.1| RNA polymerase beta subunit [Pantoea sp. 484/07]
          Length = 303

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 182/302 (60%), Positives = 231/302 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANAQLDENGGFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPV 301

Query: 789 RR 790
            R
Sbjct: 302 ER 303


>gi|254991739|ref|ZP_05273929.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL J2-064]
          Length = 173

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 73/191 (38%), Positives = 114/191 (59%), Gaps = 22/191 (11%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++K+Q ++MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  + 
Sbjct: 106 TGEVKDQEVFMGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFG 162

Query: 182 CRIIPDQGLWM 192
             +IP++G W+
Sbjct: 163 STVIPNRGAWL 173


>gi|242392294|dbj|BAH80340.1| RNA polymerase subunit B' [Halobaculum gomorrense]
          Length = 609

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 101/317 (31%), Positives = 140/317 (44%), Gaps = 72/317 (22%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 346  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEDGLVPDLVLNPHAL 405

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V        G     LG K+ SL                                
Sbjct: 406  PSRMTV--------GHVLEMLGGKVGSLEGRRVDGT------------------------ 433

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   F G +EE + S L       SG+ ++Y G+TGE  + 
Sbjct: 434  ----------------------AFQGENEEELRSSLEEHGYKSSGKEVMYSGVTGEKIEA 471

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 472  EIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGA 531

Query: 1308 AYVLQEMLTIKSD----------------DVVGRTRVYESIV-AGNDTFETGTPESFNVL 1350
            A  L+E L   SD                DV  R R+Y+ I    +D  E     +F +L
Sbjct: 532  AMALKERLLDSSDKESVYISEETGMVAVEDVEQR-RIYDPITGDEDDIHEIEISYAFKLL 590

Query: 1351 VKEMQALGLSIDLENSR 1367
            + EM+ALG+   LE   
Sbjct: 591  LDEMKALGIRPTLELED 607



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 54/359 (15%), Positives = 117/359 (32%), Gaps = 30/359 (8%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  +      ++   R  G+   +    +               +  P +  ++   +L
Sbjct: 18  GTHPDPNQLAAQIREARRRGDVSDMVNVSVKDRTDEVIVNADAGRARRPLIVVENGEPLL 77

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               ++      ++ E       +E + A+      VA      E V++    +      
Sbjct: 78  DDETIEALEAGEIEFEDLVDHGIVEFIDAEEEEDIYVA---TDEEDVNSRTTHLEIDPQL 134

Query: 752 LDPSTSGVDIYRLM-----------KFQRSNQNTCVNQR--PLVKVGDEVRRNDIIADGP 798
           +    +G+  Y                ++S      N R  P  +          +    
Sbjct: 135 IFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRIRPDTRQHLLHYPQLSMVKTQ 194

Query: 799 STD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           +T+     +    +N +VA M + G+N ED++++++  V   +  S     +E   R   
Sbjct: 195 TTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMQRSHFFRTYEGEERRYP 254

Query: 856 LGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
            G E+              E+   ++DE G++    +V+   +L+GK +P          
Sbjct: 255 GGQEDRFEVPSQDVRGARGEDAYTHLDEDGLVNPETKVDENSVLLGKTSPPRFLEEP--- 311

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                + G      R+TS+ + SG SG V  V +       K  +    +    EL  +
Sbjct: 312 ---DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 367



 Score = 43.9 bits (102), Expect = 0.18,   Method: Composition-based stats.
 Identities = 23/113 (20%), Positives = 44/113 (38%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E    +  D      V ++ A EEE+ Y+A     ++                      
Sbjct: 85  LEAGEIEFEDLVDHGIVEFIDAEEEEDIYVATDEEDVN---------------------- 122

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +   ++  P+ +  I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 123 -SRTTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPSANYRI 174


>gi|156767157|gb|ABU95093.1| ribosomal polymerase B subunit [Acinetobacter parvus DSM 16617]
          Length = 266

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 114/270 (42%), Positives = 167/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS++++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKGQESNGG-GSTKRGDKLSAEVLSGLELVDLLEIQPNDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI+ ++   K    +  LR FL+K+    G   E++    D  +L ++   ++GVP++T
Sbjct: 180  DKIEKML---KEQRTVIELREFLDKIYNKVGGEQEELDSLTDAEILALSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 237  PVFDGAEESQIKDLLELADISRTGQTVLFD 266


>gi|121699292|ref|XP_001267972.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus clavatus NRRL 1]
 gi|119396114|gb|EAW06546.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus clavatus NRRL 1]
          Length = 1234

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 97/480 (20%), Positives = 165/480 (34%), Gaps = 69/480 (14%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E    +I ++        D         +       +G      +     +   L+ 
Sbjct: 696  THIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIQYRTDNKLYRLQT 755

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-------------SVERE 962
                        +  + +  +GT   V I +  G D ++  I             ++ + 
Sbjct: 756  GQTPIVRPPLYNAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGHGTIYKT 815

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQ 1020
            +I  L  D  D +    R   ++L     G    +       +         + E     
Sbjct: 816  KIHSL--DDKDSRRSKSRREITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLVA 873

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W     D      V    + +       E+ + + I  +     + P     VK    +
Sbjct: 874  AWHTVRYDASSDSYVNVDGITHFVKYKDAEEGYIDSIRIMGAETGLEPCQALSVKY--RV 931

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+ 
Sbjct: 932  PRKPIIGDKFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESM 991

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +      +                                  
Sbjct: 992  AGKAGALHGHPQDSTPFQFSEENTAA---------------------------------- 1017

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     LR A  +  G   LY G+TG+ F   + +G ++  +L 
Sbjct: 1018 ----------------DYFGQQLRKAGYNYYGNEPLYSGITGKEFAADIFIGVVHYQRLR 1061

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1062 HMVNDKFQVRTTGPVNPLTAQPVKGRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1121



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 64/405 (15%), Positives = 129/405 (31%), Gaps = 44/405 (10%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +S  + + E +N    I+H R    + +G          +R + P  +G  CP  T +G 
Sbjct: 493 TSGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFFCPVHTPDGA 549

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL---- 634
             GL++ L     ++      +   K+    V   V   S++  E     Q +  +    
Sbjct: 550 PCGLLNHLAHKCFISTSDVNVSQLPKLL---VQLGVRSESSVSLEESVTVQLDGRIIGYC 606

Query: 635 -DEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASP------KQVVSIAASLIPFLENDD 686
             +      + V          +PRE +I ++  S         + S AA +   ++   
Sbjct: 607 SPKQARQIADTVRHWKVQGTNNIPRELEIGYVPNSNGGQYPGVYMFSQAARMYRPVKYLP 666

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            +++      ++  + +       V    T +E                    Q      
Sbjct: 667 LDKLDYVGPFEQPFMEIACLPDDLVAGVSTHIEFTPTNILSIVANMTPFSDYNQSPRNMY 726

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +  +  +    + +      K  R        Q P+V+               +  L 
Sbjct: 727 QCQMSKQTMGTPGTAIQYRTDNKLYRLQTG----QTPIVRP----------PLYNAYGLD 772

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +   G N +VA + + GY+ +D+M+I++             +       D      +  R
Sbjct: 773 NFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGHGTIYKTKIHSLDDKDSRRSKSRR 832

Query: 864 DIPNV---------SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           +I  +           E    +DE G+  VGA V  G ++    T
Sbjct: 833 EITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLVAAWHT 877



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 104/668 (15%), Positives = 195/668 (29%), Gaps = 107/668 (16%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +   R  TY   L+  L   V + D       ++ I+E    +G +P+M +       
Sbjct: 125 PSEARERHATYRGKLRARLEYQVNNGD------WMESIRE----LGQVPIMLRTNRCHLE 174

Query: 141 -----------------DGTFVIKGIQRIV---V-------SQLHRSPGIHFDHDKGRAS 173
                             G F++ G ++++   V         + R+  +   H   +  
Sbjct: 175 KATPEELVQHKEESEELGGYFIVNGNEKLIRMLVVGKRNFPMAIVRNSFVRRGHTYTKY- 233

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    +  R   R+    VP    L AL +++ +
Sbjct: 234 --GIQIRSVR--PDQTSQTNVLHYLSDGN--VTFRFSWRKSEYLVPAMMILKAL-VETND 286

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
                +  IV S                        L+    G  +              
Sbjct: 287 --REIFEGIVGSASSKGVSNTFVTDR-------VELLLRTYKGYNLHSRSSCRAY----- 332

Query: 288 LKEKGVKFLGITSD---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           L EK    LG+ +D      G      +V    G   +      D+  L      ++  +
Sbjct: 333 LGEKFKPVLGVPADMSNEDAGTEFLRKVVLPHLGNQNVTGTQDYDKFKLVMFMIRKLYAL 392

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS--TFSVAESMFNFLFFD 402
                   N +A     ++             +   +R        +S   S   F    
Sbjct: 393 VAGDCAPDNPDAVSNQEILLGGFLYGMILKERLEEWVRSFGPILRDWSNRNSGAKFTDPA 452

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            ++  LS V R                    E+I   ++  +   N   +   +D     
Sbjct: 453 FERDFLSRVVRR-----------------TNENIGGALEYFLSTGN-LVSPTGLDLQQTS 494

Query: 463 RVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
               + E +     +   RM    S   ++ +  +  ++P+      PV +         
Sbjct: 495 GYTVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFFCPVHTP---DGAPC 551

Query: 521 QLSQLEEHVNSLSR--ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE-- 576
            L     H   +S   +  ++    L Q GV    +      V     GRI    + +  
Sbjct: 552 GLLNHLAHKCFISTSDVNVSQLPKLLVQLGVRSESSVSLEESVTVQLDGRIIGYCSPKQA 611

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLD 635
                 V         N    +E  Y    +G     V   S A              LD
Sbjct: 612 RQIADTVRHWKVQGTNNIPRELEIGYVPNSNGGQYPGVYMFSQAARMYRPVKYLPLDKLD 671

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             G F +  +   C  ++++        I+ +P  ++SI A++ PF + + S R +  C 
Sbjct: 672 YVGPFEQPFMEIACLPDDLVAGVS--THIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQ 729

Query: 696 MQRQAVPL 703
           M +Q +  
Sbjct: 730 MSKQTMGT 737


>gi|242392288|dbj|BAH80381.1| RNA polymerase subunit B' [Halosimplex carlsbadense 2-9-1]
          Length = 609

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 113/607 (18%), Positives = 200/607 (32%), Gaps = 107/607 (17%)

Query: 786  DEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            + V   DI    + +    +  D     ++ VA            + +  +++       
Sbjct: 83   EAVTDGDIEFEELVERGYIEFIDAEEEEDIYVAVNEEELNEDHTHLEVDPQLMFGIGAGM 142

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R T      + +    +     +   +     +        +        
Sbjct: 143  IPYPEHNASPRITMGSG--MIKQSLGLPSANYRIRPDTR-QHLLHYPQLSLVKTQTTEQI 199

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     V    +    F R    +  R    + 
Sbjct: 200  GYDDRPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRG-LSRSHFFRTYEGEERRYPGGQE 258

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            +  E+   +       +           L     V+      ++ VL           + 
Sbjct: 259  DHFEIPDDE-------VRGARGEEAYTHLDEDGLVNPETHVGENDVLLGKTSPPRFLEEP 311

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E+         + +               ++ KV V  +
Sbjct: 312  DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLSKVSVRDE 359

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  I P EDMPF + G   D+++NP  +PSRM VG I E   
Sbjct: 360  RIPELGDKFASRHGQKGVVGHIAPQEDMPFTEQGVVPDLIINPHALPSRMTVGHILEMIG 419

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G      G+++       +   ++                                    
Sbjct: 420  GKVGSLEGRRVDGTAFTGEDEDELRG---------------------------------- 445

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           E    M    ++  SG       +TGE  +  + +G I+  KL H
Sbjct: 446  -------------SLEDHGFMSSGKEIMYSG-------ITGEQIEAEIFLGTIFYQKLYH 485

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E L  +SD 
Sbjct: 486  MVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKERLLDESDR 545

Query: 1321 ---DVVG-----------RTRVY------ESIVAGNDTFETGTPESFNVLVKEMQALGLS 1360
               +V G           + RVY      E      +  E     +F +L+ EM+ALG++
Sbjct: 546  EFINVCGECGMTAVENVEQRRVYCPNCDEE-----TEIHEVEMSYAFKLLLDEMKALGIA 600

Query: 1361 IDLENSR 1367
              +E   
Sbjct: 601  PRIELED 607



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 76/460 (16%), Positives = 136/460 (29%), Gaps = 109/460 (23%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +    +      +I   RR   + +      +       V+        P    
Sbjct: 11  YVNGSLVGTHPDPHQLADQIRQARRRGDVSEMVNVSVKNRTREVIVNADAGRARRPLLVI 70

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     ++S     A  +     E    +         + ++ A EEE+ Y+A     L+
Sbjct: 71  EDGE-PIISDEEVEAVTDGDIEFEELVER-------GYIEFIDAEEEEDIYVAVNEEELN 122

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 123 EDH-----------------------THLEVDPQLMFGIGAGMIPYPEHNASPRITMG-- 157

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
                                      SG    +                          
Sbjct: 158 ---------------------------SGMIKQSLGLPSANY------------------ 172

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    ++           Q  LVK                    D    +N +VA 
Sbjct: 173 --------RIRPDTRQHLLHYPQLSLVK----------TQTTEQIGYDDRPAAQNFVVAV 214

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VS 869
           M + G+N ED++++++  V   +  S     +E   R    G E+   +IP+        
Sbjct: 215 MSYEGFNIEDALVMNKGSVDRGLSRSHFFRTYEGEERRYPGGQED-HFEIPDDEVRGARG 273

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           EE   ++DE G++     V   D+L+GK +P               + G      R+TS+
Sbjct: 274 EEAYTHLDEDGLVNPETHVGENDVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSV 327

Query: 930 RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + SG SG V  V +       K  +    +    EL  +
Sbjct: 328 TMRSGESGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDK 367


>gi|38677886|emb|CAE30283.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 164

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 68/186 (36%), Positives = 114/186 (61%), Gaps = 22/186 (11%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           +MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYET 158

Query: 197 DSKDII 202
           D+KD++
Sbjct: 159 DAKDVV 164


>gi|83415497|gb|ABC17956.1| RNA polymerase II second largest subunit [Rozella allomycis]
          Length = 697

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 130/851 (15%), Positives = 245/851 (28%), Gaps = 173/851 (20%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              + +  + + +     +
Sbjct: 2    KRMDLAGPLLAGLFRMLFRKLTKDVGKYLQKCIDSNRDFNLTLAVKSNTITNGLRYSIAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR++      + R     + R +H +H+
Sbjct: 62   GNWGDQKKAMESRAGVSQVLNRYTYASTLSHLRRVNT----PIGRDGKLAKPRQLHNSHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY--RKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+  + ++            K+   +   ++   S      
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMSYISVGTSPAPIIDALKIYQMEYLAEISPSSIGNLTK 177

Query: 625  RYIAQANSSLDED-GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             ++      +  D      +L   R             D  +   + +        P   
Sbjct: 178  IFMNGNWIGVHSDPKRLVNDLKKFRRECAISFETSVVFDVREKEVRILTDAGRCCRPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             ++    L    + +     +        TG        +G           E +D    
Sbjct: 238  VENQTIQLKEDQLSQLQQRDI--------TGFGWQNLLENGVV---------EYLDVEEE 280

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +      +I                        D   +       PS  LG
Sbjct: 281  ETSMICMTPEDLLEAKNIT-----------------------DFPTKYTHCEIHPSMILG 317

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +     I       R   L       
Sbjct: 318  -------ICASIIPFPDHNQSPRNTYQSAMGKQAMG----INSTNFQRRMDTLNNILFYP 366

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
              P V+   ++ +                             +   +  + AI      +
Sbjct: 367  QKPLVTTRSMEYL-------------------------HFRELPAGQNAIVAIACYSGYN 401

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I  +   D+ ++  +++ E+                 +  
Sbjct: 402  QEDSVIMNQSAIDRGLF-RSICYKTYTDEEKKVGTLQVEEFMKPTFTTTVRMRHGTYDKL 460

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 +  G           K+  +  D                DE  QR     +    
Sbjct: 461  EDDGLVAPGIKISGEDIIIGKTVPIPDD---------------SDELGQRTSTHTRRDAS 505

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
            T     E    +++      D       R VK+ V+  R  Q GDK A RHG KG V   
Sbjct: 506  TPLKSNEHGIIDQVMISTNAD-----GYRFVKIRVSSVRVPQMGDKFASRHGQKGTVGIT 560

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  LG      G +  +         
Sbjct: 561  YRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLGKVSAITGDEGDATPFTDVTVE 620

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             IS     L+    +                                             
Sbjct: 621  SISETL--LKCGYQSRGFEVL--------------------------------------- 639

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                   +G S    G      +  + +G  Y  +L HMV DK++AR+ G   ++T+QP+
Sbjct: 640  ------YNGHS----GR---KLNAQIFIGPTYYQRLKHMVDDKIHARARGPVQILTRQPV 686

Query: 1284 GGKSNRGGQRL 1294
             G+S  GG R 
Sbjct: 687  EGRSRDGGLRF 697


>gi|327302082|ref|XP_003235733.1| DNA-directed RNA polymerase I [Trichophyton rubrum CBS 118892]
 gi|326461075|gb|EGD86528.1| DNA-directed RNA polymerase I [Trichophyton rubrum CBS 118892]
          Length = 1243

 Score =  296 bits (758), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 109/522 (20%), Positives = 187/522 (35%), Gaps = 60/522 (11%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  + + +  + + G   +  M I+          S HI EF+     + L      
Sbjct: 656  RMYRPVKYLPLDKLDYVGSFEQPYMEIACVASDIRNGVSTHI-EFDPTHILSILANMTPF 714

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
             D         +   + G   +G      D        + ++  TP  +  L  A   + 
Sbjct: 715  SDFNQSPRNMYQC--QMGKQAMGTPGTAIDYRTDNKLYRLQTGQTPVVRPPLYNAYGLDN 772

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  I N+   ++     ++ + +I  L  DK+       +
Sbjct: 773  FPNGMNAVVAVISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIYALD-DKESRGRGKSK 831

Query: 981  NIYSRLMEILCGQNAVSGPK--GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L     G    +  K    +         +SE      W     D      +   
Sbjct: 832  RAITKLFGFAPGGLVKAEWKAQLDEDGLPHIGAKVSEGSLVGAWHTVQYDPATDTYINVD 891

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  +       E+ F + +  +  G +    V + V +   + R    GDK + RHG KG
Sbjct: 892  KQTHFLKYKDGEEGFIDSVRVL--GSETGNEVCQAVSIKYRVPRRPVIGDKFSSRHGQKG 949

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++S++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    
Sbjct: 950  VLSQLWPATDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGSLHGLPQDSTPFQ 1009

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                   F G     
Sbjct: 1010 FSEEATAGD-------------------------------------------FFG----- 1021

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L+ A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +
Sbjct: 1022 --KQLQKAGYNFHGNEPMYSGITGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAL 1079

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1080 TGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 100/764 (13%), Positives = 200/764 (26%), Gaps = 156/764 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--------------------- 68
           I     S++                L+AA K +  I +F                     
Sbjct: 39  IRPHIDSFNALFEDTKV--------LEAALKDIG-IKSFIDGSSGTPEEKASRREDGRRA 89

Query: 69  --SGAAMLEFVSYEFDP---P---KFD-------VDDCLWRDLTYAVPLKITLRLIVFDV 113
                  +       +    P   K+          +C  R  TY   L+  L   + + 
Sbjct: 90  PKRNKLSVRITELFLEKAVLPASNKYSTRNREIYPAECRERHATYRGKLRARLEYRINNG 149

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLM-----------TKD-------------GTFVIKGI 149
           +     +           +G +P+M           T               G F++ G 
Sbjct: 150 EWKESVRE----------LGQVPIMIRSNRCHLEKATPSQLVDHKEESEELGGYFIVNGN 199

Query: 150 QRIVVSQLH--RS--PGIH---FDHDKGRASLSGKLLYACRIIPDQGLW---MDIEFDSK 199
           ++++   +   R+   GI    F       +  G  L + R  PDQ      +    D  
Sbjct: 200 EKLIRMLIVGKRNFPTGIIRNSFQKRGSAYTKFGVQLRSVR--PDQTSQTNVLHYLNDGN 257

Query: 200 DIIHVRIDRRRK---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLM 255
             +  R   R+    VPV   L AL   ++ EI      +   S   +          L+
Sbjct: 258 --VTFRFSWRKNEYLVPVMMILKALIETNDREIFERLVGREG-SLGIENTFITDRVELLL 314

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK----GVKFLGITSDCLCGLYVAED 311
              K   +         +    + +      + +E      ++ + +    L    V E 
Sbjct: 315 RTYKAYGAHSRSRCRAYLGSKFRFVLGMPEDTPEEDVGTEFLRKIVLPH--LGNQNVTET 372

Query: 312 IVNGETGEIYIEAGDVID-------EKSLEEIFHSEIRDIPILY----VDSVNNNAYIRN 360
             N +   I      + +         + + + + E+     LY     + +        
Sbjct: 373 QDNDKFNMILFMIRKLYNLVAGDCAPDNPDAVSNQEVLLGGYLYGMLLKERLEEWLKSVG 432

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            +V D     +DA     +   P     F                    + G +     L
Sbjct: 433 PMVRDWRMRNQDA-----KFTDPKFEREFLTKIIGRTNENIGGAMEYFLSTGNLVSPTGL 487

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGL 479
           +L  P           +A         +    I         +  +V ++L   +  L  
Sbjct: 488 DLQQPSGYTV------MAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCP 541

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +         + +      +          +  V      +  S      +   ++    
Sbjct: 542 VHTPDGSPCGLLNHLAHKCLISTSNLDVSGIPGVLAELGVTSESSCSIEESIPVQLDGK- 600

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
               LG     ++R   +   +                      S+   +  V  +    
Sbjct: 601 ---ILGYCTPKQSRTIADT--LRYWKVQGHKKIPVELEIGYVPSSNGGQYPGVYMFSEAA 655

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
             YR V      + + Y+ + E+    IA   S +    S                    
Sbjct: 656 RMYRPVK-YLPLDKLDYVGSFEQPYMEIACVASDIRNGVS-------------------- 694

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               I+  P  ++SI A++ PF + + S R +  C M +QA+  
Sbjct: 695 --THIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGT 736


>gi|83763769|emb|CAJ00218.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio
            alginolyticus]
          Length = 333

 Score =  296 bits (757), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 177/346 (51%), Positives = 246/346 (71%), Gaps = 13/346 (3%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AKR G+++ VDA RIV++  E +L P  +G+DIY L K+ RSNQNTC+NQRP V  G+ V
Sbjct: 1    AKRGGVIQSVDASRIVVKVNEEELVPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGEPV 60

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SER+V ED FT+IHI+E  
Sbjct: 61   SRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELT 120

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TP
Sbjct: 121  CVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTP 180

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++K++R++ +E+ Q++   
Sbjct: 181  EEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKEAK 240

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D  +E  IL+  + +R+  +L                  S   +    R +W +  ++D
Sbjct: 241  KDLTEEFQILEGGLLNRVKAVLIEGG-------------YSEAKLDTTDRKKWLELTLED 287

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
            + +Q  +E L  Q++  K+  + +F+ K  KI  GDD+ PGVL++V
Sbjct: 288  DALQTQLEQLAEQWDELKADFDKKFETKRRKITQGDDLAPGVLKIV 333


>gi|57337356|emb|CAH69686.1| RNA polymerase, beta subunit [Enterobacter cloacae]
          Length = 293

 Score =  296 bits (757), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 180/292 (61%), Positives = 223/292 (76%)

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+
Sbjct: 1   SAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRV 60

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQ
Sbjct: 61  CPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQ 120

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           ANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR
Sbjct: 121 ANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANR 180

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA RIVI+  E
Sbjct: 181 ALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNE 240

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTD
Sbjct: 241 DEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTD 292


>gi|13929088|ref|NP_113961.1| DNA-directed RNA polymerase I subunit RPA2 [Rattus norvegicus]
 gi|3914801|sp|O54888|RPA2_RAT RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2; AltName: Full=A127; AltName:
            Full=RPA135
 gi|2739048|gb|AAB94600.1| RNA polymerase I 127 kDa subunit [Rattus norvegicus]
          Length = 1135

 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 90/327 (27%), Positives = 130/327 (39%), Gaps = 76/327 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +D   G  + V V V + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ N
Sbjct: 857  NDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFN 916

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P G PSRM +G + E+  G +    G    +    +                        
Sbjct: 917  PHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY--------------- 961

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                  ML+ A  +  G   LY G++G 
Sbjct: 962  -----------------------------------FGEMLKAAGYNFYGTERLYSGISGM 986

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + 
Sbjct: 987  ELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALL 1046

Query: 1304 AYGAAYVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--ND 1337
            A+G +++L + L   SD     V    G                 R R Y   V G  + 
Sbjct: 1047 AHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTVCGRSDS 1106

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLE 1364
                  P  F   V E+ A+ + + L+
Sbjct: 1107 IDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 87/672 (12%), Positives = 198/672 (29%), Gaps = 88/672 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ +N++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFKNSVSQMLRIVMEEGCHTQKQVL--------DYL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y  +       N  + +         +   +  + + L  L  G+  
Sbjct: 305 GERFRVKLSLPDWYPNAEAAEFLFNQCICIH--LKSNTDKFYLLCLMTRKLFALARGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V + G++           + L +        ++ +    +  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRAQKTNVSINNENLMKIFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GTELTRPFEYLLATGNLRSKTGLGFMQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 +R + P  +G +CP  T +G   GL++ LT+   V            V     T
Sbjct: 480 KMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEV------------VTKFVYT 527

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQ 670
             +  L          A       +      + V       E      + +       ++
Sbjct: 528 ASIPALLCGLGVTPVDAAPCRPYSDCYPVLLDGVMVGWVDKELAPEVADTLRRFKVLRER 587

Query: 671 VVSIAASLIPFLENDDSNRV--------LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             S      P   +  +  V         +            +  A +            
Sbjct: 588 RCSSLDGGGPDSHDRKAKPVPRAVPLHHSLQAGEACAEPGAGQRRARWNYGAALHEHCHL 647

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN----- 777
            G                   VI +     D + S  ++Y+    +++     +      
Sbjct: 648 RGRGFWWSFHTPGALPSQPAEVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 707

Query: 778 ----------QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                     Q PLV+          + D    D     +G N +VA + + GY+ ED+M
Sbjct: 708 DNKLYRLQTPQSPLVRP--------CMYDHYDMDN--YPIGTNAIVAVISYTGYDMEDAM 757

Query: 828 LISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++++          S++  EF  ++   K G + +   +       ++ +D  G+  +GA
Sbjct: 758 IVNKASWERGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGA 817

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRI 944
           ++  GD   G +     +  T E  ++     E     +++  S    SG    V     
Sbjct: 818 KLEFGDPYYGYL-----NLNTGEGFVVYYKSKENCVVDNIKVCSNDTGSGKFKCVCVTVR 872

Query: 945 FNRHGIDKNERS 956
             R+    ++ +
Sbjct: 873 VPRNPTIGDKFA 884



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 49/163 (30%), Gaps = 57/163 (34%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK 85
           DL      S+++             EGL  A +++ P           L  V     PP 
Sbjct: 37  DLTRAHVDSFNY----------AVLEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPA 86

Query: 86  -----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  R  TY   L   +   V  V         K I +Q  ++G 
Sbjct: 87  VPKGTICKELNIYPAECRGRRSTYRGKLTADISWAVNGVP--------KGIIKQ--FLGX 136

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV 153
           +P+M K                         G F+I GI++++
Sbjct: 137 VPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVI 179


>gi|269912660|emb|CAY86110.1| RNA polymerase beta subunit [Neoasaia chiangmaiensis]
          Length = 287

 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 127/290 (43%), Positives = 175/290 (60%), Gaps = 28/290 (9%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EIL  FY ++ +++   
Sbjct: 61  KRKLPVTTLLYALEGENSIAARAAKAEEGGDVDAMPIRGMDQDEILGYFYNEVPFTRMPK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+   L D DTGE V E+  KLT+  ++ + E   + + +    L
Sbjct: 121 GWARPFDPE-AFRGLKLLEPLYDADTGEVVAEADAKLTARAVRKIAE-NTRVVLVGRADL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G +VA D+VN  TGEIY EAG+ + E  L  +  + + ++P+L VD   +  +IRNTL 
Sbjct: 179 LGRFVAHDLVNEHTGEIYAEAGEELTEARLAALEDAGVTELPMLSVDGQ-HGPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
            DKN  R DAL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS VGR
Sbjct: 238 VDKNMSRDDALVDIYRIMRPGEPPTPETAEAMFRGLFFDPDRYDLSAVGR 287


>gi|156767135|gb|ABU95082.1| ribosomal polymerase B subunit [Acinetobacter calcoaceticus DSM
            30006]
          Length = 266

 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 113/270 (41%), Positives = 165/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   L   ++S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERVIRLLNGQESNGG-GSTKRGDKLVDGMLSGLELVDLLEIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLSQIQVFLKEKSAEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI+ ++ + +    +  LR FL+K+    G   E +    D  VL ++   ++GVP++T
Sbjct: 180  DKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 237  PVFDGAEESQIKDLLELADISRTGQTVLFD 266


>gi|156767159|gb|ABU95094.1| ribosomal polymerase B subunit [Acinetobacter radioresistens DSM
            6976]
 gi|156767161|gb|ABU95095.1| ribosomal polymerase B subunit [Acinetobacter radioresistens]
          Length = 266

 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 117/270 (43%), Positives = 166/270 (61%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L  Q +  G    K+   LS +L+S        +    DE
Sbjct: 1    DLKEEYKIFEEAARERIVRLLKDQVSNGG-GNTKRGEKLSEELLSGLELIDLLEIQPSDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   AIAERLTQIQVFLKEKSTEIDEKFAEKKRKLSTGDELTHGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS+ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSQILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   K    I  LR FL+K+    G   E++    DD +L++A     GVP++T
Sbjct: 180  EQIDKML---KQQRAIVELRDFLDKIYNKVGGEQEQLDTLTDDEILKLAGNLSKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  SGQ IL+D
Sbjct: 237  PVFDGAEEGQIKELLELAELPRSGQQILFD 266


>gi|159124281|gb|EDP49399.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus fumigatus A1163]
          Length = 1235

 Score =  295 bits (756), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 108/532 (20%), Positives = 173/532 (32%), Gaps = 101/532 (18%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            D +  G ST +         +VA M P+  YN     +   +M  + + T     E+   
Sbjct: 688  DDLVAGVSTHIEYTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIEY--- 744

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R         T   P V                                 G        
Sbjct: 745  -RTDNKLYRLQTGQTPIVRPPLYN-------------------------AYGLDNFPNGT 778

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      D+ D  +   S                        ++ + +I  L  D
Sbjct: 779  NAVVAIISYTGYDMDDAMIINKSSHERGFG---------------YGTIYKTKIHSL--D 821

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              D +    R   ++L     G    +       +         + E      W     D
Sbjct: 822  DKDSRRSKSRREITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLIAAWHTVRYD 881

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                  V    + +       E+ + + I  +     + P     VK  +   R    GD
Sbjct: 882  AASDSYVNVDGITHFVKYKDAEEGYIDSIRIMGAETGLEPCQALSVKYRI--PRKPVIGD 939

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+  G A    
Sbjct: 940  KFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESMAGKAGALH 999

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G    S    +      +                                          
Sbjct: 1000 GHPQDSTPFQFSEENTAA------------------------------------------ 1017

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +     LR A  +  G   LY G+TG+ F   + +G ++  +L HMV+DK  
Sbjct: 1018 --------DYFGQQLRKAGYNYYGNEPLYSGITGKEFAADIFIGVVHYQRLRHMVNDKFQ 1069

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1070 VRTTGPVNQLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1121



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 125/871 (14%), Positives = 254/871 (29%), Gaps = 177/871 (20%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +   R  TY   L+  L   V + D       ++ I+E    +G +P+M +       
Sbjct: 125 PSEARERHATYRGKLRARLEYQVNNGD------WMESIRE----LGQVPIMLRTNRCHLE 174

Query: 141 -----------------DGTFVIKGIQRIV---V-------SQLHRSPGIHFDHDKGRAS 173
                             G F++ G ++++   V         + RS  +   H   +  
Sbjct: 175 KATPQELVQHKEESEELGGYFIVNGNEKLIRMLVVGKRNFPMAIVRSSFVRRGHTYTKF- 233

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    +  R   R+    +PV   + AL +++ +
Sbjct: 234 --GIQIRSVR--PDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLIPVMMIMKAL-VETND 286

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
                +  IV S              + +  +               ++    T    ++
Sbjct: 287 --REIFEGIVGSATSKGVNNTFVTDRVELLLR-------------TYKAYNLHTRSSCRA 331

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
              +  K +         L V  D+ N + G  ++    +    +       +     ++
Sbjct: 332 YLGEKFKPV---------LGVPADMSNEDAGTEFLRKIVLPHLGNQNVTEIQDYDKFKLI 382

Query: 348 YVDSVNNNAYIRNTLVTDK--NKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDS 403
                   A +      D       ++ LL   +Y ++    +  +              
Sbjct: 383 MFMIRKLYALVAGDCAPDNPDAVSNQEILLGGFLYGMILKEQLEEWM------RSFGPIL 436

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +     G    +     D    +     E+I   ++  +   N   +   +D      
Sbjct: 437 RDWSNRNGGAKFTDPAFERDFLSKIVKRTNENIGGKLEYFLSTGN-LVSPTGLDLQQVSG 495

Query: 464 VRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SS 520
              + E +     +   RM    S   ++ +  +  ++P+      PV +         +
Sbjct: 496 YTVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGLLN 555

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE--GH 578
            L+       S   ++H  +   L Q GV    +      V     GRI    + +    
Sbjct: 556 HLAHKCLIATSDVNVSHLPK--LLVQLGVRSESSVALEDSVTVQLDGRIVGYCSPKQARM 613

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLDED 637
               V         N    +E  Y    +G     +   S A              LD  
Sbjct: 614 IADTVRHWKVSGTHNIPRELEIGYVPNSNGGQYPGIYMFSQAARMYRPVKYLPLDKLDYV 673

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G F +  +   C  ++++        I+ +P  ++SI A++ PF + + S R +  C M 
Sbjct: 674 GPFEQPFMEIACLPDDLVAGVS--THIEYTPTNILSIVANMTPFSDYNQSPRNMYQCQMS 731

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +Q +          GT +E                                +  L    +
Sbjct: 732 KQTMGTP-------GTAIEYR-----------------------------TDNKLYRLQT 755

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           G                   Q P+V+               +  L +   G N +VA + 
Sbjct: 756 G-------------------QTPIVRP----------PLYNAYGLDNFPNGTNAVVAIIS 786

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV--------- 868
           + GY+ +D+M+I++             +       D      +  R+I  +         
Sbjct: 787 YTGYDMDDAMIINKSSHERGFGYGTIYKTKIHSLDDKDSRRSKSRREITKLFGFAPGGEI 846

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             E    +DE G+  VGA V  G ++    T
Sbjct: 847 RAEWRTTLDEDGLPHVGARVKEGSLIAAWHT 877


>gi|268323371|emb|CBH36959.1| DNA-directed RNA polymerase subunit B [uncultured archaeon]
          Length = 1131

 Score =  295 bits (755), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 126/324 (38%), Gaps = 84/324 (25%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 R++KV V  ++  + GDK A RHG KG++  I   EDMPF + G   D+++NP  
Sbjct: 867  SSSNRRLIKVAVRDQKIPEVGDKFASRHGQKGVIGLIARPEDMPFTEGGIIPDMIINPHA 926

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM VG + E   G      G+ I       +   D+                     
Sbjct: 927  IPSRMTVGHVLEMIGGKVGALEGRYIDGSAFSGEKEVDLRDALVRAG------------- 973

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     E +   L+                 G   D
Sbjct: 974  ------------------------FSDTGREMMWDGLK-----------------GTKID 992

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V VG +Y  KL H+VS K++AR+ G   ++T+QP  GK+  GG R GEME   +  YG
Sbjct: 993  ADVFVGVVYYQKLYHLVSAKMHARARGPVQILTRQPTEGKAREGGLRFGEMERDVLIGYG 1052

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------------DTFETGT 1343
            AA  L++ L  +SD VV        +V GN                       D +    
Sbjct: 1053 AAITLKDRLLNESDRVV-------ELVCGNCGMIACRDMKTGSSYCPNCGADTDIYPVEM 1105

Query: 1344 PESFNVLVKEMQALGLSIDLENSR 1367
              +F +L+ EM+ALG++  LE   
Sbjct: 1106 SYAFKLLLDEMKALGIAPRLELEE 1129



 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 108/656 (16%), Positives = 231/656 (35%), Gaps = 90/656 (13%)

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              +  +      +I     D      Y+   +       +++A+  + R + P     +
Sbjct: 248 MTLIRALGLESDEEIIKAVSDDPQIVKYVLENIEECDVDTQEEAIEKLGRKIAPTQAREY 307

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
                    + +  D+Y L  +               D +  +   I  + +   +L  G
Sbjct: 308 RE-----RRVNYILDRYFLPHL---------------DTKIAKAYFIGRMAESCYELYLG 347

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD------- 502
           K    D D+  N+R++  G+++++ +R+   ++ R ++ ++   ++ S   +        
Sbjct: 348 KRGEGDKDHYANKRLKLAGDLVEDLFRVSFTKLTRDMRYQLERANMRSRELKIATAIRSD 407

Query: 503 --LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
                    ++        + +SQL E  N ++ ++H RR+ +     ++R++   E RD
Sbjct: 408 VLTERIVHALATGNWVGGRAGVSQLLERSNYIATLSHLRRIIS----PLSRSQPHFEARD 463

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           +HPT +G+ICP+ET EG N GLV + +    ++     ++    + +  V      L   
Sbjct: 464 LHPTQWGKICPSETPEGPNCGLVKNFSQMVEISVGEDEKSFKDILYELGVIPPARSLEIS 523

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI----AA 676
            E    +   N       +  E  V              +++      +  + I      
Sbjct: 524 AESRTRV-FVNGDFIGFSTEPEIFVDAVRKKRRSDEISTQVNIAYYRDQSDIIINSDRGR 582

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI-- 734
           +  P +  ++   +L    +++     +  +       +E + A+    A++A       
Sbjct: 583 ARRPVMVVENKTPLLTESQIEKLRKGEMNFDDLVSVGVIEYLDAEEEENALIALNESDLT 642

Query: 735 ------------------------VEQVDAIRIVIRSVEGDLDPSTSGVDI-YRLMKFQR 769
                                   +   D       ++   +   + G+       +   
Sbjct: 643 KEGGNGYTHLELDPSLILGIVAGLIPYPDHNSSPRNTMGCAMLKQSLGLSTANYKTRADT 702

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PLV                    G    G+N +VA + + GYN ED++++
Sbjct: 703 RTHLLHSPQKPLV----------TTRTADLIQHGRRPAGQNFVVAVLSYEGYNMEDALIL 752

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV------SEEGLKNIDECGIIC 883
           ++  +   +  S     +E   R    G EE   +IP+V      S +  + +D+ GII 
Sbjct: 753 NQAAIDRGLGRSHFFRTYEGEERRYPGG-EEDIFEIPDVEIVGVRSHDAYQQLDDAGIIN 811

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
              EV P D+L+GK +P      T E            ++ RDTS+   +   G V
Sbjct: 812 SEVEVVPNDVLIGKTSPPRFLEETTELL--------SPLERRDTSICTRANERGRV 859



 Score =  152 bits (383), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 124/768 (16%), Positives = 243/768 (31%), Gaps = 164/768 (21%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS----- 69
           K + K  +I      ++ Q  S+++FL          +EG+Q     + P T  S     
Sbjct: 9   KAYLKREKI------VQHQLDSFNYFL----------DEGIQRIIDEL-PYTETSISGED 51

Query: 70  ---GAAML--EFVSYEFDPPK----------FDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
              G   L  +F       PK                  R+L Y+ P+ + ++L+     
Sbjct: 52  EEKGKYKLGVKFGKITVGIPKAREADGSYEDIFPSQARLRNLNYSAPIILDMQLV--KKY 109

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKD--------------------------------- 141
           E    + ++D  E+++ +G+LP+M K                                  
Sbjct: 110 ESGEIEIVRD--EEAVAIGELPIMLKSNRCNLSKVVIQEKLGKDLSEPEYEDWLKNEAGE 167

Query: 142 ------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG--KLLYA----CRIIPDQG 189
                 G F+I G + ++++    +P   F + + +    G    +++     R+ P + 
Sbjct: 168 DPLDPGGYFIINGSEHVIITLEDLAPNRIFVNFEEKYGSKGVVSKVFSLNQGFRV-PIR- 225

Query: 190 LWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
               +E   K I+ V      RK+   + + ALG++S+E       +I+ +   D     
Sbjct: 226 ----VEISKKGILEVSFPAVGRKIQFMTLIRALGLESDE-------EIIKAVSDDPQIVK 274

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIES-GKKLTSGLLKSLKEKGVKFL----------- 296
               ++           D+DT E+ IE  G+K+     +  +E+ V ++           
Sbjct: 275 YVLENI--------EECDVDTQEEAIEKLGRKIAPTQAREYRERRVNYILDRYFLPHLDT 326

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNA 356
            I      G   AE       G+      D    K L+           + +     +  
Sbjct: 327 KIAKAYFIGRM-AESCYELYLGKRGEGDKDHYANKRLKLAGDLVEDLFRVSFTKLTRDMR 385

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           Y           + +   L I   +R  DV T  +  ++    +          + R   
Sbjct: 386 YQLER------ANMRSRELKIATAIR-SDVLTERIVHALATGNWVGGRAGVSQLLERSNY 438

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-DDIDNLGNRRVRSVGEMLKNQY 475
              L+      +  + +       + L   + GK    +  +      V++  +M++   
Sbjct: 439 IATLSHLRRI-ISPLSRSQPHFEARDLHPTQWGKICPSETPEGPNCGLVKNFSQMVEISV 497

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
                  +  + E        S+        +  V+     F +                
Sbjct: 498 GEDEKSFKDILYELGVIPPARSLEISAESRTRVFVNGDFIGFST--------EPEIFVDA 549

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
              +R S      V  A    +   +  +  GR           + +V + T     +  
Sbjct: 550 VRKKRRSDEISTQVNIAYYRDQSDIIINSDRGRAR-------RPVMVVENKTPLLTESQI 602

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             +        D      + YL A EEEN  IA   S L ++G                 
Sbjct: 603 EKLRKGEMNFDDLVSVGVIEYLDAEEEENALIALNESDLTKEGGNG-------------- 648

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                   ++  P  ++ I A LIP+ +++ S R  MGC M +Q++ L
Sbjct: 649 -----YTHLELDPSLILGIVAGLIPYPDHNSSPRNTMGCAMLKQSLGL 691


>gi|302927105|ref|XP_003054428.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256735369|gb|EEU48715.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 1156

 Score =  295 bits (755), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 166/1131 (14%), Positives = 335/1131 (29%), Gaps = 201/1131 (17%)

Query: 269  TGEQVIESGKKLTSGLLK----SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
                ++E+ +K           + + K   ++ +  D +        +V G    I ++A
Sbjct: 193  KNRVIVEADEKNNVISASVTSSTHERKSKTYVTLKKDRIL--LTHNVLVEGIPIVIVLKA 250

Query: 325  GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
                 +  + E+       +        +      +         +  AL  I   ++ G
Sbjct: 251  LGGKSDMEIMEL-------VAGSDGRYQDEFLVNFDEATKAGIFTQHQALEYIGARVKMG 303

Query: 385  DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
                 S        +  +  +  L  +  + +      +     + I    +  + + ++
Sbjct: 304  -----SRRGQFGPQVRRNHVEEGLDALANLVIAHVPIEELDFYPKAI---YVAMMTRKVL 355

Query: 445  DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQD 502
               +    +DD D +GN+R+   G++L   +     R    +K  I       +  +P D
Sbjct: 356  MAAHNPKLVDDRDFVGNKRLELAGQLLSLLFEDLFKRFTVEVKMSIDKFLKKNNRAVPLD 415

Query: 503  LINA-----KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------- 550
             ++        +   +     +   S    ++N         RLS +   G+        
Sbjct: 416  AVHMISNHANTIGIGINRAIQTGNWSVKRFNMNRAGVTHVLSRLSYIAALGMMTRISSQF 475

Query: 551  -RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             + R     R + P+ +G +C ++T EG   GLV +L     +            V +G 
Sbjct: 476  EKTRKVSGPRALQPSQWGMLCTSDTPEGEACGLVKNLALMTHITTN---------VEEGP 526

Query: 610  VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            V   +  L+  +E       + S +  +GS+    V            R    F     +
Sbjct: 527  VKETI--LTIDKEVEAIEKFSGSMMHREGSYV-IHVNGTPFALTRNPKRFAQRFRTLRRR 583

Query: 670  QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
              +S    +      +  +       + R  + +   +       +  +           
Sbjct: 584  GGISPFVGININTHFNAIHIATDEGRICRPYIIVKNGQQKLKPEHLRLLQ---------- 633

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               G V   D +R  +       + + + + IY     Q +          L        
Sbjct: 634  --LGKVTFDDFLRQGVVEYLDVNEENDALITIYEDQVTQSTTHLEIEPFTIL-------- 683

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
               +    P                +    G     ++  ++    + +  ++       
Sbjct: 684  -GAVAGLIPFPHHNQSP-----RNTYQCAMGKQAIGAIAYNQFNRIDTLLYTLVYP---- 733

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                                       ++   I   G   +   
Sbjct: 734  ---------------------------------------QRPMVISKTIQLIGYDKLPAG 754

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +     +      D+ D  +   + +       ++F ++  +  +          +    
Sbjct: 755  QNATVVVMSYSGYDIEDALVLNKASIDRGFGRCQVFRKYTTELQKYPNGRRERIGDPQNE 814

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            +   +Q I            + G    +G    KK T L                 +  +
Sbjct: 815  EGKVKQRIKKHEGLDDDGLAIVGYRIHNGEAMIKKETPLDQT-----------TTGIGMD 863

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            +         V Y  +    +  + +K+   Q           V+KV     R  + GDK
Sbjct: 864  RGPSEYRDSSVSYRIA----DPAYIDKVMVSQ-----TEKDTTVIKVQTRQTRRPELGDK 914

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             + RHG KG+V  I+  ED+PF   G   DI+         MN                G
Sbjct: 915  FSSRHGQKGVVGIIVDQEDLPFSDKGLTPDII---------MNP--------------HG 951

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
               +  +                    G G                              
Sbjct: 952  FPSRMTVGKLLECLTGKASIIHGRPDYGFGD----------------------------- 982

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
             F     E ++ +L        G+     G+TGEP +  +  G IY  +L HMV DK+++
Sbjct: 983  AFRSHPLEEMSKVLVDHGFSWEGKDYFTSGVTGEPLEAYIFNGPIYYQRLKHMVQDKMHS 1042

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV-- 1323
            RS G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L I SD    D+   
Sbjct: 1043 RSRGPKAILTRQPTEGRSREGGLRLGEMERDCLIAYGASQLLLERLMISSDGTEIDICQQ 1102

Query: 1324 ----GRTRVYESIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
                G  + Y        +  +   P +  +LV+E+ ++ + + L+     
Sbjct: 1103 CGLFG-YKGYCHTCKSTREVTKMTMPYAAKLLVQELISMNVGVRLQMEDEF 1152



 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 134/999 (13%), Positives = 284/999 (28%), Gaps = 192/999 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY+ F+   I    R N  ++         +       LEF     D P+   
Sbjct: 44  LVKQHIDSYNFFVEQEIKDIVRANRTIR---------SDVDSNFWLEFTDIRVDRPRRQD 94

Query: 86  ---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RD+TYA P+ + ++ I          +  + I  +++ +G +P
Sbjct: 95  WQDAKSHTDVTPMECRLRDMTYAAPILVDIQYI----------RDKQRIVRKNVPLGRMP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 145 VMLKSSKCRLGGATNTQMEEMNECPLDPGGYFIIGGTEKVILIQEQLSKNRVIVEADEKN 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-----VPVTSFLMALGMDSE- 226
           ++    + +     ++          KD    RI          +P+   L ALG  S+ 
Sbjct: 205 NVISASVTSST--HERKSK-TYVTLKKD----RILLTHNVLVEGIPIVIVLKALGGKSDM 257

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI+          +  D +      A          +L  I    ++     +    + +
Sbjct: 258 EIMELVAGSDG--RYQDEFLVNFDEATKAGIFTQHQALEYIGARVKMGSRRGQFGPQVRR 315

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           +  E+G+  L      L   +V  + ++     IY+ A                     +
Sbjct: 316 NHVEEGLDALA----NLVIAHVPIEELDFYPKAIYV-AMMTRKVLMAAHNPKLVDDRDFV 370

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
                      +         +   +  + I + ++  + +    A  M +         
Sbjct: 371 GNKRLELAGQLLSLLFEDLFKRFTVEVKMSIDKFLKKNNRAVPLDAVHMISNHANTIGIG 430

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
               +     +++        V H    +     + ++  +         +     L   
Sbjct: 431 INRAIQTGNWSVKRFNMNRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPS 490

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS--S 520
           +   +      +     L    ++   I++   +  + + ++     V A+ +F  S   
Sbjct: 491 QWGMLCTSDTPEGEACGLVKNLALMTHITTNVEEGPVKETILTIDKEVEAIEKFSGSMMH 550

Query: 521 QLSQLEEHVNSLSR-ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +      HVN     +T   +  A     + R         ++   +       T EG  
Sbjct: 551 REGSYVIHVNGTPFALTRNPKRFAQRFRTLRRRGGISPFVGININTHFNAIHIATDEGRI 610

Query: 580 IGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                 V +     +      ++       D      V YL   EE +  I      + +
Sbjct: 611 CRPYIIVKNGQQKLKPEHLRLLQLGKVTFDDFLRQGVVEYLDVNEENDALITIYEDQVTQ 670

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                      ++  P  ++   A LIPF  ++ S R    C M
Sbjct: 671 S-----------------------TTHLEIEPFTILGAVAGLIPFPHHNQSPRNTYQCAM 707

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                           I   + +   + 
Sbjct: 708 GKQAIGA-----------------------------------------IAYNQFNRIDTL 726

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               +Y               QRP+V          I           L  G+N  V  M
Sbjct: 727 LYTLVYP--------------QRPMV----------ISKTIQLIGYDKLPAGQNATVVVM 762

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSE 870
            + GY+ ED++++++  +           ++    +    G  E   D  N         
Sbjct: 763 SYSGYDIEDALVLNKASIDRGFGRCQVFRKYTTELQKYPNGRRERIGDPQNEEGKVKQRI 822

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           +  + +D+ G+  VG  ++ G+ ++ K TP  ++                    R  S  
Sbjct: 823 KKHEGLDDDGLAIVGYRIHNGEAMIKKETPLDQTTTGIGMD-------------RGPSEY 869

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
             S VS  + D    ++  + + E+  +V + Q     R
Sbjct: 870 RDSSVSYRIADPAYIDKVMVSQTEKDTTVIKVQTRQTRR 908


>gi|190694913|gb|ACE88997.1| RNA polymerase beta subunit [Mycobacterium phocaicum]
          Length = 243

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 98/233 (42%), Positives = 130/233 (55%), Gaps = 40/233 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 43   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 148  -----------------LPEGMHSAPRDSIVATPVFDGARENELQGLLGSTLPNRDGDVM 190

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++TQ
Sbjct: 191  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMITQ 243



 Score = 47.0 bits (110), Expect = 0.027,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 51


>gi|76556193|emb|CAI91183.1| RNA polymerase beta subunit [Pseudomonas meliae]
          Length = 313

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 179/312 (57%), Positives = 234/312 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSMAESEGLMPLDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SP
Sbjct: 122 LVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V
Sbjct: 242 ARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRV 301

Query: 789 RRNDIIADGPST 800
           +R++ +ADGPST
Sbjct: 302 QRSNGMADGPST 313


>gi|326474430|gb|EGD98439.1| DNA-directed RNA polymerase I [Trichophyton tonsurans CBS 112818]
          Length = 1244

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 109/522 (20%), Positives = 187/522 (35%), Gaps = 60/522 (11%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  + + +  + + G   +  M I+          S HI EF+     + L      
Sbjct: 657  RMYRPVKYLPLDKLDYVGPFEQPYMEIACVASDIRNGVSTHI-EFDPTHILSILANMTPF 715

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
             D         +   + G   +G      D        + ++  TP  +  L  A   + 
Sbjct: 716  SDFNQSPRNMYQC--QMGKQAMGTPGTAIDYRTDNKLYRLQTGQTPVVRPPLYNAYGLDN 773

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  I N+   ++     ++ + +I  L  DK+       +
Sbjct: 774  FPNGMNAVVAVISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIYALD-DKESRGRGKSK 832

Query: 981  NIYSRLMEILCGQNAVSGPK--GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L     G    +  K    +         +SE      W     D      +   
Sbjct: 833  RAITKLFGFAPGGLVKAEWKAQLDEDGLPHIGAKVSEGSLVGAWHTVQYDPATDTYINVD 892

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  +       E+ F + +  +  G +    V + V +   + R    GDK + RHG KG
Sbjct: 893  KQTHFLKYKDGEEGFIDSVRVL--GSETGNEVCQAVSIKYRVPRRPVIGDKFSSRHGQKG 950

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++S++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    
Sbjct: 951  VLSQLWPATDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGSLHGLPQDSTPFQ 1010

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                   F G     
Sbjct: 1011 FSEEATAGD-------------------------------------------FFG----- 1022

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L+ A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +
Sbjct: 1023 --KQLQKAGYNFHGNEPMYSGITGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAL 1080

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1081 TGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1122



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 105/779 (13%), Positives = 219/779 (28%), Gaps = 145/779 (18%)

Query: 11  GRVRKFFGKNPEIIDIPDL---IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            R R F     +    P L   I     S++                L+AA K +  I +
Sbjct: 18  RRERLFRHPPKDKTAYPALAAAIRPHIDSFNALFEDTKV--------LEAALKDIG-IKS 68

Query: 68  F-----------------------SGAAMLEFVSYEFDP---P---KFD-------VDDC 91
           F                            +       +    P   K+          +C
Sbjct: 69  FIDGSSETPEEKASRREDGRRAPKRNKLSVRITELFLEKAVLPASNKYSTRNREIYPAEC 128

Query: 92  LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-----------TK 140
             R  TY   L+  L   V + +     +           +G +P+M           T 
Sbjct: 129 RERHATYRGKLRARLEYRVNNGEWKESVRE----------LGQVPIMIRSNRCHLEKATP 178

Query: 141 D-------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS----GKLLY 180
                         G F++ G ++++   +   R+ P     +   +   +    G  L 
Sbjct: 179 SQLVDHKEESEELGGYFIVNGNEKLIRMLIVGKRNFPTAIIRNSFQKRGSAYTKFGVQLR 238

Query: 181 ACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYP 234
           + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +     + 
Sbjct: 239 SVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVMMILKAL-IETND--REIFE 291

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           ++V  +             + +  +   +       +     G K    L      + + 
Sbjct: 292 RLVGREGSLGIENTFVTDRVELLLRTYKAYGVHSRSKCRAYLGSKFRFVL---GMPEDIP 348

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              + ++ L    V   + N    E        +    + ++++    D      D+V+N
Sbjct: 349 EEDVGTEFLR-KIVLPHLGNQNVTETQDNDKFNMILFMIRKLYNLVAGDCAPDNPDAVSN 407

Query: 355 -----NAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVS--TFSVAESMFNFLFFDSDK 405
                  Y+   L+ ++ ++   ++  + R   MR  D               +   +++
Sbjct: 408 QEVLLGGYLYGMLLKERLEEWLKSVGPMVRDWRMRNQDAKFTDPKFEREFLTRIIGRTNE 467

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
                +        L   T  D++      ++A         +    I         +  
Sbjct: 468 NIGGAMEYFLSTGNLVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMIHRGSFFAQLKTT 527

Query: 466 SVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           +V ++L   +  L  +         + +      +          +  V      +  S 
Sbjct: 528 TVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLISTSNLDVSGIPGVLAGLGVTSESS 587

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
                +   ++        LG     ++RA  +          +  P E   G      S
Sbjct: 588 CSIEESIPVQLDGK----ILGYCTPKQSRAIADTLRYWKVQGHKQIPVELEIG--YVPCS 641

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           +   +  V  +      YR V      + + Y+   E+    IA   S +    S     
Sbjct: 642 NGGQYPGVYMFSEAARMYRPVK-YLPLDKLDYVGPFEQPYMEIACVASDIRNGVS----- 695

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                              I+  P  ++SI A++ PF + + S R +  C M +QA+  
Sbjct: 696 -----------------THIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGT 737


>gi|55583686|gb|AAV53362.1| RNA polymerase II second largest subunit [Fomitopsis pinicola]
          Length = 704

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 125/844 (14%), Positives = 244/844 (28%), Gaps = 165/844 (19%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L N +R+   ++ + +    +              +    + + +     +         
Sbjct: 1    LANLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVKHNTITNGLKYSLATGNWGDQKKS 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   MASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG   GLV +L+  + ++           + +  + +         EEN + A   + + 
Sbjct: 117  EGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSATPCTKVF 168

Query: 636  EDGSF----------TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +G +           + +   R   +         D  +   +          P    D
Sbjct: 169  VNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVD 228

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D + +L   ++Q  +     A+  F            SG     +     E+   +  + 
Sbjct: 229  DQSLLLTKQHIQWLSNGKDDADNDFK-----WDSLVKSGVV---ELLDAEEEETVMICMT 280

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                      + GVD     +F  +           +K    +         PS  LG  
Sbjct: 281  PDDLETSRLQSQGVDTTADGEFDPA---------TRLKAPTNIHTWTHCEIHPSMILG-- 329

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       +
Sbjct: 330  -----VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLV 366

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 367  RM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQE 415

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    ++ R  +D  +++   + E+ E   R+          +    
Sbjct: 416  DSVIMNQSSIDRGLF-RSMYYRSYMDLEKKNGIQQLEKFEKPTRETTLRMKHGTYDKLED 474

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 475  DGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRTRNHTRRDVSTPLKSTESGIIDQVLI- 533

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VK+ V   R  Q GDK A RHG KG +     
Sbjct: 534  -------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYR 574

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +           
Sbjct: 575  QEDMPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 627

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++       LR       G+ V                   
Sbjct: 628  ------------------DLTVDSVSGFLRQRGYQSRGLEVM------------------ 651

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G
Sbjct: 652  ----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEG 700

Query: 1286 KSNR 1289
            +S  
Sbjct: 701  RSRD 704



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 81/568 (14%), Positives = 158/568 (27%), Gaps = 90/568 (15%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   S  G  ++  R    +      R          I    
Sbjct: 41  ITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPR 100

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   + + L     + +  +   + E +    ++S+      
Sbjct: 101 QLHNTHWGMVCPAETPEGQACGLVKNLSLMSCISVGSLSAPVIEFLEEWGLESL----EE 156

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NA         F     +    +  N +  I   RR   +                ++  
Sbjct: 157 NAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 216

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                 P    +  ++ L      +  ++          K      +  V  L A EEE 
Sbjct: 217 AGRVCRPLFIVDDQSLLLTKQHIQW--LSNGKDDADNDFKWDSLVKSGVVELLDAEEEET 274

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAAS 677
             I      L E      + V     GE     R             +  P  ++ + AS
Sbjct: 275 VMICMTPDDL-ETSRLQSQGVDTTADGEFDPATRLKAPTNIHTWTHCEIHPSMILGVCAS 333

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 334 IIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV--------------------------- 366

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            + + +  Y       +     +  R                  
Sbjct: 367 --------------RMDTMANILYYPQKPLATTRSMEYLRFR------------------ 394

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G+N +VA + + GYN EDS+++++  +   +F S++   +  + +   + 
Sbjct: 395 ------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDLEKKNGIQ 448

Query: 858 PEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E            +       +++ G+I  G  VN  DI++GK  P         E+L
Sbjct: 449 QLEKFEKPTRETTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPI----PPDSEEL 504

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +        DV        SG+   V+
Sbjct: 505 GQRTRNHTRRDVSTPLKSTESGIIDQVL 532


>gi|158957530|gb|ABW86307.1| RpoB [Mycobacterium sp. MMQ-5]
          Length = 243

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 103/233 (44%), Positives = 143/233 (61%), Gaps = 40/233 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      D++ PGV ++V+++VA KR I +GDK+AGRHGNKG++S+ILP EDMPFL DG
Sbjct: 43   RVFDRDNDDELAPGVNQLVRIYVAAKRKITNGDKLAGRHGNKGVISKILPIEDMPFLADG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDIVLNPLGVP RMNVGQ+ E HLGW     G KI+   +  K               
Sbjct: 103  TPVDIVLNPLGVPGRMNVGQVLELHLGWIAK-TGWKIEGEPDWVKN-------------- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD-------- 1227
                             +  +  +      ++TPVFDGA EE I+ +L   +        
Sbjct: 148  -----------------LPNMPREAPRNQTLATPVFDGAREEEISGLLDSTNVTRDGDRL 190

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +D SG++ L+DG +GEPF  P++VGY+Y+LKL+H+V DK++ARSTG YS++TQ
Sbjct: 191  IDRSGKTRLFDGRSGEPFPDPISVGYMYILKLHHLVDDKIHARSTGPYSMITQ 243



 Score = 45.8 bits (107), Expect = 0.056,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 43/51 (84%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEK+ +VRDTSL+VP G SGTV+ VR+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKSREVRDTSLKVPHGESGTVIGVRVFDRDNDD 51


>gi|70991741|ref|XP_750719.1| DNA-directed RNA polymerase I subunit beta (Rpa2) [Aspergillus
            fumigatus Af293]
 gi|66848352|gb|EAL88681.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus fumigatus Af293]
          Length = 1235

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 108/532 (20%), Positives = 173/532 (32%), Gaps = 101/532 (18%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            D +  G ST +         +VA M P+  YN     +   +M  + + T     E+   
Sbjct: 688  DDLVAGVSTHIEYTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPSTAIEY--- 744

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R         T   P V                                 G        
Sbjct: 745  -RTDNKLYRLQTGQTPIVRPPLYN-------------------------AYGLDNFPNGT 778

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      D+ D  +   S                        ++ + +I  L  D
Sbjct: 779  NAVVAIISYTGYDMDDAMIINKSSHERGFG---------------YGTIYKTKIHSL--D 821

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              D +    R   ++L     G    +       +         + E      W     D
Sbjct: 822  DKDSRRSKSRREITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLIAAWHTVRYD 881

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                  V    + +       E+ + + I  +     + P     VK  +   R    GD
Sbjct: 882  AASDSYVNVDGITHFVKYKDAEEGYIDSIRIMGAETGLEPCQALSVKYRI--PRKPVIGD 939

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+  G A    
Sbjct: 940  KFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESMAGKAGALH 999

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G    S    +      +                                          
Sbjct: 1000 GHPQDSTPFQFSEENTAA------------------------------------------ 1017

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +     LR A  +  G   LY G+TG+ F   + +G ++  +L HMV+DK  
Sbjct: 1018 --------DYFGQQLRKAGYNYYGNEPLYSGITGKEFAADIFIGVVHYQRLRHMVNDKFQ 1069

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1070 VRTTGPVNQLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1121



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 64/404 (15%), Positives = 131/404 (32%), Gaps = 44/404 (10%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G  
Sbjct: 494 SGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAP 550

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL----- 634
            GL++ L     +       +   K+    V   V   S++  E+    Q +  +     
Sbjct: 551 CGLLNHLAHKCLIATSDVNVSHLPKLL---VQLGVRSESSVALEDSVTVQLDGRIVGYCS 607

Query: 635 DEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASP------KQVVSIAASLIPFLENDDS 687
            +      + V          +PRE +I ++  S         + S AA +   ++    
Sbjct: 608 PKQARMIADTVRHWKVSGTHNIPRELEIGYVPNSNGGQYPGIYMFSQAARMYRPVKYLPL 667

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           +++      ++  + +       V    T +E                    Q       
Sbjct: 668 DKLDYVGPFEQPFMEIACLPDDLVAGVSTHIEYTPTNILSIVANMTPFSDYNQSPRNMYQ 727

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +  +  +   ++ ++     K  R        Q P+V+               +  L +
Sbjct: 728 CQMSKQTMGTPSTAIEYRTDNKLYRLQTG----QTPIVRP----------PLYNAYGLDN 773

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
              G N +VA + + GY+ +D+M+I++             +       D      +  R+
Sbjct: 774 FPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIHSLDDKDSRRSKSRRE 833

Query: 865 IPNV---------SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           I  +           E    +DE G+  VGA V  G ++    T
Sbjct: 834 ITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLIAAWHT 877



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 94/666 (14%), Positives = 199/666 (29%), Gaps = 103/666 (15%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +   R  TY   L+  L   V + D       ++ I+E    +G +P+M +       
Sbjct: 125 PSEARERHATYRGKLRARLEYQVNNGD------WMESIRE----LGQVPIMLRTNRCHLE 174

Query: 141 -----------------DGTFVIKGIQRIV---V-------SQLHRSPGIHFDHDKGRAS 173
                             G F++ G ++++   V         + RS  +   H   +  
Sbjct: 175 KATPQELVQHKEESEELGGYFIVNGNEKLIRMLVVGKRNFPMAIVRSSFVRRGHTYTKF- 233

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    +  R   R+    +PV   + AL +++ +
Sbjct: 234 --GIQIRSVR--PDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLIPVMMIMKAL-VETND 286

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
                +  IV S              + +  +               ++    T    ++
Sbjct: 287 --REIFEGIVGSATSKGVNNTFVTDRVELLLR-------------TYKAYNLHTRSSCRA 331

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
              +  K +         L V  D+ N + G  ++    +    +       +     ++
Sbjct: 332 YLGEKFKPV---------LGVPADMSNEDAGTEFLRKIVLPHLGNQNVTEIQDYDKFKLI 382

Query: 348 YVDSVNNNAYIRNTLVTDK--NKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDS 403
                   A +      D       ++ LL   +Y ++    +  +              
Sbjct: 383 MFMIRKLYALVAGDCAPDNPDAVSNQEILLGGFLYGMILKEQLEEWM------RSFGPIL 436

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +     G    +     D    +     E+I   ++  +   N   +   +D      
Sbjct: 437 RDWSNRNGGAKFTDPAFERDFLSKIVKRTNENIGGKLEYFLSTGN-LVSPTGLDLQQVSG 495

Query: 464 VRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SS 520
              + E +     +   RM    S   ++ +  +  ++P+      PV +         +
Sbjct: 496 YTVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGLLN 555

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE--GH 578
            L+       S   ++H  +   L Q GV    +      V     GRI    + +    
Sbjct: 556 HLAHKCLIATSDVNVSHLPK--LLVQLGVRSESSVALEDSVTVQLDGRIVGYCSPKQARM 613

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLDED 637
               V         N    +E  Y    +G     +   S A              LD  
Sbjct: 614 IADTVRHWKVSGTHNIPRELEIGYVPNSNGGQYPGIYMFSQAARMYRPVKYLPLDKLDYV 673

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G F +  +   C  ++++        I+ +P  ++SI A++ PF + + S R +  C M 
Sbjct: 674 GPFEQPFMEIACLPDDLVAGVS--THIEYTPTNILSIVANMTPFSDYNQSPRNMYQCQMS 731

Query: 698 RQAVPL 703
           +Q +  
Sbjct: 732 KQTMGT 737


>gi|319998247|gb|ADV91595.1| RNA polymerase B subunit [Mycobacterium noviomagense]
          Length = 247

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 99/233 (42%), Positives = 136/233 (58%), Gaps = 37/233 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G KI +                     
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKIDTA-------------------- 141

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                      +    + +L           V+TPVFDGA E  +  +L     +      
Sbjct: 142  ----GGVPDWASRLPEELLEAEPNKI----VATPVFDGAQETELQGLLSATLPNRDGEVL 193

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                G+++L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARSTG YS++TQ
Sbjct: 194  VDGDGKAVLFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYSMITQ 246



 Score = 47.0 bits (110), Expect = 0.022,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|149023254|gb|EDL80148.1| RNA polymerase 1-2 [Rattus norvegicus]
          Length = 1135

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 90/327 (27%), Positives = 130/327 (39%), Gaps = 76/327 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +D   G  + V V V + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ N
Sbjct: 857  NDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFN 916

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P G PSRM +G + E+  G +    G    +    +                        
Sbjct: 917  PHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY--------------- 961

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                  ML+ A  +  G   LY G++G 
Sbjct: 962  -----------------------------------FGEMLKAAGYNFYGTERLYSGISGM 986

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + 
Sbjct: 987  ELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALL 1046

Query: 1304 AYGAAYVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--ND 1337
            A+G +++L + L   SD     V    G                 R R Y   V G  + 
Sbjct: 1047 AHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTVCGRSDS 1106

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLE 1364
                  P  F   V E+ A+ + + L+
Sbjct: 1107 IDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 90/664 (13%), Positives = 216/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ +N++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFKNSVSQMLRIVMEEGCHTQKQVL--------DYL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y  +       N  + +         +   +  + + L  L  G+  
Sbjct: 305 GERFRVKLSLPDWYPNAEAAEFLFNQCICIH--LKSNTDKFYLLCLMTRKLFALARGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V + G++           + L +        ++ +    +  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRAQKTNVSINNENLMKIFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GTELTRPFEYLLATGNLRSKTGLGFMQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V   + +  +    +C   V
Sbjct: 480 KMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKFVYTASIPALLCGLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           +   +      +          V           E  + P  ++  I 
Sbjct: 540 TPVDAAPCRPYSDCYPVLLDGVMVGWVDKELAPEVADTLRRFKVLRERRVPPWMEVALIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELVGTMEQLFMNIAIFEDEVFGGVSTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+          + D    D     +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRP--------CMYDHYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G + +   +       ++ +D  G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGAKLEFGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YGYL-----NLNTGEGFVVYYKSKENCVVDNIKVCSNDTGSGKFKCVCVTVRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 49/163 (30%), Gaps = 57/163 (34%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK 85
           DL      S+++             EGL  A +++ P           L  V     PP 
Sbjct: 37  DLTRAHVDSFNY----------AVLEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPA 86

Query: 86  -----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  R  TY   L   +   V  V         K I +Q  ++G 
Sbjct: 87  VPKGTICKELNIYPAECRGRRSTYRGKLTADISWAVNGVP--------KGIIKQ--FLGY 136

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV 153
           +P+M K                         G F+I GI++++
Sbjct: 137 VPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVI 179


>gi|67526951|ref|XP_661537.1| hypothetical protein AN3933.2 [Aspergillus nidulans FGSC A4]
 gi|40740052|gb|EAA59242.1| hypothetical protein AN3933.2 [Aspergillus nidulans FGSC A4]
 gi|259481492|tpe|CBF75062.1| TPA: DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            (AFU_orthologue; AFUA_6G08300) [Aspergillus nidulans FGSC
            A4]
          Length = 1231

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 94/484 (19%), Positives = 165/484 (34%), Gaps = 67/484 (13%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             +      E    +I ++        D         +       +G      +     + 
Sbjct: 691  VKGLSTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIDYRTDNKL 750

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL--- 967
              L+             +  + +  +GT   V I +  G D ++ ++ + +   E     
Sbjct: 751  YRLQTGQTPIVRPPLYNAYGLDNFPNGTNAVVAIISYTGYDMDD-AMIINKSSHERGFGY 809

Query: 968  ---------ARDKDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEY 1016
                     + D+ D +    +    +L     G    +       +         I E 
Sbjct: 810  GTVYKTKVHSLDEKDSRRTKSKQAVQKLFGFAPGSEIRAEWRATLDEDGFPHIGAEIKEG 869

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                 +     D      +    + +       E  + + I  +  G +      + + V
Sbjct: 870  SIVAAYHTVRYDATSDSYINVDGITHFVKYKDSERAYIDSIRIM--GSETGTEPAQAISV 927

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
               + R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+
Sbjct: 928  KYRIPRKPIIGDKFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQM 987

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E+  G A    G         +                                     
Sbjct: 988  IESMAGKAGALHGHPQDCTPFQFSEEYT-------------------------------- 1015

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                      +T  F           LR A  +  G   LY G+TG+ F   + +G ++ 
Sbjct: 1016 ----------ATDYF--------GEQLRRAGYNYYGNEPLYSGITGKEFAADIFIGVVHY 1057

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAAY+LQ+ L 
Sbjct: 1058 QRLRHMVNDKFQVRTTGPVNNLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAYILQDRLM 1117

Query: 1317 IKSD 1320
              SD
Sbjct: 1118 NCSD 1121



 Score = 69.7 bits (169), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 96/709 (13%), Positives = 198/709 (27%), Gaps = 138/709 (19%)

Query: 69  SGAAMLEFVSYEFDPP------KFD-------VDDCLWRDLTYAVPLKITLRLIVFDVDE 115
                +       + P      K+          +C  R  TY   L+  +   V + D 
Sbjct: 93  RNKLHVRIKEVFLEKPTIPLTNKYTARNRNIYPSECRERHATYRGKLRAKIEYRVNNGD- 151

Query: 116 FTGAKSIKDIKEQSIYMGDLPLMTK------------------------DGTFVIKGIQR 151
                  + ++E    +G +P+M +                         G F++ G ++
Sbjct: 152 -----WTEQVRE----LGQVPIMLRTNRCYLEKATPAELVQHKEESEELGGYFIVNGNEK 202

Query: 152 IVVSQLHRSPGI----HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH---- 203
                L R   +    +          +    Y+   I  + +  D +    +++H    
Sbjct: 203 -----LIRMLIVGRRNYPMAIVRNTFTNRGHAYSKFGIQIRSVRPD-QTSQTNVLHYLND 256

Query: 204 ----VRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
                R   R+    +PV   L AL +++ +     +  IV S   +          + +
Sbjct: 257 GNVTFRFSWRKNEYIIPVVMILKAL-VETND--REIFEGIVGSASSEGINNTFVTDRVEL 313

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             +   +       E     G+K    L                       V  D  N E
Sbjct: 314 LLRTYKAYKLHSRSECRAFIGEKFKPVL----------------------GVPADTPNEE 351

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK--NKDRKDAL 374
            G  ++    +    +       +     +L        A +      D       ++ L
Sbjct: 352 AGTEFLRKVVLPHLGNQNVTETQDYDKFKMLMFMIRKLYALVAGDCAPDNPDAVSNQEIL 411

Query: 375 L--DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           L   +Y ++    +      +            +     G    +     D    V    
Sbjct: 412 LGGFLYGMLLKERL------DEWVRSFGPILRDWSNRNHGARFTDPAFERDFVSKVIRRS 465

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERI 490
            E+I   ++  +   N   +   +D         + E +     +   RM    S   ++
Sbjct: 466 NENIGGAMEYFLSTGN-LVSPTGLDLQQTSGYTVMAEKINFYRFISHFRMIHRGSFFAQL 524

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +  +  ++P+      PV +         + L+       S + ++H  +   L Q GV
Sbjct: 525 KTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLVATSDTDVSHLPK--LLVQLGV 582

Query: 550 ARARAGVEMRDVHPTHYGRI---CPAE------------TSEGHNIGLVSSLTSFARVNA 594
               +      V     GRI   C  +               G N   +     +   + 
Sbjct: 583 RNESSVSLDESVTVQLDGRIIGYCSPKQARVIASTLRHWKVSGTNNVPLGLEIGYVPNSN 642

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            G     Y      ++   V YL   + +  Y+        E      +LV         
Sbjct: 643 GGQYPGIYMFSQAARMYRPVKYLPLDKLD--YVGPFEQPFMEIACLPSDLVKGL------ 694

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                    I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 695 ------STHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGT 737



 Score = 65.9 bits (159), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 82/638 (12%), Positives = 190/638 (29%), Gaps = 94/638 (14%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A    +++ + E          I      +    +  T    K   R +    I  
Sbjct: 276 MILKALVETNDREIFEGIVGSASSEGINNTFVTDRVELLLRTYKAYKLHSRSECRAFIGE 335

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             +P           +       +++     + +V +    N +  +   + + + ++ +
Sbjct: 336 KFKPV----------LGVPADTPNEEAGTEFLRKVVLPHLGNQNVTETQDYDKFKMLMFM 385

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR---LGLLRM-----------ERS 485
           I+ L  L  G    D+ D + N+ +   G +     +      +R               
Sbjct: 386 IRKLYALVAGDCAPDNPDAVSNQEILLGGFLYGMLLKERLDEWVRSFGPILRDWSNRNHG 445

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNS 531
            +    + + D V      + + +  A+  F  +  L              + + E +N 
Sbjct: 446 ARFTDPAFERDFVSKVIRRSNENIGGAMEYFLSTGNLVSPTGLDLQQTSGYTVMAEKINF 505

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
              I+H R    + +G          +R + P  +G +CP  T +G   GL++ L     
Sbjct: 506 YRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCL 562

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V       +   K+       +   +S  E         + ++  DG         +   
Sbjct: 563 VATSDTDVSHLPKLLVQLGVRNESSVSLDE---------SVTVQLDGRIIGYCSPKQARV 613

Query: 652 EEILVPREKIDFIDASPK------------------QVVSIAASLIPFLENDDSNRVLMG 693
               +   K+   +  P                    + S AA +   ++    +++   
Sbjct: 614 IASTLRHWKVSGTNNVPLGLEIGYVPNSNGGQYPGIYMFSQAARMYRPVKYLPLDKLDYV 673

Query: 694 CNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              ++  + +    +  V    T +E                    Q        +  + 
Sbjct: 674 GPFEQPFMEIACLPSDLVKGLSTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQ 733

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            +    + +D     K  R        Q P+V+               +  L +   G N
Sbjct: 734 TMGTPGTAIDYRTDNKLYRLQTG----QTPIVRP----------PLYNAYGLDNFPNGTN 779

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE--FEVMARDTKLGPEEITRDIPN- 867
            +VA + + GY+ +D+M+I++             +     +  +D++    +        
Sbjct: 780 AVVAIISYTGYDMDDAMIINKSSHERGFGYGTVYKTKVHSLDEKDSRRTKSKQAVQKLFG 839

Query: 868 ------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                 +  E    +DE G   +GAE+  G I+    T
Sbjct: 840 FAPGSEIRAEWRATLDEDGFPHIGAEIKEGSIVAAYHT 877


>gi|268308297|gb|ACY95378.1| RNA polymerase beta subunit [Spiroplasma apis]
          Length = 339

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 188/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N YGFIETPYRKV +GKV  N+  YL+A +E +  +AQAN  +D +G   ++ V  
Sbjct: 1   YARINKYGFIETPYRKVENGKVLINEYEYLTADKERDYVVAQANIQIDANGKILDDSVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+VP   +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMVPPMDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VAK  GIV+ VD+ +I +          +SGV  Y L  F
Sbjct: 121 SPIVGTGVEHEAARDSGDAVVAKADGIVKYVDSRKITV--------EESSGVRNYVLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 NRSNNGTAITHIPIVKVGDKIKERDILADGPSMENGELALGQNLVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+I N+SE   K++DE GI  +G+E
Sbjct: 233 ILSERVVIDDRFTSIHIDEYTIERRQTKQGPEEITREIQNISEASKKHLDEEGIAAIGSE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|52538193|emb|CAH19198.1| RNA polymerase beta-subunit [Pseudomonas aeruginosa]
          Length = 309

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 172/297 (57%), Positives = 222/297 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L+E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNEKRVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 241 RGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 297


>gi|48477331|ref|YP_023037.1| DNA-directed RNA polymerase subunit B [Picrophilus torridus DSM 9790]
 gi|48429979|gb|AAT42844.1| DNA-directed RNA polymerase subunit B [Picrophilus torridus DSM 9790]
          Length = 1194

 Score =  295 bits (755), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 192/1149 (16%), Positives = 381/1149 (33%), Gaps = 187/1149 (16%)

Query: 258  AKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKG----VKFLGITSDCLCGLYVAED 311
             +V  S+ D+   + ++E  +K  + +   K   +KG    +  +   +D +  + +   
Sbjct: 196  ERVIVSIEDLAPNKILVEYEEKYDNKVEVAKVFSQKGNFRALTSMEKGNDGIINVSIP-T 254

Query: 312  IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +       I ++A  +  +  +     S+IR  PI+Y +           L  +      
Sbjct: 255  VAGTVPLVILMKALGMDKDIEIHNAIFSDIRMDPIIYANIEEARN--PKVLPPNGINTTD 312

Query: 372  DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            DA+  + +    G    F         +    D+  L  +G              D R+ 
Sbjct: 313  DAISYLEKRFASGQAKEFRE-----KKITQMLDRSLLPHLGDTV-----------DDRYK 356

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  + + L++L  G    DD D+  N+R++  G++L   +      + + +K ++ 
Sbjct: 357  KALYLGRMARSLLELNLGIRQEDDKDHYANKRIKLAGDLLDELFANAFQSIMKDLKYQLE 416

Query: 492  SVDIDSVMPQDLINAK---------PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                     +     +           ++        + +SQL +  +++S ++H RR+ 
Sbjct: 417  KTYNRKRGIRIRPAVRQDLLTQKILHSMATGNWIGGRTGVSQLLDRTSNVSTLSHLRRII 476

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R++   E RD+HPT +GRICP ET EG N GLV +      V      +   
Sbjct: 477  S----PLTRSQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNAALIINVTQGIDPDIII 532

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
             K+ +       +Y    EE +  I      +         +   R       + +E   
Sbjct: 533  DKIKNLG-----IYDVESEESSSRIYLNGDFIGYHNDPIAFVNTVRDLRRAGRISQELNI 587

Query: 663  FIDASPKQVVSIAAS---LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
              D    +V+          P L  +D   VL    +++  +     E       +E + 
Sbjct: 588  RYDNKTNEVIMNCDRGRLRRPLLIVNDGKTVLNRDMVEKLKMGDYTIEDLVNLGAIEWLD 647

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+                               +   S + +Y     +R      +  R
Sbjct: 648  AE-------------------------------EEENSYIAVYPFSYPERCPNCNSILYR 676

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             +V     V   +        D   L   +            +      I   M+   V 
Sbjct: 677  DMV---TWVNPGE--------DNIVLECDKCHAHFDGKSLLTSEHTHCEIDPSMILGVVA 725

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK-NIDECGIICVGAEVNPGDILVGKI 898
            + I   E     R T      +T+    +     +  +D  G   +        +    +
Sbjct: 726  SLIPYPEHNSSPRIT--MASAMTKQSIGLPAANYRIRVDTRG--HLLHYPQVPLVKTKVM 781

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                 +     +  + AI   +  +++D  +   + +    +    F R    +  R   
Sbjct: 782  DFIKYNNKPAGQNFVVAIVSYQGYNIQDAIVMNKASIERG-LGRSAFFRTYTAEEIRYPG 840

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             + ++ E+   D                   + G  A    K   +S ++  +  SE   
Sbjct: 841  GQEDRFEIPTHD-------------------VLGARAEEYYKNLDESGIIYPE--SEVNG 879

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            S          +               +S +  R             +     R+VKV V
Sbjct: 880  SDVLVGKTSPPRFLEENADKLGPMRRRESSVTMRPNESGYVDNVFLTVSESNSRIVKVKV 939

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
             M R  Q         G+K                               SR        
Sbjct: 940  RMDRTPQP--------GDK-----------------------------FASR-------- 954

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
                      G+K        + +   +      + +    S   +++      ++    
Sbjct: 955  ---------HGQKGVIGAVVPQEDMPFTEDGIIPDLLFNPHSVPSRMTLGHVLEMMGAKV 1005

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +G  + + +FDG  E+++   L+     ESG+ ++YDG+TG  F   + +G IY  K
Sbjct: 1006 STATGENIDSTIFDGEPEKSLREELKKYGFSESGEEVMYDGITGRKFKARIFIGVIYYQK 1065

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L+HMV++K +ARS G   ++T+QP  G+S +GG R GEME   + A+GA+ V+++ L  +
Sbjct: 1066 LHHMVANKFHARSRGPVQILTRQPTEGRSRQGGLRFGEMERDTLIAHGASMVIKDRLLDQ 1125

Query: 1319 SDDV---------VGRTRVY-------ESIVAGN--DTFETGTPESFNVLVKEMQALGLS 1360
            SD            G   +Y       +  V GN  + +   T  +F ++  E+ +LG+ 
Sbjct: 1126 SDGTILYVCGNPSCGHIAIYDFKRGTLKCPVCGNTGNIYPIETSYAFKLMRDELSSLGII 1185

Query: 1361 IDLENSRTK 1369
            + LE    +
Sbjct: 1186 MRLELGDMR 1194



 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 157/1035 (15%), Positives = 291/1035 (28%), Gaps = 228/1035 (22%)

Query: 16  FFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS--VF---------- 63
           +F K   +++       Q  S +HF      P+ R     Q       V           
Sbjct: 7   YFFKTESVVNY------QIESMNHFYATKDNPNNRM----QEIVDETKVSDDSEPGVILL 56

Query: 64  -PITAFSGAAMLEFVSYE------------FDPPKF----------DVDDCLWRDLTYAV 100
            P+        + F                 + P+              +   RDL Y  
Sbjct: 57  DPVKTRGKEIKIYFGRIRENGKPSGEPTIWVEKPEIKEASGASNQITPQEARIRDLNYMA 116

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------- 141
           P  + LRL +F+        +IK        +GD+P+M +                    
Sbjct: 117 P--VMLRLRIFEDGIEKDNDTIK--------IGDIPVMVRSKICTLTGNNLDIYIEKNNG 166

Query: 142 ---------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLY 180
                                G F+I G +R++VS    +P       + +       + 
Sbjct: 167 PINATRTEKLQYVGEDPNDTGGYFIIGGSERVIVSIEDLAPNKILVEYEEKYD---NKVE 223

Query: 181 ACRIIPDQG---LWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPK 235
             ++   +G       +E  +  II+V I      VP+   + ALGMD + EI +  +  
Sbjct: 224 VAKVFSQKGNFRALTSMEKGNDGIINVSIPTVAGTVPLVILMKALGMDKDIEIHNAIFSD 283

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
           I      D   +              + +   D     +E  K+  SG  K  +EK +  
Sbjct: 284 IR----MDPIIYANIEEARNPKVLPPNGINTTDDAISYLE--KRFASGQAKEFREKKITQ 337

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           +    D     ++ + + +     +Y+        +    I   + +D            
Sbjct: 338 ML---DRSLLPHLGDTVDDRYKKALYLGRMARSLLELNLGIRQEDDKD-HYANKRIKLAG 393

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             +            KD    + +            A                      +
Sbjct: 394 DLLDELFANAFQSIMKDLKYQLEKTYNRKRGIRIRPAVRQDLLTQKILHSMATGNWIGGR 453

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID-NLGNRRVRSVGEMLKNQ 474
             +   LD   +V  +       + +I+  L   +   +  D +          E  + Q
Sbjct: 454 TGVSQLLDRTSNVSTLSH-----LRRIISPLTRSQPHFEARDLHPTQWGRICPNETPEGQ 508

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA---VCEFFCSSQLSQLEEHVNS 531
               +      I           +     +    V S       +     +    + +  
Sbjct: 509 NCGLVKNAALIINVTQGIDPDIIIDKIKNLGIYDVESEESSSRIYLNGDFIGYHNDPIAF 568

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           ++ +   RR   + Q    R        D         C         + +    T   R
Sbjct: 569 VNTVRDLRRAGRISQELNIRY-------DNKTNEVIMNCDRGRLRRPLLIVNDGKTVLNR 621

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA-----------QANSSLDED--- 637
            +    ++     + D      + +L A EEEN YIA             NS L  D   
Sbjct: 622 -DMVEKLKMGDYTIEDLVNLGAIEWLDAEEEENSYIAVYPFSYPERCPNCNSILYRDMVT 680

Query: 638 ------GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                  +   E   C    +   +   +    +  P  ++ + ASLIP+ E++ S R+ 
Sbjct: 681 WVNPGEDNIVLECDKCHAHFDGKSLLTSEHTHCEIDPSMILGVVASLIPYPEHNSSPRIT 740

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           M   M +Q++ L  A                                             
Sbjct: 741 MASAMTKQSIGLPAANYRI----------------------------------------- 759

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              +   +  Y               Q PLVK                    +   G+N 
Sbjct: 760 RVDTRGHLLHYP--------------QVPLVK----------TKVMDFIKYNNKPAGQNF 795

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---- 867
           +VA + + GYN +D++++++  +   +  S     +         G E+      +    
Sbjct: 796 VVAIVSYQGYNIQDAIVMNKASIERGLGRSAFFRTYTAEEIRYPGGQEDRFEIPTHDVLG 855

Query: 868 -VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             +EE  KN+DE GII   +EVN  D+LVGK +P                     +  R+
Sbjct: 856 ARAEEYYKNLDESGIIYPESEVNGSDVLVGKTSPPRFLEE--------NADKLGPMRRRE 907

Query: 927 TSLRVPSGVSGTVVD 941
           +S+ +    SG V +
Sbjct: 908 SSVTMRPNESGYVDN 922


>gi|167537729|ref|XP_001750532.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163770953|gb|EDQ84628.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1136

 Score =  295 bits (754), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 110/503 (21%), Positives = 181/503 (35%), Gaps = 85/503 (16%)

Query: 894  LVGKITPKGESPMTPEEKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            +V   TP  +   +P              + G+      D  L   +     +V  R +N
Sbjct: 681  IVASFTPFSDFNQSPRNMYQCQMGKQTMGVPGQAIKYRADNKLYSLNSGQTPLVRPRAYN 740

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
             +G+D      +     I     D +D  +IL++    R                 K  +
Sbjct: 741  EYGVDNFPVGNNAIVCVIAYTGYDMED-AMILNKGSVERGFMHARVLATKVIDLTEKTKS 799

Query: 1007 VLSSDLISEYPRSQWWQFAVQ--DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             +        P+ +     ++  D      V +   + +   S ++        +I  G+
Sbjct: 800  RVCHYYFGVLPKDRSANLKMEKLDADGLPRVGAHIKEGDALYSYIDGSTNESRTEIYRGE 859

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
              P  + R V + +++ R    GDK A RHG KGI+S++ P  DMPF + G   DI+ NP
Sbjct: 860  --PAIIDRKVTIRLSINRNPIIGDKFASRHGQKGILSQLWPTADMPFSESGIIPDILFNP 917

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
             G PSRM +G + E+  G +    G    +    +  N                      
Sbjct: 918  HGFPSRMTIGMLIESMAGKSAALHGVAHDATPFMFNENERA------------------- 958

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                            +     LR A  +  G   +Y G+TGE 
Sbjct: 959  -------------------------------VDYFGEQLRTAGYNYHGHERMYSGITGEE 987

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F+  + +G ++  +L HMVSDK   R+ G  + +T+QP+ G+   GG R GEME   +  
Sbjct: 988  FEVDIFIGNVFYQRLRHMVSDKFQVRTQGPVNSLTRQPVKGRKKNGGIRFGEMERDALLG 1047

Query: 1305 YGAAYVLQEMLTIKSD----DVV-----------------GRTRVYESI--VAGNDTFET 1341
            +G A++LQ+ L   SD    DV                   R RV        G +    
Sbjct: 1048 HGTAFLLQDRLFNCSDRSEVDVCRKCGSLLSPYSSEKTAANRIRVLRCRGCSDGGEVVRV 1107

Query: 1342 GTPESFNVLVKEMQALGLSIDLE 1364
              P  F  L  E+ A+ + + L+
Sbjct: 1108 NLPYVFRYLTAELSAMNIRLSLD 1130



 Score = 72.0 bits (175), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 83/577 (14%), Positives = 189/577 (32%), Gaps = 69/577 (11%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           RV +      D     R +     + +I+ +  L  G    D+ D+   + +   G    
Sbjct: 341 RVLLVHIAPNDFQAKYRVL-----VGLIRRVYSLAAGSTQPDNADSQMLQELLLPGHIYC 395

Query: 469 ----EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD--LINAKPVVSAVCEFFCSSQL 522
               E +          ++  ++   +    ++   Q   +     + S +  F  +  L
Sbjct: 396 AFVKEQMSEYLVAMQKLVQTDLRMGKTVDVSNTNYLQTDVMRRCPDIGSKLEYFMSTGNL 455

Query: 523 S--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           +               + + +N L  ++H R    + +G          +R + P  +G 
Sbjct: 456 NSPTALDQMQVTGFTIVADKLNFLRYLSHFR---CVHRGAYFSQMKTTAVRKLLPEAWGF 512

Query: 569 ICPAETSEGHNIGLVSSLTSFA----RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE-E 623
           +CP  T +G   GL++ L               +      +    V+    +       +
Sbjct: 513 LCPVHTPDGAPCGLLNHLARHCLPPTEPVDISSLPPTLLGLGMIAVSEQPHFHCLDVLLD 572

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS-----PKQVVSIAASL 678
              +     +L++   F E+L   +   +E +    +I ++        P   +    + 
Sbjct: 573 GHLVGF--LALEQAPKFAEQLRILKIRDDERVPNTLEIAYVAPRAAGQFPGLYLFSTPAR 630

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           +     +   +         Q    +  +     +G E+   + +    ++  A      
Sbjct: 631 LLRPVRNLRMKSTEFVGSFEQVYLNVAVDPKEFVSG-ETTHMELTKHGFLSIVASFTPFS 689

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVGDEVRRNDIIAD 796
           D  +      +  +   T GV   + +K++  N+   +N  Q PLV+             
Sbjct: 690 DFNQSPRNMYQCQMGKQTMGVPG-QAIKYRADNKLYSLNSGQTPLVRPRAYNEYG----- 743

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF--TSIHIEEFEVMARDT 854
                + +  +G N +V  + + GY+ ED+M++++  V         +  +  ++  +  
Sbjct: 744 -----VDNFPVGNNAIVCVIAYTGYDMEDAMILNKGSVERGFMHARVLATKVIDLTEKTK 798

Query: 855 KLGPEEITRDIPNVSEEGLK--NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                     +P      LK   +D  G+  VGA +  GD L   I        +  E  
Sbjct: 799 SRVCHYYFGVLPKDRSANLKMEKLDADGLPRVGAHIKEGDALYSYI------DGSTNESR 852

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                GE A+  R  ++R+       ++  +  +RHG
Sbjct: 853 TEIYRGEPAIIDRKVTIRLSIN-RNPIIGDKFASRHG 888



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 47/282 (16%), Positives = 81/282 (28%), Gaps = 85/282 (30%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT--AFSGAAMLEFVSYEFDPPKFD--- 87
              S+++              GL+ A   + P+T  A +    L       + P      
Sbjct: 51  HVDSFNY----------MVKHGLEQAVADLDPLTFVAQNKTISLSIAKCRLEQPTVSRKE 100

Query: 88  ---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  R +TY     +T+     +V+    A  ++       Y+G LP+M
Sbjct: 101 GFSTANALYPAECRQRRVTYKGDFYLTV---NIEVEGQPNAWQVER------YVGQLPIM 151

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGR 171
                                      G F+I G ++ +V  L    R+  I  D     
Sbjct: 152 IMSNACRLNGLSPRELVMKKEEAQEMGGYFIINGNEK-IVRMLLMPRRNHPICLDRPSYV 210

Query: 172 ASLSGKLLYACR---IIPDQGLWMDIEFDSKD------IIHVRIDRRRK----VPVTSFL 218
               G   Y  +   + PDQ     +     D        +      RK    +P    L
Sbjct: 211 NRGPGYSSYGVQMRCVRPDQSAQTVVVHYKNDGTCTLGFSY------RKQQYLIPAILLL 264

Query: 219 MAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
            AL G+   +I    +  IV     + +        L    +
Sbjct: 265 RALSGVSDRQI----FMDIVRGDMSNSFLVERVEIMLRQYTR 302


>gi|302660181|ref|XP_003021772.1| hypothetical protein TRV_04103 [Trichophyton verrucosum HKI 0517]
 gi|291185687|gb|EFE41154.1| hypothetical protein TRV_04103 [Trichophyton verrucosum HKI 0517]
          Length = 1243

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 109/522 (20%), Positives = 187/522 (35%), Gaps = 60/522 (11%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  + + +  + + G   +  M I+          S HI EF+     + L      
Sbjct: 656  RMYRPVKYLPLDKLDYVGPFEQPYMEIACVASDIRNGVSTHI-EFDPTHILSILANMTPF 714

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
             D         +   + G   +G      D        + ++  TP  +  L  A   + 
Sbjct: 715  SDFNQSPRNMYQC--QMGKQAMGTPGTAIDYRTDNKLYRLQTGQTPVVRPPLYNAYGLDN 772

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  I N+   ++     ++ + +I  L  DK+       +
Sbjct: 773  FPNGMNAVVAVISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIYALD-DKESRGRGKSK 831

Query: 981  NIYSRLMEILCGQNAVSGPK--GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L     G    +  K    +         +SE      W     D      +   
Sbjct: 832  RATTKLFGFAPGGLVKAEWKAQLDEDGLPHIGAKVSEGSLVGAWHTVQYDPATDTYINVD 891

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  +       E+ F + +  +  G +    V + V +   + R    GDK + RHG KG
Sbjct: 892  KQTHFLKYKDGEEGFIDSVRVL--GSETGNEVCQAVSIKYRVPRRPVIGDKFSSRHGQKG 949

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++S++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    
Sbjct: 950  VLSQLWPATDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGSLHGLPQDSTPFQ 1009

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                   F G     
Sbjct: 1010 FSEEATAGD-------------------------------------------FFG----- 1021

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L+ A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +
Sbjct: 1022 --KQLQRAGYNFHGNEPMYSGITGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAL 1079

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1080 TGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 106/781 (13%), Positives = 222/781 (28%), Gaps = 149/781 (19%)

Query: 11  GRVRKFFGKNPEIIDIPDL---IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            R R F     +    P L   I     S++                L+AA K +  I +
Sbjct: 17  RRERLFRHPPKDKTAYPALAAAIRPHIDSFNALFEDTKV--------LEAALKDIG-IKS 67

Query: 68  F-----------------------SGAAMLEFVSYEFDP---P---KFD-------VDDC 91
           F                            +       +    P   K+          +C
Sbjct: 68  FIDGSSETPEEKASRREDGRRAPKRNKLSVRITELFLEKAVLPASNKYSTRNREIYPAEC 127

Query: 92  LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-----------TK 140
             R  TY   L+  L   + + +     +           +G +P+M           T 
Sbjct: 128 RERHATYRGRLRARLEYRINNGEWKESVRE----------LGQVPIMIRSNRCHLEKATP 177

Query: 141 D-------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS----GKLLY 180
                         G F++ G ++++   +   R+ P     +   +   +    G  L 
Sbjct: 178 SQLVDHKEESEELGGYFIVNGNEKLIRMLIVGKRNFPTAIIRNSFQKRGSAYTKFGVQLR 237

Query: 181 ACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYP 234
           + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +     + 
Sbjct: 238 SVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--REIFE 290

Query: 235 KIVYSQRGDFWCFPLSAA--DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           ++V  +              +L++    +  +         + S  +   G+ + + E+ 
Sbjct: 291 RLVGREGSLGIENTFVTDRVELLLRTYKAYGVHSRSKCRAYLGSKFRFVLGMPEDIPEED 350

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
           V         L    V   + N    E        +    + ++++    D      D+V
Sbjct: 351 VGT------ELLRKIVLPHLGNQNVTETQDNDKFNMILFMIRKLYNLVAGDCAPDNPDAV 404

Query: 353 NN-----NAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVS--TFSVAESMFNFLFFDS 403
           +N       Y+   L+ ++ ++   ++  + R   MR  D               +   +
Sbjct: 405 SNQEVLLGGYLYGMLLKERLEEWLKSVGPMVRDWRMRNQDAKFTDPKFEREFLTRIIGRT 464

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++     +        L   T  D++      ++A         +    I         +
Sbjct: 465 NENIGGAMEYFLSTGNLVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMIHRGSFFAQLK 524

Query: 464 VRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
             +V ++L   +  L  +         + +      +          +  V      +  
Sbjct: 525 TTTVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLISTSNLDVSGIPGVLAGLGVTSE 584

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           S      +   ++        LG     ++RA  +          +  P E   G     
Sbjct: 585 SSCSIEESIPVQLDGK----ILGYCTPKQSRAIADTLRYWKVQGHKQIPVELEIG--YVP 638

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            S+   +  V  +      YR V      + + Y+   E+    IA   S +    S   
Sbjct: 639 SSNGGQYPGVYMFSEAARMYRPVK-YLPLDKLDYVGPFEQPYMEIACVASDIRNGVS--- 694

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                                I+  P  ++SI A++ PF + + S R +  C M +QA+ 
Sbjct: 695 -------------------THIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMG 735

Query: 703 L 703
            
Sbjct: 736 T 736


>gi|148879043|emb|CAM07037.1| RpoB protein [Mycobacterium sp. MG7]
          Length = 228

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 99/232 (42%), Positives = 132/232 (56%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 29   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 88

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 89   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 133

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 134  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 176

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 177  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 228


>gi|196018598|ref|XP_002118836.1| hypothetical protein TRIADDRAFT_62839 [Trichoplax adhaerens]
 gi|190578036|gb|EDV18678.1| hypothetical protein TRIADDRAFT_62839 [Trichoplax adhaerens]
          Length = 617

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 172/322 (53%), Positives = 244/322 (75%), Gaps = 3/322 (0%)

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
              + TC+NQRP+VKVG  V   DI+ADG STD+G+LALG+N+LVAFMPW+GYNFEDS+L+
Sbjct: 299  GFEGTCINQRPIVKVGQYVEAGDILADGASTDMGELALGKNILVAFMPWNGYNFEDSILL 358

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V +D++TS+HI E+E++ARDT+LGPEEITRDIPNV+EE L ++DE GI+ +GA+V 
Sbjct: 359  SERLVKDDIYTSVHINEYEIVARDTRLGPEEITRDIPNVNEENLTHLDETGIVNIGAQVK 418

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            PGDILVGK+TPK ESP+TPEEKLLRAIFGEKA DVR++SLRVP G  G +VDV+IF + G
Sbjct: 419  PGDILVGKVTPKTESPLTPEEKLLRAIFGEKAADVRNSSLRVPPGEKGVIVDVKIFTKRG 478

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            + K+ER+IS+ER +IE  ++D +DE+ I++  +++++  IL G+          KS  + 
Sbjct: 479  VQKDERAISIERNEIEKFSKDMEDEKRIIEDYVFNKVKVILFGKKVK---DKSNKSITID 535

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             + + +    Q W   + D+K + +++ L+  Y+     LE  +K+K+EK+Q GDD+P G
Sbjct: 536  QNFLDDLDNKQVWSLELDDKKSKEDIQKLEEFYDNYLKKLEKDYKHKVEKLQSGDDLPQG 595

Query: 1070 VLRVVKVFVAMKRPIQSGDKMA 1091
            VL+++K++VA K  IQ GDKMA
Sbjct: 596  VLKIIKIYVANKLKIQPGDKMA 617



 Score =  208 bits (530), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 141/312 (45%), Positives = 217/312 (69%), Gaps = 1/312 (0%)

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-SDCLCGLYVAEDIVNGET 317
           K+   +VD +T E + + G ++T  +LK  ++       IT  D +   ++A+DIVN  T
Sbjct: 2   KIEKDIVDANTKEIIFKKGIRVTPRILKDFEKNNTDRYYITTEDDIKRKFLAKDIVNLTT 61

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           GE+  E+   + ++ ++ +    I +I I+ V++V++ ++IR+T+V DKNKD + AL DI
Sbjct: 62  GEVLYESTQEVTQEIIDSVKALNINEIVIIDVNNVDSGSFIRDTIVLDKNKDEEQALADI 121

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           Y+V+RPG+ ST  VA+ +F  +FFD++KYDLS VGR+K+N + +LD P     + K+DII
Sbjct: 122 YKVLRPGEPSTPEVAKQLFESMFFDNEKYDLSAVGRMKINKKHDLDVPHTTTALTKDDII 181

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            IIK L++L+ G GT+DDID+L NRRVRSVGE+++NQ+R+GL+RM++SI +R+SSV+ID+
Sbjct: 182 VIIKHLLNLKCGIGTVDDIDSLANRRVRSVGELVENQFRMGLVRMQKSIVDRMSSVEIDN 241

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           VMP DL+N+K ++S + EFF  SQLSQ  +  N L+ ITH RRLSALG GG+ R RAG E
Sbjct: 242 VMPHDLVNSKTLMSYLREFFGISQLSQFMDQTNPLAEITHKRRLSALGPGGLTRERAGFE 301

Query: 558 MRDVHPTHYGRI 569
              ++     ++
Sbjct: 302 GTCINQRPIVKV 313


>gi|148879031|emb|CAM07031.1| RpoB protein [Mycobacterium sp. MG1]
          Length = 230

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 99/232 (42%), Positives = 132/232 (56%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 230


>gi|57335863|emb|CAH23706.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 20]
          Length = 360

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 172/297 (57%), Positives = 222/297 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L+E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNEKEVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 241 RGGVIDSVDATRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 297


>gi|110666971|gb|ABG81886.1| RNA polymerase II second largest subunit [Simonyella variegata]
          Length = 717

 Score =  295 bits (754), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 131/835 (15%), Positives = 252/835 (30%), Gaps = 139/835 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + I +       +         +    + +
Sbjct: 1    DDRDHFGRKRLDLAGPLLANLFRMLFTKLTKDIYKYLERCVDNNKEFSLDLGVRHSIITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAAQAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CP+ET EG   GLV +L     V+  + G     +      +   D   
Sbjct: 117  RQLHNTHWGLVCPSETPEGQACGLVKNLALMCYVSVGSPGDPLNEFMTSLGMEPLEDYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                     ++      + ++  +    +        +      I D  +   K      
Sbjct: 177  RRYPNATKIFVNGTWVGITKNPVYLVSKIQQLRRDATLKYEVSLIRDIREREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCN--MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
              + P    D++       N  + R  +  L+        G+ +   +  G   + K AG
Sbjct: 237  RIMRPLFVIDNNPSSTNNGNLYINRTHISKLEQTKELKQAGVTNDQTQLYGWTQLVK-AG 295

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE +DA       +    D            K  +++ +     RP +           
Sbjct: 296  VVEYLDAEEEESAMIIMGPDQLGEIRRDPTGAK-SKADGDLYAPIRPRINPNTHTF--TH 352

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N                        ++     
Sbjct: 353  CEINPSMILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGK 387

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              +G      DI               +  +             +       +   +  +
Sbjct: 388  QAMGVYLTNFDIRM-----------DTMSNILYYPQKPLATTRSMEFLRFRELPAGQNAI 436

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R  I++ ++      E+ E   +    
Sbjct: 437  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYIEQEQKIGFNNLEEFEKPTKQYTT 495

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +       +  G           K++ L+                   + +Q 
Sbjct: 496  RMRPGTYDKLDDDGFVAPGVRVSGEDIIIGKTSPLT-------------------DPMQE 536

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAG 1092
              E    Q E +K  +    ++    I     +      + VK+     +  Q GDK A 
Sbjct: 537  GAEGGVRQREHTKRDISAPLRSTEAGIVDRVLLTTVEGRKCVKIRTRTTKVPQIGDKFAS 596

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 597  RHGQKGTIGITYRQEDMPFTVEGVVPDLIINPHAIPSRMTIAHLIECLLSKVAAVDGLEG 656

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 657  D-----------------------------------------------------ATP-FT 662

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            G   + I+S+L  +     G  ++Y+G TG      + +G  Y  +L HMV DK+
Sbjct: 663  GVTVQDISSLLEHSGYQSRGFEVMYNGHTGRKLVSQIFLGPTYYQRLRHMVDDKI 717


>gi|78172770|gb|ABB29455.1| RpoB [Mycobacterium jacuzzii]
          Length = 246

 Score =  295 bits (754), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 99/232 (42%), Positives = 133/232 (57%), Gaps = 37/232 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 44   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 103

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +        ++
Sbjct: 104  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPDWASKLPE------QL 156

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                + +                       VSTPVFDGA E  +  +L            
Sbjct: 157  YSAPADSI----------------------VSTPVFDGAQEGELQGLLGSTLPNRDGEVM 194

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 195  VDADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 246



 Score = 49.7 bits (117), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 52


>gi|171689286|ref|XP_001909583.1| hypothetical protein [Podospora anserina S mat+]
 gi|170944605|emb|CAP70716.1| unnamed protein product [Podospora anserina S mat+]
          Length = 1160

 Score =  295 bits (754), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 96/496 (19%), Positives = 171/496 (34%), Gaps = 90/496 (18%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   +         ++F 
Sbjct: 738  YPQRPMVITKTIQLIHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVFK 797

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            ++              ++        D    + R+   +  +   +L      +     K
Sbjct: 798  KYTT------------ELLQYPNRNKDRLGGVQRDEDGKAKDRHAVLDNDGLATPGMKMK 845

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               ++      E P  Q      +D K+        + Y+     +       ++K+   
Sbjct: 846  DGDIMIMK---ETPVDQTSTNIGEDRKITE-FRPCPISYKIKDPAI-------VDKVVI- 893

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                     ++KV     R  + GDK + RHG KG+V  I+  ED+PF   G   DI++N
Sbjct: 894  -TTKESGTPLLKVRTRQTRRPELGDKFSSRHGQKGVVGIIVDQEDLPFSDKGLTPDIIMN 952

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P G PSRM V        G     L  K   +    +                       
Sbjct: 953  PHGFPSRMTV--------GKLFECLTGKASVVAGRREYGFGD------------------ 986

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                       F     E +  +L        G+     G+TGE
Sbjct: 987  --------------------------AFRSHPVEEMGKVLIEHGFSWEGKDYFTSGITGE 1020

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P +  +  G I+  +L HMV+DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ 
Sbjct: 1021 PHEAYLFNGPIFYQRLKHMVADKMHSRSRGPRAVLTRQPTEGRSRDGGLRLGEMERDCLI 1080

Query: 1304 AYGAAYVLQEMLTIKSD----DVVGR-----TRVYESIVAGN-DTFETGTPESFNVLVKE 1353
            AYGA+ +L E L   SD    DV  R      + Y        +  +   P +  +L++E
Sbjct: 1081 AYGASQLLLERLMYSSDVTKVDVCERCGLMGYKGYCQTCKTTSNVTKMNMPYAAKLLLQE 1140

Query: 1354 MQALGLSIDLENSRTK 1369
            + ++ + + ++     
Sbjct: 1141 LISMNVGVRMQLEDQF 1156



 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 124/992 (12%), Positives = 274/992 (27%), Gaps = 194/992 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+  +I      N  ++              +  LEF       P    
Sbjct: 46  LVKQHIDSYNYFVEEDIKKIVEANRVIR---------CDQEPSFWLEFTDIRVGKPTRNE 96

Query: 86  -----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  RD TYA P+ + +               +++I+ +++ +  
Sbjct: 97  NSQLQWQSSTTVSPMECRLRDATYAAPVVVDIAY---------PKNGVRNIR-KNVQLCR 146

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
           +P+M K                         G F++ G +++++ Q   S          
Sbjct: 147 IPVMLKSSKCYLNGANNARMEELNECPLDPGGYFIVGGTEKVILIQEQLSKNRVIVEKDD 206

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-----VPVTSFLMAL-GMD 224
           +  +   +  +     ++          KD    RI          +P+   L AL G+ 
Sbjct: 207 KGGVQASVTSSTH---ERKSK-TYVVLKKD----RILLTHNILVEAIPIVIVLKALGGLS 258

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK-KLTSG 283
             +I+          Q      F  +A   +   + +   V         +    K ++G
Sbjct: 259 DYDIMELVAGGDSRYQDDFLINFEDAAKAGVYTQQQALEYVGARVKMGGPKKPSPKFSAG 318

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI------DEKSLEEIF 337
             ++  E+G+  L      L   +V    ++     IYI            + + +++  
Sbjct: 319 PRRNPIEEGLDALS----NLIVAHVTVKDLDFYPKTIYIAMMVRRILMAVHNPELVDDRD 374

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
               + + +           +    +     + +       R      +       +M  
Sbjct: 375 FVGNKRLELAGQLLSLLFEDLLKGFIGQLKANMEHFFKRPNRTSAYDPIGPIGSYGTMIT 434

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                + +    TV R  MN          + +I    ++  I    +          + 
Sbjct: 435 QGLNRAIQSGNWTVKRFGMNRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQ 494

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 + +          L    ++        + +      +  ++       + E  
Sbjct: 495 PSQWGMLCTSDTPEGEACGL----VKNLALMTHITTEAGEEKVKKCVSTLIEGIRLIEEC 550

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             ++   + E    +  +  T     L      +       R V     G      T+  
Sbjct: 551 SGTE---MHEENAFIIHVNGTPYALTLDAAAFTKRFKQFRRRGVLSAFIGIHTSHATASI 607

Query: 578 HNIGLVSSLTSFARV--NAYGFIETPYR--------KVCDGKVTNDVVYLSAMEEENRYI 627
           H       +     +  N    +E  +            D      + YL   EE +  I
Sbjct: 608 HIATDEGRICRPYIIVENGKSMLEAAHLDLLRHKKATFEDFLKKGVLEYLDVNEENDALI 667

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A   S ++                       ++   ++  P  ++   A LIPF  ++ S
Sbjct: 668 AVHESDIN-----------------------DQTTHLEIEPFTILGAVAGLIPFPHHNQS 704

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R    C M +QA+                                           I  
Sbjct: 705 PRNTYQCAMGKQAIGF-----------------------------------------IAY 723

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            + +   +     +Y               QRP+V          I           L  
Sbjct: 724 NQQNRIDTLHYTLVYP--------------QRPMV----------ITKTIQLIHYDKLPA 759

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI----TR 863
           G+N  V  M + GY+ ED++++++             +++           ++      R
Sbjct: 760 GQNATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVFKKYTTELLQYPNRNKDRLGGVQR 819

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           D    +++    +D  G+   G ++  GDI++ K TP  ++     E      F    + 
Sbjct: 820 DEDGKAKDRHAVLDNDGLATPGMKMKDGDIMIMKETPVDQTSTNIGEDRKITEFRPCPIS 879

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            +   ++ P+ V   V+  +      +    R
Sbjct: 880 YK---IKDPAIVDKVVITTKESGTPLLKVRTR 908


>gi|269912574|emb|CAY86067.1| RNA polymerase beta subunit [Gluconacetobacter hansenii]
          Length = 305

 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 144/307 (46%), Positives = 188/307 (61%), Gaps = 28/307 (9%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GM  +EIL  FY ++ + + G  W   
Sbjct: 61  VTTLLYALEGEESRAAREAKAAEGGDVDSMEIQGMSPDEILGYFYGQVEFIKSGKGWARR 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
               D   G K+   LVD DTGE V +   KLT+ +++ + E   K + +    L G ++
Sbjct: 121 FDP-DAFRGQKLLEPLVDADTGEIVAQVDTKLTARMVRKIAET-TKDVLVGPAGLIGRFI 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A D+VN +TGEI+ EAGD + E  LE +    +  +  L +D+ N   +IRNTL  DKN 
Sbjct: 179 AFDMVNPDTGEIFAEAGDELTETRLEALEADGVTKLVTLAIDATN-GPWIRNTLAIDKNT 237

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R DAL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +D PD V
Sbjct: 238 SRDDALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVDVPDTV 297

Query: 429 RHIRKED 435
           R +RKED
Sbjct: 298 RVLRKED 304


>gi|269308424|gb|ACZ34208.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5510]
 gi|269308430|gb|ACZ34211.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5478]
          Length = 339

 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 188/347 (54%), Positives = 254/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV + KV  +   YL+A +E+   +AQAN  + EDG+  ++ V  
Sbjct: 1   YAKINEYGFIETPYRKVKNKKVYLDQYEYLTADKEKEYVVAQANIKMSEDGTILDDQVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+V    +D++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMVNATDVDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLIDPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV+ VD+ +I+I           + V  Y L  F
Sbjct: 121 SPVVGTGVEFEAARDSGDAVVATEDGIVKYVDSRKIIIEQN--------NVVKNYDLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+V++ DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 NRSNNGTAITHIPIVKVGDKVKKRDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK G EEITRDIPNVSE   KN+DE GI+ +GAE
Sbjct: 233 IVSERVVIDDRFTSIHIDEYTIERRQTKQGQEEITRDIPNVSETVKKNLDEDGIVAIGAE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|52538195|emb|CAH19199.1| RNA polymerase beta-subunit [Pseudomonas frederiksbergensis]
          Length = 316

 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 225/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGSA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRHG 313


>gi|52538197|emb|CAH19200.1| RNA polymerase beta-subunit [Pseudomonas fragi]
          Length = 316

 Score =  294 bits (753), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 225/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGTA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 QRHHGRRPVHRYG 313


>gi|260505164|gb|ACX42074.1| RNA polymerase beta subunit [Leclercia sp. 349/07]
          Length = 303

 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 183/302 (60%), Positives = 231/302 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           AKR G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ +
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMHAGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPI 301

Query: 789 RR 790
            R
Sbjct: 302 ER 303


>gi|167044136|gb|ABZ08819.1| putative RNA polymerase Rpb2, domain 6 [uncultured marine
            crenarchaeote HF4000_APKG5C13]
          Length = 1114

 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 82/321 (25%), Positives = 127/321 (39%), Gaps = 76/321 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ KV +   R  + GDK A RHG KG+V  +   ED+P+  DG   D+++NP  
Sbjct: 850  SAEGGKMFKVRIRDMRLPEIGDKFASRHGQKGVVGLLAKAEDLPYTADGISPDVLINPHA 909

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM VG + E+  G A    G+K+ +     +   ++  +                  
Sbjct: 910  FPSRMTVGMMLESITGKAAAMRGRKVDASAFVGEKVDEVKSVLEDAGFKYSGKEIM---- 965

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                         G        TG+ F 
Sbjct: 966  -------------------------------------------YDG-------RTGKQFP 975

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              V +G +Y  KL+HMV+DK++AR+ G   ++T+QP  G++  GG R GEME  CI AYG
Sbjct: 976  VEVFIGVVYYQKLHHMVADKIHARARGQVQMLTKQPTEGRARGGGLRFGEMERDCIIAYG 1035

Query: 1307 AAYVLQEMLTIKSD----------------DVVGRTRVYESIV---AGNDTFETGTPESF 1347
            A+ +L++ L  +SD                D+  R R Y   V    G          +F
Sbjct: 1036 ASMILKDRLLDESDKSDIFVCERCGLVAYHDIKQR-RFY-CRVCDKKGK-VSSVSVAYAF 1092

Query: 1348 NVLVKEMQALGLSIDLENSRT 1368
             +L++EM  L ++  L     
Sbjct: 1093 KLLLQEMSCLNIAPRLLIKER 1113



 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 136/756 (17%), Positives = 273/756 (36%), Gaps = 86/756 (11%)

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           IL  F  + +     D +  P     +    +V   L D+   + ++++ K     + K+
Sbjct: 129 ILRNFSEQKLIDHAEDPYD-PGGYFIINGSERVIVGLEDLSYNKIIVDADKIGGKKVFKA 187

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                          + G     ++V  E G I         +  +  +  +   +    
Sbjct: 188 KIYS----------SIVGYRAKLELVLKEDGLIVARIPGSPVDIPIITLVRALGLESDKE 237

Query: 348 YVDSVNNNAYIRNT----LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
              +++ N  I+N         +    KDA+  I + + PG +  F +  +     +   
Sbjct: 238 IASAISLNDKIQNELEGSFEKTEISTPKDAIEYISKRIAPGMLEEFQIKRAETLLDWGL- 296

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
               L  +G+   N +  +    +               L++L+ G    DD D+ GN+ 
Sbjct: 297 ----LPHLGKQPENRKEKIQFLGEAAC-----------KLLELKLGWIQPDDKDHYGNKV 341

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSV-----------DIDSVMPQDLINAKPVVSA 512
           V+  G+ML + +R     + R +K ++               I   +  D +N    ++ 
Sbjct: 342 VKFAGQMLADLFRTAFRNLVRDMKYQLERSGQKRGINAVSAAIRPGIISDKLN--NAIAT 399

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                    ++QL +  N LS I+H RR+    Q  ++R +   E RD+H TH+GRICP+
Sbjct: 400 GNWGRGRVGVTQLLDRTNYLSTISHLRRV----QSPLSRTQPNFEARDLHSTHFGRICPS 455

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG N GLV +L   A ++     E    K+ +           +++++   +   + 
Sbjct: 456 ETPEGSNCGLVKNLALSAIISVSVPSEEIIEKMYEIGTEYFTDVKDSVKKDGTRV-FVDG 514

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI--------AASLIPFLEN 684
            L       ++L                I      P+Q  +         A  ++  L  
Sbjct: 515 KLIGYHKDGKKLASSLRELRRSSKIHPHIGISIHIPEQEGATKRLYVNCNAGRVLRSLIV 574

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
               +  +  ++  + +  L +    V  G +E + A       +      V++     I
Sbjct: 575 VKDGKSTLTPDLLDKILKKLVSWNDLVRMGVIELIDANEEENCFITFDDKHVKKHTHTEI 634

Query: 744 VI-------RSVEGDLDPSTSGVDIYRLMKFQRS--NQNTCVNQRPLVKVGDEVRRNDII 794
                     S+    + + S  + Y     ++S       +N    V+    +     I
Sbjct: 635 FPSAILGAGASIIPYPEHNQSPRNTYESAMAKQSLGFSTPMMNTSTYVRQHTMLYPQTPI 694

Query: 795 ADGPST---DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
               +     L     G+N +VA +P+ GYN ED++++S+  +   +  ++    +E  +
Sbjct: 695 VTTRAMGLLGLEKRPAGQNCVVAVLPFDGYNIEDAIVLSKSAIERGLGRTLFYRIYEAES 754

Query: 852 RDTKLGPEEITRDIP--------NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           +    G  +   +IP           E+  + +++ GI+   + V+ GDIL+GK +P   
Sbjct: 755 KQYPGGMRDNF-EIPNADDNLRGYKGEKSYRLLEDDGIVASESRVSGGDILIGKTSPPRF 813

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                E +             RDTS+ V    +G V
Sbjct: 814 MEEYHELEG-------SGPYRRDTSIGVRPSETGVV 842



 Score =  129 bits (324), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 97/722 (13%), Positives = 206/722 (28%), Gaps = 124/722 (17%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSV--FPITAFSGAAMLEFVSYEFDPPK-------- 85
           S++ FL           +GLQ     +    I        ++    +F  P+        
Sbjct: 28  SFNEFLT----------KGLQEIINEIDHIDIENAEYPYRIKLGRIQFKQPRMMELDGSV 77

Query: 86  --FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-- 141
                 +   R+++Y  PL   L   V +  +    + +         +GD+P+M K   
Sbjct: 78  THITPAEARLRNVSYVAPLM--LEASVIEDGKTLENRFLH--------IGDIPIMVKSEG 127

Query: 142 ----------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
                                 G F+I G +R++V     S   +         + GK +
Sbjct: 128 CILRNFSEQKLIDHAEDPYDPGGYFIINGSERVIVGLEDLS---YNKIIVDADKIGGKKV 184

Query: 180 YACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL----- 229
           +  +I       +   +++      +I  RI      +P+ + + ALG++S++ +     
Sbjct: 185 FKAKIYSSIVGYR-AKLELVLKEDGLIVARIPGSPVDIPIITLVRALGLESDKEIASAIS 243

Query: 230 --STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD--IDTGEQVIESGKKLTSGLL 285
                  ++  S        P  A + +        L +  I   E +++ G  L   L 
Sbjct: 244 LNDKIQNELEGSFEKTEISTPKDAIEYISKRIAPGMLEEFQIKRAETLLDWG--LLPHLG 301

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           K  + +  K   +          A  ++  + G I  +  D    K ++           
Sbjct: 302 KQPENRKEKIQFLGE-------AACKLLELKLGWIQPDDKDHYGNKVVKFAGQMLADLFR 354

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
             + + V +  Y        +  +   A       +RPG +S             +   +
Sbjct: 355 TAFRNLVRDMKYQLERSGQKRGINAVSAA------IRPGIISDKLNNA--IATGNWGRGR 406

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
             ++ +      +            + +       + L     G+  I   +        
Sbjct: 407 VGVTQLLDRTNYLSTISHLRRVQSPLSRTQPNFEARDLHSTHFGR--ICPSETPEGSNCG 464

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            V  +  +      +  E  I++            +D +        V        +   
Sbjct: 465 LVKNLALSAIISVSVPSEEIIEKMYEIGTEYFTDVKDSVKKDGTRVFVDGKL----IGYH 520

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
           ++     S +   RR S +    +  +    E        Y   C A       I +   
Sbjct: 521 KDGKKLASSLRELRRSSKIHPH-IGISIHIPEQEGATKRLYV-NCNAGRVLRSLIVVKDG 578

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            ++    +    I        D      +  + A EEEN +I                  
Sbjct: 579 KSTL-TPDLLDKILKKLVSWNDLVRMGVIELIDANEEENCFIT----------------- 620

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                        +K    +  P  ++   AS+IP+ E++ S R      M +Q++    
Sbjct: 621 -------FDDKHVKKHTHTEIFPSAILGAGASIIPYPEHNQSPRNTYESAMAKQSLGFST 673

Query: 706 AE 707
             
Sbjct: 674 PM 675


>gi|52538201|emb|CAH19202.1| RNA polymerase beta-subunit [Pseudomonas fragi]
 gi|52538203|emb|CAH19203.1| RNA polymerase beta-subunit [Pseudomonas fragi]
          Length = 327

 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 225/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGTA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRYG 313


>gi|52538205|emb|CAH19204.1| RNA polymerase beta-subunit [Pseudomonas fragi]
          Length = 329

 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 225/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGTA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRYG 313


>gi|298162154|gb|ADI59539.1| RNA polymerase B-subunit [Mycobacterium tilburgii]
          Length = 246

 Score =  294 bits (753), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 99/233 (42%), Positives = 133/233 (57%), Gaps = 40/233 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWDIEGTPDWAAN-------------- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 148  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 190

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            +D  G+ +L+DG +GE F  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQ
Sbjct: 191  VDADGKVVLFDGRSGELFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQ 243



 Score = 47.0 bits (110), Expect = 0.025,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|52538173|emb|CAH19188.1| RNA polymerase beta-subunit [Pseudomonas aeruginosa]
          Length = 360

 Score =  294 bits (752), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 172/297 (57%), Positives = 221/297 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L+E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNEKEVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA 
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAP 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 241 RGGVIDSVDATRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 297


>gi|126722435|dbj|BAF48631.1| DNA-dependent RNA polymerase subunit B' [Halorubrum vacuolatum]
          Length = 435

 Score =  294 bits (752), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 82/253 (32%), Positives = 114/253 (45%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +
Sbjct: 197  EDGSKLSKVKVRDQRVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVVNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G                                             
Sbjct: 257  PSRMTVGHVLEMLGGKV------------------------------------------- 273

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                         +      TP F G DE  +   L     + SG+ ++Y G+TGE  D 
Sbjct: 274  ----------GSLRGSRVDGTP-FQGEDEAELREGLEEFGFNSSGKEVMYSGVTGEKIDA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA
Sbjct: 323  EIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            + VL E L   SD
Sbjct: 383  SMVLNERLLQSSD 395



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 78/210 (37%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                 +  +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLMHYPQLAMVK----------TQTTEQINFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        E+   ++DE 
Sbjct: 76  ALVMNQGSVDRALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYTHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETVVDESSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    ++   EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVKVRDQRVPELGDK 218


>gi|52538177|emb|CAH19190.1| RNA polymerase beta-subunit [Pseudomonas aeruginosa]
          Length = 360

 Score =  294 bits (752), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 172/297 (57%), Positives = 222/297 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L+E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNEKEVLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 241 RGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 297


>gi|302503725|ref|XP_003013822.1| hypothetical protein ARB_07934 [Arthroderma benhamiae CBS 112371]
 gi|291177388|gb|EFE33182.1| hypothetical protein ARB_07934 [Arthroderma benhamiae CBS 112371]
          Length = 1243

 Score =  294 bits (752), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 108/522 (20%), Positives = 187/522 (35%), Gaps = 60/522 (11%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  + + +  + + G   +  M I+          S HI EF+     + L      
Sbjct: 656  RMYRPVKYLPLDKLDYVGPFEQPYMEIACVASDIRNGVSTHI-EFDPTHILSILANMTPF 714

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
             D         +   + G   +G      D        + ++  TP  +  L  A   + 
Sbjct: 715  SDFNQSPRNMYQC--QMGKQAMGTPGTAIDYRTDNKLYRLQTGQTPVVRPPLYNAYGLDN 772

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  I N+   ++     ++ + +I  L  DK+       +
Sbjct: 773  FPNGMNAVVAVISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIYALD-DKESRGRGKSK 831

Query: 981  NIYSRLMEILCGQNAVSGPK--GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L     G    +  K    +         +SE      W     D      +   
Sbjct: 832  RAITKLFGFAPGGLVKAEWKAQLDEDGLPHIGAKVSEGSLVGAWHTVQYDPATDTYINVD 891

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  +       E+ F + +  +  G +    V + + +   + R    GDK + RHG KG
Sbjct: 892  KQTHFLKYKDGEEGFIDSVRVL--GSETGNEVCQAISIKYRVPRRPVIGDKFSSRHGQKG 949

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++S++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    
Sbjct: 950  VLSQLWPATDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGSLHGLPQDSTPFQ 1009

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                   F G     
Sbjct: 1010 FSEEATAGD-------------------------------------------FFG----- 1021

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L+ A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +
Sbjct: 1022 --KQLQRAGYNFHGNEPMYSGITGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAL 1079

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1080 TGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 104/779 (13%), Positives = 219/779 (28%), Gaps = 145/779 (18%)

Query: 11  GRVRKFFGKNPEIIDIPDL---IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            R R F     +    P L   I     S++                L+AA K +  I +
Sbjct: 17  RRERLFRHPPKDKTAYPALAAAIRPHIDSFNALFEDTKV--------LEAALKDIG-IKS 67

Query: 68  F-----------------------SGAAMLEFVSYEFDP---P---KFD-------VDDC 91
           F                            +       +    P   K+          +C
Sbjct: 68  FIDGSSETPEEKASRREDGRRAPKRNKLSVRITELFLEKAVLPASNKYSTRNREIYPAEC 127

Query: 92  LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM-----------TK 140
             R  TY   L+  L   + + +     +           +G +P+M           T 
Sbjct: 128 RERHATYRGRLRARLEYRINNGEWKESVRE----------LGQVPIMIRSNRCHLEKATP 177

Query: 141 D-------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS----GKLLY 180
                         G F++ G ++++   +   R+ P     +   +   +    G  L 
Sbjct: 178 SQLVDHKEESEELGGYFIVNGNEKLIRMLIVGKRNFPTAIIRNSFQKRGSAYTKFGVQLR 237

Query: 181 ACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYP 234
           + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +     + 
Sbjct: 238 SVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--REIFE 290

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           ++V  +             + +  +   +       +     G K    L      + + 
Sbjct: 291 RLVGREGSLGIENTFVTDRVELLLRTYKAYGVHSRSKCRAYLGSKFRFVL---GMPEDIP 347

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              + ++ L    V   + N    E        +    + ++++    D      D+V+N
Sbjct: 348 EEDVGTEFLR-KIVLPHLGNQNVTETQDNDKFNMILFMIRKLYNLVAGDCAPDNPDAVSN 406

Query: 355 -----NAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVS--TFSVAESMFNFLFFDSDK 405
                  Y+   L+ ++ ++   ++  + R   MR  D               +   +++
Sbjct: 407 QEVLLGGYLYGMLLKERLEEWLKSVGPMVRDWRMRNQDAKFTDPKFEREFLTRIIGRTNE 466

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
                +        L   T  D++      ++A         +    I         +  
Sbjct: 467 NIGGAMEYFLSTGNLVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMIHRGSFFAQLKTT 526

Query: 466 SVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           +V ++L   +  L  +         + +      +          +  V      +  S 
Sbjct: 527 TVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLISTSNLDVSGIPGVLAGLGVTSESS 586

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
                +   ++        LG     ++RA  +          +  P E   G      S
Sbjct: 587 CSIEESIPVQLDGK----ILGYCTPKQSRAIADTLRYWKVQGHKQIPVELEIG--YVPSS 640

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           +   +  V  +      YR V      + + Y+   E+    IA   S +    S     
Sbjct: 641 NGGQYPGVYMFSEAARMYRPVK-YLPLDKLDYVGPFEQPYMEIACVASDIRNGVS----- 694

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                              I+  P  ++SI A++ PF + + S R +  C M +QA+  
Sbjct: 695 -----------------THIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGT 736


>gi|52694227|emb|CAG30643.1| DNA-directed RNA polymerase beta chain [Pseudomonas parafulva]
          Length = 316

 Score =  294 bits (752), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 178/315 (56%), Positives = 234/315 (74%), Gaps = 2/315 (0%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG G V 
Sbjct: 2   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGAVL 61

Query: 551 RARAGV--EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              A    + RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G
Sbjct: 62  TPSAVPASKFRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SP
Sbjct: 122 VVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPEDVTLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +V
Sbjct: 182 KQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
           A+R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V
Sbjct: 242 ARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDKV 301

Query: 789 RRNDIIADGPSTDLG 803
           +R DI+ADGPST++G
Sbjct: 302 QRGDIMADGPSTEMG 316


>gi|119469451|ref|XP_001257945.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Neosartorya fischeri NRRL 181]
 gi|119406097|gb|EAW16048.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Neosartorya fischeri NRRL 181]
          Length = 1232

 Score =  294 bits (752), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 108/532 (20%), Positives = 173/532 (32%), Gaps = 101/532 (18%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
            D +  G ST +         +VA M P+  YN     +   +M  + + T     E+   
Sbjct: 688  DDLVAGVSTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIEY--- 744

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R         T   P V                                 G        
Sbjct: 745  -RTDNKLYRLQTGQTPIVRPPLYN-------------------------AYGLDNFPNGT 778

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      D+ D  +   S                        ++ + +I  L  D
Sbjct: 779  NAVVAIISYTGYDMDDAMIINKSSHERGFG---------------YGTIYKTKIHSL--D 821

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              D +    R   ++L     G    +       +         + E      W     D
Sbjct: 822  DKDSRRSKSRREITKLFGFAPGGEIRAEWRTTLDEDGLPHVGARVKEGSLIAAWHTVRYD 881

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                  V    + +       E+ + + I  +     + P     VK  +   R    GD
Sbjct: 882  AASDSYVNVDGITHFVKYKDAEEGYIDSIRIMGAETGLEPCQALSVKYRI--PRKPVIGD 939

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + Q+ E+  G A    
Sbjct: 940  KFSSRHGQKGVCSQLWPAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESMAGKAGALH 999

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G    S    +      +                                          
Sbjct: 1000 GHPQDSTPFQFSEENTAA------------------------------------------ 1017

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +     LR A  +  G   LY G+TG+ F   + +G ++  +L HMV+DK  
Sbjct: 1018 --------DYFGQQLRKAGYNYYGNEPLYSGVTGKEFAADIFIGVVHYQRLRHMVNDKFQ 1069

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1070 VRTTGPVNQLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1121



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 130/873 (14%), Positives = 254/873 (29%), Gaps = 181/873 (20%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +   R  TY   L+  L   V + D       ++ I+E    +G +P+M +       
Sbjct: 125 PSEARERHATYRGKLRARLEYQVNNGD------WMESIRE----LGQVPIMLRTNRCHLE 174

Query: 141 -----------------DGTFVIKGIQRIV---V-------SQLHRSPGIHFDHDKGRAS 173
                             G F++ G ++++   V         + R   +   H   +  
Sbjct: 175 KATPQELVQHKEESEELGGYFIVNGNEKLIRMLVVGKRNYPMAIVRGSFVRRGHTYTKF- 233

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    +  R   R+    +PV   +  L +++ +
Sbjct: 234 --GIQIRSVR--PDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLIPVMMIMKGL-VETND 286

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK- 286
                +  IV S              + +  +               ++    T    + 
Sbjct: 287 --REIFEGIVGSATSKGVNNTFVTDRVELLLR-------------TYKAYNLHTRSSCRA 331

Query: 287 SLKEKGVKFLGITSD---CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            L EK    LG+ +D      G      IV    G   +   +  D    + I     + 
Sbjct: 332 YLGEKFKPVLGVPADMSNEDAGTEFLRKIVLPHLGNQNV--TETQDYDKFKLIMFMIRKL 389

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFF 401
             ++  D   +N               ++ LL   +Y ++    +  +            
Sbjct: 390 YALVAGDCAPDNP---------DAVSNQEILLGGFLYGMILKEQLEEWM------RSFGP 434

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +     G    +     D    +     E+I   ++  +   N   +   +D    
Sbjct: 435 ILRDWSNRNGGAKFTDPAFERDFLSKIVKRTNENIGGKLEYFLSTGN-LVSPTGLDLQQV 493

Query: 462 RRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC- 518
                + E +     +   RM    S   ++ +  +  ++P+      PV +        
Sbjct: 494 SGYTVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGL 553

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE-- 576
            + L+       S   ++H  +   L Q GV    +      V     GRI    + +  
Sbjct: 554 LNHLAHKCLIATSDVNVSHLPK--LLVQLGVRSESSVALEDSVTVQLDGRIVGYCSPKQA 611

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLD 635
                 V         N    +E  Y    +G     V   S A              LD
Sbjct: 612 RMIADTVRHWKVSGTHNIPRELEIGYVPNSNGGQYPGVYMFSQAARMYRPVKYLPLDKLD 671

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             G F +  +   C  ++++        I+ +P  ++SI A++ PF + + S R +  C 
Sbjct: 672 YVGPFEQPFMEIACLPDDLVAGVS--THIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQ 729

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +Q +          GT +E                                +  L   
Sbjct: 730 MSKQTMGTP-------GTAIEYR-----------------------------TDNKLYRL 753

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            +G                   Q P+V+               +  L +   G N +VA 
Sbjct: 754 QTG-------------------QTPIVRP----------PLYNAYGLDNFPNGTNAVVAI 784

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV------- 868
           + + GY+ +D+M+I++             +       D      +  R+I  +       
Sbjct: 785 ISYTGYDMDDAMIINKSSHERGFGYGTIYKTKIHSLDDKDSRRSKSRREITKLFGFAPGG 844

Query: 869 --SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
               E    +DE G+  VGA V  G ++    T
Sbjct: 845 EIRAEWRTTLDEDGLPHVGARVKEGSLIAAWHT 877


>gi|45545319|gb|AAS67507.1| DNA-dependent RNA polymerase II second largest subunit [Coccodinium
            bartschii]
          Length = 940

 Score =  294 bits (752), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 138/894 (15%), Positives = 269/894 (30%), Gaps = 156/894 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +++ ++    G+   DD D+LG +R+   G ++ N +R+ L    +      +
Sbjct: 172  KAFFLGYMVQRMLKCALGRTEPDDRDHLGKKRLDLSGPLMANLFRMKLDTATKDFFNYMK 231

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
                       +       + + +     +               +SQ+       S ++
Sbjct: 232  RRIEAGAGFSIKAGFKPGIITNGLKYSLATGNWGDQKKLDKAKAGVSQVLSRYTFASTLS 291

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-- 594
            H RR +A     + R     + R +H TH+G +CPAET EG   GLV +L+    V    
Sbjct: 292  HLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLSLMTMVTPSR 347

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA---NSSLDEDGSFTEELVFCRCAG 651
                   Y    + +   +        +  +  A        L +     +     R  G
Sbjct: 348  DTTPLMTYILEKNVEALEEWEP-RLNPQATKVFANGVWFAVILRDPKFLVDHFRSLRRKG 406

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLEND-------DSNRVLMGCNMQR-QAVPL 703
                      D  +   K    I   + P    D         +  L   ++ R Q    
Sbjct: 407  TIEPDISLVWDIREKEFKISGDIGRIIRPLFVVDTDKASPTHGHLKLTKEHILRLQESKA 466

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             K        G       +  A +       ++  +  + +I      L  + +  + Y 
Sbjct: 467  YKENPDQAPAGWSMANDYNWFALVNEGVVEFLDAEEEEQAMIIMTPEALSDARARAEGYL 526

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            +   +   +   V   P        +        PS  LG       +  + +P+  +N 
Sbjct: 527  IEPDEDPLRRNDVPLAP------HSKTFTHCEIHPSMILG-------VCASIIPFPDHNQ 573

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +                     E   +I    ++ L          
Sbjct: 574  SPRNTYQSAMGKQAMGV----------FLTNFDQRMETMANILYYPQKPLAR-------- 615

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
                          +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 616  -----------TQAMEFLKFRELPAGQNAIVAISCYSGYNQEDSVIMNQSSIDRGLF-RS 663

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R   D+ +    + +  +E   +    + + + +  Y ++ +   +  G        
Sbjct: 664  LFYRVYQDQEK---LIGQSVLEQFEKPTRGDTLRMRQGTYDKIDDDGIVAPGVRVRGEDI 720

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D                +E  QR  + +K          E    +++   
Sbjct: 721  IMGKTAPMAPD---------------AEELGQRQKQHVKRDASVPLRSTEAGVVDQVMLT 765

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            Q  D     + + VKV V   +  Q GDK A RHG KG +      EDMPF   G   D+
Sbjct: 766  QNAD-----MQKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTAQGVVPDL 820

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +  +          +S L   +        
Sbjct: 821  IINPHAIPSRMTIAHLIECLLSKVATLRGDEGDATPFTKVTVTQVSSLLRRMGYQSRGFE 880

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +G +    G 
Sbjct: 881  VM-----------------------------------------------YNGHT----GR 889

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                    V +G  Y  +L HMV DK+++R+ G   ++T+QP+ G++  GG R 
Sbjct: 890  ---KMVAQVFLGPTYYQRLRHMVDDKIHSRARGPTQILTRQPVEGRARDGGLRF 940



 Score =  120 bits (301), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 118/841 (14%), Positives = 262/841 (31%), Gaps = 106/841 (12%)

Query: 149 IQRIVVSQLHRSPG----IH-------FDH---DKGRASLSGKLLYACRIIPDQ------ 188
            ++++++Q  RS G    +        F H    +       +++  C +   +      
Sbjct: 1   SEKVLIAQE-RSAGNIVQVFQKVALAPFTHLAEIRSVIDKGSRMMSQCTVKLFRRAEGPD 59

Query: 189 GLWMDIEFDSKDII-----HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRG 242
           G  ++      + I     +V+ D    +P+     AL + S+ +IL          +  
Sbjct: 60  GTKIE------NPIRVQLPYVKQD----IPLVIVFRALDIVSDADILEKICFDQSDKEMM 109

Query: 243 DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
           D     L     +  A+++   +     +  +++G +     L  L ++ +  +G T D 
Sbjct: 110 DMLMGSLQEGQPIQSAELARDFIARRGNQSGLKAGDR-QKQALDILVKEFLPHIGQTPDA 168

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
                     +     +  +   +  D   L        + + +       +   + N  
Sbjct: 169 AAKKAFFLGYMVQRMLKCALGRTEPDDRDHL------GKKRLDL-------SGPLMANLF 215

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
               +   KD    + R +  G  + FS+       +  +  KY L   G      +L+ 
Sbjct: 216 RMKLDTATKDFFNYMKRRIEAG--AGFSIKAGFKPGIITNGLKYSL-ATGNWGDQKKLDK 272

Query: 423 DTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                 + + +    + +  L        R GK       +  +       E  + Q   
Sbjct: 273 AKAGVSQVLSRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQACG 332

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            +  +        S      +      N + +     E   + Q +++  +    + I  
Sbjct: 333 LVKNLSLMTMVTPSRDTTPLMTYILEKNVEALEE--WEPRLNPQATKVFANGVWFAVILR 390

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
             +        + R         +      +        G  I  +  + +      +G 
Sbjct: 391 DPKFLVDHFRSLRRKGTIEPDISLVWDIREKEFKISGDIGRIIRPLFVVDTDKASPTHGH 450

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           ++     +   + +           EN   A A  S+  D ++              LV 
Sbjct: 451 LKLTKEHILRLQESKAYK-------ENPDQAPAGWSMANDYNW------------FALVN 491

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
              ++F+DA  ++   I   ++      D+     G  ++    PL + + P        
Sbjct: 492 EGVVEFLDAEEEEQAMI---IMTPEALSDARARAEGYLIEPDEDPLRRNDVPLAPHSKTF 548

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCV 776
              +   + I+   A I+   D  +    + +  +     GV       + +        
Sbjct: 549 THCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFDQRMETMANILYY 608

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL +                    +L  G+N +VA   + GYN EDS+++++  +  
Sbjct: 609 PQKPLAR----------TQAMEFLKFRELPAGQNAIVAISCYSGYNQEDSVIMNQSSIDR 658

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    ++   +       E        D   + +     ID+ GI+  G  V   
Sbjct: 659 GLFRSLFYRVYQDQEKLIGQSVLEQFEKPTRGDTLRMRQGTYDKIDDDGIVAPGVRVRGE 718

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P     M P+ + L     +     RD S+ + S  +G V  V +     + 
Sbjct: 719 DIIMGKTAP-----MAPDAEELGQRQKQHVK--RDASVPLRSTEAGVVDQVMLTQNADMQ 771

Query: 952 K 952
           K
Sbjct: 772 K 772


>gi|315039663|ref|XP_003169207.1| DNA-directed RNA polymerase I subunit RPA2 [Arthroderma gypseum CBS
            118893]
 gi|311337628|gb|EFQ96830.1| DNA-directed RNA polymerase I subunit RPA2 [Arthroderma gypseum CBS
            118893]
          Length = 1243

 Score =  294 bits (752), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 104/496 (20%), Positives = 171/496 (34%), Gaps = 72/496 (14%)

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKIT 899
              E   +A D K G        P      L N     D         +   G   +G   
Sbjct: 679  YMEIACVASDIKNGVSTHIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGTPG 738

Query: 900  PKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPSGVSGTV----------VDVRIFN 946
               E     +   L+          +         P+G++  V           D  I N
Sbjct: 739  TAIEYRTDNKLYRLQTGQTPVVRPPLYNAYGLDNFPNGMNAVVAVISYTGYDMDDAMIIN 798

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF--KK 1004
            +   ++     ++ + +I  L  DK+       +   ++L     G    +  K    + 
Sbjct: 799  KSSHERGFGYGTIYKTKIYALD-DKESRGRGKSKRAITKLFGFAPGGLIKAEWKSQLDED 857

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                    +SE      W     D      +   K  +       E+ F + +  +  G 
Sbjct: 858  GLPHIGAKVSEGSLVCAWYTVQYDPATDTYINVDKQTHFLKYKDGEEGFVDSVRVL--GS 915

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
            +    V + V +   + R    GDK + RHG KG++S++ P  DMPF + G   D+++NP
Sbjct: 916  ETGNEVCQAVSIKYRVPRRPVIGDKFSSRHGQKGVLSQLWPSADMPFSESGIQPDVIINP 975

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
               PSRM +G   E+  G A    G    S    +                         
Sbjct: 976  HAFPSRMTIGMFVESLAGKAGSLHGLPQDSTPFQFSEETTAG------------------ 1017

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                            +     L+ A  +  G   +Y G+TG  
Sbjct: 1018 --------------------------------DYFGKQLQKAGYNFHGNEPMYSGITGRE 1045

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   + +G +Y  +L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A
Sbjct: 1046 FAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNALTGQPVKGRAKGGGIRVGEMERDALLA 1105

Query: 1305 YGAAYVLQEMLTIKSD 1320
            +GAA++LQ+ L   SD
Sbjct: 1106 HGAAFLLQDRLMNCSD 1121



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 130/985 (13%), Positives = 268/985 (27%), Gaps = 220/985 (22%)

Query: 11  GRVRKFFGKNPEIIDIPDL---IEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVF--P 64
            R R F     +    P L   I     S++  F    +      + G+++        P
Sbjct: 17  RRERLFRHPPKDKTAYPALAAAIRPHIDSFNALFEDSKVLDAALKDIGIKSFIDGNSKTP 76

Query: 65  ITAF-----------SGAAMLEFVSYEFDP---P---KFD-------VDDCLWRDLTYAV 100
                               +       +    P   K+          +C  R  TY  
Sbjct: 77  EEKAARREDGRRAPKRNKLSVRITELFLEKAVLPASNKYSTRNREIYPAECRERHATYRG 136

Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------- 141
            L+  L   V + +     +           +G +P+M +                    
Sbjct: 137 KLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRCHLEKATPAQLVDRKEE 186

Query: 142 -----GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGKLLYACRIIPDQGLW-- 191
                G FV+ G ++++   +   R+ P     +   +   +    +  +I   +     
Sbjct: 187 SEELGGYFVVNGNEKLIRMLIVGKRNFPTAIIRNSFQKRGSAYTK-FGVQIRSVRPDQTS 245

Query: 192 ----MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDF 244
               +    D    +  R   R+    VPV   L AL +++ +     + ++V  +    
Sbjct: 246 QTNVLHYLNDGN--VTFRFSWRKNEYLVPVMMILKAL-IETND--REIFERLVGGEGSLG 300

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
                    + +  +   +          + S  K  + L    +        +  +   
Sbjct: 301 IENTFVTDRVELLLRTYKAY--------GVHSRSKCRAYLGSKFRFVLGMPEDVPDED-V 351

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G      IV    G          ++   E   + +   I  +     N  A        
Sbjct: 352 GTEFLRKIVLPHLG----------NQNVTETQNNDKFNMILFMIRKLYNLVAGDCAPDNP 401

Query: 365 DKNKDRKDAL-LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLD 423
           D   +++  L   +Y ++    +  +         +      + L        +     D
Sbjct: 402 DAVSNQEVLLGGYLYGMLLKERLEEW------LKSVGPIVRDWRLKNDDAKFTDPSFERD 455

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
               V     E+I   ++  +   N   +   +D         + E +     +   RM 
Sbjct: 456 FLARVIGRTNENIGGAMEYFLSTGN-LVSPTGLDLQQPSGYTVMAEKINFYRFISHFRMI 514

Query: 484 R--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR--ITHTR 539
              S   ++ +  +  ++P+      PV +          L     H   +S   +  + 
Sbjct: 515 HRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCG---LLNHLAHKCLISTSNLDVSG 571

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE---------------GHNIGLVS 584
               L   GV    +      +     G+I    T +               GH    V 
Sbjct: 572 VPGVLAGLGVTSESSCSTEESIPVLLDGKILGYCTPKQSRVIADTLRYWKVQGHKHIPVE 631

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
               +   +  G     Y      ++   V YL     +  Y+        E      ++
Sbjct: 632 LEIGYVPSSNGGQYPGVYMFSEAARMYRPVRYLPLDRLD--YVGPFEQPYMEIACVASDI 689

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                              I+  P  ++SI A++ PF + + S R +  C M +QA+   
Sbjct: 690 KNG------------VSTHIEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGTP 737

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                  GT +E                                +  L    +G      
Sbjct: 738 -------GTAIEYR-----------------------------TDNKLYRLQTG------ 755

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q P+V+               +  L +   G N +VA + + GY+ +
Sbjct: 756 -------------QTPVVRP----------PLYNAYGLDNFPNGMNAVVAVISYTGYDMD 792

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKL-GPEEITRDIPNV---------SEEGLK 874
           D+M+I++             +       D +  G  +  R I  +           E   
Sbjct: 793 DAMIINKSSHERGFGYGTIYKTKIYALDDKESRGRGKSKRAITKLFGFAPGGLIKAEWKS 852

Query: 875 NIDECGIICVGAEVNPGDILVGKIT 899
            +DE G+  +GA+V+ G ++    T
Sbjct: 853 QLDEDGLPHIGAKVSEGSLVCAWYT 877


>gi|158954694|gb|ABW84318.1| RNA polymerase subunit B [Mycobacterium gilvum]
          Length = 248

 Score =  294 bits (752), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 136/229 (59%), Gaps = 30/229 (13%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +    + ++    + L + 
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIRLASDGADGSTEVPAWAAKLPEH 160

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
            + +                           V+TPVFDGA E  +  +L            
Sbjct: 161  MLSAPADSI---------------------VATPVFDGAQEGELQGLLGATLPNRDGETM 199

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 200  VNSDGKAVLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 248



 Score = 46.6 bits (109), Expect = 0.028,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|51035531|emb|CAH10901.1| RNA polymerase B subunit [Halorubrum coriense]
 gi|51035533|emb|CAH10902.1| RNA polymerase B subunit [Halorubrum distributum]
          Length = 435

 Score =  294 bits (752), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 83/253 (32%), Positives = 115/253 (45%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +
Sbjct: 197  EDGSKLSKVKVRDQRVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G                                             
Sbjct: 257  PSRMTVGHVLEMLGGKV------------------------------------------- 273

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                         +      TP F G DEE +   L     + SG+ ++Y G+TGE  D 
Sbjct: 274  ----------GSLRGSRVDGTP-FQGEDEEELRGQLEEYGFESSGKEVMYSGVTGEKIDA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   I  +GA
Sbjct: 323  EIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDTIIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            + VL E L   SD
Sbjct: 383  SMVLNERLLESSD 395



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 36/175 (20%), Positives = 68/175 (38%), Gaps = 11/175 (6%)

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                    +N +VA M + G+N ED++++++  V   +  S     +E   R    G E
Sbjct: 50  ISFDKRPAAQNFVVAVMSYEGFNIEDALVMNQGSVDRALTRSHFFRTYEGEERRYPGGQE 109

Query: 860 EITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           +              E+   ++DE G++    +V+   +L+GK +P              
Sbjct: 110 DRFEIPDQDVRGARGEDAYTHLDEDGLVNPETKVDESSVLLGKTSPPRFLEEP------D 163

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + G      R+TS+ + SG SG V  V +       K  +    ++   EL  +
Sbjct: 164 DMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSKVKVRDQRVPELGDK 218


>gi|52538185|emb|CAH19194.1| RNA polymerase beta-subunit [Pseudomonas taetrolens]
          Length = 327

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 176/335 (52%), Positives = 229/335 (68%), Gaps = 8/335 (2%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGSA 300

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                       G  ++ R         H Y    
Sbjct: 301 QR--------HHGRWSVHRYGRTGSGSEHAYRLHG 327


>gi|269308456|gb|ACZ34224.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5450]
          Length = 339

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 190/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V DGKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVKDGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|269859858|ref|XP_002649653.1| DNA-directed RNA polymerases I, II, and III, subunit 2
            [Enterocytozoon bieneusi H348]
 gi|220067016|gb|EED44485.1| DNA-directed RNA polymerases I, II, and III, subunit 2
            [Enterocytozoon bieneusi H348]
          Length = 1107

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 145/348 (41%), Gaps = 60/348 (17%)

Query: 1042 YETSKSILEDRFKNKIEKIQWGDD-----MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
              T  S ++ + K    K   G             +++K+ V   R ++ GDK + RHG 
Sbjct: 799  LITKVSPIDKKLKTVKYKGHPGYIDTIILSKGDDDKILKIKVRETRCVEIGDKFSSRHGQ 858

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+V  I+P  D+PF + G   DI++NP G PSRM VG+I E          G+   +  
Sbjct: 859  KGVVGLIVPQVDLPFNEYGVCPDIIMNPHGFPSRMTVGKILELIGSKVTCLTGEYTDATP 918

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             +     +       L+ +  T +      ++    +                       
Sbjct: 919  FENNTADND------LKTIFNTTNQEPLHKEHRQTEL----------------------- 949

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
              +  +L       SG+ +   G+TGE F+  +  G I+  +L HMV+DK++ RS G  +
Sbjct: 950  --LCQILIDHGYSYSGKDVFTSGITGEQFEAYIFFGPIFYQRLKHMVADKIHCRSRGPRA 1007

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD-----------VVGR 1325
            ++T+QP  G+S  GG RLGEME  C+  YGA  +L E L   SD+           +  +
Sbjct: 1008 VLTRQPTEGRSKDGGLRLGEMERDCLIGYGANSLLNERLMHCSDEFDAFICETCGIICYK 1067

Query: 1326 TRVYES-----IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             R Y       IV          P +  +L +EM A+ +   +   + 
Sbjct: 1068 ERCYWCSKKPIIVK--------MPYACKLLFQEMMAMNILPKIILEKE 1107



 Score =  144 bits (364), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 92/745 (12%), Positives = 207/745 (27%), Gaps = 138/745 (18%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK-- 85
           +L+     S+++F+   I    + N        S            L +++   + P   
Sbjct: 16  NLVRQHIESFNYFIEKEIKEIVQAN----DIIDS-----DIDRNFYLRYLNIRVEKPTMI 66

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TYA  + + +  I          K+ + I +++I MG +P+M
Sbjct: 67  ENMVEQIIYPQECRIRDITYAGNIYVDIEYI----------KNKEVIIKKNISMGKMPIM 116

Query: 139 ------------------------------------TKDGTFVIKGIQRIVVSQLHRSPG 162
                                                  G F+IKG+++++  Q  +S  
Sbjct: 117 IRSSKCHLTTHMLNSKIIMNERQKNLINYKTQECIYDNGGYFIIKGVEKVIHIQEQQSKN 176

Query: 163 -IHFDHDK-----GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR----IDRRRKV 212
            I  +  K        S S K      +I              D  +++    I+    V
Sbjct: 177 RIIIEMGKNGLYTSMTSSSIKHKNKTNVIY-----------KNDKFYIQNTIFIE---DV 222

Query: 213 PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
           P+   L  LG++++E + ++  K                 +L  G      +        
Sbjct: 223 PIVLVLKTLGLNTDEEIVSYIGKEGVELM-----------ELSFGEVYEKDIYTETDA-- 269

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           +IE  K +       LK    K + +    L         ++ +     I    +I +  
Sbjct: 270 LIELSKFI------KLKSDDNKEIKV-KSILAEKLFPNIKIDDDLKNKGICLCLMIRKLI 322

Query: 333 LEEIFHSEIRDIPIL-YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
           L +    +  D   L           +         K   +    I +++     +    
Sbjct: 323 LAKQNLLKPDDKDYLGNKRFELAGQLLSILFEDTFKKFNFELKKSIDKILSKRIRTNEFD 382

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
           A + FN             +     N  R  ++       + +   I  + ++  + +  
Sbjct: 383 ALTFFNLQTGSITTTLSRAISSGNWNLKRFKMERSGVTHVLTRYSYITALGMMTKINSHF 442

Query: 451 GTIDDID-----NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
                +      +  +  +    +  + +    +  +    +    S           + 
Sbjct: 443 EKTRKVSGPRSLHPSSWGMFCPADTPEGESCGLVKNLALLTEISTESDSDIIKNILQTLG 502

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +       F +     +  +       ++   L       + R     +   +    
Sbjct: 503 VIKLKFCQESEFYAKNKFMVFINGELFGLTSNIEYL-CCAIRKIRREGKINKFVSIFHNK 561

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP---YRKVCDGKVTNDVVYLSAMEE 622
                   T  G     +  +   +        +     Y+   D  +   + Y+   EE
Sbjct: 562 LENAIYISTDNGRICRPLIIIKKNSNFFTNYQFQCNKIKYKSFNDLLLEGLIEYVDVNEE 621

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            +  IA                           +  E    ++ +   ++S+ A LIPF 
Sbjct: 622 NDCLIA-------------------LHKSNINNLNIENYTHLEIADYSILSLIAGLIPFP 662

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAE 707
            ++ S R    C M +QA+  +   
Sbjct: 663 HHNQSPRNTYQCAMGKQAIGHIGTN 687



 Score =  106 bits (264), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 104/758 (13%), Positives = 249/758 (32%), Gaps = 73/758 (9%)

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           +   +           ++  K    + D + G  +I+  +K+    ++  + K    + +
Sbjct: 126 THMLNSKIIMNERQKNLINYKTQECIYD-NGGYFIIKGVEKVI--HIQEQQSKNRIIIEM 182

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             + L     +  I +     +  +      + +   IF  ++  + +L    +N +  I
Sbjct: 183 GKNGLYTSMTSSSIKHKNKTNVIYKNDKFYIQNT---IFIEDVPIVLVLKTLGLNTDEEI 239

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
            + +  +  +  + +  ++Y      +                D+ +  + ++   K+  
Sbjct: 240 VSYIGKEGVELMELSFGEVYEKDIYTETDALIELSKFIKLKSDDNKEIKVKSILAEKLFP 299

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
            + +D     + I    +  +I+ L+  +      DD D LGN+R    G++L   +   
Sbjct: 300 NIKIDDDLKNKGIC---LCLMIRKLILAKQNLLKPDDKDYLGNKRFELAGQLLSILFEDT 356

Query: 479 LLRME--------RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
             +          + + +RI + + D++   + +    + + +     S   +     + 
Sbjct: 357 FKKFNFELKKSIDKILSKRIRTNEFDALTFFN-LQTGSITTTLSRAISSGNWNLKRFKME 415

Query: 531 SLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                    R S +   G+         + R     R +HP+ +G  CPA+T EG + GL
Sbjct: 416 RSGVTHVLTRYSYITALGMMTKINSHFEKTRKVSGPRSLHPSSWGMFCPADTPEGESCGL 475

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL-----SAMEEENRYIAQANSSLDED 637
           V +L     ++     +     + +   T  V+ L     S    +N+++   N  L   
Sbjct: 476 VKNLALLTEISTESDSD----IIKNILQTLGVIKLKFCQESEFYAKNKFMVFINGELFGL 531

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMG 693
            S  E L              + +       +  + I+        P +    ++     
Sbjct: 532 TSNIEYLCCAIRKIRREGKINKFVSIFHNKLENAIYISTDNGRICRPLIIIKKNSNFFTN 591

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV---DAIRIVIRSVEG 750
              Q   +         +   +E V        ++A     +  +   +   + I     
Sbjct: 592 YQFQCNKIKYKSFNDLLLEGLIEYVDVNEENDCLIALHKSNINNLNIENYTHLEIADYSI 651

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR--NDIIADGPST-------- 800
               +      +     + + Q     Q  +  +G  +++  + ++     T        
Sbjct: 652 LSLIAGLIPFPHHNQSPRNTYQCAMGKQA-IGHIGTNIKKRFDLLMLQLNYTQRPLSCSK 710

Query: 801 -----DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                    +  G N +VA M + GY+ ED++++++  +          +  ++      
Sbjct: 711 ILDINKYNKIPAGINAMVAVMSYSGYDIEDAIIVNKDSIERGFMRVEVYKTIKIEFERFT 770

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK---- 911
            G  E          E      +  II VG  V  GDIL+ K++P  +   T + K    
Sbjct: 771 NGKTE----------EIYIVNGKEQIIEVGTHVMDGDILITKVSPIDKKLKTVKYKGHPG 820

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            +  I   K  D +   ++V        +  +  +RHG
Sbjct: 821 YIDTIILSKGDDDKILKIKVRE-TRCVEIGDKFSSRHG 857


>gi|269308474|gb|ACZ34233.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5862]
          Length = 339

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 191/347 (55%), Positives = 254/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV DG+V  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YAKINRYGFIETPYRKVVDGRVLNDEHVYLTADKEKDFIVAQANIQTAEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I    + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIGADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV+ VD+  I +           +GV  Y L  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVAVEDGIVKYVDSKMITV--------EGKTGVKSYSLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+V+ NDI+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 LRSNNGTAMTHLPIVKVGDKVKSNDILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDADGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|291244544|ref|XP_002742157.1| PREDICTED: RNA polymerase I polypeptide B-like [Saccoglossus
            kowalevskii]
          Length = 1133

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 70/258 (27%), Positives = 110/258 (42%), Gaps = 50/258 (19%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G+D+     + V + + ++R    GDK + RHG KG+ S++ P E+MPF + G   DI+ 
Sbjct: 851  GNDLGTAECQKVYISLRIQRNPTIGDKFSSRHGQKGVCSQLWPVENMPFSESGMTPDIIF 910

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM +G + E+  G +    G    +    +                       
Sbjct: 911  NPHGFPSRMTIGMMIESMAGKSGSLHGLSHDATPFTFSE--------------------- 949

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                         D    +    MLR A  +  G   +Y G+ G
Sbjct: 950  -----------------------------DRPAIDYFGRMLREAGYNYYGNERMYSGVDG 980

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
               +  + VG +Y  +L HMV DK   R+TG   ++T QP+ G+   GG R GEME   +
Sbjct: 981  RELEADIFVGIVYYQRLRHMVEDKFQVRTTGPIDILTHQPVKGRKRAGGIRFGEMERDAL 1040

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             ++G +++LQ+ L   SD
Sbjct: 1041 LSHGTSFLLQDRLFHCSD 1058



 Score =  108 bits (270), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 135/961 (14%), Positives = 261/961 (27%), Gaps = 227/961 (23%)

Query: 16  FFGK----NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA---F 68
            +GK      +++   +L++    S++  L           EGL  A + + P+      
Sbjct: 13  NYGKPPKSQSKVLQ--ELVKPHIESFNFMLS----------EGLNLAIQDMQPVEFALPS 60

Query: 69  SGAAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                L F       P            K    +C     TY   ++  L         +
Sbjct: 61  GEKVSLSFTDASIGVPTVAQGNIHALSLKVYPTECRQGGTTYKAKIRAHL--------CW 112

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
                +K IKE  I +G++P++ K                         G F+I GI+++
Sbjct: 113 KLNNEVKAIKE--ILLGEVPILVKSNSCNLNKLSPSELIKKNEEVEEMGGYFIINGIEKV 170

Query: 153 VVSQLHRSPGIHFDHDKGR-ASLSGKLLYACRIIPDQ-------------------GLWM 192
           +  ++   P  +F     R +  +   LY    +  +                      +
Sbjct: 171 I--RMIVLPRRNFPMALNRGSWKNRGKLYTEYGVSMRCVKPDQTAVNIILHYLTNGTAML 228

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
              + SK+   V        PV   L AL   +++     Y +++  +  D   +     
Sbjct: 229 CFSY-SKEQFFV--------PVVLILKALVDTTDQ---FIYDELM--RGKDKNTYYKGCV 274

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
             M+    +  L       + +    ++  GL     ++      I       L    D 
Sbjct: 275 TYMLRQIQTQGLTSQRKILEYLGEMFRVKLGLADWYTDRQNGEFLIKQCICVHLTNNMDK 334

Query: 313 VN---GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
            N       +++  A      ++ +   + E+     LY+  +          + D    
Sbjct: 335 FNTLVYMVRKLFAFANGECAAENADSTMNQEVLMGGHLYLMYLKEK-------MVDWLVS 387

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            + ++    +V     V   +   S             L   G +     L L     + 
Sbjct: 388 VRYSIEKQAKVKGQSFVLNSTTLNSAVGRTNLSHAVEYLLKTGNLNSKTGLGLMQATGLT 447

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +   D +  ++ L   R     I         R  SV  +L   +              
Sbjct: 448 VV--ADKLNYVRYLSHFR----CIHRGAFFSEMRTTSVRRLLPEAWGFLC-------PVH 494

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
                   ++       + V         S  L  L                  +   G 
Sbjct: 495 TPDGAPCGLLNHMAALCQVVNDQPQVSHLSRLLCNLGMTPTDGPSPGEPSECYDVLLDGR 554

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY------GFIETPYR 603
              +   EM          +   +      +  V  +    + + Y        +    R
Sbjct: 555 VLGKVDKEMAGELGNKLRILKVRKEHRVPEMLEVVLVPMTGKCSQYPGLYLFSSVARLMR 614

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +   TN    +   E+    IA   S   E                           
Sbjct: 615 PVLNLA-TNTTEMIGTFEQVYMNIAVTASEAHEG----------------------LTTH 651

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           ++ S   ++S  ASL PF + + S R +  C M +Q +         V T +     K  
Sbjct: 652 LELSESGLLSAVASLTPFSDFNQSPRNMYQCQMGKQTMGT------PVHTYLHRTDNK-- 703

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                                                 Q P+V+
Sbjct: 704 -----------------------------------------------LYRLQTPQSPIVR 716

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                          + ++ +  LG N +VA + + GY+ ED+M++++           H
Sbjct: 717 P----------CSYDTYNIDNYPLGTNAVVAVISYTGYDMEDAMILNKSSYERGFA---H 763

Query: 844 IEEFEVMARDTKLGPEEITRDIPNV------SEEGLKNIDECGIICVGAEVNPGDILVGK 897
              ++    D K    E  + I  +            ++D  G+  +GA + PGD L G 
Sbjct: 764 GTIYKTEVIDLKKISGEKGKSISLMFGCLPDDRRTEGHLDLDGLPPIGAIIEPGDPLCGY 823

Query: 898 I 898
           I
Sbjct: 824 I 824


>gi|269308466|gb|ACZ34229.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5446H]
          Length = 339

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 189/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V +GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVQNGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEEGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|190694901|gb|ACE88991.1| RNA polymerase beta subunit [Mycobacterium chimaera]
          Length = 243

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 101/232 (43%), Positives = 134/232 (57%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 44   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 103

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 104  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 149  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++T
Sbjct: 192  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMIT 243



 Score = 48.9 bits (115), Expect = 0.006,   Method: Composition-based stats.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 52


>gi|310877316|gb|ADP36993.1| RNA polymerase subunit B [Mycobacterium novocastrense]
          Length = 227

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 103/232 (44%), Positives = 138/232 (59%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +   A              
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKINGSPDWASA-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                             + +   + + G  VSTPVFDGA E  +  +L            
Sbjct: 133  -----------------LPKELLESEPGSIVSTPVFDGAREAELQGLLGSTLPNRDGETL 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +DE G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 176  VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 227


>gi|213407890|ref|XP_002174716.1| DNA-directed RNA polymerase I subunit RPA2 [Schizosaccharomyces
            japonicus yFS275]
 gi|212002763|gb|EEB08423.1| DNA-directed RNA polymerase I subunit RPA2 [Schizosaccharomyces
            japonicus yFS275]
          Length = 1170

 Score =  293 bits (751), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 91/472 (19%), Positives = 155/472 (32%), Gaps = 62/472 (13%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                  E    ++ ++        D         +   G   +G            +   
Sbjct: 665  KITTHVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQMGKQTMGTPGTAIRYRTDNKMYR 724

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L+             S  +    +G    V + +  G D  +  I  +            
Sbjct: 725  LQTGQTPIVRPRLHDSYGLDHYPNGMNAVVAVISYTGYDMEDAMILNKSAHERGFGYGTV 784

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK-- 1030
             +   +D +   R  E +          GF   +    + + +           + E   
Sbjct: 785  YKSQKIDLSEKRRRGEPVVHHF------GFAPGSTPRREWLEKLDMDGLPYIGTKVEDGE 838

Query: 1031 --VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                   ES    +  +    E  F +++  +  G+D+     +V+ +     R    GD
Sbjct: 839  PIAAYYDESTGHNFVQTYHGTEPGFVDEVRVL--GNDVGDSECQVLHIKFRNTRSPIIGD 896

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KGI S+  P  DMPF + G   DI++NP   PSRM +G   E+  G A    
Sbjct: 897  KFSSRHGQKGICSQKWPTVDMPFTESGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALH 956

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G    S    +      +                                          
Sbjct: 957  GMAQDSTPFVFSETQTAA------------------------------------------ 974

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +     L  A  +  G   +Y G+TG+     + +G +Y  +L HMVSDK  
Sbjct: 975  --------DYFGEQLVKAGYNYHGNEPMYSGITGKELHADIYIGVVYYQRLRHMVSDKFQ 1026

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             R+TG    +T+QP+ G+   GG R GEME   +  +GA++++Q+ L   SD
Sbjct: 1027 VRTTGPIHNLTRQPVKGRKRAGGIRFGEMERDAVIGHGASFLMQDRLMNCSD 1078



 Score = 75.1 bits (183), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 123/955 (12%), Positives = 255/955 (26%), Gaps = 181/955 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA----FSGAAMLEFVSYEFDPP---- 84
              S++      +      + G +  F SV         F           +   P    
Sbjct: 32  HVESFNALTEGGLLNLAVKDIGEKTVFDSVTQNEDGSMSFGNRMTFRVDEVQIAKPMLSS 91

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   K    +C  R  TY   + +     V D    +  + +          G+LP
Sbjct: 92  RERTSINRKIFPSECRERLCTYKARMVLKFSWRVNDGPWQSEMREV----------GNLP 141

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLH---RS-PGIHFDHD 168
           +M +                         G FV+ GI++ +V  L    R+ P       
Sbjct: 142 IMVRSNRCHLEGLSPAELIAHKEESEEMGGYFVVNGIEK-IVRMLILPKRNHPVALIRPS 200

Query: 169 KGRASLSGKLLYACRIIPDQGLWMD-------IEFDSKDIIHVRIDRRRK---VPVTSFL 218
            G    +   +Y    I  + +  D       + + S  +   R   R+    +P    L
Sbjct: 201 FG----NRGTMYTQYGISIRCVRPDQSSLTNTLHYLSNGVAMFRFHWRKNEYLIPSMMIL 256

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            AL   S++ +   +  IV  +  + +        L      S  L       Q + S  
Sbjct: 257 KALIETSDKEI---FEGIVGQETENTFLTDRVELMLRAYK--SYGLSTQTQSLQYLGSKF 311

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           ++  GL + L +  V    +    L  L    D        +  +   ++  +   +   
Sbjct: 312 RVVLGLAEDLTDVEVGRTLLRRVVLVNLPDNRDKFRMLLF-MIRKLYALVAGECCADNPD 370

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
           S      +L        A I    + D     +     I + +R G        +   + 
Sbjct: 371 SPQHQEILL---GGFLFAQIIKEKIDDWLTSIRA---QIQQDVRRGAAGIDFSDKKYLSR 424

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +F   +    + +        L  +T  D++      ++A         +    +     
Sbjct: 425 VFSKVNSDIGTRLQYFLSTGNLVSNTGLDLQQATGYTVVAEKLNFYRFLSHFRMVHRGAF 484

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +  SV ++L   +                      ++       + V S +     
Sbjct: 485 FAELKTTSVRKLLPEAWGFLC-------PVHTPDGSPCGLLNHLASKCEIVTSPIDVS-N 536

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA--RAGVEMRDVHPTHYGRICPAETSE 576
              L          + + +   +S    G +         +                +  
Sbjct: 537 IPALLLSLGVDPPTAVVANPDWVSVQLDGKIVGWCTHKLAKHVAAVLRQMKVRGDLASDG 596

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              +  +S        +  G     +      ++   V YL            A   LD 
Sbjct: 597 KTPLVPLSLEIGLVPPSHGGQFPGLFLFSEQARMVRPVKYL------------ATGKLDN 644

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            G F  E V+   A     +  +    ++ SP  V+SI A++ PF + + S R +  C M
Sbjct: 645 VGPF--EQVYMDIACFPREIVPKITTHVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQM 702

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +Q +                      G AI  +    + ++   +  I          +
Sbjct: 703 GKQTMGT-------------------PGTAIRYRTDNKMYRLQTGQTPIVR---PRLHDS 740

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            G+D Y                            N ++A    T                
Sbjct: 741 YGLDHYPNGM------------------------NAVVAVISYTGYDM------------ 764

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
                  ED+M++++             +  ++   + +   E +              E
Sbjct: 765 -------EDAMILNKSAHERGFGYGTVYKSQKIDLSEKRRRGEPVVHHFGFAPGSTPRRE 817

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            L+ +D  G+  +G +V  G+ +            +     ++   G +   V +
Sbjct: 818 WLEKLDMDGLPYIGTKVEDGEPIAAY------YDESTGHNFVQTYHGTEPGFVDE 866


>gi|52538171|emb|CAH19187.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 5]
          Length = 330

 Score =  293 bits (750), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 224/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRGSA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRHG 313


>gi|185179210|gb|ACC77618.1| RpoB [Mycobacterium porcinum]
          Length = 225

 Score =  293 bits (750), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 26   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 138

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 139  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 176

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS
Sbjct: 177  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYS 225


>gi|269308438|gb|ACZ34215.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4903]
 gi|269308452|gb|ACZ34222.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4900]
 gi|269308462|gb|ACZ34227.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5363]
 gi|269308468|gb|ACZ34230.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5366]
          Length = 339

 Score =  293 bits (750), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 191/347 (55%), Positives = 254/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV +GKV  ++ VYL+A +E++  +AQAN   D+DG   +E V  
Sbjct: 1   YAKINPYGFIETPYRKVLNGKVLKDEHVYLTADKEKDFIVAQANIQTDKDGKILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV+ VD+  I I           +GV  Y L  F
Sbjct: 121 SPIVGTGVEYEAARDSGDAVVATEDGIVKYVDSKTITI--------EGKNGVKSYTLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+V+ N+I+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 SRSNNGTAITHLPIVKVGDKVKANEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDLDGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|239925564|gb|ACS35440.1| RNA polymerase beta subunit [Mycobacterium sherrisii]
          Length = 244

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 98/232 (42%), Positives = 134/232 (57%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 45   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 104

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 105  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPDWAAN-------------- 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 150  -----------------LPEDLRHAQPDQIVSTPVFDGAKEEELQGLLSCTLPNRDGNVM 192

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++T
Sbjct: 193  VDADGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMIT 244



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/53 (66%), Positives = 44/53 (83%)

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 53


>gi|290965269|dbj|BAI82231.1| RNA polymerase subunit B' [halophilic archaeon]
 gi|291088182|dbj|BAI82372.1| RNA polymerase subunit B' [halophilic archaeon YSM-79]
          Length = 608

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 120/584 (20%), Positives = 200/584 (34%), Gaps = 95/584 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LVA       +    + I  +++       I   E     R T      
Sbjct: 101  EFIDAEEEEDILVAVEEDDLTDDHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +    A+   +
Sbjct: 159  MMKQSLGLPAANYRIRPDTR-QHLMHYPQKAMVNTQTTKQIGYDDRPAGQNFTVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  +     V    +    F R    +  R    + ++ E+   D       +  
Sbjct: 218  GFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQEDRFEIPDDD-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                   + L     V+      +++VL           +  +      + +R       
Sbjct: 270  ARGEDAYKHLDEDGLVNPETRVDENSVLLGKTSPPRFLEEPDEMGGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E          + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 330  SGEDGVVDTVTLMEGE------------DGSKLAKVSVRDERIPELGDKFASRHGQKGVV 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF ++G   D+VLNP  +PSRM VG + E   G +    G+ +       +
Sbjct: 378  GHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKSGALEGRTVDGTAFTGE 437

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               +I   R+ L++     S  E +                           G   E I 
Sbjct: 438  DEEEI---RNSLQERGFKSSGKEVLYS-------------------------GVSGEKI- 468

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                                     +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 469  -------------------------EAEIFVGNIFYHKLYHMVSNKMHARSKGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG---------R-- 1325
            QP  G++  GG RLGEME   + A+GAA VL+E L   SD    D+ G         R  
Sbjct: 504  QPTEGRAREGGLRLGEMERDTVIAHGAAMVLKERLLESSDQEYVDICGNCGMTAVENREQ 563

Query: 1326 TRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             RVY     G   D        +F +L+ EM+ALG++  LE   
Sbjct: 564  RRVY-CPNCGEETDVHSIEMSYAFKLLLDEMKALGIAPRLELED 606



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 61/368 (16%), Positives = 126/368 (34%), Gaps = 31/368 (8%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +S  +E   Y+  +     +D     E +   R  G+   +    +              
Sbjct: 1   MSQSQEAKVYVNGSLVGTHDDPHELAENIREARRRGDISDMVNVSVKERTGEVIVNADAG 60

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            +  P L  +D   ++   +++      ++ E       +E + A+     +VA     +
Sbjct: 61  RARRPLLVVEDGEPLVTEDDLEALENEEVEFETLVEEGKVEFIDAEEEEDILVAVEEDDL 120

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-----------RPLVKV 784
              D   + I         +            + +     + Q           RP  + 
Sbjct: 121 TD-DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQ 179

Query: 785 GDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                    + +  +T      D   G+N  VA M + G+N ED++++++  V   +  S
Sbjct: 180 HLMHYPQKAMVNTQTTKQIGYDDRPAGQNFTVAVMSYEGFNIEDALVMNKGSVERALARS 239

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILV 895
                +E   R    G E+   +IP+        E+  K++DE G++     V+   +L+
Sbjct: 240 HFFRTYEGEERRYPGGQEDRF-EIPDDDVRGARGEDAYKHLDEDGLVNPETRVDENSVLL 298

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           GK +P        E      + G      R+TS+ + SG  G V    +    G D ++ 
Sbjct: 299 GKTSPPRFLEEPDE------MGGLSPQKRRETSVTMRSGEDGVV--DTVTLMEGEDGSKL 350

Query: 956 SISVEREQ 963
           +    R++
Sbjct: 351 AKVSVRDE 358



 Score = 44.7 bits (104), Expect = 0.12,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 57/195 (29%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +   ++       I   RR   +        +       V+        P    
Sbjct: 10  YVNGSLVGTHDDPHELAENIREARRRGDISDMVNVSVKERTGEVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E                +    +E    +         V ++ A EEE+  +A     L 
Sbjct: 70  EDGE--------PLVTEDDLEALENEEVEFETLVEEGKVEFIDAEEEEDILVAVEEDDLT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DDH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPAANYRI 173


>gi|83763767|emb|CAJ00217.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio harveyi]
          Length = 336

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 173/348 (49%), Positives = 242/348 (69%), Gaps = 13/348 (3%)

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
               +G+E  V+  SG   VAKR G+++ VDA RIV++  E +L P  +G+DIY L K+ R
Sbjct: 1    LCWSGIERNVSVDSGVTAVAKRGGVIQSVDASRIVVKVNEKELVPGEAGIDIYNLTKYTR 60

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            SNQNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+
Sbjct: 61   SNQNTCINQRPCVMPGEPVSRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILV 120

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
            SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV 
Sbjct: 121  SERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVK 180

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G
Sbjct: 181  GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDG 240

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            ++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S
Sbjct: 241  VEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVRAVLIDGG-------------YS 287

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
               +    R +W +  ++D+ +Q  +E L  Q++  K+  + +F+ K 
Sbjct: 288  EAKLDTTDRKKWLELTLEDDALQTQLEQLAEQWDELKADFDKKFETKR 335


>gi|46019132|emb|CAE52030.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 160

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 68/182 (37%), Positives = 113/182 (62%), Gaps = 22/182 (12%)

Query: 23  IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD 82
           ++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y   
Sbjct: 1   VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLG 50

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  G
Sbjct: 51  EPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTG 101

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           TF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD++
Sbjct: 102 TFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVV 158

Query: 203 HV 204
           +V
Sbjct: 159 YV 160


>gi|269308436|gb|ACZ34214.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5441]
          Length = 339

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 188/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V +GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVKNGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD ++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSIKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|328770085|gb|EGF80127.1| hypothetical protein BATDEDRAFT_30022 [Batrachochytrium dendrobatidis
            JAM81]
          Length = 1147

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 75/279 (26%), Positives = 119/279 (42%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQ-WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            + +    +      +++++  GDD     L+ + + + + RP   GDK + RHG KG++S
Sbjct: 840  KVTVKEYKGMEDAYVDQVRLIGDDSGKKPLQKIHIRLRIPRPPLIGDKFSSRHGQKGVIS 899

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    +    +  
Sbjct: 900  QKWPSIDMPFSESGIIPDVIINPHAFPSRMTIGMFIESLAGKAGALHGYAQDATPFKFNE 959

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                              D A  +    
Sbjct: 960  --------------------------------------------------DHAAGDFFGE 969

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG+ F   + +G +Y  +L HMVSDK   R+TG    +TQQ
Sbjct: 970  ELRQAGFNYHGNEPMYSGITGQEFKADIYIGVVYYQRLRHMVSDKYQVRTTGPVHNLTQQ 1029

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG R GEME   + A+G +Y+L++ L   SD
Sbjct: 1030 PVKGRKRAGGIRFGEMERDSLLAHGVSYLLKDRLMNCSD 1068



 Score = 63.6 bits (153), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 98/643 (15%), Positives = 195/643 (30%), Gaps = 90/643 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRV--MRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D       I          DR + LL  +R   +     +   +       L    D+ +
Sbjct: 256 DFEIFERIIMGVYTNTFLIDRVELLLRSFRRYAIYNSTQALAYIGSKFAVMLDSPEDQLE 315

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +         M L   T    +    + +I +++ L  L +G    D+ D+L  +     
Sbjct: 316 VDAGLEFLRRMILVHLTDAKSKF---DLLIYMLQKLYSLVSGDTAPDNPDSLQFQETLLA 372

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV-------------VSAVC 514
           G M     +  L     +IK  I+      +   D  + K +                + 
Sbjct: 373 GHMFSALIKEKLADWLLAIKTTINMDIKKQISKLDFSDKKYIQKLFSKTSGMSDIGKKIE 432

Query: 515 EFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            F  +  L              + + E +N    I+H R   ++ +G          +R 
Sbjct: 433 YFLATGNLISSSNLDLQQVSGYTIIAEKLNFYRYISHFR---SIHRGAFFAELKTTTVRK 489

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC---DGKVTNDVVYL 617
           + P  +G +CP  T +G   GL++ L+    +       +    +    +     ++V  
Sbjct: 490 LLPESWGFLCPVHTPDGSPCGLLNHLSHTCEIFLDKIDVSHIPSIVAAAEFDSRENIVM- 548

Query: 618 SAMEEENRYIAQANSSLDED------GSFTEELVFCRCAGEEILVPREKIDFIDA----- 666
             ++ + + I    +S+  +            +       E   VP  K           
Sbjct: 549 -TIQLDGKVIGWGRTSVVRNIAQTLRDWKIRGINNVPLKLEIGYVPPTKGGQYPGLFLFS 607

Query: 667 SPKQVV----SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           SP +++     +A     F+   +   + + C M+   VP +     F  T M S     
Sbjct: 608 SPARMIRPVKYLATGDTDFIGPFEQVYMDIAC-MKEDVVPGITTHQEFNPTDMLS----- 661

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
               +VA      +   + R + +   G     T    ++               Q P+V
Sbjct: 662 ----VVANLTPFSDFNQSPRNMYQCQMGKQSMGTPSQSLHHRT--DNKLYRLQTGQSPIV 715

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           +                  L     G N +V  + + GY+ ED+ +I++           
Sbjct: 716 RPN----------LHNDYGLDGYPNGMNAVVCVISYTGYDMEDASIIAKSSHERGYGYGT 765

Query: 843 HI---------EEFEVMARDTKLGPEEITRDIPNVSEEGL----KNIDECGIICVGAEVN 889
                         +        G        PN+SE+ L    + ID  G+  +G  + 
Sbjct: 766 VYKGEWVDLSDFHRQGDIVTHYFGFVAWNESEPNLSEKALARALQFIDLDGLPIIGVRLT 825

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            GD +   +          E K +   + ++   + D S + P
Sbjct: 826 RGDPMYAFVDDVTGKVTVKEYKGMEDAYVDQVRLIGDDSGKKP 868



 Score = 52.8 bits (125), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 87/664 (13%), Positives = 188/664 (28%), Gaps = 115/664 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R ++Y   ++I +   V              I+ +   +G LP+M +       
Sbjct: 95  PSECRERGISYKSKMQIRINWRVNG----------GPIQSEICGLGSLPIMVRSLKCNLD 144

Query: 142 ------------------GTFVIKGIQRIVVSQLHR--------SPGIHFD---HDKGRA 172
                             G FVI GI+R     L R         P          +G  
Sbjct: 145 GKSPSEMVAHHEDADDFGGYFVINGIER-----LIRLLIVPRRNHPTAIIRPSFQKRGPT 199

Query: 173 SLSGKLLYACRIIPDQGLW---MDIEFD--------SKDIIHVRIDRRRKVPVTSFLMAL 221
                ++  C ++PDQ      M    D         K I ++       VPV   + AL
Sbjct: 200 YSKFGIIMRC-VLPDQSAQTITMHYCTDGEVTLRFFHKKIEYM-------VPVVLVMRAL 251

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
              S+ EI    + +I+     + +        L    +   ++ +       I S   +
Sbjct: 252 CNTSDFEI----FERIIMGVYTNTFLIDRVELLLRSFRR--YAIYNSTQALAYIGSKFAV 305

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                +   E       +    L  L  A+   +     +      +    S +    + 
Sbjct: 306 MLDSPEDQLEVDAGLEFLRRMILVHLTDAKSKFDL----LIYMLQKLYSLVSGDTAPDNP 361

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFL 399
                   + + +  + +    + D     K    +DI + +   D S     + +F+  
Sbjct: 362 DSLQFQETLLAGHMFSALIKEKLADWLLAIKTTINMDIKKQISKLDFSDKKYIQKLFSKT 421

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              SD      +        L   +  D++ +    IIA         +   +I      
Sbjct: 422 SGMSDIG--KKIEYFLATGNLISSSNLDLQQVSGYTIIAEKLNFYRYISHFRSIHRGAFF 479

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +  +V ++L   +                      ++       +  +  +      
Sbjct: 480 AELKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHLSHTCEIFLDKIDVSHIP 532

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S           ++      R + +    +     G     V       +   +    +N
Sbjct: 533 S----------IVAAAEFDSRENIVMTIQLDGKVIGWGRTSVVRNIAQTLRDWKIRGINN 582

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           + L   +  +      G     +      ++   V YL+  + +  +I        +   
Sbjct: 583 VPLKLEIG-YVPPTKGGQYPGLFLFSSPARMIRPVKYLATGDTD--FIGPFEQVYMDIAC 639

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E++V                   + +P  ++S+ A+L PF + + S R +  C M +Q
Sbjct: 640 MKEDVVPG------------ITTHQEFNPTDMLSVVANLTPFSDFNQSPRNMYQCQMGKQ 687

Query: 700 AVPL 703
           ++  
Sbjct: 688 SMGT 691


>gi|269308454|gb|ACZ34223.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4886]
          Length = 339

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 190/347 (54%), Positives = 254/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV +GKV  ++ VYL+A +E++  +AQAN   D+DG   +E V  
Sbjct: 1   YAKINPYGFIETPYRKVLNGKVLKDEHVYLTADKEKDFIVAQANIQTDKDGKILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV+ VD+  I I           +GV  Y L  F
Sbjct: 121 SPIVGTGVEYEAARDSGDAVVATEDGIVKYVDSKTITI--------EGKNGVKSYTLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+++ N+I+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 SRSNNGTAITHLPIVKVGDKIKANEILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDSDGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|225348572|gb|ACN87267.1| RNA polymerase beta subunit [Mycobacterium riyadhense]
          Length = 247

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 99/233 (42%), Positives = 132/233 (56%), Gaps = 37/233 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 44   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 103

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G K+ +          +       E  
Sbjct: 104  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKVDTGNGVPDWAARLPDDLLHAEPN 162

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 163  A----------------------------IVSTPVFDGAQEAELQGLLSATLPNRDGEVL 194

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                G+++L DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQ
Sbjct: 195  VDGDGKAVLLDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQ 247



 Score = 49.7 bits (117), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 52


>gi|183579281|gb|ACC63218.1| RpoB [Mycobacterium smegmatis]
          Length = 228

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 29   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 88

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +        ++
Sbjct: 89   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGVPDWASKLPE------EL 141

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                + +                       V+TPVFDGA E  +  +L            
Sbjct: 142  YSAPADST----------------------VATPVFDGAQEGELAGLLGSTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 180  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 228


>gi|254169060|ref|ZP_04875898.1| DNA-directed RNA polymerase, beta subunit, putative [Aciduliprofundum
            boonei T469]
 gi|197622030|gb|EDY34607.1| DNA-directed RNA polymerase, beta subunit, putative [Aciduliprofundum
            boonei T469]
          Length = 1201

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 183/1179 (15%), Positives = 375/1179 (31%), Gaps = 180/1179 (15%)

Query: 225  SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL---- 280
             ++IL+  Y + +     D    P     +    +V  SL D+     ++E  ++     
Sbjct: 169  DKDILNWPYKQKLEYVGEDPDD-PGGYFIIGGSERVLVSLEDLAPNRVLVEKNERYNTVV 227

Query: 281  -TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             T+ +    +      +         +     +       I ++A  +  ++ +     S
Sbjct: 228  ETAKVFSQRRGYRALTIMEKKSDGIIVVSVPAVAGTIPLVILMKALGLEKDQDIYRAIVS 287

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            + +   I   +              +  + ++DA+  + +    G    +         +
Sbjct: 288  DEKMSVIALANIEEVEN--DKLYPPNGIRTQRDAIEYLEKRFAAGQAKEYRE-----KKI 340

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                D   L  +G  K           + R  +   +  + + +++L  G    DD D+L
Sbjct: 341  SQILDSSLLPHLGTSK-----------EDRIKKAYYLGRMARRVLELHLGLRKEDDKDHL 389

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSA 512
             N+R++  G++L+  +R+    + + +K ++                 QD++  K + + 
Sbjct: 390  ANKRLKLSGDLLEELFRMAFEALMKDLKYQLERTYNRKKGIRIRVSIRQDVLTQKIMHAM 449

Query: 513  --VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                     + +SQL +  + +S ++H RR+ +     + R++   E RD+HPT +GR+C
Sbjct: 450  STGNWVGGRTGVSQLLDRTSHMSTLSHLRRVIS----PLTRSQPHFEARDLHPTQWGRLC 505

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P ET EG N GLV +      V+  G+ E    K+  G    +  Y +   E  R     
Sbjct: 506  PNETPEGQNCGLVKNAALIIDVSE-GYPEEDVLKILKGLGVEERQYETG--ELARVYLNG 562

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE-NDDSNR 689
            N                    + ++  +  I + D + + +++     I       ++  
Sbjct: 563  NLVGYHKDGLALTNEIRSRRRKGLISHQINIRYDDTTNEVMINSDKGRIRRPLLVVENGN 622

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            V      +             V  G+ E + A+    A +A                   
Sbjct: 623  VKYTSRHRELLRRGKMDIEDLVREGVVEWIDAEEEENAYIA------------------- 663

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                        +Y     +R      V  R  V   + +   +                
Sbjct: 664  ------------VYAYDVPERCPHCGRVLGRNDV---EWMNPGEGEKVTLRCKHC----- 703

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
                   +          + I   ++   V   +         R T      + +    +
Sbjct: 704  --GAEFGVEKKITKEHTHLEIDPLLILGAVAGCVPYPHHNSSPRITMGAA--MLKQSLGL 759

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                 +   +     +        +    +           +  + AI      +++D  
Sbjct: 760  PAANYRRRPDTRG-HLLHYPQAPIVRTKTMDFVNFMRRPAGQNAVVAIISYHGYNIQDAI 818

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   + V         F R    +  R    + ++ E+ + D       +   +     +
Sbjct: 819  VMNKASVERG-FGRSTFFRTYKSEERRYPGGQEDKFEIPSPD-------VRGAMTEDRYK 870

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L     +S     K   VL                     +       L    +  +S 
Sbjct: 871  LLDEDGLISPEVYVKGGDVLIGK--------------TSPPRFLEEESELLGPQKRRESS 916

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +  R + +         +     R+VKV V  +R  +         G+K           
Sbjct: 917  VTMRPEEEGWVDSVLLTVSENNSRLVKVKVRDQRIPEL--------GDK----------- 957

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
                                SR                  G+K        + +   +  
Sbjct: 958  ------------------FASR-----------------HGQKGVVGAIIPQEDMPFTES 982

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                + +I   +   +++      ++        G  V   VF G  E+A+   L     
Sbjct: 983  GIIPDLIINPHAIPSRMTVGHILEMIGGKVGSLEGRFVDGTVFSGEPEKALREALVKNGF 1042

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
              +G+ I+YDG+TG   +  + VG IY  KL+HMV+ K +ARS G   ++T+QP  G+S 
Sbjct: 1043 KYNGKEIMYDGITGRKIEAEIFVGVIYYQKLHHMVAGKFHARSRGPVQILTRQPTEGRSR 1102

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----VVG-----------RTR-VYESI 1332
             GG R GEME   +  +GAA V+++ L   SD     V G           R R +    
Sbjct: 1103 LGGLRFGEMERDTLIGHGAAMVIKDRLLDNSDGTVLYVCGNPECGHIAMFDRKRGILRCP 1162

Query: 1333 VAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            V GN  + +   T  +F ++  E+ +LG+ + ++    K
Sbjct: 1163 VCGNTTNIYPIETSYAFKLMHDELASLGVIMRMKVGDMK 1201



 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 142/989 (14%), Positives = 278/989 (28%), Gaps = 212/989 (21%)

Query: 79  YEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                P+              +   RDL+Y  PL + ++++  D D     +  + +K  
Sbjct: 83  IRIGRPEIKEATGATVQITPMEARLRDLSYLAPLYLKIKVLECD-DAGCYEREPEMVK-- 139

Query: 129 SIYMGDLPLMTKD-------------------------------------------GTFV 145
              +GD P+M K                                            G F+
Sbjct: 140 ---IGDFPVMVKSKICTLHEDNIDDYLDSISKDKDILNWPYKQKLEYVGEDPDDPGGYFI 196

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ---GLWMDIEFDSKDII 202
           I G +R++VS    +P         +      ++   ++   +        +E  S  II
Sbjct: 197 IGGSERVLVSLEDLAPNRVLVE---KNERYNTVVETAKVFSQRRGYRALTIMEKKSDGII 253

Query: 203 HVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            V +      +P+   + ALG++ ++ +   Y  IV  ++                    
Sbjct: 254 VVSVPAVAGTIPLVILMKALGLEKDQDI---YRAIVSDEKMSVIALANIEEVENDKLYPP 310

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV---------------KFLGITSDCLCGL 306
           + +       + +E  K+  +G  K  +EK +               K   I      G 
Sbjct: 311 NGIRTQRDAIEYLE--KRFAAGQAKEYREKKISQILDSSLLPHLGTSKEDRIKKAYYLGR 368

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             A  ++    G    +  D +  K L+           + +   + +  Y        K
Sbjct: 369 M-ARRVLELHLGLRKEDDKDHLANKRLKLSGDLLEELFRMAFEALMKDLKYQLERTYNRK 427

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
              R        RV    DV T  +  +M    +          + R      L+     
Sbjct: 428 KGIR-------IRVSIRQDVLTQKIMHAMSTGNWVGGRTGVSQLLDRTSHMSTLSHLR-- 478

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             R I             DL   +      +     +   + +       +     E  +
Sbjct: 479 --RVISPLTRSQPHFEARDLHPTQWGRLCPNETPEGQNCGLVKNAALIIDVSEGYPEEDV 536

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            + +  + ++                   +   + +   ++ +   + I   RR   +  
Sbjct: 537 LKILKGLGVEE-------RQYETGELARVYLNGNLVGYHKDGLALTNEIRSRRRKGLISH 589

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
               R         ++        P    E  N+   S      R             + 
Sbjct: 590 QINIRYDDTTNEVMINSDKGRIRRPLLVVENGNVKYTSRHRELLRRGKMD--------IE 641

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDE----------------DGSFTEELVFCRCA 650
           D      V ++ A EEEN YIA     + E                      E V  RC 
Sbjct: 642 DLVREGVVEWIDAEEEENAYIAVYAYDVPERCPHCGRVLGRNDVEWMNPGEGEKVTLRCK 701

Query: 651 GE-----EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                        ++   ++  P  ++   A  +P+  ++ S R+ MG  M +Q++ L  
Sbjct: 702 HCGAEFGVEKKITKEHTHLEIDPLLILGAVAGCVPYPHHNSSPRITMGAAMLKQSLGL-- 759

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                                                    +       +   +  Y   
Sbjct: 760 ---------------------------------------PAANYRRRPDTRGHLLHYP-- 778

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                       Q P+V+                 +      G+N +VA + +HGYN +D
Sbjct: 779 ------------QAPIVR----------TKTMDFVNFMRRPAGQNAVVAIISYHGYNIQD 816

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNVS----EEGLKNIDECG 880
           ++++++  V      S     ++   R    G E +     P+V     E+  K +DE G
Sbjct: 817 AIVMNKASVERGFGRSTFFRTYKSEERRYPGGQEDKFEIPSPDVRGAMTEDRYKLLDEDG 876

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I     V  GD+L+GK +P        EE  L           R++S+ +     G V 
Sbjct: 877 LISPEVYVKGGDVLIGKTSPPRFLE---EESELLGPQKR-----RESSVTMRPEEEGWVD 928

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLAR 969
            V +       +  +    ++   EL  +
Sbjct: 929 SVLLTVSENNSRLVKVKVRDQRIPELGDK 957


>gi|311324412|gb|ADP89515.1| RNA polymerase subunit B [Mycobacterium sp. NLA001000736]
          Length = 245

 Score =  293 bits (749), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 95/232 (40%), Positives = 129/232 (55%), Gaps = 37/232 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  +       +    +          
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNVDVAAGTPEWATTLPEELLESG-- 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                           +TPVFDGA EE +  +L     D      
Sbjct: 160  --------------------------PDTKTATPVFDGAQEEELQGLLASTLPDRDGNVQ 193

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++T
Sbjct: 194  VNSDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMIT 245



 Score = 47.0 bits (110), Expect = 0.021,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|51038416|gb|AAT94116.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038420|gb|AAT94118.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038424|gb|AAT94120.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|326694952|gb|AEA03699.1| RNA polymerase B [Mycobacterium sp. CST-9.1]
          Length = 240

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 153

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 154  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS
Sbjct: 192  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|190694911|gb|ACE88996.1| RNA polymerase beta subunit [Mycobacterium phocaicum]
          Length = 244

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 97/232 (41%), Positives = 129/232 (55%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 45   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 104

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 105  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 150  -----------------LPEGMHSAPRDSIVATPVFDGARENELQGLLGSTLPNRDGDVM 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 193  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 244



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 36/53 (67%), Positives = 44/53 (83%)

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           TPKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   TPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 53


>gi|52538175|emb|CAH19189.1| RNA polymerase beta-subunit [Pseudomonas aeruginosa]
          Length = 360

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 170/297 (57%), Positives = 220/297 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV  A+ EFF SSQL Q  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMGESEGLMPQDLINAKPVAGAIKEFFGSSQLLQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L+E     ++LV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNEKRVLVDKLVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           R G+++ VDA R+V+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 241 RGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 297


>gi|269308450|gb|ACZ34221.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5420]
 gi|269308478|gb|ACZ34235.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5867]
          Length = 339

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 189/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V DGKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVKDGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD ++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSIKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|254994301|ref|ZP_05276491.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes FSL
            J2-064]
          Length = 151

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 76/128 (59%), Positives = 96/128 (75%)

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +YM+KL HMV DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY L
Sbjct: 1    GVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 60

Query: 1312 QEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            QE+LTIKSDDVVGR + YE+IV G    E G PESF VL+KE+Q+LG+ + + ++  +  
Sbjct: 61   QEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQSLGMDVKMLSADEEEI 120

Query: 1372 AKMEEIPD 1379
               +   D
Sbjct: 121  EMRDMDDD 128


>gi|311336634|gb|ADP30897.2| RNA polymerase beta subunit [Acinetobacter soli]
          Length = 266

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 113/270 (41%), Positives = 164/270 (60%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L  Q +  G    K+   LS D++S             DE
Sbjct: 1    DLKEEYKIFEEAARERVVRLLTNQESNGGGTT-KRGDKLSEDMLSGLELVDLLDIQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +   + ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ G+K
Sbjct: 60   GIAERLSQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGNK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP   +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDANGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++I  ++   +    I+ LR FL+K+    G   E +    D+ +L +A   + GVP++T
Sbjct: 180  EQIDKMLQQQRT---IAELRIFLDKIYNKVGGEQEDLDSLTDEEILVLAGNLRKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +A+L  +GQ IL+D
Sbjct: 237  PVFDGAEENQIKELLELAELPRTGQQILFD 266


>gi|119193490|ref|XP_001247351.1| DNA-directed RNA polymerase I [Coccidioides immitis RS]
          Length = 1243

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 94/459 (20%), Positives = 158/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPS 933
            D         +   G   +G            +   L+          +         P+
Sbjct: 716  DFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLDNFPN 775

Query: 934  GVSGTV----------VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            G++  V           D  I N+   ++     ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALD-DKEARGRGKSRREI 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            ++L     G    +       +         ++E      W     D   +  +   K  
Sbjct: 835  TKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVDKET 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + I  +  G +      + V +   + R    GDK + RHG KG+ S
Sbjct: 895  HFLKYKDSEEGYIDSIRIL--GAETGNEACQAVSIKYRIPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G         +  
Sbjct: 953  QLWPAVDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDCTPFQFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                                   +    
Sbjct: 1013 EYTAG--------------------------------------------------DHFGE 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + VT Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGVTGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAVTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 94/705 (13%), Positives = 197/705 (27%), Gaps = 115/705 (16%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L+  L   V + D     +           +G +P+M +       
Sbjct: 124 PAECRERHATYRGRLRARLEFRVNNGDWKESVRE----------LGQVPIMLRTNRCHLE 173

Query: 141 -----------------DGTFVIKGIQRIVVSQLHRS----PGIHFDHDKGRASLSGKLL 179
                             G F++ G ++ ++  L  S    P         +   S    
Sbjct: 174 KLTPYQLVERKEESEELGGYFIVNGNEK-LIRMLIVSRRNFPMAIIRTSFTKRGASYTK- 231

Query: 180 YACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
           +  +I   +         +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 232 FGVQIRSVRPDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--R 286

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL------ 284
             + ++V  +             + +  +   +       +     G+K    L      
Sbjct: 287 EIFERLVGREGSLGINNTFVTDRMELLLRTYKAYGVHSKSKCRAYLGEKFRYVLGMADNV 346

Query: 285 -LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-------EKSLEEI 336
             + +  + ++ + +    L    V E   N +   I      +           + + +
Sbjct: 347 SDEDVGTEFLRKIVLPH--LGNQNVTEPQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAV 404

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            + E+     LY   +          +    +D  +  L         +        +  
Sbjct: 405 SNQEVLLGGFLYGMILKERLEEWLRSIGPLARDWSNRNLGALFTDPKFEKDFLGRIVART 464

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           N     + +Y LST G +     L+L  P     I      A         +    I   
Sbjct: 465 NENLGGALEYFLST-GNLVSPTGLDLQQPSGYTII------AEKINFYRFISHFRMIHRG 517

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                 +  +V ++L   +              + + D       + +  K +++     
Sbjct: 518 SFFAQLKTTTVRKLLPESWGFLCP---------VHTPDGSPCGLLNHLAHKCLIATSNLD 568

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HYGRICPAET 574
                       V S S  +    ++ L  G +    A  + R +  T  H+      + 
Sbjct: 569 VSGIPEILSTLGVGSESSSSLEESVAVLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKI 628

Query: 575 SEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                IG V +     +  V  +      YR V      + + Y+   E+    IA   S
Sbjct: 629 PTELEIGYVPNSNGGQYPGVYIFSQCARMYRPVK-YLPLDKLDYVGPFEQPFMEIACVPS 687

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +    S                        ++  P  ++SI A++ PF + + S R + 
Sbjct: 688 EITSGLS----------------------THVEFDPTHILSILANMTPFSDFNQSPRNMY 725

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            C M +QA+                +    +G   +A+       
Sbjct: 726 QCQMGKQAMGT--PGTSIAYRTDNKLYRLQTGQTPIARPPLYNAY 768



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 75/451 (16%), Positives = 148/451 (32%), Gaps = 51/451 (11%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 492 PSGYTIIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 548

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L     +              +  V+     LS +         ++S  +   
Sbjct: 549 PCGLLNHLAHKCLIAT-----------SNLDVSGIPEILSTL---GVGSESSSSLEESVA 594

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDAS--PKQVVSIAASLIPFLENDDSNRVLM---G 693
              +  +   CA ++  V  + +        PK    +    +P         V +    
Sbjct: 595 VLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKIPTELEIGYVPNSNGGQYPGVYIFSQC 654

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-----RAGIVEQVDAIRIVIRSV 748
             M R    L   +  +VG            A + ++        +      I  ++ ++
Sbjct: 655 ARMYRPVKYLPLDKLDYVG---PFEQPFMEIACVPSEITSGLSTHVEFDPTHILSILANM 711

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGP---STDLG 803
               D + S  ++Y+    +++     T +  R   K+         IA  P   +  L 
Sbjct: 712 TPFSDFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLD 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEIT 862
           +   G N +VA + + GY+ +D+M+I++             +       D +  G  +  
Sbjct: 772 NFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALDDKEARGRGKSR 831

Query: 863 RDIPN---------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT------PKGESPMT 907
           R+I           V  E   ++ E G+  VGA+V  GDI+    T       +    + 
Sbjct: 832 REITKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVD 891

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            E   L+    E+        L   +G    
Sbjct: 892 KETHFLKYKDSEEGYIDSIRILGAETGNEAC 922


>gi|46019140|emb|CAE52034.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 159

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 70/181 (38%), Positives = 112/181 (61%), Gaps = 22/181 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           +P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK
Sbjct: 1   LPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPK 50

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           + V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+
Sbjct: 51  YPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFI 101

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++VR
Sbjct: 102 INGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVR 158

Query: 206 I 206
           I
Sbjct: 159 I 159


>gi|269308448|gb|ACZ34220.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5373]
          Length = 339

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 188/347 (54%), Positives = 256/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V +GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVQNGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD ++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSIKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|269308444|gb|ACZ34218.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4908]
 gi|269308446|gb|ACZ34219.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4906]
          Length = 339

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 189/347 (54%), Positives = 255/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N +GFIETPYR+V  GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YARINEFGFIETPYRQVQKGKVLNDEHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+   + +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPKDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   G+V+ VD+ +I+I           SG   YRL  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVANEDGVVKYVDSKQIII--------EGASGPKNYRLSDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD V+  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 WRSNSGTAITHLPIVKVGDSVKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GII +G E
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTLERRQTKQGPEEITREIPNISESHKKHLDEDGIIAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|269308486|gb|ACZ34239.1| RNA polymerase beta subunit [Spiroplasma sp. BARC 4689]
 gi|269308488|gb|ACZ34240.1| RNA polymerase beta subunit [Spiroplasma sp. GSU4980]
          Length = 339

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 189/347 (54%), Positives = 250/347 (72%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV  GKV  ++ VYL+A +E++  +AQAN    +DG   +E V  
Sbjct: 1   YAKINKYGFIETPYRKVVKGKVLNDEHVYLTADKEKDFIVAQANIQTSKDGKILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV  VD+  I I           +G   Y L  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVASEDGIVRYVDSKTITI--------EGKNGPRSYTLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+++ NDI+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 YRSNNGTAITHLPIVKVGDKIKANDILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESNKKHLDSDGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|295442842|ref|NP_595819.2| DNA-directed RNA polymerase I complex subunit Rpa2
            [Schizosaccharomyces pombe 972h-]
 gi|259016134|sp|Q9P7X8|RPA2_SCHPO RecName: Full=Probable DNA-directed RNA polymerase I subunit RPA2;
            AltName: Full=DNA-directed RNA polymerase I polypeptide
            2; Short=RNA polymerase I subunit 2
 gi|254745588|emb|CAB66435.2| DNA-directed RNA polymerase I complex subunit Rpa2
            [Schizosaccharomyces pombe]
          Length = 1174

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 94/440 (21%), Positives = 163/440 (37%), Gaps = 72/440 (16%)

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            +P+        ++ +            +   R+ +G +  VV  ++ N +G+D      +
Sbjct: 697  SPRNMYQCQMGKQTMGTPGTALRYRTDNKLYRLQTGQTP-VVRPKLHNTYGLDHYPNGTN 755

Query: 959  VEREQIELLARDKDDEQVILDRNIYSR---LMEILCGQNAVSGPK-----------GFKK 1004
                 I     D +D  +IL+++ + R      +  G++     K           GF  
Sbjct: 756  AVVAVISYTGYDMED-AMILNKSAHERGFGYGTVYKGESFDLSQKRRRGEPVVHHFGFAP 814

Query: 1005 STVLSSDLISEYPRSQW----WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
             +    + + +           +    D  V    ES    +  +    E  F +++  +
Sbjct: 815  GSTPRREWLQKLDADGLPFIGIKLEDGDPIVAYYDESTGQNFIETYHGTEPGFVDEVRLL 874

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              G+D+     + + V + + R    GDK + RHG KGI S+  P  DMPF + G   DI
Sbjct: 875  --GNDVGDSECQQIHVKLRITRSPIIGDKFSSRHGQKGICSQKWPTVDMPFTESGMQPDI 932

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP   PSRM +G   E+  G A    G    S    Y      +              
Sbjct: 933  IINPHAFPSRMTIGMFIESLAGKAGACHGLAQDSTPFIYSEQQTAA-------------- 978

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                +     L  A  +  G   +Y G+
Sbjct: 979  ------------------------------------DYFGEQLVKAGYNYHGNEPMYSGI 1002

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TG+     + +G +Y  +L HMVSDK   R+TG    +T+QP+ G+   GG R GEME  
Sbjct: 1003 TGQEMKADIYIGVVYYQRLRHMVSDKFQVRTTGPIHNLTRQPVKGRKRAGGIRFGEMERD 1062

Query: 1301 CIQAYGAAYVLQEMLTIKSD 1320
             +  +G ++++Q+ L   SD
Sbjct: 1063 AVIGHGTSFLMQDRLMNCSD 1082



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 115/762 (15%), Positives = 210/762 (27%), Gaps = 156/762 (20%)

Query: 27  PDL---IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF---VSYE 80
           PDL   ++    S++      +        G + AF S   IT   G A L+F   +S+ 
Sbjct: 23  PDLQKAVKPHVDSFNALTNAGLLNYAVKEIGEKCAFDS---ITQEEGGA-LKFGNKISFR 78

Query: 81  FDP-----P------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            D      P            K    +   R  TY   L +     V      +  + + 
Sbjct: 79  VDEVQIAKPMLSSRERSSINRKVYPAEARERLTTYKSRLVLKFSWSVNGGPRQSEMREV- 137

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
                    G +P+M +                         G F++ GI++     L R
Sbjct: 138 ---------GMIPIMVRSNRCHLEGLSPAELIAHKEESEEMGGYFIVNGIEK-----LIR 183

Query: 160 S--------PGIHFDHDKGRASLSGKLLYACRIIPDQ--GLWM--DIEFDSKDIIHVRID 207
                    P             S    Y   I   +     +   + + +  +   R  
Sbjct: 184 MLILPKRNHPTAIIRPSFANRGTSYSQ-YGLSIRCVRPDQSSLTNTLHYLNNGVTMFRFH 242

Query: 208 RRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
            R+    +P    L AL   S++ +   +  IV    G+ +        L      S  L
Sbjct: 243 WRKNEYLIPSMMILKALLETSDKEI---FEGIVGKDLGNTFLTDRVELMLRAYK--SYGL 297

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED---IVNGETGEIY 321
                  Q + S  ++  G+ + L +  V    +    L  L  A+D   ++     ++Y
Sbjct: 298 YSQTETLQYLGSKFRVVLGVAEDLTDVEVGRFLLQKVVLVHLREAKDKFRLLLFMIRKLY 357

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
                     + +   H EI     LY         I    + D     +  +    R  
Sbjct: 358 ALVAGECCADNPDSPQHQEILLGGFLYGQ-------ILKEKIEDWLNSIRAQINLDVRRS 410

Query: 382 RPG----DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            PG    D    +   S  N       +Y LST G +  N  L+L              +
Sbjct: 411 APGVDFSDRKYLTRVFSKINNDIGTKLQYFLST-GNLVSNTGLDLQQATGYTV------V 463

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           A         +    +         +  +V ++L   +                      
Sbjct: 464 AEKLNFYRFLSHFRMVHRGAFFAELKTTTVRKLLPEAWGFMC-------PVHTPDGSPCG 516

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           ++       + V          S L  L       S + H      +   G        +
Sbjct: 517 LLNHLARKCEIVTHPSDVSQIPSLLLSLGVDPP--SVVGHESGWGCVQLDGKIVGWCTYK 574

Query: 558 --------MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY------R 603
                   +R +   +  ++     +E   + L   +  +   +  G     Y      R
Sbjct: 575 LAKHVADVLRLMKIEYAVKLRNGTATEPAKVPLDLEIG-YVPPSHNGQYPGLYLFSNPAR 633

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            V       T ++  L   E+    IA                           +  +  
Sbjct: 634 MVRPVKHISTGELDMLGPFEQVYMDIA----------------------CFPKEIVPKVS 671

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             ++ SP  V+SI A++ PF + + S R +  C M +Q +  
Sbjct: 672 THVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQMGKQTMGT 713



 Score = 61.6 bits (148), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 75/586 (12%), Positives = 180/586 (30%), Gaps = 59/586 (10%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
           T     S F  +   ++      VGR  +   + +   +     +   ++ +I+ L  L 
Sbjct: 303 TLQYLGSKFRVVLGVAEDLTDVEVGRFLLQKVVLVHLREAKD--KFRLLLFMIRKLYALV 360

Query: 448 NGKGTIDDIDNLGNRRVRSVG--------EMLKNQYRLGLLRMERSIK---ERISSVDID 496
            G+   D+ D+  ++ +   G        E +++       ++   ++     +   D  
Sbjct: 361 AGECCADNPDSPQHQEILLGGFLYGQILKEKIEDWLNSIRAQINLDVRRSAPGVDFSDRK 420

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLS 542
            +          + + +  F  +  L              + + E +N    ++H R   
Sbjct: 421 YLTRVFSKINNDIGTKLQYFLSTGNLVSNTGLDLQQATGYTVVAEKLNFYRFLSHFR--- 477

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            + +G          +R + P  +G +CP  T +G   GL++ L   AR        +  
Sbjct: 478 MVHRGAFFAELKTTTVRKLLPEAWGFMCPVHTPDGSPCGLLNHL---ARKCEIVTHPSDV 534

Query: 603 RKVCDGKVTNDVVYLSA-MEEENRYIAQANSSLDED-GSFTEELVFCRCAGEEILVPREK 660
            ++    ++  V   S    E      Q +  +         + V       +I    + 
Sbjct: 535 SQIPSLLLSLGVDPPSVVGHESGWGCVQLDGKIVGWCTYKLAKHVADVLRLMKIEYAVKL 594

Query: 661 IDFIDASP-KQVVSIAASLIPFLENDDSNRVLM----GCNMQRQAVPLLKAEAPFVGTG- 714
            +     P K  + +    +P   ++     L        M R    +   E   +G   
Sbjct: 595 RNGTATEPAKVPLDLEIGYVP-PSHNGQYPGLYLFSNPARMVRPVKHISTGELDMLGPFE 653

Query: 715 -MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            +   +A      +      +      +  ++ ++    D + S  ++Y+    +++   
Sbjct: 654 QVYMDIACFPKEIVPKVSTHVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQMGKQTMGT 713

Query: 774 TCVNQRPLV-KVGDEVRRNDIIADGPSTDL----GDLALGRNMLVAFMPWHGYNFEDSML 828
                R         ++        P             G N +VA + + GY+ ED+M+
Sbjct: 714 PGTALRYRTDNKLYRLQTGQTPVVRPKLHNTYGLDHYPNGTNAVVAVISYTGYDMEDAMI 773

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++             +         +   E +              E L+ +D  G+  
Sbjct: 774 LNKSAHERGFGYGTVYKGESFDLSQKRRRGEPVVHHFGFAPGSTPRREWLQKLDADGLPF 833

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           +G ++  GD +V           +  +  +    G +   V +  L
Sbjct: 834 IGIKLEDGDPIVAY------YDESTGQNFIETYHGTEPGFVDEVRL 873


>gi|148879079|emb|CAM07055.1| RpoB protein [Mycobacterium sp. MHSD11]
          Length = 231

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 131/230 (56%), Gaps = 37/230 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 144  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 182  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 231


>gi|52538169|emb|CAH19186.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 4]
          Length = 347

 Score =  292 bits (748), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 173/313 (55%), Positives = 223/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKVRIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRGST 300

Query: 791 NDIIADGPSTDLG 803
                       G
Sbjct: 301 QRHHGRRSVHRYG 313


>gi|303312029|ref|XP_003066026.1| DNA-directed RNA polymerase I polypeptide 2 , putative [Coccidioides
            posadasii C735 delta SOWgp]
 gi|240105688|gb|EER23881.1| DNA-directed RNA polymerase I polypeptide 2 , putative [Coccidioides
            posadasii C735 delta SOWgp]
          Length = 1243

 Score =  292 bits (748), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 94/459 (20%), Positives = 158/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPS 933
            D         +   G   +G            +   L+          +         P+
Sbjct: 716  DFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLDNFPN 775

Query: 934  GVSGTV----------VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            G++  V           D  I N+   ++     ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALD-DKEARGRGKSRREI 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            ++L     G    +       +         ++E      W     D   +  +   K  
Sbjct: 835  TKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVDKET 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + I  +  G +      + V +   + R    GDK + RHG KG+ S
Sbjct: 895  HFLKYKDSEEGYIDSIRIL--GAETGNEACQAVSIKYRIPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G         +  
Sbjct: 953  QLWPAVDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDCTPFQFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                                   +    
Sbjct: 1013 EYTAG--------------------------------------------------DHFGE 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + VT Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGVTGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAVTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 94/705 (13%), Positives = 197/705 (27%), Gaps = 115/705 (16%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L+  L   V + D     +           +G +P+M +       
Sbjct: 124 PAECRERHATYRGRLRARLEFRVNNGDWKESVRE----------LGQVPIMLRTNRCHLE 173

Query: 141 -----------------DGTFVIKGIQRIVVSQLHRS----PGIHFDHDKGRASLSGKLL 179
                             G F++ G ++ ++  L  S    P         +   S    
Sbjct: 174 KLTPYQLVERKEESEELGGYFIVNGNEK-LIRMLIVSRRNFPMAIIRTSFTKRGASYTK- 231

Query: 180 YACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
           +  +I   +         +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 232 FGVQIRSVRPDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--R 286

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL------ 284
             + ++V  +             + +  +   +       +     G+K    L      
Sbjct: 287 EIFERLVGREGSLGINNTFVTDRMELLLRTYKAYGVHSKSKCRAYLGEKFRYVLGMADNV 346

Query: 285 -LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-------EKSLEEI 336
             + +  + ++ + +    L    V E   N +   I      +           + + +
Sbjct: 347 SDEDVGTEFLRKIVLPH--LGNQNVTEPQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAV 404

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            + E+     LY   +          +    +D  +  L         +        +  
Sbjct: 405 SNQEVLLGGFLYGMILKERLEEWLRSIGPLARDWSNRNLGALFTDPKFEKDFLGRIVART 464

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           N     + +Y LST G +     L+L  P     I      A         +    I   
Sbjct: 465 NENLGGALEYFLST-GNLVSPTGLDLQQPSGYTII------AEKINFYRFISHFRMIHRG 517

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                 +  +V ++L   +              + + D       + +  K +++     
Sbjct: 518 SFFAQLKTTTVRKLLPESWGFLCP---------VHTPDGSPCGLLNHLAHKCLIATSNLD 568

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HYGRICPAET 574
                       V S S  +    ++ L  G +    A  + R +  T  H+      + 
Sbjct: 569 VSGIPEILSTLGVGSESSSSLEESVAVLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKI 628

Query: 575 SEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                IG V +     +  V  +      YR V      + + Y+   E+    IA   S
Sbjct: 629 PTELEIGYVPNSNGGQYPGVYIFSQCARMYRPVK-YLPLDKLDYVGPFEQPFMEIACVQS 687

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +    S                        ++  P  ++SI A++ PF + + S R + 
Sbjct: 688 EITSGLS----------------------THVEFDPTHILSILANMTPFSDFNQSPRNMY 725

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            C M +QA+                +    +G   +A+       
Sbjct: 726 QCQMGKQAMGT--PGTSIAYRTDNKLYRLQTGQTPIARPPLYNAY 768



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 75/451 (16%), Positives = 148/451 (32%), Gaps = 51/451 (11%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 492 PSGYTIIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 548

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L     +              +  V+     LS +         ++S  +   
Sbjct: 549 PCGLLNHLAHKCLIAT-----------SNLDVSGIPEILSTL---GVGSESSSSLEESVA 594

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDAS--PKQVVSIAASLIPFLENDDSNRVLM---G 693
              +  +   CA ++  V  + +        PK    +    +P         V +    
Sbjct: 595 VLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKIPTELEIGYVPNSNGGQYPGVYIFSQC 654

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-----RAGIVEQVDAIRIVIRSV 748
             M R    L   +  +VG            A + ++        +      I  ++ ++
Sbjct: 655 ARMYRPVKYLPLDKLDYVG---PFEQPFMEIACVQSEITSGLSTHVEFDPTHILSILANM 711

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGP---STDLG 803
               D + S  ++Y+    +++     T +  R   K+         IA  P   +  L 
Sbjct: 712 TPFSDFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLD 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEIT 862
           +   G N +VA + + GY+ +D+M+I++             +       D +  G  +  
Sbjct: 772 NFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALDDKEARGRGKSR 831

Query: 863 RDIPN---------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT------PKGESPMT 907
           R+I           V  E   ++ E G+  VGA+V  GDI+    T       +    + 
Sbjct: 832 REITKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVD 891

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            E   L+    E+        L   +G    
Sbjct: 892 KETHFLKYKDSEEGYIDSIRILGAETGNEAC 922


>gi|320040000|gb|EFW21934.1| DNA-directed RNA polymerase 1 [Coccidioides posadasii str. Silveira]
          Length = 1243

 Score =  292 bits (748), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 94/459 (20%), Positives = 158/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPS 933
            D         +   G   +G            +   L+          +         P+
Sbjct: 716  DFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLDNFPN 775

Query: 934  GVSGTV----------VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            G++  V           D  I N+   ++     ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALD-DKEARGRGKSRREI 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            ++L     G    +       +         ++E      W     D   +  +   K  
Sbjct: 835  TKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVDKET 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + I  +  G +      + V +   + R    GDK + RHG KG+ S
Sbjct: 895  HFLKYKDSEEGYIDSIRIL--GAETGNEACQAVSIKYRIPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G         +  
Sbjct: 953  QLWPAVDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDCTPFQFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                                   +    
Sbjct: 1013 EYTAG--------------------------------------------------DHFGE 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + VT Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGVTGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAVTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 93/705 (13%), Positives = 197/705 (27%), Gaps = 115/705 (16%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L+  L   V + D     +           +G +P+M +       
Sbjct: 124 PAECRERHATYRGRLRARLEFRVNNGDWKESVRE----------LGQVPIMLRTNRCHLE 173

Query: 141 -----------------DGTFVIKGIQRIVVSQLHRS----PGIHFDHDKGRASLSGKLL 179
                             G F++ G ++ ++  L  S    P         +   S    
Sbjct: 174 KLTPYQLVERKEESEELGGYFIVNGNEK-LIRMLIVSRRNFPMAIIRTSFTKRGASYTK- 231

Query: 180 YACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
           +  +I   +         +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 232 FGVQIRSVRPDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--R 286

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL------ 284
             + +++  +             + +  +   +       +     G+K    L      
Sbjct: 287 EIFERLIGREGSLGINNTFVTDRMELLLRTYKAYGVHSKSKCRAYLGEKFRYVLGMADNV 346

Query: 285 -LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-------EKSLEEI 336
             + +  + ++ + +    L    V E   N +   I      +           + + +
Sbjct: 347 SDEDVGTEFLRKIVLPH--LGNQNVTEPQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAV 404

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            + E+     LY   +          +    +D  +  L         +        +  
Sbjct: 405 SNQEVLLGGFLYGMILKERLEEWLRSIGPLARDWSNRNLGALFTDPKFEKDFLGRIVART 464

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
           N     + +Y LST G +     L+L  P     I      A         +    I   
Sbjct: 465 NENLGGALEYFLST-GNLVSPTGLDLQQPSGYTII------AEKINFYRFISHFRMIHRG 517

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                 +  +V ++L   +              + + D       + +  K +++     
Sbjct: 518 SFFAQLKTTTVRKLLPESWGFLCP---------VHTPDGSPCGLLNHLAHKCLIATSNLD 568

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HYGRICPAET 574
                       V S S  +    ++ L  G +    A  + R +  T  H+      + 
Sbjct: 569 VSGIPEILSTLGVGSESSSSLEESVAVLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKI 628

Query: 575 SEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                IG V +     +  V  +      YR V      + + Y+   E+    IA   S
Sbjct: 629 PTELEIGYVPNSNGGQYPGVYIFSQCARMYRPVK-YLPLDKLDYVGPFEQPFMEIACVPS 687

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +    S                        ++  P  ++SI A++ PF + + S R + 
Sbjct: 688 EITSGLS----------------------THVEFDPTHILSILANMTPFSDFNQSPRNMY 725

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            C M +QA+                +    +G   +A+       
Sbjct: 726 QCQMGKQAMGT--PGTSIAYRTDNKLYRLQTGQTPIARPPLYNAY 768



 Score = 58.9 bits (141), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 75/451 (16%), Positives = 148/451 (32%), Gaps = 51/451 (11%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 492 PSGYTIIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 548

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L     +              +  V+     LS +         ++S  +   
Sbjct: 549 PCGLLNHLAHKCLIAT-----------SNLDVSGIPEILSTL---GVGSESSSSLEESVA 594

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDAS--PKQVVSIAASLIPFLENDDSNRVLM---G 693
              +  +   CA ++  V  + +        PK    +    +P         V +    
Sbjct: 595 VLLDGRIVGYCAPKQARVIADTLRHWKVEGHPKIPTELEIGYVPNSNGGQYPGVYIFSQC 654

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-----RAGIVEQVDAIRIVIRSV 748
             M R    L   +  +VG            A + ++        +      I  ++ ++
Sbjct: 655 ARMYRPVKYLPLDKLDYVG---PFEQPFMEIACVPSEITSGLSTHVEFDPTHILSILANM 711

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGP---STDLG 803
               D + S  ++Y+    +++     T +  R   K+         IA  P   +  L 
Sbjct: 712 TPFSDFNQSPRNMYQCQMGKQAMGTPGTSIAYRTDNKLYRLQTGQTPIARPPLYNAYGLD 771

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEIT 862
           +   G N +VA + + GY+ +D+M+I++             +       D +  G  +  
Sbjct: 772 NFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYALDDKEARGRGKSR 831

Query: 863 RDIPN---------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT------PKGESPMT 907
           R+I           V  E   ++ E G+  VGA+V  GDI+    T       +    + 
Sbjct: 832 REITKLFGFAPGGLVKAEWRNHLGEDGLPHVGAKVAEGDIIAAWHTVQYDPAAETYLNVD 891

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            E   L+    E+        L   +G    
Sbjct: 892 KETHFLKYKDSEEGYIDSIRILGAETGNEAC 922


>gi|170091560|ref|XP_001877002.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164648495|gb|EDR12738.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 1179

 Score =  292 bits (748), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 69/258 (26%), Positives = 104/258 (40%), Gaps = 50/258 (19%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G D     L+ + + + + R    GDK + RHG KG+ S+  P  DMPF + G   D+++
Sbjct: 885  GFDAGDTELQKIHITLRITRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFSESGMQPDVII 944

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +G + E+  G A    G    +    +                       
Sbjct: 945  NPHAFPSRMTIGMLVESMAGKAGAMHGLAQDATPFKFSEEDTAINY-------------- 990

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                                    L  A  +  G   +Y G+TG
Sbjct: 991  ------------------------------------FGEQLLAAGYNYYGNEPMYSGITG 1014

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            + F   + +G +Y  +L HMV DK   R+TG    VT+QP+ G+   GG R GEME   +
Sbjct: 1015 QEFAADIYIGVVYYQRLRHMVLDKFQVRTTGPVDPVTRQPVKGRKRAGGIRFGEMERDAL 1074

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             A+G +++LQ+ L   SD
Sbjct: 1075 IAHGTSFLLQDRLMNCSD 1092



 Score = 72.0 bits (175), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 97/665 (14%), Positives = 195/665 (29%), Gaps = 90/665 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDL 408
           D       I          DR + LL  +++                F  +    + +  
Sbjct: 278 DKEIFEGVIMQDYENTFLTDRVELLLRSFKMFTMQTGEQCLEYLGDKFRVVLNLPEDWTN 337

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
           +  G   +   + +         +   ++ +++ L  L +G    D+ D+  ++ V   G
Sbjct: 338 AAQGAWLLRKMILVHLETPRE--KFRMLLFMLRKLYSLVSGSCCADNPDSPQHQEVLLPG 395

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCS------- 519
            +     +  L  +   I+  IS    + V     D    + VVS V     S       
Sbjct: 396 SLYGMIIKERLEEILNGIRMGISMDVRNGVAVDFNDKRYFQKVVSKVNFDIGSKLSNFLA 455

Query: 520 ---------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
                          S  + + E +N    I+H R    + +G          +R + P 
Sbjct: 456 TGNLVSPTGLDLQQASGFTIVAEKLNWQRYISHFR---CIHRGAFFAELKTTTVRKLLPE 512

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM---- 620
            +G +CP  T +G   GL++ L+   R+            +        V   +      
Sbjct: 513 AWGFLCPVHTPDGSPCGLLNHLSRSCRITTTPLAVAHIPALLAAHGMTQVFTPTIDGRKN 572

Query: 621 ---EEENRYI--------AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
              + + R I        AQ  ++L    +  +  V      E  LVP            
Sbjct: 573 LSVQLDGRVIGWARPSVAAQLATNLRIWKTEGKHEVPL--DLEIGLVPVSNGGQYPGLFL 630

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA--PFVGTGMESVVAKSSGAAI 727
              + A  + P     +     +G   Q         E     V T +E           
Sbjct: 631 FSTT-ARMMRPVKYLGNGRDDQVGPFEQVYMNIACIPEEIEEAVSTHVEHEPTNFLSILA 689

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                    Q        +  +  +    + +      K  R        Q P+V+    
Sbjct: 690 NLTPFSDFNQSPRNIYQCQMGKQSMGTPATALQHRTDNKLYRLQTG----QSPVVRP--- 742

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                  A   +  +     G N +VA + + GY+ ED+M++++             +  
Sbjct: 743 -------ALHNTYAMDSFPNGTNAIVAVISYTGYDMEDAMILNKSAHERGFGYGTVYKSQ 795

Query: 848 EVMARDTKLGPEEITRDIPNVS------------EEGLKNIDECGIICVGAEVNPGDILV 895
            +  ++ +   +  +    +                 L+ +D  G+  +GA ++ GD + 
Sbjct: 796 IIDLKEMRGASKLNSVPTLHFGLGNDIRTTGDKLHACLEFLDLDGLPFIGARLSSGDPIA 855

Query: 896 GKITPK-----------GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
             +               E     E +LL    G+  +     +LR+       V+  + 
Sbjct: 856 AYVDDTTGRTKFVRYKGDELGYIDEVRLLGFDAGDTELQKIHITLRI---TRSPVIGDKF 912

Query: 945 FNRHG 949
            +RHG
Sbjct: 913 SSRHG 917


>gi|83415487|gb|ABC17951.1| RNA polymerase II second largest subunit [Rhizophlyctis rosea]
          Length = 719

 Score =  292 bits (748), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 142/862 (16%), Positives = 275/862 (31%), Gaps = 173/862 (20%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERI--SSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ +     +  +  +         IN+K + + +     +
Sbjct: 2    KRLDLAGPLLSGLFRMLFKKLTKDTSRYMLKNVQEHKDFELASAINSKTIQNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RRL+      + R     + R +H TH+
Sbjct: 62   GNWGDQKKFMSARAGVSQVLNRYTYASTLSHLRRLNT----PIGRDGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN----DVVYLSAMEE 622
            G +CPAET EG   GLV +L+  + +            V +          V  +S  + 
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMSYITVGSPGNPVKEFVKELGTVELASQGVGEIS--QS 175

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF---IDASPKQVVSIAASLI 679
               ++  A   + +D  +    +     G E+ +    +     ++ S        A  +
Sbjct: 176  TKVFVNGAWVGVHDDPEYLVNSIREARRGAEVSLELSIVRDVREMELSLVTDAGRIARPL 235

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQV 738
              ++ D     +   N+Q             +  GM E +  +     ++A    ++   
Sbjct: 236  FIVDKDSQKLRITKDNIQEIMENEDVMFEALLTNGMVEYLDTEEEETTMIAMSPEVLADT 295

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
             A+R   + +  +    T           +R   NT              +        P
Sbjct: 296  RAMRKGTKRIITEKPDGT-----------RRLRGNTS-----------RTKEWTHCEIHP 333

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  + +   +++  ++          
Sbjct: 334  SMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYLTSYQTRM------- 377

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +             +       +   +  + AI  
Sbjct: 378  --------------------DTMANILFYPQKPLATTRSMKYLKFKELPAGQNAIVAIGC 417

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    ++ R  +D  ++      E +E    D++    + 
Sbjct: 418  YSGYNQEDSLIMNQSSIDRGLF-RSMYYRVYLDTEKKVGLTNTETLEKP--DRETTLRMR 474

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                Y +L +   ++ G+  +       K+  L  +                +E  QR  
Sbjct: 475  GGTAYDKLDDDGLVIPGKRVLGDDIIIGKTMPLQDN---------------SEELGQRRA 519

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K    T     E+   +++     G        + VKV V   R  Q GDK A RHG
Sbjct: 520  NHTKRDSSTPLKSTENGIVDQVILTTNG-----EGFKFVKVRVRSVRIPQMGDKFASRHG 574

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMPF   G   D+++NP  +PSRM +G + E  +G     +G +  + 
Sbjct: 575  QKGTVGITYRTEDMPFTAQGIVPDLIINPHAIPSRMTIGHLVECLIGKVGAIMGTEGDAT 634

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                   G +S     L                      R  E   +G            
Sbjct: 635  PFTDVTVGSVSDTLKTL------------------GFQPRGFEVLHNG------------ 664

Query: 1216 EEAINSMLRMADLDESGQ---SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                           +G+   + LY G T             Y  +L HMV DK+++R+ 
Sbjct: 665  --------------HTGKKLTAQLYFGPT-------------YYQRLKHMVDDKIHSRAR 697

Query: 1273 GSYSLVTQQPLGGKSNRGGQRL 1294
            G   ++T+QP+ G+S  GG R 
Sbjct: 698  GPVQILTRQPVEGRSRDGGLRF 719


>gi|120561279|gb|ABM27024.1| RNA polymerase II second largest subunit [Monosiga brevicollis]
          Length = 904

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 162/1053 (15%), Positives = 303/1053 (28%), Gaps = 210/1053 (19%)

Query: 271  EQVIESGKKLTSGLLKSLKE--KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
              ++E   + TS ++  +     G      T   +    +     +     ++   G   
Sbjct: 33   RSIVEDSNRPTSTMMVKMLRGGSGGTKGRATFGRVIHASLPYIRQDIPVVVLFRALGFED 92

Query: 329  DEKSLEEIFHS--EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            D   LE I +   ++  + +L              +  D    R  A + + + MR    
Sbjct: 93   DRSILEHIIYDFDDMEMMELLKPSLDEAFVVQTREVALDLIGRRSMAAVGMSKDMR---- 148

Query: 387  STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                     F       +      VG      +         R ++              
Sbjct: 149  -------VRFARDILQKEMLPHIGVGPQCEQAKAFFLGYMVHRTLQAALR---------- 191

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLI 504
               +  +DD D+ GN+R+   G ++   +R    ++ + +  K           M   L+
Sbjct: 192  ---RRELDDRDHYGNKRLDLAGSLVAYLFRTLFKQLTKKLTRKVTDLVNRNHKFMVITLL 248

Query: 505  NAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            + + + S +     +               +SQ+   +   S ++H RRL++     + R
Sbjct: 249  DVEILGSGLRYSLATGNWGDQKKAHEARAGVSQVLNRLTFASTLSHLRRLNS----PIDR 304

Query: 552  ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 + R +H TH+G ICPAET EGH +GLV +L+  A +            V D    
Sbjct: 305  TGKIAKPRQLHNTHWGYICPAETPEGHAVGLVKNLSLMASLTVGSDDTP----VHDLLGA 360

Query: 612  NDVVYL----SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            + + YL    S    +       N +     S  +ELV              ++      
Sbjct: 361  SGLDYLDRLPSRSAIKTATKVFVNGNWVGIHSHPDELVTTMRQMRRAHSVASEVSIFRNI 420

Query: 668  PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
             ++                                             E  +   SG   
Sbjct: 421  RER---------------------------------------------EVHIVTDSGRTT 435

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              +   IV + DA R         +    +    +             + QR +V+  D 
Sbjct: 436  --RPLLIVNKDDANRCRFALKNSHVMALRNDQMSWTH-----------LVQRGVVEYIDV 482

Query: 788  VRRNDIIADGPSTDLGDLAL----GRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTS 841
                  +          LAL      N       +       SM+  I   ++       
Sbjct: 483  NEEETTMIAM--YGHDPLALLALPDSNTTSYCNTYTHCEIHPSMILSICASIIPFPDHNQ 540

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                 ++       +G                 ++    +  V        +    +   
Sbjct: 541  SPRNTYQSAMGKQAMGVYITN-----------FHVRMDTLAHVLYYPQRPLVQTRSMNYL 589

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
              + +      +  I      +  D+ +     V   +     +  +       S   ER
Sbjct: 590  RFAELPAGINAIVGIMTYTGYNQEDSVIMNRYSVERGLFRSVFYRSYAA-----SEHSER 644

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
             +I  + +   +  + + R  Y +L +     + +  P             + E P    
Sbjct: 645  GEIIKIDKPSRENCIGMRRANYDKLED-----DGIVAPGIRVSGDDAIVGRLLELP---- 695

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                      +   ++   ++E     L  R             +     + VK+ V   
Sbjct: 696  ----------EATRQASGGRFEKRDKSLFLRSSESGIIDGVMISVNQKGEKFVKIRVRSV 745

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK A RHG KG        EDMPF   G   DI++NP  +PSRM +G + E  L
Sbjct: 746  RTPQIGDKFASRHGQKGTCGMQYAQEDMPFAASGVVPDIIVNPHAIPSRMTIGHLIECLL 805

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G +    G    +         D++ +     +      +  ++                
Sbjct: 806  GKSASHSGTIGDATPFTKVNVTDVADIL----EGYNFQRYGNEVM--------------- 846

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                         +G +       G      V +G  Y  +L H
Sbjct: 847  ----------------------------YNGFT-------GRKMQAQVFLGPTYYQRLKH 871

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            MV DK++AR+ G    +T+QP+ G+S  GG R 
Sbjct: 872  MVDDKIHARARGPLQNLTRQPMEGRSRDGGLRF 904



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 123/767 (16%), Positives = 227/767 (29%), Gaps = 121/767 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +PV     ALG + +  IL          +  +     L  A ++   +V+
Sbjct: 74  YIRQD----IPVVVLFRALGFEDDRSILEHIIYDFDDMEMMELLKPSLDEAFVVQTREVA 129

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L+   +   V  S           L+++ +  +G+   C          +   T +  
Sbjct: 130 LDLIGRRSMAAVGMSKDMRVRFARDILQKEMLPHIGVGPQCEQAKAFFLGYMVHRTLQAA 189

Query: 322 IEAGDVIDEKSL-EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           +   ++ D      +        +  L+              VTD        ++     
Sbjct: 190 LRRRELDDRDHYGNKRLDLAGSLVAYLFRTLFKQLTKKLTRKVTDLVNRNHKFMVIT--- 246

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
           +   ++    +  S+    + D  K   +  G  ++  RL   +      R     D   
Sbjct: 247 LLDVEILGSGLRYSLATGNWGDQKKAHEARAGVSQVLNRLTFASTLSHLRRLNSPIDRTG 306

Query: 439 IIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDID 496
            I     L N   G I   +      V  V  + L     +G            S +D  
Sbjct: 307 KIAKPRQLHNTHWGYICPAETPEGHAVGLVKNLSLMASLTVGSDDTPVHDLLGASGLDYL 366

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
             +P        + +A   F   + +         ++ +   RR  ++           +
Sbjct: 367 DRLPS----RSAIKTATKVFVNGNWVGIHSHPDELVTTMRQMRRAHSVASE--VSIFRNI 420

Query: 557 EMRDVHP-THYGR------ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             R+VH  T  GR      I   + +      L +S     R +   +     R V    
Sbjct: 421 REREVHIVTDSGRTTRPLLIVNKDDANRCRFALKNSHVMALRNDQMSWTHLVQRGV---- 476

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
               V Y+   EEE   IA             + L                    +  P 
Sbjct: 477 ----VEYIDVNEEETTMIAMYG---------HDPLALLALPDSNTTSYCNTYTHCEIHPS 523

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++SI AS+IPF +++ S R      M +QA+ +                          
Sbjct: 524 MILSICASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------- 564

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + V  Y               QRPLV+      
Sbjct: 565 ----------------------RMDTLAHVLYYP--------------QRPLVQ------ 582

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-- 847
                         +L  G N +V  M + GYN EDS++++   V   +F S+    +  
Sbjct: 583 ----TRSMNYLRFAELPAGINAIVGIMTYTGYNQEDSVIMNRYSVERGLFRSVFYRSYAA 638

Query: 848 -EVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            E   R   +  ++ +R +   +       +++ GI+  G  V+  D +VG++    E+ 
Sbjct: 639 SEHSERGEIIKIDKPSRENCIGMRRANYDKLEDDGIVAPGIRVSGDDAIVGRLLELPEAT 698

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                            + RD SL + S  SG +  V I      +K
Sbjct: 699 RQASGG---------RFEKRDKSLFLRSSESGIIDGVMISVNQKGEK 736


>gi|185179216|gb|ACC77621.1| RpoB [Mycobacterium xenopi]
          Length = 208

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 100/231 (43%), Positives = 135/231 (58%), Gaps = 37/231 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 7    RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 66

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G KI +                     
Sbjct: 67   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKIDT--------------------- 104

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                      +    + +L           V+TPVFDGA EE +  +L            
Sbjct: 105  ---SKGVPDWASRLPEELLEAEPNKI----VATPVFDGAREEELQGLLSCTLPNRDGDVL 157

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++
Sbjct: 158  VDGDGKATLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMI 208


>gi|322370000|ref|ZP_08044562.1| DNA-directed RNA polymerase subunit B' [Haladaptatus paucihalophilus
            DX253]
 gi|242392310|dbj|BAH80328.1| RNA polymerase subunit B' [Haladaptatus paucihalophilus DX253]
 gi|320550336|gb|EFW91988.1| DNA-directed RNA polymerase subunit B' [Haladaptatus paucihalophilus
            DX253]
          Length = 608

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 96/321 (29%), Positives = 138/321 (42%), Gaps = 78/321 (24%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 345  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTQEGVVPDLIVNPHAL 404

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V        G     +G K+ ++                                
Sbjct: 405  PSRMTV--------GHVLEMIGGKVGAMEGRRVDGT------------------------ 432

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   F G D+E + S L+      SG+ I+Y G+TGE  + 
Sbjct: 433  ----------------------AFSGEDKEELRSALQERGYKSSGKEIMYSGVTGEKIEA 470

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I   KL HMVS+K++ARS G   ++T+QP  G++  GG R+G ME  C   +GA
Sbjct: 471  EIFVGTILYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRIGTMERDCFVGHGA 530

Query: 1308 AYVLQEMLTIKSDDVVGRTRVY----------ESIVAG----------NDTFETGTPESF 1347
            A  L+E L   SD    R  +Y          E+I              D  E     +F
Sbjct: 531  ALALKERLLDSSD----REWIYVCGQCGMSAVENIDQNRVYCPNCEEETDIHEIDMSYAF 586

Query: 1348 NVLVKEMQALGLSIDLENSRT 1368
             +L+ EM+ALG++  LE   T
Sbjct: 587  KLLLDEMKALGIAPRLELEDT 607



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 62/374 (16%), Positives = 120/374 (32%), Gaps = 29/374 (7%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +S   E   Y+  +      D       V   R  G+   +    +    +         
Sbjct: 1   MSQGREAKVYVNGSLVGTHPDPEQLANQVREARRRGDVSEMVNVSVKGRTSEVIINADAG 60

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            +  P L  +D    +    ++      L  +       +E + A+      VA     +
Sbjct: 61  RARRPLLVVEDGETRITDEEVEALNQGDLSFDELVERGKIEFIDAEEEEDIYVAVDDDEL 120

Query: 736 EQVDAIRIVIRSV---------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR--PLVKV 784
            + D   + I                + + S          ++S      N R  P  + 
Sbjct: 121 NE-DHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSIGLPSANYRIRPDTRQ 179

Query: 785 GDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                    +    +T+     D    +N  VA M + G+N ED++++++  V   +  S
Sbjct: 180 HLFHYPQLSMVKTQTTEQIGFDDRPAAQNFTVAVMSYEGFNIEDALVMNKGSVERALARS 239

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDILV 895
                +E   R    G E+   +IP+        E+   ++DE G++     V+   +L+
Sbjct: 240 HFFRTYEGEERRYPGGQEDRF-EIPSDDVRGARGEDAYTHLDEDGLVNPETRVDENSVLL 298

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           GK +P               + G      R+TS+ + SG SG V  V +       K  +
Sbjct: 299 GKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVVDTVTLMEGEDGSKLSK 352

Query: 956 SISVEREQIELLAR 969
               +    EL  +
Sbjct: 353 VSVRDERIPELGDK 366



 Score = 47.0 bits (110), Expect = 0.024,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 23/99 (23%)

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + ++ A EEE+ Y+A  +  L+ED                          ++  P+ +
Sbjct: 98  GKIEFIDAEEEEDIYVAVDDDELNEDH-----------------------THLEIDPQLI 134

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             I A +IP+ E++ S R+ MG  M +Q++ L  A    
Sbjct: 135 FGIGAGMIPYPEHNASPRITMGAGMMKQSIGLPSANYRI 173


>gi|158954706|gb|ABW84324.1| RNA polymerase subunit B [Mycobacterium vaccae]
          Length = 244

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 130/229 (56%), Gaps = 34/229 (14%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +     + L   +   
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIQVADGTGEVPQWAAKLPEHMLSA 160

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          V+TPVFDGA E  +  +L     +      
Sbjct: 161  PPDSI-------------------------VATPVFDGAQEGELTGLLGATLPNRDGETM 195

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 196  VNADGKAVLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 244



 Score = 46.6 bits (109), Expect = 0.030,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|148879039|emb|CAM07035.1| RpoB protein [Mycobacterium sp. MG5]
          Length = 230

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 98/232 (42%), Positives = 130/232 (56%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 136  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 179  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 230


>gi|221056432|ref|XP_002259354.1| dna-directed rna polymerase, beta subunit [Plasmodium knowlesi strain
            H]
 gi|193809425|emb|CAQ40127.1| dna-directed rna polymerase, beta subunit,putative [Plasmodium
            knowlesi strain H]
          Length = 1539

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 194/1202 (16%), Positives = 371/1202 (30%), Gaps = 124/1202 (10%)

Query: 288  LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
             ++  +K+LG +S    G++          G+I +    +   +S  E F +       L
Sbjct: 348  FEKYNLKYLGNSSYFRRGIFRYNVAPGERKGKIILRYAILPHIQSYSEKFETICMMFKTL 407

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF---LFFDSD 404
                    A I    + +        LL     +    + T               F   
Sbjct: 408  IFSKFKLMAKINKDSLENHAVTTCSHLLSN---LLKEQILTCLGRLVFRYSRNFYKFYEK 464

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            KYD   V   ++ +R      D+   + ++ +  +     D    K          + + 
Sbjct: 465  KYDSFKVMVKQIYLRYKEMVMDE---LDEKHLNMVPLEGDDSDISKAADSGNQLAMSNKS 521

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS----- 519
             +V ++                       + +++      +   +   +  FF +     
Sbjct: 522  EAVKKLKSIFMDEKEKLFSSVESYIQELYNDNNLFVDISKSFITLTMPIIFFFKTGNISS 581

Query: 520  --------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                    S      + +NSL  IT+ R   A+ +G   +    +  R +    +G ICP
Sbjct: 582  ENIGYQQRSGWVIGADEINSLRFITNFR---AIHRGCFFQEVKVLSPRKLLGEAWGFICP 638

Query: 572  AETSEGHNIGLVSSLTSFARV-------NAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
              T +G   GL++ L+ F+ V       +    I+   +K+      +D   +  + E+ 
Sbjct: 639  VHTPDGSPCGLLNHLSQFSYVHNSASNESHKLNIKLYLKKIGVNVNLDDTSGIPTIYEDQ 698

Query: 625  RY-IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA-----SPKQVVSIAASL 678
               I   +  +          V  +    +         + +       P  + SI  + 
Sbjct: 699  TIPILVDSVPITYISEQDFNRVVYKLKYAKNHNLYNLKAYFEINAYLNEPLLMDSIIINT 758

Query: 679  IP-----FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
             P      L N     +       +  V +           +   + +     + +K+  
Sbjct: 759  FPGRLIRPLFNLKMKCIEYISPAYQPYVAIAINYEHIKKNNLARKMLRMKERLVRSKKGT 818

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV------KVGDE 787
              +     + +  +    L  S+ G  +      +  +  +       V          E
Sbjct: 819  QQKMTIKEQYLFHARRMKLASSSKGNALQNSSPVKEDSGASESKISRKVLQLLEDSENKE 878

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE----------- 836
                D   D    +   ++             G + + +    +R               
Sbjct: 879  REHTDSQGDITDGEDDYISSSNYDSSGDSCGEGSDDQSNRQSDDRSDKREGKYRHSVPPT 938

Query: 837  ---DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
               D   +++++ +E M    +    + T  +  +        D         +      
Sbjct: 939  SYTDSDENVNLDIYEQMPEKFEYMELKETSFLSFLGS-LTPFSDHNQSPRNIYQCQMLKQ 997

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +G  +       T +   +        V        V +  SGT   V I    G D  
Sbjct: 998  TMGIQSLNMMYTFTNKIYRMITPQYPLVVTRDYELYGVDNFPSGTNAVVAILAYTGYDME 1057

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA-----VSGPKGFKKSTVL 1008
            +  I  +      + R    + +I+D        +   G N       +G      ++  
Sbjct: 1058 DALIINKSSAERGIFRTHIYKTIIIDLKKNHGAGDFALGNNVRYTNKNAGTNATSANSTS 1117

Query: 1009 SSDLISEYPRSQWWQFAVQD--EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            ++    ++      +F  +D   +VQ+ +  L   Y       E     K ++       
Sbjct: 1118 TAKNNLKFQYEHMGKFLNKDGLPRVQQKMVELNPLYSYVNKASELTVYEKFKEHGEYYVD 1177

Query: 1067 PPGVLRVVK-----VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                 +  K     + +   RP   GDK A RHG KG+VSR+ P EDMPF + G   D++
Sbjct: 1178 CVTNYKSTKNQIGIIRLRTTRPPLVGDKFASRHGQKGVVSRLFPHEDMPFSESGIVPDVI 1237

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD-----------ISPLRS 1170
             NP G+PSRM +G + E+  G A    GK+I +                     +     
Sbjct: 1238 FNPHGIPSRMTIGMLIESICGKAACMYGKRIDATPFRKYTKQKSFNNEWIDNCGVKGFLE 1297

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS-TPVFD------GADEEAINSML 1223
             +++               ++       + K+ +P   TP  +          +    +L
Sbjct: 1298 QVKQGKNEDGKDSSSHAPGEEVGHSHKGKKKNDIPKGETPKGEKNNITYDEKIDYFAKLL 1357

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
                 D  G  +LY G+ G P    +  G IY  +L HM  DK   R TG    +T QPL
Sbjct: 1358 LNKGYDYYGTELLYSGIYGVPLQAHIFFGVIYYQRLRHMAYDKAQVRRTGPICNLTHQPL 1417

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD---------------------- 1321
             GK   GG RLGEME   + ++G ++++ E   I SD                       
Sbjct: 1418 KGKKKHGGIRLGEMERDGLISHGCSFIINERFLINSDGHECFVCPQCGLILSPIMQFTCS 1477

Query: 1322 --------VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    + GR++V      G        P     L+ E+  L ++I L     +N   
Sbjct: 1478 GEMVKGRSIGGRSKVAVCKSCGVSCKIVYVPYVLRYLLNELICLNITIRLNIKSVENMFD 1537

Query: 1374 ME 1375
            M+
Sbjct: 1538 MK 1539


>gi|269308442|gb|ACZ34217.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5400]
 gi|269308460|gb|ACZ34226.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5360]
          Length = 339

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 189/347 (54%), Positives = 250/347 (72%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N +GFIETPYRKV  GKV  ++ VYL+A +E++  +AQAN    +DG   +E V  
Sbjct: 1   YAKINKFGFIETPYRKVVKGKVLNDEHVYLTADKEKDFIVAQANIQTSKDGKILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIMADPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV  VD+  I I           +G   Y L  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVASEDGIVRYVDSKTITI--------EGKNGPRSYTLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+V+ NDI+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 YRSNNGTAITHLPIVKVGDKVKANDILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V ED FTSIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIEDRFTSIHIDEYTLERRQTKQGPEEITRDIPNISESHKKHLDNDGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|289596766|ref|YP_003483462.1| DNA-directed RNA polymerase subunit B [Aciduliprofundum boonei T469]
 gi|289534553|gb|ADD08900.1| DNA-directed RNA polymerase subunit B [Aciduliprofundum boonei T469]
          Length = 1201

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 183/1179 (15%), Positives = 375/1179 (31%), Gaps = 180/1179 (15%)

Query: 225  SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL---- 280
             ++IL+  Y + +     D    P     +    +V  SL D+     ++E  ++     
Sbjct: 169  DKDILNWPYKQKLEYVGEDPDD-PGGYFIIGGSERVLVSLEDLAPNRVLVEKNERYNTVV 227

Query: 281  -TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
             T+ +    +      +         +     +       I ++A  +  ++ +     S
Sbjct: 228  ETAKVFSQRRGYRALTIMEKKSDGIIVVSVPAVAGTIPLVILMKALGLEKDQDIYRAIVS 287

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            + +   I   +              +  + ++DA+  + +    G    +         +
Sbjct: 288  DEKMSVIALANIEEVEN--DKLYPPNGIRTQRDAIEYLEKRFAAGQAKEYRE-----KKI 340

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                D   L  +G  K           + R  +   +  + + +++L  G    DD D+L
Sbjct: 341  SQILDSSLLPHLGTSK-----------EDRIKKAYYLGRMARRVLELHLGLRKEDDKDHL 389

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSA 512
             N+R++  G++L+  +R+    + + +K ++                 QD++  K + + 
Sbjct: 390  ANKRLKLSGDLLEELFRMAFEALMKDLKYQLERTYNRKKGIRIRVSIRQDVLTQKIMHAM 449

Query: 513  --VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                     + +SQL +  + +S ++H RR+ +     + R++   E RD+HPT +GR+C
Sbjct: 450  STGNWVGGRTGVSQLLDRTSHMSTLSHLRRVIS----PLTRSQPHFEARDLHPTQWGRLC 505

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            P ET EG N GLV +      V+  G+ E    K+  G    +  Y +   E  R     
Sbjct: 506  PNETPEGQNCGLVKNAALIIDVSE-GYPEEDVLKILKGLGVEERQYETG--ELARVYLNG 562

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE-NDDSNR 689
            N                    + ++  +  I + D + + +++     I       ++  
Sbjct: 563  NLVGYHKDGLALTNEIRSKRRKGLISHQINIRYDDTTNEVMINSDKGRIRRPLLVVENGN 622

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            V      +             V  G+ E + A+    A +A                   
Sbjct: 623  VKYTSRHRELLRRGKMEIEDLVREGVVEWIDAEEEENAYIA------------------- 663

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                        +Y     +R      V  R  V   + +   +                
Sbjct: 664  ------------VYAYDVPERCPHCGRVLGRNDV---EWMNPGEGEKVTLRCKHC----- 703

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
                   +          + I   ++   V   +         R T      + +    +
Sbjct: 704  --GAEFGVEKKITKEHTHLEIDPLLILGAVAGCVPYPHHNSSPRITMGAA--MLKQSLGL 759

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                 +   +     +        +    +           +  + AI      +++D  
Sbjct: 760  PAANYRRRPDTRG-HLLHYPQAPIVRTKTMDFVNFMRRPAGQNAVVAIISYHGYNIQDAI 818

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   + V         F R    +  R    + ++ E+ + D       +   +     +
Sbjct: 819  VMNKASVERG-FGRSTFFRTYKSEERRYPGGQEDKFEIPSPD-------VRGAMTEDRYK 870

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +L     +S     K   VL                     +       L    +  +S 
Sbjct: 871  LLDEDGLISPEVYVKGGDVLIGK--------------TSPPRFLEEESELLGPQKRRESS 916

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +  R + +         +     R+VKV V  +R  +         G+K           
Sbjct: 917  VTMRPEEEGWVDSVLLTVSENNSRLVKVKVRDQRIPEL--------GDK----------- 957

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
                                SR                  G+K        + +   +  
Sbjct: 958  ------------------FASR-----------------HGQKGVVGAIIPQEDMPFTES 982

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                + +I   +   +++      ++        G  V   VF G  E+A+   L     
Sbjct: 983  GIIPDLIINPHAIPSRMTVGHILEMIGGKVGSLEGRFVDGTVFSGEPEKALREALVKNGF 1042

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
              +G+ I+YDG+TG   +  + VG IY  KL+HMV+ K +ARS G   ++T+QP  G+S 
Sbjct: 1043 KYNGKEIMYDGITGRKIEAEIFVGVIYYQKLHHMVAGKFHARSRGPVQILTRQPTEGRSR 1102

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----VVG-----------RTR-VYESI 1332
             GG R GEME   +  +GAA V+++ L   SD     V G           R R +    
Sbjct: 1103 LGGLRFGEMERDTLIGHGAAMVIKDRLLDNSDGTVLYVCGNPECGHIAMFDRKRGILRCP 1162

Query: 1333 VAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
            V GN  + +   T  +F ++  E+ +LG+ + ++    K
Sbjct: 1163 VCGNTTNIYPIETSYAFKLMHDELASLGVIMRMKVGDMK 1201



 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 144/989 (14%), Positives = 281/989 (28%), Gaps = 212/989 (21%)

Query: 79  YEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                P+              +   RDL+Y  PL + ++++  D D     +  + +K  
Sbjct: 83  IRIGRPEIKEATGATVQITPMEARLRDLSYLAPLYLKIKVLECD-DAGCYEREPEMVK-- 139

Query: 129 SIYMGDLPLMTKD-------------------------------------------GTFV 145
              +GD P+M K                                            G F+
Sbjct: 140 ---IGDFPVMVKSKICTLHEDNIDDYLDSISKDKDILNWPYKQKLEYVGEDPDDPGGYFI 196

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ---GLWMDIEFDSKDII 202
           I G +R++VS    +P         +      ++   ++   +        +E  S  II
Sbjct: 197 IGGSERVLVSLEDLAPNRVLVE---KNERYNTVVETAKVFSQRRGYRALTIMEKKSDGII 253

Query: 203 HVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
            V +      +P+   + ALG++ ++ +   Y  IV  ++                    
Sbjct: 254 VVSVPAVAGTIPLVILMKALGLEKDQDI---YRAIVSDEKMSVIALANIEEVENDKLYPP 310

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV---------------KFLGITSDCLCGL 306
           + +       + +E  K+  +G  K  +EK +               K   I      G 
Sbjct: 311 NGIRTQRDAIEYLE--KRFAAGQAKEYREKKISQILDSSLLPHLGTSKEDRIKKAYYLGR 368

Query: 307 YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK 366
             A  ++    G    +  D +  K L+           + +   + +  Y        K
Sbjct: 369 M-ARRVLELHLGLRKEDDKDHLANKRLKLSGDLLEELFRMAFEALMKDLKYQLERTYNRK 427

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
              R        RV    DV T  +  +M    +          + R      L+     
Sbjct: 428 KGIR-------IRVSIRQDVLTQKIMHAMSTGNWVGGRTGVSQLLDRTSHMSTLSHLR-- 478

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
             R I             DL   +      +     +   + +       +     E  +
Sbjct: 479 --RVISPLTRSQPHFEARDLHPTQWGRLCPNETPEGQNCGLVKNAALIIDVSEGYPEEDV 536

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            + +  + ++                   +   + +   ++ +   + I   RR   +  
Sbjct: 537 LKILKGLGVEE-------RQYETGELARVYLNGNLVGYHKDGLALTNEIRSKRRKGLISH 589

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
               R         ++        P    E  N+   S      R    G +E     + 
Sbjct: 590 QINIRYDDTTNEVMINSDKGRIRRPLLVVENGNVKYTSRHRELLR---RGKME-----IE 641

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDE----------------DGSFTEELVFCRCA 650
           D      V ++ A EEEN YIA     + E                      E V  RC 
Sbjct: 642 DLVREGVVEWIDAEEEENAYIAVYAYDVPERCPHCGRVLGRNDVEWMNPGEGEKVTLRCK 701

Query: 651 GE-----EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                        ++   ++  P  ++   A  +P+  ++ S R+ MG  M +Q++ L  
Sbjct: 702 HCGAEFGVEKKITKEHTHLEIDPLLILGAVAGCVPYPHHNSSPRITMGAAMLKQSLGL-- 759

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                                                    +       +   +  Y   
Sbjct: 760 ---------------------------------------PAANYRRRPDTRGHLLHYP-- 778

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                       Q P+V+                 +      G+N +VA + +HGYN +D
Sbjct: 779 ------------QAPIVR----------TKTMDFVNFMRRPAGQNAVVAIISYHGYNIQD 816

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNVS----EEGLKNIDECG 880
           ++++++  V      S     ++   R    G E +     P+V     E+  K +DE G
Sbjct: 817 AIVMNKASVERGFGRSTFFRTYKSEERRYPGGQEDKFEIPSPDVRGAMTEDRYKLLDEDG 876

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I     V  GD+L+GK +P        EE  L           R++S+ +     G V 
Sbjct: 877 LISPEVYVKGGDVLIGKTSPPRFLE---EESELLGPQKR-----RESSVTMRPEEEGWVD 928

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLAR 969
            V +       +  +    ++   EL  +
Sbjct: 929 SVLLTVSENNSRLVKVKVRDQRIPELGDK 957


>gi|51035553|emb|CAH10913.1| RNA polymerase B subunit [Halococcus morrhuae]
          Length = 233

 Score =  292 bits (747), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 81/262 (30%), Positives = 117/262 (44%), Gaps = 61/262 (23%)

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +PSRM VG
Sbjct: 2    KVSVRDQRVPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIVNPHALPSRMTVG 61

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E   G      G+++       +   ++                             
Sbjct: 62   HVLEMLGGKVGSLEGRRVDGTAFTGEEEEELRSSLEEHG--------------------- 100

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                            FD                  SG+ I++ G+TGE  D  + VG I
Sbjct: 101  ----------------FD-----------------SSGKEIMHSGVTGEKIDAEIFVGTI 127

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            +  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GAA  L+E 
Sbjct: 128  FYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGAAMALKER 187

Query: 1315 LTIKSDDVVGRTRVYESIVAGN 1336
            L  +SD    R  +Y   V G 
Sbjct: 188  LLDESD----REFIY---VCGE 202


>gi|67515344|gb|AAY68201.1| RNA polymerase IV second largest subunit [Lunularia cruciata]
          Length = 789

 Score =  292 bits (747), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 80/340 (23%), Positives = 127/340 (37%), Gaps = 101/340 (29%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ KV +   R  Q GDK +  HG KGIV  +   ED+PF  +G   DI++NP  
Sbjct: 509  DEEGKKIAKVKLRETRIPQVGDKFSRMHGQKGIVGMVFTQEDLPFTNEGIVPDIIINPHA 568

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSR  +GQ+ E+ LG A    G+++                                  
Sbjct: 569  FPSRQTLGQMCESALGKAIAKRGEQL---------------------------------- 594

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP    +  E+I   L  +  +  G   +Y+G TG+   
Sbjct: 595  -------------------FATPFNPASTVESITEALHESGYNGWGMETMYNGYTGKAMV 635

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G  +  +L HMV DK+  RS G    +T+QP+  +   GG + GEME  C+ A+G
Sbjct: 636  AKIFIGSTFYQRLTHMVEDKIKYRSRGHVHPLTRQPVSDRKRHGGVKFGEMERDCLIAHG 695

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESI---------------------------------- 1332
            AA  LQE     SD        Y  I                                  
Sbjct: 696  AAATLQERTFHLSD--------YHEIHICRSCKQMAHMGIDRIPTCRFCKEKNKKVVKGK 747

Query: 1333 ------VAGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                      +  +   P +  +L++E+Q++G+S+ L+  
Sbjct: 748  KTDKTETKVEEIVKVEIPYACKLLIQELQSMGISVGLDTE 787



 Score = 69.3 bits (168), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 86/552 (15%), Positives = 168/552 (30%), Gaps = 93/552 (16%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R   ++  S + +       +  K +       F S      +   NS       R    
Sbjct: 9   RKRLQKHLSKNQELSSIDKYVEDKVITRGFRNSFSSGNWMGHDLMKNSGIVFDLKRSNPI 68

Query: 544 LGQGGVARARA--------GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
                +   R         G + R    + +GR+CP +T +G   GLV ++     V++ 
Sbjct: 69  STLCQLRELRQYVPPTVKVGEDARHPTFSQWGRVCPIDTPDGEACGLVKNMALTGIVSSA 128

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE------------- 642
           G  E P     +      +  +++           N         T              
Sbjct: 129 GT-EAPVIDFLESNGMIPLESVTSDTLGMVMKVFVNGRWLGVVKHTHFEPIIKGLRALRK 187

Query: 643 ----------ELVFCRCAGEE-------------ILVPREKIDFIDASPKQVVSIAASLI 679
                     E+V  R   E              ++V   K++    S  Q +S    L 
Sbjct: 188 RPPTAELYQMEVVIIRPKFEIQVSTDSGRVLRPLLVVRHNKMNLNQDSVTQYISEKRGLP 247

Query: 680 PFLE---NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM------ESVVAKSSGAAIVAK 730
                         L+G   + +A+  L         G+      E   A+   + I+  
Sbjct: 248 HERFTWFLQKHVIELLGVEEEEKALIALHGADLEKANGLQSRKTVEFSHAEIHPSLILGL 307

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A ++      +      +       +          +   S Q+    Q  LVK     
Sbjct: 308 SASVIPFPHRNQSSRNLFQAHKHSKQAIGVYVTNLACRADTSGQHLFYPQVQLVKTN--- 364

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          ++  G+N +VA   + GYN EDS+++ +  +   +F + H   F+
Sbjct: 365 -------IVNCLQKDEIFSGQNAIVAIACYTGYNQEDSIIMDQSALDRGMFRTQHYRTFK 417

Query: 849 VMARDTKLGPEEITRDIPNVSEEGLK---NIDECGIICVGAEVNPGDILVGKITPKGESP 905
              R       + +    +     ++    +++ G+  +G  +   D++VGKI    +  
Sbjct: 418 SEERSDHETFGKPSAADDSGGPRAMRSDQILEDDGLPYIGCNLGMNDVIVGKIVTHSQ-- 475

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
                   +      +  + DTS R+ +   G V              E+ I V+ E+ +
Sbjct: 476 --------KNTQSADSARLVDTSTRLKAHEKGRV--------------EQVILVQDEEGK 513

Query: 966 LLARDKDDEQVI 977
            +A+ K  E  I
Sbjct: 514 KIAKVKLRETRI 525


>gi|269308426|gb|ACZ34209.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5603]
 gi|269308428|gb|ACZ34210.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5529]
 gi|269308434|gb|ACZ34213.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5508]
 gi|269308482|gb|ACZ34237.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5858]
          Length = 339

 Score =  292 bits (747), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 186/347 (53%), Positives = 251/347 (72%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +AR+N YGFIETPYRKV  G+V   +  YL+A +E++  +AQAN  + EDG   +E V  
Sbjct: 1   YARINEYGFIETPYRKVQKGRVLLGEYEYLTADKEKDFVVAQANIQISEDGVILDEQVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++++     ID++D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDMMATPTDIDYVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV  VD+  I I   E        G+  Y L  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVATADGIVRYVDSKLISIEQSE--------GIKNYVLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VK+GD+++  DI+ADGPS + G+LALG+N++VAF  W+GYN+ED++
Sbjct: 173 TRSNNGTAITHIPIVKLGDKIKARDILADGPSMEKGELALGQNVVVAFTTWNGYNYEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D FTSIHI+E+ +  R TK GPEEITR+IPN+SE   K++DE GI+ +GAE
Sbjct: 233 IVSERIVIDDRFTSIHIDEYTIERRQTKQGPEEITREIPNISEVSKKHLDEEGIVAIGAE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|269912618|emb|CAY86089.1| RNA polymerase beta subunit [Gluconacetobacter xylinus]
          Length = 290

 Score =  292 bits (747), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 135/293 (46%), Positives = 182/293 (62%), Gaps = 28/293 (9%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY K+ +++   
Sbjct: 61  KRKLPVTTLLYALEGAASEAARAAKAAEGGDVESMEIQGMDPDEILSYFYGKVEFTKTEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W     A D   G K+   L+D  TGE+V  +  KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDA-DAFRGQKLLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A DIVN  TGEI+ EAGD + E+ LEE+    +  +  L VD+ N   +IRNTL 
Sbjct: 179 IGRFIASDIVNEHTGEIHAEAGDELTEQKLEELEGEGLTTLTTLAVDAAN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
            DKN  R++AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKM
Sbjct: 238 VDKNASREEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKM 290


>gi|148879051|emb|CAM07041.1| RpoB protein [Mycobacterium llatzerense]
          Length = 229

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 98/232 (42%), Positives = 130/232 (56%), Gaps = 40/232 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 30   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 89

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 90   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 134

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 135  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 177

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++T
Sbjct: 178  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMIT 229


>gi|115383181|gb|ABI96811.1| RNA polymerase beta subunit [Mycobacterium fortuitum]
 gi|148879073|emb|CAM07052.1| RpoB protein [Mycobacterium sp. MHSD4]
          Length = 230

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 144  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 182  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 230


>gi|261199570|ref|XP_002626186.1| DNA-directed RNA polymerase I polypeptide 2 [Ajellomyces dermatitidis
            SLH14081]
 gi|239594394|gb|EEQ76975.1| DNA-directed RNA polymerase I polypeptide 2 [Ajellomyces dermatitidis
            SLH14081]
 gi|239615559|gb|EEQ92546.1| DNA-directed RNA polymerase I polypeptide 2 [Ajellomyces dermatitidis
            ER-3]
 gi|327354710|gb|EGE83567.1| DNA-directed RNA polymerase [Ajellomyces dermatitidis ATCC 18188]
          Length = 1243

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 96/459 (20%), Positives = 158/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G      E     +   L+             S  + +  +
Sbjct: 716  DFNQSPRNMYQCQMSKQAMGTPGSSMEYRTDNKLYRLQTGQSPVVRSPLYNSYGLDNFPN 775

Query: 937  GTVVDVRIFNRHGIDKNERSI-------------SVEREQIELLARDKDDEQVILDRNIY 983
            G    V + +  G D ++  I             ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLD-DKESRGRGKARREV 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            S+L     G            +         ++E      W     D      V   +  
Sbjct: 835  SKLFGFAPGGLVKGEWRDALDEDGLPHIGARVTEGSLVAAWHTVRFDPVSNSYVNIDRQT 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +  +  G +      + + V   + R    GDK + RHG KG+ S
Sbjct: 895  HFLKYKDTEEGYVDSVRIL--GSETGGDPCQALSVKFRIPRKPLIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   DI++NP   PSRM +G   E+  G A    G    +    +  
Sbjct: 953  QLWPAIDMPFSETGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALHGLAQDATPFRFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                             F G        
Sbjct: 1013 ENTAGD-------------------------------------------FFG-------E 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDSLLAHGAAFLLQDRLMNCSD 1121



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 84/667 (12%), Positives = 173/667 (25%), Gaps = 99/667 (14%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGRLRARLEYKVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGK 177
                                G F++ G ++++   +   R+ P     +   +   +  
Sbjct: 171 HLEKASPEQLVQRKEESEELGGYFIVNGNEKLIRMLIVGRRNFPMAIVRNSFTKRGPTYT 230

Query: 178 LLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-E 227
             Y  +I   +         +    D    +  R   R+    VPV   L AL   ++ +
Sbjct: 231 K-YGIQIRSVRPDQTSQTNVLHYLSDGN--VTFRFSWRKNEFLVPVAMILKALVETNDRD 287

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I      +       + +        L+   K        DT   + E  + +       
Sbjct: 288 IFERLVGREGSKGIQNSFVTD-RVELLLRTYKGYGLHGRDDTRAYLGEKFRPVLGMPADM 346

Query: 288 LKEK----GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID-------EKSLEEI 336
             E      ++ + +    L    V E   N +   I      +           + + I
Sbjct: 347 PDEAVGTEFLRKVVLPH--LGNQNVTESQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAI 404

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            + E+     LY   +               +D             P     F       
Sbjct: 405 SNQEVLLGGFLYGMLLKERLEEWLRSFGPVARDW-AFRNQNAPFSDPRFEKEFLSRIVTR 463

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                        + G +     L+L  P     I      A         +    I   
Sbjct: 464 TNENIGGALEYFLSTGNLVSPTGLDLQQPSGYTVI------AEKINFYRFISHFRMIHRG 517

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                 +  +V ++L   +                      ++       +   S +   
Sbjct: 518 SFFAQLKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHLAHKCEIATSNLD-- 568

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
              S + Q+  ++   S  +     S + Q            +    +   R       E
Sbjct: 569 --VSGVPQVISNLGVTSESSVALDESVVVQLDGRILGYCSPKQARMISDTLRY---WKVE 623

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           GH    V     +   +  G     Y      ++   V YL   + +  Y+        E
Sbjct: 624 GHRSLPVELEIGYVPNSNRGQYPGIYLFSQCARMLRPVKYLPLDKLD--YVGPLEQPYME 681

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                 ++                   ++  P  ++SI A++ PF + + S R +  C M
Sbjct: 682 IACLPSDITSG------------VSTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQM 729

Query: 697 QRQAVPL 703
            +QA+  
Sbjct: 730 SKQAMGT 736



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 67/436 (15%), Positives = 131/436 (30%), Gaps = 51/436 (11%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 492 PSGYTVIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 548

Query: 579 NIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GL++ L     +  +   +    + + +  VT++    S++  +   + Q +  +   
Sbjct: 549 PCGLLNHLAHKCEIATSNLDVSGVPQVISNLGVTSE----SSVALDESVVVQLDGRILGY 604

Query: 638 --------------GSFTEELVFCRCAGEEILVPREKIDFID---ASPKQVVSIAASLIP 680
                             E         E   VP              +    +      
Sbjct: 605 CSPKQARMISDTLRYWKVEGHRSLPVELEIGYVPNSNRGQYPGIYLFSQCARMLRPVKYL 664

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            L+  D    L    M+   +P        V T +E                    Q   
Sbjct: 665 PLDKLDYVGPLEQPYMEIACLPSDITSG--VSTHVEFDPTHILSIVANMTPFSDFNQSPR 722

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +  +  +    S ++     K  R        Q P+V+               S 
Sbjct: 723 NMYQCQMSKQAMGTPGSSMEYRTDNKLYRLQTG----QSPVVRS----------PLYNSY 768

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL-GPE 859
            L +   G N +VA + + GY+ +D+M+I++             +       D +  G  
Sbjct: 769 GLDNFPNGMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLDDKESRGRG 828

Query: 860 EITRDIPN---------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +  R++           V  E    +DE G+  +GA V  G ++    T + +       
Sbjct: 829 KARREVSKLFGFAPGGLVKGEWRDALDEDGLPHIGARVTEGSLVAAWHTVRFDPVSNSYV 888

Query: 911 KLLRAIFGEKAVDVRD 926
            + R     K  D  +
Sbjct: 889 NIDRQTHFLKYKDTEE 904


>gi|189187656|gb|ACD84646.1| RpoB [Mycobacterium setense]
          Length = 231

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 132/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 145  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 182

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS
Sbjct: 183  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYS 231


>gi|148879041|emb|CAM07036.1| RpoB protein [Mycobacterium sp. MG6]
          Length = 230

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 98/231 (42%), Positives = 131/231 (56%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 137  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 180  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 230


>gi|289598458|gb|ADD12741.1| RNA polymerase subunit B [Mycobacterium sp. Bejaia]
          Length = 684

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 97/233 (41%), Positives = 133/233 (57%), Gaps = 37/233 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 481  RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 540

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +       +  
Sbjct: 541  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDVAAGVPDWAEKLPEELYSAD-- 597

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--MAD------ 1227
                                           +TPVFDGA E  +  +L   +A+      
Sbjct: 598  --------------------------PDTRTATPVFDGAQENELQGLLSSTLANRDGEIM 631

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            ++  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++TQ
Sbjct: 632  VNGDGKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQ 684



 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 108/181 (59%), Positives = 148/181 (81%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL+ +ARVN +GFIETPYRKV DG V++D+ YL+A EE+   +AQANS L++
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETPYRKVNDGVVSDDIEYLTADEEDRHVVAQANSPLED 180

Query: 637 D 637
           D
Sbjct: 181 D 181


>gi|315435634|gb|ADU18207.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 237

 Score =  291 bits (746), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 151  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 42.8 bits (99), Expect = 0.40,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|4456847|emb|CAB36987.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 400

 Score =  291 bits (746), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 181/340 (53%), Positives = 242/340 (71%), Gaps = 2/340 (0%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ 
Sbjct: 58  VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQV 117

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N LS +
Sbjct: 118 RLGLSRMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSEL 177

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           +H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N Y
Sbjct: 178 SHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKY 237

Query: 596 GFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GF++TPYRKV      VTN++V+L+A EE+   +AQANS L+ DG+F E++V  R  G  
Sbjct: 238 GFVQTPYRKVDRATGEVTNEIVWLTADEEDEYTVAQANSKLNADGTFAEKVVMGRHQGVN 297

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
              P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +APFVGT
Sbjct: 298 QEYPASSVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPFVGT 357

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           GME   A  SGAA++A+  G V   DA ++ +R  +G LD
Sbjct: 358 GMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD 397


>gi|296223273|ref|XP_002807565.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase I subunit
            RPA2-like [Callithrix jacchus]
          Length = 1165

 Score =  291 bits (745), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 112/559 (20%), Positives = 183/559 (32%), Gaps = 93/559 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 668  EQIFMNVAIYEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 726

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 727  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 786

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 787  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 836

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 837  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 894

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM
Sbjct: 895  KCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPVEDMPFTESGMVPDILFNPHGFPSRM 954

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G +    G    +    +                                
Sbjct: 955  TIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY----------------------- 991

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                          ML+ A  +  G   LY G++G   +  + +
Sbjct: 992  ---------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFI 1024

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L
Sbjct: 1025 GVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLL 1084

Query: 1312 QEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETGTPE 1345
             + L   SD     V    G                 R R Y   +    +       P 
Sbjct: 1085 HDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCHRSDTIDTVSVPY 1144

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
             F   V E+ A+ + + L+
Sbjct: 1145 VFRYFVAELAAMNIKVKLD 1163



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 98/664 (14%), Positives = 223/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    ++++ RN++        ++      +V+           
Sbjct: 283 LKALVSFSDYQIFQELIKGKEDDSFFRNSVSQMLRIVMEEGCSTQKQVLN--------YL 334

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 335 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 392

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRL---GLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            D+ D+L N+ V + G++     +    G L   + + ++ +     S+   +L+    +
Sbjct: 393 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIVFDKKAQKTNLSMNTDNLMKIFTM 452

Query: 510 VSAVCEFFCS------------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              + + F                    S L  + + +N +  ++H R    + +G    
Sbjct: 453 GLDLTKPFEYLLATGNLRSKTGLGLLQASGLCVVADKLNFIRYLSHFR---CVHRGSDFA 509

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V       T     +C+  V
Sbjct: 510 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTTSIPALLCNLGV 569

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-----EELVFCRCAGEEILVPREKIDFID 665
           T           E   +      +            + L   +   E+ + P  ++  I 
Sbjct: 570 TPVDGAPHQPYSECYPVLLDGVMVGWVDKELALGIADSLRHFKVLREKRIPPWMEVVLIP 629

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            LI  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 630 MTGKPSLYPGLFLFTTPCRLIRPVQNLELGKEELIGTMEQIFMNVAIYEDEVFAGVTTHQ 689

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 690 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 745

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 746 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 795

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 796 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 855

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 856 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 910

Query: 953 NERS 956
           ++ +
Sbjct: 911 DKFA 914



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/138 (19%), Positives = 45/138 (32%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 82  EGLGLAVQAIPPFEFAFKDQRISFTILDAVISPPTVPKGTICKEASVYPAECRGRRSTYR 141

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L + +   V  +         K I +QS  +G +P+M K                   
Sbjct: 142 GKLTVDVNWAVNGI--------SKGIIKQS--LGYVPIMVKSKLCNLHNLPPQALIQHHE 191

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 192 EAEEMGGYFIINGIEKVI 209


>gi|148879033|emb|CAM07032.1| RpoB protein [Mycobacterium sp. MG2]
          Length = 229

 Score =  291 bits (745), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 98/231 (42%), Positives = 131/231 (56%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 229


>gi|269912648|emb|CAY86104.1| RNA polymerase beta subunit [Gluconobacter thailandicus]
 gi|269912650|emb|CAY86105.1| RNA polymerase beta subunit [Gluconobacter thailandicus]
 gi|269912652|emb|CAY86106.1| RNA polymerase beta subunit [Gluconobacter thailandicus]
 gi|269912654|emb|CAY86107.1| RNA polymerase beta subunit [Gluconobacter thailandicus]
          Length = 287

 Score =  291 bits (745), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 132/290 (45%), Positives = 181/290 (62%), Gaps = 28/290 (9%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GMD +EILS FY  + +++ GD
Sbjct: 61  KRKLPVTTLLYALEGANYIAQRDQKIAEGGDVEGLDIRGMDQDEILSYFYDMVPFARMGD 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P        G K+ S LVD DTGE V E+  KLT+ +++ + EK  + + +    +
Sbjct: 121 GWARPFEPE-AFRGQKLLSPLVDADTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDV 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G Y+A D+VN  TGEIY EAG+ + E  L  +    I ++P L VD  ++  +IRNTL 
Sbjct: 179 LGRYIAHDLVNEHTGEIYGEAGEELTEDRLVALEELGITELPTLSVDG-SHGPWIRNTLT 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
            DKN  R +AL+DIYR+MRPG+  T   AE+MF  LFFD D+YDLS+VGR
Sbjct: 238 VDKNNSRDEALIDIYRIMRPGEPPTKETAEAMFRGLFFDQDRYDLSSVGR 287


>gi|319919237|gb|ADV78236.1| RNA polymerase subunit B [Mycobacterium sp. NLA000302110]
          Length = 245

 Score =  291 bits (745), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 96/230 (41%), Positives = 130/230 (56%), Gaps = 35/230 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 43   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G +I +  +                  
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWEIPADASGAYPEWAA---------- 151

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                            ++            V+TPVFDGA E  +  +L     +      
Sbjct: 152  ----------------NLPEGMHSAPRDSIVATPVFDGARENELQGLLGSTLPNRDGDVM 195

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 196  VDADGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 245



 Score = 47.0 bits (110), Expect = 0.023,   Method: Composition-based stats.
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 51


>gi|13492590|gb|AAK28286.1| DNA-directed RNA polymerase III [Leishmania major]
          Length = 606

 Score =  291 bits (745), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 86/307 (28%), Positives = 128/307 (41%), Gaps = 68/307 (22%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + +KV     RP + GDK + RHG KG+V  I+   DMPF + G   D++       
Sbjct: 350  DVDQKIKVVTREVRPPEPGDKFSSRHGQKGVVGLIVNGVDMPFNERGMCPDMI------- 402

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                             +     K+ + 
Sbjct: 403  --MN----------------------------------------PHGFPSRMTVGKLLEL 420

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                   +      G       F G   ++I+  L     +  G+ + Y G+TGE     
Sbjct: 421  VCSKAAALRGSMGDGT-----AFGGESADSISQQLLSFGYNYHGKDVFYSGITGELMQGY 475

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++ARSTG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 476  VFFGPIYYQRLKHMVTDKMHARSTGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 535

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYES-----IVAGNDTFETGTPESFNVLVKEMQA 1356
             +L E L I SD        V G    Y +        G  T +   P +F +L++E+Q 
Sbjct: 536  NLLNERLLISSDMFTADICHVCG-NLGYNNRCTYCKTKGT-TSKVNMPYAFKLLIQELQG 593

Query: 1357 LGLSIDL 1363
            +G+S+ L
Sbjct: 594  MGVSLRL 600



 Score = 75.9 bits (185), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 50/350 (14%), Positives = 103/350 (29%), Gaps = 26/350 (7%)

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            ++  ++  +  +      N +L     +   L                +       ++ 
Sbjct: 7   EEIDTVTPTDFLHYCTVFLNGTLIGIHRYPNRLCAGIRTLRRSGRLHPHVSISTQPRQRT 66

Query: 672 VSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           V I +     +   +   D    +   ++ R    L            E V    S   +
Sbjct: 67  VQIGSDGGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTHNDFLAEGLTEYVDVNESNDCL 126

Query: 728 VA-KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR-PLVKVG 785
           +A   A I        + +  +      +      +     + + Q+    Q    V + 
Sbjct: 127 IAVYPADIGPYTT--HLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGTVALN 184

Query: 786 DEVRRNDIIADGPS-------------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             +R + ++  G               T    L  G N +V  M + GY+ ED+ + ++ 
Sbjct: 185 QYIRADTVLLLGAYPQRPLCRTKAMSLTHYEKLGAGINAMVCVMSYSGYDIEDAQVYNKS 244

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +       + + + EV       G  ++      N      K ++  G+   GA V   
Sbjct: 245 SLDRGYGRCVVLRKHEVDLEKYAGGEFDVILPPEKNSGTGKFKALNPDGVAGKGALVQQY 304

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           D+LV K TP       P   + +         V D  +  P G     +D
Sbjct: 305 DVLVNKFTPVAGGDPRPAPLVYKYPQ----PAVVDHVIISPPGDYDRSLD 350


>gi|47219788|emb|CAG03415.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1171

 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 99/508 (19%), Positives = 171/508 (33%), Gaps = 94/508 (18%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 738  YLLAYPQRPMVKTKTIEIIEFEKLPAGQNATVAVMSYSGYDIEDALILNKASLDRGFGRC 797

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++         R  +   +++     D    + I   NI         G+   +     
Sbjct: 798  LVYKNTKCTL-RRYTNQTFDKVMGPMLDAATRKPIWRHNILDADGICSPGERVENKQVLV 856

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                    V    ++ + ++ + QY       +    + IEK+  
Sbjct: 857  NKSMP-----------------TVTQTPLEGSTQTGQPQYRDVPICYKGSTDSYIEKVMI 899

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI+ 
Sbjct: 900  SSNAEDAF--LIKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDTGICPDII- 956

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                              G  +
Sbjct: 957  --------MN--------------------------------------------PHGYPS 964

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                    + +   A          T  F G+  + +   L     +  G+  +  G+TG
Sbjct: 965  RMTVGKLIELLAGKAGVLDGRFHYGT-AFGGSKVKDVCEDLIRHGYNYQGKDYVTSGITG 1023

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 1024 EPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCL 1083

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTRVYESI---VAGND-------------TFETG 1342
              YGA+ +L E L I SD    DV G+  +       V  +                   
Sbjct: 1084 IGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWQVKLSHLDLECHYCKSSCQVSSLR 1143

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKN 1370
             P +  +L +E+Q++ +   L+ SR   
Sbjct: 1144 IPYACKLLFQELQSMNIIPRLKLSRYNE 1171



 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 133/980 (13%), Positives = 273/980 (27%), Gaps = 207/980 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEG----------LQAAFKSVFPI--TAFSGAAML-- 74
           L++    S+++F+ + I    + NE           L++  +    I     +    L  
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANEKITSDADPMWYLKSVTRLFKYILYELQNSHYHLSK 98

Query: 75  ------EFVSYEFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
                  +++     P               +C  RD+TY+ P+ + +            
Sbjct: 99  FLCLFYRYLNIYVGMPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYT--------- 149

Query: 119 AKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVV 154
            +  + I   ++ +G +P+M                           G F++KG +++++
Sbjct: 150 -RGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFAKLNECPLDPGGYFIVKGQEKVIL 208

Query: 155 SQLHRSPG-IHFDHDK----GRASLSGKLLYACR--IIPDQGLWMDIEFDSKDIIHVRID 207
            Q   S   I  D D+    G +  S       R  +I  QG             ++R +
Sbjct: 209 IQEQLSKNRIIVDQDRKGAVGASVTSSTHEKKSRTNMIVKQG-----------RFYLRHN 257

Query: 208 R-RRKVPVTSFLMALGMDSE-EILSTFYPKIV--------YSQRGDFWCFPLSAADLMVG 257
                 P+      +G++S+ EI+     +            +      F  + A   +G
Sbjct: 258 TLSEDAPIAIIFKGMGVESDQEIVQMIGTEENVMASFAPSLEECQKAQIFTQTQALRYLG 317

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            KV    +     +  +E  ++L + L+  L    VK     + C+  L V    V    
Sbjct: 318 NKVRRQRMWGGPKKTKMEEARELLASLI--LTHVPVKEFNFRAKCIY-LAVMVRRVILAQ 374

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G+  ++  D    K LE            L+    +    I + ++  +      A  D+
Sbjct: 375 GDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQR----AAQFDV 430

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + MR   ++   V     +   +   ++ +   G  ++  RL+  +   +         
Sbjct: 431 VKHMRQDQITNGMVNA--ISTGNWSLKRFKMDRQGVTQVLSRLSFISALGMMTRISSQFE 488

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
              K+                     +    +  + +    +  +           D   
Sbjct: 489 KTRKVSGPRSLQ---------PSQWGMLCPSDTPEGEACGLVKNLALMTHITTDMEDGPI 539

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +     +  + V     E      +  +  + N L  I   ++L    +  + RA    E
Sbjct: 540 IKLAFNLGVEDVNLLCGEELSYPSVFLVFLNGNILGVIRDHQKLVGTFRL-MRRAGFINE 598

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDV 614
              +      R     +  G        +       +      +   YR   D      V
Sbjct: 599 FVSISTNLTDRCVYISSDGGRLCRPYIIVKKGQPMVKNKHMEDLSQGYRNFEDFLHDGLV 658

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   EE +  IA                           +  +    ++  P  ++ +
Sbjct: 659 EYLDVNEENDCQIAL-----------------------YEHMIHKDTTHLEIEPFTLLGV 695

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A LIP+  ++ S R    C M +QA+  +         G        +   ++A     
Sbjct: 696 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLMYLLA----- 741

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                      QRP+VK           
Sbjct: 742 -----------------------------------------YPQRPMVK----------T 750

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                 +   L  G+N  VA M + GY+ ED++++++  +       +  +  +   R  
Sbjct: 751 KTIEIIEFEKLPAGQNATVAVMSYSGYDIEDALILNKASLDRGFGRCLVYKNTKCTLRRY 810

Query: 855 KLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                +                    +D  GI   G  V    +LV K  P         
Sbjct: 811 TNQTFDKVMGPMLDAATRKPIWRHNILDADGICSPGERVENKQVLVNKSMPTVTQTPLEG 870

Query: 910 EKLLRAIFGEKAVDVRDTSL 929
                             S 
Sbjct: 871 STQTGQPQYRDVPICYKGST 890


>gi|315435628|gb|ADU18204.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-10014]
          Length = 239

 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 129/229 (56%), Gaps = 38/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I        A      + S     
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAATPEWAAKLPEQMLSAPPDS 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
            I                             V+TPVFDGA E  +  +L     +      
Sbjct: 160  I-----------------------------VATPVFDGAQEGELQGLLGATLPNRDGETM 190

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 191  VNADGKAVLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 239



 Score = 45.8 bits (107), Expect = 0.052,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|269308432|gb|ACZ34212.1| RNA polymerase beta subunit [Spiroplasma sp. GSU5490]
          Length = 339

 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 187/347 (53%), Positives = 254/347 (73%), Gaps = 9/347 (2%)

Query: 589 FARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +A++N YGFIETPYRKV +GKV  ++ VYL+A +E++  +AQAN    EDG+  +E V  
Sbjct: 1   YAKINQYGFIETPYRKVSNGKVLKDNHVYLTADKEKDFIVAQANIKTSEDGTILDESVIA 60

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R  G++I+     +DF+D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQAVPL+  E
Sbjct: 61  RYRGDDIVAEPMDVDFVDVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAVPLINPE 120

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           +P VGTG+E   A+ SG A+VA   GIV+ VD+  I +           +G+  Y L  F
Sbjct: 121 SPIVGTGVEFEAARDSGDAVVATEDGIVKYVDSKLITV--------EGKNGIKSYVLNDF 172

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSN  T +   P+VKVGD+++ NDI+ADGPS + G+LALG+N++VAF  W+GYNFED++
Sbjct: 173 SRSNNGTAITHLPIVKVGDKIKSNDILADGPSMEKGELALGQNVVVAFTTWNGYNFEDAV 232

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           ++SER+V +D F+SIHI+E+ +  R TK GPEEITRDIPN+SE   K++D  GI+ +G E
Sbjct: 233 IVSERIVIDDRFSSIHIDEYTLERRQTKQGPEEITRDIPNISESNKKHLDSDGIVAIGTE 292

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
           V  GDILVGK+TPK ++ ++PE+KLL AIFGEK+ +V+D SLRVP+G
Sbjct: 293 VKVGDILVGKVTPKSQTQLSPEDKLLHAIFGEKSRNVKDNSLRVPNG 339


>gi|52694253|emb|CAG30656.1| DNA-directed RNA polymerase beta chain [Pseudomonas syringae]
          Length = 329

 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 187/332 (56%), Positives = 246/332 (74%), Gaps = 8/332 (2%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RA
Sbjct: 1   SEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERA 60

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 61  GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASPKQVVS 673
           V+LSA+EE +  IAQA++++++     +ELV  R         R+  +  +D SPKQVVS
Sbjct: 121 VFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLKRNSPSRRQADVTLMDVSPKQVVS 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES----VVAKSSGAAIVA 729
           +AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P    G        VA+ SG  +VA
Sbjct: 181 VAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPA---GRYWPWSANVARDSGVCVVA 237

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           +R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+
Sbjct: 238 RRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQ 297

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           R+DI+ADGPST++G+LALG+NM +AFM W+G+
Sbjct: 298 RSDIMADGPSTNMGELALGQNMRIAFMAWNGF 329


>gi|52538199|emb|CAH19201.1| RNA polymerase beta-subunit [Pseudomonas frederiksbergensis]
          Length = 360

 Score =  291 bits (745), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 173/313 (55%), Positives = 223/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHY R CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYTRGCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRGSA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRHG 313


>gi|321259894|ref|XP_003194667.1| DNA-directed RNA polymerase I polypeptide 2 [Cryptococcus gattii
            WM276]
 gi|317461139|gb|ADV22880.1| DNA-directed RNA polymerase I polypeptide 2, putative [Cryptococcus
            gattii WM276]
          Length = 1192

 Score =  291 bits (744), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 114/271 (42%), Gaps = 52/271 (19%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +++  +  G D     L+ + + + + R    GDK + RHG KG+ S+  P  DM
Sbjct: 883  ETAFIDEVRVL--GSDAGDAELQKIHIKLRIPRSPVIGDKFSSRHGQKGVCSQKFPAIDM 940

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   D+++NP   PSRM +G   E+  G A    G    +    +          
Sbjct: 941  PFSESGMQPDVIINPHAFPSRMTIGMFVESMAGKAGALHGVAQDATPFKFSDKDR----- 995

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                   PV      +     LR A  +
Sbjct: 996  ---------------------------------------PV------DYFGEQLRAAGYN 1010

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   +Y G+TGE F   + +G +Y  +L HMV+DK   R+TG    +T+QP+ G+   
Sbjct: 1011 YYGNEPMYSGITGEEFHADIYLGLVYYQRLRHMVNDKFQVRTTGPVDPLTRQPVKGRKRA 1070

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + A+G +++LQ+ L   SD
Sbjct: 1071 GGIRFGEMERDALIAHGTSFLLQDRLMNCSD 1101



 Score = 90.9 bits (224), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 111/783 (14%), Positives = 211/783 (26%), Gaps = 143/783 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAA-FKSVFPITAFSGA-------AMLEFVSYE 80
           L+    +S++  +  +  P     +GL     + +     F G          L   SY 
Sbjct: 49  LVAPHISSFNALIEDDGNPGA---KGLLQMGVEDIGEKVVFDGKGSEGGLGTKL---SYR 102

Query: 81  FDP--------PKFD---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            D         P+ D           +   R  TY   L + ++  V   DE    K  +
Sbjct: 103 IDRVALSKPLVPEKDKLAVERRVFPTEARERLATYRSKLTVNIKWTV--TDEDGNRKEFE 160

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV----VS 155
           +IKE     G LP+M +                         G F++ G ++I+    V 
Sbjct: 161 EIKEC----GLLPVMVRSIRCNLQGLPATELIKHSEESTSFGGYFIVNGNEKIIRYLVVP 216

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ----------------GLWMDIEFDSK 199
           + H +P   +     +   S    Y C+I   +                G  +   +   
Sbjct: 217 RRH-NPINLYRPSFAKRGASYTP-YGCQIRCVRPDETACTNTIHYLSNGGATLRFAW--- 271

Query: 200 DIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
                     RK    +P+   L AL     +EI        +     D          L
Sbjct: 272 ----------RKVEYMIPLMLILKALVDASDKEIFE-----GLIQGEYDNTFLTDRVELL 316

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
           + G K           + + E  + +   +        V    +    L  L    D   
Sbjct: 317 LRGQKSWGLHTGAQCLDYLGEKFRVVL-NVPDDWSNVQVGGYLLRKVVLVHLPAPRDKFR 375

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +      +  + S      +         +        I      D     K  +
Sbjct: 376 M----LLFMLRKLYSQVSGATCPDNPDSPQHHEVLLPGFLYGMIIKERFDDCLNAVKSQI 431

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
               R  +           S+ +   +D        +    +     LD           
Sbjct: 432 QLDLRDGKARSFMDPKYFTSVLSKTNWDIGSKLSYFLATGNLVSPTGLDLQQTSGFTIVA 491

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           + +   + L   R     I         +  +V +++   +                   
Sbjct: 492 EKLNFYRYLSHFR----CIHRGAFFAELKTTTVRKLMPESWGFLC-------PVHTPDGS 540

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
              ++       + V S++      + LS         S I   R +     G V    +
Sbjct: 541 PCGLLNHLSHTCQIVTSSLDVSHIPALLSAQGMTQVFASSIDGRRMVCIQLDGKVIGYAS 600

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            ++ + +      R+   +T     + L   +  +  V   G     Y      ++   V
Sbjct: 601 PMKAKQLAN----RLRKLKTEADPKVPLDLEIG-YVPVTKGGQYPGLYLFSSRSRMMRPV 655

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL             N  LD  GSF  E V+   A  +  + +     ++  P  ++S+
Sbjct: 656 TYL------------ENGKLDHLGSF--EQVYMDVAITKEEIEKGVSSHLELDPTSMLSV 701

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A+L PF + + S R +  C M +Q++                +    SG   V +    
Sbjct: 702 IANLTPFSDFNQSPRNMYQCQMGKQSMGT--PSTAISKRTDNKMYRLQSGQTPVVRPDLH 759

Query: 735 VEQ 737
              
Sbjct: 760 NHY 762



 Score = 70.5 bits (171), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 81/578 (14%), Positives = 176/578 (30%), Gaps = 84/578 (14%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM-------------------LK 472
           +   ++ +++ L    +G    D+ D+  +  V   G +                   ++
Sbjct: 373 KFRMLLFMLRKLYSQVSGATCPDNPDSPQHHEVLLPGFLYGMIIKERFDDCLNAVKSQIQ 432

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-----SSQLSQLEE 527
              R G  R     K   S +   +      ++       +          +S  + + E
Sbjct: 433 LDLRDGKARSFMDPKYFTSVLSKTNWDIGSKLSYFLATGNLVSPTGLDLQQTSGFTIVAE 492

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N    ++H R    + +G          +R + P  +G +CP  T +G   GL++ L+
Sbjct: 493 KLNFYRYLSHFR---CIHRGAFFAELKTTTVRKLMPESWGFLCPVHTPDGSPCGLLNHLS 549

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE-ELVF 646
              ++       +    +   +    V + S+++       Q +  +    S  + + + 
Sbjct: 550 HTCQIVTSSLDVSHIPALLSAQGMTQV-FASSIDGRRMVCIQLDGKVIGYASPMKAKQLA 608

Query: 647 CRCAGEEILVPREK----------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            R    +     +           +      P   +  + S +        N  L     
Sbjct: 609 NRLRKLKTEADPKVPLDLEIGYVPVTKGGQYPGLYLFSSRSRMMRPVTYLENGKLDHLGS 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKS--SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             Q    +      +  G+ S +     S  +++A      +   + R + +   G    
Sbjct: 669 FEQVYMDVAITKEEIEKGVSSHLELDPTSMLSVIANLTPFSDFNQSPRNMYQCQMGKQSM 728

Query: 755 STSGVDI--YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            T    I      K  R        Q P+V+                    +   G N +
Sbjct: 729 GTPSTAISKRTDNKMYRLQSG----QTPVVRPDLHNHYG----------FDNFPNGTNAI 774

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNVSE 870
           VA + + GY+ ED+M++++               ++    D K   G     +   +   
Sbjct: 775 VAVISYTGYDMEDAMILNKSAHERGFGYGTV---YKADIFDLKGVPGASRSAKPTLHFGL 831

Query: 871 EGLKNID--------ECGIICVGAEVNPGDILVGKITPK-----------GESPMTPEEK 911
                 D        + G+  +G +V  GD L   I               E+    E +
Sbjct: 832 GRDVKEDHDARNIISQDGLPIIGTKVKTGDPLCAYIDDTTGRTKFHKYKGDETAFIDEVR 891

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           +L +  G+  +      LR+P      V+  +  +RHG
Sbjct: 892 VLGSDAGDAELQKIHIKLRIP---RSPVIGDKFSSRHG 926


>gi|291386321|ref|XP_002709638.1| PREDICTED: RNA polymerase I polypeptide B isoform 2 [Oryctolagus
            cuniculus]
          Length = 1079

 Score =  291 bits (744), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 111/559 (19%), Positives = 183/559 (32%), Gaps = 93/559 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQLFLNVAIFEDEVLAGVT-THQELFPHSMLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+          +         P G +  V           D 
Sbjct: 641  GFPLLTYQDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVTSYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 701  MIVNKASWERGFAH-GSVYKTEFIDLSEKIKQGDDSLVFG---------VKPGDPRILQR 750

Query: 1013 ISEYPRSQWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 751  LDDDGLPFIGTKLQYGDPYYGYLNLNTGESFVVYYKSKENCIVDNIKVCS--NDTGSGKF 808

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + + + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM
Sbjct: 809  KCICITMRVPRNPTIGDKFASRHGQKGILSRLWPVEDMPFTESGMVPDILFNPHGFPSRM 868

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G +    G    +    +                                
Sbjct: 869  TIGMLIESMAGKSAALHGLCHDATPFTFSEQNSAL------------------------- 903

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                     +    ML+ A  +  G   LY G++G   +  + +
Sbjct: 904  -------------------------DHFGEMLKAAGYNFYGTERLYSGISGLELEADIFI 938

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L
Sbjct: 939  GVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLL 998

Query: 1312 QEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPE 1345
             + L   SD     V    G                 R R Y   +    +       P 
Sbjct: 999  HDRLFNCSDRSIAHVCVECGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPY 1058

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
             F   V E+ A+ + + L+
Sbjct: 1059 VFRYFVAELAAMNIKVKLD 1077



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 93/673 (13%), Positives = 206/673 (30%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEADSFFRNSVSQMLRIVAEEGCFTQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 249 GECFRVKLNLPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYLLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            ++ D+L N+ V + G++           +   +        ++ +       + +    
Sbjct: 307 EENPDSLVNQEVLTPGQLFLMFLKEKMEAWLTSIKIALDKKAQKTNISINTENLLKVFSM 366

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GADLTRPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAICEVVTQFVYTTSIPPLLCSLGV 483

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V    V     +E    IA +   L       E+ +   
Sbjct: 484 TPIDGAPHRPYSECYPVLLDGVMVGWV----DKELAPGIADS---LRLFKVLREKRIPP- 535

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  LVP      +        +    + P    +     L+G   Q      +  + 
Sbjct: 536 -WMEVALVPMTGKPSLYPGLYLFTTPCRLVRPVQNLELGKEELIGTMEQLFLNVAIFEDE 594

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
              G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 595 VLAGVTTHQELFPHSMLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 651

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA   + GY+ ED+
Sbjct: 652 DNKLYRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVTSYTGYDMEDA 700

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G + +   +       L+ +D+ G+  +G
Sbjct: 701 MIVNKASWERGFAHGSVYKTEFIDLSEKIKQGDDSLVFGVKPGDPRILQRLDDDGLPFIG 760

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            ++  GD   G +     +  T E  ++   +       +++  S    SG    +    
Sbjct: 761 TKLQYGDPYYGYL-----NLNTGESFVVYYKSKENCIVDNIKVCSNDTGSGKFKCICITM 815

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 816 RVPRNPTIGDKFA 828



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 26/59 (44%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
             + K + +Q  ++G +P+M K                         G F+I GI++++
Sbjct: 67  NGTSKGVIKQ--FLGHVPIMVKSKLCNLYNLSPQALIEHHEEAEEMGGYFIINGIEKVI 123


>gi|291386319|ref|XP_002709637.1| PREDICTED: RNA polymerase I polypeptide B isoform 1 [Oryctolagus
            cuniculus]
          Length = 1135

 Score =  291 bits (744), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 111/559 (19%), Positives = 183/559 (32%), Gaps = 93/559 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQLFLNVAIFEDEVLAGVT-THQELFPHSMLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+          +         P G +  V           D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVTSYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 757  MIVNKASWERGFAH-GSVYKTEFIDLSEKIKQGDDSLVFG---------VKPGDPRILQR 806

Query: 1013 ISEYPRSQWW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 807  LDDDGLPFIGTKLQYGDPYYGYLNLNTGESFVVYYKSKENCIVDNIKVCS--NDTGSGKF 864

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + + + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM
Sbjct: 865  KCICITMRVPRNPTIGDKFASRHGQKGILSRLWPVEDMPFTESGMVPDILFNPHGFPSRM 924

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G +    G    +    +                                
Sbjct: 925  TIGMLIESMAGKSAALHGLCHDATPFTFSEQNSAL------------------------- 959

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                     +    ML+ A  +  G   LY G++G   +  + +
Sbjct: 960  -------------------------DHFGEMLKAAGYNFYGTERLYSGISGLELEADIFI 994

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L
Sbjct: 995  GVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLL 1054

Query: 1312 QEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPE 1345
             + L   SD     V    G                 R R Y   +    +       P 
Sbjct: 1055 HDRLFNCSDRSIAHVCVECGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPY 1114

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
             F   V E+ A+ + + L+
Sbjct: 1115 VFRYFVAELAAMNIKVKLD 1133



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 93/673 (13%), Positives = 206/673 (30%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEADSFFRNSVSQMLRIVAEEGCFTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNLPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYLLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            ++ D+L N+ V + G++           +   +        ++ +       + +    
Sbjct: 363 EENPDSLVNQEVLTPGQLFLMFLKEKMEAWLTSIKIALDKKAQKTNISINTENLLKVFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GADLTRPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAICEVVTQFVYTTSIPPLLCSLGV 539

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V    V     +E    IA +   L       E+ +   
Sbjct: 540 TPIDGAPHRPYSECYPVLLDGVMVGWV----DKELAPGIADS---LRLFKVLREKRIPP- 591

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  LVP      +        +    + P    +     L+G   Q      +  + 
Sbjct: 592 -WMEVALVPMTGKPSLYPGLYLFTTPCRLVRPVQNLELGKEELIGTMEQLFLNVAIFEDE 650

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
              G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 651 VLAGVTTHQELFPHSMLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 707

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA   + GY+ ED+
Sbjct: 708 DNKLYRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVTSYTGYDMEDA 756

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G + +   +       L+ +D+ G+  +G
Sbjct: 757 MIVNKASWERGFAHGSVYKTEFIDLSEKIKQGDDSLVFGVKPGDPRILQRLDDDGLPFIG 816

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            ++  GD   G +     +  T E  ++   +       +++  S    SG    +    
Sbjct: 817 TKLQYGDPYYGYL-----NLNTGESFVVYYKSKENCIVDNIKVCSNDTGSGKFKCICITM 871

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 872 RVPRNPTIGDKFA 884



 Score = 62.4 bits (150), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 43/138 (31%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLGHAVQAIAPFEFAFKDERITLTIVDAVISPPTVPKGTICREFNVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V          + K + +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWAV--------NGTSKGVIKQ--FLGHVPIMVKSKLCNLYNLSPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179


>gi|88976158|gb|ABD59039.1| RNA polymerase II second largest subunit [Macrolepiota dolichaula]
          Length = 882

 Score =  291 bits (744), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 132/895 (14%), Positives = 263/895 (29%), Gaps = 147/895 (16%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 120  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 176

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 177  GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 236

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 237  ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 292

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 293  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 344

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 345  AHSTTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIY 401

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ RV     +      LL+ +              +        + G++E +DA    
Sbjct: 402  TDAGRVCRPLFIVENQQLLLQ-KKHIRWLNSSFDEEGNEYKWEQLIKGGVIELLDAEEEE 460

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +    +   +       +    ++ +     R  +K G            PS  LG 
Sbjct: 461  TVMISMTPEDLENSRLQAAGVDPHANDGDFDPAAR--LKAGTHAHTWTHCEIHPSMILG- 517

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                        ++       +G       
Sbjct: 518  ------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFL 553

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I               +  +             +       +   +  + AI      + 
Sbjct: 554  IRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 602

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +   
Sbjct: 603  EDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLE 661

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  +  D      R++          ++     +  Q   
Sbjct: 662  DDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI 721

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       + VKV V   R  Q GDK A RHG KG +    
Sbjct: 722  --------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITY 761

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +          
Sbjct: 762  RQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------ 815

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                ++     + LR       G+ V                  
Sbjct: 816  -------------------DLTVESVSTFLRQKGYQSRGLEVM----------------- 839

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                   G +       G      V +G  Y  +L HMV DK+++R+ G   ++T
Sbjct: 840  -----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILT 882



 Score =  141 bits (355), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 98/775 (12%), Positives = 217/775 (28%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+      LG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 50  YIKVD----IPIWVVFRGLGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 105

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + +              +      + 
Sbjct: 106 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 161

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 162 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLQKCV 211

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 212 ETH--KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 268

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 269 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAP 328

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 329 VIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVS 388

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                  +   ++        P    E  N  L+        +N+    E    K     
Sbjct: 389 VVRDIREKELRIYTDAGRVCRPLFIVE--NQQLLLQKKHIRWLNSSFDEEGNEYKWEQLI 446

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               +  L A EEE   I+     L+        +      G+                 
Sbjct: 447 KGGVIELLDAEEEETVMISMTPEDLENSRLQAAGVDPHANDGDFDPAARLKAGTHAHTWT 506

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 507 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI------------ 554

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 555 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 582

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 583 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 621

Query: 843 HIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E            +       +++ G+I  G  V   DI++GK
Sbjct: 622 YYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGK 681

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 682 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 729


>gi|58268448|ref|XP_571380.1| DNA-directed RNA polymerase i polypeptide 2 [Cryptococcus neoformans
            var. neoformans JEC21]
 gi|134112740|ref|XP_774913.1| hypothetical protein CNBF0780 [Cryptococcus neoformans var.
            neoformans B-3501A]
 gi|50257561|gb|EAL20266.1| hypothetical protein CNBF0780 [Cryptococcus neoformans var.
            neoformans B-3501A]
 gi|57227615|gb|AAW44073.1| DNA-directed RNA polymerase i polypeptide 2, putative [Cryptococcus
            neoformans var. neoformans JEC21]
          Length = 1193

 Score =  291 bits (744), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 114/271 (42%), Gaps = 52/271 (19%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +++  +  G D     L+ + + + + R    GDK + RHG KG+ S+  P  DM
Sbjct: 883  ETAFIDEVRVL--GSDAGDAELQKIHIKLRIPRSPVIGDKFSSRHGQKGVCSQKFPAIDM 940

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   D+++NP   PSRM +G   E+  G A    G    +    +          
Sbjct: 941  PFSESGMQPDVIINPHAFPSRMTIGMFVESMAGKAGALHGLAQDATPFKFSDKDR----- 995

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                   PV      +     LR A  +
Sbjct: 996  ---------------------------------------PV------DYFGEQLRAAGYN 1010

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   +Y G+TGE F   + +G +Y  +L HMV+DK   R+TG    +T+QP+ G+   
Sbjct: 1011 YYGNEPMYSGITGEEFHADIYLGLVYYQRLRHMVNDKFQVRTTGPVDPLTRQPVKGRKRA 1070

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + A+G +++LQ+ L   SD
Sbjct: 1071 GGIRFGEMERDALIAHGTSFLLQDRLMNCSD 1101



 Score = 90.9 bits (224), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 107/749 (14%), Positives = 204/749 (27%), Gaps = 141/749 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAA-FKSVFPITAFSGA-------AMLEFVSYE 80
           L+     S++  +     P     +GL     + +     F G          L   SY 
Sbjct: 49  LVAPHIKSFNALIEDEGNPGA---KGLLQMGVEDIGEKVVFDGKGSEGGLGTKL---SYR 102

Query: 81  FDP--------PKFD---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
            D         P+ D           +   R  TY   L + ++  V   DE    K  +
Sbjct: 103 IDRVALSKPLVPEKDKLAVERRVFPTEARERLATYRSKLTVNIKWTV--TDEDGNRKEFE 160

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV----VS 155
           +IKE     G LP+M +                         G F++ G ++I+    V 
Sbjct: 161 EIKEC----GLLPVMVRSIRCNLQGLPATELIKHSEESTSFGGYFIVNGNEKIIRYLVVP 216

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ----------------GLWMDIEFDSK 199
           + H +P   +     +   S    Y C+I   +                G  +   +   
Sbjct: 217 RRH-NPINLYRPSFAKRGASYTP-YGCQIRCVRPDETACTNTIHYLSNGGATLRFAW--- 271

Query: 200 DIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
                     RK    +P+   L AL     +EI        +     D          L
Sbjct: 272 ----------RKVEYMIPLMLILKALVDASDKEIFE-----GLIQGEYDNTFLTDRVELL 316

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
           + G K           + + E  + +   +        V    +    L  L    D   
Sbjct: 317 LRGQKSWGLHTGAQCLDYLGEKFRVVL-NVPDDWSNVQVGGYLLRKVVLVHLPAPRDKFR 375

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
                +      +  + S      +         +        I      D     K  +
Sbjct: 376 M----LLFMLRKLYSQVSGATCPDNPDSPQHHEVLLPGFLYGMIIKERFDDCLNAVKSQI 431

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
               R  +           S+ +   +D        +    +     LD           
Sbjct: 432 QLDLRDGKARSFMDPKYFTSVLSKTNWDIGSKLSYFLATGNLVSPTGLDLQQTSGFTIVA 491

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           + +   + L   R     I         +  +V +++   +                   
Sbjct: 492 EKLNFYRYLSHFR----CIHRGAFFAELKTTTVRKLMPESWGFLC-------PVHTPDGS 540

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
              ++       + V S++      + LS         S I   R +     G V    +
Sbjct: 541 PCGLLNHLSHTCQIVTSSLDVSHIPALLSAQGMTQVFASSIDGRRMVCIQLDGKVIGYAS 600

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
            ++ + +      R+   +T     + L   +  +  V   G     Y      ++   V
Sbjct: 601 PMKAKQLAN----RLRKLKTEADSKVPLDLEIG-YVPVTKGGQYPGLYLFASRSRMMRPV 655

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL             N  LD  GSF  E V+   A  +  + +     ++  P  ++S+
Sbjct: 656 TYL------------ENGKLDHLGSF--EQVYMDVAITKEEIEKGVSSHVELDPTSMLSV 701

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            A++ PF + + S R +  C M +Q++  
Sbjct: 702 IANMTPFSDFNQSPRNMYQCQMGKQSMGT 730



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 82/578 (14%), Positives = 172/578 (29%), Gaps = 84/578 (14%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM-------------------LK 472
           +   ++ +++ L    +G    D+ D+  +  V   G +                   ++
Sbjct: 373 KFRMLLFMLRKLYSQVSGATCPDNPDSPQHHEVLLPGFLYGMIIKERFDDCLNAVKSQIQ 432

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-----SSQLSQLEE 527
              R G  R     K   S +   +      ++       +          +S  + + E
Sbjct: 433 LDLRDGKARSFMDPKYFTSVLSKTNWDIGSKLSYFLATGNLVSPTGLDLQQTSGFTIVAE 492

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N    ++H R    + +G          +R + P  +G +CP  T +G   GL++ L+
Sbjct: 493 KLNFYRYLSHFR---CIHRGAFFAELKTTTVRKLMPESWGFLCPVHTPDGSPCGLLNHLS 549

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              ++       +    +   +    V + S+++       Q +  +    S  +     
Sbjct: 550 HTCQIVTSSLDVSHIPALLSAQGMTQV-FASSIDGRRMVCIQLDGKVIGYASPMKAKQLA 608

Query: 648 RCAGEEILVPREKI-----------DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
               +       K+                 P   +  + S +        N  L     
Sbjct: 609 NRLRKLKTEADSKVPLDLEIGYVPVTKGGQYPGLYLFASRSRMMRPVTYLENGKLDHLGS 668

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKS--SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             Q    +      +  G+ S V     S  +++A      +   + R + +   G    
Sbjct: 669 FEQVYMDVAITKEEIEKGVSSHVELDPTSMLSVIANMTPFSDFNQSPRNMYQCQMGKQSM 728

Query: 755 STSGVDI--YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            T    I      K  R        Q P+V+                    +   G N +
Sbjct: 729 GTPSTAISKRTDNKMYRLQSG----QTPVVRP----------DLHNQYGFDNFPNGTNAI 774

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNVSE 870
           VA + + GY+ ED+M++++               ++    D K   G     +   +   
Sbjct: 775 VAVISYTGYDMEDAMILNKSAHERGFGYGTV---YKADIFDLKGVPGASRSAKPTLHFGL 831

Query: 871 EGLKNID--------ECGIICVGAEVNPGDILVGKITPK-----------GESPMTPEEK 911
                 D        + G+  +G  V  GD L   I               E+    E +
Sbjct: 832 GRDVKEDHDARNIISQDGLPIIGTRVKAGDPLCAYIDDTTGRTKFHKYKGDETAFIDEVR 891

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           +L +  G+  +      LR+P      V+  +  +RHG
Sbjct: 892 VLGSDAGDAELQKIHIKLRIP---RSPVIGDKFSSRHG 926


>gi|126303601|ref|XP_001373893.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 1135

 Score =  291 bits (744), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 110/538 (20%), Positives = 175/538 (32%), Gaps = 90/538 (16%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E     + +V    +   D         +   G   +G      +     +   L+ 
Sbjct: 657  THQELFPHSLLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQT 716

Query: 916  IFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
                     +         P G +  V  +        D    + +              
Sbjct: 717  PQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAH-GSVYK 775

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
             E + L   I      ++ G      P   +    L SD +        +          
Sbjct: 776  TELIDLSEKIKQGDDSLVFGVK----PGDLRVLQKLDSDGLPHIGSLLKYGDPFYSYLNI 831

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               ES    Y+  ++ L D  K         +D   G  + + + + + R    GDK A 
Sbjct: 832  NTGESFVTYYKNKENCLVDNIK------VCSNDSGNGKFKSICITMRIPRNPTIGDKFAS 885

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM +G + E+  G +    G   
Sbjct: 886  RHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCH 945

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +    +                                                     
Sbjct: 946  DATPFTFSEENSALGY-------------------------------------------- 961

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                     ML+ A  +  G   LY G++G   +  + +G +Y  +L HMVSDK   R+T
Sbjct: 962  ------FGEMLKAAGYNFYGTERLYSGISGVELEADIFIGVVYYQRLRHMVSDKFQVRTT 1015

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV---VG- 1324
            G+   VT QP+GG++ +GG R GEME   + A+G +++L + L   SD     V    G 
Sbjct: 1016 GARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGS 1075

Query: 1325 ----------------RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                            R R Y   V    +       P  F   V E+ A+ + + L+
Sbjct: 1076 LLSPLLEKPPPSWSAMRNRKYNCTVCNQSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 84/667 (12%), Positives = 212/667 (31%), Gaps = 76/667 (11%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ +       I    +     N++ RN +        ++  +   +V+          
Sbjct: 252 VLKALVAFSDYQIFQELIKGREENSFFRNCVSQMLRVVMEEGCITQKQVLN--------Y 303

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
               F       D Y         +N  + +    +    +   +  + + L      + 
Sbjct: 304 LGERFRVKLSLPDWYTNVQAAEFLLNQCVCIHLKSNEE--KFYVLCLMTRKLFTFAKEEC 361

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLL------RMERSIKERISSVDIDSVMPQDLIN 505
             ++ D+L N+ V + G ++    +  +       ++    + + ++V +++     + +
Sbjct: 362 MEENPDSLMNQEVLTPGRLILMFLKEKMEAWLVSVKIALDKRAQKTNVSMNTENLMKIFS 421

Query: 506 AKPVVSAVCEFFCS---------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
               ++   E+F +               S L  + + +N +  ++H R    + +G   
Sbjct: 422 MGLDLTRPFEYFLATGNLRSKTGLGMLQDSGLCVVADKLNFIRYLSHFR---CVHRGAAF 478

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------ 592
                  +R + P  +G +CP  T +G   GL++ +T+   V                  
Sbjct: 479 AKMRTTTVRKLLPESWGFLCPVHTPDGEPCGLMNHMTAICEVVTQAVYTSSIAPLLCSLG 538

Query: 593 --NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                G    PY +     +   +V      E++  +A A +    +     +       
Sbjct: 539 VTPFDGTPSQPYSECYPVMLNGIMV---GWVEKD--LAPAITDSLRNFKVLGKKQIPP-W 592

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E +L+P+     +        +    + P    +     L+G   Q      +      
Sbjct: 593 TEIVLIPKTGKPSLYPGLFLFTTPCRMIRPVQNLELGKEELIGTLEQIFMNIAIFENEIV 652

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            G      +   S  ++VA      +   + R + +   G        +  Y+     + 
Sbjct: 653 PGITTHQELFPHSLLSVVANFIPFSDHNQSPRNMYQCQMG-KQTMGFPLLTYQDRSDNKL 711

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+M+++
Sbjct: 712 YRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVN 760

Query: 831 ERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           +          S++  E   ++   K G + +   +       L+ +D  G+  +G+ + 
Sbjct: 761 KASWERGFAHGSVYKTELIDLSEKIKQGDDSLVFGVKPGDLRVLQKLDSDGLPHIGSLLK 820

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            GD     +               +        +++  S    +G   ++       R+ 
Sbjct: 821 YGDPFYSYLNINTGESFVTYY---KNKENCLVDNIKVCSNDSGNGKFKSICITMRIPRNP 877

Query: 950 IDKNERS 956
              ++ +
Sbjct: 878 TIGDKFA 884



 Score = 72.0 bits (175), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 112/755 (14%), Positives = 210/755 (27%), Gaps = 155/755 (20%)

Query: 20  NPEIIDIPDLIEV---QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAML 74
            P+   +P L E+      S+++             EGL  A +++ P+          L
Sbjct: 26  LPKEQQLPALQELTRAHIESFNY----------AMREGLSHAVQAIPPLEFAFKDERITL 75

Query: 75  EFVSYEFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             V     PP           K    +C  R  TY   L   +   V            K
Sbjct: 76  AIVDAVVSPPMVPKGSICKELKVYPAECRGRRSTYRGKLTADISWSVNGNP--------K 127

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH- 158
            I +QS  +G +P+M K                         G F+I GI++ ++  L  
Sbjct: 128 GIIKQS--LGYIPIMVKSRLCNLYNLPPKSLIEHHEEAEEMGGYFIINGIEK-IIRMLIM 184

Query: 159 --RSPGIHFDHDKGRASLSGKLLYACRIIPDQ---------------GLWMDIEFDSKDI 201
             R+  I     K +    G   Y   +   +               G  M      K++
Sbjct: 185 PRRNFPIAMIRPKWKTRGPGYTHYGISMHCVRDEHTAINMNLHYLENGSVMVNFIYHKEL 244

Query: 202 IHVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKV 260
                     +P+   L AL      +I   F   I   +   F+   +S          
Sbjct: 245 FF--------LPLGFVLKALVAFSDYQI---FQELIKGREENSFFRNCVSQMLR------ 287

Query: 261 SSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDI 312
                       V+E G      +L  L E+    L +          + L    V    
Sbjct: 288 -----------VVMEEGCITQKQVLNYLGERFRVKLSLPDWYTNVQAAEFLLNQCV---C 333

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           ++ ++ E       ++  K         + + P      +N        L+    K++ +
Sbjct: 334 IHLKSNEEKFYVLCLMTRKLFTFAKEECMEENP---DSLMNQEVLTPGRLILMFLKEKME 390

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST-----VGRVKMNMRLNLDTPDD 427
           A L   ++         +V+ +  N +   S   DL+      +    +  +  L    D
Sbjct: 391 AWLVSVKIALDKRAQKTNVSMNTENLMKIFSMGLDLTRPFEYFLATGNLRSKTGLGMLQD 450

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
                  D +  I+ L   R     +         R  +V ++L   +            
Sbjct: 451 SGLCVVADKLNFIRYLSHFR----CVHRGAAFAKMRTTTVRKLLPESWGFLC-------P 499

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                 +   +M       + V  AV      + L             +  +  S     
Sbjct: 500 VHTPDGEPCGLMNHMTAICEVVTQAVYTS-SIAPLLCSLGVTPFDGTPS--QPYSECYPV 556

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            +     G   +D+ P     +   +      I   + +    +          +     
Sbjct: 557 MLNGIMVGWVEKDLAPAITDSLRNFKVLGKKQIPPWTEIVLIPKTGKPSLYPGLFLFTTP 616

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            ++   V  L   +EE   I            F  E+V                   +  
Sbjct: 617 CRMIRPVQNLELGKEE--LIGTLEQIFMNIAIFENEIVPG------------ITTHQELF 662

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 663 PHSLLSVVANFIPFSDHNQSPRNMYQCQMGKQTMG 697


>gi|219671611|gb|ACL31685.1| RNA polymerase subunit B [Mycobacterium fortuitum]
 gi|219671613|gb|ACL31686.1| RNA polymerase subunit B [Mycobacterium fortuitum]
 gi|219671615|gb|ACL31687.1| RNA polymerase subunit B [Mycobacterium fortuitum]
 gi|219671617|gb|ACL31688.1| RNA polymerase subunit B [Mycobacterium fortuitum]
 gi|315435592|gb|ADU18186.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
 gi|315435614|gb|ADU18197.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
 gi|315435622|gb|ADU18201.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
 gi|326694964|gb|AEA03705.1| RNA polymerase B [Mycobacterium sp. ASCw-1.3]
          Length = 240

 Score =  291 bits (744), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 153

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 154  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 192  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 240



 Score = 45.8 bits (107), Expect = 0.060,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|258574737|ref|XP_002541550.1| DNA-directed RNA polymerase I polypeptide 2 [Uncinocarpus reesii
            1704]
 gi|237901816|gb|EEP76217.1| DNA-directed RNA polymerase I polypeptide 2 [Uncinocarpus reesii
            1704]
          Length = 1243

 Score =  291 bits (744), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 88/422 (20%), Positives = 144/422 (34%), Gaps = 72/422 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSIS 958
            G          + A+      D+ D  +   S            +       DK  R   
Sbjct: 769  GLDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYPLDDKEARGRG 828

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              + +I+ L              +         G++ +    G  K          +   
Sbjct: 829  KSKREIKKL-------FGFAPGGLVKAEWRNQLGEDGLPHVGGRVK----------DGDL 871

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W     D   +  +   K  +       E+ + + I  +  G +      + + +  
Sbjct: 872  VAAWHTVQYDPAAETYLNVDKETHFLKYKDAEEGYIDSIRIL--GSETGNEPCQAISIKY 929

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
             + R    GDK + RHG KG+ S++ P  DMPF + G   DI++NP   PSRM +G   E
Sbjct: 930  RIPRKPIIGDKFSSRHGQKGVCSQLWPAVDMPFSESGIQPDIIINPHAFPSRMTIGMFVE 989

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            +  G A    G         +                                       
Sbjct: 990  SLAGKAGALHGLAQDCTPFQFSEEYTAG-------------------------------- 1017

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                              +     LR A  +  G   +Y G+TG  F   + +G +Y  +
Sbjct: 1018 ------------------DHFGEQLRKAGYNFHGNEPMYSGVTGREFAADIYLGVVYYQR 1059

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   
Sbjct: 1060 LRHMVNDKFQVRTTGPVNALTGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNC 1119

Query: 1319 SD 1320
            SD
Sbjct: 1120 SD 1121



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 88/672 (13%), Positives = 188/672 (27%), Gaps = 115/672 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L+  +   V + D     +           +G +P+M +       
Sbjct: 124 PAECRERHATYRGRLRARVEYKVNNGDWKESVRE----------LGQVPIMLRTNRCHLE 173

Query: 141 -----------------DGTFVIKGIQRIVVSQLHRS----PGIHFDHDKGRASLSGKLL 179
                             G F++ G ++ ++  L  S    P     +   +   +    
Sbjct: 174 KLSPSQLVERKEESEELGGYFIVNGNEK-LIRMLIVSRRNFPMAIIRNSFTKRGATYTK- 231

Query: 180 YACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
           Y  +I   +         +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 232 YGVQIRSVRPDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKAL-IETND--R 286

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             + ++V  +             + +  +   +          + S  K  + L +  + 
Sbjct: 287 EIFERLVGREGSLGMKNTFVTDRMELLLRTYKAY--------GVHSRSKCRAYLGEKFRY 338

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                  +  +   G      IV    G          ++   E   + +   I  +   
Sbjct: 339 VLGMSENVPDED-VGTEFLRKIVLPHLG----------NQNVTESQDNDKFNMILFIIRK 387

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                A        D   +++  L      M   +             +   +  +    
Sbjct: 388 LYTLVAGDCAPDNPDAVSNQEVLLGGFLYGMILKERLEEW-----LRSIGPIARDWSNKN 442

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G    + R   D    +     E+I   ++  +   N   +   +D         + E 
Sbjct: 443 LGLPFTDARFEKDFISRIVARTNENIGGALEYFLSTGN-LVSPTGLDLQQPSGYTIMAEK 501

Query: 471 LKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           +     +   RM    S   ++ +  +  ++P+      PV +          L     H
Sbjct: 502 INFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCG---LLNHLAH 558

Query: 529 VNSLSR--ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI---CPAE---------- 573
              ++   +        L   GV    +      V  +  GRI   C  +          
Sbjct: 559 KCLIATSNLNVAGVPEVLSILGVGSESSSSTEESVAVSLDGRIVGYCSPKQARVISDTLR 618

Query: 574 --TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               EGH    V     +   +  G     Y      ++   V YL   + +  Y+    
Sbjct: 619 HWKVEGHPKIPVELEVGYVPNSNGGQYPGVYLFSQCARMYRPVKYLPLDKLD--YVGPFE 676

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
               E      +++                  ++  P  ++SI A++ PF + + S R +
Sbjct: 677 QPFMEIACVPSDIMSG------------ISTHVEFDPTHILSILANMTPFSDFNQSPRNM 724

Query: 692 MGCNMQRQAVPL 703
             C M +QA+  
Sbjct: 725 YQCQMGKQAMGT 736



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 94/583 (16%), Positives = 189/583 (32%), Gaps = 75/583 (12%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           ++ +    N +  +   + +   I+ II+ L  L  G    D+ D + N+ V   G    
Sbjct: 358 KIVLPHLGNQNVTESQDNDKFNMILFIIRKLYTLVAGDCAPDNPDAVSNQEVLLGGFLYG 417

Query: 469 ----EMLKNQYRL------GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               E L+   R               +    +  + D +        + +  A+  F  
Sbjct: 418 MILKERLEEWLRSIGPIARDWSNKNLGLPFTDARFEKDFISRIVARTNENIGGALEYFLS 477

Query: 519 SSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +  L              + + E +N    I+H R    + +G          +R + P 
Sbjct: 478 TGNLVSPTGLDLQQPSGYTIMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPE 534

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP  T +G   GL++ L     +              +  V      LS +    
Sbjct: 535 SWGFLCPVHTPDGSPCGLLNHLAHKCLIAT-----------SNLNVAGVPEVLSIL---G 580

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS--PKQVVSIAASLIPFL 682
                ++S+ +      +  +   C+ ++  V  + +        PK  V +    +P  
Sbjct: 581 VGSESSSSTEESVAVSLDGRIVGYCSPKQARVISDTLRHWKVEGHPKIPVELEVGYVPNS 640

Query: 683 ENDDSNRVLM---GCNMQRQAVPLLKAEAPFVGTGMESVVAKSS--GAAIVAKRAGIVEQ 737
                  V +      M R    L   +  +VG   E    + +   + I++  +  VE 
Sbjct: 641 NGGQYPGVYLFSQCARMYRPVKYLPLDKLDYVGP-FEQPFMEIACVPSDIMSGISTHVEF 699

Query: 738 VDAIRIVIRSVE-GDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDII 794
                + I +      D + S  ++Y+    +++     T ++ R   K+         I
Sbjct: 700 DPTHILSILANMTPFSDFNQSPRNMYQCQMGKQAMGTPGTSIDYRTDNKLYKLQTGQTPI 759

Query: 795 ADGP---STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           A  P   +  L +   G N +VA + + GY+ +D+M+I++             +      
Sbjct: 760 ARPPLYNAYGLDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGYGTIYKTKIYPL 819

Query: 852 RDTK-LGPEEITRDIPN---------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT-- 899
            D +  G  +  R+I           V  E    + E G+  VG  V  GD++    T  
Sbjct: 820 DDKEARGRGKSKREIKKLFGFAPGGLVKAEWRNQLGEDGLPHVGGRVKDGDLVAAWHTVQ 879

Query: 900 ----PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
                +    +  E   L+    E+        L   +G    
Sbjct: 880 YDPAAETYLNVDKETHFLKYKDAEEGYIDSIRILGSETGNEPC 922


>gi|51035515|emb|CAH10893.1| RNA polymerase B subunit [Haloarcula japonica]
          Length = 430

 Score =  291 bits (744), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 78/253 (30%), Positives = 112/253 (44%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF + G   D+++NP  +
Sbjct: 192  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFHRGGVVPDLIINPHAL 251

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 252  PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEELRGSLEDHG-------------- 297

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+  +Y G+TGE  D 
Sbjct: 298  -----------------------FD-----------------SSGKETMYSGVTGEKIDA 317

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 318  EIFVGDIFYQKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 377

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 378  AMALKERLLDESD 390



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 42/210 (20%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    D    +N +VA M + G+N ED
Sbjct: 21  RPDTRQHLLHYPQLSMVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 70

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++D+ 
Sbjct: 71  ALVMNQGSVDRALARSHFFRTYEGEERRYPGGQEDRF-EIPDDEVRGARGEEAYTHLDDD 129

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++    +V    +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 130 GLVNPETKVGENAVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 183

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 184 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 213


>gi|315435608|gb|ADU18194.1| RNA polymerase beta-subunit [Mycobacterium setense]
          Length = 240

 Score =  291 bits (744), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 132/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 153

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 154  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG YS
Sbjct: 192  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.069,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|148879081|emb|CAM07056.1| RpoB protein [Mycobacterium sp. MHSD12]
          Length = 231

 Score =  291 bits (744), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 101/230 (43%), Positives = 133/230 (57%), Gaps = 37/230 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWATKL---------- 139

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                   E +     DS+            VSTPVFDGA EE +  +L     +      
Sbjct: 140  ------PEDLYSAPVDSI------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 182  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 231


>gi|158954700|gb|ABW84321.1| RNA polymerase subunit B [Mycobacterium rhodesiae]
          Length = 241

 Score =  290 bits (743), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I  +    +   ++       E  
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVVGGTPEWAANLPQDMLSSE-- 158

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 159  --------------------------PNSIVSTPVFDGAREEELQGLLSSTLPNRDGEVL 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 193  VNGDGKAVLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 241



 Score = 46.2 bits (108), Expect = 0.038,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|158954704|gb|ABW84323.1| RNA polymerase subunit B [Mycobacterium tusciae]
          Length = 238

 Score =  290 bits (743), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +                  
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIDGSPDWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +     + + G  VSTPVFDGA E+ +  +L     +      
Sbjct: 147  -----------------LPEEMLEAEPGSIVSTPVFDGAREDELQGLLSSTLPNRDGVTL 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDSDGKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.042,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|296803847|ref|XP_002842776.1| DNA-directed RNA polymerase I subunit RPA2 [Arthroderma otae CBS
            113480]
 gi|238846126|gb|EEQ35788.1| DNA-directed RNA polymerase I subunit RPA2 [Arthroderma otae CBS
            113480]
          Length = 1243

 Score =  290 bits (743), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 107/522 (20%), Positives = 186/522 (35%), Gaps = 60/522 (11%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  R + +  + + G   +  M I+          S HI EF+     + L      
Sbjct: 656  RMYRPVRYLPLDKLDYVGPFEQPYMEIACIASDIRNGISTHI-EFDPTHILSILANMTPF 714

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
             D         +   + G   +G      D        + ++  TP  +  L  A   + 
Sbjct: 715  SDFNQSPRNMYQC--QMGKQAMGTPGTAIDYRTDNKLYRLQTGQTPVVRPPLYNAYGLDN 772

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  I N+   ++     ++ + ++  L  DK+       +
Sbjct: 773  FPNGMNAVVAVISYTGYDMDDAMIINKSSHERGFGYGTIYKTKVYALD-DKESRGRGASK 831

Query: 981  NIYSRLMEILCGQNAVSGPK--GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L     G    +  K    +         +SE      W     D      V   
Sbjct: 832  RSITKLFGFAPGGLIKAEWKAQLDEDGLPHIGAKVSEGSLVGAWHTVQYDPATDTYVNVD 891

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  +       E+ + + +  +  G +    V + V +   + R    GDK + RHG KG
Sbjct: 892  KQTHFLKYKDGEEGYVDSVRIL--GAETGNEVCQAVSIKYRVPRRPVIGDKFSSRHGQKG 949

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++S++ P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    
Sbjct: 950  VLSQLWPSTDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGSLHGLAQDSTPFQ 1009

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                         + 
Sbjct: 1010 FSEEDTAG--------------------------------------------------DY 1019

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L+ A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +
Sbjct: 1020 FGKQLQKAGYNFHGNEPMYSGITGREFAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNAL 1079

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1080 TGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1121



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 89/677 (13%), Positives = 201/677 (29%), Gaps = 119/677 (17%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGKLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS-- 175
                                G FV+ G ++++   +   R+ P     +   +   +  
Sbjct: 171 HLEKATPSQLVERKEESEELGGYFVVNGNEKLIRMLIVGKRNFPTAIIRNSFQKRGSAYT 230

Query: 176 --GKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    + +R   R+    VPV   L AL +++ +
Sbjct: 231 KFGIQIRSVR--PDQTSQTNVLHYLSDGN--VTLRFSWRKNEYLVPVMMVLKAL-IETND 285

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAA--DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
                + ++V  +              +L++    +  +         + S  +   G+ 
Sbjct: 286 --REIFERLVGREDSLGIENTFVTDRVELLLRTYKAYGVHSRSKCRAYLGSKFRFVLGMP 343

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           + + ++ V    +    L  L       + +  +  +    +    +L     +      
Sbjct: 344 EDVPDEDVGTEFLRKIVLPHLGNQNVTESQDNDKFNMILFMIRKLYTLVAGDCAPDNPDA 403

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           I   + +    Y+   L+ ++ ++   ++  I R  R  +  T                +
Sbjct: 404 ISNQEVL-LGGYLYGMLLKERLEEWLKSVGPIVRDWRMRNQDTKFTDPKF-------ERE 455

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
           +    +GR   N+   L+      ++                    +   +D        
Sbjct: 456 FLAKVIGRTNENIGGALEYFLSTGNL-------------------VSPTGLDLQQPSGYT 496

Query: 466 SVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
            + E +     +   RM    S   ++ +  +  ++P+      PV +          L 
Sbjct: 497 VMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCG---LL 553

Query: 524 QLEEHVNSLSR--ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE----- 576
               H   +S   +  +     L   GV    +      +     G+I    T +     
Sbjct: 554 NHLAHKCLISTSNLDVSGVPGVLAGLGVTSESSCSTEESIPVQLNGKILGYCTPKQSRAI 613

Query: 577 ----------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                     GH    V     +   ++ G     Y      ++   V YL   + +  Y
Sbjct: 614 ADTLRYWKVQGHKHIPVELEIGYVPSSSGGQYPGVYMFSEAARMYRPVRYLPLDKLD--Y 671

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +        E      ++                   I+  P  ++SI A++ PF + + 
Sbjct: 672 VGPFEQPYMEIACIASDIRNG------------ISTHIEFDPTHILSILANMTPFSDFNQ 719

Query: 687 SNRVLMGCNMQRQAVPL 703
           S R +  C M +QA+  
Sbjct: 720 SPRNMYQCQMGKQAMGT 736


>gi|60172310|gb|AAX14486.1| RNA polymerase beta subunit [Vibrio scophthalmi LMG 19158]
          Length = 184

 Score =  290 bits (743), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 103/187 (55%), Positives = 133/187 (71%), Gaps = 5/187 (2%)

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+ ++G PVDIVLNPLGVPSRMN+GQI E HLG A  G+G+KI  ++   K   +
Sbjct: 1    PVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGEKINKMV---KEQQE 57

Query: 1165 ISPLRSFLEKVI--GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            ++  R FL+KV   G    T  I+   D  V  +    + G+P++TPVFDGA E +I ++
Sbjct: 58   LAKFREFLQKVYDLGDTRQTVDIASLSDAEVRTLIGNLRGGLPIATPVFDGAPESSIKAL 117

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L +ADL  SGQ  L+DG TG+ F+RPVTVGY+ MLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 118  LELADLPTSGQLKLFDGRTGDSFERPVTVGYMCMLKLNHLVDDKMHARSTGSYSLVTQQP 177

Query: 1283 LGGKSNR 1289
            LGGK+  
Sbjct: 178  LGGKAQF 184


>gi|62720668|gb|AAX93870.1| RNA polymerase subunit B [Mycobacterium gadium]
          Length = 238

 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +                  
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIDGSPDWATN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +     + + G  VSTPVFDGA E+ +  +L     +      
Sbjct: 147  -----------------LPEEMLEAEPGSIVSTPVFDGAREDELQGLLSSTLPNRDGATL 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDSDGKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.041,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|115383177|gb|ABI96809.1| RNA polymerase beta subunit [Mycobacterium sp. JAN1]
 gi|115383179|gb|ABI96810.1| RNA polymerase beta subunit [Mycobacterium sp. JAN1]
          Length = 227

 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGSPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 227


>gi|297266784|ref|XP_002799417.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 [Macaca
            mulatta]
          Length = 924

 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 112/558 (20%), Positives = 183/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 427  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 485

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 486  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 545

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 546  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGIKPGDP--------RILQKL 596

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 597  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 654

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 655  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 714

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 715  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 750

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 751  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 784

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 785  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 844

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 845  DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 904

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 905  FRYFVAELAAMNIKVKLD 922



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 99/673 (14%), Positives = 215/673 (31%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 42  LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 93

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 94  GGCFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 151

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRL---GLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            D+ D+L N+ V + G++     +    G L   +   ++ +     S+   +L+    +
Sbjct: 152 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 211

Query: 510 VSAVCEFFC------------------SSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              + + F                   +S L  + + +N +  ++H R    + +G    
Sbjct: 212 GIDLTKPFEYLFATGNLRSKTGLGLLQNSGLCVVADKLNFIRYLSHFR---CVHRGADFA 268

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 269 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 328

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V   V ++         +A   +          E     
Sbjct: 329 TPVDGAPHRPYSECYPVLLDGVM--VGWVDKE------LAPGIADSLRHFKVLREKRIPP 380

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 381 -WMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDE 439

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
            F G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 440 VFAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 496

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 497 DNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 545

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G   +   I       L+ +D+ G+  +G
Sbjct: 546 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRILQKLDDDGLPFIG 605

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++     E     +++  S    SG    V    
Sbjct: 606 AKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITM 660

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 661 RVPRNPTIGDKFA 673


>gi|148879037|emb|CAM07034.1| RpoB protein [Mycobacterium sp. MG4]
          Length = 228

 Score =  290 bits (743), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 130/230 (56%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 228


>gi|148879055|emb|CAM07043.1| RpoB protein [Mycobacterium llatzerense]
          Length = 227

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 97/231 (41%), Positives = 129/231 (55%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 29   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 88

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 89   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGXPEWAAN-------------- 133

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 134  -----------------LPXGXHSAPRDSIVATPVFDGAREGELXGLLGSTLPNRDGDVM 176

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 177  VNAXGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 227


>gi|185179190|gb|ACC77608.1| RpoB [Mycobacterium chelonae]
          Length = 223

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 130/230 (56%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 26   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 130

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 131  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 173

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 174  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 223


>gi|190148976|gb|ACE63463.1| RNA polymerase subunit B [Pseudonocardia xinjiangensis]
          Length = 318

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 174/324 (53%), Positives = 238/324 (73%), Gaps = 8/324 (2%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG
Sbjct: 2   RMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQHNPLAGLTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +GFI+TPYRKV +G
Sbjct: 62  LSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPFGFIQTPYRKVSEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDAS 667
           +VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE   +    +D+ID S
Sbjct: 122 RVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVDYISPVGVDYIDVS 181

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTGME   A  +G  +
Sbjct: 182 PRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTGMELRAAVDAGDVL 241

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           VA +AG+VE++ A  I + + +G           YRL KF+RSNQ TC NQ+P++  GD 
Sbjct: 242 VADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGTCNNQKPIIDEGDR 294

Query: 788 VRRNDIIADGPSTDLGDLALGRNM 811
           V    +IADGP T+ G++ALG+N+
Sbjct: 295 VEAGQVIADGPCTENGEMALGKNL 318


>gi|4456853|emb|CAB36990.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 400

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 180/340 (52%), Positives = 243/340 (71%), Gaps = 2/340 (0%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ 
Sbjct: 58  VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQV 117

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           RLGL RMER+++ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  +  N LS +
Sbjct: 118 RLGLSRMERNVRERMSVQDNEVLTPQHIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSEL 177

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           ++ RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N Y
Sbjct: 178 SNKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKY 237

Query: 596 GFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  G  
Sbjct: 238 GFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGRHQGVN 297

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
              P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGT
Sbjct: 298 QEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPYVGT 357

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           GME   A  SGAA++A+  G V   DA ++ +R  +G LD
Sbjct: 358 GMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD 397


>gi|142094|gb|AAA22032.1| RNA polymerase beta-subunit [Anabaena variabilis]
          Length = 165

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 77/135 (57%), Positives = 98/135 (72%)

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             FDRPVT+G  YMLKL H+V DK++ARSTG YSLVTQQPLGGK+ +GGQR GEMEVW ++
Sbjct: 1    AFDRPVTIGVAYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRFGEMEVWALE 60

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            A+GAAY LQE+LT+KSDD+ GR     +IV G      GTPESF VL++E+Q+LGL I +
Sbjct: 61   AFGAAYTLQELLTVKSDDMQGRNEALNAIVKGKAIPRPGTPESFKVLMRELQSLGLDIAV 120

Query: 1364 ENSRTKNSAKMEEIP 1378
                T+      ++ 
Sbjct: 121  HKVETQADGSSLDVE 135


>gi|148879045|emb|CAM07038.1| RpoB protein [Mycobacterium sp. MG8]
          Length = 218

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 98/231 (42%), Positives = 130/231 (56%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 20   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 79

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 80   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 124

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 125  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 167

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G++ L+DG  GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 168  VDGDGKARLFDGRXGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 218


>gi|207457737|ref|NP_001128800.1| DNA-directed RNA polymerase I subunit RPA2 [Pongo abelii]
          Length = 1135

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 112/558 (20%), Positives = 183/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGMKPGDP--------RILQKL 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 926  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 961

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 962  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 93/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + ++V +++  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIPPWTEVVLIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   +       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGMKPGDPRILQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 99/721 (13%), Positives = 200/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEVSVYPAECRGRRCTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLYNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMVRPKWKTRGPGYTHYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++       +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTNVS-MNTDNLMRIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +++ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
             + +               +      ++   V  L   +EE          L       
Sbjct: 591 PWTEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V        +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|148879075|emb|CAM07053.1| RpoB protein [Mycobacterium sp. MHSD5]
          Length = 231

 Score =  290 bits (742), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 149  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 182

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 183  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 231


>gi|297266782|ref|XP_001088359.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 isoform 2
            [Macaca mulatta]
          Length = 1070

 Score =  290 bits (741), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 112/558 (20%), Positives = 183/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 573  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 631

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 632  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 691

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 692  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGIKPGDP--------RILQKL 742

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 743  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 800

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 801  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 860

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 861  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 896

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 897  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 930

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 931  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 990

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 991  DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 1050

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1051 FRYFVAELAAMNIKVKLD 1068



 Score = 86.7 bits (213), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 99/673 (14%), Positives = 215/673 (31%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 188 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 239

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 240 GGCFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 297

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRL---GLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            D+ D+L N+ V + G++     +    G L   +   ++ +     S+   +L+    +
Sbjct: 298 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 357

Query: 510 VSAVCEFFC------------------SSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              + + F                   +S L  + + +N +  ++H R    + +G    
Sbjct: 358 GIDLTKPFEYLFATGNLRSKTGLGLLQNSGLCVVADKLNFIRYLSHFR---CVHRGADFA 414

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 415 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 474

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V   V ++         +A   +          E     
Sbjct: 475 TPVDGAPHRPYSECYPVLLDGVM--VGWVDKE------LAPGIADSLRHFKVLREKRIPP 526

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 527 -WMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDE 585

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
            F G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 586 VFAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 642

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 643 DNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 691

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G   +   I       L+ +D+ G+  +G
Sbjct: 692 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRILQKLDDDGLPFIG 751

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++     E     +++  S    SG    V    
Sbjct: 752 AKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITM 806

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 807 RVPRNPTIGDKFA 819



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 34/90 (37%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L   +   V  +         K I +Q  ++G +P+M K       
Sbjct: 35  PAECRGRRSTYRGKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLH 84

Query: 142 ------------------GTFVIKGIQRIV 153
                             G F+I GI++++
Sbjct: 85  SLPPQALIEHHEEAEEMGGYFIINGIEKVI 114


>gi|240278168|gb|EER41675.1| DNA-directed RNA polymerase I [Ajellomyces capsulatus H143]
          Length = 1242

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/459 (21%), Positives = 156/459 (33%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G      E     +   L+             S  + +  +
Sbjct: 716  DFNQSPRNMYQCQMSKQAMGTPGASIEYRTDNKLYRLQTGQTPVVRTPLYNSYGLDNFPN 775

Query: 937  GTVVDVRIFNRHGIDKNERSI-------------SVEREQIELLARDKDDEQVILDRNIY 983
            G    V + +  G D ++  I             ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLD-DKESRGRGKARREV 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            S+L     G            +         ++E      W     D             
Sbjct: 835  SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +     G +      + + V   + R    GDK + RHG KG+ S
Sbjct: 895  HLLKYKDTEEGYIDNVRIF--GSETGGDPCQAISVKFRVPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   DI++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 953  QLWPAIDMPFSETGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALHGLAQDSTPFRFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                S                                            F G        
Sbjct: 1013 EHTASD-------------------------------------------FFG-------E 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDSLLAHGAAFLLQDRLMNCSD 1121



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 81/664 (12%), Positives = 181/664 (27%), Gaps = 93/664 (14%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGRLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGK 177
                                G F++ G ++++   +   R+ P         +   +  
Sbjct: 171 HLEKCSPEQLVQRKEESEELGGYFIVNGNEKLIRMLIVGRRNFPMAIIRSSFTKRGQTYT 230

Query: 178 LLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-E 227
             Y  +I   +         +    D    +  R   R+    VPV   L AL   ++ E
Sbjct: 231 K-YGIQIRSVRTDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKALVETNDRE 287

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I      +       + +        L+   K        DT   + E  + +       
Sbjct: 288 IFERLVGREGSEGIKNSFVTD-RVELLLRTYKGYKLYGRDDTRAYLGEKFRPVLGMPADI 346

Query: 288 LKE----KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             +    + ++ + +    L    V E   N +   I      +    + E    +    
Sbjct: 347 PDDMVGAEFLRKVVLPH--LGNQNVTESQDNDKFNMILFMIRKLYTLVAGECAPDNP--- 401

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVSTFSVAESMFNFL 399
              +    V     +   L+ ++ ++   A   I R      +    S     +   + +
Sbjct: 402 -DAVSNQEVLLGGSLYGMLLKERLEEWLRAFGPIARDWSFRNQNARFSDPRFEKEFLSRI 460

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              +++     +        L   T  D++      +IA         +    I      
Sbjct: 461 VSRTNENIGGALEYFLSTGNLVSPTGLDLQQPSGYTVIAEKINFYRFISHFRMIHRGSFF 520

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +  +V ++L   +                      ++       K   S        
Sbjct: 521 AQLKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHLAHECKIATSN----LDV 569

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S + Q+   +      + +   S + Q            +    +   R        G+ 
Sbjct: 570 SGVPQVISDLGVTYESSVSLDESVVVQLDGRILGYCSPKQARMISDTLRY---WKVAGNK 626

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              V     +   +  G     Y      ++   V YL   + +  Y+        E   
Sbjct: 627 SLPVELEIGYIPNSNRGQYPGIYIFSQCARMMRPVKYLPLDKLD--YVGPFEQPFMEIAC 684

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +++                  ++  P  ++SI A++ PF + + S R +  C M +Q
Sbjct: 685 VPSDIMSG------------ISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQMSKQ 732

Query: 700 AVPL 703
           A+  
Sbjct: 733 AMGT 736



 Score = 63.2 bits (152), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 95/673 (14%), Positives = 195/673 (28%), Gaps = 103/673 (15%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A    +++ + E          I      +    +  T    K   R D    +  
Sbjct: 275 MILKALVETNDREIFERLVGREGSEGIKNSFVTDRVELLLRTYKGYKLYGRDDTRAYLGE 334

Query: 380 VMRP-----GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             RP      D+    V             K  L  +G   +    + D        +  
Sbjct: 335 KFRPVLGMPADIPDDMVGAEFL-------RKVVLPHLGNQNVTESQDND--------KFN 379

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME----------- 483
            I+ +I+ L  L  G+   D+ D + N+ V   G +     +    R+E           
Sbjct: 380 MILFMIRKLYTLVAGECAPDNPDAVSNQEVLLGGSLYGMLLK---ERLEEWLRAFGPIAR 436

Query: 484 ------RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------S 523
                 ++ +      + + +        + +  A+  F  +  L              +
Sbjct: 437 DWSFRNQNARFSDPRFEKEFLSRIVSRTNENIGGALEYFLSTGNLVSPTGLDLQQPSGYT 496

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            + E +N    I+H R    + +G          +R + P  +G +CP  T +G   GL+
Sbjct: 497 VIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLL 553

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL-----DEDG 638
           + L    ++       +    V        V Y S++  +   + Q +  +      +  
Sbjct: 554 NHLAHECKIATSNLDVSG---VPQVISDLGVTYESSVSLDESVVVQLDGRILGYCSPKQA 610

Query: 639 SFTEELVFCRCAGEEILVPRE-KIDFIDASPKQVVS-------IAASLIPF----LENDD 686
               + +          +P E +I +I  S +            A  + P     L+  D
Sbjct: 611 RMISDTLRYWKVAGNKSLPVELEIGYIPNSNRGQYPGIYIFSQCARMMRPVKYLPLDKLD 670

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                    M+   VP        + T +E                    Q        +
Sbjct: 671 YVGPFEQPFMEIACVPSDIMSG--ISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQ 728

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +  +    + ++     K  R        Q P+V+               S  L +  
Sbjct: 729 MSKQAMGTPGASIEYRTDNKLYRLQTG----QTPVVR----------TPLYNSYGLDNFP 774

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF----TSIHIEEFEVMARDTKLGPEEIT 862
            G N +VA + + GY+ +D+M+I++                I   +      +       
Sbjct: 775 NGMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLDDKESRGRGKARREV 834

Query: 863 RDIPNVSEEGLKN------IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             +   +   L        +DE G+  +GA V  G I+    T + +        +    
Sbjct: 835 SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 894

Query: 917 FGEKAVDVRDTSL 929
              K  D  +  +
Sbjct: 895 HLLKYKDTEEGYI 907


>gi|62720662|gb|AAX93867.1| RNA polymerase subunit B [Mycobacterium phlei]
          Length = 238

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 132/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI+      K               
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIEGDPEWAKN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +     + +    V+TPVFDGA EE +  +L     +      
Sbjct: 147  -----------------LPEDLREAEPNSIVATPVFDGAREEELQGLLSSTLPNRDGEQM 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKAVLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 45.8 bits (107), Expect = 0.054,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|169247691|gb|ACA51679.1| RpoB [Mycobacterium abscessus]
 gi|185179196|gb|ACC77611.1| RpoB [Mycobacterium abscessus]
          Length = 225

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 98/231 (42%), Positives = 129/231 (55%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 27   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 87   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 131

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 132  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 174

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 175  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 225


>gi|148879077|emb|CAM07054.1| RpoB protein [Mycobacterium sp. MHSD6]
          Length = 230

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 148  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 182  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 230


>gi|154274906|ref|XP_001538304.1| DNA-directed RNA polymerase I polypeptide 2 [Ajellomyces capsulatus
            NAm1]
 gi|150414744|gb|EDN10106.1| DNA-directed RNA polymerase I polypeptide 2 [Ajellomyces capsulatus
            NAm1]
          Length = 1214

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/459 (21%), Positives = 157/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G      E     +   L+             S  + +  +
Sbjct: 688  DFNQSPRNMYQCQMSKQAMGTPGASIEYRTDNKLYRLQTGQTPVVRTPLYNSYGLDNFPN 747

Query: 937  GTVVDVRIFNRHGIDKNERSI-------------SVEREQIELLARDKDDEQVILDRNIY 983
            G    V + +  G D ++  I             ++ + +I  L  DK+       R   
Sbjct: 748  GMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLD-DKESRGRGKARREV 806

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            S+L     G            +         ++E      W     D             
Sbjct: 807  SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 866

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +  +  G +      + + V   + R    GDK + RHG KG+ S
Sbjct: 867  HLLKYKDTEEGYIDNVRIL--GSETGGDPCQAISVKFRVPRKPVIGDKFSSRHGQKGVCS 924

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   DI++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 925  QLWPAIDMPFSETGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALHGLAQDSTPFRFSE 984

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                S                                            F G        
Sbjct: 985  EHTASD-------------------------------------------FFG-------E 994

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 995  QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1054

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1055 PVKGRAKGGGIRVGEMERDSLLAHGAAFLLQDRLMNCSD 1093



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 67/233 (28%), Gaps = 51/233 (21%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGRLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGK 177
                                G F++ G ++++   +   R+ P         +   +  
Sbjct: 171 HLEKCSPEQLVQRKEESEELGGYFIVNGNEKLIRMLIVGRRNFPMAIIRSSFTKRGQTYT 230

Query: 178 LLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-E 227
             Y  +I   +         +    D    +  R   R+    VPV   L AL   ++ E
Sbjct: 231 K-YGIQIRSVRADQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKALVETNDRE 287

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           I      +       + +        L+   K        DT   + E  + +
Sbjct: 288 IFERLVGREGSEGIKNSFVTD-RVELLLRTYKGYKLYGRDDTRAYLGEKFRPV 339



 Score = 45.8 bits (107), Expect = 0.051,   Method: Composition-based stats.
 Identities = 32/229 (13%), Positives = 65/229 (28%), Gaps = 24/229 (10%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           + T +E                    Q        +  +  +    + ++     K  R 
Sbjct: 665 ISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQMSKQAMGTPGASIEYRTDNKLYRL 724

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q P+V+               S  L +   G N +VA + + GY+ +D+M+I+
Sbjct: 725 QTG----QTPVVR----------TPLYNSYGLDNFPNGMNAVVAVLSYTGYDMDDAMIIN 770

Query: 831 ERMVSEDVF----TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN------IDECG 880
           +                I   +      +         +   +   L        +DE G
Sbjct: 771 KSAHDRGFGWGTIYKTKIYSLDDKESRGRGKARREVSKLFGFAPGSLIKGEWRHALDEDG 830

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           +  +GA V  G I+    T + +        +       K  D  +  +
Sbjct: 831 LPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQTHLLKYKDTEEGYI 879


>gi|53854332|gb|AAU95611.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 305

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 182/304 (59%), Positives = 234/304 (76%)

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           NG G +DDID+LGNRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAK
Sbjct: 1   NGHGEVDDIDHLGNRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAK 60

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PV +A+ EFF SSQLSQ  +  N LS +T+ RR+SALG GG+ R RAG E+RDVHPTHYG
Sbjct: 61  PVSAAIKEFFGSSQLSQFMDQTNPLSEVTYKRRVSALGPGGLTRERAGFEVRDVHPTHYG 120

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    I
Sbjct: 121 RVCPIETPEGPNIGLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVI 180

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQAN+ LD DG+   +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+
Sbjct: 181 AQANADLDSDGNLIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDA 240

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR 
Sbjct: 241 NRALMGANMQRQAVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRV 300

Query: 748 VEGD 751
            + +
Sbjct: 301 HDDE 304


>gi|115383173|gb|ABI96807.1| RNA polymerase beta subunit [Mycobacterium chelonae]
 gi|115383175|gb|ABI96808.1| RNA polymerase beta subunit [Mycobacterium chelonae]
 gi|148879035|emb|CAM07033.1| RpoB protein [Mycobacterium sp. MG3]
 gi|148879071|emb|CAM07051.1| RpoB protein [Mycobacterium sp. MHSD3]
          Length = 227

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 227


>gi|325096233|gb|EGC49543.1| DNA-directed RNA polymerase I [Ajellomyces capsulatus H88]
          Length = 1242

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/459 (21%), Positives = 156/459 (33%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G      E     +   L+             S  + +  +
Sbjct: 716  DFNQSPRNMYQCQMSKQAMGTPGASIEYRTDNKLYRLQTGQTPVVRTPLYNSYGLDNFPN 775

Query: 937  GTVVDVRIFNRHGIDKNERSI-------------SVEREQIELLARDKDDEQVILDRNIY 983
            G    V + +  G D ++  I             ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLD-DKESRGRGKARREV 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            S+L     G            +         ++E      W     D             
Sbjct: 835  SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +     G +      + + V   + R    GDK + RHG KG+ S
Sbjct: 895  HLLKYKDTEEGYIDNVRIF--GSETGGDPCQAISVKFRVPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   DI++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 953  QLWPAIDMPFSETGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALHGLAQDSTPFRFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                S                                            F G        
Sbjct: 1013 EHTASD-------------------------------------------FFG-------E 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDSLLAHGAAFLLQDRLMNCSD 1121



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 82/664 (12%), Positives = 181/664 (27%), Gaps = 93/664 (14%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGRLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGK 177
                                G F++ G ++++   +   R+ P         +   +  
Sbjct: 171 HLEKCSPEQLVQRKEESEELGGYFIVNGNEKLIRMLIVGRRNFPMAIIRSSFTKRGQTYT 230

Query: 178 LLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-E 227
             Y  +I   +         +    D    +  R   R+    VPV   L AL   ++ E
Sbjct: 231 K-YGIQIRSVRTDQTSQTNVLHYLSDGN--VTFRFSWRKNEYLVPVVMILKALVETNDRE 287

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I      +       + +        L+   K        DT   + E  + +       
Sbjct: 288 IFERLVGREGSEGIKNSFVTD-RVELLLRTYKGYKLYGRDDTRAYLGEKFRPVLGMPADI 346

Query: 288 LKE----KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             +    + ++ + +    L    V E   N +   I      +    + E    +    
Sbjct: 347 PDDMVGAEFLRKVVLPH--LGNQNVTESQDNDKFNMILFMIRKLYTLVAGECAPDNP--- 401

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR----VMRPGDVSTFSVAESMFNFL 399
              +    V     +   L+ ++ ++   A   I R      +    S     +   + +
Sbjct: 402 -DAVSNQEVLLGGSLYGMLLKERLEEWLRAFGPIARDWSFRNQNARFSDPRFEKEFLSRI 460

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
              +++     +        L   T  D++      IIA         +    I      
Sbjct: 461 VSRTNENIGGALEYFLSTGNLVSPTGLDLQQPSGYTIIAEKINFYRFISHFRMIHRGSFF 520

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +  +V ++L   +                      ++       K   S        
Sbjct: 521 AQLKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHLAHECKIATSN----LDV 569

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S + Q+   +      + +   S + Q            +    +   R        G+ 
Sbjct: 570 SGVPQVISDLGVTYESSVSLDESVVVQLDGRILGYCSPKQARMISDTLRY---WKVAGNK 626

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
              V     +   +  G     Y      ++   V YL   + +  Y+        E   
Sbjct: 627 SLPVELEIGYIPNSNRGQYPGIYIFSQCARMMRPVKYLPLDKLD--YVGPFEQPFMEIAC 684

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +++                  ++  P  ++SI A++ PF + + S R +  C M +Q
Sbjct: 685 VPSDIMSG------------ISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQMSKQ 732

Query: 700 AVPL 703
           A+  
Sbjct: 733 AMGT 736



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 95/673 (14%), Positives = 195/673 (28%), Gaps = 103/673 (15%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A    +++ + E          I      +    +  T    K   R D    +  
Sbjct: 275 MILKALVETNDREIFERLVGREGSEGIKNSFVTDRVELLLRTYKGYKLYGRDDTRAYLGE 334

Query: 380 VMRP-----GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             RP      D+    V             K  L  +G   +    + D        +  
Sbjct: 335 KFRPVLGMPADIPDDMVGAEFL-------RKVVLPHLGNQNVTESQDND--------KFN 379

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME----------- 483
            I+ +I+ L  L  G+   D+ D + N+ V   G +     +    R+E           
Sbjct: 380 MILFMIRKLYTLVAGECAPDNPDAVSNQEVLLGGSLYGMLLK---ERLEEWLRAFGPIAR 436

Query: 484 ------RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------S 523
                 ++ +      + + +        + +  A+  F  +  L              +
Sbjct: 437 DWSFRNQNARFSDPRFEKEFLSRIVSRTNENIGGALEYFLSTGNLVSPTGLDLQQPSGYT 496

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            + E +N    I+H R    + +G          +R + P  +G +CP  T +G   GL+
Sbjct: 497 IIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLL 553

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL-----DEDG 638
           + L    ++       +    V        V Y S++  +   + Q +  +      +  
Sbjct: 554 NHLAHECKIATSNLDVSG---VPQVISDLGVTYESSVSLDESVVVQLDGRILGYCSPKQA 610

Query: 639 SFTEELVFCRCAGEEILVPRE-KIDFIDASPKQVVS-------IAASLIPF----LENDD 686
               + +          +P E +I +I  S +            A  + P     L+  D
Sbjct: 611 RMISDTLRYWKVAGNKSLPVELEIGYIPNSNRGQYPGIYIFSQCARMMRPVKYLPLDKLD 670

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                    M+   VP        + T +E                    Q        +
Sbjct: 671 YVGPFEQPFMEIACVPSDIMSG--ISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQ 728

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +  +    + ++     K  R        Q P+V+               S  L +  
Sbjct: 729 MSKQAMGTPGASIEYRTDNKLYRLQTG----QTPVVR----------TPLYNSYGLDNFP 774

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF----TSIHIEEFEVMARDTKLGPEEIT 862
            G N +VA + + GY+ +D+M+I++                I   +      +       
Sbjct: 775 NGMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLDDKESRGRGKARREV 834

Query: 863 RDIPNVSEEGLKN------IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             +   +   L        +DE G+  +GA V  G I+    T + +        +    
Sbjct: 835 SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 894

Query: 917 FGEKAVDVRDTSL 929
              K  D  +  +
Sbjct: 895 HLLKYKDTEEGYI 907


>gi|190694903|gb|ACE88992.1| RNA polymerase beta subunit [Mycobacterium chelonae]
          Length = 229

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 33   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 92

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 93   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 137

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 138  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 180

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 181  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 229


>gi|52538181|emb|CAH19192.1| RNA polymerase beta-subunit [Pseudomonas alcaliphila]
          Length = 316

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 169/296 (57%), Positives = 219/296 (73%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MP DLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPHDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG  +RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +  V
Sbjct: 61  RERAGFXVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVNEAMV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA+++L++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATLNDKAVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           R G+++ VDA RIV+R  + +++   +GVDIY L  + RSNQNTC+NQRPLV  GD
Sbjct: 241 RGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTXYTRSNQNTCINQRPLVSKGD 296


>gi|319998249|gb|ADV91596.1| RNA polymerase B subunit [Mycobacterium xenopi]
          Length = 243

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 100/230 (43%), Positives = 134/230 (58%), Gaps = 37/230 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G KI +                     
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKIDT--------------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                      +    + +L           V+TPVFDGA EE +  +L            
Sbjct: 141  ---SKGVPDWASRLPEELLEAEPNKI----VATPVFDGAREEELQGLLSCTLPNRDGDVL 193

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS+
Sbjct: 194  VDGDGKATLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSM 243



 Score = 47.0 bits (110), Expect = 0.027,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|55728623|emb|CAH91052.1| hypothetical protein [Pongo abelii]
          Length = 1135

 Score =  290 bits (741), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 112/558 (20%), Positives = 184/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +         +     E + L   I      ++ G               +   L
Sbjct: 757  MIVNKASWERGFAHGSA-YKSEFIDLSEKIKQGDSSLVFGMKPGDP--------RILQKL 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKACS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 926  IGMLIESMAGKSAALHGLCHGATPFIFSEENSALEY------------------------ 961

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 962  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 88.2 bits (217), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 95/664 (14%), Positives = 216/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--- 509
            D+ D+L N+ V + G++     +  L  +  SIK         + +  +  N   +   
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGLLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 422

Query: 510 ----VSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
                      F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIPPWTEVVLIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S +  EF  ++   K G   +   +       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSAYKSEFIDLSEKIKQGDSSLVFGMKPGDPRILQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKACSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 61.6 bits (148), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 101/721 (14%), Positives = 203/721 (28%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEVSVYPAECRGRRCTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLYNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   +   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMVRPKWKTRGPGYTHFGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +     +   LV+ K    K A      +       T ++       +  
Sbjct: 375 LTPGQLFLMFLKEK--LEGLLVSIKIAFDKKAQKTNVSMN------TDNLMRIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +++ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
             + +               +      ++   V  L   +EE          L       
Sbjct: 591 PWTEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V   +    +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVTTHQ----ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|4456851|emb|CAB36989.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 400

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 195/435 (44%), Positives = 267/435 (61%), Gaps = 40/435 (9%)

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
            +EAG ++    +E         I     D +N   YI N    D     +  +L  ++V
Sbjct: 1   LVEAGTIMTRSVIE--------SIESHLDDDLNKIVYIPN----DAAVVTEPVVLQKFKV 48

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           + P D                              + +  N +  D VR +   DI+A +
Sbjct: 49  VAPTDPDRV--------------------------VTIIGNANPDDKVRTVTPADILAEM 82

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
              ++L  G G +DDID+LGNRR+R+VGE+L NQ RLGL RMER+++ER+S  D + + P
Sbjct: 83  SYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQVRLGLSRMERNVRERMSVQDNEVLTP 142

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RD
Sbjct: 143 QQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEVRD 202

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLS 618
           VH THYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+
Sbjct: 203 VHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRATGEVTNEIVWLT 262

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE+   +AQANS L+ DG+F E++V  R  G     P   +D++D SPKQVV++A + 
Sbjct: 263 ADEEDEYTVAQANSKLNADGTFAEKVVMGRHQGVNQEYPASSVDYMDVSPKQVVAVATAC 322

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLENDDSNR LMG NMQRQAVPL+  +APFVGTGME   A  SGAA++A+  G V   
Sbjct: 323 IPFLENDDSNRALMGANMQRQAVPLIDPKAPFVGTGMEYQAAHDSGAAVIAQYDGKVTYA 382

Query: 739 DAIRIVIRSVEGDLD 753
           DA ++ +R  +G LD
Sbjct: 383 DADKVEVRREDGSLD 397


>gi|156767131|gb|ABU95080.1| ribosomal polymerase B subunit [Acinetobacter baylyi]
 gi|156767151|gb|ABU95090.1| ribosomal polymerase B subunit [Acinetobacter lwoffii]
 gi|156767153|gb|ABU95091.1| ribosomal polymerase B subunit [Acinetobacter lwoffii]
          Length = 266

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 112/270 (41%), Positives = 162/270 (60%), Gaps = 5/270 (1%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D  +E  I +     R++ +L GQ +  G    K+   LS D++S        +    DE
Sbjct: 1    DLKEEFKIFEEAARERIIRLLKGQESNGGGTT-KRGDKLSEDVLSGLELVDLLEVQPTDE 59

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             +   +  ++V  +     ++++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDK
Sbjct: 60   GIAERLTQIQVFLKEKSYEIDEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDK 119

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MAGRHGNKG+VS ILP EDMP    G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG
Sbjct: 120  MAGRHGNKGVVSNILPVEDMPHDIHGVPVDVVLNPLGVPSRMNVGQILETHLGMAAKGLG 179

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
             KI  ++ + +    +  LR FL+K+    G   E +    D+ +L ++   + GVP++T
Sbjct: 180  DKIDKMMKEQRT---VLELRDFLDKIYNKVGGEQEDLDSLTDEEILVLSGNLRKGVPLAT 236

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYD 1238
            PVFDGA+E  I  +L +  +  +GQ++LYD
Sbjct: 237  PVFDGAEESQIKELLELGGISRTGQTVLYD 266


>gi|157851000|gb|ABV90282.1| RpoB [Mycobacterium avium complex]
          Length = 237

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVI 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D+ G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDDDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|225557526|gb|EEH05812.1| DNA-directed RNA polymerase I [Ajellomyces capsulatus G186AR]
          Length = 1242

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/459 (21%), Positives = 156/459 (33%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G      E     +   L+             S  + +  +
Sbjct: 716  DFNQSPRNMYQCQMSKQAMGTPGASIEYRTDNKLYRLQTGQTPVVRTPLYNSYGLDNFPN 775

Query: 937  GTVVDVRIFNRHGIDKNERSI-------------SVEREQIELLARDKDDEQVILDRNIY 983
            G    V + +  G D ++  I             ++ + +I  L  DK+       R   
Sbjct: 776  GMNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLD-DKESRGRGKARREV 834

Query: 984  SRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            S+L     G            +         ++E      W     D             
Sbjct: 835  SKLFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQT 894

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +     G +      + + V   + R    GDK + RHG KG+ S
Sbjct: 895  HLLKYKDTEEGYIDNVRIF--GSETGGDPCQAISVKFRVPRKPVIGDKFSSRHGQKGVCS 952

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   DI++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 953  QLWPATDMPFSETGIQPDIIINPHAFPSRMTIGMFIESLAGKAGALHGLAQDSTPFRFSE 1012

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                S                                            F G        
Sbjct: 1013 EHTASD-------------------------------------------FFG-------E 1022

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 1023 QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1082

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1083 PVKGRAKGGGIRVGEMERDSLLAHGAAFLLQDRLMNCSD 1121



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 80/678 (11%), Positives = 192/678 (28%), Gaps = 121/678 (17%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   V + +     +           +G +P+M +    
Sbjct: 121 EIYPSECRERHATYRGRLRARLEYRVNNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLSGK 177
                                G F++ G ++++   +   R+ P         +   +  
Sbjct: 171 HLEKCSPEQLVQRKEESEELGGYFIVNGNEKLIRMLIVGRRNFPMAIIRSSFTKRGQT-- 228

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE 226
             Y    I  + + +D +    +++H         R   R+    VPV   L AL   ++
Sbjct: 229 --YTKYGIQIRSVRID-QTSQTNVLHYLSDGNVTFRFSWRKNEYLVPVVMILKALVETND 285

Query: 227 -EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            EI      +       + +        L+   K        DT   + E  + +     
Sbjct: 286 REIFERLVGREGSEGIKNSFVTD-RVELLLRTYKGYKLYGRDDTRAYLGEKFRPVLGMPA 344

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
                          D + G      +V    G            +++ E   ++  ++ 
Sbjct: 345 DIP------------DDMVGAEFLRKVVLPHLG-----------NQNVTESQDNDKFNMI 381

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLD--IYRVMRPGDVSTFSVAESMFNFLFFDS 403
           +  +  +                  ++ LL   +Y ++    +  +  A       +   
Sbjct: 382 LFMIRKLYTLVAGECAPDNPDAVSNQEVLLGGSLYGMLLKERLEEWLRAFGPIARDWSFR 441

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           ++    +      + R   +    +     E+I   ++  +   N   +   +D      
Sbjct: 442 NQNARFS------DPRFEKEFLSRIVSRTNENIGGALEYFLSTGN-LVSPTGLDLQQPSG 494

Query: 464 VRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
              + E +     +   RM    S   ++ +  +  ++P+      PV            
Sbjct: 495 YTVIAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPV------------ 542

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
                   +    + H      +    +  +     + D+  T+   +   E+      G
Sbjct: 543 ---HTPDGSPCGLLNHLAHKCEIATSNLDVSGVPQVISDLGVTYESSVSLDESVAVQLDG 599

Query: 582 LVSSLTSFARVNAYGFIETPYRKV---CDGKVTNDVVYLSAMEEEN----RYIAQANSSL 634
            +    S  +          Y KV       V  ++ Y+              +Q    +
Sbjct: 600 RILGYCSPKQARMISDT-LRYWKVAGNKSLPVELEIGYIPNSNRGQYPGIYIFSQCARMM 658

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKI---------DFIDASPKQVVSIAASLIPFLEND 685
                   + +      E+  +    +           ++  P  ++SI A++ PF + +
Sbjct: 659 RPVKYLPLDKLDYVGPFEQPFMEIACVPSDIMSGISTHVEFDPTHILSIVANMTPFSDFN 718

Query: 686 DSNRVLMGCNMQRQAVPL 703
            S R +  C M +QA+  
Sbjct: 719 QSPRNMYQCQMSKQAMGT 736



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 92/671 (13%), Positives = 197/671 (29%), Gaps = 100/671 (14%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           I     +  D +  E +   E  +  I      +    +  T    K   R D    +  
Sbjct: 276 ILKALVETNDREIFERLVGREGSE-GIKNSFVTDRVELLLRTYKGYKLYGRDDTRAYLGE 334

Query: 380 VMRP-----GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
             RP      D+    V             K  L  +G   +    + D        +  
Sbjct: 335 KFRPVLGMPADIPDDMVGAEFL-------RKVVLPHLGNQNVTESQDND--------KFN 379

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME----------- 483
            I+ +I+ L  L  G+   D+ D + N+ V   G +     +    R+E           
Sbjct: 380 MILFMIRKLYTLVAGECAPDNPDAVSNQEVLLGGSLYGMLLK---ERLEEWLRAFGPIAR 436

Query: 484 ------RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------S 523
                 ++ +      + + +        + +  A+  F  +  L              +
Sbjct: 437 DWSFRNQNARFSDPRFEKEFLSRIVSRTNENIGGALEYFLSTGNLVSPTGLDLQQPSGYT 496

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            + E +N    I+H R    + +G          +R + P  +G +CP  T +G   GL+
Sbjct: 497 VIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLL 553

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL-----DEDG 638
           + L     +       +    V        V Y S++  +     Q +  +      +  
Sbjct: 554 NHLAHKCEIATSNLDVSG---VPQVISDLGVTYESSVSLDESVAVQLDGRILGYCSPKQA 610

Query: 639 SFTEELVFCRCAGEEILVPRE-KIDFIDASPK------QVVSIAASLIPFLENDDSNRVL 691
               + +          +P E +I +I  S +       + S  A ++  ++    +++ 
Sbjct: 611 RMISDTLRYWKVAGNKSLPVELEIGYIPNSNRGQYPGIYIFSQCARMMRPVKYLPLDKLD 670

Query: 692 MGCNMQRQAVPLLKAEAPF---VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                ++  + +    +     + T +E                    Q        +  
Sbjct: 671 YVGPFEQPFMEIACVPSDIMSGISTHVEFDPTHILSIVANMTPFSDFNQSPRNMYQCQMS 730

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           +  +    + ++     K  R        Q P+V+               S  L +   G
Sbjct: 731 KQAMGTPGASIEYRTDNKLYRLQTG----QTPVVR----------TPLYNSYGLDNFPNG 776

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVF----TSIHIEEFEVMARDTKLGPEEITRD 864
            N +VA + + GY+ +D+M+I++                I   +      +         
Sbjct: 777 MNAVVAVLSYTGYDMDDAMIINKSAHDRGFGWGTIYKTKIYSLDDKESRGRGKARREVSK 836

Query: 865 IPNVSEEGLKN------IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           +   +   L        +DE G+  +GA V  G I+    T + +        +      
Sbjct: 837 LFGFAPGSLIKGEWRHALDEDGLPHIGARVTEGSIVAAWHTVRFDPVSNSYTNIDGQTHL 896

Query: 919 EKAVDVRDTSL 929
            K  D  +  +
Sbjct: 897 LKYKDTEEGYI 907


>gi|109104228|ref|XP_001088474.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 isoform 3
            [Macaca mulatta]
          Length = 1135

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 112/558 (20%), Positives = 183/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGIKPGDP--------RILQKL 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 926  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 961

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 962  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 100/673 (14%), Positives = 210/673 (31%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GGCFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQY-------------------RLGLLRMERSIKERISSV 493
            D+ D+L N+ V + G++                        +   + M      RI ++
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 422

Query: 494 DIDSVMPQDL--INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            ID   P +                  +S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQNSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V   V ++         +A   +          E     
Sbjct: 540 TPVDGAPHRPYSECYPVLLDGVM--VGWVDKE------LAPGIADSLRHFKVLREKRIPP 591

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E +L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 592 -WMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDE 650

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
            F G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 651 VFAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRS 707

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 708 DNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G   +   I       L+ +D+ G+  +G
Sbjct: 757 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRILQKLDDDGLPFIG 816

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++     E     +++  S    SG    V    
Sbjct: 817 AKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITM 871

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 872 RVPRNPTIGDKFA 884



 Score = 58.5 bits (140), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 44/138 (31%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEVSVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLHSLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179


>gi|157851025|gb|ABV90294.1| RpoB [Mycobacterium bouchedurhonense]
          Length = 237

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|157851004|gb|ABV90284.1| RpoB [Mycobacterium marseillense]
 gi|167540465|gb|ABZ81927.1| RpoB [Mycobacterium marseillense]
          Length = 237

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.091,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|67810584|gb|AAY81999.1| RNA polymerase II second largest subunit [Chara australis]
          Length = 329

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 83/385 (21%), Positives = 134/385 (34%), Gaps = 66/385 (17%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
            ++ S+ +            IF R   D+  +  S+ RE+ E   ++              
Sbjct: 4    QEDSVIMNQSSIDRGFFRSIFYRSYRDEERKQGSLMREEFEKPDKECTLGLRHGSYAKLD 63

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                +  G           K+       +     S+  +         R+         +
Sbjct: 64   DDGLVFPGLRVSGDDVIIGKTVP-----LPSPSSSEDMEMNSGPGAALRSCSDGGRMGSS 118

Query: 1045 SKSILEDRFKNKIEKIQWGDDMP-------PGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
              S    R  + + +      +           LR VK+ V   R  Q GDK + RHG K
Sbjct: 119  HVSRFHKRDSSTVLRHSENGMIDQVLLTTNDEGLRFVKLRVRSVRVPQIGDKFSSRHGQK 178

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +G++      
Sbjct: 179  GTVGMTYTQEDMPWTCEGITPDIIVNPHAIPSRMTIGQLIECIMGKVATHVGREGD---- 234

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     +
Sbjct: 235  -------------------------------------------------ATP-FTDVTVD 244

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             I+ +L        G  ++Y+G TG      + +G  Y  +L HMV DK+++R  G   L
Sbjct: 245  NISKVLHKCQYQMRGYEVMYNGHTGRRLSAHIFLGPTYYQRLKHMVDDKIHSRGRGPVQL 304

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +T+QP  G+S  GG R GEME  C+
Sbjct: 305  LTRQPAEGRSREGGLRFGEMERDCL 329



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 6/123 (4%)

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLK 874
           GYN EDS+++++  +    F SI    +    R    L  EE  +        +      
Sbjct: 1   GYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEERKQGSLMREEFEKPDKECTLGLRHGSYA 60

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +D+ G++  G  V+  D+++GK  P   SP + E+  + +  G       D      S 
Sbjct: 61  KLDDDGLVFPGLRVSGDDVIIGKTVP-LPSPSSSEDMEMNSGPGAALRSCSDGGRMGSSH 119

Query: 935 VSG 937
           VS 
Sbjct: 120 VSR 122


>gi|32344980|gb|AAM93500.1| RNA polymerase beta subunit [Rickettsia honei]
          Length = 168

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 98/166 (59%), Positives = 127/166 (76%), Gaps = 1/166 (0%)

Query: 23  IIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A LEFV YEF
Sbjct: 3   VADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANLEFVKYEF 62

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           D PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ +YMGD+PLMTK 
Sbjct: 63  DTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQEVYMGDIPLMTKS 122

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP 
Sbjct: 123 GTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPY 168


>gi|110224857|emb|CAJ29745.1| DNA-directed RNA polymerase beta chain [Pseudomonas sp. OX1]
          Length = 284

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 168/284 (59%), Positives = 217/284 (76%)

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG
Sbjct: 1   GSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEG 60

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ 
Sbjct: 61  PNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDK 120

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              T+ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 121 KVLTDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++P  +
Sbjct: 181 RQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEA 240

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD
Sbjct: 241 GVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTD 284


>gi|52694247|emb|CAG30653.1| DNA-directed RNA polymerase beta chain [Pseudomonas indica]
          Length = 314

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 172/293 (58%), Positives = 225/293 (76%), Gaps = 1/293 (0%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 22  EFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 81

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL ++AR N YGF+E+PYR V +G+VT+++V+LSA+EE +  IAQA+++L
Sbjct: 82  PEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGQVTDEIVFLSAIEEADHVIAQASATL 141

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DE+G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG 
Sbjct: 142 DENGRLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGS 201

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAK-SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           NMQRQAVP L+++ P VGTGME  V   + G+A VA+R G+++ VDA RIV+R  + +++
Sbjct: 202 NMQRQAVPTLRSDKPLVGTGMERNVGHVTPGSAWVARRGGVIDSVDASRIVVRVNDDEVE 261

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              +GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R+DI+ADGPSTD+G+  
Sbjct: 262 TGEAGVDIYNLTKYTRSNQNTCINQRPLVQKGDKVSRSDILADGPSTDMGNWR 314


>gi|52694259|emb|CAG30659.1| DNA-directed RNA polymerase beta chain [Pseudomonas corrugata]
          Length = 284

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 166/284 (58%), Positives = 216/284 (76%)

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG
Sbjct: 1   GSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEG 60

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ 
Sbjct: 61  PNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDK 120

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 121 KVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++P  +
Sbjct: 181 RQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVEPGEA 240

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPST+
Sbjct: 241 GVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTN 284


>gi|242777481|ref|XP_002479042.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Talaromyces stipitatus ATCC 10500]
 gi|218722661|gb|EED22079.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Talaromyces stipitatus ATCC 10500]
          Length = 1264

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 91/422 (21%), Positives = 151/422 (35%), Gaps = 73/422 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSIS 958
            G          + AI      D+ D  +   S            +    +  DK+ R   
Sbjct: 777  GLDNFPNGANAVVAILAYTGYDMDDAMVINKSSHERGFGHGTIYKTKFYNLDDKDSRRNK 836

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             +RE  +L               I +     L            K+ + +++        
Sbjct: 837  SKREISKLFG-------FAPGSEIKAEYRATLDEDGLPHPGAKIKEGSYVAA-------- 881

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W     D      +    + +       E+ + + +  +  G++     L+ + V  
Sbjct: 882  ---WYTVRYDAGSDSYINVDGITHFLKYKDAEEGYIDTVRLV--GNENGNEPLQAISVKF 936

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
             + R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + QI E
Sbjct: 937  RVPRRPIIGDKFSSRHGQKGVCSQLWPQIDMPFSESGIQPDLIINPHAFPSRMTIAQIIE 996

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            +  G A    G    S    +      +                                
Sbjct: 997  SMAGKAGALHGHPQDSTPFQFSEENTAA-------------------------------- 1024

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                              +     LR A  +  G   +Y G+TG+ F   + +G ++  +
Sbjct: 1025 ------------------DYFGHQLRKAGYNYHGNEPMYSGITGKEFAADIYLGVVHYQR 1066

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV+DK   R+TG  + VT QP+ G+S  GG R+GEME   + A+G A++LQ+ L   
Sbjct: 1067 LRHMVNDKFQVRTTGPVNSVTGQPVKGRSKGGGIRVGEMERDSLLAHGCAFLLQDRLMNC 1126

Query: 1319 SD 1320
            SD
Sbjct: 1127 SD 1128



 Score = 70.1 bits (170), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 85/629 (13%), Positives = 190/629 (30%), Gaps = 76/629 (12%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A    +++ + E                 +    +  T    K   R DA   + +
Sbjct: 283 MILKALVETNDREIFEGIVGNASTKGPANTFVTDRVELLLRTFKGYKIYSRSDARAYLGK 342

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             RP           +F    +  ++     + ++ +    N +      + + + ++ +
Sbjct: 343 KFRPV----------LFAPATWTHEECGAEFLRKIVLPHLGNQNVTTTQDYDKFKLMLFM 392

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK-------NQYRLGLLRMERS------- 485
           I+ L     G    D+ D + N+ V   G +          ++ L   R+ R        
Sbjct: 393 IRKLYAFVAGDCAADNPDAISNQEVMLGGYVYGMLLKERLEEWLLSFGRLVRDWSYRGGN 452

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNS 531
           +K    S + D +        + +  A+  F  +  L              + + E +N 
Sbjct: 453 LKFTDPSFEKDFIGKVIKRTNENIGGALEYFLSTGNLVSPTGLDMQQASGFTVVAEKINF 512

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
              I H R    + +G          +R + P  +G +CP  T +G   GL++ L     
Sbjct: 513 YRFIAHFR---MVHRGTFFAQLKTTAVRKLLPESWGFMCPVHTPDGSPCGLLNHLAHKCL 569

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC---- 647
           +       +   +V        +   ++ E       Q N  +    S  +  +      
Sbjct: 570 IATSDLDVSHIPRVLAQLG---IKSEASAEVTESVCVQLNGRVVGYCSPKQAKMIHDTLR 626

Query: 648 RCAGEEILVPREKIDFIDA-------SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
               E      ++++            P   +S   + +       +   L       Q 
Sbjct: 627 FWKVEGSHDIPKELEIGYVPTSNGGQYPGIYMSSQPARMYRPVKYLALDKLDYVGPFEQP 686

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
              +      + +G+ S   + +   I++  A +    D  +      +  +   T G  
Sbjct: 687 FMEIACLEEDIRSGL-STHIEFTPTNILSIIANMTPFSDNNQSPRNMYQCQMSKQTMGTP 745

Query: 761 -IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +           Q P+V+               +  L +   G N +VA + + 
Sbjct: 746 GTSFAYRTDNKLYRLQTGQTPIVRP----------PLYNAYGLDNFPNGANAVVAILAYT 795

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV---------SE 870
           GY+ +D+M+I++             +       D      +  R+I  +           
Sbjct: 796 GYDMDDAMVINKSSHERGFGHGTIYKTKFYNLDDKDSRRNKSKREISKLFGFAPGSEIKA 855

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKIT 899
           E    +DE G+   GA++  G  +    T
Sbjct: 856 EYRATLDEDGLPHPGAKIKEGSYVAAWYT 884



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 97/675 (14%), Positives = 194/675 (28%), Gaps = 121/675 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L+  L+  V + +     +           +G +PLM +       
Sbjct: 132 PAECRERHATYRGRLRARLQYQVNNGEWHESVRE----------LGQVPLMLRSNRCHLE 181

Query: 142 ------------------GTFVIKGIQRIVVSQLHRS--------PGIHFDHDKGRASLS 175
                             G F++ G ++     L R         P         +    
Sbjct: 182 SFSPQQLVDHKEESEELGGYFIVNGNEK-----LIRMLIMPKRNFPMAINRPSFQKRGA- 235

Query: 176 GKLLYACRIIPDQGLWMDIEFDSK-------DIIHVRIDRRRK---VPVTSFLMALGMDS 225
           G   +  +I   +    D    +          +  R   R++   VPV   L AL +++
Sbjct: 236 GFTTFGVQI---RSARPDQTTQTNVLHYLSDGNVTFRFSWRKQEYLVPVMMILKAL-VET 291

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +     +  IV +            A+  V  +V   L      +    S  +  + L 
Sbjct: 292 ND--REIFEGIVGNASTKG------PANTFVTDRVELLLRTFKGYKIYSRSDAR--AYLG 341

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           K  +         T +  CG      IV    G   +      D+  L      ++    
Sbjct: 342 KKFRPVLFAPATWTHEE-CGAEFLRKIVLPHLGNQNVTTTQDYDKFKLMLFMIRKLYAF- 399

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +    + +N   I N  V             +Y ++    +  + ++       +     
Sbjct: 400 VAGDCAADNPDAISNQEVMLGG--------YVYGMLLKERLEEWLLSFGRLVRDWSY--- 448

Query: 406 YDLSTVGRVKM-NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
                 G +K  +     D    V     E+I   ++  +   N   +   +D       
Sbjct: 449 ----RGGNLKFTDPSFEKDFIGKVIKRTNENIGGALEYFLSTGN-LVSPTGLDMQQASGF 503

Query: 465 RSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQ 521
             V E +     +   RM    +   ++ +  +  ++P+      PV +         + 
Sbjct: 504 TVVAEKINFYRFIAHFRMVHRGTFFAQLKTTAVRKLLPESWGFMCPVHTPDGSPCGLLNH 563

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HYGRICPAET----- 574
           L+       S   ++H  R+ A        +    E   V       G   P +      
Sbjct: 564 LAHKCLIATSDLDVSHIPRVLAQLGIKSEASAEVTESVCVQLNGRVVGYCSPKQAKMIHD 623

Query: 575 ------SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                  EG +         +   +  G     Y      ++   V YL+  + +  Y+ 
Sbjct: 624 TLRFWKVEGSHDIPKELEIGYVPTSNGGQYPGIYMSSQPARMYRPVKYLALDKLD--YVG 681

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                  E     E++                   I+ +P  ++SI A++ PF +N+ S 
Sbjct: 682 PFEQPFMEIACLEEDIRSGL------------STHIEFTPTNILSIIANMTPFSDNNQSP 729

Query: 689 RVLMGCNMQRQAVPL 703
           R +  C M +Q +  
Sbjct: 730 RNMYQCQMSKQTMGT 744


>gi|148879065|emb|CAM07048.1| RpoB protein [Mycobacterium sp. MG19]
 gi|148879067|emb|CAM07049.1| RpoB protein [Mycobacterium sp. MG20]
          Length = 227

 Score =  289 bits (740), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+          D           
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAANLPDGMHSAPRDSI- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          V+TPVFDGA E  +  +L     +      
Sbjct: 149  ------------------------------VATPVFDGARENELQGLLGSTLPNRDGDVM 178

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 179  VNADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 227


>gi|52538189|emb|CAH19196.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 18]
          Length = 319

 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 224/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 SDDIVFLSAIEEADHVIAQASAAMNEKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDNGSA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRHG 313


>gi|52538187|emb|CAH19195.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 19]
          Length = 318

 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 174/313 (55%), Positives = 224/313 (71%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++D+V+LSA+EE +  IAQA+++++E     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 SDDIVFLSAIEEADHVIAQASAAMNEKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD    
Sbjct: 241 RGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDNGSA 300

Query: 791 NDIIADGPSTDLG 803
                  P    G
Sbjct: 301 WRHHGRRPVHRHG 313


>gi|60218856|gb|AAX14841.1| RpoB [Mycobacterium septicum]
          Length = 241

 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVADGTPEWASRLPDGLHSAP-- 158

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 159  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 193  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 241



 Score = 46.2 bits (108), Expect = 0.037,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|71148461|gb|AAZ28895.1| RpoB [Mycobacterium mucogenicum]
          Length = 238

 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 42   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 147  -----------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVM 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.043,   Method: Composition-based stats.
 Identities = 33/50 (66%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 50


>gi|315435630|gb|ADU18205.1| RNA polymerase beta-subunit [Mycobacterium avium]
          Length = 237

 Score =  289 bits (739), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 30/49 (61%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ++ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   QTELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|148879069|emb|CAM07050.1| RpoB protein [Mycobacterium sp. MHSD2]
          Length = 229

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 130/230 (56%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 137  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 180  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 229


>gi|158954668|gb|ABW84305.1| RNA polymerase subunit B [Mycobacterium chelonae]
 gi|158954670|gb|ABW84306.1| RNA polymerase subunit B [Mycobacterium chelonae]
 gi|158954672|gb|ABW84307.1| RNA polymerase subunit B [Mycobacterium chelonae]
 gi|158954674|gb|ABW84308.1| RNA polymerase subunit B [Mycobacterium chelonae]
 gi|158954676|gb|ABW84309.1| RNA polymerase subunit B [Mycobacterium chelonae]
 gi|158954678|gb|ABW84310.1| RNA polymerase subunit B [Mycobacterium chelonae]
          Length = 238

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 147  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.040,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 50


>gi|55273989|gb|AAV48865.1| RNA polymerase II second largest subunit [Amanita brunnescens]
          Length = 694

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 129/824 (15%), Positives = 243/824 (29%), Gaps = 146/824 (17%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ + +    +              +  + + + +     +             
Sbjct: 1    FRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWGDQKKSMSSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L   A ++   +       + +  + +         EEN + A   + +  +G 
Sbjct: 117  CGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSAVPCTKVFVNGV 168

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR- 698
            +       R     +   ++     D SP+  V             D+ RV     +   
Sbjct: 169  WMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVEN 225

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
            Q + L K    ++  G                + GIVE +DA       +    +   + 
Sbjct: 226  QQLALQKKHVRWLSNGFNEESEDFKWE--HLVKGGIVELLDADEEETVMISMTPEDLENS 283

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                  +    ++       R  +K G            PS  LG       +  + +P+
Sbjct: 284  RLQQSGVDPNVNDGEFDPAAR--LKAGISAHAWTHCEIHPSMILG-------ICASIIPF 334

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N                        ++       +G       I             
Sbjct: 335  PDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM----------- 365

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 366  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 425

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G N    
Sbjct: 426  LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNVTGE 484

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 485  DIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI-------------- 530

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 531  ------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVP 584

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  L      +G +  +                        
Sbjct: 585  DLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-------------------- 624

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  ++     + LR       G+ V                         G +    
Sbjct: 625  -----DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGHT---- 653

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
               G      + +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 654  ---GRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 694



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 87/604 (14%), Positives = 169/604 (27%), Gaps = 101/604 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 10  KDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLN 68

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 69  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAC 128

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA   V     F     +    +  N +  I   RR
Sbjct: 129 ISVGSYSAPVIEFLEEWGLESLEENAHSAVPCTKVFVNGVWMGVHRDPANLVKTIKKLRR 188

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +                ++        P    E   + L      +  ++     E+
Sbjct: 189 KDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVRW--LSNGFNEES 246

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL----- 655
              K         V  L A EEE   I+     L+        +      GE        
Sbjct: 247 EDFKWEHLVKGGIVELLDADEEETVMISMTPEDLENSRLQQSGVDPNVNDGEFDPAARLK 306

Query: 656 --VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             +        +  P  ++ I AS+IPF +++ S R      M +QA+ +          
Sbjct: 307 AGISAHAWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI--- 363

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 364 --------------------------------------RMDTMANILYYPQKPLATTRSM 385

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 386 EYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSS 421

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E            +       +++ G+I  G  V
Sbjct: 422 IDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTNV 481

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DI++GK  P         ++        +    RD S  + S  SG V  V I    
Sbjct: 482 TGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNS 534

Query: 949 GIDK 952
              K
Sbjct: 535 EGQK 538


>gi|62720656|gb|AAX93864.1| RNA polymerase subunit B [Mycobacterium alvei]
          Length = 241

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 158

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 159  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 193  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 241



 Score = 46.2 bits (108), Expect = 0.037,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|295815617|gb|ADG36311.1| RNA polymerase beta-subunit [Mycobacterium intermedium]
          Length = 240

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI           ++         +
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKIDVANGVPDWAANLPE------DL 153

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
              +                           V+TPVFDGA E  +  +L            
Sbjct: 154  YHSEPDAI----------------------VATPVFDGAQEAELQGLLSCTLPNRDNEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.070,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|183579267|gb|ACC63211.1| RpoB [Mycobacterium intracellulare]
          Length = 227

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 136  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 179  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 227


>gi|315435638|gb|ADU18209.1| RNA polymerase beta-subunit [Mycobacterium mucogenicum]
          Length = 237

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 146  -----------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVM 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.076,   Method: Composition-based stats.
 Identities = 32/49 (65%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 49


>gi|52699898|gb|AAU87010.1| DNA-dependent RNA polymerase II second largest subunit [Thamnolia
            subuliformis]
          Length = 716

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 126/833 (15%), Positives = 247/833 (29%), Gaps = 143/833 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G ++   +R+   ++ + + +  +              + +  + + + 
Sbjct: 1    DXXGKKRLDLAGXLMAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     V      E    +    + ++  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      I D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLIRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D+     G  +  + +     +   +   M+            AK  G    
Sbjct: 237  RPLFVIDNDAKSPNKGSLVLTKELVNRLEDDKDLPADMDPDEKA-------AKTMGWDGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +   R V+  ++ + + +   V     +   R  Q               V+        
Sbjct: 290  I--KRGVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYQMPETTDDPNKRVKAPLNPTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N                        ++       +
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQAM 389

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G      D                +  +             +       +   +  + AI
Sbjct: 390  GXXXTNFDERM-----------DTMTNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 438

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R        +E+  +    + +
Sbjct: 439  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRVYTDQEKRVGM---SVVEMFEKPMRSDTL 494

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++             
Sbjct: 495  KLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL------------ 542

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +K    T     E+   +K+             LR VKV +   +  Q GDK A R
Sbjct: 543  ---HIKRDVSTPLRSTENGLVDKVLL-----TTNHEGLRFVKVRMRTTKIPQIGDKFASR 594

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 595  HGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD 654

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                 +TP F  
Sbjct: 655  -----------------------------------------------------ATP-FTE 660

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
               ++++ +LR       G  ++Y+G TG      V +G  Y  +L HMV  K
Sbjct: 661  VTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRHMVDXK 713


>gi|315435602|gb|ADU18191.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-09183]
          Length = 240

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 157

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 158  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 192  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.065,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|157851006|gb|ABV90285.1| RpoB [Mycobacterium timonense]
          Length = 237

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.093,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|295815631|gb|ADG36318.1| RNA polymerase beta-subunit [Mycobacterium europaeum]
          Length = 237

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEGLLHAQPNQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.077,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|303325236|gb|ADM14343.1| RNA polymerase subunit B [Mycobacterium sp. CST-8.2a]
 gi|303325238|gb|ADM14344.1| RNA polymerase subunit B [Mycobacterium sp. CST-8.17]
 gi|315435578|gb|ADU18179.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
 gi|315435590|gb|ADU18185.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
 gi|315435600|gb|ADU18190.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
 gi|315435640|gb|ADU18210.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-10090]
 gi|326694950|gb|AEA03698.1| RNA polymerase B [Mycobacterium sp. CST-7.10]
          Length = 237

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.072,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|295815623|gb|ADG36314.1| RNA polymerase beta-subunit [Mycobacterium parmense]
          Length = 240

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 129/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I           ++       E  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAGGTPDWAANLPEDLLHAESN 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 160  ----------------------------SIVSTPVFDGAKEEELQGLLGSTLPNRDGDVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.068,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|55273985|gb|AAV48863.1| RNA polymerase II second largest subunit [Coprinus comatus]
          Length = 699

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 125/834 (14%), Positives = 242/834 (29%), Gaps = 156/834 (18%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L N +R+   ++ + +    +              +  + + + +     +         
Sbjct: 1    LANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWGDQKKS 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   MSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            EG   GLV +L   + ++   +       + +  + +         EEN + +   + + 
Sbjct: 117  EGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSSTPCTKVF 168

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             +G +       R     +   ++     D SP+  V             D+ RV     
Sbjct: 169  VNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLF 225

Query: 696  MQRQAVPLL------KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            +      LL           +   G E              + G++E +DA       + 
Sbjct: 226  IVENQQLLLQKKHIRWLNNGYNDEGEEYK-------WEQLIKGGVIELLDAEEEETVMIS 278

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
               +   +     +         +   +    +K G            PS  LG      
Sbjct: 279  MTPEDLENSRL--QAAGVDTHANDGEFDPAARLKAGTHAHTWTHCEIHPSMILG------ 330

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N                        ++       +G       I    
Sbjct: 331  -ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM-- 369

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 370  ---------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVI 420

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +   +    I+ R  +D  ++S   + E+ E   R+          +       I
Sbjct: 421  MNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLI 479

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  +  D      R++          ++     +  Q        
Sbjct: 480  APGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI----- 534

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                  + VKV V   R  Q GDK A RHG KG +      EDM
Sbjct: 535  ---------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGITYRQEDM 579

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   DI++NP  +PSRM +G + E  L      +G +  +               
Sbjct: 580  PFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----------- 628

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                           ++     + LR       G+ +                       
Sbjct: 629  --------------DLTVESVSTFLRQKGYQSRGLEIM---------------------- 652

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
              G +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP+
Sbjct: 653  YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPV 699



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 87/604 (14%), Positives = 167/604 (27%), Gaps = 101/604 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 14  KDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLN 72

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 73  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSC 132

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA         F     +    +  N +  I   RR
Sbjct: 133 ISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRR 192

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +            +   ++        P    E  N  L+        +N     E 
Sbjct: 193 KDDISPEVSVVRDIREKELRIYTDAGRVCRPLFIVE--NQQLLLQKKHIRWLNNGYNDEG 250

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL----- 655
              K         +  L A EEE   I+     L+        +      GE        
Sbjct: 251 EEYKWEQLIKGGVIELLDAEEEETVMISMTPEDLENSRLQAAGVDTHANDGEFDPAARLK 310

Query: 656 --VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                      +  P  ++ I AS+IPF +++ S R      M +QA+ +          
Sbjct: 311 AGTHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI--- 367

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 368 --------------------------------------RMDTMANILYYPQKPLATTRSM 389

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 390 EYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSS 425

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E            +       +++ G+I  G  V
Sbjct: 426 IDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLIAPGTGV 485

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DI++GK  P         ++        +    RD S  + S  SG V  V I    
Sbjct: 486 RGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNS 538

Query: 949 GIDK 952
              K
Sbjct: 539 EGQK 542


>gi|110293951|gb|ABG66438.1| RNA polymerase-beta subunit [Staphylococcus caprae]
 gi|110293953|gb|ABG66439.1| RNA polymerase-beta subunit [Staphylococcus caprae]
          Length = 313

 Score =  289 bits (739), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 180/313 (57%), Positives = 231/313 (73%), Gaps = 3/313 (0%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+C
Sbjct: 1   ASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIA 628
           P ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +A
Sbjct: 61  PIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVA 120

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSN
Sbjct: 121 QANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 180

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS- 747
           R LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI AK  G VE V++  +++R  
Sbjct: 181 RALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEVLVRRL 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           VE +       +D Y L KF+RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++AL
Sbjct: 241 VEENGTEHEGELDRYPLAKFKRSNSGTCYNQRPIVSVGDVVEYNEILADGPSMELGEMAL 300

Query: 808 GRNMLVAFMPWHG 820
           GRN++V FM W G
Sbjct: 301 GRNVVVGFMTWDG 313


>gi|110224855|emb|CAJ29744.1| DNA-directed RNA polymerase beta chain [Pseudomonas thivervalensis]
          Length = 284

 Score =  288 bits (738), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 166/284 (58%), Positives = 215/284 (75%)

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG
Sbjct: 1   GSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEG 60

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ 
Sbjct: 61  PNIGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDK 120

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 121 KVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +
Sbjct: 181 RQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEA 240

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+ADGPSTD
Sbjct: 241 GVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIMADGPSTD 284


>gi|148879063|emb|CAM07047.1| RpoB protein [Mycobacterium llatzerense]
          Length = 229

 Score =  288 bits (738), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 97/231 (41%), Positives = 129/231 (55%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 136  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS++
Sbjct: 179  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSMI 229


>gi|32344974|gb|AAM93497.1| RNA polymerase beta subunit [Rickettsia montanensis]
 gi|32344976|gb|AAM93498.1| RNA polymerase beta subunit [Rickettsia massiliae MTU5]
 gi|32344978|gb|AAM93499.1| RNA polymerase beta subunit [Rickettsia sp. Bar29]
 gi|32344986|gb|AAM93503.1| RNA polymerase beta subunit [Rickettsia conorii]
 gi|32344988|gb|AAM93504.1| RNA polymerase beta subunit [Rickettsia conorii]
          Length = 168

 Score =  288 bits (738), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 98/166 (59%), Positives = 128/166 (77%), Gaps = 1/166 (0%)

Query: 23  IIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A LEFV YEF
Sbjct: 3   VADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANLEFVKYEF 62

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           D PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ +YMGD+PLMTK+
Sbjct: 63  DTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQEVYMGDIPLMTKN 122

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP 
Sbjct: 123 GTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPY 168


>gi|309319933|pdb|3LTI|A Chain A, Crystal Structure Of The Escherichia Coli Rna Polymerase
           Beta Subunit Beta2-Betai4 Domains
          Length = 296

 Score =  288 bits (738), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 110/295 (37%), Positives = 162/295 (54%), Gaps = 3/295 (1%)

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
           SPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD KD + VRIDRRRK+P T  L 
Sbjct: 5   SPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILR 64

Query: 220 ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           AL   +E+IL  F+ K+++  R +     L    L  G   S  +     G   +E G++
Sbjct: 65  ALNYTTEQILDLFFEKVIFEIRDNKLQXELVPERL-RGETASFDIE--ANGXVYVEXGRR 121

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +T+  ++ L++  VK + +  + + G  VA D ++  TGE+   A   +    L  +  S
Sbjct: 122 ITARHIRQLEKDDVKLIEVPVEYIAGXVVAXDYIDESTGELICAANXELSLDLLAXLSQS 181

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
             + I  L+ + +++  YI  TL  D   DR  AL++IYR  RPG+  T   AES+F  L
Sbjct: 182 GHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRXXRPGEPPTREAAESLFENL 241

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
           FF  D+YDLS VGR   N  L  +  +    +  +DII +   L+D+RNG G +D
Sbjct: 242 FFSEDRYDLSAVGRXXFNRSLLREEIEGSGILSXDDIIDVXXXLIDIRNGXGEVD 296


>gi|185179202|gb|ACC77614.1| RpoB [Mycobacterium gordonae]
          Length = 229

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 97/230 (42%), Positives = 132/230 (57%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 137  -----------------LPEDLRHAQPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            ++  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS+
Sbjct: 180  VNGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSM 229


>gi|185179192|gb|ACC77609.1| RpoB [Mycobacterium abscessus]
          Length = 223

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 128/230 (55%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 26   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 130

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 131  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 173

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 174  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 223


>gi|51035523|emb|CAH10897.1| RNA polymerase B subunit [Haloferax denitrificans]
          Length = 435

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 104/428 (24%), Positives = 161/428 (37%), Gaps = 78/428 (18%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     V    +    F R    +  R    + 
Sbjct: 51   GFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQE 109

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 110  DRFEIPSQD-------VRGARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEP 162

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
               A    + +R         E+         + +               ++ KV V  +
Sbjct: 163  DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLAKVSVRDQ 210

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF  DG   D+VLNP  +PSRM V        
Sbjct: 211  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV-------- 262

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG K+ +L                                              
Sbjct: 263  GHVLEMLGGKVGALEGRRVDGT-------------------------------------- 284

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     F G +EE + S L       SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 285  --------AFQGENEEELRSALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYH 336

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MVS+K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD 
Sbjct: 337  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSD- 395

Query: 1322 VVGRTRVY 1329
               + +VY
Sbjct: 396  ---KEKVY 400



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLMHYPQLSMVK----------TQTTEQIGFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        E+   ++DE 
Sbjct: 76  ALVMNKGSVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETVVDENSVLLGKTSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    ++   EL  +
Sbjct: 189 DTVTLMEGEDGSKLAKVSVRDQRVPELGDK 218


>gi|32344994|gb|AAM93507.1| RNA polymerase beta subunit [Rickettsia typhi str. Wilmington]
          Length = 168

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 99/166 (59%), Positives = 128/166 (77%), Gaps = 1/166 (0%)

Query: 23  IIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A LEFV YEF
Sbjct: 3   VADIPNLIEIQKNSYERNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANLEFVKYEF 62

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           D PK+DVD+C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ +YMGD+PLMTK+
Sbjct: 63  DTPKYDVDECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQEVYMGDIPLMTKN 122

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP 
Sbjct: 123 GTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPY 168


>gi|149639737|ref|XP_001515678.1| PREDICTED: similar to RNA polymerase I polypeptide B [Ornithorhynchus
            anatinus]
          Length = 1146

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 87/328 (26%), Positives = 132/328 (40%), Gaps = 76/328 (23%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G+D   G  + + + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ 
Sbjct: 867  GNDTGNGKFKCICITMRIPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILF 926

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM +G + E+  G +    G    +    +                       
Sbjct: 927  NPHGFPSRMTIGMLIESMAGKSAALHGVCHDATPFTFSEENSAL---------------- 970

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                              +   +ML+ A  +  G   LY G++G
Sbjct: 971  ----------------------------------DYFGNMLKSAGYNFYGTEKLYSGISG 996

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
               +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   +
Sbjct: 997  LELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPVGGRNVQGGIRFGEMERDAL 1056

Query: 1303 QAYGAAYVLQEMLTIKSD----DV---VG-----------------RTRVYESIVA--GN 1336
             A+G +++L + L   SD     V    G                 R R Y   V    +
Sbjct: 1057 LAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTVCRQSD 1116

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLE 1364
                   P  F   V E+ A+ + + L+
Sbjct: 1117 TIETVSVPYVFRYFVAELAAMNIKVTLD 1144



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 83/614 (13%), Positives = 189/614 (30%), Gaps = 85/614 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +N++ +N +        ++      +V+           
Sbjct: 264 LKALVGFSDHQIFQELIKGREDNSFYKNCVSQMLRMVMEEGCTTQKQVLN--------YL 315

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       + Y         +N  + +         +   +  + + L     G+  
Sbjct: 316 GERFRIKLNLPEWYRNEQAAEFLLNQCICIH--LKSNTEKFYMLCLMTRKLFAFAKGECM 373

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRL---GLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            +  D+L N+ V + G++     +      L   +   ++ +     S+  ++L+    +
Sbjct: 374 EESSDSLMNQEVLTPGQLFLMFLKEKLEAWLVSVKIAFDKRAQKTNISLNSENLMKVFSM 433

Query: 510 VSAVCEFFCS------------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +   F                      L  + + +N +  ++H R    + +G    
Sbjct: 434 GLDLTRPFEYLLATGSLRSKTGLGMLQDVGLCVVADKLNFIRYLSHFR---CVHRGAAFA 490

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ +T+   +                   
Sbjct: 491 KMRTTSVRRLLPESWGFLCPVHTPDGEPCGLMNHMTAVCEIVTQVAYTPTLPALLCSLGI 550

Query: 593 -NAYGFIETPYR----KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
               G    PYR     V DG V   V          + +A   +    +     E    
Sbjct: 551 TPVDGAPSQPYRDCYPVVLDGVVMGWVE---------KDLAPGIADSLRNFKVLGEKKIP 601

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
               E +L+P      +        +    + P    D      +G   Q      +  +
Sbjct: 602 P-WMEVVLIPMTGKPSLYPGLFLFTTPCRMIRPVRNLDLGKEEFIGTLEQTFMNIAIFED 660

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLM 765
               G      +   S  ++VA     +   D  +      +  +   T G  ++ YR  
Sbjct: 661 EIVPGITTHQELFPHSMLSVVA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLNTYRER 717

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
              +        Q PLV+                 ++ +  +G N +VA + + GY+ ED
Sbjct: 718 SDNKLY-RLHSPQSPLVRPYMY----------DYYEMDNYPIGTNAVVAVISYTGYDMED 766

Query: 826 SMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           +M++++          +++  E   ++   K G + +   +          +D+ G+  +
Sbjct: 767 AMIVNKSSWERGFAHGTVYKTERVDLSDKIKQGDDCLVFGVKPGDSRVAHKLDDDGLPYI 826

Query: 885 GAEVNPGDILVGKI 898
           GA +  GD     +
Sbjct: 827 GAVLQYGDPFYSYV 840



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 113/817 (13%), Positives = 222/817 (27%), Gaps = 156/817 (19%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPP-----------KFDVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP           K    +C  R  TY 
Sbjct: 63  EGLSQAVQAILPFEFAFRDERITLAIVDAVISPPMVPKGSICKELKVFPAECRGRRSTYR 122

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +QS  +G +P+M K                   
Sbjct: 123 GKLTADISWAVNGIP--------KGIIKQS--LGYVPIMVKSKLCNLYDLPPKALIEHHE 172

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQ---- 188
                 G F++ GI++ ++  L    R+  I     K ++   G   +   +   +    
Sbjct: 173 EPEEMGGYFIVNGIEK-IIRMLIMPRRNFPIALIRPKWKSRGPGYTHFGVSMHCVRDEHT 231

Query: 189 -----------GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-GMDSEEILSTFYPKI 236
                      G  M      K++          +P+   L AL G    +I   F   I
Sbjct: 232 AINMNLHYLENGTVMVNFIYQKELFF--------LPLGFALKALVGFSDHQI---FQELI 280

Query: 237 VYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL 296
              +   F+   +S    M                 V+E G      +L  L E+    L
Sbjct: 281 KGREDNSFYKNCVSQMLRM-----------------VMEEGCTTQKQVLNYLGERFRIKL 323

Query: 297 GITS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHS 339
            +          + L    +   + +           T +++  A     E+S + + + 
Sbjct: 324 NLPEWYRNEQAAEFLLNQCICIHLKSNTEKFYMLCLMTRKLFAFAKGECMEESSDSLMNQ 383

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           E+     L++  +          +       K A     +               +F  +
Sbjct: 384 EVLTPGQLFLMFLKEK-------LEAWLVSVKIAFDKRAQKTNIS--LNSENLMKVF-SM 433

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
             D  +     +    +  +  L    DV      D +  I+ L   R     +      
Sbjct: 434 GLDLTRPFEYLLATGSLRSKTGLGMLQDVGLCVVADKLNFIRYLSHFR----CVHRGAAF 489

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              R  SV  +L   +                  +   +M       + V          
Sbjct: 490 AKMRTTSVRRLLPESWGFLC-------PVHTPDGEPCGLMNHMTAVCEIVTQVAYTPTLP 542

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           + L  L       +     R    +   GV         +D+ P     +   +      
Sbjct: 543 ALLCSLGITPVDGAPSQPYRDCYPVVLDGVVMGWV---EKDLAPGIADSLRNFKVLGEKK 599

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I     +               +      ++   V  L   +EE  +I     +      
Sbjct: 600 IPPWMEVVLIPMTGKPSLYPGLFLFTTPCRMIRPVRNLDLGKEE--FIGTLEQTFMNIAI 657

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F +E+V                   +  P  ++S+ A+ IPF +++ S R +  C M +Q
Sbjct: 658 FEDEIVPG------------ITTHQELFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQ 705

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV----IRSVEGDLDPS 755
            +        +       +    S  + + +             +    + +V       
Sbjct: 706 TMG--FPLNTYRERSDNKLYRLHSPQSPLVRPYMYDYYEMDNYPIGTNAVVAVISYTGYD 763

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                I     ++R   +  V +   V + D++++ D
Sbjct: 764 MEDAMIVNKSSWERGFAHGTVYKTERVDLSDKIKQGD 800


>gi|157004959|gb|ABV00682.1| RpoB [Mycobacterium avium subsp. silvaticum]
 gi|157004961|gb|ABV00683.1| RpoB [Mycobacterium avium subsp. paratuberculosis]
 gi|157004963|gb|ABV00684.1| RpoB [Mycobacterium avium subsp. avium ATCC 25291]
 gi|157004971|gb|ABV00688.1| RpoB [Mycobacterium avium subsp. hominissuis]
          Length = 237

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|319998253|gb|ADV91598.1| RNA polymerase B subunit [Mycobacterium conspicuum]
          Length = 240

 Score =  288 bits (738), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 99/231 (42%), Positives = 133/231 (57%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWATNLPK----------- 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                                +      G+ VSTPVFDGA EE +  +L            
Sbjct: 150  -------------------ELQSAEPDGI-VSTPVFDGAKEEELQGLLSCTLPNRDGEVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++
Sbjct: 190  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMI 240



 Score = 45.8 bits (107), Expect = 0.047,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|113871077|gb|ABI37012.1| RNA polymerase beta subunit [Mycobacterium haemophilum]
          Length = 232

 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 33   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 92

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI       +   ++       E  
Sbjct: 93   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKIDVAGGMPEWAANLPAELLHAE-- 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 150  --------------------------PNQIVSTPVFDGAKEEELQGLLSSTLPNRDGDVM 183

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 184  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 232


>gi|51035527|emb|CAH10899.1| RNA polymerase B subunit [Halogeometricum borinquense]
          Length = 435

 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 100/419 (23%), Positives = 153/419 (36%), Gaps = 74/419 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +    A+   +  ++ D  L +  G     +    F R    +  R    + 
Sbjct: 51   GFDERPAAQNFTVAVMSYEGFNIEDA-LVMNKGSVDRAMARSHFFRTYEGEERRYPGGQE 109

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 110  DRFEVPSQD-------VRGARGEDAYNHLDDDGLVNPETVVDENSVLLGKTSPPRFLEEP 162

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                    + +R         E          + +               ++ KV V  +
Sbjct: 163  DDMGGLSPQKRRETSVTMRSGENGVVDTVTLMEGE------------DGSKLAKVSVRDQ 210

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF  DG   D+V+NP  +PSRM V        
Sbjct: 211  RIPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVINPHALPSRMTV-------- 262

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG K+ +L                                              
Sbjct: 263  GHVLEMLGGKVGALEGRRVDGT-------------------------------------- 284

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     F G DE  +   L       SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 285  --------AFQGEDESELRGALEEHGFKSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYH 336

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            MVS+K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD
Sbjct: 337  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSD 395



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 72/209 (34%), Gaps = 21/209 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N  VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDERPAAQNFTVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECG 880
           ++++++  V   +  S     +E   R    G E+              E+   ++D+ G
Sbjct: 76  ALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEDRFEVPSQDVRGARGEDAYNHLDDDG 135

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++     V+   +L+GK +P               + G      R+TS+ + SG +G V 
Sbjct: 136 LVNPETVVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGENGVVD 189

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLAR 969
            V +       K  +    ++   EL  +
Sbjct: 190 TVTLMEGEDGSKLAKVSVRDQRIPELGDK 218


>gi|157004965|gb|ABV00685.1| RpoB [Mycobacterium chimaera]
 gi|315435576|gb|ADU18178.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|315435580|gb|ADU18180.1| RNA polymerase beta-subunit [Mycobacterium chimaera]
 gi|315435582|gb|ADU18181.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
          Length = 237

 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.091,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|269912582|emb|CAY86071.1| RNA polymerase beta subunit [Gluconacetobacter johannae]
          Length = 299

 Score =  288 bits (737), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 146/301 (48%), Positives = 192/301 (63%), Gaps = 28/301 (9%)

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
           SPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L 
Sbjct: 1   SPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLY 60

Query: 220 AL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
           AL                         GMD++EIL+ FY K+V+ +    W  P  A   
Sbjct: 61  ALEGEASAAARAAKLAEGGDVDALDIQGMDADEILNYFYGKVVFVKTSKGWARPFDAE-S 119

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
             G K+   L+D +TGE V E+  KLT+ +++ + EK  K + + +  L G YVA D+VN
Sbjct: 120 FRGLKLLEPLIDAETGEVVAEADAKLTARMVRKIAEK-TKDVLVGAAGLIGRYVAYDLVN 178

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
            +TGEIY EAG+ + E  LE +  + +  +P L +D+ N   +IRNTL  DKN  R DAL
Sbjct: 179 PDTGEIYAEAGEELTEARLEALEEAGLDRLPTLAIDASN-GPWIRNTLTVDKNTTRDDAL 237

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
            DIYRVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD PD VR +RKE
Sbjct: 238 TDIYRVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLDAPDTVRVLRKE 297

Query: 435 D 435
           D
Sbjct: 298 D 298


>gi|157004969|gb|ABV00687.1| RpoB [Mycobacterium colombiense]
          Length = 237

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.085,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|62720670|gb|AAX93871.1| RNA polymerase subunit B [Mycobacterium novocastrense]
          Length = 238

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 135/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +   A              
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKINGSPDWASA-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                             + +   + + G  VSTPVFDGA E  +  +L            
Sbjct: 147  -----------------LPKELLESEPGSIVSTPVFDGAREAELQGLLGSTLPNRDGETL 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +DE G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238


>gi|221763244|gb|ABX25845.2| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 233

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 98/230 (42%), Positives = 130/230 (56%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 233



 Score = 40.8 bits (94), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|183579283|gb|ACC63219.1| RpoB [Mycobacterium chelonae]
          Length = 227

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 227


>gi|302693869|ref|XP_003036613.1| hypothetical protein SCHCODRAFT_80314 [Schizophyllum commune H4-8]
 gi|300110310|gb|EFJ01711.1| hypothetical protein SCHCODRAFT_80314 [Schizophyllum commune H4-8]
          Length = 1226

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 89/453 (19%), Positives = 152/453 (33%), Gaps = 65/453 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR---AIFGEKAVDVRDTSLRVPS 933
            D         +   G   +G  +         +   L+   +     A+         P+
Sbjct: 706  DFNQSPRNIYQCQMGKQTMGTPSTAINHRTDNKLYRLQTGQSPIVRPALHNTYAMDAFPN 765

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQI------ELLARDKDDEQVILDRNIYSRLM 987
            G +  V  +        D    + S            +    D  D++     +    L 
Sbjct: 766  GTNAIVAVISYTGYDMEDAMILNKSAHERGFGYGTVYKSAIIDLKDQKGATKSSSAPTLH 825

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
              L      +G K    +  +  D +         +    D       +           
Sbjct: 826  FGLGKDIRRTGDKAHACTEFVGEDGLPLVG----VKLTAGDPMAAFINDVTGRTQFQKYK 881

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E  + +++  +  G D     L+ ++V + + R    GDK + RHG KG+ S+  P  
Sbjct: 882  GDETAYVDQVRLL--GGDNGDTELQKIQVTLRITRSPVIGDKFSSRHGQKGVCSQKWPAV 939

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF + G   D+++NP   PSRM +G + E+  G A    G    +    +        
Sbjct: 940  DMPFSESGMQPDVIINPHAFPSRMTIGMLVESMAGKAGAMHGLAQDATPFKFSEEDTA-- 997

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                             +     L  A 
Sbjct: 998  ------------------------------------------------VDYFGKQLLAAG 1009

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
             +  G   +Y G+TG+ F   + +G +Y  +L HMV DK   R+TG    +T+QP+ G+ 
Sbjct: 1010 YNYYGNEPMYSGITGQEFAADIYLGVVYYQRLRHMVLDKFQVRTTGQVDPLTRQPVKGRK 1069

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              GG RLGEME   + A+G +++LQ+ L   SD
Sbjct: 1070 RGGGIRLGEMERDALIAHGTSFLLQDRLMNCSD 1102



 Score = 53.5 bits (127), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 93/675 (13%), Positives = 181/675 (26%), Gaps = 128/675 (18%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +   R  +Y   + +    I +          +K+        G +P+M +    
Sbjct: 124 KIFPTEARERLTSYRGRMTMK---ICWTDSHGNKNDMVKEC-------GLVPIMVRSVRC 173

Query: 142 ---------------------GTFVIKGIQRIV-----------VSQL-----HRSPGIH 164
                                G FVI G +R++           +S L     +R P  +
Sbjct: 174 NLRGMSSAQLVAHREEAEEFGGYFVINGNERLIRYLILPRRNHVISLLRPSFANRGPS-Y 232

Query: 165 FDHDK-------GRASLSGKLLYACRIIPD-QGLWMDIEFDSKDIIHVRIDRRRKVPVTS 216
             H          + S++  L Y    +   +  W   E       +V       +P+  
Sbjct: 233 TPHAVQIRCVRPDQTSVTNTLHYLSNGMAMLRFSWRKQE-------YV-------IPIML 278

Query: 217 FLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
            L AL G   +EI              DF    L+  D +     S     + TG Q +E
Sbjct: 279 ILKALVGASDKEIFE-------GVVMQDFENTFLT--DRVELLLRSFKAYTMRTGNQCLE 329

Query: 276 ---SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG---ETGEIYIEAGDVID 329
                 ++   L +      V    +    L  L    +  N       ++Y        
Sbjct: 330 YLGDRFRVVLNLPEDWTNLAVGTWLVNKMVLVHLPTPREKYNMLLFMLRKLYALVSGECC 389

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
             + +   H E+     LY         I+       N         I   +R G V  F
Sbjct: 390 ADNPDSPQHQEVLLPGTLY------GMIIKERCEEVLNG----IRAGIMSDVRNGVVVDF 439

Query: 390 SVAESMFNFLFFDSDKYDLST-VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
           +     +         +D+   +        L   T  D++      I+A         +
Sbjct: 440 NDKR--YMTKVMSKVSFDIGAKLSNFLATGNLVSPTGLDLQQASGFTIVAEKLNWQRYIS 497

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               I         +  +V ++L   +                      ++       + 
Sbjct: 498 HFRCIHRGAFFAELKTTTVRKLLPEAWGFLC-------PVHTPDGSPCGLLNHLSRTCRI 550

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
             + +      + L+          RI     +     G V         + +       
Sbjct: 551 TTTPLIVAHIPALLAAHGMTQPFAGRINGRTNICVQLDGRVIGWARPAVAQQLANN---- 606

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +   +T   H + +   +      +  G     +      +    V YL           
Sbjct: 607 LRIWKTEGMHEVPMDLEIG-LVLESKGGQYPGLFLFSSRSRFMRPVKYLPNGR------- 658

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                  +D   + E V+   A     +       ++ +P   +SI A++ PF + + S 
Sbjct: 659 -------DDQVGSFEQVYMNIACLPEEIEPGVTSHVEHNPTNFLSILANMTPFSDFNQSP 711

Query: 689 RVLMGCNMQRQAVPL 703
           R +  C M +Q +  
Sbjct: 712 RNIYQCQMGKQTMGT 726


>gi|126722433|dbj|BAF48630.1| DNA-dependent RNA polymerase subunit B' [Haloferax sp. BV2]
          Length = 435

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 102/438 (23%), Positives = 159/438 (36%), Gaps = 74/438 (16%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +        +        G       +  + A+   +  ++ D  +     V    +  
Sbjct: 32   HLMHYPQLSMVKTQYPEQIGFDERPAAQNFVVALMSYEGFNIEDALVMNKGSVE-RALAR 90

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
              F R    +  R    + ++ E+ ++D       +           L     V+     
Sbjct: 91   SHFFRTYEGEERRYPGGQEDRFEIPSQD-------VRGARGEDAYSHLDEDGLVNPETVV 143

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             +++VL           +    A    + +R         E+         + +      
Sbjct: 144  DENSVLLGKTSPPRFLEEPDDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------ 197

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                     ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF  DG   D+VL
Sbjct: 198  ------DGSKLAKVSVRDQRVPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVL 251

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM V        G     LG K+ +L                           
Sbjct: 252  NPHALPSRMTV--------GHVLEMLGGKVGALEGRRVDGT------------------- 284

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                        F G +EE + S L       SG+ ++Y G+TG
Sbjct: 285  ---------------------------AFQGENEEELRSALEERGFMSSGKEVMYSGVTG 317

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E  +  + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG RLGEME   +
Sbjct: 318  EKIEAEIFVGIIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTV 377

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
              +GAA VLQE L   SD
Sbjct: 378  IGHGAAMVLQERLLDSSD 395



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLMHYPQLSMVK----------TQYPEQIGFDERPAAQNFVVALMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        E+   ++DE 
Sbjct: 76  ALVMNKGSVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETVVDENSVLLGKTSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    ++   EL  +
Sbjct: 189 DTVTLMEGEDGSKLAKVSVRDQRVPELGDK 218


>gi|52694357|emb|CAG38018.1| RNA polymerase beta subunit [Pseudomonas syringae]
          Length = 328

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 186/330 (56%), Positives = 243/330 (73%), Gaps = 8/330 (2%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
             + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R
Sbjct: 1   MAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT
Sbjct: 61  ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVT 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASPKQ 670
            ++V+LSA+EE +  IAQA++++++     +ELV  R         R+  +  +D SPKQ
Sbjct: 121 EEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLKRNSPSRRQADVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES----VVAKSSGAA 726
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P    G        VA+ SG  
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPA---GRYWPWSANVARDSGVC 237

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD
Sbjct: 238 VVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD 297

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            V+R+DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 298 RVQRSDIMADGPSTDMGELALGQNMRIAFM 327


>gi|169247685|gb|ACA51676.1| RpoB [Mycobacterium kansasii]
          Length = 226

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 30   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 89

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 90   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 148  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 177

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 178  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 226


>gi|315435604|gb|ADU18192.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-09045]
          Length = 237

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 135/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +   A              
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKINGSPDWASA-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                             + +   + + G  VSTPVFDGA E  +  +L            
Sbjct: 146  -----------------LPKELLESEPGSIVSTPVFDGAREAELQGLLGSTLPNRDGETL 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +DE G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.073,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|295815611|gb|ADG36308.1| RNA polymerase beta-subunit [Mycobacterium florentinum]
          Length = 237

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEGLRHAQPDQTVSTPVFDGAKEEELQGLLACTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.073,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|158954690|gb|ABW84316.1| RNA polymerase subunit B [Mycobacterium chitae]
 gi|158954692|gb|ABW84317.1| RNA polymerase subunit B [Mycobacterium confluentis]
          Length = 241

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 95/229 (41%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +               
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDVAAGVPEWA------------- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--RMAD------ 1227
                           + +        +    +TPVFDGA E  +  +L   +A+      
Sbjct: 148  ---------------EGLPEDLRSAPADTKTATPVFDGAQEGELQGLLGSTLANRDGEVM 192

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 193  VNSDGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 241



 Score = 46.6 bits (109), Expect = 0.033,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|62720660|gb|AAX93866.1| RNA polymerase subunit B [Mycobacterium moriokaense]
          Length = 238

 Score =  288 bits (737), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 133/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G KI+   +                  
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWAAKA-GWKIEGNPDWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +     + +    VSTPVFDGA EE +  +L            
Sbjct: 147  -----------------LPEEMHEVEPNTIVSTPVFDGAREEELQGLLSSTLSNRDGDTL 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKAQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 45.8 bits (107), Expect = 0.046,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|169247687|gb|ACA51677.1| RpoB [Mycobacterium gordonae]
 gi|185179200|gb|ACC77613.1| RpoB [Mycobacterium gordonae]
          Length = 232

 Score =  288 bits (736), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 96/231 (41%), Positives = 131/231 (56%), Gaps = 40/231 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 34   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 93

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 94   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 138

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--- 1232
                             +            VSTPVFDGA EE +  +L     +  G   
Sbjct: 139  -----------------LPEDLRHAAPNQIVSTPVFDGAXEEELQGLLSCTLPNRDGDVM 181

Query: 1233 -----QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                 +++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS++
Sbjct: 182  VNGDXKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMI 232


>gi|295815633|gb|ADG36319.1| RNA polymerase beta-subunit [Mycobacterium genavense]
          Length = 237

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEGLRHAQPDQTVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.068,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|115383157|gb|ABI96799.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383159|gb|ABI96800.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383161|gb|ABI96801.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383165|gb|ABI96803.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383167|gb|ABI96804.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383169|gb|ABI96805.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|115383171|gb|ABI96806.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|154278271|gb|ABS72372.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 227

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 227


>gi|295815621|gb|ADG36313.1| RNA polymerase beta-subunit [Mycobacterium palustre]
          Length = 240

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G K+ +                     
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKVDT--------------------- 138

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                      +    + +L           VSTPVFDGA E  +  +L     +      
Sbjct: 139  ---EGGVPDWASKLPEELLHAEPNAI----VSTPVFDGAQEAELQGLLSATLPNRDGDVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.066,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|326915056|ref|XP_003203837.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase I subunit
            RPA2-like [Meleagris gallopavo]
          Length = 1048

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 98/465 (21%), Positives = 154/465 (33%), Gaps = 58/465 (12%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E     I +V    +   D         +   G   +G      +     +  LL  
Sbjct: 570  THQELFPHSILSVVANLIPFSDHNQSPRNMYQCQMGKQTMGFPVYNYKDRSDNKLYLLHT 629

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                           + S   GT   V + +  G D  +  I  +       A     + 
Sbjct: 630  PQSPLVRPRMYDYYGMDSYPVGTNSVVAVISYSGYDMEDAMIVNKSSWERGFAYGSVIKM 689

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
              +D ++ +             G    K    L +D +                      
Sbjct: 690  ESIDLSLKASRGGDNLVFGIRPGDPNIK--EKLDADGLPFVGSILQPGDPFYSYMNLNTG 747

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E+  V Y+  +  + D  K         +D   G  +   + V + R    GDK A RHG
Sbjct: 748  ETFTVYYQNKEVGIVDNIK------LCSNDRGTGKFKKACITVRVPRNPTVGDKFASRHG 801

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KGI+S++ P EDMPF ++G   DI+ NP G PSRM +G + E+  G +    G    + 
Sbjct: 802  QKGILSQLWPVEDMPFTENGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGAYYDAT 861

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
               +                                                        
Sbjct: 862  PFTFTEKNSALKY----------------------------------------------- 874

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                   L  A  +  G   +Y G++G   +  + VG +Y  +L HMVSDK   R+TG  
Sbjct: 875  ---FGETLVSAGYNFFGTEKMYSGISGVELEADIFVGVVYYQRLRHMVSDKFQVRTTGPR 931

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              VT QP+ G++  GG R GEME   + A+G +++L + L   SD
Sbjct: 932  DSVTNQPVKGRNVEGGIRFGEMERDALLAHGTSFLLHDRLFSCSD 976



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 34/90 (37%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C     TY   L + +   +  + +         IK Q +  G +P+M K       
Sbjct: 13  PAECRGXRSTYRGRLTVDISWSLNGIPQ-------GSIK-QPV--GYIPIMVKSKLCNLY 62

Query: 142 ------------------GTFVIKGIQRIV 153
                             G F+I G+++++
Sbjct: 63  NLSPQELIQHHEEEEEMGGYFIINGLEKVI 92


>gi|45545347|gb|AAS67521.1| DNA-dependent RNA polymerase II second largest subunit [Sphaerophorus
            globosus]
          Length = 903

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 130/864 (15%), Positives = 261/864 (30%), Gaps = 142/864 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+  +DD D+ G +R+   G +L   +R+   
Sbjct: 159  HISQSEGTETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFN 218

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ + + +  +    +         + +  + + +     +               +SQ+
Sbjct: 219  KLTKDVYKYLQRCVENNKEFNLTLAVKSTTLTNGLKYSLATGNWGDQKKAASSKAGVSQV 278

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 279  LNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 334

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +       +  +   L++      ++      +  D +    
Sbjct: 335  LALMCYITVGTPSEPIIDFMVQRGMDLLEEYEPLNSPNATKIFVNGVWVGVHRDPAHLVS 394

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAV 701
             V        +      + D  D   K          P F+ ++D      G  +  +  
Sbjct: 395  TVQNLRRRGHLSHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSNNCGNLVLTKDH 454

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
                 E   +G  M++   +          ++G+VE VDA       +    +       
Sbjct: 455  IAKLEEDKEMGMSMDAQEREDKLMGWTGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQ 514

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            I         N +  +N+R    +             PS  LG       +  + +P+  
Sbjct: 515  IQAGYTMPEQNPDD-LNKRVKAPLNQTSHTWTHCEIHPSMILG-------ICASIIPFPD 566

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +   + +  ++                                
Sbjct: 567  HNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------------------DT 597

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 598  MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 657

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R        +E   +    + + L    Y +L +   +  G     
Sbjct: 658  -RSLFYRSYTDQEKRVGM---SVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSG 713

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  +S D      R++          ++     +  Q   S            
Sbjct: 714  EDIIIGKTAPISPDAEELGQRTKQHTKRDTSTPLRSTENGIVDQVLLS------------ 761

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 762  --------TNSDGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVV 813

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +                          
Sbjct: 814  PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------ 849

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  I+Y
Sbjct: 850  -----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEIMY 879

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNH 1261
            +G TG+     V +G  Y  +L H
Sbjct: 880  NGHTGQKLRAQVFLGPTYYQRLRH 903



 Score =  155 bits (392), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 124/850 (14%), Positives = 252/850 (29%), Gaps = 154/850 (18%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR- 205
            ++++++Q  RS          + + S    Y   I    ++G  +      K  ++ + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKAQSNTP-YVAEIRSAVERGSRLISGMQIK--LYEKG 54

Query: 206 ------IDRRRK---------VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
                   +  K         +P+     ALG+   E+IL+        +Q  +     +
Sbjct: 55  EGSKGGFGQTIKCTLPYIKTEIPIAIVFRALGIVSDEDILNHICYDRKDTQMLEMLKPCI 114

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD-------C 302
             A ++   +V+   +      Q +   K++     + + +K +      S+        
Sbjct: 115 EEAFVIQDREVALDFIGKRGNSQGVTRDKRI--KYARDIMQKELLPHISQSEGTETRKAF 172

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNT 361
             G  V   ++    G   ++  D   +K L+           +L+   + +   Y++  
Sbjct: 173 FLGYMV-HRLLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQRC 231

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
           +  +K  +   A+             T  +  S+    + D  K   S  G  ++  R  
Sbjct: 232 VENNKEFNLTLAV--------KSTTLTNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYT 283

Query: 422 LDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             +      R          I     L N   G +   +    +    V  +    Y   
Sbjct: 284 FASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITV 343

Query: 479 LLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
               E  I    +     ++   P +  NA  +      F     +    +  + +S + 
Sbjct: 344 GTPSEPIIDFMVQRGMDLLEEYEPLNSPNATKI------FVNGVWVGVHRDPAHLVSTVQ 397

Query: 537 HTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
           + RR   L  +  + R     E        R   P       P   + G+ +     +  
Sbjct: 398 NLRRRGHLSHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSNNCGNLVLTKDHIAK 457

Query: 589 FARVNAYGF------IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                  G        E           +  V Y+ A EEE   I      L+       
Sbjct: 458 LEEDKEMGMSMDAQEREDKLMGWTGLVKSGVVEYVDAEEEETIMIVMTPEDLEISKQIQA 517

Query: 643 ELVFCRCAGEEILVP--------REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                    +++                  +  P  ++ I AS+IPF +++ S R     
Sbjct: 518 GYTMPEQNPDDLNKRVKAPLNQTSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 577

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+                                          V  +       
Sbjct: 578 AMGKQAMG-----------------------------------------VFLTNYDQRMD 596

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y               Q+PL                      +L  G+N +VA
Sbjct: 597 TMANILYYP--------------QKPL----------ATTRSMEFLKFRELPAGQNAIVA 632

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVS 869
              + GYN EDS+++++  +   +F S+    +    +   +   E     +  D   + 
Sbjct: 633 IACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRVGMSVVEQFEKPMRSDTLKLK 692

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ GI+  G  V+  DI++GK  P      +P+ + L     +     RDTS 
Sbjct: 693 HGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPI-----SPDAEELGQRTKQH--TKRDTST 745

Query: 930 RVPSGVSGTV 939
            + S  +G V
Sbjct: 746 PLRSTENGIV 755


>gi|158954702|gb|ABW84322.1| RNA polymerase subunit B [Mycobacterium simiae]
          Length = 238

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +  +               
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPDWAQN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +       +    VSTPVFDGA EE +  +L     +      
Sbjct: 147  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGLLGSTLPNRDGDVM 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 190  VDADGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.045,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|295815627|gb|ADG36316.1| RNA polymerase beta-subunit [Mycobacterium stomatepiae]
          Length = 237

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGTPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEGLRHAQPDQTVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|156098891|ref|XP_001615461.1| DNA-directed RNA polymerase, beta subunit [Plasmodium vivax SaI-1]
 gi|148804335|gb|EDL45734.1| DNA-directed RNA polymerase, beta subunit, putative [Plasmodium
            vivax]
          Length = 1562

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 100/403 (24%), Positives = 155/403 (38%), Gaps = 29/403 (7%)

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            D  I N+   ++      + + +I  L ++    +  L  N+      +    N  +G  
Sbjct: 1081 DALIINKSSAERGIFRTHIYKTEIIDLEKNHGRGEFTLGNNVRYTNSSVGSNANGANGNN 1140

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
              K +     + + +              +VQ+ +  L   Y       E     K +  
Sbjct: 1141 SGKSNLKFQYEHMGKMLNKDGL------PRVQQKIVELNPLYSYINKANELTVYEKFKGH 1194

Query: 1061 QWGD-----DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                     +      ++  V +   RP   GDK A RHG KG+VSR+ P EDMPF + G
Sbjct: 1195 GEYYVDCVTNYKSTRNQIAIVRLRTTRPPLVGDKFASRHGQKGVVSRLFPHEDMPFSESG 1254

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG--------DISP 1167
               D++ NP G+PSRM +G + E+  G A    GK+I +                 D   
Sbjct: 1255 IVPDVIFNPHGIPSRMTIGMLIESICGKAACIYGKRIDATPFRKYTQQRSFDNEWIDNCG 1314

Query: 1168 LRSFL--EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA--------DEE 1217
            ++ FL  +     G   E         V R  ++ K   P        A          +
Sbjct: 1315 VKGFLEGKNRGNNGGKKEGEKSSSAHDVNRSHKRKKKSDPPKGETQKNAKANITYDEKID 1374

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                +L     D  G  +LY G+ G P    +  G IY  +L HM  DK   R TG    
Sbjct: 1375 YFAKLLLNKGYDYYGTELLYSGIYGVPLQAHIFFGVIYYQRLRHMAYDKAQVRRTGPICN 1434

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +T QPL GK   GG RLGEME   + ++G ++++ E   + SD
Sbjct: 1435 LTHQPLKGKKKHGGIRLGEMERDGLISHGCSFIINERFLLNSD 1477


>gi|31442390|ref|NP_852647.1| RNA polymerase beta chain [Eimeria tenella strain Penn State]
 gi|74810522|sp|Q7YN57|RPOB_EIMTE RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|31322482|gb|AAO40248.1| RNA polymerase B [Eimeria tenella]
          Length = 1059

 Score =  288 bits (736), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 127/581 (21%), Positives = 227/581 (39%), Gaps = 60/581 (10%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G       + + +N     +  +  N  +S  +  +   E +   +++  ++++ RD   
Sbjct: 529  GAKMQSQIVPILKNKRSIIITGYEKNLLNSTNLILKAYQEGI--VVYVSSYKIIIRDL-Y 585

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
              +                +     +  G  +  G IL         S       LL + 
Sbjct: 586  NRKITYFLDKYKRSNHFTILHSKPNVWQGERIFCGQILTSTQD-ILFSEYIGGNNLLVSY 644

Query: 917  FGEKAVDVRDTSLRVPS---GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                  +  D  +           T +  +++       N+ S  +    I L  +    
Sbjct: 645  GNFFGYNFEDAIVLNKKIIYSQLFTSLHFKVYEIIFNSLNKFSFEI--STINLPKKSFYS 702

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            ++ +    I     ++L     VS          +++  IS  P           E    
Sbjct: 703  KRNLDFFGIIKEGSKVLNNDILVSKI-------FITNINISLLPLYNLIYILFGKEIKNI 755

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              +S+ V +  S  I++    +   KI+       G     +V++  +R +  GDK+ GR
Sbjct: 756  KDKSILVSFGNSGRIVKTELFSYSSKIKSY----LGYYLKCRVYICKQRLLSVGDKLCGR 811

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            +GNKGI++ ILP  D+P+   G   DI+ + LG+PSRMN+GQ+FE   G +C  L K++ 
Sbjct: 812  YGNKGIIAYILPSNDLPYTNTGIIPDIISDSLGIPSRMNIGQLFENLFGLSCYFLNKRLC 871

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                       I  +       I   S    I +                          
Sbjct: 872  ISNTFNLPKVYIKTILYNYINNIKEKSGNLWIYNSY------------------------ 907

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                              G+ +L DG  G     P  +G     KL HM+ DK++ R+ G
Sbjct: 908  ----------------SPGKILLRDGRQGYKLSEPSFLGISKYSKLIHMIKDKIHYRTIG 951

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV 1333
             Y+ + QQP+ G++ +GGQR GEME+W I+AYG++Y L+E+L  KSDD++ RT +  ++ 
Sbjct: 952  PYTELMQQPVKGRNKKGGQRFGEMEIWAIEAYGSSYNLRELLNYKSDDIIARTSLLSNLD 1011

Query: 1334 AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKM 1374
                     T ESF  L++E+ ++ L+I+  +S  +   K+
Sbjct: 1012 NNIILDNITTTESFRTLIREIHSMNLNIEAFSSIDQLEGKI 1052



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 163/742 (21%), Positives = 307/742 (41%), Gaps = 29/742 (3%)

Query: 228 ILS--TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           ILS   F+     +          ++  L+       +L +          G+     + 
Sbjct: 54  ILSDFLFFKTTNLTSNITDTVQEFNSKILIFLPLKIKNLKNNKYKIIYYLLGEIPKYTIE 113

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE-IFHSEIRDI 344
           K+L   G+K   I+      + +  +        I        D+  +   +  ++   I
Sbjct: 114 KNLIINGLKKTFISKLMFNYIGIFFNKFIKNNNNILYAKIIFNDKFIINIVLEENKCYCI 173

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS---------TFSVAESM 395
              Y   +    Y+    + D     +       + +     S               S 
Sbjct: 174 FNNYKYDLICFLYLLGISMQDIFIFSRYNKSFYLKKLLLTLPSLNINNIINYNIFKYLSF 233

Query: 396 FNFLFFDSDKYDL-STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
           F  L F  + Y + + V     ++   +    +  ++   D I I+ IL+D++  K  I 
Sbjct: 234 FFNLSFKLNTYYIFNKVLNKNNSLYSYIKNFSNSNNLIALDFINILDILLDIKYNKKNIT 293

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSA 512
           D+D L  R + ++G    NQY   L +    +         +++            +   
Sbjct: 294 DLDLLEYRSIFTLGNYFTNQYSFYLKKFSNILHNDIFKCIKNLEKYKLNTNSFKSKLYFN 353

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + E+   + L Q  E +NS S I H  R++       ++ +  +++R+++    G +C  
Sbjct: 354 LKEYLTVNPLVQYLEQINSFSEIIHKNRVTNYN----SKLKQNLQIRNINLNQLGSLCLI 409

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           +T+EG N GLV S T   ++      + PY  V + K  N + ++++  ++   +   N 
Sbjct: 410 DTTEGINCGLVISFTKNIKIEKRNNFQFPYLPVLNIKTKNFITFINSFLQQTYIVLFNNY 469

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L ++  F    +         L      + I   P  + S A +LIPF+  +D  RVLM
Sbjct: 470 YLRKNKLFNFFNLSLNKN-SFKLKNISIQNMIYIKPMDMFSFAENLIPFIFYNDPARVLM 528

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G  MQ Q VP+LK +   + TG E  +  S+   + A + GIV  V + +I+IR +    
Sbjct: 529 GAKMQSQIVPILKNKRSIIITGYEKNLLNSTNLILKAYQEGIVVYVSSYKIIIRDLYNRK 588

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                    Y L K++RSN  T ++ +P V  G+ +    I+         +   G N+L
Sbjct: 589 I-------TYFLDKYKRSNHFTILHSKPNVWQGERIFCGQILTSTQDILFSEYIGGNNLL 641

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-TKLGPEEITRDIPNVSEE 871
           V++  + GYNFED+++++++++   +FTS+H + +E++     K   E  T ++P  S  
Sbjct: 642 VSYGNFFGYNFEDAIVLNKKIIYSQLFTSLHFKVYEIIFNSLNKFSFEISTINLPKKSFY 701

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKI-TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
             +N+D  GII  G++V   DILV KI        + P   L+  +FG++  +++D S+ 
Sbjct: 702 SKRNLDFFGIIKEGSKVLNNDILVSKIFITNINISLLPLYNLIYILFGKEIKNIKDKSIL 761

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           V  G SG +V   +F+     K
Sbjct: 762 VSFGNSGRIVKTELFSYSSKIK 783


>gi|260946741|ref|XP_002617668.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
 gi|238849522|gb|EEQ38986.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
          Length = 1232

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 92/470 (19%), Positives = 159/470 (33%), Gaps = 55/470 (11%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +     E    +I ++        D         +   G   +G            + 
Sbjct: 720  EENVHTHVEFAPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALVHRSDNKL 779

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              L+                + +  +G    V + +  G D ++  I  +          
Sbjct: 780  YRLQTGQTPIVKANLYDDYGMDNFPNGMNAVVAVISYTGYDMDDAMIINKSADERGFGYG 839

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
               +   +D ++  R  + +       G    +        L  +       +    D  
Sbjct: 840  TVYKVEKVDLSLSRRRGDPITQHF---GFGSDEWPETWKEKLDDDGLPLIGVKVEEGDPI 896

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V    E+L      +    E  +  +++ +   DD      + + +   + R    GDK 
Sbjct: 897  VAYFDETLGKTKIKTYHSSEPAYIEEVKLLA--DDTGDSECQQITIKYRVTRAPLIGDKF 954

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG+ SR  P  DMP+ + G   D+++NP   PSRM +G   E+  G A    G 
Sbjct: 955  SSRHGQKGVCSRKWPTVDMPYSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGI 1014

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               S    +  +                                             TP 
Sbjct: 1015 AQDSTPWKFSEDD--------------------------------------------TPA 1030

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                  +     L++A  +  G   +Y G+TGE     + +G +Y  +L HMV+DK   R
Sbjct: 1031 ------DFFGEQLKLAGYNYHGNEPMYSGVTGEELRADIYIGVVYYQRLRHMVNDKFQVR 1084

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            STG  + +T QP+ G+   GG R+GEME   +  +G AY+LQ+ L   SD
Sbjct: 1085 STGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTAYLLQDRLLNSSD 1134



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/96 (17%), Positives = 29/96 (30%), Gaps = 39/96 (40%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L + +   V D +E +  +    +          P+M K       
Sbjct: 168 PSECRERMSTYRGKLLMKVVWSVNDGEEVSEVRDGGQV----------PIMLKSNRCHLE 217

Query: 142 ------------------GTFVIKGIQRIVVSQLHR 159
                             G F++ GI++     L R
Sbjct: 218 KLSPDELVAQKEESDELGGYFIVNGIEK-----LVR 248


>gi|326694962|gb|AEA03704.1| RNA polymerase B [Mycobacterium sp. ASCr-1.2]
          Length = 237

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLRHAQPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.077,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|254566671|ref|XP_002490446.1| RNA polymerase I subunit A135 [Pichia pastoris GS115]
 gi|238030242|emb|CAY68165.1| RNA polymerase I subunit A135 [Pichia pastoris GS115]
 gi|328350840|emb|CCA37240.1| DNA-directed RNA polymerase I subunit A2 [Pichia pastoris CBS 7435]
          Length = 1165

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 78/279 (27%), Positives = 116/279 (41%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQ-WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +T            IE+++   DD+    L++V +   + R  Q GDK + RHG KG+ S
Sbjct: 841  KTKVKTYHSSEPAYIEEVKLISDDLGDSELQMVTIKYRITRQPQIGDKFSSRHGQKGVCS 900

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 901  RKWPQIDMPFTETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWKFNE 960

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +                                             TP       +    
Sbjct: 961  DD--------------------------------------------TPA------DFFGE 970

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L  A  +  G   +Y G+TGE     + +G +Y  +L HMV+DK   RSTG  + +T Q
Sbjct: 971  QLISAGYNYHGNEPMYSGVTGEELRADIYIGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQ 1030

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG R+GEME   +  +G A++LQ+ L   SD
Sbjct: 1031 PVKGRKRNGGIRIGEMERDALIGHGTAFLLQDRLLNCSD 1069



 Score = 75.1 bits (183), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 81/593 (13%), Positives = 182/593 (30%), Gaps = 67/593 (11%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  + +        DR + LL  Y+   +     +   + +          D  D
Sbjct: 264 DREIFDGIVGSETSNSFLTDRLELLLRNYKHYKLVSKQETLAYLGDKFRVVFNATPDVSD 323

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  VG+  +   + +  PD+    +   ++ +I+ L  L +G    D+ D   ++ V   
Sbjct: 324 VD-VGKEVLRRIVLVHLPDNRD--KFRLLLFMIRKLYALVSGDCCPDNPDATQHQEVLLG 380

Query: 468 GEMLKNQYRLGLLRMERSIKERI----------SSVDIDSVMPQDLINAKPVVSAVCEFF 517
           G +     +  +     SI+ +I          +  +   +        + +   +  F 
Sbjct: 381 GFLYGMIIKEKIEEYLASIRLQIQTDINRGYPVNFDEPKYMSRVFQRINENIGKKLQYFL 440

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 441 STGNLVSQTGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLP 497

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ L    +++      +   KV      +     +A  + 
Sbjct: 498 ESWGFLCPVHTPDGSPCGLLNHLAHKCKISTEESDVSKVPKVLSKLGVSANHVFAAGPQM 557

Query: 624 NRYIAQANSSLDEDGSFTEELVF----CRCAGEEILVPREKIDFIDASPKQ-------VV 672
                Q +  +    +  +  +          E        ++     P          +
Sbjct: 558 CCV--QLDGKIVGWCTHEQAKIVADTLRFWKVEGGHGIPLDLEVGHVPPSSRGQYPGLYL 615

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
               + +                   QA   +      + + + S   + S   I++  A
Sbjct: 616 FGGRARMTRPVRYLPLDKEDIIGPFEQAYINIAVTPEEIESNVHS-HVEFSPTNILSILA 674

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    D  +      +  +   T G   +  + +           Q P+VK        
Sbjct: 675 NLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALVHRSDNKLYRLQTGQTPIVKANLYDDYG 734

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                     + +   G N +VA + + GY+ +D+M+I++               ++V  
Sbjct: 735 ----------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSSDERGFGYGT---MYKVEV 781

Query: 852 RDTKLGPEEITRDIPNVSEEG-------LKNIDECGIICVGAEVNPGDILVGK 897
            D      +      +             +N+DE G+  +G  VN GD +V  
Sbjct: 782 IDLADSRRKGDPITQHFGFGTDEWPESWKQNLDEDGLPAIGTLVNEGDPIVAY 834


>gi|158954666|gb|ABW84304.1| RNA polymerase subunit B [Mycobacterium immunogenum]
 gi|158954682|gb|ABW84312.1| RNA polymerase subunit B [Mycobacterium bolletii]
 gi|158954686|gb|ABW84314.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|158954688|gb|ABW84315.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|193093814|gb|ABW84313.1| RNA polymerase subunit B [Mycobacterium massiliense]
          Length = 238

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 147  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.043,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 50


>gi|32344990|gb|AAM93505.1| RNA polymerase beta subunit [Rickettsia aeschlimannii]
 gi|32344992|gb|AAM93506.1| RNA polymerase beta subunit [Rickettsia helvetica]
          Length = 168

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 97/166 (58%), Positives = 127/166 (76%), Gaps = 1/166 (0%)

Query: 23  IIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           + DIP+LI +QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A LEFV YEF
Sbjct: 3   VADIPNLIAIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANLEFVKYEF 62

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           D PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ +YMGD+PLMTK+
Sbjct: 63  DTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQEVYMGDIPLMTKN 122

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP 
Sbjct: 123 GTFIINGTERVVVSQMHRSPGVFFYHDEGKIHSSGKLLYSARVIPY 168


>gi|318602917|emb|CBJ04561.1| RNA polymerase beta subunit [Pseudomonas sp. R-37067]
 gi|318602936|emb|CBJ04564.1| RNA polymerase beta subunit [Pseudomonas sp. R-37092]
          Length = 288

 Score =  288 bits (736), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 169/287 (58%), Positives = 222/287 (77%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR 
Sbjct: 2   SEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYART 61

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E
Sbjct: 62  NQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNE 121

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VG
Sbjct: 122 FTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVG 181

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQ
Sbjct: 182 TGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQ 241

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           NTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+
Sbjct: 242 NTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWN 288


>gi|52538183|emb|CAH19193.1| RNA polymerase beta-subunit [Pseudomonas sp. Lineda 16]
          Length = 360

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 175/352 (49%), Positives = 230/352 (65%), Gaps = 12/352 (3%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           ++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 SDDIVFLSAIEEADHVIAQASAAMNDKKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA 
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAP 240

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
             G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD    
Sbjct: 241 PGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGD---- 296

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                       G   + R          G      +   ER+    +   +
Sbjct: 297 ----NGSAWRHHGRRPVHRYGRAG----SGSEHAHRVHGVERLQLRRLHLPV 340


>gi|47209534|emb|CAF89806.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1071

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 115/597 (19%), Positives = 190/597 (31%), Gaps = 95/597 (15%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +T    +   +N+ +      G   +  M +           + H               
Sbjct: 541  TTPCRMMRPVQNLTLGKQELIGTFEQLYMNVGVFAAEVQAGVTTH--------------Q 586

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E     + +V    +   D         +   G+   G +    ++   P          
Sbjct: 587  ELFPHSMLSVVANFIPYSDHNQSPRNMYQCQMGECRDGSVDGGKQTMGFPLHTFADRSDN 646

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
            +        S  V   +          +         S +    +  ++      E+   
Sbjct: 647  KLYRLQTPQSPLVRPSMYDHYSLDNYPSGTNAVVAVISYTGYDMEDAMIVNKASWERGFA 706

Query: 979  DRNIYSRLMEIL--CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
              +IY   +  L    +   S   G         D +               +     V+
Sbjct: 707  HGSIYKTEVVDLAERVKGDDSVVFGTTPGDPRVEDKLDADGLPHIGSVLRYGDPFYSYVD 766

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                Q   S    ++       K+   D    G  + V +   + R    GDK A RHG 
Sbjct: 767  LNTGQSSVSYYRSQEACVVDNIKVCSNDS-GAGRFKHVCITTRVPRNPTIGDKFASRHGQ 825

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KGI+SR+ P EDMPF + G   DI+ NP G PSRM +G + E+  G +    G    +  
Sbjct: 826  KGILSRLWPAEDMPFTESGMCPDILFNPHGFPSRMTIGMLIESMAGKSGALHGLSHDATP 885

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
              +                                                    D +  
Sbjct: 886  FTFSE--------------------------------------------------DTSAL 895

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            E    MLR    +  G   LY GL+G+  +  + +G +Y  +L HMVSDK   R+TG+  
Sbjct: 896  EYFGEMLRAGGYNYYGTERLYSGLSGQELEADIFIGVVYYQRLRHMVSDKFQVRTTGARD 955

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVG---- 1324
             VT QP+GG++ +GG R GEME   + A+G++++L + L   SD        D  G    
Sbjct: 956  KVTNQPVGGRNVQGGIRFGEMERDALLAHGSSFLLHDRLFNCSDRSVAQVCVD-CGSLLS 1014

Query: 1325 -------------RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                         R R    ++ G  +       P  F   V E+ A+ + + LE  
Sbjct: 1015 PLLEKPPPYWSATRHRKTVCMLCGRSDSIASLSVPYVFRYFVAELAAMNIKVKLEVK 1071



 Score = 63.2 bits (152), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 36/112 (32%), Gaps = 37/112 (33%)

Query: 69  SGAAMLEFVSYEFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
           +    + FV      P           K    +C  R  +Y   L   +   V  V    
Sbjct: 3   NDKISITFVEATILKPMVAKGTVCSQLKVYPAECRGRRCSYKGKLVADISWSVNGVPRG- 61

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKD----------------GTFVIKGIQRIV 153
                  I +Q+  +G LP+M K                 G F++ GI++++
Sbjct: 62  -------IIKQT--LGHLPIMVKSQLCNLRGLTPTQLEMGGYFIVNGIEKVI 104


>gi|195997459|ref|XP_002108598.1| hypothetical protein TRIADDRAFT_51662 [Trichoplax adhaerens]
 gi|190589374|gb|EDV29396.1| hypothetical protein TRIADDRAFT_51662 [Trichoplax adhaerens]
          Length = 780

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 90/435 (20%), Positives = 152/435 (34%), Gaps = 61/435 (14%)

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            AEV     L         + +TP     ++        +   ++  P        D +++
Sbjct: 332  AEVTTHQELSPCSMLSALARLTPFSDFNQSPRNMYQCQMGKQTMGTPIQSFKYRSDNKLY 391

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
               G D  +  I  +       A        I    + +   +   G        G   S
Sbjct: 392  RIQGYDMEDAMILNKSSVERGFA-----HATIYKSEVINLNSKTADGLEIFGQTPGTTDS 446

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
              +  D + +                    + +   Y   +  + D  K        G D
Sbjct: 447  DNIDLDGLPKIGSILNSGDPYYCTLNLSTSQCVVHYYRGQEQGIVDDVK------LLGSD 500

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 L+ + V   ++R    GDK + RHG KG+ S++ P E+MPF + G   DI+ NP 
Sbjct: 501  SGRKPLQRICVKFRIERNPIIGDKFSSRHGQKGVCSQLWPIENMPFTESGMTPDILFNPH 560

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM +G + E+  G +    G    +    +                          
Sbjct: 561  GFPSRMTIGMMIESMAGKSASLHGLCHDATPFQFSEKVSA-------------------- 600

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                           +     L  A  +  G   +YDG++GE F
Sbjct: 601  ------------------------------VDYFGKYLEKAGYNYFGTERMYDGMSGEEF 630

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  + +G +Y  +L HM+SDK   R+TG    +T+QP+ G+   GG R GEME   + ++
Sbjct: 631  EANIFIGTVYYQRLRHMISDKFQVRTTGPIDSLTRQPVQGRKRAGGVRFGEMERDALISH 690

Query: 1306 GAAYVLQEMLTIKSD 1320
            G +++LQ+ L   SD
Sbjct: 691  GTSFLLQDRLLNCSD 705



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 75/506 (14%), Positives = 160/506 (31%), Gaps = 72/506 (14%)

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK---- 472
           N+R  +    D    +   +I +I+ L  + NG+  I+  D+  N+ +   G M      
Sbjct: 8   NLRNCIAVHLDRNEDKFNLLIYMIRKLYAVANGECQIESQDSPMNQEILLGGHMYSMVLK 67

Query: 473 ---NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS------ 523
                +   +  +      + +   +++ + +   N   + + +  F  +  L       
Sbjct: 68  EKLELWLSRVKNLILKYMAKTNDEKLENAIVRAANNGTNIPNQLEYFLATGNLVARADLG 127

Query: 524 --------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                    + + +N +  ++H R   ++ +G          +R + P  +G +CP  T 
Sbjct: 128 LMQVAGYVLVADRLNFMRFVSHFR---SVHRGSFFTEMRTTAVRKLLPEAWGFLCPVHTP 184

Query: 576 EGHNIGLVSSLTSFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           +G   GL++ L +  +V     +    + T Y           + Y SA           
Sbjct: 185 DGAPCGLLNHLAASCKVVTKMSDTTKLVSTLYELGMLSLSDPLIEYSSAH---------- 234

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID-ASPKQVVSIAASLIPFLENDDSNR 689
              +  DG     +           +   KI+ +D   P   +++    I  L  +    
Sbjct: 235 --VVILDGKIVGYIQKEIGKEIADKLRYLKINNMDMVDPSTEIALVHDGISGL-YNGLYL 291

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                 M R    L   +   +GT             I A+ A          +      
Sbjct: 292 FTSPARMIRPVTNLRLQKQEMIGTF----EQVFMDICITAEEAYA-------EVTTHQEL 340

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                 ++   +     F +S +N    Q     +G  ++     +D     +       
Sbjct: 341 SPCSMLSALARLTPFSDFNQSPRNMYQCQMGKQTMGTPIQSFKYRSDNKLYRI------- 393

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
                     GY+ ED+M++++  V      +   +   +          EI    P  +
Sbjct: 394 ---------QGYDMEDAMILNKSSVERGFAHATIYKSEVINLNSKTADGLEIFGQTPGTT 444

Query: 870 EEGLKNIDECGIICVGAEVNPGDILV 895
           +    NID  G+  +G+ +N GD   
Sbjct: 445 DS--DNIDLDGLPKIGSILNSGDPYY 468


>gi|46019144|emb|CAE52036.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 159

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 65/181 (35%), Positives = 109/181 (60%), Gaps = 22/181 (12%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   
Sbjct: 1   RRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLS 50

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MG
Sbjct: 51  LEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMG 101

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++
Sbjct: 102 DFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLE 158

Query: 194 I 194
            
Sbjct: 159 Y 159


>gi|324502024|gb|ADY40894.1| DNA-directed RNA polymerase I subunit RPA2 [Ascaris suum]
          Length = 1163

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 101/254 (39%), Gaps = 54/254 (21%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            +   ++R    GDK A RHG KGI S + P E MPF + G   DI+ NP G PSRM +G 
Sbjct: 883  IQWRIQRNPIIGDKFASRHGQKGINSFLWPAESMPFSESGMMPDIIFNPHGFPSRMTIGM 942

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E+  G A    G    +    +                                    
Sbjct: 943  MIESMAGKAAAMHGAYYDASPFVFNEKKTA------------------------------ 972

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                                 +    +L +A  +  G   +Y G+ G   +  +  G +Y
Sbjct: 973  --------------------IDHFGRLLTLAGYNYYGNETMYSGVDGREMEVQIFFGIVY 1012

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM++DK   RSTG    VT QP+ G+   GG R GEME   + A+GA++ LQ+ L
Sbjct: 1013 YQRLRHMIADKFQVRSTGPIDPVTHQPVKGRKKGGGIRFGEMERDAMIAHGASFSLQDRL 1072

Query: 1316 TIKSD----DVVGR 1325
               SD     V  R
Sbjct: 1073 FNSSDKDLAHVCAR 1086



 Score = 68.6 bits (166), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 34/98 (34%)

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
             D  K    +C  R +TY  PLK ++ + +  V                  +G++P+M 
Sbjct: 99  SIDAMKIYPSECRQRGMTYRAPLKASIEIRINGVRAECCEAI----------LGEVPVML 148

Query: 140 ------------------------KDGTFVIKGIQRIV 153
                                   K G F++KG ++++
Sbjct: 149 MSSRCHLKGLSRSQLVARGEEATEKGGYFIVKGSEKVI 186


>gi|45545341|gb|AAS67518.1| DNA-dependent RNA polymerase II second largest subunit [Peltigera
            membranacea]
          Length = 895

 Score =  287 bits (735), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 154/1011 (15%), Positives = 302/1011 (29%), Gaps = 166/1011 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S +   L  KG    G          +     +   G ++   G V DE  L
Sbjct: 28   VEKGSRLISSMQIKLFAKGENHKG-GFGQTVKATLPYVKTDVPIGIVFRGLGIVSDEDIL 86

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A++         +DR+ AL  I        +S      
Sbjct: 87   NHICYDRNDTQMLEKLKPCIEEAFV--------IQDREVALDWIGSRGNSQSLSRPKRV- 137

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                       KY    + +  +      D  +  +      +  ++  ++    G+  +
Sbjct: 138  -----------KYARDIMQKELLPHISQTDGSETKK---AFFLGYMVHRMLQCALGRREV 183

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + + +  +    +         + +  + +
Sbjct: 184  DDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTTLTN 243

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 244  GLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 299

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + ++  +   
Sbjct: 300  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPCEPIIDFMNQRNMEMLEEYEP 359

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L +      ++      +  D +     V     G  I      + D  D   K      
Sbjct: 360  LRSPNATKVFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAG 419

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAG 733
                P F+ ++D+  +  G  +  +       E      GM+    ++           G
Sbjct: 420  RVCRPLFVIDNDTRSMNYGNLVLTKEHITRLEEDKEAAIGMDRDELEARQMGWDGLVNQG 479

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE VDA       +        +   I +L K    N     N+R         +    
Sbjct: 480  VVEYVDAEEEETVMIVMTPGDLETSRQI-QLGKAVPENAEDEPNKRVNAMSHRSAQTWTH 538

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   + +  ++     
Sbjct: 539  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM-- 587

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 588  -------------------------DTMANILYYPQKPMATTRSMEFLKFRELPAGQNAI 622

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    
Sbjct: 623  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRT 678

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  +  D      R++          
Sbjct: 679  DTLRLKHGTYEKLDDDGIVAPGVRVSGEDMIIGKTAPIPPDSEELGQRTKMHIKRDASTP 738

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            ++     +  Q                             LR VKV +   +  Q GDK 
Sbjct: 739  LRSTENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKF 778

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 779  ASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGF 838

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +                                                       +TP 
Sbjct: 839  EGD-----------------------------------------------------ATP- 844

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            F     ++++ +LR       G  ++Y+  TG+     V +G  Y  +L H
Sbjct: 845  FTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895



 Score =  138 bits (347), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 105/784 (13%), Positives = 223/784 (28%), Gaps = 146/784 (18%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +V+ D    VP+      LG+   E+IL+        +Q  +     +  A ++   +V+
Sbjct: 63  YVKTD----VPIGIVFRGLGIVSDEDILNHICYDRNDTQMLEKLKPCIEEAFVIQDREVA 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +      Q +   K++     + + +K +                   ++   G   
Sbjct: 119 LDWIGSRGNSQSLSRPKRV--KYARDIMQKEL----------------LPHISQTDGSET 160

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN----NAYIRNTLVTDKNKDRKDALLDI 377
            +A  +              R++                 +        NK  KD    +
Sbjct: 161 KKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYL 220

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +       F++   + +    +  KY L   G      +         + + +    
Sbjct: 221 QKCVENNR--EFNLTLGVKSTTLTNGLKYSL-ATGNWGDQKKAASSKAGVSQVLNRYTFA 277

Query: 438 AIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           + +  L        R+GK       +  +  +    E  + Q    +  +       + +
Sbjct: 278 STLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGT 337

Query: 493 VDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                +   +  N + +         +A   F     +    +  + +S +   RR   +
Sbjct: 338 PCEPIIDFMNQRNMEMLEEYEPLRSPNATKVFVNGVWVGVHRDPAHLVSNVQDLRRGHII 397

Query: 545 -GQGGVARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGF 597
             +  + R     E +    T  GR+C        +T   +   LV +     R+     
Sbjct: 398 SHEVSLVRDIRDREFK--IFTDAGRVCRPLFVIDNDTRSMNYGNLVLTKEHITRLEEDKE 455

Query: 598 ---------IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------- 641
                    +E              V Y+ A EEE   I      L+             
Sbjct: 456 AAIGMDRDELEARQMGWDGLVNQGVVEYVDAEEEETVMIVMTPGDLETSRQIQLGKAVPE 515

Query: 642 -EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             E    +          +     +  P  ++ I AS+IPF +++ S R      M +QA
Sbjct: 516 NAEDEPNKRVNAMSHRSAQTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQA 575

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +                                          V  +       + + + 
Sbjct: 576 MG-----------------------------------------VFLTNYDQRMDTMANIL 594

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA   + G
Sbjct: 595 YYPQKPMATTRSMEFLKFR------------------------ELPAGQNAIVAIACYSG 630

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        D   +     + 
Sbjct: 631 YNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRTDTLRLKHGTYEK 690

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  D+++GK  P         ++        K    RD S  + S  
Sbjct: 691 LDDDGIVAPGVRVSGEDMIIGKTAPIPPDSEELGQRT-------KMHIKRDASTPLRSTE 743

Query: 936 SGTV 939
           +G V
Sbjct: 744 NGIV 747


>gi|158954680|gb|ABW84311.1| RNA polymerase subunit B [Mycobacterium abscessus]
          Length = 238

 Score =  287 bits (735), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 127/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 147  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.037,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 50


>gi|157062992|gb|ABV04085.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|161015973|gb|ABX55984.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|219671585|gb|ACL31672.1| RNA polymerase subunit B [Mycobacterium bolletii]
 gi|219671587|gb|ACL31673.1| RNA polymerase subunit B [Mycobacterium bolletii]
 gi|219671589|gb|ACL31674.1| RNA polymerase subunit B [Mycobacterium bolletii]
 gi|219671591|gb|ACL31675.1| RNA polymerase subunit B [Mycobacterium bolletii]
 gi|219671593|gb|ACL31676.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671595|gb|ACL31677.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671597|gb|ACL31678.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671599|gb|ACL31679.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671601|gb|ACL31680.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671603|gb|ACL31681.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671605|gb|ACL31682.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671607|gb|ACL31683.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|219671609|gb|ACL31684.1| RNA polymerase subunit B [Mycobacterium massiliense]
 gi|226934684|gb|ACO92416.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|315435612|gb|ADU18196.1| RNA polymerase beta-subunit [Mycobacterium bolletii]
          Length = 237

 Score =  287 bits (735), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|110293957|gb|ABG66441.1| RNA polymerase-beta subunit [Staphylococcus aureus]
          Length = 313

 Score =  287 bits (735), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 180/313 (57%), Positives = 231/313 (73%), Gaps = 3/313 (0%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+C
Sbjct: 1   ASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIA 628
           P  T EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +A
Sbjct: 61  PIXTPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVA 120

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSN
Sbjct: 121 QANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 180

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS- 747
           R LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI AK  G VE V++  I++R  
Sbjct: 181 RALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRL 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           VE +       +D Y L KF+RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++AL
Sbjct: 241 VEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMAL 300

Query: 808 GRNMLVAFMPWHG 820
           GRN++V F+PW G
Sbjct: 301 GRNVVVGFIPWDG 313


>gi|312451970|gb|ADQ86017.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451972|gb|ADQ86018.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451974|gb|ADQ86019.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451976|gb|ADQ86020.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451978|gb|ADQ86021.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451980|gb|ADQ86022.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|312451982|gb|ADQ86023.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 236

 Score =  287 bits (735), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 100  TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 145  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 187

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 188  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 236



 Score = 44.7 bits (104), Expect = 0.12,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 48


>gi|62720658|gb|AAX93865.1| RNA polymerase subunit B [Mycobacterium flavescens]
          Length = 238

 Score =  287 bits (735), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 136/229 (59%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +                  
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKINGSPDWA---------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                           +++ +   + + G  VSTPVFDGA E  +  +L            
Sbjct: 145  ---------------NALPKELLESEPGSIVSTPVFDGARENELQGLLGSTLPNRDGETL 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +DE G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.044,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|16081519|ref|NP_393870.1| DNA-directed RNA polymerase subunit B [Thermoplasma acidophilum DSM
            1728]
 gi|548823|sp|Q03587|RPOB_THEAC RecName: Full=DNA-directed RNA polymerase subunit B
 gi|809775|emb|CAA48280.1| DNA-directed RNA polymerase [Thermoplasma acidophilum]
 gi|10639562|emb|CAC11534.1| probable DNA-directed RNA polymerase chain B [Thermoplasma
            acidophilum]
          Length = 1195

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 182/1081 (16%), Positives = 350/1081 (32%), Gaps = 179/1081 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            I ++A  +  +  + +   S     PI+Y +  ++       L  +     +DA+  + +
Sbjct: 263  ILMKALGLERDVDVHDAIASVPEMEPIIYSNIEDSKN--PKVLPPNGVNTTEDAISYLEK 320

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                G    F                 D      +  ++  +L      R  +   +  +
Sbjct: 321  RFAAGQAKEFR----------------DKKISQMLDHSLLPHLGDSPSDRIRKAIYLGRM 364

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
             + L++L  G    DD D+L N+R++  G+++   +R     + + +K ++         
Sbjct: 365  ARSLLELSLGIRKEDDKDHLANKRIKLAGDLMDELFRSAFQSVMKDLKYQLEKTYNRKRG 424

Query: 500  PQDLINAK---------PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
             +     +           +S        + +SQL + V++LS I+H RR+ +     + 
Sbjct: 425  IKIRPAVRQDLLTQRVLHAMSTGNWIGGRTGVSQLLDRVSNLSTISHLRRIIS----PLT 480

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R +   E RD+HPT +GRICP ET EG N GLV +      V      ++    +    V
Sbjct: 481  RTQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNAALLINVTQGIDPDSVMEILKGMDV 540

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID--FIDASP 668
               +      E   +     N            LV             ++++  + D + 
Sbjct: 541  REVLE-----ESPKKGRVYLNGDFIGYHDDPRYLVSRIREERRSGRMSDEVNVRYDDNTN 595

Query: 669  KQVVSIAASLI--PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            + +V+     +  P L   D   VL    ++R     +  E       +E + A+     
Sbjct: 596  EVIVNSDRGRLRRPLLILKDGKTVLDRTMIERLKHGEISFEDLVKQGAIEWLDAE----- 650

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                      +   + V +Y     ++         R +V   D
Sbjct: 651  --------------------------EEEDTYVAVYAYDIPEKCPHCNSYLYRSMV---D 681

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V   +                       +P         + I   M+   V + I   E
Sbjct: 682  WVNPGESEITLECGFC--------HQRFNVPSKLSKENTHLEIDPAMILGVVASIIPYPE 733

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                 R T              S   ++  D  G   +        +    +        
Sbjct: 734  HNSSPRITIASAMAKQSLGFAQSNVRIRP-DTRG--HLLHYPQVPLVRTRVMDYIHYDRR 790

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
               +  + A+   +  +++D  +   + +    +    F R    +  R    +      
Sbjct: 791  PAGQNFVVAVLSYEGYNIQDALVINKAAIERG-LGRSTFFRTYSAEERRYPGGQ------ 843

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                 +D+  I   +I     E        SG    +     S  LI +    ++ +   
Sbjct: 844  -----EDKFEIPTHDIIGARAEEYYKNLDDSGIIFPEAYVEGSDVLIGKTSPPRFLEEGE 898

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            +    QR  ES           +++ F            +     RVVK+ V  +R  + 
Sbjct: 899  ERLGPQRRRESSVTMRPNESGYVDNVFL----------TVSESNSRVVKIKVRSERIPEL 948

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
                    G+K                               SR                
Sbjct: 949  --------GDK-----------------------------FASR---------------- 955

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+K    +   + +   +      + +    S   +++      ++      ++G  +
Sbjct: 956  -HGQKGVVGLVVPQEDMPFTEDGIIPDLIFNPHSIPSRMTVGHILEMIGGKIASRTGRFI 1014

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
               +F G  E+++   L      +S   ++YDG+TG  F   + VG IY  KL+HMV+ K
Sbjct: 1015 DGTIFSGEPEKSLRDALVKYGFRKSSTEVMYDGITGRRFKADIFVGVIYYQKLHHMVAGK 1074

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD----V 1322
             +ARS G   ++T+QP  G+S +GG R GEME   + A+GAA V+++ L  +SD     V
Sbjct: 1075 FHARSRGPVQILTRQPTEGRSRQGGLRFGEMERDTLIAHGAAMVIKDRLLDQSDGTVLYV 1134

Query: 1323 VG------------RTRVYESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             G            R       V GN  + +   T  +F ++  E+ +LG+ + L     
Sbjct: 1135 CGNPSCGHIAIYDRRKGTLRCPVCGNTGNIYPIETSYAFKLMRDELISLGVVMRLMLGDM 1194

Query: 1369 K 1369
            K
Sbjct: 1195 K 1195



 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 133/955 (13%), Positives = 278/955 (29%), Gaps = 208/955 (21%)

Query: 79  YEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
                P+             ++   RDL Y  P  +TL+L + +     G++ IK     
Sbjct: 85  IFIGKPEIKEASGASNQITPNEARLRDLNYLAP--VTLKLRIVEDGIEKGSEIIK----- 137

Query: 129 SIYMGDLPLMT----------------------------------------KDGTFVIKG 148
              +GDLP+M                                           G F+I G
Sbjct: 138 ---VGDLPVMVRSKICTLSEENLDQYIEKNNGPIGLSRREKLQYVGEDPDDPGGYFIIGG 194

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG---LWMDIEFDSKDIIHVR 205
            +R++VS    +P       + R       +   ++   +G       +E  +   I+V 
Sbjct: 195 SERVIVSLEDLAPNKIMVEWEDRYES---KVEVSKVFSQRGGFRALTSMEKGTDGTINVS 251

Query: 206 IDR-RRKVPVTSFLMALGMDSE-EILSTF-----YPKIVYSQRGDFWCFPLSAADLMVGA 258
           I      VP+   + ALG++ + ++            I+YS   D     +   + +   
Sbjct: 252 IPSVAGTVPLVILMKALGLERDVDVHDAIASVPEMEPIIYSNIEDSKNPKVLPPNGVNTT 311

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           + + S ++           K+  +G  K  ++K +  +      L   ++ +   +    
Sbjct: 312 EDAISYLE-----------KRFAAGQAKEFRDKKISQM--LDHSLLP-HLGDSPSDRIRK 357

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            IY+        +    I   + +D  +           +     +      KD    + 
Sbjct: 358 AIYLGRMARSLLELSLGIRKEDDKD-HLANKRIKLAGDLMDELFRSAFQSVMKDLKYQLE 416

Query: 379 RVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV-----RHI 431
           +    + G     +V + +       +        GR  ++  L+  +         R I
Sbjct: 417 KTYNRKRGIKIRPAVRQDLLTQRVLHAMSTGNWIGGRTGVSQLLDRVSNLSTISHLRRII 476

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                        DL   +      +     +   + +       +       S+ E + 
Sbjct: 477 SPLTRTQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNAALLINVTQGIDPDSVMEILK 536

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            +D+  V+ +     +        +     +   ++    +SRI   RR   +      R
Sbjct: 537 GMDVREVLEESPKKGRV-------YLNGDFIGYHDDPRYLVSRIREERRSGRMSDEVNVR 589

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                    V+        P    +     L               ++       D    
Sbjct: 590 YDDNTNEVIVNSDRGRLRRPLLILKDGKTVL--------DRTMIERLKHGEISFEDLVKQ 641

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF--------------------CRCAG 651
             + +L A EEE+ Y+A     + E        ++                    C    
Sbjct: 642 GAIEWLDAEEEEDTYVAVYAYDIPEKCPHCNSYLYRSMVDWVNPGESEITLECGFCHQRF 701

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                  ++   ++  P  ++ + AS+IP+ E++ S R+ +   M +Q++   ++     
Sbjct: 702 NVPSKLSKENTHLEIDPAMILGVVASIIPYPEHNSSPRITIASAMAKQSLGFAQSNVRI- 760

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                                                      +   +  Y         
Sbjct: 761 ----------------------------------------RPDTRGHLLHYP-------- 772

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q PLV+                        G+N +VA + + GYN +D+++I++
Sbjct: 773 ------QVPLVR----------TRVMDYIHYDRRPAGQNFVVAVLSYEGYNIQDALVINK 816

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGA 886
             +   +  S     +    R    G E+      +      +EE  KN+D+ GII   A
Sbjct: 817 AAIERGLGRSTFFRTYSAEERRYPGGQEDKFEIPTHDIIGARAEEYYKNLDDSGIIFPEA 876

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            V   D+L+GK +P        E    +          R++S+ +    SG V +
Sbjct: 877 YVEGSDVLIGKTSPPRFLEEGEERLGPQRR--------RESSVTMRPNESGYVDN 923


>gi|148879057|emb|CAM07044.1| RpoB protein [Mycobacterium llatzerense]
          Length = 227

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 97/230 (42%), Positives = 128/230 (55%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 30   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 89

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 90   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 134

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 135  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 177

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS+
Sbjct: 178  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYSM 227


>gi|4456849|emb|CAB36988.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 400

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 181/340 (53%), Positives = 242/340 (71%), Gaps = 2/340 (0%)

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           + +  N +  D VR +   DI+A +   ++L  G G +DDID+LGNRR+R+VGE+L NQ 
Sbjct: 58  VTIIGNANPDDKVRTVTPADILAEMSYFLNLAEGLGRVDDIDHLGNRRIRAVGELLANQV 117

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           RLGL RMER+ +ER+S  D + + PQ +IN +PV +AV EFF SSQLSQ  E  N LS +
Sbjct: 118 RLGLSRMERNARERMSVQDNEVLTPQHIINIRPVTAAVKEFFGSSQLSQFMEQHNPLSEL 177

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           ++ RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +N Y
Sbjct: 178 SNKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHLNKY 237

Query: 596 GFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
           GF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  G  
Sbjct: 238 GFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQGVN 297

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
              P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGT
Sbjct: 298 QEYPANVVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPYVGT 357

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           GME   A  SGAA++A+  G V   DA ++ +R  +G LD
Sbjct: 358 GMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD 397


>gi|322491300|emb|CBZ26568.1| DNA-directed RNA polymerase polypeptide,putative [Leishmania mexicana
            MHOM/GT/2001/U1103]
          Length = 1132

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 87/307 (28%), Positives = 128/307 (41%), Gaps = 68/307 (22%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + VKV     RP + GDK + RHG KG+V  I+   DMPF + G   D++       
Sbjct: 876  DVDQKVKVVTREVRPPEPGDKFSSRHGQKGVVGLIVNGVDMPFNERGMCPDMI------- 928

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                             +     K+ + 
Sbjct: 929  --MN----------------------------------------PHGFPSRMTVGKLLEL 946

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                   +      G       F G   ++I+  L     +  G+ + Y G+TGE     
Sbjct: 947  VCSKAAALRGSMGDGT-----AFGGDSADSISQQLLSFGYNYHGKDVFYSGITGELMQGY 1001

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++ARSTG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 1002 VFFGPIYYQRLKHMVTDKMHARSTGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 1061

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYES-----IVAGNDTFETGTPESFNVLVKEMQA 1356
             +L E L I SD        V G    Y +        G  T +   P +F +L++E+Q 
Sbjct: 1062 NLLNERLLISSDMFTADICHVCG-NLGYNNRCTYCKTKGT-TSKVNMPYAFKLLIQELQG 1119

Query: 1357 LGLSIDL 1363
            +G+S+ L
Sbjct: 1120 MGVSLRL 1126



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 101/709 (14%), Positives = 221/709 (31%), Gaps = 53/709 (7%)

Query: 269 TGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               +IE+ +    S  ++S     +    +T      +             + ++A  +
Sbjct: 185 KNRVIIEADEHGSISAHVQSKTHYSISKCAVTFKKGSIVLTHRSFTEDIPIIVVLKALGL 244

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            +++ + +   +      IL+                     + DAL  I    +     
Sbjct: 245 ENDQHITQCIGTSPEFQAILFPCFEEA--------RLLNVVTQNDALQYIGEKRKETVWE 296

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                +   N    D     L+ V  +       +    + RH +   +  +++ +++  
Sbjct: 297 AEETQQRQVNRSKADKAAEFLANVL-LCHIREAQVQKDWNFRH-KAFYVCFMVRGMIEAS 354

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLIN 505
                +D+ D  GN+R  + G ++   +   L +  R +K          DS  P ++  
Sbjct: 355 FDASLLDERDFYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSKKDSTRPFNVKQ 414

Query: 506 -----AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RA 552
                 + + + +     S +      ++N         RLS +   G+         + 
Sbjct: 415 LMESKMEVIQNGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLGMMTRLASSFEKT 474

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           R     R + P+ +G +CP +T EG + GLV +  + ++V      +   R         
Sbjct: 475 RKVSGPRSLQPSQWGMVCPCDTPEGESCGLVKNFATLSQVTLD-LNDNYVRAAAHSLGVE 533

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++  ++  +  + Y    N +L     +   L     A          +       ++ V
Sbjct: 534 EIDTVTPTDFLHYYTVFLNGTLIGIHRYPNRLCAGIRALRRSGRLHPHVSISTQPRQRTV 593

Query: 673 SIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            I +     +   +   D    +   ++ R    L           +E V    S   ++
Sbjct: 594 QIGSDGGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTHNDFLAEGLIEYVDVNESNDCLI 653

Query: 729 A-KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR-PLVKVGD 786
           A   A I        + +  +      +      +     + + Q+    Q    V +  
Sbjct: 654 AVYPADIRPYTT--HLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGTVALNQ 711

Query: 787 EVRRNDIIADGPS-------------TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            +R + ++  G               T    L  G N +V  M + GY+ ED+ + ++  
Sbjct: 712 YIRADTVLLLGAYPQRPLCRTKAMSLTHYERLGAGINAMVCVMSYSGYDIEDAQVYNKSS 771

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +       + + + EV       G  ++      N      K ++  G+   G  V   D
Sbjct: 772 LDRGYGRCVVLRKHEVDLEKYAGGEFDVILPPEKNSGTGKFKALNPDGVASKGVLVQQYD 831

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +LV K TP       P   + +         V D  +  P G     +D
Sbjct: 832 VLVNKFTPVAGGDPRPAPLVYKYPQ----PAVVDHVIISPPGDYDRSLD 876



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 103/761 (13%), Positives = 224/761 (29%), Gaps = 137/761 (18%)

Query: 16  FFGK--NPEIIDI-PDL------IEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFP 64
            FG+    + +++ P L      +    AS+DH + +           LQ     +S   
Sbjct: 10  DFGEEYQRKKLEMLPALMGMRGILNHHIASFDHLIEVE----------LQRILLNESNVE 59

Query: 65  ITAF-SGAAMLEFVSYEFDPPK-----------FDVDDCLWRDLTYAVPLKITLRLIVFD 112
           I +      ++ + +     P+               +C  RD+TY   + + ++    D
Sbjct: 60  IKSTVDPDFVIRYQNIRICRPQEIVGKGHIPKLVTPQECRIRDMTYRGDMIVDVQYTSRD 119

Query: 113 VDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKG 148
                         E+ + +G +P+M K                         G F+IKG
Sbjct: 120 RSRAMLV-------EKDVKIGTIPIMLKSKCCNLYRKTREELVNMRECPLDPGGYFIIKG 172

Query: 149 IQRIVVSQLHRSPG-IHFDHDKGRA---SLSGKLLYA---CRIIPDQGLWMDIEFDSKDI 201
           ++++ + Q  +S   +  + D+  +    +  K  Y+   C +   +G           I
Sbjct: 173 VEKVCLVQEQQSKNRVIIEADEHGSISAHVQSKTHYSISKCAVTFKKGS----------I 222

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +         +P+   L ALG+++++ ++         Q   F CF  +    +V    +
Sbjct: 223 VLTHRSFTEDIPIIVVLKALGLENDQHITQCIGTSPEFQAILFPCFEEARLLNVVTQNDA 282

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +     E V E+ +     + +S  +K  +FL     C       +   N      Y
Sbjct: 283 LQYIGEKRKETVWEAEETQQRQVNRSKADKAAEFLANVLLCHIREAQVQKDWNFRHKAFY 342

Query: 322 IEAGDVIDEK------SLEEIFHSEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNK 368
           +        +       L+E      +          +L+ D +     +  T +  +  
Sbjct: 343 VCFMVRGMIEASFDASLLDERDFYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLS 402

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            +        + +    +        M  +   +D  +++++  G  ++  RL+      
Sbjct: 403 KKDSTRPFNVKQLMESKMEVIQNGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLG 462

Query: 428 VRHIRKEDIIAIIKILVDLR---NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL--RM 482
           +            K+        +  G +   D         V            L    
Sbjct: 463 MMTRLASSFEKTRKVSGPRSLQPSQWGMVCPCDTPEGESCGLVKNFATLSQVTLDLNDNY 522

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
            R+    +   +ID+V P D ++   V      F   + +          + I   RR  
Sbjct: 523 VRAAAHSLGVEEIDTVTPTDFLHYYTV------FLNGTLIGIHRYPNRLCAGIRALRRSG 576

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            L        +       +  +  GRI             V+S       +         
Sbjct: 577 RLHPHVSISTQPRQRTVQI-GSDGGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTH---- 631

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
               D      + Y+   E  +  IA   + +                            
Sbjct: 632 ---NDFLAEGLIEYVDVNESNDCLIAVYPADIRPY-----------------------TT 665

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            ++  P  ++ + A +IP+  ++ S R      M +QA+  
Sbjct: 666 HLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGT 706


>gi|161015975|gb|ABX55985.1| RNA polymerase beta subunit [Mycobacterium phocaicum]
          Length = 237

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 146  -----------------LPEGMHSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVM 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 32/49 (65%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 49


>gi|219671581|gb|ACL31670.1| RNA polymerase subunit B [Mycobacterium abscessus]
 gi|219671583|gb|ACL31671.1| RNA polymerase subunit B [Mycobacterium abscessus]
 gi|241897477|gb|ACS70955.1| RNA polymerase subunit B [Mycobacterium sp. P54]
 gi|315435584|gb|ADU18182.1| RNA polymerase beta-subunit [Mycobacterium abscessus]
 gi|315435594|gb|ADU18187.1| RNA polymerase beta-subunit [Mycobacterium abscessus]
 gi|315435624|gb|ADU18202.1| RNA polymerase beta-subunit [Mycobacterium abscessus]
          Length = 237

 Score =  287 bits (735), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 127/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.067,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|295673492|ref|XP_002797292.1| DNA-directed RNA polymerase I subunit RPA2 [Paracoccidioides
            brasiliensis Pb01]
 gi|226282664|gb|EEH38230.1| DNA-directed RNA polymerase I subunit RPA2 [Paracoccidioides
            brasiliensis Pb01]
          Length = 1220

 Score =  287 bits (734), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 93/459 (20%), Positives = 158/459 (34%), Gaps = 68/459 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +   G   +G      +     +   L+                + +  +
Sbjct: 694  DFNQSPRNMYQCQMGKQAMGTPGTSIQYRTDNKLYRLQTGQTPIVRPPLYNCYGLDNFPN 753

Query: 937  GTVVDVRIFNRHGIDKNERSISVERE---------QIELLARDKDDEQVILDRNIYSRLM 987
            G    V + +  G D ++ ++ + R           I        DE+    R    R +
Sbjct: 754  GMNAVVAVLSYTGYDMDD-AMIINRSAHDRGFGWGTIYKTKVYCLDEKESRGRGKAKREI 812

Query: 988  EILCGQNAVSGPKGF------KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
              L G       KG       +         ++E      W     D      +   +  
Sbjct: 813  AKLFGFAPGGLIKGEWRQTLDEDGLPHIGVRVTEGSIVAAWHTVRFDAVSNSYINIDRQT 872

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +       E+ + + +  +  G +      + + +   + R    GDK + RHG KG+ S
Sbjct: 873  HFFKYKDTEEGYIDSVRIL--GSETGGDPCQAISIKYRIPRKPVIGDKFSSRHGQKGVCS 930

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            ++ P  DMPF + G   D+++NP   PSRM +G   E+  G +    G    S    +  
Sbjct: 931  QLWPAIDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKSGALHGLAQDSTPFRFSE 990

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                             F G        
Sbjct: 991  EHTAGD-------------------------------------------FFG-------E 1000

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G+TG  F   + +G +Y  +L HMV+DK   R+TG  + +T Q
Sbjct: 1001 QLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQRLRHMVNDKFQVRTTGPVNALTGQ 1060

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1061 PVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNCSD 1099



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 80/659 (12%), Positives = 185/659 (28%), Gaps = 105/659 (15%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   + + +     +           +G +P+M +    
Sbjct: 121 EIYPAECRERHATYRGRLRARLEYRINNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS-- 175
                                G FV+ G ++++   +   R+ P         +   +  
Sbjct: 171 YLEKCSPEQLVQHKEESEELGGYFVVNGNEKLIRMLIVGRRNFPMAIIRSSFMKRGPTYT 230

Query: 176 --GKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE- 226
             G  + + R  PDQ      +    D    +  R   R+    VPV   L  L   ++ 
Sbjct: 231 KFGIQIRSVR--PDQTSQTNFLHYLSDGN--VTFRFTWRKNEYLVPVVMILKGLVQTNDR 286

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +I    + ++V  +             + +  +           +     G+K    L  
Sbjct: 287 DI----FERLVGHEGSKGIKNSFVTDRVELLLRTYKGYGIHGRDDIRAYLGEKFRPVL-- 340

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                 +    +  + L  + +     +  T        D  D      I     +   +
Sbjct: 341 -GMPTDIPDEAVGVEFLRKVVLPHLGNHSVT--------DSQDNDKFNMILFMIRKLYTL 391

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           +  D   +N               ++ LL   +Y ++    +  +             + 
Sbjct: 392 VAGDCAPDNP---------DAVSNQEVLLGGFLYGILLKERLEEW------LRSFGPIAQ 436

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            + +        + +   +    +     E+I   ++  +   N   +   +D       
Sbjct: 437 DWSVKNQNARFTDPKFEKEFLSKIVARTNENIGGALEYFLSTGN-LVSPTGLDLQQPSGY 495

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             + E +     +   RM   I        + +   + L+               S + Q
Sbjct: 496 TVMAEKINFYRFISHFRM---IHRGSFFAQLKTTTVRKLLPETHKCKIETSNLDVSGVPQ 552

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           +  ++   S  + +   S + Q            +    +   R       EG+    V 
Sbjct: 553 IISNLGVTSESSVSLEESVVVQMDGRILGYCSPKQARIISDTLRY---WKVEGNKSLPVE 609

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
               +   +  G     Y      ++   V YL   + +  Y+        E      ++
Sbjct: 610 LEIGYVPNSNRGQYPGIYLFSQCARMVRPVKYLPLDKLD--YVGPFEQPFMEIACVPSDI 667

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +                  ++  P  ++SI A++ PF + + S R +  C M +QA+  
Sbjct: 668 ISG------------VSTHVEFDPTYILSIVANMTPFSDFNQSPRNMYQCQMGKQAMGT 714



 Score = 45.5 bits (106), Expect = 0.078,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 75/227 (33%), Gaps = 26/227 (11%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V T +E         +IVA      +   + R + +   G     T G  I    +    
Sbjct: 671 VSTHVEFDPTYIL--SIVANMTPFSDFNQSPRNMYQCQMGKQAMGTPGTSI--QYRTDNK 726

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q P+V+                  L +   G N +VA + + GY+ +D+M+I+
Sbjct: 727 LYRLQTGQTPIVRP----------PLYNCYGLDNFPNGMNAVVAVLSYTGYDMDDAMIIN 776

Query: 831 ERMVSEDVFTSIHIEE--FEVMARDTKLGPEEITRDIPNV---------SEEGLKNIDEC 879
                         +   + +  ++   G  +  R+I  +           E  + +DE 
Sbjct: 777 RSAHDRGFGWGTIYKTKVYCLDEKE-SRGRGKAKREIAKLFGFAPGGLIKGEWRQTLDED 835

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           G+  +G  V  G I+    T + ++       + R     K  D  +
Sbjct: 836 GLPHIGVRVTEGSIVAAWHTVRFDAVSNSYINIDRQTHFFKYKDTEE 882


>gi|295815629|gb|ADG36317.1| RNA polymerase beta-subunit [Mycobacterium triplex]
          Length = 237

 Score =  287 bits (734), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEGLRHAQPDQTVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|118087767|ref|XP_415007.2| PREDICTED: similar to RNA polymerase I polypeptide B [Gallus gallus]
          Length = 1041

 Score =  287 bits (734), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 105/522 (20%), Positives = 171/522 (32%), Gaps = 72/522 (13%)

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +T    +   +N+L     W G    + + ++   +  DV   +                
Sbjct: 520  TTPCRMVRPVKNLLYGRKEWIGT--LEQVFMNVATMESDVMPGV------------TTHQ 565

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
            E     I +V    +   D         +   G   +G      +     +  LL     
Sbjct: 566  ELFPHSILSVVANLIPFSDHNQSPRNMYQCQMGKQTMGFPVYNYKDRSDNKLYLLHTPQS 625

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                        + S   GT   V + +  G D  +  I  +       A     +   +
Sbjct: 626  PLVRPRMYDYYGMDSYPVGTNSVVAVISYSGYDMEDAMIVNKSSWERGFAYGSVIKMESI 685

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            D ++ +             G    K    L +D +                      E+ 
Sbjct: 686  DLSLKANRGGDNLVFGIRPGDPNVK--EKLDADGLPFVGSILQPGDPFYSYMNLNTGETF 743

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             V Y+  +  + D  K         +D   G  +   + V + R    GDK A RHG KG
Sbjct: 744  TVYYQNKEVGIVDNIK------LCSNDRGTGKFKKACITVRVPRNPTVGDKFASRHGQKG 797

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S++ P EDMPF ++G   DI+ NP G PSRM +G + E+  G +    G    +    
Sbjct: 798  ILSQLWPVEDMPFTENGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGAYYDATPFT 857

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                           
Sbjct: 858  FTEKNSALKY-------------------------------------------------- 867

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                L  A  +  G   +Y G++G   +  + VG +Y  +L HMVSDK   R+TG    V
Sbjct: 868  FGETLVSAGYNFFGTEKMYSGISGVELEADIFVGVVYYQRLRHMVSDKFQVRTTGPRDSV 927

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            T QP+ G++  GG R GEME   + A+G +++L + L   SD
Sbjct: 928  TNQPIKGRNVEGGIRFGEMERDALLAHGTSFLLHDRLFSCSD 969


>gi|55273997|gb|AAV48869.1| RNA polymerase II second largest subunit [Clavaria zollingeri]
          Length = 694

 Score =  287 bits (734), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 128/829 (15%), Positives = 239/829 (28%), Gaps = 156/829 (18%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ + +    +              +  + + + +     +             
Sbjct: 1    FRMLFRKLTKDVYRYLQKCVETHKEFNIALAVKHQTITNGLKYSLATGNWGDQKKSMSSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L   A ++           + +  + +         EEN +     + +  +G 
Sbjct: 117  CGLVKNLALMACISVGSSSAPVIEFLEEWGLESL--------EENAHSTTPCTKVFVNGV 168

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR- 698
            +             I   R K    D SP+  V             D+ RV     +   
Sbjct: 169  WMGVHRDPAHLVRTIKKLRRK---DDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEN 225

Query: 699  -----QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                 Q   +      +  TG E              + GI+E +DA       +    +
Sbjct: 226  QQLALQKKHIKWLNQGYDDTGEEFR-------WEQLVKGGIIELLDAEEEETVMISMTPE 278

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               +       +    ++       R  +K G            PS  LG       +  
Sbjct: 279  DLENSRLQSTGVDPHANDGEFDPAAR--LKSGINAHTWTHCEIHPSMILG-------ICA 329

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N                        ++       +G       I        
Sbjct: 330  SIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM------ 365

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 366  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQS 420

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D  ++S   + E+ E   R+        + +       I  G 
Sbjct: 421  SIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGNYDKLESDGLIAPGT 479

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  D      R++          ++     +  Q            
Sbjct: 480  GVRGDDIIIGKTAPIPPDSEELGQRTRSHTKRDVSTPLKSTESGVIDQVLI--------- 530

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                              + VKV +   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 531  -----------TTNSEGQKFVKVRLRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTA 579

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +G + E  L      +G +  +                   
Sbjct: 580  EGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--------------- 624

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                       ++     + LR       G+ V                         G 
Sbjct: 625  ----------DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGH 652

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 653  T-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 694



 Score =  120 bits (300), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 81/592 (13%), Positives = 164/592 (27%), Gaps = 98/592 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 10  KDVYRYLQKCVETHKEFNIALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLN 68

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 69  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAC 128

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA         F     +    +  + +  I   RR
Sbjct: 129 ISVGSSSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMGVHRDPAHLVRTIKKLRR 188

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +            +   ++        P    E   + L      +  +N       
Sbjct: 189 KDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHIKW--LNQGYDDTG 246

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL----- 655
              +         +  L A EEE   I+     L+     +  +      GE        
Sbjct: 247 EEFRWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQSTGVDPHANDGEFDPAARLK 306

Query: 656 --VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             +        +  P  ++ I AS+IPF +++ S R      M +QA+ +          
Sbjct: 307 SGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI--- 363

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 364 --------------------------------------RMDTMANILYYPQKPLATTRSM 385

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 386 EYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSS 421

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E            +       ++  G+I  G  V
Sbjct: 422 IDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGNYDKLESDGLIAPGTGV 481

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
              DI++GK  P         E+L +        DV        SGV   V+
Sbjct: 482 RGDDIIIGKTAPI----PPDSEELGQRTRSHTKRDVSTPLKSTESGVIDQVL 529


>gi|62720664|gb|AAX93868.1| RNA polymerase subunit B [Mycobacterium pulveris]
          Length = 238

 Score =  287 bits (734), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 134/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G K++                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWAA-HSGWKVEGKP------------------- 141

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                      ++   D +L           VSTPVFDGA  E +  +L            
Sbjct: 142  --------DWANQLPDDLLEAEPN----TIVSTPVFDGASGEELQGLLASTLPNRDGEKL 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDSDGKAMLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.041,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|46019146|emb|CAE52037.1| RNA polymerase beta subunit [Bacillus sonorensis]
          Length = 160

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 67/182 (36%), Positives = 112/182 (61%), Gaps = 22/182 (12%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYE 80
            E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y 
Sbjct: 1   SEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYS 50

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
              PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT 
Sbjct: 51  LGDPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTD 101

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I G +R++VSQL RSP +++    G+   +GK  +   +IP++G W++ E D+KD
Sbjct: 102 TGTFIINGAERVIVSQLVRSPSVYYS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKD 158

Query: 201 II 202
           ++
Sbjct: 159 VV 160


>gi|144954314|gb|ABP04233.1| RpoB [Mycobacterium phocaicum]
          Length = 237

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 146  -----------------LPEGMHSAPRDSIVATPVFDGARENELQGLLGSTLPNRDGDVM 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.075,   Method: Composition-based stats.
 Identities = 32/49 (65%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 49


>gi|190148960|gb|ACE63455.1| RNA polymerase subunit B [Pseudonocardia hydrocarbonoxydans]
          Length = 318

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 169/324 (52%), Positives = 235/324 (72%), Gaps = 8/324 (2%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG
Sbjct: 2   RMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQTNPLAGLTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           ++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL+SFA+VN +GFI++PYRKV DG
Sbjct: 62  LSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSFAQVNPFGFIQSPYRKVEDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDAS 667
           K  + + YL+A EE+   IAQAN  LDEDG+F  + V  R   GE   +    +D+ID S
Sbjct: 122 KAGDQIDYLTADEEDRFVIAQANEPLDEDGNFIGDRVLVRRKGGEVDYISPAGVDYIDVS 181

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++++P VGTGME   A  +G  +
Sbjct: 182 PRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSDSPLVGTGMELRAAVDAGDVV 241

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           VA++AG+VE++ A  I + + +G           YRL KF+RSNQ TC NQ+P+V  G  
Sbjct: 242 VAEKAGVVEELCADFITVMADDGTR-------RTYRLHKFRRSNQGTCTNQKPIVVEGAR 294

Query: 788 VRRNDIIADGPSTDLGDLALGRNM 811
           V    ++ADGP T+ G++ALG+N+
Sbjct: 295 VEVGQVLADGPCTENGEMALGKNL 318


>gi|71148463|gb|AAZ28896.1| RpoB [Mycobacterium mucogenicum]
          Length = 238

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 42   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 147  -----------------LPEGMRSAPRDSIVATPVFDGARENELQGLLGATLPNRDGDVM 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.044,   Method: Composition-based stats.
 Identities = 33/50 (66%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 50


>gi|157868405|ref|XP_001682755.1| DNA-directed RNA polymerase polypeptide [Leishmania major strain
            Friedlin]
 gi|68126211|emb|CAJ03500.1| putative DNA-directed RNA polymerase polypeptide [Leishmania major
            strain Friedlin]
          Length = 1132

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 86/307 (28%), Positives = 128/307 (41%), Gaps = 68/307 (22%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + +KV     RP + GDK + RHG KG+V  I+   DMPF + G   D++       
Sbjct: 876  DVDQKIKVVTREVRPPEPGDKFSSRHGQKGVVGLIVNGVDMPFNERGMCPDMI------- 928

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                             +     K+ + 
Sbjct: 929  --MN----------------------------------------PHGFPSRMTVGKLLEL 946

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                   +      G       F G   ++I+  L     +  G+ + Y G+TGE     
Sbjct: 947  VCSKAAALRGSMGDGT-----AFGGESADSISQQLLSFGYNYHGKDVFYSGITGELMQGY 1001

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++ARSTG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 1002 VFFGPIYYQRLKHMVTDKMHARSTGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 1061

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYES-----IVAGNDTFETGTPESFNVLVKEMQA 1356
             +L E L I SD        V G    Y +        G  T +   P +F +L++E+Q 
Sbjct: 1062 NLLNERLLISSDMFTADICHVCG-NLGYNNRCTYCKTKGT-TSKVNMPYAFKLLIQELQG 1119

Query: 1357 LGLSIDL 1363
            +G+S+ L
Sbjct: 1120 MGVSLRL 1126



 Score =  127 bits (318), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 102/707 (14%), Positives = 224/707 (31%), Gaps = 49/707 (6%)

Query: 269 TGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               +IE+ +    S  ++S     +    +T      +             + ++A  +
Sbjct: 185 KNRVIIEADEHGNISAHVQSKTHYSISKCAVTFKKGSIVLTHRSFTEDIPIIVVLKALGL 244

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            +++ + +   +      IL+                     + DAL  I    +     
Sbjct: 245 ENDQHITQCIGTLPEFQKILFPCFEEA--------RLLNVVTQNDALQYIGEKRKETVWE 296

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                +   N    D     L+ V  +       +    + RH +   +  +++ +++  
Sbjct: 297 AEETQQRQVNRSKADKAAEFLANVL-LCHIREAQVQKDWNFRH-KAFYVCFMVRGMIEAS 354

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLIN 505
                +D+ D  GN+R  + G ++   +   L +  R +K          DS  P ++  
Sbjct: 355 FDTSLLDERDFYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSRKDSTRPFNVKQ 414

Query: 506 -----AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RA 552
                 + + + +     S +      ++N         RLS +   G+         + 
Sbjct: 415 LMESKMEVIQNGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLGMMTRLASSFEKT 474

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           R     R + P+ +G +CP +T EG + GLV +  + ++V      +   R         
Sbjct: 475 RKVSGPRSLQPSQWGMVCPCDTPEGESCGLVKNFATLSQVTLD-LNDNYVRAAAHALGVE 533

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++  ++  +  +      N +L     +   L                +       ++ V
Sbjct: 534 EIDTVTPTDFLHYCTVFLNGTLIGIHRYPNRLCAGIRTLRRSGRLHPHVSISTQPRQRTV 593

Query: 673 SIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            I +     +   +   D    +   ++ R    L            E V    S   ++
Sbjct: 594 QIGSDGGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTHNDFLAEGLTEYVDVNESNDCLI 653

Query: 729 A-KRAGIVEQVDAIRI-------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR- 779
           A   A I      + +       V+  +      + S  + ++    +++     +NQ  
Sbjct: 654 AVYPADIGPYTTHLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGTVALNQYI 713

Query: 780 ---PLVKVGDEVRRNDIIADGPS-TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
               ++ +G   +R        S T    L  G N +V  M + GY+ ED+ + ++  + 
Sbjct: 714 RADTVLLLGAYPQRPLCRTKAMSLTHYEKLGAGINAMVCVMSYSGYDIEDAQVYNKSSLD 773

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 + + + EV       G  ++      N      K ++  G+   GA V   D+L
Sbjct: 774 RGYGRCVVLRKHEVDLEKYAGGEFDVILPPEKNSGTGKFKALNPDGVAGKGALVQQYDVL 833

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           V K TP       P   + +         V D  +  P G     +D
Sbjct: 834 VNKFTPVAGGDPRPAPLVYKYPQ----PAVVDHVIISPPGDYDRSLD 876



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 99/738 (13%), Positives = 215/738 (29%), Gaps = 128/738 (17%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFPITAF-SGAAMLEFVSYEFDPPK- 85
           +    AS+DH + +           LQ     +S   I +      ++ + +     P+ 
Sbjct: 33  LNHHIASFDHLIEVE----------LQRILLNESNVEIKSTVDPDFVIRYQNIRICRPQE 82

Query: 86  ----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                         +C  RD+TY   + + ++    D              E+ + +G +
Sbjct: 83  IVGKGHIPKLVTPQECRIRDMTYRGDMIVDVQYTSRDRSRAMLV-------EKDVKIGTI 135

Query: 136 PLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M K                         G F+IKG++++ + Q  +S   +  + D+ 
Sbjct: 136 PIMLKSKCCNLYRKTREELVNMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADEH 195

Query: 171 RA---SLSGKLLYA---CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
                 +  K  Y+   C +   +G           I+         +P+   L ALG++
Sbjct: 196 GNISAHVQSKTHYSISKCAVTFKKGS----------IVLTHRSFTEDIPIIVVLKALGLE 245

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           +++ ++     +   Q+  F CF  +    +V    +   +     E V E+ +     +
Sbjct: 246 NDQHITQCIGTLPEFQKILFPCFEEARLLNVVTQNDALQYIGEKRKETVWEAEETQQRQV 305

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK------SLEEIFH 338
            +S  +K  +FL     C       +   N      Y+        +       L+E   
Sbjct: 306 NRSKADKAAEFLANVLLCHIREAQVQKDWNFRHKAFYVCFMVRGMIEASFDTSLLDERDF 365

Query: 339 SEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
              +          +L+ D +     +  T +  +   +        + +    +     
Sbjct: 366 YGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSRKDSTRPFNVKQLMESKMEVIQN 425

Query: 392 AESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR--- 447
              M  +   +D  +++++  G  ++  RL+      +            K+        
Sbjct: 426 GMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLGMMTRLASSFEKTRKVSGPRSLQP 485

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL--RMERSIKERISSVDIDSVMPQDLIN 505
           +  G +   D         V            L     R+    +   +ID+V P D ++
Sbjct: 486 SQWGMVCPCDTPEGESCGLVKNFATLSQVTLDLNDNYVRAAAHALGVEEIDTVTPTDFLH 545

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              V      F   + +          + I   RR   L        +       +  + 
Sbjct: 546 YCTV------FLNGTLIGIHRYPNRLCAGIRTLRRSGRLHPHVSISTQPRQRTVQI-GSD 598

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            GRI             V+S       +             D        Y+   E  + 
Sbjct: 599 GGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTH-------NDFLAEGLTEYVDVNESNDC 651

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA   + +                             ++  P  ++ + A +IP+  ++
Sbjct: 652 LIAVYPADIGPY-----------------------TTHLEVEPLSLLGVVAGIIPYPHHN 688

Query: 686 DSNRVLMGCNMQRQAVPL 703
            S R      M +QA+  
Sbjct: 689 QSARNTFQSAMGKQALGT 706


>gi|32344982|gb|AAM93501.1| RNA polymerase beta subunit [Rickettsia slovaca]
 gi|32344984|gb|AAM93502.1| RNA polymerase beta subunit [Rickettsia slovaca]
          Length = 168

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/166 (58%), Positives = 128/166 (77%), Gaps = 1/166 (0%)

Query: 23  IIDIPDLIEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           + DIP+LIE+QK SY+  FL +NI   ER N+GLQ+   S+FPI+  S  A +EFV YEF
Sbjct: 3   VADIPNLIEIQKNSYEKNFLQLNIKDSERKNKGLQSILNSIFPISDSSNIANIEFVKYEF 62

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           D PK+DV++C  R L+YA PLK+TLRL ++D+DE TG + IK IKEQ +YMGD+PLMTK+
Sbjct: 63  DTPKYDVEECSQRSLSYAAPLKVTLRLSIWDIDEDTGTREIKGIKEQEVYMGDIPLMTKN 122

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           GTF+I G +R+VVSQ+HRSPG+ F HD+G+   SGKLLY+ R+IP 
Sbjct: 123 GTFIINGTERVVVSQMHRSPGVFFYHDEGKVHSSGKLLYSARVIPY 168


>gi|326694958|gb|AEA03702.1| RNA polymerase B [Mycobacterium sp. HA-1]
 gi|326694960|gb|AEA03703.1| RNA polymerase B [Mycobacterium sp. ASCr-1.1]
          Length = 237

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLRHAQPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.078,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|169769719|ref|XP_001819329.1| DNA-directed RNA polymerase I subunit RPA135 [Aspergillus oryzae
            RIB40]
 gi|238487962|ref|XP_002375219.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus flavus NRRL3357]
 gi|83767188|dbj|BAE57327.1| unnamed protein product [Aspergillus oryzae]
 gi|220700098|gb|EED56437.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Aspergillus flavus NRRL3357]
          Length = 1237

 Score =  287 bits (734), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 115/276 (41%), Gaps = 52/276 (18%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E+ + + I  +     + P     VK  +   R    GDK + RHG KG+ S++ 
Sbjct: 898  KYKDAEEGYIDSIRIMGAETGIEPCQSLSVKYRI--PRKPVIGDKFSSRHGQKGVCSQLW 955

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P  DMPF + G   D+++NP   PSRM + Q+ E+  G A    G    S    +     
Sbjct: 956  PAVDMPFSESGIQPDLIINPHAFPSRMTIAQMIESMAGKAGALHGHPQDSTPFQFSEENT 1015

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             +                                                  +     LR
Sbjct: 1016 AA--------------------------------------------------DYFGHQLR 1025

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A  +  G   LY G+TG+ F   + +G ++  +L HMV+DK   R+TG  + +T QP+ 
Sbjct: 1026 KAGYNYYGNEPLYSGITGKEFAADIFIGVVHYQRLRHMVNDKFQVRTTGPVNSLTGQPVK 1085

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1086 GRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1121



 Score = 65.1 bits (157), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 102/713 (14%), Positives = 201/713 (28%), Gaps = 146/713 (20%)

Query: 69  SGAAMLEFVSYEFDPP------KFD-------VDDCLWRDLTYAVPLKITLRLIVFDVDE 115
                +       + P      KF          +C  R  TY   L+  +   V + D 
Sbjct: 93  RNKLHVRIKEVFLEKPAIPPTNKFTTRNRNIYPSECRERHATYRGKLRARIEYRVNNGDW 152

Query: 116 FTGAKSIKDIKEQSIYMGDLPLM-----------TK-------------DGTFVIKGIQR 151
               +           +G +P+M           T               G F++ G ++
Sbjct: 153 MEAVRE----------LGQVPIMMRTNRCHLEKATPAELVEHKEESEELGGYFIVNGNEK 202

Query: 152 ----IVV------SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW---MDIEFDS 198
               ++V        + R   +   H   +    G  + + R  PDQ      +    D 
Sbjct: 203 LIRMLIVGKRNFPMAIVRGSFVKRGHTYTKF---GVQIRSVR--PDQTSQTNVLHYLSDG 257

Query: 199 KDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLM 255
              +  R   R+    VPV   L AL +++ +     +  +V S   +          + 
Sbjct: 258 N--VTFRFSWRKNEYLVPVMMILKAL-VETND--REIFEGLVGSASSEGINNTFVTDRVE 312

Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLL--KSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           +  +                 G  L S       L EK    LG+  D          + 
Sbjct: 313 LLLRT--------------YKGYNLHSRSACRAYLGEKFKPVLGVPMD----------MS 348

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK--NKDRK 371
           N E G  ++    +    +       +     ++        A +      D       +
Sbjct: 349 NEEAGTEFLRKVVLPHLGNQNVTETQDYDKFKLIMFMIRKLYALVAGDCAPDNPDAVSNQ 408

Query: 372 DALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           + LL   +Y ++    +  +                + +   G    +     D    V 
Sbjct: 409 EILLGGFLYGMILKERLEEW------VRSFGPILRDWSMRNHGAKFTDPSFERDFLSKVV 462

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIK 487
               E+I   ++  +   N   +   +D         + E +     +   RM    S  
Sbjct: 463 KRSNENIGGALEYFLSTGN-LVSPTGLDLQQTSGYTVMAEKINFYRFISHFRMIHRGSFF 521

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            ++ +  +  ++P+      PV +         + L+       S   ++H  R   L Q
Sbjct: 522 AQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLISTSDIDVSHLPR--LLVQ 579

Query: 547 GGVARARAGVEMRDVHPTHYGRI----------------CPAETSEGHNIGLVSSLTSFA 590
            GV    +      V     GRI                   +    HN+     +  + 
Sbjct: 580 LGVRSESSVSLEESVTVQLDGRIVGFCSPKQARMIADTLRHWKVEGSHNVPRELEIG-YV 638

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
             +  G     Y      ++  +V YL   + +  Y+        E      +LV     
Sbjct: 639 PNSNGGQYPGIYMFSQAARMYREVKYLPLDKLD--YVGPFEQPFMEIACLPSDLVAG--- 693

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                        I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 694 ---------ISTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGT 737



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 80/561 (14%), Positives = 169/561 (30%), Gaps = 92/561 (16%)

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +   +++     + +V +    N +  +   + + + I+ +I+ L  L  G    D+ D 
Sbjct: 345 MDMSNEEAGTEFLRKVVLPHLGNQNVTETQDYDKFKLIMFMIRKLYALVAGDCAPDNPDA 404

Query: 459 LGNRRVRSVG--------EMLKNQYRLGLLRM------ERSIKERISSVDIDSVMPQDLI 504
           + N+ +   G        E L+   R     +          K    S + D +      
Sbjct: 405 VSNQEILLGGFLYGMILKERLEEWVRSFGPILRDWSMRNHGAKFTDPSFERDFLSKVVKR 464

Query: 505 NAKPVVSAVCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVA 550
           + + +  A+  F  +  L              + + E +N    I+H R    + +G   
Sbjct: 465 SNENIGGALEYFLSTGNLVSPTGLDLQQTSGYTVMAEKINFYRFISHFR---MIHRGSFF 521

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGK 609
                  +R + P  +G +CP  T +G   GL++ L     ++      +   R +    
Sbjct: 522 AQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCLISTSDIDVSHLPRLLVQLG 581

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           V            E+    + + ++  DG         +       +   K+   + S  
Sbjct: 582 V----------RSESSVSLEESVTVQLDGRIVGFCSPKQARMIADTLRHWKV---EGSHN 628

Query: 670 QVVSIAASLIPFLENDDSNRVLM---GCNMQRQAVPLLKAEAPFVG-------------- 712
               +    +P         + M      M R+   L   +  +VG              
Sbjct: 629 VPRELEIGYVPNSNGGQYPGIYMFSQAARMYREVKYLPLDKLDYVGPFEQPFMEIACLPS 688

Query: 713 -------TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                  T +E                    Q        +  +  +    + +D     
Sbjct: 689 DLVAGISTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIDYRTDN 748

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           K  R        Q P+V+               +  L +   G N +VA + + GY+ +D
Sbjct: 749 KLYRLQTG----QTPIVRP----------PLYNAYGLDNFPNGTNAVVAIISYTGYDMDD 794

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV---------SEEGLKNI 876
           +M+I++             +       + +    +  R+I  +           E    I
Sbjct: 795 AMIINKSSHERGFGHGTIYKTKVHSLDEKESRRNKSRREITKLFGFAPGGEIRAEWRNTI 854

Query: 877 DECGIICVGAEVNPGDILVGK 897
           DE G+  +GA V  G ++   
Sbjct: 855 DEDGLPHIGARVKEGSLVAAY 875


>gi|319998255|gb|ADV91599.1| RNA polymerase B subunit [Mycobacterium shimoidei]
          Length = 244

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 100/231 (43%), Positives = 134/231 (58%), Gaps = 37/231 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDTSKGVPDWAAQLP--------- 152

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                           + +L           VSTPVFDGA EE +  +L     +      
Sbjct: 153  ---------------EELLEAEPNKI----VSTPVFDGAREEELQGLLSSTLPNRDGDTL 193

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                G++ILYDG +GEPF  PVT GY+Y++KL+H+V DK++ARSTG YS++
Sbjct: 194  VDGDGKAILYDGRSGEPFPYPVTTGYMYIMKLHHLVDDKIHARSTGPYSMI 244



 Score = 46.6 bits (109), Expect = 0.028,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|57337352|emb|CAH69684.1| RNA polymerase, beta subunit [Enterobacter amnigenus]
          Length = 282

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 169/281 (60%), Positives = 213/281 (75%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS ITH RR+SAL  GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEITHKRRISALXPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQAN++LDE+G F
Sbjct: 61  GLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRF 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            ++LV CR  GE  L   +++D++D S +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQA
Sbjct: 121 VDDLVTCRSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQA 180

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP L+A+ P VGTGME  VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+D
Sbjct: 181 VPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGID 240

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           IY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTD
Sbjct: 241 IYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTD 281


>gi|311251947|ref|XP_003124850.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 2
            [Sus scrofa]
          Length = 1079

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 117/558 (20%), Positives = 189/558 (33%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQIFMNVAIFEDEVLAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+          +         P G +  V  +        D 
Sbjct: 641  GFPLLTFKDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G      P   + +  L  D 
Sbjct: 701  MILNKASWERGFAH-GSVYKSEFIDLSEKIKQGDDSLVFGVR----PGDPRVAQKLDDDG 755

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +        +             ES  V Y++ ++ + D  K        G+D   G  +
Sbjct: 756  LPFVGAQLQYGDPYYSYLNLNTGESFVVYYKSKENCIVDNIK------VCGNDTGSGRFK 809

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 810  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPVEDMPFTESGMVPDILFNPHGFPSRMT 869

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +            + K                  
Sbjct: 870  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKA----------------- 912

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                             A  +  G   LY G++G   +  + +G
Sbjct: 913  ---------------------------------AGYNYYGTERLYSGISGLELEADIFIG 939

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 940  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 999

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1000 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYSCSLCNRSDTIDTVSVPYV 1059

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1060 FRYFVAELAAMNIKVKLD 1077



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 92/611 (15%), Positives = 205/611 (33%), Gaps = 79/611 (12%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCATQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 249 GERFRVKVNLPDWYPNEQAAEFLFNECICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEML------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            ++ D+L N+ V + G++       K +  L  +++    K + +SV +++     ++N 
Sbjct: 307 EENPDSLVNQEVLTPGQLFLMFLKEKLEAWLVSIKIAIDKKAQKTSVSLNTENLMKILNL 366

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GIDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------------- 598
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTATCEVVTQFVYTASIPALLCSLGV 483

Query: 599 ----ETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 P+R+  +      + V+   A +E    IA +   L       E+ +      E
Sbjct: 484 TPVDSAPHRRYSECYPVLLDGVMVGWADKELAPSIADS---LRHFKVLREKRIPP--WME 538

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            +L+P      +        +    + P          L+G   Q      +  +    G
Sbjct: 539 VVLIPMTGKPSLYPGLYLFTTPCRLVRPVQNLGLGREELIGTMEQIFMNVAIFEDEVLAG 598

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                 +   S  +++A     +   D  +      +  +   T G   + L+ F+  + 
Sbjct: 599 VTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMG---FPLLTFKDRSD 652

Query: 773 NTCV----NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           N        Q PLV+                 D+ +  +G N +VA + + GY+ ED+M+
Sbjct: 653 NKLYRLQTPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMI 702

Query: 829 ISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +++          S++  EF  ++   K G + +   +        + +D+ G+  VGA+
Sbjct: 703 LNKASWERGFAHGSVYKSEFIDLSEKIKQGDDSLVFGVRPGDPRVAQKLDDDGLPFVGAQ 762

Query: 888 VNPGDILVGKI 898
           +  GD     +
Sbjct: 763 LQYGDPYYSYL 773



 Score = 48.1 bits (113), Expect = 0.010,   Method: Composition-based stats.
 Identities = 86/633 (13%), Positives = 176/633 (27%), Gaps = 107/633 (16%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
               K + +Q  ++G +P+M K                         G F+I GI++++ 
Sbjct: 67  NGISKGVIKQ--FLGYVPIMVKSKLCNLYSLSPRALIEHHEEAEEMGGYFIINGIEKVI- 123

Query: 155 SQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL---------WMDIEFDSKDII 202
             L    R+  I     K ++   G   Y   +   +           +++      + I
Sbjct: 124 RMLIMPRRNFPIAMVRPKWKSRGPGYTQYGVSMHCVREEHSAVNMNLHYLENGTVMLNFI 183

Query: 203 HVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           +      RK    +P+   L AL      +I    + +++  +  D +     +  L   
Sbjct: 184 Y------RKELFFLPLGFALKALVSFSDYQI----FQELIKGKEDDSFLRNSVSQMLR-- 231

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVA 309
                          V+E G      +L  L E+    + +          + L    + 
Sbjct: 232 --------------IVMEEGCATQKQVLNYLGERFRVKVNLPDWYPNEQAAEFLFNECIC 277

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             +    T + Y+         +L +    E     ++  + +         L       
Sbjct: 278 IHL-KSNTEKFYMLCLMTRKLFALAKGECMEENPDSLVNQEVLTPGQLFLMFLKEKLEAW 336

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
                + I +  +   VS  +        L  D  K     +    +  +  L    D  
Sbjct: 337 LVSIKIAIDKKAQKTSVSLNTENLMKILNLGIDLTKPFEYLLATGNLRSKTGLGFLQDSG 396

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                D +  I+ L   R     +    +    R  +V  +L   +              
Sbjct: 397 LCVVADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRLLPESWGFLC-------PVH 445

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
               +   +M       + V   V      + L  L   V  +    H RR S      +
Sbjct: 446 TPDGEPCGLMNHLTATCEVVTQFVYTASIPALLCSLG--VTPVDSAPH-RRYSECYPVLL 502

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                G   +++ P+    +   +      I     +               Y      +
Sbjct: 503 DGVMVGWADKELAPSIADSLRHFKVLREKRIPPWMEVVLIPMTGKPSLYPGLYLFTTPCR 562

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           +   V  L    EE   I            F +E++                   +  P 
Sbjct: 563 LVRPVQNLGLGREE--LIGTMEQIFMNVAIFEDEVLAG------------VTTHQELFPH 608

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 609 SLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 641


>gi|315435586|gb|ADU18183.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-09125]
          Length = 237

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 136/229 (59%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKINGSPDW----------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                   +++ + + +S+            VSTPVFDGA E  +  +L            
Sbjct: 143  --ASGLPKELLEAEPESI------------VSTPVFDGARENELQGLLGSTLPNRDGETL 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++E G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VNEDGKAQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|311251945|ref|XP_003124849.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 1
            [Sus scrofa]
          Length = 1135

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 117/558 (20%), Positives = 189/558 (33%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVLAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+          +         P G +  V  +        D 
Sbjct: 697  GFPLLTFKDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G      P   + +  L  D 
Sbjct: 757  MILNKASWERGFAH-GSVYKSEFIDLSEKIKQGDDSLVFGVR----PGDPRVAQKLDDDG 811

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +        +             ES  V Y++ ++ + D  K        G+D   G  +
Sbjct: 812  LPFVGAQLQYGDPYYSYLNLNTGESFVVYYKSKENCIVDNIK------VCGNDTGSGRFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPVEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +            + K                  
Sbjct: 926  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKA----------------- 968

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                             A  +  G   LY G++G   +  + +G
Sbjct: 969  ---------------------------------AGYNYYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYSCSLCNRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 92/611 (15%), Positives = 205/611 (33%), Gaps = 79/611 (12%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCATQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GERFRVKVNLPDWYPNEQAAEFLFNECICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            ++ D+L N+ V + G++       K +  L  +++    K + +SV +++     ++N 
Sbjct: 363 EENPDSLVNQEVLTPGQLFLMFLKEKLEAWLVSIKIAIDKKAQKTSVSLNTENLMKILNL 422

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------------- 598
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTATCEVVTQFVYTASIPALLCSLGV 539

Query: 599 ----ETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                 P+R+  +      + V+   A +E    IA +   L       E+ +      E
Sbjct: 540 TPVDSAPHRRYSECYPVLLDGVMVGWADKELAPSIADS---LRHFKVLREKRIPP--WME 594

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            +L+P      +        +    + P          L+G   Q      +  +    G
Sbjct: 595 VVLIPMTGKPSLYPGLYLFTTPCRLVRPVQNLGLGREELIGTMEQIFMNVAIFEDEVLAG 654

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                 +   S  +++A     +   D  +      +  +   T G   + L+ F+  + 
Sbjct: 655 VTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMG---FPLLTFKDRSD 708

Query: 773 NTCV----NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           N        Q PLV+                 D+ +  +G N +VA + + GY+ ED+M+
Sbjct: 709 NKLYRLQTPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMI 758

Query: 829 ISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +++          S++  EF  ++   K G + +   +        + +D+ G+  VGA+
Sbjct: 759 LNKASWERGFAHGSVYKSEFIDLSEKIKQGDDSLVFGVRPGDPRVAQKLDDDGLPFVGAQ 818

Query: 888 VNPGDILVGKI 898
           +  GD     +
Sbjct: 819 LQYGDPYYSYL 829



 Score = 69.3 bits (168), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 101/712 (14%), Positives = 197/712 (27%), Gaps = 128/712 (17%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK-----------FDVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLSHAVQAIPPFEFTFKDERISLTIVDAAISPPTVPKGSICKELNIYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K + +Q  ++G +P+M K                   
Sbjct: 112 GRLTADISWAVNGI--------SKGVIKQ--FLGYVPIMVKSKLCNLYSLSPRALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K ++   G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMVRPKWKSRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E+    + +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCATQKQVLNYLGERFRVKVNL 314

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +   +    T + Y+         +L +    E     ++  +
Sbjct: 315 PDWYPNEQAAEFLFNECICIHL-KSNTEKFYMLCLMTRKLFALAKGECMEENPDSLVNQE 373

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         L            + I +  +   VS  +        L  D  K     
Sbjct: 374 VLTPGQLFLMFLKEKLEAWLVSIKIAIDKKAQKTSVSLNTENLMKILNLGIDLTKPFEYL 433

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +    +  +  L    D       D +  I+ L   R     +    +    R  +V  +
Sbjct: 434 LATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRL 489

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                  +   +M       + V   V      + L  L   V 
Sbjct: 490 LPESWGFLC-------PVHTPDGEPCGLMNHLTATCEVVTQFVYTASIPALLCSLG--VT 540

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +    H RR S      +     G   +++ P+    +   +      I     +    
Sbjct: 541 PVDSAPH-RRYSECYPVLLDGVMVGWADKELAPSIADSLRHFKVLREKRIPPWMEVVLIP 599

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                      Y      ++   V  L    EE   I            F +E++     
Sbjct: 600 MTGKPSLYPGLYLFTTPCRLVRPVQNLGLGREE--LIGTMEQIFMNVAIFEDEVLAG--- 654

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                         +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 655 ---------VTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 697


>gi|309356743|emb|CAP36707.2| hypothetical protein CBG_19469 [Caenorhabditis briggsae AF16]
          Length = 1167

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 125/301 (41%), Gaps = 23/301 (7%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DE            + T K    +     + +I    + P G  +   +   ++R    G
Sbjct: 796  DEVYYVTFNMETGDFRTHKFHYAEPAYCGMVRIVENSEAPGGGAQHALIQWRIERNPIIG 855

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KGI S + P E +PF + G   DI+ NP G PSRM +G + E+  G     
Sbjct: 856  DKFASRHGQKGINSFLWPTESLPFSETGMVPDIIFNPHGFPSRMTIGMMIESMAGKCAAT 915

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G+   +    +K     +       K+  + + + KI                      
Sbjct: 916  HGENYDASPFVFKLVLLENGDGGEGVKLDFSQNFSPKIYAGK------------------ 957

Query: 1208 TPVF----DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +P+F    D         +L  A  +  G    Y G+ G   +  +  G +Y  +L HM+
Sbjct: 958  SPIFFSSEDNTAINHFGELLTKAGYNYYGNETFYSGVDGRQMEMQIFFGIVYYQRLRHMI 1017

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-DV 1322
            +DK   R+TG    +T QP+ G+   GG R GEME   I A+G ++VLQ+ L   SD DV
Sbjct: 1018 ADKFQVRATGPIDPITHQPVKGRKKGGGIRFGEMERDAIIAHGTSFVLQDRLLNCSDRDV 1077

Query: 1323 V 1323
             
Sbjct: 1078 A 1078



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 41/112 (36%), Gaps = 29/112 (25%)

Query: 70  GAAMLEFVSYEFDPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
               ++F S +   P  D               +C  R +TYA  LK+ + + V +    
Sbjct: 39  DNVTMKFTSAQLHKPTLDSGAKLTSDTLPLYPAECRQRGMTYAGNLKVNIDVHVNETRLD 98

Query: 117 TGAKSIKDI---------------KEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
                +  +               ++Q +  G+ P+  K G F++ G ++++
Sbjct: 99  IIETILGKVPIMLRSEGCHLRGMSRKQLVAAGEEPI-EKGGYFIVNGSEKVI 149


>gi|148879059|emb|CAM07045.1| RpoB protein [Mycobacterium llatzerense]
          Length = 226

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 127/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 30   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 89

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 90   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 134

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 135  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 177

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 178  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 226


>gi|183579271|gb|ACC63213.1| RpoB [Mycobacterium avium]
          Length = 228

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 128/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I                       
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDGNPEWAVN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 137  -----------------LPEELRHAQPNQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G ++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 180  VDGDGXAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 228


>gi|299473871|gb|ADJ18230.1| ribosomal RNA polymerase beta subunit [Mycobacterium heidelbergense]
          Length = 240

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G K+ +         ++       E  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKVDTGKGVPDWAANLPEELLHAEAD 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 160  A----------------------------IVSTPVFDGAQEGELQGLLSATLPNRDGDVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|295815619|gb|ADG36312.1| RNA polymerase beta-subunit [Mycobacterium montefiorense]
 gi|295815625|gb|ADG36315.1| RNA polymerase beta-subunit [Mycobacterium saskatchewanense]
          Length = 237

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGGPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEDLLHAQPNQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.078,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|51035525|emb|CAH10898.1| RNA polymerase B subunit [Haloferax mediterranei]
          Length = 435

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 102/419 (24%), Positives = 156/419 (37%), Gaps = 74/419 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G       +  + A+   +  ++ D  +     V    +    F R    +  R    + 
Sbjct: 51   GFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVE-RALARSHFFRTYEGEERRYPGGQE 109

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++ E+ ++D       +           L     V+      +++VL           + 
Sbjct: 110  DRFEIPSQD-------VRGARGEDAYSHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEP 162

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
               A    + +R         E+         + +               ++ KV V  +
Sbjct: 163  DDMAGLSPQKRRETSVTMRSGESGVVDTVTLMEGE------------DGSKLAKVSVRDQ 210

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+V  + P EDMPF  DG   D+VLNP  +PSRM V        
Sbjct: 211  RVPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVLNPHALPSRMTV-------- 262

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G     LG K+ +L                                              
Sbjct: 263  GHVLEMLGGKVGALEGRRVDGT-------------------------------------- 284

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     F G DE  + S L       SG+ ++Y G+TGE  +  + VG I+  KL H
Sbjct: 285  --------AFQGEDEHELRSALEERGFMSSGKEVMYSGVTGEKIEAEIFVGIIFYHKLYH 336

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            MVS+K++ARS G   ++T+QP  G++  GG RLGEME   +  +GAA VLQE L   SD
Sbjct: 337  MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRLGEMERDTVIGHGAAMVLQERLLDSSD 395



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 77/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLMHYPQLSMVK----------TQTTEQIGFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        E+   ++DE 
Sbjct: 76  ALVMNKGSVERALARSHFFRTYEGEERRYPGGQEDRF-EIPSQDVRGARGEDAYSHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V+   +L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETVVDENSVLLGKTSPPRFLEEP------DDMAGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    ++   EL  +
Sbjct: 189 DTVTLMEGEDGSKLAKVSVRDQRVPELGDK 218


>gi|158954696|gb|ABW84319.1| RNA polymerase subunit B [Mycobacterium lentiflavum]
          Length = 238

 Score =  286 bits (733), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI+                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIEGEPEWAAN-------------- 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 147  -----------------LPDGLRHAQPDQTVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 190  VNADGKARLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.045,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|226292175|gb|EEH47595.1| DNA-directed RNA polymerase I subunit RPA2 [Paracoccidioides
            brasiliensis Pb18]
          Length = 1242

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 86/422 (20%), Positives = 145/422 (34%), Gaps = 72/422 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSIS 958
            G          + A+      D+ D  +   S            +       DK  R   
Sbjct: 769  GLDNFPNGMNAVVAVLSYTGYDMDDAMIINRSAHDRGFGWGTIYKTKVYSLDDKESRGRG 828

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              + +I  L                     ++ G+   +  +            ++E   
Sbjct: 829  KAKREIAKL--------------FGFAPGGLIKGEWRQTLDED---GLPHIGVRVTEGSI 871

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W     D      +   +  +       E+ + + +  +  G +      + + +  
Sbjct: 872  VAAWHTVRFDAVSNSYINIDRQTHFLKYKDTEEGYIDSVRIL--GSETGGDPCQAISIKY 929

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
             + R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM +G   E
Sbjct: 930  RIPRKPVIGDKFSSRHGQKGVCSQLWPAIDMPFSESGIQPDVIINPHAFPSRMTIGMFVE 989

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            +  G +    G    S    +                                       
Sbjct: 990  SLAGKSGALHGLAQDSTPFRFSEEHTAGD------------------------------- 1018

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                        F G         LR A  +  G   +Y G+TG  F   + +G +Y  +
Sbjct: 1019 ------------FFG-------EQLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQR 1059

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   
Sbjct: 1060 LRHMVNDKFQVRTTGPVNALTGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNC 1119

Query: 1319 SD 1320
            SD
Sbjct: 1120 SD 1121



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 83/675 (12%), Positives = 192/675 (28%), Gaps = 115/675 (17%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   + + +     +           +G +P+M +    
Sbjct: 121 EIYPAECRERHATYRGRLRARLEYRINNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS-- 175
                                G FV+ G ++++   +   R+ P         +   +  
Sbjct: 171 YLEKCSPEQLVQHKEESEELGGYFVVNGNEKLIRMLIVGRRNFPMAIIRSSFMKRGPTYT 230

Query: 176 --GKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE- 226
             G  + + R  PDQ      +    D    +  R   R+    VPV   L  L   ++ 
Sbjct: 231 KFGIQIRSVR--PDQTSQTNFLHYLSDGN--VTFRFTWRKNEYLVPVVMILKGLVQTNDR 286

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +I    + ++V  +  +          + +  +           +     G+K       
Sbjct: 287 DI----FERLVGHEGSEGIKNSFVTDRVELLLRTYKGYGIHGRDDIRAYLGEKFRPV--- 339

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                 +       D   G+     +V    G   +   D  D      I     +   +
Sbjct: 340 ------LGMPTDIPDEAVGVEFLRKVVLPHLGNHNV--TDSQDNDKFNMILFMIRKLYTL 391

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           +  D   +N               ++ LL   +Y ++    +  +             + 
Sbjct: 392 VAGDCAPDNP---------DAVSNQEVLLGGFLYGMLLKERLEEW------LRSFGPIAQ 436

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           ++ +       ++ +   +    +     E+I   ++  +   N   +   +D       
Sbjct: 437 EWSVKNQNARFIDPKFEKEFLSRIVARTNENIGGALEYFLSTGN-LVSPTGLDLQQPSGY 495

Query: 465 RSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQ 521
             + E +     +   RM    S   ++ +  +  ++P+      PV +         + 
Sbjct: 496 TVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNH 555

Query: 522 LSQ-------LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV---HPTHYGRICP 571
           L+          +       I++    S             ++ R +    P     I  
Sbjct: 556 LAHKCKIETSNLDVSGVPQIISNLGVTSESSVSLEESVVVQMDGRILGYCSPKQARIISD 615

Query: 572 AETS---EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                  EG+    V     +   +  G     Y      ++   V YL   + +  Y+ 
Sbjct: 616 TLRYWKVEGNKSLPVELEIGYVPNSNRGQYPGIYLFSQCARMVRPVKYLPLDKLD--YVG 673

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                  E      +++                  ++  P  ++SI A++ PF + + S 
Sbjct: 674 PFEQPFMEIACVPSDIISG------------VSTHVEFDPTYILSIVANMTPFSDFNQSP 721

Query: 689 RVLMGCNMQRQAVPL 703
           R +  C M +QA+  
Sbjct: 722 RNMYQCQMGKQAMGT 736



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 88/575 (15%), Positives = 172/575 (29%), Gaps = 79/575 (13%)

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  + +V +    N +  D   + +   I+ +I+ L  L  G    D+ D + N+ V   
Sbjct: 353 VEFLRKVVLPHLGNHNVTDSQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAVSNQEVLLG 412

Query: 468 G--------EMLKNQYRLG------LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           G        E L+   R             ++ +      + + +        + +  A+
Sbjct: 413 GFLYGMLLKERLEEWLRSFGPIAQEWSVKNQNARFIDPKFEKEFLSRIVARTNENIGGAL 472

Query: 514 CEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             F  +  L              + + E +N    I+H R    + +G          +R
Sbjct: 473 EYFLSTGNLVSPTGLDLQQPSGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVR 529

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKVT------- 611
            + P  +G +CP  T +G   GL++ L    ++       +   + + +  VT       
Sbjct: 530 KLLPESWGFLCPVHTPDGSPCGLLNHLAHKCKIETSNLDVSGVPQIISNLGVTSESSVSL 589

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + Y S  +     I        +        V            R + 
Sbjct: 590 EESVVVQMDGRILGYCSPKQ---ARIISDTLRYWKVEGNKSLPVELEIGY-VPNSNRGQY 645

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             I    +    +       L+  D         M+   VP        V T +E     
Sbjct: 646 PGIYLFSQCARMVRPVKYLPLDKLDYVGPFEQPFMEIACVPS--DIISGVSTHVEFDPTY 703

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +IVA      +   + R + +   G     T G  I    +           Q P+
Sbjct: 704 IL--SIVANMTPFSDFNQSPRNMYQCQMGKQAMGTPGTSI--QYRTDNKLYRLQTGQTPI 759

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+                  L +   G N +VA + + GY+ +D+M+I+           
Sbjct: 760 VRP----------PLYNCYGLDNFPNGMNAVVAVLSYTGYDMDDAMIINRSAHDRGFGWG 809

Query: 842 IHIEEFEVMARDTKL-GPEEITRDIPNV---------SEEGLKNIDECGIICVGAEVNPG 891
              +       D +  G  +  R+I  +           E  + +DE G+  +G  V  G
Sbjct: 810 TIYKTKVYSLDDKESRGRGKAKREIAKLFGFAPGGLIKGEWRQTLDEDGLPHIGVRVTEG 869

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            I+    T + ++       + R     K  D  +
Sbjct: 870 SIVAAWHTVRFDAVSNSYINIDRQTHFLKYKDTEE 904


>gi|225681121|gb|EEH19405.1| DNA-directed RNA polymerase I polypeptide 2 [Paracoccidioides
            brasiliensis Pb03]
          Length = 1242

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 86/422 (20%), Positives = 145/422 (34%), Gaps = 72/422 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSIS 958
            G          + A+      D+ D  +   S            +       DK  R   
Sbjct: 769  GLDNFPNGMNAVVAVLSYTGYDMDDAMIINRSAHDRGFGWGTIYKTKVYSLDDKESRGRG 828

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              + +I  L                     ++ G+   +  +            ++E   
Sbjct: 829  KAKREIAKL--------------FGFAPGGLIKGEWRQTLDED---GLPHIGVRVTEGSI 871

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W     D      +   +  +       E+ + + +  +  G +      + + +  
Sbjct: 872  VAAWHTVRFDAVSNSYINIDRQTHFLKYKDTEEGYIDSVRIL--GSETGGDPCQAISIKY 929

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
             + R    GDK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM +G   E
Sbjct: 930  RIPRKPVIGDKFSSRHGQKGVCSQLWPAIDMPFSESGIQPDVIINPHAFPSRMTIGMFVE 989

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            +  G +    G    S    +                                       
Sbjct: 990  SLAGKSGALHGLAQDSTPFRFSEEHTAGD------------------------------- 1018

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                        F G         LR A  +  G   +Y G+TG  F   + +G +Y  +
Sbjct: 1019 ------------FFG-------EQLRKAGYNFHGNEPMYSGITGREFAADIYLGVVYYQR 1059

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   
Sbjct: 1060 LRHMVNDKFQVRTTGPVNALTGQPVKGRAKGGGIRVGEMERDALLAHGAAFLLQDRLMNC 1119

Query: 1319 SD 1320
            SD
Sbjct: 1120 SD 1121



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 83/675 (12%), Positives = 191/675 (28%), Gaps = 115/675 (17%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           +    +C  R  TY   L+  L   + + +     +           +G +P+M +    
Sbjct: 121 EIYPAECRERHATYRGRLRARLEYRINNGEWKESVRE----------LGQVPIMLRSNRC 170

Query: 142 ---------------------GTFVIKGIQRIVVSQLH--RS-PGIHFDHDKGRASLS-- 175
                                G FV+ G ++++   +   R+ P         +   +  
Sbjct: 171 YLEKCSPEQLVQHKEESEELGGYFVVNGNEKLIRMLIVGRRNFPMAIIRSSFMKRGPTYT 230

Query: 176 --GKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE- 226
             G  + + R  PDQ      +    D    +  R   R+    VPV   L  L   ++ 
Sbjct: 231 KFGIQIRSVR--PDQTSQTNFLHYLSDGN--VTFRFTWRKNEYLVPVVMILKGLVQTNDR 286

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +I    + ++V  +  +          + +  +           +     G+K       
Sbjct: 287 DI----FERLVGHEGSEGIKNSFVTDRVELLLRTYKGYGIHGRDDIRAYLGEKFRPV--- 339

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                 +       D   G+     +V    G   +   D  D      I     +   +
Sbjct: 340 ------LGMPTDIPDEAVGVEFLRKVVLPHLGNHNV--TDSQDNDKFNMILFMIRKLYTL 391

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           +  D   +N               ++ LL   +Y ++    +  +             + 
Sbjct: 392 VAGDCAPDNP---------DAVSNQEVLLGGFLYGMLLKERLEEW------LRSFGPIAQ 436

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            + +       ++ +   +    +     E+I   ++  +   N   +   +D       
Sbjct: 437 DWSVKNQNARFIDPKFEKEFLSRIVARTNENIGGALEYFLSTGN-LVSPTGLDLQQPSGY 495

Query: 465 RSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQ 521
             + E +     +   RM    S   ++ +  +  ++P+      PV +         + 
Sbjct: 496 TVMAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNH 555

Query: 522 LSQ-------LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV---HPTHYGRICP 571
           L+          +       I++    S             ++ R +    P     I  
Sbjct: 556 LAHKCKIETSNLDVSGVPQIISNLGVTSESSVSLEESVVVQMDGRILGYCSPKQARIISD 615

Query: 572 AETS---EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                  EG+    V     +   +  G     Y      ++   V YL   + +  Y+ 
Sbjct: 616 TLRYWKVEGNKSLPVELEIGYVPNSNRGQYPGIYLFSQCARMVRPVKYLPLDKLD--YVG 673

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                  E      +++                  ++  P  ++SI A++ PF + + S 
Sbjct: 674 PFEQPFMEIACVPSDIISG------------VSTHVEFDPTYILSIVANMTPFSDFNQSP 721

Query: 689 RVLMGCNMQRQAVPL 703
           R +  C M +QA+  
Sbjct: 722 RNMYQCQMGKQAMGT 736



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 88/575 (15%), Positives = 172/575 (29%), Gaps = 79/575 (13%)

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  + +V +    N +  D   + +   I+ +I+ L  L  G    D+ D + N+ V   
Sbjct: 353 VEFLRKVVLPHLGNHNVTDSQDNDKFNMILFMIRKLYTLVAGDCAPDNPDAVSNQEVLLG 412

Query: 468 G--------EMLKNQYRLG------LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           G        E L+   R             ++ +      + + +        + +  A+
Sbjct: 413 GFLYGMLLKERLEEWLRSFGPIAQDWSVKNQNARFIDPKFEKEFLSRIVARTNENIGGAL 472

Query: 514 CEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             F  +  L              + + E +N    I+H R    + +G          +R
Sbjct: 473 EYFLSTGNLVSPTGLDLQQPSGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVR 529

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKVT------- 611
            + P  +G +CP  T +G   GL++ L    ++       +   + + +  VT       
Sbjct: 530 KLLPESWGFLCPVHTPDGSPCGLLNHLAHKCKIETSNLDVSGVPQIISNLGVTSESSVSL 589

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + Y S  +     I        +        V            R + 
Sbjct: 590 EESVVVQMDGRILGYCSPKQ---ARIISDTLRYWKVEGNKSLPVELEIGY-VPNSNRGQY 645

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             I    +    +       L+  D         M+   VP        V T +E     
Sbjct: 646 PGIYLFSQCARMVRPVKYLPLDKLDYVGPFEQPFMEIACVPS--DIISGVSTHVEFDPTY 703

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +IVA      +   + R + +   G     T G  I    +           Q P+
Sbjct: 704 IL--SIVANMTPFSDFNQSPRNMYQCQMGKQAMGTPGTSI--QYRTDNKLYRLQTGQTPI 759

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V+                  L +   G N +VA + + GY+ +D+M+I+           
Sbjct: 760 VRP----------PLYNCYGLDNFPNGMNAVVAVLSYTGYDMDDAMIINRSAHDRGFGWG 809

Query: 842 IHIEEFEVMARDTKL-GPEEITRDIPNV---------SEEGLKNIDECGIICVGAEVNPG 891
              +       D +  G  +  R+I  +           E  + +DE G+  +G  V  G
Sbjct: 810 TIYKTKVYSLDDKESRGRGKAKREIAKLFGFAPGGLIKGEWRQTLDEDGLPHIGVRVTEG 869

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            I+    T + ++       + R     K  D  +
Sbjct: 870 SIVAAWHTVRFDAVSNSYINIDRQTHFLKYKDTEE 904


>gi|295815613|gb|ADG36309.1| RNA polymerase beta-subunit [Mycobacterium kubicae]
          Length = 239

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 130/229 (56%), Gaps = 38/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI +      A      L       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKIDADQRPEWAANLREDLLHAEPNA 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
            I                             V+TPVFDGA E  +  +L            
Sbjct: 160  I-----------------------------VATPVFDGAQEAELQGLLSYTLPNRDNEVM 190

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 191  VDGDGKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 239



 Score = 45.1 bits (105), Expect = 0.084,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|315435598|gb|ADU18189.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-09337]
          Length = 237

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   S   V+TPVFDGA E+ +  +L     +      
Sbjct: 146  -----------------LPEGMQSAPSDSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 188

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.068,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|60172312|gb|AAX14487.1| RNA polymerase beta subunit [Aliivibrio salmonicida]
          Length = 184

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 101/187 (54%), Positives = 133/187 (71%), Gaps = 5/187 (2%)

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   +
Sbjct: 1    PVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQE 57

Query: 1165 ISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            +   R+FL+KV   G   +   I+   DD V  + +    G+P++TP+FDGA E +I  +
Sbjct: 58   LHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLVKNLHGGLPIATPIFDGAPESSIKEL 117

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 118  LKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 177

Query: 1283 LGGKSNR 1289
            LGGK+  
Sbjct: 178  LGGKAQF 184


>gi|218282083|ref|ZP_03488382.1| hypothetical protein EUBIFOR_00957 [Eubacterium biforme DSM 3989]
 gi|218216876|gb|EEC90414.1| hypothetical protein EUBIFOR_00957 [Eubacterium biforme DSM 3989]
          Length = 643

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 102/497 (20%), Positives = 188/497 (37%), Gaps = 80/497 (16%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           A  +V  G    R+ + K    +++P+L+E+Q  S+  F            +G+Q  F+ 
Sbjct: 6   AYRIVSCGKKSSRRDYSKVSGKLELPNLVEIQTDSFKWFTQ----------QGIQEVFEE 55

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           ++PI  +     L F+ Y F+ PK++ ++ ++R+  +A PL   + L V   D  TG   
Sbjct: 56  IYPIENYGKNIRLNFLRYHFEEPKYNAEESMYRECNFAAPLYADMELEV--TDSETGEVV 113

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
               K + +Y+GD PLMT+ GTF+I G +R++VSQ+ RSPG +F         +GK  ++
Sbjct: 114 T---KSEEVYLGDFPLMTETGTFIINGAERVIVSQIVRSPGAYFADSYD--EKTGKQNFS 168

Query: 182 CRIIPDQGLWMDIEFDSKD-----IIHVRIDRRRKVPVTSF------------------- 217
           C +IP +G W++   + K      +I+V IDRRRKV  +                     
Sbjct: 169 CELIPSRGTWLEFMTEQKKTTNGRLINVSIDRRRKVLFSILFKAIGMSLNIGVNEDTHDT 228

Query: 218 ------LMALG---------MDSEEILSTF----------YPKIVYSQRGDFWCFPLSAA 252
                 L A+G          +  E ++ +          Y +I  S   D       A 
Sbjct: 229 SMMETFLRAMGRNWSDVATDAEDREYMNMYLLLYTAFFGKYEEIENSLLNDKVKTTQEAL 288

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKEKGVKFLGITSDCLCGLYVAE 310
                 + S  +  +D G   +   K        L       ++      D + G+ +A 
Sbjct: 289 LSFYENQRSDEIPTLD-GSITLMQAKFFDHRRYDLTKAGRYKLRKKLNAIDRMYGMSLAH 347

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
           DIV+   G +++E G ++       +         +          +       D     
Sbjct: 348 DIVDV-NGNVFMEKGTMVHRDERNALRE------ELAKGTYCVAYPFRSEFHEEDIVSIP 400

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
                 +   +   DV T       +        + D+  + +V  N+ +          
Sbjct: 401 TSWTTGLIGRVLASDVETEDA----YLDAGTVLTEQDVLAIQKVVENVDIFAGLFAQPVK 456

Query: 431 IRKEDIIAIIKILVDLR 447
           +  E++ ++      L 
Sbjct: 457 LTAENMDSVFNYGQRLY 473



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 73/330 (22%), Positives = 133/330 (40%), Gaps = 49/330 (14%)

Query: 232 FYPKIVYSQRG---DFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           F+    Y             L+A D M G  ++  +VD+  G   +E G  +      +L
Sbjct: 314 FFDHRRYDLTKAGRYKLRKKLNAIDRMYGMSLAHDIVDV-NGNVFMEKGTMVHRDERNAL 372

Query: 289 KEKGVK---------FLGITSDCLC--------GLYVAEDIVNGETGEIYIEAGDVIDE- 330
           +E+  K               + +         GL       + ET + Y++AG V+ E 
Sbjct: 373 REELAKGTYCVAYPFRSEFHEEDIVSIPTSWTTGLIGRVLASDVETEDAYLDAGTVLTEQ 432

Query: 331 ---------KSLEEIFHSEIRDIPILYVDSVNNNAY---------IRNTLVTDKNKDRKD 372
                    ++++       + + +   +  +   Y         + N    D      +
Sbjct: 433 DVLAIQKVVENVDIFAGLFAQPVKLTAENMDSVFNYGQRLYALGRLTNAQGEDIVDADME 492

Query: 373 ALLDIYRVMRPGDVSTFSVAESM--------FNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
            + + Y V    D     V   +               +   ++  +      +R+  + 
Sbjct: 493 LVANRYMVGVSPDAIDSDVETQVKQRALSEDITAWLIGACVQEVYIIDNNGDEVRVAGND 552

Query: 425 P-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           P  +   I   D+ A     +++  G GT DDID LGNRR+RSVGE+++NQ+R+GL RME
Sbjct: 553 PFANKHTITVSDMYAFFSYSLNVMEGVGTTDDIDMLGNRRIRSVGELIQNQFRIGLSRME 612

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           R +KER+S  ++DS+ P+ L N +P+ +A+
Sbjct: 613 RVVKERMSIQEMDSLTPRKLTNIRPLTAAI 642



 Score = 50.1 bits (118), Expect = 0.002,   Method: Composition-based stats.
 Identities = 43/203 (21%), Positives = 75/203 (36%), Gaps = 9/203 (4%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA----EDIVNGETGEIYIEAGD 326
           E + E  K     L+    ++  K L        G+ +     ED  +    E ++ A  
Sbjct: 180 EFMTEQKKTTNGRLINVSIDRRRKVLFSILFKAIGMSLNIGVNEDTHDTSMMETFLRAMG 239

Query: 327 VIDEKSLEEIFHSE-IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
                   +    E +    +LY         I N+L+ DK K  ++ALL  Y   R  +
Sbjct: 240 RNWSDVATDAEDREYMNMYLLLYTAFFGKYEEIENSLLNDKVKTTQEALLSFYENQRSDE 299

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
           + T   + ++    FFD  +YDL+  GR K+  +LN         +  +    I+ +  +
Sbjct: 300 IPTLDGSITLMQAKFFDHRRYDLTKAGRYKLRKKLNAIDRMYGMSLAHD----IVDVNGN 355

Query: 446 LRNGKGTIDDIDNLGNRRVRSVG 468
           +   KGT+   D     R     
Sbjct: 356 VFMEKGTMVHRDERNALREELAK 378


>gi|109104775|ref|XP_001114787.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like, partial
            [Macaca mulatta]
          Length = 449

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 91/391 (23%), Positives = 142/391 (36%), Gaps = 79/391 (20%)

Query: 1001 GFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
            G K         + +        +    D        +    +       E+   + I+ 
Sbjct: 109  GIKPGDPRILQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKV 168

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                +D   G  + V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   D
Sbjct: 169  CS--NDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPD 226

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+ NP G PSRM +G + E+  G +    G    +    +                    
Sbjct: 227  ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY----------- 275

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                      ML+ A  +  G   LY G
Sbjct: 276  ---------------------------------------FGEMLKAAGYNFYGTERLYSG 296

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            ++G   +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME 
Sbjct: 297  ISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMER 356

Query: 1300 WCIQAYGAAYVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG 1335
              + A+G +++L + L   SD     V    G                 R R Y   +  
Sbjct: 357  DALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCN 416

Query: 1336 --NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
              +       P  F   V E+ A+ + + L+
Sbjct: 417  RSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 447



 Score = 60.1 bits (144), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 71/182 (39%), Gaps = 18/182 (9%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++      
Sbjct: 32  QSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERG 81

Query: 838 V-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD    
Sbjct: 82  FAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRILQKLDDDGLPFIGAKLQYGDPYYS 141

Query: 897 KITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +     +  T E  ++     E     +++  S    SG    V       R+    ++
Sbjct: 142 YL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDK 196

Query: 955 RS 956
            +
Sbjct: 197 FA 198


>gi|168003281|ref|XP_001754341.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162694443|gb|EDQ80791.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 906

 Score =  286 bits (732), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 99/489 (20%), Positives = 179/489 (36%), Gaps = 102/489 (20%)

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            P+     T    +L+         V    L        ++V  +     G+ ++    + 
Sbjct: 498  PQKPLVTTRAASILQKPELYSGQTVIVAILCYGYNQEDSIVMNQASVDRGLFRSAHYKTY 557

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
            + E+ + +            +  Y++ ++ + G       +   K  ++   + SE    
Sbjct: 558  KGEEKKNIQEQFSKPSTSDVKGWYNKSLDKVEGDGFPCLGEKLVKGDIVIGKVTSE---- 613

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                  V + +   +   LKV  +     +    +                 R+ KV + 
Sbjct: 614  ------VHNPRQVDSSTHLKVHQKGHVDQVMLSSEE-------------DGHRIAKVRLR 654

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            + R  Q+GDK +  HG KG++  + P ED+PF + G   DI++NP  +PSR  VGQI E 
Sbjct: 655  VTRAPQAGDKFSSMHGQKGVIGALFPQEDLPFTQQGIVPDIIMNPHALPSRQTVGQILEC 714

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
                    LGK I +                                             
Sbjct: 715  L-------LGKAIAASGKRR---------------------------------------- 727

Query: 1200 WKSGVPVSTPVFDGADEEA-INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                   + P F G D    IN  L  A L   G   + +G TG+     VT+G  +  +
Sbjct: 728  ------YAIP-FSGIDNAEAINQYLHEAKLARGGCEFMSNGTTGQRLKVLVTIGPTFYQR 780

Query: 1259 LNHMVSDKVYAR-STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            L HM  DK+  R +TG  +L+T+QP+  +++ GG + GEME  C+  +GA+  L+E   +
Sbjct: 781  LEHMAEDKIKYRGNTGPVNLLTRQPVKDRNSLGGLKFGEMERDCMLGHGASATLRERYFL 840

Query: 1318 KSDDVVGRTRVY-------------ESIVA------GNDTFETGTPESFNVLVKEMQALG 1358
             SD      ++Y               I        G    +   P +  +L +E+ ++G
Sbjct: 841  LSDP----YKMYICQSCRRPATMDSSRIPKCQFCKNGKRIVQVQIPYACKLLWQELLSMG 896

Query: 1359 LSIDLENSR 1367
            + + ++  +
Sbjct: 897  ICVYMDTKK 905



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 89/707 (12%), Positives = 212/707 (29%), Gaps = 117/707 (16%)

Query: 212 VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P    + ALG    +E +      +      +     + AAD  +   ++     +   
Sbjct: 15  IPAVIIMRALGFCSDKEFMEMVCYDLSDLHLMELIRPSILAADEYMDNALAYIGSKMTNN 74

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC--------GLYVAEDIVNGETGEIYI 322
            +  E   +    L+     +G K        +         G    +D  + +   + +
Sbjct: 75  VKPDEECGRDVLNLMFHHIGQGYKQKAYFLGYMIRQICLARLGRCPEDDKEHYKNKRLDL 134

Query: 323 EAGDVID--EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
               +      ++  +     + +        +  +       +   K+ + A       
Sbjct: 135 AGQLLRHQFRAAMAHLQRDMQKQLQKHLGKEDSLGSIKTFVQESIITKNLQGAFT----- 189

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
           +   + S    +  +   +   +    +S + ++++N+       +  RH        + 
Sbjct: 190 LGNWNTSEGQRSSGVVGDIKRTNTIAMISHLRQLRLNLPPKSRPTESARHPNFSYWARVC 249

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
            +     +  G + +I   G     +  E L             +I        ++ ++P
Sbjct: 250 PVQTTDGDDCGLVKNISLTGILSSNTEEEPLM------------AILLDHGMRYLEEILP 297

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
             L +   V      F     +  L+   + ++ +   RR  A+ +         ++   
Sbjct: 298 SSLADTDKV------FLNGKWVGTLDNSQDLVNILRAHRRKGAVHEETEVVKDDHLKEVR 351

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           ++      + P    +   + L         ++     +T             V YL   
Sbjct: 352 IYTDGGRILRPLLVVQNQCLVLSKRHLKKINMDMKTG-KTAKECWQALLADGVVEYLGVE 410

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EEE   +A  +  L +       LV                   +     ++ + AS IP
Sbjct: 411 EEEGAMVALGSDDLAKARGCDGALV---------------YSHCEIDSSYLMGLGASTIP 455

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++ ++R L   +   +    L                                    
Sbjct: 456 FLEHNQASRNLFQSDKHCKQAIGLYTTNF------------------------------- 484

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                           S   ++   K   + +   + Q+P +  G  V            
Sbjct: 485 ----------QSRADASASHLFYPQKPLVTTRAASILQKPELYSGQTV------------ 522

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT--KLGP 858
                      +VA + + GYN EDS+++++  V   +F S H + ++   +    +   
Sbjct: 523 -----------IVAILCY-GYNQEDSIVMNQASVDRGLFRSAHYKTYKGEEKKNIQEQFS 570

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
           +  T D+     + L  ++  G  C+G ++  GDI++GK+T +  +P
Sbjct: 571 KPSTSDVKGWYNKSLDKVEGDGFPCLGEKLVKGDIVIGKVTSEVHNP 617


>gi|301781943|ref|XP_002926383.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 2
            [Ailuropoda melanoleuca]
          Length = 1079

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 113/558 (20%), Positives = 184/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F +I I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQIFMNIAIFEDEVLAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      ++    +   L+          +         P G +  V  +        D 
Sbjct: 641  GFPLLTYQARSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 701  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDDSLVFGVKPGDP--------RILQKL 751

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       Q    D        +    +       E+   + I+     +D   G  +
Sbjct: 752  DDDGLPFIGAQLQYGDPYYSYLNLNTGESFVMYYKSKENCIVDNIKVCS--NDTGSGKFK 809

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             + + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 810  CICITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 869

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +            L                    
Sbjct: 870  IGMLIESMAGKSAALHGLCHDATPFTFSEENSALEYFGEL-------------------- 909

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                          L+ A  +  G   LY G++G   +  + +G
Sbjct: 910  ------------------------------LKAAGYNFYGTERLYSGISGIELEADIFIG 939

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 940  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 999

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1000 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCDRSDTIDTVSVPYV 1059

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1060 FRYFVAELAAMNIKVKLD 1077



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 92/673 (13%), Positives = 208/673 (30%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEEDSFFRNSVSQMLRIVMEEGCSTQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          +  + +         +   +  + + L  L  G+  
Sbjct: 249 GECFRVKLSLPDWYPNEQAAEFLFDQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V + G++           + + +        ++ +       + +    
Sbjct: 307 EDNPDSLVNQEVLTPGQLFLMFLKEKMESWLVSIKIALDKRSQKTNVSINTENLMKIFSL 366

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GTDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASVPALLCSLGV 483

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V    V     +E    IA +   L       E+ +   
Sbjct: 484 TPVDGAPHRPYAECYPVLLDGVMVGWV----DKELAPSIADS---LRHFKVLREKRIPP- 535

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 536 -WMEVALIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNIAIFEDE 594

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
              G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 595 VLAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQARS 651

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 652 DNKLYRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G + +   +       L+ +D+ G+  +G
Sbjct: 701 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDDSLVFGVKPGDPRILQKLDDDGLPFIG 760

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++   +       +++  S    SG    +    
Sbjct: 761 AQLQYGDPYYSYL-----NLNTGESFVMYYKSKENCIVDNIKVCSNDTGSGKFKCICITM 815

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 816 RVPRNPTIGDKFA 828



 Score = 43.1 bits (100), Expect = 0.35,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 26/53 (49%)

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
           I +Q  ++G +P+M K                         G F+I GI++++
Sbjct: 73  IIKQ--FLGYVPIMVKSKLCNLHSLPPRALIEHHEEAEEMGGYFIINGIEKVI 123


>gi|255948070|ref|XP_002564802.1| Pc22g07860 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211591819|emb|CAP98074.1| Pc22g07860 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 1249

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 97/422 (22%), Positives = 145/422 (34%), Gaps = 73/422 (17%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSIS 958
            G          + AI      D+ D  +   S            +       + + R   
Sbjct: 770  GLDNFPNGMNAVVAIISYTGYDMDDAMIINKSAHERGFGHGTVYKTKVVTLAENDSRRNK 829

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
             +RE  +L      DE     RN          G     G K                  
Sbjct: 830  SKREVTKLFGFAPGDEIKDQVRNTIDEDGMPHLGARVKEGDKIAA--------------- 874

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
               W     D      V    V +       E+ + + I  +       P     +K  +
Sbjct: 875  ---WHNVRFDPASDSYVNVDGVTHYMKYKDAEEGYVDSIRIMGSESGNEPAQSLSIKYRI 931

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R    GDK + RHG KG++S++ P  DMPF + G   D+++NP   PSRM + Q+ E
Sbjct: 932  --PRKPVIGDKFSSRHGQKGVLSQLWPAVDMPFSESGMQPDLIINPHAFPSRMTIAQMIE 989

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
            +  G A    G    S    +                                       
Sbjct: 990  SMAGKAGAMHGLPQDSTPFQFSEENT---------------------------------- 1015

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +T  F           LR A  +  G   LY G+TG  F   + +G +Y  +
Sbjct: 1016 --------ATDYF--------GEQLRKAGYNYYGNEPLYSGVTGREFSADIYMGLVYYQR 1059

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   
Sbjct: 1060 LRHMVNDKFQVRTTGPVNALTGQPVKGRAKGGGIRVGEMERDSLIAHGAAFLLQDRLMNC 1119

Query: 1319 SD 1320
            SD
Sbjct: 1120 SD 1121



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 60/404 (14%), Positives = 135/404 (33%), Gaps = 46/404 (11%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 493 TSGYTVIAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 549

Query: 579 NIGLVSSLTSFARVNAYGFIETPY-RKVCDGKVTNDVVYLSAMEEENRYIAQANSSL--- 634
             GL++ L+    +       +   R +    V ++    S++  +   + Q +  +   
Sbjct: 550 PCGLLNHLSHKCLIATDNLDVSHLPRTLVQLGVRSE----SSVALDESVVVQLDGRIIGY 605

Query: 635 --DEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASP------KQVVSIAASLIPFLEND 685
              +      + +       +  +PRE ++ +I  S         + S +A +   ++  
Sbjct: 606 CSPKQAQRIADTIRYWKVEGKNNIPRELEVGYIPNSSGGQYPGVYMFSQSARMYRPVKYL 665

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             +++      ++  + +   E+  +    T +E                    Q     
Sbjct: 666 ALDKLDYVGPFEQPFMEIACVESDLIPGLSTHIEFTPTNILSIVANMTPFSDYNQSPRNM 725

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
              +  +  +    + +      K  R        Q P+V+               +  L
Sbjct: 726 YQCQMSKQTMGTPGTSIAHRTDNKLYRIQTG----QTPIVRP----------PLYNAYGL 771

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF-----EVMARDTKLG 857
            +   G N +VA + + GY+ +D+M+I++             +       E  +R  K  
Sbjct: 772 DNFPNGMNAVVAIISYTGYDMDDAMIINKSAHERGFGHGTVYKTKVVTLAENDSRRNKSK 831

Query: 858 PEEI----TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            E            + ++    IDE G+  +GA V  GD +   
Sbjct: 832 REVTKLFGFAPGDEIKDQVRNTIDEDGMPHLGARVKEGDKIAAW 875



 Score = 58.2 bits (139), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 91/708 (12%), Positives = 188/708 (26%), Gaps = 154/708 (21%)

Query: 78  SYEFDPP------KFD-------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
               + P      K+          +C  R  TY   L+  L   V + D     +    
Sbjct: 102 EIFLEKPTLPPTNKYTTRNREIYPSECRERHATYRGKLRARLEYQVNNGDWMESVRE--- 158

Query: 125 IKEQSIYMGDLPLMTK------------------------DGTFVIKGIQRIVVSQLHRS 160
                  +G++P+M +                         G +++ G ++     L R 
Sbjct: 159 -------LGNVPIMVRTNRCHLEKATPDELVRHKEESEELGGFYIVNGNEK-----LIRM 206

Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWM-------DI----------EFDSKDIIH 203
             +            GK  Y   II  +G ++                   +    +++H
Sbjct: 207 LIV------------GKRNYPMSII--RGSFVKRGQTYTKFGVQIRSVRPDQTSQTNVLH 252

Query: 204 --------VRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
                    R   R+    +PV   L AL   ++      +  IV +             
Sbjct: 253 YLSDGNVTFRFSWRKNEYLIPVMMILKALAETND---REIFEAIVGAASSKGMSNTFVTD 309

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS---DCLCGLYVA 309
            + +  +   +              K         L +     LG+ +   D   G    
Sbjct: 310 RVELLLRTYHAYQ------------KHSQYDCRSHLGKAFRPVLGVPADMPDEEVGTEFL 357

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
             +V    G   +      D+  L      ++           N +A     ++      
Sbjct: 358 RKVVLPHLGNENVTESQDWDKFKLITFMIRKLYSTVAGDCAPDNPDAVSNQEILLGGFLY 417

Query: 370 RKDALLDIYRVMRPGDVS--TFSVAESMFNFLFFDSDKYDLST-VGRVKMNMRLNLDTPD 426
                  I   +R        +S+  +   F     ++  LS  V R   N+   L+   
Sbjct: 418 GMILKERIEEWLRSFGPIARDWSIRNNGAKFTDEAFERDFLSKIVKRSNENIGNALEYFL 477

Query: 427 DVRHI-----------RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
              ++               +IA         +    I         +  +V ++L   +
Sbjct: 478 STGNLVSPTGLDLQQTSGYTVIAEKINFYRFISHFRMIHRGSFFAQLKTTTVRKLLPESW 537

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
                         + + D       + ++ K +++        S L +    +   S  
Sbjct: 538 GFLCP---------VHTPDGSPCGLLNHLSHKCLIATDN--LDVSHLPRTLVQLGVRSES 586

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           +     S + Q            +        R       EG N         +   ++ 
Sbjct: 587 SVALDESVVVQLDGRIIGYCSPKQAQRIADTIRY---WKVEGKNNIPRELEVGYIPNSSG 643

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           G     Y      ++   V YL+  + +  Y+        E      +L+          
Sbjct: 644 GQYPGVYMFSQSARMYRPVKYLALDKLD--YVGPFEQPFMEIACVESDLIPGL------- 694

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                   I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 695 -----STHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGT 737


>gi|548821|sp|P36251|RPOB_LIBAS RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
 gi|144460|gb|AAA23109.1| RNA polymerase beta-subunit [Candidatus Liberibacter asiaticus]
 gi|739027|prf||2002224F RNA polymerase:SUBUNIT=beta
          Length = 178

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 177/178 (99%), Positives = 177/178 (99%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
           SIKDIKEQSIYMGDLPLMTKDGTFVIKG QRIVVSQLHRSPGIHFDHDKGRASLSGKL
Sbjct: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGTQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178


>gi|212533185|ref|XP_002146749.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Penicillium marneffei ATCC 18224]
 gi|210072113|gb|EEA26202.1| DNA-directed RNA polymerase I subunit beta (Rpa2), putative
            [Penicillium marneffei ATCC 18224]
          Length = 1261

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 91/413 (22%), Positives = 150/413 (36%), Gaps = 73/413 (17%)

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD---VRIFNRHGIDKNERSISVEREQIELL 967
              + AI    A D+ D  +   S            +    +  DK+ R    +RE  +L 
Sbjct: 786  NAIVAILSYSAYDMDDAMIINKSSHERGFGHGTVYKTKFYNLDDKDSRRNKSKREISKLF 845

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                          I +     L            K+ + +++           W     
Sbjct: 846  G-------FAPGAEIKAEWRTTLDEDGLPHPGVKVKEGSYVAA-----------WYNVRY 887

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D      V      +       E+ + + +  +  G++     L+ + V   + R    G
Sbjct: 888  DAGSDSYVNVDGQTHFLKYKDAEEGYIDTVRLV--GNENGNEPLQAISVKYRVPRKPIIG 945

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK + RHG KG+ S++ P  DMPF + G   D+++NP   PSRM + QI E+  G A   
Sbjct: 946  DKFSSRHGQKGVCSQLWPAIDMPFSESGIMPDLIINPHAFPSRMTIAQIIESMAGKAGAL 1005

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G  +      +      +                                         
Sbjct: 1006 HGHPVDCTPFQFNEENTAA----------------------------------------- 1024

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                     +     LR A  +  G   +Y G+TG+ F   + +G ++  +L HMV+DK 
Sbjct: 1025 ---------DYFGHQLRKAGYNYHGNEPMYSGITGKEFAADIYLGVVHYQRLRHMVNDKF 1075

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              R+TG  + VT QP+ G+S  GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1076 QVRTTGPVNSVTGQPVKGRSKGGGIRVGEMERDSLLAHGCAFLLQDRLMNCSD 1128



 Score = 70.1 bits (170), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 89/637 (13%), Positives = 189/637 (29%), Gaps = 96/637 (15%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + ++A    +++ + E                 +    +  T    K   R DA   + +
Sbjct: 283 MILKALVETNDREIFEGIVGNASSKGSANTFVTDRVELLLRTFHGYKIWSRSDARAYLGK 342

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             RP           +F    +  ++     + ++ +    N +      + + + I+ +
Sbjct: 343 KFRPV----------LFAPATWTHEECGTEFLRKIVLPHLGNQNVTTTQDYDKFKLILFM 392

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK-------NQYRLGLLRMERS------- 485
           I+ L     G    D+ D + N+ +   G +          ++ L   R+ R        
Sbjct: 393 IRKLYSFVAGDCASDNPDAVSNQEIMLGGYVYGMLLKERLEEWLLSFGRLLRDWSYKGGN 452

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNS 531
           +K      + D +        + +  A+  F  +  L              + + E +N 
Sbjct: 453 LKFTDPMFEKDFISKVIKRTNENLGGALEYFLSTGNLVSPTGLDMQQASGFTVVAEKINF 512

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
              I+H R    + +G          +R + P  +G +CP  T +G   GL++ L     
Sbjct: 513 YRFISHFR---MVHRGTFFAQLKTTTVRKLLPESWGFMCPVHTPDGSPCGLLNHLAHKCL 569

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           V+          +V        +   S+ E       Q N             V   C+ 
Sbjct: 570 VSTSDLDVAHIPRVLAQLG---IKTESSAEVTESVCVQLNG-----------RVIGYCSP 615

Query: 652 EEILVPREKIDFIDASPKQVVS--IAASLIPFLENDDSNRVLMGCN---MQRQAVPLLKA 706
           ++  +  + + F        +   +    IP ++      + M      M R    L   
Sbjct: 616 KQAKMIHDTLRFWKVEGTHGIPKELEIGYIPNMQGGQYPGIYMSSQPARMYRPVKYLALD 675

Query: 707 EAPFVGTG----ME------------SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           +  +VG      ME            S   + +   + +  A +    D  +      + 
Sbjct: 676 KLDYVGPFEQPFMEIACLEEDIRSGLSTHIEFTPTNMFSIIANMTPFSDNNQSPRNMYQC 735

Query: 751 DLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            +   T G        +           Q P+V+                  L +   G 
Sbjct: 736 QMSKQTMGTPGTSIAFRTDNKMYRLQTGQTPIVRSPLYNEYG----------LDNFPNGC 785

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV- 868
           N +VA + +  Y+ +D+M+I++             +       D      +  R+I  + 
Sbjct: 786 NAIVAILSYSAYDMDDAMIINKSSHERGFGHGTVYKTKFYNLDDKDSRRNKSKREISKLF 845

Query: 869 --------SEEGLKNIDECGIICVGAEVNPGDILVGK 897
                     E    +DE G+   G +V  G  +   
Sbjct: 846 GFAPGAEIKAEWRTTLDEDGLPHPGVKVKEGSYVAAW 882



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 87/675 (12%), Positives = 192/675 (28%), Gaps = 121/675 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L+  L+  V + +     +           +G +PLM +       
Sbjct: 132 PAECRERHATYRGRLRARLQYQVNNGEWRESVRE----------LGQVPLMLRSNRCHLE 181

Query: 142 ------------------GTFVIKGIQRIVVSQLHRS--------PGIHFDHDKGRASLS 175
                             G F++ G ++     L R         P         +  + 
Sbjct: 182 SFSPQELVDHKEESEELGGYFIVNGNEK-----LIRMLIMPKRNFPMAINRPSFQKRGV- 235

Query: 176 GKLLYACRIIPDQGLWMDIEFDSK-------DIIHVRIDRRRK---VPVTSFLMALGMDS 225
           G   +  +I   +    D    +          +  R   R++   VPV   L AL +++
Sbjct: 236 GFTTFGVQI---RSARPDQTTQTNVLHYLSDGNVTFRFSWRKQEYLVPVMMILKAL-VET 291

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +     +  IV +              + +  +           +     GKK    L 
Sbjct: 292 ND--REIFEGIVGNASSKGSANTFVTDRVELLLRTFHGYKIWSRSDARAYLGKKFRPVLF 349

Query: 286 K----SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
                + +E G +FL        G        + +  ++ +          + +++    
Sbjct: 350 APATWTHEECGTEFLRKIVLPHLGNQNVTTTQDYDKFKLILF--------MIRKLYSFVA 401

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDK--NKDRKDALLDIYRVMRPG-------DVSTFSVA 392
            D      D+V+N   +    V      +  ++ LL   R++R           +     
Sbjct: 402 GDCASDNPDAVSNQEIMLGGYVYGMLLKERLEEWLLSFGRLLRDWSYKGGNLKFTDPMFE 461

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           +   + +   +++     +        L   T  D++      ++A         +    
Sbjct: 462 KDFISKVIKRTNENLGGALEYFLSTGNLVSPTGLDMQQASGFTVVAEKINFYRFISHFRM 521

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +         +  +V ++L   +                      ++           S 
Sbjct: 522 VHRGTFFAQLKTTTVRKLLPESWGFMC-------PVHTPDGSPCGLLNHLAHKCLVSTSD 574

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HYGRIC 570
           +        L+QL     S + +T +  +     G V    +  + + +H T   +    
Sbjct: 575 LDVAHIPRVLAQLGIKTESSAEVTES--VCVQLNGRVIGYCSPKQAKMIHDTLRFWKVEG 632

Query: 571 PAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                +   IG + ++    +  +         YR V      + + Y+   E+    IA
Sbjct: 633 THGIPKELEIGYIPNMQGGQYPGIYMSSQPARMYRPVK-YLALDKLDYVGPFEQPFMEIA 691

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                +    S                        I+ +P  + SI A++ PF +N+ S 
Sbjct: 692 CLEEDIRSGLS----------------------THIEFTPTNMFSIIANMTPFSDNNQSP 729

Query: 689 RVLMGCNMQRQAVPL 703
           R +  C M +Q +  
Sbjct: 730 RNMYQCQMSKQTMGT 744


>gi|315435610|gb|ADU18195.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-09258]
          Length = 237

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 134/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +   A              
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKINGSPDWASA-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             + +   + + G  VSTPVFDGA E  +  +L            
Sbjct: 146  -----------------LPKELLESEPGSIVSTPVFDGAREAELQGLLSATLPNRDGETL 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +DE G+++L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 189  VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237



 Score = 45.5 bits (106), Expect = 0.068,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|198426188|ref|XP_002131003.1| PREDICTED: similar to RNA polymerase I polypeptide B [Ciona
            intestinalis]
          Length = 1144

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 105/252 (41%), Gaps = 50/252 (19%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G  + V + + ++R    GDK A RHG KGI S+  P  ++PF + G   DIV NP G P
Sbjct: 870  GHFKRVSIVLRVQRNPIIGDKFASRHGQKGICSQKWPMANLPFTESGMFPDIVFNPHGFP 929

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +G + E+  G +    G    +    +                             
Sbjct: 930  SRMTIGMMIESMAGKSAAMHGHCYDATPFTFTE--------------------------- 962

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                   D    E    +L  A  +  G   +Y G++G   +  
Sbjct: 963  -----------------------DKPAIEFFGDLLTEAGYNYYGTETMYSGVSGLEMEAQ 999

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG   ++TQQP+ G+   GG R GEME   + A+G A
Sbjct: 1000 IFIGIVYYQRLRHMVSDKFQVRTTGPVDMITQQPVKGRKRAGGIRFGEMERDALLAHGCA 1059

Query: 1309 YVLQEMLTIKSD 1320
             +L + L   SD
Sbjct: 1060 MLLYDRLLTSSD 1071



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 126/992 (12%), Positives = 275/992 (27%), Gaps = 196/992 (19%)

Query: 16  FFGKNPEIIDIP--DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
            +GK  E    P  DL      S++ F+   +    +    L+            +    
Sbjct: 25  NYGKPEEAQHPPIQDLTRPHVDSFNWFVNDGVKLLAKGLAPLEVLIN--------NDRLA 76

Query: 74  LEFVSYEFDPPKFD------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           L F     + PK +              +C  R  TY   ++ +L   +  + + T  + 
Sbjct: 77  LSFTDISVEKPKIEDGFRNCRTTQVYPSECRQRGATYQAKIQASLSFEINGMKQGTIPR- 135

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV---V 154
                     +G +P+M K                         G FV+ G +++V   +
Sbjct: 136 ---------CLGTIPIMVKSDRCNLHGLSPKELVEKQEEEQEMGGYFVVNGNEKVVRMLI 186

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS--------KDIIHVRI 206
            Q  R+  +       +        +   +        + +  +           + + +
Sbjct: 187 MQR-RNYPVGIVRPSWKNRGQNYTEFGVSVR----SMTEDQTTAPFVLHYLSNGTVTICV 241

Query: 207 DRRRKV---PVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
             R+++   P+   L AL      +I    Y +++ ++  D +        L      + 
Sbjct: 242 YHRKEMFFLPLVLILKALVPFSDRDI----YKELIKTKEDDTYFTCCVQNMLRQAQ--AY 295

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED---IVNGETGE 319
           +L +     + +    ++         +  +    +    L  L   ED   +++  T +
Sbjct: 296 NLFEQKDFLRYLGEKFRIKLNRASWYSDTDIAHFMLKHHVLIHLDSNEDKFRLISFMTRK 355

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           ++  A         + + + E+     L+   +       N  +   ++           
Sbjct: 356 VFDLALGKCMPDDADSVQNQEVLLPGHLFQMVIKEK---LNLWLLTLSRVVLRKATAAKA 412

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                 +S+  +  SM +     S    L   G +  N  L L     +  I   D +  
Sbjct: 413 KTAIPGLSSVLIQNSMSSVPDVTSAMSYLLATGTLVSNTGLGLMQFAGLTVI--ADKLNY 470

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           ++ +   R     I         R  +V ++L   +                      +M
Sbjct: 471 MRYISHFR----CIHRGAFFAQMRTTTVRKLLPESWGFLC-------PVHTPDGSPCGLM 519

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
                  + V            L++L     + S +    +   +   G  +    + + 
Sbjct: 520 NHMSFLCEIVTHPPSNDAMLPLLNRLGMLSPTTSEVAGFGKFYPVILDG--KLIGWMPVH 577

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             H       C  +     N+ +   +               Y    + ++   V+ L  
Sbjct: 578 QGHQAVNVIRCK-KARGQDNVPITLEICLIEYTGKPTQYPGLYLMSQEARMVRPVMNL-- 634

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                        +++  GSF +  +      EE     +     + S   ++S  ASL 
Sbjct: 635 ----------ITGTVEMIGSFEQVYMNICIIPEEAH---KMTTHQELSQHSILSAVASLT 681

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           P+ + + S R +  C M +Q +                                I  + D
Sbjct: 682 PYSDFNQSPRNMYQCQMGKQTMGT--------------------------PCQAIAYRAD 715

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                I++                              Q  LV+            D   
Sbjct: 716 NKLYRIQT-----------------------------PQAALVRPYMY--------DHYK 738

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE----FEVMARDTK 855
            D      G+N +VA + + GY+ ED+M++++             +           D  
Sbjct: 739 MDN--FPFGQNAVVAVISYTGYDMEDAMILNKGSFDRGFAYGTIYKTDLIDLSSKVGDRT 796

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           +     T    +   +   N+   G+  VG  +  GD     I        +  E  +  
Sbjct: 797 VNVTFGTNPKDDRFPDL--NLGADGLPAVGQRLLTGDNYYSYI------DHSNSEMKVVK 848

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
             G++   V    +   +  +G    V I  R
Sbjct: 849 YSGQETGYVDSVRVLSNNAGTGHFKRVSIVLR 880


>gi|71005228|ref|XP_757280.1| hypothetical protein UM01133.1 [Ustilago maydis 521]
 gi|46096459|gb|EAK81692.1| hypothetical protein UM01133.1 [Ustilago maydis 521]
          Length = 1289

 Score =  286 bits (731), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 107/249 (42%), Gaps = 50/249 (20%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V++ + + R    GDK + RHG KG+ S+  P  DMPF + G   D+++NP   PSRM
Sbjct: 962  QKVQIMLRITRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFSESGMQPDVIINPHAFPSRM 1021

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G A    G    S    +  +                             
Sbjct: 1022 TIGMLIESIAGKAGAMHGIAQDSTPFTFSEDF---------------------------- 1053

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                            TP       E     L+ A  +  G   +Y G+TG+     + +
Sbjct: 1054 ----------------TP------TEFFGEQLKAAGYNHVGNEPMYSGITGQELRADIYL 1091

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMV+DK   R+TG    +T+QP+ G+   GG R GEME   + A+G +Y+L
Sbjct: 1092 GVVYYQRLRHMVNDKFQVRTTGPVHALTRQPIKGRKRAGGIRFGEMERDALLAHGTSYML 1151

Query: 1312 QEMLTIKSD 1320
            Q+ L   SD
Sbjct: 1152 QDRLMNCSD 1160



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 85/665 (12%), Positives = 197/665 (29%), Gaps = 88/665 (13%)

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY-----VDSVN 353
           ++  +    + +D +   T  ++      +  +         +  + +L       D   
Sbjct: 279 SNKAIVIRCLHKDDLISVTNAVHYLHNGGLTMRFSWRKQEYMVPVVMVLKALVDATDKEI 338

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
             + ++         DR + LL  ++               S F  +    + Y  + VG
Sbjct: 339 FASIVQGDFENTFLTDRVELLLRNFKQYSLWSGHQCLEYLGSKFRVVLGCPEDYTDAQVG 398

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
              ++  L +    D    + + +I +I+ L  L  G+   D+ D+  +  +   G    
Sbjct: 399 TELISRILLVH--LDSPRDKYKMLIFMIQKLYSLVAGESCADNADSPQHHEILMPGFLVG 456

Query: 469 ----EMLKNQYRLGLLRMERSIKERIS---SVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
               E +         ++ R ++ ++      D   +          +   +  F  +  
Sbjct: 457 QIIKERIDEAVGNIRAQIARDVRMKVKGLDFFDSKYIKKTVSKVNIDIGVKIASFLATGN 516

Query: 522 L--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           L              + + E +N    + H R   ++ +G          +R + P  +G
Sbjct: 517 LSSPSGLDLQQTSGFTIMAEKLNFARYLAHFR---SVHRGAFFAELKTTSVRKLLPEAWG 573

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY----------L 617
            +CP  T +G   GL++  +   R+       +    +  G    +  +           
Sbjct: 574 FLCPVHTPDGSPCGLLNHFSHTCRMTTRQPDVSHIHALLSGLGMTEAAFAIGAVGAASQR 633

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
                +N  + Q + ++    +                     +   D     V +  A 
Sbjct: 634 DTDARDNMVVVQLDGAILGYTTPALAKHMATALRIWKTEGLHHVPL-DLEIGFVPTSRAG 692

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIV 735
             P L             M R    L   +   VG    +   +A      +      + 
Sbjct: 693 QYPGL-----YLFSNRARMMRPVRLLHNNKIDMVGPFEQVYLDIACDPQEVVPGVSTHVE 747

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV---------------NQRP 780
               +I  V+ ++    D + S  + Y+    +++                      Q P
Sbjct: 748 LAPTSILSVLANLTPFSDYNQSPRNCYQAQMMKQTMGTASTAVSRRTDNKLYRIQTPQTP 807

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           +V+     +              D   G N +VA + + GY+ ED+M++++         
Sbjct: 808 VVRPELYNKYG----------FDDYPNGTNAIVAVISYTGYDMEDAMILNKSAHERGFGY 857

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVS--------EEGLKNIDECGIICVGAEVNPGD 892
               +   +  RD K G    +    +          E     +D+ G+  +G +V  G+
Sbjct: 858 GTVYKSETIDLRDLK-GKSSSSVPTLHFGFAPNSRPTEAQRAILDQDGLPYIGQKVMAGE 916

Query: 893 ILVGK 897
            +   
Sbjct: 917 PICAY 921



 Score = 46.2 bits (108), Expect = 0.039,   Method: Composition-based stats.
 Identities = 104/784 (13%), Positives = 206/784 (26%), Gaps = 180/784 (22%)

Query: 25  DIPDLIEVQKASYDHFLMMN--------IAPDERPNEG---LQAAFKSVFPITAFSG--- 70
           ++ +L+     S++     +        +A     NEG   L+ + + + P   F G   
Sbjct: 77  ELTELVAPNIESFNALWAEDPSLDPPASVAVSGFVNEGTGLLEKSLRRLAPRIVFDGQGD 136

Query: 71  -------AAMLEFVSYEFDPPKFD------------VDDCLWRDLTYAVPLKITLRLIVF 111
                     L   S     P  +              +   R  TY   L   L   V 
Sbjct: 137 ANNGLGNRITLRMDSVNLSKPLINERAKGVRERRVFPTEARERLFTYTGKLTARLCWSVN 196

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIK 147
              E +      DI    + +G+ P++ +                         G F++ 
Sbjct: 197 GDPEQS------DI----VTLGNCPVLVRSNRCNLRGMSSRELVAHHEEANEFGGYFLVN 246

Query: 148 GIQRIVVSQLHR--------SPGIHFDHDKGRASLSG-------KLLYACRIIP------ 186
           G +R     L R        SP         +   S        + L+   +I       
Sbjct: 247 GNER-----LIRYLIVAKANSPQAIERPSFEKRGPSYSNKAIVIRCLHKDDLISVTNAVH 301

Query: 187 --------DQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-GMDSEEIL-------- 229
                    +  W   E+               VPV   L AL     +EI         
Sbjct: 302 YLHNGGLTMRFSWRKQEYM--------------VPVVMVLKALVDATDKEIFASIVQGDF 347

Query: 230 -STFYPK---------IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
            +TF              YS      C     +   V         D   G ++I     
Sbjct: 348 ENTFLTDRVELLLRNFKQYSLWSGHQCLEYLGSKFRVVLGCPEDYTDAQVGTELISRILL 407

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +     +   +  +  +      + G   A++  + +  EI +  G ++ +   E I  +
Sbjct: 408 VHLDSPRDKYKMLIFMIQKLYSLVAGESCADNADSPQHHEILMP-GFLVGQIIKERIDEA 466

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                  +  D       +         K      +DI   +     ++F    ++ +  
Sbjct: 467 VGNIRAQIARDVRMKVKGLDFFDSKYIKKTVSKVNIDIGVKI-----ASFLATGNLSSPS 521

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
             D  +    T+   K+N           R++     +       +L+         +  
Sbjct: 522 GLDLQQTSGFTIMAEKLNF---------ARYLAHFRSVHRGAFFAELKTTSVRKLLPEAW 572

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           G                  L     + +      D+  +            +       +
Sbjct: 573 G---FLCPVHTPDGSPCGLLNHFSHTCRMTTRQPDVSHIHALLSGLGMTEAAFAIGAVGA 629

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +     +   N +                +  A  G     +       +   +T   H+
Sbjct: 630 ASQRDTDARDNMVVV-------------QLDGAILGYTTPALAKHMATALRIWKTEGLHH 676

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           + L   +  F   +  G     Y      ++   V  L             N+ +D  G 
Sbjct: 677 VPLDLEIG-FVPTSRAGQYPGLYLFSNRARMMRPVRLLH------------NNKIDMVGP 723

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F  E V+   A +   V       ++ +P  ++S+ A+L PF + + S R      M +Q
Sbjct: 724 F--EQVYLDIACDPQEVVPGVSTHVELAPTSILSVLANLTPFSDYNQSPRNCYQAQMMKQ 781

Query: 700 AVPL 703
            +  
Sbjct: 782 TMGT 785


>gi|303325240|gb|ADM14345.1| RNA polymerase subunit B [uncultured Mycobacterium sp.]
 gi|326694954|gb|AEA03700.1| RNA polymerase B [Mycobacterium sp. CSTy-8.29]
 gi|326694956|gb|AEA03701.1| RNA polymerase B [Mycobacterium sp. ASCy-1.0]
          Length = 240

 Score =  286 bits (731), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 128/229 (55%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +  G +       +  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDVANGVPEWAGKLPENLLSAQ-- 157

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 158  --------------------------PDSIVSTPVFDGAQEAELQGLLSATLPNRDGEVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VDGDGKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|55274001|gb|AAV48871.1| RNA polymerase II second largest subunit [Clitocybe subditopoda]
          Length = 693

 Score =  286 bits (731), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 126/829 (15%), Positives = 237/829 (28%), Gaps = 157/829 (18%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ + +    +              +  + + + +     +             
Sbjct: 1    FRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWGDQKKSMSSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L   A ++   +       + +  + +         EEN +     + +  +G 
Sbjct: 117  CGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSTTPCTKVFVNGV 168

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR- 698
            +       R     +   ++     D SP+  V             D+ RV     +   
Sbjct: 169  WMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEN 225

Query: 699  -----QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                 Q   +      +   G E              + GI+E +DA       +    +
Sbjct: 226  QQLALQKKHIKWLNNGYNDEGEEYK-------WEQLVKGGIIELLDAEEEETVMISMTPE 278

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               +                   +    +K G            PS  LG       +  
Sbjct: 279  DLENSRLNQSGAPHT---HEPDFDPAARLKPGLNSHTWTHCEIHPSMILG-------ICA 328

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N                        ++       +G       I        
Sbjct: 329  SIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM------ 364

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 365  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQS 419

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D  ++S   + E+ E   RD          +       I  G 
Sbjct: 420  SIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTYDKLEDDGLIAPGT 478

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  D      R++          ++     +  Q            
Sbjct: 479  GVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI--------- 529

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                              + VKV V   R  Q+GDK A RHG KG +      EDMPF  
Sbjct: 530  -----------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGITYRQEDMPFTA 578

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +G + E  L      +G +  +                   
Sbjct: 579  EGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--------------- 623

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                       ++     + LR       G+ V                         G 
Sbjct: 624  ----------DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGH 651

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            +       G      V +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 652  T-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 693



 Score =  122 bits (305), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 86/604 (14%), Positives = 169/604 (27%), Gaps = 102/604 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 10  KDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLN 68

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 69  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAC 128

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA         F     +    +  N +  I   RR
Sbjct: 129 ISVGSYSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMGVHRDPANLVKTIKKLRR 188

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +            +   ++        P    E   + L      +  +N     E 
Sbjct: 189 KDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHIKW--LNNGYNDEG 246

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-- 658
              K         +  L A EEE   I+     L E+    +         +     R  
Sbjct: 247 EEYKWEQLVKGGIIELLDAEEEETVMISMTPEDL-ENSRLNQSGAPHTHEPDFDPAARLK 305

Query: 659 -----EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                      +  P  ++ I AS+IPF +++ S R      M +QA+ +          
Sbjct: 306 PGLNSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI--- 362

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 363 --------------------------------------RMDTMANILYYPQKPLATTRSM 384

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 385 EYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSS 420

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E        +   +       +++ G+I  G  V
Sbjct: 421 IDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTYDKLEDDGLIAPGTGV 480

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DI++GK  P         ++        +    RD S  + S  SG V  V I    
Sbjct: 481 AGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNS 533

Query: 949 GIDK 952
              K
Sbjct: 534 EGQK 537


>gi|315435596|gb|ADU18188.1| RNA polymerase beta-subunit [Mycobacterium tusciae]
          Length = 237

 Score =  286 bits (731), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 97/228 (42%), Positives = 129/228 (56%), Gaps = 40/228 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI    +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIDGSPDWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +     + + G  VSTPVFDGA E+ +  +L     +      
Sbjct: 146  -----------------LPEEMLEAEPGSIVSTPVFDGAREDELQGLLSSTLPNRDGVTL 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG  
Sbjct: 189  VDSDGKAELFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPV 236



 Score = 45.5 bits (106), Expect = 0.071,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|301781941|ref|XP_002926382.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 1
            [Ailuropoda melanoleuca]
 gi|281347779|gb|EFB23363.1| hypothetical protein PANDA_016030 [Ailuropoda melanoleuca]
          Length = 1135

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 113/558 (20%), Positives = 184/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F +I I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNIAIFEDEVLAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      ++    +   L+          +         P G +  V  +        D 
Sbjct: 697  GFPLLTYQARSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDDSLVFGVKPGDP--------RILQKL 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       Q    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAQLQYGDPYYSYLNLNTGESFVMYYKSKENCIVDNIKVCS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             + + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CICITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +            L                    
Sbjct: 926  IGMLIESMAGKSAALHGLCHDATPFTFSEENSALEYFGEL-------------------- 965

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                          L+ A  +  G   LY G++G   +  + +G
Sbjct: 966  ------------------------------LKAAGYNFYGTERLYSGISGIELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCDRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 92/673 (13%), Positives = 208/673 (30%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          +  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLSLPDWYPNEQAAEFLFDQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V + G++           + + +        ++ +       + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKMESWLVSIKIALDKRSQKTNVSINTENLMKIFSL 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GTDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASVPALLCSLGV 539

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V    V     +E    IA +   L       E+ +   
Sbjct: 540 TPVDGAPHRPYAECYPVLLDGVMVGWV----DKELAPSIADS---LRHFKVLREKRIPP- 591

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 592 -WMEVALIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNIAIFEDE 650

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
              G      +   S  +++A     +   D  +      +  +   T G  +  Y+   
Sbjct: 651 VLAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQARS 707

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 708 DNKLYRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G + +   +       L+ +D+ G+  +G
Sbjct: 757 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDDSLVFGVKPGDPRILQKLDDDGLPFIG 816

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++   +       +++  S    SG    +    
Sbjct: 817 AQLQYGDPYYSYL-----NLNTGESFVMYYKSKENCIVDNIKVCSNDTGSGKFKCICITM 871

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 872 RVPRNPTIGDKFA 884



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 42/138 (30%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK-----------FDVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPMVPKGNICKELNIYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +           I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWAVNGISRG--------IIKQ--FLGYVPIMVKSKLCNLHSLPPRALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179


>gi|196011451|ref|XP_002115589.1| hypothetical protein TRIADDRAFT_59462 [Trichoplax adhaerens]
 gi|190581877|gb|EDV21952.1| hypothetical protein TRIADDRAFT_59462 [Trichoplax adhaerens]
          Length = 1016

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 85/343 (24%), Positives = 129/343 (37%), Gaps = 86/343 (25%)

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            L+ +Y              +E +    +       ++K  +   R  + GDK + RHG K
Sbjct: 736  LQPEYIDMPMTYRGPTDAYVENVMISSNNDEAF--LIKTLLRSSRRPEIGDKFSSRHGQK 793

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G+   I+  EDMPF       D ++NP G PSRM V        G     +G K   L  
Sbjct: 794  GVCGLIVNQEDMPFT------DQIMNPHGFPSRMTV--------GKLMEVIGGKASLLDG 839

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
             ++                                                  FDG   E
Sbjct: 840  KFRYGT----------------------------------------------AFDGDKLE 853

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +   L   +   +G+  L  G+TGE     +  G +Y  +L HMV DK++AR+ G  ++
Sbjct: 854  DLCQTLIDYNYSYAGKDYLTSGITGEGLSAYIFFGPVYYQRLKHMVLDKMHARAKGPRAV 913

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN- 1336
            +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD        +E  V  N 
Sbjct: 914  LTRQPTEGRSRDGGLRLGEMERDCLIAYGTSMLLVERLMISSD-------AFEVDVCNNC 966

Query: 1337 ----------------DTFETGTPESFNVLVKEMQALGLSIDL 1363
                                   P +  +L +E+Q++ +   L
Sbjct: 967  GLLAYSKWCHYCHSSCHVSSLQIPYACKLLFQELQSMNIIPRL 1009



 Score =  137 bits (344), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 147/1044 (14%), Positives = 276/1044 (26%), Gaps = 284/1044 (27%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
            L++    SY++F+   I      N         V   T       L++++          
Sbjct: 44   LVKQHIDSYNYFINCEIKKIVNAN-------NKVT--TDADTVFYLKYLNVYVGNPDIEE 94

Query: 83   -----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  P +   +C  RDLTY+ P+ + +             +  + I+ Q + +G +P+
Sbjct: 95   SFNVTKPTY-PHECRLRDLTYSAPIVVDIEYT----------RGAQRIRRQKLPIGRVPV 143

Query: 138  MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
            M                           G F++KG++++++ Q   S             
Sbjct: 144  MLRSSICVLNGKSPVELAKYNECPIDPGGYFIVKGVEKVILIQEQLSKN----------- 192

Query: 174  LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY 233
                     R+I        +E D+K                             LS   
Sbjct: 193  ---------RMI--------LEVDNKGNA--------------------------LSYIG 209

Query: 234  PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGV 293
             ++   + G        A DL+    +S     +D  +       +L   LL  L E   
Sbjct: 210  SRVRQRKWGAKKLPVDEARDLLANVVLSHIPSILDDKDYYGNKRLELAGQLLALLFEDLF 269

Query: 294  KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
            K        +    + +         +     D++     ++I +     +         
Sbjct: 270  KKFNSELKSIAEKNIPKQRAGPVNMNLRFLEFDIVKYMRQDQITNGFNLALTTGNWSIKR 329

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
                               AL  + R+    + +             +       +  G 
Sbjct: 330  YKMDRAGVTQVLSRLSYLSALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGE 389

Query: 414  VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
                  L  +           D   II +L +L      +   + L    +  V     N
Sbjct: 390  ---ACGLVKNLALMTHITTDSDDKIIINLLFNLGVEDINLLSGEELSLPHIYIV---YVN 443

Query: 474  QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
             Y LG  R  + +      +  D    Q       + + + EF                 
Sbjct: 444  GYVLGAARNYKKLIRTFRLLRRDIKTAQVKRILYLIANYINEFVSIYP------------ 491

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
               HT R   +   G                  GR+C           +V S      + 
Sbjct: 492  --NHTYRQINIALDG------------------GRVC-------RPYIIVKSEKPLVTIK 524

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                +    R   D      + YL   EE +  IA   S ++                  
Sbjct: 525  HIEELSQGIRSFDDFIRNGLIEYLDVNEENDCNIALYESDIN------------------ 566

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                  K   +D  P  ++ + A LIPF  ++ S R    C M +QA+  +         
Sbjct: 567  -----SKTTHLDIEPFTILGVCAGLIPFPHHNQSPRNTYQCAMGKQAIGTI--------- 612

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G                                                           
Sbjct: 613  GYNQRNRID----------------------------------------------TVLYQ 626

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                Q PLVK                 +   L  G+N ++A M + GY+ ED++++++  
Sbjct: 627  LVYPQVPLVK----------TKTIDLIEFDKLPAGQNAIIAVMSYSGYDIEDAVILNKAS 676

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            V                  D + G       +          +D  GI   G +V    I
Sbjct: 677  VDRGPQA------------DAQTGKTIWKHKV----------LDADGICMPGEKVESKQI 714

Query: 894  LVGKITP---------KGESPMTPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            L+ K  P          G+  + PE   +     G     V +  +   +  +  +  + 
Sbjct: 715  LINKSIPSVTSTPIAGTGQKLLQPEYIDMPMTYRGPTDAYVENVMISSNNDEAFLIKTLL 774

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILD---------RNIYSRLMEILCGQN 994
              +R     ++ S    ++ +  L  +++D               R    +LME++ G  
Sbjct: 775  RSSRRPEIGDKFSSRHGQKGVCGLIVNQEDMPFTDQIMNPHGFPSRMTVGKLMEVI-GGK 833

Query: 995  AVSGPKGFKKSTVLSSDLISEYPR 1018
            A      F+  T    D + +  +
Sbjct: 834  ASLLDGKFRYGTAFDGDKLEDLCQ 857


>gi|289617152|emb|CBI56220.1| unnamed protein product [Sordaria macrospora]
          Length = 1239

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 102/497 (20%), Positives = 173/497 (34%), Gaps = 65/497 (13%)

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             E  + SI   E EV+  D     E    +I ++        D         +   G   
Sbjct: 671  QEQPYMSIACTEQEVIPGD-STHVEFDPTNILSILANMTPFSDFNQSPRNMYQCQMGKQT 729

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +G            +   L+             +    +  +GT   V + +  G D ++
Sbjct: 730  MGTPGTALSRRTDNKMYRLQTGQTPIVRAPLHNTYGFDNFPNGTNAVVAVISYTGYDMDD 789

Query: 955  RSISVEREQIELL---ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             ++ + +   E           ++V L  +  +R  + +      +     ++ST  + D
Sbjct: 790  -AMIINKSAHERGFGHGSIYKTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDTLD 848

Query: 1012 LISEYPRSQWWQ--------FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    +  +          V  +   + V    + +       ED F  ++  I   
Sbjct: 849  NDGLPRVGRLLREGDVLCAWHTVSADYNGQLVNRDGITHYERYKDSEDAFVEEVRVIGAD 908

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +   P  L+ V + + + R    GDK + RHG KG+ S+  P  DMPF + G   D+++N
Sbjct: 909  NGTEP--LQTVSIKLRIPRSPVIGDKFSSRHGQKGVCSQKWPATDMPFSETGIQPDVIIN 966

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSRM +G   E+  G A    G    S    +                        
Sbjct: 967  PHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFDEQNRAG----------------- 1009

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                             +     L  A  +  G   LY G+TGE
Sbjct: 1010 ---------------------------------DYFGHQLMKAGYNYHGNEPLYSGITGE 1036

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F   + +G +Y  +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + 
Sbjct: 1037 EFQADIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKGRKKGGGIRVGEMERDALL 1096

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G +++LQ+ L   SD
Sbjct: 1097 AHGTSFLLQDRLLNCSD 1113



 Score = 70.5 bits (171), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 76/544 (13%), Positives = 160/544 (29%), Gaps = 83/544 (15%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           ++ +      D  +     +   ++ + + L  L  G   +D+ D + N+ +   G    
Sbjct: 353 KIVLVHLGCQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLYG 412

Query: 469 --------EMLKNQYRLG---LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                   E+L   +R      LR   ++  +  +   D  +       + +  ++  F 
Sbjct: 413 QIIKERLEELLTVSFRASLRDYLRRNPTVSFQSETFTKDFPIAIFRRANENIGQSLEYFL 472

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N L  I+H R    + +G          +R + P
Sbjct: 473 STGNLVSPSGLDLQQVSGFTVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTVRKLLP 529

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFA-----RVNAYGFIETPYRK-------------V 605
             +G +CP  T +G   GL++ L          V+A       +               V
Sbjct: 530 ESWGFLCPVHTPDGSPCGLLNHLAHKCKIMTDHVDASTIPRLAFELGVVNISSAATSESV 589

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                   V + +  E   + IA+       +G     L       E   VP        
Sbjct: 590 VVMLDGRIVGWCTPDE--CKSIAETLRYWKVNGENGVPL-----QLEIGYVPPSNGGSYP 642

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKS 722
                + S  A ++  ++     +       ++  + +   E   +    T +E      
Sbjct: 643 G--LYMSSQPARMVRPVKYLPLAKEDFVGPQEQPYMSIACTEQEVIPGDSTHVEFDPTNI 700

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                         Q        +  +  +    + +      K  R        Q P+V
Sbjct: 701 LSILANMTPFSDFNQSPRNMYQCQMGKQTMGTPGTALSRRTDNKMYRLQTG----QTPIV 756

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           +               +    +   G N +VA + + GY+ +D+M+I++           
Sbjct: 757 RA----------PLHNTYGFDNFPNGTNAVVAVISYTGYDMDDAMIINKSAHERGFGHGS 806

Query: 843 HIEEFEVMARDTKLGP-------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
             +  +V  +D                     + E     +D  G+  VG  +  GD+L 
Sbjct: 807 IYKTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDTLDNDGLPRVGRLLREGDVLC 866

Query: 896 GKIT 899
              T
Sbjct: 867 AWHT 870



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 96/750 (12%), Positives = 212/750 (28%), Gaps = 137/750 (18%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS------GAAMLEFVSYEFDP 83
           ++    S++     +  P    +  L       F                + + S E   
Sbjct: 44  VDPHIESFNALFRDDGKPSL-LDHALAEIGTKTFLDGDERADPAGKNKLTIRYKSIELQK 102

Query: 84  ----P--------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
               P        +    +C  R ++Y   L  T    + D +     +           
Sbjct: 103 SQVPPTNRWAKNREIFPAECRERHVSYRGKLSATFEYRINDGEPHEFVRE---------- 152

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDH 167
           +G +P+M K                         G FV+ GI++ ++  L  +       
Sbjct: 153 LGQMPIMVKSNKCHLQNNSPAQLVARGEESEELGGYFVVNGIEK-LIRMLLMNRRNFPLA 211

Query: 168 DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTS 216
               +  +    Y    I  + +  D E    +++H         R   R+    +PV  
Sbjct: 212 IVRPSFQNRGATYTPYGIIMRSVRPD-ETSQTNVLHYLSDGNVTFRFSWRKNEYLIPVMM 270

Query: 217 FLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
            + AL +++ +     +  +V   +            + +                    
Sbjct: 271 IMKAL-VETND--REIFEGLVGPPQSKGVANTFLTDRVEL-------------------- 307

Query: 277 GKKLTSGLLKSLKEKGVKFLGITSDCLCGLY-----VAEDIVNGETGEIYIEAGDVIDEK 331
                  LL++ K+ G+     T   L   +     VA+ + + E G  ++    ++   
Sbjct: 308 -------LLRTYKKYGLYSKTQTRAYLGQKFRVVLGVADTMSDYEVGTEFLRKIVLVHLG 360

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             +     +     +L        A +      D     ++  + +   +  G +    +
Sbjct: 361 CQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLY-GQIIKERL 419

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            E +          Y          +     D P  +     E+I   ++  +   N   
Sbjct: 420 EELLTVSFRASLRDYLRRNPTVSFQSETFTKDFPIAIFRRANENIGQSLEYFLSTGN-LV 478

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPV 509
           +   +D         V E L     +   RM    S   ++ +  +  ++P+      PV
Sbjct: 479 SPSGLDLQQVSGFTVVAEKLNFLRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPV 538

Query: 510 VSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
            +         + L+   + +      +   RL+   + GV    +      V     GR
Sbjct: 539 HTPDGSPCGLLNHLAHKCKIMTDHVDASTIPRLAF--ELGVVNISSAATSESVVVMLDGR 596

Query: 569 ICPAETSE---------------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           I    T +               G N   +     +   +  G     Y      ++   
Sbjct: 597 IVGWCTPDECKSIAETLRYWKVNGENGVPLQLEIGYVPPSNGGSYPGLYMSSQPARMVRP 656

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YL   +E+  ++              +E++                  ++  P  ++S
Sbjct: 657 VKYLPLAKED--FVGPQEQPYMSIACTEQEVIPG------------DSTHVEFDPTNILS 702

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           I A++ PF + + S R +  C M +Q +  
Sbjct: 703 ILANMTPFSDFNQSPRNMYQCQMGKQTMGT 732


>gi|198448644|gb|ABZ85927.2| RNA polymerase beta subunit [Mycobacterium pinnipedii]
          Length = 240

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 133/229 (58%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDAAKGVPDWAARLP--------- 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           D +L           VSTPVFDGA E  +  +L            
Sbjct: 151  ---------------DELLEAQPNAI----VSTPVFDGAQEAELQGLLSCTLPNRDGDVL 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 46.2 bits (108), Expect = 0.043,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDED 49


>gi|111378457|gb|ABH09240.1| RpoB [Enterobacter pyrinus]
          Length = 293

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 179/293 (61%), Positives = 226/293 (77%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG VT+++ YLSA+EE N  IAQANS+L +D  F ++LV CR  GE  L  R+++D++D
Sbjct: 121 TDGVVTDEIHYLSAIEEGNFVIAQANSNLSDDNRFVDDLVTCRSKGESSLFSRDQVDYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG 
Sbjct: 181 VSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGV 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             VAKR G V+ VDA RIVI+  + ++ P  +G+DIY L K+ RSNQNTC+NQ
Sbjct: 241 TAVAKRGGTVQYVDASRIVIKVNDDEMYPGEAGIDIYNLTKYTRSNQNTCINQ 293


>gi|170291136|ref|YP_001737952.1| DNA-directed RNA polymerase subunit B [Candidatus Korarchaeum
            cryptofilum OPF8]
 gi|170175216|gb|ACB08269.1| DNA-directed RNA polymerase subunit B [Candidatus Korarchaeum
            cryptofilum OPF8]
          Length = 1121

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 81/255 (31%), Positives = 115/255 (45%), Gaps = 54/255 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
               G  ++V+V V   RP + GDK A RHG KG++  I   EDMPF   G   DIVL+P 
Sbjct: 856  TKTGGEKLVRVNVRETRPPELGDKFATRHGQKGVLGMIYRHEDMPFTAQGIIPDIVLDPH 915

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ++E   G      G+ +                                 
Sbjct: 916  TIPSRMTIGQLYEIIAGKVGALEGRFVDG------------------------------- 944

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  TP F     E +   L     + SG+ I+YDG TG   
Sbjct: 945  ----------------------TP-FMSEPVEDLMEALVKLGFEYSGEEIMYDGRTGRMI 981

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
              PV +G  Y  +L HMV DK++AR+ G   L+T+QP+ G++  GG RLGEME   + ++
Sbjct: 982  KAPVFIGISYYQRLKHMVRDKIHARARGQMQLLTRQPVEGRARGGGLRLGEMEGEVLISH 1041

Query: 1306 GAAYVLQEMLTIKSD 1320
            GAA V+++    +SD
Sbjct: 1042 GAASVIRDRYIDQSD 1056



 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 150/1014 (14%), Positives = 310/1014 (30%), Gaps = 199/1014 (19%)

Query: 18  GKNPEIIDIP---------DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF 68
            K  E+   P         +L +VQ  S++ FL            G+Q    +   I   
Sbjct: 3   SKRSEVDFYPIVKAYFRERNLADVQIESFNRFL----------ERGIQEVVDAFKEIE-L 51

Query: 69  SGAAMLEFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
                L         P+ D           ++   R+  Y  P+++ +++    +     
Sbjct: 52  VENYKLILSRVYVGRPEIDEYDGSSLPAMPNEIRLRNADYIAPIELEIKVYAGGM----- 106

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
                ++K + + +G LP+M K                         G F+I G +R++V
Sbjct: 107 -----ELKTERVRIGHLPIMVKSKGCYLYGLDEKRLISKGEDPRDPGGYFIINGSERVLV 161

Query: 155 SQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQG---LWMDIEFDSKD-IIHVRIDRR 209
            +   +P  +  +             +  +I+  +      + +E+  +D  I       
Sbjct: 162 MRDDIAPNKVIVEQTVAENKP---YSHVAQIVSARAGLRTRLYLEYYMRDGTIKASTGAL 218

Query: 210 RKVPVTSFLMALGMDSEE-ILSTFY---PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           R +PV   L ALG++ +E I+        +I              A +           +
Sbjct: 219 RGIPVAMLLKALGLERDEDIVDAISSVDDEIRSEFLYSLDDVQRRAEEEGAQIITREEAL 278

Query: 266 DIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
           D      V    +       K  L+   +  +G++ +           +  +  ++    
Sbjct: 279 DYIGRRLVQAVPRADRIRYAKEYLRNNFLPHIGVSEEDNIVKAYFLAKMIEKLLKVVRGK 338

Query: 325 GDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
            +  D+     + +  S      +           ++       +    D  LDI R+++
Sbjct: 339 LEPDDKDHFSNKRLRLSGTLMQEVFRDSFYQLVRKLKEKADEQLSSGVYD--LDIRRIIQ 396

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
              + T  +  ++    +   D      + R      L+          R    +     
Sbjct: 397 SQKLVTQRIIRAVATGAWPGGDLGVSQNLERTNYIATLHHLR-------RVNSPLPAGLP 449

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           L ++R   GT             +   ++++      +      +  I  V      P  
Sbjct: 450 LHEVRQTHGTSIGRLCPLETPEGTNVGLVRSLAIFCDVTFGTDPEPIIELVLDWGAKPAK 509

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               + V S +   + + +L    +    L      +R     +              ++
Sbjct: 510 EAKPREVGS-LTPVYVNGRLVAFTDKPEELVSFLREKRAELNPEVNF-----------IY 557

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
               G +     +      L+        +     +++      D      V  L A EE
Sbjct: 558 NREEGAVFINADAGRMRRPLIPVSKLKEAMELLPKVDSGELSFTDLVKMGVVELLDADEE 617

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   +AQ+   +                        +K    D +P  +  +AAS IP+ 
Sbjct: 618 EYAVVAQSIEEIT-----------------------DKHTHFDFAPYAMFGVAASQIPYA 654

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           E+++  R ++G NM RQ +    A            +   S A ++              
Sbjct: 655 EHNNIPRDIIGSNMVRQGLGEYLA---------NWRLRFDSRAFLM-------------- 691

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                                              QRP+V+                T  
Sbjct: 692 --------------------------------FYPQRPIVE----------TRGAEITGY 709

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                G+N++VA +P  GYN +D++++S+  +      ++    +E  AR   +   +  
Sbjct: 710 NYRPSGQNLVVALLPMDGYNMDDALVMSKGAIDRGAARAVFFRTYETEARRHAIIEGDKF 769

Query: 863 RDIPNVS-------EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +   +        E+  + + E GI+     V  GD+L+GK +P   SP    E  + +
Sbjct: 770 ENPVALKKVSGKKEEQYYQKLGEDGIVDPETYVEGGDVLIGKTSPPRFSP----ELTVGS 825

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            + +   + RDTS+ + +   G V DV +  + G +K  R    E    EL  +
Sbjct: 826 GYPQYTFERRDTSISMRAWERGVVTDVLLATKTGGEKLVRVNVRETRPPELGDK 879


>gi|315435588|gb|ADU18184.1| RNA polymerase beta-subunit [Mycobacterium shimoidei]
          Length = 238

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 132/229 (57%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +          +          
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDTSKGVPDWAAQLP--------- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                           + +L           VSTPVFDGA EE +  +L     +      
Sbjct: 149  ---------------EELLEAEPNKI----VSTPVFDGAREEELQGLLSSTLPNRDGDTL 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ILYDG +GEPF  PVT GY+Y++KL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKAILYDGRSGEPFPYPVTTGYMYIMKLHHLVDDKIHARSTGPYS 238



 Score = 43.5 bits (101), Expect = 0.26,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 47


>gi|55583690|gb|AAV53364.1| RNA polymerase II second largest subunit [Grifola sordulenta]
          Length = 712

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 125/836 (14%), Positives = 241/836 (28%), Gaps = 141/836 (16%)

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAV 513
             D+ G +R+   G +L N +R+   ++ + +    +              +    + + +
Sbjct: 1    RDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGL 60

Query: 514  CEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
                 +               +SQ+       S ++H RR +      + R     + R 
Sbjct: 61   KYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQ 116

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G +CPAET EG   GLV +L+  A ++           + +  + +        
Sbjct: 117  LHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLEEWGLESL------- 169

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             EEN + +   + +  +G +       R     +   ++     D S +  V        
Sbjct: 170  -EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISAEVSVVRDIRERE 225

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                 D+ RV     +      LL+ +       +E ++          K      +   
Sbjct: 226  LRLYTDAGRVCRPLFIVENQQLLLQKK------HIEWLIRSKEEQTTKPKDLRFDYK--W 277

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
              ++   V   LD                      +   P       ++   I       
Sbjct: 278  DHLIRDGVIELLDAEEEET--------------VMICMTPEDLENSRLQAAGIDPHANDG 323

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            D    +  +    A+  W       SM+  +   ++            ++       +G 
Sbjct: 324  DFDPASRLKAPTNAY-TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGI 382

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                  +               +  +             +       +   +  + AI  
Sbjct: 383  YLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILC 431

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S V   +    ++ R  +D  ++S   + E  E   RD        
Sbjct: 432  YSGYNQEDSVIMNQSSVDRGLF-RSMYYRSYMDLEKKSGVQQVEAFEKPTRDTTLRMKHG 490

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +       I  G N         K+  ++ D      R++          ++   + +
Sbjct: 491  TYDKLEDDGLIAPGTNVNGEDIIIGKTAPIAPDSEELGQRTRTHTKRDVSTPLKSTEQGI 550

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                              + VK+ V   R  Q GDK A RHG KG
Sbjct: 551  IDQVLI--------------------TTNAEGQKFVKIRVRSTRIPQIGDKFASRHGQKG 590

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +    
Sbjct: 591  TIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT 650

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                      ++       LR       G+ V            
Sbjct: 651  -------------------------DLTVESVSQFLRQKGYQSRGLEVM----------- 674

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                         G +       G      V +G  Y  +L HMV DK+++R+ G 
Sbjct: 675  -----------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGP 712


>gi|331233519|ref|XP_003329420.1| DNA-directed RNA polymerase I subunit RPA2 [Puccinia graminis f. sp.
            tritici CRL 75-36-700-3]
 gi|309308410|gb|EFP85001.1| DNA-directed RNA polymerase I subunit RPA2 [Puccinia graminis f. sp.
            tritici CRL 75-36-700-3]
          Length = 1224

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 112/277 (40%), Gaps = 52/277 (18%)

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                  E+ F  ++  I  G D+P      +   + + R    GDK + RHG KG+ S+ 
Sbjct: 880  EKYKGDEEAFVEEVRMI--GGDVPSKECTKIHFKLRVPRSPVIGDKFSSRHGQKGVCSQK 937

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
             P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    +    +    
Sbjct: 938  WPSIDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGAMHGIAQDATPFRFNEQD 997

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                        TP             L
Sbjct: 998  --------------------------------------------TPS------AYFGEQL 1007

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            R A  +  G   +Y G+TG+ F+  + +G +Y  +L HMV DK   R+TG    +T+QP+
Sbjct: 1008 RAAGYNYHGNEPMYSGITGKEFEADIYIGLVYYQRLRHMVGDKWQVRTTGKVDKLTRQPV 1067

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G+   GG R GEME   + A+G +++LQ+ L   SD
Sbjct: 1068 KGRKRGGGIRFGEMERDALLAHGTSFLLQDRLMNCSD 1104



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 109/665 (16%), Positives = 216/665 (32%), Gaps = 92/665 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDL 408
           D        +N        DR + +L  ++    P   +      S F  +    D +  
Sbjct: 292 DQEIFTNLAQNAFEDTFRTDRIELMLRNFQYYSLPTASACLDFLGSKFKVVLGCPDDWGS 351

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             +GR  +   + +   D +   +   ++ +I+ L  L  G+   D+ D+  ++ +   G
Sbjct: 352 EQIGRYLLQRIVLVHLKDPIS--KYRLLLFMIQKLYALVAGECCADNPDSPQHQEILLPG 409

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC---------- 518
            +L +  +         I+ +I+S    S       + K V  A+ + +           
Sbjct: 410 HLLSSILKERFEEYLGGIQAQITSEVRKSTTGVTFSDNKFVTKAIGKVYSDIGRRVTFFL 469

Query: 519 ---------------SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
                          +S  + + E +N    I+H R    + +G          +R + P
Sbjct: 470 ATGNLVSPTGLDLQQTSGFTIIAEKLNFYRYISHFR---CVHRGAFFAELKTTTVRKLLP 526

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV----NAYGFIETPYRKVCDGKVTNDVVYLS- 618
             +G +CP  T +G   GL++      ++     +   I +    +   +  +  ++ S 
Sbjct: 527 EAWGFLCPVHTPDGSPCGLLNHFAHKCKILTSAPSVKNIPSLLLSLGMSQPFDTTIHPSK 586

Query: 619 --AMEEENRYIAQANSSLDEDG------SFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
             +++ +   I  A+SSL            TE L       E  LVPR K       P  
Sbjct: 587 FVSVQLDGEIIGWASSSLCSRMATALRTWKTEGLENIPLELEIGLVPRSKGGQY---PGL 643

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +    + +       SN+         Q    +      +  G  S   + S   +++ 
Sbjct: 644 FLFSTPARMMRPVQLLSNKKTDLVGSFEQVYMDIACSQEEIDPGF-STHVEISPTHVLSL 702

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR---PLVKVGDE 787
            A +    D  +      +  +   T G      +   R++      Q    P+V+    
Sbjct: 703 LANLTPFSDFNQSPRNMYQCQMSKQTMG--TPSGVIHHRTDNKLYRLQTGQTPIVRP--- 757

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                  A      +     G N +VA + + GY+ ED+M++++           H   +
Sbjct: 758 -------ALHDVYQMDHFPNGTNAVVAVISYTGYDMEDAMILNKSAHERGFA---HGMVY 807

Query: 848 EVMARD-TKLGPEEITRDIPNVS-----------EEGLKNIDECGIICVGAEVNPGDILV 895
           + M  D +  G    +     +                  +D  G+  VG+ V  GD L 
Sbjct: 808 KSMIVDLSPEGSRTSSEKHFGIGKSFGGSESSAFNRMCDKLDSDGVALVGSRVRSGDPLC 867

Query: 896 GKIT----------PKGESPMTPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
             +            KG+     EE +++      K        LRVP      V+  + 
Sbjct: 868 AYVDRTTGKTSFEKYKGDEEAFVEEVRMIGGDVPSKECTKIHFKLRVP---RSPVIGDKF 924

Query: 945 FNRHG 949
            +RHG
Sbjct: 925 SSRHG 929



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 97/664 (14%), Positives = 172/664 (25%), Gaps = 111/664 (16%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +   R +TYA  +   +   + +       +            G LP+M K       
Sbjct: 131 PTEARERLVTYAGKISAKVTWSLNNGPPQNEYRD----------FGLLPIMVKSEKCNLK 180

Query: 142 ------------------GTFVIKGIQRIV----------VSQLHR----SPGIHFDHD- 168
                             G FV+ G ++I+          V  L R    + G  +    
Sbjct: 181 QMSPAKLVSHHEESEEMGGYFVVNGNEKIIRCLIVPRRNHVISLIRPSFVNRGNFYTTYA 240

Query: 169 -------KGRASLSGKLLY-ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
                    + S +  L Y +   I  +  W   EF               VPV   L A
Sbjct: 241 TQIRCVRPDQTSQTNTLHYLSNGTITFRFSWRKSEFM--------------VPVVMLLKA 286

Query: 221 L-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           L G   +EI          +Q      F     +LM+      SL         + S  K
Sbjct: 287 LIGASDQEIF------TNLAQNAFEDTFRTDRIELMLRNFQYYSLPTASACLDFLGSKFK 340

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +  G       + +         L    V   + +  +    +          +     +
Sbjct: 341 VVLGCPDDWGSEQIGR------YLLQRIVLVHLKDPISKYRLLLFMIQKLYALVAGECCA 394

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +  D P  + + +     + + L     +        I   +R                 
Sbjct: 395 DNPDSPQ-HQEILLPGHLLSSILKERFEEYLGGIQAQITSEVRKSTTGVTFSDNKFVTKA 453

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                      V        L   T  D++      IIA         +    +      
Sbjct: 454 IGKVYSDIGRRVTFFLATGNLVSPTGLDLQQTSGFTIIAEKLNFYRYISHFRCVHRGAFF 513

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +  +V ++L   +                      ++       K + SA       
Sbjct: 514 AELKTTTVRKLLPEAWGFLC-------PVHTPDGSPCGLLNHFAHKCKILTSAPSVKNIP 566

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S L  L       + I      S      +     G     +       +   +T    N
Sbjct: 567 SLLLSLGMSQPFDTTIH----PSKFVSVQLDGEIIGWASSSLCSRMATALRTWKTEGLEN 622

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I L   +      +  G     +      ++   V  LS            N   D  GS
Sbjct: 623 IPLELEIG-LVPRSKGGQYPGLFLFSTPARMMRPVQLLS------------NKKTDLVGS 669

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F  E V+   A  +  +       ++ SP  V+S+ A+L PF + + S R +  C M +Q
Sbjct: 670 F--EQVYMDIACSQEEIDPGFSTHVEISPTHVLSLLANLTPFSDFNQSPRNMYQCQMSKQ 727

Query: 700 AVPL 703
            +  
Sbjct: 728 TMGT 731


>gi|55583694|gb|AAV53366.1| RNA polymerase II second largest subunit [Marasmius alliaceus]
          Length = 705

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 132/835 (15%), Positives = 247/835 (29%), Gaps = 146/835 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYMQKCVETHKEFNLTAAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   R+     D SP+  V         
Sbjct: 169  EENAHSSTPTTKVFVNGVWMG---VHRDPANLVKTIRKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG-AAIVAKRAGIVEQVDA 740
                D+ RV     +      +L+ +   V   +     + S        + GI+E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVDNQQLVLQKKH--VKWLLNGQNDEGSEFKWEHLVKHGIIELLDA 283

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     + +    ++       R  +K G            PS 
Sbjct: 284  EEEETVMISMTPEDLENSRLQQQGVDPHENDGEFDPAAR--LKAGINAHTWTHCEIHPSM 341

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 342  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 376

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 377  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 425

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 426  GYNQEDSVIMNQSSVDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTY 484

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 485  DKIEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVD 544

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 545  QVLI--------------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTI 584

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 585  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 642

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++       LR       G+ V    F G       
Sbjct: 643  -----------------------DLTVESVSMFLRQKGYQSRGLEVM---FHGHT----- 671

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
                              G         V +G  Y  +L HMV DK+++R+ G  
Sbjct: 672  ------------------GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPV 705



 Score =  121 bits (303), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 92/622 (14%), Positives = 175/622 (28%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++  ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYMQKCVETH--KEFNLTAAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPTTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +    V+  R   E      T  GR+C       +   +
Sbjct: 189 GVHRDPANLVKTIRKLRRKDDISPE-VSVVRDIREKELRLYTDAGRVCRPLFIVDNQQLV 247

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +        +N     E    K         +  L A EEE   I+     L+      +
Sbjct: 248 LQKKHVKWLLNGQND-EGSEFKWEHLVKHGIIELLDAEEEETVMISMTPEDLENSRLQQQ 306

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 307 GVDPHENDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 366

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 367 MGKQAMGIYLTNFLI-----------------------------------------RMDT 385

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 386 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 421

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  V   +F SI+   +  + + + +   E        +   +  
Sbjct: 422 LCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKH 481

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 482 GTYDKIEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 534

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 535 LKSTESGIVDQVLITTNSEGQK 556


>gi|53854340|gb|AAU95615.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 299

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 179/298 (60%), Positives = 229/298 (76%)

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+
Sbjct: 1   DDIDHLGNRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAI 60

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N L  +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 61  KEFFGSSQLSQFMDQTNPLFEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIE 120

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ 
Sbjct: 121 TPEGPNIGLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANAD 180

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           LD DG+   +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 LDSDGNLIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMG 240

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            NMQRQAVP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +
Sbjct: 241 ANMQRQAVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDE 298


>gi|75062001|sp|Q5REE8|RPA2_PONAB RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2; AltName: Full=RPA135
 gi|55726171|emb|CAH89859.1| hypothetical protein [Pongo abelii]
          Length = 1136

 Score =  285 bits (730), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 112/559 (20%), Positives = 183/559 (32%), Gaps = 92/559 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGMKPGDP--------RILQKL 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 925

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 926  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 961

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 962  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA-YVL 1311
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G + ++L
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFFLL 1055

Query: 1312 QEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPE 1345
             + L   SD     V    G                 R R Y   +    +       P 
Sbjct: 1056 HDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPY 1115

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
             F   V E+ A+ + + L+
Sbjct: 1116 VFRYFVAELAAMNIKVKLD 1134



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 93/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + ++V +++  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTNVSMNTDNLMRIFTM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIPPWTEVVLIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   +       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGMKPGDPRILQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 99/721 (13%), Positives = 200/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEVSVYPAECRGRRCTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLYNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMVRPKWKTRGPGYTHYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++       +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTNVS-MNTDNLMRIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +++ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKELAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
             + +               +      ++   V  L   +EE          L       
Sbjct: 591 PWTEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V        +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|308367814|gb|ADO29946.1| RNA polymerase subunit B [Mycobacterium setense]
          Length = 225

 Score =  285 bits (729), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 98/227 (43%), Positives = 130/227 (57%), Gaps = 37/227 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 141  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG 
Sbjct: 179  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTGP 225


>gi|62720666|gb|AAX93869.1| RNA polymerase subunit B [Mycobacterium elephantis]
          Length = 238

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 134/229 (58%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G K++                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWAA-HSGWKVEGKP------------------- 141

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                    + ++   D +L           VSTPVFDGA  + +  +L     +      
Sbjct: 142  --------EWANQLPDDLLEAEPN----TIVSTPVFDGATGDELQGLLGSTLPNRDGEKL 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDGDGKAMLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.043,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|225412292|ref|ZP_03761481.1| hypothetical protein CLOSTASPAR_05514 [Clostridium asparagiforme DSM
            15981]
 gi|225042186|gb|EEG52432.1| hypothetical protein CLOSTASPAR_05514 [Clostridium asparagiforme DSM
            15981]
          Length = 198

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 74/130 (56%), Positives = 96/130 (73%), Gaps = 1/130 (0%)

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
            +KL+H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEMEVW ++AYGA+Y LQE++T
Sbjct: 1    MKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYTLQEIMT 60

Query: 1317 IKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEE 1376
            +KSDDVVGR + YE+I+ G +  E G PESF VL+KEMQ+LGL + +           E 
Sbjct: 61   VKSDDVVGRVKTYEAIIKGENIPEPGVPESFKVLLKEMQSLGLDVQVLRDDGTEVEMAEN 120

Query: 1377 IPDFNKCELK 1386
            I D+   EL+
Sbjct: 121  I-DYGDTELR 129


>gi|60172322|gb|AAX14492.1| RNA polymerase beta subunit [Aliivibrio wodanis]
          Length = 184

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 101/187 (54%), Positives = 134/187 (71%), Gaps = 5/187 (2%)

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+ + G PVDIVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   +
Sbjct: 1    PVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQE 57

Query: 1165 ISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            +   R+FL+KV   G   +   I+   DD V  + +  + G+P++TP+FDGA E +I  +
Sbjct: 58   LHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLIKNLRGGLPIATPIFDGAPEASIKEL 117

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 118  LKLVDLPESGQLKLFDGRTGDEFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 177

Query: 1283 LGGKSNR 1289
            LGGK+  
Sbjct: 178  LGGKAQF 184


>gi|321399356|emb|CBZ08599.1| putative DNA-directed RNA polymerase polypeptide [Leishmania infantum
            JPCM5]
          Length = 1132

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 85/307 (27%), Positives = 128/307 (41%), Gaps = 68/307 (22%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + +KV     RP + GDK + RHG KG+V  I+   DMPF + G   D++       
Sbjct: 876  DVDQKIKVITREVRPPEPGDKFSSRHGQKGVVGLIVNGVDMPFNERGMCPDMI------- 928

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                             +     K+ + 
Sbjct: 929  --MN----------------------------------------PHGFPSRMTVGKLLEL 946

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                   +      G       F G   ++I+  L     +  G+ + Y G+TG+     
Sbjct: 947  VCSKAAALRGSMGDGT-----AFGGDSADSISQQLLSFGYNYHGKDVFYSGITGDLMQGY 1001

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++ARSTG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 1002 VFFGPIYYQRLKHMVTDKMHARSTGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 1061

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYES-----IVAGNDTFETGTPESFNVLVKEMQA 1356
             +L E L I SD        V G    Y +        G  T +   P +F +L++E+Q 
Sbjct: 1062 NLLNERLLISSDMFTADICHVCG-NLGYNNRCTYCKTKGT-TSKVNMPYAFKLLIQELQG 1119

Query: 1357 LGLSIDL 1363
            +G+S+ L
Sbjct: 1120 MGVSLRL 1126



 Score =  129 bits (325), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 104/707 (14%), Positives = 228/707 (32%), Gaps = 49/707 (6%)

Query: 269 TGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               +IE+ +    S  ++S     +    +T      +             + ++A  +
Sbjct: 185 KNRVIIEADEHGNISAHVQSKTHYSISKCAVTFKKGSIVLTHRSFTEDIPIIVVLKALGL 244

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            +++ + +   +      IL+                     + DAL  I    +     
Sbjct: 245 ENDQHITQCIGTSPEFQEILFPCFEEA--------RLLNVVTQNDALQYIGEKRKETVWE 296

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                +   N    D     L+ V  +       +    + RH +   +  +++ +++  
Sbjct: 297 AEETQQRQVNRSKADKAAEFLANVL-LCHIREAQVQKDWNFRH-KAFYVCFMVRGMIEAS 354

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLIN 505
                +D+ D  GN+R  + G ++   +   L +  R +K          DS  P ++  
Sbjct: 355 FDASLLDERDFYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSKKDSTRPFNVKQ 414

Query: 506 -----AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RA 552
                 + + + +     S +      ++N         RLS +   G+         + 
Sbjct: 415 LMESKMEVIQNGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLGMMTRLASSFEKT 474

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           R     R + P+ +G +CP +T EG + GLV +  + ++V      ++  R         
Sbjct: 475 RKVSGPRSLQPSQWGMVCPCDTPEGESCGLVKNFATLSQVTLD-LNDSYVRAAAHALGVE 533

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++  ++  +  + Y    N +L     +   L     A          +       ++ V
Sbjct: 534 EIDTVTPTDFLHYYTVFLNGTLIGIHRYPNRLCAGIRALRRSGRLHPHVSISTQPRQRTV 593

Query: 673 SIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            I +     +   +   D    +   ++ R    L           +E V    S   ++
Sbjct: 594 QIGSDGGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTHNDFLAEGLIEYVDVNESNDCLI 653

Query: 729 A-KRAGIVEQVDAIRI-------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR- 779
           A   A I      + +       V+  +      + S  + ++    +++     +NQ  
Sbjct: 654 AVYPADIGPYTTHLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGTVALNQYI 713

Query: 780 ---PLVKVGDEVRRNDIIADGPS-TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
               ++ +G   +R        S T    L  G N +V  M + GY+ ED+ + ++  + 
Sbjct: 714 RADTVLLLGAYPQRPLCRTKAMSLTHYEKLGAGINAMVCVMSYSGYDIEDAQVYNKSSLD 773

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 + + + EV       G  ++      N      K ++  G+   GA V   D+L
Sbjct: 774 RGYGRCVVLRKHEVDLEKYAGGEFDVILPPEKNSGTGKFKALNPDGVASKGALVQQYDVL 833

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           V K TP       P   + +         V D  +  P G     +D
Sbjct: 834 VNKFTPVAGGDPRPAPLVYKYPQ----PAVVDHVIISPPGDYDRSLD 876



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 99/738 (13%), Positives = 214/738 (28%), Gaps = 128/738 (17%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFPITAF-SGAAMLEFVSYEFDPPK- 85
           +    AS+DH + +           LQ     +S   I +      ++ + +     P+ 
Sbjct: 33  LNHHIASFDHLIEVE----------LQRILLNESNVEIKSTVDPDFVIRYQNIRICRPQE 82

Query: 86  ----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                         +C  RD+TY   + + ++    D              E+ + +G +
Sbjct: 83  IVGKGHIPKLVTPQECRVRDMTYRGDMIVDVQYTSRDRSRAMLV-------EKDVKIGTI 135

Query: 136 PLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M K                         G F+IKG++++ + Q  +S   +  + D+ 
Sbjct: 136 PIMLKSKCCNLYRKTREELVNMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADEH 195

Query: 171 RA---SLSGKLLYA---CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
                 +  K  Y+   C +   +G           I+         +P+   L ALG++
Sbjct: 196 GNISAHVQSKTHYSISKCAVTFKKGS----------IVLTHRSFTEDIPIIVVLKALGLE 245

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           +++ ++         Q   F CF  +    +V    +   +     E V E+ +     +
Sbjct: 246 NDQHITQCIGTSPEFQEILFPCFEEARLLNVVTQNDALQYIGEKRKETVWEAEETQQRQV 305

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK------SLEEIFH 338
            +S  +K  +FL     C       +   N      Y+        +       L+E   
Sbjct: 306 NRSKADKAAEFLANVLLCHIREAQVQKDWNFRHKAFYVCFMVRGMIEASFDASLLDERDF 365

Query: 339 SEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
              +          +L+ D +     +  T +  +   +        + +    +     
Sbjct: 366 YGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSKKDSTRPFNVKQLMESKMEVIQN 425

Query: 392 AESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR--- 447
              M  +   +D  +++++  G  ++  RL+      +            K+        
Sbjct: 426 GMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIASLGMMTRLASSFEKTRKVSGPRSLQP 485

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL--RMERSIKERISSVDIDSVMPQDLIN 505
           +  G +   D         V            L     R+    +   +ID+V P D ++
Sbjct: 486 SQWGMVCPCDTPEGESCGLVKNFATLSQVTLDLNDSYVRAAAHALGVEEIDTVTPTDFLH 545

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              V      F   + +          + I   RR   L        +       +  + 
Sbjct: 546 YYTV------FLNGTLIGIHRYPNRLCAGIRALRRSGRLHPHVSISTQPRQRTVQI-GSD 598

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            GRI             V+S       +             D      + Y+   E  + 
Sbjct: 599 GGRIVRLLIIVRDGKPAVTSAHLDRLRDRLCTH-------NDFLAEGLIEYVDVNESNDC 651

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA   + +                             ++  P  ++ + A +IP+  ++
Sbjct: 652 LIAVYPADIGPY-----------------------TTHLEVEPLSLLGVVAGIIPYPHHN 688

Query: 686 DSNRVLMGCNMQRQAVPL 703
            S R      M +QA+  
Sbjct: 689 QSARNTFQSAMGKQALGT 706


>gi|319998251|gb|ADV91597.1| RNA polymerase B subunit [Mycobacterium branderi]
          Length = 240

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 100/230 (43%), Positives = 132/230 (57%), Gaps = 40/230 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+                       
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDGKP------------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                      +    + +L           VSTPVFDGA EE +  +L     +      
Sbjct: 143  --------DWASKLPEELLEAEPNKI----VSTPVFDGAREEELQGLLSSTLPNRDGDVL 190

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                G++ILYDG +GEPF  PVT GY+Y++KL+H+V DK++ARSTG YS+
Sbjct: 191  VDGDGKAILYDGRSGEPFPYPVTTGYMYIMKLHHLVDDKIHARSTGPYSM 240



 Score = 46.6 bits (109), Expect = 0.031,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|301622236|ref|XP_002940443.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 2
            [Xenopus (Silurana) tropicalis]
          Length = 1079

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 119/613 (19%), Positives = 199/613 (32%), Gaps = 151/613 (24%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA-FMPWHGYNFEDSMLISERMVSEDVFT 840
            V +   V   DI+  G +T           +VA F+P+  +N     +   +M  + +  
Sbjct: 584  VFLNVAVYEGDIVP-GETTHQEFFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGF 642

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             +    ++   R         T   P V        +                       
Sbjct: 643  PL--MTYQD--RSDNKLYRLQTPQSPLVRPSMYDYYEMD--------------------- 677

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                        + A+      D+ D  +   S          ++    +D +++    E
Sbjct: 678  ----NYPIGTNAIVAVISYTGYDMEDAMVLNKSSWERGFAHGSVYKTDHVDLSKKLKDGE 733

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
               +  +  D +  +  LD +    +  +L   +   G                      
Sbjct: 734  DNLVFGIKPDDERVKGRLDSDGLPAVGAVLQFGDPYYGYLNLNTG--------------- 778

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                           ES    Y++ ++ + D  K         +D+  G  + V V + +
Sbjct: 779  ---------------ESFVAYYKSKENCVIDNIK------ICSNDIGFGKFKSVCVTMRI 817

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM +G + E+ 
Sbjct: 818  PRNPTIGDKFASRHGQKGILSRLWPSEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESM 877

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G +    G    +    +                                         
Sbjct: 878  AGKSAALHGLCHDATPFTFSEENSAL---------------------------------- 903

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            E    MLR    +  G   LY G++G   +  + +G +Y  +L 
Sbjct: 904  ----------------EYFGEMLRAGGYNFYGTEKLYSGISGLELEADIFIGVVYYQRLR 947

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L + L   SD
Sbjct: 948  HMVSDKFQVRTTGARDKVTNQPVGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1007

Query: 1321 DVVGRTRVYESIVAG------------------------------NDTFETGTPESFNVL 1350
                R+  +  I  G                              +       P  F   
Sbjct: 1008 ----RSTAHVCIECGSLLSPFLEKPPPSWSSIRNRKHHCEVCDRTDTVETVSVPYVFRYF 1063

Query: 1351 VKEMQALGLSIDL 1363
            V E+ A+ +S+ L
Sbjct: 1064 VAELAAMNISVKL 1076



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 89/664 (13%), Positives = 213/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     N++ R+ +        ++       V++          
Sbjct: 197 LKALVDYSDYQIFTELIKGKEENSFYRDCMTQMLRAVVEEGCHSQKNVLK--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F   F+  D +         ++  + +    +V   +   +  + + L         
Sbjct: 249 GERFRVKFYLPDWFTDEQAAEFLISQCICIHLKTNVE--KFYMLCMMTQKLFTFAKDGCM 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLL------RMERSIKERISSVDIDSVMPQDLINA 506
            ++ D+L  + V + G++L    +  +       ++    +    +VD+ +     +  +
Sbjct: 307 EENPDSLMYQEVMTPGQLLLMFLKEKMESWLLGVKVNLDKRAHKYTVDLSTETMMKVFTS 366

Query: 507 KPVVSAVCE---------------FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              ++  CE                  SS L  + + +N +  ++H R    + +G    
Sbjct: 367 TSDLTKTCEYLLATGNLRSKTGLGMLQSSGLVVVADKLNFIRYLSHFR---CVHRGAAFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 +R + P  +G +CP  T +G   GL++ +T+   +       T    +      
Sbjct: 424 KMRTTSVRRLLPESWGFLCPVHTPDGEPCGLMNHMTAACEIVTQTSYNTLLPLLLCSLGM 483

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V   +     + Y    + ++      T             +   + +          
Sbjct: 484 TPVDGTAGKLFADCYPVMLDGAMVGWVEKTIAPGLVSALRNYKVKHEKNVPPWTEIVLIP 543

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV---AKSSGAAIV 728
           ++  ASL P L           C M R    L   +   +GT +E V    A   G  + 
Sbjct: 544 MTGKASLYPGL-----FLFTTPCRMVRPVRNLALGKEELLGT-LEQVFLNVAVYEGDIVP 597

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN----------- 777
            +         ++  V+ +     D + S  ++Y+    +++     +            
Sbjct: 598 GETTHQEFFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGFPLMTYQDRSDNKLYR 657

Query: 778 ----QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q PLV+                 ++ +  +G N +VA + + GY+ ED+M++++  
Sbjct: 658 LQTPQSPLVRPSMY----------DYYEMDNYPIGTNAIVAVISYTGYDMEDAMVLNKSS 707

Query: 834 VSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
                   S++  +   +++  K G + +   I    E     +D  G+  VGA +  GD
Sbjct: 708 WERGFAHGSVYKTDHVDLSKKLKDGEDNLVFGIKPDDERVKGRLDSDGLPAVGAVLQFGD 767

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              G +               ++       +++  S  +  G   +V       R+    
Sbjct: 768 PYYGYLNLNTGESFVAYY---KSKENCVIDNIKICSNDIGFGKFKSVCVTMRIPRNPTIG 824

Query: 953 NERS 956
           ++ +
Sbjct: 825 DKFA 828



 Score = 43.5 bits (101), Expect = 0.26,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 26/55 (47%)

Query: 123 KDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
           K I +Q+  +G +P+M K                         G F+I GI++++
Sbjct: 71  KGIIKQT--LGHIPIMVKSKFCNLYDLNPKQLLEHHEEEQEMGGYFIINGIEKVI 123


>gi|269912580|emb|CAY86070.1| RNA polymerase beta subunit [Gluconacetobacter johannae]
          Length = 273

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 123/272 (45%), Positives = 169/272 (62%), Gaps = 28/272 (10%)

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+
Sbjct: 1   ERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRK 60

Query: 210 RKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDF 244
           RK+PVT+ L AL                         GMD++EIL+ FY K+V+ +    
Sbjct: 61  RKLPVTTLLYALEGEASAAARAAKLAEGGDVDALDIQGMDADEILNYFYGKVVFVKTSKG 120

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
           W  P  A     G K+   L+D +TGE V E+  KLT+ +++ + EK  K + + +  L 
Sbjct: 121 WARPFDAE-SFRGLKLLEPLIDAETGEVVAEADAKLTARMVRKIAEK-TKDVLVGAAGLI 178

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G YVA D+VN +TGEIY EAG+ + E  LE +  + +  +P L +D+ N   +IRNTL  
Sbjct: 179 GRYVAYDLVNPDTGEIYAEAGEELTEARLEALEEAGLDRLPTLAIDASN-GPWIRNTLTV 237

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
           DKN  R DAL DIYRVMRPG+  T   AE+MF
Sbjct: 238 DKNTTRDDALTDIYRVMRPGEPPTPETAEAMF 269


>gi|154336907|ref|XP_001564689.1| DNA-directed RNA polymerase polypeptide [Leishmania braziliensis
            MHOM/BR/75/M2904]
 gi|134061724|emb|CAM38755.1| DNA-directed RNA polymerase polypeptide [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1125

 Score =  285 bits (729), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/307 (28%), Positives = 130/307 (42%), Gaps = 68/307 (22%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + +KV     RP + GDK + RHG KG+V  I+   DMPF + G   D++       
Sbjct: 869  DVDQKIKVITREVRPPEPGDKFSSRHGQKGVVGLIVNGVDMPFNERGMCPDMI------- 921

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                              G  +      
Sbjct: 922  --MN--------------------------------------------PHGFPSRMTVGK 935

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
              + V   A   +  +   T  F G   ++I+  L     +  G+ + Y G+TGE     
Sbjct: 936  LLELVCSKAAALRGSMGDGT-AFGGDSADSISRQLLSFGYNYHGKDVFYSGITGELMQGY 994

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++ARSTG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 995  VFFGPIYYQRLKHMVTDKMHARSTGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 1054

Query: 1309 YVLQEMLTIKSD-------DVVGRTRVYES-----IVAGNDTFETGTPESFNVLVKEMQA 1356
             +L E L I SD        V G    Y +        G  T +   P +F +L++E+Q 
Sbjct: 1055 SLLNERLLISSDLFTADICHVCG-NLGYNNRCTYCKTKGT-TSKVNMPYAFKLLIQELQG 1112

Query: 1357 LGLSIDL 1363
            +G+S+ L
Sbjct: 1113 MGVSLRL 1119



 Score =  125 bits (313), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 102/707 (14%), Positives = 224/707 (31%), Gaps = 49/707 (6%)

Query: 269 TGEQVIESGKK-LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               +IE+ +    S  ++S     +    +T      +             + ++A  +
Sbjct: 178 KNRVIIEADEHGNISAHVQSKTHYSISKCAVTFKKGSIVLTHRSFTEDIPIIVVLKALGL 237

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
            +++ + +   +      IL+                     + DAL  I    +     
Sbjct: 238 ENDQHITQCIGTSPAFQKILFPCFEEA--------RGLNIFTQNDALQYIGEKRKETVWE 289

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                +   N    D     L+ V  +       +    + RH +   +  +++ +++  
Sbjct: 290 VEETQQRQVNRSKADKAAEFLANVL-LCHIRESQMQKDWNFRH-KAFYVCFMVRGMIEAS 347

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLIN 505
                +D+ D  GN+R  + G ++   +   L +  R +K          DS  P ++  
Sbjct: 348 FDASLLDERDFYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSKRDSTRPFNVKQ 407

Query: 506 -----AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARA 552
                 + + + +     S +      ++N         RLS +              + 
Sbjct: 408 LMESKMEVIQNGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIACLGMMTRLASSFEKT 467

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           R     R + P+ +G +CP +T EG + GLV +  + ++V      +   R         
Sbjct: 468 RKVSGPRSLQPSQWGMVCPCDTPEGESCGLVKNFATLSQVTLD-MNDHYVRASAHSLGVE 526

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++  ++  +    Y    N +L     +   L     A          +       ++ V
Sbjct: 527 EIDTVTPTDFLQYYSVFLNGTLIGIHRYPNRLCAGIRALRRSGRLHPHVSISMQPRQRTV 586

Query: 673 SIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
            I +     +   +        +   ++ R    L           +E V    S   ++
Sbjct: 587 QIGSDGGRIVRLLIIVRGGKPAVTSAHLDRLRDRLCTHNDFLAEGLIEYVDVNESNDCLI 646

Query: 729 A-KRAGIVEQVDAIRI-------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR- 779
           A   A I      + +       V+  +      + S  + ++    +++     +NQ  
Sbjct: 647 AVYPADIGPYTTHLEVEPLSLLGVVAGIIPYPHHNQSARNTFQSAMGKQALGTVALNQYI 706

Query: 780 ---PLVKVGDEVRRNDIIADGPS-TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
               ++ +G   +R        S T    L  G N +V  M + GY+ ED+ + ++  + 
Sbjct: 707 RADTVLLLGAYPQRPLCRTRAMSLTHYEKLGAGINAMVCVMSYSGYDIEDAQVYNKSSLD 766

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 + + + EV       G  ++      N      K ++  G+   GA V   D+L
Sbjct: 767 RGYGRCVVLRKHEVDLEKYAGGEFDVILPPEKNSGSGKFKALNPDGVASKGAFVQQYDVL 826

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           V K TP       P   + +       + V D  +  P G     +D
Sbjct: 827 VNKFTPVAGGDPRPAPLVYKYPQ----LAVVDHVIISPPGDYDRSLD 869



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 88/739 (11%), Positives = 203/739 (27%), Gaps = 130/739 (17%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF--KSVFPITAF-SGAAMLEFVSYEF----- 81
           +    AS+DH + +           LQ     +S   I +      ++ + +        
Sbjct: 26  LNHHIASFDHLIEVE----------LQRILLNESNVEIKSVVDPDFLIRYQNIRVCRPQE 75

Query: 82  --DP---PKF-DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                  PKF    +C  RD+TY   + + ++    D              E+ + +G +
Sbjct: 76  IVGKGHIPKFVTPQECRIRDMTYRGDMIVDVQYTSRDRSRAMLV-------EKDVKIGTI 128

Query: 136 PLMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
           P+M K                         G F+IKG++++ + Q  +S   +  + D+ 
Sbjct: 129 PIMLKSKCCNLYRKTREELVSMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADEH 188

Query: 171 RA---SLSGKLLYA---CRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
                 +  K  Y+   C +   +G           I+         +P+   L ALG++
Sbjct: 189 GNISAHVQSKTHYSISKCAVTFKKGS----------IVLTHRSFTEDIPIIVVLKALGLE 238

Query: 225 SEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ--VIESGKKLT 281
           +++ I         + +            ++         + +        V E+ ++  
Sbjct: 239 NDQHITQCIGTSPAFQKILFPCFEEARGLNIFTQNDALQYIGEKRKETVWEVEETQQRQV 298

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV----IDEKSLEEIF 337
           +        + +  + +           +     +   +      +     D   L+E  
Sbjct: 299 NRSKADKAAEFLANVLLCHIR-ESQMQKDWNFRHKAFYVCFMVRGMIEASFDASLLDERD 357

Query: 338 HSEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
               +          +L+ D +     +  T +  +   R        + +    +    
Sbjct: 358 FYGNKRFETTGTLMALLFEDLLKQFNRVVKTAMDQQLSKRDSTRPFNVKQLMESKMEVIQ 417

Query: 391 VAESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR-- 447
               M  +   +D  +++++  G  ++  RL+      +            K+       
Sbjct: 418 NGMRMAISSGRWDLKRFNMNRQGITQVLSRLSYIACLGMMTRLASSFEKTRKVSGPRSLQ 477

Query: 448 -NGKGTIDDIDNLGNRRVRSVGEMLKNQYRL--GLLRMERSIKERISSVDIDSVMPQDLI 504
            +  G +   D         V                  R+    +   +ID+V P D +
Sbjct: 478 PSQWGMVCPCDTPEGESCGLVKNFATLSQVTLDMNDHYVRASAHSLGVEEIDTVTPTDFL 537

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               V      F   + +          + I   RR   L        +       +   
Sbjct: 538 QYYSV------FLNGTLIGIHRYPNRLCAGIRALRRSGRLHPHVSISMQPRQRTVQIGSD 591

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
               +       G     V+S       +             D      + Y+   E  +
Sbjct: 592 GGRIVRLLIIVRGGK-PAVTSAHLDRLRDRLCTH-------NDFLAEGLIEYVDVNESND 643

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA   + +                             ++  P  ++ + A +IP+  +
Sbjct: 644 CLIAVYPADIGPY-----------------------TTHLEVEPLSLLGVVAGIIPYPHH 680

Query: 685 DDSNRVLMGCNMQRQAVPL 703
           + S R      M +QA+  
Sbjct: 681 NQSARNTFQSAMGKQALGT 699


>gi|318602987|emb|CBJ04573.1| RNA polymerase beta subunit [Pseudomonas sp. R-37176]
          Length = 287

 Score =  285 bits (728), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 168/286 (58%), Positives = 220/286 (76%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR 
Sbjct: 2   SEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYART 61

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E
Sbjct: 62  NQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHLNE 121

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VG
Sbjct: 122 FTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVG 181

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TGME  VA+ SG  +VA+R G+++ VDA RIV+   + +++   +GVDIY L K+ RSNQ
Sbjct: 182 TGMERNVARDSGVCVVARRGGVIDSVDASRIVVPVADDEVETGEAGVDIYNLTKYTRSNQ 241

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
           NTC+NQRPLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W
Sbjct: 242 NTCINQRPLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAW 287


>gi|207340417|gb|EDZ68774.1| YPR010Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 835

 Score =  285 bits (728), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 119/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 470  EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 529

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   DI++NP   PSR
Sbjct: 530  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSR 589

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 590  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD--------------------------- 622

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 623  -----------------TPA------DYFGEQLAKAGYNYHGNEPMYSGATGEELRADIY 659

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 660  VGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 719

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 720  LQDRLLNSSD 729



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 89/577 (15%), Positives = 179/577 (31%), Gaps = 83/577 (14%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR----------LGLLR 481
           +   ++ +I+ L  L  G+ + D+ D   ++ V   G +     +          +  +R
Sbjct: 2   KFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVR 61

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL--------------SQLEE 527
           M+ +    I+  D   +    +   + + S +  F  ++ L              + + E
Sbjct: 62  MDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTANLVSQSGLDLQQVSGYTVVAE 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N    I+H R    + +G          +R + P  +G +CP  T +G   GL++   
Sbjct: 122 KINFYRFISHFR---MVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFA 178

Query: 588 SFARVNAY----GFIETPYRK--VCDGKVT--------------NDVVYLSAMEEENRYI 627
              R++        I +      V     T                + ++S   E+ + I
Sbjct: 179 HKCRISTQQSDVSRIPSILYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVS--HEQGKII 236

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A        +G      +            R +   +         +       L+ +D 
Sbjct: 237 ADTLRYWKVEGKTPGLPIDLEIGY-VPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDI 295

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                   M     P        V T +E         +I+A      +   + R + + 
Sbjct: 296 VGPFEQVYMNIAVTPQEIQNN--VHTHVEFTPTNIL--SILANLTPFSDFNQSPRNMYQC 351

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             G     T GV +                Q P+VK                  + +   
Sbjct: 352 QMGKQTMGTPGVALCHRS--DNKLYRLQTGQTPIVKANLYDDYG----------MDNFPN 399

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-----RDTKLGPEEIT 862
           G N +VA + + GY+ +D+M+I++             +  +V       R   +      
Sbjct: 400 GFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGF 459

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK----------ITPKGESPMTPEEKL 912
            +     E  L+ +DE G+  +G  V  GD +              T     P   EE  
Sbjct: 460 GNDEWPKEW-LEKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVN 518

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           L      K  +++  S++     +  + D +  +RHG
Sbjct: 519 LIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSSRHG 554


>gi|221044264|dbj|BAH13809.1| unnamed protein product [Homo sapiens]
          Length = 1173

 Score =  285 bits (728), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 111/559 (19%), Positives = 182/559 (32%), Gaps = 93/559 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 676  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 734

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 735  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 794

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 795  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 844

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 845  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 902

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM
Sbjct: 903  KCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRM 962

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G +    G    +    +                                
Sbjct: 963  TIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY----------------------- 999

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                          ML+ A  +  G   LY G++G   +  + +
Sbjct: 1000 ---------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFI 1032

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R G ME   + A+G +++L
Sbjct: 1033 GVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGGMERDALLAHGTSFLL 1092

Query: 1312 QEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETGTPE 1345
             + L   SD     V    G                 R R Y   +    +       P 
Sbjct: 1093 HDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVSVPY 1152

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
             F   V E+ A+ + + L+
Sbjct: 1153 VFRYFVAELAAMNIKVKLD 1171



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 215/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 291 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 342

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 343 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 400

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 401 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 460

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 461 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 517

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 518 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 577

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 578 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 637

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 638 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 697

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 698 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 753

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 754 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 803

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 804 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 863

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 864 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 918

Query: 953 NERS 956
           ++ +
Sbjct: 919 DKFA 922



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 100/721 (13%), Positives = 200/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 90  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 149

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 150 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 199

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 200 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHS 258

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 259 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 308

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 309 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 352

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 353 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 412

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++       +  
Sbjct: 413 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMRIFTMGIDL 464

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 465 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 518

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 519 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 571

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +D+ P     +   +      I 
Sbjct: 572 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIP 628

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +               +      ++   V  L+  +EE          L       
Sbjct: 629 PWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEE----------LIGTMEQI 678

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V        +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 679 FMNVAIFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 734

Query: 702 P 702
            
Sbjct: 735 G 735


>gi|300078415|gb|ADJ67154.1| RNA polymerase B-subunit [Staphylococcus aureus subsp. anaerobius]
          Length = 317

 Score =  285 bits (728), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 181/317 (57%), Positives = 232/317 (73%), Gaps = 3/317 (0%)

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+
Sbjct: 1   MSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGL 60

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--D 607
            R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV    
Sbjct: 61  TRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDT 120

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
             +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D S
Sbjct: 121 HAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVS 180

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ SGAAI
Sbjct: 181 PKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAI 240

Query: 728 VAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
            AK  G VE V++  I++R  VE +       +D Y L KF+RSN  TC NQRP+V VGD
Sbjct: 241 TAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGD 300

Query: 787 EVRRNDIIADGPSTDLG 803
            V  N+I+ADGPS +LG
Sbjct: 301 VVECNEILADGPSMELG 317


>gi|301622234|ref|XP_002940442.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like isoform 1
            [Xenopus (Silurana) tropicalis]
          Length = 1135

 Score =  285 bits (728), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 119/613 (19%), Positives = 199/613 (32%), Gaps = 151/613 (24%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA-FMPWHGYNFEDSMLISERMVSEDVFT 840
            V +   V   DI+  G +T           +VA F+P+  +N     +   +M  + +  
Sbjct: 640  VFLNVAVYEGDIVP-GETTHQEFFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGF 698

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             +    ++   R         T   P V        +                       
Sbjct: 699  PL--MTYQD--RSDNKLYRLQTPQSPLVRPSMYDYYEMD--------------------- 733

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                        + A+      D+ D  +   S          ++    +D +++    E
Sbjct: 734  ----NYPIGTNAIVAVISYTGYDMEDAMVLNKSSWERGFAHGSVYKTDHVDLSKKLKDGE 789

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
               +  +  D +  +  LD +    +  +L   +   G                      
Sbjct: 790  DNLVFGIKPDDERVKGRLDSDGLPAVGAVLQFGDPYYGYLNLNTG--------------- 834

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                           ES    Y++ ++ + D  K         +D+  G  + V V + +
Sbjct: 835  ---------------ESFVAYYKSKENCVIDNIK------ICSNDIGFGKFKSVCVTMRI 873

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM +G + E+ 
Sbjct: 874  PRNPTIGDKFASRHGQKGILSRLWPSEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESM 933

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G +    G    +    +                                         
Sbjct: 934  AGKSAALHGLCHDATPFTFSEENSAL---------------------------------- 959

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            E    MLR    +  G   LY G++G   +  + +G +Y  +L 
Sbjct: 960  ----------------EYFGEMLRAGGYNFYGTEKLYSGISGLELEADIFIGVVYYQRLR 1003

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L + L   SD
Sbjct: 1004 HMVSDKFQVRTTGARDKVTNQPVGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063

Query: 1321 DVVGRTRVYESIVAG------------------------------NDTFETGTPESFNVL 1350
                R+  +  I  G                              +       P  F   
Sbjct: 1064 ----RSTAHVCIECGSLLSPFLEKPPPSWSSIRNRKHHCEVCDRTDTVETVSVPYVFRYF 1119

Query: 1351 VKEMQALGLSIDL 1363
            V E+ A+ +S+ L
Sbjct: 1120 VAELAAMNISVKL 1132



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 89/664 (13%), Positives = 213/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     N++ R+ +        ++       V++          
Sbjct: 253 LKALVDYSDYQIFTELIKGKEENSFYRDCMTQMLRAVVEEGCHSQKNVLK--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F   F+  D +         ++  + +    +V   +   +  + + L         
Sbjct: 305 GERFRVKFYLPDWFTDEQAAEFLISQCICIHLKTNVE--KFYMLCMMTQKLFTFAKDGCM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLL------RMERSIKERISSVDIDSVMPQDLINA 506
            ++ D+L  + V + G++L    +  +       ++    +    +VD+ +     +  +
Sbjct: 363 EENPDSLMYQEVMTPGQLLLMFLKEKMESWLLGVKVNLDKRAHKYTVDLSTETMMKVFTS 422

Query: 507 KPVVSAVCE---------------FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              ++  CE                  SS L  + + +N +  ++H R    + +G    
Sbjct: 423 TSDLTKTCEYLLATGNLRSKTGLGMLQSSGLVVVADKLNFIRYLSHFR---CVHRGAAFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                 +R + P  +G +CP  T +G   GL++ +T+   +       T    +      
Sbjct: 480 KMRTTSVRRLLPESWGFLCPVHTPDGEPCGLMNHMTAACEIVTQTSYNTLLPLLLCSLGM 539

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V   +     + Y    + ++      T             +   + +          
Sbjct: 540 TPVDGTAGKLFADCYPVMLDGAMVGWVEKTIAPGLVSALRNYKVKHEKNVPPWTEIVLIP 599

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV---AKSSGAAIV 728
           ++  ASL P L           C M R    L   +   +GT +E V    A   G  + 
Sbjct: 600 MTGKASLYPGL-----FLFTTPCRMVRPVRNLALGKEELLGT-LEQVFLNVAVYEGDIVP 653

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN----------- 777
            +         ++  V+ +     D + S  ++Y+    +++     +            
Sbjct: 654 GETTHQEFFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGFPLMTYQDRSDNKLYR 713

Query: 778 ----QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q PLV+                 ++ +  +G N +VA + + GY+ ED+M++++  
Sbjct: 714 LQTPQSPLVRPSMY----------DYYEMDNYPIGTNAIVAVISYTGYDMEDAMVLNKSS 763

Query: 834 VSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
                   S++  +   +++  K G + +   I    E     +D  G+  VGA +  GD
Sbjct: 764 WERGFAHGSVYKTDHVDLSKKLKDGEDNLVFGIKPDDERVKGRLDSDGLPAVGAVLQFGD 823

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              G +               ++       +++  S  +  G   +V       R+    
Sbjct: 824 PYYGYLNLNTGESFVAYY---KSKENCVIDNIKICSNDIGFGKFKSVCVTMRIPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/158 (17%), Positives = 50/158 (31%), Gaps = 57/158 (36%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPP------ 84
              S++              EGL  A +++ P+     +    L+ V     PP      
Sbjct: 42  HIDSFNQ----------AMTEGLSLAVQAMKPLEFTYKNDKVALQIVDAVITPPLVPKGS 91

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K    +C  R  TY   L   +   +  +         K I +Q+  +G +P+M 
Sbjct: 92  ICKEQKIYPAECRGRRSTYRGKLTADVSWSLNGLQ--------KGIIKQT--LGHIPIMV 141

Query: 140 KD------------------------GTFVIKGIQRIV 153
           K                         G F+I GI++++
Sbjct: 142 KSKFCNLYDLNPKQLLEHHEEEQEMGGYFIINGIEKVI 179


>gi|256081823|ref|XP_002577167.1| DNA-directed RNA polymerase III subunit [Schistosoma mansoni]
 gi|238662463|emb|CAZ33404.1| DNA-directed RNA polymerase III subunit, putative [Schistosoma
            mansoni]
          Length = 1126

 Score =  285 bits (728), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 109/491 (22%), Positives = 173/491 (35%), Gaps = 94/491 (19%)

Query: 888  VNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V P   LV   T +      +   +  + AI      DV D  +   + +        ++
Sbjct: 688  VYPQKPLVQSKTIQMMHFDELPAGQNAVVAIMSYSGYDVEDALVINQASIDRGFARACVY 747

Query: 946  NRHG-IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
             R G   K   +   +R     + R         +  +  R  E+L              
Sbjct: 748  RRSGVHLKMHENAVYDRLMGPSIER---------ETGVLRRGDEVLQADGVAYIGACVND 798

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              +L +  +     S     A          E+    ++      +    + +EK+ +  
Sbjct: 799  RQILINKEMPVVSSSAVLDNAGSLSLNVNTPENATE-FKRCPVDYKGIEPSYVEKVMF-- 855

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                G   VVK+ +   R  + GDK + RHG KG+V  I+  ED+PF  +G   DI++NP
Sbjct: 856  STSEGNQAVVKILLRQTRRPEVGDKFSSRHGQKGVVGLIVRQEDLPFSTNGLTPDIIMNP 915

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
             G PSRM V        G     LG K  ++    +                        
Sbjct: 916  HGFPSRMTV--------GKLLEVLGSKAGAIEGKIRDGS--------------------- 946

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                      F G   E ++ +L        G+ ILY G+TG P
Sbjct: 947  -------------------------AFSGDPAEVLSQVLIDHGYHYLGKEILYSGVTGAP 981

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
             +  +  G +Y  +L HMV DKV+ARS G  + +T+QP  G+S  GG R+GEME  C  A
Sbjct: 982  LEAFIYFGPVYYQRLKHMVMDKVHARSRGPVTALTRQPTEGRSREGGLRVGEMERDCFIA 1041

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN------------------DTFETGTPES 1346
            YG + +L E L + SD        Y++ V                            P +
Sbjct: 1042 YGTSQLLLERLLLSSD-------AYDACVCEKCGLLATSPNWCQYCRSSRQVVSVRMPYA 1094

Query: 1347 FNVLVKEMQAL 1357
              +L +E+  +
Sbjct: 1095 CKLLFQELMCM 1105



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 90/738 (12%), Positives = 203/738 (27%), Gaps = 132/738 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+++   S++HF+   I    R N            ++       LE+      PP    
Sbjct: 17  LVKLHIDSFNHFIQTEIKNIVRAN----------SRVSVPEANWWLEYNDIYIKPPTVND 66

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 +    DC  RDLTYA  + + +  +          +  + + ++ + +G +P+M
Sbjct: 67  GGVVASRVTPHDCRLRDLTYAGEILVDVTFV----------RQNEVVSKKGVLIGRMPIM 116

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGR--- 171
            K                         G F+I G +++V+ Q   S       +  +   
Sbjct: 117 LKSSICVLNGKSPSELMRLKECPLDPGGYFIIGGTEKVVLMQEQTSKNRLIIEEDSKRGL 176

Query: 172 ---ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI 228
               + S     +   I  +             I   +D    VP+     A+ + S++ 
Sbjct: 177 VCSVTSSSAQTKSKTNIVTKDD--KFYLSHNSFI---VD----VPIAILFKAMNITSDQE 227

Query: 229 L-----------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           L           + F P +      +     L A + +               + ++E  
Sbjct: 228 LLQLIGTEESVWANFVPSLKLCLEYNIH-TCLDACNWLHSRLRQPRYRTAFGADIILEIQ 286

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           + L   ++  ++ + + F         G  V   I+  E   I +   D    K +E   
Sbjct: 287 RFLRDIIITHVEMEKLNF--APRAFFLGQMVRYLILANE-KRIPVNDRDFYGNKRIELAG 343

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                                      D  K   + L      +      T         
Sbjct: 344 SLLALLFE-------------------DVFKTFNEDLWLTVSKIDTKRRCTPFDISRHIK 384

Query: 398 FLFFDSDKYDLSTVGRV--KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
                       + G    K    +       V  +     +  +  +         +  
Sbjct: 385 TWMITEQLNRAISSGNWIIKRFRMMRHGVTQVVSRLSYVAALGHMTRMTSQFEKTRKVSG 444

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             ++   +   +      +     L    ++   ++    D+ + + + N       + +
Sbjct: 445 PRSIHASQWGLICPSDTPEGEACGLVKNVALMCHVTVEVDDAHLIELISNYYTF--PLYQ 502

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              +     +  +   +    H  +L  +   G+ R+        V+     +     + 
Sbjct: 503 MRYAKNEYVIYVNGKPIGFTQHPGKL-CVLIRGLRRSGRIHGFVSVYIKQAYQCVHVVSD 561

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANS 632
            G        L +   +     ++     V +         V YL   E  +  +A   S
Sbjct: 562 GGRFCRPYIILCNGRPLVTESVLQDLRHNVLNWDDLLKKGLVEYLDVNELNDCLVAMDES 621

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L +   +                       ++  P  ++ + A LIP+ +++ S R   
Sbjct: 622 CLTDGNHY---------------------THMEIDPATILGVVAGLIPYPDHNQSPRNTY 660

Query: 693 GCNMQRQAVPLLKAEAPF 710
            C M +QA+  +      
Sbjct: 661 QCAMGKQAIGTVALNQQI 678



 Score =  121 bits (304), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 94/651 (14%), Positives = 197/651 (30%), Gaps = 68/651 (10%)

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
           K   +T D    L     IV+     ++       D++ L+ I   E             
Sbjct: 190 KTNIVTKDDKFYLSHNSFIVDVPIAILFKAMNITSDQELLQLIGTEES---------VWA 240

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           N        +        DA   ++  +R     T   A+ +               + R
Sbjct: 241 NFVPSLKLCLEYNIHTCLDACNWLHSRLRQPRYRTAFGADIIL-------------EIQR 287

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              ++ +     + +    +   +  +++ L+     +  ++D D  GN+R+   G +L 
Sbjct: 288 FLRDIIITHVEMEKLNFAPRAFFLGQMVRYLILANEKRIPVNDRDFYGNKRIELAGSLLA 347

Query: 473 NQYRLGLLRME-------------RSIKERISSVDIDSVMPQDLINA---KPVVSAVCEF 516
             +                     R       S  I + M  + +N              
Sbjct: 348 LLFEDVFKTFNEDLWLTVSKIDTKRRCTPFDISRHIKTWMITEQLNRAISSGNWIIKRFR 407

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                ++Q+   ++ ++ + H  R+++       + R     R +H + +G ICP++T E
Sbjct: 408 MMRHGVTQVVSRLSYVAALGHMTRMTS----QFEKTRKVSGPRSIHASQWGLICPSDTPE 463

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G   GLV ++     V            + +           A  E   Y+        +
Sbjct: 464 GEACGLVKNVALMCHVTVEVDDAHLIELISNYYTFPLYQMRYAKNEYVIYVNGKPIGFTQ 523

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCN 695
                  L+        I                VVS       P++   +   ++    
Sbjct: 524 HPGKLCVLIRGLRRSGRIHGFVSVYIKQAYQCVHVVSDGGRFCRPYIILCNGRPLVTESV 583

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI------------ 743
           +Q     +L  +       +E +        +VA         D                
Sbjct: 584 LQDLRHNVLNWDDLLKKGLVEYLDVNELNDCLVA--MDESCLTDGNHYTHMEIDPATILG 641

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR----PLVKVGDEVRRNDIIADG-P 798
           V+  +    D + S  + Y+    +++     +NQ+     L       ++  + +    
Sbjct: 642 VVAGLIPYPDHNQSPRNTYQCAMGKQAIGTVALNQQIRFDTLQCQMVYPQKPLVQSKTIQ 701

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA M + GY+ ED+++I++  +      +       V  +  +   
Sbjct: 702 MMHFDELPAGQNAVVAIMSYSGYDVEDALVINQASIDRGFARACVYRRSGVHLKMHENAV 761

Query: 859 EEI-TRDIPNVSEEGLKNIDE----CGIICVGAEVNPGDILVGKITPKGES 904
            +             L+  DE     G+  +GA VN   IL+ K  P   S
Sbjct: 762 YDRLMGPSIERETGVLRRGDEVLQADGVAYIGACVNDRQILINKEMPVVSS 812


>gi|62720672|gb|AAX93872.1| RNA polymerase subunit B [Mycobacterium holsaticum]
          Length = 238

 Score =  285 bits (728), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 99/229 (43%), Positives = 132/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G K++                      
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWAA-HSGWKVEGKPEWA---------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                           + +     + +    VSTPVFDGA  E +  +L            
Sbjct: 145  ---------------EQLPDDLLEAEPNTIVSTPVFDGAQGEELLGLLASTLPNRDGEKL 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG YS
Sbjct: 190  VDSDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 238



 Score = 46.2 bits (108), Expect = 0.042,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|147899772|ref|NP_001080005.1| polymerase (RNA) I polypeptide B, 128kDa [Xenopus laevis]
 gi|37589362|gb|AAH59304.1| MGC68946 protein [Xenopus laevis]
          Length = 1134

 Score =  284 bits (727), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 115/557 (20%), Positives = 193/557 (34%), Gaps = 91/557 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E VF ++ I E E++  +T    E     + +V    +   D         +   G   +
Sbjct: 637  EQVFLNVAIYEGEIVPGET-THQELFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTM 695

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 696  GFPLMTYQDRSDNKLYRLQTPQSPLVRPSMYDYYEMDNYPVGTNAIVAVISYTGYDMEDA 755

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + S         +  K D       ++  +L +          P   +    L +D 
Sbjct: 756  MVLNKSSWERGFAHGSVYKTDHV-----DLSKKLKDGEDNIVFGIKPDDERVKGRLDNDG 810

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            +        +             ES    Y++ ++ + D  K         +D+  G  +
Sbjct: 811  LPPVGAVLQFGDPYYGYLNFNTGESFVAYYKSKENCVVDNIK------ICSNDIGFGKFK 864

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 865  SVCITMRIPRNPTIGDKFASRHGQKGILSRLWPSEDMPFTESGMVPDILFNPHGFPSRMT 924

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 925  IGMLIESMAGKSAALHGLCHDATPFTFSEENSAL-------------------------- 958

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                    E    MLR    +  G   LY G++G   +  + +G
Sbjct: 959  ------------------------EYFGEMLRAGGYNFYGTEKLYSGISGLELEADIFIG 994

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 995  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPVGGRNIQGGIRFGEMERDALLAHGTSFLLH 1054

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     +    G                 R R ++ +V    +       P  
Sbjct: 1055 DRLFHCSDRSTAHMCVECGSLIAPFLEKPPPSWSSIRNRKHQCVVCNRTDTVEAVSVPYV 1114

Query: 1347 FNVLVKEMQALGLSIDL 1363
            F   V E+ A+ +++ L
Sbjct: 1115 FRYFVAELAAMNINVKL 1131



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 82/662 (12%), Positives = 197/662 (29%), Gaps = 69/662 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +N++ R+ +        ++   +   V++          
Sbjct: 253 LKALVEFSDYQIFTELIKGKEDNSFYRDCMTQMLRVVVEEGCHNQKNVLK--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F   F+  + Y         ++  + +    +V   +   +  + + L         
Sbjct: 305 GERFRVKFYLPEWYTDEQAAEFLISHCICIHLKTNVE--KFYMLCMMTQKLFTFAKDGCM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLL------RMERSIKERISSVDIDSVMPQDLINA 506
            ++ D+L  + V + G++L    +  +       ++    +           M + L + 
Sbjct: 363 EENPDSLMYQEVLTPGQLLLMFLKEKMESWLLGVKLNLDKRAHKLVDLTTETMGKILTST 422

Query: 507 KPVVSAVCE--------------FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +                       SS L  + + +N +  ++H R    + +G     
Sbjct: 423 SDLTKLCEYLLATGNLRSKTGLGMLQSSGLVVVADKLNFIRYLSHFR---CVHRGAAFAK 479

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGK 609
                +R + P  +G +CP  T +G   GL++ +T+   +    +Y              
Sbjct: 480 MRTTSVRRLLPESWGFLCPVHTPDGEPCGLMNHMTAACEIVTQTSYNTSLPLLLCSLGMT 539

Query: 610 VTND----------VVYLSAME--EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
             +            V L           +A    +         +          ++  
Sbjct: 540 PVDGAAGKSFADCYPVMLDGAMVGWVENNVAPGLVNALRIYKVKHDKNVPPWTEIVLIPM 599

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             K            +    + P          L+G   Q      +       G     
Sbjct: 600 TGKASLYPGL-FVFTTPCRLVRPIRNLALGKEELLGTLEQVFLNVAIYEGEIVPGETTHQ 658

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  ++VA     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 659 ELFPHSMLSVVA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLMTYQDRSDNKLYRLQ- 714

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 ++ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 715 TPQSPLVRPSMY----------DYYEMDNYPVGTNAIVAVISYTGYDMEDAMVLNKSSWE 764

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  +   +++  K G + I   I    E     +D  G+  VGA +  GD  
Sbjct: 765 RGFAHGSVYKTDHVDLSKKLKDGEDNIVFGIKPDDERVKGRLDNDGLPPVGAVLQFGDPY 824

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            G +               ++       +++  S  +  G   +V       R+    ++
Sbjct: 825 YGYLNFNTGESFVAYY---KSKENCVVDNIKICSNDIGFGKFKSVCITMRIPRNPTIGDK 881

Query: 955 RS 956
            +
Sbjct: 882 FA 883



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 52/167 (31%), Gaps = 60/167 (35%)

Query: 27  PDLIEV---QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEF 81
           P L E+      S++              EGL  A +++ P+     +    L+ V    
Sbjct: 33  PPLQEITRAHIDSFNQ----------AMTEGLSLAVQAMKPLEFTYRNDKVALQIVDAVL 82

Query: 82  DPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
             P           K    +C  R  TY   L   +   +  +         K I +Q+ 
Sbjct: 83  SHPLVPKGSICKEQKIYPAECRGRRSTYRGKLTADVSWSLNGMQ--------KGIIKQT- 133

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIV 153
            +G  P+M K                         G F+I GI++++
Sbjct: 134 -LGQFPIMVKSKFCNLYDLNPKQLLEHHEEEQEMGGYFIINGIEKVI 179


>gi|148879049|emb|CAM07040.1| RpoB protein [Mycobacterium sp. MG11]
          Length = 225

 Score =  284 bits (727), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 96/227 (42%), Positives = 127/227 (55%), Gaps = 40/227 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG 
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 225


>gi|327553822|gb|AEB00413.1| RNA polymerase beta-subunit [Mycobacterium sp. B10-07.09.0206]
          Length = 237

 Score =  284 bits (727), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 100/229 (43%), Positives = 131/229 (57%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+                       
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDGKP------------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                      +    + +L           VSTPVFDGA EE +  +L     +      
Sbjct: 141  --------DWAAKLPEELLEAEPNKI----VSTPVFDGAREEELQGLLSSTLPNRDGEVL 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ILYDG +GEPF  PVT GY+Y++KL+H+V DK++ARSTG YS
Sbjct: 189  VDGDGKAILYDGRSGEPFPYPVTTGYMYIMKLHHLVDDKIHARSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.089,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|83415477|gb|ABC17946.1| RNA polymerase II second largest subunit [Glomus mosseae]
          Length = 724

 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 135/855 (15%), Positives = 257/855 (30%), Gaps = 154/855 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ + +R     +   +    R              +    + +       +
Sbjct: 2    KRLDMAGPLMISLFRTLYKTVLNDMAAYFRKCISSKREFKLPLALRPHKITNGFRYSIGT 61

Query: 520  -------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                         S +S++      +S I+H RR +A       R     + R +H TH+
Sbjct: 62   GNWGDAKKAKQSRSGVSRVLNRFTYVSTISHLRRCNAPT----GREGKFTKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G ICPAET EG   GL+ +L   + V+     +     +    +  ++            
Sbjct: 118  GYICPAETPEGQACGLMKNLALMSYVSVSIPSDILNEFINSCGICQNINETPFDNIVKFT 177

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS---LIPFLE 683
                N +L        +L+      +   +P +     D    +V   + S     P   
Sbjct: 178  KVFVNGNLTCITDRPLDLIKSIREIKGNSLPADIGIVNDILVNEVRFYSDSGRMCRPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             +D + VL    + +  + + +     +   +                   +E +DA   
Sbjct: 238  VEDQHLVLTSDTLSKLKLEIAQEANQSLWEAL--------------VLERYIEYIDAEEE 283

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQ--RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
               ++            +Y L K +  R  +        L+ +     +       PS  
Sbjct: 284  E-STMICISPDELYESRLYNLRKLEGLRPRRKRRSVHERLINLPTYPNKWTHCEIHPSMI 342

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG  A       + +P+  +N       S R   +   +   +  +    R         
Sbjct: 343  LGVSA-------SLIPFSDHNQ------SPRNTYQSAMSKQAMGIYATNFR--------- 380

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                          +    +  +        +    +       +     ++ AI     
Sbjct: 381  --------------LRMDVLANLLYYPQKPLVTTKVMEYLQFRELPAGINVIVAIMCYGG 426

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S V   +     +         R +  E++   L   D      I   N
Sbjct: 427  YNQEDSLIINQSSVDRGLFRSFSY--------RRYLDQEKKVGVLNMED------ITKPN 472

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
             Y+ L         +           +  +   +    +    + +DE + +  ES    
Sbjct: 473  PYTTLGLKRGNYEKLDDDGIVPCGVRVCGN---DILIGKVSTLSPEDELLGQRKES--HV 527

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y    + L       ++++           ++VKV V   R  + GDK A RHG KG + 
Sbjct: 528  YRDVSTPLRSTEHGIVDQVIV--TTNQDGAKLVKVGVRNTRIPEIGDKFASRHGQKGTIG 585

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  DG   DI++NP  +PSRM +G + E  +G   V  G +          
Sbjct: 586  INYRQEDMPFTADGITPDIIINPHAIPSRMTIGHLIECLMGKLSVFSGSEGDVTAFSEVT 645

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               IS                                                       
Sbjct: 646  VESISRKLGSFG------------------------------------------------ 657

Query: 1222 MLRMADLD--ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
                  L+   +G +    G         + +G  Y  +L HMV DK+++R  G  +++T
Sbjct: 658  -FHRRGLEVMYNGHT----GR---KLAAQIFIGPTYYQRLKHMVQDKIHSRGRGPVNILT 709

Query: 1280 QQPLGGKSNRGGQRL 1294
            +QP+ G+S  GG R 
Sbjct: 710  RQPVEGRSREGGLRF 724



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 91/580 (15%), Positives = 175/580 (30%), Gaps = 89/580 (15%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RN 448
           ++      +  +Y + T G      +         R + +   ++ I  L        R 
Sbjct: 45  ALRPHKITNGFRYSIGT-GNWGDAKKAKQSRSGVSRVLNRFTYVSTISHLRRCNAPTGRE 103

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV-DIDSVMPQDLINAK 507
           GK T     +  +       E  + Q    +  +       +S   DI +         +
Sbjct: 104 GKFTKPRQLHNTHWGYICPAETPEGQACGLMKNLALMSYVSVSIPSDILNEFINSCGICQ 163

Query: 508 PVVS-------AVCEFFCSSQLSQLEEHV-NSLSRITHTRRLSALGQGGVARARAGVEMR 559
            +            + F +  L+ + +   + +  I   +  S     G+       E+R
Sbjct: 164 NINETPFDNIVKFTKVFVNGNLTCITDRPLDLIKSIREIKGNSLPADIGIVNDILVNEVR 223

Query: 560 DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
               +  GR+C P    E     LV +  + +++      E          +   + Y+ 
Sbjct: 224 --FYSDSGRMCRPLFVVEDQ--HLVLTSDTLSKLKLEIAQEANQSLWEALVLERYIEYID 279

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EEE+  I  +   L E   +    +                                 
Sbjct: 280 AEEEESTMICISPDELYESRLYNLRKLEGLR----------------------------- 310

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                     R       +R                      +   + I+   A ++   
Sbjct: 311 ---------PRRKRRSVHERLINLPTYPNK--------WTHCEIHPSMILGVSASLIPFS 353

Query: 739 DAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           D  +    + +  +     G+      ++           Q+PLV               
Sbjct: 354 DHNQSPRNTYQSAMSKQAMGIYATNFRLRMDVLANLLYYPQKPLV----------TTKVM 403

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-L 856
                 +L  G N++VA M + GYN EDS++I++  V   +F S     +    +    L
Sbjct: 404 EYLQFRELPAGINVIVAIMCYGGYNQEDSLIINQSSVDRGLFRSFSYRRYLDQEKKVGVL 463

Query: 857 GPEEITRDIPN----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E+IT+  P     +     + +D+ GI+  G  V   DIL+GK++      ++PE++L
Sbjct: 464 NMEDITKPNPYTTLGLKRGNYEKLDDDGIVPCGVRVCGNDILIGKVST-----LSPEDEL 518

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           L           RD S  + S   G V  V +       K
Sbjct: 519 LGQRKESHV--YRDVSTPLRSTEHGIVDQVIVTTNQDGAK 556


>gi|51038414|gb|AAT94115.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038418|gb|AAT94117.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038422|gb|AAT94119.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038426|gb|AAT94121.1| RNA polymerase beta [Mycobacterium senegalense]
 gi|51038428|gb|AAT94122.1| RNA polymerase beta [Mycobacterium senegalense]
          Length = 229

 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 98/226 (43%), Positives = 129/226 (57%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 33   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 92

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 93   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 146  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG
Sbjct: 184  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTG 229


>gi|51701984|sp|Q75DS1|RPA2_ASHGO RecName: Full=DNA-directed RNA polymerase I subunit RPA2; AltName:
            Full=DNA-directed RNA polymerase I polypeptide 2;
            Short=RNA polymerase I subunit 2
          Length = 1198

 Score =  284 bits (726), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 79/366 (21%), Positives = 131/366 (35%), Gaps = 70/366 (19%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+ +I++++   R                  +           +   +W +  +  EK+ 
Sbjct: 779  DDAMIINKSADERGFSYGTVYKTEKIDLSLSRGRGDPVTQHFGFGTDEWPKEWL--EKLD 836

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG------------------VLRVV 1074
             +   +   Y      +   F + + K +                           L+ +
Sbjct: 837  EDGLPIIGSYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVTLIGDESNKFQELQYI 896

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
             +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G
Sbjct: 897  TIKYRIRRVPQIGDKFSSRHGQKGVCSRKWPTVDMPFSETGIQPDVIINPHAFPSRMTIG 956

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
               E+  G A    G    +    +                                   
Sbjct: 957  MFVESLAGKAGALHGIAQDATPWTFSEED------------------------------- 985

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                         TP       +     L  A  +  G   +Y G TGE     + +G +
Sbjct: 986  -------------TPA------DYFGDQLLKAGYNYHGNEPMYSGATGEELRADIYIGVV 1026

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ 
Sbjct: 1027 YYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDR 1086

Query: 1315 LTIKSD 1320
            L   SD
Sbjct: 1087 LLNSSD 1092



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 72/528 (13%), Positives = 160/528 (30%), Gaps = 60/528 (11%)

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            ++  R+ L    D    +   ++ +I+ L  L  G+   D+ D   ++ V   G +   
Sbjct: 345 QELLRRIVLVHLGDENTDKSNMLMFMIRKLYSLVAGECCPDNPDATQHQEVLLGGFLYGM 404

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP-----------VVSAVCEFFCSSQL 522
             +  +    ++IK +    D++  MP D  + K            + S +  F  +  L
Sbjct: 405 IVKEKIEEYLQNIKLQ-IQADVNRGMPVDFKDRKYMTRVLTRINENIGSKLQYFLSTGNL 463

Query: 523 --------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         + + E +N    I+H R    + +G          +R + P  +G 
Sbjct: 464 VSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKLLPESWGF 520

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP  T +G   GL++      +++      +    +      +   +++A    +    
Sbjct: 521 LCPVHTPDGSPCGLLNHFAHKCKISTTQSDVSKIPTLLYSLGVSPAAHVTAA-GPSLCCV 579

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           Q +  +    S  +  +         +  +     +D     V +      P L     +
Sbjct: 580 QLDGKIVGWCSHEQGRIVADTLRYWKVEGKTDGLPLDLEIGYVPASKRGQYPGLYLFGGH 639

Query: 689 RVLM--------------GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
             +M              G   Q      +  E   + T +  +         +      
Sbjct: 640 SRMMRPVRYLPLDKQDIVGPFEQVYMDIAVTPEENPLITSILMLNFHQQIILSILANLTP 699

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                     I +       +     +    +           Q P+VK           
Sbjct: 700 FLLTLTNLPKICTNYQMGKQTMGTPGVALCHRSDNKLYRLQSGQTPIVKANLYDDYG--- 756

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA--- 851
                  + +   G N +VA + + GY+ +D+M+I++             +  ++     
Sbjct: 757 -------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFSYGTVYKTEKIDLSLS 809

Query: 852 --RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             R   +             E  L+ +DE G+  +G+ V  GD +   
Sbjct: 810 RGRGDPVTQHFGFGTDEWPKEW-LEKLDEDGLPIIGSYVEEGDPICAY 856



 Score = 43.1 bits (100), Expect = 0.32,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 33/90 (36%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +   R  TY   L + L   V D +E      ++D        G LP+M +       
Sbjct: 117 PAEARKRLTTYRGKLLLKLNWSVNDGEETFS--EVRDC-------GPLPVMLQSNRCHLH 167

Query: 142 ------------------GTFVIKGIQRIV 153
                             G F++ GI++++
Sbjct: 168 KMSPQELVEHKEESDELGGYFIVNGIEKLI 197


>gi|256270098|gb|EEU05336.1| Rpa135p [Saccharomyces cerevisiae JAY291]
          Length = 1203

 Score =  284 bits (726), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 119/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 838  EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 897

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   DI++NP   PSR
Sbjct: 898  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSR 957

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 958  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD--------------------------- 990

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 991  -----------------TPA------DYFGEQLAKAGYNYHGNEPMYSGATGEELRADIY 1027

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 1028 VGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 1087

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 1088 LQDRLLNSSD 1097



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 103/663 (15%), Positives = 205/663 (30%), Gaps = 88/663 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG----DVSTFSVAESMFNFLFFDSDK 405
           D    +  I N +      DR + LL  ++   P           + +          D+
Sbjct: 285 DREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQ 344

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            DL  VG+  ++  + +    D    +   ++ +I+ L  L  G+ + D+ D   ++ V 
Sbjct: 345 SDLE-VGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403

Query: 466 SVGEMLKNQYR----------LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             G +     +          +  +RM+ +    I+  D   +    +   + + S +  
Sbjct: 404 LGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQY 463

Query: 516 FFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           F  +  L              + + E +N    I+H R    + +G          +R +
Sbjct: 464 FLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKL 520

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY----GFIETPYRK--VCDGKVT---- 611
            P  +G +CP  T +G   GL++      R++        I +      V     T    
Sbjct: 521 LPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAG 580

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + ++S   E+ + IA        +G      +            R + 
Sbjct: 581 PSLCCVQIDGKIIGWVS--HEQGKIIADTLRYWKVEGKTPGLPIDLEIGY-VPPSTRGQY 637

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +         +       L+ +D         M     P        V T +E     
Sbjct: 638 PGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNN--VHTHVEFTPTN 695

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +I+A      +   + R + +   G     T GV +                Q P+
Sbjct: 696 IL--SILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRS--DNKLYRLQTGQTPI 751

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK                  + +   G N +VA + + GY+ +D+M+I++          
Sbjct: 752 VKANLYDDYG----------MDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYG 801

Query: 842 IHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
              +  +V       R   +       +     E  L+ +DE G+  +G  V  GD +  
Sbjct: 802 TMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEW-LEKLDEDGLPYIGTYVEEGDPICA 860

Query: 897 K----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       T     P   EE  L      K  +++  S++     +  + D +  +
Sbjct: 861 YFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSS 919

Query: 947 RHG 949
           RHG
Sbjct: 920 RHG 922



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 99/812 (12%), Positives = 222/812 (27%), Gaps = 106/812 (13%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +   R  +Y   L + L+  V + +E      ++D        G LP+M +    
Sbjct: 120 KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLF--EVRDC-------GGLPVMLQSNRC 170

Query: 142 ---------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGK 177
                                G F++ GI++++   + Q    P             S  
Sbjct: 171 HLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGAS-- 228

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE 226
             Y+   I  + +  D +    +++H         R   R+    VPV   L AL   S+
Sbjct: 229 --YSHYGIQIRSVRPD-QTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSD 285

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
                 +  I+ +   D +        L+ G K     +   T + +   G K    ++ 
Sbjct: 286 ---REIFDGIIGNDVKDSFLTD-RLELLLRGFKKRYPHLQNRT-QVLQYLGDKF--RVVF 338

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                        SD   G  V + IV    G+   +    +    + +++     +   
Sbjct: 339 QASPD-------QSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSP 391

Query: 347 LYVDSVNNNAYIRNTLVTDK--NKDRKDALLDIYRVMRPGDVSTFSVAES---MFNFLFF 401
              D+  +   +    +      +   + L +I   +R       ++        + +  
Sbjct: 392 DNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLM 451

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             ++   S +        L   +  D++ +    ++A         +    +        
Sbjct: 452 RVNENIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQ 511

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +  +V ++L   +                      ++       +            S 
Sbjct: 512 LKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSI 564

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L     S +             G +    +  + + +  T    +   +        
Sbjct: 565 LYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADT----LRYWKVEGKTPGL 620

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +     +   +  G     Y      ++   V YL   +E+   +              
Sbjct: 621 PIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKED--IVGPF----------- 667

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V+   A     +       ++ +P  ++SI A+L PF + + S R +  C M +Q +
Sbjct: 668 -EQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTM 726

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTS 757
                           +    +G   + K     +            + +V         
Sbjct: 727 GT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMD 784

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA--LGRNMLVAF 815
              I      +R      + +   V +     R D I         +        +    
Sbjct: 785 DAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDG 844

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +P+ G   E+   I      +D      I+ +
Sbjct: 845 LPYIGTYVEEGDPIC--AYFDDTLNKTKIKTY 874


>gi|151942801|gb|EDN61147.1| RNA polymerase A [Saccharomyces cerevisiae YJM789]
          Length = 1203

 Score =  284 bits (726), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 119/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 838  EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 897

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   DI++NP   PSR
Sbjct: 898  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSR 957

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 958  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD--------------------------- 990

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 991  -----------------TPA------DYFGEQLAKAGYNYHGNEPMYSGATGEELRADIY 1027

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 1028 VGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 1087

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 1088 LQDRLLNSSD 1097



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 103/663 (15%), Positives = 205/663 (30%), Gaps = 88/663 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG----DVSTFSVAESMFNFLFFDSDK 405
           D    +  I N +      DR + LL  ++   P           + +          D+
Sbjct: 285 DREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPQLQNRTQVLQYLGDKFRVVFQASPDQ 344

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            DL  VG+  ++  + +    D    +   ++ +I+ L  L  G+ + D+ D   ++ V 
Sbjct: 345 SDLE-VGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403

Query: 466 SVGEMLKNQYR----------LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             G +     +          +  +RM+ +    I+  D   +    +   + + S +  
Sbjct: 404 LGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQY 463

Query: 516 FFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           F  +  L              + + E +N    I+H R    + +G          +R +
Sbjct: 464 FLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKL 520

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY----GFIETPYRK--VCDGKVT---- 611
            P  +G +CP  T +G   GL++      R++        I +      V     T    
Sbjct: 521 LPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAG 580

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + ++S   E+ + IA        +G      +            R + 
Sbjct: 581 PSLCCVQIDGKIIGWVS--HEQGKIIADTLRYWKVEGKTPGLPIDLEIGY-VPPSTRGQY 637

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +         +       L+ +D         M     P        V T +E     
Sbjct: 638 PGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNN--VHTHVEFTPTN 695

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +I+A      +   + R + +   G     T GV +                Q P+
Sbjct: 696 IL--SILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRS--DNKLYRLQTGQTPI 751

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK                  + +   G N +VA + + GY+ +D+M+I++          
Sbjct: 752 VKANLYDDYG----------MDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYG 801

Query: 842 IHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
              +  +V       R   +       +     E  L+ +DE G+  +G  V  GD +  
Sbjct: 802 TMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEW-LEKLDEDGLPYIGTYVEEGDPICA 860

Query: 897 K----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       T     P   EE  L      K  +++  S++     +  + D +  +
Sbjct: 861 YFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSS 919

Query: 947 RHG 949
           RHG
Sbjct: 920 RHG 922



 Score = 54.3 bits (129), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 99/812 (12%), Positives = 222/812 (27%), Gaps = 106/812 (13%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +   R  +Y   L + L+  V + +E      ++D        G LP+M +    
Sbjct: 120 KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLF--EVRDC-------GGLPVMLQSNRC 170

Query: 142 ---------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGK 177
                                G F++ GI++++   + Q    P             S  
Sbjct: 171 HLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGAS-- 228

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE 226
             Y+   I  + +  D +    +++H         R   R+    VPV   L AL   S+
Sbjct: 229 --YSHYGIQIRSVRPD-QTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSD 285

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
                 +  I+ +   D +        L+ G K     +   T + +   G K    ++ 
Sbjct: 286 ---REIFDGIIGNDVKDSFLTD-RLELLLRGFKKRYPQLQNRT-QVLQYLGDKF--RVVF 338

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                        SD   G  V + IV    G+   +    +    + +++     +   
Sbjct: 339 QASPD-------QSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSP 391

Query: 347 LYVDSVNNNAYIRNTLVTDK--NKDRKDALLDIYRVMRPGDVSTFSVAES---MFNFLFF 401
              D+  +   +    +      +   + L +I   +R       ++        + +  
Sbjct: 392 DNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLM 451

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             ++   S +        L   +  D++ +    ++A         +    +        
Sbjct: 452 RVNENIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQ 511

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +  +V ++L   +                      ++       +            S 
Sbjct: 512 LKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSI 564

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L     S +             G +    +  + + +  T    +   +        
Sbjct: 565 LYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADT----LRYWKVEGKTPGL 620

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +     +   +  G     Y      ++   V YL   +E+   +              
Sbjct: 621 PIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKED--IVGPF----------- 667

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V+   A     +       ++ +P  ++SI A+L PF + + S R +  C M +Q +
Sbjct: 668 -EQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTM 726

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTS 757
                           +    +G   + K     +            + +V         
Sbjct: 727 GT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMD 784

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA--LGRNMLVAF 815
              I      +R      + +   V +     R D I         +        +    
Sbjct: 785 DAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDG 844

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +P+ G   E+   I      +D      I+ +
Sbjct: 845 LPYIGTYVEEGDPIC--AYFDDTLNKTKIKTY 874


>gi|118358942|ref|XP_001012712.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila]
 gi|89294479|gb|EAR92467.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila SB210]
          Length = 1141

 Score =  284 bits (726), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 100/508 (19%), Positives = 174/508 (34%), Gaps = 82/508 (16%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              I+          +    I   G            A+      D+ D ++   S +   
Sbjct: 702  DTILYQLIYPQTPLLKTKVIEYAGYDKFPAGHNASIAVLSYSGYDIEDATVLNKSSLDRG 761

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F ++  +  +  +S   E +    ++ +         +  +   +      + G
Sbjct: 762  FGRTMVFKKYETEIQKLKMSGLTELLRGPPKEAEGSYKKKQNRVLKKFGALDDDGTPIVG 821

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                    VL +      P     Q   +D     +V           +  + +   K+ 
Sbjct: 822  -ASINNGDVLFNKY---TPLLTLEQQRGRDILNNNSVSEYIHN----PTTFKGK---KLA 870

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            +I            ++K  V   R  + GDK + RHG KGI+  I+  EDMPF + G   
Sbjct: 871  RIDRVIRSQQDGNVIIKTIVRETRRPEYGDKFSSRHGQKGIIGLIVNQEDMPFSEKGWVP 930

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM V        G     LG K   L   +K                  
Sbjct: 931  DLIMNPHGYPSRMTV--------GKLLELLGSKAAVLSGQFKYGT--------------- 967

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                            F G     ++S+L       +G+ ++  
Sbjct: 968  -------------------------------AFGGDKMADLSSILVQNGFSYTGKDVIIS 996

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE     V  G ++  +L HMV+DKV+AR+ G  + +T+QP  G++  GG RLGEME
Sbjct: 997  GITGEYMQCYVFCGPVFYQRLKHMVADKVHARAKGRVTTLTRQPTEGRAKDGGLRLGEME 1056

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG-------------NDTFETGTPE 1345
               + A+ ++ +L E L I SD      +V E    G             +   +   P 
Sbjct: 1057 RDSLLAFASSNLLIERLMISSDKFS--VQVCEK--CGFIQHTNSCKMCQTDQVSKVVMPY 1112

Query: 1346 SFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +  +L +E+ ++ +   L          
Sbjct: 1113 ACKLLFQELLSMNIKPKLNLVDINKIEN 1140



 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 92/727 (12%), Positives = 211/727 (29%), Gaps = 109/727 (14%)

Query: 29  LIEVQKASYDHF----LMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
            +     S+++F    L   I         L               + +LE+     +PP
Sbjct: 25  FVSHHIQSFNYFINIKLQQIITSSMNKELRL-----------DTDNSFLLEYTKIYIEPP 73

Query: 85  KFD------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
             D        +    + +YA  + +   L      E +  K         + +G +P+M
Sbjct: 74  AHDNKTMMLPQEARLSNSSYAGNIYVDCELTFNGKKEDSLRK---------VNIGKMPIM 124

Query: 139 T-------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG-- 170
                                       G F+IKG++++ + Q   +   I  + DK   
Sbjct: 125 LGSSHCNLIKALELGQVHKLQECANDPRGYFIIKGVEKVFLIQEQLADNRIFIEEDKNKE 184

Query: 171 -----RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-VPVTSFLMALGMD 224
                +++          II                I+V++    K +P+  F  A G++
Sbjct: 185 LVANVKSNTVDTKSITSLII------------KNHKIYVKVSSFSKPIPLLIFFKAYGVE 232

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           SE+ +        +       C        +   + +   +      +  +  K  +   
Sbjct: 233 SEQEIFQLIGTEEHLLNRLALCLEDIEQSQVYTQQQALEYLSKRLRPKTFQDKKYSSRNP 292

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           +   ++     +     C    Y    I  G      IEA D   +    + + ++    
Sbjct: 293 VDEARDIITNVVLCHIPCKNYNYYPRAIFLGLMARRLIEALDDPSKIDKRDYYGNKRMKC 352

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
              Y++ +  + + +  ++      RK+   +I +           V   +       + 
Sbjct: 353 AGWYLELLFEDKFKQFNMMV-----RKELSKEIEKHKNKSYPIKNRVESILEKNHDIITQ 407

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNGKGTIDDIDNLGN 461
             + +         R  +DT    + + +   IA I ++  +         +    +L  
Sbjct: 408 GLNNAISTGNWTIKRFRMDTVGVTQVLARISYIAAIGMMTRMNSQFKKSRKLTGPRSLLG 467

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                V            L    S+   I+  +  +V+    +N               +
Sbjct: 468 SHWGLVCPADTPDGESCGLTKNLSLMAHITIEEKKNVLSTIALNLGMEDIGHYSSGEIHE 527

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARAR-AGVEMRDVHPTHYGRICPAETSEGHNI 580
                  +N      H    +   +    R R        +      R    +T +G   
Sbjct: 528 DKNYMVFLNGQIIGMHRDPEAFAQKLRFMRRRGKIGTTISISTNSEKRAVYLDTDDGRLC 587

Query: 581 GLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            L+  + +       +    ++   +   D      + Y+   EE+N YIA     +   
Sbjct: 588 RLLIVVENGKPLITNDHLNDLKEKRKSYLDLIRMGLIEYIDVNEEDNCYIAIKQEDIP-- 645

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                               R K   ++  P  ++ + + L+P+  ++ ++R    C M 
Sbjct: 646 -------------------NRSKTTHMEIDPLTLLGVVSGLVPYPHHNQASRNTFQCAMG 686

Query: 698 RQAVPLL 704
           +QA+ ++
Sbjct: 687 KQALGII 693



 Score =  114 bits (286), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 105/762 (13%), Positives = 240/762 (31%), Gaps = 87/762 (11%)

Query: 211 KVPVTS------FLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
           K+P+         + AL +     L                       + +   ++    
Sbjct: 120 KMPIMLGSSHCNLIKALELGQVHKLQECANDPRGYFIIKGVEKVFLIQEQLADNRI---F 176

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
           ++ D  ++++ + K  T         K +  L I +  +     +          I+ +A
Sbjct: 177 IEEDKNKELVANVKSNTVDT------KSITSLIIKNHKIYVKVSSFSKPIPLL--IFFKA 228

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
             V  E+ + ++  +E   +  L +   +            +   ++ AL  + + +RP 
Sbjct: 229 YGVESEQEIFQLIGTEEHLLNRLALCLEDIEQS--------QVYTQQQALEYLSKRLRPK 280

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
                       +    D  +  ++ V    +  +     P      R   +  + + L+
Sbjct: 281 TFQDK----KYSSRNPVDEARDIITNVVLCHIPCKNYNYYP------RAIFLGLMARRLI 330

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE----------RISSVD 494
           +  +    ID  D  GN+R++  G  L+  +     +    +++            S   
Sbjct: 331 EALDDPSKIDKRDYYGNKRMKCAGWYLELLFEDKFKQFNMMVRKELSKEIEKHKNKSYPI 390

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA---- 550
            + V      N   +   +     +   +     ++++       R+S +   G+     
Sbjct: 391 KNRVESILEKNHDIITQGLNNAISTGNWTIKRFRMDTVGVTQVLARISYIAAIGMMTRMN 450

Query: 551 ----RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
               ++R     R +  +H+G +CPA+T +G + GL  +L+  A +      +     + 
Sbjct: 451 SQFKKSRKLTGPRSLLGSHWGLVCPADTPDGESCGLTKNLSLMAHITIEEK-KNVLSTIA 509

Query: 607 DGKVTNDVVYLSAME--EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
                 D+ + S+ E  E+  Y+   N  +       E                  I   
Sbjct: 510 LNLGMEDIGHYSSGEIHEDKNYMVFLNGQIIGMHRDPEAFAQKLRFMRRRGKIGTTISIS 569

Query: 665 DASPKQVVSIAASL---IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-MESVVA 720
             S K+ V +          L   ++ + L+  +         K+    +  G +E +  
Sbjct: 570 TNSEKRAVYLDTDDGRLCRLLIVVENGKPLITNDHLNDLKEKRKSYLDLIRMGLIEYIDV 629

Query: 721 KSSGAAIVA-KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ- 778
                  +A K+  I  +     + I  +      S      +     + + Q     Q 
Sbjct: 630 NEEDNCYIAIKQEDIPNRSKTTHMEIDPLTLLGVVSGLVPYPHHNQASRNTFQCAMGKQA 689

Query: 779 ----------RPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFED 825
                     R    +   +     +      +         G N  +A + + GY+ ED
Sbjct: 690 LGIIGSTSMNRVDTILYQLIYPQTPLLKTKVIEYAGYDKFPAGHNASIAVLSYSGYDIED 749

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKL-GPEEITRDIPNVSEEGLKN--------- 875
           + ++++  +      ++  +++E   +  K+ G  E+ R  P  +E   K          
Sbjct: 750 ATVLNKSSLDRGFGRTMVFKKYETEIQKLKMSGLTELLRGPPKEAEGSYKKKQNRVLKKF 809

Query: 876 --IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             +D+ G   VGA +N GD+L  K TP           +L  
Sbjct: 810 GALDDDGTPIVGASINNGDVLFNKYTPLLTLEQQRGRDILNN 851


>gi|6325267|ref|NP_015335.1| Rpa135p [Saccharomyces cerevisiae S288c]
 gi|133320|sp|P22138|RPA2_YEAST RecName: Full=DNA-directed RNA polymerase I subunit RPA2; AltName:
            Full=DNA-directed RNA polymerase I 135 kDa polypeptide;
            Short=A135; AltName: Full=DNA-directed RNA polymerase I
            polypeptide 2; Short=RNA polymerase I subunit 2
 gi|172464|gb|AAA34993.1| RNA polymerase I (second largest subunit) [Saccharomyces cerevisiae]
 gi|887587|emb|CAA90154.1| Rpa2p [Saccharomyces cerevisiae]
 gi|939744|gb|AAA97589.1| Rpa135p [Saccharomyces cerevisiae]
 gi|1314085|emb|CAA95050.1| Rpa2p [Saccharomyces cerevisiae]
 gi|190407954|gb|EDV11219.1| RNA polymerase I subunit [Saccharomyces cerevisiae RM11-1a]
 gi|259150163|emb|CAY86966.1| Rpa135p [Saccharomyces cerevisiae EC1118]
 gi|285815545|tpg|DAA11437.1| TPA: Rpa135p [Saccharomyces cerevisiae S288c]
 gi|323350179|gb|EGA84326.1| Rpa135p [Saccharomyces cerevisiae VL3]
          Length = 1203

 Score =  284 bits (726), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 119/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 838  EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 897

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   DI++NP   PSR
Sbjct: 898  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSR 957

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 958  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD--------------------------- 990

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 991  -----------------TPA------DYFGEQLAKAGYNYHGNEPMYSGATGEELRADIY 1027

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 1028 VGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 1087

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 1088 LQDRLLNSSD 1097



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 103/663 (15%), Positives = 205/663 (30%), Gaps = 88/663 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG----DVSTFSVAESMFNFLFFDSDK 405
           D    +  I N +      DR + LL  ++   P           + +          D+
Sbjct: 285 DREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQ 344

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            DL  VG+  ++  + +    D    +   ++ +I+ L  L  G+ + D+ D   ++ V 
Sbjct: 345 SDLE-VGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403

Query: 466 SVGEMLKNQYR----------LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             G +     +          +  +RM+ +    I+  D   +    +   + + S +  
Sbjct: 404 LGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQY 463

Query: 516 FFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           F  +  L              + + E +N    I+H R    + +G          +R +
Sbjct: 464 FLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKL 520

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY----GFIETPYRK--VCDGKVT---- 611
            P  +G +CP  T +G   GL++      R++        I +      V     T    
Sbjct: 521 LPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAG 580

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + ++S   E+ + IA        +G      +            R + 
Sbjct: 581 PSLCCVQIDGKIIGWVS--HEQGKIIADTLRYWKVEGKTPGLPIDLEIGY-VPPSTRGQY 637

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +         +       L+ +D         M     P        V T +E     
Sbjct: 638 PGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNN--VHTHVEFTPTN 695

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +I+A      +   + R + +   G     T GV +                Q P+
Sbjct: 696 IL--SILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRS--DNKLYRLQTGQTPI 751

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK                  + +   G N +VA + + GY+ +D+M+I++          
Sbjct: 752 VKANLYDDYG----------MDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYG 801

Query: 842 IHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
              +  +V       R   +       +     E  L+ +DE G+  +G  V  GD +  
Sbjct: 802 TMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEW-LEKLDEDGLPYIGTYVEEGDPICA 860

Query: 897 K----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       T     P   EE  L      K  +++  S++     +  + D +  +
Sbjct: 861 YFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSS 919

Query: 947 RHG 949
           RHG
Sbjct: 920 RHG 922



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 99/812 (12%), Positives = 222/812 (27%), Gaps = 106/812 (13%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +   R  +Y   L + L+  V + +E      ++D        G LP+M +    
Sbjct: 120 KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLF--EVRDC-------GGLPVMLQSNRC 170

Query: 142 ---------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGK 177
                                G F++ GI++++   + Q    P             S  
Sbjct: 171 HLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGAS-- 228

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE 226
             Y+   I  + +  D +    +++H         R   R+    VPV   L AL   S+
Sbjct: 229 --YSHYGIQIRSVRPD-QTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSD 285

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
                 +  I+ +   D +        L+ G K     +   T + +   G K    ++ 
Sbjct: 286 ---REIFDGIIGNDVKDSFLTD-RLELLLRGFKKRYPHLQNRT-QVLQYLGDKF--RVVF 338

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                        SD   G  V + IV    G+   +    +    + +++     +   
Sbjct: 339 QASPD-------QSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSP 391

Query: 347 LYVDSVNNNAYIRNTLVTDK--NKDRKDALLDIYRVMRPGDVSTFSVAES---MFNFLFF 401
              D+  +   +    +      +   + L +I   +R       ++        + +  
Sbjct: 392 DNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLM 451

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             ++   S +        L   +  D++ +    ++A         +    +        
Sbjct: 452 RVNENIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQ 511

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +  +V ++L   +                      ++       +            S 
Sbjct: 512 LKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSI 564

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L     S +             G +    +  + + +  T    +   +        
Sbjct: 565 LYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADT----LRYWKVEGKTPGL 620

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +     +   +  G     Y      ++   V YL   +E+   +              
Sbjct: 621 PIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKED--IVGPF----------- 667

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V+   A     +       ++ +P  ++SI A+L PF + + S R +  C M +Q +
Sbjct: 668 -EQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTM 726

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTS 757
                           +    +G   + K     +            + +V         
Sbjct: 727 GT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMD 784

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA--LGRNMLVAF 815
              I      +R      + +   V +     R D I         +        +    
Sbjct: 785 DAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDG 844

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +P+ G   E+   I      +D      I+ +
Sbjct: 845 LPYIGTYVEEGDPIC--AYFDDTLNKTKIKTY 874


>gi|240972645|ref|XP_002401144.1| RNA polymerase II second largest subunit (RPB2), putative [Ixodes
            scapularis]
 gi|215490975|gb|EEC00616.1| RNA polymerase II second largest subunit (RPB2), putative [Ixodes
            scapularis]
          Length = 442

 Score =  284 bits (726), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 78/309 (25%), Positives = 117/309 (37%), Gaps = 80/309 (25%)

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R    GDK A RHG KG+ S++ P E+MPF + G   DI+ NP G PSRM +G + E+  
Sbjct: 186  RNPMIGDKFASRHGQKGVCSQLWPIENMPFTESGMTPDIIFNPHGFPSRMTIGMMIESMA 245

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G +    G    +    +  N   S                                   
Sbjct: 246  GKSATLHGFVHDATPFKFSENQPAS----------------------------------- 270

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           E    +L+ A  +  G   +Y G+ G   +  +  G +Y  +L H
Sbjct: 271  ---------------EYFGELLKKAGYNYHGTERMYSGVDGREMEADIFFGVVYYQRLRH 315

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+DK   R+TG    +T QP+ G+   GG R GEME   + A+G++++LQ+ L   SD 
Sbjct: 316  MVADKYQVRTTGPVDTLTHQPVKGRKRAGGIRFGEMERDSLLAHGSSFLLQDRLFNCSD- 374

Query: 1322 VVGRTRVYES-----------------IVA---------GNDTFETGTPESFNVLVKEMQ 1355
               R+  Y                   +V          G+       P  F  L  E+ 
Sbjct: 375  ---RSLAYVCRKCGSVLSPLIEKPDGDVVRKWVCPACQTGDFVDTISMPYVFRYLAAELA 431

Query: 1356 ALGLSIDLE 1364
             + + I L 
Sbjct: 432  GINMGIKLH 440



 Score = 47.0 bits (110), Expect = 0.026,   Method: Composition-based stats.
 Identities = 29/196 (14%), Positives = 65/196 (33%), Gaps = 27/196 (13%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           V T  E                 ++   D  +      +  +   T G    + ++++  
Sbjct: 7   VTTHQELRQTSMLSVL-----GNMIPYSDFNQSPRNMYQCQMGKQTMGTPC-QALRYRSD 60

Query: 771 NQNTCV--NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           N+   +   Q P V+                  + D   G N +VA + + GY+ ED+M+
Sbjct: 61  NKLYRIQTPQTPFVRPTAYDH----------YHMDDFPTGTNAIVAVISYTGYDMEDAMV 110

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV------SEEGLKNIDECGII 882
           +++  V        H   ++    + ++   +  R    V       +     +D  G+ 
Sbjct: 111 LNKSSVERGFK---HGCVYKTELVNLRVLAGDTGRQTSLVFGRKATDKYLEGKVDLDGLP 167

Query: 883 CVGAEVNPGDILVGKI 898
            +G +V   D +   +
Sbjct: 168 YIGVKVEQNDPVCSFV 183


>gi|302306565|ref|NP_982975.2| ABR029Wp [Ashbya gossypii ATCC 10895]
 gi|299788577|gb|AAS50799.2| ABR029Wp [Ashbya gossypii ATCC 10895]
          Length = 1196

 Score =  284 bits (726), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 79/366 (21%), Positives = 131/366 (35%), Gaps = 70/366 (19%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            D+ +I++++   R                  +           +   +W +  +  EK+ 
Sbjct: 777  DDAMIINKSADERGFSYGTVYKTEKIDLSLSRGRGDPVTQHFGFGTDEWPKEWL--EKLD 834

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG------------------VLRVV 1074
             +   +   Y      +   F + + K +                           L+ +
Sbjct: 835  EDGLPIIGSYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVTLIGDESNKFQELQYI 894

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
             +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G
Sbjct: 895  TIKYRIRRVPQIGDKFSSRHGQKGVCSRKWPTVDMPFSETGIQPDVIINPHAFPSRMTIG 954

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
               E+  G A    G    +    +                                   
Sbjct: 955  MFVESLAGKAGALHGIAQDATPWTFSEED------------------------------- 983

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                         TP       +     L  A  +  G   +Y G TGE     + +G +
Sbjct: 984  -------------TPA------DYFGDQLLKAGYNYHGNEPMYSGATGEELRADIYIGVV 1024

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ 
Sbjct: 1025 YYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDR 1084

Query: 1315 LTIKSD 1320
            L   SD
Sbjct: 1085 LLNSSD 1090



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 74/527 (14%), Positives = 165/527 (31%), Gaps = 60/527 (11%)

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
            ++  R+ L    D    +   ++ +I+ L  L  G+   D+ D   ++ V   G +   
Sbjct: 345 QELLRRIVLVHLGDENTDKSNMLMFMIRKLYSLVAGECCPDNPDATQHQEVLLGGFLYGM 404

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP-----------VVSAVCEFFCSSQL 522
             +  +    ++IK +    D++  MP D  + K            + S +  F  +  L
Sbjct: 405 IVKEKIEEYLQNIKLQ-IQADVNRGMPVDFKDRKYMTRVLTRINENIGSKLQYFLSTGNL 463

Query: 523 --------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         + + E +N    I+H R    + +G          +R + P  +G 
Sbjct: 464 VSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKLLPESWGF 520

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP  T +G   GL++      +++      +    +      +   +++A    +    
Sbjct: 521 LCPVHTPDGSPCGLLNHFAHKCKISTTQSDVSKIPTLLYSLGVSPAAHVTAA-GPSLCCV 579

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           Q +  +    S  +  +         +  +     +D     V +      P L     +
Sbjct: 580 QLDGKIVGWCSHEQGRIVADTLRYWKVEGKTDGLPLDLEIGYVPASKRGQYPGLYLFGGH 639

Query: 689 RVLMGCNMQ------------RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             +M                  Q    +      +   +     + S   I++  A +  
Sbjct: 640 SRMMRPVRYLPLDKQDIVGPFEQVYMDIAVTPEEIQNNVH-THVEFSPTNILSILANLTP 698

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             D  +      +  +   T G   +    +           Q P+VK            
Sbjct: 699 FSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQSGQTPIVKANLYDDYG---- 754

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA---- 851
                 + +   G N +VA + + GY+ +D+M+I++             +  ++      
Sbjct: 755 ------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFSYGTVYKTEKIDLSLSR 808

Query: 852 -RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            R   +             E  L+ +DE G+  +G+ V  GD +   
Sbjct: 809 GRGDPVTQHFGFGTDEWPKEW-LEKLDEDGLPIIGSYVEEGDPICAY 854



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 97/813 (11%), Positives = 215/813 (26%), Gaps = 115/813 (14%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +   R  TY   L + L   V D +E      ++D        G LP+M +       
Sbjct: 117 PAEARKRLTTYRGKLLLKLNWSVNDGEETFS--EVRDC-------GPLPVMLQSNRCHLH 167

Query: 142 ------------------GTFVIKGIQRIV---VSQ-------LHRSPGIHFDHDKGRAS 173
                             G F++ GI++++   + Q       + R P    +     + 
Sbjct: 168 KMSPQELVEHKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIR-PS-FANRGTSYSH 225

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALG 222
                 Y  +I   +      +    +++H         R   R+    VPV   L AL 
Sbjct: 226 ------YGVQIRCVRPD----QTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVLILKAL- 274

Query: 223 MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
             ++      +  IV +   + +        L    K    L++     Q +    ++  
Sbjct: 275 --TDASDREIFDGIVGADTSNSFLTDRLELLLRGFKKRFPQLLNRRQVLQYLGDKFRVVL 332

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                + +  V         L    V   + +  T +  +    +    SL         
Sbjct: 333 QASPDMSDYLVGQ------ELLRRIVLVHLGDENTDKSNMLMFMIRKLYSLVAGECCPDN 386

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
                + + +         +     +  ++  L I   +  G    F         +   
Sbjct: 387 PDATQHQEVLLGGFLYGMIVKEKIEEYLQNIKLQIQADVNRGMPVDFKD-RKYMTRVLTR 445

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            ++   S +        L   +  D++ +    ++A         +    +         
Sbjct: 446 INENIGSKLQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQL 505

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +  +V ++L   +                      ++       K   +        + L
Sbjct: 506 KTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCKISTTQSDVSKIPTLL 558

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
             L     +               G +    +  + R V  T    +   +     +   
Sbjct: 559 YSLGVSPAAHVTAAGPSLCCVQLDGKIVGWCSHEQGRIVADT----LRYWKVEGKTDGLP 614

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +     +   +  G     Y      ++   V YL   +++   +        +     E
Sbjct: 615 LDLEIGYVPASKRGQYPGLYLFGGHSRMMRPVRYLPLDKQD--IVGPFEQVYMDIAVTPE 672

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E            +       ++ SP  ++SI A+L PF + + S R +  C M +Q + 
Sbjct: 673 E------------IQNNVHTHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMG 720

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
                          +    SG   + K     +          +       S +G D+ 
Sbjct: 721 T--PGVALCHRSDNKLYRLQSGQTPIVKANLYDDY-GMDNFPNGTNAVVAVISYTGYDMD 777

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVR------RNDIIADGPSTDLGDLA--LGRNMLVA 814
             M   +S      +    V   +++       R D +         +        +   
Sbjct: 778 DAMIINKSADERGFSYGT-VYKTEKIDLSLSRGRGDPVTQHFGFGTDEWPKEWLEKLDED 836

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +P  G   E+   I      +D      I+ +
Sbjct: 837 GLPIIGSYVEEGDPIC--AYFDDTLNKTKIKTY 867


>gi|323335118|gb|EGA76408.1| Rpa135p [Saccharomyces cerevisiae Vin13]
          Length = 1046

 Score =  283 bits (725), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 119/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 731  EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 790

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   DI++NP   PSR
Sbjct: 791  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSR 850

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 851  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD--------------------------- 883

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 884  -----------------TPA------DYFGEQLAKAGYNYHGNEPMYSGATGEELRADIY 920

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            VG +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 921  VGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 980

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 981  LQDRLLNSSD 990



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 103/663 (15%), Positives = 205/663 (30%), Gaps = 88/663 (13%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG----DVSTFSVAESMFNFLFFDSDK 405
           D    +  I N +      DR + LL  ++   P           + +          D+
Sbjct: 178 DREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQ 237

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            DL  VG+  ++  + +    D    +   ++ +I+ L  L  G+ + D+ D   ++ V 
Sbjct: 238 SDLE-VGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 296

Query: 466 SVGEMLKNQYR----------LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
             G +     +          +  +RM+ +    I+  D   +    +   + + S +  
Sbjct: 297 LGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQY 356

Query: 516 FFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           F  +  L              + + E +N    I+H R    + +G          +R +
Sbjct: 357 FLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKL 413

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY----GFIETPYRK--VCDGKVT---- 611
            P  +G +CP  T +G   GL++      R++        I +      V     T    
Sbjct: 414 LPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAG 473

Query: 612 ----------NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                       + ++S   E+ + IA        +G      +            R + 
Sbjct: 474 PSLCCVQIDGKIIGWVS--HEQGKIIADTLRYWKVEGKTPGLPIDLEIGY-VPPSTRGQY 530

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             +         +       L+ +D         M     P        V T +E     
Sbjct: 531 PGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNN--VHTHVEFTPTN 588

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
               +I+A      +   + R + +   G     T GV +                Q P+
Sbjct: 589 IL--SILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRS--DNKLYRLQTGQTPI 644

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           VK                  + +   G N +VA + + GY+ +D+M+I++          
Sbjct: 645 VKANLYDDYG----------MDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYG 694

Query: 842 IHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
              +  +V       R   +       +     E  L+ +DE G+  +G  V  GD +  
Sbjct: 695 TMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEW-LEKLDEDGLPYIGTYVEEGDPICA 753

Query: 897 K----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       T     P   EE  L      K  +++  S++     +  + D +  +
Sbjct: 754 YFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSS 812

Query: 947 RHG 949
           RHG
Sbjct: 813 RHG 815



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 99/812 (12%), Positives = 222/812 (27%), Gaps = 106/812 (13%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +   R  +Y   L + L+  V + +E      ++D        G LP+M +    
Sbjct: 13  KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLF--EVRDC-------GGLPVMLQSNRC 63

Query: 142 ---------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGK 177
                                G F++ GI++++   + Q    P             S  
Sbjct: 64  HLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGAS-- 121

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE 226
             Y+   I  + +  D +    +++H         R   R+    VPV   L AL   S+
Sbjct: 122 --YSHYGIQIRSVRPD-QTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSD 178

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
                 +  I+ +   D +        L+ G K     +   T + +   G K    ++ 
Sbjct: 179 ---REIFDGIIGNDVKDSFLTD-RLELLLRGFKKRYPHLQNRT-QVLQYLGDKF--RVVF 231

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                        SD   G  V + IV    G+   +    +    + +++     +   
Sbjct: 232 QASPD-------QSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSP 284

Query: 347 LYVDSVNNNAYIRNTLVTDK--NKDRKDALLDIYRVMRPGDVSTFSVAES---MFNFLFF 401
              D+  +   +    +      +   + L +I   +R       ++        + +  
Sbjct: 285 DNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLM 344

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
             ++   S +        L   +  D++ +    ++A         +    +        
Sbjct: 345 RVNENIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQ 404

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +  +V ++L   +                      ++       +            S 
Sbjct: 405 LKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSI 457

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L     S +             G +    +  + + +  T    +   +        
Sbjct: 458 LYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADT----LRYWKVEGKTPGL 513

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +     +   +  G     Y      ++   V YL   +E+   +              
Sbjct: 514 PIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKED--IVGPF----------- 560

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            E V+   A     +       ++ +P  ++SI A+L PF + + S R +  C M +Q +
Sbjct: 561 -EQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTM 619

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTS 757
                           +    +G   + K     +            + +V         
Sbjct: 620 GT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMD 677

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA--LGRNMLVAF 815
              I      +R      + +   V +     R D I         +        +    
Sbjct: 678 DAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDG 737

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +P+ G   E+   I      +D      I+ +
Sbjct: 738 LPYIGTYVEEGDPIC--AYFDDTLNKTKIKTY 767


>gi|46019142|emb|CAE52035.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 160

 Score =  283 bits (725), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 66/182 (36%), Positives = 108/182 (59%), Gaps = 22/182 (12%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  
Sbjct: 1   YGRHRQRRSYARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIED 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+
Sbjct: 51  FTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKD 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK  +   +IP+
Sbjct: 102 QDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPN 158

Query: 188 QG 189
           +G
Sbjct: 159 RG 160


>gi|302122451|gb|ADK92896.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 318

 Score =  283 bits (725), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 190/318 (59%), Positives = 245/318 (77%)

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
           G+  T   AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L
Sbjct: 1   GEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKL 60

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           + +RNGKG +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDL
Sbjct: 61  IAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDL 120

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
           INAKP+ +AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH 
Sbjct: 121 INAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHV 180

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE 
Sbjct: 181 THYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEG 240

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IAQAN+ L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 QFVIAQANAKLNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 300

Query: 684 NDDSNRVLMGCNMQRQAV 701
           +DD+NR LMG NMQRQAV
Sbjct: 301 HDDANRALMGANMQRQAV 318


>gi|320592799|gb|EFX05208.1| DNA-directed RNA polymerase 1 subunit beta [Grosmannia clavigera
            kw1407]
          Length = 1290

 Score =  283 bits (725), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 98/497 (19%), Positives = 169/497 (34%), Gaps = 65/497 (13%)

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             E  + SI + E EV++  T    E    ++ ++        D         +   G   
Sbjct: 684  QEQPYMSIAVREQEVISGQT-THVELDPTNMLSILANMTPFSDFNQSPRNMYQCQMGKQT 742

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +G            +   L+             +    +  +GT V V + +  G D ++
Sbjct: 743  MGTPGTALAHRTDNKTYRLQTGQTPIVRAPLHNAYGFDNFPNGTNVVVAVISYTGYDMDD 802

Query: 955  RSISVEREQIEL----------LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
             ++ + +   E                 D+          ++     G       +G   
Sbjct: 803  -AMIINKSAHERGFGHGSVYKTKKITLKDDSRTRSAKHVGKMFGFAPGAFVSGQVRGLLD 861

Query: 1005 STVLSSDLISEYPRSQWWQF-AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               L    +          +  V  +     V      +       ED +  ++  I  G
Sbjct: 862  DDGLPYIGMRVKMGDPLVAWHTVSADYDGTLVNRDGQTHYEKYKDGEDAYVEEVRLI--G 919

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            ++    +L+ + V + + R    GDK + RHG KG+ S+  P  DMPF + G   ++++N
Sbjct: 920  NENGNELLQTISVKLRIPRSPTIGDKFSSRHGQKGVCSQKWPTVDMPFTESGLQPEVIIN 979

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSRM +G   E+  G A    G    S    +                        
Sbjct: 980  PHAFPSRMTIGMFIESLAGKAGALHGLAQDSTPFQFDE---------------------- 1017

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                        D    +     L  A  +  G   +Y G+TGE
Sbjct: 1018 ----------------------------DNTAGDYFGHQLMKAGFNYHGNEPMYSGITGE 1049

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
              +  + +G +Y  +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + 
Sbjct: 1050 ELEADIYIGVVYYQRLRHMVNDKFQVRTTGPVVPTTGQPIKGRKRGGGIRVGEMERDALL 1109

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G A++LQ+ L   SD
Sbjct: 1110 AHGTAFLLQDRLLNCSD 1126



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 88/539 (16%), Positives = 170/539 (31%), Gaps = 73/539 (13%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM-- 470
           ++ +    N+D  +     +   +I +I+ L  L  G   +D+ D + N+ V   G +  
Sbjct: 366 KIVLVHLGNMDVTEAQDADKFRMLIFMIRKLYALVAGDCAVDNPDAVQNQEVLLGGFLYG 425

Query: 471 --------------LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                         L+   R    R   +     +             N + + +A+  F
Sbjct: 426 QILKEKLDEFLSVSLRGALRDYWRRYPTNTMTTEAFARDFQAAVFRRSN-ENIGNALEYF 484

Query: 517 FCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
             +  L              + + E +N L  ++H R    + +G          +R + 
Sbjct: 485 LSTGNLISASGLDLQQVSGFTVVAEKLNFLRFLSHFR---MIHRGSFFAQLKTTTVRKLL 541

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAM 620
           P  +G +CP  T +G   GL++ L    R+   G I+       D  VT    V   SA 
Sbjct: 542 PESWGFLCPVHTPDGSPCGLLNHLAHKCRI-ITGTIDAS---AVDAIVTELGAVSLSSAS 597

Query: 621 EEENRYIAQANSSLDEDGSFTEELVF----CRCAGEEILVPREKIDFIDA-------SPK 669
            EE+  +   +  +    S  E             E       +++            P 
Sbjct: 598 TEES-VVVMLDGRVVGWCSPKEAKRIADTLRHWKVEGSHNIPAELEIGYVPQSNGGSYPG 656

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA--I 727
             ++ A S +       +         Q Q    +      V +G  + V         I
Sbjct: 657 VYMASAPSRMVRPVKYLALDKEDFVGPQEQPYMSIAVREQEVISGQTTHVELDPTNMLSI 716

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           +A      +   + R + +   G     T G       +           Q P+V+    
Sbjct: 717 LANMTPFSDFNQSPRNMYQCQMGKQTMGTPG--TALAHRTDNKTYRLQTGQTPIVRA--- 771

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                      +    +   G N++VA + + GY+ +D+M+I++             +  
Sbjct: 772 -------PLHNAYGFDNFPNGTNVVVAVISYTGYDMDDAMIINKSAHERGFGHGSVYKTK 824

Query: 848 EVMARD-------TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           ++  +D         +G          VS +    +D+ G+  +G  V  GD LV   T
Sbjct: 825 KITLKDDSRTRSAKHVGKMFGFAPGAFVSGQVRGLLDDDGLPYIGMRVKMGDPLVAWHT 883



 Score = 70.9 bits (172), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 95/696 (13%), Positives = 205/696 (29%), Gaps = 112/696 (16%)

Query: 69  SGAAMLEFVSYEFDP---P---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
                + +          P         +    +C  R  TY   L  T    + + D  
Sbjct: 101 RNQLHIRYKDVSLQKCYVPATNKFAKNREILPAECRERHSTYRGKLMATFEYRINNGDPV 160

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
              +           +G +P+M K                         G F++ GI++I
Sbjct: 161 EVVRD----------LGQVPIMVKSNRCHLEGLSPAALVERKEESEELGGYFIVNGIEKI 210

Query: 153 V-VSQLHRSPGIHFDHDKGRASLSGK-LLYACRIIPDQGLWMDIEFDSKDIIH------- 203
           + + Q+ R    +F H   R S   +   Y    I  + +  D E    +++H       
Sbjct: 211 IRLLQVGR---RNFPHAINRPSFQNRGAAYTPYGIITRSVRPD-ETSQTNVLHYLKDGNI 266

Query: 204 -VRIDRRRK---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
             R   R+    +PV   L AL   ++ EI              + +        L+   
Sbjct: 267 TFRFSWRKNEFLIPVMMILKALVETNDREIFEAIVGPANSKGAENTYLTD-RVELLLRTY 325

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           +         T   + E  + +  G+  ++    V              V   + N +  
Sbjct: 326 EFYGLYSKSATRAYLGEKFRVVL-GVPTTMSNYDVGT------EFLRKIVLVHLGNMDVT 378

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN----------NAYIRNTLVTDKNK 368
           E        +    + +++     D  +   D+V N             ++  L    + 
Sbjct: 379 EAQDADKFRMLIFMIRKLYALVAGDCAVDNPDAVQNQEVLLGGFLYGQILKEKLDEFLSV 438

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             + AL D +R      ++T + A      +F  S++   + +        L   +  D+
Sbjct: 439 SLRGALRDYWRRYPTNTMTTEAFARDFQAAVFRRSNENIGNALEYFLSTGNLISASGLDL 498

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIK 487
           + +    ++A     +   +    I         +  +V ++L   +  L  +       
Sbjct: 499 QQVSGFTVVAEKLNFLRFLSHFRMIHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSP 558

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
             + +                 V A+     +  L          S  +    +  +  G
Sbjct: 559 CGLLNHLAHKCRIITGTIDASAVDAIVTELGAVSL----------SSASTEESVVVMLDG 608

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
            V    +  E + +  T    +   +    HNI     +    + N  G     Y     
Sbjct: 609 RVVGWCSPKEAKRIADT----LRHWKVEGSHNIPAELEIGYVPQSN-GGSYPGVYMASAP 663

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            ++   V YL+  +E+  ++              +E++              +   ++  
Sbjct: 664 SRMVRPVKYLALDKED--FVGPQEQPYMSIAVREQEVISG------------QTTHVELD 709

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 710 PTNMLSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 745


>gi|183579269|gb|ACC63212.1| RpoB [Mycobacterium peregrinum]
          Length = 186

 Score =  283 bits (724), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/215 (43%), Positives = 120/215 (55%), Gaps = 37/215 (17%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DGTPVDI+LN  GVP RMN
Sbjct: 1    LVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDGTPVDIILNTHGVPRRMN 60

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQI ETHLGW     G  I       +    +                           
Sbjct: 61   IGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAPV------------------ 101

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE--------SGQSILYDGLTGEP 1244
                         VSTPVFDGA EE +  +L     +          G++ L+DG +GEP
Sbjct: 102  ----------DSIVSTPVFDGAREEELAGLLGSTLPNRDGDVMVNADGKATLFDGRSGEP 151

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            F  PVTVGY+Y+LKL+H+V DK++ARS G YS++T
Sbjct: 152  FPYPVTVGYMYILKLHHLVDDKIHARSXGPYSMIT 186


>gi|295815615|gb|ADG36310.1| RNA polymerase beta-subunit [Mycobacterium interjectum]
          Length = 240

 Score =  283 bits (724), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 96/229 (41%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +         ++       E  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDTGKGVPDWAANLPEDLLHAEPN 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 160  A----------------------------IVSTPVFDGAQEAELQGLLSATLPNRDGEVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+++L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VNGDGKAVLFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.8 bits (107), Expect = 0.052,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|148879053|emb|CAM07042.1| RpoB protein [Mycobacterium llatzerense]
          Length = 221

 Score =  283 bits (724), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 126/229 (55%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 25   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 130  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 172

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G+S+L+DG +GEPF  PVTVGY+Y+LKL H+V DK++ARSTG YS
Sbjct: 173  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLXHLVDDKIHARSTGPYS 221


>gi|164657975|ref|XP_001730113.1| hypothetical protein MGL_2495 [Malassezia globosa CBS 7966]
 gi|159104008|gb|EDP42899.1| hypothetical protein MGL_2495 [Malassezia globosa CBS 7966]
          Length = 517

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 108/259 (41%), Gaps = 50/259 (19%)

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G D      + V++   + R    GDK + RHG KG+ S+  P  DMPF + G   D++
Sbjct: 181  IGSDAGDTECQHVQIMFRIPRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFSESGMQPDVI 240

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP   PSRM +G + E+  G A    G    +    +  +                   
Sbjct: 241  INPHAFPSRMTIGMLIESMAGKAGAMHGLSQDATPWTFGEHD------------------ 282

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                      TPV            LR A  +  G   +Y G+T
Sbjct: 283  --------------------------TPV------SYFGEQLRAAGYNYMGNEPMYSGIT 310

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+     + +G +Y  +L HMV+DK   R+TG    +T+QP+ G+   GG R GEME   
Sbjct: 311  GQELRADIYLGVVYYQRLRHMVNDKFQVRTTGPVHALTRQPVKGRKRAGGIRFGEMERDA 370

Query: 1302 IQAYGAAYVLQEMLTIKSD 1320
            + A+G +++LQ+ L   SD
Sbjct: 371  LLAHGTSFLLQDRLLNCSD 389


>gi|318602980|emb|CBJ04571.1| RNA polymerase beta subunit [Pseudomonas sp. R-37147]
          Length = 285

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 168/285 (58%), Positives = 222/285 (77%)

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 1   RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 60

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 61  SPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAVRHLNEFTVKAPE 120

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 121 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 180

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 181 ARDSGGCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQR 240

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           PLV  GD V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFE
Sbjct: 241 PLVSKGDRVQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFE 285


>gi|315435618|gb|ADU18199.1| RNA polymerase beta-subunit [Mycobacterium massiliense]
          Length = 237

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 96/228 (42%), Positives = 127/228 (55%), Gaps = 40/228 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG  
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPV 236



 Score = 45.5 bits (106), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|154184297|gb|ABS70973.1| RNA polymerase beta subunit [Mycobacterium insubricum]
          Length = 239

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 96/228 (42%), Positives = 127/228 (55%), Gaps = 40/228 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 44   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 103

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  ++                      
Sbjct: 104  TPVDIILNTHGVPRRMNIGQILETHLGWMAKA-GWNVEGSPEWAAN-------------- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        S   V+TPVFDGA EE +  +L            
Sbjct: 149  -----------------LPEDLLHAPSDSIVATPVFDGAREEELQGLLSSTLPNRDGEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG Y
Sbjct: 192  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPY 239



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 52


>gi|145926556|gb|ABP98917.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
 gi|190612176|gb|ACE80522.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
          Length = 257

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 144/258 (55%), Positives = 185/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  D W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRQARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EA + I EKSL+ +     +D+P+L +D VN 
Sbjct: 120 ALRMSDEELVGNYLAEDLVNPKTGEIYAEASEEITEKSLKVLNEQGYKDLPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTHRTLR 257


>gi|149234772|ref|XP_001523265.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Lodderomyces
            elongisporus NRRL YB-4239]
 gi|146453054|gb|EDK47310.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Lodderomyces
            elongisporus NRRL YB-4239]
          Length = 817

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 94/473 (19%), Positives = 159/473 (33%), Gaps = 55/473 (11%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +  +     E    +I ++        D         +   G   +G           
Sbjct: 305  EEIENNVHSHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSD 364

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
             +   L+                + +  +G    V + +  G D ++  I  +       
Sbjct: 365  NKLYRLQTGQTPIVKANLYDEYGMDNFPNGMNAIVAVISYTGYDMDDAMIINKSSDERGF 424

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                  +   +D     R  + +       G    +        L  +       +    
Sbjct: 425  GYGTVYKVEKVDLGQSRRKGDPISQHF---GFGDDEWPETWKEKLDDDGLPLIGVKVEEG 481

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V    ++L      +    E  +  +++ +  GDD      + + +   + R  Q G
Sbjct: 482  DPIVAYFDDTLGKTKVKTYHSSEPAYIEEVKLL--GDDAGDKEAQQITIKYRITRQPQIG 539

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK + RHG KG++SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A   
Sbjct: 540  DKFSSRHGQKGVLSRKWPQIDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKAGAL 599

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G    S    +  +                                             
Sbjct: 600  HGIAQDSTPWKFSESD-------------------------------------------- 615

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            TP       +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+DK 
Sbjct: 616  TPA------DYFGDQLLKAGYNFHGNEPMYSGATGEELRCDIYIGCVYYQRLRHMVNDKF 669

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              RSTG  + +T QP+ G+   GG R+GEME   +  +G A++LQ+ L   SD
Sbjct: 670  QVRSTGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTAFLLQDRLLNCSD 722



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 55/394 (13%), Positives = 118/394 (29%), Gaps = 32/394 (8%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S  + + E +N    I+H R    + +G          +R + P  +G +CP  T +G  
Sbjct: 110 SGYTVVAEKINFHRFISHFR---MVHRGAFFAELKTTTVRKLLPESWGFLCPVHTPDGSP 166

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDG 638
            GL++ L+    +       +   +V        V+  +A     +  + Q +  +    
Sbjct: 167 CGLLNHLSHKCVI---ATTASDVSQVPKALTQLGVLPANAYAAGPDLCVVQLDGKIVGWT 223

Query: 639 SFTEELVF----CRCAGEEILVPREKIDFIDASPKQVVSIAASLI---PFLENDDSNRVL 691
           +  +  +          E        ++     P          I             + 
Sbjct: 224 THEQGKIIADTLRFWKVEGSHGLPLDLEIGYVPPSVNGQYPGLYIFGGHSRMMRPVKYLP 283

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGME---SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           +G          +          +E       + S   I++  A +    D  +      
Sbjct: 284 LGKEDIVGPFEQVYMNVAVTPEEIENNVHSHVEFSPTNILSILANLTPFSDFNQSPRNMY 343

Query: 749 EGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           +  +   T G      + +           Q P+VK                  + +   
Sbjct: 344 QCQMGKQTMGTPGTALVHRSDNKLYRLQTGQTPIVKANLYDEYG----------MDNFPN 393

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA----RDTKLGPEEITR 863
           G N +VA + + GY+ +D+M+I++             +  +V      R      +    
Sbjct: 394 GMNAIVAVISYTGYDMDDAMIINKSSDERGFGYGTVYKVEKVDLGQSRRKGDPISQHFGF 453

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                 E   + +D+ G+  +G +V  GD +V  
Sbjct: 454 GDDEWPETWKEKLDDDGLPLIGVKVEEGDPIVAY 487


>gi|110293955|gb|ABG66440.1| RNA polymerase-beta subunit [Staphylococcus aureus]
          Length = 313

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 176/313 (56%), Positives = 227/313 (72%), Gaps = 3/313 (0%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+C
Sbjct: 1   ASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIA 628
           P  T EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +A
Sbjct: 61  PIXTPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVA 120

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           QANS LD +G F ++ V CR  G   ++ + K+D++D SPKQVVS A + IPFLENDDSN
Sbjct: 121 QANSKLDXNGRFMDDEVVCRFRGNNTVMAKXKMDYMDVSPKQVVSAATACIPFLENDDSN 180

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS- 747
           R LMG NMQRQ VPL+  EAPFVGTGME V A+ SGAAI AK  G VE V++  I++R  
Sbjct: 181 RALMGANMQRQVVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRL 240

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           VE +       +D Y L K +RSN  TC NQRP+V VGD V  N+I+ADGPS +LG++AL
Sbjct: 241 VEENGVEHEGELDRYPLAKXKRSNSGTCYNQRPIVAVGDVVEYNEILADGPSMELGEMAL 300

Query: 808 GRNMLVAFMPWHG 820
           GRN++V F+PW G
Sbjct: 301 GRNVVVGFIPWDG 313


>gi|145926558|gb|ABP98918.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
 gi|145926560|gb|ABP98919.1| RNA polymerase beta subunit [Bradyrhizobium elkanii]
 gi|190612146|gb|ACE80507.1| RNA polymerase subunit beta [Bradyrhizobium sp. BuCeR1]
 gi|190612148|gb|ACE80508.1| RNA polymerase subunit beta [Bradyrhizobium sp. BuCeR2]
 gi|190612156|gb|ACE80512.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612158|gb|ACE80513.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612160|gb|ACE80514.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612162|gb|ACE80515.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612166|gb|ACE80517.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612168|gb|ACE80518.1| RNA polymerase subunit beta [Bradyrhizobium sp. BuMiT10]
 gi|190612178|gb|ACE80523.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612180|gb|ACE80524.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612182|gb|ACE80525.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612184|gb|ACE80526.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612186|gb|ACE80527.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612190|gb|ACE80529.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612192|gb|ACE80530.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612194|gb|ACE80531.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|190612196|gb|ACE80532.1| RNA polymerase subunit beta [Bradyrhizobium elkanii]
 gi|313670552|gb|ADR73467.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM116]
 gi|313670582|gb|ADR73482.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM131]
 gi|313670600|gb|ADR73491.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM140]
 gi|313670656|gb|ADR73519.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO168]
 gi|313670670|gb|ADR73526.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO175]
 gi|313670684|gb|ADR73533.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO182]
 gi|313670692|gb|ADR73537.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO186]
 gi|313670716|gb|ADR73549.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO198]
 gi|313670718|gb|ADR73550.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO199]
 gi|313670730|gb|ADR73556.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO205]
 gi|313670750|gb|ADR73566.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO215]
 gi|313670758|gb|ADR73570.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO219]
 gi|313670762|gb|ADR73572.1| RNA polymerase subunit beta [Bradyrhizobium sp. 61A101]
 gi|313670778|gb|ADR73580.1| RNA polymerase subunit beta [Bradyrhizobium pachyrhizi]
          Length = 257

 Score =  283 bits (723), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 145/258 (56%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMYALGLDGEQILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  D W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KITYKRTKDGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRQARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EAG+ I EKSL+ +     +D+P+L +D VN 
Sbjct: 120 ALRMSDEELVGNYLAEDLVNPKTGEIYAEAGEEITEKSLKVLNEQGYKDLPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTHRTLR 257


>gi|53854336|gb|AAU95613.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 293

 Score =  282 bits (722), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 175/292 (59%), Positives = 224/292 (76%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRRVRSVGE+ +NQ+R GL R+ER++KER++  + +++MP DLINAKPV +A+ EFF S
Sbjct: 1   GNRRVRSVGELTENQFRSGLARVERAVKERLNQAESENLMPHDLINAKPVSAAIKEFFGS 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQTNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYR+V DGKVT ++ YLSA+EE    IAQAN+ LD DG+
Sbjct: 121 IGLINSLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGN 180

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +LV CR  GE I+   +++ ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 181 LIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEHDDANRALMGANMQRQ 240

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  S  AIVA+R G+VE VDA R+VIR  + +
Sbjct: 241 AVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGVVEYVDANRVVIRVHDDE 292


>gi|189187661|gb|ACD84648.1| RpoB [Mycobacterium setense]
          Length = 228

 Score =  282 bits (722), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 98/226 (43%), Positives = 130/226 (57%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 145  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 182

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG
Sbjct: 183  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTG 228


>gi|52694351|emb|CAG38015.1| RNA polymerase beta subunit [Pseudomonas cichorii]
          Length = 372

 Score =  282 bits (722), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 182/373 (48%), Positives = 244/373 (65%), Gaps = 5/373 (1%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
              + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 2   CMAESEGLMPQDLINAKPVGAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 61

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL  +AR N YGF+E+PYR V +G V
Sbjct: 62  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAVYARTNQYGFLESPYRVVKEGLV 121

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ +V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +   D    Q
Sbjct: 122 TDKIVFLSAIEEADHVIAQASAAMNDKHELVDELVAVRHLNEFTVKAPADVTL-DGRFAQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             S   S  P        R      ++  +V L +   P     + +  A      + A 
Sbjct: 181 AGSFGRSF-PDSVPRARRRQPCIDGVRTCSVRLYQPCVPTSRWSVPAWSATLPVTPVSAS 239

Query: 731 RA---GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                 +++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD 
Sbjct: 240 WPVAAVLIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDR 299

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           V+R+DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +SER+V ED FT+IHI+E 
Sbjct: 300 VQRSDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLSERVVQEDRFTTIHIQEL 359

Query: 848 EVMARDTKLGPEE 860
             +ARDTKLGPEE
Sbjct: 360 TCVARDTKLGPEE 372


>gi|220679440|emb|CAX13206.1| novel protein (zgc:66298) [Danio rerio]
          Length = 1132

 Score =  282 bits (722), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 164/1066 (15%), Positives = 296/1066 (27%), Gaps = 200/1066 (18%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
              + A   N    D        +  IYR     ++    +  ++   + +   +     +
Sbjct: 216  EEHTAINMNLHYLDNGTVM---VNFIYRK----ELFFLPLGFALKALVDYSDYQIYQELI 268

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
               + N        + +R +  +     IK+L  L        ++         +   + 
Sbjct: 269  KGREDNSFYKSCVSEMLRIVMDQGCTTKIKVLNYLGERFRVKLNLPEWFTHEQCAHFLLD 328

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +         +E+     + +  + S   Q+ +   P      E     QL  +      
Sbjct: 329  ECLCIHLKTDVEKFYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKM 388

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
                        L    +A  +    +  + P    ++    T        + +  +   
Sbjct: 389  EGW---------LVSVKLALEKKPQRVGGLTPDSMTKLFNMGTDLTKAFEYLLATGNLMS 439

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
                G ++     V      N + YLS                             R   
Sbjct: 440  KTGLGMLQNSGLCVV-ADKLNFIRYLS----------HFRCVHRGAAFAKMRTTTVRKLL 488

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--------RQAVPL 703
             E       +   D  P  +++   +    +        L G                  
Sbjct: 489  PESWGFLCPVHTPDGEPCGLMNHMTAHCEIVAPVYPTSTLPGLLCSLGVNAADGNPGQAY 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                   +   M   V K    A     +    +V   + V    E  L P T    +Y 
Sbjct: 549  SDCYPVILDGAMIGWVEKE--VAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYP 606

Query: 764  -------LMKFQRSNQNTCV-NQRPL-----VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                     +  R+ +N  +  Q  +     V +   +   +I  DG +T          
Sbjct: 607  GLYLFTTPCRMVRTVRNLSLGKQELIGIFEQVYLNVGIFEKEI-EDGVTTHQELFPHSML 665

Query: 811  MLVA-FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +VA F+P+  +N     +   +M  + +   +H  ++    R         T   P V 
Sbjct: 666  SVVAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQY----RSDNKLYRLQTPQSPLVR 721

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 + D                                   + A+      D+ D  +
Sbjct: 722  PAMYDHYDVD-------------------------NYPIGTNAIVAVISYTGYDMEDAMI 756

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S          ++    ID +E+    +                             
Sbjct: 757  VNKSSWERGFAHGSVYKTEIIDLSEKVKGDDSIVF------------------------- 791

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
                       G K         +               +     +     Q        
Sbjct: 792  -----------GVKPGDPKVMGKLDADGLPFIGSVLKYGDPFYGYISLNTGQSHVYFYKY 840

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            ++       K+   ++   G  + + V   + R    GDK A RHG KGI+SR+ P EDM
Sbjct: 841  QESCVVDNIKV-CSNETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDM 899

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G +    G    +    +          
Sbjct: 900  PFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENSAL--- 956

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                           E    +L+ A  +
Sbjct: 957  -----------------------------------------------EHFGELLKAAGYN 969

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY GL+G   +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +
Sbjct: 970  YYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQ 1029

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVG----------------- 1324
            GG R GEME   + A+G +++L + L   SD        D  G                 
Sbjct: 1030 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMD-CGSLLSPLLEKPPPNWSAT 1088

Query: 1325 RTRVYESIV----AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            R R  ++I       +       P  F   V E+ A+ + I L+  
Sbjct: 1089 RHR--KTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 100/744 (13%), Positives = 208/744 (27%), Gaps = 129/744 (17%)

Query: 17  FGKNPEIIDIP--DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSG-AA 72
           FG   E   +P  +L++    S+D              +GL    +++ P+   + G   
Sbjct: 23  FGVPKEKQSVPVQELVKAHIESFDQ----------AVTDGLCRVVEAIPPMEFLYKGDRI 72

Query: 73  MLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            L FV      P                +C  R  TY   L   +   V  V        
Sbjct: 73  SLSFVEAIIHTPSVSKGGISRDLRVFPAECRGRRCTYRAKLVADVSWSVNGVP------- 125

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV--VS 155
            K I +QS  +G +P+M K                         G F++ GI++++  + 
Sbjct: 126 -KGIIKQS--LGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLI 182

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW------------MDIEFDSKDIIH 203
              R+  I     K ++   G   YA   I  + +             +D      + I+
Sbjct: 183 MPRRNYPIAVSRPKFKSRGQGYTQYA---ISMRCVKEEHTAINMNLHYLDNGTVMVNFIY 239

Query: 204 VRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                 RK    +P+   L AL      +I    Y +++  +  + +     +  L    
Sbjct: 240 ------RKELFFLPLGFALKALVDYSDYQI----YQELIKGREDNSFYKSCVSEML---- 285

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           ++          + +   G++    L  +L E               L +       +  
Sbjct: 286 RIVMDQGCTTKIKVLNYLGERFRVKL--NLPEWFTHEQCAHFLLDECLCIHLKTDVEKFY 343

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            + +    +      E +  +    +    +             +       K AL    
Sbjct: 344 MLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKP 403

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           + +          + +    +  D  K     +    +  +  L    +       D + 
Sbjct: 404 QRVGGLTP----DSMTKLFNMGTDLTKAFEYLLATGNLMSKTGLGMLQNSGLCVVADKLN 459

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I+ L   R     +         R  +V ++L   +                  +   +
Sbjct: 460 FIRYLSHFR----CVHRGAAFAKMRTTTVRKLLPESWGFLC-------PVHTPDGEPCGL 508

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           M     + + V            L  L  +    +     +  S      +  A  G   
Sbjct: 509 MNHMTAHCEIVAPVYPTSTLPGLLCSLGVN---AADGNPGQAYSDCYPVILDGAMIGWVE 565

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           ++V P+    +   +      +   + +    +          Y      ++   V  LS
Sbjct: 566 KEVAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYPGLYLFTTPCRMVRTVRNLS 625

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             ++E   I               E V+      E  +        +  P  ++S+ A  
Sbjct: 626 LGKQELIGI--------------FEQVYLNVGIFEKEIEDGVTTHQELFPHSMLSVVAEF 671

Query: 679 IPFLENDDSNRVLMGCNMQRQAVP 702
           IPF +++ S R +  C M +Q + 
Sbjct: 672 IPFSDHNQSPRNMYQCQMSKQTMG 695


>gi|158954698|gb|ABW84320.1| RNA polymerase subunit B [Mycobacterium murale]
          Length = 241

 Score =  282 bits (722), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 94/229 (41%), Positives = 125/229 (54%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 42   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 101

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +   ++          
Sbjct: 102  TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIDVAQGVPEWASNLPEALYSAPAD 160

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
              T                            +TPVFDG  E  +  +L     +      
Sbjct: 161  TNT----------------------------ATPVFDGTRENELTGLLGSTLPNRDGDVM 192

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVGY+ +LKL+H+V DK++ARSTG YS
Sbjct: 193  VDGDGKATLFDGRSGEPFPYPVTVGYMDILKLHHLVDDKIHARSTGPYS 241



 Score = 46.6 bits (109), Expect = 0.035,   Method: Composition-based stats.
 Identities = 32/50 (64%), Positives = 41/50 (82%)

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 50


>gi|320580927|gb|EFW95149.1| DNA-directed RNA polymerase I [Pichia angusta DL-1]
          Length = 1166

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 91/470 (19%), Positives = 159/470 (33%), Gaps = 55/470 (11%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +     E    +I ++        D         +   G   +G            + 
Sbjct: 658  ENNIHTHVEFAPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKL 717

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              L++               + +  +GT   V + +  G D ++  I  +          
Sbjct: 718  YRLQSGQTPIVKANLYDDYGMDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYG 777

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
               +   +D ++  +  + +       G    +        L ++            D  
Sbjct: 778  VVYKVEKVDLSLNRKRGDPITQHF---GFGSDEWPESWKEKLDNDGLPHIGVHVEEGDPI 834

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                 + L      +    E  F  +++ +  GDD      + + +   + R    GDK 
Sbjct: 835  CAYYDDILGKTKVKTYHSSEPAFIEEVKLL--GDDNGTSEFQTLSIKYRITRQPLIGDKF 892

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G 
Sbjct: 893  SSRHGQKGVCSRKWPQIDMPFSETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGI 952

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               +    +  +                                             TP 
Sbjct: 953  AQDATPWKFSESD--------------------------------------------TPA 968

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                  +     L+ A  +  G   LY G+TGE     + +G +Y  +L HMV+DK   R
Sbjct: 969  ------DYFGEQLQRAGYNYHGNEPLYSGVTGEELRADIYIGVVYYQRLRHMVNDKFQVR 1022

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            STG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1023 STGPVNSLTLQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1072



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 79/577 (13%), Positives = 172/577 (29%), Gaps = 69/577 (11%)

Query: 368 KDRKDALLDIYRVMR-PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
            DR + LL  Y+         T +     F  +F  +      +VG   +   + +   +
Sbjct: 283 TDRLELLLRTYKNYNLYSQKETLAYLGDKFRVVFGATPDMSDISVGEEVIKRIVLVHLEN 342

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
           +    +   ++ +I+ L  L  G  + D+ D   ++ +   G +     +  +    ++I
Sbjct: 343 NED--KFRMLLFMIRKLYSLVAGDCSPDNPDATQHQEILLGGFLYGMILKEKIEEYLQNI 400

Query: 487 KERISSVDIDSVMPQDLINAKP----------VVSAVCEFFCSSQL-------------- 522
           + ++ S     +                    +   +  F  +  L              
Sbjct: 401 RLQVQSDINRGIAVNFSDRKYMSRVFLRINENIGQKLQYFLSTGNLVSQSGLDLQQVSGY 460

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           + + E +N    I+H R    + +G          +R + P  +G +CP  T +G   GL
Sbjct: 461 TVVAEKINFHRFISHFR---MVHRGSFFAQLKTTAVRKLLPESWGFLCPVHTPDGSPCGL 517

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL-SAMEEENRYI--AQANSSLDEDGS 639
           ++ L    R+       T   KV        V    SA+      +   Q +  +    S
Sbjct: 518 LNHLAHKCRITTKASDVT---KVPKLLHKLGVSPTASAINISGPNVCCVQLDGRIIGWCS 574

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE--------NDDSNRVL 691
             +  +         +     I   D     V   +    P L               + 
Sbjct: 575 HKQGKIVADTLRFWKVEGHHDIPL-DLEIGYVPPSSGGQYPGLYLFAGASRMVRPVRYLP 633

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGME---SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           +           +      + + +E       + +   I++  A +    D  +      
Sbjct: 634 LDKEDIVGPFEQVFMNVAVIPSEIENNIHTHVEFAPTNILSILANLTPFSDFNQSPRNMY 693

Query: 749 EGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           +  +   T G   +    +           Q P+VK                  + +   
Sbjct: 694 QCQMGKQTMGTPGVALCHRSDNKLYRLQSGQTPIVKANLYDDYG----------MDNFPN 743

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G N +VA + + GY+ +D+M+I++          +    ++V   D  L  +       +
Sbjct: 744 GTNAVVAVISYTGYDMDDAMIINKSADERGFGYGVV---YKVEKVDLSLNRKRGDPITQH 800

Query: 868 VSEEG-------LKNIDECGIICVGAEVNPGDILVGK 897
                        + +D  G+  +G  V  GD +   
Sbjct: 801 FGFGSDEWPESWKEKLDNDGLPHIGVHVEEGDPICAY 837



 Score = 65.9 bits (159), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 112/827 (13%), Positives = 238/827 (28%), Gaps = 147/827 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L + +   + D +E      I +++E     G +P+M +       
Sbjct: 104 PAECRERMTTYRARLLLKVCWSINDGEE------ISEVREA----GQIPIMLQSNRCHLE 153

Query: 142 ------------------GTFVIKGIQRIV---VSQ-------LHRSPGIHFDHDKGRAS 173
                             G F++ GI++++   + Q       + R P    +     + 
Sbjct: 154 NLSPDQLVKLREESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIR-PS-FANRGTSYSH 211

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE- 226
             G  + + R  PDQ      +    D    +  R   R+    +PV   L AL   ++ 
Sbjct: 212 F-GVQIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLIPVVMILKALIETNDR 266

Query: 227 EILS---------TFYPK---------IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
           EI           +F              Y+                V    +  + DI 
Sbjct: 267 EIFDGVVGADTGNSFLTDRLELLLRTYKNYNLYSQKETLAYLGDKFRVVFGATPDMSDIS 326

Query: 269 TGEQVIESGKKLTSGLLKSLKEKG--VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            GE+VI   K++    L++ ++K   + F+      L     + D  +    +  +  G 
Sbjct: 327 VGEEVI---KRIVLVHLENNEDKFRMLLFMIRKLYSLVAGDCSPDNPDATQHQEILLGGF 383

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           +      E+I    +++I +     +N    +  +     ++       +I + +     
Sbjct: 384 LYGMILKEKIEEY-LQNIRLQVQSDINRGIAVNFSDRKYMSRVFLRINENIGQKL----- 437

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F    ++ +    D  +    TV   K+N           R I    ++        L
Sbjct: 438 QYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFH---------RFISHFRMVHRGSFFAQL 488

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
           +         ++ G                  L  +    +    + D+ + +P+ L   
Sbjct: 489 KTTAVRKLLPESWG---FLCPVHTPDGSPCGLLNHLAHKCRITTKASDV-TKVPKLLHKL 544

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
               +A         +  ++     +   +H +           +               
Sbjct: 545 GVSPTASAINISGPNVCCVQLDGRIIGWCSHKQGKIVADTLRFWK--------------- 589

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                    EGH+   +     +   ++ G     Y      ++   V YL   +E+   
Sbjct: 590 --------VEGHHDIPLDLEIGYVPPSSGGQYPGLYLFAGASRMVRPVRYLPLDKED--I 639

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +               E VF   A     +       ++ +P  ++SI A+L PF + + 
Sbjct: 640 VGPF------------EQVFMNVAVIPSEIENNIHTHVEFAPTNILSILANLTPFSDFNQ 687

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIR 742
           S R +  C M +Q +                +    SG   + K     +          
Sbjct: 688 SPRNMYQCQMGKQTMGT--PGVALCHRSDNKLYRLQSGQTPIVKANLYDDYGMDNFPNGT 745

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             + +V            I      +R      V +   V +    +R D I        
Sbjct: 746 NAVVAVISYTGYDMDDAMIINKSADERGFGYGVVYKVEKVDLSLNRKRGDPITQHFGFGS 805

Query: 803 GDLALG--RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +        +    +P  G + E+   I      +D+     ++ +
Sbjct: 806 DEWPESWKEKLDNDGLPHIGVHVEEGDPIC--AYYDDILGKTKVKTY 850


>gi|124504400|gb|AAI28811.1| Zgc:66298 [Danio rerio]
          Length = 1132

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 164/1066 (15%), Positives = 296/1066 (27%), Gaps = 200/1066 (18%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
              + A   N    D        +  IYR     ++    +  ++   + +   +     +
Sbjct: 216  EEHTAINMNLHYLDNGTVM---VNFIYRK----ELFFLPLGFALKALVDYSDYQIYQELI 268

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
               + N        + +R +  +     IK+L  L        ++         +   + 
Sbjct: 269  KGREDNSFYKSCVSEMLRIVMDQGCTTKIKVLNYLGERFRVKLNLPEWFTHEQCAHFLLD 328

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +         +E+     + +  + S   Q+ +   P      E     QL  +      
Sbjct: 329  ECLCIHLKTDVEKFYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKM 388

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
                        L    +A  +    +  + P    ++    T        + +  +   
Sbjct: 389  EGW---------LVSVKLALEKKPQRVGGLTPDSMTKLFNMGTDLTKAFEYLLATGNLMS 439

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
                G ++     V      N + YLS                             R   
Sbjct: 440  KTGLGMLQNSGLCVV-ADKLNFIRYLS----------HFRCVHRGAAFAKMRTTTVRKLL 488

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--------RQAVPL 703
             E       +   D  P  +++   +    +        L G                  
Sbjct: 489  PESWGFLCPVHTPDGEPCGLMNHMTAHCEIVAPVYPTSTLPGLLCSLGVNAADGNPGQAY 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                   +   M   V K    A     +    +V   + V    E  L P T    +Y 
Sbjct: 549  SDCYPVILDGAMIGWVEKE--VAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYP 606

Query: 764  -------LMKFQRSNQNTCV-NQRPL-----VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                     +  R+ +N  +  Q  +     V +   +   +I  DG +T          
Sbjct: 607  GLYLFTTPCRMVRTVRNLSLGKQELIGIFEQVYLNVGIFEKEI-EDGVTTHQELFPHSML 665

Query: 811  MLVA-FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +VA F+P+  +N     +   +M  + +   +H  ++    R         T   P V 
Sbjct: 666  SVVAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQY----RSDNKLYRLQTPQSPLVR 721

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 + D                                   + A+      D+ D  +
Sbjct: 722  PAMYDHYDVD-------------------------NYPIGTNAIVAVISYTGYDMEDAMI 756

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S          ++    ID +E+    +                             
Sbjct: 757  VNKSSWERGFAHGSVYKTEIIDLSEKVKGDDSIVF------------------------- 791

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
                       G K         +               +     +     Q        
Sbjct: 792  -----------GVKPGDPKVMGKLDADGLPFIGSVLKYGDPFYGYISLNTGQSHVYFYKY 840

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            ++       K+   ++   G  + + V   + R    GDK A RHG KGI+SR+ P EDM
Sbjct: 841  QESCVVDNIKV-CSNETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDM 899

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G +    G    +    +          
Sbjct: 900  PFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENSAL--- 956

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                           E    +L+ A  +
Sbjct: 957  -----------------------------------------------EHFGELLKAAGYN 969

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY GL+G   +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +
Sbjct: 970  YYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQ 1029

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVG----------------- 1324
            GG R GEME   + A+G +++L + L   SD        D  G                 
Sbjct: 1030 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMD-CGSLLSPLLEKPPPNWSAT 1088

Query: 1325 RTRVYESIV----AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            R R  ++I       +       P  F   V E+ A+ + I L+  
Sbjct: 1089 RHR--KTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 99/744 (13%), Positives = 209/744 (28%), Gaps = 129/744 (17%)

Query: 17  FG--KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSG-AA 72
           FG  K  + + + +L++    S+D              +GL    +++ P+   + G   
Sbjct: 23  FGVPKEKQRVPVQELVKAHIESFDQ----------AVTDGLCRVVEAIPPMEFLYKGDRI 72

Query: 73  MLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            L FV      P                +C  R  TY   L   +   V  V        
Sbjct: 73  SLSFVEAIIHTPSVSKGGISRDLRVFPAECRGRRCTYRAKLVADVSWSVNGVP------- 125

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV--VS 155
            K I +QS  +G +P+M K                         G F++ GI++++  + 
Sbjct: 126 -KGIIKQS--LGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLI 182

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW------------MDIEFDSKDIIH 203
              R+  I     K ++   G   YA   I  + +             +D      + I+
Sbjct: 183 MPRRNYPIAVSRPKFKSRGQGYTQYA---ISMRCVKEEHTAINMNLHYLDNGTVMVNFIY 239

Query: 204 VRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                 RK    +P+   L AL      +I    Y +++  +  + +     +  L    
Sbjct: 240 ------RKELFFLPLGFALKALVDYSDYQI----YQELIKGREDNSFYKSCVSEML---- 285

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           ++          + +   G++    L  +L E               L +       +  
Sbjct: 286 RIVMDQGCTTKIKVLNYLGERFRVKL--NLPEWFTHEQCAHFLLDECLCIHLKTDVEKFY 343

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            + +    +      E +  +    +    +             +       K AL    
Sbjct: 344 MLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKP 403

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           + +          + +    +  D  K     +    +  +  L    +       D + 
Sbjct: 404 QRVGGLTP----DSMTKLFNMGTDLTKAFEYLLATGNLMSKTGLGMLQNSGLCVVADKLN 459

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I+ L   R     +         R  +V ++L   +                  +   +
Sbjct: 460 FIRYLSHFR----CVHRGAAFAKMRTTTVRKLLPESWGFLC-------PVHTPDGEPCGL 508

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           M     + + V            L  L  +    +     +  S      +  A  G   
Sbjct: 509 MNHMTAHCEIVAPVYPTSTLPGLLCSLGVN---AADGNPGQAYSDCYPVILDGAMIGWVE 565

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           ++V P+    +   +      +   + +    +          Y      ++   V  LS
Sbjct: 566 KEVAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYPGLYLFTTPCRMVRTVRNLS 625

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             ++E   I               E V+      E  +        +  P  ++S+ A  
Sbjct: 626 LGKQELIGI--------------FEQVYLNVGIFEKEIEDGVTTHQELFPHSMLSVVAEF 671

Query: 679 IPFLENDDSNRVLMGCNMQRQAVP 702
           IPF +++ S R +  C M +Q + 
Sbjct: 672 IPFSDHNQSPRNMYQCQMSKQTMG 695


>gi|76253769|ref|NP_956812.2| DNA-directed RNA polymerase I subunit RPA2 [Danio rerio]
 gi|66911319|gb|AAH97040.1| Zgc:66298 [Danio rerio]
 gi|182890886|gb|AAI65683.1| Zgc:66298 protein [Danio rerio]
          Length = 1132

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 164/1066 (15%), Positives = 296/1066 (27%), Gaps = 200/1066 (18%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
              + A   N    D        +  IYR     ++    +  ++   + +   +     +
Sbjct: 216  EEHTAINMNLHYLDNGTVM---VNFIYRK----ELFFLPLGFALKALVDYSDYQIYQELI 268

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
               + N        + +R +  +     IK+L  L        ++         +   + 
Sbjct: 269  KGREDNSFYKSCVSEMLRIVMDQGCTTKIKVLNYLGERFRVKLNLPEWFTHEQCAHFLLD 328

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
            +         +E+     + +  + S   Q+ +   P      E     QL  +      
Sbjct: 329  ECLCIHLKTDVEKFYMLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKM 388

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
                        L    +A  +    +  + P    ++    T        + +  +   
Sbjct: 389  EGW---------LVSVKLALEKKPQRVGGLTPDSMTKLFNMGTDLTKAFEYLLATGNLMS 439

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
                G ++     V      N + YLS                             R   
Sbjct: 440  KTGLGMLQNSGLCVV-ADKLNFIRYLS----------HFRCVHRGAAFAKMRTTTVRKLL 488

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--------RQAVPL 703
             E       +   D  P  +++   +    +        L G                  
Sbjct: 489  PESWGFLCPVHTPDGEPCGLMNHMTAHCEIVAPVYPTSTLPGLLCSLGVNAADGNPGQAY 548

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                   +   M   V K    A     +    +V   + V    E  L P T    +Y 
Sbjct: 549  SDCYPVILDGAMIGWVEKE--VAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYP 606

Query: 764  -------LMKFQRSNQNTCV-NQRPL-----VKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                     +  R+ +N  +  Q  +     V +   +   +I  DG +T          
Sbjct: 607  GLYLFTTPCRMVRTVRNLSLGKQELIGIFEQVYLNVGIFEKEI-EDGVTTHQELFPHSML 665

Query: 811  MLVA-FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +VA F+P+  +N     +   +M  + +   +H  ++    R         T   P V 
Sbjct: 666  SVVAEFIPFSDHNQSPRNMYQCQMSKQTMGFPLHSYQY----RSDNKLYRLQTPQSPLVR 721

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 + D                                   + A+      D+ D  +
Sbjct: 722  PAMYDHYDVD-------------------------NYPIGTNAIVAVISYTGYDMEDAMI 756

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S          ++    ID +E+    +                             
Sbjct: 757  VNKSSWERGFAHGSVYKTEIIDLSEKVKGDDSIVF------------------------- 791

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
                       G K         +               +     +     Q        
Sbjct: 792  -----------GVKPGDPKVMGKLDADGLPFIGSVLKYGDPFYGYISLNTGQSHVYFYKY 840

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            ++       K+   ++   G  + + V   + R    GDK A RHG KGI+SR+ P EDM
Sbjct: 841  QESCVVDNIKV-CSNETGTGRFKRICVTSRVPRNPTIGDKFASRHGQKGILSRLWPAEDM 899

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF + G   DI+ NP G PSRM +G + E+  G +    G    +    +          
Sbjct: 900  PFTESGMSPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCHDATPFTFSEENSAL--- 956

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                           E    +L+ A  +
Sbjct: 957  -----------------------------------------------EHFGELLKAAGYN 969

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G   LY GL+G   +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +
Sbjct: 970  YYGTERLYSGLSGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPMGGRNVQ 1029

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------DVVG----------------- 1324
            GG R GEME   + A+G +++L + L   SD        D  G                 
Sbjct: 1030 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAQVCMD-CGSLLSTLLEKPPPNWSAT 1088

Query: 1325 RTRVYESIV----AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            R R  ++I       +       P  F   V E+ A+ + I L+  
Sbjct: 1089 RHR--KTICLLCNKSDSIETVSVPYVFKYFVAELAAMNIKIKLDVK 1132



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 99/744 (13%), Positives = 209/744 (28%), Gaps = 129/744 (17%)

Query: 17  FG--KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA-FSG-AA 72
           FG  K  + + + +L++    S+D              +GL    +++ P+   + G   
Sbjct: 23  FGVPKEKQRVPVQELVKAHIESFDQ----------AVTDGLCRVVEAIPPMEFLYKGDRI 72

Query: 73  MLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
            L FV      P                +C  R  TY   L   +   V  V        
Sbjct: 73  SLSFVEAIIHTPSVSKGGISRDLRVFPAECRGRRCTYRAKLVADVSWSVNGVP------- 125

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV--VS 155
            K I +QS  +G +P+M K                         G F++ GI++++  + 
Sbjct: 126 -KGIIKQS--LGQMPIMVKSKLCNLHGLSPKELLEHHEEAEEMGGYFIVNGIEKVIRLLI 182

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW------------MDIEFDSKDIIH 203
              R+  I     K ++   G   YA   I  + +             +D      + I+
Sbjct: 183 MPRRNYPIAVSRPKFKSRGQGYTQYA---ISMRCVKEEHTAINMNLHYLDNGTVMVNFIY 239

Query: 204 VRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                 RK    +P+   L AL      +I    Y +++  +  + +     +  L    
Sbjct: 240 ------RKELFFLPLGFALKALVDYSDYQI----YQELIKGREDNSFYKSCVSEML---- 285

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           ++          + +   G++    L  +L E               L +       +  
Sbjct: 286 RIVMDQGCTTKIKVLNYLGERFRVKL--NLPEWFTHEQCAHFLLDECLCIHLKTDVEKFY 343

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
            + +    +      E +  +    +    +             +       K AL    
Sbjct: 344 MLCLMTRKLFSFAKQECMEENPDSPMFHEVLTPGQLYLMFLKEKMEGWLVSVKLALEKKP 403

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
           + +          + +    +  D  K     +    +  +  L    +       D + 
Sbjct: 404 QRVGGLTP----DSMTKLFNMGTDLTKAFEYLLATGNLMSKTGLGMLQNSGLCVVADKLN 459

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I+ L   R     +         R  +V ++L   +                  +   +
Sbjct: 460 FIRYLSHFR----CVHRGAAFAKMRTTTVRKLLPESWGFLC-------PVHTPDGEPCGL 508

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           M     + + V            L  L  +    +     +  S      +  A  G   
Sbjct: 509 MNHMTAHCEIVAPVYPTSTLPGLLCSLGVN---AADGNPGQAYSDCYPVILDGAMIGWVE 565

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           ++V P+    +   +      +   + +    +          Y      ++   V  LS
Sbjct: 566 KEVAPSVIESLRRFKVLGEKKVPPWTEIVLVPQTGKASLYPGLYLFTTPCRMVRTVRNLS 625

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             ++E   I               E V+      E  +        +  P  ++S+ A  
Sbjct: 626 LGKQELIGI--------------FEQVYLNVGIFEKEIEDGVTTHQELFPHSMLSVVAEF 671

Query: 679 IPFLENDDSNRVLMGCNMQRQAVP 702
           IPF +++ S R +  C M +Q + 
Sbjct: 672 IPFSDHNQSPRNMYQCQMSKQTMG 695


>gi|183579285|gb|ACC63220.1| RpoB [Mycobacterium fortuitum]
 gi|183989081|gb|ACC66098.1| RpoB [Mycobacterium fortuitum]
          Length = 224

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 128/226 (56%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 141  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 178

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 179  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 224


>gi|154291829|ref|XP_001546494.1| hypothetical protein BC1G_14991 [Botryotinia fuckeliana B05.10]
 gi|150846599|gb|EDN21792.1| hypothetical protein BC1G_14991 [Botryotinia fuckeliana B05.10]
          Length = 1207

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 98/494 (19%), Positives = 170/494 (34%), Gaps = 67/494 (13%)

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            F SI + E E+ + +     E     I ++        D         +   G   +G  
Sbjct: 674  FMSIAVTEQEIESGE-HTHVEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQSMGTP 732

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                      +   L+                  +  +G    V + +  G D ++ ++ 
Sbjct: 733  GTAIRYRTDNKAYRLQTGQTPIVRAPLHNEYGFDNFPNGMNSVVAVISYTGYDMDD-AMI 791

Query: 959  VEREQIEL------LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            + +   E       + + K  E     ++  ++ ++ L G  A  G    +    +  D 
Sbjct: 792  INKSAHERGFGHGTIYKTKKYELEEGHKSRSAKNIKKLFGF-APGGLVKAEWKAAIDEDG 850

Query: 1013 ISEYPRSQWWQF------AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            +    R             V  ++  + V      +       E  F  ++  I  G++ 
Sbjct: 851  LPFIGRMVQNGDLIAAWHTVSMDENGKYVNRDGQTHFEKYKETEIAFIEEVRLI--GNEN 908

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + + V + + R    GDK + RHG KG+ S+  P  DMPF + G   D ++NP  
Sbjct: 909  GIEPCQAISVKLRIPRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFTESGIQPDTIINPHA 968

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM +G   E+  G A    G    S    +                           
Sbjct: 969  FPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFDEEHKAG-------------------- 1008

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                          +     L  A  +  G   +Y G+TGE   
Sbjct: 1009 ------------------------------DYFGHQLMKAGYNYYGNEPMYSGITGEELH 1038

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G +Y  +L HMV+DK   R+TG  + +T QP+ G+   GG R+GEME   + A+G
Sbjct: 1039 ADIYIGVVYYQRLRHMVNDKYQVRTTGPVTQLTGQPIKGRKKGGGIRVGEMERDSLLAHG 1098

Query: 1307 AAYVLQEMLTIKSD 1320
             A++LQ+ L   SD
Sbjct: 1099 TAFLLQDRLLNCSD 1112



 Score = 62.4 bits (150), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 90/677 (13%), Positives = 195/677 (28%), Gaps = 124/677 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   +   +   + + D     +           +G LPLM         
Sbjct: 118 PAECRERHVTYRGKMSARMEYSINNGDPKEFIRD----------LGQLPLMLMSNKCHLQ 167

Query: 142 ------------------GTFVIKGIQRIV----VSQ------LHRSPGIHFDHDKGRAS 173
                             G FV+ GI++I+    V++      + R P   F       +
Sbjct: 168 NNSPAQLVQKKEESEELGGYFVVNGIEKIIRLLVVNRRNFPMAIIR-PS--FKGRGPTYT 224

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G L+ + R  PDQ      +    D    +  R   R+    VP    L AL +++ +
Sbjct: 225 EFGMLIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEFLVPAMMILKAL-VETND 279

Query: 228 ILSTFYPKIVYSQRGDFWCFPLS---AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
                +  +V +                 L+   K         T   + E  +      
Sbjct: 280 --KEIFEGLVGAAGSKGAENTFLTDRVELLLRTYKAYGLYTKSKTRAYLGEKFR------ 331

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
                                L V + + N + G  ++    ++   + +     +    
Sbjct: 332 -------------------IVLGVPDTMSNYDVGTEFLRKIVLVHLGNTDVTEAQDKDKF 372

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +L   +    + +      D     ++  + +   +  G +    + + +   L     
Sbjct: 373 KMLLFMTRKLYSLVAGDCAGDNPDAVQNQEILLGGFL-FGMIIKERLEDWLHTSLRMALR 431

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            Y   +            D P  +     E +   ++  +   N   +   +D       
Sbjct: 432 DYVRRSPENNFATPEFLKDFPVKICSRTNEQVGGALEYFMSTGN-LVSPTGLDLQQTSGF 490

Query: 465 RSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQ 521
             V E +     +   RM    S   ++ +  +  ++P+      PV +         + 
Sbjct: 491 TVVAEKINFLRFIAHFRMIHRGSFFAQLKTTTVRKLLPESWGFMCPVHTPDGSPCGLLNH 550

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI---CPAE----- 573
           LS     +   S ++   +   L + GV    +      V     G+I   C  +     
Sbjct: 551 LSHKCIILTHASDVSALPK--LLSELGVVSTGSSSTDESVVVQLDGKIMGWCSPKQSLVI 608

Query: 574 -------TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                    E  +    +    +   +  G     Y      ++   V YL   +E+  +
Sbjct: 609 ADTLRYWKVEKTHGVPTNLEIGYIPNSHGGQYPGIYLSAAPARMVRPVKYLPLDKED--F 666

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           +              +E+                   ++  P  ++SI A++ PF + + 
Sbjct: 667 VGPLEQPFMSIAVTEQEIESGEH------------THVEFDPTHILSILANMTPFSDFNQ 714

Query: 687 SNRVLMGCNMQRQAVPL 703
           S R +  C M +Q++  
Sbjct: 715 SPRNMYQCQMGKQSMGT 731


>gi|60172306|gb|AAX14484.1| RNA polymerase beta subunit [Aliivibrio logei]
          Length = 184

 Score =  282 bits (721), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 100/187 (53%), Positives = 133/187 (71%), Gaps = 5/187 (2%)

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDM + + G PVDIVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   +
Sbjct: 1    PVEDMSYDEKGQPVDIVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQE 57

Query: 1165 ISPLRSFLEKVIGTGSHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
            +   R+FL+KV   G   +   I+   DD V  + +  + G+P++TP+FDGA E +I  +
Sbjct: 58   LHKFRNFLQKVYDLGETRQEVDIAALSDDEVRTLVKNLRGGLPIATPIFDGAPESSIKEL 117

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L++ DL ESGQ  L+DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARSTGSYSLVTQQP
Sbjct: 118  LKLVDLPESGQLKLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 177

Query: 1283 LGGKSNR 1289
            LGGK+  
Sbjct: 178  LGGKAQF 184


>gi|327265571|ref|XP_003217581.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like, partial
            [Anolis carolinensis]
          Length = 692

 Score =  282 bits (721), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 95/468 (20%), Positives = 158/468 (33%), Gaps = 64/468 (13%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT---PKGESPMTPEEKL 912
               E     + +V    +   D         +   G   +G      P          + 
Sbjct: 215  THQELFPHSMLSVVANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTFPYRTDDKLYRLQT 274

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
             ++     A+         P G +  V  +        D    + S         +  K 
Sbjct: 275  PQSPLVRPAMYDHYDMDSYPIGTNAIVAVISYSGYDMEDAMILNKSSWERGFAHGSIYKT 334

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            +       ++  ++ +         GP        L +D +         +    D    
Sbjct: 335  ERI-----DLTEKIKQGEDNLVFGIGPDRAATLKNLDADGLPPIGS----RLQYGDPYYS 385

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                +    + T     E    + I+     +D   G  + V + + + R    GDK A 
Sbjct: 386  YLNLNTGESFVTYHKNKEVCVVDNIKVCS--NDTGSGQFKCVCITLRVPRNPTIGDKFAS 443

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM +G + E+  G +    G   
Sbjct: 444  RHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSASLHGLCH 503

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +    +                                                     
Sbjct: 504  DATPFTFSEENSA----------------------------------------------- 516

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                E    ML+    +  G   +Y G++G   +  + +G +Y  +L HMVSDK   R+T
Sbjct: 517  ---VEYFGKMLKAGGYNYYGTERMYSGVSGVELEADIFIGVVYYQRLRHMVSDKFQVRTT 573

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G+   VT QP+GG++ +GG R GEME   + A+G +++L + L   SD
Sbjct: 574  GARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 621



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 73/459 (15%), Positives = 146/459 (31%), Gaps = 39/459 (8%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              +S LS + + +N +  ++H R    + +G          +R + P  +G +CP  T 
Sbjct: 5   MLQTSGLSVMADKLNFVRYLSHFR---CVHRGADFIKMRTTTVRKLLPESWGFLCPVHTP 61

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKVTNDVVYLSAMEEENRYI-----AQ 629
           +G   GL++ LT+   +       T     +C   VT      +    E   +       
Sbjct: 62  DGEPCGLMNHLTAPCEIVTQSLFTTSLPSLLCSLGVTPTDGVPNQPYSECYPVTLDGSLV 121

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF------IDASPKQVVSIAASLIPFLE 683
                D      E L  C+   E+ +    ++            P   +      +    
Sbjct: 122 GWIEKDLAPGLVETLRHCKAMQEKKIPVWTEVVLIPMTGKPSLYPGLFIFTTPCRMMRPV 181

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM--ESVVAKSSGAAIVAKRAGIVEQVDAI 741
            + +           Q    +      +  G+     +   S  ++VA     +   D  
Sbjct: 182 RNLALGKEEWIGTMEQVFMNIAVLENEIELGLTTHQELFPHSMLSVVA---NFIPFSDHN 238

Query: 742 RIVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +      +  +   T G   +    +           Q PLV+                 
Sbjct: 239 QSPRNMYQCQMGKQTMGFPLLTFPYRTDDKLYRLQTPQSPLVRPAMYDH----------Y 288

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPE 859
           D+    +G N +VA + + GY+ ED+M++++          SI+  E   +    K G +
Sbjct: 289 DMDSYPIGTNAIVAVISYSGYDMEDAMILNKSSWERGFAHGSIYKTERIDLTEKIKQGED 348

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
            +   I       LKN+D  G+  +G+ +  GD     +     +  T E  +      E
Sbjct: 349 NLVFGIGPDRAATLKNLDADGLPPIGSRLQYGDPYYSYL-----NLNTGESFVTYHKNKE 403

Query: 920 --KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                +++  S    SG    V       R+    ++ +
Sbjct: 404 VCVVDNIKVCSNDTGSGQFKCVCITLRVPRNPTIGDKFA 442


>gi|325140578|gb|EGC63099.1| biotin synthase [Neisseria meningitidis CU385]
          Length = 599

 Score =  282 bits (721), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 97/206 (47%), Positives = 130/206 (63%), Gaps = 20/206 (9%)

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
            +KR +Q+GDKMAGRHGNKG+VSRILP EDMP++ DG PVDIVLNPLGVPSRMN+GQI E 
Sbjct: 1    IKRRLQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVPSRMNIGQILEV 60

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
            HLGWA  G+G++I  ++ + +  G+    R FL ++       E +    D+ ++ +A  
Sbjct: 61   HLGWAAKGIGERIDRMLKEQRKAGE---SREFLNRLYNGSGKKEDLDALTDEEIIELASN 117

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMA-----------DLDES-GQSILYDGLTGEPFDR 1247
             + G   ++PVFDGA E  I  ML +A             ++S  Q  LYDG +GE FDR
Sbjct: 118  LRKGASFASPVFDGAKESEIREMLNLAYPSDDPEVEKLGFNDSKTQITLYDGRSGEAFDR 177

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTG 1273
             VTVG ++ LKL+H+V     AR  G
Sbjct: 178  KVTVGVMHYLKLHHLV-----ARLRG 198


>gi|156255565|gb|ABU62999.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 233

 Score =  282 bits (721), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 96/227 (42%), Positives = 127/227 (55%), Gaps = 40/227 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 144  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG 
Sbjct: 187  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 233



 Score = 43.5 bits (101), Expect = 0.25,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 47


>gi|156034861|ref|XP_001585849.1| hypothetical protein SS1G_13366 [Sclerotinia sclerotiorum 1980]
 gi|154698769|gb|EDN98507.1| hypothetical protein SS1G_13366 [Sclerotinia sclerotiorum 1980 UF-70]
          Length = 1165

 Score =  281 bits (720), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 100/494 (20%), Positives = 170/494 (34%), Gaps = 67/494 (13%)

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            F SI + E E+ A +     E     I ++        D         +   G   +G  
Sbjct: 632  FMSIAVTEQEIEAGE-HTHVEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQSMGTP 690

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                      +   L+                  +  +G    V + +  G D ++ ++ 
Sbjct: 691  GTAIRYRTDNKAYRLQTGQTPIVRAPLHNDYGFDNFPNGMNSVVAVISYTGYDMDD-AMI 749

Query: 959  VEREQIEL------LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
            + +   E       + + K  E     ++  +R ++ L G  A  G    +    +  D 
Sbjct: 750  INKSAHERGFGHGTIYKTKKYELEEGHKSRSARNIKKLFGF-APGGLVKAEWKAAIDEDG 808

Query: 1013 ISEYPRSQWWQF------AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            +    R             V  ++  + V      +       E  F  ++  I  G++ 
Sbjct: 809  LPFIGRMVQNGDLIAAWHTVSMDENGKYVNRDGQTHFEKYKETEIAFIEEVRLI--GNEN 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + + V + + R    GDK + RHG KG+ S+  P  DMPF + G   D ++NP  
Sbjct: 867  GIEPCQAISVKLRIPRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFTESGIQPDTIINPHA 926

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM +G   E+  G A    G    S    +                           
Sbjct: 927  FPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFDEEHKAG-------------------- 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                          +     L  A  +  G   +Y G+TGE   
Sbjct: 967  ------------------------------DYFGHQLMKAGYNYYGNEPMYSGITGEELH 996

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G +Y  +L HMV+DK   R+TG  + +T QP+ G+   GG R+GEME   + A+G
Sbjct: 997  ADIYIGVVYYQRLRHMVNDKYQVRTTGPVTQLTGQPIKGRKKGGGIRVGEMERDSLLAHG 1056

Query: 1307 AAYVLQEMLTIKSD 1320
             A++LQ+ L   SD
Sbjct: 1057 TAFLLQDRLLNCSD 1070



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 87/657 (13%), Positives = 181/657 (27%), Gaps = 126/657 (19%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   +   +   + + D     +           +G LPLM         
Sbjct: 118 PAECRERHVTYRGKMSARMEYSINNGDPKEFIRD----------LGQLPLMLMSNKCHLQ 167

Query: 142 ------------------GTFVIKGIQRIV----VSQ------LHRSPGIHFDHDKGRAS 173
                             G FV+ GI++I+    V++      + R P   F       +
Sbjct: 168 NNSPAQLVQNKEESEELGGYFVVNGIEKIIRLLVVNRRNFPMAIIR-PS--FKGRGPAYT 224

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE- 226
             G L+ + R  PDQ      +    D    +  R   R+    VP    L AL   ++ 
Sbjct: 225 EFGMLIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEFLVPAMMILKALVETNDK 280

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI              + +        L+   K         T   + E   ++  G+  
Sbjct: 281 EIFEGLVGTPGSKGTDNTFLND-RVELLLRTYKAYGLYTKSKTRAYLGEKF-RIVLGVPD 338

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           ++    V    +    L  L                   +  D+   + +     +   +
Sbjct: 339 TMSNYDVGTEFLRKIVLVHLGNTNVT-------------EAQDKDKFKMLLFMTRKLYSL 385

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           +  D   +N               ++ LL        G +    + + +   L      Y
Sbjct: 386 VAGDCAGDNP---------DAVQNQEILL---GGFLFGMIIKERLEDWLHTSLRMALRDY 433

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
              +     +      D P  +     E +   ++  +   N   +   +D         
Sbjct: 434 VRRSPENNFVTPEFLKDFPVKICSRTNEQVGGALEYFMSTGN-LVSPTGLDLQQTSGFTV 492

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           V E +     +   RM                +P+ L     V         SS    + 
Sbjct: 493 VAEKINFLRFIAHFRMIHRGSFFAQLKTTTVPLPKLLSELGVV-----STGSSSTDESVV 547

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
             ++       + + S +    +   +                      EG +    +  
Sbjct: 548 VQLDGKIMGWCSPKQSLVIADTLRYWK---------------------VEGTHGVPTNLE 586

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             +   +  G     Y      ++   V YL+  +E+  ++              +E   
Sbjct: 587 IGYIPNSHGGQYPGIYLSAAPARMVRPVKYLALDKED--FVGPLEQPFMSIAVTEQE--- 641

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                    +   +   ++  P  ++SI A++ PF + + S R +  C M +Q++  
Sbjct: 642 ---------IEAGEHTHVEFDPTHILSILANMTPFSDFNQSPRNMYQCQMGKQSMGT 689


>gi|133872967|gb|ABO40481.1| RNA polymerase subunit B [Mycobacterium setense]
          Length = 230

 Score =  281 bits (720), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 98/226 (43%), Positives = 130/226 (57%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 34   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 93

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 94   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 147  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 184

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK++ARSTG
Sbjct: 185  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDKIHARSTG 230


>gi|167945261|ref|ZP_02532335.1| DNA-directed RNA polymerase, beta subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
 gi|110589080|gb|ABG77049.1| DNA-directed RNA polymerase beta subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 314

 Score =  281 bits (720), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 177/282 (62%), Positives = 217/282 (76%)

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
           + + YLSA+EE    IAQA++S D +G+ T++LV  R   E  L   +K+ +ID SPKQ+
Sbjct: 1   DQIDYLSAIEEGRYVIAQASASTDAEGNLTDDLVSSRHQNEFTLSVADKVQYIDVSPKQI 60

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AAS+IPFLE+DD+NR LMG NMQRQAVP L+AE P VGTGME  VA  SG  +VAKR
Sbjct: 61  VSVAASMIPFLEHDDANRALMGSNMQRQAVPTLRAEKPLVGTGMERTVAVDSGVTVVAKR 120

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G +E VDA RIV+R  + + +   SGVDIY L K+ RSNQNTC+NQRPLVKVG+ + R 
Sbjct: 121 GGEIETVDAARIVVRVNDDETEAGESGVDIYNLTKYTRSNQNTCINQRPLVKVGNTIARG 180

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           D++ADGPSTD+G+LALG+N+ VAFMPW+GYNFEDS+LISER+V ED FTSIHIEE   MA
Sbjct: 181 DVLADGPSTDMGELALGQNLRVAFMPWNGYNFEDSILISERVVEEDRFTSIHIEELTCMA 240

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           RDTKLGPEEIT DIPNV E  L  +DE GI+ +GAEV  GDI
Sbjct: 241 RDTKLGPEEITGDIPNVGEAALSKLDESGIVYIGAEVKEGDI 282


>gi|52694189|emb|CAG30624.1| DNA-directed RNA polymerase beta chain [Pseudomonas luteola]
          Length = 327

 Score =  281 bits (720), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 167/285 (58%), Positives = 214/285 (75%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
               LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 43  RTTRLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 102

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D   ++D+V+LSA+EE N  IAQA+++LDE+    +ELV  
Sbjct: 103 TYARTNQYGFLESPYRVVKDAVASDDIVFLSAIEEANHVIAQASAALDENNRLVDELVAV 162

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++
Sbjct: 163 RHQNEFTVKSPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSD 222

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R    +++   +GVDIY L K+
Sbjct: 223 KPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVANAEVETGEAGVDIYNLTKY 282

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            RSNQNTC+NQRPLV  GD + R DI+ADGPSTD+G+LALG+NM 
Sbjct: 283 TRSNQNTCINQRPLVNKGDVIARGDILADGPSTDMGELALGQNMR 327


>gi|52699894|gb|AAU87008.1| DNA-dependent RNA polymerase II second largest subunit [Taphrina
            communis]
          Length = 731

 Score =  281 bits (720), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 127/837 (15%), Positives = 245/837 (29%), Gaps = 130/837 (15%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L   +R+   R+ + I++ ++              +    + + + 
Sbjct: 1    DXXGKKRIDXAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLPLAVKHTTITNGLR 60

Query: 515  EFFCSS-------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGTWGDQKKQMNARVGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL-SAM 620
            H TH+G +CPAET EG   GLV +L   + V+           + +  + +   Y  SA 
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGMESLEDYNPSAG 176

Query: 621  EEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
                +            + G   + L   R   +         D  +   +         
Sbjct: 177  RPSTKIFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK--RAGIVE 736
             P     D          + +A  L+  +             +       ++    GI E
Sbjct: 237  RPLFVVHDDESAESDPTGESEAGSLVLKKEHVQRMAYSKEHPEDEDKFGWSQVLSNGIAE 296

Query: 737  QVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +DA      +I     DL+ +   +  Y   + +         ++   +    +R    
Sbjct: 297  YLDAEEEETVMIAMTPDDLEATKHMMAGYVEPEVEEPADADERERKIAAEAAKRLRPAVN 356

Query: 794  IADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
             A    T      ++   +  + +P+  +N                        ++    
Sbjct: 357  KAQHLWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMG 398

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G       +               +  +             +       +   +  
Sbjct: 399  KQAMGXXXXXYQVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNA 447

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D  E+    + ++ E   R+  
Sbjct: 448  IVAILCYSGYNQEDSMIMNQSSIDRGLF-RSMFYRVYQDSEEKIDMNQAQEFEKPTRETT 506

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                   R+ Y +L +                 T +S + +     +   +     +   
Sbjct: 507  MRM---KRSTYDKLED----------DGLVAPGTRVSGEDVIVGKTAGLLKDENSADLAA 553

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R+    K    T     E    +K+      D       + VKV +   +  Q GDK A 
Sbjct: 554  RSATQTKRDVSTQLRSTEAGIIDKVMVSTNSD-----GHKFVKVRIRATKIPQIGDKFAS 608

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM V  + E  L       G + 
Sbjct: 609  RHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEG 668

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +                                   D +V  V+   +           
Sbjct: 669  DATPF-------------------------------TDVTVEAVSNNLR----------- 686

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                               G  I+Y+G TG      V +G  Y  +L H+V DK+ A
Sbjct: 687  ------------EQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIXA 731



 Score =  107 bits (267), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 83/637 (13%), Positives = 169/637 (26%), Gaps = 116/637 (18%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +   +     K           +       T  +  S+    + D  K   + VG  ++ 
Sbjct: 26  LTKDIRQYMTKCVDSGKEFNLPLAVKHTTITNGLRYSLATGTWGDQKKQMNARVGVSQVL 85

Query: 418 MRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
            R    +      R          I     L N    +         +      ++KN  
Sbjct: 86  NRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLA 142

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            +  + +  +    I  ++   +   +  N      +   F     L    +  + +  +
Sbjct: 143 LMSYVSVGSASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNGVWLGVHSDPGHLVKTL 202

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA---------------ETSEGHNI 580
              RR + +            +   +         P                E+  G  +
Sbjct: 203 RSLRRKTDISPEVSVVRDIREKELRLFTDAGRVCRPLFVVHDDESAESDPTGESEAGSLV 262

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                +   A    +   E  +             YL A EEE   IA     L+     
Sbjct: 263 LKKEHVQRMAYSKEHPEDEDKF-GWSQVLSNGIAEYLDAEEEETVMIAMTPDDLEATKHM 321

Query: 641 TEELVFCRCAGEEILVPREK--------------------IDFIDASPKQVVSIAASLIP 680
               V            RE+                        +  P  ++ I AS+IP
Sbjct: 322 MAGYVEPEVEEPADADERERKIAAEAAKRLRPAVNKAQHLWTHCEIHPSMILGICASIIP 381

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+                                       
Sbjct: 382 FPDHNQSPRNTYQSAMGKQAMGXXXXXYQV------------------------------ 411

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                         + + +  Y       +     +  R                     
Sbjct: 412 -----------RMDTMANILYYPQKPLATTRSMEYLKFR--------------------- 439

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-- 858
              +L  G+N +VA + + GYN EDSM++++  +   +F S+    ++       +    
Sbjct: 440 ---ELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQ 496

Query: 859 --EEITRDIPN-VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             E+ TR+    +       +++ G++  G  V+  D++VGK     +   + +     A
Sbjct: 497 EFEKPTRETTMRMKRSTYDKLEDDGLVAPGTRVSGEDVIVGKTAGLLKDENSADLAARSA 556

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    RD S ++ S  +G +  V +       K
Sbjct: 557 -----TQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHK 588


>gi|185179212|gb|ACC77619.1| RpoB [Mycobacterium kansasii]
          Length = 220

 Score =  281 bits (720), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 94/227 (41%), Positives = 127/227 (55%), Gaps = 40/227 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 26   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 144  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 173

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG 
Sbjct: 174  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 220


>gi|307204008|gb|EFN82912.1| DNA-directed RNA polymerase III subunit RPC2 [Harpegnathos saltator]
          Length = 1081

 Score =  281 bits (720), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 101/589 (17%), Positives = 184/589 (31%), Gaps = 110/589 (18%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            +AL  N + A            + +   ++            ++        G       
Sbjct: 578  IALDENEIQAETTHMEIETFTILGVCAGLIPYPHHNQSPRNTYQCAMGRQAAGT------ 631

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                     +      ++          +          + +   E  + AI      D+
Sbjct: 632  -----IGYNQRKRMDTVMYNLVYPQAPIVRTKTSEMIKYNELPAGENAIVAIMSYGGYDI 686

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D  +   + +        I+ R      +R  +   ++I   + D +  +V    +I  
Sbjct: 687  EDALVVNRASLDRGYGRCLIY-RSTKAVLKRYPNQTYDRIMGPSLDSNTNKVAWKHDILD 745

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                 + G+          K            P     +     +   +       QY  
Sbjct: 746  ADGIAMPGERVEDKKVLVNK----------SVPSQSIDRVNTGSDASPKT------QYRD 789

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            ++   +      +E+     +       ++K+ +   R  + GDK++ RHG KG++  I+
Sbjct: 790  AEIYYKGLEPAYVEQSLLTSNADDSF--LIKLLLRQTRRPEIGDKLSSRHGQKGVIGSIV 847

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              ED+PF   G   DI++NP G PSRM VG++ E   G   +  G+   S         D
Sbjct: 848  NPEDLPFNDQGIVPDIIMNPHGFPSRMTVGKLIEILAGKVGILNGEFHDSTAFGGSKVDD 907

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S                      +                                   
Sbjct: 908  LSEQMQKHGYNYLGKDCFYSGITGEPMEAYIY---------------------------- 939

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                            TG       TV   Y  +L HMV DK++AR+ G   ++T+QP  
Sbjct: 940  ----------------TG-------TV---YYQRLKHMVQDKIHARAKGPRVVMTRQPTE 973

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------------RT 1326
            G+S  GG R GEME  C+ AYGA+ +L E L + SD    DV                R+
Sbjct: 974  GRSKDGGLRFGEMERDCLVAYGASMMLIERLMLSSDGVKVDVCNSCGLMGYSGWCQSCRS 1033

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
                     ++      P +  +L+ E+Q++ +   L+    +  +  E
Sbjct: 1034 --------NSNISSVTMPYACKLLLHELQSMNIVPRLKLRDYRERSHTE 1074



 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 116/894 (12%), Positives = 250/894 (27%), Gaps = 200/894 (22%)

Query: 75  EFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
            ++      P FD            +C  RDLTYA P+ + +  I          +  + 
Sbjct: 17  RYLDIHIGEPIFDESLNDIRKLYPHECRLRDLTYAAPIIVDIEYI----------RGNQP 66

Query: 125 IKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVS--QLH 158
           I + +I +G +P+M                           G F+IKG +++++   Q+ 
Sbjct: 67  IIKNNIVIGRMPIMLRSANCRLTGLTAHELSTKDECPHDPGGYFIIKGQEKVILIQEQMV 126

Query: 159 RSPGIHFDHD----------------KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           R+  I  + D                K + S+ GK   + R            +   +I 
Sbjct: 127 RNR-ILLEKDNKENIVAYCNSSTHERKTKTSIIGK---SGR-----------YYMKHNIF 171

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                    + VT    A+G+ +++ I+     +  +  + ++        ++    +  
Sbjct: 172 Q------DDILVTIVFKAMGIHTDQNIVMLIGTEHEFQSKLEWSLRECHDLNIFTQNQAL 225

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L    T  +V  + +         L    VK        +   ++   ++  ++ +  
Sbjct: 226 MYLNSKRTQPRVFNANEMKDVLATNVLSHVPVKNFSFKLKGIHLAFMVRKVIMAQSNKKL 285

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           ++  D +  K LE            L+        +    +        K A  DI + M
Sbjct: 286 LDDRDFVGNKRLEVAGSLLSLMFEDLF----KRFNWELKQIADKNIPKIKAAQFDIVKHM 341

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
           R   ++   +     +   +   ++ +   G  ++  RL+  +   +            +
Sbjct: 342 RQDQITNGLLFA--ISTGNWKIKRFKMERQGATQVLSRLSYISALGMMTRVHSQFEKTRQ 399

Query: 442 I--LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L   +  +    +        + + L     +     E  I   +S++D+  + 
Sbjct: 400 VSGPRSLHLSQWGMLCPCDTPEGESCGLVKNLALMAHITTDEPEDHIAWLLSTLDMQEI- 458

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
               + ++ +          + + Q     +   ++ HT +        + R        
Sbjct: 459 --QSLGSQEINHKDEWLVLLNGVIQ--GVTSHYKKLVHTLKT-------LRRRGYISSFV 507

Query: 560 DVHPTHYGRICPAETSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            ++     R     T  G        V +             +    K  D   T  + Y
Sbjct: 508 SIYMQDNHRCVHISTDGGRLCRPYFIVENGRLVVTAEHMKLFQQKILKFEDFLQTGMIEY 567

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L   EE +  IA   + +                         +   ++     ++ + A
Sbjct: 568 LDVNEENDVLIALDENEIQA-----------------------ETTHMEIETFTILGVCA 604

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            LIP+  ++ S R    C M RQA   +         G                      
Sbjct: 605 GLIPYPHHNQSPRNTYQCAMGRQAAGTI---------GYNQRKRMD-------------- 641

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                                               N    Q P+V+             
Sbjct: 642 --------------------------------TVMYNLVYPQAPIVR----------TKT 659

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G N +VA M + GY+ ED+++++   +       +     + + +    
Sbjct: 660 SEMIKYNELPAGENAIVAIMSYGGYDIEDALVVNRASLDRGYGRCLIYRSTKAVLKRYPN 719

Query: 857 GPEEITRDIPNVSEEG-----LKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
              +        S           +D  GI   G  V    +LV K  P     
Sbjct: 720 QTYDRIMGPSLDSNTNKVAWKHDILDADGIAMPGERVEDKKVLVNKSVPSQSID 773


>gi|315435626|gb|ADU18203.1| RNA polymerase beta-subunit [Mycobacterium abscessus]
          Length = 235

 Score =  281 bits (720), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 96/227 (42%), Positives = 125/227 (55%), Gaps = 40/227 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG 
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 235



 Score = 45.5 bits (106), Expect = 0.066,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|255513762|gb|EET90027.1| RNA polymerase Rpb2 domain 6 [Candidatus Micrarchaeum acidiphilum
            ARMAN-2]
          Length = 607

 Score =  281 bits (719), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 113/574 (19%), Positives = 191/574 (33%), Gaps = 92/574 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D     N LVA            + I   ++      S    EF  M R       
Sbjct: 99   IEYLDAEEEENALVAINESEITEKTTHLEIDPSLMFGVTVNSSVFPEFNNMGRHAIAWNF 158

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                     +   ++  D  G   +        I          +     + L+ A+   
Sbjct: 159  MKQAQGLYATNFNMRY-DARG--YLLHYPQEPIINSITYRTMKLNRHPNGQNLVVALSTY 215

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +++D  +   + V   +     F         R+ S E  +     +D+        
Sbjct: 216  YGYNMKDAVVINRAAVDRGLGRSTFF---------RTYSDEERRYPGGQKDRFVIPAATT 266

Query: 980  RNIYSRLMEILCGQNAVSGPK-GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                        G++ +  P+    +  ++   +       +   F V +EK +      
Sbjct: 267  EGYRGEHAYAKLGEDGIVEPEMDVNEGDIIIGKVSPPRFLEEQTSFGVGEEKSRD----- 321

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                    + ++ R                G  ++VKV V   +  + GDK A R   KG
Sbjct: 322  --------NSVDLRSGEVGTVDNVMFSETTGATKIVKVRVRSNKVPEIGDKFASRQSQKG 373

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +V+ I+  EDMPF KDG   D++LNP+G+P+RM  G + E     A    G K       
Sbjct: 374  VVALIVNQEDMPFTKDGIIPDMLLNPIGLPNRMTYGHMLEMLGAKAASLKGTKFDGSAFS 433

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                                      + 
Sbjct: 434  KNGKEL---------------------------------------------------VDE 442

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
               +L     D+ G   LYDG TG+ F+  +  G +Y  +L HMVS K+  RS G   ++
Sbjct: 443  YGKILTEYGFDKFGDETLYDGRTGKRFESKLFTGVVYYHRLWHMVSLKLQVRSRGPVQIL 502

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYES 1331
            T+QP  GK  +GG + GEME   +  YGA+ +++E +  +SD          G    Y+ 
Sbjct: 503  TRQPTEGKPRKGGLKFGEMERDALVGYGASLLIKERMLDQSDKAPVWICKNCGDIGYYDY 562

Query: 1332 IVA--------GNDTFETGTPESFNVLVKEMQAL 1357
            I          GND  E     +F +L+ E++++
Sbjct: 563  IKNIPICPLCGGNDLEEIEISYAFKLLLDELKSM 596


>gi|315435642|gb|ADU18211.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
 gi|315435644|gb|ADU18212.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 238

 Score =  281 bits (719), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 128/226 (56%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 153

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 154  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 192  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 237



 Score = 45.5 bits (106), Expect = 0.063,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|186929321|emb|CAQ43102.1| RNA polymerase B-subunit [Staphylococcus rostri]
 gi|209407458|emb|CAR82638.1| RNA polymerase B-subunit [Staphylococcus rostri]
          Length = 320

 Score =  281 bits (719), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 174/316 (55%), Positives = 230/316 (72%), Gaps = 3/316 (0%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           ++S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG
Sbjct: 2   KMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--C 606
           + R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV   
Sbjct: 62  LTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIE 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
              +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +EK+D++D 
Sbjct: 122 TNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+PFVGTGME V A+ SGAA
Sbjct: 182 SPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGAA 241

Query: 727 IVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
           ++AK  G VE V +  I++R  +E +       +D Y L KF+RSN  TC NQRP++K G
Sbjct: 242 VIAKHRGRVEHVQSKEILVRRLIEENGQEYEGELDRYPLAKFKRSNSGTCYNQRPIIKAG 301

Query: 786 DEVRRNDIIADGPSTD 801
           D V + +I+ADGPS +
Sbjct: 302 DVVEKGEILADGPSME 317


>gi|290976959|ref|XP_002671206.1| predicted protein [Naegleria gruberi]
 gi|284084773|gb|EFC38462.1| predicted protein [Naegleria gruberi]
          Length = 1069

 Score =  281 bits (719), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 157/1095 (14%), Positives = 306/1095 (27%), Gaps = 214/1095 (19%)

Query: 248  PLSAADLMVGAKVSSSLVDIDT-----GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDC 302
                  L+   + +              E   + G  +     K+L  + V         
Sbjct: 81   SEVVYRLLTQQRANFPFAITRPSWMGYKEDFTDKGILVRCRHPKTLITRLVNIHYRRDGV 140

Query: 303  LCGLYVAEDIVNGETGEIYI-EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
            +     A + V      +   +A     ++ L  +  +  ++   L         + +  
Sbjct: 141  VFMR--AGNPVPFYINIVLALKALRECSDRDLFLLLTAGTKNKVTLDRVVELLGDFRKTF 198

Query: 362  LVTDKNKDRKDALLDIYRVM---RPGDVSTF-------SVAESMFNFLFFDSDKYDLSTV 411
                  +D   AL  IY      R  +                   +      K+    +
Sbjct: 199  PTVQTREDAIIALGTIYDPHGLRRLEEPVDKNKLIKSGYEKFDFLVYCVQKLYKFVDGEI 258

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                ++   N +       +     + I   +  L +G      + +    +   + +  
Sbjct: 259  AEENLDDFDNHELLTVGEVLSNVIPLIIYNKIQ-LAHGTCAKLLMKSATTMQPDMLEQKY 317

Query: 472  KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-LSQLEEHVN 530
               +R       +SI  +    DI+ +     +    V +        ++ L    E +N
Sbjct: 318  LALFRDKC----KSILSKACPNDINRLF---SVGDVSVSAPFRPELSQTRALFTKLERIN 370

Query: 531  SLSRITHTR---RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             L  I+H R   R  A       R       R + P+ +G ICP  + +GH  GLV+ L+
Sbjct: 371  FLRVISHFRATHRGIAFLDSNSTRM------RRLTPSFWGFICPVHSPDGHLCGLVNHLS 424

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                                   T ++V                 +          +V  
Sbjct: 425  ----------------------QTTEIV-----------------THQAKPKELRSVVEM 445

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                  +    EK   +    +  V +  ++I  + +D    +       + +      +
Sbjct: 446  CLKLGMLPSSTEKCISVSIEDEAPVMLDGAIIGKVSHDKLQNLADQLRYCKVSGKYGLPK 505

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               +                        +        +      L+  T      R +++
Sbjct: 506  FMEIA--------------------CQPKYSAMDIPYL----PQLNIFTDIARAVRPVRY 541

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
              + Q+  +     V +   V   DI  +    ++       + L    P+  +N     
Sbjct: 542  LPTGQDEWIGSAEQVFMNIAVTVEDIKPNTTHMEID-PTNFMSFLGNLTPFCNFNQSPRC 600

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +M  + +    H  +  V  +                        D          
Sbjct: 601  IYQCQMAKQSMAAVFHSVDHRVDTK----------------------LFDMKLPQKPLTR 638

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                       T             + A+      D+ D  +   +     ++   +F  
Sbjct: 639  TK-------HQTDLPFDEFNNGCNAVVAVISYTGYDMEDAMIMNKTSYERGMMHGTVFKT 691

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              ID  E +  +     +    D D +    +   Y  L E+              + ++
Sbjct: 692  EDIDLTEGTAFLTNRVFDKTEMDSDYQAKEFEDLDYDGLPEVGL---------PLDEGSI 742

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
             ++    E  +    ++   D     +V                       K+   D   
Sbjct: 743  FANYYDPEKQKFMPMKWKDVDSATVHSV-----------------------KVIATDPSD 779

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
               ++   +   + R    GDK + RHG KG++S + P EDMPF   G   DIV+NP   
Sbjct: 780  YKKVKHASITFRLNRNPIIGDKFSSRHGQKGVLSILWPQEDMPFTDGGIVPDIVINPHAF 839

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E+    A    G    +    +                            
Sbjct: 840  PSRMTIGMLVESMSSKAGALHGYFPDATPFSFSEENTA---------------------- 877

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                         +     L+ A  +  G  ++Y G  G     
Sbjct: 878  ----------------------------VDHFGEQLKKAGYNYHGNEVMYSGALGTTLKA 909

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G +Y  +L HMVSDK   R  G  + +T QP+ G+   GG R+GEME   + AYGA
Sbjct: 910  DIYMGVVYYQRLRHMVSDKYQCRVGGPTNAITHQPVKGRKKAGGVRMGEMERDALVAYGA 969

Query: 1308 AYVLQEML---TIKS 1319
            A V+++     T  S
Sbjct: 970  AAVVKDRFFDCTDSS 984


>gi|67626014|gb|AAY78476.1| RNA polymerase IV second largest subunit [Ginkgo biloba]
          Length = 651

 Score =  281 bits (719), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 121/337 (35%), Gaps = 74/337 (21%)

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            L+ +   K    Q          +  +V +   R    GDK +  HG KG+V  I   E+
Sbjct: 368  LKLKHTEKGRVDQVVMSANDDDKKFARVCLREVRSPSLGDKFSSMHGQKGVVGFIEEQEN 427

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF ++G   D+++NP   PSR   GQ+FE   G A    G                   
Sbjct: 428  MPFTQEGIVPDLIINPHAFPSRQTPGQLFECAFGKAIASSGVVGD--------------- 472

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP +     + I   L     
Sbjct: 473  --------------------------------------ATP-YGPVTLQYITEQLHRCGY 493

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
             + G+  +Y+G TG      + +G  Y  +L HM  DK+  R+ G    +T+QP+  +  
Sbjct: 494  QQWGKEQMYNGRTGCKLQSKIFIGPTYYQRLIHMAEDKMKYRNHGPVHPLTRQPVADRKR 553

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR------TRVYESIVAG--- 1335
             GG + GEME  C+ A+GA   L E L   SD     V  R      T +    V G   
Sbjct: 554  HGGVKFGEMERDCMLAHGATANLLERLFFLSDFSTMHVC-RECRNMATVILRDGVRGPYC 612

Query: 1336 ------NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                      +   P +  +L +E+ ++G+ +  +  
Sbjct: 613  PFCKTAKHIVKVNVPYACKMLYQELFSIGMCLRFQTE 649



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 64/446 (14%), Positives = 129/446 (28%), Gaps = 97/446 (21%)

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
              ++KN    GL+ +  +    +  ++   +   D I++  +  A   F     +   +
Sbjct: 7   NCGLVKNLAVTGLVSLHSAEDPILDILNECGITKLDQISSFNLKGAANIFINGEWVGAYD 66

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN-IGLVSS 585
           +    + ++   RR   +      +         +       + P               
Sbjct: 67  DPDFLVEKLRDLRRKQRIHPHXEIKRDKKQNEIRIFSDAGRILRPLFIVRDQRLCISQKQ 126

Query: 586 LTSFA-RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           + +F  R N + ++               +  L   EEE+  IA                
Sbjct: 127 IENFKKRGNPFKYLMER----------GIIEILGVEEEEDTKIACG-------------- 162

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           V      E            +  P  ++S++A  IPF  ++ + R L             
Sbjct: 163 VDILRMAENNRSYPS-FTHCELDPSFLLSLSAGFIPFSNHNLATRTLYQSE--------- 212

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                           K S  AI                   +       +++    Y  
Sbjct: 213 ----------------KHSKQAI---------------GHYSTNPRARCDTSAHQLFYPQ 241

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
               ++  + C+N+                             G+N +VA    +GYN E
Sbjct: 242 KPLFKTMSSECLNKM------------------------QFFNGQNAIVAVNVHYGYNQE 277

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMAR------DTKLGPEEITRDIPNVSEEGLKNIDE 878
           DS++ +   +   +F S+H   F                  E+    P      +  +D+
Sbjct: 278 DSLVANHASIDRGLFRSMHFHTFISETDHHDNDSKKSSFRVEVDFGKPQTGNLKVDKLDD 337

Query: 879 CGIICVGAEVNPGDILVGKITPKGES 904
            G+  +GA +  GDIL+GK+ P+   
Sbjct: 338 DGLPFIGASLVSGDILIGKVGPQPSD 363


>gi|148879061|emb|CAM07046.1| RpoB protein [Mycobacterium llatzerense]
          Length = 219

 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 95/227 (41%), Positives = 125/227 (55%), Gaps = 40/227 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 25   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 130  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 172

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG 
Sbjct: 173  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 219


>gi|315435636|gb|ADU18208.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-10043]
          Length = 240

 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 130/229 (56%), Gaps = 37/229 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G K+ +        G++       E  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWKVDTGKGVPDWAGNLPEDLLHAEPN 159

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 160  A----------------------------IVSTPVFDGAQEAELQGLLSATLPNRDGEVL 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                G++ L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARSTG YS
Sbjct: 192  VNGDGKAELFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARSTGPYS 240



 Score = 45.8 bits (107), Expect = 0.058,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|50303741|ref|XP_451816.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640948|emb|CAH02209.1| KLLA0B06303p [Kluyveromyces lactis]
          Length = 1203

 Score =  281 bits (718), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 120/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            + + +        +  + + +    +    + +       +    +  K+   +      
Sbjct: 837  EKLDDDGLPLIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVKLIGDESSKFQE 896

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ + +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSR
Sbjct: 897  LQAITIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDVIINPHAFPSR 956

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +  +                            
Sbjct: 957  MTIGMFVESLAGKAGALHGIAQDSTPWTFNESD--------------------------- 989

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 990  -----------------TPA------DYFGDQLAKAGYNYHGNEPMYSGATGEELRADIY 1026

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 1027 IGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 1086

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 1087 LQDRLLNCSD 1096



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 92/623 (14%), Positives = 199/623 (31%), Gaps = 95/623 (15%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP---GDVST 388
            L  +  +  R+I    V    +N+++          DR + LL  ++   P       T
Sbjct: 276 ILRALCDTNDREIFDHVVGGDTSNSFL---------TDRLELLLRGFKKRYPTLQNRKQT 326

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                  F  +F  S       VG+  +N  + +   ++ +  +   ++ +I+ L  L  
Sbjct: 327 LQYLGDKFRVVFQASPDMTDLQVGQELLNRIVLVHLGENNKD-KFNMLLFMIRKLYSLVA 385

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP----QDLI 504
           G+ + D+ D   ++ +   G +     +  +    ++I+ +I +     +      Q  +
Sbjct: 386 GECSPDNPDAAQHQEILLGGFLYGMIVKEKIEEYLQNIRLQIQTDINRGLAINFKDQKYM 445

Query: 505 N------AKPVVSAVCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSAL 544
           N       + + S +  F  +  L              + + E +N    I+H R    +
Sbjct: 446 NKVLMRVNENIGSKLQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MV 502

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            +G          +R + P  +G  CP  T +G   GL++ L+   +++           
Sbjct: 503 HRGSFFAQLKTTTVRKLLPESWGFFCPVHTPDGSPCGLLNHLSHKCKISTEQ-------- 554

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      ++Y   +      IA   S         +  +   C+ E+  V  + + F 
Sbjct: 555 -SDVSKIPSILYSLGVTPAAHVIAAGPSMCCV---QLDGKIIGWCSHEQGKVVADTLRFW 610

Query: 665 DAS---PKQVVSIAASLIPFLENDDSNRVLM---GCNMQRQAVPLLKAEAPFVG------ 712
                 P   V +    +P   +     + +      M R    L   +   VG      
Sbjct: 611 KVEGKTPGLPVDLEVGYVPPTTSGQYPGLFLFGGHSRMMRPVRYLPLDKEDIVGPFEQVY 670

Query: 713 -------TGME---SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-I 761
                    +E       + S   I++  A +    D  +      +  +   T G   +
Sbjct: 671 MNIAVTPEEIENNVHSHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGV 730

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
               +           Q P+VK                  + +   G N +VA + + GY
Sbjct: 731 ALCHRSDNKLYRLQTGQTPIVKANLYDDYG----------MDNFPNGTNAVVAVISYTGY 780

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG-------LK 874
           + +D+M+I++               ++V   +  +          +            L+
Sbjct: 781 DMDDAMIINKSADERGFGYGT---MYKVEKVNLSMNRSRGDPITQHFGFGTDEWPKEWLE 837

Query: 875 NIDECGIICVGAEVNPGDILVGK 897
            +D+ G+  +G  V  GD +   
Sbjct: 838 KLDDDGLPLIGTYVEEGDPICAY 860



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 100/840 (11%), Positives = 220/840 (26%), Gaps = 121/840 (14%)

Query: 70  GAAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
               L         P            K    +   R  +Y   + + L+  V D +E  
Sbjct: 93  NKLSLSIEQVSISKPTSNDGVSSAVERKVFPSESRQRLTSYRGKILLKLKWSVNDGEETF 152

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
               ++D        G LP+M +                         G F++ GI++++
Sbjct: 153 --TEVRDC-------GGLPIMLQSNRCHLNKMSPYELVEHREESDEFGGYFIVNGIEKLI 203

Query: 154 ---VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH------- 203
              + Q    P             S    Y+   I  + +  D +    +++H       
Sbjct: 204 RMLIVQRRNHPMAIIRPSFANRGAS----YSQYGIQIRSVRPD-QTSQTNVLHYLNDGQV 258

Query: 204 -VRIDRRRK---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
             R   R+    +PV   L AL   ++ EI                       ++  +  
Sbjct: 259 TFRFSWRKNEYLIPVVMILRALCDTNDREIFDHVVGGDT--------------SNSFLTD 304

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           ++   L         +++ K+    L    +        +T D   G  +   IV    G
Sbjct: 305 RLELLLRGFKKRYPTLQNRKQTLQYLGDKFRVVFQASPDMT-DLQVGQELLNRIVLVHLG 363

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT-DKNKDRKDALLDI 377
           E   +    +    + +++     +      D+  +   +    +     K++ +  L  
Sbjct: 364 E-NNKDKFNMLLFMIRKLYSLVAGECSPDNPDAAQHQEILLGGFLYGMIVKEKIEEYLQN 422

Query: 378 YRVMRPGDV----STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            R+    D+    +     +   N +    ++   S +        L   +  D++ +  
Sbjct: 423 IRLQIQTDINRGLAINFKDQKYMNKVLMRVNENIGSKLQYFLSTGNLVSQSGLDLQQVSG 482

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             ++A         +    +         +  +V ++L   +                  
Sbjct: 483 YTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFFC-------PVHTPDG 535

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               ++       K            S L  L     +               G +    
Sbjct: 536 SPCGLLNHLSHKCKISTEQSDVSKIPSILYSLGVTPAAHVIAAGPSMCCVQLDGKIIGWC 595

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           +  + + V  T    +   +         V     +      G     +      ++   
Sbjct: 596 SHEQGKVVADT----LRFWKVEGKTPGLPVDLEVGYVPPTTSGQYPGLFLFGGHSRMMRP 651

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YL   +E+   +               E V+   A     +       ++ SP  ++S
Sbjct: 652 VRYLPLDKED--IVGPF------------EQVYMNIAVTPEEIENNVHSHVEFSPTNILS 697

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I A+L PF + + S R +  C M +Q +                +    +G   + K   
Sbjct: 698 ILANLTPFSDFNQSPRNMYQCQMGKQTMGT--PGVALCHRSDNKLYRLQTGQTPIVKANL 755

Query: 734 IVEQ----VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
             +            + +V            I      +R      + +   V +     
Sbjct: 756 YDDYGMDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKVEKVNLSMNRS 815

Query: 790 RNDIIADGPSTDLGDLA--LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           R D I         +        +    +P  G   E+   I      +D      I+ +
Sbjct: 816 RGDPITQHFGFGTDEWPKEWLEKLDDDGLPLIGTYVEEGDPIC--AYFDDTLNKTKIKTY 873


>gi|256081821|ref|XP_002577166.1| DNA-directed RNA polymerase III subunit [Schistosoma mansoni]
 gi|238662462|emb|CAZ33403.1| DNA-directed RNA polymerase III subunit, putative [Schistosoma
            mansoni]
          Length = 1128

 Score =  280 bits (717), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 107/491 (21%), Positives = 173/491 (35%), Gaps = 105/491 (21%)

Query: 888  VNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            V P   LV   T +      +   +  + AI      DV D  +   + +        ++
Sbjct: 701  VYPQKPLVQSKTIQMMHFDELPAGQNAVVAIMSYSGYDVEDALVINQASIDRGFARACVY 760

Query: 946  NRHG-IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
             R G   K   +   +R     + R         +  +  R  E+L              
Sbjct: 761  RRSGVHLKMHENAVYDRLMGPSIER---------ETGVLRRGDEVLQADGVAYIGACVND 811

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              +L +  +     S                 +  ++++      +    + +EK+ +  
Sbjct: 812  RQILINKEMPVVSSSAVLD------------NAGSLKFKRCPVDYKGIEPSYVEKVMF-- 857

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                G   VVK+ +   R  + GDK + RHG KG+V  I+  ED+PF  +G   DI++NP
Sbjct: 858  STSEGNQAVVKILLRQTRRPEVGDKFSSRHGQKGVVGLIVRQEDLPFSTNGLTPDIIMNP 917

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
             G PSRM V        G     LG K  ++    +                        
Sbjct: 918  HGFPSRMTV--------GKLLEVLGSKAGAIEGKIRDGS--------------------- 948

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                      F G   E ++ +L        G+ ILY G+TG P
Sbjct: 949  -------------------------AFSGDPAEVLSQVLIDHGYHYLGKEILYSGVTGAP 983

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
             +  +  G +Y  +L HMV DKV+ARS G  + +T+QP  G+S  GG R+GEME  C  A
Sbjct: 984  LEAFIYFGPVYYQRLKHMVMDKVHARSRGPVTALTRQPTEGRSREGGLRVGEMERDCFIA 1043

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN------------------DTFETGTPES 1346
            YG + +L E L + SD        Y++ V                            P +
Sbjct: 1044 YGTSQLLLERLLLSSD-------AYDACVCEKCGLLATSPNWCQYCRSSRQVVSVRMPYA 1096

Query: 1347 FNVLVKEMQAL 1357
              +L +E+  +
Sbjct: 1097 CKLLFQELMCM 1107



 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 85/735 (11%), Positives = 201/735 (27%), Gaps = 113/735 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+++   S++HF+   I    R N            ++       LE+      PP    
Sbjct: 17  LVKLHIDSFNHFIQTEIKNIVRAN----------SRVSVPEANWWLEYNDIYIKPPTVND 66

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 +    DC  RDLTYA  + + +  +          +  + + ++ + +G +P+M
Sbjct: 67  GGVVASRVTPHDCRLRDLTYAGEILVDVTFV----------RQNEVVSKKGVLIGRMPIM 116

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGR--- 171
            K                         G F+I G +++V+ Q   S       +  +   
Sbjct: 117 LKSSICVLNGKSPSELMRLKECPLDPGGYFIIGGTEKVVLMQEQTSKNRLIIEEDSKRGL 176

Query: 172 ---ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-E 227
               + S     +   I  +             I   +D    VP+     A+ + S+ E
Sbjct: 177 VCSVTSSSAQTKSKTNIVTKDD--KFYLSHNSFI---VD----VPIAILFKAMNITSDQE 227

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD--IDTGEQVIESGKKLTSGLL 285
           +L     +                 ++       + L         +      +      
Sbjct: 228 LLQLIGTEESVWANFVPSLKLCLEYNIHTCLDACNWLHSRLRQPRYRTAFGAGRTLRTAA 287

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
             L+   +  +      +   +V  + +N      ++        + +  +  +  + IP
Sbjct: 288 NILETDIILEIQRFLRDIIITHVEMEKLNFAPRAFFLG-------QMVRYLILANEKRIP 340

Query: 346 ILYVDSVNNNAY-----IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
               D   N        +   L  D  K   + L      +      T            
Sbjct: 341 PDDRDFYGNKRIELAGSLLALLFEDVFKTFNEDLWLTVSKIDTKRRCTPFDISRHIKTWM 400

Query: 401 FDSDKYDLSTVGRV--KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                    + G    K    +       V  +     +  +  +         +    +
Sbjct: 401 ITEQLNRAISSGNWIIKRFRMMRHGVTQVVSRLSYVAALGHMTRMTSQFEKTRKVSGPRS 460

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           +   +   +      +     L    ++   ++    D+ + + + N       + +   
Sbjct: 461 IHASQWGLICPSDTPEGEACGLVKNVALMCHVTVEVDDAHLIELISNYYTF--PLYQMRY 518

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +     +  +   +    H  +L  +   G+ R+        V+     +     +  G 
Sbjct: 519 AKNEYVIYVNGKPIGFTQHPGKL-CVLIRGLRRSGRIHGFVSVYIKQAYQCVHVVSDGGR 577

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSSLD 635
                  L +   +     ++     V +         V YL   E  +  +A   S L 
Sbjct: 578 FCRPYIILCNGRPLVTESVLQDLRHNVLNWDDLLKKGLVEYLDVNELNDCLVAMDESCLT 637

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +   +                       ++  P  ++ + A LIP+ +++ S R    C 
Sbjct: 638 DGNHY---------------------THMEIDPATILGVVAGLIPYPDHNQSPRNTYQCA 676

Query: 696 MQRQAVPLLKAEAPF 710
           M +QA+  +      
Sbjct: 677 MGKQAIGTVALNQQI 691



 Score =  129 bits (323), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 95/651 (14%), Positives = 196/651 (30%), Gaps = 55/651 (8%)

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
           K   +T D    L     IV+     ++       D++ L+ I   E             
Sbjct: 190 KTNIVTKDDKFYLSHNSFIVDVPIAILFKAMNITSDQELLQLIGTEES---------VWA 240

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
           N        +        DA   ++  +R     T   A           +   +  + R
Sbjct: 241 NFVPSLKLCLEYNIHTCLDACNWLHSRLRQPRYRTAFGAGRTLRTAANILETDIILEIQR 300

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
              ++ +     + +    +   +  +++ L+     +   DD D  GN+R+   G +L 
Sbjct: 301 FLRDIIITHVEMEKLNFAPRAFFLGQMVRYLILANEKRIPPDDRDFYGNKRIELAGSLLA 360

Query: 473 NQYRLGLLRME-------------RSIKERISSVDIDSVMPQDLINA---KPVVSAVCEF 516
             +                     R       S  I + M  + +N              
Sbjct: 361 LLFEDVFKTFNEDLWLTVSKIDTKRRCTPFDISRHIKTWMITEQLNRAISSGNWIIKRFR 420

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                ++Q+   ++ ++ + H  R+++       + R     R +H + +G ICP++T E
Sbjct: 421 MMRHGVTQVVSRLSYVAALGHMTRMTS----QFEKTRKVSGPRSIHASQWGLICPSDTPE 476

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G   GLV ++     V            + +           A  E   Y+        +
Sbjct: 477 GEACGLVKNVALMCHVTVEVDDAHLIELISNYYTFPLYQMRYAKNEYVIYVNGKPIGFTQ 536

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS-LIPFLENDDSNRVLMGCN 695
                  L+        I                VVS       P++   +   ++    
Sbjct: 537 HPGKLCVLIRGLRRSGRIHGFVSVYIKQAYQCVHVVSDGGRFCRPYIILCNGRPLVTESV 596

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI------------ 743
           +Q     +L  +       +E +        +VA         D                
Sbjct: 597 LQDLRHNVLNWDDLLKKGLVEYLDVNELNDCLVA--MDESCLTDGNHYTHMEIDPATILG 654

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR----PLVKVGDEVRRNDIIADG-P 798
           V+  +    D + S  + Y+    +++     +NQ+     L       ++  + +    
Sbjct: 655 VVAGLIPYPDHNQSPRNTYQCAMGKQAIGTVALNQQIRFDTLQCQMVYPQKPLVQSKTIQ 714

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA M + GY+ ED+++I++  +      +       V  +  +   
Sbjct: 715 MMHFDELPAGQNAVVAIMSYSGYDVEDALVINQASIDRGFARACVYRRSGVHLKMHENAV 774

Query: 859 EEI-TRDIPNVSEEGLKNIDE----CGIICVGAEVNPGDILVGKITPKGES 904
            +             L+  DE     G+  +GA VN   IL+ K  P   S
Sbjct: 775 YDRLMGPSIERETGVLRRGDEVLQADGVAYIGACVNDRQILINKEMPVVSS 825


>gi|194762066|gb|ACF94995.1| RpoB [Bartonella sp. Lao/Nh3]
 gi|223928138|gb|ACN23837.1| RNA polymerase beta subunit [Bartonella sp. KM2519]
 gi|269930915|gb|ACZ54192.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 254/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E+VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 EAVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|258562132|gb|ACV81788.1| RNA polymerase II second largest subunit [Agaricus bisporus]
          Length = 697

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 126/827 (15%), Positives = 249/827 (30%), Gaps = 146/827 (17%)

Query: 472  KNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
            ++ +R+   ++ + +    +              +  + + + +     +          
Sbjct: 1    RHLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWGDQKKSM 60

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET E
Sbjct: 61   SSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPE 116

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G   GLV +L   + ++   +       + +  + +         EEN +     + +  
Sbjct: 117  GQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSTSPCTKVFV 168

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +G +       R     +   ++     D SP+  V             D+ RV     +
Sbjct: 169  NGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLFI 225

Query: 697  QRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
                  LL      ++ +G +    +     +   + G++E +DA       +    +  
Sbjct: 226  VENQQLLLGKRHIRWLNSGSDDEGNEYKWEQL--IKGGVIELLDAEEEETVMISMTPEDL 283

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             +       +    ++ +     R  +K G            PS  LG       +  + 
Sbjct: 284  ENSRLQAAGVDPHANDGDFDPAAR--LKAGTHAHTWTHCEIHPSMILG-------ICASI 334

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N                        ++       +G       I          
Sbjct: 335  IPFPDHNQSPRN------------------TYQSAMAKQAMGIYLTNFLIRM-------- 368

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 369  ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 425

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD          +       I  G   
Sbjct: 426  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGV 484

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          V   ++S ++       I       
Sbjct: 485  RGEDIIIGKTAPIPPDSEELGQRTR----THTRRDVSTPLKSTEIGIVDQVLI------- 533

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 534  ---------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTVGITYRQEDMPFTAEG 584

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +G + E  L      +G +  +                     
Sbjct: 585  IVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----------------- 627

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                     ++     + LR       G+ V                         G + 
Sbjct: 628  --------DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGHT- 656

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                  G      + +G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 657  ------GRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQP 697


>gi|124804526|ref|XP_001348029.1| DNA-directed RNA polymerase 1, subunit 2, putative [Plasmodium
            falciparum 3D7]
 gi|23496284|gb|AAN35942.1| DNA-directed RNA polymerase 1, subunit 2, putative [Plasmodium
            falciparum 3D7]
          Length = 1517

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 192/1181 (16%), Positives = 354/1181 (29%), Gaps = 123/1181 (10%)

Query: 228  ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK----LTSG 283
            ILS    K     +        +A   +     S  L D    +++ E          + 
Sbjct: 287  ILSPIKKKSYIFNKIKLGVENENAIKYIELFINSIFLKDTFNEKELFEKYNLSYLGRIAY 346

Query: 284  LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            L + + +  +      +  +    +   I N                   +++ +S  + 
Sbjct: 347  LRRGIFKYNLNCYEKKAKDILKYCILPHIKNNSEK-------FETMCFMFKKLIYSNFKL 399

Query: 344  IPILYVDSVNNNAYIRNTLV-----TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            I  +  DS+ N+A    + +      D+  +    L   Y         T      +   
Sbjct: 400  ITPINKDSLENHAVTTCSNLLANLLKDQVMNSLCRLYIRYTRSFFKYFETKYNTFKLSVK 459

Query: 399  LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
              +   K  +    +     +++L    +  +          K     +     I++ + 
Sbjct: 460  QIYLRYKMFVLEEMQEDRLNQISLSKSSEDINDSSYQDNNDYKNESKKKLKSIFINEKEK 519

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            L         E+  + Y            E   S    S           + S    +  
Sbjct: 520  LFRSVDNYFKELYNDNY---------MFLENCKSFSNTSSAILFFFKTGNISSENLHYQQ 570

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             S      + +N+L  IT+ R   A+ +G   +    +  R +    +G ICP  T +G 
Sbjct: 571  KSGWVIAADEINNLRLITNFR---AIHRGTFFQDVKVLTPRKLLGESWGFICPVHTPDGT 627

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVC----------DGKVTNDVVYLSAMEEENRYIA 628
              GL++ L  +  ++     E     +           +   T+ +   +  ++EN  I 
Sbjct: 628  PCGLLNHLAQYCHIHNLSSNEAHKLNIKLYLKKIGINVNLDDTSGIH--TIYDDENIPII 685

Query: 629  QANSSLDEDG-----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP--- 680
              +  +   G         +L + +      L    +I+     P  + SI  +  P   
Sbjct: 686  VDSIPITYIGEKDFNRTVYKLKYAKNNNLFNLKSYFEINAYLNEPLIMNSIIINTFPGRL 745

Query: 681  --FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
               L N  +  +       +  + +           +   + K     + + +       
Sbjct: 746  IRPLLNLKTKDIEFISPSYQPYISVAINNEDVKKNNLARKLLKKKEQVVNSMKIDRTPGS 805

Query: 739  DAIRIVIRSVEGD-----LDPSTSGVDIYRLMKFQRS---------NQNTCVNQRPLVKV 784
               + +      +        S  G   Y   K  R          N ++  N    V  
Sbjct: 806  IKQKFLYHQNRENLLWKLKKESKDGSYKYEKHKIDRKLLKILDQKKNNDSDTNTDNYVSS 865

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY--NFEDSMLI-SERMVSEDVFTS 841
             +    +D      S   GD     N         G   N   +  I S+  ++ D++  
Sbjct: 866  SEYDTDSDYDYGYDSNSDGDSKSNSNFDSKSDNISGSDNNMSTTTYIDSDENINIDMYEQ 925

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I  ++FE M          +    P          D         +       +G  +  
Sbjct: 926  IP-QKFEYMELKETSFLSFLASLTPF--------SDHNQSPRNIYQCQMLKQTMGIQSLN 976

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                 T +   +        V        V +  SGT   V I    G D  +  I  + 
Sbjct: 977  NVYTFTNKIYRMITPQFPLVVTRDYEFYGVDNFPSGTNAVVAILAYTGYDMEDALIINKA 1036

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ- 1020
                 + R    +   +D          + G N          +  L+ +   ++     
Sbjct: 1037 SADRGIFRTHIYKTEFIDLQKVGESSNFVFGNNIRYLNNNKNNNKNLAYENKGKFLNKDG 1096

Query: 1021 ---WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                 Q   +   +   +        T+     +  +  ++ +  G +      +V  V 
Sbjct: 1097 LPCVQQKITEGSPLYSYINKGNEL--TTYESFRNHGEYFVDFVSIGKNNS---NQVAVVK 1151

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   R  Q GDK A RHG KG+VSR+ P EDMPF + G   DI+ NP G+PSRM +G + 
Sbjct: 1152 LRSTRQPQVGDKFASRHGQKGVVSRLFPQEDMPFAESGIVPDIIFNPHGIPSRMTIGMLI 1211

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGD--------------------------------- 1164
            E+  G A    GK+I +                                           
Sbjct: 1212 ESICGKAASLYGKRIDATPFRKYTQQKSFNNPWIDNCGIKGFLEKNDTIKSDLDTCQKEK 1271

Query: 1165 -----ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 I+   +   K     +  +  +  D D         +        +      +  
Sbjct: 1272 DKNKNINNNNNNKIKENKYNNSNDSNASIDSDDNTNNCNDKRDEEEKKANITYDEKIDYF 1331

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L     D  G  +LY G+ G P    + +G IY  +L HM  DK   R TG    +T
Sbjct: 1332 AKLLLNKGYDYYGTELLYSGIYGVPLQAHIFIGVIYYQRLRHMAYDKAQVRRTGPVCNLT 1391

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             QPL GK   GG R+GEME   I ++G ++V+ E   + SD
Sbjct: 1392 HQPLKGKRKHGGIRVGEMERDGIISHGCSFVINERFLMSSD 1432


>gi|169792066|gb|ACA80323.1| RpoB [Fusobacterium periodonticum]
 gi|169792072|gb|ACA80326.1| RpoB [Fusobacterium periodonticum]
 gi|169792076|gb|ACA80328.1| RpoB [Fusobacterium periodonticum]
 gi|169792082|gb|ACA80331.1| RpoB [Fusobacterium periodonticum]
 gi|206967387|gb|ACI22674.1| RpoB [Fusobacterium periodonticum]
 gi|206967391|gb|ACI22676.1| RpoB [Fusobacterium periodonticum]
          Length = 143

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 89/195 (45%), Positives = 108/195 (55%), Gaps = 52/195 (26%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRMN+GQ+ E HLG A        
Sbjct: 1    RHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMRT----- 55

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  ++TPVFD
Sbjct: 56   -----------------------------------------------LNGGTCIATPVFD 68

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA EE +   L       +G+  LYDG TGE FD  VTVG +YMLKL+H+V DK++AR+ 
Sbjct: 69   GATEEQVKDYLEKQGFPRTGKVTLYDGRTGEKFDNKVTVGIMYMLKLHHLVEDKMHARAI 128

Query: 1273 GSYSLVTQQPLGGKS 1287
            G YSLVTQQPLGGK+
Sbjct: 129  GPYSLVTQQPLGGKA 143


>gi|291088178|dbj|BAI82370.1| RNA polymerase subunit B' [Halobacterium noricense]
          Length = 608

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 120/583 (20%), Positives = 195/583 (33%), Gaps = 93/583 (15%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D     ++LV        +    + I  +++       I   E     R T      
Sbjct: 101  EFIDAEEEEDVLVGVDQDELTDNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG-- 158

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            + +    +     +   +     +        +        G       +  + A+   +
Sbjct: 159  MMKQSLGLPAANYRIRPDTR-QHLLHYPQKAMVNTQTTEQIGYDDRPAGQNFVVAVMSYE 217

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              ++ D  L +  G     +    F R    +  R    + ++ E+ + D       +  
Sbjct: 218  GFNIEDA-LVMNQGSVDRALSRSHFFRTYEGEERRYPGGQEDRFEIPSDD-------VRG 269

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                     L     V+       S+VL           +         + +R       
Sbjct: 270  GRGEDAYTHLDDDGLVNPETQVDDSSVLLGKTSPPRFLEEPEDMGGLSPQKRRETSVTMR 329

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              E          + +               ++ KV V  +R  + GDK A RHG KG+V
Sbjct: 330  SGEDGVVDTVTLMEGE------------DGSKLAKVSVRDERIPELGDKFASRHGQKGVV 377

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              + P EDMPF ++G   D+VLNP  +PSRM VG + E   G A    G+ +       +
Sbjct: 378  GHLAPHEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKAGSLDGRSVDGTAFTGE 437

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                   LRS LE+     S  E +                           G   E I 
Sbjct: 438  DE---DELRSTLEERGFKSSGKEVLYS-------------------------GVSGEKI- 468

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                                     +  + VG I+  KL HMVS+K++ARS G   ++T+
Sbjct: 469  -------------------------EAEIFVGTIFYHKLYHMVSNKLHARSKGPVQVLTR 503

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR-----TRVYE- 1330
            QP  G++  GG R+GEME   +  +GAA VL+E L   SD     V G         YE 
Sbjct: 504  QPTEGRAREGGLRVGEMERDTVIGHGAAMVLKERLLDSSDREEIHVCGNCGMTAVENYEQ 563

Query: 1331 SIVAGNDTFETG------TPESFNVLVKEMQALGLSIDLENSR 1367
              V   +  E           +F +L+ EM+ALG++  LE   
Sbjct: 564  RRVYCPNCEEETDVHSLEMSYAFKLLLDEMKALGIAPRLELED 606



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 59/370 (15%), Positives = 125/370 (33%), Gaps = 35/370 (9%)

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           +S   E   Y+  +     ED       +   R  GE   +    +              
Sbjct: 1   MSTEREAKVYVNGSLVGTHEDPEELAAQIREARRRGEVSEMVNVSVKDRTNEVIVNADAG 60

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
            +  P L  +D   ++    M       +  E       +E + A+     +V       
Sbjct: 61  RARRPLLVVEDGEPLVTDEEMGAVENDDIDFEDLVRAGKVEFIDAEEEEDVLV---GVDQ 117

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK--FQRSNQNTCVNQ-----------RPLV 782
           +++      +      +    +G+  Y       + +     + Q           RP  
Sbjct: 118 DELTDNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDT 177

Query: 783 KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           +          + +  +T+     D   G+N +VA M + G+N ED++++++  V   + 
Sbjct: 178 RQHLLHYPQKAMVNTQTTEQIGYDDRPAGQNFVVAVMSYEGFNIEDALVMNQGSVDRALS 237

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDECGIICVGAEVNPGDI 893
            S     +E   R    G E+   +IP+        E+   ++D+ G++    +V+   +
Sbjct: 238 RSHFFRTYEGEERRYPGGQEDRF-EIPSDDVRGGRGEDAYTHLDDDGLVNPETQVDDSSV 296

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           L+GK +P               + G      R+TS+ + SG  G V    +    G D +
Sbjct: 297 LLGKTSPPRFLEEP------EDMGGLSPQKRRETSVTMRSGEDGVV--DTVTLMEGEDGS 348

Query: 954 ERSISVEREQ 963
           + +    R++
Sbjct: 349 KLAKVSVRDE 358



 Score = 42.0 bits (97), Expect = 0.70,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 60/195 (30%), Gaps = 31/195 (15%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           +   S +   E+     ++I   RR   + +      +       V+        P    
Sbjct: 10  YVNGSLVGTHEDPEELAAQIREARRRGEVSEMVNVSVKDRTNEVIVNADAGRARRPLLVV 69

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E     +             G +E       D      V ++ A EEE+  +      L 
Sbjct: 70  EDGEPLVTDE--------EMGAVENDDIDFEDLVRAGKVEFIDAEEEEDVLVGVDQDELT 121

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ++                          ++  P+ +  I A +IP+ E++ S R+ MG  
Sbjct: 122 DNH-----------------------THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAG 158

Query: 696 MQRQAVPLLKAEAPF 710
           M +Q++ L  A    
Sbjct: 159 MMKQSLGLPAANYRI 173


>gi|194762022|gb|ACF94993.1| RpoB [Bartonella sp. Lao/Nh1]
          Length = 298

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 254/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIVDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|116181610|ref|XP_001220654.1| hypothetical protein CHGG_01433 [Chaetomium globosum CBS 148.51]
 gi|88185730|gb|EAQ93198.1| hypothetical protein CHGG_01433 [Chaetomium globosum CBS 148.51]
          Length = 1188

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 90/455 (19%), Positives = 154/455 (33%), Gaps = 64/455 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +   G   +G            +   L+             +    +  +
Sbjct: 662  DFNQSPRNMYQCQMGKQTMGTPGTALRHRTDNKMYRLQTGQTPIVRAPLHNTYGFDNFPN 721

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELL---ARDKDDEQVILDRNIYSRLMEILCGQ 993
            G    V + +  G D ++ ++ + +   E           ++V L  +  +R  + +   
Sbjct: 722  GMNAVVAVISYTGYDMDD-AMIINKSAHERGFGHGTIYKTKKVSLKDDSRTRTSKTISKM 780

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQ--------FAVQDEKVQRNVESLKVQYETS 1045
               +     + S     D        +  +          V  +   + +    + +   
Sbjct: 781  FGFAPGSPVRASDREMLDEDGLPYVGRLVREGDILCAWHTVSADYSGQLINRDGITHWER 840

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                ED F  ++  I       P  L+ V + + + R    GDK + RHG KG+ S+  P
Sbjct: 841  YKEAEDAFIEEVRVIGSDSGTEP--LQTVSIKLRIPRSPIIGDKFSSRHGQKGVASQKWP 898

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
              DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +      
Sbjct: 899  AIDMPFSETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFNEEHTA 958

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                               +     L  
Sbjct: 959  G--------------------------------------------------DYFGHQLMK 968

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            A  +  G   +Y G+TGE F   + +G +Y  +L HMV+DK   R+TG     T QP+ G
Sbjct: 969  AGYNYHGNEPMYSGITGEEFACDIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKG 1028

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1029 RKKGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1063



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 79/537 (14%), Positives = 164/537 (30%), Gaps = 69/537 (12%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           R+ +     +D  ++    + + ++ + + L  L  G   +D+ D + N+ +   G    
Sbjct: 303 RIVLVNLGCVDVTEEQDLDKFKMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLYG 362

Query: 469 --------EMLKNQYRLG---LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                   E+L    RL     LR   S     S    D  +       + + +A+  F 
Sbjct: 363 MVLKERLDELLSVSLRLALRDYLRRNPSQSFTSSGFTKDFPIAIFRRTNENLGNALEYFL 422

Query: 518 CSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L                + E +N L  I+H R    + +G          +R + P
Sbjct: 423 STGNLQSPSGLDLQQTSGFTVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTVRKLLP 479

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ +    ++       +    V      ND  Y SA   E
Sbjct: 480 ESWGFLCPVHTPDGSPCGLLNHMAHKCKIITDSVDVSAVPGVAMELGVND--YSSAATSE 537

Query: 624 NRYIAQANSSL---DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK--------QVV 672
           +  +      +     + +        R   E        ++     P          + 
Sbjct: 538 SVVVMLDGRIIGWCTPNAAKAVADNLRRWKVEGGHGIPILLEIGYVPPSKGGSYPGIYMS 597

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVA 729
           S ++ ++  ++     +       ++  + +   +   +    T +E             
Sbjct: 598 SQSSRMVRPVKYLPLGKEDFVGPHEQPYMSIACTDGEVLPGDSTHVEFDPTHILSILANM 657

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                  Q        +  +  +    + +      K  R        Q P+V+      
Sbjct: 658 TPFSDFNQSPRNMYQCQMGKQTMGTPGTALRHRTDNKMYRLQTG----QTPIVRA----- 708

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    +    +   G N +VA + + GY+ +D+M+I++             +  +V
Sbjct: 709 -----PLHNTYGFDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGHGTIYKTKKV 763

Query: 850 MARDTKLGP-------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +D                     V     + +DE G+  VG  V  GDIL    T
Sbjct: 764 SLKDDSRTRTSKTISKMFGFAPGSPVRASDREMLDEDGLPYVGRLVREGDILCAWHT 820



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 86/637 (13%), Positives = 180/637 (28%), Gaps = 122/637 (19%)

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV----VSQ------L 157
           +G +P+M K                         G F++ GI++I+    V++      +
Sbjct: 103 LGQMPIMIKSNKCHLENNSPALLVQRKEESEELGGYFIVNGIEKIIRLLLVNRRNFPLAI 162

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRR 209
            R            +  +    Y    I  + +  D E    +++H         R   R
Sbjct: 163 IR-----------PSFTNRGPSYTPYGIIVRSVRPD-ETSQTNVLHYLNDGNVTFRFSWR 210

Query: 210 RK---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           +    VPV   L AL   ++ EI              + +        L+   K      
Sbjct: 211 KNEYLVPVMMILKALIETNDREIFEGLVGPPNSKGIENTFLTD-RVELLLRTYKTYGLYT 269

Query: 266 DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
              T   + E  + +                         L V E + + E G  ++   
Sbjct: 270 KTQTRAYLGEKFRVV-------------------------LGVPETMSDYEVGTEFLRRI 304

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
            +++   ++     ++    +L        A +      D     ++  + +   +  G 
Sbjct: 305 VLVNLGCVDVTEEQDLDKFKMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLY-GM 363

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
           V    + E +   L      Y      +   +     D P  +     E++   ++  + 
Sbjct: 364 VLKERLDELLSVSLRLALRDYLRRNPSQSFTSSGFTKDFPIAIFRRTNENLGNALEYFLS 423

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDL 503
             N   +   +D         V E L     +   RM    S   ++ +  +  ++P+  
Sbjct: 424 TGN-LQSPSGLDLQQTSGFTVVAEKLNFLRFISHFRMVHRGSFFAQLKTTTVRKLLPESW 482

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSR--ITHTRRLSALGQGGVARARAGVEMRDV 561
               PV +          L     H   +    +  +       + GV    +      V
Sbjct: 483 GFLCPVHTPDGSPCG---LLNHMAHKCKIITDSVDVSAVPGVAMELGVNDYSSAATSESV 539

Query: 562 HPTHYGRICPAETS---------------EGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                GRI    T                EG +   +     +   +  G     Y    
Sbjct: 540 VVMLDGRIIGWCTPNAAKAVADNLRRWKVEGGHGIPILLEIGYVPPSKGGSYPGIYMSSQ 599

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
             ++   V YL   +E+  ++               E++                  ++ 
Sbjct: 600 SSRMVRPVKYLPLGKED--FVGPHEQPYMSIACTDGEVLPG------------DSTHVEF 645

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 646 DPTHILSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 682


>gi|183579265|gb|ACC63210.1| RpoB [Mycobacterium phlei]
          Length = 221

 Score =  280 bits (717), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 98/226 (43%), Positives = 130/226 (57%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G KI+      K               
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWKIEGDPEWAKN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                             +     + +    V+TPVFDGA EE +  +L     +      
Sbjct: 133  -----------------LPEDLREAEPNSIVATPVFDGAREEELQGLLSSTLPNRDGEQM 175

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 176  VDGDGKAVLYDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 221


>gi|223928146|gb|ACN23841.1| RNA polymerase beta subunit [Bartonella sp. TT0105]
          Length = 298

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 217/299 (72%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E+VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 EAVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|3668171|dbj|BAA33445.1| RNA polymerase I second-largest subunit [Neurospora crassa]
          Length = 1234

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 106/497 (21%), Positives = 169/497 (34%), Gaps = 65/497 (13%)

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             E  + SI   E EV+  D     E    +I ++        D         +   G   
Sbjct: 670  QEQPYMSIACTEQEVIPGD-STHVEFDPTNILSILANMTPFSDFNQSPRNMYQCQMGKQT 728

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +G            +   L+             +    +  +G    V + +  G D ++
Sbjct: 729  MGTPATALAHRTDNKMYRLQTGQTPVVRAPLHNTYGFDNFPNGMNAVVAVISYTGYDMDD 788

Query: 955  RSISVEREQIELLA--RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD- 1011
              I  +               ++V L  +  +R  + +      +     ++ST    D 
Sbjct: 789  AMILNKSAHERGFGHGSIYKTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDMLDN 848

Query: 1012 --------LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    L+ E      W     D   Q         YE      ED F  ++  I   
Sbjct: 849  DGLPRVGRLLREGDVICAWHTVSADYNGQLVNRDGVTHYERY-KDSEDAFVEEVRVIGAD 907

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +   P  L+ V + + + R    GDK + RHG KG++S+  P  DMPF + G   D+++N
Sbjct: 908  NGTEP--LQTVSIKLRIPRSPVIGDKFSSRHGQKGVLSQKWPATDMPFSETGIQPDVIIN 965

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSRM +G   E+  G A    G    S    +                        
Sbjct: 966  PHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFDEQNTAG----------------- 1008

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                             +     L  A  +  G   LY G+TGE
Sbjct: 1009 ---------------------------------DYFGHQLMKAGYNYHGNEPLYSGITGE 1035

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F   + +G +Y  +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + 
Sbjct: 1036 EFQADIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKGRKKGGGIRVGEMERDALL 1095

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G +++LQ+ L   SD
Sbjct: 1096 AHGTSFLLQDRLLNCSD 1112



 Score = 68.6 bits (166), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 78/542 (14%), Positives = 164/542 (30%), Gaps = 79/542 (14%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           ++ +    + D  +     +   ++ + + L  L  G   +D+ D + N+ +   G    
Sbjct: 352 KIVLVHLGSQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLYG 411

Query: 469 --------EMLKNQYRLG---LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                   E+L   +R      LR   ++  +  +   D  +       + +  ++  F 
Sbjct: 412 QIIKERLEELLTVSFRASLRDYLRRNPTVSFQSDTFLKDFPIAIFRRANENIGQSLEYFL 471

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N L  I+H R    + +G          +R + P
Sbjct: 472 STGNLVSPSGLDLQQVSGFTVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTVRKLLP 528

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTND--------- 613
             +G +CP  T +G   GL++ L    ++        T  R   +  V N          
Sbjct: 529 ESWGFLCPVHTPDGSPCGLLNHLAHKCKIMTESVDASTISRLAFELGVVNISSAATSESV 588

Query: 614 VVYLS------AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           VV L          EE + IA+       +G     L       E   VP          
Sbjct: 589 VVMLDGRIVGWCTPEECKSIAETLRYWKVNGENGVPL-----QLEIGYVPPSNGGSYPG- 642

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSG 724
              + S  A ++  ++     +       ++  + +   E   +    T +E        
Sbjct: 643 -LYMSSQPARMVRPVKYLPLQKEDFVGPQEQPYMSIACTEQEVIPGDSTHVEFDPTNILS 701

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                       Q        +  +  +    + +      K  R        Q P+V+ 
Sbjct: 702 ILANMTPFSDFNQSPRNMYQCQMGKQTMGTPATALAHRTDNKMYRLQTG----QTPVVRA 757

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                         +    +   G N +VA + + GY+ +D+M++++             
Sbjct: 758 ----------PLHNTYGFDNFPNGMNAVVAVISYTGYDMDDAMILNKSAHERGFGHGSIY 807

Query: 845 EEFEVMARDTKLGP-------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +  +V  +D                     + E     +D  G+  VG  +  GD++   
Sbjct: 808 KTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDMLDNDGLPRVGRLLREGDVICAW 867

Query: 898 IT 899
            T
Sbjct: 868 HT 869



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 99/753 (13%), Positives = 208/753 (27%), Gaps = 143/753 (18%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAA----FKSVFPITAFSGA--AMLEFVSYEFDP 83
           ++    S++     +  P    +  L       F          G     + + S E   
Sbjct: 43  VDPHIESFNALFRDDGKPSL-LDHALAEIGTKTFLDGDERADPQGKNKLTIRYKSIELQK 101

Query: 84  ----P--------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
               P        +    +C  R ++Y   L  T    + D +     +           
Sbjct: 102 SQVPPTNRWAKNREIFPAECRERHVSYRGKLSATFEYRINDGEPHEFVRE---------- 151

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH--RSPGIHF 165
           +G +P+M K                         G F++ GI++++   L   R+     
Sbjct: 152 LGQMPIMVKSNKCHLQNNSPAQLVARKEESEELGGYFIVNGIEKLIRMLLVNRRN---FP 208

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPV 214
                 +  +    Y    I  + +  D E    +++H         R   R+    +PV
Sbjct: 209 LAIVRPSFQNRGASYTPYGIIMRSVRPD-ETSQTNVLHYLSDGNVTFRFSWRKNEYLIPV 267

Query: 215 TSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
              + AL   ++ EI                                             
Sbjct: 268 MMIMKALVETNDREIFEGLVGPPQSKASPTPSLTDRVEL--------------------- 306

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY-----VAEDIVNGETGEIYIEAGDVI 328
                     LL++ K+ G+     T   L   +     V + + + E G  ++    ++
Sbjct: 307 ----------LLRTYKKYGLYSKTQTRAYLGQKFRVVLGVPDTMSDYEVGTEFLRKIVLV 356

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
              S +     +     +L        A +      D     ++  + +   +  G +  
Sbjct: 357 HLGSQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLY-GQIIK 415

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
             + E +          Y          +     D P  +     E+I   ++  +   N
Sbjct: 416 ERLEELLTVSFRASLRDYLRRNPTVSFQSDTFLKDFPIAIFRRANENIGQSLEYFLSTGN 475

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINA 506
              +   +D         V E L     +   RM    S   ++ +  +  ++P+     
Sbjct: 476 -LVSPSGLDLQQVSGFTVVAEKLNFLRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFL 534

Query: 507 KPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            PV +         + L+   + +      +   RL+   + GV    +      V    
Sbjct: 535 CPVHTPDGSPCGLLNHLAHKCKIMTESVDASTISRLAF--ELGVVNISSAATSESVVVML 592

Query: 566 YGRICPAETSE---------------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            GRI    T E               G N   +     +   +  G     Y      ++
Sbjct: 593 DGRIVGWCTPEECKSIAETLRYWKVNGENGVPLQLEIGYVPPSNGGSYPGLYMSSQPARM 652

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              V YL   +E+  ++              +E++                  ++  P  
Sbjct: 653 VRPVKYLPLQKED--FVGPQEQPYMSIACTEQEVIPG------------DSTHVEFDPTN 698

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 699 ILSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 731


>gi|302785610|ref|XP_002974576.1| hypothetical protein SELMODRAFT_101823 [Selaginella moellendorffii]
 gi|300157471|gb|EFJ24096.1| hypothetical protein SELMODRAFT_101823 [Selaginella moellendorffii]
          Length = 692

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 99/455 (21%), Positives = 160/455 (35%), Gaps = 47/455 (10%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              D         +   G   +G  +   +     +   L+      A +V      +   
Sbjct: 210  WSDHNQSPRNMYQCQMGKQTLGFASQALKFRTDHKMYNLQNPQSPVARNVNYKKYNMDEF 269

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
              GT   V +    G D  +  I  +      LA  +  +   +D ++  +  + +    
Sbjct: 270  PLGTNAVVAVLAYTGFDMEDAMIMNKSSMERGLAHGQIYKTEHVDLSLLQKKSDGIVNLF 329

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK-SILEDRF 1053
            +               + +         Q     +     + ++    +  K    E+  
Sbjct: 330  SR------PTGKRNIHNFLDVDGLPHIGQTMHNGDPYCSVLNTMTGDAKLHKLKAAENVV 383

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             + +  I  G       L+ + V     R    GDK + RHG KGI+S++ P  DMPF  
Sbjct: 384  IDSVIAIGHGR----DPLQKIAVKFRHDRNPVIGDKFSSRHGQKGILSQLWPDIDMPFSA 439

Query: 1114 -DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
              G   DI++NP   PSRM +G + E+    A V  G+ + S      +    +      
Sbjct: 440  VTGMRPDIIINPHAFPSRMTIGMLMESMAAKAGVLRGEYVDSTPFRSSSAALEAKDGKTG 499

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                G   H   IS                                    L     +  G
Sbjct: 500  SGYKGKDKHYPAIS-------------------------------EFGEQLAQHGFNYHG 528

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ++Y GL G      + +G +Y  +L HMVSDK   RS G+ + VT+QP+GG+   GG 
Sbjct: 529  TEVMYSGLLGTELTCEIFIGVVYYQRLRHMVSDKFQVRSLGAINPVTRQPVGGRKLGGGI 588

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV 1323
            R GEME   + A+GAAY+L + L   SD    DV 
Sbjct: 589  RFGEMERDSLLAHGAAYLLHDRLHTSSDYHVGDVC 623



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 60/395 (15%), Positives = 125/395 (31%), Gaps = 51/395 (12%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +  S + E +N    I+H R   ++ +G     +    +R + P  +G +CP  T +G  
Sbjct: 1   NGFSVVAEKLNFFRFISHFR---SVHRGAFFARQRTTSVRKLLPESWGFLCPVHTPDGEP 57

Query: 580 IGLVSSLTSFARV-------NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE----NRYIA 628
            GL++ L+S  ++       N     +  +R +        +V +S +            
Sbjct: 58  CGLLTHLSSLCKISTDLDQNNHPKDPKVIHRTIATVLAQLGMVSISPLLALSGPPKYLAV 117

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
             +  +                 E   VP     +  A P   +    S        +  
Sbjct: 118 LLDGCVLGYMPVGNIPQTVPIDLEIGYVP---CTYAGAYPGLFLYTTPSRFLRPAYMEIA 174

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
               G   +  + P          T +E               A +    D  +      
Sbjct: 175 CPDGGNCGRTPSAPP--------ATHIELHPTAMLSVV-----ASLTPWSDHNQSPRNMY 221

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLA 806
           +  +   T G    + +KF R++      Q P   V      ++          ++ +  
Sbjct: 222 QCQMGKQTLGFAS-QALKF-RTDHKMYNLQNPQSPVARNVNYKK---------YNMDEFP 270

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD-----TKLGPEEI 861
           LG N +VA + + G++ ED+M++++  +   +    H + ++    D      K      
Sbjct: 271 LGTNAVVAVLAYTGFDMEDAMIMNKSSMERGLA---HGQIYKTEHVDLSLLQKKSDGIVN 327

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               P         +D  G+  +G  ++ GD    
Sbjct: 328 LFSRPTGKRNIHNFLDVDGLPHIGQTMHNGDPYCS 362


>gi|269930829|gb|ACZ54149.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 217/299 (72%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|85115172|ref|XP_964824.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Neurospora crassa
            OR74A]
 gi|51704242|sp|O74633|RPA2_NEUCR RecName: Full=DNA-directed RNA polymerase I subunit RPA2; AltName:
            Full=DNA-directed RNA polymerase I polypeptide 2;
            Short=RNA polymerase I subunit 2
 gi|28926619|gb|EAA35588.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Neurospora crassa
            OR74A]
          Length = 1234

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 106/497 (21%), Positives = 169/497 (34%), Gaps = 65/497 (13%)

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             E  + SI   E EV+  D     E    +I ++        D         +   G   
Sbjct: 670  QEQPYMSIACTEQEVIPGD-STHVEFDPTNILSILANMTPFSDFNQSPRNMYQCQMGKQT 728

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +G            +   L+             +    +  +G    V + +  G D ++
Sbjct: 729  MGTPATALAHRTDNKMYRLQTGQTPVVRAPLHNTYGFDNFPNGMNAVVAVISYTGYDMDD 788

Query: 955  RSISVEREQIELLA--RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD- 1011
              I  +               ++V L  +  +R  + +      +     ++ST    D 
Sbjct: 789  AMILNKSAHERGFGHGSIYKTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDMLDN 848

Query: 1012 --------LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    L+ E      W     D   Q         YE      ED F  ++  I   
Sbjct: 849  DGLPRVGRLLREGDVICAWHTVSADYNGQLVNRDGVTHYERY-KDSEDAFVEEVRVIGAD 907

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +   P  L+ V + + + R    GDK + RHG KG++S+  P  DMPF + G   D+++N
Sbjct: 908  NGTEP--LQTVSIKLRIPRSPVIGDKFSSRHGQKGVLSQKWPATDMPFSETGIQPDVIIN 965

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSRM +G   E+  G A    G    S    +                        
Sbjct: 966  PHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFDEQNTAG----------------- 1008

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                             +     L  A  +  G   LY G+TGE
Sbjct: 1009 ---------------------------------DYFGHQLMKAGYNYHGNEPLYSGITGE 1035

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F   + +G +Y  +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + 
Sbjct: 1036 EFQADIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKGRKKGGGIRVGEMERDALL 1095

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G +++LQ+ L   SD
Sbjct: 1096 AHGTSFLLQDRLLNCSD 1112



 Score = 68.9 bits (167), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 88/607 (14%), Positives = 179/607 (29%), Gaps = 85/607 (14%)

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                   +      DR + LL  Y+         T +     F  +    D      VG
Sbjct: 287 VGPPQSKGVANTFLTDRVELLLRTYKKYGLYSKTQTRAYLGQKFRVVLGVPDTMSDYEVG 346

Query: 413 -----RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                ++ +    + D  +     +   ++ + + L  L  G   +D+ D + N+ +   
Sbjct: 347 TEFLRKIVLVHLGSQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLG 406

Query: 468 G------------EMLKNQYRLG---LLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           G            E+L   +R      LR   ++  +  +   D  +       + +  +
Sbjct: 407 GFLYGQIIKERLEELLTVSFRASLRDYLRRNPTVSFQSDTFLKDFPIAIFRRANENIGQS 466

Query: 513 VCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           +  F  +  L              + + E +N L  I+H R    + +G          +
Sbjct: 467 LEYFLSTGNLVSPSGLDLQQVSGFTVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTV 523

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTND---- 613
           R + P  +G +CP  T +G   GL++ L    ++        T  R   +  V N     
Sbjct: 524 RKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCKIMTESVDASTISRLAFELGVVNISSAA 583

Query: 614 -----VVYLS------AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                VV L          EE + IA+       +G     L       E   VP     
Sbjct: 584 TSESVVVMLDGRIVGWCTPEECKSIAETLRYWKVNGENGVPL-----QLEIGYVPPSNGG 638

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVV 719
                   + S  A ++  ++     +       ++  + +   E   +    T +E   
Sbjct: 639 SYPG--LYMSSQPARMVRPVKYLPLQKEDFVGPQEQPYMSIACTEQEVIPGDSTHVEFDP 696

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                            Q        +  +  +    + +      K  R        Q 
Sbjct: 697 TNILSILANMTPFSDFNQSPRNMYQCQMGKQTMGTPATALAHRTDNKMYRLQTG----QT 752

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+V+               +    +   G N +VA + + GY+ +D+M++++        
Sbjct: 753 PVVRA----------PLHNTYGFDNFPNGMNAVVAVISYTGYDMDDAMILNKSAHERGFG 802

Query: 840 TSIHIEEFEVMARDTKLGP-------EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
                +  +V  +D                     + E     +D  G+  VG  +  GD
Sbjct: 803 HGSIYKTKKVSLKDDSRTRSAKSIVKMFGFAPNSTIRESTRDMLDNDGLPRVGRLLREGD 862

Query: 893 ILVGKIT 899
           ++    T
Sbjct: 863 VICAWHT 869



 Score = 68.6 bits (166), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 98/752 (13%), Positives = 214/752 (28%), Gaps = 141/752 (18%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAA----FKSVFPITAFSGA--AMLEFVSYEFDP 83
           ++    S++     +  P    +  L       F          G     + + S E   
Sbjct: 43  VDPHIESFNALFRDDGKPSL-LDHALAEIGTKTFLDGDERADPQGKNKLTIRYKSIELQK 101

Query: 84  ----P--------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
               P        +    +C  R ++Y   L  T    + D +     +           
Sbjct: 102 SQVPPTNRWAKNREIFPAECRERHVSYRGKLSATFEYRINDGEPHEFVRE---------- 151

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH--RSPGIHF 165
           +G +P+M K                         G F++ GI++++   L   R+     
Sbjct: 152 LGQMPIMVKSNKCHLQNNSPAQLVARKEESEELGGYFIVNGIEKLIRMLLVNRRN---FP 208

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPV 214
                 +  +    Y    I  + +  D E    +++H         R   R+    +PV
Sbjct: 209 LAIVRPSFQNRGASYTPYGIIMRSVRPD-ETSQTNVLHYLSDGNVTFRFSWRKNEYLIPV 267

Query: 215 TSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
              + AL +++ +     +  +V   +            + +                  
Sbjct: 268 MMIMKAL-VETND--REIFEGLVGPPQSKGVANTFLTDRVEL------------------ 306

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY-----VAEDIVNGETGEIYIEAGDVID 329
                    LL++ K+ G+     T   L   +     V + + + E G  ++    ++ 
Sbjct: 307 ---------LLRTYKKYGLYSKTQTRAYLGQKFRVVLGVPDTMSDYEVGTEFLRKIVLVH 357

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
             S +     +     +L        A +      D     ++  + +   +  G +   
Sbjct: 358 LGSQDVTEQQDADKFNMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLY-GQIIKE 416

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            + E +          Y          +     D P  +     E+I   ++  +   N 
Sbjct: 417 RLEELLTVSFRASLRDYLRRNPTVSFQSDTFLKDFPIAIFRRANENIGQSLEYFLSTGN- 475

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAK 507
             +   +D         V E L     +   RM    S   ++ +  +  ++P+      
Sbjct: 476 LVSPSGLDLQQVSGFTVVAEKLNFLRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLC 535

Query: 508 PVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           PV +         + L+   + +      +   RL+   + GV    +      V     
Sbjct: 536 PVHTPDGSPCGLLNHLAHKCKIMTESVDASTISRLAF--ELGVVNISSAATSESVVVMLD 593

Query: 567 GRICPAETSE---------------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
           GRI    T E               G N   +     +   +  G     Y      ++ 
Sbjct: 594 GRIVGWCTPEECKSIAETLRYWKVNGENGVPLQLEIGYVPPSNGGSYPGLYMSSQPARMV 653

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V YL   +E+  ++              +E++                  ++  P  +
Sbjct: 654 RPVKYLPLQKED--FVGPQEQPYMSIACTEQEVIPG------------DSTHVEFDPTNI 699

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +SI A++ PF + + S R +  C M +Q +  
Sbjct: 700 LSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 731


>gi|219958092|gb|ACL68100.1| DNA-directed RNA polymerase beta subunit [Mycobacterium wolinskyi]
          Length = 232

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 128/226 (56%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +        ++
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPDWASKLPE------QL 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                + +                       VSTPVFDGA E  +  +L            
Sbjct: 149  YSAPADSI----------------------VSTPVFDGAQEGELQGLLGSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 187  VDADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 232



 Score = 41.6 bits (96), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 44


>gi|300120856|emb|CBK21098.2| unnamed protein product [Blastocystis hominis]
 gi|300175006|emb|CBK20317.2| unnamed protein product [Blastocystis hominis]
          Length = 1151

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 114/278 (41%), Gaps = 50/278 (17%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +TS    +      +++++  D  P   ++ V +     R    GDK + RHG KG++S 
Sbjct: 841  KTSLRFHDSSEPAYVDEVRILDGDPALGVQRVNIKFRYNRNPVVGDKFSSRHGQKGVLSV 900

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            + P  DMPF   G   D ++NP   PSRM +G + E+  G +    G+ + +    +   
Sbjct: 901  LWPQIDMPFTASGITPDCIINPNAFPSRMTIGMLIESMAGKSGALHGQYMDATPFQFSEK 960

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                                  +     
Sbjct: 961  QCA--------------------------------------------------VDFFGEQ 970

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L+ A  +  G   LY G+ G+  +  + +G +Y  +L HMVSDK   R+ G  + +T+QP
Sbjct: 971  LKAAGFNYYGSEPLYSGIWGDLLEADIYIGVVYYQRLRHMVSDKSQVRANGPINQLTRQP 1030

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            L G+   GG R GEME   I A+GA+++L E L   SD
Sbjct: 1031 LKGRKRHGGIRFGEMERDSIIAHGASFLLHERLLNSSD 1068



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 108/773 (13%), Positives = 230/773 (29%), Gaps = 154/773 (19%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT----AFSGAAMLEFVSYEFDP 83
           DL+     SY+  L          ++GL  A + +FP+            +     +   
Sbjct: 37  DLVRFHIESYNFML----------DKGLSLAVRDIFPLEVENPDNKQVLRIWIQDVKIGY 86

Query: 84  PKFD---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           P  +           +C  R ++Y  PL   +   V D       ++          +G 
Sbjct: 87  PIKEDGSSETRLLPHECRERGISYTSPLIAYVAHQVNDGQIVVTERN----------LGQ 136

Query: 135 LPL-----------MTK-------------DGTFVIKGIQRIV----VSQLHRSPGIHFD 166
           LP+           MT               G F+  G++R++    V++ H    I   
Sbjct: 137 LPIMVGSNRCHLSRMTPAERVNCGEEVYELGGYFICNGLERMIRLLQVTRRH----IIVA 192

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-------RK----VPVT 215
            D+   +  G   Y       + +  D+   +  + ++R D R       RK    VPV 
Sbjct: 193 LDRPSFTKRGPE-YTSLGCQMKCVREDMSSMTVTLHYLR-DGRCTLRWFIRKQEFLVPVV 250

Query: 216 SFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             L AL      EI                      +  L +  + S ++      E + 
Sbjct: 251 LILKALKDCSDREIYE--------QLMRGDSNNTFLSDRLELLLRESKNMHLTTRRECLA 302

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
             G +    L  S +   V+      + L   Y+   + +        EA   +  + + 
Sbjct: 303 YLGSRFRILLYMSSRYSDVEV----GEELLKRYILVHLKSN-------EAKFALLLEMIS 351

Query: 335 EIFHSEIRDIPILYVDSVNNNAYI--RNTLVTDKNKDRKDALLDIYRVM-----RPGDVS 387
           +++    ++IP    DS+ N+  +   + +     +  ++ L+ + + +     R  +  
Sbjct: 352 KLYKLANKEIPPDNADSLMNHELLLGGHLMCMFLKEKLEEFLIGVRQNIAREVDRHKEKI 411

Query: 388 ----TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               T  + +++          Y L   G +  +  L+L        +   + +   + L
Sbjct: 412 DLYDTAWIKKALDRQSDIGKKAYYLLATGNIISSTGLDLQQAAGYTIV--AEKLNHWRYL 469

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQD 502
              R+    +         +     ++L + +  L  +         + +    +     
Sbjct: 470 SHFRS----VHRGQFFTEMKTTQPRKLLPDSWGFLCCVHTPDGAPCGLLNHLTATCSITT 525

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH----TRRLSALGQGGVARARAGVEM 558
            +   P ++ +C+            + N    +        R+ A            +++
Sbjct: 526 DVVPAPQLARLCQALGLVPADSPLVYGNHYVPVFFNGQLLGRVLAAQAAAFCDQLRLLKL 585

Query: 559 RDVH-PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
                P     +C     +G     V   T  AR+                  T    ++
Sbjct: 586 DGAKLPACLEIVCVPAGEQGGPWPCVYLSTDAARMQRP----------VRHLGTGKTEWI 635

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +E+    IA     + +                           I+ SP  ++S+ AS
Sbjct: 636 GPLEQVYLEIACVEEDIRKG----------------------VTTHIEVSPANMLSLIAS 673

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLK-AEAPFVGTGMESVVAKSSGAAIVA 729
           L PF + + S R +  C M +Q +     +      T M  +    +     A
Sbjct: 674 LTPFSDFNQSPRNMYQCQMGKQTMGTPGLSWTHRTDTKMYRLQTPQAPIVHNA 726


>gi|227937614|gb|ACP43382.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930929|gb|ACZ54199.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930933|gb|ACZ54201.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|269930871|gb|ACZ54170.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930873|gb|ACZ54171.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930875|gb|ACZ54172.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930905|gb|ACZ54187.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930909|gb|ACZ54189.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930911|gb|ACZ54190.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930913|gb|ACZ54191.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 297

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 216/298 (72%), Positives = 252/298 (84%), Gaps = 1/298 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 297


>gi|238883229|gb|EEQ46867.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Candida albicans
            WO-1]
          Length = 1166

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 96/476 (20%), Positives = 162/476 (34%), Gaps = 61/476 (12%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +  +     E    +I ++        D         +   G   +G           
Sbjct: 654  EEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSD 713

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL- 966
             +   L+                + +  +G    V + +  G D ++ ++ + +   E  
Sbjct: 714  NKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDD-AMIINKSADERG 772

Query: 967  --LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                     E+V L ++   R   I       S          L +D +         + 
Sbjct: 773  FGYGTVYKTEKVDLSQSRR-RGDPITQHFGFGSDEWPEAWKEKLDADGLPLIG----VKV 827

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D  V    ++L      +    E  +  +++ +  GDD      + + +   + R  
Sbjct: 828  EEGDPIVAYYDDTLGKTKVKTYHSSEPAYIEEVKLL--GDDSNEQEGQQITIKYRITRQP 885

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A
Sbjct: 886  LIGDKFSSRHGQKGVCSRKWPQIDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKA 945

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G    S    +                                             
Sbjct: 946  GALHGIAQDSTPWKFNEQD----------------------------------------- 964

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP       +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+
Sbjct: 965  ---TPA------DYFGEQLLKAGYNYHGNEPMYSGATGEELRCDIYIGCVYYQRLRHMVN 1015

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1016 DKFQVRSTGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1071



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 81/590 (13%), Positives = 176/590 (29%), Gaps = 61/590 (10%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  + N        DR + LL  Y+   +     +   + +          D  D
Sbjct: 266 DREIFDGIVGNDTENSFLTDRLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASPDMSD 325

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  VG+  +   + +  P++    +   ++ +I+ L  L  G    D+ D   ++ V   
Sbjct: 326 IE-VGKEVLKRIVLVHLPNNAD--KFRMLLFMIRKLYSLVAGDCAPDNPDATQHQEVLLG 382

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFF 517
           G +     +  +    ++IK +I S     V                    +   +  F 
Sbjct: 383 GFLYGMIIKEKIEEYLQNIKLQIQSDINRGVGINFDDRKYMTRVFSRINENIGQKLQYFL 442

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 443 STGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLP 499

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ L+   ++       +   K             +A    
Sbjct: 500 ESWGFLCPVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQLGVLPADSFAAGP-- 557

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQVV 672
           N    Q +  +    +  +  +         +          +I ++  S     P   +
Sbjct: 558 NLCCVQLDGKIVGWTTHEQGRIVADTLRYWKVNGGHGLPLDLEIGYVPPSNKGQYPGLYI 617

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
               S +                   Q    +      +   + S   + +   I++  A
Sbjct: 618 FGGHSRMMRPVKYLPLDKEDIVGPFEQVYMNVAVTPEEIENNIHS-HVEFTPTNILSILA 676

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    D  +      +  +   T G      + +           Q P+VK        
Sbjct: 677 NLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSDNKLYRLQTGQTPIVKANLYDDYG 736

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                     + +   G N +VA + + GY+ +D+M+I++             +  +V  
Sbjct: 737 ----------MDNFPNGMNAIVAVISYTGYDMDDAMIINKSADERGFGYGTVYKTEKVDL 786

Query: 852 ----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               R      +          E   + +D  G+  +G +V  GD +V  
Sbjct: 787 SQSRRRGDPITQHFGFGSDEWPEAWKEKLDADGLPLIGVKVEEGDPIVAY 836



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 100/762 (13%), Positives = 215/762 (28%), Gaps = 97/762 (12%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   L + +   V D +E      + +++E     G +P+M K       
Sbjct: 105 PSECRERMVTYRSRLMLNVTWSVNDGEE------VSEVREA----GQIPIMLKSNRCHLE 154

Query: 142 ------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLS----G 176
                             G F++ GI++++   + Q    P        G    S    G
Sbjct: 155 KLSPNQLVEAKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFGNRGASYTKFG 214

Query: 177 KLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
             + + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 215 IQIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEFLVPVVMILKAL-IETND--R 267

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             +  IV +   + +        L+   K  +     +T   + +  + +          
Sbjct: 268 EIFDGIVGNDTENSFLTD-RLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASP----- 321

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +  + +  + L  + +     N +   + +    +    SL     +        + +
Sbjct: 322 -DMSDIEVGKEVLKRIVLVHLPNNADKFRMLL--FMIRKLYSLVAGDCAPDNPDATQHQE 378

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         +     +  ++  L I   +  G V            +F   ++     
Sbjct: 379 VLLGGFLYGMIIKEKIEEYLQNIKLQIQSDINRG-VGINFDDRKYMTRVFSRINENIGQK 437

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +        L   +  D++ +    ++A         +    +         +  +V ++
Sbjct: 438 LQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAELKTTTVRKL 497

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                      ++       K    A         L+Q    + 
Sbjct: 498 LPESWGFLC-------PVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQ-LGVLP 549

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           + S             G +       + R V  T    +   + + GH + L   +  + 
Sbjct: 550 ADSFAAGPNLCCVQLDGKIVGWTTHEQGRIVADT----LRYWKVNGGHGLPLDLEIG-YV 604

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
             +  G     Y      ++   V YL   +E+   +               E V+   A
Sbjct: 605 PPSNKGQYPGLYIFGGHSRMMRPVKYLPLDKED--IVGPF------------EQVYMNVA 650

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                +       ++ +P  ++SI A+L PF + + S R +  C M +Q +         
Sbjct: 651 VTPEEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGT--PGTAL 708

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           V      +    +G   + K     +            I +V            I     
Sbjct: 709 VHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDDAMIINKSA 768

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +R      V +   V +    RR D I         +    
Sbjct: 769 DERGFGYGTVYKTEKVDLSQSRRRGDPITQHFGFGSDEWPEA 810


>gi|227937618|gb|ACP43384.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 219/299 (73%), Positives = 254/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|227937584|gb|ACP43367.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930917|gb|ACZ54193.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 219/299 (73%), Positives = 254/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|169792074|gb|ACA80327.1| RpoB [Fusobacterium nucleatum]
 gi|169792078|gb|ACA80329.1| RpoB [Fusobacterium nucleatum]
 gi|169792080|gb|ACA80330.1| RpoB [Fusobacterium nucleatum]
 gi|169792108|gb|ACA80344.1| RpoB [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
 gi|206967389|gb|ACI22675.1| RpoB [Fusobacterium nucleatum subsp. fusiforme]
          Length = 143

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 89/195 (45%), Positives = 108/195 (55%), Gaps = 52/195 (26%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRMN+GQ+ E HLG A        
Sbjct: 1    RHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMR------ 54

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  ++TPVFD
Sbjct: 55   ----------------------------------------------SLNGGTCIATPVFD 68

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA EE +   L       +G+  LYDG TGE FD  VTVG +YMLKL+H+V DK++AR+ 
Sbjct: 69   GATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTVGIMYMLKLHHLVEDKMHARAI 128

Query: 1273 GSYSLVTQQPLGGKS 1287
            G YSLVTQQPLGGK+
Sbjct: 129  GPYSLVTQQPLGGKA 143


>gi|315435606|gb|ADU18193.1| RNA polymerase beta-subunit [Mycobacterium peregrinum]
          Length = 230

 Score =  280 bits (716), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 125/226 (55%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 34   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 93

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 94   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 151  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 184

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 185  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 230


>gi|269930867|gb|ACZ54168.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 299

 Score =  280 bits (715), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 216/299 (72%), Positives = 252/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+ 
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSN 298


>gi|68471155|ref|XP_720354.1| hypothetical protein CaO19.7062 [Candida albicans SC5314]
 gi|77022490|ref|XP_888689.1| hypothetical protein CaO19_7062 [Candida albicans SC5314]
 gi|46442218|gb|EAL01509.1| hypothetical protein CaO19.7062 [Candida albicans SC5314]
 gi|76573502|dbj|BAE44586.1| hypothetical protein [Candida albicans]
          Length = 1166

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 96/476 (20%), Positives = 162/476 (34%), Gaps = 61/476 (12%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +  +     E    +I ++        D         +   G   +G           
Sbjct: 654  EEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSD 713

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL- 966
             +   L+                + +  +G    V + +  G D ++ ++ + +   E  
Sbjct: 714  NKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDD-AMIINKSADERG 772

Query: 967  --LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                     E+V L ++   R   I       S          L +D +         + 
Sbjct: 773  FGYGTVYKTEKVDLSQSRR-RGDPITQHFGFGSDEWPEAWKEKLDADGLPLIG----VKV 827

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D  V    ++L      +    E  +  +++ +  GDD      + + +   + R  
Sbjct: 828  EEGDPIVAYYDDTLGKTKVKTYHSSEPAYIEEVKLL--GDDSNEQEGQQITIKYRITRQP 885

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A
Sbjct: 886  LIGDKFSSRHGQKGVCSRKWPQIDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKA 945

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G    S    +                                             
Sbjct: 946  GALHGIAQDSTPWKFNEQD----------------------------------------- 964

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP       +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+
Sbjct: 965  ---TPA------DYFGEQLLKAGYNYHGNEPMYSGATGEELRCDIYIGCVYYQRLRHMVN 1015

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1016 DKFQVRSTGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1071



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 100/762 (13%), Positives = 215/762 (28%), Gaps = 97/762 (12%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   L + +   V D +E      + +++E     G +P+M K       
Sbjct: 105 PSECRERMVTYRSRLMLNVTWSVNDEEE------VSEVREA----GQIPIMLKSNRCHLE 154

Query: 142 ------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLS----G 176
                             G F++ GI++++   + Q    P        G    S    G
Sbjct: 155 KLSPNQLVEAKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFGNRGASYTKFG 214

Query: 177 KLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
             + + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 215 IQIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEFLVPVVMILKAL-IETND--R 267

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             +  IV +   + +        L+   K  +     +T   + +  + +          
Sbjct: 268 EIFDGIVGNDTENSFLTD-RLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASP----- 321

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +  + +  + L  + +     N +   + +    +    SL     +        + +
Sbjct: 322 -DMSDIEVGKEVLKRIVLVHLPNNADKFRMLL--FMIRKLYSLVAGDCAPDNPDATQHQE 378

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         +     +  ++  L I   +  G V            +F   ++     
Sbjct: 379 VLLGGFLYGMIIKEKIEEYLQNIKLQIQSDINRG-VGINFDDRKYMTRVFSRINENIGQK 437

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +        L   +  D++ +    ++A         +    +         +  +V ++
Sbjct: 438 LQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAELKTTTVRKL 497

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                      ++       K    A         L+Q    + 
Sbjct: 498 LPESWGFLC-------PVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQ-LGVLP 549

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           + S             G +       + R V  T    +   + + GH + L   +  + 
Sbjct: 550 ADSFAAGPNLCCVQLDGKIVGWTTHEQGRIVADT----LRYWKVNGGHGLPLDLEIG-YV 604

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
             +  G     Y      ++   V YL   +E+   +               E V+   A
Sbjct: 605 PPSNKGQYPGLYIFGGHSRMMRPVKYLPLDKED--IVGPF------------EQVYMNVA 650

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                +       ++ +P  ++SI A+L PF + + S R +  C M +Q +         
Sbjct: 651 VTPEEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGT--PGTAL 708

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           V      +    +G   + K     +            I +V            I     
Sbjct: 709 VHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDDAMIINKSA 768

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +R      V +   V +    RR D I         +    
Sbjct: 769 DERGFGYGTVYKTEKVDLSQSRRRGDPITQHFGFGSDEWPEA 810



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 81/590 (13%), Positives = 176/590 (29%), Gaps = 61/590 (10%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  + N        DR + LL  Y+   +     +   + +          D  D
Sbjct: 266 DREIFDGIVGNDTENSFLTDRLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASPDMSD 325

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  VG+  +   + +  P++    +   ++ +I+ L  L  G    D+ D   ++ V   
Sbjct: 326 IE-VGKEVLKRIVLVHLPNNAD--KFRMLLFMIRKLYSLVAGDCAPDNPDATQHQEVLLG 382

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFF 517
           G +     +  +    ++IK +I S     V                    +   +  F 
Sbjct: 383 GFLYGMIIKEKIEEYLQNIKLQIQSDINRGVGINFDDRKYMTRVFSRINENIGQKLQYFL 442

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 443 STGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLP 499

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ L+   ++       +   K             +A    
Sbjct: 500 ESWGFLCPVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQLGVLPADSFAAGP-- 557

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQVV 672
           N    Q +  +    +  +  +         +          +I ++  S     P   +
Sbjct: 558 NLCCVQLDGKIVGWTTHEQGRIVADTLRYWKVNGGHGLPLDLEIGYVPPSNKGQYPGLYI 617

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
               S +                   Q    +      +   + S   + +   I++  A
Sbjct: 618 FGGHSRMMRPVKYLPLDKEDIVGPFEQVYMNVAVTPEEIENNIHS-HVEFTPTNILSILA 676

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    D  +      +  +   T G      + +           Q P+VK        
Sbjct: 677 NLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSDNKLYRLQTGQTPIVKANLYDDYG 736

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                     + +   G N +VA + + GY+ +D+M+I++             +  +V  
Sbjct: 737 ----------MDNFPNGMNAIVAVISYTGYDMDDAMIINKSADERGFGYGTVYKTEKVDL 786

Query: 852 ----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               R      +          E   + +D  G+  +G +V  GD +V  
Sbjct: 787 SQSRRRGDPITQHFGFGSDEWPEAWKEKLDADGLPLIGVKVEEGDPIVAY 836


>gi|269930931|gb|ACZ54200.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 297

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 217/298 (72%), Positives = 252/298 (84%), Gaps = 1/298 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 297


>gi|171696212|ref|XP_001913030.1| hypothetical protein [Podospora anserina S mat+]
 gi|170948348|emb|CAP60512.1| unnamed protein product [Podospora anserina S mat+]
          Length = 1234

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 97/497 (19%), Positives = 169/497 (34%), Gaps = 65/497 (13%)

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             E  + SI   E E++  D     E    +I ++        D         +   G   
Sbjct: 667  YEQPYMSIACVEQEIVPGD-STHVEFDPTNILSILANMTPFSDFNQSPRNMYQCQMGKQT 725

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +G            +   ++             +    +  +G    V + +  G D ++
Sbjct: 726  MGTPGAALAHRTDNKMYRIQTGQTPVVRSPLHNTYGFDNFPNGFNAVVAVISYTGYDMDD 785

Query: 955  RSISVEREQIELL---ARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
             ++ + +   E           +++ L  +  +R  +        +     + S     D
Sbjct: 786  -AMIINKSAHERGFGHGSIYKTKKISLKDDSRTRSSKTTTKMFGFAPGSPIRASDREMLD 844

Query: 1012 LISEYPRSQWWQ--------FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                    +  +          V  +   + V    + +       ED F  ++  I  G
Sbjct: 845  EDGLPYVGRLVREGDIIAAWHTVSADYSGKLVNRDGITHWERYKEAEDAFIEEVRVI--G 902

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
             D     L+ + + + + R    GDK + RHG KG+ S+  P  DMPF + G   D+++N
Sbjct: 903  SDTGNEPLQTLSIKLRVPRSPVIGDKFSSRHGQKGVCSQKWPAVDMPFSETGIQPDVIIN 962

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSRM +G   E+  G A    G    S    +      +                 
Sbjct: 963  PHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFSEENMAA----------------- 1005

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                             +     L  A  +  G   +Y G+TGE
Sbjct: 1006 ---------------------------------DYFGHQLMKAGYNYHGNEPMYSGITGE 1032

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F   + +G +Y  +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + 
Sbjct: 1033 EFMCDIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKGRKKGGGIRVGEMERDALL 1092

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G A++LQ+ L   SD
Sbjct: 1093 AHGTAFLLQDRLLNCSD 1109



 Score = 69.7 bits (169), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 88/656 (13%), Positives = 185/656 (28%), Gaps = 82/656 (12%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R ++Y   L   L   + + D     +           +G +P+M K       
Sbjct: 115 PAECRERHVSYRGKLTAVLEYRINNGDAHEFVRE----------LGQMPIMVKSNKCHLE 164

Query: 142 ------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
                             G FVI GI++ ++  L  +           +  +    Y   
Sbjct: 165 NNSPAQLVERKEESEELGGYFVINGIEK-IIRLLLMNKRNFPLAITRPSFTNRGPSYTPH 223

Query: 184 IIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE-EILST 231
            I  + +  D E    +++H         R   R+    VPV   L AL   ++ EI  +
Sbjct: 224 GIIVRSVRPD-ETSQTNVLHYLNDGNVTFRFSWRKNEYLVPVMMILKALVETNDREIFES 282

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
                      + +        L      + +L         +    ++  G+  ++ + 
Sbjct: 283 LVGPPTSKGVENTFLTDRVELLLRTYK--TYNLYTKKQTRAYLGQKFRVVLGVPDTMTDY 340

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            V    +    L  L   +     +T +  +         +L     +      +   + 
Sbjct: 341 EVGTEFLRKVVLVHLGCNDVTEEQDTDKFKMLLFMCRKLYALVAGDCAVDNPDAVQNQEI 400

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +         L          AL    R     + +   V+ES          +     +
Sbjct: 401 LLGGFLYGMILKERLEDLLSTALRGALRDHLRRNPTDSFVSESFRKQFPGHIFRKTNENI 460

Query: 412 GR----VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           G           L   +  D++ +    ++A     +   +    +         +  +V
Sbjct: 461 GNALEYFLSTGNLQSPSGLDLQQVSGFTVVAEKLNFLRFISHFRMVHRGSFFAQLKTTTV 520

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            ++L   +                      ++       K    A         L +L  
Sbjct: 521 RKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCKITTKAADVSAVPGVLLELG- 572

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            VN+ S    T  +  +  G V    A    + +  T    +   +   GH I L   + 
Sbjct: 573 -VNNYSSAATTESVVVMLDGKVVGWCAPQNAKPLADT----LRQLKVEGGHGIPLELEIG 627

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +   +  G     Y      ++   V YL+  +E+   +              +E+V  
Sbjct: 628 -YVPTSNGGSYPGIYMASNTSRMVRPVKYLALNKED--MVGPYEQPYMSIACVEQEIVPG 684

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                           ++  P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 685 ------------DSTHVEFDPTNILSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 728



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 75/537 (13%), Positives = 162/537 (30%), Gaps = 69/537 (12%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           +V +      D  ++    + + ++ + + L  L  G   +D+ D + N+ +   G    
Sbjct: 349 KVVLVHLGCNDVTEEQDTDKFKMLLFMCRKLYALVAGDCAVDNPDAVQNQEILLGGFLYG 408

Query: 469 --------EMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLI--NAKPVVSAVCEFF 517
                   ++L    R  L   + R+  +   S       P  +     + + +A+  F 
Sbjct: 409 MILKERLEDLLSTALRGALRDHLRRNPTDSFVSESFRKQFPGHIFRKTNENIGNALEYFL 468

Query: 518 CSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L                + E +N L  I+H R    + +G          +R + P
Sbjct: 469 STGNLQSPSGLDLQQVSGFTVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTVRKLLP 525

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++      ++       +    V      N+  Y SA   E
Sbjct: 526 ESWGFLCPVHTPDGSPCGLLNHFAHKCKITTKAADVSAVPGVLLELGVNN--YSSAATTE 583

Query: 624 NRYIAQANSSL----DEDGSFTEELVFCRCAGEEILVPRE-KIDFIDAS-----PKQVVS 673
           +  +      +     ++     + +          +P E +I ++  S     P   ++
Sbjct: 584 SVVVMLDGKVVGWCAPQNAKPLADTLRQLKVEGGHGIPLELEIGYVPTSNGGSYPGIYMA 643

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV----GTGMESVVAKSSGAAIVA 729
              S +       +           Q    +      +     T +E             
Sbjct: 644 SNTSRMVRPVKYLALNKEDMVGPYEQPYMSIACVEQEIVPGDSTHVEFDPTNILSILANM 703

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                  Q        +  +  +    + +      K  R        Q P+V+      
Sbjct: 704 TPFSDFNQSPRNMYQCQMGKQTMGTPGAALAHRTDNKMYRIQTG----QTPVVRS----- 754

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    +    +   G N +VA + + GY+ +D+M+I++             +  ++
Sbjct: 755 -----PLHNTYGFDNFPNGFNAVVAVISYTGYDMDDAMIINKSAHERGFGHGSIYKTKKI 809

Query: 850 MARD-------TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +D                     +     + +DE G+  VG  V  GDI+    T
Sbjct: 810 SLKDDSRTRSSKTTTKMFGFAPGSPIRASDREMLDEDGLPYVGRLVREGDIIAAWHT 866


>gi|169792058|gb|ACA80319.1| RpoB [Fusobacterium nucleatum]
 gi|169792064|gb|ACA80322.1| RpoB [Fusobacterium nucleatum]
 gi|169792070|gb|ACA80325.1| RpoB [Fusobacterium nucleatum]
 gi|169792104|gb|ACA80342.1| RpoB [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]
 gi|169792106|gb|ACA80343.1| RpoB [Fusobacterium nucleatum subsp. polymorphum ATCC 10953]
          Length = 143

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 89/195 (45%), Positives = 108/195 (55%), Gaps = 52/195 (26%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRMN+GQ+ E HLG A        
Sbjct: 1    RHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMRT----- 55

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  ++TPVFD
Sbjct: 56   -----------------------------------------------LNGGTCIATPVFD 68

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA EE +   L       +G+  LYDG TGE FD  VTVG +YMLKL+H+V DK++AR+ 
Sbjct: 69   GATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTVGIMYMLKLHHLVEDKMHARAI 128

Query: 1273 GSYSLVTQQPLGGKS 1287
            G YSLVTQQPLGGK+
Sbjct: 129  GPYSLVTQQPLGGKA 143


>gi|223928144|gb|ACN23840.1| RNA polymerase beta subunit [Bartonella sp. KM2581]
          Length = 298

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTREVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|110618405|gb|ABG78831.1| RNA polymerase beta subunit [Bartonella washoensis subsp.
           cynomysii]
          Length = 298

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 254/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E++VA+ SGAA+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 EAIVARDSGAAVGAKRAGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|227937612|gb|ACP43381.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 300

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 218/299 (72%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|55584696|gb|AAV53579.1| RNA polymerase II second largest subunit [Collybia tuberosa]
          Length = 700

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 131/829 (15%), Positives = 247/829 (29%), Gaps = 146/829 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAH 169

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 170  SSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +   Q + L K    ++  G+           +V  + GI+E +DA     
Sbjct: 227  AGRVCRPLFIVENQQLALQKKHVRYINNGVNDEGEDYKWEQLV--KGGIIELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +          Q ++       R  +K G            PS  LG  
Sbjct: 285  VMISMTPEDLENSRLTQSGADPQVNDAEFDPAAR--LKAGINSHTWTHCEIHPSMILG-- 340

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 341  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLI 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 378  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 427  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPVRDNTLRMKHGTYDKLED 485

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 486  DGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI- 544

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q+GDK A RHG KG +     
Sbjct: 545  -------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGITYR 585

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 586  QEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 638

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++     + LR       G+ V                   
Sbjct: 639  ------------------DLTVESVSTFLRQKGYQSRGLEVM------------------ 662

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                  G +       G      V +G  Y  +L HMV DK+++R+ G 
Sbjct: 663  ----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGP 700



 Score =  127 bits (320), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 86/622 (13%), Positives = 169/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 184

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 185 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 244

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     E    K         +  L A EEE   I+     L+       
Sbjct: 245 QKKHVRY--INNGVNDEGEDYKWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLTQS 302

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                    E          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 GADPQVNDAEFDPAARLKAGINSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIFLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 382 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPVRDNTLRMKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 478 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 530

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 531 LKSTESGIVDQVLITTNSEGQK 552


>gi|50290705|ref|XP_447785.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49527096|emb|CAG60734.1| unnamed protein product [Candida glabrata]
          Length = 1202

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 118/310 (38%), Gaps = 50/310 (16%)

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            D + E        +  + + +    +    + +       +    +   +   +      
Sbjct: 835  DKLDEDGLPYIGTYVEEGDPICAYFDDTIGKTKIKTYHSSEPAYIEEVNLIGDESNKFQE 894

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ V +   ++R  Q GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSR
Sbjct: 895  LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDVIINPHAFPSR 954

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G   E+  G A    G    S    +                               
Sbjct: 955  MTIGMFVESLAGKAGALHGIAQDSTPWIFNEQD--------------------------- 987

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                             TP       +     L  A  +  G   +Y G TGE     + 
Sbjct: 988  -----------------TPA------DYFGEQLLKAGYNYHGNEPMYSGATGEELRCDIY 1024

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +Y  +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++
Sbjct: 1025 IGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFL 1084

Query: 1311 LQEMLTIKSD 1320
            LQ+ L   SD
Sbjct: 1085 LQDRLLNSSD 1094



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 91/650 (14%), Positives = 191/650 (29%), Gaps = 76/650 (11%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            +   N+ +TD+ +         Y  ++        + +          DK D   VG+ 
Sbjct: 291 GSNTNNSFLTDRLELLLRGFKKRYPQLKNRTQVLQYLGDKFRLVFQASPDKSDYE-VGQE 349

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            +N  + +    +    +   ++ +++ L  L  G+   D+ D   ++ V   G +    
Sbjct: 350 VLNRIVLVHLGSNGNMDKFRMLLFMVRKLYSLVAGECCPDNPDATQHQEVLLGGFLYGMI 409

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQD----------LINAKPVVSAVCEFFCSSQL-- 522
            +  +    + I  ++ +     V              +     + S +  F  +  L  
Sbjct: 410 LKEKIDEYLQGIVAQVRTDINRGVAINFNEKKYMSRVLMRVNDNIGSKMQYFLSTGNLVS 469

Query: 523 ------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       + + E +N    I+H R    + +G          +R + P  +G +C
Sbjct: 470 QSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKLLPESWGFLC 526

Query: 571 PAETSEGHNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           P  T +G   GL++      R++     +      +    VT      +A         Q
Sbjct: 527 PVHTPDGSPCGLLNHFAHKCRISTTQSDVSKVPELLYSLGVTPASHTFAAGPSLCCV--Q 584

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            +  +    S  +  V         +         D     V   +    P L     + 
Sbjct: 585 LDGKIIGWTSHEQGRVIADTLRFWKVEGETPGLPKDLEIGYVPPSSKGQYPGLYIFGGHS 644

Query: 690 VLMGCNMQ------------RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            +M                  Q    +      +   +     + S   I++  A +   
Sbjct: 645 RMMRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNNIH-THVEFSPTNILSILANLTPF 703

Query: 738 VDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            D  +      +  +   T G   +    +           Q P+VK             
Sbjct: 704 SDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYG----- 758

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                + +   G N +VA + + GY+ +D+M+I++               ++V   D  L
Sbjct: 759 -----MDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYGT---MYKVEKVDLSL 810

Query: 857 GPEEITRDIPNVSEEG-------LKNIDECGIICVGAEVNPGDILVGK----------IT 899
                     +            L  +DE G+  +G  V  GD +              T
Sbjct: 811 NRSRGDPVTQHFGFGTDEWPKEWLDKLDEDGLPYIGTYVEEGDPICAYFDDTIGKTKIKT 870

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                P   EE  L      K  +++  S++     +  + D +  +RHG
Sbjct: 871 YHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGD-KFSSRHG 919



 Score = 61.6 bits (148), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 105/821 (12%), Positives = 222/821 (27%), Gaps = 119/821 (14%)

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
           + P +   +   R  +Y   + + L+  V D +       ++D        G LP+M + 
Sbjct: 115 ERPVY-PSEARQRLTSYRGKILLKLKWSVNDGENVFS--EVRDC-------GGLPIMLQS 164

Query: 142 ------------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASL 174
                                   G F+I GI++++   + Q    P             
Sbjct: 165 NRCHLNKMSPHELVQHKEESDELGGYFIINGIEKLIRMLIVQRRNHPMAIIRPSFANRGA 224

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGM 223
           S    Y+   I  + +  D +    +++H         R   R+    +PV   + AL  
Sbjct: 225 S----YSQYGIQIRSVRPD-QTSQTNVLHYLNDGQVTFRFSWRKNEYLIPVVMIMKALVD 279

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
            S+      +  I+ S   + +        L+ G K     +   T + +   G K    
Sbjct: 280 TSD---REIFDGIIGSNTNNSFLTD-RLELLLRGFKKRYPQLKNRT-QVLQYLGDKF--R 332

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           L+              SD   G  V   IV    G         +    + +++     +
Sbjct: 333 LVFQASPDK-------SDYEVGQEVLNRIVLVHLGSNGNMDKFRMLLFMVRKLYSLVAGE 385

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
                 D+  +   +    +          L +       G V+      +    + F+ 
Sbjct: 386 CCPDNPDATQHQEVLLGGFLYGMI------LKEKIDEYLQGIVAQVRTDINRGVAINFNE 439

Query: 404 DKYDLSTVGRVKMNM-----------RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            KY    + RV  N+            L   +  D++ +    ++A         +    
Sbjct: 440 KKYMSRVLMRVNDNIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRM 499

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +         +  +V ++L   +                      ++       +   + 
Sbjct: 500 VHRGSFFAQLKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCRISTTQ 552

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                    L  L     S +             G +    +  + R +  T        
Sbjct: 553 SDVSKVPELLYSLGVTPASHTFAAGPSLCCVQLDGKIIGWTSHEQGRVIADTLRFWKVEG 612

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET        +     +   ++ G     Y      ++   V YL   +E+   +     
Sbjct: 613 ETPGLPKDLEIG----YVPPSSKGQYPGLYIFGGHSRMMRPVRYLPLDKED--IVGPF-- 664

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                     E V+   A     +       ++ SP  ++SI A+L PF + + S R + 
Sbjct: 665 ----------EQVYMNIAVTPQEIQNNIHTHVEFSPTNILSILANLTPFSDFNQSPRNMY 714

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSV 748
            C M +Q +                +    +G   + K     +            + +V
Sbjct: 715 QCQMGKQTMGT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGTNAVVAV 772

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA-- 806
                       I      +R      + +   V +     R D +         +    
Sbjct: 773 ISYTGYDMDDAMIINKSADERGFGYGTMYKVEKVDLSLNRSRGDPVTQHFGFGTDEWPKE 832

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
               +    +P+ G   E+   I      +D      I+ +
Sbjct: 833 WLDKLDEDGLPYIGTYVEEGDPIC--AYFDDTIGKTKIKTY 871


>gi|315435616|gb|ADU18198.1| RNA polymerase beta-subunit [Mycobacterium alvei]
          Length = 237

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 125/226 (55%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +          
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAEGTPEWASRLPDGLHSAP-- 157

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 158  --------------------------VDSIVSTPVFDGAREEELAGLLGSTLPNRDGDVM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 192  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 237



 Score = 45.5 bits (106), Expect = 0.066,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|150865654|ref|XP_001384965.2| DNA-directed RNA polymerase I [Scheffersomyces stipitis CBS 6054]
 gi|149386910|gb|ABN66936.2| DNA-directed RNA polymerase I [Scheffersomyces stipitis CBS 6054]
          Length = 1167

 Score =  280 bits (715), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 113/279 (40%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQW-GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +T            IE+++  GDD      + + +   + R    GDK + RHG KG+ S
Sbjct: 841  KTKVKTYHSSEPAYIEEVKLLGDDSGDQEGQQITIKYRITRQPNIGDKFSSRHGQKGVCS 900

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 901  RKWPQIDMPFSETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWKFSE 960

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +                                             TP       +    
Sbjct: 961  DD--------------------------------------------TPA------DYFGE 970

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G TGE     + +G +Y  +L HMV+DK   RSTG  + +T Q
Sbjct: 971  QLRSAGYNYHGNEPMYSGATGEELRADIYIGCVYYQRLRHMVNDKFQVRSTGPVNSLTMQ 1030

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG R+GEME   +  +G A++LQ+ L   SD
Sbjct: 1031 PVKGRKRSGGIRVGEMERDALIGHGTAFMLQDRLLNCSD 1069



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 96/657 (14%), Positives = 196/657 (29%), Gaps = 83/657 (12%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRV--MRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  +          DR + LL  Y+   +     +   + +          D  D
Sbjct: 264 DREIFDGIVGADSANSFLTDRLELLLRTYKQYNLYSKQETLAYLGDKFRVVFGATPDVSD 323

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  VG+  +   + +  PD+    +   ++ +I+ L  L  G  + D+ D   ++ V   
Sbjct: 324 IE-VGKEVLRRIVLVHLPDNAD--KFRMLLFMIRKLYSLVAGDCSPDNPDATQHQEVLLG 380

Query: 468 GEMLKNQYRLGLLRMERSIKERI----------SSVDIDSVMPQDLINAKPVVSAVCEFF 517
           G +     +  +    ++I  +I          +  D   +    +   + +   +  F 
Sbjct: 381 GFLYGMIIKEKIEEYLQNINLQIQSDINRGVAINFNDRKYMSRVFMRINENIGQKLQYFL 440

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 441 STGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLP 497

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ L    R+       +   K       +     +A    
Sbjct: 498 ESWGFLCPVHTPDGSPCGLLNHLAHKCRIATEASDVSQVPKTLAQLGVSPAHTFAAGP-- 555

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N    Q +  +    +  +  +          V       +D     V   A    P L 
Sbjct: 556 NLCCVQLDGKIVGWTTHEQGKIVADTL-RFWKVEGGHGLPLDLEIGYVPPSAKGQYPGLY 614

Query: 684 NDDSNRVLMGC------------NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
               +  +M                  Q    +      +   +     + S   I++  
Sbjct: 615 IFGGHSRMMRPAKYLPLDKPDVLGPFEQVYMNVAVTPAEIEGNVH-THVEFSPTNILSIL 673

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR---PLVKVGDEV 788
           A +    D  +      +  +   T G     +    RS+      Q    P+VK     
Sbjct: 674 ANLTPFSDFNQSPRNMYQCQMGKQTMG--TPGVALMHRSDNKLYRLQTGQTPIVKANLYD 731

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                        + +   G N +VA + + GY+ +D+M+I++             +  +
Sbjct: 732 DYG----------MDNFPNGMNAVVAVISYTGYDMDDAMIINKSADERGFGYGTVYKVEK 781

Query: 849 VMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG------- 896
           V       R   +       D         + +D  G+  +G +V  GD +V        
Sbjct: 782 VDLSQSRRRGDPITQHFGFGDDEWPETWR-EKLDADGLPLIGVKVEEGDPIVAFFDETSG 840

Query: 897 ----KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
               K     E     E KLL    G++         R+        +  +  +RHG
Sbjct: 841 KTKVKTYHSSEPAYIEEVKLLGDDSGDQEGQQITIKYRI---TRQPNIGDKFSSRHG 894



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 87/665 (13%), Positives = 192/665 (28%), Gaps = 115/665 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L + +   V D DE      + +I+E     G +P+M K       
Sbjct: 103 PAECRERMSTYRSRLMLKVAWSVNDGDE------VSEIREA----GQVPIMLKTNRCHLE 152

Query: 141 -----------------DGTFVIKGIQRIV---VSQ-------LHRSPGIHFDHDKGRAS 173
                             G F++ GI++++   + Q       + R P   F +     +
Sbjct: 153 KLSPQELVEQREESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIR-PS--FGNRGAAYT 209

Query: 174 LSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEE 227
             G  + + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +
Sbjct: 210 KFGIQIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVMMILKAL-IETND 264

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
                +  IV +   + +        L+   K  +     +T   + +  + +       
Sbjct: 265 --REIFDGIVGADSANSFLTD-RLELLLRTYKQYNLYSKQETLAYLGDKFRVVFGATP-- 319

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
                V  + +  + L  + +     N +   + +    +    SL     S        
Sbjct: 320 ----DVSDIEVGKEVLRRIVLVHLPDNADKFRMLL--FMIRKLYSLVAGDCSPDNPDATQ 373

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           + + +         +     +  ++  L I   +  G V+         + +F   ++  
Sbjct: 374 HQEVLLGGFLYGMIIKEKIEEYLQNINLQIQSDINRG-VAINFNDRKYMSRVFMRINENI 432

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              +        L   +  D++ +    ++A         +    +         +  +V
Sbjct: 433 GQKLQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAELKTTTV 492

Query: 468 GEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            ++L   +  L  +         + +            +    V         S      
Sbjct: 493 RKLLPESWGFLCPVHTPDGSPCGLLNHLAHKCRIATEASDVSQVPKTLAQLGVSPAHTFA 552

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
              N                G +       + + V  T    +   +   GH + L   +
Sbjct: 553 AGPNLC---------CVQLDGKIVGWTTHEQGKIVADT----LRFWKVEGGHGLPLDLEI 599

Query: 587 TSFARVNAYGFIETPY--------RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             +   +A G     Y         +       +    L   E+    +A   + ++ + 
Sbjct: 600 G-YVPPSAKGQYPGLYIFGGHSRMMRPAKYLPLDKPDVLGPFEQVYMNVAVTPAEIEGN- 657

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++ SP  ++SI A+L PF + + S R +  C M +
Sbjct: 658 ---------------------VHTHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGK 696

Query: 699 QAVPL 703
           Q +  
Sbjct: 697 QTMGT 701


>gi|157004967|gb|ABV00686.1| RpoB [Mycobacterium intracellulare]
          Length = 237

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 98/229 (42%), Positives = 130/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V +K++A STG YS
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDEKIHAPSTGPYS 237



 Score = 45.1 bits (105), Expect = 0.085,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|115503929|ref|XP_001218757.1| DNA-directed RNA polymerase III [Trypanosoma brucei TREU927]
 gi|83642239|emb|CAJ15945.1| DNA-directed RNA polymerase III, putative [Trypanosoma brucei brucei
            strain 927/4 GUTat10.1]
 gi|261325981|emb|CBH08807.1| DNA-directed RNA polymerase III, putative [Trypanosoma brucei
            gambiense DAL972]
          Length = 1129

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 83/306 (27%), Positives = 125/306 (40%), Gaps = 66/306 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
             V + +KV     R  + GDK + RHG KG+V  I    +MPF + G   D++       
Sbjct: 871  DVEQKIKVVTREVRGPEPGDKFSSRHGQKGVVGLITDGVNMPFNEQGICPDMI------- 923

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
              MN                                             +     K+ + 
Sbjct: 924  --MN----------------------------------------PHGFPSRMTVGKLLEL 941

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                V  +  ++  G       F G   E +   L     +  G+ I Y G+TGE     
Sbjct: 942  VSSKVSALTGKFGDGT-----AFGGDKAEDLGEELIRHGYNYHGKDIFYSGVTGEMLRAY 996

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV+DK++AR+TG  S++T+QP  G+S  GG R+GEME  C+  YGA+
Sbjct: 997  VFFGPIYYQRLKHMVTDKMHARATGPRSMLTRQPTEGRSRSGGLRVGEMERDCMVGYGAS 1056

Query: 1309 YVLQEMLTIKSD----DVVGR------TRVYESIVAGND-TFETGTPESFNVLVKEMQAL 1357
             +L E L + SD    D+  R         Y S     +       P +F +L++E+Q +
Sbjct: 1057 NLLNERLLVSSDLFTIDIC-RCCGFMGYNGYCSYCNAKNTVSRVNVPYAFKLLLQELQGM 1115

Query: 1358 GLSIDL 1363
            G+S  L
Sbjct: 1116 GISTRL 1121



 Score =  136 bits (342), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 139/966 (14%), Positives = 273/966 (28%), Gaps = 176/966 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+    AS+DH + + +              KS     +      + +       P+   
Sbjct: 29  LLNHHVASFDHLINVELGRILLNES--NREIKS-----SIDPDFSIRYSGIRVCRPREIV 81

Query: 86  --------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  RDLTY   + + +     D  +           E +I +G +P+
Sbjct: 82  GKGQLPKPVSPHECRTRDLTYRGDIVVDVEYTSRDRSKRICT-------ETNIKIGTIPI 134

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKG-- 170
           M K                         G F+IKG++++ + Q  +S   +  + D    
Sbjct: 135 MLKSSSCNLYGKGREELIAMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADDNGD 194

Query: 171 -RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EI 228
             A +  K  Y+            + F    I+ V    +  +P+   L ALGM+S+ +I
Sbjct: 195 IVAHVQSKTHYSI-------SKCSVTFRKGRIVMVHRSFKEDIPIVVVLKALGMESDQQI 247

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
                    + Q   F CF  +A+  +     +   +     E   E  +     + KS 
Sbjct: 248 AQHIGVSPAF-QSVLFACFEHAASLNVKTQDDALHFIGERRKETFWEMDETQQRHVQKSK 306

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            +         ++ L  + +          +       +     +  +  + +     L 
Sbjct: 307 ADS-------AAEFLANVLLCHIREGEVQRDWNFRHKALYVCFMVRRMVEASVDS--SLL 357

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR--------PGDVSTFSVAESMFNFLF 400
            +          T  T      +D L    RV++          D +     + +     
Sbjct: 358 DERDFYGNKRFETTGTLMGLLFEDLLKQYNRVVKTAMDQLLSKKDTTKPFNLKQLMESKM 417

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVR-HIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                     +   +  ++    +   +   + +   I+ I ++  L +       I   
Sbjct: 418 EVIQNGMRVALSSGRWELKRFNMSRQGITQVLSRLSYISCIGMMTRLASSFEKSRKI--- 474

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              R     +                + +  + +   ++   D        +   E    
Sbjct: 475 SGPRSLQPSQWGMVCPCDTPEGESCGLVKNFAILSQVTLDMDDSFVRAAAYNLGVEEVDC 534

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              ++  ++               L       +R    +R +  +  GR+ P  +   ++
Sbjct: 535 ISPNEFLKYYTVFL-------NGTLMGIHRYPSRLCRGVRTLRRS--GRLHPHVSIAIND 585

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
                 +         G I   Y  V DGK      +L  +      I   N  L E   
Sbjct: 586 RQKSVQIGCD-----GGRIVRLYIVVRDGKPAVTSQHLDNLSSGKCSI---NDFLAE--G 635

Query: 640 FTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             E +         I V  + I      ++  P  ++ + A +IPF  ++ S R      
Sbjct: 636 LVEFIDVNEANDCLIAVYPKDIEQYTTHLEIEPLSLLGVVAGIIPFPHHNQSARNTFQSA 695

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+                                           I   +     +
Sbjct: 696 MGKQALGT-----------------------------------------IAYNQYIRMDT 714

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +  Y               QRPL +                T+   L  G N +V  
Sbjct: 715 VLMLGAYP--------------QRPLCR----------TKAMNLTNYEILGAGINAMVCV 750

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M + GY+ ED+ + +   +       + + + EV       G  +I     + +      
Sbjct: 751 MSYSGYDIEDAQVYNRSSLDRGYGRCVVLRKHEVELERLPNGEYDIILPADS-NVGRHSA 809

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           ++  GI   GA V   DILV K TP       P   + +         V D  +  P G 
Sbjct: 810 LNSDGIASKGAVVRQFDILVNKYTPVPSMEPRPNPLVYKYPQ----PAVVDHVVISPPGD 865

Query: 936 SGTVVD 941
           S   +D
Sbjct: 866 SDRSMD 871


>gi|313670774|gb|ADR73578.1| RNA polymerase subunit beta [Bradyrhizobium iriomotense]
          Length = 257

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 140/258 (54%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D EEIL+TFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEEILNTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           +I+Y +  + W  P  A +   G   +S L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  RILYKRTKEGWRVPFDA-NRFRGYSTTSDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN 
Sbjct: 120 ALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|212373997|emb|CAP09925.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35724]
          Length = 310

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 164/282 (58%), Positives = 217/282 (76%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SAL  GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 9   PNNPLSEITHKRRVSALXPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 68

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 69  AYARTNQYGFLESPYRVVKEGVVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAV 128

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+
Sbjct: 129 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRAD 188

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+
Sbjct: 189 KPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKY 248

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            RSNQNTC+NQRPLV+ GD V+R+DI+ADGPSTD+G+LALG+
Sbjct: 249 TRSNQNTCINQRPLVRKGDRVQRSDIMADGPSTDMGELALGQ 290


>gi|227937626|gb|ACP43388.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 296

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 215/296 (72%), Positives = 250/296 (84%), Gaps = 1/296 (0%)

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS 
Sbjct: 2   FRIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSE 61

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN 
Sbjct: 62  ITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNK 121

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE +
Sbjct: 122 YGFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVL 181

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           + PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTG
Sbjct: 182 MAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTG 241

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           MESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 242 MESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 296


>gi|223928142|gb|ACN23839.1| RNA polymerase beta subunit [Bartonella sp. KM2563]
          Length = 298

 Score =  279 bits (714), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 219/299 (73%), Positives = 252/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD  G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDPKGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|315435620|gb|ADU18200.1| RNA polymerase beta-subunit [Mycobacterium avium complex]
          Length = 234

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 98/226 (43%), Positives = 129/226 (57%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPDWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEELRHAQPDQIVSTPVFDGAKEEELAGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG
Sbjct: 189  VDGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTG 234



 Score = 45.1 bits (105), Expect = 0.092,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|241957019|ref|XP_002421229.1| DNA-directed RNA polymerase I subunit, putative [Candida dubliniensis
            CD36]
 gi|223644573|emb|CAX40561.1| DNA-directed RNA polymerase I subunit, putative [Candida dubliniensis
            CD36]
          Length = 1166

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 95/476 (19%), Positives = 162/476 (34%), Gaps = 61/476 (12%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +  +     E    +I ++        D         +   G   +G           
Sbjct: 654  EEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSD 713

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL- 966
             +   L+                + +  +G    V + +  G D ++ ++ + +   E  
Sbjct: 714  NKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDD-AMIINKSADERG 772

Query: 967  --LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                     E+V L ++   R   I       +          L +D +         + 
Sbjct: 773  FGYGTVYKTEKVDLSQSRR-RGDPITQHFGFGTDEWPEAWKEKLDADGLPLIG----VKV 827

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D  V    ++L      +    E  +  +++ +  GDD      + + +   + R  
Sbjct: 828  EEGDPIVAYYDDTLGKTKVKTYHSSEPGYIEEVKLL--GDDSNEQEGQQITIKYRITRQP 885

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A
Sbjct: 886  LIGDKFSSRHGQKGVCSRKWPQIDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKA 945

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G    S    +                                             
Sbjct: 946  GALHGIAQDSTPWKFNEQD----------------------------------------- 964

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP       +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+
Sbjct: 965  ---TPA------DYFGEQLLKAGYNYHGNEPMYSGATGEELRCDIYIGCVYYQRLRHMVN 1015

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1016 DKFQVRSTGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1071



 Score = 68.6 bits (166), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 81/590 (13%), Positives = 176/590 (29%), Gaps = 61/590 (10%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  + N        DR + LL  Y+   +     +   + +          D  D
Sbjct: 266 DREIFDGIVGNDTENSFLTDRLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASPDMSD 325

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +  VG+  +   + +  P++    +   ++ +I+ L  L  G    D+ D   ++ V   
Sbjct: 326 IE-VGKEVLKRIVLVHLPNN--TDKFRMLLFMIRKLYSLVAGDCAPDNPDATQHQEVLLG 382

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFF 517
           G +     +  +    ++IK +I S     V                    +   +  F 
Sbjct: 383 GFLYGMIIKEKIEEYLQNIKLQIQSDINRGVGINFDDRKYMTRVFSRINENIGQKLQYFL 442

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 443 STGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLP 499

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             +G +CP  T +G   GL++ L+   ++       +   K             +A    
Sbjct: 500 ESWGFLCPVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQLGVLPADSFAAGP-- 557

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQVV 672
           N    Q +  +    +  +  +         +          +I ++  S     P   +
Sbjct: 558 NLCCVQLDGRIVGWTTHEQGRIVADTLRYWKVNGGHGLPLDLEIGYVPPSNKGQYPGLYI 617

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
               S +                   Q    +      +   + S   + +   I++  A
Sbjct: 618 FGGRSRMMRPVRYLPLDKEDIVGPFEQVYMNVAVTPEEIENNIHS-HVEFTPTNILSILA 676

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    D  +      +  +   T G      + +           Q P+VK        
Sbjct: 677 NLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSDNKLYRLQTGQTPIVKANLYDDYG 736

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                     + +   G N +VA + + GY+ +D+M+I++             +  +V  
Sbjct: 737 ----------MDNFPNGMNAIVAVISYTGYDMDDAMIINKSADERGFGYGTVYKTEKVDL 786

Query: 852 ----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               R      +          E   + +D  G+  +G +V  GD +V  
Sbjct: 787 SQSRRRGDPITQHFGFGTDEWPEAWKEKLDADGLPLIGVKVEEGDPIVAY 836



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 100/762 (13%), Positives = 215/762 (28%), Gaps = 97/762 (12%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   L + +   V D +E      + +++E     G +P+M K       
Sbjct: 105 PSECRERMVTYRSRLMLNVTWSVNDGEE------VSEVREA----GQIPIMLKSNRCHLE 154

Query: 142 ------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLS----G 176
                             G F++ GI++++   + Q    P        G    S    G
Sbjct: 155 KLSPNQLVEAKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFGNRGASYTKFG 214

Query: 177 KLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILS 230
             + + R  PDQ      +    D    +  R   R+    VPV   L AL +++ +   
Sbjct: 215 IQIRSVR--PDQTSQTNVLHYLNDGN--VTFRFSWRKNEFLVPVVMILKAL-IETND--R 267

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             +  IV +   + +        L+   K  +     +T   + +  + +          
Sbjct: 268 EIFDGIVGNDTENSFLTD-RLELLLRTYKTYNLYSQQETLAYLGDKFRVVFGASP----- 321

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +  + +  + L  + +     N +   + +    +    SL     +        + +
Sbjct: 322 -DMSDIEVGKEVLKRIVLVHLPNNTDKFRMLL--FMIRKLYSLVAGDCAPDNPDATQHQE 378

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         +     +  ++  L I   +  G V            +F   ++     
Sbjct: 379 VLLGGFLYGMIIKEKIEEYLQNIKLQIQSDINRG-VGINFDDRKYMTRVFSRINENIGQK 437

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +        L   +  D++ +    ++A         +    +         +  +V ++
Sbjct: 438 LQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAELKTTTVRKL 497

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                      ++       K    A         L+Q    + 
Sbjct: 498 LPESWGFLC-------PVHTPDGSPCGLLNHLSHKCKIATEASDVSQVPKALTQ-LGVLP 549

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           + S             G +       + R V  T    +   + + GH + L   +  + 
Sbjct: 550 ADSFAAGPNLCCVQLDGRIVGWTTHEQGRIVADT----LRYWKVNGGHGLPLDLEIG-YV 604

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
             +  G     Y      ++   V YL   +E+   +               E V+   A
Sbjct: 605 PPSNKGQYPGLYIFGGRSRMMRPVRYLPLDKED--IVGPF------------EQVYMNVA 650

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                +       ++ +P  ++SI A+L PF + + S R +  C M +Q +         
Sbjct: 651 VTPEEIENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGT--PGTAL 708

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           V      +    +G   + K     +            I +V            I     
Sbjct: 709 VHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDDAMIINKSA 768

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
            +R      V +   V +    RR D I         +    
Sbjct: 769 DERGFGYGTVYKTEKVDLSQSRRRGDPITQHFGFGTDEWPEA 810


>gi|156546417|ref|XP_001607116.1| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Nasonia vitripennis]
          Length = 1127

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 94/497 (18%), Positives = 166/497 (33%), Gaps = 89/497 (17%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                  +   +    I       +   +  + A+      D+ D  +   + +       
Sbjct: 705  YNLVYPHAPMVKTKTIELINFDKLPAGQNAIVAVMSYSGYDIEDALILNKASIDRGYGRC 764

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        + +     ++I   + D   ++ I   +I         G+   +     
Sbjct: 765  LVYKNAKCVLKKYANQTC-DRIMPASVDATTKKPIWQHDIIDGEGIAAPGEMVSNKKVMV 823

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KST                     +          + +Y+ +  + ++     IEK+  
Sbjct: 824  NKSTPS------------------ANTGPVTTGSQAQTEYKNANLVYKNPVPAYIEKVMI 865

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+  EDMPF   G   D++ 
Sbjct: 866  SSNAEDAY--LIKLLLRQTRRPEIGDKFSSRHGQKGVTGLIVEQEDMPFNDSGICPDMI- 922

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
                    MN                                              G  +
Sbjct: 923  --------MN--------------------------------------------PHGFPS 930

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                    + +   A   K      T  F G+  E +   L     +  G+ I Y G+TG
Sbjct: 931  RMTVGKLIELLAGKAGVLKGKFHYGT-AFGGSKVEDVCEELVSQGYNYLGKDIFYSGITG 989

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            EP    +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+
Sbjct: 990  EPLQAYIYSGPVYYQKLKHMVQDKMHARARGPRAVLTRQPTEGRSKDGGLRLGEMERDCL 1049

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVGRTR----VYESIVAGND----TFETGTPESFNVL 1350
              YGA+ +L E L + SD    DV    +     Y                  P +  +L
Sbjct: 1050 IGYGASMMLIERLMLSSDAFDVDVC--NKCGLMAYTGYCHSCRSSACVSTITMPYACKLL 1107

Query: 1351 VKEMQALGLSIDLENSR 1367
             +E+Q++ +   L    
Sbjct: 1108 FQELQSMNIVPRLTLKN 1124



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 117/973 (12%), Positives = 281/973 (28%), Gaps = 226/973 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S+++F+ + I    + NE          P+        +++++     P    
Sbjct: 35  LVKQHIDSFNYFINVEIKKIVKANE---KVLSDADPL------FYVKYLNVSIGTPDIEE 85

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDL Y+ P+ + +  +          +  + I   ++ +G +P+M
Sbjct: 86  GFSVSRPTTPHECRLRDLNYSAPITVDIEYM----------RGHQPIIRNNLLIGRMPIM 135

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+I G +++++ Q                  
Sbjct: 136 LRSSNCVLSEKSNFELAKMNECPHDPGGYFIINGQEKVILIQEQ---------------- 179

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDII-----HVRIDRRRK------------------ 211
               +   RII        +E D+K+ I         +R+ K                  
Sbjct: 180 ----MLRNRII--------LEEDNKNCIVASCNSATQERKTKTNVIGRAGKYYLRHNIFQ 227

Query: 212 --VPVTSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +PV     A+G+   +EI+     +  + ++         A +++   +    L +  
Sbjct: 228 DDIPVVIIFKAMGIVCDQEIVQLIGTEENFMKKIGASLEECHALNIVAQNQALKYLGNKR 287

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNGETGEIYI 322
             ++       +T  +   L    +  + +             L V + ++    G++  
Sbjct: 288 KQKRFTVVKSSITDEMKDVLASNILSHVPVIDFNFKLKATYLALMVRKVMIAQTDGKLVD 347

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +     +++            + +++ D      +   T+        K A  DI + MR
Sbjct: 348 DRDYYGNKRL-----ELAGSLLALMFEDLFKRFNWDLKTIADKNIPKIKAAQFDIVKHMR 402

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
             D  T  +A ++ +  +         T+ R KM           + +I    ++  +  
Sbjct: 403 H-DSITNGLAVAISSGNW---------TIKRFKMERHGVTQVLSRLSYISALGMMTRVNS 452

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
             +          +       +    +  + +    +  +           +   +    
Sbjct: 453 QFEKTRKVSGPRSLQPSQWG-MLCPSDTPEGEGCGLVKNLALMTHITTEIEEEPIMRLAF 511

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            +  + V     E   +  +  +  + N L  + +  RL  + +  + R     +   ++
Sbjct: 512 NLGVENVNILGGEEINNKDVYMVFLNGNILGIVKNYYRLVTVFRM-LRRKGLVNQFVSIY 570

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
           P H  R     +  G        +       +      +E   R   D      + YL  
Sbjct: 571 PQHQHRCVQISSDGGRLCRPYIIVEHCQPLVKAEHIKLLEQGVRSFEDFLHDGTIEYLDV 630

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            EE + +IA + S + E                        I  ++  P  ++ + A L+
Sbjct: 631 NEENDSFIAFSESHIKEG-----------------------ITHLEIEPFTLLGVCAGLV 667

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           P+  ++ S R    C M +QA+                                      
Sbjct: 668 PYPHHNQSPRNTYQCAMGKQAMGT------------------------------------ 691

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                I   + +   +     +Y      ++     +N                      
Sbjct: 692 -----IAYNQRNRIDTLMYNLVYPHAPMVKTKTIELIN---------------------- 724

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                L  G+N +VA M + GY+ ED++++++  +       +  +  + + +       
Sbjct: 725 --FDKLPAGQNAIVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNAKCVLKKYANQTC 782

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           +                    ID  GI   G  V+   ++V K TP   +         +
Sbjct: 783 DRIMPASVDATTKKPIWQHDIIDGEGIAAPGEMVSNKKVMVNKSTPSANTGPVTTGSQAQ 842

Query: 915 AIFGEKAVDVRDT 927
             +    +  ++ 
Sbjct: 843 TEYKNANLVYKNP 855


>gi|227937610|gb|ACP43380.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 300

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 217/299 (72%), Positives = 252/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS Q+T
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSIQST 298


>gi|19074837|ref|NP_586343.1| DNA-DIRECTED RNA POLYMERASE III SUBUNIT 2 (130kDa SUBUNIT)
            [Encephalitozoon cuniculi GB-M1]
 gi|19069562|emb|CAD25947.1| DNA-DIRECTED RNA POLYMERASE III SUBUNIT 2 (130kDa SUBUNIT)
            [Encephalitozoon cuniculi GB-M1]
          Length = 1110

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/342 (23%), Positives = 131/342 (38%), Gaps = 83/342 (24%)

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            ++       +  + +KI   +  D +      ++K  +   R  + GDK + RHG KG+V
Sbjct: 836  KFTGKVHRGDPAYIDKILITKSQDQV------LIKTMLRQTRVPEIGDKFSSRHGQKGVV 889

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
              ++  EDMPF   G   DI++NP G PSRM VG+I E   G A V  G+ + S      
Sbjct: 890  GLLVRQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKIVELISGKAGVLEGQILDSTAFKEN 949

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            +      L                 +                G P++  +F         
Sbjct: 950  SVEQTCELLIKHGFSYSGKDCFTSGTT---------------GAPLAAYIF--------- 985

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                                           G ++  +L HMV+DK++ R+ G  +++T+
Sbjct: 986  ------------------------------FGPVFYQRLKHMVADKIHMRARGPRAILTR 1015

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV------- 1333
            QP  G+S  GG +LGEME  C+  YGA+ ++ E L   SD       V+E+ V       
Sbjct: 1016 QPTEGRSKDGGLKLGEMERDCLIGYGASSLITERLMTSSD-------VFEAYVCRSCGVL 1068

Query: 1334 ---------AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
                      G    +   P +  +L +E+ ++ +   L   
Sbjct: 1069 AFKGCCVACKGTKPVKVKMPYACKLLFQELMSMNILPRLHIE 1110



 Score =  121 bits (303), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 96/751 (12%), Positives = 223/751 (29%), Gaps = 140/751 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+     SYD+F+   I    R N+       S            L+++      P    
Sbjct: 19  LVRQHIESYDYFVDHEIKALVRANQ----IVDS-----DIDHTFYLKYLDIRVAMPSVEE 69

Query: 86  ----FD--VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               ++    +C  RD+TY+  + + +  +          ++ + I ++ + +G +P+M 
Sbjct: 70  NMVNYNVFPIECRLRDITYSANIYVDIEYV----------RNRQIIVKRDVCIGKMPVML 119

Query: 140 KD----------------------------------GTFVIKGIQRIVVSQLHRSPGIHF 165
           +                                   G F+++GI+R+V+ Q   S     
Sbjct: 120 RSSRCHLRRETKGPMEGRKTKDRRIRESQECPLDVGGYFIVRGIERVVLIQEQLSKNRII 179

Query: 166 DHDKGR-----ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
                +      + S     +   +  +    D  +  K+ +        +VPV   + A
Sbjct: 180 IESGPKGLFASVTSSTDEHKSKTSVTTR----DDCYYLKNSMF-----SEEVPVVIMMKA 230

Query: 221 LGMDSEEILSTFYPKIVYSQR-------GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
           LG+  +  ++    K  +               F    A L + + +     D    E +
Sbjct: 231 LGLVQDREVAECVGKEYFEIMVPSFGECMSKGIFTREQALLYISSYIKLKPEDNRIEEVL 290

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
               +K+   +     +   K + I    L    +A+  +N    +   +   V +++  
Sbjct: 291 TVLSEKVLPNVQIEGCDLRKKGIYI---ALMVRRLAQTKLNILRED---DKDFVGNKRFE 344

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
                  I         +      I   L         DAL  +       ++ T ++A 
Sbjct: 345 LAGQLLSILFEDTFKRFNFELKKSIDKILSKRSRAQEFDALTFLN---LQANMITSTLAR 401

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD---LRNGK 450
           +  +   ++  ++ +   G   +  R +  +   +            K+        +  
Sbjct: 402 A-ISTGNWNLKRFRMERSGVTHVLSRHSYISALGMMTKINSHFEKTRKVSGPRSLHTSSW 460

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
           G +  +D         V  +            +  +    +   +  V    +   +   
Sbjct: 461 GMLCPVDTPEGESCGLVKNLALLAEITTNSDTKPIL---DTVYKLGVVDINSVYTREIHQ 517

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRI 569
             +   F +  +  +    + L       R   L    V+  +  VE R +H  +  GR+
Sbjct: 518 KDMFSVFLNGDIIGITNRADFLVEQFKLHRRKGLVGKFVSIYKVTVE-RVIHIASDNGRV 576

Query: 570 C-------------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--- 613
           C                +++        +++    + +   +   Y K        +   
Sbjct: 577 CRPLIIIDKNRINQTIISNQMDECLKALNISEKVAIESGKSLFDCYLKYKSFTDLLEEGF 636

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YL   EE +  +A     +                        E+   ++ S   ++ 
Sbjct: 637 IEYLDVNEENDCLVALKPEDIG-----------------------EETTHLEISEFAILG 673

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
             A L+PF  ++ S R    C M +QA+  +
Sbjct: 674 YVAGLVPFPHHNQSPRNTYQCAMGKQAIGHI 704



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 80/526 (15%), Positives = 180/526 (34%), Gaps = 69/526 (13%)

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           +++ L   +      DD D +GN+R    G++L   +     R    +K+ I  +     
Sbjct: 318 MVRRLAQTKLNILREDDKDFVGNKRFELAGQLLSILFEDTFKRFNFELKKSIDKILSKRS 377

Query: 499 MPQDLI-------NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA- 550
             Q+          A  + S +     +   +     +          R S +   G+  
Sbjct: 378 RAQEFDALTFLNLQANMITSTLARAISTGNWNLKRFRMERSGVTHVLSRHSYISALGMMT 437

Query: 551 -------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                  + R     R +H + +G +CP +T EG + GLV +L   A +      +    
Sbjct: 438 KINSHFEKTRKVSGPRSLHTSSWGMLCPVDTPEGESCGLVKNLALLAEITTNSDTKPILD 497

Query: 604 KVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            V    V + + VY   + +++ +    N  +    +  + LV          +  + + 
Sbjct: 498 TVYKLGVVDINSVYTREIHQKDMFSVFLNGDIIGITNRADFLVEQFKLHRRKGLVGKFVS 557

Query: 663 FIDASPKQVVSIA------ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG-- 714
               + ++V+ IA         +  ++ +  N+ ++   M      L  +E   + +G  
Sbjct: 558 IYKVTVERVIHIASDNGRVCRPLIIIDKNRINQTIISNQMDECLKALNISEKVAIESGKS 617

Query: 715 -------------------MESVVAKSSGAAIVAKRAGIVEQVD--------AIRIVIRS 747
                              +E +        +VA +   + +          AI   +  
Sbjct: 618 LFDCYLKYKSFTDLLEEGFIEYLDVNEENDCLVALKPEDIGEETTHLEISEFAILGYVAG 677

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST------- 800
           +      + S  + Y+    +++  +  +N    VK   +     +              
Sbjct: 678 LVPFPHHNQSPRNTYQCAMGKQAIGHISLN----VKKRFDSVILQLTYTHRPMVSTKILD 733

Query: 801 --DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
             +  ++  G+N +VA M + GY+ ED++++++  V   +F     +    + +    G 
Sbjct: 734 LINYNEIPAGQNAMVAVMSYSGYDIEDALVLNKTSVERGLFRVEVYKTTTTLLKKHSNGM 793

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            ++    P  S      +DE G+   G  V  G + V K++P   +
Sbjct: 794 SDVLWPNPKESV-----LDEDGLGKPGKMVRDGTVYVNKMSPVDGT 834


>gi|169792086|gb|ACA80333.1| RpoB [Fusobacterium nucleatum]
 gi|169792098|gb|ACA80339.1| RpoB [Fusobacterium nucleatum]
 gi|169792100|gb|ACA80340.1| RpoB [Fusobacterium nucleatum]
          Length = 143

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 89/195 (45%), Positives = 108/195 (55%), Gaps = 52/195 (26%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL+DGT +D+VLNPLGVPSRMN+GQ+ E HLG A        
Sbjct: 1    RHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMR------ 54

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  ++TPVFD
Sbjct: 55   ----------------------------------------------SLNEGTCIATPVFD 68

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA EE +   L       +G+  LYDG TGE FD  VTVG +YMLKL+H+V DK++AR+ 
Sbjct: 69   GATEEQVKDYLEKQGYPRTGKVTLYDGRTGEKFDNKVTVGIMYMLKLHHLVEDKMHARAI 128

Query: 1273 GSYSLVTQQPLGGKS 1287
            G YSLVTQQPLGGK+
Sbjct: 129  GPYSLVTQQPLGGKA 143


>gi|45120568|gb|AAO64656.2| RNA polymerase II subunit RPB2 [Echinodontium tinctorium]
          Length = 871

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 154/1012 (15%), Positives = 289/1012 (28%), Gaps = 171/1012 (16%)

Query: 275  ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            +SGK ++   +K       K  G     +    +    V+     ++   G + D   LE
Sbjct: 14   KSGKTISQFQVKMFHRSQEKTSG----NVIKATIPYIKVDIPIWVVFRALGVISDRDILE 69

Query: 335  EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
             I +       +  +    ++ ++         +DR  AL  I         +T    E 
Sbjct: 70   HICYDMSDSPMLEMLKPCIDDGFV--------IQDRDIALDFIGNR----GTTTGLSRER 117

Query: 395  MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
               +      K  L  V              +     +      +I  L+     +  +D
Sbjct: 118  RIRYAQEILQKEMLPHV-----------SMSEGSESRKAYFFGYMIHRLLLAAMERRELD 166

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSA 512
            D D+ G +R+   G +L N +R+   ++ R +   +               I    + + 
Sbjct: 167  DRDHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRHLQKCVETHKEFNLNLAIKHTTITNG 226

Query: 513  VCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            +     +               +SQ+       S ++H RR +      + R     + R
Sbjct: 227  LKYSLATGNWGDQKKAMSAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPR 282

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             +H TH+G +CPAET EG   GLV +L+  A ++      T    + +  + +       
Sbjct: 283  QLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSTSGTIVDFLEEWGLESL------ 336

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
              EEN + +   + +  +G +       R     I   ++     D  P+  +       
Sbjct: 337  --EENAHSSTLTTKVFVNGVWVG---IHRDPTNLISTLKKLRRKDDVHPEVSIVRDIRER 391

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                  D   V     +      +L+ +   +V  G                + G++E +
Sbjct: 392  ELRIYTDPGXVCRPLFVVENHQLVLEKKHVQWVSQGY-RDHPXDPFHWSQLIKTGVIEML 450

Query: 739  DAIRI-VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            DA     +       D   S +    +      +Q      R     G            
Sbjct: 451  DAEEEETVMICMTPEDLENSRLQAAGIDPHANEDQEFDPAARLKAASGLTPHTWTHCEIH 510

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 511  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 545

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   +               +  +             +       +   +  + AI 
Sbjct: 546  IYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 594

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  +++   + E+ E   RD       
Sbjct: 595  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDMEKKAGVQQVEEFEKPTRDTTLHMKH 653

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  L  D      RS+          ++     
Sbjct: 654  GTYDKIENDGLIAPGTGVNGADIIIGKTAPLPVDSEELGQRSRLHTRRDVSTPLKSTESG 713

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VK+ V   R  Q GDK A RHG K
Sbjct: 714  IVDQ--------------------VLVTTNHEGHKFVKIRVRSTRIPQIGDKFASRHGQK 753

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +   
Sbjct: 754  GTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 813

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S     L++   +                                       
Sbjct: 814  TDLTVESVSKFL--LQQGYQSRGLEVM--------------------------------- 838

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                          G +       G      V +G  Y  +L HMV DK++A
Sbjct: 839  ------------YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKIHA 871



 Score =  137 bits (345), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 98/769 (12%), Positives = 214/769 (27%), Gaps = 101/769 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  S   +     +    ++    ++
Sbjct: 45  YIKVD----IPIWVVFRALGVISDRDILEHICYDMSDSPMLEMLKPCIDDGFVIQDRDIA 100

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + ++             +      + 
Sbjct: 101 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMSEGSESRKAYFFGYMIH---RLL 156

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  +    +      +    P+L          +   +     K  +        +
Sbjct: 157 LAAMERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRHLQKCVETHKEFNLNL 216

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                  T  +  S+    + D  K   +  G  ++  R    +      R         
Sbjct: 217 AIKHTTITNGLKYSLATGNWGDQKKAMSAKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 276

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +     +I + +    ++S+
Sbjct: 277 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSTSGTIVDFLEEWGLESL 336

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 NA         F     +    +  N +S +   RR   +              
Sbjct: 337 ----EENAHSSTLTTKVFVNGVWVGIHRDPTNLISTLKKLRRKDDVHPEVSIVRDIRERE 392

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             ++        P    E H + L      +           P+        T  +  L 
Sbjct: 393 LRIYTDPGXVCRPLFVVENHQLVLEKKHVQWVSQGYRDHPXDPFH-WSQLIKTGVIEMLD 451

Query: 619 AMEEENRYIAQANSSLDEDG----------SFTEELVFCRCAGEEILVPREKIDFIDASP 668
           A EEE   I      L+             +  +E            +        +  P
Sbjct: 452 AEEEETVMICMTPEDLENSRLQAAGIDPHANEDQEFDPAARLKAASGLTPHTWTHCEIHP 511

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ I AS+IPF +++ S R      M +QA+ +                         
Sbjct: 512 SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------------ 553

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                                     + + +  Y       +     +  R         
Sbjct: 554 -----------------------RMDTMANILYYPQKPLATTRSMEYLKFR--------- 581

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          +L  G+N +VA + + GYN EDS+++++  +   +F SI+   + 
Sbjct: 582 ---------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYM 626

Query: 849 VMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            M +   +   E           ++       I+  G+I  G  VN  DI++GK  P   
Sbjct: 627 DMEKKAGVQQVEEFEKPTRDTTLHMKHGTYDKIENDGLIAPGTGVNGADIIIGKTAPL-- 684

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 E+L +        DV        SG+   V+       H   K
Sbjct: 685 --PVDSEELGQRSRLHTRRDVSTPLKSTESGIVDQVLVTTNHEGHKFVK 731


>gi|190344605|gb|EDK36311.2| conserved hypothetical protein [Meyerozyma guilliermondii ATCC 6260]
          Length = 1166

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 76/279 (27%), Positives = 113/279 (40%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQW-GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +T            IE+++  GDD      + + +   + R    GDK + RHG KG+ S
Sbjct: 841  KTKVKTYHSSEPAYIEEVKLLGDDSGNQEGQQITIKYRVTRQPLIGDKFSSRHGQKGVCS 900

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 901  RKWPQVDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIFSE 960

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +                                             TP       +    
Sbjct: 961  DD--------------------------------------------TPA------DYFGE 970

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G TGE     + +G +Y  +L HMV+DK   RSTG  + +T Q
Sbjct: 971  QLRQAGYNYHGNEPMYSGATGEELRADIYIGCVYYQRLRHMVNDKFQVRSTGPVNSLTMQ 1030

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1031 PVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1069



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 90/655 (13%), Positives = 188/655 (28%), Gaps = 79/655 (12%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRV--MRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  +          DR + LL  Y+   +     +   + +          D  D
Sbjct: 264 DREIFDGIVGADTSNSFLTDRLELLLRSYKKYNLYSKQETLAYLGDKFRVVFGATPDVSD 323

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +     V   + L        +      ++ +I+ L  L  G  + D+ D   ++ V   
Sbjct: 324 IEVGQEVLKRIVLVHLEDPKDKF---RMLLFMIRKLYTLVAGDCSPDNPDATQHQEVLLG 380

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFF 517
           G +     +  +    +SI+ +ISS     V                    +   +  F 
Sbjct: 381 GFLYGMIIKEKIEEYLQSIRLQISSDINRGVAVNFNDRRYMSRVFLRINENIGQKLQYFL 440

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 441 STGNLVSQSGLDLQQVSGYTVVAEKINFHRFISHFR---MVHRGSFFAELKTTTVRKLLP 497

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVY-----L 617
             +G +CP  T +G   GL++ L    ++      + T    +    V+    +     L
Sbjct: 498 ESWGFLCPVHTPDGSPCGLLNHLAHKCKIATEASDVSTVPAALAQLGVSPAHAFAAGPNL 557

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ------- 670
             ++ + + +      +  +              E        ++     P         
Sbjct: 558 CCIQLDGKVV----GWVTHEHGKIVADTLRFWKVEGTHGLPLDLEIGYVPPSNQGQYPGL 613

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +    S +                   Q    +    P +   +     + S   +++ 
Sbjct: 614 YIFGGHSRMMRPTKYLPLDKQDIVGPFEQVYMDIAVTPPEIENNVH-THVEFSPTNVLSI 672

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            A +    D  +      +  +   T G   +    +           Q P+VK      
Sbjct: 673 LANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALAHRSDNKLYRLQTGQTPIVKANLYDD 732

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                       + +   G N +VA + + GY+ +D+M+I++             +  +V
Sbjct: 733 YG----------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYGTVYKVEKV 782

Query: 850 MA----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--------- 896
                 R      +       +  E   + +D  G+  +G +V  GD +V          
Sbjct: 783 DLSQSRRRGDPITQHFGFGEDSWPESWKEKLDSDGLPIIGVKVEEGDPIVAYFDDTLGKT 842

Query: 897 --KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             K     E     E KLL    G +         RV       ++  +  +RHG
Sbjct: 843 KVKTYHSSEPAYIEEVKLLGDDSGNQEGQQITIKYRV---TRQPLIGDKFSSRHG 894



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 96/750 (12%), Positives = 197/750 (26%), Gaps = 155/750 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDER---PNEGLQAAFKSVFPITAFS---GAAMLEFVSYEFDP 83
           +     S++                + G +  F S               +   S +   
Sbjct: 31  VSPHIGSFNALTEGPGGGLLNLGVQDIGTKTIFDSN----DTDRLGNKLSIRVESVQLTK 86

Query: 84  P------KFD------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
           P      K          +C  R  +Y   L + +   V D +E      + +++E    
Sbjct: 87  PAVPANDKLSMNRRTYPSECRERMTSYRSRLMLKVTWSVNDGEE------VSEVREA--- 137

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV---VSQLHRSPGIH 164
            G +P+M K                         G F++ GI++++   + Q    P   
Sbjct: 138 -GQIPIMLKSNRCHLEKLSPDELVKQKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAI 196

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVT 215
                G    S    +  +I   +         +    D    +  R   R+    VPV 
Sbjct: 197 IRPSFGNRGASYTK-FGIQIRCVRPDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVM 253

Query: 216 SFLMALGMDSE-EILSTFYPKIV------------------YSQRGDFWCFPLSAADLMV 256
             + AL   S+ EI                           Y+                V
Sbjct: 254 MIMKALVETSDREIFDGIVGADTSNSFLTDRLELLLRSYKKYNLYSKQETLAYLGDKFRV 313

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG---VKFLGITSDCLCGLYVAEDIV 313
               +  + DI+ G++V+   K++    L+  K+K    +  +      + G    ++  
Sbjct: 314 VFGATPDVSDIEVGQEVL---KRIVLVHLEDPKDKFRMLLFMIRKLYTLVAGDCSPDNPD 370

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
             +  E+ +          ++E     ++ I +     +N    +        ++     
Sbjct: 371 ATQHQEVLLGGFLYGM--IIKEKIEEYLQSIRLQISSDINRGVAVNFNDRRYMSRVFLRI 428

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             +I + +       F    ++ +    D  +    TV   K+N           R I  
Sbjct: 429 NENIGQKL-----QYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFH---------RFISH 474

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             ++       +L+         ++ G                L  +         + + 
Sbjct: 475 FRMVHRGSFFAELKTTTVRKLLPESWGF---------------LCPVHTPDGSPCGLLNH 519

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                      +    V A       S         N             +   G     
Sbjct: 520 LAHKCKIATEASDVSTVPAALAQLGVSPAHAFAAGPNLC----------CIQLDGKVVGW 569

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E    H             EG +   +     +   +  G     Y      ++   
Sbjct: 570 VTHE----HGKIVADTLRFWKVEGTHGLPLDLEIGYVPPSNQGQYPGLYIFGGHSRMMRP 625

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
             YL   +++   +               E V+   A     +       ++ SP  V+S
Sbjct: 626 TKYLPLDKQD--IVGPF------------EQVYMDIAVTPPEIENNVHTHVEFSPTNVLS 671

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           I A+L PF + + S R +  C M +Q +  
Sbjct: 672 ILANLTPFSDFNQSPRNMYQCQMGKQTMGT 701


>gi|190612188|gb|ACE80528.1| RNA polymerase subunit beta [Bradyrhizobium sp. BuNoG5]
 gi|313670764|gb|ADR73573.1| RNA polymerase subunit beta [Bradyrhizobium sp. 61A124]
          Length = 257

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 138/258 (53%), Positives = 187/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|146422181|ref|XP_001487032.1| conserved hypothetical protein [Meyerozyma guilliermondii ATCC 6260]
          Length = 1166

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 76/279 (27%), Positives = 113/279 (40%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQW-GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            +T            IE+++  GDD      + + +   + R    GDK + RHG KG+ S
Sbjct: 841  KTKVKTYHSSEPAYIEEVKLLGDDSGNQEGQQITIKYRVTRQPLIGDKFSSRHGQKGVCS 900

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            R  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +  
Sbjct: 901  RKWPQVDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIFSE 960

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +                                             TP       +    
Sbjct: 961  DD--------------------------------------------TPA------DYFGE 970

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             LR A  +  G   +Y G TGE     + +G +Y  +L HMV+DK   RSTG  + +T Q
Sbjct: 971  QLRQAGYNYHGNEPMYSGATGEELRADIYIGCVYYQRLRHMVNDKFQVRSTGPVNSLTMQ 1030

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1031 PVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1069



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 89/655 (13%), Positives = 190/655 (29%), Gaps = 79/655 (12%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRV--MRPGDVSTFSVAESMFNFLFFDSDKYD 407
           D    +  +          DR + LL  Y+   +     +   + +          D  D
Sbjct: 264 DREIFDGIVGADTSNSFLTDRLELLLRSYKKYNLYSKQETLAYLGDKFRVVFGATPDVSD 323

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           +     V   + L        +      ++ +I+ L  L  G  + D+ D   ++ V   
Sbjct: 324 IEVGQEVLKRIVLVHLEDPKDKF---RMLLFMIRKLYTLVAGDCSPDNPDATQHQEVLLG 380

Query: 468 GEMLKNQYRLGLLRMERSIKERI----------SSVDIDSVMPQDLINAKPVVSAVCEFF 517
           G +     +  +    +SI+ +I          +  D   +    L   + +   +  F 
Sbjct: 381 GFLYGMIIKEKIEEYLQSIRLQILSDINRGVAVNFNDRRYMSRVFLRINENIGQKLQYFL 440

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              + + E +N    I+H R    + +G          +R + P
Sbjct: 441 STGNLVSQSGLDLQQVSGYTVVAEKINFHRFISHFR---MVHRGSFFAELKTTTVRKLLP 497

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVY-----L 617
             +G +CP  T +G   GL++ L    ++      + T    +    V+    +     L
Sbjct: 498 ESWGFLCPVHTPDGSPCGLLNHLAHKCKIATEASDVSTVPAALAQLGVSPAHAFAAGPNL 557

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ------- 670
             ++ + + +      +  +              E        ++     P         
Sbjct: 558 CCIQLDGKVV----GWVTHEHGKIVADTLRFWKVEGTHGLPLDLEIGYVPPSNQGQYPGL 613

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            +    S +                   Q    +    P +   +     + S   +++ 
Sbjct: 614 YIFGGHSRMMRPTKYLPLDKQDIVGPFEQVYMDIAVTPPEIENNVH-THVEFSPTNVLSI 672

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            A +    D  +      +  +   T G   +    +           Q P+VK      
Sbjct: 673 LANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALAHRSDNKLYRLQTGQTPIVKANLYDD 732

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                       + +   G N +VA + + GY+ +D+M+I++             +  +V
Sbjct: 733 YG----------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYGTVYKVEKV 782

Query: 850 MA----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG--------- 896
                 R      +       +  E   + +D  G+  +G +V  GD +V          
Sbjct: 783 DLSQSRRRGDPITQHFGFGEDSWPESWKEKLDSDGLPIIGVKVEEGDPIVAYFDDTLGKT 842

Query: 897 --KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             K     E     E KLL    G +         RV       ++  +  +RHG
Sbjct: 843 KVKTYHSSEPAYIEEVKLLGDDSGNQEGQQITIKYRV---TRQPLIGDKFSSRHG 894



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 96/750 (12%), Positives = 198/750 (26%), Gaps = 155/750 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDER---PNEGLQAAFKSVFPITAFS---GAAMLEFVSYEFDP 83
           +     S++                + G +  F S               +   S +   
Sbjct: 31  VSPHIGSFNALTEGPGGGLLNLGVQDIGTKTIFDSN----DTDRLGNKLSIRVESVQLTK 86

Query: 84  P------KFD------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
           P      K          +C  R  +Y   L + +   V D +E      + +++E    
Sbjct: 87  PAVPANDKLSMNRRTYPSECRERMTSYRSRLMLKVTWSVNDGEE------VSEVREA--- 137

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV---VSQLHRSPGIH 164
            G +P+M K                         G F++ GI++++   + Q    P   
Sbjct: 138 -GQIPIMLKSNRCHLEKLSPDELVKQKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMAI 196

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVT 215
                G    S    +  +I   +         +    D    +  R   R+    VPV 
Sbjct: 197 IRPSFGNRGASYTK-FGIQIRCVRPDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVM 253

Query: 216 SFLMALGMDSE-EILSTFYPKIV------------------YSQRGDFWCFPLSAADLMV 256
             + AL   S+ EI                           Y+                V
Sbjct: 254 MIMKALVETSDREIFDGIVGADTSNSFLTDRLELLLRSYKKYNLYSKQETLAYLGDKFRV 313

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG---VKFLGITSDCLCGLYVAEDIV 313
               +  + DI+ G++V+   K++    L+  K+K    +  +      + G    ++  
Sbjct: 314 VFGATPDVSDIEVGQEVL---KRIVLVHLEDPKDKFRMLLFMIRKLYTLVAGDCSPDNPD 370

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
             +  E+ +          ++E     ++ I +  +  +N    +        ++     
Sbjct: 371 ATQHQEVLLGGFLYGM--IIKEKIEEYLQSIRLQILSDINRGVAVNFNDRRYMSRVFLRI 428

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             +I + +       F    ++ +    D  +    TV   K+N           R I  
Sbjct: 429 NENIGQKL-----QYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFH---------RFISH 474

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             ++       +L+         ++ G                L  +         + + 
Sbjct: 475 FRMVHRGSFFAELKTTTVRKLLPESWGF---------------LCPVHTPDGSPCGLLNH 519

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
                      +    V A       S         N             +   G     
Sbjct: 520 LAHKCKIATEASDVSTVPAALAQLGVSPAHAFAAGPNLC----------CIQLDGKVVGW 569

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E    H             EG +   +     +   +  G     Y      ++   
Sbjct: 570 VTHE----HGKIVADTLRFWKVEGTHGLPLDLEIGYVPPSNQGQYPGLYIFGGHSRMMRP 625

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
             YL   +++   +               E V+   A     +       ++ SP  V+S
Sbjct: 626 TKYLPLDKQD--IVGPF------------EQVYMDIAVTPPEIENNVHTHVEFSPTNVLS 671

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           I A+L PF + + S R +  C M +Q +  
Sbjct: 672 ILANLTPFSDFNQSPRNMYQCQMGKQTMGT 701


>gi|223928140|gb|ACN23838.1| RNA polymerase beta subunit [Bartonella sp. KM2529]
          Length = 298

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 215/299 (71%), Positives = 253/299 (84%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ES+VA+ SGAA+ A+R+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESIVARDSGAAVAARRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|156255567|gb|ABU63000.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 231

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 143  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 185

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 186  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 231



 Score = 42.4 bits (98), Expect = 0.54,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 46


>gi|302825794|ref|XP_002994479.1| hypothetical protein SELMODRAFT_270143 [Selaginella moellendorffii]
 gi|300137562|gb|EFJ04457.1| hypothetical protein SELMODRAFT_270143 [Selaginella moellendorffii]
          Length = 1172

 Score =  279 bits (713), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 99/455 (21%), Positives = 160/455 (35%), Gaps = 47/455 (10%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              D         +   G   +G  +   +     +   L+      A +V      +   
Sbjct: 690  WSDHNQSPRNMYQCQMGKQTLGFASQALKFRTDHKMYNLQNPQSPVARNVNYKKYNMDEF 749

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
              GT   V +    G D  +  I  +      LA  +  +   +D ++  +  + +    
Sbjct: 750  PLGTNAVVAVLAYTGFDMEDAMIMNKSSMERGLAHGQIYKTEHVDLSLLQKKSDGIVNLF 809

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK-SILEDRF 1053
            +               + +         Q     +     + ++    +  K    E+  
Sbjct: 810  SR------PTGKRNIHNFLDVDGLPHIGQTMHNGDPYCSVLNTMTGDAKLHKLKAAENVV 863

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             + +  I  G       L+ + V     R    GDK + RHG KGI+S++ P  DMPF  
Sbjct: 864  IDSVIAIGHGR----DPLQKIAVKFRHDRNPVIGDKFSSRHGQKGILSQLWPDIDMPFSA 919

Query: 1114 -DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
              G   DI++NP   PSRM +G + E+    A V  G+ + S      +    +      
Sbjct: 920  VTGMRPDIIINPHAFPSRMTIGMLMESMAAKAGVLRGEYVDSTPFRSSSAALDAKDGKTG 979

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                G   H   IS                                    L     +  G
Sbjct: 980  SGYKGKDKHYPAIS-------------------------------EFGEQLAQHGFNYHG 1008

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ++Y GL G      + +G +Y  +L HMVSDK   RS G+ + VT+QP+GG+   GG 
Sbjct: 1009 TEVMYSGLLGTELTCEIFIGVVYYQRLRHMVSDKFQVRSLGAINPVTRQPVGGRKLGGGI 1068

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV 1323
            R GEME   + A+GAAY+L + L   SD    DV 
Sbjct: 1069 RFGEMERDSLLAHGAAYLLHDRLHTSSDYHVGDVC 1103



 Score = 70.5 bits (171), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 96/619 (15%), Positives = 194/619 (31%), Gaps = 49/619 (7%)

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY-----VDSVNNNAYI 358
            G  +         G I     D  D +  E++    ++                    I
Sbjct: 247 LGFVIRRQEFVIPVGIILKAFMDTSDREIFEQLSGIHVQGQEQSKGAVGSQLISQRARII 306

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
                      R D L  I  V+R             FN L     K      G   +  
Sbjct: 307 IEETQRQPCLTRLDCLRYIEDVLRRFVFVHLDNFRDKFNLLIHMLHKLFAVVDGSASI-- 364

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
               D+ D ++H        ++ I +  R              +R+      LK ++ L 
Sbjct: 365 ----DSSDTLQHQELLLPGHLMNIYLKDRLEDWL------YRCKRLLQREMQLKEEFDLS 414

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
                  I E+ ++VDI   +   L        +  +   ++  S + E +N    I+H 
Sbjct: 415 DHAKVLKIVEKNNAVDIGKRIEYLLSTGNIQSQSHMDLQQANGFSVVAEKLNFFRFISHF 474

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------ 592
           R   ++ +G     +    +R + P  +G +CP  T +G   GL++ L+S  ++      
Sbjct: 475 R---SVHRGAFFARQRTTSVRKLLPESWGFLCPVHTPDGEPCGLLTHLSSLCKISTDLDQ 531

Query: 593 -NAYGFIETPYRK---VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            N     +  +R    V        +  L A+    +Y+A     +  DG     +    
Sbjct: 532 NNHPKDPKVIHRTIATVLAQLGMVSISPLLALSGPPKYLA-----VLLDGCVLGYMPVGN 586

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                  +   K+           + A +          +R L            L +  
Sbjct: 587 IPQTVSHLRSLKVPIDLEIGYVPCTYAGAYPGLFLYTTPSRFLRPVKQLDTGAIELISAF 646

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVE-QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                 +      + G    A  A  +E    A+  V+ S     D + S  ++Y+    
Sbjct: 647 EQAYMEIACPDGGNCGRTPSAPPATHIELHPTAMLSVVASSTPWSDHNQSPRNMYQCQMG 706

Query: 768 QRS--NQNTCVNQRPLVKVGDEVRRNDIIADGPST---DLGDLALGRNMLVAFMPWHGYN 822
           +++    +  +  R   K+ +       +A   +    ++ +  LG N +VA + + G++
Sbjct: 707 KQTLGFASQALKFRTDHKMYNLQNPQSPVARNVNYKKYNMDEFPLGTNAVVAVLAYTGFD 766

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARD-----TKLGPEEITRDIPNVSEEGLKNID 877
            ED+M++++  +   +    H + ++    D      K          P         +D
Sbjct: 767 MEDAMIMNKSSMERGLA---HGQIYKTEHVDLSLLQKKSDGIVNLFSRPTGKRNIHNFLD 823

Query: 878 ECGIICVGAEVNPGDILVG 896
             G+  +G  ++ GD    
Sbjct: 824 VDGLPHIGQTMHNGDPYCS 842



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 103/755 (13%), Positives = 220/755 (29%), Gaps = 154/755 (20%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA--MLEFV-----SYE 80
           DL+     S+D+F+            GL  A K + P+    G+    L ++      + 
Sbjct: 31  DLVSPHIDSFDYFVQR----------GLVEAVKGIAPVEIEQGSTGNKLIYILWMNFGFS 80

Query: 81  FD-------------PPKFD-----------VDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
            D             PP  D             +C    L+Y   L   ++LI+ D    
Sbjct: 81  LDVVLALTLDKPVVQPPVKDLKEKAMEHRLLPKECRQGFLSYTGAL--NIQLIL-DYGSM 137

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
           T        +   + +G LP+M K                         G F++KGI+RI
Sbjct: 138 T--------RHHQLSLGKLPIMLKSSLCHLRGLSPQKLISLKEEGTEMGGYFIVKGIERI 189

Query: 153 VVSQLH--RSPGIHFDHDKGRASLSGKLLYACRIIPDQ-------GLWMDIEFDSKDI-- 201
           +   +   R+  I    +  +   +G   ++   +  +       G  + + +       
Sbjct: 190 IRMLIVPKRNHIIAIRRNAFQNRGAG---FSDIGLMMRCVRPDQTGSTIKLYYLHHGTAR 246

Query: 202 IHVRIDRRRK--VPVTSFLMA-LGMDSEEILSTFYPKIVYSQRGDF-----WCFPLSAAD 253
           +   I RR++  +PV   L A +     EI        V  Q               A  
Sbjct: 247 LGFVI-RRQEFVIPVGIILKAFMDTSDREIFEQLSGIHVQGQEQSKGAVGSQLISQRARI 305

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG--VKFLGITSDCLCGLYVAED 311
           ++   +    L  +D    + +  ++     L + ++K   +  +      +     + D
Sbjct: 306 IIEETQRQPCLTRLDCLRYIEDVLRRFVFVHLDNFRDKFNLLIHMLHKLFAVVDGSASID 365

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             +    +  +  G +++    + +     R   +L  +      +  +          K
Sbjct: 366 SSDTLQHQELLLPGHLMNIYLKDRLEDWLYRCKRLLQREMQLKEEFDLSDHAKVLKIVEK 425

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +  +DI + +                          L + G ++    ++L   +     
Sbjct: 426 NNAVDIGKRI------------------------EYLLSTGNIQSQSHMDLQQANGFSV- 460

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERI 490
                +A         +   ++        +R  SV ++L   +  L  +         +
Sbjct: 461 -----VAEKLNFFRFISHFRSVHRGAFFARQRTTSVRKLLPESWGFLCPVHTPDGEPCGL 515

Query: 491 SSVDIDSVMPQ---DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
            +            D  N       +     +         ++ L  ++   +  A+   
Sbjct: 516 LTHLSSLCKISTDLDQNNHPKDPKVIHRTIATVLAQLGMVSISPLLALSGPPKYLAVLLD 575

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G       V       +H   +      E   +   +   ++  +  Y       R V  
Sbjct: 576 GCVLGYMPVGNIPQTVSHLRSLKVPIDLEIGYV-PCTYAGAYPGLFLYTTPSRFLRPVKQ 634

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
              T  +  +SA E+    IA        DG                  P      I+  
Sbjct: 635 LD-TGAIELISAFEQAYMEIA------CPDGGNCGR---------TPSAPPA--THIELH 676

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           P  ++S+ AS  P+ +++ S R +  C M +Q + 
Sbjct: 677 PTAMLSVVASSTPWSDHNQSPRNMYQCQMGKQTLG 711


>gi|226124|prf||1411173A RNA polymerase beta
          Length = 287

 Score =  278 bits (712), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 170/287 (59%), Positives = 222/287 (77%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+LGNRRVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +A
Sbjct: 1   VDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAA 60

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 61  VKEFFGSSQLSQFMDQNNPLSEITHKRRCSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 120

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL ++AR N YGF+E+PYR V +G V++D+V+LSA+EE +  IAQA++
Sbjct: 121 ETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVSDDIVFLSAIEEADHVIAQASA 180

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           ++++     +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 181 AMNDKHQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 240

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +V +R G+++ VD
Sbjct: 241 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVRRRGGVIDSVD 287


>gi|269930823|gb|ACZ54146.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 300

 Score =  278 bits (712), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 217/301 (72%), Positives = 253/301 (84%), Gaps = 1/301 (0%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   IGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 61  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ 
Sbjct: 121 FIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMA 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME
Sbjct: 181 PRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
           SVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T  
Sbjct: 241 SVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSTKR 299

Query: 777 N 777
           N
Sbjct: 300 N 300


>gi|197944873|gb|ACH79983.1| RNA polymerase subunit B [Mycobacterium fallax]
          Length = 235

 Score =  278 bits (712), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 97/224 (43%), Positives = 128/224 (57%), Gaps = 34/224 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGWA    G  I     + +     + L + L   
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWAAKA-GWNIPGADGNGEVPEWAAKLPAELLSA 156

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 157  PSDSI-------------------------VSTPVFDGAREEELQGLLSSTLPNRDGETM 191

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARS
Sbjct: 192  VGGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARS 235



 Score = 42.8 bits (99), Expect = 0.45,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|313670776|gb|ADR73579.1| RNA polymerase subunit beta [Bradyrhizobium jicamae]
          Length = 257

 Score =  278 bits (712), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 142/258 (55%), Positives = 185/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMYALGLDGETILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  + W  P  A+    G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KINYKRAKEGWRVPFDAS-RFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EAG+ + EKSL+ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIYAEAGEELTEKSLKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLNADKNMTREDALFDIYRVMRPGEPPTIDSAQTMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTHRTLR 257


>gi|226934694|gb|ACO92421.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 233

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 40   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 99

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 100  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 145  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 187

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 188  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 233



 Score = 44.3 bits (103), Expect = 0.14,   Method: Composition-based stats.
 Identities = 30/48 (62%), Positives = 39/48 (81%)

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           + +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   TELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 48


>gi|52694245|emb|CAG30652.1| DNA-directed RNA polymerase beta chain [Pseudomonas balearica]
          Length = 366

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 169/292 (57%), Positives = 217/292 (74%), Gaps = 1/292 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 26  SSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 85

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL ++AR N YGF+E+PYR V DG+VT+++V+LSA+EE +  IAQA++ LDE  
Sbjct: 86  NIGLINSLAAYARTNQYGFLESPYRVVKDGEVTDEIVFLSAIEEADHVIAQASAKLDEPV 145

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           S  +E+V  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQR
Sbjct: 146 SLVDEIVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 205

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGA-AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           QAVP L+++ P VGTGME  V   +   A VA+R G+++ VDA RIV+R  + +++   +
Sbjct: 206 QAVPTLRSDKPLVGTGMERNVPPGNPVFASVARRGGVIDSVDASRIVVRVNDDEVETGEA 265

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           GVDIY L K+ RSNQNTC+NQRPLV+ GD+V R DI+ADGPSTD+G     R
Sbjct: 266 GVDIYNLTKYTRSNQNTCINQRPLVQKGDQVARGDIMADGPSTDMGSWRWAR 317


>gi|50425489|ref|XP_461338.1| DEHA2F22902p [Debaryomyces hansenii CBS767]
 gi|49657007|emb|CAG89744.1| DEHA2F22902p [Debaryomyces hansenii]
          Length = 1167

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 91/470 (19%), Positives = 157/470 (33%), Gaps = 55/470 (11%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +     E    +I ++        D         +   G   +G            + 
Sbjct: 655  ENNIHTHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALNHRSDNKL 714

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              L+                + +  +G    V + +  G D ++  I  +          
Sbjct: 715  YRLQTGQTPIVKASLYDDYGMDNFPNGMNAVVAVISYTGYDMDDAMIINKSADERGFGYG 774

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
               +   +D +   R  + +       G    +        L ++       +    D  
Sbjct: 775  TVYKVEKVDLSQSRRRGDPITQHF---GFGTDEWPESWREKLDADGLPLIGVKVDEGDPI 831

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            V    ++L      +    E  +  +++ +  GDD      + + +   + R    GDK 
Sbjct: 832  VAYYDDTLGRTKVKTYHSTEPAYIEEVKLL--GDDSGDQEGQQITIKYRITRQPLIGDKF 889

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G 
Sbjct: 890  SSRHGQKGVCSRKWPQVDMPFSETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGI 949

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               +    +  +                                             TP 
Sbjct: 950  AQDATPWKFSEDD--------------------------------------------TPA 965

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
                  +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+DK   R
Sbjct: 966  ------DFFGEQLSKAGYNYHGNEPMYSGATGEELRADIYIGCVYYQRLRHMVNDKFQVR 1019

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            STG  + +T QP+ G+   GG R+GEME   +  +G A++LQ+ L   SD
Sbjct: 1020 STGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTAFLLQDRLLNCSD 1069



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 79/589 (13%), Positives = 174/589 (29%), Gaps = 59/589 (10%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR-PGDVSTFSVAESMFNFLFFDSDKYDL 408
           D    +  I          DR + LL  Y+         T +     F  +F  +     
Sbjct: 264 DREIFDGIIGADTSNSFLTDRLELLLRTYKQYNLYSKQETLAYLGDKFRIVFGSAPDVSD 323

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VG+  +   + +  P+++   +   ++ +I+ L  L  G    D+ D   ++ V   G
Sbjct: 324 IEVGKEVLQRIVLVHLPNNLD--KFRMLLFMIRKLYSLVAGDCCPDNPDATQHQEVLLGG 381

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFFC 518
            +     +  +    ++IK +I S     +                    +   +  F  
Sbjct: 382 FLYGMIIKEKIDEYLQNIKLQIQSDINRGIAINFNDRKYMSRVFLRINENIGQKLQYFLS 441

Query: 519 SSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +  L              + + E +N    I+H R    + +G          +R + P 
Sbjct: 442 TGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLPE 498

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP  T +G   GL++ L+   ++       +           +     +A    N
Sbjct: 499 SWGFLCPVHTPDGSPCGLLNHLSHKCQIATEASDVSQVPVALAQLGVSPAHSFAAGP--N 556

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQVVS 673
               Q +  +    +     +         +          ++ ++  S     P   + 
Sbjct: 557 LCCVQLDGKVMGWTTHEHGKIVADTLRYWKVEGNHGLPLDLEVGYVPPSTKGQYPGLYLF 616

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
              S +                   Q    +      +   +     + S   I++  A 
Sbjct: 617 GGHSRMMRPTKYLPLNKTDILGPFEQVYMDVAVTPAEIENNIH-THVEFSPTNILSILAN 675

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           +    D  +      +  +   T G   +    +           Q P+VK         
Sbjct: 676 LTPFSDFNQSPRNMYQCQMGKQTMGTPGVALNHRSDNKLYRLQTGQTPIVKASLYDDYG- 734

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA- 851
                    + +   G N +VA + + GY+ +D+M+I++             +  +V   
Sbjct: 735 ---------MDNFPNGMNAVVAVISYTGYDMDDAMIINKSADERGFGYGTVYKVEKVDLS 785

Query: 852 ---RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              R      +          E   + +D  G+  +G +V+ GD +V  
Sbjct: 786 QSRRRGDPITQHFGFGTDEWPESWREKLDADGLPLIGVKVDEGDPIVAY 834



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 92/677 (13%), Positives = 189/677 (27%), Gaps = 139/677 (20%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------- 140
             +C  R  TY   L + +   V D DE      + +I+E     G +P+M K       
Sbjct: 103 PSECRERMSTYRSRLMLKVTWSVNDGDE------VSEIREA----GQVPVMLKTNRCHLE 152

Query: 141 -----------------DGTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGKLLY 180
                             G F++ GI++++   + Q    P        G    S    +
Sbjct: 153 KLSPSELVDQKEESDEMGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFGNRGASYTK-F 211

Query: 181 ACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-EILS 230
             +I   +         +    D    +  R   ++    VP    L AL   ++ EI  
Sbjct: 212 GIQIRCVRPDQTSQTNVLHYLNDGN--VTFRFSWKKNEYLVPAMMILKALIETNDREIFD 269

Query: 231 -TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI----------ESGKK 279
                    S   D     L             +L  +    +++          E GK+
Sbjct: 270 GIIGADTSNSFLTDRLELLLRTYKQYNLYSKQETLAYLGDKFRIVFGSAPDVSDIEVGKE 329

Query: 280 LTSGLLKSLKEKGVKFLGITSDCL-------CGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           +   ++       +    +    +        G    ++    +  E+ +          
Sbjct: 330 VLQRIVLVHLPNNLDKFRMLLFMIRKLYSLVAGDCCPDNPDATQHQEVLLGGFLYGM--I 387

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           ++E     +++I +     +N    I        ++       +I + +       F   
Sbjct: 388 IKEKIDEYLQNIKLQIQSDINRGIAINFNDRKYMSRVFLRINENIGQKL-----QYFLST 442

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            ++ +    D  +    TV   K+N           R I    ++       +L+     
Sbjct: 443 GNLVSQSGLDLQQVSGYTVVAEKINFY---------RFISHFRMVHRGSFFAELKTTTVR 493

Query: 453 IDDIDNLG-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
               ++ G     +    S   +L +      +  E S   ++        +      A 
Sbjct: 494 KLLPESWGFLCPVHTPDGSPCGLLNHLSHKCQIATEASDVSQVPVALAQLGVSPAHSFAA 553

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                  +     ++     H +        R     G  G+      +E+  V P+  G
Sbjct: 554 GPNLCCVQLDG--KVMGWTTHEHGKIVADTLRYWKVEGNHGL---PLDLEVGYVPPSTKG 608

Query: 568 RICPAETSEGHNIGLVSSLTS-FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           +        GH+  +  +      + +  G  E  Y  V           ++  E EN  
Sbjct: 609 QYPGLYLFGGHSRMMRPTKYLPLNKTDILGPFEQVYMDVA----------VTPAEIEN-- 656

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                                                ++ SP  ++SI A+L PF + + 
Sbjct: 657 --------------------------------NIHTHVEFSPTNILSILANLTPFSDFNQ 684

Query: 687 SNRVLMGCNMQRQAVPL 703
           S R +  C M +Q +  
Sbjct: 685 SPRNMYQCQMGKQTMGT 701


>gi|183579261|gb|ACC63208.1| RpoB [Mycobacterium scrofulaceum]
          Length = 224

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 127/226 (56%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I           ++       +  
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNINVAEGVPPWAANLPEDLLHAQPN 146

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                                          VSTPVFDGA E  +  +L            
Sbjct: 147  A----------------------------IVSTPVFDGAREAELQGLLSCTLPNRDNEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG
Sbjct: 179  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTG 224


>gi|255718993|ref|XP_002555777.1| KLTH0G17160p [Lachancea thermotolerans]
 gi|238937161|emb|CAR25340.1| KLTH0G17160p [Lachancea thermotolerans]
          Length = 1197

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 90/468 (19%), Positives = 160/468 (34%), Gaps = 54/468 (11%)

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +T    E    +I ++        D         +   G   +G            +   
Sbjct: 678  NTHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYR 737

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            L+                + +  +G    V + +  G D ++  I  +      L     
Sbjct: 738  LQTGQTPIVKANLYDEYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGLGYGTM 797

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
             +   +D  + +R       Q+   G   + K+ +   D + +        +  + + + 
Sbjct: 798  YKVEKVDLAL-NRSRGDPITQHFGFGDDEWPKNWL---DKLDDDGLPMIGTYVEEGDPIC 853

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
               +    + +       +    +   +   +      L+ V +   ++R  Q GDK + 
Sbjct: 854  AFFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESSKFQELQTVSIKYRIRRTPQIGDKFSS 913

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG+ SR  P  DMPF + G   DI++NP   PSRM +G   E+  G A    G   
Sbjct: 914  RHGQKGVCSRKWPTVDMPFSESGMQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGMAH 973

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +    +                                                TP   
Sbjct: 974  DATPWTFTEED--------------------------------------------TPA-- 987

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                +     L  A  +  G   +Y G TG+     + +G +Y  +L HMV+DK   RST
Sbjct: 988  ----DCFGEQLLQAGYNYHGNEPMYSGATGQELRADIYIGVVYYQRLRHMVNDKFQVRST 1043

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1044 GPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1091



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 85/607 (14%), Positives = 187/607 (30%), Gaps = 102/607 (16%)

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             + +  + + L     D  R +     + +I+ L  L  G+ + D+ D   ++ V   G
Sbjct: 346 EELLKRIVLVHLGDSNEDKSRML-----LFMIRKLYSLVAGECSPDNPDATQHQEVLLGG 400

Query: 469 EMLKNQYRLGLLRMERSIKERI----------SSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            +     +  +    ++IK +I          +  +   +    +   + + S +  F  
Sbjct: 401 FLYGMIIKEKIEEYLQNIKLQIQSDVNRGLAVNFKERKYMTRVLMRVNENIGSKLQYFLS 460

Query: 519 SSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +  L              + + E +N    I+H R    + +G          +R + P 
Sbjct: 461 TGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAQLKTTTVRKLLPE 517

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP  T +G   GL++      +++                V+     L      +
Sbjct: 518 SWGFLCPVHTPDGSPCGLLNHFAHKCKIST-----------SQSDVSRIPSLL-----YS 561

Query: 625 RYIAQANSSLDEDGSF----TEELVFCRCAGEEILVPREKIDFIDAS---PKQVVSIAAS 677
             +A A+ +     +      +  +   C+ E+  +  + + F       P   + +   
Sbjct: 562 LGVAPASHTFTAGPTMCCVQLDGKIVGWCSHEQGKIIADTLRFWKVEGETPGLPLDLEIG 621

Query: 678 LIPFLENDDSNRVLM---GCNMQRQAVPLLKAEAPFVG----------------TGMESV 718
            +P         + +      M R    L   +   VG                      
Sbjct: 622 YVPPSSRGQYPGLYLFGGHSRMMRPVKYLPLGKEDIVGPFEQVYMNIAVTPKEIQNNTHT 681

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVN 777
             + +   I++  A +    D  +      +  +   T G   +    +           
Sbjct: 682 HVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTG 741

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q P+VK                  + +   G N +VA + + GY+ +D+M+I++      
Sbjct: 742 QTPIVKANLYDEYG----------MDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERG 791

Query: 838 VFTSIHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +      +  +V       R   +       D        L  +D+ G+  +G  V  GD
Sbjct: 792 LGYGTMYKVEKVDLALNRSRGDPITQHFGFGDDEWPKNW-LDKLDDDGLPMIGTYVEEGD 850

Query: 893 ILVGK----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
            +              T     P   EE  L      K  +++  S++     +  + D 
Sbjct: 851 PICAFFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESSKFQELQTVSIKYRIRRTPQIGD- 909

Query: 943 RIFNRHG 949
           +  +RHG
Sbjct: 910 KFSSRHG 916



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 111/886 (12%), Positives = 233/886 (26%), Gaps = 121/886 (13%)

Query: 29  LIE--VQ--KASYDHFLMM---NIAPDERPNEGLQAAFKSVFPITAFS---GAAMLEFVS 78
           L+E  VQ    S++         +      + G +  F         +       L    
Sbjct: 37  LLEEAVQPHIGSFNALTEGPDGGLLNQAVKDIGGKVVFDGTKSDENPNYLGNKLTLSVEQ 96

Query: 79  YEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                P            K    +   R  +Y   L + LR  + D +E        +I+
Sbjct: 97  VSISKPVSNDGVSSAVERKVFPSESRQRLSSYRGKLLLKLRWAINDGEESFT-----EIR 151

Query: 127 EQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV---VSQLHR 159
           +     G LP+M +                         G F+I GI++++   + Q   
Sbjct: 152 DC----GGLPVMLQSNRCHLNKLSPNELVKHKEESDELGGYFIINGIEKLIRMLIVQRRN 207

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK 211
            P             S    Y+   I  + +  D +    +++H         R   R+ 
Sbjct: 208 HPMAIIRPSFANRGAS----YSQYGIQIRSVRPD-QTSQTNVLHYLNDGEVTFRFSWRKN 262

Query: 212 ---VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
              +PV   L AL  ++  EI    +  IV S   + +        L    K    L + 
Sbjct: 263 EYLIPVVMILKALCELNDREI----FDGIVGSDTSNSFLTDRLELLLRGHKKKYGELHNR 318

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
              + +   G K        L+           + L    V   + +    +  +    +
Sbjct: 319 R--QVLQYLGDKFRV----VLQASPDATDFQVGEELLKRIVLVHLGDSNEDKSRMLLFMI 372

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
               SL     S        + + +         +     +  ++  L I   +  G ++
Sbjct: 373 RKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMIIKEKIEEYLQNIKLQIQSDVNRG-LA 431

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                      +    ++   S +        L   +  D++ +    ++A         
Sbjct: 432 VNFKERKYMTRVLMRVNENIGSKLQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFI 491

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           +    +         +  +V ++L   +                      ++       K
Sbjct: 492 SHFRMVHRGSFFAQLKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHFAHKCK 544

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
              S        S L  L     S +             G +    +  + + +  T   
Sbjct: 545 ISTSQSDVSRIPSLLYSLGVAPASHTFTAGPTMCCVQLDGKIVGWCSHEQGKIIADT--- 601

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            +   +         +     +   ++ G     Y      ++   V YL   +E+   +
Sbjct: 602 -LRFWKVEGETPGLPLDLEIGYVPPSSRGQYPGLYLFGGHSRMMRPVKYLPLGKED--IV 658

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                          E V+   A     +       ++ +P  ++SI A+L PF + + S
Sbjct: 659 GPF------------EQVYMNIAVTPKEIQNNTHTHVEFTPTNILSILANLTPFSDFNQS 706

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRI 743
            R +  C M +Q +                +    +G   + K     E           
Sbjct: 707 PRNMYQCQMGKQTMGT--PGVALCHRSDNKLYRLQTGQTPIVKANLYDEYGMDNFPNGFN 764

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            + +V            I      +R      + +   V +     R D I         
Sbjct: 765 AVVAVISYTGYDMDDAMIINKSADERGLGYGTMYKVEKVDLALNRSRGDPITQHFGFGDD 824

Query: 804 DLA--LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
           +        +    +P  G   E+   I      +D      I+ +
Sbjct: 825 EWPKNWLDKLDDDGLPMIGTYVEEGDPIC--AFFDDTLNKTKIKTY 868


>gi|269930855|gb|ACZ54162.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 296

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 215/297 (72%), Positives = 251/297 (84%), Gaps = 1/297 (0%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   IGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 61  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ 
Sbjct: 121 FIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMA 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME
Sbjct: 181 PRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           SVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 241 SVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 296


>gi|313759653|gb|ADR79139.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 229

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 229


>gi|226934672|gb|ACO92410.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|226934686|gb|ACO92417.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 221

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 133  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 176  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 221


>gi|185179223|gb|ACC77624.1| RpoB [Mycobacterium abscessus]
          Length = 218

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 125/226 (55%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 25   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 130  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 172

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 173  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 218


>gi|156255571|gb|ABU63002.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|226934692|gb|ACO92420.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 232

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 144  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 187  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 232



 Score = 43.5 bits (101), Expect = 0.26,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 47


>gi|89888213|gb|ABD78650.1| DNA-directed RNA polymerase beta subunit [Bordetella hinzii]
          Length = 294

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 177/290 (61%), Positives = 229/290 (78%)

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL++S+  +AR+N YGF+ETPYRK+ DGKV++ + YLSA+EE +  IAQAN++LD
Sbjct: 1   EGPNIGLINSMALYARLNEYGFLETPYRKIIDGKVSDQIDYLSAIEESHYVIAQANAALD 60

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +G F ++LV CR AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG N
Sbjct: 61  AEGRFVDDLVACREAGETMLTSPANVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +    
Sbjct: 121 MQRQAVPCLRPEKPLVGTGIERTVAVDSGTTVQALRGGLVDHVDAERVVIRVNDEENVAG 180

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             GVDIY L+K+ RSNQNT +NQRP+VK GD V + D++ADG STDLG+LALG+NML+AF
Sbjct: 181 EVGVDIYNLIKYTRSNQNTNINQRPIVKRGDRVAKGDVLADGASTDLGELALGQNMLIAF 240

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           MPW+GYNFEDS+LISER+V++D +TS+HIEE  V+ARDTKLGPEEITRDI
Sbjct: 241 MPWNGYNFEDSILISERVVADDRYTSVHIEELTVVARDTKLGPEEITRDI 290


>gi|255731632|ref|XP_002550740.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Candida tropicalis
            MYA-3404]
 gi|240131749|gb|EER31308.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Candida tropicalis
            MYA-3404]
          Length = 1166

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 93/476 (19%), Positives = 162/476 (34%), Gaps = 61/476 (12%)

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E +  +     E    +I ++        D         +   G   +G           
Sbjct: 654  EEIENNVHSHVEFSPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSD 713

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL- 966
             +   L+                + +  +G    V + +  G D ++ ++ + +   E  
Sbjct: 714  NKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAIVAVISYTGYDMDD-AMIINKSADERG 772

Query: 967  --LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                     E++ L ++   R   I       +          L +D +         + 
Sbjct: 773  FGYGTVYKTEKIDLSQSRR-RGDPITQHFGFGTDEWPEAWKEKLDADGLPMIG----VKV 827

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D  V    ++L      +    E  +  +++ +  GD+      + + +   + R  
Sbjct: 828  EAGDPIVAYYDDTLGKTKVKTYHSSEPGYIEEVKLL--GDETSDQEGQQLTIKYRITRAP 885

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A
Sbjct: 886  LIGDKFSSRHGQKGVCSRKWPQIDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKA 945

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G    S    +                                             
Sbjct: 946  GALHGIAQDSTPWKFNEQD----------------------------------------- 964

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               TP       +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+
Sbjct: 965  ---TPA------DYFGEQLLKAGYNYHGNEPMYSGATGEELRCDIYIGCVYYQRLRHMVN 1015

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1016 DKFQVRSTGPVNSLTMQPVKGRKRSGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1071



 Score = 72.4 bits (176), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 92/649 (14%), Positives = 192/649 (29%), Gaps = 67/649 (10%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR-PGDVSTFSVAESMFNFLFFDSDKYDL 408
           D    +  + N        DR + LL  Y+         T +     F  +F  +     
Sbjct: 266 DREIFDGIVGNDTGNSFLTDRLELLLRTYKKYNLNSQQETLAYLGDKFRVVFGATPDMSD 325

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VG+  +   + +  PD+    +   ++ +I+ L  L  G    D+ D   ++ V   G
Sbjct: 326 IDVGKEVLKRIVLVHLPDN--TDKFRMLLFMIRKLYSLVAGDCAPDNPDATQHQEVLLGG 383

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP----------VVSAVCEFFC 518
            +     +  +    ++IK +I S     V                    +   +  F  
Sbjct: 384 FLYGMIIKEKIEEYLQNIKLQIQSDINRGVGINFDDRKYMTRVFSRINENIGQKLQYFLS 443

Query: 519 SSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +  L              + + E +N    I+H R    + +G          +R + P 
Sbjct: 444 TGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRGSFFAELKTTTVRKLLPE 500

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP  T +G   GL++ L    ++       +   K             +A  +  
Sbjct: 501 SWGFLCPVHTPDGSPCGLLNHLAHKCKIATVASDVSQVPKALTQLGVLPADSFAAGPDLC 560

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQVVS 673
               Q +  +    +  +  +         +          +I ++  S     P   + 
Sbjct: 561 CV--QLDGKIVGWTTHKQGKIVADTLRFWKVEGSHGLPLDLEIGYVPPSNKGQYPGLYLF 618

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
              S +                   Q    +      +   + S   + S   I++  A 
Sbjct: 619 GGHSRMMRPVKYLPLDKQDILGPFEQVYMNVAVTPEEIENNVHS-HVEFSPTNILSILAN 677

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           +    D  +      +  +   T G      + +           Q P+VK         
Sbjct: 678 LTPFSDFNQSPRNMYQCQMGKQTMGTPGTALVHRSDNKLYRLQTGQTPIVKANLYDDYG- 736

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA- 851
                    + +   G N +VA + + GY+ +D+M+I++             +  ++   
Sbjct: 737 ---------MDNFPNGMNAIVAVISYTGYDMDDAMIINKSADERGFGYGTVYKTEKIDLS 787

Query: 852 ---RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV-------GKITPK 901
              R      +          E   + +D  G+  +G +V  GD +V       GK   K
Sbjct: 788 QSRRRGDPITQHFGFGTDEWPEAWKEKLDADGLPMIGVKVEAGDPIVAYYDDTLGKTKVK 847

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG-VSGTVVDVRIFNRHG 949
                 P       + G++  D     L +        ++  +  +RHG
Sbjct: 848 TYHSSEPGYIEEVKLLGDETSDQEGQQLTIKYRITRAPLIGDKFSSRHG 896



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 112/824 (13%), Positives = 223/824 (27%), Gaps = 143/824 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R +TY   L + +   V D +E      + +++E     G +P+M K       
Sbjct: 105 PSECRERMVTYRSRLMLNVTWSVNDGEE------VSEVREA----GQIPIMLKSNRCHLE 154

Query: 142 ------------------GTFVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLSGKLLY 180
                             G F++ GI++++   + Q    P        G    S    Y
Sbjct: 155 KLTPNQLVEAKEESDELGGYFIVNGIEKLIRMLIVQRRNHPMALIRPSFGNRGASYTK-Y 213

Query: 181 ACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSE-EILS 230
             +I   +         +    D    +  R   R+    VPVT  L AL   ++ EI  
Sbjct: 214 GIQIRCVRPDQTSQTNVLHYLNDGN--VTFRFSWRKNEYLVPVTMILKALVETNDREIFD 271

Query: 231 TFYPKIV------------------YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
                                    Y+                V    +  + DID G++
Sbjct: 272 GIVGNDTGNSFLTDRLELLLRTYKKYNLNSQQETLAYLGDKFRVVFGATPDMSDIDVGKE 331

Query: 273 VIESGKKLTSGLLKSLKEKG--VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           V+   K++    L    +K   + F+      L     A D  +    +  +  G +   
Sbjct: 332 VL---KRIVLVHLPDNTDKFRMLLFMIRKLYSLVAGDCAPDNPDATQHQEVLLGGFLYGM 388

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
              E+I    +++I +     +N    I         +       +I + +       F 
Sbjct: 389 IIKEKIEEY-LQNIKLQIQSDINRGVGINFDDRKYMTRVFSRINENIGQKL-----QYFL 442

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
              ++ +    D  +    TV   K+N           R I    ++       +L+   
Sbjct: 443 STGNLVSQSGLDLQQVSGYTVVAEKINFY---------RFISHFRMVHRGSFFAELKTTT 493

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                 ++ G        +            +   +  +     + S + Q       + 
Sbjct: 494 VRKLLPESWGFLCPVHTPDGSPC-------GLLNHLAHKCKIATVASDVSQVPKALTQLG 546

Query: 511 SAVCEFF-CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
               + F     L  ++     +   TH +           +                  
Sbjct: 547 VLPADSFAAGPDLCCVQLDGKIVGWTTHKQGKIVADTLRFWK------------------ 588

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
                 EG +   +     +   +  G     Y      ++   V YL   +++      
Sbjct: 589 -----VEGSHGLPLDLEIGYVPPSNKGQYPGLYLFGGHSRMMRPVKYLPLDKQDIL---- 639

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                        E V+   A     +       ++ SP  ++SI A+L PF + + S R
Sbjct: 640 ----------GPFEQVYMNVAVTPEEIENNVHSHVEFSPTNILSILANLTPFSDFNQSPR 689

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDAIRIVI 745
            +  C M +Q +         V      +    +G   + K     +            I
Sbjct: 690 NMYQCQMGKQTMGT--PGTALVHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGMNAI 747

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            +V            I      +R      V +   + +    RR D I         + 
Sbjct: 748 VAVISYTGYDMDDAMIINKSADERGFGYGTVYKTEKIDLSQSRRRGDPITQHFGFGTDEW 807

Query: 806 ALG--RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                  +    +P  G   E    I      +D      ++ +
Sbjct: 808 PEAWKEKLDADGLPMIGVKVEAGDPIV--AYYDDTLGKTKVKTY 849


>gi|145926548|gb|ABP98913.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926554|gb|ABP98916.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|190612240|gb|ACE80554.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612242|gb|ACE80555.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612244|gb|ACE80556.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612246|gb|ACE80557.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612248|gb|ACE80558.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612250|gb|ACE80559.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612252|gb|ACE80560.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612254|gb|ACE80561.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612256|gb|ACE80562.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612258|gb|ACE80563.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612260|gb|ACE80564.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612262|gb|ACE80565.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612264|gb|ACE80566.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612266|gb|ACE80567.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612268|gb|ACE80568.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612270|gb|ACE80569.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612274|gb|ACE80571.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|190612276|gb|ACE80572.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670350|gb|ADR73366.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM15]
 gi|313670354|gb|ADR73368.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM17]
 gi|313670362|gb|ADR73372.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM21]
 gi|313670368|gb|ADR73375.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM24]
 gi|313670382|gb|ADR73382.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM31]
 gi|313670386|gb|ADR73384.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM33]
 gi|313670400|gb|ADR73391.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM40]
 gi|313670402|gb|ADR73392.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM41]
 gi|313670420|gb|ADR73401.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM50]
 gi|313670558|gb|ADR73470.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM119]
 gi|313670564|gb|ADR73473.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM122]
 gi|313670572|gb|ADR73477.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM126]
 gi|313670574|gb|ADR73478.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM127]
 gi|313670580|gb|ADR73481.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM130]
 gi|313670598|gb|ADR73490.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM139]
 gi|313670608|gb|ADR73495.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM144]
 gi|313670614|gb|ADR73498.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM147]
 gi|313670620|gb|ADR73501.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM150]
 gi|313670630|gb|ADR73506.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM155]
 gi|313670632|gb|ADR73507.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM156]
 gi|313670634|gb|ADR73508.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM157]
 gi|313670636|gb|ADR73509.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM158]
 gi|313670640|gb|ADR73511.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM160]
 gi|313670650|gb|ADR73516.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM165]
 gi|313670652|gb|ADR73517.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO166]
 gi|313670654|gb|ADR73518.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO167]
 gi|313670662|gb|ADR73522.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO171]
 gi|313670666|gb|ADR73524.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO173]
 gi|313670668|gb|ADR73525.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO174]
 gi|313670680|gb|ADR73531.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO180]
 gi|313670682|gb|ADR73532.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO181]
 gi|313670690|gb|ADR73536.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO185]
 gi|313670694|gb|ADR73538.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO187]
 gi|313670700|gb|ADR73541.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO190]
 gi|313670704|gb|ADR73543.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO192]
 gi|313670706|gb|ADR73544.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO193]
 gi|313670710|gb|ADR73546.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO195]
 gi|313670714|gb|ADR73548.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO197]
 gi|313670722|gb|ADR73552.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO201]
 gi|313670724|gb|ADR73553.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO202]
 gi|313670726|gb|ADR73554.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO203]
 gi|313670728|gb|ADR73555.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO204]
 gi|313670732|gb|ADR73557.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO206]
 gi|313670736|gb|ADR73559.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO208]
 gi|313670738|gb|ADR73560.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO209]
 gi|313670740|gb|ADR73561.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO210]
 gi|313670742|gb|ADR73562.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO211]
 gi|313670756|gb|ADR73569.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO218]
 gi|313670760|gb|ADR73571.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO220]
 gi|313670768|gb|ADR73575.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670772|gb|ADR73577.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670780|gb|ADR73581.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670782|gb|ADR73582.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670784|gb|ADR73583.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
          Length = 257

 Score =  278 bits (712), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|152926448|gb|ABS32281.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|152926450|gb|ABS32282.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|152926452|gb|ABS32283.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520233|gb|ABS82790.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520235|gb|ABS82791.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520237|gb|ABS82792.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520239|gb|ABS82793.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520241|gb|ABS82794.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|154520243|gb|ABS82795.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|219816064|gb|ACL37154.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|219958090|gb|ACL68099.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759623|gb|ADR79124.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759625|gb|ADR79125.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759627|gb|ADR79126.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759629|gb|ADR79127.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759631|gb|ADR79128.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759633|gb|ADR79129.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759635|gb|ADR79130.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759637|gb|ADR79131.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759639|gb|ADR79132.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759641|gb|ADR79133.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759643|gb|ADR79134.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759645|gb|ADR79135.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759647|gb|ADR79136.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759649|gb|ADR79137.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759651|gb|ADR79138.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759655|gb|ADR79140.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759657|gb|ADR79141.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759659|gb|ADR79142.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759661|gb|ADR79143.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759663|gb|ADR79144.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759665|gb|ADR79145.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759667|gb|ADR79146.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759671|gb|ADR79148.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759673|gb|ADR79149.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759675|gb|ADR79150.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759677|gb|ADR79151.1| RNA polymerase beta subunit [Mycobacterium bolletii]
 gi|313759679|gb|ADR79152.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759681|gb|ADR79153.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759683|gb|ADR79154.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759685|gb|ADR79155.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759687|gb|ADR79156.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759689|gb|ADR79157.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759691|gb|ADR79158.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|313759693|gb|ADR79159.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 229

 Score =  278 bits (711), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 229



 Score = 40.8 bits (94), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|156255569|gb|ABU63001.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 237

 Score =  278 bits (711), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 44   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 103

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 104  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 149  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 191

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 192  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 237



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 34/52 (65%), Positives = 43/52 (82%)

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PKGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 52


>gi|226934688|gb|ACO92418.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 234

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 234



 Score = 45.5 bits (106), Expect = 0.077,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|183579273|gb|ACC63214.1| RpoB [Mycobacterium kansasii]
 gi|183579279|gb|ACC63217.1| RpoB [Mycobacterium gastri]
          Length = 220

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 94/226 (41%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 27   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 87   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 145  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 174

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG
Sbjct: 175  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTG 220


>gi|226934674|gb|ACO92411.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 232

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 125/226 (55%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 144  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 186

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 187  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 232



 Score = 43.5 bits (101), Expect = 0.23,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 47


>gi|269930865|gb|ACZ54167.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 298

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 213/299 (71%), Positives = 250/299 (83%), Gaps = 1/299 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQAN SLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANFSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+ +PFLENDD+NR  MG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAADLPFLENDDANRASMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 298


>gi|160337110|gb|ABX25846.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 228

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 127/226 (56%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 34   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 93

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 94   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 138

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 139  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 181

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 182  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 227


>gi|67516079|ref|XP_657925.1| hypothetical protein AN0321.2 [Aspergillus nidulans FGSC A4]
 gi|40746571|gb|EAA65727.1| hypothetical protein AN0321.2 [Aspergillus nidulans FGSC A4]
          Length = 1656

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 166/1145 (14%), Positives = 329/1145 (28%), Gaps = 229/1145 (20%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +  D L   +            I ++
Sbjct: 704  IVETDPKKEIVQASVTSSSN-----ERKSKSYIILKKDRLYVKHNVLSEDIPI--VILLK 756

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  +      + A      +      ++ AL  I   ++ 
Sbjct: 757  AMGIHTDKEMMLL-------VAGVDKVYQEDFAINFEEAIKVGVFTQQQALDWIGSRIKI 809

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                       +         +  +  +  V ++     D     + I    +  + + +
Sbjct: 810  NRKQMSYRRTHV---------QEAVEAIASVIISHIEVKDMNFRPKAI---YVANMARRV 857

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            +  +N    +DD D LGN+R+   G++L   +     +    IK  I  V       +  
Sbjct: 858  LMAKNDAALVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRVEAF 917

Query: 504  INAKPVVSA-------VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
                 +          +     +   S     +          RLS +   G+       
Sbjct: 918  DAWSVIGMHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 977

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G IC A+T EG   GLV +L     +              +G
Sbjct: 978  FEKTRKVSGPRALQPSQFGMICLADTPEGEACGLVKNLALMTHITTND---------EEG 1028

Query: 609  KVTNDVVYLSAMEE----ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             + N +  L A +          A  + ++  +G+        R     +   R      
Sbjct: 1029 PIKNLIFMLGAEDIQTVGGKEIYAPGSYTISINGTPMA---LTRRPKYFLNAFRRLRRMG 1085

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              S    + I         +  +  V        + + +++     V       +   + 
Sbjct: 1086 RISEFVSIYIN-------HHQRAVHVATDDGRICRPLIIVEDGKSRVKKHHLRKLRDGTM 1138

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                    G+VE VD               + S + IY       +              
Sbjct: 1139 QFDDFLAQGLVEYVDVNE-----------ENDSLIAIYEKDITDTTTHMEI--------- 1178

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               +       +   +P+  +N          M  + +      
Sbjct: 1179 -------------------EPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA---- 1215

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                                         + +    I+ +        +    I      
Sbjct: 1216 -------------------------IASNQFLRIDSILYLMVYPQKPMVKSRTIELTKYD 1250

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +    A+      D+ D  +     V       ++F ++  +    S   +    
Sbjct: 1251 QLPAGQNATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTNMKSYSNGTKDILS 1310

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                   +++  I    +         G+   +G     KST           +S     
Sbjct: 1311 PPT---YENDAPIRKHALLESDGLAAVGEQVNAGEVYINKSTP---------DQSMSSGM 1358

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D     +     + Y     + +  + +K+              +++KV     R  
Sbjct: 1359 PGSDAGRPISYNPTPMTY----KLPDPAYIDKV-----MISATENENQIIKVLTRQTRRP 1409

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+               G  VD                         
Sbjct: 1410 EVGDKFSSRHGQKGV--------------TGIIVD------------------------- 1430

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                  +      D   N DI         ++       +++      ++       SG 
Sbjct: 1431 ------QADMPFTDQGINPDI---------IMNPHGFPSRMTVGKMLELVAGKAGVLSGQ 1475

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                  F G   E +   L        G+  L  G+TGE     V  G IY  KL HMV 
Sbjct: 1476 HGYGTCFSGTPVEQMTQTLIDKGFSYGGKDYLTSGITGEALPFYVFTGPIYYQKLKHMVQ 1535

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            DK+++R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    
Sbjct: 1536 DKMHSRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEV 1595

Query: 1321 DV------------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DV              R +   S+V          P +  +L++E+ ++ ++  L+    
Sbjct: 1596 DVCEQCGFMGYLNWCQRCKSSRSVVK------MVIPYAAKLLIQELMSMNVTARLKLEDE 1649

Query: 1369 KNSAK 1373
                K
Sbjct: 1650 FPETK 1654



 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 88/743 (11%), Positives = 211/743 (28%), Gaps = 128/743 (17%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
            L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 547  LVKQHIDSYNYLVEVQ----------LKKIVESSNTIRSDVDHNFYIKFTDIYLGFPRRA 596

Query: 86   --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                              +C  RD TYA P+++    I          +  + ++ + + 
Sbjct: 597  DEPQDVRTEFEESTVTPHECRLRDTTYAAPIQVDFEYI----------RGRQRVRRKGVS 646

Query: 132  MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
            +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 647  IGRMPVMLRSSKCVLGNKTPAQMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 706

Query: 167  HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
             D  +        S S +      II             KD ++V+ +     +P+   L
Sbjct: 707  TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDRLYVKHNVLSEDIPIVILL 755

Query: 219  MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
             A+G+ +++ +      +    + DF      A  + VG       +D       I   +
Sbjct: 756  KAMGIHTDKEMMLLVAGVDKVYQEDFAINFEEA--IKVGVFTQQQALDWIGSRIKINRKQ 813

Query: 279  KLTSGLLKSLKEKGVKFLGITSDCLCG---LYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
                        + +  + I+   +        A  + N     +  +     D   +++
Sbjct: 814  MSYRRTHVQEAVEAIASVIISHIEVKDMNFRPKAIYVANMARRVLMAKN----DAALVDD 869

Query: 336  IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
              +   + + +           +         K   D  ++I +V+   +      A S+
Sbjct: 870  RDYLGNKRLEL-------AGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRVEAFDAWSV 922

Query: 396  FNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
                     +     +     +  R  ++       + +   IA + ++  + +      
Sbjct: 923  IGMHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTR 982

Query: 455  DIDNLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
             +      +    G + L +        + +++         D   P   +        +
Sbjct: 983  KVSGPRALQPSQFGMICLADTPEGEACGLVKNLALMTHITTNDEEGPIKNLIFMLGAEDI 1042

Query: 514  CEFFCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRIC 570
                             +N        R    L     + R     E   ++  H+ R  
Sbjct: 1043 QTVGGKEIYAPGSYTISINGTPMALTRRPKYFLNAFRRLRRMGRISEFVSIYINHHQRAV 1102

Query: 571  PAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
               T +G     +  +       + +    +     +  D      V Y+   EE +  I
Sbjct: 1103 HVATDDGRICRPLIIVEDGKSRVKKHHLRKLRDGTMQFDDFLAQGLVEYVDVNEENDSLI 1162

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            A     +                        +    ++  P  ++   A LIP+  ++ S
Sbjct: 1163 AIYEKDIT-----------------------DTTTHMEIEPFTILGAVAGLIPYPHHNQS 1199

Query: 688  NRVLMGCNMQRQAVPLLKAEAPF 710
             R    C M +QA+  + +    
Sbjct: 1200 PRNTYQCAMGKQAIGAIASNQFL 1222


>gi|313759669|gb|ADR79147.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 229

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 96/226 (42%), Positives = 125/226 (55%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 229



 Score = 41.2 bits (95), Expect = 1.3,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|148879047|emb|CAM07039.1| RpoB protein [Mycobacterium sp. MG9]
          Length = 220

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 94/228 (41%), Positives = 126/228 (55%), Gaps = 40/228 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 25   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 130  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 172

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            +D  G++ L++G +GE F  PVTVGY+Y+L L+H+V DK++ARSTG Y
Sbjct: 173  VDGDGKARLFNGRSGESFPYPVTVGYMYILNLHHLVDDKIHARSTGPY 220


>gi|302759705|ref|XP_002963275.1| hypothetical protein SELMODRAFT_405033 [Selaginella moellendorffii]
 gi|300168543|gb|EFJ35146.1| hypothetical protein SELMODRAFT_405033 [Selaginella moellendorffii]
          Length = 1126

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 99/455 (21%), Positives = 160/455 (35%), Gaps = 47/455 (10%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
              D         +   G   +G  +   +     +   L+      A +V      +   
Sbjct: 644  WSDHNQSPRNMYQCQMGKQTLGFASQALKFRTDHKMYNLQNPQSPVARNVNYKKYNMDEF 703

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
              GT   V +    G D  +  I  +      LA  +  +   +D ++  +  + +    
Sbjct: 704  PLGTNAVVAVLAYTGFDMEDAMIMNKSSMERGLAHGQIYKTEHVDLSLLQKKSDGIVNLF 763

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK-SILEDRF 1053
            +               + +         Q     +     + ++    +  K    E+  
Sbjct: 764  SR------PTGKRNIHNFLDVDGLPHIGQTMHNGDPYCSVLNTMTGDAKLHKLKAAENVV 817

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             + +  I  G       L+ + V     R    GDK + RHG KGI+S++ P  DMPF  
Sbjct: 818  IDSVIAIGHGR----DPLQKIAVKFRHDRNPVIGDKFSSRHGQKGILSQLWPDIDMPFSA 873

Query: 1114 -DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
              G   DI++NP   PSRM +G + E+    A V  G+ + S      +    +      
Sbjct: 874  VTGMRPDIIINPHAFPSRMTIGMLMESMAAKAGVLRGEYVDSTPFRSSSAALDAKDGKTG 933

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                G   H   IS                                    L     +  G
Sbjct: 934  SGYKGKDKHYPAIS-------------------------------EFGEQLAQHGFNYHG 962

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
              ++Y GL G      + +G +Y  +L HMVSDK   RS G+ + VT+QP+GG+   GG 
Sbjct: 963  TEVMYSGLLGTELTCEIFIGVVYYQRLRHMVSDKFQVRSLGAINPVTRQPVGGRKLGGGI 1022

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV 1323
            R GEME   + A+GAAY+L + L   SD    DV 
Sbjct: 1023 RFGEMERDSLLAHGAAYLLHDRLHTSSDYHVGDVC 1057



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 92/619 (14%), Positives = 189/619 (30%), Gaps = 88/619 (14%)

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY-----VDSVNNNAYI 358
            G  +         G I     D  D +  E++    ++                    I
Sbjct: 240 LGFVIRRQEFVIPVGIILKAFMDTSDREIFEQLSGIHVQGQEQSKGAVGSQLISQRARII 299

Query: 359 RNTLVTDKNKDRKDALLDIYRVMR----------PGDVSTFSVAESMFNFLFFDSDKYDL 408
                      R D L  I    R            +V    +   +F  L    DK++L
Sbjct: 300 IEETQRQPCLTRLDCLRYIGETFRTPLEALSSMSNAEVGEDVLRRFVFVHLDNFRDKFNL 359

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
                 K+   ++     D     +   + +   L+++       D +     +R+    
Sbjct: 360 LIHMLHKLFAVVDGSASIDSSDTLQHQELLLPGHLMNIYLKDRLEDWL--YRCKRLLQRE 417

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
             LK ++ L        I E+ ++VDI   +   L        +  +   ++  S + E 
Sbjct: 418 MQLKEEFDLSDHAKVLKIVEKNNAVDIGKRIEYLLSTGNIQSQSHMDLQQANGFSVVAEK 477

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
           +N    I+H R   ++ +G     +    +R + P  +G +CP  T +G   GL++ L+S
Sbjct: 478 LNFFRFISHFR---SVHRGAFFARQRTTSVRKLLPESWGFLCPVHTPDGEPCGLLTHLSS 534

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             +++                                      + LD++    +  V   
Sbjct: 535 LCKIS--------------------------------------TDLDQNNHPKDPKVPI- 555

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASL--IPFLENDDSNRVLMGCNMQRQAVPLLKA 706
              E   VP     +  A P   +    S    P  + D     L+    Q         
Sbjct: 556 -DLEIGYVP---CTYAGAYPGLFLYTTPSRFLRPVKQLDTGAIELISAFEQAYMEIACPD 611

Query: 707 --EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                   +   +   +    A+++  A      D  +      +  +   T G    + 
Sbjct: 612 GGNCGRTPSAPPATHIELHPTAMLSVVASSTPWSDHNQSPRNMYQCQMGKQTLGFAS-QA 670

Query: 765 MKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           +KF R++      Q P   V      ++          ++ +  LG N +VA + + G++
Sbjct: 671 LKF-RTDHKMYNLQNPQSPVARNVNYKK---------YNMDEFPLGTNAVVAVLAYTGFD 720

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARD-----TKLGPEEITRDIPNVSEEGLKNID 877
            ED+M++++  +   +    H + ++    D      K          P         +D
Sbjct: 721 MEDAMIMNKSSMERGLA---HGQIYKTEHVDLSLLQKKSDGIVNLFSRPTGKRNIHNFLD 777

Query: 878 ECGIICVGAEVNPGDILVG 896
             G+  +G  ++ GD    
Sbjct: 778 VDGLPHIGQTMHNGDPYCS 796



 Score = 61.6 bits (148), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 115/738 (15%), Positives = 225/738 (30%), Gaps = 166/738 (22%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGAA--MLEFV-SY 79
           DL+     S+D+F+            GL  A K + P+        SG     L+ V + 
Sbjct: 31  DLVSPHIDSFDYFVQR----------GLVEAVKGIAPVEIEQDGFHSGDFGFSLDVVLAL 80

Query: 80  EFDPP----------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             D P                +    +C    L+Y   L   ++LI+ D    T      
Sbjct: 81  TLDKPVVQPPVKDLKEKAMEHRLLPKECRQGFLSYTGAL--NIQLIL-DYGSMT------ 131

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH- 158
             +   + +G LP+M K                         G F++KGI+RI+   +  
Sbjct: 132 --RYHQLSLGKLPIMLKSSLCHLRGLSPQKLISLKEEGTEMGGYFIVKGIERIIRKLIVP 189

Query: 159 -RSPGIHFDHDKGRASLSGKLLYACRIIPDQ-------GLWMDIEFDSKDI--IHVRIDR 208
            R+  I    +  +   +G   ++   +  +       G  + + +       +   I R
Sbjct: 190 KRNHIIAIRRNAFQNRGAG---FSDIGLMMRCVRPDQTGSTIKLYYLHHGTARLGFVI-R 245

Query: 209 RRK--VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R++  +PV   L A  MD+ +       + ++ Q           +   VG++    L+ 
Sbjct: 246 RQEFVIPVGIILKAF-MDTSD-------REIFEQLSGIHVQGQEQSKGAVGSQ----LIS 293

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
                 + E+ ++     L  L+  G  F     + L        + N E GE  +    
Sbjct: 294 QRARIIIEETQRQPCLTRLDCLRYIGETFRT-PLEAL------SSMSNAEVGEDVLRRFV 346

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
            +   +  + F+  I  +  L+     + +   +  +  +       L++IY   R  D 
Sbjct: 347 FVHLDNFRDKFNLLIHMLHKLFAVVDGSASIDSSDTLQHQELLLPGHLMNIYLKDRLEDW 406

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                 + +        +++DLS   +V   +  N       R           + L+  
Sbjct: 407 --LYRCKRLLQREMQLKEEFDLSDHAKVLKIVEKNNAVDIGKRI----------EYLLST 454

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLI 504
            N +      D         V E L     +   R     +   R  +  +  ++P+   
Sbjct: 455 GNIQSQSHM-DLQQANGFSVVAEKLNFFRFISHFRSVHRGAFFARQRTTSVRKLLPESWG 513

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
              PV +   E      L      +  +S                          D+   
Sbjct: 514 FLCPVHTPDGEPCG---LLTHLSSLCKIST-------------------------DLDQN 545

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           ++ +               +   ++  +  Y       R V     T  +  +SA E+  
Sbjct: 546 NHPKDPKVPIDLEIGYVPCTYAGAYPGLFLYTTPSRFLRPVKQLD-TGAIELISAFEQAY 604

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA        DG                  P      I+  P  ++S+ AS  P+ ++
Sbjct: 605 MEIA------CPDGGNCGR---------TPSAPPA--THIELHPTAMLSVVASSTPWSDH 647

Query: 685 DDSNRVLMGCNMQRQAVP 702
           + S R +  C M +Q + 
Sbjct: 648 NQSPRNMYQCQMGKQTLG 665


>gi|51035535|emb|CAH10903.1| RNA polymerase B subunit [Halosimplex carlsbadense]
          Length = 435

 Score =  278 bits (711), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 110/253 (43%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF + G   D+++NP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTEQGVVPDLIINPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 257  PSRMTVGHILEMIGGKVGSLEGRRVDGTAFTGEDEDELRGSL------------------ 298

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                         E    M    ++  SG       +TGE  + 
Sbjct: 299  -----------------------------EDHGFMSSGKEIMYSG-------ITGEQIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 323  EIFLGTIFYQKLYHMVSNKIHARSRGPVQVLTRQPTEGRAREGGLRVGEMERDVLIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L  +SD
Sbjct: 383  AMALKERLLDESD 395



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/210 (21%), Positives = 76/210 (36%), Gaps = 23/210 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  LVK                    D    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSLVK----------TQTTEQIGYDDRPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN------VSEEGLKNIDEC 879
           ++++++  V   +  S     +E   R    G E+   +IP+        EE   ++DE 
Sbjct: 76  ALVMNKGSVDRGLSRSHFFRTYEGEERRYPGGQED-HFEIPDDEVRGARGEEAYTHLDED 134

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++     V   D+L+GK +P               + G      R+TS+ + SG SG V
Sbjct: 135 GLVNPETHVGENDVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMRSGESGVV 188

Query: 940 VDVRIFNRHGIDKNERSISVEREQIELLAR 969
             V +       K  +    +    EL  +
Sbjct: 189 DTVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|185179214|gb|ACC77620.1| RpoB [Mycobacterium gordonae]
          Length = 218

 Score =  278 bits (710), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 129/226 (57%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 25   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 130  -----------------LPEDLRHAQPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 172

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            ++  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG
Sbjct: 173  VNGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTG 218


>gi|19173004|ref|NP_597555.1| DNA-DIRECTED RNA POLYMERASE I, SECOND LARGEST SUBUNIT
            [Encephalitozoon cuniculi GB-M1]
 gi|19168671|emb|CAD26190.1| DNA-DIRECTED RNA POLYMERASE I, SECOND LARGEST SUBUNIT
            [Encephalitozoon cuniculi GB-M1]
          Length = 1062

 Score =  278 bits (710), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 86/351 (24%), Positives = 139/351 (39%), Gaps = 74/351 (21%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDM--PPGVLRVVKVF------------VAMKRPIQSGD 1088
               K     R+ ++  +      +   PG++ +V+VF            + + R    GD
Sbjct: 756  RIQKDDTLYRYVDQDGREYEKRYLGTEPGIVDIVRVFENDMGERCATFTIRIVRSPMIGD 815

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+ S   P  DMPF + G   DI++NP   PSRM +G + E+  G      
Sbjct: 816  KFSSRHGQKGVCSMHWPGIDMPFTESGCVPDIIINPHAFPSRMTIGMLIESIAGKVGCLS 875

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +    +       +         +                                  
Sbjct: 876  GNEQDGTVFKKSFLLEQEEGDDEKVR---------------------------------- 901

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                   +E + S LR    +  G   +Y G+ G  F   + VG +Y  +L HMV DK  
Sbjct: 902  ------RKEYLCSELRRHGFNYYGNEPMYSGVAGNEFRADIFVGVVYYQRLKHMVGDKFQ 955

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
             R+ G+    T+QP+GG+  RGG R GEME   + ++GA+Y+LQ+ L   SD     + V
Sbjct: 956  VRTKGAVVSTTRQPVGGRKKRGGIRFGEMERDALISHGASYLLQDRLLKSSD-----STV 1010

Query: 1329 YE------SI--------VAGNDTFET-GTPESFNVLVKEMQALGLSIDLE 1364
            +E      SI        + G+   +    P  F  L  E+ A+ + + ++
Sbjct: 1011 FEYCGTCRSILFTNNGDCICGSSDLKAVEMPYVFKYLCCELLAMNIKVQID 1061



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 27/88 (30%), Gaps = 32/88 (36%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R LTY   + + + L   +    T  KS           G  P+M +       
Sbjct: 78  PRECRERGLTYKGKMVVRVSLFHDNKHVVTEDKSA----------GHFPIMVRSTLCHLN 127

Query: 142 ----------------GTFVIKGIQRIV 153
                           G F+I GI R +
Sbjct: 128 GIKNKNEVGEDEDEIGGYFIINGIDRFI 155


>gi|312214262|emb|CBX94255.1| hypothetical protein [Leptosphaeria maculans]
          Length = 941

 Score =  278 bits (710), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 116/327 (35%), Gaps = 52/327 (15%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
             A S     +        ++        W     D      +              E  F
Sbjct: 569  KAESKETLDEDGFPRIGTMLRSGDVIAAWHTVSYDPAADDYINRDGQTSFFKYKEDELAF 628

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              ++  I   D   P   + + + + + R    GDK + RHG KG+ S+  P  DMPF +
Sbjct: 629  VEEVRIIGSEDGTQP--CQKISIKLRVPRLPVIGDKFSSRHGQKGVASQKWPAIDMPFSE 686

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D+++NP   PSRM +G   E+  G A    G    S    +              
Sbjct: 687  SGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPFRFDEQNTA-------- 738

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                       +     L  A  +  G 
Sbjct: 739  ------------------------------------------VDFFGHQLMKAGYNYYGN 756

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y G+TG+     + +G +Y  +L HMV+DK   R+TG  +  T QP+ G+   GG R
Sbjct: 757  EPMYSGITGQELAADIYIGVVYYQRLRHMVNDKFQVRTTGPVNSTTGQPIKGRKKGGGIR 816

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +GEME   + A+G A++LQ+ L   SD
Sbjct: 817  VGEMERDALIAHGTAFLLQDRLMNCSD 843



 Score = 43.9 bits (102), Expect = 0.18,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 8/100 (8%)

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT----SIHIEEFEVMARDTKLGPEEITR 863
             N +VA + + GY+ +D+M++++                I + E  +R  + G      
Sbjct: 500 VMNAVVAVISYTGYDMDDAMILNKSAHERGFGYGTIYKTKICDLEEGSRKNRSGRTITKM 559

Query: 864 ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                   V  E  + +DE G   +G  +  GD++    T
Sbjct: 560 FGFAPEGFVKAESKETLDEDGFPRIGTMLRSGDVIAAWHT 599


>gi|145926532|gb|ABP98905.1| RNA polymerase beta subunit [Bradyrhizobium sp. CIAT3101]
          Length = 257

 Score =  278 bits (710), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 140/258 (54%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|76178927|gb|ABA41001.1| RNA polymerase subunit B [Aliivibrio fischeri]
          Length = 298

 Score =  278 bits (710), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 181/298 (60%), Positives = 230/298 (77%)

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER+++ER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 1   FRVGLVRVERAVRERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 60

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA+ N 
Sbjct: 61  VTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPNIGLINSLSAFAQCNE 120

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG+VT+ V YLSA+EE    IAQAN+ L E+G+F +EL+  R  GE  
Sbjct: 121 YGFLETPYRRVVDGQVTDQVDYLSAIEEGTFVIAQANAVLTEEGTFADELIIARQKGESG 180

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L PRE I ++D +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP LKA+ P VGTG
Sbjct: 181 LHPREHIQYMDVATNQVVSVAASLIPFLEHDDANRALMGANMQRQAVPTLKADKPLVGTG 240

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           +E  VA  SG   VAKR G+V+ VDA RIVI+  E +L P  +G+DIY L K+ RSNQ
Sbjct: 241 IERNVAVDSGVTAVAKRGGVVQSVDASRIVIKVNEEELVPGEAGIDIYNLTKYTRSNQ 298


>gi|145926530|gb|ABP98904.1| RNA polymerase beta subunit [Bradyrhizobium yuanmingense]
 gi|145926544|gb|ABP98911.1| RNA polymerase beta subunit [Bradyrhizobium liaoningense]
 gi|145926546|gb|ABP98912.1| RNA polymerase beta subunit [Bradyrhizobium yuanmingense]
 gi|145926550|gb|ABP98914.1| RNA polymerase beta subunit [Bradyrhizobium liaoningense]
 gi|145926552|gb|ABP98915.1| RNA polymerase beta subunit [Bradyrhizobium yuanmingense]
 gi|190612140|gb|ACE80504.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612142|gb|ACE80505.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612144|gb|ACE80506.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612150|gb|ACE80509.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612152|gb|ACE80510.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612154|gb|ACE80511.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612198|gb|ACE80533.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612200|gb|ACE80534.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612202|gb|ACE80535.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612204|gb|ACE80536.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612206|gb|ACE80537.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612208|gb|ACE80538.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612210|gb|ACE80539.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612212|gb|ACE80540.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612214|gb|ACE80541.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612216|gb|ACE80542.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612218|gb|ACE80543.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612220|gb|ACE80544.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612222|gb|ACE80545.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612224|gb|ACE80546.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612226|gb|ACE80547.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612228|gb|ACE80548.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612230|gb|ACE80549.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612232|gb|ACE80550.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612234|gb|ACE80551.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612236|gb|ACE80552.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612238|gb|ACE80553.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612278|gb|ACE80573.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612280|gb|ACE80574.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612282|gb|ACE80575.1| RNA polymerase subunit beta [Bradyrhizobium yuanmingense]
 gi|190612284|gb|ACE80576.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612286|gb|ACE80577.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612288|gb|ACE80578.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612290|gb|ACE80579.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612292|gb|ACE80580.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612294|gb|ACE80581.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612296|gb|ACE80582.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612298|gb|ACE80583.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
          Length = 257

 Score =  277 bits (709), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 185/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN 
Sbjct: 120 ALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|315435632|gb|ADU18206.1| RNA polymerase beta-subunit [Mycobacterium sp. FI-10135]
          Length = 231

 Score =  277 bits (709), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 125/226 (55%), Gaps = 40/226 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 38   RVFSREDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFMPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGEPEWAAN-------------- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +            V+TPVFDGA E  +  +L     +      
Sbjct: 143  -----------------LPEGMHSAPRDSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 185

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G+S+L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 186  VNAEGKSMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 231



 Score = 42.4 bits (98), Expect = 0.56,   Method: Composition-based stats.
 Identities = 31/46 (67%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ VR+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGVRVFSREDDD 46


>gi|313670562|gb|ADR73472.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM121]
 gi|313670576|gb|ADR73479.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM128]
 gi|313670612|gb|ADR73497.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM146]
 gi|313670622|gb|ADR73502.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM151]
          Length = 257

 Score =  277 bits (709), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 138/258 (53%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           +I+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  RILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +K+++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKNMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|327409577|ref|YP_004346997.1| DNA-directed RNA polymerase subunit 2 [Lausannevirus]
 gi|326784751|gb|AEA06885.1| DNA-directed RNA polymerase subunit 2 [Lausannevirus]
          Length = 1242

 Score =  277 bits (709), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 175/1039 (16%), Positives = 333/1039 (32%), Gaps = 129/1039 (12%)

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSD---KYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
            +  R   + +   A  MF     + +   +  L  VG  +    L        +   ++ 
Sbjct: 278  KEQRTHLIPSLEQARVMFPKSRKNREATIQKALGIVGNKQTTKSLIDLIFPHYKTAEEKI 337

Query: 436  I--IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 ++   + ++ G+   +D D+  N+RV  V  +L N +     +  ++I++     
Sbjct: 338  WFLCYMLARAIKVKCGEREPEDRDHYANKRVDCVDSLLNNLFYSMWNQTTKAIRDSCE-G 396

Query: 494  DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               +  P   I +K +   +     +   S                R + +    + +  
Sbjct: 397  KGRNSDPLKTIYSKLITKKLSMALATGNWSSFNTKK-KTGTSQFFERYNCVSASNLRKLH 455

Query: 554  -------AGVEMRDVHPTHYGRICPAETSEGHN-IGLVSSLTSFARVNAYGFIETPYRKV 605
                      + R VH + +G +CP +T E     GL   L   A V+    IE  +   
Sbjct: 456  AAIGTEGNMTKPRRVHESSFGFVCPPDTPESKERTGLSKVLALSALVSLGCSIEECF--- 512

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
               ++ + +   S    E  ++           +    +              +     D
Sbjct: 513  ---QILDAIPEFSRDFGEGTFVFLNGVIAGSTQNPEFLISVLSELKRSNNFFWDCCFVYD 569

Query: 666  ASPKQVVSIAAS---LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                +V     +   + P +   D   V    ++++     L  +       +E + A+ 
Sbjct: 570  KKFDEVRINCDAGRLIRPLMLVQDGKLVFEEEHLRKLRDGELTWQDFLSLGIVEYIDAEQ 629

Query: 723  -SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                 I      + +        I  +      S+           + S   +       
Sbjct: 630  QEHMLICPSAEELGKHKRWTHCEIHPILVYGVCSSIIPYSANNPSPRLSYFASMAKSSVA 689

Query: 782  VKVGDE--VRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            V   D   V  +  +   P              L D  + +N+++A   +  +  ED+++
Sbjct: 690  VPRLDFDEVPYDQHVLHYPQKSLASTKAARLLGLNDSPISQNIVLAVCSYEDFGMEDAII 749

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-ITRDIPNVSEEGLKNIDECGIICVGAE 887
              +         S H    +    +   G E+   R+ P++S         C     G +
Sbjct: 750  CCKSFTQFGGMVSSH---HQKPVAEIGHGQEQIDPRNEPDMSFPDFCQRLWCR--ECGKK 804

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V         + P+  S   P     + +   KA +                        
Sbjct: 805  V--------MLCPECNSEYIPTNGGFKGVMCRKAEN------------------------ 832

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
                   R   +  E I+    +  + Q  LD  +  R  E LC           +    
Sbjct: 833  -------RRREIVNEGIQKWNNNLKEGQKSLDF-LKPREWECLC----------LEVDKR 874

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW-GDDM 1066
               D + E       Q  V+D  +   V  +    +  K       K+K   +       
Sbjct: 875  PRFDHLDEAGVVDVGQI-VEDGDMLVGVADVSE--DKKKDESLYFSKDKRGIVTSVCYTQ 931

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD---GTPVDIVLN 1123
                   ++V V   R  + GDK    H  KG  S  +P E+MPF  D    +  D ++N
Sbjct: 932  NTKGHVCIRVTVVSTRVPEVGDKATSFHSQKGTFSLFVPPENMPFSSDPFAASHPDFIIN 991

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PL  PSRM +GQ  E+  G       + +   +     +   +          G     E
Sbjct: 992  PLAFPSRMTIGQPKESSAGKKTACAHRDLPDHLRFEYESLYSALSERIGRVPSGKEVAAE 1051

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
             I    + +    +  +    P  T  F     E +   L+       G+ +  DG+TG+
Sbjct: 1052 IIRKRGNPTTDGYSGSYTDCTPF-TSNF-----EIVEDELKKRGYAPGGKELYIDGMTGK 1105

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
             F   + VG +   +L HMV+DK++AR+TG    +T+QP  G+S  GG ++G ME  C+ 
Sbjct: 1106 MFSVKLFVGLVAENRLKHMVTDKMHARATGKIQSLTRQPTEGRSRNGGLKIGSMERDCLV 1165

Query: 1304 AYGAAYVLQEMLTIKSD--DV-----VGRTRVYESI-VAGN----------DTFETGTPE 1345
              GA   L++ +    D  DV      G      +I V G           +  +     
Sbjct: 1166 GNGATLCLRDRMFFSCDKYDVWCCTSCG----LIAINVEGKKICRACHGKSNVGKVAIRY 1221

Query: 1346 SFNVLVKEMQALGLSIDLE 1364
            S  +  +E+ A+G++  + 
Sbjct: 1222 STKLAFQELMAMGITPRIL 1240



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 124/1020 (12%), Positives = 272/1020 (26%), Gaps = 186/1020 (18%)

Query: 32  VQKASYDHFLMMNIAPDERPNEGLQAAFKSVF--------------PITAFSGAA---ML 74
            Q  +Y+ F+   +    R  +G     +                 P +A    +   ++
Sbjct: 24  HQIQAYNEFVQELLPNIIR-EKGRIEIDREDNNVEEDEEENEEGEKPTSAKKKKSWHQVV 82

Query: 75  EFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
           EF + EF    +             +   R + Y+ P    + +   D +     +    
Sbjct: 83  EFTNPEFGRVTYQEIDGMVQDIFPAEARKRGIPYSAPFYCDIAITTADGETKHHPRIT-- 140

Query: 125 IKEQSIYMGDLPLMT--------------------------KDGTFVIKGIQRIVVS--- 155
                  + ++P+M                           K G F++    R +V    
Sbjct: 141 -------IAEIPVMVRSCLCNLTRYNMSGDSCYKKWEDPNDKGGYFILN---REIVVICS 190

Query: 156 --------------QLHRSPGIHFDHDKGRAS-LSGKLLYACRIIPDQGLWMDIE--FDS 198
                         Q+ R    +  H + R S  S        +  + G+ +        
Sbjct: 191 ERGAFGRVYTYSEKQMLRGMPKYDVHSEIRVSATSNTRTTTAYVGLENGVAVFFGQHVSP 250

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                        +P+ + L A+G    ++L   Y K+   ++       L  A +M   
Sbjct: 251 SG-----------IPLCALLEAMGTSYLDLLK--YVKLSNKEQRTHLIPSLEQARVMFPK 297

Query: 259 KVSSSLVDIDTGEQVIESGKK------LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
              +    I     ++ + +       L     K+ +EK      + +  +       + 
Sbjct: 298 SRKNREATIQKALGIVGNKQTTKSLIDLIFPHYKTAEEKIWFLCYMLARAIKVKCGEREP 357

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            + +    Y        +  L  +F+S                  IR++          D
Sbjct: 358 EDRD---HYANKRVDCVDSLLNNLFYSMWN----------QTTKAIRDSCEGKGRNS--D 402

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            L  IY  +      T  ++ ++    +   +    +   +          +     H  
Sbjct: 403 PLKTIYSKL-----ITKKLSMALATGNWSSFNTKKKTGTSQFFERYNCVSASNLRKLHAA 457

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                 + K      +  G +   D   ++    + ++L          +   +    S 
Sbjct: 458 IGTEGNMTKPRRVHESSFGFVCPPDTPESKERTGLSKVLA---------LSALVSLGCSI 508

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            +   ++      ++        F         +     +S ++  +R +          
Sbjct: 509 EECFQILDAIPEFSRDFGEGTFVFLNGVIAGSTQNPEFLISVLSELKRSNNFF------- 561

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
                + D         C A       + +      F        +        D     
Sbjct: 562 WDCCFVYDKKFDEVRINCDAGRLIRPLMLVQDGKLVFEE-EHLRKLRDGELTWQDFLSLG 620

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V Y+ A ++E+  I  +   L +   +                        +  P  V 
Sbjct: 621 IVEYIDAEQQEHMLICPSAEELGKHKRW---------------------THCEIHPILVY 659

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKR 731
            + +S+IP+  N+ S R+    +M + +V + + +   V          + S A+  A R
Sbjct: 660 GVCSSIIPYSANNPSPRLSYFASMAKSSVAVPRLDFDEVPYDQHVLHYPQKSLASTKAAR 719

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +      + ++ +V    D       I      Q     +  +Q+P+ ++G    + 
Sbjct: 720 LLGLNDSPISQNIVLAVCSYEDFGMEDAIICCKSFTQFGGMVSSHHQKPVAEIGHGQEQI 779

Query: 792 DIIADGPSTDLGDLALGRNMLVA-------------FMPWHGYNFEDSMLISERMVSEDV 838
           D   + P     D                       ++P +G         +E    E V
Sbjct: 780 DPRNE-PDMSFPDFCQRLWCRECGKKVMLCPECNSEYIPTNGGFKGVMCRKAENRRREIV 838

Query: 839 FTSIHIEEFEVMARDTKLG---PEEITRDIPNV-SEEGLKNIDECGIICVGAEVNPGDIL 894
              I      +      L    P E       V       ++DE G++ VG  V  GD+L
Sbjct: 839 NEGIQKWNNNLKEGQKSLDFLKPREWECLCLEVDKRPRFDHLDEAGVVDVGQIVEDGDML 898

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           VG      +          +   G     V        +     +    +  R     ++
Sbjct: 899 VGVADVSEDKKKDESLYFSKDKRGI----VTSVCYTQNTKGHVCIRVTVVSTRVPEVGDK 954


>gi|316966676|gb|EFV51221.1| DNA-directed RNA polymerase I subunit RPA2 [Trichinella spiralis]
          Length = 1177

 Score =  277 bits (709), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 91/441 (20%), Positives = 149/441 (33%), Gaps = 71/441 (16%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD---VRDTSLRVPSGVSGTVV 940
            V + V+  D  +  +       +  E     AI          V   S    S     + 
Sbjct: 681  VHSLVHRTDNKMYCLRTPQSPLVKTESYDAYAIDNYPLGTNAIVAVISYTKLSIQGYDME 740

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
            D  I N+  +++      + + +      + +D         + R          V    
Sbjct: 741  DAMIINKASVERGFAHACIYKTE----RINLNDRLYDGRNVFFRRDPADATLSAFVDEDG 796

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET-SKSILEDRFKNKIEK 1059
              +   + S +      +  W  +  +  + +R +      Y         + +   +  
Sbjct: 797  LPQVGKLYSKNDPLYTGQRNWILYGEKISQFRRCIRRQYKNYWQCKWCRTVEAYLRYVS- 855

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                           K+F    R    GDK A RHG KGI S + P E+MPF + G   D
Sbjct: 856  ------------CYCKIFGDYHRNPFVGDKFASRHGQKGINSFLWPAENMPFTESGMVPD 903

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I+ NP G PSRM VG + E+  G +    G K  +    +                    
Sbjct: 904  IIFNPHGFPSRMTVGMMIESMAGKSAALHGIKHDATPFKFSDEHPA-------------- 949

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                 E    +L  A  +  G   +Y G
Sbjct: 950  ------------------------------------IEYFGQLLTKAGYNYYGNERMYSG 973

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
            + G   +  +  G +Y  +L HMVSDK   R+TG+  L+T+QP+ G+   GG R GEME 
Sbjct: 974  IDGRMLEVDIFFGVVYYQRLRHMVSDKFQVRATGAVDLLTKQPVQGRKRGGGIRFGEMER 1033

Query: 1300 WCIQAYGAAYVLQEMLTIKSD 1320
              + ++G A++L + L   SD
Sbjct: 1034 DSLISHGTAFLLHDRLFDNSD 1054



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 66/195 (33%), Gaps = 71/195 (36%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF---PITAFSG---AAMLEFVSYEFD 82
           L+E    S+++F            +G+  A ++ F   P  +  G    A+         
Sbjct: 39  LVEPHIKSFNYF----------AEQGITQAVENPFIGFPAISKDGGDANAL--------- 79

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM---- 138
             K    +C     +Y+  L  TL + + +    +  ++          +GD+P+M    
Sbjct: 80  --KLWPSECRVSCRSYSAKLLATLTIKINNQVVDSARRN----------LGDIPIMLMSN 127

Query: 139 ----TK----------------DGTFVIKGIQRIV---VSQLHRSPGI---HFDHDKGRA 172
               TK                 G F++ G +++V   ++Q  R   +   +F       
Sbjct: 128 RCHLTKLSPNQLMKEKEEMNEMGGYFIVNGQEKVVRMLIAQ--RRNYVGSLYFVSLWLLL 185

Query: 173 SLSGKLLYACRIIPD 187
             +G       IIP+
Sbjct: 186 GRNG--SNVASIIPN 198


>gi|269912620|emb|CAY86090.1| RNA polymerase beta subunit [Gluconacetobacter xylinus]
          Length = 304

 Score =  277 bits (709), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 138/301 (45%), Positives = 184/301 (61%), Gaps = 29/301 (9%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GMD +EILS FY K+ +++    W   
Sbjct: 61  VTTLLYALEGAASEAARAAKAAEGGDVESMEIQGMDPDEILSYFYGKVEFTKTEKGWARR 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             A D   G K+   L+D  TGE+V  +  KLT+ +++ + E   K + +    L G ++
Sbjct: 121 FDA-DAFRGQKLLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGLIGRFI 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN--NNAYIRNTLVTDK 366
           A DIVN  TGEI+ EAGD + E+ LEE+    +  +  L   +V+  N  +IRNTL  DK
Sbjct: 179 ASDIVNEHTGEIHAEAGDELTEQKLEELEGEGLTTLTTLTTLAVDAANGPWIRNTLAVDK 238

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
           N  R++AL DIYRVMRPG+  T   AE+MF+ LFFD D+YDLS VGRVKMNMRL +  P 
Sbjct: 239 NASREEALTDIYRVMRPGEPPTPETAEAMFSGLFFDPDRYDLSAVGRVKMNMRLGVTCPT 298

Query: 427 D 427
            
Sbjct: 299 R 299


>gi|103001677|gb|ABF71517.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 704

 Score =  277 bits (709), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 117/825 (14%), Positives = 238/825 (28%), Gaps = 145/825 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + +  +              + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                D+  +     N+   ++ +  L+ +               S     AK  G    V
Sbjct: 237  LFVIDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV 288

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q               V+         
Sbjct: 289  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHT 346

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M  + +   + +  ++         
Sbjct: 347  WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM------ 398

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                   +  +             +       +   +  + AI 
Sbjct: 399  ---------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 437

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 438  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 493

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  ++ D      R++          ++  
Sbjct: 494  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRST 553

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             L+ VKV +   +  Q GDK A RH
Sbjct: 554  ENGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRH 593

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +   
Sbjct: 594  GQKGTIGITYRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD- 652

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP F   
Sbjct: 653  ----------------------------------------------------ATP-FTEV 659

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              ++++ +LR       G  ++Y+G TG      V +G  Y  +L
Sbjct: 660  TVDSVSKLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRL 704


>gi|168042961|ref|XP_001773955.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162674799|gb|EDQ61303.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1199

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 97/451 (21%), Positives = 161/451 (35%), Gaps = 46/451 (10%)

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV---RDTSLRV 931
              D         +   G   +G      +     +   ++      A      +    + 
Sbjct: 710  WSDHNQSPRNMYQCQMGKQTMGFPAQALQCRADNKMYRIQTPQMPIAQTNAWNKYHMNQF 769

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
            P+G +  V  +        D    + S     +      K +   + +  +  R   +  
Sbjct: 770  PTGTNAIVAVLAYTGFDMEDAMILNKSSVERGLHYGQVYKSETIDLTE--LRQRGDGVTN 827

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK-SILE 1050
                      FK+    S++ I         Q   + +     V  +  Q + SK    E
Sbjct: 828  VFARSGAMARFKEQADKSANFIDIDGLPYVGQTLTEGDPYCSVVNKMTGQSKISKLKGSE 887

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                + +  I  G   P   L+ V +     R  Q GDK + RHG KG+ S++ P  DMP
Sbjct: 888  AAIVDYVAAINTGSKDP---LQKVTIRTRHPRYPQIGDKFSSRHGQKGVCSQLWPDVDMP 944

Query: 1111 FLK-DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            F    G   DI++NP   PSRM +G + E+    A    GK + +     K++ +    +
Sbjct: 945  FSAVTGMRPDIIINPHAFPSRMTIGMLLESMAAKAGALDGKFMNATPFK-KSSKEGGDGK 1003

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
             F +     G                                     + +   +     +
Sbjct: 1004 DFAKTGGNDG-----------------------------------TADLLGQQMNAHGFN 1028

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
              G  ++Y G+ G  F   + +G +Y  +L HMVSDK   RS G  + VT+QP+ G+   
Sbjct: 1029 YHGTEVMYSGVLGTEFVCEIYLGVVYYQRLRHMVSDKYQVRSMGPVNPVTRQPVKGRKVG 1088

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            GG R GEME   + A+GAAY+L + L   SD
Sbjct: 1089 GGIRFGEMERDSLLAHGAAYLLHDRLHACSD 1119



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 108/773 (13%), Positives = 215/773 (27%), Gaps = 144/773 (18%)

Query: 6   VFNGLGRVRKFFGKNPEIID---IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
            F G        G+  E +D   + DL +    S+D+F+            GL+ A + +
Sbjct: 27  SFYG--------GRKEEELDCSSLYDLTKPHTESFDYFV----------ERGLEEAVRRL 68

Query: 63  FPIT---AFSGA-AMLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLR 107
            PI      SG    L        PP  D             +C    LTY        R
Sbjct: 69  QPIELKHPISGTSLRLWVEKPNVSPPMKDLGSQALDQRLLPSECRLAGLTY--------R 120

Query: 108 LIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GT 143
            I            +  +   +I  G +P+M K                         G 
Sbjct: 121 GIFTADICMQWNNGV--VVRHNISYGKMPVMVKSSVCHLRGLNQKQLVAAKEEATEMGGY 178

Query: 144 FVIKGIQRIVVSQLHRSP------GIHFDHDKGRASL-SGKLLYACR-IIP--------- 186
           F+  G +RI+  +L   P      G+     K R    S K +   R + P         
Sbjct: 179 FICNGNERII--RLLIMPKRNYVVGVKRTSYKNRGPSYSDKGVMISRCVRPDQSAVTMRM 236

Query: 187 ---DQGL-WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQR 241
              + G   +      ++ +         +PV   L AL   +E EI          S+ 
Sbjct: 237 YYMNYGSASLGFSVRRQEFL---------IPVGIILKALIESNEYEIYEQLMSIQSDSKA 287

Query: 242 GDFWCFPLSA---ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                        A +++      SL       Q +         +    ++    ++ +
Sbjct: 288 MKGALGSQFVSQRAKIILEEVRQLSLFTRHDCLQFLGGLTCYFLLVKSVGEQVLNDYILV 347

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
             D     +     +  +   +        +  +L+         +  + V     +  +
Sbjct: 348 HLDNPLDKFNLLVFMLQKLFALVDGMAAPDNADALQNHEILLPGHLLTIVVKDRIQDWLL 407

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
           R      K    K A  D+ +   P DV+   V +        D  K     +    +  
Sbjct: 408 RVQGQLLKEMKEKPAENDLQQ---PIDVTVKHVQKVFEKVPASDVSKKVEYLLNTGNLVS 464

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RL 477
           +  LD           + +  ++ L   R+    +         R  +V ++L   +  +
Sbjct: 465 QSGLDLNQVGGFTLVAEKLNFLRYLSHFRS----VHRGAFFATLRTTTVRKLLPESWGFM 520

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAK-PVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
             +         + +    +      ++A+      +      +++      V  L +++
Sbjct: 521 CPVHTPDGSPCGLLNHLTAACQISSDLDARGNKKDPLAIRKSVTKVMVNLGLVPVLPKLS 580

Query: 537 HTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +      L     G                H  R+   + SE      ++ +   +  + 
Sbjct: 581 NMAPPEYLTVLLDGCVIGHLATGAIPSIIEHLRRLKVVDGSEVPADMEIAYIPCTSAGSY 640

Query: 595 YG-----FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            G           R V        +  +  +E       Q N  L   G+          
Sbjct: 641 PGLYLATTPSRFTRTVKQMFGDGSLELIGPLE-------QVNQFLCPGGNEPIGPKP--- 690

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                          + +    +S+ ASL P+ +++ S R +  C M +Q + 
Sbjct: 691 ------------THEEINATAFLSVVASLTPWSDHNQSPRNMYQCQMGKQTMG 731


>gi|169792052|gb|ACA80316.1| RpoB [Fusobacterium nucleatum]
 gi|169792054|gb|ACA80317.1| RpoB [Fusobacterium nucleatum]
 gi|169792056|gb|ACA80318.1| RpoB [Fusobacterium nucleatum]
 gi|169792060|gb|ACA80320.1| RpoB [Fusobacterium nucleatum]
 gi|169792062|gb|ACA80321.1| RpoB [Fusobacterium nucleatum]
 gi|169792068|gb|ACA80324.1| RpoB [Fusobacterium nucleatum]
 gi|169792084|gb|ACA80332.1| RpoB [Fusobacterium nucleatum]
 gi|169792088|gb|ACA80334.1| RpoB [Fusobacterium nucleatum]
 gi|169792090|gb|ACA80335.1| RpoB [Fusobacterium nucleatum]
 gi|169792092|gb|ACA80336.1| RpoB [Fusobacterium nucleatum]
 gi|169792094|gb|ACA80337.1| RpoB [Fusobacterium nucleatum]
 gi|169792096|gb|ACA80338.1| RpoB [Fusobacterium nucleatum]
 gi|169792102|gb|ACA80341.1| RpoB [Fusobacterium nucleatum]
          Length = 143

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 91/195 (46%), Positives = 107/195 (54%), Gaps = 52/195 (26%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR+LP EDMPFL DGT +D+VLNPLGVPSRMN+GQ+ E HLG A        
Sbjct: 1    RHGNKGVVSRVLPAEDMPFLADGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMRT----- 55

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                              G  +STPVFD
Sbjct: 56   -----------------------------------------------LNGGTYISTPVFD 68

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            GA EE I   L       +G+  LYDG TGE FD  VTVG +YMLKL+H+V DK++AR+ 
Sbjct: 69   GATEEQIKDYLEKQGFPRTGKVTLYDGRTGEKFDNEVTVGIMYMLKLHHLVEDKMHARAI 128

Query: 1273 GSYSLVTQQPLGGKS 1287
            G YSLVTQQPLGGK+
Sbjct: 129  GPYSLVTQQPLGGKA 143


>gi|197944875|gb|ACH79984.1| RNA polymerase subunit B [Mycobacterium brumae]
          Length = 235

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 100/226 (44%), Positives = 133/226 (58%), Gaps = 36/226 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  ++    +                 
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNVQVAGGEIPEWA------------ 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
               G+  E +     DS+            VSTPVFDGA EE +  +L            
Sbjct: 145  ---GNLPEDLLSAPSDSI------------VSTPVFDGAREEELQGLLSSTLPNRDGEVM 189

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARSTG
Sbjct: 190  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTG 235



 Score = 42.8 bits (99), Expect = 0.50,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|6449113|gb|AAF08832.1| RNA polymerase beta subunit [Granulicatella adiacens ATCC 49175]
          Length = 290

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 166/297 (55%), Positives = 219/297 (73%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +T+ RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+++A++
Sbjct: 1   GELTYKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSTYAKI 60

Query: 593 NAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFIETPYR+V     KVT+ + YL+A EE++  +AQANS L+EDGSF  ++V  R  
Sbjct: 61  NKYGFIETPYRRVDWNTHKVTDKIDYLTADEEDSFVVAQANSPLNEDGSFVNDVVMARYV 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E + VP E++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPLL  +APF
Sbjct: 121 SENLEVPVERVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLLNPKAPF 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           +GTGME V A  SG A++ KR G+VE VDA  + +R+ +G LD        Y + KF  S
Sbjct: 181 IGTGMEYVSAHDSGVALLCKRDGVVEFVDAKEVRVRTADGSLD-------TYHITKFHGS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N   C NQRP+V  GD+V + +I+ADGPS + G+LALG+N+LVAFM W GY +ED++
Sbjct: 234 NAGMCYNQRPIVAQGDKVVKGEILADGPSMEKGELALGQNVLVAFMTWEGYIYEDAV 290


>gi|238516704|gb|ACR43978.1| RNA polymerase subunit B [Candidatus Bartonella thailandensis]
          Length = 297

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 215/298 (72%), Positives = 250/298 (83%), Gaps = 1/298 (0%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   IGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 61  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ 
Sbjct: 121 FIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMA 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PRE +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGME
Sbjct: 181 PRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLMRSEAPFVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           SVVA+ SGAA+ AKR GIV+QVDA RIVIR+ E  +D S SGVDIYRL KFQRSNQ+T
Sbjct: 241 SVVARDSGAAVSAKRGGIVDQVDATRIVIRATEE-VDSSKSGVDIYRLQKFQRSNQST 297


>gi|254582667|ref|XP_002499065.1| ZYRO0E02838p [Zygosaccharomyces rouxii]
 gi|238942639|emb|CAR30810.1| ZYRO0E02838p [Zygosaccharomyces rouxii]
          Length = 1196

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 80/364 (21%), Positives = 136/364 (37%), Gaps = 66/364 (18%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ--DEK 1030
            D+ +I++++   R                  +S          +   +W +  ++  DE 
Sbjct: 777  DDAMIINKSADERGFAYGTMYKTEKVDLSLNRSRGDPISQHFGFGNDEWPKEWLEKLDED 836

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEK---------IQWGDDMPPGVLRV-----VKV 1076
                + +   + +   +  +D       K         I+  + +     ++     V +
Sbjct: 837  GLPFIGTYVEEGDPIVAYFDDTLNRTKVKTYHSTEPAYIEEVNLIGDESNKLQELQTVSI 896

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
               ++R  Q GDK + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G  
Sbjct: 897  KYRIRRTPQIGDKFSSRHGQKGVCSRKWPTVDMPFSETGIQPDVIINPHAFPSRMTIGMF 956

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E+  G A    G    +    +  N                                  
Sbjct: 957  VESLAGKAGTLHGVAQDASPWVFDEND--------------------------------- 983

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                       TP       +     L  +  +  G   +Y G +GE     + VG +Y 
Sbjct: 984  -----------TPA------DYFGDQLLKSGYNYHGNEPMYSGASGEELRADIYVGVVYY 1026

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV+DK   RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L 
Sbjct: 1027 QRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLL 1086

Query: 1317 IKSD 1320
              SD
Sbjct: 1087 NSSD 1090



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 103/677 (15%), Positives = 201/677 (29%), Gaps = 89/677 (13%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            ++ +     R+I             + N+ +TD+ +         Y  +R        +
Sbjct: 269 IIKALCDISDREIF-----DGIIGPDLSNSFLTDRLELLLRGFKKRYPQLRNRTQVLQYL 323

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            +          DK DL  VG+  ++  + +    D    +   ++ +I+ L  L  G  
Sbjct: 324 GDKFRIVFQAPPDKSDLD-VGKEVLHRIVLVHLNGDTNEDKCRLLLFMIRKLYSLVAGAC 382

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI----------SSVDIDSVMPQ 501
           + D+ D   ++ V   G +     +  +    +SI  +I          +  D   +   
Sbjct: 383 SPDNPDATQHQEVLLGGFLYGMILKEKVDEYMQSIIAQIRTDINRGIPANFKDRKYMTRV 442

Query: 502 DLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQG 547
            +     + S +  F  +  L              + + E +N    I+H R    + +G
Sbjct: 443 LMRVNDNIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRG 499

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN----AYGFIETPYR 603
                     +R + P  +G +CP  T +G   GL++      R++        I +   
Sbjct: 500 SFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHFAHKCRISTKQSDVSQIPSILY 559

Query: 604 KV-------------CDGKVTND---VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +                 V  D   V + S   E+ R IA        +G      +  
Sbjct: 560 SLGVSPASQAFAAGPSLCCVQIDGKIVGWTS--HEQGRIIADTLRLWKVEGKTPGLPLDL 617

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                  L  R +   +         +       L+ +D         M     P     
Sbjct: 618 EIGY-VPLSSRGQYPGLYIFGGHSRMMRPVRYLPLDKEDIVGPFEQVYMNIAVTPQELQN 676

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              V T +E                    Q        +  +  +      +      K 
Sbjct: 677 N--VHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMAKQTMGTPGVALCHRSDNKL 734

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            R        Q P+VK                  + +   G N +VA + + GY+ +D+M
Sbjct: 735 YRLQSG----QTPVVKANLYDDYG----------MDNFPNGINAVVAVISYTGYDMDDAM 780

Query: 828 LISERMVSEDVFTSIHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +I++             +  +V       R   +       +     E  L+ +DE G+ 
Sbjct: 781 IINKSADERGFAYGTMYKTEKVDLSLNRSRGDPISQHFGFGNDEWPKEW-LEKLDEDGLP 839

Query: 883 CVGAEVNPGDILVGK----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            +G  V  GD +V             T     P   EE  L      K  +++  S++  
Sbjct: 840 FIGTYVEEGDPIVAYFDDTLNRTKVKTYHSTEPAYIEEVNLIGDESNKLQELQTVSIKYR 899

Query: 933 SGVSGTVVDVRIFNRHG 949
              +  + D +  +RHG
Sbjct: 900 IRRTPQIGD-KFSSRHG 915



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 114/889 (12%), Positives = 243/889 (27%), Gaps = 134/889 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS--------GAAMLEFVSYEF 81
           ++    S++             N+G++   + V  I                +       
Sbjct: 42  VQPHIGSFNAL--TEGPEGGLLNQGIKDIGEKV--IFDGKRSDSIQLGNRLSVSVEQASI 97

Query: 82  DPPKFD------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
             P F+              +   R  +Y   L I LR  V + +E      ++D     
Sbjct: 98  TKPMFNDGVASGVERRVFPSEARQRLSSYKGKLVIKLRWEVNNGEETF--TEVRDC---- 151

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIV---VSQ------ 156
              G +P+M +                         G F+I GI++++   + Q      
Sbjct: 152 ---GAVPIMLQSNRCHLYNMPPSELVKHKEESDEFGGYFIINGIEKLIRMLIVQRRNHPM 208

Query: 157 -LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRRK- 211
            + R P   F +     S  G  + + R  PDQ      +    D    +  R   R+  
Sbjct: 209 AIIR-PS--FANRGAAYSQFGVQIRSVR--PDQTSQTNVLHYLHD--GQVTFRFSWRKNE 261

Query: 212 --VPVTSFLMAL-GMDSEEILS-TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
             +PV   + AL  +   EI      P +  S   D          L+ G K     +  
Sbjct: 262 YLIPVVMIIKALCDISDREIFDGIIGPDLSNSFLTDRL------ELLLRGFKKRYPQLRN 315

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
            T + +   G K    ++          L +  + L    +    +NG+T E        
Sbjct: 316 RT-QVLQYLGDKF--RIVFQAPPDK-SDLDVGKEVL--HRIVLVHLNGDTNEDKCRLLLF 369

Query: 328 IDEKSLEEIFHSEIRDIP--ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           +  K    +  +   D P    + + +         L    ++  +  +  I   +  G 
Sbjct: 370 MIRKLYSLVAGACSPDNPDATQHQEVLLGGFLYGMILKEKVDEYMQSIIAQIRTDINRGI 429

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
            + F         +    +    S +        L   +  D++ +    ++A       
Sbjct: 430 PANFKD-RKYMTRVLMRVNDNIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYR 488

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLI 504
             +    +         +  +V ++L   +  L  +         + +            
Sbjct: 489 FISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHFAHKCRISTKQ 548

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +    + ++      S  SQ        +             G +    +  + R +  T
Sbjct: 549 SDVSQIPSILYSLGVSPASQ--------AFAAGPSLCCVQIDGKIVGWTSHEQGRIIADT 600

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
               +   +         +     +  +++ G     Y      ++   V YL   +E+ 
Sbjct: 601 ----LRLWKVEGKTPGLPLDLEIGYVPLSSRGQYPGLYIFGGHSRMMRPVRYLPLDKED- 655

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +              +EL                   ++ +P  ++SI A+L PF + 
Sbjct: 656 -IVGPFEQVYMNIAVTPQELQNNVH------------THVEFTPTNILSILANLTPFSDF 702

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ----VDA 740
           + S R +  C M +Q +                +    SG   V K     +        
Sbjct: 703 NQSPRNMYQCQMAKQTMGT--PGVALCHRSDNKLYRLQSGQTPVVKANLYDDYGMDNFPN 760

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               + +V            I      +R      + +   V +     R D I+     
Sbjct: 761 GINAVVAVISYTGYDMDDAMIINKSADERGFAYGTMYKTEKVDLSLNRSRGDPISQHFGF 820

Query: 801 DLGDLA--LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
              +        +    +P+ G   E+   I      +D      ++ +
Sbjct: 821 GNDEWPKEWLEKLDEDGLPFIGTYVEEGDPIV--AYFDDTLNRTKVKTY 867


>gi|89888192|gb|ABD78641.1| DNA-directed RNA polymerase beta subunit [Bordetella trematum]
          Length = 292

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 175/289 (60%), Positives = 229/289 (79%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++S+  +AR+N YGF+ETPYRK+ DG+V++ + YLSA+EE +  IAQAN++LDE
Sbjct: 1   GPNIGLINSMALYARLNEYGFLETPYRKIIDGRVSDQIDYLSAIEESHYVIAQANAALDE 60

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +G F ++LV CR AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG NM
Sbjct: 61  EGRFVDDLVACREAGETMLTAPSNVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGANM 120

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
           QRQAVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +     
Sbjct: 121 QRQAVPCLRPEKPLVGTGIERTVAVDSGTTVQALRGGLVDHVDAERVVIRVNDDENVAGE 180

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            GVDIY L+K+ RSNQNT +NQRP+VK GD V + D++ADG STDLG+LALG+NML+AFM
Sbjct: 181 VGVDIYNLIKYTRSNQNTNINQRPIVKRGDRVAKGDVLADGASTDLGELALGQNMLIAFM 240

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           PW+GYNFEDS+LISE++V++D +TS+HIEE  V+ARDTKLGPEEITRDI
Sbjct: 241 PWNGYNFEDSILISEKVVADDRYTSVHIEELTVVARDTKLGPEEITRDI 289


>gi|194762044|gb|ACF94994.1| RpoB [Bartonella sp. Lao/Nh2]
          Length = 295

 Score =  277 bits (708), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 215/296 (72%), Positives = 251/296 (84%), Gaps = 1/296 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG ++RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFKVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           E+VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 241 EAVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSN 295


>gi|269912562|emb|CAY86061.1| RNA polymerase beta subunit [Gluconacetobacter entanii]
          Length = 275

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 120/278 (43%), Positives = 163/278 (58%), Gaps = 28/278 (10%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
            +R++VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR
Sbjct: 1   TERVIVSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDR 60

Query: 209 RRKVPVTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGD 243
           +RK+PVT+ L AL                         GM  +EIL  FY ++ + +   
Sbjct: 61  KRKLPVTTLLYALEGEESRAARDAKAAEGGDVESMEIRGMTPDEILGYFYGQVEFIKSEK 120

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W       D   G K+   LVD DTGE V +   KLT+ +++ + E   K + +    L
Sbjct: 121 GWARRFDP-DAFRGQKLLEPLVDADTGEIVAQVDTKLTARMVRKIAET-TKDVLVGPAGL 178

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
            G ++A D+VN ETGEI+ EAGD + E  LE +    +  +  L +D+ N   +IRNTL 
Sbjct: 179 IGRFIAFDMVNPETGEIFAEAGDELTEARLEALEADGVTKLVTLAIDATN-GPWIRNTLA 237

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
            DKN  R DAL DIYRVMRPG+  T   AE+MF+ LFF
Sbjct: 238 IDKNTSRDDALTDIYRVMRPGEPPTPETAEAMFSGLFF 275


>gi|183579263|gb|ACC63209.1| RpoB [Mycobacterium ulcerans]
          Length = 224

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 95/226 (42%), Positives = 126/226 (55%), Gaps = 37/226 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +  G +       +  
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIDVANGVPEWAGKLPENLLSAQ-- 144

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 145  --------------------------PDSIVSTPVFDGAQEAELQGLLSATLPNRDGEVL 178

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                G++ L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARSTG
Sbjct: 179  VDGDGKAKLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTG 224


>gi|326517304|dbj|BAK00019.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 1194

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 113/278 (40%), Gaps = 54/278 (19%)

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGV----LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
               E  + + +  I  G      V     R V + +  +R    GDK + RHG KG +S 
Sbjct: 883  KDHEPAYIDAVRVIGLGSSTNTKVERSNFRRVAITLRYRRNPIIGDKFSSRHGQKGTLSV 942

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            + P E+MPF + G   D+++NP   PSRM +G + E+  G A    G    +    +   
Sbjct: 943  LWPQENMPFSESGMSPDVLINPHAFPSRMTIGMLIESMAGKAGAIHGMFQDATPFQFHEE 1002

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +                                                   + +   
Sbjct: 1003 RKV--------------------------------------------------IDYVGEQ 1012

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            LR       G   LY+GLTG+     + +G ++  +L HMVSDK   RSTG  + +T+QP
Sbjct: 1013 LRACGYQYYGSEPLYNGLTGKVMQADIFIGLVFYQRLRHMVSDKSQVRSTGPVTAITRQP 1072

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            + G+   GG RLGEME   + ++G A+ LQ+ L   SD
Sbjct: 1073 VKGRKKHGGIRLGEMERDALLSHGVAFCLQDRLMNCSD 1110



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 118/873 (13%), Positives = 244/873 (27%), Gaps = 148/873 (16%)

Query: 52  NEGLQAAFKSVFPIT---AFSGAAMLEFVSYEFDPPK---------FDVDDCLWRDLTYA 99
           + GL  A   + P+           ++F S E   P              +C     +Y+
Sbjct: 3   DHGLDDALADLLPVELSINEDTHIKMQFTSLEIGYPCRPLGADIVPVTPRECRESATSYS 62

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
              K ++ + +           +K        +GDLP+M                     
Sbjct: 63  GSFKGSIEVTIEGKVNAQYVIPVK--------LGDLPIMVMSSKCNLRNLAPKKLAEMEE 114

Query: 142 ------GTFVIKGIQRIV-VSQLH-RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
                 G F++ GI+R++ + Q+  R+  +  +    R   +    Y+ + +  +     
Sbjct: 115 ESNEVGGYFIVNGIERVIRLLQIQRRNYAVAIERSTFRNRGNN---YSDKGVAMKCT--- 168

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
                KD+    I              L       L+     + +  R   +  P+    
Sbjct: 169 ----KKDLTSATIT-------------LHY-----LNNGCATLRFVLRKQEFLLPVILVA 206

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCG-------- 305
             +       L D   GE +      LT+ +   L++     L   ++CL          
Sbjct: 207 KSLMNISDKELFDRIVGENL--DNTFLTTRIELLLRDYKQYNLHSMNECLAYLGSLFRNL 264

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
           L V     + ETG + I+        +L     S    +  L        ++++   + D
Sbjct: 265 LGVTSKYSDLETGILLIKR-------NLFIHVESFGGKLDCLIFMIRKLFSFVQGKCIND 317

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                 DAL+  + ++ PG +    + E +   L           V R    M+   +  
Sbjct: 318 NA----DALM-NHDLLLPGHLLNMIIKEKLEESLTASK-----GLVIRDSRVMKGKFEAE 367

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ---YRLGLLRM 482
                          + L D   G         L +  V S   +   Q   + +   R+
Sbjct: 368 -------CLKNNKYFQRLCDRVCGNIGAKIATFLSSGNVVSSSGLDLMQKSGFTIIAERL 420

Query: 483 E--RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
              R      S               + ++     F C                + H  +
Sbjct: 421 NLFRFFSHFQSVHRGQFFTTMKTTTVRKLLPESWGFLCP----VHTPDGAPCGLLNHLAK 476

Query: 541 LSALGQGGVARARAGVEMRDV-HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            + +     ++         V  P+          S    + +   +      N  G   
Sbjct: 477 DAVILSYPPSKKPPITTTHPVAQPSAVNLDLLCSKSYLQEVLVSLGMQISGLGNYDGQAI 536

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS--LDEDGSFTEELVFCRCAGEEILVP 657
              R+     +          E+    +AQ      L + G   +         E   +P
Sbjct: 537 FNERESLSVLIDGVFAGFVQKEKAPSVVAQLRRMKSLAKYGRRADLPYILEPTTEIGFIP 596

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL---------KAEA 708
           + + D +   P   +      +     +   + +       Q    +             
Sbjct: 597 KLEFDNLGPYPGIYIFTQHGRMSRPVLNLHTKEVEWIGPMEQVFMEIACVKEDIFPSPFK 656

Query: 709 PFVGTGMESVVAKS---SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
               T +E         S   ++++ A +    D  +      +  +   T G   +   
Sbjct: 657 TASSTSVEDEGTSHIELSPTVMLSQIASLTPYSDYNQSPRNMYQCQMGKQTMGTPTH-AF 715

Query: 766 KFQRSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
           KF+  N+   +   Q P+V+                  + +   G N +VA + + GY+ 
Sbjct: 716 KFRADNKLYRILNVQAPIVQ----------TKTHGEYFMDEYPQGCNAVVAVISYTGYDM 765

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           ED+M+I++           H   ++ M  D + 
Sbjct: 766 EDAMIINKAAYERGFG---HGCVYKTMFVDLEE 795


>gi|260505174|gb|ACX42078.1| RNA polymerase beta subunit [Leclercia adecarboxylata ATCC 23216]
          Length = 289

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 176/287 (61%), Positives = 224/287 (78%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   VGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YG
Sbjct: 61  HKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           F+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L 
Sbjct: 121 FLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLF 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME
Sbjct: 181 SRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY 
Sbjct: 241 RAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYN 287


>gi|269930861|gb|ACZ54165.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930893|gb|ACZ54181.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930895|gb|ACZ54182.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930897|gb|ACZ54183.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 294

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 214/295 (72%), Positives = 249/295 (84%), Gaps = 1/295 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 294


>gi|219111265|ref|XP_002177384.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411919|gb|EEC51847.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 1147

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/447 (19%), Positives = 154/447 (34%), Gaps = 54/447 (12%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV---PS 933
            D+        +   G   +G            +   L+               ++   P+
Sbjct: 675  DQNQSPRNMYQCQMGKQTMGTPAHSLPYRPDNKLYRLQTPQAPVVQTSIHGEYKMDEYPN 734

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
            G +  V  +        D    + S         +  K  +  + +    +       G+
Sbjct: 735  GTNAVVAVLSYTGFDMEDSVILNKSSVERGFAHASVYKTIDVSLQEEAKMT--GASSSGE 792

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
            +         K   +    + +    Q      + + +   V+S+    + +    E   
Sbjct: 793  DVRMKFSNKVKFDKVMYPSLQDDGLPQVGDCMTEGDPLYCVVDSIS-GMDRAAKHKEREI 851

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                     G+D   G    V + +   R    GDK + RHG KG++S + P EDMPF +
Sbjct: 852  AYVQSVRALGNDSGKGADNKVSITLRFPRNPVLGDKFSSRHGQKGVLSILWPQEDMPFSE 911

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D+++NP   PSRM +G + E+  G +    G    +    +  +G          
Sbjct: 912  SGISPDVIINPHAFPSRMTIGMMVESMAGKSGALHGNFQNATPFSFHESG---------- 961

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                  D    +     L+ A  +  G 
Sbjct: 962  --------------------------------------DKVSVDYFGEQLQAAGYNYYGS 983

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              LY G++G      + +G +Y  +L HMV DK   R+TG  + +T+QP+ G+   GG R
Sbjct: 984  EPLYSGVSGCVMQADLYIGVVYYQRLRHMVLDKYQVRATGPTNELTRQPIKGRKKGGGIR 1043

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            LGEME   + ++G A++LQ+ L   SD
Sbjct: 1044 LGEMERDSLLSHGTAFLLQDRLLNCSD 1070



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 103/754 (13%), Positives = 214/754 (28%), Gaps = 143/754 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP----ITAFSGAAMLEFVSYEFDPP 84
           L      S+D+F            +GL    + + P    I        L         P
Sbjct: 6   LTAPHVDSFDYF----------WEQGLARGVQDIEPAEFNIVDPQK---LR--DNPIAKP 50

Query: 85  ---------KFDVDDCLWRDLTYAVPLKITL--RLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                    K    +C  R L YA  +  T   R+I         ++ ++  K      G
Sbjct: 51  AKAPGERSQKLLPRECRERKLVYAGEISATFCYRMIQRRNGVDFPSRPVRLNKT----FG 106

Query: 134 DLPLM-----------TK-------------DGTFVIKGIQRIV-VSQ---------LHR 159
           D+P+M           T               G F++ GI+R V + Q         + R
Sbjct: 107 DMPIMVMSKGCHLEGTTPKQLVKLKEEDNEFGGYFIVGGIERCVRLLQVPRRNHATAIQR 166

Query: 160 SP-----------GI---HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR 205
           S            G+      H+   ++++  + Y        G  +      ++ +   
Sbjct: 167 SSYKNRGNTYTDLGVAMRCARHNGDMSAITNTVHYLTTG----GANLKFVAKKQEFL--- 219

Query: 206 IDRRRKVPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                 +P    L AL G +S+  L   Y +IV   + + +    +   L        SL
Sbjct: 220 ------IPAILILRALSGSESQTEL---YERIVQGDQSNTFLVARAGLLLQDARARFGSL 270

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG---ETGEIY 321
              D     I +  +  S   ++  +  +    I    L  L    D +        ++Y
Sbjct: 271 NTPDECLAFIGTRFRRLSQKAETTSDVEIGHHIIRRFVLIHLPTYRDKLECLLLMLRKLY 330

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN--AYIRNTLVTDKNKDRKDALLDIYR 379
             A       + + + + EI     L    +      ++ +  +   +  RKD      +
Sbjct: 331 AFAAGDCGVDNADSLQNQEILLPGHLMCTFIKEKFEEFLSSLRLALLSDLRKDFARTSAK 390

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           +             +               + G +     L+L        +   + +  
Sbjct: 391 LTDAKYWGKMVDRHAGKASGGIGKKVQHFLSTGNIVSTSGLDLMQVSGYTIV--AERLNF 448

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSV---DI 495
           ++     R+    +         +  +V ++L +Q+  L  +         + S      
Sbjct: 449 LRYCAHFRS----VHRGQFFMEMKTTAVRKLLPDQWGFLCPVHTPDGGPCGLLSHLALKS 504

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
             +     ++AK ++                   N   RI  T     +   G     A 
Sbjct: 505 KVMAYPSRLDAKGMIDLDDLLLSLGVTPCGAGSRNGDGRIGSTHLHLPVSIDGRIVGGAS 564

Query: 556 VEMRDVHPTHYGRICPAE------TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             +  +   H  ++          T E   +   +    +  +  +       R V +  
Sbjct: 565 PSVLKIIAAHLRKLKVDNPPVVPPTLEVGLVPPGNPGAPYPGLYLFTCAARLVRPVLNRA 624

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            +    ++  +E+    IA  +  + E                            +  P 
Sbjct: 625 -SGHTEFIGPLEQGYMDIACLDEDIREG----------------------ITTHQELDPT 661

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            ++S+ A+L PF + + S R +  C M +Q +  
Sbjct: 662 NMLSLIANLTPFSDQNQSPRNMYQCQMGKQTMGT 695


>gi|160337106|gb|ABX25844.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 224

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 95/225 (42%), Positives = 126/225 (56%), Gaps = 40/225 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 137  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARST
Sbjct: 180  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARST 224


>gi|310793783|gb|EFQ29244.1| RNA polymerase Rpb2 [Glomerella graminicola M1.001]
          Length = 1225

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/454 (19%), Positives = 149/454 (32%), Gaps = 62/454 (13%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +   G   +G            +   L++            +    +  +
Sbjct: 707  DFNQSPRNMYQCQMGKQTMGTPATALRYRTDNKMYRLQSGQTPVVRSPLHNAYGFDNFPN 766

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLA--RDKDDEQVILDRNIYSRLMEILCGQN 994
            G    V + +  G D ++  I  +               +++ L     +R ++ +    
Sbjct: 767  GFNAVVAVISYTGYDMDDAMILNKSAHERGFGHGTIYKTKKITLKDESRTRSVKNISKLF 826

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQ--------FAVQDEKVQRNVESLKVQYETSK 1046
              +     K       D        +  Q          V  +   + V      +    
Sbjct: 827  GFAPGGFVKGHYRGQLDEDGLPYVGRLVQEGDVLCAWHTVSADYSGKLVNLDGQTHYEKY 886

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
               E  F  ++  I  G +      + + + + + R    GDK + RHG KG+ S+  P 
Sbjct: 887  KDSETAFVEEVRVI--GSETGNEPAQTISIKLRVPRSPVIGDKFSSRHGQKGVASQKWPA 944

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
             DMPF + G   D+++NP   PSRM +G   E+  G A    G    S    +      +
Sbjct: 945  VDMPFSESGMQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFNEENTAA 1004

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                              +     L  A
Sbjct: 1005 --------------------------------------------------DYFGHQLMKA 1014

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
              +  G   +Y G+TGE     + VG +Y  +L HMV+DK   R+TG     T QP+ G+
Sbjct: 1015 GYNYHGNEPMYSGITGEELAADIYVGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKGR 1074

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
               GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1075 KRGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1108



 Score = 69.7 bits (169), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 84/656 (12%), Positives = 181/656 (27%), Gaps = 82/656 (12%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L  T    + D D     +           +G +P+M K       
Sbjct: 114 PAECRERHCTYRGRLSATFEYRINDGDPKEFVRE----------LGQVPIMVKSNRCHLE 163

Query: 142 ------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
                             G F++ GI++ ++  L  +           +  +    Y   
Sbjct: 164 GNSPAQLVQRKEESEELGGYFIVNGIEK-IIRMLQVNRRNFPMAINRPSFQNRGQGYTPY 222

Query: 184 IIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSE-EILST 231
            I  + +  D E    +++H         R   R+    VPV   L +L   ++ EI   
Sbjct: 223 GIILRSVRPD-ETSQTNVLHYLSDGNMTFRFSWRKNEYLVPVMMILKSLVETNDREIFEG 281

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
                      + +        L+   K        +T   + E  + +  G+  ++   
Sbjct: 282 LIGLSGSKSSKNTFLTD-RVELLLRTYKSYCLYSKTETRAYLGEKFRVVL-GVPDTMSNY 339

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            V    +    L  L         +  +  +    +    +L     S      +   + 
Sbjct: 340 DVGTEFLRKIVLVHLGNINVTEKEDNDKFRMLLFMIRKLYALVAGDCSVDNPDAVQNQEV 399

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           +         L     +    A+    R       +T   ++        +  ++    +
Sbjct: 400 LLGGFLYGMILKERLEEFLTTAVRLSLREWTRKHPATPFTSQDFAKEFPANIFRHANENL 459

Query: 412 GR----VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
           G           L   +  D++      ++A     +   +    I         +  +V
Sbjct: 460 GNGLEYFLSTGNLTSPSGLDLQQTAGFTVVAEKLNFLRFLSHFRMIHRGAFFAELKTTTV 519

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
            ++L   +                      ++       K +  AV        L     
Sbjct: 520 RKLLPESWGFMC-------PVHTPDGAPCGLLNHLAHKCKIMTEAVDASKIP-GLVAELG 571

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            V + S  T    +  L    V        +R      Y ++      EG +   +    
Sbjct: 572 AVETSSAATDESVVIMLDGRIVGFCTPRESLRIADTLRYWKV------EGTHGVPLQLEV 625

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +   +  G     Y      ++   V YL   +E+  ++              +E+V  
Sbjct: 626 GYVPPSNGGSYPGIYLASAPARMVRPVKYLPLDKED--FVGPHEQPYMSIAVVEDEIVSG 683

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                       +   ++ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 684 ------------ESTHVEFTPTNMLSILANMTPFSDFNQSPRNMYQCQMGKQTMGT 727



 Score = 68.2 bits (165), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 60/407 (14%), Positives = 127/407 (31%), Gaps = 50/407 (12%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++  + + E +N L  ++H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 483 TAGFTVVAEKLNFLRFLSHFR---MIHRGAFFAELKTTTVRKLLPESWGFMCPVHTPDGA 539

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ L    ++            V   K+   V  L A  E +      +  +  DG
Sbjct: 540 PCGLLNHLAHKCKI--------MTEAVDASKIPGLVAELGA-VETSSAATDESVVIMLDG 590

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQV------------------VSIAASLIP 680
                            +   K++     P Q+                   S  A ++ 
Sbjct: 591 RIVGFCTPRESLRIADTLRYWKVEGTHGVPLQLEVGYVPPSNGGSYPGIYLASAPARMVR 650

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            ++    ++       ++  + +   E   V    ES   + +   +++  A +    D 
Sbjct: 651 PVKYLPLDKEDFVGPHEQPYMSIAVVEDEIVSG--ESTHVEFTPTNMLSILANMTPFSDF 708

Query: 741 IRIVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            +      +  +   T G        +           Q P+V+               +
Sbjct: 709 NQSPRNMYQCQMGKQTMGTPATALRYRTDNKMYRLQSGQTPVVRS----------PLHNA 758

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +   G N +VA + + GY+ +D+M++++             +  ++  +D      
Sbjct: 759 YGFDNFPNGFNAVVAVISYTGYDMDDAMILNKSAHERGFGHGTIYKTKKITLKDESRTRS 818

Query: 860 EITRDIPN-------VSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                          V       +DE G+  VG  V  GD+L    T
Sbjct: 819 VKNISKLFGFAPGGFVKGHYRGQLDEDGLPYVGRLVQEGDVLCAWHT 865


>gi|145521170|ref|XP_001446440.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124413918|emb|CAK79043.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1131

 Score =  276 bits (707), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 103/500 (20%), Positives = 190/500 (38%), Gaps = 84/500 (16%)

Query: 880  GIICVGAEVNPGDILVGKITPKGE--SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            GII +  ++     L   I P+      ++ E      +       V   S         
Sbjct: 682  GIIGMNTQIRCDTQLYQLIYPQTPLVRTVSMEAVNQHRLPAGHNAQVAVMSYSCYDIEDA 741

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +++    +R          SV   +I    ++    + I +    +            +
Sbjct: 742  LIMNKSSLDRGFGRTAVYKKSVTECEINQRNKESRFNERIDEPPTKTH----------NT 791

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK---VQRNVESLKVQYETSKSILEDRFK 1054
              K  KK   L +D I++            ++K   V  N ++  +Q   + S+ ++++ 
Sbjct: 792  KKKFIKKYHALDNDGITKVGAQLHHGDIYVNKKTPQVPDNPQTENIQIADTPSVFKEKWP 851

Query: 1055 NKIEKIQWGDDMPPGV--LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              ++++   ++   G   ++ +K      R  + GDK + RHG KG+V  I+  EDMPF 
Sbjct: 852  YTVDRVLIINNTNDGTEKIKTIKTIFRQIRRPEFGDKFSSRHGQKGVVGLIVNQEDMPFN 911

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            + G   D+++NP G                                              
Sbjct: 912  ERGWCPDLIMNPHG---------------------------------------------- 925

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                 +     K+ +     +  +  ++K G       F G +   +   L        G
Sbjct: 926  ---YPSRMTIAKLMELLCGKLGALEGKFKYGT-----AFGGENVLQVGEELLKRGFHYQG 977

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L  G+TGE  +  V  G I+  +L HMV DK++AR+ G    +T+QP+ G++  GGQ
Sbjct: 978  KDCLISGITGEYMECYVYQGPIFYQRLKHMVIDKIHARAKGPMEKLTRQPVEGRAKDGGQ 1037

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVAG---NDTFETG 1342
            R+GEME  C  AYGA+ +L E L I SD       ++ G  +  +S+  G   +  ++  
Sbjct: 1038 RIGEMERDCFLAYGASNLLIERLLISSDPFNVYVCEICGMFKS-DSVCRGCNTDKVYQIR 1096

Query: 1343 TPESFNVLVKEMQALGLSID 1362
             P    +L +E+  L ++I 
Sbjct: 1097 LPYCCKLLFQEL--LAMNIK 1114



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 125/967 (12%), Positives = 269/967 (27%), Gaps = 227/967 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS--VFPITAFSGA-AMLEFVSYEFDPPK 85
           L +    S+++F+           + L+   KS     IT  S +  +LE++S   + P 
Sbjct: 18  LQKQHIDSFNYFI----------EQRLEQIVKSPLNQRITCESDSSFLLEYLSIRVENPT 67

Query: 86  FD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           F                +C   D TYA  + + +R+ +   +          I+E+ + +
Sbjct: 68  FTSSWDKYSLKSLLYPHECRLNDQTYAGDIYVNVRIHMKGREP---------IEEKDVLI 118

Query: 133 GDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHD 168
           G +P+M                           G F+I+G +++++              
Sbjct: 119 GRMPIMLGSKKCNLSGKTEAEIFQYGECPYDPKGYFIIEGNEKVILILEQVVDNRIIVDV 178

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIEFD-------SKDIIHVRIDRRRKVPVTSFLMAL 221
             +        Y   +         +E          K+  +V+    +  P+     AL
Sbjct: 179 DNKTDQ-----YVSTVQSY-----QLETKSKASIILKKNKFYVKSSSFKDAPLFIVFKAL 228

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G+ ++ EI+     +    ++        S   +         +     G+ +       
Sbjct: 229 GIVNDKEIIELIGTEPSIVEKLLMSFQDSSDEKIKTQLDALQYI-----GKLITSKFGGQ 283

Query: 281 TSGLLKSLKEK----------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           +S L    +EK            K+         G  V   I+  E      +     ++
Sbjct: 284 SSNLADQAREKLAQVFLAHVNCKKYDFYPKAIYLGQMVRRLILAMEDKRFVDDKDYYGNK 343

Query: 331 KSLEEIFHSEIRDIP--------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +        E+            I  +               D     K+  +DI + + 
Sbjct: 344 RMRCAGNLLELLFEDLFKGLNSTISSILKKELGKANCKFTPKDVTMKMKEFGVDITKGLN 403

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
               +     +         +    L+ +        L        + ++     A++  
Sbjct: 404 RAIKTGKWTIQRFHMDRQGVTQL--LARISYTSALGMLTKMRSQVQKTLKVSGPRALVGS 461

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              +     T D  D    + +  +  + +   +  + +    I   +   DI    P +
Sbjct: 462 QFGMICPADTPDGEDCGLVKTLALLTHITQEDIQDSVYK----IILSMGVEDICHFKPSE 517

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
                 V          ++  +  + +                   + R     E   +H
Sbjct: 518 FHKNYIVYLNGIIVGMHARPQEFVDQLRI-----------------LRRRGKINEFVSIH 560

Query: 563 PTHYGRICPAETSEG----HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN-DVVYL 617
                ++       G      I +        +++   F +   + V    V N  + YL
Sbjct: 561 KDDLRKVVNISGDSGRLVRPLILVKDGKPQLIQIDMIDFKQNDAKTVFSSFVKNGKIEYL 620

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              E +N +IA   + +                         +   ++     ++S    
Sbjct: 621 DVNESDNAFIALTINDVTM-----------------------ETTHLEIDQMTILSCVTG 657

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           L+PF  ++ S R    C M +Q++ ++                                 
Sbjct: 658 LVPFPHHNQSARNTFQCQMGKQSLGIIGMNTQI--------------------------- 690

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            +     IY      R+     VNQ                   
Sbjct: 691 --------------RCDTQLYQLIYPQTPLVRTVSMEAVNQH------------------ 718

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE----EFEVMARD 853
                  L  G N  VA M +  Y+ ED++++++  +      +   +    E E+  R+
Sbjct: 719 ------RLPAGHNAQVAVMSYSCYDIEDALIMNKSSLDRGFGRTAVYKKSVTECEINQRN 772

Query: 854 TKLGPEEITRDIPNVSE-------EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +    E   + P  +        +    +D  GI  VGA+++ GDI V K TP+     
Sbjct: 773 KESRFNERIDEPPTKTHNTKKKFIKKYHALDNDGITKVGAQLHHGDIYVNKKTPQVPDNP 832

Query: 907 TPEEKLL 913
             E   +
Sbjct: 833 QTENIQI 839


>gi|62903510|gb|AAY19522.1| RpoB [uncultured Bartonella sp.]
          Length = 294

 Score =  276 bits (707), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 215/294 (73%), Positives = 249/294 (84%), Gaps = 1/294 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           + SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 242 RDSGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 294


>gi|269930919|gb|ACZ54194.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 294

 Score =  276 bits (707), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 215/295 (72%), Positives = 249/295 (84%), Gaps = 1/295 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 294


>gi|227937594|gb|ACP43372.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 294

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 216/295 (73%), Positives = 250/295 (84%), Gaps = 1/295 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 294


>gi|145926508|gb|ABP98893.1| RNA polymerase beta subunit [Bradyrhizobium genosp. beta]
 gi|145926524|gb|ABP98901.1| RNA polymerase beta subunit [Bradyrhizobium genosp. beta]
          Length = 257

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN 
Sbjct: 120 ALRMSDEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKGLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|302122497|gb|ADK92919.1| RNA polymerase subunit B [Vibrio parahaemolyticus]
          Length = 311

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 188/310 (60%), Positives = 242/310 (78%)

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG
Sbjct: 2   AEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKG 61

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +
Sbjct: 62  EVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISA 121

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
           AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP
Sbjct: 122 AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCP 181

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN
Sbjct: 182 IETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQAN 241

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR L
Sbjct: 242 AKLNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRAL 301

Query: 692 MGCNMQRQAV 701
           MG NMQRQAV
Sbjct: 302 MGANMQRQAV 311


>gi|89888206|gb|ABD78647.1| DNA-directed RNA polymerase beta subunit [Achromobacter
           xylosoxidans]
          Length = 300

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 178/298 (59%), Positives = 232/298 (77%)

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
            G NIGL+ S+  +AR+N YGF+ETPYRK+ DG+V+  + YLSA+EE +  IAQAN++LD
Sbjct: 1   GGPNIGLIXSMALYARLNEYGFLETPYRKIIDGRVSEQIDYLSAIEESHYVIAQANAALD 60

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           E+G F ++LV CR AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG N
Sbjct: 61  EEGRFVDDLVACREAGETMLTAPANVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +    
Sbjct: 121 MQRQAVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGLVDHVDAERVVIRVNDEENVAG 180

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             GVDIY L+K+ RSNQNT +NQRP+VK GD V + D++ADG STDLG+LALG+NML+AF
Sbjct: 181 EVGVDIYNLIKYTRSNQNTNINQRPIVKRGDRVAKGDVLADGASTDLGELALGQNMLIAF 240

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           MPW+GYNFEDS+LISE++V++D +TS+HIEE  V+ARDTKLGPEEITRDI N++E  L
Sbjct: 241 MPWNGYNFEDSILISEKVVADDRYTSVHIEELTVVARDTKLGPEEITRDISNLAETQL 298


>gi|227937590|gb|ACP43370.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 293

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 212/294 (72%), Positives = 248/294 (84%), Gaps = 1/294 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           E++VA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQR
Sbjct: 241 EAIVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQR 293


>gi|227937586|gb|ACP43368.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 293

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 214/293 (73%), Positives = 248/293 (84%), Gaps = 1/293 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 242 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 293


>gi|145926514|gb|ABP98896.1| RNA polymerase beta subunit [Bradyrhizobium sp. BC-P6]
          Length = 257

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 140/258 (54%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ D L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN 
Sbjct: 120 ALRMSDDELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKGLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|145926510|gb|ABP98894.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926520|gb|ABP98899.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926522|gb|ABP98900.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926534|gb|ABP98906.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926536|gb|ABP98907.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926562|gb|ABP98920.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|145926564|gb|ABP98921.1| RNA polymerase beta subunit [Bradyrhizobium japonicum]
 gi|190612272|gb|ACE80570.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670322|gb|ADR73352.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM1]
 gi|313670324|gb|ADR73353.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM2]
 gi|313670326|gb|ADR73354.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM3]
 gi|313670328|gb|ADR73355.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM4]
 gi|313670330|gb|ADR73356.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM5]
 gi|313670334|gb|ADR73358.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM7]
 gi|313670336|gb|ADR73359.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM8]
 gi|313670340|gb|ADR73361.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM10]
 gi|313670342|gb|ADR73362.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM11]
 gi|313670344|gb|ADR73363.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM12]
 gi|313670346|gb|ADR73364.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM13]
 gi|313670352|gb|ADR73367.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM16]
 gi|313670356|gb|ADR73369.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM18]
 gi|313670358|gb|ADR73370.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM19]
 gi|313670360|gb|ADR73371.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM20]
 gi|313670364|gb|ADR73373.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM22]
 gi|313670366|gb|ADR73374.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM23]
 gi|313670370|gb|ADR73376.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM25]
 gi|313670372|gb|ADR73377.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM26]
 gi|313670378|gb|ADR73380.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM29]
 gi|313670384|gb|ADR73383.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM32]
 gi|313670388|gb|ADR73385.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM34]
 gi|313670390|gb|ADR73386.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM35]
 gi|313670394|gb|ADR73388.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM37]
 gi|313670396|gb|ADR73389.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM38]
 gi|313670398|gb|ADR73390.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM39]
 gi|313670404|gb|ADR73393.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM42]
 gi|313670406|gb|ADR73394.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM43]
 gi|313670408|gb|ADR73395.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM44]
 gi|313670410|gb|ADR73396.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM45]
 gi|313670412|gb|ADR73397.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM46]
 gi|313670414|gb|ADR73398.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM47]
 gi|313670416|gb|ADR73399.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM48]
 gi|313670418|gb|ADR73400.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM49]
 gi|313670422|gb|ADR73402.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM51]
 gi|313670424|gb|ADR73403.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM52]
 gi|313670426|gb|ADR73404.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM53]
 gi|313670428|gb|ADR73405.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM54]
 gi|313670430|gb|ADR73406.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM55]
 gi|313670432|gb|ADR73407.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO56]
 gi|313670436|gb|ADR73409.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO58]
 gi|313670438|gb|ADR73410.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO59]
 gi|313670442|gb|ADR73412.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO61]
 gi|313670444|gb|ADR73413.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO62]
 gi|313670446|gb|ADR73414.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO63]
 gi|313670448|gb|ADR73415.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO64]
 gi|313670450|gb|ADR73416.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO65]
 gi|313670454|gb|ADR73418.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO67]
 gi|313670456|gb|ADR73419.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO68]
 gi|313670458|gb|ADR73420.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO69]
 gi|313670460|gb|ADR73421.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO70]
 gi|313670462|gb|ADR73422.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO71]
 gi|313670464|gb|ADR73423.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO72]
 gi|313670466|gb|ADR73424.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO73]
 gi|313670470|gb|ADR73426.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO75]
 gi|313670472|gb|ADR73427.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO76]
 gi|313670476|gb|ADR73429.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO78]
 gi|313670478|gb|ADR73430.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO79]
 gi|313670480|gb|ADR73431.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO80]
 gi|313670484|gb|ADR73433.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO82]
 gi|313670486|gb|ADR73434.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO83]
 gi|313670494|gb|ADR73438.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO87]
 gi|313670496|gb|ADR73439.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO88]
 gi|313670498|gb|ADR73440.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO89]
 gi|313670500|gb|ADR73441.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO90]
 gi|313670502|gb|ADR73442.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO91]
 gi|313670504|gb|ADR73443.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO92]
 gi|313670506|gb|ADR73444.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO93]
 gi|313670510|gb|ADR73446.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO95]
 gi|313670512|gb|ADR73447.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO96]
 gi|313670514|gb|ADR73448.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO97]
 gi|313670516|gb|ADR73449.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO98]
 gi|313670524|gb|ADR73453.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO102]
 gi|313670526|gb|ADR73454.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO103]
 gi|313670528|gb|ADR73455.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO104]
 gi|313670530|gb|ADR73456.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO105]
 gi|313670532|gb|ADR73457.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO106]
 gi|313670534|gb|ADR73458.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO107]
 gi|313670536|gb|ADR73459.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO108]
 gi|313670538|gb|ADR73460.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO109]
 gi|313670540|gb|ADR73461.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO110]
 gi|313670542|gb|ADR73462.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM111]
 gi|313670544|gb|ADR73463.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM112]
 gi|313670546|gb|ADR73464.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM113]
 gi|313670548|gb|ADR73465.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM114]
 gi|313670550|gb|ADR73466.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM115]
 gi|313670554|gb|ADR73468.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM117]
 gi|313670560|gb|ADR73471.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM120]
 gi|313670566|gb|ADR73474.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM123]
 gi|313670568|gb|ADR73475.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM124]
 gi|313670570|gb|ADR73476.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM125]
 gi|313670578|gb|ADR73480.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM129]
 gi|313670584|gb|ADR73483.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM132]
 gi|313670586|gb|ADR73484.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM133]
 gi|313670588|gb|ADR73485.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM134]
 gi|313670590|gb|ADR73486.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM135]
 gi|313670592|gb|ADR73487.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM136]
 gi|313670594|gb|ADR73488.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM137]
 gi|313670596|gb|ADR73489.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM138]
 gi|313670602|gb|ADR73492.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM141]
 gi|313670604|gb|ADR73493.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM142]
 gi|313670606|gb|ADR73494.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM143]
 gi|313670610|gb|ADR73496.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM145]
 gi|313670616|gb|ADR73499.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM148]
 gi|313670618|gb|ADR73500.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM149]
 gi|313670624|gb|ADR73503.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM152]
 gi|313670626|gb|ADR73504.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM153]
 gi|313670628|gb|ADR73505.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM154]
 gi|313670638|gb|ADR73510.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM159]
 gi|313670642|gb|ADR73512.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM161]
 gi|313670644|gb|ADR73513.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM162]
 gi|313670646|gb|ADR73514.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM163]
 gi|313670648|gb|ADR73515.1| RNA polymerase subunit beta [Bradyrhizobium sp. HM164]
 gi|313670658|gb|ADR73520.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO169]
 gi|313670660|gb|ADR73521.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO170]
 gi|313670664|gb|ADR73523.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO172]
 gi|313670672|gb|ADR73527.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO176]
 gi|313670674|gb|ADR73528.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO177]
 gi|313670676|gb|ADR73529.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO178]
 gi|313670678|gb|ADR73530.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO179]
 gi|313670686|gb|ADR73534.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO183]
 gi|313670688|gb|ADR73535.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO184]
 gi|313670696|gb|ADR73539.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO188]
 gi|313670698|gb|ADR73540.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO189]
 gi|313670702|gb|ADR73542.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO191]
 gi|313670708|gb|ADR73545.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO194]
 gi|313670712|gb|ADR73547.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO196]
 gi|313670720|gb|ADR73551.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO200]
 gi|313670734|gb|ADR73558.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO207]
 gi|313670746|gb|ADR73564.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO213]
 gi|313670748|gb|ADR73565.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO214]
 gi|313670752|gb|ADR73567.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO216]
 gi|313670766|gb|ADR73574.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|313670770|gb|ADR73576.1| RNA polymerase subunit beta [Bradyrhizobium japonicum]
 gi|320152320|gb|ADR73469.2| RNA polymerase subunit beta [Bradyrhizobium sp. HM118]
          Length = 257

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|313670376|gb|ADR73379.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM28]
 gi|313670744|gb|ADR73563.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO212]
 gi|313670754|gb|ADR73568.1| RNA polymerase subunit beta [Bradyrhizobium sp. HO217]
          Length = 257

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 138/258 (53%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K++Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KVLYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|255927057|gb|ACU40914.1| RNA polymerase beta subunit [Pantoea sp. 1400/07]
 gi|260594185|gb|ACX46387.1| RNA polymerase beta subunit [Pantoea sp. A11/07]
          Length = 288

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 176/288 (61%), Positives = 222/288 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVI 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D++D 
Sbjct: 121 DGVVSDEIHYLSAIEEGNYVIAQANAQLDENGGFVDDLVTCRSKGESSLFSRDQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNT
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNT 288


>gi|302122443|gb|ADK92892.1| RNA polymerase subunit B [Vibrio alginolyticus]
          Length = 311

 Score =  276 bits (706), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 187/310 (60%), Positives = 242/310 (78%)

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG
Sbjct: 2   AEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKG 61

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +
Sbjct: 62  EVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISA 121

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
           AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP
Sbjct: 122 AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCP 181

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN
Sbjct: 182 IETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQAN 241

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR L
Sbjct: 242 AKLNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRAL 301

Query: 692 MGCNMQRQAV 701
           MG NMQRQAV
Sbjct: 302 MGANMQRQAV 311


>gi|6449123|gb|AAF08836.1| RNA polymerase beta subunit [Streptococcus constellatus]
          Length = 290

 Score =  276 bits (705), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 165/297 (55%), Positives = 213/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L EDG F + +V  R  
Sbjct: 61  NKYGFIQTPYRKVDRETGLVTNEIVWLTADEEDEYIVAQANSKLTEDGRFAKAIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP+
Sbjct: 121 GNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAIIAQHDGKVVYSDAAKVEVRREDGSLD-------VYHITKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  TC NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTCYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|190612164|gb|ACE80516.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612170|gb|ACE80519.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612172|gb|ACE80520.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
 gi|190612174|gb|ACE80521.1| RNA polymerase subunit beta [Bradyrhizobium liaoningense]
          Length = 257

 Score =  276 bits (705), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 184/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEPGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L +  + L G YVAED+VN +TGEI+ EAG+ I +K ++ +     +++P+L +D VN 
Sbjct: 120 ALRMADEELVGNYVAEDLVNPKTGEIHAEAGEEITDKLMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLESAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|145926538|gb|ABP98908.1| RNA polymerase beta subunit [Bradyrhizobium sp. IRBG 127]
          Length = 257

 Score =  276 bits (705), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 184/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMFALGLDGEQILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K++Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + +     +D+P+L +D VN 
Sbjct: 120 ALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKVLNEQGYKDLPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTQRTLR 257


>gi|313670348|gb|ADR73365.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM14]
 gi|313670380|gb|ADR73381.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM30]
 gi|313670392|gb|ADR73387.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM36]
          Length = 257

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 138/258 (53%), Positives = 187/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILS FY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSAFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|227937606|gb|ACP43378.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 293

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 213/294 (72%), Positives = 248/294 (84%), Gaps = 1/294 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           ESVVA+ SGAA+ AKR+GIV+QVDA RIV+R+ E  LDPS SGVDIYRL KFQR
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVVRATED-LDPSKSGVDIYRLQKFQR 293


>gi|224053240|ref|XP_002297732.1| predicted protein [Populus trichocarpa]
 gi|222844990|gb|EEE82537.1| predicted protein [Populus trichocarpa]
          Length = 1109

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 79/340 (23%), Positives = 122/340 (35%), Gaps = 77/340 (22%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D      L+ V +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 811  DTKSKKHLQKVNIRFRHPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLII 870

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         G  + +           +       + +      
Sbjct: 871  NPHAFPSRMTIAMLLESLAAKGGSLNGNFVDATPFASTVRASNAGEAKSEPESL------ 924

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                              + +  ML+    +  G  +LY G+ G
Sbjct: 925  ---------------------------------VDELGKMLKSKGFNHHGVEVLYSGVYG 951

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T+QP+ G+   GG R GEME   +
Sbjct: 952  TELTCEIFIGPVYYQRLRHMVSDKFQVRSTGPVDQITRQPIKGRKRGGGIRFGEMERDSM 1011

Query: 1303 QAYGAAYVLQEMLTIKSD----DVVG-------------R-----------TRVYESIV- 1333
             A+GAAY+L + L   SD    DV               R            +  + +V 
Sbjct: 1012 LAHGAAYLLHDRLHTCSDYHIADVCSICGSILTTHYQPQRRIVRDIGGLPPVKAPKKVVC 1071

Query: 1334 ------AGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                   G        P  F  L  E+ A+ + + L  + 
Sbjct: 1072 HACQTSKG--IETVAMPYVFRYLAAELAAMNIKMTLHLND 1109



 Score = 63.6 bits (153), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 88/567 (15%), Positives = 182/567 (32%), Gaps = 65/567 (11%)

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG---LLRMERSIKERISSV 493
           I +++ L    +     D+ D+L N+ +   G ++    +      LR  +S+ +   + 
Sbjct: 287 IFMLQKLFSFVDHTSAPDNPDSLQNQDILLPGHLMTIYLKEKLEDWLRKAKSLVQDELTK 346

Query: 494 DI--------DSVMPQDLINAKPVVSAVCEFFCSSQLSQL--EEHVNSLSRITHTRRLSA 543
           +         D     D  +   V +AV     S +L+     +            RL+ 
Sbjct: 347 NNTFNFLAVGDVRKVMDKNSPVTVSTAVESMLRSGRLATQTGLDLQQRAGYTVQAERLNY 406

Query: 544 LGQGGVARA---------RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           L      RA              +R + P  +G +CP  T +G   GL++ +T   RV +
Sbjct: 407 LRFLSFFRAVHRGASFAGGRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTCSCRVTS 466

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENR-YIAQANSS----LDEDGSFTEELVFCRC 649
           Y   +   +   D + +   V  S     +   + QA       +  DG     L     
Sbjct: 467 YFDSQGVVKDFFDIRKSILGVLTSLGMIASLPKLVQAGPPKALSVLLDGRVIGSLPSSEI 526

Query: 650 AGEEILVPREKIDFIDASP------KQVVSIAASLIPFLENDDSNR-----VLMGCNMQR 698
                 + R K+    A P         +SI  +      +   +R       +    + 
Sbjct: 527 EKVIAHLRRLKVSATSAIPDDMEVGYVPLSIGGAYPGLYISTYPSRFIRPVRNISIPCEE 586

Query: 699 QAVPLLKAEAPFVGT------GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           +    L      V T         +   +     +++  A +    D  +      +  +
Sbjct: 587 RQDIELIGPFEQVSTEFSFLNAFPATHEEIHPTNMLSVVANLTPWSDHNQSPRNMYQCQM 646

Query: 753 DPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              T    +     +  +   +    Q P+V+ G   +            + +   G N 
Sbjct: 647 AKQTMAFSLQSLRFRADQKIYHLQTPQTPIVRTGAYTK----------YSIDEHPTGTNA 696

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
           +VA + + GY+ ED+M++++  V   +F     +   +   D     +   R     + +
Sbjct: 697 IVAVLAYTGYDMEDAMILNKSSVDRGMFHGQIYQTETIDLSDEGSRSDRSHRRFRRSNTD 756

Query: 872 GLKN--IDECGIICVGAEVNPGDILVG-------KITPKGESPMTPEEKLLRAIFGEKAV 922
              +  ID  G+  VG  +NP +              PK      P      A+  +   
Sbjct: 757 RSSHSLIDSDGLPYVGQIINPNEPYCSIYNDITNTSKPKYRKGSEPAIVDYVAVDTKSKK 816

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            ++  ++R        ++  +  +RHG
Sbjct: 817 HLQKVNIRFRH-PRNPIIGDKFSSRHG 842


>gi|9972352|gb|AAG10602.1|AC008030_2 Similar to DNA-directed RNA polymerase subunit [Arabidopsis thaliana]
          Length = 1233

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 85/344 (24%), Positives = 127/344 (36%), Gaps = 80/344 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D       +   +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 928  DMKSKKHPQRANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIDMPFNGVTGMRPDLII 987

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +              R  ++K  G     
Sbjct: 988  NPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPF-----------RDAVKKTNGEEESK 1036

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                               + + SML+    +  G   LY G  G
Sbjct: 1037 SSLL-----------------------------VDDLGSMLKEKGFNHYGTETLYSGYLG 1067

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T QP+ G+   GG R GEME   +
Sbjct: 1068 VELKCEIFMGPVYYQRLRHMVSDKFQVRSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSL 1127

Query: 1303 QAYGAAYVLQEMLTIKSD----DVV----------------------------GRT--RV 1328
             A+GA+Y+L + L   SD    DV                             GRT  +V
Sbjct: 1128 LAHGASYLLHDRLHTSSDHHIADVCSLCGSLLTSSVVNVQQKKLIQEIGKLPPGRTPKKV 1187

Query: 1329 --YESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
              Y      G +T     P  F  L  E+ ++ + + L+ S  +
Sbjct: 1188 TCYSCKTSKGMET--VAMPYVFRYLAAELASMNIKMTLQLSDRE 1229


>gi|227937596|gb|ACP43373.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 294

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 213/294 (72%), Positives = 248/294 (84%), Gaps = 1/294 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS+Q+T
Sbjct: 242 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSSQST 294


>gi|67810790|gb|AAY82004.1| RNA polymerase IV second largest subunit [Arabidopsis thaliana]
          Length = 333

 Score =  276 bits (705), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 119/316 (37%), Gaps = 69/316 (21%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 60   VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 119

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 120  LLEAALSKGIAC-------------------------------------PIQKKEGSSAA 142

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 143  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSLIFMGPTF 197

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  +KV  R+TG    +T+QP+  +   GG R GEME  C+ A+GA+  L E L
Sbjct: 198  YQRLVHMSENKVKFRNTGPVHPLTRQPVADRKRFGGIRFGEMERDCLIAHGASANLHERL 257

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 258  FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCASSDHVVRVYVPYGAKLL 315

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 316  CQELFSMGITLNFDTK 331


>gi|145926528|gb|ABP98903.1| RNA polymerase beta subunit [Bradyrhizobium sp. BTAi1]
          Length = 257

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 184/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E+ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKIPVTSLMFALGLDGEQILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K++Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRTARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + +     +D+P+L +D VN 
Sbjct: 120 ALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKVLNEQGYKDLPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTQRTLR 257


>gi|169600505|ref|XP_001793675.1| hypothetical protein SNOG_03089 [Phaeosphaeria nodorum SN15]
 gi|160705450|gb|EAT89820.2| hypothetical protein SNOG_03089 [Phaeosphaeria nodorum SN15]
          Length = 1616

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 83/348 (23%), Positives = 124/348 (35%), Gaps = 58/348 (16%)

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS------DLISEYPRSQWWQFAVQDEKVQ 1032
             RN   R +  L G    S     +K T+          L+        W     D    
Sbjct: 1224 RRNRSGRTISKLFGFAPDSLVPASRKETLDEDGLPRIGTLLRNGDAIAAWHTVSYDAASD 1283

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              V              E  F  ++  I   D   P   + + + + + R    GDK + 
Sbjct: 1284 DYVNRDANTNYFKYKEDELAFVEEVRIIGSEDGTQP--CQKLSIKLRVPRSPVIGDKFSS 1341

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG+ S+  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G   
Sbjct: 1342 RHGQKGVCSQKWPSIDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQ 1401

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S    +                                                     
Sbjct: 1402 DSTPFRFDEQNTA----------------------------------------------- 1414

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                +     L  A  +  G   +Y G+TG+     + +G +Y  +L HMV+DK   R+T
Sbjct: 1415 ---VDFFGHQLMKAGYNYYGNEPMYSGITGQELAADIYIGVVYYQRLRHMVNDKYQVRTT 1471

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G  +  T QP+ G+   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1472 GPINSTTGQPIKGRKKGGGIRVGEMERDALIAHGTAFLLQDRLMNCSD 1519



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 102/741 (13%), Positives = 203/741 (27%), Gaps = 149/741 (20%)

Query: 30  IEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAF-----SGAAMLEFVSYEFDP 83
           ++    S++  F       +   + G    F    P              +       D 
Sbjct: 44  VDPHINSFNSIFAAGGQLEEALKDIG-TKVFLDGNPYARPEEVGQRNRLSVRIQDVFLDK 102

Query: 84  ----PKFD---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
               P              +C  R  TY   L+  L   V + D             + +
Sbjct: 103 SVLPPSNKVALKNRNILPAECRERHATYRGKLRARLEWKVNNGDWR-----------EEV 151

Query: 131 Y-MGDLPLMTK-----------DGTFVIKGIQRIV-VSQLHR-------SPGIHFDHDKG 170
             +G +P+M +            G F++ GI++I+ + Q++R         G   +   G
Sbjct: 152 CDLGAVPIMLRLVKAKEESEELGGYFIVNGIEKIIRMLQVNRRNFPMAIKRGAFTNRGPG 211

Query: 171 RASLSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRRR---KVPVTSFLMALGMD 224
                G LL + R  PDQ      +    D    +++R   R+    VPV   L +L   
Sbjct: 212 YTQY-GILLRSMR--PDQTSQTNALHYLSDGN--VNLRFSWRKAEYLVPVMMVLKSLVET 266

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           ++ EI              +          L+   KV        T   + +  K +   
Sbjct: 267 NDREIFEGLVGAAGSEGLAEKQFVTDRVELLLRTYKVYGLHSKAKTRAYLGQKFKVV--- 323

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                                 L + ED  + E G  ++    +    +       +   
Sbjct: 324 ----------------------LQIPEDTSDEEAGTEFLRRIVLPHLGAYHITPAQDADK 361

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF-LFFD 402
             +L        + +      D      DA +    ++  G +    + E + ++     
Sbjct: 362 FRMLLFMIRKLYSLVEGECCVDNP----DA-VQNQEILLGGQLYGMIMKERLDDWLQSMR 416

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGN 461
               D       +             + +R+        +   L  G   +   +D    
Sbjct: 417 PVLQDWGRRTEWRPFTSQEFQKDFISKILRRSQTDIGRAMEYFLSTGNLISPTGLDLQQT 476

Query: 462 RRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                V E +     +   RM    +    + +  +  ++P+      PV +        
Sbjct: 477 AGFVVVAEKINFYRFISHFRMVHRGAFFAELKTTTVRKLLPESWGFMCPVHTP---DGAP 533

Query: 520 SQLSQLEEHVNSLSR--ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI-------- 569
             L     H   L+   +  +     + Q GV+   +      V     GR+        
Sbjct: 534 CGLLNHFSHKCKLATQNVDVSAIPKLVAQLGVSSKSSASIEASVVVQLDGRVLGFCSPKQ 593

Query: 570 --------CPAETSEGHNIGLVSSLTS--------FARVNAYGFIETPYRKVCDGKVTND 613
                      +    HN+ L   +          +  V     +   YR V      + 
Sbjct: 594 AKVIADTLRYWKVEGSHNVPLEMEIGYVPNSNGGQYPGVYMMSQVARMYRPVK-YLPLDK 652

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   E+    IA  ++ +    S                        ++  P  + S
Sbjct: 653 LDYVGPFEQPYMSIACTDAEIVSGDS----------------------THVEYDPTNIFS 690

Query: 674 IAASLIPFLENDDSNRVLMGC 694
           I A++ PF + + S R +  C
Sbjct: 691 IVANMTPFSDFNQSPRNMYQC 711



 Score = 48.5 bits (114), Expect = 0.009,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 45/130 (34%), Gaps = 18/130 (13%)

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q P+V+                    +   G N +VA + + GY+ +D+M++++      
Sbjct: 1156 QTPVVRP----------PLHNEYGFDNFPNGTNAVVAVISYTGYDMDDAMILNKSAHERG 1205

Query: 838  VFT----SIHIEEFEVMARDTKLGPEEI----TRDIPNVSEEGLKNIDECGIICVGAEVN 889
                      I + E  AR  + G              V     + +DE G+  +G  + 
Sbjct: 1206 FGHGTIYKTKICDLEEGARRNRSGRTISKLFGFAPDSLVPASRKETLDEDGLPRIGTLLR 1265

Query: 890  PGDILVGKIT 899
             GD +    T
Sbjct: 1266 NGDAIAAWHT 1275


>gi|227937602|gb|ACP43376.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 293

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 213/294 (72%), Positives = 248/294 (84%), Gaps = 1/294 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFAEEFVVCRHAGEVLMAPRDY 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRSEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 293


>gi|302122449|gb|ADK92895.1| RNA polymerase subunit B [Vibrio alginolyticus]
 gi|302122511|gb|ADK92926.1| RNA polymerase subunit B [Vibrio sp. JF7]
          Length = 313

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 187/310 (60%), Positives = 242/310 (78%)

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG
Sbjct: 4   AEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKG 63

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +
Sbjct: 64  EVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISA 123

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
           AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP
Sbjct: 124 AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCP 183

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN
Sbjct: 184 IETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQAN 243

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR L
Sbjct: 244 AKLNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRAL 303

Query: 692 MGCNMQRQAV 701
           MG NMQRQAV
Sbjct: 304 MGANMQRQAV 313


>gi|170032393|ref|XP_001844066.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Culex
            quinquefasciatus]
 gi|167872352|gb|EDS35735.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Culex
            quinquefasciatus]
          Length = 1129

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 105/593 (17%), Positives = 183/593 (30%), Gaps = 113/593 (19%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              +    N+    +   G   +  M I           + H +E    +  + L      
Sbjct: 613  RMMRPVINLDANKVELIGTFEQVYMDICITAREAYPKVTTH-KELSKTSFLSNLAMLIPM 671

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEK 920
             D         +   + G   +G   +   +       + ++P TP  + +    I  + 
Sbjct: 672  PDCNQSPRNMYQC--QMGKQTMGTPCHNWQLQCIAKFYRLQTPATPLFRPVHHDNIDLDN 729

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
                 +  + V S     + D  I N+   ++     +V + ++  L  D          
Sbjct: 730  YAMGTNAIVAVISYTGYDMEDAMIINKSAFERGFAHGTVYKNELIELKGD----SFFARD 785

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                RL + L            +    +     +        +F   ++ +  N++    
Sbjct: 786  PRDERLKQFLDNDGLPYRSALLQHRNPMYCYFDTNDHTYHVVKFDHHEDGIVDNIKLC-- 843

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                                  G        + V  +  + R    GDK A R G KGI 
Sbjct: 844  ----------------------GTTSASAPKKAVITY-RIVRNPNVGDKFASRAGQKGIC 880

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            S+  P  D+PF + G   DI+ NP G PSRM +  + ET  G      G    +    Y 
Sbjct: 881  SQKWPAVDLPFTESGMIPDIIFNPHGFPSRMTIAMMIETMAGKTGACHGLVHDATPFRYT 940

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                                    +   
Sbjct: 941  EENTA--------------------------------------------------IDYFG 950

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +L  +  +  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG    +T 
Sbjct: 951  RLLESSGYNYFGTERMYSGVDGREMKADIFFGVVHYQRLRHMVSDKWQVRSTGPLDQLTH 1010

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG---RT----------- 1326
            QP  G+S  GG R GEME   + A+GA+++LQ+ L   SD +     R+           
Sbjct: 1011 QPNKGRSRGGGVRFGEMERDALIAHGASFLLQDRLFHGSDKITTLVCRSCGTLIGPISSI 1070

Query: 1327 --RVYESIVAGNDTFE-------------TGTPESFNVLVKEMQALGLSIDLE 1364
              +V  +      T                  P  F  LV ++ A+ +++ L+
Sbjct: 1071 TKKVATNATETERTPATCRLCRSDQGIGHVEIPYIFKFLVSQLTAMNINVKLD 1123



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 92/618 (14%), Positives = 189/618 (30%), Gaps = 71/618 (11%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
            +     L+ +      +I    +     + Y ++ +     +  ++    I+  +   D
Sbjct: 238 FIPIMMLLKALSDYTDNEIYKRLIVGYEEDQYYKHCIQNMLRELHEE---GIHNQVECKD 294

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                    ++    + +D      + +  + + L+ D        +   ++ +++ L  
Sbjct: 295 YMGKVFRTKLYYLPAWYTDAQRTDHLLKTCVLIHLDDDLD------KFNLLVFMMQKLFT 348

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID-------SV 498
              G+  ++ +D+   + +   G + +   R   L     +K  +  +  D       + 
Sbjct: 349 AAQGRCKLESVDSTMMQELLLGGHLYQKLLREHFLTFLNGMKYNMLKLCSDADAHLGQNE 408

Query: 499 MPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSAL 544
                 NA     A   FF +              S L  + E++N +  ++H R   A+
Sbjct: 409 AVMACKNASNFDRAFSNFFATGNLQKASEMGLMQDSGLVIIAENINRMRYMSHFR---AI 465

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI-----E 599
            +G         E R + P  +G ICP  T +G   GL++ LT+  RV+           
Sbjct: 466 HRGSFFVTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTTNCRVSNSPDPGKVKNI 525

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYI-----AQANSSLDEDGSFTEELVFCRCAGEEI 654
             Y         N V        E   +               G   ++L   +  GEEI
Sbjct: 526 EKYLIQYGMTPANSVALSGGGVGEGYTVMVEGRIAGRIPKAVVGQAVQQLRMLKIGGEEI 585

Query: 655 LVPREKIDFIDASPKQV------VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               E +        Q       V  A  + P +  D +   L+G   Q      + A  
Sbjct: 586 PEATEIVFIPSKEGGQYPGLYIFVGAARMMRPVINLDANKVELIGTFEQVYMDICITARE 645

Query: 709 PF--VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            +  V T  E           +        Q        +  +  +        +  + K
Sbjct: 646 AYPKVTTHKELSKTSFLSNLAMLIPMPDCNQSPRNMYQCQMGKQTMGTPCHNWQLQCIAK 705

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F R         RP+                 + DL + A+G N +VA + + GY+ ED+
Sbjct: 706 FYRLQTPATPLFRPV--------------HHDNIDLDNYAMGTNAIVAVISYTGYDMEDA 751

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           M+I++           H   ++    + K              E   + +D  G+    A
Sbjct: 752 MIINKSAFERGFA---HGTVYKNELIELKGDSFFARDP---RDERLKQFLDNDGLPYRSA 805

Query: 887 EVNPGDILVGKITPKGES 904
            +   + +         +
Sbjct: 806 LLQHRNPMYCYFDTNDHT 823


>gi|227937592|gb|ACP43371.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 293

 Score =  275 bits (704), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 213/294 (72%), Positives = 247/294 (84%), Gaps = 1/294 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR  MG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRAFMGSNMQRQAVPLVRAEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 293


>gi|11496555|ref|NP_044569.1| RNA polymerase beta chain [Toxoplasma gondii RH]
 gi|74824911|sp|Q9MTD3|RPOB_TOXGO RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|5231258|gb|AAD41152.1|U87145_21 RNA polymerase B [Toxoplasma gondii]
          Length = 1051

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 125/540 (23%), Positives = 209/540 (38%), Gaps = 58/540 (10%)

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
             + E +V       IHI++         L   + +     + ++ L    E   +     
Sbjct: 550  ALQEGIVLNASSLKIHIKDLFNREIVYYLSKYKKSNQNTIIHQKPLVWNGER--VFTNQL 607

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            +     ++      G + +          F E AV V    L      S  +        
Sbjct: 608  LTQHQDIIDSEFAIGNNLLFYYGNFCGYDF-EDAVIVSKRVLYQQLFSSLHMDIYEFNFC 666

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK--KS 1005
            +  + +    ++E  +     +   D   I+         +IL G   ++  K  K   +
Sbjct: 667  YNNENDIEFSTLEIPKQSYYIKKNLDSLGIIKEG-----EKILTGSILLTKIKVAKPTYT 721

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                  LI                 +Q        + E     +  R K K         
Sbjct: 722  YKSIFKLIYSIFGKTIRNIKDNSLYIQTGKSGRVSKIELFLVNISSRHKYK--------- 772

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                     ++F+  +R +  GDK+ GR+GNKGI+S I    D+PFL++    DI++  L
Sbjct: 773  TYNNSYLKCRIFICKQRFLTVGDKLCGRYGNKGILSYIAENADLPFLQNSFYPDIIVGAL 832

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G+PSRMN+GQ+FE  +G        +I        +N   + L+  +   +         
Sbjct: 833  GIPSRMNLGQLFEALVGKISFSYNIRI-LPSFTTSSNLYFNYLKILIYNFL--------- 882

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                      +   +K G                 + L   +L   G+ I+ DG TG   
Sbjct: 883  ----------MFNNFKKGF----------------NWLYNFNLP--GKFIIRDGRTGVKL 914

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               V  G     KL H++ DK++ R+TG Y+ + QQPL GK N GGQR GEME+W ++A+
Sbjct: 915  KSSVLCGVSRYSKLIHLIKDKLHFRTTGPYTEILQQPLKGKKNLGGQRFGEMEIWALEAF 974

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            GA+Y L+E+L  KSDD   R  + E ++    +   +   ESF V++KE   L L+++L 
Sbjct: 975  GASYNLKEILNYKSDDCFARNNLKEYLLFRNTELQNSTITESFRVILKEFNGLILNLELF 1034



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 158/719 (21%), Positives = 293/719 (40%), Gaps = 42/719 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F   + Y         PL   +L        +L+  +     +          L  LK+ 
Sbjct: 68  FLDNVQYINSLIKIFLPLKFQNLKTNKVFFKNLLIFE-----LPKYNSYNYCYLNGLKKI 122

Query: 292 GVKFLGITSDCLCGLYVAEDI---------VNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
            +     ++      Y+              N     I ++        S++ +  + I 
Sbjct: 123 FISKYFTSNGIFFNKYLKRKYNIYYAKLLLTNSNFFNIILDLKLKQIYLSIKNLKFNFIL 182

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            +  L + + +   Y R             AL       +   +   +  +S+F     +
Sbjct: 183 FLYYLGIKNTDILKYSRYKNSKILKLLIFSALQTDLVNNKKIILKNLNYLKSIFKLTILN 242

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              Y    + + K+N            ++   D I I+ +L+DL++ K     ID+L N+
Sbjct: 243 -KNYKNFIISKDKLN---YNYGDFSKNNLLIIDFIFILDLLLDLQSKKLCFKTIDHLDNK 298

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            + ++G   ++ ++  L +    I   I       +                E    + L
Sbjct: 299 HINTIGNYFQHNFKFYLKKFISIIPNLIKLQKFSLLKV----------YNFKELLILNPL 348

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            Q  E +NS S + H  +L+          +  + +R++     G++C  +T+EG N GL
Sbjct: 349 IQYLEQINSFSELMHKYKLNNYNSFS----KGILNLREICLNQLGKLCLIDTTEGINCGL 404

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           V S     R+   G I+  +  +   K    + + +++++E   I   N +L +      
Sbjct: 405 VVSFAKHIRIYKKGIIQVYFSSIFKNKTKEFLNFKTSLDQELYLIQFNNINLRKIKYLMN 464

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             +        I     K   +      + S   +LIPF++ +D  R LMG  MQ Q+VP
Sbjct: 465 VRLVYNKNNFRIKFFSNKKSIL-LEFTDLFSFTENLIPFIKYNDPARCLMGAKMQSQSVP 523

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL  +  FV TG E  +   S   I A + GIV    +++I I+ +            +Y
Sbjct: 524 LLNKKKSFVITGYEKEIITKSDTTIKALQEGIVLNASSLKIHIKDLFNREI-------VY 576

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L K+++SNQNT ++Q+PLV  G+ V  N ++         + A+G N+L  +  + GY+
Sbjct: 577 YLSKYKKSNQNTIIHQKPLVWNGERVFTNQLLTQHQDIIDSEFAIGNNLLFYYGNFCGYD 636

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGI 881
           FED++++S+R++ + +F+S+H++ +E           E +  +IP  S    KN+D  GI
Sbjct: 637 FEDAVIVSKRVLYQQLFSSLHMDIYEFNFCYNNENDIEFSTLEIPKQSYYIKKNLDSLGI 696

Query: 882 ICVGAEVNPGDILVGKI-TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           I  G ++  G IL+ KI   K         KL+ +IFG+   +++D SL + +G SG V
Sbjct: 697 IKEGEKILTGSILLTKIKVAKPTYTYKSIFKLIYSIFGKTIRNIKDNSLYIQTGKSGRV 755


>gi|12324162|gb|AAG52049.1|AC022455_3 DNA-directed RNA polymerase subunit, putative; 8546-1198 [Arabidopsis
            thaliana]
          Length = 1114

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 85/344 (24%), Positives = 127/344 (36%), Gaps = 80/344 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D       +   +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 809  DMKSKKHPQRANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIDMPFNGVTGMRPDLII 868

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +              R  ++K  G     
Sbjct: 869  NPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPF-----------RDAVKKTNGEEESK 917

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                               + + SML+    +  G   LY G  G
Sbjct: 918  SSLL-----------------------------VDDLGSMLKEKGFNHYGTETLYSGYLG 948

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T QP+ G+   GG R GEME   +
Sbjct: 949  VELKCEIFMGPVYYQRLRHMVSDKFQVRSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSL 1008

Query: 1303 QAYGAAYVLQEMLTIKSD----DVV----------------------------GRT--RV 1328
             A+GA+Y+L + L   SD    DV                             GRT  +V
Sbjct: 1009 LAHGASYLLHDRLHTSSDHHIADVCSLCGSLLTSSVVNVQQKKLIQEIGKLPPGRTPKKV 1068

Query: 1329 --YESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
              Y      G +T     P  F  L  E+ ++ + + L+ S  +
Sbjct: 1069 TCYSCKTSKGMET--VAMPYVFRYLAAELASMNIKMTLQLSDRE 1110


>gi|313670332|gb|ADR73357.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM6]
 gi|313670338|gb|ADR73360.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM9]
 gi|313670374|gb|ADR73378.1| RNA polymerase subunit beta [Bradyrhizobium sp. OM27]
 gi|313670434|gb|ADR73408.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO57]
 gi|313670440|gb|ADR73411.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO60]
 gi|313670452|gb|ADR73417.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO66]
 gi|313670468|gb|ADR73425.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO74]
 gi|313670474|gb|ADR73428.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO77]
 gi|313670482|gb|ADR73432.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO81]
 gi|313670488|gb|ADR73435.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO84]
 gi|313670490|gb|ADR73436.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO85]
 gi|313670492|gb|ADR73437.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO86]
 gi|313670508|gb|ADR73445.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO94]
 gi|313670518|gb|ADR73450.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO99]
 gi|313670520|gb|ADR73451.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO100]
 gi|313670522|gb|ADR73452.1| RNA polymerase subunit beta [Bradyrhizobium sp. OO101]
          Length = 257

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 140/258 (54%), Positives = 187/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L +  + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRMADEELVGNYIAEDLVNPKTGEIHAEAGEEITDKSMKVLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|79356046|ref|NP_564341.2| NRPA2; DNA binding / DNA-directed RNA polymerase/ ribonucleoside
            binding [Arabidopsis thaliana]
 gi|332193031|gb|AEE31152.1| nuclear RNA polymerase A2 [Arabidopsis thaliana]
          Length = 1178

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 85/344 (24%), Positives = 127/344 (36%), Gaps = 80/344 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D       +   +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 873  DMKSKKHPQRANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIDMPFNGVTGMRPDLII 932

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +              R  ++K  G     
Sbjct: 933  NPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPF-----------RDAVKKTNGEEESK 981

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                               + + SML+    +  G   LY G  G
Sbjct: 982  SSLL-----------------------------VDDLGSMLKEKGFNHYGTETLYSGYLG 1012

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T QP+ G+   GG R GEME   +
Sbjct: 1013 VELKCEIFMGPVYYQRLRHMVSDKFQVRSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSL 1072

Query: 1303 QAYGAAYVLQEMLTIKSD----DVV----------------------------GRT--RV 1328
             A+GA+Y+L + L   SD    DV                             GRT  +V
Sbjct: 1073 LAHGASYLLHDRLHTSSDHHIADVCSLCGSLLTSSVVNVQQKKLIQEIGKLPPGRTPKKV 1132

Query: 1329 --YESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
              Y      G +T     P  F  L  E+ ++ + + L+ S  +
Sbjct: 1133 TCYSCKTSKGMET--VAMPYVFRYLAAELASMNIKMTLQLSDRE 1174



 Score = 52.4 bits (124), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 96/759 (12%), Positives = 191/759 (25%), Gaps = 144/759 (18%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM------LE--- 75
           ++ +L+     S+D+             +GL   F  + P++ +           LE   
Sbjct: 18  ELHNLVTHHIESFDY----------MTLKGLDVMFNRIKPVSVYDPNTENELSIWLENPL 67

Query: 76  --------FVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                   F S     P     +C    ++Y       +     D               
Sbjct: 68  VFAPQKESFKSTSRKEPLL-PFECRQAKISYTGTFMADVCFKYNDGVVVRDKFD------ 120

Query: 128 QSIYMGDLPLMTKD------------------------GTFVIKGIQRI---VVS----- 155
                G  P+M                           G F++ GI+R+   V++     
Sbjct: 121 ----FGQFPIMLMSKLCSLKGADCRKLLKCKESTSEMGGYFILNGIERVFRCVIAPKRNH 176

Query: 156 --QLHR-----------SPGIHFDHDKGRASLSGKLLY-----ACRIIPDQGLWMDIEFD 197
              + R           S  +     +   S     LY     + R+    G W+     
Sbjct: 177 PTSMIRNSFRDRKEGYSSKAVVTRCVRDDQSSVTVKLYYLRNGSARV----GFWI----- 227

Query: 198 SKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTF--YPKIVYSQRGDFWCFPLSAADL 254
                   + R   +PV   L AL     EEI  +        Y +        L     
Sbjct: 228 --------VGREYLLPVGLVLKALTNSCDEEIYESLNCCYSEHYGRGDGAIGTQLVRERA 279

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF-------LGITSDCLCGLY 307
            +       L     G    E  +K            GVK          +  D L    
Sbjct: 280 KIILDEVRDL-----GLFTREQCRKHLGQH-FQPVLDGVKKESLSIVAEAVLRDYLFVHL 333

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR-NTLVTDK 366
             +         I  +   ++D+ SL +   S      ++    +      +    +   
Sbjct: 334 DNDHDKFNLLIFIIQKLYSLVDQTSLPDNPDSLQNQEILVPGHVITIYLKEKLEEWLRKC 393

Query: 367 NKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD 426
               KD L +         ++      +        +    L   G +K    L+L    
Sbjct: 394 KSLLKDELDNTNSKFSFESLADVKKLINKNPPRSIGTSIETLLKTGALKTQSGLDLQQRA 453

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
                        +  L  L   +         G R       + ++   L  +      
Sbjct: 454 GYTV-----QAERLNFLRFLSFFRAVHRGASFAGLRTTTVRKLLPESWGFLCPVHTPDGT 508

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
              + +    +       ++K  +    +   S     + + +     +    +L   G 
Sbjct: 509 PCGLLNHMTRTSRITSQFDSKGNIRDFLKIRKS-----VVDVLTGAGMVPSLPKLVRAGP 563

Query: 547 GGVARARAGVEMRD-VHPTHYGRICPAETS---EGHNIGLVSSLTSFARVNAYGFIETPY 602
             V       ++   +      ++         E  ++        +   +  G     Y
Sbjct: 564 PKVIHVLLDGQVVGTLSSNLVTKVVSYIRRLKVEAPSVIPEDLEVGYVPTSMGGSYPGLY 623

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
              C  +    V  +S        I   N  L          + C   G           
Sbjct: 624 LASCPARFIRPVKNIS--------IPSDNIELIGPFEQVFMEISCPDGGNGGRNNSSLAT 675

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
             +  P  ++S+ A+L P+ +++ S R +  C M +Q +
Sbjct: 676 HEEIHPTGMISVVANLTPWSDHNQSPRNMYQCQMAKQTM 714


>gi|185179219|gb|ACC77622.1| RpoB [Mycobacterium kansasii]
          Length = 217

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 93/225 (41%), Positives = 126/225 (56%), Gaps = 40/225 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 25   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 84

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I    +      +        +  
Sbjct: 85   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIAGSPDWAANLPEALRSAEPNQI- 142

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     +      
Sbjct: 143  ------------------------------VSTPVFDGAQEAELQGLLSSTLPNRDGDVL 172

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARST
Sbjct: 173  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARST 217


>gi|289616941|emb|CBI56331.1| unnamed protein product [Sordaria macrospora]
          Length = 1274

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 149/986 (15%), Positives = 290/986 (29%), Gaps = 170/986 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+   DD D+ G +R+   G +L   +R  + 
Sbjct: 416  HISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVR 475

Query: 481  RMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ + +    +              I A  + + +     +               +SQ+
Sbjct: 476  RLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNGLKYSLATGNWGDQKKAMSSTAGVSQV 535

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     +             P ET EG   GLV +
Sbjct: 536  LNRYTFASTLSHLRRTNT----PIGRDGKLAK-------------PPETPEGQACGLVKN 578

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L+    V+     +    +    + +V  +   L        ++      + +D      
Sbjct: 579  LSLMCFVSVGTLADPIIEFMVARNMEVLEEYEPLRYPNATKVFVNGTWVGVHQDPKHLVT 638

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV        I      +  I     ++ S A  ++  L   +          + Q +  
Sbjct: 639  LVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVMRPLFTVEQEDNGESGVEKGQLILT 698

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             +               +          +G +E +DA       +    +     +D YR
Sbjct: 699  KEHIRRLEQDKELGKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTPED----LDTYR 754

Query: 764  LMKFQ----RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              KF+      +     N R   K              PS  LG       +  + +P+ 
Sbjct: 755  QHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPSMLLG-------ICASIIPFP 807

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     +  +                                
Sbjct: 808  DHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------------------------D 838

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 839  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGI 898

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D  +R      EQ E   R           +       I  G       
Sbjct: 899  F-RSLFFRSYTDCEKRVGINIVEQFEKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDD 957

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K++ ++ D                 E  QR  + +K    T     E    + +  
Sbjct: 958  IIIGKTSPINPD---------------NQELGQRTAQHVKRDASTPLRSTESGIVDSVAF 1002

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV V   +  Q GDK A                            
Sbjct: 1003 TTNQDGL-----RYVKVRVRTTKIPQIGDKFA---------------------------- 1029

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                     SR         H     +G+  + + +    +              +    
Sbjct: 1030 ---------SR---------HGQKGTIGVTYRQEDMPFTAEGITPDI-------IINPHA 1064

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
              +     +  + +L      K     +TP F     ++++++LR       G  I+Y G
Sbjct: 1065 IPSRMTIAHLIECLLSKVGSLKGMEGDATP-FTDVTVDSVSNLLREHGYQSRGFEIMYHG 1123

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TG      V  G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME 
Sbjct: 1124 HTGRKLRAQVFFGPTYYQRLRHMVDDKIHARARGPVQIMTRQPVEGRARDGGLRFGEMER 1183

Query: 1300 WCIQAYGAAYVLQEMLTIKSD-------DVVGRTRVYESIVA-------GND---TFETG 1342
             C+ A+GAA  L+E L   SD       ++ G      ++           +     +  
Sbjct: 1184 DCMIAHGAASFLKERLFEVSDAFRVHICEICGLMTPIANLTKQSFECRPCKNKTKIAQVH 1243

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRT 1368
             P +  +L +E+ ++ ++  +  SR+
Sbjct: 1244 MPYAAKLLFQELMSMNIASRMFTSRS 1269



 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 138/1052 (13%), Positives = 283/1052 (26%), Gaps = 218/1052 (20%)

Query: 20   NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE---- 75
                 D+  L+  Q  S++ F    +         L        P        +L     
Sbjct: 52   ISSYFDLKGLVSQQIDSFNEFTTDTVQSLIDEYADL--TLDHPSPGDDDGRDIILRRYDV 109

Query: 76   -FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITL---------------RLI 109
             F       P               +C  R+LTY+ P+   +               +L 
Sbjct: 110  HFGEIIISRPTLTEATGETISLLPYECRDRNLTYSAPIYCKVTKRARIAVSEKKPLNQLT 169

Query: 110  VFDVDEFTGA-----------------------KSIKDIKEQSIYMGDLPLMTKD----- 141
              + D                            K   +  +  +++G +P+M K      
Sbjct: 170  DDEHDHMARTGEHPTVLRWIEEESAPPEPPKEDKVNAENLKGYLFLGKIPIMVKSKICHL 229

Query: 142  -------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
                               G F+I G ++++++Q  RS          +    G + Y  
Sbjct: 230  YMEDDESLFTLNECPYDQGGYFIINGSEKVLIAQE-RSAANI--VQVFKKPPGGSVSYQA 286

Query: 183  RIIP--DQGLWMDIEFDSKDIIHVRIDRRR-----KVPVT-----------SFLMALG-M 223
             I    ++G  +         +H + D+ +      V VT               ALG +
Sbjct: 287  EIRSALEKGSRLISSLQM--RLHTKADQNKGRLANTVSVTLPYVKEEVSLAIVFRALGVV 344

Query: 224  DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID-TGEQVIESGKKLTS 282
              E+IL+        SQ  +     +  A  +   +V+   +     G   +    ++ +
Sbjct: 345  SDEDILNHICYDRRDSQMLEALRPCIEEAFCIQDREVALDYIGKRGNGGAGVNRNARIKA 404

Query: 283  GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
                 L+++ +  +     C          +  +  +  +   D  D            +
Sbjct: 405  AK-DMLQKELLPHISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDH------FGKK 457

Query: 343  DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
             + +           +         +  +D +  + R +       FS+A  +      +
Sbjct: 458  RLDL-------AGPLLAKLFRGIVRRLTQDLMGYMKRCVDTN--KHFSLALGIKASTLTN 508

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              KY L   G      +    T    + + +    + +  L       G    +      
Sbjct: 509  GLKYSL-ATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPPET 567

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
                   ++KN   +  + +       I  +   ++   +        +A   F   + +
Sbjct: 568  PEGQACGLVKNLSLMCFVSVGTLADPIIEFMVARNMEVLEEYEPLRYPNATKVFVNGTWV 627

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE------ 576
               ++  + ++ + + RR + +                +       + P  T E      
Sbjct: 628  GVHQDPKHLVTLVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVMRPLFTVEQEDNGE 687

Query: 577  -----GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
                 G  I     +    +    G     Y        +  + YL A EEE   I    
Sbjct: 688  SGVEKGQLILTKEHIRRLEQDKELGKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTP 747

Query: 632  SSLDE------DGSFTEELVFCRCAGEEILVPR---EKIDFIDASPKQVVSIAASLIPFL 682
              LD        G   E+    R                   +  P  ++ I AS+IPF 
Sbjct: 748  EDLDTYRQHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPSMLLGICASIIPFP 807

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            +++ S R      M +QA+                                         
Sbjct: 808  DHNQSPRNTYQSAMGKQAMGFFLTNYS--------------------------------- 834

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                        + + +  Y       +     +  R                       
Sbjct: 835  --------RRMDTMANILYYPQKPLATTRSMEYLKFR----------------------- 863

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E  
Sbjct: 864  -ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGIFRSLFFRSYTDCEKRVGINIVEQF 922

Query: 863  -----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                  +           ++  GII  G  V   DI++GK +P         ++  + + 
Sbjct: 923  EKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPDNQELGQRTAQHVK 982

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                   RD S  + S  SG V  V       
Sbjct: 983  -------RDASTPLRSTESGIVDSVAFTTNQD 1007


>gi|185179221|gb|ACC77623.1| RpoB [Mycobacterium gordonae]
          Length = 218

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 94/225 (41%), Positives = 128/225 (56%), Gaps = 40/225 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 26   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 130

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  +L            
Sbjct: 131  -----------------LPEDLRHAQPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 173

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            ++  G+S+L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARST
Sbjct: 174  VNGDGKSVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARST 218


>gi|52699833|gb|AAU86978.1| DNA-dependent RNA polymerase II second largest subunit [Lobaria
            quercizans]
          Length = 717

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 127/839 (15%), Positives = 241/839 (28%), Gaps = 148/839 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ + + + +               + +  + + + 
Sbjct: 1    DHXGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIV 735
             P    D+  +     N+   ++ V  L+ +      T  E    K  G        G+V
Sbjct: 237  RPLFVIDNDPKSPNRGNLVLTKEHVNKLEDDKELGPDTDPEGREDKFRG-WKGLVNQGVV 295

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDII 794
            E VDA            + +   V     ++  R  Q   V   P +      V+     
Sbjct: 296  EYVDAEE----------EETVMIVMTPEDLEISRQIQAGYVMPEPSIDDPNKRVKAPLNP 345

Query: 795  ADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                 T      ++   +  + +P+  +N                        ++     
Sbjct: 346  TAHTWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGX 387

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              +G      D                +  +             +       +   +  +
Sbjct: 388  QAMGXXXXNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 436

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    
Sbjct: 437  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRS 492

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  ++ D      R++          
Sbjct: 493  DTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTP 552

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            ++     +  Q                             LR VKV +   +  Q GDK 
Sbjct: 553  LRSTENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKF 592

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 593  ASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 652

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          +S L    E    +                                
Sbjct: 653  EGDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM-------------------------- 684

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                +G +    G         V +G  Y  +L HMV DK++A
Sbjct: 685  -------------------YNGHT----GR---KLHAQVFLGPTYYQRLRHMVDDKIHA 717


>gi|4336509|gb|AAD17842.1| DNA dependent RNA polymerase beta subunit [Toxoplasma gondii]
          Length = 1051

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 109/409 (26%), Positives = 176/409 (43%), Gaps = 50/409 (12%)

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK--KSTVLSSDLISEY 1016
            +E   +E+  +    ++ +    I     +IL G   ++  K  K   +      LI   
Sbjct: 673  IEFSTLEIPKQSYYIKKNLDSLGIIKEGEKILTGSILLTKIKVAKPTYTYKSIFKLIYSI 732

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                          +Q        + E     +  R K K                  ++
Sbjct: 733  FGKTIRNIKDNSLYIQTGKSGRVSKIELFLVNISSRHKYK---------TYNNSYLKCRI 783

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
            F+  +R +  GDK+ GR+GNKGI+S I    D+PFL++    DI++  LG+PSRMN+GQ+
Sbjct: 784  FICKQRFLTVGDKLCGRYGNKGILSYIAENADLPFLQNSFYPDIIVGALGIPSRMNLGQL 843

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE  +G        +I        +N   + L+  +   +                   +
Sbjct: 844  FEALVGKISFSYNIRI-LPSFTTSSNLYFNYLKILIYNFL-------------------M 883

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
               +K G                 + L   +L   G+ I+ DG TG      V  G    
Sbjct: 884  FNNFKKGF----------------NWLYNFNLP--GKFIIRDGRTGVKLKSSVLCGVSRY 925

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             KL H++ DK++ R+TG Y+ + QQPL GK N GGQR GEME+W ++A+GA+Y L+E+L 
Sbjct: 926  SKLIHLIKDKLHFRTTGPYTEILQQPLKGKKNLGGQRFGEMEIWALEAFGASYNLKEILN 985

Query: 1317 IKSDDVVGRTRVYESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             KSDD   R  + E ++    +   +   ESF V++KE   L L+++L 
Sbjct: 986  YKSDDCFARNNLKEYLLFRNTELQNSTITESFRVILKEFNGLILNLELF 1034



 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 158/719 (21%), Positives = 294/719 (40%), Gaps = 42/719 (5%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F   + Y         PL   +L        +L+  +     +          L  LK+ 
Sbjct: 68  FLDNVQYINSLIKIFLPLKFQNLKTNKVFFKNLLIFE-----LPKYNSYNYCYLNGLKKI 122

Query: 292 GVKFLGITSDCLCGLYVAEDI---------VNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
            +     ++      Y+              N     I ++        S++ +  + I 
Sbjct: 123 FISKYFTSNGIFFNKYLKRKYNIYYAKLLLTNSNFFNIILDLKLKQIYLSIKNLKFNFIL 182

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            +  L + + +   Y R             AL       +   +   +  +S+F     +
Sbjct: 183 FLYYLGIKNTDILKYSRYKNSKILKLLIFSALQTDLVNNKKIILKNLNYLKSIFKLTILN 242

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              Y    + + K+N            ++   D I I+ +L+DL++ K     ID+L N+
Sbjct: 243 -KNYKNFIISKDKLN---YNYGDFSKNNLLIIDFIFILDLLLDLQSKKLCFKTIDHLDNK 298

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            + ++G   ++ ++  L +    I   I       +                E    + L
Sbjct: 299 HINTIGNYFQHNFKFYLKKFISIIPNLIKLQKFSLLKV----------YNFKELLILNPL 348

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            Q  E +NS S + H  +L+          +  + +R++     G++C  +T+EG N GL
Sbjct: 349 IQYLEQINSFSELMHKYKLNNYNSFS----KGILNLREICLNQLGKLCLIDTTEGINCGL 404

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           V S     R+   G I+  +  +   K    + + +++++E   I   N +L +      
Sbjct: 405 VVSFAKHIRIYKKGIIQVYFSSIFKNKTKEFLNFKTSLDQELYLIQFNNINLRKIKYLMN 464

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             +        I     K   +      + S   +LIPF++ +D  R LMG  MQ Q+VP
Sbjct: 465 VRLVYNKNNFRIKFFSNKKSIL-LEFTDLFSFTENLIPFIKYNDPARCLMGAKMQSQSVP 523

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           LL  +  FV TG E  +   S   I A + GIV    +++I I+ +            +Y
Sbjct: 524 LLNKKKSFVITGYEKEIITKSDTTIKALQEGIVLNASSLKIHIKDLFNREI-------VY 576

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L K+++SNQNT ++Q+PLV  G+ V  N ++         + A+G N+L+ +  + GY+
Sbjct: 577 YLSKYKKSNQNTIIHQKPLVWNGERVFTNQLLTQHQDIIDSEFAIGNNLLIYYGNFCGYD 636

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGI 881
           FED++++S+R++ + +F+S+H++ +E           E +  +IP  S    KN+D  GI
Sbjct: 637 FEDAVIVSKRVLYQQLFSSLHMDIYEFNFCYNNENDIEFSTLEIPKQSYYIKKNLDSLGI 696

Query: 882 ICVGAEVNPGDILVGKI-TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           I  G ++  G IL+ KI   K         KL+ +IFG+   +++D SL + +G SG V
Sbjct: 697 IKEGEKILTGSILLTKIKVAKPTYTYKSIFKLIYSIFGKTIRNIKDNSLYIQTGKSGRV 755


>gi|302122513|gb|ADK92927.1| RNA polymerase subunit B [Vibrio sp. JF46]
          Length = 312

 Score =  275 bits (703), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 187/310 (60%), Positives = 242/310 (78%)

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           AE++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG
Sbjct: 3   AEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKG 62

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            +DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +
Sbjct: 63  EVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISA 122

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
           AV EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP
Sbjct: 123 AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGITRERAGFEVRDVHVTHYGRLCP 182

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            ET EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN
Sbjct: 183 IETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQAN 242

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE+DD+NR L
Sbjct: 243 AKLNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLEHDDANRAL 302

Query: 692 MGCNMQRQAV 701
           MG NMQRQAV
Sbjct: 303 MGANMQRQAV 312


>gi|268561614|ref|XP_002646487.1| Hypothetical protein CBG19469 [Caenorhabditis briggsae]
          Length = 1131

 Score =  275 bits (703), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 76/297 (25%), Positives = 112/297 (37%), Gaps = 51/297 (17%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            DE            + T K    +     + +I    + P G  +   +   ++R    G
Sbjct: 796  DEVYYVTFNMETGDFRTHKFHYAEPAYCGMVRIVENSEAPGGGAQHALIQWRIERNPIIG 855

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KGI S + P E +PF + G   DI+ NP G PSRM +G + E+  G     
Sbjct: 856  DKFASRHGQKGINSFLWPTESLPFSETGMVPDIIFNPHGFPSRMTIGMMIESMAGKCAAT 915

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G+   +    +                                                
Sbjct: 916  HGENYDASPFVFNE---------------------------------------------- 929

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                D         +L  A  +  G    Y G+ G   +  +  G +Y  +L HM++DK 
Sbjct: 930  ----DNTAINHFGELLTKAGYNYYGNETFYSGVDGRQMEMQIFFGIVYYQRLRHMIADKF 985

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-DVV 1323
              R+TG    +T QP+ G+   GG R GEME   I A+G ++VLQ+ L   SD DV 
Sbjct: 986  QVRATGPIDPITHQPVKGRKKGGGIRFGEMERDAIIAHGTSFVLQDRLLNCSDRDVA 1042



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 41/112 (36%), Gaps = 29/112 (25%)

Query: 70  GAAMLEFVSYEFDPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
               ++F S +   P  D               +C  R +TYA  LK+ + + V +    
Sbjct: 39  DNVTMKFTSAQLHKPTLDSGAKLTSDTLPLYPAECRQRGMTYAGNLKVNIDVHVNETRLD 98

Query: 117 TGAKSIKDI---------------KEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
                +  +               ++Q +  G+ P+  K G F++ G ++++
Sbjct: 99  IIETILGKVPIMLRSEGCHLRGMSRKQLVAAGEEPI-EKGGYFIVNGSEKVI 149


>gi|145926492|gb|ABP98885.1| RNA polymerase beta subunit [Bradyrhizobium genosp. alpha bv.
           genistearum]
          Length = 257

 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 188/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI+Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KILYKRTKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDEELVGNYLAEDLVNPKTGEIHAEAGEEITDKSMKVLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|67515342|gb|AAY68200.1| RNA polymerase IV second largest subunit [Antirrhinum majus]
          Length = 821

 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 84/345 (24%), Positives = 123/345 (35%), Gaps = 82/345 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E     K+      D    GV     V +   R    GDK +  HG KG++  + 
Sbjct: 534  KLKHTERGMVQKVVLSSNDDGKNFGV-----VSLRQVRSPCLGDKFSSMHGQKGVLGFLE 588

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              E+ PF K+G   DIV+NP   PSR   GQ+ E  LG      G               
Sbjct: 589  SQENFPFTKEGIVPDIVINPHAFPSRQTPGQLLEAALGKGIALGG--------------- 633

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                K   P STP       + I + L 
Sbjct: 634  ----------------------------------ALKYATPFSTP-----SVDDITAQLH 654

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                   G   +YDG TGE  +  + +G  +  +L HM  DK+  R+TG    +T+QP+ 
Sbjct: 655  RLGFSRWGDERVYDGRTGEKVESLIFMGPTFYQRLTHMAEDKIKFRNTGPVHPLTRQPVA 714

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYE 1330
             +   GG + GEME  C+ A+GAA  L E L   SD              +V+ R+    
Sbjct: 715  DRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSSQMHVCRKCQNMANVIQRSVFGG 774

Query: 1331 SIVAG---------NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              + G          D      P    +L +E+ ++G+S+  +  
Sbjct: 775  RKIRGPYCRFCDSVEDVVRLNVPYGAKLLCQELFSMGISLKFDTE 819



 Score =  116 bits (290), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 87/576 (15%), Positives = 205/576 (35%), Gaps = 62/576 (10%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI---KE 488
           +   +  ++K L++   G+  +D+ D+  N+R+   GE+L+ + R+ +   ER +    +
Sbjct: 8   KARLLGYMVKCLLEAYRGRRKVDNRDDFRNKRLELAGELLERELRVHIKHAERRMTKAMQ 67

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS-RITHTRRLSALGQG 547
           R    D +       ++A  + + +   F +   S   + +  +S  +   RR + L   
Sbjct: 68  RDLYRDREIQSIDSYLDASIITNGLSRAFSTGAWSHPYKRMERISGVVATLRRTNPLQTM 127

Query: 548 GVARARAGV--------EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
              R             + R  HP+H+G+IC   T +G N GLV +L S   V+     +
Sbjct: 128 ADMRKTRQQVSYTGRVGDARYPHPSHWGKICFLSTPDGENCGLVKNLASMGLVSTNVLEQ 187

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
               +         +V  ++   E ++ A  +         ++  V        ++    
Sbjct: 188 ESLLRQFHVCGMEKLVDDTSSVLEGKHKAFLDGEWVGMCKDSKSFVAKLRRKRRMMEMPY 247

Query: 660 KID-FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +++   D   ++V   A +           ++     ++ +       +   V    E +
Sbjct: 248 QVEIKRDVRHREVRIFADAGRILRPLLLVQKLKKIKELKGEFSFQSLLDNGIV----EFI 303

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD----------------PSTSGVDIY 762
            A+       A     +   D  + +++    +LD                   +   +Y
Sbjct: 304 GAEEEEDCRTAWGIKYLFSADKEKPLVKYTHCELDCSFLLGLSCGLIPFANHDHARRVLY 363

Query: 763 RLMKFQR----------------SNQNTCVNQRPL--VKVGDEVRRNDIIADGPST-DLG 803
           +  K  +                ++ N    QRP+    + D + ++   +         
Sbjct: 364 QSEKHSQQAIGFSTTNPSIRVDTNSHNLYYPQRPIFGTMLSDSLGKSKYSSHHKGMLPHP 423

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +   G+  +VA     GYN EDS++++   +   +F + H+  ++    ++    +++  
Sbjct: 424 EFFNGQCAIVAVNVHLGYNQEDSIVMNRASMERGMFRTEHVRSYKAEVDNSDAPGKKLKP 483

Query: 864 DIPNV------SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM----TPEEKLL 913
           D              + ++D+ G   +GA +  GDI++GK    G          E  ++
Sbjct: 484 DDLVDFGKTESKIGRVDSLDDDGFPFIGANLQTGDIVIGKHAASGVDHSIKLKHTERGMV 543

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           + +      D ++  +     V    +  +  + HG
Sbjct: 544 QKVVLSSNDDGKNFGVVSLRQVRSPCLGDKFSSMHG 579


>gi|269930859|gb|ACZ54164.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 212/293 (72%), Positives = 247/293 (84%), Gaps = 1/293 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQ
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQ 292


>gi|197944877|gb|ACH79985.1| RNA polymerase subunit B [Mycobacterium triviale]
          Length = 232

 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 92/224 (41%), Positives = 122/224 (54%), Gaps = 37/224 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILATEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I            +       +  
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPDWATKLPEELLSAQ-- 154

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                           +TPVFDGA EE +  +L     D      
Sbjct: 155  --------------------------PDTKTATPVFDGAQEEELQGLLASTLPDRDGNVL 188

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                G+++LYDG +GEPF  PVTVGY+Y++KL+H+V DK++ARS
Sbjct: 189  VNGDGKAVLYDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARS 232



 Score = 42.8 bits (99), Expect = 0.43,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|46370310|gb|AAS89954.1| RpoB [Bartonella rattimassiliensis]
          Length = 294

 Score =  275 bits (702), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 215/294 (73%), Positives = 248/294 (84%), Gaps = 1/294 (0%)

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH
Sbjct: 2   GLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITH 61

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF
Sbjct: 62  KRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGF 121

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           IE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ P
Sbjct: 122 IESPYRKIIDGKVTREVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAP 181

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES
Sbjct: 182 RDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMES 241

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 242 VVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSN 294


>gi|269930809|gb|ACZ54139.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930821|gb|ACZ54145.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930833|gb|ACZ54151.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930879|gb|ACZ54174.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930881|gb|ACZ54175.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  275 bits (702), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 212/293 (72%), Positives = 247/293 (84%), Gaps = 1/293 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 292


>gi|157851002|gb|ABV90283.1| RpoB [Mycobacterium avium complex]
          Length = 237

 Score =  275 bits (702), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 97/229 (42%), Positives = 129/229 (56%), Gaps = 40/229 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAVN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 146  -----------------LPEQLRHAQPDQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++AR T SYS
Sbjct: 189  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARPTVSYS 237



 Score = 45.1 bits (105), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 49


>gi|269930815|gb|ACZ54142.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  275 bits (702), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 211/293 (72%), Positives = 246/293 (83%), Gaps = 1/293 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+ 
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQSN 292


>gi|89888199|gb|ABD78644.1| DNA-directed RNA polymerase beta subunit [Bordetella petrii]
          Length = 293

 Score =  275 bits (702), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 176/288 (61%), Positives = 229/288 (79%)

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL++S+  +AR+N YGF+ETPYRK+ DGKV++ + YLSA+EE N  IAQAN++LD++
Sbjct: 2   PNIGLINSMALYARLNEYGFLETPYRKIIDGKVSDQIDYLSAIEESNYVIAQANAALDDE 61

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G F ++LV CR AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQ
Sbjct: 62  GRFVDDLVACREAGETMLTAPANVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQ 121

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +      
Sbjct: 122 RQAVPCLRPEKPVVGTGVERTVAVDSGTTVQALRGGVVDHVDAERVVIRVNDDENVAGEV 181

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
           GVDIY L+K+ RSNQNT +NQRP+VK GD+V + D++ADG STDLG+LALG+NML+AFMP
Sbjct: 182 GVDIYNLIKYTRSNQNTNINQRPIVKRGDKVAKGDVLADGASTDLGELALGQNMLIAFMP 241

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           W+GYNFEDS+LISE++V++D +TSIHIEE  V+ARDTKLGPEEITRDI
Sbjct: 242 WNGYNFEDSILISEKVVADDRYTSIHIEELTVVARDTKLGPEEITRDI 289


>gi|269930827|gb|ACZ54148.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930831|gb|ACZ54150.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930845|gb|ACZ54157.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930849|gb|ACZ54159.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930863|gb|ACZ54166.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930877|gb|ACZ54173.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930891|gb|ACZ54180.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 291

 Score =  274 bits (701), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 211/292 (72%), Positives = 246/292 (84%), Gaps = 1/292 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 291


>gi|51970364|dbj|BAD43874.1| putative DNA-directed RNA polymerase subunit [Arabidopsis thaliana]
          Length = 639

 Score =  274 bits (701), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 119/316 (37%), Gaps = 70/316 (22%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 367  VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 426

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 427  LLEAALSKGIAC--------------------------------------PIQKEGSSAA 448

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 449  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTF 503

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GA+  L E L
Sbjct: 504  YQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERL 563

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 564  FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLL 621

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 622  CQELFSMGITLNFDTE 637



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 85/261 (32%), Gaps = 23/261 (8%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF-----VGTGMESVVAKSSGAAIVAKR 731
           S  PF    D   + +    + +                + T  E  ++   G +     
Sbjct: 113 SQYPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEPKIYTHCELDLSFLLGVSCAVVP 172

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                  D  R V+   +     +         ++    +Q     Q+PL K        
Sbjct: 173 FANH---DHGRRVLYQSQKHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFK-------- 221

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G+N +VA     GYN EDS+++++  +   +F S  I  ++   
Sbjct: 222 --TLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEV 279

Query: 852 -----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                   K   E +     +     + ++++ G   +GA ++ GDI++G+ T  G    
Sbjct: 280 DAKDSEKRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESGADHS 339

Query: 907 TPEEKLLRAIFGEKAVDVRDT 927
              +   R I  +  +   D 
Sbjct: 340 IKLKHTERGIVQKVVLSSNDE 360


>gi|269930853|gb|ACZ54161.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  274 bits (701), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 212/293 (72%), Positives = 246/293 (83%), Gaps = 1/293 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIERPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQ
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQ 292


>gi|296087844|emb|CBI35100.3| unnamed protein product [Vitis vinifera]
          Length = 1113

 Score =  274 bits (701), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 84/313 (26%), Positives = 122/313 (38%), Gaps = 59/313 (18%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVLNPLGVPSR 1130
            + V +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++NP   PSR
Sbjct: 841  QKVNIRFRRPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSR 900

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E+         GK + +               S    +               
Sbjct: 901  MTIAMLLESVAAKGGSLHGKFVDATPFSDSLRKANGEAGSESSSL--------------- 945

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                      + + SML     +  G  +LY G  G      + 
Sbjct: 946  -------------------------VDELGSMLTSYGFNYHGVEVLYSGFYGTELTCEIF 980

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +Y  +L HMVSDK   RSTG+   VT+QP+ G+   GG R GEME   + A+GAAY+
Sbjct: 981  IGPVYYQRLRHMVSDKFQVRSTGTVDQVTRQPIKGRKRGGGIRFGEMERDSMLAHGAAYL 1040

Query: 1311 LQEMLTIKSD----DV---VGRTRVYESIV--------AGNDTFETGTPESFNVLVKEMQ 1355
            L + L   SD    DV    G      SI+         G +T     P  F  L  E+ 
Sbjct: 1041 LHDRLHTCSDHHIADVCSLCGSILT-TSIIQPQKRATSKGMET--VSMPYIFRFLAAELA 1097

Query: 1356 ALGLSIDLENSRT 1368
            A+ + + L+ S  
Sbjct: 1098 AMNIKMTLQLSNG 1110



 Score = 70.1 bits (170), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 131/958 (13%), Positives = 258/958 (26%), Gaps = 233/958 (24%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C    ++Y+  L   +     +            I+E+   +G  P+M K       
Sbjct: 44  PFECRQAKISYSGKLLADVCFQYGNGVA---------IREKF-NLGQFPIMLKSKLCHLR 93

Query: 142 ------------------GTFVIKGIQRIV-----------VSQLHRSPGIHFDHDKGRA 172
                             G F++ G++R+V           +S + R      D  +G  
Sbjct: 94  GADPQKLVSCKEESSEMGGYFILNGLERVVRLLILPKRNYPMS-MVR--NSFRDRREGYT 150

Query: 173 SLS-------------GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
             +                LY  R   +    +      ++ +         +PV   L 
Sbjct: 151 DKAVVIRCVREDQSAVTVKLYYLR---NGSARLGFWIQGREYL---------LPVGVVLK 198

Query: 220 ALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           AL   ++ EI    Y  +                +   G K +        G Q++    
Sbjct: 199 ALIDTTDHEI----YESLTCCYS-----------EKYEGGKGAV-------GTQLVGERV 236

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           K+    ++ L                   +  D +  E+  I  +A   +  + +     
Sbjct: 237 KIILDEVRDL--SLFTRHQCLQHIGEHFQLVMDGLENESYSIVADA---VLREYIFVHLD 291

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
           +      +L        + I  T V D        +L    V+ PG + T  + E +  +
Sbjct: 292 NNYDKFNLLIFMVQKLFSLIDQTSVPDNPD-----VLQNQEVLLPGHLITIYLKEKLQEW 346

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI-- 456
           L+            R               + + K     I   + ++      +     
Sbjct: 347 LYKARRLLQDEINKRKNFEFSSLAHV---KKVMDKNPSRQISLAVENMLKTGRLVTQSGL 403

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRME---------RSIKERISSVDIDSVMPQDLINAK 507
           D      +    E L     L   R           R+   R    +    +        
Sbjct: 404 DLQQRAGMTVQAERLNFLRFLSHFRAVHRGASFAGLRTTSVRKLLPEAWGFLCPVHTPDG 463

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD------V 561
                +     + +++   +   +       R        G+    A  ++        +
Sbjct: 464 EPCGLLNHMASTCRITSYFDSRGNTRDFFKIRMSILSVLIGIGMTPALPKLVQAGPPEVL 523

Query: 562 HPTHYGRIC------PAETSEGHNIGLVSSLTS---------FARVNAYGFIETPYRKVC 606
                GR+         ET+  H   L  S  S         +  ++  G     Y    
Sbjct: 524 SVILDGRVVGSIPSSEVETAVNHLRRLKVSAISVIPDDLEVGYIPLSMGGAYPGLYLFTS 583

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
             +    V  +S   EE   I      L          + C    +            + 
Sbjct: 584 PSRFVRPVRNISIPSEEGHDI-----ELIGPFEQVYMEIRCPDGSDGGRRNIFPATHEEI 638

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++S+ ASL P+ +++ S R +  C M +Q +                     S  A
Sbjct: 639 HPTGMLSVVASLTPWSDHNQSPRNMYQCQMGKQTMA-------------------FSSQA 679

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           I  +                          +   +Y L   Q           P+V+   
Sbjct: 680 INCR--------------------------ADQKLYHLQTPQT----------PIVRTSA 703

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
            V+            + +   G N +VA + + GY+ ED+M++++  V   +    H + 
Sbjct: 704 YVK----------YSMDEFPTGTNAIVAVLAYSGYDMEDAMILNKSSVDRGL---CHGQI 750

Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKN-----IDECGIICVGAEVNPGDILVG----- 896
           ++    D      +  R         +       ID  G+  VG  +NP +         
Sbjct: 751 YQTETIDLSDENNKSDRGQRMFRRSNVDKSANSLIDSDGLPYVGQMINPNEPYCSIYNEV 810

Query: 897 -----KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    KG  P+  +   L A   +    V     R  +     ++  +  +RHG
Sbjct: 811 TSSTRATKLKGSEPVIVDYVALDAKNKKHPQKVNIRFRRPRN----PIIGDKFSSRHG 864


>gi|227937608|gb|ACP43379.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 291

 Score =  274 bits (701), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 213/292 (72%), Positives = 247/292 (84%), Gaps = 1/292 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+
Sbjct: 241 DSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQS 291


>gi|255070151|ref|XP_002507157.1| predicted protein [Micromonas sp. RCC299]
 gi|226522432|gb|ACO68415.1| predicted protein [Micromonas sp. RCC299]
          Length = 1192

 Score =  274 bits (701), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 76/262 (29%), Positives = 113/262 (43%), Gaps = 47/262 (17%)

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK-DGTPV 1118
            I  G          + V V   R    GDK + RHG KG++S + P ED+P+++  G+  
Sbjct: 883  ISSGKASKGQTETKMSVTVRCDRNPIIGDKFSSRHGQKGVLSFLCPEEDLPYIEKSGSRP 942

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP   PSRM +G + E+    A    G+ I +       +                
Sbjct: 943  DILINPHAFPSRMTIGMLLESMASKAGALDGRFIDASPFQAANDE--------------- 987

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                       + +P            MLR    + SG   + +
Sbjct: 988  -------------------------THIISP------TREYGEMLRKHGYNYSGSETMVN 1016

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            GLTGE FD  + VG +Y  +L HMVSDK   RS G  + +TQQP+ G+   GG R GEME
Sbjct: 1017 GLTGERFDVDIFVGLVYYQRLRHMVSDKFQVRSLGPNNPLTQQPIKGRKAGGGIRFGEME 1076

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD 1320
               + A+G++Y++ + L   SD
Sbjct: 1077 RDALIAHGSSYLIHDRLHACSD 1098



 Score = 95.5 bits (236), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 133/969 (13%), Positives = 257/969 (26%), Gaps = 246/969 (25%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFK-----SVFPI----TAFSGAAMLEFVSYEFDP 83
             AS+D+FL          + GL    +     S+ P     T+ S    + F +     
Sbjct: 29  HLASFDYFL----------DHGLSDVVRCLDNISIQPSGAQNTSSSPRFKMWFENISIGR 78

Query: 84  P-------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           P             +    +C     TY  P+  T+     DV            +E  I
Sbjct: 79  PIREDTTAVRARDPRVFPRECRESSNTYKAPMLATVAWTFGDVGAIFR-------REFRI 131

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIV---VSQ------- 156
            M   P+M                           G F++ G +RI+   V Q       
Sbjct: 132 CM--FPVMVASKVCNLFGFSQDELICRGEEGHEMGGYFILNGNERIIRLLVQQRRHYIMG 189

Query: 157 LHR----SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK- 211
           + R    S G  + H       S    +   +       +    D    + V + RR++ 
Sbjct: 190 MKRKAYSSRGPIYTHYATAIRCSANDEHTSTV------RIHYTSDGSARL-VFVHRRKEY 242

Query: 212 -VPVTSFLMAL--------------GMDS--------EEILSTFYPKIVYSQRGDFWCFP 248
            VP    L AL              G+          E I         +          
Sbjct: 243 FVPAGIILRALAEFSDSVVQAIVARGLTGLGAQVFAIERIRIILGEAATFGIHNKVQALA 302

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                       +    + D G+++I     +     +      +  +      + G   
Sbjct: 303 YLGEHFRAQLDANPWETNFDVGKRLICEHIFIHLQSDEDKFNLVLLMMQKLYALVAGQCS 362

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A++  +    EI +    +      E++  +  +    L  +   N     N    D   
Sbjct: 363 ADNPDSLMHHEILLPGILMQIF-VREKLQDALHKAKIALNREFEEN----PNHASADD-- 415

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
                          G+  +    E++         +Y L+T     ++ R  L      
Sbjct: 416 ---------------GEWLSQVAIEAITKTNIGRLAEYFLATG---NLSSRTGLGLTQTS 457

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
                 D +  ++ +   R+    +         R  +V ++L   +             
Sbjct: 458 GFTIVADKLNYMRYISHFRS----VHRGAYFAELRTTTVRKLLPESWG------------ 501

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            +  V      P  L+N       +     S+  ++       L  +      S+ G   
Sbjct: 502 FLCPVHTPDGSPCGLLNHLAASCYIHVACESTGEARDRARSQVLKVL------SSAGALI 555

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC-- 606
           +  + +       H T              +  +V S    A+V+    + +        
Sbjct: 556 LHGSTSLGSAPPAHLTVMLDGLILGFVADSDAKVVVSALRAAKVSGSNGVSSHLEIAHIP 615

Query: 607 ------DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-E 659
                  G      ++ ++       I Q N   +  GS  +  +  RC           
Sbjct: 616 LSSCGYGGAFPGLYLFSTSSRMMRPVIQQQNRITENIGSLEQAFMSIRCPDGRQKPTCIA 675

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           +    +  P  ++S+ ASL P+ + + S R +  C M +Q + +      +         
Sbjct: 676 EHAHEENGPGTILSVVASLTPWSDFNQSPRNMYQCQMAKQTMGMPLHSFCY--------- 726

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                                    IYRL   Q          R
Sbjct: 727 ------------------------------------RPDTKIYRLHTPQ----------R 740

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P+   G   +            + +  LG N +VA +   GY+ ED+M++++  +   + 
Sbjct: 741 PVAMTGQYDK----------YQMDNYPLGTNAVVAVIAHTGYDMEDAMIVNKGAMERGLG 790

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNV------------SEEGLKNIDECGIICVGAE 887
              H   ++        G +E       +                  +ID  G    G+ 
Sbjct: 791 ---HATLYKTETVTLVAGSDENFGQCNVIQQKLGSPIAFTEKHPFDPDIDTDGAPRPGSI 847

Query: 888 VNPGDILVG 896
              G  L  
Sbjct: 848 KQAGSTLCS 856


>gi|17506623|ref|NP_492476.1| hypothetical protein F14B4.3 [Caenorhabditis elegans]
 gi|3875865|emb|CAA99827.1| C. elegans protein F14B4.3, partially confirmed by transcript
            evidence [Caenorhabditis elegans]
          Length = 1127

 Score =  274 bits (701), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 70/257 (27%), Positives = 101/257 (39%), Gaps = 51/257 (19%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                +   +   ++R    GDK A RHG KGI S + P E +PF + G   DI+ NP G 
Sbjct: 835  DSGAKHALIQWRIERNPIIGDKFASRHGQKGINSFLWPVESLPFSETGMVPDIIFNPHGF 894

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E+  G A    G+   +    +                            
Sbjct: 895  PSRMTIGMMIESMAGKAAATHGENYDASPFVFNE-------------------------- 928

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                    D         +L  A  +  G    Y G+ G   + 
Sbjct: 929  ------------------------DNTAINHFGELLTKAGYNYYGNETFYSGVDGRQMEM 964

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G +Y  +L HM++DK   R+TG    +T QP+ G+   GG R GEME   I A+G 
Sbjct: 965  QIFFGIVYYQRLRHMIADKFQVRATGPIDPITHQPVKGRKKGGGIRFGEMERDAIIAHGT 1024

Query: 1308 AYVLQEMLTIKSD-DVV 1323
            ++VLQ+ L   SD DV 
Sbjct: 1025 SFVLQDRLLNCSDRDVA 1041



 Score = 69.3 bits (168), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 47/119 (39%)

Query: 72  AMLEFVSYEFDPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
             ++F S +   P  D               +C  R LTYA  LK+ + + V        
Sbjct: 41  VTMKFTSAQLHKPTLDTGAKLTSDTLPLLPAECRQRGLTYAGNLKVGIDVHV-------- 92

Query: 119 AKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIV 153
             S  DI E  I +G +P+M                         K G F++ G ++++
Sbjct: 93  NGSRLDIIE--IILGKVPIMLRSEGCHLRGMSRKELVVAGEEPIEKGGYFIVNGSEKVI 149


>gi|46370312|gb|AAS89955.1| RpoB [Bartonella phoceensis]
          Length = 293

 Score =  274 bits (701), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 213/291 (73%), Positives = 246/291 (84%), Gaps = 1/291 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 3   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 62

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 63  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 122

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 123 PYRKIVDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDH 182

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 183 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 242

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 243 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSN 292


>gi|227937582|gb|ACP43366.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  274 bits (701), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 215/293 (73%), Positives = 248/293 (84%), Gaps = 1/293 (0%)

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH
Sbjct: 1   GLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITH 60

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGF
Sbjct: 61  KRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGF 120

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           IE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ P
Sbjct: 121 IESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAP 180

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES
Sbjct: 181 RDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMES 240

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 VVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 292


>gi|145926540|gb|ABP98909.1| RNA polymerase beta subunit [Bradyrhizobium sp. IRBG 131]
          Length = 257

 Score =  274 bits (700), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 183/258 (70%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI+  RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVFARIDRRRKLPVTSLMFALGLDGETILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           K++Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + L+EKG+K
Sbjct: 61  KLIYKRIKEGWRVPFDA-NRFRGYSTVNDLIDADTGKVVLEAGKKLTVRAARQLQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++ + L G Y+AED+VN +TGEIY EAG+ I +K  + +     +D+P+L +D VN 
Sbjct: 120 ALRMSDEELLGNYIAEDLVNPKTGEIYAEAGEEITDKLFKVLNEQGYKDLPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             YIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GPYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL LD PD  R +R
Sbjct: 240 KMNMRLELDAPDTQRTLR 257


>gi|328853401|gb|EGG02540.1| hypothetical protein MELLADRAFT_49804 [Melampsora larici-populina
            98AG31]
          Length = 1214

 Score =  274 bits (700), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 109/278 (39%), Gaps = 52/278 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                   E+ F  +I  I  G+D        +   + + R    GDK + RHG KG+ S+
Sbjct: 874  WEKYKGDEEAFVEEIRLI--GNDSSTTECTKIHFKLRIPRSPVIGDKFSSRHGQKGVCSQ 931

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
              P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    +    +   
Sbjct: 932  KWPAVDMPFTESGMQPDVIINPHAFPSRMTIGMFVESLAGKAGAMHGIAQDATPFRFNEK 991

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                         TP       E   + 
Sbjct: 992  D--------------------------------------------TPS------EYFGTQ 1001

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            L  +  +  G   +Y G+TGE F   + +G +Y  +L HMV DK   R+TG     T QP
Sbjct: 1002 LLASGFNYHGNEPMYSGITGEEFVADIYIGLVYYQRLRHMVGDKWQVRTTGQVEKTTHQP 1061

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            + G+   GG R GEME   + A+G +++LQ+ L   SD
Sbjct: 1062 IKGRKRGGGIRFGEMERDALLAHGTSFLLQDRLMNCSD 1099



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 99/652 (15%), Positives = 206/652 (31%), Gaps = 90/652 (13%)

Query: 359 RNTLVTDKNKDRKDALLDIYR-VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +N        DR + LL  ++    P          S F  +    D +    VGR  ++
Sbjct: 302 QNAFDDTFRTDRIELLLRSFKNYHLPTSALCLHFLGSKFRIVLNCPDDWSDERVGRFLLD 361

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             + +    +    +   ++ +I+ L  L  G+   D+ D+  ++ +   G +L +  + 
Sbjct: 362 RVVLVH--LNNATSKYRLLLFMIQKLYALVGGECCADNPDSPQHQEILMPGHLLSSILKE 419

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPV-----------VSAVCEFFCSSQL---- 522
                   I+ +++S     V   +  + K V              +  F  +  L    
Sbjct: 420 RFEEYIGGIRNQMASDVRRGVASANFRDPKYVQKTMARVDCDAGKRITYFLATGNLVSPT 479

Query: 523 ----------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     + + E +N    I+H R    + +G          +R + P  +G +CP 
Sbjct: 480 GLDLQQMSGFTLIAEKLNFYRYISHFR---CVHRGAFFAELKTTTVRKLLPEAWGFLCPV 536

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            T +G   GL++      ++ +     +    +      +   + SA++ +N    Q + 
Sbjct: 537 HTPDGSPCGLLNHFAHQCQILSSPSPSSHVPALLTSLGMSQP-FDSAVDVKNYVCVQLDG 595

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV------------------SI 674
            +    S     +         L   +        P   V                  + 
Sbjct: 596 EVIGWAS-----LSLCFKMATALRLWKTEGLEKIPPGLEVGFVPRVTGGQYPGLFLFSTP 650

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A  + P     +    L+G     Q    +      +  G+ S   + S   I++  A +
Sbjct: 651 ARMMRPVQLISNGKTELIGP--FEQVYLDIACTESEIEKGI-STHVEISPTHILSLLANL 707

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR---PLVKVGDEVRRN 791
               D  +      +  +   T G          R++      Q    P+V+        
Sbjct: 708 TPFSDFNQSPRNMYQCQMSKQTMG--TPSSAFNHRTDNKLYRLQTGQTPIVRP------- 758

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
              A      +     G N +VA + + GY+ ED+M++++             +   V  
Sbjct: 759 ---ALHDHYHMDHFPNGTNAVVAVISYTGYDMEDAMILNKSGHERGFGHGTIYKSQIVDL 815

Query: 852 R-DTKLGPEEITRD--IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT--------- 899
           + D   G  E        +  ++  +++   GI  +G+ +  GD L   +          
Sbjct: 816 QPDRGRGSSERHFGLGDDHKLKDMAQHLGADGIAMIGSRLKRGDPLCAYVDRVTGKGGWE 875

Query: 900 -PKGESPMTPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             KG+     EE +L+               LR+P      V+  +  +RHG
Sbjct: 876 KYKGDEEAFVEEIRLIGNDSSTTECTKIHFKLRIP---RSPVIGDKFSSRHG 924


>gi|255578257|ref|XP_002529996.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis]
 gi|223530519|gb|EEF32401.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis]
          Length = 1159

 Score =  274 bits (700), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 74/265 (27%), Positives = 109/265 (41%), Gaps = 44/265 (16%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D      L+ V +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 856  DTKNKKHLQKVNIRFRHPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLII 915

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +                   K +  G   
Sbjct: 916  NPHAFPSRMTIAMLLESLAAKGGSLNGKFVDATPFTSS------------VKNVNGGEAK 963

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
             +                                + + +MLR    +  G  +LY G+ G
Sbjct: 964  SESESL---------------------------VDDLGNMLRSHGFNYHGVEVLYSGVYG 996

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG+   +T+QP+ G+   GG R GEME   +
Sbjct: 997  TELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTVDQITRQPIKGRKRGGGIRFGEMERDAM 1056

Query: 1303 QAYGAAYVLQEMLTIKSD----DVV 1323
             A+GAAY+L + L   SD    DV 
Sbjct: 1057 LAHGAAYLLHDRLHTCSDYHIADVC 1081



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 84/585 (14%), Positives = 180/585 (30%), Gaps = 93/585 (15%)

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM--------LKNQYRLGLLRMERSIKE 488
           I +++ L  L +    +D+ D+L N+ V   G +        L+   R     ++  I +
Sbjct: 324 IFMLQKLFSLVDQTSVVDNPDSLQNQEVLLPGHLVTIYLKEKLEEWLRKAKKVLQEEIAK 383

Query: 489 RISSV---DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL--EEHVNSLSRITHTRRLSA 543
             +      +D     D   +  +  AV     + +L      +            RL+ 
Sbjct: 384 NNNFNFLSVLDVKKVIDKNPSTTISLAVENMLKTGRLVTQTGLDLQQRAGYTVQAERLNF 443

Query: 544 LGQGGVARAR---------AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           L      RA              +R + P  +G +CP  T +G   GL++ +T   R+ +
Sbjct: 444 LRFLSFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTRSCRITS 503

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           Y   +   +   D + +   V  S           ++          + L          
Sbjct: 504 YFDSQGAVKDFFDIRKSILGVLTSLGM-------TSSLPKLVQAGPPQVLSVLLDGRVVG 556

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN-----MQRQAVPLLKAEAP 709
            +P  +++ +    +++   A+S+IP         + MG       +       ++    
Sbjct: 557 SIPSSQVEKVVVHLRRLKVAASSVIPDDLEVGYVPLSMGGAFPGLYLFTSPSRFIRPVKN 616

Query: 710 FVGTGMESVVAKSSG------AAIVAKRAGIVEQVDA---IRIVIRSVEGDL-------- 752
                 E    +  G        I     G   + DA       I   +           
Sbjct: 617 ISIPAGEGENIELIGPFEQVFMEIRCPDGGNGGRSDAFPATHEEIHPTDMLSVVANLTPW 676

Query: 753 -DPSTSGVDIYRLMKFQRSNQNTCVN---------------QRPLVKVGDEVRRNDIIAD 796
            D + S  ++Y+    +++   +  +               Q P+V+     +       
Sbjct: 677 SDHNQSPRNMYQCQMAKQTMAFSLQSLRFRADQKLYHLQTPQTPIVRTSSYTK------- 729

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                + +   G N +VA + + GY+ ED+M++++  V   +    H + ++    D   
Sbjct: 730 ---YCVDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVERGM---CHGQIYQTETIDLSE 783

Query: 857 GPEEITRDIPNVSEEGLKN-----IDECGIICVGAEVNPGDILVG-------KITPKGES 904
                 R         +       ID  G+  VG  ++P +                   
Sbjct: 784 EGSRSDRAQRMFRRSNIDKSLHSVIDSDGLPYVGQMIHPNEPYCSIYNEITNTTRTNNRK 843

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              P      AI  +    ++  ++R        ++  +  +RHG
Sbjct: 844 GSDPVIVDYVAIDTKNKKHLQKVNIRFRH-PRNPIIGDKFSSRHG 887



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 96/794 (12%), Positives = 203/794 (25%), Gaps = 184/794 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L      S+D+ +            GL+    ++ P ++ +    L              
Sbjct: 24  LTRHHIDSFDYMI----------ERGLEIMLDNIKPESSRTKHKRL------------LP 61

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------- 141
            +C    ++Y    +  +                K +  +    G LP+M K        
Sbjct: 62  FECRQAKISYTGKFEADV----------CFEYHGKAVIREKYNFGQLPIMLKSRLCHLYG 111

Query: 142 -----------------GTFVIKGIQRI-------------------------------V 153
                            G F++ G++R+                               V
Sbjct: 112 VDSQQLVSFNEESAEMGGYFILNGLERVVRLLIMPKRNYPMSTVRGSFRDRREGYTDKAV 171

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLY----ACRIIPDQGLWM---DIEFDSKDIIHVRI 206
           V +  R    +      ++S+S KL Y    + R+    G W+   +             
Sbjct: 172 VIRCVRE---YQSSLTDQSSVSVKLYYLRSGSARL----GFWIQGREYL----------- 213

Query: 207 DRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
                +P    L AL   ++      Y K+       +     +    +VG +    L +
Sbjct: 214 -----LPAGIVLKALAETTD---REIYEKLTCCYDEKYEKAKGAVGSQLVGERAKIILDE 265

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKF-------LGITSDCLCGLYVAEDIVNGETGE 319
           +       +S      G        G++          +  D +    V  +  + +   
Sbjct: 266 VRDLSLFTQSECLRHIGEHFQPVMDGLEKETFSNVAHAVLKDYIF---VHLNNYDDKFNL 322

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +      +        +  +         +   +         + +  +  K  L +   
Sbjct: 323 LIFMLQKLFSLVDQTSVVDNPDSLQNQEVLLPGHLVTIYLKEKLEEWLRKAKKVLQEEIA 382

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                +  +    + + +     +       V  +    RL   T  D++      + A 
Sbjct: 383 KNNNFNFLSVLDVKKVIDKNPSTTISL---AVENMLKTGRLVTQTGLDLQQRAGYTVQAE 439

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL-------------LRMERSI 486
               +   +    +    +    R  SV ++L   +                   M RS 
Sbjct: 440 RLNFLRFLSFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTRSC 499

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +   S  D    +       K ++  +     +S L +          ++       +G 
Sbjct: 500 RIT-SYFDSQGAVKDFFDIRKSILGVLTSLGMTSSLPK-LVQAGPPQVLSVLLDGRVVGS 557

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY--GFIETPYRK 604
              +     VE   VH         +   +   +G V      A    Y         R 
Sbjct: 558 IPSS----QVEKVVVHLRRLKVAASSVIPDDLEVGYVPLSMGGAFPGLYLFTSPSRFIRP 613

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +       + + A E E       N  L          + C   G             
Sbjct: 614 VKN-------ISIPAGEGE-------NIELIGPFEQVFMEIRCPDGGNGGRSDAFPATHE 659

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ----------------AVPLLKAEA 708
           +  P  ++S+ A+L P+ +++ S R +  C M +Q                   L   + 
Sbjct: 660 EIHPTDMLSVVANLTPWSDHNQSPRNMYQCQMAKQTMAFSLQSLRFRADQKLYHLQTPQT 719

Query: 709 PFVGTGMESVVAKS 722
           P V T   +     
Sbjct: 720 PIVRTSSYTKYCVD 733


>gi|37725758|gb|AAO32827.1| RNA polymerase beta subunit [Bartonella vinsonii subsp. arupensis]
          Length = 292

 Score =  274 bits (700), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 213/291 (73%), Positives = 245/291 (84%), Gaps = 1/291 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 3   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 62

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 63  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 122

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 123 PYRKIVDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDH 182

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 183 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 242

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           + SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 243 RDSGAAVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSN 292


>gi|302411196|ref|XP_003003431.1| DNA-directed RNA polymerase I subunit RPA2 [Verticillium albo-atrum
            VaMs.102]
 gi|261357336|gb|EEY19764.1| DNA-directed RNA polymerase I subunit RPA2 [Verticillium albo-atrum
            VaMs.102]
          Length = 1208

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 88/455 (19%), Positives = 145/455 (31%), Gaps = 64/455 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA---IFGEKAVDVRDTSLRVPS 933
            D         +   G   +G            +   ++          +         P+
Sbjct: 685  DFNQSPRNMYQCQMGKQTMGTPATALAHRTDNKLYRIQTGQTPVVRSPLHNEYGFDNFPN 744

Query: 934  GVSGTVVDVRIFNRHGID-----KNERSISVEREQIELLAR-DKDDEQVILDRNIYSRLM 987
            G++  V  +        D     K+          I  + +    D+         ++L 
Sbjct: 745  GMNSVVAVISYTGYDMDDAMILNKSSHERGFGHGTIYKVKKVSLKDDSRSRTAKQVTKLF 804

Query: 988  EILCGQNAVSGPKGF--KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                        +    +        ++ E      +     D          + QYE  
Sbjct: 805  GFAPNSFVKGEYRSMLDEDGLPYVGRMVQEGDILCAYHTVTADFNGNLTNLDGQTQYE-K 863

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E  F  ++  I   +   P   + V + + + R    GDK + RHG KG+ S+  P
Sbjct: 864  YKESEQAFIEEVRIIGSENGNEPA--QTVSIKLRVPRAPVIGDKFSSRHGQKGVASQKWP 921

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
              DMPF + G   D ++NP   PSRM +G   E+  G A    G    S    +      
Sbjct: 922  ATDMPFTESGMQPDTIINPHAFPSRMTIGMFVESLAGKAGALHGLAQDSTPFKFNEENTA 981

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            +                                                  +     L  
Sbjct: 982  A--------------------------------------------------DYFGHQLMK 991

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
            A  +  G   +Y G+TGE     + +G +Y  +L HMV+DK   R+TG     T QP+ G
Sbjct: 992  AGYNYHGNEPMYSGITGEELSADIYIGVVYYQRLRHMVNDKYQVRTTGPVVPTTGQPIKG 1051

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1052 RKKGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1086



 Score = 70.9 bits (172), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 82/540 (15%), Positives = 169/540 (31%), Gaps = 67/540 (12%)

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             + R+ +    N+D  +     + + ++ +I+ L  L  G+ ++D+ D + N+ V   G
Sbjct: 322 EFLKRIVLVHLGNVDVTEQQDSDKFKMLLFMIRKLYALVAGECSVDNPDAIQNQEVLLGG 381

Query: 469 EMLKNQYRLGLLRM-----ERSIKERISSVDIDSVMPQDLIN----------AKPVVSAV 513
            +     +  L          S+++        +   QD              + + S +
Sbjct: 382 FLYGMILKERLDEFLSTAVRASLRDYHRKFPAKTFTSQDFQKDFPATIFRLANESLGSGL 441

Query: 514 CEFFCSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             F  +  L+               + E +N L  I+H R    + +G          +R
Sbjct: 442 EYFMSTGNLTSPSGLDLQQTAGYTVVAEKLNFLRFISHFR---MIHRGAFFAELKTTTVR 498

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVYLS 618
            + P  +G +CP  T +G   GL++ L    R+        T    V +      V   S
Sbjct: 499 KLLPESWGFLCPVHTPDGSPCGLLNHLAHKCRIMTDPVDTSTLPALVAEM---GAVSTSS 555

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVF---CRCAGEEILVPREKIDFIDASPKQ----- 670
           A  +E+  +      L          +         E       +++     P       
Sbjct: 556 AATDESVVVMLDGRVLGFSTPQESIRIADTLRYWKVEGTHGVPLELEIGYVPPSNGGSYP 615

Query: 671 ---VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
              + S AA ++  ++     +       ++  + +   E   +    ES   +     +
Sbjct: 616 GLYIASKAARMVRPVKYLPLQKQDYVGPHEQPYMSIAVVEKEIISG--ESTHVEFDPTNM 673

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           ++  A +    D  +      +  +   T G        +           Q P+V+   
Sbjct: 674 LSILANMTPFSDFNQSPRNMYQCQMGKQTMGTPATALAHRTDNKLYRIQTGQTPVVRS-- 731

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +   G N +VA + + GY+ +D+M++++             + 
Sbjct: 732 --------PLHNEYGFDNFPNGMNSVVAVISYTGYDMDDAMILNKSSHERGFGHGTIYKV 783

Query: 847 FEVMARDTKLGPEEIT-------RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            +V  +D                     V  E    +DE G+  VG  V  GDIL    T
Sbjct: 784 KKVSLKDDSRSRTAKQVTKLFGFAPNSFVKGEYRSMLDEDGLPYVGRMVQEGDILCAYHT 843



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 90/732 (12%), Positives = 197/732 (26%), Gaps = 124/732 (16%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF-------PITAFSGAAMLEFVSYEFD 82
           +     S++     +  P    + GL       F       P         + +      
Sbjct: 40  VSPHIESFNALFRNDGKPSL-LDHGLADIGTKTFLDGDDRTP-QGQRNKLTIRYKGVSLQ 97

Query: 83  P----P--KFD------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
                P  K+         +C  R +TY   L  T    + D D     +          
Sbjct: 98  KSQLPPSNKYAKTREIFPAECRERHVTYRGKLSATFEFRINDGDAKEFTRD--------- 148

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIV-VSQLHRSPGIHF 165
            +G +P+M K                         G F++ GI++I+ + Q++R      
Sbjct: 149 -LGQMPIMVKSNRCHLEGNSPDLLVKRKEESEELGGYFIVNGIEKIIRLLQVNR------ 201

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII-HVRIDRRRKVP--VTSFLMALG 222
              +     S          P +G      +    I    ++   +     V   L AL 
Sbjct: 202 ---RNFPMPSTDPAS-----PTRGA----GYSPHGIHSFAQLGPTKPFSTNVMMILKALV 249

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
             ++ EI              + +        L+            +T   + E  + + 
Sbjct: 250 ETNDREIFEGLIGSKGSKSAQNTFLTD-RVELLLRTYTSYGLYTKTETRAYLGEKFRVVL 308

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
                      +    + ++ L    V   + N +  E        +    + +++    
Sbjct: 309 ------GVPDTMSHYDVGTEFLK-RIVLVHLGNVDVTEQQDSDKFKMLLFMIRKLYALVA 361

Query: 342 RDIPILYVDSVNN---------NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
            +  +   D++ N            I    + +       A L  Y    P    T    
Sbjct: 362 GECSVDNPDAIQNQEVLLGGFLYGMILKERLDEFLSTAVRASLRDYHRKFPAKTFTSQDF 421

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNM-RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
           +  F    F      L +     M+   L   +  D++      ++A     +   +   
Sbjct: 422 QKDFPATIFRLANESLGSGLEYFMSTGNLTSPSGLDLQQTAGYTVVAEKLNFLRFISHFR 481

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
            I         +  +V ++L   +                      ++       + +  
Sbjct: 482 MIHRGAFFAELKTTTVRKLLPESWGFLC-------PVHTPDGSPCGLLNHLAHKCRIMTD 534

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
            V        L      V++ S  T    +  L    +  +     +R      Y ++  
Sbjct: 535 PVDTS-TLPALVAEMGAVSTSSAATDESVVVMLDGRVLGFSTPQESIRIADTLRYWKV-- 591

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
               EG +   +     +   +  G     Y      ++   V YL   +++  Y+    
Sbjct: 592 ----EGTHGVPLELEIGYVPPSNGGSYPGLYIASKAARMVRPVKYLPLQKQD--YVGPHE 645

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                     +E++              +   ++  P  ++SI A++ PF + + S R +
Sbjct: 646 QPYMSIAVVEKEIISG------------ESTHVEFDPTNMLSILANMTPFSDFNQSPRNM 693

Query: 692 MGCNMQRQAVPL 703
             C M +Q +  
Sbjct: 694 YQCQMGKQTMGT 705


>gi|157427473|gb|ABV56119.1| RNA polymerase beta subunit [Candidatus Bartonella rudakovii]
          Length = 292

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 211/291 (72%), Positives = 243/291 (83%), Gaps = 1/291 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 3   RMERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 62

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 63  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 122

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 123 PYRKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDTEGRFTEEFVVCRHAGEVLMAPRDH 182

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA
Sbjct: 183 IDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVA 242

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
             SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 243 CDSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQRSN 292


>gi|269930795|gb|ACZ54132.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 214/293 (73%), Positives = 247/293 (84%), Gaps = 1/293 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 DSGAAVSAKRDGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 292


>gi|269930807|gb|ACZ54138.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 292

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 214/293 (73%), Positives = 247/293 (84%), Gaps = 1/293 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 DSGAAVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 292


>gi|145613510|ref|XP_363646.2| hypothetical protein MGG_01572 [Magnaporthe oryzae 70-15]
 gi|145020582|gb|EDK04711.1| hypothetical protein MGG_01572 [Magnaporthe oryzae 70-15]
          Length = 1240

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 89/456 (19%), Positives = 153/456 (33%), Gaps = 66/456 (14%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +   G   +G            +   ++                  +  +
Sbjct: 708  DFNQSPRNMYQCQMGKQTMGTPGAAISRRTDNKMYRIQTGQTPIVRAPLHNEYGFDNFPN 767

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELL---ARDKDDEQVILDRNIYSRLMEILCGQ 993
            G    V + +  G D ++ ++ + +   E           +++ L  +  +R  + +   
Sbjct: 768  GMNAVVAVISYTGYDMDD-AMIINKSAHERGFGHGTIYKTKKITLKDDSRTRSTKHITKM 826

Query: 994  NAVSGPKGFKKSTVLSSDL---------ISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
               +     K   +   DL         + +      W     D   Q         YE 
Sbjct: 827  FGFAPNTTVKARDLEKLDLDGLPRIGSKVEQGDIIAAWHTVSADYSDQLVNRDGLTHYE- 885

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E  F  +I  +  G++     L+ V +   + R    GDK + RHG KG+ S+  
Sbjct: 886  KYKDSETAFVEEIRLV--GNENGTEPLQTVSIKFRIPRSPVIGDKFSSRHGQKGVASQKW 943

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P  DMPF + G   D+++NP   PSRM +G   E+  G +    G    S    +     
Sbjct: 944  PMIDMPFSESGMQPDVIINPHAFPSRMTIGMFVESLAGKSGALHGLAQDSTPFKFDEQNT 1003

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             +                                                  +     L 
Sbjct: 1004 AA--------------------------------------------------DYFGHQLM 1013

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A  +  G   +Y G+TG+     + +G +Y  +L HMV+DK   R+TG     T QP+ 
Sbjct: 1014 KAGYNYHGNEPMYSGITGQELAADIYIGVVYYQRLRHMVNDKFQVRTTGPVVPTTGQPIK 1073

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G+   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1074 GRKRGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1109



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 59/410 (14%), Positives = 123/410 (30%), Gaps = 56/410 (13%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +S    + E +N L  I+H R    + +G          +R + P  +G +CP  T +G 
Sbjct: 484 TSGFVVVAEKLNFLRFISHFR---MVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGS 540

Query: 579 NIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GL++ L    ++      +    R   +  V +     SA  EE       +  +  D
Sbjct: 541 PCGLLNHLAHKCKIMTDAVDVSAIPRLATELGVVDT---SSADTEE-------SVPVMLD 590

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQV------------------VSIAASLI 679
           G         +       +   K++     P  +                   S  + ++
Sbjct: 591 GKILGWCSPKQSRTIADTLRYWKVEGSHGVPVHMEIGLVPPSNGGSYPGIYMASQPSRMV 650

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG---TGMESVVAKSSGAAIVAKRAGIVE 736
             ++     +       ++  + +   E   V    T +E                    
Sbjct: 651 RPVKYLPLEKEDYVGTHEQPYMSIACTEPEIVSGESTHVEFDPTNMLSILANMTPFSDFN 710

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
           Q        +  +  +    + +      K  R        Q P+V+             
Sbjct: 711 QSPRNMYQCQMGKQTMGTPGAAISRRTDNKMYRIQTG----QTPIVRA----------PL 756

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +   G N +VA + + GY+ +D+M+I++             +  ++  +D   
Sbjct: 757 HNEYGFDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGHGTIYKTKKITLKDDSR 816

Query: 857 GPEEITR-------DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                             V    L+ +D  G+  +G++V  GDI+    T
Sbjct: 817 TRSTKHITKMFGFAPNTTVKARDLEKLDLDGLPRIGSKVEQGDIIAAWHT 866


>gi|103001497|gb|ABF71510.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 695

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 116/816 (14%), Positives = 236/816 (28%), Gaps = 145/816 (17%)

Query: 467  VGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--- 521
             G +L N +R+   ++ + + +  +    +         + +  + + +     +     
Sbjct: 1    CGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGD 60

Query: 522  ----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                      +SQ+       S ++H RR +      + R     + R +H TH+G +CP
Sbjct: 61   QKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCP 116

Query: 572  AETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            AET EG   GLV +L     +      E    +    + +V  +     +      ++  
Sbjct: 117  AETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNG 176

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSN 688
                +  D +     V        I      + D  D   K          P    D+  
Sbjct: 177  VWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDP 236

Query: 689  RVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            +     N+   ++ +  L+ +               S     AK  G    V     V+ 
Sbjct: 237  KSTNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVE 286

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DL 805
             V+ + + +   V     ++  R  Q           +   V+          T      
Sbjct: 287  YVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHP 346

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ++   +  + +P+  +N          M  + +   + +  ++                 
Sbjct: 347  SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM-------------- 390

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 391  -------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 437

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +
Sbjct: 438  DSVIMNQSSIDHGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDK 493

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   +  G           K+  ++ D      R++          ++     +  Q 
Sbjct: 494  LDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQV 553

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        LR VKV +   +  Q GDK A RHG KG +  
Sbjct: 554  LL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGI 593

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF K+G   D+++NP  +PSRM +  + E  L       G +           
Sbjct: 594  TYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------- 644

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     ++++ +
Sbjct: 645  --------------------------------------------ATP-FTEVTVDSVSKL 659

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            LR       G  ++Y+G TG      V +G  Y  +
Sbjct: 660  LREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 695


>gi|55583684|gb|AAV53361.1| RNA polymerase II second largest subunit [Flammulina velutipes]
          Length = 691

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 125/821 (15%), Positives = 240/821 (29%), Gaps = 146/821 (17%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ R +    +              +  + + + +     +             
Sbjct: 1    FRMLFRKLTRDVYRYLQKCVETRKEFNVNVGVKHQTITNGLKYSLATGNWGDQKKSMSSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L   + ++   +       + +  + +         EEN +     + +  +G 
Sbjct: 117  CGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSTTPCTKVFVNGV 168

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            +       R     +   ++     D SP+  +             D  RV     +   
Sbjct: 169  WMG---VHRDPANLVKTIKKLRRKDDISPEVSLVRDIREKELRLYTDPGRVCRPLFIVEN 225

Query: 700  AVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
               +L+ +   ++  G +    +     +   + GI+E +DA       +    D   + 
Sbjct: 226  QQLVLQKKHVKWIVRGSDDDGQEYKWEQL--IKTGIIELLDAEEEETVMISMSPDDLETS 283

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +    +    +        R  +K G            PS  LG       +  + +P+
Sbjct: 284  RNQQSGLDTHTNEGEFDPAAR--LKAGVNAHTWTHCEIHPSMILG-------ICASIIPF 334

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N                        ++       +G       I             
Sbjct: 335  PDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM----------- 365

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S V   
Sbjct: 366  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRG 425

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S     E+ E   RD          +       I  G      
Sbjct: 426  LF-RSIYYRSYMDVEKKSGVQALEEFEKPQRDTTLRMKHGTYDKLEDDGLIAPGTGVRGE 484

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 485  DIIIGKTAPIPPDSEELGQRTRLHTRRDVSTPLKSTESGIIDQVLI-------------- 530

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q+GDK A RHG KG +      EDMPF  +G   
Sbjct: 531  ------TTNAEGQKFVKVRVRATRIPQTGDKFASRHGQKGTIGITYRQEDMPFTCEGIVP 584

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      +G +  +                        
Sbjct: 585  DIIINPHAIPSRMTIGHLVECLLSKVATLIGHEGDATPFT-------------------- 624

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  ++     + LR       G+ V                         G +    
Sbjct: 625  -----DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGHT---- 653

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               G      V +G  Y  +L HMV DK+++R+ G   ++T
Sbjct: 654  ---GRKLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQILT 691



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 83/602 (13%), Positives = 162/602 (26%), Gaps = 99/602 (16%)

Query: 376 DIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           D+YR + +  +                 +        G      +         + + + 
Sbjct: 11  DVYRYLQKCVETRKEFNVNVGVKHQTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRY 70

Query: 435 DIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
              + +  L        R GK       +  +  +    E  + Q    +  +       
Sbjct: 71  TYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCIS 130

Query: 490 ISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           + S     +             NA         F     +    +  N +  I   RR  
Sbjct: 131 VGSYSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKD 190

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +            +   ++        P    E   + L      +  +      +   
Sbjct: 191 DISPEVSLVRDIREKELRLYTDPGRVCRPLFIVENQQLVLQKKHVKW--IVRGSDDDGQE 248

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL------- 655
            K      T  +  L A EEE   I+ +   L+   +    L      GE          
Sbjct: 249 YKWEQLIKTGIIELLDAEEEETVMISMSPDDLETSRNQQSGLDTHTNEGEFDPAARLKAG 308

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V        +  P  ++ I AS+IPF +++ S R      M +QA+ +            
Sbjct: 309 VNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI----- 363

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                                  + + +  Y       +     
Sbjct: 364 ------------------------------------RMDTMANILYYPQKPLATTRSMEY 387

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +  R                        +L  G+N +VA + + GYN EDS+++++  V 
Sbjct: 388 LKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSVD 423

Query: 836 EDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNP 890
             +F SI+   +  + + +     EE  +        +       +++ G+I  G  V  
Sbjct: 424 RGLFRSIYYRSYMDVEKKSGVQALEEFEKPQRDTTLRMKHGTYDKLEDDGLIAPGTGVRG 483

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P         ++        +    RD S  + S  SG +  V I      
Sbjct: 484 EDIIIGKTAPIPPDSEELGQRT-------RLHTRRDVSTPLKSTESGIIDQVLITTNAEG 536

Query: 951 DK 952
            K
Sbjct: 537 QK 538


>gi|45545331|gb|AAS67513.1| DNA-dependent RNA polymerase II second largest subunit [Hydnum
            repandum]
          Length = 887

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 132/872 (15%), Positives = 246/872 (28%), Gaps = 146/872 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 147  RYAQEILQKEMLPHVSMGEGSESKK---AFFFGYMIHRLLLAALERRELDDRDHFGKKRL 203

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L + +R+   ++ + +   +               + +  + + +     +   
Sbjct: 204  DLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHKDFNISIAVKSNTITNGLKYSLATGNW 263

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 264  GDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKPRQLHNTHWGMV 319

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  A ++  G +  P  +         +   +A    +     
Sbjct: 320  CPAETPEGQACGLVKNLSLMACIS-VGSLSAPVIEFLQEWGLESLE-ENANAHGSATKVF 377

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
             N            LV                   D S +  +             D+ R
Sbjct: 378  VNGVWMGVHRDAPNLVKTLRRLRRKD---------DISSEVSIVRDIREKELRLYTDAGR 428

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            V     +      LLK E       +               + G++E +DA       + 
Sbjct: 429  VCRPLFIVENQQLLLKKEHV---NMLNDKSRTDPYKWTHLVKDGVIELLDAEEEETVMIC 485

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
               D   +           R+NQ         V  G          D  +     +    
Sbjct: 486  MTPDDLEN----------SRTNQA--------VAAGYVSNAGASDHDVAARVRSTMTAHT 527

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
                   P         + I   ++            ++       +G       +    
Sbjct: 528  WTHCEIHPSM------ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRM-- 579

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +    AI      +  D+ +
Sbjct: 580  ---------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVI 630

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +   +    ++ R   D  ++   +  E+ E   RD                  I
Sbjct: 631  MNQSSIDRGLF-RSMYYRSYTDAEKKVGVLPLEEFEKPTRDTTLRMKHGTYEKLEDDGLI 689

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  L  D                +E  QR     +    T     
Sbjct: 690  APGTGVAGEDIIIGKTAPLPPD---------------SEELGQRMRTHTRRDVSTPLKST 734

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E+   +++      D +     + VK+ +   R  Q GDK A RHG KG V      EDM
Sbjct: 735  ENGIVDQVLVTTNQDGL-----KFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDM 789

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   DI++NP  +PSRM +G + E  L      +G +                  
Sbjct: 790  PFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGD---------------- 833

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                 +TP F     E+++ +LR     
Sbjct: 834  -------------------------------------ATP-FTELTVESVSQLLRENGYQ 855

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G  ++Y G +G      V +G  Y  +L H
Sbjct: 856  SRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887



 Score =  140 bits (353), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 99/772 (12%), Positives = 219/772 (28%), Gaps = 113/772 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +P+     ALG+ S+ +IL         +Q  +     +    ++   +V+
Sbjct: 72  YIRDD----IPIWVVFRALGITSDRDILEHICYDTNDTQMVEMLKPCIDEGFVIQEREVA 127

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L+        +   K+L     + L+++ +  + +              +      + 
Sbjct: 128 LDLIGKRGTTTGLSKDKRLRYAQ-EILQKEMLPHVSMGEGSESKKAFFFGYMIH---RLL 183

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  +    +      +    P+L          +   +     K  +        +
Sbjct: 184 LAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHKDFNISI 243

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   S  G  ++  R    +      R         
Sbjct: 244 AVKSNTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNTPLGRDG 303

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +  +   + E +    ++S+
Sbjct: 304 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLQEWGLESL 363

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 +     SA   F     +    +  N +  +   RR   +            + 
Sbjct: 364 EENANAH----GSATKVFVNGVWMGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIREKE 419

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             ++        P    E   + L     +   +N     +    K         +  L 
Sbjct: 420 LRLYTDAGRVCRPLFIVENQQLLLKKEHVNM--LNDKSRTDP--YKWTHLVKDGVIELLD 475

Query: 619 AMEEENRYIAQANSSLDE-------------DGSFTEELVFCRCAGEEILVPREKIDFID 665
           A EEE   I      L+              +   ++  V  R       +        +
Sbjct: 476 AEEEETVMICMTPDDLENSRTNQAVAAGYVSNAGASDHDVAARVR---STMTAHTWTHCE 532

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R      M +QA+ +                      
Sbjct: 533 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQV--------------- 577

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + +  Y       +     +  R      
Sbjct: 578 --------------------------RMDTMANILYYPQKPLATTRSMEYLRFR------ 605

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N  VA + + GYN EDS+++++  +   +F S++  
Sbjct: 606 ------------------ELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYR 647

Query: 846 EFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +    +   + P E            +     + +++ G+I  G  V   DI++GK  P
Sbjct: 648 SYTDAEKKVGVLPLEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGVAGEDIIIGKTAP 707

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    +++       +    RD S  + S  +G V  V +       K
Sbjct: 708 LPPDSEELGQRM-------RTHTRRDVSTPLKSTENGIVDQVLVTTNQDGLK 752


>gi|269913261|emb|CAY86057.1| RNA polymerase beta subunit [Gluconacetobacter diazotrophicus]
          Length = 293

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 141/296 (47%), Positives = 185/296 (62%), Gaps = 28/296 (9%)

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL-- 221
            FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL  
Sbjct: 1   FFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEG 60

Query: 222 -----------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                                  GMD++EIL  FY ++V+++    W  P  A     G 
Sbjct: 61  ASSAAARAAKVAEGGDVDALEIRGMDADEILGYFYNQVVFTKGPKGWARPFDAE-SFRGL 119

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
           K+   LVD  +GE V E+  KLT+ +++ + E   K + +    L G YVA D+VN ETG
Sbjct: 120 KLLEPLVDAQSGEVVAEADAKLTARMVRKIAET-TKEVLVGPAGLIGRYVAHDLVNMETG 178

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           EIY EAG+ + E  LE +  + +  +P L VD+ N   +IRNTL  DKN  R+DAL DIY
Sbjct: 179 EIYAEAGEELTEARLEALEEAGVDQLPTLAVDASN-GPWIRNTLTVDKNTSREDALTDIY 237

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           RVMRPG+  T   AE+MF+ LFFD+D+YDLS VGRVKMNMRL LD PD +R +RKE
Sbjct: 238 RVMRPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKMNMRLGLDAPDTIRVLRKE 293


>gi|46370308|gb|AAS89953.1| RpoB [Bartonella rattimassiliensis]
          Length = 291

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 212/291 (72%), Positives = 245/291 (84%), Gaps = 1/291 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTREVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSN
Sbjct: 242 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSN 291


>gi|260594189|gb|ACX46389.1| RNA polymerase beta subunit [Pantoea sp. 1378/07]
          Length = 285

 Score =  273 bits (699), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 171/285 (60%), Positives = 219/285 (76%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           +V DG V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D+
Sbjct: 121 RVIDGVVSDEIHYLSAIEEGNYVIAQANAQLDENGGFVDDLVTCRSKGESSLFSRDQVDY 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 181 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           G   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ 
Sbjct: 241 GVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYT 285


>gi|83763759|emb|CAJ00213.1| putative DNA-directed RNA polymerase, beta subunit [Vibrio sp. 12F08]
          Length = 307

 Score =  273 bits (698), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 171/318 (53%), Positives = 227/318 (71%), Gaps = 13/318 (4%)

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            GTG+E  VA  SG   VAKR G V+ VDA RIVI+  E +L P  +G+DIY L K+ RSN
Sbjct: 1    GTGIERNVAVDSGVTAVAKRGGTVQSVDASRIVIKVNEDELIPGEAGIDIYNLTKYTRSN 60

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            QNTC+NQRP V  G+ V R D++ADGPSTDLG+LALG+NM +AFMPW+GYNFEDS+L+SE
Sbjct: 61   QNTCINQRPTVLPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSE 120

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            R+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E  L  +DE GI+ +GAEV  G
Sbjct: 121  RVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGG 180

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            DILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP+ VSGT++DV++F R G++
Sbjct: 181  DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVE 240

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L                  S  
Sbjct: 241  KDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLLQGG-------------YSDA 287

Query: 1012 LISEYPRSQWWQFAVQDE 1029
             +    R +W +  ++D+
Sbjct: 288  KLDTIDRKKWLELTLEDD 305


>gi|303388613|ref|XP_003072540.1| DNA-directed RNA polymerase subunit B [Encephalitozoon intestinalis
            ATCC 50506]
 gi|303301681|gb|ADM11180.1| DNA-directed RNA polymerase subunit B [Encephalitozoon intestinalis
            ATCC 50506]
          Length = 1047

 Score =  273 bits (698), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 90/349 (25%), Positives = 144/349 (41%), Gaps = 73/349 (20%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMP--PGVLRVVKVF------------VAMKRPIQSGD 1088
            +  K  +  ++ +  ++      +    GV+  V+VF            + M R    GD
Sbjct: 744  KIQKDSILYKYVDLEDREYQTRYLETEDGVIDSVRVFESDAGERCALLTIRMVRNPTIGD 803

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K + RHG KG+ S   P  DMPF + G   DI++NP   PSRM +G + E+  G      
Sbjct: 804  KFSSRHGQKGVCSVHWPSIDMPFTESGYVPDIIINPHAFPSRMTIGMLMESIAGKVGCLS 863

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G        +                        + +S  +D+  +              
Sbjct: 864  GNTQDGTAFE------------------------KNLSQGEDEETVG------------- 886

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                   +E I S L+    +  G   +Y G++G  F   V VG +Y  +L HMV DK  
Sbjct: 887  ------RKEYICSELQKYGFNYYGNEPMYSGVSGNEFRVDVFVGVVYYQRLKHMVGDKFQ 940

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
             R+ G+    T+QP+GG+  +GG R GEME   + ++GA+++LQ+ L   SD   G T  
Sbjct: 941  VRTKGAIVSTTRQPVGGRKRQGGIRFGEMERDTLISHGASHLLQDRLLKCSD---GTTFE 997

Query: 1329 Y----ESI--------VAG-NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            Y    +SI        + G +D      P  F  L  E+ A+ + + L+
Sbjct: 998  YCGACKSILFTSSGDCICGSSDIRIVEMPYVFKYLCYELLAMNIRVKLD 1046



 Score = 51.6 bits (122), Expect = 0.001,   Method: Composition-based stats.
 Identities = 93/664 (14%), Positives = 184/664 (27%), Gaps = 135/664 (20%)

Query: 90  DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-------- 141
           +C  R LTY   + I + L   +    T  K            G  P+M +         
Sbjct: 68  ECRERGLTYKGKIIIRISLFHDNKHIMTEDKLA----------GYFPIMVRSSLCHLRNA 117

Query: 142 --------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS----LSGKL--LYA 181
                         G F+I G  + +     R     F   + R       + K    + 
Sbjct: 118 KNMNKVGEDEDEVGGYFIINGFDKFI-----R-----FTITQKRNHIFAFKTRKRESFFT 167

Query: 182 CRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLMALGMDSEEILS 230
              +  + +  D E    + ++        +++  RR     P+   L AL   ++E L 
Sbjct: 168 GYGVSMRCVGKD-EIGHMNNLYYCTDGNVVLKMYYRRSEFFFPLVLILRALVNTTDEEL- 225

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
             Y  +   +R        +  ++    +    +    +      S  ++   +L     
Sbjct: 226 --YEALGQGERAIHLLKCFAEYNVFSRKECLDYIGSRFSSMANFGSKIEVAEEILSKYIA 283

Query: 291 KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
             +       + L     A+ + +    EI  E  D      L          +      
Sbjct: 284 SHLSSHLDKFNFLI--LAAKKLFSFVNNEIAEEDFDSSGNHELHTTTQILSSLLR----- 336

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
                  I   + +     +K  L       R  + S   V + ++          ++  
Sbjct: 337 -----DKIEEFMRSLPIAYKKAYLKSEGEKRRLEEDSDSEVVDGIYEDKLDILKIKEIFK 391

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
              + +  ++ L        +     I        L       +     GN R  + G  
Sbjct: 392 KAVMNIGQKVELFLSSGNIFLSCCSDI---LQTTGLSITLERTNFYRYFGNLRSINRGTH 448

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           + +                     I  + P+      PV +                   
Sbjct: 449 IPSL-----------------VTRIRKLRPESWGFICPVHTPDGACCG------------ 479

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG-RICPAETSEGHNIGLVSSLTSF 589
               + H  + + +           +    V PT  G R+      +G  IG  SS    
Sbjct: 480 ---VLLHMAKGADIVSRANDFDTEILFELGVVPTIRGVRMEVPVLVDGKVIGSTSSPQFL 536

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+           KV +     ++VY      E   +  +       G F  +++  R 
Sbjct: 537 VRM-------LREYKVKNRLKI-EIVY-----SEGTKVFSSVCIFSSMGRFIRKVMNQRL 583

Query: 650 AGEEILVPREKI-----------DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
             EE +   E++           D+ +     ++ I A L P+ E++ S R +  C M +
Sbjct: 584 GSEEWVGIMEQVSLNIDLERGEGDYHEIDKSNILGIIAGLTPYSEHNQSPRNMYQCQMAK 643

Query: 699 QAVP 702
           QA+ 
Sbjct: 644 QAMG 647


>gi|307343502|emb|CBJ18668.1| RNA polymerase B subunit [Micromonospora sp. SG2]
          Length = 226

 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 103/228 (45%), Positives = 134/228 (58%), Gaps = 39/228 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++     +K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAAWKKQLRSID---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEPDTNVATPVFDGAREEEISGLLSSTLPNRDGKQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V D+   RSTG YS+
Sbjct: 180  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVDDRSR-RSTGPYSM 226


>gi|108885399|gb|ABG23216.1| DNA-directed RNA polymerase [Geobacillus caldoproteolyticus]
          Length = 145

 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 67/167 (40%), Positives = 102/167 (61%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  FK + PI  F+G   LEFV Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFAGNLSLEFVDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYSVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++    G+   +GK  ++  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGFSATVIPNRGAW 145


>gi|9501921|gb|AAF87946.1| RNA polymerase beta-subunit [Helicobacter pylori]
          Length = 230

 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 92/234 (39%), Positives = 149/234 (63%), Gaps = 5/234 (2%)

Query: 65  ITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS-IK 123
           I        LE+   EF   K+ V + + R +TY++PLKI +RLI+++ D  +G K+ IK
Sbjct: 1   IQDEHTRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIK 60

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           DIKEQSI++ ++PLMT+  +F+I G++R+V +QLHRSPG+ F  ++   SL+ KL+Y  +
Sbjct: 61  DIKEQSIFIREIPLMTERTSFIINGVERVVFNQLHRSPGVIFKEEESSTSLN-KLIYTGQ 119

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
           IIPD+G W+  E+DSKD+++ RI++RRKVPVT    A+    ++I+  FYP +      D
Sbjct: 120 IIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYEND 179

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
            +  P ++ D     ++   L D   G+ ++ +GKKLTS  +K LKE  ++++ 
Sbjct: 180 KYLIPFASLD--ANQRMEFDLKDPQ-GKVILLAGKKLTSRKIKELKENHLEWVE 230


>gi|145338664|ref|NP_188437.2| NRPD2b; DNA binding / DNA-directed RNA polymerase/ ribonucleoside
            binding [Arabidopsis thaliana]
          Length = 1055

 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 119/316 (37%), Gaps = 69/316 (21%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 782  VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 841

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 842  LLEAALSKGIAC-------------------------------------PIQKKEGSSAA 864

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 865  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSLIFMGPTF 919

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  +KV  R+TG    +T+QP+  +   GG R GEME  C+ A+GA+  L E L
Sbjct: 920  YQRLVHMSENKVKFRNTGPVHPLTRQPVADRKRFGGIRFGEMERDCLIAHGASANLHERL 979

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 980  FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCASSDHVVRVYVPYGAKLL 1037

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 1038 CQELFSMGITLNFDTK 1053



 Score =  112 bits (280), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 127/899 (14%), Positives = 258/899 (28%), Gaps = 188/899 (20%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDV-----------DEFTGAKSIKDIKEQSIYMGDLPLMT 139
           C  +++TY+  +K+  ++ VF              +    K I D+K+Q I +G +P+M 
Sbjct: 3   CRLQNMTYSARIKVNAQVEVFKKIVIKHDKFKTGQDEYVEKEILDVKKQDILIGSIPVMV 62

Query: 140 KD-----------------------GTFVIKGIQRIVVSQLHR---------SP-GIHFD 166
           K                        G FVIKG +++ ++Q            SP  + F 
Sbjct: 63  KSVLCKTSEKGKENCKKGNCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWISNSPWTVSFR 122

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK---DIIHVRIDRRRKVPVTSFLMALGM 223
            +  R           R I  +    +   D K    ++ V       +PV     ALG+
Sbjct: 123 SETKRN----------RFI-VRLSENEKAEDYKIMEKVLTVYFLSTE-IPVWLLFFALGV 170

Query: 224 DSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
            S+ E +             D        A +     V  +    +     +E   K T 
Sbjct: 171 SSDKEAMDLI-----AFDGDDASITNSLIASIHEADAVCEAFRCGNNALTYVEHQIKSTK 225

Query: 283 GLLKSLKEKGVKFLGIT-------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
                  +  ++                 G  V   +++   G+   E  D    K +E 
Sbjct: 226 FPPAESVDDCLRLYLFPCLQGLKKKARFLGYMVKC-LLSAYAGKRKCENRDSFRNKRIEL 284

Query: 336 IFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                 R+I + L          ++  L  D +    +  LD   +    + +  + A S
Sbjct: 285 AGELLEREIRVHLAHARRKMTRAMQKQLSGDGDLKPIEHYLDASVITNGLNRAFSTGAWS 344

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
                        ++ +GR      L        + +     +   +       G+    
Sbjct: 345 HPFRKMERVSG-VVANLGRANPLQTLIDLRRTRQQVL-YTGKVGDARHPHPSHWGRVCFL 402

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
              +  N  +     +L      GL  +   +        ++          K +     
Sbjct: 403 STPDGENCGLVKNMSLLGLVSTQGLESVVEMLFTCGMEELMNDTSTPLCGKHKVL----- 457

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAE 573
                  +    +  + +  +   RR S L  +  + R +   E+R              
Sbjct: 458 --LNGDWVGLCADSESFVGELKSRRRQSELPLEMEIKRDKDDNEVR------------IF 503

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T  G  +  +  + +  ++      + P++ + D  +                       
Sbjct: 504 TDAGRLLRPLLVVENLHKLKQDKPTQYPFKHLLDQGIL---------------------- 541

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  G   EE        +++L   +     +     ++ ++ +++PF  +D   RVL  
Sbjct: 542 -ELIGIEEEEDCTTAWGIKQLLKEPKNYTHCELDLSFLLGVSCAIVPFANHDHGKRVLYQ 600

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                                               K         +    IR       
Sbjct: 601 SQ----------------------------------KHCQQAIGFSSTNPNIRCD----- 621

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                            +Q     Q+PL K                 +   L  G+N +V
Sbjct: 622 ---------------TLSQQLFYPQKPLFK----------TLASECLEKEVLFNGQNAIV 656

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-----RDTKLGPEEITRDIPNV 868
           A     GYN EDS+++++  +   +F S  I  ++           K   E +       
Sbjct: 657 AVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDTKDSEKRKKMDELVQFGKTYS 716

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
               + ++++ G   +GA ++ GDI++G+ T  G       +   R I  +  +   D 
Sbjct: 717 KIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDE 775


>gi|269930887|gb|ACZ54178.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930899|gb|ACZ54184.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930901|gb|ACZ54185.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 289

 Score =  273 bits (698), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 210/290 (72%), Positives = 244/290 (84%), Gaps = 1/290 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           + SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 RDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 289


>gi|227937620|gb|ACP43385.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 290

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 211/290 (72%), Positives = 244/290 (84%), Gaps = 1/290 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 242 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 290


>gi|183989083|gb|ACC66099.1| RpoB [Mycobacterium kansasii]
          Length = 203

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 93/225 (41%), Positives = 126/225 (56%), Gaps = 40/225 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 11   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 70

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW C   G +I+          +        +  
Sbjct: 71   TPVDIILNTHGVPRRMNIGQILETHLGW-CAHSGWQIEGSPEWAANLPEALRSAEPNQI- 128

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  +  +L     D      
Sbjct: 129  ------------------------------VSTPVFDGAQEAELQGLLSSTLPDRDGDVL 158

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                G+++L+DG +GEPF  PVTVG++Y++KL+H+V DK++ARST
Sbjct: 159  VDGDGKAVLFDGRSGEPFPYPVTVGFMYIMKLHHLVDDKIHARST 203


>gi|109289916|gb|ABG29322.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative [Solanum
            bulbocastanum]
          Length = 304

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 118/313 (37%), Gaps = 76/313 (24%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   E+ PF   G   DIV+NP   PSR   GQ
Sbjct: 44   VNLEHVRSPCLGDKFSSMHGQKGVLGYLESQENFPFTVQGIVPDIVINPHAFPSRQTPGQ 103

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  LG   + LG                                              
Sbjct: 104  LLEASLGK-GIALG---------------------------------------------- 116

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                   G   +TP F     +AI   L        G   +Y+G TGE     + +G  +
Sbjct: 117  ------GGEKYATP-FSTLSVDAILKQLHGRGFSRWGNERVYNGRTGEMVHSLIFMGPTF 169

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L
Sbjct: 170  YQRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERL 229

Query: 1316 TIKSD----DVVGRTRVYESI---------VAG---------NDTFETGTPESFNVLVKE 1353
               SD     + G+ +   ++         + G          D  +   P    +L +E
Sbjct: 230  FTLSDSSQMHICGKCKNMANVIQRSAPGGKIRGPFCRFCESVEDIVKVDVPYGAKLLCQE 289

Query: 1354 MQALGLSIDLENS 1366
            + ++G+S+  +  
Sbjct: 290  LFSMGISLKFDTE 302


>gi|255548744|ref|XP_002515428.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis]
 gi|223545372|gb|EEF46877.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis]
          Length = 1203

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 98/511 (19%), Positives = 166/511 (32%), Gaps = 93/511 (18%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L  P    G      I  + 
Sbjct: 749  KHSQQAIGFPTTNPNIRVDTLSHQLYYPQRPLFRTVTSDCLGKPGDTRG---HNGIVPKP 805

Query: 949  GIDKNERSISVEREQIELLARD-KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
             +   + +I      +     D     +  L+R ++ R   I   +  V   +   K   
Sbjct: 806  ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMF-RSEHIRSYKADVDNKELLDKRRK 864

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED---RFKNKIEKIQWG- 1063
               ++      S+  +    D+     + +     +       +       K++  + G 
Sbjct: 865  YDDNVNFGKIPSKIGRVDSLDDDGFPFIGANLQSGDIVIGRCAESGPDHSIKLKHTERGM 924

Query: 1064 ------DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                       G    V V +   R    GDK +  HG KG++  +   E+ PF + G  
Sbjct: 925  VQKVVLSSNDEGKNFAV-VSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTRQGIV 983

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             DIV+NP   PSR   GQ+ E  LG      G                            
Sbjct: 984  PDIVINPHSFPSRQTPGQLLEAALGKGIACGGS--------------------------- 1016

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                      +  +TP F     EAI + L  A     G   +Y
Sbjct: 1017 --------------------------MKYATP-FSTLSVEAITNQLHRAGFSRWGNERVY 1049

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            +G TGE     + +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GEM
Sbjct: 1050 NGRTGEMVRSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEM 1109

Query: 1298 EVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESI----------VAG-------- 1335
            E  C+ A+GA+  L E L   SD     +  + +   ++          + G        
Sbjct: 1110 ERDCLIAHGASANLHERLFTLSDSSQMHICQKCKNVANVIQRAVPGGRKIRGPYCRVCES 1169

Query: 1336 -NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
             ++  +   P    +L +E+ ++G+S+  E 
Sbjct: 1170 VDEIVKVNVPYGAKLLCQELFSMGISLKFET 1200



 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 129/956 (13%), Positives = 261/956 (27%), Gaps = 213/956 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+          N G+Q AF S     V P    S         A ++F
Sbjct: 76  LISHQINSYNDFI----------NNGIQKAFDSFGELVVEPGYDPSKKGENEWRYASVKF 125

Query: 77  VSYEFDPPKFD---------VDDCLWRDLTYAVPLKITLRLIVFD---VDEFTGAKSIKD 124
                + P F                +++TY+  +K+ + + V+    V           
Sbjct: 126 GKVALEKPTFWSGADEHKMLPRHARLQNMTYSSKMKVNVSVEVYTRKVVRSDKFKTGKDQ 185

Query: 125 IKEQSIY--------MGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
             ++ +         +G LP+M K                   G F+IKG +++ ++Q  
Sbjct: 186 YVDKEVLNTDNRNITIGSLPVMVKSDLCWMKTAEKGDCDFDHGGYFLIKGAEKVFIAQEQ 245

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQ------G-LWMDIEFDSKDIIHVRIDRRRK 211
               I              + Y   I  ++      G   ++     K  + V       
Sbjct: 246 ----ICLKRLWISNIQGWTVSYKSEIKRNRLIVRLVGLSALEDVKAEKKCLTVYFLSTE- 300

Query: 212 VPVTSFLMALGMDSEE--------------ILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           +P+     ALG+ S++              I++ F+  I  +            A   V 
Sbjct: 301 IPLWILFFALGVTSDKEVIDLIGYGSNDARIVNIFFASIHDADEKTEGFRRGKEALEYVV 360

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            ++  +       E         T   L+         +        G     +  +   
Sbjct: 361 RQIRGTRFPPGENEDFFLLYLFPTLHSLRQKARFLGYMVKCLLQAYNGQR-KCNNWDSFR 419

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD--------KNKD 369
            + +  A ++++ +    I H+  R    L  D   +          D            
Sbjct: 420 NKRFELAKELLERELKVHIAHARRRMAKALQKDLYGDRDVRPIEHYLDASIVTNGLSRAF 479

Query: 370 RKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
              A    Y+ M    G V+    A  +   +     +Y +   G+V            D
Sbjct: 480 STGAWSHPYKRMERISGVVANLGRANPLQTMVDLRKTRYHVQYTGKVG-----------D 528

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
            R         +  +        G + ++   G   V  +  ++      G+ ++     
Sbjct: 529 ARFPHPSHWGRVCFLSTPDGENCGLVKNLATTGLVSVNILEPLIDKLIARGMEKVPEDSH 588

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
             +   D                     F     +   E+    ++ +          + 
Sbjct: 589 SDLDEKDK-------------------VFLNGEWVGVCEDSRLFVAELR-------RLRR 622

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                +     RD           A       + + +     A        ++   K   
Sbjct: 623 RKKLPQQVEIKRDEQQQEVRIFSDAGRILRPLLVVQNLHKIEAFKGGNCTFQSLLDK--- 679

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 + ++   EEE+   A         G   ++ +              K    +  
Sbjct: 680 ----GIIEFVGTEEEEDCSTA-WGIKFLLSGVDGKQSL--------------KYTHCELD 720

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
              ++ ++  +IPF  +D + RVL       Q                            
Sbjct: 721 MSFLLGLSCGIIPFANHDHARRVLYQAQKHSQQAIGFPT--------------------- 759

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                              +       + S    Y      R+  + C+           
Sbjct: 760 -------------------TNPNIRVDTLSHQLYYPQRPLFRTVTSDCLG---------- 790

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +  D           +L  G+N +VA     GYN EDS++++   +   +F S HI  +
Sbjct: 791 -KPGDTRGHNGIVPKPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSY 849

Query: 848 EVMARDTKLGPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +    + +L  +    D              + ++D+ G   +GA +  GDI++G+
Sbjct: 850 KADVDNKELLDKRRKYDDNVNFGKIPSKIGRVDSLDDDGFPFIGANLQSGDIVIGR 905


>gi|227937588|gb|ACP43369.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 290

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 212/290 (73%), Positives = 245/290 (84%), Gaps = 1/290 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 2   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 61

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 62  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 121

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 122 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDH 181

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 182 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 241

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 242 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 290


>gi|163785806|ref|ZP_02180292.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
 gi|159878925|gb|EDP72943.1| RNA polymerase beta subunit [Hydrogenivirga sp. 128-5-R1-1]
          Length = 355

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 206/350 (58%), Positives = 264/350 (75%), Gaps = 4/350 (1%)

Query: 659  EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            E++DF+D SPKQVVS++ASLIPFLE+DD+NR LMG NMQRQAVPLLK E P  GTG+E +
Sbjct: 1    EEVDFMDVSPKQVVSVSASLIPFLEHDDANRALMGSNMQRQAVPLLKTEYPLAGTGIERI 60

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE---GDLDPSTSGVDIYRLMKFQRSNQNTC 775
            VAK+SG+A+VA+R GIVE V   +IVI+  +    + DP   G+D+Y+L KF+ SNQ TC
Sbjct: 61   VAKNSGSAVVAERGGIVESVSGNKIVIKVNKEEINENDPLDIGIDVYKLKKFKGSNQATC 120

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +NQRPLVK GD V    IIADGPST  G+L+LG+N+LVAFMPW GYNFED+++ISER+V 
Sbjct: 121  INQRPLVKKGDVVEAGAIIADGPSTYKGELSLGKNVLVAFMPWRGYNFEDAIVISERLVK 180

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +DVFTSIHIEEF+V AR+TKLG EEITR+IP +SE+ L N+DE GI+ VGA V PGDILV
Sbjct: 181  DDVFTSIHIEEFDVEARETKLGSEEITRNIPGISEKALANLDEHGIVRVGAYVKPGDILV 240

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID-KNE 954
            GK+TPKGE+  TPEEKLL AIFGEKA DV+D+SLRVP+GV G V+DV++F R   D KN 
Sbjct: 241  GKVTPKGETQPTPEEKLLLAIFGEKASDVKDSSLRVPAGVEGIVIDVQVFARKKADRKNA 300

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
                + +E+IE L ++ +D++  +       L +++ G       K   K
Sbjct: 301  YLDKLIKEEIEELEKELEDKKRFIQERRDEELKKVILGAEISKDVKLAGK 350


>gi|103001706|gb|ABF71518.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 695

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 116/815 (14%), Positives = 236/815 (28%), Gaps = 145/815 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +    +         + +  + + +     +      
Sbjct: 2    GPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  +
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                 N+   ++ +  L+ +               S     AK  G    V     V+  
Sbjct: 238  STNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVEY 287

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLA 806
            V+ + + +   V     ++  R  Q           +   V+          T      +
Sbjct: 288  VDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMNPTAHTWTHCEIHPS 347

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            +   +  + +P+  +N          M  + +   + +  ++                  
Sbjct: 348  MILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM--------------- 390

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 391  ------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 438

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L
Sbjct: 439  SVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKL 494

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  ++ D      R++          ++     +  Q  
Sbjct: 495  DDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVL 554

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                       LR VKV +   +  Q GDK A RHG KG +   
Sbjct: 555  L--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 594

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF K+G   D+++NP  +PSRM +  + E  L       G +            
Sbjct: 595  YRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------- 644

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     ++++ +L
Sbjct: 645  -------------------------------------------ATP-FTEVTVDSVSKLL 660

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            R       G  ++Y+G TG      V +G  Y  +
Sbjct: 661  REHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 695


>gi|227937598|gb|ACP43374.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 289

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 211/290 (72%), Positives = 244/290 (84%), Gaps = 1/290 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 289


>gi|185179206|gb|ACC77616.1| RpoB [Mycobacterium gordonae]
          Length = 218

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 92/224 (41%), Positives = 126/224 (56%), Gaps = 40/224 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 27   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+   +                  
Sbjct: 87   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGAPDWAAN-------------- 131

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +            VSTPVFDGA EE +  +L            
Sbjct: 132  -----------------LPEDLRHAAPNQIVSTPVFDGAKEEELQGLLSCTLPNRDGDVM 174

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            ++  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK++ARS
Sbjct: 175  VNGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARS 218


>gi|90399221|emb|CAJ86030.1| B0414F07.4 [Oryza sativa Indica Group]
          Length = 1343

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 107/613 (17%), Positives = 181/613 (29%), Gaps = 101/613 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT-----SIHIEE 846
              +      +   +    ++  A+   + +  E+   + +   +EDVF         +  
Sbjct: 792  QWLMQQEIIEFIGVEEEEDIRSAWGIRNLFESEEEAPMVKMNKAEDVFNVKRKIGGEVSG 851

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     D           IP        N +    +   +E       +G  T      +
Sbjct: 852  YTHCELDLSFLLGLSCGIIP------FANHNFARRVLYQSE-KHSQQAIGYSTTNPHIRV 904

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
                  L          V    +   S  +    D      +   +N        +    
Sbjct: 905  DTLSHQLYYPQRPLFKTVIADCIG-RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQ 963

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  +   +      +        +    G  G  K   +   +     +S+  +   
Sbjct: 964  EDSLVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDN 1023

Query: 1027 QDEKVQRNVESLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKV 1076
             D+     V +     +      S   +    K++  + G            G    V V
Sbjct: 1024 LDDDGLPYVGASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-V 1082

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+
Sbjct: 1083 TLRQVRSPCLGDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQL 1142

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  LG      G                                               
Sbjct: 1143 LEAALGKGIALGGT---------------------------------------------- 1156

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   +  +TP F  A  + I   L  A     G   + +G TGE     + +G  + 
Sbjct: 1157 -------MRYATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFY 1208

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L 
Sbjct: 1209 QRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLF 1268

Query: 1317 IKSD----DVVG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKE 1353
            + SD     V     R   V    V G                +      P    +L +E
Sbjct: 1269 MLSDFSQMHVCQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQE 1328

Query: 1354 MQALGLSIDLENS 1366
            + ++G+ +  E  
Sbjct: 1329 LFSMGICLRFETE 1341



 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 148/1026 (14%), Positives = 298/1026 (29%), Gaps = 236/1026 (23%)

Query: 14   RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
            R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 132  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 181

Query: 57   AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
              F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 182  ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 241

Query: 91   CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
               +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 242  ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 301

Query: 140  ----------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDK---GRASLSGKLLY 180
                              G F+IKG+++    +L    G  +  +    G+     + ++
Sbjct: 302  NLCWLHKLKESDCQFDSGGYFLIKGMEK---DELQGCGGKLYSRNLCLNGKLETPTQKVF 358

Query: 181  AC-------RI-IPDQGLWMDIEFDSKDIIHVRIDRRR-----------------KV--- 212
                     RI + D+  WM             I RRR                 K+   
Sbjct: 359  IAQEQKCLTRIWVEDRPCWMVSFLSP-------IRRRRIYIKLIDSANNEDASGGKIISI 411

Query: 213  -------PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                   P+     ALG+ S+ +I      +   +   +     +  +D +      S  
Sbjct: 412  SFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDK 471

Query: 265  VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYI 322
                  E +  S           + +     +          G  V   ++   TG+   
Sbjct: 472  ARQYVDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKC 530

Query: 323  EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
            +  D    K L+       R++   ++               +  ++ ++    +   + 
Sbjct: 531  DNKDDFRNKRLDLAGELLGRELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASII 589

Query: 383  PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
               ++      S  +    +     +    R    +++  D     + +         + 
Sbjct: 590  TNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARY 649

Query: 443  LVDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
                  GK   +   D      V+++        R+    ++R I   ++ +        
Sbjct: 650  PNPSYWGKLCFMSTPDGENCGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL-------- 701

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
              I  + V      F     +    +  + + R+   RR   +      +         V
Sbjct: 702  HEIPTEEVPRMDKIFLNGDWVGSCSDPASFVLRLRCMRRSGLIDPQVEIKWDKHQREVRV 761

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                   + P    E  N       +S++                       + ++   E
Sbjct: 762  FSDAGRILRPLLVVENLNKIRRPKGSSYS--------------FQWLMQQEIIEFIGVEE 807

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK------IDFIDASPKQVVSIA 675
            EE+   A    +L E       +V    A +   V R+           +     ++ ++
Sbjct: 808  EEDIRSAWGIRNLFES-EEEAPMVKMNKAEDVFNVKRKIGGEVSGYTHCELDLSFLLGLS 866

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
              +IPF  ++ + RVL                             K S  AI        
Sbjct: 867  CGIIPFANHNFARRVLYQSE-------------------------KHSQQAIGYSTTNPH 901

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             +VD                               +      QRPL     +    D I 
Sbjct: 902  IRVD-----------------------------TLSHQLYYPQRPL----FKTVIADCIG 928

Query: 796  DGPSTDLG-------DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                T          +   G+N +VA     G+N EDS++++   +   +F + H   ++
Sbjct: 929  RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQEDSLVMNRASLERGMFRTEHFRNYK 988

Query: 849  VMARDTKL--------GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
                +             ++I           + N+D+ G+  VGA +  GDI++GK++ 
Sbjct: 989  AEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVGASLQSGDIVIGKVSE 1048

Query: 901  KGESPM 906
             GE   
Sbjct: 1049 SGEDHS 1054


>gi|226934690|gb|ACO92419.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 227

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 94/224 (41%), Positives = 125/224 (55%), Gaps = 40/224 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++ARS
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARS 227



 Score = 40.8 bits (94), Expect = 1.6,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|108885361|gb|ABG23197.1| DNA-directed RNA polymerase [Geobacillus thermoleovorans subsp.
           stromboliensis]
 gi|108885363|gb|ABG23198.1| DNA-directed RNA polymerase [Geobacillus thermocatenulatus]
 gi|108885365|gb|ABG23199.1| DNA-directed RNA polymerase [Geobacillus lituanicus]
 gi|108885369|gb|ABG23201.1| DNA-directed RNA polymerase [Geobacillus thermoleovorans]
 gi|108885371|gb|ABG23202.1| DNA-directed RNA polymerase [Bacillus caldotenax]
 gi|108885373|gb|ABG23203.1| DNA-directed RNA polymerase [Bacillus caldolyticus]
 gi|108885375|gb|ABG23204.1| DNA-directed RNA polymerase [Geobacillus sp. S9]
 gi|108885377|gb|ABG23205.1| DNA-directed RNA polymerase [Bacillus caldovelox]
 gi|108885379|gb|ABG23206.1| DNA-directed RNA polymerase [Geobacillus sp. A83]
 gi|108885383|gb|ABG23208.1| DNA-directed RNA polymerase [Geobacillus gargensis]
 gi|108885385|gb|ABG23209.1| DNA-directed RNA polymerase [Geobacillus jurassicus]
 gi|108885387|gb|ABG23210.1| DNA-directed RNA polymerase [Geobacillus sp. S23]
          Length = 145

 Score =  273 bits (697), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 66/167 (39%), Positives = 101/167 (60%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAW 145


>gi|269930835|gb|ACZ54152.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 291

 Score =  272 bits (696), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 211/292 (72%), Positives = 246/292 (84%), Gaps = 1/292 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 SGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 291


>gi|145926498|gb|ABP98888.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926506|gb|ABP98892.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926512|gb|ABP98895.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926516|gb|ABP98897.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926518|gb|ABP98898.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
          Length = 257

 Score =  272 bits (696), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSMKALNEQGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|38344903|emb|CAD41847.2| OSJNBb0079B02.6 [Oryza sativa Japonica Group]
          Length = 1343

 Score =  272 bits (696), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 107/613 (17%), Positives = 181/613 (29%), Gaps = 101/613 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT-----SIHIEE 846
              +      +   +    ++  A+   + +  E+   + +   +EDVF         +  
Sbjct: 792  QWLMQQEIIEFIGVEEEEDIRSAWGIRNLFESEEEAPMVKMNKAEDVFNVKRKIGGEVSG 851

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     D           IP        N +    +   +E       +G  T      +
Sbjct: 852  YTHCELDLSFLLGLSCGIIP------FANHNFARRVLYQSE-KHSQQAIGYSTTNPHIRV 904

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
                  L          V    +   S  +    D      +   +N        +    
Sbjct: 905  DTLSHQLYYPQRPLFKTVIADCIG-RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQ 963

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  +   +      +        +    G  G  K   +   +     +S+  +   
Sbjct: 964  EDSVVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDN 1023

Query: 1027 QDEKVQRNVESLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKV 1076
             D+     V +     +      S   +    K++  + G            G    V V
Sbjct: 1024 LDDDGLPYVGASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-V 1082

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+
Sbjct: 1083 TLRQVRSPCLGDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQL 1142

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  LG      G                                               
Sbjct: 1143 LEAALGKGIALGGT---------------------------------------------- 1156

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   +  +TP F  A  + I   L  A     G   + +G TGE     + +G  + 
Sbjct: 1157 -------MRYATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFY 1208

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L 
Sbjct: 1209 QRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLF 1268

Query: 1317 IKSD----DVVG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKE 1353
            + SD     V     R   V    V G                +      P    +L +E
Sbjct: 1269 MLSDFSQMHVCQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQE 1328

Query: 1354 MQALGLSIDLENS 1366
            + ++G+ +  E  
Sbjct: 1329 LFSMGICLRFETE 1341



 Score =  141 bits (355), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 148/1026 (14%), Positives = 298/1026 (29%), Gaps = 236/1026 (23%)

Query: 14   RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
            R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 132  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 181

Query: 57   AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
              F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 182  ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 241

Query: 91   CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
               +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 242  ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 301

Query: 140  ----------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDK---GRASLSGKLLY 180
                              G F+IKG+++    +L    G  +  +    G+     + ++
Sbjct: 302  NLCWLHKLKESDCQFDSGGYFLIKGMEK---DELQGCGGKLYSRNLCLNGKLETPTQKVF 358

Query: 181  AC-------RI-IPDQGLWMDIEFDSKDIIHVRIDRRR-----------------KV--- 212
                     RI + D+  WM             I RRR                 K+   
Sbjct: 359  IAQEQKCLTRIWVEDRPCWMVSFLSP-------IRRRRIYIKLIDSANNEDASGGKIISI 411

Query: 213  -------PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                   P+     ALG+ S+ +I      +   +   +     +  +D +      S  
Sbjct: 412  SFLYANMPIWLMFFALGISSDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDK 471

Query: 265  VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYI 322
                  E +  S           + +     +          G  V   ++   TG+   
Sbjct: 472  ARQYVDELIKNSKFPPAEPFDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKC 530

Query: 323  EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
            +  D    K L+       R++   ++               +  ++ ++    +   + 
Sbjct: 531  DNKDDFRNKRLDLAGELLGRELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASII 589

Query: 383  PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
               ++      S  +    +     +    R    +++  D     + +         + 
Sbjct: 590  TNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARY 649

Query: 443  LVDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
                  GK   +   D      V+++        R+    ++R I   ++ +        
Sbjct: 650  PNPSYWGKLCFMSTPDGENCGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL-------- 701

Query: 502  DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
              I  + V      F     +    +  + + R+   RR   +      +         V
Sbjct: 702  HEIPTEEVPRMDKIFLNGDWVGSCSDPASFVLRLRCMRRSGLIDPQVEIKRDKHQREVRV 761

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                   + P    E  N       +S++                       + ++   E
Sbjct: 762  FSDAGRILRPLLVVENLNKIRRPKGSSYS--------------FQWLMQQEIIEFIGVEE 807

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK------IDFIDASPKQVVSIA 675
            EE+   A    +L E       +V    A +   V R+           +     ++ ++
Sbjct: 808  EEDIRSAWGIRNLFES-EEEAPMVKMNKAEDVFNVKRKIGGEVSGYTHCELDLSFLLGLS 866

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
              +IPF  ++ + RVL                             K S  AI        
Sbjct: 867  CGIIPFANHNFARRVLYQSE-------------------------KHSQQAIGYSTTNPH 901

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             +VD                               +      QRPL     +    D I 
Sbjct: 902  IRVD-----------------------------TLSHQLYYPQRPL----FKTVIADCIG 928

Query: 796  DGPSTDLG-------DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                T          +   G+N +VA     G+N EDS++++   +   +F + H   ++
Sbjct: 929  RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQEDSVVMNRASLERGMFRTEHFRNYK 988

Query: 849  VMARDTKL--------GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
                +             ++I           + N+D+ G+  VGA +  GDI++GK++ 
Sbjct: 989  AEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVGASLQSGDIVIGKVSE 1048

Query: 901  KGESPM 906
             GE   
Sbjct: 1049 SGEDHS 1054


>gi|145926496|gb|ABP98887.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926500|gb|ABP98889.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926502|gb|ABP98890.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926526|gb|ABP98902.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
 gi|145926542|gb|ABP98910.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
          Length = 257

 Score =  272 bits (696), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSIKVLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLAADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|108885381|gb|ABG23207.1| DNA-directed RNA polymerase [Geobacillus stearothermophilus]
          Length = 145

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 67/167 (40%), Positives = 101/167 (60%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAW 145


>gi|109287887|ref|YP_654581.1| hypothetical protein MIV009R [Invertebrate iridescent virus 3]
 gi|123868018|sp|Q197F1|RPB2_IIV3 RecName: Full=Probable DNA-directed RNA polymerase II subunit RPB2
            homolog
 gi|106073510|gb|ABF82039.1| hypothetical protein MIV009R [Aedes taeniorhynchus iridescent virus]
          Length = 1140

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 93/481 (19%), Positives = 154/481 (32%), Gaps = 82/481 (17%)

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
             +        +    E   L          V        +     +++    +R      
Sbjct: 731  TLNYPQKPLVTTSFAEYNQLNEYPNGINAIVAIACYTGYNQEDSIILNKSSIDRGLFGT- 789

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
                           ++   E+ I   +   ++ +   G     G    ++       LI
Sbjct: 790  ----ITYNTFTAQEKKNGIIEERIEIPSNAIKIRDCNYGLVGPDGIVRLRQRVKKGDVLI 845

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             +              K +   E L       +   E      ++ +  G        R+
Sbjct: 846  CKVTI-----------KNKNQDEKLVDSSVIVQHGEEGYVDRIVDNVIDG-------CRI 887

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  + GDK       KG    I P EDMPF   G   DI++NP  +PSRM +
Sbjct: 888  VKVVIGQMRTPEIGDKFCSGMAQKGTCGMIFPQEDMPFTASGMTPDIIINPNCIPSRMTI 947

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
             QI  T +G                            +         +     +  +  +
Sbjct: 948  NQIISTVMGKL--------------------------YTVNPNPRFRNGNSFQENSNTIL 981

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
              +                          L++   D SG  ++Y G TGE     + +G 
Sbjct: 982  KELCHH-----------------------LKLNGFDPSGSEVMYSGFTGERIQSTIFMGP 1018

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             Y  +L HMV DK++ARS G  + + +QP  G+S  GG R GEME  CI  +GA   L E
Sbjct: 1019 TYYHRLKHMVKDKMHARSHGQVTTLHRQPNCGRSQGGGLRFGEMEKDCILVHGATQFLNE 1078

Query: 1314 MLTIKSD----DVVGRTRVYESIVA------GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             + + SD    DV     +  S           +      P S   L++E+  +G+   +
Sbjct: 1079 RMFLNSDPFQIDVCKDCGMMSSTSKKCHHCGSINVKRCNIPYSCKNLLQELNGMGIKTKI 1138

Query: 1364 E 1364
            +
Sbjct: 1139 D 1139



 Score =  107 bits (266), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 104/651 (15%), Positives = 210/651 (32%), Gaps = 61/651 (9%)

Query: 297 GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE-----KSLEEIFHSEIRDIPILYVDS 351
            I +  +  L +   +++   G ++   G   D+     +SL  +     + I  +  D 
Sbjct: 224 MIKNKIMVSLKLKRKLIDIPVGIVFKCLGYNPDQMGSKFRSLFNLPPEYEKYIDAIKNDC 283

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF---SVAESMFNFLFFDSDKYDL 408
           +   AY       D +                 +       +++ S+       +    +
Sbjct: 284 LEEFAYGIAVSAADGDNSDSGGESGGEEEADQEEHIVKVFRNMSTSVDKDGGMAATGITI 343

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             V +               R  R + +  ++K  +     K  +D+ D+  ++RV + G
Sbjct: 344 EDVQKSLDMDLFPHLGITSTRKQRVDLLAFMVKKYLLTLTRKIPVDNRDDYNHKRVETAG 403

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS-------- 520
           E+    +RL   + +++   +I +   D     + +    + + +   F S         
Sbjct: 404 ELYSFLFRLLYKKFQKTCITQIRNRKPD---ISNFLRTSGITTGILYSFSSGYWGVQRNT 460

Query: 521 ----QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                +SQ+     SL     + R   + +    +     E+R +HP+    +CP ET E
Sbjct: 461 YIRTGVSQVVNPKVSLLANYSSLRRVVIPESKDGKEAKTSEIRQIHPSSSFLVCPVETPE 520

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G  +G V ++  F +V   G          D    +   + +  +  N  +   N S   
Sbjct: 521 GKGVGTVLNMAVFCQVTT-GISTCEIMDQIDSFGVDLKCHCTIKDPNNCLLLLINGSPYG 579

Query: 637 DGSFTEELVFCRCAGEEILVPREK-----------------IDFIDASPKQVVSIAASLI 679
           +G               I +   +                 I  +D        I  S  
Sbjct: 580 NGHANVIHRLNFLNDTNISIVVNRALGVIEIFSDAGRFIRPIFDLDKICNFEGEIVPSFK 639

Query: 680 PFLENDDSNRVLM---GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            FL+N     + +     N     +  L          ME       G       AGI+ 
Sbjct: 640 WFLDNQLIRYIDINEAAANSIAIELRDLSTNPNTRYNLMELDPCGMFGIV-----AGIIP 694

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             D  +         +     G      +K +  +      Q+PLV            + 
Sbjct: 695 FPDRTQSARNCFYSSMVKQAIGFVPCHNLKTETVSHTLNYPQKPLV----------TTSF 744

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                L +   G N +VA   + GYN EDS+++++  +   +F +I    F    +   +
Sbjct: 745 AEYNQLNEYPNGINAIVAIACYTGYNQEDSIILNKSSIDRGLFGTITYNTFTAQEKKNGI 804

Query: 857 GPE--EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             E  EI  +   + +     +   GI+ +   V  GD+L+ K+T K ++ 
Sbjct: 805 IEERIEIPSNAIKIRDCNYGLVGPDGIVRLRQRVKKGDVLICKVTIKNKNQ 855



 Score =  102 bits (253), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 107/764 (14%), Positives = 222/764 (29%), Gaps = 147/764 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L++ Q  +++HF+           +GL+    +   I         L+F +   + P   
Sbjct: 32  LVKHQIETFNHFIS----------KGLKTIINNESSIKYQSHDNYSLKFTNIYVEYPSII 81

Query: 87  ---------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK--DIKEQ-SIYMGD 134
                       +   +DL+Y          +  +V E    K  K   I EQ  + +  
Sbjct: 82  DDDRTIRDLYPQEARNKDLSYTGN-------VCVNVIEMVENKEGKPPQISEQYRVPIAK 134

Query: 135 LPLMT-------------------------KDGTFVIKGIQRIVVSQLHR---SPGIHFD 166
           +P+M                          + G F+I G +R+++SQ  R   +  + F 
Sbjct: 135 IPIMLGSDVCHLSKYTPLENEQINGHSQADQGGYFIINGKERVLISQ-VRKAYNKPVCFV 193

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEF--------DSKDIIHVRIDRRRK---VPVT 215
                 S    +L     I +     +  F          K+ I V +  +RK   +PV 
Sbjct: 194 KS---TSQKEDVL-----ICEMRSMCEETFHSTSVQVKMIKNKIMVSLKLKRKLIDIPVG 245

Query: 216 SFLMALGMDSEEILSTF---------YPKIVYSQRGD-------FWCFPLSAADLMVGAK 259
                LG + +++ S F         Y K + + + D             +  D      
Sbjct: 246 IVFKCLGYNPDQMGSKFRSLFNLPPEYEKYIDAIKNDCLEEFAYGIAVSAADGDNSDSGG 305

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKS--LKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            S    + D  E +++  + +++ + K   +   G+    +       L+    I +   
Sbjct: 306 ESGGEEEADQEEHIVKVFRNMSTSVDKDGGMAATGITIEDVQKSLDMDLFPHLGITSTRK 365

Query: 318 GEIYIEAG-------DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             + + A         +  +  ++       + +             +            
Sbjct: 366 QRVDLLAFMVKKYLLTLTRKIPVDNRDDYNHKRVETAGELYSFLFRLLYKKFQKTCITQI 425

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM-RLNLDTPDDVR 429
           ++   DI   +R   ++T  +      +     + Y  + V +V      L  +     R
Sbjct: 426 RNRKPDISNFLRTSGITTGILYSFSSGYWGVQRNTYIRTGVSQVVNPKVSLLANYSSLRR 485

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +  E          ++R    +   +              + N      +    S  E 
Sbjct: 486 VVIPESKDGKEAKTSEIRQIHPSSSFLVCPVETPEGKGVGTVLNMAVFCQVTTGISTCEI 545

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +  +D   V  +     K   + +      S       + N  + + H  RL+ L    +
Sbjct: 546 MDQIDSFGVDLKCHCTIKDPNNCLLLLINGS------PYGNGHANVIH--RLNFLNDTNI 597

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
           +             +  GR                        N  G I   ++   D +
Sbjct: 598 SIVVNRALGVIEIFSDAGRFIRPIFDLDKIC------------NFEGEIVPSFKWFLDNQ 645

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           +   + Y+   E      A ANS   E               +    P  + + ++  P 
Sbjct: 646 L---IRYIDINE------AAANSIAIE-------------LRDLSTNPNTRYNLMELDPC 683

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +  I A +IPF +   S R     +M +QA+  +        T
Sbjct: 684 GMFGIVAGIIPFPDRTQSARNCFYSSMVKQAIGFVPCHNLKTET 727


>gi|9294064|dbj|BAB02021.1| DNA-dependent RNA polymerase II [Arabidopsis thaliana]
          Length = 1119

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 119/316 (37%), Gaps = 69/316 (21%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 846  VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 905

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 906  LLEAALSKGIAC-------------------------------------PIQKKEGSSAA 928

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 929  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSLIFMGPTF 983

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  +KV  R+TG    +T+QP+  +   GG R GEME  C+ A+GA+  L E L
Sbjct: 984  YQRLVHMSENKVKFRNTGPVHPLTRQPVADRKRFGGIRFGEMERDCLIAHGASANLHERL 1043

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 1044 FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCASSDHVVRVYVPYGAKLL 1101

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 1102 CQELFSMGITLNFDTK 1117



 Score =  111 bits (278), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 143/955 (14%), Positives = 272/955 (28%), Gaps = 210/955 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           LI  Q  SY+ F+            GLQ  F+S              F       P FDV
Sbjct: 39  LISHQLNSYNFFI----------EHGLQNVFES--------------FGDI-LVEPSFDV 73

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTG-----AKSIKDIKEQSIYMGDLPLMTKD-- 141
                 D  YA    +  ++++      TG      K I D+K+Q I +G +P+M K   
Sbjct: 74  IKKKDGDWRYA---TVFKKIVIKHDKFKTGQDEYVEKEILDVKKQDILIGSIPVMVKSVL 130

Query: 142 ---------------------GTFVIKGIQRIVVSQLHR---------SP-GIHFDHDKG 170
                                G FVIKG +++ ++Q            SP  + F  +  
Sbjct: 131 CKTSEKGKENCKKGNCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWISNSPWTVSFRSETK 190

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSK---DIIHVRIDRRRKVPVTSFLMALGMDSE- 226
           R           R I  +    +   D K    ++ V       +PV     ALG+ S+ 
Sbjct: 191 RN----------RFI-VRLSENEKAEDYKIMEKVLTVYFLSTE-IPVWLLFFALGVSSDK 238

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           E +             D        A +     V  +    +     +E   K T     
Sbjct: 239 EAMDLI-----AFDGDDASITNSLIASIHEADAVCEAFRCGNNALTYVEHQIKSTKFPPA 293

Query: 287 SLKEKGVKFLGIT-------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
              +  ++                 G  V   +++   G+   E  D    K +E     
Sbjct: 294 ESVDDCLRLYLFPCLQGLKKKARFLGYMVKC-LLSAYAGKRKCENRDSFRNKRIELAGEL 352

Query: 340 EIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             R+I + L          ++  L  D +    +  LD   +    + +  + A S    
Sbjct: 353 LEREIRVHLAHARRKMTRAMQKQLSGDGDLKPIEHYLDASVITNGLNRAFSTGAWSHPFR 412

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                    ++ +GR      L        + +     +   +       G+       +
Sbjct: 413 KMERVSG-VVANLGRANPLQTLIDLRRTRQQVL-YTGKVGDARHPHPSHWGRVCFLSTPD 470

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
             N  +     +L      GL  +   +        ++          K +         
Sbjct: 471 GENCGLVKNMSLLGLVSTQGLESVVEMLFTCGMEELMNDTSTPLCGKHKVL-------LN 523

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +    +  + +  +   RR S L  +  + R +   E+R              T  G
Sbjct: 524 GDWVGLCADSESFVGELKSRRRQSELPLEMEIKRDKDDNEVR------------IFTDAG 571

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             +  +  + +  ++      + P++ + D                          L+  
Sbjct: 572 RLLRPLLVVENLHKLKQDKPTQYPFKHLLDQG-----------------------ILELI 608

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G   EE        +++L   +     +     ++ ++ +++PF  +D   RVL      
Sbjct: 609 GIEEEEDCTTAWGIKQLLKEPKNYTHCELDLSFLLGVSCAIVPFANHDHGKRVLYQSQ-- 666

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                                           K         +    IR           
Sbjct: 667 --------------------------------KHCQQAIGFSSTNPNIRCD--------- 685

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                        +Q     Q+PL K                 +   L  G+N +VA   
Sbjct: 686 -----------TLSQQLFYPQKPLFK----------TLASECLEKEVLFNGQNAIVAVNV 724

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEG 872
             GYN EDS+++++  +   +F S  I  ++           K   E +           
Sbjct: 725 HLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDTKDSEKRKKMDELVQFGKTYSKIGK 784

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           + ++++ G   +GA ++ GDI++G+ T  G       +   R I  +  +   D 
Sbjct: 785 VDSLEDDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDE 839


>gi|297830452|ref|XP_002883108.1| NRPD2a [Arabidopsis lyrata subsp. lyrata]
 gi|297328948|gb|EFH59367.1| NRPD2a [Arabidopsis lyrata subsp. lyrata]
          Length = 1169

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 75/316 (23%), Positives = 119/316 (37%), Gaps = 69/316 (21%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 896  VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 955

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 956  LLEAALSK-------------------------------------GIASPIQKKEGSSAA 978

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 979  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSLIFMGPTF 1033

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  DKV  R+TG    +T+QP+  K   GG + GEME  C+ A+GA+  L E L
Sbjct: 1034 YQRLVHMSEDKVKFRNTGPVHPLTRQPVADKKRFGGIKFGEMERDCLIAHGASANLHERL 1093

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 1094 FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCASSDHVVRVYVPYGAKLL 1151

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 1152 CQELFSMGITLNFDTK 1167



 Score =  134 bits (338), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 145/988 (14%), Positives = 286/988 (28%), Gaps = 231/988 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFP----ITAFSGA---AMLEF 76
           LI  Q  SY+ F+            GL+  F+S     V P    I    G    A ++F
Sbjct: 44  LISHQLNSYNFFI----------EHGLRNVFESFGEMLVEPSFDVIKKKDGDWRYATVKF 93

Query: 77  VSYEFDPPKF--DVDD-------CLWRDLTYAVPLKITLRLIVFDV-----------DEF 116
               F+ P F  D  +          +++TY+  +K+ +++ VF              + 
Sbjct: 94  GEVTFEKPTFFSDDKELEFLPWHARLQNMTYSARIKVNVQVEVFKKTVVKSDKFKTGQDE 153

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD-----------------------GTFVIKGIQRIV 153
              K I D+K+Q I +G +P+M K                        G FVIKG +++ 
Sbjct: 154 YVEKEILDVKKQDILIGSIPVMVKSVLCKTSEKGKENCKKGDCAFDQGGYFVIKGAEKVF 213

Query: 154 VSQLHR---------SP-GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK---D 200
           ++Q            SP  + F  +  R           R I  +    +   D K    
Sbjct: 214 IAQEQMCTKRLWISNSPWTVSFRSETKRN----------RFI-VRLSENEKADDYKRREK 262

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGA 258
           ++ V       +PV     ALG+ S+ E +    +  +      D        A +    
Sbjct: 263 VLTVYFLSTE-IPVWLLFFALGVSSDKEAMDLIAFDGV------DASITNSLIASIHEAD 315

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLYVAED 311
            V  +    +     +E   K T        +  ++                 G  V   
Sbjct: 316 AVCEAFRCGNNALTYVEHQIKSTKFPPAESVDDCLRLYLFPGLQGLKKKARFLGYMVKC- 374

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +++   G+   E  D    K +E       R+I +    +       + T    K    +
Sbjct: 375 LLSAYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARR-----KMTRAMQKQLSGE 429

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD------LSTVGRVKMNMRLNLDTP 425
             L  I   +    V T  +  +     +    +        ++ +GR      L     
Sbjct: 430 GELKPIEHYLDAS-VITNGLNRAFSTGAWSHPFRKMERVSGVVANLGRANPLQSLIDLRR 488

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              + +     +   +       G+       +  N  +     +L       L  +   
Sbjct: 489 TRQQVL-YTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQVLESVVEM 547

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL- 544
           +        +D          K +            +    +  + ++ +   RR S L 
Sbjct: 548 LYACGMEELMDDTSTPLCGKHKVL-------LNGDWVGLCADSESFVAELKSRRRQSELP 600

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            +  + R +   E+R              T  G  +  +  + +  ++      + P++ 
Sbjct: 601 REMEIKRDKDDNEVR------------IFTDAGRLLRPLLVVENLHKLKQDKPTQYPFKH 648

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + D  +                        +  G   EE        +++L   +     
Sbjct: 649 LLDQGIL-----------------------ELIGIEEEEDCNTAWGIKQLLKEPKNYTHC 685

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +     ++ ++ +++PF  +D   RVL                                 
Sbjct: 686 ELDLSFLLGVSCAIVPFANHDHGKRVLYQSQ----------------------------- 716

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                K         +    IR                        +Q     Q+PL K 
Sbjct: 717 -----KHCQQAIGFSSTNPNIRCD--------------------TLSQQLFYPQKPLFK- 750

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               L  G+N +VA     GYN EDS+++++  +   +F S  I
Sbjct: 751 ---------TVASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQI 801

Query: 845 EEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             ++           K   E +           + ++++ G   +GA ++ GDI++G+ T
Sbjct: 802 RSYKAEVDTKDSEKRKKMDELVKFGKTYSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCT 861

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDT 927
             G       +   R I  +  +   D 
Sbjct: 862 DSGADHSIKLKHTERGIVQKVVLSSNDE 889


>gi|308485788|ref|XP_003105092.1| hypothetical protein CRE_20709 [Caenorhabditis remanei]
 gi|308257037|gb|EFP00990.1| hypothetical protein CRE_20709 [Caenorhabditis remanei]
          Length = 1127

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 79/346 (22%), Positives = 127/346 (36%), Gaps = 73/346 (21%)

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDE-KVQRNVESLKVQYETSKSILEDRF------ 1053
            GF   TV+  + I+     +      ++  +  + V +  +     +  L++ +      
Sbjct: 746  GFAHGTVIKVERINLVTDRERKTIFYKNPREDMKTVSADGLPIPGRRYFLDEVYYVTFNM 805

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKV---------------FVAMKRPIQSGDKMAGRHGNKG 1098
            +    +        P    +V++                  ++R    GDK A RHG KG
Sbjct: 806  ETGDFRSHKFHYAEPAYCGMVRIVEQSESGSGAQHALIQWRIERNPIIGDKFASRHGQKG 865

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I S + P E +PF + G   DI+ NP G PSRM +G + E+  G A    G+   +    
Sbjct: 866  INSFLWPIESLPFSETGMVPDIIFNPHGFPSRMTIGMMIESMAGKAAATHGENYDASPFV 925

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
            +                                                    D      
Sbjct: 926  FNE--------------------------------------------------DKTAINH 935

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
               +L  A  +  G    Y G+ G   +  +  G +Y  +L HM++DK   R+TG    +
Sbjct: 936  FGELLTKAGYNYYGNETFYSGVDGRQMEMQIFFGIVYYQRLRHMIADKFQVRATGPIDPI 995

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-DVV 1323
            T QP+ G+   GG R GEME   I A+G ++VLQ+ L   SD DV 
Sbjct: 996  THQPVKGRKKGGGIRFGEMERDAIIAHGTSFVLQDRLLNCSDRDVA 1041



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 36/119 (30%), Gaps = 47/119 (39%)

Query: 72  AMLEFVSYEFDPPKFD-------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
             ++F S +   P  D               +C  R LTYA  LK+ + + V        
Sbjct: 41  VTMKFTSAQLHKPTLDNGAKLTSDTLPLYPAECRQRGLTYAGNLKVGIDVHVNGTRLDII 100

Query: 119 AKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIV 153
                        +G +P+M                         K G F++ G ++++
Sbjct: 101 ETI----------LGKVPIMLRSEGCNLRGMSRKELVAAGEEPIEKGGYFIVNGSEKVI 149


>gi|38347314|emb|CAE05960.2| OSJNBa0063C18.1 [Oryza sativa Japonica Group]
          Length = 1316

 Score =  272 bits (696), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 107/613 (17%), Positives = 181/613 (29%), Gaps = 101/613 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT-----SIHIEE 846
              +      +   +    ++  A+   + +  E+   + +   +EDVF         +  
Sbjct: 765  QWLMQQEIIEFIGVEEEEDIRSAWGIRNLFESEEEAPMVKMNKAEDVFNVKRKIGGEVSG 824

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     D           IP        N +    +   +E       +G  T      +
Sbjct: 825  YTHCELDLSFLLGLSCGIIP------FANHNFARRVLYQSE-KHSQQAIGYSTTNPHIRV 877

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
                  L          V    +   S  +    D      +   +N        +    
Sbjct: 878  DTLSHQLYYPQRPLFKTVIADCIG-RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQ 936

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  +   +      +        +    G  G  K   +   +     +S+  +   
Sbjct: 937  EDSVVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDN 996

Query: 1027 QDEKVQRNVESLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKV 1076
             D+     V +     +      S   +    K++  + G            G    V V
Sbjct: 997  LDDDGLPYVGASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-V 1055

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+
Sbjct: 1056 TLRQVRSPCLGDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQL 1115

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  LG      G                                               
Sbjct: 1116 LEAALGKGIALGGT---------------------------------------------- 1129

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   +  +TP F  A  + I   L  A     G   + +G TGE     + +G  + 
Sbjct: 1130 -------MRYATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFY 1181

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L 
Sbjct: 1182 QRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLF 1241

Query: 1317 IKSD----DVVG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKE 1353
            + SD     V     R   V    V G                +      P    +L +E
Sbjct: 1242 MLSDFSQMHVCQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQE 1301

Query: 1354 MQALGLSIDLENS 1366
            + ++G+ +  E  
Sbjct: 1302 LFSMGICLRFETE 1314



 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 142/1007 (14%), Positives = 295/1007 (29%), Gaps = 225/1007 (22%)

Query: 14   RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
            R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 132  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 181

Query: 57   AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
              F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 182  ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 241

Query: 91   CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
               +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 242  ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 301

Query: 140  ----------------KDGTFVIKGIQRIVVSQLHR-----------SPGIHFDHDKGRA 172
                              G F+IKG++++ ++Q  +              + F     R 
Sbjct: 302  NLCWLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRR 361

Query: 173  SLSGKLLYAC--------RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
             +  KL+ +         +II      +         ++        +P+     ALG+ 
Sbjct: 362  RIYIKLIDSANNEDASGGKIIS-----ISF-------LYA------NMPIWLMFFALGIS 403

Query: 225  SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
            S+ +I      +   +   +     +  +D +      S        E +  S       
Sbjct: 404  SDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQYVDELIKNSKFPPAEP 463

Query: 284  LLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
                + +     +          G  V   ++   TG+   +  D    K L+       
Sbjct: 464  FDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKCDNKDDFRNKRLDLAGELLG 522

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
            R++   ++               +  ++ ++    +   +    ++      S  +    
Sbjct: 523  RELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKR 581

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
            +     +    R    +++  D     + +         +       GK   +   D   
Sbjct: 582  NERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGEN 641

Query: 461  NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
               V+++        R+    ++R I   ++ +          I  + V      F    
Sbjct: 642  CGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL--------HEIPTEEVPRMDKIFLNGD 693

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +    +  + + R+   RR   +      +         V       + P    E  N 
Sbjct: 694  WVGSCSDPASFVLRLRCMRRSGLIDPQVEIKRDKHQREVRVFSDAGRILRPLLVVENLNK 753

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                  +S++                       + ++   EEE+   A    +L E    
Sbjct: 754  IRRPKGSSYS--------------FQWLMQQEIIEFIGVEEEEDIRSAWGIRNLFES-EE 798

Query: 641  TEELVFCRCAGEEILVPREK------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
               +V    A +   V R+           +     ++ ++  +IPF  ++ + RVL   
Sbjct: 799  EAPMVKMNKAEDVFNVKRKIGGEVSGYTHCELDLSFLLGLSCGIIPFANHNFARRVLYQS 858

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                                      K S  AI         +VD               
Sbjct: 859  E-------------------------KHSQQAIGYSTTNPHIRVD--------------- 878

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-------DLAL 807
                            +      QRPL     +    D I     T          +   
Sbjct: 879  --------------TLSHQLYYPQRPL----FKTVIADCIGRSEYTFGRKDDFARPEYFN 920

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--------GPE 859
            G+N +VA     G+N EDS++++   +   +F + H   ++    +             +
Sbjct: 921  GQNAIVAVNVHQGFNQEDSVVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKD 980

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +I           + N+D+ G+  VGA +  GDI++GK++  GE   
Sbjct: 981  KIDFGKMQSKRGRVDNLDDDGLPYVGASLQSGDIVIGKVSESGEDHS 1027


>gi|301119239|ref|XP_002907347.1| DNA-directed RNA polymerase I subunit RPA2, putative [Phytophthora
            infestans T30-4]
 gi|262105859|gb|EEY63911.1| DNA-directed RNA polymerase I subunit RPA2, putative [Phytophthora
            infestans T30-4]
          Length = 1179

 Score =  272 bits (695), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 97/499 (19%), Positives = 169/499 (33%), Gaps = 81/499 (16%)

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL--VGKITPKGESPMT 907
              +       E    +  V  +     D+        E+ P ++L  V  +TP  +   +
Sbjct: 652  PVKQMDTKRIEYIGPMEQVFMDIACTKDDIRPATTHMEIKPTNMLSLVASLTPFSDYNQS 711

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE------- 960
            P       +  +       + +         +   +I         E  +          
Sbjct: 712  PRNMYQCQMAKQTMGTPAHSIVHRSDNKMYRIQSPQIPIVQNERLREYQLDEYPLGTNAV 771

Query: 961  REQIELLARDKDDEQVILDRNIYSR------LMEILCGQNAVSGPKGFKKSTVLSSD--- 1011
               I     D +D  +IL+++ Y R      + + L    + +G +G   S    S+   
Sbjct: 772  VAVISYTGFDMED-AMILNKSSYERGFGHASVYKQLTVDISSNGKQGSATSKKYFSNIKT 830

Query: 1012 ---------LISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQ 1061
                      +         Q     + V   + E+  +         E     ++  I 
Sbjct: 831  DGSGDYCSTKLDRDGFPHIGQVVNHGDPVASWIDETTGLPSVQKHKESEPAIIEQVNMI- 889

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G+           + +   R    GDK + RHG KG++S + P  DMPF + G   DI+
Sbjct: 890  -GNSSSSSEFTKASIKLRFCRNPTIGDKFSSRHGQKGVMSILWPQADMPFSESGISPDII 948

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP   PSRM VG + E+         GK + +    +     +                
Sbjct: 949  INPHAFPSRMTVGMLIESMAAKTGALKGKYMDATPFQFSEKDRV---------------- 992

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                               +   S L+    +  G   LY G++
Sbjct: 993  ----------------------------------IDYFGSQLKEHGYNYMGSEPLYSGIS 1018

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G      + +G +Y  +L HMVSDK   R+TG  + +T+QP+ G+   GG RLGEME   
Sbjct: 1019 GTVMQADIYIGVVYYQRLRHMVSDKSQVRATGPMNSLTRQPVKGRKKGGGIRLGEMERDS 1078

Query: 1302 IQAYGAAYVLQEMLTIKSD 1320
            + A+G A+++Q+ L   SD
Sbjct: 1079 LLAHGCAFLVQDRLLNCSD 1097



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 59/180 (32%)

Query: 18  GKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF--PITAFSG-AAML 74
            K+ E +    L+     S++ FL           EGL  A   +   P+   +     +
Sbjct: 35  AKSNEKLQK--LVSPHLDSFNFFLT----------EGLDLAVADMCKVPVELPNQHRMDI 82

Query: 75  EFVSYEFDPP----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
              + +   P          K    +C  R ++Y  PL +TL         F G+++++ 
Sbjct: 83  WIENAQIGYPTTENQITGEQKLLPSECRQRGVSYTAPLVVTL------ARSFGGSQNVE- 135

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV-VSQLHR 159
            + Q + +G++P+M +                         G F+  G +R V + Q+ R
Sbjct: 136 -RLQRV-VGEIPIMVRSKRCHLNGMAPTDLVKAREEANEMGGYFICNGNERCVRLLQMPR 193


>gi|115460882|ref|NP_001054041.1| Os04g0641000 [Oryza sativa Japonica Group]
 gi|113565612|dbj|BAF15955.1| Os04g0641000 [Oryza sativa Japonica Group]
          Length = 1270

 Score =  272 bits (695), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 107/613 (17%), Positives = 181/613 (29%), Gaps = 101/613 (16%)

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT-----SIHIEE 846
              +      +   +    ++  A+   + +  E+   + +   +EDVF         +  
Sbjct: 719  QWLMQQEIIEFIGVEEEEDIRSAWGIRNLFESEEEAPMVKMNKAEDVFNVKRKIGGEVSG 778

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +     D           IP        N +    +   +E       +G  T      +
Sbjct: 779  YTHCELDLSFLLGLSCGIIP------FANHNFARRVLYQSE-KHSQQAIGYSTTNPHIRV 831

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
                  L          V    +   S  +    D      +   +N        +    
Sbjct: 832  DTLSHQLYYPQRPLFKTVIADCIG-RSEYTFGRKDDFARPEYFNGQNAIVAVNVHQGFNQ 890

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  +   +      +        +    G  G  K   +   +     +S+  +   
Sbjct: 891  EDSVVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDN 950

Query: 1027 QDEKVQRNVESLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKV 1076
             D+     V +     +      S   +    K++  + G            G    V V
Sbjct: 951  LDDDGLPYVGASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-V 1009

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+
Sbjct: 1010 TLRQVRSPCLGDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQL 1069

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  LG      G                                               
Sbjct: 1070 LEAALGKGIALGGT---------------------------------------------- 1083

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   +  +TP F  A  + I   L  A     G   + +G TGE     + +G  + 
Sbjct: 1084 -------MRYATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFY 1135

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L 
Sbjct: 1136 QRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLF 1195

Query: 1317 IKSD----DVVG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKE 1353
            + SD     V     R   V    V G                +      P    +L +E
Sbjct: 1196 MLSDFSQMHVCQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQE 1255

Query: 1354 MQALGLSIDLENS 1366
            + ++G+ +  E  
Sbjct: 1256 LFSMGICLRFETE 1268



 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 142/1007 (14%), Positives = 295/1007 (29%), Gaps = 225/1007 (22%)

Query: 14  RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
           R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 86  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 135

Query: 57  AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
             F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 136 ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 195

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
              +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 196 ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 255

Query: 140 ----------------KDGTFVIKGIQRIVVSQLHR-----------SPGIHFDHDKGRA 172
                             G F+IKG++++ ++Q  +              + F     R 
Sbjct: 256 NLCWLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRR 315

Query: 173 SLSGKLLYAC--------RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
            +  KL+ +         +II      +         ++        +P+     ALG+ 
Sbjct: 316 RIYIKLIDSANNEDASGGKIIS-----ISF-------LYA------NMPIWLMFFALGIS 357

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           S+ +I      +   +   +     +  +D +      S        E +  S       
Sbjct: 358 SDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQYVDELIKNSKFPPAEP 417

Query: 284 LLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + +     +          G  V   ++   TG+   +  D    K L+       
Sbjct: 418 FDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKCDNKDDFRNKRLDLAGELLG 476

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R++   ++               +  ++ ++    +   +    ++      S  +    
Sbjct: 477 RELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKR 535

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
           +     +    R    +++  D     + +         +       GK   +   D   
Sbjct: 536 NERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGEN 595

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              V+++        R+    ++R I   ++ +          I  + V      F    
Sbjct: 596 CGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL--------HEIPTEEVPRMDKIFLNGD 647

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +    +  + + R+   RR   +      +         V       + P    E  N 
Sbjct: 648 WVGSCSDPASFVLRLRCMRRSGLIDPQVEIKRDKHQREVRVFSDAGRILRPLLVVENLNK 707

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                 +S++                       + ++   EEE+   A    +L E    
Sbjct: 708 IRRPKGSSYS--------------FQWLMQQEIIEFIGVEEEEDIRSAWGIRNLFES-EE 752

Query: 641 TEELVFCRCAGEEILVPREK------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              +V    A +   V R+           +     ++ ++  +IPF  ++ + RVL   
Sbjct: 753 EAPMVKMNKAEDVFNVKRKIGGEVSGYTHCELDLSFLLGLSCGIIPFANHNFARRVLYQS 812

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                                     K S  AI         +VD               
Sbjct: 813 E-------------------------KHSQQAIGYSTTNPHIRVD--------------- 832

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-------DLAL 807
                           +      QRPL     +    D I     T          +   
Sbjct: 833 --------------TLSHQLYYPQRPL----FKTVIADCIGRSEYTFGRKDDFARPEYFN 874

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL--------GPE 859
           G+N +VA     G+N EDS++++   +   +F + H   ++    +             +
Sbjct: 875 GQNAIVAVNVHQGFNQEDSVVMNRASLERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKD 934

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +I           + N+D+ G+  VGA +  GDI++GK++  GE   
Sbjct: 935 KIDFGKMQSKRGRVDNLDDDGLPYVGASLQSGDIVIGKVSESGEDHS 981


>gi|145926504|gb|ABP98891.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
          Length = 257

 Score =  272 bits (695), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 139/258 (53%), Positives = 186/258 (72%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  + W  P  A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KIQYKRIKEGWRVPFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSIKVLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|79416709|ref|NP_189020.2| NRPD2A; DNA binding / DNA-directed RNA polymerase [Arabidopsis
            thaliana]
 gi|9293951|dbj|BAB01854.1| DNA-directed RNA polymerase, subunit B [Arabidopsis thaliana]
 gi|57791156|gb|AAW56422.1| polymerase IV second largest subunit [Arabidopsis thaliana]
 gi|62183738|gb|AAX73261.1| RNA polymerase IV second-largest subunit [Arabidopsis thaliana]
          Length = 1172

 Score =  272 bits (695), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 119/316 (37%), Gaps = 70/316 (22%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R    GDK +  HG KG++  +   ++ PF   G   DIV+NP   PSR   GQ
Sbjct: 900  VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQ 959

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  L                                                + S   
Sbjct: 960  LLEAALSKGIAC--------------------------------------PIQKEGSSAA 981

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
              +  +   P STP   G  E  I   L  A     G   +Y+G +GE     + +G  +
Sbjct: 982  YTKLTRHATPFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTF 1036

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
              +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GA+  L E L
Sbjct: 1037 YQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERL 1096

Query: 1316 TIKSD----DVVGRTRVYESIVAGNDTFETG---------------------TPESFNVL 1350
               SD     +  + + Y +++    T  +G                      P    +L
Sbjct: 1097 FTLSDSSQMHICRKCKTYANVI--ERTPSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLL 1154

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ ++G++++ +  
Sbjct: 1155 CQELFSMGITLNFDTK 1170



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 149/983 (15%), Positives = 289/983 (29%), Gaps = 221/983 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY++F+            GLQ  F+S     V P              A ++F
Sbjct: 48  LISHQLNSYNYFI----------EHGLQNVFQSFGEMLVEPSFDVVKKKDNDWRYATVKF 97

Query: 77  VSYEFDPPKF--DVDD-------CLWRDLTYAVPLKITLRLIVFDVDEFTG--------- 118
                + P F  D  +          +++TY+  +K+ +++ VF                
Sbjct: 98  GEVTVEKPTFFSDDKELEFLPWHARLQNMTYSARIKVNVQVEVFKNTVVKSDKFKTGQDN 157

Query: 119 --AKSIKDIKEQSIYMGDLPLMTKD-----------------------GTFVIKGIQRIV 153
              K I D+K+Q I +G +P+M K                        G FVIKG +++ 
Sbjct: 158 YVEKKILDVKKQDILIGSIPVMVKSILCKTSEKGKENCKKGDCAFDQGGYFVIKGAEKVF 217

Query: 154 VSQLHR---------SP-GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK---D 200
           ++Q            SP  + F  +  R           R I  +    +   D K    
Sbjct: 218 IAQEQMCTKRLWISNSPWTVSFRSENKRN----------RFI-VRLSENEKAEDYKRREK 266

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           ++ V       +PV     ALG+ S+ E +             D        A + V   
Sbjct: 267 VLTVYFLSTE-IPVWLLFFALGVSSDKEAMDLI-----AFDGDDASITNSLIASIHVADA 320

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLYVAEDI 312
           V  +    +     +E   K T        ++ +                  G  V   +
Sbjct: 321 VCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLFPGLQSLKKKARFLGYMVKC-L 379

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRK 371
           +N   G+   E  D    K +E       R+I + L          ++  L  D +    
Sbjct: 380 LNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARRKMTRAMQKHLSGDGDLKPI 439

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +  LD   V+  G    FS       F   +     ++ +GR      L        + +
Sbjct: 440 EHYLDA-SVITNGLSRAFSTGAWSHPFRKMERVSGVVANLGRANPLQTLIDLRRTRQQVL 498

Query: 432 RKEDIIAIIKILVDLRNGKGT-IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                +   +       G+   +   D      V+++  +     +     +E+     +
Sbjct: 499 -YTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFACGM 557

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGV 549
             +  D+  P        +            +    +  + ++ +   RR S L  +  +
Sbjct: 558 EELMDDTCTP--------LFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEI 609

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R +   E+R              T  G  +  +  + +  ++      + P+  + D  
Sbjct: 610 KRDKDDNEVR------------IFTDAGRLLRPLLVVENLQKLKQEKPSQYPFDHLLDHG 657

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           +                        +  G   EE        +++L   +     +    
Sbjct: 658 IL-----------------------ELIGIEEEEDCNTAWGIKQLLKEPKIYTHCELDLS 694

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ ++ +++PF  +D   RVL                                      
Sbjct: 695 FLLGVSCAVVPFANHDHGRRVLYQSQ---------------------------------- 720

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           K         +    IR                        +Q     Q+PL K      
Sbjct: 721 KHCQQAIGFSSTNPNIRCD--------------------TLSQQLFYPQKPLFK------ 754

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                          L  G+N +VA     GYN EDS+++++  +   +F S  I  ++ 
Sbjct: 755 ----TLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKA 810

Query: 850 MA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                     K   E +     +     + ++++ G   +GA ++ GDI++G+ T  G  
Sbjct: 811 EVDAKDSEKRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESGAD 870

Query: 905 PMTPEEKLLRAIFGEKAVDVRDT 927
                +   R I  +  +   D 
Sbjct: 871 HSIKLKHTERGIVQKVVLSSNDE 893


>gi|325192359|emb|CCA26801.1| DNAdirected RNA polymerase I complex subunit Rpa2 p [Albugo laibachii
            Nc14]
          Length = 1198

 Score =  272 bits (695), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 104/247 (42%), Gaps = 56/247 (22%)

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK + RHG KG++S + P  DMPF + G   DI++NP   PSRM +G +
Sbjct: 922  KLRFCRNPVIGDKFSSRHGQKGVLSILWPQTDMPFTESGMSPDIIINPHAFPSRMTIGML 981

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E+    A    G+ +                                            
Sbjct: 982  LESMAAKAGALGGEYVD------------------------------------------- 998

Query: 1197 AEQWKSGVPVSTPV-FDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                      +TP  FD  +   +     L+    +  G   LY G++G      + +G 
Sbjct: 999  ----------ATPFKFDEKNRVVDHFGEKLKQFGYNYMGTEPLYSGISGTIMQADIYIGV 1048

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
            +Y  +L HMVSDK   R+TG  + +T+QP+ G+   GG R GEME   + A+G +++LQ+
Sbjct: 1049 VYYQRLRHMVSDKSQVRATGPMNSLTRQPVKGRKKGGGIRFGEMERDSLLAHGCSFLLQD 1108

Query: 1314 MLTIKSD 1320
             L   SD
Sbjct: 1109 RLMNCSD 1115



 Score = 95.9 bits (237), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 141/1031 (13%), Positives = 282/1031 (27%), Gaps = 256/1031 (24%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAF-SGAAMLEFVSYEFDPP 84
           +L+     S+++ L           EGL  A   +    I         +     +   P
Sbjct: 57  NLVSPHINSFNYLLT----------EGLHLAIADIARVSIQLPGQNKLSIWIEDAQVGLP 106

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                     K    +C  R ++Y  PL +TL              S    + Q + +GD
Sbjct: 107 FSTNAVKGEQKLLPAECRQRGISYTAPLVLTL--------ARAFNGSNTVERLQRV-VGD 157

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV-VSQLHRSPGIHFDHDK 169
           +P+M +                         G F+  G +R + + Q+ R         +
Sbjct: 158 IPIMVRSKRCHLHHLSPQRLVQAKEEAYEVGGYFICNGNERCIRLLQMPR---------R 208

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDII-HVRIDRR------------------- 209
                  +  +      ++G   ++  D    +  VR D+                    
Sbjct: 209 HHVMAVRRGAFT-----NRG---ELYTDMAVFMKCVRRDQSSVTVTLHYLEDGSATVRFS 260

Query: 210 -RK----VPVTSFLMAL-GMDSEEILS---------TFYP---KIVYSQRGDFWCFPLSA 251
            RK    +PV   L A+  +   EI           TF     ++V  Q   F  +    
Sbjct: 261 VRKQEFMIPVVLVLKAMYSLTDREIYDRVLRGEHTNTFLALRMEVVIQQAKAFGVYTKEE 320

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           A   +G      L + D     ++ G  L    +     KG K     ++ L    +   
Sbjct: 321 ALTYLGKHFRYVLQNSDDA-SHLQVGMSLIDEFVFVHLPKGEKGGSQKAELL--CLMLRK 377

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +     G+I  +  D +  + L    H  +  +     + + +           K     
Sbjct: 378 LYAFAKGDICEDNSDSVMNQELLLPGHLYLNILKEKIQEGLQSLRIQILKECAKKTGVMD 437

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           DA +   R +      T ++ ++M  FL   + K              +  +  +  R++
Sbjct: 438 DAFM---RRLWD---RTPNIGQAMMYFLNTGNLKSSSGLDLMQVAGYTIVAEKLNFYRYL 491

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGN---------RRVRSVGEMLKNQYRLGLLRM 482
                +   +   +++         D+ G               +  +      +     
Sbjct: 492 SHFRSVHRGQFFTEMKTTAVRKLLPDSWGFLCPVHTPDGSPCGLLNHLATECQVVCEPAF 551

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           E +   +        +    +I +            S         V   +  +      
Sbjct: 552 EATTILQNELKLARFLSSLGMIPSNGFSDGALIMPSSYLPILFNGKVIGCA-PSDLCVTI 610

Query: 543 ALGQGGVARARAGVEMRDVH-PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
                 +   R+  + R  H       IC   ++ G     +      AR+         
Sbjct: 611 QRALRSIKSTRSQADKRCEHGIIANLEICLILSTLGGPFPGLFLSADAARLTRP------ 664

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                    T ++ ++  ME+    IA     +                           
Sbjct: 665 ----IKQLDTEEIEWIGPMEQVFMNIACTEKDIRP-----------------------AT 697

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
             I+  P  ++S+ ASL PF + + S R +  C M +Q +                    
Sbjct: 698 THIEIKPTNMLSLVASLTPFSDYNQSPRNMYQCQMAKQTMGT------------------ 739

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                       +  + D+    I++                              Q P+
Sbjct: 740 --------PCHSLSHRGDSKMYRIQT-----------------------------PQSPI 762

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V   + +R   +          +  LG N +VA + + GY+ ED+M++++          
Sbjct: 763 V-QNERLREYQL---------DEYPLGTNAVVAVISYTGYDMEDAMILNKSSYERGFA-- 810

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN---------------IDECGIICVGA 886
            H   ++ +  D     ++      + S+    N               +D  G   VG 
Sbjct: 811 -HASVYKHVTVDIGSDGKQQRTQKQDSSKAYFTNVISDSDSDLQFYSPELDYDGFPHVGK 869

Query: 887 EVNPGDIL-------VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP-SGVSGT 938
            V  GD L        GK + +      P       + G+       T   +        
Sbjct: 870 TVYQGDPLACWVDETTGKQSYQKHKESEPAVVEQVTLLGKSTQTCDFTKANLKLRFCRNP 929

Query: 939 VVDVRIFNRHG 949
           V+  +  +RHG
Sbjct: 930 VIGDKFSSRHG 940


>gi|41614952|ref|NP_963450.1| DNA-directed RNA polymerase subunit B' [Nanoarchaeum equitans Kin4-M]
 gi|40068676|gb|AAR39011.1| NEQ156 [Nanoarchaeum equitans Kin4-M]
          Length = 603

 Score =  272 bits (695), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/320 (25%), Positives = 126/320 (39%), Gaps = 74/320 (23%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                  V+V + M+RP + GDK + RHG KG++  I+P  DMPF   G   D++ NP G+
Sbjct: 341  EDSNLKVRVRIRMERPTEIGDKFSSRHGQKGVIGLIVPPSDMPFTASGIVPDLIFNPHGL 400

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +GQI E   G                                             
Sbjct: 401  PSRMTIGQIIELVAGK-------------------------------------------- 416

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                 V  +  +   G P      +    E +   L      E G   +YD +TGE +  
Sbjct: 417  -----VASLRGKAVDGTPW-----EEEPVEDLRKQLLRLGFREDGTETMYDPITGEEYKV 466

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG ++  KL  + ++K++AR+ G  +++T+QP  GKS  GG R GEME   I ++GA
Sbjct: 467  KIFVGVMWYHKLKFLAANKLHARARGPMAILTRQPTEGKSREGGLRFGEMETDVILSHGA 526

Query: 1308 AYVLQEMLTIKSDDV-------VGRTRVYESIVAG----------NDTFETGTPESFNVL 1350
            A  L E     SD V        G   + E+   G                    +F + 
Sbjct: 527  AISLYERF--GSDLVKVPVCEKCGAIAI-ENKEKGTAYCPVCGETEKISYVEMSYAFKLF 583

Query: 1351 VKEMQALGLSIDLENSRTKN 1370
            + E+ +LG+   L      +
Sbjct: 584  LDELTSLGIWPRLRLKHKFD 603



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 69/364 (18%), Positives = 125/364 (34%), Gaps = 48/364 (13%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKID-FIDASPKQVVSIAASLI--PFLENDDS 687
           N          E+ V        +    E ++ ++D      +      I  P +  ++ 
Sbjct: 8   NGKYIGKTDNPEKFVQEFRKKRRLGYLPETVNIYLDEQNDIYIYTDGGRIVRPLIVVENG 67

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI------------- 734
              L   +++  A   LK +       +E + A     A +A                  
Sbjct: 68  KPKLTQKHIELLAQGKLKWDDLVKQGIIEYLDAAEEENAYIALDIEDLTPEHTHLEIGPQ 127

Query: 735 ---------VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM-KFQRSNQNTCVNQRPLVKV 784
                    V      +    +          G+       +F+         Q+PLV+ 
Sbjct: 128 VILGILSAAVPYARFNQSARLNRGERTQRQALGLYSVAYPLRFESDVHVAQTLQKPLVR- 186

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                              +   G NM+VA M + GYN +D+++I+   +      +++ 
Sbjct: 187 ---------TIVHDLIRFDERPAGYNMVVAVMAYEGYNTQDALVINRNAIDFGFTRTMYF 237

Query: 845 EEFEVMARDTKLG-PEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +E + R   LG  +EIT   P+V     E+  ++++  GI+   AEV   D+L+G+I+
Sbjct: 238 RPYEAVERKYALGLSDEITVPSPDVRGYKGEKHYRHLESDGIVYPEAEVKGKDVLIGRIS 297

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           P        E  LL A   +K    RD+S+ V S   G V    +    G D N +    
Sbjct: 298 PPRFLE-GGELALLGAATLQK----RDSSITVRSEEEGIV--DSVLVTEGEDSNLKVRVR 350

Query: 960 EREQ 963
            R +
Sbjct: 351 IRME 354


>gi|108885389|gb|ABG23211.1| DNA-directed RNA polymerase [Geobacillus subterraneus]
 gi|108885391|gb|ABG23212.1| DNA-directed RNA polymerase [Geobacillus uzenensis]
 gi|108885393|gb|ABG23213.1| DNA-directed RNA polymerase [Geobacillus sp. I112]
 gi|108885395|gb|ABG23214.1| DNA-directed RNA polymerase [Geobacillus sp. T45]
 gi|108885397|gb|ABG23215.1| DNA-directed RNA polymerase [Geobacillus thermodenitrificans]
          Length = 145

 Score =  272 bits (695), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 67/167 (40%), Positives = 101/167 (60%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYSVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAW 145


>gi|330819047|ref|XP_003291577.1| RNA polymerase I, second largest subunit [Dictyostelium purpureum]
 gi|325078245|gb|EGC31907.1| RNA polymerase I, second largest subunit [Dictyostelium purpureum]
          Length = 1117

 Score =  272 bits (695), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 86/447 (19%), Positives = 147/447 (32%), Gaps = 58/447 (12%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +       +G            +   ++ I             RV     
Sbjct: 659  DYNQSPRNMYQCQMAKQTMGTPLHSYPFRTDNKLYKIQNIQKPIVHTKNQFKYRVNDYAH 718

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELL---ARDKDDEQVILDRNIYSRLMEILCGQ 993
            G    + + +  G D  E ++ + +   E          +E + LD  +     +     
Sbjct: 719  GCNAVIAVISNTGYDM-EDAMIINKSAYERGFGHGSVYKNEYIDLDEGLSRFESKKTFFG 777

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               S          +  D +    R               + + +   Y+  +    +  
Sbjct: 778  RPNSSVDNL--GDFIDVDGLPFVGRLIKPGEPYYTYIRPSDGKQVVKDYKGKEEAYIE-- 833

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + +I     G    P  +  + V +   R    GDK + RHG KG++S++ P  +MPF +
Sbjct: 834  EVRILFASGGTGREPSKINNICVKLRYNRNPVIGDKFSSRHGQKGVLSQLWPEVNMPFTE 893

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D+++NP   PSRM +G + E   G A    GK   +    +              
Sbjct: 894  SGMKPDVIINPNAFPSRMTIGMLVEILAGKAGAIHGKFQDATAFQFDEKNTAID------ 947

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                 F G         L  +  +  G 
Sbjct: 948  -------------------------------------FFG-------EQLSKSGFNRFGN 963

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y G TG+ F+  +  G  Y  +L HMV DK   R+ G  + +T+QP+ G+   GG R
Sbjct: 964  ETMYSGTTGKEFEAEIFFGVCYYQRLRHMVKDKYQVRALGKVNALTRQPIKGRKVGGGIR 1023

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             GEME   + A+GA++ L + L   SD
Sbjct: 1024 FGEMERDSLLAHGASFCLNDRLMKSSD 1050



 Score =  102 bits (255), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 118/863 (13%), Positives = 234/863 (27%), Gaps = 131/863 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFSGAAMLEFVSYEFDPP-- 84
           LI+    S+D F           + G+    KS  P           ++F   +   P  
Sbjct: 8   LIQPHIDSFDFF----------TDHGIDLILKSNEPLYFEHKERQYKIKFTQLKLGKPVH 57

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  +F  ++     +TY  P K  + L      +    K         + +G +P+
Sbjct: 58  NFKEKEVRFYPNEAREAGVTYDAPFKGEVSLYEGVDSDEPIHKV-------DVDLGRMPI 110

Query: 138 MTKD------------------------GTFVIKGIQRIV-----------VSQLHRSPG 162
           M K                         G F++ G +++V           V+ LHR   
Sbjct: 111 MVKSRFCHLNGLSSEELIEKREEELEQGGYFIVNGNEKVVRMLVMTKANHPVA-LHR--- 166

Query: 163 IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-------RIDRRRK---V 212
                   +A  +    Y    I  + +  D    + ++ ++       R   RR+   +
Sbjct: 167 --------KAWTNRGPGYTKFGITIRCVRPDRTSITNNLHYISDGQITLRFLYRRQEFFL 218

Query: 213 PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
           P T  L AL   +E      Y  +V     + +        L      + +  +    E 
Sbjct: 219 PATLLLKALKDTTE---REIYENLVQGDNENTFLTDRVELSLREQKINNINTQE----EV 271

Query: 273 VIESGKKLTSG--LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           +   G +  +   L  S     +    I S     L   +D  N     I      V  +
Sbjct: 272 LDYIGSRFRARSQLPSSFSNTQIGQWFIDSYVFVHLPNYKDKYNLLVLMIQKLYSMVAGK 331

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
              + I  +   ++ +         + +   L       R   L       +  D     
Sbjct: 332 SGTDNIDSAAFHEVLLA---GQIFGSILGEKLTEYLESTRSFTLKHFEDKKKENDKLENV 388

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             +++                G ++ N  L+L        I      A     +   +  
Sbjct: 389 FKKTVEKNFKIGDRFNYFLATGNLRSNSGLDLQQTSGFVVI------ADKLNFLRFISHF 442

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            +I         +  S+ +++   +  L  +         + +    + +          
Sbjct: 443 RSIHRGAFFATMKTTSIRKLMPESWGFLCPVHTPDGAPCGLLNHLTSACLVTVDPLQDQK 502

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           V        S   +     ++  +  +H      L    + +         V    Y R 
Sbjct: 503 VLKARPLIPSFLATHGMLPIDMTTVFSHQYLTITLDGCVIGKIEQKAGEELVTMLRYLRS 562

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
              E +    I +  S  S    + Y  I          +    V+ L++ +EE   I  
Sbjct: 563 VGTEPAIPKTIEISYSPPSSVENSQYPGISLF---TSGARFMRPVINLTSGKEE--LIGP 617

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                 E      E++                  I+ SP  + S+ A+L PF + + S R
Sbjct: 618 QEQLYMEIAVVPNEVIKG------------VTTHIETSPTAMFSLLANLTPFSDYNQSPR 665

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD--AIRIVIRS 747
            +  C M +Q +       PF        +       +  K        D       + +
Sbjct: 666 NMYQCQMAKQTMGTPLHSYPFRTDNKLYKIQNIQKPIVHTKNQFKYRVNDYAHGCNAVIA 725

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV--RRNDIIADGPSTDLGDL 805
           V  +         I     ++R   +        V   + +         +   T  G  
Sbjct: 726 VISNTGYDMEDAMIINKSAYERGFGHGS------VYKNEYIDLDEGLSRFESKKTFFGRP 779

Query: 806 ALGRNMLVAFMPWHGYNFEDSML 828
               + L  F+   G  F   ++
Sbjct: 780 NSSVDNLGDFIDVDGLPFVGRLI 802


>gi|301500937|ref|YP_003795402.1| RNA polymerase beta subunit [Alveolata sp. CCMP3155]
 gi|300069483|gb|ADJ66590.1| RNA polymerase beta subunit [Chromerida sp. RM11]
          Length = 1069

 Score =  271 bits (694), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 104/303 (34%), Positives = 146/303 (48%), Gaps = 49/303 (16%)

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +    L V +  +   R I++GDK+ GRHGNKG+VS I P  D P+  DG   DI+++P
Sbjct: 806  QLGLDDLPVFRCVLGKFRHIEAGDKLCGRHGNKGVVSAIWPQADFPYTADGLIPDILVSP 865

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            LGVPSRMNVGQI ET  G      G    S      +  +   +R     +    +    
Sbjct: 866  LGVPSRMNVGQILETLFGL----TGFFSDSRCKVNVSAENDYEIRHKRNVLYHKLN---- 917

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                            +  ++   + +    G+ +L DG T   
Sbjct: 918  ------------------------------SVQEYSNYKTLFNPFVPGKVLLRDGRT--- 944

Query: 1245 FDRPVT----VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
              R V     +G  Y+ KL HMV DK+ ARS G Y+ +TQQP+ GK   GGQR GEME W
Sbjct: 945  -SRAVFGGSVLGLSYIFKLTHMVQDKITARSQGVYAEITQQPVRGKWKLGGQRFGEMEAW 1003

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF---ETGTPESFNVLVKEMQAL 1357
             ++A+GAAY L+++LT+KSD    R   YE+I          E G PE ++VLVK + +L
Sbjct: 1004 AMEAFGAAYELRDLLTLKSDATGYRDIAYETIFFDQLNPRSSEMGFPECWHVLVKHLNSL 1063

Query: 1358 GLS 1360
            G+ 
Sbjct: 1064 GIE 1066



 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 127/499 (25%), Positives = 225/499 (45%), Gaps = 30/499 (6%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR--------RVRS 466
           ++  RL+ D      +  K D++ ++ +  D   G  +  + D++G+R         +  
Sbjct: 260 QIQSRLSSDKNSTALYCSKYDLLHVLDVFFDSIVGGRSSINTDHMGHRIVSTWNFALLEC 319

Query: 467 VGEMLKNQYRLGLLRM-ERSIKERISSVDIDSVMPQD-----LINAKPVVSAVCEFFCSS 520
           +  +L   +  G L + E       ++ D D  +P+          + V+  + E    +
Sbjct: 320 IQSVLSQVFSTGDLLVSEPDPSGSRTTCDTDEELPESLTKAFKTMNQKVMDGIYEILTVN 379

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            LSQ  +  N L+   H  +LS+   GG +        RDV P+ +G++C   T +G N 
Sbjct: 380 PLSQYLDQTNVLAEYVHLHKLSSKALGGSSPTALL---RDVAPSSFGKLCSLYTIDGENA 436

Query: 581 GLVSSLTSFARVNAYGFIETPYRKV-CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           G V+   S AR +  G ++T  R        T+ V  ++ +E E   ++           
Sbjct: 437 GTVNQYASLARGSQGGELKTIVRLAPRGSCHTDRVALVNTIELEETPVSIHPLIWRRSEV 496

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                   +   E       K+          ++   +LIPFL +DD  R LMG NMQRQ
Sbjct: 497 SVLPRAVVQERNEFKTREITKVSLFCPDSTSFLAPQVNLIPFLWHDDPTRCLMGANMQRQ 556

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AV LL A+   V TGM+++++  +G  + +   G+V  V    I +R         +   
Sbjct: 557 AVSLLSAQKSVVSTGMDTLLSSLNGNGLHSLTEGVVTCVTQNAIYMRD--------SFNR 608

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           ++  L  F  SNQ    +  P+V  G+ V    ++A       G+L LG+N+ VA+  W+
Sbjct: 609 ELRYLFPFTISNQKQIRHYYPVVWEGERVFPGQLLAQNQGVHEGELCLGQNLFVAYASWY 668

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GY +ED++L++ER+V E   TS+ + + +VM  +     EEIT  +P V  + L  +++ 
Sbjct: 669 GYTYEDAILLNERLVYERTLTSVSMAQKDVMLEE----HEEITSFLPGVDFKDLCLLNQV 724

Query: 880 GIICVGAEVNPGDILVGKI 898
           GI  +G+ V     ++GK+
Sbjct: 725 GIAPLGSLVEREMAIIGKV 743


>gi|170516901|gb|ACB15386.1| RpoB [Bifidobacterium longum]
          Length = 469

 Score =  271 bits (694), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 167/363 (46%), Positives = 248/363 (68%), Gaps = 16/363 (4%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
            +   + + L  +  + + +AL+D+YR +RP D  T    +++ +  +F++ +YDL+ VG
Sbjct: 106 KDYPLVLDALEKETLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVG 165

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDID 457
           R K+N +L ++   + R + +EDIIA IK LV L +G               +  +DDID
Sbjct: 166 RYKINRKLGVEADFNDRSLHQEDIIATIKYLVALHDGAATFPGKRNGEDVDLRVDVDDID 225

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           + GNRR+R VGE+++NQ R GL RMER ++ER+++ D +++ PQ LIN +PV + + EFF
Sbjct: 226 HFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDAEAITPQSLINIRPVNATIKEFF 285

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            +SQLSQ  +  N LS +T+ RRLSALG GG++R RA +E+RDVHP+H+GR+CP E+ EG
Sbjct: 286 GTSQLSQFMDQNNPLSGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEG 345

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL +F RVN +GFIETPYRKV +G VT++V Y++A  + +  IAQAN  LDE+
Sbjct: 346 PNIGLIGSLATFGRVNPFGFIETPYRKVVNGHVTDEVEYMTADRDLDHVIAQANQELDEN 405

Query: 638 GSFTEELVFCRCAGEE-ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           G+F ++    R   EE + VP   +D++D SP+Q+VS+ ASLIPFLE+D+ +R LMG NM
Sbjct: 406 GNFVQKSALARVGEEEAVDVPVSSVDYMDVSPRQMVSLGASLIPFLEHDEGHRALMGTNM 465

Query: 697 QRQ 699
           QRQ
Sbjct: 466 QRQ 468



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 62/181 (34%), Positives = 97/181 (53%), Gaps = 6/181 (3%)

Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
           K Q+++MGD PL T  GTF+I G +R++VSQL RSPG++FD  + R   S K ++  +II
Sbjct: 1   KSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRQQDRT--SDKEVFGAKII 58

Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGD 243
           P +G W++ E D KD   VR+DR+RK     FLMA+GM   EI   F  YP ++ +   +
Sbjct: 59  PSRGAWLEFEIDKKDQPQVRVDRKRKQSAIVFLMAIGMTKSEIAQAFKDYPLVLDALEKE 118

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSD 301
                  A   +      +     + G+ +++S    T    L +  + K  + LG+ +D
Sbjct: 119 TLETQDEALVDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLGVEAD 178

Query: 302 C 302
            
Sbjct: 179 F 179


>gi|530427|emb|CAA83749.1| DNA-directed RNA polymerase (beta) [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 356

 Score =  271 bits (694), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 171/348 (49%), Positives = 243/348 (69%), Gaps = 8/348 (2%)

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           +N         + + +   T    YL+A +E+N  IAQ+N + DE+G   +E++  R  G
Sbjct: 5   MNMDLLQXHIEKLLMELFKTIKFEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSRFNG 64

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           ++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K E+P V
Sbjct: 65  DDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIKPESPIV 124

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L  ++RSN
Sbjct: 125 ATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILSDYERSN 176

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
             T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED++++SE
Sbjct: 177 NGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFEDAIVMSE 236

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V +D FTSIHI+E+ +  R+TK G EE+TR+IPN+SE+  +++D  GI+ +G EV  G
Sbjct: 237 RIVIDDRFTSIHIDEYTLEVRNTKQGQEEVTREIPNMSEQAKRHLDAEGIVAIGTEVKVG 296

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           D+LVGK+TPKG+  ++PE+KLL AIFGEK+ +V+D SLRVP+G  G V
Sbjct: 297 DVLVGKVTPKGQVQLSPEDKLLHAIFGEKSRNVKDNSLRVPNGGEGLV 344


>gi|74826449|sp|Q9NJN5|RPOB_NEOCA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|6492294|gb|AAF14261.1|AF138960_2 DNA dependent RNA polymerase beta subunit [Neospora caninum]
          Length = 1050

 Score =  271 bits (694), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 109/407 (26%), Positives = 181/407 (44%), Gaps = 48/407 (11%)

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            +E   +E+  +    ++ +    I     +IL G   ++  K  K +   +   I +   
Sbjct: 674  IEFSTLEIPKQSYYIKKSLDSLGIVKEGEKILTGNILLTKIKVTKPN--YTYKSIFKLIY 731

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
            S  +   +++ K              SK  L     N   K      +        ++F+
Sbjct: 732  S-IFGKTIRNIKDNSLYIQTGKNGRVSKIELFLINTNSHYKTYNNSYL------KCRIFI 784

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
              +R +  GDK+ GR+GNKGI+S I    D+PFL++    DI++  LG+PSRMN+GQ+FE
Sbjct: 785  CKQRFLTVGDKLCGRYGNKGILSYIAENADLPFLQNSFYPDIIVGALGIPSRMNLGQLFE 844

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G        +I        +N   + L+  +   +                   +  
Sbjct: 845  ALVGKIGFSYNIRI-LPSFTSSSNAYFNYLKILIYNFL-------------------MFN 884

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              K G                 + L   +L   G+ ++ DG TG      V  G     K
Sbjct: 885  NLKKGF----------------NWLYNFNLP--GKFLIRDGRTGIKLKSSVLCGVSRYSK 926

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            L HM+ DK++ R+TG Y+ + QQPL GK N GGQR GEME+W ++A+GA+Y L+E+L  K
Sbjct: 927  LIHMIKDKLHFRTTGPYTEILQQPLKGKKNLGGQRFGEMEIWALEAFGASYNLKEILNYK 986

Query: 1319 SDDVVGRTRVYESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLE 1364
            SDD   R  + + ++   ++   +   ESF V++KE   L L+++L 
Sbjct: 987  SDDCFARNNLKDYLLFRNSELQNSTITESFRVILKEFNGLILNLELF 1033



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 156/723 (21%), Positives = 294/723 (40%), Gaps = 47/723 (6%)

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID------------TGEQVIESGK 278
            F   + Y         PL   +L        +L+  +             G + I   K
Sbjct: 67  HFLDNVQYINSLIKIFLPLKFQNLKTNQIFFKNLLIFELPKYNSHNYCYLNGLKKIFISK 126

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
             TS  +   K    K+    +  L       +IV     +    +   +    +  +++
Sbjct: 127 YFTSNGIFFHKYLKRKYDIYYAKILLTNSNFFNIVLDLKLKQIYLSIKNLKFNFILFLYY 186

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             I +  IL       +  ++  + T    +  +    I + +            +    
Sbjct: 187 LGINNKDILKYSRYKKSKILKLLIFTALQTNLINNKKFILKNLNYLKSIFKVTNLNKNYK 246

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
            F  +        G    N  L +            D I I+ +L+DL++ K    +ID+
Sbjct: 247 HFIINKNKLNYNYGNFNKNNFLTI------------DFIFILDLLLDLQSKKLCFKNIDH 294

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L N+ + ++G   ++ ++  L +    I   I       +                E   
Sbjct: 295 LDNKHINTIGNYFQHNFKFYLKKFISIIPNLIKLKKFSLLKV----------YNFKELLI 344

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            + L Q  E +NS S +TH  +L+          +  + +R++     G++C  +T+EG 
Sbjct: 345 LNPLIQYLEQINSFSELTHKYKLNNYNSS----LKGILNLREICLNQIGKLCLIDTTEGI 400

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           N GL+ +     R+   G I+     V   K    + + +++++E   I   N +L ++ 
Sbjct: 401 NCGLIVNFAKHIRIYKKGIIQIYVSPVFKNKTKEFINFKTSLDQELYLIQFNNINLRKNK 460

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            F E +          +               + S   +LIPF++ +D  R LMG  MQ 
Sbjct: 461 LFNENIKVVYNKNNFRIKFISNKKSFLLKFADLFSFTENLIPFIKYNDPARCLMGAKMQS 520

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           Q+VPLL  +  FV TG E  +   S   I A + GIV    +++I I+ +          
Sbjct: 521 QSVPLLNKKKSFVVTGYEKEIITKSDITIKALQEGIVLNASSLKIHIKDLFNREI----- 575

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +Y L K+++SNQNT ++Q+PLV  G+ V  N ++         + A+G N+L+ +  +
Sbjct: 576 --VYYLSKYKKSNQNTLIHQKPLVWNGERVFTNQLLTQHQDIIDSEFAIGNNLLIYYGNF 633

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVSEEGLKNID 877
            GY+FED+++ S+R++ + +F+S+H++ +E           E +  +IP  S    K++D
Sbjct: 634 CGYDFEDAVIGSKRVLYQQLFSSLHMDIYEFNFGYNNENDIEFSTLEIPKQSYYIKKSLD 693

Query: 878 ECGIICVGAEVNPGDILVGKI-TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             GI+  G ++  G+IL+ KI   K         KL+ +IFG+   +++D SL + +G +
Sbjct: 694 SLGIVKEGEKILTGNILLTKIKVTKPNYTYKSIFKLIYSIFGKTIRNIKDNSLYIQTGKN 753

Query: 937 GTV 939
           G V
Sbjct: 754 GRV 756


>gi|297851416|ref|XP_002893589.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp.
            lyrata]
 gi|297339431|gb|EFH69848.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp.
            lyrata]
          Length = 1188

 Score =  271 bits (694), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 77/348 (22%), Positives = 124/348 (35%), Gaps = 76/348 (21%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D       +   +     R    GDK + RHG KG+ S++ P  +MPF    G   D+++
Sbjct: 881  DMKSKKHPQKANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIEMPFNGVTGMRPDLII 940

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +              R  ++K  G     
Sbjct: 941  NPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPF-----------RDAVKKTNGEKESK 989

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                               + + SML+    +  G   LY G  G
Sbjct: 990  SSLL-----------------------------VDDLGSMLKEKGFNYYGTETLYSGSLG 1020

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T QP+ G+   GG R GEME   +
Sbjct: 1021 VELKCEIFMGPVYYQRLRHMVSDKFQVRSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSL 1080

Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVY--------------ESIVAGNDTFETG------ 1342
             A+GA+Y+L + L   SD  +                    + ++  N     G      
Sbjct: 1081 LAHGASYLLHDRLHTSSDHHIADVCSLCGSLLTSSVVNVQQKKLIKVNGKLPPGRTPKKV 1140

Query: 1343 ---------------TPESFNVLVKEMQALGLSIDLENSRTKNSAKME 1375
                            P  F  L  E+ ++ + + L+ S    + + +
Sbjct: 1141 TCHSCGTSKGMETVAMPYVFRYLAAELASMNIKMTLQLSDRGVADEEK 1188



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 85/619 (13%), Positives = 191/619 (30%), Gaps = 83/619 (13%)

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F  +    +K     V    +   L +   +D  H +   +I II+ L  L +     D+
Sbjct: 312 FQPVLDGLEKESHPMVAEAVLRDYLFVHLDND--HDKFNLLIFIIQKLYSLVDQTSLPDN 369

Query: 456 IDNLGNRRVRSVG--------EMLKNQYRLGLLRMERSIKERISSVDIDSV----MPQDL 503
            D+L N+ +   G        E L++  R     ++  +    S    +S+       + 
Sbjct: 370 PDSLQNQEILVPGHVITIYLKEKLEDWLRKCKSLLKDELLNTSSKFSFESLADVKKLINK 429

Query: 504 INAKPVVSAVCEFFCSSQLSQL--EEHVNSLSRITHTRRLSALGQGGVARAR-------- 553
              + + +++     +  L      +            RL+ L      RA         
Sbjct: 430 NPPRSIGTSIETLLKTGALKTQSGLDLQQRAGYTVQAERLNFLRFLSFFRAVHRGASFAG 489

Query: 554 -AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG---- 608
                +R + P  +G +CP  T +G   GL++ +T  +R+ +    +   R         
Sbjct: 490 LRTTTVRKLLPESWGFLCPVHTPDGTPCGLLNHMTCTSRITSQFDSKGNIRDFLKIRKSV 549

Query: 609 --------KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF---CRCAGEEILVP 657
                    V++    + A   +  ++      +    S     V     R   E   V 
Sbjct: 550 VEVLTGAGMVSSLPKLVRAGPPKVIHVLLDGQVVGTLSSNLVTKVVSYLRRLKVEAPSVI 609

Query: 658 RE--KIDFIDASP---KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            E  ++ ++  S       + +A+    F+    +  +             +  E     
Sbjct: 610 PEDLEVGYVPISMGGSYPGLYLASCPARFIRPVKNISIPSENIELIGPFEQVFMEISCPD 669

Query: 713 TGM-------ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-L 764
            G         +   +     +++  A +    D  +      +  +   T         
Sbjct: 670 GGNGGRNNSSPATHEEIHPTGMISVVANLTPWSDHNQSPRNMYQCQMAKQTMAYSTQALQ 729

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +  +   +    Q P+V+               +  + +   G N +VA +   G++ E
Sbjct: 730 FRADQKIYHLQTPQSPVVRTKTYT----------TYSIDENPTGTNAIVAVLAHTGFDME 779

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARD-------TKLGPEEITRDIPNVSEEGLKNID 877
           D+M++++  V   +    H + ++    D          G +   R   + S+     ID
Sbjct: 780 DAMILNKSSVERGM---CHGQIYQTENIDLSDQNSRYDSGHKSFRRSTTDKSDHS--RID 834

Query: 878 ECGIICVGAEVNPGDILV-------GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
             G+  VG ++ P +          GK          P      ++  +     +  ++R
Sbjct: 835 ADGLPYVGQKIYPDEPYCRIYDEVTGKQRLMKGKGTDPVIVDFVSVDMKSKKHPQKANIR 894

Query: 931 VPSGVSGTVVDVRIFNRHG 949
                   ++  +  +RHG
Sbjct: 895 FRHA-RNPIIGDKFSSRHG 912



 Score = 48.9 bits (115), Expect = 0.006,   Method: Composition-based stats.
 Identities = 96/762 (12%), Positives = 190/762 (24%), Gaps = 143/762 (18%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM------LEFVS 78
           ++ +L+     S+D+             +GL   F  + P++ +           L F+ 
Sbjct: 18  ELHNLVTHHIESFDYMTQ----------KGLDVMFNRIKPVSVYDPNTENELSNILFFMI 67

Query: 79  YEFDPP-KFDVD----------------DCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
              + P  F                   +C    ++Y       +     D         
Sbjct: 68  LWLENPVVFAPQKESFRSTSRKEPLLPFECRQAKISYTGTFMADVCFKYNDGVVVRDRFD 127

Query: 122 IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI---VV 154
                      G  P+M                           G F++ GI+R+   V+
Sbjct: 128 ----------FGQFPIMLMSKLCSLRGADCRKLLKCKESTSEMGGYFILNGIERVFRCVI 177

Query: 155 S-------QLHRSPGIHFDHDKGRA-------------SLSGKLLY-----ACRIIPDQG 189
           +        + R      D  +G               S     LY     + R+    G
Sbjct: 178 APKRNHPTSMIR--NSFRDRKEGYTEKAVVTRCVRDDQSSVTVKLYYLRNGSARV----G 231

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD-SEEILSTF--YPKIVYSQRGDFWC 246
            W+             + R   +PV   L AL     EEI  +        Y +      
Sbjct: 232 FWI-------------VGREYLLPVGLVLKALTNTCDEEIYESLNCCYSEHYGRGDGAIG 278

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF------LGITS 300
             L      +       L     G    E  +K      + + +   K         +  
Sbjct: 279 TQLIRERAKIILDEVRDL-----GLFTREQCRKHLGQHFQPVLDGLEKESHPMVAEAVLR 333

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR- 359
           D L      +         I  +   ++D+ SL +   S      ++    +      + 
Sbjct: 334 DYLFVHLDNDHDKFNLLIFIIQKLYSLVDQTSLPDNPDSLQNQEILVPGHVITIYLKEKL 393

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
              +       KD LL+         ++      +        +    L   G +K    
Sbjct: 394 EDWLRKCKSLLKDELLNTSSKFSFESLADVKKLINKNPPRSIGTSIETLLKTGALKTQSG 453

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
           L+L                 +  L  L   +         G R       + ++   L  
Sbjct: 454 LDLQQRAGYTV-----QAERLNFLRFLSFFRAVHRGASFAGLRTTTVRKLLPESWGFLCP 508

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +         + +    +       ++K  +    +   S  +  L       S     R
Sbjct: 509 VHTPDGTPCGLLNHMTCTSRITSQFDSKGNIRDFLKIRKSV-VEVLTGAGMVSSLPKLVR 567

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
                    +   +    +     T           E  ++        +  ++  G   
Sbjct: 568 AGPPKVIHVLLDGQVVGTLSSNLVTKVVSYLRRLKVEAPSVIPEDLEVGYVPISMGGSYP 627

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
             Y   C  +    V  +S   E        N  L          + C   G        
Sbjct: 628 GLYLASCPARFIRPVKNISIPSE--------NIELIGPFEQVFMEISCPDGGNGGRNNSS 679

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                +  P  ++S+ A+L P+ +++ S R +  C M +Q +
Sbjct: 680 PATHEEIHPTGMISVVANLTPWSDHNQSPRNMYQCQMAKQTM 721


>gi|300708202|ref|XP_002996285.1| hypothetical protein NCER_100631 [Nosema ceranae BRL01]
 gi|239605574|gb|EEQ82614.1| hypothetical protein NCER_100631 [Nosema ceranae BRL01]
          Length = 1054

 Score =  271 bits (694), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 123/312 (39%), Gaps = 56/312 (17%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
                 +   + R    GDK   RHG KG+ S   P  DMPF + G   DI++NP   PSR
Sbjct: 789  NLCANIKFRIIRNPNIGDKFCSRHGQKGVCSMHWPSIDMPFTESGIVPDIIINPHAFPSR 848

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G + E+  G +   LG+   +   +     + + ++                     
Sbjct: 849  MTIGMLIESMAGKSGCCLGEIQDATPFEKNTFLNNNDVQR-------------------- 888

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                    +E +I   L     +  G   +Y G+TG  F   + 
Sbjct: 889  ------------------------NEPSIGDQLIQHGFNYYGNEPMYSGITGTEFKTDIF 924

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G ++  +L HMV+DK   R++G+    T+QP+GG+ N GG R GEME   + A+G  Y+
Sbjct: 925  IGVVFYQRLRHMVNDKYQVRASGAVVATTRQPVGGRKNLGGVRFGEMERDAMIAHGTPYL 984

Query: 1311 LQEMLTIKSDD-VVGRTRVYESI--------VAGNDTFE-TGTPESFNVLVKEMQALGLS 1360
            L + L   SD  V       +SI        + G   F     P  F  L  E+  L ++
Sbjct: 985  LNDRLLKCSDHSVFTFCCTCKSILFANNDKCICGGKIFNTVEMPYVFKYLCSEL--LAMN 1042

Query: 1361 IDLENSRTKNSA 1372
            I +     +   
Sbjct: 1043 IRVILDVKQPVI 1054



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 124/948 (13%), Positives = 247/948 (26%), Gaps = 208/948 (21%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD----- 87
              SY+      +          +   K V P+T   G+  +E   +    P        
Sbjct: 10  HIESYNALFYNKVF---------KNIIKKVKPLT--IGSFRMEIADFTVHQPFITERNNI 58

Query: 88  -------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
                    +    + TY   + I   L   D    +  +            G  P+M K
Sbjct: 59  SLDRRLLPREARLTNTTYKGKIFIKFSLFYDDKLISSEFRPC----------GGFPIMVK 108

Query: 141 DGT----------------------FVIKGIQRIV---VSQLHRSPGIHFDHDKGRASLS 175
            G                       F+I GI +++   + Q    P       K +   +
Sbjct: 109 SGYCHLLDEPNPNSIDEDENDIGGYFIINGIDKLIRFHIMQKRNYPFALCRPQKNKN-YT 167

Query: 176 GKLLYACRIIPDQG-------LWMDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDS 225
              +Y    I   G        ++    D  D+ + R  RRR    +P+   L AL   +
Sbjct: 168 DNYIY----IRSVGDDELGHVGYLHYSIDG-DVFY-RFFRRRNEFHIPIIIILKALVNTT 221

Query: 226 E-EILSTFYPKIVYSQRGDFWCFPLSAAD----LMVGAKVSSSLVDIDTGEQVIESGKKL 280
           + EI       I  +            +       +GA+   S+      E  IE     
Sbjct: 222 DQEIYKMLNNDIYITVALKKATKEEVFSRAECIEYIGARFKQSMNASTNEEACIEILDTY 281

Query: 281 TSGLLKSLKEKG---VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
               L   ++K    +  +      + G  + ED  +  + E+  E     +      IF
Sbjct: 282 VCPHLTKNQDKFNFLIYSIKKLFSLVKGEIIPEDSDSPASHEMLTETQLFAN------IF 335

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
             ++ D+   +   +      +N    D  K+++  L            S  +   +   
Sbjct: 336 KDKLEDLKRSFKAQIMRTFLRKNGKRKDYEKNKEPIL-----------PSLENCMHAFKY 384

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                  +   S +    +N++ + D           + I   + +   R+    ++   
Sbjct: 385 LDCASVGRAFESFLSTGNINIQNSSDILQSAGFSIMAERINFYRYISHFRS----LNRGS 440

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                R   V ++    +              + + D         + +   +      F
Sbjct: 441 FFQEVRTTGVRKLRSESWGFFCP---------VHTPDGTPCGLLTHLTSAASLVNFTNNF 491

Query: 518 CSSQLSQLEEHVNSLSRITHTR--RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
             + L       +    I          L            ++R     +   +     S
Sbjct: 492 DYNLLYSFGIIPSHRQFINGISVFYNGLLIGYTFNPCDLTNKLRKYRRDNNLSLEIIHYS 551

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                     L  +  V  Y  +    R V   K +  +  +  ME+    I   + ++ 
Sbjct: 552 G---------LKLYETVLIYNTVSRLIRPVL-HKESGKIEMVGIMEQVFLDINLNDMTVY 601

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +D                     +  ++ +   + + SI ASL PF E + S R +  C 
Sbjct: 602 KDSPNI----------------SKCFEYQEVDNQNIFSIVASLTPFSEYNQSPRNMYQCQ 645

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +Q++                     S                                
Sbjct: 646 MAKQSMG---------HPAHNIKTRNDS-------------------------------- 664

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                                 Q P+V+        D              LG N +VA 
Sbjct: 665 --------------KIYMLNYTQHPIVQNKKYSLVQD------------YPLGLNCIVAV 698

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + +  Y+ ED+M+I++  +   +FT    +  ++                   + + L  
Sbjct: 699 LSYTAYDMEDAMVINKGSMERGLFTGYVYKVDKIELPKDCCFSYLPDVGCKINTGDILYK 758

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             + G           D  + +     E+         R I      D
Sbjct: 759 YTDFGGKETSVLCKSSDGYIIESVDIFENENLCANIKFRIIRNPNIGD 806


>gi|6449128|gb|AAF08838.1| RNA polymerase beta subunit [Streptococcus cristatus ATCC 51100]
          Length = 290

 Score =  271 bits (693), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 163/297 (54%), Positives = 213/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R  
Sbjct: 61  NKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|311033950|gb|ADP55401.1| RNA polymerase beta subunit [Bacillus atrophaeus]
          Length = 148

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 64/160 (40%), Positives = 101/160 (63%), Gaps = 12/160 (7%)

Query: 58  AFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
            F+ + PI  F+G   LEF+ Y    PK+ V++   RD+TY+ PL++ +RLI        
Sbjct: 1   MFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLI-------- 52

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
             K   ++K+Q ++MGD P+MT  GTF+I G +R++VSQL RSP ++F    G+   +GK
Sbjct: 53  -NKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNGK 108

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
             +   +IP++G W++ E D+KD+++VRIDR RK+PV   
Sbjct: 109 KGFTTTVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVWVL 148


>gi|108885357|gb|ABG23195.1| DNA-directed RNA polymerase [Geobacillus toebii]
          Length = 145

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 67/167 (40%), Positives = 101/167 (60%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYKWFL----------DEGLREMFKEISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYSEKVDK---NGKRGYSATVIPNRGAW 145


>gi|50552684|ref|XP_503752.1| YALI0E09845p [Yarrowia lipolytica]
 gi|49649621|emb|CAG79343.1| YALI0E09845p [Yarrowia lipolytica]
          Length = 1165

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 111/276 (40%), Gaps = 53/276 (19%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E  F  ++ K+   D +  G L+ + V + + R    GDK + RHG KG+ S+  
Sbjct: 847  KYKSGETGFVEEV-KLLGDDSL--GELQKITVKLRIPRSPVIGDKFSSRHGQKGVCSQKW 903

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P  DMPF + G   D+++NP   PSRM +G   E+    +    G    +    +     
Sbjct: 904  PTYDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAAKSGALHGMAQDATPWQFSETNT 963

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
             +                                                  E     L 
Sbjct: 964  AA--------------------------------------------------EYFGEQLL 973

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A  +  G   +Y G+TG+     + VG ++  +L HMV+DK   RSTG  + +T QP+ 
Sbjct: 974  KAGYNYHGNEPMYSGVTGQELRCDIYVGVVFYQRLRHMVNDKFQVRSTGPVNPLTMQPVK 1033

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G+   GG R+GEME   +  +G +Y+LQ+ L   SD
Sbjct: 1034 GRKRSGGIRVGEMERDALIGHGTSYLLQDRLLNCSD 1069



 Score = 76.3 bits (186), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 88/597 (14%), Positives = 176/597 (29%), Gaps = 76/597 (12%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR-PGDVSTFSVAESMFNFLFFDSDKYDL 408
           D    +  + +        DR + LL  Y+  +        +     F  +         
Sbjct: 266 DREIFDGIVASEGSNSFLTDRLELLLRNYKSYKLTSKQENLAFLGEKFRIVMDAPKDMSN 325

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR+ +   + +   D+    +   ++ +I+ L  L   + + D+ D + ++ V   G
Sbjct: 326 EDVGRLMLKRVILVHLQDN--TDKFRMLLFMIRKLYALVASECSPDNPDAVQHQEVLLGG 383

Query: 469 EMLKNQY----------RLGLLRMERSIKERISSVDIDSVMPQDLIN-AKPVVSAVCEFF 517
            +                   +R E   K++   +D   +M +      + +   +  F 
Sbjct: 384 FLYGMIIKERMEEYLSNFCATVRTELQKKKQSLHLDDPKIMQRICPRINEDIGRKLHYFL 443

Query: 518 CSSQLSQLE--------------EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L                  E +N    I H R    + +G         ++R + P
Sbjct: 444 STGNLVSHTGLDLQQTTGYTVIVEKINFHRFIAHFR---MIHRGSFFAELKTTDVRKLLP 500

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG-----------KVTN 612
             +G +CP  T +G   GL++ L     ++           V +                
Sbjct: 501 ESWGFLCPVHTPDGSPCGLLNHLAHKCLISVKKSDVGDIDSVLNQLGISPAGALANTPQK 560

Query: 613 DVVYLSAMEEE--NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
            VV L           IAQ  ++       T +        E  LVP  +       P  
Sbjct: 561 SVVMLDGKIIGWCTHEIAQQAANTIRQWKVTGDARLP-QDLEVGLVPPSRGGQY---PGL 616

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL---KAEAPFVGTGMESVVAKSSGAAI 727
            +   AS         +           Q    +     E   V + +E      S   I
Sbjct: 617 YLFAEASRFMRPVKHLATEKEDIVGPFEQVYLNVAVTPDEITNVHSHVEY-----SPTNI 671

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           ++  A +    D  +      +  +     G       +           Q P+V+ G  
Sbjct: 672 LSILANMTPFSDFNQSPRNMYQCQMGKQAMGTPGVLTHRSDNKMYRLQTGQSPIVRAGLF 731

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                         L +   G N +VA + + GY+ +D+M+I++           H   +
Sbjct: 732 DEYG----------LDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFG---HGTIY 778

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKN-------IDECGIICVGAEVNPGDILVGK 897
           +    D     +     + +               +D  G+  VGA+++ GD +   
Sbjct: 779 KTEKVDLTEKQKPGDPTLLHFGFGPDNWPREWTQTLDVDGLPLVGAKLSNGDPIAAY 835



 Score = 65.1 bits (157), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 96/795 (12%), Positives = 215/795 (27%), Gaps = 112/795 (14%)

Query: 66  TAFSGAAMLEFVSYEFDPPKFD------------VDDCLWRDLTYAVPLKITLRLIVFDV 113
                   +   + +   P                 +C  R  TY   + +TL   V   
Sbjct: 71  ENLGNRLAIRVANVQLGRPTVSANDKTTINRKVFPSECRERMATYRARMVLTLGYSVNGG 130

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGI 149
            E   ++ +          G +P+M                         + G FVI G+
Sbjct: 131 PEKFESRDV----------GMIPIMMGSNRCHLEGMGPKDMVAHKEESEEQGGYFVINGL 180

Query: 150 QRIV---VSQLHRSPGIHFDHDKGRASLS----GKLLYACRIIPDQGLW---MDIEFDSK 199
           ++++   + Q    P         +   +    G  + + R  PDQ      +    D  
Sbjct: 181 EKLIRLLIVQRRNHPLAIIRKSFTKRGSNYTTFGVQIRSVR--PDQSSQTNVLHYLSD-- 236

Query: 200 DIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
             I +R   R+    VPV   L AL +++ +     +  IV S+  + +        L+ 
Sbjct: 237 GGITMRFSWRKNEYLVPVMMILKAL-VETND--REIFDGIVASEGSNSFLTD-RLELLLR 292

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGE 316
             K S  L         +    ++     K +  + V  L +    L  L    D     
Sbjct: 293 NYK-SYKLTSKQENLAFLGEKFRIVMDAPKDMSNEDVGRLMLKRVILVHLQDNTDKFRML 351

Query: 317 TG---EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                ++Y          + + + H E+     LY         I+  +    +      
Sbjct: 352 LFMIRKLYALVASECSPDNPDAVQHQEVLLGGFLY------GMIIKERMEEYLSNFCATV 405

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             ++ +  +   +    + + +   +  D  +     +    +     LD      +   
Sbjct: 406 RTELQKKKQSLHLDDPKIMQRICPRINEDIGRKLHYFLSTGNLVSHTGLDLQQTTGYTVI 465

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISS 492
            + I   + +   R     I         +   V ++L   +  L  +         + +
Sbjct: 466 VEKINFHRFIAHFR----MIHRGSFFAELKTTDVRKLLPESWGFLCPVHTPDGSPCGLLN 521

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
                 +     +    + +V      S              + +T + S +   G    
Sbjct: 522 HLAHKCLISVKKSDVGDIDSVLNQLGIS----------PAGALANTPQKSVVMLDGKIIG 571

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E   +       I   + +    +     +      +  G     Y      +   
Sbjct: 572 WCTHE---IAQQAANTIRQWKVTGDARLPQDLEVG-LVPPSRGGQYPGLYLFAEASRFMR 627

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            V +L+  +E+   I      +  + + T + +                  ++ SP  ++
Sbjct: 628 PVKHLATEKED---IVGPFEQVYLNVAVTPDEITNVH------------SHVEYSPTNIL 672

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           SI A++ PF + + S R +  C M +QA+             M  +    S         
Sbjct: 673 SILANMTPFSDFNQSPRNMYQCQMGKQAMGTPGVLTHRSDNKMYRLQTGQSPIVRAGLFD 732

Query: 733 GIVEQVDAI-RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                        + +V            I      +R   +  + +   V + ++ +  
Sbjct: 733 EYGLDNFPNGMNAVVAVISYTGYDMDDAMIINKSAHERGFGHGTIYKTEKVDLTEKQKPG 792

Query: 792 DIIADGPSTDLGDLA 806
           D           +  
Sbjct: 793 DPTLLHFGFGPDNWP 807


>gi|269930839|gb|ACZ54154.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 290

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 210/291 (72%), Positives = 245/291 (84%), Gaps = 1/291 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           GAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 GAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 290


>gi|103001423|gb|ABF71507.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 693

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 115/814 (14%), Positives = 235/814 (28%), Gaps = 145/814 (17%)

Query: 469  EMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----- 521
             +L N +R+   ++ + + +  +    +         + +  + + +     +       
Sbjct: 1    PLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQK 60

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+       S ++H RR +      + R     + R +H TH+G +CPAE
Sbjct: 61   KAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAE 116

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            T EG   GLV +L     +      E    +    + +V  +     +      ++    
Sbjct: 117  TPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 176

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +  D +     V        I      + D  D   K          P    D+  + 
Sbjct: 177  VGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 236

Query: 691  LMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                N+   ++ +  L+ +               S     AK  G    V     V+  V
Sbjct: 237  TNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVEYV 286

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 287  DAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMNPTAHTWTHCEIHPSM 346

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 347  ILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------- 388

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 389  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 437

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 438  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 493

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D      R++          ++     +  Q   
Sbjct: 494  DDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 553

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      LR VKV +   +  Q GDK A RHG KG +    
Sbjct: 554  --------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 593

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +             
Sbjct: 594  RQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------- 642

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     ++++ +LR
Sbjct: 643  ------------------------------------------ATP-FTEVTVDSVSKLLR 659

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                   G  ++Y+G TG      V +G  Y  +
Sbjct: 660  EHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 693


>gi|6449148|gb|AAF08846.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 290

 Score =  271 bits (693), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 163/297 (54%), Positives = 214/297 (72%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  
Sbjct: 61  NKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|269930811|gb|ACZ54140.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930841|gb|ACZ54155.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930847|gb|ACZ54158.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930857|gb|ACZ54163.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|269930869|gb|ACZ54169.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 288

 Score =  271 bits (693), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 209/289 (72%), Positives = 243/289 (84%), Gaps = 1/289 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 288


>gi|56694296|gb|AAW22888.1| RNA polymerase II second largest subunit [Psilotum nudum]
          Length = 573

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 120/721 (16%), Positives = 212/721 (29%), Gaps = 148/721 (20%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   + +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMSYITVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +   G +             +   R ++   D   +  V     L       
Sbjct: 54   AVIPQATKIFVXGCWVGIHRDPELLVRTLRQLRRQV---DVXTEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +      L+K          ES  +  +   +VAK  G +E VD      
Sbjct: 111  DYGRCSRPLFIVENQRLLIKKSHIRALQQKESTXS--AWYDLVAK--GFIEYVDTEEEET 166

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +  +     +  D                                     PS  LG  
Sbjct: 167  TMISMNXSDXEAARDHPEEA---------------------YSDTYTHCEIHPSMILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCASIIPFPDHNQSPRNTXQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLFYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        IF R   D+  +  ++ +E+ E   R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSIFYRSYRDEEXKQGTLVKEEFERPNRETXTNMRHGSYDKLXX 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T LS                  D+   +     K    T 
Sbjct: 349  DGLTPPGTRVSGEDVIIGKTTPLSQ-----------------DDTGNQAQRYSKRDQSTC 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK+ V   R  Q GDK + RHG KG V     
Sbjct: 392  LRXSESGMIDQVLLTTNADGL-----RFVKIRVRSIRVPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ ++G   DI++NP  +PSRM +GQ+ E  +G     +G++              
Sbjct: 447  QEDMPWTQEGISPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGREGD------------ 494

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++I+  L  
Sbjct: 495  -----------------------------------------ATP-FTDVTVDSISKALHK 512

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G   +Y+G T    +  + +G  Y  +L HMV DK+++R  G   ++T+QP  G
Sbjct: 513  CGYQMRGFETMYNGHTXRXLNAMIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEG 572

Query: 1286 K 1286
            +
Sbjct: 573  R 573



 Score = 62.0 bits (149), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 53/329 (16%), Positives = 101/329 (30%), Gaps = 36/329 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 11  EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVXGCWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 71  IHRDPELLVRTLRQLRRQVDVXTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVENQRLLI 129

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S    A           Y  V  G     + Y+   EEE   I+   S  +      E
Sbjct: 130 KKS-HIRALQQKESTXSAWYDLVAKGF----IEYVDTEEEETTMISMNXSDXEAARDHPE 184

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E               +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 185 E------------AYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTXQSAMGKQAMG 232

Query: 703 LL----------------KAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           +                   + P V T  ME +  +   A I A  A            +
Sbjct: 233 IYVTNYQLRMDTLAYVLFYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 292

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 293 IMNQSSIDRGFFRSIFYRSYRDEEXKQGT 321


>gi|66800165|ref|XP_629008.1| RNA polymerase I, second largest subunit [Dictyostelium discoideum
            AX4]
 gi|74896752|sp|Q54BM1|RPA2_DICDI RecName: Full=DNA-directed RNA polymerase I subunit rpa2; AltName:
            Full=DNA-directed RNA polymerase I polypeptide 2;
            Short=RNA polymerase I subunit 2
 gi|60462371|gb|EAL60592.1| RNA polymerase I, second largest subunit [Dictyostelium discoideum
            AX4]
          Length = 1130

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 72/284 (25%), Positives = 111/284 (39%), Gaps = 52/284 (18%)

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +   Y+  +    +    +I     G    P  +  + V +   R    GDK + RHG 
Sbjct: 832  QVTKDYKGKEEAYIE--DVRIIFGPNGATRDPSKINNICVKLRFNRNPVIGDKFSSRHGQ 889

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++S++ P  +MPF + G   D+++NP   PSRM +G + E   G A    GK   +  
Sbjct: 890  KGVLSQLWPEINMPFTESGMKPDVIINPNAFPSRMTIGMLVEILAGKAGAIHGKFQDATA 949

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
              +  N                                                F G   
Sbjct: 950  FQFDENNTAID-------------------------------------------FFG--- 963

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                  L  A  +  G   +Y G TG+ F+  +  G  Y  +L HMV DK   R+ G  +
Sbjct: 964  ----EQLAKAGFNRFGNEQMYSGTTGKEFECEIFFGVCYYQRLRHMVKDKYQVRALGKVN 1019

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             +T+QP+ G+   GG R GEME   + A+GA++ L + L   SD
Sbjct: 1020 ALTRQPIKGRKVGGGIRFGEMERDSLLAHGASFCLNDRLMKSSD 1063



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 110/755 (14%), Positives = 226/755 (29%), Gaps = 150/755 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFSGAAMLEFVSYEFDPP-- 84
           LI+    S+D F           + G+    K   P      S    + F   +   P  
Sbjct: 8   LIQPHIDSFDFF----------TDHGIDLVLKDSEPLYFEHNSTQYKIRFTDLKLSRPTR 57

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLI-VFDVDEFTGAKSIKDIKEQ-----SIY 131
                  K   ++      TY  P K  + L  V ++DE      +   K++      + 
Sbjct: 58  NIVEKEIKLYPNESRETGTTYNAPFKGAIGLYEVNEMDEMDDGTEVDYNKQEPTHTFEVD 117

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV-----------VSQ 156
           +G LP+M K                         G F++ G +++V           V+ 
Sbjct: 118 LGRLPIMVKSRYCHLNGMSPEKLIESREEELEQGGYFIVNGNEKVVRMLVMTKANHPVA- 176

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV-------RIDRR 209
           LHR           +A  +    Y    I  + +  D    + ++ ++       R   R
Sbjct: 177 LHR-----------KAWTNRGPGYTKNGITIRCVRPDRSSITNNLHYINDGQTTLRFLYR 225

Query: 210 RK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R+   +P T  L AL   +E+ +   Y  IV     + +        L         + +
Sbjct: 226 RQEFFLPATLLLKALKDTTEKEI---YENIVQGDNENTFLTDRVELSLREQK-----INN 277

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+T E+V+                          D +   + A          I I    
Sbjct: 278 INTQEEVL--------------------------DYIGSRFRARTQFPPSFSNIKIGRWF 311

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL--DIYRVMRPG 384
           +     +    +++  ++ IL +  +      +       +   ++ LL   IY ++   
Sbjct: 312 INQFVFVHLPNYNDKYNLLILMIQKLYAMVGGKCGTDNIDSPAFQEVLLAGHIYGMILKE 371

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
            ++ +  +   F    F+  K     +                 + + K   IA      
Sbjct: 372 KLTEYLESTKSFVLKSFEDKKKSGDKL------------PDALKKVLDKNFKIADRFSYF 419

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQD 502
                  +   ID         + + L     +   R     +    + +  I  +MP+ 
Sbjct: 420 LATGNLRSSSGIDLQQTSGFCVIADKLNFLRFISHFRSIHRGAFFATMKTTAIRKLMPES 479

Query: 503 LINAKPVVSAVCEFFC------SSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR--ARA 554
                PV +             S+ L  ++   +   +   T   S L   G+      +
Sbjct: 480 WGFFCPVHTPDGAPCGLLNHLSSNCLVTVDAAQDPTVQKAQTLLPSFLAAHGMLPIDMVS 539

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR------KVCDG 608
             + + +  T  GR+      +     +       +  N     +T          V +G
Sbjct: 540 VYQHQYLTITLDGRVLGKIEPKAGEEMVKMLRYLRSMGNEPSIPKTMEISYAPPTNVENG 599

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           + +   ++ +        +   +   +  G   +E ++   A     V +     I+ SP
Sbjct: 600 QYSGISLFTTGARFMRPVVNLTSGQNELIG--PQEQLYMEIAVVPHEVIKGVTTHIETSP 657

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             + S+ A+L PF + + S R +  C M +Q +  
Sbjct: 658 TAMFSLLANLTPFSDYNQSPRNMYQCQMAKQTMGT 692


>gi|225430474|ref|XP_002283296.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 1198

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 104/527 (19%), Positives = 170/527 (32%), Gaps = 94/527 (17%)

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              N D    +   +E       +G  T      +      L          +    L  P
Sbjct: 729  YANHDHARRVLYQSE-KHSQQAIGFSTTNPNIRVDTLSHQLYYPQRPLFRTMISDCLGKP 787

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD-KDDEQVILDRNIYSRLMEILC 991
                G      I  R      + +I      +     D     +  L+R ++ R   I  
Sbjct: 788  GYSEG---HKGIVPRPEYFNGQIAIVAVNVHLGYNQEDSLVMNRASLERGMF-RSEHIRS 843

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
             ++ V   +   K       +     +S+  +    D+     + +     +       +
Sbjct: 844  YKSEVDNNESLDKKRKSEDSVHFGKMQSKIGRVDSLDDDGFPFIGANLQNGDIVIGRCAE 903

Query: 1052 ---RFKNKIEKIQWG-------DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                   K++  + G            G    V V +   R    GDK +  HG KG++ 
Sbjct: 904  SGVDHSIKLKHTERGMVQKVVVSANDDGKNFAV-VSLRQVRTPCLGDKFSSMHGQKGVLG 962

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             +   E+ PF   G   DIV+NP   PSR   GQ+ E     A +G G     L+     
Sbjct: 963  FLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLE-----AALGKGIACGGLLRH--- 1014

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     +AI  
Sbjct: 1015 ---------------------------------------------ATP-FSTLSVDAIAD 1028

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L  A     G   +Y+G TGE     + +G  +  +L HM  DKV  R+TG    +T+Q
Sbjct: 1029 QLHRAGFSRWGHERVYNGRTGEMLRSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQ 1088

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESI----- 1332
            P+  +   GG + GEME  C+ A+GAA  L E L   SD     +  R +   ++     
Sbjct: 1089 PVSDRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSAYMHICRRCKNISNVIQRSV 1148

Query: 1333 -----VAG---------NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                 V G          +  +   P    +L +E+ ++G+S+  E 
Sbjct: 1149 AGGRKVRGPYCRYCESSEEIVKVNVPYGAKLLCQELFSMGISLKFET 1195



 Score =  139 bits (351), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 136/965 (14%), Positives = 274/965 (28%), Gaps = 223/965 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-----TAFSGA-------AMLEF 76
           LI+ Q  S++ F+            G+Q  F S   I        S         A + F
Sbjct: 63  LIQHQINSFNDFI----------KNGIQRVFDSFGEIPVEPGYDPSKRGEGDWRYASVRF 112

Query: 77  VSYEFDPPK-------------FDVDDCLWRDLTYAVPLKITLRLIVF-----DVDEFTG 118
                + P+             F       +++TY+  +K  +   V+       D++  
Sbjct: 113 GKVTLERPRVWAGESDGKESLNFLPRHARLQNMTYSSRMKAQVHFQVYTQKLVRSDKYKT 172

Query: 119 AKSIKDIKEQSIY-------MGDLPLMTKD------------------GTFVIKGIQRIV 153
            K  K ++++ I+       +G +P+M K                   G F+IKG ++  
Sbjct: 173 GKDNKYVEKKVIFEDNRDILIGRIPVMVKSELCWMNGVERGDCEYDHGGYFLIKGAEKTF 232

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW--------MDIEFDSKD----- 200
           ++Q            K     S            + +W        ++   D  +     
Sbjct: 233 IAQEQ-------ICLKRLWVSSNPTWMVA----YRPIWKRKRVYVKLEPPKDENNRGGEK 281

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           ++ V       +P+     ALG  S+ E++      I  +   +     +  AD     K
Sbjct: 282 VLTVYFSSTE-IPIWILFFALGASSDKEVVDLIDFNIDDAGISNILVASIHEADREAEKK 340

Query: 260 VSS--------SLVDIDTGEQVIESGKKLTSGLLKSLKEK--GVKFLGITSDCLCGLYVA 309
                      S VD          G+ +   + K L     GVK          G  V 
Sbjct: 341 GMYFRRQGNAISFVDKLVKSCKFPPGESIQECISKYLFPNFSGVKQ----KARFLGYMVK 396

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD--IPILYVDSVNNNAYIRNTLVTDKN 367
             ++   TG    +  D    K LE       R+  + I + +     A  R        
Sbjct: 397 C-LLQAYTGRRKCDNRDDFRNKRLELAGELLERELRVHIRHAERRMVKAMQRELYGDRDL 455

Query: 368 KDRKDAL------LDIYRVMRPGDVSTFSVAESMFNFLFFDSDK---YDLSTVGRVKMNM 418
           +  ++ L        + R    G  S         + +     +     ++   R     
Sbjct: 456 RPIENYLDASIITNGLSRAFSTGQWSHPFKRMERISGVVATLRRTNPLQMTADMRKTRQQ 515

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                   D R+        +  +        G + ++   G      +  ++   +  G
Sbjct: 516 VQYTGKVGDARYPHPSHWGKVCFLSTPDGENCGLVKNLAITGLVSTEVLDPLVDKLFDCG 575

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           + ++      ++S  +                     F     +   E+ ++ +  +   
Sbjct: 576 MEKLVDDTSTKLSGKNK-------------------VFLDGDWVGVCEDPISFVVELRTK 616

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR   L Q    +         +       + P    E              +V  +   
Sbjct: 617 RRHKELPQQVEIKRDEQQGEVRIFSDAGRILRPLLVVENLK-----------KVKTFKGD 665

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           +  ++ + D      V  + A EEE+   A     L +                    P 
Sbjct: 666 DFTFQSLLD---KGIVELIGAEEEEDCSTAWGIKYLLKGHDD----------------PP 706

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K    +     ++ ++  +IP+  +D + RVL       Q                   
Sbjct: 707 VKYTHCELDMSFLLGLSCGIIPYANHDHARRVLYQSEKHSQQAIGFST------------ 754

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                                       +       + S    Y      R+  + C+  
Sbjct: 755 ----------------------------TNPNIRVDTLSHQLYYPQRPLFRTMISDCLG- 785

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           +P    G +      I   P    G +A     +VA     GYN EDS++++   +   +
Sbjct: 786 KPGYSEGHKG-----IVPRPEYFNGQIA-----IVAVNVHLGYNQEDSLVMNRASLERGM 835

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGD 892
           F S HI  ++    + +   ++   +              + ++D+ G   +GA +  GD
Sbjct: 836 FRSEHIRSYKSEVDNNESLDKKRKSEDSVHFGKMQSKIGRVDSLDDDGFPFIGANLQNGD 895

Query: 893 ILVGK 897
           I++G+
Sbjct: 896 IVIGR 900


>gi|227937600|gb|ACP43375.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
 gi|227937628|gb|ACP43389.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 288

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 211/289 (73%), Positives = 244/289 (84%), Gaps = 1/289 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 DSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 288


>gi|269930817|gb|ACZ54143.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 289

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 208/288 (72%), Positives = 243/288 (84%), Gaps = 1/288 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYR 287


>gi|83415495|gb|ABC17955.1| RNA polymerase II second largest subunit precursor [Spiromyces
            aspiralis]
          Length = 1058

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 123/826 (14%), Positives = 226/826 (27%), Gaps = 149/826 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    +M + +    +    +     P   I +  + + +     +
Sbjct: 2    KRMDLAGPLLAMLFRNLFRKMTKDVTRYMQKCIDNDREFRPNIAIKSTTITTGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A V      +  +  + +     ++  L      +  
Sbjct: 118  GIVCPAETPEGQACGLVKNLALMAHVTISCSAQPIHDFL-NDWGMENLEELQVTSIADAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFL 682
                N           +LV               I    D  +   +          P  
Sbjct: 177  KIFVNGVWLGIHREANKLVPQLRQMRRETSLSFDISIVRDIREKELRIYTDEGRVCRPLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D    +   ++ R                             +    G+VE +DA  
Sbjct: 237  VVEDLRLKVTNDHINRLIELNEIGGGEEGE------------GWQMLISDGVVEYLDAEE 284

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D      + ++             + R   +    +         PS  L
Sbjct: 285  EETAMICMTPDELRESYEYHQTG--VEPPMEVDPSFRIRSRRNIYINTWTHCEIHPSMIL 342

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +                        
Sbjct: 343  G-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV---------------------- 373

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                 ++   L+      +  V         +   +       +   +  + AI      
Sbjct: 374  ----MLTNYQLRM---DTLSNVLYYPQKPLAITRAMDYLKFRQLPAGQNAIVAILCYSGY 426

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+  R  S    + E   R+            
Sbjct: 427  NQEDSIIMNQSSIDRGLF-RSLFFRTYQDEENREGSAHVGRFEKPTRETTLRLKHGTYEK 485

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  +  G   V       K+T + +D +    R++        + ++     +  + 
Sbjct: 486  LDEDGLVAPGTRVVGDDIIIGKTTPIPADSLELGQRTKNHTKLDASKPLRSTEHGIVDRV 545

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        +R VKV V   R  Q GDK A RHG KG V  
Sbjct: 546  ML--------------------TTNADGIRFVKVRVRSTRVPQIGDKFASRHGQKGTVGM 585

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   D+++NP  +PSRM +G + E  L      LG+   +        
Sbjct: 586  TYRTEDMPFTAEGIVPDLIINPHAIPSRMTIGHLIECLLSKLSTLLGQDGDATPFTDVTV 645

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS  R    +                                                
Sbjct: 646  EAIS--RELHSRGYHPRGFEVM-------------------------------------- 665

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +G +    G         V +G  Y  +L HMV DK++
Sbjct: 666  -------YNGHT----GR---KLAAQVFLGPTYXQRLKHMVDDKIH 697



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 91/618 (14%), Positives = 176/618 (28%), Gaps = 93/618 (15%)

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           P+L +   N    +   +     K   +       +       T  +  S+    + D  
Sbjct: 9   PLLAMLFRNLFRKMTKDVTRYMQKCIDNDREFRPNIAIKSTTITTGLKYSLATGNWGDQK 68

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           K   S  G  ++  R    +      R          I     L N    I         
Sbjct: 69  KAMQSRAGVSQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGIVCPAETPEG 128

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +      ++KN   +  + +  S +     ++   +   + +    +  A   F     L
Sbjct: 129 QACG---LVKNLALMAHVTISCSAQPIHDFLNDWGMENLEELQVTSIADATKIFVNGVWL 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               E    + ++   RR ++L            +   ++        P    E   + +
Sbjct: 186 GIHREANKLVPQLRQMRRETSLSFDISIVRDIREKELRIYTDEGRVCRPLFVVEDLRLKV 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +   +                         V YL A EEE   I      L E   + +
Sbjct: 246 TNDHINRLIELNEIGGGEEGEGWQMLISDGVVEYLDAEEEETAMICMTPDELRESYEYHQ 305

Query: 643 ELV-------FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             V                 +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 306 TGVEPPMEVDPSFRIRSRRNIYINTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 365

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ ++                                                  +
Sbjct: 366 MGKQAMGVMLTNYQL-----------------------------------------RMDT 384

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRP--LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S V  Y               Q+P  + +  D ++               L  G+N +V
Sbjct: 385 LSNVLYYP--------------QKPLAITRAMDYLKFRQ------------LPAGQNAIV 418

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP----EEITRD-IPNV 868
           A + + GYN EDS+++++  +   +F S+    ++              E+ TR+    +
Sbjct: 419 AILCYSGYNQEDSIIMNQSSIDRGLFRSLFFRTYQDEENREGSAHVGRFEKPTRETTLRL 478

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                + +DE G++  G  V   DI++GK TP     +   ++        K     D S
Sbjct: 479 KHGTYEKLDEDGLVAPGTRVVGDDIIIGKTTPIPADSLELGQRT-------KNHTKLDAS 531

Query: 929 LRVPSGVSGTVVDVRIFN 946
             + S   G V  V +  
Sbjct: 532 KPLRSTEHGIVDRVMLTT 549


>gi|320165771|gb|EFW42670.1| DNA-directed RNA polymerase I complex subunit Rpa2 [Capsaspora
            owczarzaki ATCC 30864]
          Length = 1126

 Score =  271 bits (692), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 125/331 (37%), Gaps = 82/331 (24%)

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+  G+       R + +   ++R    GDK A RHG KG+ S++ P E MPF + G   
Sbjct: 847  KLIAGEGSDQRAQRAI-IRFRLRRNPVIGDKFASRHGQKGVCSQLWPSEGMPFCESGMVP 905

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI+ NP G PSRM +G   ET  G +                                  
Sbjct: 906  DILFNPHGFPSRMTIGMWIETMAGKSAA-------------------------------- 933

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSI 1235
                                     V  ++P VF+      +     L  A  +  G   
Sbjct: 934  ---------------------LHGVVHDASPFVFNEKSRAVDYFGEQLAKAGYNYYGSER 972

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +Y G+TG+ FD  + +G +Y  +L HMV DK   R+TG    +T QP+ G+   GG R G
Sbjct: 973  MYSGVTGKEFDAEIFMGVVYYQRLRHMVLDKYQVRTTGPVHNLTHQPIKGRKRAGGIRFG 1032

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRT-RVYESI----------------VAG--- 1335
            EME   + A+G A++L + L   SD       +   SI                V     
Sbjct: 1033 EMERDSLLAHGTAFLLHDRLMNCSDYSYSYVCKACGSILSPMLEQATQISGKRNVKCRSC 1092

Query: 1336 ---NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                +      P  F  L+ E+  L ++I +
Sbjct: 1093 QSSKNVEIIAVPYVFRYLLSEL--LAMNIRV 1121



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 92/668 (13%), Positives = 202/668 (30%), Gaps = 110/668 (16%)

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-- 141
           P     +C  R  TY   L +TL+  V D       +           +G +P+M K   
Sbjct: 82  PAVFPTECRERASTYKSDLHVTLKWKVDDGPVNQTERK----------LGQIPIMVKSQR 131

Query: 142 ----------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK-L 178
                                 G F+I GI+R  + ++   P  ++     R S   +  
Sbjct: 132 CNLRDLSPTELVANQEEAEEMGGYFIINGIER--IMRMLLLPRRNYVMALDRPSFRKRGP 189

Query: 179 LYA--CRIIPDQGLWMD---------IEFDSKDIIHVRIDRRRK---VPVTSFLMALGMD 224
            Y     +I  +   +D            D   +  VR   R+    VP    L AL   
Sbjct: 190 EYTTFGTMI--RCTRLDQTSQTITVHFLQDGNCM--VRFSYRKNEYLVPAVLILKALVTT 245

Query: 225 SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
           +++ +   + +IV S + D +        L     +   + +       +    ++   +
Sbjct: 246 TDQEI---FERIVGSSKLDSFLTDRVELMLRSATDMH--VHNSKQARVFLGERFRIALDV 300

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
            + + ++ V  L +    L  L   +D  +                  +++++     D 
Sbjct: 301 PEDMSDEDVGRLLLRKLMLIHLDNDQDKFDLLVF-------------MIQKLYKVVSGDC 347

Query: 345 PILYVDSVNNNAYIRNT--LVTDKNKDRKDALLDIYRVM-----RPGDVSTFSVAESMFN 397
                DS  N+  + +    +    +  ++ L     V+     R  +  +FS     F 
Sbjct: 348 CTENADSPMNHEILTSGQLYLMFLKEKMEEYLTACKAVVAQDLRRNPEQVSFSAGSQYFT 407

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                +       +  +     L   T  D++ +    ++A     +   +    I    
Sbjct: 408 KSLSKNPVDIGRRLEYLMATGNLASATGLDLQQVSGFTVVADKLNFLRYLSHFRCIHRGA 467

Query: 458 NLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                +  +V ++L   +  +  +         + +      +  D +     V A+   
Sbjct: 468 FFAEMKTTTVRKLLPEAWGFVCPVHTPDGAPCGLLNHLAAKCLVVDEVADASRVPAMLIE 527

Query: 517 FCSSQLSQLEEHVN-SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              + +     + +  L+ +   R +  L     A+  A    R                
Sbjct: 528 LGMAPIDHKIHYPSDYLNVLLDGRIIGKLAPENAAQITAHFRYRKAQG-----HKDLPRY 582

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               + L S    F  +  +  +    R V +  + N V Y+ + E+    IA   + + 
Sbjct: 583 MESALVLPSERGQFPGLFIFTSLCRMVRPVQN-LIANTVEYIGSFEQVYMDIAVLEADIV 641

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                                        + SP  ++S+ A + P+ +++ S R +  C 
Sbjct: 642 ----------------------PGVTTHHELSPTAMLSVNALMTPYSDHNQSPRNMYQCQ 679

Query: 696 MQRQAVPL 703
           M +Q +  
Sbjct: 680 MGKQTMGT 687


>gi|103001447|gb|ABF71508.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 692

 Score =  271 bits (692), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 115/813 (14%), Positives = 235/813 (28%), Gaps = 145/813 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L N +R+   ++ + + +  +    +         + +  + + +     +        
Sbjct: 1    LLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKST 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   ++ +  L+ +               S     AK  G    V     V+  V+
Sbjct: 237  NCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVEYVD 286

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q           +   V+          T      ++ 
Sbjct: 287  AEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMNPTAHTWTHCEIHPSMI 346

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N          M  + +   + +  ++                    
Sbjct: 347  LGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----------------- 387

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 388  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 437

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 438  IMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDD 493

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 494  DGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL- 552

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 553  -------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 593

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF K+G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 594  QEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------ 641

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 642  -----------------------------------------ATP-FTEVTVDSVSKLLRE 659

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                  G  ++Y+G TG      V +G  Y  +
Sbjct: 660  HGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 692


>gi|322694313|gb|EFY86146.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Metarhizium
            acridum CQMa 102]
          Length = 1231

 Score =  270 bits (691), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 111/300 (37%), Gaps = 54/300 (18%)

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W            N++ +           E  F  ++  I  G +     L+ V +   +
Sbjct: 864  WHTVTPDYNGNLVNLDGITHY--EKYKDGETGFVEEVRLI--GAETGSETLQTVSIKFRI 919

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+ S+  P  DMPF + G   D+++NP   PSRM +G   E+ 
Sbjct: 920  PRSPIIGDKFSSRHGQKGVASQKWPAIDMPFSESGIQPDVIINPHAFPSRMTIGMFVESL 979

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +                                         
Sbjct: 980  AGKAGALHGLAQDSTPFKFDEEDTA----------------------------------- 1004

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     L  A     G   +Y G+TGE     + +G +Y  +L 
Sbjct: 1005 ---------------VDYFGHQLMKAGYSYHGNEPMYSGITGEELGADIYIGVVYYQRLR 1049

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG     T QP+ G+   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1050 HMVNDKFQVRTTGPVVPTTGQPIKGRKRGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1109



 Score = 70.1 bits (170), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 96/613 (15%), Positives = 187/613 (30%), Gaps = 99/613 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVG- 412
                         DR + LL  Y+         T +     F  +    +      VG 
Sbjct: 285 GPMGSKATENTFLTDRVELLLRTYKRYGLYSKSQTRAYLGEKFRVVLGVPETMSDYEVGT 344

Query: 413 ----RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               R+ +    N++  ++    +   ++ +++ L  L  G+  +D+ D L N+ +   G
Sbjct: 345 EFLRRIVLVHLGNVNVAEEQDLDKFRMLLFMVRKLYALAAGECAVDNPDALQNQEILLGG 404

Query: 469 --------EMLKNQYRLGLLRMERSIKERI-----SSVDIDSVMPQDLIN--AKPVVSAV 513
                   E L     +G+    R    R      +S D     P  +     + + +A+
Sbjct: 405 FLYSQILKERLDEFVSVGVRSSLRDFLRRHPQVSFTSEDFRKEFPGTIFRKANENLGNAL 464

Query: 514 CEFFCSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
             F  +  L                + E +N L  I+H R    + +G          +R
Sbjct: 465 EYFLSTGNLQSPSGLDLQQTAGFTVVAEKLNFLRFISHFR---MVHRGAFFAQLKTTAVR 521

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY----------------- 602
            + P  +G +CP  T +G   GL++ L    ++       +                   
Sbjct: 522 KLLPESWGFMCPVHTPDGSPCGLLNHLAHKCKIVTDHVDVSKLPALARELGVVDTSSALT 581

Query: 603 -RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL------VFCRCAGEEIL 655
              V        + + S  E  +  IA        +G+    L      V     G    
Sbjct: 582 SENVVVMMDGKILGWCSPKE--SLRIADCLRYWKVEGTHGVPLQLEIGYVPASNGGSYPG 639

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           V           P + +         L+ +D         M    VP  +     V T +
Sbjct: 640 VYITSTPARMVRPVKYLP--------LQKEDFVGPYEQPYMSIAVVP--QETESGVSTHV 689

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E         +I+A      +   + R + +   G     T G  I    +++  N++  
Sbjct: 690 EFDPTNML--SILANMTPFSDFNQSPRNMYQCQMGKQTMGTPGTAI----RYRTDNKSYR 743

Query: 776 VN--QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           +   Q P+V+                    +   G N +VA + + GY+ +D+M++++  
Sbjct: 744 IQTGQTPIVRA----------PLHNDYGFDNFPNGMNAVVAVISYTGYDMDDAMILNKSA 793

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEI-------TRDIPNVSEEGLKNIDECGIICVGA 886
                      +  ++  +D                     VS      +D+ G+  VG 
Sbjct: 794 HERGFGHGTIYKTKKITLKDDSRTRAAKSVTKAFGFAPHSYVSASYQGMLDDDGLPHVGR 853

Query: 887 EVNPGDILVGKIT 899
            V  GD++    T
Sbjct: 854 LVQEGDVICAWHT 866



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 94/746 (12%), Positives = 207/746 (27%), Gaps = 135/746 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS------GAAMLEFVSYEFDPP-- 84
              S++  +  +       + GL       F                +   +     P  
Sbjct: 43  HIESFNR-IFGDDGKKGLLDYGLTDIGTKTFLDGDERSGPEGKNRLHIRIKNVSLQKPQI 101

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                     +    +C  R ++Y   L  T    +   D     +           +G 
Sbjct: 102 PPSNKMARNREILPAECRERHVSYRGRLSATFEYSINGGDPIEFVRE----------LGQ 151

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
           +P+M K                         G F++ GI++ ++  L  +          
Sbjct: 152 VPIMIKSNRCHLENNSPAQLVERKEESEELGGYFIVNGIEK-IIRLLQVNKRNFPMAINR 210

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTSFLM 219
            +  +    Y    I  + +  D E    +++H         R   R+    +PV   L 
Sbjct: 211 PSFQNRGAGYTSYGIIVRSVRPD-ETSQTNVLHYLNDGNITFRFSWRKNEYLIPVIMILK 269

Query: 220 ALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
           AL   ++ EI       +      + +        L+   K         T   + E  +
Sbjct: 270 ALVETNDREIFEGLIGPMGSKATENTFLTD-RVELLLRTYKRYGLYSKSQTRAYLGEKFR 328

Query: 279 KLTSGLLKSLKEKGVKFLGITS---DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
            +               LG+     D   G      IV    G + +     +D+  +  
Sbjct: 329 VV---------------LGVPETMSDYEVGTEFLRRIVLVHLGNVNVAEEQDLDKFRMLL 373

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
               ++  +      +V+N   ++N  +          L +     R  +  +  V  S+
Sbjct: 374 FMVRKLYALA-AGECAVDNPDALQNQEILLGGFLYSQILKE-----RLDEFVSVGVRSSL 427

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            +FL         S   R +    +     +++      + +       +L++  G    
Sbjct: 428 RDFLRRHPQVSFTSEDFRKEFPGTIFRKANENLG-----NALEYFLSTGNLQSPSG---- 478

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQDLINAKPVVSAV 513
           +D         V E L     +   RM    +   ++ +  +  ++P+      PV    
Sbjct: 479 LDLQQTAGFTVVAEKLNFLRFISHFRMVHRGAFFAQLKTTAVRKLLPESWGFMCPV---- 534

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                           +    + H      +    V  ++     R++          +E
Sbjct: 535 -----------HTPDGSPCGLLNHLAHKCKIVTDHVDVSKLPALARELGVVDTSSALTSE 583

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN---DVVYLSAMEEENR---YI 627
                  G +    S  + +        Y KV          ++ Y+ A    +    YI
Sbjct: 584 NVVVMMDGKILGWCSP-KESLRIADCLRYWKVEGTHGVPLQLEIGYVPASNGGSYPGVYI 642

Query: 628 AQANSSLDEDGSFT-----EELVFCRCAGEEILVPREKI-----DFIDASPKQVVSIAAS 677
               + +     +      + +         I V  ++        ++  P  ++SI A+
Sbjct: 643 TSTPARMVRPVKYLPLQKEDFVGPYEQPYMSIAVVPQETESGVSTHVEFDPTNMLSILAN 702

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPL 703
           + PF + + S R +  C M +Q +  
Sbjct: 703 MTPFSDFNQSPRNMYQCQMGKQTMGT 728


>gi|67515338|gb|AAY68198.1| RNA polymerase IV second largest subunit [Rhododendron macrophyllum]
          Length = 1019

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/534 (18%), Positives = 164/534 (30%), Gaps = 106/534 (19%)

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              N D    +   +E       +G  T      +      L          +    L  P
Sbjct: 550  FANHDHARRVLYQSE-KHSQQAMGFNTTNPNIRVDTNTHQLYYPQRPLFRTMVSDCLGKP 608

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD-KDDEQVILDRNIYSRLMEILC 991
                  +    I  R      + +I      +     D     +  L+R ++ R   I  
Sbjct: 609  G---YPLGHNGIVPRAEYFNGQCAIVAVNVHLGYNQEDSLVMNRASLERGMF-RSEHIRS 664

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
             +  V   +   K       +     +S+  +    D+     + +     +       +
Sbjct: 665  YKADVDNKESVGKKPKFEDSVNFGKVQSKIGRVDSLDDDGFPFIGANLQNGDIVVGRCAE 724

Query: 1052 ---RFKNKIEKIQWG-------DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                   K++  + G            G    V V +   R    GDK +  HG KG++ 
Sbjct: 725  SGADHSIKLKHTERGMVQKVVLSANDEGKNFAV-VSLRQVRTPCLGDKFSSMHGQKGVLG 783

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             +   E+ PF   G   DIV+NP   PSR   GQ+ E  LG      G +          
Sbjct: 784  FLESQENFPFTIQGIVPDIVVNPHAFPSRQTPGQLLEAALGKGIACGGLQ---------- 833

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     +A+  
Sbjct: 834  -------------------------------------------KYATP-FSTLSVDAVTD 849

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L  A     G   +Y+G TGE     V +G  +  +L HM  DKV  R+TG    +T+Q
Sbjct: 850  QLHRAGFSRWGSERVYNGRTGEMIHSLVFMGPTFYQRLTHMSEDKVKFRNTGPVHPLTRQ 909

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV-------------- 1323
            P+  +   GG + GEME  C+ A+GAA  L E L   SD     +               
Sbjct: 910  PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSSQMHICRKCNNIANVIQRAV 969

Query: 1324 --GRTRVYESIVAG---------NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              GR       + G          +      P    +L +E+ ++G+++  +  
Sbjct: 970  PGGRK------IRGPYCRFCESVEEIVRVNVPYGAKLLAQELFSMGITMKFDTE 1017



 Score = 99.4 bits (246), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 93/516 (18%), Positives = 180/516 (34%), Gaps = 51/516 (9%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI---KE 488
           +   +  ++K L+    G+  ID+ D+  N+R+   GE+L+ + R+ +   ER +    +
Sbjct: 207 KARFLGYMVKCLLQAYTGRRKIDNRDDFRNKRLELAGELLERELRVHVKHAERRMVKAMQ 266

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS-RITHTRRLSALGQG 547
           R    +      +  ++A  + + +   F +   S   + +  +S  +   RR + L   
Sbjct: 267 RDLYGERVIHAIEHYLDASIITNGLSRAFSTGAWSHPYKKMERISGVVATLRRTNPLQTI 326

Query: 548 GVARARAGV--------EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
              R             + R  HP+H+G+IC   T +G N GLV +L     V+     E
Sbjct: 327 ADMRKTRQQVSYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLAITGLVSTN-IEE 385

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
               K+ D  +   V   S +      +    + +   G     +   R       VP +
Sbjct: 386 HFLDKLLDSGMEKLVDDTSTLLSGKVKVFLDGNWVGVCGDSVSFVAALRRKRRRKEVPHQ 445

Query: 660 -KIDFIDASPKQVVSIAASLI--PFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGM 715
            +I   +   +  V   A  I  P L  ++  ++            LL      F+GT  
Sbjct: 446 VEIKRDEQHREVRVFSDAGRILRPLLVVENLGKIKASKGGDYSFQSLLDKGVIEFIGTEE 505

Query: 716 ESVVAKSSGAAIVAKRAGIVEQV-------------------------DAIRIVIRSVEG 750
           E     + G   +         V                         D  R V+   E 
Sbjct: 506 EEDCRTAWGINYLFMENEAKATVKYTHCELDMSFLLGLSAAIIPFANHDHARRVLYQSEK 565

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEV-RRNDIIADGPSTDLGDLAL 807
               +         ++   +       QRPL    V D + +    +         +   
Sbjct: 566 HSQQAMGFNTTNPNIRVDTNTHQLYYPQRPLFRTMVSDCLGKPGYPLGHNGIVPRAEYFN 625

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-- 865
           G+  +VA     GYN EDS++++   +   +F S HI  ++    + +   ++   +   
Sbjct: 626 GQCAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKADVDNKESVGKKPKFEDSV 685

Query: 866 ----PNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                      + ++D+ G   +GA +  GDI+VG+
Sbjct: 686 NFGKVQSKIGRVDSLDDDGFPFIGANLQNGDIVVGR 721


>gi|145542267|ref|XP_001456821.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124424634|emb|CAK89424.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1115

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 74/279 (26%), Positives = 112/279 (40%), Gaps = 54/279 (19%)

Query: 1044 TSKSILEDRFKN--KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                +   +     +IE++   +     V  ++K  +   R    GDK + RHG KG++S
Sbjct: 814  QQVKVYHSKDSETARIEQVAVVNKSENDVSVMIKYRI--NRNPIIGDKFSSRHGQKGVMS 871

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             + P  DMPF + G   DI++NP   PSRM +G + E+    A V  G+  ++       
Sbjct: 872  LLWPQIDMPFSESGMVPDIIINPHAFPSRMTIGMLIESMAAKANVLQGEMFETHPFQNYE 931

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            N ++                                                   +    
Sbjct: 932  NDNV--------------------------------------------------VDYFGK 941

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L     +  G   LY G+ G P    +  G +Y  +L HMVSDK  ARS G   ++TQQ
Sbjct: 942  QLIKHGYNYHGNETLYSGIYGTPLKVDIYFGVVYYQRLRHMVSDKSQARSMGPVDVLTQQ 1001

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG RLGEME   + A+G AY + + L   SD
Sbjct: 1002 PIKGRKKGGGIRLGEMERDALIAHGVAYCINDRLLKCSD 1040



 Score = 97.1 bits (240), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 107/755 (14%), Positives = 222/755 (29%), Gaps = 162/755 (21%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFS---GAAMLEFVSYE 80
           +    S+++              GL    + + PI                  +     +
Sbjct: 14  KHHIESFNYL----------YTHGLIEICRHLSPIEVCVPGNRDIRLPFKNMKIWIEELQ 63

Query: 81  FDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              P         +     C     +Y  P+  T+   + D  + T   S          
Sbjct: 64  IGMPTQQGMLGDNRVLPTQCRQMKKSYTAPMLATICREIDDNPKETVRLS---------- 113

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV---VSQLHRSPGIH 164
           +G++P++ K                         G F+I G ++I+   + Q  R+  I 
Sbjct: 114 LGEIPILVKSQKCHLNGLSAEELVQQQEDCNEFGGYFIINGNEKIIRMLIIQ-KRNYPIA 172

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVT 215
           F     +        +A ++   +         +    D    +++RI  ++K   +PV 
Sbjct: 173 FKRPGYKNKGFNFSPFAVQMKCVRSDQYARTITLHYLMDGN--VYLRIILKKKELQMPVI 230

Query: 216 SFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT-GEQV 273
             L AL  M+  +I    Y +IV SQ                  +V   + D  + G   
Sbjct: 231 ILLRALTDMNDYQI----YQQIVRSQADKSDISD----------RVEVMIADAKSRGINT 276

Query: 274 IESGKKLTSGLLK---SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            +   +    LL+   ++       L +    L          + +   I +        
Sbjct: 277 QKDALEYIGRLLRVELNIFNPETTDLQVGRIFLREHICVHLENDQDKASILLLC------ 330

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +E+++   I +I    +DS+ N   + +  +       ++ L D+   +R   +   S
Sbjct: 331 --IEKLYALFIDEINPDNLDSLVNQEVLLSGHL--YTAYLREKLEDLLVGVREKILKDAS 386

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             +S    L +    +DL T    K+   L          +   +      I   L N +
Sbjct: 387 KEQSKLKDLAYFKRCFDLQTTVGEKLENFLATGNLRSQTGLDLMEASGFTIIADKLNNMR 446

Query: 451 -----GTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLI 504
                 ++         +  +V ++L + +  +  +         + +    S +P    
Sbjct: 447 FLSHFRSVHRGSYFAQMKTTTVRKLLPDVWGFVCPVHTPDGGPCGLLNHITMSCVPLTHP 506

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           + + V   +      SQ                           +     G     + PT
Sbjct: 507 DEQDVEELLFPLGVQSQ---------------RLIYSKNDLPVVLNGKLIGYLNSSLLPT 551

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY---------RKVCDGKVTNDVV 615
               +   +++ G             + N        Y         R V + K  N + 
Sbjct: 552 FEHTLRVYKSN-GTIKETTEVACLPRQENKSPLFPGIYINTTVARLMRPVINLK-LNTIE 609

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           ++S +E+ N  IA   + +  D                         + +  P  ++SI 
Sbjct: 610 WISPLEQINMSIACTQADIRTD-----------------------TQYQEIDPAYILSIL 646

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           AS +PFL  + S R +  C M +Q +       P+
Sbjct: 647 ASNVPFLNYNQSPRNMYQCQMAKQTMGSPCHNYPY 681


>gi|227937604|gb|ACP43377.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 290

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 210/288 (72%), Positives = 244/288 (84%), Gaps = 1/288 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           ESVVA+ SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 ESVVARDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYR 287


>gi|225465805|ref|XP_002263835.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 825

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 70/251 (27%), Positives = 101/251 (40%), Gaps = 41/251 (16%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVLNPLGVPSR 1130
            + V +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++NP   PSR
Sbjct: 531  QKVNIRFRRPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSR 590

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E+         GK + +               S    +               
Sbjct: 591  MTIAMLLESVAAKGGSLHGKFVDATPFSDSLRKANGEAGSESSSL--------------- 635

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                      + + SML     +  G  +LY G  G      + 
Sbjct: 636  -------------------------VDELGSMLTSYGFNYHGVEVLYSGFYGTELTCEIF 670

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G +Y  +L HMVSDK   RSTG+   VT+QP+ G+   GG R GEME   + A+GAAY+
Sbjct: 671  IGPVYYQRLRHMVSDKFQVRSTGTVDQVTRQPIKGRKRGGGIRFGEMERDSMLAHGAAYL 730

Query: 1311 LQEMLTIKSDD 1321
            L + L   SD 
Sbjct: 731  LHDRLHTCSDH 741



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 73/463 (15%), Positives = 146/463 (31%), Gaps = 54/463 (11%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           E +N L  ++H R +         R  +   +R + P  +G +CP  T +G   GL++ +
Sbjct: 106 ERLNFLRFLSHFRAVHRGASFAGLRTTS---VRKLLPEAWGFLCPVHTPDGEPCGLLNHM 162

Query: 587 TSFARVNAYGFIETPYRKVCDGK-----VTNDVVYLSAMEEENRYIAQANSS----LDED 637
            S  R+ +Y       R     +     V   +    A+      + QA       +  D
Sbjct: 163 ASTCRITSYFDSRGNTRDFFKIRMSILSVLIGIGMTPAL----PKLVQAGPPEVLSVILD 218

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASP------KQVVSIAASLIPFLENDDSNR-- 689
           G     +           + R K+  I   P         +S+  +          +R  
Sbjct: 219 GRVVGSIPSSEVETAVNHLRRLKVSAISVIPDDLEVGYIPLSMGGAYPGLYLFTSPSRFV 278

Query: 690 ---VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                +    +      L      V   +        G   +            +  V+ 
Sbjct: 279 RPVRNISIPSEEGHDIELIGPFEQVYMEIRCPDGSDGGRRNIFPATHEEIHPTGMLSVVA 338

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGPST---D 801
           S+    D + S  ++Y+    +++    +  +N R   K+         I    +     
Sbjct: 339 SLTPWSDHNQSPRNMYQCQMGKQTMAFSSQAINCRADQKLYHLQTPQTPIVRTSAYVKYS 398

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
           + +   G N +VA + + GY+ ED+M++++  V   +    H + ++    D      + 
Sbjct: 399 MDEFPTGTNAIVAVLAYSGYDMEDAMILNKSSVDRGL---CHGQIYQTETIDLSDENNKS 455

Query: 862 TRDIPNVSEEGLKN-----IDECGIICVGAEVNPGDILVG----------KITPKGESPM 906
            R         +       ID  G+  VG  +NP +                  KG  P+
Sbjct: 456 DRGQRMFRRSNVDKSANSLIDSDGLPYVGQMINPNEPYCSIYNEVTSSTRATKLKGSEPV 515

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             +   L A   +    V     R  +     ++  +  +RHG
Sbjct: 516 IVDYVALDAKNKKHPQKVNIRFRRPRN----PIIGDKFSSRHG 554


>gi|160337112|gb|ABX25847.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 227

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 94/225 (41%), Positives = 125/225 (55%), Gaps = 40/225 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 35   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 94

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 95   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 139

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 140  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 182

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V D ++ARST
Sbjct: 183  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDXIHARST 227


>gi|269930885|gb|ACZ54177.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 286

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 207/287 (72%), Positives = 241/287 (83%), Gaps = 1/287 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           + SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 RDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 286


>gi|189192000|ref|XP_001932339.1| DNA-directed RNA polymerase I polypeptide 2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
 gi|187973945|gb|EDU41444.1| DNA-directed RNA polymerase I polypeptide 2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
          Length = 1178

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/525 (19%), Positives = 174/525 (33%), Gaps = 67/525 (12%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                  + + +  + + G   +  M IS          S H+E          +   +  
Sbjct: 616  RMYRPVKYLPLNKLDYVGPFEQPYMSISCTDAEIVSGDSTHVE--FDPTNILSIVSNQTP 673

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAIFGEK 920
                N S   L    + G   +G      D        + ++  TP  +  L      + 
Sbjct: 674  FSDYNQSPRNLYRSCQMGKQSMGTPATSLDYRTDNKAYRLQTGQTPIARPPLHNKYGLDN 733

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  +  + V S     + D  + +R   ++     +V + +I  L       +    +
Sbjct: 734  FPNGMNAVVAVISYTGYDMDDGFVLSRGAHERGFGHGTVYKTKILDLEEGSRKNRS---K 790

Query: 981  NIYSRLMEILCGQNAVSGPKGF--KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               ++L          S PK             ++        W     D  +       
Sbjct: 791  RTVTKLFGFAPDSLVESKPKETLDADGLPRVGTMLRSGDVIAAWHTVSYDTAMDDYTNKD 850

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
                       E  +  ++  I   D   P   + + + + + R    GDK + RHG KG
Sbjct: 851  GQTQFFKYKEDEVAYVEQVRIIGSEDGTQP--CQKLSIKLRIPRSPIVGDKFSSRHGQKG 908

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +VS+     DMPF + G   D+++NP   PSRM +G   E+  G +    G         
Sbjct: 909  VVSQKFSVADMPFSETGIQPDVIINPHAFPSRMTIGMFIESLAGKSGALHGMAQD----- 963

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV-FDGAD-- 1215
                                                            +TP  FD  +  
Sbjct: 964  ------------------------------------------------ATPFQFDEQNTA 975

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             +     L  A  +  G   +Y G TGE     + +G +Y  +L HM++DK   R+TG  
Sbjct: 976  VDHFGQQLMKAGYNYYGNEPMYSGFTGEELHADIYIGVVYYQRLRHMINDKFQVRTTGPV 1035

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +  T QP+ G+   GG R+GEME   + A+G A++LQ+ +   SD
Sbjct: 1036 NPTTGQPVKGRKKGGGIRVGEMERDALIAHGTAFLLQDRMMNCSD 1080



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/312 (13%), Positives = 81/312 (25%), Gaps = 84/312 (26%)

Query: 30  IEVQKASYDH-FLMMNIAPDERPNEGLQAAFKSVFPITAF-----SGAAMLEFVSYEFDP 83
           +     S++  F       +   + G    F    P  A           L       D 
Sbjct: 44  VAPHTESFNAIFCAGGQLSEGIKDIG-TKIFLDGNPYAAPEEAGARNRLSLRIQDVFLDK 102

Query: 84  PK-------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
           P                  +   R  TY   ++  L+  +             D +E+  
Sbjct: 103 PALPSTNKVALKNRNILPSEARERHATYRGKMRARLQWRINQ----------GDWQEEMA 152

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIV----VSQ------ 156
            +G +P+M +                         G F++ G ++++    V++      
Sbjct: 153 DLGSVPIMLRSNRCHLEGLSPAALVKSKEESEECGGYFIVNGNEKMIRPLQVNRRNYPMA 212

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRR 210
           + R  G   +   G         Y  +I   +         +    D    ++ R   R+
Sbjct: 213 IKR--GAFTNRGPGYTQ------YGIQIRSMRPDQTSQTNALHYLDDGN--VNFRFSWRK 262

Query: 211 K---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               VP+   + AL   ++ EI              +          L+   KV      
Sbjct: 263 SEYLVPLVMIMKALVETNDREIFEGLVGAAGSKGLREKQFVSDRVELLLRTFKVYGLHTK 322

Query: 267 IDTGEQVIESGK 278
             T   + +  K
Sbjct: 323 AKTRAFLGQKFK 334


>gi|269930837|gb|ACZ54153.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 288

 Score =  270 bits (691), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 209/289 (72%), Positives = 243/289 (84%), Gaps = 1/289 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           GAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ
Sbjct: 241 GAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQ 288


>gi|145489775|ref|XP_001430889.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124397990|emb|CAK63491.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1115

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 112/276 (40%), Gaps = 52/276 (18%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 +D    +IE++   +     V  ++K  +   R    GDK + RHG KG++S + 
Sbjct: 817  KVHHSKDSETARIEQVAVVNKSENDVSVMIKYRI--NRNPIIGDKFSSRHGQKGVMSLLW 874

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P  DMPF + G   DI++NP   PSRM +G + E+    A V  G+  ++       N +
Sbjct: 875  PQIDMPFSESGMVPDIIINPHAFPSRMTIGMLIESMAAKANVLQGEMFETHPFQNYENDN 934

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +                                                   +     L 
Sbjct: 935  V--------------------------------------------------VDYFGKQLI 944

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G P    +  G +Y  +L HMVSDK  ARS G   ++TQQP+ 
Sbjct: 945  KHGYNYHGNETLYSGIYGTPLKVDIYFGVVYYQRLRHMVSDKSQARSMGPVDVLTQQPIK 1004

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            G+   GG RLGEME   + A+G AY + + L   SD
Sbjct: 1005 GRKKGGGIRLGEMERDALIAHGVAYCINDRLLKCSD 1040



 Score = 97.8 bits (242), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 107/755 (14%), Positives = 222/755 (29%), Gaps = 162/755 (21%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------AFS---GAAMLEFVSYE 80
           +    S+++              GL    + + PI                  +     +
Sbjct: 14  KHHIESFNYL----------YTHGLVEICRHLSPIEVCVPGNRDIRLPFKNMKIWIEELQ 63

Query: 81  FDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
              P         +     C     +Y  P+  T+   + D  + T   S          
Sbjct: 64  IGMPTQQGMLGDNRVLPTQCRQMKKSYTAPMLATICREIDDNPKETVRLS---------- 113

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIV---VSQLHRSPGIH 164
           +G++P++ K                         G F+I G ++I+   + Q  R+  I 
Sbjct: 114 LGEIPILVKSQKCHLNGLSAEELVQQQEDCNEFGGYFIINGNEKIIRMLIIQ-KRNYPIA 172

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLW------MDIEFDSKDIIHVRIDRRRK---VPVT 215
           F     +        YA ++   +         +    D    +++RI  ++K   +PV 
Sbjct: 173 FKRPGYKNKGFNFSPYAVQMKCVRSDQYARTITLHYLMDGN--VYLRIILKKKELQMPVI 230

Query: 216 SFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT-GEQV 273
             L AL  M+  +I    Y +IV SQ                  +V   + D  + G   
Sbjct: 231 ILLRALTDMNDYQI----YQQIVRSQADKSDISD----------RVEVMIADAKSRGINT 276

Query: 274 IESGKKLTSGLLK---SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            +   +    LL+   ++       L +    L          + +   I +        
Sbjct: 277 QKDALEYIGRLLRVELNIFNPETTDLQVGRIFLREHICVHLDNDQDKASILLLC------ 330

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
             +E+++   I +I    +DS+ N   + +  +       ++ L D+   +R   +   +
Sbjct: 331 --IEKLYALFIDEINPDNLDSLVNQEVLLSGHL--YTAYLREKLEDLLVGVREKILKDAT 386

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
             +S    L +    +DL T    K+   L          +   +      I   L N +
Sbjct: 387 KEQSKLKDLAYFKRCFDLQTTVGEKLENFLATGNLRSQTGLDLMEASGFTIIADKLNNMR 446

Query: 451 -----GTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLI 504
                 ++         +  +V ++L + +  +  +         + +    S +P    
Sbjct: 447 FLSHFRSVHRGSYFAQMKTTTVRKLLPDVWGFVCPVHTPDGGPCGLLNHITMSCVPLTHP 506

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           + + +   +      SQ                           +     G     + PT
Sbjct: 507 DEQDIEELLFPLGVQSQ---------------RLIYSKNDLPVVLNGKLIGYLNSSLLPT 551

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY---------RKVCDGKVTNDVV 615
               I   +++ G             + N        Y         R V + K  N + 
Sbjct: 552 FEHTIRVYKSN-GTIKETTEVACLPRQENKSPLFPGIYINTTVARLMRPVINLK-LNTIE 609

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           ++S +E+ N  IA   + +  D                         + +  P  ++SI 
Sbjct: 610 WISPLEQINMSIACTQADIRTD-----------------------TQYQEIDPAYILSIL 646

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           AS +PFL  + S R +  C M +Q +       P+
Sbjct: 647 ASNVPFLNYNQSPRNMYQCQMAKQTMGSPCHNYPY 681


>gi|108885401|gb|ABG23217.1| DNA-directed RNA polymerase [Geobacillus tepidamans]
          Length = 145

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 67/167 (40%), Positives = 102/167 (61%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  FK + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFKEISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYSVEESKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++    G+   +GK  ++  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---GKVDKNGKRGFSATVIPNRGAW 145


>gi|120561263|gb|ABM27016.1| RNA polymerase II second largest subunit [Catenaria anguillulae]
          Length = 892

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 154/947 (16%), Positives = 286/947 (30%), Gaps = 165/947 (17%)

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
              I   + D              D  +D++ AL  I R  R            + N    
Sbjct: 84   ETICYHFDDDQMLEMLKPCIEQADVIQDQELALDHIGRRGR------------VTNMHRD 131

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               +Y    + R  +         +  +      I  ++  ++    G+  IDD D+ G 
Sbjct: 132  QRIRYARDLLERETLPHIGTTPGCETRKAW---FIGYMVHRMLLAALGRRPIDDRDHFGK 188

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD---LINAKPVVSAVCEFFC 518
            +R+   G +L + ++    +  + I    +     S  P     ++    + + +     
Sbjct: 189  KRLDLAGPLLASLFKTFFSKFVKDITREFTKSIERSQGPFHLASVVKPGIITNGLRYALA 248

Query: 519  SSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +               +SQ+       S ++H RRL+      + R     + R +H TH
Sbjct: 249  TGNWGDQKKFMETRAGVSQVLNRYTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTH 304

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEE 623
            +G +CPAET EG   GLV +L   A ++     E     + +  +    ++   SA+ + 
Sbjct: 305  WGMVCPAETPEGQACGLVKNLALMAYISVGTSAEPVVEALQEYGIENLEEISDASAVADA 364

Query: 624  NRYIAQ-ANSSLDEDGSFTEELVFCRCAGEEILVPREK-------IDFIDASPKQVVSIA 675
             +     A   +  D +   + +       ++  P           D  D   +      
Sbjct: 365  TKVFVNGAWVGIHSDPADLFKTLREMRRMGDLTPPHLDEPEVSIVRDIRDNEIRIYTDPG 424

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
              + P F+ N+D+ R+ +       A+  LK +     T  E   +  S   ++ +    
Sbjct: 425  RIMRPLFVVNEDTQRLKLRKAHVAAALEALKVDDDVKETD-EMRDSLMSWRNLLRQGVLE 483

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +   +   + + S+       + G  +    KF ++ +          K G+  +R    
Sbjct: 484  LMDTEEEEMAMISMTPADLAESRGDKVVDKSKFDKTARLKSR------KPGEYCKRWTHC 537

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               PS  LG       +  + +P+  +N       S R   +       +  F    +  
Sbjct: 538  EIHPSMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVFLTNFQ-- 582

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                                 +    +  +        +    +T      +   +  + 
Sbjct: 583  ---------------------LRMDTLANILYYPQRPLVTTRSMTYLRFRELPAGQNAIV 621

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    I+ R   D  ++S  VE E  E   RD    
Sbjct: 622  AITCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYFDSEKKSGGVEEEVFEKPNRDTTMR 680

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  ++      I  G           K+  L  D+     R+               
Sbjct: 681  LRRGTYDLLDDDGIISPGTQVKGDDIILGKTAPLPDDVSEMGARTT-------------- 726

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K    TS    E  + + +      D++     + VKV V   R  Q GDK A RH
Sbjct: 727  --QTKKDVSTSLKATEKGYVDHVIVTTNADNL-----KFVKVRVRSTRVPQMGDKFASRH 779

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMPF   G   D+++NP  +PSRM +G + E  L      +G +  +
Sbjct: 780  GQKGTVGVTYRQEDMPFSALGVTPDLIVNPHAIPSRMTIGHLVECLLSKVGALVGTEGDA 839

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS   +                                            
Sbjct: 840  TPFTDLTVQEISQQLAQHGFQQRGFEVM-------------------------------- 867

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                            +G +    G      D  V  G  Y  +L H
Sbjct: 868  ---------------YNGHT----GR---KLDAQVFFGPTYYQRLKH 892



 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 121/861 (14%), Positives = 257/861 (29%), Gaps = 161/861 (18%)

Query: 149 IQRIVVSQL--------HRS-PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK 199
            ++++++Q           S PG  +  +    S +G+   +  I               
Sbjct: 1   SEKVIIAQERTATNTVFVFSKPGGAYQAEIRSQSDAGQRTLSSFI--------------- 45

Query: 200 DIIHVRIDRRRKV-----------PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCF 247
               VR+D++R++           P+     ALG+ S+ +IL T        Q  +    
Sbjct: 46  ----VRMDKQRRITCSLPYIQEEIPLPIVFRALGVHSDKQILETICYHFDDDQMLEMLKP 101

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGIT------S 300
            +  AD++   +++   +        +   +++     +  L+ + +  +G T       
Sbjct: 102 CIEQADVIQDQELALDHIGRRGRVTNMHRDQRI--RYARDLLERETLPHIGTTPGCETRK 159

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
               G  V   ++    G   I+  D   +K L+             +   V +      
Sbjct: 160 AWFIGYMVHRMLL-AALGRRPIDDRDHFGKKRLDLAGPLLASLFKTFFSKFVKDITREFT 218

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG-RVKMNMR 419
             +         A      V++PG + T  +  ++    + D  K+  +  G    +N  
Sbjct: 219 KSIERSQGPFHLA-----SVVKPG-IITNGLRYALATGNWGDQKKFMETRAGVSQVLNRY 272

Query: 420 LNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
               T   +R +         +     L N    +         +   + + L     + 
Sbjct: 273 TFASTLSHLRRLNTPIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAYIS 332

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           +      + E +    I+++  +++ +A  V  A   F   + +    +  +    +   
Sbjct: 333 VGTSAEPVVEALQEYGIENL--EEISDASAVADATKVFVNGAWVGIHSDPADLFKTLREM 390

Query: 539 RRLSALGQGGV-------ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS------ 585
           RR+  L    +        R     E+R ++      + P          L         
Sbjct: 391 RRMGDLTPPHLDEPEVSIVRDIRDNEIR-IYTDPGRIMRPLFVVNEDTQRLKLRKAHVAA 449

Query: 586 ----LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               L     V     +        +      +  +   EEE   I+   + L E     
Sbjct: 450 ALEALKVDDDVKETDEMRDSLMSWRNLLRQGVLELMDTEEEEMAMISMTPADLAESRGDK 509

Query: 642 -----EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                +     R    +     ++    +  P  ++ I AS+IPF +++ S R      M
Sbjct: 510 VVDKSKFDKTARLKSRKPGEYCKRWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 569

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                                                   + 
Sbjct: 570 GKQAMGVFLTNFQL-----------------------------------------RMDTL 588

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           + +  Y               QRPLV                     +L  G+N +VA  
Sbjct: 589 ANILYYP--------------QRPLV----------TTRSMTYLRFRELPAGQNAIVAIT 624

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEE 871
            + GYN EDS+++++  +   +F SI+   +    + +    EE+           +   
Sbjct: 625 CYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYFDSEKKSGGVEEEVFEKPNRDTTMRLRRG 684

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ GII  G +V   DI++GK  P  +         +  +        +D S  +
Sbjct: 685 TYDLLDDDGIISPGTQVKGDDIILGKTAPLPDD--------VSEMGARTTQTKKDVSTSL 736

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            +   G V  V +       K
Sbjct: 737 KATEKGYVDHVIVTTNADNLK 757


>gi|103001538|gb|ABF71512.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 692

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 115/813 (14%), Positives = 235/813 (28%), Gaps = 145/813 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L N +R+   ++ + + +  +    +         + +  + + +     +        
Sbjct: 1    LLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKST 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   ++ +  L+ +               S     AK  G    V     V+  V+
Sbjct: 237  NCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVEYVD 286

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q           +   V+          T      ++ 
Sbjct: 287  AEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSMI 346

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N          M  + +   + +  ++                    
Sbjct: 347  LGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----------------- 387

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 388  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 437

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 438  IMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDD 493

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 494  DGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL- 552

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 553  -------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 593

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF K+G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 594  QEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------ 641

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 642  -----------------------------------------ATP-FTEVTVDSVSKLLRE 659

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                  G  ++Y+G TG      V +G  Y  +
Sbjct: 660  HGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 692


>gi|226934678|gb|ACO92413.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 224

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 93/223 (41%), Positives = 124/223 (55%), Gaps = 40/223 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 34   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 93

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 94   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 138

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 139  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 181

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++AR
Sbjct: 182  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHAR 224


>gi|110589622|gb|ABG77313.1| RNA polymerase beta subunit [Enterobacter helveticus]
          Length = 280

 Score =  270 bits (690), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 167/279 (59%), Positives = 212/279 (75%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKY 280


>gi|160330991|ref|XP_001712203.1| rpc2 [Hemiselmis andersenii]
 gi|159765650|gb|ABW97878.1| rpc2 [Hemiselmis andersenii]
          Length = 1100

 Score =  270 bits (689), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 92/398 (23%), Positives = 154/398 (38%), Gaps = 60/398 (15%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            ++   +    R++ +R  +IL   +   G K F++          +  +       V   
Sbjct: 751  NRSSIERGFFRSVIARKHKILLKNSDFLGAKSFERPLPNLEKFEEKKIKKIENYGEVVKF 810

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
            + ++N      +   S+  L++     IEK+    +     +  VK+ +   R  + GDK
Sbjct: 811  QKKKNQFLNFEKQIFSRLSLKEFKGEMIEKVIISSNFLE--IFFVKLILRQIRQPEVGDK 868

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             + RHG KG+   I   +D+PF  DG   D+++NP G PSRM VG++ E          G
Sbjct: 869  FSSRHGQKGVCGAICFQKDLPFSNDGIIPDLIMNPHGFPSRMTVGKVIEIM--------G 920

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             KI S+   +         +    K     +                             
Sbjct: 921  AKIGSIFGKFIDGTPFIESKIAKIKKKLKIA----------------------------- 951

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                  G+   + G+TG P    V  G ++  KL HMV DK++A
Sbjct: 952  -----------------GYSSEGKEFFFSGITGVPMLMDVFSGPVFYQKLKHMVKDKIHA 994

Query: 1270 RSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG----R 1325
            R  G  S +T+QP+ G+S  GG R GEME  C+ +YGA+  + E L I SD         
Sbjct: 995  RGKGPCSNITRQPIEGRSRGGGLRFGEMERDCLISYGASEAIIERLLISSDLTQANFDLH 1054

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            T  +       +      P +  +L +E+Q++ +   L
Sbjct: 1055 TGFFTDKKKSLNIVSLKLPYACKLLFQELQSMNILPRL 1092



 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 128/916 (13%), Positives = 268/916 (29%), Gaps = 194/916 (21%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           K F     I+    LI  Q  S+++FL  +I      N+      K +F       +  L
Sbjct: 7   KNFNLVSYILKSKGLIWQQIESFNYFLNTDIKKIIFMNQ------KKIF---DSDDSFFL 57

Query: 75  EFVSYEFD---------PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           +F   +                   C   D +Y   +   L   +             + 
Sbjct: 58  KFSKLKIGLASEYLNFMEMPISPYQCRTTDSSYTGTIFFDLSFKI-------------EK 104

Query: 126 KEQSIY---MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLH 158
           K+ +++   +G +P+M                           G F++KG +++++ Q  
Sbjct: 105 KKFNVFNFNLGKIPIMLQSNKCILFSKNENEFLSLNECPLDPGGYFILKGTEKVILIQEQ 164

Query: 159 RSPG-IHFDHDKGRAS-------LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR 210
            S   I+ + D+  +         S K +     + +Q   +      K  + V      
Sbjct: 165 VSANRINIEQDQHGSICAVVNSFSSNKKIRNVVFLKNQ--KLYF----KHKLFVE----- 213

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           ++P+  FL +LG + + EIL     +         W    +    +   K +   +    
Sbjct: 214 EIPLFIFLKSLGFEKDREILDLIGKEYENILE---WSLFETKLAGITSKKQAIFYIVQRF 270

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV--NGETGEIYIEAGDV 327
              + E      +   KS  E    F    +  +      +     N E   I++     
Sbjct: 271 NFNLFEKKFSDNAFKSKSYSENEFFFKEGLTKFILTHLTPKVFYGGNLEEKGIFLSLMVK 330

Query: 328 IDEKSLEEIFHSEIRD-------------IPILYVDSVNNNAYI-RNTLVTDKNKDRKDA 373
               +L +   ++ +D             + IL+ D               +  K +K+ 
Sbjct: 331 KIFSNLNQPMITDNKDYYGNKRLGLAGNLVSILFEDFFRKTLKEGYKYYKLNSTKLKKNQ 390

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            L++   +R   ++                 K + + V +    +          +   +
Sbjct: 391 HLELISFLRQDIITNGLEYSFSTGNWIVKKLKIEKNGVTQTLSRLSFISSISIVTKITSQ 450

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
            + I  I+    L + +  +    +        + + L     + +    R I +    +
Sbjct: 451 NEKIRKIRGPRSLHSSQWGMICPTDTPEGESCGLVKDLTILAHISVKIKTRFITQLCYDL 510

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            I++++     N          F     L         +      RR   +         
Sbjct: 511 GIENLIHPKKKNFFLEKKICKIFLNGRYLGIHNNPSYFMYSFRSMRRSGMINYYVSIFWD 570

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E   +         P    +   + + +      + N             D  +T  
Sbjct: 571 TFSEEIVIFTDEGRICRPFLIVDLGKVKIKNFEKKLLKKNLT--------FCKDLFLTGL 622

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + +L   E+ N +IAQ+                             K   ++ SP+ V+ 
Sbjct: 623 LEFLDVNEQNNAFIAQS-----------------------PQYINNKTTHLEISPEIVLG 659

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           I ASLIPFL+++ S R    C M +QA+                                
Sbjct: 660 ICASLIPFLDHNQSPRNTYQCAMGKQAIGS------------------------------ 689

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                      I   +     +   + IY               Q+PLVK          
Sbjct: 690 -----------ISLNQNQRCDTILSLLIYP--------------QKPLVKTKMVYFSG-- 722

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N  V  + + G++ ED+++++   +    F S+   + +++ ++
Sbjct: 723 --------NNRLTSGINACVCILSYSGFDIEDAIILNRSSIERGFFRSVIARKHKILLKN 774

Query: 854 TK-LGPEEITRDIPNV 868
           +  LG +   R +PN+
Sbjct: 775 SDFLGAKSFERPLPNL 790


>gi|45545311|gb|AAS67503.1| DNA-dependent RNA polymerase II second largest subunit [Candida
            parapsilosis]
          Length = 892

 Score =  270 bits (689), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 139/856 (16%), Positives = 258/856 (30%), Gaps = 146/856 (17%)

Query: 425  PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
             +     +   +  ++  L+     +   DD D+ G +R+   G +L N +R+   ++ +
Sbjct: 159  EEGFETRKAFFLGYMVNRLLLCALERKEPDDRDHFGKKRLDLAGPLLANLFRILFKKLTK 218

Query: 485  SIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHV 529
             I    +    +         + ++ +   +     +               +SQ+    
Sbjct: 219  DIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRY 278

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  
Sbjct: 279  TYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM 334

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            + ++     E     + D  +     Y+ +   +   +      +         + + R 
Sbjct: 335  SCISVGTPSEPISSFLRDWGLEPLEDYVPSNSPDATRVFVNGVWVGVHREPASLVDYMRD 394

Query: 650  AGEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                  +  E     D   K             P    DD+       +++ +   +   
Sbjct: 395  LRRNGDISPEVSIIRDIREKELKIFTDAGRVYRPLFIVDDNPDSETKGDLKLKKEHV--- 451

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYR 763
                + +  +    + S       R GIVE VDA      +I     DL+ S S +   +
Sbjct: 452  -NRLLESSYDGDEDEPSYTWSSLVREGIVEYVDAEEEETIMIAMTPDDLEASKSNLTETQ 510

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                Q   Q     +R                  PS  LG  A       + +P+  +N 
Sbjct: 511  QQDLQMEEQELDPAKRIKPTGSSNTHTFTHCEIHPSMILGVAA-------SIIPFPDHNQ 563

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +   + +  + V                               +  
Sbjct: 564  SPRNTYQSAMGKQAMG--VFLTNYAVRM---------------------------DTMAN 594

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +        
Sbjct: 595  ILYYPQKPLATTRAMEHLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGFF-RS 653

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +D  +R      + +E   +    + + L    Y +L +   I  G        
Sbjct: 654  LFFRSYMDLEKRQGM---KALETFEKPSRSDTLRLKHGTYEKLDDDGLIAPGVRVSGEDI 710

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+T +  D      R+Q+                 K    T     E    +++   
Sbjct: 711  IIGKTTPIPPDTEELGQRTQYHT---------------KRDASTPLRSTESGIVDQVLLT 755

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD       + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 756  TNGD-----GAKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFTAEGIVPDL 810

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM V  + E  L       G +                             
Sbjct: 811  IINPHAIPSRMTVAHLIECLLSKVSSLSGLEGD--------------------------- 843

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      ++P F     EAI+ +LR       G  ++Y+G 
Sbjct: 844  --------------------------ASP-FTDVTAEAISKLLREHGYQSRGFEVMYNGH 876

Query: 1241 TGEPFDRPVTVGYIYM 1256
            TG+     V  G  Y 
Sbjct: 877  TGKKLMAQVFFGPTYY 892



 Score = 97.1 bits (240), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 75/531 (14%), Positives = 151/531 (28%), Gaps = 48/531 (9%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD---- 266
           +P+     ALG+  + +IL          Q  +     +    ++   +V+   +     
Sbjct: 73  IPIVIVFRALGVVPDGDILEHICYDANDWQMLEMLKPCVEEGFVIQEREVALDFIGRRGV 132

Query: 267 --IDTGEQVIESGKKLTSGLLKSL--KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             I   +++  +   L   LL ++  +E            +    +   +   E      
Sbjct: 133 LGIRREKRIQYAKDILQKELLPNITQEEGFETRKAFFLGYMVNRLLLCALERKEP----- 187

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +  D   +K L+           IL+   + +   Y++  +  DK  +   A+       
Sbjct: 188 DDRDHFGKKRLDLAGPLLANLFRILFKKLTKDIYNYMQRCVENDKEFNLTLAV------- 240

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
                 T  +  S+    + +  K   S  G  ++  R    +      R          
Sbjct: 241 -KSQTITDGLRYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGK 299

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           I     L N    +         +      ++KN   +  + +    +   S +    + 
Sbjct: 300 IAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGTPSEPISSFLRDWGLE 356

Query: 500 PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVE- 557
           P +         A   F     +    E  + +  +   RR   +     + R     E 
Sbjct: 357 PLEDYVPSNSPDATRVFVNGVWVGVHREPASLVDYMRDLRRNGDISPEVSIIRDIREKEL 416

Query: 558 ------MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                  R   P       P   ++G        +      +  G  + P          
Sbjct: 417 KIFTDAGRVYRPLFIVDDNPDSETKGDLKLKKEHVNRLLESSYDGDEDEPSYTWSSLVRE 476

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR------------E 659
             V Y+ A EEE   IA     L+   S   E        EE  +               
Sbjct: 477 GIVEYVDAEEEETIMIAMTPDDLEASKSNLTETQQQDLQMEEQELDPAKRIKPTGSSNTH 536

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                +  P  ++ +AAS+IPF +++ S R      M +QA+ +       
Sbjct: 537 TFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYAV 587


>gi|113957834|gb|ABI49125.1| RNA polymerase II second largest subunit [Megalospora tuberculosa]
          Length = 718

 Score =  270 bits (689), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 132/840 (15%), Positives = 245/840 (29%), Gaps = 148/840 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + I +  +              +    + S
Sbjct: 1    DDRDHFGKKRLDLAGPLLATLFRTLFSKLSKDIYKYLQKCVESNREFNLTLGVKQNTLTS 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGEQKKAAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     ++     E    Y      ++  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYISVGSPAEPIVDYLIQRGMEILEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  TRSPNATKVFVNGVWVGVHHDPALLVSNVQELRRTNIIPHEASLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                P F+ N+D      G  +  + +     +   V   M     + +G +I  +    
Sbjct: 237  RVCRPLFVVNNDFKSDNAGSLVLTKEMVQKVEDERDVVIAM--DPEERAGTSIGWQGLVY 294

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDI 793
                      I+ V+ + + +   V     ++  R  Q      +P        V+    
Sbjct: 295  A-------RAIQYVDAEEEETIMIVMTPEDLEISRQVQAGYDAPQPSADAPNSRVKAAVN 347

Query: 794  IADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                  T      ++   +  + +P+  +N          M  + +              
Sbjct: 348  PTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV------------ 395

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                L N DE    +  +             +       +   +
Sbjct: 396  -------------------FLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQ 436

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R  ++  +R      + +E   + 
Sbjct: 437  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVNTEKRVGM---QVLESFEKP 492

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               E + L    Y +L     +  G           K+T ++ D                
Sbjct: 493  LRSETLKLKHGTYDKLDNDGLVAPGVRVSGDDVIIGKTTPIAPD---------------A 537

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            +E  QR    +K    T     E+   +++             L+ VKV +   +  Q G
Sbjct: 538  EEMGQRTKAHIKKDASTPLRSTENGIVDRVLL-----STNSEGLKFVKVRMRTTKIPQIG 592

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L      
Sbjct: 593  DKFASRHGQKGTIGITYRQEDMPFTSEGMVPDIIINPHAIPSRMTIAHLIECQLSKVSSL 652

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +          +S L    E    +                             
Sbjct: 653  RGYEGDATPFTEITVDSVSNLLR--EHGYQSRGFEVM----------------------- 687

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                   +G +    G         V +G  Y  +L HMV DK+
Sbjct: 688  ----------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 718


>gi|145926494|gb|ABP98886.1| RNA polymerase beta subunit [Bradyrhizobium canariense]
          Length = 257

 Score =  270 bits (689), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 137/258 (53%), Positives = 185/258 (71%), Gaps = 1/258 (0%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP 234
           SGKL++A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS + ALG+D E ILSTFY 
Sbjct: 1   SGKLVFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLMFALGLDGEAILSTFYK 60

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
           KI Y +  + W     A +   G    + L+D DTG+ V+E+GKKLT    + ++EKG+K
Sbjct: 61  KIQYKRIKEGWRVQFDA-NRFRGYSTINDLIDADTGKVVLEAGKKLTVRGARQMQEKGLK 119

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L ++   L G Y+AED+VN +TGEI+ EAG+ I +KS++ +     +++P+L +D VN 
Sbjct: 120 ALRLSDAELVGNYIAEDLVNPKTGEIHAEAGEEITDKSIKVLNEHGYKELPLLDIDHVNV 179

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            AYIRNTL  DKN  R+DAL DIYRVMRPG+  T   A++MF  LFFD+++YDLS VGRV
Sbjct: 180 GAYIRNTLSADKNMTREDALFDIYRVMRPGEPPTLDSAQAMFQSLFFDAERYDLSAVGRV 239

Query: 415 KMNMRLNLDTPDDVRHIR 432
           KMNMRL+LD PD  R +R
Sbjct: 240 KMNMRLDLDAPDTQRTLR 257


>gi|120561265|gb|ABM27017.1| RNA polymerase II second largest subunit [Coelomomyces stegomyiae]
          Length = 862

 Score =  270 bits (689), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 142/952 (14%), Positives = 278/952 (29%), Gaps = 185/952 (19%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            ++   G + D   LE I +       +  +    + A+  N         ++ AL  I +
Sbjct: 73   VFRALGLLTDRDILERICYDFNDHQMLEMLKPCIDEAFQVN--------TQELALDHIGK 124

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
              +   ++                 +Y    + R  +       T       +   I  +
Sbjct: 125  RGKNVGLT------------RERRIRYACDLLERELLPHI---GTTPGCETRKSYFIGYM 169

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDS 497
            I  L+    G+  +DD D+ G +R+   G +L + +R    ++ + +             
Sbjct: 170  INRLLSTALGRREVDDRDHFGKKRLDLAGPLLASLFRTFFQKLTKDVGRYFTNCLERSRP 229

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSAL 544
                  IN+  + + +     +               +SQ+       S ++H RRL+  
Sbjct: 230  FNLNMAINSNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFASTLSHLRRLNT- 288

Query: 545  GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                + R     + R +H TH+G +CPAET EG   GLV +L   + ++     E  +  
Sbjct: 289  ---PIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSIISVGSASEPIHEF 345

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----FCRCAGEEILVPREK 660
            + +   T ++  +S            N +        + LV      R A +        
Sbjct: 346  LSEW-TTENLEEISPSTIGPNTKVFVNGAWIGIHREPDSLVKTLKTLRRATDIDSEVSVV 404

Query: 661  IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ----RQAVPLLKAEAPFVGTGME 716
             D  +   +          P    +++ ++++          +    +      +  G+ 
Sbjct: 405  HDIRENELRIYTDPGRICRPLFVVNENQQLVLKKEHILKLSEEDEDAIWGWEKLLINGI- 463

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                              VE +D        +    D            K    ++   +
Sbjct: 464  ------------------VEYLDTEEEETVMISMSPDDLAEARGALIFDKSLDRDRTARL 505

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
              R   K GD  +        P+  LG       +  + +P+  +N       S R   +
Sbjct: 506  KAR---KPGDYCKTWTHCEIHPAMILG-------ICASIIPFPDHNQ------SPRNTYQ 549

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                   +  +    +                       +    +  +        +   
Sbjct: 550  SAMGKQAMGVYLTNFQ-----------------------LRMDTLANILYYPQKPLVTTR 586

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +   +  + AI      +  D+ +   S +   +    I+ R  +D  +++
Sbjct: 587  NMQYLRFRELPAGQNAIVAIAAYSGYNQEDSLIMSQSAIDRGLF-RSIYYRSYVDAEKKT 645

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
               + E+ E   R+   +              +  G           K+  L  D     
Sbjct: 646  GFTQLEEFERPTRETTLKLRQGSYEKLEDDGFVAPGTRVNGDDIIIGKTAPLPMDHSELG 705

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             R+                   K    T     E+   + +     GD       + VK+
Sbjct: 706  TRTT----------------QTKKDVSTGLKSSENGIVDHVMVTTNGD-----GYKFVKI 744

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             V   R  Q GDK A RHG KG V      EDMPF  +G   D+++NP  +PSRM +G +
Sbjct: 745  RVRSTRVPQIGDKFASRHGQKGTVGMTYRQEDMPFTAEGLTPDLIINPHAIPSRMTIGHL 804

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  LG      G +                                             
Sbjct: 805  VECLLGKVSSLTGSEGD------------------------------------------- 821

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                      +TP F     + I+ +LR     + G  ++Y+G TG+     
Sbjct: 822  ----------ATP-FTDVTVQQISDLLRECGYQQRGFEVMYNGHTGKKLSAQ 862



 Score =  154 bits (388), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 118/838 (14%), Positives = 250/838 (29%), Gaps = 132/838 (15%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK--DIIHVRI 206
            ++++++Q   +    F     + +L   + Y   I          E   K      V++
Sbjct: 1   SEKVIIAQERTATNTVF---VFKKALPSPVEYQAEIRSQ------AETGPKTMSSFIVKM 51

Query: 207 DR-----------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
            R            + +P+     ALG+ ++ +IL          Q  +     +  A  
Sbjct: 52  SRQHHITATLPYINQDIPIVIVFRALGLLTDRDILERICYDFNDHQMLEMLKPCIDEAFQ 111

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYV 308
           +   +++   +        +   +++       L+ + +  +G T           G  +
Sbjct: 112 VNTQELALDHIGKRGKNVGLTRERRIRYA-CDLLERELLPHIGTTPGCETRKSYFIGYMI 170

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKN 367
              +++   G   ++  D   +K L+             +   + +   Y  N L   + 
Sbjct: 171 -NRLLSTALGRREVDDRDHFGKKRLDLAGPLLASLFRTFFQKLTKDVGRYFTNCLERSRP 229

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG-RVKMNMRLNLDTPD 426
            +   A+          +  T  +  ++    + D  K+  +  G    +N      T  
Sbjct: 230 FNLNMAI--------NSNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFASTLS 281

Query: 427 DVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
            +R +         +     L N    +         +      ++KN   + ++ +  +
Sbjct: 282 HLRRLNTPIGREGKLAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSIISVGSA 338

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
            +     +   +    + I+   +      F   + +    E  + +  +   RR + + 
Sbjct: 339 SEPIHEFLSEWTTENLEEISPSTIGPNTKVFVNGAWIGIHREPDSLVKTLKTLRRATDID 398

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V+      E      T  GRIC        N  LV       +++     E      
Sbjct: 399 SE-VSVVHDIRENELRIYTDPGRICRPLFVVNENQQLVLKKEHILKLSEED--EDAIWGW 455

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG------SFTEELVFCRCAGEEILVPRE 659
               +   V YL   EEE   I+ +   L E           +     R    +     +
Sbjct: 456 EKLLINGIVEYLDTEEEETVMISMSPDDLAEARGALIFDKSLDRDRTARLKARKPGDYCK 515

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                +  P  ++ I AS+IPF +++ S R      M +QA+ +                
Sbjct: 516 TWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNFQL--------- 566

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                                              + + +  Y               Q+
Sbjct: 567 --------------------------------RMDTLANILYYP--------------QK 580

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PLV             +       +L  G+N +VA   + GYN EDS+++S+  +   +F
Sbjct: 581 PLV----------TTRNMQYLRFRELPAGQNAIVAIAAYSGYNQEDSLIMSQSAIDRGLF 630

Query: 840 TSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            SI+   +    + T     EE  R        + +   + +++ G +  G  VN  DI+
Sbjct: 631 RSIYYRSYVDAEKKTGFTQLEEFERPTRETTLKLRQGSYEKLEDDGFVAPGTRVNGDDII 690

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P                        +D S  + S  +G V  V +       K
Sbjct: 691 IGKTAPLPMDHSELGT--------RTTQTKKDVSTGLKSSENGIVDHVMVTTNGDGYK 740


>gi|6449118|gb|AAF08834.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 290

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 165/297 (55%), Positives = 211/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L EDG F E +V  R  
Sbjct: 61  NKYGFIQTPYRKVNRETGLVTNEIVWLTADEEDEFIVAQANSKLTEDGRFAEAIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP+
Sbjct: 121 GNNQEFPSDQVDFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA +A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAADIAQHDGKVVYSDAAKVEVRREDGSLD-------VYHITKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTSYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|213402277|ref|XP_002171911.1| DNA-directed RNA polymerase III subunit RPC2 [Schizosaccharomyces
            japonicus yFS275]
 gi|211999958|gb|EEB05618.1| DNA-directed RNA polymerase III subunit RPC2 [Schizosaccharomyces
            japonicus yFS275]
          Length = 1160

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 155/969 (15%), Positives = 299/969 (30%), Gaps = 192/969 (19%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---- 487
            +   +  + + ++        +DD D +GN+R+   G++L   +     +    +K    
Sbjct: 351  KAVYVAMMARRVLMAMVDPSQVDDRDYVGNKRLELAGQLLALLFEDLFKKFNSDLKLNID 410

Query: 488  ---ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               ++ +         Q  ++   +   +     +   S     +          RLS +
Sbjct: 411  KVLKKPNRTQEFDAYNQLSMHGDHITQGMVRALSTGNWSLKRFKMERAGVTHVLSRLSFI 470

Query: 545  GQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
               G+         + R     R + P+ +G +C ++T EG   GLV +L     +    
Sbjct: 471  SALGMMTRITSQFEKTRKVSGPRSLQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTD- 529

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
              E P  ++       DV  ++  E     +AQ +  +  +GS        R     +  
Sbjct: 530  EEEGPLIRLAYAFGVEDVHTVTGRE----ILAQDSYLVYINGSILG---ITRYPSRFVSC 582

Query: 657  PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             R        SP   + I         + D  R+     +    +P +  E         
Sbjct: 583  FRRLRRSGRISPFVGIFINEHQRAVFISADGGRICRPLIVVENGLPRVTNE-------HI 635

Query: 717  SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
              +           +AG VE VD               + S + +Y       +      
Sbjct: 636  RKLKNGEMVFEDFLKAGYVEYVDVNE-----------ENDSLIAVYEKDIAPDTTH---- 680

Query: 777  NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                             +   P T LG +A         +P+  +N          M  +
Sbjct: 681  -----------------LEIEPFTILGAVA-------GVIPYPHHNQSPRNTYQCAMGKQ 716

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
             +                             +    L+ ID   ++ +        +   
Sbjct: 717  AIGA---------------------------IGYNQLQRIDT--LLYLMVYPQQPMVKTK 747

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             I   G   +   +  + AI      D+ D  +   + +       ++F++H     +  
Sbjct: 748  TIELIGYDKLPAGQNAMVAIMSYSGYDIEDALVLNKASLDRGFGRCQVFHKHSAIIRK-Y 806

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
             +   ++I    RD ++ +VI    I         G    SG     K T  +       
Sbjct: 807  PNGTHDRIGDPQRDPENGKVIWKHKILEDDGLAGVGCQVQSGQVYINKQTPTN------- 859

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                    A+ +       ++ +  Y  +    +      I+K+            +VKV
Sbjct: 860  --------ALDNTIALGQPQTTESGYRATPMTYKAPEPAYIDKVML--TNSDADQTLVKV 909

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
                 R  + GDK +                                     SR      
Sbjct: 910  LTRQTRRPELGDKFS-------------------------------------SR------ 926

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
                        G+K    +   + +   + +    + ++       +++      +L  
Sbjct: 927  -----------HGQKGVCGVIIQQEDMPFNDIGICPDIIMNPHGFPSRMTVGKMIELLSG 975

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                  G       F G+  E ++ +L     + SG+ +L  G+TGE  +  +  G IY 
Sbjct: 976  KAGVLRGTLEYGTCFGGSRVEDMSRILVEHGYNYSGKDMLTSGITGEQLEAYIFFGPIYY 1035

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L 
Sbjct: 1036 QKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIAYGASQLLLERLM 1095

Query: 1317 IKSD----DVVGRTRVYESI----VAG--------NDTFETGTPESFNVLVKEMQALGLS 1360
            + SD    DV       E+       G            +   P +  +L +E+ ++ + 
Sbjct: 1096 LSSDAFEVDVC------ENCGLLGYKGWCNSCESSKHVVKMTIPYAAKLLFQELMSMNII 1149

Query: 1361 IDLENSRTK 1369
              L      
Sbjct: 1150 PRLALEDEF 1158



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 113/945 (11%), Positives = 259/945 (27%), Gaps = 204/945 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ +++      N   Q     V P         L+++      P    
Sbjct: 58  LVKQHLDSYNYFVDVDLKKIVEAN---QKITSDVEP------WFYLKYLDIRVGQPVRTD 108

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY   + + +             +  + ++ +++ +G +P+M
Sbjct: 109 LDAIQHSISPHECRLRDLTYGANIFVDIEYT----------RGRQVVRRRNVPIGRMPVM 158

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR-- 171
                                      G FV+KG +++++ Q   S   I  + +  +  
Sbjct: 159 LRSNKCVLYGKSEKELAALNECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVEAEPSKEM 218

Query: 172 --------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALG 222
                           Y                     ++++ +     +P+   L A+G
Sbjct: 219 WQASVTSSTHERKSKTYVVT--------------KNGRLYMKHNSVNEDIPIVIALKAMG 264

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           + S+ EI           Q         +A   +   + + + +                
Sbjct: 265 LQSDREIFELVAGSEANYQDLFAPSVEEAAKLNVYTTEQALNYIG--------------- 309

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGL------YVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
              +K  +  G   L    + L  L      +++   ++     +Y+ A           
Sbjct: 310 -SHVKVNRRAGAARLPPHEEALEVLAAVVLAHISVVNLDFRPKAVYV-AMMARRVLMAMV 367

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
                     +           +         K   D  L+I +V++  + +    A + 
Sbjct: 368 DPSQVDDRDYVGNKRLELAGQLLALLFEDLFKKFNSDLKLNIDKVLKKPNRTQEFDAYNQ 427

Query: 396 FNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
            +       +  +  +     +  R  ++       + +   I+ + ++  + +      
Sbjct: 428 LSMHGDHITQGMVRALSTGNWSLKRFKMERAGVTHVLSRLSFISALGMMTRITSQFEKTR 487

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLL-RMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
            +    + +    G +  +    G    + +++         +   P   +     V  V
Sbjct: 488 KVSGPRSLQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTDEEEGPLIRLAYAFGVEDV 547

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALG---QGGVARARAGVEMRDVHPTHYGRIC 570
                   L+Q    V     I    R  +        + R+        +    + R  
Sbjct: 548 HTVTGREILAQDSYLVYINGSILGITRYPSRFVSCFRRLRRSGRISPFVGIFINEHQRAV 607

Query: 571 PAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
                 G     +  + +            ++       D      V Y+   EE +  I
Sbjct: 608 FISADGGRICRPLIVVENGLPRVTNEHIRKLKNGEMVFEDFLKAGYVEYVDVNEENDSLI 667

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +  D                          ++  P  ++   A +IP+  ++ S
Sbjct: 668 AVYEKDIAPD-----------------------TTHLEIEPFTILGAVAGVIPYPHHNQS 704

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R    C M +QA+                                           I  
Sbjct: 705 PRNTYQCAMGKQAIGA-----------------------------------------IGY 723

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +     +   + +Y               Q+P+VK                     L  
Sbjct: 724 NQLQRIDTLLYLMVYP--------------QQPMVK----------TKTIELIGYDKLPA 759

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G+N +VA M + GY+ ED++++++  +           +   + R    G  +   D   
Sbjct: 760 GQNAMVAIMSYSGYDIEDALVLNKASLDRGFGRCQVFHKHSAIIRKYPNGTHDRIGDPQR 819

Query: 868 VSEE-----GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
             E        K +++ G+  VG +V  G + + K TP      T
Sbjct: 820 DPENGKVIWKHKILEDDGLAGVGCQVQSGQVYINKQTPTNALDNT 864


>gi|6449158|gb|AAF08850.1| RNA polymerase beta subunit [Streptococcus sanguinis SK1]
          Length = 290

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 162/297 (54%), Positives = 213/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L+E G F E +V  R  
Sbjct: 61  NKYGFIQTPYRKVDREAGVVTNEIVWLTADEEDEFIVAQANSKLNEKGGFAEPIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GNNQEFPSDQVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++A+  G V   D  ++ +R  +G LD       +Y++ KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVIAQHDGKVTYADPDKVEVRREDGSLD-------VYQIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTSYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|6449163|gb|AAF08852.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 290

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 164/297 (55%), Positives = 211/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++  RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSDKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV      VTN++V+L+A EE+   +AQANS L E+G F E +V  R  
Sbjct: 61  NKYGFIQTPYRKVDRKAGIVTNEIVWLTADEEDEYIVAQANSKLTENGRFAEAIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+   AP+
Sbjct: 121 GNNQEFPSDQVDFMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPHAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAAI+A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAIIAQHDGKVVYSDAAKVEVRREDGSLD-------VYHITKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTSYNQRTLVKVGDTVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|159485654|ref|XP_001700859.1| hypothetical protein CHLREDRAFT_113199 [Chlamydomonas reinhardtii]
 gi|158281358|gb|EDP07113.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 720

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 70/286 (24%), Positives = 111/286 (38%), Gaps = 52/286 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            ++    L+      ++++        G+ +   + +   R    GDK A RHG KG++S 
Sbjct: 405  KSKSHKLKGEEVAVVDQVGVEGRGLGGLPQQANIRLRFNRNPMIGDKFASRHGQKGVLSI 464

Query: 1103 ILPCEDMPFLK-DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            + P  DMPF    G   D+++NP   PSRM +G + E+ +       G+ + +       
Sbjct: 465  LWPDTDMPFCAATGIRPDLIINPHAFPSRMTIGMLVESLVSKGGALAGQFVDASPFQRAD 524

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
              +                                                         
Sbjct: 525  GVEKGNATERWGAY---------------------------------------------- 538

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L        GQ  +  G+TG+     + +G +Y  +L HMVSDK   RSTG  + +T+Q
Sbjct: 539  -LERQGFSRYGQETMISGVTGQEMPCDIYIGPVYYQRLRHMVSDKFQVRSTGPINAMTRQ 597

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV 1323
            P+ G+   GG R GEME   + A+GAAY+L + L   SD    DV 
Sbjct: 598  PIKGRKFGGGIRFGEMERDSLLAHGAAYLLHDRLHACSDYHVADVC 643


>gi|83415461|gb|ABC17938.1| RNA polymerase II second largest subunit [Spizellomyces punctatus]
          Length = 721

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 125/853 (14%), Positives = 245/853 (28%), Gaps = 153/853 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI-KERISSVDID-SVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++   + +     VD          I    +   +     +
Sbjct: 2    KRLNLAGPLLSGLFRMLFRKLTNDVTRYTRKVVDSRGEFNLTMAIKGGTITRGLQYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RRL+      + R     + R +H TH+
Sbjct: 62   GNWGDQKKFMQARAGVSQVLNRYTYASTLSHLRRLNT----PIGRDGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + V   G    P     +     ++  ++        
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMSYVT-VGHSVAPILDFLNEFNMENLEEITPDRIPKAT 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N          + LV         +         D +P+  +    +        D
Sbjct: 177  KVFVNGQWLGIHDDPDTLVKTLRNLRRNV---------DVTPELSIVRDVADKELRLYTD 227

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
              R+     +  +   L   +   + T  +              R      +    +V  
Sbjct: 228  GGRISRPLFIVEEDQTLSLTKEIALKTKTDPDTQ---------MRQCDWNYLLEEGVVEY 278

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD---EVRRNDIIADGPSTDLG 803
                + +     +D+  L + +   Q     Q   V+  D    +R N + A   +    
Sbjct: 279  LDTEEEETVMIAMDVEDLKRVRLLGQG----QELQVRKDDATARLRSNAVYARNYTHCEI 334

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
              ++   +  + +P+  +N          M  + +   I +  +++              
Sbjct: 335  HPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNYQIRM------------ 380

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             +  +             +       +   +  + AI      +
Sbjct: 381  ---------------DTMANILFYPQKPLATTRAMEFMHFRELPAGQNAVVAIAVYSGYN 425

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    ++ R  +D  ++   +  E  E  +RD             
Sbjct: 426  QEDSLIMSQSSIDRGLF-RSMYYRVYMDTEKKVGMMASETFEKPSRDSCLRLKHGTYEKL 484

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R+           ++     +  +  
Sbjct: 485  DNDGLIAPGVRVGGEDIIIGKTVPIKEDSAEMGQRTAAHTKRDASTPLKSTENGIIDRVM 544

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             + +    +F     +                         Q GDK A RHG KG V   
Sbjct: 545  VTTNEAGFKFVKVRVRSVRV--------------------PQMGDKFAXRHGQKGTVGIT 584

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               ED+PF  +G   D+++NP  +PSRM +G + E  L       G +  +         
Sbjct: 585  YRQEDLPFSAEGISPDLIINPHAIPSRMTIGHLVECLLSKLATLTGVEGDATPFTDLTVD 644

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             IS                                                         
Sbjct: 645  QISRALEQFGY------------------------------------------------- 655

Query: 1224 RMADLD--ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +    +   +G +    G         V  G  Y  +L HMV DK+++R+ G   ++T+Q
Sbjct: 656  QKRGFEVLYNGHT----GR---KLQAQVFFGPTYYQRLKHMVDDKIHSRARGPVQILTRQ 708

Query: 1282 PLGGKSNRGGQRL 1294
            P+ G+S  GG RL
Sbjct: 709  PVEGRSRDGGLRL 721


>gi|148357799|gb|ABQ59235.1| RNA polymerase beta subunit [Bartonella melophagi]
          Length = 289

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 210/289 (72%), Positives = 243/289 (84%), Gaps = 1/289 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           AI AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRSNQ+T
Sbjct: 241 AIGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSNQST 288


>gi|52694233|emb|CAG30646.1| DNA-directed RNA polymerase beta chain [Pseudomonas putida]
          Length = 326

 Score =  269 bits (688), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 160/277 (57%), Positives = 213/277 (76%)

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RL     GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 50  RLCTRPGGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 109

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G V++D+V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E
Sbjct: 110 SPYRVVKEGVVSDDIVFLSAIEEADHVIAQASAAMNDKKQLIDELVAVRHLNEFTVKAPE 169

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 170 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 229

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQR
Sbjct: 230 ARDSGVCVVARRGGVIDSVDASRIVVRVNDDEVETGEAGVDIYNLTKYTRSNQNTCINQR 289

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           PLV  GD+V+R+DI+ADGPSTD+G+LALG+NM +AFM
Sbjct: 290 PLVSKGDKVQRSDIMADGPSTDMGELALGQNMRIAFM 326


>gi|296082132|emb|CBI21137.3| unnamed protein product [Vitis vinifera]
          Length = 1220

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 96/516 (18%), Positives = 160/516 (31%), Gaps = 86/516 (16%)

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              N D    +   +E       +G  T      +      L          +     R  
Sbjct: 765  YANHDHARRVLYQSE-KHSQQAIGFSTTNPNIRVDTLSHQLYYPQRPLFRTMISDLPRPE 823

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
                   +     +     ++   ++    +  +   +           + +        
Sbjct: 824  YFNGQIAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEH---IRSYKSEVDNNESLDKKR 880

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
            ++  S   G  +S +   D + +             + V        V +       E  
Sbjct: 881  KSEDSVHFGKMQSKIGRVDSLDDDGFPFIGANLQNGDIVIGRCAESGVDHSIKLKHTERG 940

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+      D     V     V +   R    GDK +  HG KG++  +   E+ PF 
Sbjct: 941  MVQKVVVSANDDGKNFAV-----VSLRQVRTPCLGDKFSSMHGQKGVLGFLESQENFPFT 995

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
              G   DIV+NP   PSR   GQ+ E     A +G G     L+                
Sbjct: 996  IQGIVPDIVINPHAFPSRQTPGQLLE-----AALGKGIACGGLLRH-------------- 1036

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     +AI   L  A     G
Sbjct: 1037 ----------------------------------ATP-FSTLSVDAIADQLHRAGFSRWG 1061

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
               +Y+G TGE     + +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG 
Sbjct: 1062 HERVYNGRTGEMLRSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQPVSDRKRFGGI 1121

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESI----------VAG--- 1335
            + GEME  C+ A+GAA  L E L   SD     +  R +   ++          V G   
Sbjct: 1122 KFGEMERDCLIAHGAAANLHERLFTLSDSAYMHICRRCKNISNVIQRSVAGGRKVRGPYC 1181

Query: 1336 ------NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                   +  +   P    +L +E+ ++G+S+  E 
Sbjct: 1182 RYCESSEEIVKVNVPYGAKLLCQELFSMGISLKFET 1217



 Score =  135 bits (341), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 139/965 (14%), Positives = 272/965 (28%), Gaps = 237/965 (24%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-----TAFSGA-------AMLEF 76
           LI+ Q  S++ F+            G+Q  F S   I        S         A + F
Sbjct: 99  LIQHQINSFNDFI----------KNGIQRVFDSFGEIPVEPGYDPSKRGEGDWRYASVRF 148

Query: 77  VSYEFDPPK-------------FDVDDCLWRDLTYAVPLKITLRLIVF-----DVDEFTG 118
                + P+             F       +++TY+  +K  +   V+       D++  
Sbjct: 149 GKVTLERPRVWAGESDGKESLNFLPRHARLQNMTYSSRMKAQVHFQVYTQKLVRSDKYKT 208

Query: 119 AKSIKDIKEQSIY-------MGDLPLMTKD------------------GTFVIKGIQRIV 153
            K  K ++++ I+       +G +P+M K                   G F+IKG ++  
Sbjct: 209 GKDNKYVEKKVIFEDNRDILIGRIPVMVKSELCWMNGVERGDCEYDHGGYFLIKGAEKTF 268

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW--------MDIEFDSKD----- 200
           ++Q            K     S            + +W        ++   D  +     
Sbjct: 269 IAQEQ-------ICLKRLWVSSNPTWMVA----YRPIWKRKRVYVKLEPPKDENNRGGEK 317

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
           ++ V       +P+     ALG  S+ E++      I  +   +     +  AD     K
Sbjct: 318 VLTVYFSSTE-IPIWILFFALGASSDKEVVDLIDFNIDDAGISNILVASIHEADREAEKK 376

Query: 260 VSS--------SLVDIDTGEQVIESGKKLTSGLLKSLKEK--GVKFLGITSDCLCGLYVA 309
                      S VD          G+ +   + K L     GVK          G  V 
Sbjct: 377 GMYFRRQGNAISFVDKLVKSCKFPPGESIQECISKYLFPNFSGVKQ----KARFLGYMVK 432

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD--IPILYVDSVNNNAYIRNTLVTDKN 367
             ++   TG    +  D    K LE       R+  + I + +     A  R        
Sbjct: 433 C-LLQAYTGRRKCDNRDDFRNKRLELAGELLERELRVHIRHAERRMVKAMQRELYGDRDL 491

Query: 368 KDRKDAL------LDIYRVMRPGDVSTFSVAESMFNFLFFDSDK---YDLSTVGRVKMNM 418
           +  ++ L        + R    G  S         + +     +     ++   R     
Sbjct: 492 RPIENYLDASIITNGLSRAFSTGQWSHPFKRMERISGVVATLRRTNPLQMTADMRKTRQQ 551

Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                   D R+        +  +        G + ++   G      +  ++   +  G
Sbjct: 552 VQYTGKVGDARYPHPSHWGKVCFLSTPDGENCGLVKNLAITGLVSTEVLDPLVDKLFDCG 611

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           + ++      ++S  +                     F     +   E+ ++ +  +   
Sbjct: 612 MEKLVDDTSTKLSGKNK-------------------VFLDGDWVGVCEDPISFVVELRTK 652

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR   L Q    +         +       + P    E              +V  +   
Sbjct: 653 RRHKELPQQVEIKRDEQQGEVRIFSDAGRILRPLLVVENLK-----------KVKTFKGD 701

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           +  ++ + D      V  + A EEE+   A     L +                    P 
Sbjct: 702 DFTFQSLLD---KGIVELIGAEEEEDCSTAWGIKYLLKGHDD----------------PP 742

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            K    +     ++ ++  +IP+  +D + RVL                           
Sbjct: 743 VKYTHCELDMSFLLGLSCGIIPYANHDHARRVLYQSE----------------------- 779

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             K S  AI         +VD                               +      Q
Sbjct: 780 --KHSQQAIGFSTTNPNIRVD-----------------------------TLSHQLYYPQ 808

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           RPL       R        P    G +A     +VA     GYN EDS++++   +   +
Sbjct: 809 RPL------FRTMISDLPRPEYFNGQIA-----IVAVNVHLGYNQEDSLVMNRASLERGM 857

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGD 892
           F S HI  ++    + +   ++   +              + ++D+ G   +GA +  GD
Sbjct: 858 FRSEHIRSYKSEVDNNESLDKKRKSEDSVHFGKMQSKIGRVDSLDDDGFPFIGANLQNGD 917

Query: 893 ILVGK 897
           I++G+
Sbjct: 918 IVIGR 922


>gi|71663340|ref|XP_818664.1| DNA-directed RNA polymerase III subunit [Trypanosoma cruzi strain CL
            Brener]
 gi|70883928|gb|EAN96813.1| DNA-directed RNA polymerase III subunit, putative [Trypanosoma cruzi]
          Length = 382

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 129/329 (39%), Gaps = 83/329 (25%)

Query: 1055 NKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + +  +  GD      V + +KV     R  + GDK + RHG KG+V  I    +MPF +
Sbjct: 109  DHVVILPPGDSERSMDVEQKIKVITREVRVPEPGDKFSSRHGQKGVVGLITDGVNMPFNE 168

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D++         MN                                         
Sbjct: 169  KGISPDMI---------MN----------------------------------------P 179

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +     K+ +     V  +   +  G       F G + E +   L     +  G+
Sbjct: 180  HGFPSRMTVGKLLELVSSKVSALTGTFGDGT-----AFGGDNAEDLGMHLLRNGFNYHGK 234

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             + Y G+TGE     V  G IY  +L HMV+DK++AR+TG  S++T+QP  G+S  GG R
Sbjct: 235  DVFYSGITGEIMQAYVFFGPIYYQRLKHMVTDKMHARATGPRSMLTRQPTEGRSRSGGLR 294

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR---------------TRVYESIVA 1334
            +GEME  C+  YGA+ +L E L + SD    D   R               T+       
Sbjct: 295  VGEMERDCMVGYGASNLLNERLLLSSDLFTVDTC-RSCGFLGYCGYCPYCNTK------- 346

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             N       P +F +L++E+Q +G+S  L
Sbjct: 347  -NTVSHVNVPYAFKLLLQELQGMGISTRL 374


>gi|322518472|gb|ADX06996.1| RNA polymerase beta subunit [Enterobacter cloacae]
          Length = 267

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 166/267 (62%), Positives = 208/267 (77%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 1   LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 60

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  R+++D+
Sbjct: 61  KVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDY 120

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 121 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 180

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V 
Sbjct: 181 GVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVS 240

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRN 810
           +G+ V R D++ADGPSTDLG+LALG+N
Sbjct: 241 LGEPVERGDVLADGPSTDLGELALGQN 267


>gi|312370727|gb|EFR19060.1| hypothetical protein AND_23137 [Anopheles darlingi]
          Length = 501

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 106/598 (17%), Positives = 184/598 (30%), Gaps = 137/598 (22%)

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            +   +N+L       G   +  + I           + H+ E    A  + L       D
Sbjct: 1    MRPVKNLLANRTELIGTFEQVYLDICITPEETYPELTTHM-ELSKTAFLSNLAQLIPMPD 59

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                     +   + G   +G   +   +       + ++P TP  + +           
Sbjct: 60   CNQSPRNMYQC--QMGKQTMGTPCHNWAMQCTSKFYRLQTPATPLFRPVHY--------D 109

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
                     G +  V  +        D    + S            K++   +L  + ++
Sbjct: 110  NIDLDNYAMGTNAIVAVISYTGYDMEDAMIINKSAYERGFAAGTVYKNEFFALLGNSFFA 169

Query: 985  RLMEILCGQNAVSGPKGFKKSTVL-SSDLISEY--PRSQWWQFAVQDEKVQRNVESLKVQ 1041
            R  +       +       + +VL ++D +  Y       +   VQD+++  N + L + 
Sbjct: 170  RNPKDETLTAFLDNDGLPCQGSVLSTNDPLYSYFDTNDHLYHVQVQDKQLSENGKQLIIT 229

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y                                     + R    GDK A R G KGI S
Sbjct: 230  Y------------------------------------RVPRNPSVGDKFASRAGQKGICS 253

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
            +  P  D+PF + G   DI+ NP G PSRM +  + ET  G      G    +    +  
Sbjct: 254  QKWPAIDLPFTESGMIPDIIFNPHGFPSRMTIAMMIETMAGKTGACHGLVHDATPFRFDE 313

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            N                                                           
Sbjct: 314  NNTAIDY--------------------------------------------------FGR 323

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L  +  +  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG    +T Q
Sbjct: 324  LLETSGYNYYGTERMYSGVDGREMKADIFFGIVHYQRLRHMVSDKWQVRSTGPIDQLTHQ 383

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG---------- 1324
            P  G++  GG R GEME   + ++GA+++LQ+ L   SD V        G          
Sbjct: 384  PNKGRARGGGVRFGEMERDGLISHGASFLLQDRLFHGSDKVMTLICQRCGSLLGPLDSVT 443

Query: 1325 -RTRVYESIVAGNDTFET---------------GTPESFNVLVKEMQALGLSIDLENS 1366
             R     +I +                        P  F  LV ++ ++ +++ L+ S
Sbjct: 444  RRV----AINSNEFQQTPASCRLCQDDCEIGHVEIPYIFKFLVSQLSSVNINVKLQLS 497


>gi|110740195|dbj|BAF01996.1| putative DNA-directed RNA polymerase subunit [Arabidopsis thaliana]
          Length = 578

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 126/344 (36%), Gaps = 80/344 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL-KDGTPVDIVL 1122
            D       +   +     R    GDK + RHG KG+ S++ P  DMPF    G   D+++
Sbjct: 273  DMKSKKHPQRANIRFRHARNPIIGDKFSSRHGQKGVCSQLWPDIDMPFNGVTGMRPDLII 332

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +  + E+         GK + +              R  ++K  G     
Sbjct: 333  NPHAFPSRMTIAMLLESIAAKGGSLHGKFVDATPF-----------RDAVKKTNGEEESK 381

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
              +                               + + SML+    +      LY G  G
Sbjct: 382  SSLL-----------------------------VDDLGSMLKEKGFNHYDTETLYSGYLG 412

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                  + +G +Y  +L HMVSDK   RSTG    +T QP+ G+   GG R GEME   +
Sbjct: 413  VELKCEIFMGPVYYQRLRHMVSDKFQVRSTGQVDQLTHQPIKGRKRGGGIRFGEMERDSL 472

Query: 1303 QAYGAAYVLQEMLTIKSD----DVV----------------------------GRT--RV 1328
             A+GA+Y+L + L   SD    DV                             GRT  +V
Sbjct: 473  LAHGASYLLHDRLHTSSDHHIADVCSLCGSLLTSSVVNVQQKKLIQEIGKLPPGRTPKKV 532

Query: 1329 --YESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTK 1369
              Y      G +T     P  F  L  E+ ++ + + L+ S  +
Sbjct: 533  TCYSCKTSKGMET--VAMPYVFRYLAAELASMNIKMTLQLSDRE 574


>gi|103001984|gb|ABF71530.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 719

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 122/838 (14%), Positives = 242/838 (28%), Gaps = 145/838 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  QRSPNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P    D+  +     N+   ++ +  L+ +               S     AK  G
Sbjct: 237  RVCRPLFVIDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFG 288

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                V     V+  V+ + + +   V     ++  R  Q           +   V+    
Sbjct: 289  WDGLV--NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMN 346

Query: 794  IADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                  T      ++   +  + +P+  +N          M  + +   + +  ++    
Sbjct: 347  PTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM- 403

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 404  --------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 437

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 438  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMR 493

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 494  SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVST 553

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q                             LR VKV +   +  Q GDK
Sbjct: 554  PLRSTENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDK 593

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G
Sbjct: 594  FASRHGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 653

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L    E    +                               
Sbjct: 654  FEGDATPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------- 686

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                 +G +    G         V +G  Y  +L HMV DK+
Sbjct: 687  --------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 717


>gi|322815966|gb|EFZ24456.1| DNA-directed RNA polymerase III subunit, putative [Trypanosoma cruzi]
          Length = 1130

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 129/329 (39%), Gaps = 83/329 (25%)

Query: 1055 NKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + +  +  GD      V + +KV     R  + GDK + RHG KG+V  I    +MPF +
Sbjct: 857  DHVVILPPGDSERSMDVEQKIKVITREVRVPEPGDKFSSRHGQKGVVGLITDGVNMPFNE 916

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D++         MN                                         
Sbjct: 917  KGISPDMI---------MN----------------------------------------P 927

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +     K+ +     V  +   +  G       F G + E +   L     +  G+
Sbjct: 928  HGFPSRMTVGKLLELVSSKVSALTGTFGDGT-----AFGGDNAEDLGMHLLRNGFNYHGK 982

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             + Y G+TGE     V  G IY  +L HMV+DK++AR+TG  S++T+QP  G+S  GG R
Sbjct: 983  DVFYSGITGEIMQAYVFFGPIYYQRLKHMVTDKMHARATGPRSMLTRQPTEGRSRSGGLR 1042

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR---------------TRVYESIVA 1334
            +GEME  C+  YGA+ +L E L + SD    D   R               T+       
Sbjct: 1043 VGEMERDCMVGYGASNLLNERLLLSSDLFTVDTC-RSCGFLGYCGYCPYCNTK------- 1094

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             N       P +F +L++E+Q +G+S  L
Sbjct: 1095 -NTVSHVNVPYAFKLLLQELQGMGISTRL 1122



 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 144/981 (14%), Positives = 271/981 (27%), Gaps = 206/981 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+    AS+DH + + +              KS     +      + + +     P+   
Sbjct: 30  LLNHHIASFDHLINVELKRILLNES--NREIKS-----SIDPDFSIRYTNIRVCQPREIV 82

Query: 86  --------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  RDLTY   + + +     D ++           E  I +G +P+
Sbjct: 83  GKGQLPKVVSPHECRTRDLTYRGDMIVDVEYTSRDRNKRPCT-------ETDIKIGTIPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSP----------GI 163
           M K                         G F+IKG++++ + Q  +S           G 
Sbjct: 136 MLKSSSCNLFGKTREELVAMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADDNGN 195

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK--VPVTSFLMAL 221
              H + +   S   +  C +              K  I V + R  K  +P+   L AL
Sbjct: 196 IVAHVQSKTHYS---ISKCSV-----------TFKKGRI-VMVHRSFKEDIPIVVMLKAL 240

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           GM+S+ +I         +     F CF  +AA  +     +   +     E   E     
Sbjct: 241 GMESDQQIAQHIGTTPAFESVL-FACFEQAAALGVKTQDDALHFIGERRKETSWEVDDA- 298

Query: 281 TSGLLKSLKEKGVKFLG---ITSDCLCGLYVAEDIVNGETGEIYIEAGDVI----DEKSL 333
               ++  K           +      G    +     +   +      +I    D   L
Sbjct: 299 QQRHIQKSKADNAAEFLGNVLLCHIREGQVQRDWNFRHKALYVCFMVRRMIEASVDSSLL 358

Query: 334 EEIFHSEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           +E      +          +L+ D +     +  T +  +   +        + +    +
Sbjct: 359 DERDFYGNKRFETTGTLMGLLFEDLLKQFNRVVKTAMDQQLSKKDTTKPFNVKQLMESKL 418

Query: 387 STFSVAESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                   +  +   ++  ++++S  G  ++  RL+      +            KI   
Sbjct: 419 EVIQSGMRVALSSGRWELKRFNMSRQGITQVLSRLSYIACIGMMTRLASSFEKSRKISGP 478

Query: 446 LR---NGKGTIDDIDNLGNRRVRSVGEM--LKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                +  G +   D         V     L            R+    +   ++DS+  
Sbjct: 479 RSLQPSQWGMVCPCDTPEGESCGLVKNFGILSQVTLDMDDSFVRAAAHNLGVEEVDSISS 538

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           ++ +N   V      F   + +            +   RR   L            +   
Sbjct: 539 REFLNYYTV------FLNGTLIGIHRYPNRLCRGVRALRRSGRLHPHVSIAINDRQKSVQ 592

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           +     GRI        H    V+S            +      + D      V ++   
Sbjct: 593 I-GCDGGRIVRLYIVVNHAKPAVTSAHLD-------QLSAGQCSINDFLAEGLVEFIDVN 644

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E  +  IA     ++                            ++  P  ++ + A +IP
Sbjct: 645 EANDCLIAVYPRDIE-----------------------TYTTHLEVEPLSLLGVVAGIIP 681

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F  ++ S R      M +QA+                                       
Sbjct: 682 FPHHNQSARNTFQSAMGKQALGT------------------------------------- 704

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               I   +     +   V  Y               QRPL +                T
Sbjct: 705 ----IAYNQYIRTDTVLMVGAYP--------------QRPLCR----------TKAMDLT 736

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
               L  G N +V  M + GY+ ED+ + +   +       + + + EV       G  E
Sbjct: 737 HYEKLGAGINAMVCVMSYSGYDIEDAQVYNRCSLDRGYGRCVVLRKHEVDLERLPNGEYE 796

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           I    P+ +    K ++  GI   GA V   DILV K TP       P   + +      
Sbjct: 797 IILP-PDSNAGKCKALNSDGIASKGAIVRQFDILVNKYTPVASLEPRPNPLVYKYPQ--- 852

Query: 921 AVDVRDTSLRVPSGVSGTVVD 941
              V D  + +P G S   +D
Sbjct: 853 -PAVVDHVVILPPGDSERSMD 872


>gi|224812783|gb|ACN65025.1| RpoB [Cronobacter malonaticus]
          Length = 281

 Score =  269 bits (687), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 167/279 (59%), Positives = 213/279 (76%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++
Sbjct: 121 VTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
              VAKR G V+ VDA RIVI+  E ++ P  + +DIY 
Sbjct: 241 VTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEASIDIYN 279


>gi|183579277|gb|ACC63216.1| RpoB [Mycobacterium terrae]
          Length = 211

 Score =  268 bits (686), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 93/225 (41%), Positives = 130/225 (57%), Gaps = 35/225 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 10   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 69

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 70   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWTIEK--------------------- 107

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
              +G      +D   + +       ++    +TPVFDGA E  +  +L            
Sbjct: 108  -DSGGSVPDWADKLPEELHSAGPDTRT----ATPVFDGAQESELQGLLSSTLANRDGEVM 162

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            ++  G+++L+DG +GEPF  PVTVGY Y++KL+H+V DK++ARST
Sbjct: 163  VNGDGKAMLFDGRSGEPFPYPVTVGYXYIMKLHHLVDDKIHARST 207


>gi|103001521|gb|ABF71511.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 692

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 114/813 (14%), Positives = 234/813 (28%), Gaps = 145/813 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L   +R+   ++ + + +  +    +         + +  + + +     +        
Sbjct: 1    LLAXLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKST 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   ++ +  L+ +               S     AK  G    V     V+  V+
Sbjct: 237  NCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--NNGVVEYVD 286

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q           +   V+          T      ++ 
Sbjct: 287  AEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSMI 346

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N          M  + +   + +  ++                    
Sbjct: 347  LGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----------------- 387

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 388  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 437

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 438  IMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDD 493

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 494  DGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL- 552

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 553  -------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 593

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF K+G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 594  QEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------ 641

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 642  -----------------------------------------ATP-FTEVTVDSVSKLLRE 659

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                  G  ++Y+G TG      V +G  Y  +
Sbjct: 660  HGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 692


>gi|108885359|gb|ABG23196.1| DNA-directed RNA polymerase [Geobacillus kaustophilus]
          Length = 145

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 65/167 (38%), Positives = 100/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KE  ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKELDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAW 145


>gi|330946830|ref|XP_003306806.1| hypothetical protein PTT_20049 [Pyrenophora teres f. teres 0-1]
 gi|311315505|gb|EFQ85085.1| hypothetical protein PTT_20049 [Pyrenophora teres f. teres 0-1]
          Length = 484

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 115/300 (38%), Gaps = 53/300 (17%)

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W   +          +  + Q+   K   E  F +++  I   D   P   + + + + +
Sbjct: 140  WHTVSYDTAMDDYTNKDGQTQFFKYKED-EVAFIDQVRLIGSEDGTQP--CQKLSIKLRI 196

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+VS+     DMPF + G   D+++NP   PSRM +G   E+ 
Sbjct: 197  PRSPIVGDKFSSRHGQKGVVSQKFSVADMPFSETGIQPDVIINPHAFPSRMTIGMFIESL 256

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G +    G    S    +                                         
Sbjct: 257  AGKSGALHGMAQDSTPFQFDEQNTA----------------------------------- 281

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     L  A  +  G   +Y G TGE     + +G +Y  +L 
Sbjct: 282  ---------------VDHFGQQLMKAGYNYYGNEPMYSGFTGEELHADIYIGVVYYQRLR 326

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HM++DK   R+TG  +  T QP+ G+   GG R+GEME   + A+G A++LQ+ +   SD
Sbjct: 327  HMINDKFQVRTTGPVNPTTGQPVKGRKKGGGIRVGEMERDALIAHGTAFLLQDRMMNCSD 386


>gi|51035517|emb|CAH10894.1| RNA polymerase B subunit [Halobaculum gomorrense]
          Length = 435

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 84/253 (33%), Positives = 115/253 (45%), Gaps = 54/253 (21%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF +DG   D+VLNP  +
Sbjct: 197  EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEDGLVPDLVLNPHAL 256

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V        G     LG K+ SL                                
Sbjct: 257  PSRMTV--------GHVLEMLGGKVGSLEGRRVDGT------------------------ 284

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   F G +EE + S L       SG+ ++Y G+TGE  + 
Sbjct: 285  ----------------------AFQGENEEELRSSLEEHGYKSSGKEVMYSGVTGEKIEA 322

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + VG I+  KL HMVS+K++ARS G   ++T+QP  G++  GG R+GEME   +  +GA
Sbjct: 323  EIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGA 382

Query: 1308 AYVLQEMLTIKSD 1320
            A  L+E L   SD
Sbjct: 383  AMALKERLLDSSD 395



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 73/209 (34%), Gaps = 21/209 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q  +VK                    +    +N +VA M + G+N ED
Sbjct: 26  RPDTRQHLLHYPQLSMVK----------TQTTEQIGFDERPAAQNFVVAVMSYEGFNIED 75

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECG 880
           ++++++  V   +  S     +E   R    G E+              E+   ++DE G
Sbjct: 76  ALVMNKGSVDRAMQRSHFFRTYEGEERRYPGGQEDRFEVPSQDVRGARGEDAYTHLDEDG 135

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++    +V+   +L+GK +P               + G      R+TS+ + SG SG V 
Sbjct: 136 LVNPETKVDENSVLLGKTSPPRFLEEP------DDMGGLSPQKRRETSVTMXSGESGVVD 189

Query: 941 DVRIFNRHGIDKNERSISVEREQIELLAR 969
            V +       K  +    +    EL  +
Sbjct: 190 TVTLMEGEDGSKLSKVSVRDERIPELGDK 218


>gi|171187549|gb|ACB41378.1| RpoB [Bartonella sp. 1-1C]
          Length = 286

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 207/287 (72%), Positives = 239/287 (83%), Gaps = 1/287 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID
Sbjct: 121 RKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHID 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KFQR
Sbjct: 241 SGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKFQR 286


>gi|269930883|gb|ACZ54176.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 285

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 206/286 (72%), Positives = 240/286 (83%), Gaps = 1/286 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 285


>gi|269912594|emb|CAY86077.1| RNA polymerase beta subunit [Gluconacetobacter nataicola]
          Length = 301

 Score =  268 bits (686), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 123/275 (44%), Positives = 165/275 (60%), Gaps = 28/275 (10%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GMD +EILS FY K+ +++    W   
Sbjct: 61  VTTLLYALEGAASEAARAAKAAEGGDVESMEIQGMDPDEILSYFYGKVEFTKTEKGWARR 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
             A     G K+   L+D  TGE+V  +  KLT+ +++ + E   K + +    L G ++
Sbjct: 121 FDAE-AFRGQKLLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGLIGRFI 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A DIVN  TGEIY EAGD + E+ LEE+    +  +  L VD+ N   +IRNTL  DKN 
Sbjct: 179 ASDIVNEHTGEIYAEAGDELTEQKLEELESEGLTTLTTLAVDAAN-GPWIRNTLAVDKNA 237

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            R++AL DIYRVMRPG+  T   AE+MF+ LFFD 
Sbjct: 238 SREEALTDIYRVMRPGEPPTPETAEAMFSGLFFDP 272


>gi|83415453|gb|ABC17934.1| RNA polymerase II second largest subunit precursor [Batrachochytrium
            dendrobatidis]
          Length = 1202

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 114/732 (15%), Positives = 203/732 (27%), Gaps = 131/732 (17%)

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             +     CPAET EG   GLV +L+    +   G    P  +  +      +  +S    
Sbjct: 602  NSIVSHNCPAETPEGQACGLVKNLSLMGYIT-VGSPAPPILEFLEEWTMESLEEISPSTI 660

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                    N          ++LV         +         D SP+  V          
Sbjct: 661  PTATKIFLNGQWVGIHRDPDQLVSTLRRLRRSV---------DVSPEVSVVRDVRDRELR 711

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
               D+ R+     +      L+  +        + +  K   +       G+VE +D   
Sbjct: 712  LCTDAGRIARSLFVVTPEQSLVLTKEMVQQLHEDQIQWKDLLS------YGVVEYIDTEE 765

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D              +R    T   +   V   +           PS  L
Sbjct: 766  EETVMICMTPDDLAEARMAAAGQVVERHQVGTGRLKSATVYTRNY----THCEIHPSMIL 821

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N     +    M  + +                        
Sbjct: 822  G-------ICASIIPFPDHNQSPRSVYQSAMGKQAMG----------------------- 851

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                 ++   L+      +  +             +       +      + AI      
Sbjct: 852  ---LFLTNFQLRM---DTMSNILFYPQKPLATTRAMEFMHFRDLPAGINAVVAIACYSGY 905

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D+ ++   +  E +E  +RD            
Sbjct: 906  NQEDSLIMNQSSIDRGLF-RSLYYRVYMDQEKKVGMISTETLEKPSRDTTLRLKHGTYEK 964

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +++D      R+           ++     +  Q 
Sbjct: 965  LEDDGLIAPGVRVSGEDIIIGKTVPIAADSTELGQRTTMHTKRDASTPLKSTENGIVDQV 1024

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R    GDK A RHG KG V  
Sbjct: 1025 LI--------------------TTNQDGFKFVKVRVRSIRIPHMGDKFASRHGQKGTVGI 1064

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  DG   D+++NP  +PSRM +G + E  L       G +  +        
Sbjct: 1065 TYRTEDMPFTADGITPDLIINPHAIPSRMTIGHLVECLLSKVSTFTGDEGDATPFTDVTV 1124

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              IS       +  G      ++                                     
Sbjct: 1125 EAISQAL----QGYGYQRRGFEVL------------------------------------ 1144

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
                    +G +    G      +  V  G  Y  +L HMV DK+++R+ G   ++T+QP
Sbjct: 1145 -------YNGHT----GR---KLNAQVYTGPTYYQRLKHMVDDKIHSRARGPLQILTRQP 1190

Query: 1283 LGGKSNRGGQRL 1294
            + G+S  GG R 
Sbjct: 1191 VEGRSRDGGLRF 1202



 Score = 74.3 bits (181), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 60/479 (12%), Positives = 126/479 (26%), Gaps = 47/479 (9%)

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
                   +E+          +L+       A      +   N            ++   
Sbjct: 493 WIKGSLFFIEQHRSKCQHAFELLHTGLGTKAAVSAEINMPHHNPSH---------MLNVK 543

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
           ++ T    E  +       D+Y      R       +++     R     D   + +   
Sbjct: 544 EIPTAPADE--YITWIEFKDRYVHKESPRFVWVTIHSIEEAPAER---LYDFNTVSQNHS 598

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
              N   + +        +      ++KN   +G + +       +  ++  ++   + I
Sbjct: 599 FFANSIVSHNCPAETPEGQACG---LVKNLSLMGYITVGSPAPPILEFLEEWTMESLEEI 655

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +   + +A   F     +    +    +S +   RR   +             +RDV   
Sbjct: 656 SPSTIPTATKIFLNGQWVGIHRDPDQLVSTLRRLRRSVDVSP-------EVSVVRDVRDR 708

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                  A         +    +          +     +  D      V Y+   EEE 
Sbjct: 709 ELRLCTDAGRIARSLFVVTPEQSLVLTKEMVQQLHEDQIQWKDLLSYGVVEYIDTEEEET 768

Query: 625 RYIAQANSSLDEDGSFTEELVFCRC-----AGEEILVPREKIDFIDASPKQVVSIAASLI 679
             I      L E        V  R        +   V        +  P  ++ I AS+I
Sbjct: 769 VMICMTPDDLAEARMAAAGQVVERHQVGTGRLKSATVYTRNYTHCEIHPSMILGICASII 828

Query: 680 PFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKS 722
           PF +++ S R +    M +QA+                 L   + P   T  ME +  + 
Sbjct: 829 PFPDHNQSPRSVYQSAMGKQAMGLFLTNFQLRMDTMSNILFYPQKPLATTRAMEFMHFRD 888

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
             A I A    I       +     +            +Y  +   +  +   ++   L
Sbjct: 889 LPAGINA-VVAIACYSGYNQEDSLIMNQSSIDRGLFRSLYYRVYMDQEKKVGMISTETL 946



 Score = 48.5 bits (114), Expect = 0.008,   Method: Composition-based stats.
 Identities = 20/130 (15%), Positives = 48/130 (36%), Gaps = 19/130 (14%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G +L   +R+   ++ + +    +I+            + +  + +       +
Sbjct: 2   KRLDLAGPLLGGLFRMLFRKLTKDVSRYLQITMESGREFNLSLAVKSSTITNGPKYSLAT 61

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RRL+      + R     + R +H TH+
Sbjct: 62  GNWGDQKKFMQARAGVSQVLNRYTFASTLSHLRRLNT----PIGRDGKLAKPRQLHNTHW 117

Query: 567 GRICPAETSE 576
           G +C +  +E
Sbjct: 118 GMVCLSGDTE 127


>gi|321468089|gb|EFX79076.1| hypothetical protein DAPPUDRAFT_305037 [Daphnia pulex]
          Length = 1134

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 151/1014 (14%), Positives = 299/1014 (29%), Gaps = 197/1014 (19%)

Query: 390  SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK--EDIIAIIKILVDLR 447
             +   +    FF   K   +   R  +   +    P +  + +     +  +I+ ++   
Sbjct: 285  HLGNKLRQKRFFGGPKKTATEEARETLATTILAHVPVENFNFKAKAMYLALMIRRVIQAE 344

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DL 503
            N   ++DD D  GN+R+   G +L   +     RM   +K+            Q      
Sbjct: 345  NDPTSVDDRDYYGNKRLELAGSLLSLLFEDLFKRMNFELKQIADKNIPKIKAAQFDVIKH 404

Query: 504  INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAG 555
            I    + + +     +   +     ++         RLS +   G+         + R  
Sbjct: 405  IRTDHITNGLENAISTGNWTIKRFRMDRQGVTQMLCRLSYISGLGMMTRVNSQFEKTRKV 464

Query: 556  VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
               R + P+ +G +CP++T EG   GLV +L     +      E   R   +  V  D+ 
Sbjct: 465  SGPRSLQPSQWGMLCPSDTPEGEGCGLVKNLALMTHITTEAEEEPISRIAQNMGV-EDIN 523

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
              S  E  +  I     + +  G   + L   R              F  A     ++  
Sbjct: 524  LFSGEEISDPSIYTVFLNGNILGLVKDYLRLIRY-------------FKLARRHGFINAF 570

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
             S+ P  +         G  + R  + + K +A    T         S            
Sbjct: 571  VSIYPHFQTRSVYISSDGGRLCRPYIIVRKGKAAL--TDKHMQELADS----------FR 618

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
               D I   +       + + S + +Y                       D       + 
Sbjct: 619  TFEDFIHDGLIEYLDVNEENDSNIAVYES---------------------DINEETTHLE 657

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              P T LG       +    +P+  +N       S R   +       +       R+  
Sbjct: 658  IEPFTLLG-------VCAGLIPYPHHNQ------SPRNTYQCAMGKQAMGTIACNQRNRI 704

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     ++      +   +    I       +   +  + A
Sbjct: 705  -----------------------DTLLYNLVYPHKPMVKTRTIELINFENLPAGQNAMVA 741

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            +      D+ D ++   + +        ++        +R  +   +++     D   ++
Sbjct: 742  VMSYSGFDIEDATVLNKASLDRGYGRCLVYKNAKCAL-KRYNNQSSDRVNGPILDAASKK 800

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             I   +I         GQ          K+           P +     A          
Sbjct: 801  PIWKHDILDADGFAAVGQPVEPKQVLINKA----------MPTAPVVTVAPGAPAAVPLP 850

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            E     Y       +    + +EK+ +  +       ++K+ +   R  + GDK +    
Sbjct: 851  E-----YRDVPIAYKGAIPSYVEKVMFSSNAEEA--HIIKIQLRQTRRPEIGDKFS---- 899

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
                                             SR                  G+K  + 
Sbjct: 900  ---------------------------------SR-----------------HGQKGVTA 909

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
            +   + +   + L    + ++       +++      +L        G       F G+ 
Sbjct: 910  LVAEQEDLPFTELGICPDVIMNPHGFPSRMTVGKLIELLAGKAGLLEGKFHYGTAFGGSK 969

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
             + ++  L     +  G+  +  G TGE     +  G +Y  KL HMV DK++ARS G  
Sbjct: 970  VQDVSEELIKHGYNYQGKECMTSGTTGEQLSAYIYFGPVYYQKLKHMVMDKMHARSRGPR 1029

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--DVVGRTRVYESIV 1333
            +++T+QP  G++  GG RLGEME  C+ AYG++ ++ E L I SD  DV          V
Sbjct: 1030 AVLTRQPTEGRAREGGLRLGEMERDCLIAYGSSMLILERLMISSDAFDVD---------V 1080

Query: 1334 AGN-----------------DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                                       P +  +L +E+QA+ ++  L+  +  +
Sbjct: 1081 CNQCGLMGYFGWCHYCKSSASVSSIRIPYACKLLFQELQAMNIAPRLKLDKYFD 1134



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 111/992 (11%), Positives = 273/992 (27%), Gaps = 198/992 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY++F+ ++I    + NE           ++       ++++      P    
Sbjct: 38  LVKQHIDSYNYFINVDIKKIVKANE---KV------VSHSDQTFYIKYLDIHVGKPDSIE 88

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I    I +G +P+M
Sbjct: 89  DMNHSRLTTPHECRLRDMTYSAPVTVDIEYT----------RGQQRIVRNGIPIGRMPIM 138

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            +                         G F+++G +++++ Q   S       ++     
Sbjct: 139 LRSSNCTLAGISPAEMAKKNECPYDCGGYFIVRGNEKVILIQEQMS------KNRMIVEQ 192

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMALGM- 223
             K   +C++             +K   +V +++ +           +PV     A+G+ 
Sbjct: 193 DRKGNMSCQVTSS-------THGTKTRTNVVVNKGKYYLKQNSFQDDIPVAIVFKAMGIV 245

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +EI+                      A +    +    L +    ++     KK  + 
Sbjct: 246 SDQEIVQMIGTDDRVMTSFAPSLEECVRASIFTQQQALGHLGNKLRQKRFFGGPKKTATE 305

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL---EEIFHSE 340
             +      +    +  +       A  +       I  E      +       +     
Sbjct: 306 EARETLATTILAH-VPVENFNFKAKAMYLALMIRRVIQAENDPTSVDDRDYYGNKRLELA 364

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
              + +L+ D      +    +        K A  D+ + +R   ++             
Sbjct: 365 GSLLSLLFEDLFKRMNFELKQIADKNIPKIKAAQFDVIKHIRTDHITNGLENAISTGNWT 424

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
               + D   V ++   +          R   + +    +     L+  +  +    +  
Sbjct: 425 IKRFRMDRQGVTQMLCRLSYISGLGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTP 484

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +     E  I     ++ ++ +            S    F   +
Sbjct: 485 EGEGCGLVKNLALMTHITTEAEEEPISRIAQNMGVEDINLFSGEEISDP-SIYTVFLNGN 543

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC--PAETSEGH 578
            L  +++++  +      RR   +                +  +  GR+C       +G 
Sbjct: 544 ILGLVKDYLRLIRYFKLARRHGFINAFVSIYPHFQTRSVYI-SSDGGRLCRPYIIVRKGK 602

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
                  +   A           +R   D      + YL   EE +  IA   S ++   
Sbjct: 603 AALTDKHMQELA---------DSFRTFEDFIHDGLIEYLDVNEENDSNIAVYESDIN--- 650

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                               E+   ++  P  ++ + A LIP+  ++ S R    C M +
Sbjct: 651 --------------------EETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 690

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+                                           I   + +   +   
Sbjct: 691 QAMGT-----------------------------------------IACNQRNRIDTLLY 709

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             +Y                +P+VK                 +  +L  G+N +VA M +
Sbjct: 710 NLVYP--------------HKPMVK----------TRTIELINFENLPAGQNAMVAVMSY 745

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP-----NVSEEGL 873
            G++ ED+ ++++  +       +  +  +   +       +                  
Sbjct: 746 SGFDIEDATVLNKASLDRGYGRCLVYKNAKCALKRYNNQSSDRVNGPILDAASKKPIWKH 805

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPK----------GESPMTPEEKLLRAIFGEKAVD 923
             +D  G   VG  V P  +L+ K  P             +   PE + +   +      
Sbjct: 806 DILDADGFAAVGQPVEPKQVLINKAMPTAPVVTVAPGAPAAVPLPEYRDVPIAYKGAIPS 865

Query: 924 VRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNE 954
             +  +   +     ++ +++   R     ++
Sbjct: 866 YVEKVMFSSNAEEAHIIKIQLRQTRRPEIGDK 897


>gi|227937624|gb|ACP43387.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 288

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 210/289 (72%), Positives = 244/289 (84%), Gaps = 1/289 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS+Q+T
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRSSQST 288


>gi|294876076|ref|XP_002767539.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative
            [Perkinsus marinus ATCC 50983]
 gi|239869199|gb|EER00257.1| DNA-directed RNA polymerase II 135 kDa polypeptide, putative
            [Perkinsus marinus ATCC 50983]
          Length = 1255

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 78/341 (22%), Positives = 124/341 (36%), Gaps = 34/341 (9%)

Query: 984  SRLMEILCGQNAVSGPKGFKK----STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            SRL +     ++V G K  K             + E             E      +  +
Sbjct: 863  SRLAQFRADNHSVKGEKVVKDLDYDGIPYIGQQVHEGDPICRVLNKGTGEAKLEKYKEGE 922

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V +    +++                        + + + + R    GDK + RHG KG+
Sbjct: 923  VAWVEQVNMIGGGGWWGGGAGARNPGGIKDGSERMSIKLRLPRNPVVGDKFSSRHGQKGV 982

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P  DMPF   G   DI+ NP G+PSRM +G + E   G A    G  +       
Sbjct: 983  MAILWPQADMPFSTSGISPDIMFNPHGMPSRMTIGMLIEFMAGKAAALTGMPV------- 1035

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                           V        +     D       + +  G   +         E  
Sbjct: 1036 ---------------VNANSFRQYRGKGLLDTEHNNEKDPYAPGDTTA--------HEYF 1072

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L+    +  G   LY G+ GEP    + +G +Y  +L HMV DK   R+TG    +T
Sbjct: 1073 GETLKKFGYEYLGAEELYSGMHGEPLKTHIYMGVVYYQRLRHMVLDKFQVRATGPIDPLT 1132

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +QP+ G+   GG R GEME   + ++G + +L + L   SD
Sbjct: 1133 RQPVKGRKKHGGVRFGEMERDSLISHGTSALLADRLLKCSD 1173



 Score = 69.3 bits (168), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 68/404 (16%), Positives = 139/404 (34%), Gaps = 33/404 (8%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++  + + + +N+   ++H R   A+ +G   +      +R + P  +G +CP  T +G 
Sbjct: 506 TTGFTVVADKLNAYRYLSHFR---AVHRGSFFQEMKTTSVRKLLPETWGFLCPVHTPDGT 562

Query: 579 NIGLVSSLTSFAR-VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI-AQANSSLDE 636
             GL++ L +  + V      E     + +   +  V  + + +       A  N+ +  
Sbjct: 563 PCGLLNHLAAPCQPVVRIASPEGVIPGLEEELASLGVQLVRSSKTSTANYGAGENAYVTL 622

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG-CN 695
           DG    ++   R       + R KID     P     +         + +   +  G C 
Sbjct: 623 DGRVLGKVARSRLEAVAEELRRLKIDKD--CPGVPADLEIVACQTPASFEGLWLFTGPCR 680

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGA---------------AIVAKRAGIVEQVDA 740
           M R    L       VG  ME V  K +                  I  K   I     +
Sbjct: 681 MVRPVRDLATGNEELVGP-MEQVFLKIAATREDLEASTKTSSVPENIPMKYTHIELSPIS 739

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDEVRRNDIIADG- 797
           +  VI  +    + + S  ++Y+    +++     +N   R   KV         +    
Sbjct: 740 MLSVIAGLTPFSNHNQSPRNMYQCQMLKQTMAIPYLNHPYRTDNKVYKITYPQFPMVRTT 799

Query: 798 --PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                +      G N +VA +   G++ ED+++IS+             +   +      
Sbjct: 800 VLSEANFDVKPAGTNAIVAVIAHSGFDMEDALIISKGSYDRGFKHGSVYKTKVINCPPKG 859

Query: 856 LG----PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                  +    +     E+ +K++D  GI  +G +V+ GD + 
Sbjct: 860 TVGSRLAQFRADNHSVKGEKVVKDLDYDGIPYIGQQVHEGDPIC 903



 Score = 50.8 bits (120), Expect = 0.001,   Method: Composition-based stats.
 Identities = 118/766 (15%), Positives = 239/766 (31%), Gaps = 118/766 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNE-GLQAAFKSVFP--ITAFSGA--------AMLE--F 76
           ++    S++ F++  + P+      GL      + P  +T   G           L    
Sbjct: 47  VKPHVDSFNLFVITGLTPEATNEILGL--LPDDISPAEMTWHDGTTVRCWLSDLSLHQPI 104

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
              +   P+     C    +TY+  L  T+     +V   TG   ++  +   + +G +P
Sbjct: 105 RGEDVLDPRLLPTHCRQAHITYSGELSATV-----NVSLGTGEPPVQMAR---VPLGLVP 156

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M +                         G F++ G ++++  +L   P  +F     R 
Sbjct: 157 IMVRSEACHLHGMPPSKMVQCGEDPDERGGYFIVNGNEKVI--RLLIMPKSNFPVALYRP 214

Query: 173 SLSGK-LLYACRIIPDQGLWMDIEFDS------KD-IIHVRIDRRRK---VPVTSFLMAL 221
           S S +  LY+   +  + +  D+   +      KD    VR    +    +P+   L  L
Sbjct: 215 SFSNRGPLYSAYAVQMRSMRPDLTTQTVTMHYRKDGTCWVRFTYLKNEYLIPLMLLLKCL 274

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL----MVGAKVSSSLVDIDTGEQVIESG 277
              + + L++   + ++    D        A+     +   +    L  + + E  +   
Sbjct: 275 ---APDELNS--ERSLFELLCDGLMADTFVAERVTCMLEQMRTHPELKHVHSREDALYYL 329

Query: 278 KKLTSGLLKSLKEKGV------------------KFLGITSDCLCGLYVAEDIVNGETGE 319
                 + +  +  GV                  K + +    L  L +       E G+
Sbjct: 330 GSKFEVVFREKRGAGVSLDGIALEVDDAAMSPVEKSVSVARRLLDSLMLVHCPKGAEGGK 389

Query: 320 IYIEAGDVIDEKSLEEIF------HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD- 372
             ++   +I  K +  +       +++  D+  L +      A ++  L +   +     
Sbjct: 390 AKVDCLVLIFRKLMALVRGDIAPDNADAMDVQELLLPGQLFGALLKEVLQSSLLRLEGAL 449

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFF--DSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           A       +  G   T   AE + N      D  K   S +    +  R  LD       
Sbjct: 450 AKKSRQAQVGKGRAPTVLSAELIRNTFMGVCDVTKRMESFLATGNITSRSGLDLQQTTGF 509

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKER 489
               D +   + L   R     +         +  SV ++L   +  L  +         
Sbjct: 510 TVVADKLNAYRYLSHFR----AVHRGSFFQEMKTTSVRKLLPETWGFLCPVHTPDGTPCG 565

Query: 490 ISSVDIDSVMPQDLI-NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ-- 546
           + +       P   I + + V+  + E   S  +  +     S +               
Sbjct: 566 LLNHLAAPCQPVVRIASPEGVIPGLEEELASLGVQLVRSSKTSTANYGAGENAYVTLDGR 625

Query: 547 --GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
             G VAR+R      ++      + CP        I    +  SF  +  +       R 
Sbjct: 626 VLGKVARSRLEAVAEELRRLKIDKDCP-GVPADLEIVACQTPASFEGLWLFTGPCRMVRP 684

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V D    N+   +  ME+    IA     L+     +          E I +    I+  
Sbjct: 685 VRDLATGNE-ELVGPMEQVFLKIAATREDLEASTKTSS-------VPENIPMKYTHIEL- 735

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             SP  ++S+ A L PF  ++ S R +  C M +Q + +     P+
Sbjct: 736 --SPISMLSVIAGLTPFSNHNQSPRNMYQCQMLKQTMAIPYLNHPY 779


>gi|6449153|gb|AAF08848.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 290

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 162/297 (54%), Positives = 214/297 (72%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +++ RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSYKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  
Sbjct: 61  NKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEYTVAQANSRLNEDGTFAEKIVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P   +D++D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GVNQEYPANIVDYMDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLINPQAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|110669610|gb|ABG81900.1| RNA polymerase II second largest subunit [Hypocenomyce scalaris]
          Length = 708

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 123/828 (14%), Positives = 238/828 (28%), Gaps = 143/828 (17%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+ S G +L   +R+   ++ R + + +     +         + +    + +     + 
Sbjct: 1    RLDSCGPLLAGLFRMLFNKLARDVAKYLEKCVENNREFNLTLGVKSTTPTNGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     +      E    +    + +V  +     +      
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQRSPNATKV 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLE 683
            ++      +  D +     V        I      + D  D   K          P F+ 
Sbjct: 177  FVNGVWVGVHRDPAHLVSTVQNLRRNHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVI 236

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            N+D      G  +  +       +   +G  M++           AK  G    V   + 
Sbjct: 237  NNDPKSPNKGNLVLTKEHVNRLEDDKELGADMDAEEKA-------AKFMGWEGLV--NQG 287

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+  V+ + + +   V     ++  R  Q   V Q         V+          T   
Sbjct: 288  VVEYVDAEEEETVMIVMTPEDLEISRQLQAGYVIQESTDDPNKRVKAPMNPTAHTWTHCE 347

Query: 804  -DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
               ++   +  + +P+  +N          M  + +   + +  +E              
Sbjct: 348  IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM----------- 394

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 395  ----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGY 438

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    
Sbjct: 439  NQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGT 494

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L +   +  G           K+  ++ D      R++          ++     + 
Sbjct: 495  YDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTESGIV 554

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                             LR VKV +   +  Q GDK A RHG KG 
Sbjct: 555  DQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGT 594

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +     
Sbjct: 595  IGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTE 654

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 +S L    E    +                                         
Sbjct: 655  VTVDSVSRLLR--EHGYQSRGFEVM----------------------------------- 677

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                       +G +    G         V +G  Y  +L HMV DK+
Sbjct: 678  ----------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 708


>gi|57337358|emb|CAH69687.1| RNA polymerase, beta subunit [Enterobacter cloacae]
          Length = 265

 Score =  268 bits (685), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 163/264 (61%), Positives = 204/264 (77%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF
Sbjct: 1   KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGF 60

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L  
Sbjct: 61  LETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFS 120

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME 
Sbjct: 121 RDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMER 180

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+N
Sbjct: 181 AVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCIN 240

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD 801
           Q P V +G+ V R D++ADGPSTD
Sbjct: 241 QMPCVSLGEPVERGDVLADGPSTD 264


>gi|269930813|gb|ACZ54141.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 285

 Score =  268 bits (685), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 206/286 (72%), Positives = 241/286 (84%), Gaps = 1/286 (0%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           ESVVA+ SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 ESVVARDSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 285


>gi|224141967|ref|XP_002324332.1| predicted protein [Populus trichocarpa]
 gi|222865766|gb|EEF02897.1| predicted protein [Populus trichocarpa]
          Length = 1160

 Score =  268 bits (684), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 97/501 (19%), Positives = 159/501 (31%), Gaps = 84/501 (16%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNR 947
                  +G  T      +      L          +    L +P        +  +  N 
Sbjct: 717  KHSQQAIGFSTTNPNIRVDTLSHQLHYPQRPLFRTMISDCLVLPKPELFNGQNAIVAVNV 776

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
            H     E S+ + R  +E     + +        + ++ +     ++  S   G  +S +
Sbjct: 777  HLGYNQEDSLVMNRASLER-GMFRSEHIRSYKAEVDNKELTDKRRKSEDSITFGKIQSKI 835

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
               D + +             + V          +       E     K+          
Sbjct: 836  GRVDSLDDDGFPFIGANMQSGDIVIGKCAESGADHSVKLKHTERGMVQKV----VLSSND 891

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
             G    V V +   R    GDK +  HG KG++  +   E+ PF   G   DIV+NP   
Sbjct: 892  EGKNFAV-VSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGVVPDIVINPHAF 950

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSR   GQ+ E  LG      G K                                    
Sbjct: 951  PSRQTPGQLLEAALGKGIACGGSK------------------------------------ 974

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                               +TP F     + I   L  A     G   +Y+G TGE    
Sbjct: 975  -----------------RYATP-FSTLSVDDIIDQLHRAKFSRWGNERVYNGRTGEMVRS 1016

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             + +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+ A+GA
Sbjct: 1017 LIFMGPTFYQRLVHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGA 1076

Query: 1308 AYVLQEMLTIKSD----DVVGRTR-VYESIVAG------------------NDTFETGTP 1344
            +  L E L   SD     +  + + V   I  G                  +D  +   P
Sbjct: 1077 SANLHERLFTLSDSSEMHICQKCKNVANVIQRGVPGGRKIRGPYCRVCESVDDLVKVSVP 1136

Query: 1345 ESFNVLVKEMQALGLSIDLEN 1365
                +L +E+ ++G+S+  + 
Sbjct: 1137 YGAKLLCQELFSMGISLKFDT 1157



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 132/951 (13%), Positives = 253/951 (26%), Gaps = 210/951 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSG-------AAMLEF 76
           LI  Q  SY+ F+          N GLQ  F S     V P    S         A + F
Sbjct: 40  LISHQINSYNSFI----------NSGLQRVFDSFGEVAVEPGYDSSKQKDGEWRRASVRF 89

Query: 77  VSYEFDPPKFD------------VDDCLWRDLTYAVPLK--ITLRLIVFDVDEFTGAKSI 122
                D P F                   +++TY+  +K  + +++    V      K+ 
Sbjct: 90  GKVTLDRPSFWGGTSSDAEHNMFPRHARLQNMTYSARMKIHVNVQVYTQTVGRSDKFKTG 149

Query: 123 KDIKEQ---------SIYMGDLPLMTKD------------------GTFVIKGIQRIVVS 155
            D   Q          I +G +P+M K                   G F+IKG +++ ++
Sbjct: 150 IDKVVQKNVVHTENREIIIGRIPVMVKSDLCWLTTVEKGDCDFDHGGYFLIKGAEKVFIA 209

Query: 156 QLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ-------GLWMDIEFDSKDIIHVRIDR 208
           Q      I         S    + Y   +  ++          ++     K  + V    
Sbjct: 210 QEQ----ICMKRLWISNSQGWTVSYKSEVKRNRLIVRLVELSKLEYIKGEKKGLCVYFLS 265

Query: 209 RRKVPVTSFLMALGMDSE-EILSTF-YPKIVYSQRGDFWCFPLSAADL---MVGAKVSSS 263
              +P+     ALG+ S+ E++    Y     S    F+     A +          +  
Sbjct: 266 TE-IPLWILFFALGVRSDKEVIDLIDYASNDASIVNIFFASIHDADEKCEHFRREDRALD 324

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            VD    +      + +   +   L  +             G  V   ++   TG    +
Sbjct: 325 YVDKLLKKTRFPPKESIEDAISAYLFPRLNSR--RHKARFLGYMVKC-LLEAYTGHRKCD 381

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY-----IRNTLVTDKNKDRKDALLDIY 378
             D    K  E       R++ +    ++          +         +   DA +   
Sbjct: 382 NRDSFRNKRFELASELLERELKVHVSHALRRMTKALQRDLYGDRDVHPIEHYLDASIVTN 441

Query: 379 RVMRPGDVSTFSVAESMFNF------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            + R      +                   ++        R      L      D R+  
Sbjct: 442 GLTRAFSTGAWCHPFKWMERVSGVVGNLGRANPLQTMIDLRKTRQQVLYTGKVGDARYPH 501

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                 +  +        G + ++   G         ++   +  G+ ++          
Sbjct: 502 PSHWGRVCFLSTPDGENCGLVKNLAVTGVVSTNISESLVDKLFDSGMEKLVDD------- 554

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
                           +      F     +   E+    +  +   RR   L      + 
Sbjct: 555 ------------TYTKLDGKHKVFLNGEWVGVCEDSCLFVGELRSMRRRRELPYQVEIKR 602

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
                   +       + P    E  +        ++   +                   
Sbjct: 603 DEQQREVRIFSDAGRILRPLLVVENLDKIKAFKGGNYIFTSLL--------------DKG 648

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + ++   EEE+   A     L  D                      K    +     ++
Sbjct: 649 IIEFIGTEEEEDCCTAWGIKFLLAD---------------IEGKQPMKYSHCELDMSFLL 693

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            ++  +IPF  +D + RVL                             K S  AI     
Sbjct: 694 GLSCGIIPFANHDHARRVLYQAQ-------------------------KHSQQAIGFSTT 728

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
               +VD                               +      QRPL           
Sbjct: 729 NPNIRVD-----------------------------TLSHQLHYPQRPL--------FRT 751

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
           +I+D       +L  G+N +VA     GYN EDS++++   +   +F S HI  ++    
Sbjct: 752 MISDCLVLPKPELFNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVD 811

Query: 853 DTKLGPEEITRDI------PNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           + +L  +    +              + ++D+ G   +GA +  GDI++GK
Sbjct: 812 NKELTDKRRKSEDSITFGKIQSKIGRVDSLDDDGFPFIGANMQSGDIVIGK 862


>gi|323575418|dbj|BAJ78237.1| RNA polymerase [Spiroplasma sp. Ozg]
          Length = 480

 Score =  268 bits (684), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 183/345 (53%), Positives = 241/345 (69%), Gaps = 8/345 (2%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V  GK+TN++ YL+A EE+N  IAQAN  LD +       V  R  G+ I+V   K+++I
Sbjct: 1   VIAGKITNEIKYLTAGEEKNYIIAQANIELDTNNVIKNNNVIARSNGQNIIVGPNKVEYI 60

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VSIA S IPFLENDD+NR LMG NMQRQA+PLLK + P VGTG+E  VA  SG
Sbjct: 61  DVSPKQIVSIATSCIPFLENDDANRALMGANMQRQAIPLLKPQTPIVGTGVEYAVAHDSG 120

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            AIVA   G+V+ VD+           +  S   +  Y L +F+RSNQ T V   PLVKV
Sbjct: 121 LAIVANLPGVVQYVDS--------HEIIIKSEEEITTYELSRFERSNQGTAVTHVPLVKV 172

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
           GD+V  N I+ADGPS   G+LALG+N+++AFM WHGYN+ED+++ISER+V +DV+TS+HI
Sbjct: 173 GDKVEVNQILADGPSMKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVYTSMHI 232

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           EE+ +  R TK G EEITR+IPN SE+  + +D+ GI+ +G EV  G ILVGK+TPKG++
Sbjct: 233 EEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDEGIVLIGTEVKEGGILVGKVTPKGQT 292

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             T EEKLL AIFGEK+ +V+D SLRVP+G +G V  ++ + R  
Sbjct: 293 QSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIVQGIKRYKRED 337



 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 110/385 (28%), Positives = 156/385 (40%), Gaps = 79/385 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V    IL    +   +  +   + ++ A       +  D  +     V   V 
Sbjct: 169  LVKVGDKVEVNQILADGPS-MKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVY 227

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ++  +     E    +I    E   R  DDE  I+      +   IL G+ 
Sbjct: 228  TSMHIEEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDE-GIVLIGTEVKEGGILVGKV 286

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L + +  E  R+               V+ +                
Sbjct: 287  TPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIVQGI---------------- 330

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K + G D+P  V  VVKVF+  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+D
Sbjct: 331  -KRYKREDGFDLPSEVEEVVKVFIVQKRKIREGDKMAGRHGNKGVISKVLPIEDMPFLED 389

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            GTPVDI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+  +    + 
Sbjct: 390  GTPVDIMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGAKNQDLLDIMKEAK- 448

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                FD                    + 
Sbjct: 449  -YND--------------------------------FD--------------------KL 455

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKL 1259
             LYDGLTGE F + ++VG +YMLKL
Sbjct: 456  TLYDGLTGEKFAKKISVGVMYMLKL 480


>gi|67515340|gb|AAY68199.1| RNA polymerase IV second largest subunit [Isoetes sp. JL-2005]
          Length = 623

 Score =  268 bits (684), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 75/329 (22%), Positives = 118/329 (35%), Gaps = 56/329 (17%)

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G+ + S   G+KK +    + +               + +   + +         +  + 
Sbjct: 307  GEPSESDVGGYKKQSHY--EKLDSDGLPHVGAALSSSDVIIGKLFTAGADVREVDASQKL 364

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            +   +    Q            VKV +   R  Q GDK +  HG KG+V      ED+PF
Sbjct: 365  KHTERGRVDQVVIAAKNDAETDVKVRLRECRTPQVGDKFSSMHGQKGVVGMCFHQEDLPF 424

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +DG   D+++NP   P+R  +GQ+ E   G A     ++                    
Sbjct: 425  TRDGIVPDLIINPHAFPTRQTLGQLMECLAGKAAAVSAREQD------------------ 466

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F        +  L  A    +
Sbjct: 467  -----------------------------------ATP-FVERSLPRFSEELHKAGFQRT 490

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G   +Y G  G      V +G  +  +L HM  DK+  R TGS   +T+QP+  +   GG
Sbjct: 491  GMECMYSGRVGTRMKVRVNIGVTFYQRLTHMAEDKMKYRRTGSVHPLTRQPIVDRKRHGG 550

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             R GEME  C+ A+GA+  LQE L + SD
Sbjct: 551  IRFGEMERDCMIAHGASATLQERLFLLSD 579



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 53/337 (15%), Positives = 110/337 (32%), Gaps = 42/337 (12%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS--IAASLIPFLENDDSN 688
             ++  D       +F     E  +      +     P+      +   +I F+  ++  
Sbjct: 92  EINIFSDAGRLLRPLFIVDNDELCITKEHLFELRRKKPQDGFEYLVKEGVIEFVGAEEEY 151

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R  +  ++Q    P          T ME   A        A  A ++  V+  +      
Sbjct: 152 RASIAGSIQDLKRPR---SHHVRYTHMELRPASLL-----AIGAFVIPFVNHNQSSRVMQ 203

Query: 749 EGDLDPST--SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           +                 ++   ++      QRPLV+                    +L 
Sbjct: 204 QSRKHCRQAIGFNCSNLRVRCDTTSHELLYPQRPLVR----------TQAMTLIGRPELH 253

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR---DTKLGPEEITR 863
            G+N +VA +   GYN EDS+++++  +   +F S+H    +   +   D + G    + 
Sbjct: 254 NGQNPIVAVLSDTGYNQEDSIILNQSSLDRGMFRSMHFHTHKDALKPTLDQRFGEPSESD 313

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                 +   + +D  G+  VGA ++  D+++GK+   G                     
Sbjct: 314 VGGYKKQSHYEKLDSDGLPHVGAALSSSDVIIGKLFTAGADVRE---------------- 357

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
             D S ++     G V  V I  ++  + + +    E
Sbjct: 358 -VDASQKLKHTERGRVDQVVIAAKNDAETDVKVRLRE 393


>gi|6449143|gb|AAF08844.1| RNA polymerase beta subunit [Streptococcus parasanguinis ATCC
           15912]
          Length = 290

 Score =  268 bits (684), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 162/297 (54%), Positives = 213/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGFI+TPYRKV    G VTN++V+L+A EE+   +AQANS L+E+G F E +V  R  
Sbjct: 61  NKYGFIQTPYRKVDREKGVVTNEIVWLTADEEDEYIVAQANSKLNEEGGFAEPIVMGRHR 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P +++D++  SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GNNQEFPSDQVDYMAVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++A+  G V   DA ++ +   +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVIAQYDGKVTYADADKVKVCREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTGYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|332017159|gb|EGI57958.1| DNA-directed RNA polymerase III subunit RPC2 [Acromyrmex echinatior]
          Length = 1113

 Score =  268 bits (684), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 104/585 (17%), Positives = 190/585 (32%), Gaps = 98/585 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT-KLGP 858
             +  D+    + L+A            + I+E  +       I         R+T +   
Sbjct: 607  IEYLDVNEENDSLIACTESEINENTTHLEIAEFTILGVCAGLIPYPHHNQSPRNTYQCAM 666

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             +    I   ++    +     ++     +    +    I       +   E  + A+  
Sbjct: 667  GKQAMGIIGYNQRNRIDTVMYNLVYPQTPI----VKTRAIELINYDKLPAGENAIVAVMS 722

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                D+ D  +   + +        ++        + +    ++ I     D + ++ I 
Sbjct: 723  YSGYDIEDALIFNKASIDRGYGRCLVYRNAKCILKKYANRT-QDTIMGPMLDGNTKKPIT 781

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
               +      +L G+   +      KS    S+ I           AV+           
Sbjct: 782  KHEVLDVDGIVLPGEMVENKTVMVNKSVPTPSENIGPVSSGTIQTQAVE----------- 830

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
               Y  ++   +      +EK+    +     L   K+ +   R  + GDK + RHG KG
Sbjct: 831  ---YRNAEIPFKGMVPAYVEKVIVTSNADDCFLT--KLLLRQTRRPEIGDKFSSRHGQKG 885

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            ++  I+  EDMP            N  G+                               
Sbjct: 886  VIGLIVEQEDMP-----------FNDHGI------------------------------- 903

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                          + ++       +++      +L       +G       F GA  E 
Sbjct: 904  ------------CPDIIMNPHGFPSRMTVGKLIELLAGKAGVVNGKFHDATAFGGAKVED 951

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I   L     +  G+   Y+G+TG+P    +  G +Y  KL HMV DK++AR+ G   ++
Sbjct: 952  IREELAKNGYNYLGKDFFYNGMTGKPLIGYIYSGPVYYQKLKHMVQDKMHARARGPRVVL 1011

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG---------- 1324
            T+QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV            
Sbjct: 1012 TRQPTEGRSREGGLRLGEMERDCLIGYGASMLLVERLMISSDAFKVDVCNKCGLIGYNGW 1071

Query: 1325 --RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              R +   S            P +  +L +E+Q++ +   L    
Sbjct: 1072 CQRCKSSSS------VSTITMPYACKLLFQELQSMNVVPRLSLKD 1110



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 127/961 (13%), Positives = 278/961 (28%), Gaps = 238/961 (24%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     SY++F+   I    + NE +Q         +       L++++ +   P+   
Sbjct: 15  LVNQHIDSYNYFINEEIKNIVKANEKVQ---------SDEDPHFYLKYLNIKVGLPEVQE 65

Query: 87  ----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RDL Y+  + + +  I          +S + I   ++ +G +P
Sbjct: 66  SSNSIRTIPTTPHECRLRDLNYSASIIVDVEYI----------RSNQRIIRHNMVIGKMP 115

Query: 137 LMTKD------------------------GTFVIKGIQRIVVS--QLHRSPGIHFDHDKG 170
           +M +                         G F+I G +++++   Q+ R+          
Sbjct: 116 IMLRSSNCVLTKKSESELAKMNECLYDSGGYFIINGQEKVILIQEQMVRN---------- 165

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDII-----HVRIDRRRK-------------- 211
                       RII        +E DSK+ I         D++ K              
Sbjct: 166 ------------RII--------LEEDSKNCIVAACNSFTHDKKTKTNVVGKTGKYYIRH 205

Query: 212 ------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                 + +T    A+G+ S+ EI+     +  Y  +            +    +    L
Sbjct: 206 NMFQDDILITIIFKAMGIVSDLEIMQMVGTQETYLNKFAASLEDCQELGIFSQNQALKYL 265

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA-----EDIVNGETGE 319
            +     +       +T  +   L    +  + +         +        ++N ++  
Sbjct: 266 NNKRKQMRFHVPKSHVTDEMKDVLATNILSHVPVVDFNFRPKALYLALMIRRVINAQSDH 325

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
             I+  D    K LE            L+         I N  +       K A  DI  
Sbjct: 326 SLIDDKDYYGNKRLELAGSLLALMFEDLFKRFNWELKKIANKNI----PKTKAAAFDIVN 381

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            MR            +       +      T+ R +M              +     + +
Sbjct: 382 HMR----------HDLITNGLVFAISSGNWTIKRFRMERHGVTQVLSR---LSYISALGM 428

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +  +         +    +L   +   +      +     L    ++   I++   + ++
Sbjct: 429 MTRVHSQFEKTRKVSGPRSLQGSQWGMLCPNDTPEGEACGLVKNLALMAHITTEVPEELI 488

Query: 500 PQDLIN--AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + ++N   + + +   E   S  +  +  +   +  + + +RL    +  + R      
Sbjct: 489 IKLVLNLGVENIYTLAGEELTSEDIYSVFVNGIMVGIVQNHKRLVRQFRL-LRRRGYINS 547

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV---CDGKVTNDV 614
              ++  H  +     +  G     +  + +   +     IE   R +    D      +
Sbjct: 548 FVSIYTQHRHKCIQISSDGGRLCRPLIIVKNAKSLVKPKHIENLERNITSFEDFLYDGLI 607

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   EE +  IA   S ++E+                          ++ +   ++ +
Sbjct: 608 EYLDVNEENDSLIACTESEINEN-----------------------TTHLEIAEFTILGV 644

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A LIP+  ++ S R    C M +QA+ ++         G                    
Sbjct: 645 CAGLIPYPHHNQSPRNTYQCAMGKQAMGII---------GYNQRNRID------------ 683

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                 N    Q P+VK           
Sbjct: 684 ----------------------------------TVMYNLVYPQTPIVK----------T 699

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE-------EF 847
                 +   L  G N +VA M + GY+ ED+++ ++  +       +          ++
Sbjct: 700 RAIELINYDKLPAGENAIVAVMSYSGYDIEDALIFNKASIDRGYGRCLVYRNAKCILKKY 759

Query: 848 EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
               +DT +GP         +++  +  +D  GI+  G  V    ++V K  P     + 
Sbjct: 760 ANRTQDTIMGPMLDGNTKKPITKHEV--LDVDGIVLPGEMVENKTVMVNKSVPTPSENIG 817

Query: 908 P 908
           P
Sbjct: 818 P 818


>gi|45330861|gb|AAS57791.1| RNA polymerase II second largest subunit [Cortinarius iodes]
          Length = 878

 Score =  268 bits (684), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 150/1002 (14%), Positives = 291/1002 (29%), Gaps = 173/1002 (17%)

Query: 286  KSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G      +    V+     ++   G + D   LE I +   
Sbjct: 30   KTISQFQVKMFHRNQERSLGNVMKATIPYIKVDIPIWVVFRALGVISDRDILEHICYDLQ 89

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I         +T    E    +   
Sbjct: 90   DSQMLEMLKPCIDDGFV--------IQDREVALDFIGNR----GTTTGLSRERRIRYAQE 137

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               K  L  V              +   + +      +I  L+     +  +DD D+ G 
Sbjct: 138  ILQKEMLPHVAMK-----------EGSEYQKAHFFGYMIHRLLLAALERRELDDRDHFGK 186

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 187  KRLDLAGPLLSNLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLAT 246

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 247  GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 302

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN-DVVYLSAMEEENR 625
            G +CPAET EG   GLV +L   A ++           + +  + + +    S       
Sbjct: 303  GMVCPAETPEGQACGLVKNLALMACISVGSIAAPGIEFLEEWGLESLEEHSHSPAPSTKI 362

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            ++      +  D +   + +      ++I      +  I     +V S A  +   L   
Sbjct: 363  FVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISIVRDIREKELRVYSDAGRVCRPLFIV 422

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            ++ R+++     R     +  E      G E    +         + GI+E +DA     
Sbjct: 423  ENQRLILQKRHVRWLNNGINDE------GEEFKWDRL-------IKGGIIELLDAEEEET 469

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +       +  Q +        R  +K G            PS  LG  
Sbjct: 470  VMISMTPEDLENSRLQRPGVDPQANEGEFDPAAR--LKAGTHAHTLTHCEIHPSMILG-- 525

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 526  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLI 562

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 563  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 611

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +    
Sbjct: 612  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRLKHGTYDKLED 670

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 671  DGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI- 729

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q GDK A RHG KG V     
Sbjct: 730  -------------------TTNSEGQKFVKVRVRSSRIPQIGDKFASRHGQKGTVGITYR 770

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 771  QEDMPFTAEGIVPDVIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 823

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++       LR       G+ V                   
Sbjct: 824  ------------------DLTVESVSIFLRQKGYQSRGLEVM------------------ 847

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                  G +       G      V +G  Y  +L HMV DK+
Sbjct: 848  ----YHGHT-------GRKLQAQVYLGPTYYQRLKHMVDDKI 878



 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 100/775 (12%), Positives = 220/775 (28%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  SQ  +     +    ++   +V+
Sbjct: 58  YIKVD----IPIWVVFRALGVISDRDILEHICYDLQDSQMLEMLKPCIDDGFVIQDREVA 113

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G     S ++      + L+++ +  + +                     + 
Sbjct: 114 LDFIGNR-GTTTGLSRERRIRYAQEILQKEMLPHVAMKEGSEYQK---AHFFGYMIHRLL 169

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 170 LAALERRELDDRDHFGKKRLDL----------AGPLLSNLFRMLFRKLTKDVYRYLQKCV 219

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 220 --ETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 276

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S+   
Sbjct: 277 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSIAAP 336

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             ++     +   F     +    +  N +  +   RR   +     
Sbjct: 337 GIEFLEEWGLESLEEHSHSPAPSTKIFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEIS 396

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                  +   V+        P    E   + L      +  +N     E    K     
Sbjct: 397 IVRDIREKELRVYSDAGRVCRPLFIVENQRLILQKRHVRW--LNNGINDEGEEFKWDRLI 454

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               +  L A EEE   I+     L+        +      GE               + 
Sbjct: 455 KGGIIELLDAEEEETVMISMTPEDLENSRLQRPGVDPQANEGEFDPAARLKAGTHAHTLT 514

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 515 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI------------ 562

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 563 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 590

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 591 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 629

Query: 843 HIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E        +   +       +++ G+I  G  V   DI++GK
Sbjct: 630 YYRSYMDLEKKSGIQQLEEFEKPTRENTLRLKHGTYDKLEDDGLIAPGTGVAGEDIIIGK 689

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 690 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 737


>gi|269930819|gb|ACZ54144.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 286

 Score =  268 bits (684), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 207/287 (72%), Positives = 241/287 (83%), Gaps = 1/287 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           GAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 GAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 286


>gi|110734400|gb|ABG88855.1| RNA polymerase II second largest subunit [Mrakia frigida]
          Length = 705

 Score =  267 bits (683), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 125/822 (15%), Positives = 233/822 (28%), Gaps = 135/822 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + +    +           +  +    + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLAGLFRMLFKKLTKDVFRYLQKCVETRKEFKLESAVRQATITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   + ++           + +  +     Y  
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPILEFLDEWGLEALEEYAG 176

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAAS 677
            A      ++      +  D +   E +       +I      + D  +   +        
Sbjct: 177  APSATKVFVNGVWVGVHRDANQLTEHLIRLRRCSDIKSEVSVVRDIRERELRLYTDAGRV 236

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
              P    + S++      ++++ V  L               ++           G +E 
Sbjct: 237  CRPLFVVNQSDQ---QLALKKEDVGKLTNSKDENLN----DESEDHYTWTHLLEEGKIEL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +  +           Q     Q      G +    D+    
Sbjct: 290  LDAEEEETVMIAMTPEDLAAAREAESQADMSVREQQRVQMQ-----TGQDY---DVAGRA 341

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTK 855
             ST                 +       SM+  I   ++                     
Sbjct: 342  KSTSFSH------------TFTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXKQA 389

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G       I               +  +             +       +   +  + A
Sbjct: 390  MGIYLTNYQIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVA 438

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    ++ R   D  +++  V  E+ E   RD     
Sbjct: 439  ILCYSGYNQEDSVIMNQSSIDRGLF-RSMYYRSYQDVEKKNGMVSLEEFEKPTRDSTLRL 497

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +       +  G           K+  +  D                +E  QR  
Sbjct: 498  KQGTYDKLDADGLVSPGVGVNGEDIIIGKTAPIPKD---------------SEELGQRQA 542

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K    T     E    +++      D +     + VK+ V   R  Q GDK A RHG
Sbjct: 543  THTKRDVSTPLKSTEQGIVDQVLVTTNADGL-----KFVKIRVRSTRVPQIGDKFASRHG 597

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMPF  +G   DI++NP  +PSRM +G + E  L      LG +    
Sbjct: 598  QKGTVGITYRQEDMPFTSEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLLGTEGD-- 655

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP F    
Sbjct: 656  ---------------------------------------------------ATP-FTDLT 663

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             EA+++ L+       G  ++Y G TG      V +G  Y  
Sbjct: 664  VEAVSARLKDKGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQ 705



 Score =  105 bits (262), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 88/591 (14%), Positives = 160/591 (27%), Gaps = 86/591 (14%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F +  ++      +  KY L   G      +         + + +    + +  L   
Sbjct: 45  KEFKLESAVRQATITNGLKYSL-ATGNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRC 103

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI------ 495
                R+GK       +  +  +    E  + Q    +  +       + S         
Sbjct: 104 NTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPILEFL 163

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARA 554
           D    + L       SA   F     +    +       +   RR S +  +  V R   
Sbjct: 164 DEWGLEALEEYAGAPSATKVFVNGVWVGVHRDANQLTEHLIRLRRCSDIKSEVSVVRDIR 223

Query: 555 GVEMRDVHPTHYGRICPAETSEGH-------NIGLVSSLTSFARVNAYGFIETPYRKVCD 607
             E+R    T  GR+C                   V  LT+    N     E  Y     
Sbjct: 224 ERELR--LYTDAGRVCRPLFVVNQSDQQLALKKEDVGKLTNSKDENLNDESEDHY-TWTH 280

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 +  L A EEE   IA     L                        E    +   
Sbjct: 281 LLEEGKIELLDAEEEETVMIAMTPEDLAAAR------------------EAESQADMSVR 322

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            +Q V                       MQ      +   A            +   + I
Sbjct: 323 EQQRV----------------------QMQTGQDYDVAGRAKSTSFSHTFTHCEIHPSMI 360

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +               G+      ++           Q+PL     
Sbjct: 361 LGICASIIPFPDHNQXXXXXXXXXXXKQAMGIYLTNYQIRMDTMANILYYPQKPL----- 415

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F S++   
Sbjct: 416 -----ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRS 470

Query: 847 FEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           ++ + +   +   E            + +     +D  G++  G  VN  DI++GK  P 
Sbjct: 471 YQDVEKKNGMVSLEEFEKPTRDSTLRLKQGTYDKLDADGLVSPGVGVNGEDIIIGKTAPI 530

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +      ++       +     RD S  + S   G V  V +       K
Sbjct: 531 PKDSEELGQR-------QATHTKRDVSTPLKSTEQGIVDQVLVTTNADGLK 574


>gi|227937622|gb|ACP43386.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 286

 Score =  267 bits (683), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 209/287 (72%), Positives = 242/287 (84%), Gaps = 1/287 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           GAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KFQRS
Sbjct: 241 GAAVNAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKFQRS 286


>gi|126023772|gb|ABN71366.1| RNA polymerase beta subunit [Oenococcus kitaharae]
          Length = 300

 Score =  267 bits (683), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 161/304 (52%), Positives = 202/304 (66%), Gaps = 9/304 (2%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+AV EFF SSQLSQ  +  N L  + H RRLSALG GG+ R RAG E+RDVH +
Sbjct: 4   NIRPVVAAVKEFFGSSQLSQFMDQTNPLGELNHKRRLSALGPGGLTRDRAGYEVRDVHYS 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEE 622
           HYGRI P ET EG NIGL++SL  + R+N YGFIETPYR+V     KVT+ + YL+A  E
Sbjct: 64  HYGRIDPIETPEGPNIGLITSLAVYGRINEYGFIETPYRRVDWDTHKVTDKIDYLTADVE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +N  IAQANS L++DGS     V  R     I  P E +D++D SPKQ+V+++ + IPFL
Sbjct: 124 DNYTIAQANSELNDDGSLVNATVTARHGDNNIETPIEDVDYMDVSPKQIVAVSTAAIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           ENDDSNR LMG NMQRQAVPL+   +P VGTG+E   A  SG A + +  G VE VD   
Sbjct: 184 ENDDSNRALMGANMQRQAVPLVAPHSPIVGTGIEYRAAVDSGLAQIDEAKGTVEYVDGRD 243

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           I +R  +G        +  Y LMKFQRSN     NQ P+VKVG+ V + D++ADGPS + 
Sbjct: 244 IKVREDDG-------NLHEYPLMKFQRSNGGKNYNQTPIVKVGETVEKGDVLADGPSMEN 296

Query: 803 GDLA 806
           G+LA
Sbjct: 297 GELA 300


>gi|108885367|gb|ABG23200.1| DNA-directed RNA polymerase [Geobacillus sp. N60]
          Length = 145

 Score =  267 bits (683), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 65/167 (38%), Positives = 100/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+ IE+Q +SY  FL          +EGL+  F+ + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNSIEIQTSSYQWFL----------DEGLREMFREISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYS---DKVDKNGKRGYSATVIPNRGAW 145


>gi|119644256|gb|ABL85615.1| RNA polymerase II second largest subunit [Degelia plumbea]
          Length = 718

 Score =  267 bits (683), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 126/834 (15%), Positives = 237/834 (28%), Gaps = 136/834 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + + +  +              I +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGIKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + ++  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIDFMMKRNMEILEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L +      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LRSPNATKVFVNGVWVGVHRDPAHLVSNVQSLRRRHWISHEVSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAG 733
                P F+  +D+     G  +  +   L   E   +G  M+    +            G
Sbjct: 237  RVCRPLFVIENDAKNPNCGNLVLTKGHILRLEEDKELGADMDPEEREERFMGWEGLVNQG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE VDA       +    +       + +         +   N+R   K+         
Sbjct: 297  VVEYVDAEEEETVMIVMTPEDLDISRQV-QAGHDPEPPPDDDPNRRVKAKMSPTAHTWTH 355

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   + +  +E     
Sbjct: 356  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM-- 404

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 405  -------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 439

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R      EQ E   +    
Sbjct: 440  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGMTIVEQFEKPMKSDTL 498

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            +      +       +  G           K+  ++ D      R++          ++ 
Sbjct: 499  KLKHGTYDKLDDDGIVSPGVRVFGDDIVIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 558

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 559  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDKFASR 598

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 599  HGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 658

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 659  ATPFTEVTVDSVSRLLR--EHGYQSRGFEVM----------------------------- 687

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                             +G +    G         V +G  Y  +L HMV DK+
Sbjct: 688  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 718



 Score =  121 bits (303), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 90/585 (15%), Positives = 160/585 (27%), Gaps = 107/585 (18%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 59  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 118

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   P  
Sbjct: 119 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIDFMMKRNMEILEEYEPLR 178

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS-ALGQGGVARARAGVEM--- 558
             NA  V      F     +    +  + +S +   RR      +  + R     E    
Sbjct: 179 SPNATKV------FVNGVWVGVHRDPAHLVSNVQSLRRRHWISHEVSLVRDIRDREFKIF 232

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG------FIETPYRKVCDG 608
               R   P           + G+ +     +         G        E  +      
Sbjct: 233 TDAGRVCRPLFVIENDAKNPNCGNLVLTKGHILRLEEDKELGADMDPEEREERFMGWEGL 292

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLD--------EDGSFTEELVFCRCAGEEILVPREK 660
                V Y+ A EEE   I      LD         D     +    R    ++      
Sbjct: 293 VNQGVVEYVDAEEEETVMIVMTPEDLDISRQVQAGHDPEPPPDDDPNRRVKAKMSPTAHT 352

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +         T  E  + 
Sbjct: 353 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFL-------TNYEQRMD 405

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             +                                                      Q+P
Sbjct: 406 TMANIL------------------------------------------------YYPQKP 417

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           L                      +L  G+N +VA   + GYN EDS+++++  +   +F 
Sbjct: 418 L----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFR 467

Query: 841 SIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           S+    +    +   +   E     +  D   +       +D+ GI+  G  V   DI++
Sbjct: 468 SLFYRSYTDQEKRVGMTIVEQFEKPMKSDTLKLKHGTYDKLDDDGIVSPGVRVFGDDIVI 527

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           GK  P         E+L +        DV        +G+   V+
Sbjct: 528 GKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 568


>gi|113957140|gb|ABI49100.1| RNA polymerase II second largest subunit [Lobaria scrobiculata]
          Length = 714

 Score =  267 bits (683), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 124/834 (14%), Positives = 243/834 (29%), Gaps = 144/834 (17%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCE 515
            + G  R+   G +L   +R+   ++ + + + +               + +  + + +  
Sbjct: 1    HFGKNRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLKY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLATGNWGGQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAM 620
             TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L + 
Sbjct: 117  NTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSP 176

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLI 679
                 ++      +  D +     V        I      + D  D   K          
Sbjct: 177  NATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCR 236

Query: 680  P-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            P F+ ++D      G  +  +       +   +G  ++    +        K  G    V
Sbjct: 237  PLFVIDNDPKSPNRGNLVLTKEHVNKLEDDKELGPDVDPEGRED-------KFRGWKGLV 289

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADG 797
               + V+  V+ + + +   V     ++  R  Q   V   P +      V+        
Sbjct: 290  --NQGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYVMPEPSIDAPNKRVKAPLNPTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N                        ++       +
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQAM 389

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G      D                +  +             +       +   +  + AI
Sbjct: 390  GVFLTNFDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 438

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S     +    +F R   D+ +R   +    +E   +    + +
Sbjct: 439  ACYSGYNQEDSVIMNQSSTDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTL 494

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D                +E  QR
Sbjct: 495  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPD---------------AEEMGQR 539

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +K    T     E+   +++             LR VKV +   +  Q GDK A R
Sbjct: 540  TKAHIKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASR 594

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 595  HGQKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVGTLRGLEGD 654

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L                                             
Sbjct: 655  ATPFTDVTVDSVSKLL-------------------------------------------- 670

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                      R  ++   G +    G         V +G  Y  +L HMV DK+
Sbjct: 671  ---RDHGYQSRGFEIMYHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDKI 714


>gi|224812771|gb|ACN65019.1| RpoB [Cronobacter dublinensis subsp. dublinensis]
          Length = 275

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 166/274 (60%), Positives = 210/274 (76%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 IVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIY 275


>gi|116199389|ref|XP_001225506.1| hypothetical protein CHGG_07850 [Chaetomium globosum CBS 148.51]
 gi|88179129|gb|EAQ86597.1| hypothetical protein CHGG_07850 [Chaetomium globosum CBS 148.51]
          Length = 1155

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 95/501 (18%), Positives = 167/501 (33%), Gaps = 100/501 (19%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  ++   I       +   +     +      D+ D  +   +         ++F 
Sbjct: 733  YPQRPMVITKTIQLIHYDKLPAGQNATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVF- 791

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R    + ++  +  ++++  + +D+     I       +    + G    SG     K T
Sbjct: 792  RKYTAELQQYPNGRKDRLGGIQKDEAGN-TIAKHACLDKDGLAVVGYRVHSGETMIMKET 850

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +                 +  ++   +       Y  +    +  + +K+         
Sbjct: 851  PIDQTSTG-----------IGSDRGSDDFRPAATNYRIA----DPAYIDKV-----MISN 890

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  +VKV     R  + GDK + RHG KG+V  I   EDMPF   G   DI+     
Sbjct: 891  TEKNTSIVKVQTRQTRRPELGDKFSSRHGQKGVVGIIADQEDMPFSDSGLVPDII----- 945

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
                MN                G   +  +                E+  G G       
Sbjct: 946  ----MNP--------------HGFPSRMTVGKLFECLTGKASVVAGERDYGFGD------ 981

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F     E +  +L        G+     G+TGEP +
Sbjct: 982  -----------------------AFRSHPVEEMGKVLVEHGFSWEGKDYFTSGITGEPHE 1018

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  +L HMV DK+++RS G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1019 AYLFNGPIYYQRLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYG 1078

Query: 1307 AAYVLQEMLTIKSD----DVV------GRTRVYESIVAG--------NDTFETGTPESFN 1348
            A+ +L E L I SD    D+       G    Y     G        +   +   P +  
Sbjct: 1079 ASQLLLERLMISSDGTQVDICELCGLLG----Y----KGFCQTCGSTSQVTQMTMPYAAK 1130

Query: 1349 VLVKEMQALGLSIDLENSRTK 1369
            +LV+E+ ++ + + ++     
Sbjct: 1131 LLVQELISMNVGVRMQLEDKF 1151



 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 130/945 (13%), Positives = 260/945 (27%), Gaps = 202/945 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY+ F+   I    + N  ++         +       LEF       P    
Sbjct: 44  LVKQHIDSYNFFVEQEIKDIVKANRSIR---------SDQEKDFWLEFTDIRVGTPTRND 94

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   +    +C  RD+TYA P+ + +          T ++  K I  + I +  +P
Sbjct: 95  YTDFKARDEVTPMECRLRDMTYAAPVVVDI----------TYSRDRKRIVRKDIPLCRIP 144

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G +++++ Q   S          + 
Sbjct: 145 VMLKSAKCCLSGANNAQMEIMNECPLDPGGYFIINGTEKVILIQEQLSKNRVIVEADEKT 204

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR----------KVPVTSFLMAL- 221
                 + +               + K   +V + + R           +P+   L AL 
Sbjct: 205 GGVSASVTSST------------HERKSKTYVILKKDRIVLNHNVLVEPIPIVIVLKALG 252

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           G+   EI+          Q      F  +A   +   + +   V         + G+ + 
Sbjct: 253 GLSDYEIMEVVAGGDARYQDDFLINFEEAAKAGVFTQQQALEYVGSRVKMGGPKKGRSMA 312

Query: 282 SGLLKSLKEKG-------------VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
           +   +S  E+G             +K L      +    +   ++        ++  D +
Sbjct: 313 APR-RSPVEEGLDALANIIIAHVTIKDLDFYPKSIYISMMVRRVLMAAHNPRLVDDRDFV 371

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             K LE            ++   V       N     K  +R  A   +  +   G   T
Sbjct: 372 GNKRLELAGQLLSLLFEDMFKMFV--GGLKGNMEYFFKKPNRTSAYDPVGPISSQGQYIT 429

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR- 447
             +  +      ++  +++++  G   +  RL+      +            K+      
Sbjct: 430 QGLNRA-IQSGNWNVKRFNMNRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRAL 488

Query: 448 --NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
             +  G +   D         V  +    +       E         +     +     +
Sbjct: 489 QPSQWGMLCPSDTPEGEACGLVKNLALMTHITTNAEEEPVKNWIFGLIPGVEPIRMYTGS 548

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-T 564
                 +       +  +  +      SR   TRR   +                +H  T
Sbjct: 549 EMHKRGSYMIHLNGTPFAITKHPKEFASRFKTTRRRGHISP--FIGIHINEHFSAIHIAT 606

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    +     L        ++    F +   R V        + YL   EE 
Sbjct: 607 DEGRICRPYIIVKDGKPKLKKEHLRLLQLGKATFDDFLKRSV--------IEYLDVNEEN 658

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           +  IA     ++                            ++  P  ++   A LIPF  
Sbjct: 659 DALIAIREDDVN-----------------------HSTTHMEIEPFTILGAVAGLIPFPH 695

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R    C M +QA+                                          
Sbjct: 696 HNQSPRNTYQCAMGKQAIGA---------------------------------------- 715

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            I   + +   +     +Y               QRP+V          I          
Sbjct: 716 -IAYNQFNRIDTLLYTLVYP--------------QRPMV----------ITKTIQLIHYD 750

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            L  G+N  V  M + GY+ ED++++++              ++    +    G ++   
Sbjct: 751 KLPAGQNATVVVMSYSGYDIEDALVLNKASCDRGFGRCQVFRKYTAELQQYPNGRKDRLG 810

Query: 864 DIPNVSEEG----LKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            I              +D+ G+  VG  V+ G+ ++ K TP  ++
Sbjct: 811 GIQKDEAGNTIAKHACLDKDGLAVVGYRVHSGETMIMKETPIDQT 855


>gi|124491185|gb|ABN12927.1| RNA polymerase beta chain [Rhizobium sp. IRBG74]
          Length = 237

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 142/238 (59%), Positives = 177/238 (74%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +ILSTFY K  Y + GD W  P     L   AKV + ++D DTGE V+E+GKKLT  L++
Sbjct: 61  DILSTFYTKASYERDGDGWRIPFQPEAL-KNAKVVTDMIDADTGEVVVEAGKKLTPRLIR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L EKG+K L  T + L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I  S   +IP+
Sbjct: 120 QLSEKGLKALKATDEDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLGLILQSGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D VN  AYIRNTL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LNIDHVNVGAYIRNTLSADKNENRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAE 237


>gi|259489446|tpe|CBF89725.1| TPA: DNA-directed RNA polymerase III, beta subunit, putative
            (AFU_orthologue; AFUA_1G02460) [Aspergillus nidulans FGSC
            A4]
          Length = 1225

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 166/1145 (14%), Positives = 329/1145 (28%), Gaps = 229/1145 (20%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +  D L   +            I ++
Sbjct: 273  IVETDPKKEIVQASVTSSSN-----ERKSKSYIILKKDRLYVKHNVLSEDIPI--VILLK 325

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            A  +  +K +  +       +  +      + A      +      ++ AL  I   ++ 
Sbjct: 326  AMGIHTDKEMMLL-------VAGVDKVYQEDFAINFEEAIKVGVFTQQQALDWIGSRIKI 378

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                       +         +  +  +  V ++     D     + I    +  + + +
Sbjct: 379  NRKQMSYRRTHV---------QEAVEAIASVIISHIEVKDMNFRPKAI---YVANMARRV 426

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
            +  +N    +DD D LGN+R+   G++L   +     +    IK  I  V       +  
Sbjct: 427  LMAKNDAALVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRVEAF 486

Query: 504  INAKPVVSA-------VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
                 +          +     +   S     +          RLS +   G+       
Sbjct: 487  DAWSVIGMHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 546

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G IC A+T EG   GLV +L     +              +G
Sbjct: 547  FEKTRKVSGPRALQPSQFGMICLADTPEGEACGLVKNLALMTHITTND---------EEG 597

Query: 609  KVTNDVVYLSAMEE----ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             + N +  L A +          A  + ++  +G+        R     +   R      
Sbjct: 598  PIKNLIFMLGAEDIQTVGGKEIYAPGSYTISINGTPMA---LTRRPKYFLNAFRRLRRMG 654

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              S    + I         +  +  V        + + +++     V       +   + 
Sbjct: 655  RISEFVSIYIN-------HHQRAVHVATDDGRICRPLIIVEDGKSRVKKHHLRKLRDGTM 707

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                    G+VE VD               + S + IY       +              
Sbjct: 708  QFDDFLAQGLVEYVDVNE-----------ENDSLIAIYEKDITDTTTHMEI--------- 747

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               +       +   +P+  +N          M  + +      
Sbjct: 748  -------------------EPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA---- 784

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
                                         + +    I+ +        +    I      
Sbjct: 785  -------------------------IASNQFLRIDSILYLMVYPQKPMVKSRTIELTKYD 819

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +    A+      D+ D  +     V       ++F ++  +    S   +    
Sbjct: 820  QLPAGQNATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTNMKSYSNGTKDILS 879

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                   +++  I    +         G+   +G     KST           +S     
Sbjct: 880  PPT---YENDAPIRKHALLESDGLAAVGEQVNAGEVYINKSTP---------DQSMSSGM 927

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
               D     +     + Y     + +  + +K+              +++KV     R  
Sbjct: 928  PGSDAGRPISYNPTPMTY----KLPDPAYIDKV-----MISATENENQIIKVLTRQTRRP 978

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+               G  VD                         
Sbjct: 979  EVGDKFSSRHGQKGV--------------TGIIVD------------------------- 999

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                  +      D   N DI         ++       +++      ++       SG 
Sbjct: 1000 ------QADMPFTDQGINPDI---------IMNPHGFPSRMTVGKMLELVAGKAGVLSGQ 1044

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                  F G   E +   L        G+  L  G+TGE     V  G IY  KL HMV 
Sbjct: 1045 HGYGTCFSGTPVEQMTQTLIDKGFSYGGKDYLTSGITGEALPFYVFTGPIYYQKLKHMVQ 1104

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            DK+++R+ G  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    
Sbjct: 1105 DKMHSRARGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEV 1164

Query: 1321 DV------------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
            DV              R +   S+V          P +  +L++E+ ++ ++  L+    
Sbjct: 1165 DVCEQCGFMGYLNWCQRCKSSRSVVK------MVIPYAAKLLIQELMSMNVTARLKLEDE 1218

Query: 1369 KNSAK 1373
                K
Sbjct: 1219 FPETK 1223



 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 88/743 (11%), Positives = 211/743 (28%), Gaps = 128/743 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 116 LVKQHIDSYNYLVEVQ----------LKKIVESSNTIRSDVDHNFYIKFTDIYLGFPRRA 165

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    I          +  + ++ + + 
Sbjct: 166 DEPQDVRTEFEESTVTPHECRLRDTTYAAPIQVDFEYI----------RGRQRVRRKGVS 215

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 216 IGRMPVMLRSSKCVLGNKTPAQMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 275

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      II             KD ++V+ +     +P+   L
Sbjct: 276 TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDRLYVKHNVLSEDIPIVILL 324

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +++ +      +    + DF      A  + VG       +D       I   +
Sbjct: 325 KAMGIHTDKEMMLLVAGVDKVYQEDFAINFEEA--IKVGVFTQQQALDWIGSRIKINRKQ 382

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCG---LYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
                       + +  + I+   +        A  + N     +  +     D   +++
Sbjct: 383 MSYRRTHVQEAVEAIASVIISHIEVKDMNFRPKAIYVANMARRVLMAKN----DAALVDD 438

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
             +   + + +           +         K   D  ++I +V+   +      A S+
Sbjct: 439 RDYLGNKRLEL-------AGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRVEAFDAWSV 491

Query: 396 FNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
                    +     +     +  R  ++       + +   IA + ++  + +      
Sbjct: 492 IGMHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTR 551

Query: 455 DIDNLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
            +      +    G + L +        + +++         D   P   +        +
Sbjct: 552 KVSGPRALQPSQFGMICLADTPEGEACGLVKNLALMTHITTNDEEGPIKNLIFMLGAEDI 611

Query: 514 CEFFCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRIC 570
                            +N        R    L     + R     E   ++  H+ R  
Sbjct: 612 QTVGGKEIYAPGSYTISINGTPMALTRRPKYFLNAFRRLRRMGRISEFVSIYINHHQRAV 671

Query: 571 PAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              T +G     +  +       + +    +     +  D      V Y+   EE +  I
Sbjct: 672 HVATDDGRICRPLIIVEDGKSRVKKHHLRKLRDGTMQFDDFLAQGLVEYVDVNEENDSLI 731

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +                        +    ++  P  ++   A LIP+  ++ S
Sbjct: 732 AIYEKDIT-----------------------DTTTHMEIEPFTILGAVAGLIPYPHHNQS 768

Query: 688 NRVLMGCNMQRQAVPLLKAEAPF 710
            R    C M +QA+  + +    
Sbjct: 769 PRNTYQCAMGKQAIGAIASNQFL 791


>gi|108885349|gb|ABG23191.1| DNA-directed RNA polymerase [Geobacillus sp. T38]
 gi|108885351|gb|ABG23192.1| DNA-directed RNA polymerase [Geobacillus sp. A60]
          Length = 145

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 63/167 (37%), Positives = 100/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD PLMT+ GTF
Sbjct: 51  KYSVEEAKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           VI G +R++VSQL RSP +++     +   +GK  +   +IP++G W
Sbjct: 102 VINGAERVIVSQLVRSPSVYYS---DKIDKNGKKGFTATVIPNRGAW 145


>gi|194766529|ref|XP_001965377.1| GF20648 [Drosophila ananassae]
 gi|190617987|gb|EDV33511.1| GF20648 [Drosophila ananassae]
          Length = 1129

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 127/350 (36%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    ++ I+        V ++V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCFVDSIRQLGSFDVSVKKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +    G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKSAAMHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQQIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G+         P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSAHPKTCRLCGDSSAVSMIEIPFSFKFLVTELSSVNINARFKLNE 1128



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 91/612 (14%), Positives = 216/612 (35%), Gaps = 66/612 (10%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLIQGYESDQYYLSCVQSMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T S   S               +  D+     + + ++ + L+          + + I+
Sbjct: 294 YTHSQCRSFIGNLFRSRFPEVPEWQPDEDVTDFILKERIMVHLDSYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +++ L     GK  ++++D+   + V   G +    +  +    ++++ R +++++++ 
Sbjct: 348 FMVQKLFQCAQGKQKVENVDSAMMQEVLVPGILYQKYIGERIETWMMQVRRCLQKKLTTP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     ++M Q +  A  V  ++  F  +              S L  + E++N +  ++
Sbjct: 408 DSLVNSALMTQCMRQAGGVGRSMESFLATGNIVSRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISKRP 524

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             E              ++ LS   + +  +      +  DG              +   
Sbjct: 525 DPELVKAIPSKLIEMG-MLPLSNRRDPDAKL----YVVFLDGRHL-----GHIHQSDATK 574

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             E++            +    IPF +N              M R    L   +  ++GT
Sbjct: 575 IVEELRHGKIFGSLPQMMEIGFIPFKKNGQFPGLFLATGPARMMRPVWNLKWKKVEYIGT 634

Query: 714 G--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              +   +A             +          + ++    D + S  ++Y+    +++ 
Sbjct: 635 LEQLYMEIAIDPKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTM 694

Query: 772 QNTCVN--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDS 826
              C+N  ++   K+         +      D     D A+G N +VA + + GY+ ED+
Sbjct: 695 GTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIKLDDFAMGTNAIVAVISYTGYDMEDA 754

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M+I++        + SI+  +F  + + +                E +K +D  G+   G
Sbjct: 755 MIINKAAYERGFAYGSIYKTKFVSLDKKSSYFCRHPHMP------ELVKYLDTDGLPHPG 808

Query: 886 AEVNPGDILVGK 897
           ++++ G+ L   
Sbjct: 809 SKLSYGNPLYCY 820


>gi|113957110|gb|ABI49098.1| RNA polymerase II second largest subunit [Letrouitia domingensis]
          Length = 708

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 128/828 (15%), Positives = 239/828 (28%), Gaps = 144/828 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + + + +               + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRMLFQKLTKDVYKYLQKCVEMNREFNLTLGVKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H  R +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAAQSRAGVSQVLNRYTFASTLSHLCRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     ++     E    +      +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIVDFMIQRGMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFC-RCAGEEILVPREKIDFIDASPKQVVSIA 675
            + +      ++      + +D +     V   R  G          D  D   K      
Sbjct: 177  VRSPNATKVFVNGVWVGIHQDPAHLVSTVQELRRRGHIPHETSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKRAG 733
                P F+ ++D      G  +  +   +   E    G  M+    A++S         G
Sbjct: 237  RVCRPLFVIDNDPRNPNRGSLVLTKDHIMKLEEDREAGLDMDPEEKAQTSMGWQSLVDTG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             VE VDA       +    +       I         + N              V+    
Sbjct: 297  AVEYVDAEEEETIMIVMTPEDLEISRQIQAGYTMPDRSDNA---------PNQRVKAPMS 347

Query: 794  IADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
             +    T      ++   +  + +P+  +N          M  + +              
Sbjct: 348  ASSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXXXXX 407

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                             E                                   +   +  
Sbjct: 408  XXXXXXXXXXXXXXXXME-----------------------------FLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R  +D  +R        IE   +   
Sbjct: 439  IVAIACYSGFNQEDSVIMNQSSIDRGLF-RSLFYRAYVDAEKRVGM---AVIERFEKPLR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             E + L    Y +L +   +  G           K+  ++ D                +E
Sbjct: 495  SETLKLKHGTYDKLDDDGLVAPGVRVSGEDVIIGKTQPIAPD---------------AEE 539

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR    +K    T     E+   +++             L+ VKV +   +  Q GDK
Sbjct: 540  MGQRTKMHVKRDASTPLRSTENGIVDRVLL-----STNQEGLKFVKVRMRTTKVPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 655  FEGD-----------------------------------------------------ATP 661

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             F     ++++ +LR       G  ++Y+G TG      V +G  Y  
Sbjct: 662  -FTEITVDSVSKLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQ 708



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 48/339 (14%), Positives = 93/339 (27%), Gaps = 27/339 (7%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 59  TNGLKYSLATGNWGDQKKAAQSRAGVSQVLNRYTFASTLSHLCRTNTPIGRDGKIAKPRQ 118

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +      ++KN   +  + +    +  +  +    +   +   
Sbjct: 119 LHNTHWGLVCPAETPEGQACG---LVKNLALMCYISVGTPSEPIVDFMIQRGMEVLEEYE 175

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM------ 558
                +A   F     +   ++  + +S +   RR   +  +  + R     E       
Sbjct: 176 PVRSPNATKVFVNGVWVGIHQDPAHLVSTVQELRRRGHIPHETSLVRDIRDREFKIFTDA 235

Query: 559 -RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV------T 611
            R   P       P   + G  +     +         G    P  K            T
Sbjct: 236 GRVCRPLFVIDNDPRNPNRGSLVLTKDHIMKLEEDREAGLDMDPEEKAQTSMGWQSLVDT 295

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDF 663
             V Y+ A EEE   I      L+               +    +     +         
Sbjct: 296 GAVEYVDAEEEETIMIVMTPEDLEISRQIQAGYTMPDRSDNAPNQRVKAPMSASSHTWTH 355

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            +  P  ++ I AS+IPF +++ S R      M +QA+ 
Sbjct: 356 CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 394


>gi|71419186|ref|XP_811091.1| DNA-directed RNA polymerase III subunit [Trypanosoma cruzi strain CL
            Brener]
 gi|70875716|gb|EAN89240.1| DNA-directed RNA polymerase III subunit, putative [Trypanosoma cruzi]
          Length = 1130

 Score =  267 bits (682), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 128/329 (38%), Gaps = 83/329 (25%)

Query: 1055 NKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
            + +  +  GD      V + +KV     R  + GDK + RHG KG+V  I    +MPF +
Sbjct: 857  DHVVILPPGDSERSMDVEQKIKVITREVRVPEPGDKFSSRHGQKGVVGLITDGVNMPFNE 916

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   D++         MN                                         
Sbjct: 917  KGISPDMI---------MN----------------------------------------P 927

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +     K+ +     V  +   +  G       F G + E +   L     +  G+
Sbjct: 928  HGFPSRMTVGKLLELVSSKVSALTGTFGDGT-----AFGGDNAEDLGMHLLRNGFNYHGK 982

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
               Y G+TGE     V  G IY  +L HMV+DK++AR+TG  S++T+QP  G+S  GG R
Sbjct: 983  DAFYSGITGEIMQAYVFFGPIYYQRLKHMVTDKMHARATGPRSMLTRQPTEGRSRSGGLR 1042

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR---------------TRVYESIVA 1334
            +GEME  C+  YGA+ +L E L + SD    D   R               T+       
Sbjct: 1043 VGEMERDCMVGYGASNLLNERLLLSSDLFTVDTC-RSCGFLGYCGYCPYCNTK------- 1094

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             N       P +F +L++E+Q +G+S  L
Sbjct: 1095 -NTVSHVNVPYAFKLLLQELQGMGISTRL 1122



 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 143/981 (14%), Positives = 271/981 (27%), Gaps = 206/981 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+    AS+DH + + +              KS     +      + + +     P+   
Sbjct: 30  LLNHHIASFDHLINVELKRILLNES--NREIKS-----SIDPDFSIRYTNIRVCQPREIV 82

Query: 86  --------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  RDLTY   + + +     D ++           E  I +G +P+
Sbjct: 83  GKGQLPKAVSPHECRTRDLTYRGDMIVDVEYTSRDRNKRPCT-------ETDIKIGTIPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSP----------GI 163
           M K                         G F+IKG++++ + Q  +S           G 
Sbjct: 136 MLKSSSCNLFGRTREELVAMRECPLDPGGYFIIKGVEKVCLVQEQQSKNRVIIEADDNGN 195

Query: 164 HFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK--VPVTSFLMAL 221
              H + +   S   +  C +              K  I V + R  K  +P+   L AL
Sbjct: 196 IVAHVQSKTHYS---ISKCSV-----------TFKKGRI-VMVHRSFKEDIPIVVMLKAL 240

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           GM+S+ +I         +     F CF  +AA  +     +   +     E   E     
Sbjct: 241 GMESDQQIAQHIGTTPAFESVL-FACFEQAAALGVKTQDDALHFIGERRKETSWEVDDA- 298

Query: 281 TSGLLKSLKEKGVKFLG---ITSDCLCGLYVAEDIVNGETGEIYIEAGDVI----DEKSL 333
               ++  K           +      G    +     +   +      +I    D   L
Sbjct: 299 QQRHIQKSKADNAAEFLGNVLLCHIREGQVQRDWNFRHKALYVCFMVRRMIEASVDSSLL 358

Query: 334 EEIFHSEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           +E      +          +L+ D +     +  T +  +   +        + +    +
Sbjct: 359 DERDFYGNKRFETTGTLMGLLFEDLLKQFNRVVKTAMDQQLSKKDTTKAFNVKQLMESKL 418

Query: 387 STFSVAESM-FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                   +  +   ++  ++++S  G  ++  RL+      +            KI   
Sbjct: 419 EVIQSGMRVALSSGRWELKRFNMSRQGITQVLSRLSYIACIGMMTRLASSFEKSRKISGP 478

Query: 446 LR---NGKGTIDDIDNLGNRRVRSVGEM--LKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                +  G +   D         V     L            R+    +   ++DS+  
Sbjct: 479 RSLQPSQWGMVCPCDTPEGESCGLVKNFGILSQVTLDMDDSFVRAAAHNLGVEEVDSISS 538

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           ++ +N   V      F   + +            +   RR   L            +   
Sbjct: 539 REFLNYYTV------FLNGTLIGIHRYPNRLCRGVRALRRSGRLHPHVSIAINDRQKSVQ 592

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           +     GRI        H    V+S            +      + D      V ++   
Sbjct: 593 I-GCDGGRIVRLYIVVNHAKPAVTSAHLD-------QLSAGQYSINDFLAEGLVEFIDVN 644

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           E  +  IA     ++                            ++  P  ++ + A +IP
Sbjct: 645 EANDCLIAVYPRDIE-----------------------TYTTHLEVEPLSLLGVVAGIIP 681

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F  ++ S R      M +QA+                                       
Sbjct: 682 FPHHNQSARNTFQSAMGKQALGT------------------------------------- 704

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               I   +     +   +  Y               QRPL +                T
Sbjct: 705 ----IAYNQYIRTDTVLMLGAYP--------------QRPLCR----------TKAMDLT 736

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
               L  G N +V  M + GY+ ED+ + +   +       + + + EV       G  E
Sbjct: 737 HYEKLGAGINAMVCVMSYSGYDIEDAQVYNRCSLDRGYGRCVVLRKHEVDLERLPNGEYE 796

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           I    P+ +    K ++  GI   GA V   DILV K TP       P   + +      
Sbjct: 797 IILP-PDSNAGKCKALNSDGIASKGAIVRQFDILVNKYTPVASLEPRPNPLVYKYPQ--- 852

Query: 921 AVDVRDTSLRVPSGVSGTVVD 941
              V D  + +P G S   +D
Sbjct: 853 -PAVVDHVVILPPGDSERSMD 872


>gi|323448349|gb|EGB04249.1| hypothetical protein AURANDRAFT_55255 [Aureococcus anophagefferens]
          Length = 1148

 Score =  266 bits (681), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 112/303 (36%), Gaps = 50/303 (16%)

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +    D       E    +        E  + + +  I   +     + R   + +   R
Sbjct: 823  KICHGDSLWCAFYELSCKKVIGVHKDAETAYVDAVRFIGHANKGQKSIQRKASITLRFPR 882

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
                GDK + RHG KG++S + P  DMPF + G   DI++NP   PSRM +G + E+  G
Sbjct: 883  NPVIGDKFSSRHGQKGVLSVLWPECDMPFTESGITPDILINPHAFPSRMTIGMLVESMAG 942

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             +    G         +  + +                                      
Sbjct: 943  KSASLQGNHQDGTPFIFHGDCNA------------------------------------- 965

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                          +   S L  A  +  G   +Y G +G      + +G +Y  +L HM
Sbjct: 966  -------------IDYFGSQLCAAGYEYFGSEAVYSGFSGLLVRMQIFIGVVYYQRLRHM 1012

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
            VSDK   RSTG    +T QP+ G+   GG RLGEME   + A+G A++L + L   SD  
Sbjct: 1013 VSDKSQVRSTGPVHQLTHQPIKGRKRHGGIRLGEMERDALLAHGVAFLLHDRLVFCSDGH 1072

Query: 1323 VGR 1325
              R
Sbjct: 1073 RAR 1075



 Score = 49.7 bits (117), Expect = 0.004,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 69/251 (27%), Gaps = 92/251 (36%)

Query: 33  QKASYDHFLMM-------NIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDP 83
              S++ F+          + P +   EG         P         + F   S     
Sbjct: 11  HIQSFNQFMDETLAIGVTGVPPQKFVLEG---------P---SKERLHVSFCVASVNIGH 58

Query: 84  PK-----------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
           P                +     +TY+ P+ +T    V         +S          +
Sbjct: 59  PTVLDDDFVSVIHLTPRESRECKVTYSAPMDVTFECCVDGRTVEIFTRS----------I 108

Query: 133 GDLPLMT------------------------KDGTFVIKGIQRIV-VSQLH--------- 158
           G LP+M                           G F++ G+++I+ + Q+          
Sbjct: 109 GHLPIMVLSHRCHLWGLKKNGLISSREEDFEYGGYFIVNGLEKILRLLQVVPMRNMALAI 168

Query: 159 -----RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-- 211
                R+ G  F         +      C I         + + S   + +R+  R++  
Sbjct: 169 KRPAYRNRGTFFTEYAVMMRCARPDQSTCTI--------TLHYLSNGTLRLRVSIRKQEM 220

Query: 212 -VPVTSFLMAL 221
            +P+   L AL
Sbjct: 221 MIPLCIILKAL 231


>gi|89888220|gb|ABD78653.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888227|gb|ABD78656.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888234|gb|ABD78659.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888241|gb|ABD78662.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888248|gb|ABD78665.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888262|gb|ABD78671.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
          Length = 280

 Score =  266 bits (681), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 170/277 (61%), Positives = 219/277 (79%)

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR+N YGF+ETPYRK+ DGKV++ + YLSA+EE +  IAQAN++LD +G F ++LV CR
Sbjct: 3   YARLNEYGFLETPYRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDAEGHFVDDLVACR 62

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
            AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E 
Sbjct: 63  EAGETMLTSPVNVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEK 122

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ 
Sbjct: 123 PLVGTGVERTVAVDSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYT 182

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQNT +NQRP+VK GD V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+L
Sbjct: 183 RSNQNTNINQRPIVKRGDRVSKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSIL 242

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ISER+V++D +TS+HIEE  V+ARDTKLGPEEITRDI
Sbjct: 243 ISERVVADDRYTSVHIEELTVVARDTKLGPEEITRDI 279


>gi|110618403|gb|ABG78830.1| RNA polymerase beta subunit [Bartonella sp. CL6416co]
          Length = 276

 Score =  266 bits (681), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 198/275 (72%), Positives = 233/275 (84%)

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
           R+GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I
Sbjct: 1   RIGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEI 60

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN Y
Sbjct: 61  THKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKY 120

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++
Sbjct: 121 GFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLM 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
            PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGM
Sbjct: 181 APRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGM 240

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           E++VA+ SGAA+ AKRAGIV+QVDA RIVIR+ E 
Sbjct: 241 EAIVARDSGAAVGAKRAGIVDQVDATRIVIRATED 275


>gi|296421900|ref|XP_002840501.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636719|emb|CAZ84692.1| unnamed protein product [Tuber melanosporum]
          Length = 422

 Score =  266 bits (681), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 126/322 (39%), Gaps = 55/322 (17%)

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQD--EKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
            GF+   +          R  W +    D    + + V      +    S      + ++ 
Sbjct: 77   GFETKFIFGKAYQRIGIRQDWLRIVDMDGLPTIGQLVRDGDAVFIYRGSEDAYIDEVRLL 136

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              + GD  P   ++ + +   + RP   GDK + RHG KG+ S+  P  DMPF + G   
Sbjct: 137  GSEGGDSKP---MQEISIKYRIPRPPNIGDKFSSRHGQKGVCSQKWPSIDMPFTESGMQP 193

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP   PSRM +G   E+  G +    G    S    +      +            
Sbjct: 194  DIIINPHAFPSRMTIGMFVESLAGKSGALHGIAQDSTPFRFDEENTAA------------ 241

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  +     L++A  +  G   +Y 
Sbjct: 242  --------------------------------------DYFGHQLKVAGYNYHGNEPMYS 263

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE     + +G +Y  +L HMV+DK   R+TG  S +T QP+ G+   GG R+GEME
Sbjct: 264  GITGEELHADIYIGVVYYQRLRHMVNDKYQVRTTGKISELTHQPIKGRKKGGGIRVGEME 323

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD 1320
               + A+G A++LQ+ L   SD
Sbjct: 324  RDSLLAHGGAFLLQDRLFNCSD 345


>gi|269930889|gb|ACZ54179.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 284

 Score =  266 bits (681), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 205/285 (71%), Positives = 239/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|255927066|gb|ACU40918.1| RNA polymerase beta subunit [Pantoea sp. A18/07]
          Length = 275

 Score =  266 bits (681), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 166/274 (60%), Positives = 211/274 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANAQLDENGGFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           AKR G V+ VDA RIVI+  E ++ P  +G+DIY
Sbjct: 242 AKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIY 275


>gi|269930825|gb|ACZ54147.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 284

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 205/285 (71%), Positives = 239/285 (83%), Gaps = 1/285 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYRL K
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQK 284


>gi|67968293|dbj|BAE00193.1| RNA polymerase beta chain [Selaginella uncinata]
          Length = 1071

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 135/536 (25%), Positives = 197/536 (36%), Gaps = 55/536 (10%)

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +    R T +  EE T D  +V      N         G     G    G+I     +  
Sbjct: 585  YTDGERTTSVNGEE-TIDTESVMYRSPNNSTRVHQRPNGRFGKGGFPRKGQIAADSGAAE 643

Query: 907  TPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNERSISVEREQI 964
              E    +         +  ++   VP+       D     +    +   R       +I
Sbjct: 644  GGESASGINISTAYTPREGHNSEDSVPTSERPAFGDTYTSIHTEKYEMEARVTPQGTAEI 703

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                    D+  +   +       +  G    +G     K T  + +   + P S   Q 
Sbjct: 704  ITGEIPHSDDYFLRHSDESG---LVSPGSRVETGDVSVGKPTPRNPEESPKAPESNLPQA 760

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                     ++ + +       +    R  +             G  RVV  +    R  
Sbjct: 761  VPG-----IDITAARETCPRVPTGGRGRIIDVKWIYPED---TSGHTRVVHAYAPQARET 812

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDK AGRHGNKGI  +I P +DMP L+DGT +D++L+P GVP RMNVGQI E   G A
Sbjct: 813  QVGDKAAGRHGNKGITPKIAPRQDMPHLQDGTSIDMILSPSGVPPRMNVGQISERVPGPA 872

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                 +  + + +D +   +    +    +       T      +               
Sbjct: 873  GYHPERHHRIIPSDERYEREAPR-KPVFPETYEASEQTANPRSLE--------------- 916

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                   L   G+S   DG TGE  ++PVT G  +M K  H   
Sbjct: 917  -----------------------LGNPGKSRPIDGRTGEVSEQPVTAGKAHMPKSVHQAD 953

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
             K +ARS+G +  VTQQPL GKS +GGQR+GEMEV   +  G +++ QEM T K D V  
Sbjct: 954  GKTHARSSGPHPRVTQQPLKGKSKQGGQRMGEMEVRAPEGSGVSHIPQEMPTTKPDHVQA 1013

Query: 1325 RTRVYESIVAGNDT--FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            R  V  +IVAG      ET TPES    V+E + L   +DL     +         
Sbjct: 1014 RREVVGTIVAGEPVYGPETTTPESPRSPVREPRRLAPDLDLAVVEKELIPNNRSRE 1069



 Score =  250 bits (639), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 175/560 (31%), Positives = 272/560 (48%), Gaps = 18/560 (3%)

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           + ++  +GR   N + + D P +      +D+ A     + +  G GT+DD D+  NRR+
Sbjct: 250 RSEIGEIGRANSNKKPDPDVPKNEIFPLPKDVSAATDHSIGIGIGIGTLDDTDHPKNRRI 309

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQL 522
           R+  +  ++Q R    R    ++  IS           + + N+ P  + + EF  S   
Sbjct: 310 RTAADSSQDQSRSASERPADPMRGGISRAARRKNVSTMRGVANSSPSSTTLKEFSGSHPP 369

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            Q  +  N  +++ H R+ S+ G GG  R  A  ++RD+HP+HYGR  P  TSEG N G 
Sbjct: 370 PQSPDQTNPSTQMVHKRKPSSPGPGGPTRRTASSQVRDIHPSHYGRARPIGTSEGTNAGP 429

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDV--VYLSAMEEENRYIAQANSSLDEDGSF 640
           + S    A VN +G+  +P  ++       D+   Y+SA +E    I     S       
Sbjct: 430 IPSSALHADVNHWGYSTSPSHRISGVSSGGDIAAAYVSAEDE-GSRITTGTCSSVYRKDR 488

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            E+ +  R   E +   R++I      P Q     A LIP  E++D+NR   G N QRQA
Sbjct: 489 GEQAIEARYRQESVTPARDQIHSRSIPPSQNPPAGAPLIPSPESNDANRTPTGSNTQRQA 548

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            PLL++E   VGTG+E  +A      I A + G  +  D  R    + E  +D  +    
Sbjct: 549 APLLRSEQRIVGTGLEGQIASDPRDTITAAQGGKTDYTDGERTTSVNGEETIDTES---- 604

Query: 761 IYRLMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               + ++  N +T V+QRP  +   G   R+  I AD  + + G+ A G N+  A+ P 
Sbjct: 605 ----VMYRSPNNSTRVHQRPNGRFGKGGFPRKGQIAADSGAAEGGESASGINISTAYTPR 660

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNVSEEGLKNID 877
            G+N EDS+  SER    D +TSIH E++E+ AR T  G  E IT +IP+  +  L++ D
Sbjct: 661 EGHNSEDSVPTSERPAFGDTYTSIHTEKYEMEARVTPQGTAEIITGEIPHSDDYFLRHSD 720

Query: 878 ECGIICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           E G++  G+ V  GD+ VGK TP+   ESP  PE  L +A+ G      R+T  RVP+G 
Sbjct: 721 ESGLVSPGSRVETGDVSVGKPTPRNPEESPKAPESNLPQAVPGIDITAARETCPRVPTGG 780

Query: 936 SGTVVDVRIFNRHGIDKNER 955
            G ++DV+         + R
Sbjct: 781 RGRIIDVKWIYPEDTSGHTR 800



 Score =  110 bits (275), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 60/296 (20%), Positives = 110/296 (37%), Gaps = 39/296 (13%)

Query: 21  PEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYE 80
            E+  +PD  E Q  ++   +      +   + G Q   + + P   F G        Y 
Sbjct: 7   REMFVMPDPGEAQSEAFSRSINRGSMEEPNDSPGTQDTDREIGP-RPFDGR-------YH 58

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK----EQSIYMGDLP 136
              P  D      RD  Y          I +  + +   +S +  K    EQ +Y G  P
Sbjct: 59  VIEPLSD-----ERDAVYES--------IAYPPESYVLPRSTRKGKACAGEQIVYTGSTP 105

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF 196
           L +  GT V+ GI R+ ++Q+ RSPG    H       SG  +Y    IP +G     E 
Sbjct: 106 LTSPRGTLVVNGIDRVTINQISRSPG---THHNLERGPSGDPVYTGTTIPSRGGKSKSEP 162

Query: 197 DSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST--FYPKIVYSQRGDFWCFPLSAADL 254
           D K+ I VR+ ++RK P+    +A+G  +++I     +      ++  D W    +  + 
Sbjct: 163 DGKNRIWVRVRKKRKTPIQLPSLAMGSSTKDISDNACYPDTSRETRENDVWSGEHAVPES 222

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK------FLGITSDCLC 304
              +  +    ++     + E  ++ +      + E G           +  + + 
Sbjct: 223 RRLSYGTDEYPELPD---IFEESRQKSPQPRSEIGEIGRANSNKKPDPDVPKNEIF 275


>gi|52694321|emb|CAG38000.1| RNA polymerase beta subunit [Pseudomonas sp. LMG 13965]
          Length = 346

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 184/350 (52%), Positives = 238/350 (68%), Gaps = 9/350 (2%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG
Sbjct: 1   VKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL-----TSFARVNAYGFIET 600
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL         R+        
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLGGLRPHQPVRLPGKPVPRG 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             R+          V +      +R+         ++    +ELV  R   E  +   E 
Sbjct: 121 EGRRCQRRHR----VPVGNRRGGSRHRTGFGRDERQESQLIDELVAVRHLNEFTVKAPED 176

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 177 VTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 236

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
           + SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRP
Sbjct: 237 RDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRP 296

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           LV  GD+V+R DI+ADGPSTD+G+LALG+NM +AFM W+G+NFEDS+ +S
Sbjct: 297 LVSKGDKVQRGDIMADGPSTDMGELALGQNMRIAFMAWNGFNFEDSICLS 346


>gi|83415447|gb|ABC17931.1| RNA polymerase II second largest subunit precursor [Coelomomyces
            stegomyiae]
          Length = 1080

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 125/830 (15%), Positives = 236/830 (28%), Gaps = 162/830 (19%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++ + +                   IN+  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRTFFQKLTKDVGRYFTNCLERSRPFNLNMAINSNTITNGLRYALAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RRL+      + R     + R +H TH+
Sbjct: 62   GNWGDQKKFMETRAGVSQVLNRYTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++     E  +  + +   T ++  +S        
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSIISVGSASEPIHEFLSEW-TTENLEEISPSTIGPNT 176

Query: 627  IAQANSSLDEDGSFTEELV----FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                N +        + LV      R A +         D  +   +          P  
Sbjct: 177  KVFVNGAWIGIHREPDSLVKTLKTLRRATDIDSEVSVVHDIRENELRIYTDPGRICRPLF 236

Query: 683  ENDDSNRVLMGCNMQ----RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
              +++ ++++          +    +      +  G+                   VE +
Sbjct: 237  VVNENQQLVLKKEHILKLSEEDEDAIWGWEKLLINGI-------------------VEYL 277

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            D        +    D            K    ++   +  R   K GD  +        P
Sbjct: 278  DTEEEETVMISMSPDDLAEARGALIFDKSLDRDRTARLKAR---KPGDYCKTWTHCEIHP 334

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +  LG       +  + +P+  +N       S R   +       +  +    +      
Sbjct: 335  AMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVYLTNFQ------ 375

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                             +    +  +        +    +       +   +  + AI  
Sbjct: 376  -----------------LRMDTLANILYYPQKPLVTTRNMQYLRFRELPAGQNAIVAIAA 418

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    I+ R  +D  +++   + E+ E   R+   +    
Sbjct: 419  YSGYNQEDSLIMSQSAIDRGLF-RSIYYRSYVDAEKKTGFTQLEEFERPTRETTLKLRQG 477

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      +  G           K+  L  D      R+                   
Sbjct: 478  SYEKLEDDGFVAPGTRVNGDDIIIGKTAPLPMDHSELGTRT----------------TQT 521

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K    T     E+   + +     GD       + VK+ V   R  Q GDK A RHG KG
Sbjct: 522  KKDVSTGLKSSENGIVDHVMVTTNGD-----GYKFVKIRVRSTRVPQIGDKFASRHGQKG 576

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             V      EDMPF  +G   D+++NP  +PSRM +G + E  LG      G +  +    
Sbjct: 577  TVGMTYRQEDMPFTAEGLTPDLIINPHAIPSRMTIGHLVECLLGKVSSLTGSEGDATPFT 636

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  IS L                           V     +G  +S  +F G     
Sbjct: 637  DVTVQQISDLLR---------------ECGYQQRGFEVMYNGHTGKKLSAQIFLG----- 676

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                                Y  +L HMV DK++
Sbjct: 677  ----------------------------------PTYYQRLKHMVDDKIH 692



 Score = 58.5 bits (140), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            +RS G   ++T+QP+ G+S  GG R 
Sbjct: 1055 SRSRGPLQILTRQPVEGRSRDGGLRF 1080


>gi|218195684|gb|EEC78111.1| hypothetical protein OsI_17620 [Oryza sativa Indica Group]
          Length = 1177

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/423 (21%), Positives = 142/423 (33%), Gaps = 89/423 (21%)

Query: 978  LDRNIY-SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            L+R ++ +        +    G  G  K   +   +     +S+  +    D+     V 
Sbjct: 808  LERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVG 867

Query: 1037 SLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKVFVAMKRPIQS 1086
            +     +      S   +    K++  + G            G    V V +   R    
Sbjct: 868  ASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-VTLRQVRSPCL 926

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+ E  LG    
Sbjct: 927  GDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQLLEAALGKGIA 986

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G                                                      +  
Sbjct: 987  LGGT-----------------------------------------------------MRY 993

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TP F  A  + I   L  A     G   + +G TGE     + +G  +  +L HM  DK
Sbjct: 994  ATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFYQRLIHMAEDK 1052

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV 1322
            V  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L + SD     V
Sbjct: 1053 VKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLFMLSDFSQMHV 1112

Query: 1323 VG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                 R   V    V G                +      P    +L +E+ ++G+ +  
Sbjct: 1113 CQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQELFSMGICLRF 1172

Query: 1364 ENS 1366
            E  
Sbjct: 1173 ETE 1175



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 97/740 (13%), Positives = 214/740 (28%), Gaps = 146/740 (19%)

Query: 14  RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
           R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 68  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 117

Query: 57  AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
             F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 118 ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 177

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
              +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 178 ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 237

Query: 140 ----------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS------GK 177
                             G F+IKG++++ ++Q  +     +  D+    +S       +
Sbjct: 238 NLCWLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRR 297

Query: 178 LLY-------------ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
            +Y               +II      +         ++        +P+     ALG+ 
Sbjct: 298 RIYIKLIDSANNEDASGGKIIS-----ISF-------LYA------NMPIWLMFFALGIS 339

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           S+ +I      +   +   +     +  +D +      S        E +  S       
Sbjct: 340 SDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQYVDELIKNSKFPPAEP 399

Query: 284 LLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + +     +          G  V   ++   TG+   +  D    K L+       
Sbjct: 400 FDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKCDNKDDFRNKRLDLAGELLG 458

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R++   ++               +  ++ ++    +   +    ++      S  +    
Sbjct: 459 RELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKR 517

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
           +     +    R    +++  D     + +         +       GK   +   D   
Sbjct: 518 NERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGEN 577

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              V+++        R+    ++R I   ++ +          I  + V      F    
Sbjct: 578 CGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL--------HEIPTEEVPRMDKIFLNGD 629

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +    +  + + R+   RR   +      +         V       + P    E  N 
Sbjct: 630 WVGSCSDPASFVLRLRCMRRSGLIDPQVEIKWDKHQREVRVFSDAGRILRPLLVVENLNK 689

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                 +S++                       + ++   EEE+   A    +L E    
Sbjct: 690 IRRPKGSSYS--------------FQWLMQQEIIEFIGVEEEEDIRSAWGIRNLFES-EE 734

Query: 641 TEELVFCRCAGEEILVPREK 660
              +V    A +   V R+ 
Sbjct: 735 EAPMVKMNKAEDVFNVKRKI 754



 Score = 91.3 bits (225), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 88/613 (14%), Positives = 190/613 (30%), Gaps = 55/613 (8%)

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           +   G+I   +    +       F   I     ++      +    +  V +        
Sbjct: 311 DASGGKIISISFLYANMPIWLMFFALGISSDKDIFDVINMED---CDACVINTITATIKE 367

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             ++    R  D +   V + +     F   +     + +                  + 
Sbjct: 368 SDELCEGFRKSDKARQYV-DELIKNSKFPPAEPFDDYIAKYLFPSISGNRN-------KA 419

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI---KERI 490
             +  ++K L+    GK   D+ D+  N+R+   GE+L  + R  +   ER +    +R 
Sbjct: 420 LFLGYMVKCLLMAFTGKRKCDNKDDFRNKRLDLAGELLGRELRAHIRHAERLMVKALQRD 479

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT-HTRRLSALGQGGV 549
            + + +       ++A  + + +   F +       +     + I    RR + L     
Sbjct: 480 LNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISD 539

Query: 550 ARARAGV--------EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            R             + R  +P+++G++C   T +G N GLV +L   A V++       
Sbjct: 540 LRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGENCGLVKNLAVTATVSSRVAPPLI 599

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            R +      N +  +   E         N       S     V          +     
Sbjct: 600 DRFIS--CGMNKLHEIPTEEVPRMDKIFLNGDWVGSCSDPASFVLRLRCMRRSGL----- 652

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
                 P+  +             D+ R+L    +      + +              + 
Sbjct: 653 ----IDPQVEIKWDKHQREVRVFSDAGRILRPLLVVENLNKIRRP-----------KGSS 697

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            S   ++ +       V+     IRS  G  +   S  +   ++K  ++     V ++  
Sbjct: 698 YSFQWLMQQEIIEFIGVE-EEEDIRSAWGIRNLFESEEEA-PMVKMNKAEDVFNVKRKIG 755

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            +V       +I+     T          M        G N EDS++++   +   +F +
Sbjct: 756 GEVSGYTHYQNILLGERMTLPDQSISMAKMQYGSECSSGVNQEDSLVMNRASLERGMFRT 815

Query: 842 IHIEEFEVMARDTKL--------GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            H   ++    +             ++I           + N+D+ G+  VGA +  GDI
Sbjct: 816 EHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVGASLQSGDI 875

Query: 894 LVGKITPKGESPM 906
           ++GK++  GE   
Sbjct: 876 VIGKVSESGEDHS 888


>gi|113957204|gb|ABI49108.1| RNA polymerase II second largest subunit [Anaptychia palmatula]
          Length = 707

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 125/827 (15%), Positives = 241/827 (29%), Gaps = 144/827 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + +    ++   +    +    I +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRTLFNKLTKDVEKYLKVCIENNKEFILTLGIKSSTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGEQKEAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V+     +   P+      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCHVSVGTPSDGIVPFLLQRQMESLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
             ++      ++      +  +       V        +      I D  D   + +    
Sbjct: 177  HTSPNATKIFVNGVWVGVHRNPVHLVNAVQTLRRKHVLEPEVSLIRDIRDREFRILTDQG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
              L P F+ ++D+     G  +  +       +   V   M+  V +     I      I
Sbjct: 237  RVLRPLFVVDNDAKSPNCGNLVFNKEHSQRLDDDDSVPFDMDKEVREK---MIFGWNGLI 293

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                     V+  V+ + + +   V   + +   R  Q       P              
Sbjct: 294  ------NEGVVEYVDAEEEETVMIVMTPQDLAMSRQLQAGYALAEP-------------- 333

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMAR 852
               P      +    N       W       SM+  I   ++            ++    
Sbjct: 334  --DPDEPNRRVTAPINPTAH--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 389

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G           +           +  +             +       +   +  
Sbjct: 390  KQAMGXXXXXXXXRMET-----------MSHILYYPQKPLATTRSMEYLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGTNVLERFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L E   I+ G           K+  ++ D      R++         
Sbjct: 495  SDTLKLKHGTYDKLDEDGLIIPGARVSGEDIIIGKTAPIAPDAEEMGQRTKLHTKRDAST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     L  Q                             LR VKV +   +  Q GDK
Sbjct: 555  PLRSTESGLVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 655  FEGD-----------------------------------------------------ATP 661

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
             F     ++++ +LR       G  ++Y+G TG      V +G  Y 
Sbjct: 662  -FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYY 707


>gi|323434950|gb|ADX66435.1| RNA polymerase beta subunit [uncultured Bartonella sp.]
          Length = 284

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 204/285 (71%), Positives = 237/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DG+VT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID
Sbjct: 121 RKIVDGRVTKEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRDHID 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|120561249|gb|ABM27009.1| RNA polymerase II second largest subunit [Mucor hiemalis]
          Length = 884

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 130/857 (15%), Positives = 235/857 (27%), Gaps = 157/857 (18%)

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
                 +      +I  L+     +  +DD D+ G +R+   G ++   +RL   ++ + +
Sbjct: 165  KTETRKSYFFGYMIHRLLLAALERRELDDRDHYGKKRMDLAGVLMSGLFRLLFKKLTKDV 224

Query: 487  --KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNS 531
                +              + +  + + +     +               +SQ+      
Sbjct: 225  AKYLQKCIESSREFNLTLAVKSNTITNGLKYSLATGNWGDQKKAAQARAGVSQVLNRYTF 284

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
             S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L   + 
Sbjct: 285  ASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSY 340

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            ++  G   TP     +     ++  LSA    +      N           EL+      
Sbjct: 341  IS-VGSAATPLIMFLEEWAMENLEELSATSIADATKVFVNGVWIGIHRDPGELINSLKQM 399

Query: 652  EE-ILVPREKIDFIDASPK---QVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKA 706
               + +  E     D   K             P FL  +   R+     M+ Q       
Sbjct: 400  RRSVDISPEVSIVRDIREKELRMYTDAGRCCRPLFLVENQQLRLNREHIMRIQDTEDDFG 459

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                +  G+                   VE VDA       +    +         +   
Sbjct: 460  WQDMIADGI-------------------VEYVDADEEETAMICMTPEDLAESRMTAQYGA 500

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
              +  ++     +   + G            PS  LG       +  + +P+  +N    
Sbjct: 501  PLQETRDLASRVKS--QTGSYSHTWTHCEIHPSMILG-------ICASIIPFPDHNQ--- 548

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
               S R   +       +  +    +                            +  +  
Sbjct: 549  ---SPRNTYQSAMGKQAMGVYLTNFQTRM-----------------------DTLANILY 582

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 583  YPQKPLTTTRSMEFLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFF 641

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D  +++  +  E+ E   RD                  I  G           K+ 
Sbjct: 642  RTYMDAEKKAGMMFMEEFEKPTRDSTLRLKHGTYEKLEDDGLIAPGTRVSGDDIIIGKTA 701

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             + +D      R+           ++     +  Q                         
Sbjct: 702  PIPADSEELGQRTTTHNKRDASTPLRSTETGIVDQVML--------------------TT 741

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV V   R  Q GDK A RHG KG +      ED PF  +G   D+++NP  
Sbjct: 742  NQDGLKFVKVRVRSTRVPQMGDKFASRHGQKGTIGMTYRQEDFPFSAEGITPDLIINPHA 801

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +G + E  LG      G +  +          IS                    
Sbjct: 802  IPSRMTIGHMIECLLGKVSTLTGNEGDATPFTDVTVEAIS-------------------- 841

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                   L+       G  V    F G                                +
Sbjct: 842  -----QALQAQGYQSRGFEVMYNGFTG-----------------------------RKLN 867

Query: 1247 RPVTVGYIYMLKLNHMV 1263
              V +G  Y  +L HMV
Sbjct: 868  VQVFLGPTYYQRLKHMV 884



 Score =  100 bits (249), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 91/752 (12%), Positives = 205/752 (27%), Gaps = 91/752 (12%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           VP+     ALG  ++ ++L          +  +     +  A ++    V+   +    G
Sbjct: 76  VPIVIVFRALGQVADRDVLEHICYDRNDYEMLELLKPSIEEAFVIQDQDVALDFIGKR-G 134

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
             V  + ++      + L+++ +  +G               +      + + A +  + 
Sbjct: 135 TTVGATRERRIKYASEILQKELLPHVGTAYKTETRKSYFFGYMIH---RLLLAALERREL 191

Query: 331 KSLEEIFHSEIRDIPILYVDSVNN-NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
              +      +    +L           +   +     K  + +      +    +  T 
Sbjct: 192 DDRDHYGKKRMDLAGVLMSGLFRLLFKKLTKDVAKYLQKCIESSREFNLTLAVKSNTITN 251

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLR 447
            +  S+    + D  K   +  G  ++  R    +      R          I     L 
Sbjct: 252 GLKYSLATGNWGDQKKAAQARAGVSQVLNRYTFASTLSHLRRCNTPIGRDGKIAKPRQLH 311

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
           N    +         +      ++KN   +  + +  +    I  ++  ++   + ++A 
Sbjct: 312 NTHWGLVCPAETPEGQACG---LVKNLALMSYISVGSAATPLIMFLEEWAMENLEELSAT 368

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            +  A   F     +    +    ++ +   RR   +            +   ++     
Sbjct: 369 SIADATKVFVNGVWIGIHRDPGELINSLKQMRRSVDISPEVSIVRDIREKELRMYTDAGR 428

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              P    E   + L        +     F         D      V Y+ A EEE   I
Sbjct: 429 CCRPLFLVENQQLRLNREHIMRIQDTEDDFG------WQDMIADGIVEYVDADEEETAMI 482

Query: 628 AQANSSLDEDGSFT-------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                 L E            E          +           +  P  ++ I AS+IP
Sbjct: 483 CMTPEDLAESRMTAQYGAPLQETRDLASRVKSQTGSYSHTWTHCEIHPSMILGICASIIP 542

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                   + A I+      +    +
Sbjct: 543 FPDHNQSPRNTYQSAMGKQAMGVYLT---------NFQTRMDTLANILYYPQKPLTTTRS 593

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +  +          +   +  Y              NQ                    S 
Sbjct: 594 MEFLRFRELPAGQNAIVAILCYSG-----------YNQE------------------DSV 624

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +   ++ R +  +       + E    +            + +EEFE   RD+      
Sbjct: 625 IMNQSSIDRGLFRSLFFRTYMDAEKKAGM------------MFMEEFEKPTRDS------ 666

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                  +     + +++ G+I  G  V+  DI++GK  P         ++         
Sbjct: 667 ----TLRLKHGTYEKLEDDGLIAPGTRVSGDDIIIGKTAPIPADSEELGQRT-------T 715

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             + RD S  + S  +G V  V +       K
Sbjct: 716 THNKRDASTPLRSTETGIVDQVMLTTNQDGLK 747


>gi|86161664|gb|ABC86967.1| RNA polymerase beta subunit [Bartonella bovis]
 gi|86161674|gb|ABC86972.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 284

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 207/285 (72%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|317016962|gb|ADU86030.1| RNA polymerase beta-subunit [Bartonella sp. R4(2010)]
          Length = 284

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 207/285 (72%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|320202799|emb|CBZ01636.1| RNA polymerase beta-subunit [Mycobacterium sp. BFLP-6]
          Length = 238

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 92/222 (41%), Positives = 122/222 (54%), Gaps = 34/222 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPF+ DG
Sbjct: 43   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAVEDMPFMPDG 102

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +     S L   L   
Sbjct: 103  TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIQVAEGATEVPAWASKLPEELRSA 161

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                                          V+TPVFDGA E  +  +L     +      
Sbjct: 162  EPNSI-------------------------VATPVFDGAREGELEGLLGSTLPNRDGDVM 196

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V DK++A
Sbjct: 197  VNAEGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHA 238



 Score = 47.0 bits (110), Expect = 0.023,   Method: Composition-based stats.
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KGE+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   KGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 51


>gi|227937616|gb|ACP43383.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 284

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 207/285 (72%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDGEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL K
Sbjct: 241 DSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQK 284


>gi|222629653|gb|EEE61785.1| hypothetical protein OsJ_16357 [Oryza sativa Japonica Group]
          Length = 1185

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/423 (21%), Positives = 142/423 (33%), Gaps = 89/423 (21%)

Query: 978  LDRNIY-SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            L+R ++ +        +    G  G  K   +   +     +S+  +    D+     V 
Sbjct: 816  LERGMFRTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVG 875

Query: 1037 SLKVQYE---TSKSILEDRFKNKIEKIQWG-------DDMPPGVLRVVKVFVAMKRPIQS 1086
            +     +      S   +    K++  + G            G    V V +   R    
Sbjct: 876  ASLQSGDIVIGKVSESGEDHSIKLKHTEKGMVQRVLLSANDEGKNFAV-VTLRQVRSPCL 934

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK +  HG KG+V  +   E+ PF   G   DIV+NP   P+R   GQ+ E  LG    
Sbjct: 935  GDKFSSMHGQKGVVGFLESQENFPFTYQGIVPDIVINPHAFPTRQTPGQLLEAALGKGIA 994

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G                                                      +  
Sbjct: 995  LGGT-----------------------------------------------------MRY 1001

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TP F  A  + I   L  A     G   + +G TGE     + +G  +  +L HM  DK
Sbjct: 1002 ATP-FTTASFDVITDQLHKAGFSRWGAESVLNGRTGERMHSLIFMGPTFYQRLIHMAEDK 1060

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV 1322
            V  R+TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L + SD     V
Sbjct: 1061 VKFRNTGPVHPLTRQPVADRKRFGGVKFGEMERDCLLAHGAAANLHERLFMLSDFSQMHV 1120

Query: 1323 VG---RT-RVYESIVAG---------------NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                 R   V    V G                +      P    +L +E+ ++G+ +  
Sbjct: 1121 CQTCERVANVIMRPVPGGKKIRGPYCGFCRSSENIVRINVPYGAKLLYQELFSMGICLRF 1180

Query: 1364 ENS 1366
            E  
Sbjct: 1181 ETE 1183



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 97/740 (13%), Positives = 214/740 (28%), Gaps = 146/740 (19%)

Query: 14  RKFFGKNPEIIDIPDL-----------------IEVQKASYDHFLMMNIAPDERPNEGLQ 56
           R  + + P  + IP L                 I  Q  SY+ F+            GLQ
Sbjct: 68  RDSYAQIPVDMSIPSLEKFCKEASRSFFDEIGLISHQINSYNEFVS----------HGLQ 117

Query: 57  AAFKS-----VFPITAFSGA-------AMLEFVSYEFDPPKF-----DVDD--------- 90
             F S     V P    S         A+++F   + + P F     D+D+         
Sbjct: 118 ELFDSLGEVTVEPSYDPSNRGPGGWRHAIIKFGRVQLEEPVFWSHGCDIDEQSLKLKPRH 177

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD-------IKEQSIY--MGDLPLMT-- 139
              +++TY+  +K+ +   V+ +++   AK+  D       I  ++ Y  +G LP+M   
Sbjct: 178 ARLQNMTYSSKMKVEVHFQVYSMEKSDKAKTGNDKFGYKRNIINETYYINIGRLPVMVMS 237

Query: 140 ----------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS------GK 177
                             G F+IKG++++ ++Q  +     +  D+    +S       +
Sbjct: 238 NLCWLHKLKESDCQFDSGGYFLIKGMEKVFIAQEQKCLTRIWVEDRPCWMVSFLSPIRRR 297

Query: 178 LLY-------------ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMD 224
            +Y               +II      +         ++        +P+     ALG+ 
Sbjct: 298 RIYIKLIDSANNEDASGGKIIS-----ISF-------LYA------NMPIWLMFFALGIS 339

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           S+ +I      +   +   +     +  +D +      S        E +  S       
Sbjct: 340 SDKDIFDVINMEDCDACVINTITATIKESDELCEGFRKSDKARQYVDELIKNSKFPPAEP 399

Query: 284 LLKSLKEKGVKFLG--ITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
               + +     +          G  V   ++   TG+   +  D    K L+       
Sbjct: 400 FDDYIAKYLFPSISGNRNKALFLGYMVKCLLM-AFTGKRKCDNKDDFRNKRLDLAGELLG 458

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
           R++   ++               +  ++ ++    +   +    ++      S  +    
Sbjct: 459 RELR-AHIRHAERLMVKALQRDLNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKR 517

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLG 460
           +     +    R    +++  D     + +         +       GK   +   D   
Sbjct: 518 NERCAGIVATLRRTNPLQMISDLRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGEN 577

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
              V+++        R+    ++R I   ++ +          I  + V      F    
Sbjct: 578 CGLVKNLAVTATVSSRVAPPLIDRFISCGMNKL--------HEIPTEEVPRMDKIFLNGD 629

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +    +  + + R+   RR   +      +         V       + P    E  N 
Sbjct: 630 WVGSCSDPASFVLRLRCMRRSGLIDPQVEIKRDKHQREVRVFSDAGRILRPLLVVENLNK 689

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
                 +S++                       + ++   EEE+   A    +L E    
Sbjct: 690 IRRPKGSSYS--------------FQWLMQQEIIEFIGVEEEEDIRSAWGIRNLFES-EE 734

Query: 641 TEELVFCRCAGEEILVPREK 660
              +V    A +   V R+ 
Sbjct: 735 EAPMVKMNKAEDVFNVKRKI 754



 Score = 92.1 bits (227), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 87/615 (14%), Positives = 192/615 (31%), Gaps = 51/615 (8%)

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
           +   G+I   +    +       F   I     ++      +    +  V +        
Sbjct: 311 DASGGKIISISFLYANMPIWLMFFALGISSDKDIFDVINMED---CDACVINTITATIKE 367

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             ++    R  D +   V + +     F   +     + +                  + 
Sbjct: 368 SDELCEGFRKSDKARQYV-DELIKNSKFPPAEPFDDYIAKYLFPSISGNRN-------KA 419

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI---KERI 490
             +  ++K L+    GK   D+ D+  N+R+   GE+L  + R  +   ER +    +R 
Sbjct: 420 LFLGYMVKCLLMAFTGKRKCDNKDDFRNKRLDLAGELLGRELRAHIRHAERLMVKALQRD 479

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT-HTRRLSALGQGGV 549
            + + +       ++A  + + +   F +       +     + I    RR + L     
Sbjct: 480 LNSERELQEFDHYLDASIITNGLNRAFSTGSWCHPYKRNERCAGIVATLRRTNPLQMISD 539

Query: 550 ARARAGV--------EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            R             + R  +P+++G++C   T +G N GLV +L   A V++       
Sbjct: 540 LRKTRQRVAYAGKAGDARYPNPSYWGKLCFMSTPDGENCGLVKNLAVTATVSSRVAPPLI 599

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
            R +      N +  +   E         N       S     V          +     
Sbjct: 600 DRFIS--CGMNKLHEIPTEEVPRMDKIFLNGDWVGSCSDPASFVLRLRCMRRSGL----- 652

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
                 P+  +             D+ R+L    +      + + +        + ++ +
Sbjct: 653 ----IDPQVEIKRDKHQREVRVFSDAGRILRPLLVVENLNKIRRPKGSSY--SFQWLMQQ 706

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                I  +    +     IR +  S E       +  +    +K +   + +       
Sbjct: 707 EIIEFIGVEEEEDIRSAWGIRNLFESEEEAPMVKMNKAEDVFNVKRKIGGEVSGYTHLIA 766

Query: 782 VKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             +G  +           P    G     +N +VA     G+N EDS++++   +   +F
Sbjct: 767 DCIGRSEYTFGRKDDFARPEYFNG-----QNAIVAVNVHQGFNQEDSLVMNRASLERGMF 821

Query: 840 TSIHIEEFEVMARDTKL--------GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            + H   ++    +             ++I           + N+D+ G+  VGA +  G
Sbjct: 822 RTEHFRNYKAEVENKGGPGGNKRLKMKDKIDFGKMQSKRGRVDNLDDDGLPYVGASLQSG 881

Query: 892 DILVGKITPKGESPM 906
           DI++GK++  GE   
Sbjct: 882 DIVIGKVSESGEDHS 896


>gi|205289912|gb|ACI02328.1| RNA polymerase beta subunit [Bartonella rochalimae]
          Length = 286

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 202/281 (71%), Positives = 234/281 (83%), Gaps = 1/281 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 7   MERAIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 66

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 67  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 126

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ I
Sbjct: 127 YRKIIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHI 186

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA 
Sbjct: 187 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVAC 246

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
            SGAAI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDIY
Sbjct: 247 DSGAAIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDIY 286


>gi|269913225|emb|CAY86039.1| RNA polymerase beta subunit [Acidomonas methanolica]
 gi|269913229|emb|CAY86041.1| RNA polymerase beta subunit [Acidomonas methanolica]
          Length = 288

 Score =  266 bits (680), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 131/291 (45%), Positives = 175/291 (60%), Gaps = 28/291 (9%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----- 221
           HDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL     
Sbjct: 1   HDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGENS 60

Query: 222 --------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                               GMD +EIL+ FY  + ++     W  P    D   G K+ 
Sbjct: 61  IAARAAKAAAGGDVESLPIRGMDQDEILAYFYGTVPFTHTSKGWSRPFDP-DAFRGQKLL 119

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L D +TGE V E+  KLT+   + + EK  K + +    L G ++A+D+VN  TGEIY
Sbjct: 120 EPLFDAETGEVVAEADAKLTARACRKIAEK-TKDVLVGRADLLGRFIAKDLVNPATGEIY 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            EAG+ + E  L  +  S I ++P+L VD   +  +IRNTL  DKN  R DAL+DIYR+M
Sbjct: 179 AEAGEELTEARLVALEESGITELPMLAVDPA-HGPWIRNTLAVDKNVSRDDALVDIYRIM 237

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           RPG+  T   AE+MF  LFFD D+YDLS VGRVKMNMRL +D PD +R +R
Sbjct: 238 RPGEPPTPETAEAMFQGLFFDHDRYDLSAVGRVKMNMRLEVDVPDTMRVLR 288


>gi|113957802|gb|ABI49123.1| RNA polymerase II second largest subunit [Teloschistes exilis]
          Length = 709

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 139/830 (16%), Positives = 242/830 (29%), Gaps = 146/830 (17%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L + +R+   ++ + I +  +              +    + S +     + 
Sbjct: 1    RLDLAGPLLASLFRMLFQKLTKDIYKYLQKCVESNREFNLTLGVKQNTISSGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGDQKKAAQAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     ++     E  T Y      +V  +            
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCFISVGSPAEPITDYLIQRGMEVLEEYEPTRMPNATKV 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN 684
            ++      +  D +     V        IL     + D  D   K          P    
Sbjct: 177  FVNGVWVGVHHDPAHLVPNVQELRRKGIILHEASLVRDIRDREFKIFTDAGRVCRPLFVV 236

Query: 685  DDSNRVLMGC--NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            D+  +        + ++ V  ++ E   V T      A+ S        +G +E VDA  
Sbjct: 237  DNDPKSGNAGYLALTKEMVQRVEDERDTVITMDREERAEQSIGWQGLVDSGAIEYVDAEE 296

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +       +        SN++   NQR    V             PS  L
Sbjct: 297  EETIMIAMTPEDLEISRHVQAGYPMPESNEDA-PNQRVKAPVNPTAHTWTHCEIHPSMIL 355

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +                        
Sbjct: 356  G-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV---------------------- 386

Query: 863  RDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                      L N DE    +  +             +       +   +  + AI    
Sbjct: 387  ---------FLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 437

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R  +D  +R        +E   R    E + L  
Sbjct: 438  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYVDTEKRVGM---TVLEKFERPLRSETLKLKH 493

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+T ++ D                +E  QR    
Sbjct: 494  GTYDKLDDDGLVAPGVRVSGDDVIIGKTTPIAPD---------------AEEMGQRTKNH 538

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +K    T     E+   +K+             L+ VKV +   +  Q GDK A RHG K
Sbjct: 539  IKKDTSTPLRSTENGIVDKVLL-----STNSEGLKFVKVRMRTTKVPQIGDKFASRHGQK 593

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 594  GTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPF 653

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 654  TEITVDSVSKLLR--EHGYQSRGFEVM--------------------------------- 678

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                         +G +    G         V +G  Y  +L HMV DK+
Sbjct: 679  ------------YNGHT----GR---KLVVQVFLGPTYYQRLRHMVDDKI 709


>gi|124491193|gb|ABN12931.1| RNA polymerase beta chain [Agrobacterium rubi]
          Length = 237

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 141/238 (59%), Positives = 182/238 (76%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KD+++ RIDRRRK+P TS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDVVYARIDRRRKLPATSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EILSTFY K  Y + G+ W +P    D++ GAK  + LVD DTGE V+E+GKKLT  L++
Sbjct: 61  EILSTFYTKANYVRDGEGWRYPYQP-DVLKGAKAITELVDADTGEVVVEAGKKLTPRLIR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            + +KG+KFL  +++ L G Y+AEDIVN ETGEIY+EAGD IDEK+L+ I  S   +IPI
Sbjct: 120 QMSDKGLKFLKASNEDLYGNYLAEDIVNYETGEIYLEAGDEIDEKTLKLILDSGFDEIPI 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D +N  AYIRNTL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFDS+
Sbjct: 180 LNIDHINVGAYIRNTLAADKNENRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDSE 237


>gi|148357793|gb|ABQ59232.1| RNA polymerase beta subunit [Bartonella tamiae]
          Length = 291

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 210/289 (72%), Positives = 242/289 (83%), Gaps = 1/289 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT DVVYLSAMEE   Y+AQANSSLD +  FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTDVVYLSAMEESKHYVAQANSSLDAEARFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           AI A+RAGIV+QVDA RIVI + E  LDP+ SGVDIYRL KFQRSNQ+T
Sbjct: 241 AIGARRAGIVDQVDATRIVIHATED-LDPTKSGVDIYRLQKFQRSNQST 288


>gi|8474|emb|CAA35185.1| RNA polymerase 3, second largest subunit [Drosophila melanogaster]
          Length = 1129

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 126/350 (36%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          ++V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPTKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 94/617 (15%), Positives = 216/617 (35%), Gaps = 76/617 (12%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYESDQYYVSCVQAMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D      + R ++ + L+          + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILRERVMIHLDTYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    + ++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSSMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  A+  F  +              S L  + E++N +  ++
Sbjct: 408 DALVTSAVMTQCMRQAGGVGRAIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIE-----TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
             +       +         ++  YL    E+   +      L        E +      
Sbjct: 525 DPKLVKAIPKHLIDMGMMPLSNRRYLG---EKLYVVFLDGKHLGHIHQSEAEKIV----- 576

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEA 708
                  +++ +          +    IPF +N              + R    L     
Sbjct: 577 -------DELRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYIATGPARLMRPVWNLKWKRV 629

Query: 709 PFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            ++GT   +   +A  +          +          + ++    D + S  ++Y+   
Sbjct: 630 EYIGTLEQLYMEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQM 689

Query: 767 FQRSNQNTCVN--QRPLVKVGDEVRRNDIIA---DGPSTDLGDLALGRNMLVAFMPWHGY 821
            +++    C+N  ++   K+         +          L D A+G N +VA + + GY
Sbjct: 690 GKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDIIQLDDFAMGTNAIVAVISYTGY 749

Query: 822 NFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           + ED+M+I++        + SI+  +F  + + +                E +K++D  G
Sbjct: 750 DMEDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELIKHLDTDG 803

Query: 881 IICVGAEVNPGDILVGK 897
           +   G++++ G  L   
Sbjct: 804 LPHPGSKLSYGSPLYCY 820


>gi|291168943|gb|ADD81876.1| RNA polymerase beta subunit [Candidatus Bartonella antechini]
          Length = 284

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 207/285 (72%), Positives = 239/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIVDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDNVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR G+V+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAIGAKRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|119644141|gb|ABL85608.1| RNA polymerase II second largest subunit [Punctelia rudecta]
          Length = 718

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 129/838 (15%), Positives = 243/838 (28%), Gaps = 144/838 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P    D+  R     N+         L      +  T  +       G   + K  
Sbjct: 237  RVCRPLFVIDNDPRSSNRGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKE- 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +        +N +  +N+R    +        
Sbjct: 296  GVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   + +  +E    
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM- 404

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 405  --------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                           V     +G  + T 
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGKKLVTQ 699

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            VF                                       +G  Y  +L HMV DK+
Sbjct: 700  VF---------------------------------------LGPTYYQRLRHMVDDKI 718



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 85/625 (13%), Positives = 174/625 (27%), Gaps = 115/625 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 15  GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 191

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 192 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 251

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +                  E              V Y+ A EEE   I
Sbjct: 252 SNRGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMI 311

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 312 VMTPEDLEISRQLQAGYAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 371

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +         T  E  +   +                
Sbjct: 372 PFPDHNQSPRNTYQSAMGKQAMGVFL-------TNYEQRMDTMANIL------------- 411

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                                 Q+PL                  
Sbjct: 412 -----------------------------------YYPQKPL----------ATTRSMEF 426

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 427 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVV 486

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   +       +D+ G++  G  V+  DI++GK  P         ++   
Sbjct: 487 EQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-- 544

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                K    RDTS  + S  +G V
Sbjct: 545 -----KLHVKRDTSTPLRSTENGIV 564


>gi|242080725|ref|XP_002445131.1| hypothetical protein SORBIDRAFT_07g004600 [Sorghum bicolor]
 gi|241941481|gb|EES14626.1| hypothetical protein SORBIDRAFT_07g004600 [Sorghum bicolor]
          Length = 1251

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 89/356 (25%), Positives = 124/356 (34%), Gaps = 80/356 (22%)

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  +    E   + L    K  ++K+        GV     V +   R    GDK A  H
Sbjct: 950  IGKVSESGEDHSAKLMHTEKGMVDKVVL-SANDDGVN-FATVTLRQSRSPCVGDKFASMH 1007

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG+V  +   E+ PF   G   DIV+NP G P+R   GQ+ E  LG      GK    
Sbjct: 1008 GQKGVVGLLDSQENFPFTCQGIVPDIVINPHGFPTRQTPGQLLEAALGKGIAMGGK---- 1063

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                             V  +TP F   
Sbjct: 1064 -------------------------------------------------VRYATP-FTTP 1073

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              + I   L  A     G+  + +G TGE     V +G  +  +L HM  DKV  R+TG 
Sbjct: 1074 TVDVITEQLHKAGFSRWGEESVLNGQTGERMKSLVFMGPTFYQRLVHMAEDKVKFRNTGP 1133

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV-GRTRVY 1329
               VT+QP+  K   GG + GEME  C+ A+GAA  L E L   SD     +     RV 
Sbjct: 1134 VHPVTRQPVEDKKRFGGVKFGEMERDCMLAHGAAANLHERLFTLSDFSQMHICQACQRVA 1193

Query: 1330 ESI----------VAG---------NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              I          V G                 P    +L +E+  +G+ +  +  
Sbjct: 1194 NVIMRPAEGGSKKVHGPYCMFCRSAERIVRVNVPYGSKLLYQELFCMGICLKFDTE 1249



 Score =  140 bits (353), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 135/977 (13%), Positives = 273/977 (27%), Gaps = 238/977 (24%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---AFS--------GAAMLEFV 77
           L+  Q  SY+ F+            GLQ  F S+  IT    +           A ++F 
Sbjct: 124 LVSHQINSYNQFVS----------HGLQDLFDSLGEITVEPDYDPSNKSGAWKHATIKFG 173

Query: 78  SYEFDPP--------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             E   P              KF       + +TYA  + + +   V+ +D+   AK+ K
Sbjct: 174 RVELSEPVFMVDNLDLEQQDLKFKPRHARLQRMTYASRMNVEMTAQVYILDKSDKAKTGK 233

Query: 124 D---------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVV-- 154
           D          + + + MG LP+M K                   G F+IKG +++ +  
Sbjct: 234 DTHVHRREIMTETKQVSMGLLPVMVKSNLCWLHKLQESDCQFDFGGYFLIKGTEKVFIAE 293

Query: 155 ---------------------SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
                                SQ+ R      +    +   S K   +C++I        
Sbjct: 294 EQRFLSRIWITDYPSWDASYLSQIKR------EKINIKLVPS-KRNESCKVI-------- 338

Query: 194 IEFDSKDIIHV--RIDRRRKVPVTSFLMALGMDSE-------EILSTFYPKIVYSQRGDF 244
                   I+    I     +P+     ALG+ S+       +IL       + +     
Sbjct: 339 -------TIYFMGTI-----IPIWVVFFALGVSSDKEAFDMIDILD--CDASIVNIISST 384

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE--KGVKFLGITSDC 302
                   +       +   VD    +      +     + + +     GV+   +    
Sbjct: 385 IKESHEEFEGFRAPGRACQYVDKLIRKSKFPPKESFDEYVCRYMFPSVNGVRSKALFLGY 444

Query: 303 LCGLYV-------AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           +    +         D  +    +    A  ++  +    I  +E R + ++  D  N+ 
Sbjct: 445 MVKCLLMAYSGNRKCDNKDDFRNKRLGLACQLLRRELWTHIKRAEWRMVKLMQRDLSNDG 504

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                    D +       L+                 S        ++   + +  R  
Sbjct: 505 NLQDLRRYVDASIITNG--LNRAFSTGSWRHPYLKARCSGVVATLRRTNPLQMMSDLRKT 562

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
                      D R+        +  +        G + ++             ++    
Sbjct: 563 RQWVAYSGAVGDARYPNPSFWGKLCFLSTPDGEKCGFVKNLAVTAVVSSVVRKPLIDTFV 622

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             G+ ++                   D I+ + +      F   S L    +      R+
Sbjct: 623 SCGMKKL-------------------DDISLQDISGKDRIFLNGSLLGVCADPHELTLRL 663

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
              RR   +              RD H      +C      G  +  +  + +  R+   
Sbjct: 664 RSLRRSKLIDP-------QVEIKRDKHHKEVRVLCD----PGRILRPLLVVENLRRITRP 712

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                 ++++ D    N V  +   EEE+   A     L                     
Sbjct: 713 KDGLYSFQELIDQ---NIVELIGVEEEEDIQCASGIRHLFSGEKEDR------------- 756

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                    +  P  ++ ++ SLIPF  +D+  RVLM      Q                
Sbjct: 757 --SSGYTHCELDPSFLLGLSCSLIPFANHDNGKRVLMQAEKISQQAIGYSP--------- 805

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                          +       + S    Y             
Sbjct: 806 -------------------------------TNSHTRLDTLSHQIFYPQRP--------- 825

Query: 776 VNQRPLVKVG-DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              + +V  G  +             +  +   G+N +V+     G+N EDS++++   +
Sbjct: 826 -LFKTVVSYGLGKAETAYSFGRKDDFNTPEYFNGQNAIVSINVHQGFNQEDSLVLNRASL 884

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV-----SEEGLKNIDECGIICVGAEVN 889
              +F ++H++ ++    + ++      R+  N          + ++D  G+  VGA + 
Sbjct: 885 ERGMFRTLHLKSYKAQVENKEITRRLKHRESINFGKVQSKRGKVDSLDSEGLPYVGASLQ 944

Query: 890 PGDILVGKITPKGESPM 906
            GDI++GK++  GE   
Sbjct: 945 SGDIVIGKVSESGEDHS 961


>gi|198385434|gb|ACH86036.1| RpoB [Bartonella sp. Cr28647]
          Length = 284

 Score =  266 bits (679), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 205/285 (71%), Positives = 238/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA  
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVACD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|321160842|gb|ADW66606.1| RNA polymerase beta subunit [Bartonella coopersplainsensis]
          Length = 284

 Score =  266 bits (679), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 206/285 (72%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|88601072|gb|ABD46532.1| RNA polymerase II second largest subunit [Vuilleminia comedens]
          Length = 880

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 135/874 (15%), Positives = 251/874 (28%), Gaps = 155/874 (17%)

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+ 
Sbjct: 139  YAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGKKRLD 195

Query: 466  SVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL- 522
              G +L N +R+   ++ R +    +              +    + + +     +    
Sbjct: 196  LAGPLLANLFRMLFRKLTRDVYRYLQKCVETSKEFNISLAVKHNTITNGLKYSLATGNWG 255

Query: 523  ------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                        SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 256  DQKKSMASKAGXSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVC 311

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            PAET EG   GLV +L   + ++   +       + +  + +     +A  +        
Sbjct: 312  PAETPEGQACGLVKNLALMSTISVGSYSAPVIEFLEEWGLESLEE--NAHSQTPCTKVFV 369

Query: 631  NSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
            N            LV      R   +         D  +   +          P    ++
Sbjct: 370  NGVWMGVHRDPANLVKTIKQLRRKDDISPEVSVVRDIRERELRIATDAGRVCRPLFIVNN 429

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTG----MESVVAKSSGAAIVAKRAGIVEQVDAIR 742
                L     +++ + LL     +V T      E      S       + G++E +DA  
Sbjct: 430  KELAL-----KKKHIDLLNVGKHYVTTADGVQEEQDYKFDSLV-----KEGVIEYLDAEE 479

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +            I    K    ++      R  ++              PS  L
Sbjct: 480  EETVMICMTPTELDRARRIELGAKPDDEDEEYDPAAR--IETATLAHTWTHCEIHPSMIL 537

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 538  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 572

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              +               +  +             +       +   +  + AI      
Sbjct: 573  FLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIMCYSGY 621

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S V   +    ++ R  +D  ++S   E E+     RD          + 
Sbjct: 622  NQEDSVIMNQSSVDRGLF-RSMYYRSYMDVEKKSGVQELEKFMKPTRDTTLRMKHGTYDK 680

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G N         K+  +  D                +E  QR     +   
Sbjct: 681  IEDDGLIAPGTNVNGEDIIIGKTAPIPPD---------------SEELGQRTRGHTRRDV 725

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             T     E    +++      D       + VKV +   R  Q GDK A RHG KG V  
Sbjct: 726  STPLKSTEQGTVDQVLLTTNAD-----GQKFVKVRIRSTRIPQIGDKFASRHGQKGTVGI 780

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      LG++           
Sbjct: 781  TYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLLGQEGD--------- 831

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     E+++  
Sbjct: 832  --------------------------------------------ATP-FTELTVESVSKY 846

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            LR       G  I+Y G TG+  +  + +G  Y 
Sbjct: 847  LRDRGYQSRGLEIMYHGHTGKKLNAQIYLGPTYY 880



 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 105/771 (13%), Positives = 218/771 (28%), Gaps = 125/771 (16%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +     +   +V 
Sbjct: 63  YIKVD----IPIWIXFRALGVISDRDILEHICYDMQDTQMLEMLKPCIDDGIFVQDREVC 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G     S ++      + L+++ +  + +              +      + 
Sbjct: 119 LDYIGNR-GTTTGLSRERRLXYAQEILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 174

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  +D    + + +
Sbjct: 175 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTRDVYRYLQKCV 224

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F+++ ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 225 ETS--KEFNISLAVKHNTITNGLKYSL-ATGNWGDQKKSMASKAGXSQVLNRYTYASTLS 281

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 282 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSTISVGSYSAP 341

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 342 VIEFLEEWGLESLEENAHSQTPCTKVFVNGVWMGVHRDPANLVKTIKQLRRKDDISPE-- 399

Query: 550 ARARAGVEMRDVHP-THYGRIC-------PAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
                 +  R++   T  GR+C         E +       + ++       A G  E  
Sbjct: 400 VSVVRDIRERELRIATDAGRVCRPLFIVNNKELALKKKHIDLLNVGKHYVTTADGVQEEQ 459

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--- 658
             K         + YL A EEE   I    + LD                E     R   
Sbjct: 460 DYKFDSLVKEGVIEYLDAEEEETVMICMTPTELDRARRIELGAKPDDEDEEYDPAARIET 519

Query: 659 ----EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                     +  P  ++ I AS+IPF +++ S R      M +QA+ +           
Sbjct: 520 ATLAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---- 575

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                                                   + + +  Y       +    
Sbjct: 576 -------------------------------------RMDTMANILYYPQKPLATTRSME 598

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +  R                        +L  G+N +VA M + GYN EDS+++++  V
Sbjct: 599 YLKFR------------------------ELPAGQNAIVAIMCYSGYNQEDSVIMNQSSV 634

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +  + + + +   E            +       I++ G+I  G  VN
Sbjct: 635 DRGLFRSMYYRSYMDVEKKSGVQELEKFMKPTRDTTLRMKHGTYDKIEDDGLIAPGTNVN 694

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +   G    DV         G    V+
Sbjct: 695 GEDIIIGKTAPI----PPDSEELGQRTRGHTRRDVSTPLKSTEQGTVDQVL 741


>gi|17136446|ref|NP_476708.1| RNA polymerase I 135kD subunit [Drosophila melanogaster]
 gi|78099796|sp|P20028|RPA2_DROME RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2; AltName: Full=RPA135
 gi|7296211|gb|AAF51503.1| RNA polymerase I 135kD subunit [Drosophila melanogaster]
 gi|18447630|gb|AAL68376.1| SD02110p [Drosophila melanogaster]
 gi|220947372|gb|ACL86229.1| RpI135-PA [synthetic construct]
          Length = 1129

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 126/350 (36%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          ++V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPKKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 95/617 (15%), Positives = 216/617 (35%), Gaps = 76/617 (12%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYESDQYYVSCVQAMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D      + R ++ + L+          + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILRERVMIHLDTYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    + ++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  A+  F  +              S L  + E++N +  ++
Sbjct: 408 DALVTSAVMTQCMRQAGGVGRAIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIE-----TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
             +       +         ++  YL    E+   +      L        E +      
Sbjct: 525 DPKLVKAIPKHLIDMGMMPLSNRRYLG---EKLYVVFLDGKHLGHIHQSEAEKIV----- 576

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEA 708
                  +++ +          +    IPF +N              M R    L     
Sbjct: 577 -------DELRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYIATGPARMMRPVWNLKWKRV 629

Query: 709 PFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            ++GT   +   +A  +          +          + ++    D + S  ++Y+   
Sbjct: 630 EYIGTLEQLYMEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQM 689

Query: 767 FQRSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGY 821
            +++    C+N  ++   K+         +      D     D A+G N +VA + + GY
Sbjct: 690 GKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGY 749

Query: 822 NFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           + ED+M+I++        + SI+  +F  + + +                E +K++D  G
Sbjct: 750 DMEDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELIKHLDTDG 803

Query: 881 IICVGAEVNPGDILVGK 897
           +   G++++ G  L   
Sbjct: 804 LPHPGSKLSYGSPLYCY 820


>gi|281210835|gb|EFA85001.1| RNA polymerase I [Polysphondylium pallidum PN500]
          Length = 1109

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 86/480 (17%), Positives = 149/480 (31%), Gaps = 59/480 (12%)

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I       RD+    E     + +V        D         +       +G       
Sbjct: 618  ISIMPEEVRDSTTHCELSPTAMFSVEANLTPFSDYNQSPRNMYQCQMAKQTMGTPLHSYA 677

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRV---PSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +   ++ I          +  R+   P G +  +  V        D    + S  
Sbjct: 678  YRTDNKLYKVQNIQRPIVATENQSKYRINDYPHGCNAVIAVVSNTGYDMEDAMIINKSAF 737

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
                   +  K++   I +      + +    +   +     +         I    +  
Sbjct: 738  ERGFGHGSVYKNEFVDIDEGKSRLEMGKTSISRPNYTSDNLDQWIDRDGLPYIGRLIKPG 797

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
               + V      + V      Y+  +   +   +  +            ++    V +  
Sbjct: 798  EPYYTVFSTIENKQVT---KNYKGKE---DAWIEEIMILGGSTQVRASTMITKFVVKLRF 851

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG++S++ P  +MPF + G   D+++NP   PSRM +G + E  
Sbjct: 852  DRNPVIGDKFSSRHGQKGVLSQLWPEINMPFTESGLKPDVIINPNAFPSRMTIGMLVEIL 911

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
               A    GK   +    +                                         
Sbjct: 912  AAKAGAIHGKFQDATAFRFNEKNSA----------------------------------- 936

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            E     L+ A  +  G   +Y G TGE F   +  G  Y  +L 
Sbjct: 937  ---------------VEFFGEQLKQAGFNYYGNEPMYSGTTGEEFHANIFFGICYYQRLR 981

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV DK   R+TG  + +T+QP+ G+   GG R GEME   + A+G ++ L + L   SD
Sbjct: 982  HMVKDKYQVRATGRVNNITRQPIKGRKVGGGIRFGEMERDSLLAHGTSFCLNDRLMKSSD 1041



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 96/744 (12%), Positives = 193/744 (25%), Gaps = 149/744 (20%)

Query: 29  LIEVQKASYDHF-------LMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           L+     SYD F       ++  + P    N    A         +      L+F     
Sbjct: 8   LVTPHIDSYDFFAEKALSIIVAGLPPVYINNRAENA--------DSTQKHWRLKFKDVTI 59

Query: 82  DPPKFD------VDDCLWRDLTYAVPLKITLRLI---VFDVDEFTGAKSIKDIKEQSIYM 132
             P           +      +Y+ P+  T+ L+     D +  T            + +
Sbjct: 60  SKPIKSDNRQLFPTESRQSGTSYSAPMVGTVALLKSPTSDEEHETYN----------VQL 109

Query: 133 GDLPLMTKD------------------------GTFVIKGIQRI---VVS---------- 155
           G++P+M                           G F+I G +++   +V+          
Sbjct: 110 GNIPVMVNSSRCHLRGLTSAQLVKNHEEELEVGGYFIINGNEKVMRMLVANKANHPIALT 169

Query: 156 -Q--LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW---MDIEFDSKDIIHVRIDRR 209
            Q   +R PG          +  G  L + R  PD+      +    D    I  R   R
Sbjct: 170 RQGWTNRGPG---------YTKFGVTLRSVR--PDRSSLTNNLHYISD--GQITFRFYFR 216

Query: 210 RK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R+   +PVT  L AL   +++    F   +       F    +         K    L  
Sbjct: 217 RQEYFIPVTLLLKALVDTTDK--EIFTQIVQGDFENTFLTDRVELTLREQKVKG---LNT 271

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            D     I S  +  + L  S   + +    I +  L  L    D  N     + +    
Sbjct: 272 KDEILDYIGSRYRHKANLPDSFTNQQIAEYMIDNFFLVHLPDYRDKFNI----LIVMIQK 327

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           +      +    +         +       Y+  +          +A   I   +     
Sbjct: 328 LYAVVQGKNGCDNIDATSFHEVLLPERLTEYLEVSRAMYLKA--INAQKTINEDLAFKK- 384

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                  +    L            G +  +  L+L        I   D +  I+ +   
Sbjct: 385 -------AFDRSLNIGEKFNYFLATGNLVSSSGLDLQQTSGFAII--ADKLNFIRYISHF 435

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           R+    I         +  S+ +++   +  L  +         + +    + +     +
Sbjct: 436 RS----IHRGAFFATMKTTSIRKLMPESFGFLCPVHTPDGAPCGLLNHLSANCIITKDPS 491

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                        S             S    T          +     G     +    
Sbjct: 492 QDEKSKEGVRLLPS-----FLMAHGVTSIDVTTNFQPNSLPVMLNGKLIGRINDGLAQDL 546

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
              +   +++        +   ++A    +  G     +      +    V+ L      
Sbjct: 547 VDLLRYLKSTGDEKAVPQTMEVAYAPKEQSKGGQYPGIFLFTTGARFMRTVINL------ 600

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLI 679
                             E +         I +  E++       + SP  + S+ A+L 
Sbjct: 601 -------------KSGKNELIGPQEQLYMNISIMPEEVRDSTTHCELSPTAMFSVEANLT 647

Query: 680 PFLENDDSNRVLMGCNMQRQAVPL 703
           PF + + S R +  C M +Q +  
Sbjct: 648 PFSDYNQSPRNMYQCQMAKQTMGT 671



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 97/674 (14%), Positives = 204/674 (30%), Gaps = 91/674 (13%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNT-------LVTDKNKDRKDALLDIYRVMRPG 384
            L+ +  +  ++I    V     N ++ +                + + L  I    R  
Sbjct: 227 LLKALVDTTDKEIFTQIVQGDFENTFLTDRVELTLREQKVKGLNTKDEILDYIGSRYRHK 286

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
                S           D+         R K N+ +                  +I+ L 
Sbjct: 287 ANLPDSFTNQQIAEYMIDNFFLVHLPDYRDKFNILIV-----------------MIQKLY 329

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            +  GK   D+ID      V    E L     +      ++I  + +  + D    +   
Sbjct: 330 AVVQGKNGCDNIDATSFHEVLLP-ERLTEYLEVSRAMYLKAINAQKTINE-DLAFKKAFD 387

Query: 505 NAKPVVSAVCEFFCSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  +      F  +  L                + + +N +  I+H R   ++ +G   
Sbjct: 388 RSLNIGEKFNYFLATGNLVSSSGLDLQQTSGFAIIADKLNFIRYISHFR---SIHRGAFF 444

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY-GFIETPYRKVC--- 606
                  +R + P  +G +CP  T +G   GL++ L++   +       E     V    
Sbjct: 445 ATMKTTSIRKLMPESFGFLCPVHTPDGAPCGLLNHLSANCIITKDPSQDEKSKEGVRLLP 504

Query: 607 ---------------DGKVTNDVVYLSAMEEENRY--IAQANSSLDEDGSFTEELVFCRC 649
                          + +  +  V L+          +AQ    L      T +      
Sbjct: 505 SFLMAHGVTSIDVTTNFQPNSLPVMLNGKLIGRINDGLAQDLVDLLRYLKSTGDEKAVPQ 564

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD-SNRVLMGCNMQRQAVPLLKAEA 708
             E    P+E+          + +  A  +  + N       L+G   Q      +  E 
Sbjct: 565 TMEVAYAPKEQSKGGQYPGIFLFTTGARFMRTVINLKSGKNELIGPQEQLYMNISIMPEE 624

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
               T       + S  A+ +  A +    D  +      +  +   T G  +  Y    
Sbjct: 625 VRDST----THCELSPTAMFSVEANLTPFSDYNQSPRNMYQCQMAKQTMGTPLHSYAYRT 680

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +   + QRP+V   ++ +            + D   G N ++A +   GY+ ED+
Sbjct: 681 DNKLYKVQNI-QRPIVATENQSK----------YRINDYPHGCNAVIAVVSNTGYDMEDA 729

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL------KNIDECG 880
           M+I++           H   ++    D   G   +     ++S          + ID  G
Sbjct: 730 MIINKSAFERGFG---HGSVYKNEFVDIDEGKSRLEMGKTSISRPNYTSDNLDQWIDRDG 786

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +  +G  + PG+      +      +T   K     + E+ + +  ++    S +    V
Sbjct: 787 LPYIGRLIKPGEPYYTVFSTIENKQVTKNYKGKEDAWIEEIMILGGSTQVRASTMITKFV 846

Query: 941 DVRIFNRHGIDKNE 954
               F+R+ +  ++
Sbjct: 847 VKLRFDRNPVIGDK 860


>gi|300394684|gb|ADK11880.1| DNA-directed RNA polymerase II subunit two [Coniophora arida]
          Length = 687

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 125/815 (15%), Positives = 238/815 (29%), Gaps = 144/815 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   F       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTVCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      LL+ +   ++  G                + G++E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDA 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +         +   +    +K G            PS 
Sbjct: 286  EEEETVMISMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSM 343

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 344  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 378

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 379  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 427

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 428  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTY 486

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 487  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 546

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 547  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 586

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +         
Sbjct: 587  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 639

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 640  ----------------------------------------------ATP-FTDLTVESVS 652

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            + LR       G  ++Y G TG      V +G  Y
Sbjct: 653  TFLRQKGYQSRGLEVMYHGHTGRKLQAQVYLGPTY 687



 Score =  118 bits (296), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 166/610 (27%), Gaps = 96/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNISLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESLEENAHSSTVCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +          T   K         +  L A EEE   I+     L+     + 
Sbjct: 249 QKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEEEETVMISMTPEDLENSRLQSA 308

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +   +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 309 GIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLV-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 484 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 539

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 540 TENGIVDQVL 549


>gi|198385439|gb|ACH86038.1| RpoB [Bartonella sp. Cr28649]
          Length = 284

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 206/285 (72%), Positives = 239/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME VVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|118640735|gb|ABL09935.1| RNA polymerase beta subunit [Aeromonas sp. 2433-05]
          Length = 290

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 167/290 (57%), Positives = 225/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF +++YDLSTVGR+K N RL  +    V  + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSAERYDLSTVGRMKFNRRLGREDETGVGVLTKDDIVEVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLE 290


>gi|664896|emb|CAA58965.1| RNA polymerase subunit beta [Arabidopsis thaliana]
          Length = 368

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 153/371 (41%), Positives = 227/371 (61%), Gaps = 10/371 (2%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ+L+ + P+ +    FF    LSQ+ +  N L++I H R+LS LG GG+    A   +
Sbjct: 6   TPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTANFRI 65

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV--Y 616
           RD+HP+HYGRICP +TSEG N+GL+ SL+  AR+  +G +E+P+ ++ +      +   +
Sbjct: 66  RDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKKARIRMLF 125

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           LS  ++E   IA  NS     G   E+ V  R   E + +  E++      P Q  SI A
Sbjct: 126 LSPSQDEYYMIAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGA 185

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPF+E++D+NR LM  NMQRQAVPL ++E   VGTG+E  VA  SG   +A+  G + 
Sbjct: 186 SLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKIL 245

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             D  +IV+                  L+ +QRSN+NTC++Q+P V+ G  +++  I+AD
Sbjct: 246 YTDTEKIVLSGN--------GDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILAD 297

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+LALG+N+LVA+MPW GYNFED++LISE +V  D++TS HI ++E+    T  
Sbjct: 298 GAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQ 357

Query: 857 GPEEITRDIPN 867
           GPE IT++IP+
Sbjct: 358 GPERITKEIPH 368


>gi|197091100|gb|ACH41902.1| RpoB [Agrobacterium tumefaciens]
          Length = 237

 Score =  265 bits (678), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 140/238 (58%), Positives = 176/238 (73%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EILSTFY K  Y + GD W  P    D +  AKV + ++D DTGE V+E GKKLT  L++
Sbjct: 61  EILSTFYTKATYERSGDGWRIPFQP-DALKNAKVITDMIDADTGEVVVEGGKKLTPRLIR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L +KG+K L  T + L G ++AEDIVN  TGEIY+EAGD IDEK+L  I  S   +IP+
Sbjct: 120 QLVDKGLKALKATDEDLYGNFLAEDIVNYSTGEIYLEAGDEIDEKTLGLILQSGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D VN  AYIRNTL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LNIDHVNVGAYIRNTLSADKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAE 237


>gi|195470252|ref|XP_002087422.1| GE16780 [Drosophila yakuba]
 gi|194173523|gb|EDW87134.1| GE16780 [Drosophila yakuba]
          Length = 1129

 Score =  265 bits (678), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 125/350 (35%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPKKTVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKFLVTELSSVNINARFKLNE 1128



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 97/613 (15%), Positives = 212/613 (34%), Gaps = 68/613 (11%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDFTDEEIYNRLVKGYESDQYYVSCVQSMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D+     + R ++ + L+          + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDEDVTDFILRERVMIHLDNYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    + ++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLGERVESWVSQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  A+  F  +              S L  + E++N +  ++
Sbjct: 408 DALLTSAVMTQCMRQAGGVGRAIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                  K+     T  +           Y  +    +  DG              E   
Sbjct: 525 DP-----KLVKAIPTQLIDMGMIPLSNRSYSGEKLYVVFLDGKHL-----GHIHQSEANK 574

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             + + +          +    IPF +N              M R    L   +  ++GT
Sbjct: 575 IVDDLRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYLATGPARMMRPVWNLKWNKVEYIGT 634

Query: 714 G--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              +   +A             +          + ++    D + S  ++Y+    +++ 
Sbjct: 635 LEQLYMEIAIDQKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTM 694

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIA------DGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
              C+N  P        R               +  L D A+G N +VA + + GY+ ED
Sbjct: 695 GTPCLN-WPKQAANKLYRLQTPATPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMED 753

Query: 826 SMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           +M+I++        + SI+  +F  + + +                E +K++D  G+   
Sbjct: 754 AMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELVKHLDTDGLPHP 807

Query: 885 GAEVNPGDILVGK 897
           G++++ G  L   
Sbjct: 808 GSKLSYGSPLYCY 820


>gi|322510564|gb|ADX05878.1| putative DNA-directed RNA polymerase [Organic Lake phycodnavirus 1]
          Length = 1164

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 120/604 (19%), Positives = 207/604 (34%), Gaps = 100/604 (16%)

Query: 781  LVKVGDEVRRNDIIADGPSTD--------LGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            LV+   +V+ N I+    +            DL L  N+  + + +     +++ +I   
Sbjct: 620  LVRPLFKVKNNKILLTNNTIQRLKEDELSWRDLLLPLNIDESIIEYIDSAEQNNSMIC-- 677

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE-GLKNIDECGIICVGAEVNPG 891
             +  + F   +      +   T  G        P  ++          G   +G  V+  
Sbjct: 678  -MKPNQFKEEYNYTHCEIHPSTIFGVLASCIPFPQHNQSPRNTYQCAMGKQAIGIYVSNF 736

Query: 892  DILVGKITPKGESPMTP--EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            +  + K        M P  E +++  +   +        + + +       D  +FNR  
Sbjct: 737  NKRMDKTAYILNYTMRPLVETRVMNMMKLNQLPCGNQVIVAIMTHGGYNQEDSLLFNRGS 796

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D       +    I    +D+D +    +         I       +  K  K+  +  
Sbjct: 797  LD-----RGLFHATIYHTEKDEDKKINGEEELRVKPNPNITRNMKFGNYDKINKQGVIDE 851

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            ++LI +       +  V  E    N + +K  YE          +  ++K     +    
Sbjct: 852  NELIEDKDII-ISKVVVIKENKNDNTKLIK--YEDQSKSYRTTEECYVDKNYIDRNGDGH 908

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
                 KV V   R    GDK + RHG KG +  I+  EDMP+ KDG   DI++NP  +PS
Sbjct: 909  --TFCKVRVRSTRKPNIGDKFSSRHGQKGTIGNIINEEDMPYTKDGLRPDIIINPHAIPS 966

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM + Q+ ET +G   + LG              +                         
Sbjct: 967  RMTIAQLKETLIGKLLLKLGLFGDGTSFGEMDMEE------------------------- 1001

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                                VF    +    S  R  +L   G+       TGE  +  +
Sbjct: 1002 --------------------VFKELKKHDYES--RGNELLYDGK-------TGEQIETSI 1032

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             +G +Y  +L HMV+DK ++R  G    +T+QP  G+S  GG R GEME  C+ ++GA+ 
Sbjct: 1033 FIGPVYYQRLKHMVNDKQHSRCIGPMVNLTRQPAEGRSRDGGLRFGEMERDCMISHGASK 1092

Query: 1310 VLQEMLTIKSD----DV---VGRTRVYESIVAGNDT------------FETGTPESFNVL 1350
              +E +   SD    +V    G   VY                          P S  +L
Sbjct: 1093 FTKERIYDVSDKYAVNVCKKCGMIAVYN---DKEHIHLCNVCENRTDFSNVKIPYSCKLL 1149

Query: 1351 VKEM 1354
             +E+
Sbjct: 1150 FQEL 1153



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 138/1019 (13%), Positives = 280/1019 (27%), Gaps = 210/1019 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFS------GAAMLE----F 76
           L++ Q  SY+ F+             L    +   P  I +            LE    F
Sbjct: 25  LVKHQVDSYNDFVQNQ----------LIKTIEMFNPLIIKSPHDYLPEYKKYRLEVEINF 74

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRL-IVFDVDEFTGAKSIKDI 125
           V+     P+              D   R  TY+    + + +            +  K I
Sbjct: 75  VNLSIYRPEIHENNGSSKLMFPSDARLRSFTYSSNFTLDMNIKYTIRKGANLENEEFKHI 134

Query: 126 KEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSP 161
               I  G +P+M                           G F+I G ++  + Q   + 
Sbjct: 135 HLSKIQFGKIPIMLNSCICVLKQYPHIHPDNIDECKMDPGGYFIINGSEKTCLGQEKTAD 194

Query: 162 GIHFDHDKGRASLSGKLLYACRI--------IPDQGLWMDIEFDSK------DIIHVRID 207
              F     +   S K L+            I  +   + +  +SK      DI+ V++ 
Sbjct: 195 NKVF---CFKQKQSNKWLWTAEFRSVPDWKCISPK--QIYMMLNSKLSAYGHDIL-VQLP 248

Query: 208 RRRK-VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
           R +K +P+     ALG++S+         I+ +   +        A +  GA       +
Sbjct: 249 RLKKPIPLFVLFRALGIESD---KKICNIILLNSNKESKLLEYLKASIYEGA----EYNN 301

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            +   Q I S    T  +     E   K      D L            E   IY+    
Sbjct: 302 YEDALQYIISNVIYTP-INMDKDEGHRKKTEFAKDVLSNDLFPHCKTKEEK--IYLLGFM 358

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG-- 384
                        +                 + N      NK  KD    + R +  G  
Sbjct: 359 TKKIILAYSGIEKQTDRDSYENKRVELTGTLLNNLFRNYFNKVVKDIQKQVIREINNGSW 418

Query: 385 -------DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
                  ++ T +    +      ++      + G   +            + + +   +
Sbjct: 419 KSSEDYFNIITLTNIYKIVKSTTIENGLKRALSTGDFGIKSMNTNKVGV-AQVLNRLTYL 477

Query: 438 AIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           + +  L  +     ++GK       +          E  + Q  +G+++    +    + 
Sbjct: 478 STLSHLRRVNTPIDKSGKLVEPRKLHGSTWGFLCPAETPEGQ-SVGVVKNISYMTNVSTY 536

Query: 493 VDI--------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            D           + P D    +     V  F     +      +     +   +    +
Sbjct: 537 SDSTPIYEFIKPYLYPLDHYETEDFYDKVKVFVNGRWIGITHNPITLFKDLKQKKHNGMI 596

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
                       +   V       + P    + + I L ++     + +   + +     
Sbjct: 597 HIYCSIVFNYQNKEIYVCNDCGRLVRPLFKVKNNKILLTNNTIQRLKEDELSWRD---LL 653

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           +      + + Y+ + E+ N  I    +   E+ ++                        
Sbjct: 654 LPLNIDESIIEYIDSAEQNNSMICMKPNQFKEEYNY---------------------THC 692

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  +  + AS IPF +++ S R    C M +QA+ +  +                  
Sbjct: 693 EIHPSTIFGVLASCIPFPQHNQSPRNTYQCAMGKQAIGIYVSNFN--------------- 737

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                KR      +             L+ +   +   R+M   + NQ  C NQ      
Sbjct: 738 -----KRMDKTAYI-------------LNYTMRPLVETRVMNMMKLNQLPCGNQ------ 773

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                                     ++VA M   GYN EDS+L +   +   +F +   
Sbjct: 774 --------------------------VIVAIMTHGGYNQEDSLLFNRGSLDRGLFHATIY 807

Query: 845 EEFEVMARDTKLGPEEITRDIP----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
              +   +      E   +  P    N+       I++ G+I     +   DI++ K+  
Sbjct: 808 HTEKDEDKKINGEEELRVKPNPNITRNMKFGNYDKINKQGVIDENELIEDKDIIISKVVV 867

Query: 901 KGESPMTPEEKLLRAIFGEKAVD----VRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNE 954
             E+     + +      +          D +    +G   T   VR+   R     ++
Sbjct: 868 IKENKNDNTKLIKYEDQSKSYRTTEECYVDKNYIDRNGDGHTFCKVRVRSTRKPNIGDK 926


>gi|301500896|ref|YP_003795308.1| RNA polymerase beta subunit [Chromera velia]
 gi|300069442|gb|ADJ66550.1| RNA polymerase beta subunit [Chromera velia]
          Length = 1421

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 95/278 (34%), Positives = 147/278 (52%), Gaps = 39/278 (14%)

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
            +Q GDK+ G+HGNKGIVS +L   DMP+L+DGT  D++++ LGVPSRMN+GQ++E  LG 
Sbjct: 1153 MQLGDKVCGKHGNKGIVSALLDTPDMPYLEDGTSPDMIVSALGVPSRMNIGQLYECILGL 1212

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                L  ++K   +D    G+                            +          
Sbjct: 1213 TAEWLNSRLKYSQDDKLFCGE--------------------------QYLRENIYNLMKQ 1246

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            V + T           N+       +  G+ +L +G +G+     V  G  Y+ KL HMV
Sbjct: 1247 VALFT-----------NNAWFYNPYNP-GKILLREGASGQLIQGGVFYGMTYLFKLIHMV 1294

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV 1323
              K++ R  G Y+L+TQQP  G+   GGQRLGEMEVW IQA+ A+Y L+E+L +KSDD+ 
Sbjct: 1295 EKKIHTRPVGPYTLITQQPPRGRRQEGGQRLGEMEVWAIQAFSASYTLKELLVLKSDDLF 1354

Query: 1324 GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
             R ++++ +V+       G  E+F +L++++  LG+ +
Sbjct: 1355 YRQQIHDRLVSAEKLS-FGYSETFKLLIRDLNILGVGV 1391



 Score =  128 bits (321), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 110/405 (27%), Positives = 187/405 (46%), Gaps = 25/405 (6%)

Query: 511  SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--RARAGVEMRDVHPTHYGR 568
             +V EF   S L Q  + +N L+ I H RR+SALG GG++  R R   E RDV+P++YG+
Sbjct: 699  WSVREFLIESPLLQYLDEINPLTEIVHKRRISALGLGGISANRERPETEERDVYPSYYGK 758

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +C  ET EG   GLV S T F+R+     +   +  +  G++   + +L+  E      A
Sbjct: 759  LCAVETLEGERAGLVVSHTIFSRLTRNHNLSIAHFSLLHGRLEPTLKFLNFTE------A 812

Query: 629  QANSSLDEDGSFTEELVFC--RCAGEEILVPREKID----FIDASPKQVVSIAASLIPFL 682
              N+            +F   R           K+     ++  S   + S AA+L PF+
Sbjct: 813  STNAMPYYKIVKRRSKIFNGLRHLFGTGEYAFTKLHLHFRYLPMSHTVMFSPAAALTPFM 872

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             ++D  R LM  NMQRQA PLL  +   +  G+ES  +  +    ++   GIV      +
Sbjct: 873  FHNDPTRTLMAANMQRQATPLLYTQPSALSFGLESTWSVDTAYTAISLNEGIVMTSSPWQ 932

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            I +R               Y L    ++NQ+T   Q P V  G+ +    ++  G +   
Sbjct: 933  IEVR-------DIAYRDIQYLLKNLLQTNQSTVNQQVPCVWPGERIFPGQLLTSGYAQKN 985

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
             +LALG N  V +  ++GY FED++L++   + + +FTS+ + E +++  +         
Sbjct: 986  YELALGINTRVCYGVYYGYTFEDAILLNSTCIQKHMFTSLQLYEKKLLLGNLSHTS---- 1041

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 + +E L N+   G++   + + P  +L+ KI     + +T
Sbjct: 1042 LMSLLLPQESLINVSSHGMLKPNSLIYPSQLLISKIEDTRPNFLT 1086


>gi|118640737|gb|ABL09936.1| RNA polymerase beta subunit [Aeromonas veronii]
          Length = 290

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 166/290 (57%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF +++YDLSTVGR+K N RL  +       + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSAERYDLSTVGRMKFNRRLGREDETGAGVLTKDDIVDVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLE 290


>gi|325658930|gb|ADZ39773.1| RNA polymerase beta subunit [Bartonella sp. OS09]
 gi|325658932|gb|ADZ39774.1| RNA polymerase beta subunit [Bartonella sp. OS23]
          Length = 284

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 206/285 (72%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+GIV+QVDA RIVIR++E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVSAKRSGIVDQVDATRIVIRAIED-LDPSKSGVDIYRLQKF 284


>gi|269930903|gb|ACZ54186.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 282

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 203/282 (71%), Positives = 237/282 (84%), Gaps = 1/282 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            SGAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 DSGAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYR 281


>gi|321160840|gb|ADW66605.1| RNA polymerase beta subunit [Bartonella sp. WC1]
          Length = 284

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 206/285 (72%), Positives = 237/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD  G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIVDGKVTTEVIYLSAMEESKHYVAQANSSLDAGGRFTEEFVVCRHAGEVLMAPRDNVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR G+V+ VDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAIGAKRGGVVDHVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|325658934|gb|ADZ39775.1| RNA polymerase beta-subunit [Bartonella sp. OS02]
          Length = 284

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 205/285 (71%), Positives = 240/285 (84%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F+EE V CR AGE ++ PRE +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFSEEFVVCRHAGEVLMAPREHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAA+ AKR+GIV+QVDA RIV+R+ E  LDPS SGVDIYRL KF
Sbjct: 241 SGAAVAAKRSGIVDQVDATRIVVRATED-LDPSRSGVDIYRLQKF 284


>gi|124491195|gb|ABN12932.1| RNA polymerase beta chain [Agrobacterium tumefaciens]
          Length = 237

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 141/238 (59%), Positives = 177/238 (74%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EILSTFY K  Y + GD W  P    D +  AKV + ++D DTGE V+E GKKLT  L++
Sbjct: 61  EILSTFYTKATYERAGDGWRIPFQP-DALKNAKVITDMIDADTGEVVVEGGKKLTPRLIR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L +KG+K L  T + L G ++AEDIVN ETGEIY+EAGD IDEK+L  I  S   +IP+
Sbjct: 120 QLVDKGLKALKATDEDLYGNFLAEDIVNYETGEIYLEAGDEIDEKTLGLILQSGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D VN  AYIRNTL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LNIDHVNVGAYIRNTLSVDKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAE 237


>gi|124491191|gb|ABN12930.1| RNA polymerase beta chain [Rhizobium huautlense]
          Length = 237

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 143/238 (60%), Positives = 179/238 (75%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PV+S LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVSSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +ILSTFY K  Y + GD W  P     L  GAK  S ++D DTGE V+ESGKKLT  LL+
Sbjct: 61  DILSTFYSKSNYERDGDGWRIPFQPETL-KGAKTLSDMIDADTGEVVVESGKKLTPRLLR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L +KG+K L  T+D L G Y+AEDIVN ETGEIY+EAGD IDEK+L  I ++   +IP+
Sbjct: 120 QLSDKGLKALKATNDDLYGNYLAEDIVNMETGEIYLEAGDEIDEKTLPVILNAGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LGIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAE 237


>gi|194853433|ref|XP_001968165.1| GG24715 [Drosophila erecta]
 gi|190660032|gb|EDV57224.1| GG24715 [Drosophila erecta]
          Length = 1129

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 125/350 (35%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPKKTVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKFLVTELSSVNINARFKLNE 1128



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 97/613 (15%), Positives = 213/613 (34%), Gaps = 68/613 (11%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYESDQYYVSCVQSMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D+     + R ++ + L+ +        + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDEDVTDFILRERVMIHLDTNED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    +L++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLGERVESWVLQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  ++  F  +              S L  + E++N +  ++
Sbjct: 408 DGLLTSAVMTQCMRQAGGVGRSIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                  K+        +           Y+      +  DG              E   
Sbjct: 525 DP-----KLVKAIPKQLIDMGMMPLSNRSYLGDKLYVVFLDGKHL-----GHIYQSEATK 574

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             + + +          +    IPF +N              M R    L      ++GT
Sbjct: 575 IVDDLRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYLATGPARMMRPVWNLKWNRVEYIGT 634

Query: 714 G--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
              +   +A  S          +          + ++    D + S  ++Y+    +++ 
Sbjct: 635 LEQLYMEIAIDSKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTM 694

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIA------DGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
              C+N  P        R               +  L D A+G N +VA + + GY+ ED
Sbjct: 695 GTPCLN-WPKQAANKLYRLQTPATPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMED 753

Query: 826 SMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           +M+I++        + SI+  +F  + + +                E +K++D  G+   
Sbjct: 754 AMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELVKHLDTDGLPHP 807

Query: 885 GAEVNPGDILVGK 897
           G++++ G  L   
Sbjct: 808 GSKLSYGSPLYCY 820



 Score = 42.0 bits (97), Expect = 0.75,   Method: Composition-based stats.
 Identities = 96/756 (12%), Positives = 208/756 (27%), Gaps = 139/756 (18%)

Query: 14  RKFFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT--AFS 69
           R  F + P+ +   + +L      S+D  L +          GL    K + PI   + +
Sbjct: 18  RPEFKQIPKKLSRHLANLGAPHVDSFDEMLTL----------GLDNTAKHMIPIHWLSPA 67

Query: 70  G-AAMLEFVSYEFDPPK------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
           G    ++  S     PK                D     ++Y+    + L   V  V++ 
Sbjct: 68  GEKISMKVESIWISKPKVPQDVIDVRTREIYPTDSRQLHISYSGMCSVRLGWTVNGVEKS 127

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
                          +G++P+M +                         G FVI+G ++ 
Sbjct: 128 AINMD----------LGEVPIMLRSKACNLGQASPEEMVKHGEHDSEWGGIFVIRGNEK- 176

Query: 153 VVSQLH---RSPGIHFD----HDKGRASLS-GKLLYACRIIPDQGLWMDIEFDSKDII-- 202
           +V  L    R+  I        D+G+     G L+   R         + E    +++  
Sbjct: 177 IVRMLIMTRRNHPICVKRSSWKDRGQNFSDLGMLVQTVR---------EDESSLSNVVHY 227

Query: 203 ---------HVRIDRRRKVPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
                       + R   VPV   L  L     EEI    Y ++V     D +      +
Sbjct: 228 LNNGTAKFMFSHVKRLSYVPVCLILKCLMDYTDEEI----YNRLVQGYESDQYYVSCVQS 283

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            L    +  +          +    +     + +   ++ V    +    +  L   ED 
Sbjct: 284 ML-REVQNENVYTHAQCKSFIGNLFRARFPEVPEWQPDEDVTDFILRERVMIHLDTNEDK 342

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
                  I         +  +E +  + ++++ +              + V    +    
Sbjct: 343 FQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLGERVESWVLQVRRC--- 399

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
               + + +   D    S   +          +   S +    +  R  L    +   + 
Sbjct: 400 ----LQKKLTSPDGLLTSAVMTQCMRQAGGVGRSIESFLATGNIASRTGLGLMQNSGLVI 455

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERIS 491
             + I  ++ +   R     I         R     ++L + +  +  +         + 
Sbjct: 456 MAENINRMRYMSHFR----AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLL 511

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           +    +       + K V +   +             +++ S +     +  L    +  
Sbjct: 512 NHLTLTCEISMRPDPKLVKAIPKQLIDMG-----MMPLSNRSYLGDKLYVVFLDGKHLGH 566

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                  + V    YG+I    T                +         P R +      
Sbjct: 567 IYQSEATKIVDDLRYGKIF--GTLPQMMEIGFIPFKKNGQFPGLYLATGPARMMRPVWNL 624

Query: 612 --NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
             N V Y+  +E+    IA                       +   +  +    ++ +  
Sbjct: 625 KWNRVEYIGTLEQLYMEIA----------------------IDSKEMYPDFTTHLELAKT 662

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             +S  A+LIP  + + S R +  C M +Q +    
Sbjct: 663 HFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPC 698


>gi|118640717|gb|ABL09926.1| RNA polymerase beta subunit [Salmonella enterica subsp. enterica
           serovar Typhimurium]
          Length = 290

 Score =  265 bits (677), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 175/290 (60%), Positives = 229/290 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  D+YDLS VGR+K N  L  D  +    + K+DII ++K L+D+RNGKG +
Sbjct: 1   SLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKDDIIDVMKKLIDIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS+
Sbjct: 181 TPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEGNYVIAQANSN 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 241 LDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 290


>gi|110618407|gb|ABG78832.1| RNA polymerase beta subunit [Bartonella sp. CL8134co]
          Length = 275

 Score =  265 bits (677), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 197/274 (71%), Positives = 232/274 (84%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +GLLRMER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS IT
Sbjct: 1   IGLLRMERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEIT 60

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YG
Sbjct: 61  HKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYG 120

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           FIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ 
Sbjct: 121 FIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMA 180

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME
Sbjct: 181 PRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGME 240

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           ++VA+ SGAA+ AKRAGIV+QVDA RIVIR+ E 
Sbjct: 241 AIVARDSGAAVGAKRAGIVDQVDATRIVIRATED 274


>gi|58697117|ref|ZP_00372555.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
           endosymbiont of Drosophila simulans]
 gi|58536592|gb|EAL59929.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
           endosymbiont of Drosophila simulans]
          Length = 226

 Score =  265 bits (677), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 84/216 (38%), Positives = 133/216 (61%), Gaps = 20/216 (9%)

Query: 14  RKFFGKNPEIID-IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           R  + ++ ++ D + DL++VQK SYD F      P  + NE L+  F ++FPI      A
Sbjct: 16  RVSYSRSIDLKDSLLDLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLRRA 70

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDV--------------DEFTG 118
            +EF+S   D PK+D  +C+ R +T++  +  ++RL+V                 D    
Sbjct: 71  TIEFISCRVDDPKYDESECIKRGVTFSAQVIASIRLVVMQDGISLDEYKSIKESGDHSKL 130

Query: 119 AKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
           A  +K I+EQ ++   LP+MT  GTF+I G+++++VSQ+HRSPG+ FD DKG+   SGKL
Sbjct: 131 ATVVKSIEEQKVHFCGLPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

Query: 179 LYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           +Y+ RIIP +G W+DIEFD KD ++ R+DR++K+P+
Sbjct: 191 IYSARIIPYRGSWLDIEFDVKDHLYFRVDRKKKMPI 226


>gi|269930935|gb|ACZ54202.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 282

 Score =  265 bits (677), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 204/282 (72%), Positives = 237/282 (84%), Gaps = 1/282 (0%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           MER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   MERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 DSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYR 281


>gi|119644095|gb|ABL85606.1| RNA polymerase II second largest subunit [Parmotrema reticulatum]
          Length = 718

 Score =  265 bits (677), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 126/837 (15%), Positives = 244/837 (29%), Gaps = 142/837 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQTLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAG 733
                P F+ ++D      G  +  +           +G        + +        + G
Sbjct: 237  RVCRPLFVIDNDPRSSNRGNLVLTKEHVQKLELDERIGLIQNLTSGEETNMGWQGLVKEG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE VDA       +    +       +        +N +  +N+R    +         
Sbjct: 297  VVEYVDAEEEETIMIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWTH 355

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   + +  +E     
Sbjct: 356  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM-- 404

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 405  -------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 439

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    
Sbjct: 440  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRS 495

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  ++ D      R++          
Sbjct: 496  DTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTP 555

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            ++     +  Q   S                         LR VKV +   +  Q GDK 
Sbjct: 556  LRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDKF 595

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 596  ASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGF 655

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          +S L                           V     +G  + T V
Sbjct: 656  EGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGKKLVTQV 700

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            F                                       +G  Y  +L HMV DK+
Sbjct: 701  F---------------------------------------LGPTYYQRLRHMVDDKI 718



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 87/625 (13%), Positives = 175/625 (28%), Gaps = 115/625 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 15  GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 191

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  +   RR   +  +  + R     E        R   P       P  
Sbjct: 192 VGVHRDPAHLVGTVQTLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 251

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +         G I      E              V Y+ A EEE   I
Sbjct: 252 SNRGNLVLTKEHVQKLELDERIGLIQNLTSGEETNMGWQGLVKEGVVEYVDAEEEETIMI 311

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 312 VMTPEDLEISRQLQAGYAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 371

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +         T  E  +   +                
Sbjct: 372 PFPDHNQSPRNTYQSAMGKQAMGVFL-------TNYEQRMDTMANIL------------- 411

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                                 Q+PL                  
Sbjct: 412 -----------------------------------YYPQKPL----------ATTRSMEF 426

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 427 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVV 486

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   +       +D+ G++  G  V+  DI++GK  P         ++   
Sbjct: 487 EQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-- 544

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                K    RDTS  + S  +G V
Sbjct: 545 -----KLHVKRDTSTPLRSTENGIV 564


>gi|6449138|gb|AAF08842.1| RNA polymerase beta subunit [Streptococcus oralis ATCC 35037]
          Length = 290

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 161/297 (54%), Positives = 215/297 (72%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +++ RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSYKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGF++TPYRKV      VTN++V+L+A EE+   +AQANS L+EDG+F E++V  R  
Sbjct: 61  NKYGFVQTPYRKVDRETGVVTNEIVWLTADEEDEFTVAQANSRLNEDGTFAEKVVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P E +D++D SPKQVV++A + IPFLEN+DSNR LMG NMQRQAVPL+  +AP+
Sbjct: 121 GVNQEYPAEVVDYMDVSPKQVVAVATACIPFLENNDSNRALMGANMQRQAVPLIDPKAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E   A  SGAA++A+  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGLEYQAAHDSGAAVIAQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTAYNQRTLVKVGDVVEKGDFIADGPSMEKGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|304653525|gb|ADM47774.1| RNA polymerase beta-subunit [Bartonella capreoli]
          Length = 284

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 205/284 (72%), Positives = 239/284 (84%), Gaps = 1/284 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 2   RAIKERMSSVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 61

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 62  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 121

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D 
Sbjct: 122 KIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDL 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ S
Sbjct: 182 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDS 241

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           GAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 242 GAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|22128702|gb|AAM92814.1| putative DNA-directed RNA polymerase I subunit, 5'-partial [Oryza
            sativa Japonica Group]
          Length = 855

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 110/262 (41%), Gaps = 56/262 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGV 1127
              L+   + +   R    GDK + RHG KG+ S++ P  DMPF  + G   D+++NP   
Sbjct: 555  DRLQKANIRLRRVRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSANTGMRPDLIINPHAF 614

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +  + E+    A    GK I                                   
Sbjct: 615  PSRMTIAMLLESIAAKAGSLKGKFI----------------------------------- 639

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                             P ++ V + ++   + +  ML     +  G  ILY G+ G   
Sbjct: 640  --------------DATPFASSVKERSNSIVDELGPMLASYGFNYHGTEILYSGVFGTEM 685

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  +L HMVSDK   R+TG    +T+QP+GG+   GG R GEME   + A+
Sbjct: 686  KCEIFLGPVYYQRLRHMVSDKFQVRTTGRIDQITRQPIGGRKYGGGIRFGEMERDALLAH 745

Query: 1306 GAAYVLQEMLTIKSD----DVV 1323
            GA+Y+L + L   SD    DV 
Sbjct: 746  GASYLLHDRLHSCSDYHIADVC 767



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 71/442 (16%), Positives = 145/442 (32%), Gaps = 37/442 (8%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            ++   E +N    I+H R   ++ +G          +R + P  +G +CP  T +G   
Sbjct: 164 GMTIHAERLNFHRYISHFR---SVHRGSSFAKMRTTSVRKLLPESWGFLCPVHTPDGEPC 220

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-- 638
           GL++ +TS  R++++   E   +     K++     + A        AQ    ++  G  
Sbjct: 221 GLLNHMTSTCRISSFYNSEGATKDFQKIKMSLIARLVGAGM------AQLLPRIERTGPP 274

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP--FLENDDSNRVLMGCNM 696
                 V     G       E++   D     V        P  +L  + +  +      
Sbjct: 275 EVLHVHVDGCIVGSIASAKIEEVIPEDLEVGYVPLSHGGAYPGLYLFTNPARFLRPAFME 334

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            R                 E    +    AI++  A +    D  +      +  +   T
Sbjct: 335 IRCPDGGDGGRNKLFPATHE----EIHPTAILSVVANLTPWSDHNQSPRNMYQCQMAKQT 390

Query: 757 SGVDIYRLMKFQRSNQNTCV--NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            G    + +KF+   +   +   Q P+V+     +            + +   G N +VA
Sbjct: 391 MGFCG-QALKFRTDVKAFHLQTPQTPIVRTATYSK----------YCMDEFPSGTNAIVA 439

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            + + GY+ ED+M++++  V   +F     +   +                 N+S +   
Sbjct: 440 VLSYTGYDMEDAMILNKSAVDRGMFRGHIFQTECIDLSAKSRDNVTEFFCKSNLSRDTTA 499

Query: 875 NIDECGIICVGAEVNPGDILV-------GKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            I+  G+  +G  + P +          G + P       P      A+ G    D    
Sbjct: 500 AIESDGLPRIGENIFPNEQYYSVCNNLTGTVRPIKLKGSEPAAIDYVAVNGTNFKDRLQK 559

Query: 928 SLRVPSGVSGTVVDVRIFNRHG 949
           +      V   ++  +  +RHG
Sbjct: 560 ANIRLRRVRNPIIGDKFSSRHG 581


>gi|118640719|gb|ABL09927.1| RNA polymerase beta subunit [Yersinia sp. 2447-04]
          Length = 290

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 176/290 (60%), Positives = 228/290 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  D+YDLS VGR+K N  L  D  +    + KEDI  ++K L+D+RNGKG +
Sbjct: 1   NLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKEDITEVMKKLIDIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS+
Sbjct: 181 TPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSN 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           LDEDG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 241 LDEDGRFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 290


>gi|321160844|gb|ADW66607.1| RNA polymerase beta subunit [Bartonella sp. BA1]
          Length = 284

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 206/285 (72%), Positives = 239/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +VVYLSAMEE   Y+AQANSSL+ +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVVYLSAMEESKHYVAQANSSLNAEGRFTEEFVVCRHAGEVLMAPRDNVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL  F
Sbjct: 241 SGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQNF 284


>gi|119644344|gb|ABL85619.1| RNA polymerase II second largest subunit [Xanthoria elegans]
          Length = 718

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 135/841 (16%), Positives = 244/841 (29%), Gaps = 150/841 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + I +  +              +    + S
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRMLFQKLTKDIYKYLQKCVESNREFNLTLGVKQNTLSS 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     ++     +    Y      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPADPIVDYLTNRGMESLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              A      ++         D +     +        I      + D  D   K      
Sbjct: 177  TRAPHATKVFVNGTWIGCHNDPAHLVPHIQEVRRKGIIAHEASLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P F+ ++D     MG   + +  V  L+ E   V T      A+        +  G
Sbjct: 237  RVCRPLFVIDNDPKSENMGNLALTKDMVQKLEDERDMVLTMDPEERAE--------QVIG 288

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRND 792
                VD+    +  V+ + + +         ++  R  Q       P        V+   
Sbjct: 289  WEALVDS--GAVEYVDAEEEETIMIAMTPEDLEISRQIQAGYAAPVPSEDAPNQRVKAPL 346

Query: 793  IIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                   T      ++   +  + +P+  +N          M  + +             
Sbjct: 347  NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------- 395

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                 L N DE    +  +             +       +   
Sbjct: 396  --------------------FLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAG 435

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R  +D  +R        +E   +
Sbjct: 436  QNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVDTEKRVGM---TVLEKFEK 491

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                E + L    Y +L +   +  G           K+T ++ D               
Sbjct: 492  PLRTETLKLKHGTYDKLDDDGLVAPGVRVSGEDVIIGKTTPIAPD--------------- 536

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
              E  QR    +K    T     E+   +K+             L+ VKV +   +  Q 
Sbjct: 537  AQEMGQRTKSHIKKDASTPLRSTENGIVDKVLL-----STNSEGLKFVKVRMRTTKIPQI 591

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L     
Sbjct: 592  GDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSS 651

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +          +S L    E    +                            
Sbjct: 652  LRGYEGDATPFTEITVDSVSKLLR--EHGYQSRGFEVM---------------------- 687

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                    +G +    G         V +G  Y  +L HMV DK
Sbjct: 688  -----------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDK 717

Query: 1267 V 1267
            +
Sbjct: 718  I 718



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/345 (13%), Positives = 96/345 (27%), Gaps = 31/345 (8%)

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           +  S+    + D  K   +  G  ++  R    +      R          I     L N
Sbjct: 62  LKYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHN 121

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +         +   + + L     + +      I + +++  ++S+   +   A  
Sbjct: 122 THWGLVCPAETPEGQACGLVKNLALMCYISVGTPADPIVDYLTNRGMESLEEYEPTRAPH 181

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYG 567
                      + +    +  + +  I   RR   +  +  + R     E +    T  G
Sbjct: 182 ATKVF---VNGTWIGCHNDPAHLVPHIQEVRRKGIIAHEASLVRDIRDREFK--IFTDAG 236

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-------------- 613
           R+C       ++    +        +    +E     V                      
Sbjct: 237 RVCRPLFVIDNDPKSENMGNLALTKDMVQKLEDERDMVLTMDPEERAEQVIGWEALVDSG 296

Query: 614 -VVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDFI 664
            V Y+ A EEE   IA     L+               E    +     +          
Sbjct: 297 AVEYVDAEEEETIMIAMTPEDLEISRQIQAGYAAPVPSEDAPNQRVKAPLNPTAHTWTHC 356

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           +  P  ++ I AS+IPF +++ S R      M +QA+ +      
Sbjct: 357 EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYD 401


>gi|212373995|emb|CAP09924.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35723]
          Length = 272

 Score =  265 bits (676), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 155/266 (58%), Positives = 207/266 (77%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR
Sbjct: 1   LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYR 60

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  
Sbjct: 61  VVKEGVVTDEIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTL 120

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 121 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 180

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+
Sbjct: 181 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVR 240

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGR 809
            GD V+R+DI+ADGPSTD+G+LALG+
Sbjct: 241 KGDRVQRSDIMADGPSTDMGELALGQ 266


>gi|298912927|emb|CAZ66631.1| RNA polymerase beta subunit [Aeromonas enteropelogenes]
          Length = 289

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 166/289 (57%), Positives = 224/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF +++YDLSTVGR+K N RL  +    V  + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSAERYDLSTVGRMKFNRRLGREDETGVGVLTKDDIVEVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFL
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFL 289


>gi|195147244|ref|XP_002014590.1| GL18874 [Drosophila persimilis]
 gi|194106543|gb|EDW28586.1| GL18874 [Drosophila persimilis]
          Length = 1127

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 87/353 (24%), Positives = 133/353 (37%), Gaps = 83/353 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++ +  ++ I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 827  KVEKMDEKEECFVDSIRQLGSFDLTPKKTVCITLRVPRPATIGDKFASRAGQKGICSQKY 886

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +    G               
Sbjct: 887  PAEDLPFTESGMIPDIVFNPHGFPSRMTIAMMIETMAGKSAAVHG--------------- 931

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI---NS 1221
                                                  GV  +TP        AI     
Sbjct: 932  --------------------------------------GVYDATPFRFSEKNTAIDYFGK 953

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    TQQ
Sbjct: 954  MLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGTVEARTQQ 1013

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRT-RVYESIV 1333
            P+ G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + I+
Sbjct: 1014 PIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHSCGSILSPLQQII 1073

Query: 1334 A----GNDTFETG---------------TPESFNVLVKEMQALGLSIDLENSR 1367
                 G  + +                  P SF  LV E+ ++ ++   + ++
Sbjct: 1074 KRNERGGLSSKPQTCRLCGDSSSVSMIEIPFSFKFLVTELSSVNINARFKLNK 1126



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 72/421 (17%), Positives = 143/421 (33%), Gaps = 35/421 (8%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           +S L  + E++N +  ++H R   A+ +G         E R + P  +G ICP  T +G 
Sbjct: 448 NSGLVIMAENINRMRYMSHFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGT 504

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ LT    ++          K+        +              Q N       
Sbjct: 505 PCGLLNHLTLTCEISKRPDP-----KLVQAIPPKLIEM-----GMLPLSCQRNPDSKMYV 554

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCN 695
              +          +     E + +   +      +    IPF +N              
Sbjct: 555 VLLDGKHLGHIFQSDACKIVEDLRYEKITGAVPQMMEIGFIPFKKNGQFPGLYLSTGPAR 614

Query: 696 MQRQAVPLLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M R    +   +  ++GT   +   +A             +          + ++    D
Sbjct: 615 MMRPVWNIKWKQVEYIGTLEQLYMEIAIDPKEMYPDFTTHLELAKTHFMSNLANLIPMPD 674

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALG 808
            + S  ++Y+    +++    C+N  ++   K+         +      D     D A+G
Sbjct: 675 YNQSPRNMYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMG 734

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            N +VA + + GY+ ED+M+I++        + SI+  +F  + + +           P+
Sbjct: 735 TNAIVAVISYTGYDMEDAMIINKSAYERGFAYGSIYKSKFVQLPKKSS-----YFARHPH 789

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKI-----TPKGESPMTPEEKLLRAIFGEKAV 922
           + E   K +D  G+   GA++  G  L         T K E     EE  + +I    + 
Sbjct: 790 MPELA-KYLDTDGLPHPGAKLTFGCPLYCYFDGEVATYKVEKMDEKEECFVDSIRQLGSF 848

Query: 923 D 923
           D
Sbjct: 849 D 849


>gi|108885403|gb|ABG23218.1| DNA-directed RNA polymerase [Bacillus sp. A49]
 gi|108885405|gb|ABG23219.1| DNA-directed RNA polymerase [Bacillus licheniformis]
          Length = 145

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 63/167 (37%), Positives = 100/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF
Sbjct: 51  KYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAW 145


>gi|195350089|ref|XP_002041574.1| GM16738 [Drosophila sechellia]
 gi|194123347|gb|EDW45390.1| GM16738 [Drosophila sechellia]
          Length = 1129

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 125/350 (35%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPKKTVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 95/615 (15%), Positives = 219/615 (35%), Gaps = 72/615 (11%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYESDQYYVSCVQSMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D+     + R ++ + L+          + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDEDVTDFILRERVMIHLDTYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    + ++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  A+  F  +              S L  + E++N +  ++
Sbjct: 408 DALVTSAVMTQCMRQAGGVGRAIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIETPYRKVCDGKVTNDVVYLSAME---EENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                 + +    +   ++ LS+     E+   +      L        E +        
Sbjct: 525 DP-NLVKAIPKHLIDMGMMPLSSRRYLGEKLYVVFLDGKHLGHIHQSEAEKIV------- 576

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPF 710
                +++ +          +    IPF +N              M R    L      +
Sbjct: 577 -----DELRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYLATGPARMMRPVWNLKWKRVEY 631

Query: 711 VGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           +GT   +   +A  +          +          + ++    D + S  ++Y+    +
Sbjct: 632 IGTLEQLYMEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGK 691

Query: 769 RSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNF 823
           ++    C+N  ++   K+         +      D     D A+G N +VA + + GY+ 
Sbjct: 692 QTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDM 751

Query: 824 EDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           ED+M+I++        + SI+  +F  + + +                E +K++D  G+ 
Sbjct: 752 EDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELIKHLDTDGLP 805

Query: 883 CVGAEVNPGDILVGK 897
             G++++ G  L   
Sbjct: 806 HPGSKLSYGSPLYCY 820


>gi|298912919|emb|CAZ66627.1| RNA polymerase beta subunit [Aeromonas hydrophila]
          Length = 289

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 167/289 (57%), Positives = 224/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF S++YDLSTVGR+K N RL  +    V  + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSSERYDLSTVGRMKFNRRLAREDETGVGTLTKDDIVDVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFL
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFL 289


>gi|124491197|gb|ABN12933.1| RNA polymerase beta chain [Agrobacterium tumefaciens]
          Length = 237

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 141/238 (59%), Positives = 177/238 (74%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKLPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EILSTFY K  Y + GD W  P    D +  AKV + ++D DTGE V+E GKKLT  L++
Sbjct: 61  EILSTFYTKATYERAGDGWRIPFQP-DALKNAKVITDMMDADTGEVVVEGGKKLTPRLIR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L +KG+K L  T + L G ++AEDIVN ETGEIY+EAGD IDEK+L  I  S   +IP+
Sbjct: 120 QLVDKGLKALKATDEDLYGNFLAEDIVNYETGEIYLEAGDEIDEKTLGLILQSGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D VN  AYIRNTL  DKN++R++AL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LNIDHVNVGAYIRNTLSVDKNQNRQEALFDIYRVMRPGEPPTMDSAEAMFNSLFFDAE 237


>gi|298912917|emb|CAZ66626.1| RNA polymerase beta subunit [Aeromonas caviae]
          Length = 289

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 167/289 (57%), Positives = 224/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF S++YDLSTVGR+K N RL  +    V  + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSSERYDLSTVGRMKFNRRLGREDETGVGVLTKDDIVEVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFL
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFL 289


>gi|258562146|gb|ACV81795.1| RNA polymerase II second largest subunit [Wallemia sebi]
          Length = 680

 Score =  265 bits (676), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 122/766 (15%), Positives = 215/766 (28%), Gaps = 135/766 (17%)

Query: 519  SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
             + +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 46   RAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQ 101

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV +L   A V+  G    P +         ++   +     N+     N       
Sbjct: 102  ACGLVKNLALMANVST-GSSSAPIQDFLQEWGMEELEEFNPR--SNQVKVFVNGVWIGVH 158

Query: 639  SFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                 LV            + ++    D  +   K          P    D+        
Sbjct: 159  RDPTNLVKTLRKLRREGDIQHEVSVVRDVREKEIKVFTDAGRVCRPLFLVDEET------ 212

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
              Q+  +           T  E                G++E +DA       +    + 
Sbjct: 213  --QQLEINKSHIAKIEAHTNGEDEDPDQPYNWAKLMSDGVMELLDAEEEETVMICMTPEE 270

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                   +     +        +   L     +          PS  LG       +  +
Sbjct: 271  LEHSRQGFIPQDEEFDPAARIKSASTL-----DTHTWTHCEIHPSMILG-------ICAS 318

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +   +H+  F+                          
Sbjct: 319  IIPFPDHNQSPRNTYQAAMGKQAMG--VHLTNFQQRM----------------------- 353

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 354  ----DTLSNILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSA 409

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    IF R  +D  ++  ++  E+ E   R+          +       I  G  
Sbjct: 410  IDRGLF-RSIFYRSYMDTEKKVGTMLLEEFEKPTRETCLRMKHGTYDKIENDGLIAPGTA 468

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +  D      R++          ++     +  Q             
Sbjct: 469  VTGDDIIIGKTAPIPPDSEELGQRTKLHTKRDVSTPLKSTENGIVDQ------------- 515

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            L+  KV +   R  Q GDK A RHG KG +      EDMPF  D
Sbjct: 516  -------VLVTTNADGLKFSKVRMRSTRIPQIGDKFASRHGQKGTIGITYRNEDMPFTSD 568

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +G + E  L       G +  +          IS        
Sbjct: 569  GITPDLIINPHAIPSRMTIGHLVECLLSKVATLQGSEGDATPFTEVTVESISS------- 621

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                              +L      K G+ V                        +G +
Sbjct: 622  ------------------ILHEKGYQKRGLEVM----------------------YNGHT 641

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                G         V +G  Y  +L HMV DK++AR+ G   ++T+
Sbjct: 642  ----GR---KLQAQVYIGPTYYQRLKHMVDDKIHARARGPVQILTR 680


>gi|171186405|ref|YP_001795324.1| DNA-directed RNA polymerase subunit B [Thermoproteus neutrophilus
            V24Sta]
 gi|170935617|gb|ACB40878.1| RNA polymerase Rpb2 domain 6 [Thermoproteus neutrophilus V24Sta]
          Length = 1127

 Score =  264 bits (675), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 101/606 (16%), Positives = 198/606 (32%), Gaps = 105/606 (17%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            V+ GD     D +      +  D     N  +A  P    +    + I    +   V + 
Sbjct: 604  VRRGDLT--WDDLVKMGVIEYLDADEEENAHIAVDPDVDLSNYTHVEIVPSSILGAVGSI 661

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R+               S      +D  G   +        +    +   
Sbjct: 662  IPYLEHNQSPRNQYEAAMAKQSLGLPQSNFLY-KLDSRG--HMLYYPERPIVTTRGLELV 718

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G S     +  + A+      ++ D  +   + V   +    +F R    + ++    E 
Sbjct: 719  GYSRRPAGQNAVVALLTYTGYNIEDAVILNKASVERGMF-RSVFYRTYETEEQKYPGGEE 777

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++IE+                       + G           +  +   ++         
Sbjct: 778  DKIEIPD-------------------SSVKGYRGPEAYSHLDEDGIAPPEVYVSSNEVLV 818

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
             + +          E +  +   +   +    K  ++++       P   ++VKV +   
Sbjct: 819  GKTSPPRFYTTLEAERILKERRDASVAVRRGEKGIVDRVII--TESPEGNKLVKVRLREL 876

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+                                 VG +     
Sbjct: 877  RVPELGDKFASRHGQKGV---------------------------------VGMLL---- 899

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                     + + +                 + ++   +   +++       +       
Sbjct: 900  ---------RHEDMPFTEDGIVP--------DIIVNPHALPSRMTVAQLLESMAGKVGAS 942

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G  V    F+G  EE +  +L        G+ ++Y G+TGE     + +G +Y  KL+H
Sbjct: 943  LGALVDATAFEGVKEEDLRKLLLKLGYKWDGKEVMYSGITGERLVADIFIGVVYYQKLHH 1002

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MV+DK++AR+ G   ++T+QP  G+S  GG RLGEME   + A+GA+ +L E L   SD 
Sbjct: 1003 MVADKIHARARGPVQILTRQPTEGRSREGGLRLGEMERDVLIAHGASALLYERLVESSD- 1061

Query: 1322 VVGRTRVY------------------ESIVAGN--DTFETGTPESFNVLVKEMQALGLSI 1361
               +  +Y                  +  + G+     +   P ++ +L++E+ ALG+  
Sbjct: 1062 ---KYTMYVCELCGLPAYLDAKSNKPKCPIHGDTGQFAKVVVPYAYKLLLQELIALGIYP 1118

Query: 1362 DLENSR 1367
             LE + 
Sbjct: 1119 KLELTE 1124



 Score =  154 bits (390), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 108/738 (14%), Positives = 226/738 (30%), Gaps = 137/738 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFV 77
           L   Q  S++ FL   +          E   +GL+   + +   +P I    G+  + + 
Sbjct: 37  LANHQIKSFNDFLDKKLPKIVEDFKVVETEIKGLKLVLERIEVGWPKIKESDGSESIIY- 95

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +   R+ TY+ PL +T  L V D    T             Y+G+LP+
Sbjct: 96  ----------PMEARLRNATYSAPLYLTATLYVDDEPYVTETF----------YIGELPI 135

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGR 171
           M K                         G F+I G +R+++SQ  L     I+   DK  
Sbjct: 136 MVKSKRCNLTRLRPGEYIKKFEDPQDFGGYFIINGSERVIISQEDLVADRPIYDRGDKPS 195

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEILS 230
                K +     I  +   + +E +   +I+V +     K+P   ++ ALG++++E   
Sbjct: 196 VKYIAKTI--STGIGYR-STLTVELNRDGVIYVTLSAMPVKIPFPIYMKALGLETDE--- 249

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVS---SSLVDIDTGEQVIESGKKLTSGLLKS 287
                +V +   D          L+   +++      +D   G+  +   K +       
Sbjct: 250 ----DVVKAVSDDPEIQKELLPSLIAANQIAITREDALDFIGGKVAVGQPKPIRVEKAYQ 305

Query: 288 L--------------KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           L               EK  + + +    + G  + + +V  + G    +  D +  K +
Sbjct: 306 LLDKYFLPHLGTTTPDEKRQQEIRLKKALMLGQ-IVKGLVELQLGRRKPDDKDHVANKRV 364

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
             +     +    +    +                        I  ++RP D+ T  V +
Sbjct: 365 RLVGDLMTQLFRTVLKQFLQELKSQLEKYYARGRIPH------IQTIVRP-DIITERVRQ 417

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-GT 452
           ++    +          + R      L+      V  + +       + L   + G+   
Sbjct: 418 ALATGNWVGGKTGVSQILDRTNYMSTLSYLRRV-VSSLSRTQPHFEARDLHPTQWGRLCA 476

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           ++  +      V+++  + +    +    +E+ +    +   +  +  ++       V  
Sbjct: 477 VETPEGQNVGLVKNLALLAEITTGVDEGEVEQLLY---NLGVVPLLKAREEGIRGAEVYI 533

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                                 +   RR   +          G     V+        P 
Sbjct: 534 NGRLIGVHP-----NPEELAKTVRGMRRQGKISDEINIAYLDGSVY--VNCDGGRIRRPL 586

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
              EG  + L   +    R     +         D      + YL A EEEN +IA    
Sbjct: 587 LVVEGGRLKLTKEIVEKVRRGDLTW--------DDLVKMGVIEYLDADEEENAHIAV--- 635

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                               +  V       ++  P  ++    S+IP+LE++ S R   
Sbjct: 636 --------------------DPDVDLSNYTHVEIVPSSILGAVGSIIPYLEHNQSPRNQY 675

Query: 693 GCNMQRQAVPLLKAEAPF 710
              M +Q++ L ++   +
Sbjct: 676 EAAMAKQSLGLPQSNFLY 693


>gi|89888255|gb|ABD78668.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
          Length = 280

 Score =  264 bits (675), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 169/277 (61%), Positives = 218/277 (78%)

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR+N YGF+ETPYRK+ DGKV++ + YLSA+EE +  IAQAN++LD +G F ++LV CR
Sbjct: 3   YARLNEYGFLETPYRKIIDGKVSDQIDYLSAIEESHYVIAQANAALDAEGHFVDDLVACR 62

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
            AGE +L     + ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E 
Sbjct: 63  EAGETMLTSPVNVHYMDVAPSQIVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEK 122

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +      GVDIY L+K+ 
Sbjct: 123 PLVGTGVERTVAVDSGTTVQALRGGLVDHVDAERVVIRVNDEENVAGEVGVDIYNLIKYT 182

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSNQNT +NQRP+VK GD V + D++ADG STDLG+LALG+NML+AFMPW+GYNFEDS+L
Sbjct: 183 RSNQNTNINQRPIVKRGDRVSKGDVLADGASTDLGELALGQNMLIAFMPWNGYNFEDSIL 242

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ISER+V++D +TS+H EE  V+ARDTKLGPEEITRDI
Sbjct: 243 ISERVVADDRYTSVHXEELTVVARDTKLGPEEITRDI 279


>gi|190694917|gb|ACE88999.1| RNA polymerase beta subunit [Mycobacterium conceptionense]
          Length = 206

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 92/219 (42%), Positives = 121/219 (55%), Gaps = 37/219 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 17   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 76

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 77   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 129

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 130  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 167

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK
Sbjct: 168  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDK 206


>gi|103001369|gb|ABF71504.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 699

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 115/820 (14%), Positives = 235/820 (28%), Gaps = 145/820 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + +  +              + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                D+  +     N+   ++ +  L+ +               S     AK  G    V
Sbjct: 237  LFVIDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV 288

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q               V+         
Sbjct: 289  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHT 346

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M  + +   + +  ++         
Sbjct: 347  WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM------ 398

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                   +  +             +       +   +  + AI 
Sbjct: 399  ---------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 437

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 438  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 493

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  ++ D      R++          ++  
Sbjct: 494  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRST 553

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             L+ VKV +   +  Q GDK A RH
Sbjct: 554  ENGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRH 593

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +   
Sbjct: 594  GQKGTIGITYRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD- 652

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP F   
Sbjct: 653  ----------------------------------------------------ATP-FTEV 659

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
              ++++ +LR       G  ++Y+G TG      V +G  
Sbjct: 660  TVDSVSKLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPT 699


>gi|298912921|emb|CAZ66628.1| RNA polymerase beta subunit [Aeromonas veronii bv. veronii]
 gi|298912923|emb|CAZ66629.1| RNA polymerase beta subunit [Aeromonas jandaei]
          Length = 289

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 165/289 (57%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF +++YDLSTVGR+K N RL  +       + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSAERYDLSTVGRMKFNRRLGREDETGAGVLTKDDIVDVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFL
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFL 289


>gi|48188|emb|CAA77863.1| N-terminus of beta subunit of RNA polymerase [Thermotoga maritima
           MSB8]
          Length = 404

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 113/421 (26%), Positives = 181/421 (42%), Gaps = 75/421 (17%)

Query: 11  GRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA--- 67
            R R  FGK+ E + IPDL+E+QK+SY  FL           EGL    K   PI +   
Sbjct: 8   RRTRVSFGKSREPLPIPDLVEIQKSSYRRFL----------EEGLLEVLKKFSPIYSQAT 57

Query: 68  ------FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                       LEFVS     P  D  +C  + LTY+VP+  T RL             
Sbjct: 58  RSDLRKSDRGFALEFVSTRTGEPAIDPLECKAKGLTYSVPIYATARLTDM---------K 108

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYA 181
             ++KE+ +++G +P MT  GTF+I G +R+VV+Q+  SPG++F  +        +  Y 
Sbjct: 109 SGEMKEEEVFLGYIPYMTDRGTFIINGAERVVVNQIVVSPGLYFSSE-----YIDREEYG 163

Query: 182 CRIIPDQGLWMDIEFDSKD-IIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQ 240
              +P +G W+++  D  D +++  +D  +KV +  FL  +G + +E + + YP  + + 
Sbjct: 164 GYFLPSRGAWLEVILDPYDGVLYAGLD-GKKVNLFLFLKTIGYEKDEDILSLYPTYLDAD 222

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             D          L VG+ +   + D   G ++ E    LT  L +           I  
Sbjct: 223 DEDSLL-------LHVGSILLEDIYD--GGRKIAEKWDILTKDLAER----------ILM 263

Query: 301 DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
                       +   T E  +E      E+  EE   ++I  +                
Sbjct: 264 IDDINQIKIVHPIAQNTFEKMLEVVSSSSEEGEEEEEKTKIYGL---------------- 307

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
                      DA L+I+R +RP ++   + A+   + LFF+ ++YDLS VGR K+N RL
Sbjct: 308 -----NEVTVVDAYLEIFRRLRPEELPRINAAKRYLHDLFFNPERYDLSEVGRYKVNERL 362

Query: 421 N 421
            
Sbjct: 363 R 363


>gi|195575535|ref|XP_002077633.1| GD23021 [Drosophila simulans]
 gi|194189642|gb|EDX03218.1| GD23021 [Drosophila simulans]
          Length = 1129

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 125/350 (35%), Gaps = 77/350 (22%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    +E I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 829  KVVKMDEKEDCIVESIRQLGSFDLSPKKTVAITLRVPRPATIGDKFASRAGQKGICSQKY 888

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G    +    +     
Sbjct: 889  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENT 948

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 949  A--------------------------------------------------IDYFGKMLE 958

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 959  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1018

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIVA-- 1334
            G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV   
Sbjct: 1019 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQRIVKRN 1078

Query: 1335 ---------------GND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                           G++        P SF  LV E+ ++ ++   + + 
Sbjct: 1079 ETGGLSSQPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 94/615 (15%), Positives = 220/615 (35%), Gaps = 72/615 (11%)

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
                 ++ + +  +  I    +D  +   Y R     + ++     +  + R ++  +V
Sbjct: 234 KFMFSHVKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYESDQYYVSCVQSMLREVQNENV 293

Query: 387 STFSVAESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            T +  +S               +  D+     + R ++ + L+          + + I+
Sbjct: 294 YTHAQCKSFIGNLFRARFPEVPEWQPDEDVTDFILRERVMIHLDNYED------KFQLIV 347

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSV 493
            +I+ L     GK  ++++D+   + V   G +    L  +    + ++ R ++++++S 
Sbjct: 348 FMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP 407

Query: 494 D---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRIT 536
           D     +VM Q +  A  V  A+  F  +              S L  + E++N +  ++
Sbjct: 408 DALVTSAVMTQCMRQAGGVGRAIESFLATGNIASRTGLGLMQNSGLVIMAENINRMRYMS 467

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H R   A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++   
Sbjct: 468 HFR---AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRP 524

Query: 597 FIETPYRKVCDGKVTNDVVYLSAME---EENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
             +   + +    +   ++ LS+     E+   +      L        + +        
Sbjct: 525 DPKLV-KAIPKHLIDMGMMPLSSRRYLGEKLYVVFLDGKHLGHIHQSEADKIV------- 576

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPF 710
                +++ +          +    IPF +N              M R    L      +
Sbjct: 577 -----DELRYGKIFGTLPQMMEIGFIPFKKNGQFPGLYLATGPARMMRPVWNLKWKRVEY 631

Query: 711 VGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
           +GT   +   +A  +          +          + ++    D + S  ++Y+    +
Sbjct: 632 IGTLEQLYMEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGK 691

Query: 769 RSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNF 823
           ++    C+N  ++   K+         +      D     D A+G N +VA + + GY+ 
Sbjct: 692 QTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDM 751

Query: 824 EDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           ED+M+I++        + SI+  +F  + + +                E +K++D  G+ 
Sbjct: 752 EDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFARHPHMP------ELIKHLDTDGLP 805

Query: 883 CVGAEVNPGDILVGK 897
             G++++ G  L   
Sbjct: 806 HPGSKLSYGSPLYCY 820


>gi|294871589|ref|XP_002765980.1| DNA-directed RNA polymerase I subunit, putative [Perkinsus marinus
            ATCC 50983]
 gi|239866470|gb|EEQ98697.1| DNA-directed RNA polymerase I subunit, putative [Perkinsus marinus
            ATCC 50983]
          Length = 510

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 78/341 (22%), Positives = 124/341 (36%), Gaps = 34/341 (9%)

Query: 984  SRLMEILCGQNAVSGPKGFKK----STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            SRL +     ++V G K  K             + E             E      +  +
Sbjct: 136  SRLAQFRADNHSVKGEKVVKDLDYDGIPYIGQQVHEGDPICRVLNKGTGEAKLEKYKEGE 195

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
            V +    +++                        + + + + R    GDK + RHG KG+
Sbjct: 196  VAWVEQVNMIGGGGWWGGGAGARNPGGIKDGSERMSIKLRLPRNPVVGDKFSSRHGQKGV 255

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            ++ + P  DMPF   G   DI+ NP G+PSRM +G + E   G A    G  +       
Sbjct: 256  MAILWPQADMPFSTSGISPDIMFNPHGMPSRMTIGMLIEFMAGKAAALTGMPV------- 308

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                           V        +     D       + +  G   +         E  
Sbjct: 309  ---------------VNANSFRQYRGKGLLDTEHNNEKDPYAPGDTTA--------HEYF 345

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L+    +  G   LY G+ GEP    + +G +Y  +L HMV DK   R+TG    +T
Sbjct: 346  GETLKKFGYEYLGAEELYSGMHGEPLKTHIYMGVVYYQRLRHMVLDKFQVRATGPIDPLT 405

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +QP+ G+   GG R GEME   + ++G + +L + L   SD
Sbjct: 406  RQPVKGRKKHGGVRFGEMERDSLISHGTSALLADRLLKCSD 446



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 62/175 (35%), Gaps = 9/175 (5%)

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDE 787
           K   I     ++  VI  +    + + S  ++Y+    +++     +N   R   KV   
Sbjct: 2   KYTHIELSPISMLSVIAGLTPFSNHNQSPRNMYQCQMLKQTMAIPYLNHPYRTDNKVYKI 61

Query: 788 VRRNDIIADG---PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                 +         +      G N +VA +   G++ ED+++IS+             
Sbjct: 62  TYPQFPMVRTTVLSEANFDVKPAGTNAIVAVIAHSGFDMEDALIISKGSYDRGFKHGSVY 121

Query: 845 EEFEVMARDTKLG----PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           +   +             +    +     E+ +K++D  GI  +G +V+ GD + 
Sbjct: 122 KTKVINCPPKGTVGSRLAQFRADNHSVKGEKVVKDLDYDGIPYIGQQVHEGDPIC 176


>gi|270012190|gb|EFA08638.1| hypothetical protein TcasGA2_TC006301 [Tribolium castaneum]
          Length = 848

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 118/325 (36%), Gaps = 83/325 (25%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             R       + R    GDK A R G KGI S+  P ED+PF + G   DIV NP G PSR
Sbjct: 574  NRTACFTFRVPRNPNVGDKFASRAGQKGICSQKWPMEDLPFTETGLVPDIVFNPHGFPSR 633

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E   G +                                              
Sbjct: 634  MTIAMMIEVMAGKSAA-------------------------------------------- 649

Query: 1191 DSVLRVAEQWKSGVPVSTPV-F--DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                         V  +TP  F  +    +    +L     +  G   +Y G+ G     
Sbjct: 650  ---------LHGLVHDATPFKFTEEDTAIDYFGRLLEAGGYNYYGTETMYSGIDGREMTA 700

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G ++  +L HMVSDK   RSTG   ++T+QPL G+   GG R GEME   + ++GA
Sbjct: 701  QIFFGIVHYQRLRHMVSDKWQVRSTGPTDILTRQPLKGRKRGGGVRFGEMERDSLISHGA 760

Query: 1308 AYVLQEMLTIKSDD-----------------VVGRT--RVYESIVA--------GNDTFE 1340
            +++LQ+ L   SD                  V+ R   +  +S           G D  E
Sbjct: 761  SFLLQDRLFHCSDKTTAFICTSCGTLLGPVTVITRVAEKANQSTCKETCRLCGHGRDISE 820

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
               P  F   V +M +  +++ +  
Sbjct: 821  IQIPYIFKFFVTQMASCNINVKMLT 845



 Score = 72.0 bits (175), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 69/391 (17%), Positives = 135/391 (34%), Gaps = 29/391 (7%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            L+ + E++N +  ++H     A+ +G   +     E+R + P  +G ICP  T +G   
Sbjct: 169 GLTIVAENINRMRYMSH---FKAVHRGAFFQEMRTTEVRQLLPDAWGFICPVHTPDGAPC 225

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++ LT+   V          RKV +      ++         +Y+A            
Sbjct: 226 GLLNHLTTNCSVTDV----PDARKVENIP----IILTRLGMVALKYVASVGFD-QNYVVV 276

Query: 641 TEELVFCRCAGEEILVPREKIDFIDAS-PKQVVSIAASLIPFLENDDSNRVLM----GCN 695
            +  V      +      E++        +   ++   L+P ++       L        
Sbjct: 277 LDGRVLGYVRRDLAPKLVEQLRLCKIKGEEVPNTLEIVLVPLMKVTAQFPGLYLFTGPAR 336

Query: 696 MQRQAVPLLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M R  + L   E  FVGT   +   +  S           +     A    +  +    D
Sbjct: 337 MMRPLLNLKTKEVEFVGTFEQVYMDICVSPDEYYKGVTTHMELSKLAFLSNLAQLIPMPD 396

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPL--VKVGDEVRRNDIIADGPSTDL---GDLALG 808
            + S  ++Y+    +++    C N R     K+         +      D     D A+G
Sbjct: 397 CNQSPRNMYQCQMGKQTMGTPCHNWRSQSETKLYRLQTPATPLFRPVHYDNINLDDFAMG 456

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            N +VA + + GY+ ED+M+I++           H   ++      +       R+    
Sbjct: 457 TNAIVAVISYTGYDMEDAMIINKAADERGFA---HGSIYKTEFVTLEHESSYFCRNPE-- 511

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             E  + +D  G+  +G  +  GD L    +
Sbjct: 512 KPELAEFLDTDGLPIIGRRMKDGDPLYCYYS 542


>gi|294668295|ref|ZP_06733399.1| hypothetical protein NEIELOOT_00208 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
 gi|291309749|gb|EFE50992.1| hypothetical protein NEIELOOT_00208 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
          Length = 316

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 155/316 (49%), Positives = 227/316 (71%), Gaps = 1/316 (0%)

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +R  + +      GVDIY L+KF RSNQ+T +NQRP VK GD ++R D++ADG STDLG+
Sbjct: 1    MRVHDDEAVAGEVGVDIYNLVKFTRSNQSTNINQRPAVKAGDVLQRGDLVADGASTDLGE 60

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            LALG+NM++AFMPW+GYN+EDS+LISE++ ++D +TSIHIEE  V+ARDTKLG E+ITRD
Sbjct: 61   LALGQNMVIAFMPWNGYNYEDSILISEKVAADDRYTSIHIEELNVVARDTKLGAEDITRD 120

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            IPN+SE     +DE GI+ +GAEV  GD+LVGK+TPKGE+ +TPEEKLLRAIFGEKA DV
Sbjct: 121  IPNLSERMQSRLDESGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDV 180

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
            +DTSLR+P+G+SGTV+DV++F R GI +++R+ ++   +++    D +D+  I D + + 
Sbjct: 181  KDTSLRMPTGMSGTVIDVQVFTREGIQRDKRAQAIIDAELKRYRLDLNDQLRIFDNDAFD 240

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP-RSQWWQFAVQDEKVQRNVESLKVQYE 1043
            R+  ++ GQ A  GP    K + ++++ ++  P +  W+   V DE + + +E +K   +
Sbjct: 241  RIERMIVGQKANGGPMKLAKGSKITAEYLAGLPSKHDWFDVRVADENIAKQLELIKGSLQ 300

Query: 1044 TSKSILEDRFKNKIEK 1059
              +   E  F+ K +K
Sbjct: 301  DKREEAETLFEIKKKK 316


>gi|242074526|ref|XP_002447199.1| hypothetical protein SORBIDRAFT_06g030300 [Sorghum bicolor]
 gi|241938382|gb|EES11527.1| hypothetical protein SORBIDRAFT_06g030300 [Sorghum bicolor]
          Length = 1239

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 96/510 (18%), Positives = 155/510 (30%), Gaps = 89/510 (17%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      +    D      +
Sbjct: 785  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYTAFGRKDDYTRPEY 844

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 845  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKTDVENKDGTKRLKLKE 903

Query: 1007 VLS-------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             +           +               +     +  +    E     L+   K  ++K
Sbjct: 904  KIDFGKTESKRGRVDNLDDDGLPYIGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 963

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +        G    V V +   R    GDK +  HG KG+V  +   E+ PF  +G   D
Sbjct: 964  VLL-SANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHEGIVPD 1021

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IV+NP   P+R   GQ+ E     A +G G   K                          
Sbjct: 1022 IVINPHAFPTRQTPGQLLE-----AALGKGIACKGT------------------------ 1052

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                    +  +TP F  A  + I   L  A     G   + +G
Sbjct: 1053 ------------------------MRYATP-FTTASVDVIAEQLHKAGYSRWGAENVLNG 1087

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TGE     V +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GEME 
Sbjct: 1088 RTGERMQSLVFMGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMER 1147

Query: 1300 WCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYESIVAG---------N 1336
             C+ A+G+A  L E L + SD              +VV R+      + G          
Sbjct: 1148 DCLLAHGSAANLHERLFMLSDFSQMHICQTCERVANVVMRSVPGGKKIRGPYCGFCKSSE 1207

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +      P    +L +E+ ++G+ +  +  
Sbjct: 1208 NIVRINVPYGAKLLYQELFSMGICLKFDTE 1237



 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 139/969 (14%), Positives = 278/969 (28%), Gaps = 223/969 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 114 LISHQINSYNEFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 163

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  LK+ + + V+ +++   +K+  + 
Sbjct: 164 GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLKVEVTIQVYSLEKSDKSKTGNEG 223

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 224 FVQKRNFMNETHWIFIGLLPVMVKSNLCLLHSLKESECLFDAGGYFLVKGMEKVFIAQEQ 283

Query: 159 RS-----------PGIHFDHDKGRASLSGKLLYACRIIPDQGLW-MDIEFDSKDIIHVRI 206
           R              I F H+  R  +  KL+ + R     G   + I F     ++   
Sbjct: 284 RCLKRLWVSDRPFWMISFMHEIKRRRIYIKLVESTRSEDFSGSKVISISF-----LYAT- 337

Query: 207 DRRRKVPVTSFLMALGMDSE----EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                +PV     ALG+ S+    +++        V +                  +  +
Sbjct: 338 -----MPVWLLFFALGISSDKEAFDVIDMQDCDASVINTISATIKESDELCKGFRKSDKA 392

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              VD           +     + + L                G  V   ++   TG+  
Sbjct: 393 RQYVDELVKSSRFPPAESFDDYVARFLFPDING--NRNKAFFLGYMVKCLLM-AFTGKRK 449

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIP-----ILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
            +  D    K L+       R++      +           + N       +   DA + 
Sbjct: 450 CDNKDDFRNKRLDLPGELLGRELRAQLRLLERRMVKAIQRDLNNDRELQDLERYIDASIV 509

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
              + R     ++                   ++   + +  R             D R+
Sbjct: 510 TNGLNRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTRQRVAYAGKAGDARY 569

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                   +  +        G + ++        R    ++++    G+ ++     E I
Sbjct: 570 PNPSYWGKLCFLSTPDGENCGLVKNLAVTAIVSSRVGQPLIESFISCGMSKLNDIPTEHI 629

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
             +D                     F   + +   ++  + + R+   RR S +      
Sbjct: 630 QRMDK-------------------IFLNGNWVGSCKDSASFVFRLRCMRRSSMIDPQVEI 670

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           +     +   V       + P    E  N        SF+                +   
Sbjct: 671 KRDKHHKEVRVFSDAGRILRPLLVVENLNKIRKPKGRSFS--------------FQELMQ 716

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + ++   EEE+   A     L E                            +  P  
Sbjct: 717 QEIIEFIGVEEEEDIQCAWGIRHLFESEGAI-----------------SSYTHCELDPSF 759

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ ++  +IPF  ++ + RVL                             K S  AI   
Sbjct: 760 LMGLSCGIIPFANHNFARRVLYQSE-------------------------KHSQQAIGYS 794

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                 +VD                               +      QRPL     +   
Sbjct: 795 TTNPHIRVD-----------------------------TLSHQLYYPQRPL----FKTVI 821

Query: 791 NDIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            D +     T  G        +   G+N +VA     G+N EDS++++   +   +F + 
Sbjct: 822 ADCLGRSDYTAFGRKDDYTRPEYFNGQNAIVAVNVHQGFNQEDSLVMNRASLERGMFRTE 881

Query: 843 HIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           H+  ++    +          E+I           + N+D+ G+  +GA +   DI++GK
Sbjct: 882 HLRSYKTDVENKDGTKRLKLKEKIDFGKTESKRGRVDNLDDDGLPYIGASLQTNDIVIGK 941

Query: 898 ITPKGESPM 906
           ++  GE   
Sbjct: 942 VSESGEDHS 950


>gi|298912925|emb|CAZ66630.1| RNA polymerase beta subunit [Aeromonas schubertii]
          Length = 289

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 166/289 (57%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF S++YDLSTVGR+K N RL  +    V  + K+DI+ ++K L+D+RNG   +
Sbjct: 1   QLFENLFFSSERYDLSTVGRMKFNRRLGREDETGVGVLTKDDIVDVMKRLIDIRNGNDEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDALMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N  S +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPQSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVEYLSAIEEGKYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             EDG   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFL
Sbjct: 241 TTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFL 289


>gi|156627827|gb|ABU88901.1| RNA polymerase II second largest subunit [Phymatotrichopsis omnivora]
 gi|156627829|gb|ABU88902.1| RNA polymerase II second largest subunit [Phymatotrichopsis omnivora]
 gi|156627831|gb|ABU88903.1| RNA polymerase II second largest subunit [Phymatotrichopsis omnivora]
 gi|156627833|gb|ABU88904.1| RNA polymerase II second largest subunit [Phymatotrichopsis omnivora]
          Length = 884

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 128/933 (13%), Positives = 263/933 (28%), Gaps = 150/933 (16%)

Query: 346  ILYVDSVNNNAYIRNT--LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +     ++ +        
Sbjct: 82   VSDEDILNHVCYDRNDTEMLEMMKPCIEEAFVIQDREVALDFIGKRGNSQGV---NKEKR 138

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +Y    + +  +      +  +  +      +  ++  ++     +  +DD D+ G +R
Sbjct: 139  IRYARDIMQKELLPHISQKEGSETRK---AFFLGYMVHRMLQCALERREVDDRDHFGKKR 195

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    ++ + + + +               + +  + + +     +  
Sbjct: 196  LDLAGPLLAQLFRNLWKQLTKEVYKYLEKCVEGSKEFNLNLAVKSNTITTGLKYSLATGN 255

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 256  WASQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 311

Query: 569  ICPAETSEGHNIGLVSSLTS--FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L    +  V   G     +    + +   +     +      +
Sbjct: 312  VCPAETPEGQACGLVKNLALMSYITVGTPGDPIVDFMAQRNMEFLEEYEPQRSPNATKIF 371

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
            +      +  D       V        I      I D  D   K          P    D
Sbjct: 372  VNGVWVGIHRDPLQLVRTVQKLRRTGVISHEVSVIRDIRDREFKIFTDAGRVCRPLFAID 431

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            +         +  Q   + + E        E    K   +       G VE +DA     
Sbjct: 432  NDPTSERRGQLVLQKEHIERLEDDHSLPEEERFGWKGLLSV------GAVEYLDAEEEET 485

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +       +    +           + P+                PS  LG  
Sbjct: 486  VMIVMTPEDLELSRQVQAGYEVAEETDMGKRVKAPI---NPATHTWTHCEIHPSMILG-- 540

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   + +  F                  
Sbjct: 541  -----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM-------------- 579

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 580  -------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 626

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R  +D+ +R      E+ E   R    +      +    
Sbjct: 627  DSVIMNQSSIDRGLF-RSLFYRSYMDQEKRIGMQIVEEFEKPMRSNTLKLKHGTYDKLDE 685

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ DL     R ++         ++     +  Q    
Sbjct: 686  DGLVAPGVRVSGEDIIIGKTAPIAPDLDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML- 744

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV +   +  Q GDK A RHG KG +     
Sbjct: 745  -------------------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYR 785

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 786  MEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD------------ 833

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 834  -----------------------------------------ATP-FTDVTVDSVSQLLRQ 851

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                  G  ++Y+G TG      V +G  Y  +
Sbjct: 852  EGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 884



 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 108/790 (13%), Positives = 225/790 (28%), Gaps = 142/790 (17%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+   E+IL+        ++  +     +  A ++   +V+
Sbjct: 65  YIKSD----IPIVIVFRALGVVSDEDILNHVCYDRNDTEMLEMMKPCIEEAFVIQDREVA 120

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +      Q +   K++     + + +K +                   ++ + G   
Sbjct: 121 LDFIGKRGNSQGVNKEKRI--RYARDIMQKEL----------------LPHISQKEGSET 162

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            +A  +            E R++                 L        K    ++Y+ +
Sbjct: 163 RKAFFLGYMVHRMLQCALERREVDDRDHFGKKRLDLAGPLLAQLFRNLWKQLTKEVYKYL 222

Query: 382 RPGDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                    F++  ++ +       KY L   G      +         + + +    + 
Sbjct: 223 EKCVEGSKEFNLNLAVKSNTITTGLKYSL-ATGNWASQKKAASSKAGVSQVLNRYTFAST 281

Query: 440 IKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           +  L        R+GK       +  +  +    E  + Q    +  +       + +  
Sbjct: 282 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYITVGTPG 341

Query: 495 IDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
              V      N + +         +A   F     +    + +  +  +   RR   +  
Sbjct: 342 DPIVDFMAQRNMEFLEEYEPQRSPNATKIFVNGVWVGIHRDPLQLVRTVQKLRRTGVIS- 400

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
                      +RD+    +     A         + +  TS  R       E   R   
Sbjct: 401 ------HEVSVIRDIRDREFKIFTDAGRVCRPLFAIDNDPTSERRGQLVLQKEHIERLED 454

Query: 607 DGKVTND-------------VVYLSAMEEENRYIAQANSSL------DEDGSFTEELVFC 647
           D  +  +             V YL A EEE   I      L             EE    
Sbjct: 455 DHSLPEEERFGWKGLLSVGAVEYLDAEEEETVMIVMTPEDLELSRQVQAGYEVAEETDMG 514

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +     I          +  P  ++ I AS+IPF +++ S R      M +QA+ +    
Sbjct: 515 KRVKAPINPATHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN 574

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                                A+R   +  +                             
Sbjct: 575 --------------------FAERMDTMANI----------------------------- 585

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                     Q+PL                      +L  G+N +VA + + GYN EDS+
Sbjct: 586 ------LYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 629

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGII 882
           ++++  +   +F S+    +    +   +   E     +  +   +       +DE G++
Sbjct: 630 IMNQSSIDRGLFRSLFYRSYMDQEKRIGMQIVEEFEKPMRSNTLKLKHGTYDKLDEDGLV 689

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             G  V+  DI++GK  P         ++       +K    RD S  + S  +G V  V
Sbjct: 690 APGVRVSGEDIIIGKTAPIAPDLDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQV 742

Query: 943 RIFNRHGIDK 952
            +       K
Sbjct: 743 MLTTNAEGLK 752


>gi|110669604|gb|ABG81897.1| RNA polymerase II second largest subunit [Bacidia schweinitzii]
          Length = 720

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 128/835 (15%), Positives = 241/835 (28%), Gaps = 136/835 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + +    +              + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLAGLFRMLFYKLTKDVFKYLQKCVESNKEFNLTLAVKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L+       ++      +    +     +        I      + D  D   K      
Sbjct: 177  LNNPNATKVFVNGVWVGVHSQPANLVNTIKSLRRQGLISYEVSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAG 733
                P F+ ++D      G  +  +       +    G GM++   +          + G
Sbjct: 237  RVCRPLFVVDNDPKSNNYGNLVLTKDHIQKLVDDEEAGAGMDAQEREEKLIGWQGLVKNG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG-DEVRRND 792
            +VE VDA       +    +   +   ++        +     N R   +    +     
Sbjct: 297  VVEYVDAEEEETIMIVMTPEDLETSRQLHAGYTLPPPDLIEDPNARVKAQTNPTQQHAWT 356

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   + +  ++V   
Sbjct: 357  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM- 406

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 407  --------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 440

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R      EQ E   R   
Sbjct: 441  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGMNVVEQFEKPMRSDT 499

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
             +      +       +  G           K+  ++ D      R++          ++
Sbjct: 500  LKLKHGTYDKLDDDGIVAPGVRMSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLR 559

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q   S                         LR VKV +   +  Q GDK A 
Sbjct: 560  STENGIVDQVLLS--------------------TNSEGLRFVKVRMRTTKVPQIGDKFAS 599

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 600  RHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSALQGCEG 659

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L                         LRV      G  V      
Sbjct: 660  DATPFTEVTVDSVSKL-------------------------LRVHGYQSRGFEVM----- 689

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                              +G +    G         V +G  Y  +L HMV DK+
Sbjct: 690  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 720



 Score = 69.3 bits (168), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 56/352 (15%), Positives = 94/352 (26%), Gaps = 35/352 (9%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 59  TNGLKYSLATGNWGDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 118

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   P +
Sbjct: 119 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLN 178

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM--- 558
             NA  V          SQ        N ++ I   RR   +  +  + R     E    
Sbjct: 179 NPNATKVFVNGVWVGVHSQ------PANLVNTIKSLRRQGLISYEVSLVRDIRDREFKIF 232

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG------FIETPYRKVCDG 608
               R   P       P   + G+ +     +         G        E         
Sbjct: 233 TDAGRVCRPLFVVDNDPKSNNYGNLVLTKDHIQKLVDDEEAGAGMDAQEREEKLIGWQGL 292

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGS----------FTEELVFCRCAGEEILVPR 658
                V Y+ A EEE   I      L+                 E    R   +     +
Sbjct: 293 VKNGVVEYVDAEEEETIMIVMTPEDLETSRQLHAGYTLPPPDLIEDPNARVKAQTNPTQQ 352

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 +  P  ++ I AS+IPF +++ S R      M +QA+ +       
Sbjct: 353 HAWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDV 404


>gi|6449133|gb|AAF08840.1| RNA polymerase beta subunit [Streptococcus mitis]
          Length = 290

 Score =  264 bits (675), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 159/297 (53%), Positives = 212/297 (71%), Gaps = 9/297 (3%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ++H RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+S+  +
Sbjct: 1   SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSYGHL 60

Query: 593 NAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N YGF++TPYRKV    G VTN++V+L+A EE+   +AQA S L+E+ +F E++V  R  
Sbjct: 61  NKYGFVQTPYRKVDREKGVVTNEIVWLTADEEDEFTVAQAYSCLNEEWTFAEKVVMGRHQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           G     P   +D++D SPKQVV++A + IPFLENDDS R LMG NMQRQAVPL+  +AP+
Sbjct: 121 GVNQEYPANVVDYMDVSPKQVVAVATACIPFLENDDSTRALMGANMQRQAVPLINPKAPY 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME   A  SGAA++++  G V   DA ++ +R  +G LD       +Y + KF+RS
Sbjct: 181 VGTGMEYQAAHDSGAAVISQYDGKVTYADADKVEVRREDGSLD-------VYHIQKFRRS 233

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           N  T  NQR LVKVGD V + D IADGPS + G++ALG+N +VA+M W GYNFED++
Sbjct: 234 NSGTAYNQRTLVKVGDVVEKGDFIADGPSMENGEMALGQNPIVAYMTWEGYNFEDAV 290


>gi|156845523|ref|XP_001645652.1| hypothetical protein Kpol_541p37 [Vanderwaltozyma polyspora DSM
            70294]
 gi|156116318|gb|EDO17794.1| hypothetical protein Kpol_541p37 [Vanderwaltozyma polyspora DSM
            70294]
          Length = 1204

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 92/473 (19%), Positives = 162/473 (34%), Gaps = 60/473 (12%)

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              +     E    +I ++        D         +   G   +G            + 
Sbjct: 682  ENNIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKL 741

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              L++               + +  +GT   V + +  G D ++  I  +          
Sbjct: 742  YRLQSGQTPIVKANLYDDYGMDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYG 801

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
               +   +D ++ +R       Q+   GP  + K  +   + + E        +  + + 
Sbjct: 802  TMYKVEKVDLSM-NRSRGDPITQHFGFGPDEWPKEWL---EKLDEDGLPYIGTYVEEGDP 857

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            +    +    + +       +    +   +   +      L+ V +   ++R  Q GDK 
Sbjct: 858  ICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKF 917

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E     A      
Sbjct: 918  SSRHGQKGVCSRKWPTIDMPFSETGIQPDVIINPHAFPSRMTIGMFVE---SLAGK---- 970

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP- 1209
                                                          A         +TP 
Sbjct: 971  ----------------------------------------------AGALHGTAHDATPW 984

Query: 1210 VFDGADE--EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
             FD +D   +     L  A  +  G   +Y G TGE     + +G +Y  +L HMV+DK 
Sbjct: 985  TFDESDTPADYFGDQLLKAGYNYHGNEPMYSGATGEELRADIYIGVVYYQRLRHMVNDKF 1044

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              RSTG  + +T QP+ G+   GG R+GEME   +  +G +++LQ+ L   SD
Sbjct: 1045 QVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNCSD 1097



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 101/671 (15%), Positives = 209/671 (31%), Gaps = 77/671 (11%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ +  +  R+I           + I+N+ +TD+ +         Y  ++        +
Sbjct: 276 ILKALCDTSDREIF-----DGIIGSDIKNSFLTDRLELLLRGFKKRYPQLQNRTQVLQYI 330

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            +          DK D   VG+  +N  + +         +   ++ +I+ L  L  G+ 
Sbjct: 331 GDKFRVVFQASPDKSDYD-VGQEVLNRIVLVHLGTGNNEDKSRMLMFMIRKLYSLVAGEC 389

Query: 452 TIDDIDNLGNRRVRSVGEM----------LKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
             D+ D   ++ V   G +             Q  +  +R + +    I+  D   +   
Sbjct: 390 CPDNPDATQHQEVLLGGFLYGMILKEKMDEYLQSIIAQIRADINRGMAINFKDRKYMSRV 449

Query: 502 DLINAKPVVSAVCEFFCSSQL--------------SQLEEHVNSLSRITHTRRLSALGQG 547
            +   + + S +  F  +  L              + + E +N    I+H R    + +G
Sbjct: 450 LMRVNENIGSKLQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFR---MVHRG 506

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                     +R + P  +G +CP  T +G   GL++      R++    I++   K+ +
Sbjct: 507 SFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRIST---IQSDVSKIPE 563

Query: 608 GKVTNDVVYLSAMEEEN--RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
              +  V   S            Q +  +    S  E  +         +  +     +D
Sbjct: 564 LLYSLGVTPASQTVAAGPSLCCVQLDGKIVGWVSHDEGKIVADTLRFWKVEGKTPGLPLD 623

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNM------QRQAVPLLKAEAPFVGTGMESVV 719
                V   ++   P L     +  +M          +    P  +       T  E   
Sbjct: 624 LEIGYVPPSSSGQYPGLYIFGGHSRMMRPVRYLPLGKEDIVGPFEQVYMNIAVTPQEIEN 683

Query: 720 AKSSGA-----AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQN 773
              S        I++  A +    D  +      +  +   T G   +    +       
Sbjct: 684 NIHSHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYR 743

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q P+VK                  + +   G N +VA + + GY+ +D+M+I++  
Sbjct: 744 LQSGQTPIVKANLYDDYG----------MDNFPNGTNAVVAVISYTGYDMDDAMIINKSA 793

Query: 834 VSEDVFTSIHIEEFEVMA-----RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
                      +  +V       R   +             E  L+ +DE G+  +G  V
Sbjct: 794 DERGFGYGTMYKVEKVDLSMNRSRGDPITQHFGFGPDEWPKEW-LEKLDEDGLPYIGTYV 852

Query: 889 NPGDILVGK----------ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
             GD +              T     P   EE  L      K  +++  S++     +  
Sbjct: 853 EEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQ 912

Query: 939 VVDVRIFNRHG 949
           + D +  +RHG
Sbjct: 913 IGD-KFSSRHG 922



 Score = 62.4 bits (150), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 101/839 (12%), Positives = 216/839 (25%), Gaps = 118/839 (14%)

Query: 70  GAAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
               +         P            KF   +   R  +Y   L + L+  V D +E  
Sbjct: 93  NKLSISIEQVSIAKPTSNDGVSSAVERKFYPSEARQRLTSYRGKLLMKLKWSVNDGEEVL 152

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
                          G LP+M +                         G F++ GI++++
Sbjct: 153 TDMRDG---------GGLPIMLQSNRCHLNKLSPYDLVQRKEESDELGGYFIVNGIEKLI 203

Query: 154 ---VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH------- 203
              + Q    P             S    Y  +I   +      +    +++H       
Sbjct: 204 RMLIVQRRNHPMAIIRPSFANRGASYTQ-YGIQIRSVRND----QTSQTNVLHYLNDGQV 258

Query: 204 -VRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
             R   R+    +P    L AL   S+      +  I+ S   + +        L+ G K
Sbjct: 259 TFRFSWRKNEYLIPAVMILKALCDTSD---REIFDGIIGSDIKNSFLTD-RLELLLRGFK 314

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                +   T + +   G K    ++              SD   G  V   IV    G 
Sbjct: 315 KRYPQLQNRT-QVLQYIGDKF--RVVFQASPDK-------SDYDVGQEVLNRIVLVHLGT 364

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK--NKDRKDALLDI 377
              E    +    + +++     +      D+  +   +    +      +   + L  I
Sbjct: 365 GNNEDKSRMLMFMIRKLYSLVAGECCPDNPDATQHQEVLLGGFLYGMILKEKMDEYLQSI 424

Query: 378 YRVMRPGD---VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
              +R      ++         + +    ++   S +        L   +  D++ +   
Sbjct: 425 IAQIRADINRGMAINFKDRKYMSRVLMRVNENIGSKLQYFLSTGNLVSQSGLDLQQVSGY 484

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
            ++A         +    +         +  +V ++L   +                   
Sbjct: 485 TVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLC-------PVHTPDGS 537

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
              ++       +              L  L     S +             G +    +
Sbjct: 538 PCGLLNHFAHKCRISTIQSDVSKIPELLYSLGVTPASQTVAAGPSLCCVQLDGKIVGWVS 597

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             E + V  T    +   +         +     +   ++ G     Y      ++   V
Sbjct: 598 HDEGKIVADT----LRFWKVEGKTPGLPLDLEIGYVPPSSSGQYPGLYIFGGHSRMMRPV 653

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   +E+   +               E V+   A     +       ++ +P  ++SI
Sbjct: 654 RYLPLGKED--IVGPF------------EQVYMNIAVTPQEIENNIHSHVEFTPTNILSI 699

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A+L PF + + S R +  C M +Q +                +    SG   + K    
Sbjct: 700 LANLTPFSDFNQSPRNMYQCQMGKQTMGT--PGVALCHRSDNKLYRLQSGQTPIVKANLY 757

Query: 735 VEQ----VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            +            + +V            I      +R      + +   V +     R
Sbjct: 758 DDYGMDNFPNGTNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKVEKVDLSMNRSR 817

Query: 791 NDIIADGPSTDLGDLA--LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            D I         +        +    +P+ G   E+   I      +D      I+ +
Sbjct: 818 GDPITQHFGFGPDEWPKEWLEKLDEDGLPYIGTYVEEGDPIC--AYFDDTLNKTKIKTY 874


>gi|119644161|gb|ABL85609.1| RNA polymerase II second largest subunit [Vulpicida pinastri]
          Length = 718

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 132/838 (15%), Positives = 250/838 (29%), Gaps = 144/838 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVLNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RA 732
                P    D+  R     N+   ++ V  L+ +     T  E  V + +        + 
Sbjct: 237  RVCRPLFVIDNDPRSSNEGNLVLTKEHVQKLELDRENWAT-TEPDVREDTNMGWQGLVKE 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       V    +       I    + + SN +  +++R    +        
Sbjct: 296  GVVEYVDAEEEETIMVVMTPEDLEISRQIRAGFEPEASNPDE-LSRRVKTPMKQTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   + +  ++    
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM- 404

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 405  --------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L E   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLRLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                           V     +G  + T 
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQ 699

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            VF                                       +G  Y  +L HMV DK+
Sbjct: 700  VF---------------------------------------LGPTYYQRLRHMVDDKI 718



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 78/621 (12%), Positives = 166/621 (26%), Gaps = 102/621 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 15  GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 191

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 192 VGVHRDPAHLVGTVLNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 251

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++EG+ +     +                  E              V Y+ A EEE   +
Sbjct: 252 SNEGNLVLTKEHVQKLELDRENWATTEPDVREDTNMGWQGLVKEGVVEYVDAEEEETIMV 311

Query: 628 AQANSSLDEDGSFTEELVF--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                 L+                    R     +          +  P  ++ I AS+I
Sbjct: 312 VMTPEDLEISRQIRAGFEPEASNPDELSRRVKTPMKQTAHTWTHCEIHPSMILGICASII 371

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                   + A I+      +    
Sbjct: 372 PFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYQQRMDTMANILYYPQKPLATTR 422

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           ++  +          +   +  Y              NQ                    S
Sbjct: 423 SMEFLKFRELPAGQNAIVAIACYSG-----------YNQE------------------DS 453

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +   ++ R +  +       + E  + +S             +E+FE   R       
Sbjct: 454 VIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS------------VVEQFEKPMR------- 494

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               D   +       +DE G++  G  V+  DI++GK  P         E+L +     
Sbjct: 495 ---SDTLRLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLH 547

Query: 920 KAVDVRDTSLRVPSGVSGTVV 940
              DV        +G+   V+
Sbjct: 548 VKRDVSTPLRSTENGIVDQVL 568


>gi|55273993|gb|AAV48867.1| RNA polymerase II second largest subunit [Armillaria mellea]
          Length = 884

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 151/1011 (14%), Positives = 293/1011 (28%), Gaps = 173/1011 (17%)

Query: 278  KKLTSGLLKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSL 333
            + L     K++ +  VK      +   G      +    V+     ++   G + D   L
Sbjct: 27   RSLVKKGGKTISQFQVKMFHRHQERSLGNVMKATIPYIKVDIPIWVVFRALGVISDRDIL 86

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E I +       +  +    ++ ++         +DR+ AL  I         +T    E
Sbjct: 87   EHICYDMQDAQMLEMLKPCIDDGFV--------IQDREVALDFIGNR----GTTTGLSRE 134

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  V              +     +      +I  L+     +  +
Sbjct: 135  RRIRYAQEILQKEMLPHV-----------SMSEGSESKKAYFFGYMIHRLLLAALERREL 183

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+LG  R+   G +L N +R+   +  R +    +              +  + + +
Sbjct: 184  DDRDHLGKNRLDLAGPLLANLFRMLFRKFNRDVYRYLQKCVETHKEFNVSVGVKHQTITN 243

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 244  GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 299

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   + ++   +       + +  +        
Sbjct: 300  RQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLE------- 352

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
               EEN + A   + +  +G +       R     +   ++     D SP+  V      
Sbjct: 353  -TLEENAHSATPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRE 408

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                   D+ RV     +      +L+ +   ++  G      +     +   + G++E 
Sbjct: 409  KELRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLVRGTNDDGEEYKWEQL--IKGGVIEL 466

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +       +    ++ +     R  +K G            
Sbjct: 467  LDAEEEETVMISMTPEDLENSRLQQSGVDIHANDGDFDPAAR--LKAGINAHTWTHCEIH 524

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 525  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 559

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   I               +  +             +       +   +  + AI 
Sbjct: 560  IYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 608

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  + +     E  E   R+       
Sbjct: 609  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDVEKNNGIHSMEVFEKPMRESTLRMKH 667

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G   V       K+  +  +      R++          ++     
Sbjct: 668  GTYDKLEDDGLIAPGTGVVGEDIIIGKTAPIPPESEELGQRTRMHTRRDVSTPLKNTERG 727

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VKV V   R  Q GDK A RHG K
Sbjct: 728  IVDQ--------------------VLVTTNYEGQKFVKVRVRSTRIPQIGDKFASRHGQK 767

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +   
Sbjct: 768  GTIGITYRQEDMPFTCEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 827

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                       ++     + LR       G+ V           
Sbjct: 828  T-------------------------DLTVESVSTFLRQKGYQSRGLEVM---------- 852

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                          G +    G         V +G  Y  +L HMV DK++
Sbjct: 853  ------------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIH 884



 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 98/767 (12%), Positives = 222/767 (28%), Gaps = 104/767 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 63  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + ++             +      + 
Sbjct: 119 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMSEGSESKKAYFFGYMIH---RLL 174

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  +    + +  + +    P+L              +     K  +        V
Sbjct: 175 LAALERRELDDRDHLGKNRLDLAGPLLANLFRMLFRKFNRDVYRYLQKCVETHKEFNVSV 234

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                  T  +  S+    + D  K   S  G  ++  R    +      R         
Sbjct: 235 GVKHQTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREG 294

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +   + + L     + +      + E +    ++++
Sbjct: 295 KIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLETL 354

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                 NA         F     +    +  N +  I   RR   +            + 
Sbjct: 355 ----EENAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKE 410

Query: 559 RDVHPTHYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
             ++        P    E    +     +    R       E  + ++  G V   +  L
Sbjct: 411 LRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLVRGTNDDGEEYKWEQLIKGGV---IELL 467

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQ 670
            A EEE   I+     L+        +      G+          +        +  P  
Sbjct: 468 DAEEEETVMISMTPEDLENSRLQQSGVDIHANDGDFDPAARLKAGINAHTWTHCEIHPSM 527

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS+IPF +++ S R      M +QA+ +                           
Sbjct: 528 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI-------------------- 567

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + +  Y       +     +  R           
Sbjct: 568 ---------------------RMDTMANILYYPQKPLATTRSMEYLKFR----------- 595

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  +
Sbjct: 596 -------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDV 642

Query: 851 ARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            ++  +   E     +      +       +++ G+I  G  V   DI++GK  P     
Sbjct: 643 EKNNGIHSMEVFEKPMRESTLRMKHGTYDKLEDDGLIAPGTGVVGEDIIIGKTAPI---- 698

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             PE + L           RD S  + +   G V  V +   +   K
Sbjct: 699 -PPESEELGQRTRMH--TRRDVSTPLKNTERGIVDQVLVTTNYEGQK 742


>gi|46411496|gb|AAS94318.1| RNA polymerase II [Ostropa barbara]
          Length = 719

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 136/841 (16%), Positives = 250/841 (29%), Gaps = 149/841 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    R+   + + ++    D         + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLAKLFRNLFRRLTGDVYKYLTKCVSDNKEFNLTLGVKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V         +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIIEFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L +      ++      +  D +   + V        I      I D  D   K      
Sbjct: 177  LRSPNATKVFVNGVWVGVHRDPAHLVKTVQHLRRSHLISHEVSLIRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA--IVAKRA 732
                P F+ ++D +    G  +  +       +   +   M++    +SG          
Sbjct: 237  RVCRPLFVIDNDVDSANKGNLVLNKEHIRRLEDDQTMPANMDAEQKANSGFFGFQGLIND 296

Query: 733  GIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            G+VE VDA      +I     DLD S      Y++    R + +  +N+R    +     
Sbjct: 297  GVVEYVDAEEEETVMIVMTPEDLDISRQLQAGYQI----RPDDSGDLNKRVKAPMNPTAH 352

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    PS  LG       +  + +P+  +N                        ++ 
Sbjct: 353  IWTHCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQS 387

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                  +G      D                +  +             +       +   
Sbjct: 388  AMGKQAMGVFLTNFDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAG 436

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   + +   +    +F R   D+ +R   +    +E   +
Sbjct: 437  QNAIVAIACYSGYNQEDSVIMNQTSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEK 492

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                + + L    Y +L E   I  G           K+  ++ D      R++      
Sbjct: 493  PYRADTLKLKHGTYDKLDEDGIIAPGVRVSGEDIIIGKTAPMAPDAEELGQRTKAHTKRD 552

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                ++     +  Q                             LR VKV +   +  Q 
Sbjct: 553  ASTPLRSTENGIVDQVLI--------------------TTNAEGLRFVKVRMRTTKIPQI 592

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF + G   D+++NP  +PSRM +  + E  L     
Sbjct: 593  GDKFASRHGQKGTIGITYRQEDMPFTRQGIVPDLIINPHAIPSRMTIAHLIECQLSKVST 652

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +          +S L                                      
Sbjct: 653  LRGLEGDATPFTEVTVDSVSKLL------------------------------------- 675

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                             R  ++   G +    G         V +G  Y  +L HMV DK
Sbjct: 676  ----------RDHGYQSRGFEIMYHGHT----GR---KMMAQVFLGPTYYQRLRHMVDDK 718

Query: 1267 V 1267
            +
Sbjct: 719  I 719


>gi|242041665|ref|XP_002468227.1| hypothetical protein SORBIDRAFT_01g042100 [Sorghum bicolor]
 gi|241922081|gb|EER95225.1| hypothetical protein SORBIDRAFT_01g042100 [Sorghum bicolor]
          Length = 1228

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 95/510 (18%), Positives = 155/510 (30%), Gaps = 89/510 (17%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      +    D  +   +
Sbjct: 774  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYTTFGRKDDFMRPEY 833

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 834  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKE 892

Query: 1007 VLS-------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
             +           +               +     +  +    E     L+   K  ++K
Sbjct: 893  KIDFGKTESKRGRVDNLDDDGLPYIGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 952

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
            +        G    V V +   R    GDK +  HG KG+V  +   E+ PF   G   D
Sbjct: 953  VLL-SANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHKGIVPD 1010

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IV+NP   P+R   GQ+ E     A +G G   K                          
Sbjct: 1011 IVINPHAFPTRQTPGQLLE-----AALGKGIACKGT------------------------ 1041

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                    +  +TP F  A  + I   L  A     G   + +G
Sbjct: 1042 ------------------------MRYATP-FTTASVDVIAEQLHRAGYSRWGTENVLNG 1076

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
             TGE     + +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GEME 
Sbjct: 1077 RTGERMQSLIFMGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGEMER 1136

Query: 1300 WCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYESIVAG---------N 1336
             C+ A+G+A  L E L + SD              +VV R+      + G          
Sbjct: 1137 DCLLAHGSAANLHERLFMLSDFSQMHICQTCERVANVVMRSVSGGKKIRGPYCGFCKSSE 1196

Query: 1337 DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            +      P    +L +E+ ++G+ +  +  
Sbjct: 1197 NIVRINVPYGAKLLYQELFSMGICLKFDTE 1226



 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 139/968 (14%), Positives = 281/968 (29%), Gaps = 221/968 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 103 LISHQINSYNDFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 152

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  L + + + V+ +++   +K+  D 
Sbjct: 153 GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLIVEVNIQVYSLEKSDKSKTGNDG 212

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 213 FVQKRDFMNETHWIFIGLLPVMVKSNLCLLHSLKESECLFDAGGYFLVKGMEKVFIAQEL 272

Query: 159 R-----------SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID 207
           R              I F  +  R  +  KL+ + R     G  +     S   ++    
Sbjct: 273 RCLKRLWIIDRPCWMISFMSEMKRRRIYIKLVESTRSEDFSGSKII----SISFLYAT-- 326

Query: 208 RRRKVPVTSFLMALGMDSE----EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
               +PV     ALG+ S+    +++        V +             +    +  + 
Sbjct: 327 ----MPVWLLFFALGISSDKEAFDVIDMQDCDASVINTISATIKESDELCEGFRKSDKAR 382

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
             VD           +     + + L                G  V   ++   TG+   
Sbjct: 383 QYVDELVKSSRFPPAESFDDYIARFLFPDISG--NRNKALFLGYMVKCLLM-AFTGKRKC 439

Query: 323 EAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNTLVTDKNKDRK---DALLDI 377
           +  D    K L+       R++   +   +     A  R+     + +D +   DA +  
Sbjct: 440 DNKDDFRNKRLDLPGELLGRELRAHLRLAEKRMVKAIQRDLNSDRELQDLERYIDASIVT 499

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
             + R     ++                   ++   + +  R             D R+ 
Sbjct: 500 NGLSRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTRQRVAYAGKAGDARYP 559

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                  +  +        G + ++        R V  ++++    G+ ++     E I 
Sbjct: 560 NPSYWGKLCFMSTPDGENCGLVKNLAVTAIVSSRVVQPLIESFISCGMSKLNDIPTEHIQ 619

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
            +D                     F   + +   ++  + + R+   RR S +      +
Sbjct: 620 RMDK-------------------IFLNGNWVGSCKDSASFVFRLRCMRRSSLIDPQVEIK 660

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                +   V       + P    E           SF+                +    
Sbjct: 661 RDKHHKEVRVFSDAGRILRPLLVVENLKKIRKPKGRSFS--------------FQELMQQ 706

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + ++   EEE+   A     L E                            +  P  +
Sbjct: 707 EIIEFIGVEEEEDIQCAWGIRHLFESEGAI-----------------SSYTHCELDPSFL 749

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + ++  +IPF  ++ + RVL                             K S  AI    
Sbjct: 750 LGLSCGIIPFANHNFARRVLYQSE-------------------------KHSQQAIGYST 784

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                +VD                               +      QRPL     +    
Sbjct: 785 TNPHIRVD-----------------------------TLSHQLYYPQRPL----FKTVIA 811

Query: 792 DIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
           D +     T  G        +   G+N +VA     G+N EDS++++   +   +F + H
Sbjct: 812 DCLGRSDYTTFGRKDDFMRPEYFNGQNAIVAVNVHQGFNQEDSLVMNRASLERGMFRTEH 871

Query: 844 IEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
           +  ++    +          E+I           + N+D+ G+  +GA +   DI++GK+
Sbjct: 872 LRSYKADVENKDGTKRLKLKEKIDFGKTESKRGRVDNLDDDGLPYIGASLQTNDIVIGKV 931

Query: 899 TPKGESPM 906
           +  GE   
Sbjct: 932 SESGEDHS 939


>gi|108885353|gb|ABG23193.1| DNA-directed RNA polymerase [Geobacillus pallidus]
          Length = 145

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 63/167 (37%), Positives = 99/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD PLMT+ GTF
Sbjct: 51  KYSVEEAKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           VI G +R++VSQL RSP +++     +   +GK      +IP++G W
Sbjct: 102 VINGAERVIVSQLVRSPSVYYS---DKIDKNGKKGLTATVIPNRGAW 145


>gi|52699816|gb|AAU86970.1| DNA-dependent RNA polymerase II second largest subunit [Gyalecta
            jenensis]
          Length = 714

 Score =  264 bits (675), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 131/841 (15%), Positives = 249/841 (29%), Gaps = 155/841 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++   +R+   ++ + + +  +              + +  + + + 
Sbjct: 1    DHXGKKRLDLAGPLMAGLFRMLFNKLTKDVYQYLQKCVESGKEFNLALGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E     +   + +V  +      
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFIVSRNMEVLEEYEPTRN 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PHSTKVFVNGVWVGVHRDPAHLVSTVQTLRRQNMISSEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM---ESVVAKSSGAAIVAKRAGI 734
             P F+ ++D      G  +  + +     +   +   M   E        A +VA  A  
Sbjct: 237  RPLFVVDNDKKSPNKGALVLTKELINKLEDDRELPADMDPDEKKERYFGWAGLVANGAIE 296

Query: 735  VEQVDAIRI-VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                +     +I     DL+ S      Y +       QNT +N R   K+         
Sbjct: 297  FLDAEEEETVMIAMTPEDLEISRHMQMGYTIE------QNTDINARVKAKINARTT-WTH 349

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 350  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV------------- 389

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                               L N DE    +  +             +       +   + 
Sbjct: 390  ------------------FLTNFDERMDTMSNILYYPQKPLGTTRAMEFLKFRELPAGQN 431

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    +F R  +++ +R        +E   +  
Sbjct: 432  AIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMEQEKRVGI---SLVEQFEKPL 487

Query: 972  DDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              E + +    Y +L +   I  G           K+  ++ D      R+++       
Sbjct: 488  RSETLRVKHGTYDKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEEMGQRTKFHTKRDAS 547

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +                  ++K+          L+ VKV +   +  Q GD
Sbjct: 548  TPLRSTENGI------------------VDKVLV--TTNAEGLKFVKVRMRTTKVPQIGD 587

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  DG P D+++NP  +PSRM +  + E  L       
Sbjct: 588  KFASRHGQKGTIGITYRQEDMPFTADGIPPDLIINPHAIPSRMTIAHLIECLLSKVSALR 647

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +                                    D  +        G    +
Sbjct: 648  GCEGDATPFT--------------------------------DITVDSVSDLLRGHGYQS 675

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
              F+               +  +G +    G         + +G  Y  +L HMV DK+ 
Sbjct: 676  RGFE---------------IMYNGHT----GR---KLVAQIFLGPTYYQRLRHMVDDKIX 713

Query: 1269 A 1269
            A
Sbjct: 714  A 714



 Score =  114 bits (286), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 85/638 (13%), Positives = 169/638 (26%), Gaps = 118/638 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        NK  KD    + + +  G    F++A  + +    +  KY L   G  
Sbjct: 12  GPLMAGLFRMLFNKLTKDVYQYLQKCVESG--KEFNLALGVKSTTLTNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +      N + +          +   F     
Sbjct: 129 TPEGQACGLVKNLALMCYITVGSPSEPIIEFIVSRNMEVLEEYEPTRNPHSTKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR + +                +         P    +     
Sbjct: 189 VGVHRDPAHLVSTVQTLRRQNMISSEVSLVRDIRDREFKIFTDAGRVCRPLFVVDNDKKS 248

Query: 582 LVSSLTSFAR--VN------------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
                    +  +N                 +  Y           + +L A EEE   I
Sbjct: 249 PNKGALVLTKELINKLEDDRELPADMDPDEKKERYFGWAGLVANGAIEFLDAEEEETVMI 308

Query: 628 AQANSSL-----DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           A     L      + G   E+        +  +  R      +  P  ++ I AS+IPF 
Sbjct: 309 AMTPEDLEISRHMQMGYTIEQNTDINARVKAKINARTTWTHCEIHPSMILGICASIIPFP 368

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +         T  +  +   S                   
Sbjct: 369 DHNQSPRNTYQSAMGKQAMGVFL-------TNFDERMDTMSNIL---------------- 405

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                                              Q+PL                 + + 
Sbjct: 406 --------------------------------YYPQKPL-------------GTTRAMEF 420

Query: 803 GDLALGRNMLVAFM---PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                      A +    + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 421 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMEQEKRVGISLV 480

Query: 860 EIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E        +   V       +D+ GII  G  V+  DI++GK  P         ++   
Sbjct: 481 EQFEKPLRSETLRVKHGTYDKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEEMGQRT-- 538

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                K    RD S  + S  +G V  V +       K
Sbjct: 539 -----KFHTKRDASTPLRSTENGIVDKVLVTTNAEGLK 571


>gi|198473780|ref|XP_001356442.2| GA17896 [Drosophila pseudoobscura pseudoobscura]
 gi|198138104|gb|EAL33506.2| GA17896 [Drosophila pseudoobscura pseudoobscura]
          Length = 1126

 Score =  264 bits (674), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 88/353 (24%), Positives = 133/353 (37%), Gaps = 83/353 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++ +  ++ I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 826  KVEKMDEKEECFVDSIRQLGSFDLTPKKTVCITLRVPRPATIGDKFASRAGQKGICSQKY 885

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +    G               
Sbjct: 886  PAEDLPFTESGMIPDIVFNPHGFPSRMTIAMMIETMAGKSAAVHG--------------- 930

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI---NS 1221
                                                  GV  +TP        AI     
Sbjct: 931  --------------------------------------GVYDATPFRFSEKNTAIDYFGK 952

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    TQQ
Sbjct: 953  MLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGTVEARTQQ 1012

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRT-RVYESIV 1333
            P+ G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + IV
Sbjct: 1013 PIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHSCGSILSPLQQIV 1072

Query: 1334 A----GNDTFETG---------------TPESFNVLVKEMQALGLSIDLENSR 1367
                 G  + +                  P SF  LV E+ ++ ++   + ++
Sbjct: 1073 KRNERGGLSSKPQTCRLCGDSSSVSMIEIPFSFKFLVTELSSVNINARFKLNK 1125



 Score = 71.6 bits (174), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 98/638 (15%), Positives = 215/638 (33%), Gaps = 71/638 (11%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            ++ + +  +  I    +D  +   Y R     +K++    ++  + R +    V T + 
Sbjct: 236 HIKRLSYVPVCLILKCLMDYTDEEIYNRLVQGYEKDQYYVSSVQTMLRDVHNEGVYTHAQ 295

Query: 392 AESMFNF---------LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
             S               +  D+     + R ++ + L+          + + I+ +++ 
Sbjct: 296 CRSFIGTLFRSRFNVVPEWQPDEDVTDFILRERILVHLDTYEE------KFQLIVFMVQK 349

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLK-------NQYRLGLLRMERSIKERISSVDI 495
           L     GK  ++++D+   + V   G + +         +   + R+ +       S+  
Sbjct: 350 LFQCAQGKHKVENVDSAMMQEVLLPGHLYQKYLGERIENWVAMVRRVLQKKLSTPDSLLT 409

Query: 496 DSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRL 541
            S++ Q +  A  V  ++  F  +              S L  + E++N +  ++H R  
Sbjct: 410 SSILTQSMRQAGGVGKSIESFLATGNIASNTGLGLMQNSGLVIMAENINRMRYMSHFR-- 467

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            A+ +G         E R + P  +G ICP  T +G   GL++ LT    ++        
Sbjct: 468 -AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISKRPDP--- 523

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
             K+        +              Q N          +          +     E +
Sbjct: 524 --KLVQAIPPKLIEM-----GMLPLSCQRNPDSKMYVVLLDGKHLGHIFQSDACKIVEDL 576

Query: 662 DFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGTG--ME 716
            +   +      +    IPF +N              M R    +   +  ++GT   + 
Sbjct: 577 RYEKITGAVPQMMEIGFIPFKKNGQFPGLYLSTGPARMMRPVWNIKWKQVEYIGTLEQLY 636

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
             +A             +          + ++    D + S  ++Y+    +++    C+
Sbjct: 637 MEIAIDPKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCL 696

Query: 777 N--QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISE 831
           N  ++   K+         +      D     D A+G N +VA + + GY+ ED+M+I++
Sbjct: 697 NWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINK 756

Query: 832 RMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                   + SI+  +F  + + +           P++ E   K +D  G+   GA++  
Sbjct: 757 SAYERGFAYGSIYKSKFVQLPKKSS-----YFARHPHMPELA-KYLDTDGLPHPGAKLTF 810

Query: 891 GDILVGKI-----TPKGESPMTPEEKLLRAIFGEKAVD 923
           G  L         T K E     EE  + +I    + D
Sbjct: 811 GCPLYCYFDGEVATYKVEKMDEKEECFVDSIRQLGSFD 848


>gi|103001472|gb|ABF71509.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 686

 Score =  264 bits (674), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 113/807 (14%), Positives = 232/807 (28%), Gaps = 145/807 (17%)

Query: 476  RLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------ 521
            R+   ++ + + +  +    +         + +  + + +     +              
Sbjct: 1    RMLFXKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAASSKA 60

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 61   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 116

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +      E    +    + +V  +     +      ++      +  D 
Sbjct: 117  GLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVGVHRDP 176

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            +     V        I      + D  D   K          P    D+  +     N+ 
Sbjct: 177  AHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNCGNLV 236

Query: 698  --RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
              ++ +  L+ +               S     AK  G    V     V+  V+ + + +
Sbjct: 237  LTKEHINKLEDDKDLPA-------NMDSED-KEAKFFGWDGLV--NNGVVEYVDAEEEET 286

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVA 814
               V     ++  R  Q           +   V+          T      ++   +  +
Sbjct: 287  VMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMNPTAHTWTHCEIHPSMILGICAS 346

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +   + +  ++                          
Sbjct: 347  IIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----------------------- 381

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 382  ----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 437

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  
Sbjct: 438  IDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAP 493

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D      R++          ++     +  Q          
Sbjct: 494  GVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL------- 546

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                               LR VKV +   +  Q GDK A RHG KG +      EDMPF
Sbjct: 547  -------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPF 593

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             K+G   D+++NP  +PSRM +  + E  L       G +                    
Sbjct: 594  TKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------ 635

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++ +LR       
Sbjct: 636  -----------------------------------ATP-FTEVTVDSVSKLLREHGYQSR 659

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G  ++Y+G TG+     V +G  Y  +
Sbjct: 660  GFEVMYNGHTGQKLVAQVFLGPTYYQR 686


>gi|86161672|gb|ABC86971.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 285

 Score =  264 bits (674), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 198/285 (69%), Positives = 232/285 (81%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR+GIV+QVDA RIVIR+ E      +     YRL KF
Sbjct: 241 SGAAIGAKRSGIVDQVDATRIVIRATEDLDPSKSGVEYSYRLQKF 285


>gi|55831373|gb|AAV66545.1| RNA polymerase II second largest subunit [Fomitiporia mediterranea]
          Length = 898

 Score =  264 bits (674), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 133/884 (15%), Positives = 258/884 (29%), Gaps = 121/884 (13%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 115  RYAQEILQKEMLPHISMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGKKRL 171

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   ++ + +    +              I  + + + +     +   
Sbjct: 172  DLAGPLLTGLFRMLFRKLTKDVYRYLQKCVETHKEFNINMAIKTQTLTNGLKYSLATGNW 231

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 232  GDQKKAMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 287

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   A ++  G +  P     +      +   +  +  N     
Sbjct: 288  CPAETPEGQACGLVKNLALMAVIS-VGSVSGPVIDFLEEWGLETLEENT--QSTNLTKVF 344

Query: 630  ANSSL----DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             N        +  +    L   R   +         D  +   +        L P    +
Sbjct: 345  VNGVWLGVCRDPLNMVNTLRTLRRMQDFDSEVSIVRDIREREIRIYSDAGRVLRPLFIVE 404

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D    L   +++         E P+V     +    S G  +  +  G           +
Sbjct: 405  DHKLKLKRQHLRWLQEKWRIEERPYVPREERNKEEVSEGETVADEEEGRPIM--RDERRV 462

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
            +  +     S+   D    +      +   +   P   +   + R  +     + D    
Sbjct: 463  KRKKKPFTWSSLIRDGVIELLDAEEEETVMICMTPDDLLESRLLRRGLDPRAEA-DFNPA 521

Query: 806  ALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            A  + + +A   W       SM+  I   ++            ++       +G      
Sbjct: 522  ARLKPLPIAH-TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNF 580

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 581  LMRQ-----------DTMANILYYPQKPLATTRAMEYLKFRELPAGQNAIVAILCYSGYN 629

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    ++ R  +D+ +RS ++  ++ E   RD          +  
Sbjct: 630  QEDSVIMNQSSIDRGLF-RSLYYRTYMDQEKRSGAIIVDEFEKPTRDTTLRMKHGTYDKL 688

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G N         K+  +  D                +E  QR     K    
Sbjct: 689  EDDGLIAPGVNVRGDDIIIGKTAPIPPD---------------SEELGQRTRGHTKRDIS 733

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
            T     E    +++              + VK+ V   R  Q GDK A RHG KG +   
Sbjct: 734  TPLKSTEQGIVDQVVV-----TTNAEGTKFVKIRVRSTRIPQIGDKFASRHGQKGTIGIT 788

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 789  YRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATIVGNEGDATPFTDLTVD 848

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             +S +    EK   +                                             
Sbjct: 849  SVSSVLR--EKGYQSRGLEVM--------------------------------------- 867

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                    G +    G         V +G  Y  +L HMV DK+
Sbjct: 868  ------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKI 898



 Score =  126 bits (316), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 103/808 (12%), Positives = 220/808 (27%), Gaps = 148/808 (18%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  S   +     +    ++   +V+
Sbjct: 40  YIKVD----IPIWVVFRALGVISDRDILEHICFDMNDSSMLEMLKPCIDDGFVIQDREVA 95

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   K+L     + L+++ +  + +            G  +   ++  
Sbjct: 96  LDFIGNRGTATGLNRDKRLRYAQ-EILQKEMLPHISMAEGSESKKAYFFGYMIHRLLLAA 154

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 155 LERRELDDRDHFGKKRLDLAGPLLTGLFRMLFRKLTKDVYRYLQKCVETHKEFNINMAI- 213

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 214 -------KTQTLTNGLKYSLATGNWGDQKKAMSSKAGVSQVLNRYTYASTLSHLRRCNTP 266

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + +     
Sbjct: 267 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAVISVGSVSGPVIDF---- 322

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++    + L       +    F     L    + +N ++ +   RR+            
Sbjct: 323 -LEEWGLETLEENTQSTNLTKVFVNGVWLGVCRDPLNMVNTLRTLRRMQDFDSEVSIVRD 381

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL--------------------------- 586
                  ++      + P    E H + L                               
Sbjct: 382 IREREIRIYSDAGRVLRPLFIVEDHKLKLKRQHLRWLQEKWRIEERPYVPREERNKEEVS 441

Query: 587 --TSFARVNAYGFIETPYRKVCDGKV---------TNDVVYLSAMEEENRYIAQANSSLD 635
              + A       I    R+V   K             +  L A EEE   I      L 
Sbjct: 442 EGETVADEEEGRPIMRDERRVKRKKKPFTWSSLIRDGVIELLDAEEEETVMICMTPDDLL 501

Query: 636 EDGSFTEELVFCRCAGEEILVP------REKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           E       L     A                    +  P  ++ I AS+IPF +++ S R
Sbjct: 502 ESRLLRRGLDPRAEADFNPAARLKPLPIAHTWTHCEIHPSMILGICASIIPFPDHNQSPR 561

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                 M +QA+ +                                              
Sbjct: 562 NTYQSAMGKQAMGIYLTNFLM--------------------------------------- 582

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                + + +  Y       +     +  R                        +L  G+
Sbjct: 583 --RQDTMANILYYPQKPLATTRAMEYLKFR------------------------ELPAGQ 616

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP----EEITRD- 864
           N +VA + + GYN EDS+++++  +   +F S++   +    + +        E+ TRD 
Sbjct: 617 NAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYMDQEKRSGAIIVDEFEKPTRDT 676

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +++ G+I  G  V   DI++GK  P         ++        +    
Sbjct: 677 TLRMKHGTYDKLEDDGLIAPGVNVRGDDIIIGKTAPIPPDSEELGQRT-------RGHTK 729

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           RD S  + S   G V  V +       K
Sbjct: 730 RDISTPLKSTEQGIVDQVVVTTNAEGTK 757


>gi|189240038|ref|XP_972683.2| PREDICTED: similar to RNA polymerase I 135kD subunit CG4033-PA
            [Tribolium castaneum]
          Length = 993

 Score =  264 bits (674), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 118/325 (36%), Gaps = 83/325 (25%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             R       + R    GDK A R G KGI S+  P ED+PF + G   DIV NP G PSR
Sbjct: 719  NRTACFTFRVPRNPNVGDKFASRAGQKGICSQKWPMEDLPFTETGLVPDIVFNPHGFPSR 778

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E   G +                                              
Sbjct: 779  MTIAMMIEVMAGKSAA-------------------------------------------- 794

Query: 1191 DSVLRVAEQWKSGVPVSTPV-F--DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                         V  +TP  F  +    +    +L     +  G   +Y G+ G     
Sbjct: 795  ---------LHGLVHDATPFKFTEEDTAIDYFGRLLEAGGYNYYGTETMYSGIDGREMTA 845

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             +  G ++  +L HMVSDK   RSTG   ++T+QPL G+   GG R GEME   + ++GA
Sbjct: 846  QIFFGIVHYQRLRHMVSDKWQVRSTGPTDILTRQPLKGRKRGGGVRFGEMERDSLISHGA 905

Query: 1308 AYVLQEMLTIKSDD-----------------VVGRT--RVYESIVA--------GNDTFE 1340
            +++LQ+ L   SD                  V+ R   +  +S           G D  E
Sbjct: 906  SFLLQDRLFHCSDKTTAFICTSCGTLLGPVTVITRVAEKANQSTCKETCRLCGHGRDISE 965

Query: 1341 TGTPESFNVLVKEMQALGLSIDLEN 1365
               P  F   V +M +  +++ +  
Sbjct: 966  IQIPYIFKFFVTQMASCNINVKMLT 990



 Score = 72.8 bits (177), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 88/605 (14%), Positives = 191/605 (31%), Gaps = 67/605 (11%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD-------KNKDRKDALLDIYRVMRPG 384
            L+ +     + I    +    +++Y  + +               +D  + + ++ R  
Sbjct: 113 ILKCLCDYCDQFIYQKLIQGYQHDSYYLDCVQNMLRNLHIENLHTHEDCKVYLGKMFR-- 170

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
                      +    + +D      + +  + + L+          +   ++ + + L 
Sbjct: 171 --------VKFYECPDWLTDSEIADFILKKCIMIHLDKPED------KFNMLVFMCQKLF 216

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ---------YRLGLLRMERSIKERISSVDI 495
                K   +  D +  + +   G +             + L    ++RS          
Sbjct: 217 VFVQDKCKPEGADAVMMQELLLGGHLYLQLIKERLQGWLFGLKSNILKRSSTLTGHLSQT 276

Query: 496 DSVMPQDL----INAKPVVSAVCEFFCSSQLSQLEEHVNSL--SRITHTRRLS---ALGQ 546
           + +          NA  +  A      SS L  +++   ++    I   R +S   A+ +
Sbjct: 277 EILQAAKRSGGLENAFEMFLATGNITSSSGLGLMQDKGLTIVAENINRMRYMSHFKAVHR 336

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           G   +     E+R + P  +G ICP  T +G   GL++ LT+   V          RKV 
Sbjct: 337 GAFFQEMRTTEVRQLLPDAWGFICPVHTPDGAPCGLLNHLTTNCSVTDV----PDARKVE 392

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           +      ++         +Y+A             +  V      +      E++     
Sbjct: 393 NIP----IILTRLGMVALKYVASVGFD-QNYVVVLDGRVLGYVRRDLAPKLVEQLRLCKI 447

Query: 667 S-PKQVVSIAASLIPFLENDDSNRVLM----GCNMQRQAVPLLKAEAPFVGTG--MESVV 719
              +   ++   L+P ++       L        M R  + L   E  FVGT   +   +
Sbjct: 448 KGEEVPNTLEIVLVPLMKVTAQFPGLYLFTGPARMMRPLLNLKTKEVEFVGTFEQVYMDI 507

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
             S           +     A    +  +    D + S  ++Y+    +++    C N R
Sbjct: 508 CVSPDEYYKGVTTHMELSKLAFLSNLAQLIPMPDCNQSPRNMYQCQMGKQTMGTPCHNWR 567

Query: 780 PL--VKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
                K+         +      D     D A+G N +VA + + GY+ ED+M+I++   
Sbjct: 568 SQSETKLYRLQTPATPLFRPVHYDNINLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAD 627

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                   H   ++      +       R+      E  + +D  G+  +G  +  GD L
Sbjct: 628 ERGFA---HGSIYKTEFVTLEHESSYFCRNPE--KPELAEFLDTDGLPIIGRRMKDGDPL 682

Query: 895 VGKIT 899
               +
Sbjct: 683 YCYYS 687


>gi|86161666|gb|ABC86968.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 284

 Score =  264 bits (674), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 206/284 (72%), Positives = 239/284 (84%), Gaps = 1/284 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL K
Sbjct: 241 SGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQK 283


>gi|110704328|gb|ABG88064.1| RNA polymerase II second largest subunit [Microbotryum violaceum]
          Length = 699

 Score =  264 bits (674), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 130/827 (15%), Positives = 244/827 (29%), Gaps = 145/827 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R+   ++ + +   +        S      + +  + + +   
Sbjct: 1    FGAKRLDLAGPLLAALFRMLFRKLTKDVYRHLQKCVETQKSFNLNTAVRSNTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +A     + R     + R +H 
Sbjct: 61   LATGNWGDQKKAMSAKAGVSQVLNRYTFASTLSHLRRCNA----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   + ++  G    P  +  +     ++   S+   +
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMSYIS-VGSPSAPIVEFLEEWGMENLEEFSSEMSK 175

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
               +   N            LV                   D + +  V           
Sbjct: 176  GTKV-FVNGVWQGVHRDPAHLVQTIKRLR---------RCGDIAYEVSVVRDVRERELRL 225

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            + D+ RV     +      +L          ++++  + S      KR    + +     
Sbjct: 226  HTDAGRVCRPLFIVEDHRLVLTRH------HIDALQNEDSEDRPDEKRLKWTDLI--ETG 277

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+  V+ + + +         ++  R  Q T   Q                 D  +T  G
Sbjct: 278  VVEYVDAEEEETVMICMTPEDLETSRLFQETGQIQV-------------DTFDPSATVKG 324

Query: 804  DLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +       V    W       SM+  I   ++            ++       +G    
Sbjct: 325  SMG------VNTHTWTHCEIHPSMILGICASIIPXXXXXXSPRNTYQSAMGKQAMGVFLT 378

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +               +  V             +       +   +  + AI     
Sbjct: 379  NYQVRM-----------DTMANVLYYPQKPLATTRSMEYLHFRELPAGQNAIVAIMCYSG 427

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +     + R  +D+ ++S +++ E+ E   RD           
Sbjct: 428  YNQEDSVILNQSSIDRGLF-RSFYYRSYMDQEKKSGAIQMEEFEKPTRDTTLRLKHGTYE 486

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G+          K+  L  D                +E  QR     K  
Sbjct: 487  KLEADGIIGLGERVAGEDIIIGKTAPLPPD---------------SEELGQRLKNHTKRD 531

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
              T     E+   +++      D +     + VK+ V   R  + GDK A RHG KG + 
Sbjct: 532  VSTPLKSTENGIVDQVLVTTNQDGL-----KFVKIRVRSTRIPEIGDKFASRHGQKGTIG 586

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +GT  DI++NP  +PSRM +G + E  L       G +  +       
Sbjct: 587  ITYRHEDMPFSAEGTIPDIIINPHAIPSRMTIGHLVECLLSKVSTISGNEGDATPFSEVT 646

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               IS L   +     +                                           
Sbjct: 647  VEAISTLLKEMG--YHSRGLEVM------------------------------------- 667

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                     +G +    G         V +G  Y  +L HMV+DK++
Sbjct: 668  --------YNGHT----GR---KLQAQVYLGPTYYQRLKHMVNDKIH 699


>gi|318602924|emb|CBJ04562.1| RNA polymerase beta subunit [Pseudomonas sp. R-37082]
          Length = 263

 Score =  264 bits (674), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 153/263 (58%), Positives = 199/263 (75%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++A
Sbjct: 1   PLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R  
Sbjct: 61  RTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVRHL 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P 
Sbjct: 121 NEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPL 180

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RS
Sbjct: 181 VGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRS 240

Query: 771 NQNTCVNQRPLVKVGDEVRRNDI 793
           NQNTC+NQRPLV  GD V+RNDI
Sbjct: 241 NQNTCINQRPLVSKGDRVQRNDI 263


>gi|70794976|gb|AAZ08462.1| RNA polymerase II second largest subunit [Platanus orientalis]
          Length = 923

 Score =  264 bits (674), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 139/927 (14%), Positives = 273/927 (29%), Gaps = 173/927 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       ++   ++       ++A +   + +    +       S          KY 
Sbjct: 155  DILEHICYDFLDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 211

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 212  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 268

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 269  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQA 328

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 329  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 384

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 385  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 437

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             +   R ++   D + +  V     L       D  R    
Sbjct: 438  IFVNGCWVGIHRNPELLVNTLRKLRRQV---DVNTEVGVIRDIHLKELRLYTDYGRCSRP 494

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                K   A    +        D   +  I  V+ + 
Sbjct: 495  LFIVEKQRLLI--------------KKKDIRALQQRETPEDGGWHDLVAKGYIEYVDTEE 540

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 541  EETTMISMTINDLVTARLNPEEAYS-----------ETYTHCEIHPSLILG-------VC 582

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 583  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 616

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 617  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 673

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 674  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 732

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T ++ +                 E   +     +  + TS    E  
Sbjct: 733  TRVSGEDVIIGKTTPIAQE-----------------EPQGQASRYTRRDHSTSLRHSESG 775

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 776  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 830

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 831  VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 871

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 872  ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 896

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +Y+G TG      + +G  Y  +L
Sbjct: 897  FETMYNGHTGRKLSAMIFLGPTYYQRL 923



 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 116/879 (13%), Positives = 252/879 (28%), Gaps = 169/879 (19%)

Query: 120 KSIKDIKE-QSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
           + + + +E   +++G +P+M +                         G F+I G +++++
Sbjct: 9   EEVTETQEFTKVFIGKVPIMLRSSYCTLFQNSEKDLTELGECPYDQGGYFIINGSEKVLI 68

Query: 155 SQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR---- 208
           +Q   S   ++      +     K  Y   +        + +      + VR+  R    
Sbjct: 69  AQEKMSTNHVY----VFKKRQPNKYAYVAEVR----SMAESQNRPPSSMFVRMLSRASAK 120

Query: 209 ---------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
                          R ++P+     ALG  ++ +IL       + +Q  +     L  A
Sbjct: 121 GGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFLDTQMMELLRPSLEEA 180

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            ++   +V+   +        +   K++     + L+++ +  +G+   C          
Sbjct: 181 FVIQNQQVALDYIGKRGSTVGVTREKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYFGY 239

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +      + + A     E   +   +  +    P+L          +   +     K   
Sbjct: 240 IIH---RLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVD 296

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
           +      +        T  +  S+    +  ++           +N      T   +R +
Sbjct: 297 NGKEVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRL 356

Query: 432 -RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
                    +     L N    +         +      ++KN   +  + +  +    +
Sbjct: 357 NSPIGREGKLAKPRQLHNSHWGMMCPAETPEGQACG---LVKNLALMVYITVGSAANPIL 413

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGV 549
             ++  S    + I+   +  A   F     +         ++ +   RR   +  + GV
Sbjct: 414 EFLEEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVNTLRKLRRQVDVNTEVGV 473

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGH----NIGLVSSLTSFARVNAYGFIETPYRKV 605
            R     E+R ++  +     P    E          + +L         G+        
Sbjct: 474 IRDIHLKELR-LYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRETPEDGGW-------- 524

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            D      + Y+   EEE   I+              +LV  R   E      E     +
Sbjct: 525 HDLVAKGYIEYVDTEEEETTMISM----------TINDLVTARLNPE--EAYSETYTHCE 572

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ + AS+IPF +++ S R      M +QA+ +                      
Sbjct: 573 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------- 617

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                R   +  V                                       Q+PLV   
Sbjct: 618 -----RMDTLAYV-----------------------------------LYYPQKPLV--- 634

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                              L  G N +VA   + GYN EDS+++++  +    F S+   
Sbjct: 635 -------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFR 687

Query: 846 EFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +    +      +E        +   +       +D+ G+   G  V+  D+++GK TP
Sbjct: 688 SYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 747

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +                     RD S  +    SG V
Sbjct: 748 IAQEEP---------QGQASRYTRRDHSTSLRHSESGMV 777


>gi|110289329|gb|ABB47823.2| DNA-directed RNA polymerase, beta subunit family protein, expressed
            [Oryza sativa Japonica Group]
          Length = 1044

 Score =  264 bits (674), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 110/262 (41%), Gaps = 56/262 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGV 1127
              L+   + +   R    GDK + RHG KG+ S++ P  DMPF  + G   D+++NP   
Sbjct: 744  DRLQKANIRLRRVRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSANTGMRPDLIINPHAF 803

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +  + E+    A    GK I                                   
Sbjct: 804  PSRMTIAMLLESIAAKAGSLKGKFI----------------------------------- 828

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                             P ++ V + ++   + +  ML     +  G  ILY G+ G   
Sbjct: 829  --------------DATPFASSVKERSNSIVDELGPMLASYGFNYHGTEILYSGVFGTEM 874

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  +L HMVSDK   R+TG    +T+QP+GG+   GG R GEME   + A+
Sbjct: 875  KCEIFLGPVYYQRLRHMVSDKFQVRTTGRIDQITRQPIGGRKYGGGIRFGEMERDALLAH 934

Query: 1306 GAAYVLQEMLTIKSD----DVV 1323
            GA+Y+L + L   SD    DV 
Sbjct: 935  GASYLLHDRLHSCSDYHIADVC 956



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 72/449 (16%), Positives = 144/449 (32%), Gaps = 29/449 (6%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            ++   E +N    I+H R   ++ +G          +R + P  +G +CP  T +G   
Sbjct: 331 GMTIHAERLNFHRYISHFR---SVHRGSSFAKMRTTSVRKLLPESWGFLCPVHTPDGEPC 387

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG-- 638
           GL++ +TS  R++++   E   +     K++     + A        AQ    ++  G  
Sbjct: 388 GLLNHMTSTCRISSFYNSEGATKDFQKIKMSLIARLVGAGM------AQLLPRIERTGPP 441

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                 V     G       E++   D     V        P L    +    +      
Sbjct: 442 EVLHVHVDGCIVGSIASAKIEEVIPEDLEVGYVPLSHGGAYPGLYLFTNPARFLRPVRSL 501

Query: 699 QAVPLLKAEAPFVGTG----MESVVAK--SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             +         +G      ME         G   +           AI  V+ ++    
Sbjct: 502 LGLSNGGPNIELIGPFEQAFMEIRCPDGGDGGRNKLFPATHEEIHPTAILSVVANLTPWS 561

Query: 753 DPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGPST---DLGDLAL 807
           D + S  ++Y+    +++       +  R  VK          I    +     + +   
Sbjct: 562 DHNQSPRNMYQCQMAKQTMGFCGQALKFRTDVKAFHLQTPQTPIVRTATYSKYCMDEFPS 621

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G N +VA + + GY+ ED+M++++  V   +F     +   +                 N
Sbjct: 622 GTNAIVAVLSYTGYDMEDAMILNKSAVDRGMFRGHIFQTECIDLSAKSRDNVTEFFCKSN 681

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILV-------GKITPKGESPMTPEEKLLRAIFGEK 920
           +S +    I+  G+  +G  + P +          G + P       P      A+ G  
Sbjct: 682 LSRDTTAAIESDGLPRIGENIFPNEQYYSVCNNLTGTVRPIKLKGSEPAAIDYVAVNGTN 741

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D    +      V   ++  +  +RHG
Sbjct: 742 FKDRLQKANIRLRRVRNPIIGDKFSSRHG 770


>gi|120561257|gb|ABM27013.1| RNA polymerase II second largest subunit [Gigaspora gigantea]
          Length = 894

 Score =  263 bits (673), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 128/938 (13%), Positives = 278/938 (29%), Gaps = 150/938 (15%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            V++  +++       +    +AL            +  +            + +      
Sbjct: 80   VSDQDFLQYVCYDPNDNQMMEALKPCIEEAFAVQSTEVAADWIGRRGTTTGATRDKRIKY 139

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDII--AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +  +   L      +    +++      ++  L+    G+  +DD D+ G +R+   G 
Sbjct: 140  AKEILQKELLPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRRELDDRDHYGKKRMDLAGP 199

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L + +R+   ++ + I    R              I A+ + + +     +        
Sbjct: 200  LLASLFRMLFKKLTKDISIYLRKCIDTSREFNLHLAIKAQTITNGLKYSLATGNWGDQKK 259

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 260  AMQSRAGVSQVLNRYTFASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHWGMVCPAET 315

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L+  + ++     +             +   ++  ++ +    + N+ +
Sbjct: 316  PEGQACGLVKNLSLMSYISVGSSSKPI------VDFLEEYGMINLNQQFDPANIRDNTKV 369

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              +G +             +   R  +   D SP+  V             D+ RV    
Sbjct: 370  FVNGKWAGISTAPEQLANTLRGLRRSV---DVSPEVSVVRDIREKELRIYTDAGRVCRPL 426

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI---RIVIRSVEGD 751
             +      ++  E   +   ++ +  +++      +R      V         I  ++ +
Sbjct: 427  FIVEDQCLVISKE--LIDN-LDDIHGENAEKQSQKRRQDRQVYVWHDLISNGAIEYIDAE 483

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD---EVRRNDIIADGPSTDLG-DLAL 807
             + +         +   R+   T ++Q       D    V+    ++    T      ++
Sbjct: 484  EEETVMICMTPEDLAASRNYYQTGISQASKAHEKDIAARVKSESNLSIHTWTHCEIHPSM 543

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   I++  ++                   
Sbjct: 544  ILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------- 582

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +    +  +        +    +       +   +  + AI      +  D+
Sbjct: 583  --------LRMDTLANILYYPQKPLVTTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDS 634

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    IF R  +D+ ++   +    IE   +   +  + L    Y +L 
Sbjct: 635  VIMNQSSIDRGLF-RSIFYRSYMDQEKKVGILS---IEEFDKPTRETTLRLKHGTYEKLE 690

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   I  G           K T +    I    R            ++     +  Q   
Sbjct: 691  DDGLIAPGTRVSGDDIIIGKVTPIPEHTIELGQRKDSHTHRDASTPMRSTENGIVDQ--- 747

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      ++ VKV V   R  Q GDK A RHG KG +    
Sbjct: 748  -----------------VMVTTNAEGMKFVKVRVRSTRIPQMGDKFASRHGQKGTIGITY 790

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +G + E  LG      G++  +          
Sbjct: 791  RQEDMPFTSEGITPDLIINPHAIPSRMTIGHLVECLLGKVSTLTGQEGDATPFTDVTVEA 850

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            IS      +    +                                              
Sbjct: 851  ISHSLR--QNGYHSRGFEVM---------------------------------------- 868

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                  +G +    G         V +G  Y  +L HM
Sbjct: 869  -----YNGHT----GR---KLAAQVFLGPTYYQRLKHM 894



 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 103/772 (13%), Positives = 214/772 (27%), Gaps = 106/772 (13%)

Query: 209 RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++ VPV     ALG +  ++ L         +Q  +     +  A  +   +V++  +  
Sbjct: 65  KKDVPVVIAFRALGAVSDQDFLQYVCYDPNDNQMMEALKPCIEEAFAVQSTEVAADWIGR 124

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                     K++     K + +K +    ++++  C    A  +       +    G  
Sbjct: 125 RGTTTGATRDKRI--KYAKEILQKEL-LPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRR 181

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +              P+L          +   +     K    +      +       
Sbjct: 182 ELDDRDHYGKKRMDLAGPLLASLFRMLFKKLTKDISIYLRKCIDTSREFNLHLAIKAQTI 241

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 242 TNGLKYSLATGNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNTPMGRDGKIAKPRQ 301

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +   + + L     + +    + I + +    + ++  Q   +
Sbjct: 302 LHNTHWGMVCPAETPEGQACGLVKNLSLMSYISVGSSSKPIVDFLEEYGMINLNQQ--FD 359

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
              +      F                + +   RR   +            +   ++   
Sbjct: 360 PANIRDNTKVFVNGKWAGISTAPEQLANTLRGLRRSVDVSPEVSVVRDIREKELRIYTDA 419

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFI----------ETPYRKVCDGKVTNDVV 615
                P    E     ++S        + +G            +       D      + 
Sbjct: 420 GRVCRPLFIVEDQ-CLVISKELIDNLDDIHGENAEKQSQKRRQDRQVYVWHDLISNGAIE 478

Query: 616 YLSAMEEENRYIAQANSSLDEDGSF----------TEELVFCRCAGEEILVPREKIDFID 665
           Y+ A EEE   I      L    ++            E         E  +        +
Sbjct: 479 YIDAEEEETVMICMTPEDLAASRNYYQTGISQASKAHEKDIAARVKSESNLSIHTWTHCE 538

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R      M +QA+ +                      
Sbjct: 539 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------- 583

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + +  Y               Q+PLV   
Sbjct: 584 --------------------------RMDTLANILYYP--------------QKPLV--- 600

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N +VA + + GYN EDS+++++  +   +F SI   
Sbjct: 601 -------TTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIFYR 653

Query: 846 EFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +    +    L  EE  +        +     + +++ G+I  G  V+  DI++GK+TP
Sbjct: 654 SYMDQEKKVGILSIEEFDKPTRETTLRLKHGTYEKLEDDGLIAPGTRVSGDDIIIGKVTP 713

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    E  +     + +   RD S  + S  +G V  V +       K
Sbjct: 714 IP-------EHTIELGQRKDSHTHRDASTPMRSTENGIVDQVMVTTNAEGMK 758


>gi|70794972|gb|AAZ08460.1| RNA polymerase II second largest subunit [Eschscholzia californica]
          Length = 951

 Score =  263 bits (673), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 140/927 (15%), Positives = 274/927 (29%), Gaps = 173/927 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  REILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCAIGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAAHPILEFLEEWSTEN-------FEEISPAVIPQSTK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIHLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K +        E   +   G        G +E VD        +   ++
Sbjct: 523  LFIVEKQRLLIKKKDIQALQLRE---SPEEGGWHDLVAKGFIEYVDTEEEETTMISMTIN 579

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD-EVRRNDIIADGPSTDLGDLALGRNML 812
               S                        V   +            PS  LG       + 
Sbjct: 580  DLVSA----------------------RVNPKEAYSETYTHCEIHPSLILG-------VC 610

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 611  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 644

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 645  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 701

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 702  SSIDRGFF-RSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 760

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T ++                  D+   +     +  + TS    E  
Sbjct: 761  TRVSGEDVIIGKTTPIAQ-----------------DDSQGQASRYTRRDHSTSLRHSESG 803

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 804  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 858

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 859  VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 899

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 900  ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 924

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +Y+G TG      + +G  Y  +L
Sbjct: 925  FETMYNGHTGRKLTAMIFLGPTYYQRL 951



 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 124/912 (13%), Positives = 263/912 (28%), Gaps = 173/912 (18%)

Query: 88  VDDCLWRDLTYAVPLKITL--RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD---- 141
                 R+LTY+ PL + +  R+I    D    A++    K   +++G +P+M +     
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCEEVAETQDFTK---VFIGRVPIMLRSSYCT 63

Query: 142 --------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLY 180
                               G F+I G ++++++Q   S   ++      +     K  Y
Sbjct: 64  LYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAY 119

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMA 220
              +        + +      + VR+  R                   R ++P+     A
Sbjct: 120 VAEVR----SMAESQNRPPSSMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRA 175

Query: 221 LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG  ++ +IL         +Q  +     L  A ++   +V+   +        +   K+
Sbjct: 176 LGFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKR 235

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +     + L+++ +  +G+   C          +      + + A     E   +   + 
Sbjct: 236 IKYAR-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCAIGRRPEDDRDHYGNK 291

Query: 340 EIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            +    P+L          +   +     K   +      +        T  +  S+   
Sbjct: 292 RLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATG 351

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDID 457
            +  ++           +N      T   +R +         +     L N    +    
Sbjct: 352 NWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPA 411

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                +      ++KN   +  + +  +    +  ++  S    + I+   +  +   F 
Sbjct: 412 ETPEGQACG---LVKNLALMVYITVGSAAHPILEFLEEWSTENFEEISPAVIPQSTKIFV 468

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSE 576
               +         +  +   RR   +  + GV R     E+R ++  +     P    E
Sbjct: 469 NGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIHLKELR-LYTDYGRCSRPLFIVE 527

Query: 577 GH----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                     + +L         G+         D      + Y+   EEE   I+    
Sbjct: 528 KQRLLIKKKDIQALQLRESPEEGGW--------HDLVAKGFIEYVDTEEEETTMISM--- 576

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                     +LV  R          E     +  P  ++ + AS+IPF +++ S R   
Sbjct: 577 -------TINDLVSARVNP--KEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTY 627

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              M +QA+ +                           R   +  V              
Sbjct: 628 QSAMGKQAMGIYVTNYQL--------------------RMDTLAYV-------------- 653

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    Q+PLV                      L  G N +
Sbjct: 654 ---------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAI 682

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPN 867
           VA   + GYN EDS+++++  +    F S+    +    +      +E        +   
Sbjct: 683 VAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMG 742

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP  +           +         RD 
Sbjct: 743 MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------SQGQASRYTRRDH 793

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 794 STSLRHSESGMV 805


>gi|301616295|ref|XP_002937598.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2 [Xenopus
            (Silurana) tropicalis]
          Length = 1151

 Score =  263 bits (673), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 70/277 (25%), Positives = 107/277 (38%), Gaps = 73/277 (26%)

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   DI++NP  +PSRM VG + E   G      G+                 
Sbjct: 930  DMPFTCEGITPDIIINPHAIPSRMTVGHLIECLQGKVSANKGEIGD-------------- 975

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP  D  + + I+++L    
Sbjct: 976  ---------------------------------------ATPFNDAVNVQKISNLLSDYG 996

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G  +LY+G TG      + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S
Sbjct: 997  YHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRS 1056

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIV 1333
              GG R GEME  C  A+GAA  L+E L   SD     V            RT  YE   
Sbjct: 1057 RDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGLMAIANTRTHTYEC-- 1114

Query: 1334 AG----NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             G            P +  +L +E+ ++ ++  +  S
Sbjct: 1115 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMTS 1151



 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 135/1009 (13%), Positives = 277/1009 (27%), Gaps = 208/1009 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHTTGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVVKEGEEQI-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK----- 211
            ++    K       K  Y           ++        I V +  R     +K     
Sbjct: 204 TVYVFAKKDS-----KYAYTAECR----SCLENSSRPTSSIWVSMLARGGQGAKKSAIGQ 254

Query: 212 ------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                       VP+     ALG  S+ +IL          +  +     L  A ++   
Sbjct: 255 RIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQ 314

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
            V+ + +     +  +   K++     + L+++ +  +G++  C          +     
Sbjct: 315 NVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH--- 370

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A    +    +   +  +    P+L          +   +     K         
Sbjct: 371 RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFN 430

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKED 435
             +     + +  +  S+    + D  K   +  G  ++  RL   +      R      
Sbjct: 431 LELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIG 490

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +     L N    +                ++KN   +  + +       +  ++ 
Sbjct: 491 RDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEE 547

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R  
Sbjct: 548 WSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDI 607

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E      T  GRIC         +     L     ++     E       D   +  V 
Sbjct: 608 REREIRIYTDAGRIC----RPLLIVEKQKLLLKRRHIDQLKEREYNNYSWQDLVASGVVE 663

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+  +EEE   +A     L E G                +         +  P  ++ + 
Sbjct: 664 YIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILGVC 707

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +                                
Sbjct: 708 ASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------- 742

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                              + + V  Y               Q+PLV             
Sbjct: 743 ----------------RMDTLAHVLYYP--------------QKPLV----------TTR 762

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM-------VSEDVFTSIHIEEFE 848
                   +L  G N +VA                  +          +   S+    ++
Sbjct: 763 SMEYLRFRELPAGINSIVAXXXXXXXXXXXXXXXXXHISLATNIKHPSECQESVFYRSYK 822

Query: 849 VMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
                     EE+           +       +D+ G+I  G  V+  D+++GK     E
Sbjct: 823 EQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPE 882

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +    E          +    RD S  + +  +G V  V +       K
Sbjct: 883 NEDELEST-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 924


>gi|119644321|gb|ABL85618.1| RNA polymerase II second largest subunit [Xanthoria polycarpa]
          Length = 718

 Score =  263 bits (673), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 132/841 (15%), Positives = 238/841 (28%), Gaps = 150/841 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + I +  +              +    + S
Sbjct: 1    DDSDHFGKKRLDLAGPLLAGLFRMLFQKLTKDIYKYLQKCVESNREFNLALGVKQNTLSS 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      +    Y      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPADPIVDYLTNRGMESLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              A      ++         D +     +        I      + D  D   K      
Sbjct: 177  TRAPHATKVFVNGTWIGCHNDPAHLVTHIQEIRRKGIIAHEASLVRDIRDREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P    D+  +     N+   +  V  L+ E   V T      A+        +  G
Sbjct: 237  RVCRPLFVIDNDPKSENNGNLALTKDMVQKLEDERDMVLTMDPEERAE--------QVIG 288

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRND 792
                VD+    +  V+ + + +         ++  R  Q       P        V+   
Sbjct: 289  WEALVDS--GAVEYVDAEEEETIMIAMTPEDLEISRHIQAGYAAPVPSEDAPNQRVKAPL 346

Query: 793  IIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                   T      ++   +  + +P+  +N          M  + +             
Sbjct: 347  NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------- 395

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                 L N DE    +  +             +       +   
Sbjct: 396  --------------------FLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAG 435

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R  +D  +R        +E   +
Sbjct: 436  QNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVDTEKRVGM---TVLENFEK 491

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                E + L    Y +L +   +  G           K+T ++ D               
Sbjct: 492  PLRTETLKLKHGTYDKLDDDGLVAPGVRVSGEDVIIGKTTPIAPD--------------- 536

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
              E  QR    +K    T     E+   +K+             L+ VKV +   +  Q 
Sbjct: 537  AQEMGQRTKSHIKKDASTPLRSTENGIVDKVLL-----STNSEGLKFVKVRMRTTKIPQI 591

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L     
Sbjct: 592  GDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSS 651

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +          +S L                                      
Sbjct: 652  LRGYEGDATPFTEITVDSVSKLLREHSYQSRGFEVM------------------------ 687

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                    +G +    G         V +G  Y  +L HMV DK
Sbjct: 688  -----------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDK 717

Query: 1267 V 1267
            +
Sbjct: 718  I 718



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 51/374 (13%), Positives = 105/374 (28%), Gaps = 42/374 (11%)

Query: 375 LDIYRVMRPGDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            DIY+ ++        F++A  +         KY L   G      +         + + 
Sbjct: 31  KDIYKYLQKCVESNREFNLALGVKQNTLSSGLKYSL-ATGNWGDQKKAASAKAGVSQVLN 89

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R+GK       +  +  +    E  + Q    +  +     
Sbjct: 90  RYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 149

Query: 488 ERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             + +     V        + +          A   F   + +    +  + ++ I   R
Sbjct: 150 ITVGTPADPIVDYLTNRGMESLEEYEPTRAPHATKVFVNGTWIGCHNDPAHLVTHIQEIR 209

Query: 540 RLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           R   +  +  + R     E +    T  GR+C       ++    ++       +    +
Sbjct: 210 RKGIIAHEASLVRDIRDREFK--IFTDAGRVCRPLFVIDNDPKSENNGNLALTKDMVQKL 267

Query: 599 ETPYRKVCDGKVTND---------------VVYLSAMEEENRYIAQANSSLDEDGSFT-- 641
           E     V                       V Y+ A EEE   IA     L+        
Sbjct: 268 EDERDMVLTMDPEERAEQVIGWEALVDSGAVEYVDAEEEETIMIAMTPEDLEISRHIQAG 327

Query: 642 ------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                  E    +     +          +  P  ++ I AS+IPF +++ S R      
Sbjct: 328 YAAPVPSEDAPNQRVKAPLNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 387

Query: 696 MQRQAVPLLKAEAP 709
           M +QA+ +      
Sbjct: 388 MGKQAMGVFLTNYD 401


>gi|218184815|gb|EEC67242.1| hypothetical protein OsI_34174 [Oryza sativa Indica Group]
          Length = 1086

 Score =  263 bits (672), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 110/262 (41%), Gaps = 56/262 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGV 1127
              L+   + +   R    GDK + RHG KG+ S++ P  DMPF  + G   D+++NP   
Sbjct: 786  DRLQKANIRLRRVRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSANTGMRPDLIINPHAF 845

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +  + E+    A    GK I                                   
Sbjct: 846  PSRMTIAMLLESIAAKAGSLKGKFI----------------------------------- 870

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                             P ++ V + ++   + +  ML     +  G  ILY G+ G   
Sbjct: 871  --------------DATPFASSVKERSNSIVDELGPMLASYGFNYHGTEILYSGVFGTEM 916

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  +L HMVSDK   R+TG    +T+QP+GG+   GG R GEME   + A+
Sbjct: 917  KCEIFLGPVYYQRLRHMVSDKFQVRTTGRIDQITRQPIGGRKYGGGIRFGEMERDALLAH 976

Query: 1306 GAAYVLQEMLTIKSD----DVV 1323
            GA+Y+L + L   SD    DV 
Sbjct: 977  GASYLLHDRLHSCSDYHIADVC 998



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 92/600 (15%), Positives = 191/600 (31%), Gaps = 55/600 (9%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
             F  +    +K D  TV    +   + +   ++  H +   +I +++ L  + +   + 
Sbjct: 224 KYFRSVMEGFEKDDFETVAEAVLKDYIFVHLQNN--HDKFNLLIFMLQKLYAIVDQTASP 281

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRL-------GLLRMERSIKERISSVDIDS-------VM 499
           D  D L  + V   G ++    +           R+      +  S D++        + 
Sbjct: 282 DKADALQYQEVLLPGHLITVFLKDRLQDWLRKSKRLIVEEATKNKSFDLNDSQEVRKFLS 341

Query: 500 PQDLINAKPVVSAVCEFFCSSQ----------LSQLEEHVNSLSRITHTRRLSALGQGGV 549
                  K + S +     +SQ          ++   E +N    I+H R   ++ +G  
Sbjct: 342 KTSAYVGKAIQSMIKVGKVNSQSGLDLPQRDGMTIHAERLNFHRYISHFR---SVHRGSS 398

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                   +R + P  +G +CP  T +G   GL++ +TS  R++++   E   +     K
Sbjct: 399 FAKMRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRISSFYNSEGATKDFQKIK 458

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRCAGEEILVPREKIDFIDAS 667
           ++     + A        AQ    ++  G        V     G       E++   D  
Sbjct: 459 MSLIARLVGAGM------AQLLPRIERTGPPEVLHVHVDGCIVGSIASAKIEEVIPEDLE 512

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG----TGMESVVAK-- 721
              V        P L    +    +        +         +G      ME       
Sbjct: 513 VGYVPLSHGGAYPGLYLFTNPARFLRPVRSLLGLSNGGPNIELIGPFEQAFMEIRCPDGG 572

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQR 779
             G   +           AI  V+ ++    D + S  ++Y+    +++       +  R
Sbjct: 573 DGGRNKLFPATHEEIHPTAILSVVANLTPWSDHNQSPRNMYQCQMAKQTMGFCGQALKFR 632

Query: 780 PLVKVGDEVRRNDIIADGPST---DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
             VK          I    +     + +   G N +VA + + GY+ ED+M++++  V  
Sbjct: 633 TDVKAFHLQTPQTPIVRTATYSKYCMDEFPSGTNAIVAVLSYTGYDMEDAMILNKSAVDR 692

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV- 895
            +F     +   +                 N+S +    I+  G+  +G  + P +    
Sbjct: 693 GMFRGHIFQTECIDLSAKSRDNVTEFFCKSNLSRDTTAAIESDGLPRIGENIFPNEQYYS 752

Query: 896 ------GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                 G + P       P      A+ G    D    +      V   ++  +  +RHG
Sbjct: 753 VCNNLTGTVRPIKLKGSEPAAIDYVAVNGTNFKDRLQKANIRLRRVRNPIIGDKFSSRHG 812


>gi|222613075|gb|EEE51207.1| hypothetical protein OsJ_32024 [Oryza sativa Japonica Group]
          Length = 1150

 Score =  263 bits (672), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 110/262 (41%), Gaps = 56/262 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGV 1127
              L+   + +   R    GDK + RHG KG+ S++ P  DMPF  + G   D+++NP   
Sbjct: 850  DRLQKANIRLRRVRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSANTGMRPDLIINPHAF 909

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +  + E+    A    GK I                                   
Sbjct: 910  PSRMTIAMLLESIAAKAGSLKGKFI----------------------------------- 934

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                             P ++ V + ++   + +  ML     +  G  ILY G+ G   
Sbjct: 935  --------------DATPFASSVKERSNSIVDELGPMLASYGFNYHGTEILYSGVFGTEM 980

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  +L HMVSDK   R+TG    +T+QP+GG+   GG R GEME   + A+
Sbjct: 981  KCEIFLGPVYYQRLRHMVSDKFQVRTTGRIDQITRQPIGGRKYGGGIRFGEMERDALLAH 1040

Query: 1306 GAAYVLQEMLTIKSD----DVV 1323
            GA+Y+L + L   SD    DV 
Sbjct: 1041 GASYLLHDRLHSCSDYHIADVC 1062



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 153/978 (15%), Positives = 284/978 (29%), Gaps = 187/978 (19%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFSGAAMLEFVSYEFDPPKFDVDD 90
              S+D+F+          +EGL    +S+ P  IT       L  +  E   PK     
Sbjct: 25  HIDSFDYFI----------DEGLDKMLQSIRPVEITVPKSPTTLRNILPELGTPK----- 69

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD----LPLMTKDGTFVI 146
                   A  LK  +++    V +    +      E+ I+ G+    +      G F+ 
Sbjct: 70  --------ASILK-KVQIHHILVSKLCHLRGADS--EKLIFHGEEATEM-----GGYFIC 113

Query: 147 KGIQR---IVVSQ-------LHRSPGIHFDHDKGRAS-------------LSGKLLY--- 180
            G++R   I++ Q       L R  G   +   G                     LY   
Sbjct: 114 GGMERLVRILILQKRNYPMGLIR--GSFVNRGAGYTDKAVIIRCVQDDQSSVTIKLYYLL 171

Query: 181 --ACRIIPDQGLWM---DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILS--TF 232
             + R+    G W+   +                  +PV   L AL   S+ EI +  T 
Sbjct: 172 NGSARL----GFWLGGREFL----------------LPVGIVLKALIDTSDREIFTSLTC 211

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
                Y +        L      +       L      E ++  GK   S +    K+  
Sbjct: 212 CYSDHYERGKGVVSTQLIGERAQIILDEVRDLSLFTRTECLLHLGKYFRSVMEGFEKDDF 271

Query: 293 VK-FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
                 +  D +                                   +      +L    
Sbjct: 272 ETVAEAVLKDYIFVHL------------------------------QNNHDKFNLLIFML 301

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
               A +  T   DK     DAL     V+ PG + T  + + + ++      K     V
Sbjct: 302 QKLYAIVDQTASPDKA----DALQY-QEVLLPGHLITVFLKDRLQDW----LRKSKRLIV 352

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
                N   +L+   D R    E  +     +++  +GK            R        
Sbjct: 353 EEATKNKSFDLN---DFRDFILEGQVKGTSRVIETSSGKPCWLMRIGAQEVRKFLSKTSA 409

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
                     + ++I+  I    ++S    DL     +                 E +N 
Sbjct: 410 Y---------VGKAIQSMIKVGKVNSQSGLDLPQRDGMT-------------IHAERLNF 447

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
              I+H R   ++ +G          +R + P  +G +CP  T +G   GL++ +TS  R
Sbjct: 448 HRYISHFR---SVHRGSSFAKMRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCR 504

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRC 649
           ++++   E   +     K++     + A        AQ    ++  G        V    
Sbjct: 505 ISSFYNSEGATKDFQKIKMSLIARLVGAGM------AQLLPRIERTGPPEVLHVHVDGCI 558

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            G       E++   D     V        P L    +    +        +        
Sbjct: 559 VGSIASAKIEEVIPEDLEVGYVPLSHGGAYPGLYLFTNPARFLRPVRSLLGLSNGGPNIE 618

Query: 710 FVG----TGMESVVAK--SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            +G      ME         G   +           AI  V+ ++    D + S  ++Y+
Sbjct: 619 LIGPFEQAFMEIRCPDGGDGGRNKLFPATHEEIHPTAILSVVANLTPWSDHNQSPRNMYQ 678

Query: 764 LMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADGPST---DLGDLALGRNMLVAFMPW 818
               +++       +  R  VK          I    +     + +   G N +VA + +
Sbjct: 679 CQMAKQTMGFCGQALKFRTDVKAFHLQTPQTPIVRTATYSKYCMDEFPSGTNAIVAVLSY 738

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GY+ ED+M++++  V   +F     +   +                 N+S +    I+ 
Sbjct: 739 TGYDMEDAMILNKSAVDRGMFRGHIFQTECIDLSAKSRDNVTEFFCKSNLSRDTTAAIES 798

Query: 879 CGIICVGAEVNPGDILV-------GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            G+  +G  + P +          G + P       P      A+ G    D    +   
Sbjct: 799 DGLPRIGENIFPNEQYYSVCNNLTGTVRPIKLKGSEPAAIDYVAVNGTNFKDRLQKANIR 858

Query: 932 PSGVSGTVVDVRIFNRHG 949
              V   ++  +  +RHG
Sbjct: 859 LRRVRNPIIGDKFSSRHG 876


>gi|1350832|sp|P28365|RPA2_EUPOC RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2
 gi|578407|emb|CAA47067.1| DNA-directed RNA polymerase [Euplotes octocarinatus]
          Length = 1166

 Score =  263 bits (672), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/562 (18%), Positives = 182/562 (32%), Gaps = 114/562 (20%)

Query: 766  KFQRSNQNTCVNQ----RPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHG 820
            +F R  +N   N      PL ++   +   D      +T    D     +++ +   +  
Sbjct: 620  RFTRPVKNLHYNCIEWISPLEQMNLSIACTDEDITPETTHQELDPINILSIVASVGVFAE 679

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            YN     +   +M  + + T  H  +F    +  +L         P V      + D   
Sbjct: 680  YNQSPRNMYQCQMAKQTMGTPYHNHQFRTDNKIYRLLFPHR----PIVKTRTQVDFD--- 732

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS--GT 938
               +    +  + +V  I+  G            +        V   S       S   +
Sbjct: 733  ---IEEYPSGTNAVVAVISYTGYDLEDAMIINKSSYERGFGHGVVYKSYTHDLNESNSQS 789

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
               ++   R+    N       + ++E +  D           +     ++  G+  +  
Sbjct: 790  TRGIKSSVRYKFLNNVSQKDKSKIKLENIDPD----------GLPKIGSQLTKGKPELCI 839

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                K+   LS    SE  R +  +    D+K                            
Sbjct: 840  FDTLKRGAKLSKFKDSEKARIETVRVCGNDDKNP-------------------------- 873

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D++  G        +   R    GDK + RHG KG++S + P  DMPF ++G   
Sbjct: 874  -----DNLSIGYT------IRYSRIPVIGDKFSSRHGQKGVLSVLWPQVDMPFTENGITP 922

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP   PSRM +G + ++    +    G+           + DI             
Sbjct: 923  DLIINPHAFPSRMTMGMLIQSMAAKSGSLRGEFKTVETFQRYDDNDI------------- 969

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                        L     +  G  ++Y 
Sbjct: 970  -------------------------------------VGHFGKELLDKGFNYHGNELMYS 992

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+ G P    + +G +Y  +L HMVSDK  AR TG   ++T QP+ G+   GG R GEME
Sbjct: 993  GIFGTPLKADIFIGVVYYQRLRHMVSDKSQARGTGPIDILTHQPVKGRKKGGGIRFGEME 1052

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD 1320
               + A+GAAY L + L   SD
Sbjct: 1053 RDSLLAHGAAYCLNDRLFRSSD 1074



 Score =  102 bits (255), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 136/969 (14%), Positives = 279/969 (28%), Gaps = 231/969 (23%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---G 70
           RK   K  + I           S+D    M+   +      L   F  + P  + S    
Sbjct: 9   RKEISKIYKNIA-----RHHIDSFD--FAMSTCLNRACEHMLP--FDYIVPEESASCGFK 59

Query: 71  AAMLEFVSYEFDPPK-----FD-----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
              L + S+E   P      +D       +C  R +TY +PL  T+    FD +     K
Sbjct: 60  KLTLWYDSFELGQPSLGEIDYDSHILYPSECRQRKMTYTIPLFATI-FKKFDDEMVDNFK 118

Query: 121 SIKDIKEQSIYMGDLPLM-----------TK-------------DGTFVIKGIQRIVVSQ 156
                    + +GD+P M           TK              G F++ G ++++   
Sbjct: 119 ---------VKLGDIPTMGRKKFCNLKGLTKKELAKRGEDMLEFGGYFIVNGNEKVIRML 169

Query: 157 LH--RSPGIHFDHDKGRASLSGKLLYACRIIPDQ---------------GL-WMDIEFDS 198
           +   R+  I F   K          Y  ++   +               G   + + +  
Sbjct: 170 IVPKRNFPIAFKRSKFLERGKDFTDYGVQMRCVRDDFTAQTITLTYLSDGSVSLRLIYQK 229

Query: 199 KDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
           ++ +         +P+   L AL   ++      Y +IV              A L VG 
Sbjct: 230 QEFL---------IPIILILKALKNCTD---RQIYERIVKGNFNQRQISDRVEAILAVGK 277

Query: 259 KVSSSLVDIDTGEQVIESGKKL-TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +  ++ D D  + +I S  ++  +G+     +     L ++                  
Sbjct: 278 DL--NIYDSDQSKALIGSRFRIVLAGITSETSDIDAGDLFLSKHICIHTDS--------- 326

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK--DALL 375
                EA        +++++ S   ++ +  +DSV     +    +  +    K  D L 
Sbjct: 327 ----YEAKFDTLILMIDKLYASVANEVELDNLDSVAMQDVLLGGHLYLQILSEKLFDCLH 382

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
              R     ++   +     F  +  +        +   +M   L         ++    
Sbjct: 383 INLRARLNKELKRHNFDPMKFRDVLTNQKINCGIGLIGKRMENFLATGNLISRTNLDLMQ 442

Query: 436 IIAIIKILVDLRN-----GKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKER 489
                 I   L N        +I        ++  SV ++L   +  +  +         
Sbjct: 443 TSGFCIIGDKLNNIRFLSHFRSIHRGQYFAEQKTTSVRKLLPESWGFICPVHTPDGAPCG 502

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + +    S +P      +  +                  +NS+S        +       
Sbjct: 503 LLNHISMSCVPIGSEEKQIDIDKFRNILGELG-------MNSISSDLCLNYHTGYYPVIF 555

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF------------ 597
                G   +D+  +    +   + ++      +      A +   G+            
Sbjct: 556 DGIHLGYVEKDIGESFVEGLRYLKCTQSQPDYAIPRTLEIAFIPFSGYSRNLQWPGIFLA 615

Query: 598 --IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                  R V +    N + ++S +E+ N  IA  +  +                     
Sbjct: 616 STPARFTRPVKNLHY-NCIEWISPLEQMNLSIACTDEDITP------------------- 655

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
               +    +  P  ++SI AS+  F E + S R +  C M +Q +        F     
Sbjct: 656 ----ETTHQELDPINILSIVASVGVFAEYNQSPRNMYQCQMAKQTMGTPYHNHQF----- 706

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                                    +   IYRL+   R      
Sbjct: 707 ----------------------------------------RTDNKIYRLLFPHR------ 720

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
               P+VK   +V            D+ +   G N +VA + + GY+ ED+M+I++    
Sbjct: 721 ----PIVKTRTQVD----------FDIEEYPSGTNAVVAVISYTGYDLEDAMIINKSSYE 766

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDI-----------PNVSEEGLKNIDECGIICV 884
                 +  + +     ++        +              + S+  L+NID  G+  +
Sbjct: 767 RGFGHGVVYKSYTHDLNESNSQSTRGIKSSVRYKFLNNVSQKDKSKIKLENIDPDGLPKI 826

Query: 885 GAEVNPGDI 893
           G+++  G  
Sbjct: 827 GSQLTKGKP 835


>gi|313212713|emb|CBY36648.1| unnamed protein product [Oikopleura dioica]
          Length = 1140

 Score =  263 bits (672), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 88/337 (26%), Positives = 133/337 (39%), Gaps = 58/337 (17%)

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLIS-EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +  G      P   K    ++ D +  +        F  QD       E  +        
Sbjct: 767  LRLGCRDRFDPNELKAYRKIAGDKLDIDGLPFPGGIFTYQDAYYCYYNEHEQKYSVGKYD 826

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
               +    +  ++        G  +   +   + RPI  GDKMA RHG KGI SR+    
Sbjct: 827  SHAEDAIVESVRVFTNKRPQEGGFQQAAIQFRIARPINIGDKMASRHGQKGICSRLWATT 886

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+ ++G   D++ NP G PSRM VG + E   G A +  G+                 
Sbjct: 887  DMPWTENGIVPDLIFNPHGFPSRMTVGMMIEFIAGKAAMVNGR----------------- 929

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFD--GADEEAINSMLR 1224
                                                V  STP VFD     +E    +L+
Sbjct: 930  ------------------------------------VYDSTPFVFDENYTADEHFGKVLK 953

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS-TGSYSLVTQQPL 1283
             A L+  G   +Y G++GE  +  +  G +Y  +L HMV DK  AR+  G     TQQP+
Sbjct: 954  EAGLNYHGYERMYSGISGEELEADIFFGPVYYQRLRHMVYDKFQARADKGPIDPYTQQPV 1013

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G++  GG R+GEME   + ++GAA++ ++ L   SD
Sbjct: 1014 KGRARGGGVRMGEMERDGLISHGAAFICRDRLFHCSD 1050



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 74/598 (12%), Positives = 158/598 (26%), Gaps = 69/598 (11%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD----KYDL 408
           +   Y           +   A+  + + +        + A+ +             K D+
Sbjct: 231 DLEIYREFMQTMSDEPNYDSAVKRMLKKLVKIQHHFLTQAKFLGQSFRIFDICPAWKSDV 290

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
                      L     D+ +      +      +         ID  ++        + 
Sbjct: 291 EAGQAFLKRYCLIYLNNDEDKVRAFALMARKAFRISHNTCATDDIDSPESHDVLLPGHLF 350

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA--------KPVVSAVCEFFCSS 520
           + +  ++     R    I  +  S  ++    +   N           +         + 
Sbjct: 351 QSMTLEFFESYQRSVSMIMAKEYSKQLEKGNDEVGQNMLSFAINKIGNMNQHFKYLIATG 410

Query: 521 QLSQLE--------------EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            L   +              E +N     +H R    + +G           R +    +
Sbjct: 411 NLKTNDGLGMQQLAGIVVGAEKINFARFYSHFR---CIHRGAFFMEMRATSPRKLSTAAW 467

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--AMEEEN 624
           G ICP  T +G   GL++ L    R+N          K+ +  +   V   S  A E + 
Sbjct: 468 GFICPVHTPDGPPCGLLNHLAHTVRINVK---RENTAKLEELLLEIGVKPCSIKANEFDI 524

Query: 625 RYIAQA-NSSLDEDGSFTEELVFCRCAGEEILVPR-----EKIDFIDASPKQVVSIAASL 678
             I          +G   + +       +     R     E +       K    +   +
Sbjct: 525 PVIIDGKQIGWIANGWRAQAVEKYLRRLKTSSSDRVPDTLEIVHCPAPENKGEAVMFPGI 584

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-----GMESVVAKSS-GAAIVAKRA 732
               E     R L+     +  +  +  +     T       E    +    AA++++ A
Sbjct: 585 NLLTEPARMYRPLLNLREDKIEMIGIMEQVWLHVTVNQKESHELTEYQELYPAALLSELA 644

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    +        ++  +   T G   Y    +           Q PLV+        
Sbjct: 645 CMSPFSNMNAGARVILQCQMAKQTFGWPSYTLNHRSDNKMYRILTPQEPLVRSH------ 698

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  S  + D  LG N+++A + + GY+ ED+  +S+      +      +   V  
Sbjct: 699 ----LHDSWGMDDYPLGTNVMIAVISYTGYDLEDATCVSKMSRERGMMYGTIYKTKMVDL 754

Query: 852 RDT------------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +DT                     ++    +     +D  G+   G      D     
Sbjct: 755 QDTAQSMGYRSGLRLGCRDRFDPNELKAYRKIAGDKLDIDGLPFPGGIFTYQDAYYCY 812



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 50/187 (26%), Gaps = 61/187 (32%)

Query: 10  LGRVRKFFGKNPE--IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT- 66
               R  +GK PE     +  + +    S+D FL           EGL     SV P   
Sbjct: 19  KQTSRVNYGKLPEDKNKQLKFISDTHVQSFDWFL----------EEGLPNIPNSVAPYEF 68

Query: 67  -----AFSGAAMLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLRLIV 110
                       LE    E   P  +             +C  +   Y  P+ +T  LI 
Sbjct: 69  EMEANNDQMRFRLEVEHIEVGQPTLESSIVCKDRRLFPSECRQKKTDYTAPVHVTFNLIN 128

Query: 111 FDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVI 146
               E         ++        +PLM                           G F+ 
Sbjct: 129 LSSGETQVVTKKDLLQ--------MPLMVMSSKCHLRGLSPEELVARKEDHFEIGGYFIA 180

Query: 147 KGIQRIV 153
            G ++++
Sbjct: 181 SGNEKVI 187


>gi|124491189|gb|ABN12929.1| RNA polymerase beta chain [Agrobacterium vitis]
          Length = 237

 Score =  263 bits (672), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 142/238 (59%), Positives = 176/238 (73%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI+H RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVHARIDRRRKIPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EILSTFY K  Y + G  W  P  A  L  G+K    +VD D+GE V+E+GKKLT  LL+
Sbjct: 61  EILSTFYSKSDYKRDGKGWRVPFQAETL-KGSKTLVDMVDADSGEVVVEAGKKLTPRLLR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
            L++KG+K L  T + L G Y+AEDIVN  TGEIY+EAGD IDEK+L  I  +   +IP+
Sbjct: 120 QLQDKGLKALKATDEDLYGNYLAEDIVNFATGEIYLEAGDEIDEKTLPIILEAGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFDS+
Sbjct: 180 LGIDHINVGAYIRNTLAADKNENRQDALFDIYRVMRPGEPPTMDSAEAMFNSLFFDSE 237


>gi|269930791|gb|ACZ54130.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 280

 Score =  263 bits (672), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 202/281 (71%), Positives = 235/281 (83%), Gaps = 1/281 (0%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER+IKER+SSV+ID+VMPQDLINA    +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RMERAIKERMSSVEIDTVMPQDLINANHAAAAVREFFGSSQLSQFMDQTNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           LSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+
Sbjct: 61  LSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIES 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ 
Sbjct: 121 PYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDH 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA
Sbjct: 181 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVA 240

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           + SGAA+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 RDSGAAVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 280


>gi|151545|gb|AAA25985.1| RNA polymerase [Pseudomonas aeruginosa]
          Length = 281

 Score =  263 bits (672), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 161/280 (57%), Positives = 208/280 (74%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +A  EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 2   KERLSMAESEGLMPQDLINAKPVAAADKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 61

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++A  N YGF+E+PYR V 
Sbjct: 62  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYAAPNKYGFLESPYRVVK 121

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D  VT+++V+LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E  D +D 
Sbjct: 122 DSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDADLMDV 181

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  
Sbjct: 182 SPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 241

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +VA+R G+++ VDA R+V+R  + +++   +GVDIY L K
Sbjct: 242 VVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTK 281


>gi|190694915|gb|ACE88998.1| RNA polymerase beta subunit [Mycobacterium conceptionense]
          Length = 220

 Score =  263 bits (672), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 93/219 (42%), Positives = 122/219 (55%), Gaps = 37/219 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 143

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML--------RMAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 144  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 181

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +D  G++ L+DG +GEPF  PVTVGY+YMLKL+H+V DK
Sbjct: 182  VDSDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDDK 220


>gi|110669596|gb|ABG81893.1| RNA polymerase II second largest subunit [Pertusaria dactylina]
          Length = 714

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 126/837 (15%), Positives = 241/837 (28%), Gaps = 149/837 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++   +R+   ++ + + +  +              + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLMAGLFRMLFKKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     V      E    +      +V  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMISRSMEVLEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  + +    +V        I      + D  D   K         
Sbjct: 177  PNATKIFVNGVWIGVHRNPTDLVRIVQGLRRNGMISHEVSLVRDIRDREFKIFTDAGRVT 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+  +     N+   ++ V  L+ +            A        AK  G   
Sbjct: 237  RPLFVIDNDPKSSNKGNLVLTKEIVNRLEDDKDL--------PADMDPDEKAAKTMGWDG 288

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V A   V+  ++ + + +   V     +   R  Q               V+       
Sbjct: 289  LVKA--GVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYQMPETTDDPNKRVKAPVNPTA 346

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +                 
Sbjct: 347  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV--------------- 391

Query: 856  LGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                             L N DE    +  +             +       +   +  +
Sbjct: 392  ----------------FLTNFDERMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAI 435

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    
Sbjct: 436  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRS 491

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  ++ D      R++          
Sbjct: 492  DTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL--------- 542

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                   +K    T     E+   +K+             LR VKV +   +  Q GDK 
Sbjct: 543  ------HIKRDASTPLRTTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKF 591

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 592  ASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 651

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          +S L    E    +                                
Sbjct: 652  EGDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM-------------------------- 683

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                +G +    G         V +G  Y  +L HMV DK+
Sbjct: 684  -------------------YNGHT----GR---KLVVQVFLGPTYYQRLRHMVDDKI 714


>gi|168053094|ref|XP_001778973.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162669645|gb|EDQ56228.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1238

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 127/317 (40%), Gaps = 70/317 (22%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 R+ KV +   R  Q+GDK +  HG KG++  +L  ED+PF + G   DI++NP  
Sbjct: 973  EEDGHRIAKVRLRCSRRPQAGDKFSSMHGQKGVIGAVLNQEDLPFTRQGVVPDIIINPHA 1032

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +P+R  VGQ+ E+ LG      G +        ++                         
Sbjct: 1033 LPNRQTVGQLLESLLGKLMAVRGTQQSVAPFQKQS------------------------- 1067

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +T  F           L  ++    G   + +G TG   +
Sbjct: 1068 --------------------ATRKF--------MDQLHQSEYQRGGSESMTNGTTGMRLN 1099

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYAR-STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
              +++G  +  +L+HMV DK+  R S G    +T+QP+  + N GG + GEME  C+  +
Sbjct: 1100 SLISIGATFYQRLDHMVEDKIKYRGSGGPVDALTRQPVKNRKNMGGVKFGEMERDCMIGH 1159

Query: 1306 GAAYVLQEMLTIKSDD----VV------------GRTRVYESIVAGNDTFETGTPESFNV 1349
            GA+  L+E   + SD     V              R R  +    G    +   P S  +
Sbjct: 1160 GASVTLRERCFLLSDPYAMLVCSSCRRPSGHTDPSRRRFCKFCCTGKHVVQIQIPYSCKL 1219

Query: 1350 LVKEMQALGLSIDLENS 1366
            L +E+ ++G+++ LE  
Sbjct: 1220 LWQELLSMGITLFLETK 1236



 Score =  129 bits (323), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 114/722 (15%), Positives = 235/722 (32%), Gaps = 70/722 (9%)

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           +    +          ++  +    +   S L   DT         +  +    +  +  
Sbjct: 240 FDDGGFFIIKGSEKVLIAQEEKAHQSIYVSYLKRTDTWIATYSPTWRGFNSNQMNRGKTF 299

Query: 293 VKFLGITSDCLCGLYVAEDIVNGETGEIYIEA-GDVIDEKSLEEIF-HSEIRDIPILYVD 350
           VK        L        +       I   A G   D++ LE I   S       L + 
Sbjct: 300 VKLRMRKKAELL--VGVPGLTEPVPLVILFRALGTSSDKEFLESICYDSTDSRFHDLLLS 357

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
           S+ +   I     +  +     A     + +R   +S   +   + N     S +   + 
Sbjct: 358 SIWDADLILEEFQSRISYP---AGASAIKSVRDQILSVRFLGTKLRNSRHVPSVEAGKTI 414

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +G++ ++        +     +   +  ++  L     G+   DD D+  N+R+   G++
Sbjct: 415 IGQLFVH-------TEGGYTRKAMLLGYMVNQLCSTFLGRRLEDDKDHFKNKRLDLTGQL 467

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDS--------------VMPQDLINAKPVVSAVCEF 516
           L +Q+R  +  +ER +K R+    +                V  Q             E 
Sbjct: 468 LSHQFRKAMAHLERDVKRRLHPYLVKGRDLAPLKTYVTEAIVTKQMQSAFTLGNWNTNEG 527

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             SS +  + + +N ++ ++H R+        +         R  + +++GRICP +TS+
Sbjct: 528 LKSSGVVAVLKRMNPMATLSHLRQFRLNLPPPMKPTDP---ARHPNYSYWGRICPTQTSD 584

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENRYIAQANSSL 634
           G   GL+ SL     V++    E     + D       ++  L+    E  ++      +
Sbjct: 585 GAECGLIKSLALTCVVSSDTPEEPVLHVLSDCGMHSLEEITPLTISMAEKIFVNGRWVGI 644

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI---AASLIPFLENDDSNRVL 691
             D + T  +V          +   +I+       + V I   A  L+  L      ++ 
Sbjct: 645 FYDYNATLAIVATLRQLRREQLLHGEIEVARDPKTKAVHIHTDAGRLLRPLLIVKEQKLA 704

Query: 692 MGCNMQRQAVPLLKAEAPFVGTG--MESV--------------VAKSSGAAIVAKRAGIV 735
           M     +    + K E+        +E                +A +      A++    
Sbjct: 705 MSKQHLKTLRAMSKQESAEACWNFLLEQQVVELLGTEEEEGALIALNRDDLERARKDPDA 764

Query: 736 EQVDAIRIVIRSVEG-------DLDPSTSGVDIYRLMKFQRSNQNTCVNQ---RPLVKVG 785
                  I +  + G        LD + +  ++Y+  K  +       +    R      
Sbjct: 765 PLYTHSEIDVSYIFGLGASVIPFLDHNQASRNLYQAEKHCKQAMGFYTSNLSGRSDCSGH 824

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMP--WHGYNFEDSMLISERMVSEDVFTSIH 843
                   +    + D        N  VA +     GYN EDS++++   +   +F S+H
Sbjct: 825 QLFYPQKPLVTTRTWDYLKKPEITNGQVAIVSIQCCGYNQEDSIIMNRASIDRGLFRSMH 884

Query: 844 IEEFEVMARDTKLGPEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            + +    R      E   +   ++        L  IDE G   +G  +  GDI++GK+T
Sbjct: 885 FKTYRGEER--HNVIEHFAKPSISIAKRSRNASLNKIDEDGFPHLGDYLEKGDIIIGKLT 942

Query: 900 PK 901
            +
Sbjct: 943 AE 944



 Score =  103 bits (256), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 111/778 (14%), Positives = 214/778 (27%), Gaps = 151/778 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP---ITAFS----------GAAMLE 75
           L+E    S++ F+            GL A F+       I   S            A + 
Sbjct: 89  LVEHHLRSFNEFM----------EYGLPAMFEEAGSFDCIPDHSVLVDSGIGVRKWARIV 138

Query: 76  FVSYEFDPPKFD--------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           +       P +                 +   R+L+Y+  L + + L V       G K 
Sbjct: 139 YGEVAVGKP-YTTFTREGVKEVVDLLPHEARLRNLSYSAHLYVNMTLEV----RSQGNKK 193

Query: 122 IK------DIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQR 151
            +      + K  +I +G +P+M                           G F+IKG ++
Sbjct: 194 TQNPEDMIETKTDTICVGKVPVMVNSSFCHLHGLSEKDSVAKGHCSFDDGGFFIIKGSEK 253

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACR----IIPDQGLWMDIEF--DSKDIIHVR 205
           ++++Q              +A  S  + Y  R    I      W        ++    V+
Sbjct: 254 VLIAQE------------EKAHQSIYVSYLKRTDTWIATYSPTWRGFNSNQMNRGKTFVK 301

Query: 206 IDRRRK-------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
           +  R+K             VP+     ALG  S+ E L +       S+  D     +  
Sbjct: 302 LRMRKKAELLVGVPGLTEPVPLVILFRALGTSSDKEFLESICYDSTDSRFHDLLLSSIWD 361

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           ADL++    S   +    G   I+S +     +     +        + +   G  +   
Sbjct: 362 ADLILEEFQSR--ISYPAGASAIKSVRDQILSVRFLGTKLRNSRHVPSVE--AGKTIIGQ 417

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +     G    +A  +    +         R                   L     K   
Sbjct: 418 LFVHTEGGYTRKAMLLGYMVNQLCSTFLGRRLEDDKDHFKNKRLDLTGQLLSHQFRKAMA 477

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
               D+ R + P  V    +A            K   S       N    L +   V  +
Sbjct: 478 HLERDVKRRLHPYLVKGRDLAPLKTYVTEAIVTKQMQSAFTLGNWNTNEGLKSSGVVAVL 537

Query: 432 RKEDIIAIIKILVDLRNG------------------KGTIDDIDNLGNRRVRSVGEMLKN 473
           ++ + +A +  L   R                     G I             +  +   
Sbjct: 538 KRMNPMATLSHLRQFRLNLPPPMKPTDPARHPNYSYWGRICPTQTSDGAECGLIKSLALT 597

Query: 474 QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
                    E  +          ++ + P  +  A+ +                   +  
Sbjct: 598 CVVSSDTPEEPVLHVLSDCGMHSLEEITPLTISMAEKIFVNGRWVGI---FYDYNATLAI 654

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS-SLTSFA 590
           ++ +   RR   L            +   +H      + P    +   + +    L +  
Sbjct: 655 VATLRQLRREQLLHGEIEVARDPKTKAVHIHTDAGRLLRPLLIVKEQKLAMSKQHLKTLR 714

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            ++     E  +  + + +V   V  L   EEE   IA             ++L   R  
Sbjct: 715 AMSKQESAEACWNFLLEQQV---VELLGTEEEEGALIALN----------RDDLERARKD 761

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN-MQRQAVPLLKAE 707
            +  L    +ID           + AS+IPFL+++ ++R L       +QA+    + 
Sbjct: 762 PDAPLYTHSEIDVSYI-----FGLGASVIPFLDHNQASRNLYQAEKHCKQAMGFYTSN 814


>gi|108885355|gb|ABG23194.1| DNA-directed RNA polymerase [Geobacillus sp. O83]
          Length = 145

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 66/167 (39%), Positives = 99/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE   +SY  FL          +EGL+  FK + PI  FSG   LEF+ Y    P
Sbjct: 1   ELPNLIERSTSSYKWFL----------DEGLREMFKEISPIEDFSGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TYA PL++ +RLI          K   ++KEQ ++MGD PLMT+ GTF
Sbjct: 51  KYTVEEAKERDVTYAAPLRVKVRLI---------NKETGEVKEQDVFMGDFPLMTETGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP +++     +   +GK  Y+  +IP++G W
Sbjct: 102 IINGAERVIVSQLVRSPSVYYSEKVDK---NGKRGYSATVIPNRGAW 145


>gi|323434942|gb|ADX66432.1| RNA polymerase beta subunit [uncultured Bartonella sp.]
          Length = 284

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 202/285 (70%), Positives = 238/285 (83%), Gaps = 1/285 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           S AA+ A+R+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 SXAAVAARRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 284


>gi|120561255|gb|ABM27012.1| RNA polymerase II second largest subunit [Glomus mosseae]
          Length = 883

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 133/936 (14%), Positives = 270/936 (28%), Gaps = 156/936 (16%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            V++  +++       +    +AL               +            + +      
Sbjct: 80   VSDQDFLQYVCYDPSDHQMLEALKPCIEEAFAVQSMEVAADWIGRRGTTTGATRDKRIKY 139

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDII--AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +  +   L      +    +++      ++  L+    G+  +DD D+ G +R+   G 
Sbjct: 140  AKDILQKELLPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRRELDDRDHYGKKRMDLAGP 199

Query: 470  MLKNQYRLGLLRMERS--IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L + +R+   ++ +   I  R              I A+ + + +     +        
Sbjct: 200  LLASLFRMLFKKLTKDVSIYLRKCIDSNREFNLNLAIKAQTITNGLKYSLATGNWGDQKK 259

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 260  AMQSRAGVSQVLNRYTFASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHWGMVCPAET 315

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L+  + ++     +             +   ++  ++ +    + N+ +
Sbjct: 316  PEGQACGLVKNLSLMSYISVGSASKPI------IDFLEEYGMINLNQQFDPANIKDNTKV 369

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL--- 691
              +G +             +   R  +   D SP+  V             D+ RV    
Sbjct: 370  FVNGKWAGISSSPEQLSYTLKGLRRTV---DVSPEVSVVRDIRERELRIYTDAGRVCRPL 426

Query: 692  --MGCNMQRQAVPLLKAEAPFVGTGMES-VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              +     R    L++    F    M        S + I        E +DA       +
Sbjct: 427  FIVENERLRITKGLIQKLDVFKMKKMTFGWQDLISNSVI--------EYIDAEEEETVMI 478

Query: 749  EGDLDPSTSGVDIYRLMKFQRSN-QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                +   +    +   + ++       V  R   +   ++         PS  LG    
Sbjct: 479  CMTPEDLAAARVFHETGETKQEKAHERDVAARVKSETNLKIHSWTHCEIHPSMILG---- 534

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   I++  ++                   
Sbjct: 535  ---ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------- 570

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +    +  +        +    +       +   +  + AI      +  D+
Sbjct: 571  --------LRMDTLANILYYPQKPLVTTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDS 622

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    IF R  +D+ ++   +  E+ E   ++                 
Sbjct: 623  VIMNQSSIDRGLF-RSIFYRSYMDQEKKVGMLTIEEFEKPTKETTLRLKHGTYEKLEEDG 681

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K T +S D +    R            ++     +  Q      
Sbjct: 682  LIAPGTRVSGDDIIIGKVTPISPDTVELGQRKTTHTKRDASTPMRSTETGIVDQ------ 735

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                                   ++ VKV V   R  Q GDK A RHG KG +      E
Sbjct: 736  --------------VMVTTNAEGMKFVKVRVRSTRVPQMGDKFASRHGQKGTIGITYRQE 781

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+V+NP  +PSRM +G + E  LG      G++  +          IS 
Sbjct: 782  DMPFTAEGITPDLVINPHAIPSRMTIGHMVECLLGKVSTLTGQEGDATPFTDVTVEAISQ 841

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                  +   +                                                 
Sbjct: 842  SLR--SQGYQSRGFEVM------------------------------------------- 856

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +G +    G         V +G  Y  +L HMV
Sbjct: 857  --YNGHT----GR---KLSAQVFLGPTYYQRLKHMV 883



 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 107/767 (13%), Positives = 211/767 (27%), Gaps = 108/767 (14%)

Query: 209 RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++ VPV     ALG +  ++ L          Q  +     +  A  +   +V++  +  
Sbjct: 65  KKDVPVVIAFRALGAVSDQDFLQYVCYDPSDHQMLEALKPCIEEAFAVQSMEVAADWIGR 124

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                     K++     K + +K +    ++++  C    A  +       +    G  
Sbjct: 125 RGTTTGATRDKRI--KYAKDILQKEL-LPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRR 181

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +              P+L          +   +     K           +       
Sbjct: 182 ELDDRDHYGKKRMDLAGPLLASLFRMLFKKLTKDVSIYLRKCIDSNREFNLNLAIKAQTI 241

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 242 TNGLKYSLATGNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNTPMGRDGKIAKPRQ 301

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE----RISSVDIDSVMPQ 501
           L N    +         +   + + L     + +    + I +               P 
Sbjct: 302 LHNTHWGMVCPAETPEGQACGLVKNLSLMSYISVGSASKPIIDFLEEYGMINLNQQFDPA 361

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           ++ +   V         SS   Q          +   RR   +                +
Sbjct: 362 NIKDNTKVFVNGKWAGISSSPEQ------LSYTLKGLRRTVDVSPEVSVVRDIRERELRI 415

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           +        P    E   + +   L     V     ++       D    + + Y+ A E
Sbjct: 416 YTDAGRVCRPLFIVENERLRITKGLIQKLDV---FKMKKMTFGWQDLISNSVIEYIDAEE 472

Query: 622 EENRYIAQANSSL-----------DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           EE   I      L            +     E  V  R   E   +        +  P  
Sbjct: 473 EETVMICMTPEDLAAARVFHETGETKQEKAHERDVAARVKSET-NLKIHSWTHCEIHPSM 531

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS+IPF +++ S R      M +QA+ +                           
Sbjct: 532 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL-------------------- 571

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + +  Y               Q+PLV        
Sbjct: 572 ---------------------RMDTLANILYYP--------------QKPLV-------- 588

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G+N +VA + + GYN EDS+++++  +   +F SI    +   
Sbjct: 589 --TTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIFYRSYMDQ 646

Query: 851 ARDTKL-GPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +   +   EE  +        +     + ++E G+I  G  V+  DI++GK+TP     
Sbjct: 647 EKKVGMLTIEEFEKPTKETTLRLKHGTYEKLEEDGLIAPGTRVSGDDIIIGKVTPISPDT 706

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +   ++       +     RD S  + S  +G V  V +       K
Sbjct: 707 VELGQR-------KTTHTKRDASTPMRSTETGIVDQVMVTTNAEGMK 746


>gi|190694907|gb|ACE88994.1| RNA polymerase beta subunit [Mycobacterium fortuitum]
          Length = 197

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 91/219 (41%), Positives = 121/219 (55%), Gaps = 37/219 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 8    RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 67

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 68   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 120

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 121  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 158

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK
Sbjct: 159  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDK 197


>gi|52699827|gb|AAU86975.1| DNA-dependent RNA polymerase II second largest subunit [Lecanora
            concolor]
          Length = 708

 Score =  263 bits (671), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 129/830 (15%), Positives = 241/830 (29%), Gaps = 150/830 (18%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   ++ + + +  +    +     P   + +  + + +     +   
Sbjct: 2    DLAGPLLAGLFRMLFHKLTKDVYKYLQKCVENGKEFNPTLAVKSSTLTNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L    +  V +       +    +  V  +   L+       ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYITVGSPSDPIIDFMVQRNMDVLEEYEPLTFPNATKIFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  + +     V        I      + D  D   K          P    D+
Sbjct: 178  NGVWVGVHREPAHLVSNVQALRRNGLISHEVSLVRDVRDREFKIFTDAGRVCRPLFVIDN 237

Query: 687  SNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
              +     N+         + +     +G   E       G      + G+VE VDA   
Sbjct: 238  DPKSSNCGNLVLTKEIVQQVEEDRDTLIGMDPEERERLDLG-WKRLIKQGVVEYVDAEEE 296

Query: 744  ---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               +I      L+ S   +  Y L +      +  +N+R   KV    R        PS 
Sbjct: 297  ETIMITMTPQQLEESRQVLQGYTLPE----PGDDELNKRVTAKVNTSARNWTHCEIHPSM 352

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 353  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGVFL 387

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               D                +  +             +       +   +  + AI    
Sbjct: 388  TNFDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYT 436

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +    +    +E   +    E + L  
Sbjct: 437  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYSDQEK---QIGHSVLEQFEKPMRSETLKLKH 492

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  +++D                +E  QR    
Sbjct: 493  GTYDKLDDDGLVAPGVRVSGEDIIIGKTAPITAD---------------AEELGQRTKAH 537

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             K    T     E+   +++      D +     R  KV +   +  Q GDK A RHG K
Sbjct: 538  TKRDISTPLRSTENGIVDQVLMSTNADGL-----RFAKVRMRTTKIPQIGDKFASRHGQK 592

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 593  GTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPF 652

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 653  TEVTVDSVSRLLR--ENGYHSRGFEVM--------------------------------- 677

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                         +G +       G      V +G  Y  +L HMV  K+
Sbjct: 678  ------------YNGHT-------GRKLVAQVFLGPTYYQRLRHMVDXKI 708


>gi|195437584|ref|XP_002066720.1| GK24411 [Drosophila willistoni]
 gi|194162805|gb|EDW77706.1| GK24411 [Drosophila willistoni]
          Length = 1122

 Score =  262 bits (670), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/353 (22%), Positives = 126/353 (35%), Gaps = 85/353 (24%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    ++ I+          + V + + + RP   GDK A R G KGI S+  
Sbjct: 822  KVMKMDEKEDCFVDSIRQLGSFELQPRKSVCITLRVPRPATIGDKFASRAGQKGICSQKY 881

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +    G    +    +     
Sbjct: 882  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKSAAVHGNVYDATPFRFSEQNT 941

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    ML 
Sbjct: 942  A--------------------------------------------------IDYFGKMLE 951

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
                +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T QP+ 
Sbjct: 952  AGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIK 1011

Query: 1285 GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES------------I 1332
            G+   GG R GEME   + ++GAA++LQ+ L   SD    +T                 I
Sbjct: 1012 GRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSD----KTHTLVCHKCGSILSPLQQI 1067

Query: 1333 VA----GNDTFET---------------GTPESFNVLVKEMQALGLSIDLENS 1366
            V     G  + +                  P SF  LV E+ ++ ++   + +
Sbjct: 1068 VKRNETGGLSSKPETCRLCGDSSSVSMIEIPFSFKFLVTELSSVNINARFKLN 1120



 Score = 71.6 bits (174), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 88/623 (14%), Positives = 204/623 (32%), Gaps = 97/623 (15%)

Query: 320 IYIEAGDVIDEKSLE-------EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
           + ++      ++ +        E     I  +  +  D  N   Y               
Sbjct: 243 LILKCLMDYTDEEIYNRLIQGYETDQYYISCVQTMLRDVQNEGVYTHAQCRNFIGTLF-- 300

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
                    R  +V  +  AE++ +F            + R ++ + L+          +
Sbjct: 301 -------RSRIAEVPEWEPAEAVTDF------------ILRERIMVHLDSYED------K 335

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKE 488
            + I+ +++ L     GK  ++++D+   + V   G +    L  +  + + ++ + + +
Sbjct: 336 FQLIVFMVQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLGERIEMWMFQLRKCLLK 395

Query: 489 RISSVD---IDSVMPQDLINAKPVVSAVCEFFCS--------------SQLSQLEEHVNS 531
           ++++ D     S + Q +  A  V  ++  F  +              S L  + E++N 
Sbjct: 396 KLTTPDALLSSSTLTQCMRQAGGVGRSIESFLATGNIASRSGLGLMQNSGLVIMAENINR 455

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           +  ++H R   A+ +G         E R + P  +G +CP  T +G   GL++ LT    
Sbjct: 456 MRYMSHFR---AIHRGSYFTTMRTTEARQLLPDAWGFVCPVHTPDGTPCGLLNHLTLTCE 512

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVY------LSAMEEENRYIAQANSSLDEDGSFTEELV 645
           ++          K+        +             E   Y+   +              
Sbjct: 513 ISKRPDP-----KLVKAIPAKLIEMGMLPLSHRPQPESKLYVVFLDGRH----------- 556

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD---SNRVLMGCNMQRQAVP 702
                  +     E + +     +    +    IPF +N              M R    
Sbjct: 557 LGHIYQSDATKIVEDLRYGKIMGELPKMLEIGFIPFKKNGQFPGLFLATSPARMMRPVWN 616

Query: 703 LLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           L      ++GT   +   +A             +          + ++    D + S  +
Sbjct: 617 LKWQRVEYIGTLEQLYMEIAIDEKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRN 676

Query: 761 IYRLMKFQRSNQNTCVN--QRPLVKVGDEVRRNDIIA---DGPSTDLGDLALGRNMLVAF 815
           +Y+    +++    C+N  ++   K+         +       +  L D A+G N +VA 
Sbjct: 677 MYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHHDNIQLDDFAMGTNAIVAV 736

Query: 816 MPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           + + GY+ ED+M+I++        + SI+  +F  + + +                E  K
Sbjct: 737 ISYTGYDMEDAMIINKAAYERGFAYGSIYKSKFVQLPKKSSYFARHPHMP------ELQK 790

Query: 875 NIDECGIICVGAEVNPGDILVGK 897
            +D  G+   G +++ G  +   
Sbjct: 791 YLDTDGLPHPGTKLSYGCPMYCY 813


>gi|118396434|ref|XP_001030557.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila]
 gi|89284864|gb|EAR82894.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila SB210]
          Length = 1178

 Score =  262 bits (670), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 88/416 (21%), Positives = 151/416 (36%), Gaps = 58/416 (13%)

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR-HGIDKNERSISVEREQI 964
            M PE   L          V   S          +++   + R  G     ++ S +  ++
Sbjct: 739  MDPESYGLSDYPSGTNAIVAVISYTGYDMEDAMILNKSSYERGFGHGCVYKNYSYDVAEL 798

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                  K      +     S++ E L G    +     KK T +               F
Sbjct: 799  NKEKNSKFKMLNEVKNIDKSQIAEGLEGDGIPAIGSVIKKGTAV---------------F 843

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             + D +            E  +        ++  K              V+  + + R  
Sbjct: 844  QIYDTQKNAMKTFYHKDSELGRLDGIALVHDEKTKEPR-----------VEYRIRIPRNP 892

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDK + RHG KG++S + P  DMPF + G   D+++NP   PSRM +G+         
Sbjct: 893  IIGDKFSSRHGQKGVLSVLWPHIDMPFTESGITPDVIINPHAFPSRMTIGKF-------- 944

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                 +++ + +N  K    I  +      + G    T+   +Y DD ++          
Sbjct: 945  -TLYSRRLTNQLNFNKKGMLIESMAGKSGALNGNILETQPFQNYQDDDIVNY-------- 995

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                              L+    +  G  ++Y G  G      + +G +Y  +L HMVS
Sbjct: 996  --------------FGKQLQSHGYNYYGNEVMYSGTYGCMMKVDIYMGIVYYQRLRHMVS 1041

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK  ARSTG   ++TQQP+ G+   GG R+GEME   + ++G ++ + +     SD
Sbjct: 1042 DKAQARSTGPVDMLTQQPIKGRKRGGGIRMGEMERDALLSHGISFCMHDRFLNCSD 1097



 Score =  104 bits (260), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 106/757 (14%), Positives = 220/757 (29%), Gaps = 148/757 (19%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV-SY------------ 79
              S++ F+          +EGL+   + + P+         E+  SY            
Sbjct: 32  HIDSFN-FI---------YDEGLKKITQYLQPVEIIKEQRSEEYKQSYLPFKSMKVWIEN 81

Query: 80  -EFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
            E   P           K   ++C     TY  PL   +   +      +          
Sbjct: 82  LEIATPIRADSGVAEDNKLMPEECRIGRKTYGAPLFAKVARSIDGGKPESIN-------- 133

Query: 128 QSIYMGDLPL-----------MTK-------------DGTFVIKGIQRIVVSQLH---RS 160
             I +GD+P+           MT               G F++ G ++ +V  L    R+
Sbjct: 134 --IRLGDIPIIVRSDHCHLAKMTPKELVKAHEDCNEFGGYFIVNGNEK-IVRMLILQKRN 190

Query: 161 PGIHFDH----DKGRASLS--------GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
             I F      ++G              + LY+  I       +    D    + +RI  
Sbjct: 191 YPIAFIRAGYVNRGPNYTPFAVQMKCVREDLYSKTIT------LHYVSD--GSVFLRILH 242

Query: 209 RRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLV 265
           R++   +P    L AL     +I        +   +            L+ G+K  S   
Sbjct: 243 RKQEFLIPAIVILKAL----ADISDLQIYNKLVKGQSSKSAISDRVEVLIRGSKAMSLNT 298

Query: 266 DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG---ETGEIYI 322
             +    + ++ + + +     + +K V  + +  +    L    D +N       ++Y 
Sbjct: 299 KEECLAHLGKNFRVVLNITNPEITDKQVGEIFMNENICVHLNNNIDKLNTICVMISKLYA 358

Query: 323 EAGDVIDEKSLEEIFHS-----EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
              D I   +L+ + +          + IL          IR  +  D ++  +   +  
Sbjct: 359 LVSDEICPDNLDSLQNQEVLLPGHLYMMILREKLEEMLLGIRAKVFKDGSRPEEAIRIPH 418

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
              ++       S+   +  FL   + K              +  D  +++R +     +
Sbjct: 419 IAYLKKAIEFQGSIGNKIEYFLSTGNLKSQTGLDLMQAKGFTIIADKLNNMRFLSHFRSV 478

Query: 438 AIIKILVDLRNGKGTIDDIDNLGN----RRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                  +++         +N G              L N        + R   +     
Sbjct: 479 HRGAYFTEMKTTTVRKLLPENWGFICPVHTPDGGPCGLLNHISQSCKPLTRPGYDGNIHF 538

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           ++  V     I   P+V+ +   F  + ++ + +    +  I      +        +  
Sbjct: 539 NL--VTLCTEIGMNPIVNDLSIVFPPTSVTIMLD-GRVIGYIESKNAQTFCQSLKYLKIM 595

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                R +         P    E  NI     L +          E  + +       N 
Sbjct: 596 QDP-TRLIPADLEIGYVPKLNLEKQNIFPGIFLHTN---------EARFVRPVKHLKLNA 645

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + +++  E+ +  IA     +  D                        ++ + SP  ++S
Sbjct: 646 LEWITPFEQVHLSIACIEEDIRND-----------------------TEYQELSPSYILS 682

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           I  S IPFL  + S R +  C M +Q +       P+
Sbjct: 683 ILPSQIPFLNYNQSPRNMYQCQMAKQTMGTSMHNFPY 719


>gi|52699853|gb|AAU86988.1| DNA-dependent RNA polymerase II second largest subunit [Placynthium
            nigrum]
          Length = 716

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 120/836 (14%), Positives = 244/836 (29%), Gaps = 144/836 (17%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L   +R+   ++ + + +  +              + +  + + +  
Sbjct: 1    HFGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLKY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAM 620
             TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L + 
Sbjct: 117  NTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSP 176

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLI 679
                 ++      +  D +     V        I      + D  D   K          
Sbjct: 177  NATKVFVNGVWVGVHRDPAHLVSTVLSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCR 236

Query: 680  P-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            P F+ ++D      G  +  +   L   +   +G  M+    +       AK  G    V
Sbjct: 237  PLFVIDNDPKSANCGSLVLTKEHILKLEDDKELGANMDPEERE-------AKFMGWQGLV 289

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADG 797
               + V+  V+ + + +   V     ++  +  Q     + P +      V+        
Sbjct: 290  --NQGVVEYVDAEEEETVMIVMTPEDLEISKHLQAGFPLEEPSIDDPNRRVKAPLNPTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +   + +  +         
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNY--------- 396

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                              ++    +  +             +       +   +  + AI
Sbjct: 397  ------------------DLRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 438

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + +
Sbjct: 439  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTL 494

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++          ++ 
Sbjct: 495  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 554

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 555  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 594

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 595  HGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 654

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 655  ATPFTEVTVDSVSRLLR--EHGYQSRGFEVM----------------------------- 683

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 684  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 716


>gi|120561253|gb|ABM27011.1| RNA polymerase II second largest subunit [Glomus mosseae]
          Length = 883

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 133/936 (14%), Positives = 270/936 (28%), Gaps = 156/936 (16%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            V++  +++       +    +AL               +            + +      
Sbjct: 80   VSDQDFLQYVCYDPSDHQMLEALKPCIEEAFAVQSMEVAADWIGRRGTTTGATRDKRIKY 139

Query: 412  GRVKMNMRLNLDTPDDVRHIRKEDII--AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +  +   L      +    +++      ++  L+    G+  +DD D+ G +R+   G 
Sbjct: 140  AKDILQKELLPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRRELDDRDHYGKKRMDLAGP 199

Query: 470  MLKNQYRLGLLRMERS--IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L + +R+   ++ +   I  R              I A+ + + +     +        
Sbjct: 200  LLASLFRMLFKKLTKDVSIYLRKCIDSNREFNLNLAIKAQTITNGLKYSLATGNWGDQKK 259

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 260  AMQSRAGVSQVLNRYTFASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHWGMVCPAET 315

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L+  + ++     +             +   ++  ++ +    + N+ +
Sbjct: 316  PEGQACGLVKNLSLMSYISVGSASKPI------IDFLEEYGMINLNQQFDPANIKDNTKV 369

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL--- 691
              +G +             +   R  +   D SP+  V             D+ RV    
Sbjct: 370  FVNGKWAGISSSPEQLSYTLKGLRRTV---DVSPEVSVVRDIRERELRIYTDAGRVCRPL 426

Query: 692  --MGCNMQRQAVPLLKAEAPFVGTGMES-VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              +     R    L++    F    M        S + I        E +DA       +
Sbjct: 427  FIVENERLRITKGLIQKLDVFKMKKMTFGWQDLISNSVI--------EYIDAEEEETVMI 478

Query: 749  EGDLDPSTSGVDIYRLMKFQRSN-QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                +   +    +   + ++       V  R   +   ++         PS  LG    
Sbjct: 479  CMTPEDLAAARVFHETGETKQEKAHERDVAARVKSETNLKIHSWTHCEIHPSMILG---- 534

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   I++  ++                   
Sbjct: 535  ---ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------- 570

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                    +    +  +        +    +       +   +  + AI      +  D+
Sbjct: 571  --------LRMDTLANILYYPQKPLVTTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDS 622

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    IF R  +D+ ++   +  E+ E   ++                 
Sbjct: 623  VIMNQSSIDRGLF-RSIFYRSYMDQEKKVGMLTIEEFEKPTKETTLRLKHGTYEKLEEDG 681

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K T +S D +    R            ++     +  Q      
Sbjct: 682  LIAPGTRVSGDDIIIGKVTPISPDTVELGQRKTSHTKRDASTPMRSTETGIVDQ------ 735

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                                   ++ VKV V   R  Q GDK A RHG KG +      E
Sbjct: 736  --------------VMVTTNAEGMKFVKVRVRSTRVPQMGDKFASRHGQKGTIGITYRQE 781

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+V+NP  +PSRM +G + E  LG      G++  +          IS 
Sbjct: 782  DMPFTAEGITPDLVINPHAIPSRMTIGHMVECLLGKVSTLTGQEGDATPFTDVTVEAISQ 841

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                  +   +                                                 
Sbjct: 842  SLR--SQGYQSRGFEVM------------------------------------------- 856

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +G +    G         V +G  Y  +L HMV
Sbjct: 857  --YNGHT----GR---KLSAQVFLGPTYYQRLKHMV 883



 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 107/767 (13%), Positives = 212/767 (27%), Gaps = 108/767 (14%)

Query: 209 RRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           ++ VPV     ALG +  ++ L          Q  +     +  A  +   +V++  +  
Sbjct: 65  KKDVPVVIAFRALGAVSDQDFLQYVCYDPSDHQMLEALKPCIEEAFAVQSMEVAADWIGR 124

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                     K++     K + +K +    ++++  C    A  +       +    G  
Sbjct: 125 RGTTTGATRDKRI--KYAKDILQKEL-LPHVSTEYGCEKRKAFFLGYMVHRLLLAALGRR 181

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +              P+L          +   +     K           +       
Sbjct: 182 ELDDRDHYGKKRMDLAGPLLASLFRMLFKKLTKDVSIYLRKCIDSNREFNLNLAIKAQTI 241

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 242 TNGLKYSLATGNWGDQKKAMQSRAGVSQVLNRYTFASTLSHLRRCNTPMGRDGKIAKPRQ 301

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE----RISSVDIDSVMPQ 501
           L N    +         +   + + L     + +    + I +               P 
Sbjct: 302 LHNTHWGMVCPAETPEGQACGLVKNLSLMSYISVGSASKPIIDFLEEYGMINLNQQFDPA 361

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           ++ +   V         SS   Q          +   RR   +                +
Sbjct: 362 NIKDNTKVFVNGKWAGISSSPEQ------LSYTLKGLRRTVDVSPEVSVVRDIRERELRI 415

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           +        P    E   + +   L     V     ++       D    + + Y+ A E
Sbjct: 416 YTDAGRVCRPLFIVENERLRITKGLIQKLDV---FKMKKMTFGWQDLISNSVIEYIDAEE 472

Query: 622 EENRYIAQANSSL-----------DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           EE   I      L            +     E  V  R   E   +        +  P  
Sbjct: 473 EETVMICMTPEDLAAARVFHETGETKQEKAHERDVAARVKSET-NLKIHSWTHCEIHPSM 531

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ++ I AS+IPF +++ S R      M +QA+ +                           
Sbjct: 532 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL-------------------- 571

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                   + + +  Y               Q+PLV        
Sbjct: 572 ---------------------RMDTLANILYYP--------------QKPLV-------- 588

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                        +L  G+N +VA + + GYN EDS+++++  +   +F SI    +   
Sbjct: 589 --TTRAMEFLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIFYRSYMDQ 646

Query: 851 ARDTKL-GPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +   +   EE  +        +     + ++E G+I  G  V+  DI++GK+TP     
Sbjct: 647 EKKVGMLTIEEFEKPTKETTLRLKHGTYEKLEEDGLIAPGTRVSGDDIIIGKVTPISPDT 706

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +   ++       + +   RD S  + S  +G V  V +       K
Sbjct: 707 VELGQR-------KTSHTKRDASTPMRSTETGIVDQVMVTTNAEGMK 746


>gi|68131916|gb|AAY85236.1| RNA polymerase II second largest subunit [Vitis piasezkii]
          Length = 951

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 139/927 (14%), Positives = 275/927 (29%), Gaps = 173/927 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                +   A  + +        D   +  I  V+ + 
Sbjct: 523  LFIVEKQRLLI--------------KKRDIRALQLRESPEDGGWHDLVSKGFIEYVDTEE 568

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 569  EETTMISMTINDLISARLNPEEAYS-----------ETYTHCEIHPSLILG-------VC 610

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 611  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 644

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 645  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 701

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 702  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 760

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T +S                  D+   +     +  + TS    E  
Sbjct: 761  TRVSGEDVIIGKTTPISQ-----------------DDSQGQASRYTRRDHSTSLRHSESG 803

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 804  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 858

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 859  VEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 899

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 900  ----------------------------------ATP-FTDVTVDNISKALHKCGYQMRG 924

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +Y+G TG      + +G  Y  +L
Sbjct: 925  FETMYNGHTGRRLTAMIFLGPTYYQRL 951



 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 120/911 (13%), Positives = 261/911 (28%), Gaps = 171/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +           + + +E   +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDLE--EVTETQEFTKVFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  +   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQSTKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L         G+         D      + Y+   EEE   I+     
Sbjct: 529 QRLLIKKRDIRALQLRESPEDGGW--------HDLVSKGFIEYVDTEEEETTMISM---- 576

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +L+  R   E      E     +  P  ++ + AS+IPF +++ S R    
Sbjct: 577 ------TINDLISARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 628

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                           R   +  V               
Sbjct: 629 SAMGKQAMGIYVTNYQL--------------------RMDTLAYV--------------- 653

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 654 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 683

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 684 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGM 743

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           +         RD S
Sbjct: 744 RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------SQGQASRYTRRDHS 794

Query: 929 LRVPSGVSGTV 939
             +    SG V
Sbjct: 795 TSLRHSESGMV 805


>gi|88601066|gb|ABD46529.1| RNA polymerase II second largest subunit [Tulasnella violea]
          Length = 676

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 126/810 (15%), Positives = 239/810 (29%), Gaps = 150/810 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              +    +   +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFKKLTKDVFRHLQKCVETHKDFTLGAAVKNTTITQGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++           + +  +     + +       +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSCISVGTLSAPIIEFLQEWDIEPLEEHANGSGATKVF 177

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
            +      +  D       +      ++I      +  I     ++ + A  +   L   +
Sbjct: 178  VNGVWVGVHRDAQELVMTLRRLRRKDDISAEVSIVRDIRERELRLYTDAGRVCRPLFIVE 237

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            ++ +L+     RQ       E P+  T +          A   +   I    + +   +R
Sbjct: 238  NHELLIRKKHVRQLQEN-SPEQPYGWTNLLHDGVIELLDAEEEETVMICMTPEDLENSLR 296

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            + +  +  +      Y + K               VK              PS  LG   
Sbjct: 297  TKDEFMQDAD-----YDVAK--------------RVKATMNAHTWTHCEIHPSMILG--- 334

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N          M  + +   I +  +++                 
Sbjct: 335  ----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNYQIRVDTMSN---------- 378

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                             +             +       +   +  + AI      +  D
Sbjct: 379  -----------------ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 421

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S V   +    ++ R  +D  ++S +V  E+ E   RD          +     
Sbjct: 422  SVIMNQSSVDRGLF-RSMYYRSYMDVEKKSGAVSVEEFEKPTRDTTLRMKHGTYDKLEDD 480

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G           K+  +  D                +E  QR     K    T  
Sbjct: 481  GLIAPGTGVSGEDIIIGKTAPIPPD---------------SEELGQRTQTHTKRDVSTPL 525

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
               E+   +++     G       L+ VK+ V   R  Q GDK A RHG KG V      
Sbjct: 526  KSTENGIIDQVLLTTNG-----EGLKFVKIRVRSTRIPQVGDKFASRHGQKGTVGITYRQ 580

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF  +G   DIV+NP  +PSRM +G + E  L      LG +               
Sbjct: 581  EDMPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKLATLLGNEGD------------- 627

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                    +TP F     E+++ +L+  
Sbjct: 628  ----------------------------------------ATP-FTDLTVESVSHLLKAR 646

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                 G  ++Y G TG+     V +G  Y 
Sbjct: 647  GYQSRGLEVMYHGHTGKKLQAQVYLGPTYY 676


>gi|113957144|gb|ABI49101.1| RNA polymerase II second largest subunit [Pseudocyphellaria anomala]
          Length = 715

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 120/835 (14%), Positives = 239/835 (28%), Gaps = 146/835 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R+   ++ + + + +               + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQTLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                D+  +     N+   ++ V  L+ +         E    +        K  G    
Sbjct: 237  LFVIDNDPKSPNRGNLVLTKEHVNKLEDDKELGPELDAEGREKED-------KFRGWKGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIAD 796
            V   + V+  V+ + + +   V     ++  R  Q   V   P +      V+       
Sbjct: 290  V--NQGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYVMPEPSIDDPNKRVKAPLNPTA 347

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +   + +  ++       
Sbjct: 348  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---- 401

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 402  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 438

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 439  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDT 494

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 495  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLR 554

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 555  STENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFAS 594

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 595  RHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 654

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 655  DATPFTEVTVDSVSRLLR--EHGYQSRGFEVM---------------------------- 684

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                              +G +    G         V +G  Y  +L HMV DK+
Sbjct: 685  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 715


>gi|45545345|gb|AAS67520.1| DNA-dependent RNA polymerase II second largest subunit [Pneumocystis
            carinii]
          Length = 898

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 139/939 (14%), Positives = 265/939 (28%), Gaps = 151/939 (16%)

Query: 348  YVDSVNNNAYIRNTLVT--DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
              D + +  Y  N            ++A +   R +    +     A  +         +
Sbjct: 89   DRDIMEHICYDPNDHQMLEMLKPCIEEAFVIQEREVALDFIGKRGSAVGI---NREKRLR 145

Query: 406  YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            Y    + +  +       T +     +   +  +I  L+     +   DD D+ G +R+ 
Sbjct: 146  YAQDILQKELLPHIT---TTEGYETRKAFFLGYMIHRLLLCALERRDPDDRDHFGKKRLD 202

Query: 466  SVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G +L N +R+   ++ + +    +              + +  +   +     +    
Sbjct: 203  LAGPLLANLFRMLFKKLTKDVYKYMQKCVETNREFNLTLAVKSNTITHGLRYSLATGNWG 262

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 263  DQKKIMSARVGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKVAKPRQLHNTHWGLVC 318

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL-SAMEEENRYIAQ 629
            PAET EG   GLV +L+  + V+           + +  + N   Y  SA     +    
Sbjct: 319  PAETPEGQACGLVKNLSLMSYVSVGSASAPIIEFLEEWGMENLEDYNPSATPNTTKVFVN 378

Query: 630  A-NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDS 687
                 +  D     E +       +I V    + D  +   +          P    D++
Sbjct: 379  GVWLGVHRDPYHLVETIKSLRRKLDISVEVSVVRDIREKELRIFTDAGRVCRPLFIVDNN 438

Query: 688  NRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                    +   ++ V  +           ES    SS  A      GIVE +DA     
Sbjct: 439  PESNSRGQLMLKKEHVQKIIDNKNRTELDNESKFGWSSLVA-----NGIVEYIDAEEEET 493

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +   I    K            +PLV     +         PS  LG  
Sbjct: 494  VMIAMTPEDLEATRQIQAGYKIADEID-PARRVKPLVSPNTYL--WTHCEIHPSMILG-- 548

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   + +  ++V                
Sbjct: 549  -----ICASIIPFPDHNQSPRNTYQSAMGKQAIG--VFLTNYQVRM-------------- 587

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 588  -------------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQE 634

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    IF R  +D+ ++      E+ E   R+   +      +    
Sbjct: 635  DSVIMNQSSIDRGLF-RSIFYRSYMDQEKKIGMQIMEEFEKPMRNNCLKLKHGTYDKIED 693

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  +      R+++         ++     +  Q    
Sbjct: 694  DGLIAPGTRVSGDDIIIGKTAPIPPNAEELGQRTKFHTKRDVSTPLRSTESGIIDQ---- 749

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV +   R  Q GDK A RHG KG +     
Sbjct: 750  ----------------VMVSTNAEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGITYR 793

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM V  + E  L       G +  +          I
Sbjct: 794  HEDMPFTSEGIVPDIIINPHAIPSRMTVAHLIECLLSKVSALSGYEGDATPFTDVTVEAI 853

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S +    +    +                                               
Sbjct: 854  SKMLR--QHGYQSRGFEVM----------------------------------------- 870

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                 +G +    G         V +G  Y  +L HMV 
Sbjct: 871  ----YNGHT----GR---KLVAQVFLGPTYYQRLKHMVD 898



 Score =  157 bits (398), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 116/850 (13%), Positives = 244/850 (28%), Gaps = 136/850 (16%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          +      + Y   I    ++   +   F  K ++   I
Sbjct: 1   SEKVIIAQE-RS--AANTVQVFKKPAPSAVSYVAEIRSAIEKSSKLMSNFQIK-LMSKSI 56

Query: 207 DR-------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAA 252
           ++             R  +P+     ALG+  + +I+          Q  +     +  A
Sbjct: 57  EKGAGQTIRACLPYIRNDIPIVIVFRALGVVPDRDIMEHICYDPNDHQMLEMLKPCIEEA 116

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
            ++   +V+   +        I   K+L       L+++ +  +  T             
Sbjct: 117 FVIQEREVALDFIGKRGSAVGINREKRLRYAQ-DILQKELLPHITTTEGYETRKAFFLGY 175

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRK 371
           +      + + A +  D    +      +    P+L          +   +     K  +
Sbjct: 176 MIH---RLLLCALERRDPDDRDHFGKKRLDLAGPLLANLFRMLFKKLTKDVYKYMQKCVE 232

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--R 429
                   +    +  T  +  S+    + D  K   + VG  ++  R    +      R
Sbjct: 233 TNREFNLTLAVKSNTITHGLRYSLATGNWGDQKKIMSARVGVSQVLNRYTFASTLSHLRR 292

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                     +     L N    +         +      ++KN   +  + +  +    
Sbjct: 293 TNTPIGRDGKVAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSYVSVGSASAPI 349

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           I  ++   +   +  N     +    F     L    +  + +  I   RR        +
Sbjct: 350 IEFLEEWGMENLEDYNPSATPNTTKVFVNGVWLGVHRDPYHLVETIKSLRR-------KL 402

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             +     +RD+          A         + ++  S +R       E   + + +  
Sbjct: 403 DISVEVSVVRDIREKELRIFTDAGRVCRPLFIVDNNPESNSRGQLMLKKEHVQKIIDNKN 462

Query: 610 VTN----------------DVVYLSAMEEENRYIAQ------ANSSLDEDGSFTEELVFC 647
            T                  V Y+ A EEE   IA       A   +       +E+   
Sbjct: 463 RTELDNESKFGWSSLVANGIVEYIDAEEEETVMIAMTPEDLEATRQIQAGYKIADEIDPA 522

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           R     +          +  P  ++ I AS+IPF +++ S R      M +QA+ +    
Sbjct: 523 RRVKPLVSPNTYLWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAIGVFLTN 582

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                                                          + + +  Y     
Sbjct: 583 YQV-----------------------------------------RMDTMANILYYPQKPL 601

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             +     +  R                        +L  G+N +VA + + GYN EDS+
Sbjct: 602 ATTRSMEYLRFR------------------------ELPAGQNAIVAILCYSGYNQEDSV 637

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGII 882
           ++++  +   +F SI    +    +   +   E     +  +   +       I++ G+I
Sbjct: 638 IMNQSSIDRGLFRSIFYRSYMDQEKKIGMQIMEEFEKPMRNNCLKLKHGTYDKIEDDGLI 697

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             G  V+  DI++GK  P    P   EE   R     K    RD S  + S  SG +  V
Sbjct: 698 APGTRVSGDDIIIGKTAPI---PPNAEELGQRT----KFHTKRDVSTPLRSTESGIIDQV 750

Query: 943 RIFNRHGIDK 952
            +       K
Sbjct: 751 MVSTNAEGLK 760


>gi|313246967|emb|CBY35812.1| unnamed protein product [Oikopleura dioica]
          Length = 1185

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 88/337 (26%), Positives = 133/337 (39%), Gaps = 58/337 (17%)

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLIS-EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
            +  G      P   K    ++ D +  +        F  QD       E  +        
Sbjct: 807  LRLGCRDRFDPNELKAYRKIAGDKLDIDGLPFPGGIFTYQDAYYCYYNEHEQKYSVGKYD 866

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
               +    +  ++        G  +   +   + RPI  GDKMA RHG KGI SR+    
Sbjct: 867  SHAEDAIVESVRVFTNKRPQEGGFQQAAIQFRIARPINIGDKMASRHGQKGICSRLWATT 926

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMP+ ++G   D++ NP G PSRM VG + E   G A +  G+                 
Sbjct: 927  DMPWTENGIVPDLIFNPHGFPSRMTVGMMIEFIAGKAAMVNGR----------------- 969

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFD--GADEEAINSMLR 1224
                                                V  STP VFD     +E    +L+
Sbjct: 970  ------------------------------------VYDSTPFVFDENYTADEHFGKVLK 993

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS-TGSYSLVTQQPL 1283
             A L+  G   +Y G++GE  +  +  G +Y  +L HMV DK  AR+  G     TQQP+
Sbjct: 994  EAGLNYHGYERMYSGISGEELEADIFFGPVYYQRLRHMVYDKFQARADKGPIDPYTQQPV 1053

Query: 1284 GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             G++  GG R+GEME   + ++GAA++ ++ L   SD
Sbjct: 1054 KGRARGGGVRMGEMERDGLISHGAAFICRDRLFHCSD 1090



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 74/598 (12%), Positives = 158/598 (26%), Gaps = 69/598 (11%)

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD----KYDL 408
           +   Y           +   A+  + + +        + A+ +             K D+
Sbjct: 271 DLEIYREFMQTMSDEPNYDSAVKRMLKKLVKIQHHFLTQAKFLGQSFRIFDICPAWKSDV 330

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
                      L     D+ +      +      +         ID  ++        + 
Sbjct: 331 EAGQAFLKRYCLIYLNNDEDKVRAFALMARKAFRISHNTCATDDIDSPESHDVLLPGHLF 390

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA--------KPVVSAVCEFFCSS 520
           + +  ++     R    I  +  S  ++    +   N           +         + 
Sbjct: 391 QSMTLEFFESYQRSVSMIMAKEYSKQLEKGNDEVGQNMLSFAINKIGNMNQHFKYLIATG 450

Query: 521 QLSQLE--------------EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
            L   +              E +N     +H R    + +G           R +    +
Sbjct: 451 NLKTNDGLGMQQLAGIVVGAEKINFARFYSHFR---CIHRGAFFMEMRATSPRKLSTAAW 507

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--AMEEEN 624
           G ICP  T +G   GL++ L    R+N          K+ +  +   V   S  A E + 
Sbjct: 508 GFICPVHTPDGPPCGLLNHLAHTVRINVK---RENTAKLEELLLEIGVKPCSIKANEFDV 564

Query: 625 RYIAQA-NSSLDEDGSFTEELVFCRCAGEEILVPR-----EKIDFIDASPKQVVSIAASL 678
             I          +G   + +       +     R     E +       K    +   +
Sbjct: 565 PVIIDGKQIGWIANGWRAQAVEKYLRRLKTSSSDRVPDTLEIVHCPAPENKGEAVMFPGI 624

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-----GMESVVAKSS-GAAIVAKRA 732
               E     R L+     +  +  +  +     T       E    +    AA++++ A
Sbjct: 625 NLLTEPARMYRPLLNLREDKIEMIGIMEQVWLHVTVNQKESHELTEYQELYPAALLSELA 684

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            +    +        ++  +   T G   Y    +           Q PLV+        
Sbjct: 685 CMSPFSNMNAGARVILQCQMAKQTFGWPSYTLNHRSDNKMYRILTPQEPLVRSH------ 738

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  S  + D  LG N+++A + + GY+ ED+  +S+      +      +   V  
Sbjct: 739 ----LHDSWGMDDYPLGTNVMIAVISYTGYDLEDATCVSKMSRERGMMYGTIYKTKMVDL 794

Query: 852 RDT------------KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +DT                     ++    +     +D  G+   G      D     
Sbjct: 795 QDTAQSMGYRSGLRLGCRDRFDPNELKAYRKIAGDKLDIDGLPFPGGIFTYQDAYYCY 852



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 50/187 (26%), Gaps = 61/187 (32%)

Query: 10  LGRVRKFFGKNPE--IIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT- 66
               R  +GK PE     +  + +    S+D FL           EGL     SV P   
Sbjct: 19  KQTSRVNYGKLPEDKNKQLKFISDTHVQSFDWFL----------EEGLPNIPNSVAPYEF 68

Query: 67  -----AFSGAAMLEFVSYEFDPPKFD-----------VDDCLWRDLTYAVPLKITLRLIV 110
                       LE    E   P  +             +C  +   Y  P+ +T  LI 
Sbjct: 69  EMEANNDQMRFRLEVEHIEVGQPTLESSIVCKDRRLFPSECRQKKTDYTAPVHVTFNLIN 128

Query: 111 FDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVI 146
               E         ++        +PLM                           G F+ 
Sbjct: 129 LSSGESQVVTKKDLLQ--------MPLMVMSSKCHLRGLSPEELVARKEDHFEIGGYFIA 180

Query: 147 KGIQRIV 153
            G ++++
Sbjct: 181 SGNEKVI 187


>gi|310697221|gb|ADP06540.1| RpoB [Bartonella sp. R-191]
          Length = 280

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 204/280 (72%), Positives = 235/280 (83%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR  +D 
Sbjct: 121 KIVDGKVTTEVVYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMTPRSHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++ EAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRTEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAAIVAKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAIVAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|86161670|gb|ABC86970.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 285

 Score =  262 bits (670), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 206/286 (72%), Positives = 239/286 (83%), Gaps = 2/286 (0%)

Query: 483 ERSIK-ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           ER+IK  R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRL
Sbjct: 1   ERAIKARRMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRL 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +
Sbjct: 121 YRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+
Sbjct: 181 DLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVAR 240

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
            SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL KF
Sbjct: 241 DSGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQKF 285


>gi|110169467|gb|ABG53986.1| RNA polymerase II second largest subunit [Exobasidium gracile]
          Length = 705

 Score =  262 bits (669), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 126/843 (14%), Positives = 237/843 (28%), Gaps = 163/843 (19%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ R I    +    +      Q  + +  + + +    
Sbjct: 1    GKKRLDLAGPLLSGLFRMLFKKLTRDIYRHLQRCVEESKEFTLQAAVKSSTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKFMSAKAGVSQVLNRYTYASTLSHLRRCNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L+  + ++           + +  + + V    A  +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSLMSMISVGSPSGPIIEFLEEYGLDSLVDMQIADAKAT 176

Query: 625  RYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            +         + D      E L   R   +  +      D  +   +          P  
Sbjct: 177  KVFVNGVWMGTCDTPTGLVETLRDLRRKDDISIEVSVVHDIREKELRLYTDAGRVQRPLF 236

Query: 683  ENDDSNRVLM-------GCNMQRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGI 734
              +  ++ L            Q +        +  V  G +E + A+     ++      
Sbjct: 237  IVNPEDKTLYVKPKHVNWIETQERPDGSPYGWSQLVRDGLIELLDAEEEETVMICMSPQD 296

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +E            E       SG    RL+  Q    +T                    
Sbjct: 297  LESS------RMYNENPDSIKLSGDPTARLVPVQTYAPST----------------WTHC 334

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               P+  LG        ++ F P            S R V +       +  +    +  
Sbjct: 335  EIHPAMILG----VCASIIPFPPXQ----------SPRNVYQSAMGKQAMGVYLTNYQMR 380

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                                      +  +             +       +   +  + 
Sbjct: 381  M-----------------------DTMANILYYPQKPLATTHSMHYLKFRELPAGQNAIV 417

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    ++ R  +D  +++  +  E+ E  +R+    
Sbjct: 418  AILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTHMDMEKKTGMILLEEFEKPSRETAVR 476

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T L  D      RS+          ++  
Sbjct: 477  LKHGTYDKIDADGFCAPGTRVSGEDIIIGKTTPLPPDSEELGLRSKLHTKKDVSTPLKST 536

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q   S                          + VKV +   R  Q+GDK A RH
Sbjct: 537  ENGIVDQVLVS--------------------TNAEGNKFVKVRIRSTRIPQTGDKFASRH 576

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  +
Sbjct: 577  GQKGTIGITYRQEDMPFTIEGVTPDIIINPHAIPSRMTIGHLVECLLSKVGALSGQEGDA 636

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S                           L V     +G  +   V+ G 
Sbjct: 637  TPFTDLTVEAVSHQLR---------------QHGYQSRGLEVMYNGHTGKKLQAQVYLGP 681

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                                                    Y  +L HMV DK+++R+ G 
Sbjct: 682  T---------------------------------------YYQRLKHMVDDKIHSRARGP 702

Query: 1275 YSL 1277
              +
Sbjct: 703  VQI 705



 Score = 68.9 bits (167), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 88/602 (14%), Positives = 165/602 (27%), Gaps = 98/602 (16%)

Query: 376 DIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           DIYR + R  + S     ++        +        G      +         + + + 
Sbjct: 26  DIYRHLQRCVEESKEFTLQAAVKSSTITNGLKYSLATGNWGDQKKFMSAKAGVSQVLNRY 85

Query: 435 DIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
              + +  L        R+GK       +  +  +    E  + Q    +  +       
Sbjct: 86  TYASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSMIS 145

Query: 490 ISSVD------IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           + S        ++      L++ +   +   + F +       +    L       R   
Sbjct: 146 VGSPSGPIIEFLEEYGLDSLVDMQIADAKATKVFVNGVWMGTCDTPTGLVETLRDLRRKD 205

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                V+      E      T  GR+                 T + +     +IET  R
Sbjct: 206 DISIEVSVVHDIREKELRLYTDAGRVQRPLFIVNPE-----DKTLYVKPKHVNWIETQER 260

Query: 604 K------VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-------CA 650
                           +  L A EEE   I  +   L+    + E     +         
Sbjct: 261 PDGSPYGWSQLVRDGLIELLDAEEEETVMICMSPQDLESSRMYNENPDSIKLSGDPTARL 320

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                         +  P  ++ + AS+IPF     S R +    M +QA+ +       
Sbjct: 321 VPVQTYAPSTWTHCEIHPAMILGVCASIIPFP-PXQSPRNVYQSAMGKQAMGVYLT---- 375

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                   +   + A I+      +    ++                       +KF+  
Sbjct: 376 -----NYQMRMDTMANILYYPQKPLATTHSMH---------------------YLKFREL 409

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                     L   G   + + +I +  S D G         + +        +  M++ 
Sbjct: 410 PAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRS-----LYYRTHMDMEKKTGMILL 463

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           E              EFE  +R+T +           +       ID  G    G  V+ 
Sbjct: 464 E--------------EFEKPSRETAV----------RLKHGTYDKIDADGFCAPGTRVSG 499

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK TP    P   EE  LR+    K    +D S  + S  +G V  V +      
Sbjct: 500 EDIIIGKTTP---LPPDSEELGLRS----KLHTKKDVSTPLKSTENGIVDQVLVSTNAEG 552

Query: 951 DK 952
           +K
Sbjct: 553 NK 554


>gi|46411504|gb|AAS94322.1| RNA polymerase II [Astrothelium cinnamomeum]
          Length = 722

 Score =  262 bits (669), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 125/842 (14%), Positives = 240/842 (28%), Gaps = 148/842 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS--VDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    R+ + + + +     +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLASLFRTLFQRLTKDVYQHLQKAIENNREFSITLAVKSAHITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLSTGNWGEQRKAMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V+     E     +   + ++  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVSVGTPSEPIVEFMNRNNMEILEEYDP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            ++       ++      +  D S   + +        I      + D  +   K      
Sbjct: 177  VAFPNATKIFVNGVWVGVSRDPSRLVKTIQDVRRRGMISFEVSLVRDVREREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVP---LLKAEAPFVGTGMESVVAKSSGA--AIVAK 730
              + P    D   R     N+  Q  P    L+ +             + S         
Sbjct: 237  RVMRPLFVIDTDPRSENRGNLIYQKDPHVYRLQEDERIKKDPTLDDEQRESMRYGWQGLV 296

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            R G++E +DA       +    +  ++   +         +       R   K    V+ 
Sbjct: 297  RDGVIEYLDAEEEETAMIMMFPEDISTHQAMKAGRIIVEDDGQKDPLARVQAKPNPNVKN 356

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   P+  LG       +  + +P+  +N                        ++  
Sbjct: 357  YTHCEIHPAMILG-------ICASIIPFPDHNQSPRN------------------TYQSA 391

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                 +G                       ++ V             +       +   +
Sbjct: 392  MGKQAMGVMLTNFASRM-----------DTMVNVLYYPQKPLATTHSMKYLNFQELPAGQ 440

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   + 
Sbjct: 441  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGSTVLEEFEKP 496

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + + L R  Y +L     I  G           K+  ++ D+     R++       
Sbjct: 497  MRSDTLRLKRGTYDKLDNDGIISPGVRVSGEDIIIGKTAPIAPDVEELGQRTKLHTKRDV 556

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +  Q                             L+ VKV     +  Q G
Sbjct: 557  STPLRSTENGIVDQVVL--------------------TTNTEGLKFVKVRTRTTKVPQIG 596

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  L      
Sbjct: 597  DKFASRHGQKGTIGITYRQEDMPFTSQGITPDLIINPHAIPSRMTIAHLVECLLSKLGSL 656

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +         DIS                                         
Sbjct: 657  TGNEGDATPFSPITVSDISNFLR------------------------------------- 679

Query: 1208 TPVFDGADEEAINSMLRMADLD--ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                         +  +    +   +G +    G         V  G  Y  +L HMV D
Sbjct: 680  ------------ENGFQSRGFEVMYNGHT----GR---KLRAQVFFGPTYYQRLRHMVDD 720

Query: 1266 KV 1267
            K+
Sbjct: 721  KI 722


>gi|86559341|gb|ABD04078.1| RNA polymerase II second largest subunit [Aureoboletus thibetanus]
          Length = 692

 Score =  262 bits (669), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 123/829 (14%), Positives = 239/829 (28%), Gaps = 161/829 (19%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
              VG +L N +R+   ++ + +    +              +  + + + +     +   
Sbjct: 1    DLVGPLLANLFRMAFKKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLATGNW 60

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 61   GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 116

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   + ++   +       + +  + +         EEN + + 
Sbjct: 117  CPAETPEGQACGLVRNLALMSGISVGSYSAPVIEFLEEWGLESL--------EENAHSST 168

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 169  PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGR 225

Query: 690  VLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            V     +       L+ +   ++  G               +     + V +    I  +
Sbjct: 226  VCRPLFIVENQQLALQKKHIKWLNQGYRDDDG---------EEFKWEQLVKSGI--IELL 274

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV--------KVGDEVRRNDIIADGPST 800
            + + + +         ++  RS       Q   V        K G            PS 
Sbjct: 275  DAEEEETVMISMTPEDLENSRSQSAGINTQESEVDHDPAARLKAGITAHTWTHCEIHPSM 334

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 335  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 369

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 370  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 418

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 419  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTY 477

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G N         K+  +  D      R++          ++     +  
Sbjct: 478  DKLEDDGLIAPGTNVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 537

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 538  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 577

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +      
Sbjct: 578  GITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 635

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 636  -----------------------DLTVESVSTFLRQKGYQSRGLEVM------------- 659

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                       G +       G+     + +G  Y  +L HMV DK+++
Sbjct: 660  ---------YHGHT-------GKKLQAQIYLGPTYYQRLKHMVDDKIHS 692



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 80/618 (12%), Positives = 169/618 (27%), Gaps = 111/618 (17%)

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
               + N       K  KD    + + +       F+++ ++ +    +  KY L   G 
Sbjct: 3   VGPLLANLFRMAFKKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGN 59

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVG 468
                +         + + +    + +  L        R GK       +  +  +    
Sbjct: 60  WGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPA 119

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQ 521
           E  + Q    +  +       + S     +             NA         F     
Sbjct: 120 ETPEGQACGLVRNLALMSGISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVW 179

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  N +  I   RR   +                ++        P    E   + 
Sbjct: 180 MGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLA 239

Query: 582 LVSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           L              ++   YR       K      +  +  L A EEE   I+     L
Sbjct: 240 LQKK--------HIKWLNQGYRDDDGEEFKWEQLVKSGIIELLDAEEEETVMISMTPEDL 291

Query: 635 DEDGSFTEELVFCRCAGE-------EILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +   S +  +       +       +  +        +  P  ++ + AS+IPF +++ S
Sbjct: 292 ENSRSQSAGINTQESEVDHDPAARLKAGITAHTWTHCEIHPSMILGVCASIIPFPDHNQS 351

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +                                            
Sbjct: 352 PRNTYQSAMGKQAMGIYLTNFLV------------------------------------- 374

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  + + +  Y       +     +  R                        +L  
Sbjct: 375 ----RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPA 406

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD--- 864
           G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E       
Sbjct: 407 GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTR 466

Query: 865 --IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                +       +++ G+I  G  V   DI++GK  P         E+L +        
Sbjct: 467 DTTLRMKHGTYDKLEDDGLIAPGTNVRGEDIIIGKTAPI----PPDSEELGQRTRTHTRR 522

Query: 923 DVRDTSLRVPSGVSGTVV 940
           DV        +G+   V+
Sbjct: 523 DVSTPLKSTENGIVDQVL 540


>gi|73975055|ref|XP_860639.1| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide
            B isoform 4 [Canis familiaris]
          Length = 221

 Score =  262 bits (669), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 106/275 (38%), Gaps = 73/275 (26%)

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  +PSRM +G + E   G      G+                  
Sbjct: 1    MPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--------------- 45

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP  D  + + I+++L     
Sbjct: 46   --------------------------------------ATPFNDAVNVQKISNLLSDYGY 67

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSN 1288
               G  +LY+G TG      + +G  Y  +L HMV DK+++R+ G   ++ +QP+ G+S 
Sbjct: 68   HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 127

Query: 1289 RGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG----------RTRVYESIVA 1334
             GG R GEME  C  A+GAA  L+E L   SD     V            RT  YE    
Sbjct: 128  DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC--R 185

Query: 1335 G----NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            G            P +  +L +E+ ++ ++  + +
Sbjct: 186  GCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 220


>gi|124491187|gb|ABN12928.1| RNA polymerase beta chain [Rhizobium leguminosarum bv. viciae]
          Length = 237

 Score =  262 bits (669), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 139/238 (58%), Positives = 175/238 (73%), Gaps = 1/238 (0%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
           HDKG++  SGKLL+A R+IP +G W+DIEFD+KDI++ RIDRRRK+PVTS LMALGMD E
Sbjct: 1   HDKGKSHSSGKLLFAARVIPYRGSWLDIEFDAKDIVYARIDRRRKIPVTSLLMALGMDGE 60

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EIL TFY K +Y + G+ W  P     L  GAK  + +VD DTGE V+E+GKKLT  LL+
Sbjct: 61  EILDTFYTKSLYKRDGEGWRIPFKPETL-KGAKAITEMVDADTGEVVVEAGKKLTPRLLR 119

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
           +L +KG+K L    D L G Y+A DIVN  TGEIY+EAGD IDEK+L  I  +   +IP+
Sbjct: 120 TLSDKGLKALKAADDDLYGNYLAGDIVNYSTGEIYLEAGDEIDEKTLGIILANGFDEIPV 179

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           L +D +N  AYIRNTL  DKN++R+DAL DIYRVMRPG+  T   AE+MFN LFFD++
Sbjct: 180 LGIDHINVGAYIRNTLTADKNENRQDALFDIYRVMRPGEPPTMESAEAMFNSLFFDAE 237


>gi|269930851|gb|ACZ54160.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 280

 Score =  261 bits (668), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 201/280 (71%), Positives = 235/280 (83%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAA+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|45545323|gb|AAS67509.1| DNA-dependent RNA polymerase II second largest subunit [Cryptococcus
            neoformans]
          Length = 1114

 Score =  261 bits (668), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 133/860 (15%), Positives = 251/860 (29%), Gaps = 146/860 (16%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++ T +     +   +  ++  L     G+  +DD D+ GN+R+   G ++   + +   
Sbjct: 382  HVSTAEGFESKKAYFLGYMVHRLCMAALGRRELDDRDHFGNKRLDLAGPLMAEMFNVVFG 441

Query: 481  RMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ----------LSQLEEH 528
            ++   +   +               I    +   +     +            +SQ+   
Sbjct: 442  KLREDMYRYLKKCVEQNKEFALNMAIRPNTITDGLKYALATGNWGKRDNTRAGVSQVLNS 501

Query: 529  VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
                S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L  
Sbjct: 502  YTFTSTLSHLRRTNT----PIGRDSKAAKPRQLHDTHWGMVCPAETPEGSACGLVKNLAL 557

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             + ++   +       + +  + +   Y  A      ++      +  D       +   
Sbjct: 558  MSYISVGSYSAPVMEFLEEWGLEDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQM 617

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              G ++      + D  +   +          P    D   + L         +  +  E
Sbjct: 618  RRGGQLKYEVSIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQMADE 677

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRL 764
                           SGA       GIVE VDA       I     DL  + +    + L
Sbjct: 678  GLL------------SGAWDKLLSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHEL 725

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            ++ + ++     +    +K     ++   +   PS  LG       +  + +P+  +N  
Sbjct: 726  VRDRAAHNLESFDPAARIKSTVWSQQYTHMEIHPSMILG-------VCASIIPFPDHNQS 778

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +   +                                 +    ++ V
Sbjct: 779  PRNTYQSAMGKQAMGVCL-----------------------------TNYQLRMDTMVNV 809

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +     S +   +  + AI      +  D+ +   S +   +    +
Sbjct: 810  LYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSL 868

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPKG 1001
            + R   D  +    V+ E IE   R++         + Y++L     +  G N       
Sbjct: 869  YFRSYTDTEKMKGMVKAETIEKPDRNETLRMKHGTGDRYAKLDVDGLVAPGTNVNGDDIL 928

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  L  D      R+Q                  K    T     E    +++    
Sbjct: 929  IGKTAPLPEDSEELGQRTQLHT---------------KRDISTPLKSTEQGVVDQVMLST 973

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             G          VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 974  NG-----EGNMFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDII 1028

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L       G +  +          +S +     K   +   
Sbjct: 1029 INPHAIPSRMTIGHLVECLLSKVSTLTGAEGDATPFTELTVEAVSKVLR--AKGYQSRGF 1086

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                    +L        G +    G  
Sbjct: 1087 ---------------------------------------ELL------YHGHT----GR- 1096

Query: 1242 GEPFDRPVTVGYIYMLKLNH 1261
                   V  G  Y  +L H
Sbjct: 1097 --KLQAQVYFGPTYYQRLKH 1114



 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 128/1034 (12%), Positives = 283/1034 (27%), Gaps = 199/1034 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT------------AFSGAAMLEF 76
           L+  Q  S++ F+   +          Q        +T              +    + F
Sbjct: 58  LVRQQLESFNEFIETTM----------QEIVDDHSRLTLDQFTQYTGVAGDETRRYEISF 107

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLI------VFDVDEFTGAK 120
                                  +   R+LTY+ PL + ++        V D  E     
Sbjct: 108 GQIYLARVNHTEMDGRTNMLFPQEARLRNLTYSAPLYVDIKKRTLTASGVDDPVEADWQP 167

Query: 121 SIKD------IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
           ++ D       +E+   +G +P+M +                         G F+I G +
Sbjct: 168 AVGDDGEVEGAEEEKTSIGKVPVMVRSNFCLLHGLPDDQCHEIGECPYDQGGYFIISGSE 227

Query: 151 RIVVSQLHRSPG-------------IHFDHDKGRASLSGKLLYACRIIPD-Q-----GLW 191
           +++++Q   +                +F     +    G++     +    +     G  
Sbjct: 228 KVLIAQERMATNHVFVFLKAAPARFTYFAEINSQKEKGGRVANHTEVRMYARASGTTGGV 287

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           + +      + + ++D    +P+     ALG+  + ++LS            +     + 
Sbjct: 288 IRVS-----LPYTKVD----IPLVVVFRALGIVPDRDVLSHICFGAEDEALLEMLQPSIE 338

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF------LGITSDCLC 304
            +  +     +   +      +     ++  +     L ++ +                 
Sbjct: 339 ESFAVQDRDTALDFIGRRGQHEKAPRAQRQRAA-FDILHKEFLPHVSTAEGFESKKAYFL 397

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLV 363
           G  V    +    G   ++  D    K L+           +++     +   Y++  + 
Sbjct: 398 GYMVHRLCM-AALGRRELDDRDHFGNKRLDLAGPLMAEMFNVVFGKLREDMYRYLKKCVE 456

Query: 364 TDKNKDRKDALLDIYRVMRPGDVST-FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            +K      A       +RP  ++     A +  N+   D+ +  +S V           
Sbjct: 457 QNKEFALNMA-------IRPNTITDGLKYALATGNWGKRDNTRAGVSQVLNSYTFTSTLS 509

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                   I ++   A  + L D   G     +          S   ++KN   +  + +
Sbjct: 510 HLRRTNTPIGRDSKAAKPRQLHDTHWGMVCPAETP------EGSACGLVKNLALMSYISV 563

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                  +  ++   +  +DL   +   +A   F     +    +     + +   RR  
Sbjct: 564 GSYSAPVMEFLEEWGL--EDLSEYQDAPTATKVFVNGVWMGIHRDAPTLHNNLLQMRRGG 621

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            L                ++        P    +     L        R++         
Sbjct: 622 QLKYEVSIVRDIRERELRLYTDAGRVCRPLFIVDQPTQTLRLKRDHIDRIDQMADEGLLS 681

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG--SFTEELVFCRCAGEEILVPR-- 658
                      V Y+ A EEE   IA     L          ELV  R A          
Sbjct: 682 GAWDKLLSEGIVEYVDAAEEETILIAMTPEDLVNARTAHSKHELVRDRAAHNLESFDPAA 741

Query: 659 --------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   ++   ++  P  ++ + AS+IPF +++ S R      M +QA+ +       
Sbjct: 742 RIKSTVWSQQYTHMEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVCLTNYQL 801

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                       +   ++      +    ++  +  S       +   +  Y        
Sbjct: 802 ---------RMDTMVNVLYYPQKPLATTRSMEYLKFSELPAGQNAIVAIMCYSG------ 846

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                 NQ            + +I +  S D G         + F  +        M+ +
Sbjct: 847 -----YNQ-----------EDSVIMNQSSIDRGLFRS-----LYFRSYTDTEKMKGMVKA 885

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           E +   D   ++            K G             +    +D  G++  G  VN 
Sbjct: 886 ETIEKPDRNETL----------RMKHGT-----------GDRYAKLDVDGLVAPGTNVNG 924

Query: 891 GDILVGKITPKGESPMTPEEKL-------LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            DIL+GK  P  E      ++        +          V D  +   +G     V +R
Sbjct: 925 DDILIGKTAPLPEDSEELGQRTQLHTKRDISTPLKSTEQGVVDQVMLSTNGEGNMFVKIR 984

Query: 944 I-FNRHGIDKNERS 956
           +   R     ++ +
Sbjct: 985 VRSTRVPQIGDKFA 998


>gi|224812773|gb|ACN65020.1| RpoB [Cronobacter dublinensis subsp. lausanensis]
          Length = 270

 Score =  261 bits (668), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 164/270 (60%), Positives = 206/270 (76%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D 
Sbjct: 121 DGIVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            VAKR G V+ VDA RIVI+  E ++ P  
Sbjct: 241 AVAKRGGTVQYVDASRIVIKVNEDEMYPGE 270


>gi|310697223|gb|ADP06541.1| RpoB [Bartonella sp. E1-105]
          Length = 280

 Score =  261 bits (668), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 205/280 (73%), Positives = 234/280 (83%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +VVYLSAMEE   Y+AQANSSLD DG F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTTEVVYLSAMEESKHYVAQANSSLDADGRFIEEFVVCRHAGEVLMAPRDYVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAAI AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAIGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|123979420|gb|ABM81535.1| RNA polymerase II second largest subunit [Dirinaria applanata]
          Length = 705

 Score =  261 bits (668), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 120/829 (14%), Positives = 234/829 (28%), Gaps = 155/829 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    ++ + +    +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRTLFNKLNKDVEKYLKNCIENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKASSSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     V+     E    +      +   +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYVSVGTPSEGIVDFLLSRQMEPLEEYDPLASPHATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      + +  +     V        I      I D  D   K +      L P   
Sbjct: 178  IFVNGVWVGIHQKPALLVSAVQSLRRKHFIEHEVSLIRDIRDREFKILTDQGRVLRPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD---- 739
             +D               P +      V T       ++     +       E++     
Sbjct: 238  VED--------------DPKMHDHGNLVLTKDHVERLEADRDVPLDMDKEERERITFGWH 283

Query: 740  --AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                  V+  V+ + + +   V     +   R  Q   V                +    
Sbjct: 284  GLINEGVVEYVDAEEEETIMIVMTPYDLNVSRQIQAGYV----------------LPEAD 327

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +    N       W       SM+  I   ++            ++       
Sbjct: 328  SDDPNRRVKAPINPTAH--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQA 385

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G      D    +           +  +             +       +   +  + A
Sbjct: 386  MGVFLTNFDQRMET-----------MSHILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 434

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +     F R   D+ ++   +    +E   +    + 
Sbjct: 435  IACYSGYNQEDSVIMNQSSIDRGLF-RSPFYRSYTDQEKK---IGMYTMEQFEKPARTDT 490

Query: 976  VILDRNIYSRLME----ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
            + L    Y +L +    I+ G           K+  ++ D      R++          +
Sbjct: 491  LKLKHGTYDKLDDTDGIIIPGARVSGEDIIIGKTAPIAPDAEELGQRTKLHNKRDASTPL 550

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     L  Q   + +                       LR VKV +   +  Q GDK A
Sbjct: 551  RSTESGLVDQVLLTVN--------------------SEGLRFVKVRMRTTKIPQIGDKFA 590

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +
Sbjct: 591  SRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFE 650

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                                   +TP F
Sbjct: 651  GD-----------------------------------------------------ATP-F 656

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                 ++++S+LR       G  ++Y+G TG      V +G  Y  +L 
Sbjct: 657  TEVTVDSVSSLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLR 705


>gi|190694909|gb|ACE88995.1| RNA polymerase beta subunit [Mycobacterium fortuitum]
          Length = 222

 Score =  261 bits (667), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 91/219 (41%), Positives = 121/219 (55%), Gaps = 37/219 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 33   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 92

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 93   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 146  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 183

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK
Sbjct: 184  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHHLVDDK 222


>gi|310697225|gb|ADP06542.1| RpoB [Bartonella sp. E2-114]
          Length = 280

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 204/280 (72%), Positives = 234/280 (83%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTTEVVYLSAMEESKHYVAQANSSLDAEGRFIEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAAI AKR GIV+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAIGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|328868020|gb|EGG16401.1| RNA polymerase I [Dictyostelium fasciculatum]
          Length = 1010

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 112/311 (36%), Gaps = 52/311 (16%)

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLK-VQYETSKSILEDRFKNKIEKIQW-GDDMPPG 1069
             +         ++    E +   V  L   Q        E+ +  +++ I        P 
Sbjct: 682  YLDVDGLPHVGRYVTGHEPLYTFVNELDGKQVVEMIKSKEEAWIEEVKIIGNLTSMNAPR 741

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             +    V     R    GDK A RHG KG++S++ P  +MPF + G   D+++NP   PS
Sbjct: 742  TVTKFTVKYRFDRNPVIGDKFASRHGQKGVLSQLWPEINMPFSESGLKPDVIINPNAFPS 801

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +G + E     A    G   +     +                              
Sbjct: 802  RMTIGMLIEIMAAKAGAVNGIFQQGTAFSFDEKNTAVK---------------------- 839

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                                 F G         L  A  +  G   +Y G TGE F   +
Sbjct: 840  ---------------------FFG-------EQLAKAGYNYYGNEPMYSGTTGEEFHADI 871

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
              G  Y  +L HMV DK   R+TG  + +T+QP+ G+   GG R GEME   + A+G ++
Sbjct: 872  FFGVCYYQRLRHMVKDKYQVRATGKVNALTRQPVKGRKIGGGIRFGEMERDSMLAHGTSF 931

Query: 1310 VLQEMLTIKSD 1320
             L + L   SD
Sbjct: 932  CLNDRLMKSSD 942



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 95/652 (14%), Positives = 194/652 (29%), Gaps = 97/652 (14%)

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVT 364
           G      +       + +     I   + ++  +  +           +    +      
Sbjct: 93  GQVTYRFLYKRHEYFLPVAMLLRILGDTTDKEIYQHVVQGDTENTFLTDRIELMLREQRI 152

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D    + +AL  +    R                  F  D +    +    +N  + +  
Sbjct: 153 DHVNTQAEALDYLGSRFRHK---------------AFLPDNFTNRQIAEYMINNYILVHL 197

Query: 425 PDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           P+     +   I  +++ L     GK   D+ID      V   G +  +  +  L     
Sbjct: 198 PNWRD--KFNLICLMVQKLYSSVQGKSDCDNIDATSFHEVLLGGHLFCSMLKERLQEYLE 255

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-------------------------S 519
           +++                 N + ++    +                            +
Sbjct: 256 TVRFHFLHGVEIEKKNGKNPNHEAILKKSFDRAGAIGPKFESFLATGNLASNSGLDVQQT 315

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S  + + E +N L  I+H R   ++ +G          +R + P  +G +CP  T +G  
Sbjct: 316 SGFTIIAEKLNFLRYISHFR---SIHRGAFFATMKTSSIRKLMPESFGFLCPVHTPDGAP 372

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME---EENRYIAQANSSLDE 636
            GL++ L+S   +      E   RKV +  +T     LS      E        +  +  
Sbjct: 373 CGLLNHLSSNCLITKDPLQE---RKVLESNLTLTKFLLSNGVTSIETTSTFRPGSLPVTF 429

Query: 637 DGS--------FTEELVFC-RCAGEEILVPREKIDFIDASPKQVVSIAAS---------- 677
           +G           +ELV   R               I  +PK    I             
Sbjct: 430 NGRLIGMADEDTCDELVNTLRYLRSVGHENVPSTLEIAYAPKNRPGIVGGQFPGISLFST 489

Query: 678 ----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
               + P +      + L+G   Q      +  E   V  G+     + S  A+++  A 
Sbjct: 490 GARFMRPVINVKSGKQELIGPQEQLYMNIAIYPEE--VKKGIT-THVELSPTAMLSVVAN 546

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN-QRPLVKVGDEVRRND 792
           +    D  +      +  +   T G  ++       +      N Q+P+V+  ++ +   
Sbjct: 547 LTPFSDYNQSPRNMYQCQMAKQTMGTPMHSYAYRADNKLFKIQNPQKPIVRTINQSK--- 603

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                    + D   G N ++A +   GY+ ED+M+I++           H   ++ +  
Sbjct: 604 -------YHVNDYPHGCNAVIAVISNTGYDMEDAMIINKSSYERGFG---HGSVYKTVFY 653

Query: 853 DTKLGPEEITRDIPNVSEEGLK------NIDECGIICVGAEVNPGDILVGKI 898
           D   G         +VS    +       +D  G+  VG  V   + L   +
Sbjct: 654 DLDEGKLRAQTGRTSVSRPDYQTDGLDQYLDVDGLPHVGRYVTGHEPLYTFV 705


>gi|70794974|gb|AAZ08461.1| RNA polymerase II second largest subunit [Liriodendron tulipifera]
          Length = 942

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 138/926 (14%), Positives = 273/926 (29%), Gaps = 172/926 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +                  KY 
Sbjct: 175  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGQTVGVTKEKRIKYA 231

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 232  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 288

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 289  GPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 348

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 349  NAAGTRAGVSQVLNRLTFASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 404

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 405  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 457

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 458  IFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 514

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+                K   +    +           +  I  V+ + +
Sbjct: 515  LFIVEKQRLLI--------------KKKHIRSLQQRETQDEGWHDLVAKGFIEYVDTEEE 560

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N +   +                    PS  LG       +  
Sbjct: 561  ETTMISMTISDLVSARLNPDEAYS-----------ETYTHCEIHPSLILG-------VCA 602

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 603  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 635

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 636  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 693

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 694  SIDRGFF-RSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGT 752

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++                  DE   +     +  + TS    E   
Sbjct: 753  RVSGEDVIIGKTTPIAQ-----------------DESQGQASRYTRRDHSTSLRHSESGM 795

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 796  VDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 850

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G   V +GK+                      
Sbjct: 851  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAVHMGKEGD-------------------- 890

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 891  ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 916

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +Y+G TG      + +G  Y  +L
Sbjct: 917  ETMYNGHTGRRLTAMIFLGPTYYQRL 942



 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 122/904 (13%), Positives = 261/904 (28%), Gaps = 164/904 (18%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD-------- 141
              R+LTY+ PL + +   V             +D  +  +++G +P+M +         
Sbjct: 2   ARLRNLTYSAPLYVDVTKRVIKKGHDCEEVTETQDFTK--VFIGKVPIMLRSSYCTLYQN 59

Query: 142 ----------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRI 184
                           G F+I G ++++++Q   S   ++      +     K  Y   +
Sbjct: 60  SEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYVAEV 115

Query: 185 IPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMALGMD 224
                   + +      + VR+  R                   R ++P+     ALG  
Sbjct: 116 R----SMAESQNRPPSSMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFV 171

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           ++ +IL         +Q  +     L  A ++   +V+   +        +   K++   
Sbjct: 172 ADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGQTVGVTKEKRIKYA 231

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L+++ +  +G+   C          +      + + A     E   +   +  +  
Sbjct: 232 K-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKRLDL 287

Query: 344 I-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
             P+L          +   +     K   +      +        T  +  S+    +  
Sbjct: 288 AGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 347

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           ++           +N      T   +R +         +     L N    +        
Sbjct: 348 ANAAGTRAGVSQVLNRLTFASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAETPE 407

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F     
Sbjct: 408 GQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCW 464

Query: 522 LSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +         +  +   RR   +  + GV R     E+R ++  +     P    E   +
Sbjct: 465 VGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRL 523

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +         + +    ET      D      + Y+   EEE   I+            
Sbjct: 524 LIKKK-----HIRSLQQRETQDEGWHDLVAKGFIEYVDTEEEETTMISM----------T 568

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             +LV  R   +      E     +  P  ++ + AS+IPF +++ S R      M +QA
Sbjct: 569 ISDLVSARLNPD--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 626

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                           R   +  V                      
Sbjct: 627 MGIYVTNYQL--------------------RMDTLAYV---------------------- 644

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+PLV                      L  G N +VA   + G
Sbjct: 645 -------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSG 681

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 682 YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDK 741

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           +         RD S  +    
Sbjct: 742 LDDDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLRHSE 792

Query: 936 SGTV 939
           SG V
Sbjct: 793 SGMV 796


>gi|185179204|gb|ACC77615.1| RpoB [Mycobacterium chelonae]
          Length = 213

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 91/220 (41%), Positives = 121/220 (55%), Gaps = 40/220 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 26   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 85

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 86   TPVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 130

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 131  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 173

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK+
Sbjct: 174  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKI 213


>gi|119644179|gb|ABL85610.1| RNA polymerase II second largest subunit [Buellia stillingiana]
          Length = 717

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 120/840 (14%), Positives = 233/840 (27%), Gaps = 149/840 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R    ++ + ++   +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRTLFNKLNKDVERYLKNCIENNREFNLTLGVKSTHITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V+    IE    +      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVSVGAPIEGVVDFLFQRQMESLEEYDP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +    +     V      + I      + D  D   K +    
Sbjct: 177  LTSPHATKIFVNGVWVGVHRSPAALVNAVQDLRRKQVIAYEVSLVRDIRDREFKILTDQG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKRAGI 734
              L P    ++                 +  +       +E     +     I  +    
Sbjct: 237  RVLRPLFVVEN------------DPKSPICGDLVLNKGHIEKLESDRDIPLDIDKEERVK 284

Query: 735  VEQVDA---IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                        V+  V+ D + +   V     +   R  Q               V+  
Sbjct: 285  KTYGWHGLVNEGVVEYVDADEEETVMIVMTPYDLNVSRQVQAGYALPEDNDDPNARVKAP 344

Query: 792  DIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                    T      ++   + V+ +P+  +N          M  + +   + +  ++  
Sbjct: 345  INPTAHTWTHCEIHPSMILGVCVSIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQR 402

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                          +  +             +       +   +
Sbjct: 403  MET---------------------------MAHILYYPQKPLATTRSMEFLKFRELPAGQ 435

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +     F R   D+  R   +    IE   + 
Sbjct: 436  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSPFFRSYSDQEGR---IGLNVIEQFEKP 491

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
                 + L    Y +L +   I+ G           K+  +++D        +  +    
Sbjct: 492  MRSNTMKLKHGTYEKLDDDGLIIPGARVSGEDIIIGKTAPITADAEELGQGIKIRERRDA 551

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     L  Q                              + VKV +   +  Q G
Sbjct: 552  STPLRSTESGLVDQVAL--------------------TTNAEGHKFVKVRMRTTKIPQIG 591

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L      
Sbjct: 592  DKFASRHGQKGTIGITYRQEDMPFTSEGLVPDIIINPHAIPSRMTIAHLIECQLSKVSSL 651

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +          +S L    E    +                             
Sbjct: 652  RGFEGDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM----------------------- 686

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                   +G +    G         V +G  Y  +L HMV DK+
Sbjct: 687  ----------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 717


>gi|68131842|gb|AAY85199.1| RNA polymerase II second largest subunit [Cissus tuberosa]
          Length = 951

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 140/926 (15%), Positives = 275/926 (29%), Gaps = 171/926 (18%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++   +   ++A +   + +    +       S          KY 
Sbjct: 183  DILEHTCYDFSGTQMMELPHPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                 +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEIFQKEMLPHVGVGEYCETKK---AYYFGYIIHQLLLCAFGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K +        ES         +              +  I  V+ + +
Sbjct: 523  LFIVEKQRLLIKKKDIRALQLRESPEDGGWHDLV-------------SKGFIEYVDTEEE 569

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 570  ETTMISMTINDLVSARLNPEEAYS-----------ETYTHCEIHPSLILG-------VCA 611

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 612  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 644

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 645  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 702

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 703  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGT 761

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S                  D+   +     +  + TS    E   
Sbjct: 762  RVSGEDVIIGKTTPISQ-----------------DDSQGQPSRYTRRDHSTSLRHSESGM 804

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 805  VDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 859

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 860  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 899

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 900  ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 925

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +Y+G TG      + +G  Y  +L
Sbjct: 926  ETMYNGHTGRRLTAMIFLGPTYYQRL 951



 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 119/911 (13%), Positives = 257/911 (28%), Gaps = 171/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +           + + +E   +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVNVTKRIIRKGHDLE--EVTETQEFTKVFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YHNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSDNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + V++  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSSMFVQMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHTCYDFSGTQMMELPHPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                K + +K +       +                 ++ + A     E   +   +  
Sbjct: 237 --KYAKEIFQKEMLPHVGVGEYCETKKAYYFGYIIH--QLLLCAFGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  +   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQSTKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L         G+         D      + Y+   EEE   I+     
Sbjct: 529 QRLLIKKKDIRALQLRESPEDGGW--------HDLVSKGFIEYVDTEEEETTMISM---- 576

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +LV  R   E      E     +  P  ++ + AS+IPF +++ S R    
Sbjct: 577 ------TINDLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 628

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                           R   +  V               
Sbjct: 629 SAMGKQAMGIYVTNYQL--------------------RMDTLAYV--------------- 653

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 654 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 683

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 684 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGM 743

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           +         RD S
Sbjct: 744 RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------SQGQPSRYTRRDHS 794

Query: 929 LRVPSGVSGTV 939
             +    SG V
Sbjct: 795 TSLRHSESGMV 805


>gi|103001649|gb|ABF71516.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 691

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 115/810 (14%), Positives = 234/810 (28%), Gaps = 143/810 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 2    GPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSN 688
               +  D +     V        I      + D  D   K          P F+ ++D  
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G  +  +       +   +   M+    +       AK  G    V     V+  V
Sbjct: 238  STNCGNLVLTKEHINKLEDDRDLPAIMDFEEKE-------AKFFGWDGLV--NNGVVEYV 288

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 289  DAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSM 348

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 349  ILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------- 390

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 391  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 439

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 440  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 495

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +S D      R++          ++     +  Q   
Sbjct: 496  DDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 555

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      L+ VKV +   +  Q GDK A RHG KG +    
Sbjct: 556  --------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 595

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +             
Sbjct: 596  RQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------- 644

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     ++++ +LR
Sbjct: 645  ------------------------------------------ATP-FTEVTVDSVSKLLR 661

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                   G  ++Y+G TG      V +G  
Sbjct: 662  EHGYQSRGFEVMYNGHTGRKLVAQVFLGPT 691


>gi|67810699|gb|AAY82002.1| RNA polymerase II second largest subunit [Selaginella erythropus]
          Length = 581

 Score =  261 bits (667), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 116/728 (15%), Positives = 214/728 (29%), Gaps = 148/728 (20%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   A +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMAYITVGSAANPILVFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +   ++ +  +G++           + +   R ++   D + +  V     L       
Sbjct: 54   AVIPNSTKIFVNGAWVGIHREPEHLVKTLRQLRRQV---DVNTEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+                    A    +           +  I
Sbjct: 111  DYGRCSRPLFIVEKQRLLI--------------KKSDIRALQQKEAGENGWHELVAKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              V+ + + +T        +   R N +   +                    PS  LG  
Sbjct: 157  EYVDTEEEETTMISMTILDLVNARLNPDEAYS-----------DTYTHCEIHPSMILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   IH+  ++                 
Sbjct: 204  -----VCGSIIPFPDHNQSPRNTYQSAMGKQAMG--IHVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        IF R   D+ +++ ++ +E+ E   R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSIFYRSYRDEEKKAGTLVKEEFERPNRETTTGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T ++                  DE   +     K    T 
Sbjct: 349  DGIAPPGTRVSGEDVIIGKTTPVTQ-----------------DETSTQAQRYTKRDQSTC 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK  V   R  Q GDK + RHG KG +     
Sbjct: 392  LRHSESGMIDQVLLTTNADGL-----RFVKTRVRSIRIPQIGDKFSSRHGQKGTIGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF ++G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 447  QEDMPFTQEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAALMGKEGDATPFTDVTVDNI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 507  SKALHKCGYQMRGFETM------------------------------------------- 523

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 +G +    G      +  + +G  Y  +L HMV DK+++R  G   ++T+QP  G
Sbjct: 524  ----YNGHT----GR---RLNAMIFIGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEG 572

Query: 1286 KSNRGGQR 1293
            +S  GG R
Sbjct: 573  RSRDGGXR 580



 Score =  118 bits (295), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 75/482 (15%), Positives = 145/482 (30%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + ++   F   + + 
Sbjct: 11  EGQACGLVKNLALMAYITVGSAANPILVFLEEWSTENFEEISPAVIPNSTKIFVNGAWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              E  + +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 71  IHREPEHLVKTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 129

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      + A    E       +      + Y+   EEE   I+              
Sbjct: 130 KKS-----DIRALQQKEAGENGWHELVAKGFIEYVDTEEEETTMISM----------TIL 174

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   +      +     +  P  ++ +  S+IPF +++ S R      M +QA+ 
Sbjct: 175 DLVNARLNPD--EAYSDTYTHCEIHPSMILGVCGSIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 233 IHVTNYQL--------------------RMDTLAYV------------------------ 248

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 249 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 287

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNID 877
            EDS+++++  +    F SI    +    +    L  EE  R        +       +D
Sbjct: 288 QEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKAGTLVKEEFERPNRETTTGMRHGSYDKLD 347

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GI   G  V+  D+++GK TP  +   +            +    RD S  +    SG
Sbjct: 348 DDGIAPPGTRVSGEDVIIGKTTPVTQDETST---------QAQRYTKRDQSTCLRHSESG 398

Query: 938 TV 939
            +
Sbjct: 399 MI 400


>gi|310697229|gb|ADP06544.1| RpoB [Bartonella sp. Ew-111]
          Length = 280

 Score =  261 bits (667), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 203/280 (72%), Positives = 236/280 (84%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D 
Sbjct: 121 KIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGHFTEEFVVCRHAGEVLMAPRDHVDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAA+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAVSAKRAGIVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|103001255|gb|ABF71499.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 691

 Score =  261 bits (667), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 113/811 (13%), Positives = 231/811 (28%), Gaps = 145/811 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 2    GPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  +
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                 N+   ++ +  L+ +               S     AK  G    V     V+  
Sbjct: 238  STNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEY 287

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLA 806
            V+ + + +   V     ++  R  Q               V+          T      +
Sbjct: 288  VDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPS 347

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            +   +  + +P+  +N          M  + +   + +  ++                  
Sbjct: 348  MILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM--------------- 390

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 391  ------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 438

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L
Sbjct: 439  SVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKL 494

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  ++ D      R++          ++     +  Q  
Sbjct: 495  DDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVL 554

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                       L+ VKV +   +  Q GDK A RHG KG +   
Sbjct: 555  L--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 594

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +  + E  L       G +            
Sbjct: 595  YRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------- 644

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     ++++ +L
Sbjct: 645  -------------------------------------------ATP-FTEVTVDSVSKLL 660

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            R       G  ++Y+G TG      V +G  
Sbjct: 661  REHGYQSRGFEVMYNGHTGRKLVAQVFLGPT 691


>gi|118640715|gb|ABL09925.1| RNA polymerase beta subunit [Grimontia hollisae]
          Length = 290

 Score =  261 bits (667), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 172/290 (59%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF  D+YDLS VGR+K N  L  +       +  +DII +++ L+D+RNG G +
Sbjct: 1   QLFESLFFSEDRYDLSAVGRMKFNSSLGREEMTGSGVLSHDDIIEVMRKLIDIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYRKV DGKVT+++ YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARTNPYGFLETPYRKVVDGKVTDEIDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDGSF +EL+  R  GE  L PR+ + ++D +  QVVS+AASLIPFLE
Sbjct: 241 LNEDGSFADELITARQKGESGLHPRDHVQYMDVATNQVVSVAASLIPFLE 290


>gi|52699778|gb|AAU86951.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            laqueata]
          Length = 711

 Score =  261 bits (667), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 123/833 (14%), Positives = 239/833 (28%), Gaps = 145/833 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L N +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DXXGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYAFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L    +  V         +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSQPIIDFMIQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V      + I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVLALRRQDAISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D      G  +  ++      +   +    E       G   + KR G+VE 
Sbjct: 237  RPLFVIDNDPRSPNCGNLVLTKSDIQKLEDDKDLPPDYEIDEKNPPGWNGLVKR-GVVEY 295

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            VDA            + +   V     ++  R  Q           +   V+        
Sbjct: 296  VDAEE----------EETVMIVMTPEDLEISRQLQAGYHLPETSDDLNKRVKAPMNPTAH 345

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N                        ++       +
Sbjct: 346  TWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAM 387

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G      D                +  +             +       +   +  + AI
Sbjct: 388  GVXLXNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 436

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + +
Sbjct: 437  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTL 492

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++          ++ 
Sbjct: 493  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 552

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 553  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 592

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 593  HGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 652

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 653  ATPFTEVTVDSVSKLLR--EHGYQSRGFEAM----------------------------- 681

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                             +G +    G         V +G  Y  +L HMV DK
Sbjct: 682  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDK 711


>gi|56692710|ref|YP_164168.1| DNA-directed RNA polymerase II second largest subunit [Singapore
            grouper iridovirus]
 gi|42517422|gb|AAS18088.1| DNA-directed RNA polymerase II second largest subunit [Singapore
            grouper iridovirus]
          Length = 1103

 Score =  261 bits (666), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 87/339 (25%), Positives = 141/339 (41%), Gaps = 71/339 (20%)

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             ++      +    E+ + +KI +     D+ P   ++VKV +   R  + GDK A    
Sbjct: 824  TTVCKDISLAIKASEEGYLDKIVQ-----DVDPDGRKIVKVRLRTPRIPEMGDKFASFTA 878

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG    +   EDMPF KDG   D+++NP   PSRM V  + +   G A   LGK+    
Sbjct: 879  QKGTCGAVKSQEDMPFDKDGVVPDLIINPHAFPSRMTVNYLLQMCFGLAGCKLGKRYD-- 936

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +T  F+ AD
Sbjct: 937  ---------------------------------------------------AT-AFERAD 944

Query: 1216 -EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              + I    + A ++    S++Y G+TG  F   + +      +L HMVS K+++R +G 
Sbjct: 945  IVKDIADAAKEAGIEHW-DSVMYSGITGRRFPAKIFMAPCPYQRLRHMVSGKIHSRVSGP 1003

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD-------VVGRTR 1327
               +T+QP+ G+S  GG ++GEME WC  ++GA+  L+E +   SD          GR  
Sbjct: 1004 VDALTRQPVAGRSRDGGIKIGEMEQWCKISHGASESLKESMFDTSDKYSVPVCQTCGRIS 1063

Query: 1328 ---VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                Y  +    D   T  P +  +L +E++A+G+SI  
Sbjct: 1064 DHFEYCRLCDAVDIRLTYLPYTTKLLFQELKAIGISITF 1102



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 89/597 (14%), Positives = 192/597 (32%), Gaps = 74/597 (12%)

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             +    +    +++    +    +++  I   ++   +   +DAL ++ + +       
Sbjct: 206 TAEEAVALCGLGVKEGD-SFSCHTSSHQTIAALIIEQYSNCPEDALQELAKYV------- 257

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                             D     +  +N  L L       H+       ++K L     
Sbjct: 258 -----------PDTKKSSDKREYVKTVLNRELFLHGGHGASHLGW-----MVKKLAQTAA 301

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           G     D D++ N+RV + G ++       L +  + +  + +    +      L N++ 
Sbjct: 302 GISKPLDRDDIANKRVDTTGHLIMFLLDGLLKQYVK-LFLKSAECQKNLCPYTVLQNSQV 360

Query: 509 VVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + +++   F +                 +SQ+  + N  ++++H RR+       V+   
Sbjct: 361 ITNSLHLCFATGNWTVKRIGPPSYVRVGVSQILSNNNFGAKLSHLRRI----MHAVSFKG 416

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD------ 607
             ++MR +H +HYG +CP ET EG  +G+V ++   A V+ Y   E     +        
Sbjct: 417 KNIKMRQLHTSHYGFLCPYETPEGERVGIVLNMAESAAVSDYTPREEITAILDRAGGMPG 476

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            + T ++ +L+    +       +  L    +   E V        I +  +     D  
Sbjct: 477 YEKTAELSHLAWSSSDTFSAVVVDGRLAGFTTEPREFVKEAK----IRLSAQVGVCWDKI 532

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ--AVPLLKAEAPFVGTGMESVVAKSSGA 725
             ++  +           D  R+                   AP VG   E      S  
Sbjct: 533 EDEIHLLGCEGRFMRRMLDPARLRGEPIEIEPLSLSKTRTVTAPSVGRLEEHKTQNLSKY 592

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNTCVNQR---PL 781
             +  +      V    +   + E   D  ++ +  Y      + + Q+    Q    P 
Sbjct: 593 IYLCIQEINCGTVGKDYLDPPASEILTDVMSAVIPFYDHTQSPRNAYQSNMGKQAIGFPA 652

Query: 782 VKVGDEVRRNDIIADGPST-----------DLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           +   D         D P +           +   +A G   +VA M   G+N EDS++++
Sbjct: 653 INCEDRYDATLHRLDYPQSALTESRAIERVNFDTMAHGALPVVAIMTAEGFNQEDSIVLN 712

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNIDECGIICV 884
              +   +F+ +    F    +       E            +     +DE G+I  
Sbjct: 713 ASSLDRGLFSCVTYRTFAANDKRRSKYDSEQICLPEYGNRNKDWDYTLLDENGVINP 769



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 75/243 (30%), Gaps = 81/243 (33%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+     SY+  L  +        +          PI       +++F S  ++ P    
Sbjct: 4   LVAHHLDSYESMLWRDFPNLIAREK----------PIE--VKGYVIKFESLYYEMPVKEA 51

Query: 85  ---KF-DVDDCLWRDLTYAVP---------------LKITLRLI---VFDVDEFTGAKSI 122
              K+        +DLTY                  +   L L    V         +  
Sbjct: 52  DLTKYLTPAIARRQDLTYQAAACCVLNVVDPHGRETIYPRLELCKLPVMVGSSLCWTRQR 111

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           +D++      G+ PL    G F+IKG +R+++      P I   +D              
Sbjct: 112 QDMR------GECPL-DPGGYFIIKGKERVII------PHIRPAYDHPVVHEQEGP---- 154

Query: 183 RIIPDQGLWMDIEFDSKD-------IIHVRIDRRRKV-----------PVTSFLMALGMD 224
                   W+  EF S +       ++  R D RR +           PV +   ALG  
Sbjct: 155 -------SWL-CEFRSVNPLTQQSVLVQARTDCRRSLEFSLPYIKQYVPVGTTFKALGKT 206

Query: 225 SEE 227
           +EE
Sbjct: 207 AEE 209


>gi|103001231|gb|ABF71498.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            scabrida]
          Length = 713

 Score =  261 bits (666), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 121/835 (14%), Positives = 239/835 (28%), Gaps = 147/835 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +    +         + +  + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     +      E    +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 177  TKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPL 236

Query: 682  LENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQV 738
               D+  +     N+   ++ +  L+ +     T   E            AK  G    V
Sbjct: 237  FVIDNDPKSTHCGNLALTKEHINKLEDDKDLPATMDTEEKD---------AKFFGWDGLV 287

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q           +   V+         
Sbjct: 288  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYTIPETSDDLNKRVKAPMNPTAHT 345

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M  + +   + +  ++         
Sbjct: 346  WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM------ 397

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                   +  +             +       +   +  + AI 
Sbjct: 398  ---------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 436

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 437  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 492

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L E   +  G           K+  ++ D      R++          ++  
Sbjct: 493  LKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRST 552

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             LR VKV +   +  Q GDK A RH
Sbjct: 553  ENGIVDQVLI--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRH 592

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 593  GQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 652

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 653  TPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------ 680

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 681  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 713


>gi|310697227|gb|ADP06543.1| RpoB [Bartonella sp. E3-106]
          Length = 280

 Score =  261 bits (666), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 203/280 (72%), Positives = 234/280 (83%), Gaps = 1/280 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+I+ER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSA
Sbjct: 1   RAIRERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           K+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE V CR +GE ++ PR  ID 
Sbjct: 121 KIIDGKVTTEVVYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHSGEVLMAPRNHIDL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++ EAPFVGTGMESVVA+ S
Sbjct: 181 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRTEAPFVGTGMESVVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           GAAIVAKR G+V+QVDA RIVIR+ E  LDPS SGVDIYR
Sbjct: 241 GAAIVAKRGGVVDQVDATRIVIRATED-LDPSKSGVDIYR 279


>gi|118640709|gb|ABL09922.1| RNA polymerase beta subunit [Grimontia hollisae]
 gi|118640711|gb|ABL09923.1| RNA polymerase beta subunit [Grimontia hollisae]
 gi|118640713|gb|ABL09924.1| RNA polymerase beta subunit [Grimontia hollisae]
 gi|118640721|gb|ABL09928.1| RNA polymerase beta subunit [Grimontia hollisae]
          Length = 290

 Score =  261 bits (666), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 172/290 (59%), Positives = 223/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF  D+YDLS VGR+K N  L  +       +  +DII +++ L+D+RNG G +
Sbjct: 1   QLFESLFFSEDRYDLSAVGRMKFNSSLGREEMTGSGVLSHDDIIEVMRKLIDIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYRKV DGKVT+++ YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARTNPYGFLETPYRKVVDGKVTDEIDYLSAIEEGQFVIAQANAV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDGSF +EL+  R  GE  L PR+ + ++D +  QVVS+AASLIPFLE
Sbjct: 241 LNEDGSFADELITARQKGESGLHPRDHVQYMDVATNQVVSVAASLIPFLE 290


>gi|119644004|gb|ABL85600.1| RNA polymerase II second largest subunit [Lecidea fuscoatra]
          Length = 707

 Score =  261 bits (666), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 123/826 (14%), Positives = 233/826 (28%), Gaps = 142/826 (17%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   ++ + + +  +              + +  + + +     +   
Sbjct: 1    DLAGPLLAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLKYSLATGNW 60

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 61   GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 116

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +   L +      ++
Sbjct: 117  CPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPNATKVFV 176

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  D +     V        I      + D  D   K          P    D+
Sbjct: 177  NGVWVGVHRDPAHLVSTVLSLRRHHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDN 236

Query: 687  SNRVLMGCNMQ--RQAVPLLKAEAPFVG-TGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
              +     N+   ++ V  L+ +   +  T  E  VAK  G        G+VE VDA   
Sbjct: 237  DPKSSNRGNLVLTKEHVQKLEDDREIIASTDPEDRVAKFMG-WEGLVHQGVVEYVDAEE- 294

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADGPSTDL 802
                     + +   V     ++  R  Q   V   P +      V+          T  
Sbjct: 295  ---------EETVMIVMTPEDLEISRQIQAGFVLPDPSIDDPNKRVKAPLNPTAHTWTHC 345

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N          M  + +   + +  ++             
Sbjct: 346  EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------- 393

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 394  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 436

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R      E+ E   R    +      +
Sbjct: 437  YNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGMSVVEEFEKPMRSDTLKLKHGTYD 495

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   +  G           K+  ++ D      R++          ++     +  Q
Sbjct: 496  KLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLRSTENGIVDQ 555

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                         LR VKV +   +  Q GDK A RHG KG + 
Sbjct: 556  VLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIG 595

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +       
Sbjct: 596  ITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVT 655

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               +S L    E    +                                           
Sbjct: 656  VDSVSRLLR--EHGYQSRGFEVM------------------------------------- 676

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                     +G +    G         V +G  Y  +L HMV DK+
Sbjct: 677  --------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 707


>gi|113957191|gb|ABI49106.1| RNA polymerase II second largest subunit [Diploschistes
            cinereocaesius]
          Length = 709

 Score =  261 bits (666), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 126/832 (15%), Positives = 235/832 (28%), Gaps = 149/832 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ + +R    R+ + + + +               + +  + + +     +
Sbjct: 1    KRLDLAGPLMASLFRSLFNRLTKDVLKYLQKCIEGNRDFNIALGVKSTTLTNGLKYSLAT 60

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   GNWSEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L    +  V + G     +    + +V  +     +     
Sbjct: 117  GLVCPAETPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPNITK 176

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF-- 681
             ++      +  D +     V        I      I D  D   K          P   
Sbjct: 177  VFVNGVWVGVHRDPAHLYNTVLSLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVARPLFV 236

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            ++ND  +       + ++ V  L+ +             +         ++G VE +DA 
Sbjct: 237  IDNDKRSSRRGELVLSKELVNRLEDDRELPPGLDPDEKKEKYFGWEGLIKSGAVEYLDAE 296

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +               R  Q       P        +          T 
Sbjct: 297  EEETVMIAMTPEDLDI----------SRQVQAGYAPPEPSTDQNARFKAPINANVHTWTH 346

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N          M  + +                      
Sbjct: 347  CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV-------------------- 386

Query: 861  ITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                        L N DE    +  +             +       +   +  + AI  
Sbjct: 387  -----------FLTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILC 435

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R  +++ +R        +E   +    E + L
Sbjct: 436  YSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPLRSETLRL 491

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                Y +L +   I  G           K+  ++ D                DE  QR  
Sbjct: 492  KHGTYEKLDDDGLIAPGVRVSGEDVIIGKTAPIAPD---------------TDELGQRTK 536

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K    T     E+   +K+             L+ VKV +   +  Q GDK A RHG
Sbjct: 537  LHSKRDASTPLRSTENGIVDKVLL-----TTNQEGLKFVKVRMRTTKIPQIGDKFASRHG 591

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 592  QKGTIGITYRQEDMPFTAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDAT 651

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S L    E    +                                     
Sbjct: 652  PFTDVTVDSVSRLLR--EHGYQSRGFEVM------------------------------- 678

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                           +G +    G         V  G  Y  +L HMV DK+
Sbjct: 679  --------------YNGHT----GR---KLRAQVFFGPTYYQRLRHMVDDKI 709


>gi|307343584|emb|CBJ18707.1| RNA polymerase B subunit [Micromonospora pattaloongensis]
          Length = 211

 Score =  261 bits (666), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K+     ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVDGDDAEWKTALRSIG---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------ADESEPDTNVATPVFDGAKEEEISGLLSSTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 177  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 211


>gi|55583700|gb|AAV53369.1| RNA polymerase II second largest subunit [Pluteus romellii]
          Length = 646

 Score =  261 bits (666), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 118/752 (15%), Positives = 222/752 (29%), Gaps = 131/752 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 25   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 80

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++   +       + +  + +         EEN +     + +  +G +
Sbjct: 81   GLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSTTPCTKVFVNGVW 132

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 133  MG---VHRNPANLVKTIKKLRRKDDISPEVSVVRDTREKELRLYTDAGRVCRPLFIVENQ 189

Query: 701  VPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
              +L+ +   ++ +G      +     +   + G++E VDA       +    +   +  
Sbjct: 190  QLVLQKKHIKWLNSGYNEDGEEFKWEQL--IKGGVIELVDAEEEETVMISMTPEDLENSR 247

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                      ++       R  +K G            PS  LG       +  + +P+ 
Sbjct: 248  LRQSGQDPHMNDGEFDPAAR--LKAGTHAHTWTHCEIHPSMILG-------ICASIIPFP 298

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N                        ++       +G       I              
Sbjct: 299  DHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM-----------D 329

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 330  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 389

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                I+ R  +D  ++S   + E+ E  +R+          +       I  G       
Sbjct: 390  F-RSIYYRSYMDLEKKSGIQQLEEFEKPSRETTLRMKHGTYDKLEDDGLIAPGTGVRGED 448

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  D      R++          ++     +  Q                  
Sbjct: 449  IIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLL--------------- 493

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                        + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 494  -----TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVPD 548

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +V+NP  +PSRM +G + E  L      +G +  +          +S      +K   + 
Sbjct: 549  LVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVEAVSSFLR--QKGYQSR 606

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                       L +     +G+      
Sbjct: 607  G------------------------------------------LEVMYHGHTGK------ 618

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                     V +G  Y  +L HMV DK+++R+
Sbjct: 619  ----KLQAQVYLGPTYYQRLKHMVDDKIHSRA 646



 Score =  117 bits (293), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 75/567 (13%), Positives = 149/567 (26%), Gaps = 98/567 (17%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R GK       +  +  +
Sbjct: 9   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGM 68

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFF 517
               E  + Q    +  +       + S     +             NA         F 
Sbjct: 69  VCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSTTPCTKVFV 128

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
               +       N +  I   RR   +            +   ++        P    E 
Sbjct: 129 NGVWMGVHRNPANLVKTIKKLRRKDDISPEVSVVRDTREKELRLYTDAGRVCRPLFIVEN 188

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L      +  +N+    +    K         +  + A EEE   I+     L+  
Sbjct: 189 QQLVLQKKHIKW--LNSGYNEDGEEFKWEQLIKGGVIELVDAEEEETVMISMTPEDLENS 246

Query: 638 GSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                        GE                   +  P  ++ I AS+IPF +++ S R 
Sbjct: 247 RLRQSGQDPHMNDGEFDPAARLKAGTHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRN 306

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                                               
Sbjct: 307 TYQSAMGKQAMGIFLTNFLI---------------------------------------- 326

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               + + +  Y       +     +  R                        +L  G+N
Sbjct: 327 -RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQN 361

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----I 865
            +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E          
Sbjct: 362 AIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPSRETT 421

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +++ G+I  G  V   DI++GK  P         ++        +    R
Sbjct: 422 LRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-------RTHTRR 474

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           D S  + S  SG V  V +       K
Sbjct: 475 DVSTPLKSTESGIVDQVLLTTNSEGQK 501


>gi|52699784|gb|AAU86954.1| DNA-dependent RNA polymerase II second largest subunit [Athelia
            bombacina]
          Length = 698

 Score =  261 bits (666), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 130/827 (15%), Positives = 245/827 (29%), Gaps = 146/827 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + +    +              +  + + + +   
Sbjct: 2    FGKKRLDLXGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYS 61

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 62   LATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHN 117

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   + ++   +       + +         L ++EE 
Sbjct: 118  THWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWG-------LESLEEN 170

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
                A + S L +       +   R     +   ++     D SP+  V           
Sbjct: 171  ----AHSTSPLTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRL 226

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D+ RV     +      +LK +   ++  G+     +         ++GI+E +DA  
Sbjct: 227  YTDAGRVCRPLFIVEDHQLVLKKKHIRWLSQGLNDEKEEFKWE--HLVKSGIIELLDAEE 284

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   S     + +    ++ +     R  +K G            PS  L
Sbjct: 285  EETVMISMTPEDLESTRMKMQGLDPHANDGDFDPAAR--LKAGVNATTWTHCEIHPSMIL 342

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 343  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXFLTN 377

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 378  FLIRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGY 426

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E  +RD          + 
Sbjct: 427  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPSRDSTLRMKHGTYDK 485

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R+           ++   + +  Q 
Sbjct: 486  LEDDGMIAPGTRVNGEDIIIGKTAPIPPDSEELGQRTNLHTRRDVSTPLKSTEKGIVDQV 545

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 546  LI--------------------TTNSEGQKFVKVRVRSSRVPQIGDKFASRHGQKGTIGI 585

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 586  TYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT---- 641

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                  ++     + LR       G+ V                
Sbjct: 642  ---------------------DLTVESVSAYLRQKGYQSRGLEVM--------------- 665

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                     G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 666  -------YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDKIXA 698



 Score =  122 bits (306), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 89/622 (14%), Positives = 169/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 11  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 67

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 68  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 127

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 128 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSTSPLTKVFVNGVWM 187

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E H   L
Sbjct: 188 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEDH--QL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           V        ++     E    K      +  +  L A EEE   I+     L+      +
Sbjct: 246 VLKKKHIRWLSQGLNDEKEEFKWEHLVKSGIIELLDAEEEETVMISMTPEDLESTRMKMQ 305

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            L      G+          V        +  P  ++ I AS+IPF +++ S R      
Sbjct: 306 GLDPHANDGDFDPAARLKAGVNATTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 365

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M  QA+                                                     +
Sbjct: 366 MGXQAMGXFLTNFLI-----------------------------------------RMDT 384

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 385 MANILYYPQKPLATTRSMEYLRFR------------------------ELPAGQNAIVAI 420

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 421 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPSRDSTLRMKH 480

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  VN  DI++GK  P         ++             RD S  
Sbjct: 481 GTYDKLEDDGMIAPGTRVNGEDIIIGKTAPIPPDSEELGQRT-------NLHTRRDVSTP 533

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S   G V  V I       K
Sbjct: 534 LKSTEKGIVDQVLITTNSEGQK 555


>gi|327311708|ref|YP_004338605.1| DNA-directed RNA polymerase subunit beta [Thermoproteus uzoniensis
            768-20]
 gi|326948187|gb|AEA13293.1| DNA-directed RNA polymerase subunit beta [Thermoproteus uzoniensis
            768-20]
          Length = 1127

 Score =  261 bits (666), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 98/582 (16%), Positives = 190/582 (32%), Gaps = 105/582 (18%)

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               N  +A  P    +    M I    +   + + I   E     R+             
Sbjct: 627  EEENAYIAVGPEPDMSKYTHMEIVPSSILGAIASIIPYLEHNQSPRNQYEAAMAKQSLGL 686

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
              +      +D  G   +        +    +   G S     +  + A+      ++ D
Sbjct: 687  PQANFMY-KLDSRG--HMLYYPERPIVTTRGLELIGYSRKPAGQNAVVALLTYTGYNIED 743

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              +   S V   +     +         R+   E ++      D+ +      R      
Sbjct: 744  AVIMNKSSVDRGLFRSNFY---------RTYETEEQKYPGGEEDRIEVPDSSARGYRGPE 794

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
                  ++ ++ P+ +        ++I        +   ++ EK+           +  +
Sbjct: 795  AYSHLDEDGIAPPEVYVTG----GEVIIGKTAPPRFYMTLETEKI----------LKERR 840

Query: 1047 SILEDRFKNKIEKIQWGDDMP-PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                   + +   +        P   ++VKV +   R  + GDK A RHG KG++     
Sbjct: 841  DASIPVRRGERGIVDRVVITESPEGNKLVKVRLRELRVPELGDKFASRHGQKGVI----- 895

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
                                        G +              + + +          
Sbjct: 896  ----------------------------GMLL-------------RQEDMPFTEDGIVPD 914

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                     V      +        +S+   A      +  +TP F+G  E  +  +L  
Sbjct: 915  I-------IVNPHAMPSRMTVGQLLESIAGKAGALTGQLIDATP-FEGVTEGELRELLMK 966

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G+ ++Y G+TGE     + +G +Y  KL+HMV+DK++ARS G   ++T+QP  G
Sbjct: 967  LGFRWDGKEVMYSGITGEKLVADIFIGIVYYQKLHHMVADKIHARSRGPVQILTRQPTEG 1026

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVY---------------- 1329
            +S  GG RLGEME   + A+GA+ +L E   ++S D   +  +Y                
Sbjct: 1027 RSREGGLRLGEMERDVLIAHGASALLYER-MVESSD---KYTMYVCELCGLPAYLDAKTN 1082

Query: 1330 --ESIVAGN--DTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              +  + G      +   P +F +L++E+ ALG+   LE + 
Sbjct: 1083 RPKCPIHGESGQFAKVVVPYAFKLLLQELIALGIYPKLELAE 1124



 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 129/641 (20%), Positives = 235/641 (36%), Gaps = 74/641 (11%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            R DAL  +   +  G      +  ++        DKY L  +   K + +      ++ 
Sbjct: 278 TRDDALDFVGGKIAVGQPRPIRIERAL-----QILDKYFLPNLNPQKPDEK----AMEEA 328

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R  +   +  ++K L++++ G+   DD D++ N+RVR V ++L   +R  + +  + +K 
Sbjct: 329 RIKKALLLGQVVKGLIEMQLGRRKPDDKDHVANKRVRLVNDLLAQLFRTVMKQFLQELKN 388

Query: 489 RISSVDIDSVMPQ---------DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           ++        +P               K  ++        + +SQ+ +  N LS +++ R
Sbjct: 389 QLEKYYARGKIPHLQTIVRPDIITERVKQALATGNWVGGKTGVSQILDRTNYLSTLSYLR 448

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+ +     ++R +   E RD+HPT +GR+C  ET EG N+GLV +L   A +       
Sbjct: 449 RVVS----SLSRTQPHFEARDLHPTQWGRLCAVETPEGQNVGLVKNLALLAEITIGVDEA 504

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
              + + +  V   +       E        N  L       EELV             +
Sbjct: 505 VVEKTLNELGVVPVLEARRGGLEGAEVYL--NGRLIGIHQNPEELVKTLRKMRRQGKISD 562

Query: 660 KIDFIDASPKQVVSIAASLI--PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           +++         V+     I  P L  +D    L   ++Q+ A   L          +E 
Sbjct: 563 EVNVAHLGDAVYVNCDGGRIRRPLLVIEDGKLKLTKEHVQKLASGELTWNDLVKMGVVEY 622

Query: 718 VVAKSSGAAIVA--------KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           + A     A +A        K   +     +I   I S+   L+ + S  + Y     ++
Sbjct: 623 LDADEEENAYIAVGPEPDMSKYTHMEIVPSSILGAIASIIPYLEHNQSPRNQYEAAMAKQ 682

Query: 770 SN---------------QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           S                      +RP+V                         G+N +VA
Sbjct: 683 SLGLPQANFMYKLDSRGHMLYYPERPIV----------TTRGLELIGYSRKPAGQNAVVA 732

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP------NV 868
            + + GYN ED++++++  V   +F S     +E   +    G EE   ++P        
Sbjct: 733 LLTYTGYNIEDAVIMNKSSVDRGLFRSNFYRTYETEEQKYPGG-EEDRIEVPDSSARGYR 791

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
             E   ++DE GI      V  G++++GK  P         EK+L+        + RD S
Sbjct: 792 GPEAYSHLDEDGIAPPEVYVTGGEVIIGKTAPPRFYMTLETEKILK--------ERRDAS 843

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           + V  G  G V  V I      +K  +    E    EL  +
Sbjct: 844 IPVRRGERGIVDRVVITESPEGNKLVKVRLRELRVPELGDK 884



 Score =  151 bits (381), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 113/741 (15%), Positives = 240/741 (32%), Gaps = 145/741 (19%)

Query: 30  IEVQKASYDHFLMMNIAPD-------ERPNEGLQAAFKSV---FP-ITAFSGAAMLEFVS 78
           ++ Q  +++ F+   +          E   +GL+ A + V   +P I    G+  + +  
Sbjct: 38  VDHQIRAFNDFIDRKLPKIIEEMGVVETEIKGLKVAIERVEIGWPRIKEPDGSETVIY-- 95

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +   R+ TY+ P+ +T+ L V D    T            IY G+LP+M
Sbjct: 96  ---------PMEARLRNATYSAPMYLTVTLYVDDEPYATET----------IYAGELPIM 136

Query: 139 TKD------------------------GTFVIKGIQRIVVSQ--LHRSPGIHFDHDKGRA 172
            K                         G F+I G +R+V+SQ  L     I+   DK   
Sbjct: 137 VKSKKCNLTRLKPEEYPKRFEDPEDPGGYFIINGSERVVISQEDLVTDRPIYDVGDKP-- 194

Query: 173 SLSGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEE 227
                + Y  ++I      +   M +E+    +I+V +     ++P T ++ A+G++S++
Sbjct: 195 ----TIRYLAKVISTGPGYR-ATMTVEYHKDGVIYVTLSAIPVRIPFTVYMRAMGLESDQ 249

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS---SLVDIDTGEQVIESGKKLTSGL 284
                   IV +   D          L+ G ++++     +D   G+  +   + +    
Sbjct: 250 -------DIVLAVSDDPDIQKELLPSLLAGQEIAATRDDALDFVGGKIAVGQPRPIRIER 302

Query: 285 L--------------KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
                          +   EK ++   I    L G  V + ++  + G    +  D +  
Sbjct: 303 ALQILDKYFLPNLNPQKPDEKAMEEARIKKALLLGQ-VVKGLIEMQLGRRKPDDKDHVAN 361

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
           K +  +     +    +    +     ++N L     + +   L  I R     D+ T  
Sbjct: 362 KRVRLVNDLLAQLFRTVMKQFLQE---LKNQLEKYYARGKIPHLQTIVRP----DIITER 414

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
           V +++    +          + R      L+      V  + +       + L   + G+
Sbjct: 415 VKQALATGNWVGGKTGVSQILDRTNYLSTLSYLRRV-VSSLSRTQPHFEARDLHPTQWGR 473

Query: 451 -GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              ++  +      V+++  + +    +    +E+++         +  +   L   +  
Sbjct: 474 LCAVETPEGQNVGLVKNLALLAEITIGVDEAVVEKTL--------NELGVVPVLEARRGG 525

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
           +     +     +   +     +  +   RR   +            +   V+       
Sbjct: 526 LEGAEVYLNGRLIGIHQNPEELVKTLRKMRRQGKISDE--VNVAHLGDAVYVNCDGGRIR 583

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            P    E   + L               + +      D      V YL A EEEN YIA 
Sbjct: 584 RPLLVIEDGKLKLTKEHVQ--------KLASGELTWNDLVKMGVVEYLDADEEENAYIAV 635

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
                                         K   ++  P  ++   AS+IP+LE++ S R
Sbjct: 636 GPEP-----------------------DMSKYTHMEIVPSSILGAIASIIPYLEHNQSPR 672

Query: 690 VLMGCNMQRQAVPLLKAEAPF 710
                 M +Q++ L +A   +
Sbjct: 673 NQYEAAMAKQSLGLPQANFMY 693


>gi|295658889|ref|XP_002790004.1| DNA-directed RNA polymerase III subunit RPC2 [Paracoccidioides
            brasiliensis Pb01]
 gi|226282087|gb|EEH37653.1| DNA-directed RNA polymerase III subunit RPC2 [Paracoccidioides
            brasiliensis Pb01]
          Length = 1205

 Score =  261 bits (666), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 164/1122 (14%), Positives = 331/1122 (29%), Gaps = 225/1122 (20%)

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            + K   ++ +  + +   +   +        I ++A  +  +K +  +       +  + 
Sbjct: 270  ERKSKSYIILKKERIYVRHNVLNEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 320

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + A      V      +  AL  I   ++             F  +  +  +  +
Sbjct: 321  STYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRKPNN------FGVIRRNYVQEAI 374

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 375  EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 431

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQ 521
            ++L   +     + +  IK  I  V    V  +          +   +   +     +  
Sbjct: 432  QLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNRAISTGN 491

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAE 573
             S     +          RLS +   G+         + R     R + P+ +G +CP++
Sbjct: 492  WSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPSQFGMLCPSD 551

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQAN 631
            T EG   GLV +L     +      E P RK+       DV  +   E   +  YI   N
Sbjct: 552  TPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGRELHGQGTYIVFLN 610

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDS 687
             S        +  +             E I       ++ V IA        P +  +D 
Sbjct: 611  GSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRAVHIATDDGRICRPLIIVEDG 670

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               +   ++                  ME     + G           E +D       +
Sbjct: 671  KSRVQARHL-----------RALRSGSMEFDDFLAHGLV---------EYLDCNEENDSN 710

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +                                 V   D V     +   P T LG +A 
Sbjct: 711  I--------------------------------AVYENDIVDSTTHLEIEPFTILGAVA- 737

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                    +P+  +N          M  + +                             
Sbjct: 738  ------GLIPYPHHNQSPRNTYQCAMGKQAIGA--------------------------- 764

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                  + +    ++          +    I       +   +    A+      D+ D 
Sbjct: 765  --IANNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDRLPAGQAATVAVMSYSGYDIEDA 822

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +     +       ++F R      +   +  +++++   R         +  +  R  
Sbjct: 823  LVLNKGSIDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------ENGLPVRKH 872

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +L      +  +   +  V  + +  E   S        D             Y  S  
Sbjct: 873  ALLDNDGLAAVGEKVNQGEVYINKVTPENALSS--GITGSDAGRPIT-------YIPSPQ 923

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              +    + I+K+           +++KV     R  + GDK +                
Sbjct: 924  TYKLPDPSYIDKVMISS--TEAENQLIKVQTRQTRRPEVGDKFS---------------- 965

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
                                 SR                  G+K    I   +A+   S 
Sbjct: 966  ---------------------SR-----------------HGQKGVVGIIAEQADMPFSD 987

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            L    + ++       +++      ++       SG       F G+  E ++++L    
Sbjct: 988  LGIVPDIIMNPHGFPSRMTVGKMLELVAGKAGILSGQFSYGTAFGGSPVEEMSAILVKHG 1047

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+  L  G+TGE     V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S
Sbjct: 1048 FSYGGKDCLTSGITGESLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRS 1107

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYES 1331
              GG RLGEME  C+ AYG + +L E L I SD    DV              R +    
Sbjct: 1108 RDGGLRLGEMERDCLIAYGTSQLLLERLMISSDQYEVDVCESCGFMGYSGWCQRCKSSRG 1167

Query: 1332 IVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            +V          P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1168 VVK------MIIPYAAKLLVQELFSMNVVARLKLADEFPEDR 1203



 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/739 (11%), Positives = 200/739 (27%), Gaps = 118/739 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 94  LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGTPRRAD 144

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 145 EEQDSNFNAASTITPNECRLRDMTYASPILVDFEYV----------RGRQRVKRNGTAIG 194

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 195 RMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 254

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             K+ I+VR +     VP+   L A
Sbjct: 255 LKKEIVQASVTSSSNERKSKSYII-----------LKKERIYVRHNVLNEDVPIVILLKA 303

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      I  + + DF      A  L +     +   +          +   
Sbjct: 304 MGIQSDKEMLLLVAGIDSTYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRKPNNFG 363

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +          + +  + I+   +  L                 A         +     
Sbjct: 364 VIRRNYVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMARRVLMAKHDPSL 415

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +           +         K + D  ++I +V++    +    A  +    
Sbjct: 416 VDDRDYVGNKRLELAGQLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIH 475

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDD 455
                +     +     +++        V H    +     + ++  +         +  
Sbjct: 476 GNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 535

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
              L   +   +      +     L    ++   I++ D +  + + +            
Sbjct: 536 PRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLIFALGAEDVQTVG 595

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAET 574
                        +N        R    L     + R     E   V   H+ R     T
Sbjct: 596 GRELHGQGTYIVFLNGSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRAVHIAT 655

Query: 575 SEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            +G     +  +       +      + +   +  D      V YL   EE +  IA   
Sbjct: 656 DDGRICRPLIIVEDGKSRVQARHLRALRSGSMEFDDFLAHGLVEYLDCNEENDSNIAVYE 715

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + +                        +    ++  P  ++   A LIP+  ++ S R  
Sbjct: 716 NDI-----------------------VDSTTHLEIEPFTILGAVAGLIPYPHHNQSPRNT 752

Query: 692 MGCNMQRQAVPLLKAEAPF 710
             C M +QA+  +      
Sbjct: 753 YQCAMGKQAIGAIANNQFL 771


>gi|52699857|gb|AAU86990.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 714

 Score =  261 bits (666), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 118/835 (14%), Positives = 236/835 (28%), Gaps = 145/835 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + +  +              + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIXDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                D   +     N+   ++ +  L+ +               S     AK  G    V
Sbjct: 237  XFVXDXDPKSTNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV 288

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q               V+ +       
Sbjct: 289  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKASMNPTAHT 346

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M  + +   + +  ++         
Sbjct: 347  WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM------ 398

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                   +  +             +       +   +  + AI 
Sbjct: 399  ---------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 437

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 438  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 493

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  ++ D      R++          ++  
Sbjct: 494  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRST 553

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             L+ VKV +   +  Q GDK A RH
Sbjct: 554  ENGIXDQVLL--------------------TTXAEGLKFVKVRMRTTKIPQIGDKFASRH 593

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 594  GQKGTIGITYRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 653

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 654  TPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------ 681

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 682  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 714


>gi|113707353|gb|ABI36584.1| RNA polymerase II second largest subunit [Icmadophila ericetorum]
          Length = 708

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 116/812 (14%), Positives = 232/812 (28%), Gaps = 126/812 (15%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            ++   +R    ++ + + +  +              + +  + + +     +        
Sbjct: 1    LMAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYSLATGNWGEQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     V      E    +    + ++  +   L +      ++     
Sbjct: 117  PEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRV 690
             +  D +     V        I      + D  D   K          P F+ ++D+   
Sbjct: 177  GVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDAKSP 236

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              G  +  + +     +   +   M+            AK  G    +   R V+  ++ 
Sbjct: 237  NKGSLVLTKELVQRLEDDKDLPADMDPDEKA-------AKTMGWDGLI--KRGVVEYLDA 287

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGR 809
            + + +   V     +   R  Q               V+          T      ++  
Sbjct: 288  EEEETVMIVMTPEDLDISRQLQAGYQLPETTDDPNKRVKAPLNPTAHTWTHCEIHPSMIL 347

Query: 810  NMLVAFMPWHGYNFE--DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
             +  + +P+  +N      +L  E ++                         E   +  N
Sbjct: 348  GVCASIIPFPDHNQVSITKVLNLEMLIRNSXXXXXXXXXXXXXXXIFLTNFSERMDNAFN 407

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                            +             +       +   +  + AI      +  D+
Sbjct: 408  ----------------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 451

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    ++ R   D+ +R      EQ E   R    +      +      
Sbjct: 452  VIMNQSSIDRGLF-RSLYYRTYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDG 510

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++      +   ++     L         
Sbjct: 511  LVAPGVRVSGEDIIIGKTEPIAPDSEELGQRTKLHVKRDKSTPLRTTENGL--------- 561

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                     I+K+          LR VK+     +  Q GDK A RHG KG +      E
Sbjct: 562  ---------IDKVML--STNAEGLRFVKIRTRTTKIPQIGDKFASRHGQKGTIGITYRQE 610

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 611  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD-------------- 656

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 657  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 676

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                G  ++Y+G TG      V +G  Y  +L
Sbjct: 677  YQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRL 708



 Score = 97.5 bits (241), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 72/539 (13%), Positives = 155/539 (28%), Gaps = 83/539 (15%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R+GK       +  +  +
Sbjct: 51  ATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 110

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEF 516
               E  + Q    +  +       + S     +      N + +         +A   F
Sbjct: 111 VCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVF 170

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                +    +  + +S +   RR   +             +RD+      R     T  
Sbjct: 171 VNGVWVGVHRDPAHLVSTVMSLRRRGLIS-------HEVSLVRDIR----DREFKIFTDA 219

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G     +  + + A+    G +      V       D   L A  +              
Sbjct: 220 GRVCRPLFVIDNDAKSPNKGSLVLTKELVQR---LEDDKDLPADMD-------------- 262

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                +E        +  L+ R  ++++DA  ++ V I    +   E+ D +R L     
Sbjct: 263 ----PDEKAAKTMGWD-GLIKRGVVEYLDAEEEETVMI----VMTPEDLDISRQLQAGYQ 313

Query: 697 QRQA--VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI--------- 745
             +    P  + +AP   T       +   + I+   A I+   D  ++ I         
Sbjct: 314 LPETTDDPNKRVKAPLNPTAHTWTHCEIHPSMILGVCASIIPFPDHNQVSITKVLNLEML 373

Query: 746 -------RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                                      +   +       Q+PL                 
Sbjct: 374 IRNSXXXXXXXXXXXXXXXIFLTNFSERMDNAFNILYYPQKPL----------ATTRSME 423

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA   + GYN EDS+++++  +   +F S++   +    +   +  
Sbjct: 424 FLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSV 483

Query: 859 EE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            E     +  D   +       +D+ G++  G  V+  DI++GK  P         ++ 
Sbjct: 484 VEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTEPIAPDSEELGQRT 542


>gi|52699847|gb|AAU86985.1| DNA-dependent RNA polymerase II second largest subunit [Pertusaria
            amara]
          Length = 716

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 127/835 (15%), Positives = 241/835 (28%), Gaps = 141/835 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++   +R    ++ R + +  +              + +  + + + 
Sbjct: 1    DHXGKKRLDLAGPLMAGLFRNLFKKLTRDVFKYLQKCVETNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+    V      E    +    + ++  +   +++
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMCCVTVGSPSEPIINFMIQRNMEILEEYEPMNS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PHATKIFVNGVWVGVHRDAASLVSNVIQLRRRGVIEPEVSMVRDIRDREFKIFTDAGRVQ 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D      G  +  + +     +   +   M+    +       AK  G    
Sbjct: 237  RPLFVVDNDVKSSNKGSLVLTKELVSRLEDDKELPDDMDPDEKE-------AKMLGWKGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            V   R V+  ++ + + +   V     ++  R  Q       P  +    V+        
Sbjct: 290  V--ERGVVEYLDAEEEETVMIVMTPEDLEISRQIQAGYQMPEPTDEPNKRVKAPLNRTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +                  
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGV---------------- 391

Query: 857  GPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                            L N DE    +  +             +       +   +  + 
Sbjct: 392  ---------------FLTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIV 436

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   D+ +R      EQ E   R    +
Sbjct: 437  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLK 495

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +       I  G           K+  ++ D      R++              
Sbjct: 496  LKHGTYDKLDEDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL------------- 542

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +K    T     E+   +K+             LR VKV     +  Q GDK A RH
Sbjct: 543  --HVKRDVSTPLRSTENGIVDKVLL-----TTNAEGLRFVKVRTRTTKVPQIGDKFASRH 595

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 596  GQKGTIGITYRMEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 655

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 656  TPFTEVTVDSVSRLLR--EHGYQSRGFEVM------------------------------ 683

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 684  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 716


>gi|258562140|gb|ACV81792.1| RNA polymerase II second largest subunit [Ramaria stricta]
          Length = 679

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 113/759 (14%), Positives = 219/759 (28%), Gaps = 132/759 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 50   GVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 105

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++           + +  +  + +  +A           N         
Sbjct: 106  GLVKNLALMACISVGSASPPVIEFLEEWGL--ETLEENAHSTTPCTKVFVNGVWLGVHRD 163

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSI---AASLIPFLENDDSNRVLMGCNMQ 697
               LV              ++  +    +Q + +   A  +   L   ++ ++++     
Sbjct: 164  PANLVKTLKKLRRKADIPAEVSIVRDIREQELRVYTDAGRVCRPLFVVENQQLVLQKKHI 223

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            +      + + P        +    SG         I+E +DA       +    +   +
Sbjct: 224  KWLQQGYRDDDPAQAP-YRWITMVKSG---------IIELLDAEEEETVMISMTPEDLET 273

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                 +    + +  ++  +    +K              PS  LG       +  + +P
Sbjct: 274  SRL--QQQGMESAVNDSEFDPAARLKAVMHAHTWTHCEIHPSMILG-------ICASIIP 324

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N                        ++       +G       +            
Sbjct: 325  FPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM---------- 356

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  + AI      +  D+ +   S +  
Sbjct: 357  -DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 415

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +    ++ R  +D  + S   + E+     RD          +       I  G     
Sbjct: 416  GLF-RSMYYRSYMDMEKTSGIHQLEEFSKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRG 474

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  +  +                +E  Q+     +    T     E    +++
Sbjct: 475  EDIIIGKTAPIPPE---------------SEELGQKTSNHTRRDVSTPLKSTESGIVDQV 519

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                  D       R VKV V   R  Q+GDK A RHG KG +      EDMPF  +G  
Sbjct: 520  LITTNSD-----GHRFVKVRVRSTRIPQTGDKFASRHGQKGTIGITYRQEDMPFTVEGIT 574

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             DI++NP  +PSRM +G + E  L      +G +  +          +S L    ++   
Sbjct: 575  PDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTELTVESVSTLLR--KQGYH 632

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
            +                                                     G +   
Sbjct: 633  SRGLEVM---------------------------------------------YHGHT--- 644

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
             G         V +G  Y  +L HMV DK+++R+ G   
Sbjct: 645  -GR---KLQAQVYLGPTYYQRLKHMVDDKIHSRARGPVQ 679



 Score =  122 bits (306), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 87/593 (14%), Positives = 170/593 (28%), Gaps = 114/593 (19%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F++  ++      +  KY L   G      +         + + +    + +  L   
Sbjct: 12  KEFNLNLAVKPNTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRC 70

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +       + S     +   
Sbjct: 71  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSASPPVIEFL 130

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA         F     L    +  N +  +   RR + +    V+  R 
Sbjct: 131 EEWGLETLEENAHSTTPCTKVFVNGVWLGVHRDPANLVKTLKKLRRKADI-PAEVSIVRD 189

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR---------KV 605
             E      T  GR+C         + +V +     +     +++  YR         + 
Sbjct: 190 IREQELRVYTDAGRVC-------RPLFVVENQQLVLQKKHIKWLQQGYRDDDPAQAPYRW 242

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPR 658
                +  +  L A EEE   I+     L+      + +       E          +  
Sbjct: 243 ITMVKSGIIELLDAEEEETVMISMTPEDLETSRLQQQGMESAVNDSEFDPAARLKAVMHA 302

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                 +  P  ++ I AS+IPF +++ S R      M +QA+ +               
Sbjct: 303 HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV-------- 354

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                                               + + +  Y       +     +  
Sbjct: 355 ---------------------------------RMDTMANILYYPQKPLATTRSMEYLKF 381

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           R                        +L  G+N +VA + + GYN EDS+++++  +   +
Sbjct: 382 R------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 417

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           F S++   +  M + + +   E            +       +++ G+I  G  V   DI
Sbjct: 418 FRSMYYRSYMDMEKTSGIHQLEEFSKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDI 477

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           ++GK  P       PE + L           RD S  + S  SG V  V I  
Sbjct: 478 IIGKTAPI-----PPESEELGQ--KTSNHTRRDVSTPLKSTESGIVDQVLITT 523


>gi|56418253|gb|AAV91067.1| DNA-directed RNA polymerase [Grouper iridovirus]
          Length = 1103

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 87/339 (25%), Positives = 141/339 (41%), Gaps = 71/339 (20%)

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             ++      +    E+ + +KI +     D+ P   ++VKV +   R  + GDK A    
Sbjct: 824  TTVCKDISLTVKASEEGYLDKIVQ-----DVDPDGRKIVKVRLRTPRIPEMGDKFASFTA 878

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG    +   EDMPF KDG   D+++NP   PSRM V  + +   G A   LGK+    
Sbjct: 879  QKGTCGAVKSQEDMPFDKDGVVPDLIINPHAFPSRMTVNYLLQMCFGLAGCKLGKRYD-- 936

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +T  F+ AD
Sbjct: 937  ---------------------------------------------------AT-AFERAD 944

Query: 1216 -EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              + I    + A ++    S++Y G+TG  F   + +      +L HMVS K+++R +G 
Sbjct: 945  IVKDIADAAKEAGIEHW-DSVMYSGITGRRFPAKIFMAPCPYQRLRHMVSGKIHSRVSGP 1003

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD-------VVGRTR 1327
               +T+QP+ G+S  GG ++GEME WC  ++GA+  L+E +   SD          GR  
Sbjct: 1004 VDALTRQPVAGRSRDGGIKIGEMEQWCKISHGASESLKESMFDTSDKYSVPVCQTCGRIS 1063

Query: 1328 ---VYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                Y  +    D   T  P +  +L +E++A+G+SI  
Sbjct: 1064 DHFEYCRLCDAVDIRLTYLPYTTKLLFQELKAIGISITF 1102



 Score = 92.8 bits (229), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 88/597 (14%), Positives = 190/597 (31%), Gaps = 74/597 (12%)

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             +    +    ++D    +    +++  I   ++       +DAL ++ + +       
Sbjct: 206 TAEEAVALCGLGVKDGD-SFSCHTSSHQTIAALIIEQYANCPEDALQELAKYV------- 257

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                             D     +  +N  L L       H+       ++K L     
Sbjct: 258 -----------PDTKKSSDKREYVKTVLNRELFLHGGHGASHLGW-----MVKKLAQTAA 301

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
           G     D D++ N+RV + G ++       L +  + +  + +    +      L N++ 
Sbjct: 302 GISKPLDRDDIANKRVDTTGHLIMFLLDGLLKQYVK-LFLKSAECQKNLCPYTVLQNSQV 360

Query: 509 VVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           + +++   F +                 +SQ+  + N  ++++H RR+       V+   
Sbjct: 361 ITNSLHLCFATGNWTVKRIGPPSYVRVGVSQILSNNNFGAKLSHLRRI----MHAVSFKG 416

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD------ 607
             ++MR +H +HYG +CP ET EG  +G+V ++   A V+ Y   E     +        
Sbjct: 417 KNIKMRQLHTSHYGFLCPYETPEGERVGIVLNMAESAAVSDYTPREEITAILDRTGGMPG 476

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
            + T ++ +L+    +       +  L    +   E V        I +P +     D  
Sbjct: 477 YEKTAELSHLAWSSSDTFSAVVVDGRLAGFTTEPREFVKEAK----IRLPAQVGVCWDKI 532

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF--VGTGMESVVAKSSGA 725
             ++  +           D  R+                      VG   E      +  
Sbjct: 533 EDEIHLLGCEGRFMRRMLDPARLRGEPIEIEPLSLSETRTVTAPSVGRLEEHKTQNLAKY 592

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNTCVNQR---PL 781
             +  +      V    +   + E   D  ++ +  Y      + + Q+    Q    P 
Sbjct: 593 VYLCIQEINCGTVGKDYLDPPASEILTDVMSAVIPFYDHTQSPRNAYQSNMGKQAIGFPA 652

Query: 782 VKVGDEVRRNDIIADGPST-----------DLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           +   D         D P +           +   +A G   +VA M   G+N EDS++++
Sbjct: 653 INCEDRYDATLHRLDYPQSALTESRAIERVNFDTMAHGALPVVAIMTAEGFNQEDSIVLN 712

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNIDECGIICV 884
              +   +F+ +    F    +       E            +     +DE G+I  
Sbjct: 713 ASSLDRGLFSCVTYRTFAANDKRRSKYDSEQICLPEYGNRNKDWDYTLLDENGVISP 769



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 76/243 (31%), Gaps = 81/243 (33%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L+     SY+  L  +        +          PI       +++F S  ++ P    
Sbjct: 4   LVAHHLDSYESMLWRDFPNLIAREK----------PI--NVKGYIIKFESLYYEMPVKEA 51

Query: 85  ---KF-DVDDCLWRDLTYAVP----LKIT--------------LRLIVFDVDEFTGAKSI 122
              K+        +DLTY       L +                +L V         +  
Sbjct: 52  DPTKYLTPAIARRQDLTYQAAACCVLNVVDPHGRETTYPRLELCKLPVMVGSSLCWTRQK 111

Query: 123 KDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
           +D+K      G+ PL    G F+IKG +R+++      P I   +D              
Sbjct: 112 QDMK------GECPL-DPGGYFIIKGKERVII------PHIRPAYDHPVVHEQEGP---- 154

Query: 183 RIIPDQGLWMDIEFDSKD-------IIHVRIDRRRKV-----------PVTSFLMALGMD 224
                   W+  EF S +       ++  R D RR +           PV +   ALG  
Sbjct: 155 -------SWL-CEFRSVNPLTQQSVLVQARTDCRRSLEFSLPYIKQYVPVGTTFKALGKT 206

Query: 225 SEE 227
           +EE
Sbjct: 207 AEE 209


>gi|52699831|gb|AAU86977.1| DNA-dependent RNA polymerase II second largest subunit [Leptogium
            cyanescens]
          Length = 713

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 126/832 (15%), Positives = 242/832 (29%), Gaps = 144/832 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ R + +  +              I +  + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFNKLTRDVYKYLQKCVETNREFNLTLGIKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   L +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D       V        I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPVHLVSTVQTLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D      G  +  +   L   E   +G  M+    +       AK  G    V   +
Sbjct: 238  IENDPKSPNRGNLVLTKEHILRLEEDKELGPDMDPDERE-------AKFMGWEGLV--NQ 288

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADGPSTD 801
             V+  V+ + + +   V     ++  ++ Q     + P +      V+          T 
Sbjct: 289  GVVEYVDAEEEETVMIVMTPEDLEISKNVQMGYAVEEPSIDDPNRRVKAPVNPTAHTWTH 348

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N          M  + +   + +  +E            
Sbjct: 349  CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYEQRM--------- 397

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 398  ------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRTDTLKLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K+  LS+D      R++          ++     
Sbjct: 496  GTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLSADNEELGQRTKMHVKRDVSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGVTYRQEDMPFTSEGQVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPF 655

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 656  TEVTVDSVSRLLR--EHGYQSRGFEVM--------------------------------- 680

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                         +G +    G         + +G  Y  +L HMV DK+ A
Sbjct: 681  ------------YNGHT----GR---KLVAQIFLGPTYYQRLRHMVDDKIXA 713


>gi|86161676|gb|ABC86973.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 284

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 202/284 (71%), Positives = 236/284 (83%), Gaps = 1/284 (0%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           SGAAI AKR+GIV+QVDA RIVIR+ E  LDPS SGVD   + K
Sbjct: 241 SGAAIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDTLIVYK 283


>gi|261194511|ref|XP_002623660.1| DNA-directed RNA polymerase III polypeptide [Ajellomyces dermatitidis
            SLH14081]
 gi|239588198|gb|EEQ70841.1| DNA-directed RNA polymerase III polypeptide [Ajellomyces dermatitidis
            SLH14081]
          Length = 1204

 Score =  260 bits (665), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 170/1129 (15%), Positives = 345/1129 (30%), Gaps = 207/1129 (18%)

Query: 288  LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            L ++ +    +  +      + +  V   + E   ++  ++ +  +    +    D+PI+
Sbjct: 238  LVQEQLSKNRVIVETDLKKEIVQASVTSSSNERKSKSYIIMKKDRIYMRHNVLNEDVPIV 297

Query: 348  ----------YVDSVNNNAYIRNTLVTDKNKDRKDAL-LDIYRVMRPGDVSTFSVAESMF 396
                        + +   A I +T   D + + ++A+ L IY   +  +     +  +  
Sbjct: 298  ILLKAMGIQSDKEMLLLVAGIDSTYQEDFSINFEEAVKLGIYTQHQALEYIGSRIKINRK 357

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLRNGKGTIDD 455
               F  + +  +        ++ ++    +++    K   +A + + ++  ++    +DD
Sbjct: 358  PNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKALYVAHMARRVLMAKHDPSLVDD 417

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKP 508
             D +GN+R+   G++L   +     + +  IK  I  V    V  +          +   
Sbjct: 418  RDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNH 477

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRD 560
            +   +     +   S     +          RLS +   G+         + R     R 
Sbjct: 478  ITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRA 537

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            + P+ +G +CP++T EG   GLV +L     +      E P RK+       DV  +   
Sbjct: 538  LQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGR 596

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            E       Q    +  +GS        R     +   R        S    V I      
Sbjct: 597  ELHG----QGAYIIFLNGSPIA---LTRRPKFFLNSFRRLRRTGRVSEFISVFIN----- 644

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
               + ++  +        + + +++     V       +   S         G+VE +D 
Sbjct: 645  --HHQNAVHIATDDGRICRPLIVVEDGKSKVTKSHLWALRSGSMEFDDFLAHGLVEYLDC 702

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +                                 V   D       +   P T
Sbjct: 703  NEENDSYI--------------------------------AVYEEDITDSTTHLEIEPFT 730

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG +A         +P+  +N          M  + +                      
Sbjct: 731  ILGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------------------- 763

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                         + +    ++          +    I       +   +    A+    
Sbjct: 764  ---------IANNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDKLPAGQSATVAVMSYS 814

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              D+ D  +   S V       ++F R      +   +  +++++   R         + 
Sbjct: 815  GYDIEDALVLNKSSVDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------EN 864

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +  R   +L      +  +   +  V  + +  E   S        D            
Sbjct: 865  GLPIRKHALLDSDGLAAVGEKVNQGEVYINKVTPENALSS--GITGSDAGRPIA------ 916

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             Y  S    +    + I+K+           +++KV     R  + GDK +         
Sbjct: 917  -YIPSPQTYKLPDPSYIDKVMI--SATEAENQLIKVQTRQTRVPEVGDKFS--------- 964

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                                        SR                  G+K    I    
Sbjct: 965  ----------------------------SR-----------------HGQKGVVGIIAEY 979

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            A+   S L    + ++       +++      ++       SG       F G+  E ++
Sbjct: 980  ADMPFSDLGIVPDIIMNPHGFPSRMTVGKMLELIAGKAGILSGQFGYGTAFGGSPVEEMS 1039

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            ++L        G+  L  G+TGEP    V +G IY  KL HMV DK+++R+ G  +++T+
Sbjct: 1040 AILVDHGFSYGGKDYLTSGITGEPLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTR 1099

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VG 1324
            QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV              
Sbjct: 1100 QPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCESCGFMGYLGWCQ 1159

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            R +    +V          P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1160 RCKTSRGVVK------MVIPYAAKLLVQELFSMNVVARLKLADEFPEER 1202



 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 88/739 (11%), Positives = 200/739 (27%), Gaps = 118/739 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 93  LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGNPRRAD 143

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 144 EEQDSKFDVASTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 193

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 194 RMPVMLRSSKCVLSNKSEAEMQLLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 253

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             KD I++R +     VP+   L A
Sbjct: 254 LKKEIVQASVTSSSNERKSKSYII-----------MKKDRIYMRHNVLNEDVPIVILLKA 302

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      I  + + DF      A  L +     +   +          +   
Sbjct: 303 MGIQSDKEMLLLVAGIDSTYQEDFSINFEEAVKLGIYTQHQALEYIGSRIKINRKPNSFG 362

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +T         + +  + I+   +  L                 A         +     
Sbjct: 363 ITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMARRVLMAKHDPSL 414

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +           +         K + D  ++I +V++    +    A  +    
Sbjct: 415 VDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIH 474

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDD 455
                +     +     +++        V H    +     + ++  +         +  
Sbjct: 475 GNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 534

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
              L   +   +      +     L    ++   I++ D +  + + +            
Sbjct: 535 PRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLIFALGAEDVQTVG 594

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAET 574
                        +N        R    L     + R     E   V   H+       T
Sbjct: 595 GRELHGQGAYIIFLNGSPIALTRRPKFFLNSFRRLRRTGRVSEFISVFINHHQNAVHIAT 654

Query: 575 SEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            +G     +  +         +    + +   +  D      V YL   EE + YIA   
Sbjct: 655 DDGRICRPLIVVEDGKSKVTKSHLWALRSGSMEFDDFLAHGLVEYLDCNEENDSYIAVYE 714

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +                        +    ++  P  ++   A LIP+  ++ S R  
Sbjct: 715 EDIT-----------------------DSTTHLEIEPFTILGAVAGLIPYPHHNQSPRNT 751

Query: 692 MGCNMQRQAVPLLKAEAPF 710
             C M +QA+  +      
Sbjct: 752 YQCAMGKQAIGAIANNQFL 770


>gi|298912929|emb|CAZ66632.1| RNA polymerase beta subunit [Grimontia hollisae]
          Length = 289

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 171/289 (59%), Positives = 222/289 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF  D+YDLS VGR+K N  L  +       +  +DII +++ L+D+RNG G +
Sbjct: 1   QLFESLFFSEDRYDLSAVGRMKFNSSLGREEMTGSGVLSHDDIIEVMRKLIDIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYRKV DGKVT+++ YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARTNPYGFLETPYRKVVDGKVTDEIDYLSAIEEGQFVIAQANAV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L+EDGSF +EL+  R  GE  L PR+ + ++D +  QVVS+AASLIPFL
Sbjct: 241 LNEDGSFADELITARQKGESGLHPRDHVQYMDVATNQVVSVAASLIPFL 289


>gi|70794970|gb|AAZ08459.1| RNA polymerase II second largest subunit [Astilbe sp. Yoshikawa s.n.]
          Length = 951

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 154/967 (15%), Positives = 283/967 (29%), Gaps = 190/967 (19%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +    V+     ++   G V D+  LE I +       +  +      A++         
Sbjct: 160  LPYIRVDIPIIIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQV--- 216

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
                 AL  I +              S          KY    + +  +      +  + 
Sbjct: 217  -----ALDYIGKR------------GSTVGVTREKRIKYAREILQKEMLPHVGMAEYCET 259

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +         II  L+ +  G+   DD D+ GN+R+   G +L   +R+   ++ R ++
Sbjct: 260  KK---AYYFGYIIHRLLLVALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVR 316

Query: 488  --ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLS 533
               +    +   V  Q  I AK + S +     +              +SQ+   +   S
Sbjct: 317  GYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYAS 376

Query: 534  RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
             ++H RRL++     + R     + R +H + +G +CPAET EG   GLV +L     + 
Sbjct: 377  TLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 432

Query: 594  AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
                       + +    N        EE +  +    + +  +G +       R     
Sbjct: 433  VGSAAYPILEFLEEWGTEN-------FEEISPAVIPEATKIFVNGCWVG---IHRDPDML 482

Query: 654  ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
            +   R     +D + +  V     L       D  R      +  +   L+         
Sbjct: 483  VKTLRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLI--------- 533

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                   K   A    +        D   +  I  V+ + + +T        +   R N 
Sbjct: 534  -----KKKDIQALQQRETPEDGGWHDLVAKGFIEYVDTEEEETTMISMTINDLVSARLNP 588

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                +                    PS  LG       +  + +P+  +N          
Sbjct: 589  EEAYS-----------EYYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSA 630

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            M  + +     I       R   L         P V+   ++++                
Sbjct: 631  MGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL---------------- 670

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                         +      + AI      +  D+ +   S +        +F R   D+
Sbjct: 671  ---------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDE 720

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
             ++  ++ +E      R+          +          G           K++ ++   
Sbjct: 721  EKKMGTLVKEDFGRPNRNDTMNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQ-- 778

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                           DE   +     K  + TS    E    +++      D +     R
Sbjct: 779  ---------------DESQGQASRYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----R 818

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM 
Sbjct: 819  FVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMT 878

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E  +G     +GK+                                         
Sbjct: 879  IGQLIECIMGKVAAHMGKEGD--------------------------------------- 899

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                          +TP F     + I+  L        G   +Y+G TG      + +G
Sbjct: 900  --------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLG 944

Query: 1253 YIYMLKL 1259
              Y  +L
Sbjct: 945  PTYYQRL 951



 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 123/912 (13%), Positives = 262/912 (28%), Gaps = 173/912 (18%)

Query: 88  VDDCLWRDLTYAVPLKITL--RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD---- 141
                 R+LTY+ PL + +  R+I    D     ++    K   +++G +P+M +     
Sbjct: 7   PKAARLRNLTYSAPLYVDVSKRVIKKGHDGEEVTETQDFTK---VFIGKVPIMLRSSYCT 63

Query: 142 --------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLY 180
                               G F+I G ++++++Q   S   ++      +     K  Y
Sbjct: 64  LFQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAY 119

Query: 181 ACRIIPDQGL----------WMDIEFDSKD----------IIHVRIDRRRKVPVTSFLMA 220
              +                 M     +K           + ++R+D    +P+     A
Sbjct: 120 VAEVRSMAESQNRPPSTMFVRMLARTSAKGGSSGQYIRATLPYIRVD----IPIIIVFRA 175

Query: 221 LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG  ++ +IL         +Q  +     L  A ++   +V+   +        +   K+
Sbjct: 176 LGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKR 235

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +     + + +K +      ++                  + + A     E   +   + 
Sbjct: 236 I--KYAREILQKEMLPHVGMAEYCETKKAYYFGYIIHR--LLLVALGRRAEDDRDHYGNK 291

Query: 340 EIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            +    P+L          +   +     K   +      +        T  +  S+   
Sbjct: 292 RLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATG 351

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDID 457
            +  ++           +N      T   +R +         +     L N +  +    
Sbjct: 352 NWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPA 411

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                +      ++KN   +  + +  +    +  ++       + I+   +  A   F 
Sbjct: 412 ETPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPEATKIFV 468

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSE 576
               +    +    +  +   RR   +  + GV R     E+R ++  +     P    E
Sbjct: 469 NGCWVGIHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVE 527

Query: 577 GH----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                     + +L         G+         D      + Y+   EEE   I+    
Sbjct: 528 KQRLLIKKKDIQALQQRETPEDGGW--------HDLVAKGFIEYVDTEEEETTMISM--- 576

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                     +LV  R   E      E     +  P  ++ + AS+IPF +++ S R   
Sbjct: 577 -------TINDLVSARLNPE--EAYSEYYTHCEIHPSLILGVCASIIPFPDHNQSPRNTY 627

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              M +QA+ +      F                    R   +  V              
Sbjct: 628 QSAMGKQAMGIYVTNYQF--------------------RMDTLAYV-------------- 653

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    Q+PLV                      L  G N +
Sbjct: 654 ---------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAI 682

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPN 867
           VA   + GYN EDS+++++  +    F S+    +    +      +E        D  N
Sbjct: 683 VAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRNDTMN 742

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK +P  +           +         RD 
Sbjct: 743 MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDE---------SQGQASRYTKRDH 793

Query: 928 SLRVPSGVSGTV 939
           S  +    +G V
Sbjct: 794 STSLRHSETGMV 805


>gi|117675885|emb|CAL69213.1| RNA polymerase subunit B [Rathayibacter festucae]
          Length = 424

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 171/394 (43%), Positives = 241/394 (61%), Gaps = 34/394 (8%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I      G+ +        T  ++++A  +  E+ LE+   +    I +        
Sbjct: 48  EFEIDKRDQVGVRIDRKRKQSVT--VFLKALGLTSEEILEQF--AGYESIEL-------- 95

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                 TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR 
Sbjct: 96  ------TLEKDNILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRY 149

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNL 459
           K+N +L +D       +  EDIIA IK LV L +G+                 +DDID+ 
Sbjct: 150 KINRKLGIDKALSDSVLTVEDIIATIKYLVALHDGRTNLPGVRDGAAVDLRLDVDDIDHF 209

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 210 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 269

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 270 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 329

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL+ SL SFAR+N++GFIETPYRKV DG VT  + YL+A EE+   +AQAN+ L  D  
Sbjct: 330 IGLIGSLASFARINSFGFIETPYRKVVDGVVTAQIDYLTASEEDEYLVAQANAPLTSDMR 389

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVV 672
           F E  V  R   GE  LV  E++ ++D SP+Q+V
Sbjct: 390 FAEGKVLVRPKGGEVELVDAERVHYMDVSPRQMV 423



 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 57/161 (35%), Positives = 84/161 (52%), Gaps = 6/161 (3%)

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           FVI G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W++ E D +D + 
Sbjct: 1   FVINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAWLEFEIDKRDQVG 58

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D       A   +      
Sbjct: 59  VRIDRKRKQSVTVFLKALGLTSEEILEQFAGYESIELTLEKDNILTKEDALRDIYRKLRP 118

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              V  +    ++++    +    L K  + K  + LGI  
Sbjct: 119 GEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIDK 159


>gi|66356143|gb|AAY45706.1| RNA polymerase IV second largest subunit [Zea mays]
          Length = 1170

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 98/512 (19%), Positives = 154/512 (30%), Gaps = 95/512 (18%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      S    +      +
Sbjct: 716  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYASFGRKNDFARPEY 775

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 776  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKE 834

Query: 1007 VLS----------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             +            D + +            ++ V   V      +       E     K
Sbjct: 835  KIDFGKTESKRGRXDNLDDDGLPYVGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 894

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +           G    V V +   R    GDK +  HG KG+V  +   E+ PF  +G 
Sbjct: 895  VLL----SANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHEGI 949

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DIV+NP   P+R   GQ+ E     A +G G   K                       
Sbjct: 950  VPDIVINPHAFPTRQTPGQLLE-----AALGKGIACKGT--------------------- 983

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                       +  +TP F  A  + I   L  A     G   +
Sbjct: 984  ---------------------------MRYATP-FTTASVDVIAEQLHRAGYSRWGSENV 1015

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
             +G TGE     V +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GE
Sbjct: 1016 LNGRTGERVQSLVFMGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGE 1075

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYESIVAG------- 1335
            ME  C+ A+G+A  L E L + SD              +VV R+      + G       
Sbjct: 1076 MERDCLLAHGSAANLHERLFLLSDFSQMHICQTCERVANVVMRSVPGGKKIRGPYCGFCK 1135

Query: 1336 --NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
               +      P    +L +E+ ++G+ +  E 
Sbjct: 1136 SSENIVRINVPYGAKLLYQELFSMGICLKFET 1167



 Score =  144 bits (364), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 142/977 (14%), Positives = 288/977 (29%), Gaps = 239/977 (24%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 45  LISHQINSYNEFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 94

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  L + + + V+ +++   +K+  D 
Sbjct: 95  GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLIVEVTIQVYSLEKSDKSKTGNDG 154

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 155 FVQKRNFMNETHWIFIGLLPVMVKSNLCLLHSLNESECLFDAGGYFLVKGMEKVFIAQEQ 214

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW-MDIEFDSK-DIIHVR-IDRRR----- 210
           R                 + L+    I D+  W +    + K   I+++ ++  R     
Sbjct: 215 RC---------------LRRLW----ISDRPCWTISFMSEIKRRRIYIKLVESTRSEDFS 255

Query: 211 --KVPVTS-FLM----------ALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMV 256
             K+ +T  FL           ALG+ S+ E+      +   +   +     +  +D + 
Sbjct: 256 ESKI-ITISFLYATMPVWLXXFALGISSDKEVFDMIXMQDCDASVINTISATIKESDKLC 314

Query: 257 GAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL---GITSDCLCGLYVAEDIV 313
                S        E +++S +   +        + +              G  V   ++
Sbjct: 315 EDFRKSDKARQYVDE-LVKSSRFPPAESFDDYIARFLFPDISGNRNKALFLGYMVKCLLM 373

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNTLVTDKNKDRK 371
              TG+   +  D    K L+       R++   +   +     A  R+     + +D +
Sbjct: 374 -AFTGKRKCDNKDDFRNKRLDLPGELLGRELRAQLRLAEKRMVKAIQRDLNSDRELQDLE 432

Query: 372 ---DALLDIYRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKMNMRLNL 422
              DA +    + R     ++                   ++   + +  R         
Sbjct: 433 RYIDASIVTNGLNRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTRQRVAYA 492

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
               D R+        +  +        G + ++        R +  ++++    G+ ++
Sbjct: 493 GKAGDARYPNPSYWGKLCFMSTPDGENCGLVKNLAVTAIVSSRVMQPLIESFISCGMSKL 552

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                E I  +D                     F   + +   E   + + R+   RR S
Sbjct: 553 NDIPTEHIQRMDK-------------------IFLNGNWVGSCENSASFVFRLRCMRRSS 593

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +      +         V       + P    E  N        SF+            
Sbjct: 594 LIDPQVEIKRDKHHNEVRVFTDAGRILRPLLVVENLNKIRKPKGRSFS------------ 641

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
               +      + ++   EEE+   A     L E                          
Sbjct: 642 --FHELMQQEIIEFIGVEEEEDIQCAWGIRHLFESEGAI-----------------SSYT 682

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ ++  +IPF  ++ + RVL                             K 
Sbjct: 683 HCELDPSFLLGLSCGIIPFANHNFARRVLYQSE-------------------------KH 717

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           S  AI         +VD                               +      QRPL 
Sbjct: 718 SQQAIGYSTTNPHIRVD-----------------------------TLSHQLYYPQRPL- 747

Query: 783 KVGDEVRRNDIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
               +    D +        G        +   G+N +VA     G+N EDS++++   +
Sbjct: 748 ---FKTVIADCLGRSDYASFGRKNDFARPEYFNGQNAIVAVNVHQGFNQEDSLVMNRASL 804

Query: 835 SEDVFTSIHIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F + H+  ++    +          E+I             N+D+ G+  VGA + 
Sbjct: 805 ERGMFRTEHLRSYKADVENKDGTKRLKLKEKIDFGKTESKRGRXDNLDDDGLPYVGASLQ 864

Query: 890 PGDILVGKITPKGESPM 906
             DI++GK++  GE   
Sbjct: 865 TNDIVIGKVSESGEDHS 881


>gi|45120572|gb|AAO64666.2| RNA polymerase II subunit RPB2 [Lycoperdon pyriforme]
          Length = 849

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 129/871 (14%), Positives = 260/871 (29%), Gaps = 149/871 (17%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 112  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 168

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 169  GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 228

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 229  ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 284

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 285  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 336

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + A   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 337  AHSATPCTKVFVNGVWMG---VHRDPANLMKTIKKLRRKDDISPEVSVVRDIREKELRIY 393

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      LL+ +   ++ +G +   ++     +   + G++E +DA   
Sbjct: 394  TDAGRVCRPLFIVENQQLLLQKKHIRWLNSGFDEEGSEYKWEQM--IKGGVIELLDAEEE 451

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +       +    ++ +     R  +K G            PS  LG
Sbjct: 452  ETVMISMTPEDLENSRLQAAGVDPHANDGDFDPAAR--LKAGTHAHTWTHCEIHPSMILG 509

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 510  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 544

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 545  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 593

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          +  
Sbjct: 594  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKL 652

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 653  EDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVL 712

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 713  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 752

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +            
Sbjct: 753  YRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------- 802

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     E++++ L
Sbjct: 803  -------------------------------------------ATP-FTDLTVESVSTFL 818

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            R       G  ++Y G TG      V +G  
Sbjct: 819  RQKGYQSRGLEVMYHGHTGRKLQAQVYLGPT 849



 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 98/775 (12%), Positives = 217/775 (28%), Gaps = 120/775 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+      LG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 42  YIKVD----IPIWVVFRGLGVISDRDILEHICYDMQDTQMLEMLKPCIDDGFVIQDREVA 97

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   +++     + L+++ +  + +              +      + 
Sbjct: 98  LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIH---RLL 153

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  KD    + + +
Sbjct: 154 LAALERRELDDRDHFGKKRLDL----------AGPLLANLFRMLFRKLTKDVYRYLQKCV 203

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F++A ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 204 ETH--KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 260

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 261 HLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAP 320

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +  I   RR   +     
Sbjct: 321 VIEFLEEWGLESLEENAHSATPCTKVFVNGVWMGVHRDPANLMKTIKKLRRKDDISPEVS 380

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                  +   ++        P    E  N  L+        +N+    E    K     
Sbjct: 381 VVRDIREKELRIYTDAGRVCRPLFIVE--NQQLLLQKKHIRWLNSGFDEEGSEYKWEQMI 438

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKID 662
               +  L A EEE   I+     L+        +      G+                 
Sbjct: 439 KGGVIELLDAEEEETVMISMTPEDLENSRLQAAGVDPHANDGDFDPAARLKAGTHAHTWT 498

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 499 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI------------ 546

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 547 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 574

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 575 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 613

Query: 843 HIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  + + + +   E            +       +++ G+I  G  V   DI++GK
Sbjct: 614 YYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGK 673

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 674 TAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 721


>gi|321471157|gb|EFX82130.1| hypothetical protein DAPPUDRAFT_316708 [Daphnia pulex]
          Length = 1135

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 146/1043 (13%), Positives = 291/1043 (27%), Gaps = 208/1043 (19%)

Query: 360  NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
               V      ++ AL  + + +R             F              +    +   
Sbjct: 269  EECVRASIFTQQQALNHLGKKLRQK---------RFFGGPKKTPLDEAREALAETVLAHV 319

Query: 420  LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGL 479
              L+     +      +  +I+ ++       ++DD D  GN+R    G ++   +    
Sbjct: 320  PVLNFNFKAK---AMYLALMIRRVIQAERDPTSVDDRDYYGNKRCELAGSLISLLFEDLF 376

Query: 480  LRMERSIKERISSVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
             RM   +K             Q      I    +   +     +   +     +      
Sbjct: 377  KRMNFELKSIADKNIPKVKAAQFDVIKHIRTDTLTLGLENAIATGNWTIKRFRMERQGVT 436

Query: 536  THTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                RLS +   G+         + R     R + P+ +G +CP++T EG   GLV +L 
Sbjct: 437  QMLCRLSYISGLGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEGCGLVKNLA 496

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDEDGSFTEELV 645
                +      E P  K+       D+   S  E  +  I     N ++         L+
Sbjct: 497  LMTHITTE-AEEEPIIKIAQNMGVEDINLFSGEEISDPSIYTVFLNGNILGLVKDYLRLI 555

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                           +        + V I+          DS R+     + RQ  P + 
Sbjct: 556  RYFKLARRHGFINAFVSIYPHFLTRSVYISC---------DSGRLCRPYIIVRQGRPAV- 605

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                   T         S               D I   +       + + S + +Y   
Sbjct: 606  -------TEHHMQELADS----------FRTFEDFIHDGLVEYLDVNEENDSNIAVYES- 647

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                                D       +   P T LG       +    +P+  +N   
Sbjct: 648  --------------------DINEETTHLEIEPFTLLG-------VCAGLIPYPHHNQ-- 678

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                S R   +       +       R+                          G++   
Sbjct: 679  ----SPRNTYQCAMGKQAMGTIACNQRNRI-----------------------DGLLYNL 711

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
               +   +    I       +   +  + A+      D+ D ++   + +        ++
Sbjct: 712  VYPHKPMVKTRTIEMVNFENIPAGQNAMVAVMSYSGFDIEDATVLNKASLDRGYGRCIVY 771

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
                    +R  +   +++     D   ++      I         GQ          K 
Sbjct: 772  KNAKCVL-KRYNNATSDRVNGPMIDPVTKKPAWKHEIIDIDGFACVGQPVQPKQVLINK- 829

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                       P                 +     +Y       +    + +EK+ +  +
Sbjct: 830  ---------IMPTVPAVAVTPGVPAAAAPL----PEYRDVPITYKGPIPSYVEKVMFSSN 876

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 +  +K+ +   R  + GDK +                                  
Sbjct: 877  AEEANI--IKIQLRQTRRPEIGDKFS---------------------------------- 900

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
               SR                  G+K  + +   + +   + L    + ++       ++
Sbjct: 901  ---SR-----------------HGQKGVTALVAEQEDLPFTELGICPDVIMNPHGFPSRM 940

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
            +      +L        G       F G+  + ++  L     +  G+  +  G TGE  
Sbjct: 941  TVGKLIELLAGKAGLMEGKFHYGTAFGGSKVQDVSEELMKHGFNYQGKECMTSGTTGEQL 1000

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               +  G +Y  KL HMV DK++ARS G  +++T+QP  G++  GG RLGEME  C+ AY
Sbjct: 1001 TAYIYFGPVYYQKLKHMVMDKMHARSQGPRAILTRQPTEGRARDGGLRLGEMERDCLIAY 1060

Query: 1306 GAAYVLQEMLTIKSD----DVVG--------------RTRVYESIVAGNDTFETGTPESF 1347
            G++ ++ E L I SD    DV                R+                 P + 
Sbjct: 1061 GSSMLILERLMISSDAFNVDVCNQCGLIGYFGWCHFCRSSA--------SVSSLRIPYAC 1112

Query: 1348 NVLVKEMQALGLSIDLENSRTKN 1370
             +L +E+Q++ ++  L+  +  +
Sbjct: 1113 KLLFQELQSMNIAPRLKLDKYFD 1135



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 125/994 (12%), Positives = 283/994 (28%), Gaps = 201/994 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    SY++F+ + I    + NE           I+       L+++      P    
Sbjct: 38  LVKQHIDSYNYFINVEIKKIVKANE---KV------ISFADPTFYLKYLDIHVGKPDSIE 88

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + +    I +G +P+M
Sbjct: 89  DMHHSRLTTPHECRLRDMTYSAPVTVDIEYT----------RGQQRVVRNGIAIGRMPIM 138

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            +                         G F+++G +++++ Q   S          + ++
Sbjct: 139 LRSSNCTLAGILPAEMAKKNECPYDCGGYFIVRGNEKVILIQEQMSKNRMIVEQDRKGNM 198

Query: 175 SGKLLYACR-------IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGM-DSE 226
           S ++  +         +I ++G                   +  +PV     A+G+   +
Sbjct: 199 SCQVTSSTHGTKTRTNVIMNKG---KYYLKQNSF-------QDDIPVVIAFKAMGIVSDQ 248

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           EI+                      A +    +  + L      ++     KK      +
Sbjct: 249 EIVQMIGTDDHVMTSFAPSLEECVRASIFTQQQALNHLGKKLRQKRFFGGPKKTPLDEAR 308

Query: 287 S-LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE----EIFHSEI 341
             L E  +  + + +            +      +     D       +    +      
Sbjct: 309 EALAETVLAHVPVLN---FNFKAKAMYLALMIRRVIQAERDPTSVDDRDYYGNKRCELAG 365

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             I +L+ D      +   ++        K A  D+ + +R  D  T  +  +      +
Sbjct: 366 SLISLLFEDLFKRMNFELKSIADKNIPKVKAAQFDVIKHIR-TDTLTLGLENA-IATGNW 423

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---NGKGTIDDIDN 458
              ++ +   G  +M  RL+  +   +            K+        +  G +   D 
Sbjct: 424 TIKRFRMERQGVTQMLCRLSYISGLGMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDT 483

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                   V  +    +       E  IK   +    D  +      + P +  V  F  
Sbjct: 484 PEGEGCGLVKNLALMTHITTEAEEEPIIKIAQNMGVEDINLFSGEEISDPSIYTV--FLN 541

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY-GRICPAETSEG 577
            + L  +++++  +      RR   +              R V+ +   GR+C       
Sbjct: 542 GNILGLVKDYLRLIRYFKLARRHGFINAFVSIYPHFL--TRSVYISCDSGRLCRPYIIVR 599

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
                V+             +   +R   D      V YL   EE +  IA   S ++  
Sbjct: 600 QGRPAVTEHHMQ-------ELADSFRTFEDFIHDGLVEYLDVNEENDSNIAVYESDIN-- 650

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                                E+   ++  P  ++ + A LIP+  ++ S R    C M 
Sbjct: 651 ---------------------EETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 689

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+                                           I   + +      
Sbjct: 690 KQAMGT-----------------------------------------IACNQRNRIDGLL 708

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
              +Y                +P+VK                 +  ++  G+N +VA M 
Sbjct: 709 YNLVYP--------------HKPMVK----------TRTIEMVNFENIPAGQNAMVAVMS 744

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + G++ ED+ ++++  +       I  +  + + +       +         +       
Sbjct: 745 YSGFDIEDATVLNKASLDRGYGRCIVYKNAKCVLKRYNNATSDRVNGPMIDPVTKKPAWK 804

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITP-----------KGESPMTPEEKLLRAIFGEKA 921
            + ID  G  CVG  V P  +L+ KI P              +   PE + +   +    
Sbjct: 805 HEIIDIDGFACVGQPVQPKQVLINKIMPTVPAVAVTPGVPAAAAPLPEYRDVPITYKGPI 864

Query: 922 VDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNE 954
               +  +   +     ++ +++   R     ++
Sbjct: 865 PSYVEKVMFSSNAEEANIIKIQLRQTRRPEIGDK 898


>gi|52699774|gb|AAU86949.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            complanata]
          Length = 730

 Score =  260 bits (664), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 124/841 (14%), Positives = 242/841 (28%), Gaps = 139/841 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     ++     E    +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D       V     G  I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHSDPVHLVNTVQAVRRGHMISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+  +     N+   ++ +  L+          E +  K      V +      
Sbjct: 237  RPLFVIDNDPKSPRCGNLVLTKEHINKLEDYKDLSAEMQEKIREKEEVEKEVKEDGTPYG 296

Query: 737  QVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV---KVGDEVRRND 792
                  R V+  V+ + + +   V     ++  R  Q   V   P      +   V+   
Sbjct: 297  WNGLIKRGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYVLPEPSNTSEALMKRVKAPM 356

Query: 793  IIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                   T      ++   +  + +P+  +N          M  + +       E  +  
Sbjct: 357  NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGXXXXNYEQRMDT 416

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                                         +  +             +       +   + 
Sbjct: 417  -----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQN 447

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +  
Sbjct: 448  AIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPM 503

Query: 972  DDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              + + L    Y +L +   +  G           K+  ++ D      R++        
Sbjct: 504  RSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVS 563

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +  Q                             LR VKV +   +  Q GD
Sbjct: 564  TPLRSTENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGD 603

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       
Sbjct: 604  KFASRHGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLR 663

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +          +S L    E    +                              
Sbjct: 664  GFEGDATPFTEITVDSVSKLLR--EHGYQSRGFEVM------------------------ 697

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                                  +G +    G         V +G  Y  +L HMV DK+ 
Sbjct: 698  ---------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIX 729

Query: 1269 A 1269
            A
Sbjct: 730  A 730


>gi|268563827|ref|XP_002647022.1| Hypothetical protein CBG24045 [Caenorhabditis briggsae]
          Length = 1078

 Score =  260 bits (663), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 152/1004 (15%), Positives = 297/1004 (29%), Gaps = 196/1004 (19%)

Query: 407  DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            +   V  +  +M  ++  PD    ++   +  + + L+    G+  +DD D  GN+R+  
Sbjct: 231  EHEAVDFLSNSMITHIACPDGNFKMKAIYLGQMTRRLIQTEMGENELDDRDFYGNKRLEL 290

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDIDS----VMPQDLINAKPVVSAVCEFFCSSQL 522
             G +L   +     R    +K    +  + +    +     +    + + +     +   
Sbjct: 291  AGSLLALLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQDMITNTIVNAMSTGNW 350

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAET 574
                  +  L       RLS +   G+         + R     R + P+ +G +CP++T
Sbjct: 351  IIKRFRMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDT 410

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L   + +      +   R + +  V           E+       N   
Sbjct: 411  PEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGV-----------EDLH-----NVHF 454

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI--DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                     L+F         V  E++     D     ++S   S+   + N        
Sbjct: 455  SHVNKPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSMTNRSVFISSD 514

Query: 693  GCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            G  + R  + +   +     T + E    K              + VD   +    V   
Sbjct: 515  GGRLCRPYIIVRHGKPMLTETHVQELKEGK----------RIFEDFVDDGIVEYLDVNEM 564

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
             D   +                        V   +       +   P T LG       +
Sbjct: 565  NDALIA------------------------VYENEIGAETTHLEIEPFTLLG-------V 593

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
                +P+  +N          M  + + T      +    R   +         P V  +
Sbjct: 594  CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIA----YNQQKRIDSIMYLLCYPQRPLVKSK 649

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                                      I       +      + A+      D+ D  +  
Sbjct: 650  T-------------------------IELTNFEKLPAGANGIIAVMSYSGYDIEDALVLN 684

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
             + +        ++ +H     ++  +   +++   A D    + I       +   +  
Sbjct: 685  KASLDRGYGRCLVY-KHVKGTAKKYPNQTYDRLLGPAVDSVTLKPIFKHKNLDQEGIVFT 743

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G   +       K   + S        +     A +D           V Y+      + 
Sbjct: 744  GARILPKQTIINKYMPVVSAESGSAASANTIGIAGRD-----------VAYKDVSITYKT 792

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +  E++    +       + KV +   R  + GDK +                    
Sbjct: 793  PTPSYAERVLLTYNEDEA--HLFKVLLRQTRRPELGDKFS-------------------- 830

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    +   + +   + L   
Sbjct: 831  -----------------SR-----------------HGQKGVCGLIAQQEDMPFNDLGMV 856

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++    +  +++      +L       +G       F G   + +   L     +  
Sbjct: 857  PDMIMNPHGYPSRMTVGKLMELLSGKAGVMNGTYHYGTAFGGDQVKDVCEELAARGYNYM 916

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+ +L  G+TG+P    +  G IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG
Sbjct: 917  GKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGG 976

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-----------------DVVGRTRVYESIVA 1334
             RLGEME  C+ AYGA+ +L E L + SD                 DV     V  S   
Sbjct: 977  LRLGEMERDCLIAYGASMLLIERLMVSSDEFKVLFRSFVPLIPIEVDVCTGCGVIGS--K 1034

Query: 1335 G--------NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            G                P +  +L +E+Q++ +   L+ +R   
Sbjct: 1035 GWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLDLARYTE 1078



 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 118/903 (13%), Positives = 268/903 (29%), Gaps = 182/903 (20%)

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT------- 139
              +C  RD+TY+ P+ + +             +  + + ++ + +G +P+M        
Sbjct: 14  SESECRLRDMTYSAPISVDIEYT----------RGHQRVYKKDLVIGRMPIMLRSSKCIL 63

Query: 140 -----------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
                              G FV+KG +++++ Q   S       ++     +      C
Sbjct: 64  RDLAEEELARVQECPHDPGGYFVVKGSEKVILIQEQLS------KNRIMVGRNSSKELQC 117

Query: 183 RIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIV 237
            ++     +          K    VR ++    VPV+    A+G++S+ +I+ST   +  
Sbjct: 118 EVLSSTSERKSK-TYVTVKKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGHEEK 176

Query: 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLG 297
           Y             A +    +  + +       +    G    + +      K  + + 
Sbjct: 177 YVSAFAQTLEECINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLTAPKEHEAVD 236

Query: 298 ITSDCLCGLYVAEDIVNGETGEIYIEAG------DVIDEKSLEEIFHSEIRDIP------ 345
             S+ +   ++A    N +   IY+           + E  L++      + +       
Sbjct: 237 FLSNSMI-THIACPDGNFKMKAIYLGQMTRRLIQTEMGENELDDRDFYGNKRLELAGSLL 295

Query: 346 -ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +L+ D           +  +       A LDI + MR  D+ T ++  +M +   +   
Sbjct: 296 ALLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQ-DMITNTIVNAM-STGNWIIK 353

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
           ++ +  +G  ++  R           +     + ++  +         +    +L   + 
Sbjct: 354 RFRMERLGVTQVLSR-----------LSYISALGMMTRINSTFEKTRKVSGPRSLQPSQW 402

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             +      +     L    ++   I++   +  + + L+N+        E   +   S 
Sbjct: 403 GMLCPSDTPEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGV------EDLHNVHFSH 456

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           + +  N+L  +      +A+    V +A   +    +                       
Sbjct: 457 VNKPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSMTNRSVFISSDGG 516

Query: 585 SLTSFARVNAYG----------FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            L     +  +G           ++   R   D      V YL   E  +  IA   + +
Sbjct: 517 RLCRPYIIVRHGKPMLTETHVQELKEGKRIFEDFVDDGIVEYLDVNEMNDALIAVYENEI 576

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                    +   ++  P  ++ + A LIP+  ++ S R    C
Sbjct: 577 GA-----------------------ETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQC 613

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+  +                  S                               
Sbjct: 614 AMGKQAMGTI---------AYNQQKRIDS------------------------------- 633

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                               C  QRPLVK                T+   L  G N ++A
Sbjct: 634 ---------------IMYLLCYPQRPLVKS----------KTIELTNFEKLPAGANGIIA 668

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVS 869
            M + GY+ ED++++++  +       +  +  +  A+       +         +    
Sbjct: 669 VMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTYDRLLGPAVDSVTLKP 728

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
               KN+D+ GI+  GA + P   ++ K  P   +               + V  +D S+
Sbjct: 729 IFKHKNLDQEGIVFTGARILPKQTIINKYMPVVSAESGSAASANTIGIAGRDVAYKDVSI 788

Query: 930 RVP 932
              
Sbjct: 789 TYK 791


>gi|225728467|gb|ACO24290.1| RNA polymerase beta subunit [Bartonella henselae]
          Length = 280

 Score =  260 bits (663), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 200/281 (71%), Positives = 235/281 (83%), Gaps = 1/281 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           A+ A+R+GIV+QVDA RIVIR+ E  LDPS SGVDIYRL K
Sbjct: 241 AVAARRSGIVDQVDATRIVIRATED-LDPSKSGVDIYRLQK 280


>gi|239613518|gb|EEQ90505.1| DNA-directed RNA polymerase III polypeptide [Ajellomyces dermatitidis
            ER-3]
 gi|327357033|gb|EGE85890.1| DNA-directed RNA polymerase [Ajellomyces dermatitidis ATCC 18188]
          Length = 1228

 Score =  260 bits (663), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 170/1129 (15%), Positives = 345/1129 (30%), Gaps = 207/1129 (18%)

Query: 288  LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            L ++ +    +  +      + +  V   + E   ++  ++ +  +    +    D+PI+
Sbjct: 262  LVQEQLSKNRVIVETDLKKEIVQASVTSSSNERKSKSYIIMKKDRIYMRHNVLNEDVPIV 321

Query: 348  ----------YVDSVNNNAYIRNTLVTDKNKDRKDAL-LDIYRVMRPGDVSTFSVAESMF 396
                        + +   A I +T   D + + ++A+ L IY   +  +     +  +  
Sbjct: 322  ILLKAMGIQSDKEMLLLVAGIDSTYQEDFSINFEEAVKLGIYTQHQALEYIGSRIKINRK 381

Query: 397  NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLRNGKGTIDD 455
               F  + +  +        ++ ++    +++    K   +A + + ++  ++    +DD
Sbjct: 382  PNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKALYVAHMARRVLMAKHDPSLVDD 441

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKP 508
             D +GN+R+   G++L   +     + +  IK  I  V    V  +          +   
Sbjct: 442  RDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNH 501

Query: 509  VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRD 560
            +   +     +   S     +          RLS +   G+         + R     R 
Sbjct: 502  ITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRA 561

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            + P+ +G +CP++T EG   GLV +L     +      E P RK+       DV  +   
Sbjct: 562  LQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGR 620

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            E       Q    +  +GS        R     +   R        S    V I      
Sbjct: 621  ELHG----QGAYIIFLNGSPIA---LTRRPKFFLNSFRRLRRTGRVSEFISVFIN----- 668

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
               + ++  +        + + +++     V       +   S         G+VE +D 
Sbjct: 669  --HHQNAVHIATDDGRICRPLIVVEDGKSKVTKSHLWALRSGSMEFDDFLAHGLVEYLDC 726

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +                                 V   D       +   P T
Sbjct: 727  NEENDSYI--------------------------------AVYEEDITDSTTHLEIEPFT 754

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG +A         +P+  +N          M  + +                      
Sbjct: 755  ILGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------------------- 787

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                         + +    ++          +    I       +   +    A+    
Sbjct: 788  ---------IANNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDKLPAGQSATVAVMSYS 838

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              D+ D  +   S V       ++F R      +   +  +++++   R         + 
Sbjct: 839  GYDIEDALVLNKSSVDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------EN 888

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +  R   +L      +  +   +  V  + +  E   S        D            
Sbjct: 889  GLPIRKHALLDSDGLAAVGEKVNQGEVYINKVTPENALSS--GITGSDAGRPIA------ 940

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             Y  S    +    + I+K+           +++KV     R  + GDK +         
Sbjct: 941  -YIPSPQTYKLPDPSYIDKVMI--SATEAENQLIKVQTRQTRVPEVGDKFS--------- 988

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                                        SR                  G+K    I    
Sbjct: 989  ----------------------------SR-----------------HGQKGVVGIIAEY 1003

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            A+   S L    + ++       +++      ++       SG       F G+  E ++
Sbjct: 1004 ADMPFSDLGIVPDIIMNPHGFPSRMTVGKMLELIAGKAGILSGQFGYGTAFGGSPVEEMS 1063

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
            ++L        G+  L  G+TGEP    V +G IY  KL HMV DK+++R+ G  +++T+
Sbjct: 1064 AILVDHGFSYGGKDYLTSGITGEPLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTR 1123

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VG 1324
            QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV              
Sbjct: 1124 QPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCESCGFMGYLGWCQ 1183

Query: 1325 RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
            R +    +V          P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1184 RCKTSRGVVK------MVIPYAAKLLVQELFSMNVVARLKLADEFPEER 1226



 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 88/739 (11%), Positives = 200/739 (27%), Gaps = 118/739 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 117 LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGNPRRAD 167

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +    +          +  + +K     +G
Sbjct: 168 EEQDSKFDVASTITPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTAIG 217

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   +  + D
Sbjct: 218 RMPVMLRSSKCVLSNKSEAEMQLLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVETD 277

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             KD I++R +     VP+   L A
Sbjct: 278 LKKEIVQASVTSSSNERKSKSYII-----------MKKDRIYMRHNVLNEDVPIVILLKA 326

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESGKK 279
           +G+ S++ +      I  + + DF      A  L +     +   +          +   
Sbjct: 327 MGIQSDKEMLLLVAGIDSTYQEDFSINFEEAVKLGIYTQHQALEYIGSRIKINRKPNSFG 386

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +T         + +  + I+   +  L                 A         +     
Sbjct: 387 ITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMARRVLMAKHDPSL 438

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +           +         K + D  ++I +V++    +    A  +    
Sbjct: 439 VDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIH 498

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDD 455
                +     +     +++        V H    +     + ++  +         +  
Sbjct: 499 GNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 558

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
              L   +   +      +     L    ++   I++ D +  + + +            
Sbjct: 559 PRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLIFALGAEDVQTVG 618

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAET 574
                        +N        R    L     + R     E   V   H+       T
Sbjct: 619 GRELHGQGAYIIFLNGSPIALTRRPKFFLNSFRRLRRTGRVSEFISVFINHHQNAVHIAT 678

Query: 575 SEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            +G     +  +         +    + +   +  D      V YL   EE + YIA   
Sbjct: 679 DDGRICRPLIVVEDGKSKVTKSHLWALRSGSMEFDDFLAHGLVEYLDCNEENDSYIAVYE 738

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +                        +    ++  P  ++   A LIP+  ++ S R  
Sbjct: 739 EDIT-----------------------DSTTHLEIEPFTILGAVAGLIPYPHHNQSPRNT 775

Query: 692 MGCNMQRQAVPLLKAEAPF 710
             C M +QA+  +      
Sbjct: 776 YQCAMGKQAIGAIANNQFL 794


>gi|120561259|gb|ABM27014.1| RNA polymerase II second largest subunit [Allomyces macrogynus]
          Length = 867

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 148/971 (15%), Positives = 284/971 (29%), Gaps = 184/971 (18%)

Query: 308  VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
            +     +     ++   G V D   LE I +    D  +  +    +NA+          
Sbjct: 61   LPYIQQDIPIMVLFRALGLVADRDILERICYDFSDDQMLEMLKPSIDNAF--------TI 112

Query: 368  KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            ++R+ AL  I +  R                      +Y    + R  +           
Sbjct: 113  QEREIALDFIGKRGRN------------IGLTRDKRIRYAHDLLERELLPHI---GITPG 157

Query: 428  VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
             +  +   I  ++  L+    G+  +DD D+ G +R+   G +L + +R    ++ + + 
Sbjct: 158  CQTRKSYFIGYMVHRLLLAALGRRQVDDRDHFGKKRLDLAGPLLASLFRTFFQKLTKDVS 217

Query: 488  ERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSL 532
               +              IN+  + + +     +               +SQ+       
Sbjct: 218  RYFTVCIERGREFNLNMAINSNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFA 277

Query: 533  SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
            S ++H RRL+      + R     + R +H TH+G +CPAET EG   GLV +L   A +
Sbjct: 278  STLSHLRRLNT----PIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAYI 333

Query: 593  NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----FCR 648
            +  G    P  +  +   T ++  ++A    +      N S        + LV      R
Sbjct: 334  S-VGSASGPILEFLEEWTTENLEEITASAIGSNTKVFVNGSWVGIHRQPDSLVQTLISLR 392

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             +G+ +       D  D   +          P    ++  ++++  +   +         
Sbjct: 393  RSGDIMPEVSVVRDVRDNELRIYTDAGRICRPLFIVNEQQQLVLRRDHVARLEVGEWGWE 452

Query: 709  PFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
              +  G+ E +  +     ++                +   +          D  +L K 
Sbjct: 453  DLLANGIVEYLDTEEEETTMIC---------------MTPDDLAESRGDPIPDKSKLDKT 497

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             R             K GD  ++       PS  LG       +  + +P+  +N     
Sbjct: 498  ARLKSR---------KAGDVCKQWSHCEIHPSMILG-------ICASIIPFPDHNQ---- 537

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
              S R   +       +  +    +                       +    +  +   
Sbjct: 538  --SPRNTYQSAMGKQAMGLYLTNFQ-----------------------LRMDTLANILYY 572

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                 +    +       +   +  + AI      +  D+ +   S +   +    I+ R
Sbjct: 573  PQKPLVATRSMKYLRFRELPAGQNAVVAIAVYSGYNQEDSIIMNQSSIDRGLF-RSIYYR 631

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +D+ ++S   + E  E   R+   +      +       +  G           K+  
Sbjct: 632  AYMDQEKKSGFSDVETFEKPTRETTLKLRHGSYDKIEEDGLVAPGTRVTGDDIIIGKTAP 691

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L  D      R+                   K    TS    E    + +      D   
Sbjct: 692  LPPDTSEMGARTT----------------QTKKDVSTSLKSTEQGIVDHVMLTTNND--- 732

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                + VKV V   R  Q GDK A RHG KG V      EDMPF  DG   D+++NP  +
Sbjct: 733  --GYKFVKVRVRSTRVPQMGDKFASRHGQKGTVGMTYRQEDMPFSADGVTPDLIVNPHAI 790

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E  L       G +  +         +I+                     
Sbjct: 791  PSRMTIGHLVECLLSKVGSLTGTEGDATPFTDITVQEIA--------------------- 829

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  LR     + G  +                        +G +       G+    
Sbjct: 830  ----DRLRSCGYQQRGFEIM----------------------YNGHT-------GKKLAA 856

Query: 1248 PVTVGYIYMLK 1258
             V  G  Y  +
Sbjct: 857  QVFFGPTYYQR 867



 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 105/749 (14%), Positives = 218/749 (29%), Gaps = 110/749 (14%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG+ ++ +IL          Q  +     +  A  +   +++   +     
Sbjct: 68  IPIMVLFRALGLVADRDILERICYDFSDDQMLEMLKPSIDNAFTIQEREIALDFIGKRGR 127

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEA 324
              +   K++       L+ + +  +GIT           G  V   ++    G   ++ 
Sbjct: 128 NIGLTRDKRIRYAH-DLLERELLPHIGITPGCQTRKSYFIGYMVHRLLL-AALGRRQVDD 185

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
            D   +K L+             +   + + + Y    +   +  +   A+         
Sbjct: 186 RDHFGKKRLDLAGPLLASLFRTFFQKLTKDVSRYFTVCIERGREFNLNMAI--------N 237

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVG-RVKMNMRLNLDTPDDVRHI-RKEDIIAIIK 441
            +  T  +  ++    + D  K+  +  G    +N      T   +R +         + 
Sbjct: 238 SNTITNGLRYALATGNWGDQKKFMETRAGVSQVLNRYTFASTLSHLRRLNTPIGREGKLA 297

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +         +      ++KN   +  + +  +    +  ++  +    
Sbjct: 298 KPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMAYISVGSASGPILEFLEEWTTENL 354

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           + I A  + S    F   S +    +  + +  +   RR   +             +RDV
Sbjct: 355 EEITASAIGSNTKVFVNGSWVGIHRQPDSLVQTLISLRRSGDIMP-------EVSVVRDV 407

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                     A         +        R +    +E       D      V YL   E
Sbjct: 408 RDNELRIYTDAGRICRPLFIVNEQQQLVLRRDHVARLEVGEWGWEDLLANGIVEYLDTEE 467

Query: 622 EENRYIAQANSSLDEDGSFTEELVF-----CRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           EE   I      L E                R    +     ++    +  P  ++ I A
Sbjct: 468 EETTMICMTPDDLAESRGDPIPDKSKLDKTARLKSRKAGDVCKQWSHCEIHPSMILGICA 527

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ L                                 
Sbjct: 528 SIIPFPDHNQSPRNTYQSAMGKQAMGLYLTNFQL-------------------------- 561

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y               Q+PLV              
Sbjct: 562 ---------------RMDTLANILYYP--------------QKPLVA----------TRS 582

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA   + GYN EDS+++++  +   +F SI+   +    + +  
Sbjct: 583 MKYLRFRELPAGQNAVVAIAVYSGYNQEDSIIMNQSSIDRGLFRSIYYRAYMDQEKKSGF 642

Query: 857 GPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E            +       I+E G++  G  V   DI++GK  P     + P+  
Sbjct: 643 SDVETFEKPTRETTLKLRHGSYDKIEEDGLVAPGTRVTGDDIIIGKTAP-----LPPDTS 697

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            + A   +   DV  +      G+   V+
Sbjct: 698 EMGARTTQTKKDVSTSLKSTEQGIVDHVM 726


>gi|118640703|gb|ABL09919.1| RNA polymerase beta subunit [Photobacterium damselae subsp.
           damselae]
 gi|118640705|gb|ABL09920.1| RNA polymerase beta subunit [Photobacterium damselae subsp.
           damselae]
 gi|118640707|gb|ABL09921.1| RNA polymerase beta subunit [Photobacterium damselae subsp.
           damselae]
          Length = 290

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 223/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +F  LFF  ++YDLS VGR+K N  L  D       +  +DII +++ L+D+RNGKG +
Sbjct: 1   QLFESLFFSEERYDLSAVGRMKFNSSLLRDETTGPGTLDNQDIIDVMRKLIDIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+ FAR N YGF+ETPYRKV DGKV+ ++ YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSVFARCNPYGFLETPYRKVVDGKVSEEIEYLSAIEEGQYVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDGSF +EL+  R  G+  L PR+ + ++D +  QVVS+AASLIPFLE
Sbjct: 241 LNEDGSFADELITARQKGDSGLHPRDHVQYMDVATNQVVSVAASLIPFLE 290


>gi|45545307|gb|AAS67501.1| DNA-dependent RNA polymerase II second largest subunit [Candida
            glabrata]
          Length = 885

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 135/846 (15%), Positives = 247/846 (29%), Gaps = 147/846 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KER 489
            +   +  +I  L+     +   DD D+ G +R+   G +L   ++    ++ + I    +
Sbjct: 165  KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTKDIFRYMQ 224

Query: 490  ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRIT 536
             +  + +    +  INAK + S +     +               +SQ+       S ++
Sbjct: 225  RTVEEANDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLS 284

Query: 537  HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
            H RR +      + R     + R +H TH+G +CPAET EG   GLV +L+  + ++   
Sbjct: 285  HLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGA 340

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF----TEELVFCRCAGE 652
                    + +  +     Y+   +  +      N              E L   R  G+
Sbjct: 341  DPMPIITFLSEWGMEPLEDYV-PHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGD 399

Query: 653  EILVPREKIDFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLK-AEAPF 710
                     D  +   K          P F+  DD         +++  V  L   E   
Sbjct: 400  INPEVSMIRDIREQELKIFTDAGRVYRPLFIVEDDEELGRKELKVRKGHVAKLMATEYQD 459

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            +  G E     +  + +     G+VE +DA       +    +          + K    
Sbjct: 460  IEGGFEDAEDYTWSSLL---NEGLVEYIDAEEEESILIAMQPEDLEPTAVEQDIPK---- 512

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                 V+    +KV             PS  LG  A       + +P+  +N        
Sbjct: 513  ---ENVDLAKRIKVTHHATTFTHCEIHPSMILGVAA-------SIIPFPDHNQSPRNTYQ 562

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
              M  + +   +    F +                               +  +      
Sbjct: 563  SAMGKQAMGVFLTNYNFRMDT-----------------------------MANILYYPQK 593

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                   +       +   +  + AI      +  D+ +   S +   +    +F R  +
Sbjct: 594  PLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF-RSLFFRSYM 652

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSS 1010
            D+ ++      E  E   R           +       I  G           K+T ++ 
Sbjct: 653  DQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDEDGLIAPGVRVSGEDIIIGKTTPIAP 712

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
            D      R+ +         ++     +  Q                             
Sbjct: 713  DEEELGQRTAYHSKRDASTPLRSTENGIVDQVLI--------------------TTNQDG 752

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            L+ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSR
Sbjct: 753  LKFVKVRVRTTKVPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR 812

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M V  + E  L       G +                                       
Sbjct: 813  MTVAHLIECLLSKVAALSGNEGD------------------------------------- 835

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                            ++P F     E I+ +LR       G  ++Y+G TG+     + 
Sbjct: 836  ----------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIF 878

Query: 1251 VGYIYM 1256
             G  Y 
Sbjct: 879  FGPTYY 884



 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 102/773 (13%), Positives = 215/773 (27%), Gaps = 107/773 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+  + EIL      +   Q  +     +    ++   + +
Sbjct: 66  YIKQD----IPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETA 121

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        I+  K++       L+++ +  +                +      + 
Sbjct: 122 LDFIGRRGTALGIKKEKRIQYAK-DILQKEFLPHITQLEGFESRKAFFLGYM---INRLL 177

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A D  D+   +      +    P+L          +   +     +  ++A     ++
Sbjct: 178 LCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFRKLTKDIFRYMQRTVEEANDFNMKL 237

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
                  T  +  ++    + +  K   S  G  ++  R    +      R         
Sbjct: 238 AINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDG 297

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            +     L N    +         +      ++KN   +  + +       I+ +    +
Sbjct: 298 KLAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMSCISVGADPMPIITFLSEWGM 354

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            P +         A   F               +  +   RR   +            + 
Sbjct: 355 EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREQE 414

Query: 559 RDVHPTHYGRICPAETSE------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--- 609
             +         P    E         + +     +      Y  IE  +    D     
Sbjct: 415 LKIFTDAGRVYRPLFIVEDDEELGRKELKVRKGHVAKLMATEYQDIEGGFEDAEDYTWSS 474

Query: 610 --VTNDVVYLSAMEEENRYIAQANSSLDE---DGSFTEELVFCRCAGEEILVPREKIDFI 664
                 V Y+ A EEE+  IA     L+    +    +E V      +            
Sbjct: 475 LLNEGLVEYIDAEEEESILIAMQPEDLEPTAVEQDIPKENVDLAKRIKVTH-HATTFTHC 533

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ +AAS+IPF +++ S R      M +QA+ +      F              
Sbjct: 534 EIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNF-------------- 579

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         + + +  Y       +     +  R     
Sbjct: 580 ---------------------------RMDTMANILYYPQKPLGTTRAMEYLKFR----- 607

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                              +L  G+N +VA   + GYN EDSM++++  +   +F S+  
Sbjct: 608 -------------------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFF 648

Query: 845 EEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +    +   +   E        +   +       +DE G+I  G  V+  DI++GK T
Sbjct: 649 RSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDEDGLIAPGVRVSGEDIIIGKTT 708

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           P         ++             RD S  + S  +G V  V I       K
Sbjct: 709 PIAPDEEELGQRTAY-------HSKRDASTPLRSTENGIVDQVLITTNQDGLK 754


>gi|326422564|gb|EGD71959.1| RNA polymerase beta subunit [Candidatus Parvarchaeum acidophilus
            ARMAN-5_'5-way FS']
          Length = 600

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/313 (26%), Positives = 126/313 (40%), Gaps = 72/313 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + V + +   R ++ GDK   R G KG+V  +L  EDMPF   G   D++ +P  
Sbjct: 338  TAEGNKYVSLKIRQDRKVEIGDKFGPRSGQKGVVGMLLNQEDMPFTYSGIIPDLIFSPYS 397

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +P+RM++  + E   G      G+ I                                  
Sbjct: 398  IPTRMSMAYLLELIGGKVGALGGRYIDG-------------------------------- 425

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 TP F G  EE + + L      E+G   +Y+G+TGE   
Sbjct: 426  ---------------------TP-FIGEKEEDLRNELLEYGFRENGVETMYNGITGEEMQ 463

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + VG +  ++L H V++K+  R+ G   L+ +QP  GKS  GG RLGEME  C  AYG
Sbjct: 464  VKIFVGDMTYIRLKHFVANKIQWRARGPIQLLNRQPTEGKSKSGGLRLGEMEKDCFVAYG 523

Query: 1307 AAYVLQEMLTIKSDDV-------VGRTRVYE-------SIVAGND--TFETGTPESFNVL 1350
            +A  L+E     SD +        G T VY          + G D          SF +L
Sbjct: 524  SAMALKERF--DSDKITIPVCSKCGMTAVYNVRKKTGYCPIDGEDTQIKLIEVSASFKIL 581

Query: 1351 VKEMQALGLSIDL 1363
            + E++A+G+   +
Sbjct: 582  LDELKAVGIYPKM 594



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 55/304 (18%), Positives = 112/304 (36%), Gaps = 30/304 (9%)

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +A   I + +  D  ++      + +       E           +   S     A    
Sbjct: 79  LAEGHITWQDLIDKGKIEYLDADEEELAYTAITEEELTPAHTHLEITPLSVFGTQASLLP 138

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV---NQRPLVKVGDEVRR 790
            +   +A R V       +     GV IY      R + ++ +    Q P+V        
Sbjct: 139 FINHSNAHRNVTA-----VKSVQQGVGIYSTNYLIRHDNDSMIAIDQQTPIVTTKIYNNE 193

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                     D G    G+N++VA + + GYN +D+++I++  V   +F ++    ++V 
Sbjct: 194 ----------DFGSHVFGQNIVVAVLSYLGYNMDDAIIINKSSVDRGLFRAMFFRPYKVE 243

Query: 851 ARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                 G  ++  +         SE   K +DE GI  V + VN GD+L+G+++P     
Sbjct: 244 ETKYVGGQSDLITNPDKDVAGYRSEAAYKYLDEDGIAAVNSHVNSGDVLIGRVSPPRFVS 303

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
              + +L             ++S+   +G  G V +V + +    +K       +  ++E
Sbjct: 304 SIDKFRL-------GVQKQVESSIECRTGEGGIVENVFVTSTAEGNKYVSLKIRQDRKVE 356

Query: 966 LLAR 969
           +  +
Sbjct: 357 IGDK 360


>gi|269930937|gb|ACZ54203.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 279

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 199/279 (71%), Positives = 232/279 (83%), Gaps = 1/279 (0%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSAL
Sbjct: 1   AIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +
Sbjct: 121 IIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SG
Sbjct: 181 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           AAI AKR GIV+QVDA+RIVIR+ E  L+PS SGVDIYR
Sbjct: 241 AAIGAKRGGIVDQVDAMRIVIRATED-LNPSKSGVDIYR 278


>gi|307343586|emb|CBJ18708.1| RNA polymerase B subunit [Micromonospora peucetia]
          Length = 210

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 125/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     D+K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDTDWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|290558923|gb|EFD92311.1| RNA polymerase Rpb2 domain 6 [Candidatus Parvarchaeum acidophilus
            ARMAN-5]
          Length = 426

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/313 (26%), Positives = 126/313 (40%), Gaps = 72/313 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + V + +   R ++ GDK   R G KG+V  +L  EDMPF   G   D++ +P  
Sbjct: 164  TAEGNKYVSLKIRQDRKVEIGDKFGPRSGQKGVVGMLLNQEDMPFTYSGIIPDLIFSPYS 223

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +P+RM++  + E   G      G+ I                                  
Sbjct: 224  IPTRMSMAYLLELIGGKVGALGGRYIDG-------------------------------- 251

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                 TP F G  EE + + L      E+G   +Y+G+TGE   
Sbjct: 252  ---------------------TP-FIGEKEEDLRNELLEYGFRENGVETMYNGITGEEMQ 289

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + VG +  ++L H V++K+  R+ G   L+ +QP  GKS  GG RLGEME  C  AYG
Sbjct: 290  VKIFVGDMTYIRLKHFVANKIQWRARGPIQLLNRQPTEGKSKSGGLRLGEMEKDCFVAYG 349

Query: 1307 AAYVLQEMLTIKSDDV-------VGRTRVYE-------SIVAGND--TFETGTPESFNVL 1350
            +A  L+E     SD +        G T VY          + G D          SF +L
Sbjct: 350  SAMALKERF--DSDKITIPVCSKCGMTAVYNVRKKTGYCPIDGEDTQIKLIEVSASFKIL 407

Query: 1351 VKEMQALGLSIDL 1363
            + E++A+G+   +
Sbjct: 408  LDELKAVGIYPKM 420



 Score = 69.7 bits (169), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 79/174 (45%), Gaps = 12/174 (6%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           D G    G+N++VA + + GYN +D+++I++  V   +F ++    ++V       G  +
Sbjct: 20  DFGSHVFGQNIVVAVLSYLGYNMDDAIIINKSSVDRGLFRAMFFRPYKVEETKYVGGQSD 79

Query: 861 ITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           +  +         SE   K +DE GI  V + VN GD+L+G+++P        + +L   
Sbjct: 80  LITNPDKDVAGYRSEAAYKYLDEDGIAAVNSHVNSGDVLIGRVSPPRFVSSIDKFRL--- 136

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
                     ++S+   +G  G V +V + +    +K       +  ++E+  +
Sbjct: 137 ----GVQKQVESSIECRTGEGGIVENVFVTSTAEGNKYVSLKIRQDRKVEIGDK 186


>gi|520505|gb|AAC83398.1| RNA polymerase II, second largest subunit [Artemia salina]
          Length = 862

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 133/962 (13%), Positives = 270/962 (28%), Gaps = 178/962 (18%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 60   GQRIIAIVPYIKQEIPIMIVFRALGFVADRDILEHIIYEFDDPEMMEMVKPSLDEAFVIQ 119

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 120  EQNVALNFIGARGARPGV---TKDKRIKYAREILQKEMLPHVGISDFCETKK---AYFLG 173

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G ++   +R     + + ++          
Sbjct: 174  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLMSLLFRGLFKTLTKEVRMYAQKFIDRG 233

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  K +   +     +               +SQ+   +   S ++H RR++
Sbjct: 234  KDFNIELAIKPKFITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVN 293

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 294  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPIL 349

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  +    ++      +  D       L   R   + I+    
Sbjct: 350  EFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVS 409

Query: 660  KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
             +  I     ++ + A  +   L   ++ R+L+      Q                    
Sbjct: 410  MVRDIQDREIRIYTDAGRICRPLLIVENQRLLLKKTHIEQLKEKEYNNFV-------WND 462

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
              +SG           E VD +      +    D      + Y                 
Sbjct: 463  LVASGVV---------EYVDTLEEETAMIAMAPDDIRLDNEGY----------------- 496

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                              P+  LG       +  + +P+  +N          M  + + 
Sbjct: 497  --------CATYTHCEIHPAMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG 541

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              ++I  F                           ++    +  V        +    + 
Sbjct: 542  --VYITNF---------------------------HVRMDTLAHVLCYPQKPLVTTRSME 572

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +      + AI      +  D+ L   S V         F  +   + +R+++ 
Sbjct: 573  YLRFRELPAGINSIVAILCYTGYNQEDSVLMNASAVDRGFFRSVFFRSYKDAETKRAMAG 632

Query: 960  EREQ-IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              E+  E  +RD                     G              ++ +  I     
Sbjct: 633  ASEETFEKPSRD------------------TCQGMKHPQSYDKLDNDGII-APGIRVSGD 673

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   V   +    + S   +Y         R        Q    +     +  K+ V
Sbjct: 674  DVVIGKTVTMPENDDELSSAAKRYSKRDCSTFLRNSETGITDQVMLTLNTEGFKFCKIRV 733

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK A RHG KG        EDMPF  +GT  DI++NP  +PSRM +G + E
Sbjct: 734  RSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFSAEGTAPDIIINPHAIPSRMTIGHLIE 793

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
               G      G+   +   +                                        
Sbjct: 794  CIQGKVSANKGEIGDATPFN---------------------------------------- 813

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                         D  + + I+++L+       G  ++Y+G TG      V +G  Y  +
Sbjct: 814  -------------DAVNVQKISNLLQDYGYQLRGNEVMYNGFTGRKLVSQVFLGPTYYQR 860

Query: 1259 LN 1260
            L 
Sbjct: 861  LK 862



 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 109/741 (14%), Positives = 208/741 (28%), Gaps = 119/741 (16%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG  ++ +IL     +    +  +     L  A ++    V+ + +     
Sbjct: 74  IPIMIVFRALGFVADRDILEHIIYEFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGA 133

Query: 271 EQVIESGKKLTSGL----LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
              +   K++         + L   G+     T       Y+   ++    G   ++  D
Sbjct: 134 RPGVTKDKRIKYAREILQKEMLPHVGISDFCETKKAYFLGYMVHRLLLAALGRRELDDRD 193

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
               K L+            L+         +   +     K           +      
Sbjct: 194 HYGNKRLDLAGPLMSLLFRGLFKT-------LTKEVRMYAQKFIDRGKDFNIELAIKPKF 246

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  RL   +      R          +    
Sbjct: 247 ITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPR 306

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +                ++KN   +  + +       +  ++  S+   + I
Sbjct: 307 QLHNTLWGMICPAETPEGAAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLEEI 363

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
               +  A   F     +    +    ++ +   RR   +    V+  R   +      T
Sbjct: 364 APSAIADATKIFVNGCWVGIHRDPEQLMTTLRKLRRQMDIIVSEVSMVRDIQDREIRIYT 423

Query: 565 HYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             GRIC P    E   + L  +      +      E       D   +  V Y+  +EEE
Sbjct: 424 DAGRICRPLLIVENQRLLLKKT-----HIEQLKEKEYNNFVWNDLVASGVVEYVDTLEEE 478

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              IA A   +  D                           +  P  ++ + AS+IPF +
Sbjct: 479 TAMIAMAPDDIRLDNE----------------GYCATYTHCEIHPAMILGVCASIIPFPD 522

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                                        
Sbjct: 523 HNQSPRNTYQSAMGKQAMGVYITNFHV--------------------------------- 549

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                      + + V  Y               Q+PLV                     
Sbjct: 550 --------RMDTLAHVLCYP--------------QKPLV----------TTRSMEYLRFR 577

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV-MARDTKLGPEEIT 862
           +L  G N +VA + + GYN EDS+L++   V    F S+    ++    +    G  E T
Sbjct: 578 ELPAGINSIVAILCYTGYNQEDSVLMNASAVDRGFFRSVFFRSYKDAETKRAMAGASEET 637

Query: 863 RDIP-------NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            + P           +    +D  GII  G  V+  D+++GK     E+           
Sbjct: 638 FEKPSRDTCQGMKHPQSYDKLDNDGIIAPGIRVSGDDVVIGKTVTMPENDDELSSAA--- 694

Query: 916 IFGEKAVDVRDTSLRVPSGVS 936
               K    RD S  + +  +
Sbjct: 695 ----KRYSKRDCSTFLRNSET 711


>gi|269930939|gb|ACZ54204.1| RNA polymerase beta-subunit [uncultured Bartonella sp.]
          Length = 278

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 199/279 (71%), Positives = 232/279 (83%), Gaps = 1/279 (0%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSAL
Sbjct: 1   AIKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +
Sbjct: 121 IIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SG
Sbjct: 181 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           AAI AKR GIV+QVDA+RIVIR+ E  L+PS SGVDIYR
Sbjct: 241 AAIGAKRGGIVDQVDAMRIVIRATED-LNPSKSGVDIYR 278


>gi|190148974|gb|ACE63462.1| RNA polymerase subunit B [Pseudonocardia thermophila]
          Length = 270

 Score =  259 bits (662), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 153/277 (55%), Positives = 205/277 (74%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+  L++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGYLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG+VT+++ YL+A EEE   IAQAN+ LD++G+F E+ V  R   GE  
Sbjct: 61  GFIQTPYRKVVDGRVTDEIDYLTADEEERFVIAQANAPLDDEGNFIEDRVLVRRKGGEPD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +D+ID SP+Q+VS+ ++LIPFLE+DD+NR LMG NMQRQAVPLL++EAP VGTG
Sbjct: 121 LIAPSGVDYIDVSPRQMVSVGSALIPFLEHDDANRALMGANMQRQAVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE+V A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVAEKAGVVEEVCADYITVMADDGTR-------KTYRLYKFRRSNQTT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C+NQ+P+V  G  V    ++ADGP T+ G+LALG+N+
Sbjct: 234 CINQKPIVDEGQRVEAGQVLADGPCTENGELALGKNL 270


>gi|298566250|ref|NP_001177299.1| required to maintain repression7 [Zea mays]
 gi|283443696|gb|ADB19857.1| required to maintain repression 7/RNA polymerase D second largest
            subunit [Zea mays]
 gi|297185477|gb|ADI24118.1| RPD2/E2a [Zea mays]
          Length = 1229

 Score =  259 bits (662), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 98/512 (19%), Positives = 154/512 (30%), Gaps = 95/512 (18%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      S    +      +
Sbjct: 775  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYASFGRKNDFARPEY 834

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 835  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKE 893

Query: 1007 VLS----------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             +            D + +            ++ V   V      +       E     K
Sbjct: 894  KIDFGKTESKRGRVDNLDDDGLPYVGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 953

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +           G    V V +   R    GDK +  HG KG+V  +   E+ PF  +G 
Sbjct: 954  V----LLSANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHEGI 1008

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DIV+NP   P+R   GQ+ E     A +G G   K                       
Sbjct: 1009 VPDIVINPHAFPTRQTPGQLLE-----AALGKGIACKGT--------------------- 1042

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                       +  +TP F  A  + I   L  A     G   +
Sbjct: 1043 ---------------------------MRYATP-FTTASVDVIAEQLHRAGYSRWGSENV 1074

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
             +G TGE     V +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GE
Sbjct: 1075 LNGRTGERVQSLVFMGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGE 1134

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYESIVAG------- 1335
            ME  C+ A+G+A  L E L + SD              +VV R+      + G       
Sbjct: 1135 MERDCLLAHGSAANLHERLFLLSDFSQMHICQTCERVANVVMRSVPGGKKIRGPYCGFCK 1194

Query: 1336 --NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
               +      P    +L +E+ ++G+ +  E 
Sbjct: 1195 SSENIVRINVPYGAKLLYQELFSMGICLKFET 1226



 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 143/983 (14%), Positives = 286/983 (29%), Gaps = 251/983 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 104 LISHQINSYNEFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 153

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  L + + + V+ +++   +K+  D 
Sbjct: 154 GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLIVEVTIQVYSLEKSDKSKTGNDG 213

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 214 FVQKRNFMNETHWIFIGLLPVMVKSNLCLLHSLNESECLFDAGGYFLVKGMEKVFIAQEQ 273

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW-MDIEFDSK-DIIHVR-IDRRR----- 210
           R                 + L+    I D+  W +    + K   I+++ ++  R     
Sbjct: 274 RC---------------LRRLW----ISDRPCWTISFMSEIKRRRIYIKLVESTRSEDFS 314

Query: 211 --KV----------PVTSFLMALGMDSE----EILSTFYPKIVYSQRGDFWCFPLSAADL 254
             K+          PV     ALG+ S+    +++          Q  D       +A +
Sbjct: 315 ESKIITISFLYATMPVWLLFFALGISSDKEVFDMIDM--------QDCDASVINTISATI 366

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLY 307
               K+       D   Q ++   K +        +  +                  G  
Sbjct: 367 KESDKLCEDFRKSDKARQYVDELVKSSRFPPAESFDDYIARFLFPDISGNRNKALFLGYM 426

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNTLVTD 365
           V   ++   TG+   +  D    K L+       R++   +   +     A  R+     
Sbjct: 427 VKCLLM-AFTGKRKCDNKDDFRNKRLDLPGELLGRELRAQLRLAEKRMVKAIQRDLNSDR 485

Query: 366 KNKDRK---DALLDIYRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKM 416
           + +D +   DA +    + R     ++                   ++   + +  R   
Sbjct: 486 ELQDLERYIDASIVTNGLNRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTR 545

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     D R+        +  +        G + ++        R +  ++++   
Sbjct: 546 QRVAYAGKAGDARYPNPSYWGKLCFMSTPDGENCGLVKNLAVTAIVSSRVMQPLIESFIS 605

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            G+ ++     E I  +D                     F   + +   E   + + R+ 
Sbjct: 606 CGMSKLNDIPTEHIQRMDK-------------------IFLNGNWVGSCENSASFVFRLR 646

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             RR S +      +         V       + P    E  N        SF+      
Sbjct: 647 CMRRSSLIDPQVEIKRDKHHNEVRVFTDAGRILRPLLVVENLNKIRKPKGRSFS------ 700

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                     +      + ++   EEE+   A     L E                    
Sbjct: 701 --------FHELMQQEIIEFIGVEEEEDIQCAWGIRHLFESEGAI--------------- 737

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ ++  +IPF  ++ + RVL                         
Sbjct: 738 --SSYTHCELDPSFLLGLSCGIIPFANHNFARRVLYQSE--------------------- 774

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
               K S  AI         +VD                               +     
Sbjct: 775 ----KHSQQAIGYSTTNPHIRVD-----------------------------TLSHQLYY 801

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSML 828
            QRPL     +    D +        G        +   G+N +VA     G+N EDS++
Sbjct: 802 PQRPL----FKTVIADCLGRSDYASFGRKNDFARPEYFNGQNAIVAVNVHQGFNQEDSLV 857

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIIC 883
           ++   +   +F + H+  ++    +          E+I           + N+D+ G+  
Sbjct: 858 MNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKEKIDFGKTESKRGRVDNLDDDGLPY 917

Query: 884 VGAEVNPGDILVGKITPKGESPM 906
           VGA +   DI++GK++  GE   
Sbjct: 918 VGASLQTNDIVIGKVSESGEDHS 940


>gi|111378445|gb|ABH09235.1| RNA polymerase beta subunit [uncultured Bartonella sp.]
          Length = 277

 Score =  259 bits (662), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 198/277 (71%), Positives = 230/277 (83%), Gaps = 1/277 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D
Sbjct: 121 VDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           AI AKR GIV+QVDA+RIVIR+ E  LDPS SGV+IY
Sbjct: 241 AIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVEIY 276


>gi|303274472|ref|XP_003056556.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226462640|gb|EEH59932.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 1198

 Score =  259 bits (662), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 107/244 (43%), Gaps = 47/244 (19%)

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK-DGTPVDIVLNPLGVPSRMNVGQI 1136
            +   R    GDK + RHG KG++S + P E +P+++  G   DI++NP   PSRM +G +
Sbjct: 909  LRYNRNPIIGDKFSSRHGQKGVLSFLWPEESLPYVERTGIRPDIIINPHAFPSRMTIGML 968

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E+    +    G  I +                                        + 
Sbjct: 969  VESMASKSGALDGACINASPF-------------------------------------KA 991

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            A++ K+  P +               LR    D  G   + +GLTGE F   + +G +Y 
Sbjct: 992  AQKEKTYSPPA---------AEYGETLRKHGYDYCGSETMVNGLTGEAFGVDIYIGLVYY 1042

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMVSDK   RS G  + +TQQP  G+ + GG R GEME   + A+GAAY++ + L 
Sbjct: 1043 QRLRHMVSDKFQVRSVGPNNSLTQQPTKGRKSGGGIRFGEMERDALLAHGAAYLIHDRLH 1102

Query: 1317 IKSD 1320
              SD
Sbjct: 1103 ACSD 1106



 Score = 56.2 bits (134), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/162 (14%), Positives = 44/162 (27%), Gaps = 63/162 (38%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFK---SVF---PITAF-SGAAMLEFVSYEFD------ 82
           S+++F+            GL    K   SV    P T+  S    L F            
Sbjct: 28  SFNYFV----------EHGLAEVIKRMASVSVQAPGTSAQSSRIRLWFSGVSMKTPVRER 77

Query: 83  -------PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                   P+    +C     TY  P+   +   V +           ++    + +   
Sbjct: 78  DGLSLARDPRVFPRECREAGSTYKAPMTANICWSVGEA---------GEVYHHELQLCQF 128

Query: 136 PLMTKD------------------------GTFVIKGIQRIV 153
           P+M                           G F++ G +R++
Sbjct: 129 PVMVSSTRCHLASASRAELINRGEEGREIGGYFILNGNERMI 170


>gi|300394694|gb|ADK11885.1| DNA-directed RNA polymerase II subunit two [Coniophora marmorata]
          Length = 686

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 124/814 (15%), Positives = 237/814 (29%), Gaps = 144/814 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   F       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTVCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      LL+ +   ++  G                + G++E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLLLQKKHIKWLNQGYRDDEPAEEFKWDQLVKGGVIELLDA 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +         +   +    +K G            PS 
Sbjct: 286  EEEETVMIAMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSM 343

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 344  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 378

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 379  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 427

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 428  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTY 486

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 487  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 546

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 547  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 586

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +         
Sbjct: 587  GITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 639

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 640  ----------------------------------------------ATP-FTDLTVESVS 652

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            + LR       G  ++Y G TG      V +G  
Sbjct: 653  TFLRQKGYQSRGLEVMYHGHTGRKLQAQVYLGPT 686



 Score =  121 bits (303), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 165/610 (27%), Gaps = 96/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNISLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESLEENAHSSTVCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +              K         +  L A EEE   IA     L+     + 
Sbjct: 249 QKKHIKWLNQGYRDDEPAEEFKWDQLVKGGVIELLDAEEEETVMIAMTPEDLENSRLQSA 308

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +   +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 309 GIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLV-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 484 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 539

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 540 TENGIVDQVL 549


>gi|300394674|gb|ADK11875.1| DNA-directed RNA polymerase II subunit two [Amylocorticium
            cebennense]
          Length = 689

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 122/817 (14%), Positives = 231/817 (28%), Gaps = 147/817 (17%)

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAV 513
             D+ G +R+   G +L N +R+   ++ R +    +              +  + + + +
Sbjct: 3    DDHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNVSLAVKHQTITNGL 62

Query: 514  CEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
                 +               +SQ+       S ++H RR +      + R     + R 
Sbjct: 63   KYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQ 118

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G +CPAET EG   GLV +L   A ++           + +  + +        
Sbjct: 119  LHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSISAPVIEFLEEWGLESL------- 171

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             EEN + +   + +  +G +       R  G  +   ++     D SP+  V        
Sbjct: 172  -EENAHSSTPCTKVFVNGVWMG---VHRDPGNLVKTIKKLRRKDDISPEVSVVRDIREKE 227

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                 D+ RV     +      +L+ +                       R       D 
Sbjct: 228  LRLYTDAGRVCRPLFIVENQQLILQKKH---------------------IRWLDQGYTDD 266

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
            +    +  E         +D           +   +   P       +++  +       
Sbjct: 267  VEETFKWDELVKHGIIELLD-------AEEEETVMIAMTPEDLDNSRLQQGALDLRKLDE 319

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +    A  +  + A   W       SM+  I   ++            ++       +G 
Sbjct: 320  EFDPAARLKAGVNAH-TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGI 378

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                  +               +  +             +       +   +  + AI  
Sbjct: 379  YLTNFLVRM-----------DTMANILYYPQKPLATTRSMMYLKFRELPAGQNAIVAILC 427

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    I+ R  +D  ++S   + EQ E   RD        
Sbjct: 428  YSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEQFEKPTRDNTLRMKHG 486

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +       I  G           K+  +  D      R++          ++     +
Sbjct: 487  TYDKIEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTETGI 546

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                              + VKV V   R  Q GDK A RHG KG
Sbjct: 547  VDQVLI--------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKG 586

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +       
Sbjct: 587  TIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD----- 641

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     E+
Sbjct: 642  ------------------------------------------------ATP-FTDLTVES 652

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
            ++  L        G  ++Y G TG      + +G  Y
Sbjct: 653  VSKFLLQKGYQSRGMEVMYHGHTGRKLQAQIYLGPTY 689



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 88/622 (14%), Positives = 173/622 (27%), Gaps = 100/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+V+ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNVSLAVKHQTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLALMACISVGSISAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 192 GVHRDPGNLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLIL 251

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +        +E  + K  +      +  L A EEE   IA     LD       
Sbjct: 252 QKKHIRWLDQGYTDDVEETF-KWDELVKHGIIELLDAEEEETVMIAMTPEDLDNSRLQQG 310

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            L   +   E          V        +  P  ++ I AS+IPF +++ S R      
Sbjct: 311 ALDLRKLDEEFDPAARLKAGVNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 370

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 371 MGKQAMGIYLTNFLV-----------------------------------------RMDT 389

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 390 MANILYYPQKPLATTRSMMYLKFR------------------------ELPAGQNAIVAI 425

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 426 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEQFEKPTRDNTLRMKH 485

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 486 GTYDKIEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 538

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  +G V  V I       K
Sbjct: 539 LKSTETGIVDQVLITTNSEGQK 560


>gi|52699884|gb|AAU87003.1| DNA-dependent RNA polymerase II second largest subunit [Stereocaulon
            paschale]
          Length = 717

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 129/837 (15%), Positives = 245/837 (29%), Gaps = 144/837 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAGLFRMLFHKLTKDVYKYLQKCVENNKDFNMALAVKSTTLTNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L++
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLNS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      I D  D   K         
Sbjct: 177  PNATKIFVNGVWVGVHRDPAHLVGTVQNLRRKGNISYEVSLIRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIV 735
             P    D+  R     N+   +Q V  L+ +  +  T   E     + G      R+G+V
Sbjct: 237  RPLFVIDNDPRSSNCGNLVLTKQLVAQLEEDREYGATLDPEEKEKANIG-WQRLLRSGVV 295

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA       +    +       +        ++ +  +N+R         R      
Sbjct: 296  EYVDAEEEETIMIVMTPEDLEMSRQLEAGFSMPPADPDD-LNKRVKATPNPTARTWTHCE 354

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N                        ++       
Sbjct: 355  IHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGXXX 389

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             G      D+               +  +             +       +   +  + A
Sbjct: 390  XGVFLTNYDVRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 438

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 439  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMALVEEFEKPMRSDT 494

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 495  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLR 554

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q   S                         LR  KV +   +  Q GDK A 
Sbjct: 555  STENGIVDQVLLS--------------------TNADGLRFAKVRMRTTKIPQIGDKFAS 594

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 595  RHGQKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 654

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 655  DATPFTEVTVDSVSRLLR--EHGYQSRGFEVM---------------------------- 684

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                              +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 685  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 717


>gi|283443700|gb|ADB19859.1| mutant required to maintain repression 7-2/ RNA polymerase D second
            largest subunit 2-2 [Zea mays]
          Length = 1229

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 98/512 (19%), Positives = 154/512 (30%), Gaps = 95/512 (18%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      S    +      +
Sbjct: 775  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYASFGRKNDFARPEY 834

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 835  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKE 893

Query: 1007 VLS----------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             +            D + +            ++ V   V      +       E     K
Sbjct: 894  KIDFGKTESKRGRVDNLDDDGLPYVGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 953

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +           G    V V +   R    GDK +  HG KG+V  +   E+ PF  +G 
Sbjct: 954  VLL----SANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHEGI 1008

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DIV+NP   P+R   GQ+ E     A +G G   K                       
Sbjct: 1009 VPDIVINPHAFPTRQTPGQLLE-----AALGKGIACKGT--------------------- 1042

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                       +  +TP F  A  + I   L  A     G   +
Sbjct: 1043 ---------------------------MRYATP-FTTASVDVIAEQLHRAGYSRWGSENV 1074

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
             +G TGE     V +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GE
Sbjct: 1075 LNGRTGERVQSLVFMGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGVKFGE 1134

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD--------------DVVGRTRVYESIVAG------- 1335
            ME  C+ A+G+A  L E L + SD              +VV R+      + G       
Sbjct: 1135 MERDCLLAHGSAANLHERLFLLSDFSQMHICQTCERVANVVMRSVPGGKKIRGPYCGFCK 1194

Query: 1336 --NDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
               +      P    +L +E+ ++G+ +  E 
Sbjct: 1195 SSENIVRINVPYGAKLLYQELFSMGICLKFET 1226



 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 143/983 (14%), Positives = 286/983 (29%), Gaps = 251/983 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 104 LISHQINSYNEFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 153

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  L + + + V+ +++   +K+  D 
Sbjct: 154 GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLIVEVTIQVYSLEKSDKSKTGNDG 213

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 214 FVQKRNFMNETHWIFIGLLPVMVKSNLCLLHSLNESECLFDAGGYFLVKGMEKVFIAQEQ 273

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW-MDIEFDSK-DIIHVR-IDRRR----- 210
           R                 + L+    I D+  W +    + K   I+++ ++  R     
Sbjct: 274 RC---------------LRRLW----ISDRPCWTISFMSEIKRRRIYIKLVESTRSEDFS 314

Query: 211 --KV----------PVTSFLMALGMDSE----EILSTFYPKIVYSQRGDFWCFPLSAADL 254
             K+          PV     ALG+ S+    +++          Q  D       +A +
Sbjct: 315 ESKIITISFLYATMPVWLLFFALGISSDKEVFDMIDM--------QDCDASVINTISATI 366

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLY 307
               K+       D   Q ++   K +        +  +                  G  
Sbjct: 367 KESDKLCEDFRKSDKARQYVDELVKSSRFPPAESFDDYIARFLFPDISGNRNKALFLGYM 426

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNTLVTD 365
           V   ++   TG+   +  D    K L+       R++   +   +     A  R+     
Sbjct: 427 VKCLLM-AFTGKRKCDNKDDFRNKRLDLPGELLGRELRAQLRLAEKRMVKAIQRDLNSDR 485

Query: 366 KNKDRK---DALLDIYRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKM 416
           + +D +   DA +    + R     ++                   ++   + +  R   
Sbjct: 486 ELQDLERYIDASIVTNGLNRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTR 545

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     D R+        +  +        G + ++        R +  ++++   
Sbjct: 546 QRVAYAGKAGDARYPNPSYWEKLCFMSTPDGENCGLVKNLAVTAIVSSRVMQPLIESFIS 605

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            G+ ++     E I  +D                     F   + +   E   + + R+ 
Sbjct: 606 CGMSKLNDIPTEHIQRMDK-------------------IFLNGNWVGSCENSASFVFRLR 646

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             RR S +      +         V       + P    E  N        SF+      
Sbjct: 647 CMRRSSLIDPQVEIKRDKHHNEVRVFTDAGRILRPLLVVENLNKIRKPKGRSFS------ 700

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                     +      + ++   EEE+   A     L E                    
Sbjct: 701 --------FHELMQQEIIEFIGVEEEEDIQCAWGIRHLFESEGAI--------------- 737

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ ++  +IPF  ++ + RVL                         
Sbjct: 738 --SSYTHCELDPSFLLGLSCGIIPFANHNFARRVLYQSE--------------------- 774

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
               K S  AI         +VD                               +     
Sbjct: 775 ----KHSQQAIGYSTTNPHIRVD-----------------------------TLSHQLYY 801

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSML 828
            QRPL     +    D +        G        +   G+N +VA     G+N EDS++
Sbjct: 802 PQRPL----FKTVIADCLGRSDYASFGRKNDFARPEYFNGQNAIVAVNVHQGFNQEDSLV 857

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIIC 883
           ++   +   +F + H+  ++    +          E+I           + N+D+ G+  
Sbjct: 858 MNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKEKIDFGKTESKRGRVDNLDDDGLPY 917

Query: 884 VGAEVNPGDILVGKITPKGESPM 906
           VGA +   DI++GK++  GE   
Sbjct: 918 VGASLQTNDIVIGKVSESGEDHS 940


>gi|224008096|ref|XP_002293007.1| DNA directed RNA polymerase i, second largest subunit [Thalassiosira
            pseudonana CCMP1335]
 gi|220971133|gb|EED89468.1| DNA directed RNA polymerase i, second largest subunit [Thalassiosira
            pseudonana CCMP1335]
          Length = 1069

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 87/459 (18%), Positives = 156/459 (33%), Gaps = 76/459 (16%)

Query: 877  DECGIICVGAEVNPGDILVG---KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            D         +   G   +G      P        + +  +A   + AV         P+
Sbjct: 584  DYNQSPRNMYQCQMGKQTMGTPCHSLPYRADNKMYKIQTPQAPLVQTAVHGEYKMDEYPN 643

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
            G +  V  +        D              ++      E+     ++Y  +   LC +
Sbjct: 644  GTNAVVAVLSYTGFDMED-------------AMILNKSSYERGFGHASVYKTIKIRLCNK 690

Query: 994  NAVSGPKGFKKSTVLS------SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSK 1046
                      +  + +         + E    +  Q+  + + +    +      Y    
Sbjct: 691  TKRVKIPPENEGDLPTFRHDPVYPHLDEDGLPRVGQWVEEGDALYCLADDDGNKGYPGKH 750

Query: 1047 SILEDRFKNKIEKIQWGDDMPP-----GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
               E      I ++  G          G    + + +   R    GDK + RHG KG++S
Sbjct: 751  KEKEKACVQTIRRLNTGGTSSASRGSKGTDDALSITLRFPRNPVIGDKFSSRHGQKGVLS 810

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
             + P  DMPF + G   D+++NP   PSRM +G + E+  G +    G    +    +  
Sbjct: 811  ILWPQTDMPFSESGISPDVIINPHAFPSRMTIGMLIESMAGKSGASHGMFQDATPFSFHE 870

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +G                                                D    +    
Sbjct: 871  SG------------------------------------------------DKIAVDYFGE 882

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L+ A  +  G   LY G++G      + +G ++  +L HMVSDK   R+TG+ + +T+Q
Sbjct: 883  QLQAAGYNYYGSEPLYSGVSGCLMHADLYIGVVFYQRLRHMVSDKYQVRATGTVNPLTRQ 942

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            P+ G+   GG RLGEME   + ++G A++L + L   SD
Sbjct: 943  PIKGRKKGGGIRLGEMERDSLLSHGTAFLLHDRLLNCSD 981



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 88/610 (14%), Positives = 191/610 (31%), Gaps = 81/610 (13%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE--SMFNFLFFDSDKY 406
            D    N  ++        + R + LL   +           +A   S F  +   ++  
Sbjct: 144 TDEELYNRIVQGDESNTFVRARAELLLREAKQFNGMQTPEECLAFVGSRFRLMSMKANST 203

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
               +G   +N  + +  P     +  E  + +++ L     G   +D+ D+L N+ +  
Sbjct: 204 SDVEIGHYIINRYILIHLPSYGDKL--EYTLFMLRKLYSFAAGDCGVDNADSLQNQEILL 261

Query: 467 VGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQD-----------LINAKPV 509
            G ++    +      L  +R+    + R+    + + +PQ            ++++  +
Sbjct: 262 PGHLMCTFVKEKFDETLANIRLGLLKEMRMDYTKLLTSVPQVKFWTKCVDRYGMLSSGGI 321

Query: 510 VSAVCEFFCSSQ--------LSQLEEHVNSLSRITHTR---RLSALGQGGVARARAGVEM 558
              V  F  +          L Q+  +     ++   R      ++ +G          +
Sbjct: 322 GKKVQHFLSTGNIISSTGLDLMQVSGYTIVAEKLNFLRFCAHFRSVHRGQFFMEMKTTAV 381

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY------GFIETPYRKVCDGKVTN 612
           R + P  +G +CP  T +G   GL+S +    +  AY      G ++     +    VT 
Sbjct: 382 RKLLPDQWGFLCPVHTPDGGPCGLLSHMALKCQCMAYPADAKDGEMQDLDELLISWGVTP 441

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP---- 668
                   +         N  +  +G          C      +   K+      P    
Sbjct: 442 AGTGGEGGD-GRTISNFTNLPVMVNGRVVGGASVKLCKSIAFQLRSLKVQEKPTVPPTLE 500

Query: 669 ---------------KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF--- 710
                            + +IAA ++  +    + R      M++  + +          
Sbjct: 501 VAYIPPGMKGGPYPGLFLFTIAARVVRPVLQRATGRTEYIGPMEQPFMDIACLPEDIREG 560

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQR 769
           + T  E   A        +  A +    D  +      +  +   T G   +    +   
Sbjct: 561 ITTHQELDPANML-----SLIASLTPFSDYNQSPRNMYQCQMGKQTMGTPCHSLPYRADN 615

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q PLV+           A      + +   G N +VA + + G++ ED+M++
Sbjct: 616 KMYKIQTPQAPLVQ----------TAVHGEYKMDEYPNGTNAVVAVLSYTGFDMEDAMIL 665

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKL---GPEEITRDIPNVSEEG-LKNIDECGIICVG 885
           ++         +   +  ++   +       P E   D+P    +    ++DE G+  VG
Sbjct: 666 NKSSYERGFGHASVYKTIKIRLCNKTKRVKIPPENEGDLPTFRHDPVYPHLDEDGLPRVG 725

Query: 886 AEVNPGDILV 895
             V  GD L 
Sbjct: 726 QWVEEGDALY 735


>gi|300394750|gb|ADK11913.1| DNA-directed RNA polymerase II subunit two [Serpula himantioides]
          Length = 685

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 121/814 (14%), Positives = 232/814 (28%), Gaps = 145/814 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+   +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFVKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +      + K   I      
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEEYKWEHLVKGGIIELLDAE 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +       D   S +    +            +    +K G+           PS 
Sbjct: 286  EEETVMISMTPEDLENSKLQSAGIDPHTNDGD---YDPAARLKAGNNSHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 378  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 486  DKLEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VK+ V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +         
Sbjct: 586  GITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 638

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 639  ----------------------------------------------ATP-FTDLTVESVS 651

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            + LR       G  ++Y G TG      V +G  
Sbjct: 652  TFLRQKGYQSRGLEVMYHGHTGRKLQAQVYLGPT 685



 Score =  118 bits (295), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 168/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +     Y   +    K         +  L A EEE   I+     L+     + 
Sbjct: 249 QKKHIKWLN-QGYRDDDGEEYKWEHLVKGGIIELLDAEEEETVMISMTPEDLENSKLQSA 307

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+     R             +  P  ++ + AS+IPF +++ S R      
Sbjct: 308 GIDPHTNDGDYDPAARLKAGNNSHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 367

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 368 MGKQAMGIYLTNFLV-----------------------------------------RMDT 386

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 387 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 422

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 423 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKH 482

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 483 GTYDKLEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 538

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 539 TENGIVDQVL 548


>gi|45120578|gb|AAO64677.2| RNA polymerase II subunit RPB2 [Henningsomyces candidus]
          Length = 848

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 133/864 (15%), Positives = 260/864 (30%), Gaps = 148/864 (17%)

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
              +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +
Sbjct: 116  RIRYAQEILQKEMIPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHFGKK 172

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L N +R+   ++ + +    +              +  + + + +     + 
Sbjct: 173  RLDLAGPLLANLFRMLFRKLSKDVYRYLQKCVEAQKEFNLALAVKHQTITNGLKYSLATG 232

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 233  NWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWG 288

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
             +CPAET EG   GLV +L   A ++           + +  + +         E+N + 
Sbjct: 289  MVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL--------EDNAHS 340

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                + +  +G +       R  G  +   ++     D SP+  V             D+
Sbjct: 341  TVPCTKVFVNGVWMG---VHRDPGNLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDA 397

Query: 688  NRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             RV     +      +L+ +   ++G G +   +K    ++   + GIVE +DA      
Sbjct: 398  GRVCRPLFIVENQQLVLQKKHVKWLGQGTDDQGSKFLWESL--IKTGIVELLDAEEEETV 455

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +    +   +              +    +    +K G            PS  LG   
Sbjct: 456  MISMTPEDLETSRLQQSGADPHTHEEEE-FDPAARLKAGSNSHTWTHCEIHPSMILG--- 511

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N                        ++       +G       I 
Sbjct: 512  ----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIR 549

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 550  M-----------DTMANILFYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 598

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    I+ R  +D  ++S   + E+ E   RD          +     
Sbjct: 599  SVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVAQLEEFEKPTRDNTLRMKHGTYDKLDED 657

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G           K+  +  D      R++                          
Sbjct: 658  GLISPGVGVSGEDIIIGKTAPIPPDSEELGQRTRL------------------HTRRDVS 699

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
            + L+     KI+++           + VKV +   R  Q GDK A RHG KG +      
Sbjct: 700  TPLKSTENGKIDQVLI--TTNSEGQKFVKVRIRSIRIPQIGDKFASRHGQKGTIGITYRQ 757

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF ++G   DI++NP  +PSRM +G + E  L      LG +               
Sbjct: 758  EDMPFTREGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLLGNEGD------------- 804

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                    +TP F     E++++ LR  
Sbjct: 805  ----------------------------------------ATP-FTELTVESVSTYLRQK 823

Query: 1227 DLDESGQSILYDGLTGEPFDRPVT 1250
                 G  ++Y G TG      V 
Sbjct: 824  GYQSRGLEVMYHGHTGRKLQAQVY 847



 Score =  140 bits (352), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 103/760 (13%), Positives = 222/760 (29%), Gaps = 110/760 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 43  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDAQILEMLKPCIDDGFVIQDREVA 98

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   K++     + L+++ +  + +            G  +   ++  
Sbjct: 99  LDFIGNRGTTTGLSRDKRIRYAQ-EILQKEMIPHVSMAEGSESKKAYFFGYMIHRLLL-A 156

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                 ++  D   +K L+           +L+   ++ + Y       +  K+   AL 
Sbjct: 157 ALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRK-LSKDVYRYLQKCVEAQKEFNLALA 215

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
             ++ +  G      +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 216 VKHQTITNG------LKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTP 269

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + E +   
Sbjct: 270 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEW 329

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++S+      NA   V     F     +    +  N +  I   RR   +         
Sbjct: 330 GLESL----EDNAHSTVPCTKVFVNGVWMGVHRDPGNLVKTIKKLRRKDDISPEVSVVRD 385

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L      +  +      +           T  
Sbjct: 386 IRERELRLYTDAGRVCRPLFIVENQQLVLQKKHVKW--LGQGTDDQGSKFLWESLIKTGI 443

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL--------VPREKIDFID 665
           V  L A EEE   I+     L+                EE                   +
Sbjct: 444 VELLDAEEEETVMISMTPEDLETSRLQQSGADPHTHEEEEFDPAARLKAGSNSHTWTHCE 503

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R      M +QA+ +                      
Sbjct: 504 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI--------------- 548

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                        + + +  Y       +     +  R      
Sbjct: 549 --------------------------RMDTMANILFYPQKPLATTRSMEYLKFR------ 576

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N +VA + + GYN EDS+++++  +   +F SI+  
Sbjct: 577 ------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYR 618

Query: 846 EFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +  + + + +   E        +   +       +DE G+I  G  V+  DI++GK  P
Sbjct: 619 SYMDLEKKSGVAQLEEFEKPTRDNTLRMKHGTYDKLDEDGLISPGVGVSGEDIIIGKTAP 678

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                    E+L +        DV        +G    V+
Sbjct: 679 I----PPDSEELGQRTRLHTRRDVSTPLKSTENGKIDQVL 714


>gi|119644183|gb|ABL85611.1| RNA polymerase II second largest subunit [Phaeophyscia orbicularis]
          Length = 718

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 117/840 (13%), Positives = 233/840 (27%), Gaps = 150/840 (17%)

Query: 455  DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSA 512
            D D+ G +R+   G +L   +R    ++ + +    ++   +    +    + +  + + 
Sbjct: 2    DRDHFGKKRLDLAGPLLAGLFRTLFNKLTKDLEKYLKVCIENSKEFILNLGVKSSTLTNG 61

Query: 513  VCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
            +     +               +SQ+       S ++H RR +      + R     + R
Sbjct: 62   LKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPR 117

Query: 560  DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYL 617
             +H TH+G +CPAET EG   GLV +L     V+     E   P+      +   +    
Sbjct: 118  QLHNTHWGLVCPAETPEGQACGLVKNLALMCHVSVGTPSEGIVPFLLQRQMESLEEYEPH 177

Query: 618  SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            ++      ++      +  + +     V                      P+  +     
Sbjct: 178  ASPNATKIFVNGVWVGVHRNPAHLVTAVQSLRRKHV------------LEPEVSLIRDIR 225

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
               F    D  RVL    +                 G  + +           +    + 
Sbjct: 226  EREFRILTDQGRVLRPLFVVETDPKSPNCGNLVFNKGHSNKLDDDQEVPHDMDKELREKM 285

Query: 738  VDA-----IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRN 791
            +          V+  V+ + + +   V   + +   R  Q       P   +    V   
Sbjct: 286  IFGWNGLINEGVVEYVDAEEEETVMIVMTPQDLAMSRQLQAGYALAEPDPDEPNRRVTAP 345

Query: 792  DIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                    T      ++   +  + +P+  +N          M  + +   + +  ++  
Sbjct: 346  MNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQR 403

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                             +             +       +   +
Sbjct: 404  METMS---------------------------HILYYPQKPLATTRSMEYLKFRELPAGQ 436

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D+ +R  +     +E   + 
Sbjct: 437  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGT---NVLEQFEKP 492

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + + L    Y +L +   I+ G           K+  +S D      R++       
Sbjct: 493  MRADTLKLKHGTYDKLDDDGIIIPGARVSGDDVIIGKTAPISPDAEELGQRTKLHTKRDA 552

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     L  Q                             LR VKV +   +  Q G
Sbjct: 553  STPLRSTESGLVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIG 592

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L      
Sbjct: 593  DKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLIECQLSKVASL 652

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G +  +          +S L    E    +                             
Sbjct: 653  RGLEGDATPFTEITVDSVSRLLR--EHGYQSRGFEVM----------------------- 687

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                   +G +    G         V +G  Y  +L HMV DK+
Sbjct: 688  ----------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 718


>gi|52694127|emb|CAG30593.1| DNA-directed RNA polymerase beta chain [Pseudomonas aurantiaca]
          Length = 260

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 152/260 (58%), Positives = 200/260 (76%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 1   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKR 60

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 61  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 120

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V +G VT+++V+LSA+EE +  IAQA++++++ G   +ELV  R   E  +   E
Sbjct: 121 SPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKGQLIDELVAVRHLNEFTVKAPE 180

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  V
Sbjct: 181 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNV 240

Query: 720 AKSSGAAIVAKRAGIVEQVD 739
           A+ SG  +VA+R G+++ VD
Sbjct: 241 ARDSGVCVVARRGGVIDSVD 260


>gi|295815637|gb|ADG36321.1| RNA polymerase beta-subunit [Mycobacterium europaeum]
          Length = 222

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 92/219 (42%), Positives = 121/219 (55%), Gaps = 40/219 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPQEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAAN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 141  -----------------LPEGLLHAQPNQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK
Sbjct: 184  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDK 222



 Score = 40.8 bits (94), Expect = 1.6,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 44


>gi|153958188|gb|ABS53384.1| RpoB [Bacteriovorax sp. SAN2]
          Length = 368

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 176/371 (47%), Positives = 248/371 (66%), Gaps = 10/371 (2%)

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+ES VA+ SGA + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQN
Sbjct: 1    GIESTVARDSGAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQN 58

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC NQ+ LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+
Sbjct: 59   TCNNQKALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERL 118

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            ++ DVFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDI
Sbjct: 119  LARDVFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDI 178

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++  
Sbjct: 179  LVGKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELC 238

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKST 1006
             RS  +  ++  L+ RD+  E   +  +   ++ ++L G              +   K  
Sbjct: 239  ARSKEIIEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGA 298

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+S++++  P        ++   ++  +           + +  +  ++I K   GD++
Sbjct: 299  DLTSEVLASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDEL 357

Query: 1067 PPGVLRVVKVF 1077
            PPGV++ V ++
Sbjct: 358  PPGVIKKVTIY 368


>gi|22086608|gb|AAM90690.1|AF403008_1 RNA polymerase beta subunit [Rickettsia africae]
          Length = 290

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 191/291 (65%), Positives = 240/291 (82%), Gaps = 2/291 (0%)

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++S+ ++AR+N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG
Sbjct: 1   EYGLINSMATYARINKHGFIESPYRRVKDGCVTDEVVYLSAIEEGKYKIGQANSKINKDG 60

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               E + CR   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQ
Sbjct: 61  KLQGEFINCRVEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQ 120

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL+K +APFVGTG+E +VAK SGA+++A   GIVEQVD+ RIVIR++E      + 
Sbjct: 121 RQAVPLIKTDAPFVGTGVEGIVAKDSGASVLALHDGIVEQVDSNRIVIRTLE-QKVDGSP 179

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            VDIY L+KFQ+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+P
Sbjct: 180 SVDIYNLLKFQKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLP 239

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           W+GYNFEDS+LISER+V EDVFTSIHIEEFEV+ARDT+LGPEEITRDIPNV
Sbjct: 240 WNGYNFEDSILISERIVKEDVFTSIHIEEFEVIARDTRLGPEEITRDIPNV 290


>gi|113957845|gb|ABI49126.1| RNA polymerase II second largest subunit [Ramalina complanata]
          Length = 709

 Score =  259 bits (661), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 120/827 (14%), Positives = 233/827 (28%), Gaps = 143/827 (17%)

Query: 466  SVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G +L+  +R+   ++ + + +  +    +         + +  + + +     +    
Sbjct: 1    LAGPLLEGLFRMLFYKLTKDVYKYLQRCVENNKEFNLTLAVKSTTLTNGLKYSLATGNWG 60

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 61   DQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 116

Query: 571  PAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            PAET EG   GLV +L    +  V   G     +      ++  +   LS       ++ 
Sbjct: 117  PAETPEGQACGLVKNLALMCYITVGTPGQPIVDFMMQRQMELLEEYEPLSNPNATKIFVN 176

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDS 687
                 +    +     V        I      + D  D   K          P    + +
Sbjct: 177  GVWVGVHSQPAILTATVMSLRRKGLISYEVSLVRDIRDREFKIFTDAGRVCRPLFVVESN 236

Query: 688  NRV-LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVI 745
             R    G  +  +           + + M++   +          + G VE VDA     
Sbjct: 237  PRDQNFGNLVLTKHDVQELDHNRELISSMDAQDREDQAIGWQGLVKNGKVEYVDAEEEET 296

Query: 746  RSVEGDLDPST--SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
              +    +          Y        +     N+R  V+     +        PS  LG
Sbjct: 297  IMIVMTPEDLEISKHYSTYGDDALAGDDNKDDPNKRMKVRPKAIRQAWTHCEIHPSMILG 356

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   + +  ++V              
Sbjct: 357  -------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM------------ 395

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             +  +             +       +   +  + AI      +
Sbjct: 396  ---------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYN 440

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R   D+ +R        +E   +    + + L    Y
Sbjct: 441  QEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---SVVEQFEKPMRSDTLSLKHGTY 496

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   +  G           K+  ++ D      R++          ++     +  
Sbjct: 497  DKLDDDGIVSPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVD 556

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q   S                         LR VKV +   +  Q GDK A RHG KG +
Sbjct: 557  QVLLS--------------------TNSDGLRFVKVRMRTTKIPQIGDKFASRHGQKGTI 596

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 597  GITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEV 656

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L    E    +                                          
Sbjct: 657  TVDSVSRLLR--EHGYQSRGFEVM------------------------------------ 678

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                      +G +    G         V +G  Y  +L HMV DK+
Sbjct: 679  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 709


>gi|123979408|gb|ABM81529.1| RNA polymerase II second largest subunit [Masonhalea richardsonii]
          Length = 704

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 121/822 (14%), Positives = 242/822 (29%), Gaps = 142/822 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++   + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRGTFNKLTNDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      + D  D   K          P F+
Sbjct: 178  IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAI 741
             ++D      G  +  +             T  E  V + +        + G+VE VDA 
Sbjct: 238  IDNDPRSSNKGNLVLTKEHVQKLELDRENWTTTEPDVREKTDMGWQGLVKEGVVEYVDAE 297

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +       +   ++    N N  +N+R    +             PS  
Sbjct: 298  EEETIMIVMTPEDLDISRQLQAGLEPPGPNPNE-LNRRVKAPMNPTAHTWTHCEIHPSMI 356

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +   + +  ++             
Sbjct: 357  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM---------- 397

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 398  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 440

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R        +E   +    + + L   
Sbjct: 441  HNQEDSVIVNQSSIDRGLF-RSLFYRAYTDQEKRVGM---SVVEQFEKPMQSDTLKLKHG 496

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 497  TYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGI 556

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q   S                         LR VKV +   +  Q GD+ A RHG KG
Sbjct: 557  VDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDRFASRHGQKG 596

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E                    
Sbjct: 597  TIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIEC------------------- 637

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                              +L      +     +TP F     ++
Sbjct: 638  ----------------------------------LLSKVSSLRGFEGDATP-FTEVTVDS 662

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++ +LR       G  ++Y+G TG      V +G  Y  +L 
Sbjct: 663  VSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLR 704



 Score = 70.1 bits (170), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 63/463 (13%), Positives = 125/463 (26%), Gaps = 55/463 (11%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK   D    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 8   GPLLASLFRGTFNKLTNDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 185 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 244

Query: 574 TSEGHNIGLVSSLTSF--ARVNAYGFIETPYRKVCDGKV----TNDVVYLSAMEEENRYI 627
           +++G+ +     +      R N          K   G         V Y+ A EEE   I
Sbjct: 245 SNKGNLVLTKEHVQKLELDRENWTTTEPDVREKTDMGWQGLVKEGVVEYVDAEEEETIMI 304

Query: 628 AQANSSLDEDGSFTEELVF--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                 LD        L           R     +          +  P  ++ I AS+I
Sbjct: 305 VMTPEDLDISRQLQAGLEPPGPNPNELNRRVKAPMNPTAHTWTHCEIHPSMILGICASII 364

Query: 680 PFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GMESVVAKS 722
           PF +++ S R      M +QA+                 L   + P   T  ME +  + 
Sbjct: 365 PFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRE 424

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
             A   A  A            +   +  +D        YR  
Sbjct: 425 LPAGQNAIVAIACYSGHNQEDSVIVNQSSIDRGLFRSLFYRAY 467


>gi|120561273|gb|ABM27021.1| RNA polymerase II second largest subunit [Monoblepharis macrandra]
          Length = 879

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 132/844 (15%), Positives = 249/844 (29%), Gaps = 161/844 (19%)

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDID 496
            +I  L+     +   DD D+ G +R+   G ++ N +R+   R+ + I    R +     
Sbjct: 176  MIHRLLLCALERREADDRDHFGKKRLDLAGPLMANLFRMLFRRLTQDISRALRKAVESHR 235

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSA 543
                   +  + +   +     +               +SQ+       S ++H RRL++
Sbjct: 236  EFNMVSAVQHQIITRGLQFSLATGNWGDQRKMMQTRAGVSQVLSRYTYASTLSHLRRLNS 295

Query: 544  LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                 + R     + R +H TH+G +CPAET EG   GLV +L   A ++    +E    
Sbjct: 296  ----PIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAYISVGSPVEPLVD 351

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID- 662
             + +     D+  LSA +  ++     N          EEL+         +    ++  
Sbjct: 352  FLQEW-TLEDLEELSADDIRDKCKVFLNGVWIGVHRNPEELMRIFRDYRRKISISAEVSA 410

Query: 663  FIDASPKQVVSIAAS---LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
              D   K++  ++ +     P    ++   + +      +           V  G+    
Sbjct: 411  VWDVREKELRFLSDAGRICRPLFVVNNMQ-LEIRKGHIAKLQNQTWKWGDLVSNGL---- 465

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                           VE VD        +    D     +          + Q   V  R
Sbjct: 466  ---------------VEYVDTDEEETTMIAMSFDDLRDSMI---------AAQGEEVMAR 501

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE--D 837
               +V + +R   ++    +      ++   +  + +P+  +N          M  +   
Sbjct: 502  SDWEVTERLRGGTVLTRYWTHAEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 561

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            VF +          R   +         P V+   ++++                     
Sbjct: 562  VFLTNF------QLRMDTMSNILYYPQKPLVTTRAMEHL--------------------- 594

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
                    +   +  + AI      +  D+ +   S +   +    ++ R  +D  ++  
Sbjct: 595  ----HFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLYYRAYMDSEKKLG 649

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
              + E  E   RD   +      +       +  G     G     K+  L         
Sbjct: 650  IQQAETFEKPVRDATIKMRGTSYDTLEDDGFVAPGTRVSDGDILIGKTVPL--------- 700

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                        K    + +   ++E   +    R        Q           +VKV 
Sbjct: 701  -----------PKGSEELGARTARHEKKDASTTMRGAETGIIDQVMLSTDSQGQNMVKVR 749

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   R  Q GDK A RHG KG V      EDMPF  +G   DI++NP  +PSRM +G + 
Sbjct: 750  IRSTRIPQMGDKFASRHGQKGTVGITYRHEDMPFTAEGICPDIIINPHAIPSRMTIGHLV 809

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  LG      G++  +        G IS     L                         
Sbjct: 810  ECLLGKVSALAGEEGDATPFMETTVGAISSALKGLGYQQRGYEVL--------------- 854

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                                             +G +    G         + +G  Y  
Sbjct: 855  --------------------------------YNGHT----GR---KLQAQIFLGPTYYQ 875

Query: 1258 KLNH 1261
            +L H
Sbjct: 876  RLKH 879



 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 110/782 (14%), Positives = 228/782 (29%), Gaps = 126/782 (16%)

Query: 212 VPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           VPV     ALG +   EIL         SQ  +     +   + +   +V+   +     
Sbjct: 75  VPVVVLFRALGVLSDREILEHCCYDFDDSQMLEMLRPSIEEGNEIQEREVALDFIGKRAQ 134

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
              +   K++ +   + L+++ +  +GI +    G                 +A  +   
Sbjct: 135 TMGLSRDKRI-AFAAQILQKELLPHIGIQA-RSEGR----------------KAWFLGYM 176

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG-DVSTF 389
                +   E R+                  +        +    DI R +R   +    
Sbjct: 177 IHRLLLCALERREADDRDHFGKKRLDLAGPLMANLFRMLFRRLTQDISRALRKAVESHRE 236

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL--- 446
               S                 G      ++        + + +    + +  L  L   
Sbjct: 237 FNMVSAVQHQIITRGLQFSLATGNWGDQRKMMQTRAGVSQVLSRYTYASTLSHLRRLNSP 296

Query: 447 --RNGKGTIDDIDNLGNRRVRSVGE--------MLKNQYRLGLLRMERSIKERISSVDID 496
             R GK       +  +  +    E        ++KN   +  + +   ++  +  +   
Sbjct: 297 IGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAYISVGSPVEPLVDFLQEW 356

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           ++   + ++A  +      F     +         +      RR  ++    V+      
Sbjct: 357 TLEDLEELSADDIRDKCKVFLNGVWIGVHRNPEELMRIFRDYRRKISISAE-VSAVWDVR 415

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           E      +  GRIC         + +V+++    R      ++    K  D      V Y
Sbjct: 416 EKELRFLSDAGRIC-------RPLFVVNNMQLEIRKGHIAKLQNQTWKWGDLVSNGLVEY 468

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEIL------VPREKIDFIDASPK 669
           +   EEE   IA +   L +     + E V  R   E         V        +  P 
Sbjct: 469 VDTDEEETTMIAMSFDDLRDSMIAAQGEEVMARSDWEVTERLRGGTVLTRYWTHAEIHPS 528

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IPF +++ S R      M +QA+ +                          
Sbjct: 529 MILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFQL------------------- 569

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + S +  Y               Q+PLV       
Sbjct: 570 ----------------------RMDTMSNILYYP--------------QKPLV------- 586

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA   + GYN EDS+++++  +   +F S++   +  
Sbjct: 587 ---TTRAMEHLHFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRAYMD 643

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +   +   E            +       +++ G +  G  V+ GDIL+GK  P  + 
Sbjct: 644 SEKKLGIQQAETFEKPVRDATIKMRGTSYDTLEDDGFVAPGTRVSDGDILIGKTVPLPKG 703

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
                 +  R        + +D S  +  G    ++D  + +     +N   + +   +I
Sbjct: 704 SEELGARTAR-------HEKKDASTTMR-GAETGIIDQVMLSTDSQGQNMVKVRIRSTRI 755

Query: 965 EL 966
             
Sbjct: 756 PQ 757


>gi|51869981|ref|YP_073534.1| RNA polymerase beta subunit [Lymphocystis disease virus - isolate
            China]
 gi|51858189|gb|AAU10873.1| RNA polymerase beta subunit [Lymphocystis disease virus - isolate
            China]
          Length = 1017

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 92/420 (21%), Positives = 154/420 (36%), Gaps = 83/420 (19%)

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            + E      D E  I   +   R  ++  G    +G    K          S        
Sbjct: 663  ETEKYKSKHDSEL-IAHPDFLIRNRDLDYGLLGKTGVLDIKLGKKNKKYQGSICNSLWIP 721

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
               V   KV + +    + Y+     ++   +  ++++     +  G  RVVK+ +   +
Sbjct: 722  AGTVLVGKVSKKLIDGVIVYKDVSLTVKADEEGYLDELLDYYMVETG--RVVKIKLRSSK 779

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              + GDK A     KG    I   EDMPF KDG   D+++NP   PSRM +  I +   G
Sbjct: 780  IPEIGDKFASFTAQKGTCGMIYRQEDMPFTKDGIVPDLIINPHAFPSRMTLNYILQMCYG 839

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
             A    GK   +         D                                      
Sbjct: 840  LAACKTGKIYDATPFKRYNLTD-------------------------------------- 861

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                            +  +     L+   ++ +Y GLTG+ F   + +G     +L H+
Sbjct: 862  ---------------ELRELALELKLETW-ETTMYCGLTGKKFASKIFIGPCDYQRLRHL 905

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML------- 1315
            V++K+++R +G    +T QP+ G+S  GG ++GEME WC  ++GA+  L+E L       
Sbjct: 906  VTNKIHSRISGPIDNLTHQPVAGRSRYGGIKVGEMEQWCKLSHGASAALKESLFDMSDKY 965

Query: 1316 ------TIK--SDDVVGRTRVYESIVAGNDTFETGT---PESFNVLVKEMQALGLSIDLE 1364
                  T K  SDD       +E     +D  E      P +  +L +E+ A+G+ +  E
Sbjct: 966  TIPICKTCKTISDD-------FEYCRKCDDI-EIELKNCPYTSKLLFQELMAIGIHVQFE 1017



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 30/146 (20%), Positives = 53/146 (36%), Gaps = 47/146 (32%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L      SYD FL  +I      ++ ++AA               ++F    ++ PK   
Sbjct: 5   LTAHHIESYDKFLFFDIPTIVAQDKIIKAA------------NFTVKFKKIIYNKPKLTP 52

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------- 141
            +   +DLTY++ +         D +     KS+       I+   LPLM K        
Sbjct: 53  LEAKQKDLTYSISI---------DYEIDFNGKSVVL----EIF--SLPLMLKSKLCLTCE 97

Query: 142 -------------GTFVIKGIQRIVV 154
                        G F++KG +R+++
Sbjct: 98  EGETFELCPNDPGGYFIVKGKERVLI 123



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 79/487 (16%), Positives = 153/487 (31%), Gaps = 74/487 (15%)

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
            N    D + Y  + + +   N   +    +  RH+       ++  L  + +G+  + D
Sbjct: 240 LNVKCDDKESYVEAILKKEIFNHLEDHSPFNVARHL-----GYMVDRLATIASGEAALTD 294

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            D+L  +RV + G +++  ++    +  R I+  + ++         + N   + + +  
Sbjct: 295 KDDLAYKRVDTSGVLIEFLFKGLFKQYVRLIRNSLETLKNPDP-INVVKNVNVITNGLNL 353

Query: 516 FFCSSQ---------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            F +                 +SQ+  + N  SR++H RR        V       ++R 
Sbjct: 354 CFATGNWSVKKTGPPSYMRVGVSQVLCNHNYGSRLSHLRR----LMHAVGFKGKNFKIRR 409

Query: 561 VHPTHYGRICPAETSEGHNIGLVSS------LTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           +H +HYG ICP ET EG  +G+V +       +     N    +  PY K          
Sbjct: 410 LHASHYGFICPYETPEGERVGVVLNTALSTAFSQGIPKNQIKPLMMPYLK---------- 459

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF-IDASPKQVVS 673
                  E   +    N  +    +   E V    +     V      F  +     V S
Sbjct: 460 -------ESGYFRVVLNGEIVGYVNDPNETVKLLKSVLPDGVSVFCFRFTPEIKECHVFS 512

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                +  +  +D    +    +   A   L A +                  ++A    
Sbjct: 513 DQGRFLRPVLINDKIVRVCAQEIHHIAYKELPAYSIMTD--------------VMASVIP 558

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                 + RI  +S  G               ++  +       Q+ L           I
Sbjct: 559 FYNHAPSPRIAYQSNMG-KQAVGITTLTGGKDRYDPTFYVLDYPQKAL--------ARTI 609

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
             D        +  G   +VA     GYN EDS+++++  V   +F     + F    + 
Sbjct: 610 CYDR--YKFDIMCHGAIPIVAVSTMDGYNQEDSVILNKSSVDRGLFVITCYKTFVETEKY 667

Query: 854 TKLGPEE 860
                 E
Sbjct: 668 KSKHDSE 674


>gi|307343540|emb|CBJ18687.1| RNA polymerase B subunit [Micromonospora carbonacea]
          Length = 210

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 125/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|123469849|ref|XP_001318134.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
 gi|121900885|gb|EAY05911.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
          Length = 1104

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 69/279 (24%), Positives = 109/279 (39%), Gaps = 51/279 (18%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +      +D     ++K+          +  V +   M R    GDK + RHG KG+ S 
Sbjct: 795  KERIMSYKDGEDGFVDKVITTTSDDGKRVLSVVLKFRMVRTPTIGDKFSSRHGQKGVFSF 854

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA-CVGLGKKIKSLINDYKA 1161
              P E+MPF ++G   D+++NP   PSRM +G + E+  G            +    +  
Sbjct: 855  PWPQENMPFCENGITPDVIINPHAFPSRMTIGMLIESMCGKLRASQDCAFFDATPFTHDE 914

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               I+                                                  + +  
Sbjct: 915  KNRIT--------------------------------------------------DEVGQ 924

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   +Y G+TGE F   + +G +Y  +L HMV DK   R+TG  + +T+Q
Sbjct: 925  MLAKEGFEYYGNEAMYSGITGEQFKADIFMGVVYYQRLRHMVGDKYQVRATGKMNNITRQ 984

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            PL G+   GG RLGEME   + A G  ++L++     SD
Sbjct: 985  PLKGRKKGGGIRLGEMERDGLLAQGVTFLLRDRFMWCSD 1023



 Score = 79.3 bits (194), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 84/580 (14%), Positives = 174/580 (30%), Gaps = 44/580 (7%)

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM----FNFLFFDSDKYD 407
           V++     +    + +    D ++   R     D+ T + A       F  +      + 
Sbjct: 235 VDDRTIYESICGQNPDSFYSDRVIATLRYASELDIHTRAGARDFLGAHFRTVLQCPRHFT 294

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                 V +   L     D+    + + +I + + L+ L  G+   D++D      + + 
Sbjct: 295 NEECCEVLLKRNLFPHLSDEAPSKKFDLLIYMTRRLLQLVKGEILPDNMDANSAHELLTP 354

Query: 468 GEMLKNQYRLGLLRMERSIK------ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS- 520
           G +        +    ++        E+ +  D D++      NA  V + +   F +  
Sbjct: 355 GTLWLPALSDAITDFLKATAANVYKDEKNAIDDFDALQTILKKNASGVENRMRYLFSTGS 414

Query: 521 -------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                         LS + E +N    + H R   ++ +G          +R + P  +G
Sbjct: 415 LRGNSTLGLSQTEGLSIIAERINYCRYLAHFR---SVHRGAFFTTMKTTAVRYLLPESWG 471

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            +CP  T +G   GL++ L  F  +   G  +     V        V +L + +     I
Sbjct: 472 FMCPVHTPDGGLCGLLTHLARFCEIVT-GDSQGFKEIVQIFTNYGMVPFLGSGD-MVPVI 529

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI-PFLENDD 686
                        +   V          +  +  +  D             +        
Sbjct: 530 VDGRVVGSIRERLSSAAVEALKTARRKGIIPKMAEIADLPAGSFTRSIYVFLNQQRMMRP 589

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
              V          +  +  +             +    A+++  A +    D  +    
Sbjct: 590 VFNVKAQEQEYAGPLEQIFMDIASNPKDESKAYREIHHTAMLSLIASLTPFSDYNQSPRN 649

Query: 747 SVEGDLDPSTSGVDIYRLMKFQR-SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
             +  +   T G   +R          +    QRP+V+  ++              L D 
Sbjct: 650 MYQCQMAKQTMGYPSHREAASTEVKTYHVHYPQRPIVRTMEQDSH----------ALEDF 699

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            LG N  VA + + GY+ ED++LI++  V        H   ++      +          
Sbjct: 700 LLGTNACVAVLSYTGYDMEDALLINKCSVERGFG---HGCIYKTHRYTAEEIESNSYFCN 756

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                    ++D  G+  VG  V+ G  L+    PK    
Sbjct: 757 TKDGVIVDPDLDADGLPFVGQRVSKGCKLLRVYNPKENKE 796


>gi|110669594|gb|ABG81892.1| RNA polymerase II second largest subunit [Mycoblastus sanguinarius]
          Length = 709

 Score =  258 bits (660), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 120/829 (14%), Positives = 240/829 (28%), Gaps = 144/829 (17%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R+   ++ + + +  +    +         + +  + + +     + 
Sbjct: 1    RLDLAGPLLAGLFRMLFHKLTKDVFKYLQKCVENNKEFNMTLAVKSTTLTNGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     +      E    +    + +V  +   LS+      
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNATKI 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLE 683
            ++      +  D +     V        I      + D  D   K          P F+ 
Sbjct: 177  FVNGVWVGVHRDPAHLVRTVQNLRRKGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVI 236

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIR 742
            ++DS     G  +  +   +   +   +   M++   +  G       + G+VE VDA  
Sbjct: 237  DNDSKSDNRGGLVLTKEDVIKLEDDREIAAEMDAQEKEEQGVGWQGLVKKGVVEYVDAEE 296

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +       I        +N +          +   V+          T  
Sbjct: 297  EETIMIVMTPEDLEISRQIQAGYTLPEANPDD---------LNKRVKAPLKATAHTWTHC 347

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N          M  + +   + +  ++             
Sbjct: 348  EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------- 395

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 396  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 438

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L   
Sbjct: 439  YNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHG 494

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 495  TYEKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGI 554

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q   S                         LR VKV +   +  Q GDK A RHG KG
Sbjct: 555  VDQVLLS--------------------TNSDGLRFVKVRMRTTKIPQIGDKFASRHGQKG 594

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 595  TIGITYRQEDMPFTGEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFT 654

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 655  EVTVDSVSRLLR--EHGYQSRGFEVM---------------------------------- 678

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                        +G +    G         V +G  Y  +L HMV DK+
Sbjct: 679  -----------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 709



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 76/592 (12%), Positives = 164/592 (27%), Gaps = 112/592 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        +K  KD    + + +       F++  ++ +    +  KY L   G  
Sbjct: 6   GPLLAGLFRMLFHKLTKDVFKYLQKCVENN--KEFNMTLAVKSTTLTNGLKYSL-ATGNW 62

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 63  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 122

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 123 TPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNATKIFVNGVW 182

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +    +  + +  + + RR   +  +  + R     E +    T  GR+C       ++ 
Sbjct: 183 VGVHRDPAHLVRTVQNLRRKGLISHEVSLVRDIRDREFK--IFTDAGRVCRPLFVIDNDS 240

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---------------VVYLSAMEEENR 625
              +             +E       +                     V Y+ A EEE  
Sbjct: 241 KSDNRGGLVLTKEDVIKLEDDREIAAEMDAQEKEEQGVGWQGLVKKGVVEYVDAEEEETI 300

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGE--------EILVPREKIDFIDASPKQVVSIAAS 677
            I      L+                +         +          +  P  ++ I AS
Sbjct: 301 MIVMTPEDLEISRQIQAGYTLPEANPDDLNKRVKAPLKATAHTWTHCEIHPSMILGICAS 360

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+                                    
Sbjct: 361 IIPFPDHNQSPRNTYQSAMGKQAMG----------------------------------- 385

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                 V  +       + + +  Y               Q+PL                
Sbjct: 386 ------VFLTNYDQRMDTMANILYYP--------------QKPL----------ATTRSM 415

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   + 
Sbjct: 416 EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMS 475

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             E     +  D   +     + +D+ GI+  G  V+  DI++GK  P    
Sbjct: 476 VVEQFEKPMRSDTLKLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPIAPD 527


>gi|213876751|gb|ACJ54372.1| RNA polymerase subunit B [Mycobacterium setense]
          Length = 226

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 92/218 (42%), Positives = 122/218 (55%), Gaps = 37/218 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 38   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 98   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNINVAEGTPEWASKLPE------QL 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                  +                       VSTPVFDGA EE +  +L            
Sbjct: 151  YSAPVDSI----------------------VSTPVFDGAREEELAGLLASTLPNRDGDVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            ++E G++ L+DG +GEPF  PVTVGY+YMLKL+H+V D
Sbjct: 189  VNEDGKATLFDGRSGEPFPYPVTVGYMYMLKLHHLVDD 226



 Score = 42.8 bits (99), Expect = 0.50,   Method: Composition-based stats.
 Identities = 30/46 (65%), Positives = 38/46 (82%)

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   LTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 46


>gi|8895188|gb|AAF80844.1| RNA polymerase beta subunit [Bartonella bacilliformis]
          Length = 275

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 202/276 (73%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++VPR+ ID +D
Sbjct: 121 TDGKVTTEVVYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMVPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AASLIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAASLIPFLENDDANRALMGSNMQRQAVPLIRSEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AISAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|118640669|gb|ABL09902.1| RNA polymerase beta subunit [Vibrio vulnificus]
 gi|118640671|gb|ABL09903.1| RNA polymerase beta subunit [Vibrio vulnificus]
 gi|118640673|gb|ABL09904.1| RNA polymerase beta subunit [Vibrio vulnificus]
 gi|118640675|gb|ABL09905.1| RNA polymerase beta subunit [Vibrio vulnificus]
 gi|118640677|gb|ABL09906.1| RNA polymerase beta subunit [Vibrio vulnificus]
 gi|118640729|gb|ABL09932.1| RNA polymerase beta subunit [Vibrio vulnificus]
          Length = 290

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 174/290 (60%), Positives = 227/290 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  D  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGRDDAEEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDG+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LNEDGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|300394692|gb|ADK11884.1| DNA-directed RNA polymerase II subunit two [Coniophora arida var.
            suffocata]
          Length = 686

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 127/813 (15%), Positives = 243/813 (29%), Gaps = 144/813 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ R +    +              +  + + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   + ++   F       + +  + +      
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL----- 171

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
               EEN + +   + +  +G +       R     +   ++     D SP+  V      
Sbjct: 172  ---EENAHSSTVCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRE 225

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                   D+ RV     +      LL+ +   ++  G                + G++E 
Sbjct: 226  RELRLYTDAGRVCRPLFIVENQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIEL 285

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +       +  ++S+++  +  R  +K G            
Sbjct: 286  LDAEEEETVMISMTPEDLENCRLQSAGIDTRQSDEDYDLAAR--LKSGINAHTWTHCEIH 343

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 344  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 378

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   +               +  +             +       +   +  + AI 
Sbjct: 379  IYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 427

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD       
Sbjct: 428  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKH 486

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  +  D      R++          ++     
Sbjct: 487  GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDGSTPLKSTENG 546

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VKV V   R  Q GDK A RHG K
Sbjct: 547  IVDQVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQK 586

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +      
Sbjct: 587  GTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---- 642

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     E
Sbjct: 643  -------------------------------------------------ATP-FTDLTVE 652

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            ++++ LR       G  ++Y G TG      V 
Sbjct: 653  SVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQVY 685



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 85/623 (13%), Positives = 171/623 (27%), Gaps = 101/623 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNISLAVKHQTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESLEENAHSSTVCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 192 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 251

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +          T   K         +  L A EEE   I+     L E+     
Sbjct: 252 QKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEEEETVMISMTPEDL-ENCRLQS 310

Query: 643 ELVFCRCAGEEIL--------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +  R + E+          +        +  P  ++ I AS+IPF +++ S R     
Sbjct: 311 AGIDTRQSDEDYDLAARLKSGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 370

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 371 AMGKQAMGIYLTNFLV-----------------------------------------RMD 389

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 390 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 425

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            + + GYN EDS+++++  +   +F SI+   +  + + + +   E            + 
Sbjct: 426 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMK 485

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 I++ G+I  G  V+  DI++GK  P         ++        +    RD S 
Sbjct: 486 HGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDGST 538

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S  +G V  V I       K
Sbjct: 539 PLKSTENGIVDQVLITTNSEGQK 561


>gi|52699796|gb|AAU86960.1| DNA-dependent RNA polymerase II second largest subunit [Cudonia
            circinans]
          Length = 718

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 129/837 (15%), Positives = 240/837 (28%), Gaps = 143/837 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R    R+   + +  +              + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAKLFRNLWKRLTGDVYKYLQTCVEKQSEFNLTLAVKSSTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+   +  V         +       V  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPSDPIVEFMIQRGMDVLEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +    +     V        I      I D  D   K         
Sbjct: 177  PNSTKVFVNGVWVGVHSHPARLVRNVQGLRRQHLISHEVSLIRDIRDREFKVFTDAGRVC 236

Query: 679  IPFL--ENDDSNRVLMGCNMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIV 735
             P    E D+ +       + +  +  L+ +    +   +E               +G+V
Sbjct: 237  RPLFIVETDEESPNKGNLVLNKDHIKKLEDDQAMPLQMALEVKNKHGYFGFNGLLDSGVV 296

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA       +    +       I   ++ Q  + +  +N+R    V           
Sbjct: 297  EYVDAEEEETIMIVMTPEDLEISRQIQAGLE-QLPDDSGDLNKRVKAPVNPTAHIWTHCE 355

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N          M  + +   + +  ++       
Sbjct: 356  IHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM---- 402

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 403  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 439

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R        IE   +    + 
Sbjct: 440  IACYAGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---ATIESFEKPNRSDT 495

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L E   +  G           K+  ++ D      R++          ++
Sbjct: 496  IRLKTATYDKLDEDGIVSPGVRVSGEDIIIGKTAPIAPDAEELGQRTKAHTKRDASTPLR 555

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 556  STENGIVDQVLL--------------------TTNADGLRFVKVRMRTTKIPQIGDKFAS 595

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMPF ++G   DI++NP  +PSRM +  + E  L       G + 
Sbjct: 596  RHGQKGTVGITYRQEDMPFTREGIVPDIIINPHAIPSRMTIAHLIECQLSKVSTLRGLEG 655

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L                                            
Sbjct: 656  DATPFTEVTVDSVSKLL------------------------------------------- 672

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                       R  ++  +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 673  ----RDHGYQSRGFEIMYNGHT----GR---KLRAQVFLGPTYYQRLRHMVDDKIXA 718



 Score = 59.7 bits (143), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 49/361 (13%), Positives = 102/361 (28%), Gaps = 43/361 (11%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL- 446
            F++  ++ +    +  KY L   G      +    T    + + +    + +  L    
Sbjct: 43  EFNLTLAVKSSTITNGLKYSL-ATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTN 101

Query: 447 ----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
               R+GK       +  +  +    E  + Q    +  +  S+   ++       + + 
Sbjct: 102 TPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL--SLMCYVTVGTPSDPIVEF 159

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
           +I     V    E   S   +++  +   +   +H  RL    Q G+ R         + 
Sbjct: 160 MIQRGMDVLEEYEPLRSPNSTKVFVNGVWVGVHSHPARLVRNVQ-GLRRQHLISHEVSLI 218

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------------------------ 598
                R     T  G     +  + +       G +                        
Sbjct: 219 RDIRDREFKVFTDAGRVCRPLFIVETDEESPNKGNLVLNKDHIKKLEDDQAMPLQMALEV 278

Query: 599 --ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--------VFCR 648
             +  Y        +  V Y+ A EEE   I      L+        L           +
Sbjct: 279 KNKHGYFGFNGLLDSGVVEYVDAEEEETIMIVMTPEDLEISRQIQAGLEQLPDDSGDLNK 338

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                +          +  P  ++ I AS+IPF +++ S R      M +QA+ +     
Sbjct: 339 RVKAPVNPTAHIWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNY 398

Query: 709 P 709
            
Sbjct: 399 Q 399


>gi|307343514|emb|CBJ18674.1| RNA polymerase B subunit [Micromonospora sp. SGA5]
          Length = 211

 Score =  258 bits (659), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 125/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAGWKKALRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 211


>gi|108885407|gb|ABG23220.1| DNA-directed RNA polymerase [Bacillus sp. T107]
          Length = 145

 Score =  258 bits (659), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 62/167 (37%), Positives = 99/167 (59%), Gaps = 22/167 (13%)

Query: 25  DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP 84
           ++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    P
Sbjct: 1   ELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEP 50

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF
Sbjct: 51  KYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTF 101

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           +I G +R++VSQL RSP ++F    G+   +GK  +   +IP++  W
Sbjct: 102 IINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRAQW 145


>gi|82795299|gb|ABB91665.1| RNA polymerase beta subunit [Mycobacterium immunogenum]
          Length = 217

 Score =  258 bits (659), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 91/219 (41%), Positives = 120/219 (54%), Gaps = 40/219 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V DK
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDK 217


>gi|307343486|emb|CBJ18660.1| RNA polymerase B subunit [Micromonospora sp. GUI61]
          Length = 211

 Score =  258 bits (659), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 126/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 136  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 177  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 211


>gi|195032695|ref|XP_001988542.1| GH11221 [Drosophila grimshawi]
 gi|193904542|gb|EDW03409.1| GH11221 [Drosophila grimshawi]
          Length = 1125

 Score =  258 bits (658), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 85/352 (24%), Positives = 129/352 (36%), Gaps = 83/352 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    ++ ++          + V + + + RP   GDK A R G KGI S+  
Sbjct: 825  KVVKMDEKEDCIVDSVRQLGSFELTPRKTVCITLRVARPATIGDKFASRAGQKGICSQKY 884

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G      G               
Sbjct: 885  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKNAAVHG--------------- 929

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV-F--DGADEEAINS 1221
                                                  GV  +TP  F  D    +    
Sbjct: 930  --------------------------------------GVYDATPFRFSEDNTAIDYFGK 951

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T Q
Sbjct: 952  MLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTNQ 1011

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRTRV-YESIV 1333
            P+ G+   GG R GEME   + ++GAA++LQ+ L   SD          G      + I+
Sbjct: 1012 PIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLKQII 1071

Query: 1334 A-----------------GND--TFETGTPESFNVLVKEMQALGLSIDLENS 1366
                              G+         P SF  LV E+ ++ ++   + +
Sbjct: 1072 KRNEAGGLSSMPDTCRLCGDSSGVSMIEIPFSFKFLVTELSSVNINARFKLN 1123



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 88/538 (16%), Positives = 191/538 (35%), Gaps = 61/538 (11%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                  +  D+     + R ++ + L  +        + + I+ +++ L     GK  +
Sbjct: 306 RFPEVPEWLPDEAVTEFILRERIMVHLQTNEE------KFQLIVFMVQKLFQCAQGKFKV 359

Query: 454 DDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSVDI---DSVMPQDLINA 506
           +++D+   + V   G +    L  +  + L+++ + + +++S+ D     S+M Q +  A
Sbjct: 360 ENVDSAMMQEVLLPGHLYQKYLGERIEMWLMQLRKCLLKKLSTADSLVSSSIMTQCMRQA 419

Query: 507 KPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             V  ++  F  +              S L  + E++N +  ++H R   A+ +G     
Sbjct: 420 GGVGRSIESFLATGNVASRSGLGLMQSSGLVIMAENINRMRYMSHFR---AIHRGSYFTT 476

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E R + P  +G ICP  T +G   GL++ LT    ++     +     V       
Sbjct: 477 MRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISKRPDPK----LVQGIPALL 532

Query: 613 -DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            ++  L   ++++         +  DG              E     E + +   + +  
Sbjct: 533 FEMGMLPLTQQDHPD--AKLYVVFLDGKHL-----GHIFQTEADKIVEDLRYAKITGQVP 585

Query: 672 VSIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGTG--MESVVAKSSGAA 726
             +    IPF +N              M R    L   +  ++GT   +   +A      
Sbjct: 586 KMMEIGFIPFKKNGQFPGLFLSTGPARMMRPVWNLKWKQVEYIGTLEQLYMEIAIDEKEM 645

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                  +          + ++    D + S  ++Y+    +++    C+N  P      
Sbjct: 646 YPDFTTHLELSKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLN-WPKQAANK 704

Query: 787 EVRRNDIIA------DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-F 839
             R               +  L D A+G N +VA + + GY+ ED+M+I++        +
Sbjct: 705 LYRLQTPATPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAY 764

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            SI+  +F  +A+                  E +K +D  G+   GA+++ G      
Sbjct: 765 GSIYKSKFVQLAKKQSYFARHPNMP------ELIKYLDTDGLPQPGAKLSYGCPFYCY 816



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 101/767 (13%), Positives = 207/767 (26%), Gaps = 161/767 (20%)

Query: 14  RKFFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
           R  F + P  ++  + +L      S+D  L + +    +     Q  F+     TA    
Sbjct: 14  RPEFKQIPNKLNKHLANLGAPHVDSFDEMLSVGLENMAKYMTPQQ--FQ-----TAAGER 66

Query: 72  AMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
             L+  S     P            +    D      +Y+    + L   V D+D+    
Sbjct: 67  IHLKVESIWIAKPQVPLDVIDVRTREIYPTDARQLHASYSGQCSLRLGWSVNDLDKSAIN 126

Query: 120 KSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVS 155
                     + +G++P+M +                         G FVI+G ++ +V 
Sbjct: 127 ----------VDLGEVPIMLRSQACNLGQASPTEMVKHGEHDSEWGGIFVIRGNEK-IVR 175

Query: 156 QLH-----------RSP-----------GIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
            L            RS            G+     +         L+      + G    
Sbjct: 176 MLIMTRRNHPICVKRSSWKDRGHNFSELGVMVQTVRDDELSLTNTLHYL----NNGT-AR 230

Query: 194 IEFDS-KDIIHVRIDRRRKVPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSA 251
             F   K + +V        PV   L  L     E+I    Y  +V     D +      
Sbjct: 231 FMFSHMKRLSYV--------PVCLILKCLMDYTDEQI----YNCLVQGYESDQYYLTCVQ 278

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
           + L    +             +    +     + + L ++      +T   L    +   
Sbjct: 279 SML-RDVQNEGVYTSAQCRSFIGTLFRSRFPEVPEWLPDE-----AVTEFILRERIMVHL 332

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
             N E  ++ +          ++++F        +  VDS      +    +    K   
Sbjct: 333 QTNEEKFQLIVF--------MVQKLFQCAQGKFKVENVDSAMMQEVLLPGHL--YQKYLG 382

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV--------KMNMRLNLD 423
           + +      +R   +   S A+S+ +             VGR          +  R  L 
Sbjct: 383 ERIEMWLMQLRKCLLKKLSTADSLVSSSIMTQCMRQAGGVGRSIESFLATGNVASRSGLG 442

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRM 482
                  +   + I  ++ +   R     I         R     ++L + +  +  +  
Sbjct: 443 LMQSSGLVIMAENINRMRYMSHFR----AIHRGSYFTTMRTTEARQLLPDAWGFICPVHT 498

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                  + +    +       + K V       F    L   ++             + 
Sbjct: 499 PDGTPCGLLNHLTLTCEISKRPDPKLVQGIPALLFEMGMLPLTQQDHP-----DAKLYVV 553

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET-- 600
            L    +         + V    Y +I    T +   +  +  +         G   +  
Sbjct: 554 FLDGKHLGHIFQTEADKIVEDLRYAKI----TGQVPKMMEIGFIPFKKNGQFPGLFLSTG 609

Query: 601 PYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           P R +          V Y+  +E+    IA                       +E  +  
Sbjct: 610 PARMMRPVWNLKWKQVEYIGTLEQLYMEIA----------------------IDEKEMYP 647

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
           +    ++ S    +S  A+LIP  + + S R +  C M +Q +    
Sbjct: 648 DFTTHLELSKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPC 694


>gi|307343580|emb|CBJ18705.1| RNA polymerase B subunit [Micromonospora olivasterospora]
          Length = 210

 Score =  258 bits (658), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|307343510|emb|CBJ18672.1| RNA polymerase B subunit [Micromonospora sp. SG16]
          Length = 214

 Score =  258 bits (658), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 125/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 180  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 214


>gi|126636179|gb|ABO25740.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 272

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 197/273 (72%), Positives = 229/273 (83%), Gaps = 1/273 (0%)

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+
Sbjct: 1   MSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGL 60

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGK
Sbjct: 61  TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGK 120

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPK
Sbjct: 121 VTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPK 180

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           Q+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGAAI A
Sbjct: 181 QLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGAAIGA 240

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           KR+GIV+QVDA RIVIR+ E  LDPS SGVDIY
Sbjct: 241 KRSGIVDQVDATRIVIRATED-LDPSKSGVDIY 272


>gi|119644196|gb|ABL85612.1| RNA polymerase II second largest subunit [Physconia muscigena]
          Length = 718

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 127/838 (15%), Positives = 241/838 (28%), Gaps = 144/838 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + +    ++   +    +    I +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRTLFNKLTKDVEKYLKVCIENNKEFILNLGIKSSTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V+     +   P+      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCHVSVGTPSDGIVPFLLQRQMESLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
             ++      ++      +  +       V        +      I D  D   + +    
Sbjct: 177  HTSPNATKIFVNGVWVGVHRNPVHLVNAVQTLRRKHVLEPEVSLIRDIRDREFRILTDQG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
              L P F+ ++D+     G  +  +       +   V   M+  V +     I      I
Sbjct: 237  RVLRPLFVVDNDAKSPNCGNLVFNKEHSQRLDDDDSVPYDMDKEVREK---IIFGWNGLI 293

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                     V+  V+ + + +   V   + +   R  Q       P              
Sbjct: 294  ------NEGVVEYVDAEEEETVMIVMTPQDLAMSRQLQAGYALAEP-------------- 333

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMAR 852
               P      +    N       W       SM+  I   ++            ++    
Sbjct: 334  --DPDEPNRRVTAPINPTAH--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 389

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G      D    +           +  +             +       +   +  
Sbjct: 390  KQAMGVFLTNYDQRMET-----------MSHILYYPQKPLATTRSMEYLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGTNVLEKFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L E   I+ G           K+  ++ D      R++         
Sbjct: 495  SDTLKLKHGTYDKLDEDGLIIPGARVSGEDIIIGKTAPIAPDAEEMGQRTKLHTKRDAST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     L  Q                             LR VKV +   +  Q GDK
Sbjct: 555  PLRSTESGLVDQVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L    E    +                               
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM------------------------- 687

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                 +G +    G         V +G  Y  +L HMV DK+
Sbjct: 688  --------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 718


>gi|118640603|gb|ABL09869.1| RNA polymerase beta subunit [Vibrio mimicus]
          Length = 290

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 173/290 (59%), Positives = 227/290 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF +++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGIVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+GSF +ELV  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LAEEGSFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|8895198|gb|AAF80849.1|AF165993_1 RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659052|dbj|BAG12735.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659054|dbj|BAG12736.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659056|dbj|BAG12737.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659058|dbj|BAG12738.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659060|dbj|BAG12739.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|262117888|dbj|BAI47969.1| RNA polymerase beta subunit [Bartonella sp. SR23-1]
 gi|262117898|dbj|BAI47974.1| RNA polymerase beta subunit [Bartonella sp. SR79-1]
          Length = 275

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343548|emb|CBJ18691.1| RNA polymerase B subunit [Micromonospora citrea]
          Length = 209

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 126/214 (58%), Gaps = 38/214 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K+     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVDGDDAEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLV 209


>gi|52699906|gb|AAU87014.1| DNA-dependent RNA polymerase II second largest subunit [Xanthoria
            elegans]
          Length = 717

 Score =  258 bits (658), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 133/840 (15%), Positives = 241/840 (28%), Gaps = 150/840 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L   +R+   ++ + I +  +              +    + S + 
Sbjct: 1    DXXGKKRLDLAGPLLAGLFRMLFQKLTKDIYKYLQKCVESNREFNLTLGVKQNTLSSGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     ++     +    Y      +   +     A
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPADPIVDYLTNRGMESLEEYEPTRA 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++         D +     +        I      + D  D   K         
Sbjct: 177  PHATKVFVNGTWIGCHNDPAHLVPHIQEVRRKGIIAHEASLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P F+ ++D     MG   + +  V  L+ E   V T      A+        +  G   
Sbjct: 237  RPLFVIDNDPKSENMGNLALTKDMVQKLEDERDMVLTMDPEERAE--------QVIGWEA 288

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRNDIIA 795
             VD+    +  V+ + + +         ++  R  Q       P        V+      
Sbjct: 289  LVDS--GAVEYVDAEEEETIMIAMTPEDLEISRQIQAGYAAPVPSEDAPNQRVKAPLNPT 346

Query: 796  DGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T      ++   +  + +P+  +N          M  + +                
Sbjct: 347  AHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV-------------- 392

Query: 855  KLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                              L N DE    +  +             +       +   +  
Sbjct: 393  -----------------FLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 435

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R  +D  +R        +E   +   
Sbjct: 436  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVDTEKRVGM---TVLEKFEKPLR 491

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             E + L    Y +L +   +  G           K+T ++ D                 E
Sbjct: 492  TETLKLKHGTYDKLDDDGLVAPGVRVSGEDVIIGKTTPIAPD---------------AQE 536

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR    +K    T     E+   +K+             L+ VKV +   +  Q GDK
Sbjct: 537  MGQRTKSHIKKDASTPLRSTENGIVDKVLL-----STNSEGLKFVKVRMRTTKIPQIGDK 591

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 592  FASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 651

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L    E    +                               
Sbjct: 652  YEGDATPFTEITVDSVSKLLR--EHGYQSRGFEVM------------------------- 684

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                 +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 685  --------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 717



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/345 (13%), Positives = 96/345 (27%), Gaps = 31/345 (8%)

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           +  S+    + D  K   +  G  ++  R    +      R          I     L N
Sbjct: 59  LKYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHN 118

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +         +   + + L     + +      I + +++  ++S+   +   A  
Sbjct: 119 THWGLVCPAETPEGQACGLVKNLALMCYISVGTPADPIVDYLTNRGMESLEEYEPTRAPH 178

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYG 567
                      + +    +  + +  I   RR   +  +  + R     E +    T  G
Sbjct: 179 ATKVF---VNGTWIGCHNDPAHLVPHIQEVRRKGIIAHEASLVRDIRDREFK--IFTDAG 233

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-------------- 613
           R+C       ++    +        +    +E     V                      
Sbjct: 234 RVCRPLFVIDNDPKSENMGNLALTKDMVQKLEDERDMVLTMDPEERAEQVIGWEALVDSG 293

Query: 614 -VVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDFI 664
            V Y+ A EEE   IA     L+               E    +     +          
Sbjct: 294 AVEYVDAEEEETIMIAMTPEDLEISRQIQAGYAAPVPSEDAPNQRVKAPLNPTAHTWTHC 353

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           +  P  ++ I AS+IPF +++ S R      M +QA+ +      
Sbjct: 354 EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYD 398


>gi|118640599|gb|ABL09867.1| RNA polymerase beta subunit [Vibrio mimicus]
 gi|118640601|gb|ABL09868.1| RNA polymerase beta subunit [Vibrio mimicus]
 gi|118640605|gb|ABL09870.1| RNA polymerase beta subunit [Vibrio mimicus]
 gi|118640725|gb|ABL09930.1| RNA polymerase beta subunit [Vibrio mimicus]
          Length = 290

 Score =  258 bits (658), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 173/290 (59%), Positives = 227/290 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF +++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGIVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+GSF +ELV  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGSFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|224812777|gb|ACN65022.1| RpoB [Cronobacter genomosp. 1]
          Length = 260

 Score =  258 bits (658), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 161/260 (61%), Positives = 202/260 (77%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           ++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SAL
Sbjct: 1   AVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++
Sbjct: 121 VTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG
Sbjct: 181 DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIV 744
              VAKR G V+ VDA RIV
Sbjct: 241 VTAVAKRGGTVQYVDASRIV 260


>gi|52699855|gb|AAU86989.1| DNA-dependent RNA polymerase II second largest subunit [Placopsis
            perrugosa]
          Length = 693

 Score =  258 bits (658), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 114/813 (14%), Positives = 235/813 (28%), Gaps = 143/813 (17%)

Query: 469  EMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----- 521
             ++   +R+   ++ + + +  +              + +  + + +     +       
Sbjct: 1    PLMAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLKYSLATGNWGDQK 60

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+       S ++H RR +      + R     + R +H TH+G +CPAE
Sbjct: 61   KAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAE 116

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            T EG   GLV +L     +      E    +    + +V  +     +      ++    
Sbjct: 117  TPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPTRSPNATKVFVNGVW 176

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNR 689
              +  D S     V        I      I D  D   K          P F+ ++D+  
Sbjct: 177  VGVHRDPSHLVSTVQSLRRRGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDAKS 236

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               G  +  +       +   +   ++             +  G    V A    +  ++
Sbjct: 237  ANKGALVLTKEHINKLEDDKELPPDLDPDEKAE-------RYFGWDGLVKA--GAVEFLD 287

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q       P       V+          T      ++ 
Sbjct: 288  AEEEETVMIVMTPEDLEISRQVQAGYGLPEPSSDPNARVKAPISAGAHTWTHCEIHPSMI 347

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G      D    
Sbjct: 348  LGICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGXXXXXXDERM- 388

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 389  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 438

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R  +D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 439  IMNQSSIDRGLF-RSLFYRTYVDQEKR---IGLSVVEQFEKPMRSDTLRLKHGTYDKLDD 494

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ +      R++                 +K    T 
Sbjct: 495  DGIVAPGVRVSGEDIIIGKTAPIAPNAEELGQRTKL---------------HIKRDTSTP 539

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E+   +K+             LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 540  LRSTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYL 594

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 595  QEDMPFSSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------ 642

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 643  -----------------------------------------ATP-FTDVTVDSVSRLLRE 660

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                  G  ++Y+G TG      V +G  Y  +
Sbjct: 661  HGYQSRGFEVMYNGHTGRKLVAQVFLGXTYYQR 693



 Score = 63.6 bits (153), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 54/343 (15%), Positives = 93/343 (27%), Gaps = 36/343 (10%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 44  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 103

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   P  
Sbjct: 104 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPTR 163

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDV 561
             NA  V      F     +    +  + +S +   RR   +  +  + R     E +  
Sbjct: 164 SPNATKV------FVNGVWVGVHRDPSHLVSTVQSLRRRGMISHEVSLIRDIRDREFK-- 215

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE---------------TPYRKVC 606
             T  GR+C       ++    +             +E                 Y    
Sbjct: 216 IFTDAGRVCRPLFVIDNDAKSANKGALVLTKEHINKLEDDKELPPDLDPDEKAERYFGWD 275

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLD-------EDGSFTEELVFCRCAGEEILVPRE 659
                  V +L A EEE   I      L+         G               I     
Sbjct: 276 GLVKAGAVEFLDAEEEETVMIVMTPEDLEISRQVQAGYGLPEPSSDPNARVKAPISAGAH 335

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                +  P  ++ I AS+IPF +++ S R      M +QA+ 
Sbjct: 336 TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 378


>gi|262117896|dbj|BAI47973.1| RNA polymerase beta subunit [Bartonella sp. SR71-1]
          Length = 275

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|118640607|gb|ABL09871.1| RNA polymerase beta subunit [Vibrio cholerae]
 gi|118640609|gb|ABL09872.1| RNA polymerase beta subunit [Vibrio cholerae]
 gi|118640611|gb|ABL09873.1| RNA polymerase beta subunit [Vibrio cholerae]
 gi|118640613|gb|ABL09874.1| RNA polymerase beta subunit [Vibrio cholerae]
 gi|118640615|gb|ABL09875.1| RNA polymerase beta subunit [Vibrio cholerae]
 gi|118640617|gb|ABL09876.1| RNA polymerase beta subunit [Vibrio cholerae]
          Length = 290

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 173/290 (59%), Positives = 226/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF +++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   SLFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +ELV  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|300394754|gb|ADK11915.1| DNA-directed RNA polymerase II subunit two [Suillus bresadolae]
          Length = 694

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 125/823 (15%), Positives = 233/823 (28%), Gaps = 145/823 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAGLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMSSKAGVSQVLNRYTYASTLSHLRRTNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +   Q + L K    ++  G      +      + K   I      
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHVKWLNQGYREDDGEEFKWEQLVKNGIIELLDAE 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +       D   S +    +   Q        +    +K G            PS 
Sbjct: 286  EEETVMICMTPEDLENSRLQSAGIDPHQNDGD---YDPAARLKAGINSHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 378  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 486  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +      
Sbjct: 586  GITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 643

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 644  -----------------------DLTVESVSTFLRQKGYQSRGLEVM------------- 667

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                       G +       G      V +G  Y  +L HMV
Sbjct: 668  ---------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 694



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 80/598 (13%), Positives = 166/598 (27%), Gaps = 111/598 (18%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           D+YR ++        F+++ ++ +    +  KY L   G      +         + + +
Sbjct: 29  DVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL-ATGNWGDQKKAMSSKAGVSQVLNR 87

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R GK       +  +  +    E  + Q    +  +      
Sbjct: 88  YTYASTLSHLRRTNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCI 147

Query: 489 RISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +             NA         F     +    +  N +  I   RR 
Sbjct: 148 SVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRK 207

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +                ++        P    E   + L              ++   
Sbjct: 208 DDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVK--------WLNQG 259

Query: 602 YR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YR       K         +  L A EEE   I      L+     +  +   +  G+  
Sbjct: 260 YREDDGEEFKWEQLVKNGIIELLDAEEEETVMICMTPEDLENSRLQSAGIDPHQNDGDYD 319

Query: 655 L-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                   +        +  P  ++ + AS+IPF +++ S R      M +QA+ +    
Sbjct: 320 PAARLKAGINSHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTN 379

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                                                          + + +  Y     
Sbjct: 380 FLV-----------------------------------------RMDTMANILYYPQKPL 398

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             +     +  R                        +L  G+N +VA + + GYN EDS+
Sbjct: 399 ATTRSMEYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSV 434

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGII 882
           ++++  +   +F SI+   +  + + + +   E            +       I++ G+I
Sbjct: 435 IMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLI 494

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             G  V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 495 APGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 548


>gi|53854338|gb|AAU95614.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 263

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 157/263 (59%), Positives = 199/263 (75%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG 
Sbjct: 1   KERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEVTHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPYR+V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPYRRVI 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+   +++ ++D 
Sbjct: 121 DGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIMATPDRVQYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           +  QVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+ E P VGTG+E  VA  S  A
Sbjct: 181 ATGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPMVGTGIERSVAVDSATA 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVE 749
           IVA+R G+VE VDA R+VIR  +
Sbjct: 241 IVARRGGVVEYVDANRVVIRVHD 263


>gi|307343590|emb|CBJ18710.1| RNA polymerase B subunit [Micromonospora rifamycinica]
          Length = 215

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLSSTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 181  SSGKARLFDGRSGEPLPDPIAVGYIYILKLNHLVD 215


>gi|190148950|gb|ACE63450.1| RNA polymerase subunit B [Pseudonocardia benzenivorans]
          Length = 270

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 155/277 (55%), Positives = 205/277 (74%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG VT  + YL+A EE+   IAQAN+ L++DGSFTE+ V  R   GE  
Sbjct: 61  GFIQTPYRKVVDGVVTEQIDYLTADEEDRFVIAQANAPLNDDGSFTEDRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+P   +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++EAP VGTG
Sbjct: 121 LIPPTGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVAEKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMALGKNL 270


>gi|52694195|emb|CAG30627.1| DNA-directed RNA polymerase beta chain [Pseudomonas monteilii]
          Length = 337

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 181/339 (53%), Positives = 229/339 (67%), Gaps = 5/339 (1%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR---VNAYGFIETPYR 603
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL S      V   G      R
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLGSLCPYQPVRLPGKPVP--R 118

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                      V +      +R+         E+    +ELV  R   E  +   E +  
Sbjct: 119 CEGRRCQRRHRVPVGHRRSRSRHRPGFGRDEREESQLIDELVAVRHLNEFTVKAPEDVTL 178

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 179 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 238

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 239 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 298

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            GD+V+R DI+ADGPSTD+G+LALG+NM +AFM W+G+ 
Sbjct: 299 KGDKVQRGDIMADGPSTDMGELALGQNMRIAFMAWNGFY 337


>gi|307343546|emb|CBJ18690.1| RNA polymerase B subunit [Micromonospora chokoriensis]
          Length = 214

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAEWKRQLRSID---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V 
Sbjct: 180  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVD 214


>gi|296011772|gb|ADG65540.1| RNA polymerase beta subunit [Mycobacterium sp. NL-JvIW-016]
          Length = 212

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 91/217 (41%), Positives = 118/217 (54%), Gaps = 34/217 (15%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 22   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 81

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +     S L   L   
Sbjct: 82   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDGADGAGEVPAWASNLPQGLLSA 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA E  ++ +L     +      
Sbjct: 141  PADSI-------------------------VSTPVFDGAQEGELSGLLGSTLPNRDGDVM 175

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H+V 
Sbjct: 176  VNADGKSQLFDGRSGEPFPYPVTVGYMYILKLHHLVD 212


>gi|103001354|gb|ABF71503.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 687

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 112/808 (13%), Positives = 229/808 (28%), Gaps = 145/808 (17%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L N +R+   ++ + + +  +              + +  + + +     +         
Sbjct: 1    LANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKA 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   ASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     +      E    +    + +V  +     +      ++      
Sbjct: 117  EGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVG 176

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  D +     V        I      + D  D   K          P    D+  +   
Sbjct: 177  VHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTN 236

Query: 693  GCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              N+   ++ +  L+ +               S     AK  G    V     V+  V+ 
Sbjct: 237  CGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEYVDA 286

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGR 809
            + + +   V     ++  R  Q               V+          T      ++  
Sbjct: 287  EEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPSMIL 346

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N          M  + +   + +  ++                     
Sbjct: 347  GICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM------------------ 386

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 387  ---------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVI 437

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME- 988
               S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L + 
Sbjct: 438  MNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDD 493

Query: 989  --ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              +  G           K+  ++ D      R++          ++     +  Q     
Sbjct: 494  GIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL-- 551

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                                    L+ VKV +   +  Q GDK A RHG KG +      
Sbjct: 552  ------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQ 593

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF  +G   D+++NP  +PSRM +  + E  L       G +               
Sbjct: 594  EDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------- 640

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                    +TP F     ++++ +LR  
Sbjct: 641  ----------------------------------------ATP-FTEVTVDSVSKLLREH 659

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                 G  ++Y+G TG      V +G  
Sbjct: 660  GYQSRGFEVMYNGHTGRKLVAQVFLGPT 687


>gi|118364886|ref|XP_001015664.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila]
 gi|89297431|gb|EAR95419.1| DNA-directed RNA polymerase, beta subunit family protein [Tetrahymena
            thermophila SB210]
          Length = 1226

 Score =  257 bits (657), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 77/311 (24%), Positives = 117/311 (37%), Gaps = 74/311 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                + +VKV +   R  Q GDK A RHG KG     +  ED+P+  +G   ++V+NP  
Sbjct: 954  DKDGMYIVKVKLRSNRIPQIGDKFASRHGQKGTCGMTIRGEDLPYNIEGIIAELVINPHC 1013

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +G + E          G                                     
Sbjct: 1014 IPSRMTIGHMIEGLNSKLSSLKGIWGD--------------------------------- 1040

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F G   + I S L        G  +LY+  TG    
Sbjct: 1041 --------------------ATP-FSGIKLQDIASELHTYGYQRYGNEVLYNPYTGMRLS 1079

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G  +  +L H+V DK+Y+RS G    + +QP  G+S  GG R GEME  CI A+G
Sbjct: 1080 TQIYYGPTFYQRLRHLVDDKMYSRSRGPVVAIVRQPTHGRSRGGGLRFGEMERDCIIAHG 1139

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRVY-ESIVA-----------GND----TFETGTPES 1346
             +  L+E     SD     V  R  ++ ++ V            G+       +   P +
Sbjct: 1140 TSNFLKERTFGVSDQFRTHVCSRCGLFAKADVTNHKYDCTGCSQGDKKHYKIVQVYLPYA 1199

Query: 1347 FNVLVKEMQAL 1357
               L++E+ A+
Sbjct: 1200 AKQLIQELMAM 1210



 Score =  109 bits (272), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 97/652 (14%), Positives = 223/652 (34%), Gaps = 87/652 (13%)

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
               D++ +E IF++         ++ + ++  +          ++++AL+ I   +   
Sbjct: 302 CVESDKEMMERIFYNLKDPKNEQMMEMLRSSLLLAQHC-----NNKREALIFIGYRINAT 356

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
             + +  ++            Y L  +G             D+ + +    I  +I+ L+
Sbjct: 357 --TNYRGSQEAMQSAEDTLKLYLLPHIG---------TQESDNDKKL--FFIGYMIQKLL 403

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY----RLGLLRMERSIKERISSVDIDSVM- 499
           +   GK   DD D+ G +R+   G ++   +    R+     +++++++I+ +  D+   
Sbjct: 404 NAALGKTQEDDRDHYGKKRLDMAGALISQLFKERLRIFQKNAKKNLQQKINDISRDAQKS 463

Query: 500 ---PQDLINAKPVVSAVCEFFCSSQLSQLEE--------------HVNSLSRITHTRRLS 542
                D+ + K +   +     +    Q  +                +  + ++H RR++
Sbjct: 464 LNVIVDIFDHKLISDHIRLALATGNWGQTADGEVVKTGVAQVLKRDTSLFATMSHMRRVN 523

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           A     +  A      R +H THYG ICPAET EG  IG+V +L+  A+V+     +   
Sbjct: 524 A----PMKSAAKLARPRQLHNTHYGLICPAETPEGQKIGMVKNLSLLAQVSLGLSSQDNL 579

Query: 603 RK---VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +    + +     D++ L   +   +     N +        E+++        +     
Sbjct: 580 KIQEQLEEQINQFDILNLKLEKIPYQTKVFFNGNWIGFTETPEQIIDVFKEIRRLQKIDG 639

Query: 660 KIDFIDA---SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL------KAEAPF 710
                D      +        + P     +         + +  +  +      KA    
Sbjct: 640 FSIVRDIINKEIRIYTDQGRGMRPVFTVQEICEGKNRLKITKSKLYAILQQFEGKAFQKL 699

Query: 711 VGTG-MESVVAKSSGAAIVAKRAGIVEQVDA--------IRIVIRSVEGDLDPSTSGVDI 761
           +  G +E +  +    A++A         D             I         ++     
Sbjct: 700 IDEGFIELLDVEEEEGALIAVDINDFYHTDDPRRTNLPFTHCEIHPAMILGVCASVIPFG 759

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL--------------GDLAL 807
           +     + + Q+    Q   +   +   R D +                       D+ +
Sbjct: 760 HHNQGPRNTLQSAMGKQAMGLNSTNFHMRLDTLCHILYYPQIALASSKSLQYITAKDIPI 819

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG--------PE 859
           G N +VA   + GYN EDS++I++  +   +F SI    ++   +   +G          
Sbjct: 820 GSNAVVAIACFTGYNQEDSIIINQSAIDRGLFRSILYRTYKTTEKKEHMGLNPVIEHIRF 879

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              +     +      +D  GII  G +V   D+L+GK+    ++  + ++ 
Sbjct: 880 PDEKKTIIPASYSFLKLDYDGIIPPGTQVTGEDVLIGKVVELPKTEGSDKQY 931



 Score = 97.8 bits (242), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 97/692 (14%), Positives = 208/692 (30%), Gaps = 100/692 (14%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVF----DVDEFTGAKSIKDIKEQSIYMGDLPLMTK 140
           K         DL Y V +KI ++L+      D  E     + +D  +  I +  LP+M +
Sbjct: 130 KIYPMMARISDLDYFVEIKIPVQLVRTIKHPDGTEQKELITSRDKNQNLITLFKLPVMVQ 189

Query: 141 D------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLS 175
                                    G F+IKG ++++++Q   +   ++    K      
Sbjct: 190 SMYCSLAGENLEGRIKHGECQFDQGGYFIIKGSEKVIIAQERMAFNFVYVFQQKDP---- 245

Query: 176 GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK------------------VPVTSF 217
            K+ +   I   +        D  + +  +   + K                  +P+   
Sbjct: 246 -KMPWIAEIRSIR--------DKTNAVQSKFALKLKLRDGEYQLYARCKLINEDIPIFVL 296

Query: 218 LMALGM--DSEEILS-TFY--PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
           L ALG     +E++   FY        Q  +     L  A      + +   +       
Sbjct: 297 LKALGCVESDKEMMERIFYNLKDPKNEQMMEMLRSSLLLAQHCNNKREALIFIGYRINAT 356

Query: 273 VIESGKKLTSGLLKS------LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
               G +      +       L   G +            Y+ + ++N   G+   +  D
Sbjct: 357 TNYRGSQEAMQSAEDTLKLYLLPHIGTQESDNDKKLFFIGYMIQKLLNAALGKTQEDDRD 416

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
              +K L+       +           N        + D ++D + +L  I  +     +
Sbjct: 417 HYGKKRLDMAGALISQLFKERLRIFQKNAKKNLQQKINDISRDAQKSLNVIVDIFDHK-L 475

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR---LNLDTPDDVRHIRKEDIIAIIKIL 443
            +  +  ++    +  +   ++   G  ++  R   L        R        A +   
Sbjct: 476 ISDHIRLALATGNWGQTADGEVVKTGVAQVLKRDTSLFATMSHMRRVNAPMKSAAKLARP 535

Query: 444 VDLRNGK-GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
             L N   G I   +    +++  V  +         L  + ++K +    +  +     
Sbjct: 536 RQLHNTHYGLICPAETPEGQKIGMVKNLSLLAQVSLGLSSQDNLKIQEQLEEQINQFDIL 595

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            +  + +      FF  + +   E     +      RRL  +    + R     E+R ++
Sbjct: 596 NLKLEKIPYQTKVFFNGNWIGFTETPEQIIDVFKEIRRLQKIDGFSIVRDIINKEIR-IY 654

Query: 563 PTHYGRICPAETS----EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
                 + P  T     EG N   ++    +A +  +      ++K+ D      +  L 
Sbjct: 655 TDQGRGMRPVFTVQEICEGKNRLKITKSKLYAILQQFEG--KAFQKLIDEGF---IELLD 709

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EEE   IA                +      ++           +  P  ++ + AS+
Sbjct: 710 VEEEEGALIAVD--------------INDFYHTDDPRRTNLPFTHCEIHPAMILGVCASV 755

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           IPF  ++   R  +   M +QA+ L       
Sbjct: 756 IPFGHHNQGPRNTLQSAMGKQAMGLNSTNFHM 787


>gi|262117936|dbj|BAI47993.1| RNA polymerase beta subunit [Bartonella sp. FN16-1]
 gi|262117940|dbj|BAI47995.1| RNA polymerase beta subunit [Bartonella sp. FN18-1]
          Length = 275

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343598|emb|CBJ18714.1| RNA polymerase B subunit [Micromonospora siamensis]
          Length = 215

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDEEWKRQLRSIE---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V 
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVD 215


>gi|82581192|dbj|BAE48669.1| RNA polymerase beta subunit [Bartonella sp. Fuji 12-1]
 gi|124358802|dbj|BAF46070.1| RNA polymerase beta subunit [Bartonella sp. Okinawa 45-1]
 gi|159137653|gb|ABW88906.1| RNA polymerase beta-subunit [Bartonella queenslandensis]
 gi|159137657|gb|ABW88908.1| RNA polymerase beta-subunit [Bartonella queenslandensis]
 gi|262072881|dbj|BAI47750.1| RNA polymerase beta subunit [Bartonella sp. Kuchinoshima 2-1]
          Length = 275

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|170584696|ref|XP_001897130.1| DNA-directed RNA polymerase, beta subunit family protein [Brugia
            malayi]
 gi|158595460|gb|EDP34013.1| DNA-directed RNA polymerase, beta subunit family protein [Brugia
            malayi]
          Length = 1108

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 108/306 (35%), Gaps = 64/306 (20%)

Query: 1026 VQDEKVQRNVESLKVQYE-TSKSILEDRFKNKIEKIQWGDDMPPGVLRV-VKVFVAMKRP 1083
            ++ +      E     Y+       E  F   +  ++ G+ +     +    +    +R 
Sbjct: 784  MEGDPYYSVYEIDTNNYKVHKYKYAEAAFCGSVRIVEEGEHIGNSKGKCHALIQWRTQRN 843

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
               GDK A RHG KGI S + P E MPF + G   DI+ NP         G + E+  G 
Sbjct: 844  PIIGDKFASRHGQKGINSFLWPTESMPFSESGMVPDIIFNPH--------GMMIESMAGK 895

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
            A    G    S    +                                            
Sbjct: 896  AGAMHGSTYDSSPFVFNEKKTA-------------------------------------- 917

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                         +    +L  A  +  G   +Y G+ G   +  +  G +Y  +L HM+
Sbjct: 918  ------------IDHFGQLLVRAGYNYYGNETMYSGVDGRELEVQIFFGIVYYQRLRHMI 965

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD--- 1320
            +DK   RSTG    VT QP+ G+   GG R GEME   + A+GAA+ LQ+ L   SD   
Sbjct: 966  ADKFQVRSTGPTDPVTLQPVKGRKKGGGIRFGEMERDAMIAHGAAFTLQDRLFNCSDRDI 1025

Query: 1321 -DVVGR 1325
              +  R
Sbjct: 1026 AHICAR 1031



 Score = 65.1 bits (157), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 39/120 (32%), Gaps = 48/120 (40%)

Query: 72  AMLEFVSYEFDPP--------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
             L + S +   P              K    +C  R LTY  PLK+++ + +  V    
Sbjct: 41  VELRYTSAQLGYPMVEVKQGSSVVDSLKLFPSECRQRGLTYRGPLKVSVEIRLNGVKMDF 100

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
                       + +G++P+M K                         G F+ KG ++++
Sbjct: 101 C----------EVIVGEVPIMLKSNRCHLRWLTREQLVAHGEEGTEKGGYFICKGTEKVI 150



 Score = 52.0 bits (123), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 64/381 (16%), Positives = 123/381 (32%), Gaps = 94/381 (24%)

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             VGR  + + + +   +D    +   +  + + L+ L  G+   +  DN   +     G
Sbjct: 294 EDVGRFLLRVCVAIHLDNDED--KFFLLSYMAQKLIALAKGECAAESPDNPQFQEAAVSG 351

Query: 469 --------EMLKNQYRLGLLRMERSIKERISSV---DIDSVMPQDLINAKPVVSAVCEFF 517
                   E L+N   +   ++E   K +  S      + +       +  +   +  F 
Sbjct: 352 HILLLIIRERLENTLSIARRKIELEAKRKAESFLLSSHELIRAMGTQRSGEITRGLEYFI 411

Query: 518 CSSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L              S + E +N L  ++H R   A+ +G         ++R + P
Sbjct: 412 ATGNLITKGGLTLQQNNGFSVIAERINQLRFVSHFR---AIHRGAFFMEMRTTDVRKLRP 468

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARV------------------------------- 592
             +G ICP  T +G   GL++ +T+  R+                               
Sbjct: 469 EAWGFICPVHTPDGAPCGLLNHVTASVRIVTHYSNTSELPKLLGELGMMYPVLVDGKFVG 528

Query: 593 ----NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE--NRYIAQANSSLDEDGSFTE---- 642
               +    IE   R +    V++DV   S  E     + I   N  +   G +      
Sbjct: 529 YISQSEASHIERQLRFLK---VSDDVRLPSCAEIILVQKSIDPINILVQYPGLYIFTEPA 585

Query: 643 --------------------ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                               E V+     +            +  P  + S AA+LIPF 
Sbjct: 586 RLIRPVRYLPSNRIEFIGTFEQVYLSICIDPEEAEPNVTMHQEIHPSCLFSFAANLIPFP 645

Query: 683 ENDDSNRVLMGCNMQRQAVPL 703
           +++ S R +  C M +Q + +
Sbjct: 646 DHNQSPRNVYQCQMGKQTMGI 666


>gi|298912937|emb|CAZ66636.1| RNA polymerase beta subunit [Vibrio vulnificus]
          Length = 289

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 173/289 (59%), Positives = 226/289 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  D  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGRDDAEEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L+EDG+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LNEDGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|307343594|emb|CBJ18712.1| RNA polymerase B subunit [Micromonospora saelicesensis]
          Length = 211

 Score =  257 bits (657), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V 
Sbjct: 177  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVD 211


>gi|40643998|emb|CAD91516.1| RNA polymerase II second largest subunit [Garrya elliptica]
          Length = 576

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 86/506 (16%), Positives = 153/506 (30%), Gaps = 91/506 (17%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
              T    L+   N   A+   +       S++  +   ++            ++      
Sbjct: 159  SMTINDLLSAKLNPEDAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 218

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G          V+    +      +  V        +    +       +      + 
Sbjct: 219  AMG--------IYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 267

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R     
Sbjct: 268  AIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 326

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T ++                  D+   + 
Sbjct: 327  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ-----------------DDSQGQA 369

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K  + TS    E    +++      D +     R VKV V   R  Q GDK + RH
Sbjct: 370  SRYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRH 424

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 425  GQKGTIGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 484

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS         +                                      
Sbjct: 485  TPFTDVTVDNISKALHKCGYQMRGFETM-------------------------------- 512

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                            +G +    G         + +G  Y  +L HMV DK+++R  G 
Sbjct: 513  ---------------YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 550

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVW 1300
              ++T+QP  G+S  GG R GEME  
Sbjct: 551  VQILTRQPAEGRSRDGGLRFGEMERD 576



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 70/476 (14%), Positives = 140/476 (29%), Gaps = 97/476 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++       + I+   +  A   F     +    +  
Sbjct: 5   LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPD 64

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + GV R     E+R ++  +     P    E   + L+     
Sbjct: 65  MLVRTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRL-LIKKKDI 122

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A        +       D      + Y+   EEE   I+              +L+  +
Sbjct: 123 QALQQRESPEDGG---WHDLVAKGFIEYIDTEEEETTMISM----------TINDLLSAK 169

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E      +     +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 170 LNPE--DAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 227

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            F                    R   +  V                              
Sbjct: 228 QF--------------------RMDTLAYV------------------------------ 237

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PLV                      L  G N +VA   + GYN EDS++
Sbjct: 238 -----LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVI 282

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++  +    F S+    +    +      +E        +   +       +D+ G+  
Sbjct: 283 MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAP 342

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  D+++GK TP  +           +         RD S  +    +G V
Sbjct: 343 PGTRVSGEDVIIGKTTPIAQDD---------SQGQASRYTKRDHSTSLRHSETGMV 389


>gi|307343582|emb|CBJ18706.1| RNA polymerase B subunit [Micromonospora pallida]
          Length = 210

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 86   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWKVEGDDEDWKRALRGIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + ++   V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AAEAEADTNVATPVFDGAREEEISGLLAATLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|118640581|gb|ABL09858.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640583|gb|ABL09859.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640585|gb|ABL09860.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640587|gb|ABL09861.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640589|gb|ABL09862.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640591|gb|ABL09863.1| RNA polymerase beta subunit [Vibrio fluvialis]
 gi|118640593|gb|ABL09864.1| RNA polymerase beta subunit [Vibrio furnissii]
 gi|118640595|gb|ABL09865.1| RNA polymerase beta subunit [Vibrio furnissii]
 gi|118640597|gb|ABL09866.1| RNA polymerase beta subunit [Vibrio furnissii]
          Length = 290

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +     ++   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIERADAEEQGTLDETDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +ELV  R  GE  L PRE ++++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELVTARQKGESGLHPREHVNYMDVATNQVVSIAASLIPFLE 290


>gi|52699866|gb|AAU86994.1| DNA-dependent RNA polymerase II second largest subunit [Rhizocarpon
            disporum]
          Length = 716

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 120/836 (14%), Positives = 235/836 (28%), Gaps = 143/836 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R    ++ + +    +              + +  + S + 
Sbjct: 1    DHXGKKRLDLAGPLLAGLFRTLFKKLTKDVFKYLQKCVEQNREFNLTLGVKSTTLTSGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   G+V +L     +      E    +       +  +    S 
Sbjct: 117  HNTHWGLVCPAETPEGQACGVVKNLALMCYITVGTPSEPIIDFMVQRSMDLLEEYEPQSY 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PNATKIFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D      G  +  +       E   +G  M+    +       +K  G    
Sbjct: 237  RPLFVIDNDPRSPNRGSLVLTKQHIQKLEEDHEIGADMDPEERE-------SKFMGWEGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            V   + V+  V+ + + +   V     ++  R  Q               V+        
Sbjct: 290  V--NQGVVEYVDAEEEETVMIVMTPADLEISRQLQQGYTLPETSDDPNRRVKAPMNPTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +   + +  ++        
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----- 400

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 401  ----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 438

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S V   +    +F R   D+ +R  +     +E   +    + +
Sbjct: 439  ACYSGYNQEDSVIMNQSSVDRGLF-RSLFYRAYTDQEKRVGT---SVVEQFEKPMRSDTL 494

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++          ++ 
Sbjct: 495  KLKHGTYDKLDDDGIVAPGVRISGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 554

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 555  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 594

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 595  HGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 654

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 655  ATPFTDVTVDSVSSLLR--EHGYQSRGFEVM----------------------------- 683

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 684  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVXXKIXA 716


>gi|262117954|dbj|BAI48002.1| RNA polymerase beta subunit [Bartonella sp. TM21-1]
          Length = 275

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124490808|gb|ABN12774.1| RNA polymerase beta subunit [Bartonella sp. RN24BJ]
          Length = 278

 Score =  257 bits (657), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 186/274 (67%), Positives = 219/274 (79%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
           +IK      +ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSAL
Sbjct: 1   AIKSVCHRSEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSAL 60

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 61  GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 120

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +
Sbjct: 121 IIDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SG
Sbjct: 181 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSG 240

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           AA+ AKR+GIV+QVDA RIVIR+ E      + G
Sbjct: 241 AAVSAKRSGIVDQVDATRIVIRATEDLDPSKSGG 274


>gi|207109765|ref|ZP_03243927.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            HPKX_438_CA4C1]
          Length = 157

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 73/146 (50%), Positives = 97/146 (66%), Gaps = 8/146 (5%)

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+  GGQR GEMEVW ++AYGA
Sbjct: 1    RVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGA 60

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            A+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F VL KE+Q+L L I++    
Sbjct: 61   AHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDD 120

Query: 1368 TKNSA-----KMEEIP---DFNKCEL 1385
                       ++E     DF+  +L
Sbjct: 121  VDEDGAPKPIVIKEDDRPKDFSSFQL 146


>gi|159137651|gb|ABW88905.1| RNA polymerase beta-subunit [Bartonella queenslandensis]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHP+HYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPSHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|169659046|dbj|BAG12732.1| RNA polymerase beta subunit [Bartonella grahamii]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGCFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343450|emb|CBJ18642.1| RNA polymerase B subunit [Micromonospora sp. GUI2]
          Length = 214

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 127/215 (59%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V 
Sbjct: 180  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLVD 214


>gi|86161668|gb|ABC86969.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 285

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 192/285 (67%), Positives = 225/285 (78%)

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           ER+IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLS
Sbjct: 1   ERAIKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLS 60

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PY
Sbjct: 61  ALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPY 120

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           RK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D
Sbjct: 121 RKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVD 180

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ 
Sbjct: 181 LMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARD 240

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           SGAAI AKR+GIV+QVDA         G        +   RL KF
Sbjct: 241 SGAAIGAKRSGIVDQVDAHTYCYSCNGGSRSFKVLVLIFTRLQKF 285


>gi|159137655|gb|ABW88907.1| RNA polymerase beta-subunit [Bartonella queenslandensis]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699802|gb|AAU86963.1| DNA-dependent RNA polymerase II second largest subunit [Diaporthe
            phaseolorum]
          Length = 726

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 130/844 (15%), Positives = 246/844 (29%), Gaps = 149/844 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R  + ++   +    +    +         I    + + + 
Sbjct: 1    DHXGKKRLDLAGPLLAKLFRNIVKKLTGDLMAYMKRCIQEEKGFDLTLGIRHGTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMSSTAGVSQVLNRYTFSSTLSHLRRTNT----PIGRDGKLAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+    V+     +    +    + +V  +    S 
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPADPIRDFMIQRNMEVLEEYDPASN 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  +I      + +D      LV        I      + D  D   K        +
Sbjct: 177  PYATKIFINGTWVGVHQDPKHLVGLVQDLRRKSIISHEVSLVRDIRDREFKIFSDAGRVM 236

Query: 679  IPFLENDDSNRVLMGC-----NMQRQAVPLLKAEAPFVGTGME---SVVAKSSGAAIV-- 728
             P    +  +    G       + ++ +  L+A+        +       + SG      
Sbjct: 237  RPLFVVEQDDNPDTGAMKGTLVLNKEHIRRLEADQNLNPADEDYFGWDSLQHSGVIEYLD 296

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+         +   +    E    P  +  + ++    + ++++T +N R   K+  ++
Sbjct: 297  AEEEETAMICMSPEDLDEYREAKKRPKQTEEEHHQEKLDRLNDESTDLNARVKTKINTDI 356

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                     PS  LG       +  + +P+  +N                        ++
Sbjct: 357  NMYTHCEIHPSMLLG-------ICASIIPFPDHNQSPRN------------------TYQ 391

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                   +G                       +  +             +       +  
Sbjct: 392  SAMGKQAMGXXXXXXXXXM-----------DTMANILYYPQKPLATTRSMEFLKFRELPA 440

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    +F R   D  +R        +E   
Sbjct: 441  GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYTDSEKRVGI---NVVESFE 496

Query: 969  RDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            +    + + L    Y +L +   I  G           K++ ++ D              
Sbjct: 497  KPFRSDTLRLKHGTYDKLDDDGIIAPGVRVSGEDIIIGKTSPINPD-------------- 542

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               E  QR  + +K    T     E    + +      D +     R VKV V   +  Q
Sbjct: 543  -NQELGQRTAQHVKRDASTPLRSTESGIIDSVVVTTNQDGL-----RYVKVRVRTTKIPQ 596

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L    
Sbjct: 597  IGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHAIPSRMTIAHLIECLLSKVS 656

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G +  +          +S L                                     
Sbjct: 657  TLKGMEGDATPFTDVTVDSVSDLLHAHGYQSRGFEVL----------------------- 693

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                     +G +    G         V  G  Y  +L HMV D
Sbjct: 694  ------------------------YNGHT----GR---KLKAQVFFGPTYYQRLRHMVDD 722

Query: 1266 KVYA 1269
            K+ A
Sbjct: 723  KIXA 726


>gi|115334877|gb|ABI94045.1| RNA polymerase beta subunit [Bartonella rochalimae ATCC BAA-1498]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 228/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D
Sbjct: 121 IDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME+ VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAKVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA+RIVIR+ E  LDPS SGV+I
Sbjct: 241 AIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVNI 275


>gi|126513819|gb|ABO16006.1| RNA polymerase-beta-subunit [Bartonella sp. Sm7680bgl]
 gi|169659044|dbj|BAG12731.1| RNA polymerase beta subunit [Bartonella grahamii]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|225678942|gb|EEH17226.1| DNA-directed RNA polymerase III subunit RPC2 [Paracoccidioides
            brasiliensis Pb03]
          Length = 1232

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 164/1118 (14%), Positives = 329/1118 (29%), Gaps = 232/1118 (20%)

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            + K   ++ +  + +   +   +        I ++A  +  +K +  +       +  + 
Sbjct: 312  ERKSKSYIILKKERIYVRHNVLNEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 362

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + A      V      +  AL  I   ++             F  +  +  +  +
Sbjct: 363  STYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRKPNN------FGVIRRNYVQEAI 416

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 417  EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 473

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQ 521
            ++L   +     + +  IK  I  V    V  +          +   +   +     +  
Sbjct: 474  QLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNRAISTGN 533

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAE 573
             S     +          RLS +   G+         + R     R + P+ +G +CP++
Sbjct: 534  WSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPSQFGMLCPSD 593

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQAN 631
            T EG   GLV +L     +      E P RK+       DV  +   E   +  YI   N
Sbjct: 594  TPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGRELHGQGAYIVFLN 652

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDS 687
             S        +  +             E I       ++ V IA        P +  +D 
Sbjct: 653  GSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRAVHIATDDGRICRPLIIVEDG 712

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
             +  +  +  R                ME     + G           E +D        
Sbjct: 713  -KSKVQAHHLR----------ALRSGSMEFDDFLAHGLV---------EYLDCNE----- 747

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                   + S + +Y                       D V     +   P T LG +A 
Sbjct: 748  ------ENDSNIAVYED---------------------DIVDSTTHLEIEPFTILGAVA- 779

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                    +P+  +N          M  + +                             
Sbjct: 780  ------GLIPYPHHNQSPRNTYQCAMGKQAIGA--------------------------- 806

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                  + +    ++          +    I       +   +    A+      D+ D 
Sbjct: 807  --IANNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDRLPAGQAATVAVMSYSGYDIEDA 864

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +     +       ++F R      +   +  +++++   R         +  +  R  
Sbjct: 865  LVLNKGSIDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------ENGLPVRKH 914

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +L      +  +      V  + +  E   S        D             Y  S  
Sbjct: 915  ALLDNDGLAAVGEKVNHGEVYINKVTPENALSS--GITGSDAGRPIT-------YIPSPQ 965

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              +    + I+K+           +++KV     R  + GDK +                
Sbjct: 966  TYKLPDPSYIDKVMISS--TEAENQLIKVQTRQTRRPEVGDKFS---------------- 1007

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
                                 SR                  G+K    I   +A+   S 
Sbjct: 1008 ---------------------SR-----------------HGQKGVVGIIAEQADMPFSD 1029

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
            L    + ++       +++      ++       SG       F G+  E ++++L    
Sbjct: 1030 LGIVPDIIMNPHGFPSRMTVGKMLELVAGKAGILSGQFSYGTAFGGSPVEEMSAVLVKHG 1089

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                G+  L  G+TGE     V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S
Sbjct: 1090 FSYGGKDCLTSGITGESLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRS 1149

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESF 1347
              GG RLGEME  C+ AYG + +L E L I SD                  +E    ES 
Sbjct: 1150 RDGGLRLGEMERDCLIAYGTSQLLLERLMISSD-----------------QYEVDVCESC 1192

Query: 1348 ------------NVLVKEMQALGLSIDLENSRTKNSAK 1373
                         +LV+E+ ++ +   L+ +      +
Sbjct: 1193 GFMGYSGWCQRSKLLVQELFSMNVVARLKLADEFPEDR 1230



 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 87/744 (11%), Positives = 205/744 (27%), Gaps = 114/744 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA-----MLEFVSYEFDP 83
           L++    SY++F+ + +    + +  +++     F I + +  +     +  F       
Sbjct: 122 LVKQHIDSYNYFVEVQLKKIVQASAEIRSDVDPNFYIRSSAKTSHSVFRVFRFHDIYLGT 181

Query: 84  PK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           P+                  ++C  RD+TYA P+ +    +          +  + +K  
Sbjct: 182 PRRADEEQDSNFNAASTITPNECRLRDMTYASPILVDFEYV----------RGRQRVKRN 231

Query: 129 SIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-I 163
              +G +P+M                           G F++ G +++++ Q   S   +
Sbjct: 232 GTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQEQLSKNRV 291

Query: 164 HFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVT 215
             + D  +        S S +      II             K+ I+VR +     VP+ 
Sbjct: 292 IVETDLKKEIVQASVTSSSNERKSKSYII-----------LKKERIYVRHNVLNEDVPIV 340

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVI 274
             L A+G+ S++ +      I  + + DF      A  L +     +   +         
Sbjct: 341 ILLKAMGIQSDKEMLLLVAGIDSTYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRK 400

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            +   +          + +  + I+   +  L                 A         +
Sbjct: 401 PNNFGVIRRNYVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMARRVLMAK 452

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                      +           +         K + D  ++I +V++    +    A  
Sbjct: 453 HDPSLVDDRDYVGNKRLELAGQLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYG 512

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGK 450
           +         +     +     +++        V H    +     + ++  +       
Sbjct: 513 VVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKT 572

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +     L   +   +      +     L    ++   I++ D +  + + +       
Sbjct: 573 RKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLIFALGAED 632

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRI 569
                             +N        R    L     + R     E   V   H+ R 
Sbjct: 633 VQTVGGRELHGQGAYIVFLNGSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRA 692

Query: 570 CPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
               T +G     +  +       + +    + +   +  D      V YL   EE +  
Sbjct: 693 VHIATDDGRICRPLIIVEDGKSKVQAHHLRALRSGSMEFDDFLAHGLVEYLDCNEENDSN 752

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IA     +                        +    ++  P  ++   A LIP+  ++ 
Sbjct: 753 IAVYEDDI-----------------------VDSTTHLEIEPFTILGAVAGLIPYPHHNQ 789

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPF 710
           S R    C M +QA+  +      
Sbjct: 790 SPRNTYQCAMGKQAIGAIANNQFL 813


>gi|262117926|dbj|BAI47988.1| RNA polymerase beta subunit [Bartonella sp. KS2-1]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            +GKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 INGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|257465800|dbj|BAI23358.1| RNA polymerase beta subunit [Bartonella washoensis]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS+LD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSALDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ +  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATDD-LDPSKSGVDI 275


>gi|300394688|gb|ADK11882.1| DNA-directed RNA polymerase II subunit two [Coniophora puteana]
          Length = 686

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 125/810 (15%), Positives = 235/810 (29%), Gaps = 144/810 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   F       + +         L ++E
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWG-------LESLE 169

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E     A A + +  +G +       R     +   ++     D SP+  V         
Sbjct: 170  ENAHSSA-ACTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      LL+ +   ++  G                + G++E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVEDQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDA 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +         +   +    +K G            PS 
Sbjct: 286  EEEETVMIAMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSM 343

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 344  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 378

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 379  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 427

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 428  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTY 486

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 487  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 546

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 547  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 586

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +         
Sbjct: 587  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 639

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 640  ----------------------------------------------ATP-FTDLTVESVS 652

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + LR       G  ++Y G TG      V 
Sbjct: 653  TFLRQKGYQSRGLEVMYHGHTGRKLQAQVY 682


>gi|124358810|dbj|BAF46074.1| RNA polymerase beta subunit [Bartonella sp. Shimane 84-1]
 gi|262072910|dbj|BAI47763.1| RNA polymerase beta subunit [Bartonella grahamii]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148942|gb|ACE63446.1| RNA polymerase subunit B [Pseudonocardia antarctica]
          Length = 269

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 154/276 (55%), Positives = 200/276 (72%), Gaps = 8/276 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL SFARVN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFIETPYRKV DG VT+ + YL+A EE+   +AQAN+ L+EDGSF EE V  R   GE  
Sbjct: 61  GFIETPYRKVVDGVVTSQIDYLTADEEDRFVVAQANARLNEDGSFAEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPSGVEYIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  + A+ AG+VE++ A  I +   EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVTAESAGVVEELCADYITVMDDEGQRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMALGKN 269


>gi|124358804|dbj|BAF46071.1| RNA polymerase beta subunit [Bartonella sp. Yoroshima 11-1]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIV+R+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVVRATED-LDPSKSGVDI 275


>gi|37725756|gb|AAO32826.1| RNA polymerase beta subunit [Bartonella bovis]
 gi|37726549|gb|AAO39776.1| RNA polymerase beta subunit [Bartonella schoenbuchensis R1]
 gi|124358768|dbj|BAF46053.1| RNA polymerase beta subunit [Bartonella capreoli]
          Length = 275

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AIGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|520507|gb|AAA50224.1| RNA polymerase II, second largest subunit [Caenorhabditis elegans]
          Length = 859

 Score =  257 bits (656), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 129/968 (13%), Positives = 274/968 (28%), Gaps = 193/968 (19%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 60   GQRIIGILPYIKQEIPIMIVFRALGFVSDRDILGHIIYDFNDPEMMEMVKPSLDEAFVIQ 119

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +     +   +     +   I 
Sbjct: 120  EQNVALNFIGARGAKPGV---TREQRIKYAREILQKELLPH---VGVSEHCETKKAFFIG 173

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDI 495
             ++  L+    G+  +DD D++GN+R+   G +L   +R     + + ++   +      
Sbjct: 174  YMVHRLLLAALGRRELDDRDHIGNKRLDLAGPLLAFLFRSLFRNLLKEMRMTAQKYINKN 233

Query: 496  DSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
            D       +    +   +     +               +SQ+   +   + ++H RR +
Sbjct: 234  DDFALDVCVKTSTITRGLTYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRAN 293

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G +CPAET EG  +GLV +L   A ++     E   
Sbjct: 294  S----PIGREGKLAKPRQLHNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPIL 349

Query: 603  RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPR 658
              + +     ++  +S     +      N +        ++L+      R   + I+   
Sbjct: 350  EFLEEWS-MENLEEVSPSAIADATKIFVNGAWVGIHREPDQLMTTLKKLRRQMDIIVSEV 408

Query: 659  EKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL----KAEAPFVGT 713
              + D  D   +          P L  ++    L   ++ +             +  VG 
Sbjct: 409  SMVRDIRDREIRIYTDAGRVCRPLLIVENQKLALKKRHIDQLKEAADEANKYTWSDLVGG 468

Query: 714  GM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            G+ E + +     +++A     +                                     
Sbjct: 469  GVVELIDSMEEETSMIAMMPEDL------------------------------------- 491

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                      + G     +      P+  LG       +  + +P+  +N       S R
Sbjct: 492  ----------RSGGYCDTHTHCEIHPAMILG-------VCASIIPFPDHNQ------SPR 528

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
               +       +  +                           ++    +  V        
Sbjct: 529  NTYQSAMGKQAMGVYTTNF-----------------------HVRMDTLAHVLYYPQKPL 565

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +    +     + +      + AI      +  D+ +   S +   +    +F R   D 
Sbjct: 566  VTTRSMEYLRFNELPAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLF-RSVFYRSYRDN 624

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
                 +   E IE   R+K         +       I  G           K+  L    
Sbjct: 625  EANLDNANEELIEKPTREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVAL---- 680

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
                              +  ++++   +Y    +    R        Q    +     +
Sbjct: 681  ----------------PDIDDDLDASGKKYPKRDASTFLRSSETGIVDQVMLSLNSDGNK 724

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VK+ +   R  Q GDK A RHG KG +  +   EDMPF  +G   DI++NP  VPSRM 
Sbjct: 725  FVKIRMRSVRLPQIGDKFASRHGQKGTMGIMYRQEDMPFTAEGLTPDIIINPHAVPSRMT 784

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E   G      G+   +   +                                  
Sbjct: 785  IGHLIECLQGKLSANKGEIGDATPFN---------------------------------- 810

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                               D  + + I+ +L        G  ++Y+G TG+     +  G
Sbjct: 811  -------------------DTVNVQKISGLLCEYGYHLRGNEVMYNGHTGKKLTTQIFFG 851

Query: 1253 YIYMLKLN 1260
              Y  +L 
Sbjct: 852  PTYYQRLK 859



 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 110/752 (14%), Positives = 223/752 (29%), Gaps = 112/752 (14%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG  S+ +IL          +  +     L  A ++    V+ + +     
Sbjct: 74  IPIMIVFRALGFVSDRDILGHIIYDFNDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGA 133

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
           +  +   +++     + L+++ +  +G++  C          +        +   ++ D 
Sbjct: 134 KPGVTREQRIKYAR-EILQKELLPHVGVSEHCETKKAFFIGYMVHRLLLAALGRRELDDR 192

Query: 331 KSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             +  + +  +      +      N    +R T     NK+   AL    +        T
Sbjct: 193 DHIGNKRLDLAGPLLAFLFRSLFRNLLKEMRMTAQKYINKNDDFALDVCVK----TSTIT 248

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDL 446
             +  S+    + D  K   S  G  ++  RL          R          +     L
Sbjct: 249 RGLTYSLATGNWGDQKKAHQSRAGVSQVLNRLTYTATLSHLRRANSPIGREGKLAKPRQL 308

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            N +  +         +   + + L     + +  +   I E +    ++++   + ++ 
Sbjct: 309 HNTQWGMVCPAETPEGQAVGLVKNLALMAYISVGSLPEPILEFLEEWSMENL---EEVSP 365

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
             +  A   F   + +    E    ++ +   RR   +    V+  R   +      T  
Sbjct: 366 SAIADATKIFVNGAWVGIHREPDQLMTTLKKLRRQMDIIVSEVSMVRDIRDREIRIYTDA 425

Query: 567 GRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
           GR+C P    E   + L        +       E       D      V  + +MEEE  
Sbjct: 426 GRVCRPLLIVENQKLALKKRHIDQLK---EAADEANKYTWSDLVGGGVVELIDSMEEETS 482

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA     L   G                    +     +  P  ++ + AS+IPF +++
Sbjct: 483 MIAMMPEDLRSGG------------------YCDTHTHCEIHPAMILGVCASIIPFPDHN 524

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R      M +QA+ +                                          
Sbjct: 525 QSPRNTYQSAMGKQAMGVYTTNFHV----------------------------------- 549

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                    + + V  Y               Q+PLV                     +L
Sbjct: 550 ------RMDTLAHVLYYP--------------QKPLV----------TTRSMEYLRFNEL 579

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----- 860
             G N +VA + + GYN EDS++++   +   +F S+    +     +     EE     
Sbjct: 580 PAGINAIVAILSYSGYNQEDSVIMNNSAIDRGLFRSVFYRSYRDNEANLDNANEELIEKP 639

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                  +       +DE GII  G  V+  D+++GK     +     +    +      
Sbjct: 640 TREKCSGMRHSLYDKLDEDGIISPGMRVSGDDVIIGKTVALPDIDDDLDASGKKYPK--- 696

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               RD S  + S  +G V  V +      +K
Sbjct: 697 ----RDASTFLRSSETGIVDQVMLSLNSDGNK 724


>gi|298912935|emb|CAZ66635.1| RNA polymerase beta subunit [Vibrio mimicus]
          Length = 289

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 172/289 (59%), Positives = 226/289 (78%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF +++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGIVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+GSF +ELV  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGSFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|124358806|dbj|BAF46072.1| RNA polymerase beta subunit [Bartonella sp. Okinawa 19-1]
 gi|126513821|gb|ABO16007.1| RNA polymerase-beta-subunit [Bartonella sp. Sm7688bgl]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|82581200|dbj|BAE48673.1| RNA polymerase beta subunit [Bartonella sp. Fuji 4-1]
 gi|103484133|dbj|BAE94839.1| RNA polymerase beta subunit [Bartonella sp. Aomori 36-2]
 gi|103484135|dbj|BAE94840.1| RNA polymerase beta subunit [Bartonella sp. Aomori 23-1]
 gi|124358796|dbj|BAF46067.1| RNA polymerase beta subunit [Bartonella sp. Hokkaido 19-1]
 gi|169659038|dbj|BAG12728.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|262072867|dbj|BAI47743.1| RNA polymerase beta subunit [Bartonella sp. Koshimizu 15-1]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|298912933|emb|CAZ66634.1| RNA polymerase beta subunit [Vibrio cholerae]
          Length = 289

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 172/289 (59%), Positives = 225/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF +++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   SLFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V +G VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G F +ELV  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGGFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|262117932|dbj|BAI47991.1| RNA polymerase beta subunit [Bartonella sp. FN12-1]
 gi|262117934|dbj|BAI47992.1| RNA polymerase beta subunit [Bartonella sp. FN15-1]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117892|dbj|BAI47971.1| RNA polymerase beta subunit [Bartonella sp. SR36-1]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS+L  +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSALYSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|6606095|gb|AAF19060.1|AF107788_1 DNA-dependent RNA polymerase II RPB140 [Pichia kudriavzevii]
          Length = 905

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 139/938 (14%), Positives = 256/938 (27%), Gaps = 152/938 (16%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            + +   +++    D +    + L               ++             +      
Sbjct: 85   IEDGDILQHICYDDDDWQMLEMLKPCIEEGFLIQSQEVALDYIGRRGNAVGIKRERRIQF 144

Query: 412  GRVKMNMRLNLDTPDDVRHIR--KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             +  +          D  H          II  L+     +   DD D+ G +R+   G 
Sbjct: 145  AKDILQREFLPHISQDGGHETNKAYFFGYIINRLLLCALERKEQDDRDHFGKKRLDLAGP 204

Query: 470  MLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L N +R+   ++ R I    +      +       + +  + S +     +        
Sbjct: 205  LLANLFRILFRKLSRDIYRYMQRCIEHGEDFNIVSAVKSTTITSGLKYSLATGNWGEQKK 264

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 265  AMSSKAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAET 320

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L+  + ++     E     + +      +      E +       N + 
Sbjct: 321  PEGQACGLVKNLSLMSCISVGSASEPITYLLEEW-GLEPISDYDPQEHKLSTRVFLNGNW 379

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRV 690
                     LV              ++    D  +   K          P    DD    
Sbjct: 380  VGTHRDPGMLVDTMRQLRRSGTISSEVSLIRDIREREFKIFTDAGRVYRPLFIVDDDPDS 439

Query: 691  LMGCN----------MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                           +  + V  +  +  F   G      +           GIVE +DA
Sbjct: 440  ENKGGLKLTKEHCRKILDREVEEIPQDDEFDENGEPLEPLQRIYGWESLLSEGIVEYLDA 499

Query: 741  IRIVI----RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                      S E     + +G D   + +    N N   + +  +K             
Sbjct: 500  EEEETVLIAMSSEDLSFNNQNGEDDEHMNQDHDENGNLIQSDK-RIKSHINSHSFTHCEI 558

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             PS  LG  A       + +P+  +N          M  + +   + +  + V       
Sbjct: 559  HPSMILGVAA-------SIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYNVRM----- 604

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 605  ----------------------DTMANILYYPQKPLAKTQSMEFLKFRELPAGQNAIVAI 642

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R  +D+  R+     E+ E   R       
Sbjct: 643  CCYSGYNQEDSMIMNQSSIDRGLF-RSLFFRSYMDQERRNGISVVEEFEKPMRSNTLGFK 701

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                        I  G           K+  +  D      R+++         ++    
Sbjct: 702  AGTYEKLDDDGLISPGVRVSGDDIIIGKTVPIPPDTEELGQRTKYHTKRDASTPLRATES 761

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  Q                             LR VKV +   +  Q GDK A RHG 
Sbjct: 762  GIVDQVLL--------------------TTNSEGLRFVKVRMRTTKVPQIGDKFASRHGQ 801

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   D+++NP  +PSRM V  + E  L       G +     
Sbjct: 802  KGTIGITYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLIECLLSKVASLRGYEGD--- 858

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                              +TP F     
Sbjct: 859  --------------------------------------------------ATP-FTDLTV 867

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            +A++ +LR       G  ++Y+G TG+     V  G  
Sbjct: 868  DAVSKLLRENGYQSRGFEVMYNGHTGKKLMAQVFFGPT 905



 Score =  135 bits (341), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 103/762 (13%), Positives = 229/762 (30%), Gaps = 90/762 (11%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    VP+     ALG+  + +IL          Q  +     +    L+   +V+
Sbjct: 68  YIKTD----VPIVIVFRALGVIEDGDILQHICYDDDDWQMLEMLKPCIEEGFLIQSQEVA 123

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        I+  +++       L+ + +  +                +      + 
Sbjct: 124 LDYIGRRGNAVGIKRERRIQFAK-DILQREFLPHISQDGGHETNKAYFFGYI---INRLL 179

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  ++   +      +                + N       K  +D    + R +
Sbjct: 180 LCALERKEQDDRDHFGKKRLDL----------AGPLLANLFRILFRKLSRDIYRYMQRCI 229

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
             G+   F++  ++ +       KY L   G      +         + + +    + + 
Sbjct: 230 EHGE--DFNIVSAVKSTTITSGLKYSL-ATGNWGEQKKAMSSKAGVSQVLNRYTYSSTLS 286

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLLRMERSIKE 488
            L        R+GK       +  +  +    E  + Q          +  + +  + + 
Sbjct: 287 HLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGSASEP 346

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
               ++   + P    + +    +   F   + +    +    +  +   RR   +    
Sbjct: 347 ITYLLEEWGLEPISDYDPQEHKLSTRVFLNGNWVGTHRDPGMLVDTMRQLRRSGTISSEV 406

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVC 606
                    +RD+    +     A         +          N  G    +   RK+ 
Sbjct: 407 SL-------IRDIREREFKIFTDAGRVYRPLFIVD---DDPDSENKGGLKLTKEHCRKIL 456

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D     +V  +   +E             ++     E +      E +L     ++++DA
Sbjct: 457 DR----EVEEIPQDDE------------FDENGEPLEPLQRIYGWESLLSEG-IVEYLDA 499

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME---SVVAKSS 723
             ++ V IA S      N+ +       N        L      + + +        +  
Sbjct: 500 EEEETVLIAMSSEDLSFNNQNGEDDEHMNQDHDENGNLIQSDKRIKSHINSHSFTHCEIH 559

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLV 782
            + I+   A I+   D  +    + +  +     GV      ++           Q+PL 
Sbjct: 560 PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLA 619

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
           K                    +L  G+N +VA   + GYN EDSM++++  +   +F S+
Sbjct: 620 K----------TQSMEFLKFRELPAGQNAIVAICCYSGYNQEDSMIMNQSSIDRGLFRSL 669

Query: 843 HIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               +    R   +   E     +  +         + +D+ G+I  G  V+  DI++GK
Sbjct: 670 FFRSYMDQERRNGISVVEEFEKPMRSNTLGFKAGTYEKLDDDGLISPGVRVSGDDIIIGK 729

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             P    P   EE   R     K    RD S  + +  SG V
Sbjct: 730 TVPI---PPDTEELGQRT----KYHTKRDASTPLRATESGIV 764


>gi|8895192|gb|AAF80846.1|AF165990_1 RNA polymerase beta subunit [Bartonella clarridgeiae]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DG+VT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D
Sbjct: 121 VDGRVTKEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDI
Sbjct: 241 AIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDI 275


>gi|257153209|dbj|BAI23159.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153213|dbj|BAI23161.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|289576609|dbj|BAI23160.2| RNA polymerase beta subunit [Bartonella washoensis]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|8895196|gb|AAF80848.1|AF165992_1 RNA polymerase beta subunit [Bartonella elizabethae]
 gi|103484139|dbj|BAE94842.1| RNA polymerase beta subunit [Bartonella sp. Fuji 9-1]
 gi|103484141|dbj|BAE94843.1| RNA polymerase beta subunit [Bartonella sp. Fuji 8-1]
 gi|124358798|dbj|BAF46068.1| RNA polymerase beta subunit [Bartonella sp. Nagano 12-1]
 gi|124358800|dbj|BAF46069.1| RNA polymerase beta subunit [Bartonella sp. Ehime 5-1]
 gi|159885665|dbj|BAE94841.2| RNA polymerase beta subunit [Bartonella sp. Fuji 17-1]
 gi|169659040|dbj|BAG12729.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659042|dbj|BAG12730.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|169659048|dbj|BAG12733.1| RNA polymerase beta subunit [Bartonella grahamii]
 gi|262072885|dbj|BAI47752.1| RNA polymerase beta subunit [Bartonella sp. Tokushima 10-1]
 gi|262117902|dbj|BAI47976.1| RNA polymerase beta subunit [Bartonella sp. BR10-1]
 gi|262117908|dbj|BAI47979.1| RNA polymerase beta subunit [Bartonella sp. OY1-1]
 gi|262117922|dbj|BAI47986.1| RNA polymerase beta subunit [Bartonella sp. KT25-1]
 gi|262117928|dbj|BAI47989.1| RNA polymerase beta subunit [Bartonella sp. KS4-1]
 gi|262117942|dbj|BAI47996.1| RNA polymerase beta subunit [Bartonella sp. OE1-1]
 gi|262117968|dbj|BAI48009.1| RNA polymerase beta subunit [Bartonella sp. DS1-1]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699882|gb|AAU87002.1| DNA-dependent RNA polymerase II second largest subunit [Sporastatia
            testudinea]
          Length = 700

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 117/816 (14%), Positives = 223/816 (27%), Gaps = 135/816 (16%)

Query: 473  NQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------- 521
              +R+   ++ + + +  +              I A  + + +     +           
Sbjct: 1    GLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGIKASTLTNGLKYSLATGNWGDQKKAAS 60

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 61   SKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 116

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L     V      E    +    + +V  +     +      +I      + 
Sbjct: 117  QACGLVKNLALMCYVTVGSPSEPIVDFMIQRNMEVLEEYEPQRSPNATKIFINGVWVGVH 176

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             D +     V        I      I D  D   K          P    D+  +     
Sbjct: 177  RDPAHLVSTVQALRRKNVISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNRG 236

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            N+      + + E      G E    +  G  +              + V+  V+ + + 
Sbjct: 237  NLVLTKEHVAQLEEDK-EKGAEMDPEEKEGKVMGWNSLV-------NQGVVEYVDAEEEE 288

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +   V     ++  R  Q        +      V+    +     T      ++   +  
Sbjct: 289  TVMIVMTPEDLEISRQLQAGFAMPETVDDPNRRVKAPVNLTAHTWTHCEIHPSMILGICA 348

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   + +  ++                         
Sbjct: 349  SIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------------- 384

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 385  -----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 439

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    +F R   D+ +R      EQ E   R    +      +       +  G 
Sbjct: 440  SIDRGLF-RSLFYRSYTDQEKRVGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGV 498

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  ++ D      R++          ++     +  Q            
Sbjct: 499  RVSGEDIVIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQVLL--------- 549

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             LR VKV +   +  Q GDK A RHG KG +      EDMPF  
Sbjct: 550  -----------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTS 598

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +  +          +S L    E
Sbjct: 599  EGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKLLR--E 656

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +                                                    +G 
Sbjct: 657  HGYQSRGFEVM---------------------------------------------YNGH 671

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
            +    G         V +G  Y  +L HMV DK+ A
Sbjct: 672  T----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 700


>gi|257153201|dbj|BAI23155.1| RNA polymerase beta subunit [Bartonella washoensis]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ P + +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPCDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|103002002|gb|ABF71531.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            cf. chlorophanum Lunke 97]
          Length = 711

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 118/832 (14%), Positives = 237/832 (28%), Gaps = 145/832 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 1    KRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLAT 60

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +     +     
Sbjct: 117  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATK 176

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177  VFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 236

Query: 684  NDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             D+  +     N+   ++ +  L+ +               S     AK  G    V   
Sbjct: 237  IDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV--N 286

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              V+  V+ + + +   V     ++  R  Q           +   V+          T 
Sbjct: 287  NGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTH 346

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N          M  + +   + +  ++            
Sbjct: 347  CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTXYDQRM--------- 395

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 396  ------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 437

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 438  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKH 493

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 494  GTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENG 553

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 554  IVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKXASRHGQK 593

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +       DMPF K+G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 594  GTIGITYRQXDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPF 653

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 654  TEVTVDSVSKLLR--EHGYQSRGFEVM--------------------------------- 678

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                         +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 679  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 711


>gi|125213028|dbj|BAF46395.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153191|dbj|BAI23150.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153197|dbj|BAI23153.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153199|dbj|BAI23154.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|262117884|dbj|BAI47967.1| RNA polymerase beta subunit [Bartonella sp. RJ31-1]
 gi|262117886|dbj|BAI47968.1| RNA polymerase beta subunit [Bartonella sp. RJ37-1]
          Length = 275

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRAGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343462|emb|CBJ18648.1| RNA polymerase B subunit [Micromonospora sp. GUI15]
          Length = 213

 Score =  256 bits (655), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 96/213 (45%), Positives = 125/213 (58%), Gaps = 38/213 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G +++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWQVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A+  +    V+TPVFDGA EE I  +L     +        
Sbjct: 140  -------------------ADSSEPDTNVATPVFDGAREEEIAGLLSSTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
              G++ L+DG +GEP   P+ VGYIY+LKLNH+
Sbjct: 181  ASGKAQLFDGRSGEPLPSPIAVGYIYILKLNHL 213


>gi|190148988|gb|ACE63469.1| RNA polymerase subunit B [Pseudonocardia sp. W101]
          Length = 267

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 156/274 (56%), Positives = 204/274 (74%), Gaps = 8/274 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT+ + YL+A EE+   IAQAN+ L++DGSFTEE V  R   GE  
Sbjct: 61  GFIQTPYRKVEEGRVTDQIDYLTADEEDRFVIAQANAPLNDDGSFTEERVLVRRKGGELD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+P   +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 LIPPTAVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           C NQ+P+V  GD V    +IADGP T+ G++ALG
Sbjct: 234 CNNQKPIVDEGDRVEVGQVIADGPCTENGEMALG 267


>gi|224797495|gb|ACN62777.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            melanogaster]
          Length = 424

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 171/369 (46%), Positives = 247/369 (66%), Gaps = 8/369 (2%)

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1    RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61   GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118  -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAF  W+GYN+ED++++SER+VS+DVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173  VAFTTWNGYNYEDAIIVSERLVSDDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233  RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G  G +  ++ F R   + +   + V +  I    + ++ +++         + +IL  
Sbjct: 293  NGGEGIIQAIKRFPREKYELSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPL 352

Query: 993  QNAVSGPKG 1001
            ++      G
Sbjct: 353  EDMPHMEDG 361



 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 81/293 (27%), Positives = 135/293 (46%), Gaps = 14/293 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVKQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSDDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGGEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSADVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  +     
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNEELIEIMEKAN 419


>gi|262117950|dbj|BAI48000.1| RNA polymerase beta subunit [Bartonella sp. OE6-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117964|dbj|BAI48007.1| RNA polymerase beta subunit [Bartonella sp. FG5-1]
 gi|262117966|dbj|BAI48008.1| RNA polymerase beta subunit [Bartonella sp. FG6-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDNEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|46411502|gb|AAS94321.1| RNA polymerase II [Punctelia hypoleucites]
          Length = 705

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 124/824 (15%), Positives = 234/824 (28%), Gaps = 144/824 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L + +R    ++ + + +  +    +         + +  + + +     +      
Sbjct: 2    GPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +   L++      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  R
Sbjct: 178  WVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPR 237

Query: 690  VLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                 N+         L      +  T  +       G   + K  G+VE VDA      
Sbjct: 238  SSNRGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKE-GVVEYVDAEEEETI 296

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +    +       +        +N +  +N+R    +             PS  LG   
Sbjct: 297  MIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWTHCEIHPSMILG--- 352

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N          M  + +   + +  +E                  
Sbjct: 353  ----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM--------------- 391

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 392  ------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 439

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R        +E   +    + + L    Y +L
Sbjct: 440  SVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---SVVEQFEKPMRSDTLRLKHGTYDKL 495

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  ++ D      R++          ++     +  Q  
Sbjct: 496  DDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVL 555

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             S                         LR VKV +   +  Q GDK A RHG KG +   
Sbjct: 556  LS--------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 595

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +         
Sbjct: 596  YRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVD 655

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             +S L                           V     +G  + T VF            
Sbjct: 656  SVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQVF------------ 688

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                       +G  Y  +L HMV DK+
Sbjct: 689  ---------------------------LGPTYYQRLRHMVDDKI 705



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 85/625 (13%), Positives = 174/625 (27%), Gaps = 115/625 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 2   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 58

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 59  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 118

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 119 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 178

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 179 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 238

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +                  E              V Y+ A EEE   I
Sbjct: 239 SNRGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMI 298

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 299 VMTPEDLEISRQLQAGYAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 358

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +         T  E  +   +                
Sbjct: 359 PFPDHNQSPRNTYQSAMGKQAMGVFL-------TNYEQRMDTMANIL------------- 398

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                                 Q+PL                  
Sbjct: 399 -----------------------------------YYPQKPL----------ATTRSMEF 413

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 414 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRVGMSVV 473

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   +       +D+ G++  G  V+  DI++GK  P         ++   
Sbjct: 474 EQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-- 531

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                K    RDTS  + S  +G V
Sbjct: 532 -----KLHVKRDTSTPLRSTENGIV 551


>gi|262117958|dbj|BAI48004.1| RNA polymerase beta subunit [Bartonella sp. FG2-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD  G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSKGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117876|dbj|BAI47963.1| RNA polymerase beta subunit [Bartonella sp. AR15-3]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+S V+ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSLVEIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D
Sbjct: 121 IDGKVTKEVIYLSAMEESKHYVAQANSSLDTEGRFTEEFVVCRHAGEVLMAPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA+RIVIR+ E  LDPS SGVDI
Sbjct: 241 AIGAKRGGIVDQVDAMRIVIRATED-LDPSKSGVDI 275


>gi|190148970|gb|ACE63460.1| RNA polymerase subunit B [Pseudonocardia sulfidoxydans]
          Length = 270

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 152/277 (54%), Positives = 203/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG VT  + YL+A EE+   +AQAN+ L++DGSFTEE V  R   GE  
Sbjct: 61  GFIQTPYRKVVDGVVTEQIDYLTADEEDRYVVAQANAPLNDDGSFTEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 YITPAGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVAEKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMALGKNL 270


>gi|257153205|dbj|BAI23157.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153207|dbj|BAI23158.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|262117890|dbj|BAI47970.1| RNA polymerase beta subunit [Bartonella sp. SR26-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS+LD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSALDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343534|emb|CBJ18684.1| RNA polymerase B subunit [Micromonospora sp. SR15]
          Length = 210

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 125/215 (58%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 86   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWNVEGDEADWKRALRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AAEAEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|262117912|dbj|BAI47981.1| RNA polymerase beta subunit [Bartonella sp. OY9-1]
 gi|262117920|dbj|BAI47985.1| RNA polymerase beta subunit [Bartonella sp. HT3-1]
 gi|262117944|dbj|BAI47997.1| RNA polymerase beta subunit [Bartonella sp. OE2-1]
 gi|262117946|dbj|BAI47998.1| RNA polymerase beta subunit [Bartonella sp. OE3-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|82581196|dbj|BAE48671.1| RNA polymerase beta subunit [Bartonella sp. Aomori 21-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ EG LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATEG-LDPSKSGVDI 275


>gi|56541588|dbj|BAD77831.1| RNA polymerase beta subunit [Bartonella birtlesii]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDAVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262072863|dbj|BAI47741.1| RNA polymerase beta subunit [Bartonella sp. Koshimizu 6-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSL+ +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLNAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358812|dbj|BAF46075.1| RNA polymerase beta subunit [Bartonella sp. Nakanoshima 3-1]
 gi|124358814|dbj|BAF46076.1| RNA polymerase beta subunit [Bartonella sp. Nakanoshima 4-1]
 gi|262072873|dbj|BAI47746.1| RNA polymerase beta subunit [Bartonella sp. Amami 5-1]
          Length = 275

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTREVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|312204322|gb|ADQ47478.1| RNA polymerase II second largest subunit [Cryptodiscus rhopaloides]
          Length = 711

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 121/807 (14%), Positives = 235/807 (29%), Gaps = 122/807 (15%)

Query: 474  QYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + I + +               + +  + + +     +            
Sbjct: 1    LFRTLFGKLVKDIFKYLQKCIEAGKEFNLTLGVKSTLLTNGLKYSLATGNWGEQKKAAST 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +    + +V  +     A      ++      +  
Sbjct: 117  ACGLVKNLALMCYITVGSPAEPIIEFMVQRNMEVLEEYEPTRAPNSTKVFVNGVWVGVHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMG 693
            D +     V        I      I D  D   K          P   ++ND+ +    G
Sbjct: 177  DPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDNKSPNKGG 236

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              + ++ V  L+ +       +E    K  G   +                +  ++ + +
Sbjct: 237  LVLTKELVNKLEDDRDLHELSLEEKKDKYFGWNGL-----------LNSGAVEFLDAEEE 285

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNML 812
             +   V     ++  R  Q   V   P V      +    +     T      ++   + 
Sbjct: 286  ETVMIVMTPDELETSRQKQAGYVIDDPNVDSNARFKGTANVDTNTWTHCEIHPSMILGVC 345

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N    + +S   +                                      
Sbjct: 346  ASIIPFPDHN---QVCVSLSXMLYLTNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 402

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 403  XTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 462

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R  +++ +R   +    +E   +    E        Y +L +  
Sbjct: 463  NQSSIDRGLF-RSLFYRSYVEQEKR---LGMSMLEQFEKPMKSEVFRTKHGTYEKLDDDG 518

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K+  ++ +                +E  QR     K    T   
Sbjct: 519  IIAPGVRVSGEDIIIGKTAPMAPE---------------SEELGQRTKAHTKRDASTPLR 563

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             L+ VKV +   +  Q GDK A RHG KG +      E
Sbjct: 564  STENGIVDKVLL-----TTNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQE 618

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 619  DMPFTCEGVTPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 664

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 665  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 684

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYI 1254
                G  I+Y+G TG+     V +G  
Sbjct: 685  YQSRGFEIMYNGHTGKKLVAQVFLGPT 711



 Score =  121 bits (304), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 88/629 (13%), Positives = 169/629 (26%), Gaps = 85/629 (13%)

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
             T   K  KD    + + +  G    F++   + + L  +  KY L   G      +  
Sbjct: 2   FRTLFGKLVKDIFKYLQKCIEAG--KEFNLTLGVKSTLLTNGLKYSL-ATGNWGEQKKAA 58

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                  + + +    + +  L        R+GK       +  +  +    E  + Q  
Sbjct: 59  STKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 118

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEH 528
             +  +       + S     +      N + +         ++   F     +    + 
Sbjct: 119 GLVKNLALMCYITVGSPAEPIIEFMVQRNMEVLEEYEPTRAPNSTKVFVNGVWVGVHRDP 178

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL------ 582
            + +S +   RR + +                +         P    +  N         
Sbjct: 179 AHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDNKSPNKGGLV 238

Query: 583 -----VSSLTSFARVNAYGFIETP--YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                V+ L     ++     E    Y        +  V +L A EEE   I      L+
Sbjct: 239 LTKELVNKLEDDRDLHELSLEEKKDKYFGWNGLLNSGAVEFLDAEEEETVMIVMTPDELE 298

Query: 636 EDGSFTEELVFCRCAGE-------EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                    V      +          V        +  P  ++ + AS+IPF +++   
Sbjct: 299 TSRQKQAGYVIDDPNVDSNARFKGTANVDTNTWTHCEIHPSMILGVCASIIPFPDHNQVC 358

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
             L                                                         
Sbjct: 359 VSLSXMLYLTNXXXXXXXXXXXXX---------------------------XXXXXXXXX 391

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                            +           Q+PL                      +L  G
Sbjct: 392 XXXXXXXXXXXXTNFDERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAG 441

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
           +N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     +  
Sbjct: 442 QNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYVEQEKRLGMSMLEQFEKPMKS 501

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           ++        + +D+ GII  G  V+  DI++GK  P     M PE + L      KA  
Sbjct: 502 EVFRTKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAP-----MAPESEELGQR--TKAHT 554

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            RD S  + S  +G V  V +       K
Sbjct: 555 KRDASTPLRSTENGIVDKVLLTTNSEGLK 583


>gi|113957162|gb|ABI49104.1| RNA polymerase II second largest subunit [Lobariella pallida]
          Length = 700

 Score =  256 bits (655), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 120/819 (14%), Positives = 235/819 (28%), Gaps = 148/819 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCS 519
            + +   G +L   +R+   ++ + + + +               + +  + + +     +
Sbjct: 1    KHLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLKYSLAT 60

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   L +     
Sbjct: 117  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPNATK 176

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177  VFVNGVWVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 236

Query: 684  NDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             D+  +     N+   ++ V  L+ +      T  E    K  G        G+VE VDA
Sbjct: 237  IDNDPKSPNRGNLVLTKEHVNKLEDDKELGPDTDPEGREDKFRG-WKGLVNQGVVEYVDA 295

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADGPS 799
                        + +   V     ++  R  Q   V   P +      V+          
Sbjct: 296  EE----------EETVMIVMTPEDLEISRQIQAGYVMPEPSIDDPNKRVKAPLNPTAHTW 345

Query: 800  TDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T      ++   +  + +P+  +N          M  + +   + +  ++          
Sbjct: 346  THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM------- 396

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +                         +  + AI  
Sbjct: 397  --------------------DTMANILXYPQKPXXXXXXXXXXXXXXXXAGQNAIVAIAC 436

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L
Sbjct: 437  YSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKL 492

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                Y +L +   +  G           K+  ++ D      R++          ++   
Sbjct: 493  KHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTE 552

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +  Q                             LR VKV +   +  Q GDK A RHG
Sbjct: 553  NGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHG 592

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +    
Sbjct: 593  QKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD-- 650

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP F    
Sbjct: 651  ---------------------------------------------------ATP-FTEVT 658

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
             ++++ +LR       G   +Y+G TG      V +G  
Sbjct: 659  VDSVSRLLREHGYQSRGFEEMYNGHTGRKLMAQVFLGPT 697



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 73/566 (12%), Positives = 144/566 (25%), Gaps = 99/566 (17%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R+GK       +  +  +
Sbjct: 59  ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 118

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEF 516
               E  + Q    +  +       + +     +      N + +         +A   F
Sbjct: 119 VCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPNATKVF 178

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLS-ALGQGGVARARAGVEM-------RDVHPTHYGR 568
                +    +  + +S +   RR      +  + R     E        R   P     
Sbjct: 179 VNGVWVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRPLFVID 238

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGF------IETPYRKVCDGKVTNDVVYLSAMEE 622
             P   + G+ +     +         G        E  +R          V Y+ A EE
Sbjct: 239 NDPKSPNRGNLVLTKEHVNKLEDDKELGPDTDPEGREDKFRGWKGLVNQGVVEYVDAEEE 298

Query: 623 ENRYIAQANSSLDEDGSFTEELV--------FCRCAGEEILVPREKIDFIDASPKQVVSI 674
           E   I      L+         V          +     +          +  P  ++ I
Sbjct: 299 ETVMIVMTPEDLEISRQIQAGYVMPEPSIDDPNKRVKAPLNPTAHTWTHCEIHPSMILGI 358

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++ S R      M +QA+ +                   + A I+      
Sbjct: 359 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYDQRMDTMANILXYPQKP 409

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                               +   +  Y              NQ                
Sbjct: 410 XXXXXXXXXXXXXXXXAGQNAIVAIACYSG-----------YNQE--------------- 443

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               S  +   ++ R +  +       + E  + +S             +E+FE   R  
Sbjct: 444 ---DSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMS------------VVEQFEKPMR-- 486

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                    D   +       +D+ GI+  G  V+  DI++GK  P         E+L +
Sbjct: 487 --------SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQ 534

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   DV        +G+   V+
Sbjct: 535 RTKLHVKRDVSTPLRSTENGIVDQVL 560


>gi|190148936|gb|ACE63443.1| RNA polymerase subunit B [Pseudonocardia alaniniphila]
          Length = 270

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 153/277 (55%), Positives = 203/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVDNGRVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 FISPTGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P++  GD V    +IADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIIDEGDRVEAGQVIADGPCTENGEMALGKNL 270


>gi|103001800|gb|ABF71522.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 716

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 118/834 (14%), Positives = 229/834 (27%), Gaps = 145/834 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L N +R+   ++ + + +  +              + +  + + + 
Sbjct: 1    DXXGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+  +     N+   ++ +  L+ +               S     AK  G   
Sbjct: 237  RPLFVIDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDG 288

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V     V+  V+ + + +   V     ++  R  Q               V+       
Sbjct: 289  LV--NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTA 346

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +                 
Sbjct: 347  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSXMGKQAMXXXXXXXXXXXXXXXXX 406

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                                      +       +   +  + A
Sbjct: 407  X-----------------------------YYPQKPLATTRSMEFLKFRELPAGQNAIVA 437

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 438  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDT 493

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 494  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLR 553

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             L+ VKV +   +  Q GDK A 
Sbjct: 554  STENGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFAS 593

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 594  RHGQKGTIGITYRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 653

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 654  DATPFTEVTVDSVSKLLR--EHGYQSRGFEVM---------------------------- 683

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                              +G +    G         V +G  Y  +L HMV DK
Sbjct: 684  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDK 713



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 83/619 (13%), Positives = 165/619 (26%), Gaps = 99/619 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N      NK  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFNKLTKDVYKYLQKCVESNR--EFNLTLGVKSTTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 129 TPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +S +   RR   +  +  + R     E        R   P       P  
Sbjct: 189 VGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 248

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           T+ G+ +     +           I      E  +           V Y+ A EEE   I
Sbjct: 249 TNCGNLVLTKEHINKLEDDKDLPAIMDSEEKEAKFFGWDGLVNNGVVEYVDAEEEETVMI 308

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                 L                              + S +     A       E  D 
Sbjct: 309 VMTPEDL------------------------------EISRQIQAGYA-----MPETSDD 333

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               +   M                T       +   + I+   A I+   D  +    +
Sbjct: 334 PNKRVKAPM--------------NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNT 379

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +  +                          Q+PL                      +L 
Sbjct: 380 YQSXMGKQAMXXXXXXXXXXXXXXXXXXYYPQKPL----------ATTRSMEFLKFRELP 429

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----I 861
            G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     +
Sbjct: 430 AGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPM 489

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             D   +       +D+ GI+  G  V+  DI++GK  P         E+L +       
Sbjct: 490 RSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHVK 545

Query: 922 VDVRDTSLRVPSGVSGTVV 940
            DV        +G+   V+
Sbjct: 546 RDVSTPLRSTENGIVDQVL 564


>gi|124358826|dbj|BAF46082.1| RNA polymerase beta subunit [Bartonella sp. Yoroshima 7-2]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699780|gb|AAU86952.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            macrospora subsp. macrospora]
          Length = 706

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 123/829 (14%), Positives = 235/829 (28%), Gaps = 147/829 (17%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L N +R+   ++ + + +  +    +         + +  + + +     + 
Sbjct: 1    RLDXAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L    +  V         +    + +V  +     +      
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYITVGTPSQPIIDFMIQRNMEVLEEYEPQRSPNATKV 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN 684
            ++      +  D +     V        I      + D  D   K          P    
Sbjct: 177  FVNGVWVGVHRDPAHLVSTVLALRRANAISHEVSLVRDIRDREFKIFTDAGRVCRPLFVI 236

Query: 685  DDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            ++  R     N+   +Q +  L+ +        E       G   + K  GIVE VDA  
Sbjct: 237  NNDPRSKNCGNLVLTKQDIHKLEDDKDLPD-DYEIDEKNPPGWNGLIKH-GIVEYVDAEE 294

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                      + +   V     ++  R  Q           +   V+          T  
Sbjct: 295  ----------EETVMIVMTPEDLEISRQLQAGYNLPDTSDDLIKRVKAPMNPTAHTWTHC 344

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N                        ++       +G    
Sbjct: 345  EIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXLT 386

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              D                +  +             +       +   +  + AI     
Sbjct: 387  NYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 435

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L   
Sbjct: 436  YNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHG 491

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 492  TYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGI 551

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                             LR VKV +   +  Q GDK A RHG KG
Sbjct: 552  VDQVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKG 591

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 592  TIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 651

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 652  EVTVDSVSKLLR--EHGYQSRGFEVM---------------------------------- 675

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                        +G +    G         V +G  Y  +L HMV DK+
Sbjct: 676  -----------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 706


>gi|307343570|emb|CBJ18702.1| RNA polymerase B subunit [Micromonospora inositola]
          Length = 210

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 124/215 (57%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +      +K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAAWKKQLRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEGDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V 
Sbjct: 176  SSGKAQLFDGGSGEPLPDPIAVGYIYILKLNHLVD 210


>gi|298912941|emb|CAZ66638.1| RNA polymerase beta subunit [Vibrio furnissii]
          Length = 289

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 170/289 (58%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +     ++   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIERADAEEQGTLDETDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G F +ELV  R  GE  L PRE ++++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGGFADELVTARQKGESGLHPREHVNYMDVATNQVVSIAASLIPFL 289


>gi|190148958|gb|ACE63454.1| RNA polymerase subunit B [Pseudonocardia halophobica]
          Length = 269

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 154/276 (55%), Positives = 202/276 (73%), Gaps = 8/276 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG VT  + YL+A EE+   IAQAN+ L+ DGSFTE+ V  R   GE  
Sbjct: 61  GFIQTPYRKVVDGVVTEQIDYLTADEEDRFVIAQANAPLNADGSFTEDRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+P   +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++EAP VGTG
Sbjct: 121 LIPPTGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +V ++AG+VE++ A  I + S +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVTEKAGVVEELCADYITVMSDDGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMALGKN 269


>gi|94410936|gb|ABF18586.1| RNA polymerase II second largest subunit [Camarophyllopsis
            hymenocephala]
          Length = 696

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 127/831 (15%), Positives = 237/831 (28%), Gaps = 156/831 (18%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + +    +              +  + + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +      
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL----- 171

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
               EEN + +   + +  +G +       R     +   ++     D SP+  V      
Sbjct: 172  ---EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKXIKKLRRKDDISPEVSVVRDIRE 225

Query: 679  IPFLENDDSNRVLMGCNMQR------QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                   D+ RV     +        Q   +      +   G E              + 
Sbjct: 226  RELRLYTDAGRVCRPLFIVENQQLALQKKHIRWLNQGYDDGGEEYK-------WEQLIKG 278

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            GI+E +DA       +    +   +       +    ++       R  +KVG +     
Sbjct: 279  GIIELLDAEEEETVMISMTPEDLENSRLQSSGVDPHANDGEFDPAAR--LKVGIDAHTWT 336

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N                        ++    
Sbjct: 337  HCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMG 371

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G       I               +  +             +       +   +  
Sbjct: 372  KQAMGIYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNA 420

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD  
Sbjct: 421  IVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTT 479

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       I  G           K+  +  D      R++          ++
Sbjct: 480  LRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLK 539

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                              + VKV V   R  Q GDK A 
Sbjct: 540  STESGIVDQVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFAS 579

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G + 
Sbjct: 580  RHGQKGTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEG 639

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S      +K   +                                  
Sbjct: 640  DATPFTELTVESVSTFLR--QKGYQSRGLEVM---------------------------- 669

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                               G +    G         V +G  Y  +L HMV
Sbjct: 670  -----------------YHGHT----GR---KLQAQVYLGPTYYQRLKHMV 696



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 87/623 (13%), Positives = 170/623 (27%), Gaps = 103/623 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH-NIG 581
               +  N +  I   RR   +                ++        P    E      
Sbjct: 192 GVHRDPANLVKXIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 251

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +    +    G  E    K         +  L A EEE   I+     L+     +
Sbjct: 252 QKKHIRWLNQGYDDGGEE---YKWEQLIKGGIIELLDAEEEETVMISMTPEDLENSRLQS 308

Query: 642 EELVFCRCAGEEILVPREKI-------DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +      GE     R K+          +  P  ++ I AS+IPF +++ S R     
Sbjct: 309 SGVDPHANDGEFDPAARLKVGIDAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 368

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 369 AMGKQAMGIYLTNFLI-----------------------------------------RMD 387

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 388 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 423

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            + + GYN EDS+++++  +   +F SI+   +  + + + +   E            + 
Sbjct: 424 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMK 483

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +++ G+I  G  V   DI++GK  P         ++        +    RD S 
Sbjct: 484 HGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVST 536

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S  SG V  V I       K
Sbjct: 537 PLKSTESGIVDQVLITTNSEGQK 559


>gi|52699851|gb|AAU86987.1| DNA-dependent RNA polymerase II second largest subunit [Petractis
            luetkemuelleri]
          Length = 716

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 117/838 (13%), Positives = 239/838 (28%), Gaps = 147/838 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D  G +R    G ++   +R+   ++ + + + +     +         + +  + + + 
Sbjct: 1    DXFGKKRXDLAGPLMAGLFRMLFYKLFKDVNQYLKKCVDNGKEFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      I D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVNTVQSLRRRNMISSEVSLIRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D+     G  +  + +     +   +   M+    K        K  G    
Sbjct: 237  RPLFVIDNDNKSPNKGSLVLTKELVNKLEDDRELPPDMDPDEKKL-------KYFGWAGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            V +    +  ++ + + +         ++  R  Q       P       V+     A  
Sbjct: 290  VAS--GAVEFLDAEEEETVMIAMTPEDLEISRQVQAGYALPEPSSDPNARVKAPVSAAQQ 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  +                    
Sbjct: 348  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQ-------------------- 387

Query: 857  GPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                              N DE    +  +             +       +   +  + 
Sbjct: 388  -----------AXXXXXTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIV 436

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    ++ R  +++ +R   +    +E   +    E
Sbjct: 437  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLYYRVYVEQEKR---IGMSLVEQFEKPLRSE 492

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + +    Y +L +   I  G           K+  ++ D      R++          +
Sbjct: 493  TLRVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPL 552

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +                  ++K+          L+ VKV +   +    GDK A
Sbjct: 553  RSTENGI------------------VDKVLL--TTNAEGLKFVKVRMRTTKVPXIGDKFA 592

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +
Sbjct: 593  SRHGQKGTIGITYRQEDMPFSAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFE 652

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S L    E    +                                 
Sbjct: 653  GDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM--------------------------- 683

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                               +G +    G         V  G  Y  +L HMV  K++A
Sbjct: 684  ------------------YNGHT----GR---KLVAQVFFGPTYYQRLRHMVXXKIHA 716



 Score =  103 bits (256), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 82/630 (13%), Positives = 156/630 (24%), Gaps = 100/630 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +         K  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 12  GPLMAGLFRMLFYKLFKDVNQYLKKCVDNG--KEFNLTLGVKSTTLTNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +      N + +         +A   F     
Sbjct: 129 TPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRSPNATKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + ++ +   RR + +                +         P    +  N  
Sbjct: 189 VGVHRDPAHLVNTVQSLRRRNMISSEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDNKS 248

Query: 582 LVSSLTSFAR--VN------------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
                    +  VN                 +  Y        +  V +L A EEE   I
Sbjct: 249 PNKGSLVLTKELVNKLEDDRELPPDMDPDEKKLKYFGWAGLVASGAVEFLDAEEEETVMI 308

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     L+         V    A  E             S  Q                 
Sbjct: 309 AMTPEDLE-----ISRQVQAGYALPEPSSDPNARVKAPVSAAQQTW-------------- 349

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                                    T  E   +   G            Q          
Sbjct: 350 -------------------------THCEIHPSMILGICASIIPFPDHNQSPRNT----Y 380

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  +          +           Q+PL                      +L  
Sbjct: 381 QSAMGKQAXXXXXTNFDERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPA 430

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT----- 862
           G+N +VA   + GYN EDS+++++  +   +F S++   +    +   +   E       
Sbjct: 431 GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRVYVEQEKRIGMSLVEQFEKPLR 490

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +   V     + +D+ GII  G  V+  DI++GK  P         ++        K  
Sbjct: 491 SETLRVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLH 543

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             RD S  + S  +G V  V +       K
Sbjct: 544 TKRDASTPLRSTENGIVDKVLLTTNAEGLK 573


>gi|8895194|gb|AAF80847.1|AF165991_1 RNA polymerase beta subunit [Bartonella doshiae]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AIGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358794|dbj|BAF46066.1| RNA polymerase beta subunit [Bartonella sp. Nagano 14-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 196/275 (71%), Positives = 230/275 (83%), Gaps = 1/275 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVD
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVD 274


>gi|52694119|emb|CAG30589.1| DNA-directed RNA polymerase beta chain [Pseudomonas
           anguilliseptica]
          Length = 258

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 150/252 (59%), Positives = 192/252 (76%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH R
Sbjct: 5   VRVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKR 64

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E
Sbjct: 65  RVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLE 124

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           +PYR V DG  T+++V+LSA+EE N  IAQA++ LDE+    +ELV  R   E  +   E
Sbjct: 125 SPYRMVKDGVATDEIVFLSAIEEANHVIAQASAGLDENNRLIDELVAVRHLNEFTVKAPE 184

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            +  +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+++ P VGTGME  V
Sbjct: 185 DVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSDKPLVGTGMERNV 244

Query: 720 AKSSGAAIVAKR 731
           A+ SG  +VA+R
Sbjct: 245 ARDSGVCVVARR 256


>gi|309366827|emb|CAP20749.2| hypothetical protein CBG_24045 [Caenorhabditis briggsae AF16]
          Length = 1160

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 152/1014 (14%), Positives = 297/1014 (29%), Gaps = 206/1014 (20%)

Query: 407  DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            +   V  +  +M  ++  PD    ++   +  + + L+    G+  +DD D  GN+R+  
Sbjct: 303  EHEAVDFLSNSMITHIACPDGNFKMKAIYLGQMTRRLIQTEMGENELDDRDFYGNKRLEL 362

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDIDS----VMPQDLINAKPVVSAVCEFFCSSQL 522
             G +L   +     R    +K    +  + +    +     +    + + +     +   
Sbjct: 363  AGSLLALLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQDMITNTIVNAMSTGNW 422

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAET 574
                  +  L       RLS +   G+         + R     R + P+ +G +CP++T
Sbjct: 423  IIKRFRMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDT 482

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L   + +      +   R + +  V           E+       N   
Sbjct: 483  PEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGV-----------EDLH-----NVHF 526

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI--DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                     L+F         V  E++     D     ++S   S+   + N        
Sbjct: 527  SHVNKPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSMTNRSVFISSD 586

Query: 693  GCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            G  + R  + +   +     T + E    K              + VD   +    V   
Sbjct: 587  GGRLCRPYIIVRHGKPMLTETHVQELKEGK----------RIFEDFVDDGIVEYLDVNEM 636

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
             D   +                        V   +       +   P T LG       +
Sbjct: 637  NDALIA------------------------VYENEIGAETTHLEIEPFTLLG-------V 665

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
                +P+  +N          M  + + T      +    R   +         P V  +
Sbjct: 666  CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIA----YNQQKRIDSIMYLLCYPQRPLVKSK 721

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                                      I       +      + A+      D+ D  +  
Sbjct: 722  T-------------------------IELTNFEKLPAGANGIIAVMSYSGYDIEDALVLN 756

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
             + +        ++ +H     ++  +   +++   A D    + I       +   +  
Sbjct: 757  KASLDRGYGRCLVY-KHVKGTAKKYPNQTYDRLLGPAVDSVTLKPIFKHKNLDQEGIVFT 815

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G   +       K   + S        +     A +D           V Y+      + 
Sbjct: 816  GARILPKQTIINKYMPVVSAESGSAASANTIGIAGRD-----------VAYKDVSITYKT 864

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +  E++    +       + KV +   R  + GDK +                    
Sbjct: 865  PTPSYAERVLLTYNEDEA--HLFKVLLRQTRRPELGDKFS-------------------- 902

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    +   + +   + L   
Sbjct: 903  -----------------SR-----------------HGQKGVCGLIAQQEDMPFNDLGMV 928

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++    +  +++      +L       +G       F G   + +   L     +  
Sbjct: 929  PDMIMNPHGYPSRMTVGKLMELLSGKAGVMNGTYHYGTAFGGDQVKDVCEELAARGYNYM 988

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+ +L  G+TG+P    +  G IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG
Sbjct: 989  GKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGG 1048

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD---------------------------DVVG 1324
             RLGEME  C+ AYGA+ +L E L + SD                           DV  
Sbjct: 1049 LRLGEMERDCLIAYGASMLLIERLMVSSDEFKVLFRSFVPLIPIEVFFVRRCFQCVDVCT 1108

Query: 1325 RTRVYESIVAG--------NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
               V  S   G                P +  +L +E+Q++ +   L+ +R   
Sbjct: 1109 GCGVIGS--KGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLDLARYTE 1160



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 130/961 (13%), Positives = 287/961 (29%), Gaps = 195/961 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L++    S+DHF+ + I      N+ +          +  +    L ++      P    
Sbjct: 41  LVKQHLVSFDHFVNVEIRNIMLSNQKIT---------SDANPNFHLTYLDIRVGKPSK-- 89

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT--------- 139
             C  RD+TY+ P+ + +             +  + + ++ + +G +P+M          
Sbjct: 90  --CRLRDMTYSAPISVDIEYT----------RGHQRVYKKDLVIGRMPIMLRSSKCILRD 137

Query: 140 ---------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
                            G FV+KG +++++ Q   S              S K L  C +
Sbjct: 138 LAEEELARVQECPHDPGGYFVVKGSEKVILIQEQLSKNRI-----MVGRNSSKEL-QCEV 191

Query: 185 IPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIVYS 239
           +     +          K    VR ++    VPV+    A+G++S+ +I+ST   +  Y 
Sbjct: 192 LSSTSERKSK-TYVTVKKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGHEEKYV 250

Query: 240 QRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
                       A +    +  + +       +    G    + +      K  + +   
Sbjct: 251 SAFAQTLEECINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLTAPKEHEAVDFL 310

Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAG------DVIDEKSLEEIFHSEIRDIP-------I 346
           S+ +   ++A    N +   IY+           + E  L++      + +        +
Sbjct: 311 SNSMI-THIACPDGNFKMKAIYLGQMTRRLIQTEMGENELDDRDFYGNKRLELAGSLLAL 369

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L+ D           +  +       A LDI + MR  D+ T ++  +M +   +   ++
Sbjct: 370 LFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQ-DMITNTIVNAM-STGNWIIKRF 427

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            +  +G  ++  R           +     + ++  +         +    +L   +   
Sbjct: 428 RMERLGVTQVLSR-----------LSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGM 476

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           +      +     L    ++   I++   +  + + L+N+        E   +   S + 
Sbjct: 477 LCPSDTPEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGV------EDLHNVHFSHVN 530

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N+L  +      +A+    V +A   +    +                        L
Sbjct: 531 KPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSMTNRSVFISSDGGRL 590

Query: 587 TSFARVNAYG----------FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                +  +G           ++   R   D      V YL   E  +  IA   + +  
Sbjct: 591 CRPYIIVRHGKPMLTETHVQELKEGKRIFEDFVDDGIVEYLDVNEMNDALIAVYENEIGA 650

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                  +   ++  P  ++ + A LIP+  ++ S R    C M
Sbjct: 651 -----------------------ETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAM 687

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+  +                  S                                 
Sbjct: 688 GKQAMGTI---------AYNQQKRIDS--------------------------------- 705

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                             C  QRPLVK                T+   L  G N ++A M
Sbjct: 706 -------------IMYLLCYPQRPLVKS----------KTIELTNFEKLPAGANGIIAVM 742

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEE 871
            + GY+ ED++++++  +       +  +  +  A+       +         +      
Sbjct: 743 SYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTYDRLLGPAVDSVTLKPIF 802

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
             KN+D+ GI+  GA + P   ++ K  P   +               + V  +D S+  
Sbjct: 803 KHKNLDQEGIVFTGARILPKQTIINKYMPVVSAESGSAASANTIGIAGRDVAYKDVSITY 862

Query: 932 P 932
            
Sbjct: 863 K 863


>gi|159137659|gb|ABW88909.1| RNA polymerase beta-subunit [Bartonella queenslandensis]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++  R+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAARDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|169659050|dbj|BAG12734.1| RNA polymerase beta subunit [Bartonella grahamii]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  L+PS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LNPSKSGVDI 275


>gi|52694397|emb|CAG38038.1| RNA polymerase beta subunit [Pseudomonas oleovorans]
          Length = 338

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 179/338 (52%), Positives = 227/338 (67%), Gaps = 5/338 (1%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 3   KERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGP 62

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR---VNAYGFIETPYR 603
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL        V   G       
Sbjct: 63  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLGCLCPHQPVRLPGKPVPR-- 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                      V +      +R+         E+    +ELV  R   E  +   E +  
Sbjct: 121 GEGRRGQRRHRVPVGHRRGGSRHRPGFGRDEREESQLIDELVAVRHLNEFTVKAPEDVTL 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ S
Sbjct: 181 MDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDS 240

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
           G  +VA+R G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV 
Sbjct: 241 GVCVVARRGGVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVS 300

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            GD+V+R DI+ADGPSTD+G+LALG+NM +AFM W+G+
Sbjct: 301 KGDKVQRGDIMADGPSTDMGELALGQNMRIAFMAWNGF 338


>gi|257153193|dbj|BAI23151.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153195|dbj|BAI23152.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|262117878|dbj|BAI47964.1| RNA polymerase beta subunit [Bartonella sp. RJ23-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRAGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|159137641|gb|ABW88900.1| RNA polymerase beta-subunit [Bartonella rattaustraliani]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRAGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|257153203|dbj|BAI23156.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153215|dbj|BAI23162.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|257153217|dbj|BAI23163.1| RNA polymerase beta subunit [Bartonella washoensis]
 gi|262117952|dbj|BAI48001.1| RNA polymerase beta subunit [Bartonella sp. DR7-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|159137661|gb|ABW88910.1| RNA polymerase beta-subunit [Bartonella coopersplainsensis]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699808|gb|AAU86966.1| DNA-dependent RNA polymerase II second largest subunit [Diploschistes
            scruposus]
          Length = 713

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 125/836 (14%), Positives = 236/836 (28%), Gaps = 149/836 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFF 517
            G +R    G ++ + +R    R+ + + + +               + +  + + +    
Sbjct: 1    GKKRXDLAGPLMASLFRSLFNRLTKDVLKYLQKCIEGNRDFNIALGVKSTTLTNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWSEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L    +  V + G     +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPNI 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      +  D +     V        I      I D  D   K          P 
Sbjct: 177  TKVFVNGVWVGVHRDPAHLYNTVLSLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVARPL 236

Query: 682  --LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
              ++ND  +       + ++ V  L+ +             +        K  G    V 
Sbjct: 237  FVIDNDKRSSRRGELVLSKELVNRLEDDRELPPDLDPDEKKE--------KYFGWEGLVK 288

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            +    +  ++ + + +         +   R  Q       P        +          
Sbjct: 289  S--GAVEYLDAEEEETVMIAMTPEDLDISRQVQAGYAPPEPSTDQNARFKAPVNTNVHTW 346

Query: 800  TDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T      ++   +  + +P+  +N          M  + +                    
Sbjct: 347  THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGV------------------ 388

Query: 859  EEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                          L N DE    +  +             +       +   +  + AI
Sbjct: 389  -------------FLTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 435

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R  +++ +R        +E   +    E +
Sbjct: 436  LCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPLRSETL 491

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   I  G           K+  ++ D                DE  QR
Sbjct: 492  RLKHGTYEKLDDDGLIAPGVRVSGEDVIIGKTAPIAPD---------------TDELGQR 536

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                 K    T     E+   +K+             L+ VKV +   +  Q GDK A R
Sbjct: 537  TKLHSKRDASTPLRSTENGIVDKVLL-----TTNQEGLKFVKVRMRTTKIPQIGDKFASR 591

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 592  HGQKGTIGITYRQEDMPFTAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 651

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 652  ATPFTDVTVDSVSRLLR--EHGYQSRGFEVM----------------------------- 680

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V  G  Y  +L HMV  K+ A
Sbjct: 681  ----------------YNGHT----GR---KLRAQVFFGPTYYQRLRHMVDXKIXA 713



 Score = 70.9 bits (172), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 53/389 (13%), Positives = 108/389 (27%), Gaps = 37/389 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +   +  N+  KD L  + + +       F++A  + +    +  KY L   G  
Sbjct: 9   GPLMASLFRSLFNRLTKDVLKYLQKCIEGNR--DFNIALGVKSTTLTNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 66  SEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNTPLGRDGKIAKPRQLHNTHWGLVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +      N + +         +    F     
Sbjct: 126 TPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPNITKVFVNGVW 185

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  +  + +   RR + +  +  + R     E        R   P          
Sbjct: 186 VGVHRDPAHLYNTVLSLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVARPLFVIDNDKRS 245

Query: 574 TSEGHNI---GLVSSLTSFARVNAYGFI---ETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           +  G  +    LV+ L     +         +  Y        +  V YL A EEE   I
Sbjct: 246 SRRGELVLSKELVNRLEDDRELPPDLDPDEKKEKYFGWEGLVKSGAVEYLDAEEEETVMI 305

Query: 628 AQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           A     LD                         +          +  P  ++ I AS+IP
Sbjct: 306 AMTPEDLDISRQVQAGYAPPEPSTDQNARFKAPVNTNVHTWTHCEIHPSMILGICASIIP 365

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           F +++ S R      M  QA+ +      
Sbjct: 366 FPDHNQSPRNTYQSAMGXQAMGVFLTNFD 394


>gi|262072883|dbj|BAI47751.1| RNA polymerase beta subunit [Bartonella sp. Kumamoto 35-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IK+R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKDRMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117962|dbj|BAI48006.1| RNA polymerase beta subunit [Bartonella sp. FG4-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 201/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHIDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148962|gb|ACE63456.1| RNA polymerase subunit B [Pseudonocardia kongjuensis]
          Length = 270

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 154/277 (55%), Positives = 204/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+SFARVN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSFARVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFIETPYRKV DG VT+ + YL+A EE+   +AQAN+ L++DGSF E+ V  R   GE  
Sbjct: 61  GFIETPYRKVVDGVVTSQIDYLTADEEDRFVVAQANARLNDDGSFAEDRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +D+ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPSGVDYIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I +   EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVAEQAGVVEELCADYITVMDDEGQRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIVDEGARVEVGQVLADGPCTENGEMALGKNL 270


>gi|262117948|dbj|BAI47999.1| RNA polymerase beta subunit [Bartonella sp. OE5-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPASAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRSEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|168809732|gb|ACA29585.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 225

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 99/294 (33%), Positives = 137/294 (46%), Gaps = 71/294 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 1    DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 49

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 50   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 103

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 104  RHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 163

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D+                                              D
Sbjct: 164  ATPVFDGATSEDLW---------------------------------------------D 178

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
              +E         A +    +++LYDG TGEPFD  V+VG +YM+KL+HMV DK
Sbjct: 179  TVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDK 223



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 48/75 (64%), Positives = 57/75 (76%)

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  
Sbjct: 1   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGD 60

Query: 937 GTVVDVRIFNRHGID 951
           G V DV+IF R   D
Sbjct: 61  GVVRDVKIFTRANGD 75


>gi|78100240|gb|ABB20921.1| RNA polymerase II second largest subunit [Rhodotorula hordea]
          Length = 695

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 130/825 (15%), Positives = 243/825 (29%), Gaps = 149/825 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ + +   +               + +  + + +    
Sbjct: 1    GAKRLDLAGPLLAALFRMLFRKLTKDVYRHLQKCVETQKPFNLNSAVKSNTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAMSAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++           + +  + N   + S M +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPIVEFLEEWGMENLEEFSSEMSKGT 176

Query: 625  RYIAQA-NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL 682
            +         +  D +   E +       +I      + D  +   +          P  
Sbjct: 177  KVFVNGVWQGVHRDPAHLVETIKRLRRCGDISNEVSVVRDVRERELRLFTDAGRVCRPLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D   VL   N++   +              E    +           G+VE VDA  
Sbjct: 237  IVEDHRLVLTRANVEALQIEE-----------SEDRPDEKRMKWTDLLETGVVEYVDAEE 285

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK--VGDEVRRNDIIADGPST 800
                 +    +     +D  RL +     Q    +    VK  +G            PS 
Sbjct: 286  EETVMICMTPED----LDTSRLFQETGQVQVDTFDASATVKGSMGVNTHTWTHCEIHPSM 341

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   + +  ++V           
Sbjct: 342  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQVRM--------- 383

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 384  ------------------DTMANILYYPQKPLATTRSMEYLHFRELPAGQNAIVAIMCYS 425

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +     + R  +D+ ++S +++ E+ E   RD          
Sbjct: 426  GYNQEDSVILNQSSIDRGLF-RSFYYRSYMDQEKKSGAIQMEEFEKPTRDTTLRLKHGTY 484

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                    I  G+          K+  L  D                +E  QR+    K 
Sbjct: 485  EKLEADGIIGLGERVAGEDIIIGKTAPLPPD---------------SEELGQRSKNHTKR 529

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++      D +     + VK+ V   R  + GDK A RHG KG +
Sbjct: 530  DVSTPMKSTENGIIDQVLVTTNQDGL-----KFVKIRVRSTRVPEIGDKFASRHGQKGTI 584

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +GT  DI++NP  +PSRM +G + E  L       G +  +      
Sbjct: 585  GITYRHEDMPFSGEGTTPDIIINPHAIPSRMTIGHLVECLLSKVSTISGNEGDATPFSEV 644

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                IS L   +     +                                          
Sbjct: 645  TVEAISTLLKEMG--YHSRGLEVM------------------------------------ 666

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                      +G +    G         V +G  Y  +L HMV D
Sbjct: 667  ---------YNGHT----GR---KLQAQVYLGPTYYQRLKHMVDD 695


>gi|103001177|gb|ABF71496.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            molybdina]
          Length = 709

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 120/829 (14%), Positives = 235/829 (28%), Gaps = 145/829 (17%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + + +  +    +         + +  + + +     +   
Sbjct: 2    DLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTISNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +     +      ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMVQRNMEVLEEYEPQRSPNATKVFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  D +     V        I      + D  D   K          P    ++
Sbjct: 178  NGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVVEN 237

Query: 687  SNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
              +     N+   ++ +  L+ +     T          G    AK  G    V     V
Sbjct: 238  DPKSTHCGNLVLTKEHINKLEDDKDLPPTA--------EGEEKDAKFFGWDGLV--NNGV 287

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG- 803
            +  V+ + + +   V     ++  R  Q           +   V+          T    
Sbjct: 288  VEYVDAEEEETVMIVMTPEDLEISRQIQAGYTIPETSDDLIKRVKAPMNPTAHTWTHCEI 347

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
              ++   +  + +P+  +N                        ++       +G      
Sbjct: 348  HPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGXXXXXX 389

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                             +  +             +       +   +  + AI      +
Sbjct: 390  XXXM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYN 438

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R   D+ +R        +E   +    + + L    Y
Sbjct: 439  QEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGM---SVVEQFEKPMRSDTLKLKHGTY 494

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   +  G           K+  +S D      R++                 +K 
Sbjct: 495  DKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKL---------------HVKR 539

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++             L+ VKV +   +  Q GDK A RHG KG +
Sbjct: 540  DCSTPLRSTENGIVDQVLI-----TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTI 594

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF KDG   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 595  GITYRQEDMPFTKDGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEV 654

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L    E    +                                          
Sbjct: 655  TVDSVSKLLR--EHGYQSRGFEVM------------------------------------ 676

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                      +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 677  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 709


>gi|8895206|gb|AAF80853.1|AF165997_1 RNA polymerase beta subunit [Bartonella vinsonii subsp. vinsonii]
 gi|82581210|dbj|BAE48678.1| RNA polymerase beta subunit [Bartonella japonica]
 gi|124358816|dbj|BAF46077.1| RNA polymerase beta subunit [Bartonella sp. Nakanoshima 13-1]
 gi|124358818|dbj|BAF46078.1| RNA polymerase beta subunit [Bartonella sp. Nakanoshima 25-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117930|dbj|BAI47990.1| RNA polymerase beta subunit [Bartonella sp. FN6-1]
 gi|262117970|dbj|BAI48010.1| RNA polymerase beta subunit [Bartonella sp. DS3-1]
 gi|262117972|dbj|BAI48011.1| RNA polymerase beta subunit [Bartonella sp. DS7-1]
          Length = 275

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGHFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|224797499|gb|ACN62779.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797501|gb|ACN62780.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797503|gb|ACN62781.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797507|gb|ACN62783.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797509|gb|ACN62784.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797511|gb|ACN62785.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797513|gb|ACN62786.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797515|gb|ACN62787.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797517|gb|ACN62788.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797523|gb|ACN62791.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797527|gb|ACN62793.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797529|gb|ACN62794.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797531|gb|ACN62795.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797533|gb|ACN62796.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797535|gb|ACN62797.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797537|gb|ACN62798.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797539|gb|ACN62799.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797541|gb|ACN62800.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797543|gb|ACN62801.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797545|gb|ACN62802.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797547|gb|ACN62803.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797549|gb|ACN62804.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797551|gb|ACN62805.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797553|gb|ACN62806.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797555|gb|ACN62807.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797557|gb|ACN62808.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797559|gb|ACN62809.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
          Length = 424

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 172/369 (46%), Positives = 247/369 (66%), Gaps = 8/369 (2%)

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1    RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61   GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118  -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173  VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233  RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G  G +  ++ F R   + +   + V +  I    + ++ +++         + +IL  
Sbjct: 293  NGGEGIIQAIKRFPREKYELSVDVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPL 352

Query: 993  QNAVSGPKG 1001
            ++      G
Sbjct: 353  EDMPHMEDG 361



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 81/293 (27%), Positives = 135/293 (46%), Gaps = 14/293 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVKQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGGEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSVDVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  +     
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNEELIEIMEKAN 419


>gi|118640619|gb|ABL09877.1| RNA polymerase beta subunit [Vibrio metschnikovii]
 gi|118640621|gb|ABL09878.1| RNA polymerase beta subunit [Vibrio metschnikovii]
          Length = 290

 Score =  256 bits (654), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 223/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +     ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSPERYDLSTVGRMKFNSSIERTDAEEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L +D  F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTDDSRFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|8895186|gb|AAF80843.1| RNA polymerase beta subunit [Bartonella alsatica]
          Length = 275

 Score =  256 bits (653), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358770|dbj|BAF46054.1| RNA polymerase beta subunit [Bartonella chomelii]
          Length = 275

 Score =  256 bits (653), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDLEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AIGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|159137645|gb|ABW88902.1| RNA polymerase beta-subunit [Bartonella rattaustraliani]
          Length = 275

 Score =  256 bits (653), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +VVYLSAMEE   Y+AQANSSLD  G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVVYLSAMEESKHYVAQANSSLDAQGRFVEEFVVCRHAGEVLMAPRDNVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|294992900|gb|ADF57570.1| RNA polymerase [Mycobacterium sp. NL-HBW-26]
          Length = 209

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 90/218 (41%), Positives = 120/218 (55%), Gaps = 35/218 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 19   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 78

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+   N                  
Sbjct: 79   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWDIRKDGNAEIPAWA----------- 126

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                            ++    +   +    +TPVFDGA EE +  +L            
Sbjct: 127  ---------------QNLPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 171

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V D
Sbjct: 172  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDD 209


>gi|8895202|gb|AAF80851.1|AF165995_1 RNA polymerase beta subunit [Bartonella taylorii]
 gi|124358820|dbj|BAF46079.1| RNA polymerase beta subunit [Bartonella sp. Hokkaido 16-3]
 gi|124358822|dbj|BAF46080.1| RNA polymerase beta subunit [Bartonella sp. Hokkaido 25-2]
 gi|262072871|dbj|BAI47745.1| RNA polymerase beta subunit [Bartonella sp. Yatsugatake 16-1]
 gi|262072875|dbj|BAI47747.1| RNA polymerase beta subunit [Bartonella sp. Sendai 5-1]
          Length = 275

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|164472697|gb|ABY59020.1| RNA polymerase beta subunit [Mycobacterium parascrofulaceum]
          Length = 221

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 89/219 (40%), Positives = 119/219 (54%), Gaps = 37/219 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +IL  EDMPFL DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILAQEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I           ++       +  
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNINVAEGVPPWAANLPEDLLHAQPN 150

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                                          VSTPVFDGA E  +  +L            
Sbjct: 151  A----------------------------IVSTPVFDGAREAELQGLLSATLPNRDNEVM 182

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V DK
Sbjct: 183  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDK 221


>gi|22086602|gb|AAM90688.1|AF403006_1 RNA polymerase beta subunit [Rickettsia mongolotimonae]
          Length = 288

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 189/289 (65%), Positives = 237/289 (82%), Gaps = 2/289 (0%)

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL +S+ ++A +N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG  
Sbjct: 1   GLTNSMATYATINKHGFIESPYRRVKDGCVTDEVVYLSAIEEGKYKIGQANSKINKDGKL 60

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E + CR   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQRQ
Sbjct: 61  QGEFINCRVEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQ 120

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           AVPL+K +APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E      +  V
Sbjct: 121 AVPLIKTDAPFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLE-QKVDGSPSV 179

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           DIY L+KFQ+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+PW+
Sbjct: 180 DIYNLLKFQKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLPWN 239

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
           GYNFEDS+LISER+V EDVFTSIHIEEFEV+ARDT+LGPEEITR IP+V
Sbjct: 240 GYNFEDSILISERIVKEDVFTSIHIEEFEVIARDTRLGPEEITRAIPSV 288


>gi|118640699|gb|ABL09917.1| RNA polymerase beta subunit [Vibrio sp. 2423-01]
          Length = 290

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 225/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   D   + + DI+ ++K L+ +RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDALDQGTLDETDIVEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVIDGIVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|224797521|gb|ACN62790.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           hydei]
          Length = 328

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 168/332 (50%), Positives = 233/332 (70%), Gaps = 8/332 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SL VP
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLXVP 292

Query: 933 SGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
           +G  G +  ++ F R   + +   + V +  I
Sbjct: 293 NGGEGIIQAIKRFPREKYELSVDVLEVIKIYI 324


>gi|195388314|ref|XP_002052825.1| GJ17773 [Drosophila virilis]
 gi|194149282|gb|EDW64980.1| GJ17773 [Drosophila virilis]
          Length = 1122

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 85/346 (24%), Positives = 130/346 (37%), Gaps = 83/346 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    ++ ++          + V + + + RP   GDK A R G KGI S+  
Sbjct: 822  KVVKMDEKEDCVVDSVRQLGSFELMPRKTVCITLRVARPATIGDKFASRAGQKGICSQKY 881

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +    G               
Sbjct: 882  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKSAAVHG--------------- 926

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV-F--DGADEEAINS 1221
                                                  GV  +TP  F  D    +    
Sbjct: 927  --------------------------------------GVYDATPFRFSEDNTAIDYFGK 948

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T Q
Sbjct: 949  MLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTNQ 1008

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD------------------VV 1323
            P+ G+   GG R GEME   + ++GAA++LQ+ L   SD                   ++
Sbjct: 1009 PIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLRQII 1068

Query: 1324 GRTRV--YESI-----VAGND--TFETGTPESFNVLVKEMQALGLS 1360
             R       S+     + G+         P SF  LV E+ ++ ++
Sbjct: 1069 KRNETGGLSSMPDTCRLCGDSSGVSMIEIPFSFKFLVTELSSVNIN 1114



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 89/536 (16%), Positives = 190/536 (35%), Gaps = 55/536 (10%)

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             +      D      V    M  R+ +    +    + + I+ +++ L     GK  ++
Sbjct: 300 FRSRFPEVPDWLPDEAVTEYIMRERIMVHLATNEE--KFQLIVFMVQKLFQCAQGKYKVE 357

Query: 455 DIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSVDI---DSVMPQDLINAK 507
           ++D+   + V   G +    L  +  + LL++ R + +++++ D     S+M Q +  A 
Sbjct: 358 NVDSAMMQEVLLPGHLYQKYLGERIEMWLLQLRRCLLKKLNAPDSLASSSIMTQCMRQAG 417

Query: 508 PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            V  A+  F  +              S L  + E++N +  ++H R   A+ +G      
Sbjct: 418 GVGRAMESFLATGNVASRTGLGLMQSSGLVIMAENINRMRYMSHFR---AIHRGSYFTTM 474

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
              E R + P  +G ICP  T +G   GL++ LT    ++     +          +  +
Sbjct: 475 RTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISKRPDPKLVQAI---PAMLLE 531

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +  +   ++      Q ++ L     F +          E     E + +   + +    
Sbjct: 532 MGMMPLSQQ-----GQPDAKLYV--VFLDGKHLGHIFQTEATKMVEDLRYAKITGQVPEM 584

Query: 674 IAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGTG--MESVVAKSSGAAIV 728
           +    IP+ +N              M R    L      ++GT   +   +A        
Sbjct: 585 MEIGFIPYKKNGQFPGLFLSTGPTRMMRPVWNLKWQRVEYIGTLEQLYMEIAIDEKEMYP 644

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                +          + ++    D + S  ++Y+    +++    C+N  P        
Sbjct: 645 DFTTHLELSKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLN-WPKQAANKLY 703

Query: 789 RRNDIIA------DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTS 841
           R               +  L D A+G N +VA + + GY+ ED+M+I++        + S
Sbjct: 704 RLQTPATPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKSAYERGFAYGS 763

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           I+  +F  +A+                  E +K++D  G+   G +++ G  L   
Sbjct: 764 IYKSKFVQLAKKQSYFARHPHMP------ELIKHLDTDGLPHPGTKLSYGSPLYCY 813



 Score = 42.8 bits (99), Expect = 0.40,   Method: Composition-based stats.
 Identities = 94/763 (12%), Positives = 206/763 (26%), Gaps = 153/763 (20%)

Query: 14  RKFFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFS 69
           R  F + PE ++  + +L      S+D  L +          GL+   + + P      +
Sbjct: 11  RPEFKQIPEKLNKHLANLGAPHVDSFDEMLSV----------GLEHVARYMVPQQFQTPA 60

Query: 70  G-AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEF 116
           G    +   S     P            +    D      +Y+    + L   V D+++ 
Sbjct: 61  GERISINIESIWITKPQVPMDVIDVRTREIYPTDARQLHASYSGVCSVRLGWSVNDLEKT 120

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRI 152
                          +G++P+M +                         G FVI+G ++ 
Sbjct: 121 PINMD----------LGEVPVMLRSRACNLGKATPQDMVKHGEHDSEWGGIFVIRGNEK- 169

Query: 153 VVSQLH-----------RSP-----------GIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +V  L            RS            G+     +        +L+      + G 
Sbjct: 170 IVRMLIMTRRNHPICVKRSSWKDRGHNFSELGVMVQTVRDDELSLTNVLHYL----NNGT 225

Query: 191 WMDIEFDS-KDIIHVRIDRRRKVPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFP 248
                F   K + +V        PV   L  L     E+I    Y  +V     D +   
Sbjct: 226 -ARFMFSHVKRLSYV--------PVCLILKCLMDYTDEQI----YNCLVQGYESDQYYLT 272

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
              + L    +             +    +     +   L ++ V    +    +  L  
Sbjct: 273 CVQSML-RDVQNEGVYTSAQCRSFIGTLFRSRFPEVPDWLPDEAVTEYIMRERIMVHLAT 331

Query: 309 AED---IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
            E+   ++     +++  A      ++++     E+     LY   +     +    +  
Sbjct: 332 NEEKFQLIVFMVQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLGERIEMWLLQLR- 390

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
                      + + +   D    S   +          +   S +    +  R  L   
Sbjct: 391 ---------RCLLKKLNAPDSLASSSIMTQCMRQAGGVGRAMESFLATGNVASRTGLGLM 441

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMER 484
                +   + I  ++ +   R     I         R     ++L + +  +  +    
Sbjct: 442 QSSGLVIMAENINRMRYMSHFR----AIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPD 497

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                + +    +       + K V +       +  L      ++   +      +  L
Sbjct: 498 GTPCGLLNHLTLTCEISKRPDPKLVQA-----IPAMLLEMGMMPLSQQGQPDAKLYVVFL 552

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
               +         + V    Y +I   +  E   IG +    +  +         P R 
Sbjct: 553 DGKHLGHIFQTEATKMVEDLRYAKIT-GQVPEMMEIGFIPYKKN-GQFPGLFLSTGPTRM 610

Query: 605 VCDGKVTN--DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           +          V Y+  +E+    IA                       +E  +  +   
Sbjct: 611 MRPVWNLKWQRVEYIGTLEQLYMEIA----------------------IDEKEMYPDFTT 648

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
            ++ S    +S  A+LIP  + + S R +  C M +Q +    
Sbjct: 649 HLELSKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPC 691


>gi|224812775|gb|ACN65021.1| RpoB [Cronobacter dublinensis subsp. lactaridi]
          Length = 255

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 157/254 (61%), Positives = 196/254 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 IVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   V
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAV 241

Query: 729 AKRAGIVEQVDAIR 742
           AKR G V+ VDA R
Sbjct: 242 AKRGGTVQYVDASR 255


>gi|194320284|gb|ACF48382.1| RNA polymerase II second largest subunit [Pycnothelia papillaria]
          Length = 693

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 125/816 (15%), Positives = 238/816 (29%), Gaps = 154/816 (18%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS---- 523
            +L   +R    ++ + + +  +    +         + +  + + +     +        
Sbjct: 1    LLAGLFRTLFHKLTKDVYKYLQKCVENNKDFNMALAVKSTHITNGLRYSLATGNWRDQKK 60

Query: 524  ---------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                     Q+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +   LS+      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNAAKIFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNR 689
             +  D +     V        I      I D  D   K          P   +EN+ ++ 
Sbjct: 177  GVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIENNPASP 236

Query: 690  VLMGCNMQRQAVPLLKAEAP-----FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI- 743
                  + +Q +  L+ +         GT  +       G        G+VE VDA    
Sbjct: 237  NRGNLVLTKQMLEQLEQDKQELAARAAGTDTDDTDKNKLG-WYRLINNGVVEYVDAEEEE 295

Query: 744  --VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              +I     DL  S      Y L     ++ +  +N+R                  PS  
Sbjct: 296  TIMIVMTPEDLLISQQLQQGYSLP----ADDSNDLNKRVKATPNPTAHTWTHCEIHPSMI 351

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +   + +  + V            
Sbjct: 352  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYNVRM---------- 392

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 393  -----------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 435

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L   
Sbjct: 436  YNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHG 491

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 492  TYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDSEELGQRTKLHVKRDASTPLRSTENGI 551

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q   S                         LR  KV +   +  Q GDK A RHG KG
Sbjct: 552  VDQVVLS--------------------TNADGLRFAKVRMRTTKIPQIGDKFASRHGQKG 591

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +       
Sbjct: 592  TIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD----- 646

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     ++
Sbjct: 647  ------------------------------------------------ATP-FTEVTVDS 657

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            ++ +LR       G  ++Y+G TG      V +G  
Sbjct: 658  VSRLLRENGYQSRGFEVMYNGHTGRKLVAQVFLGPT 693



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 83/621 (13%), Positives = 172/621 (27%), Gaps = 117/621 (18%)

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
             T  +K  KD    + + +       F++A ++ +    +  +Y L   G  +   +  
Sbjct: 6   FRTLFHKLTKDVYKYLQKCVENN--KDFNMALAVKSTHITNGLRYSL-ATGNWRDQKKAA 62

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                  + + +    + +  L        R+GK       +  +  +    E  + Q  
Sbjct: 63  QSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 122

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEH 528
             +  +       + +     +      N + +         +A   F     +    + 
Sbjct: 123 GLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNAAKIFVNGVWVGVHRDP 182

Query: 529 VNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + +S + + RR   +  +  + R     E        R   P       PA  + G+ +
Sbjct: 183 AHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIENNPASPNRGNLV 242

Query: 581 GLVSSLTSFARV--------------NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                L    +               +        YR + +G     V Y+ A EEE   
Sbjct: 243 LTKQMLEQLEQDKQELAARAAGTDTDDTDKNKLGWYRLINNGV----VEYVDAEEEETIM 298

Query: 627 IAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           I      L               +     +                +  P  ++ I AS+
Sbjct: 299 IVMTPEDLLISQQLQQGYSLPADDSNDLNKRVKATPNPTAHTWTHCEIHPSMILGICASI 358

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                   + A I+      +   
Sbjct: 359 IPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV---------RMDTMANILYYPQKPLATT 409

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            ++  +          +   +  Y              NQ                    
Sbjct: 410 RSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE------------------D 440

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           S  +   ++ R +  +       + E  + +S             +E+FE   R      
Sbjct: 441 SVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS------------VVEQFEKPMR------ 482

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                D   +       +D+ GI+  G  V+  DI++GK  P         ++       
Sbjct: 483 ----SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDSEELGQRT------ 532

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K    RD S  + S  +G V
Sbjct: 533 -KLHVKRDASTPLRSTENGIV 552


>gi|159137647|gb|ABW88903.1| RNA polymerase beta-subunit [Bartonella rattaustraliani]
          Length = 275

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD  G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAQGRFVEEFVVCRHAGEVLMAPRDNVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358824|dbj|BAF46081.1| RNA polymerase beta subunit [Bartonella sp. Hokkaido 17-1]
          Length = 275

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343480|emb|CBJ18657.1| RNA polymerase B subunit [Micromonospora sp. GUI41]
          Length = 214

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 96/214 (44%), Positives = 125/214 (58%), Gaps = 38/214 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K           +     
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSIDAHESVGD--- 146

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                                        V+TPVFDGA EE I+ +L     +        
Sbjct: 147  --------------------------TNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLV 214


>gi|262117894|dbj|BAI47972.1| RNA polymerase beta subunit [Bartonella sp. SR37-1]
          Length = 275

 Score =  256 bits (653), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 195/276 (70%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS+L  +G FTE  V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSALYSEGRFTEGFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124490804|gb|ABN12772.1| RNA polymerase beta subunit [Bartonella sp. RN2BJ]
          Length = 276

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 188/273 (68%), Positives = 221/273 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 2   RMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D SP
Sbjct: 122 KVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ 
Sbjct: 182 KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVS 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AKR+GIV+QVDA RIVIR+ E      + G   
Sbjct: 242 AKRSGIVDQVDATRIVIRATEDLDPSKSGGDIT 274


>gi|262117924|dbj|BAI47987.1| RNA polymerase beta subunit [Bartonella sp. KT27-1]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             GKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IGGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|159137649|gb|ABW88904.1| RNA polymerase beta-subunit [Bartonella rattaustraliani]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +VVYLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVVYLSAMEESKHYVAQANSSLDTEGHFIEEFVVCRHAGEVLMAPRDNVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|269912584|emb|CAY86072.1| RNA polymerase beta subunit [Gluconacetobacter johannae]
          Length = 272

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 127/275 (46%), Positives = 171/275 (62%), Gaps = 28/275 (10%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----- 221
           HDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL     
Sbjct: 1   HDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGEAS 60

Query: 222 --------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                               GMD++EIL+ FY K+V+ +    W  P  A     G K+ 
Sbjct: 61  AAARAAKLAEGGDVDALDIQGMDADEILNYFYGKVVFVKTSKGWARPFDAE-SFRGLKLL 119

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L+D +TGE V E+  KLT+ +++ + EK  K + + +  L G YVA D+VN +TGEIY
Sbjct: 120 EPLIDAETGEVVAEADAKLTARMVRKIAEK-TKDVLVGAAGLIGRYVAYDLVNPDTGEIY 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            EAG+ + E  LE +  + +  +P L +D+ N   +IRNTL  DKN  R DAL DIYRVM
Sbjct: 179 AEAGEELTEARLEALEEAGLDRLPTLAIDASN-GPWIRNTLTVDKNTTRDDALTDIYRVM 237

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           RPG+  T   AE+MF+ LFFD+D+YDLS VGRVKM
Sbjct: 238 RPGEPPTPETAEAMFSGLFFDADRYDLSAVGRVKM 272


>gi|52699786|gb|AAU86955.1| DNA-dependent RNA polymerase II second largest subunit [Baeomyces
            placophyllus]
          Length = 717

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 119/839 (14%), Positives = 241/839 (28%), Gaps = 148/839 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+   +R+   G ++   +R+   ++ + +   +               + +  + + + 
Sbjct: 1    DHXXXKRLDLAGPLMAGLFRMLFNKLVKDVYNYLKKCVESNREFNLSLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+    +      E    +      +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMCYITVGTPNEPIIDFMIQRSMEVLEEYEPTRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + +  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVREIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+  +D+ +   G  +  + +     +   + T ++            A+  G    
Sbjct: 237  RPLFVIENDAKKANKGSLVLTKELVNRLEDDKDIPTDLDPDERA-------ARYFGWDGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRNDIIAD 796
            V +    +  ++ + + +   V     ++  R  Q          V     ++     + 
Sbjct: 290  VKS--GAVEFLDAEEEETVMIVMTPEDLEISRQLQMGYTMPSSSNVDPNSRIKVPIKASS 347

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +                 
Sbjct: 348  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGV--------------- 392

Query: 856  LGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                             L N DE    +  +             +       +   +  +
Sbjct: 393  ----------------XLTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 436

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    
Sbjct: 437  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYTDQEKR---IGMSVVEQFEKPMRS 492

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  ++ D      R++          
Sbjct: 493  DTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEEMGQRTKL--------- 543

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                   +K    T     E+   +K+             LR VKV +   +  Q GDK 
Sbjct: 544  ------HIKRDVSTPLRTTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKF 592

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 593  ASRHGQKGTIGITYRMEDMPFTAEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 652

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          IS L                                          
Sbjct: 653  EGDATPFTEVTVDSISNLLREHGYQSRGFEIM---------------------------- 684

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 685  -------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 717



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 77/578 (13%), Positives = 152/578 (26%), Gaps = 93/578 (16%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 56  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 115

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +   + + L     + +      I + +    ++ +   +   
Sbjct: 116 LHNTHWGLVCPAETPEGQACGLVKNLSLMCYITVGTPNEPIIDFMIQRSMEVLEEYEPTR 175

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPT 564
           +               +    +  + +S +   RR S +  +  + R     E + +   
Sbjct: 176 SPNATKVF---VNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVREIRDREFK-IFTD 231

Query: 565 HYGRICPAETSEG-----HNIGLVSSLTSFARVNAYGFIET---------PYRKVCDGKV 610
                 P    E      +   LV +     R+     I T          Y        
Sbjct: 232 AGRVCRPLFVIENDAKKANKGSLVLTKELVNRLEDDKDIPTDLDPDERAARYFGWDGLVK 291

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV--------FCRCAGEEILVPREKID 662
           +  V +L A EEE   I      L+                          I        
Sbjct: 292 SGAVEFLDAEEEETVMIVMTPEDLEISRQLQMGYTMPSSSNVDPNSRIKVPIKASSHTWT 351

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M  QA+ +                   
Sbjct: 352 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGVXLT---------NYDERMD 402

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           + A I+      +    ++  +          +   +  Y              NQ    
Sbjct: 403 TMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE--- 448

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           S  +   ++ R +  +       + E  + +S            
Sbjct: 449 ---------------DSVIMNQSSIDRGLFRSLFFRTYTDQEKRIGMS------------ 481

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +E+FE   R           D   +       +D+ GI+  G  V+  DI++GK  P  
Sbjct: 482 VVEQFEKPMR----------SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIA 531

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                  E++ +        DV        +G+   V+
Sbjct: 532 PDA----EEMGQRTKLHIKRDVSTPLRTTENGIVDKVL 565


>gi|262117918|dbj|BAI47984.1| RNA polymerase beta subunit [Bartonella sp. OY12-1]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAG+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRAGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|520515|gb|AAA50228.1| RNA polymerase II, second largest subunit [Helobdella stagnalis]
          Length = 859

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 132/876 (15%), Positives = 243/876 (27%), Gaps = 170/876 (19%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 KY    + +  +      D  +  +      +  ++  L+    G+  +DD D+ 
Sbjct: 139  REKRIKYAKEILQKEMLPHVGISDFCETRK---AYFLGYMVHRLLLAALGRREVDDRDHY 195

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFF 517
            GN+R+   G +L   +R     + + I+               +  I  + +   +    
Sbjct: 196  GNKRLDLAGPLLAYLFRGLFRNLSKEIRLYAQKFIDRGKDFNLELAIKTRTITDGLKYSL 255

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+   +   S ++H RRL++     + R       R +H T
Sbjct: 256  ATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNS----PIGRDGKLARPRQLHNT 311

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             +G ICPAET EG  +GLV +L   A ++           + +     ++  +S     +
Sbjct: 312  LWGMICPAETPEGCAVGLVKNLALMAYISVGSQPSPILEFLEEWS-MENLEEISPSAIMD 370

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N          E+L+         +             +  V            
Sbjct: 371  ATRIFVNGCWVGIHRDPEQLMNTLKKLRRQMDI--------IVSEVSVIRDIRDREIRIY 422

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ R+     +      LL  +   +    E      S   +VA               
Sbjct: 423  TDAGRICRPLLIVENQKLLL--KKRHIDLLKEREYNNYSWQDLVA--------------- 465

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                        +GV  Y     + +       +  + K G            PS  LG 
Sbjct: 466  ------------NGVVEYIDTMEEETVMLAMTPEDFIEKGGQYCSTYTHCEIHPSMILG- 512

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N          M  + +   ++I  +                 
Sbjct: 513  ------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYITNY----------------- 547

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                      ++    +  V        +    +       +      + AI      + 
Sbjct: 548  ----------HVRMDTLAHVLFYPQKPLVTTRSMEYLKFRELPAGINSITAIASYTGYNQ 597

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S V        +F R   D   +    + E  E   R           N Y 
Sbjct: 598  EDSVIMNESAVDRGFF-RSVFYRSYKDAESKKGFDQEEVFEKPDRSYVQGMR---ANSYD 653

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +L                   T +S D              +   + +  +E    +Y  
Sbjct: 654  KL----------DDDGIISPGTRVSGD-------DALVGKTISLPENEDELEGQARRYTK 696

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                +  R        Q    +     +  K+ V   +  Q GDK A RHG KG      
Sbjct: 697  RDCSVFMRKSETGVVGQVMVTINQDGFKFTKIRVRTVKTPQIGDKFASRHGQKGTCGMRY 756

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM VG + E   G      G+   +   +      
Sbjct: 757  RQEDMPFTAEGITPDIIINPHAIPSRMTVGHLIECLQGKVAANRGEIADATPFN------ 810

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                           D  +   I+ +L+
Sbjct: 811  -----------------------------------------------DTVNVRKISDVLK 823

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                   G  +LY+G TG      + +G  Y  +L 
Sbjct: 824  EYGYHMHGNEVLYNGHTGRKIVSQIFLGPTYYQRLK 859



 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 114/756 (15%), Positives = 214/756 (28%), Gaps = 120/756 (15%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG  S+ +IL          +  +     +  A  +    V+ + +     
Sbjct: 74  IPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSIDEAFCVQDQPVALNFIGGRGS 133

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEA 324
              +   K++     + L+++ +  +GI+           G  V   ++    G   ++ 
Sbjct: 134 RPGVTREKRIKYAK-EILQKEMLPHVGISDFCETRKAYFLGYMVHRLLL-AALGRREVDD 191

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
            D    K L+            L+ +            +        +       +    
Sbjct: 192 RDHYGNKRLDLAGPLLAYLFRGLFRNLSKEIRLYAQKFIDRGKDFNLE-------LAIKT 244

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKI 442
              T  +  S+    + D  K   +  G  ++  RL   +      R          +  
Sbjct: 245 RTITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAR 304

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              L N    +                ++KN   +  + +       +  ++  S+   +
Sbjct: 305 PRQLHNTLWGMICPAETP---EGCAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLE 361

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            I+   ++ A   F     +    +    ++ +   RR   +    V+  R   +     
Sbjct: 362 EISPSAIMDATRIFVNGCWVGIHRDPEQLMNTLKKLRRQMDIIVSEVSVIRDIRDREIRI 421

Query: 563 PTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            T  GRIC P    E   + L         ++     E       D      V Y+  ME
Sbjct: 422 YTDAGRICRPLLIVENQKLLLKKR-----HIDLLKEREYNNYSWQDLVANGVVEYIDTME 476

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           EE   +A       E G                          +  P  ++ I AS+IPF
Sbjct: 477 EETVMLAMTPEDFIEKGGQ----------------YCSTYTHCEIHPSMILGICASIIPF 520

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            +++ S R      M +QA+ +                                      
Sbjct: 521 PDHNQSPRNTYQSAMGKQAMGVYITNYHV------------------------------- 549

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                        + + V  Y               Q+PLV                   
Sbjct: 550 ----------RMDTLAHVLFYP--------------QKPLV----------TTRSMEYLK 575

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +L  G N + A   + GYN EDS++++E  V    F S+    ++          EE+
Sbjct: 576 FRELPAGINSITAIASYTGYNQEDSVIMNESAVDRGFFRSVFYRSYKDAESKKGFDQEEV 635

Query: 862 TRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      +       +D+ GII  G  V+  D LVGK     E+    E +  R  
Sbjct: 636 FEKPDRSYVQGMRANSYDKLDDDGIISPGTRVSGDDALVGKTISLPENEDELEGQARR-- 693

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   RD S+ +    +G V  V +       K
Sbjct: 694 -----YTKRDCSVFMRKSETGVVGQVMVTINQDGFK 724


>gi|37725754|gb|AAO32825.1| RNA polymerase beta subunit [Bartonella koehlerae]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F+EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFSEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVAAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117910|dbj|BAI47980.1| RNA polymerase beta subunit [Bartonella sp. OY2-1]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|118640623|gb|ABL09879.1| RNA polymerase beta subunit [Vibrio cincinnatiensis]
          Length = 290

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  D  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   SLFESLFFSPERYDLSTVGRMKFNSSIERDDAEEQGTLDETDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFIIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L ++  F +EL+  R  GE  L PRE ++++D +  QVVSIAASLIPFLE
Sbjct: 241 LTDENRFADELITARQKGESGLHPREHVNYMDVATNQVVSIAASLIPFLE 290


>gi|224797519|gb|ACN62789.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           hydei]
          Length = 323

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 167/329 (50%), Positives = 232/329 (70%), Gaps = 8/329 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SL VP
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLXVP 292

Query: 933 SGVSGTVVDVRIFNRHGIDKNERSISVER 961
           +G  G +  ++ F R   + +   + V +
Sbjct: 293 NGGEGIIQAIKRFPREKYELSVDVLEVIK 321


>gi|52699880|gb|AAU87001.1| DNA-dependent RNA polymerase II second largest subunit [Sporastatia
            polyspora]
          Length = 713

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 120/829 (14%), Positives = 224/829 (27%), Gaps = 135/829 (16%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ + + +  +              I A  + + +    
Sbjct: 1    GKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGIKASTLTNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     V      E    +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYVTVGSPSEPIVDFMIQRNMEVLEEYEPQRSPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               +I      +  D +     V        I      I D  D   K          P 
Sbjct: 177  TKIFINGVWVGVHRDPAHLVSTVQALRRKNVISHEVSLIRDIRDREFKIFTDAGRVCRPL 236

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               D+  +     N+      + + E      G E    +  G  +              
Sbjct: 237  FVIDNDPKSTNRGNLVLTKEHVAQLEEDK-EKGAEMDPEEKEGKVMGWNSLV-------N 288

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            + V+  V+ + + +   V     ++  R  Q        +      V+    +     T 
Sbjct: 289  QGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGFAMPETIDDPNRRVKAPVNLTAHTWTH 348

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N                        ++       +G   
Sbjct: 349  CEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXX 390

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                                 +       +   +  + AI    
Sbjct: 391  XXXXXXXXXXXX-----------XLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R      EQ E   R    +      
Sbjct: 440  GYNQEDSVIMXXSSIDRGLF-RSLFYRSYTDQEKRVGMSIVEQFEKPMRSDTLKLKHGTY 498

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       +  G           K+  ++ D      R++          ++     +  
Sbjct: 499  DKLDDDGIVAPGVRVSGEDIVIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVD 558

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                             LR VKV +   +  Q GDK A RHG KG +
Sbjct: 559  QVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTI 598

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 599  GITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEV 658

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L    E    +                                          
Sbjct: 659  TVDSVSKLLR--EHGYQSRGFEVM------------------------------------ 680

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                      +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 681  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 713



 Score =  107 bits (267), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 81/542 (14%), Positives = 145/542 (26%), Gaps = 90/542 (16%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 53  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 112

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E       + +   ++   PQ 
Sbjct: 113 LHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGSPSEPIVDFMIQRNMEVLEEYEPQR 172

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM--- 558
             NA  +      F     +    +  + +S +   RR + +  +  + R     E    
Sbjct: 173 SPNATKI------FINGVWVGVHRDPAHLVSTVQALRRKNVISHEVSLIRDIRDREFKIF 226

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG---FIETPYRKVCDGK-- 609
               R   P       P  T+ G+ +     +         G     E    KV      
Sbjct: 227 TDAGRVCRPLFVIDNDPKSTNRGNLVLTKEHVAQLEEDKEKGAEMDPEEKEGKVMGWNSL 286

Query: 610 -VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+ A EEE   I      L+                +      E ID  +   
Sbjct: 287 VNQGVVEYVDAEEEETVMIVMTPEDLE-----------ISRQLQAGFAMPETIDDPNRRV 335

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           K  V++                                      T       +   + I+
Sbjct: 336 KAPVNL--------------------------------------TAHTWTHCEIHPSMIL 357

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDE 787
              A I+   D  +    + +  +     G                    Q+PL      
Sbjct: 358 GICASIIPFPDHNQSPRNTYQSAMGXQAMGXXXXXXXXXXXXXXXXLYYPQKPL------ 411

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA   + GYN EDS+++    +   +F S+    +
Sbjct: 412 ----ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMXXSSIDRGLFRSLFYRSY 467

Query: 848 EVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
               +   +   E     +  D   +       +D+ GI+  G  V+  DI++GK  P  
Sbjct: 468 TDQEKRVGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIVIGKTAPIA 527

Query: 903 ES 904
             
Sbjct: 528 PD 529


>gi|190148938|gb|ACE63444.1| RNA polymerase subunit B [Pseudonocardia alni]
          Length = 269

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 154/276 (55%), Positives = 200/276 (72%), Gaps = 8/276 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL SFARVN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFIETPYRKV DG VT+ + YL+A EE+   +AQAN+ L+EDGSF EE V  R   GE  
Sbjct: 61  GFIETPYRKVVDGVVTSQIDYLTADEEDRFVVAQANAQLNEDGSFAEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +++ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPSGVEYIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  + A+ AG+VE++ A  I +   EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVTAESAGVVEELCADYITVMDDEGQRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N
Sbjct: 234 CNNQKPIVDEGARVEVGQVLADGPCTENGEMALGKN 269


>gi|169247689|gb|ACA51678.1| RpoB [Mycobacterium abscessus]
 gi|185179198|gb|ACC77612.1| RpoB [Mycobacterium abscessus]
          Length = 208

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 90/218 (41%), Positives = 117/218 (53%), Gaps = 40/218 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 23   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 82

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 83   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 127

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 128  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 170

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V D
Sbjct: 171  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDD 208


>gi|307343460|emb|CBJ18647.1| RNA polymerase B subunit [Micromonospora sp. GUI14]
 gi|307343464|emb|CBJ18649.1| RNA polymerase B subunit [Micromonospora sp. GUI16]
 gi|307343484|emb|CBJ18659.1| RNA polymerase B subunit [Micromonospora sp. GUI43]
          Length = 214

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 127/214 (59%), Gaps = 38/214 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLV 214


>gi|159137643|gb|ABW88901.1| RNA polymerase beta-subunit [Bartonella rattaustraliani]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDTEGHFVEEFVVCRHAGEVLMAPRDNVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262072879|dbj|BAI47749.1| RNA polymerase beta subunit [Bartonella sp. Nakanoshima 61-1]
          Length = 275

 Score =  255 bits (652), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR  E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRXXED-LDPSKSGVDI 275


>gi|55273983|gb|AAV48862.1| RNA polymerase II second largest subunit [Agaricostilbum hyphaenes]
          Length = 693

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 120/756 (15%), Positives = 216/756 (28%), Gaps = 129/756 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 65   GVSQVLNRYTYASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQAC 120

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++  G    P  +  +      +  L+A   +   +   N         
Sbjct: 121  GLVKNLALMSYIS-VGTPSAPIIEFLEEWNMESLEDLTADLGKGTKV-FVNGVWQGIHRD 178

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
              +LV                       K  ++   S++  +   +         + R  
Sbjct: 179  PAQLVT---------------TLKTLRRKGDINKEVSVVRDVRERELRIFTDAGRVCRPV 223

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
              + +     V       + + S A                   + S E   +    G  
Sbjct: 224  FIVDEQTQELVLQKEHVRMLEDSQA-----------------DDVDSEEFGWNNLVEGGV 266

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               L   +      C++   L     +V      A+      G           F     
Sbjct: 267  AELLDAEEEETVMICMSPEDLQMSKIQVESGKAAANPDLGAGGARLRQIQSTRTF---TH 323

Query: 821  YNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
                 +M+  +   ++            ++       +G    +  +   +         
Sbjct: 324  CEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTSFQVRMDNSSN------ 377

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
                 +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 378  -----ILYYPQKPLATTRSMEYLHFRDLPAGQNAIVAILCYSGYNQEDSVIMSQSAIDRG 432

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     + R  +D+ +R  ++  E+ E   R +         +       I  G+N V  
Sbjct: 433  LF-RSFYYRTYMDQEKRKGNILMEEFEKPMRQQTLRMKHGTYDKIDSDGLINPGENVVGD 491

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L  D                +E  QR  + +K    T     E  + +++ 
Sbjct: 492  DILIGKTAPLPPD---------------TEELGQRTKDHVKRDVSTPLKTTERGYVDQVM 536

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D+      R  KV     R  Q GDK A RHG KG +      EDMPF  DG   
Sbjct: 537  LTTNADN-----DRFAKVRTRATRIPQVGDKFASRHGQKGTIGITYRQEDMPFTVDGITP 591

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L       G +  +          IS L         +
Sbjct: 592  DIIINPHAIPSRMTIGHLVECLLSKVSTITGNEGDATPFTNVTVEAISDLLK--ANGYHS 649

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 650  RGLEVM---------------------------------------------YNGHT---- 660

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
            G         V +G  Y  +L HMV DK+++R+   
Sbjct: 661  GR---KLKAQVYLGPTYYQRLKHMVDDKIHSRARAP 693



 Score = 45.5 bits (106), Expect = 0.064,   Method: Composition-based stats.
 Identities = 48/427 (11%), Positives = 113/427 (26%), Gaps = 39/427 (9%)

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-- 446
           F +  ++ + +  +  +Y L   G      +         + + +    + +  L     
Sbjct: 29  FRLXSAIKSSIITNGLRYSL-ATGNWGDQKKSLSAKAGVSQVLNRYTYASTLSHLRRCNT 87

Query: 447 ---RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
              R+GK       +  +  +    E  + Q    +  +       + +     +   + 
Sbjct: 88  PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSYISVGTPSAPIIEFLEE 147

Query: 504 INAKPVVSAVCEFFCSSQLS-------QLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
            N + +     +    +++           +    ++ +   RR   + +          
Sbjct: 148 WNMESLEDLTADLGKGTKVFVNGVWQGIHRDPAQLVTTLKTLRRKGDINKEVSVVRDVRE 207

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLV--SSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
               +         P    +     LV           +    +++      +       
Sbjct: 208 RELRIFTDAGRVCRPVFIVDEQTQELVLQKEHVRMLEDSQADDVDSEEFGWNNLVEGGVA 267

Query: 615 VYLSAMEEENRYIAQANSSLD------EDGSFTEELVFCRCAGEEILVPREK-IDFIDAS 667
             L A EEE   I  +   L       E G                 +   +     +  
Sbjct: 268 ELLDAEEEETVMICMSPEDLQMSKIQVESGKAAANPDLGAGGARLRQIQSTRTFTHCEIH 327

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFV 711
           P  ++ + AS+IPF +++ S R      M +QA+                 L   + P  
Sbjct: 328 PAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTSFQVRMDNSSNILYYPQKPLA 387

Query: 712 GT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            T  ME +  +   A   A  A +          +   +  +D        YR    Q  
Sbjct: 388 TTRSMEYLHFRDLPAGQNAIVAILCYSGYNQEDSVIMSQSAIDRGLFRSFYYRTYMDQEK 447

Query: 771 NQNTCVN 777
            +   + 
Sbjct: 448 RKGNILM 454


>gi|257153086|dbj|BAI23101.1| RNA polymerase beta subunit [Bartonella washoensis]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA  SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVACDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358790|dbj|BAF46064.1| RNA polymerase beta subunit [Bartonella sp. Nagano 3-1]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 188/272 (69%), Positives = 223/272 (81%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           A+ AKR+G+V+QVDA RIVIR+ E      + 
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATEDLDSSKSG 272


>gi|45545353|gb|AAS67524.1| DNA-dependent RNA polymerase II second largest subunit [Usnea
            cornuta]
          Length = 903

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 150/1012 (14%), Positives = 293/1012 (28%), Gaps = 168/1012 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S +   L EKG    G     +    +           ++   G V DE  L
Sbjct: 36   VEKGSRLISSMQMKLYEKGEGSKGGFGQTIK-CTLPYIKTEIPIAIVFRALGVVSDEDIL 94

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +      A++         +DR+ AL  I +      V+      
Sbjct: 95   NHICYDRKDTQMLEMLKPCIEEAFV--------IQDREVALDFIGKRGNSQGVT------ 140

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                       KY    + +  +     ++  +  +      +  ++  L+    G+  +
Sbjct: 141  ------RDKRIKYARDIMQKELLPHISQVEGSETRK---AFFLGYMVHRLLQCALGRREV 191

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 192  DDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 251

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 252  GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 307

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 308  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 367

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 368  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAG 427

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLL---KAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P    D+  R     N+      +L        +  T  +       G   + K  
Sbjct: 428  RVCRPLFVIDNDPRSSNRGNLVLTKDHVLKLEMDRENWATTEPDVREETDMGWQGLVKE- 486

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +        +N    +N+R    +        
Sbjct: 487  GVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYVMPEANPEE-LNKRVKAPMNPTAHTWT 545

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   + +  ++    
Sbjct: 546  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM- 595

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 596  --------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNA 629

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 630  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 685

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 686  SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 745

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 746  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 785

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 786  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 845

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                           V     +G  + T 
Sbjct: 846  FEGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQ 890

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            VF                                       +G  Y  +L H
Sbjct: 891  VF---------------------------------------LGPTYYQRLRH 903



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 107/849 (12%), Positives = 231/849 (27%), Gaps = 152/849 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVR- 205
            ++++++Q  RS          + + S    Y   I    ++G  +      K  ++ + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKAQSNTP-YVAEIRSAVEKGSRLISSMQMK--LYEKG 54

Query: 206 ------IDRRRK---------VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
                   +  K         +P+     ALG+   E+IL+        +Q  +     +
Sbjct: 55  EGSKGGFGQTIKCTLPYIKTEIPIAIVFRALGVVSDEDILNHICYDRKDTQMLEMLKPCI 114

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A ++   +V+   +      Q +   K++                      +    + 
Sbjct: 115 EEAFVIQDREVALDFIGKRGNSQGVTRDKRIKYAR-----------------DIMQKELL 157

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN----NAYIRNTLVTD 365
             I   E  E   +A  +              R++                 + +     
Sbjct: 158 PHISQVEGSE-TRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGT 216

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            NK  KD    + + +       F++  ++ +    +  +Y L   G      +      
Sbjct: 217 FNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNWGDQKKAASVKA 273

Query: 426 DDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              + + +    + +  L        R+GK       +  +  +    E  + Q    + 
Sbjct: 274 GVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVK 333

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSL 532
            +       + +     V      N + +         +A   F     +    +  + +
Sbjct: 334 NLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVWVGVHRDPAHLV 393

Query: 533 SRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVS 584
             + + RR   +  +  + R     E        R   P       P  ++ G+ +    
Sbjct: 394 GTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGNLVLTKD 453

Query: 585 SLTSFAR------VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            +                  E              V Y+ A EEE   I      L+   
Sbjct: 454 HVLKLEMDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLEISR 513

Query: 639 SFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                 V      EE+                  +  P  ++ I AS+IPF +++ S R 
Sbjct: 514 QLQAGYVMPEANPEELNKRVKAPMNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRN 573

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                   + A I+      +    ++  +      
Sbjct: 574 TYQSAMGKQAMGVFLT---------NYQQRMDTMANILYYPQKPLATTRSMEFLKFRELP 624

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               +   +  Y              NQ                    S  +   ++ R 
Sbjct: 625 AGQNAIVAIACYSG-----------YNQE------------------DSVIMNQSSIDRG 655

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
           +  +       + E  + +S             +E+FE   R           D   +  
Sbjct: 656 LFRSLFYRAYTDQEKRIGMS------------VVEQFEKPMR----------SDTLKLKH 693

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +D+ G++  G  V+  DI++GK  P         ++        K    RDTS  
Sbjct: 694 GTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTP 746

Query: 931 VPSGVSGTV 939
           + S  +G V
Sbjct: 747 LRSTENGIV 755


>gi|9309389|gb|AAF87050.1|AF171071_1 RNA polymerase beta subunit [Bartonella henselae]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ A+R+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVAARRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148984|gb|ACE63467.1| RNA polymerase subunit B [Pseudonocardia sp. S053]
          Length = 266

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 196/273 (71%), Gaps = 8/273 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ L +DG F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVENGRVTEQIDYLTADEEDRFVIAQANAPLHDDGRFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++EAP VGTG
Sbjct: 121 YISPAGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           C NQ+P+V  G  V    ++ADGP T+ G++AL
Sbjct: 234 CNNQKPIVDEGQRVEAGQVLADGPCTENGEMAL 266


>gi|262117960|dbj|BAI48005.1| RNA polymerase beta subunit [Bartonella sp. FG3-1]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPASAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFIEEFVVCRHAGEVLMAPRDYVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRSEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|124358792|dbj|BAF46065.1| RNA polymerase beta subunit [Bartonella sp. Hokkaido 29-1]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVGIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699896|gb|AAU87009.1| DNA-dependent RNA polymerase II second largest subunit [Thelocarpon
            laureri]
          Length = 715

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 129/835 (15%), Positives = 236/835 (28%), Gaps = 142/835 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L N +R+   ++ + + +  +              + A  + + + 
Sbjct: 1    DXXGKKRLXLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKASTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +      ++  + +   +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPLVDFMVARGMEILEEYIPSKS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  +     + V        I      I D  D   +         
Sbjct: 177  PNATKIFVNGVWVGVHNNPKRLADTVSEVRKQHSIPPEVSMIRDIRDREFRISSDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+  +D      G     +    L      +    E    + +        AG+VE 
Sbjct: 237  RPLFVIENDPKEENYGQLRLTKEHVKLLDNDANIEXETEEEREEKTFGWKGLVDAGVVEY 296

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            VDA      ++   + P    +       +Q    NT    R    +             
Sbjct: 297  VDAEEEE--TIMIVMTPEDLEISRXLRAGYQLPEDNTSSIXRVKAPLNPTAHTWTHCEIH 354

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++        G
Sbjct: 355  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKXAXG 389

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                  D                +  +             +       +   +  + AI 
Sbjct: 390  XXXXXFDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 438

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    IE   +    + + 
Sbjct: 439  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSTIEQFEKPMRGDTLK 494

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   I  G           K+  ++ D      R++          ++  
Sbjct: 495  LKHGTYDKLDDDGIIAPGVRVSGEDVIIGKTAPIAPDAEELGQRTKMHIKRDVSTPLRST 554

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             LR VKV +   +  Q GDK A RH
Sbjct: 555  ESGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKVPQIGDKFASRH 594

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +GT  D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 595  GQKGTIGITYRQEDMPFTSEGTIPDLIINPHAIPSRMTIAHLIECQLSKVASLKGYEGDA 654

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 655  TPFTDVTVDSVSGLLR--EHGYQSRGFEVM------------------------------ 682

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 683  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 715


>gi|262072877|dbj|BAI47748.1| RNA polymerase beta subunit [Bartonella sp. Sendai 6-1]
          Length = 275

 Score =  255 bits (652), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++  R+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMASRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|82581218|dbj|BAE48682.1| RNA polymerase beta subunit [Bartonella silvatica]
 gi|103484145|dbj|BAE94845.1| RNA polymerase beta subunit [Bartonella sp. Fuji 25-1]
 gi|103484147|dbj|BAE94846.1| RNA polymerase beta subunit [Bartonella sp. Aomori 32-1]
 gi|262072869|dbj|BAI47744.1| RNA polymerase beta subunit [Bartonella sp. Shimokita 30-1]
          Length = 275

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PRE +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRENVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLMRSEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  +D S SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATEE-VDSSKSGVDI 275


>gi|298912939|emb|CAZ66637.1| RNA polymerase beta subunit [Vibrio metschnikovii]
          Length = 289

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 170/289 (58%), Positives = 222/289 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +     ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSPERYDLSTVGRMKFNSSIERTDAEEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L +D  F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LTDDSRFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|103484129|dbj|BAE94837.1| RNA polymerase beta subunit [Bartonella sp. Aomori 32-2]
          Length = 275

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++S  +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSSATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117938|dbj|BAI47994.1| RNA polymerase beta subunit [Bartonella sp. FN17-1]
          Length = 275

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++  R+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGHFTEEFVVCRHAGEVLMASRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|307343572|emb|CBJ19216.1| RNA polymerase B subunit [Micromonospora lupini]
          Length = 214

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 127/214 (59%), Gaps = 38/214 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDTDWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+V
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHLV 214


>gi|299748143|ref|XP_001837493.2| DNA-directed RNA polymerase I polypeptide 2 [Coprinopsis cinerea
            okayama7#130]
 gi|298407835|gb|EAU84409.2| DNA-directed RNA polymerase I polypeptide 2 [Coprinopsis cinerea
            okayama7#130]
          Length = 1203

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 94/258 (36%), Gaps = 66/258 (25%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G D     L+ V V + + R    GDK + RHG KG+ S+  P  DMPF + G   D+++
Sbjct: 890  GSDAGDSELQKVHVTLRIPRAPVIGDKFSSRHGQKGVCSQKWPAIDMPFSESGIQPDVII 949

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP   PSRM +G + E+  G A    G    +    +                       
Sbjct: 950  NPHAFPSRMTIGMLVESMAGKAGAMHGLAQDATPFKFTEEDTA----------------- 992

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                              +     L  A  +  G   +Y G+TG
Sbjct: 993  ---------------------------------IDYFGKQLLAAGYNYYGNEPMYSGITG 1019

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            + F   +  G +Y  +L HMV DK                  G+   GG R GEME   +
Sbjct: 1020 QEFAADIYFGVVYYQRLRHMVLDKFQ----------------GRKRAGGIRFGEMERDAL 1063

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             A+G +++LQ+ L   SD
Sbjct: 1064 IAHGTSFLLQDRLMNCSD 1081



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 78/580 (13%), Positives = 176/580 (30%), Gaps = 83/580 (14%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER-- 489
           +   ++ +++ +  L +G+   D+ D+  ++ V   G +     +  +  +  +I+    
Sbjct: 364 KFRMLLYMLRKMYSLISGECCADNPDSPQHQEVLLPGSLYGMIIKERMEEILNAIRATIA 423

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCS----------------------SQLSQLEE 527
           +      +V   D      V++ V     S                      S  + + E
Sbjct: 424 MDVRTGANVDFHDKKYFAKVLTKVNFDIGSKMSNFLATGNLVSPTGLDLQQASGFTIVAE 483

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N    I+H R    + +G          +R + P  +G +CP  T +G   GL++ L+
Sbjct: 484 KLNWQRYISHFR---CIHRGAFFAELKTTTVRKLLPEAWGFLCPVHTPDGSPCGLLNHLS 540

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------ 641
              R+            +          + ++++       Q +  +             
Sbjct: 541 RTCRIITSPLTVAHIPNLLAAHGMTQ-SFATSIDGRKNLCVQLDGRVIGWARPVVAAQLA 599

Query: 642 -EELVFCRCAGEEILVPREKIDFIDASPKQVVSI------AASLIPFLENDDSNRVLMGC 694
               ++      E+ +  E     ++   Q   +      A  + P     +     +G 
Sbjct: 600 TNLRIWKTEGKYEVPLDLEIGFVPESHGGQYPGLFLFSTKARFMRPVKYLANGKDDQIGS 659

Query: 695 NMQRQAVPLLKAEA--PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             Q         E     V T +E                    Q        +  +  +
Sbjct: 660 FEQVYMNIACTPEEIEEGVSTHVEHDPTNFLSILANMTPFSDFNQSPRNIYQCQMGKQTM 719

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
               + +      K  R        Q P+V+           +   +  +     G N +
Sbjct: 720 GTPATAIQHRTDNKLYRLQTG----QSPIVRP----------SLHNTYGMDAFPNGTNAV 765

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VA + + GY+ ED+M++++             +   +  ++ +   +  +    +    G
Sbjct: 766 VAVISYTGYDMEDAMILNKSAHERGFTYGTIYKSQIIDLKEVRGASKSSSTPTLHFGIAG 825

Query: 873 LKNI------------DECGIICVGAEVNPGDILVGKITPK-----------GESPMTPE 909
              +            D+ G+   G  V PGD L   I               E+    +
Sbjct: 826 DIRLTGDNAHPCAEFVDKDGLPFPGVRVKPGDPLAAYIDDTTGRTRFVKYKGDETAYVDQ 885

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            +LL +  G+  +     +LR+P      V+  +  +RHG
Sbjct: 886 VRLLGSDAGDSELQKVHVTLRIP---RAPVIGDKFSSRHG 922



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 103/750 (13%), Positives = 194/750 (25%), Gaps = 142/750 (18%)

Query: 29  LIEVQKASYDH-FLMMNIAPDERPNEGLQA-AFKSVFPITAFSGA----------AMLEF 76
            +     S++  F    +   +    GL + A K +    AF G             +  
Sbjct: 39  FVAPHIESFNALFDDSGLPSGDGDGRGLLSLALKDIGERVAFDGRGADPESWGNRMRIWI 98

Query: 77  VSYEFDPPKFD------------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD 124
                  P                 +   R  +Y   + + L    +        +  KD
Sbjct: 99  EQVTIARPMVSDRDRTARERRVFPSEARERLTSYRGRMTVKL---CWTDPSGQKHEMPKD 155

Query: 125 IKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV------- 153
                   G +P+M +                         G FVI G +R++       
Sbjct: 156 C-------GLIPIMVRSVRCNLRTLSSAELVQRHEEPEEFGGYFVINGNERLIRYLILPR 208

Query: 154 ---VSQLHR--------SPGIHFDHDK----GRASLSGKLLY----ACRIIPDQGLWMDI 194
              V  L R        S   +    +     + S++  L Y    +      +  W   
Sbjct: 209 RNHVISLIRPSFSNRGPSYTQYAVQIRCVRPDQTSVTNTLHYLANGSA---MFRFTWRKQ 265

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
           E       +V       +P+   L AL     +EI        V  Q  D          
Sbjct: 266 E-------YV-------IPIMLILKALVNASDKEIFE-----GVVMQDYDNTFLTDRVEL 306

Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
           L+   K+ +        E + +  + +   L +      +    I    L  L    D  
Sbjct: 307 LLRSFKMYTMHTGEQCLEYLGDKFRVVL-NLPEDWTNAAIGAWLIQKLVLVHLETPRDKF 365

Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                 +  +   +I  +   +   S      +L     +    I    + +     +  
Sbjct: 366 RMLLY-MLRKMYSLISGECCADNPDSPQHQEVLL---PGSLYGMIIKERMEEILNAIRAT 421

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           +    R     D         +   + FD      S +        L   T  D++    
Sbjct: 422 IAMDVRTGANVDFHDKKYFAKVLTKVNFDIG----SKMSNFLATGNLVSPTGLDLQQASG 477

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             I+A         +    I         +  +V ++L   +                  
Sbjct: 478 FTIVAEKLNWQRYISHFRCIHRGAFFAELKTTTVRKLLPEAWGFLC-------PVHTPDG 530

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
               ++       + + S +      + L+      +  + I   + L     G V    
Sbjct: 531 SPCGLLNHLSRTCRIITSPLTVAHIPNLLAAHGMTQSFATSIDGRKNLCVQLDGRVIGW- 589

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                R V             +EG     +     F   +  G     +      +    
Sbjct: 590 ----ARPVVAAQLATNLRIWKTEGKYEVPLDLEIGFVPESHGGQYPGLFLFSTKARFMRP 645

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V YL            AN   D+ GSF  E V+   A     +       ++  P   +S
Sbjct: 646 VKYL------------ANGKDDQIGSF--EQVYMNIACTPEEIEEGVSTHVEHDPTNFLS 691

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           I A++ PF + + S R +  C M +Q +  
Sbjct: 692 ILANMTPFSDFNQSPRNIYQCQMGKQTMGT 721


>gi|8895190|gb|AAF80845.1|AF165989_1 RNA polymerase beta subunit [Bartonella vinsonii subsp. berkhoffii]
          Length = 275

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR  +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRNHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148978|gb|ACE63464.1| RNA polymerase subunit B [Pseudonocardia yunnanensis]
          Length = 270

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 153/277 (55%), Positives = 203/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVDNGRVTTQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 FISPTGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P++  GD V    +IADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIIDEGDRVEAGQVIADGPCTENGEMALGKNL 270


>gi|124502488|gb|ABN13625.1| RNA polymerase beta subunit [Bartonella sp. SD8HB]
          Length = 273

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 189/265 (71%), Positives = 222/265 (83%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEG 750
           A+ AKR GIV+QVDA RIVIR+ E 
Sbjct: 241 AVGAKRGGIVDQVDATRIVIRATED 265


>gi|52699772|gb|AAU86948.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            cervina]
          Length = 714

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 122/837 (14%), Positives = 240/837 (28%), Gaps = 147/837 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L N +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DXXGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L    +  V         +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSQPIIDFMIQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V      + I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVISLRRHDAISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+  R     N+   ++ +  L+ +        E       G   + K+ G+VE
Sbjct: 237  RPLFVIDNDPRSTNCGNLVLTKEHIQKLEDDKDLPP-DYEIDEKNPPGWNGLVKK-GVVE 294

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VDA            + +   V     ++  R  Q           +   V+       
Sbjct: 295  YVDAEE----------EETVMIVMTPEDLEISRQLQAGYNLPDTSDDLIKRVKAPMNPTA 344

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +   + +  ++       
Sbjct: 345  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM---- 398

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 399  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 435

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 436  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDT 491

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 492  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLR 551

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 552  STENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFAS 591

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 592  RHGQKGTIGITYRQEDMPFTNQGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 651

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 652  DATPFTEVTVDSVSKLLR--EHGYQSRGFEVM---------------------------- 681

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                              +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 682  -----------------YNGHT----GR---KLVGQVFLGPTYYQRLRHMVDXKIXA 714


>gi|298912953|emb|CAZ66644.1| RNA polymerase beta subunit [Aliivibrio fischeri]
          Length = 289

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 167/289 (57%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  D  +    + + DII +++ L+D+RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGRDNDEGAGVLDETDIIEVMRKLIDIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER+++ER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVRERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FA+ N YGF+ETPYR+V DG+VT+ V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFAQCNEYGFLETPYRRVVDGQVTDQVDYLSAIEEGTFVIAQANAV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G+F +EL+  R  GE  L PRE I ++D +  QVVS+AASLIPFL
Sbjct: 241 LTEEGTFADELIIARQKGESGLHPREHIQYMDVATNQVVSVAASLIPFL 289


>gi|113707349|gb|ABI36582.1| RNA polymerase II second largest subunit [Usnea antarctica]
          Length = 711

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 118/811 (14%), Positives = 233/811 (28%), Gaps = 125/811 (15%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + + +  +    +         + +  + + +     +            
Sbjct: 2    LFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGNWGDQKKAASV 61

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 62   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 117

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +    + +V  +   L++      ++      +  
Sbjct: 118  ACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVWVGVHR 177

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D +     V        I      + D  D   K          P    D+  R     N
Sbjct: 178  DPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGN 237

Query: 696  MQRQAVPLL---KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            +      +L        +  T  +       G   + K  G+VE VDA       +    
Sbjct: 238  LVLTKDHVLKLEMDRENWATTEPDVREETDMGWQGLVKE-GVVEYVDAEEEETIMIVMTP 296

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +       +        +N    +N+R    +             PS  LG       + 
Sbjct: 297  EDLEISRQLQAGYVMPEANPEE-LNKRVKAPMNPTAHTWTHCEIHPSMILG-------IC 348

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          +  +   +    +                      V    
Sbjct: 349  ASIIPFPDHNQ---------VSFDTWMSGYSTDTLSXXXXXXXXXXXXXXXXXXXVFLTN 399

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +      +  +             +       +   +  + AI      +  D+ +   
Sbjct: 400  YQQR-MDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 458

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---I 989
            S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +
Sbjct: 459  SSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLV 514

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  ++ D      R++          ++     +  Q   S    
Sbjct: 515  APGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDTSTPLRSTENGIVDQVLLS---- 570

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                 LR VKV +   +  Q GDK A RHG KG +      EDM
Sbjct: 571  ----------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDM 614

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   D++++P  +PSRM +  + E                               
Sbjct: 615  PFTSEGMVPDLIISPHAIPSRMTIAHLIEC------------------------------ 644

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                   +L      +     +TP F     ++++ +LR     
Sbjct: 645  -----------------------LLSKVSSLRGFEGDATP-FTEVTVDSVSRLLREHGYQ 680

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G  ++Y+G TG      V +G  Y  +L 
Sbjct: 681  SRGFEVMYNGHTGRKLVTQVFLGPTYYQRLR 711



 Score =  104 bits (260), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 82/616 (13%), Positives = 165/616 (26%), Gaps = 100/616 (16%)

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            NK  KD    + + +       F++  ++ +    +  +Y L   G      +      
Sbjct: 7   FNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNWGDQKKAASVKA 63

Query: 426 DDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              + + +    + +  L        R+GK       +  +  +    E  + Q    + 
Sbjct: 64  GVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVK 123

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSL 532
            +       + +     V      N + +         +A   F     +    +  + +
Sbjct: 124 NLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVWVGVHRDPAHLV 183

Query: 533 SRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVS 584
             + + RR   +  +  + R     E        R   P       P  ++ G+ +    
Sbjct: 184 GTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGNLVLTKD 243

Query: 585 SLTSFAR------VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            +                  E              V Y+ A EEE   I      L+   
Sbjct: 244 HVLKLEMDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLEISR 303

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                 V      EE+    +                                       
Sbjct: 304 QLQAGYVMPEANPEELNKRVK--------------------------------------- 324

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV-------IRSVEGD 751
                    AP   T       +   + I+   A I+   D  ++          +    
Sbjct: 325 ---------APMNPTAHTWTHCEIHPSMILGICASIIPFPDHNQVSFDTWMSGYSTDTLS 375

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALG 808
                                 T   QR              +A   S +     +L  G
Sbjct: 376 XXXXXXXXXXXXXXXXXXXVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAG 435

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
           +N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     +  
Sbjct: 436 QNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRS 495

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           D   +       +D+ G++  G  V+  DI++GK  P         ++        K   
Sbjct: 496 DTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHI 548

Query: 924 VRDTSLRVPSGVSGTV 939
            RDTS  + S  +G V
Sbjct: 549 KRDTSTPLRSTENGIV 564


>gi|124358808|dbj|BAF46073.1| RNA polymerase beta subunit [Bartonella sp. Okinawa 36-1]
          Length = 275

 Score =  255 bits (651), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S A
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSRA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262117916|dbj|BAI47983.1| RNA polymerase beta subunit [Bartonella sp. OY14-1]
          Length = 275

 Score =  255 bits (651), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 200/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDIEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|224812779|gb|ACN65023.1| RpoB [Cronobacter sakazakii]
          Length = 255

 Score =  255 bits (651), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 158/255 (61%), Positives = 199/255 (78%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SA
Sbjct: 1   RAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR
Sbjct: 61  LGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYR 120

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
           KV DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D+
Sbjct: 121 KVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDY 180

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  S
Sbjct: 181 MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDS 240

Query: 724 GAAIVAKRAGIVEQV 738
           G   VAKR GIV+ V
Sbjct: 241 GVTAVAKRGGIVQYV 255


>gi|103001625|gb|ABF71515.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            sp. Hertel 39.701]
          Length = 691

 Score =  255 bits (651), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 113/752 (15%), Positives = 217/752 (28%), Gaps = 126/752 (16%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 52   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 107

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     ++     E    +    + +V  +     +      ++      +  D 
Sbjct: 108  GLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRSPNATKVFVNGVWVGVHSDP 167

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
                  V     G  I      + D  D   K          P F+ ++D      G  +
Sbjct: 168  VHLVNTVQAVRRGHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSPRCGSLV 227

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA---IRIVIRSVEGDLD 753
              +       +   +   M     +         +             R V+  V+ + +
Sbjct: 228  LTKEHINKLEDYKDLSAEM-QEKIREKEEVEKEVKEDGTPYGWNGLIKRGVVEYVDAEEE 286

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLV---KVGDEVRRNDIIADGPSTDLG-DLALGR 809
             +   V     ++  R  Q   V   P      +   V+          T      ++  
Sbjct: 287  ETVMIVMTPEDLEISRQLQAGYVLPEPSDTSEALMKRVKAPMNPTAHTWTHCEIHPSMIL 346

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N          M  + +   + +  +E                     
Sbjct: 347  GICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM------------------ 386

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 387  ---------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVI 437

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME- 988
               S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L + 
Sbjct: 438  MNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDD 493

Query: 989  --ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              +  G           K+  ++ D      R++          ++     +  Q     
Sbjct: 494  GIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRSTENGIVDQVLL-- 551

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                                    LR VKV +   +  Q GDK A RHG KG +      
Sbjct: 552  ------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQ 593

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF K+G   D+++NP  +PSRM +  + E  L       G +               
Sbjct: 594  EDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------- 640

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                    +TP F     ++++ +LR  
Sbjct: 641  ----------------------------------------ATP-FTEITVDSVSKLLREH 659

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                 G  ++Y+G TG      V +G  Y  +
Sbjct: 660  GYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQR 691


>gi|190148944|gb|ACE63447.1| RNA polymerase subunit B [Pseudonocardia asaccharolytica]
          Length = 269

 Score =  255 bits (651), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 153/276 (55%), Positives = 197/276 (71%), Gaps = 8/276 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG+VT  + YL+A EE+   IAQAN+ L +DG F E  V  R   GE  
Sbjct: 61  GFIQTPYRKVEDGRVTEQIDYLTADEEDRFVIAQANAPLTDDGHFQENRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++EAP VGTG
Sbjct: 121 FISPAGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + S EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMSDEGVRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N
Sbjct: 234 CNNQKPIVDEGQRVEAGQVLADGPCTENGEMALGKN 269


>gi|120561251|gb|ABM27010.1| RNA polymerase II second largest subunit [Basidiobolus ranarum]
          Length = 883

 Score =  255 bits (651), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 124/880 (14%), Positives = 245/880 (27%), Gaps = 152/880 (17%)

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            D      + + + +    +  +   + +  +      ++  L+     +  +DD D+ G 
Sbjct: 138  DKRIKYATEILQKEFLPHVATEAHTETK--KAYFFGYMVHRLLLAALERRDLDDRDHYGK 195

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              + +  + + +     +
Sbjct: 196  KRMDLAGPLLAMLFRMLFRKLTKDVGRYLQKCIDSNREFNLTLAVKSNTITNGLKYSLAT 255

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 256  GNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 311

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++  G    P  +V        +   SA    +  
Sbjct: 312  GMVCPAETPEGQACGLVKNLALMSYIS-VGNPSAPVVEVLADWAMESLEQFSANNIADAT 370

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N            L+                  +D SP+  +             D
Sbjct: 371  KIFVNGVWVGIHRDPGNLIETMRRFR---------RRVDISPEVSIVRDIRDKEIRFYTD 421

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + RV     +       L+ E        E          +V    GIVE +DA    + 
Sbjct: 422  AGRVCRPLYVVENQRITLRKEHVVALQMREYDGEPFGWQDLV--VNGIVEYLDAEEEEVS 479

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DL 805
             +    +  +            R            V V   V+ +  +     T      
Sbjct: 480  MICMTPEDLSE----------SRMYSKLGYIPEREVDVASRVKSSAALITHTWTHCEIHP 529

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ++   +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 530  SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 570

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  +             +       +   +  + AI      +  
Sbjct: 571  ----------LRMDTMANILYYPQKPLCTTRAMEYLRFRELPAGQNAIVAILCYSGYNQE 620

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   + +   +    IF R  +D+ ++   +  E+ E   R+               
Sbjct: 621  DSLIMNQTSIDRGLF-RSIFYRSYMDQEKKVGMMVMEEFEKPTRESTLRLKHGTYEKLEG 679

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 680  DGLIAPGTRVSGDDIIIGKTAPIPPDSEELGQRTKTHSKRDASTPLRSTENGIVDQVML- 738

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV V   R  Q GDK A RHG KG +     
Sbjct: 739  -------------------TTNQEGLKFVKVRVRSTRVPQMGDKFASRHGQKGTIGVTYR 779

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +G + E  L       G +  +          I
Sbjct: 780  QEDMPFNNEGIVPDLIINPHAIPSRMTIGHMVECLLSKVSTLSGNEGDATPFTEVTVEAI 839

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S                                                         + 
Sbjct: 840  SHALQEHGY-------------------------------------------------QK 850

Query: 1226 ADLD--ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               +   +G +    G         +  G  Y  +L HMV
Sbjct: 851  RGFEVLYNGHT----GR---KLTAQIYFGPTYYQRLKHMV 883



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 110/768 (14%), Positives = 222/768 (28%), Gaps = 106/768 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    VP+     ALG+ ++ +IL             +     +  A ++    V+
Sbjct: 67  YIRQD----VPIVVVFRALGLVADRDILEHICYDQEDYAMLELLKPCIEEAFVIQEQHVA 122

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        I   K++     + L+++ +  +   +            +      + 
Sbjct: 123 LDYIGKRGTTVGINKDKRIKYAT-EILQKEFLPHVATEAHTETKKAYFFGYMVH---RLL 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           + A +  D    +      +    P+L +        +   +     K           +
Sbjct: 179 LAALERRDLDDRDHYGKKRMDLAGPLLAMLFRMLFRKLTKDVGRYLQKCIDSNREFNLTL 238

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIA 438
               +  T  +  S+    + D  K   +  G  ++  R    +      R         
Sbjct: 239 AVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVLNRYTFASTLSHLRRCNTPIGRDG 298

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            I     L N    +         +      ++KN   +  + +       +  +   ++
Sbjct: 299 KIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSYISVGNPSAPVVEVLADWAM 355

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVE 557
              +  +A  +  A   F     +    +  N +  +   RR   +     + R     E
Sbjct: 356 ESLEQFSANNIADATKIFVNGVWVGIHRDPGNLIETMRRFRRRVDISPEVSIVRDIRDKE 415

Query: 558 MRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
           +R    T  GR+C P    E   I L        ++  Y           D  V   V Y
Sbjct: 416 IR--FYTDAGRVCRPLYVVENQRITLRKEHVVALQMREYDGEPFG---WQDLVVNGIVEY 470

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTE-ELVFCRCAGEEILVPR------EKIDFIDASPK 669
           L A EEE   I      L E   +++   +  R       V              +  P 
Sbjct: 471 LDAEEEEVSMICMTPEDLSESRMYSKLGYIPEREVDVASRVKSSAALITHTWTHCEIHPS 530

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IPF +++ S R      M +QA+ +                          
Sbjct: 531 MILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL------------------- 571

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 572 ----------------------RMDTMANILYYPQKPLCTTRAMEYLRFR---------- 599

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI    +  
Sbjct: 600 --------------ELPAGQNAIVAILCYSGYNQEDSLIMNQTSIDRGLFRSIFYRSYMD 645

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +   +   E            +     + ++  G+I  G  V+  DI++GK  P    
Sbjct: 646 QEKKVGMMVMEEFEKPTRESTLRLKHGTYEKLEGDGLIAPGTRVSGDDIIIGKTAPIPPD 705

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                ++        K    RD S  + S  +G V  V +       K
Sbjct: 706 SEELGQRT-------KTHSKRDASTPLRSTENGIVDQVMLTTNQEGLK 746


>gi|262117914|dbj|BAI47982.1| RNA polymerase beta subunit [Bartonella sp. OY10-1]
          Length = 275

 Score =  255 bits (650), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++V   SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVVCDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRGGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262072861|dbj|BAI47740.1| RNA polymerase beta subunit [Bartonella sp. Koshimizu 5-1]
          Length = 275

 Score =  255 bits (650), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+Q+DA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQIDATRIVIRATED-LDPSKSGVDI 275


>gi|300394756|gb|ADK11916.1| DNA-directed RNA polymerase II subunit two [Serpula himantioides]
          Length = 682

 Score =  255 bits (650), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 121/810 (14%), Positives = 231/810 (28%), Gaps = 145/810 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +      + K   I      
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEEYKWEHLVKGGIIELLDAE 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +       D   S +    +            +    +K G+           PS 
Sbjct: 286  EEETVMISMTPEDLENSRLQSAGIDPHTNDGD---YDPAARLKAGNNSHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 378  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 486  DKLEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VK+ V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +         
Sbjct: 586  GITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 638

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 639  ----------------------------------------------ATP-FTDLTVESVS 651

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
            + LR       G  ++Y G TG      V 
Sbjct: 652  TFLRQKGYQSRGLEVMYHGHTGRKLQAQVY 681



 Score =  118 bits (295), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 168/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +     Y   +    K         +  L A EEE   I+     L+     + 
Sbjct: 249 QKKHIKWLN-QGYRDDDGEEYKWEHLVKGGIIELLDAEEEETVMISMTPEDLENSRLQSA 307

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+     R             +  P  ++ + AS+IPF +++ S R      
Sbjct: 308 GIDPHTNDGDYDPAARLKAGNNSHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 367

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 368 MGKQAMGIYLTNFLV-----------------------------------------RMDT 386

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 387 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 422

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 423 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKH 482

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 483 GTYDKLEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 538

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 539 TENGIVDQVL 548


>gi|298912943|emb|CAZ66639.1| RNA polymerase beta subunit [Vibrio cincinnatiensis]
          Length = 289

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 170/289 (58%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  D  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   SLFESLFFSPERYDLSTVGRMKFNSSIERDDAEEQGTLDETDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFIIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L ++  F +EL+  R  GE  L PRE ++++D +  QVVSIAASLIPFL
Sbjct: 241 LTDENRFADELITARQKGESGLHPREHVNYMDVATNQVVSIAASLIPFL 289


>gi|330038752|ref|XP_003239690.1| second-largest subunit of RNA polymerase III [Cryptomonas paramecium]
 gi|327206614|gb|AEA38792.1| second-largest subunit of RNA polymerase III [Cryptomonas paramecium]
          Length = 1087

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 87/395 (22%), Positives = 152/395 (38%), Gaps = 63/395 (15%)

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            ++  +      I  G       K  K        L + Y +SQ + F+++        + 
Sbjct: 737  IEDAMTLNRSSIQRGFMKSVLLKKSKIILKDKKSLSTLYKKSQEFFFSIKKNFFSIKKKK 796

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                       +    + + +K+              VK      R  + GDK + RHG 
Sbjct: 797  NFKNSNEKMPYIISPRRTENQKMYNSILTHNNHDFVFVKFVFRETRTPEVGDKFSSRHGQ 856

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+   +   ED PF  +G+  DI++NP G PSRM +G+I E          GK  +   
Sbjct: 857  KGVCGIVNFYEDFPFSNEGSVPDIIMNPHGFPSRMTIGKIVELLGSKLSCLSGKFFEGTP 916

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                                                                 VF+    
Sbjct: 917  FKKFNRI----------------------------------------------VFE---- 926

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                 +L++   +++ + I + G +G+P    V  G ++  KL HMV+DK+Y+RS G  S
Sbjct: 927  ---KKILKL-GYNKNCKDIFFSGTSGQPLYAFVFSGPVFYQKLKHMVADKIYSRSRGIKS 982

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG--RTRVYESIVA 1334
             +T+QP+ G++  GG R GEME  C+ +YGA+ +  E L I SD  +G   T+   +I  
Sbjct: 983  KLTRQPVEGRNKGGGLRFGEMERDCLVSYGASELTLERLMISSDIYLGSFDTKT-GTITH 1041

Query: 1335 GNDTFETGT-----PESFNVLVKEMQALGLSIDLE 1364
              ++ +        P +  +L +E+ ++ +   + 
Sbjct: 1042 VTNSNKHSITLIKFPYACKLLFQELYSMNIIPRIY 1076



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 96/724 (13%), Positives = 200/724 (27%), Gaps = 110/724 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-AMLEFVSYEFD------ 82
           I  Q  S++ FL          N GL+        I           F + +        
Sbjct: 21  IWQQIESFNFFL----------NVGLKKTLYKFKCINNLQENNLSYNFSNLKLGSTTSCN 70

Query: 83  ---PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA----------KSIKDI---K 126
                    ++C  RD++Y  P+ + +                       +S   I   K
Sbjct: 71  ESTEYTVTPNECRIRDISYMAPILVDVCYFFKKKFFSRMNLTLCILPIMIRSTGCIFFNK 130

Query: 127 EQS--IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
            ++  +   + PL    G F+IKGI+R+ VS   R   + F+         G L     +
Sbjct: 131 SENFFVKFKECPL-DGGGYFIIKGIERV-VSIRER---LTFNKINIEKDQDGNL--CACV 183

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRK-----------VPVTSFLMALGMDSE-EILSTF 232
           I      +  E   K+ I   I + +K           + V     A+ +  E + +   
Sbjct: 184 I----SCL-AERRVKNSI---ILKNKKFYFRSNIFLEDILVLILYKAINITDEKDFIGLV 235

Query: 233 ---YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
              +  I+     +     +      +        + +   +Q  +     T   +K + 
Sbjct: 236 GFQFENILNFTVDEMKIMGIFTQKQALLYIYQRLDLKVWKYKQFFKKNAGNTYEFIKKIV 295

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                F   +   L  +   +   +   G+I            +++I  S  + I I   
Sbjct: 296 -----FNVFSKYILIHVISQKKTRDNFYGKIMF------ISIMIKKILASIDQTICIDNK 344

Query: 350 DSVNN------NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           D   N         +         +         + + +           S F+  F  S
Sbjct: 345 DYYGNKRFELSGQIMIKLFENVFKRSVFQMEKKYFSLSKKIKGRIECDVFSFFHSNFISS 404

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 + G   ++               +     I+ +  +    N    I  + +L  
Sbjct: 405 SFEYSLSSGNWILSKFSQEKQGMTQILSRLSFISSISSVNKINSTYNKSTKILTLRSLYP 464

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   V      +     +    SI   IS  + +  +     +      +  +      
Sbjct: 465 SQWGVVCPSDTPEGESCGIIKNLSILTYISLDEKNKYIKNLCFDLGVEFLSFSKVKTVPM 524

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
                   N+   +             + R     +   +      R     T  G    
Sbjct: 525 DMVFLN--NNYIGLHANTPRFLFVFRKMRRDTIISQNTSIFWDTVNRFVFIWTDRGRACR 582

Query: 582 LVSSLTSFARVNAYGFIET-PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
               +     ++ +    T       + +  N V +L   E+ N  IA  +  ++     
Sbjct: 583 PFFIIKLNESIDKFKKRNTAKIFSWKNLQRENFVEFLDTYEQNNALIANESKKIN----- 637

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                              K   ++ SP+ ++ I A+ IPF  ++ S R    C M +Q+
Sbjct: 638 ------------------SKTTHLEISPEIILGICANNIPFPNHNQSPRNTYQCAMGKQS 679

Query: 701 VPLL 704
           +  +
Sbjct: 680 IGFI 683



 Score = 91.7 bits (226), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 89/627 (14%), Positives = 213/627 (33%), Gaps = 40/627 (6%)

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
              I   E+V+   ++LT   +   K++          CL    V   I+       +  
Sbjct: 148 YFIIKGIERVVSIRERLTFNKINIEKDQDGNLCACVISCLAERRVKNSIILKNKKFYFRS 207

Query: 324 AGDVIDEKSLEEIFHSEIRD----IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
              + D   L       I D    I ++     N   +  + +       +K ALL IY+
Sbjct: 208 NIFLEDILVLILYKAINITDEKDFIGLVGFQFENILNFTVDEMKIMGIFTQKQALLYIYQ 267

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +           +      +    K   +   +  +   ++     D  + +   I  +
Sbjct: 268 RLDLKVWKYKQFFKKNAGNTYEFIKKIVFNVFSKYILIHVISQKKTRDNFYGKIMFISIM 327

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGE----MLKNQYRLGLLRMER---SIKERISS 492
           IK ++   +    ID+ D  GN+R    G+    + +N ++  + +ME+   S+ ++I  
Sbjct: 328 IKKILASIDQTICIDNKDYYGNKRFELSGQIMIKLFENVFKRSVFQMEKKYFSLSKKIKG 387

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG---- 548
                V      N             +  LS+  +    +++I       +         
Sbjct: 388 RIECDVFSFFHSNFISSSFEYSLSSGNWILSKFSQEKQGMTQILSRLSFISSISSVNKIN 447

Query: 549 --VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
               ++   + +R ++P+ +G +CP++T EG + G++ +L+    ++     +     + 
Sbjct: 448 STYNKSTKILTLRSLYPSQWGVVCPSDTPEGESCGIIKNLSILTYISLDEKNKY----IK 503

Query: 607 DGKVTNDVVYLS----AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           +      V +LS         +      N       +     VF +   + I+     I 
Sbjct: 504 NLCFDLGVEFLSFSKVKTVPMDMVFLNNNYIGLHANTPRFLFVFRKMRRDTIISQNTSIF 563

Query: 663 FIDASPKQVVSI--AASLIPFL-----ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +   +    +      +  PF      E+ D  +      +        +    F+ T  
Sbjct: 564 WDTVNRFVFIWTDRGRACRPFFIIKLNESIDKFKKRNTAKIFSWKNLQRENFVEFLDT-Y 622

Query: 716 ESVVAKSSGAA--IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           E   A  +  +  I +K   +    + I  +  +     + + S  + Y+    ++S   
Sbjct: 623 EQNNALIANESKKINSKTTHLEISPEIILGICANNIPFPNHNQSPRNTYQCAMGKQSIGF 682

Query: 774 TCVNQ----RPLVKVGDEVRRNDI-IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
             +NQ      ++ +    ++  +       +    L  G N  +  M + G++ ED+M 
Sbjct: 683 IGLNQIYRADTILSLLVYPQKPIVGTKITELSGNNRLTGGINACICVMSYRGHDIEDAMT 742

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTK 855
           ++   +      S+ +++ +++ +D K
Sbjct: 743 LNRSSIQRGFMKSVLLKKSKIILKDKK 769


>gi|262072865|dbj|BAI47742.1| RNA polymerase beta subunit [Bartonella sp. Koshimizu 7-1]
          Length = 275

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID  +PQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDPAIPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148956|gb|ACE63453.1| RNA polymerase subunit B [Pseudonocardia dioxanivorans CB1190]
          Length = 267

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 154/274 (56%), Positives = 202/274 (73%), Gaps = 8/274 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG VT  + YL+A EE+   IAQAN+ L++DGSFTE+ V  R   GE  
Sbjct: 61  GFIQTPYRKVVDGVVTEQIDYLTADEEDRFVIAQANAPLNDDGSFTEDRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+P   +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++EAP VGTG
Sbjct: 121 LIPPTGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVAEKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           C NQ+P+V  G  V    ++ADGP T+ G++ALG
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMALG 267


>gi|124490812|gb|ABN12776.1| RNA polymerase beta subunit [Bartonella sp. RN27BJ]
          Length = 271

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 189/264 (71%), Positives = 222/264 (84%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG 
Sbjct: 1   KERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKII 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D 
Sbjct: 121 DGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA
Sbjct: 181 SPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAA 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEG 750
           + AKR+GIV+QVDA RIVIR+ E 
Sbjct: 241 VSAKRSGIVDQVDATRIVIRATED 264


>gi|195118276|ref|XP_002003666.1| GI21635 [Drosophila mojavensis]
 gi|193914241|gb|EDW13108.1| GI21635 [Drosophila mojavensis]
          Length = 1122

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 84/353 (23%), Positives = 133/353 (37%), Gaps = 83/353 (23%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                ++++    ++ ++          + V + + + RP   GDK A R G KGI S+  
Sbjct: 822  KVVKMDEKEDCIVDSVRQLGSFEIMPRKTVCITLRVARPATIGDKFASRAGQKGICSQKY 881

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PF + G   DIV NP G PSRM +  + ET  G +                    
Sbjct: 882  PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKSAA------------------ 923

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV-F--DGADEEAINS 1221
                                                  GV  +TP  F  D    +    
Sbjct: 924  -----------------------------------LHGGVYDATPFRFSEDNTAIDYFGK 948

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G   LY G+ G      +  G ++  +L HMV DK   RSTG+    T Q
Sbjct: 949  MLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTNQ 1008

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD------------------VV 1323
            P+ G+   GG R GEME   + ++GAA++LQ+ L   SD                   ++
Sbjct: 1009 PIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAPLQQII 1068

Query: 1324 GRTRV--YESI-----VAGND--TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             R +     S+     + G+         P SF  LV E+ ++ ++   + ++
Sbjct: 1069 KRNQTGGLSSMPETCRLCGDSSGVSMIEIPFSFKFLVTELSSVNINARFKLNQ 1121



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 87/536 (16%), Positives = 194/536 (36%), Gaps = 57/536 (10%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                  +  D+     + R ++ + LN +        + + I+ +++ L     GK  +
Sbjct: 303 RFQEVPEWMPDEAVTEFIIRERIMVHLNTNEE------KFQLIVFMVQKLFQCAQGKFKV 356

Query: 454 DDIDNLGNRRVRSVGEM----LKNQYRLGLLRMERSIKERISSVDI---DSVMPQDLINA 506
           +++D+   + V   G +    L  +  + L+ + + + +++++ D     S+M Q +  A
Sbjct: 357 ENVDSAMMQEVLLPGHLYQKYLGERLEMWLMHLRKCLLKKLNTPDSLVSSSIMTQCMRQA 416

Query: 507 KPVVSAVCEFFCSSQ--------------LSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             V  A+  F  +                L  + E++N +  ++H R   A+ +G     
Sbjct: 417 GGVGRAMESFLATGNVASRTGLGLMQSTGLVIMAENINRMRYMSHFR---AIHRGSYFTT 473

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E R + P  +G ICP  T +G   GL++ LT    ++     +   + +    +  
Sbjct: 474 MRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISKRPDPKLV-QAIPSMLLEM 532

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            ++ LS          Q ++ L     F +          E     E + +   + K   
Sbjct: 533 GMIPLSQQ-------GQPDAKLYV--VFLDGKHLGHIFQTEANKIVEDLRYAKITGKVPE 583

Query: 673 SIAASLIPFLENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGTG--MESVVAKSSGAAI 727
            +    IP+ +N              M R    L      ++GT   +   +A       
Sbjct: 584 MMEIGFIPYKKNGQFPGLFLCTGPTRMMRPVWNLKWRRVEYIGTLEQLYMEIAIDEKEMY 643

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVG 785
                 +          + ++    D + S  ++Y+    +++    C+N  ++   K+ 
Sbjct: 644 PDFTTHLELSKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWSKQAANKLY 703

Query: 786 DEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTS 841
                   +      D     D A+G N +VA + + GY+ ED+M+I++        + S
Sbjct: 704 RLQTPATPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKSAYERGFAYGS 763

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           I+  +F  +++                  E +K++D  G+   G +++ G  L   
Sbjct: 764 IYKSKFVQLSKKQSYFARHPHMP------ELIKHLDTDGLPHPGTKLSYGSPLYCY 813


>gi|57337350|emb|CAH69683.1| RNA polymerase, beta subunit [uncultured bacterium]
          Length = 253

 Score =  255 bits (650), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 151/251 (60%), Positives = 192/251 (76%)

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG V
Sbjct: 2   RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVV 61

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L   +++D++D S +Q
Sbjct: 62  TDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYMDVSTQQ 121

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 122 VVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 181

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
           R G V+ VDA RIVI+  E ++    +G+DIY L K+ RSNQNTC+NQ P V +G+ V R
Sbjct: 182 RGGTVQYVDASRIVIKVNEDEMLAGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVER 241

Query: 791 NDIIADGPSTD 801
            D++ADGPSTD
Sbjct: 242 GDVLADGPSTD 252


>gi|103001965|gb|ABF71529.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            cf. chlorophanum Nash 26]
          Length = 714

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 120/832 (14%), Positives = 231/832 (27%), Gaps = 145/832 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + + +               + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFNKLTKDVXKYLXKCVESGREFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                D+  +     N+   ++ +  L+ +               S     AK  G    V
Sbjct: 237  LFVIDNDPKSTNCGNLVLTKEHINKLEDDRDLPA-------IMDSEE-KEAKFFGWDGLV 288

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q           +   V+         
Sbjct: 289  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHT 346

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M                        
Sbjct: 347  WTHCEIHPSMILGICASIIPFPDHNQSPXNTYQSXM---------------------GXX 385

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                         +   N        +             +       +   +  + AI 
Sbjct: 386  XXXXXXXXXXQRMDTXAN--------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 437

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 438  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 493

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  +S D      R++          ++  
Sbjct: 494  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRST 553

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             L+ VKV +   +  Q GDK A RH
Sbjct: 554  ENGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRH 593

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 594  GQKGTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 653

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 654  TPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------ 681

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                            +G +    G         V +G  Y  +L HMV DK
Sbjct: 682  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDK 711



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 84/619 (13%), Positives = 167/619 (26%), Gaps = 99/619 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N      NK  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 10  GPLLANLFRMLFNKLTKDVXKYLXKCVESGR--EFNLTLGVKSTTITNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 67  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 127 TPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 186

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +S +   RR   +  +  + R     E        R   P       P  
Sbjct: 187 VGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 246

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           T+ G+ +     +           I      E  +           V Y+ A EEE   I
Sbjct: 247 TNCGNLVLTKEHINKLEDDRDLPAIMDSEEKEAKFFGWDGLVNNGVVEYVDAEEEETVMI 306

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                 L                              + S +     A       E  D 
Sbjct: 307 VMTPEDL------------------------------EISRQIQAGYA-----MPEASDD 331

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               +   M                T       +   + I+   A I+   D  +    +
Sbjct: 332 LNKRVKAPM--------------NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPXNT 377

Query: 748 VEGDL-DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +  +              +           Q+PL                      +L 
Sbjct: 378 YQSXMGXXXXXXXXXXXXQRMDTXANILYYPQKPL----------ATTRSMEFLKFRELP 427

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----I 861
            G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     +
Sbjct: 428 AGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPM 487

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             D   +       +D+ GI+  G  V+  DI++GK  P         E+L +       
Sbjct: 488 RSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDA----EELGQRTKLHVK 543

Query: 922 VDVRDTSLRVPSGVSGTVV 940
            DV        +G+   V+
Sbjct: 544 RDVSTPLRSTENGIVDQVL 562


>gi|52699812|gb|AAU86968.1| DNA-dependent RNA polymerase II second largest subunit [Glypholecia
            scabra]
          Length = 722

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 118/836 (14%), Positives = 240/836 (28%), Gaps = 140/836 (16%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +    +         + +  + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L    +  V         +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSQPIIDFMIQRNMEVLEEYEPQRSPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP- 680
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 177  TKVFVNGVWVGVHRDPAHLVSTVIALRRLNAISHEVSLVRDIRDREFKIFTDAGRVCRPL 236

Query: 681  FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            F+ ++D      G  +  +  +  L+ +        E +   ++    V          D
Sbjct: 237  FVIDNDPKSHNRGSLVLTKDHIHKLEDDKELTP---EQIAELAAEVDPVTGHKKTSPGWD 293

Query: 740  A--IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                  V+  V+ + + +   V     ++  R  Q           +   V+        
Sbjct: 294  GLVETGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGFTFPETSDDLNKRVKAPMNPTAH 353

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +   + +  ++        
Sbjct: 354  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM----- 406

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 407  ----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 444

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + +
Sbjct: 445  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTL 500

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++          ++ 
Sbjct: 501  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 560

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 561  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 600

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 601  HGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 660

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 661  ATPFTEVTVDSVSKLLR--EHGYQSRGFEVM----------------------------- 689

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 690  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 722


>gi|225728460|gb|ACO24287.1| RNA polymerase beta subunit [Bartonella koehlerae]
          Length = 269

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 189/265 (71%), Positives = 223/265 (84%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F+EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFSEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEG 750
           A+ AKR+GIV+QVDA RIVIR+ E 
Sbjct: 241 AVAAKRSGIVDQVDATRIVIRATED 265


>gi|8895204|gb|AAF80852.1|AF165996_1 RNA polymerase beta subunit [Bartonella tribocorum]
          Length = 275

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 232/276 (84%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y++QANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVSQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|262072914|dbj|BAI47765.1| RNA polymerase beta subunit [Bartonella grahamii]
          Length = 275

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 195/276 (70%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA  E+RDVHPTHYGRICP ET +G NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAAFEVRDVHPTHYGRICPIETPKGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|55273995|gb|AAV48868.1| RNA polymerase II second largest subunit [Calostoma cinnabarinum]
          Length = 680

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 122/809 (15%), Positives = 235/809 (29%), Gaps = 145/809 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ R +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMAAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGXIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      +L+ +   ++  G      +      + K   +         
Sbjct: 226  TDAGRVCRPLFIVENQQLVLQKKHIQWLSQGYRDEANEEFKWEHLVKNGIVELLDAEEEE 285

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +       D   S +    +  ++   +    +    +K              PS  LG
Sbjct: 286  TVMISMTPEDLENSRLQSAGINPYENDGE---YDPTARLKARTSAHTWTHCEIHPSMILG 342

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 343  -------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 377

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 378  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIMCYSGYN 426

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 427  QEDSVIMNQSSIDRGLF-RSIYYRSYMDMEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKL 485

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  +      R++          V   ++S +    
Sbjct: 486  EEDGLIAPGTGVQGEDIIIGKTAPIPPESEELGQRTR----THTRRDVSTPLKSTEKGTI 541

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                I                       + VKV V   R  Q GDK A RHG KG +   
Sbjct: 542  DQVLI----------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 585

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      LG +            
Sbjct: 586  YRQEDMPFTAEGISPDIIINPHAIPSRMTIGHLVECLLSKVATLLGNEGD---------- 635

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                                       +TP F     E+++S L
Sbjct: 636  -------------------------------------------ATP-FTELTVESVSSFL 651

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            R       G  ++Y G TG      + +G
Sbjct: 652  RQKGYQSRGLEVMYHGHTGRKLQAQIYLG 680



 Score =  125 bits (314), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 88/623 (14%), Positives = 169/623 (27%), Gaps = 102/623 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R G        +  +  +    E
Sbjct: 66  GDQKKSMAAKAGVSQVLNRYTYASTLSHLRRCNTPLGREGXIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH-NIG 581
               +  N +  I   RR   +                ++        P    E    + 
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLVL 245

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +   ++       E    K         V  L A EEE   I+     L+     +
Sbjct: 246 QKKHIQWLSQGYRDEANEE--FKWEHLVKNGIVELLDAEEEETVMISMTPEDLENSRLQS 303

Query: 642 EELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +      GE     R             +  P  ++ + AS+IPF +++ S R     
Sbjct: 304 AGINPYENDGEYDPTARLKARTSAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 363

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 364 AMGKQAMGIYLTNFLV-----------------------------------------RMD 382

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 383 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 418

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            M + GYN EDS+++++  +   +F SI+   +  M + + +   E            + 
Sbjct: 419 IMCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKKSGVQQLEEFEKPTRDTTLRMK 478

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 ++E G+I  G  V   DI++GK  P       PE + L           RD S 
Sbjct: 479 HGTYDKLEEDGLIAPGTGVQGEDIIIGKTAPI-----PPESEELGQRTRTH--TRRDVST 531

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S   GT+  V I       K
Sbjct: 532 PLKSTEKGTIDQVLITTNSEGQK 554


>gi|298912959|emb|CAZ66647.1| RNA polymerase beta subunit [Vibrio campbellii]
          Length = 289

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 169/289 (58%), Positives = 222/289 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L EDG F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFL
Sbjct: 241 LTEDGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFL 289


>gi|185179208|gb|ACC77617.1| RpoB [Mycobacterium smegmatis]
          Length = 215

 Score =  254 bits (649), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 90/220 (40%), Positives = 118/220 (53%), Gaps = 40/220 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 133  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V D +
Sbjct: 176  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVDDXI 215


>gi|82581204|dbj|BAE48675.1| RNA polymerase beta subunit [Bartonella sp. Fuji 6-1]
          Length = 275

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLEND +NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDGANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|103001206|gb|ABF71497.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            fulvoviridula]
          Length = 708

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 119/830 (14%), Positives = 236/830 (28%), Gaps = 147/830 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + +  +    +         + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                D+  +     N+   ++ +  L+ +      T  E            AK  G    
Sbjct: 237  LFVIDNDPKSTHCGNLVLTKEHINKLEDDKDLPATTDTEEKD---------AKFFGWDGL 287

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            V     V+  V+ + + +   V     ++  R  Q           +   V+        
Sbjct: 288  V--NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYTIPETSDDLNKRVKAPMNPTAH 345

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +   + +  ++        
Sbjct: 346  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----- 398

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                    +  +             +       +   +  + AI
Sbjct: 399  ----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 436

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + +
Sbjct: 437  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTL 492

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L E   +  G           K+  ++ D      R++          ++ 
Sbjct: 493  KLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 552

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 553  TENGIVDQVLI--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 592

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 593  HGQKGTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 652

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 653  ATPFTEVTVDSVSKLLR--EHGYQSRGFEVM----------------------------- 681

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                             +G +    G         V +G  Y  +L HMV
Sbjct: 682  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 708


>gi|118640625|gb|ABL09880.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640627|gb|ABL09881.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640629|gb|ABL09882.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640631|gb|ABL09883.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640633|gb|ABL09884.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640635|gb|ABL09885.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640639|gb|ABL09887.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640723|gb|ABL09929.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640727|gb|ABL09931.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
          Length = 290

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 172/290 (59%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|118640665|gb|ABL09900.1| RNA polymerase beta subunit [Vibrio sp. 9866-84]
          Length = 290

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + ++DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIEREDALEQGTLDEQDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|221110129|ref|XP_002162413.1| PREDICTED: similar to DNA-DIRECTED RNA POLYMERASE II SECOND LARGEST
            SUBUNIT [Hydra magnipapillata]
          Length = 1117

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 162/1091 (14%), Positives = 332/1091 (30%), Gaps = 174/1091 (15%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKDRKDALLDIY 378
            I   A  +  ++ + EI   +  D  ++ +  V+       N     K + +++A+  + 
Sbjct: 146  ILFRALGIESDRDIIEICAYDKTDYHMIELLRVSLETCVNDNDDQEHKIQTQEEAIDLLI 205

Query: 379  RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
              M+     T +   + F            ++       +     +P +    +   +  
Sbjct: 206  TKMKVLKNYTNTNLSTRFEQKKLHLLDLLKTS------FLPHIEGSPSNPYREKAYYLGY 259

Query: 439  IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
            II  L+ +  G+  +D+ D    +R+ ++ E+L+               ++ ++   D  
Sbjct: 260  IINKLLKVELGRAPVDNRDAYTKKRIDNIRELLEEIMIQQYKNNMNECSKQFTARMGDDG 319

Query: 499  MPQDLIN--AKPVVSAVCEFFCSS----------QLSQLEEHVNSLSRITHTRRLSALGQ 546
               D  N   +       + F +S           +SQ+ +  + +  +T   R+ +   
Sbjct: 320  DAADPYNVIHQFKAGTFEQGFKASIMIGNWSRKKGVSQMLQRNSYMQLLTSLSRIDSQSS 379

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK-- 604
               A      + R V P+    +C   T E  NIGLV  L+    +       T   K  
Sbjct: 380  TQSA--GRLTKPRHVDPSTVPFLCVVSTPEHGNIGLVKHLSMIGSITIGDKDNTEIVKEF 437

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            +    +  D+  +   E +N +    N    +    + ++         I    +    +
Sbjct: 438  IMTHPLVKDISEVPVYELKNMFKVFLNGEWLKVVENSYDVGDNYYDNPVIKFYSDA--KV 495

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
                 +      S++   ++++         + R  + +       +   M         
Sbjct: 496  KKISCEFNPQMTSVVFDYKDNEIRFNTDSGRLYRPVIRINGDNEMMLTKEMIDK------ 549

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              I  K   + +  D     I+             +    M      +     ++ ++  
Sbjct: 550  --ISLKATDVGKISDWDEFYIQY---PYPIEFIDSEEQPFMLIAEDRKVLNFERKKIIDS 604

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
               V + +        D             F+ +       S+L+SE      + T+I  
Sbjct: 605  EKHVFKGEESKIVNRFDD----------KFFLRYDSIEIHPSVLLSE------IATNIPF 648

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             E     R+         +    V     ++  +   I    EV   +    K T     
Sbjct: 649  CEKNCSTRNI--YQYAQGKQGMGVYCTAYRSRTDLSFILYNPEVPVVNTRTSKYTYT--D 704

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             + P    + AI      +  D+ +   + +   +       ++       + + E    
Sbjct: 705  ILPPGSNAVVAIACYSGYNQEDSIVFNMTSLQRGLFRSMSLYKYISSI---TKNQETSGN 761

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            +   +   D+        Y +L E       +       K  V+   +      +   + 
Sbjct: 762  DKFMKPPPDKMAGTKNGNYDKLNE----HGYIPEETQITKGDVIFGKVTPINDTTNTGRI 817

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                             ++ S    +      I+++   D          K  V  +R  
Sbjct: 818  -----------------FKDSSEQYKSYADGVIDRVYT-DIKNQDGYETRKALVRSERFP 859

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK   RHG KG +   L   DMPF K G   DI++NP  +PSRM++ Q+ E   G  
Sbjct: 860  RIGDKFCSRHGQKGTIGISLRGIDMPFTKWGIRPDIIVNPNAIPSRMSIAQLCECLFGKV 919

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                G  +     +      +  +   L        +                       
Sbjct: 920  GALKGMNMDGTAFEDYDIDAMKDMLESLGYQRECEEYLY--------------------- 958

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                           N ML        G+ I             + +G  Y  +L HMV 
Sbjct: 959  ---------------NGML--------GKMI----------KHMIFIGPTYYQRLRHMVQ 985

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK++AR  G  +++T+Q   G+S  GG RLGEME   +  +G A  L+E +   +D    
Sbjct: 986  DKIHARGRGPVTILTRQAPEGRSREGGLRLGEMERDAVITHGIAKFLKERMLDCAD---- 1041

Query: 1325 RTRVYESIVAG--------------NDTFETG------------------TPESFNVLVK 1352
                Y + V G                T                       P +F ++++
Sbjct: 1042 ---AYSTYVCGICGMFARREDSRFSEPTPGPDDVYYCPKCNNYTDIHQIMIPYAFKLMLQ 1098

Query: 1353 EMQALGLSIDL 1363
            E+ A+ ++  +
Sbjct: 1099 ELMAMNIAPRI 1109



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 101/803 (12%), Positives = 235/803 (29%), Gaps = 90/803 (11%)

Query: 140 KDGTFVIKGIQRIVV---SQLHRSPGIHFDHDKGRASLSGKLL----YACRIIPDQGLWM 192
             G F+I G +++V+   S +   P +    +   +++S K++     +          +
Sbjct: 67  PGGYFIINGSEKVVICQDSMIKNHPMVFIKKN---SNVSNKVVQVNSKSNDPTSMMQSVL 123

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSA 251
            I+     I+ V+I    +V V     ALG++S+ +I+             D   + +  
Sbjct: 124 -IKIKKDGIMTVKISVLYEVNVMILFRALGIESDRDIIEI--------CAYDKTDYHMIE 174

Query: 252 ADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAED 311
              +      +   D +   Q  E    L    +K LK      L    +      +   
Sbjct: 175 LLRVSLETCVNDNDDQEHKIQTQEEAIDLLITKMKVLKNYTNTNLSTRFEQKKLHLLDLL 234

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN----------- 360
             +         +    ++        +++  + +      N +AY +            
Sbjct: 235 KTSFLPHIEGSPSNPYREKAYYLGYIINKLLKVELGRAPVDNRDAYTKKRIDNIRELLEE 294

Query: 361 -TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             +   KN   + +     R+   GD +        F    F+        +G       
Sbjct: 295 IMIQQYKNNMNECSKQFTARMGDDGDAADPYNVIHQFKAGTFEQGFKASIMIGNWSRKKG 354

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL-- 477
           ++         +++   + ++  L  + +   T         R V               
Sbjct: 355 VSQM-------LQRNSYMQLLTSLSRIDSQSSTQSAGRLTKPRHVDPSTVPFLCVVSTPE 407

Query: 478 -GLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
            G + + + +     I+  D D+            +          +L  + +   +   
Sbjct: 408 HGNIGLVKHLSMIGSITIGDKDNTEIVKEFIMTHPLVKDISEVPVYELKNMFKVFLNGEW 467

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +        +G           +   +      ++          +  V        +  
Sbjct: 468 LKVVENSYDVGDN-------YYDNPVIKFYSDAKVKKISCEFNPQMTSVVFDYKDNEIRF 520

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
                  YR V      N++  L+    +   I+   + + +   + E  +      E I
Sbjct: 521 NTDSGRLYRPVIRINGDNEM-MLTKEMIDK--ISLKATDVGKISDWDEFYIQYPYPIEFI 577

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                       S +Q   + A     L  +    +    +               V  G
Sbjct: 578 D-----------SEEQPFMLIAEDRKVLNFERKKIIDSEKH---------------VFKG 611

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
            ES +          +   I      +   I +     + + S  +IY+  + ++     
Sbjct: 612 EESKIVNRFDDKFFLRYDSIEIHPSVLLSEIATNIPFCEKNCSTRNIYQYAQGKQGMGVY 671

Query: 775 CVNQRPLVKVGDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           C   R    +   +   ++          T    L  G N +VA   + GYN EDS++ +
Sbjct: 672 CTAYRSRTDLSFILYNPEVPVVNTRTSKYTYTDILPPGSNAVVAIACYSGYNQEDSIVFN 731

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKL--GPEEITRDIPNV----SEEGLKNIDECGIICV 884
              +   +F S+ + ++       +   G ++  +  P+            ++E G I  
Sbjct: 732 MTSLQRGLFRSMSLYKYISSITKNQETSGNDKFMKPPPDKMAGTKNGNYDKLNEHGYIPE 791

Query: 885 GAEVNPGDILVGKITPKGESPMT 907
             ++  GD++ GK+TP  ++  T
Sbjct: 792 ETQITKGDVIFGKVTPINDTTNT 814


>gi|103484143|dbj|BAE94844.1| RNA polymerase beta subunit [Bartonella sp. Gunma 2-1]
          Length = 275

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 228/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G F EE V  R AGE ++ PRE +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFIEEFVVRRHAGEVLMAPRENVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL+++EAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLMRSEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  +D S SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATEE-VDSSKSGVDI 275


>gi|46411490|gb|AAS94316.1| RNA polymerase II [Acarosporina microspora]
          Length = 717

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 117/839 (13%), Positives = 242/839 (28%), Gaps = 147/839 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++ + +R    ++ + + +  +              + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLMASLFRGLFQKLVKDVFKYLQKCVESGKEFNLTLGVKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAMSAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V +       Y    +  V  +   
Sbjct: 117  RQLHCTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSAPIIDYLVSRNMDVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                     ++      +  + +   + +      + +      + D  D   K      
Sbjct: 177  TRHPNSTKIFVNGVWVGVHRNPAQLVQHMQVLRRKKYLSFELSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                P F+  +D      G  +  + +     +   +   +     +        +  G 
Sbjct: 237  RVCRPLFVIENDPRNPNKGNLILTKDLINKLEDDRDLPPDLTKEEREE-------RYFGW 289

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
               V +   V+  ++ + + +   V     ++  R  Q       P       V+    +
Sbjct: 290  DGLVGS--GVVEFLDAEEEETVMIVMTPEDLEVSRQVQAGYAPPEPNNDPNARVKGKVNL 347

Query: 795  ADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                 T      ++   +  + +P+  +N          M  + +               
Sbjct: 348  QQHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSTMGKQAMGV------------- 394

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                               L N DE    +  +             +       +   + 
Sbjct: 395  ------------------FLTNFDERIDTMSNILYYPQKPLATTRSMEFLKFRELPAGQN 436

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    +F R  +++ +R   +    +E   +  
Sbjct: 437  AIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKR---IGMSLVETFEKPM 492

Query: 972  DDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              + + L    Y +L +   +  G           K+  +  D      R++        
Sbjct: 493  RSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIPPDSEEMGQRTKLHTKRDAS 552

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +                  ++K+          L+ VKV     +  Q GD
Sbjct: 553  TPLRSTENGI------------------VDKVLL--TTNAEGLKFVKVRTRTTKIPQIGD 592

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       
Sbjct: 593  KFASRHGQKGTIGVTYRMEDMPFSSEGITPDIIINPHAIPSRMTIAHLIECQLSKVSSLR 652

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +          +S L    E    +                              
Sbjct: 653  GFEGDATPFTEVTVDSVSRLLR--EHGYQSRGFEVM------------------------ 686

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                  +G +    G         V  G  Y  +L HMV DK+
Sbjct: 687  ---------------------YNGHT----GR---KLVSQVFFGPTYYQRLKHMVDDKI 717


>gi|190148982|gb|ACE63466.1| RNA polymerase subunit B [Pseudonocardia sp. S010]
          Length = 270

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 153/277 (55%), Positives = 203/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVSEGRVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 YISPVGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P++  GD V    +IADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIIDEGDRVEAGQVIADGPCTENGEMALGKNL 270


>gi|73852908|ref|YP_294192.1| putative DNA-directed RNA polymerase II subunit [Emiliania huxleyi
            virus 86]
 gi|72415624|emb|CAI65861.1| putative DNA-directed RNA polymerase II subunit [Emiliania huxleyi
            virus 86]
          Length = 1156

 Score =  254 bits (649), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 92/418 (22%), Positives = 145/418 (34%), Gaps = 99/418 (23%)

Query: 971  KDDEQ---VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
            +D+E+     ++R    + +    G       K   K   +               F   
Sbjct: 793  RDEEKGTGADIERFENPKNIPGCSGMKEADYSKIDDKGMPIIGK-----------TFYNG 841

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD----------MPPGVLRVVKVF 1077
            D  + + V    +Q +  +  +    K     +   D+            P     VKV 
Sbjct: 842  DVLIGKVVSMSLLQADPKEGEVRRDTKRDRSHVLRTDEPVVVDAVFLSKTPEGHGYVKVR 901

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                R    GDK + RHG KG+    +P  D P   DG   DI++NP  +PSRM +G + 
Sbjct: 902  TRAIRIPMVGDKFSARHGQKGVCGVTMPAADFPCTADGVAPDIIINPHAIPSRMTIGMLM 961

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G+                                               
Sbjct: 962  EMVLSKVACYEGETQDG------------------------------------------- 978

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                      TP F G + E I   L    +   G  +LY+G++GE  +  + +   Y  
Sbjct: 979  ----------TP-FTGNNIELIADRLETHGMQRYGNEMLYNGMSGEMLESMIFIAPCYYQ 1027

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
            +L HMV DK +AR+ G+  L+T+ P  G+S  GG R+GEME   I ++GA  V ++ L  
Sbjct: 1028 RLKHMVVDKSHARNRGAQQLLTRAPTEGRSRDGGLRIGEMEKDSIISHGAGDVAKDRLFE 1087

Query: 1318 KSDDVV----------GRTRVYESIVA-----------GNDTFETGTPESFNVLVKEM 1354
            +SD              R    ++ V            G     T  P S  +L++E+
Sbjct: 1088 QSDIFECVACEKCGHFAREGTDDTSVKNSGMWCEHCKTGKHCTHTQLPYSMKLLIQEL 1145



 Score =  127 bits (320), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 135/971 (13%), Positives = 284/971 (29%), Gaps = 195/971 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDPP--- 84
           +  Q  SYDHF+   +       EG       +  + + SG     + F +   + P   
Sbjct: 23  VAHQIESYDHFIENQLPYIIS--EG-----SDISYMHS-SGKVSHHVHFTNPSVNRPAIQ 74

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE--QSIYMGDL 135
                           R LTY+  + + +   + D    T +      ++  +++ +  +
Sbjct: 75  ESDGFYKPITPHIARLRGLTYSSTVVVDV---IHDRINHTVSPPTLINRKVFRNVIIAQI 131

Query: 136 PLMT---------------------------KDGTFVIKGIQRIVVSQ-LHRSPGIH-FD 166
           P+M                              G F+I G ++ ++ Q   R+  +  F 
Sbjct: 132 PVMVRSKLCYLADVSENDLSADAKKHECKVDPGGYFIISGNEKTLIPQTKIRTNHVFIFP 191

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMD----IEFDSKDIIHVRID-RRRKVP-------V 214
              G         Y   +       +     I  +  DI +  +     K+P       V
Sbjct: 192 SKHGEKHK-----YTAEVRSCHEAKLRSTSTIYMNINDISNGEVPVITCKLPFLKSNLSV 246

Query: 215 TSFLMALGM-DSEEILSTFYPKIVYSQ--------RGDFWCFPLSAADLMVGAKVSSSLV 265
                 LG   +++I++        ++              +   A    VG  V+S   
Sbjct: 247 FILFRMLGAESTDDIINYIGNIPKDTEAILRIMLDSDTKQNYSRDAIMDWVGRNVTSDTT 306

Query: 266 DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
                 +       +TS L   +                G  +   +      E+  +  
Sbjct: 307 RATKESREKYIDHIITSELAPHMGLVNNPETNKKKMIFIGHMIQRLMSVATGQEVVDDRD 366

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D I++     I  +      +L      N     +T +  + +  ++A  ++  ++    
Sbjct: 367 DFINK----RIDSAGALLALLLRQHHRGNAMQGLSTQLRKQVESPREATFNVGEIVSHKK 422

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-----DVRHIRKEDIIAII 440
           + T  +  +     +  S     +  G+  +   L   T         +           
Sbjct: 423 I-TSGLKFAFATGTWGISRGGGTANGGQTGVVQILPRLTTMATLGASRKINTPIAREGRT 481

Query: 441 KILVDLR-NGKGTIDDIDNLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSV 498
                L  +  G +   D    +    V  + +  + R+G      +I        ID  
Sbjct: 482 AGPRMLHPSSWGLVCCSDTPEGQACGLVSNLAITTRIRIGAPMQPIAILLMTLDHTIDIS 541

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                   + +  A+         +   + +  ++    + R         + + +    
Sbjct: 542 TATSHE--RYIGYALHVNGTIVGYAITIDQIKEIATQMRSLRRHGNLPFDCSISISNDNS 599

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             V+  H   + P    + ++  +  ++ + A V           K         + Y+ 
Sbjct: 600 LFVNSDHGALLRPLIIRDRYHDFVCMAMQNPAVVPN---------KYTRMLREGIIEYID 650

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           + E+ N  +A  ++ +++D                      +   I+  P  +  I  S 
Sbjct: 651 SAEQTNMRVAIHHTDIEQD----------------------EYTHIEIHPALLTGICVSQ 688

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R+       +QA+ L                         A+R   V  V
Sbjct: 689 IPFCDHNQSPRIAYQAAQCKQAIGLYTTN--------------------FAERLDTVGHV 728

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A                                     Q+PLV       R + +    
Sbjct: 729 LAT-----------------------------------PQKPLV-----TTRLEELLGTS 748

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
               G +      +VA M + G+N +DS+L+++  +   +FTS          + T    
Sbjct: 749 VVRSGAVP-----IVAIMCYSGFNQDDSVLLNQSSIDRGLFTSFAYHTIRDEEKGTGADI 803

Query: 859 E--EITRDIP---NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           E  E  ++IP    + E     ID+ G+  +G     GD+L+GK+         P+E  +
Sbjct: 804 ERFENPKNIPGCSGMKEADYSKIDDKGMPIIGKTFYNGDVLIGKVVSMSLLQADPKEGEV 863

Query: 914 RAIFGEKAVDV 924
           R         V
Sbjct: 864 RRDTKRDRSHV 874


>gi|307343574|emb|CBJ18703.1| RNA polymerase B subunit [Micromonospora matsumotoense]
          Length = 215

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 96/213 (45%), Positives = 124/213 (58%), Gaps = 38/213 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDTDWKRQLRSIE---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEPDTNVATPVFDGAREEEISGLLSSTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
              G++ L+DG +GEP   P+ VGYIY+LKLNH+
Sbjct: 181  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHL 213


>gi|118640637|gb|ABL09886.1| RNA polymerase beta subunit [Vibrio parahaemolyticus]
 gi|118640641|gb|ABL09888.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640643|gb|ABL09889.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640645|gb|ABL09890.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640647|gb|ABL09891.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640649|gb|ABL09892.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640651|gb|ABL09893.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640653|gb|ABL09894.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640655|gb|ABL09895.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640731|gb|ABL09933.1| RNA polymerase beta subunit [Vibrio alginolyticus]
 gi|118640739|gb|ABL09937.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 290

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|115396768|ref|XP_001214023.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Aspergillus
            terreus NIH2624]
 gi|114193592|gb|EAU35292.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Aspergillus
            terreus NIH2624]
          Length = 1219

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 169/1139 (14%), Positives = 339/1139 (29%), Gaps = 221/1139 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S   KS     +K   +         V  +++N +   + + 
Sbjct: 267  IVETDPKKEIVQASVTSSSNERKSKSYIVLKKDKLY--------VKHNVLNEDIPIVILL 318

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                I+      +  + +  +           A         +  D   A + I R    
Sbjct: 319  KAMGINTDKEMLLLVAGVDKVYQEDFAINFEEAINLGIYTQQQALDWIGARIKINRKQAS 378

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
               +    A      +        +S +    MN R            +   +  + + +
Sbjct: 379  YRRTHVQEAIEAIASVI-------ISHIEVKNMNFRP-----------KAIYVAHMARRV 420

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE-------RISSVDID 496
            +  +N    +DD D LGN+R+   G++L   +     +    IK        + +  +  
Sbjct: 421  LMAKNDPTLVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNVDKVLNKRNRAEAF 480

Query: 497  SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
                   ++   +   +     +   S     +          RLS +   G+       
Sbjct: 481  DAWSVMSMHTNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 540

Query: 551  --RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
              + R     R + P+ +G +CPA+T EG   GLV +L     +      E P R +   
Sbjct: 541  FEKTRKVSGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTN-DEEGPIRNLIFM 599

Query: 609  KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                D+  L   E           ++  +G+ T      R     +   R        S 
Sbjct: 600  LGAEDIQTLGGKE----LYGPGCYTISINGTPTA---LTRRPKYFLNAFRRLRRMGRISE 652

Query: 669  KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
               + I         +  +  V        + + +++     V T     + + +     
Sbjct: 653  FVSIYIN-------HHQHAVHVATDDGRICRPLIVVENGKSTVQTHHLEKLREGTMQFDD 705

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                G+VE +D               + S + IY                       D  
Sbjct: 706  FLAQGLVEYLDVNE-----------ENDSLIAIYEK---------------------DIS 733

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                 +   P T LG +A         +P+  +N          M  + +          
Sbjct: 734  ETTTHLEIEPFTILGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA-------- 778

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                     + +    I+ +        +    I       +  
Sbjct: 779  ---------------------IASNQFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPA 817

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + A+      D+ D  +     V       ++F ++  +    S   +     L  
Sbjct: 818  GQNAIVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTNLKSYSNGTKDM---LTP 874

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
               +++  I    +         G+   +G     KST           ++  +     D
Sbjct: 875  PSYENDAPIRKHALLESDGLAAVGEQVNAGEVYINKSTP---------DQANSFGIGGPD 925

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
                 N     + Y     + +  + +++        +     ++VKV     R  + GD
Sbjct: 926  PNRPINYMPTPMTY----KLPDPAYIDQVLL-----SVTENENQLVKVLTRQTRRPEVGD 976

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K +                                     SR                  
Sbjct: 977  KFS-------------------------------------SR-----------------H 982

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G+K    I   +A+   +      + ++       +++      ++       SG     
Sbjct: 983  GQKGVVGIIADQADMPFTDQGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLSGQHGYG 1042

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
              F G+  E ++ +L        G+  L  G+TGE     V  G IY  KL HMV DK++
Sbjct: 1043 TCFGGSPVEEMSQILIDKGFSYGGKDYLTSGITGEALPFYVFTGPIYYQKLKHMVQDKMH 1102

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV-- 1322
            +R+ G  +++T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    DV  
Sbjct: 1103 SRARGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCE 1162

Query: 1323 ----------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                        R +   S+V          P +  +L++E+ ++ ++  L+       
Sbjct: 1163 KCGFMGYLNWCQRCKSSRSVVK------MVIPYAAKLLIQELMSMNVTARLKLEDEFPE 1215



 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 87/748 (11%), Positives = 215/748 (28%), Gaps = 138/748 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F       P+  
Sbjct: 110 LVKQHIDSYNYLVEVQ----------LKKIVESSSIIRSDVDHNFYIKFTDIYLGAPRRA 159

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    +          +  + ++++   
Sbjct: 160 DESQDAGPAFTGSTVTPQECRLRDTTYAAPIQVDFDYV----------RGRQRVRKRGYA 209

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 210 IGRMPVMLRSSKCVLANKSPAEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 269

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 270 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLNEDIPIVILL 318

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESG 277
            A+G+++++ +      +    + DF      A +L +   + +   +         ++ 
Sbjct: 319 KAMGINTDKEMLLLVAGVDKVYQEDFAINFEEAINLGIYTQQQALDWIGARIKINRKQAS 378

Query: 278 KK-------LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            +       + +     +    VK +      +   ++A  ++  +     ++  D +  
Sbjct: 379 YRRTHVQEAIEAIASVIISHIEVKNMNFRPKAIYVAHMARRVLMAKNDPTLVDDRDYLGN 438

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
           K LE            L+                   K   D  +++ +V+   + +   
Sbjct: 439 KRLELAGQLLALLFEDLF------------------KKFCFDIKMNVDKVLNKRNRAEAF 480

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
            A S+ +       +     +     +  R  ++       + +   IA + ++  + + 
Sbjct: 481 DAWSVMSMHTNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQ 540

Query: 450 KGTIDDIDNLGNRRVRSVGEML-KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
                 +      +    G +   +        + +++         D   P   +    
Sbjct: 541 FEKTRKVSGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPIRNLIFML 600

Query: 509 VVSAVCEFFCS--SQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTH 565
               +                 +N        R    L     + R     E   ++  H
Sbjct: 601 GAEDIQTLGGKELYGPGCYTISINGTPTALTRRPKYFLNAFRRLRRMGRISEFVSIYINH 660

Query: 566 YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR---KVCDGKVTNDVVYLSAMEE 622
           +       T +G     +  + +         +E       +  D      V YL   EE
Sbjct: 661 HQHAVHVATDDGRICRPLIVVENGKSTVQTHHLEKLREGTMQFDDFLAQGLVEYLDVNEE 720

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            +  IA     +                        E    ++  P  ++   A LIP+ 
Sbjct: 721 NDSLIAIYEKDI-----------------------SETTTHLEIEPFTILGAVAGLIPYP 757

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            ++ S R    C M +QA+  + +    
Sbjct: 758 HHNQSPRNTYQCAMGKQAIGAIASNQFL 785


>gi|307343476|emb|CBJ18655.1| RNA polymerase B subunit [Micromonospora sp. GUI37]
          Length = 212

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 96/214 (44%), Positives = 125/214 (58%), Gaps = 38/214 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 29   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 88

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 89   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWNVEGDDADWKRALRSID---------- 137

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 138  -------------------AAEAEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 178

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              G++ L+DG +GEP   P+ VGYIY+LKLNH+V
Sbjct: 179  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHLV 212


>gi|262072859|dbj|BAI47739.1| RNA polymerase beta subunit [Bartonella sp. Nagano 20-1]
          Length = 275

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYR++
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ S A
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSRA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|103001310|gb|ABF71501.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 683

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 110/804 (13%), Positives = 227/804 (28%), Gaps = 145/804 (18%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ + + +  +              + +  + + +     +             
Sbjct: 1    FRMLFXKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAASSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L     +      E    +    + +V  +     +      ++      +  D
Sbjct: 117  CGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVGVHRD 176

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             +     V        I      + D  D   K          P    D+  +     N+
Sbjct: 177  PAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNCGNL 236

Query: 697  Q--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
               ++ +  L+ +               S     AK  G    V     V+  V+ + + 
Sbjct: 237  VLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEYVDAEEEE 286

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +   V     ++  R  Q               V+          T      ++   +  
Sbjct: 287  TVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPSMILGICA 346

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   + +  ++                         
Sbjct: 347  SIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------------- 382

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 383  -----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 437

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   + 
Sbjct: 438  SIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVA 493

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +  Q         
Sbjct: 494  PGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL------ 547

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                L+ VKV +   +  Q GDK A RHG KG +      EDMP
Sbjct: 548  --------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMP 593

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+++NP  +PSRM +  + E  L       G +                   
Sbjct: 594  FTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------- 636

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     ++++ +LR      
Sbjct: 637  ------------------------------------ATP-FTEVTVDSVSKLLREHGYQS 659

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYI 1254
             G  ++Y+G TG      V +G  
Sbjct: 660  RGFEVMYNGHTGRKLVAQVFLGPT 683


>gi|190148948|gb|ACE63449.1| RNA polymerase subunit B [Pseudonocardia autotrophica]
          Length = 270

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 154/277 (55%), Positives = 204/277 (73%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+SFARVN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSFARVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFIETPYRKV +G VT  + YL+A EE+   +AQAN+ L+EDGSF E+ V  R   GE  
Sbjct: 61  GFIETPYRKVVEGVVTTQIDYLTADEEDRFVVAQANARLNEDGSFAEDRVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +D+ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPAGVDYIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I +   EG  +        YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVARQAGVVEELCADYITVMDDEGQRE-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N+
Sbjct: 234 CNNQKPIVDEGARVEVGQVLADGPCTENGEMALGKNL 270


>gi|124490816|gb|ABN12778.1| RNA polymerase beta subunit [Bartonella sp. RN52BJ]
          Length = 266

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 187/262 (71%), Positives = 219/262 (83%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 2   RMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT +V+YLSAMEE   Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D SP
Sbjct: 122 KVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ 
Sbjct: 182 KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVS 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEG 750
           AKR+GIV+QVDA RIVIR+ E 
Sbjct: 242 AKRSGIVDQVDATRIVIRATED 263


>gi|118640681|gb|ABL09908.1| RNA polymerase beta subunit [Vibrio orientalis]
          Length = 290

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNG G +
Sbjct: 1   SLFESLFFSEERYDLSTVGRMKFNSSIEREDAQEQGTLDETDIIEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIQEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F EEL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFAEELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|190148952|gb|ACE63451.1| RNA polymerase subunit B [Pseudonocardia chloroethenivorans]
          Length = 266

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 150/273 (54%), Positives = 201/273 (73%), Gaps = 8/273 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL +FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLATFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV DG+VT  + YL+A EE+   IAQAN+ LD+DG F E+ V  R   G+  
Sbjct: 61  GFIQTPYRKVEDGRVTEQIDYLTADEEDRFVIAQANAPLDDDGHFQEDRVMVRRKGGDVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           LVP   +D+ID SP+Q+VS A +LIPF+E+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 LVPPTGVDYIDVSPRQMVSAATALIPFVEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I++ + +G           YRL KF+RSNQ +
Sbjct: 181 MELRAAVDAGDVVVADKAGVVEELCADYIMVMADDGTRQ-------TYRLHKFRRSNQGS 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           C+NQ+P+V+ G  V    ++ADGP T+ G++AL
Sbjct: 234 CINQKPIVEEGARVEVGQVLADGPCTEDGEMAL 266


>gi|118640683|gb|ABL09909.1| RNA polymerase beta subunit [Vibrio nigripulchritudo]
          Length = 290

 Score =  254 bits (648), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 226/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFAEERYDLSTVGRMKFNSSIEREDALEQGTLDELDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQANS 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFIIAQANSG 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F EELV  R  GE  L PR+++D++D +  QVVS+AASLIPFLE
Sbjct: 241 LTEEGTFVEELVTARQKGESGLHPRDQVDYMDVATNQVVSVAASLIPFLE 290


>gi|103001877|gb|ABF71525.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 714

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 119/834 (14%), Positives = 237/834 (28%), Gaps = 145/834 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +              + +  + + +    
Sbjct: 2    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSL 61

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 62   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 117

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     +      E    +    + +V  +     +   
Sbjct: 118  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNA 177

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 178  TKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPL 237

Query: 682  LENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
               D+  +     N+   ++ +  L+ +               S     AK  G    V 
Sbjct: 238  FVIDNDPKSTNCGNLVLTKEHINKLEDDRDLPA-------IIDSEE-KEAKFFGWDGLV- 288

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                V+  V+ + + +   V     ++  R  Q           +   V+          
Sbjct: 289  -NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTW 347

Query: 800  TDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T      ++   +  + +P+  +N          M  + +   + +  ++          
Sbjct: 348  THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM------- 398

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +             +       +   +  + AI  
Sbjct: 399  --------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAC 438

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L
Sbjct: 439  YSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKL 494

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                Y +L +   +  G           K+  +S D      R++          ++   
Sbjct: 495  KHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTE 554

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +  Q                             L+ VKV +   +  Q GDK A RHG
Sbjct: 555  NGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHG 594

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 595  QKGTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDAT 654

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S L    E    +                                     
Sbjct: 655  PFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------- 681

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                           +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 682  --------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVXXKIXA 714


>gi|52699806|gb|AAU86965.1| DNA-dependent RNA polymerase II second largest subunit [Coenogonium
            luteum]
          Length = 714

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 122/838 (14%), Positives = 231/838 (27%), Gaps = 151/838 (18%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEF 516
             G +R+   G ++   +R    ++ + + + +               + +  + + +   
Sbjct: 1    FGKKRLDLAGPLMAGLFRQLFSKLTKDVSKYLQKCVEGGKEFNLTLGVKSTTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               ++Q+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGEQKKAASSKAGVAQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +       V  +     +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRQMDVLEEYEPTRSPH 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D       V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDSGHLVSTVQSLRRRNMISSEVTLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  -FLENDDSNRVLMGC-NMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             F+ ++D      G   M ++ V  L+ +         E    +  G             
Sbjct: 237  LFVIDNDPKSSNKGSLVMTKEMVNKLEDDREIPADLDPEEKKKRHFGW--------NGLL 288

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            V+     + + E +        +    ++  R  Q       P       V+        
Sbjct: 289  VNGAVEFLDAEEEETVMIAMSPE---DLEISRMVQAGYAPPEPSADPNARVKAPVKAIQQ 345

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M  + +                  
Sbjct: 346  TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGV---------------- 389

Query: 857  GPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                            L N DE    +  +             +       +   +  + 
Sbjct: 390  ---------------FLTNFDERMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIV 434

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R  +++ +    +  E +E   +    E
Sbjct: 435  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYVEQEK---HLGMEVVEQFEKPLRSE 490

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + L    Y +L +   I  G           K+  + S+      R++           
Sbjct: 491  TLRLKHGTYDKLDDDGIIAPGIRVSGEDIIIGKTAPMRSNDEELGQRTKLHT-------- 542

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                   K    T+    E    +K+             L+ VKV     +  Q GDK A
Sbjct: 543  -------KRDASTALRSTESGLVDKVLI-----TTNAEGLKFVKVRTRTTKVPQIGDKFA 590

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  L       G +
Sbjct: 591  SRHGQKGTIGITYRQEDMPFSAQGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFE 650

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S L                           +     +G  +   VF
Sbjct: 651  GDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEIMYNGHTGKKLVAQVF 695

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                                    G  Y  +L HMV DK+ A
Sbjct: 696  ---------------------------------------FGPTYYQRLRHMVDDKIXA 714



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 90/637 (14%), Positives = 182/637 (28%), Gaps = 114/637 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        +K  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 10  GPLMAGLFRQLFSKLTKDVSKYLQKCVEGG--KEFNLTLGVKSTTITNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 67  GEQKKAASSKAGVAQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +          +          A   F     
Sbjct: 127 TPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRQMDVLEEYEPTRSPHATKVFVNGVW 186

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGG-VARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +S +   RR + +     + R     E        R   P       P  
Sbjct: 187 VGVHRDSGHLVSTVQSLRRRNMISSEVTLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 246

Query: 574 TSEGHNIG---LVSSLTSFARVNAYGFIETPYRK---VCDGKVTNDVVYLSAMEEENRYI 627
           +++G  +    +V+ L     + A    E   ++        V   V +L A EEE   I
Sbjct: 247 SNKGSLVMTKEMVNKLEDDREIPADLDPEEKKKRHFGWNGLLVNGAVEFLDAEEEETVMI 306

Query: 628 AQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           A +   L+                         +   ++     +  P  ++ + AS+IP
Sbjct: 307 AMSPEDLEISRMVQAGYAPPEPSADPNARVKAPVKAIQQTWTHCEIHPSMILGVCASIIP 366

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +++ S R      M +QA+ +                                     
Sbjct: 367 FPDHNQSPRNTYQSAMGKQAMGVFLTNF-------------------------------- 394

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                     +   + + +  Y       +     +  R                     
Sbjct: 395 ---------DERMDTMANILYYPQKPLATTRSMEYLKFR--------------------- 424

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E
Sbjct: 425 ---ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYVEQEKHLGMEVVE 481

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   +   +       +D+ GII  G  V+  DI++GK  P   +     ++    
Sbjct: 482 QFEKPLRSETLRLKHGTYDKLDDDGIIAPGIRVSGEDIIIGKTAPMRSNDEELGQRT--- 538

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               K    RD S  + S  SG V  V I       K
Sbjct: 539 ----KLHTKRDASTALRSTESGLVDKVLITTNAEGLK 571


>gi|118640657|gb|ABL09896.1| RNA polymerase beta subunit [Vibrio campbellii]
 gi|118640659|gb|ABL09897.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 290

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 169/290 (58%), Positives = 223/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|124502490|gb|ABN13626.1| RNA polymerase beta subunit [Bartonella sp. SD16HB]
          Length = 269

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 188/264 (71%), Positives = 221/264 (83%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG 
Sbjct: 1   KERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKII 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D 
Sbjct: 121 DGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGAA
Sbjct: 181 SPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGAA 240

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEG 750
           + AKR GIV+QVDA RIVIR+ E 
Sbjct: 241 VGAKRGGIVDQVDATRIVIRATED 264


>gi|52699770|gb|AAU86947.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            canadensis]
          Length = 713

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 122/832 (14%), Positives = 233/832 (28%), Gaps = 143/832 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G  R+   G +L N +R+   ++ + + +  +    +         + +  + + +    
Sbjct: 3    GKXRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSL 62

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 63   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 118

Query: 565  HYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L    +  V         +    + +V  +     +   
Sbjct: 119  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSQPIVDFMIQRNMEVLEEYEPQRSPNA 178

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 179  TKVFVNGVWVGVHRDPAHLVSTVLALRRANAISHEVSLVRDIRDREFKIFTDAGRVCRPL 238

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               ++  R     N+      + K E          +  K+        + GIVE VDA 
Sbjct: 239  FVINNDPRSTNCGNLVLTKPDIHKLEDDKDLPEDYEIDEKNPPGWNGLIKKGIVEYVDAE 298

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                       + +   V     ++  R  Q           +   V+          T 
Sbjct: 299  E----------EETVMIVMTPEDLEISRQLQAGYHLPDTSDDLIKRVKAPMNPTAHTWTH 348

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N                        ++       +G   
Sbjct: 349  CEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGVXL 390

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               D                +  +             +       +   +  + AI    
Sbjct: 391  TNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 496  GTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPF 655

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 656  TEVTVDSVSKLLR--EHGYQSRGFEVM--------------------------------- 680

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                         +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 681  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 713


>gi|300394768|gb|ADK11922.1| DNA-directed RNA polymerase II subunit two [Leucogyrophana mollusca]
          Length = 875

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 127/880 (14%), Positives = 247/880 (28%), Gaps = 148/880 (16%)

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                 +Y    + +  +      +  +  +         +I  L+     +  +DD D+ 
Sbjct: 128  RERRIRYAQEILQKEMLPHVSMAEGSESKK---AYFFGYMIHRLLLAALERRELDDRDHF 184

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ R +    +              +  + + + +    
Sbjct: 185  GKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL 244

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 245  ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 300

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +         EEN
Sbjct: 301  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EEN 352

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 353  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLY 409

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +   Q + L K    ++  G      +      + K   I         
Sbjct: 410  TDAGRVCRPLFIVENQQLALQKKHVKWLNQGFRDDDGEEYKWEQLVKGGIIELLDAEEEE 469

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +       D   S +    +            +    +K G            PS  LG
Sbjct: 470  TVMISMTPEDLENSRMQSAGIDPHSNDAD---YDPAARLKAGINAHTWTHCEIHPSMILG 526

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 527  -------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 561

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             +               +  +             +       +   +  + AI      +
Sbjct: 562  LVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 610

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 611  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKI 669

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 670  EDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 729

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 730  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 769

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D ++NP  +P RM +G + E  L      +G +  +         
Sbjct: 770  YRQEDMPFTAEGIVPDXIINPHAIPXRMTIGHLVECLLSKVATLIGNEGDATPFT----- 824

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 825  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 848

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    G +       G      V +G  Y  +L HMV
Sbjct: 849  ------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 875



 Score =  138 bits (348), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 94/759 (12%), Positives = 213/759 (28%), Gaps = 108/759 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R+D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +V+
Sbjct: 58  YIRVD----IPIWVVFRALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVA 113

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNG 315
              +        +   +++     + L+++ +  + +            G  +   ++  
Sbjct: 114 LDFIGNRGTTTGLSRERRIRYAQ-EILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAA 172

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K  +   A+ 
Sbjct: 173 LERRELDDRDHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAV- 231

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 232 -------KHQTITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 284

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +      ++KN   +  + +       I  +
Sbjct: 285 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACG---LVKNLALMSCISVGSYSAPVIEFL 341

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +      NA         F     +    +  N +  I   RR   +         
Sbjct: 342 EEWGLE-SLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRD 400

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + L      +            Y K         
Sbjct: 401 IRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNQGFRDDDGEEY-KWEQLVKGGI 459

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDA 666
           +  L A EEE   I+     L+     +  +       +          +        + 
Sbjct: 460 IELLDAEEEETVMISMTPEDLENSRMQSAGIDPHSNDADYDPAARLKAGINAHTWTHCEI 519

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 520 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 563

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 564 -------------------------RMDTMANILYYPQKPLATTRSMEYLKFR------- 591

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F SI+   
Sbjct: 592 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRS 634

Query: 847 FEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E            +       I++ G+I  G  V+  DI++GK  P 
Sbjct: 635 YMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI 694

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   E+L +        DV        +G+   V+
Sbjct: 695 ----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 729


>gi|262117900|dbj|BAI47975.1| RNA polymerase beta subunit [Bartonella sp. BR1-1]
 gi|262117904|dbj|BAI47977.1| RNA polymerase beta subunit [Bartonella sp. BR11-1]
          Length = 275

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 229/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P RK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPCRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS LD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSPLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|190148940|gb|ACE63445.1| RNA polymerase subunit B [Pseudonocardia ammonioxydans]
          Length = 269

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 150/276 (54%), Positives = 202/276 (73%), Gaps = 8/276 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+SFARVN +
Sbjct: 1   THKRRLSALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSSFARVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFIETPYRKV +G VT  + YL+A EE+   +AQAN+ L++DGSF E+ +  R   GE  
Sbjct: 61  GFIETPYRKVTEGVVTEQIDYLTADEEDRFVVAQANAVLNDDGSFAEDRILVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    ++++D SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPAGVEYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I +   EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVAEQAGVVEELCADYITVMDDEGQRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N
Sbjct: 234 CNNQKPIVDEGARVEVGQVLADGPCTENGEMALGKN 269


>gi|300394670|gb|ADK11873.1| DNA-directed RNA polymerase II subunit two [Anomoloma albolutescens]
          Length = 686

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 128/815 (15%), Positives = 242/815 (29%), Gaps = 145/815 (17%)

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAV 513
             D+ G +R+   G +L N +R+   ++ R +    +              +  + + + +
Sbjct: 1    DDHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGL 60

Query: 514  CEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
                 +               +SQ+       S ++H RR +      + R     + R 
Sbjct: 61   KYSLATGNWGDQTKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQ 116

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +        
Sbjct: 117  LHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL------- 169

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             EEN + +   + +  +G +       R     +   ++     D SP+  V        
Sbjct: 170  -EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKE 225

Query: 681  FLENDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
                 D+ RV     +   Q + L K    ++  G      +      + K +GI+E +D
Sbjct: 226  LRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNQGYRDDDQEEFKWEQLVK-SGIIELLD 284

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A       +    +   +       +    ++ +     R  +K G            PS
Sbjct: 285  AEEEETVMISMTPEDLENSRLQQSGVDPHANDGDFDPAAR--LKAGINAHTWTHCEIHPS 342

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N                        ++       +G  
Sbjct: 343  MILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIY 377

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I               +  +             +       +   +  + AI   
Sbjct: 378  LTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCY 426

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD         
Sbjct: 427  SGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPNRDNTLRMKHGT 485

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G          + +  +  D      R++          ++     + 
Sbjct: 486  YDKIREDGLIAPGTGVTGEDIILENTAPIPPDSEELGQRTRTHSRRDVSTPLKSTENGIV 545

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q GDK A RHG KG 
Sbjct: 546  DQVLI--------------------TTNHEGQKFVKVRVRSTRISQIGDKFASRHGQKGT 585

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +        
Sbjct: 586  IGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------ 639

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                           +TP F     E++
Sbjct: 640  -----------------------------------------------ATP-FTDLTVESV 651

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            ++ LR       G  ++Y G TG      V +G  
Sbjct: 652  STFLRQKGYQSRGLEVMYHGHTGRKLQAQVYLGPT 686



 Score =  113 bits (282), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 84/622 (13%), Positives = 174/622 (27%), Gaps = 100/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 13  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 69

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 70  GDQTKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 129

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 130 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 189

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 190 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 249

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         +  + K      +  +  L A EEE   I+     L+       
Sbjct: 250 QKKHVKWLNQGYRDDDQEEF-KWEQLVKSGIIELLDAEEEETVMISMTPEDLENSRLQQS 308

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 309 GVDPHANDGDFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLI-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPNRDNTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I E G+I  G  V   DI++     +  +P+ P+ + L       +   RD S  
Sbjct: 484 GTYDKIREDGLIAPGTGVTGEDIIL-----ENTAPIPPDSEELGQRTRTHSR--RDVSTP 536

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  +G V  V I   H   K
Sbjct: 537 LKSTENGIVDQVLITTNHEGQK 558


>gi|124490806|gb|ABN12773.1| RNA polymerase beta subunit [Bartonella sp. RN2BJ]
          Length = 270

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 187/262 (71%), Positives = 220/262 (83%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 2   RMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SP
Sbjct: 122 KVTKEVIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ 
Sbjct: 182 KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVS 241

Query: 729 AKRAGIVEQVDAIRIVIRSVEG 750
           AKR+GIV+QVDA RIVIR+ E 
Sbjct: 242 AKRSGIVDQVDATRIVIRATED 263


>gi|118640667|gb|ABL09901.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 290

 Score =  254 bits (648), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|52699768|gb|AAU86946.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            bullata]
          Length = 727

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 121/836 (14%), Positives = 238/836 (28%), Gaps = 135/836 (16%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +    +         + +  + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     ++     E    +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRSPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF 681
               ++      + +D       V     G  I      + D  D   K          P 
Sbjct: 177  TKVFVNGVWVGVHQDPVHLVNTVQAVRRGHMISHEVSLVRDIRDREFKVFTDAGRVCRPL 236

Query: 682  LENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMES-VVAKSSGAAIVAKRAGIVEQV 738
               D+  + L   ++   ++ +  L+          E     + +   +           
Sbjct: 237  FVIDNDPKSLKCGSLVLTKEHINKLEDYKDLTAEMQERIREKEEAEKGVKEDGTPYGWNG 296

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
               R V+  V+ + + +   V     ++  R  Q       P              +D  
Sbjct: 297  LIKRGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYRLPEP--------------SDTS 342

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKL 856
               +  +    N       W       SM+  I   ++            ++       +
Sbjct: 343  EALMKRVKAPLNPTAH--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAM 400

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G      D                +  +             +       +   +  + AI
Sbjct: 401  GVYLTNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 449

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + +
Sbjct: 450  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTL 505

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  ++ D      R++          ++ 
Sbjct: 506  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRS 565

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                             LR VKV +   +  Q GDK A R
Sbjct: 566  TENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASR 605

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 606  HGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 665

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L    E    +                                   
Sbjct: 666  ATPFTEITVDSVSKLLR--EHGYQSRGFEVM----------------------------- 694

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 695  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 727


>gi|118640661|gb|ABL09898.1| RNA polymerase beta subunit [Vibrio harveyi]
 gi|118640663|gb|ABL09899.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 290

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 169/290 (58%), Positives = 223/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|88601070|gb|ABD46531.1| RNA polymerase II second largest subunit [Punctularia strigosozonata]
          Length = 701

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 123/819 (15%), Positives = 235/819 (28%), Gaps = 141/819 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + +    + S            +    + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKSIETGKQFNLSLAVKHNTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L+  A ++  G I  P  +  +      +   +
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLSLMATIS-VGSISAPVIEFLEEWGLESLE-EN 174

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSI 674
            A           N            LV      R             D  +   +     
Sbjct: 175  AHSSTPCTKVFVNGVWMGVHRDPLNLVKTIKKLRRKDNISPETSVVRDIRERELRISTDA 234

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKA--EAPFVGTGMESVVAKSSGAAIVAK-R 731
                 P    ++   VL   ++++      +   +     T  E+   +          +
Sbjct: 235  GRVCRPLFIVENQQLVLKKSHIEKLHKHNTEPVLDDAGAPTFDENGKQRFFQYQFDELVK 294

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
             G++E +DA       +    +   +     +     + + +     R  +K G +    
Sbjct: 295  EGVIEYLDAEEEETVMICMTPEDLENARLKQQGHDPSQDDPDFDPAAR--IKTGTQAHLW 352

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  PS  LG       +  + +P+  +N                        ++   
Sbjct: 353  THCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAM 387

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                +G       +               +  +             +       +   + 
Sbjct: 388  GKQAMGIYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQN 436

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    ++ R  +D  ++S   + E+ E   RD 
Sbjct: 437  AIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSMYFRSYMDMEKKSGIQQLEEFEKPTRDT 495

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                     +       I  G N         K+  +  D      R++          +
Sbjct: 496  TLRMKHGTYDKLEDDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRGHTRRDVSTPL 555

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +   +    Q                              + VKV +   R  Q GDK A
Sbjct: 556  KSTEQGTVDQVLI--------------------TTNSEGQKFVKVRIRSTRIPQIGDKFA 595

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +
Sbjct: 596  SRHGQKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNE 655

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                                   +TP F
Sbjct: 656  GD-----------------------------------------------------ATP-F 661

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                 E+++  LR       G  ++Y G TG      + 
Sbjct: 662  TDLTVESVSQFLRQRGYQSRGLEVMYHGHTGRKLQAQIY 700


>gi|312086795|ref|XP_003145218.1| RNA polymerase III 128kD subunit-PA [Loa loa]
 gi|307759618|gb|EFO18852.1| RNA polymerase III 128kD subunit-PA [Loa loa]
          Length = 1040

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 150/1029 (14%), Positives = 307/1029 (29%), Gaps = 176/1029 (17%)

Query: 360  NTLVTDKNKDRKDALLDI--YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
                + +   ++ AL  I     MR             F      +   +   +  +   
Sbjct: 164  EECASHQIVTQEGALQYIASKVKMRKFGP---------FASGTSSTLPREHEAIDFLSNL 214

Query: 418  MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
            M  ++  PD    ++   +  +I+ L+    G    DD D  GN+R+   G +L   +  
Sbjct: 215  MIAHVPCPDGNMKMKAIYLGLMIRRLMQAEVGDTECDDRDFYGNKRLELAGSLLALLFED 274

Query: 478  GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
               R    +K        D+ + + L     +V  + +   ++ L       N   +   
Sbjct: 275  VFKRFNSELKRI-----ADNSLGKTLAAPLDIVKHMRQDLITNALVDALATGNWTIKRFK 329

Query: 538  TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
              R               V  R  + +  G +    ++         S     + + +G 
Sbjct: 330  MERQGV----------TQVLSRLSYISVLGMMTRINST--FEKTRKVSGPRSLQPSQWGM 377

Query: 598  IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            +                      E E+  + +  + +    + ++E    R      +  
Sbjct: 378  LCPS----------------DTPEGESCGLVKNLALISHITTDSDEEPVIRLLYNSGVED 421

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
             + + F          +  + +      D  R++      R+    L  E   V T    
Sbjct: 422  VKSLHFSAIHSPVYHIVFLNGVIVGLTIDPQRIVSTIRAVRRH--GLLNEFVSVST---- 475

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                       A+R+  +            +  +  P  +   I  L K  R  +     
Sbjct: 476  ---------NAAQRSVYIASDGGRLCRPYIIVKNGVPQVTQEHIEELKKGCRIFE----- 521

Query: 778  QRPLVKVGDEVRRNDI-IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                    D V    I   D    +   +A+  N +              + +   ++  
Sbjct: 522  --------DFVDDGLIEYLDVNEMNDASIAVYENQIKPNTTHLEIEPFTLLGVCAGLIPY 573

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                      ++       +G          +     K ID   ++ +        +   
Sbjct: 574  PHHNQSPRNTYQCAMGKQAMGT---------IGYNQQKRIDS--LMYLLVYPQRPLVKTK 622

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             I       +   +  + A+      D+ D  +   + +        ++ +H      + 
Sbjct: 623  TIEFCNFEKLPAGQNAVIAVMSYSGYDIEDALVLNKASLDRGYGRCLVY-KHAKATARKY 681

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
             +   +++     +    + I    +  +   +  G    S      K   + S      
Sbjct: 682  PNQTFDRLMGPTVEATTRKPIYKHQVLDQEGIVYVGACIHSKQVMINKHMPVVSTEAGAT 741

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
              S      V   +V+         Y+    +  +   +  E++    +       ++KV
Sbjct: 742  TSSNNDGTNVSSHEVE---------YKDVSVVYRNPVPSYAERVLLTYNEDDA--HLIKV 790

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R  + GDK + RHG KG+   I   E           D+  N LG    M    I
Sbjct: 791  LLRQTRRPELGDKFSSRHGQKGVCGLIAQQE-----------DMPFNDLG----MCPDMI 835

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
               H                                     +     K+ +        +
Sbjct: 836  MNPH----------------------------------GYPSRMTVGKLMELLSGKNAVL 861

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            + ++  G       F G   + +   L     +  G+ +L  G+TG+     +  G IY 
Sbjct: 862  SGKFHYGT-----AFGGDQVDVVCEELAARGFNYLGKDMLTSGITGQQLCAYIYFGPIYY 916

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             KL HMV DK++AR+ G  +++T+QP  G++  GG RLGEME  C+ AYGA+ +L E L 
Sbjct: 917  QKLKHMVLDKMHARARGPRAVLTRQPTEGRARDGGLRLGEMERDCLIAYGASMLLMERLM 976

Query: 1317 IKSD----DVVG--------------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            + SD    DV                R+    + +          P +  +L +E+Q++ 
Sbjct: 977  VSSDEFKVDVCSQCGLIGYKGWCQMCRSSRTMATIK--------IPYACKLLFQELQSMN 1028

Query: 1359 LSIDLENSR 1367
            +   +  S+
Sbjct: 1029 IVPKISLSK 1037



 Score =  139 bits (350), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 120/885 (13%), Positives = 258/885 (29%), Gaps = 165/885 (18%)

Query: 96  LTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT---------------- 139
           +TY+ P+ + +             +  + +    + +G +P+M                 
Sbjct: 1   MTYSAPISVDIEYT----------RGSQRVLRNGLVIGKMPVMLRSSKCVLKNMNESELA 50

Query: 140 --------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD---Q 188
                     G F+I+G +++V+ Q   S       ++     + K    C I+     +
Sbjct: 51  HVQECPYDPGGYFIIRGSEKVVLIQEQLS------KNRIMIGRNSKKELQCEILSSTQER 104

Query: 189 GLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWC 246
                     K   +VR ++    VPV     A+G +S+ +I+S    +  +        
Sbjct: 105 KSK-TYIASKKQRYYVRHNQLSDDVPVAIVFKAMGFESDHDIVSAVGLEEKFVAAMAPSI 163

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQV--IESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
              ++  ++        +       +     SG   T        +     +     C  
Sbjct: 164 EECASHQIVTQEGALQYIASKVKMRKFGPFASGTSSTLPREHEAIDFLSNLMIAHVPCPD 223

Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD-----IPILYVDSVNNNAYIR 359
           G    + I  G      ++A     E    + + ++  +     + +L+ D         
Sbjct: 224 GNMKMKAIYLGLMIRRLMQAEVGDTECDDRDFYGNKRLELAGSLLALLFEDVFKRFNSEL 283

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
             +  +       A LDI + MR  D+ T ++ +++    +    ++ +   G  ++  R
Sbjct: 284 KRIADNSLGKTLAAPLDIVKHMRQ-DLITNALVDALATGNWTI-KRFKMERQGVTQVLSR 341

Query: 420 LNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           L+  +   +        E    +        +  G +   D         V  +    + 
Sbjct: 342 LSYISVLGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDTPEGESCGLVKNLALISHI 401

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
                 E  I+   +S   D           PV   V  F     +    +    +S I 
Sbjct: 402 TTDSDEEPVIRLLYNSGVEDVKSLHFSAIHSPVYHIV--FLNGVIVGLTIDPQRIVSTIR 459

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
             RR   L +            R V+  +  GR+C         I + + +    +    
Sbjct: 460 AVRRHGLLNE--FVSVSTNAAQRSVYIASDGGRLC------RPYIIVKNGVPQVTQ-EHI 510

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
             ++   R   D      + YL   E  +  IA   + +  +                  
Sbjct: 511 EELKKGCRIFEDFVDDGLIEYLDVNEMNDASIAVYENQIKPN------------------ 552

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                   ++  P  ++ + A LIP+  ++ S R    C M +QA+  +         G 
Sbjct: 553 -----TTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GY 598

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                  S                                                    
Sbjct: 599 NQQKRIDS----------------------------------------------LMYLLV 612

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             QRPLVK                 +   L  G+N ++A M + GY+ ED++++++  + 
Sbjct: 613 YPQRPLVK----------TKTIEFCNFEKLPAGQNAVIAVMSYSGYDIEDALVLNKASLD 662

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                 +  +  +  AR       +                  + +D+ GI+ VGA ++ 
Sbjct: 663 RGYGRCLVYKHAKATARKYPNQTFDRLMGPTVEATTRKPIYKHQVLDQEGIVYVGACIHS 722

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV--RDTSLRVPS 933
             +++ K  P   +                + +V  +D S+   +
Sbjct: 723 KQVMINKHMPVVSTEAGATTSSNNDGTNVSSHEVEYKDVSVVYRN 767


>gi|212373953|emb|CAP09903.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35702]
 gi|212373991|emb|CAP09922.1| DNA-directed RNA polymerase beta subunit [Pseudomonas sp. R-35721]
          Length = 253

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 147/253 (58%), Positives = 197/253 (77%)

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+
Sbjct: 1   RAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTD 60

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVV
Sbjct: 61  EIVFLSAIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVV 120

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
           S+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R 
Sbjct: 121 SVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRG 180

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
           G+++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV+ GD V+R+D
Sbjct: 181 GVIDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVRKGDRVQRSD 240

Query: 793 IIADGPSTDLGDL 805
           I+ADGPSTD+G+L
Sbjct: 241 IMADGPSTDMGEL 253


>gi|103001574|gb|ABF71513.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            gobiense]
          Length = 709

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 117/829 (14%), Positives = 235/829 (28%), Gaps = 145/829 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + + +  +    +         + +  + + +   
Sbjct: 2    FGKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYS 61

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 62   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 117

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +  
Sbjct: 118  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPN 177

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 178  ATKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 237

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                D+  +     N+   ++ +  L+ +               S     AK  G    V
Sbjct: 238  LFVIDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------NMDSEE-KEAKFFGWDGLV 289

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 V+  V+ + + +   V     ++  R  Q           +   V+         
Sbjct: 290  --NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDLNKRVKAPMNPTAHT 347

Query: 799  STDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             T      ++   +  + +P+  +N          M  + +   + +  ++         
Sbjct: 348  WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQSMG--VFLTNYDQRM------ 399

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                   +  +             +       +   +  + AI 
Sbjct: 400  ---------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 438

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 439  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 494

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  ++ D      R++          ++  
Sbjct: 495  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRST 554

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             LR VKV +   +  Q GDK A RH
Sbjct: 555  ENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRH 594

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 595  GQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 654

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 655  TPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------ 682

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                            +G +    G         V +G  Y  +L HMV
Sbjct: 683  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 709


>gi|110666973|gb|ABG81887.1| RNA polymerase II second largest subunit [Physcia aipolia]
          Length = 718

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 122/837 (14%), Positives = 240/837 (28%), Gaps = 142/837 (16%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ + +++ + S        +    + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLAGLFRTLFNKLTKDVEKYLKSCIELNKEFILTLGVKSATLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V+     +   P+      +   +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCNVSVGTPSDGIVPFLLQRQMESLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
             +A      ++      +    +     V        +      I D  +   + +    
Sbjct: 177  HTAPNATKIFVNGVWVGVHRHPAHLVNAVQSLRRKHVLEPEVSLIRDIREREFRILTDQG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAG 733
              L P F+ ++D      G  +  +       E   V   M+  V +            G
Sbjct: 237  RVLRPLFVVDNDPKSNRCGDLVFNKEHSQKLDEDDAVPYDMDKEVREKLTFGWNGLIDEG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE VDA       +            +       + + +   N+R    +         
Sbjct: 297  VVEYVDAEEEETVMIVMTPQDLAMSRQLRAGYTLDQPDPDE-PNRRVTAPLNPTAHTWTH 355

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   + +  ++     
Sbjct: 356  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRMET 406

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                          +             +       +   +  +
Sbjct: 407  MS---------------------------HILYYPQKPLATTRSMEYLKFRELPAGQNAI 439

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ ++   +    +E   +    
Sbjct: 440  VAIACYSGYNQGDSVIMNQSSIDRGLF-RSLFYRSYTDQEKK---IGAHVVEAFEKPMRS 495

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + +      Y +L +   I+ G           K+  ++ D      R++          
Sbjct: 496  DTLRTKNGTYDKLDDDGLIVPGARVSGEDIIIGKTAPIAPDAEEMGQRTKLHTKRDASTP 555

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            ++     L  Q                             L+ VKV +   +  Q GDK 
Sbjct: 556  LRSTESGLVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKF 595

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 596  ASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 655

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          +S L                                          
Sbjct: 656  EGDATPFTEVTVDSVSRLLHEHGYQSRGFEIM---------------------------- 687

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                +G +    G         V +G  Y  +L HMV DK+
Sbjct: 688  -------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 718


>gi|297595846|gb|ADI48232.1| RNA polymerase beta subunit [Erwinia sp. CECT 5264]
          Length = 249

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 153/249 (61%), Positives = 197/249 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V +G VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R++
Sbjct: 121 PYRRVREGVVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVA 240

Query: 721 KSSGAAIVA 729
             SG   VA
Sbjct: 241 VDSGVTAVA 249


>gi|52699794|gb|AAU86959.1| DNA-dependent RNA polymerase II second largest subunit [Coenogonium
            leprieurii]
          Length = 716

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 121/840 (14%), Positives = 231/840 (27%), Gaps = 151/840 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVC 514
            D  G +R+   G ++   +R    ++ + + + +               + +  + + + 
Sbjct: 1    DXFGKKRLDLAGPLMAGLFRQLFSKLTKDVSKYLQKCVEGGKEFNLTLGVKSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               ++Q+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAASSKAGVAQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +       V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRQMDVLEEYEPTRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D       V        I      + D  D   K         
Sbjct: 177  PHATKVFVNGVWVGVHRDPGHLVSTVQSLRRRNMISSEVTLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGC-NMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIV 735
             P F+ ++D      G   M ++ V  L+ +         E    +  G           
Sbjct: 237  RPLFVIDNDPKSPNKGSLVMTKEMVNKLEDDRELPADLEPEERKKRHFGW--------NG 288

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              V+     + + E +        D    ++  R  Q       P       V+      
Sbjct: 289  LLVNGAVEFLDAEEEETVMIAMTPD---DLEISRLVQAGYALPEPSSDPNARVKAPVKAI 345

Query: 796  DGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T      ++   +  + +P+  +N          M  + +                
Sbjct: 346  QQTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGV-------------- 391

Query: 855  KLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                              L N DE    +  +             +       +   +  
Sbjct: 392  -----------------FLTNFDERMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNA 434

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R  +++ +    +  E +E   +   
Sbjct: 435  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYVEQEK---HLGMEVVEQFEKPLR 490

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             E + L    Y +L +   I  G           K+  + ++      R++         
Sbjct: 491  SETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPMRTNDEELGQRTKLHT------ 544

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
                     K    T+    E+   +K+             L+ VKV     +  Q GDK
Sbjct: 545  ---------KRDASTALRSTENGIIDKVLI-----TTNAEGLKFVKVRTRTTKVPQIGDK 590

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  L       G
Sbjct: 591  FASRHGQKGTIGITYRQEDMPFSAQGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRG 650

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                                         
Sbjct: 651  FEGDATPFTEVTVDSVSRLLREHGYQSRGFEIM--------------------------- 683

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                 +G +    G         +  G  Y  +L HMV  K+ A
Sbjct: 684  --------------------YNGHT----GR---KLVAQIFFGPTYYQRLRHMVDXKIXA 716



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 89/642 (13%), Positives = 176/642 (27%), Gaps = 124/642 (19%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        +K  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 12  GPLMAGLFRQLFSKLTKDVSKYLQKCVEGG--KEFNLTLGVKSTTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GEQKKAASSKAGVAQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +          +          A   F     
Sbjct: 129 TPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRQMDVLEEYEPTRSPHATKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR + +                +         P    +     
Sbjct: 189 VGVHRDPGHLVSTVQSLRRRNMISSEVTLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 248

Query: 582 LVSSLTSFA--RVNA-------YGFIETPYRK-----VCDGKVTNDVVYLSAMEEENRYI 627
                       VN           +E   RK          V   V +L A EEE   I
Sbjct: 249 PNKGSLVMTKEMVNKLEDDRELPADLEPEERKKRHFGWNGLLVNGAVEFLDAEEEETVMI 308

Query: 628 A------------QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           A            QA  +L E  S     V        +   ++     +  P  ++ + 
Sbjct: 309 AMTPDDLEISRLVQAGYALPEPSSDPNARVKA-----PVKAIQQTWTHCEIHPSMILGVC 363

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +                                
Sbjct: 364 ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNF--------------------------- 396

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                          +   + + +  Y       +     +  R                
Sbjct: 397 --------------DERMDTMANILYYPQKPLATTRSMEYLKFR---------------- 426

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 427 --------ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYVEQEKHLG 478

Query: 856 LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +   E        +   +     + +D+ GII  G  V+  DI++GK  P   +     +
Sbjct: 479 MEVVEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPMRTNDEELGQ 538

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +        K    RD S  + S  +G +  V I       K
Sbjct: 539 RT-------KLHTKRDASTALRSTENGIIDKVLITTNAEGLK 573


>gi|110704333|gb|ABG88065.1| RNA polymerase II second largest subunit [Microstroma juglandis]
          Length = 716

 Score =  253 bits (647), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 123/831 (14%), Positives = 241/831 (29%), Gaps = 138/831 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ R I   +     +         + +  + + + 
Sbjct: 1    DHFGKKRLDLGGPLLAGLFRMLFRKLTRDIYRHLQKCVEEQREFHLTAAVKSSTITNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL--SA 619
            H TH+G +CPAET EG   GLV +L+  + ++  G    P  +  D    +++V +  SA
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMSLIS-VGSPSAPLHQFLDEFGLDNLVDMQVSA 175

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             +    ++    +    + S   E +      ++I      +  +     ++ + +  ++
Sbjct: 176  AKATKVFVNGVWAGTHNEPSALVETLRDLRRKDDITTEVSVVHDVREKELRLYTDSGRVL 235

Query: 680  PFLENDDSN--RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS---GAAIVAKRAGI 734
              L   D    R+L+     +      K       T ME    +      + +VA+    
Sbjct: 236  RPLFIVDPKSMRLLITREHIQWLNADEKPGGMLDETNMEPDEDERERFQWSQLVAEGVIE 295

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV-RRNDI 793
                D    V+ S+       +  +                  QR  +  G+        
Sbjct: 296  YLDADEEETVMISMSPQDLAKSRRL------------------QRTGLITGEANGLDGLP 337

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
             A                     P         + +   ++            ++     
Sbjct: 338  DASARLVSSRYYEPSTWTHCEIHPAM------ILGVCASIIPFPDHNQSPRNTYQSAMGK 391

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              +G       +               +  +             +       +   +  +
Sbjct: 392  QAMGVYLTNYQMRM-----------DTMANILYYPQKPLATTRSMEHLNFRELPAGQNAI 440

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    ++ R   D  ++     +E+ E   RD   
Sbjct: 441  VAILCYSGYNQEDSVILNQSSIDRGLF-RSLYYRTYTDFEKKVGFTLQEEFEKPVRDTAI 499

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +       +  G           K+  L  D      RS+          ++ 
Sbjct: 500  RLKHGTYDKIDADGLVAPGTRVSGEDIIIGKTAPLPPDSEELGLRSKTHTKRDVSTPLKS 559

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q   S                          + VKV V   R  Q+GDK A R
Sbjct: 560  TESGIVDQVLVS--------------------TNQEGSKFVKVRVRSTRVPQTGDKFASR 599

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  
Sbjct: 600  HGQKGTIGITYRQEDMPFTIEGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGD 659

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S + + L                            K G+ +       
Sbjct: 660  ATPFTDLTVEAVSSILAKL-------------------------GYQKRGLEIM------ 688

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                             +G +       G      V +G  Y  +L HMV 
Sbjct: 689  ----------------YNGHT-------GRKLQAQVYLGPTYYQRLKHMVD 716



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 87/623 (13%), Positives = 172/623 (27%), Gaps = 119/623 (19%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR ++    +   F +  ++ +    +  +Y L   G      +         + + +
Sbjct: 29  DIYRHLQKCVEEQREFHLTAAVKSSTITNGLRYSL-ATGNWGDQKKFMQAKAGVSQVLNR 87

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 88  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSLI 147

Query: 489 RISSVDIDSVMPQDLINAKPVVSA-------VCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S         D      +V            F          E    +  +   RR 
Sbjct: 148 SVGSPSAPLHQFLDEFGLDNLVDMQVSAAKATKVFVNGVWAGTHNEPSALVETLRDLRRK 207

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI--- 598
             +            +   ++      + P    +  ++ L+ +      +NA       
Sbjct: 208 DDITTEVSVVHDVREKELRLYTDSGRVLRPLFIVDPKSMRLLITREHIQWLNADEKPGGM 267

Query: 599 -----------ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF- 646
                      E    +         + YL A EEE   I+ +   L +        +  
Sbjct: 268 LDETNMEPDEDERERFQWSQLVAEGVIEYLDADEEETVMISMSPQDLAKSRRLQRTGLIT 327

Query: 647 ------------CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                         +  P  ++ + AS+IPF +++ S R     
Sbjct: 328 GEANGLDGLPDASARLVSSRYYEPSTWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQS 387

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 388 AMGKQAMGVYLTNYQM-----------------------------------------RMD 406

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +N R                        +L  G+N +VA
Sbjct: 407 TMANILYYPQKPLATTRSMEHLNFR------------------------ELPAGQNAIVA 442

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVS 869
            + + GYN EDS+++++  +   +F S++   +    +      +E            + 
Sbjct: 443 ILCYSGYNQEDSVILNQSSIDRGLFRSLYYRTYTDFEKKVGFTLQEEFEKPVRDTAIRLK 502

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 ID  G++  G  V+  DI++GK  P    P   EE  LR+    K    RD S 
Sbjct: 503 HGTYDKIDADGLVAPGTRVSGEDIIIGKTAP---LPPDSEELGLRS----KTHTKRDVST 555

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S  SG V  V +       K
Sbjct: 556 PLKSTESGIVDQVLVSTNQEGSK 578


>gi|126009543|gb|ABK63973.2| RNA polymerase beta subunit [Bartonella tamiae]
          Length = 275

 Score =  253 bits (646), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 199/276 (72%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SS++ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT DVVYLSAMEE   Y+AQANSSLD +  FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTDVVYLSAMEESKHYVAQANSSLDAEARFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           AI A+RAGIV+QVDA RIVI + E  LDP+ SGVDI
Sbjct: 241 AIGARRAGIVDQVDATRIVIHATED-LDPTKSGVDI 275


>gi|103484131|dbj|BAE94838.1| RNA polymerase beta subunit [Bartonella sp. Fuji 34-1]
          Length = 275

 Score =  253 bits (646), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 196/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+ QANSSLD +G F EE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTKEVIYLSAMEEAKHYVPQANSSLDNEGRFIEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+G+V+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGVVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699818|gb|AAU86971.1| DNA-dependent RNA polymerase II second largest subunit [Gyalecta
            ulmi]
          Length = 711

 Score =  253 bits (646), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 115/836 (13%), Positives = 230/836 (27%), Gaps = 153/836 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++   +R+   ++ + + +  +              + +  + + +     +
Sbjct: 1    KRLDLAGPLMAGLFRMLFNKLTKDVYKYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLAT 60

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   GNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +           
Sbjct: 117  GLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRNPHSTK 176

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      I D  D   K          P F+
Sbjct: 177  VFVNGVWVGVHRDPAHLVSTVQSLRRQNMISSEVSLIRDIRDREFKIFTDAGRVCRPLFV 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM---ESVVAKSSGAAIVAKRAGIVEQVD 739
              +D      G  +  + +     +   +   M   E        A ++A          
Sbjct: 237  IENDKKSPNKGALVLTKELVRKLEDDRDLPPDMDPDEKKEKYFGWAGLLA---------- 286

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                 +  ++ + + +         +   R  Q       P       V+          
Sbjct: 287  --NGAVEFLDAEEEETVMIAMTPEDLDISRQVQAGFAPPEPSSDPNARVKAPVSANQHTW 344

Query: 800  TDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            T      ++   +  + +P+  +N          M  + +                    
Sbjct: 345  THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV------------------ 386

Query: 859  EEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                          L N DE    +  +             +       +   +  + AI
Sbjct: 387  -------------FLTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 433

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R  +++ +R        +E   +    E +
Sbjct: 434  ACYSGYNQEDSVIMSQSSIDRGLF-RSLFYRSYVEQEKRVGM---SLVEQFEKPLRSETL 489

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             +    Y +L +   I  G           K+  ++ D      R++          ++ 
Sbjct: 490  RVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRT 549

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  +                             L+ VKV +   +  Q GDK A R
Sbjct: 550  TESGIVDRVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASR 589

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 590  HGQKGTIGITYRQEDMPFSREGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 649

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L                                             
Sbjct: 650  ATPFTEVTVDSVSRLLREHGYQSRGFEMM------------------------------- 678

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                             +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 679  ----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 711



 Score = 68.6 bits (166), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 48/390 (12%), Positives = 99/390 (25%), Gaps = 39/390 (10%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        NK  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 7   GPLMAGLFRMLFNKLTKDVYKYLQKCVESG--KEFNLTLGVKSTTLTNGLKYSL-ATGNW 63

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 64  GDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 123

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +      N + +          +   F     
Sbjct: 124 TPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRNPHSTKVFVNGVW 183

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR + +                +         P    E     
Sbjct: 184 VGVHRDPAHLVSTVQSLRRQNMISSEVSLIRDIRDREFKIFTDAGRVCRPLFVIENDKKS 243

Query: 582 LVSSLTSFAR---------------VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                    +               ++     E  Y           V +L A EEE   
Sbjct: 244 PNKGALVLTKELVRKLEDDRDLPPDMDPDEKKEK-YFGWAGLLANGAVEFLDAEEEETVM 302

Query: 627 IAQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           IA     LD                         +   +      +  P  ++ I AS+I
Sbjct: 303 IAMTPEDLDISRQVQAGFAPPEPSSDPNARVKAPVSANQHTWTHCEIHPSMILGICASII 362

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           PF +++ S R      M +QA+ +      
Sbjct: 363 PFPDHNQSPRNTYQSAMGKQAMGVFLTNFD 392


>gi|307343490|emb|CBJ18662.1| RNA polymerase B subunit [Micromonospora sp. CR18]
          Length = 215

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 94/213 (44%), Positives = 124/213 (58%), Gaps = 38/213 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEPDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHL 213


>gi|52538191|emb|CAH19197.1| RNA polymerase beta-subunit [Pseudomonas frederiksbergensis]
          Length = 259

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 150/259 (57%), Positives = 194/259 (74%)

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           S  + + +MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ 
Sbjct: 1   SMAESEGLMPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLT 60

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  V
Sbjct: 61  RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKDALV 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+++V+LSA+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQ
Sbjct: 121 TDEIVFLSAIEEADHVIAQASATMNDKKMLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           VVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+
Sbjct: 181 VVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVAR 240

Query: 731 RAGIVEQVDAIRIVIRSVE 749
           R G+++ VDA RIV+R  +
Sbjct: 241 RGGVIDSVDASRIVVRVAD 259


>gi|298912931|emb|CAZ66633.1| RNA polymerase beta subunit [Vibrio alginolyticus]
          Length = 289

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 170/289 (58%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAK 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L+EDG+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFL
Sbjct: 241 LNEDGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFL 289


>gi|110631663|gb|ABG81106.1| RNA polymerase beta subunit [Bartonella rochalimae]
 gi|110631670|gb|ABG81109.1| RNA polymerase beta subunit [Bartonella rochalimae]
          Length = 261

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 183/257 (71%), Positives = 213/257 (82%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R R
Sbjct: 4   EIDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRER 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +
Sbjct: 64  AGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKE 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D SPKQ+VS
Sbjct: 124 VIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLMDVSPKQLVS 183

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGAAI AKR G
Sbjct: 184 VAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGAAIGAKRGG 243

Query: 734 IVEQVDAIRIVIRSVEG 750
           IV+QVDA+RIVIR+ E 
Sbjct: 244 IVDQVDAMRIVIRATED 260


>gi|190148980|gb|ACE63465.1| RNA polymerase subunit B [Pseudonocardia zijingensis]
          Length = 267

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 148/274 (54%), Positives = 201/274 (73%), Gaps = 8/274 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+++A+VN +
Sbjct: 1   THKRRLNALGPGGLSRERAGMEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTYAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT+ + YL+A EE+   +AQAN+ LD+DG+F E+ V  R   GE  
Sbjct: 61  GFIQTPYRKVENGRVTDQIDYLTADEEDRFVVAQANAPLDDDGNFLEDRVLVRRKGGELD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+ ++LIPFLE+DD+NR LMG NMQRQAVPLL++EAP VGTG
Sbjct: 121 YISPATVDYIDVSPRQMVSVGSALIPFLEHDDANRALMGANMQRQAVPLLRSEAPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
           C NQ+P+V  G  V    +IADGP T+ G++ALG
Sbjct: 234 CNNQKPIVDEGQRVEAGQVIADGPCTEDGEMALG 267


>gi|298912947|emb|CAZ66641.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 289

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 168/289 (58%), Positives = 222/289 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFL 289


>gi|168809734|gb|ACA29586.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 208

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 88/211 (41%), Positives = 115/211 (54%), Gaps = 54/211 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P EDMP+L DG
Sbjct: 51   KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVEDMPYLPDG 110

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+          
Sbjct: 111  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLW--------- 161

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D  +E         A +    +++
Sbjct: 162  ------------------------------------DTVNE---------AGMASDAKTV 176

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            LYDG TGEPFD  V+VG +YM+KL+HMV DK
Sbjct: 177  LYDGRTGEPFDNRVSVGVMYMIKLHHMVDDK 207



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 37/59 (62%), Positives = 45/59 (76%)

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           ILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 1   ILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRANGD 59


>gi|118640687|gb|ABL09911.1| RNA polymerase beta subunit [Vibrio pectenicida]
          Length = 290

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 169/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F+ LFF  ++YDLSTVGR+K N  +  D   +   + + DII ++K L+ +RNG G +
Sbjct: 1   SLFDSLFFSEERYDLSTVGRMKFNSSIERDDAQEQGTLDELDIIEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+++PQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAILPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N +GF+ETPYR+V DG VT +V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEFGFLETPYRRVVDGVVTGEVDYLSAIQEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F EEL+  R  GE  L PR+ +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LSEEGTFAEELITARQKGESGLHPRDHVDYMDVATNQVVSIAASLIPFLE 290


>gi|71013466|ref|XP_758593.1| hypothetical protein UM02446.1 [Ustilago maydis 521]
 gi|46098251|gb|EAK83484.1| hypothetical protein UM02446.1 [Ustilago maydis 521]
          Length = 1169

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 146/974 (14%), Positives = 290/974 (29%), Gaps = 199/974 (20%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI- 490
            +   I ++++ ++     +  +DD D +GN+R+   G++L   +     +    +K  I 
Sbjct: 355  KAIYIASMVRRVLMAMQDEKKVDDRDYVGNKRLELAGQLLSLLFEDLFKKFNSDLKMNID 414

Query: 491  ------SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
                  +         Q   N   + S       +   S     +          RLS +
Sbjct: 415  KVLKKPNRTVEFDAFNQFHFNGDYITSGFVRAISTGNWSLKRFKMERAGITHVLSRLSFI 474

Query: 545  GQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
               G+         + R     R + P+ +G +CP++T EG   GLV +L     +    
Sbjct: 475  AALGMMTRISSQFEKTRKVSGPRALQPSQWGMLCPSDTPEGEACGLVKNLALTTHITTDV 534

Query: 597  FIETPYRKVCDGKVTNDVVYLSAMEEE--NRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
              E   R      V  D+  L+  E    + Y+   N ++     F +  V         
Sbjct: 535  EEEPIARIAFTLGV-EDIHLLTGAELYRPDSYVVYLNGNVLGVTRFPQRFVLQFRRLRRA 593

Query: 655  LVPREKIDFIDASPKQVVSIAAS----LIPFLEND--DSNRVLMGCNMQRQAVPLLKAEA 708
                E +        Q V IA+       P +  D    +  +   +MQ+      + + 
Sbjct: 594  GRVSEFVSVYTNHHHQTVYIASDGGRICRPLIIVDAFTGHPRVTESHMQQLKSGARRFDD 653

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                                    G++E VD               + + + +Y      
Sbjct: 654  FL--------------------HNGLIEYVDVNE-----------ENDANIAMYEHE--- 679

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                              + +    +   P T LG +A         +P+  +N      
Sbjct: 680  -----------------IKPQYTTHLEIEPFTILGAVA-------GLIPYPHHNQSPRNT 715

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
                M  +          +  + R   L    +    P V                    
Sbjct: 716  YQCAMGKQGQGAIG----YNQLIRIDTLLYLMLYPQQPMVKSRT---------------- 755

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     I   G   +      + A+      D+ D  +   + +       +   + 
Sbjct: 756  ---------IELIGYDKLPAGTNSMVAVMSYSGYDIEDALVLNKASLDRGFGRSQTMKKS 806

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 +   +   +++     D    +     +I         G+    G     K T +
Sbjct: 807  STVIRK-YPNGTHDRLADAPVDDTTGKRQKRYDILEADGIAGVGERVEQGDVYVNKQTPV 865

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            +++  S                +  +  +  V Y+++    +      I+++   D    
Sbjct: 866  NANDNSSAAI-----------MIGASNAAASVAYKSAPLSYKPPVSGYIDQVLITD--TD 912

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                ++K  +   R  + GDK +                                     
Sbjct: 913  SDQTLIKALIRQTRRPELGDKFS------------------------------------- 935

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SR         H      GL  + + +    +            + ++       +++  
Sbjct: 936  SR---------HGQKGVCGLIVQQEDMPFTDQGINP--------DIIMNPHGFPSRMTVG 978

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                +L       +G       F G+  E ++++L     + +G+  L  G+TG+P +  
Sbjct: 979  KMIELLSGKAGVITGTLQYGTAFGGSKVEDMSALLVENGYNYAGKETLTSGITGQPLECY 1038

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G IY  +L HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  YGA 
Sbjct: 1039 VYFGPIYYQRLKHMVQDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGAT 1098

Query: 1309 YVLQEMLTIKSDDVVGRTRVYESIVAG---------------NDTFETGTPESFNVLVKE 1353
             +L E L I SD          +                       +   P    ++++E
Sbjct: 1099 QLLLERLMISSD-----AFTVHACQKCGLMGYNGFCPYCSSSKHVVQLTIPYGTKLMLQE 1153

Query: 1354 MQALGLSIDLENSR 1367
            + A+ +   L    
Sbjct: 1154 LMAMQVVPRLVLED 1167



 Score =  206 bits (524), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 124/971 (12%), Positives = 292/971 (30%), Gaps = 189/971 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+  +          L+   K+   IT        L++       P+  
Sbjct: 62  LVKQHIDSYNYFVDHD----------LKNIIKANEKITSDIDPKFYLKYTDITVGEPRRY 111

Query: 86  --------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       +C  RD+TY+  + + +             +  K I+ +++ +G +P+
Sbjct: 112 DGDALQRPITPHECRLRDITYSAHIFVNIEYT----------RGGKIIRRKNVAIGRIPV 161

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRA 172
           M                           G FV+KG +++++ Q   S   I  + D  + 
Sbjct: 162 MLRSNKCVLANKSEKELAKMSECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVEADTKKG 221

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILS 230
           ++S  +  +     ++     +       I+++ +     +P+     A+G+ ++ EIL 
Sbjct: 222 TVSASVTSSTH---ERKSKSYVLT-KHGKIYLKHNSLHEDIPIAVAFKAMGIQADREILQ 277

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE 290
                    +         +A   +   K +   +             +    + + L E
Sbjct: 278 LVAGHDDIHKELFAINLEEAARLGIYTRKQALDFIGAR------AKASRKPLSMRRPLSE 331

Query: 291 KGVKFL------GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
           + +  L       +  + L     A  I +     +        DEK +++  +   + +
Sbjct: 332 EALDVLATVIMAHVPVERLNFRPKAIYIASMVRRVLMAM----QDEKKVDDRDYVGNKRL 387

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            +           +         K   D  ++I +V++  + +    A + F+F      
Sbjct: 388 EL-------AGQLLSLLFEDLFKKFNSDLKMNIDKVLKKPNRTVEFDAFNQFHFNGDYIT 440

Query: 405 KYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG--- 460
              +  +     +  R  ++       + +   IA + ++  + +       +       
Sbjct: 441 SGFVRAISTGNWSLKRFKMERAGITHVLSRLSFIAALGMMTRISSQFEKTRKVSGPRALQ 500

Query: 461 --NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                +    +  + +    +  +  +        +         +  + +         
Sbjct: 501 PSQWGMLCPSDTPEGEACGLVKNLALTTHITTDVEEEPIARIAFTLGVEDIHLLTGAELY 560

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
                 +  + N L      +R   L    + RA    E   V+  H+ +     +  G 
Sbjct: 561 RPDSYVVYLNGNVLGVTRFPQRF-VLQFRRLRRAGRVSEFVSVYTNHHHQTVYIASDGGR 619

Query: 579 NIGLVSSLTSF-----ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
               +  + +F        +    +++  R+  D      + Y+   EE +  IA     
Sbjct: 620 ICRPLIIVDAFTGHPRVTESHMQQLKSGARRFDDFLHNGLIEYVDVNEENDANIAMYE-- 677

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                                 +  +    ++  P  ++   A LIP+  ++ S R    
Sbjct: 678 --------------------HEIKPQYTTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQ 717

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +Q                                          +  I   +    
Sbjct: 718 CAMGKQG-----------------------------------------QGAIGYNQLIRI 736

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +   + +Y               Q+P+VK                     L  G N +V
Sbjct: 737 DTLLYLMLYP--------------QQPMVKS----------RTIELIGYDKLPAGTNSMV 772

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----V 868
           A M + GY+ ED++++++  +      S  +++   + R    G  +   D P       
Sbjct: 773 AVMSYSGYDIEDALVLNKASLDRGFGRSQTMKKSSTVIRKYPNGTHDRLADAPVDDTTGK 832

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            ++    ++  GI  VG  V  GD+ V K TP   +  +    ++ A     +V  +   
Sbjct: 833 RQKRYDILEADGIAGVGERVEQGDVYVNKQTPVNANDNSSAAIMIGASNAAASVAYKSAP 892

Query: 929 LRVPSGVSGTV 939
           L     VSG +
Sbjct: 893 LSYKPPVSGYI 903


>gi|242808107|ref|XP_002485094.1| DNA-directed RNA polymerase III, beta subunit, putative [Talaromyces
            stipitatus ATCC 10500]
 gi|218715719|gb|EED15141.1| DNA-directed RNA polymerase III, beta subunit, putative [Talaromyces
            stipitatus ATCC 10500]
          Length = 1212

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 166/1143 (14%), Positives = 345/1143 (30%), Gaps = 224/1143 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +  D L   Y+  ++++ +   + + 
Sbjct: 259  IVETDPKKEIVQASVTSSSN-----ERKSKSYIILKKDRL---YLRHNVLSEDVPLVIVL 310

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                +       +  + I D+         + A      +      ++ AL  I   ++ 
Sbjct: 311  KAMGVHSDKEMMLLVAGIDDV------YQEDFAINFEEAIKQNVFTQQQALDWIGSKIKI 364

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                     ++             +S V    M+ R            +   +  + + +
Sbjct: 365  NRGKVGGYKKTHIEEAIEAISSVVISHVEVTNMDFRP-----------KAIYVANMARRV 413

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS------VDIDS 497
            +  ++    +DD D +GN+R+   G++L   +     +    IK  I+        +I  
Sbjct: 414  LMAKHDPSMVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNITKVLGKRRREIFD 473

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------- 550
             M    ++   +   +     +   S     +          RLS +   G+        
Sbjct: 474  AMSVVALHGNHITHGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQF 533

Query: 551  -RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             + R     R + P+ +G +CP++T EG   GLV +L     +      E P  K+    
Sbjct: 534  EKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTN-DEEGPVSKLVFML 592

Query: 610  VTNDVVYLSAMEEEN---RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
               D+  LS  E        I+   + +             R     +   R        
Sbjct: 593  GAEDITTLSGKEIYGLGAYIISMNGTPIA----------MTRRPKHFLNSFRRLRRMGRV 642

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            S    + I         +  +  +        + + +++   P V +     +   S   
Sbjct: 643  SEFVSIYIN-------HHQRAVHIATDDGRICRPLIVVENGKPLVNSRHLGKLRDGSMQF 695

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                  G+VE +D               + S + IY                       D
Sbjct: 696  DDFLAQGLVEYLDVNE-----------ENDSNIAIYEK---------------------D 723

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             V     +   P T LG +A         +P+  +N          M  + +        
Sbjct: 724  VVDITTHLEIEPFTILGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA------ 770

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                                       + +    ++ +        +    I       +
Sbjct: 771  -----------------------IASNQFLRIDSLLYLMVYPQKPMVKTRTIELIKYDHL 807

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
               +    A+      D+ D  +     V       ++F ++  +        E      
Sbjct: 808  PAGQNATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVANLKSYPNGSE------ 861

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
               D+     I + N+      +L      +  +   +  V  +  +     S       
Sbjct: 862  ---DRLRGPEIGENNVPIAKHALLDSDGLAAVGEVVSQGQVYINKEVPAAAFSA--GITG 916

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D     +     + Y     + +  + +K+        +  G  ++ KV     R  + 
Sbjct: 917  SDAGRPTDYNPAPMTY----KLPDPSYIDKV-----MVSVTEGESKIYKVQTRQTRRPEV 967

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK +                                     SR                
Sbjct: 968  GDKFS-------------------------------------SR---------------- 974

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+K    I   +A+   +      + ++       +++      ++       SG   
Sbjct: 975  -HGQKGVVGIIAEQADMPFTDQGIVPDIIMNPHGFPSRMTVGKLLELVAGKAGVLSGQHG 1033

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                F G+  E ++++L        G+  L  G+TG+P    V  G IY  KL HMV DK
Sbjct: 1034 YGTAFGGSPVEEMSAILVDKGFSYGGKDYLTSGITGDPLPFYVFTGPIYYQKLKHMVQDK 1093

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV 1322
            +++RSTG  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L + SD    D+
Sbjct: 1094 MHSRSTGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMLSSDKHEVDI 1153

Query: 1323 ------------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                          R R    +V          P +  +L++E+ ++ ++  L+      
Sbjct: 1154 CEKCGFMGYQNWCQRCRSSRGVVK------MTIPYAAKLLIQELLSMNVTARLKLEDEFP 1207

Query: 1371 SAK 1373
              +
Sbjct: 1208 EDR 1210



 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 95/738 (12%), Positives = 209/738 (28%), Gaps = 120/738 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   ++   I +       L+F       P+  
Sbjct: 104 LVKQHIDSYNYFIEVQ----------LKKIVEASSTIYSDADSHFFLKFTDIYVGSPRRS 153

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +            T  +   ++ ++ + +G
Sbjct: 154 DEPKDSVESDSTVTPNECRLRDMTYAAPIFVDF----------TYKRGKDNVTQRRVPIG 203

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   I  + D
Sbjct: 204 RMPIMLRSSKCVLSNKKPNELHLLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVETD 263

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             KD +++R +     VP+   L A
Sbjct: 264 PKKEIVQASVTSSSNERKSKSYII-----------LKKDRLYLRHNVLSEDVPLVIVLKA 312

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           +G+ S++ +      I    + DF      A        +  ++         I S  K+
Sbjct: 313 MGVHSDKEMMLLVAGIDDVYQEDFAINFEEA--------IKQNVFTQQQALDWIGSKIKI 364

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
             G +   K+  ++        +   +V    ++     IY+ A         +      
Sbjct: 365 NRGKVGGYKKTHIEEAIEAISSVVISHVEVTNMDFRPKAIYV-ANMARRVLMAKHDPSMV 423

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                +           +         K   D  ++I +V+          A S+     
Sbjct: 424 DDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNITKVLGK-RRREIFDAMSVVALHG 482

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDI 456
                     +     +++        V H    +     + ++  +         +   
Sbjct: 483 NHITHGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGP 542

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
             L   +   +      +     L    ++   I++ D +  + + +             
Sbjct: 543 RALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEGPVSKLVFMLGAEDITTLSG 602

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETS 575
                L      +N        R    L     + R     E   ++  H+ R     T 
Sbjct: 603 KEIYGLGAYIISMNGTPIAMTRRPKHFLNSFRRLRRMGRVSEFVSIYINHHQRAVHIATD 662

Query: 576 EGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           +G     +  + +          G +     +  D      V YL   EE +  IA    
Sbjct: 663 DGRICRPLIVVENGKPLVNSRHLGKLRDGSMQFDDFLAQGLVEYLDVNEENDSNIAIYEK 722

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +                        +    ++  P  ++   A LIP+  ++ S R   
Sbjct: 723 DV-----------------------VDITTHLEIEPFTILGAVAGLIPYPHHNQSPRNTY 759

Query: 693 GCNMQRQAVPLLKAEAPF 710
            C M +QA+  + +    
Sbjct: 760 QCAMGKQAIGAIASNQFL 777


>gi|300394698|gb|ADK11887.1| DNA-directed RNA polymerase II subunit two [Ceraceomyces borealis]
          Length = 693

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 120/822 (14%), Positives = 230/822 (27%), Gaps = 145/822 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      +L+ +   ++  G      +      + K   I      
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLVLQKKHIKWLNQGYRDEDGEEFKWEQLIKGGIIELLDAE 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                +       D   S +            +    +    +K G            PS 
Sbjct: 286  EEETVMISMTPEDLENSRLQQSGTDPHANDEE---FDPAARLKAGTNAHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 378  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 486  DKIEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      LG +  +      
Sbjct: 586  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLLGNEGDATPFTDL 645

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S     L+K   +                                          
Sbjct: 646  TVESVSKFL--LQKGYQSRGLEVM------------------------------------ 667

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                       G +       G      V +G  Y  +L HM
Sbjct: 668  ---------YHGHT-------GRKLQAQVYLGPTYYQRLKHM 693



 Score =  118 bits (296), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 82/610 (13%), Positives = 165/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLVL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +     Y   +    K         +  L A EEE   I+     L+       
Sbjct: 249 QKKHIKWLN-QGYRDEDGEEFKWEQLIKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 307

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                    E     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 308 GTDPHANDEEFDPAARLKAGTNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 367

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 368 MGKQAMGIYLTNFLI-----------------------------------------RMDT 386

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 387 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 422

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 423 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKH 482

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V   DI++GK  P         E+L +        DV      
Sbjct: 483 GTYDKIEDDGLIAPGTGVAGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 538

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 539 TENGIVDQVL 548


>gi|190148972|gb|ACE63461.1| RNA polymerase subunit B [Pseudonocardia tetrahydrofuranoxydans]
          Length = 265

 Score =  253 bits (646), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 147/272 (54%), Positives = 198/272 (72%), Gaps = 8/272 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G VT  + YL+A EE+   +AQAN+ L++DG+FTEE V  R   GE  
Sbjct: 61  GFIQTPYRKVVEGVVTEQIDYLTADEEDRYVVAQANAPLNDDGTFTEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +++ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 YIAPTGVEYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVAEKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           C NQ+P+V  G  V    ++ADGP T+ G++A
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGEMA 265


>gi|300394686|gb|ADK11881.1| DNA-directed RNA polymerase II subunit two [Coniophora cerebella]
          Length = 685

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 124/808 (15%), Positives = 233/808 (28%), Gaps = 144/808 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ R +    +              +  + + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   + ++   F       + +         L ++EE 
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWG-------LESLEEN 169

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
                A A + +  +G +       R     +   ++     D SP+  V           
Sbjct: 170  AHSSA-ACTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRL 225

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D+ RV     +      LL+ +   ++  G                + G++E +DA  
Sbjct: 226  YTDAGRVCRPLFIVEDQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEE 285

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   +     +         +   +    +K G            PS  L
Sbjct: 286  EETVMIAMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMIL 343

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 344  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 378

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              +               +  +             +       +   +  + AI      
Sbjct: 379  FLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 427

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          + 
Sbjct: 428  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDK 486

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 487  IEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQV 546

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 547  LI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGI 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +           
Sbjct: 587  TYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------- 637

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     E++++ 
Sbjct: 638  --------------------------------------------ATP-FTDLTVESVSTF 652

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVT 1250
            LR       G  ++Y G TG      V 
Sbjct: 653  LRQKGYQSRGLEVMYHGHTGRKLQAQVY 680


>gi|68131848|gb|AAY85202.1| RNA polymerase II second largest subunit [Dianthus caryophyllus]
          Length = 674

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 135/826 (16%), Positives = 240/826 (29%), Gaps = 167/826 (20%)

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINA 506
            G+   DD D+ GN+R+   G +L   +R    ++ R ++   + +      +     I A
Sbjct: 1    GRREEDDRDHYGNKRLDLAGPLLGGLFRQLFRKLTRDVRAYVQKNVDQGKDLNLTFAIKA 60

Query: 507  KPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
            K + S +     +              +SQ+   +   S ++H RRL++     + R   
Sbjct: 61   KTITSGLKYSLATGNWGAANAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGK 116

Query: 555  GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              + R +H + +G +CPAET EG   GLV +L     +            + +    N  
Sbjct: 117  LAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWSTEN-- 174

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
                  EE +  +    + +  +G +       R     +   RE    +D + +  V  
Sbjct: 175  -----FEEISPAVIPQATKIFVNGGWVG---IHRDPDLLVKTLRELRRRVDVNTEVGVVR 226

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
               L       D  R      +  +   L+                K   A    +    
Sbjct: 227  DIRLKELRIYTDYGRCSRPLFIVEKQRLLI--------------KKKDIRALQQRETPED 272

Query: 735  VEQVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                D   +  I  ++ + + +T        +   R N     +                
Sbjct: 273  GGWHDLVAKGFIEYIDTEEEETTMISMTINDLVSARLNPEESYS-----------GTYTH 321

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +     I       R 
Sbjct: 322  CEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRM 370

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              L         P V+   ++++                             +      +
Sbjct: 371  DTLAYVLYYPQKPLVTTRAMEHL-------------------------HFRQLPAGINAI 405

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R    
Sbjct: 406  VAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTM 464

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +          G           K+T LS +                      
Sbjct: 465  GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPLSPEEAQGP----------------- 507

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                   +Y      +  R        Q         LR VKV V   R  Q GDK + R
Sbjct: 508  -----AARYSRKDHSISLRHSESGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSR 562

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  
Sbjct: 563  HGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHVGKEGD 622

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                 +TP F  
Sbjct: 623  -----------------------------------------------------ATP-FTD 628

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               + I+  L+       G   +Y+G TG      + +G  Y  +L
Sbjct: 629  VTVDNISKALQKCGYQMRGFETMYNGHTGRKLSAMIFLGPTYYQRL 674


>gi|103001922|gb|ABF71527.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 701

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 118/821 (14%), Positives = 231/821 (28%), Gaps = 143/821 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 1    GPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWGDQ 60

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 61   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 116

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 117  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 176

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSN 688
               +  D +     V        I      + D  D   K          P F+ ++D  
Sbjct: 177  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 236

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G  +  +       +   +   M+S   +       AK  G    V     V+  V
Sbjct: 237  STNCGNLVLTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVEYV 287

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 288  DAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSM 347

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N                        ++       +G      D   
Sbjct: 348  ILGICASIIPFPDHNQSPRN------------------TYQSXMGKQAMGVFLTNYDQRM 389

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 390  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 438

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 439  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 494

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +S D      R++          ++     +  Q   
Sbjct: 495  DDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 554

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      L+ VKV +   +  Q GDK A RHG KG +    
Sbjct: 555  --------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 594

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 595  RQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDS 654

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 655  VSKLLR--EHGYQSRGFEVM---------------------------------------- 672

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                  +G +    G         V +G  Y  +L HMV D
Sbjct: 673  -----YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDD 701


>gi|320172600|gb|ADW24183.1| RNA polymerase II second largest subunit [Veluticeps berkeleyi]
          Length = 679

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 124/808 (15%), Positives = 233/808 (28%), Gaps = 147/808 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +    + + + 
Sbjct: 2    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLSLAVKHNTITNGLK 61

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 62   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 117

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++           + +  + +         
Sbjct: 118  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL-------- 169

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +       R   + +   ++     D SP+  V         
Sbjct: 170  EENAHSATPCTKVFVNGVWMG---VHRNPQDLVKTIKKLRRKDDISPEVSVVRDIREREL 226

Query: 682  LENDDSNRVLMGCNMQR--QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
                D+ RV     +    Q + L K    ++  G      +      + K   I    D
Sbjct: 227  RLYTDAGRVCRPLFIVEENQQLALHKKHVRWLKQGYRDDDGEPWKWDQLVKNGIIELL-D 285

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A       +    +   +       +  +    +   +    +K              PS
Sbjct: 286  AEEEETVMISMTPEDLENSRLPAGAVDPR---ADEEFDPAARLKAATHSHTWTHCEIHPS 342

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N                        ++       +G  
Sbjct: 343  MILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIY 377

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 +               +  +             +       +   +  + AI   
Sbjct: 378  LTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCY 426

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD         
Sbjct: 427  SGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGT 485

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G           K+  +  D                +E  QR     +
Sbjct: 486  YDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPD---------------SEELGQRTRSHTR 530

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                T+    E    +++              + VKV +   R  Q GDK A RHG KG 
Sbjct: 531  RDVSTAMKSTEQGIVDQVLI-----TTNHEGQKFVKVRIRSTRVPQIGDKFASRHGQKGT 585

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G +        
Sbjct: 586  IGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLTGNEGD------ 639

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                           +TP F     E++
Sbjct: 640  -----------------------------------------------ATP-FTDLTVESV 651

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDR 1247
            +  LR       G  ++Y G TG     
Sbjct: 652  SQFLREKGYQSRGLEVMYHGHTGRKLQA 679



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 87/629 (13%), Positives = 173/629 (27%), Gaps = 114/629 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 13  GPLLANLFRMLFRKLTKDVYRYLQKCVESH--KEFNLSLAVKHNTITNGLKYSL-ATGNW 69

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 70  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 129

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 130 TPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 189

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                  + +  I   RR   +             +RD+          A         +
Sbjct: 190 GVHRNPQDLVKTIKKLRRKDDISP-------EVSVVRDIRERELRLYTDAGRVCRPLFIV 242

Query: 583 VSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
             +           +++  YR       K         +  L A EEE   I+     L 
Sbjct: 243 EENQQLALHKKHVRWLKQGYRDDDGEPWKWDQLVKNGIIELLDAEEEETVMISMTPEDL- 301

Query: 636 EDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           E+       V  R   E                   +  P  ++ + AS+IPF +++ S 
Sbjct: 302 ENSRLPAGAVDPRADEEFDPAARLKAATHSHTWTHCEIHPSMILGVCASIIPFPDHNQSP 361

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 362 RNTYQSAMGKQAMGIYLTNFLV-------------------------------------- 383

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 384 ---RMDTMANILYYPQKPLATTRSMEYLRFR------------------------ELPAG 416

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD---- 864
           +N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        
Sbjct: 417 QNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRD 476

Query: 865 -IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
               +       +++ G+I  G  VN  DI++GK  P         ++        ++  
Sbjct: 477 TTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRT-------RSHT 529

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            RD S  + S   G V  V I   H   K
Sbjct: 530 RRDVSTAMKSTEQGIVDQVLITTNHEGQK 558


>gi|298912951|emb|CAZ66643.1| RNA polymerase beta subunit [Vibrio natriegens]
          Length = 289

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 169/289 (58%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFL 289


>gi|298912945|emb|CAZ66640.1| RNA polymerase beta subunit [Vibrio harveyi]
 gi|298912957|emb|CAZ66646.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 289

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 168/289 (58%), Positives = 222/289 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFL 289


>gi|118640695|gb|ABL09915.1| RNA polymerase beta subunit [Vibrio aestuarianus]
          Length = 290

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNG G +
Sbjct: 1   SLFESLFFSEERYDLSTVGRMKFNSSIEREDAGEQGTLDETDIIEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANAI 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|88601060|gb|ABD46526.1| RNA polymerase II second largest subunit [Sistotrema coronilla]
          Length = 688

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 125/810 (15%), Positives = 232/810 (28%), Gaps = 145/810 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R+   ++ + +   +               + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHKEFSLSLAVKSNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  A ++  G +  P  +         +   +A    +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMACIS-VGSLSAPVIEFLQEWGLEGLE-ENANSHGSAT 175

Query: 627  IAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQ---VVSIAASLIPFL 682
                N            LV   R    +  +  E     D   K+            P  
Sbjct: 176  KVFVNGVWMGVHRDAPNLVKTLRRLRRKDDISPEVSVVRDIREKELRLYTDAGRXCRPLF 235

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS--GAAIVAKRAGIVEQVDA 740
              ++    +   ++ +              T ++      S   +     R G++E +DA
Sbjct: 236  IVENQQLAVKKAHIHKL-------NDHAPVTSIDPDGQAHSVPYSWSHLVRDGVIELLDA 288

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +        +         +  +   +  +    VK              PS 
Sbjct: 289  EEEETVMICMTPXDLEASRTSQAAAGYVXNVGASDHDVAARVKSTMNAHTWTHCEIHPSM 348

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N       S R   +       +  +    +        
Sbjct: 349  ILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVRM----- 390

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +T      +   +    AI    
Sbjct: 391  ------------------DTMANILYYPQKPLATTRSMTYLRFRELPAGQNATVAILCYS 432

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    ++ R   D  ++   +  E+     RD          
Sbjct: 433  GYNQEDSVIMNQSSIDRGLF-RSMYYRSYSDTEKKVGILPLEEFARPTRDDTLRLKHGSY 491

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
                    I  G   V       K+  L  D                +E  QR     K 
Sbjct: 492  EKLDDDGLIAPGTGVVGEDIIIGKTAPLPPD---------------SEELGQRLRTHSKR 536

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++     GD +     + VKV +   R  Q GDK A RHG KG V
Sbjct: 537  DVSTPLKSTENGIVDQVVVTTNGDGL-----KFVKVRIRSTRIPQVGDKFASRHGQKGTV 591

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L       G++         
Sbjct: 592  GITYRHEDMPFSAEGVTPDIIINPHAIPSRMTIGHLIECLLSKLATLTGREGD------- 644

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 645  ----------------------------------------------ATP-FTELTVESVS 657

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
             +LR       G  ++Y G TG+     V 
Sbjct: 658  QLLREYGYQSRGLEVMYHGHTGKKLQVQVY 687


>gi|190148966|gb|ACE63458.1| RNA polymerase subunit B [Pseudonocardia petroleophila]
          Length = 270

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 148/277 (53%), Positives = 199/277 (71%), Gaps = 8/277 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL SFA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI++PYRKV DGK T  + YL+A EE+   IAQAN  LDEDG+F  + V  R   G+  
Sbjct: 61  GFIQSPYRKVEDGKATEQIDYLTADEEDRFIIAQANEPLDEDGNFVGDRVLVRRKGGDVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A ++IPFLE+DD+NR LMG NMQRQ+VPLL++++P VGTG
Sbjct: 121 YISPAGVDYIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQSVPLLRSDSPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVAEKAGVVEELCADFITVMADDGTR-------RTYRLHKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           C NQ+P+V  G  V    ++ADGP T+ G++ALG+N+
Sbjct: 234 CTNQKPIVLEGARVEVGQVLADGPCTENGEMALGKNL 270


>gi|224797565|gb|ACN62812.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
          Length = 424

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 168/337 (49%), Positives = 235/337 (69%), Gaps = 8/337 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLIAPNSPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLV+ G ++ +  ++ADGPS D  +LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVRQGQKIEKGQVLADGPSIDKEELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933 SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +G  G +  ++ F R   + +   + V +  I    +
Sbjct: 293 NGGEGIIQAIKRFPREKYELSADVLEVIKVYIVQKRK 329



 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 81/292 (27%), Positives = 134/292 (45%), Gaps = 14/292 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVRQGQKIEKGQVLADGPS-IDKEELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D     ++  +    
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGITXEELVEIMDKA 418



 Score = 39.7 bits (91), Expect = 3.9,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 29/90 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +       + ++ ++       +++      +       K 
Sbjct: 335  KMAGRHGNKGVISKILPLEDMPHMEDGTPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKL 394

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            G  +STPVFDG   E +  ++  A +   G
Sbjct: 395  GQKISTPVFDGITXEELVEIMDKAGMKNFG 424


>gi|224797563|gb|ACN62811.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
 gi|224797567|gb|ACN62813.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
 gi|224797569|gb|ACN62814.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
 gi|224797571|gb|ACN62815.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
 gi|224797573|gb|ACN62816.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           wheeleri]
 gi|224797575|gb|ACN62817.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797577|gb|ACN62818.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797579|gb|ACN62819.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797581|gb|ACN62820.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797583|gb|ACN62821.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797585|gb|ACN62822.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797587|gb|ACN62823.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797589|gb|ACN62824.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
 gi|224797591|gb|ACN62825.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           aldrichi]
          Length = 424

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 168/337 (49%), Positives = 235/337 (69%), Gaps = 8/337 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLIAPNSPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLV+ G ++ +  ++ADGPS D  +LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVRQGQKIEKGQVLADGPSIDKEELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933 SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +G  G +  ++ F R   + +   + V +  I    +
Sbjct: 293 NGGEGIIQAIKRFPREKYELSADVLEVIKVYIVQKRK 329



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 82/292 (28%), Positives = 135/292 (46%), Gaps = 14/292 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVRQGQKIEKGQVLADGPS-IDKEELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +    
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGITNEELVEIMDKA 418



 Score = 39.7 bits (91), Expect = 3.7,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 29/90 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +       + ++ ++       +++      +       K 
Sbjct: 335  KMAGRHGNKGVISKILPLEDMPHMEDGTPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKL 394

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            G  +STPVFDG   E +  ++  A +   G
Sbjct: 395  GQKISTPVFDGITNEELVEIMDKAGMKNFG 424


>gi|52699825|gb|AAU86974.1| DNA-dependent RNA polymerase II second largest subunit [Lasallia
            pennsylvanica]
          Length = 716

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 126/838 (15%), Positives = 239/838 (28%), Gaps = 147/838 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIV 735
             P    D+  +     N+   ++ +  L+ +      T  E   AK  G   + K  G+V
Sbjct: 237  RPLFVIDNDPKSPNNGNLVLTKEHINRLEDDKDLGPDTDPEERTAKYMGWEGLVK-QGVV 295

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E VDA            + +   V     ++  R  Q               V+      
Sbjct: 296  EYVDAEE----------EETVMIVMTPEDLEISRQIQAGYTMPETTDDPNKRVKAPMNPT 345

Query: 796  DGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T      ++   +  + +P+  +N                        ++      
Sbjct: 346  AHTWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQ 387

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G      D                +  +             +       +   +  + 
Sbjct: 388  AMGVFLTNFDQRM-----------DTMANILYYPQXPLATTRSMEFLKFRELPAGQNAIV 436

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    +
Sbjct: 437  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSD 492

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             +      Y +L +   +  G           K+  ++                  +E  
Sbjct: 493  TLRXKHGTYXKLDDDGXVAPGVRVXGEDVIIGKTAPIA---------------PXAEELG 537

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR    +K          E    +++             LR VKV        Q GDK A
Sbjct: 538  QRTKSHIKRDVSXPLRSTEXGXVDQVXL-----TXNAEGLRFVKVRXRTTXXPQIGDKFA 592

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +
Sbjct: 593  SRHGQKGTIGITYRXEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECXLXKVSSLRGFE 652

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S  R   E    +                                 
Sbjct: 653  GDATPFTEVTVDSVS--RXLREHGYQSRGFEVM--------------------------- 683

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                               +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 684  ------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 716



 Score =  110 bits (274), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 84/577 (14%), Positives = 149/577 (25%), Gaps = 97/577 (16%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 56  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 115

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E       + +   ++   PQ 
Sbjct: 116 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPQR 175

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM--- 558
             NA  V      F     +    +  + +S +   RR S +  +  + R     E    
Sbjct: 176 SPNATKV------FVNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVRDIRDREFKIF 229

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF------IETPYRKVCDG 608
               R   P       P   + G+ +     +         G           Y      
Sbjct: 230 TDAGRVCRPLFVIDNDPKSPNNGNLVLTKEHINRLEDDKDLGPDTDPEERTAKYMGWEGL 289

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+ A EEE   I      L+                                 
Sbjct: 290 VKQGVVEYVDAEEEETVMIVMTPEDLEISRQIQ--------------------------- 322

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
                   +     E  D     +   M                T       +   + I+
Sbjct: 323 --------AGYTMPETTDDPNKRVKAPM--------------NPTAHTWTHCEIHPSMIL 360

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              A I+   D  +    + +  +     GV       +           Q PL      
Sbjct: 361 GICASIIPFPDHNQSPRNTYQSAMGXQAMGVFLTNFDQRMDTMANILYYPQXPL------ 414

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA   + GYN EDS+++++  +   +F S+    +
Sbjct: 415 ----ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRCY 470

Query: 848 EVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
               +   +   E     +  D           +D+ G +  G  V   D+++GK  P  
Sbjct: 471 TDQEKRIGMSVVEQFEKPMRSDTLRXKHGTYXKLDDDGXVAPGVRVXGEDVIIGKTAPIA 530

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  ++        K+   RD S  + S   G V
Sbjct: 531 PXAEELGQRT-------KSHIKRDVSXPLRSTEXGXV 560


>gi|110669588|gb|ABG81889.1| RNA polymerase II second largest subunit [Anisomeridium polypori]
          Length = 719

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 133/839 (15%), Positives = 246/839 (29%), Gaps = 145/839 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++ N +R+  L+M +   +  +    +      Q  + A  V +
Sbjct: 1    DDRDHFGKKRLDLAGPLIANLFRILFLKMTKDAYKYLQKCVENNQDFNVQIAVKASVVTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      V R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    V+        T +    +  +  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSTGSESTPITEFMLQRNMDLLEEYDP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            +        ++      +    S    +V        +      I D  D   K      
Sbjct: 177  VVNPTATKVFVNGVWVGVHSQASQLVSVVNELRRSGTLSFEMSLIRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAV--PLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
              + P F+   D  +   G  +  ++    L++     +   M       S     +  +
Sbjct: 237  RVMRPLFVVETDYRKPNRGSLVLTKSHVQKLIEDRRLILRGSMTRTRLIXSLGGEGSFES 296

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-RPLVKVGDEVRRN 791
            G++E +DA       +    +      D+ + +            + +P  K    V+  
Sbjct: 297  GVIEYLDAEEEETAMIIMTPEDLDEHRDLMQGIPVPEGMAADRHKRIKP--KPNPTVKTY 354

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  PS  LG       +  + +P+  +N          M  + +   +   E  +  
Sbjct: 355  THCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFERRMET 407

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                                         +  +             +       +   + 
Sbjct: 408  -----------------------------MANILYYPQKPLARTMAMEYLKFRGLPAGQN 438

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +     +  +     E+   V     E   R  
Sbjct: 439  AIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQ----EQERMVGNGVFEASERPV 494

Query: 972  DDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
              E + + +  Y +L +   I  GQ  V       K+T ++ D+     R +        
Sbjct: 495  RSETMRMKQGSYEKLDQDGIITPGQRVVGEDIIMGKTTPMAHDVEELGQRQKAHTKRDVS 554

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +  Q                              R  KV V   +  Q GD
Sbjct: 555  VPLRSTEAGVIDQVML--------------------TTTADGNRFAKVRVRTTKVPQIGD 594

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF +DG   DI++NP  +PSRM +  + E  L       
Sbjct: 595  KFASRHGQKGTIGVTYRNEDMPFSRDGIVPDIIINPHAIPSRMTIAHLVECQLSKVATLR 654

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +          IS +    ++   +       + Y                    
Sbjct: 655  GDEGDATPFTKVTVTQISKILR--DQGYQSRGFEVMYNGYT------------------- 693

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                          G         V  G  Y  +L HMV DK+
Sbjct: 694  ------------------------------GR---KLVSQVFFGPTYYQRLRHMVDDKI 719


>gi|212537851|ref|XP_002149081.1| DNA-directed RNA polymerase III, beta subunit, putative [Penicillium
            marneffei ATCC 18224]
 gi|210068823|gb|EEA22914.1| DNA-directed RNA polymerase III, beta subunit, putative [Penicillium
            marneffei ATCC 18224]
          Length = 1212

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 164/1143 (14%), Positives = 344/1143 (30%), Gaps = 224/1143 (19%)

Query: 264  LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +V+ D  ++++++    +S      + K   ++ +  D L   Y+  ++++ +   + + 
Sbjct: 259  IVETDPKKEIVQASVTSSSN-----ERKSKSYIILKKDRL---YLKHNVLSEDVPLVIVL 310

Query: 324  AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
                +       +  + + D+         + A      +      ++ AL  I   ++ 
Sbjct: 311  KAMGVHSDKEMMLLVAGVDDV------YQEDFAINFEEAIKQNVFTQQQALDWIGSKIK- 363

Query: 384  GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                   +             +  +  +  V ++     D     + I    +  + + +
Sbjct: 364  -------INRGKIGGYKKTHIEEAIEAISSVIISHVEVTDMDFRPKAI---YVANMARRV 413

Query: 444  VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS------VDIDS 497
            +  ++    +DD D +GN+R+   G++L   +     + +  IK  I+        +I  
Sbjct: 414  LMAKHDSDMVDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNITKVLGKRRREIFD 473

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------- 550
             M    ++   +   +     +   S     +          RLS +   G+        
Sbjct: 474  AMSVVTLHGNHITHGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQF 533

Query: 551  -RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
             + R     R + P+ +G +CP++T EG   GLV +L     +      E P  K+    
Sbjct: 534  EKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTN-DEEGPVSKLVFML 592

Query: 610  VTNDVVYLSAMEEEN---RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
               D+  LS  E        I+   + +             R     +   R        
Sbjct: 593  GAEDITTLSGKEIYGLGAYIISMNGTPIA----------LTRRPKYFLNAFRRLRRMGRI 642

Query: 667  SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            S    + I         +  +  +        + + +++   P V       +   S   
Sbjct: 643  SEFVSIYIN-------HHQRAVHIATDDGRICRPLIVVENGKPLVKASHLEKLRDGSMQF 695

Query: 727  IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                  G+VE +D               + S + IY                       D
Sbjct: 696  DDFLAQGLVEYLDVNE-----------ENDSNIAIYEK---------------------D 723

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
             +     +   P T LG +A         +P+  +N          M  + +        
Sbjct: 724  VIDITTHLEIEPFTILGAVA-------GLIPYPHHNQSPRNTYQCAMGKQAIGA------ 770

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                                       + +    ++ +        +    I       +
Sbjct: 771  -----------------------IASNQFLRIDSLLYLMVYPQKPMVKTRTIELIKYDQL 807

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
               +    A+      D+ D  +     V       ++F R  +   +   +   +++  
Sbjct: 808  PAGQNATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVF-RKYVANLKSYPNGSEDRLRG 866

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
               D ++   I    +         G     G     K              +       
Sbjct: 867  PELD-EEGAPITKHALLDTDGLAAVGAVVSQGQVYINK---------EVPAAAFSAGITG 916

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             D     +     + Y     + +  + +K+        +  G  ++ KV     R  + 
Sbjct: 917  SDVGRPPDYNPAPMTY----KLPDPSYIDKV-----MVSVTEGESKIYKVQTRQTRRPEV 967

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK +                                     SR                
Sbjct: 968  GDKFS-------------------------------------SR---------------- 974

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+K    I   +A+   +      + ++       +++      ++       SG   
Sbjct: 975  -HGQKGVVGIIAEQADMPFNDQGIVPDIIMNPHGFPSRMTVGKLLELVAGKAGVLSGQHG 1033

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                F G+  E ++++L        G+  L  G+TGEP    V +G IY  KL HMV DK
Sbjct: 1034 YGTAFGGSPVEQMSAILVDKGFSYGGKDYLTSGITGEPLPFYVFMGPIYYQKLKHMVQDK 1093

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV 1322
            +++RSTG  + +T+QP  G+S  GG RLGEME  C+ AYG + +L E L + SD    D+
Sbjct: 1094 MHSRSTGPRATLTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMLSSDKHEVDI 1153

Query: 1323 ------------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                          R R    +V          P +  +L++E+ ++ ++  L+      
Sbjct: 1154 CEKCGFMGYQNWCQRCRSSRGVVK------MTIPYAAKLLIQELLSMNVTARLKLGDEFP 1207

Query: 1371 SAK 1373
              K
Sbjct: 1208 ENK 1210



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 93/738 (12%), Positives = 211/738 (28%), Gaps = 120/738 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   ++   I +    A  L+F       P+  
Sbjct: 104 LVKQHIDSYNYFIEVQ----------LKKIVEASSTIYSDADSAFFLKFTDIYVGSPRRS 153

Query: 86  ------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
                          ++C  RD+TYA P+ +            T  +    + ++ + +G
Sbjct: 154 DEPKDSVESDSTVTPNECRLRDMTYAAPIFVDF----------TYKRGKDKVTQRRVPIG 203

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD 168
            +P+M                           G F++ G +++++ Q   S   I  + D
Sbjct: 204 RMPIMLRSSKCVLSNKKPNEMHLLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVETD 263

Query: 169 KGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLMA 220
             +        S S +      II             KD ++++ +     VP+   L A
Sbjct: 264 PKKEIVQASVTSSSNERKSKSYII-----------LKKDRLYLKHNVLSEDVPLVIVLKA 312

Query: 221 LGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           +G+ S++ +      +    + DF      A        +  ++         I S  K+
Sbjct: 313 MGVHSDKEMMLLVAGVDDVYQEDFAINFEEA--------IKQNVFTQQQALDWIGSKIKI 364

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
             G +   K+  ++        +   +V    ++     IY+ A         +      
Sbjct: 365 NRGKIGGYKKTHIEEAIEAISSVIISHVEVTDMDFRPKAIYV-ANMARRVLMAKHDSDMV 423

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
                +           +         K + D  ++I +V+          A S+     
Sbjct: 424 DDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNITKVLGK-RRREIFDAMSVVTLHG 482

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDI 456
                     +     +++        V H    +     + ++  +         +   
Sbjct: 483 NHITHGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGP 542

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
             L   +   +      +     L    ++   I++ D +  + + +             
Sbjct: 543 RALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEGPVSKLVFMLGAEDITTLSG 602

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETS 575
                L      +N        R    L     + R     E   ++  H+ R     T 
Sbjct: 603 KEIYGLGAYIISMNGTPIALTRRPKYFLNAFRRLRRMGRISEFVSIYINHHQRAVHIATD 662

Query: 576 EGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           +G     +  + +     + +    +     +  D      V YL   EE +  IA    
Sbjct: 663 DGRICRPLIVVENGKPLVKASHLEKLRDGSMQFDDFLAQGLVEYLDVNEENDSNIAIYEK 722

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +                        +    ++  P  ++   A LIP+  ++ S R   
Sbjct: 723 DVI-----------------------DITTHLEIEPFTILGAVAGLIPYPHHNQSPRNTY 759

Query: 693 GCNMQRQAVPLLKAEAPF 710
            C M +QA+  + +    
Sbjct: 760 QCAMGKQAIGAIASNQFL 777


>gi|224797597|gb|ACN62828.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           hydei]
          Length = 423

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 168/336 (50%), Positives = 235/336 (69%), Gaps = 8/336 (2%)

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LMG
Sbjct: 1   LSDKGEILDEQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALMG 60

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E    
Sbjct: 61  ANMQRQAIPLIAPNSPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATRIVLKTKE---- 116

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               G+  Y L  F RSNQ T +   PLV+ G ++ +  ++ADGPS D  +LALG+N++V
Sbjct: 117 ----GLKNYNLDTFVRSNQGTSLTHVPLVRQGQKIEKGQVLADGPSIDKEELALGQNVVV 172

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE   
Sbjct: 173 AFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENAR 232

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP+
Sbjct: 233 KFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPN 292

Query: 934 GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           G  G +  ++ F R   + +   + V +  I    +
Sbjct: 293 GGEGIIQAIKRFPREKYELSADVLEVIKVYIVQKRK 328



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 82/292 (28%), Positives = 135/292 (46%), Gaps = 14/292 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 140  LVRQGQKIEKGQVLADGPS-IDKEELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 198

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 199  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 252

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 253  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 310

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 311  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 365

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +    
Sbjct: 366  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGITNEELIEIMDKA 417



 Score = 39.7 bits (91), Expect = 4.1,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 29/90 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +       + ++ ++       +++      +       K 
Sbjct: 334  KMAGRHGNKGVISKILPLEDMPHMEDGTPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKL 393

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            G  +STPVFDG   E +  ++  A +   G
Sbjct: 394  GQKISTPVFDGITNEELIEIMDKAGMKNFG 423


>gi|94410910|gb|ABF18576.1| RNA polymerase II second largest subunit [Gymnopus contrarius]
          Length = 693

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 126/823 (15%), Positives = 239/823 (29%), Gaps = 146/823 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYMQKCVEQHKEFNLALAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN +     + +  +G +       R     +   R+     D SP+  V         
Sbjct: 169  EENAHSTTPTTKVFVNGVWMG---VHRDPANLVKTIRKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      +L+ +   ++ +G     ++         ++GI+E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLVLQKKHIKWLSSGQNDEGSEFKWE--HLVKSGIIELLDA 283

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     + +    ++ +     R  +K G            PS 
Sbjct: 284  EEEETVMISMTPEDLENSRLQQQGVDPHTNDGDFDPAAR--LKAGINAHTWTHCEIHPSM 341

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG                         I   ++            ++       +G   
Sbjct: 342  ILG-------------------------ICASIIPFXXXXXSPRNTYQSAMGKQAMGIYL 376

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 377  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 425

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 426  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTY 484

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 485  DKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVD 544

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q+GDK A RHG KG +
Sbjct: 545  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTI 584

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 585  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 642

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++       LR       G+ V    F G       
Sbjct: 643  -----------------------DLTVESVSMFLRQKGYQSRGLEVM---FHGHT----- 671

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                              G         V +G  Y  +L HMV
Sbjct: 672  ------------------GR---KLQAQVYLGPTYYQRLKHMV 693


>gi|118640685|gb|ABL09910.1| RNA polymerase beta subunit [Listonella pelagia]
          Length = 290

 Score =  253 bits (645), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 169/290 (58%), Positives = 226/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +  ++   + + DII ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIEREEEEERGTLDESDIIEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNDYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PR+ +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPRDHVDYMDVATNQVVSIAASLIPFLE 290


>gi|94410922|gb|ABF18580.1| RNA polymerase II second largest subunit [Hygrophorus auratocephalus]
          Length = 701

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 120/821 (14%), Positives = 234/821 (28%), Gaps = 137/821 (16%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPIIEFLEEWGMESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +           + I+  R K    D SP+  V            
Sbjct: 169  AHSSTPCTKVFVNGVWMGIHRNAAHLIDTIVKLRRK---DDISPEVSVVRDIRERKLRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D  RV     +      +L+ +                   I     G  ++++     
Sbjct: 226  TDPGRVYRPLFIVNNQQLVLQKKH------------------IRWLNRGYGDKLEFNEKT 267

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
             +         +   +    +      +   ++  P       ++++ +      +D   
Sbjct: 268  GKMEPVKFKWESLVKEGIIELLDAEEEETVMISMTPEDLENSRLQQSGVDPHSNDSDFD- 326

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
             A      V    W       SM+  I   ++            ++       +G     
Sbjct: 327  PAQRLKAGVNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTN 386

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 387  FLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNTIVAILCYSGY 435

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          + 
Sbjct: 436  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKHGTYDK 494

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 495  LEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRSHTRRDVSTPMKSTESGIVDQV 554

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 555  LI--------------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGI 594

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 595  TYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGDATPFT---- 650

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                  ++     + LR       G+ V                
Sbjct: 651  ---------------------DLTVESVSTFLRQKGYQSRGLEVM--------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                     G +       G      V +G  Y  +L HMV
Sbjct: 675  -------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 701



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 85/631 (13%), Positives = 168/631 (26%), Gaps = 108/631 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVESH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSV-------MPQDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +       M     NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPIIEFLEEWGMESLEENAHSSTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                  + +  I   RR   +                ++        P        + L
Sbjct: 186 GIHRNAAHLIDTIVKLRRKDDISPEVSVVRDIRERKLRLYTDPGRVYRPLFIVNNQQLVL 245

Query: 583 VSSL---------TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                                 G +E    K         +  L A EEE   I+     
Sbjct: 246 QKKHIRWLNRGYGDKLEFNEKTGKMEPVKFKWESLVKEGIIELLDAEEEETVMISMTPED 305

Query: 634 LDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           L+        +       +          V        +  P  ++ I AS+IPF +++ 
Sbjct: 306 LENSRLQQSGVDPHSNDSDFDPAQRLKAGVNAHTWTHCEIHPSMILGICASIIPFPDHNQ 365

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           S R      M +QA+ +                                           
Sbjct: 366 SPRNTYQSAMGKQAMGIYLTNFLI------------------------------------ 389

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                   + + +  Y       +     +  R                        +L 
Sbjct: 390 -----RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELP 420

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT---- 862
            G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E      
Sbjct: 421 AGQNTIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPT 480

Query: 863 -RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             +   +       +++ G+I  G  V   DI++GK  P         ++        ++
Sbjct: 481 RENTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-------RS 533

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              RD S  + S  SG V  V I       K
Sbjct: 534 HTRRDVSTPMKSTESGIVDQVLITTNSEGQK 564


>gi|224797593|gb|ACN62826.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797595|gb|ACN62827.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
 gi|224797599|gb|ACN62829.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            hydei]
          Length = 424

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 171/369 (46%), Positives = 247/369 (66%), Gaps = 8/369 (2%)

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1    RLSDKGEILDEQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E   
Sbjct: 61   GANMQRQAIPLIAPNSPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATRIVLKTKE--- 117

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G+  Y L  F RSNQ T +   PLV+ G ++ +  ++ADGPS D  +LALG+N++
Sbjct: 118  -----GLKNYNLDTFVRSNQGTSLTHVPLVRQGQKIEKGQVLADGPSIDKEELALGQNVV 172

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE  
Sbjct: 173  VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENA 232

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233  RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G  G +  ++ F R   + +   + V +  I    + ++ +++         + +IL  
Sbjct: 293  NGGEGIIQAIKRFPREKYELSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPL 352

Query: 993  QNAVSGPKG 1001
            ++      G
Sbjct: 353  EDMPHMEDG 361



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 82/292 (28%), Positives = 135/292 (46%), Gaps = 14/292 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVRQGQKIEKGQVLADGPS-IDKEELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +    
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGITNEELIEIMDKA 418



 Score = 39.7 bits (91), Expect = 4.2,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 29/90 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +       + ++ ++       +++      +       K 
Sbjct: 335  KMAGRHGNKGVISKILPLEDMPHMEDGTPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKL 394

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            G  +STPVFDG   E +  ++  A +   G
Sbjct: 395  GQKISTPVFDGITNEELIEIMDKAGMKNFG 424


>gi|307343554|emb|CBJ18694.1| RNA polymerase B subunit [Micromonospora coxensis]
          Length = 211

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 95/213 (44%), Positives = 124/213 (58%), Gaps = 38/213 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
              G++ L+DG +GEP   P+ VGYIY+LKLNH+
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNHL 209


>gi|45545337|gb|AAS67516.1| DNA-dependent RNA polymerase II second largest subunit [Neofusicoccum
            mangiferae]
          Length = 910

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 133/850 (15%), Positives = 266/850 (31%), Gaps = 95/850 (11%)

Query: 352  VNNNAYIRNTLVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
            V++   I +      +    +A+       V+    VS         +       K +  
Sbjct: 88   VSDEDIISHICFDKNDTQIMEAIRPSIEESVLIQDRVSALDFIGRRGSNPSTGGTKRERV 147

Query: 410  TVGRVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             + R  +           +     +   +  +I  L+    G+   DD D+ G +R+   
Sbjct: 148  KLARDIIQKEFLPHISQAEGSETKKAFFLGYMIYRLLQCHLGRRDEDDRDHFGKKRLDLA 207

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R   L++ R +   +            Q  +    + + +     +      
Sbjct: 208  GPLLANLFRSLFLKLTRDVYNYLKKCIEAGRPFSLQSAVKQGTITNGLKYSLATGNWGDQ 267

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 268  KKAASSKAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPA 323

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L+    V     +     +    + ++  +     +      +I   
Sbjct: 324  ETPEGQACGLVKNLSLMCNVTVGSDVTPIQDFMTQRNMELLEEYEPNVSPNATKIFINGV 383

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +    +V        +      I D  D   K          P    DD   
Sbjct: 384  WVGVHRDPTQLVSVVKKLRRDGTLSAEMSLIRDVRDREFKIFTDAGRVCRPLFIIDDDPF 443

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIR 746
                 N+   R+ +  L+A+     +GM                ++G+VE +DA    + 
Sbjct: 444  SPNKGNLVLAREHIDKLEADQEIDVSGMNDDERDEKRYGWKGLLQSGVVEYMDAEEEEVA 503

Query: 747  SVEGDLDPSTSGVDIYR---LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             +    D   +     +     + + S +N   ++R +      V++       PS  LG
Sbjct: 504  MITMTPDDLRAHHRARQGIIDEEDEESKRNRDPHERVVPAPNPSVKQYTHCEIHPSMILG 563

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +   +   E                 
Sbjct: 564  -------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVCLTNYE----------------- 599

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                        +    ++ V             +       +   +  + AI      +
Sbjct: 600  ------------LRMDTMVNVLYYPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYN 647

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +     +  +   + +  ++V    +E   +    + + L    Y
Sbjct: 648  QEDSVIMNQSSIDRGLFRSLFYRSYTDQEKKVGMAV----VEQFEKPLRSDTMRLKHGTY 703

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   +  G           K+  ++ D                +E  QR    +K 
Sbjct: 704  DKLDDDGVVAPGVRVSGEDIIIGKTAPIAPD---------------AEELGQRTKMHIKR 748

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   + +      D +     + VKV     +  Q GDK A RHG KG +
Sbjct: 749  DVSTPLRSTENGIVDSVLLTTNSDGL-----KFVKVRTRTTKIPQIGDKFASRHGQKGTI 803

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF ++G   DI++NP  +PSRM +  + E  L       G++  +      
Sbjct: 804  GITYRHEDMPFTREGLTPDIIINPHAIPSRMTIAHLIECLLSKVGALRGQEGDATPFTDV 863

Query: 1161 ANGDISPLRS 1170
                +S L  
Sbjct: 864  TVTQVSSLLR 873



 Score = 97.1 bits (240), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 68/547 (12%), Positives = 156/547 (28%), Gaps = 56/547 (10%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +V+ D    +P+     ALG+   E+I+S        +Q  +     +  + L+     +
Sbjct: 71  YVKAD----IPIPIVFRALGIVSDEDIISHICFDKNDTQIMEAIRPSIEESVLIQDRVSA 126

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGI------TSDCLCGLYVAEDIVN 314
              +            K+    L +  ++++ +  +              G  +   ++ 
Sbjct: 127 LDFIGRRGSNPSTGGTKRERVKLARDIIQKEFLPHISQAEGSETKKAFFLGYMIYR-LLQ 185

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDA 373
              G    +  D   +K L+            L++  + +   Y++  +   +    + A
Sbjct: 186 CHLGRRDEDDRDHFGKKRLDLAGPLLANLFRSLFLKLTRDVYNYLKKCIEAGRPFSLQSA 245

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHI 431
           +             T  +  S+    + D  K   S  G  ++  R    +      R  
Sbjct: 246 VKQ--------GTITNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTYSSTLSHLRRTN 297

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
                   +     L N    +         +      ++KN   +  + +   +     
Sbjct: 298 TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG---LVKNLSLMCNVTVGSDVTPIQD 354

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVA 550
            +   ++   +        +A   F     +    +    +S +   RR   L  +  + 
Sbjct: 355 FMTQRNMELLEEYEPNVSPNATKIFINGVWVGVHRDPTQLVSVVKKLRRDGTLSAEMSLI 414

Query: 551 RARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSF--------ARVNAY 595
           R     E        R   P       P   ++G+ +     +           + +N  
Sbjct: 415 RDVRDREFKIFTDAGRVCRPLFIIDDDPFSPNKGNLVLAREHIDKLEADQEIDVSGMNDD 474

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
              E  Y        +  V Y+ A EEE   I      L       + ++       +  
Sbjct: 475 ERDEKRY-GWKGLLQSGVVEYMDAEEEEVAMITMTPDDLRAHHRARQGIIDEEDEESKRN 533

Query: 656 VPREK------------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               +                +  P  ++ I AS+IPF +++ S R      M +QA+ +
Sbjct: 534 RDPHERVVPAPNPSVKQYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV 593

Query: 704 LKAEAPF 710
                  
Sbjct: 594 CLTNYEL 600


>gi|52699860|gb|AAU86991.1| DNA-dependent RNA polymerase II second largest subunit [Porpidia
            albocaerulescens]
          Length = 715

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 123/837 (14%), Positives = 241/837 (28%), Gaps = 148/837 (17%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R    G +L   +R+   ++ + + +  +    +         + +  + + +   
Sbjct: 1    FGKKRXDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTLTNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   L +  
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPN 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ATKVFVNGVWVGVHRDPAHLVSTVQNLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRP 236

Query: 681  FLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVG-TGMESVVAKSSGAAIVAKRAGIVEQ 737
                D+  +     N+   ++ V  L+ +   +  T  E            AK  G    
Sbjct: 237  LFVIDNDPKSSNRGNLVLTKEHVQKLEEDREIIASTDPEERE---------AKLMGWEGL 287

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIAD 796
            V   + V+  V+ + + +   V     ++  R  Q   V   P +      V+       
Sbjct: 288  V--NQGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGFVLPEPSIDDPNKRVKAPLNPTA 345

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +   + +  ++V      
Sbjct: 346  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM---- 399

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 400  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 436

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 437  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMNVVEEFEKPMRSDT 492

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 493  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLR 552

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 553  STENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFAS 592

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 593  RHGQKGTIGITYRQEDMPFSSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 652

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L                           V     +G  +   VF 
Sbjct: 653  DATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGKKLVAQVF- 696

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                                  +G  Y  +L HMV  K+ A
Sbjct: 697  --------------------------------------LGPTYYQRLRHMVDXKIXA 715


>gi|219689348|gb|ACL31694.1| RNA polymerase subunit beta [Bartonella sp. Tel Aviv Rr]
          Length = 265

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 183/257 (71%), Positives = 215/257 (83%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R R
Sbjct: 3   EIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRER 62

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +
Sbjct: 63  AGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKE 122

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS
Sbjct: 123 VIYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVS 182

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           +AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGAA+ AKR+G
Sbjct: 183 VAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGAAVSAKRSG 242

Query: 734 IVEQVDAIRIVIRSVEG 750
           IV+QVDA RIVIR+ E 
Sbjct: 243 IVDQVDATRIVIRATED 259


>gi|118640689|gb|ABL09912.1| RNA polymerase beta subunit [Listonella anguillarum]
 gi|118640691|gb|ABL09913.1| RNA polymerase beta subunit [Listonella anguillarum]
 gi|118640693|gb|ABL09914.1| RNA polymerase beta subunit [Vibrio ordalii]
          Length = 290

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 225/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  +   ++  + + DII ++K L+ +RNG G +
Sbjct: 1   SLFESLFFSEERYDLSTVGRMKFNSSIEREDAGELGTLDETDIIEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQFVIAQANAI 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|262117906|dbj|BAI47978.1| RNA polymerase beta subunit [Bartonella sp. BR12-1]
          Length = 275

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 197/276 (71%), Positives = 228/276 (82%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+P RK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPCRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANS LD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSPLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ S A
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSRA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR GIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRGGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|294660111|ref|XP_002777730.1| DEHA2G23232p [Debaryomyces hansenii CBS767]
 gi|199434470|emb|CAR66041.1| DEHA2G23232p [Debaryomyces hansenii]
          Length = 1165

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 171/1127 (15%), Positives = 349/1127 (30%), Gaps = 195/1127 (17%)

Query: 269  TGEQVIESGKKLT---SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
                ++E+ +K     + +  S  E+  K   IT +    L       +     I   AG
Sbjct: 204  KNRIIVEADEKKNIVQASVTSSTHERKSKTYVITKNDNIYLKHNSISEDIPIVIILKAAG 263

Query: 326  DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
               D + L+ +   + +   +  V+               +   ++ AL  + + ++   
Sbjct: 264  ITSDLEILQLVCGQDPQYQDLFVVNFEEA--------AKLEIFTQQQALNYVGKRVK--- 312

Query: 386  VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                                     +  +   +  +L   D     +   I A+ + ++ 
Sbjct: 313  ---------TIRRAGAPKLSQMQEGIEAIATTIIAHLTVSDLQFREKALYIAAMARRVLM 363

Query: 446  LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS-------- 497
              +    +DD D +GN+R+   G+++   +     +     K  I  +            
Sbjct: 364  TMHNPKMVDDRDYVGNKRLELAGQLMSLLFEDLFKKFNSDFKANIDKILKKPSRASEFDA 423

Query: 498  -VMPQDLINAKPVVSAVCEFFCSSQLSQL-EEHVNSLSRITHTRRLSALGQG-----GVA 550
             +      N   +         +  L +   E       ++    +SALG          
Sbjct: 424  LLSINIHSNNITMGLNRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFE 483

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            ++R     R + P+ +G +C A+T EG   GLV +L     + +    E P +K+C    
Sbjct: 484  KSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITSD-DEELPIKKLCYVLG 542

Query: 611  TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              D++ + +        A  N  +  +G+     +          V     DF +     
Sbjct: 543  CEDILGIDSA----TLYADGNFGVCVNGT-----LIGCTRFPVKFVS----DFRNLRRSG 589

Query: 671  VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             VS   S+         +    G  + R  + + +     V     + +     A     
Sbjct: 590  KVSAFISIYTNSHQKAVHIATDGGRICRPLIIIGEKNKSKVNEHHLAKLLSGKWAFDDFL 649

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            + G+VE +D               + S + +Y     + S Q                  
Sbjct: 650  KDGLVEYLDVNE-----------ENDSLIALYEHDLVEHSYQTF---------------- 682

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
               +   P T LG +A         +P+  +N          M  +    +I +  +   
Sbjct: 683  -THMEIEPFTVLGAVA-------GLIPYPHHNQSPRNTYQCAMGKQ----AIGVIGYNQF 730

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
             R   L    +    P V  + ++ ID                            +   +
Sbjct: 731  RRIDTLLYLMVYPQQPMVKTKTIELIDYD-------------------------KLPAGQ 765

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + A+      D+ D  +   S +       ++  R      +R  +  ++ +  +  D
Sbjct: 766  NAVVAVMSYSGYDIEDALVLNKSSIDRGFGRCQVL-RKNTITLKRYPNHTKDLVSGMRVD 824

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            ++ E  I              G    +G     K              +   +  +    
Sbjct: 825  ENGEP-IFPHAALGPDGLGEVGMKVENGQVYVNK-----------CVPNNAGESVLGSND 872

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             Q N +     +    +  +      ++++     +      ++KV +   R  + GDK 
Sbjct: 873  QQHNQQQTAESHREVPAFYKAPEPAYVDQVMM--SVSDNDQALIKVLLRQTRRPELGDKF 930

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            +                                     SR                  G+
Sbjct: 931  S-------------------------------------SR-----------------HGQ 936

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            K    I   + +   +      + ++       +++      ++       +G       
Sbjct: 937  KGVCGIIVQQEDLPFNDDGISPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTC 996

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F G+  E ++  L       SG+ +LY G+TGE     +  G IY  KL HMV DK++AR
Sbjct: 997  FGGSKLEEMSRTLVDKGFSYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHAR 1056

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--- 1323
            + G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD    D+    
Sbjct: 1057 ARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMLSSDAFEVDICNQC 1116

Query: 1324 ---GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               G      S  +     +   P +  +L +E+ ++ ++  L+   
Sbjct: 1117 GLMGYNSWCTSCKSSEYIIKMTIPYAAKLLFQELLSMNIAPRLKLGD 1163



 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 130/951 (13%), Positives = 274/951 (28%), Gaps = 174/951 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    S+++F+ +++    + NE        V P         L+++          P
Sbjct: 57  LVKQHLDSFNYFVDVDLKKIIKANE---LVLSDVDP------EFYLKYLDIRIGHKSTSP 107

Query: 84  P-----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           P          +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 108 PGTKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIMHKDLEIGRMPIM 157

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++ G +++++ Q   S          + ++
Sbjct: 158 LRSNKCILDGIDEQQMARFDECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKNI 217

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++           D I+++ +     +P+   L A G+ S+ EIL   
Sbjct: 218 VQASVTSST--HERKSK-TYVITKNDNIYLKHNSISEDIPIVIILKAAGITSDLEILQLV 274

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL--LKSLKE 290
             +    Q      F  +A   +   + + + V             KL+     ++++  
Sbjct: 275 CGQDPQYQDLFVVNFEEAAKLEIFTQQQALNYVGKRVKTIRRAGAPKLSQMQEGIEAIAT 334

Query: 291 KGVKFLGITSDCLCGLYV-----AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
             +  L ++        +     A  ++        ++  D +  K LE           
Sbjct: 335 TIIAHLTVSDLQFREKALYIAAMARRVLMTMHNPKMVDDRDYVGNKRLELAGQLMSLLFE 394

Query: 346 ILYVDSVNN-NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
            L+    ++  A I   L         DALL I                   +   +   
Sbjct: 395 DLFKKFNSDFKANIDKILKKPSRASEFDALLSINIHSNN----ITMGLNRAISTGNWSLK 450

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLGNR 462
           ++ +   G   +  RL+  +   +            K+     L+  +  +    +    
Sbjct: 451 RFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEG 510

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
               + + L     +     E  IK+    +  + ++  D        +        + +
Sbjct: 511 EACGLVKNLALMTHITSDDEELPIKKLCYVLGCEDILGIDSATLYADGN-FGVCVNGTLI 569

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                 V  +S   + RR   +         +  +   +  T  GRIC      G     
Sbjct: 570 GCTRFPVKFVSDFRNLRRSGKVSAFISIYTNSHQKAVHI-ATDGGRICRPLIIIGEKNKS 628

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             +    A+      + +      D      V YL   EE +  IA              
Sbjct: 629 KVNEHHLAK------LLSGKWAFDDFLKDGLVEYLDVNEENDSLIA-------------- 668

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    + +    +    ++  P  V+   A LIP+  ++ S R    C M +QA+ 
Sbjct: 669 -----LYEHDLVEHSYQTFTHMEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIG 723

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
                                                    VI   +     +   + +Y
Sbjct: 724 -----------------------------------------VIGYNQFRRIDTLLYLMVY 742

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+P+VK                 D   L  G+N +VA M + GY+
Sbjct: 743 P--------------QQPMVK----------TKTIELIDYDKLPAGQNAVVAVMSYSGYD 778

Query: 823 FEDSMLISERMVSEDVFTSIHIEE-------FEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            ED++++++  +         + +       +    +D   G        P         
Sbjct: 779 IEDALVLNKSSIDRGFGRCQVLRKNTITLKRYPNHTKDLVSGMRVDENGEPIFPHAA--- 835

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           +   G+  VG +V  G + V K  P             +    + A   R+
Sbjct: 836 LGPDGLGEVGMKVENGQVYVNKCVPNNAGESVLGSNDQQHNQQQTAESHRE 886


>gi|307343602|emb|CBJ18716.1| RNA polymerase B subunit [Polymorphospora rubra]
          Length = 211

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 123/212 (58%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K+     ++K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVDGDDAEWKKALRSID---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I  +L     +        
Sbjct: 139  -------------------AHESEPDTNVATPVFDGAKEEEITGLLSSTLPNRDGEQLVG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGYIY+LKLNH
Sbjct: 180  GSGKAQLFDGRSGEPLPDPIAVGYIYILKLNH 211


>gi|224812781|gb|ACN65024.1| RpoB [Cronobacter muytjensii]
          Length = 252

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 156/252 (61%), Positives = 195/252 (77%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVT 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D 
Sbjct: 121 DGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 240

Query: 727 IVAKRAGIVEQV 738
            VAKR G V+ V
Sbjct: 241 AVAKRGGTVQYV 252


>gi|307343468|emb|CBJ18651.1| RNA polymerase B subunit [Micromonospora sp. GUI23]
          Length = 213

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 96/213 (45%), Positives = 126/213 (59%), Gaps = 38/213 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
              G++ L+DG +GEP   P+ VGY+Y+LKLNH+
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNHL 213


>gi|262117882|dbj|BAI47966.1| RNA polymerase beta subunit [Bartonella sp. RJ27-1]
          Length = 275

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 231/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS I+  RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEISLKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRAGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|52699835|gb|AAU86979.1| DNA-dependent RNA polymerase II second largest subunit [Maronea
            chilensis]
          Length = 718

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 118/832 (14%), Positives = 237/832 (28%), Gaps = 136/832 (16%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L N +R    ++   + +              Q  + +  + S +  
Sbjct: 1    HXGKKRLDXAGPLLANLFRQVFTKLIGDMNKYLSRCIDSGREFNLQLAVKSNTITSGLRY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLSTGNWSDQKNAATAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAM 620
             TH+G +CPAET EG   GLV +L     V+     +    +    + +V  +     + 
Sbjct: 117  NTHWGLVCPAETPEGQACGLVKNLALMCYVSVGTPSDPILDFLVQRNMEVLEEYEPQRSP 176

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLI 679
                 ++      +  +       V        +      + D  D   K          
Sbjct: 177  NATKVFVNGVWVGVHRNPIHLVNTVQKLRRTSVLSYEISLVHDIRDREFKIFTDAGRVCR 236

Query: 680  P-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            P F+   D      G  +  +       +        E+++ K   A +  K   ++   
Sbjct: 237  PLFVVETDPKSANNGNLVLTKEHVNKLEDHK------ETMMDKDRMARMSEKDKELLGWS 290

Query: 739  DA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                + ++  V+ + + +   V     ++  R  Q       P V   +   +  I    
Sbjct: 291  GLVKQGMVEYVDAEEEETVMIVMTPEDLEISRQIQAGYALPEPSVDEPNRRVKAPINPTA 350

Query: 798  PSTDLGDL--ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
             +    ++  ++   +  + +P+  +N                        +        
Sbjct: 351  HTWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYXSAMGKQA 392

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G      D                +  +             +       +   +  + A
Sbjct: 393  MGVYLTNFDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 441

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R      EQ E   R    + 
Sbjct: 442  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKRIGMNVVEQFEKPMRSDTLKL 500

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             +   +       +  G           K+  +++D      R++               
Sbjct: 501  KMGTYDKIDADGIVAPGSRVSGEDIIIGKTAPMAADAEELGQRTKL-------------- 546

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +K    T     E    +++             L+ VKV +   +  Q GDK A RHG
Sbjct: 547  -HIKRDVSTPLRSTESGIVDRVL-----YTTNSEGLKFVKVRMRTTKVPQIGDKFASRHG 600

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 601  QKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDAT 660

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S L    E    +                                     
Sbjct: 661  PFTDVTVDSVSRLLR--EHGYQSRGFEVM------------------------------- 687

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                           +G +    G         V +G  Y  +L HMV D +
Sbjct: 688  --------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDXI 718


>gi|124263396|gb|ABH09761.2| RNA polymerase II second largest subunit [Urocystis colchici]
          Length = 707

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 121/829 (14%), Positives = 243/829 (29%), Gaps = 139/829 (16%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G ++ + +R+   ++ R I    +    +      Q  + +  + + +    
Sbjct: 1    GKKRLDLAGPLMASLFRMLFRKLTRDIYRHLQRCVEEHKEFHIQAAVKSSTITNGLRYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY-LSAMEEE 623
            H+G +CPAET EG   GLV +L+  + ++           + +  + + V   ++  +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSLMSNISVGTPSAPIIEFLEEFGLDSLVDMQVTNAKAT 176

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              ++        +D     + +      +            D S +  V           
Sbjct: 177  KVFVNGVWMGTHDDPGQLVDTLRDLRRKD------------DISHEVSVVRDIREKELRL 224

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D+ RVL    +       L  +   V   G  + + +      + +  G++E +DA  
Sbjct: 225  YTDAGRVLRPLFIVNPMDMTLLIKKHHVAMLGQTTELGEEFRWTQLVQ-QGVIEYLDAE- 282

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                  E  +    S  D+ +  +++  N      Q P                   T  
Sbjct: 283  -----EEETVMICMSPTDLEQSREYKARNG-----QMP-----------------AETAD 315

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
                L      A   W       +M++                               + 
Sbjct: 316  PSARLKSPHTFAPDTWTHCEIHPAMILGICASIIPFPXXXXXXX-XXXXXXXXXYQSAMG 374

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +    V     +      +  +             +       +   +  + AI      
Sbjct: 375  KQSMGVYLTNYQMR-MDTMANILYYPQKPLATTRSMEHLRFRELPAGQNAIVAILCYSGY 433

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  + + ++   +  E+ E  +RD          + 
Sbjct: 434  NQEDSVIMNQSSIDRGLF-RSLYYRAYMAEEKKVGVMIMEEFEKPSRDNTIRLKHGTYDK 492

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  +  G           K+  L  D      RS+        + V  +++S +   
Sbjct: 493  IDADGMVPPGTRVSGDDIIIGKTAPLPPDSEELGLRSK----THTKKDVSISLKSTENGI 548

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 +                       + VKV V   R  Q+GDK A RHG KG +  
Sbjct: 549  IDQVLL----------------TTNANGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGI 592

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  +        
Sbjct: 593  TYRQEDMPFTSEGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGDATPFTELTV 652

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S +   L     +                                            
Sbjct: 653  EAVSSILRGLG--YHSRGLEVM-------------------------------------- 672

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                    +G +    G           +G  Y  +L HMV DK+++R+
Sbjct: 673  -------YNGHT----GR---KLQAQCYLGPTYYQRLKHMVDDKIHSRA 707



 Score = 62.0 bits (149), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 54/449 (12%), Positives = 123/449 (27%), Gaps = 50/449 (11%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR ++    +   F +  ++ +    +  +Y L   G      +         + + +
Sbjct: 26  DIYRHLQRCVEEHKEFHIQAAVKSSTITNGLRYSL-ATGNWGDQKKFMQAKAGVSQVLNR 84

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 85  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSNI 144

Query: 489 RISSVDI------DSVMPQDLINAKPVVSAVCEFF-CSSQLSQLEEHVNSLSRITHTRRL 541
            + +         +      L++ +   +   + F     +   ++    +  +   RR 
Sbjct: 145 SVGTPSAPIIEFLEEFGLDSLVDMQVTNAKATKVFVNGVWMGTHDDPGQLVDTLRDLRRK 204

Query: 542 SAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
             +  +  V R     E+R ++      + P       ++ L+      A +     +  
Sbjct: 205 DDISHEVSVVRDIREKELR-LYTDAGRVLRPLFIVNPMDMTLLIKKHHVAMLGQTTELGE 263

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--------VFCRCAGE 652
            +R          + YL A EEE   I  + + L++   +                    
Sbjct: 264 EFR-WTQLVQQGVIEYLDAEEEETVMICMSPTDLEQSREYKARNGQMPAETADPSARLKS 322

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFL-----------------------ENDDSNR 689
                 +     +  P  ++ I AS+IPF                        ++     
Sbjct: 323 PHTFAPDTWTHCEIHPAMILGICASIIPFPXXXXXXXXXXXXXXXXYQSAMGKQSMGVYL 382

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                 M   A  L   + P   T  ME +  +   A   A  A +          +   
Sbjct: 383 TNYQMRMDTMANILYYPQKPLATTRSMEHLRFRELPAGQNAIVAILCYSGYNQEDSVIMN 442

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
           +  +D        YR    +       + 
Sbjct: 443 QSSIDRGLFRSLYYRAYMAEEKKVGVMIM 471


>gi|52699908|gb|AAU87015.1| DNA-dependent RNA polymerase II second largest subunit [Xanthomendoza
            fallax]
          Length = 717

 Score =  252 bits (644), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 129/838 (15%), Positives = 238/838 (28%), Gaps = 146/838 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G +L   +R+   ++ + I +  +              +    + S + 
Sbjct: 1    DXXGKKRLDXAGPLLAGLFRMLFQKLTKDIYKYLQKCVESNREFNLTLGVKQNTLSSGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     ++     +    Y      +   +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPADPIIDYLSNRGMENLEEYEPARS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     +        I      + D  D   K         
Sbjct: 177  PHATKIFVNGTWIGVHNDPANLVPHIQDVRRKGIIAHEASLVRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+  R     N+   +  V  L+ E   V T M+            A       
Sbjct: 237  RPLFVIDNDPRSENMGNLALTKDMVQKLEDERDVVLT-MDPEERADHVIGWEA------- 288

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRNDIIA 795
             VDA    I  V+ + + +         ++  R  Q       P        V+      
Sbjct: 289  LVDA--GAIEYVDAEEEETIMIAMTPEDLEISRQIQAGYAAPVPSEDAPNQRVKAPLNPT 346

Query: 796  DGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T      ++   +  + +P+  +N          M  + +   + +  ++      
Sbjct: 347  AHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTXYDERM--- 401

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                                      +  +             +       +   +  + 
Sbjct: 402  ------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIV 437

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R  +D  +R        +E   +    E
Sbjct: 438  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVDTEKRVGM---TVLEKFEKPLRTE 493

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + L    Y +L +   +  G           K+T ++ D                 E  
Sbjct: 494  TLKLKHGTYDKLDDDGLVAPGVRVSGEDVIIGKTTPIAPD---------------AQEMG 538

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR    +K    T     E+   +K+             L+ VKV +   +  Q GDK A
Sbjct: 539  QRTKNHVKKDASTPLRSTENGIVDKVLL-----STNSEGLKFVKVRMRTTKVPQIGDKFA 593

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +
Sbjct: 594  SRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYE 653

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S L    E    +                                 
Sbjct: 654  GDATPFTEITVDSVSKLLR--EHGYQSRGFEVM--------------------------- 684

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                               +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 685  ------------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVXXKIXA 717


>gi|118640679|gb|ABL09907.1| RNA polymerase beta subunit [Vibrio nereis]
          Length = 290

 Score =  252 bits (643), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 168/290 (57%), Positives = 222/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIEREDAQEQGTLDETDIIEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIQEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|45545329|gb|AAS67512.1| DNA-dependent RNA polymerase II second largest subunit [Diploschistes
            muscorum]
          Length = 901

 Score =  252 bits (643), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 125/867 (14%), Positives = 248/867 (28%), Gaps = 149/867 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  ++ +  G+   DD D+ G +R+   G ++ + +R    
Sbjct: 158  HISQSEGSETRKAFFLGYMVHRMLQVALGRREPDDRDHFGKKRLDLAGPLMASLFRSLFN 217

Query: 481  RMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ + + + +               + +  + + +     +               +SQ+
Sbjct: 218  RLTKDVLKYLQKCIEGNRDFNIALGVKSTTLTNGLKYSLATGNWSEQKKAAQGKAGVSQV 277

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 278  LNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 333

Query: 586  LT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L    +  V + G     +    + +V  +     +      ++      +  D +    
Sbjct: 334  LALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPNITKVFVNGVWVGVHRDPAHLYN 393

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMGCNMQRQA 700
             V        I      I D  D   K          P   ++ND  +       + ++ 
Sbjct: 394  TVLSLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVARPLFVIDNDKRSSRRGELVLSKEL 453

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            V  L+ +             +        K  G    V +    +  ++ + + +     
Sbjct: 454  VNRLEDDRELPPDLDPDEKKE--------KYFGWEGLVKS--GAVEYLDAEEEETVMIAM 503

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWH 819
                +   R  Q       P        +          T      ++   +  + +P+ 
Sbjct: 504  TPEDLDISRQVQAGYAPPEPSTDQNARFKAPINTNVHTWTHCEIHPSMILGICASIIPFP 563

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE- 878
             +N          M  + +                                  L N DE 
Sbjct: 564  DHNQSPRNTYQSAMGKQAMGV-------------------------------FLTNFDER 592

Query: 879  -CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  + AI      +  D+ +   S +  
Sbjct: 593  MDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 652

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R  +++ +R        +E   +    E + L    Y +L +   I  G  
Sbjct: 653  GLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYEKLDDDGLIAPGVR 708

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  ++ D                DE  QR     K    T     E+   
Sbjct: 709  VSGEDVIIGKTAPIAPD---------------TDELGQRTKLHSKRDASTPLRSTENGIV 753

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +
Sbjct: 754  DKVLL-----TTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTAE 808

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G +  +          +S L    E 
Sbjct: 809  GITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVDSVSRLLR--EH 866

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
               +                                                    +G +
Sbjct: 867  GYQSRGFEVM---------------------------------------------YNGHT 881

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G         V  G  Y  +L H
Sbjct: 882  ----GR---KLRAQVFFGPTYYQRLRH 901



 Score = 95.5 bits (236), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 77/614 (12%), Positives = 176/614 (28%), Gaps = 77/614 (12%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS        K       ++ Y   I    ++G  +      K   H R 
Sbjct: 1   SEKVLIAQE-RSAANIVQVYK---RSDDRIPYLAEIRSAVEKGTRLISSMSVK--YHSRK 54

Query: 207 DRRRK---------------VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLS 250
           D ++                + V     ALG+   E+IL+        +Q  +     + 
Sbjct: 55  DDKKSFGSSIKVTLPYVKEEIAVAIVFRALGVVSDEDILNHICFDRRDTQMMEMLKPCIE 114

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGITSDCLCGLYVA 309
            A ++   +V+   +   +        K++     +  ++++ +  +  +          
Sbjct: 115 EAFVVQDREVALDHIGKRSNALGQPRDKRI--RHARDIMQKELLPHISQSEGSETRKAFF 172

Query: 310 EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
              +     ++ +   +  D            + + +           + +   +  N+ 
Sbjct: 173 LGYMVHRMLQVALGRREPDDRDH------FGKKRLDL-------AGPLMASLFRSLFNRL 219

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            KD L  + + +       F++A  + +    +  KY L   G      +         +
Sbjct: 220 TKDVLKYLQKCIEGNR--DFNIALGVKSTTLTNGLKYSL-ATGNWSEQKKAAQGKAGVSQ 276

Query: 430 HIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
            + +    + +  L        R+GK       +  +  +    E  + Q    +  +  
Sbjct: 277 VLNRYTFASTLSHLRRTNTPLGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 336

Query: 485 SIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRIT 536
                + S     +      N + +         +    F     +    +  +  + + 
Sbjct: 337 MCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPNITKVFVNGVWVGVHRDPAHLYNTVL 396

Query: 537 HTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI---GLVSS 585
             RR + +  +  + R     E        R   P          +  G  +    LV+ 
Sbjct: 397 SLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVARPLFVIDNDKRSSRRGELVLSKELVNR 456

Query: 586 LTSFARVNAYGFI---ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           L     +         +  Y        +  V YL A EEE   IA     LD       
Sbjct: 457 LEDDRELPPDLDPDEKKEKYFGWEGLVKSGAVEYLDAEEEETVMIAMTPEDLDISRQVQA 516

Query: 643 ELVFCR-------CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                             I          +  P  ++ I AS+IPF +++ S R      
Sbjct: 517 GYAPPEPSTDQNARFKAPINTNVHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 576

Query: 696 MQRQAVPLLKAEAP 709
           M +QA+ +      
Sbjct: 577 MGKQAMGVFLTNFD 590


>gi|224797561|gb|ACN62810.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            mojavensis]
          Length = 424

 Score =  252 bits (643), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 172/369 (46%), Positives = 247/369 (66%), Gaps = 8/369 (2%)

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1    RLSDKGEILDEQVVARFQGENIIAGRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G V+ VDA RIV+++ E   
Sbjct: 61   GANMQRQAIPLIAPNSPYVGTGVEYAAARDSGLAIVSQYDGTVDFVDATRIVLKTKE--- 117

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 G+  Y L  F RSNQ T +   PLV+ G ++ +  I+ADGPS D  +LALG+N++
Sbjct: 118  -----GLKNYNLDTFVRSNQGTSLTHVPLVRQGQKIEKGQILADGPSIDKEELALGQNVV 172

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
            VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK GPEEITR+IPN+SE  
Sbjct: 173  VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGPEEITREIPNISENA 232

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D SLRVP
Sbjct: 233  RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVP 292

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            +G  G +  ++ F R   + +   + V +  I    + ++ +++         + +IL  
Sbjct: 293  NGGEGIIQAIKRFPREKYELSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPL 352

Query: 993  QNAVSGPKG 1001
            ++      G
Sbjct: 353  EDMPHMEDG 361



 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 83/292 (28%), Positives = 135/292 (46%), Gaps = 14/292 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G ++  G IL    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 141  LVRQGQKIEKGQILADGPS-IDKEELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 199

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 200  TSIHIEEYTIERRQTKQGPEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 253

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 254  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 311

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+KV++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 312  -----LSADVLEVIKVYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 366

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +LNPLGVPSRMN+GQ+ E HLG A   LG+KI + + D   N ++  +    
Sbjct: 367  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKISTPVFDGITNEELIEIMDKA 418



 Score = 39.7 bits (91), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 29/90 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +       + ++ ++       +++      +       K 
Sbjct: 335  KMAGRHGNKGVISKILPLEDMPHMEDGTPIDIMLNPLGVPSRMNIGQVLEIHLGMAAKKL 394

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            G  +STPVFDG   E +  ++  A +   G
Sbjct: 395  GQKISTPVFDGITNEELIEIMDKAGMKNFG 424


>gi|46277289|gb|AAS86835.1| RNA polymerase II second largest subunit [Camellia japonica]
          Length = 591

 Score =  252 bits (643), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 120/735 (16%), Positives = 217/735 (29%), Gaps = 147/735 (20%)

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            + R +H +H+G +CPAET EG   GLV +L     +            + +    N    
Sbjct: 4    KPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVGSAAHPILEFLEEWSTEN---- 59

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
                EE +  +    + +  +G +           + +   R ++   D + +  V    
Sbjct: 60   ---FEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDI 113

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             L       D  R      +  +   L+K +   +    E    + SG        G +E
Sbjct: 114  RLKELRLYTDYGRCSRPLFIVDKQRLLIKKKDILILQQRE--SPEESG-WHDLVAKGFIE 170

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VD             + +T        +   R N +   +                   
Sbjct: 171  YVDTEE----------EETTMISMTINDLVTSRVNPDEAYS-----------ETYTHCEI 209

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             PS  LG       +  + +P+  +N          M  + +   I++  ++        
Sbjct: 210  HPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ-------- 252

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                               +    +  V        +    +       +        AI
Sbjct: 253  -------------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINATVAI 293

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +        +F R   D+ ++  ++ +E      RD      
Sbjct: 294  ACYSGYNQEDSLIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLIKEDFGCPNRDNTMGMR 352

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +          G           K+T +  +                 E    +  
Sbjct: 353  HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPMVPE-----------------ETQGPSSR 395

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
              +  + T+    E    +++      D +     R VKV +   R  Q GDK + RHG 
Sbjct: 396  YTRRDHSTALRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQ 450

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG V      EDMP+  +G   DI++NP  +PSRM VGQ+ E  +G     +GKK  +  
Sbjct: 451  KGTVGMTYTQEDMPWSIEGITPDIIVNPHAIPSRMTVGQLIECIMGKVAAHVGKKGDATP 510

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                   +IS         +                                        
Sbjct: 511  FTDVTLDNISKALHKCGYQMRGFETM---------------------------------- 536

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
                          +G +    G         + +G  Y  +L HMV DK+++R  G   
Sbjct: 537  -------------YNGHT----GR---QLTSMIFLGPTYYQRLKHMVDDKIHSRGRGPVQ 576

Query: 1277 LVTQQPLGGKSNRGG 1291
            ++T+QP  G+S  GG
Sbjct: 577  ILTRQPAEGRSRDGG 591


>gi|194272794|gb|ACF37257.1| RNA polymerase beta subunit [Bartonella clarridgeiae]
          Length = 263

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 182/256 (71%), Positives = 212/256 (82%)

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           ID++MPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RA
Sbjct: 1   IDTIMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERA 60

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DG+VT +V
Sbjct: 61  GFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIVDGRVTKEV 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           +YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D SPKQ+VS+
Sbjct: 121 IYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRDHIDLMDVSPKQLVSV 180

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGAAI AKR GI
Sbjct: 181 AAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGAAIGAKRGGI 240

Query: 735 VEQVDAIRIVIRSVEG 750
           V+QVDA+RIVIR+ E 
Sbjct: 241 VDQVDAMRIVIRATED 256


>gi|118640733|gb|ABL09934.1| RNA polymerase beta subunit [Vibrio harveyi]
          Length = 290

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 169/290 (58%), Positives = 222/290 (76%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNGKG +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDELDIVEVMKKLIAIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL +SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLFNSLSAFARCNEYGFLETPYRRVVDGIVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G F +EL+  R  GE  L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGGFADELITARQKGESGLHPREHAQYMDVATNQVVSIAASLIPFLE 290


>gi|45545357|gb|AAS67526.1| DNA-dependent RNA polymerase II second largest subunit [Xanthoria
            polycarpa]
          Length = 893

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 131/868 (15%), Positives = 247/868 (28%), Gaps = 150/868 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  +I  ++    G+  +DD D+ G +R+   G +L   +R+   
Sbjct: 149  HISQTEGSETRKAFFLGYMIHRMLQCALGRRDVDDRDHFGKKRLDLAGPLLAGLFRMLFQ 208

Query: 481  RMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ + I +  +              +    + S +     +               +SQ+
Sbjct: 209  KLTKDIYKYLQKCVESNREFNLALGVKQNTLSSGLKYSLATGNWGDQKKAASAKAGVSQV 268

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 269  LNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 324

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      +    Y      +   +     A      ++         D +    
Sbjct: 325  LALMCYITVGTPADPIVDYLTNRGMESLEEYEPTRAPHATKVFVNGTWIGCHNDPAHLVT 384

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQA 700
             +        I      + D  D   K          P    D+  +     N+   +  
Sbjct: 385  HIQEIRRKGIIAHEASLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSENNGNLALTKDM 444

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            V  L+ E   V T      A+        +  G    VD+    +  V+ + + +     
Sbjct: 445  VQKLEDERDMVLTMDPEERAE--------QVIGWEALVDS--GAVEYVDAEEEETIMIAM 494

Query: 761  IYRLMKFQRSNQNTCVNQRPL-VKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPW 818
                ++  R  Q       P        V+          T      ++   +  + +P+
Sbjct: 495  TPEDLEISRHIQAGYAAPVPSEDAPNQRVKAPLNPTAHTWTHCEIHPSMILGICASIIPF 554

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N          M  + +                                  L N DE
Sbjct: 555  PDHNQSPRNTYQSAMGKQAMGV-------------------------------FLTNYDE 583

Query: 879  --CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 584  RMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSID 643

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R  +D  +R        +E   +    E + L    Y +L +   +  G 
Sbjct: 644  RGLF-RSLFYRAYVDTEKRVGM---TVLENFEKPLRTETLKLKHGTYDKLDDDGLVAPGV 699

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++ D                 E  QR    +K    T     E+  
Sbjct: 700  RVSGEDVIIGKTTPIAPD---------------AQEMGQRTKSHIKKDASTPLRSTENGI 744

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  
Sbjct: 745  VDKVLL-----STNSEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTS 799

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +  +          +S L    E
Sbjct: 800  EGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEITVDSVSKLLR--E 857

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                +                                                    +G 
Sbjct: 858  HGYQSRGFEVM---------------------------------------------YNGH 872

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +    G         V +G  Y  +L H
Sbjct: 873  T----GR---KLVAQVFLGPTYYQRLRH 893



 Score = 95.5 bits (236), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 74/532 (13%), Positives = 158/532 (29%), Gaps = 47/532 (8%)

Query: 211 KVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           KVP      ALG+   E+IL+            +    PL  A L+   +V+   +    
Sbjct: 65  KVPAMILFRALGVVSDEDILNHICYDRADGDMLEMLKPPLEEAWLIQDREVALDFLGKRG 124

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIE 323
             Q +   +++       L+++ +  +  T           G  +   ++    G   ++
Sbjct: 125 KNQKMSRNERIKFAR-DVLQKELLPHISQTEGSETRKAFFLGYMI-HRMLQCALGRRDVD 182

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
             D   +K L+           +L+   +  + Y       + N++   AL      +  
Sbjct: 183 DRDHFGKKRLDLAGPLLAGLFRMLFQK-LTKDIYKYLQKCVESNREFNLALGVKQNTLSS 241

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIK 441
           G      +  S+    + D  K   +  G  ++  R    +      R          I 
Sbjct: 242 G------LKYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIA 295

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L N    +         +   + + L     + +      I + +++  ++S+   
Sbjct: 296 KPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPADPIVDYLTNRGMESLEEY 355

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRD 560
           +   A             + +    +  + ++ I   RR   +  +  + R     E + 
Sbjct: 356 EPTRAPHATKVF---VNGTWIGCHNDPAHLVTHIQEIRRKGIIAHEASLVRDIRDREFK- 411

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND------- 613
              T  GR+C       ++    ++       +    +E     V               
Sbjct: 412 -IFTDAGRVCRPLFVIDNDPKSENNGNLALTKDMVQKLEDERDMVLTMDPEERAEQVIGW 470

Query: 614 --------VVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVP 657
                   V Y+ A EEE   IA     L+               E    +     +   
Sbjct: 471 EALVDSGAVEYVDAEEEETIMIAMTPEDLEISRHIQAGYAAPVPSEDAPNQRVKAPLNPT 530

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
                  +  P  ++ I AS+IPF +++ S R      M +QA+ +      
Sbjct: 531 AHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYD 582


>gi|45545351|gb|AAS67523.1| DNA-dependent RNA polymerase II second largest subunit [Thamnolia
            vermicularis]
          Length = 893

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 133/943 (14%), Positives = 277/943 (29%), Gaps = 155/943 (16%)

Query: 346  ILYVDSVNNNAYIRN--TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +     ++ +        
Sbjct: 79   VSDEDILNHICYDRNDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGNSQGI---TRDKR 135

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             KY    + +  +     ++  +  +      +  ++  ++ +  G+   DD D+ G +R
Sbjct: 136  IKYARDIMQKELLPHISQVEGSETRK---AFFLGYMVHRMLQVALGRRDPDDRDHFGKKR 192

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G ++   +R+   ++ + + +  +              + +  + + +     +  
Sbjct: 193  LDLAGPLMAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLKYSLATGN 252

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 253  WGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 308

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L     V      E    +    + ++  +   L +      +
Sbjct: 309  VCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVF 368

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLEN 684
            +      +  D +     V        I      I D  D   K          P F+ +
Sbjct: 369  VNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLIRDIRDREFKIFTDAGRVCRPLFVID 428

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
            +D+     G  +  + +     +   +   M+            AK  G    +   R V
Sbjct: 429  NDAKSPNKGSLVLTKELVNRLEDDKDLPADMDPDEKA-------AKTMGWDGLI--KRGV 479

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG- 803
            +  ++ + + +   V     +   R  Q               V+          T    
Sbjct: 480  VEYLDAEEEETVMIVMTPEDLDISRQLQAGYQMPETTDDPNKRVKAPLNPTAHTWTHCEI 539

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
              ++   +  + +P+  +N          M  + +                         
Sbjct: 540  HPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV----------------------- 576

Query: 864  DIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                     L N DE    +  +             +       +   +  + AI     
Sbjct: 577  --------FLTNFDERMDTMTNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 628

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R        +E+  +    + + L   
Sbjct: 629  YNQEDSVIMNQSSIDRGLF-RSLFYRVYTDQEKRVGM---SVVEMFEKPMRSDTLKLKHG 684

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++                 +
Sbjct: 685  TYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL---------------HI 729

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K    T     E+   +K+             LR VKV +   +  Q GDK A RHG KG
Sbjct: 730  KRDVSTPLRSTENGLVDKVLL-----TTNHEGLRFVKVRMRTTKIPQIGDKFASRHGQKG 784

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 785  TIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFT 844

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 845  EVTVDSVSRLLR--EHGYQSRGFEVM---------------------------------- 868

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        +G +    G         V +G  Y  +L H
Sbjct: 869  -----------YNGHT----GR---KLVAQVFLGPTYYQRLRH 893



 Score = 99.8 bits (247), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 98/768 (12%), Positives = 202/768 (26%), Gaps = 124/768 (16%)

Query: 212 VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG+   E+IL+        +Q  +     +  A ++   +V+   +     
Sbjct: 67  IPIVIVFRALGVVSDEDILNHICYDRNDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGN 126

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            Q I   K++       ++++ +  +                +     ++ +   D  D 
Sbjct: 127 SQGITRDKRIKYAR-DIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVALGRRDPDDR 185

Query: 331 KSL-EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
               ++        +  L+    N         +    +  ++  L +          T 
Sbjct: 186 DHFGKKRLDLAGPLMAGLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVK---STTLTN 242

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLR 447
            +  S+    + D  K   S  G  ++  R    +      R          I     L 
Sbjct: 243 GLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLH 302

Query: 448 N-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLI 504
           N   G +   +    +    V  +            E  I    + +   ++   P    
Sbjct: 303 NTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSP 362

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NA  V      F     +    +  + +S +   RR   +             +RD+   
Sbjct: 363 NATKV------FVNGVWVGVHRDPAHLVSTVMSLRRRGLIS-------HEVSLIRDIR-- 407

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND----------- 613
              R     T  G     +  + + A+    G +      V   +   D           
Sbjct: 408 --DREFKIFTDAGRVCRPLFVIDNDAKSPNKGSLVLTKELVNRLEDDKDLPADMDPDEKA 465

Query: 614 --------------VVYLSAMEEENRYIAQANSSLDEDGS-------FTEELVFCRCAGE 652
                         V YL A EEE   I      LD                   +    
Sbjct: 466 AKTMGWDGLIKRGVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYQMPETTDDPNKRVKA 525

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
            +          +  P  ++ I AS+IPF +++ S R      M +QA+ +         
Sbjct: 526 PLNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT------ 579

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                     +   I+      +    ++  +          +   +  Y          
Sbjct: 580 ---NFDERMDTMTNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG-------- 628

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
               NQ                    S  +   ++ R +  +       + E  + +S  
Sbjct: 629 ---YNQE------------------DSVIMNQSSIDRGLFRSLFYRVYTDQEKRVGMSVV 667

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            + E    S                      D   +       +D+ G++  G  V+  D
Sbjct: 668 EMFEKPMRS----------------------DTLKLKHGTYDKLDDDGLVAPGVRVSGED 705

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I++GK  P         E+L +        DV        +G+   V+
Sbjct: 706 IIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRSTENGLVDKVL 749


>gi|256014678|gb|ACU56887.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 215

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 88/217 (40%), Positives = 118/217 (54%), Gaps = 40/217 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V 
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVD 215


>gi|52699878|gb|AAU87000.1| DNA-dependent RNA polymerase II second largest subunit [Sphaerophorus
            globosus]
          Length = 735

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 124/834 (14%), Positives = 233/834 (27%), Gaps = 122/834 (14%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAGLFRMLFNKLTKDVYKYLQRCVENNKEFNLTLAVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +      E    +       +  +   L++
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMVQRGMDLLEEYEPLNS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        +      + D  D   K         
Sbjct: 177  PNATKIFVNGVWVGVHRDPAHLVSTVQNLRRRGHLSHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVE 736
             P F+ ++D      G  +  +       E   +G  M++   +          ++G+VE
Sbjct: 237  RPLFVIDNDPKSNNCGNLVLTKDHIAKLEEDKEMGMSMDAQEREDKLMGWTGLVKSGVVE 296

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VDA       +    +       I         N +  +N+R    +            
Sbjct: 297  YVDAEEEETIMIVMTPEDLEISKQIQAGYTMPEQNPDD-LNKRVKAPLNQTSHTWTHCEI 355

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             PS  LG  A      +   P                                      +
Sbjct: 356  HPSMILGIWAS-----IIPFPDQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXM 410

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G      D                +  +             +       +   +  + AI
Sbjct: 411  GVFXTNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 459

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +R        +E   +    + +
Sbjct: 460  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGM---SVVEQFEKPMRSDTL 515

Query: 977  ILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             L    Y +L +   +  G           K+  +S D      R++          ++ 
Sbjct: 516  KLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKQHTKRDTSTPLRS 575

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q   S                         LR VKV +   +  Q GDK A R
Sbjct: 576  TENGIVDQVLLS--------------------TNSDGLRFVKVRMRTTKIPQIGDKFASR 615

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 616  HGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD 675

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S L                           +     +G  +   VF  
Sbjct: 676  ATPFTEVTVDSVSRLLR---------------EHGYQSRGFEIMYNGHTGQKLRAQVF-- 718

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                                 +G  Y  +L HMV DK+
Sbjct: 719  -------------------------------------LGPTYYQRLRHMVDDKI 735


>gi|307343588|emb|CBJ18709.1| RNA polymerase B subunit [Micromonospora purpureochromogenes]
          Length = 209

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 94/212 (44%), Positives = 122/212 (57%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKKALRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA E  I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREAEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGYIY+LKLNH
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNH 207


>gi|118640701|gb|ABL09918.1| RNA polymerase beta subunit [Vibrio halioticoli]
          Length = 290

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 168/290 (57%), Positives = 220/290 (75%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           S+F  LFF  ++YDLSTVGR+K N  +  +   +   + + DII ++K L+ +RNGKG +
Sbjct: 1   SLFASLFFSEERYDLSTVGRMKFNSSIMREDAGEQGILDETDIIEVMKKLISIRNGKGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL+++AR N +GF+ETPYR+V DG VT +V YLSA+EE    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAYARCNEFGFLETPYRRVVDGVVTEEVDYLSAIEEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L  D  F +EL+  R  GE  L PRE + ++D +  QVVSIAASLIPFLE
Sbjct: 241 LTADNLFADELITARLKGESGLHPRENVSYMDVATNQVVSIAASLIPFLE 290


>gi|46277283|gb|AAS86832.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum]
          Length = 580

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 112/727 (15%), Positives = 205/727 (28%), Gaps = 147/727 (20%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L     +            + +    N        EE +  +    +
Sbjct: 1    ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPLAT 53

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +G +             +   R ++   D + +  V     L       D  R   
Sbjct: 54   KIFVNGCWVGIHRNPELLVRTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDCGRCSR 110

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  +    +K +        ES         +     G +E VD        +   +
Sbjct: 111  PLFIVEKQKLQIKKKDILALQQRESPEEVGWHDLVA---KGYIEYVDTEEEETTMISMTI 167

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +  TS                                        PS  LG       + 
Sbjct: 168  NDLTSARLCPDDA---------------------YSETYTHCEIHPSLILG-------VC 199

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 200  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 233

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 234  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 290

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        IF R   D+ ++  ++ +E      R+          +          G
Sbjct: 291  SSIDRGFF-RSIFYRSYRDEEKKMGTLVKEDFGCPNRENTMGMRHGSYDKLDDDGFAPPG 349

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T ++                  D+   +     +  + T     E  
Sbjct: 350  TRVAGEDVIIGKTTPIAP-----------------DDAQGQTARYTRRDHSTCLRHSESG 392

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VK+ +   R  Q GDK + RHG KG +      EDMP+ 
Sbjct: 393  MVDQVLLTTNADGL-----RFVKMRMRSIRIPQIGDKFSSRHGQKGTIGMAYTQEDMPWT 447

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS      
Sbjct: 448  IEGICPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKC 507

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
               +                                                      +G
Sbjct: 508  GYQMRGFERM-----------------------------------------------YNG 520

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
             +    G    P    + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG 
Sbjct: 521  HT----GR---PLTYTIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGL 573

Query: 1293 RLGEMEV 1299
            R GEME 
Sbjct: 574  RFGEMER 580



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 73/482 (15%), Positives = 133/482 (27%), Gaps = 97/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPLATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++        P    E   +  
Sbjct: 64  IHRNPELLVRTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDCGRCSRPLFIVEKQKLQ- 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +      A        E       D      + Y+   EEE   I+   + L       +
Sbjct: 122 IKKKDILALQQRESPEEVG---WHDLVAKGYIEYVDTEEEETTMISMTINDLTSARLCPD 178

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +               E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 179 D------------AYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 226

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 227 IYVTNYQL--------------------RMDTLAYV------------------------ 242

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 243 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 281

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F SI    +    +      +E        +   +       +D
Sbjct: 282 QEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKMGTLVKEDFGCPNRENTMGMRHGSYDKLD 341

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G    G  V   D+++GK TP              A         RD S  +    SG
Sbjct: 342 DDGFAPPGTRVAGEDVIIGKTTPIAPDD---------AQGQTARYTRRDHSTCLRHSESG 392

Query: 938 TV 939
            V
Sbjct: 393 MV 394


>gi|298912949|emb|CAZ66642.1| RNA polymerase beta subunit [Vibrio navarrensis]
          Length = 289

 Score =  252 bits (643), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 169/289 (58%), Positives = 224/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIVEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGLGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN++
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVIDGIVTDEVDYLSAIEEGQFVIAQANAA 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G+F +EL+  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|225030859|gb|ACN79530.1| RNA polymerase beta subunit [Mycobacterium massiliense]
 gi|225030861|gb|ACN79531.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 220

 Score =  251 bits (642), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 89/217 (41%), Positives = 118/217 (54%), Gaps = 40/217 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V 
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLVD 220



 Score = 41.2 bits (95), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|307343578|emb|CBJ19217.1| RNA polymerase B subunit [Micromonospora nigra]
          Length = 210

 Score =  251 bits (642), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 93/215 (43%), Positives = 121/215 (56%), Gaps = 38/215 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIDAHEAAPD--- 141

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                                        V+TPVFDGA EE I+ +L     +        
Sbjct: 142  --------------------------TNVATPVFDGAREEEISGLLSSTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
              G++ L+DG +GEP   P+ VGY+Y+ KLNH+V 
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYLYIRKLNHLVE 210


>gi|45545355|gb|AAS67525.1| DNA-dependent RNA polymerase II second largest subunit [Ustilago
            maydis]
          Length = 887

 Score =  251 bits (642), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 131/859 (15%), Positives = 257/859 (29%), Gaps = 147/859 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++ T +     +      +I  L+     +  IDD D+ G +R+   G ++ N +R+   
Sbjct: 158  HISTSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFR 217

Query: 481  RMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ R +   +     +      Q  + +  + + +     +               +SQ+
Sbjct: 218  KVTRDVYRHLQKCVEEHREFHIQAAVKSSTITNGLRYSLATGNWGDQKKAMQAKAGVSQV 277

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 278  LNRFAFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKN 333

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEE 643
            L+  A V            + +  + + V    A  +  +         + D+ G   + 
Sbjct: 334  LSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHAKATKIFVNGVWMGTHDDPGQLVDT 393

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            L   R   +         D  +   +     +  L P    +  +  L+      + +  
Sbjct: 394  LRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIVNPHDMSLLIKKRHVEMIGQ 453

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
               E     TG E              + G++E +DA        E  +    S  D+ +
Sbjct: 454  PIPE-----TGEEFR-------WTHLVQEGVIEYLDAE------EEESVLICMSTTDLEQ 495

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYN 822
              +++  N    +N          ++    IA    T      A+   +  + +P+  +N
Sbjct: 496  SREYKARNGQINLNSA---DPSARLKSVHTIAPDTWTHCEIHPAMVLGICASIVPFPDHN 552

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                 +    M  +    +I I    + +R   +    +    P  +   ++++      
Sbjct: 553  QSPRNVYQSAMGKQ----AIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHL------ 602

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
                                   +   +  + AI      +  D+ +   S +   +   
Sbjct: 603  -------------------RFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-R 642

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++ R  + + ++   ++ E+ E   RD          +          G          
Sbjct: 643  SMYYRGYMAEEKKVGVMQLEEFEKPHRDTTIRMKHGTYDKIDADGLCAPGTRVSGDDVII 702

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+  L  D      RS+          ++     +  Q                     
Sbjct: 703  GKTAPLPPDSEELGMRSKLHTKKDASVSLKSTENGIIDQ--------------------V 742

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                     + VKV V   R  Q+GDK A RHG KG +      EDMPF  +G   DI++
Sbjct: 743  LVTTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIII 802

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +G + E  L       G++  +          +S +   L          
Sbjct: 803  NPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVM 862

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                                             G +    G   
Sbjct: 863  -----------------------------------------------YHGHT----GR-- 869

Query: 1243 EPFDRPVTVGYIYMLKLNH 1261
                  V +G  Y  +L H
Sbjct: 870  -KLQAQVYLGPTYYQRLKH 887



 Score =  102 bits (254), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 101/774 (13%), Positives = 227/774 (29%), Gaps = 115/774 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +P+     ALG+  + E+L         +   +     +  A ++    V+
Sbjct: 70  YIRND----IPIVIVFRALGIVPDREVLQHICYDFNDTPMLEMLKPCIEEAFVIQDRDVA 125

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +        +   K+                  + +  +    +   I   E G   
Sbjct: 126 LDFIGRRGTTTGLSRAKR-----------------TVYAQEILQKEMLPHISTSE-GSNT 167

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            +A           +   + R+I                 +        +    D+YR +
Sbjct: 168 KKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHL 227

Query: 382 RPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
           +    +   F +  ++ +    +  +Y L   G      +         + + +    + 
Sbjct: 228 QKCVEEHREFHIQAAVKSSTITNGLRYSL-ATGNWGDQKKAMQAKAGVSQVLNRFAFAST 286

Query: 440 IKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           +  L        R+GK       +  +  +    E  + Q    +  +       + +  
Sbjct: 287 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMATVTVGTPS 346

Query: 495 I------DSVMPQDLINAKPVVSAVCEFF-CSSQLSQLEEHVNSLSRITHTRRLSAL-GQ 546
                  +      L++ +   +   + F     +   ++    +  +   RR   +  +
Sbjct: 347 APIVEFLEEFGLDSLVDMQLAHAKATKIFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHE 406

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
             V R     E+R ++      + P      H++ L+        +           +  
Sbjct: 407 VSVVRDIRERELR-IYTDASRVLRPVFIVNPHDMSLLIKKRHVEMIGQPIPETGEEFRWT 465

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF--------TEELVFCRCAGEEILVPR 658
                  + YL A EEE+  I  + + L++   +                       +  
Sbjct: 466 HLVQEGVIEYLDAEEEESVLICMSTTDLEQSREYKARNGQINLNSADPSARLKSVHTIAP 525

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
           +     +  P  V+ I AS++PF +++ S R +    M +QA+ +  +            
Sbjct: 526 DTWTHCEIHPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQ--------- 576

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               S A  +A      ++       +                   ++F+          
Sbjct: 577 ----SRADSMAHVLLYPQKPLGTTRSM-----------------EHLRFRELPAGQNAIV 615

Query: 779 RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
             +   G   + + +I +  S D G            M + GY  E+  +          
Sbjct: 616 AIMCYSG-YNQEDSVIMNQSSIDRGLFRS--------MYYRGYMAEEKKV---------- 656

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              + +EEFE   RDT             +       ID  G+   G  V+  D+++GK 
Sbjct: 657 -GVMQLEEFEKPHRDT----------TIRMKHGTYDKIDADGLCAPGTRVSGDDVIIGKT 705

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P    P   EE  +R+    K    +D S+ + S  +G +  V +      +K
Sbjct: 706 AP---LPPDSEELGMRS----KLHTKKDASVSLKSTENGIIDQVLVTTNSHGNK 752


>gi|269913231|emb|CAY86042.1| RNA polymerase beta subunit [Acidomonas methanolica]
          Length = 281

 Score =  251 bits (642), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 128/284 (45%), Positives = 171/284 (60%), Gaps = 28/284 (9%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------- 221
           SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL             
Sbjct: 1   SGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGENSIAARAAKA 60

Query: 222 ------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                       GMD +EIL+ FY  + ++     W  P    D   G K+   L D +T
Sbjct: 61  AAGGDVESLPIRGMDQDEILAYFYGTVPFTHTSKGWSRPFDP-DAFRGQKLLEPLFDAET 119

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE V E+  KLT+   + + EK  K + +    L G ++A+D+VN  TGEIY EAG+ + 
Sbjct: 120 GEVVAEADAKLTARACRKIAEK-TKDVLVGRADLLGRFIAKDLVNPATGEIYAEAGEELT 178

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E  L  +  S I ++P+L VD   +  +IRNTL  DKN  R DAL+DIYR+MRPG+  T 
Sbjct: 179 EARLVALEESGITELPMLAVDPA-HGPWIRNTLAVDKNVSRDDALVDIYRIMRPGEPPTP 237

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             AE+MF  LFFD D+YDLS VGRVKMNMRL +D PD +R +RK
Sbjct: 238 ETAEAMFQGLFFDHDRYDLSAVGRVKMNMRLEVDVPDTMRVLRK 281


>gi|190148986|gb|ACE63468.1| RNA polymerase subunit B [Pseudonocardia sp. S073]
          Length = 266

 Score =  251 bits (642), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 151/273 (55%), Positives = 199/273 (72%), Gaps = 8/273 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVSEGRVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 YISPVGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           C NQ+P++  GD V    +IADGP T+ G++AL
Sbjct: 234 CNNQKPIIDEGDRVEAGQVIADGPCTENGEMAL 266


>gi|114159826|gb|ABI53720.1| RNA polymerase [Pichia pastoris]
          Length = 273

 Score =  251 bits (642), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 93/227 (40%), Gaps = 50/227 (22%)

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+ SR  P  DMPF + G   D+++NP   PSRM +G   E+  G A    G    
Sbjct: 1    HGQKGVCSRKWPQIDMPFTETGIQPDVIINPHAFPSRMTIGMFVESLAGKAGALHGIAQD 60

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            S    +  +                                             TP    
Sbjct: 61   STPWKFNEDD--------------------------------------------TPA--- 73

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
               +     L  A  +  G   +Y G+TGE     + +G +Y  +L HMV+DK   RSTG
Sbjct: 74   ---DFFGEQLISAGYNYHGNEPMYSGVTGEELRADIYIGVVYYQRLRHMVNDKFQVRSTG 130

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              + +T QP+ G+   GG R+GEME   +  +G A++LQ+ L   SD
Sbjct: 131  PVNSLTMQPVKGRKRNGGIRIGEMERDALIGHGTAFLLQDRLLNCSD 177


>gi|45120564|gb|AAO64650.2| RNA polymerase II subunit RPB2 [Bondarzewia montana]
          Length = 867

 Score =  251 bits (641), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 127/860 (14%), Positives = 245/860 (28%), Gaps = 146/860 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +     ++  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 138  RYAQEILQKEMLPHISMMEGSESKK---AYFFGYMIHRLLLAAMERRELDDXDHFGKKRL 194

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ R +    +              +    + + +     +   
Sbjct: 195  DLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKYSLATGNW 254

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 255  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGRXGKIAKPRQLHNTHWGMV 310

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   A ++           + +  + +         EEN + A 
Sbjct: 311  CPAETPEGQACGLVKNLALMATISVGSPSGPVIDFLEEWGLESL--------EENAHSAT 362

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     I   ++     D  P+  V             D  R
Sbjct: 363  PTTKIFVNGIWMG---VHRDPANLISTIKKLRRKDDIHPEVSVVRDIRERELRLYTDPGR 419

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRSV 748
            V     +       L+ +               +     +  + G+VE +DA       +
Sbjct: 420  VCRPLFIVEDQQLALQ-KKHIXWLNQGWRDDDGTPFKWNSLIKNGVVELLDAEEEETVMI 478

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +   +       +    ++ +     R     G            PS  LG     
Sbjct: 479  CMTPEDLQNSRLQGSGVDPHANDGDFDPAARLKAASGINTHTWTHCEIHPSMILG----- 533

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G       +   
Sbjct: 534  --ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM- 572

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 573  ----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 622

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    I+ R  +D  ++S   + E+ E   RD          +       
Sbjct: 623  IMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGL 681

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  +  D      R++          ++     +  Q       
Sbjct: 682  IAPGTGVTGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI---- 737

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   + VKV V   R  Q GDK A RHG KG +      ED
Sbjct: 738  ----------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQED 781

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  +PSRM +G + E  L      +G +                 
Sbjct: 782  MPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------- 826

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     E++++ LR    
Sbjct: 827  --------------------------------------ATP-FTELTVESVSAFLRQQGY 847

Query: 1229 DESGQSILYDGLTGEPFDRP 1248
               G  ++Y G TG      
Sbjct: 848  QSRGLEVMYHGHTGRKLQAQ 867



 Score =  137 bits (345), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 100/777 (12%), Positives = 216/777 (27%), Gaps = 121/777 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  SQ  +     +    ++   +++
Sbjct: 63  YIKVD----IPIWVVFRALGVISDRDILEHICYDMQDSQMLEMLKPCIDDGFVIQDREIA 118

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G     S ++      + L+++ +  + +              +      + 
Sbjct: 119 LDFIGNR-GTTTGLSRERRLRYAQEILQKEMLPHISMMEGSESKKAYFFGYMIH---RLL 174

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A +  +    +      +                + N       K  +D    + + +
Sbjct: 175 LAAMERRELDDXDHFGKKRLDL----------AGPLLANLFRMLFRKLTRDVYRYLQKCV 224

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                  F+++ ++ +    +  KY L   G      +         + + +    + + 
Sbjct: 225 ETH--KEFNLSLAVKHNTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS 281

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 282 HLRRCNTPLGRXGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMATISVGSPSGP 341

Query: 497 SVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
            +             NA         F     +    +  N +S I   RR   +     
Sbjct: 342 VIDFLEEWGLESLEENAHSATPTTKIFVNGIWMGVHRDPANLISTIKKLRRKDDIHPEVS 401

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
                      ++        P    E   + L      +          TP+ K     
Sbjct: 402 VVRDIRERELRLYTDPGRVCRPLFIVEDQQLALQKKHIXWLNQGWRDDDGTPF-KWNSLI 460

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLD---------EDGSFTEELVFCRCAGEEILVPREK 660
               V  L A EEE   I      L          +  +   +            +    
Sbjct: 461 KNGVVELLDAEEEETVMICMTPEDLQNSRLQGSGVDPHANDGDFDPAARLKAASGINTHT 520

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 521 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 570

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 571 -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 598

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 599 -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 635

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       I++ G+I  G  V   DI++
Sbjct: 636 SIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVTGEDIII 695

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 696 GKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 745


>gi|324502244|gb|ADY40989.1| DNA-directed RNA polymerase III subunit RPC2 [Ascaris suum]
          Length = 1135

 Score =  251 bits (641), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 102/596 (17%), Positives = 190/596 (31%), Gaps = 111/596 (18%)

Query: 786  DEVRRNDI-IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            D V    I   D    +   +A+  N + A            + +   ++          
Sbjct: 618  DFVDEGLIEYLDVNEMNDASIAVYENQIKADTTHLEIEPFTLLGVCAGLIPYPHHNQSPR 677

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              ++       +G          +     K ID   ++ +        +    I      
Sbjct: 678  NTYQCAMGKQAMGT---------IGYNQQKRIDS--LMYLLVYPQRPLVKSKTIEMCNFE 726

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +  + A+      D+ D  +   + +        ++ +H     ++  +   +++
Sbjct: 727  KLPAGQNAIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVY-KHAKGTAKKYPNQTFDRL 785

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
                 +    + I    +  +   +  G    S      K   +          S   Q 
Sbjct: 786  MGPTIEATTRKPIYKHQVLDQEGIVFAGARIRSKQVMINKHMPIV-----SLEASAVAQS 840

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +   +   RNVE     Y+           +  E++    +       ++KV +   R  
Sbjct: 841  SGVVQAGNRNVE-----YKDVSISYRSPVPSYAERVLLTYNEDDA--HLIKVVLRQTRRP 893

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDK + RHG KG+   I   E           D+  N LG    M    I   H    
Sbjct: 894  ELGDKFSSRHGQKGVCGLIAQQE-----------DMPFNDLG----MCPDMIMNPH---- 934

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                                             +     K+ +        ++ ++  G 
Sbjct: 935  ------------------------------GYPSRMTVGKLMELLSGKNAILSGRFHYGT 964

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                  F G     +   L     +  G+ +L  G+TG+     +  G IY  KL HMV 
Sbjct: 965  -----AFAGDQVADVCEELAARGFNYLGKDMLTSGITGQQLSAYIYFGPIYYQKLKHMVL 1019

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            DK++ARS G  +++T+QP  G++  GG RLGEME  C+ AYGA+ +L E L + SD    
Sbjct: 1020 DKMHARSRGPRAVLTRQPTEGRARDGGLRLGEMERDCLIAYGASMLLMERLMVSSDEFHV 1079

Query: 1321 DV-----------------VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            DV                   RT    + +          P +  +L +E+Q++ +
Sbjct: 1080 DVCSQCGLIGYKGWCQKCRCSRTM---ATIK--------IPYACKLLFQELQSMNI 1124



 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 122/967 (12%), Positives = 275/967 (28%), Gaps = 196/967 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++   AS+D+F+  +I    R NE +          +  + +  ++++      P    
Sbjct: 30  LVKQHIASFDYFINEDIKNILRANERIT---------SDVNPSFYVKYLDIRVGTPSSEE 80

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  RD+TY+ P+++ +             +  + +    I +G +P+
Sbjct: 81  GFTQLNEKISPHECRLRDMTYSAPIQVDIEYT----------RGNQRVLRNGIVIGRMPI 130

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F+I+G +++V+ Q   S       ++    
Sbjct: 131 MLRCSKCVLKDMNEEELARVQECPYDPGGYFIIRGSEKVVLIQEQLS------KNRIMIG 184

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-----------VPVTSFLMALG 222
            + K    C ++           D K   +V I ++++           +P+     A+G
Sbjct: 185 RNSKKELQCEVLSS-------TSDRKSKTYV-ISKKQRYYLKHNQLSDDIPIAIIFKAMG 236

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
            +S+ +I+S    +  +           +A  ++        +       +    G   T
Sbjct: 237 FESDYDIVSAVGLEEKFVAAMAPSIEECAAHQIVTQESALQFIASKVKMRKFGTGGSGPT 296

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
                   +     +        G    + I  G      ++A     E    + + ++ 
Sbjct: 297 PPKEHEAIDFLTSLMICHIPSHDGNMKLKAIYVGLMVRRLMQAEMGYTECDDRDFYGNKR 356

Query: 342 RDIP-----ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            ++      +L+ D           +  +       A LDI + MR          + + 
Sbjct: 357 LELAGSLMGLLFEDVFKRFNSELKRIADNSLGKTLAAPLDIVKHMR----------QDLV 406

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                ++       + R +M              +    ++ ++  +         +   
Sbjct: 407 TNAMVNAIATGNWIIKRFRMERHGVTQVLSR---LSYISVLGMMTRINSTFEKTRKVSGP 463

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
            +L   +   +      +     L    ++   I++   +  + + L N+         F
Sbjct: 464 RSLQPSQWGMLCPSDTPEGESCGLVKNLALISHITTDSDEKPVIRLLYNSGVEDLQSLHF 523

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETS 575
                       +N             +     V R     E   V      R     + 
Sbjct: 524 SLVHSPEYHLVFLNGAIVGITIDPQRIVSTIRAVRRNGLLSEFVSVSTNAAQRSVYIASD 583

Query: 576 EGHNI-GLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            G      +       R+  +   E    +R   D      + YL   E  +  IA   +
Sbjct: 584 GGRLCRPYIIVTDGKPRITQHDIDELKKGHRIFEDFVDEGLIEYLDVNEMNDASIAVYEN 643

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  D                          ++  P  ++ + A LIP+  ++ S R   
Sbjct: 644 QIKAD-----------------------TTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 680

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +         G        S                             
Sbjct: 681 QCAMGKQAMGTI---------GYNQQKRIDS----------------------------- 702

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                    QRPLVK                 +   L  G+N +
Sbjct: 703 -----------------LMYLLVYPQRPLVKS----------KTIEMCNFEKLPAGQNAI 735

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPN 867
           +A M + GY+ ED++++++  +       +  +  +  A+       +            
Sbjct: 736 IAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHAKGTAKKYPNQTFDRLMGPTIEATTR 795

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF-GEKAVDVRD 926
                 + +D+ GI+  GA +    +++ K  P      +   +    +  G + V+ +D
Sbjct: 796 KPIYKHQVLDQEGIVFAGARIRSKQVMINKHMPIVSLEASAVAQSSGVVQAGNRNVEYKD 855

Query: 927 TSLRVPS 933
            S+   S
Sbjct: 856 VSISYRS 862


>gi|300394728|gb|ADK11902.1| DNA-directed RNA polymerase II subunit two [Piloderma fallax]
          Length = 686

 Score =  251 bits (641), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 125/816 (15%), Positives = 243/816 (29%), Gaps = 146/816 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
             D D+ G +R+   G +L N +R+   ++ + +    +              +  + + +
Sbjct: 1    YDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   A ++           + +  + +      
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL----- 171

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
               EEN + +   + +  +G +       R     +   ++     D SP+  V      
Sbjct: 172  ---EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRE 225

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
                   D+ RV     +       L+ +   ++  G +    +     +V  + GI+E 
Sbjct: 226  KELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGFDDEDEEFKWEQLV--KGGIIEL 283

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +       +    ++ +     R  +K G +          
Sbjct: 284  LDAEEEETVMISMTPEDLENSRLQSSGVDPHANDSDFDPAAR--LKAGTDAHTWTHCEIH 341

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 342  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 376

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   I               +  +             +       +   +  + AI 
Sbjct: 377  IYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 425

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+       
Sbjct: 426  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKH 484

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  +  D      R++          ++     
Sbjct: 485  GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHNRRDVSTPLKSTENG 544

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VKV V   R  Q GDK A RHG K
Sbjct: 545  IVDQVLI--------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQK 584

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +      
Sbjct: 585  GTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---- 640

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     E
Sbjct: 641  -------------------------------------------------ATP-FTDLTVE 650

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            ++++ LR       G  ++Y G +G      V +G 
Sbjct: 651  SVSTFLRQKGYQSRGLEVMYHGHSGRKLQAQVYLGP 686



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 85/622 (13%), Positives = 174/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 192 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 251

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     E    K         +  L A EEE   I+     L+     + 
Sbjct: 252 QKKHIKW--LNQGFDDEDEEFKWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQSS 309

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +       +     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 310 GVDPHANDSDFDPAARLKAGTDAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 369

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 370 MGKQAMGIYLTNFLI-----------------------------------------RMDT 388

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 389 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 424

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 425 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRMKH 484

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         ++        +  + RD S  
Sbjct: 485 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRT-------RTHNRRDVSTP 537

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  +G V  V I       K
Sbjct: 538 LKSTENGIVDQVLITTNSEGQK 559


>gi|168809736|gb|ACA29587.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
 gi|168809738|gb|ACA29588.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
 gi|168809740|gb|ACA29589.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 230

 Score =  251 bits (641), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 99/300 (33%), Positives = 138/300 (46%), Gaps = 72/300 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 3    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 55

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 56   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 104

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 105  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 164

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 165  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 186

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM+KL+HMV 
Sbjct: 187  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVD 230



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/84 (63%), Positives = 64/84 (76%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDT
Sbjct: 1   VGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDT 60

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SLRVP G  G V DV+IF R   D
Sbjct: 61  SLRVPHGGDGVVRDVKIFTRANGD 84


>gi|103001826|gb|ABF71523.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 688

 Score =  251 bits (641), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 112/808 (13%), Positives = 228/808 (28%), Gaps = 145/808 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + + +  +              + +  + + +     +
Sbjct: 1    KRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLAT 60

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +     +     
Sbjct: 117  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATK 176

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177  VFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 236

Query: 684  NDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             D+  +     N+   ++ +  L+ +               S     AK  G    V   
Sbjct: 237  IDNDPKSTNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--N 286

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
            + V+  V+ + + +   V     ++  R  Q               V+          T 
Sbjct: 287  KGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTH 346

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N                        ++       +G   
Sbjct: 347  CEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGXXX 388

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                   +             +       +   +  + AI    
Sbjct: 389  XXXXXXXXXXXX-----------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 437

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 438  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKH 493

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 494  GTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENG 553

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             L+ VKV +   +  Q GDK A RHG K
Sbjct: 554  IVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQK 593

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +      
Sbjct: 594  GTIGITYRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---- 649

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     +
Sbjct: 650  -------------------------------------------------ATP-FTEVTVD 659

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPF 1245
            +++ +LR       G  ++Y+G TG   
Sbjct: 660  SVSKLLREHGYQSRGFEVMYNGHTGRKL 687



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 84/619 (13%), Positives = 166/619 (26%), Gaps = 99/619 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N      NK  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 7   GPLLANLFRMLFNKLTKDVYKYLQKCVESNR--EFNLTLGVKSTTITNGLKYSL-ATGNW 63

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 64  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 123

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 124 TPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 183

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +S +   RR   +  +  + R     E        R   P       P  
Sbjct: 184 VGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKS 243

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           T+ G+ +     +           I      E  +           V Y+ A EEE   I
Sbjct: 244 TNCGNLVLTKEHINKLEDDKDLPAIMDSEEKEAKFFGWDGLVNKGVVEYVDAEEEETVMI 303

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
                 L                              + S +     A       E  D 
Sbjct: 304 VMTPEDL------------------------------EISRQIQAGYA-----MPETSDD 328

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               +   M                T       +   + I+   A I+   D  +    +
Sbjct: 329 PNKRVKAPM--------------NPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNT 374

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +  +     G                    Q+PL                      +L 
Sbjct: 375 YQSAMGKQAMGXXXXXXXXXXXXXXXILYYPQKPL----------ATTRSMEFLKFRELP 424

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----I 861
            G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E     +
Sbjct: 425 AGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPM 484

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             D   +       +D+ GI+  G  V+  DI++GK  P         E+L +       
Sbjct: 485 RSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHVK 540

Query: 922 VDVRDTSLRVPSGVSGTVV 940
            DV        +G+   V+
Sbjct: 541 RDVSTPLRSTENGIVDQVL 559


>gi|52699888|gb|AAU87005.1| DNA-dependent RNA polymerase II second largest subunit [Strangospora
            pinicola]
          Length = 698

 Score =  251 bits (641), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 124/817 (15%), Positives = 236/817 (28%), Gaps = 144/817 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++   +RL   ++ R I+  +S              + +  +   +     +
Sbjct: 2    KRLDLAGPLMAQVFRLKFAQLVRDIRLYLSRCVEQGKDFNLTLAVKSNIITGGLRYCLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       + ++H RR +      + R     + R +H +H+
Sbjct: 62   GNWGDQKKASSAKAGVSQVLNRYTYAACLSHLRRTNT----PIGRDGKIAKPRQLHNSHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+    V+          +    + ++  +    +      
Sbjct: 118  GLVCPAETPEGQACGLVKNLSLMCYVSVGTPAGPIIEFMNQRNMELLEEYDPKNNPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D S     V        +      + D  D   K        + P L 
Sbjct: 178  IFVNGVWVGVHRDPSQLVNTVIDLRRNNTLSFEISLVRDVRDREFKIFTDAGRVMRPLLV 237

Query: 684  NDDSNRVLMGC-NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAI 741
             D++     G   ++R  +  L  +     TGM                + GIVE +DA 
Sbjct: 238  VDNTPGENQGTLALKRDNIDKLLRDNELDTTGMNDDDRDELVYGWKGLVKDGIVEYLDAE 297

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN-TCVNQRPLVKVGDEVRRNDIIADGPST 800
                  +    +       +    +    N        +P  K    VR+       P+ 
Sbjct: 298  EEETTMIVMSPEDLEEHRQMRMGNQIVEDNSGDPHRRFKP--KPNPAVRKYTHCEIHPAM 355

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                       E  +           
Sbjct: 356  ILG-------VCASIIPFPDHNQSPRNCYQSAXXXXXXXXXXXXXEARMDTMSN------ 402

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                   +             +       +   +  + AI    
Sbjct: 403  -----------------------ILYYPQKPLATTSSMEYLKFRDLPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +   +E   +  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPIRNETFKMKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K+  +++D      R++  Q       ++     
Sbjct: 496  GTYDKLDEDGIVAPGIRISGEDIIIGKTAPMTADAEELGQRTKAHQKRDTSTPLRTTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             +R VKV   M +  Q GDK A RHG K
Sbjct: 556  IVDQVLL--------------------TTNAEGMRFVKVRTRMTKVPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G++      
Sbjct: 596  GTIGITYRQEDMPFTSEGLVPDIIINPHAIPSRMTIAHLIECQLSKVSSLTGREGD---- 651

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     +
Sbjct: 652  -------------------------------------------------ATP-FTEVTVD 661

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            +++ +LR       G  ++Y+G TG      V +G  
Sbjct: 662  SVSKLLRENGYQSRGFEVMYNGHTGRKLVAQVFLGPT 698



 Score =  105 bits (263), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 79/579 (13%), Positives = 154/579 (26%), Gaps = 90/579 (15%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             ++ T  +   +    + D  K   +  G  ++  R           R          I
Sbjct: 47  KSNIITGGLRYCLATGNWGDQKKASSAKAGVSQVLNRYTYAACLSHLRRTNTPIGRDGKI 106

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +         +   + + L     + +      I E ++  +++ +  
Sbjct: 107 AKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAGPIIEFMNQRNMELLEE 166

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM- 558
            D  N                +    +    ++ +   RR + L  +  + R     E  
Sbjct: 167 YDPKNNPNATKIF---VNGVWVGVHRDPSQLVNTVIDLRRNNTLSFEISLVRDVRDREFK 223

Query: 559 ------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN-------AYGFIETPYRKV 605
                 R + P       P E   G       ++    R N            +      
Sbjct: 224 IFTDAGRVMRPLLVVDNTPGENQ-GTLALKRDNIDKLLRDNELDTTGMNDDDRDELVYGW 282

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
                   V YL A EEE   I  +   L+E                ++ +  + ++   
Sbjct: 283 KGLVKDGIVEYLDAEEEETTMIVMSPEDLEE--------------HRQMRMGNQIVEDNS 328

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P +            + + + R                       T  E   A   G 
Sbjct: 329 GDPHRRFK--------PKPNPAVRK---------------------YTHCEIHPAMILGV 359

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                      Q                            +    +      Q+PL    
Sbjct: 360 CASIIPFPDHNQSPRNC----YQSAXXXXXXXXXXXXXEARMDTMSNILYYPQKPL---- 411

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                    +        DL  G+N +VA   + GYN EDS+++++  +   +F S+   
Sbjct: 412 ------ATTSSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYR 465

Query: 846 EFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +    +   +   E        +   +       +DE GI+  G  ++  DI++GK  P
Sbjct: 466 AYTDQEKRIGMSVVEQFEKPIRNETFKMKHGTYDKLDEDGIVAPGIRISGEDIIIGKTAP 525

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    ++        KA   RDTS  + +  +G V
Sbjct: 526 MTADAEELGQRT-------KAHQKRDTSTPLRTTENGIV 557


>gi|307343558|emb|CBJ18696.1| RNA polymerase B subunit [Micromonospora echinaurantiaca]
          Length = 207

 Score =  251 bits (640), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 95/212 (44%), Positives = 123/212 (58%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGYIY+LKLNH
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLNH 207


>gi|262117956|dbj|BAI48003.1| RNA polymerase beta subunit [Bartonella sp. FG1-1]
          Length = 275

 Score =  251 bits (640), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 VDGKVTTEVIYLSAMEESKHYVAQANSSLDNEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKR+GIV QV+A  IVIR+ E  LDPS SGVDI
Sbjct: 241 AVSAKRSGIVTQVNAPGIVIRATED-LDPSKSGVDI 275


>gi|52699776|gb|AAU86950.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            hilaris]
          Length = 726

 Score =  251 bits (640), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 119/837 (14%), Positives = 237/837 (28%), Gaps = 141/837 (16%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     ++     E    +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D       V     G  I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHSDPVHLVNTVQAVRRGHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-- 740
             ++D      G  +  +       +   +   M     +         +           
Sbjct: 238  IDNDPKSPRCGSLVLTKEHINKLEDYKDLSAEM-QEKIREKEEVEKEVKEDGTPYGWNGL 296

Query: 741  -IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV---KVGDEVRRNDIIAD 796
              R V+  V+ + + +   V     ++  R  Q   V   P      +   V+       
Sbjct: 297  IKRGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYVLPEPSDTSEALMKRVKAPMNPTA 356

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +   +   E  +      
Sbjct: 357  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVXLTXYEQRMDT---- 412

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 413  -------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 447

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 448  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDT 503

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 504  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLR 563

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 564  STENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFAS 603

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 604  RHGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 663

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 664  DATPFTEITVDSVSKLLR--EHGYQSRGFEVM---------------------------- 693

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                              +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 694  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 726


>gi|52699814|gb|AAU86969.1| DNA-dependent RNA polymerase II second largest subunit [Graphina
            poitiaei]
          Length = 730

 Score =  251 bits (640), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 119/831 (14%), Positives = 233/831 (28%), Gaps = 125/831 (15%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEF 516
             G +R+   G ++   +R    R+ + + + +               + +  + + +   
Sbjct: 1    FGKKRLXLAGPLMAGLFRSLFNRLTKDVYKYLQKCVEGGKEFNITLGVKSTTLTNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWSEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            TH+G +CPAET EG   GLV +L    +  V + G     +    + +V  +     + +
Sbjct: 117  THWGLVCPAETPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPQ 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP 680
                ++      +  D +     V        I      + D  D   K          P
Sbjct: 177  ITKVFVNGVWVGVHRDPTHLYNTVLSLRRRNMISHEVSLVRDIRDQEFKIFTDAGRVSRP 236

Query: 681  -FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
             F+ ++D+     G  +  + +     +   +   ++    K        K  G    + 
Sbjct: 237  LFVIDNDNRSPNKGSLILTKELVNKLEDDRELPPDLDPEEKKE-------KYFGWEGLIK 289

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            +    +  ++ + + +         ++  R  Q       P       V+    +A    
Sbjct: 290  S--GAVEYLDAEEEETVMIAMTPEDLEISRQVQAGYAPPEPSSDPNARVKAPVNLAAHTW 347

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
            T           + A +          +   ++                           
Sbjct: 348  THCEIHPSMILGICASI----------IPFPDQXXXXXXXXXXXXXXXXXXXXXXXXXXX 397

Query: 860  EITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                             DE    +  +             +       +   +  + AI 
Sbjct: 398  XXXXXXXXXXXXXXXXXDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 457

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R  +++ +R        +E   +    E + 
Sbjct: 458  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVGL---AAVETFEKPLRSETLR 513

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                 Y +L +   I  G           K+  L+ D                +E  QR 
Sbjct: 514  TKHGTYEKLDDDGLIAPGVRVSGEDIIIGKTAPLALD---------------TEELGQRT 558

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K    T     E+   +K+             L+ VKV +   +  Q GDK A RH
Sbjct: 559  KNQTKRDVSTPLRSTENGIVDKVLL-----TTNQEGLKFVKVRMRTTKIPQIGDKFASRH 613

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 614  GQKGTIGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGAEGDA 673

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E+   +                                    
Sbjct: 674  TPFTAVTVDSVSRLLR--EQGYQSRGFEVM------------------------------ 701

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                            +G +    G         V  G  Y  +L HMV D
Sbjct: 702  ---------------YNGHT----GR---KLRAQVFFGPTYYQRLRHMVDD 730



 Score =  106 bits (264), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 82/625 (13%), Positives = 162/625 (25%), Gaps = 91/625 (14%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +     +  N+  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 10  GPLMAGLFRSLFNRLTKDVYKYLQKCVEGG--KEFNITLGVKSTTLTNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 67  SEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNTPLGRDGKIAKPRQLHNTHWGLVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA--------VCEFFCSSQ 521
             + Q    +  +       + S     +      N + +              F     
Sbjct: 127 TPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMEVLEEYEPTRSPQITKVFVNGVW 186

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  +  + +   RR + +  +  + R     E        R   P          
Sbjct: 187 VGVHRDPTHLYNTVLSLRRRNMISHEVSLVRDIRDQEFKIFTDAGRVSRPLFVIDNDNRS 246

Query: 574 TSEGHNI---GLVSSLTSFARVNAYGFIETP---YRKVCDGKVTNDVVYLSAMEEENRYI 627
            ++G  I    LV+ L     +      E     Y        +  V YL A EEE   I
Sbjct: 247 PNKGSLILTKELVNKLEDDRELPPDLDPEEKKEKYFGWEGLIKSGAVEYLDAEEEETVMI 306

Query: 628 AQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           A     L+                         + +        +  P  ++ I AS+IP
Sbjct: 307 AMTPEDLEISRQVQAGYAPPEPSSDPNARVKAPVNLAAHTWTHCEIHPSMILGICASIIP 366

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           F +                                                         
Sbjct: 367 FPDQXXXXXXXXXXXXXXXXXXXXXXXXXX------------------------------ 396

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                    +           Q+PL                   
Sbjct: 397 -----XXXXXXXXXXXXXXXXXXDERMDTMANILYYPQKPL----------ATTRSMEFL 441

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E
Sbjct: 442 KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKRVGLAAVE 501

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   +         + +D+ G+I  G  V+  DI++GK  P         E+L + 
Sbjct: 502 TFEKPLRSETLRTKHGTYEKLDDDGLIAPGVRVSGEDIIIGKTAPLALDT----EELGQR 557

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVV 940
              +   DV        +G+   V+
Sbjct: 558 TKNQTKRDVSTPLRSTENGIVDKVL 582


>gi|113957816|gb|ABI49124.1| RNA polymerase II second largest subunit [Gyalideopsis vulgaris]
          Length = 725

 Score =  251 bits (640), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 131/842 (15%), Positives = 239/842 (28%), Gaps = 145/842 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ +      + +     S+  Q +I    + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRTLYYKLTKDANRSLQKAVESGKSLELQSIIKPGILTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWSEQKKAAQGKAGVSQVLNRYTYASTLSHLRRTNT----PLGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V + G+    + +  + ++  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGSPGWPVIDFLQSRNMELLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                     ++      +    +     +        I      + D  +   K      
Sbjct: 177  SRNPHATKVFVNGTWVGVHPSPAHLHSQILALRRNNTISHEVSIVRDIREREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPL-----LKAEAPFVGTGMESVVAKSSGAAIVAK 730
                P    D+  R     ++      L      + E P+V    +              
Sbjct: 237  RVSRPLFVVDNDKRSERQGHLVLTKDLLAQLEEDREEPPWVPPAHDPSARPPLRGWDRLI 296

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            + G VE +DA       +    +      +           +      R   K+      
Sbjct: 297  QGGTVEYLDAEEEETVMICMTPEDLEIHREKQAGYDEVGPQEGDDPVSRIKTKLSQPPHV 356

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   PS  LG       +  + +P+  +N          M  + +            
Sbjct: 357  YTHCEIHPSMILG-------ICASIIPFPDHNQSPRNCYQSAMGKQAMGV---------- 399

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTP 908
                                  L N DE    +  +             +       +  
Sbjct: 400  ---------------------FLTNFDERMDTMANILYYPQKPLGTTRSMEFLKFRELPA 438

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    +F R  +++ +R      + +E   
Sbjct: 439  GQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYVEQEKRVGV---QLVEQFE 494

Query: 969  RDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            +    E + L +  Y +L +   I  G           K+  L+ D              
Sbjct: 495  KPLRSETLRLKQGTYEKLDDDGLIAPGTRVSGEDIIIGKTAPLAQD------------IN 542

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               E  QR     K    T     E    +K+      D +     + VK+     +  Q
Sbjct: 543  TNSEMGQRTKMHTKRDASTPLRSTESGIIDKVLLTTNSDAL-----KFVKIRTRTTKVPQ 597

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  +    L    
Sbjct: 598  IGDKFASRHGQKGTIGITYRSEDMPFTSEGITPDLIINPHAIPSRMTIAHLVGRQLSKVS 657

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G +  +          IS L                           V     +G  
Sbjct: 658  SLRGFEGDATPFTDVTVQGISALLR---------------EHGYQSRGFEVMYNGHTGKK 702

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +   VF                                        G  Y  +L HMV D
Sbjct: 703  LRGQVF---------------------------------------FGPTYYQRLRHMVDD 723

Query: 1266 KV 1267
            K+
Sbjct: 724  KI 725


>gi|294471038|gb|ADE80780.1| RNA polymerase beta subunit [Lactococcus lactis]
 gi|294471042|gb|ADE80782.1| RNA polymerase beta subunit [Lactococcus lactis]
          Length = 163

 Score =  251 bits (640), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 69/185 (37%), Positives = 101/185 (54%), Gaps = 22/185 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK +FPI  
Sbjct: 1   YGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K   ++K 
Sbjct: 51  FAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NKETGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +   +G   +    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESFGHTTIPN 158

Query: 188 QGLWM 192
           +G W+
Sbjct: 159 RGAWL 163


>gi|318602930|emb|CBJ04563.1| RNA polymerase beta subunit [Pseudomonas sp. R-37088]
          Length = 260

 Score =  251 bits (640), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 149/259 (57%), Positives = 195/259 (75%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           MPQDLINAKPV +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+
Sbjct: 1   MPQDLINAKPVAAAVKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT+++V+LS
Sbjct: 61  RDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGVVTDEIVFLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE +  IAQA++++++     +ELV  R   E  +   E +  +D SPKQVVS+AASL
Sbjct: 121 AIEEADHVIAQASATMNDQKVLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ V
Sbjct: 181 IPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSV 240

Query: 739 DAIRIVIRSVEGDLDPSTS 757
           DA RIV+R  + +++   +
Sbjct: 241 DASRIVVRVADDEVETGEA 259


>gi|103001854|gb|ABF71524.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            discurrens]
          Length = 702

 Score =  250 bits (639), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 116/822 (14%), Positives = 230/822 (27%), Gaps = 143/822 (17%)

Query: 466  SVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G +L N +R+   ++ + + +  +              + +  + + +     +    
Sbjct: 1    LAGPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWG 60

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 61   DQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 116

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            PAET EG   GLV +L     +      E    +    + +V  +     +      ++ 
Sbjct: 117  PAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVN 176

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDD 686
                 +  D +     V        I      + D  D   K          P F+ ++D
Sbjct: 177  GVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDND 236

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                  G  +  +       +   +   M+S   +       AK  G    V     V+ 
Sbjct: 237  PKSTNCGNLVLTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVE 287

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DL 805
             V+ + + +   V     ++  R  Q           +   V+          T      
Sbjct: 288  YVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHP 347

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            ++   +  + +P+  +N                        ++       +G      D 
Sbjct: 348  SMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXXXNYDQ 389

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 390  RM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 438

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +
Sbjct: 439  DSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDK 494

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   +  G           K+  ++ D      R++          ++     +  Q 
Sbjct: 495  LDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQV 554

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        L+ VKV +   +  Q GDK A RHG KG +  
Sbjct: 555  LL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGI 594

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +        
Sbjct: 595  TYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTV 654

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S L    E    +                                            
Sbjct: 655  DSVSKLLR--EHGYQSRGFEAM-------------------------------------- 674

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                    +G +    G         V +G  Y  +L HMV 
Sbjct: 675  -------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVD 702


>gi|18656504|gb|AAL77805.1|AF389451_12 DNA-directed RNA polymerase II second largest subunit-like protein
            [Tiger frog virus]
          Length = 1219

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/305 (25%), Positives = 123/305 (40%), Gaps = 64/305 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF KDG   D+++NP  
Sbjct: 966  DSDGKKLVKVRLRTPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKDGVVPDLIINPHA 1025

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 1026 FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 1061

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                            I    + A +D    S+L+ G TG    
Sbjct: 1062 -----------------------------VRDIAEAAKEAGIDCW-DSVLHSGSTGRRLP 1091

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 1092 TKIFMAPCPYQRLKHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 1151

Query: 1307 AAYVLQEMLTIKSD--DV-----VGRTR---VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+  L+E +   SD  +V      GR      Y  +    D      P +  +L +E+++
Sbjct: 1152 ASESLKESVYDMSDKYEVPVCKECGRISDHFEYCRMCDATDVSLVKLPYTTKILFQELRS 1211

Query: 1357 LGLSI 1361
            +G+SI
Sbjct: 1212 IGISI 1216



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 85/487 (17%), Positives = 163/487 (33%), Gaps = 41/487 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 403 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYIK-LFVKSAG 461

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 462 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 521

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++   A  +    
Sbjct: 522 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGAGFSLETP 577

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--VFCRCAGEEIL 655
            E     V  GK      +  A        A  ++S+D DG                 + 
Sbjct: 578 REVVMATVRMGKGLPGF-FEGAPARLAWSGAAGSASVDVDGVLCGVTGDPVGFVREARLC 636

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +P   + +     +  +            D       G +             P   +  
Sbjct: 637 LPGVSVVWKKVEREIHLLGCQGRFVRRVLDPEGIRGSGYDSPPAPEERDIEMDPAPSSSP 696

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNT 774
              +    G  + A+   +    D       + E   D  +S +  Y      + + Q+ 
Sbjct: 697 SDSLPCPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQSN 756

Query: 775 CVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWHG 820
              Q    P V   D         D P                ++A G   +VA M   G
Sbjct: 757 MGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAGG 816

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEV-MARDTKLGPEEITRDIPNVSEEG--LKNID 877
           +N EDS++++   +   +F+ +          R TK   E +      +         + 
Sbjct: 817 FNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNRKWDYDLLG 876

Query: 878 ECGIICV 884
           + G+I  
Sbjct: 877 DDGVIDP 883



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 65/241 (26%), Gaps = 85/241 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--- 84
           + +     S+D  L           +          P+        ++F +  ++PP   
Sbjct: 100 NFVRHHIESFDDMLWNEFPAMVAREK----------PV--SVKGYRVKFGTVRYEPPCPD 147

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K         D TY       L +      E    +           +  +P+M 
Sbjct: 148 GKPWEKLTPAMARRTDATYHSAAVCDLTVTDPKGLETVYPRLE---------LCKIPVMV 198

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G F+IKG +R+VV      P I   +D+     +G  
Sbjct: 199 GSAVCWTRTEGSPLPGECPSDPGGYFIIKGKERVVV------PHIRPAYDQPCVYKTGD- 251

Query: 179 LYACRIIPDQGLWM-DI-----EFDSKDIIHVRIDRRRKV-----------PVTSFLMAL 221
                       W+ +      E     ++  + D RRK+           PV     AL
Sbjct: 252 -----------GWLCEFRSVNRETMQTVLVQAKTDCRRKLEFSLPYIKQYVPVGLVFKAL 300

Query: 222 G 222
           G
Sbjct: 301 G 301


>gi|302804103|ref|XP_002983804.1| hypothetical protein SELMODRAFT_118653 [Selaginella moellendorffii]
 gi|300148641|gb|EFJ15300.1| hypothetical protein SELMODRAFT_118653 [Selaginella moellendorffii]
          Length = 762

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 124/319 (38%), Gaps = 71/319 (22%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +A  R  Q+GDK +  HG KG++   L  ED+PF + G   D+++NP   P+R  +
Sbjct: 497  VKVKIASTRAPQAGDKFSSMHGQKGVIGCCLSQEDLPFTRQGIVPDVIINPHAFPTRQTL 556

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E+  G A   +G ++ +                                       
Sbjct: 557  GQMLESIAGKAAA-MGVRVNTTPFSS---------------------------------- 581

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         ++P   GA        L      +SG    Y GL G      + VG 
Sbjct: 582  -------------ASPDQLGA-------ALHRCGFQKSGNERFYSGLYGSMIKAEIFVGV 621

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             +  KL  M  DK+  R  G +  +T+QP+  +   GG +  +ME   + A+GAA  +QE
Sbjct: 622  CFYQKLMQMADDKIKWRRIGRHDSITRQPIKDRQKYGGIKFSQMERSSLVAHGAAASIQE 681

Query: 1314 MLTIKSD----DVV---------GRTRVYESIVAGNDTF---ETGTPESFNVLVKEMQAL 1357
             +   SD    +V          GR+R        +          P S  +LV+E+ ++
Sbjct: 682  RMFHLSDPHQVEVCTRCDRMASIGRSRAPSCRFCKDKFPGFARLEIPYSCKLLVQELNSM 741

Query: 1358 GLSIDLENSRTKNSAKMEE 1376
            G+ + L    + +    E+
Sbjct: 742  GIDLRLVTDSSASLRGRED 760



 Score = 89.4 bits (220), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 81/504 (16%), Positives = 152/504 (30%), Gaps = 61/504 (12%)

Query: 504 INAKPVVSAVCEFFCSSQLSQL----------EEHVNSLSRITHTRRLSALGQGGVARAR 553
            N K V     + F     +Q            +  N    + H R +    Q     + 
Sbjct: 9   FNDKIVTCDFRDAFKRGVWAQPQTYGSGVVEALKRQNVTCTLAHLRHVRTPSQ----YSG 64

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-----------NAYGFIE--- 599
              + R  + +H GR CP ET EG N G + +L  FA +           N  G+++   
Sbjct: 65  KVNDSRYPNKSHTGRFCPVETPEGENCGHLKTLALFAMISSHRDETDVLDNLSGYLQDVD 124

Query: 600 ----TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                         +   ++ LS  +E     A+A      +      +           
Sbjct: 125 EVPLQQLHVFDKVFLNGRLLGLSTRDE-----AKAAVLHLRNRRRRGAIHSEVRVLTFPA 179

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF----- 710
              E   F D               +L  DD+   L G N   + V  L  E        
Sbjct: 180 FHGELQIFTDGGRVLRPVFIVENNEWLLTDDNVSELHGLNNGEEKVRFLLQEGLVELLGP 239

Query: 711 --------------VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV--EGDLDP 754
                         + +G+     +   AA+++  A  +           +   +     
Sbjct: 240 EEEEQCVIASRYSDLRSGIRYTHMELHPAAMLSITASTIPFAQHNLSTRVTYQAQKHSKH 299

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           +          +F  ++ +    Q+ LV        +   +         L  G++ +VA
Sbjct: 300 AIGYYSCNPSKRFDTTSDSLFYPQKQLVSTSMCRLLSPNDSAMMRGWPEKLMHGQSCVVA 359

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS--EEG 872
              + GYN EDS++ ++  +   +F SIH         + +   E   R +      ++ 
Sbjct: 360 VACYDGYNQEDSLIFNQAAIDRGLFRSIHERTHRYNI-NLQSSEESFGRPVEEDGSPQQR 418

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            +++DE G   +GA +     ++GK     E  ++     L+        +V        
Sbjct: 419 YQHLDEDGFPEIGARLQSSQAVIGKTRKLKEGTVSNSSIFLKNFEEGSVKEVVRLPKIAQ 478

Query: 933 SGVSGTVVDVRIFNRHGIDKNERS 956
                 V        HG  K + +
Sbjct: 479 GSHDVNVKTASASFPHGGVKVKIA 502


>gi|228861272|ref|YP_002854295.1| DNA-dependent RNA polymerase II largest subunit [Soft-shelled turtle
            iridovirus]
 gi|194307552|gb|ACF42282.1| DNA-dependent RNA polymerase II largest subunit [Soft-shelled turtle
            iridovirus]
          Length = 1221

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/305 (25%), Positives = 124/305 (40%), Gaps = 64/305 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF KDG   D+++NP  
Sbjct: 968  DSDGKKLVKVRLRTPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKDGVVPDLIINPHA 1027

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 1028 FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 1063

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                          + I    + A +D    S+L+ G TG    
Sbjct: 1064 -----------------------------VKDIAEAAKEAGIDCW-DSVLHSGSTGRRLP 1093

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 1094 TKIFMAPCPYQRLKHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 1153

Query: 1307 AAYVLQEMLTIKSD--DV-----VGRTR---VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+  L+E +   SD  +V      GR      Y  +    D      P +  +L +E+++
Sbjct: 1154 ASESLKESVYDMSDKYEVPVCKECGRISDHFEYCRMCDATDMSLVKLPYTTKILFQELRS 1213

Query: 1357 LGLSI 1361
            +G+SI
Sbjct: 1214 IGISI 1218



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 82/487 (16%), Positives = 161/487 (33%), Gaps = 41/487 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 405 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYVK-LFVKSAG 463

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 464 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 523

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++   A  +    
Sbjct: 524 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGAGFSLETP 579

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--VFCRCAGEEIL 655
            E     +  GK      +  A        A  ++S+D DG                 + 
Sbjct: 580 REVVMATIRLGKGLPGF-FEGAPARLAWSGAAGSASVDVDGVLCGVTGDPVGFVREARLC 638

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +P   + +     +  +            D       G +             P   +  
Sbjct: 639 LPGVSVVWKKVEREIHLLGCQGRFVRRVLDPEGIRGSGYDSPPAPKERDIEMDPAPSSSP 698

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNT 774
              +    G  + A+   +    D       + E   D  +S +  Y      + + Q+ 
Sbjct: 699 SDSLPCPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQSN 758

Query: 775 CVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWHG 820
              Q    P V   D         D P                ++A G   +VA M   G
Sbjct: 759 MGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAGG 818

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNID 877
           +N EDS++++   +   +F+ +         +       E+           E     + 
Sbjct: 819 FNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNREWDYDLLG 878

Query: 878 ECGIICV 884
           + G+I  
Sbjct: 879 DDGVIDP 885



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 65/241 (26%), Gaps = 85/241 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--- 84
           + +     S+D  L           +          P+        ++F +  ++PP   
Sbjct: 96  NFVRHHIESFDDMLWNEFPAMVAREK----------PV--SVKGYRVKFGTVRYEPPCPD 143

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K         D TY       L +      E    +           +  +P+M 
Sbjct: 144 GKPWEKLTPAMARRTDATYHSAAVCDLTVTDPKGLETVYPRLE---------LCKIPVMV 194

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G F+IKG +R+VV      P I   +D+     +G  
Sbjct: 195 GSAVCWTRTEGSPLPGECPSDPGGYFIIKGKERVVV------PHIRPAYDQPCVYKNGD- 247

Query: 179 LYACRIIPDQGLWM-DI-----EFDSKDIIHVRIDRRRKV-----------PVTSFLMAL 221
                       W+ +      E     ++  + D RRK+           PV     AL
Sbjct: 248 -----------GWLCEFRSVNRETRQTVLVQAKTDCRRKLEFSLPYIKQYVPVGLVFKAL 296

Query: 222 G 222
           G
Sbjct: 297 G 297


>gi|190148954|gb|ACE63452.1| RNA polymerase subunit B [Pseudonocardia compacta]
          Length = 266

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 198/273 (72%), Gaps = 8/273 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVTEGQVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 YISPVGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA++AG+VE++ A  + + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVAEKAGVVEELCADYVTVMADDGTR-------LTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           C NQ+P+V  G  V    +IADGP T+ G++AL
Sbjct: 234 CNNQKPIVDEGQRVEVGQVIADGPCTEDGEMAL 266


>gi|113957148|gb|ABI49103.1| RNA polymerase II second largest subunit [Lobariella pallida]
          Length = 695

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 121/813 (14%), Positives = 232/813 (28%), Gaps = 148/813 (18%)

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ + + + +               + +  + + +     +      
Sbjct: 2    GPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +   L + E    ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPECNQVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  +
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                 N+   ++ V  L+ +      T  E    K  G        G+VE VDA      
Sbjct: 238  SPNRGNLVLTKEHVNKLEDDKELAPDTDPEGREDKFRG-WKGLVNQGVVEYVDAEE---- 292

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP-LVKVGDEVRRNDIIADGPSTDLG-D 804
                  + +   V     ++  R  Q   V   P +      V+          T     
Sbjct: 293  ------EETVMIVMTPEDLEISRQIQAGYVMPEPSIDDPNKRVKAPLNPTAHTWTHCEIH 346

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
             ++   +  + +P+  +N          M  + +   + +  ++                
Sbjct: 347  PSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRMDTXXXXXXXXXXX 404

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                                                         +  + AI      + 
Sbjct: 405  XXXXXX---------------------------XXXXXXXXXXAGQNAIVAIASYSGYNQ 437

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y 
Sbjct: 438  EDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYD 493

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   +  G           K+  ++ D      R++          ++     +  Q
Sbjct: 494  KLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQ 553

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                         LR VKV +   +  Q GDK A RHG KG + 
Sbjct: 554  VLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIG 593

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF ++G   D+++NP  +PSRM +  + E  L       G +          
Sbjct: 594  ITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD-------- 645

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     ++++ 
Sbjct: 646  ---------------------------------------------ATP-FTEVTVDSVSR 659

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
            +LR       G   +Y+G TG      V +G  
Sbjct: 660  LLREHGYQSRGFEEMYNGHTGRKLMAQVFLGPT 692


>gi|49237360|ref|YP_031641.1| DNA-dependent RNA polymerase II second largest subunit domain 6,7,3,2
            beta subunit [Frog virus 3]
 gi|47060178|gb|AAT09722.1| DNA-dependent RNA polymerase II second largest subunit domain 6,7,3,2
            beta subunit [Frog virus 3]
          Length = 1221

 Score =  250 bits (639), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/305 (25%), Positives = 123/305 (40%), Gaps = 64/305 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF KDG   D+++NP  
Sbjct: 968  DSDGKKLVKVRLRTPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKDGVVPDLIINPHA 1027

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 1028 FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 1063

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                            I    + A +D    S+L+ G TG    
Sbjct: 1064 -----------------------------VRDIAEAAKEAGIDCW-DSVLHSGSTGRRLP 1093

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 1094 TKIFMAPCPYQRLKHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 1153

Query: 1307 AAYVLQEMLTIKSD--DV-----VGRTR---VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+  L+E +   SD  +V      GR      Y  +    D      P +  +L +E+++
Sbjct: 1154 ASESLKESVYDMSDKYEVPVCKECGRISDHFEYCRMCDATDMSLVKLPYTTKILFQELRS 1213

Query: 1357 LGLSI 1361
            +G+SI
Sbjct: 1214 IGISI 1218



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 83/487 (17%), Positives = 161/487 (33%), Gaps = 41/487 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 405 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYVK-LFVKSAG 463

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 464 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 523

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++   A  +    
Sbjct: 524 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGAGFSLETP 579

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--VFCRCAGEEIL 655
            E     V  GK      +  A        A  ++S+D DG                 + 
Sbjct: 580 REVVLATVRLGKGLPGF-FEGAPARLAWSGAAGSASVDVDGVLCGVTGDPVGFVREARLC 638

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +P   + +     +  +            D       G +             P   +  
Sbjct: 639 LPGVSVVWKKVEREIHLLGCQGRFVRRVLDPEGIRGSGYDSPPAPEERDIEMDPAPSSSP 698

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNT 774
              +    G  + A+   +    D       + E   D  +S +  Y      + + Q+ 
Sbjct: 699 SDSLPCPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQSN 758

Query: 775 CVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWHG 820
              Q    P V   D         D P                ++A G   +VA M   G
Sbjct: 759 MGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAGG 818

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNID 877
           +N EDS++++   +   +F+ +         +       E+           E     + 
Sbjct: 819 FNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNREWDYDLLG 878

Query: 878 ECGIICV 884
           + G+I  
Sbjct: 879 DDGVIDP 885



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 65/241 (26%), Gaps = 85/241 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--- 84
           + +     S+D  L           +          P+        ++F +  ++PP   
Sbjct: 96  NFVRHHIESFDDMLWNEFPAMVAREK----------PV--SVKGYRVKFGTVRYEPPCPD 143

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K         D TY       L +      E    +           +  +P+M 
Sbjct: 144 GKPWEKLTPAMARRTDATYHSAAVCDLTVTDPKGLETVYPRLE---------LCKIPVMV 194

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G F+IKG +R+VV      P I   +D+     +G  
Sbjct: 195 GSAVCWTRTEGSPLPGECPSDPGGYFIIKGKERVVV------PHIRPAYDQPCVYKNGD- 247

Query: 179 LYACRIIPDQGLWM-DI-----EFDSKDIIHVRIDRRRKV-----------PVTSFLMAL 221
                       W+ +      E     ++  + D RRK+           PV     AL
Sbjct: 248 -----------GWLCEFRSVNRETRQTVLVQAKTDCRRKLEFSLPYIKQYVPVGLVFKAL 296

Query: 222 G 222
           G
Sbjct: 297 G 297


>gi|168809716|gb|ACA29577.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 227

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 98/296 (33%), Positives = 137/296 (46%), Gaps = 72/296 (24%)

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            +D  DE  I+      +  +IL G+    G K       L   +  +  R          
Sbjct: 4    KDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR---------- 52

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
             +V+     +    +     +      KI     GD++  GV  +V+V++A KR I+ GD
Sbjct: 53   -EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGD 105

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            KMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 106  KMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 165

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G  I + + D   + D+                                           
Sbjct: 166  GIHIATPVFDGATSEDLW------------------------------------------ 183

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               D  +E         A +    +++LYDG TGEPFD  V+VG +YM+KL+HMV 
Sbjct: 184  ---DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVD 227



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 50/80 (62%), Positives = 61/80 (76%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRV
Sbjct: 2   ALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRV 61

Query: 932 PSGVSGTVVDVRIFNRHGID 951
           P G  G V DV+IF R   D
Sbjct: 62  PHGGDGVVRDVKIFTRANGD 81


>gi|93278283|gb|ABF06597.1| RNA polymerase II second largest subunit [Baeospora myosura]
          Length = 690

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 125/820 (15%), Positives = 238/820 (29%), Gaps = 146/820 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSTTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +       L+ +   ++G G      +     +V  + GI+E +DA   
Sbjct: 226  TDAGRVCRPLFIVENQQLALQKKHIKWIGQGTNDDGEEYKWEQLV--KGGIIELLDAEEE 283

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +       +    ++       R  +K G            PS  LG
Sbjct: 284  ETVMISMTPEDLENSRLQQSGVDIHANDGEFDPAAR--LKAGINAHTWTHCEIHPSMILG 341

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 342  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNF 376

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 377  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 425

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E  AR+          +  
Sbjct: 426  QEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPARENTLRMKHGTYDKL 484

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 485  EEDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 544

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VK+ V   R  Q GDK A RHG KG +   
Sbjct: 545  I--------------------TTNSEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGIT 584

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 585  YRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT----- 639

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++       LR       G+ V                 
Sbjct: 640  --------------------DLTVESVSMYLRQKGYQSRGLEVM---------------- 663

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    G +    G         V +G  Y  +L HMV
Sbjct: 664  ------YHGHT----GR---KLQAQVYLGPTYYQRLKHMV 690



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 82/610 (13%), Positives = 167/610 (27%), Gaps = 98/610 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +      +    K         +  L A EEE   I+     L+       
Sbjct: 246 QKKHIKW--IGQGTNDDGEEYKWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 303

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 304 GVDIHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 363

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 364 MGKQAMGIFLTNFLI-----------------------------------------RMDT 382

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 383 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 418

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 419 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPARENTLRMKH 478

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                ++E G+I  G  V   DI++GK  P         E+L +        DV      
Sbjct: 479 GTYDKLEEDGLIAPGTGVRGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 534

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 535 TENGIVDQVL 544


>gi|307343552|emb|CBJ18693.1| RNA polymerase B subunit [Micromonospora coriariae]
          Length = 211

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 124/212 (58%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 139  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGYIY+LKLNH
Sbjct: 180  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLNH 211


>gi|52699890|gb|AAU87006.1| DNA-dependent RNA polymerase II second largest subunit [Strangospora
            pinicola]
          Length = 703

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 125/825 (15%), Positives = 233/825 (28%), Gaps = 145/825 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVENNKEFNLTLAVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   LS+     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLSSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      I D  D   K          P   
Sbjct: 178  IFVNGVWVGVHRDPAHLVSTVLNLRRRGLISHEVSLIRDIRDREFKIFTDAGRVCRPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIR 742
             D       G  +  +       E   +G  M++   +          ++G+VE VDA  
Sbjct: 238  IDQ----KTGQLVLTKGHIAKLEEDKELGLSMDAQEKEDKLMGWQGLVKSGVVEYVDAEE 293

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D       I        +N +  +N+R    +             PS  L
Sbjct: 294  EETIMIVMTPDDLDISRQIQAGYSIPEANPDD-LNKRVKAPLNPTAHTWTHCEIHPSMIL 352

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                     +  +E              
Sbjct: 353  G-------ICASIIPFPDHNQSPRNTYQSAXXX--XXXXXFLTNYEARMDTMSN------ 397

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                                 +             +       +   +  + AI      
Sbjct: 398  ---------------------ILYYPQKPLATTSSMEYLKFRDLPAGQNAIVAIACYSGY 436

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+ +R   +    +E   +   +E   +    
Sbjct: 437  NQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPIRNETFKMKHGT 492

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L E   +  G           K+  +++D      R++  Q       ++     + 
Sbjct: 493  YDKLDEDGIVAPGIRISGEDIIIGKTAPMTADAEELGQRTKAHQKRDTSTPLRTTENGIV 552

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                             +R VKV   M +  Q GDK A RHG KG 
Sbjct: 553  DQVLL--------------------TTNAEGMRFVKVRTRMTKVPQIGDKFASRHGQKGT 592

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G++  +     
Sbjct: 593  IGITYRQEDMPFTSEGLVPDIIINPHAIPSRMTIAHLIECQLSKVSSLTGREGDATPFTE 652

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 +S L    E    +                                         
Sbjct: 653  VTVDSVSKLLR--ENGYQSRGFEVM----------------------------------- 675

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                       +G +    G         V +G  Y  +L HMV 
Sbjct: 676  ----------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVD 703



 Score =  112 bits (279), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 88/614 (14%), Positives = 176/614 (28%), Gaps = 98/614 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        NK  KD    + + +       F++  ++ +    +  KY L   G  
Sbjct: 8   GPLLAGLFRMLFNKLTKDVYKYLQKCVENN--KEFNLTLAVKSTTLTNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLSSPNATKIFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +    +  + +S + + RR   +  +  + R     E + +         P    +    
Sbjct: 185 VGVHRDPAHLVSTVLNLRRRGLISHEVSLIRDIRDREFK-IFTDAGRVCRPLFVIDQKTG 243

Query: 581 GLVSSLTSFARVNAYGFI---------ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            LV +    A++     +         E           +  V Y+ A EEE   I    
Sbjct: 244 QLVLTKGHIAKLEEDKELGLSMDAQEKEDKLMGWQGLVKSGVVEYVDAEEEETIMIVMTP 303

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             L                              D S +     A   IP    DD N+ +
Sbjct: 304 DDL------------------------------DISRQIQ---AGYSIPEANPDDLNKRV 330

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                          +AP   T       +   + I+   A I+   D  +    + +  
Sbjct: 331 ---------------KAPLNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 375

Query: 752 LDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                          +    +      Q+PL             +        DL  G+N
Sbjct: 376 XXXXXXXXFLTNYEARMDTMSNILYYPQKPL----------ATTSSMEYLKFRDLPAGQN 425

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDI 865
            +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        + 
Sbjct: 426 AIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPIRNET 485

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +DE GI+  G  ++  DI++GK  P         ++        KA   R
Sbjct: 486 FKMKHGTYDKLDEDGIVAPGIRISGEDIIIGKTAPMTADAEELGQRT-------KAHQKR 538

Query: 926 DTSLRVPSGVSGTV 939
           DTS  + +  +G V
Sbjct: 539 DTSTPLRTTENGIV 552


>gi|45545339|gb|AAS67517.1| DNA-dependent RNA polymerase II second largest subunit [Opegrapha
            varia]
          Length = 894

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 153/1014 (15%), Positives = 296/1014 (29%), Gaps = 172/1014 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G +L S       E  +  +  T        +     +     ++   G V DE  L
Sbjct: 27   VEKGTRLISSFSIKWAENSM-IIKRTPGPFVYAMLPYIKADVPMAVVFRALGVVSDEDIL 85

Query: 334  EEIFHSEIRDIPI-LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              I +       + L   S+   A I+         DR++AL  I R        T    
Sbjct: 86   NHICYDRNDTGMLELLKPSIEEGAMIQ---------DRENALDWIARRGN-----TTGTK 131

Query: 393  ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
            +    F      +  L  + +            +     +      +I  L+    G+  
Sbjct: 132  DRRLKFARDIMQREFLPHISQK-----------EGSDTRKAFFFGYMIHRLLQCVLGRRE 180

Query: 453  IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVV 510
             DD D+ G +R+   G ++ N +R+  L++ + + +  +    +      Q  + A  + 
Sbjct: 181  EDDRDHFGKKRLDLAGPLIANLFRVLFLKLTKDVFKYLQKCVENSTEFNVQMAVKASVIT 240

Query: 511  SAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
            + +     +               +SQ+       S ++H RR +      V R     +
Sbjct: 241  NGLKYSLATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAK 296

Query: 558  MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVV 615
             R +H TH+G +CPAET EG   GLV +L+    V+        T +    + ++  +  
Sbjct: 297  PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMGQRNMELLEEYD 356

Query: 616  YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSI 674
             +        ++      +  +      +V        +      I D  D   K     
Sbjct: 357  PVVNPTATKVFVNGVWVGVHSNPGQLVSVVQELRRNGTLSYEMTLIRDIRDREFKIFTDA 416

Query: 675  AASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KR 731
               + P F+   D  +   G  +  +Q V  + A+      G     A            
Sbjct: 417  GRVMRPLFVVEQDVRKPNKGSLVLTKQHVQQILADKDIDTKGYSDEEAAEMKFGWKGLIH 476

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK-FQRSNQNTCVNQRPLVKVGDEVRR 790
            AG+VE +DA       +    +      D+ + +   +    +     +P  K    V+ 
Sbjct: 477  AGVVEYLDAEEEETAMIIMTPEDLEEHRDLMQGIPAPEGVPSDRHKRIKP--KPNPSVKT 534

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   PS  LG       +  + +P+  +N          M  + +  ++      + 
Sbjct: 535  YTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRME 587

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                             V             +       +   +
Sbjct: 588  TMMN-----------------------------VLYYPQKPLATTRSMEYLKFRELPAGQ 618

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   + 
Sbjct: 619  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEKP 674

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + + L    Y +L +   +  G           K+  +++D      ++        
Sbjct: 675  MRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIAADAKELGQKTTMHTKRDV 734

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +  Q                             LR VKV     +  Q G
Sbjct: 735  STPLRSTENGIVDQ--------------------VLFTTNTEGLRFVKVRTRTTKVPQIG 774

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L      
Sbjct: 775  DKFASRHGQKGTIGITYRQEDMPFTREGLVPDIIINPHAIPSRMTIAHLVECLLSKVGSL 834

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             GK+  +          +S L +        G          +                 
Sbjct: 835  EGKEGDATPFTDVTVESVSKLLA------NNGYQQRGFEVMYNG---------------- 872

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                   +G+               + +G  Y  +L H
Sbjct: 873  ----------------------HTGK----------KLRAQIFLGPTYYQRLRH 894



 Score = 88.2 bits (217), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 71/550 (12%), Positives = 148/550 (26%), Gaps = 59/550 (10%)

Query: 203 HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    VP+     ALG +  E+IL+        +   +     +    ++   + +
Sbjct: 62  YIKAD----VPMAVVFRALGVVSDEDILNHICYDRNDTGMLELLKPSIEEGAMIQDRENA 117

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G       ++L       ++ + +  +                +     +  
Sbjct: 118 LDWI-ARRGNTTGTKDRRLKFAR-DIMQREFLPHISQKEGSDTRKAFFFGYMIHRLLQCV 175

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +   +  D            + + +           I N       K  KD    + + +
Sbjct: 176 LGRREEDDRDH------FGKKRLDL-------AGPLIANLFRVLFLKLTKDVFKYLQKCV 222

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                + F+V  ++   +  +  KY L   G      +         + + +    + + 
Sbjct: 223 ENS--TEFNVQMAVKASVITNGLKYSL-ATGNWGDQKKAASAKAGVSQVLNRYTYASTLS 279

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
            L        R+GK       +  +  +    E  + Q    +  +       + S    
Sbjct: 280 HLRRTNTPVGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTP 339

Query: 497 SVMPQDLINAKPVVSA--------VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QG 547
                   N + +              F     +         +S +   RR   L  + 
Sbjct: 340 ITDFMGQRNMELLEEYDPVVNPTATKVFVNGVWVGVHSNPGQLVSVVQELRRNGTLSYEM 399

Query: 548 GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTS-----FARVNAY 595
            + R     E        R + P         + ++G  +     +             Y
Sbjct: 400 TLIRDIRDREFKIFTDAGRVMRPLFVVEQDVRKPNKGSLVLTKQHVQQILADKDIDTKGY 459

Query: 596 GFIETPYRK--VCDGKVTNDVVYLSAMEEENRYIAQANSSLDED-----GSFTEELVFCR 648
              E    K           V YL A EEE   I      L+E      G    E V   
Sbjct: 460 SDEEAAEMKFGWKGLIHAGVVEYLDAEEEETAMIIMTPEDLEEHRDLMQGIPAPEGVPSD 519

Query: 649 CAGEEILVPREKI---DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                   P   +      +  P  ++ I AS+IPF +++ S R      M +QA+ +  
Sbjct: 520 RHKRIKPKPNPSVKTYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVAL 579

Query: 706 AEAPFVGTGM 715
                    M
Sbjct: 580 TNYALRMETM 589


>gi|307343482|emb|CBJ18658.1| RNA polymerase B subunit [Micromonospora sp. GUI42]
          Length = 212

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 125/212 (58%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGY+Y+LKLNH
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNH 212


>gi|190148946|gb|ACE63448.1| RNA polymerase subunit B [Pseudonocardia aurantiaca]
          Length = 266

 Score =  250 bits (638), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 149/273 (54%), Positives = 196/273 (71%), Gaps = 8/273 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEI 654
           GFI+TPYRKV +G+VT  + YL+A EE+   IAQAN+ L ++G F EE V  R   GE  
Sbjct: 61  GFIQTPYRKVDEGQVTEQIDYLTADEEDRFVIAQANAPLTDEGHFQEERVLVRRKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQAVPLL++E+P VGTG
Sbjct: 121 YISPTGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQAVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +VA +AG+VE++ A  I + + +G           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVLVADKAGVVEELCADYITVMADDGTR-------TTYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           C NQ+P+V  G  V    +IADGP T+ G++AL
Sbjct: 234 CNNQKPIVDEGARVEVGQVIADGPCTEDGEMAL 266


>gi|302814812|ref|XP_002989089.1| hypothetical protein SELMODRAFT_129173 [Selaginella moellendorffii]
 gi|300143190|gb|EFJ09883.1| hypothetical protein SELMODRAFT_129173 [Selaginella moellendorffii]
          Length = 766

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 124/319 (38%), Gaps = 71/319 (22%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +A  R  Q+GDK +  HG KG++   L  ED+PF + G   D+++NP   P+R  +
Sbjct: 501  VKVKIASTRAPQAGDKFSSMHGQKGVIGCCLSQEDLPFTRQGIVPDVIINPHAFPTRQTL 560

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E+  G A   +G ++ +                                       
Sbjct: 561  GQMLESIAGKAAA-MGVRVNTTPFSS---------------------------------- 585

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                         ++P   GA        L      +SG    Y GL G      + VG 
Sbjct: 586  -------------ASPDQLGA-------ALHRCGFQKSGNERFYSGLYGSMIKAEIFVGV 625

Query: 1254 IYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
             +  KL  M  DK+  R  G +  +T+QP+  +   GG +  +ME   + A+GAA  +QE
Sbjct: 626  CFYQKLMQMADDKIKWRRIGRHDSITRQPIKDRQKYGGIKFSQMERSSLVAHGAAASIQE 685

Query: 1314 MLTIKSD----DVV---------GRTRVYESIVAGNDTF---ETGTPESFNVLVKEMQAL 1357
             +   SD    +V          GR+R        +          P S  +LV+E+ ++
Sbjct: 686  RMFHLSDPHQVEVCTRCDRMASIGRSRAPSCRFCKDKFPGFARLEIPYSCKLLVQELNSM 745

Query: 1358 GLSIDLENSRTKNSAKMEE 1376
            G+ + L    + +    E+
Sbjct: 746  GIDLRLVTHSSASLRGRED 764



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 75/481 (15%), Positives = 154/481 (32%), Gaps = 51/481 (10%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            S + +  +  N    + H R +    Q     +    + R  + +H GR CP ET EG 
Sbjct: 34  GSGVVEALKRQNVTCTLAHLRHVRTPSQ----YSGKVNDSRYPNKSHTGRFCPVETPEGE 89

Query: 579 NIGLVSSLTSFARV-----------NAYGFIE-------TPYRKVCDGKVTNDVVYLSAM 620
           N G + +L  FA +           N  G+++                 +   ++ LS  
Sbjct: 90  NCGHLKTLALFAMISSYRDETDVLDNLSGYLQDVDEVPLQQLHVFDKVFLNGRLLGLSTR 149

Query: 621 EEENRYIA-------------------QANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           +E    +                    Q   + ++ G         R      +V   + 
Sbjct: 150 DEAKAAVLHLRNRRRRGAIHSERLFSSQVEIAPNKHGELQIFTDGGRVLRPVFIVENNEW 209

Query: 662 DFID--ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE--APFVGTGMES 717
              D   S  + +S     + FL  +    +L     ++  +    ++  +    T ME 
Sbjct: 210 LLTDDNVSELRELSNGEEKVRFLLQEGLVELLGPEEEEQCVIASRYSDLRSGICYTHMEL 269

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A     +I A      +   + R+  ++ +     +          +F  ++ +    
Sbjct: 270 HPAAML--SITASTIPFAQHNLSTRVTYQA-QKHSKHAIGYYSCNPSKRFDTTSDSLFYP 326

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+ LV        +   +         L  G++ +VA   + GYN EDS++ ++  +   
Sbjct: 327 QKQLVSTSMCRLLSPNDSAMMRGWPEKLMHGQSCVVAVACYDGYNQEDSLIFNQAAIDRG 386

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVS--EEGLKNIDECGIICVGAEVNPGDILV 895
           +F SIH         + +   E   R +      ++  +++DE G   +GA +     ++
Sbjct: 387 LFRSIHERTHRYNI-NLQSSEESFGRPVEEDGSPQQRYQHLDEDGFPEIGARLQSSQAVI 445

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           GK     E  ++     L+        +V                       HG  K + 
Sbjct: 446 GKTRKLKEGTVSNSSIFLKNFEEGSVKEVVRLPKIAQGSHDVNFKTASASFPHGGVKVKI 505

Query: 956 S 956
           +
Sbjct: 506 A 506


>gi|295815635|gb|ADG36320.1| RNA polymerase beta-subunit [Mycobacterium europaeum]
          Length = 215

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 90/216 (41%), Positives = 119/216 (55%), Gaps = 40/216 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 32   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 91

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 92   TPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWNIEGSPEWAAN-------------- 136

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +       +    VSTPVFDGA EE +  ML            
Sbjct: 137  -----------------LPEGLLHAQPNQIVSTPVFDGAKEEELQGMLSCTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +D  G+++L+DG +GEPF  PVTVGY+Y++KL+H+V
Sbjct: 180  VDGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLV 215


>gi|158853042|gb|ABW82121.1| RpoB [Bacteriovorax sp. NZAH11]
          Length = 361

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 170/364 (46%), Positives = 240/364 (65%), Gaps = 10/364 (2%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGA + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+
Sbjct: 1    ARDSGAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQK 58

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVF
Sbjct: 59   ALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVF 118

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKIT
Sbjct: 119  TSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKIT 178

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +
Sbjct: 179  PKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEI 238

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDL 1012
              ++  L+ RD+  E   +  +   ++ ++L G              +   K   L+S++
Sbjct: 239  IEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEV 298

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            ++  P        ++   ++  +           + +  +  ++I K   GD++  GV++
Sbjct: 299  LASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDELTAGVIK 357

Query: 1073 VVKV 1076
             V +
Sbjct: 358  KVTI 361


>gi|110669602|gb|ABG81896.1| RNA polymerase II second largest subunit [Lecanora hybocarpa]
          Length = 703

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 123/825 (14%), Positives = 235/825 (28%), Gaps = 145/825 (17%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   ++ + + +  +              + +  + + +     +   
Sbjct: 2    DLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEHNKEFNLTLAVKSTTLTNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +      +V  +   +++      ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYITVGTPSEPLIDFMISKSMEVLEEYEPVNSPHATKIFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  D +   ++V     G  I      + D  D   K          P    D 
Sbjct: 178  NGVWVGVHRDPARLVQMVLALRRGLTISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDQ 237

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVI 745
                  G  +  +      A    +   +++   +            G+VE VDA     
Sbjct: 238  ----KTGDLVLTKDDIEKLAVDKEISASLDAQEREDRHLGWHGLVERGVVEYVDAEEEET 293

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    D       I +            VN+R                  PS  LG  
Sbjct: 294  IMIVMTPDDLEISRCI-QAGMTIPEEDPEDVNKRRKANASAHAHTWTHCEIHPSMILG-- 350

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   + +  +E                 
Sbjct: 351  -----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYEQRM-------------- 389

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 390  -------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 436

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +
Sbjct: 437  DSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGLAVLEQFEKPMRSDTLKLKHGTYDK 492

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   +  G           K+  ++ D                +E  QR     K   
Sbjct: 493  LDDDGVVAPGVRVSGEDIIIGKTAPMAPD---------------AEELGQRTKAHTKRDV 537

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             T     E+   +++      D +     R VKV +   +  Q GDK A RHG KG +  
Sbjct: 538  STPLRSTENGIVDQVLMSTNADGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGI 592

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +        
Sbjct: 593  TYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTV 652

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S L    +    +                                            
Sbjct: 653  DSVSRLLR--QNGYQSRGFEVM-------------------------------------- 672

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                    +G +    G         V +G  Y  +L HMV DK+
Sbjct: 673  -------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 703


>gi|113957175|gb|ABI49105.1| RNA polymerase II second largest subunit [Heterodermia vulgaris]
          Length = 698

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 115/817 (14%), Positives = 229/817 (28%), Gaps = 144/817 (17%)

Query: 465  RSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R    ++ + +    +    +    +    + +  + + +     +   
Sbjct: 2    DLAGPLLAGLFRTLFNKLTKDVEKYLKNCIENNREFILTLGVKSATLTNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     V+     +   P+      +   +    +       ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCHVSVGTPSDGIVPFLLQRQMESLEEYDPHTFPNATKVFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLEND 685
                  +  + +   + V        +      I D  D   + +      L P F+ ++
Sbjct: 178  NGVWVGVHRNAAHLVQAVQSLRRKHVLEPEVSLIRDIRDREFRILTDQGRVLRPLFVVDN 237

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D+     G  +  +       E   V   ++    +        +  G    +D    V+
Sbjct: 238  DAKSNNCGNLVFNKEHSKKLDEDDSVPFDIDRENREK-------ETFGWNGLID--EGVV 288

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              V+ + + +   V   + +   R  Q      +P                 P      +
Sbjct: 289  EYVDAEEEETVMIVMTPQDLAMSRQLQAGYTLAQP----------------DPDEPNRRV 332

Query: 806  ALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                N       W       SM+  I   ++            +                
Sbjct: 333  TAPMNPTAH--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYXXXXXXXXXXXXXXXX 390

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                                                      +   +  + AI      +
Sbjct: 391  XXXXXXXXXXX-----------XXXXXXXXXXXXXXXXXXXELPAGQNAIVAIACYSGYN 439

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    +F R   D+ +R   + +  +E   +    + + L    Y
Sbjct: 440  QEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGQHIVEAFEKPMRSDTLRLKHGTY 495

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I+ G           K+  ++ D      R++          ++     L  
Sbjct: 496  DKLDDDGIIVPGARVSGEDIIIGKTAPIAPDAEEMGQRTKLHTKRDASTPLRSTESGLVD 555

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                             L+ VKV +   +  Q GDK A RHG KG +
Sbjct: 556  QVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTI 595

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +  + E  L       G +         
Sbjct: 596  GITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------- 648

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     ++++
Sbjct: 649  ----------------------------------------------ATP-FTEVTVDSVS 661

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             +LR       G  ++Y+G TG      V +G  Y  
Sbjct: 662  RLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQ 698



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/329 (13%), Positives = 82/329 (24%), Gaps = 27/329 (8%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + +  K   S  G  ++  R    +      R          I     
Sbjct: 49  TNGLKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPRQ 108

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +   + + L     + +      I   +    ++S+   D   
Sbjct: 109 LHNTHWGLVCPAETPEGQACGLVKNLALMCHVSVGTPSDGIVPFLLQRQMESLEEYDPHT 168

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDV--- 561
                           +       + +  +   RR   L     + R     E R +   
Sbjct: 169 FPNATKVF---VNGVWVGVHRNAAHLVQAVQSLRRKHVLEPEVSLIRDIRDREFRILTDQ 225

Query: 562 ----HPTHYGRICPAETSEGH---NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND- 613
                P           + G+   N      L     V      E   ++        D 
Sbjct: 226 GRVLRPLFVVDNDAKSNNCGNLVFNKEHSKKLDEDDSVPFDIDRENREKETFGWNGLIDE 285

Query: 614 --VVYLSAMEEENRYIAQANSSLDEDGS--------FTEELVFCRCAGEEILVPREKIDF 663
             V Y+ A EEE   I      L               +     R     +         
Sbjct: 286 GVVEYVDAEEEETVMIVMTPQDLAMSRQLQAGYTLAQPDPDEPNRRVTAPMNPTAHTWTH 345

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  P  ++ I AS+IPF +++ S R   
Sbjct: 346 CEIHPSMILGICASIIPFPDHNQSPRNTY 374


>gi|52699804|gb|AAU86964.1| DNA-dependent RNA polymerase II second largest subunit [Dibaeis
            baeomyces]
          Length = 711

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 118/828 (14%), Positives = 230/828 (27%), Gaps = 137/828 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G ++   +R    ++ + + +  +              + +  + + + 
Sbjct: 1    DXXGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     V      E    +    + ++  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D +     V        I      + D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+ ++D+     G  +  + +     +   +   M+            AK  G    
Sbjct: 237  RPLFVIDNDAKSPNKGSLVLTKELVSRLEDDKDLPADMDPDEKA-------AKTMGWDGL 289

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +   R V+  ++ + + +   V     +   R  Q               V+        
Sbjct: 290  I--KRGVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYQLPETTDDPNKRVKAPLNPTAH 347

Query: 798  PSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
              T      ++   +  + +P+  +N          M                       
Sbjct: 348  TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAM----------------------- 384

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G + +       SE             +             +       +   +  + AI
Sbjct: 385  GXQAMGXXXXXFSERM------DNAXNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 438

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    ++ R   D+ +R      EQ E   R    +  
Sbjct: 439  ACYSGYNQEDSVIMNXSSIDRGLF-RSLYYRTYTDQEKRVGMSVVEQFEKPMRSDTLKLK 497

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +       +  G           K+  ++ D      R++      +   ++    
Sbjct: 498  HGTYDKLDDDGLVAPGVRISGEDIIIGKTEPIAPDSEELGQRTKLHVKRDKSTPLRTTEN 557

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L                  ++K+          LR VKV     +  Q GDK A RHG 
Sbjct: 558  GL------------------VDKVML--STNAEGLRFVKVRTRTTKIPQIGDKFASRHGQ 597

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 598  KGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATP 657

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E    +                                      
Sbjct: 658  FTEVTVDSVSRLLR--EHGYQSRGFEVM-------------------------------- 683

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                          +G +    G         V +G  Y  +L HMV 
Sbjct: 684  -------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVD 711



 Score =  102 bits (254), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 84/607 (13%), Positives = 182/607 (29%), Gaps = 75/607 (12%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +     T  NK  KD    + + +       F++   + +    +  +Y L   G  
Sbjct: 12  GPLMAGLFRTLFNKLTKDVYKYLQKCVESNR--EFNLTLGVKSTTLTNGLRYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + S     +      N + +         +A   F     
Sbjct: 129 TPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR   +             +RD+      R     T  G    
Sbjct: 189 VGVHRDPAHLVSTVMSLRRRGLIS-------HEVSLVRDIR----DREFKIFTDAGRVCR 237

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +  + + A+    G +      V       D   L A  +                   
Sbjct: 238 PLFVIDNDAKSPNKGSLVLTKELVSR---LEDDKDLPADMD------------------P 276

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA- 700
           +E        +  L+ R  ++++DA  ++ V I    +   E+ D +R L       +  
Sbjct: 277 DEKAAKTMGWD-GLIKRGVVEYLDAEEEETVMI----VMTPEDLDISRQLQAGYQLPETT 331

Query: 701 -VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             P  + +AP   T       +   + I+   A I+   D  +    + +  +     G 
Sbjct: 332 DDPNKRVKAPLNPTAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGXQAMGX 391

Query: 760 DIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                  +   +       Q+PL                      +L  G+N +VA   +
Sbjct: 392 XXXXFSERMDNAXNILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACY 441

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS++++   +   +F S++   +    +   +   E     +  D   +     
Sbjct: 442 SGYNQEDSVIMNXSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTY 501

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G++  G  ++  DI++GK  P         E+L +        D         +
Sbjct: 502 DKLDDDGLVAPGVRISGEDIIIGKTEPIAPDS----EELGQRTKLHVKRDKSTPLRTTEN 557

Query: 934 GVSGTVV 940
           G+   V+
Sbjct: 558 GLVDKVM 564


>gi|307343488|emb|CBJ18661.1| RNA polymerase B subunit [Micromonospora sp. GUI63]
          Length = 211

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 125/212 (58%), Gaps = 38/212 (17%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G++ L+DG +GEP   P+ VGY+Y+LKLNH
Sbjct: 180  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLNH 211


>gi|52699870|gb|AAU86996.1| DNA-dependent RNA polymerase II second largest subunit [Sarcogyne
            regularis var. regularis]
          Length = 702

 Score =  249 bits (637), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 120/825 (14%), Positives = 235/825 (28%), Gaps = 147/825 (17%)

Query: 469  EMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----- 521
             +L N +R+   ++ + + +  +    +         + +  + + +     +       
Sbjct: 1    PLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQK 60

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+       S ++H RR +      + R     + R +H TH+G +CPAE
Sbjct: 61   KAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAE 116

Query: 574  TSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
            T EG   GLV +L    +  V         +    + +V  +     +      ++    
Sbjct: 117  TPEGQACGLVKNLALMCYITVGTPSQPIVDFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 176

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV 690
              +  D +     V        I      + D  D   K          P    ++  R 
Sbjct: 177  VGVHRDPAHLVSTVLTLRRANAISHEVSLVRDIRDREFKIFTDAGRVCRPLFVINNDPRS 236

Query: 691  LMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                N+   +Q +  L+ +        E       G   + K+ GIVE VDA        
Sbjct: 237  TNCGNLVLTKQDIHKLEDDKDLPD-DYEIDEKNPPGWNGLIKK-GIVEYVDAEE------ 288

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
                + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 289  ----EETVMIVMTPEDLEISRQLQAGYNLPDTSDDLIKRVKAPMNPTAHTWTHCEIHPSM 344

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 345  ILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM---------------- 386

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 387  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 435

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 436  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 491

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D      R++          ++     +  Q   
Sbjct: 492  DDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 551

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      LR VKV +   +  Q GDK A RHG KG +    
Sbjct: 552  --------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 591

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 592  RQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDS 651

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 652  VSKLLR--EHGYQSRGFEVM---------------------------------------- 669

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                  +G +    G         V +G  Y  +L HMV  K+ A
Sbjct: 670  -----YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIXA 702


>gi|226934682|gb|ACO92415.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 211

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 89/216 (41%), Positives = 118/216 (54%), Gaps = 40/216 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 133  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H+V
Sbjct: 176  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHHLV 211


>gi|168809722|gb|ACA29580.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 218

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 95/276 (34%), Positives = 129/276 (46%), Gaps = 60/276 (21%)

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G     G     K T      +S   R     F  +  +V+     +    +     
Sbjct: 3    IRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRD 62

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +      KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P ED
Sbjct: 63   V------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVED 116

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+   
Sbjct: 117  MPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLW-- 174

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                       D  +E         A +
Sbjct: 175  -------------------------------------------DTVNE---------AGM 182

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                +++LYDG TGEPFD  V+VG +YM+KL+HMV 
Sbjct: 183  ASDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVD 218



 Score = 68.6 bits (166), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 46/72 (63%), Positives = 55/72 (76%)

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V
Sbjct: 1   GIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVV 60

Query: 940 VDVRIFNRHGID 951
            DV+IF R   D
Sbjct: 61  RDVKIFTRANGD 72


>gi|262117880|dbj|BAI47965.1| RNA polymerase beta subunit [Bartonella sp. RJ24-1]
          Length = 275

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 198/276 (71%), Positives = 230/276 (83%), Gaps = 1/276 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           IKER+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG
Sbjct: 1   IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKI 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT +V+YLSAM     Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D
Sbjct: 121 IDGKVTTEVIYLSAMVVSKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
            SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME+VVA+ SGA
Sbjct: 181 VSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAVVARDSGA 240

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           A+ AKRAGIV+QVDA RIVIR+ E  LDPS SGVDI
Sbjct: 241 AVGAKRAGIVDQVDATRIVIRATED-LDPSKSGVDI 275


>gi|67515348|gb|AAY68203.1| RNA polymerase IV second largest subunit [Psilotum nudum]
          Length = 364

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 75/336 (22%), Positives = 130/336 (38%), Gaps = 70/336 (20%)

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             ++E +   ++ +   L+   K +++++     +     ++VKV +  +R    GDK + 
Sbjct: 81   ESLEPVNNVFKDTSVKLKSTEKGRVDQVXL--TVNDDEKKIVKVRLRERRLPVVGDKFSS 138

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
             HG KG++      E++PF K+G   DI++NP   PSR  V Q+ E  L       GKK 
Sbjct: 139  LHGQKGVIGGTFSQEELPFTKNGIVPDIIINPHAFPSRQTVAQLLEIGLAKVTSVAGKKC 198

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 199  D-----------------------------------------------------ATP-FS 204

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                + I   L        G  ++ +G TG  F+  + +G  Y  +L +M  D++  RS 
Sbjct: 205  NVKVDKIVEELHRLGYGNWGSEVMVNGQTGHQFEAVIFIGPAYYQRLVYMAEDRIKYRSL 264

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------DV 1322
            G   ++T QP+  +   GG ++GEME  C+ A+GA   +QE L + SD           +
Sbjct: 265  GPTHILTHQPVSDRKRHGGVKIGEMERDCLLAHGACANVQERLFLLSDPYIMYICSKCHM 324

Query: 1323 VG--RTRVYESIVA--GNDTFETGTPESFNVLVKEM 1354
            V    T+ Y            +   P +  +L +E+
Sbjct: 325  VAAKDTKGYHCRFCRSNYHIVQVHMPYACKLLYQEL 360



 Score = 47.8 bits (112), Expect = 0.013,   Method: Composition-based stats.
 Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 12/87 (13%)

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE-------EG 872
           GYN EDS+++++  +   +F S+H   F V         E+ +   P+VS+         
Sbjct: 1   GYNQEDSIVMNQSSIDRGLFNSMHYYGFRVELD-----GEDESLMKPSVSDINSAXQSSQ 55

Query: 873 LKNIDECGIICVGAEVNPGDILVGKIT 899
              +D  G+  +GA +   DI++GK +
Sbjct: 56  YSKLDSDGLPYIGANLFSYDIIIGKES 82


>gi|94410920|gb|ABF18579.1| RNA polymerase II second largest subunit [Hemimycena gracilis]
          Length = 689

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 125/823 (15%), Positives = 231/823 (28%), Gaps = 153/823 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++   +       + +  + +     +A  +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEE--NAHSQNP 174

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N            LV                   D SP+  V            
Sbjct: 175  CTKVFVNGVWMGVHRDPANLVKTIKKLRRKD---------DISPEVSVVRDIRERELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK----SSGAAIVAKRAGIVEQVDA 740
             D+ RV     +       L+ +   V    E    +      G  +   R GIVE +DA
Sbjct: 226  ADAGRVCRPLFIVENQQLALQKKH--VRWITEGKDDQGEQFKWGDLV---RRGIVELLDA 280

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +       +++   +    +K G            PS 
Sbjct: 281  EEEETVMISMTPEDLETSRLQQQG---MNQDEDEDFDPAARLKAGINSHTWTHCEIHPSM 337

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 338  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFL 372

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 373  TNFLIRM-----------DTMANILCYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 421

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ +   RD          
Sbjct: 422  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGINQLEEFDKPTRDTTLRMKHGTY 480

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G   V       K+  +  D      R++          ++     +  
Sbjct: 481  DKLEDDGLIAPGTGVVGEDIIIGKTAPIPPDSEELGQRTRMHTRRDVSTPLKSTESGVVD 540

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 541  QVLI--------------------TTNSDGQKFVKVRVRSIRVPQIGDKFASRHGQKGTI 580

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 581  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 638

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 639  -----------------------DLTVESVSTFLRQKGYQSRGLEVM------------- 662

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                       G +       G      V +G  Y  +L HMV
Sbjct: 663  ---------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 689



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 97/636 (15%), Positives = 176/636 (27%), Gaps = 104/636 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSQNPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYADAGRVCRPLFIVENQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         E    K  D      V  L A EEE   I+     L E     +
Sbjct: 246 QKKHVRWITEGKDDQGEQ--FKWGDLVRRGIVELLDAEEEETVMISMTPEDL-ETSRLQQ 302

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           + +      +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 QGMNQDEDEDFDPAARLKAGINSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIFLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y               Q+PL                      +L  G+N +VA 
Sbjct: 382 MANILCYP--------------QKPL----------ATTRSMEYLKFRELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGINQLEEFDKPTRDTTLRMKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P    P   EE   R          RD S  
Sbjct: 478 GTYDKLEDDGLIAPGTGVVGEDIIIGKTAPI---PPDSEELGQRTRM----HTRRDVSTP 530

Query: 931 VPSGVSGTVVDVRIFNRHGIDK--NERSISVEREQI 964
           + S  SG V  V I       K    R  S+   QI
Sbjct: 531 LKSTESGVVDQVLITTNSDGQKFVKVRVRSIRVPQI 566


>gi|153958173|gb|ABS53377.1| RpoB [Bacteriovorax sp. NZAH13]
          Length = 358

 Score =  249 bits (636), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 173/361 (47%), Positives = 239/361 (66%), Gaps = 10/361 (2%)

Query: 711  VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            VGTG+ES VA+ S A + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+
Sbjct: 1    VGTGIESTVARDSRAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRT 58

Query: 771  NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
            NQNTC NQ+ LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+
Sbjct: 59   NQNTCNNQKALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILIN 118

Query: 831  ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
            ER+++ DVFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + P
Sbjct: 119  ERLLARDVFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKP 178

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            GDILVGKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G+
Sbjct: 179  GDILVGKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGV 238

Query: 951  DKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFK 1003
            +   RS  +  ++  L+ RD+  E   +  +   ++ ++L G              +   
Sbjct: 239  ELCARSKEIIEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLP 298

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K   L+S++++  P        ++   ++  +           + +  +  ++I K   G
Sbjct: 299  KGADLTSEVLASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRG 357

Query: 1064 D 1064
            D
Sbjct: 358  D 358


>gi|190148968|gb|ACE63459.1| RNA polymerase subunit B [Pseudonocardia saturnea]
          Length = 271

 Score =  249 bits (636), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 151/278 (54%), Positives = 202/278 (72%), Gaps = 9/278 (3%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVH +HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHTSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDG-KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEE 653
           GFI+TPYRKV D  +VT  + YL+A EE+   IAQAN+ LD+DG+F EE V  R   GE 
Sbjct: 61  GFIQTPYRKVDDEGRVTEQIDYLTADEEDRFVIAQANAPLDDDGNFQEERVLVRRKGGEV 120

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             +  + +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGT
Sbjct: 121 DYISPKGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGT 180

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           GME   A  +G  +VA++AG+VE++ A  I + + +G           YRL KF+RSNQ 
Sbjct: 181 GMELRAAVDAGDVLVAEKAGVVEELCADYITVMADDGTR-------LTYRLNKFRRSNQG 233

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           TC NQ+P+V  G  V    +IADGP T+ G++ALG+N+
Sbjct: 234 TCNNQKPIVDEGQRVEVGQVIADGPCTEDGEMALGKNL 271


>gi|317408995|gb|ADV17879.1| RNA polymerase II second largest subunit [Veluticeps fimbriata]
          Length = 682

 Score =  249 bits (636), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 123/808 (15%), Positives = 230/808 (28%), Gaps = 144/808 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS--VMPQDLINAKPVVSAVC 514
            D+ G +R+     +L N +R    ++ + +   +               +    + + + 
Sbjct: 3    DHFGKKRLDPRCPLLANLFRNVFRKLTKDVYRYLQKCVETPKWFNLSLEVKHNTITNGLK 62

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR        + R     + R +
Sbjct: 63   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRC----DTPLGRKGKITKPRQL 118

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++           + +  + +         
Sbjct: 119  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL-------- 170

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +             I   R K    D SP+  V         
Sbjct: 171  EENAHSATPYTKVFVNGVWMGVHGDPGNLVRTIKKLRRK---DDISPEVSVVRDIREREL 227

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +         + G++E +DA
Sbjct: 228  RLYTDAGRVCRPLFIVENQQLALQKKHIRWLNQGYREDDPEDIWKWDQLVKNGVIELLDA 287

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +             +    +K   +          PS 
Sbjct: 288  EEEETVMISMTPEDLENSRL--QSAGIDTHLNEGEYDPAVRLKAPTQGHTWTHCEIHPSM 345

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 346  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 380

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 381  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYS 429

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D   +S   + E+ E   RD          
Sbjct: 430  GYNQVDSVIMNQSSIDRGLF-RSIYYRSYMDLEIKSGIQQLEEFEKPTRDTTLRMKHGTY 488

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      RS+                  + 
Sbjct: 489  DKIEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRSRLHT---------------RR 533

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T+    E    +++      D       + VKV V   R  Q GDK A RHG KG +
Sbjct: 534  DVSTALKSTESGIVDQVLITTNSD-----GQKFVKVRVRATRVPQIGDKFASRHGQKGTI 588

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +         
Sbjct: 589  GITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------- 641

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                                          +TP F     E+++
Sbjct: 642  ----------------------------------------------ATP-FTDLTVESVS 654

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRP 1248
            + LR       G  ++Y G TG      
Sbjct: 655  TFLRQKGYQSRGLEVMYHGHTGRKLQAQ 682



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 85/603 (14%), Positives = 160/603 (26%), Gaps = 97/603 (16%)

Query: 375 LDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            D+YR + +  +   +             +        G      +         + + +
Sbjct: 30  KDVYRYLQKCVETPKWFNLSLEVKHNTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNR 89

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R GK T     +  +  +    E  + Q    +  +      
Sbjct: 90  YTYASTLSHLRRCDTPLGRKGKITKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCI 149

Query: 489 RISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S+    +             NA         F     +    +  N +  I   RR 
Sbjct: 150 SVGSLSAPVIEFLEEWGLESLEENAHSATPYTKVFVNGVWMGVHGDPGNLVRTIKKLRRK 209

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +                ++        P    E   + L      +            
Sbjct: 210 DDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIRWLNQGYREDDPED 269

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--- 658
             K         +  L A EEE   I+     L+     +  +      GE     R   
Sbjct: 270 IWKWDQLVKNGVIELLDAEEEETVMISMTPEDLENSRLQSAGIDTHLNEGEYDPAVRLKA 329

Query: 659 ----EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                     +  P  ++ + AS+IPF +++ S R      M +QA+ +           
Sbjct: 330 PTQGHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---- 385

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                                                   + + +  Y       +    
Sbjct: 386 -------------------------------------RMDTMANILYYPQKPLATTRSME 408

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +  R                        +L  G+N +VA + + GYN  DS+++++  +
Sbjct: 409 YLRFR------------------------ELPAGQNAIVAILCYSGYNQVDSVIMNQSSI 444

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F SI+   +  +   + +   E            +       I++ G+I  G  VN
Sbjct: 445 DRGLFRSIYYRSYMDLEIKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVN 504

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P    P   EE   R+         RD S  + S  SG V  V I     
Sbjct: 505 GEDIIIGKTAPI---PPDSEELGQRSRL----HTRRDVSTALKSTESGIVDQVLITTNSD 557

Query: 950 IDK 952
             K
Sbjct: 558 GQK 560


>gi|45545327|gb|AAS67511.1| DNA-dependent RNA polymerase II second largest subunit [Dibaeis
            baeomyces]
          Length = 893

 Score =  249 bits (636), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 121/871 (13%), Positives = 245/871 (28%), Gaps = 139/871 (15%)

Query: 413  RVKMNMRLNLDTP--DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
            R  M   L       +     +   +  ++  ++ +  G+   DD D+ G +R+   G +
Sbjct: 140  RDIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPL 199

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            +   +R    ++ + + +  +              + +  + + +     +         
Sbjct: 200  MAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYSLATGNWGEQKKA 259

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 260  ASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 315

Query: 576  EGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     V      E    +    + ++  +   L +      ++      
Sbjct: 316  EGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVFVNGVWVG 375

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVL 691
            +  D +     V        I      + D  D   K          P F+ ++D+    
Sbjct: 376  VHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDAKSPN 435

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             G  +  + +     +   +   M+            AK  G    +   R V+  ++ +
Sbjct: 436  KGSLVLTKELVSRLEDDKDLPADMDPDEKA-------AKIMGWDGLI--KRGVVEYLDAE 486

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRN 810
             + +   V     +   R  Q               V+          T      ++   
Sbjct: 487  EEETVMIVMTPEDLDISRQLQAGYQLPETTDDPNKRVKAPLNPTAHTWTHCEIHPSMILG 546

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +  + +P+  +N          M  + +   I +  F     +                 
Sbjct: 547  VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNFSERMDNAFN-------------- 590

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                         +             +       +   +  + AI      +  D+ + 
Sbjct: 591  -------------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 637

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
              S +   +    ++ R   D+ +R      EQ E   R    +      +       + 
Sbjct: 638  NQSSIDRGLF-RSLYYRTYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVA 696

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++      +   ++     L            
Sbjct: 697  PGVRISGEDIIIGKTEPIAPDSEELGQRTKLHVKRDKSTPLRTTENGL------------ 744

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                  ++K+          LR VKV     +  Q GDK A RHG KG +      EDMP
Sbjct: 745  ------VDKVML--STNAEGLRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMP 796

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 797  FTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSRLLR 856

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
              E    +                                                    
Sbjct: 857  --EHGYQSRGFEVM---------------------------------------------Y 869

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +G +    G         V +G  Y  +L H
Sbjct: 870  NGHT----GR---KLVAQVFLGPTYYQRLRH 893



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 66/533 (12%), Positives = 150/533 (28%), Gaps = 56/533 (10%)

Query: 212 VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG+   E+IL+        +Q  +     +  A ++   +V+   +     
Sbjct: 67  IPIVIVFRALGVVSDEDILNHICYDRKDTQMLEMLKPCIEEAFVIQDREVALDFIGKRGN 126

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
            Q I   K++       ++++ +  +                +     ++ +   D  D 
Sbjct: 127 SQGITRDKRIKYAR-DIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVTLGRRDPDDR 185

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
                      + + +           +     T  NK  KD    + + +       F+
Sbjct: 186 DH------FGKKRLDL-------AGPLMAGLFRTLFNKLTKDVYKYLQKCVESNR--EFN 230

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---- 446
           +   + +    +  +Y L   G      +         + + +    + +  L       
Sbjct: 231 LTLGVKSTTLTNGLRYSL-ATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPI 289

Query: 447 -RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            R+GK       +  +  +    E  + Q    +  +       + S     +      N
Sbjct: 290 GRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRN 349

Query: 506 AKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGV 556
            + +         +A   F     +    +  + +S +   RR   +  +  + R     
Sbjct: 350 MEILEEYEPLRSPNATKVFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDR 409

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--- 613
           E +    T  GR+C       ++    +  +          +E       D         
Sbjct: 410 EFK--IFTDAGRVCRPLFVIDNDAKSPNKGSLVLTKELVSRLEDDKDLPADMDPDEKAAK 467

Query: 614 ------------VVYLSAMEEENRYIAQANSSLDEDGS-------FTEELVFCRCAGEEI 654
                       V YL A EEE   I      LD                   +     +
Sbjct: 468 IMGWDGLIKRGVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYQLPETTDDPNKRVKAPL 527

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                     +  P  ++ + AS+IPF +++ S R      M +QA+ +    
Sbjct: 528 NPTAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTN 580


>gi|119644030|gb|ABL85602.1| RNA polymerase II second largest subunit [Flavopunctelia flaventior]
          Length = 708

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 120/828 (14%), Positives = 245/828 (29%), Gaps = 144/828 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++ N +R+   ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLMANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+    +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYITVGTPSEPIIDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              +      +       +  D +    ++        I      + D  D   K      
Sbjct: 177  QRSPNATKVFANGVWVGVHRDPAHLTSVMLKLRRTHAISHETSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVV-AKSSGAAIVAKRA 732
                P    D+  +      +   +Q +  L+ +     + +      + +         
Sbjct: 237  RVCRPLFVIDNDVKSERAGELVLTKQHIMKLEDDRDIKDSDLPQEEKDERTWGWKGLVEE 296

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            GIVE +DA       +    +       + R       + N   N+R    +        
Sbjct: 297  GIVEYLDAEEEETAMIVMTPEDLEISKQVRRGEVI--IDDNPDPNKRVKTPINPTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +  ++   E  +   
Sbjct: 355  HSEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMXXTLTNYEQRMDT- 406

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 407  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  +             
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLI------------ 642

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
                                                     + +L      +     +TP
Sbjct: 643  -----------------------------------------ECLLSKVSSLRGFEGDATP 661

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
             F     ++++ +LR       G  ++Y+G TG      V +G  Y  
Sbjct: 662  -FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQ 708


>gi|55583708|gb|AAV53373.1| RNA polymerase II second largest subunit [Hymenopellis radicata]
          Length = 669

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 120/808 (14%), Positives = 223/808 (27%), Gaps = 164/808 (20%)

Query: 476  RLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------ 521
            R+   ++ R +    +          P D +  + + + +     +              
Sbjct: 1    RMLFRKLTRDVYRYLQKCVETRKEFNPNDGVKRQTITNGLKYSLATGNWGDQKKSMSSKA 60

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 61   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 116

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++   +       + +  + +     +A           N         
Sbjct: 117  GLVKNLALMACISVGSYSAPVIEFLEEWGLESLEE--NAHSTTPFTKVFVNGVWMGVHRD 174

Query: 641  TEELVFCRCA-GEEILVPREKIDFIDASPKQ---VVSIAASLIPFLENDDSNRVLMGCNM 696
               LV        +  +  E     D   K+            P    +D    L   ++
Sbjct: 175  PANLVNTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEDQQLALQKKHV 234

Query: 697  Q-----RQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            +     +            + TG+ E + A+     +++         D     ++    
Sbjct: 235  KWILQGKDDEGGEYKWEQLIKTGIVELLDAEEEETVMISMTPE-----DLETSRLQQNGL 289

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
            D   +    D    +K                  G            PS  LG       
Sbjct: 290  DATANDGEFDPAARLK-----------------AGINAHTWTHCEIHPSMILG------- 325

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +  + +P+  +N                        ++       +G       I     
Sbjct: 326  ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM--- 364

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                      +  +             +       +   +  + AI      +  D+ + 
Sbjct: 365  --------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIM 416

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
              S +   +    I+ R  +D  ++S     E+ E  +R+          +       I 
Sbjct: 417  NQSSIDRGLF-RSIYYRSYMDVEKKSGVQALEEFEKPSRESTLRMKHGTYDKLEDDGLIA 475

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G   V       K+  +  D      R++          ++     +  Q         
Sbjct: 476  PGTGVVGEDIIIGKTAPIPPDSEELGQRTRMHTRRDVSTPLKSTESGIIDQVLI------ 529

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                 + VKV V   R  Q+GDK A RHG KG +      EDMP
Sbjct: 530  --------------TTNADGQKFVKVRVRATRIPQTGDKFASRHGQKGTIGITYRQEDMP 575

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   DI++NP  +PSRM +G + E  L      +G +                   
Sbjct: 576  FTCEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGHEGD----------------- 618

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     E++++ LR      
Sbjct: 619  ------------------------------------ATP-FTDLTVESVSTFLRQKGYQS 641

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
             G  ++Y G TG      V +G  Y  +
Sbjct: 642  RGLEVMYHGHTGRKLQAQVYLGPTYYQR 669



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 87/602 (14%), Positives = 161/602 (26%), Gaps = 99/602 (16%)

Query: 376 DIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           D+YR + +  +                 +        G      +         + + + 
Sbjct: 10  DVYRYLQKCVETRKEFNPNDGVKRQTITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRY 69

Query: 435 DIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
              + +  L        R GK       +  +  +    E  + Q    +  +       
Sbjct: 70  TYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS 129

Query: 490 ISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
           + S     +             NA         F     +    +  N ++ I   RR  
Sbjct: 130 VGSYSAPVIEFLEEWGLESLEENAHSTTPFTKVFVNGVWMGVHRDPANLVNTIKKLRRKD 189

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +            +   ++        P    E   + L      +         E   
Sbjct: 190 DISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEDQQLALQKKHVKWIL--QGKDDEGGE 247

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL------- 655
            K      T  V  L A EEE   I+     L+        L      GE          
Sbjct: 248 YKWEQLIKTGIVELLDAEEEETVMISMTPEDLETSRLQQNGLDATANDGEFDPAARLKAG 307

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +        +  P  ++ I AS+IPF +++ S R      M +QA+ +            
Sbjct: 308 INAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI----- 362

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                                  + + +  Y       +     
Sbjct: 363 ------------------------------------RMDTMANILYYPQKPLATTRSMEY 386

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +  R                        +L  G+N +VA + + GYN EDS+++++  + 
Sbjct: 387 LKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 422

Query: 836 EDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNP 890
             +F SI+   +  + + +     EE  +        +       +++ G+I  G  V  
Sbjct: 423 RGLFRSIYYRSYMDVEKKSGVQALEEFEKPSRESTLRMKHGTYDKLEDDGLIAPGTGVVG 482

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P    P   EE   R          RD S  + S  SG +  V I      
Sbjct: 483 EDIIIGKTAPI---PPDSEELGQRTRM----HTRRDVSTPLKSTESGIIDQVLITTNADG 535

Query: 951 DK 952
            K
Sbjct: 536 QK 537


>gi|153958313|gb|ABS53445.1| RpoB [Bacteriovorax sp. MANZ5]
          Length = 348

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 166/351 (47%), Positives = 235/351 (66%), Gaps = 10/351 (2%)

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
             RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V +  +IADGP T
Sbjct: 1    NRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDVVSKGMVIADGPGT 58

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +EV ARDTKLG EE
Sbjct: 59   HLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESYEVEARDTKLGKEE 118

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
            ITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++PEEKLL+AIFG+K
Sbjct: 119  ITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLSPEEKLLKAIFGDK 178

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
            A DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+ RD+  E   +  
Sbjct: 179  AGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLIRRDERIEIKAIQT 238

Query: 981  NIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
            +   ++ ++L G              +   K   L+S++++  P        ++   ++ 
Sbjct: 239  SSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFELIGYLPLE-PALEE 297

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
             +           + +  +  ++I K   GD++PPGV++ V ++VA+KR +
Sbjct: 298  RLSEYFADVRNRINRVRQKANDEIAKHHRGDELPPGVIKKVTIYVAIKRKL 348


>gi|86559351|gb|ABD04083.1| RNA polymerase II second largest subunit [Botryobasidium
            subcoronatum]
          Length = 677

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 121/805 (15%), Positives = 228/805 (28%), Gaps = 146/805 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              +    + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFRKLTKDVYRYLQKCVETHREFNLNVAVKHNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  A ++  G +  P  +         +   +A  + N  
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMACIS-VGSLSAPVIEFLQEWGLEGLE-ENATHQGNAT 175

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                N            LV                   D SP+  V             D
Sbjct: 176  KVFVNGVWMGIHRDAPNLVKTLRRLRRKD---------DISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG-IVEQVDAIRIVI 745
            + RV     +       LK +   V   M+                  +VE +DA     
Sbjct: 227  AGRVCRPLFIVENHELSLKKKH--VKWIMDRQDENGQPYGWSNLVTSGVVELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-D 804
              +             Y         +            G  V+   ++     T     
Sbjct: 285  VMICMSSQDLDDSRQQYMSGYVPGPREVEHHA-----SGGARVKA--VLNSHTWTHCEIH 337

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
             ++   +  + +P+  +N          M  + +   I++  ++V               
Sbjct: 338  PSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYLTNYQVRM------------- 382

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                            +  +             +       +   +  + AI      + 
Sbjct: 383  --------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 428

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    ++ R  +D  ++   +  E+ E    D          +   
Sbjct: 429  EDSVIMNQSSIDRGLF-RSMYYRSHMDSEKKVGVLPVEEFEKPTPDTTLRMKRGTYDKLD 487

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  L  D                 E++ +     +    T
Sbjct: 488  DDGLIPPGTGVNGEDVIIGKTAPLPPD----------------SEELGQRKSHTRRDAST 531

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            +    E+   +++      D +     + VK+ V   R  Q GDK A RHG KG +    
Sbjct: 532  ALKSTENGIIDQVLVTTNADGL-----KFVKIRVRSTRIPQVGDKFASRHGQKGTIGITY 586

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +             
Sbjct: 587  RQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNEGD----------- 635

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     E+++ +LR
Sbjct: 636  ------------------------------------------ATP-FTELTVESVSKLLR 652

Query: 1225 MADLDESGQSILYDGLTGEPFDRPV 1249
                   G  ++Y G TG      V
Sbjct: 653  ERGYQSRGLEVMYHGHTGRKLQAQV 677


>gi|294471028|gb|ADE80775.1| RNA polymerase beta subunit [Lactococcus lactis subsp. hordniae]
          Length = 163

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 70/185 (37%), Positives = 102/185 (55%), Gaps = 22/185 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK +FPI  
Sbjct: 1   YGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K   ++K 
Sbjct: 51  FAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NKETGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +A  +G   +    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKADKNGLESFGHTTIPN 158

Query: 188 QGLWM 192
           +G W+
Sbjct: 159 RGAWL 163


>gi|103001406|gb|ABF71506.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 707

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 120/829 (14%), Positives = 233/829 (28%), Gaps = 147/829 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +              + +  + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     +      E    +    + +V  +     +   
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP- 680
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 177  TKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPL 236

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            F+ ++D      G  +  +       +   +   M+    +       AK  G    V  
Sbjct: 237  FVIDNDPKSTNCGNLVLTKEHISKLEDDRDLPAIMDPEEKE-------AKFFGWDGLV-- 287

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               V+  V+ + + +   V     ++  R  Q           +   V+          T
Sbjct: 288  NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWT 347

Query: 801  DLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                  ++   +  + +P+  +N          M                          
Sbjct: 348  HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGK------------------------ 383

Query: 860  EITRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                         L N D+    +  +             +       +   +  + AI 
Sbjct: 384  -------XXXXXXLTNYDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 436

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 437  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLK 492

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   +  G           K+  +S D      R++          ++  
Sbjct: 493  LKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRST 552

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             L+ VKV +   +  Q GDK A RH
Sbjct: 553  ENGIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRH 592

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 593  GQKGTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 652

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 653  TPFTEVTVDSVSKLLR--EHGYQSRGFEVM------------------------------ 680

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                            +G +    G         V +G  Y  +L HMV
Sbjct: 681  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 707


>gi|45686052|ref|YP_003815.1| DNA dependent RNA polymerase II [Ambystoma tigrinum virus]
 gi|37722476|gb|AAP33221.1| DNA dependent RNA polymerase II [Ambystoma tigrinum stebbensi virus]
          Length = 1221

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 77/305 (25%), Positives = 122/305 (40%), Gaps = 64/305 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF K+G   D+++NP  
Sbjct: 968  DSDGKKLVKVRLRTPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKNGVVPDLIINPHA 1027

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 1028 FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 1063

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                            I    + A +D    S+LY G TG    
Sbjct: 1064 -----------------------------VRDIAEAAKEAGIDCW-DSVLYSGSTGRRLP 1093

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 1094 TKIFMAPCPYQRLRHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 1153

Query: 1307 AAYVLQEMLTIKSD--DV-----VGRTR---VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
             +  L+E +   SD  +V      GR      Y  +    D      P +  +L +E+++
Sbjct: 1154 VSESLKESVYDTSDKYEVPVCKECGRISDHFEYCRMCDATDVSLVKLPYTTKILFQELRS 1213

Query: 1357 LGLSI 1361
            +G+SI
Sbjct: 1214 IGISI 1218



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 83/488 (17%), Positives = 162/488 (33%), Gaps = 43/488 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 405 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYVK-LFVKSAG 463

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 464 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 523

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++      +    
Sbjct: 524 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGVGFSLETP 579

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEI 654
            E     V  GK      +  A        A  ++S+D DG     T + V         
Sbjct: 580 REAVLATVRLGKGLPGF-FEGAPARLAWSGAAGSASVDVDGVLCGVTGDPVGFVREARLC 638

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    + +     +  +            D         +             P   + 
Sbjct: 639 LLGVSVV-WKKVEREIHLLGCQGRFVRRVLDPEGIRGSRYDNPPPPEERDIEMDPAPSSS 697

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQN 773
               + +  G  + A+   +    D       + E   D  +S +  Y      + + Q+
Sbjct: 698 PSDFLPRPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQS 757

Query: 774 TCVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWH 819
               Q    P V   D         D P                ++A G   +VA M   
Sbjct: 758 NMGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAG 817

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNI 876
           G+N EDS++++   +   +F+ +         +       E+           E     +
Sbjct: 818 GFNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNREWDYDLL 877

Query: 877 DECGIICV 884
            + G+I  
Sbjct: 878 GDDGVIDP 885



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 65/241 (26%), Gaps = 85/241 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--- 84
           + +     S+D  L           +          P+        ++F +  ++PP   
Sbjct: 96  NFVRHHIESFDDMLWNEFPAMVAREK----------PV--SVKGYRVKFGTVRYEPPCPD 143

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K         D TY       L +               +I    + +  +P+M 
Sbjct: 144 GKPWEKLTPAMARRTDATYHSAAVCDLTVT---------DPKGLEIVYPRLELCKIPVMV 194

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G F+IKG +R+VV   H  P   +D      +  G  
Sbjct: 195 GSAVCWTRTEGSPLPGECPSDPGGYFIIKGKERVVVP--HIRPA--YDQPCVYKNCDG-- 248

Query: 179 LYACRIIPDQGLWM-DI-----EFDSKDIIHVRIDRRRKV-----------PVTSFLMAL 221
                       W+ +      E     ++  + D RRK+           PV     AL
Sbjct: 249 ------------WLCEFRSVNRETRQTVLVQAKTDCRRKLEFSLPYIKQYVPVGLVFKAL 296

Query: 222 G 222
           G
Sbjct: 297 G 297


>gi|15128155|gb|AAK84400.1|AF397202_1 LCDV orf3-like protein [Regina ranavirus]
          Length = 950

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/312 (24%), Positives = 119/312 (38%), Gaps = 78/312 (25%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF K+G   D+++NP  
Sbjct: 697  DSDGKKLVKVRLRTPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKNGVVPDLIINPHA 756

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 757  FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 792

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                            I    + A +D    S+LY G TG    
Sbjct: 793  -----------------------------VRDIAEAAKEAGIDCW-DSVLYSGSTGRRLP 822

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 823  TKIFMAPCPYQRLRHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 882

Query: 1307 AAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPESFNV 1349
             +  L+E +   SD        YE  V                    D      P +  +
Sbjct: 883  VSESLKESVYDTSD-------KYEVPVCKECGRISDHFEYCRMCDRTDVSLVKLPYTTKI 935

Query: 1350 LVKEMQALGLSI 1361
            L +E++++G+SI
Sbjct: 936  LFQELRSIGISI 947



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 84/488 (17%), Positives = 164/488 (33%), Gaps = 43/488 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 134 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYVK-LFVKSAG 192

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 193 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 252

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++      +    
Sbjct: 253 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGVGFSLETP 308

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---SFTEELVFCRCAGEEI 654
            E     V  GK      +  A        A  ++S+D DG     T + V         
Sbjct: 309 REAVLATVRLGKGLPGF-FEGAPARLAWSGAAGSASVDVDGVLCGVTGDPVGFVREARLC 367

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    + +     +  +            D       G +             P   + 
Sbjct: 368 LLGVSVV-WKKVEREIHLLGCQGRFVRRVLDPEGIRGSGYDSPPPPEERDIEMDPAPSSS 426

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQN 773
               +++  G  + A+   +    D       + E   D  +S +  Y      + + Q+
Sbjct: 427 PSDFLSRPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQS 486

Query: 774 TCVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWH 819
               Q    P V   D         D P                ++A G   +VA M   
Sbjct: 487 NMGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAG 546

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNI 876
           G+N EDS++++   +   +F+ +         +       E+           E     +
Sbjct: 547 GFNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNREWDYDLL 606

Query: 877 DECGIICV 884
            + G+I  
Sbjct: 607 GDDGVIDP 614


>gi|153958259|gb|ABS53419.1| RpoB [Bacteriovorax sp. T10]
          Length = 357

 Score =  249 bits (635), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 170/360 (47%), Positives = 242/360 (67%), Gaps = 10/360 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                 ++   ++  +           S +  +  ++I K+  GD++PPGV++ V V+VA+
Sbjct: 299  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRGDELPPGVIKKVIVYVAI 357


>gi|294471022|gb|ADE80772.1| RNA polymerase beta subunit [Lactococcus chungangensis]
 gi|294471036|gb|ADE80779.1| RNA polymerase beta subunit [Lactococcus raffinolactis]
          Length = 163

 Score =  249 bits (635), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 68/185 (36%), Positives = 100/185 (54%), Gaps = 22/185 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E++D+P+LIE+Q  SY  FL          ++ L   FK + PI  
Sbjct: 1   YGKHRTRRSFSRIKEVLDLPNLIEIQTDSYQRFL----------DQSLADVFKEMLPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ +++    D  Y+ PL +T RL+          K   ++K 
Sbjct: 51  FAGTKDLEFVGYEMKEPKYTIEEARAHDANYSAPLFVTFRLV---------DKESGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+I G +RI+VSQL RSPG +F     +   +G   Y    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFIINGAERIIVSQLVRSPGTYFHPKVDK---NGLESYGHTTIPN 158

Query: 188 QGLWM 192
           +G W+
Sbjct: 159 RGAWL 163


>gi|113957206|gb|ABI49109.1| RNA polymerase II second largest subunit [Pyxine subcinerea]
          Length = 709

 Score =  249 bits (635), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 125/828 (15%), Positives = 234/828 (28%), Gaps = 142/828 (17%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R    ++ + +    +    +         + +  + + +     + 
Sbjct: 1    RLDLAGPLLAGLFRTLFNKLNKDVEKYLKNCIENNREFNLTLGVKSTTITNGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGEQKKASSSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     V+     E    +      +   +   L++      
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYVSVGTPSEGIVEFLLSRQMEPLEEYDPLASPHATKI 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLE 683
            ++      +  + +     V        I      I D  D   K +      L P F+ 
Sbjct: 177  FVNGVWVGIHRNPAHLVLAVQSLRRRHVIEHEVSLIRDIRDREFKILTDQGRVLRPLFVV 236

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIR 742
             +D+     G  +  +           V   M+    +           AG+VE VDA  
Sbjct: 237  ENDAKEQNYGNLVLTKEHVEKLEADRDVPLDMDKEEREQLTFGWHGLINAGVVEYVDAEE 296

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +            I         N     N+R    +             PS  L
Sbjct: 297  EETIMIVMTPYDLNVSRQIQAGYVLPEEND-ENPNRRVKAPINPTAHTWTHCEIHPSMIL 355

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 356  G-------LCASIIPFPDHNQSPRN------------------TYQSXMGKQAMGVFLTN 390

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             D    +           +  +             +       +   +  + AI      
Sbjct: 391  FDQRMET-----------MSHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGY 439

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+ ++   +    +E   +    + + L    
Sbjct: 440  NQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKK---IGMYTMEQFEKPLRSDTLKLKHGT 495

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L +   I+ G           K+  ++ D      R++          ++     L 
Sbjct: 496  YEKLDDDGIIIPGARVSGEDIIIGKTAPIAPDAEELGQRTKLHNKRDASTPLRSTESGLV 555

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q   + +                       LR VKV +   +  Q GDK A RHG KG 
Sbjct: 556  DQVLLTVN--------------------SEGLRFVKVRMRTTKVPQIGDKFASRHGQKGT 595

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +     
Sbjct: 596  IGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTD 655

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 +S L    E    +                                         
Sbjct: 656  VTVDSVSRLLR--EHGYQSRGFEVM----------------------------------- 678

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                       +G +    G         V +G  Y  +L HMV DK+
Sbjct: 679  ----------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 709



 Score =  114 bits (286), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 83/561 (14%), Positives = 172/561 (30%), Gaps = 62/561 (11%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + +  K   S  G  ++  R    +      R          I    
Sbjct: 49  ITNGLKYSLATGNWGEQKKASSSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPR 108

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +      ++KN   +  + +    +  +  +    + P +  
Sbjct: 109 QLHNTHWGLVCPAETPEGQACG---LVKNLALMCYVSVGTPSEGIVEFLLSRQMEPLEEY 165

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +      A   F     +       + +  +   RR   +             +RD+   
Sbjct: 166 DPLASPHATKIFVNGVWVGIHRNPAHLVLAVQSLRRRHVI-------EHEVSLIRDIRDR 218

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +  +    T +G  +  +  + + A+   YG +      V   +   DV  L   +EE 
Sbjct: 219 EFKIL----TDQGRVLRPLFVVENDAKEQNYGNLVLTKEHVEKLEADRDV-PLDMDKEER 273

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +      L   G                      ++++DA  ++ + I  +      +
Sbjct: 274 EQLTFGWHGLINAG---------------------VVEYVDAEEEETIMIVMTPYDLNVS 312

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                       +    P  + +AP   T       +   + I+   A I+   D  +  
Sbjct: 313 RQIQ-AGYVLPEENDENPNRRVKAPINPTAHTWTHCEIHPSMILGLCASIIPFPDHNQSP 371

Query: 745 IRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             + +  +     GV       + +  +      Q+PL                      
Sbjct: 372 RNTYQSXMGKQAMGVFLTNFDQRMETMSHILYYPQKPL----------ATTRSMEFLKFR 421

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT- 862
           +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E   
Sbjct: 422 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKKIGMYTMEQFE 481

Query: 863 ----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                D   +     + +D+ GII  GA V+  DI++GK  P         ++       
Sbjct: 482 KPLRSDTLKLKHGTYEKLDDDGIIIPGARVSGEDIIIGKTAPIAPDAEELGQRT------ 535

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K  + RD S  + S  SG V
Sbjct: 536 -KLHNKRDASTPLRSTESGLV 555


>gi|133420|sp|P08036|RPOB_SAPOF RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|929885|emb|CAA30075.1| RNA polymerase [Saponaria officinalis]
          Length = 417

 Score =  249 bits (635), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 121/467 (25%), Positives = 190/467 (40%), Gaps = 53/467 (11%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
               G   E    +   +++        I         +  G       +          +
Sbjct: 3    CIVGTGLERQAALDSGVLAIVEHEGKIIYTDTDKIILSGNGDTHSIPLVLYQRFNKNTCM 62

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             +   I  G  +  G IL       G   +   + +L A    +  +  D  L     +S
Sbjct: 63   HQNPRIPGGKCIKKGQILADGAATVG-GELGLGKNVLVAYMPWEGYNFEDAVL-----IS 116

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +V   I+    I K E    V  +  E +  +    +  L RN+  +   +  G    
Sbjct: 117  ERLVYEDIYTSFHIRKYEIQTYVTSQGPERVTSEIPHLEAHLLRNL-DKNGIVGLGSWVE 175

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G     K T   +   S  P  +  +  +  +        LK+       +++ R+  K
Sbjct: 176  TGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 235

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                  G +  P     + +++  KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DG 
Sbjct: 236  K----GGSNYNP---ETIHIYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGR 288

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D +   + S    F  ++ 
Sbjct: 289  PVDMVFNPLGVPSRMNVGQIFECSLGLAGGLLDRHYRITPFDERYEHEASRKLVF-SELY 347

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                 T K   ++ +                                        G+S +
Sbjct: 348  QASKQTAKPWIFEPE--------------------------------------YPGKSRI 369

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPL 1283
            +DG TG+PF++PV +G  Y+LKL H V DK++ RS+G Y+LVTQQPL
Sbjct: 370  FDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGHYALVTQQPL 416



 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 97/245 (39%), Positives = 148/245 (60%), Gaps = 10/245 (4%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E   VGTG+E   A  SG   + +  G +   D         +  +           L+ 
Sbjct: 1   EKCIVGTGLERQAALDSGVLAIVEHEGKIIYTD--------TDKIILSGNGDTHSIPLVL 52

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QR N+NTC++Q P +  G  +++  I+ADG +T  G+L LG+N+LVA+MPW GYNFED+
Sbjct: 53  YQRFNKNTCMHQNPRIPGGKCIKKGQILADGAATVGGELGLGKNVLVAYMPWEGYNFEDA 112

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V ED++TS HI ++E+    T  GPE +T +IP++    L+N+D+ GI+ +G+
Sbjct: 113 VLISERLVYEDIYTSFHIRKYEIQTYVTSQGPERVTSEIPHLEAHLLRNLDKNGIVGLGS 172

Query: 887 EVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            V  GDILVGK+TP+     +  PE++LLRAI G +    ++T L++P G  G V+DVR 
Sbjct: 173 WVETGDILVGKLTPQMAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRW 232

Query: 945 FNRHG 949
             + G
Sbjct: 233 IQKKG 237


>gi|294471024|gb|ADE80773.1| RNA polymerase beta subunit [Lactococcus garvieae]
          Length = 163

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 72/185 (38%), Positives = 102/185 (55%), Gaps = 22/185 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E+I +P+LIEVQ ASY +FL          +EGL   FK +FPI  
Sbjct: 1   YGNHRTRRSFSRIKEVIGLPNLIEVQTASYQNFL----------DEGLANVFKEMFPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ VD+    D  Y+ P+ +T RL+          K   ++K 
Sbjct: 51  FAGTMELEFVGYEMKAPKYTVDEARAHDANYSAPIHVTFRLV---------NKETGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +   +G   Y    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESYGHTTIPN 158

Query: 188 QGLWM 192
           +G W+
Sbjct: 159 RGAWL 163


>gi|300394702|gb|ADK11889.1| DNA-directed RNA polymerase II subunit two [Coniophora sp. Braz-6]
          Length = 693

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 122/821 (14%), Positives = 235/821 (28%), Gaps = 144/821 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNISLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   F       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTVCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +      LL+ +   ++  G                + G++E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLLLQKKHIKWLNQGYRDDEPAEEFKWDQLVKGGVIELLDA 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +     +         +   +    +K G            PS 
Sbjct: 286  EEEETVMIAMTPEDLENSRL--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSM 343

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 344  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 378

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 379  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRGLPAGQNAIVAILCYS 427

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 428  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTY 486

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 487  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 546

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 547  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 586

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +      
Sbjct: 587  GITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 644

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 645  -----------------------DLTVESVSTFLRQKGYQSRGLEVM------------- 668

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                       G +       G      V +G  Y  +L H
Sbjct: 669  ---------YHGHT-------GRKLRAQVYLGPTYYQRLKH 693



 Score =  118 bits (296), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 79/610 (12%), Positives = 164/610 (26%), Gaps = 96/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNISLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESLEENAHSSTVCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLLL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +              K         +  L A EEE   IA     L+     + 
Sbjct: 249 QKKHIKWLNQGYRDDEPAEEFKWDQLVKGGVIELLDAEEEETVMIAMTPEDLENSRLQSA 308

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +   +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 309 GIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLV-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R L                          G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLKFRGL------------------------PAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 484 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 539

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 540 TENGIVDQVL 549


>gi|190148964|gb|ACE63457.1| RNA polymerase subunit B [Pseudonocardia oroxyli]
          Length = 263

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 147/270 (54%), Positives = 197/270 (72%), Gaps = 8/270 (2%)

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL++FA+VN +
Sbjct: 1   THKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSTFAQVNPF 60

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEI 654
           GFI+TPYR+V +GKVT+ + YL+A EE+   +AQAN+ L+ DGSFTE+ V  R   GE  
Sbjct: 61  GFIQTPYRRVVEGKVTDQIDYLTADEEDRFVVAQANAPLNADGSFTEDRVLVRMKGGEVD 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           L+    +D+ID SP+Q+VS+A +LIPFLE+DD+NR LMG NMQRQ+VPLL++E+P VGTG
Sbjct: 121 LISPTGVDYIDVSPRQMVSVATALIPFLEHDDANRALMGANMQRQSVPLLRSESPLVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME   A  +G  +V ++AG+VE++ A  I + + EG           YRL KF+RSNQ T
Sbjct: 181 MELRAAVDAGDVVVTEKAGVVEELCADYITVMADEGTRQ-------TYRLNKFRRSNQGT 233

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           C NQ+P+V  G  V    ++ADGP T+ G+
Sbjct: 234 CNNQKPIVDEGQRVEVGQVLADGPCTENGE 263


>gi|103001731|gb|ABF71519.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 700

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 116/819 (14%), Positives = 232/819 (28%), Gaps = 143/819 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 2    GPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSN 688
               +  D +     V        I      + D  D   K          P F+ ++D  
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G  +  +       +   +   M+S   +       AK  G    V     V+  V
Sbjct: 238  STNCGNLVLTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVEYV 288

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 289  DAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSM 348

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 349  ILGICASIIPFPDHNQSPRNTYQSAMGKQSMG--VFLTNYDQRM---------------- 390

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 391  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 439

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 440  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 495

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +S D      R++          ++     +  Q   
Sbjct: 496  DDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 555

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      L+ VKV +   +  Q GDK A RHG KG +    
Sbjct: 556  --------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 595

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 596  RQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDS 655

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 656  VSKLLR--EHGYQSRGFEVM---------------------------------------- 673

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                  +G +    G         V +G  Y  +L HMV
Sbjct: 674  -----YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 700


>gi|153958202|gb|ABS53391.1| RpoB [Bacteriovorax sp. MANZ3]
          Length = 356

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 169/358 (47%), Positives = 238/358 (66%), Gaps = 10/358 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 2    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 59

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 60   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 119

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 120  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 179

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 180  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 239

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 240  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 299

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                 ++   ++  +           + +  +  ++I K   GD++PPGV++ V ++V
Sbjct: 300  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDELPPGVIKKVTIYV 356


>gi|307343564|emb|CBJ18699.1| RNA polymerase B subunit [Micromonospora endolithica]
          Length = 207

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 120/211 (56%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     D+K           +     
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDADWKKALRSIDAHESVGD--- 142

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                                        V+TPVFDGA EE I+ +L     +        
Sbjct: 143  --------------------------TNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  ATGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|225734465|gb|ACO25233.1| DNA dependent RNA polymerase b subunit [Epizootic haematopoietic
            necrosis virus]
          Length = 1227

 Score =  248 bits (634), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 78/305 (25%), Positives = 123/305 (40%), Gaps = 64/305 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++VKV +   R  + GDK A     KG    +L  EDMPF KDG   D+++NP  
Sbjct: 974  DSDGKKLVKVRLRAPRHPEMGDKFASFTAQKGTCGAVLTQEDMPFDKDGVVPDLIINPHA 1033

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             PSRM V  + +   G A   LGK   +   + +                          
Sbjct: 1034 FPSRMTVNYLLQMCFGTAACKLGKTYDATAFEREDV------------------------ 1069

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                            I    + A +D    S+L+ G TG    
Sbjct: 1070 -----------------------------VRDIAEAAKEAGIDCW-DSVLHSGSTGRRLP 1099

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +      +L HMVS K+++R+ G    +T+QP+ G+S  GG ++GEME WC  ++G
Sbjct: 1100 TKIFMAPCLYQRLRHMVSGKMHSRTHGPTDALTRQPVAGRSREGGIKIGEMEQWCKISHG 1159

Query: 1307 AAYVLQEMLTIKSD--DV-----VGRTR---VYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+  L+E +   SD  +V      GR      Y  +    D      P +  +L +E+++
Sbjct: 1160 ASESLKESVYDTSDKYEVPVCKECGRISDHFEYCRMCDATDVSLVKLPYTTKILFQELRS 1219

Query: 1357 LGLSI 1361
            +G+SI
Sbjct: 1220 IGISI 1224



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 83/487 (17%), Positives = 162/487 (33%), Gaps = 41/487 (8%)

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
            E +  ++K + D  +G GT  D D+L N+RV + G ++       L +  + +  + + 
Sbjct: 411 AEHLGWMVKRMADAASGIGTCTDRDDLANKRVDATGPLIAFLLDGLLKQYVK-LFVKSAG 469

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------LSQLEEHVNSLSRITH 537
              +      L N+  + +++   F +                 +SQ+  + N  +R++H
Sbjct: 470 CQKNLCPYTVLQNSMVMTNSLHMCFATGNWTVKRLGPPSYVRVGVSQVLSNNNYGARVSH 529

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR+       V+     + MR +H +HYG +CP ET EG  +G+V ++   A  +    
Sbjct: 530 LRRI----MHAVSFRGKNIRMRQLHSSHYGFLCPYETPEGEKVGIVLNMAEGAGFSLETP 585

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF--CRCAGEEIL 655
            E     V  GK      +  A        A  ++S+D DG                 + 
Sbjct: 586 REAVLATVRLGKGLPGF-FEGAPARLAWSGAVGSASVDVDGVLCGVTGDPAGFVREARLC 644

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +P   + +     +  +            D       G +             P   +  
Sbjct: 645 LPGVSVVWKKVEREIHLLGCQGRFVRRVLDPEGIRGPGYDSPPAPEERDIEMDPAPSSSP 704

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY-RLMKFQRSNQNT 774
              + +  G  + A+   +    D       + E   D  +S +  Y      + + Q+ 
Sbjct: 705 SDSLPRPPGVYVCAQELSVCSLGDGEYADPPASEILTDAMSSVIPFYDHTQSPRNAYQSN 764

Query: 775 CVNQR---PLVKVGDEVRRNDIIADGPS-----------TDLGDLALGRNMLVAFMPWHG 820
              Q    P V   D         D P                ++A G   +VA M   G
Sbjct: 765 MGKQAIGFPAVNCSDRYDATLHRLDYPQKSLVDSRSVKRLGFDEMAHGALPVVAIMTAGG 824

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN---VSEEGLKNID 877
           +N EDS++++   +   +F+ +         +       E+           E     + 
Sbjct: 825 FNQEDSVVLNASSLDRGLFSCVTYRTVSCADKRRTKYDSEVVCLPDWGLRNREWDYDLLG 884

Query: 878 ECGIICV 884
           + G+I  
Sbjct: 885 DDGVINP 891



 Score = 62.0 bits (149), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 64/241 (26%), Gaps = 85/241 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--- 84
           + +     S+D  L           +          PI        ++F +  ++PP   
Sbjct: 96  NFVRHHIESFDDMLWNEFPAMVAREK----------PI--SVKGYRVKFGTVRYEPPCPD 143

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                K         D TY       L +      E    +           +  +P+M 
Sbjct: 144 GKPWEKLTPAMARRTDATYHSAAVCDLTVTDPKGLETVYPRLE---------LCKIPVMV 194

Query: 140 ---------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKL 178
                                  G F+IKG +R+VV      P I   +D+     +   
Sbjct: 195 GSAVCWTRTEGSPLPGECPSDPGGYFIIKGKERVVV------PHIRPAYDQPCVYKNDD- 247

Query: 179 LYACRIIPDQGLWM-DI-----EFDSKDIIHVRIDRRRKV-----------PVTSFLMAL 221
                       W+ +      E     ++  + D RRK+           PV     AL
Sbjct: 248 -----------GWLCEFRSVNRETRQTVLVQAKTDCRRKLEFSLPYIKQYVPVGLVFKAL 296

Query: 222 G 222
           G
Sbjct: 297 G 297


>gi|6606097|gb|AAF19061.1|AF107789_1 DNA-dependent RNA polymerase II RPB140 [Neurospora crassa]
          Length = 903

 Score =  248 bits (634), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 124/771 (16%), Positives = 231/771 (29%), Gaps = 86/771 (11%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  L+    G+   DD D+ G +R+   G +L   +R  + 
Sbjct: 161  HISQAEGCETRKAFFLGYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVR 220

Query: 481  RMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            R+ + +    +              I A  + + +     +               +SQ+
Sbjct: 221  RLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNGLKYSLATGNWGDQKKAMSSTAGVSQV 280

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 281  LNRYTFSSTLSHLRRTNT----PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKN 336

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L+    V+     +    +    + +V  +   L        ++      + +D      
Sbjct: 337  LSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLRYPNATKVFVNGTWVGVHQDPKHLVT 396

Query: 644  LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            LV        I      +  I     ++ S A  ++  L   +          + Q +  
Sbjct: 397  LVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVMRPLFVVEQEDNSESGVEKGQLILT 456

Query: 704  LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
             +           +   +          +G +E +DA       +    +     +D YR
Sbjct: 457  KEHIRRLEQDKELAKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTPED----LDTYR 512

Query: 764  LMKFQ----RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              KF+      +     N R   K              PS  LG       +  + +P+ 
Sbjct: 513  QHKFKGREFEDDAANRGNSRIKTKFNPTTHMYTHCEIHPSMLLG-------ICASIIPFP 565

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     +  +                                
Sbjct: 566  DHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM---------------------------D 596

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 597  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGI 656

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D  +R      EQ E   R           +       I  G       
Sbjct: 657  F-RSLFFRSYTDCEKRVGINIVEQFEKPDRSNTLRPKHGTYDKLENDGIIAPGIRVTGDD 715

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K++ ++ D                 E  QR  + +K    T     E    + +  
Sbjct: 716  IIIGKTSPINPD---------------NQELGQRTAQHVKRDASTPLRSTESGIVDSVAF 760

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV V   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 761  TTNQDGL-----RYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTAEGITPD 815

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            I++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 816  IIINPHAIPSRMTIAHLIECLLSKVGALKGMEGDATPFTDVTVDSVSNLLR 866



 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 113/851 (13%), Positives = 240/851 (28%), Gaps = 136/851 (15%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS          +    G + Y   I    ++G  +         +H + 
Sbjct: 1   SEKVLIAQE-RSAANI--VQVFKKPPGGSVSYQAEIRSALEKGSRLISSLQM--RLHTKA 55

Query: 207 DRRR-----KVPVT-----------SFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPL 249
           D+ +      V VT               ALG+   E+IL+        SQ  +     +
Sbjct: 56  DQNKGRLANTVSVTLPYVKEEVSLAIVFRALGVVSDEDILNHICYDRRDSQMLEALRPCI 115

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA 309
             A  +   +V+   +          +         + L+++ +  +     C       
Sbjct: 116 EEAFCIQDREVALDYIGKRGNGSTGINRNGRIKAAKEMLQKELLPHISQAEGCETRKAFF 175

Query: 310 EDIVNGETGEIYIEAGDVIDEKSL--EEIFHSEIRDIPIL--YVDSVNNNAYIRNTLVTD 365
              +  +  +  +   D  D      + +  +      +    V  +  +         D
Sbjct: 176 LGYMVHKLLQCVLGRRDTDDRDHFGKKRLDLAGPLLAKLFRGIVRRLTQDLMGYMKRCVD 235

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            NK    AL      +  G      +  S+    + D  K   ST G  ++  R    + 
Sbjct: 236 TNKHFSLALGIKASTLTNG------LKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFSST 289

Query: 426 DDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
                R          +     L N    +         +   + + L     + +  + 
Sbjct: 290 LSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTLA 349

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
             I E + + +++ +   + +               + +   ++  + ++ + + RR + 
Sbjct: 350 DPIIEFMIARNMEVLEEYEPLRYPNATKVF---VNGTWVGVHQDPKHLVTLVQNLRRKNI 406

Query: 544 LG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           +  +  + R     E        R + P           S      L+ +     R+   
Sbjct: 407 ISFEVSLVRDIRDREFKIFSDAGRVMRPLFVVEQEDNSESGVEKGQLILTKEHIRRLEQD 466

Query: 596 GFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSSLDE------DGSFTEELVF 646
             +   +      +   +   + YL A EEE   I      LD        G   E+   
Sbjct: 467 KELAKYHEDYFGWQGLLESGAIEYLDAEEEETAMICMTPEDLDTYRQHKFKGREFEDDAA 526

Query: 647 CRCAGEEILVPR---EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            R                   +  P  ++ I AS+IPF +++ S R      M +QA+  
Sbjct: 527 NRGNSRIKTKFNPTTHMYTHCEIHPSMLLGICASIIPFPDHNQSPRNTYQSAMGKQAMGF 586

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                              + + +  Y 
Sbjct: 587 FLTNYS-----------------------------------------RRMDTMANILYYP 605

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                 +     +  R                        +L  G+N +VA   + GYN 
Sbjct: 606 QKPLATTRSMEYLKFR------------------------ELPAGQNAIVAIACYSGYNQ 641

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDE 878
           EDS+++++  +   +F S+    +    +   +   E        +           ++ 
Sbjct: 642 EDSVIMNQSSIDRGIFRSLFFRSYTDCEKRVGINIVEQFEKPDRSNTLRPKHGTYDKLEN 701

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII  G  V   DI++GK +P         ++  + +        RD S  + S  SG 
Sbjct: 702 DGIIAPGIRVTGDDIIIGKTSPINPDNQELGQRTAQHVK-------RDASTPLRSTESGI 754

Query: 939 VVDVRIFNRHG 949
           V  V       
Sbjct: 755 VDSVAFTTNQD 765


>gi|315258109|gb|ADT91642.1| RNA polymerase beta subunit [Lactococcus lactis subsp. cremoris]
          Length = 162

 Score =  248 bits (633), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 69/184 (37%), Positives = 100/184 (54%), Gaps = 22/184 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK +FPI  
Sbjct: 1   YGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K   ++K 
Sbjct: 51  FAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NKETGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +   +G   +    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESFGHTTIPN 158

Query: 188 QGLW 191
           +G W
Sbjct: 159 RGAW 162


>gi|22086605|gb|AAM90689.1|AF403007_1 RNA polymerase beta subunit [Rickettsia australis]
          Length = 281

 Score =  248 bits (633), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 185/280 (66%), Positives = 232/280 (82%), Gaps = 2/280 (0%)

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A +N +GFIE+PYRKV DG+VT++V+YLSA+EE    I QANS +D+DG    E + C
Sbjct: 2   TYATINKHGFIESPYRKVKDGRVTDEVIYLSAIEEGKYKIGQANSKVDKDGKLQGEFINC 61

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K 
Sbjct: 62  RVEGGNFVMVEPHEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKT 121

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           +APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E  +D  +  VDIY L+K
Sbjct: 122 DAPFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLEQKID-GSPSVDIYNLLK 180

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQ+SN NTC+NQ+PLV+VG  V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS
Sbjct: 181 FQKSNHNTCINQKPLVQVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDS 240

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           +LISER+V EDVFTSIHIEEFEV+ARDT+LGP EITR IP
Sbjct: 241 ILISERIVKEDVFTSIHIEEFEVIARDTRLGPVEITRAIP 280


>gi|52699788|gb|AAU86956.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            clauzadeana]
          Length = 723

 Score =  248 bits (633), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 121/833 (14%), Positives = 235/833 (28%), Gaps = 139/833 (16%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + + +  +    +         + +  + + +     +   
Sbjct: 2    DLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     ++     E    +    + +V  +     +      ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRSPNATKVFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  D       V     G  I      + D  D   K          P    D+
Sbjct: 178  NGVWVGVHSDPVHLVNTVQAVRRGHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDN 237

Query: 687  SNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRI 743
              +     N+   ++ +  L+          E +  K      V +            R 
Sbjct: 238  DPKSPRCGNLVLTKEHINKLEDYKDLSAEMQEKIREKEEVEKEVKEDGTPYGWNGLIKRG 297

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV---KVGDEVRRNDIIADGPST 800
            V+  V+ + + +   V     ++  R  Q   V   P      +   V+          T
Sbjct: 298  VVEYVDAEEEETVMIVMTPEDLEISRQLQAGYVLPEPSDTSEALMKRVKAPMNPTAHTWT 357

Query: 801  DLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                  ++   +  + +P+  +N          M  + +       E  +          
Sbjct: 358  HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXYEQRMDT-------- 409

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                                 +  +             +       +   +  + AI   
Sbjct: 410  ---------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACY 448

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L 
Sbjct: 449  SGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLK 504

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               Y +L +   +  G           K+  ++ D      R++          ++    
Sbjct: 505  HGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRSTEN 564

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  Q                             LR VKV +   +  Q GDK A RHG 
Sbjct: 565  GIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQ 604

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 605  KGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATP 664

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L                           V     +G  +   VF     
Sbjct: 665  FTEITVDSVSKLLR---------------EHGYQSRGFEVMHNGHTGRKLVAQVF----- 704

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                              +G  Y  +L HMV DK+ A
Sbjct: 705  ----------------------------------LGPTYYQRLRHMVDDKIXA 723


>gi|224797605|gb|ACN62832.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           tenebrosa]
          Length = 424

 Score =  248 bits (633), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 168/317 (52%), Positives = 223/317 (70%), Gaps = 8/317 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L  D       V  R  G+ I+V  +++++ID SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   ELTPDNIIKNNNVIARSNGQNIIVGPKEVEYIDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PLLK + P VGTG+E  VA+ SG A+VA   GIV+ VD+  I+I+S +   
Sbjct: 61  GANMQRQAIPLLKPQTPIVGTGVEYAVARDSGLAVVANLPGIVQYVDSNEIIIKSKDE-- 118

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 V  Y L +F+RSNQ T V   PLVK GD V  N I+ADGPS   G+LALG+N++
Sbjct: 119 ------VTTYELSRFERSNQGTSVTHIPLVKAGDVVEANQILADGPSMKDGELALGQNVI 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           +AFM WHGYN+ED+++ISER+V +DV+TS+HIEE+ +  R TK G EEIT +IPN SE+ 
Sbjct: 173 IAFMTWHGYNYEDAIIISERLVKDDVYTSMHIEEYNLECRKTKQGKEEITPEIPNTSEQS 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + +D+ GI+ +G EV  GDILVGK+TPKG++  T EEKLL AIFGEK+ +V+D SLRVP
Sbjct: 233 RRYLDDEGIVLIGTEVKEGDILVGKVTPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVP 292

Query: 933 SGVSGTVVDVRIFNRHG 949
           +G +G V  ++ + R  
Sbjct: 293 NGGAGIVQGIKRYKRED 309



 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 90/299 (30%), Positives = 130/299 (43%), Gaps = 25/299 (8%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G  V    IL    +   +  +   + ++ A       +  D  +     V   V 
Sbjct: 141  LVKAGDVVEANQILADGPS-MKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVY 199

Query: 941  DVRIFNRHGIDKNERSISVER------EQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ++  +     E          E   R  DDE  I+      +  +IL G+ 
Sbjct: 200  TSMHIEEYNLECRKTKQGKEEITPEIPNTSEQSRRYLDDE-GIVLIGTEVKEGDILVGKV 258

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L + +  E  R+               V+ +                
Sbjct: 259  TPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIVQGI---------------- 302

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K + G D+P  V  VVKVF+  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+D
Sbjct: 303  -KRYKREDGFDLPSEVEEVVKVFIVQKRKIREGDKMAGRHGNKGVISKVLPEEDMPFLED 361

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            GTPVDI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+  +    +
Sbjct: 362  GTPVDIMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGAKNQDLLDIMKEAK 420


>gi|258562136|gb|ACV81790.1| RNA polymerase II second largest subunit [Termitomyces poonensis]
          Length = 664

 Score =  248 bits (633), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 118/747 (15%), Positives = 213/747 (28%), Gaps = 132/747 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 49   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 104

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++   +       + +  + +         EEN + +   + +  +G +
Sbjct: 105  GLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSSTPCTKVFVNGVW 156

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 157  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQ 213

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
               L  E   V           +     +  + G+VE +DA       +    +   +  
Sbjct: 214  QLAL--EKKHVRWLSNGKDDNGTEYKWESLVKGGVVELLDAEEEETVMISMTPEDLETSR 271

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +       N   +    +K G            PS  LG       +  + +P+ 
Sbjct: 272  LQQSGVNPAV---NEDFDPAARLKAGINSHTWTHCEIHPSMILG-------ICASIIPFP 321

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N                        ++       +G       I              
Sbjct: 322  DHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM-----------D 352

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 353  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 412

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                I+ R  +D  ++S   + E+ E  +RD          +       I  G       
Sbjct: 413  F-RSIYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLEDDGLIAPGTGVAGED 471

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  +      R++          ++     +  Q                  
Sbjct: 472  IIIGKTAPIPPESEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI--------------- 516

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                        + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 517  -----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPD 571

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +G + E  L      +G +  +                         
Sbjct: 572  IIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--------------------- 610

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                 ++     + L        G+ V                         G +    G
Sbjct: 611  ----DLTVESVSTFLXQKGYQSRGLEVM----------------------YHGHT----G 640

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                     V +G  Y  +L HMV DK
Sbjct: 641  R---KLQAQVYLGPTYYQRLKHMVDDK 664



 Score =  118 bits (296), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 85/590 (14%), Positives = 163/590 (27%), Gaps = 100/590 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F++A ++ +    +  KY L   G      +         + + +    + +  L   
Sbjct: 11  KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSAKAGVSQVLNRYTYASTLSHLRRC 69

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +       + S     +   
Sbjct: 70  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFL 129

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA         F     +    +  N +  I   RR   +          
Sbjct: 130 EEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDI 189

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             +   ++        P    E   + L      +  ++          K         V
Sbjct: 190 REKELRLYTDAGRVCRPLFIVENQQLALEKKHVRW--LSNGKDDNGTEYKWESLVKGGVV 247

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDAS 667
             L A EEE   I+     L E     +  V      +          +        +  
Sbjct: 248 ELLDAEEEETVMISMTPEDL-ETSRLQQSGVNPAVNEDFDPAARLKAGINSHTWTHCEIH 306

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ I AS+IPF +++ S R      M +QA+ +                        
Sbjct: 307 PSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI----------------- 349

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + +  Y       +     +  R        
Sbjct: 350 ------------------------RMDTMANILYYPQKPLATTRSMEYLKFR-------- 377

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +
Sbjct: 378 ----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSY 421

Query: 848 EVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             + + + +   E        +   +       +++ G+I  G  V   DI++GK  P  
Sbjct: 422 MDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPI- 480

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                PE + L           RD S  + S  SG V  V I       K
Sbjct: 481 ----PPESEELGQRTRTH--TRRDVSTPLKSTESGIVDQVLITTNSEGQK 524


>gi|99866478|gb|ABF67584.1| RNA polymerase II second largest subunit [Auricularia auricula-judae]
          Length = 690

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 133/826 (16%), Positives = 247/826 (29%), Gaps = 158/826 (19%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L + +R+   ++ + +    +              + A  + + +    
Sbjct: 1    GKKRLDLAGPLLASLFRMLFRKLTKDVYRYLQKCVEARKDFNLNLAVKANTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSAKAGVSQVLNRYTFASTLSHLRRTNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++           + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +    ++ +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSGIPSTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS-----SGAAIVAKRAGIVEQVD 739
             D+ RV     +      ++K         +E +  K      S       + G++E +D
Sbjct: 226  TDAGRVCRPLFIVEDQQLVIKKH------HVEWIQNKEDEHGASFKWDNLIKTGLIELLD 279

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ--NTCVNQRPLVKVGDEVRRNDIIADG 797
            A       +    D   +     R M  + ++   +     + +V               
Sbjct: 280  AEEEETVMICMTSDDLENSRLQSRGMAPRDADNEFDPAARLKSIVNAHTW----THCEIH 335

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N       S R   +       +  +    +     
Sbjct: 336  PSMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVR--- 379

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                +  +  +             +       +   +  + AI 
Sbjct: 380  --------------------QDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 419

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  ++S  V  E+ E  +RD       
Sbjct: 420  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDVEKKSGMVALEEFEKPSRDTTLRMKH 478

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  L  D                +E  QR    
Sbjct: 479  GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPLPQD---------------SEELGQRTRTH 523

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             K    T     E+   +++      D       + VK+ +   R  Q GDK A RHG K
Sbjct: 524  QKRDVSTPLKSTENGIVDQVLITTNQD-----GQKFVKIRIRSTRVPQIGDKFASRHGQK 578

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +   
Sbjct: 579  GTIGITYRQEDMPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 638

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                       ++      VLR +     G+ V           
Sbjct: 639  T-------------------------DLTVESVSQVLRSSGYHSRGLEVM---------- 663

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                          G +       G      V +G  Y  +L HMV
Sbjct: 664  ------------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 690


>gi|19881439|ref|NP_612256.1| putative DNA-directed RNA polymerase II [Infectious spleen and kidney
            necrosis virus]
 gi|19773644|gb|AAL98758.1|AF371960_34 putative DNA-directed RNA polymerase II [infectious spleen and kidney
            necrosis virus]
          Length = 1044

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 80/341 (23%), Positives = 124/341 (36%), Gaps = 103/341 (30%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +K+              + VK+ +   R  + GDK A     KG    +    DM
Sbjct: 782  EGYFDDKLV------FNMADGCKCVKIKLRKIRIPEMGDKFASFTAQKGTCGMMYDQWDM 835

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETH--LGWACVGLGKKIKSLINDYKANGDISP 1167
            PF  DG   D+V+NP   PSRM V  + +    LG A  G GK   +   +         
Sbjct: 836  PFTADGVVPDLVINPHAFPSRMTVHYLLQMCFELG-AVAGGGKGYDATAFNS-------- 886

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        DGA    +   L    
Sbjct: 887  --------------------------------------------DGA---DLLKTLEELG 899

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 + ++Y G TG  F+  V +      KL H+V++KV+AR+TG    +T+QP+ G+S
Sbjct: 900  YA---KQVMYCGRTGRRFESLVFMAPCPYQKLKHLVANKVHARTTGPVDPLTRQPVAGRS 956

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-----------------DVVGR----- 1325
              GG ++GEME WC  ++GAA  L E +T  SD                 DV  R     
Sbjct: 957  RDGGIKIGEMEQWCKISHGAAAALHESMTTMSDPYTVPVCSVCHVMTDSYDVC-RHCRSV 1015

Query: 1326 -TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
              + Y              P +  +  +++ ++G+   + +
Sbjct: 1016 SVQTYA------------MPYTSKLFFQQLASIGIKTRIMD 1044



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 87/469 (18%), Positives = 156/469 (33%), Gaps = 65/469 (13%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--------MERSIKERISSVDIDSVMPQ 501
            G + D DNL  +RV + G ++   +R    +        ME+S    +  +   S    
Sbjct: 300 VGAVHDKDNLRWKRVDTSGALILFLFRNLFKQWVCTVKRVMEKSCVVGVPDLQGKSGSVN 359

Query: 502 DLINAKPVVSAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALG 545
            + N    V  +     +                  +SQL    N  +RI++ RR++   
Sbjct: 360 AITNVITNVLHLAFATGNWLVRKNSGTSKNTYTPRGVSQLMCVQNYGARISNLRRMT--- 416

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V      +++R +H +H G ICP ET EG  +G V  L   A +     +    R +
Sbjct: 417 -HAVGFKGKNIKVRQLHNSHNGYICPYETPEGDRVGNVVQLALSATIT----VPVCPRNI 471

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-----EELVFCRCAGEEILVPREK 660
               ++    +            Q N  +  +G          L            P   
Sbjct: 472 RTLMMSALPRFADP---------QGNQPVLLNGEIVGWVKDRMLCGMAIMHMLWDYPDVT 522

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           + F       V S     +  L +    R++    +Q   V    +         E VV+
Sbjct: 523 VVFRHGYGVHVYSEGGRFMRPLIHRGQYRMVCPSLVQELLVRPFPSPT-------ERVVS 575

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             S  A      GIV   DA+  VI       + + S  + Y+    +++    C+N   
Sbjct: 576 MDSMRADFMDLPGIVVLTDAMSAVI----PFYNHTQSPRNAYQSNMGKQAVGLPCLNYMS 631

Query: 781 L--VKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              V +   +     ++   + D      +  G   +VA + + GYN EDS++++   V 
Sbjct: 632 RWDVTLDVLMYPQVPLSRSKAMDALSFDTMPHGACPIVAVLTFDGYNQEDSIILNRSSVQ 691

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---LKNIDECGI 881
             +F S   +      +  K    E    +P            + + GI
Sbjct: 692 RGMFVSTTYKTLCECEKHVKRCEFERIMRVPVDKRRPGLVYDYLGDDGI 740



 Score = 44.7 bits (104), Expect = 0.12,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 60/189 (31%), Gaps = 47/189 (24%)

Query: 71  AAMLEFVSYEFDPPK-FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
              + F    +  P           D TY   +     L        TGAK ++ I    
Sbjct: 44  NHSVTFGDVAYSKPSPETPGHARAYDETYETTVSCKAYLTCM----ATGAKHVQHIHN-- 97

Query: 130 IYMGDLPLMT---------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
             +  +P+M                  G F++KG +RI++  +H +  I           
Sbjct: 98  --LAKMPVMVRAPPLCQGIGECEKDPGGYFIVKGKERIIIPHIHTAYNIPITM-----HC 150

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDII-HVRIDR-----------RRKVPVTSFLMALG 222
           + K    C +          E    +++  VR+ +           +  +P  +   ALG
Sbjct: 151 TTKKTLVCEM------RTHNETTGNNLLVKVRLMQGCIIEMSVPYIKSFLPAGAVFNALG 204

Query: 223 MDSEEILST 231
           +  E++L  
Sbjct: 205 VSEEDMLRY 213


>gi|55831371|gb|AAV66544.1| RNA polymerase II second largest subunit [Hygrocybe aff. conica PBM
            918]
          Length = 686

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 126/814 (15%), Positives = 243/814 (29%), Gaps = 152/814 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKVFNVALAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSQSAAVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +       R A   +   ++     D   +  V         
Sbjct: 169  EENAHSATPCTKVFVNGVWMG---VHRDAANLVKTIKKLRRKRDIESEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
              + D+ RVL    +      +L+ +   ++  G + V         V +R      VD 
Sbjct: 226  RLSTDAGRVLRPLFVVENQQLVLQKKHVKWLIDGTDGVWELDPDGKPVLRRFNWDSLVD- 284

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ------RPLV--KVGDEVRRND 792
             R ++  ++ + + +         ++  R  Q             P V  K G       
Sbjct: 285  -RGIVELLDAEEEETVMIAMTQEDLENSRLQQQGIDPHANDGDFDPAVRLKAGINSHTWT 343

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +   IH+  F +   
Sbjct: 344  HCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IHLTNFLIRM- 393

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 394  --------------------------DTMANILYYPQKPLATTRAMEYLRFRELPAGQNA 427

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    ++ R  +D  +++   + E+ E   R+  
Sbjct: 428  IVAILCYSGYNQEDSVIMNQSSIDRGLF-RSMYYRCYMDLEKKNGVQQLEEFEKPTRENT 486

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       I  G           K+  +  D      R++          ++
Sbjct: 487  LRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRSHTRRDVSTPLK 546

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                              + VK+ V   R  Q GDK A 
Sbjct: 547  STENGIVDQVLI--------------------TTNAEGHKFVKIRVRATRVPQIGDKFAS 586

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G + 
Sbjct: 587  RHGQKGTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEG 646

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 647  D-----------------------------------------------------ATP-FT 652

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                E++++ LR       G  ++Y G TG    
Sbjct: 653  ELTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQ 686



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 84/618 (13%), Positives = 170/618 (27%), Gaps = 104/618 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +    V  F+VA ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVETHKV--FNVALAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSQSAAVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                +       + P    E   + L
Sbjct: 189 GVHRDAANLVKTIKKLRRKRDIESEVSVVRDIRERELRLSTDAGRVLRPLFVVENQQLVL 248

Query: 583 VSSLTSFARVNAYGFIE------TPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSL 634
                 +      G  E         R+     + +   V  L A EEE   IA     L
Sbjct: 249 QKKHVKWLIDGTDGVWELDPDGKPVLRRFNWDSLVDRGIVELLDAEEEETVMIAMTQEDL 308

Query: 635 DEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +      + +      G+          +        +  P  ++ + AS+IPF +++ S
Sbjct: 309 ENSRLQQQGIDPHANDGDFDPAVRLKAGINSHTWTHCEIHPSMILGVCASIIPFPDHNQS 368

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +                                            
Sbjct: 369 PRNTYQSAMGKQAMGIHLTNFLI------------------------------------- 391

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  + + +  Y       +     +  R                        +L  
Sbjct: 392 ----RMDTMANILYYPQKPLATTRAMEYLRFR------------------------ELPA 423

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT----- 862
           G+N +VA + + GYN EDS+++++  +   +F S++   +  + +   +   E       
Sbjct: 424 GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRCYMDLEKKNGVQQLEEFEKPTR 483

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +   +       +++ G+I  G  V   DI++GK  P         E+L +        
Sbjct: 484 ENTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPI----PPDSEELGQRTRSHTRR 539

Query: 923 DVRDTSLRVPSGVSGTVV 940
           DV        +G+   V+
Sbjct: 540 DVSTPLKSTENGIVDQVL 557


>gi|327396886|dbj|BAK14252.1| DNA dependent RNA polymerase second largest subunit [Red sea bream
            iridovirus]
          Length = 1052

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 107/273 (39%), Gaps = 67/273 (24%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +K+              + VK+ +   R  + GDK A     KG    +    DM
Sbjct: 790  EGYFDDKLV------FNMADGCKCVKIKLRKIRIPEMGDKFASFTAQKGTCGMMYDQWDM 843

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETH--LGWACVGLGKKIKSLINDYKANGDISP 1167
            PF  DG   D+V+NP   PSRM V  + +    LG A  G GK   +   +         
Sbjct: 844  PFTADGVVPDLVINPHAFPSRMTVHYLLQMCFELG-AVAGGGKGYDATAFNS-------- 894

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        DGA    +   L    
Sbjct: 895  --------------------------------------------DGA---DLLKTLEELG 907

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 + ++Y G TG  F+  V +      KL H+V++KV+AR+TG    +T+QP+ G+S
Sbjct: 908  YA---KQVMYCGRTGRRFESLVFMAPCPYQKLKHLVANKVHARTTGPVDPLTRQPVAGRS 964

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              GG ++GEME WC  ++GAA  L E +T  SD
Sbjct: 965  RDGGIKIGEMEQWCKISHGAAAALHESMTTMSD 997



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 96/498 (19%), Positives = 169/498 (33%), Gaps = 69/498 (13%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--------MERSIKERISSVDIDSVMPQ 501
            G + D DNL  +RV + G ++   +R    +        ME+S    +  +   S    
Sbjct: 308 VGAVHDKDNLRWKRVDTSGALILFLFRNLFKQWVCTVKRVMEKSCVVGVPDLQGKSGSVN 367

Query: 502 DLINAKPVVSAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALG 545
            + N    V  +     +                  +SQL    N  +RI++ RR++   
Sbjct: 368 AITNVITNVLHLAFATGNWLVRKNSGTSKNTYTPRGVSQLMCVQNYGARISNLRRMT--- 424

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V      +++R +H +H G ICP ET EG  +G V  L   A V     +    R +
Sbjct: 425 -HAVGFKGKNIKVRQLHNSHNGYICPYETPEGDRVGNVVQLALSATVT----VPVCPRNI 479

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-----EELVFCRCAGEEILVPREK 660
               ++   ++            Q N  +  +G          L            P   
Sbjct: 480 RTLMMSVLRLFADP---------QGNQPVLLNGEIVAWVRDRMLCGMAMMHVLWDYPNVT 530

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           + F       V S    L+  L +    R++    +Q   V    +         E VV+
Sbjct: 531 VVFRHGYGVHVYSEGGRLVRPLIHRGQYRMVCPSLVQELLVRPFPSPT-------ERVVS 583

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             S  A      GIV   DA+  VI       + + S  + Y+    +++    C+N   
Sbjct: 584 MDSMRAEFMDLPGIVVLTDAMSAVI----PFYNHTQSPRNAYQSNMGKQAVGLPCLNYMS 639

Query: 781 L--VKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
              V +   +     ++   + D      +  G   +VA + + GYN EDS++++   V 
Sbjct: 640 RWDVTLDVLMYPQVPLSRSKAMDALSFDTMPHGACPIVAVLTFDGYNQEDSIILNRSSVQ 699

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---LKNIDECGIICV----GAEV 888
             +F S   +      +  K    E    +P            + + GI       G  V
Sbjct: 700 RGMFVSTTYKTLCECEKHVKRCEFERIMCVPVDKRRPGLVYDYLGDDGIFDPALARGMFV 759

Query: 889 NPGDILVGKITPKGESPM 906
             G ++VGK++     P 
Sbjct: 760 TAGVVVVGKMSFDQSRPE 777


>gi|62421225|gb|AAX82345.1| DNA-directed RNA polymerase II second largest subunit-like protein
            [Orange-spotted grouper iridovirus]
          Length = 1052

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 107/273 (39%), Gaps = 67/273 (24%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +K+              + VK+ +   R  + GDK A     KG    +    DM
Sbjct: 790  EGYFDDKLV------FNMADGCKCVKIKLRKIRIPEMGDKFASFTAQKGTCGMMYDQWDM 843

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETH--LGWACVGLGKKIKSLINDYKANGDISP 1167
            PF  DG   D+V+NP   PSRM V  + +    LG A  G GK   +   +         
Sbjct: 844  PFTADGVVPDLVINPHAFPSRMTVHYLLQMCFELG-AVAGGGKGYDATAFNS-------- 894

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        DGA    +   L    
Sbjct: 895  --------------------------------------------DGA---DLLKTLEELG 907

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 + ++Y G TG  F+  V +      KL H+V++KV+AR+TG    +T+QP+ G+S
Sbjct: 908  YA---KQVMYCGRTGRRFESLVFMAPCPYQKLKHLVANKVHARTTGPVDPLTRQPVAGRS 964

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              GG ++GEME WC  ++GAA  L E +T  SD
Sbjct: 965  RDGGIKIGEMEQWCKISHGAAAALHESMTTMSD 997



 Score = 89.0 bits (219), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 98/500 (19%), Positives = 168/500 (33%), Gaps = 73/500 (14%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--------MERSIKERISSVDIDSVMPQ 501
            G + D DNL  +RV + G ++   +R    +        ME+S    +  +   S    
Sbjct: 308 VGAVHDKDNLRWKRVDTSGALILFLFRNLFKQWVCTVKRVMEKSCVVGVPDLQGKSGSVN 367

Query: 502 DLINAKPVVSAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALG 545
            + N    V  +     +                  +SQL    N  +RI++ RR++   
Sbjct: 368 AITNVITNVLHLAFATGNWLVRKNSGTSKNTYTPRGVSQLMCVQNYGARISNLRRMT--- 424

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V      +++R +H +H G ICP ET EG  +G V  L   A V            V
Sbjct: 425 -HAVGFKGKNIKVRQLHNSHNGYICPYETPEGDRVGNVVQLALSATVT-----------V 472

Query: 606 CDGKVTNDVVYLSAMEEENRYIA--QANSSLDEDGSFT-----EELVFCRCAGEEILVPR 658
                    + +SA+       A  Q N  +  +G          L            P 
Sbjct: 473 PVCPRNIRTLMMSALR----LFADPQGNQPVLLNGEIVAWVRDRMLCGMAMMHVLWDYPH 528

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             + F       V S     +  L +    R++    +Q   V    +         E V
Sbjct: 529 VTVVFRHGYGVHVYSEGGRFVRPLIHRGQYRMVCPSLVQELLVRPFPSPT-------ERV 581

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
           V+  S  A      GIV   DA+  VI       + + S  + Y+    +++    C+N 
Sbjct: 582 VSMDSMRAEFMDLPGIVVLTDAMSAVI----PFYNHTQSPRNAYQSNMGKQAVGLPCLNY 637

Query: 779 RPL--VKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                V +   +     ++   + D      +  G   +VA + + GYN EDS++++   
Sbjct: 638 MSRWDVTLDVLMYPQVPLSRSKAMDALSFDTMPHGACPIVAVLTFDGYNQEDSIILNRSS 697

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---LKNIDECGIICV----GA 886
           V   +F S   +      +  K    E    +P            + + GI       G 
Sbjct: 698 VQRGMFVSTTYKTLCECEKHVKRCEFERIMCVPVDKRRPGLVYDYLGDDGIFDPALARGM 757

Query: 887 EVNPGDILVGKITPKGESPM 906
            V  G ++VGK++     P 
Sbjct: 758 FVTAGVVVVGKMSFDQSRPE 777


>gi|52699820|gb|AAU86972.1| DNA-dependent RNA polymerase II second largest subunit [Gyromitra
            esculenta]
          Length = 699

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 117/828 (14%), Positives = 230/828 (27%), Gaps = 153/828 (18%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L   +R    ++ + + + +               + +  + + +     + 
Sbjct: 1    RLDLAGPLLAGLFRTLWKKLTKDVYKYLEKCVETAKEFNLTLAVKSNTITNGLKYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L+  + +     G+    +    D ++  +     +      
Sbjct: 117  LVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPNATKV 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN 684
            ++         D     ++V        +      I D  D   K          P    
Sbjct: 177  FVNGVWVGTHRDPLMLHKVVQDVRRQGVVSHEVSIIRDIRDREFKIFTDAGRVCRPLFVI 236

Query: 685  DDSNRV--LMGCNMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            D+  R        + ++ V  L+ +    V           SG+          E +DA 
Sbjct: 237  DNDPRSERRGQLVLLKEHVEKLEDDHTLPVDERFGWEGLLYSGSV---------EYLDAE 287

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +       +    +      +    + P+                PS  
Sbjct: 288  EEETAMIVMTPEDLEMSRQVQLGYEEPHDQYSAKRFKAPINA--HTAHTWTHCEIHPSMI 345

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +   +    F              
Sbjct: 346  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFXTNFSERM---------- 386

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 387  -----------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 429

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R  +D+ +R   +  + +E   +      + L + 
Sbjct: 430  YNQEDSVIMNQSSIDRGLF-RSLFYRAYMDQEKR---IGMQVVEEFEKPTRSNTLKLKQG 485

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L E   +  G           K+  ++ D+     R ++         ++     +
Sbjct: 486  TYEKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGI 545

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                             L+ VKV +   +  Q GDK A RHG KG
Sbjct: 546  VDQVML--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKG 585

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             V      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 586  TVGITYRQEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 645

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    +    +       + Y                              
Sbjct: 646  DVTVESVSTLLR--QNGYQSRGFEVMYNGYT----------------------------- 674

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                G         V +G  Y  +L HMV DK
Sbjct: 675  --------------------GR---KLVAQVFLGPTYYQRLRHMVDDK 699



 Score =  116 bits (291), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 82/617 (13%), Positives = 171/617 (27%), Gaps = 99/617 (16%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +   +     K  + A      +    +  T  +  S+    + +  K   S  G  ++ 
Sbjct: 20  LTKDVYKYLEKCVETAKEFNLTLAVKSNTITNGLKYSLATGNWGEQKKAASSKAGVSQVL 79

Query: 418 MRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
            R    +      R          I     L N    +         +   + + L    
Sbjct: 80  NRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 139

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
            + +      + + +SS D++ +   +   +               +    + +     +
Sbjct: 140 YITIGTPGYPLVDFLSSNDMELLEEYEPQRSPNATKVF---VNGVWVGTHRDPLMLHKVV 196

Query: 536 THTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              RR   +  +  + R     E        R   P       P     G  + L   + 
Sbjct: 197 QDVRRQGVVSHEVSIIRDIRDREFKIFTDAGRVCRPLFVIDNDPRSERRGQLVLLKEHVE 256

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS-------F 640
                + +               +  V YL A EEE   I      L+            
Sbjct: 257 KLE--DDHTLPVDERFGWEGLLYSGSVEYLDAEEEETAMIVMTPEDLEMSRQVQLGYEEP 314

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            ++    R                +  P  ++ I AS+IPF +++ S R      M +QA
Sbjct: 315 HDQYSAKRFKAPINAHTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQA 374

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                                               +   + + + 
Sbjct: 375 MGVFXTNFS-----------------------------------------ERMDTMANIL 393

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            Y       +     +  R                        +L  G+N +VA + + G
Sbjct: 394 YYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILCYSG 429

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +   + +   + 
Sbjct: 430 YNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRIGMQVVEEFEKPTRSNTLKLKQGTYEK 489

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G++  G  V+  DI++GK  P         ++       +K    RD S  + S  
Sbjct: 490 LDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTE 542

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 543 NGIVDQVMLTTNAEGLK 559


>gi|207691933|gb|ACI25201.1| RNA polymerase beta [Mycobacterium sp. ATCC 21498]
          Length = 215

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 90/214 (42%), Positives = 118/214 (55%), Gaps = 37/214 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I  +    +   ++       E  
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVVGGAPEWAANLPQDMLSSE-- 147

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                                          VSTPVFDGA EE +  +L     +      
Sbjct: 148  --------------------------PNSIVSTPVFDGAREEELQGLLSSTLPNRDGEVL 181

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G+++LYDG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 182  VNGDGKAVLYDGRSGEPFPYPVTVGYMYILKLHH 215


>gi|119644059|gb|ABL85604.1| RNA polymerase II second largest subunit [Hypotrachyna degelii]
          Length = 708

 Score =  248 bits (632), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 115/741 (15%), Positives = 221/741 (29%), Gaps = 90/741 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P    D+  R     N+         L      +  T  +       G        
Sbjct: 237  RVCRPLFVIDNDPRSSNRGNLVLTKEHVQKLELDRENWATTEPDVREETDMG-WQGLVEE 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +        +N +  +N+R    +        
Sbjct: 296  GVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +       E  +   
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXSFNYEQRMDT- 406

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 407  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRS 1170
             +  +          +S L  
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR 675


>gi|89274888|gb|ABD65885.1| RNA polymerase II second largest subunit [Rickenella fibula]
          Length = 657

 Score =  248 bits (632), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 115/740 (15%), Positives = 206/740 (27%), Gaps = 130/740 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 46   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 101

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++           + +  + +         EEN + A   + +  +G +
Sbjct: 102  GLVKNLALMATISVGSLSAPVIEFLEEWGLESL--------EENAHSAIPLTKVFVNGVW 153

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 154  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVE-- 208

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
                      V T                         D  +   +  +        GV 
Sbjct: 209  ------NQQLVLTKKHIK-----------WLNLGYRDDDPEQKPYKWEQLVH----GGVI 247

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             Y         +   +   P       +    I       +    A  +    A + W  
Sbjct: 248  EYLDA---EEEETVMICMMPEDLENSRLMAQGIDPHANDGEFDPAARLKAPTTAHI-WTH 303

Query: 821  YNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
                 SM+  I   ++            ++       +G       +             
Sbjct: 304  CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM----------- 352

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 353  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 412

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  +D  ++S   + E+ E  +R+          +       I  G      
Sbjct: 413  LF-RSMYYRSYMDLEKKSGIQQLEEFEKPSRETTLRMKHGTYDKLEDDGLIAPGTIVNGE 471

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 472  DIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQ----------------- 514

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 515  ---VLVTTNSEGQKFVKVRVRSARIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 571

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      +G +                           
Sbjct: 572  DIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 606

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E++++ LR       G  ++Y 
Sbjct: 607  ----------------------------ATP-FTELTVESVSTFLRQKGYQSRGLEVMYH 637

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V +G  Y  +
Sbjct: 638  GHTGRKLQAQVYLGPTYYQR 657



 Score =  124 bits (312), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 82/591 (13%), Positives = 163/591 (27%), Gaps = 98/591 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F++A ++ +    +  KY L   G      +         + + +    + +  L   
Sbjct: 8   KDFNIALAVKHNTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRC 66

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +       + S+    +   
Sbjct: 67  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMATISVGSLSAPVIEFL 126

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA   +     F     +    +  N +  I   RR   +          
Sbjct: 127 EEWGLESLEENAHSAIPLTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDI 186

Query: 555 GVEMRDVHPTHYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             +   ++        P    E    +     +            E    K         
Sbjct: 187 REKELRLYTDAGRVCRPLFIVENQQLVLTKKHIKWLNLGYRDDDPEQKPYKWEQLVHGGV 246

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDA 666
           + YL A EEE   I      L+      + +      GE     R             + 
Sbjct: 247 IEYLDAEEEETVMICMMPEDLENSRLMAQGIDPHANDGEFDPAARLKAPTTAHIWTHCEI 306

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  ++ I AS+IPF +++ S R      M +QA+ +                       
Sbjct: 307 HPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------------- 350

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       + + +  Y       +     +  R       
Sbjct: 351 -------------------------RMDTMANILYYPQKPLATTRSMEYLKFR------- 378

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA + + GYN EDS+++++  +   +F S++   
Sbjct: 379 -----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRS 421

Query: 847 FEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +  + + + +   E            +       +++ G+I  G  VN  DI++GK  P 
Sbjct: 422 YMDLEKKSGIQQLEEFEKPSRETTLRMKHGTYDKLEDDGLIAPGTIVNGEDIIIGKTAPI 481

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++        +    RD S  + S  SG V  V +       K
Sbjct: 482 PPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLVTTNSEGQK 525


>gi|103001284|gb|ABF71500.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            cf. chlorophanum Feuerer 18.2.2003]
          Length = 699

 Score =  248 bits (632), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 115/820 (14%), Positives = 226/820 (27%), Gaps = 145/820 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 1    GPLLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQ 60

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 61   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 116

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 117  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 176

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  +
Sbjct: 177  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 236

Query: 690  VLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                 N+   ++ +  L+ +               S     AK  G    V     V+  
Sbjct: 237  STNCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEY 286

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLA 806
            V+ + + +   V     ++  R  Q               V+          T      +
Sbjct: 287  VDAEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPS 346

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            +   +  + +P+  +N                        ++       +G      D  
Sbjct: 347  MILGICASIIPFPDHNQSPRN------------------TYQSAMGKXXMGVFLTNYDQR 388

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 389  M-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 437

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L
Sbjct: 438  SVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKL 493

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             E   +  G           K+  ++ D      R++          ++     +  Q  
Sbjct: 494  DEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVL 553

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                       L+ VKV +   +  Q GDK A RHG KG +   
Sbjct: 554  L--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 593

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +         
Sbjct: 594  YRQEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVD 653

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             +S L    E    +                                             
Sbjct: 654  SVSKLLR--EHGYQSRGFEVM--------------------------------------- 672

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                   +G +    G         V +G  Y  +L HMV
Sbjct: 673  ------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 699


>gi|88976107|gb|ABD59032.1| RNA polymerase II second largest subunit [Cantharocybe gruberi]
          Length = 675

 Score =  248 bits (632), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 121/804 (15%), Positives = 236/804 (29%), Gaps = 146/804 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAH 169

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 170  SSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +       L+ +   ++  G            +V  + GI+E +DA     
Sbjct: 227  AGRVCRPLFIVENQQLALQKKHIKWLNQGYNDEGEDFKWEQLV--KGGIIELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +    ++ +    ++       R  +K G            PS  LG  
Sbjct: 285  VMISMTPEDLENSRLQHQGVDPHANDGEFDPAAR--LKAGTHAHTWTHCEIHPSMILG-- 340

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 341  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLI 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 378  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 427  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPLRDNTLRMKHGTYDKLED 485

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 486  DGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI- 544

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q GDK A RHG KG +     
Sbjct: 545  -------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYR 585

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +              
Sbjct: 586  QEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------ 633

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     E++++ LR 
Sbjct: 634  -----------------------------------------ATP-FTDLTVESVSTFLRQ 651

Query: 1226 ADLDESGQSILYDGLTGEPFDRPV 1249
                  G  +++ G TG      V
Sbjct: 652  KGYQSRGLEVMFHGHTGRKLQAQV 675



 Score =  125 bits (315), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 87/622 (13%), Positives = 171/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 184

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 185 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 244

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     E    K         +  L A EEE   I+     L+      +
Sbjct: 245 QKKHIKW--LNQGYNDEGEDFKWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQHQ 302

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE                   +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 GVDPHANDGEFDPAARLKAGTHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIYLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 382 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPLRDNTLRMKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 478 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 530

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 531 LKSTESGIVDQVLITTNSEGQK 552


>gi|123979392|gb|ABM81521.1| RNA polymerase II second largest subunit [Gyalidea hyalinus]
          Length = 701

 Score =  248 bits (632), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 113/751 (15%), Positives = 215/751 (28%), Gaps = 120/751 (15%)

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              + +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 63   GKAGVSQVLNRYTYASTLSHLRRTNT----PLGRDGKIAKPRQLHNTHWGLVCPAETPEG 118

Query: 578  HNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L    +  V + G+    + +    ++  +            ++      + 
Sbjct: 119  QACGLVKNLALMCYVTVGSPGWPVIDFLQSRSMELLEEYEPSRNPHITKVFVNGTWVGVH 178

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             + +     +        I      + D  +   K          P    ++  R     
Sbjct: 179  PNPANLHTQILALRRNNTISHEVSIVRDIREREFKIFTDAGRVSRPLFVVENDIRSERKG 238

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            +        L      + T +E    +    A               R++   V   LD 
Sbjct: 239  H--------LVLTKELLAT-LELDREEPPWIAPPGDPGARPPLRGWDRLIRGGVIEYLDA 289

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  +  +                       V+   + A    +D     +   +   
Sbjct: 290  EEEETVMICMTPEDLEIHRD-------------VQAGYLEAAKQESDDPVSRIKTILSQP 336

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
               +       SM++                       +  L                L 
Sbjct: 337  PHTYTHCEIHPSMILGICASIIPFPDH-----------NQSLXXXXXXXXXXXXXXVFLT 385

Query: 875  NIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            N DE    +  +             +       +   +  + AI      +  ++ +   
Sbjct: 386  NFDERMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQENSVIMNQ 445

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---I 989
            S +   +    +F R  +++ +R  +   + +E   +    E + L +  Y +L +   I
Sbjct: 446  SAIDRGLF-RSLFYRTYVEQEKRVGA---QLVEQFEKPLRSETLRLKQGTYEKLDDDGLI 501

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  L+ D                 E  QR     K    T     
Sbjct: 502  APGTRVSGEDIIIGKTAPLAQD------------INTNSEVGQRTKLHTKRDASTPLRST 549

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E+   +++             L+ VK+     +  Q GDK A RHG KG +      EDM
Sbjct: 550  ENGIVDRVLL-----TTNSEALKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRHEDM 604

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   D+++NP  +PSRM +  + E  L       G +                  
Sbjct: 605  PFTVEGITPDLIMNPHAIPSRMTIAHLVECQLSKVSSLRGFEGD---------------- 648

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                 +TP F     + I+++LR     
Sbjct: 649  -------------------------------------ATP-FTDVTVQGISALLREHGYQ 670

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G  ++Y+G TG+     + +G  Y  +L 
Sbjct: 671  SRGFEVMYNGHTGKKLRGQIFLGPTYYQRLR 701



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 58/436 (13%), Positives = 112/436 (25%), Gaps = 49/436 (11%)

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
           L++  V++P  + T  +  S+    + +  K      G  ++  R    +      R   
Sbjct: 30  LELESVIKPAIL-TNGLKYSLATGNWSEQKKAAQGKAGVSQVLNRYTYASTLSHLRRTNT 88

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  I     L N    +         +   + + L     + +      + + + S
Sbjct: 89  PLGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGSPGWPVIDFLQS 148

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVAR 551
             ++ +   +      +          + +       N  ++I   RR + +  +  + R
Sbjct: 149 RSMELLEEYEPSRNPHITKVF---VNGTWVGVHPNPANLHTQILALRRNNTISHEVSIVR 205

Query: 552 ARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSF---------ARVNAY 595
                E        R   P            +GH +     L +                
Sbjct: 206 DIREREFKIFTDAGRVSRPLFVVENDIRSERKGHLVLTKELLATLELDREEPPWIAPPGD 265

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
                P R          + YL A EEE   I      L+         +       +  
Sbjct: 266 PGARPPLRGWDRLIRGGVIEYLDAEEEETVMICMTPEDLEIHRDVQAGYLEAAKQESDDP 325

Query: 656 V---------PREKIDFIDASPKQVVSIAASLIPFLENDDS----------------NRV 690
           V         P       +  P  ++ I AS+IPF +++ S                   
Sbjct: 326 VSRIKTILSQPPHTYTHCEIHPSMILGICASIIPFPDHNQSLXXXXXXXXXXXXXXVFLT 385

Query: 691 LMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                M   A  L   + P   T  ME +  +   A   A  A            +   +
Sbjct: 386 NFDERMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQENSVIMNQ 445

Query: 750 GDLDPSTSGVDIYRLM 765
             +D        YR  
Sbjct: 446 SAIDRGLFRSLFYRTY 461


>gi|292658990|gb|ADE34378.1| DNA-directed RNA polymerase II second largest subunit-like protein
            [Turbot reddish body iridovirus]
          Length = 1050

 Score =  248 bits (632), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 73/273 (26%), Positives = 107/273 (39%), Gaps = 67/273 (24%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +K+              + VK+ +   R  + GDK A     KG    +    DM
Sbjct: 788  EGYFDDKLV------FNMADGCKCVKIKLRKIRIPEMGDKFASFTAQKGTCGMMYDQWDM 841

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETH--LGWACVGLGKKIKSLINDYKANGDISP 1167
            PF  DG   D+V+NP   PSRM V  + +    LG A  G GK   +   +         
Sbjct: 842  PFTADGVVPDLVINPHAFPSRMTVHYLLQMCFELG-AVAGGGKGYDATAFNS-------- 892

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        DGA    +   L    
Sbjct: 893  --------------------------------------------DGA---DLLKTLEELG 905

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
                 + ++Y G TG  F+  + +      KL H+V++KV+AR+TG    +T+QP+ G+S
Sbjct: 906  YA---KQVMYCGRTGRRFESLIFMAPCPYQKLKHLVANKVHARTTGPVDPLTRQPVAGRS 962

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              GG ++GEME WC  ++GAA  L E +T  SD
Sbjct: 963  RDGGIKIGEMEQWCKISHGAAAALHESMTTMSD 995



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 84/494 (17%), Positives = 155/494 (31%), Gaps = 64/494 (12%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--------MERSIKERISSVDIDSVMPQ 501
            G + D DNL  +RV + G ++   +R    +        ME+S    +  +   S    
Sbjct: 309 VGAVHDKDNLRWKRVDTSGALILFLFRNLFKQWVCTVKRVMEKSCVVGVPDLQGKSGSVN 368

Query: 502 DLINAKPVVSAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALG 545
            + N    V  +     +                  +SQL    N  +RI++ RR++   
Sbjct: 369 AITNVITNVLHLAFATGNWLVRKNSGTSKNTYTPRGVSQLMCVQNYGARISNLRRMT--- 425

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V      +++R +H +H G ICP ET EG  +G V  L   A V     +    R +
Sbjct: 426 -HAVGFKGKNIKVRQLHNSHNGYICPYETPEGDRVGNVVQLALSATVT----VPVCPRNI 480

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT----EELVFCRCAGEEILVPRE-K 660
               +    +++           Q N  +  +G       + ++        +    +  
Sbjct: 481 RALMMYTLPLFVDP---------QGNQPVLLNGEIVAWVRDRMLCGMAIMHVLWDYPDVT 531

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV-PLLKAEAPFVGTGMESVV 719
           + F       V S     +  L +    R++    +Q   V P        V    E + 
Sbjct: 532 VVFRHGYGVHVYSEGGRFVRPLIHRGQYRMVCPSLVQELLVKPFPSPTERMVSMDAEFMD 591

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                    A  A I                    +     +    ++  +       Q 
Sbjct: 592 LPGIVVLTDAMSAVIPFYNHTQSPRNAYQSNMGKQAVGLPCLNYASRWDVTLDVLMYPQV 651

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL +               +     +  G   +VA + + GYN EDS++++   V   +F
Sbjct: 652 PLSRS----------KAMDALSFDTMPHGACPIVAVLTFDGYNQEDSIILNRSSVQRGMF 701

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---LKNIDECGI----ICVGAEVNPGD 892
            S   +      +  K    E    +P            + + GI    +  G  V  G 
Sbjct: 702 VSTTYKTLCECEKHVKRCEFERIMRVPVDKRRPGLVYDYLGDDGIFDSALARGMFVTAGV 761

Query: 893 ILVGKITPKGESPM 906
           ++VGK++     P 
Sbjct: 762 VVVGKMSFDQSRPE 775


>gi|83415457|gb|ABC17936.1| RNA polymerase II second largest subunit [Monoblepharella sp. M15]
          Length = 655

 Score =  247 bits (631), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 117/730 (16%), Positives = 214/730 (29%), Gaps = 103/730 (14%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ N +R+   R+ + I    R +            +  + +   +     +
Sbjct: 2    KRLDLAGPLMANLFRMLFRRLTQDISRALRKAVESHREFNMFSAVQHQIITRGLQFSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RRL++     + R     + R +H TH+
Sbjct: 62   GNWGDQRKMMQTRAGVSQVLSRYTYASTLSHLRRLNS----PIGREGKLAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++    +E     + +     D+  LS  +  +  
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMAYISVGSPVEPIVEFLHEW-TLEDLEELSPPDMRDSC 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID-FIDASPKQVVSIAAS---LIPFL 682
                N          EELV         +    ++    D   K++  +  +     P  
Sbjct: 177  KVFLNGVWIGVHRNPEELVRVFRLYRRRISISAEVSAVWDVREKELRFLTDAGRICRPLF 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D   + +      +           V  G+                   VE VD   
Sbjct: 237  VVEDMQ-LKIRKGHIAKLTSQEWKWGELVSNGL-------------------VEYVDTDE 276

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    D                           +V  G+EV              
Sbjct: 277  EETTMIAMSFDDLRDS---------------------MIVAQGEEVAARSDWEVTERLRG 315

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G +           P         + I   ++            ++       +G     
Sbjct: 316  GTVLTRYWTHAEIHPSM------ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN 369

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                         +    +  +        +    +       +   +  + AI      
Sbjct: 370  FQ-----------LRMDTMSNILYYPQKPLVTTRAMEHLHFRELPAGQNAIVAIACYSGY 418

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D+ ++  S ++E  E   RD   +      + 
Sbjct: 419  NQEDSVIMNQSSIDRGLF-RSLYYRAYMDQQKKIGSQQQEIFEKPLRDTTVKMRGASYDT 477

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  +  G     G     K+  L                     K    + +   ++
Sbjct: 478  LDEDGFVAPGTRVSDGDILIGKTIPL--------------------PKGSEELGARTARH 517

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            E   +    R        Q           +VKV +   R  Q GDK A RHG KG V  
Sbjct: 518  EKRDASTAMRGAETGIIDQVMLSTDSQGQNMVKVRIRSTRIPQMGDKFASRHGQKGTVGI 577

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  LG      G++  +        
Sbjct: 578  TYRQEDMPFTAEGICPDIIINPHAIPSRMTIGHLVECLLGKVSALAGEEGDATPFMDTTV 637

Query: 1163 GDISPLRSFL 1172
            G IS     L
Sbjct: 638  GAISNALKGL 647


>gi|190694905|gb|ACE88993.1| RNA polymerase beta subunit [Mycobacterium fortuitum]
          Length = 223

 Score =  247 bits (631), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 88/214 (41%), Positives = 117/214 (54%), Gaps = 37/214 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 39   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 98

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I       +    +        ++
Sbjct: 99   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVAAGTPEWASKLPE------QL 151

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE----- 1230
                  +                       VSTPVFDGA EE +  +L     +      
Sbjct: 152  YSAPVDSI----------------------VSTPVFDGAREEELAGLLGSTLPNRDGDVM 189

Query: 1231 ---SGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 190  VNADGKATLFDGRSGEPFPYPVTVGYMYILKLHH 223



 Score = 43.9 bits (102), Expect = 0.20,   Method: Composition-based stats.
 Identities = 30/47 (63%), Positives = 38/47 (80%)

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDD 47


>gi|300394668|gb|ADK11872.1| DNA-directed RNA polymerase II subunit two [Athelia sp. HHB-15599]
          Length = 676

 Score =  247 bits (631), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 126/805 (15%), Positives = 238/805 (29%), Gaps = 146/805 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++           + +  + +         EEN +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL--------EENAH 169

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 170  SSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +   Q + L K    ++  G +    +     +V  ++GIVE +DA     
Sbjct: 227  AGRVCRPLFIVENQQLALQKKHVHWINRGYDDDNEEFKWEQLV--KSGIVELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +     +L     +  +   +    +K G            PS  LG  
Sbjct: 285  VMISMTPEDLENSRL--QLSGVDTTQNDGEFDPAARLKAGTNTHTWTHCEIHPSMILG-- 340

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 341  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLI 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 378  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S V   +    I+ R  +D  ++S   + E+ E   RD          +    
Sbjct: 427  DSVIMNQSSVDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYDKIED 485

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  +  D      R++          ++     +  Q    
Sbjct: 486  DGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI- 544

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV V   R  Q GDK A RHG KG V     
Sbjct: 545  -------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTVGITYR 585

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +              
Sbjct: 586  QEDMPFTAEGIVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGD------------ 633

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     E++++ LR 
Sbjct: 634  -----------------------------------------ATP-FTDLTVESVSTFLRQ 651

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVT 1250
                  G  ++Y G +G      V 
Sbjct: 652  KGYQSRGLEVMYHGHSGRKLQAQVY 676



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 85/610 (13%), Positives = 172/610 (28%), Gaps = 98/610 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 184

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 185 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 244

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     +    K      +  V  L A EEE   I+     L+       
Sbjct: 245 QKKHVHW--INRGYDDDNEEFKWEQLVKSGIVELLDAEEEETVMISMTPEDLENSRLQLS 302

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +  GE     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 GVDTTQNDGEFDPAARLKAGTNTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIFLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 382 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  V   +F SI+   +  + + + +   E        +   +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 478 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 533

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 534 TENGIVDQVL 543


>gi|94410934|gb|ABF18585.1| RNA polymerase II second largest subunit [Hygrophorus pudorinus]
          Length = 691

 Score =  247 bits (631), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 127/822 (15%), Positives = 234/822 (28%), Gaps = 149/822 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSQTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +   Q + L K    ++  G      +      + K   I    DA   
Sbjct: 226  TDAGRVCRPLFIVENQQLALQKKHVKWLNQGYRDDDGEEYKWEQLIKGGIIELL-DAEEE 284

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV--KVGDEVRRNDIIADGPSTD 801
                +    +   +            ++ +      P V  K G            PS  
Sbjct: 285  ETVMISMTPEDLENSRLQQSGQDPHENDGDF----DPAVRLKAGINAHTWTHCEIHPSMI 340

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 341  LG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLT 375

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 376  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 424

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 425  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYD 483

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G   +       K+  +  D      R++          ++     +  Q
Sbjct: 484  KLEDDGLIAPGTGVIGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ 543

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VKV V   R  Q GDK A RHG KG + 
Sbjct: 544  VLI--------------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIG 583

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +       
Sbjct: 584  ITYGQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--- 640

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                   ++     + LR       G+ V    F G        
Sbjct: 641  ----------------------DLTVESVSTFLRQKGYQSRGLEVM---FHGHT------ 669

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                             G         V +G  Y  +L HMV
Sbjct: 670  -----------------GR---KLQAQVYLGPTYYQRLKHMV 691



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 81/610 (13%), Positives = 166/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVESH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSQTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +     Y   +    K         +  L A EEE   I+     L+       
Sbjct: 246 QKKHVKWLN-QGYRDDDGEEYKWEQLIKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 304

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                   G+          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 305 GQDPHENDGDFDPAVRLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 364

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 365 MGKQAMGIYLTNFLI-----------------------------------------RMDT 383

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 384 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 419

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 420 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKH 479

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         E+L +        DV      
Sbjct: 480 GTYDKLEDDGLIAPGTGVIGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 535

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 536 TENGIVDQVL 545


>gi|294471034|gb|ADE80778.1| RNA polymerase beta subunit [Lactococcus plantarum]
          Length = 163

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 67/185 (36%), Positives = 99/185 (53%), Gaps = 22/185 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E++D+P+LIE+Q  SY  FL           + L   FK + PI  
Sbjct: 1   YGKHRTRRSFSRIKEVLDLPNLIEIQTDSYQRFL----------EQSLADVFKEMLPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ +++    D  Y+ PL +T RL+          K   ++K 
Sbjct: 51  FAGTKDLEFVGYEMKEPKYTIEEARAHDANYSAPLFVTFRLV---------DKESGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD P+MT+ GTF+I G +RI+VSQL RSPG +F     +   +G   Y    IP+
Sbjct: 102 QEVFFGDFPIMTEMGTFIINGAERIIVSQLVRSPGTYFHPKVDK---NGLESYGHTTIPN 158

Query: 188 QGLWM 192
           +G W+
Sbjct: 159 RGAWL 163


>gi|88601064|gb|ABD46528.1| RNA polymerase II second largest subunit [Tulasnella sp. FCUG 2668]
          Length = 670

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 123/804 (15%), Positives = 237/804 (29%), Gaps = 150/804 (18%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + +    +              +    +  
Sbjct: 2    DDRDHFGKKRLDLAGPLLAGLFRMLFKKLTKDVFRHLQKCVETHKDFTLGAXVKNTTITQ 61

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 62   GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKP 117

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L   + ++           + +  +     + +
Sbjct: 118  RQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGTLSAPIIEFLQEWDIEPLEEHAN 177

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
                   ++      +  D       +      ++I      +  I     ++ + A  +
Sbjct: 178  GAGATKVFVNGVWVGVHRDAQELVMTLRRLRRKDDISAEVSIVRDIRERELRLYTDAGRV 237

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
               L   +++ +L+     RQ       E P+  T +          A   +   I    
Sbjct: 238  CRPLFIVENHELLIRKRHVRQLQEN-SPEQPYGWTNLLHDGVIELLDAEEEETVMICMTP 296

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            + +   +R+ +  +  +      Y + K               VK              P
Sbjct: 297  EDLENSLRTKDEFMQDAD-----YDVAK--------------RVKATMNAHTWTHCEIHP 337

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  + +   I++  ++V         
Sbjct: 338  SMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IYLTNYQVRM------- 381

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +             +       +   +    AI  
Sbjct: 382  --------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNATVAILC 421

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    ++ R   D  ++   +  E+ E   RD        
Sbjct: 422  YSGYNQEDSVIMNQSSIDRGLF-RSMYYRSYTDAEKKVGILPLEEFEKPTRDTTLRMKHG 480

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      I  G           K+  L  D                +E  QR     
Sbjct: 481  TYEKLEDDGLIAPGTGVTGEDIIIGKTAPLPPD---------------SEELGQRLRSHT 525

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T     E+   +++     GD +     + VK+ +   R  Q GDK A RHG KG
Sbjct: 526  RRDVSTPLKSTENGIVDQVLVTTNGDGL-----KFVKIRIRSTRIPQVGDKFASRHGQKG 580

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             V      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +       
Sbjct: 581  TVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGD----- 635

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     E+
Sbjct: 636  ------------------------------------------------ATP-FTELTVES 646

Query: 1219 INSMLRMADLDESGQSILYDGLTG 1242
            ++ +LR       G  ++Y G TG
Sbjct: 647  VSELLRQHGYQSRGLEVMYHGHTG 670


>gi|52699904|gb|AAU87013.1| DNA-dependent RNA polymerase II second largest subunit [Umbilicaria
            muehlenbergii]
          Length = 709

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 124/831 (14%), Positives = 238/831 (28%), Gaps = 147/831 (17%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R    G +L   +R+   ++ + + +  +    +         + +  + + +  
Sbjct: 1    HFGKKRXDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTLTNGLKY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAM 620
             TH+G +CPAET EG   GLV +L     +      E    +    + +V  +     + 
Sbjct: 117  NTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQRSP 176

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLI 679
                 ++      +  D +     V        I      + D  D   K          
Sbjct: 177  NATKVFVNGVWVGVHRDPAHLVSTVQSLRRRNLISHEVSLVRDIRDREFKIFTDAGRVCR 236

Query: 680  PFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVE 736
            P    D+  +     N+   ++ +  L+ +      T  E   AK  G   + K  G+VE
Sbjct: 237  PLFVIDNDPKSPNNGNLVLTKEHINRLEDDKDLGPDTDPEEKAAKFMGWEGLVK-QGVVE 295

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VDA            + +   V     ++  R  Q               V+       
Sbjct: 296  YVDAEE----------EETVMIVMTPEDLEISRQIQAGYAMPETTDDPNKRVKAPMNPTA 345

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N                        ++       
Sbjct: 346  HTWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQA 387

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G      D                +  +             +       +   +  + A
Sbjct: 388  MGXFLTNFDXRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 436

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 437  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRCYTDQEKR---IGMSVVEQXEKPMRSDT 492

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D                +E  Q
Sbjct: 493  LRLXHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPD---------------AEELGQ 537

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R    +K    T     E+   +++             LR V V +   +  Q GDK A 
Sbjct: 538  RTKSHVKRDVSTPLRSTENGIVDQVLX-----TTNAEGLRFVXVRMRTTKIPQIGDKFAS 592

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 593  RHGQKGTIGITYRSEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 652

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 653  DATPFTEVTVDSVSRLLR--EHGYQSRGFEVM---------------------------- 682

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                              +G +    G         V +G  Y  +L HMV
Sbjct: 683  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 709


>gi|45545305|gb|AAS67500.1| DNA-dependent RNA polymerase II second largest subunit [Baeomyces sp.
            SLJ472]
          Length = 894

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 119/867 (13%), Positives = 251/867 (28%), Gaps = 148/867 (17%)

Query: 421  NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            ++   +     +   +  ++  ++ +  G+   DD D+ G +R+   G ++   +R+   
Sbjct: 150  HISQTEGSETRKAFFLGYMVHRMLQVVLGRREPDDRDHFGKKRLDLAGPLMAGLFRMLFN 209

Query: 481  RMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQL 525
            ++ + +   +               + +  + + +     +               +SQ+
Sbjct: 210  KLVKDVYNYLKKCVESNREFNLSLGVKSTTLTNGLKYSLATGNWGDQKKAASSKAGVSQV 269

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 270  LNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 325

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L+    +      E    +      +V  +     +      ++      +  D +    
Sbjct: 326  LSLMCYITVGTPNEPIIDFMIQRSMEVLEEYEPTRSPNATKVFVNGVWVGVHRDPAHLVS 385

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAV 701
             V        I      + D  D   K          P F+  +D+ +   G  +  + +
Sbjct: 386  TVQSLRRRSLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIENDAKKANKGSLVLTKEL 445

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
                 +   + + ++            A+  G    V +    +  ++ + + +   V  
Sbjct: 446  VNRLEDDKDIPSDLDPDERA-------ARYFGWDGLVKS--GAVEFLDAEEEETVMIVMT 496

Query: 762  YRLMKFQRSNQNTCVNQRPL-VKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWH 819
               ++  R  Q          V     ++     +    T      ++   +  + +P+ 
Sbjct: 497  PEDLEISRQLQMGYTMPSSNNVDPNSRIKVPIKASSHTWTHCEIHPSMILGICASIIPFP 556

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE- 878
             +N          M  + +                                  L N DE 
Sbjct: 557  DHNQSPRNTYQSAMGKQAMGV-------------------------------FLTNYDER 585

Query: 879  -CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  + AI      +  D+ +   S +  
Sbjct: 586  MDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDR 645

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G  
Sbjct: 646  GLF-RSLFFRTYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 701

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  ++ D      R++                 +K    T     E+   
Sbjct: 702  VSGEDIIIGKTAPIAPDAEELGQRTKL---------------HIKRDVSTPLRTTENGIV 746

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +K+             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +
Sbjct: 747  DKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTAE 801

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G +  +          IS L      
Sbjct: 802  GIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSISSLLREHGY 861

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                    +G +
Sbjct: 862  QSRGFEIM-----------------------------------------------YNGHT 874

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G         V +G  Y  +L H
Sbjct: 875  ----GR---KLVAQVFLGPTYYQRLRH 894



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 96/758 (12%), Positives = 205/758 (27%), Gaps = 103/758 (13%)

Query: 212 VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           VP+     ALG+   E+IL+        +   +     +  A ++   +V+   +     
Sbjct: 67  VPIAIVFRALGVVSDEDILNHICYDRQDTPMLELLKPCIEEAFVIQDREVALDFIGKRGN 126

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDE 330
              I   K++       + ++ +  +  T             +     ++ +   +  D 
Sbjct: 127 SNSITRDKRIKYAR-DIVVKELLPHISQTEGSETRKAFFLGYMVHRMLQVVLGRREPDDR 185

Query: 331 KSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDK----NKDRKDALLDIYRVMRPGDV 386
                      + + +           + N LV D      K  +        +      
Sbjct: 186 DH------FGKKRLDLAGPLMAGLFRMLFNKLVKDVYNYLKKCVESNREFNLSLGVKSTT 239

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   S  G  ++  R    +      R          I    
Sbjct: 240 LTNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPR 299

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   + + L     + +      I + +    ++ +   +  
Sbjct: 300 QLHNTHWGLVCPAETPEGQACGLVKNLSLMCYITVGTPNEPIIDFMIQRSMEVLEEYEPT 359

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM----- 558
            +               +    +  + +S +   RR S +  +  + R     E      
Sbjct: 360 RSPNATKVF---VNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVRDIRDREFKIFTD 416

Query: 559 --RDVHPTHYGRICPAETSEGHNI---GLVSSLTSFARVNAYGFIETP---YRKVCDGKV 610
             R   P         + ++G  +    LV+ L     + +    +     Y        
Sbjct: 417 AGRVCRPLFVIENDAKKANKGSLVLTKELVNRLEDDKDIPSDLDPDERAARYFGWDGLVK 476

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCAGEEILVPREKID 662
           +  V +L A EEE   I      L+                +         I        
Sbjct: 477 SGAVEFLDAEEEETVMIVMTPEDLEISRQLQMGYTMPSSNNVDPNSRIKVPIKASSHTWT 536

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 537 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYDERMD 587

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           + A I+      +    ++  +          +   +  Y              NQ    
Sbjct: 588 TMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE--- 633

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           S  +   ++ R +  +       + E  + +S            
Sbjct: 634 ---------------DSVIMNQSSIDRGLFRSLFFRTYTDQEKRIGMS------------ 666

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            +E+FE   R           D   +       +D+ GI+  G  V+  DI++GK  P  
Sbjct: 667 VVEQFEKPMR----------SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIA 716

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                  E+L +        DV        +G+   V+
Sbjct: 717 PDA----EELGQRTKLHIKRDVSTPLRTTENGIVDKVL 750


>gi|156839387|ref|XP_001643385.1| hypothetical protein Kpol_479p15 [Vanderwaltozyma polyspora DSM
            70294]
 gi|156113993|gb|EDO15527.1| hypothetical protein Kpol_479p15 [Vanderwaltozyma polyspora DSM
            70294]
          Length = 1139

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 100/546 (18%), Positives = 182/546 (33%), Gaps = 82/546 (15%)

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             I  +E    +     E     +       +             +   G   +G I    
Sbjct: 651  FIALYEKDINENVTHMEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQ 710

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSL---RVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
               +     L+               +   ++P+G + TV  +        D    + S 
Sbjct: 711  FKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSS 770

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
                       +      + +   +   +I+ G       K   +   L  D + E    
Sbjct: 771  IDRGFGRCETRRKT--TTVLKKYPNHTQDIIGGMRVDENGKPIWQHEPLGPDGLGEVGVQ 828

Query: 1020 QWWQFAVQDEKVQRN-----VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                    ++ V  N     + + + QY+ +  I      ++I+++     +      ++
Sbjct: 829  VTSGQIYINKSVPTNSGEGVLANTQAQYKETPVIYRAPEPSRIDQVMM--SVSDNDQALI 886

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  + GDK + RHG KG+                    I++N           
Sbjct: 887  KVLLRQNRRPELGDKFSSRHGQKGVCG------------------IIVN----------- 917

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
                              + +      +  ISP          +     K+ +       
Sbjct: 918  -----------------HEDMPF---NDDGISPDIIMNPHGFPSRMTVGKMIELVSGKAG 957

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
             +    + G       F G+  E ++ +L     + SG+ +LY G+TGE     +  G I
Sbjct: 958  VLNGSLEYGTC-----FGGSKLEDMSRILVDKGFNYSGKDMLYSGITGECLQAYIFFGPI 1012

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E 
Sbjct: 1013 YYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLER 1072

Query: 1315 LTIKSD----DVV---------GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
            L I SD    DV          G     +S        +   P +  +L +E+ ++ ++ 
Sbjct: 1073 LMISSDAFEVDVCDKCGLMGYSGWCSTCKS---AEHNNKMTIPYAAKLLFQELLSMNIAP 1129

Query: 1362 DLENSR 1367
             L    
Sbjct: 1130 RLRLED 1135



 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 122/930 (13%), Positives = 262/930 (28%), Gaps = 186/930 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP----- 83
           L++    S+++F+ +++    + N   Q     V P         L++V           
Sbjct: 50  LVKQHLDSFNYFVDVDLKKIIKAN---QLILSDVDP------EFYLKYVDIRIGQRSSSS 100

Query: 84  ------PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                 P     +C  RD+TY+ P+ + +             +    I  + + +G +P+
Sbjct: 101 SKDYLTP---PHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKDVEIGRMPI 147

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++ G +++++ Q   S          +  
Sbjct: 148 MLRSNKCILNGADDSMMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEK-- 205

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EI 228
              K +    +      +     +       I+++ +    +VP+   L A G+ S+ EI
Sbjct: 206 ---KEIVQASVTSSTHERKSKTYVVT-KNGKIYLKHNSIAEEVPIAIVLKACGIISDLEI 261

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +          Q         +A   +   + +   +     + +      +    ++++
Sbjct: 262 MQLVCGNDSSYQDIFAVNLEEAAKYNIYTQRQALEYIGGKV-KTIRRQKLSILQEGIEAI 320

Query: 289 KEKGVKFLGIT-----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
               +  L +         L    +A  +V        ++  D +  K LE         
Sbjct: 321 ATTVIAHLTVEALDFREKALYVAMMARRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLL 380

Query: 344 IPILYVDSVNN-NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              L+    ++  A I   L         DALL I            S      +   + 
Sbjct: 381 FEDLFKKFNSDFKASIDKVLKKPNRAMEYDALLSINVHSNN----ITSGLNRAISTGNWS 436

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
             ++ +   G   +  R           +     + ++  +         +     L   
Sbjct: 437 LKRFKMERAGVTHVLSR-----------LSYISALGMMTRISSQFEKSRKVSGPRALQPS 485

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           +   +      +     L    ++   I++ D +  +             + +       
Sbjct: 486 QFGMLCTADTPEGEACGLVKNLALMTHITTDDEEEPIKNLCFVLGVENICLVDSATLHLN 545

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI-G 581
             +  +   +  I    R  +     + R     E   ++   + R     T  G     
Sbjct: 546 YTVHLNGTLIGTIRFPARFVS-QFRHLRRTGKVSEFISIYTNSHQRAVHIATDGGRICRP 604

Query: 582 LVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L+      + VNA    E    K+   D      V YL   EE + +IA     ++E+  
Sbjct: 605 LIIVTAGKSHVNAEHLKELLEGKLVFDDFLKLGLVEYLDVNEENDSFIALYEKDINEN-- 662

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                +  ++  P  V+   A LIP+  ++ S R    C M +Q
Sbjct: 663 ---------------------VTHMEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQ 701

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           A+                                           I   +     +   +
Sbjct: 702 AIGA-----------------------------------------IAYNQFKRIDTLLYL 720

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            IY               Q+P+VK                 D   L  G+N  VA M + 
Sbjct: 721 MIYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYS 756

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN---- 875
           GY+ ED++++++  +           +   + +      ++I   +              
Sbjct: 757 GYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTQDIIGGMRVDENGKPIWQHEP 816

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESP 905
           +   G+  VG +V  G I + K  P     
Sbjct: 817 LGPDGLGEVGVQVTSGQIYINKSVPTNSGE 846


>gi|103001947|gb|ABF71528.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            cf. chlorophanum Riefner 87-426]
          Length = 673

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 114/754 (15%), Positives = 214/754 (28%), Gaps = 128/754 (16%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 37   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 92

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +      E    +    + +V  +     +      ++      +  D 
Sbjct: 93   GLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVGVHRDP 152

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
            +     V        I      + D  D   K          P F+ ++D      G  +
Sbjct: 153  AHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNCGNLV 212

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              +       +   +   M+S   +       AK  G    V     V+  V+ + + + 
Sbjct: 213  LTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVEYVDAEEEETV 263

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAF 815
              V     ++  R  Q           +   V+          T      ++   +  + 
Sbjct: 264  MIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSMILGICASI 323

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N          M  + +   + +  +                            
Sbjct: 324  IPFPDHNQXXXNTYQSXMGKQAMG--VFLXNYXQRM------------------------ 357

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 358  ---DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 414

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G
Sbjct: 415  DRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPG 470

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +S D      R++          ++     +  Q           
Sbjct: 471  VRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL-------- 522

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              L+ VKV +   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 523  ------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 570

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            K+G   D+++NP  +PSRM +  + E  L       G +  +          +S L    
Sbjct: 571  KEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKLLR-- 628

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            E    +                                                    +G
Sbjct: 629  EHGYQSRGFEVM---------------------------------------------YNG 643

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
             +    G         V +G  Y  +L HMV DK
Sbjct: 644  HT----GR---KLVAQVFLGPTYYQRLRHMVDDK 670


>gi|229915242|gb|ACQ90683.1| RpoB [Corynebacterium pyruviciproducens]
          Length = 169

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 82/201 (40%), Positives = 108/201 (53%), Gaps = 40/201 (19%)

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +V +ILP EDMPF++DGTP+DI+LN  GVP RMN+GQ+ E HLGW     G  I+   + 
Sbjct: 1    VVGKILPQEDMPFMEDGTPIDIILNTHGVPRRMNIGQVLEVHLGWLAKS-GWAIEGDPDW 59

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             K   D                                  +      ++TPVFDGA  E 
Sbjct: 60   AKRIPDD-------------------------------LREVPPNSLLATPVFDGATNEE 88

Query: 1219 INSMLRMADLDES--------GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            I  +L     D          G++ L+DG +GEPF  PV VG  YMLKL+H+V +K++AR
Sbjct: 89   IEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLKLHHLVDEKIHAR 148

Query: 1271 STGSYSLVTQQPLGGKSNRGG 1291
            STG YS++TQQPLGGK+  GG
Sbjct: 149  STGPYSMITQQPLGGKAQFGG 169


>gi|169806377|ref|XP_001827933.1| DNA-directed RNA polymerase [Enterocytozoon bieneusi H348]
 gi|161779001|gb|EDQ31028.1| DNA-directed RNA polymerase [Enterocytozoon bieneusi H348]
          Length = 1066

 Score =  247 bits (630), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 84/395 (21%), Positives = 144/395 (36%), Gaps = 74/395 (18%)

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
            L +    +   +G     +  +L  +    Y      +    D  +    + +       
Sbjct: 726  LNKASVNRGMFNGFITMNEKIILEKNDKILYTPPIESKLKTNDIMLTYKSDGIIKTVRYE 785

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               +    K ++ +    + +       V     + R    GDK   RHG KGI + +  
Sbjct: 786  NIEMGSVEKIRVFQ----NSLTEKSNLTVIFTFRILRNPVVGDKFCSRHGQKGICAFLWN 841

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
              DMPF ++G   DI++NP   PSRM +G + E+  G A V  GK +         N DI
Sbjct: 842  EIDMPFTENGLKPDIIINPHAFPSRMTIGMLIESMCGKAAVKFGKFVNGDPFIDNKNNDI 901

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            +  +                                                 +N  L+ 
Sbjct: 902  NVNKFN-----------------------------------------------VNRKLKE 914

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
               +  G   +Y G+ G      + +G +Y  +L HMVSDK   R  G+ +  TQQP+ G
Sbjct: 915  CGFNYYGNEPMYSGVFGTELKTDIFIGLVYYQRLKHMVSDKFQVRVGGAITSTTQQPVKG 974

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTF------ 1339
            + N+GG R GEME   + A+G++ ++++ L   SD        ++      +        
Sbjct: 975  RKNKGGIRFGEMEKDTLIAHGSSALIKDRLLDCSD-----KTTFKYCYKCKNILFSSPND 1029

Query: 1340 --ETG--------TPESFNVLVKEMQALGLSIDLE 1364
              + G         P  F  L+ E+  +G++I LE
Sbjct: 1030 KCKCGGIKSKNIKMPYVFKYLLAEL--MGMNIKLE 1062



 Score = 74.3 bits (181), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 127/862 (14%), Positives = 251/862 (29%), Gaps = 169/862 (19%)

Query: 72  AMLEFVSYEFDPP---------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
            ++ F   E   P         +    +C     TY+  + + ++L+  +   F   +  
Sbjct: 38  FVMNFEKIEIHKPYVLKQDVDNRLLPHECRETGRTYSGNIFVKIKLMYKNEILFHDYRGA 97

Query: 123 KD----IKEQSIYMGDLPLMTK-------------DGTFVIKGIQRIV---VSQLHRSPG 162
                 +K     M  L +MT               G F+I G  RI+   ++  H+   
Sbjct: 98  GQLPIMVKSN---MCHLSMMTDQELLAVKEDPNEHGGFFIINGYDRIIRFHIA--HKRNW 152

Query: 163 IHFDHDKGRAS-LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-----------RRR 210
           +   + K + S  SG   Y+C I        D E   K+ I   +D           +  
Sbjct: 153 VFGIYSKPKNSIFSG---YSCSIR----SVCDDEIGQKNEIVHTVDGNIFLKCFFYHKGY 205

Query: 211 KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            +P+   L AL   ++ EI +         +       P    D  +    S        
Sbjct: 206 LIPIIYILRALQNTTDKEIYTLLNQNPRAIEFLTKSNQPYYNKDECLNYLGSRFKHIFRI 265

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKF------LGITSDCLCGLYVAEDIVNGETGEIYIE 323
                E+G++L + +L  L     KF      +      + G   +EDI      E+Y E
Sbjct: 266 DN-YKEAGEELLNRILIHLSSHIDKFNLLIYSINKLFKLIDGKIKSEDIDLSSNHELYTE 324

Query: 324 AG--DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           A    +  ++ LEE        I  L+   V  N Y  N   T+      D    I    
Sbjct: 325 AQLIPLCIKEHLEEFKKLFKTRIIKLFKREV-KNQYRDNETDTEITTQIDD----IMSTN 379

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
           R  +++     + +F+  F      +L     + +  +++               +    
Sbjct: 380 RSTNINDTVEFDKLFSDEFMIKKIVELFKKTDLDIGTKIHKFLSTGNITTYNCSDLLQTS 439

Query: 442 ILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               L    G I+  +   +    S G    N                     +  + P+
Sbjct: 440 GFTFLS---GRINYWEFASHFYSVSRGAFFSNL----------------KITSVRKLQPE 480

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                 P+ +          L         ++   +    + L Q GV+       M  V
Sbjct: 481 SFGFFCPINTPDGSLCG---LLTYLTQQCEITCSKYIFDTNILYQLGVSFINLNNNMIPV 537

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                           + I L+  L ++   N    IE  Y         ++++  S  +
Sbjct: 538 FYN-----GKIMGYTSYPIKLIEDLRNYRCKNKL-KIEIVYEFGDKI---DEII--SICD 586

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           + +  I +  +  +    +           E   V     ++ +     + SI A+ IPF
Sbjct: 587 DISLLIRKVWNKKNNMEEYIGIKEQVFLDIELGTVH-NTFNYKEIDINNMFSIIANTIPF 645

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            +++ S R +  C M +QA+ +                                      
Sbjct: 646 ADHNPSPRNIYQCQMAKQAMGIA------------------------------------- 668

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                        +      Y      +++   C  + PL                    
Sbjct: 669 ----AYNIKYRVDNKLYNINYLQHPLIQTSNYQCFEKFPL-------------------- 704

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                 G N +VA + + GY+ ED++++++  V+  +F        +++           
Sbjct: 705 ------GFNCIVAVLSYTGYDMEDAIILNKASVNRGMFNGFITMNEKIILEKNDKILYTP 758

Query: 862 TRDIPNVSEEGLKNIDECGIIC 883
             +    + + +      GII 
Sbjct: 759 PIESKLKTNDIMLTYKSDGIIK 780


>gi|120561269|gb|ABM27019.1| RNA polymerase II second largest subunit [Chytriomyces hyalinus]
          Length = 883

 Score =  246 bits (629), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 142/980 (14%), Positives = 277/980 (28%), Gaps = 178/980 (18%)

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +    +     +     ++   G + D++ +E+I +       +  +      A+     
Sbjct: 61   VIKTSLPYIKQDVPIVVVFRALGIISDKEIMEKICYDFDDTPMLELLKPCIEEAF----- 115

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                 + R+ AL  I R       S  +  E    +      K  L  VG          
Sbjct: 116  ---PIQTREVALDYIGRR----GQSVGATKEKRIKYAMDILQKEMLPHVG---------- 158

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             T       +      +I  L+     +   DD D+ G +R+   G ++   +R+   ++
Sbjct: 159  -TKAHQETRKAYFFGYMIHRLLLATMQRRDFDDRDHFGKKRLDLAGPLMTQLFRILFRKL 217

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF------------------CSSQLSQ 524
             + I  ++      +         + + + V +                      + +SQ
Sbjct: 218  TKDITRQLQKHVESNKAFNIQSLERSLDANVLKNGLKYSLATGNWGDQSKASQARAGVSQ 277

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            +       S ++H RRL++       R     + R +H T +G +CPAET EG   GLV 
Sbjct: 278  VLNRYTFASTLSHLRRLNSPT----DRDGKLAKPRQLHNTQWGMVCPAETPEGQACGLVK 333

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +++  A +                    ++   + +EE    + +  + +  +G +    
Sbjct: 334  NMSLMAIITVGTSSGPFIE------HLEELSMET-LEEVGPSVLKDATKVFLNGMWLGVH 386

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                   E +   R      + SP+  +    +        D+ R+     +  +    L
Sbjct: 387  REPENLVENLRSTRRNC---EVSPEVSIVHDVTECELRLYTDAGRISRPLFIVDKESQKL 443

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDI 761
              +   V           +   +     G+VE +D       +I     DL+ +      
Sbjct: 444  LIQRAHVL--ALRDPETDA-TFVDLLSEGVVEYIDTEEEETAMIAMSPDDLESARKAARG 500

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
               +K +R+          L                PS  LG       +  + +P+  +
Sbjct: 501  IPEIKKERNRTERSQTISAL------TLNWTHCEIHPSMILG-------ICASIIPFPDH 547

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +   I +  F+     T        + +                
Sbjct: 548  NQSPRNCYQSAMGKQAMG--IFLTSFQYRMDQTMNILFYPQKPLACTRSMEY-------- 597

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
                                    +   +  +  I      +  D+ +   S +   +  
Sbjct: 598  -------------------LRFRELPAGQNAIVCICCYSGYNQEDSLIMNQSSIDKGLF- 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ +  ID  ++    + E IE   R+          +       +  G         
Sbjct: 638  RSLYFKVYIDTEKKEGMTQLETIEKPMRENTLRMRQGSYDKLDVDGLVSPGVRVSGDDIL 697

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  L  D      R+           ++     +  Q                    
Sbjct: 698  IGKTVPLPKDSEEMGQRTSGHTKRDDSTPLKSTEAGIIDQ-------------------- 737

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VKV +   R  Q GDK A RHG KG        EDMPF +DG   DI+
Sbjct: 738  VMVTTNADGYKFVKVRMRSIRVPQIGDKFASRHGQKGTCGITYRNEDMPFTRDGITPDII 797

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  LG      G +  +         +IS               
Sbjct: 798  INPHAIPSRMTIGHLVECLLGKVATHTGHEGDATPFTDVNVEEISRELEAFG-------- 849

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                      +          +L++G T
Sbjct: 850  -----------------------------------------FQKRGF-----EVLFNGHT 863

Query: 1242 GEPFDRPVTVGYIYMLKLNH 1261
            G+  +  V  G  Y  +L H
Sbjct: 864  GKKLNAQVYTGPTYYQRLKH 883



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 71/528 (13%), Positives = 146/528 (27%), Gaps = 42/528 (7%)

Query: 203 HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    VP+     ALG +  +EI+         +   +     +  A  +   +V+
Sbjct: 68  YIKQD----VPIVVVFRALGIISDKEIMEKICYDFDDTPMLELLKPCIEEAFPIQTREVA 123

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G+ V  + +K     +  L+++ +  +G  +            +      + 
Sbjct: 124 LDYIGRR-GQSVGATKEKRIKYAMDILQKEMLPHVGTKAHQETRKAYFFGYMIH---RLL 179

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +      D    +      +                +         K  KD    + + +
Sbjct: 180 LATMQRRDFDDRDHFGKKRLDL----------AGPLMTQLFRILFRKLTKDITRQLQKHV 229

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                      E   +     +        G      + +       + + +    + + 
Sbjct: 230 ESNKAFNIQSLERSLDANVLKNGLKYSLATGNWGDQSKASQARAGVSQVLNRYTFASTLS 289

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER------- 489
            L  L     R+GK       +     +    E  + Q    +  M              
Sbjct: 290 HLRRLNSPTDRDGKLAKPRQLHNTQWGMVCPAETPEGQACGLVKNMSLMAIITVGTSSGP 349

Query: 490 -ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            I  ++  S+   + +    +  A   F     L    E  N +  +  TRR   +    
Sbjct: 350 FIEHLEELSMETLEEVGPSVLKDATKVFLNGMWLGVHREPENLVENLRSTRRNCEVSPEV 409

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                       ++        P    +  +      L   A V A    ET    V D 
Sbjct: 410 SIVHDVTECELRLYTDAGRISRPLFIVDKESQ---KLLIQRAHVLALRDPETDATFV-DL 465

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPRE---KID 662
                V Y+   EEE   IA +   L+          E+   R   E             
Sbjct: 466 LSEGVVEYIDTEEEETAMIAMSPDDLESARKAARGIPEIKKERNRTERSQTISALTLNWT 525

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +  P  ++ I AS+IPF +++ S R      M +QA+ +      +
Sbjct: 526 HCEIHPSMILGICASIIPFPDHNQSPRNCYQSAMGKQAMGIFLTSFQY 573


>gi|120561271|gb|ABM27020.1| RNA polymerase II second largest subunit [Chytriomyces hyalinus]
          Length = 883

 Score =  246 bits (629), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 142/980 (14%), Positives = 277/980 (28%), Gaps = 178/980 (18%)

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            +    +     +     ++   G + D++ +E+I +       +  +      A+     
Sbjct: 61   VIKTSLPYIKQDVPIVVVFRALGIISDKEIMEKICYDFDDTPMLELLKPCIEEAF----- 115

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
                 + R+ AL  I R       S  +  E    +      K  L  VG          
Sbjct: 116  ---PIQTREVALDYIGRR----GQSVGATKEKRIKYAMDILQKEMLPHVG---------- 158

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
             T       +      +I  L+     +   DD D+ G +R+   G ++   +R+   ++
Sbjct: 159  -TKAHQETRKAYFFGYMIHRLLLATMQRRDFDDRDHFGKKRLDLAGPLMTQLFRILFRKL 217

Query: 483  ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF------------------CSSQLSQ 524
             + I  ++      +         + + + V +                      + +SQ
Sbjct: 218  TKDITRQLQKHVESNKAFNIQSLERSLDANVLKNGLKYSLATGNWGDQSKASQARAGVSQ 277

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            +       S ++H RRL++       R     + R +H T +G +CPAET EG   GLV 
Sbjct: 278  VLNRYTFASTLSHLRRLNSPT----DRDGKLAKPRQLHNTQWGMVCPAETPEGQACGLVK 333

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +++  A +                    ++   + +EE    + +  + +  +G +    
Sbjct: 334  NMSLMAIITVGTSSGPFIE------HLEELSMET-LEEVGPSVLKDATKVFLNGMWLGVH 386

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                   E +   R      + SP+  +    +        D+ R+     +  +    L
Sbjct: 387  REPENLVENLRSTRRNC---EVSPEVSIVHDVTECELRLYTDAGRISRPLFIVDKESQKL 443

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDI 761
              +   V           +   +     G+VE +D       +I     DL+ +      
Sbjct: 444  LIQRAHVL--ALRDPETDA-TFVDLLSEGVVEYIDTEEEETAMIAMSPDDLESARKAARG 500

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
               +K +R+             V             PS  LG       +  + +P+  +
Sbjct: 501  IPEIKKERNRTERSQT------VSALTLNWTHCEIHPSMILG-------ICASIIPFPDH 547

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +   I +  F+     T        + +                
Sbjct: 548  NQSPRNCYQSAMGKQAMG--IFLTSFQYRMDQTMNILFYPQKPLACTRSMEY-------- 597

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
                                    +   +  +  I      +  D+ +   S +   +  
Sbjct: 598  -------------------LRFRELPAGQNAIVCICCYSGYNQEDSLIMNQSSIDKGLF- 637

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ +  ID  ++    + E IE   R+          +       +  G         
Sbjct: 638  RSLYFKVYIDTEKKEGMTQLETIEKPMRENTLRMRQGSYDKLDVDGLVSPGVRVSGDDIL 697

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  L  D      R+           ++     +  Q                    
Sbjct: 698  IGKTVPLPKDSEEMGQRTSGHTKRDDSTPLKSTEAGIIDQ-------------------- 737

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VKV +   R  Q GDK A RHG KG        EDMPF +DG   DI+
Sbjct: 738  VMVTTNADGYKFVKVRMRSIRVPQIGDKFASRHGQKGTCGITYRNEDMPFTRDGITPDII 797

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  LG      G +  +         +IS               
Sbjct: 798  INPHAIPSRMTIGHLVECLLGKVATHTGHEGDATPFTDVNVEEISRELEAFG-------- 849

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                      +          +L++G T
Sbjct: 850  -----------------------------------------FQKRGF-----EVLFNGHT 863

Query: 1242 GEPFDRPVTVGYIYMLKLNH 1261
            G+  +  V  G  Y  +L H
Sbjct: 864  GKKLNAQVYTGPTYYQRLKH 883



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 71/528 (13%), Positives = 146/528 (27%), Gaps = 42/528 (7%)

Query: 203 HVRIDRRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    VP+     ALG +  +EI+         +   +     +  A  +   +V+
Sbjct: 68  YIKQD----VPIVVVFRALGIISDKEIMEKICYDFDDTPMLELLKPCIEEAFPIQTREVA 123

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +    G+ V  + +K     +  L+++ +  +G  +            +      + 
Sbjct: 124 LDYIGRR-GQSVGATKEKRIKYAMDILQKEMLPHVGTKAHQETRKAYFFGYMIH---RLL 179

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +      D    +      +                +         K  KD    + + +
Sbjct: 180 LATMQRRDFDDRDHFGKKRLDL----------AGPLMTQLFRILFRKLTKDITRQLQKHV 229

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIK 441
                      E   +     +        G      + +       + + +    + + 
Sbjct: 230 ESNKAFNIQSLERSLDANVLKNGLKYSLATGNWGDQSKASQARAGVSQVLNRYTFASTLS 289

Query: 442 ILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER------- 489
            L  L     R+GK       +     +    E  + Q    +  M              
Sbjct: 290 HLRRLNSPTDRDGKLAKPRQLHNTQWGMVCPAETPEGQACGLVKNMSLMAIITVGTSSGP 349

Query: 490 -ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
            I  ++  S+   + +    +  A   F     L    E  N +  +  TRR   +    
Sbjct: 350 FIEHLEELSMETLEEVGPSVLKDATKVFLNGMWLGVHREPENLVENLRSTRRNCEVSPEV 409

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                       ++        P    +  +      L   A V A    ET    V D 
Sbjct: 410 SIVHDVTECELRLYTDAGRISRPLFIVDKESQ---KLLIQRAHVLALRDPETDATFV-DL 465

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE---ELVFCRCAGEEILVPRE---KID 662
                V Y+   EEE   IA +   L+          E+   R   E             
Sbjct: 466 LSEGVVEYIDTEEEETAMIAMSPDDLESARKAARGIPEIKKERNRTERSQTVSALTLNWT 525

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
             +  P  ++ I AS+IPF +++ S R      M +QA+ +      +
Sbjct: 526 HCEIHPSMILGICASIIPFPDHNQSPRNCYQSAMGKQAMGIFLTSFQY 573


>gi|307343522|emb|CBJ18678.1| RNA polymerase B subunit [Micromonospora sp. SGA21]
          Length = 206

 Score =  246 bits (629), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 93/210 (44%), Positives = 120/210 (57%), Gaps = 38/210 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +      +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAAWKKQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              G++ L+DG +GEP   P+ VGYIY+LKL
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKL 206


>gi|307343518|emb|CBJ18676.1| RNA polymerase B subunit [Micromonospora sp. SGA16]
          Length = 200

 Score =  246 bits (629), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 20   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 79

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 80   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 128

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 129  -------------------AHESEPDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 169

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 170  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLN 200


>gi|119644045|gb|ABL85603.1| RNA polymerase II second largest subunit [Hypotrachyna caraccensis]
          Length = 708

 Score =  246 bits (629), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 116/741 (15%), Positives = 224/741 (30%), Gaps = 90/741 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P    D+  R     N+         L      +  T  +       G   + K  
Sbjct: 237  RVCRPLFVIDNDPRSSNRGNLVLTKEHVQKLELDRENWATTEPDVREEADMGWQGLVKE- 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +        +N +  +N+R    +        
Sbjct: 296  GVVEYVDAEEEETIMIVMTPEDLEISRQLQAGFDMPEANPDE-LNKRVKAPMNPTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +    +  E  +   
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXSYNYEQRMDT- 406

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 407  ----------------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRS 1170
             +  +          +S L  
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR 675


>gi|255713708|ref|XP_002553136.1| KLTH0D09812p [Lachancea thermotolerans]
 gi|238934516|emb|CAR22698.1| KLTH0D09812p [Lachancea thermotolerans]
          Length = 1144

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 75/346 (21%), Positives = 138/346 (39%), Gaps = 66/346 (19%)

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +   + QY  +  +      + I+++     +      ++KV +   R  + GDK + RH
Sbjct: 854  LTQSQAQYRETPVVYRAPEPSHIDQVMM--SVSENDQALIKVLLRQNRRPELGDKFSSRH 911

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG+                    I++N                             + 
Sbjct: 912  GQKGVCG------------------IIVN----------------------------HED 925

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
            L  + +            + ++       +++      ++       +G       F G+
Sbjct: 926  LPFNDQGVVP--------DIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGS 977

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              E ++ +L     + SG+ +LY G+TGE     +  G IY  KL HMV DK++AR+ G 
Sbjct: 978  KLENMSQILVNHGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGP 1037

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRV-- 1328
             +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L I SD    DV  +  +  
Sbjct: 1038 RAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCNKCGLMG 1097

Query: 1329 YE---SIVAG-NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
            Y    +   G  +  +   P +  +L +E+ ++ ++  L+      
Sbjct: 1098 YSGWCTSCKGAENVIKMTIPYAAKLLFQELLSMNIAPRLKLEDVFE 1143



 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 114/926 (12%), Positives = 262/926 (28%), Gaps = 176/926 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP----- 83
           L++    S+++F+ +++    + N   Q     V P         L++V           
Sbjct: 55  LVKQHLDSFNYFVDVDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGHRSTSS 105

Query: 84  ------PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                 P     +C  RD+TY+ P+ + +             +    I  + + +G +P+
Sbjct: 106 SKDYIVP---PHECRLRDMTYSAPVYVDIEYT----------RGRNIIMHRDVEIGRMPI 152

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++ G +++++ Q   S          + +
Sbjct: 153 MLRSNKCILNGASEKDMAKINECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKA 212

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILST 231
           +    + +     ++           D I+++ +    +VP+   L A G+ S+ EI+  
Sbjct: 213 IVQASVTSST--HERKSK-TYVITKNDKIYLKHNSIAEEVPIVLVLKACGIVSDLEIMQL 269

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
                   Q      F   A   +   + +   +         +    L  G ++++   
Sbjct: 270 VCGNDSSYQDIFAVNFEEVAKMKIYTQQQALEYIGSKVKTVRRQKLSTLQEG-IEAIATT 328

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +  L + +       +    +   T  + +   +       + + +  +          
Sbjct: 329 VIAHLTVEALDFREKAL---YIAVMTRRVVMAMHNPKMVDDRDYVGNKRLEL-------- 377

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                 +         K   D   +I +V++  + +    A    N    +        +
Sbjct: 378 --AGQLMSLLFEDLFKKFNNDFKANIDKVLKKPNRAMEYDALLSINVHSNNISSGLNRAI 435

Query: 412 GRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                +++        V H    +     + ++  +         +     L   +   +
Sbjct: 436 STGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGML 495

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
                 +     L    ++   I++ D +  + +           V +         +  
Sbjct: 496 CTSDTPEGEACGLVKNLALMTHITTDDEEEPIKKLCFLLGVECINVVDSDSLHLNYCVYL 555

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL---VS 584
           +   +  I    +  +     + R+    E   ++   + +     T  G        V+
Sbjct: 556 NGTIVGVIRFPTKFVS-HFRNLRRSGKVSEFISIYTNSHQKAVHIATDGGRICRPLIIVN 614

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
              S         +   + +  D      V YL   EE + +IA     L+         
Sbjct: 615 EGKSLVTAQHLRQLLDGHLQFDDFLKLGLVEYLDVNEENDSFIALYERDLEP-------- 666

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                          +I  ++  P  V+   A LIP+  ++ S R    C M +QA+   
Sbjct: 667 ---------------RITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA- 710

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                                                   I   +     +   + IY  
Sbjct: 711 ----------------------------------------IAYNQFKRIDTLLYLMIYP- 729

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q+P+VK                 D   L  G+N  VA M + GY+ E
Sbjct: 730 -------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDIE 766

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----DIPNVSEEGLKNIDECG 880
           D++++++  +           +   + +      +++      D         K +   G
Sbjct: 767 DALVLNKSSIDRGFGRCETRRKLTTVLKRYPNHTQDMVGGMRVDESGEPIWQHKPLGPDG 826

Query: 881 IICVGAEVNPGDILVGKITPKGESPM 906
           +  VG +V  G I V K  P   S  
Sbjct: 827 LGEVGMKVESGQIYVNKSVPTNASDS 852


>gi|55583702|gb|AAV53370.1| RNA polymerase II second largest subunit [Ramaria rubella]
          Length = 677

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 122/805 (15%), Positives = 235/805 (29%), Gaps = 145/805 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L + +R+   ++ + +    +              +    + + + 
Sbjct: 1    DHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVKPNTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSPSPPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSATPCTKVFVNGVWLG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVA-KRAGIVEQVD 739
                D+ RV     +       L+ +   ++  G              +  + G++E +D
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLHQGYSDEDPAREQYKWDSLIKGGVIELLD 285

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A       +    +   +     +    Q +  +   +    +K              PS
Sbjct: 286  AEEEETVMISMTPEDLENSRL--QQQGMQTNVNDGEFDPAARLKSVMHAHTWTHCEIHPS 343

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N                        ++       +G  
Sbjct: 344  MILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIY 378

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I               +  +             +       +   +  + AI   
Sbjct: 379  LTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCY 427

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    ++ R  +D  + S   + E+     RD         
Sbjct: 428  SGYNQEDSVIMNQSSIDRGLF-RSMYYRSYMDMEKSSGIHQLEEFTKPTRDTTLRMKHGT 486

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G           K+  +  +                +E  Q+     +
Sbjct: 487  YDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPE---------------SEELGQKTSSHTR 531

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                T     E    +++      D       R VKV V   R  Q GDK A RHG KG 
Sbjct: 532  RDVSTPLKSTESGIVDQVLITTGSD-----GHRFVKVRVRSTRIPQIGDKFASRHGQKGT 586

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +        
Sbjct: 587  IGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------ 640

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                                                           +TP F     E++
Sbjct: 641  -----------------------------------------------ATP-FTELTVESV 652

Query: 1220 NSMLRMADLDESGQSILYDGLTGEP 1244
            ++ LR       G  ++Y G TG  
Sbjct: 653  STXLRKQGYHSRGLEVMYHGHTGRK 677



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 87/617 (14%), Positives = 169/617 (27%), Gaps = 100/617 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +       K  KD    + + +       F++  ++      +  KY L   G  
Sbjct: 12  GPLLASLFRMLFRKLTKDVYRYLQKCVETH--KEFNLNLAVKPNTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     L
Sbjct: 129 TPEGQACGLVKNLALMACISVGSPSPPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWL 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH-NIG 581
               +  N +  I   RR   +                ++        P    E      
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +    +  +         K         +  L A EEE   I+     L+      
Sbjct: 249 QKKHIKWLHQGYSDEDPAREQYKWDSLIKGGVIELLDAEEEETVMISMTPEDLENSRLQQ 308

Query: 642 EELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           + +      GE          +        +  P  ++ I AS+IPF +++ S R     
Sbjct: 309 QGMQTNVNDGEFDPAARLKSVMHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 368

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 369 AMGKQAMGIYLTNFLI-----------------------------------------RMD 387

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 388 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 423

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVS 869
            + + GYN EDS+++++  +   +F S++   +  M + + +   EE T+        + 
Sbjct: 424 ILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDMEKSSGIHQLEEFTKPTRDTTLRMK 483

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +++ G+I  G  V   DI++GK  P       PE + L       +   RD S 
Sbjct: 484 HGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPI-----PPESEELGQ--KTSSHTRRDVST 536

Query: 930 RVPSGVSGTVVDVRIFN 946
            + S  SG V  V I  
Sbjct: 537 PLKSTESGIVDQVLITT 553


>gi|90101523|gb|ABD85200.1| RpoB [Staphylococcus aureus]
          Length = 271

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 159/271 (58%), Positives = 201/271 (74%), Gaps = 3/271 (1%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFI
Sbjct: 1   RRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFI 60

Query: 599 ETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++
Sbjct: 61  ETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVM 120

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME
Sbjct: 121 AKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGME 180

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF+RSN  TC
Sbjct: 181 HVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTC 240

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            NQRP+V VGD V  N+I+ADGPS +LG++A
Sbjct: 241 YNQRPIVAVGDVVEYNEILADGPSMELGEMA 271


>gi|315258105|gb|ADT91640.1| RNA polymerase beta subunit [Lactococcus lactis subsp. hordniae]
 gi|315258107|gb|ADT91641.1| RNA polymerase beta subunit [Lactococcus lactis subsp. lactis]
          Length = 162

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 70/184 (38%), Positives = 101/184 (54%), Gaps = 22/184 (11%)

Query: 8   NGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITA 67
            G  R R+ F +  E+I +P+LIEVQ  SY +FL          +EGL   FK +FPI  
Sbjct: 1   YGKHRTRRSFSRIKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDN 50

Query: 68  FSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
           F+G   LEFV YE   PK+ V++    D  Y+ P+ +T RL+          K   ++K 
Sbjct: 51  FAGTMELEFVGYEMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NKETGELKT 101

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
           Q ++ GD PLMT+ GTF+  G +R++VSQL RSPG +F     +A  +G   +    IP+
Sbjct: 102 QEVFFGDFPLMTEMGTFINNGSERLIVSQLVRSPGSYFH---LKADKNGLESFGHTTIPN 158

Query: 188 QGLW 191
           +G W
Sbjct: 159 RGAW 162


>gi|295981674|emb|CBL88370.1| RNA polymerase beta subunit [Streptococcus sp. 2777-2-07]
          Length = 237

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 98/290 (33%), Positives = 135/290 (46%), Gaps = 71/290 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 19   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 67

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 68   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 121

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 122  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 181

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 182  ATPVFDGASSEDLW---------------------------------------------- 195

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
             A  +        A +D   ++ILYDG TGEPFD  V+VG +YM+KL+HM
Sbjct: 196  -ATVKE-------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIKLHHM 237



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 59/93 (63%), Positives = 72/93 (77%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNV E+ L+ +DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG
Sbjct: 1   EEITREIPNVGEDALRQLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  DKSREVRDTSLRVPHGADGVVRDVKIFTRANGD 93


>gi|126636177|gb|ABO25739.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 257

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 179/250 (71%), Positives = 208/250 (83%)

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           QDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RD
Sbjct: 1   QDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 60

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAM
Sbjct: 61  VHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAM 120

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIP
Sbjct: 121 EESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIP 180

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGAAI AKR+GIV+QVDA
Sbjct: 181 FLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSGAAIGAKRSGIVDQVDA 240

Query: 741 IRIVIRSVEG 750
            RIVIR+ E 
Sbjct: 241 TRIVIRATED 250


>gi|307343478|emb|CBJ18656.1| RNA polymerase B subunit [Micromonospora sp. GUI40]
          Length = 211

 Score =  246 bits (629), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 123/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 140  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 181  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLN 211


>gi|109289351|gb|ABG29164.1| RNA polymerase II second largest subunit [Entyloma arnoseridis]
          Length = 695

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 131/830 (15%), Positives = 248/830 (29%), Gaps = 158/830 (19%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ R I   +     D         + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLSGLFRMLFKKLTRDIYRHLEKCVEDQKEFFINTAVKSATITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  + ++     +     + +    + +  +   E
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMSLISVGSQSQPIIEFLEEF-GLDQLTDMR-RE 174

Query: 622  EENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            +        N            LV      R   +         D  +   +        
Sbjct: 175  DARSTKVFVNGVWLGTHQDPTGLVSTLRGLRRKDDISTEVSVVHDIREKELRLYTDAGRV 234

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            + P    +  +R L    ++R+ +  L+        G E          +     G++E 
Sbjct: 235  MRPLFIVNKDDRSLF---IKRKHMNWLQH-------GTEDGSDFGWEDLVQ---CGVIEY 281

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP---LVKVGDEV-RRNDI 793
            +DA        E  +   +     Y     Q +N        P   LV +          
Sbjct: 282  LDAEE-----EETVMISMSIEDLNYSRAYHQNTNSVRDTLSDPSARLVSLHTYSGDTWTH 336

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                P+  LG       +  + +P+  +N          M  + +   +++  +    R 
Sbjct: 337  CEIHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYLTNY--QMRM 385

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              +         P  +   ++++                             +   +  +
Sbjct: 386  DTMANILYYPQKPLGTTRAMQHL-------------------------KFRELPAGQNAI 420

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    ++ R   D  ++S  VE E  E  +R+   
Sbjct: 421  VAILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTYTDLEKKSGMVEMEVFEKPSRETTI 479

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +          G           K+  L  D      RS+          +  
Sbjct: 480  RLKHGTYDKLDADGLCAPGTRVSGEDIIIGKTVPLPCDSEELGLRSKLHTKRDASMPL-- 537

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                            E    +++     GD      ++ VKV V   R  Q+GDK A R
Sbjct: 538  -------------KSTESGIVDQVLVTTNGD-----GVKFVKVRVRSTRVPQTGDKFASR 579

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  
Sbjct: 580  HGQKGTIGITYRQEDMPFTVEGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGD 639

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S                         +VL+       G+ +       
Sbjct: 640  ATPFTSLTVEAVS-------------------------NVLKGFGYQSRGLEIM------ 668

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                             +G +    G         V +G  Y  +L HMV
Sbjct: 669  ----------------YNGHT----GR---KLQAQVYLGPTYYQRLKHMV 695


>gi|307343516|emb|CBJ18675.1| RNA polymerase B subunit [Micromonospora sp. SGA9]
          Length = 207

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAAWKKQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I  +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|94410924|gb|ABF18581.1| RNA polymerase II second largest subunit [Porotheleum fimbriatum]
          Length = 689

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 128/822 (15%), Positives = 240/822 (29%), Gaps = 151/822 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLSLAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +         L A+EE N
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWG-------LEALEE-N 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
               A A++ +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  ANTA-ASTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 224

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ RV     +      +LK +     T  E+   +      + K   +          
Sbjct: 225  TDAGRVCRPLFIVDNQELVLKKKHVRWLTQGETDEGEEFKWEQLVKGGVVELLDAEEEET 284

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +       D  TS +    +       +    +    +K G            PS  LG 
Sbjct: 285  VMISMTPEDLETSRLQQAGVDPHANDGE---FDPAARLKAGINAHTWTHCEIHPSMILG- 340

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                        ++       +G       
Sbjct: 341  ------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFL 376

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I               +  +             +       +   +  + AI      + 
Sbjct: 377  IRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 425

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S      Q+E   +      + +    Y 
Sbjct: 426  EDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGI---AQLEEFEKPLRQNTLRMKHGTYD 481

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   I  G   V       K+  +  D      R++          ++     +  Q
Sbjct: 482  KLDDDGLISPGTGVVGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ 541

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VKV V   R  Q GDK A RHG KG + 
Sbjct: 542  VLI--------------------TTNSEGQKFVKVRVRSIRVPQIGDKFASRHGQKGTIG 581

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +       
Sbjct: 582  ITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--- 638

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                   ++     + LR     + G+ V               
Sbjct: 639  ----------------------DLTVESVSAYLRQKGYQQRGLEVM-------------- 662

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                      G +    G         V +G  Y  +L HMV
Sbjct: 663  --------YHGHT----GR---KLQAQVYLGPTYYQRLKHMV 689



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 88/635 (13%), Positives = 177/635 (27%), Gaps = 102/635 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVESH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI------DSVMPQDLINAKPVVSAVCEFFCSSQLS 523
             + Q    +  +       + S         +    + L       ++   F     + 
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLEALEENANTAASTKVFVNGVWMG 185

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
              +  N +  I   RR   +            +   ++        P    +   + L 
Sbjct: 186 VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVDNQELVLK 245

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
                +  +      E    K         V  L A EEE   I+     L+        
Sbjct: 246 KKHVRW--LTQGETDEGEEFKWEQLVKGGVVELLDAEEEETVMISMTPEDLETSRLQQAG 303

Query: 644 LVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +      GE          +        +  P  ++ I AS+IPF +++ S R      M
Sbjct: 304 VDPHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 363

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                                                   + 
Sbjct: 364 GKQAMGIFLTNFLI-----------------------------------------RMDTM 382

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           + +  Y       +     +  R                        +L  G+N +VA +
Sbjct: 383 ANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAIL 418

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
            + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +   
Sbjct: 419 CYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIAQLEEFEKPLRQNTLRMKHG 478

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G+I  G  V   DI++GK  P         ++        +    RD S  +
Sbjct: 479 TYDKLDDDGLISPGTGVVGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPL 531

Query: 932 PSGVSGTVVDVRIFNRHGIDK--NERSISVEREQI 964
            S  +G V  V I       K    R  S+   QI
Sbjct: 532 KSTENGIVDQVLITTNSEGQKFVKVRVRSIRVPQI 566


>gi|254803156|gb|ACT82828.1| RNA polymerase B-subunit [Staphylococcus nepalensis]
          Length = 270

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 156/270 (57%), Positives = 200/270 (74%), Gaps = 3/270 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRKRAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIETNSITDQIDYLTADEEDSYVVAQANSNLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGM 180

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E V A+ SGAAIVAK  G VE V++  I++R  +E D       +D Y L KF+RSN  T
Sbjct: 181 EHVAARDSGAAIVAKNKGRVEHVESNEILVRQLIEEDGQEYEGEIDRYPLAKFKRSNTGT 240

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           C NQRP+V  GD V + +I+ADGPS +LG+
Sbjct: 241 CYNQRPIVATGDVVAKGEILADGPSMELGE 270


>gi|52699868|gb|AAU86995.1| DNA-dependent RNA polymerase II second largest subunit [Rhytisma
            acerinum]
          Length = 708

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 128/826 (15%), Positives = 242/826 (29%), Gaps = 143/826 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    R+ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLAKLFRGLFRRLTQDVYKYLQRCVENNREFNLTLGVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L    +  V         +    + +V  +   L +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIIEFMIQRNMEVLEEYEPLRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +   + V        I      I D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPAHLVKTVQDLRRQHMISHEVSLIRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA--KRAGIVEQVDA 740
             ++D +    G  +  +       +   +   M+    +  G          G+VE VDA
Sbjct: 238  VDNDHDSPNKGNLVLNKTHISRLEDDQTMPINMDEAQREEHGYFGFKGLIDNGVVEYVDA 297

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +       I    +  + +++  +N+R    V             PS 
Sbjct: 298  EEEETIMIVMTPEDLDISRQIQAGYQI-QPDESGDLNKRVKAPVNPTAHIWTHCEIHPSM 356

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 357  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXL 391

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               D                +  +             +       +   +  + AI    
Sbjct: 392  TNFDXRM-----------DTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 440

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +   ++ + L  
Sbjct: 441  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNLVEAFEKPYRNDTLKLKH 496

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K+  L+ D                +E  QR    
Sbjct: 497  GTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAPD---------------NEELGQRTKGH 541

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +K    T     E+   +++             LR VKV +   +  Q GDK A RHG K
Sbjct: 542  VKRDASTPLRSTENGIVDQVLV-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 596

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF + G   DI++NP  +PSRM +  + E  L       G +  +   
Sbjct: 597  GTIGITYRQEDMPFTRQGIVPDIIINPHAIPSRMTIAHLIECQLSKVGTLRGLEGDATPF 656

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    +    +                                       
Sbjct: 657  TEVTVDSVSKLLR--DHGYQSRGFEVM--------------------------------- 681

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                          G +    G      +  V +G  Y  +L HMV
Sbjct: 682  ------------YHGHT----GR---KMNAQVFLGPTYYQRLRHMV 708


>gi|307343532|emb|CBJ18683.1| RNA polymerase B subunit [Micromonospora sp. SR6]
          Length = 207

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAGWKKALRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|307343568|emb|CBJ18701.1| RNA polymerase B subunit [Micromonospora halophytica]
          Length = 206

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 123/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPF++DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFMEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++    ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVQGDDAEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 206


>gi|307343524|emb|CBJ18679.1| RNA polymerase B subunit [Micromonospora sp. SGB14]
          Length = 207

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAGWKKALRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|207692935|gb|ACI25202.1| RNA polymerase beta [Mycobacterium aurum]
          Length = 214

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 89/214 (41%), Positives = 115/214 (53%), Gaps = 38/214 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I        A      + S     
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIDVASTPEWAANLPEDMLSAPADS 149

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
            I                             V+TPVFDGA E  +  +L     +      
Sbjct: 150  I-----------------------------VATPVFDGAREGELEGLLGSTLPNRDGDVM 180

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 181  VNAEGKSQLFDGRSGEPFPYPVTVGYMYILKLHH 214


>gi|307343550|emb|CBJ18692.1| RNA polymerase B subunit [Micromonospora coerulea]
          Length = 207

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAAWKKQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLSSTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|307343494|emb|CBJ18664.1| RNA polymerase B subunit [Micromonospora sp. CR30]
          Length = 207

 Score =  246 bits (628), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 123/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 136  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  ASGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|140084150|gb|ABO84924.1| RpoB [Paenibacillus amylolyticus]
          Length = 239

 Score =  246 bits (627), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 89/209 (42%), Positives = 116/209 (55%), Gaps = 54/209 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 85   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 144

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV IVLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 145  TPVQIVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGAKEYD----------- 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 194  ----------------------------------VFD---------TMEEAGMQRNGKTV 210

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            LYDG TGE F+R VTVG ++M+KL HMV 
Sbjct: 211  LYDGRTGEEFEREVTVGVMHMIKLAHMVD 239



 Score = 89.7 bits (221), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 63/93 (67%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 61  EKAREVRDTSLRVPHGTDGIVVDVKVFTRENGD 93


>gi|14601675|ref|NP_148216.1| DNA-directed RNA polymerase subunit beta [Aeropyrum pernix K1]
 gi|5105547|dbj|BAA80860.1| DNA-directed RNA polymerase subunit B [Aeropyrum pernix K1]
          Length = 1169

 Score =  246 bits (627), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 133/333 (39%), Gaps = 70/333 (21%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            R   K               ++VKV V   R  + GDK A RHG KG+            
Sbjct: 879  RLGEKGVVDMVVISTTVERNKLVKVRVRNLRIPEIGDKFASRHGQKGV------------ 926

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                                 +G IF             +      +     D+      
Sbjct: 927  ---------------------IGMIF------------PRYDMPYTEEGIEPDVILNPHA 953

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            +   +  G   E+I+        R  +        +TP F   D + +   L     D +
Sbjct: 954  IPSRMTVGQLLEEIAGKLGAIKGRFVD--------ATPFF-KEDIDGLRIELLKEGYDPN 1004

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             + ++YDG TG+  + P+T+G  Y  +L HMV+DK++AR+TG   L+T+QP  GK+ +GG
Sbjct: 1005 AREVMYDGRTGQIIEAPITIGVAYYQRLYHMVADKIHARATGRVHLLTRQPTEGKARQGG 1064

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVAGN- 1336
             R GEME  C+  +GA+ +L++ +   SD       +  G       R +V E  + G  
Sbjct: 1065 LRFGEMERDCLVGHGASMLLRDRMLDNSDAYVMYVCNTCGNIAWFNRRKKVLECPIHGEE 1124

Query: 1337 -DTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             D      P +F +L++E+ ++ +  +L+ +  
Sbjct: 1125 GDIRPVKVPYAFKLLLQEITSMMIKPELKVADK 1157



 Score =  145 bits (367), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 110/631 (17%), Positives = 224/631 (35%), Gaps = 74/631 (11%)

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
            ++DAL  +   + PG                   D   L  +G              + 
Sbjct: 296 TKEDALKYLGNRIAPGQPLDVR-----IRRAEEFLDTQLLPHLGNR-----------PED 339

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR--------LGLL 480
           R  +   +  +   ++ L  GK   DD D LGN+R+R  G+++   +R            
Sbjct: 340 RIKKAYFLAEMANRVLQLYLGKRGEDDKDFLGNKRLRLAGDLIAELFRESLEALANTMAQ 399

Query: 481 RMERSIKERISSVDIDSVMPQDLINA-KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           ++E  + ER        V P  + +  K  ++        + +SQ  +  N +S ++H R
Sbjct: 400 KLEEQLAERRQIRLDFLVRPTIISDRLKGAIATGNWGQDRTGISQQLDRTNWISLLSHLR 459

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN---AYG 596
           R+ +     ++R +A  E RD+H +H+GR CP ET EG N GLV +L   A ++      
Sbjct: 460 RVIS----PLSRGQAHFEARDLHGSHWGRYCPFETPEGINCGLVKNLALSAYISVGVDES 515

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT----------EELVF 646
            +E    K         ++  +    E   I    + +  +G              ++  
Sbjct: 516 VVEEILVKDLGVAPLERILEEAKQAGEPPEIMLKGTKVFINGRPLGYHPNGAELARKIRE 575

Query: 647 CRCAGEEILVPREKIDFIDASP------KQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            R + +  +    ++                      + P +  ++    L   ++++ +
Sbjct: 576 LRRSDKLEVERPWEVSVYHLREGEIDELYVNTDSGRLMRPVVVVENGEPKLTREHVEKLS 635

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVA--------KRAGIVEQVDAIRIVIRSVEGDL 752
              +          +E +  +    A++A        +   +   V AI  V  +  G L
Sbjct: 636 RGEITFWDLVKQGVVEMLDPEEEQNALIAELPWEVTKEHTHMELWVPAIVGVAAATIGYL 695

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS-----TDLGDLAL 807
           + + S  + Y+    +++     +N R  +     + +   +    +         +   
Sbjct: 696 EHNQSPRNTYQAAMAKQALGVYALNYRIRLDSHSYLLQYPQVPIVQTRMLDIMGYNERPA 755

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP- 866
           G+NM+VA M + GYN ED+++ ++  +   +  +     +  +  +   G  +       
Sbjct: 756 GQNMVVAIMSYTGYNIEDALIFNKGSIDMGLARAYFFRVYTGIENEYPGGERDRITLPKP 815

Query: 867 -----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                         ++  GI+    EV  G+IL+G+++P       P       +     
Sbjct: 816 DEVYDYRGAAAYAKLEADGIVAPETEVEGGEILIGRVSP-------PRFLGEGRVISMAT 868

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           V  RDTS+ +  G  G V  V I      +K
Sbjct: 869 VRRRDTSIPMRLGEKGVVDMVVISTTVERNK 899



 Score =  110 bits (274), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 92/685 (13%), Positives = 198/685 (28%), Gaps = 90/685 (13%)

Query: 71  AAMLEFVSYEFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
              + F    F  P           +    +C  R +TY+ PL + + ++  ++ E T  
Sbjct: 84  DVKIVFGKARFKEPMAREVIESFDRRVTPFECRVRGITYSAPLMVEMTIVQDNMIEKTRE 143

Query: 120 KSIKD----IK-----------EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
             I D    +K           E  I MG+ P     G F+I G ++++V+Q   +    
Sbjct: 144 VKIADFPVMVKSVLDPLSKYDEETVIEMGEDPG-DPGGYFIINGSEKVIVAQEDLAVNRI 202

Query: 165 FDHDKGRASLSGKLLYACRIIPD-----QGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFL 218
                   + + ++ +  + +       +   +D   D    +   + R R ++P+   L
Sbjct: 203 IV--NKSTAATARITHTAKAVSTVLGLRRQAIVDRMSD--GTLEASLSRLRYRIPLVVLL 258

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI-DTGEQVIESG 277
            ALG++ +        +I+ +   D          L  G  ++ +  D        I  G
Sbjct: 259 RALGLEKD-------MEIMLAVSADPDVQREMLPSLEKGRALAPTKEDALKYLGNRIAPG 311

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           + L   + ++ +    + L    +           +      +         E   + + 
Sbjct: 312 QPLDVRIRRAEEFLDTQLLPHLGNRPEDRIKKAYFLAEMANRVLQLYLGKRGEDDKDFLG 371

Query: 338 HSEIRDIPILYVDSVNNN--AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
           +  +R    L  +    +  A         + +  +   + +  ++RP  +S   +  ++
Sbjct: 372 NKRLRLAGDLIAELFRESLEALANTMAQKLEEQLAERRQIRLDFLVRPTIISD-RLKGAI 430

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
               +          + R      L+       R I             DL         
Sbjct: 431 ATGNWGQDRTGISQQLDRTNWISLLSHLR----RVISPLSRGQAHFEARDLHGSHWGRYC 486

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                      + + L     + +   E  ++E +      + + + L  AK        
Sbjct: 487 PFETPEGINCGLVKNLALSAYISVGVDESVVEEILVKDLGVAPLERILEEAKQAGEPPEI 546

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
               +++      +          R        + R+      R    + Y  +   E  
Sbjct: 547 MLKGTKVFINGRPLGYHPNGAELARKI----RELRRSDKLEVERPWEVSVYH-LREGEID 601

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVC----------DGKVTNDVVYLSAMEEENR 625
           E +       L     V   G  +     V           D      V  L   EE+N 
Sbjct: 602 ELYVNTDSGRLMRPVVVVENGEPKLTREHVEKLSRGEITFWDLVKQGVVEMLDPEEEQNA 661

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA                       E      ++   ++     +V +AA+ I +LE++
Sbjct: 662 LIA-----------------------ELPWEVTKEHTHMELWVPAIVGVAAATIGYLEHN 698

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPF 710
            S R      M +QA+ +       
Sbjct: 699 QSPRNTYQAAMAKQALGVYALNYRI 723


>gi|300394726|gb|ADK11901.1| DNA-directed RNA polymerase II subunit two [Pseudomerulius curtisii]
          Length = 652

 Score =  246 bits (627), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 121/727 (16%), Positives = 228/727 (31%), Gaps = 91/727 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSATPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +      + K  GIVE +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLSQGFRDEDGEEFKWEHLVKG-GIVELLDA 284

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    D   +     + +    ++ +     R  +K G            PS 
Sbjct: 285  EEEETVMISMTPDDLENSRLQSQGIDPHANDGDYDPAAR--LKAGTNAHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AIF   
Sbjct: 378  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIFCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDMEKKSGVQQLEEFEKPTRDNTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 486  DKLEDDGLIAPGSGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q      ++   F+                 + VKV V   R  Q GDK A RHG KG +
Sbjct: 546  Q-----VLISTNFE---------------GQKFVKVRVRSSRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +      
Sbjct: 586  GITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDL 645

Query: 1161 ANGDISP 1167
                +S 
Sbjct: 646  TVESVST 652



 Score =  120 bits (300), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 84/623 (13%), Positives = 172/623 (27%), Gaps = 102/623 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH-NIG 581
               +  N +  I   RR   +            +   ++        P    E      
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +   ++       E    K         V  L A EEE   I+     L+     +
Sbjct: 249 QKKHIKWLSQGFRDEDGEE--FKWEHLVKGGIVELLDAEEEETVMISMTPDDLENSRLQS 306

Query: 642 EELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           + +      G+     R             +  P  ++ I AS+IPF +++ S R     
Sbjct: 307 QGIDPHANDGDYDPAARLKAGTNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 366

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 367 AMGKQAMGIYLTNFLI-----------------------------------------RMD 385

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 386 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 421

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVS 869
              + GYN EDS+++++  +   +F SI+   +  M + + +   E        +   + 
Sbjct: 422 IFCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKKSGVQQLEEFEKPTRDNTLRMK 481

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +++ G+I  G+ V+  DI++GK  P         ++        +    RD S 
Sbjct: 482 HGTYDKLEDDGLIAPGSGVSGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVST 534

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S  +G V  V I       K
Sbjct: 535 PLKSTENGIVDQVLISTNFEGQK 557


>gi|307343520|emb|CBJ18677.1| RNA polymerase B subunit [Micromonospora sp. SGA18]
          Length = 207

 Score =  246 bits (627), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGEDAEWKRQLRSIE---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|46277275|gb|AAS86828.1| RNA polymerase II second largest subunit [Acer circinatum]
          Length = 580

 Score =  246 bits (627), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 112/727 (15%), Positives = 207/727 (28%), Gaps = 147/727 (20%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +   ++ +  +G +       R     +   R     +D + +  V     L       
Sbjct: 54   AVIPQSTKIFVNGCWVG---IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+K         + ++  + S              +     + 
Sbjct: 111  DYGRCSRPLFIVEKQRLLIKKRD------IHALQQRESTEVGGWHELVSKGFI---EYID 161

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               E     S +  D+ +         + C     +                        
Sbjct: 162  TEEEETTMISMTINDLVQARLNPEDAYSGCYTHCEI----------------------HP 199

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            +L   +  + +P+  +N          M  + +     I       R   L         
Sbjct: 200  SLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQK 255

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            P V+   ++++                             +      + AI      +  
Sbjct: 256  PLVTTRAMEHL-------------------------HFRQLPAGINAIVAIACYSGYNQE 290

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ ++  ++ +E      R           +    
Sbjct: 291  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRCNTMGMRHGSYDKLDD 349

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T ++                  DE   ++    +  +  S
Sbjct: 350  DGLAPPGTRVSGEDVIIGKTTPIAQ-----------------DEAQGQSSRYTRRDHSIS 392

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VKV V   R  Q GDK + RHG KG V     
Sbjct: 393  LRHSETGIVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYT 447

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 448  QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNI 507

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 508  SKALHKCGYQMRGFETM------------------------------------------- 524

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                 +G +    G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G
Sbjct: 525  ----YNGHT----GR---RLPAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEG 573

Query: 1286 KSNRGGQ 1292
            +S  GG 
Sbjct: 574  RSRDGGL 580



 Score =  111 bits (277), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 72/496 (14%), Positives = 143/496 (28%), Gaps = 101/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++       + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAAYPILEFLEEWGTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             +   F     +    +    +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQSTKIFVNGCWVGIHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +        +      +   +  V  G     + Y+   EEE   I+
Sbjct: 116 SRPLFIVEKQRLLIKKRDIHALQQRESTEVGGWHELVSKGF----IEYIDTEEEETTMIS 171

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R   E+           +  P  ++ + AS+IPF +++ S 
Sbjct: 172 M----------TINDLVQARLNPEDAYSGC--YTHCEIHPSLILGVCASIIPFPDHNQSP 219

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +      F                    R   +  V          
Sbjct: 220 RNTYQSAMGKQAMGIYVTNYQF--------------------RMDTLAYV---------- 249

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 250 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 274

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----R 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 275 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRC 334

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK TP  +           A        
Sbjct: 335 NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE---------AQGQSSRYT 385

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S+ +    +G V
Sbjct: 386 RRDHSISLRHSETGIV 401


>gi|123979394|gb|ABM81522.1| RNA polymerase II second largest subunit [Thelotrema lepadinum]
          Length = 703

 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 114/824 (13%), Positives = 235/824 (28%), Gaps = 147/824 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ + +R    R+ + + +  +              + +  + + +     +
Sbjct: 2    KRLDLAGPLMASLFRNLFNRLTKDVYKYLQKCVESNQPFNVTLGVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWTEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L    +  V + G     +    + ++  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGSPGEPIIEFMVQRNMELLEEYEPTRSPHITK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      I D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPTHLYNTVLSLRRRNMISHEVSLIRDIRDQEFKIFTDAGRVSRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             ++D+     G  M  +       +   + T ++    +        +  G    + A  
Sbjct: 238  IDNDNRSPSKGSLMLTKEHIHRLEDDRELPTDLDPDEKQE-------RYFGWEGLIKA-- 288

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
              +  ++ + + +         ++  R  Q       P       V+    +A    T  
Sbjct: 289  GAVEYLDAEEEETVMIAMTPEDLEISRQVQAGYAPPEPSDDPNSRVKAPVNLAAHTWTHC 348

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N          M  + +                       
Sbjct: 349  EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV--------------------- 387

Query: 862  TRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                       L N DE    +  +             +       +   +  + AI   
Sbjct: 388  ----------FLTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACY 437

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R  +++ +R        +E   +    E + L 
Sbjct: 438  SGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPLRSETLRLK 493

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               Y +L +   I  G           K+  ++ D      R++          ++    
Sbjct: 494  HGTYEKLDDDGLIAPGVRVSGEDVIIGKTAPIAPDTEELGQRTKLHNKRDASTPLRSTEN 553

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +                  ++K+          L+ VKV +   +  Q GDK A RHG 
Sbjct: 554  GI------------------VDKVLL--TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQ 593

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 594  KGTIGITYRQEDMPFTAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATP 653

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E    +                                      
Sbjct: 654  FTEVTVDSVSRLLR--EHGYQSRGFEVM-------------------------------- 679

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                          +G +    G         V  G  Y  +L 
Sbjct: 680  -------------YNGHT----GR---KLRAQVFFGPTYYQRLR 703


>gi|123979384|gb|ABM81517.1| RNA polymerase II second largest subunit [Parmeliella sp. AFTOL 334]
          Length = 631

 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 112/739 (15%), Positives = 214/739 (28%), Gaps = 129/739 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 13   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 68

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +      E    +    + ++  +   L +      ++      +  D 
Sbjct: 69   GLVKNLALMCYITVGSPSEPIIEFMITRNMEILEEYEPLRSPNATKVFVNGVWVGVHRDP 128

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
            +    +V        I      + D  D   K          P F+  +D      G  +
Sbjct: 129  AHLVSVVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIENDHKSPNYGNLV 188

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              +   L   E   +G  ++    +       AK  G    V   + V+  V+ + + + 
Sbjct: 189  LTKEHILRLEEDKELGGDIDPEERE-------AKFMGWEGLV--NQGVVEYVDAEEEETV 239

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVK-VGDEVRRNDIIADGPSTDLG-DLALGRNMLVA 814
              V     ++  R  Q     + P        V+          T      ++   +  +
Sbjct: 240  MIVMTPEDLEISRHIQAGFAIEEPSDDDPNRRVKAPMNPTAHTWTHCEIHPSMILGICAS 299

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                        ++       +G                 
Sbjct: 300  IIPFPDHNQSPRN------------------TYQSAMGKQAMGXXXXXXXXXX------- 334

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 335  ----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 390

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  
Sbjct: 391  IDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMKSDTLKLKHGTYDKLDDDGIVAP 446

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D      R++          ++     +  Q          
Sbjct: 447  GVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL------- 499

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                               LR VKV +   +  Q GDK A RHG KG +      EDMPF
Sbjct: 500  -------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPF 546

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   D+++NP  +PSRM +  + E  L       G +                    
Sbjct: 547  TSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------ 588

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++ +LR       
Sbjct: 589  -----------------------------------ATP-FTEVTVDSVSRLLREHGYQSR 612

Query: 1232 GQSILYDGLTGEPFDRPVT 1250
            G  ++Y+G TG      V 
Sbjct: 613  GFEVMYNGHTGRKLVAQVF 631



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 76/532 (14%), Positives = 154/532 (28%), Gaps = 67/532 (12%)

Query: 428 VRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
            + + +    + +  L        R+GK       +  +  +    E  + Q    +  +
Sbjct: 15  SQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 74

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSR 534
                  + S     +      N + +         +A   F     +    +  + +S 
Sbjct: 75  ALMCYITVGSPSEPIIEFMITRNMEILEEYEPLRSPNATKVFVNGVWVGVHRDPAHLVSV 134

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +   RR   +             +RD+    +     A         + +   S    N 
Sbjct: 135 VQSLRRRHWIS-------HEVSLVRDIRDREFKIFTDAGRVCRPLFVIENDHKSPNYGNL 187

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
               E   R   D ++  D+       EE          L   G                
Sbjct: 188 VLTKEHILRLEEDKELGGDIDP-----EEREAKFMGWEGLVNQG---------------- 226

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                 ++++DA  ++ V I       LE     +            P  + +AP   T 
Sbjct: 227 -----VVEYVDAEEEETVMIVM-TPEDLEISRHIQAGFAIEEPSDDDPNRRVKAPMNPTA 280

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                 +   + I+   A I+   D  +    + +  +     G           +  N 
Sbjct: 281 HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXXDTMANI 340

Query: 775 -CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
               Q+PL                      +L  G+N +VA   + GYN EDS+++++  
Sbjct: 341 LYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 390

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  V
Sbjct: 391 IDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMKSDTLKLKHGTYDKLDDDGIVAPGVRV 450

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 451 SGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 498


>gi|307343528|emb|CBJ18681.1| RNA polymerase B subunit [Micromonospora sp. SR2]
          Length = 206

 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 124/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 176  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLN 206


>gi|307343556|emb|CBJ18695.1| RNA polymerase B subunit [Micromonospora eburnea]
          Length = 207

 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 177  SSGKARLFDGRSGEPLPDPIAVGYIYILKLN 207


>gi|307343566|emb|CBJ18700.1| RNA polymerase B subunit [Micromonospora fulviviridis]
          Length = 206

 Score =  246 bits (627), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDTEWKRQLRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 176  RSGKAQLFDGRSGEPLPDPIAVGYVYILKLN 206


>gi|300394706|gb|ADK11891.1| DNA-directed RNA polymerase II subunit two [Gyrodon lividus]
          Length = 690

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 122/819 (14%), Positives = 240/819 (29%), Gaps = 145/819 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +      + K +GI+E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEDFKWEHLVK-SGIIELLDA 284

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +       +    ++ +     R  +K G            PS 
Sbjct: 285  EEEETVMISMTPEDLENSRLQSAGINPHENDGDFDPAAR--LKAGISAHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 378  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFERPTRDSTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G N         K+  +  D      R++          ++     +  
Sbjct: 486  DKLEDDGLIAPGTNVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VK+ V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKIRVRSTRVPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +      
Sbjct: 586  GITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 643

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 644  -----------------------DLTVESVSTFLRQKGYQSRGLEVM------------- 667

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                       G +       G+     V +G  Y  +L
Sbjct: 668  ---------YHGHT-------GKKIQAQVYLGPTYYQRL 690



 Score =  122 bits (305), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 81/617 (13%), Positives = 170/617 (27%), Gaps = 111/617 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                         ++   YR       K      +  +  L A EEE   I+     L+
Sbjct: 249 QKK--------HIKWLNQGYRDDDGEDFKWEHLVKSGIIELLDAEEEETVMISMTPEDLE 300

Query: 636 EDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                +  +      G+          +        +  P  ++ + AS+IPF +++ S 
Sbjct: 301 NSRLQSAGINPHENDGDFDPAARLKAGISAHTWTHCEIHPSMILGVCASIIPFPDHNQSP 360

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 361 RNTYQSAMGKQAMGIYLTNFLV-------------------------------------- 382

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 383 ---RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAG 415

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD--- 864
           +N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   EE  R    
Sbjct: 416 QNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFERPTRD 475

Query: 865 -IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
               +       +++ G+I  G  V   DI++GK  P         E+L +        D
Sbjct: 476 STLRMKHGTYDKLEDDGLIAPGTNVRGEDIIIGKTAPI----PPDSEELGQRTRTHTRRD 531

Query: 924 VRDTSLRVPSGVSGTVV 940
           V        +G+   V+
Sbjct: 532 VSTPLKSTENGIVDQVL 548


>gi|300394714|gb|ADK11895.1| DNA-directed RNA polymerase II subunit two [Leucogyrophana
            olivascens]
          Length = 677

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 124/807 (15%), Positives = 235/807 (29%), Gaps = 146/807 (18%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ R +    +              +  + + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         EE
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EE 168

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            N + +   + +  +G +       R     +   ++     D SP+  V           
Sbjct: 169  NAHSSSPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRL 225

Query: 684  NDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D+ RV     +   Q + L K    ++  G      +     +V  + GI+E +DA  
Sbjct: 226  YTDAGRVCRPLFIVENQQLSLQKKHVKWLNQGQNDEGEEYKWEQLV--KGGIIELLDAEE 283

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   +       +    + +      R  +K G            PS  L
Sbjct: 284  EETVMISMTPEDLENSRLQSAGIDPHTNEEEYDPAAR--LKAGINAHTWTHCEIHPSMIL 341

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 342  G-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 376

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              +               +  +             +       +   +  + AI      
Sbjct: 377  FLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 425

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          + 
Sbjct: 426  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDK 484

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 485  IEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQV 544

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 545  LI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGI 584

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +           
Sbjct: 585  TYRQEDMPFTSEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------- 635

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     E+++  
Sbjct: 636  --------------------------------------------ATP-FTDLTVESVSKF 650

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPV 1249
            L        G  ++Y G TG      V
Sbjct: 651  LYQKGYQSRGLEVMYHGHTGRKLQAQV 677


>gi|307343544|emb|CBJ18689.1| RNA polymerase B subunit [Micromonospora chersina]
          Length = 201

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 21   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 80

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 81   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDEEWKRQLRSIE---------- 129

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 130  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 170

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 171  RSGKAQLFDGRSGEPLPDPIAVGYVYILKLN 201


>gi|52699792|gb|AAU86958.1| DNA-dependent RNA polymerase II second largest subunit [Calicium
            viride]
          Length = 714

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 125/835 (14%), Positives = 236/835 (28%), Gaps = 146/835 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R    ++ + +++  +    +         + +  + + +    
Sbjct: 1    GKKRLDLAGPLLAGLFRTLFXKLNKDVEKXLKNCIENNREFNLTLGVKSTTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +  T
Sbjct: 61   ATGNWGEQKKASSSKAGVSQVLXRFTXASTLSHLRRTNT----PIGRDGKIAKPRQLXNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV        V+    ++    +      +   +   L++   
Sbjct: 117  HWGLVCPAETPEGQACGLVXXXALMCXVSVGTPVDGIVEFLLQRQMETLEEYDPLTSPXA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP- 680
               ++      +  + +     V     G  I      + D  D   K +      L P 
Sbjct: 177  TKIFLNGVWVGIHRNPAHLVSAVQSLRRGHVIAHEVSLVRDIRDREFKILTDQGRVLRPL 236

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVD 739
            F+  +D      G  +  +           +   M+    +            G+VE VD
Sbjct: 237  FVIENDVKSPXSGALVLNKEHIERLESDRXIPXDMDKEEREKLTFGWHGLINEGVVEYVD 296

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A            + +   V     +   RS Q   V                +  D   
Sbjct: 297  AEE----------EETVMIVMTPYDLSVSRSVQAGYV----------------LPEDDND 330

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +    N       W       SM+  I   ++            ++       +G
Sbjct: 331  DPNRRVKAPINPTAP--TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG 388

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                  D    +           +  +             +       +   +  + AI 
Sbjct: 389  XXXXXXDQRMET-----------MAHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 437

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + 
Sbjct: 438  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMNTLEQFEKPMRSDTLR 493

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L E   I+ G           K+  + +D      R+++         ++  
Sbjct: 494  LKHGTYEKLDEDGIIIPGARVSGEDIIIGKTAPIPADAEELGQRTKYHSKRDASTPLRST 553

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               L  Q                             LR VKV +   +  Q GDK A RH
Sbjct: 554  ESGLVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRH 593

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 594  GQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 653

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L    E    +                                    
Sbjct: 654  TPFTEVTVDSVSRLLR--EHGYQSRGFEVM------------------------------ 681

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV DK+ A
Sbjct: 682  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIXA 714



 Score =  112 bits (279), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 88/575 (15%), Positives = 159/575 (27%), Gaps = 90/575 (15%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + +  K   S  G  ++  R    +      R          I    
Sbjct: 52  ITNGLKYSLATGNWGEQKKASSSKAGVSQVLXRFTXASTLSHLRRTNTPIGRDGKIAKPR 111

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   +         + +      I E +    ++++   D +
Sbjct: 112 QLXNTHWGLVCPAETPEGQACGLVXXXALMCXVSVGTPVDGIVEFLLQRQMETLEEYDPL 171

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM----- 558
            +               +       + +S +   RR   +  +  + R     E      
Sbjct: 172 TSPXATKIF---LNGVWVGIHRNPAHLVSAVQSLRRGHVIAHEVSLVRDIRDREFKILTD 228

Query: 559 --RDVHPTHYGRICPAETSEGH---NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-- 611
             R + P             G    N   +  L S   +      E   +          
Sbjct: 229 QGRVLRPLFVIENDVKSPXSGALVLNKEHIERLESDRXIPXDMDKEEREKLTFGWHGLIN 288

Query: 612 -NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              V Y+ A EEE   I      L    S     V                         
Sbjct: 289 EGVVEYVDAEEEETVMIVMTPYDLSVSRSVQAGYV------------------------- 323

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
                   +P  +NDD NR +               +AP   T       +   + I+  
Sbjct: 324 --------LPEDDNDDPNRRV---------------KAPINPTAPTWTHCEIHPSMILGI 360

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVR 789
            A I+   D  +    + +  +     G        + +         Q+PL        
Sbjct: 361 CASIIPFPDHNQSPRNTYQSAMGXQAMGXXXXXXDQRMETMAHILYYPQKPL-------- 412

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA   + GYN EDS+++++  +   +F S+    +  
Sbjct: 413 --ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTD 470

Query: 850 MARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
             +   +   E     +  D   +     + +DE GII  GA V+  DI++GK  P    
Sbjct: 471 QEKRIGMNTLEQFEKPMRSDTLRLKHGTYEKLDEDGIIIPGARVSGEDIIIGKTAPIPAD 530

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                ++        K    RD S  + S  SG V
Sbjct: 531 AEELGQRT-------KYHSKRDASTPLRSTESGLV 558


>gi|307343542|emb|CBJ18688.1| RNA polymerase B subunit [Micromonospora chalcea]
          Length = 210

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDEEWKRQLRSIN---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 180  GSGKAQLFDGRSGEPLPDPIAVGYVYILKLN 210


>gi|307343506|emb|CBJ18670.1| RNA polymerase B subunit [Micromonospora sp. SG10]
 gi|307343526|emb|CBJ18680.1| RNA polymerase B subunit [Micromonospora sp. SR1]
          Length = 207

 Score =  245 bits (626), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 124/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 177  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLN 207


>gi|258562148|gb|ACV81796.1| RNA polymerase II second largest subunit [Entorrhiza casparyana]
          Length = 646

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 123/735 (16%), Positives = 211/735 (28%), Gaps = 132/735 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 43   GVSQVLNRYTFASTLSHLRRCNT----PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQAC 98

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA-NSSLDEDGS 639
            GLV +L   A ++           + +  + N   + S      +         +  D +
Sbjct: 99   GLVKNLALMAYISVGSASAPIIEFLEEWGMENLDEFSSNSPHATKVFVNGVWIGVHRDPA 158

Query: 640  FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                 +       +I      +  I     ++ + A  +   L   ++N++L+       
Sbjct: 159  HLVTTIRRLRRCVDISPEVSVVRDIREKELRLYTDAGRVCRPLFVVENNQLLLAKPHVEW 218

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                        G G                  GIVE +DA       +    +      
Sbjct: 219  LRNHQTPSGDDFGWGSLV-------------ENGIVEFIDAEEEETVMICMTPEDLEHSR 265

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                             +    VK+             PS  LG       +  + +P+ 
Sbjct: 266  RYQETGIM---PAQITDDPSARVKMFTFAHTWTHCEIHPSMILG-------ICASIIPFP 315

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N          M  + +     I       R   +         P      ++++   
Sbjct: 316  DHNQSPRNTYQSAMGKQAMG----IYVTNFQVRMDTMANILYYPQKPLAITRSMEHL--- 368

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                                      +   +  + AI      +  D+ +   S +   +
Sbjct: 369  ----------------------RFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 406

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                IF R  +D  ++   +  E+ E   RD                  I  G       
Sbjct: 407  F-RSIFYRTYMDSEKKMGMMVMEEFERPTRDTTLRLKHGTYEKLEGDGLIAPGTRVSGED 465

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  D                +E  QR     K    T     E+   +++  
Sbjct: 466  IIIGKTAPIPPD---------------AEELGQRTKTHTKRDVSTPLRSTENGIVDQVMI 510

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
               G       L+ VKV V   R  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 511  TTNG-----EGLKFVKVRVRSTRVPQVGDKFASRHGQKGTIGVTYRQEDMPFTVEGITPD 565

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +G + E  L       G +                            
Sbjct: 566  LIINPHAIPSRMTIGHLVECLLSKVSTIAGNEGD-------------------------- 599

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     EA++ +LR       G  ++Y+G
Sbjct: 600  ---------------------------ATP-FTDVTVEAVSKILRANGYQSRGFEVMYNG 631

Query: 1240 LTGEPFDRPVTVGYI 1254
             TG+     V +G  
Sbjct: 632  HTGQKLAAQVFLGPT 646


>gi|52699902|gb|AAU87012.1| DNA-dependent RNA polymerase II second largest subunit [Trichoglossum
            hirsutum]
          Length = 709

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 121/829 (14%), Positives = 240/829 (28%), Gaps = 145/829 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFKKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L    +  V         +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSDPIIEFMVQRNMEVLEEYEPQRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF-- 681
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 178  VFVNGVWVGVHRDAAHLVRTVQHLRRTHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            ++N+ ++       + ++ +  L+ +         E    +  G        GIVE VDA
Sbjct: 238  IDNNPASPNRGNLVLNKEHIMKLEDDKDLDPALDPEQREGQMFG-WKGLVNQGIVEYVDA 296

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                  +V   + P    +       +     N+  N+R    +             PS 
Sbjct: 297  EEEE--TVMIVMTPEDLEISRQLQAGYAVPEDNSDPNKRVKAPINPTAHTWTHCEIHPSM 354

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  +     + +  ++            
Sbjct: 355  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQ--AXGVFLTNYDQRM--------- 396

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 397  ------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 438

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 439  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYSDQEKR---IGMNILETFEKPMRSDTLKLKH 494

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  +S +      R+++         ++     
Sbjct: 495  GTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPESEELGQRTKYHVKRDVSTPLRSTENG 554

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 555  IVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 594

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 595  GTIGITYRSEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPF 654

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 655  TEVTVDSVSKLLR--EHGYQSRGFEVM--------------------------------- 679

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                         +G +    G         V +G  Y  +L HMV  K
Sbjct: 680  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXK 709



 Score =  129 bits (323), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 92/636 (14%), Positives = 176/636 (27%), Gaps = 138/636 (21%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFKKLTKDVYKYLQKCVENNR--EFNLTLGVKSTTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSDPIIEFMVQRNMEVLEEYEPQRSPNATKVFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +  + H RR   +             +RD+    +     A         
Sbjct: 185 VGVHRDAAHLVRTVQHLRRTHLIS-------HEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 582 LVSSLTSFARVN---------------------AYGFIETPYRKVCDGKVTNDVVYLSAM 620
           + ++  S  R N                          E              V Y+ A 
Sbjct: 238 IDNNPASPNRGNLVLNKEHIMKLEDDKDLDPALDPEQREGQMFGWKGLVNQGIVEYVDAE 297

Query: 621 EEENRYIA------------QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           EEE   I             QA  ++ ED S   + V                   +  P
Sbjct: 298 EEETVMIVMTPEDLEISRQLQAGYAVPEDNSDPNKRVKAPINP-----TAHTWTHCEIHP 352

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
             ++ I AS+IPF +++ S R      M +QA                            
Sbjct: 353 SMILGICASIIPFPDHNQSPRNTYQSAMGKQAXG-------------------------- 386

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                          V  +       + + +  Y               Q+PL       
Sbjct: 387 ---------------VFLTNYDQRMDTMANILYYP--------------QKPL------- 410

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                          +L  G+N +VA   + GYN EDS+++++  +   +F S+    + 
Sbjct: 411 ---ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYS 467

Query: 849 VMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              +   +   E     +  D   +       +D+ GI+  G  V+  DI++GK  P   
Sbjct: 468 DQEKRIGMNILETFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPI-- 525

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
              +PE + L           RD S  + S  +G V
Sbjct: 526 ---SPESEELGQRTKYHVK--RDVSTPLRSTENGIV 556


>gi|88601058|gb|ABD46525.1| RNA polymerase II second largest subunit [Sistotrema confluens]
          Length = 680

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 125/808 (15%), Positives = 229/808 (28%), Gaps = 143/808 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R+   ++ + +   +               + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVESHKDFNISIAVKSNTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L+  A ++  G +  P  +         +   +
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACIS-VGSLSAPVIEFLQEWGLESLE-EN 174

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            A    +      N            LV                   D S +  +      
Sbjct: 175  ANAHGSATKVFVNGVWMGVHRDAPNLVKTLRRLRRKD---------DISSEVSIVRDIRE 225

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                   D+ RV     +      LLK E           +    G     K   +V+  
Sbjct: 226  KELRLYTDAGRVCRPLFIVENQQLLLKKEHV--------NMLNDKGRNEPYKWTHLVKD- 276

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 VI  ++ + + +         ++  R+NQ         V  G          D  
Sbjct: 277  ----GVIELLDAEEEETVMICMTPDDLENSRTNQA--------VAAGYVSNAGASDHDVA 324

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +     +           P         + I   ++            ++       +G 
Sbjct: 325  ARVRSTMTAHTWTHCEIHPSM------ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGI 378

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                  +               +  +             +       +   +    AI  
Sbjct: 379  YLTNYQVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILC 427

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    ++ R   D  ++   +  E+ E   RD        
Sbjct: 428  YSGYNQEDSVIMNQSSIDRGLF-RSMYYRSYTDAEKKVGILPLEEFEKPTRDTTLRMKHG 486

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      I  G           K+  L  D                +E  QR     
Sbjct: 487  TYEKLEDDGLIAPGTGVTGEDIIIGKTAPLPPD---------------SEELGQRMRTHT 531

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T     E+   +++      D +     + VK+ +   R  Q GDK A RHG KG
Sbjct: 532  RRDVSTPLKSTENGIVDQVLVTTNQDGL-----KFVKIRIRATRIPQVGDKFASRHGQKG 586

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             V      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +       
Sbjct: 587  TVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGD----- 641

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     E+
Sbjct: 642  ------------------------------------------------ATP-FTELTVES 652

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFD 1246
            ++ +LR       G  ++Y G TG+   
Sbjct: 653  VSQLLRQHGYQSRGLEVMYHGHTGKKLQ 680


>gi|156937444|ref|YP_001435240.1| DNA-directed RNA polymerase subunit B [Ignicoccus hospitalis KIN4/I]
 gi|156566428|gb|ABU81833.1| DNA-directed RNA polymerase, subunit B' [Ignicoccus hospitalis
            KIN4/I]
          Length = 1132

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 109/604 (18%), Positives = 209/604 (34%), Gaps = 94/604 (15%)

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
            VK G+   + D++  G   +L D     N L+A  P         M I    V   V ++
Sbjct: 604  VKKGEWTFK-DLLMRGI-VELLDADEEENALIAIEPEDITPKHTHMEIWVPAVFGVVAST 661

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
            I   E     R++              +   L+  D  G   +             +   
Sbjct: 662  IPYLEHNQSPRNSYQSAMAKQALGLYAANFMLRT-DTRG--YLLHYPEKPLAQTKHLEII 718

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
            G +     +  + AI      ++ D  +   S +    +      R    + ++      
Sbjct: 719  GYNKRPAGQNAVAAILSYTGYNIEDAIIMNQSSIDRGFMRATFM-RLYQTEEQKYPGGAE 777

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++IE    D      + +   Y +L E               ++ V+  D++        
Sbjct: 778  DKIEKPKPD-QRLVGMREPKAYEKLDE---------DGIVEPETYVVGGDVLIGKSSPPR 827

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
            +    ++      +E+ +     +    E+   + +   +  D      +++VKV V   
Sbjct: 828  FTEEYKE---MGILETRRRDASVAVRHGEEGVVDTVILTENID-----GIKMVKVRVRSL 879

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK A RHG KG+                                 +G +     
Sbjct: 880  RIPEIGDKFASRHGQKGV---------------------------------IGMVL---- 902

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                           +++    DI          +  G   E I+          A  ++
Sbjct: 903  --------PHYDMPYSEFGLVPDIILNPHAFPSRMTLGQLIESIAAK--------AAAFR 946

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                 +TP F     + +  +L        G  +++DG TGE   RPV +G ++  +L H
Sbjct: 947  GREVDATP-FYKEPLDNLRKILVERGFPPDGTEVMFDGRTGEMIARPVFIGVVFYQRLYH 1005

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            MVSDK++AR+ G   ++T+QP  G++ +GG R GEME   + A+GA+ +L E L   SD 
Sbjct: 1006 MVSDKIHARARGPVQILTRQPTEGRTRKGGLRFGEMERDVLVAHGASQLLVERLLKSSDA 1065

Query: 1322 V-------VGRTRVYES-------IVAGN--DTFETGTPESFNVLVKEMQALGLSIDLEN 1365
                     G    +++        + G   + ++     +F +L++E+ ++G++  L  
Sbjct: 1066 TKVWVCAKCGHIGWWDANKGKPVCPIHGERGEMYQVELSYAFKLLIQEILSMGIAARLRL 1125

Query: 1366 SRTK 1369
                
Sbjct: 1126 GDKF 1129



 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 112/649 (17%), Positives = 223/649 (34%), Gaps = 75/649 (11%)

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
            S+     ++  D       + +           DAL  I   +  G             
Sbjct: 237 ESDKDITSLVSFDPEVQQELLPSIEQAASVPTVDDALDFIGARIAIGMPRDKR-----IE 291

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                 D   L  +G+             + R  +   +  + + L+++   K   DD D
Sbjct: 292 RAKQVLDNNLLPHLGKR-----------PEDRIKKAIFLAHMARKLLEVYLEKREPDDKD 340

Query: 458 NLGNRRVRSVGEMLKNQYRLGLL--------RMERSIKERISSVDIDSVMPQDLINAKPV 509
           +  NRR++  G+ML   +R  L         ++ERS+ +    + +  ++  + +  K  
Sbjct: 341 HYANRRLKLAGDMLAALFRTHLRGLLNDVGYQLERSVLKGEERLKLRILIRSNYLTDKVR 400

Query: 510 VS--AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            +          + +SQL +  N LS ++H RR+ +     +AR +   E R++H T +G
Sbjct: 401 QALATGNWVGNRTGVSQLLDRTNWLSTLSHLRRVVS----PLARNQPHYEARELHMTQWG 456

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD------------GKVTNDVV 615
           RICP ET EG NIGLV +L   A ++  G  E    KV D                ++ V
Sbjct: 457 RICPFETPEGPNIGLVKNLALSAHIS-VGVPEEEVEKVLDELGVIRVEEVLEKVKNDEPV 515

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA-----SPKQ 670
              A+     ++        +D     + +       ++        + +          
Sbjct: 516 PEEAISGARVFLNGRPVGYYKDAHELAQKIRQLRRQGKLHYEVSVGVYENDDGTIKEVYI 575

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA- 729
                  + P    ++    L   ++++        +   +   +E + A     A++A 
Sbjct: 576 NTDPGRVMRPVFVVENGELKLKPEHVEKVKKGEWTFKDLLMRGIVELLDADEEENALIAI 635

Query: 730 -------KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                  K   +   V A+  V+ S    L+ + S  + Y+    +++      N     
Sbjct: 636 EPEDITPKHTHMEIWVPAVFGVVASTIPYLEHNQSPRNSYQSAMAKQALGLYAANFMLRT 695

Query: 783 KVGDEV-----RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
                +     +                  G+N + A + + GYN ED++++++  +   
Sbjct: 696 DTRGYLLHYPEKPLAQTKHLEIIGYNKRPAGQNAVAAILSYTGYNIEDAIIMNQSSIDRG 755

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIP-------NVSEEGLKNIDECGIICVGAEVNP 890
              +  +  ++   +    G E+                 +  + +DE GI+     V  
Sbjct: 756 FMRATFMRLYQTEEQKYPGGAEDKIEKPKPDQRLVGMREPKAYEKLDEDGIVEPETYVVG 815

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GD+L+GK +P   +    E  +L           RD S+ V  G  G V
Sbjct: 816 GDVLIGKSSPPRFTEEYKEMGILETRR-------RDASVAVRHGEEGVV 857



 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 99/731 (13%), Positives = 215/731 (29%), Gaps = 112/731 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+  Q  SY+ F+   +         L      V P  +      LEF+   +  P    
Sbjct: 26  LVSQQLESYNKFVTETMQK-------LIEELGEVEPFES---GYKLEFIKIRYGEPIIKE 75

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ-SIYMGDLPL 137
                      +C  RDLTYA P+ + +RL               +IK++  + +G +P+
Sbjct: 76  KSGGTRPVTPTECRIRDLTYAAPIYVYMRLRNPK----------GEIKDEGWVEIGMMPV 125

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++ G ++++V+Q              +  
Sbjct: 126 MVRSILDPLSKKSPEELVEAGEDPRDPGGYFIVDGSEKVIVTQEDL---ALNKVLVDKGG 182

Query: 174 LSGKLLYACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEI 228
               + +  +++      + + + +E      +H        K+P+   + ALG++S++ 
Sbjct: 183 PQSTVTHTAKVLSTTLGYR-VQVIVERQKDGTLHAIFPPLPGKIPLVVLIRALGIESDKD 241

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS- 287
           +       + S   +     L + +           +D       I   +       K  
Sbjct: 242 I-----TSLVSFDPEVQQELLPSIEQAASVPTVDDALDFIGARIAIGMPRDKRIERAKQV 296

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS-LEEIFHSEIRDIPI 346
           L    +  LG   +      +    +  +  E+Y+E  +  D+              +  
Sbjct: 297 LDNNLLPHLGKRPEDRIKKAIFLAHMARKLLEVYLEKREPDDKDHYANRRLKLAGDMLAA 356

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L+   +          +       ++ L    R++   +  T  V +++    +  +   
Sbjct: 357 LFRTHLRGLLNDVGYQLERSVLKGEERLKL--RILIRSNYLTDKVRQALATGNWVGNRTG 414

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI-DDIDNLGNRRVR 465
               + R      L+         + +       + L   + G+    +  +      V+
Sbjct: 415 VSQLLDRTNWLSTLSHLRRVVSP-LARNQPHYEARELHMTQWGRICPFETPEGPNIGLVK 473

Query: 466 SVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           ++         +    +E+ +     I   ++   +  D    +  +S    F     + 
Sbjct: 474 NLALSAHISVGVPEEEVEKVLDELGVIRVEEVLEKVKNDEPVPEEAISGARVFLNGRPVG 533

Query: 524 QLEEHVNSLSRITHTRRLSALGQG----GVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             ++      +I   RR   L               ++   ++      + P    E   
Sbjct: 534 YYKDAHELAQKIRQLRRQGKLHYEVSVGVYENDDGTIKEVYINTDPGRVMRPVFVVENGE 593

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           + L        +   + F         D  +   V  L A EEEN  IA     +     
Sbjct: 594 LKLKPEHVEKVKKGEWTF--------KDLLMRGIVELLDADEEENALIAIEPEDITPKH- 644

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                   ++     V  + AS IP+LE++ S R      M +Q
Sbjct: 645 ----------------------THMEIWVPAVFGVVASTIPYLEHNQSPRNSYQSAMAKQ 682

Query: 700 AVPLLKAEAPF 710
           A+ L  A    
Sbjct: 683 ALGLYAANFML 693


>gi|320172580|gb|ADW24173.1| RNA polymerase II second largest subunit [Donkioporia expansa]
          Length = 683

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 121/819 (14%), Positives = 232/819 (28%), Gaps = 161/819 (19%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L N +R+   ++ + +    +              +    + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNVSLAVKHNTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKTMSAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L+  + ++  G +  P  +  +      +   +
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLSLMSCIS-VGTLSAPVIEFLEEWGLESLE-EN 174

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVF---CRCAGEEILVPREKIDFIDASPKQVVSIA 675
            A           N           +LV         ++I      +  I     ++ + A
Sbjct: 175  AHASTPCTKVFVNGVWMGVHRDPVKLVSTLRKLRRKDDINCEVSVVRDIRERELRLYTDA 234

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVP-------LLKAEAPFVGTGMESVVAKSSGAAIV 728
              +   L   ++ ++L+        V            +       +E + A+     ++
Sbjct: 235  GRVCRPLFIVENQQLLIQKRHIENLVRAKDDPTITYNWDNLLKDGVIELLDAEEEETVMI 294

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            +         D     +++   D        D    +K   S                  
Sbjct: 295  SMTPE-----DLENSRLQATGVDPHADEENDDPSARLKAPTSAH---------------- 333

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
                     PS  LG       +  + +P+  +N       +                ++
Sbjct: 334  -TWTHCEIHPSMILG-------VCASIIPFPDHNQSLQSPRN---------------TYQ 370

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                   +G       I               +  +             +       +  
Sbjct: 371  SAMGKQAMGIYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPA 419

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   
Sbjct: 420  GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPT 478

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            RD          +       I  G N         K+  +  D      R++        
Sbjct: 479  RDTTLRMKHGTYDKLEDDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRTRTHTKRDVS 538

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++   + +  Q                              + VK+ V   R  Q GD
Sbjct: 539  TPLKSTEQGIVDQVLI--------------------TTNAEGQKFVKIRVRSTRVPQIGD 578

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +
Sbjct: 579  KFASRHGQKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKLATLI 638

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +                                                       +T
Sbjct: 639  GNEGD-----------------------------------------------------AT 645

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
            P F     E ++  LR       G  ++Y G TG     
Sbjct: 646  P-FTDLTVETVSQYLRQKGYQSRGLEVMYHGHTGRKLQA 683


>gi|258562138|gb|ACV81791.1| RNA polymerase II second largest subunit [Agaricostilbum
            pulcherrimum]
          Length = 652

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 123/739 (16%), Positives = 217/739 (29%), Gaps = 135/739 (18%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 44   GVSQVLNRYTYASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQAC 99

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++  G    P  +  +      +  L+A   +   +   N         
Sbjct: 100  GLVKNLALMSYIS-VGTPSAPIIEFLEEWNMESLEDLTADLGKGTKV-FVNGVWQGIHRD 157

Query: 641  TEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCN 695
              +LV      R  G+         D  +   +          P    D+S + LM    
Sbjct: 158  PAQLVTTLKTLRRKGDINKEVSVVRDVRERELRIFTDAGRVCRPVFIVDESTQELMLQKE 217

Query: 696  MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
              RQ       +               S                       +V   + P 
Sbjct: 218  HVRQLEDAQADDV-------------DSEMFGWNNLVEGGVAELLDAEEEETVMICMSPE 264

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
               +  Y++   + +           ++     R        P+  LG       +  + 
Sbjct: 265  DLQLSKYQVEHGKAAADPDLGAGGARLRQIQSTRTFTHCEIHPAMILG-------VCASI 317

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N          M  + +   + +  F+V   ++                     
Sbjct: 318  IPFPDHNQSPRNTYQSAMGKQAMG--VFLTSFQVRMDNSSN------------------- 356

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                    +             +       +   +  + AI      +  D+ +   S +
Sbjct: 357  --------ILYYPQKPLATTRSMEYLHFRDLPAGQNAIVAILCYSGYNQEDSVIMSQSAI 408

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +     + R  +D+ +R  ++  E+ E   R +         +       +  G+N 
Sbjct: 409  DRGLF-RSFYYRTYMDQEKRKGNILMEEFEKPTRQQTLRMKHGTYDKIDSDGLVNPGENV 467

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            V       K+  L  D                +E  QR  + +K    T     E  + +
Sbjct: 468  VGDDILIGKTAPLPPD---------------TEELGQRTKDHIKRDVSTPLKTTERGYVD 512

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      D+      R  KV     R  Q GDK A RHG KG +      EDMPF  DG
Sbjct: 513  QVMLTTNADN-----DRFAKVRTRATRIPQVGDKFASRHGQKGTIGITYRQEDMPFTVDG 567

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L       G +                        
Sbjct: 568  ITPDIIINPHAIPSRMTIGHLVECLLSKVSTITGNEGD---------------------- 605

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     EAI+ +L+       G  +
Sbjct: 606  -------------------------------ATP-FTNVTVEAISDLLKANGYHSRGLEV 633

Query: 1236 LYDGLTGEPFDRPVTVGYI 1254
            +Y+G TG      V +G  
Sbjct: 634  MYNGHTGRKLRAQVYLGPT 652



 Score = 43.9 bits (102), Expect = 0.21,   Method: Composition-based stats.
 Identities = 57/432 (13%), Positives = 124/432 (28%), Gaps = 49/432 (11%)

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-- 446
           F +  ++ + +  +  +Y L   G      +         + + +    + +  L     
Sbjct: 8   FRLRSAIKSSIITNGLRYSL-ATGNWGDQKKSLSAKAGVSQVLNRYTYASTLSHLRRCNT 66

Query: 447 ---RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
              R+GK       +  +  +    E  + Q    +  +       + +     +   + 
Sbjct: 67  PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSYISVGTPSAPIIEFLEE 126

Query: 504 INAKPVVSAVCEFFCSSQLS-------QLEEHVNSLSRITHTRRLSALG-QGGVARARAG 555
            N + +     +    +++           +    ++ +   RR   +  +  V R    
Sbjct: 127 WNMESLEDLTADLGKGTKVFVNGVWQGIHRDPAQLVTTLKTLRRKGDINKEVSVVRDVRE 186

Query: 556 VEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            E+R    T  GR+C         T E             A+ +        +  + +G 
Sbjct: 187 RELR--IFTDAGRVCRPVFIVDESTQELMLQKEHVRQLEDAQADDVDSEMFGWNNLVEGG 244

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLD------EDGSFTEELVFCRCAGEEILVPREK-ID 662
           V   +    A EEE   I  +   L       E G    +            +   +   
Sbjct: 245 VAELLD---AEEEETVMICMSPEDLQLSKYQVEHGKAAADPDLGAGGARLRQIQSTRTFT 301

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKA 706
             +  P  ++ + AS+IPF +++ S R      M +QA+                 L   
Sbjct: 302 HCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTSFQVRMDNSSNILYYP 361

Query: 707 EAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
           + P   T  ME +  +   A   A  A +          +   +  +D        YR  
Sbjct: 362 QKPLATTRSMEYLHFRDLPAGQNAIVAILCYSGYNQEDSVIMSQSAIDRGLFRSFYYRTY 421

Query: 766 KFQRSNQNTCVN 777
             Q   +   + 
Sbjct: 422 MDQEKRKGNILM 433


>gi|208343773|gb|ACI26262.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 204

 Score =  245 bits (626), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 88/214 (41%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 23   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 82

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 83   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 127

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 128  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 170

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 171  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHH 204


>gi|307343538|emb|CBJ18686.1| RNA polymerase B subunit [Micromonospora auratinigra]
          Length = 205

 Score =  245 bits (625), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 25   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 84

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 85   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDEEWKRQLRSIN---------- 133

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 134  -------------------AHESEPDSNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 174

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 175  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLN 205


>gi|93278291|gb|ABF06601.1| RNA polymerase II second largest subunit [Cheimonophyllum
            candidissimum]
          Length = 690

 Score =  245 bits (625), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 122/825 (14%), Positives = 241/825 (29%), Gaps = 156/825 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N + +   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFXMLFRKLTKDVYRYLQKCVEAHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKTMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSSTPTTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +  +    L+ +   ++  G      K  G     +       V+    
Sbjct: 226  TDAGRVCRPLFIVEEQQLALQKKHVKWLAQGH-----KDDGEVYKWEHLVKGGIVE---- 276

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                                 +      +   ++  P       ++++ +       +  
Sbjct: 277  ---------------------LLDAEEEEXVMISMTPEDLENSRLQQSGVDPHANDGEFD 315

Query: 804  DLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
              A  +  + A   W       SM+  I   ++            ++       +G    
Sbjct: 316  PAARLKADINAH-TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLT 374

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 375  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 423

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S     +Q+E   +    + + +   
Sbjct: 424  YNQEDSVIMNQSSIDRGLF-RSIYYRGYMDLEKKSGI---QQLEEFEKPSRQQTLRMKHG 479

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   I  G           K+  +  D                +E  QR     
Sbjct: 480  TYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPD---------------SEELGQRTPTHT 524

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T     E    +++      D       + VKV +   R  Q GDK A RHG KG
Sbjct: 525  RRDVSTPLKSTESGMVDQVLITTNHD-----GQKFVKVRIRSTRIPQIGDKFASRHGQKG 579

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +    
Sbjct: 580  TIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT 639

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                      ++       LR       G+ V            
Sbjct: 640  -------------------------DLTVESVSMYLRQKGYQSRGLEVM----------- 663

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                         G +    G         V +G  Y  +L HMV
Sbjct: 664  -----------YHGHT----GR---KLQAQVYLGPTYYQRLKHMV 690



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 93/622 (14%), Positives = 171/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFXMLFRKLTKDVYRYLQKCVEAH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKTMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPTTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEEQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         E    K         V  L A EEE   I+     L+       
Sbjct: 246 QKKHVKWLAQGHKDDGEV--YKWEHLVKGGIVELLDAEEEEXVMISMTPEDLENSRLQQS 303

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 304 GVDPHANDGEFDPAARLKADINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 363

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 364 MGKQAMGIYLTNFLI-----------------------------------------RMDT 382

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 383 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 418

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 419 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRGYMDLEKKSGIQQLEEFEKPSRQQTLRMKH 478

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  VN  DI++GK  P    P   EE   R          RD S  
Sbjct: 479 GTYDKLEDDGLIAPGTGVNGEDIIIGKTAPI---PPDSEELGQRTP----THTRRDVSTP 531

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I   H   K
Sbjct: 532 LKSTESGMVDQVLITTNHDGQK 553


>gi|207692937|gb|ACI25203.1| RNA polymerase beta [Mycobacterium sp. ATCC 25793]
          Length = 212

 Score =  245 bits (625), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 115/214 (53%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E  +  +L     +      
Sbjct: 136  -----------------LPEDLKSAPADSIVATPVFDGAREGELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAEGKSQLFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|307343576|emb|CBJ18704.1| RNA polymerase B subunit [Micromonospora mirobrigensis]
          Length = 207

 Score =  245 bits (625), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 124/211 (58%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDEEWKRQLRSIE---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+Y+LKLN
Sbjct: 177  RTGKAQLFDGRSGEPLPDPIAVGYVYILKLN 207


>gi|255017616|ref|ZP_05289742.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes FSL
            F2-515]
          Length = 417

 Score =  245 bits (625), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 104/328 (31%), Positives = 151/328 (46%), Gaps = 62/328 (18%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
            K++   S+  E+ E  ARD       + R+I +   + L   +     +      V  +D
Sbjct: 146  KDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGA--EVKDND 203

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNV--ESLKVQYETSKSILED----RFKNKIEKIQWGDD 1065
            L+      +       +E++   +  E  +   +TS  +           KI   + GD+
Sbjct: 204  LLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREAGDE 263

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            +PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+ DGTPVDI+LNPL
Sbjct: 264  LPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIMLNPL 323

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            GVPSRMN+GQ+ E HLG A   LG  + + + D     D+                    
Sbjct: 324  GVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARDAK------ 377

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                  T ++DG                           +GE F
Sbjct: 378  ----------------------TILYDG--------------------------RSGEAF 389

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            D  ++VG +YM+KL HMV DK++ARSTG
Sbjct: 390  DNRISVGVMYMIKLAHMVDDKLHARSTG 417



 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 168/262 (64%), Positives = 200/262 (76%), Gaps = 1/262 (0%)

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE- 749
           LMG NMQRQAVPL+  EAPFVGTGME V AK SGAA+ AK  GIVE V+A  I +R V  
Sbjct: 1   LMGANMQRQAVPLMHPEAPFVGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSL 60

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
            D    T G+D Y L KF RSNQ TC NQRP V  GD V + +I+ +GPS D G+LALGR
Sbjct: 61  VDGKEVTGGIDKYTLRKFVRSNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGR 120

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N+LVAFM W GYN+ED++++SER+V +DV+TSIHIEEFE  ARDTKLGPEE+TRDIPNV 
Sbjct: 121 NVLVAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVG 180

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E+ L+++DE GII VGAEV   D+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSL
Sbjct: 181 EDALRDLDERGIIRVGAEVKDNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSL 240

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
           RVP G  G V+DV+IF R   D
Sbjct: 241 RVPHGGGGIVLDVKIFTREAGD 262


>gi|161899447|ref|XP_001712950.1| RBP2 DNA-directed RNA polymerase II second largest subunit
            [Bigelowiella natans]
 gi|75756444|gb|ABA27338.1| RBP2 DNA-directed RNA polymerase II second largest subunit
            [Bigelowiella natans]
          Length = 1159

 Score =  244 bits (624), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 81/422 (19%), Positives = 150/422 (35%), Gaps = 74/422 (17%)

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL-ISEYPRSQ 1020
             Q + L  +    +  L R I  +        N     +  +  +  S+   +      +
Sbjct: 789  NQEDSLIINHSSVERGLFRTIIYKTFAERENTNVNGIIEKIELESKSSNLFGLDIDGTRK 848

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD----MPPGVLRVVKV 1076
                   D+ +      L  + +T  + +    K  +      D     +  G  +++KV
Sbjct: 849  IETLVNGDDVLISKTIKLTGKGDTKVNTIHSDLKLPLNSQGVVDSIMYSLDEGGYKIIKV 908

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R    GDK +  HG KGI+        +P        D+++NP  +PSRM +G +
Sbjct: 909  RIRSIREPVIGDKFSSLHGQKGIIGYSYRQSLLPTTATSVTPDLIMNPHAIPSRMTIGHM 968

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  +       GK   +        G I    S                          
Sbjct: 969  IEMLMSKVSSHSGKLGDATAFSEGNIGKIIGHLSKF------------------------ 1004

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                            G     +  M+  +  +            G+   + + VG IY 
Sbjct: 1005 ----------------GIHHFGLEKMI--SGFN------------GDILQKSILVGPIYY 1034

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV DK ++RS G Y ++T+QP+ GK+  GG R GEME  C+ ++G++  L+E L 
Sbjct: 1035 QRLKHMVVDKFFSRSRGPYEILTRQPVEGKTREGGLRFGEMERDCVLSHGSSLFLKERLM 1094

Query: 1317 IKSD----DVVGRT--------RV---YESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
             +SD     +  ++        +    + +I       +   P +  +L +E+ A+ ++ 
Sbjct: 1095 DESDKFRVHICEKSGLFCPANLKTQTFWSTIYHSKSICQIFIPYACKLLFQELIAMCIAP 1154

Query: 1362 DL 1363
             L
Sbjct: 1155 RL 1156



 Score =  134 bits (336), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 103/766 (13%), Positives = 240/766 (31%), Gaps = 131/766 (17%)

Query: 30  IEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVFPITA--------FSGAAML----E 75
           I+ Q  S++ F+        D+ PN  +Q ++K+   I          ++    +    E
Sbjct: 23  IKQQIISFNDFIRKESQHIIDKIPNLVIQISYKNSNKIVNRILLLKQLYTEKPRIIKTRE 82

Query: 76  FVSYEFDPPKFDVDD-------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
              Y    P +D  +          R++TY+  ++I +   + D  +    K + +  ++
Sbjct: 83  L--YNLVEPSYDEGELNISPNKSRLRNITYSSKVRIQVFDEITDKHDANLKKKVVNKSKK 140

Query: 129 SIYMGDLPLM------------------------TKDGTFVIKGIQRIVVSQ--LHRSPG 162
            IY+G  P M                         + G F+I G ++++V+Q  L ++  
Sbjct: 141 FIYIGKFPCMIKSDTCYLNNFSEISLARNDECPFDEGGYFIINGNEKVLVAQERLVKNKV 200

Query: 163 IHFDHDKGRASLSGKLLYACRIIPDQGL--------WMDIEFDSKDI------IHVRIDR 208
             F     +     K     +               ++ +  D  +       I V+I  
Sbjct: 201 YIFSKIFDK-----KTRVMAQCRSYDSSLYNQGYMVYLKLVTDKSNNPNQCSEITVKIAS 255

Query: 209 RR-KVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
            R ++P+   L  LG  ++ EI+++ +     S++ +           +     +   + 
Sbjct: 256 LRAEIPLVILLKFLGFKNDKEIINSIFKNNSNSKKLNMLYNSFLGVTKVQTISHALRYI- 314

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
                      +  +    K L  +      I    L  +  + +    +   I   A  
Sbjct: 315 ---------VDRSFSKSNNKKLDPEKTAREIIDKKLLPHMGTSINSRFRKGLFICYMAHR 365

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           +I+  +L EI                 +     +       +  KD    + + ++  D 
Sbjct: 366 LIN--TLNEI-EQPDDKDSYKNKRVDISGHLFSSLFNNLIKRSIKDVKNQLLKKVKKSDA 422

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
           +     E +F+     +        G   ++  L+  T      + +   +++I  L  L
Sbjct: 423 TEL---EELFSSNILTNGFRYSLATGNWIIDGMLDYKTGVSQ-VLNRMSYLSMISHLSRL 478

Query: 447 RNG-----------------KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            +                   G +  ++    +    V       +      ++++I + 
Sbjct: 479 NSSYTSNGKILDIRRVHTSYWGIVCPVETPEGQTCGIVKNFAFLAHVTNSHHIQKNIIQF 538

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           +  + I +   + +I  K     +  F   S +    E+ + +  +   RR   +     
Sbjct: 539 LKKIMIKNSFTKPMIKTKKDKPDISIFVNGSWIGNTFEYFSLMKYLITLRRQEII----- 593

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY-----GFIETPYRK 604
                  ++  V      RI            L     S +  N         I+  + +
Sbjct: 594 -----PFDVSIVFNEKNKRIFIWSDPGRIKRPLFVLKNSNSFFNHSIEKIAKKIKDNFHR 648

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
                  + V YL   E EN  I                        ++  + ++ I+F 
Sbjct: 649 WYFYIKNSIVEYLDTEEIENIVI------------KLNYYNNTELIVDQTQIYKKMINFS 696

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +     ++ ++AS +PF +++ S R     +M +QA+ +  +    
Sbjct: 697 EIHASSILGVSASQVPFSQHNQSPRNTYQSSMGKQAIGINYSNFQL 742


>gi|307343596|emb|CBJ18713.1| RNA polymerase B subunit [Micromonospora sagamiensis]
          Length = 206

 Score =  244 bits (624), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 86   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWNVEGDDADWKRALRSIE---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AAEAEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKLN 206


>gi|52699800|gb|AAU86962.1| DNA-dependent RNA polymerase II second largest subunit [Dermatocarpon
            luridum]
          Length = 717

 Score =  244 bits (624), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 119/833 (14%), Positives = 233/833 (27%), Gaps = 136/833 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +RL   ++ R      +        +  +  + +  + + + 
Sbjct: 1    DHFGKKRLDLAGPLMANLFRLQFQKVVRDFSRYMQKQVESDREINLKVGLKSNIITNGLK 60

Query: 515  EFFCSS-------------QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +A     + R     + R +
Sbjct: 61   YSLATGSWGDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVY-LS 618
            H TH+G +CPAET EG   GLV +L     V  +        Y      +   +    LS
Sbjct: 117  HNTHWGYVCPAETPEGQACGLVKNLALMTMVTNSHNTGPLEEYILGRGVESLEEWEPRLS 176

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAAS 677
                +        + + +D     +        E +      + D  D   +        
Sbjct: 177  PQATKVFLNGVWFAVVIKDPKHLVDHFKLFRRAESLDPQISMVWDIRDKEFRISGDAGRI 236

Query: 678  LIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
            + P F+   D ++   G  +  +             T   +      G            
Sbjct: 237  IRPLFVVERDPSKDNYGNLVLNKNHI-----QRLDNTVYNTEAQLPMGQW---PEPPFGW 288

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +      V+  ++ + + +   +     +   ++    C  +       D + R D +  
Sbjct: 289  KDLLKEGVVEYLDAEEEETAMIIMTPEDLNTSKAKHMGCTTEETD----DPLARYDPL-- 342

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                         N           +    + +   ++            ++       +
Sbjct: 343  ------------LNPHSHTFTHCEIHPSMILGVCASVIPFPDHNQSPRNTYQSAMGKQAM 390

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G                                        +       +   +  + AI
Sbjct: 391  GXXXXXXXXXXXXXX-----------XXLYYPQKPLARTMSMEYLKFRELPAGQNAIVAI 439

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    +F R   D+ +       EQ E   R+      
Sbjct: 440  ACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKVVGHNVVEQFEKPTRNDTLRMK 498

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +       +  GQ          K+  ++ D                +E  QR  +
Sbjct: 499  HGTYDKLDADGIVEVGQRVSGEDIIIGKTAPMAPD---------------AEELGQRQKQ 543

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             LK    T     E    +++     GD       + VKV V   +  Q GDK A RHG 
Sbjct: 544  HLKRDVSTPLRSTESGIVDQVLVTTSGD-----GQKFVKVRVRTTKIPQIGDKFASRHGQ 598

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 599  KGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATP 658

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                   ++S +   +                                            
Sbjct: 659  FTKVTVTNVSNILRSMGYQSRGFEVM---------------------------------- 684

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                          +G +    G         V +G  Y  +L HMV  K++A
Sbjct: 685  -------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDXKIHA 717



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 54/384 (14%), Positives = 111/384 (28%), Gaps = 40/384 (10%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +         V   + + +  +  KY L   G  
Sbjct: 12  GPLMANLFRLQFQKVVRDFSRYMQKQVESDREINLKVG--LKSNIITNGLKYSL-ATGSW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++N       + + +    + +  L        R+GK       +  +       E
Sbjct: 69  GDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGYVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDID---------SVMPQDLINAKPVVSAVCEFFCSS 520
             + Q    +  +        S                  ++        +         
Sbjct: 129 TPEGQACGLVKNLALMTMVTNSHNTGPLEEYILGRGVESLEEWEPRLSPQATKVFLNGVW 188

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARAR--------AGVEMRDVHPTHYGRICPA 572
               +++  + +      RR  +L                 +G   R + P       P+
Sbjct: 189 FAVVIKDPKHLVDHFKLFRRAESLDPQISMVWDIRDKEFRISGDAGRIIRPLFVVERDPS 248

Query: 573 ETSEGHNIGLVSSLTSF--------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           + + G+ +   + +           A++    + E P+    D      V YL A EEE 
Sbjct: 249 KDNYGNLVLNKNHIQRLDNTVYNTEAQLPMGQWPEPPF-GWKDLLKEGVVEYLDAEEEET 307

Query: 625 RYIAQANSSLD-----EDGSFTEELVFCRCAGEEILVPREK-IDFIDASPKQVVSIAASL 678
             I      L+       G  TEE        + +L P        +  P  ++ + AS+
Sbjct: 308 AMIIMTPEDLNTSKAKHMGCTTEETDDPLARYDPLLNPHSHTFTHCEIHPSMILGVCASV 367

Query: 679 IPFLENDDSNRVLMGCNMQRQAVP 702
           IPF +++ S R      M +QA+ 
Sbjct: 368 IPFPDHNQSPRNTYQSAMGKQAMG 391


>gi|307343492|emb|CBJ18663.1| RNA polymerase B subunit [Micromonospora sp. CR21]
          Length = 206

 Score =  244 bits (624), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 94/210 (44%), Positives = 123/210 (58%), Gaps = 38/210 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              G++ L+DG +GEP   P+ VGY+Y+LKL
Sbjct: 177  RTGKAQLFDGRSGEPLPDPIAVGYVYILKL 206


>gi|140084144|gb|ABO84921.1| RpoB [Paenibacillus sp. FSL_F4-243]
          Length = 230

 Score =  244 bits (624), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 88/209 (42%), Positives = 116/209 (55%), Gaps = 54/209 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 76   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 135

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 136  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 184

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 185  ----------------------------------VFD---------TMEEAGMQRNGKTV 201

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            LYDG TGE F+R VTVG ++M+KL HMV 
Sbjct: 202  LYDGRTGERFEREVTVGVMHMIKLAHMVD 230



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/84 (63%), Positives = 66/84 (78%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDT
Sbjct: 1   VGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 60

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SLRVP G  G +VDV++F R   D
Sbjct: 61  SLRVPHGSDGIIVDVKVFTRENGD 84


>gi|307343600|emb|CBJ18715.1| RNA polymerase B subunit [Micromonospora viridifaciens]
          Length = 206

 Score =  244 bits (624), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 94/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++    ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVQGDDEEWKRQLRSIN---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I  +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAQEEEIAGLLESTLPNRDGQQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGYIY+LKLN
Sbjct: 176  RTGKARLFDGRSGEPLPDPIAVGYIYILKLN 206


>gi|94410928|gb|ABF18583.1| RNA polymerase II second largest subunit [Hygrocybe coccinea]
          Length = 655

 Score =  244 bits (623), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 117/723 (16%), Positives = 226/723 (31%), Gaps = 95/723 (13%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +   +               +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVEMHKEFNLALAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R A   +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDAANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G    +A   G  +  K   +V+    
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIRWLNNGFRDDMADDEGTPLEFKWEQLVK--GG 283

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN---QRPLV--KVGDEVRRNDIIA 795
            I  ++ + E +    +   +     + Q+S  +   N     P V  K G          
Sbjct: 284  IVELLDAEEEETVMISMTPEDLENSRLQQSGVDPHANDGEFDPAVRLKAGINTHTWTHCE 343

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N                        ++       
Sbjct: 344  IHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQA 378

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G       I               +  +             +       +   +  + A
Sbjct: 379  MGIYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVA 427

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD     
Sbjct: 428  ILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRM 486

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +       I  G           K+  +  D      R++          ++   
Sbjct: 487  KHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTE 546

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +  Q                              + VK+ V   R  Q GDK A RHG
Sbjct: 547  NGIVDQVLI--------------------TTNSEGQKFVKIRVRATRVPQIGDKFASRHG 586

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  + 
Sbjct: 587  QKGTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDAT 646

Query: 1156 IND 1158
               
Sbjct: 647  PFT 649



 Score =  119 bits (297), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 83/617 (13%), Positives = 169/617 (27%), Gaps = 105/617 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVEMH--KEFNLALAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
               +  N +  I   RR   +            +   ++        P    E      
Sbjct: 189 GVHRDAANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 579 ---NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
              +I  +++       +  G       K         V  L A EEE   I+     L+
Sbjct: 249 QKKHIRWLNNGFRDDMADDEGTPLE--FKWEQLVKGGIVELLDAEEEETVMISMTPEDLE 306

Query: 636 EDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                   +      GE          +        +  P  ++ I AS+IPF +++ S 
Sbjct: 307 NSRLQQSGVDPHANDGEFDPAVRLKAGINTHTWTHCEIHPSMILGICASIIPFPDHNQSP 366

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 367 RNTYQSAMGKQAMGIYLTNFLI-------------------------------------- 388

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 389 ---RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAG 421

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----- 863
           +N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        
Sbjct: 422 QNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRD 481

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +++ G+I  G  V   DI++GK  P         E+L +        D
Sbjct: 482 NTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPI----PPDSEELGQRTRTHTRRD 537

Query: 924 VRDTSLRVPSGVSGTVV 940
           V        +G+   V+
Sbjct: 538 VSTPLKSTENGIVDQVL 554


>gi|320172588|gb|ADW24177.1| RNA polymerase II second largest subunit [Gloeophyllum trabeum]
          Length = 648

 Score =  244 bits (623), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 117/734 (15%), Positives = 210/734 (28%), Gaps = 129/734 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 44   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 99

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L+  A ++           + +  + +         EEN + A   + +  +G +
Sbjct: 100  GLVKNLSLMACISVGSLSAPVIEFLEEWGLESL--------EENAHSATPCTKVFVNGVW 151

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 152  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQ 208

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
               L+ +        E+   +      + K   +          +       D   S + 
Sbjct: 209  QLALQKKHVRWLNQGENDDGEPWKWDQLVKNGIVELLDAEEEETVMISMTPEDLENSRLQ 268

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               +            +    +K              PS  LG       +  + +P+  
Sbjct: 269  SAGIDPHANEGD---FDPSARLKAPTHGHTWTHCEIHPSMILG-------VCASIIPFPD 318

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N                        ++       +G       +               
Sbjct: 319  HNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM-----------DT 349

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 350  MANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 409

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+ R  +D  ++S   + E+ E   RD          +       I  G        
Sbjct: 410  -RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVNGDDI 468

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  D                +E  QR     +    T+    E    +++   
Sbjct: 469  IIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTALKSTESGIVDQVLI- 512

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   DI
Sbjct: 513  ----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDI 568

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +G + E  L      +G +                             
Sbjct: 569  IINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------------------- 601

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E++++ LR       G  ++Y G 
Sbjct: 602  --------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHGH 634

Query: 1241 TGEPFDRPVTVGYI 1254
            TG      V +G  
Sbjct: 635  TGRKLQAQVYLGPT 648



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 85/580 (14%), Positives = 163/580 (28%), Gaps = 92/580 (15%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   S  G  ++  R    +      R          I    
Sbjct: 19  ITNGLKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPR 78

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   + + L     + +  +   + E +    ++S+      
Sbjct: 79  QLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLEEWGLESL----EE 134

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NA         F     +    +  N +  I   RR   +                ++  
Sbjct: 135 NAHSATPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTD 194

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                 P    E   + L      +  +N     +    K         V  L A EEE 
Sbjct: 195 AGRVCRPLFIVENQQLALQKKHVRW--LNQGENDDGEPWKWDQLVKNGIVELLDAEEEET 252

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAAS 677
             I+     L+     +  +      G+     R             +  P  ++ + AS
Sbjct: 253 VMISMTPEDLENSRLQSAGIDPHANEGDFDPSARLKAPTHGHTWTHCEIHPSMILGVCAS 312

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IPF +++ S R      M +QA+ +                                  
Sbjct: 313 IIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV--------------------------- 345

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                            + + +  Y       +     +  R                  
Sbjct: 346 --------------RMDTMANILYYPQKPLATTRSMEYLRFR------------------ 373

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + + 
Sbjct: 374 ------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQ 427

Query: 858 PEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E            +       I++ G+I  G  VN  DI++GK  P         ++ 
Sbjct: 428 QLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVNGDDIIIGKTAPIPPDSEELGQRT 487

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                  ++   RD S  + S  SG V  V I       K
Sbjct: 488 -------RSHTRRDVSTALKSTESGIVDQVLITTNSEGQK 520


>gi|153958198|gb|ABS53389.1| RpoB [Bacteriovorax sp. NZAH14]
 gi|153958200|gb|ABS53390.1| RpoB [Bacteriovorax sp. SAN5]
          Length = 352

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 168/355 (47%), Positives = 236/355 (66%), Gaps = 10/355 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V
Sbjct: 1    AKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDVV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +E
Sbjct: 59   SKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESYE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+ 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLIR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ ++L G              +   K   L+S++++  P    
Sbjct: 239  RDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                ++   ++  +           + +  +  ++I K   GD++PPGV++ V +
Sbjct: 299  GYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDELPPGVIKKVTI 352


>gi|256014682|gb|ACU56889.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|256014686|gb|ACU56891.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|256014688|gb|ACU56892.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|256014692|gb|ACU56894.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 208

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 87/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 27   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 87   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 131

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 132  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 174

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 175  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHH 208


>gi|50546993|ref|XP_500966.1| YALI0B16258p [Yarrowia lipolytica]
 gi|49646832|emb|CAG83219.1| YALI0B16258p [Yarrowia lipolytica]
          Length = 1169

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 82/509 (16%), Positives = 171/509 (33%), Gaps = 94/509 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I       +   +    A+      D+ D  +   S +   
Sbjct: 733  DTLLYLMVYPQQPMVKTRTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRG 792

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDD---EQVILDRNIYSRLMEILCGQNA 995
                ++  ++       + S   ++++ +  ++     +    +  +  +    + G + 
Sbjct: 793  FGRCQVLKKNTTVLKRYAGSDAVDRLDGVKMERRKCAWDPNSFEEVVTEQHE--VLGPDG 850

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            +       K++ +  +       S         + +     S   +Y  +         +
Sbjct: 851  LGEVGKPVKNSQVYVNRCIPVNNS---------DSLLNQSTSSSTEYREAPVTYRGPEPS 901

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             I+K+     +    L ++KV +   R  + GDK + RHG KG+                
Sbjct: 902  IIDKVMV--SVTDKELYLIKVLLRQTRRPELGDKFSSRHGQKGVCG-------------- 945

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                I++N                                    + +   S      + +
Sbjct: 946  ----IIVN------------------------------------QEDMPFSDSGVCPDII 965

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +       +++      ++        G       F G+  E ++ +L       SG+ +
Sbjct: 966  MNPHGFPSRMTVGKMIELISGKAGVLDGSLQYGTCFGGSKLEDMSKILVDHGYSYSGKDM 1025

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            LY G +GE     +  G IY  KL HMV DK++AR  G  +++T+QP  G+S  GG RLG
Sbjct: 1026 LYSGTSGECLQAYIFFGPIYYQKLKHMVMDKMHARPRGPRAVLTRQPTEGRSRDGGLRLG 1085

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DT 1338
            EME  C+ AYGA+ +L E L   SD        +E+ V                      
Sbjct: 1086 EMERDCVIAYGASQLLLERLMYSSD-------AFEADVCQKCGLLGYQGWCNSCQTTAHV 1138

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSR 1367
             +   P +  +L +E+ ++ ++  L+   
Sbjct: 1139 VKMTLPYAAKLLFQELVSMNIAPRLKLKE 1167



 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 126/963 (13%), Positives = 261/963 (27%), Gaps = 200/963 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP--KF 86
           L++    S+++F+ +++      N   Q     V P         L++       P  KF
Sbjct: 61  LVKQHLDSFNYFVDVDLKKILAAN---QMVLSDVDP------EFYLKYKDIRVGKPGIKF 111

Query: 87  D---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI------------ 125
           D           +C  RD+TYA P+ + +               I  +            
Sbjct: 112 DDKNDDNAIFPHECRLRDMTYAAPIYVDIEYTKERKIVIQRNLEIGKMPIMLRSSKCHLQ 171

Query: 126 ---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS-----------PGIHFDHDKGR 171
              +E+   MG+ PL    G F++ G +++++ Q   S            G+        
Sbjct: 172 DQTEEKMAAMGECPL-DPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKGVVQASVTSS 230

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVR---I--DRRRKVPVTSFLMALGMDSE 226
                   Y                   D I+++   I  D    +P+   L A G+ ++
Sbjct: 231 THERRSKTYVLT--------------KNDKIYLKNNSIVED----IPIVLILKAAGLVTD 272

Query: 227 -EILST------FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
            EI+         Y +I      +     +      +    S       +  ++    + 
Sbjct: 273 LEIMQAVAGQNPVYQEIFAVNFEECSKLGVFTQRQALEYLGSKVKTSRRSNVKLTHYQEG 332

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           L +     +    +  +  T   L    +   ++        I+  D +  K LE     
Sbjct: 333 LEAVATSIIAHISINNMDFTEKALYIAVMTRRVIMAMADPKMIDDRDYVGNKRLELAGQL 392

Query: 340 EIRDIPILYVDSV-NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  L+     +  A I   L         DALL+    +     S  S      + 
Sbjct: 393 LSLLFEDLFKKFNSDFKANIDKILKRPNRASMFDALLN----LETHRGSITSGMNRAIST 448

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             +   ++ +   G   +  R           +     + ++  +         +     
Sbjct: 449 GNWSLKRFKMERAGVTHVLSR-----------LSYISALGMMTRISSQFEKSRKVSGPRA 497

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L   +   +      +     L    ++   I++ D ++ +            +V     
Sbjct: 498 LQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTDDEEAPVRNLCYLLGAENISVIGGAE 557

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEG 577
                    ++N             +       R     E   ++   +       T  G
Sbjct: 558 LHAEGSFGVYLNGTLIGITKFPTKFVSSFRQFRRTGKVSEFISIYINRHHAAVHIATDGG 617

Query: 578 HNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                +  + +     +V     +        D      V YL   EE + +IA     L
Sbjct: 618 RICRPLIIVENEHPRVQVEHLKKLRDGEMTFDDFLKQGLVEYLDVNEENDSFIA-----L 672

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            E+                      +   ++  P  V+   A LIP+  ++ S R    C
Sbjct: 673 YENNINA------------------ETTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQC 714

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+                                           I   + +   
Sbjct: 715 AMGKQAIGA-----------------------------------------IAYNQLNRID 733

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           +   + +Y               Q+P+VK                 D   L  G+N  VA
Sbjct: 734 TLLYLMVYP--------------QQPMVK----------TRTIELIDYDKLPAGQNATVA 769

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK--------LGPEEITRDIP 866
            M + GY+ ED++++++  +         +++   + +            G +   R   
Sbjct: 770 VMSYSGYDIEDALVLNKSSIDRGFGRCQVLKKNTTVLKRYAGSDAVDRLDGVKMERRKCA 829

Query: 867 NVSE-------EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                      E  + +   G+  VG  V    + V +  P   S     +    +    
Sbjct: 830 WDPNSFEEVVTEQHEVLGPDGLGEVGKPVKNSQVYVNRCIPVNNSDSLLNQSTSSSTEYR 889

Query: 920 KAV 922
           +A 
Sbjct: 890 EAP 892


>gi|208343771|gb|ACI26261.1| RNA polymerase beta subunit [Mycobacterium massiliense]
          Length = 217

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 88/214 (41%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 36   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 95

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 96   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 140

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 141  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 183

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 184  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHH 217



 Score = 41.2 bits (95), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/44 (65%), Positives = 36/44 (81%)

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           PEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   PEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 44


>gi|258562142|gb|ACV81793.1| RNA polymerase II second largest subunit [Calocera viscosa]
          Length = 660

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 118/757 (15%), Positives = 202/757 (26%), Gaps = 151/757 (19%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R       R +H TH+G +CPAET EG   
Sbjct: 44   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIARPRQLHNTHWGMVCPAETPEGQAC 99

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++     +     + +  +  + +     E         N         
Sbjct: 100  GLVKNLALMACISVGSLSQPVVEFLEEWGL--EPLGERTDEGLMATKVFVNGVWMGIHRD 157

Query: 641  TEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC-- 694
             + LV              +I    D  +   +          P    ++  + L+    
Sbjct: 158  PQHLVNTVRTLRRSDGISSEISVVRDIRERELRLYTDAGRVCRPLFIVNEQTQNLVISKK 217

Query: 695  -----NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                   Q          +  V  GM                   VE +DA       + 
Sbjct: 218  EINYLQNQEDDEGQPYGWSQLVSNGM-------------------VELLDAEEEETVMIS 258

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
               +   +              QN  V  + +V               PS  LG      
Sbjct: 259  MTPEDLEASKTKRGTGYISNEPQNAAVRIKSIVH----HEHWSHCEIHPSMILG------ 308

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N       S R   +       +  +    +                 
Sbjct: 309  -ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVRM-------------- 347

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 348  ---------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVI 398

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +   +    I+ R   D  + +  V  E+ E   RD          +       +
Sbjct: 399  MNQSSIDRGLF-RSIYYRSYTDMEKTTGIVPVEEFEKPHRDTTVRMKHGTYDKLEADGLV 457

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  L  D      R++          ++     +  Q   S +  
Sbjct: 458  APGIGINGEDIIIGKTAPLPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLISTNE- 516

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                 ++ VKV +   R  Q GDK A RHG KG +      EDM
Sbjct: 517  -------------------SGVKFVKVRIRSTRVPQIGDKFASRHGQKGTIGMTYRQEDM 557

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   DI++NP  +PSRM +G + E  L      +G +  +          +S L 
Sbjct: 558  PFAANGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNEGDATPFTDLTVESVSSLL 617

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                   G G     +                                            
Sbjct: 618  R------GKGYQQRGLEVM----------------------------------------- 630

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
              G +    G         V +G  Y  +L HMV DK
Sbjct: 631  YHGHT----GR---KLQAQVYLGPTYYQRLKHMVDDK 660



 Score =  111 bits (278), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 75/566 (13%), Positives = 159/566 (28%), Gaps = 85/566 (15%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K+  +  G  ++  R    +      R          I    
Sbjct: 19  ITNGLKYSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIARPR 78

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   + + L     + +  + + +   +  ++   + P    
Sbjct: 79  QLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSQPV---VEFLEEWGLEPLGER 135

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             + +++          +    +  + ++ +   RR   +                ++  
Sbjct: 136 TDEGLMATKVFVNG-VWMGIHRDPQHLVNTVRTLRRSDGISSEISVVRDIRERELRLYTD 194

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                 P          LV S      +      E              V  L A EEE 
Sbjct: 195 AGRVCRPLFIVNEQTQNLVISKKEINYLQNQEDDEGQPYGWSQLVSNGMVELLDAEEEET 254

Query: 625 RYIAQANSSLDEDG-----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
             I+     L+         +            + +V  E     +  P  ++ I AS+I
Sbjct: 255 VMISMTPEDLEASKTKRGTGYISNEPQNAAVRIKSIVHHEHWSHCEIHPSMILGICASII 314

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 315 PFPDHNQSPRNTYQSAMGKQAMGIYLTNFQV----------------------------- 345

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + +  Y       +     +  R                    
Sbjct: 346 ------------RMDTMANILYYPQKPLATTRSMEYLKFR-------------------- 373

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  M + T + P 
Sbjct: 374 ----ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYTDMEKTTGIVPV 429

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E            +       ++  G++  G  +N  DI++GK  P         E+L +
Sbjct: 430 EEFEKPHRDTTVRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPL----PPDSEELGQ 485

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   DV        +G+   V+
Sbjct: 486 RTRTHTRRDVSTPLKSTENGIVDQVL 511


>gi|290745668|gb|ADD51568.1| RNA polymerase beta subunit [Mycobacterium sp. NL-JvIW-001]
          Length = 213

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 88/214 (41%), Positives = 117/214 (54%), Gaps = 35/214 (16%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 27   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+   N                  
Sbjct: 87   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWDIRKDGNAEIPAWA----------- 134

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                            ++    +   +    +TPVFDGA EE +  +L            
Sbjct: 135  ---------------QNLPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 179

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 180  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHH 213


>gi|307343508|emb|CBJ18671.1| RNA polymerase B subunit [Micromonospora sp. SG15]
          Length = 206

 Score =  244 bits (623), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 94/210 (44%), Positives = 122/210 (58%), Gaps = 38/210 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDTDWKRQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLSSTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              G++ L+DG +GEP   P+ VGYIY+LKL
Sbjct: 177  SSGKAQLFDGRSGEPLPDPIAVGYIYILKL 206


>gi|168010233|ref|XP_001757809.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691085|gb|EDQ77449.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 472

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 85/360 (23%), Positives = 140/360 (38%), Gaps = 59/360 (16%)

Query: 1007 VLSSDLISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            +   D++ +          V+D + +   +   + +    K +L+     +++K+     
Sbjct: 148  IPDGDILRDNDGIVLIGQKVKDGDTIAAKLVITEKKQSIEKIVLKSFVSGRVDKVTK--H 205

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  ++V+V + + R    GDK   RH  KG++  IL  ED+PF KDG   D+++NP 
Sbjct: 206  TSAEGNKIVRVRILLYRFPIVGDKFTSRHSQKGVIGAILSQEDLPFTKDGIVPDLIINPH 265

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +G + E  +               N+ +     S  RS     I   +  +  
Sbjct: 266  AIPSRMTMGHLLEMVMCKI-------YVLDSNNARDPTLPSKPRSRESSCIDATAFNKAY 318

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
              +                           E  I  +          +  +Y G TG P 
Sbjct: 319  RSF---------------------------EVDIAKL---------SKEKMYCGTTGLPI 342

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V  G  Y   L H   DK ++ S G    +T+QP+ G+S +GG R GEME  C+ A+
Sbjct: 343  EARVATGICYYHALRHQARDKAHSISKGVIQSLTKQPVEGRSRKGGLRFGEMEKDCLIAH 402

Query: 1306 GAAYVLQEMLTIKSD-----------DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GAA +L E L   SD            +            G +T E   P SF +L +E+
Sbjct: 403  GAASMLLEKLKNTSDLCEVWICHGCSTICSSNPCVNC--NGRNTKEHHLPYSFKLLAQEL 460


>gi|269913247|emb|CAY86050.1| RNA polymerase beta subunit [Asaia siamensis]
          Length = 243

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 104/246 (42%), Positives = 147/246 (59%), Gaps = 28/246 (11%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQ+HRSPG+ FDHDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+P
Sbjct: 1   VSQMHRSPGVFFDHDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLP 60

Query: 214 VTSFLMAL-------------------------GMDSEEILSTFYPKIVYSQRGDFWCFP 248
           VT+ L AL                         GMD +EIL+ FY  + +++    W  P
Sbjct: 61  VTTLLYALEGEHSIAARAAKAAEGGDVESMAIRGMDQDEILAYFYGTVPFTRMPKGWARP 120

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                   G K+   L D DTGE V E+  KLT+ +++ + E   K + +    L G ++
Sbjct: 121 FDPE-AFRGMKLLEPLYDADTGEVVAEADAKLTARMVRKIAET-TKDVLVGRADLLGRFM 178

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
           A+D+VN ETGEIY EAG+ + E  LE +  S + ++P+L VDS ++  +IRNTL  DKN 
Sbjct: 179 AQDLVNEETGEIYAEAGEELTEARLEALEESGVTELPMLAVDS-SHGPWIRNTLAVDKNN 237

Query: 369 DRKDAL 374
            R +AL
Sbjct: 238 RRDEAL 243


>gi|110669592|gb|ABG81891.1| RNA polymerase II second largest subunit [Roccella fuciformis]
          Length = 716

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 125/837 (14%), Positives = 238/837 (28%), Gaps = 144/837 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++   +R    ++ + +    +    +         +    + +
Sbjct: 1    DDRDHFGRKRLDLAGPLMAGLFRTPFQKLHKDVFRFLQRCVENDKPFSMDIAVKTNIITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAMQTKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CP+ET EG   GLV +L+    V+     E     +           L 
Sbjct: 117  RQLHNTHWGLVCPSETPEGQACGLVKNLSLMCTVSVGKPGEPIAEFLFGKD-------LE 169

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             +EE     A   + +  +G +          G+ +L  R      D +P+  +      
Sbjct: 170  PVEEYEPQKAPNATKVFLNGVWLGTHRNPTRLGDFMLSLRRS---ADIAPEVSIVRDIRE 226

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA----AIVAKRAGI 734
                   D+ RV+    +        K     +       +A          I       
Sbjct: 227  RELKIYTDAGRVMRPLLIVDNEPRSPKNGQLVLDFHHMEKIANDMEIRNDPTIHKDEKPK 286

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            +       +    +E           I   +     NQ+    +    K+GD +      
Sbjct: 287  LIYGFNGLVKDGVIEFLDAEEEESAMIVMNVAHLPGNQDPSRVKEY--KLGDRIEMKPSK 344

Query: 795  ADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                 T      ++   +  + +P+  +N          M  + +   + +  F      
Sbjct: 345  NANIFTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAQRMDT 402

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                          +             +       +   +  +
Sbjct: 403  MSN---------------------------ILYYPQKPLASTHSMNYLKFRDLPAGQNAI 435

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +     +  +     E+  SV    +E   + +  
Sbjct: 436  VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----EQQQSVGFNALEEFEKPRRG 491

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            E + +    Y +L +   +  G           K+    + +                E 
Sbjct: 492  EVLRMRPGTYEKLDDDGLVPPGVRVSGEDIIIGKTAPFQAPMQENA------------EG 539

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR  +  K          E    +++              R VKV     +  Q GDK 
Sbjct: 540  GQRTKDHTKRDVSAPLRSTEAGIIDRVL------LTTTEGKRSVKVRTRTTKVPQIGDKF 593

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + E  L       G+
Sbjct: 594  ASRHGQKGTIGITYRQEDMPFTTDGVVPDLIINPHAIPSRMTIAHLIECLLSKVSTVTGE 653

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +         +IS L  F                         A     G  +    
Sbjct: 654  EGDATPFTDVTVSNISELLKF-------------------------AGYQSRGFEMM--- 685

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                +G +    G      +  V +G  Y  +L HMV DK+
Sbjct: 686  -------------------HNGHT----GR---KLNAQVFLGPTYYQRLRHMVDDKI 716


>gi|52699876|gb|AAU86999.1| DNA-dependent RNA polymerase II second largest subunit [Sordaria
            macrospora]
          Length = 707

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 130/832 (15%), Positives = 232/832 (27%), Gaps = 152/832 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R  + R+ + +    +              I A  + + + 
Sbjct: 1    DHFGKKRLDLAGPLLAKLFRGIVRRLTQDLMGYMKRCVDTNKHFSLALGIKASTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKLAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+    V+     +    +    + +V  +   L  
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLRY 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      + +D      LV        I      + D  D   K        +
Sbjct: 177  PNATKVFVNGTWVGVHQDPKHLVTLVQNLRRKNIISFEVSLVRDIRDREFKIFSDAGRVM 236

Query: 679  IPFL-----ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
             P       +N DS        + ++ +  L+ +             +          +G
Sbjct: 237  RPLFTVEQEDNGDSGVEKGQLILTKEHIRRLEQDKEL------GKYHEDYFGWQGLLESG 290

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ----RSNQNTCVNQRPLVKVGDEVR 789
             +E +DA       +    +     +D YR  KF+      +     N R   K      
Sbjct: 291  AIEYLDAEEEETAMICMTPED----LDTYRQHKFKGREFEDDSANRGNSRIKTKFNPTTH 346

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    PS  LG       +  + +P+  +N             +     +      +
Sbjct: 347  MYTHCEIHPSMLLG-------ICASIIPFPDHNQSPRNTYQSAXGXQAXXXXLTNYSRRM 399

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                                           +  +             +       +   
Sbjct: 400  DT-----------------------------MANILYYPQKPLATTRSMEYLKFRELPAG 430

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R   D  +R      EQ E   R
Sbjct: 431  QNAIVAIACYSGYNQEDSVIMNQSSIDRGIF-RSLFFRSYTDCEKRVGINIVEQFEKPDR 489

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
                       +       I  G           K++ ++ D                 E
Sbjct: 490  SNTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPD---------------NQE 534

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  + +K    T     E    + +      D +     R VKV V   +  Q GDK
Sbjct: 535  LGQRTAQHVKRDASTPLRSTESGIVDSVAFTTNQDGL-----RYVKVRVRTTKIPQIGDK 589

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G
Sbjct: 590  FASRHGQKGTIGVTYRQEDMPFTAEGITPDIIINPHAIPSRMTIAHLIECLLSKVGSLKG 649

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +                              ++     ++LR       G  +   
Sbjct: 650  MEGDATPFT-------------------------DVTVDSVSNLLREHGYQSRGFEIM-- 682

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                  G +    G         V  G  Y  +L H
Sbjct: 683  --------------------YHGHT----GR---KLRAQVFFGPTYYQRLRH 707



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 77/584 (13%), Positives = 150/584 (25%), Gaps = 92/584 (15%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   ST G  ++  R    +      R          +     
Sbjct: 56  TNGLKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQ 115

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L N    +         +   + + L     + +  +   I E + + +++ +   + + 
Sbjct: 116 LHNTHWGLVCPAETPEGQACGLVKNLSLMCFVSVGTLADPIIEFMIARNMEVLEEYEPLR 175

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
                         + +   ++  + ++ + + RR + +                +    
Sbjct: 176 YPNATKVF---VNGTWVGVHQDPKHLVTLVQNLRRKNIISFEVSLVRDIRDREFKIFSDA 232

Query: 566 YGRICPAETSE-----------GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
              + P  T E           G  I     +    +    G     Y        +  +
Sbjct: 233 GRVMRPLFTVEQEDNGDSGVEKGQLILTKEHIRRLEQDKELGKYHEDYFGWQGLLESGAI 292

Query: 615 VYLSAMEEENRYIAQANSSLDE------DGSFTEELVFCRCAGEEILVPR---EKIDFID 665
            YL A EEE   I      LD        G   E+    R                   +
Sbjct: 293 EYLDAEEEETAMICMTPEDLDTYRQHKFKGREFEDDSANRGNSRIKTKFNPTTHMYTHCE 352

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R         QA                      + A
Sbjct: 353 IHPSMLLGICASIIPFPDHNQSPRNTYQSAXGXQAXXXXLTNYS---------RRMDTMA 403

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
            I+      +    ++  +          +   +  Y              NQ       
Sbjct: 404 NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSG-----------YNQ------- 445

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                + +I +  S D G         + F  +        + I E+    D        
Sbjct: 446 ----EDSVIMNQSSIDRGIFRS-----LFFRSYTDCEKRVGINIVEQFEKPDRS------ 490

Query: 846 EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                             +           ++  GII  G  V   DI++GK +P     
Sbjct: 491 ------------------NTLRPKHGTYDKLENDGIIAPGIRVTGDDIIIGKTSPINPDN 532

Query: 906 MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
               ++  + +        RD S  + S  SG V  V       
Sbjct: 533 QELGQRTAQHVK-------RDASTPLRSTESGIVDSVAFTTNQD 569


>gi|103001775|gb|ABF71521.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 697

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 112/818 (13%), Positives = 226/818 (27%), Gaps = 145/818 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L N +R+   ++ + + +  +              + +  + + +     +        
Sbjct: 1    LLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASILSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKST 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   ++ +  L+ +               S     AK  G    V     V+  V+
Sbjct: 237  NCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEYVD 286

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q               V+          T      ++ 
Sbjct: 287  AEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPSMI 346

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N          M  + +   + +  ++                    
Sbjct: 347  LGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM----------------- 387

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 388  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 437

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 438  IMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDD 493

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 494  DGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL- 552

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV +   +  Q GDK A RHG KG +     
Sbjct: 553  -------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 593

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          +
Sbjct: 594  QEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSV 653

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S L    E    +                                               
Sbjct: 654  SKLLR--EHGYQSRGFEVM----------------------------------------- 670

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                 +G +    G         V  G  Y  +L HMV
Sbjct: 671  ----YNGHT----GR---KLVAQVFXGPTYYQRLRHMV 697


>gi|140084108|gb|ABO84903.1| RpoB [Paenibacillus sp. FSL_F4-100]
          Length = 238

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 89/208 (42%), Positives = 117/208 (56%), Gaps = 54/208 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 85   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 144

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + S + D  +  D           
Sbjct: 145  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVASPVFDGASEYD----------- 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 194  ----------------------------------VFD---------TMEEAGMQRNGKTV 210

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            LYDG TGE F+R VTVG ++M+KL HMV
Sbjct: 211  LYDGRTGERFEREVTVGVMHMIKLAHMV 238



 Score = 89.0 bits (219), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 63/93 (67%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE LKN+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALKNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  EKAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 93


>gi|295814678|gb|ADG35927.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814680|gb|ADG35928.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814682|gb|ADG35929.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814684|gb|ADG35930.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814686|gb|ADG35931.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814688|gb|ADG35932.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814690|gb|ADG35933.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814692|gb|ADG35934.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814694|gb|ADG35935.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814696|gb|ADG35936.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814698|gb|ADG35937.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814700|gb|ADG35938.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814702|gb|ADG35939.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814704|gb|ADG35940.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814706|gb|ADG35941.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814708|gb|ADG35942.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814710|gb|ADG35943.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814712|gb|ADG35944.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814714|gb|ADG35945.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814716|gb|ADG35946.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814718|gb|ADG35947.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814720|gb|ADG35948.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814722|gb|ADG35949.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814724|gb|ADG35950.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814726|gb|ADG35951.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814728|gb|ADG35952.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814730|gb|ADG35953.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814732|gb|ADG35954.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814734|gb|ADG35955.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814736|gb|ADG35956.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814738|gb|ADG35957.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814740|gb|ADG35958.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814742|gb|ADG35959.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
 gi|295814744|gb|ADG35960.1| RNA polymerase beta-subunit [Mycobacterium neoaurum]
          Length = 204

 Score =  244 bits (622), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 23   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 82

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 83   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 127

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   S   V+TPVFDGA E+ +  +L     +      
Sbjct: 128  -----------------LPEGMQSAPSDSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 170

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 171  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 204


>gi|23451720|gb|AAN32831.1|AF440728_1 RNA polymerase beta-subunit [Rickettsia rhipicephali]
          Length = 281

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 181/281 (64%), Positives = 225/281 (80%), Gaps = 2/281 (0%)

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +       +N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG    E
Sbjct: 2   TLWQLMLPINKHGFIESPYRRVKDGYVTDEVVYLSAIEEGKYKIGQANSKVNKDGKLQGE 61

Query: 644 LVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
            + CR   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQRQAVP
Sbjct: 62  FINCRVEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQAVP 121

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L+K +APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E      +  VDIY
Sbjct: 122 LIKTDAPFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIY 180

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+KFQ+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYN
Sbjct: 181 NLLKFQKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYN 240

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           FEDS+LISER+V EDVFTSIHIEEFEV+ARDT+LGP EITR
Sbjct: 241 FEDSILISERIVKEDVFTSIHIEEFEVIARDTRLGPVEITR 281


>gi|153958177|gb|ABS53379.1| RpoB [Bacteriovorax sp. MNZ4]
          Length = 355

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 170/358 (47%), Positives = 236/358 (65%), Gaps = 10/358 (2%)

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+ES VA+ S A + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQN
Sbjct: 1    GIESTVARDSRAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQN 58

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC NQ+ LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+
Sbjct: 59   TCNNQKALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERL 118

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            ++ DVFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDI
Sbjct: 119  LARDVFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDI 178

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++  
Sbjct: 179  LVGKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELC 238

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKST 1006
             RS  +  ++  L+ RD+  E   +  +   ++ ++L G              +   K  
Sbjct: 239  ARSKEIIEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGA 298

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
             L+S++++  P        ++   ++  +           + +  +  ++I K   GD
Sbjct: 299  DLTSEVLASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGD 355


>gi|82504135|gb|ABB80490.1| RNA polymerase II subunit [Symbiotaphrina kochii]
          Length = 714

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 113/830 (13%), Positives = 226/830 (27%), Gaps = 140/830 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R    G +L N +R+   ++ + + +  +    +         + +  + + + 
Sbjct: 2    DHXGKKRXDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLK 61

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 62   YSLATGNWGDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 117

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L    +  V         +    + +V  +     +
Sbjct: 118  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSDPIVDFMIQRNMEVLEEYEPQRS 177

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  D S     V        I      + +  D   K         
Sbjct: 178  PNATKVFVNGVWVGVHRDPSHLVRDVQDLRRKHLISHEVSLVREIRDREFKIFTDAGRVC 237

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    +++ R      +   ++ +  L+ +               S      +  G   
Sbjct: 238  RPLFVINNNPRSDQCGTLVLTKEHIARLEDDKDL--------DPDLSPEEREERLFGWQG 289

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             V     ++  ++ + + +   V     ++  R  Q                       +
Sbjct: 290  LV--NNGIVEYMDAEEEETAMIVMTPEDLEISRQMQAGY------------------RVE 329

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
               T+  +  +   +      W       SM+  I   ++            ++      
Sbjct: 330  EEETEDLNKRVKAPLKPTAHSWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQ 389

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G      D                +  +             +       +   +  + 
Sbjct: 390  AMGVYLTNFDSRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIV 438

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   D+ +R      EQ E   R    +
Sbjct: 439  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGMSVVEQFEKPMRSDTLK 497

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +       +  G           K+  ++ D      R++          ++  
Sbjct: 498  LKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRST 557

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +  Q                             LR VKV +   +  Q GDK A RH
Sbjct: 558  ENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRH 597

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 598  GQKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 657

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L                                              
Sbjct: 658  TPFTEVTVDSVSRLLREHGYQSRGFEIM-------------------------------- 685

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                            +G +    G         V +G  Y  +L HMV 
Sbjct: 686  ---------------YNGHT----GR---KLRAQVFLGPTYYQRLRHMVD 713



 Score =  126 bits (316), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 88/626 (14%), Positives = 173/626 (27%), Gaps = 112/626 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N      NK  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 13  GPLLANLFRMLFNKLTKDVYKYLQKCVENNR--EFNLTLGVKSTTITNGLKYSL-ATGNW 69

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 70  GDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 129

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 130 TPEGQACGLVKNLALMCYITVGTPSDPIVDFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 189

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  +   RR   +  +  + R     E        R   P       P  
Sbjct: 190 VGVHRDPSHLVRDVQDLRRKHLISHEVSLVREIRDREFKIFTDAGRVCRPLFVINNNPRS 249

Query: 574 TSEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYI 627
              G  +     ++ L     ++     E    ++   +       V Y+ A EEE   I
Sbjct: 250 DQCGTLVLTKEHIARLEDDKDLDPDLSPEEREERLFGWQGLVNNGIVEYMDAEEEETAMI 309

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                E++                  +  P  ++ I AS+I
Sbjct: 310 VMTPEDLEISRQMQAGYRVEEEETEDLNKRVKAPLKPTAHSWTHCEIHPSMILGICASII 369

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M  QA+ +                   S    +A          
Sbjct: 370 PFPDHNQSPRNTYQSAMGXQAMGVYLTNF-------------DSRMDTMA---------- 406

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                                 Q+PL                  
Sbjct: 407 --------------------------------NILYYPQKPL----------ATTRSMEF 424

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 425 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRVGMSVV 484

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   +       +DE GI+  G  V+  DI++GK  P         E+L +
Sbjct: 485 EQFEKPMRSDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQ 540

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   DV        +G+   V+
Sbjct: 541 RTKLHIKRDVSTPLRSTENGIVDQVL 566


>gi|256014684|gb|ACU56890.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 209

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 87/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 88   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 133  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 176  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLHH 209


>gi|89090012|gb|ABD59028.1| RNA polymerase II second largest subunit [Guepiniopsis buccina]
          Length = 676

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 122/817 (14%), Positives = 227/817 (27%), Gaps = 170/817 (20%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R+   R+ + +    +              +    + + +   
Sbjct: 1    FGKKRLDLAGPLLATLFRMLFRRLTKDVYRYMQKCVETHREFNINAAVKPATITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R       R +H 
Sbjct: 61   LATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIARPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A ++     +     + +  +  + +   A E  
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMACISVGSLSQPVVEFLEEWGL--EPLGERADEPL 174

Query: 624  NRYIAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDASPKQ---VVSIAASLI 679
                   N          + LV   R       +  E     D   ++            
Sbjct: 175  TATKVFVNGVWMGVHRDPQHLVDTVRVLRRSAGINTEISVVRDIRERELRLYTDAGRVCR 234

Query: 680  PFLENDDSNRVLM----GCNMQRQAVPLLKAEA-----PFVGTGM-ESVVAKSSGAAIVA 729
            P    ++  + L        M R        ++       + TGM E + A+     ++A
Sbjct: 235  PLFVVNEPTQSLTITKREIGMLRSPPRDDDPDSRYGWSQLLTTGMVEMLDAEEEETVMIA 294

Query: 730  KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                 +E   + R    +     + +T          +                      
Sbjct: 295  MTPEDLESSRSKRGTGYASNEPPNAATRIKSTVHHEHWS--------------------- 333

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    PS  LG       +  + +P+  +N       S R   +       +  +  
Sbjct: 334  ---HCEIHPSMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLT 377

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
              +                            +  +             +       +   
Sbjct: 378  NFQVRM-----------------------DTMANILYYPQKPLATTRSMEYLKFRELPAG 414

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    I+ R   D  + +  V  E+ E   R
Sbjct: 415  QNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYTDMEKTTGIVPVEEFEKPHR 473

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
            D          +       +  G           K+  L  D      R++         
Sbjct: 474  DTTVRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPLPPDSEELGQRTRTHTRRDVST 533

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S +                       ++ VKV +   R  Q GDK
Sbjct: 534  PLKSTENGIVDQVLISTNE--------------------SGVKFVKVRIRSTRIPQIGDK 573

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G
Sbjct: 574  FASRHGQKGTIGMTYRQEDMPFAANGITPDIVINPHAIPSRMTIGHLVECLLSKLATLIG 633

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +                                                       +TP
Sbjct: 634  NEGD-----------------------------------------------------ATP 640

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
             F     E+++++LR     + G  ++Y G TG    
Sbjct: 641  -FTDLTVESVSALLRGKGYQQRGLEVMYHGHTGRKLQ 676


>gi|55140711|gb|AAQ01544.3| RNA polymerase II second largest subunit [Phaeomarasmius proximans]
          Length = 687

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 123/819 (15%), Positives = 240/819 (29%), Gaps = 152/819 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++  G I  P  +  +      +       EEN +
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMSCIS-VGTISAPVIEFLEEWGLESL-------EENAH 169

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                 + +  +G +       R A   +   ++     D SP+  V             D
Sbjct: 170  STTPFTKVFVNGVWIG---VHRDAANLVKTLKKLRRKDDLSPEVSVVRDIREKELRVYTD 226

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +      +L+ +   ++  G+    ++         R G +E +DA     
Sbjct: 227  AGRVCRPLFIVENQQLMLQKKHIRWLNNGVNDEGSEFKWE--HLIRGGTIELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +     +         +   +    +K G            PS  LG  
Sbjct: 285  VMISMTPEDLENSRL--QQRGIDVPVNDGEYDPAARLKAGTHAHTWTHCEIHPSMILG-- 340

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 341  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLI 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 378  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S     +Q+E   +   +  + L    Y +
Sbjct: 427  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGV---QQLEEFEKPTRENTLRLKHGTYDK 482

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 483  LEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQV 542

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 543  LL--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGI 582

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 583  TYRQEDMPFTSEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT---- 638

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                  ++     + LR       G+ V                
Sbjct: 639  ---------------------DLTVESVSTFLRQKGYQSRGLEVM--------------- 662

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                     G +       G      V +G  Y  +L H
Sbjct: 663  -------YHGHT-------GRKLQAQVYLGPTYYQRLKH 687



 Score =  124 bits (310), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 87/622 (13%), Positives = 171/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + ++    +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMSCISVGTISAPVIEFLEEWGLESLEENAHSTTPFTKVFVNGVWI 184

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  +   RR   L            +   V+        P    E  N  L
Sbjct: 185 GVHRDAANLVKTLKKLRRKDDLSPEVSVVRDIREKELRVYTDAGRVCRPLFIVE--NQQL 242

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +        +N     E    K         +  L A EEE   I+     L+       
Sbjct: 243 MLQKKHIRWLNNGVNDEGSEFKWEHLIRGGTIELLDAEEEETVMISMTPEDLENSRLQQR 302

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE                   +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 GIDVPVNDGEYDPAARLKAGTHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIYLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 382 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRENTLRLKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 478 GTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 530

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V +       K
Sbjct: 531 LKSTESGIVDQVLLTTNSEGQK 552


>gi|140084102|gb|ABO84900.1| RpoB [Paenibacillus xylanilyticus]
 gi|140084120|gb|ABO84909.1| RpoB [Paenibacillus amylolyticus]
 gi|140084136|gb|ABO84917.1| RpoB [Paenibacillus amylolyticus]
 gi|140084138|gb|ABO84918.1| RpoB [Paenibacillus amylolyticus]
          Length = 238

 Score =  244 bits (622), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 89/208 (42%), Positives = 116/208 (55%), Gaps = 54/208 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 85   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 144

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV IVLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 145  TPVQIVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGAKEYD----------- 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 194  ----------------------------------VFD---------TMEEAGMQRNGKTV 210

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            LYDG TGE F+R VTVG ++M+KL HMV
Sbjct: 211  LYDGRTGEEFEREVTVGVMHMIKLAHMV 238



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 63/93 (67%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 61  EKAREVRDTSLRVPHGTDGIVVDVKVFTRENGD 93


>gi|224797525|gb|ACN62792.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           hydei]
          Length = 288

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 159/296 (53%), Positives = 216/296 (72%), Gaps = 8/296 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D S
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNS 288


>gi|103001385|gb|ABF71505.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 709

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 117/827 (14%), Positives = 232/827 (28%), Gaps = 143/827 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + + +  +              + +  + + +    
Sbjct: 3    GKKRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSL 62

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 63   ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 118

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     +      E    +    + +V  +     +   
Sbjct: 119  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNA 178

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP- 680
               ++      +  D +     V        I      + D  D   K          P 
Sbjct: 179  TKVFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPL 238

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
            F+ ++D      G  +  +       +   +   M+    +       AK  G    V  
Sbjct: 239  FVIDNDPKSTNCGNLVLTKEHISKLEDDRDLPAIMDPEEKE-------AKFFGWDGLV-- 289

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               V+  V+ + + +   V     ++  R  Q           +   V+          T
Sbjct: 290  NNGVVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWT 349

Query: 801  DLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                  ++   +  + +P+  +N                        ++       +G  
Sbjct: 350  HCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKXXMGVF 391

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                D                +  +             +       +   +  + AI   
Sbjct: 392  LTNYDQRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACY 440

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L 
Sbjct: 441  SGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLK 496

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               Y +L +   +  G           K+  +S D      R++          ++    
Sbjct: 497  HGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTEN 556

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  Q                             L+ VKV +   +  Q GDK A RHG 
Sbjct: 557  GIVDQVLL--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQ 596

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 597  KGTIGITYRQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATP 656

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E    +                                      
Sbjct: 657  FTEVTVDSVSKLLR--EHGYQSRGFEVM-------------------------------- 682

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                          +G +    G         V +G  Y  +L  MV
Sbjct: 683  -------------YNGHT----GR---KLVAQVFLGPTYYQRLRXMV 709


>gi|320172596|gb|ADW24181.1| RNA polymerase II second largest subunit [Neolentinus lepideus]
          Length = 655

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 114/732 (15%), Positives = 220/732 (30%), Gaps = 100/732 (13%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L N +R+   ++ + +    +              +    + + +  
Sbjct: 4    HFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKY 63

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 64   SLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLH 119

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             TH+G +CPAET EG   GLV +L   + ++           + +  + +         E
Sbjct: 120  NTHWGMVCPAETPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL--------E 171

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            EN + A   + +  +G +       R     +   ++     D SP+  V          
Sbjct: 172  ENAHSATPCTKVFVNGVWMG---VHRDPANLVRTIKKLRRKDDISPEVSVVRDIRERELR 228

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG-----IVEQ 737
               D+ RV     +       L+ +       +  +    S      K        IVE 
Sbjct: 229  LYTDAGRVCRPLFIVENQQLALQKK------HVRWLNQGYSDDGEPWKWDQLVKNGIVEL 282

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +       +   +++     + R  +K              
Sbjct: 283  LDAEEEETVMISMTPEDLENSRLQSAGIDPHQNDGEFDPSAR--LKAATHGHTWTHCEIH 340

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 341  PSMILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 375

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   +               +  +             +       +   +  + AI 
Sbjct: 376  IYLTNFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAIL 424

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD       
Sbjct: 425  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKH 483

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  +  D                +E  QR    
Sbjct: 484  GTYDKLEDDGLIAPGTGVTGDDIIIGKTAPIPPD---------------SEELGQRTRSH 528

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             +    T+    E    +++              + VKV V   R  Q GDK A RHG K
Sbjct: 529  TRRDVSTALKSTEQGIVDQVLI-----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQK 583

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +   
Sbjct: 584  GTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 643

Query: 1158 DYKANGDISPLR 1169
                   +S   
Sbjct: 644  TDLTVESVSTFL 655



 Score =  121 bits (303), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 85/622 (13%), Positives = 172/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 14  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHNTITNGLKYSL-ATGNW 70

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 71  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 130

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 131 TPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 190

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 191 GVHRDPANLVRTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 250

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     +    K         V  L A EEE   I+     L+     + 
Sbjct: 251 QKKHVRW--LNQGYSDDGEPWKWDQLVKNGIVELLDAEEEETVMISMTPEDLENSRLQSA 308

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +  GE     R             +  P  ++ + AS+IPF +++ S R      
Sbjct: 309 GIDPHQNDGEFDPSARLKAATHGHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 368

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 369 MGKQAMGIYLTNFLV-----------------------------------------RMDT 387

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 388 MANILYYPQKPLATTRSMEYLRFR------------------------ELPAGQNAIVAI 423

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 424 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKH 483

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        ++   RD S  
Sbjct: 484 GTYDKLEDDGLIAPGTGVTGDDIIIGKTAPIPPDSEELGQRT-------RSHTRRDVSTA 536

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S   G V  V I       K
Sbjct: 537 LKSTEQGIVDQVLITTNSEGQK 558


>gi|307343530|emb|CBJ18682.1| RNA polymerase B subunit [Micromonospora sp. SR4]
          Length = 205

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 93/210 (44%), Positives = 121/210 (57%), Gaps = 38/210 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 86   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWNVEGDEADWKRALRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AAEAEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              G++ L+DG +GEP   P+ VGYIY+LKL
Sbjct: 176  SSGKAQLFDGRSGEPLPDPIAVGYIYILKL 205


>gi|113707359|gb|ABI36587.1| RNA polymerase II second largest subunit [Opegrapha dolomitica]
          Length = 702

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 125/823 (15%), Positives = 222/823 (26%), Gaps = 156/823 (18%)

Query: 474  QYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + I +       +         +    + + +     +            
Sbjct: 1    LFRTLFTKLTKDIFKYLERCVENNKDFSLDVGVRHSIITNGLRYSLATGNWGEQKKAQQT 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV +L     V+     E  Y    + +    +    A    N      N +     
Sbjct: 117  ACGLVKNLALMCYVSVGSPGEPFYE-YPNEQGMEPIEDYEARRFPNATKIFVNGTWIGVS 175

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                 LV                     SP+  +        F    D+ RV+       
Sbjct: 176  RNPSILVSDMQKLRRDGSM---------SPEVSLVRDIREREFKIFTDAGRVM------- 219

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                      P     ++     +   AI A     +E+ + I+      + + + +   
Sbjct: 220  ---------RPLFVVDIDPKSPNNGDLAINASHIDRLEEWNQIKGQYTRAQLEEEHAEQD 270

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            +                  Q  LVK G  + +   +  +     D   L    N      
Sbjct: 271  L------------GMFGWTQ--LVKTGVIEYLDAEEEESAMIIMDPSQLGQTSNNP---- 312

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---- 872
                   E+  L         +  ++H      +     LG        P          
Sbjct: 313  EEAAKEGEEDKLAPPSKPQSQISRNVHTYTHCEINPSMILGVCASIIPSPTXXXXXXXXX 372

Query: 873  ------------LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                        L N DE    +  +             +       +   +  + AI  
Sbjct: 373  XXXXXXXXXXVFLTNFDERMDTMANILYYPQKPLATTRSMEFLRFRDLPAGQNAIVAIAC 432

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R  I+  +       E  E   R       + 
Sbjct: 433  YSGYNQEDSVIMNQSAIDRGLF-RSLFYRTYIESEQTVGINNLEHFEKPVRQLTMRMSMG 491

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      +  G     G     K+  L+  +                          
Sbjct: 492  TYEKLDDDGLVPPGMRVSGGDIIIGKTMPLTGPMQEGAEGGS------------------ 533

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            ++     K +       +   I           + VKV     +  Q GDK A RHG KG
Sbjct: 534  RLAAHEKKDVSAALRSTEAGIIDRVILTTNDGRKSVKVRTRTTKVPQVGDKFASRHGQKG 593

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+V+NP  +PSRM +  + E  L       G +       
Sbjct: 594  TIGITYRQEDMPFTSEGLTPDLVINPHAIPSRMTIAHLIECLLSKVAACEGVEGD----- 648

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     + 
Sbjct: 649  ------------------------------------------------ATP-FTPVTVQD 659

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
            I+S+L  A   + G  I+++G TG+     + +G  Y  +L H
Sbjct: 660  ISSLLESAGYQQRGSEIMHNGHTGQKLKAQIFLGPTYYQRLRH 702


>gi|94410904|gb|ABF18573.1| RNA polymerase II second largest subunit [Fistulina antarctica]
          Length = 690

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 121/830 (14%), Positives = 227/830 (27%), Gaps = 165/830 (19%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + +   +               + ++ + + +   
Sbjct: 1    FGKKRLDLAGPLLSNLFRMLFRKVTKDVYRYLQKCVEMRKDFHLNMAVKSQTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R  H 
Sbjct: 61   LATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQXHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A ++   +       + +  + +     +A    
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIDFLEEWGLESLXE--NAHSST 174

Query: 624  NRYIAQANSSLDEDGSFTEEL-VFCRCAGEEILVPREKIDFIDASPK---QVVSIAASLI 679
                   N            L    R    +  +  E     D   K             
Sbjct: 175  PCTKVFVNGVWMGVHRDPANLAKXIRKLRRKDDISPEVSVVRDVREKELRIFTDAGRVCR 234

Query: 680  PFLENDDSNRVLMGCNMQ------RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
            P    ++   +L   ++Q      +      + E       +E + A+     +++    
Sbjct: 235  PLFIVENQQLLLQKKHIQWLNAGVKDDGSTFQWEQLIKDGIIELLDAEEEETVMISMTPE 294

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
             +E        I + + +     +                        +K G        
Sbjct: 295  DLETSRLQSSGIETQDEEDFDPAA-----------------------RLKAGINTHTWTH 331

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N                        ++     
Sbjct: 332  CEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGK 366

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
              +G       I               +  +             +       +   +  +
Sbjct: 367  QAMGIFLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAI 415

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R  +D  + S   + EQ E  +RD   
Sbjct: 416  VAILCYSGYNQEDSVIMNQSSIDRGLF-RSMFYRSYMDLEKTSGVQQLEQFEKPSRDTTI 474

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +       I  G           K+  +  D                +E  QR
Sbjct: 475  RMKHGTYDKLDDDGLIAPGTGVNGEDIIIGKTAPIPPD---------------SEELGQR 519

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                 +    T     E    +++      D       + VK+ V   R  Q GDK A R
Sbjct: 520  TRNHTRRDVSTPLKSTESGIVDQVLVTTNAD-----GHKFVKIRVRSTRVPQIGDKFASR 574

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  
Sbjct: 575  HGQKGTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD 634

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +          +S      +K   +                                   
Sbjct: 635  ATPFTDLTVESVSRFLR--QKGYHSRGLEVM----------------------------- 663

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                              G +       G      V +G  Y  +L HMV
Sbjct: 664  ----------------YHGHT-------GRKLQAQVYLGPTYYQRLKHMV 690



 Score =  119 bits (298), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 82/610 (13%), Positives = 164/610 (26%), Gaps = 99/610 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F +  ++ +    +  KY L   G  
Sbjct: 10  GPLLSNLFRMLFRKVTKDVYRYLQKCVEM--RKDFHLNMAVKSQTITNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 67  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQXHNTHWGMVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 127 TPEGQACGLVKNLALMACISVGSYSAPVIDFLEEWGLESLXENAHSSTPCTKVFVNGVWM 186

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N    I   RR   +            +   +         P    E   + L
Sbjct: 187 GVHRDPANLAKXIRKLRRKDDISPEVSVVRDVREKELRIFTDAGRVCRPLFIVENQQLLL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +NA    +    +         +  L A EEE   I+     L E      
Sbjct: 247 QKKHIQW--LNAGVKDDGSTFQWEQLIKDGIIELLDAEEEETVMISMTPEDL-ETSRLQS 303

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             +  +   +          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 304 SGIETQDEEDFDPAARLKAGINTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 363

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 364 MGKQAMGIFLTNFLI-----------------------------------------RMDT 382

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 383 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 418

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F S+    +  + + + +   E            +  
Sbjct: 419 LCYSGYNQEDSVIMNQSSIDRGLFRSMFYRSYMDLEKTSGVQQLEQFEKPSRDTTIRMKH 478

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +D+ G+I  G  VN  DI++GK  P         E+L +        DV      
Sbjct: 479 GTYDKLDDDGLIAPGTGVNGEDIIIGKTAPI----PPDSEELGQRTRNHTRRDVSTPLKS 534

Query: 931 VPSGVSGTVV 940
             SG+   V+
Sbjct: 535 TESGIVDQVL 544


>gi|140084114|gb|ABO84906.1| RpoB [Paenibacillus sp. FSL_F4-122]
          Length = 240

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 88/209 (42%), Positives = 116/209 (55%), Gaps = 54/209 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 86   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 145

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 146  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 194

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 195  ----------------------------------VFD---------TMEEAGMQRNGKTV 211

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            LYDG TGE F+R VTVG ++M+KL HMV 
Sbjct: 212  LYDGRTGERFEREVTVGVMHMIKLAHMVD 240



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 63/94 (67%), Positives = 76/94 (80%)

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIF
Sbjct: 1   PEEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIF 60

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  GEKAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 94


>gi|295814658|gb|ADG35917.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814660|gb|ADG35918.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814662|gb|ADG35919.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814664|gb|ADG35920.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814666|gb|ADG35921.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814668|gb|ADG35922.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814670|gb|ADG35923.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814672|gb|ADG35924.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814674|gb|ADG35925.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
 gi|295814676|gb|ADG35926.1| RNA polymerase beta-subunit [Mycobacterium bacteremicum]
          Length = 204

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 85/214 (39%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 23   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 82

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 83   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAGN-------------- 127

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 128  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGEVM 170

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 171  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 204


>gi|108885423|gb|ABG23221.1| RNA polymerase II second largest subunit [Bannoa sp. MP3490]
          Length = 646

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 111/717 (15%), Positives = 218/717 (30%), Gaps = 90/717 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L   +R+   ++ + +   +            +  I +  + + + 
Sbjct: 1    DHFGRKRLDLAGPLLGALFRMLFRKLTKDVYRHLQKCVETQKDFHLEQAIRSTTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H R  +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMQAKAGVSQVLNRYTFASTLSHLRXCNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H +H+G +CPAET EG   GLV +L   A ++           + +  + N        E
Sbjct: 117  HNSHWGMVCPAETPEGQACGLVKNLALMAYISVGSPSAPIVEFLEEWGMEN-------FE 169

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E +  +A  ++ +  +G +       R   + +   ++     D S +  V         
Sbjct: 170  EFSSDLA-KSTKVFVNGVWQG---IHRDPQQLVHTIKKLRRCADISCEVSVVRDVREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                DS R      +  + + L                  +          GIVE +DA 
Sbjct: 226  RIFTDSGRXARPLFIVEEDMSLALKRKHINWLTDSMDDEGNPYTWQSMVDTGIVEYLDAE 285

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +      D     K     Q      +P V      +        P+  
Sbjct: 286  EEETVMISMTPEDLDQVRDYVNTGKVVEKPQELGARVKPSVAT--YSQTWTHCEIHPAMI 343

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M        +++  + V            
Sbjct: 344  LG-------ICASIIPFPDHNQSPRNTYQSAMKQ---AMGVYLTNYLVRM---------- 383

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 384  -----------------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSG 426

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    ++ R  +D+ ++  ++  E+ E   R+          +
Sbjct: 427  YNQEDSVIMNQSSIDRGLF-RSLYYRSYMDQEKKQGNITMEEFEKPMRETTLRLKHGTYD 485

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  +                +E  QR+    K  
Sbjct: 486  KLDTDGLIAPGSRVSGEDIIIGKTAPIMGE---------------SEELGQRSKTQTKRD 530

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
              T     E+   +++             L+ VKV V   R  Q GDK A RHG KG + 
Sbjct: 531  VSTPLKSTENGIVDQVLV-----TTNSEGLKFVKVRVRSTRVPQIGDKFASRHGQKGTIG 585

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                 EDMPF   G   D+++NP  +PSRM +G + E  L       G +  +   +
Sbjct: 586  ITYRQEDMPFSNQGITPDLIINPHAIPSRMTIGHLVECLLSKVSCIHGNEGDATPFN 642


>gi|254803160|gb|ACT82830.1| RNA polymerase B-subunit [Staphylococcus xylosus]
          Length = 267

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 156/267 (58%), Positives = 197/267 (73%), Gaps = 3/267 (1%)

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIE
Sbjct: 1   RLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIE 60

Query: 600 TPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           TPYRKV      +T  + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ 
Sbjct: 61  TPYRKVDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTVMA 120

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME 
Sbjct: 121 KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEH 180

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
           V A+ SGAAIVAKR G VE V++  +++R  +E D       +D Y L KF+RSN  TC 
Sbjct: 181 VAARDSGAAIVAKRKGRVEHVESNEVLVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTCY 240

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLG 803
           NQRP+V  GD V R +I+ADGPS +LG
Sbjct: 241 NQRPIVSPGDVVTRGEILADGPSMELG 267


>gi|46277271|gb|AAS86826.1| RNA polymerase II second largest subunit [Antirrhinum majus]
          Length = 575

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/500 (16%), Positives = 149/500 (29%), Gaps = 91/500 (18%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
              T    L+   N   A+   +       S++  +   ++            ++      
Sbjct: 164  SMTINDLLSAKVNPTEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 223

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G          V+    +      +  V        +    +       +      + 
Sbjct: 224  AMG--------IYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 272

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R     
Sbjct: 273  AIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMG 331

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T +S                  D+   + 
Sbjct: 332  MRHGSYDKLDDDGLAPPGTRCSGEDVIIGKTTPISP-----------------DDAQGQA 374

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K  + TS    E    +++      D +     R VKV V   R  Q GDK + RH
Sbjct: 375  ARYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRH 429

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 430  GQKGTVGMTYTQEDMPWTVEGISPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 489

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS         +                                      
Sbjct: 490  TPFTDVTVDNISKALHKCGYQMRGFETM-------------------------------- 517

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                            +G +    G         + +G  Y  +L HMV DK+++R  G 
Sbjct: 518  ---------------YNGHT----GR---RLSSMIFLGPTYYQRLKHMVDDKIHSRGRGP 555

Query: 1275 YSLVTQQPLGGKSNRGGQRL 1294
              ++T+QP  G+S  GG R 
Sbjct: 556  VQILTRQPAEGRSRDGGLRF 575



 Score =  102 bits (255), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 70/486 (14%), Positives = 136/486 (27%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGLWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +S +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHRNPDMLVSTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSS----LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
                  L      +  G+ E              + Y+   EEE   I+   + L    
Sbjct: 123 KKKDVQALQQRESPDDGGWHELV--------AKGFIEYIDTEEEETTMISMTINDLLS-- 172

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                               +     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 173 ----------AKVNPTEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G   +  D+++GK TP              A         RD S  +  
Sbjct: 338 DKLDDDGLAPPGTRCSGEDVIIGKTTPISPDD---------AQGQAARYTKRDHSTSLRH 388

Query: 934 GVSGTV 939
             +G V
Sbjct: 389 SETGMV 394


>gi|207690921|gb|ACI25195.1| RNA polymerase beta [Mycobacterium neoaurum]
 gi|207690923|gb|ACI25196.1| RNA polymerase beta [Mycobacterium neoaurum]
 gi|207691927|gb|ACI25198.1| RNA polymerase beta [Mycobacterium sp. ATCC 27277]
          Length = 212

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   S   V+TPVFDGA E+ +  +L     +      
Sbjct: 136  -----------------LPEGMQSAPSDSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|88976144|gb|ABD59037.1| RNA polymerase II second largest subunit [Inocybe cookei]
          Length = 688

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 124/829 (14%), Positives = 230/829 (27%), Gaps = 168/829 (20%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   F       + +  + +     +A     
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSFSGPVIEFLEEWGLESLEE--NAHSSTA 174

Query: 625  RYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                  N            LV      R   +         D  +   +          P
Sbjct: 175  FTKVFVNGVWIGVHRDAANLVKTLKRLRRRDDISTEISXVRDIREREMRVYTDAGRVCRP 234

Query: 681  FLENDDSNRVLMGCNM------QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
                +D   VL   ++              K E    G  +E + ++     +++     
Sbjct: 235  LFIVEDQQLVLQKKHVRWLNSGVDDEGQEFKWEQMIKGGIIELLDSEEEETVMISMTPED 294

Query: 735  VEQVDAIRIVI--RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            +E     +  I   + +G+ DP+                          +K G       
Sbjct: 295  LENSRLQQRGIDPHANDGEFDPAA------------------------RLKAGTHAHTWT 330

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N                        ++    
Sbjct: 331  HCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMG 365

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G       I               +  +             +       +   +  
Sbjct: 366  KQAMGIYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNA 414

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD  
Sbjct: 415  IVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTT 473

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       I  G           K+  +  D                +E  Q
Sbjct: 474  LRMKHGTYDKLEDDGFIAPGTGVRGEDIIIGKTAPIPPD---------------SEELGQ 518

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R     +    T     E    +++              + VKV V   R  Q GDK A 
Sbjct: 519  RTRTHTRRDVSTPLKSTESGSVDQVLI-----TTNSEGQKFVKVRVRSIRIPQIGDKFAS 573

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +G + E  L      +G + 
Sbjct: 574  RHGQKGTIGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEG 633

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +                              ++     + LR       G+ V      
Sbjct: 634  DATPFT-------------------------DLTVESVSTFLRQRGYQSRGLEVM----- 663

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                               G +       G      V +G  Y  +L H
Sbjct: 664  -----------------YHGHT-------GRKLQAQVYLGPTYYQRLKH 688


>gi|300394682|gb|ADK11879.1| DNA-directed RNA polymerase II subunit two [Boletus edulis]
          Length = 673

 Score =  243 bits (621), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 114/729 (15%), Positives = 217/729 (29%), Gaps = 89/729 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + A   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSATPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +       L+ +                       + GI+E +DA 
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDGDGEEFKWEQLVKTGIIELLDAE 285

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +   +       +    ++       R  +K G            PS  
Sbjct: 286  EEETVMISMTPEDLENSRLQSAGINPHENDGEFDPAAR--LKAGINAHTWTHCEIHPSMI 343

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 344  LG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLT 378

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +               +  +             +       +   +  + AI     
Sbjct: 379  NFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 427

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 428  YNQEDSVIMNQSSIDRGLF-RSIYYRGYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYD 486

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G N         K+  +  D      R++          ++     +  Q
Sbjct: 487  KLEDDGLIAPGTNVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ 546

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VKV V   R  Q GDK A RHG KG + 
Sbjct: 547  VLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIG 586

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +       
Sbjct: 587  ITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLT 646

Query: 1162 NGDISPLRS 1170
               +S    
Sbjct: 647  VESVSTFLR 655



 Score =  125 bits (315), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 80/611 (13%), Positives = 166/611 (27%), Gaps = 99/611 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSATPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH-NIG 581
               +  N +  I   RR   +                ++        P    E      
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +    +    G  E    K      T  +  L A EEE   I+     L+     +
Sbjct: 249 QKKHIKWLNQGYRDGDGEE--FKWEQLVKTGIIELLDAEEEETVMISMTPEDLENSRLQS 306

Query: 642 EELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +      GE          +        +  P  ++ + AS+IPF +++ S R     
Sbjct: 307 AGINPHENDGEFDPAARLKAGINAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 366

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 367 AMGKQAMGIYLTNFLV-----------------------------------------RMD 385

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 386 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 421

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            + + GYN EDS+++++  +   +F SI+   +  + + + +   E            + 
Sbjct: 422 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRGYMDLEKKSGIQQLEEFEKPTRDTTLRMK 481

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +++ G+I  G  V   DI++GK  P         E+L +        DV     
Sbjct: 482 HGTYDKLEDDGLIAPGTNVRGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLK 537

Query: 930 RVPSGVSGTVV 940
              +G+   V+
Sbjct: 538 STENGIVDQVL 548


>gi|224797607|gb|ACN62833.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           atripex]
 gi|224797609|gb|ACN62834.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           ananassae]
          Length = 424

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 169/317 (53%), Positives = 226/317 (71%), Gaps = 8/317 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            LD +       V  R  G+ I+V   ++++ID SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   ELDTNNVIKNNNVIARSNGQNIIVGPNEVEYIDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PLLK + P VGTG+E  VA+ SG AIVA   G+V+ VD+  I+I+S +   
Sbjct: 61  GANMQRQAIPLLKPQTPIVGTGVEYAVARDSGLAIVANLPGVVQYVDSHEIIIKSEDE-- 118

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 +  Y L +F+RSNQ T V   PLVKVGD+V  N I+ADGPS   G+LALG+N++
Sbjct: 119 ------ITTYELSRFERSNQGTAVTHVPLVKVGDKVEVNQILADGPSMKDGELALGQNVI 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           +AFM WHGYN+ED+++ISER+V +DV+TS+HIEE+ +  R TK G EEITR+IPN SE+ 
Sbjct: 173 IAFMTWHGYNYEDAIIISERLVKDDVYTSMHIEEYNLECRKTKQGKEEITREIPNTSEQS 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + +D+ GI+ +G EV  GDILVGK+TPKG++  T EEKLL AIFGEK+ +V+D SLRVP
Sbjct: 233 RRYLDDEGIVLIGTEVKEGDILVGKVTPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVP 292

Query: 933 SGVSGTVVDVRIFNRHG 949
           +G +G V  ++ + R  
Sbjct: 293 NGGAGIVQGIKRYKRED 309



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 92/299 (30%), Positives = 134/299 (44%), Gaps = 25/299 (8%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V    IL    +   +  +   + ++ A       +  D  +     V   V 
Sbjct: 141  LVKVGDKVEVNQILADGPS-MKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVY 199

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ++  +     E    +I    E   R  DDE  I+      +  +IL G+ 
Sbjct: 200  TSMHIEEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDE-GIVLIGTEVKEGDILVGKV 258

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L + +  E  R+               V+ +                
Sbjct: 259  TPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIVQGI---------------- 302

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K + G D+P  V  VVKVF+  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+D
Sbjct: 303  -KRYKREDGFDLPSEVEEVVKVFIVQKRKIREGDKMAGRHGNKGVISKVLPIEDMPFLED 361

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            GTPVDI+LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+  +    +
Sbjct: 362  GTPVDIMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGAKNQDLLDIMKEAK 420


>gi|52699822|gb|AAU86973.1| DNA-dependent RNA polymerase II second largest subunit [Peltula
            umbilicata]
          Length = 704

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 120/824 (14%), Positives = 233/824 (28%), Gaps = 140/824 (16%)

Query: 466  SVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G +L N +R    ++ R I +  +              +    + + +     +    
Sbjct: 1    LAGPLLANLFRGLFAKLTRDIYKYLQKCVESNREFNLNIGVKQATITNGLKYSLATGNWG 60

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 61   DQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 116

Query: 571  PAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            PAET EG   GLV +L    +  V +       Y    + ++  +     +      ++ 
Sbjct: 117  PAETPEGQACGLVKNLALMCYITVGSESLPIIQYMTSRNMEMLEEYEPQRSPNATKVFLN 176

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LEND 685
                 + +D +   + V        +      + D  D   K          P   +EN 
Sbjct: 177  GVWVGVHDDPAHLVQSVLALRRECVMSYEVSLVRDIRDREFKIFTDAGRVCRPLFVIENR 236

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
              +       +++  +  L+ +     T             + +   G+VE VDA     
Sbjct: 237  TGHPNHGALVLKKSHLRELEKKKDTPSTDQSEEKDNGWQFLVSS---GVVEYVDAEEEET 293

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +   I    + +    +   N+R    +   +R        PS  LG  
Sbjct: 294  LMIVMTPEELEASRQIRAGYEVKEPEYDP--NRRLKAPLNPTLRSWTHCEIHPSMILG-- 349

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G        
Sbjct: 350  -----ICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXXXXXXX 386

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 387  RM-----------DTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQE 435

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ +R+     EQ E   R           +    
Sbjct: 436  DSVIMNQSSIDRGLF-RSLFYRAYTDQEKRAGMQVVEQFEKPMRSDTVRLKHGTYDKLDE 494

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  ++ D      R+++         ++     +  Q    
Sbjct: 495  DGIINPGVRVSGEDIIIGKTAPIAPDAEELGQRTKYHNKRDVSTPLRSTESGIVDQ---- 550

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 551  ----------------VLVTTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYR 594

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +          +
Sbjct: 595  QEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSALKGFEGDATPFTDVTVDSV 654

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S L                        +     Q +    +                   
Sbjct: 655  SAL------------------------LREHGYQSRGXEVM------------------- 671

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                 +G +    G         + +G  Y  +L HMV  K+ A
Sbjct: 672  ----YNGHT----GR---KLVAQIFLGPTYYQRLRHMVDXKIXA 704


>gi|140084124|gb|ABO84911.1| RpoB [Paenibacillus sp. FSL_F4-134]
 gi|140084128|gb|ABO84913.1| RpoB [Paenibacillus sp. FSL_F4-144]
 gi|140084142|gb|ABO84920.1| RpoB [Paenibacillus sp. FSL_F4-242]
 gi|140084146|gb|ABO84922.1| RpoB [Paenibacillus sp. FSL_F4-248]
          Length = 239

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 88/209 (42%), Positives = 116/209 (55%), Gaps = 54/209 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 85   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 144

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 145  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 194  ----------------------------------VFD---------TMEEAGMQRNGKTV 210

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
            LYDG TGE F+R VTVG ++M+KL HMV 
Sbjct: 211  LYDGRTGERFEREVTVGVMHMIKLAHMVD 239



 Score = 88.6 bits (218), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 62/93 (66%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  EKAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 93


>gi|46277261|gb|AAS86821.1| RNA polymerase II second largest subunit [Akebia longeracemosa]
          Length = 575

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 86/494 (17%), Positives = 153/494 (30%), Gaps = 83/494 (16%)

Query: 804  DLALGRNMLVA--FMPWHGYNFE-DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             +++  N LV+  F P   Y+       I   ++     + I   +     R+T      
Sbjct: 162  MISMTINDLVSARFNPEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 221

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                   V+   L+      +  V        +    +       +      + AI    
Sbjct: 222  KQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 278

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +        +  R   D+ ++  ++ +E      RD          
Sbjct: 279  GYNQEDSVIMNQSSIDRGFF-RSLSFRSYRDEEKKMGTLVKEDFGRPNRDNTMGMRHGSY 337

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +          G           K+T ++ +                 E   +     + 
Sbjct: 338  DKLDDDGLAPPGIRVSGEDVIIGKTTPIAQE-----------------ESQGQASRYTRR 380

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             + TS    E    +++      D +     R VKV +   R  Q GDK + RHG KG V
Sbjct: 381  DHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTV 435

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +      
Sbjct: 436  GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 495

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               +IS         +                                            
Sbjct: 496  TVDNISKALHKCGYQMRGFETM-------------------------------------- 517

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      +G +    G         + +G  Y  +L HMV DK+++R  G   ++T+
Sbjct: 518  ---------YNGHT----GR---KLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTR 561

Query: 1281 QPLGGKSNRGGQRL 1294
            QP  G+S  GG R 
Sbjct: 562  QPAEGRSRDGGLRF 575



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 74/486 (15%), Positives = 140/486 (28%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  + +  +  ++  S    + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAARPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
                   +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 64  IHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQQLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L         G+ E              + Y+   EEE   I+          
Sbjct: 123 KKKDIRALQQRETPEEGGWHELV--------AKGFIEYVDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLVSARFNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +                           R   +  V                    
Sbjct: 223 QAMGIYVTNYQL--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSLSFRSYRDEEKKMGTLVKEDFGRPNRDNTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP  +           +         RD S  +  
Sbjct: 338 DKLDDDGLAPPGIRVSGEDVIIGKTTPIAQEE---------SQGQASRYTRRDHSTSLRH 388

Query: 934 GVSGTV 939
             SG V
Sbjct: 389 SESGMV 394


>gi|7021502|gb|AAF35377.1|AF226074_1 RNA polymerase beta subunit [Bacillus licheniformis]
 gi|7021504|gb|AAF35378.1|AF226075_1 RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 134

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 57/150 (38%), Positives = 92/150 (61%), Gaps = 19/150 (12%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           +MT  GTF+I G +R++VSQL RSP ++F 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYFS 131


>gi|224797611|gb|ACN62835.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           ananassae]
          Length = 424

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 168/317 (52%), Positives = 226/317 (71%), Gaps = 8/317 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            LD +       V  R  G+ I+V   ++++ID SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   ELDTNNVIKNNNVIARSNGQNIIVGPNEVEYIDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PLLK + P VGTG+E  VA+ SG AIVA   G+V+ VD+  I+I+S +   
Sbjct: 61  GANMQRQAIPLLKPQTPIVGTGVEYAVARDSGLAIVANLPGVVQYVDSHEIIIKSEDE-- 118

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 +  Y L +F+RSNQ T V   PLVKVGD+V  N I+ADGPS   G+LALG+N++
Sbjct: 119 ------ITTYELSRFERSNQGTAVTHVPLVKVGDKVEVNQILADGPSMKDGELALGQNVI 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           +AFM WHGYN+ED+++ISER+V +DV++S+HIEE+ +  R TK G EEITR+IPN SE+ 
Sbjct: 173 IAFMTWHGYNYEDAIIISERLVKDDVYSSMHIEEYNLECRKTKQGKEEITREIPNTSEQS 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            + +D+ GI+ +G EV  GDILVGK+TPKG++  T EEKLL AIFGEK+ +V+D SLRVP
Sbjct: 233 RRYLDDEGIVLIGTEVKEGDILVGKVTPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVP 292

Query: 933 SGVSGTVVDVRIFNRHG 949
           +G +G V  ++ + R  
Sbjct: 293 NGGAGIVQGIKRYKRED 309



 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 91/299 (30%), Positives = 133/299 (44%), Gaps = 25/299 (8%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ VG +V    IL    +   +  +   + ++ A       +  D  +     V   V 
Sbjct: 141  LVKVGDKVEVNQILADGPS-MKDGELALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVY 199

Query: 941  DVRIFNRHGIDKNERSISVER--EQI----ELLARDKDDEQVILDRNIYSRLMEILCGQN 994
                   + ++  +     E    +I    E   R  DDE  I+      +  +IL G+ 
Sbjct: 200  SSMHIEEYNLECRKTKQGKEEITREIPNTSEQSRRYLDDE-GIVLIGTEVKEGDILVGKV 258

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G         L + +  E  R+               V+ +                
Sbjct: 259  TPKGQTQSTAEEKLLAAIFGEKSRNVKDNSLRVPNGGAGIVQGI---------------- 302

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K + G D+P  V  VVKVF+  KR I+ GDKMAGRHGNKG++S++LP EDMPFL+D
Sbjct: 303  -KRYKREDGFDLPSEVEEVVKVFIVQKRKIREGDKMAGRHGNKGVISKVLPIEDMPFLED 361

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            GTPVD +LNPLGVPSRMN+GQI E HLG A   LG K+ + + D   N D+  +    +
Sbjct: 362  GTPVDXMLNPLGVPSRMNIGQILELHLGMAAKTLGIKVATPVFDGAKNQDLLDIMKEAK 420


>gi|110169452|gb|ABG53982.1| RNA polymerase II second largest subunit [Entyloma calendulae]
          Length = 693

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 130/828 (15%), Positives = 246/828 (29%), Gaps = 158/828 (19%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R+   ++ R I   +     D         + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLSGLFRMLFKKLTRDIYRHLEKCVEDQKEFFINTAVKSATITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L+  + ++     +     + +    + +  +   E+ 
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLSLMSLISVGSQSQPIIEFLEEF-GLDQLTDMR-REDA 174

Query: 624  NRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                   N            LV      R   +         D  +   +        + 
Sbjct: 175  RSTKVFVNGVWLGTHQDPTGLVSTLRGLRRKDDISTEVSVVHDIREKELRLYTDAGRVMR 234

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P    +  +R L    ++R+ +  L+        G E          +     G++E +D
Sbjct: 235  PLFIVNKDDRSLF---IKRKHMNWLQH-------GTEDGSDFGWEDLVQ---CGVIEYLD 281

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP---LVKVGDEV-RRNDIIA 795
            A        E  +   +     Y     Q +N        P   LV +            
Sbjct: 282  AEE-----EETVMISMSIEDLNYSRAYHQNTNSVRDTLSDPSARLVSLHTYSGDTWTHCE 336

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              P+  LG       +  + +P+  +N          M  + +   +++  +    R   
Sbjct: 337  IHPAMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYLTNY--QMRMDT 385

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +         P  +   ++++                             +   +  + A
Sbjct: 386  MANILYYPQKPLGTTRAMQHL-------------------------KFRELPAGQNAIVA 420

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    ++ R   D  ++S  VE E  E  +R+     
Sbjct: 421  ILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTYTDLEKKSGMVEMEVFEKPSRETTIRL 479

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +          G           K+  L  D      RS+          +    
Sbjct: 480  KHGTYDKLDADGLCAPGTRVSGEDIIIGKTVPLPGDSEELGLRSKLHTKRDASMPL---- 535

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
                          E    +++     GD      ++ VKV V   R  Q+GDK A RHG
Sbjct: 536  -----------KSTESGIVDQVLVTTNGD-----GVKFVKVRVRSTRVPQTGDKFASRHG 579

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  + 
Sbjct: 580  QKGTIGITYRQEDMPFTVEGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGDAT 639

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S                         +VL+       G+ +         
Sbjct: 640  PFTSLTVEAVS-------------------------NVLKGFGYQSRGLEIM-------- 666

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                           +G +    G         V +G  Y  +L HMV
Sbjct: 667  --------------YNGHT----GR---KLQAQVYLGPTYYQRLKHMV 693


>gi|207690909|gb|ACI25189.1| RNA polymerase beta [Mycobacterium sp. ATCC 25798]
 gi|207690913|gb|ACI25191.1| RNA polymerase beta [Mycobacterium sp. ATCC 25799]
 gi|207690915|gb|ACI25192.1| RNA polymerase beta [Mycobacterium sp. ATCC 25800]
 gi|207690917|gb|ACI25193.1| RNA polymerase beta [Mycobacterium sp. ATCC 25803]
          Length = 212

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 85/214 (39%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAGN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 136  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGEVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|307343592|emb|CBJ18711.1| RNA polymerase B subunit [Micromonospora rosaria]
          Length = 206

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 122/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 26   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 85

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  ++    ++K                 
Sbjct: 86   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVEGDDAEWKRQLRSID---------- 134

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 135  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 175

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VG IY+LKLN
Sbjct: 176  SSGKARLFDGRSGEPLPDPIAVGNIYILKLN 206


>gi|123979404|gb|ABM81527.1| RNA polymerase II second largest subunit [Asahinea scholanderi]
          Length = 701

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 119/778 (15%), Positives = 226/778 (29%), Gaps = 105/778 (13%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 178  IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 237

Query: 684  NDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             D+  R     N+         L      +  T  +       G   + K  G+VE VDA
Sbjct: 238  IDNDPRSSNRGNLVLTKEHVQKLELDRENWATTEPDVREEADMGWQGLVKE-GVVEYVDA 296

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +       +        +N +  +N+R    +             PS 
Sbjct: 297  EEEETIMIVMTPEDLEISRQLQAGFDMPEANPDE-LNKRVKAPMNPTAHTWTHCEIHPSM 355

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +       E  +           
Sbjct: 356  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXFSNYEQRMDT--------- 399

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 400  --------------------MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 496  GTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q   S                         LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTSEGMVPDIIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPF 655

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                   +S L                           V     +G  + T VF G  
Sbjct: 656  TEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQVFXGPT 698



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 84/625 (13%), Positives = 174/625 (27%), Gaps = 115/625 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 8   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 185 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 244

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +                  E              V Y+ A EEE   I
Sbjct: 245 SNRGNLVLTKEHVQKLELDRENWATTEPDVREEADMGWQGLVKEGVVEYVDAEEEETIMI 304

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 305 VMTPEDLEISRQLQAGFDMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 364

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+    +                                 
Sbjct: 365 PFPDHNQSPRNTYQSAMGKQAMGXXFS--------------------------------- 391

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + +  Y               Q+PL                  
Sbjct: 392 --------NYEQRMDTMANILYYP--------------QKPL----------ATTRSMEF 419

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   
Sbjct: 420 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVV 479

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   +       +D+ G++  G  V+  DI++GK  P         ++   
Sbjct: 480 EQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-- 537

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTV 939
                K    RDTS  + S  +G V
Sbjct: 538 -----KLHVKRDTSTPLRSTENGIV 557


>gi|46277253|gb|AAS86817.1| RNA polymerase II second largest subunit [Sequoia sempervirens]
          Length = 556

 Score =  243 bits (620), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 81/469 (17%), Positives = 144/469 (30%), Gaps = 80/469 (17%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 168  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 224

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 225  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 283

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R+ ++ +E+     R+          +          G           K
Sbjct: 284  FFRSYRDEEKRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 343

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++ D        Q  ++  +D+                    E    +++      D
Sbjct: 344  TTPIAQDD----SAGQVSKYPKRDQSTS-------------LRHSESGMVDQVLLTTNQD 386

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 387  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 441

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 442  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 499

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 500  ---------------------------------------------YNGHT----GR---K 507

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
                + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 508  LSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 556



 Score =  112 bits (280), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 69/453 (15%), Positives = 131/453 (28%), Gaps = 102/453 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +    GV R 
Sbjct: 19  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 78

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVT 611
               E+R ++  +     P    E   + +     +  + +   G+ E            
Sbjct: 79  IRLRELR-LYTDYGRCSRPLFVVENQRLKIRKQDINNLQASREDGWHEL--------ITQ 129

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+              +LV  R   E            +  P  +
Sbjct: 130 GCIEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLI 177

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                           R
Sbjct: 178 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------R 217

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 218 MDTLAYV-----------------------------------LYYPQKPLV--------- 233

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N +VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 234 -TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 292

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E        +   +       +D+ G+   G  V+  D+++GK TP  +   
Sbjct: 293 KRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD- 351

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   +         RD S  +    SG V
Sbjct: 352 --------SAGQVSKYPKRDQSTSLRHSESGMV 376


>gi|296041315|gb|ADG85651.1| RNA-polymerase beta subunit [Mycobacterium lacticola]
          Length = 203

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 85/214 (39%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 22   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 81

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 82   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAGN-------------- 126

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 127  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGEVM 169

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 170  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 203


>gi|207690911|gb|ACI25190.1| RNA polymerase beta [Mycobacterium bacteremicum]
          Length = 212

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 84/214 (39%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  ++                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNVEGSPEWAGN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 136  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGEVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|78100234|gb|ABB20918.1| RNA polymerase II second largest subunit [Tilletiopsis sp. CBS
            111593]
          Length = 674

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 131/809 (16%), Positives = 248/809 (30%), Gaps = 158/809 (19%)

Query: 456  IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAV 513
             D+ G +R+   G +L   +R+   ++ R I   +     D         + +  + + +
Sbjct: 1    RDHFGKKRLDLAGPLLSGLFRMLFKKLTRDIYRHLEKCVEDQKEFFINSAVKSATITNGL 60

Query: 514  CEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
                 +               +SQ+       S ++H RR +      + R     + R 
Sbjct: 61   KYSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQ 116

Query: 561  VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
            +H TH+G +CPAET EG   GLV +L+  + ++     +     + +    + +  +   
Sbjct: 117  LHNTHWGMVCPAETPEGQACGLVKNLSLMSLISVGSQSQPIIEFLEEF-GLDQLTDMR-R 174

Query: 621  EEENRYIAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAA 676
            E+        N            LV      R   +         D  +   +       
Sbjct: 175  EDARSTKVFVNGVWLGTHQDPTGLVSTLRGLRRKDDISTEVSVVHDIREKELRLYTDAGR 234

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             + P    ++ +R L    ++R+ +  L+        G E          +     G++E
Sbjct: 235  VMRPLFIVNNVDRSLF---IKRKHMNWLQH-------GTEDGSDFGWEDLVQ---CGVIE 281

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP---LVKVGDEV-RRND 792
             +DA        E  +   +     Y     Q +N        P   LV +         
Sbjct: 282  YLDAEE-----EETVMISMSIEDLNYSRAYHQNTNSVRDTLSDPSARLVSLHTYAGDTWT 336

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 P+  LG       +  + +P+  +N          M  + +  ++++  +    R
Sbjct: 337  HCEIHPAMILG-------ICASIIPFPDHNQXXXXXYQSAMGKQAM--AVYLTNY--QMR 385

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +         P  +   ++++                             +   +  
Sbjct: 386  MDTMANILYYPQKPLGTTRAMQHL-------------------------KFRELPAGQNA 420

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    ++ R   D  ++S  VE E  E  +R+  
Sbjct: 421  IVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTYTDLEKKSGMVEMEVFEKPSRETT 479

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+  L  D      RS+          + 
Sbjct: 480  IRLKHGTYDKLDADGLCAPGTRVSGEDIIIGKTVPLPGDSEELGLRSKLHTKRDASMPL- 538

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                             E    +++     GD      ++ VKV V   R  Q+GDK A 
Sbjct: 539  --------------KSTESGIVDQVLVTTNGD-----GVKFVKVRVRSTRVPQTGDKFAS 579

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   DI++NP  +PSRM +GQ+ E  L      LG++ 
Sbjct: 580  RHGQKGTIGITYRQEDMPFTVEGVTPDIIINPHAIPSRMTIGQLVECLLSKVATLLGQEG 639

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 640  D-----------------------------------------------------ATP-FT 645

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLT 1241
                EA++++L+       G  I+Y+G T
Sbjct: 646  SVTVEAVSNVLKGFGYQSRGLEIMYNGHT 674



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 86/599 (14%), Positives = 165/599 (27%), Gaps = 91/599 (15%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR +     D   F +  ++ +    +  KY L   G      +         + + +
Sbjct: 30  DIYRHLEKCVEDQKEFFINSAVKSATITNGLKYSL-ATGNWGDQKKFMQAKAGVSQVLNR 88

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 89  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSLI 148

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCE-------FFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +   +      +     E       F     L   ++    +S +   RR 
Sbjct: 149 SVGSQSQPIIEFLEEFGLDQLTDMRREDARSTKVFVNGVWLGTHQDPTGLVSTLRGLRRK 208

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +            +   ++      + P       +  L         +  +G  +  
Sbjct: 209 DDISTEVSVVHDIREKELRLYTDAGRVMRPLFIVNNVDRSLFIKRKHMNWL-QHGTEDGS 267

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR--------CAGEE 653
                D      + YL A EEE   I+ +   L+   ++ +     R             
Sbjct: 268 DFGWEDLVQCGVIEYLDAEEEETVMISMSIEDLNYSRAYHQNTNSVRDTLSDPSARLVSL 327

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                +     +  P  ++ I AS+IPF +++          M +QA+ +          
Sbjct: 328 HTYAGDTWTHCEIHPAMILGICASIIPFPDHNQXXXXXYQSAMGKQAMAVYLT------- 380

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                +   + A I+                                  + +KF+     
Sbjct: 381 --NYQMRMDTMANILY---------------------YPQKPLGTTRAMQHLKFRELPAG 417

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
                  L   G   + + +I +  S D G                  + E    + E  
Sbjct: 418 QNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLYY-------RTYTDLEKKSGMVE-- 467

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
                     +E FE  +R+T             +       +D  G+   G  V+  DI
Sbjct: 468 ----------MEVFEKPSRET----------TIRLKHGTYDKLDADGLCAPGTRVSGEDI 507

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           ++GK  P        EE  LR+    K    RD S+ + S  SG V  V +       K
Sbjct: 508 IIGKTVPLPGDS---EELGLRS----KLHTKRDASMPLKSTESGIVDQVLVTTNGDGVK 559


>gi|307343458|emb|CBJ18646.1| RNA polymerase B subunit [Micromonospora sp. GUI13]
          Length = 209

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/209 (44%), Positives = 120/209 (57%), Gaps = 38/209 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDAAWKKQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I  +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              G++ L+DG +GEP   P+ VGYIY+LK
Sbjct: 181  ASGKAQLFDGRSGEPLPDPIAVGYIYILK 209


>gi|207690919|gb|ACI25194.1| RNA polymerase beta [Mycobacterium sp. ATCC 23071]
 gi|207690925|gb|ACI25197.1| RNA polymerase beta [Mycobacterium neoaurum]
          Length = 212

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAK-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   S   V+TPVFDGA E+ +  +L     +      
Sbjct: 136  -----------------LPEGMQSAPSDSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|295814746|gb|ADG35961.1| RNA polymerase beta-subunit [Mycobacterium sp. AR-07]
          Length = 204

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 23   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 82

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 83   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAK-------------- 127

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 128  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 170

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 171  VNAQGKSELFDGRSGEPFPYPVTVGYMYILKLHH 204


>gi|307343474|emb|CBJ18654.1| RNA polymerase B subunit [Micromonospora sp. GUI34]
          Length = 209

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 91/209 (43%), Positives = 120/209 (57%), Gaps = 38/209 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIN---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              G++ L+DG +GEP   P+ VGY+Y+LK
Sbjct: 181  GSGKAQLFDGRSGEPLPDPIAVGYVYILK 209


>gi|115740280|ref|XP_001185416.1| PREDICTED: similar to RNA polymerase I second largest subunit,
            partial [Strongylocentrotus purpuratus]
 gi|115908664|ref|XP_791874.2| PREDICTED: similar to RNA polymerase I second largest subunit,
            partial [Strongylocentrotus purpuratus]
          Length = 210

 Score =  243 bits (619), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 90/232 (38%), Gaps = 50/232 (21%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G+D+   V +   + + ++R    GDK + RHG KG+ S+  P EDMPF + G   DI+ 
Sbjct: 29   GNDLGNQVCQRAFIQLRIQRNPIIGDKFSSRHGQKGVCSQRWPTEDMPFTESGMTPDILF 88

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM +G + E+  G +    G    +    +                       
Sbjct: 89   NPHGFPSRMTIGMMIESMAGKSASLHGLCHDATPFTFSEEQPA----------------- 131

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                              +    +L     +  G   +Y G +G
Sbjct: 132  ---------------------------------VDYFGKLLTAGGYNYYGTERMYSGTSG 158

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
               +  + +G +Y  +L HMVSDK   RSTG   ++T QP+ G+   GG R 
Sbjct: 159  VELEADIFIGVVYYQRLRHMVSDKFQVRSTGPVDILTHQPVKGRKRAGGIRF 210


>gi|307343466|emb|CBJ18650.1| RNA polymerase B subunit [Micromonospora sp. GUI19]
          Length = 209

 Score =  243 bits (619), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 93/209 (44%), Positives = 121/209 (57%), Gaps = 38/209 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 140  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLK 1258
              G++ L+DG +GEP   P+ VGYIY+LK
Sbjct: 181  ASGKAQLFDGRSGEPLPDPIAVGYIYILK 209


>gi|92090854|gb|ABE73203.1| RNA polymerase II second largest subunit [Hydropus cf. scabripes PBM
            2513]
          Length = 687

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 126/816 (15%), Positives = 236/816 (28%), Gaps = 146/816 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ R +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETQKEFKLAVAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN  
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAN 169

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
                 + +  +G +       R     +   ++     D SP+  V             D
Sbjct: 170  STTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            + RV     +  +    LK +   ++ TG      +         + GI+E +DA     
Sbjct: 227  AGRVCRPLFIVEKQKLALKKQHIKWLSTGQTDDGEEFKWE--HLVKGGIIELLDAEEEET 284

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +   +       +    ++       R  +K G            PS  LG  
Sbjct: 285  VMISMTPEDLENSRLQQSGVSSHANDGEFDPAAR--LKAGINAHTWTHCEIHPSMILG-- 340

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 341  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLI 377

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 378  RM-----------DTMANILFYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 426

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++      E+    +R+          +    
Sbjct: 427  DSVIMNQSSIDRGLF-RSIYYRSYMDLAKKVGQNAGEEFGKPSRENTLRMKHGTYDKLED 485

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G   V       K+  +  +                +E  QR  +  K    T 
Sbjct: 486  DGLIAPGTGVVGEDIIIGKTAPIPPE---------------SEELGQRTSKHTKRDVSTP 530

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E+   +++      D         VKV V   R  Q GDK A RHG KG +     
Sbjct: 531  LKSTENGTVDQVLITTNSD-----GQTFVKVRVRSIRIPQIGDKFASRHGQKGTIGITYR 585

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 586  QEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 638

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++       LR       G+ V                   
Sbjct: 639  ------------------DLTVESVSEYLRQKGYQSRGLEVM------------------ 662

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                  G +       G      V +G  Y  +L H
Sbjct: 663  ----YHGHT-------GRKLQAQVYLGPTYYQRLKH 687



 Score =  122 bits (307), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 88/616 (14%), Positives = 169/616 (27%), Gaps = 101/616 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F +A ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTRDVYRYLQKCVETQ--KEFKLAVAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENANSTTPCTKVFVNGVWM 184

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 185 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVEKQKLAL 244

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         E    K         +  L A EEE   I+     L+       
Sbjct: 245 KKQHIKWLSTGQTDDGEE--FKWEHLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 302

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 303 GVSSHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 362

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 363 MGKQAMGIFLTNFLI-----------------------------------------RMDT 381

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 382 MANILFYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  +A+       E        +   +  
Sbjct: 418 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLAKKVGQNAGEEFGKPSRENTLRMKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P       PE + L     +     RD S  
Sbjct: 478 GTYDKLEDDGLIAPGTGVVGEDIIIGKTAPI-----PPESEELGQRTSKH--TKRDVSTP 530

Query: 931 VPSGVSGTVVDVRIFN 946
           + S  +GTV  V I  
Sbjct: 531 LKSTENGTVDQVLITT 546


>gi|300244845|gb|ADJ93855.1| RNA polymerase B subunit [Staphylococcus succinus subsp. casei]
          Length = 266

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 153/266 (57%), Positives = 196/266 (73%), Gaps = 3/266 (1%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFI
Sbjct: 1   RRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFI 60

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++
Sbjct: 61  ETPYRKVDLETHSITDKIDYLTADEEDSYVVAQANSVLDENGRFVDDEVVCRFRGNNTVM 120

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME
Sbjct: 121 AKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGME 180

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            V A+ SGAA+V KR G VE V++  I++R  +E D       +D Y L KF+RSN  TC
Sbjct: 181 HVAARDSGAAVVVKRTGRVEHVESNEILVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTC 240

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTD 801
            NQRP+V  GD V + +I+ADGPS +
Sbjct: 241 YNQRPIVSAGDVVTKGEILADGPSME 266


>gi|209943912|gb|ACI96264.1| RNA polymerase B-subunit [Staphylococcus simiae CCM 7213]
          Length = 266

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 157/266 (59%), Positives = 195/266 (73%), Gaps = 3/266 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V CR  G   +
Sbjct: 61  IETPYRKVDIDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFIEDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGM 180

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E V A+ SGAAI AK  G VE V++  I++R  VE +       +D Y L KF+RSN  T
Sbjct: 181 EHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGT 240

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPST 800
           C NQRP+V VGD V  N+I+ADGPS 
Sbjct: 241 CYNQRPIVAVGDVVEYNEILADGPSM 266


>gi|207691931|gb|ACI25200.1| RNA polymerase beta [Mycobacterium sp. ATCC 23070]
          Length = 212

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 85/214 (39%), Positives = 113/214 (52%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+          +           
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAKLPEGMLSAPADSI- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                                          V+TPVFDGA E  +  +L     +      
Sbjct: 149  ------------------------------VATPVFDGAQEGELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G++ L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKAELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|207691929|gb|ACI25199.1| RNA polymerase beta [Mycobacterium neoaurum]
          Length = 212

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 116/214 (54%), Gaps = 40/214 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++   +  D++P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPF+ DG
Sbjct: 31   RVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPIEDMPFMPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 91   TPVDIILNTHGVPRRMNIGQILETHLGWVAKA-GWNIEGSPEWAAK-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES---- 1231
                             +    +   +   V+TPVFDGA E+ +  +L     +      
Sbjct: 136  -----------------LPEGMQSAPADSIVATPVFDGAQEKELEGLLGSTLPNRDGDVM 178

Query: 1232 ----GQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G+S L+DG +GEPF  PVTVGY+Y+LKL+H
Sbjct: 179  VNAQGKSELFDGRSGEPFPYPVTVGYMYILKLHH 212


>gi|13358406|ref|NP_078633.1| DNA-directed RNA polymerase subunit 2 [Lymphocystis disease virus 1]
          Length = 1024

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 92/415 (22%), Positives = 161/415 (38%), Gaps = 73/415 (17%)

Query: 962  EQIELLARDKDDEQVIL-DRNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             + E      D E +      I +R L   L G+  V  PK  K +   +  + +     
Sbjct: 669  AETEKYKSKHDSEMIAYPKFTIRNRDLDYSLLGKTGVLDPKLGKNNKKYTGKICNVLWIP 728

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                  V   K+ + + S  V Y+     ++   +  ++++     +  G  R+VK+ + 
Sbjct: 729  A---GTVLVGKISKKLISGVVVYKDVSLAIKVDEEGYLDELLDYYTVETG--RIVKIKLR 783

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  + GDK A     KG    I   E+MPF KDG   D+++NP   PSRM +  I + 
Sbjct: 784  SPKIPEIGDKFASFTAQKGTCGMIYAQENMPFTKDGIVPDLIINPHAFPSRMTINYILQM 843

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
                A    GK   +         +                                   
Sbjct: 844  CYNLAACLQGKTYDATAFKRYNTTE----------------------------------- 868

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                               +NS+L+  +L  S ++ +Y G TG+ F   + +      +L
Sbjct: 869  ------------------DLNSILQELNL-TSWETEMYCGFTGKKFPSKIFIAPCDYQRL 909

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKS 1319
             H+V +K+++R +G    +T QP+ G+S  GG ++GEME WC  ++G + VL+E L   S
Sbjct: 910  RHLVVNKIHSRISGPIDNLTHQPVAGRSRYGGIKVGEMEQWCKLSHGVSTVLKESLFDMS 969

Query: 1320 DD----VVGRTRV----YESIVAGNDTFETGT---PESFNVLVKEMQALGLSIDL 1363
            D     V    +     +E     +D  E      P +  +L +E+ A+G++I  
Sbjct: 970  DKYQIPVCKLCKTISDDFEYCRKCDDI-EIELKNCPYTSKLLFQELMAIGINIKF 1023



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 72/501 (14%), Positives = 156/501 (31%), Gaps = 58/501 (11%)

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           ++ +       +S ++++ +++  D       T  +  +   +     D         + 
Sbjct: 223 HKALIDILFKQYSDSKTIADYVPADVKCKCKETYVKTILEKEIFNHLEDHSGKNVALHLG 282

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-VDID 496
            +I+ L+ + +G+  + D D+L  +RV + G +++  +R    +  R IK  +    + D
Sbjct: 283 YMIERLIAVVSGEAQLTDKDDLAYKRVDTSGVLIEFLFRGLFKQYIRLIKNNLEILKNPD 342

Query: 497 SVMPQDLINAKPVVSAVCEFFCSS-------------QLSQLEEHVNSLSRITHTRRLSA 543
            +     IN       +C    +               +SQ+  + N  SR++H RR   
Sbjct: 343 PINIIKSINVITNGLNLCFATGNWSVKKTGPPSYMRVGVSQVLCNHNYGSRLSHLRR--- 399

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                V       ++R +H +HYG ICP ET EG  +G+V +     R            
Sbjct: 400 -LMHAVGFKGKNFKIRRLHASHYGFICPYETPEGERVGVVLNTALSVRFTLG-------- 450

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                              +   I        ++    + ++     G    + +     
Sbjct: 451 ------------------IDKAEIKPLIQPYLDNSKKFKVILNGEIIGFTQDLDKFITAL 492

Query: 664 IDASPKQVVSIAASLIPFLENDDS---NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               P++         P+++                 ++ V      A    T  + + A
Sbjct: 493 KLILPQETSIFKYYFTPYIKECHILSDQGRFTRKVFLKENVLDYVCAAAIHHTEYKDLPA 552

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                 ++A          + RI  +S  G               ++  +       Q+ 
Sbjct: 553 SLMFTDVMASVIPFYNHTQSPRIAYQSNMG-KQAVGITTLTNGKDRYDPTFYILDYPQKA 611

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           L                       +  G   +VA     GYN EDS+++++  +   +F 
Sbjct: 612 LTY----------TTCYKKFKFDVMCHGAMPIVAVATMDGYNQEDSIILNKSSIDRGLFV 661

Query: 841 SIHIEEFEVMARDTKLGPEEI 861
               + F    +       E+
Sbjct: 662 ITCYKTFAETEKYKSKHDSEM 682



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 26/154 (16%), Positives = 47/154 (30%), Gaps = 54/154 (35%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
            L      SYD FL ++I               +   I       + + ++Y    PK  
Sbjct: 4   YLTAHHIESYDRFLFIDIP----------KIIAANNTIKTAQHTIIFKEINYCI--PKIT 51

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT-------- 139
             +   +DLTY + ++  L +    V                I+   +PLM         
Sbjct: 52  PLEAKQKDLTYNISIEYKLEINTKIVVL-------------EIF--TIPLMLRSHLCITN 96

Query: 140 -------------------KDGTFVIKGIQRIVV 154
                                G F++KG +R+++
Sbjct: 97  DSYYNLSLETAQFKLCPNDPGGYFIVKGKERVLI 130


>gi|55273991|gb|AAV48866.1| RNA polymerase II second largest subunit [Ampulloclitocybe clavipes]
          Length = 654

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 113/730 (15%), Positives = 221/730 (30%), Gaps = 92/730 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G            +V  + GI+E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVDNQQLALQKKHIKWLNQGYNDTDQDFKWEQLV--KGGIIELLDA 283

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +       +    ++       R  +K G            PS 
Sbjct: 284  EEEETVMISMTPEDLENSRLQQSGVDPHANDGEFDPPAR--LKAGTHAHTWTHCEIHPSM 341

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 342  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 376

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 377  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 425

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 426  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTY 484

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 485  DKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVD 544

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 545  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTI 584

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 585  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDL 644

Query: 1161 ANGDISPLRS 1170
                +S    
Sbjct: 645  RVESVSTFLR 654


>gi|88976114|gb|ABD59033.1| RNA polymerase II second largest subunit [Clavaria inaequalis]
          Length = 667

 Score =  242 bits (618), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 119/797 (14%), Positives = 230/797 (28%), Gaps = 146/797 (18%)

Query: 469  EMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----- 521
             +L N +R+   ++ + +    +              +  + + + +     +       
Sbjct: 1    PLLANLFRMLFRKLTKDVYRYLQKCVESHKEFNLALAVKHQTITNGLKYSLATGNWGDQK 60

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+       S ++H RR +      + R     + R +H TH+G +CPAE
Sbjct: 61   KSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAE 116

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L   A ++   +       + +  + +         EEN +     + 
Sbjct: 117  TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSTTPCTK 168

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +             I   R K    D SP+  V             D+ RV   
Sbjct: 169  VFVNGVWMGVHRDPAHLVRTIKKLRRK---DDISPEVSVVRDIRERELRLYTDAGRVCRP 225

Query: 694  CNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              +       L+ +   ++  G +    +     +V  + GI+E +DA       +    
Sbjct: 226  LFIVENQQLALQKKHIKWLNQGYDDNGEEFRWEQLV--KGGIIELLDAEEEETVMISMTP 283

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +   +     +      +  +   +    +K G            PS  LG       + 
Sbjct: 284  EDLENSRL--QSSVVDPNAIDPDFDPAARLKAGINAHTWTHCEIHPSMILG-------IC 334

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N                        ++       +G       I       
Sbjct: 335  ASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM----- 371

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +  + AI      +  D+ +   
Sbjct: 372  ------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQ 425

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +   +    I+ R  +D  ++S   + E+ E   R+          +       +  G
Sbjct: 426  SSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGSYDKLESDGLVAPG 484

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  D      R++          ++     +  Q           
Sbjct: 485  TRVRGDDIIIGKTAPIPPDSEELGQRTRSHTKRDVSTPLKSTENGVIDQVLI-------- 536

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                               + VKV +   R  Q GDK A RHG KG +      EDMPF 
Sbjct: 537  ------------TTNSEGQKFVKVRLRSIRVPQIGDKFASRHGQKGTIGITYRQEDMPFT 584

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +G + E  L      +G +                     
Sbjct: 585  AEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------- 625

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     E++++ LR       G
Sbjct: 626  ----------------------------------ATP-FTDLTVESVSTFLRQKGYQSRG 650

Query: 1233 QSILYDGLTGEPFDRPV 1249
              ++Y G TG      V
Sbjct: 651  LEVMYHGHTGRKLQAQV 667



 Score =  124 bits (312), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 82/633 (12%), Positives = 171/633 (27%), Gaps = 99/633 (15%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             + N       K  KD    + + +       F++A ++ +    +  KY L   G   
Sbjct: 1   PLLANLFRMLFRKLTKDVYRYLQKCVESH--KEFNLALAVKHQTITNGLKYSL-ATGNWG 57

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEM 470
              +         + + +    + +  L        R GK       +  +  +    E 
Sbjct: 58  DQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAET 117

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLS 523
            + Q    +  +       + S     +             NA         F     + 
Sbjct: 118 PEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMG 177

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
              +  + +  I   RR   +                ++        P    E   + L 
Sbjct: 178 VHRDPAHLVRTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQ 237

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
                +  +N          +         +  L A EEE   I+     L+     +  
Sbjct: 238 KKHIKW--LNQGYDDNGEEFRWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQSSV 295

Query: 644 LVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +       +          +        +  P  ++ I AS+IPF +++ S R      M
Sbjct: 296 VDPNAIDPDFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 355

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                                                   + 
Sbjct: 356 GKQAMGIYLTNFLI-----------------------------------------RMDTM 374

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           + +  Y       +     +  R                        +L  G+N +VA +
Sbjct: 375 ANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAIL 410

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEE 871
            + GYN EDS+++++  +   +F SI+   +  + + + +   E            +   
Sbjct: 411 CYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHG 470

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               ++  G++  G  V   DI++GK  P         E+L +        DV       
Sbjct: 471 SYDKLESDGLVAPGTRVRGDDIIIGKTAPI----PPDSEELGQRTRSHTKRDVSTPLKST 526

Query: 932 PSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
            +GV   V+ +   +        R  S+   QI
Sbjct: 527 ENGVIDQVL-ITTNSEGQKFVKVRLRSIRVPQI 558


>gi|189006590|gb|ABF18587.2| RNA polymerase II second largest subunit [Infundibulicybe gibba]
          Length = 689

 Score =  242 bits (617), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 124/824 (15%), Positives = 232/824 (28%), Gaps = 156/824 (18%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + +    +              +  + + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         EE
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EE 168

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            N + +   + +  +G +       R     +   ++     D SP+  V           
Sbjct: 169  NAHSSTPCTKVFVNGVWMG---VXRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRL 225

Query: 684  NDDSNRVLMGCNMQRQAVPLL------KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
              D+ RV     +      +L               G E              + GI+E 
Sbjct: 226  YTDAGRVCRPLFIVENQQLVLQKKHVKWLNHGINDDGDEFK-------WEQLIKGGIIEL 278

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            +DA       +    +   +       +    ++       R  +K G            
Sbjct: 279  LDAEEEETVMISMTPEDLENSRLQQSGVDPHANDGEFDPAAR--LKAGINAHTWTHCEIH 336

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 337  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 371

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   I               +  +             +       +   +  + AI 
Sbjct: 372  IYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIL 420

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD       
Sbjct: 421  CYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPMRDNTLRMKH 479

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G           K+  +  D      R++          ++     
Sbjct: 480  GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESG 539

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                              + VKV V   R  Q+GDK A RHG K
Sbjct: 540  IVDQVLI--------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQK 579

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +   
Sbjct: 580  GTIGITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 639

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                       ++     + LR       G+ V    F G    
Sbjct: 640  T-------------------------DLTVESVSTFLRQKGYQSRGLEVM---FHGHT-- 669

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                 G         V +G  Y  +L H
Sbjct: 670  ---------------------GR---KLQAQVYLGPTYYQRLKH 689



 Score =  124 bits (311), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 86/622 (13%), Positives = 172/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 10  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 67  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 127 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 186

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 187 GVXRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLVL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     +    K         +  L A EEE   I+     L+       
Sbjct: 247 QKKHVKW--LNHGINDDGDEFKWEQLIKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 304

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 305 GVDPHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 364

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 365 MGKQAMGIYLTNFLI-----------------------------------------RMDT 383

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 384 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 419

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E     +  +   +  
Sbjct: 420 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPMRDNTLRMKH 479

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 480 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 532

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 533 LKSTESGIVDQVLITTNSEGQK 554


>gi|52699843|gb|AAU86983.1| DNA-dependent RNA polymerase II second largest subunit [Peltula
            obscurans]
          Length = 713

 Score =  242 bits (617), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 124/832 (14%), Positives = 230/832 (27%), Gaps = 138/832 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+   +R+   G +L N +R    ++ R I +  +              +    + + + 
Sbjct: 1    DHFXKKRLDLAGPLLANLFRGLFAKLXRDIYKYLQKCVESNREFNLNLGVKQSTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRXL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP--YRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     +   G  +    +    + +V  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGGAADPIVAFMAQRNMEVLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      + +D +   + V      + +      I D  D   K         
Sbjct: 177  PNATKVFVNGVWVGVHDDPAHLAQDVVKLRRSKVLSYEVSLIRDIRDREFKIFTDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+  ++      G  + ++           V     +         +V +  G+VE 
Sbjct: 237  RPLFVIENEPGNPDHGTLILKKEHLRRIENTKEVPLADRTEENYFGWQQLVNE--GVVEY 294

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            VDA       V    +   +   I     +   ++N  +N+R    +             
Sbjct: 295  VDAEEEETIMVVMTPEDLETSRQIRAG--YDVRDENPDLNKRVKTPMNPTAHSWTHCEIH 352

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N          M  + +          +        
Sbjct: 353  PSMILG-------ICASIIPFPDHNQSPRNTYXSAMGKQAMGXXXXNFPHRMDTMSN--- 402

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                      +             +       +   +  + AI 
Sbjct: 403  --------------------------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIA 436

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +R      EQ E   R        
Sbjct: 437  VYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRVGMXIVEQFEKPMRSDTVRLXH 495

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
                       I  G           K+  +S+D      R++          ++     
Sbjct: 496  GTYXKLDEDGVINPGVRVSGEDIIIGKTAPISADAEXLGQRTKLHVKRDXSTPLRSTESG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQ--------------------VLVTTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   D+++ P  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTREGIVPDLIIXPHAIPSRMTIAHLIECQLSKVSALKGFEGDATPF 655

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L                           V     +G  +   +F G    
Sbjct: 656  TDVTVDSVSGLLR---------------EHGYQSRGFEVMHNGHTGRKLVAQIFLG---- 696

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                                 Y  +L HMV  K+ A
Sbjct: 697  -----------------------------------PTYYQRLRHMVDXKIXA 713


>gi|269912596|emb|CAY86078.1| RNA polymerase beta subunit [Gluconacetobacter oboediens]
          Length = 282

 Score =  242 bits (617), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 131/285 (45%), Positives = 173/285 (60%), Gaps = 28/285 (9%)

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL---------------- 221
            L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                
Sbjct: 1   RLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGAESEAARAAKAAEG 60

Query: 222 ---------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ 272
                    GM  +EILS FY K+ +++    W     A D   G K+   L+D  TGE+
Sbjct: 61  GDVESMEIQGMSPDEILSYFYGKVEFAKTEKGWARRFDA-DAFRGMKLLEPLIDAQTGEE 119

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           V     KLT+ +++ + E   K + +    L G ++A DIVN  TGEIY EAGD + E+ 
Sbjct: 120 VAPVDAKLTARMVRKIAET-TKEVLVGPAGLIGRFIASDIVNENTGEIYAEAGDELTEQK 178

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           LEE+  + +  +  L VD+ N   +IRNTL  DKN  R +AL DIYRVMRPG+  T   A
Sbjct: 179 LEELEEAGLTTLSTLAVDAAN-GPWIRNTLAVDKNASRDEALTDIYRVMRPGEPPTPETA 237

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           E+MF+ LFFD D+YDLS VGRVKMNMRL +D PD VR +RKEDI+
Sbjct: 238 EAMFSGLFFDPDRYDLSAVGRVKMNMRLGVDVPDTVRVLRKEDIL 282


>gi|113957201|gb|ABI49107.1| RNA polymerase II second largest subunit [Coccocarpia erythroxyli]
          Length = 669

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 115/743 (15%), Positives = 212/743 (28%), Gaps = 129/743 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 47   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 102

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +      E    +    + +V  +   L +      ++      +  D 
Sbjct: 103  GLVKNLALMCYITVGTPSEPIIEFMIGRNMEVLEEYEPLRSPNATKVFVNGVWVGVHRDP 162

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
            +     V     G  I      + D  D   K          P F+   D      G  +
Sbjct: 163  AHLVSTVQSLRRGHTISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIESDPKSPNCGSLV 222

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              +   L   E   +G  M+    +       +K  G    V   + V+  V+ + + + 
Sbjct: 223  LTKEHILRLEEDKELGPDMDPEERE-------SKYLGWDGLV--NQGVVEYVDAEEEETV 273

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVK-VGDEVRRNDIIADGPSTDLG-DLALGRNMLVA 814
              V     ++  R  Q     + P V      V+          T      ++   +  +
Sbjct: 274  MIVMTPEDLEVSRQLQAGYAIEEPSVDDPNRRVKAPLNPTAHTWTHCEIHPSMILGICAS 333

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                                                    
Sbjct: 334  IIPFPDHNQSPRNX-----------------------------XXXXXXXXXXXXXXXXX 364

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 365  XXXMDTMANILYYPQKPWHTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 424

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D+ +    + R  +E   +    + + L    Y +L +   +  
Sbjct: 425  IDRGLF-RSLFYRSYTDQEK---QIGRSVVEQFEKPMRSDTLRLKHGTYEKLDDDGIVAP 480

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D      R+++         ++     +  Q          
Sbjct: 481  GVRVSGEDIIIGKTAPIAPDAEELGQRTKYHVKRDVSTPLRSTENGIVDQ---------- 530

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                               LR VKV +   +  Q GDK A RHG KG +      EDMPF
Sbjct: 531  ----------VLVTTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPF 580

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   D+++NP  +PSRM +  + E  L       G +                    
Sbjct: 581  TAEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------ 622

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++ +LR       
Sbjct: 623  -----------------------------------ATP-FTEVTVDSVSRLLREHGYQSR 646

Query: 1232 GQSILYDGLTGEPFDRPVTVGYI 1254
            G  ++Y+G TG      V  G  
Sbjct: 647  GFEVMYNGHTGRKLVAQVFGGPT 669



 Score =  112 bits (280), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 77/564 (13%), Positives = 147/564 (26%), Gaps = 95/564 (16%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R+GK       +  +  +
Sbjct: 31  ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 90

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEF 516
               E  + Q    +  +       + +     +      N + +         +A   F
Sbjct: 91  VCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIGRNMEVLEEYEPLRSPNATKVF 150

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGR 568
                +    +  + +S +   RR   +  +  + R     E        R   P     
Sbjct: 151 VNGVWVGVHRDPAHLVSTVQSLRRGHTISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIE 210

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGF------IETPYRKVCDGKVTNDVVYLSAMEE 622
             P   + G  +     +         G        E+ Y           V Y+ A EE
Sbjct: 211 SDPKSPNCGSLVLTKEHILRLEEDKELGPDMDPEERESKYLGWDGLVNQGVVEYVDAEEE 270

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   I      L+                                       A   I   
Sbjct: 271 ETVMIVMTPEDLEVSRQLQ---------------------------------AGYAIEEP 297

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             DD NR +               +AP   T       +   + I+   A I+   D  +
Sbjct: 298 SVDDPNRRV---------------KAPLNPTAHTWTHCEIHPSMILGICASIIPFPDHNQ 342

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTD 801
                                      +  N     Q+P                     
Sbjct: 343 SPRNXXXXXXXXXXXXXXXXXXXXXMDTMANILYYPQKP----------WHTTRSMEFLK 392

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE- 860
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       E 
Sbjct: 393 FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKQIGRSVVEQ 452

Query: 861 ----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
               +  D   +     + +D+ GI+  G  V+  DI++GK  P         E+L +  
Sbjct: 453 FEKPMRSDTLRLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRT 508

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVV 940
                 DV        +G+   V+
Sbjct: 509 KYHVKRDVSTPLRSTENGIVDQVL 532


>gi|140084140|gb|ABO84919.1| RpoB [Paenibacillus sp. FSL_F4-235]
          Length = 228

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 88/208 (42%), Positives = 116/208 (55%), Gaps = 54/208 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 75   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 134

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 135  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 183

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 184  ----------------------------------VFD---------TMEEAGMQRNGKTV 200

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            LYDG TGE F+R VTVG ++M+KL HMV
Sbjct: 201  LYDGRTGERFEREVTVGVMHMIKLAHMV 228



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 52/83 (62%), Positives = 65/83 (78%)

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTS
Sbjct: 1   GEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTS 60

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           LRVP G  G +VDV++F R   D
Sbjct: 61  LRVPHGSDGIIVDVKVFTRENGD 83


>gi|300244843|gb|ADJ93854.1| RNA polymerase B subunit [Staphylococcus succinus subsp. succinus]
          Length = 266

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 153/266 (57%), Positives = 196/266 (73%), Gaps = 3/266 (1%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFI
Sbjct: 1   RRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFI 60

Query: 599 ETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           ETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++
Sbjct: 61  ETPYRKVDLETHSITDKIDYLTADEEDSYVVAQANSVLDENGRFVDDEVVCRFRGNNTVM 120

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
            +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME
Sbjct: 121 AKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGME 180

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            V A+ SGAA+V KR G VE V++  I++R  +E D       +D Y L KF+RSN  TC
Sbjct: 181 HVAARDSGAAVVVKRKGRVEHVESNEILVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTC 240

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTD 801
            NQRP+V  GD V + +I+ADGPS +
Sbjct: 241 YNQRPIVSAGDVVTKGEILADGPSME 266


>gi|9880|emb|CAA36427.1| RNA polymerase beta subunit (697 AA) [Plasmodium falciparum]
          Length = 697

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 114/507 (22%), Positives = 199/507 (39%), Gaps = 69/507 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +VN G IL    +    S  +    LL         +  D  +     +   + 
Sbjct: 246  IVWVGEKVNIGQILAI-NSNLLNSEYSLGNNLLVGYGSYLGYEYEDAIIISRKILYNNLY 304

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKD-----DEQVILDRNIYSRLMEILCGQNA 995
                 N + I  N  +   E   I L           D+  I+    Y     IL  +  
Sbjct: 305  TSLHLNIYEISLNIINNIPEICSINLSKMYYKNIKHLDKYGIIKEGTYILANNILISKLM 364

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    KS +   + +             +++ +   +  +         IL +   N
Sbjct: 365  FMPFIFNNKSLINIINFLFGSKLR-----IFKNKPIISTIHDIGR--VIKIEILPNHLYN 417

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K EK          +    ++++ +++ +Q GDK+  RHG+KGI+S I    D+P+L + 
Sbjct: 418  KTEK--------NNIYLKFRIYIGIQKYLQLGDKICNRHGHKGIISYISEINDIPYLNNK 469

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI ++ + +PSR+N+GQIFE   G   + L  +     N  K   +         K 
Sbjct: 470  IQPDIFISAISIPSRINIGQIFEGIYGLNSLYLNTRYIISNNLNKNYYNNYNHIFNYYKY 529

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                +         + +                                        +  
Sbjct: 530  NYNNNFNINSKMSYNYN----------------------------------------KYY 549

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L +  TG   +  + +  IY  KL HM+ DK   R  G YS +TQQP+ G + +GGQR G
Sbjct: 550  LKNPFTGNMINNSICLNNIYYYKLIHMIKDKFRYRFIGLYSELTQQPIKGNTKQGGQRFG 609

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV----AGNDTFETGTPESFNVLV 1351
            EMEVW ++A+GA+Y+ +E  T KSDD+  R ++ ++ +       +TF     E+F +++
Sbjct: 610  EMEVWALEAFGASYLFKEFFTYKSDDIKSR-KILKNYLFNNYKIKNTF---ISETFKLIL 665

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIP 1378
            KE+Q+L ++I+        +  +E +P
Sbjct: 666  KELQSLAINIEAFCIFNDTNNLLENLP 692



 Score =  132 bits (332), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 98/430 (22%), Positives = 197/430 (45%), Gaps = 10/430 (2%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           + VN+LS I    +++ +  G  ++     ++R++     G I    T+EG   GLV+ L
Sbjct: 1   DQVNNLSEINQKFKINMITTGLNSKFILNNDLRELPRNILGYISLINTNEGLTCGLVNYL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           T+   +N        Y+ +   +    +  L+   +    I+  N  L ++ +F +  + 
Sbjct: 61  TTNIFLNLKYLFVIYYKHIFYNRYNFKL-LLNIFNKNFYNISFNNIYLKKNINFNKTTIL 119

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                   +    + + I      ++S   +LIPF+  +DS R LM   M  Q VP++  
Sbjct: 120 TINKNTFKICNITQ-NIIYIPFNYLLSFIENLIPFIHYNDSIRNLMSIKMHTQIVPIIYP 178

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
               + T    ++ K     I++ + GIV  V  I+I+IR +            IY L  
Sbjct: 179 NLSNIITNYNFILNKYLNHLIISYQEGIVIYVSCIKIIIRDLFNRQI-------IYYLNN 231

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +++ NQN  +  +P+V VG++V    I+A   +    + +LG N+LV +  + GY +ED+
Sbjct: 232 YKKINQNILLIYKPIVWVGEKVNIGQILAINSNLLNSEYSLGNNLLVGYGSYLGYEYEDA 291

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++IS +++  +++TS+H+  +E+        PE  + ++  +  + +K++D+ GII  G 
Sbjct: 292 IIISRKILYNNLYTSLHLNIYEISLNIINNIPEICSINLSKMYYKNIKHLDKYGIIKEGT 351

Query: 887 EVNPGDILVGKITPKGESPMTPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
            +   +IL+ K+              ++  +FG K    ++  +       G V+ + I 
Sbjct: 352 YILANNILISKLMFMPFIFNNKSLINIINFLFGSKLRIFKNKPIISTIHDIGRVIKIEIL 411

Query: 946 NRHGIDKNER 955
             H  +K E+
Sbjct: 412 PNHLYNKTEK 421


>gi|154362131|gb|ABS80904.1| RNA polymerase beta subunit [Burkholderia ambifaria]
          Length = 234

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 137/232 (59%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++DE+G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQ 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LVDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|224797505|gb|ACN62782.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           hydei]
          Length = 287

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 158/295 (53%), Positives = 215/295 (72%), Gaps = 8/295 (2%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L + G   +E V  R  GE I+  R  +D++D SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   RLSDKGEILDEQVVARFQGENIIATRNDVDYVDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RIV+++ E   
Sbjct: 61  GANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRIVLKTKE--- 117

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G+LALG+N++
Sbjct: 118 -----GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKGELALGQNVV 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR+IPN+SE  
Sbjct: 173 VAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITREIPNISENA 232

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +V+D 
Sbjct: 233 RKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDN 287


>gi|52699782|gb|AAU86953.1| DNA-dependent RNA polymerase II second largest subunit [Acarospora
            schleicheri]
          Length = 720

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 116/831 (13%), Positives = 234/831 (28%), Gaps = 141/831 (16%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     ++     E    +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMVQRNMEVLEEYEPQRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D       V     G  I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHSDPVHLVNTVQAVRRGHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-- 740
             ++D      G  +  +       +   +   M     +         +           
Sbjct: 238  IDNDPKSPRCGSLVLTKEHINKLEDYKDLSAEM-QEKIREKEEVEKEVKEDGTPYGWNGL 296

Query: 741  -IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV---KVGDEVRRNDIIAD 796
              R V+  V+ + + +   V     ++  R  Q   V   P      +   V+       
Sbjct: 297  IKRGVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYVLPEPSDTSEALMKRVKAPMNPTA 356

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N          M  + +   + +  +        
Sbjct: 357  HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTXYXQRM---- 410

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                     +  +             +       +   +  + A
Sbjct: 411  -----------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 447

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 448  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDT 503

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++          ++
Sbjct: 504  LKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLR 563

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +  Q                             LR VKV +   +  Q GDK A 
Sbjct: 564  STENGIVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFAS 603

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G + 
Sbjct: 604  RHGQKGTIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEG 663

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 664  DATPFTEITVDSVSKLLR--EHGYQSRGFEVM---------------------------- 693

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                              +G +    G         V +G  Y  +L HMV
Sbjct: 694  -----------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 720


>gi|154362123|gb|ABS80900.1| RNA polymerase beta subunit [Burkholderia gladioli]
 gi|154362125|gb|ABS80901.1| RNA polymerase beta subunit [Burkholderia gladioli]
          Length = 234

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+S+DE+G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVTDSKVTDQIDYLSAIEEGRYVIAQANASVDENGE 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSAREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAYRGGVVDYVDAGRIVIRVNDDE 232


>gi|46277273|gb|AAS86827.1| RNA polymerase II second largest subunit [Antirrhinum majus]
          Length = 573

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 88/520 (16%), Positives = 161/520 (30%), Gaps = 96/520 (18%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV+ G  + V   +      S  + DL   R N   A+   +       S++  +   ++
Sbjct: 144  LVRNGSVEYVDTEEEETTMISMTINDLINSRHNPDAAYSETYTHCEIHPSLVLGVCASII 203

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 204  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 252

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 253  TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 311

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +  ++ +E      RD          +          G           K+T  + D   
Sbjct: 312  KMGTLVKEDFGCPNRDNTMGMRHGSYDKLEDDGFAPPGTRVSGDDVIIGKTTPFTPDE-- 369

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                              +N+   +  + +S    E    +++      D +     R V
Sbjct: 370  -----------------NQNIRFTRQDHSSSLRHSESGVVDQVLLTTNADGL-----RFV 407

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG +      +DMP+  +G   DI++NP  +PSRM +G
Sbjct: 408  KVRIRSVRIPQIGDKFSSRHGQKGTIGMTYTQDDMPWSIEGITPDIIVNPHAIPSRMTIG 467

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+  +         +IS         +                  
Sbjct: 468  QLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------ 515

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                +G +    G    P    + +G  
Sbjct: 516  -----------------------------------YNGHT----GR---PLTSMIFLGPT 533

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R 
Sbjct: 534  YYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRF 573



 Score =  112 bits (279), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 74/482 (15%), Positives = 135/482 (28%), Gaps = 99/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  +D  S    + I+   +  A   F   + + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLDEWSTENFEEISPAVIPQATKIFVNGNWIG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + G+ R     E+R    T YGR             +
Sbjct: 64  IHRNPELLVRTLRQLRRQVDVNTEVGIIRDIHLKELR--LYTDYGRCSRPLFIVDKQRLV 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +      A        E       D      V Y+   EEE   I+              
Sbjct: 122 IKKKDILALQQRESADEYG---WHDLVRNGSVEYVDTEEEETTMISM----------TIN 168

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +L+  R   +      E     +  P  V+ + AS+IPF +++ S R      M +QA+ 
Sbjct: 169 DLINSRHNPD--AAYSETYTHCEIHPSLVLGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 226

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 227 IYVTNYQL--------------------RMDTLAYV------------------------ 242

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 243 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 281

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       ++
Sbjct: 282 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGCPNRDNTMGMRHGSYDKLE 341

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G    G  V+  D+++GK TP                        +D S  +    SG
Sbjct: 342 DDGFAPPGTRVSGDDVIIGKTTPFTPDE-----------NQNIRFTRQDHSSSLRHSESG 390

Query: 938 TV 939
            V
Sbjct: 391 VV 392


>gi|124502492|gb|ABN13627.1| RNA polymerase beta subunit [Bartonella sp. SD35HB]
          Length = 245

 Score =  242 bits (617), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 173/243 (71%), Positives = 204/243 (83%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+SSV+ID+VMPQDLINAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 2   RMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ +D +D SP
Sbjct: 122 KVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
           KQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGME++VA+ SGAA+ 
Sbjct: 182 KQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEAIVARDSGAAVG 241

Query: 729 AKR 731
           AKR
Sbjct: 242 AKR 244


>gi|300394752|gb|ADK11914.1| DNA-directed RNA polymerase II subunit two [Serpula lacrymans]
          Length = 659

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 118/729 (16%), Positives = 229/729 (31%), Gaps = 90/729 (12%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L N +R+   ++ R +    +              +  + + + +  
Sbjct: 5    HFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKY 64

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 65   SLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLH 120

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             TH+G +CPAET EG   GLV +L   + ++   +       + +  + +         E
Sbjct: 121  NTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------E 172

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            EN + +   + +  +G +       R     +   ++     D SP+  V          
Sbjct: 173  ENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELR 229

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               D+ RV     +       L+ +   ++  G      +      + K +GI+E +DA 
Sbjct: 230  LYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEEYKWEHLVK-SGIIELLDAE 288

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +   +       +    ++ +     R  +K G+           PS  
Sbjct: 289  EEETVMISMTPEDLENSRLQSAGIDPHTNDGDYDPAAR--LKAGNNSHTWTHCEIHPSMI 346

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N       S R   +       +  +        L   + 
Sbjct: 347  LG-------VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNF----LVRMDT 389

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              +I    ++ L       I                  P     +   +  + AI     
Sbjct: 390  MANILYYPQKPLATTRSMDI------------------PDQFRELPAGQNAIVAILCYSG 431

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 432  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTYD 490

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  D      R++          ++     +  Q
Sbjct: 491  KLEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPIKSTENGIVDQ 550

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VK+ V   R  Q GDK A RHG KG + 
Sbjct: 551  VLI--------------------TTNSEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIG 590

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +       
Sbjct: 591  ITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLT 650

Query: 1162 NGDISPLRS 1170
               +S    
Sbjct: 651  VESVSTFLR 659



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 81/605 (13%), Positives = 159/605 (26%), Gaps = 86/605 (14%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 15  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 72  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 132 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 191

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 192 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 251

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +     Y   +    K      +  +  L A EEE   I+     L+     + 
Sbjct: 252 QKKHIKWLN-QGYRDDDGEEYKWEHLVKSGIIELLDAEEEETVMISMTPEDLENSRLQSA 310

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+     R             +  P  ++ + AS+IPF +++ S R      
Sbjct: 311 GIDPHTNDGDYDPAARLKAGNNSHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 370

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +           M                             I         +
Sbjct: 371 MGKQAMGIYLTNFLVRMDTM---------------------------ANILYYPQKPLAT 403

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
           T  +DI    +F+            L   G   + + +I +  S D G          ++
Sbjct: 404 TRSMDI--PDQFRELPAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSIYY--RSY 458

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           M     +    +                 EEFE   RD              +       
Sbjct: 459 MDLEKKSGVQQL-----------------EEFEKPTRDN----------TLRMKHGTYDK 491

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 492 LEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPIKSTENGI 547

Query: 936 SGTVV 940
              V+
Sbjct: 548 VDQVL 552


>gi|300394748|gb|ADK11912.1| DNA-directed RNA polymerase II subunit two [Ramariopsis kunzei]
          Length = 678

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 123/806 (15%), Positives = 230/806 (28%), Gaps = 143/806 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFKKLTKDVYRYLQKCVETRKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNRGDQKKSTASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HRGTVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSPIPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ RV     +       L+ +            A+         + GIVE +DA    
Sbjct: 226  TDAGRVCRPLFIVENQQLALQKKHIRWLVQGHRDDAEDDFKWEHLVKGGIVELLDAEEEE 285

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +    +   +       +    ++       R  +K G            PS  LG 
Sbjct: 286  TVMISMTPEDLENSRLQSSGVDPHANDGEFDPAAR--LKAGINAHTWTHCEIHPSMILG- 342

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N                        ++       +G       
Sbjct: 343  ------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFL 378

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I               +  +             +       +   +  + AI      + 
Sbjct: 379  IRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 427

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +   
Sbjct: 428  EDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYDKLE 486

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  +  D      R++          ++     +  Q   
Sbjct: 487  DDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI 546

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       + VKV V   R  Q GDK A RHG KG +    
Sbjct: 547  --------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITY 586

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +             
Sbjct: 587  RQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD----------- 635

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     E++++ L+
Sbjct: 636  ------------------------------------------ATP-FTELTVESVSTFLK 652

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVT 1250
                   G  ++Y G TG      V 
Sbjct: 653  QKGYLSRGLEVMYHGHTGRKLQALVY 678



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 84/610 (13%), Positives = 169/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFKKLTKDVYRYLQKCV--ETRKEFNLALAVKHQTITNGLKYSL-ATGNR 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +R      E
Sbjct: 66  GDQKKSTASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHRGTVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA   +     F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSPIPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         E  + K         V  L A EEE   I+     L+     + 
Sbjct: 246 QKKHIRWLVQGHRDDAEDDF-KWEHLVKGGIVELLDAEEEETVMISMTPEDLENSRLQSS 304

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 305 GVDPHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 364

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 365 MGKQAMGIYLTNFLI-----------------------------------------RMDT 383

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 384 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 419

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 420 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKH 479

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         E+L +        DV      
Sbjct: 480 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 535

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 536 TENGIVDQVL 545


>gi|52699874|gb|AAU86998.1| DNA-dependent RNA polymerase II second largest subunit [Seynesia
            erumpens]
          Length = 673

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 117/742 (15%), Positives = 213/742 (28%), Gaps = 126/742 (16%)

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             ++ +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG
Sbjct: 52   STAGVSQVLNRYTFASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPEG 107

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L+    ++     E    Y    + +V  +   L        ++  +   + 
Sbjct: 108  QACGLVKNLSLMCSISVGTSTEPIIDYMITRNMEVLEEYEPLRYPNATKIFLNGSWIGVH 167

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            +D     + V       +I      + D  D   K        + P    +  +    G 
Sbjct: 168  QDPKALVKDVQQLRRTNQIPAEVSLVRDIRDREFKIFSDAGRVMRPLFVVEQEDNPETGA 227

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                  +         V   +    ++           G++E +DA       +    + 
Sbjct: 228  GKGTLVLNKETVRRLEVDQTLPP-GSEDYFGWQGLVNGGMIEYLDAEEEETAMICMTPED 286

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                      ++  + N     N+R   K+             PS  LG       +  +
Sbjct: 287  LELYRLAKAGIESHQDN-TDNPNKRIRTKMNPTTHMYTHCEIHPSMLLG-------ICAS 338

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                                                    
Sbjct: 339  IIPFPDHNQSPXXX-----------------------------XXXXXXXXXXXXXXXXX 369

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 370  XRRMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 429

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D  +R        +E   +    + + L +  Y +L +   +  
Sbjct: 430  IDRGLF-RSLFFRAYSDSEKRVGI---NTVEQFEKPFRADTLRLKQGTYDKLDDDGIVAP 485

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K++ ++ D      R++                 +K    T     E 
Sbjct: 486  GVRVTGEDIIIGKTSPINPDNEEMGQRTKV---------------HVKRDASTPLRSTES 530

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++      D +     R VKV V   +  Q GDK A RHG KG +      EDMPF
Sbjct: 531  GIIDQVVVTTNADGL-----RFVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPF 585

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             ++G   DI++NP  +PSRM +  + E  L       G +                    
Sbjct: 586  TREGITPDIIINPHAIPSRMTIAHLIECLLSKVATLKGMEGD------------------ 627

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++ +LR       
Sbjct: 628  -----------------------------------ATP-FTDVTVDSVSGLLREHGYQSR 651

Query: 1232 GQSILYDGLTGEPFDRPVTVGY 1253
            G  ILY G TG      V  G 
Sbjct: 652  GFEILYHGHTGRKLRTQVFFGP 673


>gi|7453595|gb|AAF62904.1| RpoB [Bacillus sonorensis]
 gi|7453597|gb|AAF62905.1| RpoB [Bacillus sonorensis]
 gi|7453599|gb|AAF62906.1| RpoB [Bacillus sonorensis]
 gi|7453601|gb|AAF62907.1| RpoB [Bacillus sonorensis]
 gi|7453603|gb|AAF62908.1| RpoB [Bacillus sonorensis]
 gi|7453605|gb|AAF62909.1| RpoB [Bacillus sonorensis]
          Length = 134

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 56/150 (37%), Positives = 92/150 (61%), Gaps = 19/150 (12%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           +MT  GTF+I G +R++VSQL RSP +++ 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYYS 131


>gi|300394678|gb|ADK11877.1| DNA-directed RNA polymerase II subunit two [Athelia sp. FP-133442]
          Length = 674

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 112/729 (15%), Positives = 216/729 (29%), Gaps = 89/729 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSIPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +       L+ +             +         + GI+E +DA 
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHVKWLNQGYRDGDEEEFRWEHLVKGGIIELLDAE 285

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +   +            ++       R  +K G +          PS  
Sbjct: 286  EEETVMISMTPEDLENSRLQQTGADPHANDGEFDPAAR--LKAGSDAHTWTHCEIHPSMI 343

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 344  LG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLT 378

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 379  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 427

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 428  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYD 486

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  D      R++          ++     +  Q
Sbjct: 487  KIEDDGLIAPGTVVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ 546

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VKV V   R  Q GDK A RHG KG + 
Sbjct: 547  VLI--------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIG 586

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +       
Sbjct: 587  ITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLT 646

Query: 1162 NGDISPLRS 1170
               +S    
Sbjct: 647  VESVSTFLR 655



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 83/610 (13%), Positives = 169/610 (27%), Gaps = 97/610 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA   +     F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESLEENAHSSIPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         E  +R          +  L A EEE   I+     L+       
Sbjct: 249 QKKHVKWLNQGYRDGDEEEFR-WEHLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQT 307

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                   GE     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 308 GADPHANDGEFDPAARLKAGSDAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 367

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 368 MGKQAMGIFLTNFLI-----------------------------------------RMDT 386

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 387 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 422

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 423 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKH 482

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 483 GTYDKIEDDGLIAPGTVVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 538

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 539 TENGIVDQVL 548


>gi|154362139|gb|ABS80908.1| RNA polymerase beta subunit [Burkholderia vietnamiensis]
          Length = 234

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 137/232 (59%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++DE+G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQ 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LIDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|307343536|emb|CBJ18685.1| RNA polymerase B subunit [Micromonospora aurantiaca]
          Length = 210

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 92/211 (43%), Positives = 121/211 (57%), Gaps = 38/211 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 30   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 89

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 90   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIN---------- 138

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 139  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 179

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              G++ L+DG +GEP   P+ VGY+ +LKLN
Sbjct: 180  GSGKAQLFDGRSGEPLPDPIAVGYVCILKLN 210


>gi|123979364|gb|ABM81507.1| RNA polymerase II second largest subunit [Myelochroa aurulenta]
          Length = 704

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 111/733 (15%), Positives = 220/733 (30%), Gaps = 90/733 (12%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   LS+     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLSSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 178  IFVNGVWVGVHRDPAHLVGTVQNLRRRGMISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 237

Query: 684  NDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             D++       N+         L      +  T  +       G   + K  G+VE VDA
Sbjct: 238  IDNNPSSDTRGNLVLTKEHVQKLEIDRENWATTEPDVRDQTDMGWQGLVKE-GVVEYVDA 296

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +       +        +N +  +N+R    +             PS 
Sbjct: 297  EEEETIMIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWTHCEIHPSM 355

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   + +  ++            
Sbjct: 356  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM--------- 397

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 398  ------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 496  GTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDTSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q   S                         LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPF 655

Query: 1158 DYKANGDISPLRS 1170
                   +S L  
Sbjct: 656  TEVTVDSVSRLLR 668



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 80/627 (12%), Positives = 170/627 (27%), Gaps = 119/627 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 8   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLSSPNATKIFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +  + + RR   +             +RD+    +     A         
Sbjct: 185 VGVHRDPAHLVGTVQNLRRRGMIS-------HEVSLVRDIRDREFKVFTDAGRVCRPLFV 237

Query: 582 LVSSLTSFARVNAYGFIET--PYRKVCDGKVTND-------------------VVYLSAM 620
           + ++ +S  R N     E         +   T +                   V Y+ A 
Sbjct: 238 IDNNPSSDTRGNLVLTKEHVQKLEIDRENWATTEPDVRDQTDMGWQGLVKEGVVEYVDAE 297

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVV 672
           EEE   I      L+                +E+                  +  P  ++
Sbjct: 298 EEETIMIVMTPEDLEISRQLQAGYAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMIL 357

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            I AS+IPF +++ S R      M +QA+ +                   + A I+    
Sbjct: 358 GICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYQQRMDTMANILYYPQ 408

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +    ++  +          +   +  Y              NQ              
Sbjct: 409 KPLATTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE------------- 444

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 S  +   ++ R +  +       + E  + +S             +E+FE   R
Sbjct: 445 -----DSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS------------VVEQFEKPMR 487

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                      D   +       +D+ G++  G  V+  DI++GK  P         ++ 
Sbjct: 488 ----------SDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT 537

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  K    RDTS  + S  +G V
Sbjct: 538 -------KLHIKRDTSTPLRSTENGIV 557


>gi|312204316|gb|ADQ47475.1| RNA polymerase II second largest subunit [Cryptodiscus gloeocapsa]
          Length = 708

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 119/799 (14%), Positives = 226/799 (28%), Gaps = 117/799 (14%)

Query: 470  MLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
             +   +R    R+ + I   +               + +  + + +     +        
Sbjct: 1    FIGQLFRTLYARLTKDIFNYLKKCVETGKEFNLTLGVKSNTLTNGLKYSLATGNWGEQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +   + G     +    + +V  +   +        ++    +
Sbjct: 117  PEGQACGLVKNLALMCNITVGSPGDPIIDFMVQRNMEVLEEFEPMRTPNATKIFVNGTWT 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D       +      + I V    + D  D   K          P    D+  R  
Sbjct: 177  GIHRDPIHLVRTIQSLRRRKLIDVETSLVHDIRDREFKIFTDAGRVSRPVFVIDNDERSS 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   R  V  L+ +        E          +++   G VE +DA       + 
Sbjct: 237  NKGNLVLTRDMVQRLEDDKELDLEDEEQKKMFFGWNGLLS--TGAVEYLDAEEEETVMIA 294

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
               +       +    + +   +      +P V               PS  LG      
Sbjct: 295  MTPEDLEISRQVQAGYEIEEGPRELSARIKPKVNPAQHT--WTHCEIHPSMILG------ 346

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N    + +       D                                
Sbjct: 347  -ICASIIPFPDHNQVRVIPLFVAAS-TDRNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 404

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  V             +       +   +  + AI      +  D+ +
Sbjct: 405  XXXXXXXXXXXMANVLYYPQKPLATTQSMEFLKFRELPAGQNAIVAISTYSGYNQEDSVI 464

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME- 988
               S V   +    +F R  +++ +R   +     E   +    + + L    Y +L + 
Sbjct: 465  MNQSSVDRGLF-RSLFYRSYVEQEKR---IGMSMAEQFEKPLRSDTLRLKHGTYEKLDDD 520

Query: 989  --ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G           K+  ++ D      R++                  K    T  
Sbjct: 521  GIIAPGVRVSGEDIIIGKTAPIAPDAEEMGQRTKLHT---------------KRDASTPL 565

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
               E+   +K+      D +     + VKV +   +  Q GDK A RHG KG +      
Sbjct: 566  RSTENGIVDKVLLTTNADGL-----KFVKVRMRTTKIPQVGDKFASRHGQKGTIGITYRQ 620

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF  +G   DI++NP  +PSRM +  + E  L       G +               
Sbjct: 621  EDMPFTAEGLTPDIIINPHAIPSRMTIAHLVECLLSKVGAIRGNEGD------------- 667

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                    +TP F     ++++ +LR  
Sbjct: 668  ----------------------------------------ATP-FTEVTVDSVSRLLREQ 686

Query: 1227 DLDESGQSILYDGLTGEPF 1245
                 G  I+Y+G +G   
Sbjct: 687  GYQSRGFEIMYNGHSGRKL 705


>gi|300394712|gb|ADK11894.1| DNA-directed RNA polymerase II subunit two [Leucogyrophana
            lichenicola]
          Length = 664

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 116/793 (14%), Positives = 220/793 (27%), Gaps = 144/793 (18%)

Query: 476  RLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------ 521
            R+   ++ R +    +              +  + + + +     +              
Sbjct: 1    RMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLATGNWGDQKKSMASKA 60

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 61   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 116

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++   +       + +  + +         EEN + +   + +  +G +
Sbjct: 117  GLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSSTPCTKVFVNGVW 168

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 169  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQ 225

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
               L+ +        E+   +      + K   I          +       D   S + 
Sbjct: 226  QLALQKKHVKWLNQGETDEREEYKWEHLVKGGVIELLDAEEEETVMIAMTPEDLENSRLQ 285

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               +            +    +K G            PS  LG       +  + +P+  
Sbjct: 286  SAGIDPHANDGD---YDPAARLKAGINTHTWTHCEIHPSMILG-------VCASIIPFPD 335

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N                        ++       +G       +               
Sbjct: 336  HNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM-----------DT 366

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 367  MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 426

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+ R  +D  ++S   + E+ E   RD          +       I  G        
Sbjct: 427  -RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDI 485

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  D      R++          ++     +  Q                   
Sbjct: 486  IIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI---------------- 529

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   DI
Sbjct: 530  ----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVPDI 585

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +G + E  L      +G +                             
Sbjct: 586  IINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------------------- 618

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E++++ LR       G  ++Y G 
Sbjct: 619  --------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHGH 651

Query: 1241 TGEPFDRPVTVGY 1253
            TG      V +G 
Sbjct: 652  TGRKLQAQVYLGP 664



 Score =  122 bits (305), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 81/591 (13%), Positives = 166/591 (28%), Gaps = 98/591 (16%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           D+YR ++        F+++ ++ +    +  KY L   G      +         + + +
Sbjct: 10  DVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL-ATGNWGDQKKSMASKAGVSQVLNR 68

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R GK       +  +  +    E  + Q    +  +      
Sbjct: 69  YTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCI 128

Query: 489 RISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +             NA         F     +    +  N +  I   RR 
Sbjct: 129 SVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRK 188

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +                ++        P    E   + L      +  +N     E  
Sbjct: 189 DDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKW--LNQGETDERE 246

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL------ 655
             K         +  L A EEE   IA     L+     +  +      G+         
Sbjct: 247 EYKWEHLVKGGVIELLDAEEEETVMIAMTPEDLENSRLQSAGIDPHANDGDYDPAARLKA 306

Query: 656 -VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            +        +  P  ++ + AS+IPF +++ S R      M +QA+ +           
Sbjct: 307 GINTHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---- 362

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                                                   + + +  Y       +    
Sbjct: 363 -------------------------------------RMDTMANILYYPQKPLATTRSME 385

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +  R                        +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 386 YLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 421

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F SI+   +  + + + +   E            +       I++ G+I  G  V+
Sbjct: 422 DRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVS 481

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 482 GEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 528


>gi|154362155|gb|ABS80916.1| RNA polymerase beta subunit [Burkholderia plantarii]
          Length = 234

 Score =  241 bits (616), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+S+DE G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVTDSKVTDQIDYLSAIEEGRYVIAQANASVDEAGE 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSAREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A+R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAERGGVVDYVDAGRIVIRVNDDE 232


>gi|307949498|gb|ADN96585.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
 gi|307949500|gb|ADN96586.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
 gi|307949502|gb|ADN96587.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
 gi|307949504|gb|ADN96588.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
 gi|307949508|gb|ADN96590.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
 gi|307949512|gb|ADN96592.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
          Length = 243

 Score =  241 bits (616), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 138/243 (56%), Positives = 184/243 (75%)

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 1   GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 60

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 61  VFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 120

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 121 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 180

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 181 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 240

Query: 795 ADG 797
           ADG
Sbjct: 241 ADG 243


>gi|154362133|gb|ABS80905.1| RNA polymerase beta subunit [Burkholderia pyrrocinia]
 gi|154362137|gb|ABS80907.1| RNA polymerase beta subunit [Burkholderia cepacia ATCC 25416]
 gi|154362141|gb|ABS80909.1| RNA polymerase beta subunit [Burkholderia stabilis]
 gi|154362143|gb|ABS80910.1| RNA polymerase beta subunit [Burkholderia cepacia]
 gi|154362145|gb|ABS80911.1| RNA polymerase beta subunit [Burkholderia cepacia]
          Length = 234

 Score =  241 bits (616), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 137/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++DE+G+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LIDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|154362157|gb|ABS80917.1| RNA polymerase beta subunit [Burkholderia glumae]
          Length = 234

 Score =  241 bits (616), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 140/232 (60%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+S+DE G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVTDGKVTDQIDYLSAIEEGRYVIAQANASVDEAGE 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSAREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A+R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAERGGVVDYVDAGRIVIRVNDDE 232


>gi|145343599|ref|XP_001416405.1| DNA-directed RNA polymerase I polypeptide 2 [Ostreococcus lucimarinus
            CCE9901]
 gi|144576630|gb|ABO94698.1| DNA-directed RNA polymerase I polypeptide 2 [Ostreococcus lucimarinus
            CCE9901]
          Length = 1145

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 106/274 (38%), Gaps = 53/274 (19%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +    +K+   Q          +   + +   R    GDK + RHG KG++S + P EDM
Sbjct: 850  DAAVVDKVVLTQSVKQAATKNDKRAAITLRYDRNPVIGDKFSSRHGQKGVLSFLWPEEDM 909

Query: 1110 PFLK-DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            PF    G   D+++NP   PSRM +G + E+    A    G    +    +         
Sbjct: 910  PFSDRTGLRPDVIINPHAFPSRMTIGMLVESLAAKAGASTGIFADATPFKHSDKEISPT- 968

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                            E    +LR +  
Sbjct: 969  ------------------------------------------------EEYGKLLRESGY 980

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS--DKVYARSTGSYSLVTQQPLGGK 1286
            +  G   L +G TGE F   + +G +Y  +L HMVS     + RSTG  + +T QP+ G+
Sbjct: 981  NFCGSERLVNGCTGESFSVDIFIGLVYYQRLRHMVSLFHTFHVRSTGPNNPLTMQPIKGR 1040

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
             + GG R GEME   + A+G AY L  +L I SD
Sbjct: 1041 KSGGGIRFGEMERDSLLAHGVAY-LVSLLHICSD 1073



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 34/91 (37%)

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD----- 141
               C     +Y  PL +      + +D     + +       + +GD P+M K      
Sbjct: 103 TPRGCREGGESYKAPLSVQF---CWQIDGENVQRRV-------VNLGDCPVMVKSDVCSL 152

Query: 142 -------------------GTFVIKGIQRIV 153
                              G F+I GI+R++
Sbjct: 153 ALLSPAQLVARGEEAHEAGGYFIINGIERMI 183


>gi|154316380|ref|XP_001557511.1| hypothetical protein BC1G_04121 [Botryotinia fuckeliana B05.10]
 gi|150845921|gb|EDN21114.1| hypothetical protein BC1G_04121 [Botryotinia fuckeliana B05.10]
          Length = 450

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 88/504 (17%), Positives = 168/504 (33%), Gaps = 92/504 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I       +   +    A+      D+ D  +   +     
Sbjct: 18   DTLLYLMVYPQQPMVKTRTIELIKYDKLPAGQNATVAVMSFSGYDIEDALVLNKASCDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++F ++     +     +    + +  +  + + I    I       L G+   +G
Sbjct: 78   FGRCQVFRKYSTQLKKYPNRSQDRIADRVIGE--NGKPIAKHRILGTDGIALVGERINAG 135

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K +  + +                                    + +  + +K+ 
Sbjct: 136  EVYLNKESPSNPNSTGMGNDFNLNDMKPAPMG---------------YKLHDHAYIDKV- 179

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
             +    +   GVL   KV     R  + GDK + RHG KG+V                  
Sbjct: 180  -MLSQTENESGVL---KVQTRQTRRPELGDKFSSRHGQKGVVG----------------- 218

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
             I++N                                    + +   +      + ++  
Sbjct: 219  -IIVN------------------------------------QEDMPFADSGVTPDIIMNP 241

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 +++      +L       +G       F G++ + +  +L       SG+  +  
Sbjct: 242  HGFPSRMTVGKMLELLSGKAGVINGSLEYGTCFGGSNVDVMGQILIDNGFSYSGKDFVTS 301

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE     V  G IY  KL HMV DK+++RS G  +++T+QP  G+S  GG RLGEME
Sbjct: 302  GITGESLPAYVFFGPIYYQKLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEME 361

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVV---------GRTRVYESIVAGNDTFETGTPE 1345
              C+ AYGA+ +L E L + SD    D+          G  +  +S   G  T     P 
Sbjct: 362  RDCLIAYGASQLLLERLMLSSDAHQVDICETCGLMGYSGWCQTCKS-SKGVSTM--TMPY 418

Query: 1346 SFNVLVKEMQALGLSIDLENSRTK 1369
            +  +LV+EM ++ + + L+     
Sbjct: 419  AAKLLVQEMLSMNVLVRLKLEDEF 442


>gi|52699810|gb|AAU86967.1| DNA-dependent RNA polymerase II second largest subunit [Fuscidea
            lygaea]
          Length = 737

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 114/825 (13%), Positives = 226/825 (27%), Gaps = 112/825 (13%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R    ++   + +              Q  I +  + S +     +
Sbjct: 2    KRLDLAGPLLANLFRQVFTKLIGDMNKYLSRCIDSGRDFNLQLAIKSNTITSGLRYSLST 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWSDQKNAATSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     V+     +    +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYVSVGTPSDPILDFLVQRNMEVLEEYEPQRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  +       V        +      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRNPIHLVTTVQRLRRTSVLSYEISLVHDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
               D      G  +  +       +   +    E +    S +    +  G    V   +
Sbjct: 238  VETDPKSSNNGNLVLTKEYVNKLEDHKEIVMDKERMA---SMSEKEKELLGWAGLV--KQ 292

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             ++  V+ + + +   V     ++  R  Q       P +   +   +  I     +   
Sbjct: 293  GMVEYVDAEEEETVMIVMTPEDLEISRQIQAGYAMPEPSIDEPNRRVKAPINPTAHTWTH 352

Query: 803  GDL--ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             ++  ++   +  +  P+                                          
Sbjct: 353  CEIHPSMILGICASIXPFPXXXXXXXXXXXXXXXXXXXXXX-------XXXXXXXXXXXX 405

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                          +     +  +             +       +   +  + AI    
Sbjct: 406  XXXXXXXXXXXXNFDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 465

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R      EQ E   R    +  +   
Sbjct: 466  GYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKRIGMNVVEQFEKPMRSDTLKIKMGTY 524

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       +  G           K+  +++D      R++                 +K 
Sbjct: 525  DKLDVDGIVAPGNRVSGEDIIIGKTAPMAADAEELGQRTKL---------------HIKR 569

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E    +++             L+ VKV +   +  Q GDK A RHG KG +
Sbjct: 570  DVSTPLRSTESGIVDRV-----MYTTNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTI 624

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +      
Sbjct: 625  GITYRQEDMPFTSEGVIPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDV 684

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L    E    +                                          
Sbjct: 685  TVDSVSRLLR--EHGYQSRGFEVM------------------------------------ 706

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                      +G +    G         V +G  Y  +L HMV D
Sbjct: 707  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDD 735


>gi|110669606|gb|ABG81898.1| RNA polymerase II second largest subunit [Umbilicaria mammulata]
          Length = 701

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 127/817 (15%), Positives = 236/817 (28%), Gaps = 137/817 (16%)

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
            + +  +R     M   +K+ + S    ++      N             +          
Sbjct: 3    LFRGLFRKANKDMTTYLKKAVESAKEFNMTLAVRTNTITNGLKYSLATGNWGDQKKAAQS 62

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               + Q+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 63   KAGVPQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 118

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     ++    +     + K    ++  +     +      ++      +  
Sbjct: 119  ACGLVKNLALMCYISVGSPMTPIVDFMKQRGMELLEEYEPHRSPNATKVFVNGVWVGVHR 178

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D +    LV+       I      + D  D   K          P    D+  +     N
Sbjct: 179  DPTHLVGLVYHLRRTGIIHPEVGLVRDIRDREFKIFTDAGRVCRPLFVVDNDPKSANNGN 238

Query: 696  MQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            +   ++ + LLK +             +         ++G+VE VDA       +    +
Sbjct: 239  LVLTKEHIRLLKKDDDVPKDLQPDERRELIFGWEGLIKSGVVEYVDAEEEETVMIVMTPE 298

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   +    + +       +N+R    V   VR +      PS  LG       +  
Sbjct: 299  DLEISRQVQAGYEAEDEVDEEDLNKRVKATVDKNVRIHTHCEIHPSMILG-------ICA 351

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N                        +        +G      D         
Sbjct: 352  SIIPFPDHNQSPRN------------------TYRSAMGKQAMGVFLTNFDQRM------ 387

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 388  -----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 442

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R   D+ +R   +    +E   R    + + L    Y +L +   + 
Sbjct: 443  SIDRGLF-RSLFYRCYTDQEKR---IGMSVVEQFERPMRSDTLRLKHGTYDKLDDDGIVA 498

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D                +E  QR    +K    T     E
Sbjct: 499  PGVRVSGEDIIIGKTAPIAPD---------------AEELGQRTKTHVKRDVSTPLRSTE 543

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
            +   +++             LR VKV +   +  Q GDK A RHG KG +      EDMP
Sbjct: 544  NGIVDQVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMP 598

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 599  FTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSRLLR 658

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
              E    +                                                    
Sbjct: 659  --EHGYQSRGFEVM---------------------------------------------Y 671

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            +G +    G         V +G  Y  +L HMV DK+
Sbjct: 672  NGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKI 701


>gi|154362127|gb|ABS80902.1| RNA polymerase beta subunit [Burkholderia thailandensis]
 gi|154362129|gb|ABS80903.1| RNA polymerase beta subunit [Burkholderia thailandensis]
          Length = 234

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++  DGS
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAISNDGS 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LVDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRIVIRVNDDE 232


>gi|118640697|gb|ABL09916.1| RNA polymerase beta subunit [Vibrio sp. 2419-00]
          Length = 290

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 170/290 (58%), Positives = 224/290 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIVEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT+DV YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDDVDYLSAIQEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L E+G+F EEL+  R  GE  L PRE +D++D +  QVVSIAASLIPFLE
Sbjct: 241 LTEEGTFAEELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLE 290


>gi|115475001|ref|NP_001061097.1| Os08g0171600 [Oryza sativa Japonica Group]
 gi|113623066|dbj|BAF23011.1| Os08g0171600 [Oryza sativa Japonica Group]
          Length = 462

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 101/525 (19%), Positives = 155/525 (29%), Gaps = 120/525 (22%)

Query: 891  GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
                +G  T      +      L          V    L      SG+  D         
Sbjct: 7    SQQAIGYSTTNPLFRVDTHSHQLYYPQRPLFKTVAADCLGKRDYTSGSKHDFARPEYFNG 66

Query: 951  DK------------NERSISVEREQIEL----LARDKDDEQVILDRNIYSRLMEILCGQN 994
                           E S+ + R  +E         K  + +I ++ I  RL      +N
Sbjct: 67   QNAIVSISVHQGFNQEDSLVLNRASLERGMFRTQHFKSYKALIENKEITKRLKH---KEN 123

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
               G    KK  V S D+          Q    ++ +   V      +       E    
Sbjct: 124  INFGKTPSKKGLVDSLDIDGLPYIGASLQ---SNDIIIGKVSDSGEDHSIKLLHTEKGIV 180

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K+      D           V +   R  + GDK A  HG KG++  +   E+ PF   
Sbjct: 181  EKVVLSATDDGTNSAF-----VTLRQTRSPRIGDKFASMHGQKGVIGFLDSQENFPFTHQ 235

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DIV+NP G P+R   GQ+ E  LG      G    +      +   I+        
Sbjct: 236  GIVPDIVINPHGFPTRQTPGQLLEAALGKGIALGGATRYATPFTSPSVEVITEQLHKAGF 295

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                G                     ++G   ++PVF                       
Sbjct: 296  SRWGG---------------ESVINGRTGERAASPVFT---------------------- 318

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
                             G  +  +L+HM  DKV  R+TG    +T+QP+  +   GG + 
Sbjct: 319  -----------------GPTFYQRLHHMAEDKVKFRNTGPVHPLTRQPVEDRRRYGGVKF 361

Query: 1295 GEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--------------------GRTRVYE 1330
            GEME  C+ A+GAA  L E L + SD     V                     GR     
Sbjct: 362  GEMERDCLLAHGAAANLHERLFLLSDVSRLHVCRRCQRAAVVVSPAVAADGGGGRK---- 417

Query: 1331 SIVAG---------NDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
              V G          +      P    +L +E+ ++G+ +  +  
Sbjct: 418  --VRGPYCRFCRSAEEVVRVSVPYGAKILYQELFSMGICLKFDTE 460



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 64/154 (41%), Gaps = 8/154 (5%)

Query: 761 IYRLMKFQRSNQNTCVNQRPL---VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
              L +    +      QRPL   V      +R+            +   G+N +V+   
Sbjct: 16  TNPLFRVDTHSHQLYYPQRPLFKTVAADCLGKRDYTSGSKHDFARPEYFNGQNAIVSISV 75

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV-----SEEG 872
             G+N EDS++++   +   +F + H + ++ +  + ++      ++  N       +  
Sbjct: 76  HQGFNQEDSLVLNRASLERGMFRTQHFKSYKALIENKEITKRLKHKENINFGKTPSKKGL 135

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           + ++D  G+  +GA +   DI++GK++  GE   
Sbjct: 136 VDSLDIDGLPYIGASLQSNDIIIGKVSDSGEDHS 169


>gi|140084096|gb|ABO84897.1| RpoB [Paenibacillus sp. FSL_F4-077]
 gi|140084100|gb|ABO84899.1| RpoB [Paenibacillus sp. FSL_F4-085]
          Length = 237

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 88/208 (42%), Positives = 116/208 (55%), Gaps = 54/208 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 84   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 143

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 144  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 192

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 193  ----------------------------------VFD---------TMEEAGMQRNGKTV 209

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            LYDG TGE F+R VTVG ++M+KL HMV
Sbjct: 210  LYDGRTGERFEREVTVGVMHMIKLAHMV 237



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 61/92 (66%), Positives = 74/92 (80%)

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
           EITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGE
Sbjct: 1   EITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGE 60

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           KA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  KAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 92


>gi|307343560|emb|CBJ18697.1| RNA polymerase B subunit [Micromonospora echinofusca]
          Length = 221

 Score =  241 bits (615), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 91/201 (45%), Positives = 117/201 (58%), Gaps = 38/201 (18%)

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             RVV+V+VA KR IQ GDK+AGRHGN+G++S+ILP EDMPFL+DGTPVDIVLNPLGVPSR
Sbjct: 51   QRVVRVYVAQKRKIQDGDKLAGRHGNQGVISKILPIEDMPFLEDGTPVDIVLNPLGVPSR 110

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            MN+GQ+ ETHLGW     G  +     ++K                              
Sbjct: 111  MNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIE----------------------- 146

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES--------GQSILYDGLTG 1242
                  A + +    V+TPVFDGA EE I+ +L     +          G++ L+DG +G
Sbjct: 147  ------AHESEPDTNVATPVFDGAREEEISGLLSSTLPNRDGKQLIGSTGKAQLFDGRSG 200

Query: 1243 EPFDRPVTVGYIYMLKLNHMV 1263
            EP   P+ VGYIY+LKLNH+V
Sbjct: 201  EPLPDPIAVGYIYILKLNHLV 221


>gi|154362117|gb|ABS80897.1| RNA polymerase beta subunit [Burkholderia pseudomallei]
          Length = 234

 Score =  241 bits (615), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 137/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++ +DG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIGDDGA 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LVDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRIVIRVNDDE 232


>gi|300244847|gb|ADJ93856.1| RNA polymerase B subunit [Staphylococcus sp. 462]
          Length = 266

 Score =  241 bits (615), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 155/265 (58%), Positives = 197/265 (74%), Gaps = 3/265 (1%)

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           RLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIE
Sbjct: 1   RLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIE 60

Query: 600 TPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           TPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G FT + V CR  G   ++ 
Sbjct: 61  TPYRKVDLETNAITDQIDYLTADEEDSYVVAQANSTLDENGRFTADEVVCRFRGNNTVMA 120

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
           +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME 
Sbjct: 121 KEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEH 180

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
           V A+ SGAAIVAKR G VE V++  I++R  +E D       +D Y L KF+RSN  TC 
Sbjct: 181 VAARDSGAAIVAKRKGRVEHVESNEILVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTCY 240

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTD 801
           NQRP+V  GD V + +I+ADGPS +
Sbjct: 241 NQRPIVTSGDVVAKGEILADGPSME 265


>gi|307949510|gb|ADN96591.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
          Length = 243

 Score =  241 bits (615), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 139/243 (57%), Positives = 185/243 (76%)

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 1   GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 60

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+EE +  IAQA++++++    T+ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 61  VFLSAIEEADHVIAQASAAMNDKQELTDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 120

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 121 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 180

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 181 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 240

Query: 795 ADG 797
           ADG
Sbjct: 241 ADG 243


>gi|113957146|gb|ABI49102.1| RNA polymerase II second largest subunit [Flavocetraria nivalis]
          Length = 699

 Score =  241 bits (615), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 118/774 (15%), Positives = 225/774 (29%), Gaps = 99/774 (12%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L + +R    ++ + + +  +    +         + +  + + +     + 
Sbjct: 1    RLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     +      E    +    + +V  +   L++      
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKI 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN 684
            ++      +  D +     V        I      + D  D   K          P    
Sbjct: 177  FVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVI 236

Query: 685  DDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            D+  R     N+         L      +  T  +       G   + K  G+VE VDA 
Sbjct: 237  DNDPRSSNKGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKE-GVVEYVDAE 295

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +       +   ++    N +  +N+R    +             PS  
Sbjct: 296  EEETIMIVMTPEDLDISHQLQAGLQPPEPNPDE-LNRRVKAPLNPTAHTWTHCEIHPSMI 354

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N          M  + +   + +  ++             
Sbjct: 355  LG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM---------- 395

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +     + +   +  + AI     
Sbjct: 396  -----------------DTMANILYYPQKPLATTRSVEFLKFTELPAGQNAIVAIACYSG 438

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R      EQ E   R    +      +
Sbjct: 439  YNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYD 497

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   +  G           K+  ++ D      R++          ++     +  Q
Sbjct: 498  KLDEDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQ 557

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
               S                         LR VKV +   +  Q GDK A RHG KG + 
Sbjct: 558  VLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIG 597

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +       
Sbjct: 598  ITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVT 657

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
               +S L                         L V     +G  + T VF G  
Sbjct: 658  VDSVSRLLR---------------EHGYQSRGLEVMYNGHTGRKLVTQVFLGPT 696



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 82/621 (13%), Positives = 170/621 (27%), Gaps = 102/621 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 6   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 62

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 63  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 122

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 123 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 182

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 183 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 242

Query: 574 TSEGHNIGLVSSLTSF--ARVNA----YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           +++G+ +     +      R N         E              V Y+ A EEE   I
Sbjct: 243 SNKGNLVLTKEHVQKLELDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMI 302

Query: 628 AQANSSLDEDGSFTEELVF--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                 LD        L           R     +          +  P  ++ I AS+I
Sbjct: 303 VMTPEDLDISHQLQAGLQPPEPNPDELNRRVKAPLNPTAHTWTHCEIHPSMILGICASII 362

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                   + A I+      +    
Sbjct: 363 PFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYQQRMDTMANILYYPQKPLATTR 413

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           ++  +  +       +   +  Y              NQ                    S
Sbjct: 414 SVEFLKFTELPAGQNAIVAIACYSG-----------YNQE------------------DS 444

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +   ++ R +  +       + E  + +S             +E+FE   R       
Sbjct: 445 VIMNQSSIDRGLFRSLFYRAYTDQEKRVGMS------------VVEQFEKPMR------- 485

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               D   +       +DE G++  G  V+  DI++GK  P         E+L +     
Sbjct: 486 ---SDTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLH 538

Query: 920 KAVDVRDTSLRVPSGVSGTVV 940
              DV        +G+   V+
Sbjct: 539 VKRDVSTPLRSTENGIVDQVL 559


>gi|140084106|gb|ABO84902.1| RpoB [Paenibacillus sp. FSL_F4-097]
 gi|140084116|gb|ABO84907.1| RpoB [Paenibacillus sp. FSL_F4-125]
 gi|140084118|gb|ABO84908.1| RpoB [Paenibacillus sp. FSL_F4-126]
 gi|140084134|gb|ABO84916.1| RpoB [Paenibacillus sp. FSL_F4-190]
          Length = 238

 Score =  241 bits (614), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 88/208 (42%), Positives = 116/208 (55%), Gaps = 54/208 (25%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 85   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 144

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 145  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 194  ----------------------------------VFD---------TMEEAGMQRNGKTV 210

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            LYDG TGE F+R VTVG ++M+KL HMV
Sbjct: 211  LYDGRTGERFEREVTVGVMHMIKLAHMV 238



 Score = 89.0 bits (219), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 62/93 (66%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  EKAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 93


>gi|110666975|gb|ABG81888.1| RNA polymerase II second largest subunit [Dermatocarpon miniatum]
          Length = 716

 Score =  241 bits (614), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 120/828 (14%), Positives = 233/828 (28%), Gaps = 134/828 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+LG +R+   G ++ N +RL   ++ R      +        +  +  + +  + + + 
Sbjct: 4    DHLGKKRLDLAGPLMANLFRLQFQKVVRDFSRYMQKQVESDREINLKVGLKSNIITNGLK 63

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +A     + R     + R +
Sbjct: 64   YSLATGNWGDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQL 119

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVY-LS 618
            H TH+G +CPAET EG   GLV +L     V  +        Y      +   D    LS
Sbjct: 120  HNTHWGYVCPAETPEGQACGLVKNLALMTMVTNSHNTAPLEDYILGQSVEPLEDWEPRLS 179

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAAS 677
                +        + + +D     +L         +      + D  D   K        
Sbjct: 180  PQATKVFLNGVWFAVVIKDPKNLVDLFKNFRRMGRLDPQISMVWDIRDKEFKISGDAGRI 239

Query: 678  LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            + P    +         N+      + + +   V T  E+ +                 +
Sbjct: 240  IRPLFVVETDPSKDNQGNLVLNKNHIQRLDNTVVNT--EAQLPID-----QWPEPPFGWK 292

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                  V+  ++ + + +   +     +   ++       +       D + R D +   
Sbjct: 293  DLLKEGVVEYLDAEEEETAMIIMTPEDLNTSKARHMGYTTEETD----DPLARYDPL--- 345

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                        N           +    + +   ++            ++       +G
Sbjct: 346  -----------LNPHAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 394

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                  D    +           +  +             +       +   +  + AI 
Sbjct: 395  VFLTNFDQRMET-----------MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIA 443

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R   D+ +       EQ E   R        
Sbjct: 444  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKVVGHNVVEQFEKPTRSDTLRMKH 502

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       +  GQ          K+  ++ D                +E  QR  + 
Sbjct: 503  GTYDKIDADGIVEVGQRVSGEDIIIGKTAPMAPD---------------AEELGQRQKQH 547

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            LK    T     E    +++     GD       + VKV V   +  Q GDK A RHG K
Sbjct: 548  LKRDVSTPLRSTESGIVDQVLVTTSGD-----GQKFVKVRVRTTKIPQIGDKFASRHGQK 602

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 603  GTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPF 662

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                  ++S +   +                                             
Sbjct: 663  TKVTVTNVSNILRSMGYQSRGFEVM----------------------------------- 687

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                         +G +    G         V +G  Y  +L HMV D
Sbjct: 688  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDD 716



 Score =  123 bits (308), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 91/639 (14%), Positives = 178/639 (27%), Gaps = 117/639 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +         V   + + +  +  KY L   G  
Sbjct: 15  GPLMANLFRLQFQKVVRDFSRYMQKQVESDREINLKVG--LKSNIITNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++N       + + +    + +  L        R+GK       +  +       E
Sbjct: 72  GDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGYVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDID---------SVMPQDLINAKPVVSAVCEFFCSS 520
             + Q    +  +        S                  +D        +         
Sbjct: 132 TPEGQACGLVKNLALMTMVTNSHNTAPLEDYILGQSVEPLEDWEPRLSPQATKVFLNGVW 191

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARAR--------AGVEMRDVHPTHYGRICPA 572
               +++  N +    + RR+  L                 +G   R + P       P+
Sbjct: 192 FAVVIKDPKNLVDLFKNFRRMGRLDPQISMVWDIRDKEFKISGDAGRIIRPLFVVETDPS 251

Query: 573 ETSEGHNIGLVSSLTSF--------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           + ++G+ +   + +           A++    + E P+    D      V YL A EEE 
Sbjct: 252 KDNQGNLVLNKNHIQRLDNTVVNTEAQLPIDQWPEPPF-GWKDLLKEGVVEYLDAEEEET 310

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR------EKIDFIDASPKQVVSIAASL 678
             I      L+   +                               +  P  ++ + AS+
Sbjct: 311 AMIIMTPEDLNTSKARHMGYTTEETDDPLARYDPLLNPHAHTFTHCEIHPSMILGVCASI 370

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 371 IPFPDHNQSPRNTYQSAMGKQAMGVFLTNF------------------------------ 400

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + +  Y      R+     +                      
Sbjct: 401 -----------DQRMETMANILYYPQKPLARTMSMEYL---------------------- 427

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA   + GYN EDS+++++  +   +F S+    ++   +      
Sbjct: 428 --KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKVVGHNV 485

Query: 859 EEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            E        D   +       ID  GI+ VG  V+  DI++GK  P     M P+ + L
Sbjct: 486 VEQFEKPTRSDTLRMKHGTYDKIDADGIVEVGQRVSGEDIIIGKTAP-----MAPDAEEL 540

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                +     RD S  + S  SG V  V +       K
Sbjct: 541 GQRQKQHLK--RDVSTPLRSTESGIVDQVLVTTSGDGQK 577


>gi|154362113|gb|ABS80895.1| RNA polymerase beta subunit [Burkholderia caledonica]
          Length = 234

 Score =  241 bits (614), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDGKVTDQIDYLSAIEEGRYVIAQANAAVAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E   VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +
Sbjct: 181 AVPCLRPEKAVVGTGIERTVAVDSGTTVQAFRGGVVDYVDAGRMVIRVNDDE 232


>gi|94410908|gb|ABF18575.1| RNA polymerase II second largest subunit [Gloiocephala aquatica]
          Length = 685

 Score =  241 bits (614), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 121/816 (14%), Positives = 231/816 (28%), Gaps = 147/816 (18%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ R +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETRKEFNVNVGVKRQTIXNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +     + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSTTPFTKVFVNGVWMG---VHRDPANLVNTIKKLRRKDDISPEVSVVRDIREKXLXLY 225

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +   Q + L K    ++ +G++      SG     ++      V+ +  
Sbjct: 226  TDAGRVCRPLFIVENQQLSLQKKHVKWIQSGVD-----DSGEEYKWEQLIKTGIVELLDA 280

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                       +    +                +    +K G            PS  LG
Sbjct: 281  EEEETVMISMSTEDLENSRTQSAGDVPMNEGEFDPAARLKAGTNAHTWTHCEIHPSMILG 340

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 341  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNF 375

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 376  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 424

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S     E+ E   R+          +  
Sbjct: 425  QEDSVIMNQSSIDRGLF-RSIYYRSYMDVEKKSGIQALEEFEKPQRESTLRMKHGTYDKL 483

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G   V       K+  +  D      R++          ++     +  Q  
Sbjct: 484  EDDGLIAPGTGVVGEDIIIGKTAPIPPDSEELGQRTRMHTRRDVSTPLKSTESGIIDQVL 543

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q+GDK A RHG KG +   
Sbjct: 544  I--------------------TTNSDGQKFVKVRVRATRIPQTGDKFASRHGQKGTIGIT 583

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 584  YRQEDMPFTSEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGHEGDATPFT----- 638

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                                 ++     + LR       G+ V                 
Sbjct: 639  --------------------DLTVESVSTFLRQKGYQSRGLEVM---------------- 662

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    G +       G      V +G  Y  +L
Sbjct: 663  ------YHGHT-------GRKLQAQVYLGPTYYQRL 685


>gi|123487429|ref|XP_001324946.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
 gi|121907837|gb|EAY12723.1| DNA-directed RNA polymerase, beta subunit family protein [Trichomonas
            vaginalis G3]
          Length = 1142

 Score =  241 bits (614), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 175/1119 (15%), Positives = 330/1119 (29%), Gaps = 213/1119 (19%)

Query: 299  TSDCLCGLYVAE----DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI-LYVDSVN 353
              + +   ++A      +VN  T         +  + +L    ++   DIPI +   ++ 
Sbjct: 184  PYNRILIEHLANGNKTAVVNSSTSTHKTRVELIWKKDTLALHHNALSEDIPIFVLFRAMG 243

Query: 354  NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL----------FFDS 403
              +      + D        L+   + +   ++ST   A  +                  
Sbjct: 244  VTSDQEVIQLVDPTGAVGHLLMSSLQEIIKLEISTQDQAIQLIERRLKFLTITGIDATRE 303

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII--AIIKILVDLRNGKGTIDDIDNLGN 461
            ++      GR  +   +    P  +   R++ +    + + L+        ID  D  GN
Sbjct: 304  ERNMKGYKGREFLRSMVLPHIPSTLTDFRRKSVFVGFMTRWLLLSAIDPRMIDGRDFFGN 363

Query: 462  RRVRSVGEMLKNQ----YRLGLLRMERSIKERISSVD-IDSVMPQDLINAKPVVSAVCEF 516
            +R+   GE+L+      ++     M++++   I+    ID       ++++ +   +   
Sbjct: 364  KRLELAGELLELLFEDLFKTFNASMQKTVSRTINKSKGIDPSNIAQAMHSETITHGLKYA 423

Query: 517  FCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAGVEMRDVHPTHYGR 568
              S   +     +          R+S L              + +     R ++P+ +G 
Sbjct: 424  ISSGNWNITRFKMMRAGVSQLLGRMSYLQFVSMVTRISSHFEKTQKVAGARLLYPSQFGF 483

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            ICP++T EG   GL+ +      V  +       R + D  V   VV+ S  E  N YI 
Sbjct: 484  ICPSDTPEGAQCGLIKNFALTVHVTVWADPAPARRTLLDLGVEELVVF-SGEEISNNYIV 542

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              N      G   +    CR   +                   + I  +      + ++ 
Sbjct: 543  MLNGE--PIGIIDDPYSICRRFRQVRRRHW-------VDKFAAIWIVEAKKCINVSTEAG 593

Query: 689  RVLMGCNMQRQAVPLLKAE--APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            RV     +       L  E         +       +G         I+E VD   +   
Sbjct: 594  RVCRPLIIVEDHKSKLTQELMDQVNRGEINFDYLLDNG---------IIEYVDVNEMT-- 642

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                          I    K     +  CVN                          D  
Sbjct: 643  -----------DCLIAFNDKDIEEERKNCVN--------------------------DPP 665

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
            L +  L  F     +N +  + +   +V            ++       +GP  +     
Sbjct: 666  LAKGELRYFTHLEIHNAQ-MLGVCAGVVPCPHHNQSPRNTYQCAMGKQAIGPTALNIMHR 724

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                                      +    I       M   +  + AI      D+ D
Sbjct: 725  VDKSTYFNC-----------YPQQPMVQTRTIRLSRYHEMPCGQNAMVAIMSYSGHDIED 773

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
              L   + +          ++  +        V  ++I  L R++ +       ++    
Sbjct: 774  ALLMNKASLDRGFGRRYYLSKLDLMLKNYQGGVIGDRIAPLDRERPENIASPQYSLLDAD 833

Query: 987  MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G+    G     K   L+ +       +Q                          
Sbjct: 834  GIIRPGERIEKGMIYANKYVPLNFEESPVKFMAQ-------------------------- 867

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                 R+      IQ          +V+K+  A  R  + GDK +               
Sbjct: 868  ---PARYNYYPVMIQNVSVYTTETTQVIKIKTADFRRPELGDKFS--------------- 909

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
                                  SR                  G+K    +   + +   +
Sbjct: 910  ----------------------SR-----------------HGQKGVIGLIVPQEDMPYT 930

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                  + ++       +++      ++       +G   +   F     + I   L  A
Sbjct: 931  EDGICPDMIMNPHGFPSRMTVGKMIELVSGKVGILTGRIGNGTAFSSDRVKDIADDLIAA 990

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                SG+ +L  G+TGEP    +  G ++   L HMV DK+ AR+TG    +T+QP  G+
Sbjct: 991  GYSYSGKDMLMSGITGEPLYAYIFFGPVFYQSLKHMVKDKMQARATGQVQYLTRQPTQGR 1050

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGR--------------TRV 1328
            S +GG RLGEME  C+  YGAA +L E + I SD    +V  +              T+ 
Sbjct: 1051 SRQGGMRLGEMERDCLIGYGAASILYERMLISSDVYEANVCAKCGFIGYEGYCTHCKTKE 1110

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGL--SIDLEN 1365
            Y  IV          P +  +L  E+ A+G+   + LE+
Sbjct: 1111 YMKIVR--------MPYACKLLFYELMAMGIAPKVRLED 1141



 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 125/992 (12%), Positives = 274/992 (27%), Gaps = 172/992 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           LI++Q  S++ F+   +      N+           I + +    + + +   D PK   
Sbjct: 43  LIKLQLNSFNDFIESGLTKIMNANK---EV------IFSENPRVYIRYKNIYVDRPKIRN 93

Query: 87  ---DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT---- 139
                  C   D TY+  + +    +     +    +           +  LP+M     
Sbjct: 94  QILTPQMCRLSDETYSGNVLVDYDFVNGSTVKSFNNQ----------CIAKLPIMLQSNR 143

Query: 140 --------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDH----DKGRAS 173
                                 G FVI G +R+V  Q   SP   I  +H    +K    
Sbjct: 144 CYLYNASDETFAKYDECRYDPGGYFVINGTERVVHVQEQ-SPYNRILIEHLANGNKTAVV 202

Query: 174 LSGKLLYACRI--IPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILS 230
            S    +  R+  I     W       KD + +  +     +P+     A+G+ S++ + 
Sbjct: 203 NSSTSTHKTRVELI-----W------KKDTLALHHNALSEDIPIFVLFRAMGVTSDQEVI 251

Query: 231 TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE--SGKKLTSGLLKSL 288
                                   +     +  L++       I      +    +    
Sbjct: 252 QLVDPTGAVGHLLMSSLQEIIKLEISTQDQAIQLIERRLKFLTITGIDATREERNMKGYK 311

Query: 289 KEKGVKFLGITS--DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
             + ++ + +      L         V   T  + + A D       +   +  +     
Sbjct: 312 GREFLRSMVLPHIPSTLTDFRRKSVFVGFMTRWLLLSAIDPRMIDGRDFFGNKRLELAGE 371

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDI----YRVMRPGDVSTFSVAESMFNFLFFD 402
           L      +     N  +        +    I           +  T  +  ++ +  +  
Sbjct: 372 LLELLFEDLFKTFNASMQKTVSRTINKSKGIDPSNIAQAMHSETITHGLKYAISSGNWNI 431

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIR--KEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           +    +       +     L     V  I    E    +    +   +  G I   D   
Sbjct: 432 TRFKMMRAGVSQLLGRMSYLQFVSMVTRISSHFEKTQKVAGARLLYPSQFGFICPSDTPE 491

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             +   +       +         + +  +     + V+       + + +         
Sbjct: 492 GAQCGLIKNFALTVHVTVWADPAPARRTLLDLGVEELVVFS----GEEISNNYIVMLNGE 547

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH-PTHYGRIC-PAETSEGH 578
            +  +++  +   R    RR   +     A        + ++  T  GR+C P    E H
Sbjct: 548 PIGIIDDPYSICRRFRQVRRRHWV--DKFAAIWIVEAKKCINVSTEAGRVCRPLIIVEDH 605

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              L   L    +VN  G I   Y           + Y+   E  +  IA  +  ++E+ 
Sbjct: 606 KSKLTQEL--MDQVNR-GEINFDYLL-----DNGIIEYVDVNEMTDCLIAFNDKDIEEER 657

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++    Q++ + A ++P   ++ S R    C M +
Sbjct: 658 KNCVNDPPLAKGELRYF------THLEIHNAQMLGVCAGVVPCPHHNQSPRNTYQCAMGK 711

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+           T +  +                                        
Sbjct: 712 QAIG---------PTALNIMHRVD------------------------------------ 726

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                     +S    C  Q+P+V+                +   ++  G+N +VA M +
Sbjct: 727 ----------KSTYFNCYPQQPMVQ----------TRTIRLSRYHEMPCGQNAMVAIMSY 766

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP------EEITRDIPNVSEEG 872
            G++ ED++L+++  +        ++ + ++M ++ + G               N++   
Sbjct: 767 SGHDIEDALLMNKASLDRGFGRRYYLSKLDLMLKNYQGGVIGDRIAPLDRERPENIASPQ 826

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D  GII  G  +  G I   K  P        +     A +    V +++ S+   
Sbjct: 827 YSLLDADGIIRPGERIEKGMIYANKYVPLNFEESPVKFMAQPARYNYYPVMIQNVSVYTT 886

Query: 933 SGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
                  +    F R  +     S   ++  I
Sbjct: 887 ETTQVIKIKTADFRRPELGDKFSSRHGQKGVI 918


>gi|123979382|gb|ABM81516.1| RNA polymerase II second largest subunit [Parmeliella appalachensis]
          Length = 704

 Score =  241 bits (614), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 115/823 (13%), Positives = 233/823 (28%), Gaps = 144/823 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + + + +               + +  + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVEGNREFNLTLGVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRANT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + ++  +   L +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMITRNMEILEEYEPLRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPAHLVSTVQSLRRRHWISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D      G  +  +   L   E   +G  M+    +       AK  G    V   +
Sbjct: 238  IENDHKSPNYGNLVLTKEHILRLEEDKELGGDMDLEERE-------AKFMGWEGLV--NQ 288

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK-VGDEVRRNDIIADGPSTD 801
             V+  V+ + + +   V     ++  R  Q     + P        V+          T 
Sbjct: 289  GVVEYVDAEEEETVMIVMTPEDLEISRHIQAGFAIEEPSDDDPNRRVKAPMNPTAHTWTH 348

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N          M  + +   + +  ++            
Sbjct: 349  CEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM--------- 397

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 398  ------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMKSDTLKLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   +  G           K+  ++ D      R++          ++     
Sbjct: 496  GTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPF 655

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 656  TEVTVDSVSRLLR--EHGYQSRGFEVM--------------------------------- 680

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                         +G +    G         V +G  Y  +L 
Sbjct: 681  ------------YNGHT----GR---KLVAQVFLGPTYYQRLR 704


>gi|154362149|gb|ABS80913.1| RNA polymerase beta subunit [Burkholderia graminis]
          Length = 234

 Score =  241 bits (614), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++ EDGS
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGS 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E   VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKAVVGTGIERTVAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDEE 232


>gi|123979390|gb|ABM81520.1| RNA polymerase II second largest subunit [Fissurina insidiosa]
          Length = 703

 Score =  241 bits (614), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 114/824 (13%), Positives = 226/824 (27%), Gaps = 147/824 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCS 519
             R+   G ++ N +R    ++ + + + +               + +  + + +     +
Sbjct: 2    ERLDLAGPLMANLFRTLFNKLNKDVYKYLQRCVELGKEFNLNLGVKSTTLTNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWTEQKKAAQGKAGVSQVLNRYTFASTLSHLRRTNT----PLGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GL+ +L    +  V + G     +      +V  +     A     
Sbjct: 118  GLVCPAETPEGQACGLIKNLALMCYITVGSPGEPIIEFMVQRGMEVLEEYEPTRAPHITK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +    +V        +      + D  +   K          P   
Sbjct: 178  VFVNGVWVGVHRDPAHLYNVVLGLRRKNMVSHEVSLVRDIREQEFKIFTDAGRVARPLFV 237

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ +R      +      ++K         +E             K+         IR 
Sbjct: 238  IDNDSRSPNKGQLVLTKALVMK---------LEDDRDLPENMDPDEKKEKYFGWDGLIRT 288

Query: 744  -VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
              +  ++ + + +         ++  R  Q       P       V+    +A    T  
Sbjct: 289  GAVEYLDAEEEETVMIAMTPDDLEVSRQVQAGYAPPEPSSDPNARVKAPINMAAHAWTHC 348

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N          M  + +                       
Sbjct: 349  EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGI--------------------- 387

Query: 862  TRDIPNVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                       L N DE    +  V             +       +   +  + AI   
Sbjct: 388  ----------FLTNFDERMDTMANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACY 437

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    +F R  I++ +R        +E   +    E + L 
Sbjct: 438  SGYNQEDSVIMNQSSIDRGLF-RSLFYRAYIEQEKRVGM---SLVEQFEKPLRSETLRLK 493

Query: 980  RNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               Y +L E   I  G           K+  ++ D      R++          ++    
Sbjct: 494  HGTYEKLDEDGLIAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRSTEN 553

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  +                             L+ VKV +   +  Q GDK A RHG 
Sbjct: 554  GIVDKALL--------------------TTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQ 593

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 594  KGTIGITYRQEDMPFTAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATP 653

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E    +                                      
Sbjct: 654  FTDVTVDSVSRLLR--EHGYQSRGFEVM-------------------------------- 679

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                          +G +    G         V  G  Y  +L 
Sbjct: 680  -------------YNGHT----GR---KLRAQVFFGPTYYQRLR 703


>gi|256014690|gb|ACU56893.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 191

 Score =  241 bits (614), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 86/213 (40%), Positives = 115/213 (53%), Gaps = 40/213 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 11   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 70

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 71   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 115

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 116  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 158

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+
Sbjct: 159  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLH 191


>gi|154362119|gb|ABS80898.1| RNA polymerase beta subunit [Burkholderia caribensis]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVMDSKVTDQIDYLSAIEEGRYVIAQANAAVAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRIVIRVNDDE 232


>gi|110348037|gb|ABG72747.1| RNA polymerase II second largest subunit [Exobasidium rhododendri]
          Length = 693

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 120/827 (14%), Positives = 231/827 (27%), Gaps = 156/827 (18%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L   +R+   ++ R I    +    +      Q  + +  + + +   
Sbjct: 1    FGKKRLDLAGPLLSGLFRMLFKKLTRDIYRHLQRCVEESKDFTLQAAVKSSTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKFMSAKAGVSQVLNRYTYASTLSHLRRCNT----PIGRDGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L+  A ++           + +  + + V    A  + 
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLSLMAMISVGSPSGPIIEFLEEYGLDSLVDMQIADAKA 176

Query: 624  NRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
             +         + D      + L   R   +  +      D  +   +          P 
Sbjct: 177  TKVFVNGVWMGTCDAPSGLVDTLRDLRRKDDISIEVSVVHDIREKELRLYTDAGRVQRPL 236

Query: 682  LENDDSNRVLM-GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
               D  ++ L          V   K +    G G                          
Sbjct: 237  FIVDPEDKTLYVKPKHVDWVVNQEKPDGTPYGWGQLVRDGLI------------------ 278

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP---LVKVGDEV-RRNDIIAD 796
              ++    E  +    S  D+     +     +  ++  P   LV V   +         
Sbjct: 279  -ELLDAEEEETVMICMSPQDLESSRMYNEDPDSVKLSGDPTARLVSVKTYLPNTWTHCEI 337

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             P+  LG       +  + +P+  +N     +    M  + +   +++  +++       
Sbjct: 338  HPAMILG-------VCASIIPFPDHNQSPRNVYQSAMGKQAMG--VYLTNYQMRMDTMSN 388

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                                       +             +       +   +  + AI
Sbjct: 389  ---------------------------ILYYPQKPLATTHSMGYLKFRELPAGQNAIVAI 421

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D+ +   S +   +    ++ R  +D  +++  +  E+ E  +RD      
Sbjct: 422  LCYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTHMDMEKKAGMILLEEFEKPSRDTSVRLK 480

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
                +          G           K+T L  D      RS+          ++    
Sbjct: 481  HGTYDKIDADGFCAPGTRVSGEDIIIGKTTPLPPDSEELGLRSKLHTKKDVSTPLKSTEN 540

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             +  Q   S                          + VKV +   R  Q+GDK A RHG 
Sbjct: 541  GIVDQVLVS--------------------TNSEGNKFVKVRIRSTRIPQTGDKFASRHGQ 580

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  +  
Sbjct: 581  KGTIGITYRQEDMPFTIEGVTPDIIINPHAIPSRMTIGHLVECLLSKVGALSGQEGDATP 640

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S                           L V     +G  +   V+ G   
Sbjct: 641  FTDLTVEAVSHQLR---------------QHGYQSRGLEVMYNGHTGKKLQAQVYLGPT- 684

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                                  Y  +L HMV
Sbjct: 685  --------------------------------------YYQRLKHMV 693



 Score =  110 bits (275), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 92/603 (15%), Positives = 174/603 (28%), Gaps = 99/603 (16%)

Query: 376 DIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
           DIYR + R  + S     ++        +        G      +         + + + 
Sbjct: 27  DIYRHLQRCVEESKDFTLQAAVKSSTITNGLKYSLATGNWGDQKKFMSAKAGVSQVLNRY 86

Query: 435 DIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
              + +  L        R+GK       +  +  +    E  + Q    +  +       
Sbjct: 87  TYASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAMIS 146

Query: 490 ISSVD------IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           + S        ++      L++ +   +   + F +       +  + L       R   
Sbjct: 147 VGSPSGPIIEFLEEYGLDSLVDMQIADAKATKVFVNGVWMGTCDAPSGLVDTLRDLRRKD 206

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRI--CPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
                V+      E      T  GR+               V        VN      TP
Sbjct: 207 DISIEVSVVHDIREKELRLYTDAGRVQRPLFIVDPEDKTLYVKPKHVDWVVNQEKPDGTP 266

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-------CAGEEI 654
           Y           +  L A EEE   I  +   L+    + E+    +             
Sbjct: 267 Y-GWGQLVRDGLIELLDAEEEETVMICMSPQDLESSRMYNEDPDSVKLSGDPTARLVSVK 325

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                     +  P  ++ + AS+IPF +++ S R +    M +QA+ +           
Sbjct: 326 TYLPNTWTHCEIHPAMILGVCASIIPFPDHNQSPRNVYQSAMGKQAMGVYLTNYQM---- 381

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                                                   + S +  Y       ++   
Sbjct: 382 -------------------------------------RMDTMSNILYYPQKPLATTHSMG 404

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +  R                        +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 405 YLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 440

Query: 835 SEDVFTSIHIEEFEVMARDTKLG----PEEITRDI-PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++      M +   +      E+ +RD    +       ID  G    G  V+
Sbjct: 441 DRGLFRSLYYRTHMDMEKKAGMILLEEFEKPSRDTSVRLKHGTYDKIDADGFCAPGTRVS 500

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK TP    P   EE  LR+    K    +D S  + S  +G V  V +     
Sbjct: 501 GEDIIIGKTTP---LPPDSEELGLRS----KLHTKKDVSTPLKSTENGIVDQVLVSTNSE 553

Query: 950 IDK 952
            +K
Sbjct: 554 GNK 556


>gi|153958180|gb|ABS53380.1| RpoB [Bacteriovorax sp. NZ8]
          Length = 349

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 167/352 (47%), Positives = 232/352 (65%), Gaps = 10/352 (2%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGA + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+
Sbjct: 1    ARDSGAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQK 58

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVF
Sbjct: 59   ALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVF 118

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKIT
Sbjct: 119  TSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKIT 178

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +
Sbjct: 179  PKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEI 238

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDL 1012
              ++  L+ RD+  E   +  +   ++ ++L G              +   K   L+S++
Sbjct: 239  IEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEV 298

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            ++  P        ++   ++  +           + +  +  ++I K   GD
Sbjct: 299  LASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGD 349


>gi|154362147|gb|ABS80912.1| RNA polymerase beta subunit [Burkholderia ubonensis]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 137/232 (59%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++DE G+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDESGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             +ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LIDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|154362121|gb|ABS80899.1| RNA polymerase beta subunit [Burkholderia glathei]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYVIAQANAAVGEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E   VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKAVVGTGIERTVAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|23451718|gb|AAN32830.1|AF440727_1 RNA polymerase beta-subunit [Rickettsia sibirica]
          Length = 281

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 181/279 (64%), Positives = 225/279 (80%), Gaps = 2/279 (0%)

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
             R+N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG    E + CR
Sbjct: 2   MLRINKHGFIESPYRRVKDGCVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINCR 61

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +
Sbjct: 62  VEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTD 121

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E  +D     + I   +KF
Sbjct: 122 APFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLEQKVDGLLRLIFI-TYLKF 180

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           Q+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+PW GYNFEDS+
Sbjct: 181 QKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLPWSGYNFEDSI 240

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LISER+V EDVFTSIHIEEFEV+ARDT+LGPEEITR +P
Sbjct: 241 LISERIVKEDVFTSIHIEEFEVIARDTRLGPEEITRAVP 279


>gi|154362135|gb|ABS80906.1| RNA polymerase beta subunit [Burkholderia multivorans ATCC BAA-247]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+++D++G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVVDGKVTDQIDYLSAIEEGRYMIAQANAAIDDEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E   A  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDE 232


>gi|300394676|gb|ADK11876.1| DNA-directed RNA polymerase II subunit two [Athelia epiphylla]
          Length = 653

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 116/729 (15%), Positives = 225/729 (30%), Gaps = 92/729 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +   Q + L K    ++  G +    +     +V  ++GI E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHVHWINRGYDDAEEEFKWEQLV--KSGIFELLDA 283

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +       +    ++ +     R  +K G            PS 
Sbjct: 284  EEEETVMISMTPEDLENSRLQLSGVDPTVNDGDFDPAAR--LKAGTNAHTWTHCEIHPSM 341

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 342  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFL 376

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 377  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 425

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V   +    I+ R  +D  ++S   + E+ E   R+          
Sbjct: 426  GYNQEDSVIMNQSSVDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTY 484

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          ++     +  
Sbjct: 485  DKIEDDGLIAPGTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 544

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q+GDK A RHG KG V
Sbjct: 545  QVLI--------------------TTNSEGQKFVKVRVRATRIPQTGDKFASRHGQKGTV 584

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 585  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGDATPFTDL 644

Query: 1161 ANGDISPLR 1169
                +S   
Sbjct: 645  TVESVSAFL 653



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 83/610 (13%), Positives = 169/610 (27%), Gaps = 98/610 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N          K      +     L A EEE   I+     L+       
Sbjct: 249 QKKHVHW--INRGYDDAEEEFKWEQLVKSGIFELLDAEEEETVMISMTPEDLENSRLQLS 306

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 307 GVDPTVNDGDFDPAARLKAGTNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 366

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 367 MGKQAMGIFLTNFLI-----------------------------------------RMDT 385

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 386 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 421

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  V   +F SI+   +  + + + +   E        +   +  
Sbjct: 422 LCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKH 481

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 482 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 537

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 538 TENGIVDQVL 547


>gi|154362111|gb|ABS80894.1| RNA polymerase beta subunit [Burkholderia fungorum]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVTDGKVTDQIDYLSAIEEGRYVIAQANAAVAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E   VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +
Sbjct: 181 AVPCLRPEKAVVGTGIERTVAVDSGTTVQAFRGGVVDYVDAGRMVIRVNDDE 232


>gi|298912955|emb|CAZ66645.1| RNA polymerase beta subunit [Vibrio proteolyticus]
          Length = 289

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 169/289 (58%), Positives = 223/289 (77%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
           ++F  LFF  ++YDLSTVGR+K N  +  +   +   + + DI+ ++K L+ +RNG G +
Sbjct: 1   ALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGTLDETDIVEVMKKLIAIRNGIGEV 60

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+LGNRR+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV
Sbjct: 61  DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAV 120

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP E
Sbjct: 121 KEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIE 180

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG NIGL++SL++FAR N YGF+ETPYR+V DG VT+DV YLSA++E    IAQAN+ 
Sbjct: 181 TPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDDVDYLSAIQEGQYVIAQANTV 240

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           L E+G+F EEL+  R  GE  L PRE +D++D +  QVVSIAASLIPFL
Sbjct: 241 LTEEGTFAEELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFL 289


>gi|300394734|gb|ADK11905.1| DNA-directed RNA polymerase II subunit two [Porphyrellus
            porphyrosporus]
          Length = 689

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 120/818 (14%), Positives = 236/818 (28%), Gaps = 145/818 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+LG +R+   G +L N +R+   ++ R +    +              +  + + + + 
Sbjct: 1    DHLGKKRLDLAGPLLANLFRMLFKKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D+ RV     +       L+ +   ++  G      +      + K  GI+E +DA
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEKFKWEQLVK-TGIIELLDA 284

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +       +    ++ +     R  +K G            PS 
Sbjct: 285  EEEETVMISMTPEDLENSRLQSAGINPHENDGDFDPAAR--LKAGINAHTWTHCEIHPSM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 343  ILG-------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 377

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                +               +  +             +       +   +  + AI    
Sbjct: 378  TNFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G N         K+  +  D      R++          ++     +  
Sbjct: 486  DKLEDDGLIAPGTNVKGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVD 545

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q GDK A RHG KG +
Sbjct: 546  QVLI--------------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTI 585

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 586  GITYRQEDMPFTAEGVVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDL 645

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S      +K   +                                          
Sbjct: 646  TVESVSTFLR--QKGYHSRGLEVM------------------------------------ 667

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                       G +       G+     + +G  Y  +
Sbjct: 668  ---------YHGHT-------GKKLQAQIYLGPTYYQR 689



 Score =  125 bits (313), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 80/617 (12%), Positives = 169/617 (27%), Gaps = 111/617 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFKKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E   + L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLAL 248

Query: 583 VSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                         ++   YR       K      T  +  L A EEE   I+     L+
Sbjct: 249 QKK--------HIKWLNQGYRDDDGEKFKWEQLVKTGIIELLDAEEEETVMISMTPEDLE 300

Query: 636 EDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                +  +      G+          +        +  P  ++ + AS+IPF +++ S 
Sbjct: 301 NSRLQSAGINPHENDGDFDPAARLKAGINAHTWTHCEIHPSMILGVCASIIPFPDHNQSP 360

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 361 RNTYQSAMGKQAMGIYLTNFLV-------------------------------------- 382

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 383 ---RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAG 415

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----- 863
           +N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        
Sbjct: 416 QNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRD 475

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +++ G+I  G  V   DI++GK  P         E+L +        D
Sbjct: 476 NTLRMKHGTYDKLEDDGLIAPGTNVKGEDIIIGKTAPI----PPDSEELGQRTRTHTRRD 531

Query: 924 VRDTSLRVPSGVSGTVV 940
           V        +G+   V+
Sbjct: 532 VSTPLKSTENGIVDQVL 548


>gi|7453593|gb|AAF62903.1| RpoB [Bacillus sonorensis]
          Length = 134

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 55/150 (36%), Positives = 92/150 (61%), Gaps = 19/150 (12%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  ++G   LEF
Sbjct: 1   YARIXEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDYTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           +MT  GTF+I G +R++VSQL RSP +++ 
Sbjct: 102 IMTDTGTFIINGAERVIVSQLVRSPSVYYS 131


>gi|154362151|gb|ABS80914.1| RNA polymerase beta subunit [Burkholderia sp. CIP 105081]
 gi|154362153|gb|ABS80915.1| RNA polymerase beta subunit [Burkholderia sp. CIP 105143]
          Length = 234

 Score =  240 bits (613), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 176/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+++ +DG+
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVADGKVTDQIDYLSAIEEGRYVIAQANAAVADDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRIVIRVNDDE 232


>gi|154362159|gb|ABS80918.1| RNA polymerase beta subunit [Burkholderia plantarii]
          Length = 234

 Score =  240 bits (612), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+S+DE G 
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVTDSKVTDQIDYLSAIEEGRYVIAQANASVDEAGE 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSAREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AV  L+ E P VGTG+E   A  SG  + A+R G+V+ VDA RIVIR  + +
Sbjct: 181 AVRCLRPEKPVVGTGIERTCAVDSGTTVQAERGGVVDYVDAGRIVIRVNDDE 232


>gi|322511148|gb|ADX06461.1| putative DNA directed RNA polymerase II [Organic Lake phycodnavirus
            2]
          Length = 1162

 Score =  240 bits (612), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 151/968 (15%), Positives = 289/968 (29%), Gaps = 210/968 (21%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  +   L+    G     + D+  N+RV   G +L N +R    ++ + I++++ 
Sbjct: 349  KVYLLGFMTNKLIKCFCGMEQQTNRDSYENKRVELTGTLLNNLFRNYFNKVVKDIQKQVI 408

Query: 492  SVDIDS--VMPQDLINAKPVVSAVCEFFCSS------------------------QLSQL 525
                +      +D  N   + +       ++                         ++Q+
Sbjct: 409  REINNGSWKSSEDYSNIITLTNIYKIVKSTTIENGIKRALSTGDFGIKSMNTNKVGVAQV 468

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +  LS ++H RR++      + ++   VE R +H + +G +CPAET EG ++G+V +
Sbjct: 469  LNRLTYLSTLSHLRRVNT----PIDKSGKLVEPRKLHGSTWGFLCPAETPEGQSVGVVKN 524

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L+    V+ Y      Y  +                      A  + +  E     +  V
Sbjct: 525  LSYMTNVSTYSDSTPIYEYIQP-----------------YLFALDHYNTTEFYDKVKIFV 567

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
              R  G         +   +   K ++ I  S I F        V   C    + +  +K
Sbjct: 568  NGRWIGVTNQPNELFLSLKEKKYKGMIHIYCS-IVFNYKLKEIYVCNECGRLVRPLFKVK 626

Query: 706  AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                 +   M   + +     +       ++  D+I   I + E +        ++++  
Sbjct: 627  QNKILLTKDMTEQIKED--KLVWRDLILPLKTEDSIIEYIDAEEQNTSMICMKPNLFQDN 684

Query: 766  KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
                                            PST  G LA         +P+  +N   
Sbjct: 685  -----------------------YSYTHCEIHPSTIFGVLASC-------IPFPQHNQSP 714

Query: 826  SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
                   M  + +   I++  F      T        R +       +  ++E       
Sbjct: 715  RNTYQCAMGKQAIG--IYVSNFNKRMDKTAYVLNYTMRPLVETRVMNMMKLNE------- 765

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
                                +    +++ AI      +  D+ L     +   +    I+
Sbjct: 766  --------------------LPCGNQVIVAIMTHSGYNQEDSVLINKGSLDRGLFHATIY 805

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
            +                      +D+D +    +         +       +  K  K  
Sbjct: 806  HT--------------------EKDEDKKINGEEELRIKPNPNLTRNMKFGNYDKINKMG 845

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
             +  +++I +          ++D K              S    E+ + +K    + GD 
Sbjct: 846  VMNENEIIEDKDIIISKVVVIKDHKNDNTKLVKYEDQSKSYRTTEECYVDKTYIDRNGD- 904

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                     KV +   R    GDK + RHG KG                           
Sbjct: 905  ----GYTFCKVRIRAMRKPNIGDKFSSRHGQKG--------------------------- 933

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
                   VG I E            +            DI      +   +      E +
Sbjct: 934  ------TVGNIIE------------EQDMPFTKEGVRPDIIINPHAIPSRMTIAQLKETL 975

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                   +    +            F   D   +   L+  + +  G  +LYDG TGE  
Sbjct: 976  VGKLLLKLGLFGDGTS---------FGEMDMNEVYKELQKHNYESKGNEVLYDGKTGEQI 1026

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               + +G +Y  +L HMV+DK ++R  G    +T+QP  G+S  GG R GEME  C+ ++
Sbjct: 1027 KTSIFIGPVYYQRLKHMVNDKQHSRCIGPMVNLTRQPAEGRSRDGGLRFGEMERDCMISH 1086

Query: 1306 GAAYVLQEMLTIKSD----DV---VGRTRVYESIVAGNDTFETG------------TPES 1346
            GA+   +E +   SD    +V    G   VY                          P S
Sbjct: 1087 GASKFTKERIYDVSDKYAVNVCKKCGMIAVYN---DKEHIHICNVCENRTDFSYVKIPYS 1143

Query: 1347 FNVLVKEM 1354
              +L +E+
Sbjct: 1144 CKLLFQEL 1151



 Score =  129 bits (324), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 127/940 (13%), Positives = 261/940 (27%), Gaps = 203/940 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS---VFP-ITAFSGAAMLEFVSYEFDPP 84
           L++ Q  SY+ F+   +         L    KS    FP    +     + F +     P
Sbjct: 23  LVKHQVDSYNDFIQNQMMKTIDMFNPL--VVKSPHDYFPEYKTYRLEVEIVFENLSIYRP 80

Query: 85  KFD----------VDDCLWRDLTYAVPLKITLRL-IVFDVDEFTGAKSIKDIKEQSIYMG 133
           +              D   R+ TY+  + + +++  +    E    +  K I    I  G
Sbjct: 81  EIHENNGSTKLMFPSDARLRNFTYSSNITLDMKIKYIIRNGERLENEEYKYIHLSKIQFG 140

Query: 134 DLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
            +P+M                           G F+I G ++  + Q   +    F    
Sbjct: 141 KIPIMLNSCICVLKQYPNIHPDNIDECKMDPGGYFIINGSEKTCLGQEKPADNKIF---C 197

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH---------------VRIDRRRK-VP 213
            +     K L+       +    D +  S   I+               V++ R +K +P
Sbjct: 198 FKQKPGNKWLWTAE---YR-SVPDWKCISPKQIYMMVHSKLSCYGHEILVQLPRLKKPIP 253

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS--SSLVDIDTGE 271
           +     ALG++S+         +V     +        A +  G   +     ++     
Sbjct: 254 LFVLFRALGVESD---KQICSLVVLDIEKETSILDYLKASIYEGTSYNNYEDSLEYIISN 310

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
            +      +     +  K+K    L + S+ L            +T E  +     +  K
Sbjct: 311 VI---YTPINMDKDEGHKKKTEFALDVLSNDLFPHC--------KTKEEKVYLLGFMTNK 359

Query: 332 SLEEIF--HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG----- 384
            ++       +                 + N      NK  KD    + R +  G     
Sbjct: 360 LIKCFCGMEQQTNRDSYENKRVELTGTLLNNLFRNYFNKVVKDIQKQVIREINNGSWKSS 419

Query: 385 ----DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
               ++ T +    +      ++      + G   +            + + +   ++ +
Sbjct: 420 EDYSNIITLTNIYKIVKSTTIENGIKRALSTGDFGIKSMNTNKVGV-AQVLNRLTYLSTL 478

Query: 441 KILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR----MERSIKERIS 491
             L  +     ++GK       +          E  + Q  +G+++    M        S
Sbjct: 479 SHLRRVNTPIDKSGKLVEPRKLHGSTWGFLCPAETPEGQ-SVGVVKNLSYMTNVSTYSDS 537

Query: 492 SVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           +   + + P     D  N       V  F     +    +       +   +    +   
Sbjct: 538 TPIYEYIQPYLFALDHYNTTEFYDKVKIFVNGRWIGVTNQPNELFLSLKEKKYKGMIHIY 597

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                   ++   V       + P    + + I L   +T   + +   +     R +  
Sbjct: 598 CSIVFNYKLKEIYVCNECGRLVRPLFKVKQNKILLTKDMTEQIKEDKLVW-----RDLIL 652

Query: 608 GKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
              T D  + Y+ A E+    I    +   ++ S+                        +
Sbjct: 653 PLKTEDSIIEYIDAEEQNTSMICMKPNLFQDNYSY---------------------THCE 691

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  +  + AS IPF +++ S R    C M +QA+ +  +                   
Sbjct: 692 IHPSTIFGVLASCIPFPQHNQSPRNTYQCAMGKQAIGIYVSNFN---------------- 735

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
               KR      V                                        RPLV+  
Sbjct: 736 ----KRMDKTAYV-----------------------------------LNYTMRPLVE-- 754

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                           L +L  G  ++VA M   GYN EDS+LI++  +   +F +    
Sbjct: 755 --------TRVMNMMKLNELPCGNQVIVAIMTHSGYNQEDSVLINKGSLDRGLFHATIYH 806

Query: 846 EFEVMARDTKLGPEEITRDIP----NVSEEGLKNIDECGI 881
             +   +      E   +  P    N+       I++ G+
Sbjct: 807 TEKDEDKKINGEEELRIKPNPNLTRNMKFGNYDKINKMGV 846


>gi|110669608|gb|ABG81899.1| RNA polymerase II second largest subunit [Agonimia sp. AFTOL 684]
          Length = 718

 Score =  240 bits (612), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 132/841 (15%), Positives = 239/841 (28%), Gaps = 150/841 (17%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
            DD D+LG +R+   G ++ N +RL   ++ R      +        +  +  + +  + +
Sbjct: 1    DDRDHLGKKRLDLAGPLMANLFRLQFQKVVRDFFRYMQKQVESDREINLKVGLKSNIITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +A     + R     + 
Sbjct: 61   GLKYXLATGNWGDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     V  +        Y      +   D   
Sbjct: 117  RQLHNTHWGYVCPAETPEGQACGLVKNLALMTMVTNSHNTAPLQDYIMEQGVZPLEDWEP 176

Query: 617  -LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSI 674
             LS    +        + + +D     +          +      + D  D   K     
Sbjct: 177  RLSPQATKIFLNGVWFAVVIKDPKHLVDQFKGLRRRGFLDPQISMVWDIRDKEFKISGDA 236

Query: 675  AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG-----AAIVA 729
               + P    +         N+      + + +   V +  E+ +   +           
Sbjct: 237  GRIIRPLFVVETDPSSDNHGNLVLTKYHIQRLDNTVVNS--EAQLPIDAWPEPPFVWKDF 294

Query: 730  KRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
               G+VE +DA      +I     DL  S +    Y   +             P      
Sbjct: 295  LTNGVVEYLDAEEEETAMIIMTPEDLATSKAKHMGYTSEETDDPLARYDPLLNP------ 348

Query: 787  EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                       PS  LG       +  + +P+  +N          M  + +        
Sbjct: 349  HAHTFTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV------ 395

Query: 847  FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                         E   +I    ++ L                        +       +
Sbjct: 396  ----FLTNFDQRMETMANILYYPQKPLAR-------------------TMSMEYLKFREL 432

Query: 907  TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIEL 966
               +  + AI      +  D+ +   S +   +    +F R   D+ +       EQ E 
Sbjct: 433  PAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKVVGHNVLEQFER 491

Query: 967  LARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
              R           +       +  G           K+  ++ D               
Sbjct: 492  PTRADTLRMKHGTYDKIDIDGIVEVGARVYGEDIIIGKTAPMAPD--------------- 536

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
             +E  QR  + LK    T     E    +++     GD       + VKV V   +  Q 
Sbjct: 537  AEELGQRQKQHLKRDVSTPLRSTETGIVDQVLVTTTGD-----GNKFVKVRVRTTKIPQI 591

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDM F ++G   D+++NP  +PSRM +  + E  L     
Sbjct: 592  GDKFASRHGQKGTIGITYRQEDMSFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVAT 651

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +         ++S +   +                                  
Sbjct: 652  LRGDEGDATPFTKVTVTNVSNILRSMGYQSRGFEVM------------------------ 687

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                    +G +    G         + +G  Y  +L HMV DK
Sbjct: 688  -----------------------YNGHT----GR---KLVAQIFLGPTYYQRLRHMVDDK 717

Query: 1267 V 1267
            +
Sbjct: 718  I 718



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 95/639 (14%), Positives = 184/639 (28%), Gaps = 117/639 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +         V   + + +  +  KY L   G  
Sbjct: 15  GPLMANLFRLQFQKVVRDFFRYMQKQVESDREINLKVG--LKSNIITNGLKYXL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++N       + + +    + +  L        R+GK       +  +       E
Sbjct: 72  GDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGYVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKE---------RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             + Q    +  +               +   ++      +D        +         
Sbjct: 132 TPEGQACGLVKNLALMTMVTNSHNTAPLQDYIMEQGVZPLEDWEPRLSPQATKIFLNGVW 191

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARAR--------AGVEMRDVHPTHYGRICPA 572
               +++  + + +    RR   L                 +G   R + P       P+
Sbjct: 192 FAVVIKDPKHLVDQFKGLRRRGFLDPQISMVWDIRDKEFKISGDAGRIIRPLFVVETDPS 251

Query: 573 ETSEGHNIGLVSSLTSF--------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             + G+ +     +           A++    + E P+    D      V YL A EEE 
Sbjct: 252 SDNHGNLVLTKYHIQRLDNTVVNSEAQLPIDAWPEPPF-VWKDFLTNGVVEYLDAEEEET 310

Query: 625 RYIAQ-----ANSSLDEDGSFTEELVFCRCAGEEILVPR-EKIDFIDASPKQVVSIAASL 678
             I       A S     G  +EE        + +L P        +  P  ++ + AS+
Sbjct: 311 AMIIMTPEDLATSKAKHMGYTSEETDDPLARYDPLLNPHAHTFTHCEIHPSMILGVCASI 370

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R      M +QA+ +                                   
Sbjct: 371 IPFPDHNQSPRNTYQSAMGKQAMGVFLTNF------------------------------ 400

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + + +  Y      R+     +                      
Sbjct: 401 -----------DQRMETMANILYYPQKPLARTMSMEYL---------------------- 427

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA   + GYN EDS+++++  +   +F S+    ++   +      
Sbjct: 428 --KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKVVGHNV 485

Query: 859 EEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            E        D   +       ID  GI+ VGA V   DI++GK  P     M P+ + L
Sbjct: 486 LEQFERPTRADTLRMKHGTYDKIDIDGIVEVGARVYGEDIIIGKTAP-----MAPDAEEL 540

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                +     RD S  + S  +G V  V +      +K
Sbjct: 541 GQRQKQHLK--RDVSTPLRSTETGIVDQVLVTTTGDGNK 577


>gi|52699837|gb|AAU86980.1| DNA-dependent RNA polymerase II second largest subunit [Morchella
            esculenta]
          Length = 708

 Score =  240 bits (612), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 129/843 (15%), Positives = 237/843 (28%), Gaps = 165/843 (19%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVC 514
            D  G  R+   G +L   +R    ++ + + + +               + +  + + + 
Sbjct: 1    DXXGXXRLDLAGPLLAGLFRTLWKKLTKDVYKYLEKCVETGRDFNLTLAVKSNTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L+  + +     G+    +    D ++  +     +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++         D     ++V        +      I D  D   K         
Sbjct: 177  PNATKVFVNGVWVGTHRDPLMLHKVVQDVRRQGVVNHEVSIIRDIRDREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRV--LMGCNMQRQAVPLLKAEAPFVGTGME----SVVAKSSGAAIVAKRA 732
             P    D+  R        +Q++ +  L+ +       ME          SG        
Sbjct: 237  RPLFVIDNDPRSERRGQLVLQKEHIEKLEDDHALP---MEDRFGWEGLLFSGTV------ 287

Query: 733  GIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
               E +DA      +I     DLD S      Y   K + S +       P         
Sbjct: 288  ---EYLDAEEEETVMIVMTPEDLDMSRQMQLGYEEPKDEFSAKRVKAPINP-----HTAH 339

Query: 790  RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    PS  LG       +  + +P+  +N          M                
Sbjct: 340  TWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAM---------------- 376

Query: 850  MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                   G + +       SE          +  +             +       +   
Sbjct: 377  -------GXQAMGXXXXXFSERM------DTMANILYYPQKPLATTRSMEYLKFRELPAG 423

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R  +D+ +R   +  + +E   +
Sbjct: 424  QNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMDQEKR---IGMQVVEEFEK 479

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                  + L    Y +L E   +  G           K+  ++ D+     R ++     
Sbjct: 480  PTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPITPDVDEMGQRQKYHTKRD 539

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                ++     +  Q                             L+ VKV +   +  Q 
Sbjct: 540  VSTPLRSTENGIVDQVML--------------------TTNAEGLKFVKVRMRTTKIPQI 579

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG V      EDMPF  +G   D+++NP  +PSRM +  + E  L     
Sbjct: 580  GDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSS 639

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G +  +          +S L    +    +       + Y                  
Sbjct: 640  LRGFEGDATPFTDVTVESVSTLLR--QNGYQSRGFEVMYNGYT----------------- 680

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                                            G         V +G  Y  +  HMV  K
Sbjct: 681  --------------------------------GR---KLVCQVFLGPTYYQRXRHMVXXK 705

Query: 1267 VYA 1269
            + A
Sbjct: 706  IXA 708



 Score =  105 bits (261), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 85/625 (13%), Positives = 169/625 (27%), Gaps = 98/625 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +     T   K  KD    + + +  G    F++  ++ +    +  KY L   G  
Sbjct: 12  GPLLAGLFRTLWKKLTKDVYKYLEKCVETGR--DFNLTLAVKSNTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSV--------DIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
             + Q    +  +       I +           + +   +    +   +A   F     
Sbjct: 129 TPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPNATKVFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    + +     +   RR   +  +  + R     E        R   P       P  
Sbjct: 189 VGTHRDPLMLHKVVQDVRRQGVVNHEVSIIRDIRDREFKIFTDAGRVCRPLFVIDNDPRS 248

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
              G  +     +      + +               +  V YL A EEE   I      
Sbjct: 249 ERRGQLVLQKEHIEKLE--DDHALPMEDRFGWEGLLFSGTVEYLDAEEEETVMIVMTPED 306

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           LD                        ++      PK   S      P   +         
Sbjct: 307 LD---------------------MSRQMQLGYEEPKDEFSAKRVKAPINPH--------- 336

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                              T       +   + I+   A I+   D  +    + +  + 
Sbjct: 337 -------------------TAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 377

Query: 754 PSTSGVDIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
               G        +           Q+PL                      +L  G+N +
Sbjct: 378 XQAMGXXXXXFSERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAI 427

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA + + GYN EDS+++++  +   +F S+    +    +   +   E        +   
Sbjct: 428 VAILCYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLK 487

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +DE G++  G  V+  DI++GK  P      TP+   +     +K    RD 
Sbjct: 488 LKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDV 540

Query: 928 SLRVPSGVSGTVVDVRIFNRHGIDK 952
           S  + S  +G V  V +       K
Sbjct: 541 STPLRSTENGIVDQVMLTTNAEGLK 565


>gi|153958204|gb|ABS53392.1| RpoB [Bacteriovorax sp. JDF]
          Length = 347

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 167/350 (47%), Positives = 232/350 (66%), Gaps = 10/350 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 59   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
                 ++   ++  +           + +  +  ++I K   GD++PPGV
Sbjct: 299  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDELPPGV 347


>gi|111283868|gb|ABH09223.1| RNA polymerase II second largest subunit [Schizonella melanogramma]
          Length = 694

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 121/824 (14%), Positives = 235/824 (28%), Gaps = 148/824 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +R+   ++ R +    +    +      Q  + +  + + + 
Sbjct: 1    DHFGKKRIDLAGPLMANLFRMLFRKVTRDVYRHLQRCVEEHREFHIQAAVKSSTITNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMSAKVGVSQVLNRFAFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  A V            + +  + + V       
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQVTNA 176

Query: 622  EENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            +  +         + D+ G   + L   R   +         D  +   +     +    
Sbjct: 177  KATKVFVNGVWMGTHDDPGQLVDTLRDLRRKDDISQEVSVVRDIREKELRIYTDSSRVTR 236

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P    +  +  L+      Q +           TG E              + G++E +D
Sbjct: 237  PLFIVNPHDMTLLIKKHHVQRIG------KPTETGEEFR-------WTQLVQQGVIEYLD 283

Query: 740  AIRIV-IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A     +       D   S     R       + +     + ++ +             P
Sbjct: 284  AEEEESVLISMSTTDLEQSREYKMRNGHVNFDSADPSARLKSILTI--APDTWTHCEIHP 341

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            +  LG       +  + +P+  +N     +       + V  +I         R   +  
Sbjct: 342  AMVLG-------ICASIIPFPDHNQSPRNVYQXXXXKQAVSVNISNF----XTRQDTMNH 390

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                   P  +   ++++                             +   +  + AI  
Sbjct: 391  VLYYPQKPLGTTRSMEHL-------------------------KFRELPAGQNAIVAIMC 425

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    ++ R  + + ++   ++ E+ E  +RD        
Sbjct: 426  YSGYNQEDSVIMNQSSIDRGLF-RSLYYRGYLAEEKKVGVMQLEEFEKPSRDTTIRMKHG 484

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +          G           K+  L  D      RS+          ++     +
Sbjct: 485  TYDKIEADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRSKLHTKKDASISLKSTEHGV 544

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                              + V+V V   R  Q+GDK A RHG KG
Sbjct: 545  IDQVLL--------------------TTNAAGNKFVRVRVRNSRIPQTGDKFASRHGQKG 584

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  DG   DI++NP  +PSRM +G + E  L       G++  +    
Sbjct: 585  TIGITYRQEDMPFSADGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFT 644

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S +   L     +                                        
Sbjct: 645  ELTVEAVSSILRGLG--YHSRGLEVM---------------------------------- 668

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                         G S    G         V +G  Y  +L HM
Sbjct: 669  -----------YHGHS----GR---KXPAQVYLGPTYYQRLKHM 694



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 88/600 (14%), Positives = 173/600 (28%), Gaps = 82/600 (13%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           +  ++      +        T  +  S+    + D  K   + VG  ++  R    +   
Sbjct: 36  RCVEEHREFHIQAAVKSSTITNGLRYSLATGNWGDQKKAMSAKVGVSQVLNRFAFASTLS 95

Query: 428 V--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
              R          I     L N    +         +   + + L     + +      
Sbjct: 96  HLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAP 155

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           I E +    +DS++   + NAK     V        +   ++    +  +   RR   + 
Sbjct: 156 IVEFLEEFGLDSLVDMQVTNAKATKVFV----NGVWMGTHDDPGQLVDTLRDLRRKDDIS 211

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
           Q          +   ++        P      H++ L+       R+         +R  
Sbjct: 212 QEVSVVRDIREKELRIYTDSSRVTRPLFIVNPHDMTLLIKKHHVQRIGKPTETGEEFR-W 270

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL--------VFCRCAGEEILVP 657
                   + YL A EEE+  I+ + + L++   +                     + + 
Sbjct: 271 TQLVQQGVIEYLDAEEEESVLISMSTTDLEQSREYKMRNGHVNFDSADPSARLKSILTIA 330

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            +     +  P  V+ I AS+IPF +++ S R +      +QAV +  +        M  
Sbjct: 331 PDTWTHCEIHPAMVLGICASIIPFPDHNQSPRNVYQXXXXKQAVSVNISNFXTRQDTMNH 390

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
           V+                                             +KF+         
Sbjct: 391 VLY------------------------------YPQKPLGTTRSMEHLKFRELPAGQNAI 420

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
              +   G   + + +I +  S D G                GY  E+  +         
Sbjct: 421 VAIMCYSG-YNQEDSVIMNQSSIDRGLFRSLYY--------RGYLAEEKKV--------- 462

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               + +EEFE  +RDT             +       I+  G+   G  V+  D+++GK
Sbjct: 463 --GVMQLEEFEKPSRDT----------TIRMKHGTYDKIEADGLCAPGTRVSGDDVIIGK 510

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
             P    P   EE  +R+    K    +D S+ + S   G +  V +      +K  R  
Sbjct: 511 TAP---LPPDSEELGMRS----KLHTKKDASISLKSTEHGVIDQVLLTTNAAGNKFVRVR 563


>gi|111183476|gb|ABH07989.1| RNA polymerase II second largest subunit [Tilletiopsis minor]
          Length = 695

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 123/821 (14%), Positives = 227/821 (27%), Gaps = 144/821 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ R I   +     +         + A  + + +    
Sbjct: 1    GKKRLDMAGPLLAGLFRMLFRKLTRDIYRHLQKCVEEKKDFHITQAVKAATITNGLKYSI 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKFMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L+  + ++           + +  + +      A  +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSLMSTISVGSPSFPIIEFLQEFGLDSLEDMQVASSKAT 176

Query: 625  RYIAQA-NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            +           +D       +      ++I      +  I     ++ + A  ++  L 
Sbjct: 177  KVFVNGVWMGTHDDPGTLVSFIRELRRKDDISTEVSMVHDIREKELRLYTDAGRVLRPLF 236

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
              D  +  M   ++RQ +  L  +      G E                          +
Sbjct: 237  IVD--QDTMTLRIKRQHMDWLHDQQT--PDGQEWK---------------------WNEL 271

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V  ++   LD           M       +   NQ P   VG             ST   
Sbjct: 272  VTNALIEYLDAEEEET-TLICMSPTDLENSRVYNQDPKSYVG-----------PRSTRDP 319

Query: 804  DLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
               L      A   W       +M+  I   ++            ++       +G    
Sbjct: 320  SARLVSTAFFAPKTWTHCEIHPAMILGICASIIPFPXHNQSPRNTYQSAMGKQAMGVYLT 379

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +               +  +             +       +   +  + AI     
Sbjct: 380  NYQMRM-----------DTMANILYYPQKPLATTRSMEHLRFRELPAGQNAIVAILCYSG 428

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    ++ R   D  ++   +  E  E   RD          +
Sbjct: 429  YNQEDSVIMSQSAIDRGLF-RSLYYRTYTDMEKKLGVIMLETFEKPTRDTTLRMKHGTYD 487

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   +  G           K+T L  D      RS           ++     +  Q
Sbjct: 488  KLDEDGLVAPGTRVSGEDIIIGKTTPLPPDTEELGLRSASHTKRDVSTPLKSTENGIVDQ 547

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
               + S                        R VKV V   R  Q+GDK A RHG KG + 
Sbjct: 548  VLLTVS-------------------HDHSQRFVKVRVRSTRVPQTGDKFASRHGQKGTIG 588

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF ++G   DI++NP  +PSRM +G + E  L       G++  +       
Sbjct: 589  ITYRQEDMPFTREGVTPDIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGDATPFTDLT 648

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               +S +   +                                                 
Sbjct: 649  VEAVSEILREMGYQSRGLEVM--------------------------------------- 669

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                     +G +    G         V +G  Y  +L HM
Sbjct: 670  --------YNGHT----GR---KLQAQVYLGPTYYQRLKHM 695


>gi|209943906|gb|ACI96261.1| RNA polymerase B-subunit [Staphylococcus microti]
 gi|209943908|gb|ACI96262.1| RNA polymerase B-subunit [Staphylococcus microti]
          Length = 266

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 150/266 (56%), Positives = 194/266 (72%), Gaps = 3/266 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+PFVGTGM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGM 180

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E V A+ SGAA++AK  G VE V +  I++R  +E +       +D Y L KF+RSN  T
Sbjct: 181 EHVAARDSGAAVIAKHRGRVEHVQSKEILVRRLIEENGQEYEGELDRYPLAKFKRSNSGT 240

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPST 800
           C NQRP+++ GD V + +I+ADGPS 
Sbjct: 241 CYNQRPIIQAGDVVEKGEILADGPSM 266


>gi|154362105|gb|ABS80891.1| RNA polymerase beta subunit [Comamonas aquatica]
          Length = 234

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 137/230 (59%), Positives = 170/230 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD +G 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDEIDYLSAIEEGKYIIAQANAELDAEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              ELV  R  GE  L+  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LVGELVSAREKGESTLLSPERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
           AVP+L+ E P VGTG+E V A  SG  + A+R G V+ VDA RIVIR  +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTARRGGTVDYVDATRIVIRVND 230


>gi|300709367|ref|XP_002996849.1| hypothetical protein NCER_100041 [Nosema ceranae BRL01]
 gi|239606175|gb|EEQ83178.1| hypothetical protein NCER_100041 [Nosema ceranae BRL01]
          Length = 1091

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 68/314 (21%), Positives = 121/314 (38%), Gaps = 77/314 (24%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   ++K+ +   R  + GDK + RHG KG+V  I+P  +MPF   G   DI+    
Sbjct: 835  TKSEDQTLIKICLRQTRVPEIGDKFSSRHGQKGVVGLIVPQINMPFTDSGLVPDII---- 890

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
                 MN                                              G  +   
Sbjct: 891  -----MN--------------------------------------------PHGFPSRMT 901

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                 + +   A   +  +  +T +F   + + +  +L     +  G+   Y G++GEP 
Sbjct: 902  VGKIIELLTGKAGIIEGKISDAT-IFKKNEVDLVCDILSNNGFNFGGKDCFYSGISGEPI 960

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               +  G ++  +L HMV+DK++ R+ G  +++T+QP  G+S  GG RLGEME  C+  Y
Sbjct: 961  YAYIFYGPVFYQRLKHMVADKIHMRARGPRAILTRQPTEGRSRDGGLRLGEMERDCLIGY 1020

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESI---------------VAGNDTFET-GTPESFNV 1349
            GA+ ++ E L   SD       ++E+                V  +        P +  +
Sbjct: 1021 GASSLIVERLMESSD-------LFETFCCKNCGILVPKNGCNVCNDTNPLPIRLPYACKL 1073

Query: 1350 LVKEMQALGLSIDL 1363
            L +E+ ++ +   L
Sbjct: 1074 LFQELMSMNILPKL 1087



 Score =  136 bits (343), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 97/754 (12%), Positives = 198/754 (26%), Gaps = 132/754 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L      S+++F+   IA   + N        S            L++       P    
Sbjct: 19  LARQHIESFNYFINHEIASIVKAN----DIVDS-----DIDHTFYLKYTDVRISVPSLEE 69

Query: 85  ---KFD--VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
              K      +C  RDLTYA  L I +  +          ++ + I+++ +++G +P+M 
Sbjct: 70  NMIKHTLYPMECRLRDLTYASNLYIDIEYV----------RNKQIIRKKDVFIGRIPIML 119

Query: 140 KD----------------------------------GTFVIKGIQRIVVSQLHRSPGIHF 165
           +                                   G F+IKGI+++++ Q   S     
Sbjct: 120 QSDKCLLKSKNNEQKLSEESLNANLFFSQECPYDIGGYFIIKGIEKVILIQEQLSKNRII 179

Query: 166 DHDKGR------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH-VRIDRRRKVPVTSFL 218
             D  +       S + +      +I  +           D  + V       +PV + +
Sbjct: 180 IEDGPKGFFSSMTSSTHEQKSKTSVI-YK----------NDCYYLVNSSFSEDIPVVAII 228

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A  M S                 D         +      +S   +         E+  
Sbjct: 229 KACNMIS-----------------DKEIVECIGKEFADQIVLSFEEIYKHKIHTSKEAAL 271

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            L   +        ++ +           V  D V+     I I         + + I  
Sbjct: 272 YLAGFIKMKPDANKLEEVRNVIVEKILPNVKFDGVDLRNKGIMICLMVRRLIFTQKNIIT 331

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
            E +D  I           +         K   +    I +++     +    A + FN 
Sbjct: 332 EEDKDF-IGNKRFELAGQLLSILFEDSFKKFNWELKRSIDKILTKRLRAQEFDALTFFNL 390

Query: 399 LFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIA---IIKILVDLRNGKGTID 454
                       +     N  R  +D       + +   I+   ++  +         + 
Sbjct: 391 QTNIITTSMQRAISSGNWNLRRFRMDRSGVTHVLIRHSYISAVGMMTKVNSHFEKTRKVS 450

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
               L              +     L    S+   +++      +   L +   + + V 
Sbjct: 451 GPRALHTSSWGMFCPADTPEGESCGLVKNLSLLAEVTTDSDLDTIIYILSSLGVIQTGVL 510

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAE 573
                         +N             +       R     +   ++     +     
Sbjct: 511 YTHEMVSDEMYLVFLNGDIFGVTQNCFGLVKNFRNYRRKGVINKYVSIYIDENLKSVNIA 570

Query: 574 TSEGHNIGLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              G     +  +T   R N          +E  Y+   D      + YL A EE +  I
Sbjct: 571 ADNGRLCRPLIIITDEVRQNLKKGLFVISDLEMKYKSFDDLVEDGRIEYLDANEENDALI 630

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +                        +K   ++ +   ++   A LIPF  ++ S
Sbjct: 631 ALKIEDI-----------------------SDKTTHLEIADFAILGYVAGLIPFPNHNQS 667

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            R    C M +QA+  +   +     G+   +  
Sbjct: 668 PRNTYQCAMGKQAIGYIALNSKKRFDGISLQLCN 701



 Score =  122 bits (306), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 110/724 (15%), Positives = 236/724 (32%), Gaps = 97/724 (13%)

Query: 225 SEEILS--TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
           SEE L+   F+ +      G ++        +++  ++S + + I+ G       K   S
Sbjct: 136 SEESLNANLFFSQECPYDIGGYFIIKGIEKVILIQEQLSKNRIIIEDG------PKGFFS 189

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
            +  S  E+  K   I  +    L  +    +     I      + D++ +E I      
Sbjct: 190 SMTSSTHEQKSKTSVIYKNDCYYLVNSSFSEDIPVVAIIKACNMISDKEIVECIGKEFAD 249

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            I + + +   +            +  ++ AL     +    D +      ++       
Sbjct: 250 QIVLSFEEIYKHK----------IHTSKEAALYLAGFIKMKPDANKLEEVRNVIVEKILP 299

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           + K+D   +    + + L                  +++ L+  +    T +D D +GN+
Sbjct: 300 NVKFDGVDLRNKGIMICL------------------MVRRLIFTQKNIITEEDKDFIGNK 341

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCE 515
           R    G++L   +     +    +K  I  +    +  Q+             + +++  
Sbjct: 342 RFELAGQLLSILFEDSFKKFNWELKRSIDKILTKRLRAQEFDALTFFNLQTNIITTSMQR 401

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYG 567
              S   +     ++         R S +   G+         + R     R +H + +G
Sbjct: 402 AISSGNWNLRRFRMDRSGVTHVLIRHSYISAVGMMTKVNSHFEKTRKVSGPRALHTSSWG 461

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND-VVYLSAMEEENRY 626
             CPA+T EG + GLV +L+  A V     ++T    +    V    V+Y   M  +  Y
Sbjct: 462 MFCPADTPEGESCGLVKNLSLLAEVTTDSDLDTIIYILSSLGVIQTGVLYTHEMVSDEMY 521

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFL 682
           +   N  +         LV          V  + +        + V+IAA       P +
Sbjct: 522 LVFLNGDIFGVTQNCFGLVKNFRNYRRKGVINKYVSIYIDENLKSVNIAADNGRLCRPLI 581

Query: 683 ENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQVD 739
              D  R  +   +          K+    V  G +E + A     A++A +   +    
Sbjct: 582 IITDEVRQNLKKGLFVISDLEMKYKSFDDLVEDGRIEYLDANEENDALIALKIEDISDKT 641

Query: 740 --------AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ---------------NTCV 776
                   AI   +  +    + + S  + Y+    +++                   C 
Sbjct: 642 THLEIADFAILGYVAGLIPFPNHNQSPRNTYQCAMGKQAIGYIALNSKKRFDGISLQLCN 701

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                  TD  ++  G+N +VA M + GY+ ED+++I++  +  
Sbjct: 702 TQKPL----------TTTQILNITDYNEIPAGQNAMVAVMSYSGYDIEDALIINKDSLDR 751

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               +   +    + +       ++              +D+ GI   G  +  G + + 
Sbjct: 752 GFARTEVYKTHCYVLKKYSDNRSDVILPDIKNPI-----LDKDGIGKPGELLLEGTVYIN 806

Query: 897 KITP 900
           K +P
Sbjct: 807 KNSP 810


>gi|119644024|gb|ABL85601.1| RNA polymerase II second largest subunit [Cetraria islandica]
          Length = 708

 Score =  240 bits (612), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 121/741 (16%), Positives = 226/741 (30%), Gaps = 90/741 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G RR+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKRRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVLNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RA 732
                P    D+  R     N+   ++ V  L+ +     T  E  V + +        + 
Sbjct: 237  RVCRPLFVIDNDPRSSNEGNLVLTKEHVQKLELDRENWAT-TEPDVREDTNMGWQGLVKE 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       V    +       I    + ++SN +  +N+R    +        
Sbjct: 296  GVVEYVDAEEEETIMVVMTPEDLEISRQIRAGFEPEQSNPDE-LNRRVKTPMKQTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXXXXX 407

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                                                 +   +  
Sbjct: 408  XXXXXXXXXXXXXXXXXXX-----------------------------XXXRELPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L E   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLRLKHGTYDKLDEDGPVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRS 1170
             +  +          +S L  
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR 675



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 48/383 (12%), Positives = 105/383 (27%), Gaps = 38/383 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 15  GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 191

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 192 VGVHRDPAHLVGTVLNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 251

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++EG+ +     +                  E              V Y+ A EEE   +
Sbjct: 252 SNEGNLVLTKEHVQKLELDRENWATTEPDVREDTNMGWQGLVKEGVVEYVDAEEEETIMV 311

Query: 628 AQANSSLDEDGSFTEELVF--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                 L+                    R     +          +  P  ++ I AS+I
Sbjct: 312 VMTPEDLEISRQIRAGFEPEQSNPDELNRRVKTPMKQTAHTWTHCEIHPSMILGICASII 371

Query: 680 PFLENDDSNRVLMGCNMQRQAVP 702
           PF +++ S R      M +QA+ 
Sbjct: 372 PFPDHNQSPRNTYQSAMGKQAMG 394


>gi|226934680|gb|ACO92414.1| RNA polymerase beta subunit [Mycobacterium bolletii]
          Length = 221

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 87/213 (40%), Positives = 115/213 (53%), Gaps = 40/213 (18%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 41   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 100

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 101  TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGDPEWAQN-------------- 145

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 146  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 188

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +D  G++ L+DG +GEPF  PVTVGY+Y+LKL+
Sbjct: 189  VDGDGKARLFDGRSGEPFPYPVTVGYMYILKLH 221



 Score = 45.5 bits (106), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 40/49 (81%)

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           E+ +TPEE+LLRAIFGEKA +VRDTSL+VP G SG V+ +R+F+R   D
Sbjct: 1   ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSRDDDD 49


>gi|52699829|gb|AAU86976.1| DNA-dependent RNA polymerase II second largest subunit [Lempholemma
            polyanthes]
          Length = 714

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 126/834 (15%), Positives = 234/834 (28%), Gaps = 141/834 (16%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVC 514
            D  G  R+   G +L   +R+   ++ R + + +               I    + + + 
Sbjct: 1    DXFGKXRLDLAGPLLAGLFRMLFTKLTRDVYKYLQKCVELKREFNLNLGIKQATLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L    +  V +       +    +  +  +    ++
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSPPIIEFMIQRNMDMLEEFDPRNS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  + +     V        +      + D  +   K         
Sbjct: 177  PTATKVFVNGVWVGIHHNPTHLAIDVLQLRRHNFVSPEISVVRDIREREFKIFTDAGRVC 236

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
             P    +          +  +   L++ E        E                GIVE V
Sbjct: 237  RPLFVIETRKGQPDTGRLTLKKHHLIRLENDKDVPFHEKDREDKIYGWQGLVHDGIVEYV 296

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            DA       +    +       +     ++  N +   N+R        V         P
Sbjct: 297  DAEEEETIMIVMTPEDLEISRQVRAGFPWKDDNMDP--NKRIKAPPNPSVHTWTHCEIHP 354

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  + +   I +  +           
Sbjct: 355  SMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNYIQRMDTMSN-- 403

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                     +             +       +   +  + AI  
Sbjct: 404  -------------------------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAV 438

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +     +  +   + +  +S    Q+E   R   D+ + +
Sbjct: 439  YSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKKLGMS----QMESFERPMRDDTLRI 494

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             R  Y ++ E   I  G   +       K+  L+ D                +E  QR  
Sbjct: 495  KRGTYDKIDEDGIIAPGVRVIGDDIIIGKTAPLAPD---------------AEELGQRTK 539

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K    T     E    +++      D       R VKV +   +  Q GDK A RHG
Sbjct: 540  GQTKRDVSTPLRSTEQGIVDRVLVTVNAD-----GQRFVKVRMRTTKVPQIGDKFASRHG 594

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 595  QKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVAALQGFEGDAT 654

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S L                           V     +G  +   VF    
Sbjct: 655  PFTDITVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGKKLVAQVF---- 695

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                                               +G  Y  +L HMV  K+ A
Sbjct: 696  -----------------------------------LGPTYYQRLRHMVDXKIXA 714


>gi|52699841|gb|AAU86982.1| DNA-dependent RNA polymerase II second largest subunit [Peltigera
            canina]
          Length = 704

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 121/823 (14%), Positives = 233/823 (28%), Gaps = 142/823 (17%)

Query: 466  SVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G +L   +R+   ++ + + +  +    +         + +  + + +     +    
Sbjct: 1    LAGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWG 60

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 61   DQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 116

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            PAET EG   GLV +L     +      E    +    + ++  +   L +      ++ 
Sbjct: 117  PAETPEGQACGLVKNLALMCYITVGTPCEPIIDFMNQRNMEMLEEYEPLRSPNATKVFVN 176

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDD 686
                 +  D +     V     G  I      + D  D   K          P F+ ++D
Sbjct: 177  GVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDND 236

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVI 745
            +  +  G  +  +       E      GM+    ++           G+VE VDA     
Sbjct: 237  TRSMNYGNLVLTKEHITRLEEDKEAAIGMDRDELEARQMGWDGLVNQGVVEYVDAEEEET 296

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +        +   I +L K    N     N+R         +        PS  LG  
Sbjct: 297  VMIVMTPGDLETSRQI-QLGKAVPGNAEDEPNKRVNAMSHRSAQTWTHCEIHPSMILG-- 353

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   +    +                  
Sbjct: 354  -----ICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFXXNYXQRM-------------- 392

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 393  -------------DTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 439

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +
Sbjct: 440  DSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRTDTLRLKHGTYEK 495

Query: 986  LME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            L +   +  G           K+  +  D      R++          ++     +  Q 
Sbjct: 496  LDDDGIVAPGVRVSGEDMIIGKTAPIPPDSEELGQRTKMHIKRDASTPLRSTENGIVDQV 555

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                        LR VKV +   +  Q GDK A RHG KG +  
Sbjct: 556  LL--------------------TTNAEGLRFVKVRMRXXKIPQIGDKFASRHGXKGTIGI 595

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +        
Sbjct: 596  TYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTV 655

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S +                 +         V     +G  +   VF           
Sbjct: 656  DSVSKILR---------------AHGYQSRGFEVMYNAHTGQKLVAQVF----------- 689

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                        +G  Y  +L HMV D
Sbjct: 690  ----------------------------LGPTYYQRLRHMVDD 704



 Score =  108 bits (269), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 81/606 (13%), Positives = 180/606 (29%), Gaps = 77/606 (12%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        NK  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 3   GPLLAGLFRMLFNKLTKDVFKYLQKCVENNR--EFNLTLGVKSTTLTNGLKYSL-ATGNW 59

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 60  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 119

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +   +  N + +         +A   F     
Sbjct: 120 TPEGQACGLVKNLALMCYITVGTPCEPIIDFMNQRNMEMLEEYEPLRSPNATKVFVNGVW 179

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR   +             +RD+      R     T  G    
Sbjct: 180 VGVHRDPAHLVSNVQDLRRGHIIS-------HEVSLVRDIR----DREFKIFTDAGRVCR 228

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
            +  + +  R   YG +                 +++ +EE+              G   
Sbjct: 229 PLFVIDNDTRSMNYGNLVLTK------------EHITRLEEDK---------EAAIGMDR 267

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA--SLIPFLENDDSNRVLMGCNMQRQ 699
           +EL   +   +  LV +  ++++DA  ++ V I      +         + + G      
Sbjct: 268 DELEARQMGWD-GLVNQGVVEYVDAEEEETVMIVMTPGDLETSRQIQLGKAVPGNAEDEP 326

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
              +         T       +   + I+   A I+   D  +    + +  +     GV
Sbjct: 327 NKRVNAMSHRSAQT---WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGV 383

Query: 760 DIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                  +           Q+P+                      +L  G+N +VA   +
Sbjct: 384 FXXNYXQRMDTMANILYYPQKPM----------ATTRSMEFLKFRELPAGQNAIVAIACY 433

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +   +F S+    +    +   +   E        D   +     
Sbjct: 434 SGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRTDTLRLKHGTY 493

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           + +D+ GI+  G  V+  D+++GK  P         ++        K    RD S  + S
Sbjct: 494 EKLDDDGIVAPGVRVSGEDMIIGKTAPIPPDSEELGQRT-------KMHIKRDASTPLRS 546

Query: 934 GVSGTV 939
             +G V
Sbjct: 547 TENGIV 552


>gi|328771672|gb|EGF81711.1| hypothetical protein BATDEDRAFT_29606 [Batrachochytrium dendrobatidis
            JAM81]
          Length = 1167

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 160/1090 (14%), Positives = 330/1090 (30%), Gaps = 200/1090 (18%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            + ++A  V  ++ + E+   +      L+  S+   A +       K   ++ AL  I  
Sbjct: 238  VIMKAMGVESDREIAELICGDDLKYLALFSPSLEEGASL-------KISTQRQALEYIGA 290

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
             ++     TF          + +  +  L+T     + +  +     + R       + I
Sbjct: 291  KVK----VTFKTNRVGIRRDWVEEARDLLATTVLAHVPVEADDAGVLNFRPKAIYIALMI 346

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL-------GLLRMERSIKERISS 492
             ++L  ++ G G +DD D +GN+R+   G+++   +          + R      +R + 
Sbjct: 347  RRVLQAVKEG-GIVDDRDFIGNKRLELAGQLMSLLFEDLFKSWISAIKRAVDIQLKRTNR 405

Query: 493  VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG---- 548
                         ++ +   +     S   S     +          RLS +   G    
Sbjct: 406  TSQYDAAAAVSQTSRFITDGMFRAISSGNWSVKRFKMERAGVTQVLSRLSYVSALGMLTR 465

Query: 549  ----VARARAGVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
                  + R     R +  + +G IC   +T +G   GL+ +L     +      +   R
Sbjct: 466  ISSQFEKTRKVAGPRSLQTSQWGMICLSGDTEQGEACGLIKNLALMTYITTDSN-DVSLR 524

Query: 604  KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            K+     T D+  +S  +      A + + L     F   ++       E  V       
Sbjct: 525  KLAFVLGTEDINLVSGSD----LYATSETFLV----FLNGVIMGVHRNAEQFVS------ 570

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
             D    +     ++ +          + +  +  R   PL+      V  G+  V  +  
Sbjct: 571  -DLRRLRRAGRTSAFVSIYRTVSQRTINISSDGGRVCRPLI-----IVERGIPKVTEEDI 624

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
               I                 + + E                                  
Sbjct: 625  RGIIHGILRFDDLIAQGKIEYLDTNEETDSDIA--------------------------- 657

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGR--NMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                V+ N ++ D P+T   ++A       +   +P+  +N          M  + + T 
Sbjct: 658  ----VKINSVLIDQPNTTHLEIAPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGT- 712

Query: 842  IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
                                      ++   L  ID   ++ +    +   +    I   
Sbjct: 713  --------------------------IAYNQLTRIDT--LLYLMVYPHHPMVRTRTIEMI 744

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS--- 958
            G   +   +    A+      D+ D  +   + V       ++  +              
Sbjct: 745  GFDKLPAGQNATVAVMSYSGYDIEDALVLNKASVDRGYGRCQVMRKSSTMIKSYPNQTFD 804

Query: 959  -VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL-SSDLISEY 1016
             +    ++ L     +   ILD +          G+          K T   +S  +S  
Sbjct: 805  RLADPVLDPLTGQVQERYNILDND-----GICGVGERVYPNQIVINKQTPTETSPRVSAP 859

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                          + R V+   + ++ +    +      I+++            ++KV
Sbjct: 860  TNGGGSDDESSAPMLGRAVDPSSIPFKNTPMSFKYPGDAVIDQVLL--TTNEEDQTLIKV 917

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
             +   R  + GDK +                                     SR      
Sbjct: 918  LIRQTRRPELGDKFS-------------------------------------SR------ 934

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
                        G+K    I   + +   S      + ++       +++      +L  
Sbjct: 935  -----------HGQKGVCGIIVSQEDMPFSENGVVPDVIMNPHGFPSRMTVGKMIELLAG 983

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                 +G       F G+  E ++ +L       SG+ +L  G+TGEP    +  G +Y 
Sbjct: 984  KAGLFAGQVQYGTAFGGSKVEDMSRILVENGYSYSGKDMLTSGITGEPLQAYIFFGPVYY 1043

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             KL HMV DK++ARS G  + +T+QP  G+S  GG R+GEME  C+  +GA+ +L E L 
Sbjct: 1044 QKLKHMVMDKMHARSRGPRATLTRQPTEGRSRDGGLRVGEMERDCLIGHGASSLLIERLL 1103

Query: 1317 IKSD----DVVGR-------------TRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
              SD    +V  R              ++   +V          P +  +L +E+ ++ +
Sbjct: 1104 YSSDAYDVEVCSRCGIIGAWHGYCPFCKMRSGVV------TVKMPYACKLLFQELMSMNV 1157

Query: 1360 SIDLENSRTK 1369
               ++    K
Sbjct: 1158 VPRVQVDDLK 1167



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 124/937 (13%), Positives = 267/937 (28%), Gaps = 179/937 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++FL  +I    + N         + P         L F+     PP    
Sbjct: 37  LVKQHLDSFNYFLETDIKLIVQANA---KVDSDIDP------HFFLRFLDIRIKPPQAED 87

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  +    +C  RD+TYA  + + +  +          +  + I +++I +G +P+
Sbjct: 88  IQKGVVYELTPQECRLRDITYAGTICVDIEYV----------RGKQVIVKRNIEIGRMPI 137

Query: 138 MTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKG-- 170
           M K                         G F+I+G +++++ Q   S   I  + D+   
Sbjct: 138 MLKSSYCVLTNKSPDEIADLGECPLDPGGYFIIRGTEKVILIQEQLSRNRIIVETDRFGC 197

Query: 171 --RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-E 227
                 S  L    + I   G    +      +         +VPVT  + A+G++S+ E
Sbjct: 198 ICSNVTSSTLEKKSKTIVACGKTGKMVLKHNSL-------TAEVPVTVIMKAMGVESDRE 250

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
           I        +             A+  +   + +   +     +   ++ +         
Sbjct: 251 IAELICGDDLKYLALFSPSLEEGASLKISTQRQALEYIGAKV-KVTFKTNRVGIRRDWVE 309

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI-RDIPI 346
                +         L  + V  D               ++  + L+ +    I  D   
Sbjct: 310 EARDLLATTV-----LAHVPVEADDAGVLNFRPKAIYIALMIRRVLQAVKEGGIVDDRDF 364

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDI--YRVMRPGDVSTFSVAESMFNFLFFDSD 404
           +    +     + + L  D  K    A+      ++ R    S +  A ++     F +D
Sbjct: 365 IGNKRLELAGQLMSLLFEDLFKSWISAIKRAVDIQLKRTNRTSQYDAAAAVSQTSRFITD 424

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN------GKGTIDDIDN 458
               +         R  ++     + + +   ++ + +L  + +             +  
Sbjct: 425 GMFRAISSGNWSVKRFKMERAGVTQVLSRLSYVSALGMLTRISSQFEKTRKVAGPRSLQT 484

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
                +   G+  + +    +  +         S D+       ++  + +         
Sbjct: 485 SQWGMICLSGDTEQGEACGLIKNLALMTYITTDSNDVSLRKLAFVLGTEDINLVSGSDLY 544

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICPAETSEG 577
           ++        +N +    H      +     + RA        ++ T   R     +  G
Sbjct: 545 ATS-ETFLVFLNGVIMGVHRNAEQFVSDLRRLRRAGRTSAFVSIYRTVSQRTINISSDGG 603

Query: 578 HNIGLVSS----LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                +      +      +  G I    R   D      + YL   EE +  IA     
Sbjct: 604 RVCRPLIIVERGIPKVTEEDIRGIIHGILR-FDDLIAQGKIEYLDTNEETDSDIA----- 657

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                               +L+ +     ++ +P  ++   A LIP+  ++ S R    
Sbjct: 658 ---------------VKINSVLIDQPNTTHLEIAPFTILGAVAGLIPYPHHNQSPRNTYQ 702

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+                                           I   +    
Sbjct: 703 CAMGKQAIGT-----------------------------------------IAYNQLTRI 721

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +   + +Y      R+                                  L  G+N  V
Sbjct: 722 DTLLYLMVYPHHPMVRTR------------------------TIEMIGFDKLPAGQNATV 757

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS---- 869
           A M + GY+ ED++++++  V         + +   M +       +   D         
Sbjct: 758 AVMSYSGYDIEDALVLNKASVDRGYGRCQVMRKSSTMIKSYPNQTFDRLADPVLDPLTGQ 817

Query: 870 -EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +E    +D  GI  VG  V P  I++ K TP   SP
Sbjct: 818 VQERYNILDNDGICGVGERVYPNQIVINKQTPTETSP 854


>gi|148628040|gb|ABQ97025.1| RNA polymerase II second largest subunit [Eupenicillium javanicum]
          Length = 705

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 133/831 (16%), Positives = 239/831 (28%), Gaps = 154/831 (18%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK--PVVSAVCEFFCSSQ- 521
               G +L   +R+   R+ R ++  +      +  P   I  K   +   +     +   
Sbjct: 2    DLAGPLLAGLFRVLFTRVTRDLQRYMQRCVETNKEPNLRIGLKAATLTGGLKYALATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GEQKKAASSKAGVSQVLSRYTFASSLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +            ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEFEPQVTPNATKVFV 177

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
                  +  D +     +        I      I D  D   K          P    D+
Sbjct: 178  NGVWVGIHRDPTHLVNTMQSLRRRNMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVVDN 237

Query: 687  SNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI- 743
              +     ++   ++ + LL+ +           + +         R+G+VE VDA    
Sbjct: 238  DPKSENAGSLVLNKEHIRLLELDKDLQRELPPEQLREQGFGWDGLVRSGVVEYVDAEEEE 297

Query: 744  --VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK-VGDEVRRNDIIADGPST 800
              +I     DL+ S      Y L +  +++ N        V+ V             PS 
Sbjct: 298  TIMIVMTPEDLEISKHLQAGYSLPEDDKNDPNK------RVRTVTQRAHTWTHCEIHPSM 351

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                 T                   E
Sbjct: 352  ILG-------VCASIIPFPDHNQSPRNTYQXXXXXXVFLT-------------NFAQRME 391

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               +I    ++ L                        +       +   +  + AI    
Sbjct: 392  TMANILYYPQKPLA-------------------TTRSMEFLRFRELPAGQNAIVAIATYS 432

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D  +   +V    +E   +    E + + +
Sbjct: 433  GYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEK---TVGTSFVESFEKPMRTETLGMRK 488

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K   L+ D      R++          ++     
Sbjct: 489  GTYDKLDEDGIVAPGVRVSGEDIIIGKVAPLAPDAEELGQRTKAHTKIDVSTPLRSTENG 548

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q   S                         L+  KV +   +  Q GDK A RHG K
Sbjct: 549  IVDQVVIS--------------------TANDGLKFAKVRMRTTKIPQIGDKFASRHGQK 588

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   DI++NP  +PSRM +  + E  L       G +  +   
Sbjct: 589  GTIGITYRQEDMPFSREGLTPDIIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPF 648

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 649  TDVTVDSVSRLLR--EHGYQSRGFEVM--------------------------------- 673

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                         +G +    G         V +G  Y  +L HMV DK++
Sbjct: 674  ------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIH 705


>gi|7021500|gb|AAF35376.1|AF226073_1 RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 134

 Score =  239 bits (611), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 57/150 (38%), Positives = 92/150 (61%), Gaps = 19/150 (12%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHFD 166
           +MT  GTF+I G +R++VSQL RSP ++F 
Sbjct: 102 IMTDIGTFIINGAERVIVSQLVRSPSVYFS 131


>gi|124490814|gb|ABN12777.1| RNA polymerase beta subunit [Bartonella sp. RN29BJ]
          Length = 242

 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 171/240 (71%), Positives = 199/240 (82%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP  +AV EFF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPT
Sbjct: 3   NAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPT 62

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE  
Sbjct: 63  HYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAK 122

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            Y+AQANSSLD +G F EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEN
Sbjct: 123 HYVAQANSSLDSEGRFIEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEN 182

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ AKR+GIV+QVDA RIV
Sbjct: 183 DDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSGAAVSAKRSGIVDQVDATRIV 242


>gi|78190671|gb|ABB29657.1| RNA polymerase I second largest subunit [Suberites fuscus]
          Length = 536

 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 95/250 (38%), Gaps = 52/250 (20%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E  F ++I+ +  G++     L+   + + + R    GDK A R G KGI S+  
Sbjct: 339  RYKSSEPAFVDQIKLL--GNETGDSPLQRAFIKLRICRNPIIGDKFASRAGQKGICSQKW 396

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P E+MPF + G   DI+ NP G PSRM +G + E   G +    G         +  +  
Sbjct: 397  PSENMPFTESGMVPDIIFNPHGFPSRMTIGMMVEMMAGKSAALHGLCHDCTPFKFSEDNP 456

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                                +    +L 
Sbjct: 457  A--------------------------------------------------VDHFGKLLV 466

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG 1284
             A  +  G   LY G+ G  F+  + +G +Y  +L HMVSDK   R+TG   ++T QP+ 
Sbjct: 467  KAGYNYFGNERLYSGIDGREFEADIFLGVVYYQRLRHMVSDKFQVRTTGPIDILTHQPVQ 526

Query: 1285 GKSNRGGQRL 1294
            G+   GG R 
Sbjct: 527  GRRRAGGIRF 536



 Score = 52.8 bits (125), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 77/224 (34%), Gaps = 16/224 (7%)

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           A  + P      ++R L+G   Q      +  E      G  + +    G    A  A +
Sbjct: 117 ARMMRPVRNLATNSRELIGSFEQVYMDIAVIPEE--AHQGHTTHLELDEGIMFSAI-ATL 173

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
               D  +      +  +   T G  +     +           Q P+V+          
Sbjct: 174 TPYSDFNQSPRNMYQCQMAKQTMGTPLQSFPYRMDSKLYRLQSPQAPMVRTSTY------ 227

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMAR 852
             +  S D  +  LG N +VA + + GY+ ED+M++++  V       +++  E   ++ 
Sbjct: 228 --NHYSMD--EYPLGTNAIVAVISYTGYDMEDAMILNKASVERGFKHANVYKSEVISISS 283

Query: 853 DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            +  G       I    +E  + +D+ G   +G  +  GD    
Sbjct: 284 PSDRGRPSKMFGILPGDKEA-EKLDQDGFPPIGTLLQEGDPYYS 326


>gi|55584700|gb|AAV53581.1| RNA polymerase II second largest subunit [Peniophorella praetermissa]
          Length = 671

 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 125/802 (15%), Positives = 228/802 (28%), Gaps = 149/802 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ + +    +              +    + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRMLFRKLTKDVYRYLQKCVETHKDFNIALAVKHNTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKSASSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++           + +         L  +EE    
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMATISVGSLSAPVIEFLEEWG-------LEPLEEN--- 167

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             A +++ L +       +   R     +   ++     D SP+  V             D
Sbjct: 168  -AHSSTPLTKVXVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTD 226

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG--AAIVAKRAGIVEQVDAIRIV 744
            + RV     +       L  +               S         + G++E +DA    
Sbjct: 227  AGRVCRPLFIVEDNQLALTKKHIRWLNQNRRDDDPESEKYNWDSLVKGGVIEYLDAEEEE 286

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +    +     V     +     + +  +   P V+              PS  LG 
Sbjct: 287  TVMICMSPEELDDNVQEQPSINDPDYDPSARLKG-PRVR-----HNWTHCEIHPSMILG- 339

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N          M  + +   I +  F V               
Sbjct: 340  ------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNFLVRM------------- 378

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                            +  +             +       +   +  + AI      + 
Sbjct: 379  --------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIMCYSGYNQ 424

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +   
Sbjct: 425  EDSVIMNQSSIDRGLF-RSIYYRSYMDMEKKSGVQQLEEFEKPTRDTTVRMKHGTYDKIE 483

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                I  G           K+  L++D      R++          ++     +  Q   
Sbjct: 484  DDGLIAPGTGVRGEDIIIGKTAPLAADSEELGQRTRTHTRRDVSTPLKSTESGMVDQVLL 543

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                       + VKV V   R  Q+GDK A RHG KG +    
Sbjct: 544  --------------------TTNHEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGITY 583

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L      LG +             
Sbjct: 584  RQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLLGNEGD----------- 632

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     E+++  LR
Sbjct: 633  ------------------------------------------ATP-FTELTVESVSEYLR 649

Query: 1225 MADLDESGQSILYDGLTGEPFD 1246
                   G  I+Y G TG    
Sbjct: 650  QKGYQSRGLEIMYHGHTGRKLQ 671


>gi|103001903|gb|ABF71526.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 699

 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 114/818 (13%), Positives = 230/818 (28%), Gaps = 143/818 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + + +  +              + +  + + +     +      
Sbjct: 2    GPLLANLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSN 688
               +  D +     V        I      + D  D   K          P F+ ++D  
Sbjct: 178  WVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPK 237

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G  +  +       +   +   M+S   +       AK  G    V     V+  V
Sbjct: 238  STNCGNLVLTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVEYV 288

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  R  Q           +   V+          T      ++
Sbjct: 289  DAEEEETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSM 348

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 349  ILGICASIIPFPDHNQSPRNTYQSAMGXQAMG--VFLTNYDQRM---------------- 390

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 391  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 439

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L 
Sbjct: 440  VIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLD 495

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +S D      R++          ++     +  Q   
Sbjct: 496  DDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL 555

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      L+ VKV +   +  Q GDK A RHG KG +    
Sbjct: 556  --------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 595

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 596  RQEDMPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDS 655

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 656  VSKLLR--EHGYQSRGFEVM---------------------------------------- 673

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                  +G +    G         V +G  Y  +  HM
Sbjct: 674  -----YNGHT----GR---KLVAQVFLGPTYYQRXRHM 699


>gi|147903615|ref|NP_001083372.1| polymerase (RNA) II (DNA directed) polypeptide B, 140kDa [Xenopus
           laevis]
 gi|38014674|gb|AAH60458.1| MGC68569 protein [Xenopus laevis]
          Length = 949

 Score =  239 bits (610), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 143/1002 (14%), Positives = 288/1002 (28%), Gaps = 201/1002 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHTTGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVVKEGEEQI-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK----- 211
            ++    K       K  Y           ++        I V +  R     +K     
Sbjct: 204 TVYVFAKKDS-----KYAYTAECR----SCLENSSRPTSSIWVSMLARGGQGAKKSAIGQ 254

Query: 212 ------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGA 258
                       VP+     ALG  S+ +IL          +  +     L  A ++   
Sbjct: 255 RIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQ 314

Query: 259 KVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG 318
            V+ + +     +  +   K++     + L+++ +  +G++  C          +     
Sbjct: 315 NVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH--- 370

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            + + A    +    +   +  +    P+L          +   +     K         
Sbjct: 371 RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFN 430

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKED 435
             +     + +  +  S+    + D  K   +  G  ++  RL   +      R      
Sbjct: 431 LELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIG 490

Query: 436 IIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI 495
               +     L N    +                ++KN   +  + +       +  ++ 
Sbjct: 491 RDGKLAKPRQLHNTLWGMICPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLEE 547

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
            S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R  
Sbjct: 548 WSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDI 607

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E      T  GRIC         +     L     ++     E       D   +  V 
Sbjct: 608 REREIRIYTDAGRIC----RPLLIVEKQKLLLKRRHIDQLKEREYNNYSWQDLVASGVVE 663

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           Y+  +EEE   +A     L E G                +         +  P  ++ + 
Sbjct: 664 YIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILGVC 707

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +                                
Sbjct: 708 ASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV------------------------- 742

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                              + + V  Y               Q+PLV             
Sbjct: 743 ----------------RMDTLAHVLYYP--------------QKPLV----------TTR 762

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G N +VA   + GYN EDS++++   V    F S+    ++       
Sbjct: 763 SMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKG 822

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
              EE+           +       +D+ G+I  G  V+  D+++GK     E+    E 
Sbjct: 823 FDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELES 882

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    +    RD S  + +  +G V  V +       K
Sbjct: 883 T-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|300394690|gb|ADK11883.1| DNA-directed RNA polymerase II subunit two [Coniophora puteana]
          Length = 648

 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 117/731 (16%), Positives = 211/731 (28%), Gaps = 129/731 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 44   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 99

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++   F       + +         L ++EE     A A + +  +G +
Sbjct: 100  GLVKNLALMSCISVGSFSAPVIEFLEEWG-------LESLEENAHSSA-ACTKVFVNGVW 151

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 152  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVEDQ 208

Query: 701  VPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
              LL+ +   ++  G                + G++E +DA       +    +   +  
Sbjct: 209  QLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVIELLDAEEEETVMIAMTPEDLENSR 268

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
               +         +   +    +K G            PS  LG       +  + +P+ 
Sbjct: 269  L--QSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIHPSMILG-------ICASIIPFP 319

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N                        ++       +G       +              
Sbjct: 320  DHNQSPRN------------------TYQSAMGKQAMGIYLTNFLVRM-----------D 350

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 351  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 410

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                I+ R  +D  ++S   + E+ E   RD          +       I  G       
Sbjct: 411  F-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGED 469

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  D      R++          ++     +  Q                  
Sbjct: 470  IIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI--------------- 514

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                        + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 515  -----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVPD 569

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +G + E  L      +G +                            
Sbjct: 570  IIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD-------------------------- 603

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     E++++ LR       G  ++Y G
Sbjct: 604  ---------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHG 635

Query: 1240 LTGEPFDRPVT 1250
             TG      V 
Sbjct: 636  HTGRKLQAQVY 646



 Score =  121 bits (303), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 77/578 (13%), Positives = 159/578 (27%), Gaps = 94/578 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F+++ ++ +    +  KY L   G      +         + + +    + +  L   
Sbjct: 6   KEFNISLAVKHQTITNGLKYSL-ATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRC 64

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +       + S     +   
Sbjct: 65  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFL 124

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA    +    F     +    +  N +  I   RR   +          
Sbjct: 125 EEWGLESLEENAHSSAACTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDI 184

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
                 ++        P    E   + L      +          T   K         +
Sbjct: 185 RERELRLYTDAGRVCRPLFIVEDQQLLLQKKHIKWLNQGYRDDDPTEEFKWDQLVKGGVI 244

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDAS 667
             L A EEE   IA     L+     +  +   +   +          +        +  
Sbjct: 245 ELLDAEEEETVMIAMTPEDLENSRLQSAGIDTRQSDEDYDPAARLKSGINAHTWTHCEIH 304

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ I AS+IPF +++ S R      M +QA+ +                        
Sbjct: 305 PSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV----------------- 347

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + +  Y       +     +  R        
Sbjct: 348 ------------------------RMDTMANILYYPQKPLATTRSMEYLKFR-------- 375

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +
Sbjct: 376 ----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSY 419

Query: 848 EVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             + + + +   E            +       I++ G+I  G  V+  DI++GK  P  
Sbjct: 420 MDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI- 478

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                  E+L +        DV        +G+   V+
Sbjct: 479 ---PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 513


>gi|307213328|gb|EFN88780.1| DNA-directed RNA polymerase I subunit RPA2 [Harpegnathos saltator]
          Length = 1119

 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 72/347 (20%), Positives = 115/347 (33%), Gaps = 93/347 (26%)

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
               +    ++ ++    +    +R   +   + R    GDK A R G KGI S+  P ED
Sbjct: 829  YYSKEDAYVDNVKLCGTLNSKNVRRACITFRISRNPNVGDKFASRAGQKGICSQKWPAED 888

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            +PF + G   DI+ NP G PSRM +  + E   G +    G    +    +         
Sbjct: 889  LPFTESGLIPDIIFNPHGFPSRMTIAMMIEVMAGKSAAVHGLVHDATPFRFDEENTAIDY 948

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
               L                                                  L  A  
Sbjct: 949  FGKL--------------------------------------------------LEHAGY 958

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG---- 1284
            +  G   +Y G+ G   +  +  G ++  +L HMVSDK   RSTG   L+T+QP+     
Sbjct: 959  NYYGTERMYSGVDGREMNADIFFGIVHYQRLRHMVSDKWQVRSTGPVDLLTRQPIKGRRR 1018

Query: 1285 -------GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG------ 1324
                              EME   + ++G +Y+LQ+ L   SD +        G      
Sbjct: 1019 GGGVRFG-----------EMERDALLSHGCSYLLQDRLFHCSDKISTSVCQSCGTLLGPA 1067

Query: 1325 --RTRVYESIVAG------NDTFETGTPESFNVLVKEMQALGLSIDL 1363
               T  YE  +                P  F  LV ++ +  +++ L
Sbjct: 1068 IEMTSSYERSIKCRLCGNDESIKTIEVPYIFRFLVTQLASCNINVKL 1114



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 69/445 (15%), Positives = 153/445 (34%), Gaps = 25/445 (5%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S+ L+ + E++N +  ++H R   A+ +G   +     E R + P  +G ICP  T +G 
Sbjct: 445 STGLTIVAENINRMRYMSHFR---AIHRGSFFQEMRTTETRQLLPDAWGFICPVHTPDGT 501

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++ LT    V  +   +              +    A   +N Y    +  +    
Sbjct: 502 PCGLLNHLTMNCIVTKHPDCKLKAAIPRILVDLGMIPLSIANNWKNSYTVMLDGKVI--- 558

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              E+ +  R   +   +   K++  +      +++        +            M R
Sbjct: 559 GLIEDNIINRVTCKLREL---KVNGEEVPNTLEIALVPKKTIPAQYPGLYLFTNAARMMR 615

Query: 699 QAVPLLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
             + L   +   +GT   +   +      A     +        I   +  +    D + 
Sbjct: 616 PVINLATQKIELIGTFEQVYLDICVIPEEAYDGLTSHQELSNTTILSNLACLIPMPDCNQ 675

Query: 757 SGVDIYRLMKFQRSNQNTCVN-----QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
           S  ++Y+    +++    C N     Q  L ++              + ++ D A+G N 
Sbjct: 676 SPRNMYQCQMGKQTMGTPCHNWQLQSQTKLYRLQTPATPFFRPVHYDNINMDDFAMGTNA 735

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
           ++A + + GY+ ED+M+I++          + I + E +  + +        D   + E 
Sbjct: 736 IIAVISYTGYDMEDAMVINKAAYDRGFAYGM-IYKSEFVDLNDQRSYFARNPDKTCLGET 794

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D  G+  +G  +  GDI          + +T       +       +V+      
Sbjct: 795 ----LDVDGLPMIGTRIKEGDIYYCYYDADQSTYVT---GTYYSKEDAYVDNVKLCGTLN 847

Query: 932 PSGVSGTVVDVRIFNRHGIDKNERS 956
              V    +  RI +R+    ++ +
Sbjct: 848 SKNVRRACITFRI-SRNPNVGDKFA 871



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 56/179 (31%), Gaps = 61/179 (34%)

Query: 16  FFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---AFSG 70
            FGK P+  +  + +L      S+++ L           +GL    K   P+      + 
Sbjct: 13  NFGKPPDKQNRLLQNLGIPHIESFNYML----------EDGLLEGLKDSPPVYLNLPNND 62

Query: 71  AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
              L         P            K    +C  R  TY   + + L   +  V + T 
Sbjct: 63  KIALWLDDVCIYQPTVPTGVIGVKNYKIYPTECRQRGSTYRGKITVKLGWSINGVQQETL 122

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
            K           +G++P+M K                         G F+IKG++RIV
Sbjct: 123 EKD----------LGEVPIMVKSNRCYLNKMNPKQLVEHGEHEQEWGGYFIIKGLERIV 171


>gi|312204294|gb|ADQ47464.1| RNA polymerase II second largest subunit [Absconditella sphagnorum]
          Length = 712

 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 110/805 (13%), Positives = 229/805 (28%), Gaps = 119/805 (14%)

Query: 471  LKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            +   +R    ++ R +    +              + +  + + +     +         
Sbjct: 1    MAGLFRTLFTKLTRDVFKYLQKCVESGKEFNLTLGVKSTTLTNGLKYALATGNWGEQKKA 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   ATAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     +      E    +    + +V  +            ++      
Sbjct: 117  EGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRHPNSTKVFVNGVWVG 176

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVL 691
            +  D +     V        I      I D  D   K          P F+ ++DS    
Sbjct: 177  VHRDPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDSKSPN 236

Query: 692  MGCNMQ-RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             G  +  ++ V  L+ +         E    +  G A +                +  ++
Sbjct: 237  KGSLVLSKEIVNRLEDDRDIPADLDPEERAKRYFGWAGL-----------LGTGAVEFLD 285

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q       P       V+    +     T      ++ 
Sbjct: 286  AEEEETVMIVMTPEDLEISRQVQAGYGLPEPSADPNARVKAKINMGQHTWTHCEIHPSMI 345

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N +  + + +R  +                                 
Sbjct: 346  LGICASIIPFPDHN-QVCLSMLKRRDNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 404

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 405  XXXXXXXXXXXTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 464

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R  +++ +R        +E   +    + + L    Y +L +
Sbjct: 465  IMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPMRSDTLRLKHGTYEKLDD 520

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +       
Sbjct: 521  DGMVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRSTENGI------- 573

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                       ++K+          L+ VKV +   +  Q GDK A RHG KG +     
Sbjct: 574  -----------VDKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 620

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +              
Sbjct: 621  QEDMPFSAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------ 668

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     ++++ +LR 
Sbjct: 669  -----------------------------------------ATP-FTEVTVDSVSRLLRE 686

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVT 1250
                  G  ++Y+G TG      V 
Sbjct: 687  HGYQSRGFEVMYNGHTGRKLVAQVF 711



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 84/596 (14%), Positives = 161/596 (27%), Gaps = 81/596 (13%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   +  G  ++  R    +      R          I     
Sbjct: 42  TNGLKYALATGNWGEQKKAATAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 101

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   P  
Sbjct: 102 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTR 161

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEM--- 558
             N+  V      F     +    +  + +S +   RR + +     + R     E    
Sbjct: 162 HPNSTKV------FVNGVWVGVHRDPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIF 215

Query: 559 -------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP---YRKVCDG 608
                  R +         P + S   +  +V+ L     + A    E     Y      
Sbjct: 216 TDAGRVCRPLFVIDNDSKSPNKGSLVLSKEIVNRLEDDRDIPADLDPEERAKRYFGWAGL 275

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLD-------EDGSFTEELVFCRCAGEEILVPREKI 661
             T  V +L A EEE   I      L+         G              +I + +   
Sbjct: 276 LGTGAVEFLDAEEEETVMIVMTPEDLEISRQVQAGYGLPEPSADPNARVKAKINMGQHTW 335

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
              +  P  ++ I AS+IPF +++     ++                             
Sbjct: 336 THCEIHPSMILGICASIIPFPDHNQVCLSMLKRRDNXXXXXXXXXXXXXXX--------- 386

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                                                   Q+PL
Sbjct: 387 ------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXTMANILYYPQKPL 428

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                 +L  G+N +VA   + GYN EDS+++++  +   +F S
Sbjct: 429 ----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 478

Query: 842 IHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +   +   E     +  D   +     + +D+ G++  G  V+  DI++G
Sbjct: 479 LFYRAYVEQEKRVGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGMVAPGVRVSGEDIIIG 538

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K  P         ++        K    RD S  + S  +G V  V +       K
Sbjct: 539 KTAPIAPDAEELGQRT-------KLHTKRDASTPLRSTENGIVDKVLLTTNAEGLK 587


>gi|103001602|gb|ABF71514.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 694

 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 113/815 (13%), Positives = 227/815 (27%), Gaps = 145/815 (17%)

Query: 473  NQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------- 521
            N +R+   ++ + + +  +              + +  + + +     +           
Sbjct: 1    NLFRMLFNKLTKDVYKYLQKCVESGREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAAS 60

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 61   SKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 116

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L     +      E    +    + +V  +     +      ++      + 
Sbjct: 117  QACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVGVH 176

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             D +     V        I      + D  D   K          P    D+  +     
Sbjct: 177  RDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNCG 236

Query: 695  NMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            N+   ++ +  L+ +               S     AK  G    V     V+  V+ + 
Sbjct: 237  NLVLTKEHINKLEDDRDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEXVDAEE 286

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNM 811
            + +   V     ++  R  Q           +   V+          T      ++   +
Sbjct: 287  EETVMIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSMILGI 346

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N          M  + +   + +  ++                       
Sbjct: 347  CASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM-------------------- 384

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                     +  +             +       +   +  + AI      +  D+ +  
Sbjct: 385  -------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMN 437

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--- 988
             S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   
Sbjct: 438  QSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGI 493

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +  G           K+  +S D      R++          ++     +  Q       
Sbjct: 494  VAPGVRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL---- 549

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                  L+ VKV +   +  Q GDK A RHG KG +      ED
Sbjct: 550  ----------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQED 593

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF K+G   D+++NP  +PSRM +  + E  L       G +  +          +S L
Sbjct: 594  MPFTKEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKL 653

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                E    +                                                  
Sbjct: 654  LR--EHGYQSRGFEVM-------------------------------------------- 667

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
              +G +    G         V +G  Y  +L HMV
Sbjct: 668  -YNGHT----GR---KLVAQVFLGPTYYQRLRHMV 694


>gi|73975057|ref|XP_860670.1| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa
           polypeptide (RNA polymerase II subunit 2) (RPB2) isoform
           5 [Canis familiaris]
          Length = 932

 Score =  239 bits (610), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 146/1004 (14%), Positives = 294/1004 (29%), Gaps = 205/1004 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         SG        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E                  +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEK----------------EVAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F S+    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESK 820

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                EE+           +       +D+ G+I  G  V+  D+++GK     E+    
Sbjct: 821 KGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 880

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E          +    RD S  + +  +G V  V +       K
Sbjct: 881 EGT-------NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYK 917


>gi|153958206|gb|ABS53393.1| RpoB [Bacteriovorax sp. ORF]
 gi|153958210|gb|ABS53395.1| RpoB [Bacteriovorax sp. JS1]
          Length = 349

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 167/350 (47%), Positives = 231/350 (66%), Gaps = 10/350 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRDK--FDEGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   L+ ++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIAEMLKGAKTTDRLVSEDGSSELLPKGAELTGEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
                 ++   ++  +           + +  +  ++I K   GD++PPGV
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDELPPGV 349


>gi|6606107|gb|AAF19066.1|AF107794_1 DNA-dependent RNA polymerase II RPB140 [Byssochlamys nivea]
          Length = 905

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 160/1011 (15%), Positives = 293/1011 (28%), Gaps = 165/1011 (16%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G ++ S L   L  KG    G     +    +     +     ++   G V DE  L
Sbjct: 37   VEKGSRILSQLSLKLFSKGDSAKGGFGPTIRST-LPYIKTDIPIVVVFRALGVVSDEDIL 95

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
              I +       +  +       ++         +DR+ AL  I +    G   T    E
Sbjct: 96   NHICYDRNDTPMLEMLKPCIEEGFV--------IQDREVALDFISKR---GSSQTSMNHE 144

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
                +      K  L  +              +     +   +  ++  L+    G+  +
Sbjct: 145  RRVRYAREIMQKEFLPHI-----------SQSEGSETRKAFFLGYMVHRLLQCALGRRDV 193

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    R+ R ++   +        +     + A  +  
Sbjct: 194  DDRDHFGKKRLDLAGPLLATLFRTLFTRVTRDLQRYVQRCVETNREIYLNIGVKASTLTG 253

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 254  GLKYALATGNWGEQKKAASSKAGVSQVLSRYTYSSTLSHLRRTNT----PIGRDGKIAKP 309

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 310  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEP 369

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                     ++      +  D S     V        I      + D  D   K      
Sbjct: 370  QVTPNATKVFVNGVWVGIHRDPSHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAG 429

Query: 676  ASLIP-FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                P F+ ++D      G  +  ++ +  L+ +             +         R+G
Sbjct: 430  RVCRPLFVIDNDPKSENCGSLVLNKEHIRKLEQDKELPPDLSPEERRERYFGWDGLVRSG 489

Query: 734  IVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            +VE VDA      +I     DL+ S      Y L +    ++    N+R    +  +   
Sbjct: 490  VVEYVDAEEEETIMIVMTPEDLEISKQLQAGYALPE----DEGNDPNKRVRSVLSQKAHT 545

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   PS  LG       +  + +P+  +N          M  + +            
Sbjct: 546  WTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGV---------- 588

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                     E   +I    ++ L                        +       +   +
Sbjct: 589  FLTNFDQRMETMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQ 629

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D  +       E+ E   R 
Sbjct: 630  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMVGLTVVERFEKPMRS 688

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
                      +       I  G           K+  L+ +                +E 
Sbjct: 689  DTIGMRKGTYDKIDEDGIIAPGVRVSGEDIIIGKTAPLAPE---------------AEEL 733

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR     K+   T     E+   +++      DD+     + VKV +   +  Q GDK 
Sbjct: 734  GQRTKAHTKLDVSTPLRSTENGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQVGDKF 788

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 789  ASRHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGF 848

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
            +  +          +S L    E    +                                
Sbjct: 849  EGDATPFTDVTVDSVSRLLR--EHGYQSRGFEVM-------------------------- 880

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                                +G +    G         V +G  Y  +L H
Sbjct: 881  -------------------YNGHT----GR---KLVAQVFLGPTYYQRLRH 905



 Score =  119 bits (297), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 119/858 (13%), Positives = 241/858 (28%), Gaps = 142/858 (16%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIE-----FDSKDI 201
            ++++++Q  RS G        + +      Y   I    ++G  +  +     F   D 
Sbjct: 1   SEKVLIAQE-RSAGNI--AQVFKKAPPSPTPYVAEIRSAVEKGSRILSQLSLKLFSKGDS 57

Query: 202 I-------------HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCF 247
                         +++ D    +P+     ALG+   E+IL+        +   +    
Sbjct: 58  AKGGFGPTIRSTLPYIKTD----IPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKP 113

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SD 301
            +    ++   +V+   +      Q   + ++      + ++++ +  +  +        
Sbjct: 114 CIEEGFVIQDREVALDFISKRGSSQTSMNHERRVRYAREIMQKEFLPHISQSEGSETRKA 173

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
              G  V   ++    G   ++  D   +K L+            L+     +       
Sbjct: 174 FFLGYMV-HRLLQCALGRRDVDDRDHFGKKRLDLAGPLLATLFRTLFTRVTRD----LQR 228

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
            V    +  ++  L+I          T  +  ++    + +  K   S  G  ++  R  
Sbjct: 229 YVQRCVETNREIYLNIGVK---ASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLSRYT 285

Query: 422 LDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
             +      R          I     L N   G +   +    +    V  +    Y   
Sbjct: 286 YSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITV 345

Query: 479 LLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
               E  I    + +   ++   PQ   NA  V      F     +    +  + +S + 
Sbjct: 346 GTPSEPIIDFMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPSHLVSTVQ 399

Query: 537 HTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             RR + +  +  + R     E        R   P       P   + G  +     +  
Sbjct: 400 SLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSENCGSLVLNKEHIRK 459

Query: 589 FARVNA------YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS--- 639
             +                Y        +  V Y+ A EEE   I      L+       
Sbjct: 460 LEQDKELPPDLSPEERRERYFGWDGLVRSGVVEYVDAEEEETIMIVMTPEDLEISKQLQA 519

Query: 640 -----FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  E     +     +          +  P  ++ I AS+IPF +++ S R     
Sbjct: 520 GYALPEDEGNDPNKRVRSVLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 579

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                   D     + ++      
Sbjct: 580 AMGKQAMGVFLTNF------------------------------DQRMETMANILYYPQK 609

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             +       +KF+                G   + + +I +  S D G         + 
Sbjct: 610 PLATTRSMEFLKFRELPAGQNAIVAIACYSG-YNQEDSVIMNQSSIDRGLFRS-----LF 663

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
           +  +        + + ER              FE   R   +G          + +    
Sbjct: 664 YRTYTDSEKMVGLTVVER--------------FEKPMRSDTIG----------MRKGTYD 699

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            IDE GII  G  V+  DI++GK  P     + PE + L      KA    D S  + S 
Sbjct: 700 KIDEDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR--TKAHTKLDVSTPLRST 752

Query: 935 VSGTVVDVRIFNRHGIDK 952
            +G V  V +   +   K
Sbjct: 753 ENGIVDQVLVSTSNDDLK 770


>gi|241813048|ref|XP_002416483.1| DNA-directed RNA polymerase II, putative [Ixodes scapularis]
 gi|215510947|gb|EEC20400.1| DNA-directed RNA polymerase II, putative [Ixodes scapularis]
          Length = 1142

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 154/1142 (13%), Positives = 323/1142 (28%), Gaps = 229/1142 (20%)

Query: 29   LIEVQKASYDHFLMMNIAP--DERPNEGLQAAFKSVF-PITAFSGAAMLEFVSYEFDPPK 85
            L+  Q  S+D F+ M++    ++ P   LQA  +     I       +L+F       P 
Sbjct: 39   LVRQQLDSFDEFIQMSVQRIVEDTPQIDLQAEAQHASGEIENP-PRYLLKFEQIYLSKPT 97

Query: 86   FD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                         ++   R+LTY+ PL + +   V    E        + + Q  ++G +
Sbjct: 98   HWEKDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEPV-----ETQHQKTFIGKI 152

Query: 136  PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKG 170
            P+M                           G F+I G ++++++Q   +   ++    K 
Sbjct: 153  PIMLRSTYCLLNSLTDRDLSELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFQMKD 212

Query: 171  RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK-------------- 211
                  K ++           ++        + V +  R     RK              
Sbjct: 213  S-----KFVFKAECR----SCLEHSSRPTSTLWVNMLARGGQGVRKSAIGQRIIAILPYI 263

Query: 212  ---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
               +P+     ALG  ++ +IL          +  +     L  A ++    V+ + +  
Sbjct: 264  KQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGA 323

Query: 268  DTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIY 321
                  +   +++     + L+++ +  +G++           G  V   ++    G   
Sbjct: 324  RGAHPGVTKERRIKYSR-EILQKEMLPHVGVSDFCETKKAYYLGYMVHRLLL-AALGRRE 381

Query: 322  IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            ++  D    K L+            L+ +            +        +       + 
Sbjct: 382  LDDRDHYGNKRLDLAGPLMAFLFRGLFRNLTKEVRMYAQKFIDRGKDFNLE-------LA 434

Query: 382  RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAI 439
                + T  +  S+    + D  K   +  G  ++  RL   +      R          
Sbjct: 435  IKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTYASTLSHLRRVNSPIGRDGK 494

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
            +     L N    +                ++KN   +  + +       +  ++  S+ 
Sbjct: 495  LAKPRQLHNTLWGMICPAETPEGHAVG---LVKNLALMSYISVGSQPSPILEFLEEWSME 551

Query: 500  PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMR 559
              + I    +  A   F     +    +    ++ +   RR   +    V+  R   +  
Sbjct: 552  NLEEIAPSAIAEATKIFVNGCWVGIHRDPDQLMNTLRKLRRQMDIIVSEVSMVRDIRDRE 611

Query: 560  DVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
                T  GRIC P    E   +     L     +++    E       D   +  V Y+ 
Sbjct: 612  IRIYTDAGRICRPLLIVEDQKL-----LLKRRHIDSLKEREYNNYSWQDLVASGVVEYID 666

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             +EEE   ++     L + G                          +  P  ++ + AS+
Sbjct: 667  TLEEETVMLSMTPDDLQDKG----------------FAYCSTYTHCEIHPSMILGVCASI 710

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            IPF +++ S R      M +QA+ +                                   
Sbjct: 711  IPFPDHNQSPRNTYQSAMGKQAMGIYITNFHV---------------------------- 742

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                            + + V  Y       +     +  R                   
Sbjct: 743  -------------RMDTLAHVLYYPHKPLTTTRSMEYLRFR------------------- 770

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                 +L  G N +VA M + GYN EDS++++   V    F S+    ++          
Sbjct: 771  -----ELPAGINSIVAIMSYTGYNQEDSIIVNASAVDRGFFRSVFYRSYKDSECKRVGDQ 825

Query: 859  EEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            EE            +       +D+ GII  G  V+  D+++GK     E+    E    
Sbjct: 826  EEQFEKPTRETCQGMRNAIYDKLDDDGIIAPGTRVSGDDVIIGKTITLPENDDDLEST-- 883

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                  +    RD S  + +  +G V  V +       K                + +  
Sbjct: 884  -----NRRFTKRDASTFLRNSETGIVDQVMLTVNAEGYK--------------FCKIRVR 924

Query: 974  EQVI--LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               I  +     SR      GQ    G    ++    ++D ++            +  K+
Sbjct: 925  SVRIPQIGDKFASRH-----GQKGTCGITYRQEDMPFTADGLTPDIIINPHAIPSRMTKI 979

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIE-------------KIQWGDDMPPGVLRVVKVFV 1078
               ++        ++ +       K+              K    D +       V++ V
Sbjct: 980  SNLLQEYGYHLRGNEVMYNGHTGRKVNAQIFLGPTYYQRLKHMVDDKIHSRARGPVQILV 1039

Query: 1079 AM 1080
              
Sbjct: 1040 RQ 1041



 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 115/837 (13%), Positives = 237/837 (28%), Gaps = 134/837 (16%)

Query: 318  GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
            G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 253  GQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQ 312

Query: 378  YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             + +    +        +         KY    + +  +      D  +  +      + 
Sbjct: 313  EQNVALNFIGARGAHPGV---TKERRIKYSREILQKEMLPHVGVSDFCETKK---AYYLG 366

Query: 438  AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
             ++  L+    G+  +DD D+ GN+R+   G ++   +R     + + ++          
Sbjct: 367  YMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLMAFLFRGLFRNLTKEVRMYAQKFIDRG 426

Query: 497  -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                 +  I  + +   +     +               +SQ+   +   S ++H RR++
Sbjct: 427  KDFNLELAIKTRIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTYASTLSHLRRVN 486

Query: 543  ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            +     + R     + R +H T +G ICPAET EGH +GLV +L   + ++         
Sbjct: 487  S----PIGRDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMSYISVGSQPSPIL 542

Query: 603  RKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFT-EELVFCRCAGEEILVPRE 659
              + +  +    ++   +  E    ++      +  D       L   R   + I+    
Sbjct: 543  EFLEEWSMENLEEIAPSAIAEATKIFVNGCWVGIHRDPDQLMNTLRKLRRQMDIIVSEVS 602

Query: 660  KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
             + D  D   +          P L  +D   +L   ++                      
Sbjct: 603  MVRDIRDREIRIYTDAGRICRPLLIVEDQKLLLKRRHIDSLKEREYNN--------YSWQ 654

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
               +SG           E +D +      +    D        Y                
Sbjct: 655  DLVASGVV---------EYIDTLEEETVMLSMTPDDLQDKGFAY---------------- 689

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
                               PS  LG       +  + +P+  +N          M  + +
Sbjct: 690  ---------CSTYTHCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAM 733

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
               I+I  F                           ++    +  V    +        +
Sbjct: 734  G--IYITNF---------------------------HVRMDTLAHVLYYPHKPLTTTRSM 764

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V         +  +   + +R   
Sbjct: 765  EYLRFRELPAGINSIVAIMSYTGYNQEDSIIVNASAVDRGFFRSVFYRSYKDSECKRVGD 824

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             E    E   +   +    +   IY +L +   I  G           K+  L  +    
Sbjct: 825  QE----EQFEKPTRETCQGMRNAIYDKLDDDGIIAPGTRVSGDDVIIGKTITLPENDDDL 880

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
               ++ +        ++ +   +  Q   + +                        +  K
Sbjct: 881  ESTNRRFTKRDASTFLRNSETGIVDQVMLTVNA--------------------EGYKFCK 920

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            + V   R  Q GDK A RHG KG        EDMPF  DG   DI++NP  +PSRM 
Sbjct: 921  IRVRSVRIPQIGDKFASRHGQKGTCGITYRQEDMPFTADGLTPDIIINPHAIPSRMT 977



 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 42/168 (25%), Positives = 78/168 (46%), Gaps = 20/168 (11%)

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                I+++L+       G  ++Y+G TG   +  + +G  Y  +L HMV DK+++R+ G 
Sbjct: 975  RMTKISNLLQEYGYHLRGNEVMYNGHTGRKVNAQIFLGPTYYQRLKHMVDDKIHSRARGP 1034

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG------ 1324
              ++ +QP+ G++  GG R GEME  C  ++GAA  L+E L   SD     +        
Sbjct: 1035 VQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRAHICNLCGLLA 1094

Query: 1325 ----RTRVYESIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                R   +E    G        +   P +  +L +E+ ++ ++  + 
Sbjct: 1095 IANLRNNTFEC--KGCRNKTQISQIRLPYACKLLFQELMSMSIAPRMM 1140


>gi|67515352|gb|AAY68205.1| RNA polymerase IV second largest subunit [Sphagnum sp. JL-2005]
          Length = 650

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 123/317 (38%), Gaps = 72/317 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  R+ KV +   R  Q+GDK +  HG KG++  + P ED+P+ + G   DI++NP 
Sbjct: 388  NEEDGHRISKVRLRFTRAPQAGDKFSSLHGQKGVIGAVFPQEDLPYTRQGIVPDIIINPH 447

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSR   GQI E  LG      GK         +A           +   G G      
Sbjct: 448  ALPSRQTFGQIMECLLGEVVATSGK----PCFATRAETPQRVNELLFQYHYGRGGA---- 499

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                                              + +G TG P 
Sbjct: 500  ------------------------------------------------EYMCNGTTGMPL 511

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARST-GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +  +T+G  +  +L+HMV DK+  R   GS + +T QP+  +++ GG + GEME  C+  
Sbjct: 512  EALITMGPTFYQRLDHMVEDKIKFRGIGGSINPLTHQPVRDRNSLGGVKFGEMERDCMLG 571

Query: 1305 YGAAYVLQEMLTIKSD----DVVG---RTRVYESIV--------AGNDTFETGTPESFNV 1349
            +GA+  L+    + SD    ++     R    ++           G    +   P +  +
Sbjct: 572  HGASSTLRXRYFLLSDPYKMNICAACRRPATMDTKXTPKCXXCKNGKRIVQIQIPYACKL 631

Query: 1350 LVKEMQALGLSIDLENS 1366
            L +E+ ++G+S+ ++  
Sbjct: 632  LWQELLSMGISVYMDTK 648



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 60/477 (12%), Positives = 126/477 (26%), Gaps = 94/477 (19%)

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
             +  +   S+   +  N   +      F   + +  + +   +++ +   RR   L   
Sbjct: 19  MVMCVLSEHSMENLEETNPANLQYKDKVFVNGTWVGVMIDPEKAVNELREIRRSHHLHSE 78

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
                        ++      + P       N  LV S     ++     +         
Sbjct: 79  VEVVRDPVRREVFIYTDGGRILRPL--LLVQNQRLVLSRQHLKKLKVMMRLHGAGACWTY 136

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 V  L   EEE   +A     L++   +    V+                  +  
Sbjct: 137 LLKEGVVELLGIEEEEKVMVATNGQDLEKAREYAHAPVY---------------THSEID 181

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
              ++ + A +IPFL+++ + R L       +          +                 
Sbjct: 182 SSFLLGLGAVMIPFLQHNQALRNLHQSEKHCRQAIGYYCTNLW----------------- 224

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      S++    Y       +    C+ Q+P       
Sbjct: 225 -----------------------SRADSSAHHLFYPQKPLVTTRAADCL-QKP------- 253

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+  +VA   +  YN EDS+++++  +   +F S H +  
Sbjct: 254 ----------------ELMNGQVAIVAIQSFA-YNQEDSIVMNQASIDRGLFRSAHYKIH 296

Query: 848 EVMARDTKLGPEEITRDIPNVS----------EEGLKNIDECGIICVGAEVNPGDILVGK 897
               R              +            +  L  +D+ G  CVG  +  G+I++GK
Sbjct: 297 RGEERKNVDEHFSKPSISDHKGWTHAWSGLDYKACLDKVDDDGFPCVGENLTKGNIVIGK 356

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           +T +   P          +  +    V    L               F R     ++
Sbjct: 357 LTAEQGRPKLSNTSTHLKLHQK--GHVDQVLLANEEDGHRISKVRLRFTRAPQAGDK 411


>gi|269986413|gb|EEZ92700.1| RNA polymerase Rpb2 domain 6 [Candidatus Parvarchaeum acidiphilum
            ARMAN-4]
          Length = 600

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/313 (26%), Positives = 123/313 (39%), Gaps = 72/313 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 + V + +   RP++ GD    R G KG+V  +L  EDMPF   G   D++ +P  
Sbjct: 338  TSEGNKYVSLKIRQDRPVEIGDIFGPRSGQKGVVGMLLNQEDMPFTYSGIVPDLIFSPYS 397

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM++  + E          G K+ +L   +                           
Sbjct: 398  IPSRMSMSYLLELI--------GGKVGALGGRHVDGTS---------------------- 427

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                    F G  EE++   L      E+G   +Y+G+TGE   
Sbjct: 428  ------------------------FTGETEESLRQELMKYGFRENGVETMYNGITGEEMK 463

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + VG +  ++L H V  K+  R+ G   L+ +QP  GKS RGG RLGEME  C  AYG
Sbjct: 464  VRIFVGDMTYIRLKHFVEYKIQWRARGPIQLLNRQPTEGKSKRGGLRLGEMEKDCFVAYG 523

Query: 1307 AAYVLQEMLTIKSDDV-------VGRTRVYE-------SIVAGND--TFETGTPESFNVL 1350
             A  L+E     SD V        G   VY          + G D          SF +L
Sbjct: 524  TALALKERF--DSDKVTIPVCSKCGMVAVYNVKKKTGYCPIDGEDAQIKLIEVSASFKIL 581

Query: 1351 VKEMQALGLSIDL 1363
            + E++++G+   +
Sbjct: 582  LDELKSVGIYPKM 594


>gi|57337354|emb|CAH69685.1| RNA polymerase, beta subunit [Escherichia coli]
          Length = 238

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 145/237 (61%), Positives = 183/237 (77%)

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N
Sbjct: 1   HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGN 60

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+
Sbjct: 61  YVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEH 120

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR G+V+ VDA RIV
Sbjct: 121 DDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIV 180

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           I+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ V R D++ADGPSTD
Sbjct: 181 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTD 237


>gi|158853036|gb|ABW82118.1| RpoB [Bacteriovorax sp. SAN4]
          Length = 349

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 166/352 (47%), Positives = 231/352 (65%), Gaps = 10/352 (2%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ S A + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+
Sbjct: 1    ARDSRAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQK 58

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVF
Sbjct: 59   ALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVF 118

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKIT
Sbjct: 119  TSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKIT 178

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +
Sbjct: 179  PKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEI 238

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDL 1012
              ++  L+ RD+  E   +  +   ++ ++L G              +   K   L+S++
Sbjct: 239  IEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEV 298

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            ++  P        ++   ++  +           + +  +  ++I K   GD
Sbjct: 299  LASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGD 349


>gi|154362115|gb|ABS80896.1| RNA polymerase beta subunit [Burkholderia tuberum STM678]
          Length = 234

 Score =  239 bits (609), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 175/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A +N YGF+ETPYRKV DGKVT+ + YLSA+EE    IAQAN+++ +D +
Sbjct: 61  IGLINSLALYAHLNEYGFLETPYRKVADGKVTDQIDYLSAIEEGRYVIAQANAAVADDRT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T+ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTDELVSSREAGETLMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA RIVIR  + +
Sbjct: 181 AVPCLRPEKPVVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRIVIRVNDDE 232


>gi|115906100|ref|XP_797294.2| PREDICTED: similar to RNA polymerase III subunit RPC2, partial
            [Strongylocentrotus purpuratus]
 gi|115954383|ref|XP_001182073.1| PREDICTED: similar to RNA polymerase III subunit RPC2, partial
            [Strongylocentrotus purpuratus]
          Length = 313

 Score =  239 bits (609), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 99/268 (36%), Gaps = 80/268 (29%)

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP G PSRM VG++ E   G                                      
Sbjct: 108  IMNPHGFPSRMTVGKLIEFLAGK------------------------------------- 130

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                            A   +      T  F G     I   LR    +  G+  L  G+
Sbjct: 131  ----------------AGVLEGKFHYGT-AFGGDKVVDICEDLRKHGFNYLGKDFLTSGI 173

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP    +  G +Y  KL HMV DK++AR+ G  +++T+QP  G++  GG RLGEME  
Sbjct: 174  TGEPLTAYIYFGPVYYQKLKHMVLDKMHARAKGPRAVLTRQPTEGRARDGGLRLGEMERD 233

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------------NDTFETG 1342
            C+  YGA+ +L E L I SD    DV G          G               +     
Sbjct: 234  CLIGYGASMLLLERLMISSDQFQVDVCGD--------CGLIGHSGWCPYCHCSQNISSLR 285

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKN 1370
             P +  +L +E+Q++ +   L   +   
Sbjct: 286  IPYACKLLFQELQSMNIIPRLRLKKYTE 313


>gi|154362107|gb|ABS80892.1| RNA polymerase beta subunit [Herbaspirillum huttiense]
          Length = 234

 Score =  239 bits (609), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 140/232 (60%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV   KVTN + YLSA+EE    IAQAN+++D +G 
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVEGSKVTNQIDYLSAIEEGRYVIAQANATIDGEGK 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            ++ELV  R AGE ILV  E++ ++D +P QVVS+AASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LSDELVSAREAGETILVSPERVQYMDVAPGQVVSVAASLIPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG  + A R G+V+ VDA R+VIR  + +
Sbjct: 181 AVPCLRPEKPLVGTGIERTVAVDSGTTVQALRGGVVDYVDAGRVVIRVNDEE 232


>gi|154362095|gb|ABS80886.1| RNA polymerase beta subunit [Comamonas terrigena]
          Length = 234

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 139/232 (59%), Positives = 172/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD +G 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDEIDYLSAIEEGKYVIAQANAELDAEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              ELV  R AGE  L+  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LVGELVSAREAGESTLLSPERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIVIR  + +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTATRGGIVDYVDATRIVIRVNDEE 232


>gi|40645025|emb|CAD92461.1| RNA polymerase II [Valeriana officinalis]
          Length = 364

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 75/416 (18%), Positives = 129/416 (31%), Gaps = 77/416 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 26   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 85

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 86   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPAGTRVSGE 144

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T ++                  D+   +     +  + TS    E    +++ 
Sbjct: 145  DVIIGKTTPIAQ-----------------DDAQGQASRYTRRDHSTSLRHSETGMVDQVL 187

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 188  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 242

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +  
Sbjct: 243  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRG 302

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 303  FETM-----------------------------------------------YNGHT---- 311

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R 
Sbjct: 312  GR---RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRF 364



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 60/198 (30%), Gaps = 24/198 (12%)

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
                   +          +           Q+PLV                      L 
Sbjct: 5   YQSAMGKQAMGIYVTNFQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLP 54

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR--- 863
            G N +VA   + GYN EDS+++++  +    F S+    +    +      +E      
Sbjct: 55  AGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPD 114

Query: 864 --DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             +   +       +D+ G+   G  V+  D+++GK TP  +           A      
Sbjct: 115 RANTMGMRHGSYDKLDDDGLAPAGTRVSGEDVIIGKTTPIAQDD---------AQGQASR 165

Query: 922 VDVRDTSLRVPSGVSGTV 939
              RD S  +    +G V
Sbjct: 166 YTRRDHSTSLRHSETGMV 183


>gi|82504133|gb|ABB80489.1| RNA polymerase II subunit [Symbiotaphrina buchneri]
          Length = 706

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 117/815 (14%), Positives = 222/815 (27%), Gaps = 129/815 (15%)

Query: 473  NQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------- 521
            N +R+   ++ + +K   +    +         + +  + + +     +           
Sbjct: 1    NLFRMLFHKLTKDVKAYLQKCFENHREFNITLAVKSTTITNGLKYSLATGNWGDQKKAMS 60

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 61   SKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 116

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L+    +      E    Y      +V  +     +      ++      + 
Sbjct: 117  QACGLVKNLSLMCYITVGTPSEPIVDYMVTRSMEVLEEYEPQRSPNATKIFLNGVWVGVH 176

Query: 636  EDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             + S    E++  R  G  +       D  D   +          P    D+  R     
Sbjct: 177  HNPSHLVREMLSLRRKGSLLSEVGLVRDIRDREFRIFTDAGRICRPLFVVDNDPRNESCG 236

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            N+      L K EA     G   +  +     + +               +  ++ + + 
Sbjct: 237  NLVLTKEHLTKLEADKDILGDPQLSLEQKADLLESNPDVFGWNGLMKSGAVEYLDAEEEE 296

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            +   V     +   R  Q     Q P           D       T +   A        
Sbjct: 297  TAMIVMTPDDLXISRQIQAGY--QMP--------EEEDSTXXRVKTPMKXTAQ------- 339

Query: 815  FMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               W       SM+  I   ++            ++       +G      +        
Sbjct: 340  --TWTHXEIHPSMILGICAXIIPXPXHNQSPRNTYQSAMGKQAMGVFXXXFNYRM----- 392

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +  + AI      +  D+ +   
Sbjct: 393  ------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQ 446

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +   +    +F R   D+ +R      EQ E   R    +      +       +  G
Sbjct: 447  SSIDRGLF-RSLFYRSYTDQEKRVGMSVVEQFEKPTRADTLKLKHGTYDKLDEDGLVAPG 505

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  ++ D      R++          ++     +  Q           
Sbjct: 506  VRVNGEDMIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRTTESGIVDQVLL-------- 557

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              LR VKV +   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 558  ------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 605

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   D+++NP  +PSRM +  + E  L       G +  +          +S L    
Sbjct: 606  REGIVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTDVTVDGVSRLLR-- 663

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            +    +                                                    +G
Sbjct: 664  DNGYQSRGFEVM---------------------------------------------YNG 678

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
             +    G         V +G  Y  +L HMV  K+
Sbjct: 679  HT----GR---KLVAQVFLGPTYYQRLRHMVDXKI 706



 Score =  107 bits (268), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 96/618 (15%), Positives = 167/618 (27%), Gaps = 106/618 (17%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +   +     K  ++       +       T  +  S+    + D  K   S  G  ++ 
Sbjct: 10  LTKDVKAYLQKCFENHREFNITLAVKSTTITNGLKYSLATGNWGDQKKAMSSKAGVSQVL 69

Query: 418 MRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            R    +      R          I     L N   G +   +    +    V  +    
Sbjct: 70  NRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC 129

Query: 475 YRLGLLRMERSIKER--ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           Y       E  +      S   ++   PQ   NA  +      F     +       + +
Sbjct: 130 YITVGTPSEPIVDYMVTRSMEVLEEYEPQRSPNATKI------FLNGVWVGVHHNPSHLV 183

Query: 533 SRITHTRRL-SALGQGGVARARAGVEMRDVHPTHYGRIC---------PAETSEGHNIGL 582
             +   RR  S L + G+ R     E R    T  GRIC         P   S G+ +  
Sbjct: 184 REMLSLRRKGSLLSEVGLVRDIRDREFR--IFTDAGRICRPLFVVDNDPRNESCGNLVLT 241

Query: 583 VSSLTSF-ARVNAYGFIETPYRK-------------VCDGKVTNDVVYLSAMEEENRYIA 628
              LT   A  +  G  +    +                   +  V YL A EEE   I 
Sbjct: 242 KEHLTKLEADKDILGDPQLSLEQKADLLESNPDVFGWNGLMKSGAVEYLDAEEEETAMIV 301

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                L                                          +     E +DS 
Sbjct: 302 MTPDDLXISRQIQ-----------------------------------AGYQMPEEEDST 326

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              +   M+               T       +   + I+   A I+      +    + 
Sbjct: 327 XXRVKTPMK--------------XTAQTWTHXEIHPSMILGICAXIIPXPXHNQSPRNTY 372

Query: 749 EGDLDPSTSGVDIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
           +  +     GV       +           Q+PL                      +L  
Sbjct: 373 QSAMGKQAMGVFXXXFNYRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPA 422

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR---- 863
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E       
Sbjct: 423 GQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRVGMSVVEQFEKPTR 482

Query: 864 -DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +DE G++  G  VN  D+++GK  P         E+L +        
Sbjct: 483 ADTLKLKHGTYDKLDEDGLVAPGVRVNGEDMIIGKTAPIAPDA----EELGQRTKLHIKR 538

Query: 923 DVRDTSLRVPSGVSGTVV 940
           DV        SG+   V+
Sbjct: 539 DVSTPLRTTESGIVDQVL 556


>gi|46277257|gb|AAS86819.1| RNA polymerase II second largest subunit [Dioscorea sansibarensis]
          Length = 572

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 82/499 (16%), Positives = 151/499 (30%), Gaps = 91/499 (18%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
              T    +   +N   A+   +       S++  +   ++            ++      
Sbjct: 162  SMTINDLINARQNPEEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 221

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G          V+   L+      +  V        +    +       +      + 
Sbjct: 222  AMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 270

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R+    
Sbjct: 271  AIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGKPNRENTMG 329

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K++ +                  QDE   + 
Sbjct: 330  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPI-----------------PQDESQGQA 372

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                +  + TS    E    +++      D +     R VKV +   R  Q GDK + RH
Sbjct: 373  SRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRH 427

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 428  GQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 487

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS         +                                      
Sbjct: 488  TPFTDVTVDNISKALHKCGYQMRGFETM-------------------------------- 515

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                            +G +    G         + +G  Y  +L HMV DK+++R  G 
Sbjct: 516  ---------------YNGHT----GR---KLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 553

Query: 1275 YSLVTQQPLGGKSNRGGQR 1293
              ++T+QP  G+S  GG R
Sbjct: 554  VQILTRQPAEGRSRDGGLR 572



 Score =  116 bits (291), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 70/452 (15%), Positives = 130/452 (28%), Gaps = 98/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   +  A   F     +         +  +   RR   +  + GV R 
Sbjct: 33  EEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPDLLVKTLRKLRRQIDINTEVGVIRD 92

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +         + A    ET      D     
Sbjct: 93  IRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKK-----DIRALQERETSEEGWHDLVAKG 146

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +L+  R   E      +     +  P  ++
Sbjct: 147 FIEYIDTEEEETTMISM----------TINDLINARQNPE--EAYSDTYTHCEIHPSLIL 194

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 195 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 234

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 235 DTLAYV-----------------------------------LYYPQKPLV---------- 249

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 250 TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 309

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK +P  +    
Sbjct: 310 KMGTLVKEDFGKPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDE-- 367

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  +         RD S  +    SG V
Sbjct: 368 -------SQGQASRYTRRDHSTSLRHSESGMV 392


>gi|312204346|gb|ADQ47490.1| RNA polymerase II second largest subunit [Odontotrema phacidioides]
          Length = 707

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 108/799 (13%), Positives = 220/799 (27%), Gaps = 115/799 (14%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + +    +              + +  + + +     +            
Sbjct: 1    LFRQLFRKLTKDVYSYLQRCVEGNKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       + ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLSRYTFAATLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L+    +      E    +    + +V  +     + +    ++      +  
Sbjct: 117  ACGLVKNLSLMCYITVGSPSEPIIEFMVQRNMEVLEEYDSTRSPDSTKIFVNGVWVGVHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
            D +     V        I      I D  D   K          P F+ ++D      G 
Sbjct: 177  DPTHLVSTVQSLRRKGMISPEVSLIRDVRDQEFKIFTDAGRVCRPLFVIDNDPKSSNKGG 236

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +  +AV     +   +   M+             K              +  ++ + + 
Sbjct: 237  LVLTKAVVNKLEDDMALPADMDPDEK---------KEKYFGWNGLMGTGAVEFLDAEEEE 287

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +         ++  R  Q       P   +   V+     A    T      ++   +  
Sbjct: 288  TVMIAMTPEDLEISRQVQAGYGMPEPSTDLNARVKAPVSAAQQTWTHCEIHPSMILGICA 347

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N   ++  S                                           
Sbjct: 348  SIIPFPDHNQVCNVYHSGY-RYTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 406

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 407  XXXXXXXMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMGQS 466

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R  +++ +R        +E   +    E + L    Y +L E   I 
Sbjct: 467  SIDRGLF-RSLFFRSYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYEKLDEDGIIA 522

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +  +         
Sbjct: 523  PGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRTTENGIVDRVLL------ 576

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                L+ VKV     +  Q GDK A RHG KG +      EDMP
Sbjct: 577  --------------TTNAEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMP 622

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+++NP  +PSRM +  + E  L       G +                   
Sbjct: 623  FSAEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------- 665

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     ++++ +LR      
Sbjct: 666  ------------------------------------ATP-FTEVTVDSVSRLLREHGYQS 688

Query: 1231 SGQSILYDGLTGEPFDRPV 1249
             G  ++Y+G TG      V
Sbjct: 689  RGFEVMYNGHTGRKLVAQV 707


>gi|1710670|sp|P21421|RPOB_PLAFA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|587604|emb|CAA53232.1| beta subunit RNA polymerase [Plasmodium falciparum]
 gi|1171587|emb|CAA64572.1| rpoB [Plasmodium falciparum]
          Length = 1024

 Score =  238 bits (608), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 114/507 (22%), Positives = 199/507 (39%), Gaps = 69/507 (13%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            I+ VG +VN G IL    +    S  +    LL         +  D  +     +   + 
Sbjct: 573  IVWVGEKVNIGQILAI-NSNLLNSEYSLGNNLLVGYGSYLGYEYEDAIIISRKILYNNLY 631

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKD-----DEQVILDRNIYSRLMEILCGQNA 995
                 N + I  N  +   E   I L           D+  I+    Y     IL  +  
Sbjct: 632  TSLHLNIYEISLNIINNIPEICSINLSKMYYKNIKHLDKYGIIKEGTYILANNILISKLM 691

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    KS +   + +             +++ +   +  +         IL +   N
Sbjct: 692  FMPFIFNNKSLINIINFLFGSKLR-----IFKNKPIISTIHDIGR--VIKIEILPNHLYN 744

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K EK          +    ++++ +++ +Q GDK+  RHG+KGI+S I    D+P+L + 
Sbjct: 745  KTEK--------NNIYLKFRIYIGIQKYLQLGDKICNRHGHKGIISYISEINDIPYLNNK 796

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI ++ + +PSR+N+GQIFE   G   + L  +     N  K   +         K 
Sbjct: 797  IQPDIFISAISIPSRINIGQIFEGIYGLNSLYLNTRYIISNNLNKNYYNNYNHIFNYYKY 856

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                +         + +                                        +  
Sbjct: 857  NYNNNFNINSKMSYNYN----------------------------------------KYY 876

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            L +  TG   +  + +  IY  KL HM+ DK   R  G YS +TQQP+ G + +GGQR G
Sbjct: 877  LKNPFTGNMINNSICLNNIYYYKLIHMIKDKFRYRFIGLYSELTQQPIKGNTKQGGQRFG 936

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV----AGNDTFETGTPESFNVLV 1351
            EMEVW ++A+GA+Y+ +E  T KSDD+  R ++ ++ +       +TF     E+F +++
Sbjct: 937  EMEVWALEAFGASYLFKEFFTYKSDDIKSR-KILKNYLFNNYKIKNTF---ISETFKLIL 992

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIP 1378
            KE+Q+L ++I+        +  +E +P
Sbjct: 993  KELQSLAINIEAFCIFNDTNNLLENLP 1019



 Score =  136 bits (342), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 127/678 (18%), Positives = 273/678 (40%), Gaps = 17/678 (2%)

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            +   +  ++    + F+      L GLY     +  +  +I+I      ++  +    +
Sbjct: 87  NINKIIKFNILIFILPFIYNNIIILNGLYKTCIQLFKKNNKIFIIKFKNNNKNIIYVYIY 146

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             +    I  +  +N + Y  N              + I + +     +     + +   
Sbjct: 147 ISLGLRIIFKISKLNIDCYFNNFKFNFLILLLYLNNIYINKNISLFIYNNIINKKILIYN 206

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                 K+  S    +   + L L      +       +  I   + L     +   I+N
Sbjct: 207 Y----IKFIYSKYNNINNIISLKLFIIKLNKFNNIYINLLNILFSIKLNFSYYSDFYINN 262

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           + N++  S+   + N        ++    + ++           L+N K  ++ + E   
Sbjct: 263 IYNKKFYSI---IDNLLIKSKKYLKIFKYQLLNINRNIYNNITLLLNNKKYINIILENIN 319

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            + L Q  + VN+LS I    +++ +  G  ++     ++R++     G I    T+EG 
Sbjct: 320 INPLVQYSDQVNNLSEINQKFKINMITTGLNSKFILNNDLRELPRNILGYISLINTNEGL 379

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GLV+ LT+   +N        Y+ +   +    +  L+   +    I+  N  L ++ 
Sbjct: 380 TCGLVNYLTTNIFLNLKYLFVIYYKHIFYNRYNFKL-LLNIFNKNFYNISFNNIYLKKNI 438

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           +F +  +         +    + + I      ++S   +LIPF+  +DS R LM   M  
Sbjct: 439 NFNKTTILTINKNTFKICNITQ-NIIYIPFNYLLSFIENLIPFIHYNDSIRNLMSIKMHT 497

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           Q VP++      + T    ++ K     I++ + GIV  V  I+I+IR +          
Sbjct: 498 QIVPIIYPNLSNIITNYNFILNKYLNHLIISYQEGIVIYVSCIKIIIRDLFNRQI----- 552

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             IY L  +++ NQN  +  +P+V VG++V    I+A   +    + +LG N+LV +  +
Sbjct: 553 --IYYLNNYKKINQNILLIYKPIVWVGEKVNIGQILAINSNLLNSEYSLGNNLLVGYGSY 610

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GY +ED+++IS +++  +++TS+H+  +E+        PE  + ++  +  + +K++D+
Sbjct: 611 LGYEYEDAIIISRKILYNNLYTSLHLNIYEISLNIINNIPEICSINLSKMYYKNIKHLDK 670

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEE-KLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            GII  G  +   +IL+ K+              ++  +FG K    ++  +       G
Sbjct: 671 YGIIKEGTYILANNILISKLMFMPFIFNNKSLINIINFLFGSKLRIFKNKPIISTIHDIG 730

Query: 938 TVVDVRIFNRHGIDKNER 955
            V+ + I   H  +K E+
Sbjct: 731 RVIKIEILPNHLYNKTEK 748


>gi|154362093|gb|ABS80885.1| RNA polymerase beta subunit [Comamonas testosteroni]
          Length = 234

 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 142/232 (61%), Positives = 174/232 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+D+ YLSA+EE    IAQAN+ LD +G+
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDDIDYLSAIEEGKYVIAQANADLDAEGN 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              ELV  R AGE  LV  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LVGELVSAREAGESTLVSAERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + AKR GIV+ VDA RIVIR  + +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTAKRGGIVDYVDATRIVIRVNDDE 232


>gi|312204342|gb|ADQ47488.1| RNA polymerase II second largest subunit [Odontotrema diffindens]
          Length = 706

 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 110/795 (13%), Positives = 224/795 (28%), Gaps = 115/795 (14%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + + +  +              + +  + + +     +            
Sbjct: 1    LFRNLFTKLTKDVYKYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +    + +V  +     +      ++      +  
Sbjct: 117  ACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRSPNSTKVFVNGVWVGVHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
            D +     V        I      I D  D   K          P F+ ++DS     G 
Sbjct: 177  DPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDSKSTNKGA 236

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +  + +     +   +   +E            AKR      + A    +  ++ + + 
Sbjct: 237  LVLTKEIVNKLEDDKELPADLEEEE--------RAKRYFGWAGLLAS-GAVEFLDAEEEE 287

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +         +   R  Q       P   +   V+    +A    T      ++   +  
Sbjct: 288  TVMIAMTPEDLDISRQVQAGYAMPEPSTDLNARVKAKVNLAAHTWTHCEIHPSMILGICA 347

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N +                                                 
Sbjct: 348  SIIPFPDHN-QVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 406

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                      +             +       +   +  + AI      +  D+ +   S
Sbjct: 407  XXXXXXXXXXILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 466

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R  +++ +R   +    +E   +    + + L    Y +L +   I 
Sbjct: 467  SIDRGLF-RSLFYRAYVEQEKR---IGISLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIA 522

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +            
Sbjct: 523  PGVRVSGEDIIIGKTAPIAPDDEELGQRTKLHTKRDASTPLRSTESGI------------ 570

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                  ++K+          L+ VKV +   +  Q GDK A RHG KG V      EDMP
Sbjct: 571  ------VDKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMP 622

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   DI++NP  +PSRM +  + E  L       G +                   
Sbjct: 623  FSSEGIVPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------- 665

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     ++++ +LR      
Sbjct: 666  ------------------------------------ATP-FTEVTVDSVSRLLREHGYQS 688

Query: 1231 SGQSILYDGLTGEPF 1245
             G  ++Y+G TG   
Sbjct: 689  RGFEVMYNGHTGRKL 703


>gi|288563351|gb|ADC53593.1| RNA polymerase beta subunit [Pharus latifolius]
          Length = 167

 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 65/151 (43%), Positives = 102/151 (67%), Gaps = 3/151 (1%)

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
             +  G+S ++DG TG+PF++PV +G  Y+LKL H V +K++ RSTG YSLVTQQP+ G++
Sbjct: 16   PEYPGKSRIFDGRTGDPFEQPVLIGKSYILKLIHQVDEKIHGRSTGPYSLVTQQPVRGRA 75

Query: 1288 NRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFET-GTPES 1346
             +GGQR+GEMEVW ++ +G A++LQE+LT KSD ++ R  +  + + G         PES
Sbjct: 76   KQGGQRVGEMEVWALEGFGVAHILQEILTYKSDHLIARQEILSATIFGKRVPNYEDPPES 135

Query: 1347 FNVLVKEMQALGLSID--LENSRTKNSAKME 1375
            F VLV+E+++L L ++  L + +     + E
Sbjct: 136  FRVLVRELRSLALELNHFLVSEKNFRVNREE 166


>gi|88601062|gb|ABD46527.1| RNA polymerase II second largest subunit [Tulasnella pruinosa]
          Length = 656

 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 126/791 (15%), Positives = 233/791 (29%), Gaps = 150/791 (18%)

Query: 474  QYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R+   ++ + +    +              +    +   +     +            
Sbjct: 1    LFRMLFRKLTKDVFRHLQKCVEANKDFTLASAVKHTTITQGLKYSLATGNWGDQKKSMSA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              GLV +L   + ++           + +         L  +EE +   A A + +  +G
Sbjct: 117  ACGLVKNLALMSCISVGSLSAPIIEFLEEWG-------LEPLEEHSLNPASA-TKVFVNG 168

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
             +       R A E +   R      D S +  +             D+ RV     +  
Sbjct: 169  VWMG---VHRDAHELVKTLRRLRRKDDISAEVSIVRDIRERELRLYTDAGRVCRPLFIVE 225

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                L+K +  +          ++SGA      + + E V  +          +  ++  
Sbjct: 226  DQELLIKKKHIY--------KLQNSGADAFGWSSLLNEGVIELLDAEEEETVMICMTSED 277

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
            ++     K +  +       +  VK              PS  LG       +  + +P+
Sbjct: 278  LEASARPKDEFMDDPEFDPAK-RVKAQMNAHTWTHCEIHPSMILG-------ICASIIPF 329

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N          M  + +   I +  +++                             
Sbjct: 330  PDHNQSPRNTYQSAMGKQAMG--IFLTNYQIRMDTMSN---------------------- 365

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
                 +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 366  -----ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 420

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  +D  ++S +   E+ E   RD          +       I  G      
Sbjct: 421  LF-RSMYYRSYMDVEKKSGNQNLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVSGE 479

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     K    T     E+   +++ 
Sbjct: 480  DIIIGKTAPIPPD---------------SEELGQRTQTHSKRDVSTPLKSTENGIIDQVL 524

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                G       L+ VK+ V   R  Q GDK A RHG KG V      EDMPF   G   
Sbjct: 525  ITTNG-----EGLKFVKIRVRSTRIPQVGDKFASRHGQKGTVGITYRQEDMPFTAQGITP 579

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      LG +                           
Sbjct: 580  DIIINPHAIPSRMTIGHLVECLLSKLATLLGNEGD------------------------- 614

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y 
Sbjct: 615  ----------------------------ATP-FTDLTVESVSTLLRAKGYQSRGLEVMYH 645

Query: 1239 GLTGEPFDRPV 1249
            G TG+     V
Sbjct: 646  GHTGKKLQAQV 656


>gi|88976100|gb|ABD59031.1| RNA polymerase II second largest subunit [Bolbitius vitellinus]
          Length = 674

 Score =  238 bits (608), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 119/817 (14%), Positives = 232/817 (28%), Gaps = 169/817 (20%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLSNLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL 60

Query: 518  CSSQ-----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
             +             +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61   ATGNWGDQKKATKAGVSQVLNRYTYASTLSHLRRCNT----PMGRDGKIAKPRQLHNTHW 116

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR- 625
            G +CPAET EG   GLV +L+  A ++           + +         L ++EE    
Sbjct: 117  GMVCPAETPEGQACGLVKNLSLMACISVGHQSGVVVDFLQEWG-------LESLEENAHS 169

Query: 626  -------YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAAS 677
                   ++      +  D S  E+ +      E +      + D  +   +        
Sbjct: 170  NIPCSKVFVNGVWVGVHRDPSNLEKTLLRLRGKEALPSEISIVRDIREREFRIYTDAGRV 229

Query: 678  LIPFLENDDSNRVLM----GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
              P    D  ++ L+       + ++           V  G+  ++          +   
Sbjct: 230  CRPLFVVDKVSQKLLLRKKHVRLLQEGGDNGWKWENLVKEGLIELLDAEE------EEQV 283

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            ++          R  +G+ +   +  D     + +                         
Sbjct: 284  MICMTPEDLETSRLNQGETEAVLATEDFDPAARLKAKTHA---------------HSWTH 328

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   I +  F V    
Sbjct: 329  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNFLVRM-- 377

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 378  -------------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAI 412

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E  +RD   
Sbjct: 413  VAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPSRDTTL 471

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +       I  G           K+  +  D      R++          ++ 
Sbjct: 472  RMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKS 531

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
                +  Q                              + VK+ V   R  Q GDK A R
Sbjct: 532  TESGIVDQVLI--------------------TTNSEGQKFVKIRVRSTRIPQIGDKFASR 571

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  
Sbjct: 572  HGQKGTIGITYRQEDMPFTNEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD 631

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
                                                                 +TP F  
Sbjct: 632  -----------------------------------------------------ATP-FTN 637

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
               EA++++LR       G  I+Y G TG      V 
Sbjct: 638  LTVEAVSAVLRSKGYQSRGLEIMYHGHTGRKLQAQVY 674



 Score =  112 bits (279), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 83/578 (14%), Positives = 156/578 (26%), Gaps = 91/578 (15%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
            T  +  S+    + D  K   + V +V              R          I     L
Sbjct: 52  ITNGLKYSLATGNWGDQKKATKAGVSQVLNRYTYASTLSHLRRCNTPMGRDGKIAKPRQL 111

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
            N    +         +   + + L     + +      + + +    ++S+      N 
Sbjct: 112 HNTHWGMVCPAETPEGQACGLVKNLSLMACISVGHQSGVVVDFLQEWGLESLEENAHSNI 171

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                    F     +    +  N    +   R   AL    ++  R   E      T  
Sbjct: 172 P----CSKVFVNGVWVGVHRDPSNLEKTLLRLRGKEAL-PSEISIVRDIREREFRIYTDA 226

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+C            +       R+   G       K  +      +  L A EEE   
Sbjct: 227 GRVCRPLFVVDKVSQKLLLRKKHVRLLQEGGDNG--WKWENLVKEGLIELLDAEEEEQVM 284

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLI 679
           I      L+       E        +                   +  P  ++ I AS+I
Sbjct: 285 ICMTPEDLETSRLNQGETEAVLATEDFDPAARLKAKTHAHSWTHCEIHPSMILGICASII 344

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 345 PFPDHNQSPRNTYQSAMGKQAMGIFLTNFLV----------------------------- 375

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + +  Y       +     +  R                    
Sbjct: 376 ------------RMDTMANILYYPQKPLATTRSMEYLKFR-------------------- 403

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   
Sbjct: 404 ----ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQL 459

Query: 860 EITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E            +       +++ G+I  G  V   DI++GK  P         ++   
Sbjct: 460 EEFEKPSRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-- 517

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                +    RD S  + S  SG V  V I       K
Sbjct: 518 -----RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 550


>gi|159171910|gb|ABW96214.1| DNA-directed RNA polymerase beta subunit [Peredibacter starrii]
          Length = 345

 Score =  238 bits (607), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 162/346 (46%), Positives = 230/346 (66%), Gaps = 10/346 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A   G V  VD+ RIVI+    +     SGVD+++L+K+QRSNQNT +NQ+ LVK GD 
Sbjct: 3    FAGHDGKVIFVDSNRIVIQRD--NFKEEESGVDVHKLVKYQRSNQNTSINQKALVKEGDR 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V   D+IADGP+T  GDLALG+N+LVAFMPW GYN+EDS+LI+E+++++DVFT+IHIE +
Sbjct: 61   VHAGDVIADGPATQFGDLALGQNILVAFMPWGGYNYEDSILINEKILAQDVFTTIHIENY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA V PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIVKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D  +F R G++ + RS ++  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDAHVFTREGVELDARSKAIIEKETALI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD++ E   + R+   ++ ++L G              +  KK T ++ +++   P   
Sbjct: 241  RRDENIEIKAIQRSAIKKIADMLGGAVTEDKLVSEDGSSELLKKGTKITDEVLYSIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                 ++   ++  +           + +  +   +I K+  GD++
Sbjct: 301  IGYLPLK-ADLEEKLSEYFADIRNRINRVRAKANEEIAKLHKGDEL 345


>gi|307949506|gb|ADN96589.1| RNA polymerase beta subunit [Pseudomonas syringae pv. syringae]
          Length = 243

 Score =  238 bits (607), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 137/243 (56%), Positives = 184/243 (75%)

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
           G E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V +G VT ++
Sbjct: 1   GFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESPYRVVKEGLVTEEI 60

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           V+LSA+E+ +  IAQA++++++     +ELV  R   E  +     +  +D SPKQVVS+
Sbjct: 61  VFLSAIEKADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLMDVSPKQVVSV 120

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+
Sbjct: 121 AASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGV 180

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           ++ VDA RIV+R  + +++   +GVDIY L K+ RSNQNTC+NQRPLV  GD V+R+DI+
Sbjct: 181 IDSVDASRIVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDRVQRSDIM 240

Query: 795 ADG 797
           ADG
Sbjct: 241 ADG 243


>gi|307343456|emb|CBJ18645.1| RNA polymerase B subunit [Micromonospora sp. GUI12]
          Length = 207

 Score =  238 bits (607), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 89/207 (42%), Positives = 118/207 (57%), Gaps = 38/207 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIN---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYM 1256
              G++ L+DG +GEP   P+ VGY+Y+
Sbjct: 181  GSGKAQLFDGRSGEPLPDPIAVGYVYI 207


>gi|52699849|gb|AAU86986.1| DNA-dependent RNA polymerase II second largest subunit [Gyalecta
            hypoleuca]
          Length = 705

 Score =  238 bits (607), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 112/829 (13%), Positives = 230/829 (27%), Gaps = 153/829 (18%)

Query: 466  SVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-- 521
              G ++ + +R+   ++ + + + +               + +  + + +     +    
Sbjct: 1    LAGPLMASLFRMLFNKLTKDVYQYLXKCVESGKEFNLTMGVKSTTLTNGLKYSLATGNWG 60

Query: 522  -----------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                       +SQ+       S ++H RR +      + R     + R +H TH+G +C
Sbjct: 61   DQKKAMSTKAGVSQVLSRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVC 116

Query: 571  PAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEE--NRY 626
            PAET EG   GLV +L     +      E    +    D  V   V  +   E+     +
Sbjct: 117  PAETPEGQACGLVKNLALMCYITVGSPSEPIVDFMISLDMHVLEAVD-IDKDEQNLTKVF 175

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
            +      + ++   T   +     G  I      + D  D   K          P    +
Sbjct: 176  VNGVWVGVHKNPGNTINTITNLRRGNLISSEVSLVRDIRDREFKIFTDAGRVCRPLFVVN 235

Query: 686  -DSNRVLMGCNMQRQAVPLLKAEAPFVGTGM---ESVVAKSSGAAIVAKRAGIVEQVDAI 741
             D +R   G     + +     +   +   M   E        A + ++ A      +  
Sbjct: 236  TDKSRADYGTLRLTKNLINKLEDDRELPADMDADEKKEKYFGWAGLASQGAVEFLDAEEE 295

Query: 742  RI-VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               +I     DL+ S      Y++ + +            + +  + +         PS 
Sbjct: 296  ETVMIAMSPDDLEHSRQLQLXYKVEEPELGPNAR------VKRKMNALTMWTHCEIHPSM 349

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                                      
Sbjct: 350  ILG-------VCASIIPFPDHNQSPR-----------------------------NTXXX 373

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                          +     +  +             +       +   +  + AI    
Sbjct: 374  XXXXXXXXXXXXXFDERMDTMSNILFYPQKPLGTTRAMEYLKFRHLPAGQNAIVAIACYS 433

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   ++ +R        +E   +    E + +  
Sbjct: 434  GYNQEDSVIMNQSSIDRGLF-RSLFYRVYTEQEKRVGI---SLVEQFEKPLRSETLRVKH 489

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   I  G           K+  ++ D      R+++         ++     
Sbjct: 490  GTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEEMGQRTKFHTKRDASTPLRSTENG 549

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +                  ++K+          L+ VKV +   +  Q GDK A RHG K
Sbjct: 550  I------------------VDKVMV--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQK 589

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  +       G +  +   
Sbjct: 590  GTIGITYRQEDMPFTAEGITPDLIINPHAIPSRMTIAHLIECLISKVASLSGCEGDATPF 649

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S                                                   
Sbjct: 650  TDITVDSVSDALRKHGYQSRGFEVM----------------------------------- 674

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                         +G +    G         + +G  Y  +L HMV DK
Sbjct: 675  ------------YNGHT----GR---KLVAQIFLGPTYYQRLRHMVDDK 704



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 92/633 (14%), Positives = 171/633 (27%), Gaps = 106/633 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +  G    F++   + +    +  KY L   G  
Sbjct: 3   GPLMASLFRMLFNKLTKDVYQYLXKCVESG--KEFNLTMGVKSTTLTNGLKYSL-ATGNW 59

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 60  GDQKKAMSTKAGVSQVLSRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 119

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI---------DSVMPQDLINAKPVVSAVCEFFCSS 520
             + Q    +  +       + S            D  + + +   K   +    F    
Sbjct: 120 TPEGQACGLVKNLALMCYITVGSPSEPIVDFMISLDMHVLEAVDIDKDEQNLTKVFVNGV 179

Query: 521 QLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            +   +   N+++ IT+ RR + +  +  + R     E +    T  GR+C        +
Sbjct: 180 WVGVHKNPGNTINTITNLRRGNLISSEVSLVRDIRDREFK--IFTDAGRVCRPLFVVNTD 237

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---------------VVYLSAMEEEN 624
                  T     N    +E       D                     V +L A EEE 
Sbjct: 238 KSRADYGTLRLTKNLINKLEDDRELPADMDADEKKEKYFGWAGLASQGAVEFLDAEEEET 297

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IA +   L+                        K++  +  P   V            
Sbjct: 298 VMIAMSPDDLEHSRQLQLXY---------------KVEEPELGPNARV------------ 330

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
               R +    M                T  E   +   G            Q       
Sbjct: 331 ---KRKMNALTMW---------------THCEIHPSMILGVCASIIPFPDHNQSPRNTXX 372

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                          D     +    +      Q+PL                       
Sbjct: 373 XXXXXXXXXXXXXXFD----ERMDTMSNILFYPQKPL----------GTTRAMEYLKFRH 418

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-- 862
           L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E    
Sbjct: 419 LPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRVYTEQEKRVGISLVEQFEK 478

Query: 863 ---RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               +   V     + +D+ GII  G  V+  DI++GK  P         ++        
Sbjct: 479 PLRSETLRVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEEMGQRT------- 531

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K    RD S  + S  +G V  V +       K
Sbjct: 532 KFHTKRDASTPLRSTENGIVDKVMVTTNAEGLK 564


>gi|40253865|dbj|BAD05800.1| putative DNA-dependent RNA polymerase II [Oryza sativa Japonica
            Group]
          Length = 1136

 Score =  238 bits (607), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 89/429 (20%), Positives = 137/429 (31%), Gaps = 104/429 (24%)

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            K  + +I ++ I  RL      +N   G    KK  V S D+          Q    ++ 
Sbjct: 777  KSYKALIENKEITKRLKH---KENINFGKTPSKKGLVDSLDIDGLPYIGASLQ---SNDI 830

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            +   V      +       E     K+      D           V +   R  + GDK 
Sbjct: 831  IIGKVSDSGEDHSIKLLHTEKGIVEKVVLSATDDGTNSAF-----VTLRQTRSPRIGDKF 885

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A  HG KG++  +   E+ PF   G   DIV+NP G P+R   GQ+ E  LG      G 
Sbjct: 886  ASMHGQKGVIGFLDSQENFPFTHQGIVPDIVINPHGFPTRQTPGQLLEAALGKGIALGGA 945

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               +      +   I+            G                     ++G   ++PV
Sbjct: 946  TRYATPFTSPSVEVITEQLHKAGFSRWGG---------------ESVINGRTGERAASPV 990

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F                                        G  +  +L+HM  DKV  R
Sbjct: 991  FT---------------------------------------GPTFYQRLHHMAEDKVKFR 1011

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--- 1323
            +TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L + SD     V    
Sbjct: 1012 NTGPVHPLTRQPVEDRRRYGGVKFGEMERDCLLAHGAAANLHERLFLLSDVSRLHVCRRC 1071

Query: 1324 -----------------GRTRVYESIVAG---------NDTFETGTPESFNVLVKEMQAL 1357
                             GR       V G          +      P    +L +E+ ++
Sbjct: 1072 QRAAVVVSPAVAADGGGGRK------VRGPYCRFCRSAEEVVRVSVPYGAKILYQELFSM 1125

Query: 1358 GLSIDLENS 1366
            G+ +  +  
Sbjct: 1126 GICLKFDTE 1134



 Score =  113 bits (282), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 116/944 (12%), Positives = 249/944 (26%), Gaps = 215/944 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA------AMLEFV 77
           L+  Q  SY+ F+            GLQ  F S     V P    S        A ++F 
Sbjct: 49  LVSHQINSYNDFVS----------HGLQKMFDSLDEVTVEPDYDPSKKVGPWRHATIKFG 98

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI-KE-QSIYMGDL 135
             E                 Y+      L                KDI KE + + +G L
Sbjct: 99  RVELV---------------YS------LHKSDKAKTGEDPYIQRKDIMKETKWVTIGKL 137

Query: 136 PLMTKD------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
           P+M K                   G F+IKG++++ V++  R           R  ++  
Sbjct: 138 PVMVKSNLCWLHKLQESECEYDFGGYFLIKGMEKVFVAEEQRC--------LSRIWINDS 189

Query: 178 LLYACRIIPDQGLWMDIE------FDSKDIIHVRIDRRRK----------VPVTSFLMAL 221
             +       Q   +  E        S D         RK          +P+     AL
Sbjct: 190 PTWEA---CYQRSQIRREKISIKPVQSNDGF-------RKVINLYFLGATIPIWIMFFAL 239

Query: 222 GMDSE----EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES 276
           G+ S+    +I+        + +             +       +S  +D          
Sbjct: 240 GVSSDKEAFDIIDIQECDASMANIISATITESHEQCEGFQREGRASEYIDKLIRNTKFPP 299

Query: 277 GKKLTSGLLKSLKEK--GVKFLGITSDCLCGLYV-------AEDIVNGETGEIYIEAGDV 327
                  + + +     G +   +    +    +         D  +    +    A ++
Sbjct: 300 KGSFDEYIGRHMFPDVSGNRSKALFLGYMVRCLLLASSGNRKSDNRDDFRNKRLDLACEL 359

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +  +    I H++ R + ++      +            +    + L   +         
Sbjct: 360 LQRELWVHIMHAQKRMVKVMQRHLSGDGDLQPLECYVHASIVT-NGLNRAFSTGSWCHPF 418

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                 S        ++   + +  R             D R+        +  +     
Sbjct: 419 NKRERCSGIVATLRRTNPLQMMSDMRKTRQWVAYAGKAGDARYPNPSYWGKLCFLSTPDG 478

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
              G + ++         +    +      G+ ++                   D +  +
Sbjct: 479 EKCGFVKNLAITAIVSCLAREPSVDALVSCGMKKL-------------------DELLLQ 519

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            +      F   + +    + V  +  +   RR   +      +     +   +      
Sbjct: 520 EISGKDRIFLNGNLVGVCADSVEFVLHLRSMRRRKQIDAQVEIKRDKQNKEVRIFSDPGR 579

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
            + P    E       +      R N             +    N +  +   EEE+   
Sbjct: 580 ILRPLLIVE-------NLRNIMNRKNGS-------YSFQELMDQNIIELIGVEEEEDIRC 625

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     L                              +  P  ++ ++ S+IPF  +D +
Sbjct: 626 AYGIRHLFAGDEEKN---------------FSFYTHCELDPSFLLGLSCSIIPFANHDTA 670

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R+LM      Q         P                                      
Sbjct: 671 KRILMQAEKISQQAIGYSTTNPL------------------------------------- 693

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                  + S    Y      ++    C+ +R      D    +      P    G    
Sbjct: 694 ---FRVDTHSHQLYYPQRPLFKTVAADCLGKR------DYTSGSKHDFARPEYFNG---- 740

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            +N +V+     G+N EDS++++   +   +F + H + ++ +  + ++      ++  N
Sbjct: 741 -QNAIVSISVHQGFNQEDSLVLNRASLERGMFRTQHFKSYKALIENKEITKRLKHKENIN 799

Query: 868 V-----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                  +  + ++D  G+  +GA +   DI++GK++  GE   
Sbjct: 800 FGKTPSKKGLVDSLDIDGLPYIGASLQSNDIIIGKVSDSGEDHS 843


>gi|300394744|gb|ADK11910.1| DNA-directed RNA polymerase II subunit two [Pterula echo]
          Length = 682

 Score =  238 bits (607), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 107/730 (14%), Positives = 222/730 (30%), Gaps = 78/730 (10%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLSNLFRMLFKKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKMMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H +H+G +CPAET EG   GLV +L   + ++   F       + +  + +         
Sbjct: 117  HNSHWGMVCPAETPEGQACGLVKNLALMSCISVGSFSGPVLDFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN +     + +  +G +       R +   +   ++     D S +  +         
Sbjct: 169  EENAHSTTPYTKVFLNGVWIG---VHRDSANLVKTIKKLRRRDDISSEVSIVRDIREKEL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +      +L  E       +E +  K +          ++      
Sbjct: 226  RIYTDAGRVCRPLLIVENQQLMLTKE------HIEWLTNKQTPLGRPFFWEDMM-----K 274

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              +I  ++ + + +         ++  R+  +    Q    +                 D
Sbjct: 275  HGLIELLDAEEEETVMICMSPEDLEESRTKNSRGAIQEAKEEEEGMTEEEKKKKKEEDFD 334

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                A           W       SM+  I   ++            ++       +G  
Sbjct: 335  ---PAARLKAAANQSTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVF 391

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I               +  +             +       +   +  + AI   
Sbjct: 392  LTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCY 440

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    ++ R  +D  ++S   + E+ E  +R+         
Sbjct: 441  SGYNQEDSVIMNQSSIDRGLF-RSLYYRSYMDLEKKSGVQQLEEFEKPSRENTLRMKHGT 499

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G N +       K+  +  D      R++          ++   + + 
Sbjct: 500  YDKLEDDGLIAPGTNVLGEDIIIGKTAPIPPDSEELGQRTRSHTRRDVSTPLKSTEKGIV 559

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q GDK A RHG KG 
Sbjct: 560  DQVLI--------------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGT 599

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF  DG   DI++NP  +PSRM +G + E  L      +G++  +     
Sbjct: 600  IGITYRQEDMPFTADGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGQEGDATPFSD 659

Query: 1160 KANGDISPLR 1169
                ++S   
Sbjct: 660  LTVEEVSKTL 669



 Score =  115 bits (288), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 88/638 (13%), Positives = 176/638 (27%), Gaps = 117/638 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 12  GPLLSNLFRMLFKKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++        + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKMMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNSHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMSCISVGSFSGPVLDFLEEWGLESLEENAHSTTPYTKVFLNGVWI 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 189 GVHRDSANLVKTIKKLRRRDDISSEVSIVRDIREKELRIYTDAGRVCRPLLIVENQQLML 248

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG---- 638
                 +   N    +  P+    D      +  L A EEE   I  +   L+E      
Sbjct: 249 TKEHIEWL-TNKQTPLGRPFF-WEDMMKHGLIELLDAEEEETVMICMSPEDLEESRTKNS 306

Query: 639 ------------SFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLI 679
                         TEE    +   +     R             +  P  ++ I AS+I
Sbjct: 307 RGAIQEAKEEEEGMTEEEKKKKKEEDFDPAARLKAAANQSTWTHCEIHPSMILGICASII 366

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                                    
Sbjct: 367 PFPDHNQSPRNTYQSAMGKQAMGVFLTNFLI----------------------------- 397

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                          + + +  Y       +     +  R                    
Sbjct: 398 ------------RMDTMANILYYPQKPLATTRSMEYLKFR-------------------- 425

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA + + GYN EDS+++++  +   +F S++   +  + + + +   
Sbjct: 426 ----ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLYYRSYMDLEKKSGVQQL 481

Query: 860 EIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E        +   +       +++ G+I  G  V   DI++GK  P         ++   
Sbjct: 482 EEFEKPSRENTLRMKHGTYDKLEDDGLIAPGTNVLGEDIIIGKTAPIPPDSEELGQRT-- 539

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                ++   RD S  + S   G V  V I       K
Sbjct: 540 -----RSHTRRDVSTPLKSTEKGIVDQVLITTNSEGQK 572


>gi|300394760|gb|ADK11918.1| DNA-directed RNA polymerase II subunit two [Tapinella atrotomentosa]
          Length = 653

 Score =  238 bits (606), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 112/728 (15%), Positives = 222/728 (30%), Gaps = 91/728 (12%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L N +R+   ++ R +    +              +  + + + +  
Sbjct: 1    HFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             TH+G +CPAET EG   GLV +L   A ++   +       + +  + +         E
Sbjct: 117  NTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------E 168

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            EN + +   + +  +G +       R     +   ++     D SP+  V          
Sbjct: 169  ENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELR 225

Query: 683  ENDDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               D+ RV     +   Q + L K    ++  G  +   +      + K   I    DA 
Sbjct: 226  LYTDAGRVCRPLFIVENQQLALKKKHVKWLSRGYRNDETEEYKWEHLVKGGIIELL-DAE 284

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +    +   +       +    ++ +     R  +K              PS  
Sbjct: 285  EEETVMISMTPEDLENSRLQQAGVDPHANDGDFDPAAR--LKASTNAHTWTHCEIHPSMI 342

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 343  LG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLT 377

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 378  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 426

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +
Sbjct: 427  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYD 485

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  D      R++          ++     +  Q
Sbjct: 486  KLEDDGLIAPGTGVTGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ 545

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                  ++   F+                 + VK+ V   R  Q GDK A RHG KG + 
Sbjct: 546  -----VLISTNFE---------------GQKFVKIRVRSTRIPQIGDKFASRHGQKGTIG 585

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +       
Sbjct: 586  ITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTELT 645

Query: 1162 NGDISPLR 1169
               +S   
Sbjct: 646  VEAVSAFL 653



 Score =  122 bits (305), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 84/622 (13%), Positives = 169/622 (27%), Gaps = 100/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 11  GPLLANLFRMLFRKLTRDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 67

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 68  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 127

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 128 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 187

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 188 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 247

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +         ET   K         +  L A EEE   I+     L+       
Sbjct: 248 KKKHVKWLSRGYRND-ETEEYKWEHLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQA 306

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      G+     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 307 GVDPHANDGDFDPAARLKASTNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 366

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 367 MGKQAMGIFLTNFLI-----------------------------------------RMDT 385

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 386 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 421

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +  
Sbjct: 422 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKH 481

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 482 GTYDKLEDDGLIAPGTGVTGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 534

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  +G V  V I       K
Sbjct: 535 LKSTENGIVDQVLISTNFEGQK 556


>gi|103001753|gb|ABF71520.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            chlorophanum]
          Length = 699

 Score =  238 bits (606), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 112/820 (13%), Positives = 218/820 (26%), Gaps = 145/820 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L N +R+   ++ + + +  +              + +  + + +     +        
Sbjct: 1    LLANLFRMLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKST 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               N+   ++ +  L+ +               S     AK  G    V     V+  V+
Sbjct: 237  NCGNLVLTKEHINKLEDDKDLPA-------IMDSEE-KEAKFFGWDGLV--NNGVVEYVD 286

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
             + + +   V     ++  R  Q               V+          T      ++ 
Sbjct: 287  AEEEETVMIVMTPEDLEISRQIQAGYAMPETSDDPNKRVKAPMNPTAHTWTHCEIHPSMI 346

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +    +P+  +N          M                                   
Sbjct: 347  LGICAXIIPFPDHNQSPRNTYQSAMGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXT--- 403

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                                         +       +   +  + AI      +  D+ 
Sbjct: 404  --------------------------TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 437

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 438  IMNQSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDD 493

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 494  DGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL- 552

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     L+ VKV +   +  Q GDK A RHG KG +     
Sbjct: 553  -------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 593

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          +
Sbjct: 594  QEDMPFTMEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSV 653

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S L    E    +                                               
Sbjct: 654  SKLLR--EHGYQSRGFEVM----------------------------------------- 670

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                 +G +    G         V +G  Y  +L HM  D
Sbjct: 671  ----YNGHT----GR---KLVAQVFLGPTYYQRLRHMXDD 699


>gi|56553332|gb|AAV97828.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  238 bits (606), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 75/172 (43%), Positives = 106/172 (61%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D        AD + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFDKVNVRIDKDKLMME-VVADRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+   A 
Sbjct: 119 VETGRRISARHTRALEKAGLNELEVPADYLIGRVYAATYVNEDTGEVIASAN 170


>gi|170579233|ref|XP_001894738.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Brugia malayi]
 gi|158598542|gb|EDP36414.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Brugia malayi]
          Length = 1104

 Score =  238 bits (606), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 70/279 (25%), Positives = 107/279 (38%), Gaps = 80/279 (28%)

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF   G   D+++NP G PSRM V        G     L  K   L   +       
Sbjct: 885  EDMPFNDLGMCPDMIMNPHGYPSRMTV--------GKLMELLSGKNAVLSGKFHYGT--- 933

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
                                                        F G   + +   L   
Sbjct: 934  -------------------------------------------AFGGDQVDIVCEELAAR 950

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
              +  G+ +L  G+TG+     +  G IY  KL HMV DK++AR+ G  +++T+QP  G+
Sbjct: 951  GFNYLGKDMLTSGITGQQLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1010

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG--------------RTRV 1328
            +  GG RLGEME  C+ AYGA+ +L E L + SD    DV                R+  
Sbjct: 1011 ARDGGLRLGEMERDCLIAYGASMLLMERLMVSSDEFKVDVCSQCGLIGYKSWCQMCRSSR 1070

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              + +          P +  +L +E+Q++ +   +  S+
Sbjct: 1071 TMATIK--------IPYACKLLFQELQSMNIVPKISLSK 1101



 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 129/962 (13%), Positives = 287/962 (29%), Gaps = 184/962 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++   ASYD+F+   I    R N+ +          +  + +  L+++      P    
Sbjct: 28  LVKQHIASYDYFVSTEIKKILRANDKIT---------SDANPSFYLKYLDIHVGMPSSEE 78

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  RD+TY+ P+ + +             +  + +    + +G +P+
Sbjct: 79  GFNQINDKISPHECRLRDMTYSAPISVDIEYT----------RGSQRVLRNGLIIGKMPV 128

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F+I+G +++V+ Q   S       ++    
Sbjct: 129 MLRSSKCVLKNMNESELARVQECPYDPGGYFIIRGSEKVVLIQEQLS------KNRIMIG 182

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EI 228
            + K    C I+     +          K   +VR ++    VP+     A+G +S+ +I
Sbjct: 183 RNSKKELQCEILSSTQERKSK-TYIASKKQRYYVRHNQLSDDVPIAIIFKAMGFESDHDI 241

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +S    +  +            A+  +V  + +   +      +        TS L +  
Sbjct: 242 VSAVGLEEKFVAAMAP-SIEECASHQIVTQEGALQYIASKVKIRKFGPATSGTSTLPREH 300

Query: 289 KEKG------VKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL-EEIFHSEI 341
           +         +  +      +    V   ++     +  +   +  D      +      
Sbjct: 301 EAIDFLSNLMIAHVPCPDGNMKMKAVYLGLMVRRLMQAEVGDTECDDRDFYGNKRLELAG 360

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
             + +L+ D           +  +       A LDI + +R  D+ T ++ +++    + 
Sbjct: 361 SLLALLFEDVFKRFNSELKRIADNSLGKTLAAPLDIVKHVRQ-DLITNALVDALATGNWT 419

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNL 459
              ++ +   G  ++  RL+  +   +            K+     L+  +  +    + 
Sbjct: 420 I-KRFKMERQGVTQVLSRLSYISVLGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDT 478

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                  + + L     +     E+ +   + +  ++ V              +  F   
Sbjct: 479 PEGESCGLVKNLALLSHITTDSDEKPVIRLLYNAGVEDVKSLHFSAIHNPAYHIV-FLNG 537

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGH 578
             +    +    +S I   RR   L +            R V+  +  GR+C        
Sbjct: 538 VIVGLTIDPQRIVSTIRAVRRHGLLNE--FVSVSTNAAQRSVYIASDGGRLC------RP 589

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            I + +S+    +      ++  YR   D      + YL   E  +  IA   + +    
Sbjct: 590 YIIVKNSIPQVTQ-EHIEELKKGYRIFEDFVDDGLIEYLDVNEMNDASIAVYENQIKP-- 646

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                    ++  P  ++ + A LIP+  ++ S R    C M +
Sbjct: 647 ---------------------TTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 685

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+  +         G        S                                   
Sbjct: 686 QAMGTI---------GYNQQKRIDS----------------------------------- 701

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              QRPLVK                 +   L  G+N ++A M +
Sbjct: 702 -----------LMYLLVYPQRPLVK----------TKTIEFCNFEKLPAGQNAIIAVMSY 740

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI-----PNVSEEGL 873
            GY+ ED++++++  +       +  +  +  AR       +                  
Sbjct: 741 SGYDIEDALVLNKASLDRGYGRCLVYKHAKATARKYPNQTFDRLMGPTIEAATRKPIYKH 800

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRV 931
           + +D+ GI+ VGA +    +++ K  P                 I G   V+ +D S+  
Sbjct: 801 QVLDQEGIVYVGACIRSKQVMINKHMPVVSMEAGATVSNNDGTNIGGSHEVEYKDVSVVY 860

Query: 932 PS 933
            +
Sbjct: 861 RN 862


>gi|154362103|gb|ABS80890.1| RNA polymerase beta subunit [Comamonas kerstersii]
          Length = 234

 Score =  238 bits (606), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 138/230 (60%), Positives = 171/230 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD +G 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTHEIDYLSAIEEGKYVIAQANAELDAEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              ELV  R  GE  L+  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LVGELVSAREKGESTLLSPERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
           AVP+L+ E P VGTG+E V A  SG  + A+R GIV+ VDA RIVIR  +
Sbjct: 181 AVPVLRPEKPVVGTGIERVAAVDSGTVVTARRGGIVDYVDATRIVIRVND 230


>gi|45120580|gb|AAO64681.2| RNA polymerase II subunit RPB2 [Stereum hirsutum]
          Length = 801

 Score =  238 bits (606), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 118/761 (15%), Positives = 231/761 (30%), Gaps = 93/761 (12%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         +I  L+     +  +DD D+ G +R+
Sbjct: 118  RYAQEILQKEMLPHISMSEGSESKK---AYFFGYMIHRLLLAGMERRELDDRDHFGKKRL 174

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ R +    +              +    + + +     +   
Sbjct: 175  DLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKDFNLNLAVKHNTITNGLKYSLATGNW 234

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 235  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMV 290

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L+  A ++           + +  + +         EEN + A 
Sbjct: 291  CPAETPEGQACGLVKNLSLMATISVGSLSLPVIDFLEEWGLESL--------EENAHSAT 342

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     I   ++     D  P+  +             D+ R
Sbjct: 343  PTTKVFVNGVWMG---VHRDPANLIKTIKKLRRKDDIHPEVSIVRDIRERELRLYTDAGR 399

Query: 690  VLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            V     +   Q + + K     +  G +    +     +   ++G+VE +DA       +
Sbjct: 400  VCRPLFVVEDQXLAVTKKHINMLTRGTDDNGEEFKWNNL--IKSGVVEYLDAEEEETVMI 457

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +   +       +     + +     R     G            PS  LG     
Sbjct: 458  CMTPEDLENSRLQSSGINPHAEDSDFDPAARLKASSGLNTHTWTHCEIHPSMILG----- 512

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G       +   
Sbjct: 513  --ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYXTNFLVRM- 551

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 552  ----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 601

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    I+ R  +D  ++S   + E+ E   RD          +       
Sbjct: 602  IMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGL 660

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  +  D      R++          ++     +  Q       
Sbjct: 661  IAPGTGVNGEDIIIGKTAPIPPDSEELGQRTRIHTRRDVSTPLKSTESGIVDQVLI---- 716

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   + VKV V   R  Q GDK A RHG KG +      ED
Sbjct: 717  ----------------TTNHEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGITYRQED 760

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            MPF  +G   DIV+NP  +PSRM +G + E  L      +G
Sbjct: 761  MPFTAEGITPDIVINPHAIPSRMTIGHLVECLLSKVATLIG 801



 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 102/773 (13%), Positives = 224/773 (28%), Gaps = 114/773 (14%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++++D    +P+     ALG+ S+ +IL      +  +Q  +     +    ++   +++
Sbjct: 43  YIKVD----IPIWVVFRALGVISDRDILEHICYDMEDAQMLEMLKPCIDDGFVIQDREIA 98

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              +    G     S ++      + L+++ +  + ++           G  +   ++ G
Sbjct: 99  LDFIGNR-GTTTGLSRERRLRYAQEILQKEMLPHISMSEGSESKKAYFFGYMIHRLLLAG 157

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALL 375
                  +      ++              +    + +   Y++  + T K+ +   A+ 
Sbjct: 158 MERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKDFNLNLAVK 217

Query: 376 DIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRK 433
                       T  +  S+    + D  K   S  G  ++  R    +      R    
Sbjct: 218 HNT--------ITNGLKYSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTP 269

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                 I     L N    +         +   + + L     + +  +   + + +   
Sbjct: 270 LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMATISVGSLSLPVIDFLEEW 329

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            ++S+      NA         F     +    +  N +  I   RR   +         
Sbjct: 330 GLESL----EENAHSATPTTKVFVNGVWMGVHRDPANLIKTIKKLRRKDDIHPEVSIVRD 385

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
                  ++        P    E   + +     +          E    K  +   +  
Sbjct: 386 IRERELRLYTDAGRVCRPLFVVEDQXLAVTKKHINMLTRGTDDNGEE--FKWNNLIKSGV 443

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR---------EKIDFI 664
           V YL A EEE   I      L+     +  +       +     R               
Sbjct: 444 VEYLDAEEEETVMICMTPEDLENSRLQSSGINPHAEDSDFDPAARLKASSGLNTHTWTHC 503

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ I AS+IPF +++ S R      M +QA+ +                     
Sbjct: 504 EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYXTNFLV-------------- 549

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         + + +  Y       +     +  R     
Sbjct: 550 ---------------------------RMDTMANILYYPQKPLATTRSMEYLKFR----- 577

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                              +L  G+N +VA + + GYN EDS+++++  +   +F SI+ 
Sbjct: 578 -------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYY 618

Query: 845 EEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +  + + + +   E            +       +++ G+I  G  VN  DI++GK  
Sbjct: 619 RSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTA 678

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           P         ++        +    RD S  + S  SG V  V I   H   K
Sbjct: 679 PIPPDSEELGQRT-------RIHTRRDVSTPLKSTESGIVDQVLITTNHEGQK 724


>gi|56553334|gb|AAV97829.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553336|gb|AAV97830.1| RNA polymerase B subunit [Alteromonas macleodii ATCC 27126]
 gi|56553338|gb|AAV97831.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553340|gb|AAV97832.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|170671553|gb|ACB29614.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  238 bits (606), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 107/172 (62%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFDKVSVRIDKDKLMMEVVP-DRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKAGLTELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|125602346|gb|EAZ41671.1| hypothetical protein OsJ_26208 [Oryza sativa Japonica Group]
          Length = 1257

 Score =  238 bits (606), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 89/429 (20%), Positives = 137/429 (31%), Gaps = 104/429 (24%)

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            K  + +I ++ I  RL      +N   G    KK  V S D+          Q    ++ 
Sbjct: 898  KSYKALIENKEITKRLKH---KENINFGKTPSKKGLVDSLDIDGLPYIGASLQ---SNDI 951

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
            +   V      +       E     K+      D           V +   R  + GDK 
Sbjct: 952  IIGKVSDSGEDHSIKLLHTEKGIVEKVVLSATDDGTNSAF-----VTLRQTRSPRIGDKF 1006

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A  HG KG++  +   E+ PF   G   DIV+NP G P+R   GQ+ E  LG      G 
Sbjct: 1007 ASMHGQKGVIGFLDSQENFPFTHQGIVPDIVINPHGFPTRQTPGQLLEAALGKGIALGGA 1066

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
               +      +   I+            G                     ++G   ++PV
Sbjct: 1067 TRYATPFTSPSVEVITEQLHKAGFSRWGG---------------ESVINGRTGERAASPV 1111

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F                                        G  +  +L+HM  DKV  R
Sbjct: 1112 FT---------------------------------------GPTFYQRLHHMAEDKVKFR 1132

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV--- 1323
            +TG    +T+QP+  +   GG + GEME  C+ A+GAA  L E L + SD     V    
Sbjct: 1133 NTGPVHPLTRQPVEDRRRYGGVKFGEMERDCLLAHGAAANLHERLFLLSDVSRLHVCRRC 1192

Query: 1324 -----------------GRTRVYESIVAG---------NDTFETGTPESFNVLVKEMQAL 1357
                             GR       V G          +      P    +L +E+ ++
Sbjct: 1193 QRAAVVVSPAVAADGGGGRK------VRGPYCRFCRSAEEVVRVSVPYGAKILYQELFSM 1246

Query: 1358 GLSIDLENS 1366
            G+ +  +  
Sbjct: 1247 GICLKFDTE 1255



 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 122/953 (12%), Positives = 269/953 (28%), Gaps = 203/953 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA------AMLEFV 77
           L+  Q  SY+ F+            GLQ  F S     V P    S        A ++F 
Sbjct: 140 LVSHQINSYNDFVS----------HGLQKMFDSLDEVTVEPDYDPSKKVGPWRHATIKFG 189

Query: 78  SYEFDPPKFDVDDC--------------LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
             E + P F VD+C                + +TY+  +K+ + + V+ + +   AK+ +
Sbjct: 190 RVELEEPVFWVDNCDLDVETLKLKPKHARLQKMTYSSKMKVEMTVQVYSLHKSDKAKTGE 249

Query: 124 D--------IKE-QSIYMGDLPLMTK------DGTFVIKGIQRIVVSQLHRSPGIHFDHD 168
           D        +KE + + +G LP+M         G F+IKG++++ V++  R         
Sbjct: 250 DPYIQRKDIMKETKWVTIGKLPVMESECEYDFGGYFLIKGMEKVFVAEEQRC-------- 301

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIE------FDSKDIIHVRIDRRRK----------V 212
             R  ++    +       Q   +  E        S D         RK          +
Sbjct: 302 LSRIWINDSPTWEA---CYQRSQIRREKISIKPVQSNDGF-------RKVINLYFLGATI 351

Query: 213 PVTSFLMALGMDSE----EILSTF-YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           P+     ALG+ S+    +I+        + +             +       +S  +D 
Sbjct: 352 PIWIMFFALGVSSDKEAFDIIDIQECDASMANIISATITESHEQCEGFQREGRASEYIDK 411

Query: 268 DTGEQVIESGKKLTSGLLKSLKEK--GVKFLGITSDCLCGLYV-------AEDIVNGETG 318
                           + + +     G +   +    +    +         D  +    
Sbjct: 412 LIRNTKFPPKGSFDEYIGRHMFPDVSGNRSKALFLGYMVRCLLLASSGNRKSDNRDDFRN 471

Query: 319 EIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY 378
           +    A +++  +    I H++ R + ++      +            +    + L   +
Sbjct: 472 KRLDLACELLQRELWVHIMHAQKRMVKVMQRHLSGDGDLQPLECYVHASIVT-NGLNRAF 530

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
                          S        ++   + +  R             D R+        
Sbjct: 531 STGSWCHPFNKRERCSGIVATLRRTNPLQMMSDMRKTRQWVAYAGKAGDARYPNPSYWGK 590

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           +  +        G + ++         +    +      G+ ++                
Sbjct: 591 LCFLSTPDGEKCGFVKNLAITAIVSCLAREPSVDALVSCGMKKL---------------- 634

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
              D +  + +      F   + +    + V  +  +   RR   +      +     + 
Sbjct: 635 ---DELLLQEISGKDRIFLNGNLVGVCADSVEFVLHLRSMRRRKQIDAQVEIKRDKQNKE 691

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             +       + P    E       +      R N             +    N +  + 
Sbjct: 692 VRIFSDPGRILRPLLIVE-------NLRNIMNRKNGS-------YSFQELMDQNIIELIG 737

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EEE+   A     L                              +  P  ++ ++ S+
Sbjct: 738 VEEEEDIRCAYGIRHLFAGDEEKN---------------FSFYTHCELDPSFLLGLSCSI 782

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF  +D + R+LM      Q         P                             
Sbjct: 783 IPFANHDTAKRILMQAEKISQQAIGYSTTNPL---------------------------- 814

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + S    Y      ++    C+ +R      D    +      P
Sbjct: 815 ------------FRVDTHSHQLYYPQRPLFKTVAADCLGKR------DYTSGSKHDFARP 856

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
               G     +N +V+     G+N EDS++++   +   +F + H + ++ +  + ++  
Sbjct: 857 EYFNG-----QNAIVSISVHQGFNQEDSLVLNRASLERGMFRTQHFKSYKALIENKEITK 911

Query: 859 EEITRDIPNV-----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
               ++  N       +  + ++D  G+  +GA +   DI++GK++  GE   
Sbjct: 912 RLKHKENINFGKTPSKKGLVDSLDIDGLPYIGASLQSNDIIIGKVSDSGEDHS 964


>gi|153958254|gb|ABS53417.1| RpoB [Bacteriovorax sp. MIA2]
          Length = 353

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 167/355 (47%), Positives = 235/355 (66%), Gaps = 10/355 (2%)

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E +VAK SG  + A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC
Sbjct: 2    EKIVAKDSGVILFAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTC 59

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             NQ+ LVK GD V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE +++
Sbjct: 60   NNQKALVKEGDIVKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLA 119

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +DVFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILV
Sbjct: 120  QDVFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILV 179

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   R
Sbjct: 180  GKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSR 239

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVL 1008
            S  +  ++  L+ RD+  E   +  +   R+ ++L G              +   K T +
Sbjct: 240  SKDIIEQETTLIRRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEV 299

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            +S++++  P        ++   ++  +           S +  +  ++I K+  G
Sbjct: 300  TSEVLAGVPFELIGYLPLE-AALEERLSEYFADIRNRISRVRQKATDEIAKLHRG 353


>gi|86559353|gb|ABD04084.1| RNA polymerase II second largest subunit [Cantharellus cibarius]
          Length = 649

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 114/721 (15%), Positives = 206/721 (28%), Gaps = 91/721 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + +   +               +    + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLASLFRXLFRKLTKDVYRHLQKCVETHKEFTIGQAVKPSTITN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                   +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GXKYSLATGNWGDQKKAMSSKAGVSQVLNRXTFASTLSHLRRCNT----PLGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            R +H TH+G +CPAET EG   GLV +L+  A ++  G I  P  +         +   S
Sbjct: 117  RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACIS-VGSISAPVIEFLQEWGLESLEENS 175

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
            A    N      N            LV                   D S +  +      
Sbjct: 176  AH--GNATKVFVNGVWLGVHRDAPNLVKTLRRLRRKD---------DISSEVSIVRDIRE 224

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
                   D+ RV     +      +LK E         +         +   R G++E +
Sbjct: 225  RELRLYTDAGRVCRPLFIVEDQQLMLKKEHINKLNDRNATQPYKWSDLV---RDGVIELL 281

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            DA       +    D   +         +  +   +  +    ++              P
Sbjct: 282  DAEEEETVMICMTPDDLENSRTNAATAGYVSNVGASDHDVAARIRSTMTAHTWTHCEIHP 341

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N       S R   +       +  +    +      
Sbjct: 342  SMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVRM--- 385

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +             +       +   +    AI  
Sbjct: 386  --------------------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILC 425

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    ++ R   D  +++  +  E+ E   RD        
Sbjct: 426  YSGYNQEDSVIMNQSSIDRGLF-RSMYYRSYTDTEKKAGLLTLEEFEKPTRDTTLRMKHG 484

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      I  G   V       K+  L  D      R +          ++     +
Sbjct: 485  TYEKLEDDGLIAPGTGVVGEDIIIGKTAPLPPDSEELGQRLRTHTRRDVSTPLKSTENGI 544

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                             L+ VK+ +   R  Q GDK A RHG KG
Sbjct: 545  VDQVLI--------------------TTNAEGLKFVKIRIRATRVPQVGDKFASRHGQKG 584

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             V      EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +    
Sbjct: 585  TVGITYRHEDMPFTAEGITPDLVINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFT 644

Query: 1159 Y 1159
             
Sbjct: 645  E 645



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 84/585 (14%), Positives = 163/585 (27%), Gaps = 103/585 (17%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T     S+    + D  K   S  G  ++  R    +      R          I    
Sbjct: 58  ITNGXKYSLATGNWGDQKKAMSSKAGVSQVLNRXTFASTLSHLRRCNTPLGRDGKIAKPR 117

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +   + + L     + +  +   + E +    ++S+      
Sbjct: 118 QLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSISAPVIEFLQEWGLESLEENSAH 177

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
                 +A   F     L    +  N +  +   RR   +                ++  
Sbjct: 178 -----GNATKVFVNGVWLGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIRERELRLYTD 232

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
                 P    E   + L     +  ++N     +    K  D      +  L A EEE 
Sbjct: 233 AGRVCRPLFIVEDQQLMLKKEHIN--KLNDRNATQP--YKWSDLVRDGVIELLDAEEEET 288

Query: 625 RYIAQ------------ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
             I              A +    +   ++  V  R       +        +  P  ++
Sbjct: 289 VMICMTPDDLENSRTNAATAGYVSNVGASDHDVAARIR---STMTAHTWTHCEIHPSMIL 345

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            I AS+IPF +++ S R      M +QA+ +                             
Sbjct: 346 GICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFQV---------------------- 383

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
                                 + + +  Y       +     +  R             
Sbjct: 384 -------------------RMDTMANILYYPQKPLATTRSMEYLRFR------------- 411

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                      +L  G+N  VA + + GYN EDS+++++  +   +F S++   +    +
Sbjct: 412 -----------ELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYTDTEK 460

Query: 853 DTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
               L  EE  +        +     + +++ G+I  G  V   DI++GK  P       
Sbjct: 461 KAGLLTLEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGVVGEDIIIGKTAPLPPDSEE 520

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++L       +    RD S  + S  +G V  V I       K
Sbjct: 521 LGQRL-------RTHTRRDVSTPLKSTENGIVDQVLITTNAEGLK 558


>gi|209943910|gb|ACI96263.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
          Length = 266

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 150/266 (56%), Positives = 193/266 (72%), Gaps = 3/266 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+PFVGTGM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGM 180

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E V A+ SGAA+++K  G VE V +  I++R  VE +       +D Y L KF+RSN  T
Sbjct: 181 EHVAARDSGAAVISKYRGRVEHVQSSEILVRRLVEENGQEVDGTLDRYPLAKFKRSNSGT 240

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPST 800
           C NQRP++  GD V + +I+ADGPS 
Sbjct: 241 CYNQRPIIAKGDIVEKGEILADGPSM 266


>gi|154362101|gb|ABS80889.1| RNA polymerase beta subunit [Comamonas testosteroni]
          Length = 234

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 142/232 (61%), Positives = 173/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+D+ YLSA+EE    IAQAN+ LD  G+
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDDIDYLSAIEEGKYVIAQANADLDAAGN 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              ELV  R AGE  LV  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LVGELVSAREAGESTLVSAERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + AKR GIV+ VDA RIVIR  + +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTAKRGGIVDYVDATRIVIRVNDDE 232


>gi|56553344|gb|AAV97834.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|170671543|gb|ACB29609.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|170671545|gb|ACB29610.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|170671547|gb|ACB29611.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 106/172 (61%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G      ++D + G  V
Sbjct: 61  ATIILRALEMSSEEILDTFFDKVSVRIDKDKLMMEVVP-DRLRGETAQFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKAGLTELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|30141058|gb|AAP21840.1| RNA polymerase beta subunit [Streptococcus oralis ATCC 35037]
          Length = 231

 Score =  237 bits (605), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 99/295 (33%), Positives = 135/295 (45%), Gaps = 72/295 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARTLGIHIATPVFDGASSEDLW-------------------------------------- 192

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   D   E         A +D   ++ILYDG TGEPFD  V+VG +YM+KL
Sbjct: 193  -------DTVKE---------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIKL 231



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGADGVVRDVKIFTRANGD 90


>gi|307343454|emb|CBJ18644.1| RNA polymerase B subunit [Micromonospora sp. GUI8]
          Length = 207

 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 91/207 (43%), Positives = 120/207 (57%), Gaps = 38/207 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYIYM 1256
              G++ L+DG +GEP   P+ VGY+Y+
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVGYVYI 207


>gi|3133329|gb|AAC38465.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYREVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE+G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDENGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAXD 231


>gi|170671549|gb|ACB29612.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 75/172 (43%), Positives = 107/172 (62%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D        AD + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFDKVNVRIDKDKLMME-VVADRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKAGLNELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|56553312|gb|AAV97818.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553314|gb|AAV97819.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553316|gb|AAV97820.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553320|gb|AAV97822.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553322|gb|AAV97823.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553324|gb|AAV97824.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553326|gb|AAV97825.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553328|gb|AAV97826.1| RNA polymerase B subunit [Alteromonas macleodii]
 gi|56553330|gb|AAV97827.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 107/172 (62%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFDKVNVRIDKDKLMMEVVP-DRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKAGLNELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|89090016|gb|AAO64654.3| RNA polymerase II subunit RPB2 [Dacrymyces chrysospermus]
          Length = 870

 Score =  237 bits (605), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 140/1012 (13%), Positives = 271/1012 (26%), Gaps = 182/1012 (17%)

Query: 274  IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            +E G K  S L   +  + ++    ++  L    +     +     ++   G V D   L
Sbjct: 19   VEKGGKQISLLQIKMTHRNLEK---STGSLMRAQLPYIRNDIPIVVVFRALGIVPDRDVL 75

Query: 334  EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAE 393
            E I +       +  +      A++         +DR+ AL  I R              
Sbjct: 76   EHICYDPDDHAMLEMLKPCIEEAFV--------IQDREVALDYIGRR------------G 115

Query: 394  SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI 453
            +          +Y    + +  +      +  +  +         ++  LV     +  +
Sbjct: 116  TTTGLSREKRLRYAQEILQKEMLPHISTQEGAESKK---AYFFGYMVHRLVLAALDRREL 172

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   R+ + +    +              +    + +
Sbjct: 173  DDRDHFGKKRLDLAGPLLATLFRMLFRRLTKDVYRYMQKCVETHREFNINAAVKPATITN 232

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R       
Sbjct: 233  GLKYSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIARP 288

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK----VTNDV 614
            R +H  H+G +       G   GLV +L   A ++     +     + +           
Sbjct: 289  RQLHNHHWGMVXXXXXXXGQACGLVKNLALMACISVGTLSQPVVEFLEEWGLEPLGERTD 348

Query: 615  VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVS 673
              L+A      ++      +  D       V      + I      + D  +   +    
Sbjct: 349  EPLTAT---KVFVNGVWMGIHRDPQHLVNTVRTLRRSDGISSEISVVRDIRERELRLYTD 405

Query: 674  IAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKA-EAPFVGTGMESVVAKSSGAAIVAKR 731
                  P F+ N+ +  +++            K  E   V          +SG       
Sbjct: 406  AGRVCRPLFIVNEQTQNLVISKREINWLHAREKPGEKDKVYG---WSQLVTSGMV----- 457

Query: 732  AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                E +DA       +                     + +N  V  +  V         
Sbjct: 458  ----ELLDAEEEETVMIAMTPQDLDQSKTKRGTGYVSNNPENAAVRIKSTVH----HEHW 509

Query: 792  DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                  PS  LG       +  + +P+  +N       S R   +       +  +    
Sbjct: 510  SHCEIHPSMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNF 556

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
            +                            +  +             +       +   + 
Sbjct: 557  QVRM-----------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQN 593

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +   +    I+ R   D  + +  V  E+ E   RD 
Sbjct: 594  AIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYTDMEKTTGIVPVEEFEKPHRDT 652

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                     +       +  G           K+  L  D      R++          +
Sbjct: 653  TVRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPLPPDSEELGQRTRTHTRRDVSTPL 712

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            +     +  Q   S +                       ++ VKV +   R  Q GDK A
Sbjct: 713  KSTENGIVDQVLISTNE--------------------SGVKFVKVRIRSTRIPQIGDKFA 752

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +
Sbjct: 753  SRHGQKGTIGMTYRQEDMPFAGNGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNE 812

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
              +          +S L        G G     +                          
Sbjct: 813  GDATPFTDLTVESVSSLLR------GKGYQQRGLEVM----------------------- 843

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                G +    G         V +G  Y  +L HMV
Sbjct: 844  ------------------YHGHT----GR---KLQAQVYLGPTYYQRLKHMV 870



 Score =  133 bits (334), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 105/763 (13%), Positives = 224/763 (29%), Gaps = 115/763 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++R D    +P+     ALG+  + ++L             +     +  A ++   +V+
Sbjct: 52  YIRND----IPIVVVFRALGIVPDRDVLEHICYDPDDHAMLEMLKPCIEEAFVIQDREVA 107

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFL------GITSDCLCGLYVAEDIVNG 315
              +        +   K+L     + L+++ +  +              G  V   +V  
Sbjct: 108 LDYIGRRGTTTGLSREKRLRYAQ-EILQKEMLPHISTQEGAESKKAYFFGYMV-HRLVLA 165

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDAL 374
                 ++  D   +K L+           +L+   + +   Y++  + T +  +   A+
Sbjct: 166 ALDRRELDDRDHFGKKRLDLAGPLLATLFRMLFRRLTKDVYRYMQKCVETHREFNINAAV 225

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIR 432
                        T  +  S+    + D  K+  +  G  ++  R    +      R   
Sbjct: 226 KPAT--------ITNGLKYSLATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRTNT 277

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  I     L N    +         +      ++KN   +  + +    +  +  
Sbjct: 278 PIGRDGKIARPRQLHNHHWGMVXXXXXXXGQACG---LVKNLALMACISVGTLSQPVVEF 334

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
           ++   + P      +P+ +    F     +    +  + ++ +   RR   +        
Sbjct: 335 LEEWGLEPLGERTDEPLTATKV-FVNGVWMGIHRDPQHLVNTVRTLRRSDGISSEISVVR 393

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK-----VCD 607
                   ++        P          LV S      +N     E P  K        
Sbjct: 394 DIRERELRLYTDAGRVCRPLFIVNEQTQNLVISK---REINWLHAREKPGEKDKVYGWSQ 450

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDG-----SFTEELVFCRCAGEEILVPREKID 662
              +  V  L A EEE   IA     LD+        +            +  V  E   
Sbjct: 451 LVTSGMVELLDAEEEETVMIAMTPQDLDQSKTKRGTGYVSNNPENAAVRIKSTVHHEHWS 510

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +++ S R      M +QA+ +                   
Sbjct: 511 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFQV------------ 558

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                                           + + +  Y       +     +  R   
Sbjct: 559 -----------------------------RMDTMANILYYPQKPLATTRSMEYLKFR--- 586

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA + + GYN EDS+++++  +   +F SI
Sbjct: 587 ---------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSI 625

Query: 843 HIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           +   +  M + T + P E            +       ++  G++  G  +N  DI++GK
Sbjct: 626 YYRSYTDMEKTTGIVPVEEFEKPHRDTTVRMKHGTYDKLEADGLVAPGIGINGEDIIIGK 685

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             P         E+L +        DV        +G+   V+
Sbjct: 686 TAPL----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 724


>gi|3133321|gb|AAC38461.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133351|gb|AAC38476.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133383|gb|AAC38492.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133385|gb|AAC38493.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133387|gb|AAC38494.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133389|gb|AAC38495.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133391|gb|AAC38496.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133393|gb|AAC38497.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133395|gb|AAC38498.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133397|gb|AAC38499.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133403|gb|AAC38502.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133489|gb|AAC38545.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
          Length = 234

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN YGFIETPYRKV +G VT+
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPYGFIETPYRKVVNGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++VYL+A EE+   +AQANS +DEDG FTE  V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 EIVYLTADEEDRHVVAQANSPIDEDGRFTEPRVLVRRKGGEVEYVSSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|158853038|gb|ABW82119.1| RpoB [Bacteriovorax sp. MIA4]
          Length = 351

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 165/354 (46%), Positives = 234/354 (66%), Gaps = 10/354 (2%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            AK S   + A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+
Sbjct: 1    AKDSAVILFAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQK 58

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             LVK GD V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVF
Sbjct: 59   ALVKEGDIVKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVF 118

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKIT
Sbjct: 119  TSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKIT 178

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +
Sbjct: 179  PKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDI 238

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDL 1012
              ++  L+ RD+  E   +  +   R+ ++L G              +   K T ++S++
Sbjct: 239  IEQETTLIRRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEV 298

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            ++  P        ++   ++  +           S +  +  ++I K+  GD++
Sbjct: 299  LAGVPFELIGYLPLE-AALEERLSEYFADIRNRISRVRQKATDEIAKLHRGDEL 351


>gi|119644368|gb|ABL85620.1| RNA polymerase II second largest subunit [Lopezaria versicolor]
          Length = 660

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 116/725 (16%), Positives = 227/725 (31%), Gaps = 88/725 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R+   ++ + + +  +    +         + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLLAGLFRMLFYKLTKDVFKYLQKCVENNKEFNLTLAVKSTTLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L+       ++      +  + +     V        I      + D  D   K      
Sbjct: 177  LNNPNATKIFVNGVWVGVHSNPALLVSTVLNLRRRGLISYEVSLVRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAG 733
                P F+ ++D+     G     +           +G  M++   +          + G
Sbjct: 237  RVCRPLFVVDNDAKSNNYGGLALTKQDIAKLEADRELGIDMDAQEKEDKLMGWQGLVKKG 296

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            IVE VDA       V    +       I    + Q  + +   N+R    +         
Sbjct: 297  IVEYVDAEEEETIMVVMTPEDLDLSRQIQAGYR-QEEDPDENPNRRKRADLNPTQHAWTH 355

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +   + +  ++V    
Sbjct: 356  CEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM-- 404

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                                       +  +             +       +   +  +
Sbjct: 405  -------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAI 439

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D+ +R        +E   +    
Sbjct: 440  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---SVVESFEKPMRS 495

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y +L +   +  G           K+  +S D      R++          
Sbjct: 496  DTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRTKL--------- 546

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
                   +K    T     E+   +++      D +     R VKV +   +  Q GDK 
Sbjct: 547  ------HIKRDTSTPLRSTENGIVDQVLLSTNSDGL-----RSVKVRMRTTKVPQIGDKF 595

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 596  ASRHGQKGTIGITYRQEDMPFTSQGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGY 655

Query: 1151 KIKSL 1155
            +  + 
Sbjct: 656  EGDAT 660



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 80/623 (12%), Positives = 167/623 (26%), Gaps = 111/623 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +         K  KD    + + +       F++  ++ +    +  KY L   G  
Sbjct: 15  GPLLAGLFRMLFYKLTKDVFKYLQKCVENN--KEFNLTLAVKSTTLTNGLKYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             + Q    +  +       + +     +      N + +     E   +   +++  + 
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEE--YEPLNNPNATKIFVNG 189

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
             +   ++   L +     + R         +      R     T  G     +  + + 
Sbjct: 190 VWVGVHSNPALLVSTV-LNLRRRGLISYEVSLVRDIRDREFKIFTDAGRVCRPLFVVDND 248

Query: 590 ARVNAYGFI-------------------------ETPYRKVCDGKVTNDVVYLSAMEEEN 624
           A+ N YG +                         E              V Y+ A EEE 
Sbjct: 249 AKSNNYGGLALTKQDIAKLEADRELGIDMDAQEKEDKLMGWQGLVKKGIVEYVDAEEEET 308

Query: 625 RYIAQANSSLDEDGSFTEELV--------FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
             +      LD                    R    ++   +      +  P  ++ I A
Sbjct: 309 IMVVMTPEDLDLSRQIQAGYRQEEDPDENPNRRKRADLNPTQHAWTHCEIHPSMILGICA 368

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +               V   + A I+      + 
Sbjct: 369 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYDVRMDTMANILYYPQKPLA 419

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
              ++  +          +   +  Y              NQ                  
Sbjct: 420 TTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE----------------- 451

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             S  +   ++ R +  +       + E  + +S             +E FE   R    
Sbjct: 452 -DSVIMNQSSIDRGLFRSLFYRAYTDQEKRVGMS------------VVESFEKPMR---- 494

Query: 857 GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                  D   +       +D+ GI+  G  V+  DI++GK  P         ++     
Sbjct: 495 ------SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPISPDAEELGQRT---- 544

Query: 917 FGEKAVDVRDTSLRVPSGVSGTV 939
              K    RDTS  + S  +G V
Sbjct: 545 ---KLHIKRDTSTPLRSTENGIV 564


>gi|170671551|gb|ACB29613.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 107/172 (62%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFEKVSVRIDKDKLMMEVVP-DRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRVSARHTRALEKAGLSELEVPADYLIGRVFAATYVNEDTGEVIVSAN 170


>gi|94410944|gb|ABF18590.1| RNA polymerase II second largest subunit [Kuehneromyces rostratus]
          Length = 669

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 111/728 (15%), Positives = 220/728 (30%), Gaps = 92/728 (12%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEF 516
             G +R+   G +L N +R+   ++ + +    +              +  + + + +   
Sbjct: 1    FGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYS 60

Query: 517  FCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +               +SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L   A ++           + +  + +         EE
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL--------EE 168

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            N +     + +  +G +       R A   +   ++     D SP+  V           
Sbjct: 169  NAHSTTPCTKVFVNGVWMG---VHRDAANLVKTLKKLRRRDDISPEVSVVRDIREKELRL 225

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              D+ RV     +       L+ +   ++  G      +     +   + G++E +DA  
Sbjct: 226  YTDAGRVCRPLFIVENQQLALQKKHIRWINNGTHDDGEEYKWEQM--IKGGVIELLDAEE 283

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   +       +  +++        R  +K G            PS  L
Sbjct: 284  EETVMISMTPEDLENSRLQQSGIAPEQNTGEFDPAAR--LKAGTPAHTWTHCEIHPSMIL 341

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 342  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 376

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 377  FLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 425

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          + 
Sbjct: 426  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRLKHGTYDK 484

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 485  LEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQV 544

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q+GDK A RHG KG +  
Sbjct: 545  LI--------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGI 584

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 585  TYRQEDMPFTCEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTELTV 644

Query: 1163 GDISPLRS 1170
              +S    
Sbjct: 645  ESVSTFLR 652



 Score =  127 bits (318), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 86/622 (13%), Positives = 173/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 10  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 66

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 67  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 126

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 127 TPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWM 186

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  +   RR   +            +   ++        P    E   + L
Sbjct: 187 GVHRDAANLVKTLKKLRRRDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     +    K         +  L A EEE   I+     L+       
Sbjct: 247 QKKHIRW--INNGTHDDGEEYKWEQMIKGGVIELLDAEEEETVMISMTPEDLENSRLQQS 304

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +   +  GE           P       +  P  ++ I AS+IPF +++ S R      
Sbjct: 305 GIAPEQNTGEFDPAARLKAGTPAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 364

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 365 MGKQAMGIYLTNFLI-----------------------------------------RMDT 383

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 384 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 419

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 420 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRLKH 479

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 480 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 532

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 533 LKSTESGIVDQVLITTNSEGQK 554


>gi|3133325|gb|AAC38463.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133335|gb|AAC38468.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYREVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE+G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDENGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|3133379|gb|AAC38490.1| RNA polymerase beta-subunit [Mycobacterium avium]
          Length = 234

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINXRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAXD 231


>gi|52699798|gb|AAU86961.1| DNA-dependent RNA polymerase II second largest subunit [Dendrographa
            leucophaea f. minor]
          Length = 735

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 125/841 (14%), Positives = 234/841 (27%), Gaps = 134/841 (15%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +R    RM R +    ++   +         +    V + + 
Sbjct: 1    DHFGRKRLDLAGPLMANLFRQLFQRMSRDVFRHLQLCVENNKQFSMDVAVKTNVVTNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGEQKKAMQTKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY--GFIETPYRKVCDGKVTNDVVYLSA 619
            H TH+G +CP+ET EG   GLV +L+    V+    G   T +    D +   D     A
Sbjct: 117  HNTHWGLVCPSETPEGQACGLVKNLSLMCTVSVGKTGEPITEFLFGKDTEPVEDYEPQKA 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                  ++         +    EE VF    G                P+  +       
Sbjct: 177  PNATKVFLNGVWLGTHNNPRVLEEAVFATRRGAV------------LDPEVSIVRDIRER 224

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
             F    D+ RV+    +        K     +       ++         ++   + + D
Sbjct: 225  EFKIFTDAGRVMRPLLVVDNDPRSSKNGQLVLDFHHLEKLSSD----QDIRKDPNLAEAD 280

Query: 740  AIRIVI----RSVEGDLDPSTSGVDIYRLMKFQ--RSNQNTCVNQRPLVKVGDEVRRNDI 793
              +          +G ++   +  +   ++             N + + K+GD +     
Sbjct: 281  KKKQYYGFRGLVDDGVIEFLDAEEEESAMILMSVAHLPGAQDPNHQKVYKLGDRIEMKPS 340

Query: 794  IADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
             A    T      ++   +  + +P+                                  
Sbjct: 341  SAANIFTHCEIHPSMILGICASIIPFPDQXXXXXXXXXXXXXXXXXXX---------XXX 391

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                        +  +             +       +   +  
Sbjct: 392  XXXXXXXXXXXXXXXXXXXXXFAQRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNA 451

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     E+  SV    +E   R + 
Sbjct: 452  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----EQQQSVGFNALEEFERPQR 507

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             E +      Y +L +   +  G           K+    + +                 
Sbjct: 508  AETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPM----------------- 550

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV-VKVFVAMKRPIQSGD 1088
              Q N E  +   +  K  +    ++    I     +     +  VKV     +  Q GD
Sbjct: 551  --QENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRTTKVPQIGD 608

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + E  L       
Sbjct: 609  KFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSRMTIAHLIECLLSKVSTIT 668

Query: 1149 GKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            G +  +          IS L SF                                     
Sbjct: 669  GHEGDATPFTDITVSSISDLLSFAGYQSRGFE---------------------------- 700

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                               L  +G +    G      +  V +G  Y  +L HMV DK+ 
Sbjct: 701  -------------------LMYNGHT----GR---KLNAQVFLGPTYYQRLRHMVDDKIX 734

Query: 1269 A 1269
            A
Sbjct: 735  A 735



 Score =  105 bits (261), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 80/599 (13%), Positives = 157/599 (26%), Gaps = 74/599 (12%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             +V T  +  S+    + +  K   +  G  ++  R    +      R          I
Sbjct: 51  KTNVVTNGLRYSLATGNWGEQKKAMQTKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKI 110

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +         +   + + L     + + +    I E +   D +   P
Sbjct: 111 AKPRQLHNTHWGLVCPSETPEGQACGLVKNLSLMCTVSVGKTGEPITEFLFGKDTE---P 167

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            +    +   +A   F     L            +  TRR + L                
Sbjct: 168 VEDYEPQKAPNATKVFLNGVWLGTHNNPRVLEEAVFATRRGAVLDPEVSIVRDIREREFK 227

Query: 561 VHPTHYGRICPA-----ETSEGHNIGLVSSLTSFARVNAYGFI-----------ETPYRK 604
           +       + P      +     N  LV       ++++   I           +  Y  
Sbjct: 228 IFTDAGRVMRPLLVVDNDPRSSKNGQLVLDFHHLEKLSSDQDIRKDPNLAEADKKKQYYG 287

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLD--EDGSFTEELVFCRCAGEEILVPREKID 662
                    + +L A EEE+  I  + + L   +D +  +          +         
Sbjct: 288 FRGLVDDGVIEFLDAEEEESAMILMSVAHLPGAQDPNHQKVYKLGDRIEMKPSSAANIFT 347

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P  ++ I AS+IPF +                                       
Sbjct: 348 HCEIHPSMILGICASIIPFPDQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 407

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                 A+R   +  +                                       Q+PL 
Sbjct: 408 XXXXXFAQRMDTMSNI-----------------------------------LYYPQKPL- 431

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA   + GYN EDS+++++  +   +F S+
Sbjct: 432 ---------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 482

Query: 843 HIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               +    +       EE  R              + +D+ G +  G  V+  DI++GK
Sbjct: 483 FYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGK 542

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             P         E   +     K  DV        +G+   V+      +  +    R+
Sbjct: 543 TAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRT 600


>gi|108885433|gb|ABG23223.1| RNA polymerase II second largest subunit [Cintractia axicola]
          Length = 692

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 118/821 (14%), Positives = 231/821 (28%), Gaps = 146/821 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G ++ N +R+   ++ R +   +     +      Q  + +  + + +    
Sbjct: 1    GKKRIDLAGPLMANLFRMLFRKVTRDVYRHLQKCVEEHKEFHIQAAVKSATITNGLRYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKAMQAKAGVSQVLNRFAFTSTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY-LSAMEEE 623
            H+G +CPAET EG   GLV +L+  A V            + +  + + V   ++  +  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQVTNAKAT 176

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
              ++        +D     + +      +            D S +  V           
Sbjct: 177  KVFVNGVWMGTHDDPGQLVDTLRDLRRKD------------DISQEVSVVRDIREKELRI 224

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              DS+RV     +       L  +   V   G  +   +      + ++  I        
Sbjct: 225  YTDSSRVTRPLFIVNPHDMTLLIKKHHVQMIGQTTESGEEFRWTQLVQQGVIEFLDAEEE 284

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
              +       D   S     R       + +     +  + +             P+  L
Sbjct: 285  ESVLICMSTTDLEQSREYKIRNGHVNFESADPSARLKSALTI--MPDTWTHCELHPAMVL 342

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N     +    M  +    S+ I       R   +      
Sbjct: 343  G-------ICASIIPFPDHNQSPRNVYESAMAKQ----SVSINISNFHTRHDTMNHVLHY 391

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
               P  +   ++++                             +   +  + AI      
Sbjct: 392  PQKPLGTTRSMEHL-------------------------KFRELPAGQNAIVAIMCYSGY 426

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  + + ++   ++ E+ E   RD          + 
Sbjct: 427  NQEDSVIMNQSSIDRGLF-RSLYYRGYLAEEKKVGVMQLEEFEKPNRDITIRMKHGTYDK 485

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                     G           K+  L  D      R++          ++     +  Q 
Sbjct: 486  LDADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRTKMHTKKDASIALKSTENGIIDQV 545

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q+GDK A RHG KG V  
Sbjct: 546  LL--------------------TTNAAGNKFVKVRVRNSRIPQTGDKFASRHGQKGTVGI 585

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L       G++  +        
Sbjct: 586  TYRQEDMPFSAEGLTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTV 645

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
              +S +   L                                                  
Sbjct: 646  EAVSSILRGLGYQSRGLEVM---------------------------------------- 665

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    +G +    G         V +G  Y  +L HMV
Sbjct: 666  -------YNGHT----GR---KMQAQVYLGPTYYQRLKHMV 692



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 79/618 (12%), Positives = 175/618 (28%), Gaps = 91/618 (14%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +   +   F +  ++ +    +  +Y L   G  
Sbjct: 9   GPLMANLFRMLFRKVTRDVYRHLQKCV--EEHKEFHIQAAVKSATITNGLRYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 66  GDQKKAMQAKAGVSQVLNRFAFTSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI------DSVMPQDLINAKPVVSAVCEFF-CSSQL 522
             + Q    +  +       + +         +      L++ +   +   + F     +
Sbjct: 126 TPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQVTNAKATKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              ++    +  +   RR   + Q          +   ++        P      H++ L
Sbjct: 186 GTHDDPGQLVDTLRDLRRKDDISQEVSVVRDIREKELRIYTDSSRVTRPLFIVNPHDMTL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT- 641
           +        +         +R          + +L A EEE+  I  + + L++   +  
Sbjct: 246 LIKKHHVQMIGQTTESGEEFR-WTQLVQQGVIEFLDAEEEESVLICMSTTDLEQSREYKI 304

Query: 642 -------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  E           + +  +     +  P  V+ I AS+IPF +++ S R +   
Sbjct: 305 RNGHVNFESADPSARLKSALTIMPDTWTHCELHPAMVLGICASIIPFPDHNQSPRNVYES 364

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +Q+V +  +                                      +  V      
Sbjct: 365 AMAKQSVSINISNFH------------------------------TRHDTMNHVLHYPQK 394

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                     +KF+            +   G   + + +I +  S D G           
Sbjct: 395 PLGTTRSMEHLKFRELPAGQNAIVAIMCYSG-YNQEDSVIMNQSSIDRGLFRSLYY---- 449

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
                GY  E+  +             + +EEFE   RD              +      
Sbjct: 450 ----RGYLAEEKKV-----------GVMQLEEFEKPNRDI----------TIRMKHGTYD 484

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +D  G+   G  V+  D+++GK  P    P   EE  +R     K    +D S+ + S 
Sbjct: 485 KLDADGLCAPGTRVSGDDVIIGKTAP---LPPDSEELGMRT----KMHTKKDASIALKST 537

Query: 935 VSGTVVDVRIFNRHGIDK 952
            +G +  V +      +K
Sbjct: 538 ENGIIDQVLLTTNAAGNK 555


>gi|3133465|gb|AAC38533.1| RNA polymerase beta-subunit [Mycobacterium tuberculosis]
          Length = 234

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 136/231 (58%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++VYL+A EE+   +AQANS +D DG F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|312204368|gb|ADQ47501.1| RNA polymerase II second largest subunit [Stictis brunnescens]
          Length = 696

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 108/742 (14%), Positives = 197/742 (26%), Gaps = 100/742 (13%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 47   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLVCPAETPEGQAC 102

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L+    +      E    +    + +V  +     +      ++      +  + 
Sbjct: 103  GLVKNLSLMCYITVGSPSEPIVEFMVQRNMEVLEEYEPTKSPNATKVFVNGVWVGVHREP 162

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            +     +        I      I D  D   K          P    D   +     N+ 
Sbjct: 163  AHLVRTMQHLRRKNLISYEVSLIRDIRDREFKIFTDAGRVCRPLFVIDTDPKSANKGNLV 222

Query: 698  --RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
              ++ +  L+ +     T  E   A+         + G VE VDA       +    +  
Sbjct: 223  LTKEIINKLEDDKDLPPTLTEDEKAERFFGWNGLLQNGAVEFVDAEEEETVMIIMTPEDL 282

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                         R  Q       P       V+    +     T               
Sbjct: 283  EV----------SRQVQAGYAPPEPSEDPNARVKGKVNLTQHIWTHCEIXXXXXXXXXXX 332

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
                                                                        
Sbjct: 333  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 392

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 393  XRIDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 452

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    +F R  +++ +R        +E   +    + + L    Y +L +   +  G
Sbjct: 453  DRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPMRADTLRLKHGTYEKLDDDGLVAPG 508

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  D      R++          ++     L              
Sbjct: 509  VRVSGEDIIIGKTAPIPPDSEEMGQRTKLHTKRDASTPLRSTESGL-------------- 554

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                ++K+          L+ VKV     +  Q GDK A RHG KG +      EDMPF 
Sbjct: 555  ----VDKVML--TTNAEGLKFVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFS 608

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +  + E  L       G +                     
Sbjct: 609  AEGVVPDIIINPHAIPSRMTIAHLVECQLSKVSSLRGYEGD------------------- 649

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     ++++ +LR       G
Sbjct: 650  ----------------------------------ATP-FTDVTVDSVSRLLREHGYQSRG 674

Query: 1233 QSILYDGLTGEPFDRPVTVGYI 1254
              ++Y+G TG      V +G  
Sbjct: 675  FEVMYNGHTGRKLTAQVFLGPT 696


>gi|3133317|gb|AAC38459.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133345|gb|AAC38473.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133353|gb|AAC38477.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133357|gb|AAC38479.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133359|gb|AAC38480.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133409|gb|AAC38505.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133411|gb|AAC38506.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133413|gb|AAC38507.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133415|gb|AAC38508.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133417|gb|AAC38509.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133421|gb|AAC38511.1| RNA polymerase beta-subunit [Mycobacterium avium]
 gi|3133461|gb|AAC38531.1| RNA polymerase beta-subunit [Mycobacterium avium]
          Length = 234

 Score =  237 bits (604), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|3133401|gb|AAC38501.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
          Length = 234

 Score =  236 bits (603), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN YGFIETPYRKV +G VT+
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPYGFIETPYRKVVNGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++VYL+A EE+   +AQANS +DEDG FTE  V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 EIVYLTADEEDRHVVAQANSPIDEDGRFTEPRVLVRRKGGEVEYVSSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL++ EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRXEAPLVGTGMELRAAID 231


>gi|194320289|gb|ACF48385.1| RNA polymerase II second largest subunit [Dactylina arctica]
          Length = 689

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 112/727 (15%), Positives = 221/727 (30%), Gaps = 90/727 (12%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L + +R    ++ + + +  +    +         + +  + + +     +      
Sbjct: 1    GPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGNWGDQ 60

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 61   KKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 116

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +   L++      ++   
Sbjct: 117  ETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGV 176

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNR 689
               +  D +     V        I      + D  D   K          P    D+  R
Sbjct: 177  WVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPR 236

Query: 690  VLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
                 N+         L      +  T  +       G   + K  G+VE VDA      
Sbjct: 237  SSNSGNLVLTKEHVQKLEMDRENWATTEPDVREEADMGWQGLVKE-GVVEYVDAEEEETI 295

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +    +       +   +     N +  +N+R    +             PS  LG   
Sbjct: 296  MIVMTPEDLEISRQLQAGLAPPEPNPDE-LNRRVKAPINLTAHTWTHCEIHPSMILG--- 351

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N          M  + +   + +  ++                  
Sbjct: 352  ----ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM--------------- 390

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                          +  +             +       +   +  + AI      +  D
Sbjct: 391  ------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 438

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L
Sbjct: 439  SVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKL 494

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  ++ D      R++                 +K    
Sbjct: 495  DDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL---------------HVKRDVS 539

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
            T     E+   +++     G       LR VKV +   +  Q GDK A RHG KG +   
Sbjct: 540  TPLRSTENGIVDQVLLSTNG-----EGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 594

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +         
Sbjct: 595  YRQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVD 654

Query: 1164 DISPLRS 1170
             +S L  
Sbjct: 655  SVSRLLR 661



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 79/621 (12%), Positives = 167/621 (26%), Gaps = 102/621 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 1   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 57

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 58  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 117

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 118 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 177

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 178 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 237

Query: 574 TSEGHNIGLVSSLTSFAR------VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +                  E              V Y+ A EEE   I
Sbjct: 238 SNSGNLVLTKEHVQKLEMDRENWATTEPDVREEADMGWQGLVKEGVVEYVDAEEEETIMI 297

Query: 628 AQANSSLDEDGSFTEELVF--------CRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
                 L+        L           R     I +        +  P  ++ I AS+I
Sbjct: 298 VMTPEDLEISRQLQAGLAPPEPNPDELNRRVKAPINLTAHTWTHCEIHPSMILGICASII 357

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PF +++ S R      M +QA+ +                   + A I+      +    
Sbjct: 358 PFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYQQRMDTMANILYYPQKPLATTR 408

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           ++  +          +   +  Y              NQ                    S
Sbjct: 409 SMEFLKFRELPAGQNAIVAIACYSG-----------YNQE------------------DS 439

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +   ++ R +  +       + E  + +S             +E+FE   R       
Sbjct: 440 VIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS------------VVEQFEKPMR------- 480

Query: 860 EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               D   +       +D+ G++  G  V+  DI++GK  P         E+L +     
Sbjct: 481 ---SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLH 533

Query: 920 KAVDVRDTSLRVPSGVSGTVV 940
              DV        +G+   V+
Sbjct: 534 VKRDVSTPLRSTENGIVDQVL 554


>gi|94410930|gb|ABF18584.1| RNA polymerase II second largest subunit [Hygrocybe miniata f.
            longipes]
          Length = 670

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 118/759 (15%), Positives = 216/759 (28%), Gaps = 142/759 (18%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 39   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 94

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR--------YIAQANS 632
            GLV +L   A ++   +       + +         L ++EE           ++     
Sbjct: 95   GLVKNLALMACISVGSYSAPVIEFLEEWG-------LESLEENAHSSTPCTKVFVNGVWM 147

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  D +   + +      ++I      +  I     ++ + A  +   L   ++ R+++
Sbjct: 148  GVHRDAANLVKTIKKLRRKDDISPEVSIVRDIREKELRLYTDAGRVCRPLFIVENQRLVL 207

Query: 693  GCNMQRQAVPLLKAEA-----PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                 R      + E             E    +      + K   +          +  
Sbjct: 208  RKKHIRWLNAGERPETLKKKAQVPPPDPEQKSTREFXWEQLIKGGVVELLDAEEEETVMI 267

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV--KVGDEVRRNDIIADGPSTDLGDL 805
                 D   S +    +       +       P V  K G            PS  LG  
Sbjct: 268  SMTPEDLENSRLQQRGIDPHANDGEFD-----PAVRLKAGINTHTWTHCEIHPSMILG-- 320

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N                        ++       +G       I
Sbjct: 321  -----ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLI 357

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 358  RM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 406

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+               
Sbjct: 407  DSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGSYEKLED 465

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G N +       K+  +  D                +E  QR     +    T 
Sbjct: 466  DGLIAPGTNVIGEDIIIGKTAPIPPD---------------SEELGQRTRTHTRRDVSTP 510

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      DD      + VK+ V   R  Q GDK A RHG KG +     
Sbjct: 511  LKSTESGIVDQVLITTNADD-----QKFVKIRVRATRIPQIGDKFASRHGQKGTIGITYR 565

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +           
Sbjct: 566  QEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT------- 618

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                               ++     + LR       G+ V                   
Sbjct: 619  ------------------DLTVESVSTFLRQKGYQSRGLEVM------------------ 642

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                  G +       G      + +G  Y  +L HMV 
Sbjct: 643  ----YHGHT-------GRKLQAQIYLGPTYYQRLKHMVD 670



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 85/605 (14%), Positives = 167/605 (27%), Gaps = 112/605 (18%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F++A ++ +    +  KY L   G      +         + + +    + +  L   
Sbjct: 1   KEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRC 59

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +       + S     +   
Sbjct: 60  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFL 119

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA         F     +    +  N +  I   RR   +          
Sbjct: 120 EEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDAANLVKTIKKLRRKDDISPEVSIVRDI 179

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVS-------------SLTSFARVNAYGFIETP 601
             +   ++        P    E   + L               +L   A+V      +  
Sbjct: 180 REKELRLYTDAGRVCRPLFIVENQRLVLRKKHIRWLNAGERPETLKKKAQVPPPDPEQKS 239

Query: 602 YRK--VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL---- 655
            R+           V  L A EEE   I+     L+        +      GE       
Sbjct: 240 TREFXWEQLIKGGVVELLDAEEEETVMISMTPEDLENSRLQQRGIDPHANDGEFDPAVRL 299

Query: 656 ---VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
              +        +  P  ++ I AS+IPF +++ S R      M +QA+ +         
Sbjct: 300 KAGINTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI-- 357

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                                                     + + +  Y       +  
Sbjct: 358 ---------------------------------------RMDTMANILYYPQKPLATTRS 378

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
              +  R                        +L  G+N +VA + + GYN EDS+++++ 
Sbjct: 379 MEYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQS 414

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F SI+   +  + + + +   E        +   +     + +++ G+I  G  
Sbjct: 415 SIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGSYEKLEDDGLIAPGTN 474

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V   DI++GK  P         ++        +    RD S  + S  SG V  V I   
Sbjct: 475 VIGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTN 527

Query: 948 HGIDK 952
               K
Sbjct: 528 ADDQK 532


>gi|3133337|gb|AAC38469.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133341|gb|AAC38471.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V  G VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRRVVSGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE+G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDENGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|119644119|gb|ABL85607.1| RNA polymerase II second largest subunit [Platismatia glauca]
          Length = 708

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 122/786 (15%), Positives = 228/786 (29%), Gaps = 105/786 (13%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L + +R    ++ + + +  +    +         + +  + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L     +      E    +    + +V  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            L++      ++      +  D +     V        I      + D  D   K      
Sbjct: 177  LNSPNATKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE---APFVGTGMESVVAKSSGAAIVAKRA 732
                P    D+  R     N+      + K E     +  T  +       G   + K  
Sbjct: 237  RVCRPLFVIDNDPRSSNRGNLALTKDHVQKLELDRENWATTEPDVREEADMGWQGLVKE- 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE VDA       +    +       +        +N +  +N+R    +        
Sbjct: 296  GVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYAMPEANPDE-LNKRVKAPMNPTAHTWT 354

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 355  HCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXXXXX 407

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                                                                 +   +  
Sbjct: 408  XXXXXXXXXXX-----------------------------XXXXXXXXXXXXXLPAGQNA 438

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 439  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 494

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 495  SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 554

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 555  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 594

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 595  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 654

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                           V     +G  + T 
Sbjct: 655  FEGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQ 699

Query: 1210 VFDGAD 1215
            VF G  
Sbjct: 700  VFLGPT 705



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 48/383 (12%), Positives = 104/383 (27%), Gaps = 38/383 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 15  GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 71

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 72  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 131

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 132 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 191

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R     E        R   P       P  
Sbjct: 192 VGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRS 251

Query: 574 TSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+       +                  E              V Y+ A EEE   I
Sbjct: 252 SNRGNLALTKDHVQKLELDRENWATTEPDVREEADMGWQGLVKEGVVEYVDAEEEETIMI 311

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 312 VMTPEDLEISRQLQAGYAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 371

Query: 680 PFLENDDSNRVLMGCNMQRQAVP 702
           PF +++ S R      M +QA+ 
Sbjct: 372 PFPDHNQSPRNTYQSAMGKQAMG 394


>gi|154362099|gb|ABS80888.1| RNA polymerase beta subunit [Delftia acidovorans]
          Length = 234

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 136/230 (59%), Positives = 170/230 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNLLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD +G 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVADGKVTDEIDYLSAIEEGKYIIAQANAELDAEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +LV  R  G+  LV  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LIGDLVSAREKGDSTLVSAERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIV+R  +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTATRGGIVDYVDATRIVVRVND 230


>gi|45545325|gb|AAS67510.1| DNA-dependent RNA polymerase II second largest subunit [Dermatocarpon
            reticulatum]
          Length = 907

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 131/887 (14%), Positives = 257/887 (28%), Gaps = 142/887 (16%)

Query: 398  FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             L F   +   + + + +    +  +  +  +  +   +  ++  ++    G+   DD D
Sbjct: 140  NLKFAERQKHTTDILQKEFLPHIGQEPSNSSQSRKAFFLGYMVNRMLKCALGRSEPDDRD 199

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
            +LG +R+   G ++ N +RL   ++ R      +        +  +  + +  + + +  
Sbjct: 200  HLGKKRLDLAGPLMANLFRLQFQKVVRDFSRYMQKQVESDREINLKVGLKSNIITNGLKY 259

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +A     + R     + R +H
Sbjct: 260  SLATGNWGDQKKVNQAKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQLH 315

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY-LSA 619
             TH+G +CPAET EG   GLV +L     V      E    Y    D +   +    LS 
Sbjct: 316  NTHWGYVCPAETPEGQACGLVKNLALMTMVTNSHNTEPLVDYILEQDVESLEEWEPRLSP 375

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
               +        + + +D              +++      + D  D   +        +
Sbjct: 376  QATKVFLNGVWFAVVIKDPKHLVNRFKELRRTDQLDPQISIVWDIRDKEFRISGDAGRII 435

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG----MESVVAKSSGAAIVAKRAGI 734
             P    +         N+      + + +     T     +E       G      + G+
Sbjct: 436  RPLFVVERDPSKDNEGNLVLNKNHIQRLDNTVYYTEAQRPIEQWQEPPFG-WKDLLKEGV 494

Query: 735  VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
            VE +DA       +    +   +    + + +      +      PL+            
Sbjct: 495  VEYLDAEEEETAMIIMTPEDLNTSNAKH-MGRTTEETDDPLARYDPLLNPHAHTF--THC 551

Query: 795  ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
               PS  LG       +  + +P+  +N          M  + +                
Sbjct: 552  EIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLTN 594

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
                 E   +I    ++ L                        +       +   +  + 
Sbjct: 595  FDQRMETMANILYYPQKPLAR-------------------TMSMEYLKFRELPAGQNAIV 635

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   D+ +       EQ E   R     
Sbjct: 636  AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKVVGHNVVEQFEKPTRSDTLR 694

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +       +  GQ          K+  ++ D                +E  QR 
Sbjct: 695  MKHGTYDKIDADGIVEVGQRVSGEDIIIGKTAPMAPD---------------AEELGQRQ 739

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + LK    T     E    +++     GD       + VKV V   +  Q GDK A RH
Sbjct: 740  KQHLKRDVSTPLRSTESGIVDQVLVTTSGD-----GQKFVKVRVRTTKIPQIGDKFASRH 794

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 795  GQKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDA 854

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     ++S +   +                                          
Sbjct: 855  TPFTKVTVTNVSNILRSMGYQSRGFEVM-------------------------------- 882

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                            +G +    G         V +G  Y  +L H
Sbjct: 883  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRH 907



 Score =  145 bits (367), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 113/864 (13%), Positives = 240/864 (27%), Gaps = 152/864 (17%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRI 206
            ++++++Q  RS G        + +      +   I    D+G  M  +   K  ++ ++
Sbjct: 1   SEKVLIAQE-RSAGNI--VQVFKKAAPSPFTHIAEIRSSVDRGSRMLSQCTVK--LYRQV 55

Query: 207 DR-----------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFP 248
           D                  ++ +P+     AL + S+ +IL          +  D     
Sbjct: 56  DGPEQTKIPNPIRIQLPYVKQDIPLVVVFRALDIVSDADILEKICFDQSDKEMMDLLMGS 115

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
           L     +  A  +   +        ++  ++        L+++ +  +G           
Sbjct: 116 LQEGQPIQSADTARDYIARRGNNPNLKFAER-QKHTTDILQKEFLPHIGQEPSN-SSQSR 173

Query: 309 AEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNK 368
               +      +   A    +    + +    +                + N       K
Sbjct: 174 KAFFLGYMVNRMLKCALGRSEPDDRDHLGKKRLDL----------AGPLMANLFRLQFQK 223

Query: 369 DRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV 428
             +D    + + +         V   + + +  +  KY L   G      ++N       
Sbjct: 224 VVRDFSRYMQKQVESDREINLKVG--LKSNIITNGLKYSL-ATGNWGDQKKVNQAKAGVS 280

Query: 429 RHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME 483
           + + +    + +  L        R+GK       +  +       E  + Q    +  + 
Sbjct: 281 QVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLA 340

Query: 484 RSIKERISSV---------DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                  S           + D    ++        +             +++  + ++R
Sbjct: 341 LMTMVTNSHNTEPLVDYILEQDVESLEEWEPRLSPQATKVFLNGVWFAVVIKDPKHLVNR 400

Query: 535 ITHTRRLSALGQ--------GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
               RR   L                 +G   R + P       P++ +EG+ +   + +
Sbjct: 401 FKELRRTDQLDPQISIVWDIRDKEFRISGDAGRIIRPLFVVERDPSKDNEGNLVLNKNHI 460

Query: 587 TSFARVNAYGFIETPYRKV-------CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
                   Y   + P  +         D      V YL A EEE   I      L+   +
Sbjct: 461 QRLDNTVYYTEAQRPIEQWQEPPFGWKDLLKEGVVEYLDAEEEETAMIIMTPEDLNTSNA 520

Query: 640 FTEELVFCRCAGEEILVPR------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                                          +  P  ++ + AS+IPF +++ S R    
Sbjct: 521 KHMGRTTEETDDPLARYDPLLNPHAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQ 580

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                                                  
Sbjct: 581 SAMGKQAMGVFLTNF-----------------------------------------DQRM 599

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            + + +  Y      R+     +                           +L  G+N +V
Sbjct: 600 ETMANILYYPQKPLARTMSMEYL------------------------KFRELPAGQNAIV 635

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNV 868
           A   + GYN EDS+++++  +   +F S+    ++   +       E        D   +
Sbjct: 636 AIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKVVGHNVVEQFEKPTRSDTLRM 695

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  ID  GI+ VG  V+  DI++GK  P     M P+ + L     +     RD S
Sbjct: 696 KHGTYDKIDADGIVEVGQRVSGEDIIIGKTAP-----MAPDAEELGQRQKQHLK--RDVS 748

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  SG V  V +       K
Sbjct: 749 TPLRSTESGIVDQVLVTTSGDGQK 772


>gi|269913259|emb|CAY86056.1| RNA polymerase beta subunit [Gluconacetobacter azotocaptans]
          Length = 276

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 132/278 (47%), Positives = 175/278 (62%), Gaps = 28/278 (10%)

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------------------- 221
           IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                       
Sbjct: 1   IPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGEASAAARAAKVAEGGDVDSLD 60

Query: 222 --GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
             GMD++EIL+ FY K+V+ +    W  P  A     G K+   L+D ++GE V E+  K
Sbjct: 61  IQGMDADEILNYFYGKVVFVKTSKGWARPFDAE-SFRGLKLLEPLIDAESGEVVAEADAK 119

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           LT+ +++ + EK  K + + +  L G YVA D+VN +TGEIY EAG+ + E  LE +  +
Sbjct: 120 LTARMVRKIAEK-TKDVLVGAAGLIGRYVAYDLVNQDTGEIYAEAGEELTEARLEALEEA 178

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
            +  +P L VD+ N   +IRNTL  DKN  R DAL DIYRVMRPG+  T   AE+MF+ L
Sbjct: 179 GLDRLPTLAVDASN-GPWIRNTLTVDKNTTRDDALTDIYRVMRPGEPPTPETAEAMFSGL 237

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
           FFD+D+YDLS VGRVKMNMRL LD PD VR +RKEDI+
Sbjct: 238 FFDADRYDLSAVGRVKMNMRLGLDAPDTVRVLRKEDIL 275


>gi|3133355|gb|AAC38478.1| RNA polymerase beta-subunit [Mycobacterium scrofulaceum]
          Length = 234

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 136/231 (58%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++VYL+A EE+   +AQANS +D DG F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIVYLTADEEDRHVVAQANSPIDADGRFVEGRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|3133399|gb|AAC38500.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
          Length = 234

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVIDGLVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D DG F E  V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVASSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|80973529|gb|ABB53502.1| RNA polymerase beta subunit [Streptococcus thoraltensis]
          Length = 226

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 96/294 (32%), Positives = 134/294 (45%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV ++V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNKLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D   + D+                                       
Sbjct: 167  ARNLGIHMATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                     A  E        A +D   +++LYDG TGEPFD  V+VG +YM+K
Sbjct: 189  ---------ATVEE-------AGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 58/111 (52%), Positives = 77/111 (69%), Gaps = 7/111 (6%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           DTSLRVP G  G V DV+IF R        G++K  R    ++ +I++  +
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNKLVRVYIAQKRKIKVGDK 111


>gi|269913227|emb|CAY86040.1| RNA polymerase beta subunit [Acidomonas methanolica]
          Length = 250

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 106/253 (41%), Positives = 145/253 (57%), Gaps = 28/253 (11%)

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----- 221
           HDKG+   SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL     
Sbjct: 1   HDKGKTHSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGENS 60

Query: 222 --------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
                               GMD +EIL+ FY  + ++Q    W  P    D   G K+ 
Sbjct: 61  IAARAAKAAAGGDVESLPIRGMDQDEILAYFYGTVPFTQTSKGWARPFDP-DAFRGQKLL 119

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             L D +TGE V E+  KLT+   + + EK  K + +    L G ++A D+VN  TGEIY
Sbjct: 120 EPLFDAETGEVVAEADAKLTARACRKIAEK-TKDVLVGRADLLGRFIANDLVNPATGEIY 178

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            EAG+ + E  L  +  S I ++P+L VD   +  +IRNTL  DKN  R DAL+DIYR+M
Sbjct: 179 AEAGEELTEARLVALEESGITELPMLAVDPA-HGPWIRNTLAVDKNVSRDDALVDIYRIM 237

Query: 382 RPGDVSTFSVAES 394
           RPG+  T   AE+
Sbjct: 238 RPGEPPTPETAEA 250


>gi|254803158|gb|ACT82829.1| RNA polymerase B-subunit [Staphylococcus pettenkoferi]
          Length = 266

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 147/266 (55%), Positives = 196/266 (73%), Gaps = 3/266 (1%)

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPY
Sbjct: 1   ALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPY 60

Query: 603 RKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV      +T+ + YL+A EE++  +AQANS  DE+G F ++ V CR  G   ++ +EK
Sbjct: 61  RKVDIEKNAITDQIDYLTADEEDSYVVAQANSRTDEEGRFLDDEVVCRFRGNNTVMAKEK 120

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME V A
Sbjct: 121 MDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEHVAA 180

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           + SGAA++A+  G VE V++ ++++R  +E D       VD Y L KF+RSN  TC NQR
Sbjct: 181 RDSGAAVIARHRGRVEHVESNQVLVRRLIEEDGQEYEGEVDRYPLAKFKRSNSGTCYNQR 240

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDL 805
           P++  GD V + +I+ADGPS +LG++
Sbjct: 241 PIISTGDIVDKGEILADGPSMELGEM 266


>gi|154362097|gb|ABS80887.1| RNA polymerase beta subunit [Delftia acidovorans]
          Length = 234

 Score =  236 bits (603), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 136/230 (59%), Positives = 170/230 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNLLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+++ YLSA+EE    IAQAN+ LD +G 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVADGKVTDEIDYLSAIEEGKYIIAQANADLDAEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +LV  R  G+  LV  E++ ++D SP Q+VS+AASLIPFLE+DD+NR LMG NM RQ
Sbjct: 121 LIGDLVSAREKGDSTLVSAERVQYMDVSPAQIVSVAASLIPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIV+R  +
Sbjct: 181 AVPVLRPEKPMVGTGIERVAAVDSGTVVTATRGGIVDYVDATRIVVRVND 230


>gi|55583698|gb|AAV53368.1| RNA polymerase II second largest subunit [Pleurotus ostreatus]
          Length = 645

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 120/730 (16%), Positives = 208/730 (28%), Gaps = 129/730 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 44   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 99

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++  G I  P  +  +      +   +A           N         
Sbjct: 100  GLVKNLALMSCIS-GGSISAPVIEFLEEWGLESLE-ENAHSSIPCTKVFVNGVWMGVHRD 157

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
               LV                   D SP+  V             D+ RV     +    
Sbjct: 158  PANLVKTLKKLRRKD---------DISPEVSVVRDIREKELRVYTDAGRVCRPLFIVENH 208

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
              LL+ +            A          R+G++E +DA       +    +   +   
Sbjct: 209  QLLLQ-KKHIRWLNQTVDDAGEPFKWDGLIRSGVIEMLDAEEEETVMISMTPEDLENSRL 267

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             +  +       +   +    +K              PS  LG       +  + +P+  
Sbjct: 268  QHAGV--DTRVNDGEYDPAARLKASTHAHTWTHCEIHPSMILG-------ICASIIPFPD 318

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N                        ++       +G       I               
Sbjct: 319  HNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM-----------DT 349

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S V   + 
Sbjct: 350  MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRGLF 409

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               ++ R  +D  ++S   + E+ E  +RD          +       I  G        
Sbjct: 410  -RSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLEDDGLIAPGTGVDGEDI 468

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  D                +E  QR     +    T     E+ F +++   
Sbjct: 469  IIGKTAPIPPD---------------SEELGQRTRTHTRRDVSTPLKSTENGFVDQVLI- 512

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI
Sbjct: 513  ----TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDI 568

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +G + E  L      +G +                             
Sbjct: 569  IINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------------------- 601

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E++++ LR       G  ++Y G 
Sbjct: 602  --------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEVMYHGH 634

Query: 1241 TGEPFDRPVT 1250
            TG      V 
Sbjct: 635  TGRKLQAQVY 644



 Score =  117 bits (292), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 82/590 (13%), Positives = 164/590 (27%), Gaps = 99/590 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             F++  ++ +    +  KY L   G      +         + + +    + +  L   
Sbjct: 6   KEFNLTLAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRC 64

Query: 447 -----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP- 500
                R GK       +  +  +    E  + Q    +  +         S+    +   
Sbjct: 65  NTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISGGSISAPVIEFL 124

Query: 501 ------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
                     NA   +     F     +    +  N +  +   RR   +          
Sbjct: 125 EEWGLESLEENAHSSIPCTKVFVNGVWMGVHRDPANLVKTLKKLRRKDDISPEVSVVRDI 184

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDV 614
             +   V+        P    E H + L      +         E    K      +  +
Sbjct: 185 REKELRVYTDAGRVCRPLFIVENHQLLLQKKHIRWLNQTVDDAGEP--FKWDGLIRSGVI 242

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDAS 667
             L A EEE   I+     L+        +      GE                   +  
Sbjct: 243 EMLDAEEEETVMISMTPEDLENSRLQHAGVDTRVNDGEYDPAARLKASTHAHTWTHCEIH 302

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ I AS+IPF +++ S R      M +QA+ +                        
Sbjct: 303 PSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI----------------- 345

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
                                      + + +  Y       +     +  R        
Sbjct: 346 ------------------------RMDTMANILYYPQKPLATTRSMEYLKFR-------- 373

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +L  G+N +VA + + GYN EDS+++++  V   +F S++   +
Sbjct: 374 ----------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRGLFRSMYYRSY 417

Query: 848 EVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             + + + +   E        +   +       +++ G+I  G  V+  DI++GK  P  
Sbjct: 418 MDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLEDDGLIAPGTGVDGEDIIIGKTAPIP 477

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                  ++        +    RD S  + S  +G V  V I   H   K
Sbjct: 478 PDSEELGQRT-------RTHTRRDVSTPLKSTENGFVDQVLITTNHEGQK 520


>gi|123979372|gb|ABM81511.1| RNA polymerase II second largest subunit [Rhizocarpon superficiale]
          Length = 703

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 113/822 (13%), Positives = 226/822 (27%), Gaps = 143/822 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    ++ + +    +              + +  + S +     +
Sbjct: 2    KRLDLAGPLLAGLFRTLFKKLSKDVFKYLQKCVEQNREFNLTLGVKSTTLTSGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +       +  +    S      
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMVQRSMDLLEEYEPQSYPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     +        I      + D  D   K          P F+
Sbjct: 178  IFVNGVWVGVHRDPAHLVSTIQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             ++D      G  +  +       E   +G  M+    +       +K  G    V   +
Sbjct: 238  IDNDPRSPNRGSLVLTKQHIQKLEEDHEIGADMDPGERE-------SKFMGWEGLV--NQ 288

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             V+  V+ + + +   V     ++  R  Q               V+          T  
Sbjct: 289  GVVEYVDAEEEETVMIVMTPADLEISRQLQQGYTLPEASDDPNRRVKAPMNPTAHTWTHC 348

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N          M  + +   + +  ++             
Sbjct: 349  EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------- 396

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                               +  +             +       +   +  + AI     
Sbjct: 397  -----------------DTMANILYYPQNPLATTRSMEFLKFRELPAGQNAIVAIACYSG 439

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S V   +    +F R   D+ +R  +     +E   +    + + L   
Sbjct: 440  YNQEDSVIMNQSSVDRGLF-RSLFYRAYTDQEKRVGT---SVVEQFEKPMRSDTLKLKHG 495

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 496  TYDKLDDDGIVAPGVRISGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGI 555

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                             LR VKV +   +  Q GDK A RHG KG
Sbjct: 556  VDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKG 595

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 596  TIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 655

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 656  DVTVDSVSSLLR--EHGYQSRGFEVM---------------------------------- 679

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                        +G +    G         V +G  Y  +L 
Sbjct: 680  -----------YNGHT----GR---KLAAQVFLGPTYYQRLR 703


>gi|254055181|gb|ACT64190.1| RpoB [Pseudomonas aeruginosa]
 gi|254055183|gb|ACT64191.1| RpoB [Pseudomonas aeruginosa]
 gi|254055185|gb|ACT64192.1| RpoB [Pseudomonas aeruginosa]
 gi|254055187|gb|ACT64193.1| RpoB [Pseudomonas aeruginosa]
          Length = 231

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 138/231 (59%), Positives = 179/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +A+ EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA+++L+E G   +
Sbjct: 121 INSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVD 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|52699862|gb|AAU86992.1| DNA-dependent RNA polymerase II second largest subunit [Pyrenula
            cruenta]
          Length = 716

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 132/839 (15%), Positives = 245/839 (29%), Gaps = 151/839 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G ++   +R    ++ +  +   +    +   +  +       + + + 
Sbjct: 1    DXXGKKRLDLAGPLMAKLFRTQFHKVVKDFQRYMQKQVENGQEINLKVGFKPNIITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +A     + R     + R +
Sbjct: 61   YSLATGNWGEQKKANRNTAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY----L 617
            H TH+G ICPAET EG   GLV +L   + V   G  +   + + D +    +      L
Sbjct: 117  HNTHWGFICPAETPEGQACGLVKNLALMSAVTTGGPSQPIMKYLLDKRHVEPLEDWEPQL 176

Query: 618  SAMEEENRYIAQANSSL--DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            +        I     ++  +E     E     R       +     D  D   +      
Sbjct: 177  TPHA-TKIIINGVWFAVIKEEPRFLVEHFRDLRRKTHLPDMTALVWDIRDREFRINTDAG 235

Query: 676  ASLIPFL--ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKRA 732
              + P    E++ ++       + +  V  L A       G       +         + 
Sbjct: 236  RIVRPLFVVESNPAHPNKGNLVLNKSHVARLSATREARLAGQPIEEYEQEPFEWPDLVKE 295

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            GI++ VDA       +    D       IY+        ++      PL+          
Sbjct: 296  GIIDWVDAEEEETLMIVMSPDELE-NSRIYQSGYSLPPPEDPLERVAPLLNP--YAHTFT 352

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N                        +     
Sbjct: 353  HCEIHPSMILG-------VCASIIPFPDHNQSPRN------------------TYXXXXX 387

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G      D    +           +  +         +   +       +   +  
Sbjct: 388  XXXMGVFLTNFDQRMET-----------MANILYYPQKPLAITSSMEYLRFRDLPAGQNA 436

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +   +      V    +E   +   
Sbjct: 437  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQE----KQVGHNVLERFEKPVR 492

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L R  Y ++ E   +  G           K+  ++SD                +E
Sbjct: 493  ADTLKLKRGTYDKVDEDGIVAPGVRVSGEDIIMGKTAPMASD---------------TEE 537

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  + +K    T     E    +++      D       + VKV V   +  Q GDK
Sbjct: 538  LGQRTKQHIKRDVSTPLRSTESGIVDQVLVTSTQDA-----AKFVKVRVRTTKVPQIGDK 592

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 593  FASRHGQKGTIGITYRQEDMPFSREGVTPDLIINPHAIPSRMTIAHLIECQLSKLASLTG 652

Query: 1150 KKIKSLINDYKANGDIS-PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVST 1208
            ++  +          IS  LR F  +  G                               
Sbjct: 653  QEGDATPFTAVTVTAISQRLRDFGFQSRGFEVM--------------------------- 685

Query: 1209 PVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                                  +G +    G         V  G  Y  +L HMV DK+
Sbjct: 686  ---------------------YNGHT----GR---KLVAQVFFGPTYYQRLRHMVDDKI 716



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 94/609 (15%), Positives = 170/609 (27%), Gaps = 56/609 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +     T  +K  KD    + + +  G      V       +  +  KY L   G  
Sbjct: 12  GPLMAKLFRTQFHKVVKDFQRYMQKQVENGQEINLKVGFK--PNIITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               + N +T    + + +    + +  L        R+GK       +  +       E
Sbjct: 69  GEQKKANRNTAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGFICPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             + Q    +  +               +           +              +    
Sbjct: 129 TPEGQACGLVKNLALMSAVTTGGPSQPIMKYLLDKRHVEPLEDWEPQLTPHATKIIIN-G 187

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
              + I    R        + R     +M  +      R     T  G  +        F
Sbjct: 188 VWFAVIKEEPRFLVEHFRDLRRKTHLPDMTALVWDIRDREFRINTDAGRIVRP-----LF 242

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
              +           +    V      LSA  E               G   EE      
Sbjct: 243 VVESNPAHPNKGNLVLNKSHVAR----LSATREARL-----------AGQPIEEYEQEPF 287

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
                LV    ID++DA  ++ + I  S     E ++S     G ++     PL +    
Sbjct: 288 EW-PDLVKEGIIDWVDAEEEETLMIVMSP---DELENSRIYQSGYSLPPPEDPLERVAPL 343

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQ 768
                      +   + I+   A I+   D  +    +          GV       + +
Sbjct: 344 LNPYAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYXXXXXXXXMGVFLTNFDQRME 403

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PL           I +        DL  G+N +VA   + GYN EDS++
Sbjct: 404 TMANILYYPQKPL----------AITSSMEYLRFRDLPAGQNAIVAIACYSGYNQEDSVI 453

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++  +   +F S+    ++   +       E        D   +       +DE GI+ 
Sbjct: 454 MNQSSIDRGLFRSLFYRTYQDQEKQVGHNVLERFEKPVRADTLKLKRGTYDKVDEDGIVA 513

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            G  V+  DI++GK  P         ++  + I        RD S  + S  SG V  V 
Sbjct: 514 PGVRVSGEDIIMGKTAPMASDTEELGQRTKQHIK-------RDVSTPLRSTESGIVDQVL 566

Query: 944 IFNRHGIDK 952
           + +     K
Sbjct: 567 VTSTQDAAK 575


>gi|312204350|gb|ADQ47492.1| RNA polymerase II second largest subunit [Odontotrema sp. 2 EB-2010]
          Length = 707

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 110/795 (13%), Positives = 226/795 (28%), Gaps = 115/795 (14%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + + +  +              + +  + + +     +            
Sbjct: 2    LFRNLFTKLTKDVYKYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 61

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 62   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 117

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +    + +V  +     +      ++      +  
Sbjct: 118  ACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRSPNSTKVFVNGVWVGVHR 177

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
            D +     V        I      I D  D   K          P F+  +D+     G 
Sbjct: 178  DPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIENDNKSSNKGN 237

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +  +       +   +   +E            AKR      + A    +  ++ + + 
Sbjct: 238  LVLTKETVNKLEDDKDIPADLEEEE--------RAKRYFGWAGLLAS-GAVEFLDAEEEE 288

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +         ++  R  Q       P   +   V+    +A    T      ++   +  
Sbjct: 289  TVMIAMTPEDLEISRQVQAGYALPEPSTDLNARVKAKVNVAQHTWTHCEIHPSMILGICA 348

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N   +++   + V                                       
Sbjct: 349  SIIPFPDHNQVSAVVPWLK-VPCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 407

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                      +             +       +   +  + AI      +  D+ +   S
Sbjct: 408  XXXXXXXXXHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 467

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R  +++ +R   +    +E   +    + + L    Y +L +   I 
Sbjct: 468  SIDRGLF-RSLFYRAYVEQEKR---IGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIA 523

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +            
Sbjct: 524  PGVRVSGEDIIIGKTAPIAPDDEELGQRTKLHTKRDASTPLRSTESGI------------ 571

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                  ++K+          L+ VKV +   +  Q GDK A RHG KG V      EDMP
Sbjct: 572  ------VDKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMP 623

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   DI++NP  +PSRM +  + E  L       G +                   
Sbjct: 624  FSSEGIVPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------- 666

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     ++++ +LR      
Sbjct: 667  ------------------------------------ATP-FTEVTVDSVSRLLREHGYQS 689

Query: 1231 SGQSILYDGLTGEPF 1245
             G  + Y+G TG   
Sbjct: 690  RGFEVXYNGHTGRKL 704


>gi|80973507|gb|ABB53491.1| RNA polymerase beta subunit [Streptococcus hyovaginalis]
          Length = 226

 Score =  236 bits (602), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 97/294 (32%), Positives = 133/294 (45%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                     A  E        A +D   +++LYDG TGEPFD  V+VG +YM+K
Sbjct: 189  ---------ATVEE-------AGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|3133423|gb|AAC38512.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133425|gb|AAC38513.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133427|gb|AAC38514.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133429|gb|AAC38515.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133431|gb|AAC38516.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133433|gb|AAC38517.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133435|gb|AAC38518.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133437|gb|AAC38519.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133439|gb|AAC38520.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133443|gb|AAC38522.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133445|gb|AAC38523.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
 gi|3133477|gb|AAC38539.1| RNA polymerase beta-subunit [Mycobacterium intracellulare ATCC
           13950]
 gi|3133479|gb|AAC38540.1| RNA polymerase beta-subunit [Mycobacterium intracellulare]
          Length = 234

 Score =  236 bits (601), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDAKGRFEESRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|3133381|gb|AAC38491.1| RNA polymerase beta-subunit [Mycobacterium avium]
          Length = 234

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDDKGRFEEXRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|46019136|emb|CAE52032.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 133

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 57/155 (36%), Positives = 90/155 (58%), Gaps = 22/155 (14%)

Query: 35  ASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWR 94
           +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++   R
Sbjct: 1   SSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKER 50

Query: 95  DLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVV 154
           D+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +R++V
Sbjct: 51  DVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIV 101

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           SQL RSP ++F    G+   +GK  +   +IP++G
Sbjct: 102 SQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRG 133


>gi|3133405|gb|AAC38503.1| RNA polymerase beta-subunit [Mycobacterium xenopi]
 gi|3133467|gb|AAC38534.1| RNA polymerase beta-subunit [Mycobacterium smegmatis]
          Length = 234

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 178/231 (77%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVENGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS  DE+G FTE+ V  R   GE   V  +++D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPTDENGRFTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|50295197|gb|AAT72971.1| RpoB [Streptococcus thermophilus]
          Length = 240

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 95/296 (32%), Positives = 132/296 (44%), Gaps = 71/296 (23%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSEDLWDTVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
               +    ++L        G        TGEPFD  V+VG +YM+KL+HMV DK+ 
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLHHMVDDKLQ 240



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNVSEE LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   RELPNVSEEALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|154362091|gb|ABS80884.1| RNA polymerase beta subunit [Acidovorax cattleyae]
          Length = 234

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/232 (58%), Positives = 170/232 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+ + YLSA+EE    IAQAN+ LDEDG 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDQIDYLSAIEEGKYVIAQANAQLDEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +  +LV  R  G  +    E++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQ
Sbjct: 121 WPGDLVSARGTGPSLHGHAERVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIV+R  + +
Sbjct: 181 AVPVLRPEKPMVGTGIERVRAVDSGTVVTATRGGIVDYVDATRIVVRVNDDE 232


>gi|154362089|gb|ABS80883.1| RNA polymerase beta subunit [Acidovorax avenae subsp. avenae]
          Length = 234

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/232 (58%), Positives = 172/232 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEIRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT+ + YLSA+EE    IAQAN+ LDEDG 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTDQIDYLSAIEEGKYVIAQANAELDEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +  ELV  R +G+ +    E++ ++D SP Q+VS+AASL+PFLE+DD+NR L+G NM RQ
Sbjct: 121 WPGELVSARGSGQTLHGRAERVQYMDVSPAQIVSVAASLVPFLEHDDANRALIGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIV+R  + +
Sbjct: 181 AVPVLRPEKPMVGTGIERVRAVDSGTVVTATRGGIVDYVDATRIVVRVNDDE 232


>gi|119644234|gb|ABL85614.1| RNA polymerase II second largest subunit [Coccocarpia domingensis]
          Length = 667

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 108/731 (14%), Positives = 219/731 (29%), Gaps = 90/731 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G +L   +R    ++ +      + +     S+  Q +I    + +
Sbjct: 1    DDSDHFGKKRLDLAGPLLAGLFRTLYYKLTKDANRALQKAVESGKSLELQSIIKPGILTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLKYSLATGNWSEQKKAAQGKAGVSQVLNRYTYASTLSHLRRTNT----PLGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V + G+    + +  + ++  +   
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGSPGWPVIDFLQSRNMELLEEYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
                     ++      +    +     +        I      + D  +   K      
Sbjct: 177  SRNPHATKVFVNGTWVGVHPSPAHLHSRILALRRNNTISHEVSIVRDIREREFKIFTDAG 236

Query: 676  ASLIPFLENDDSNRVLMGCNMQRQAVPL-----LKAEAPFVGTGMESVVAKSSGAAIVAK 730
                P    D+  R     ++      L      + E P++    +              
Sbjct: 237  RVSRPLFVVDNDKRSERQGHLVLTKDLLAQLEEDREEPPWIPPSNDPTARPPLRGWDRLI 296

Query: 731  RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
            + G VE +DA       +    +      +         + +      R   K+      
Sbjct: 297  QGGTVEYLDAEEEETVMICMTPEDLEIHREKQAGYDEVGTQEGDDPVSRIKTKLSQPPHV 356

Query: 791  NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVM 850
                   PS  LG       +  + +P+  +N          M  + +   + +  ++  
Sbjct: 357  YTHCEIHPSMILG-------ICASIIPFPDHNQSPRNCYQSAMGKQAMG--VFLTNYDQR 407

Query: 851  ARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
                                          +  +             +       +   +
Sbjct: 408  M---------------------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQ 440

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R   D+ +    + R  +E   + 
Sbjct: 441  NAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEK---QIGRSVVEQFEKP 496

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + + L    Y +L +   +  G           K+  ++ D      R+++      
Sbjct: 497  MRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKYHVKRDV 556

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +  Q                             LR VKV +   +  Q G
Sbjct: 557  STPLRSTENGIVDQ--------------------VLVTTNAEGLRFVKVRMRTTKIPQIG 596

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK A RHG KG V      EDMPF  +G   D+++NP  +PSRM +  + E  L      
Sbjct: 597  DKFASRHGQKGTVGITYRQEDMPFTAEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSL 656

Query: 1148 LGKKIKSLIND 1158
             G +  +    
Sbjct: 657  RGFEGDATPFT 667


>gi|3133469|gb|AAC38535.1| RNA polymerase beta-subunit [Mycobacterium scrofulaceum]
          Length = 234

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDASGRFEESRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|156619305|gb|ABU88332.1| RNA polymerase beta subunit [Chlamydomonas moewusii]
          Length = 1661

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 82/224 (36%), Positives = 116/224 (51%), Gaps = 39/224 (17%)

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             +S      K K   +Q         +  ++V++A +R +Q GDKMAGRHGNKGI+S IL
Sbjct: 683  QRSSTGQNLKTKKTGMQALYLKSTSSVSSIQVYLAERRRVQVGDKMAGRHGNKGIISEIL 742

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P ED+PFL DGTP+D+VLNPLGVPSRMNVGQI+E  LG A   LG+  K    D      
Sbjct: 743  PIEDLPFLPDGTPLDMVLNPLGVPSRMNVGQIYECLLGLAGKHLGENYKVFPFD------ 796

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                     ++ G  +    +     ++ ++  + W                        
Sbjct: 797  ---------EIYGAEASRSFVYSKLYNASVKTGKTW------------------------ 823

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            + + +  G+  LYDG TGE F + +TVGY Y+L+L HMV DK++
Sbjct: 824  LFNPNLPGKIGLYDGRTGESFHQAITVGYAYILRLVHMVDDKMH 867



 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 57/97 (58%), Positives = 71/97 (73%), Gaps = 1/97 (1%)

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RSTG YSLVTQQPL G+S  GGQRLGEMEVW ++ YGAA+ L EMLTIKSDD+ GR  +
Sbjct: 1563 SRSTGPYSLVTQQPLRGRSKHGGQRLGEMEVWALEGYGAAFTLLEMLTIKSDDMSGRMTL 1622

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLEN 1365
            + +++   +    GTPESF VL+ E+QAL L I L  
Sbjct: 1623 WSNLILNKEIS-IGTPESFKVLICELQALCLDIGLFR 1658



 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 96/249 (38%), Positives = 151/249 (60%), Gaps = 1/249 (0%)

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
            +I + S +   +        Y L K+ RSNQ+TC+  +P V  G  V   D++AD  ++
Sbjct: 242 TKIKVNSYKIIENCDNYLSMEYSLEKYHRSNQDTCLVHKPAVVEGQWVESGDLLADCSAS 301

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+LALG+N+L+ +MPW GYNFED++LISER+V +D++TSIHIE +EV   ++KLG ++
Sbjct: 302 VGGELALGQNILIGYMPWEGYNFEDAILISERLVYDDLYTSIHIERYEVNIEESKLGMDK 361

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITR+IP V  + LKN++  GII +G+ V  GDILVGK+TP  +   +  +KLL  I  + 
Sbjct: 362 ITREIPEVDSDSLKNLNSLGIIKIGSWVQEGDILVGKVTPVNKKNQSNYQKLLYLILDKT 421

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIF-NRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
              VRD+SLR P G+   V+ +++F N   +D+ E   S+  +  +   + K +      
Sbjct: 422 VSPVRDSSLRAPKGIKAKVIGLQVFKNNTNLDRIESPHSIASKNTKSSQKIKANLSFSGL 481

Query: 980 RNIYSRLME 988
           +NI ++   
Sbjct: 482 QNINNKEKN 490


>gi|320172598|gb|ADW24182.1| RNA polymerase II second largest subunit [Veluticeps abietina]
          Length = 673

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 111/728 (15%), Positives = 213/728 (29%), Gaps = 89/728 (12%)

Query: 458  NLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCE 515
            + G +R+   G +L N +R+   ++ + +    +              +    + + +  
Sbjct: 1    HFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLKY 60

Query: 516  FFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
               +               +SQ+       S ++H RR +      + R     + R +H
Sbjct: 61   SLATGNWGDQKKSMSTKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLH 116

Query: 563  PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             TH+G +CPAET EG   GLV +L     ++           + +  + +         E
Sbjct: 117  NTHWGMVCPAETPEGQACGLVKNLALMGWISVGSLSAPVIEFLEEWGLESL--------E 168

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            EN + A   + +  +G +       R     +   ++     D SP+  V          
Sbjct: 169  ENAHSATPCTKVFVNGVWMG---VHRDPANLVRTIKKLRRKDDISPEVSVVRDIRERELR 225

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
               D+ RV     +       L+ +                       + GI+E +DA  
Sbjct: 226  LYTDAGRVCRPLFIVENQQLALQKKHIRWLNQGYRDDDMEPWKWDQLVKNGIIELLDAEE 285

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                 +    +   +     +             +    +K   +          PS  L
Sbjct: 286  EETVMISMTPEDLENSRL--QSAGIDTHLNEGEYDPAVRLKAPTQGHTWTHCEIHPSMIL 343

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N       S R   +  +    +  +               
Sbjct: 344  G-------VCASIIPFPDHNQ------SPRNTYQSAWGKQAMGIYLTNF----------- 379

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                      L  +D  G   +             +       +   +     I G    
Sbjct: 380  ----------LVRMDTMG--NILYYPQKPLATTRSMEYLKFRELPAGQNAFGVILGYSGY 427

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  ++ +   S +   +    I+ R  +D  ++S   + E+ E   RD          + 
Sbjct: 428  NQENSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDK 486

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 487  LEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRTRLHTRRDVSTALKSTESGIVDQV 546

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 547  LI--------------------TTNSEGQKFVKVRVRATRVPQIGDKFASRHGQKGTIGI 586

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +        
Sbjct: 587  TYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTV 646

Query: 1163 GDISPLRS 1170
              +S    
Sbjct: 647  ESVSTFLR 654



 Score = 70.5 bits (171), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 60/456 (13%), Positives = 117/456 (25%), Gaps = 56/456 (12%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 11  GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHNTITNGLKYSL-ATGNW 67

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 68  GDQKKSMSTKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 127

Query: 470 --------MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                   ++KN   +G + +       I  ++   +      NA         F     
Sbjct: 128 TPEGQACGLVKNLALMGWISVGSLSAPVIEFLEEWGLE-SLEENAHSATPCTKVFVNGVW 186

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  N +  I   RR   +                ++        P    E   + 
Sbjct: 187 MGVHRDPANLVRTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLA 246

Query: 582 LVSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           L              ++   YR       K         +  L A EEE   I+     L
Sbjct: 247 LQKKHIR--------WLNQGYRDDDMEPWKWDQLVKNGIIELLDAEEEETVMISMTPEDL 298

Query: 635 DEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +     +  +      GE     R             +  P  ++ + AS+IPF +++ S
Sbjct: 299 ENSRLQSAGIDTHLNEGEYDPAVRLKAPTQGHTWTHCEIHPSMILGVCASIIPFPDHNQS 358

Query: 688 NRVLMGC----------------NMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAK 730
            R                      M      L   + P   T  ME +  +   A   A 
Sbjct: 359 PRNTYQSAWGKQAMGIYLTNFLVRMDTMGNILYYPQKPLATTRSMEYLKFRELPAGQNAF 418

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
              +          +   +  +D        YR   
Sbjct: 419 GVILGYSGYNQENSVIMNQSSIDRGLFRSIYYRSYM 454


>gi|242003016|ref|XP_002422580.1| DNA-directed RNA polymerase I 135 kDa polypeptide, putative
            [Pediculus humanus corporis]
 gi|212505370|gb|EEB09842.1| DNA-directed RNA polymerase I 135 kDa polypeptide, putative
            [Pediculus humanus corporis]
          Length = 1114

 Score =  236 bits (601), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 107/595 (17%), Positives = 185/595 (31%), Gaps = 135/595 (22%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                +    N+ +      G   +  + I  ++       + H +E       + L    
Sbjct: 619  PNRLMRPVLNLALNKTELIGTFEQVYLEICLKLNEAYEGLTTH-KELSHTTFLSNLACLI 677

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               D         +   + G   +G  V+  DI       +   P +P            
Sbjct: 678  PMPDCNQSPRNMYQC--QMGKQSMGTPVHTWDIQAETKLYRLLLPSSPLF--------RP 727

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
                       P GV+  V  +        D                        +I+++
Sbjct: 728  GHYDAIKLDDFPMGVNAVVAVISYTGYDMED-----------------------AMIINK 764

Query: 981  NIYSR---LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW---WQFAVQDEKVQRN 1034
            + + R      IL  +     P  + +     ++LIS+              +++ +   
Sbjct: 765  SSFERGFGHGTILKSEFFHLNPDSYFERDPSKAELISKLDDDGLPFPGTLVEENDPICCY 824

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                  +Y   K   ++       ++  G+ +       V +   + R    GDK A R 
Sbjct: 825  FNGELSKYVVEKFHGKEIAYVDNVRLCCGETLNSA---SVCITFRVPRNPVVGDKFASRA 881

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KGI S++ PCED+PF   G   D+V NP G PSRM +  + E   G +    GK    
Sbjct: 882  GQKGICSQMWPCEDLPFTDSGLVPDVVFNPHGFPSRMTIAMMIELMAGKSASVHGK---- 937

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VF-- 1211
                                                             V  +TP +F  
Sbjct: 938  -------------------------------------------------VHDATPFIFSE 948

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            D +  +    +L  A  +  G   +Y G+ G   +  +  G +Y  +L HMV DK   RS
Sbjct: 949  DNSAIDYFGKLLEAAGYNYYGTEKMYSGVDGREMNAAIFFGIVYYQRLRHMVLDKWQVRS 1008

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLG-----------EMEVWCIQAYGAAYVLQEMLTIKSD 1320
            TG    +TQQP+                       EME   + ++GA+ +L + L   SD
Sbjct: 1009 TGPVDTLTQQPIK-----------GRRRGGGVRFGEMERDSLISHGASALLHDRLFECSD 1057

Query: 1321 DVVGRTRVYESI---VA---------GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                R+ ++      V          G +      P  F  L+  +Q   ++I L
Sbjct: 1058 KYKARSALFRCPKTGVKKEVCRLCSDGGNVKTIEIPYIFRYLL--IQLAAVNIHL 1110



 Score = 74.3 bits (181), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 59/441 (13%), Positives = 132/441 (29%), Gaps = 44/441 (9%)

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS----SQLSQLEEHVNSL 532
           L   ++    + +++S    +   +  +N                    L  + E++N +
Sbjct: 408 LSEGKLNSISQIQMASFCKRAGGIEKAMNNFVATGNCHNSLSGLPQDKGLVIMAENINRM 467

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             ++H     A+ +G         + R + P  +G ICP  T +G   GL++ L+    V
Sbjct: 468 RYMSH---FKAIHRGAYFTTMRTTDGRQLLPEAWGFICPVHTPDGSPCGLLNHLSKDCIV 524

Query: 593 NAYGFIETPYRKVCD-------------GKVTNDVVYLSAMEEENR--YIAQANSSLDED 637
                    Y  + +               V     Y   + +     Y+A  N+     
Sbjct: 525 TNV----PDYEILKNLSCVLTDLGVMPLEIVEKKNNYYDVLLDGKLIGYVADTNAQNLVQ 580

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                ++          +V   K D     P   +    + +     + +          
Sbjct: 581 SLRVLKIEGNVVPNTLEIVLVPKKDSESQYPGIFLFTGPNRLMRPVLNLALNKTELIGTF 640

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            Q    +  +      G+     + S    ++  A ++   D  +      +  +   + 
Sbjct: 641 EQVYLEICLKLNEAYEGLT-THKELSHTTFLSNLACLIPMPDCNQSPRNMYQCQMGKQSM 699

Query: 758 GVDIY-RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           G  ++   ++ +       +   PL + G             +  L D  +G N +VA +
Sbjct: 700 GTPVHTWDIQAETKLYRLLLPSSPLFRPGHY----------DAIKLDDFPMGVNAVVAVI 749

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            + GY+ ED+M+I++           H    +                      E +  +
Sbjct: 750 SYTGYDMEDAMIINKSSFERGFG---HGTILKSEFFHLNPDSYFERDPS---KAELISKL 803

Query: 877 DECGIICVGAEVNPGDILVGK 897
           D+ G+   G  V   D +   
Sbjct: 804 DDDGLPFPGTLVEENDPICCY 824



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 94/742 (12%), Positives = 213/742 (28%), Gaps = 138/742 (18%)

Query: 30  IEVQKASYDHFLMMNIAPDERP-----NEGLQAAFKSVFPITAF--SGAAMLEFVSYEFD 82
           +++Q    + FL     P         ++GL    K++ PI     S    ++  +    
Sbjct: 30  LDIQ----NEFLQTLGKPHVDSFNLLIDKGLNLICKNLIPIHFSVGSDRYTVQIENLRLL 85

Query: 83  PP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSI 130
            P            K    +C  R  TY+  L   +   V  V++    K          
Sbjct: 86  YPVMPDGSFALKTQKIFPCECRQRASTYSGNLFGKITWSVNGVNQHPIEKD--------- 136

Query: 131 YMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFD 166
             G +P+M K                         G F++KG ++     L R       
Sbjct: 137 -FGKIPIMIKSNRCHLKNLTPRELVEKNEHEDEWGGYFILKGHEK-----LIRM---LIA 187

Query: 167 HDKGRASLSGKLLYACRI--IPDQGLWM----DIEFDSKDIIHVRIDRRRK--------- 211
             +       +  +  R     ++G+ +    + E  + +++H   D   K         
Sbjct: 188 TRRNYPIALSRRTWKQRGASFSEKGILLRCVSEDETSTNNVLHFVTDGTVKVMLSYGRSL 247

Query: 212 --VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
             +P+   L +L   S+      + ++   +  DF+        L     V       + 
Sbjct: 248 YFIPLCLILKSLINVSD---LYVFKRLTEGRDDDFYFKSCIKTMLY-DVHVQGIDTHEEA 303

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---GETGEIYIEAGD 326
              + ++ +           +  +  L +       L   +D  N     T +++     
Sbjct: 304 KCFIGKTFRLKFPDQSPWFTDAQICDLIMEKCLAIHLNDNKDKFNLLIFMTQKLFAFVQG 363

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNN--NAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
              E++ + +   EI     +Y   + +    ++ N  +    K  +  L  I +     
Sbjct: 364 QCCEENADSLMVQEILTGGSIYQQVLKDRLQGFLNNLRLVASKKLSEGKLNSISQ----- 418

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILV 444
                 +  + F       +K   + V     +  L+    D    I  E+ I  ++ + 
Sbjct: 419 ------IQMASFCKRAGGIEKAMNNFVATGNCHNSLSGLPQDKGLVIMAEN-INRMRYMS 471

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDIDSVMPQDL 503
             +     I         R     ++L   +  +  +         + +      +  ++
Sbjct: 472 HFK----AIHRGAYFTTMRTTDGRQLLPEAWGFICPVHTPDGSPCGLLNHLSKDCIVTNV 527

Query: 504 INAKPVVS--AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            + + + +   V        L  +E+  N    +   + +  +         A   ++ +
Sbjct: 528 PDYEILKNLSCVLTDLGVMPLEIVEKKNNYYDVLLDGKLIGYVADTN-----AQNLVQSL 582

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
                       T E   +    S + +  +  +       R V +              
Sbjct: 583 RVLKIEGNVVPNTLEIVLVPKKDSESQYPGIFLFTGPNRLMRPVLN-------------- 628

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                +A   + L      T E V+     +            + S    +S  A LIP 
Sbjct: 629 -----LALNKTELIG----TFEQVYLEICLKLNEAYEGLTTHKELSHTTFLSNLACLIPM 679

Query: 682 LENDDSNRVLMGCNMQRQAVPL 703
            + + S R +  C M +Q++  
Sbjct: 680 PDCNQSPRNMYQCQMGKQSMGT 701


>gi|262193255|gb|ACY30630.1| RNA polymerase beta subunit [Xanthomonas axonopodis pv.
           malvacearum]
          Length = 241

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 144/241 (59%), Positives = 179/241 (74%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ+LIN KPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+
Sbjct: 1   TPQELINPKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+C  ET EG NIGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLS
Sbjct: 61  RDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE    IAQAN+  D     TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L
Sbjct: 121 AIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAAL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           +PFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+E  VA+ SG  + A R G++EQ+
Sbjct: 181 VPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQI 240

Query: 739 D 739
           D
Sbjct: 241 D 241


>gi|103001334|gb|ABF71502.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            flavum]
          Length = 690

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 111/751 (14%), Positives = 211/751 (28%), Gaps = 128/751 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 60   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 115

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +      E    +    + +V  +     +      ++      +  D 
Sbjct: 116  GLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVGVHRDP 175

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
            +     V        I      + D  D   K          P F+ ++D      G  +
Sbjct: 176  AHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSTNCGNLV 235

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              +       +   +   M+S   +       AK  G    V     V+  V+ + + + 
Sbjct: 236  LTKEHINKLEDDRDLPAIMDSEEKE-------AKFFGWDGLV--NNGVVEYVDAEEEETV 286

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAF 815
              V     ++  R  Q           +   V+          T      ++   +  + 
Sbjct: 287  MIVMTPEDLEISRQIQAGYAMPEASDDLNKRVKAPMNPTAHTWTHCEIHPSMILGICASI 346

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N               +   + +  ++                           
Sbjct: 347  IPFPDHNQSPRXXXXXXXXXXXMG--VFLTNYDQRM------------------------ 380

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 381  ---DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 437

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G
Sbjct: 438  DRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPG 493

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +S D      R++          ++     +  Q           
Sbjct: 494  VRVSGEDIIIGKTAPISPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL-------- 545

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              L+ VKV +   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 546  ------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 593

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            K+G   D+++NP  +PSRM +  + E  L       G +  +          +S L    
Sbjct: 594  KEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKLLR-- 651

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            E    +                                                    +G
Sbjct: 652  EHGYQSRGFEVM---------------------------------------------YNG 666

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
             +    G         V +G  Y  +L HMV
Sbjct: 667  HT----GR---KLVAQVFLGPTYYQRLRHMV 690



 Score =  115 bits (288), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 88/579 (15%), Positives = 154/579 (26%), Gaps = 94/579 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   S  G  ++  R    +      R          I    
Sbjct: 35  ITNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPR 94

Query: 445 DLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQ 501
            L N   G +   +    +    V  +    Y       E  I    + +   ++   PQ
Sbjct: 95  QLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQ 154

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-- 558
              NA  V      F     +    +  + +S +   RR   +  +  + R     E   
Sbjct: 155 RSPNATKV------FVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKI 208

Query: 559 -----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCD 607
                R   P       P  T+ G+ +     +           I      E  +     
Sbjct: 209 FTDAGRVCRPLFVIDNDPKSTNCGNLVLTKEHINKLEDDRDLPAIMDSEEKEAKFFGWDG 268

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 V Y+ A EEE   I      L                              + S
Sbjct: 269 LVNNGVVEYVDAEEEETVMIVMTPEDL------------------------------EIS 298

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            +     A       E  D     +   M                T       +   + I
Sbjct: 299 RQIQAGYA-----MPEASDDLNKRVKAPM--------------NPTAHTWTHCEIHPSMI 339

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +               GV       +           Q+PL     
Sbjct: 340 LGICASIIPFPDHNQSPRXXXXXXXXXXXMGVFLTNYDQRMDTMANILYYPQKPL----- 394

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA   + GYN EDS+++++  +   +F S+    
Sbjct: 395 -----ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 449

Query: 847 FEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E     +  D   +       +D+ GI+  G  V+  DI++GK  P 
Sbjct: 450 YTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPI 509

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                   E+L +        DV        +G+   V+
Sbjct: 510 SPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 544


>gi|112382379|gb|ABI17421.1| RNA polymerase II second largest subunit [Sarcomyxa serotina]
          Length = 659

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 115/727 (15%), Positives = 219/727 (30%), Gaps = 92/727 (12%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLAXLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +           + I   R K    D SP+  V            
Sbjct: 169  AHSSTPCTKVFVNGVWMGVHXDPANLVKTIKKLRRK---DDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +   Q + L K    ++  G      +     +V  + GI+E +DA   
Sbjct: 226  TDAGRVCRPLFIVENQQLALQKKHVKWLNEGSRDDGEEFKWEQLV--KGGIIELLDAEEE 283

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +     +         +   +    +K G            PS  LG
Sbjct: 284  ETVMISMTPEDLENSRL--QQSGVDTLTHDGXFDPAARLKAGVNAHTWTHCEIHPSMVLG 341

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 342  -------VCASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNF 376

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 377  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAVVAILCYSGYN 425

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          +  
Sbjct: 426  QEDSVIMNQSSIDRGLF-XSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTYDKL 484

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G           K+  +  D      R++          ++     +  Q  
Sbjct: 485  EDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 544

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                        + VKV V   R  Q GDK A RHG KG +   
Sbjct: 545  I--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGIT 584

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +         
Sbjct: 585  YRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVE 644

Query: 1164 DISPLRS 1170
             +S    
Sbjct: 645  SVSTFLR 651



 Score =  122 bits (305), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 81/592 (13%), Positives = 165/592 (27%), Gaps = 98/592 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 25  KDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLN 83

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 84  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMAC 143

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA         F     +    +  N +  I   RR
Sbjct: 144 ISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHXDPANLVKTIKKLRR 203

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +            +   ++        P    E   + L      +  +N     + 
Sbjct: 204 KDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVKW--LNEGSRDDG 261

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL----- 655
              K         +  L A EEE   I+     L+        +      G         
Sbjct: 262 EEFKWEQLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQSGVDTLTHDGXFDPAARLK 321

Query: 656 --VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             V        +  P  V+ + AS+IPF +++ S R      M +QA+ +          
Sbjct: 322 AGVNAHTWTHCEIHPSMVLGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI--- 378

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 379 --------------------------------------RMDTMANILYYPQKPLATTRSM 400

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 401 EYLKFR------------------------ELPAGQNAVVAILCYSGYNQEDSVIMNQSS 436

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E        +   +       +++ G+I  G  V
Sbjct: 437 IDRGLFXSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTYDKLEDDGLIAPGTGV 496

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
              DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 497 AGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 544


>gi|80973515|gb|ABB53495.1| RNA polymerase beta subunit [Streptococcus ovis]
          Length = 226

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 95/286 (33%), Positives = 131/286 (45%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSEDLW---------------------------------------------- 188

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
             A  +        A +D   ++ILYDG TGEPFD  V+VG +YM+K
Sbjct: 189  -ATVKE-------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|30141097|gb|AAP21858.1| RNA polymerase beta subunit [Streptococcus equinus]
          Length = 231

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 96/295 (32%), Positives = 134/295 (45%), Gaps = 72/295 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 171  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 192

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM+KL
Sbjct: 193  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIKL 231



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|52699872|gb|AAU86997.1| DNA-dependent RNA polymerase II second largest subunit [Sarcogyne
            similis]
          Length = 704

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 112/823 (13%), Positives = 226/823 (27%), Gaps = 143/823 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            + +   G +L N +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KXLDLAGPLLANLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPAHLVSTVQSLRRRHLISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              +D      G  +  +    +      +   M+    +        K  G    V    
Sbjct: 238  IENDPKDPNCGNLVLTKEHINMLENDKDLPADMDPEEKEK-------KFFGWDGLV--NN 288

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             V+  V+ + + +   V     ++  R  Q           +   V+          T  
Sbjct: 289  GVVEYVDAEEEETVMIVMTPEDLEISRQLQAGYAMPEASDDLIKRVKAPMNPTAHTWTHC 348

Query: 803  G-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                ++   +  + +P+  +N                        ++       +G    
Sbjct: 349  EIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGXQAMGXXXX 390

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                                  +             +       +   +  + AI     
Sbjct: 391  XXXXXXXXXXX-----------ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAXYSG 439

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L   
Sbjct: 440  YNQEDSVIMNXSSIDRGLF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHG 495

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   +  G           K+  ++ D      R++          ++     +
Sbjct: 496  TYDKLDDDGIVAPGVRVSGEDIVIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGI 555

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                             LR VKV +   +  Q GDK A RHG KG
Sbjct: 556  VDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKG 595

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF K+G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 596  TIGITYRQEDMPFTKEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 655

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 656  EVTVDSVSKLLR--EHGYQSRGFEVM---------------------------------- 679

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                        +G +    G         V +G  Y  +L H
Sbjct: 680  -----------YNGHT----GR---KLVAQVFLGPTYYQRLRH 704



 Score =  108 bits (270), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 81/606 (13%), Positives = 172/606 (28%), Gaps = 73/606 (12%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N      NK  KD    + + +       F++   + +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFNKLTKDVYKYLQKCVENNR--EFNLTLGVKSTTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIIEFMIQRNMEVLEEYEPQRSPNATKVFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +    +  + +S +   RR   +             +RD+    +     A         
Sbjct: 185 VGVHRDPAHLVSTVQSLRRRHLIS-------HEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           + +        N     E       D    +    +   E+E ++       L  +G   
Sbjct: 238 IENDPKDPNCGNLVLTKEHINMLEND---KDLPADMDPEEKEKKFF--GWDGLVNNG--- 289

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                              ++++DA  ++ V I  +      +        G  M   + 
Sbjct: 290 ------------------VVEYVDAEEEETVMIVMTPEDLEISRQLQ---AGYAMPEASD 328

Query: 702 PLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
            L+K    P   T       +   + I+   A I+   D  +    + +  +     G  
Sbjct: 329 DLIKRVKAPMNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGXQAMGXX 388

Query: 761 IYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                             Q+PL                      +L  G+N +VA   + 
Sbjct: 389 XXXXXXXXXXXXXILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIAXYS 438

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLK 874
           GYN EDS++++   +   +F S+    +    +   +   E     +  D   +      
Sbjct: 439 GYNQEDSVIMNXSSIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYD 498

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +D+ GI+  G  V+  DI++GK  P         E+L +        DV        +G
Sbjct: 499 KLDDDGIVAPGVRVSGEDIVIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENG 554

Query: 935 VSGTVV 940
           +   V+
Sbjct: 555 IVDQVL 560


>gi|3133471|gb|AAC38536.1| RNA polymerase beta-subunit [Mycobacterium scrofulaceum]
          Length = 234

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNTFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDASGRFEESRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|161331483|gb|ABX60659.1| RpoB [Paenibacillus lactis]
          Length = 232

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVATPVFDGANEYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE LKN+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALKNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|161331441|gb|ABX60638.1| RpoB [Paenibacillus sp. FSL_h8457]
          Length = 232

 Score =  235 bits (600), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 86/204 (42%), Positives = 114/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + S + D  +  D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAALQLGIHVASPVFDGASEYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE LKN+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALKNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|3133323|gb|AAC38462.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133327|gb|AAC38464.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133331|gb|AAC38466.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133333|gb|AAC38467.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
 gi|3133481|gb|AAC38541.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDESGRFAEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|153958175|gb|ABS53378.1| RpoB [Bacteriovorax sp. NZ9]
          Length = 340

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 168/343 (48%), Positives = 230/343 (67%), Gaps = 13/343 (3%)

Query: 714  GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
            G+ES VA+ S A + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQN
Sbjct: 1    GIESTVARDSRAILFAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQN 58

Query: 774  TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
            TC NQ+ LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+
Sbjct: 59   TCNNQKALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERL 118

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            ++ DVFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDI
Sbjct: 119  LARDVFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDI 178

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            LVGKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++  
Sbjct: 179  LVGKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELC 238

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKST 1006
             RS  +  ++  L+ RD+  E   +  +   ++ ++L G              +   K  
Sbjct: 239  ARSKEIIEQETTLIRRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGA 298

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
             L+S++++  P        ++        E L   +   ++ +
Sbjct: 299  DLTSEVLASIPFELIGYLPLE----PALEERLSEYFADVRNRI 337


>gi|3133347|gb|AAC38474.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133361|gb|AAC38481.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133363|gb|AAC38482.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133367|gb|AAC38484.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133369|gb|AAC38485.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133371|gb|AAC38486.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133419|gb|AAC38510.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133441|gb|AAC38521.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133463|gb|AAC38532.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133473|gb|AAC38537.1| RNA polymerase beta-subunit [Mycobacterium kansasii ATCC 12478]
 gi|3133475|gb|AAC38538.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
 gi|3133493|gb|AAC38547.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
          Length = 234

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVIDGLVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D +G F E  V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDAEGRFVEPRVLVRRKAGEVEYVASSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|94410948|gb|ABF18592.1| RNA polymerase II second largest subunit [Lachnella villosa]
          Length = 660

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 112/729 (15%), Positives = 216/729 (29%), Gaps = 95/729 (13%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +R+   ++ + +   +               +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLMANLFRMLFRKLTKDVYRHLQKCVETRKEFSVNLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  + V   G      R   +      +       
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMSCVT-IGTESNIVRDFLEEWGLESL------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E+N       + +  +G +             ++  R      +  P+  +         
Sbjct: 169  EDNANSTVPCTKIFVNGVWVGVHRDAGHLVRNMVRLR---RLGNLRPQTSIVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +  +   +L        T  E    + S   +V++  G++E +DA 
Sbjct: 226  RIYTDAGRVCRPLFVVEKQELVLHKGHIAALT-HEDKEERLSWDKLVSQ--GVIEMLDAE 282

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +   +D       I      +         QR  +K              PS  
Sbjct: 283  EEETVMIAMSIDDLEVARTIRMGGTVEDDPDPG---QR--LKPRHIAHTWTHCEIHPSMI 337

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 338  LG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLT 372

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +             +       +   +  + AI     
Sbjct: 373  NFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 421

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  +++   + E  E   RD          +
Sbjct: 422  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKTGIQQVEDFEKPTRDTTLRMKHGTYD 480

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  D      R++          ++        Q
Sbjct: 481  KLESDGFIAPGVGVRGDDIIIGKTAPIPPDSEELGQRTRLHTRRDVSTPLKSTESGQVDQ 540

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VK+ +   R  Q GDK A RHG KG + 
Sbjct: 541  VLI--------------------TTNSEGQKFVKIRIRATRVPQIGDKFASRHGQKGTIG 580

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +       
Sbjct: 581  ITYRQEDMPFTNEGVVPDIVINPHAIPSRMTIGHLVECLLSKVATVIGNEGDATPFTDLT 640

Query: 1162 NGDISPLRS 1170
               +S +  
Sbjct: 641  VDGVSRVLR 649



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 91/620 (14%), Positives = 167/620 (26%), Gaps = 102/620 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       FSV  ++ +    +  KY L   G  
Sbjct: 12  GPLMANLFRMLFRKLTKDVYRHLQKCV--ETRKEFSVNLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       I +                   NA   V     F     +
Sbjct: 129 TPEGQACGLVKNLSLMSCVTIGTESNIVRDFLEEWGLESLEDNANSTVPCTKIFVNGVWV 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  + +  +   RRL  L                ++        P    E     L
Sbjct: 189 GVHRDAGHLVRNMVRLRRLGNLRPQTSIVRDIRERELRIYTDAGRVCRPLFVVE--KQEL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD-----ED 637
           V      A +      E              +  L A EEE   IA +   L+       
Sbjct: 247 VLHKGHIAALTHEDKEER--LSWDKLVSQGVIEMLDAEEEETVMIAMSIDDLEVARTIRM 304

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           G   E+        +   +        +  P  ++ I AS+IPF +++ S R      M 
Sbjct: 305 GGTVEDDPDPGQRLKPRHIA-HTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 363

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 364 KQAMGIFLTNFLI-----------------------------------------RMDTMA 382

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y       +     +  R                        +L  G+N +VA + 
Sbjct: 383 NILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILC 418

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEG 872
           + GYN EDS+++++  +   +F SI+   +  + + T +   E            +    
Sbjct: 419 YSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKTGIQQVEDFEKPTRDTTLRMKHGT 478

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              ++  G I  G  V   DI++GK  P         ++        +    RD S  + 
Sbjct: 479 YDKLESDGFIAPGVGVRGDDIIIGKTAPIPPDSEELGQRT-------RLHTRRDVSTPLK 531

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           S  SG V  V I       K
Sbjct: 532 STESGQVDQVLITTNSEGQK 551


>gi|156059482|ref|XP_001595664.1| hypothetical protein SS1G_03753 [Sclerotinia sclerotiorum 1980]
 gi|154701540|gb|EDO01279.1| hypothetical protein SS1G_03753 [Sclerotinia sclerotiorum 1980 UF-70]
          Length = 1230

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 90/504 (17%), Positives = 177/504 (35%), Gaps = 92/504 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I       +   +    A+      D+ D  +   +     
Sbjct: 798  DTLLYLMVYPQQPMVKTRTIELIKYDKLPAGQNATVAVMSFSGYDIEDALVLNKASCDRG 857

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++F R    + ++  +  +++I    +  ++ + I    I       + G+   +G
Sbjct: 858  FGRCQVF-RKYSTQLKKYPNRSQDRIAD-RQVGENGKPIAKHRILGVDGIAMVGERINAG 915

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K              S      + ++    +++   + Y     + +  + +K+ 
Sbjct: 916  ETYLNKE-----------SPSNPNSSGMGNDYGSNDMKPAPMGY----KLHDYAYIDKV- 959

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
             +    +    VL   KV     R  + GDK + RHG KG+V                  
Sbjct: 960  -MLSQTENESTVL---KVQTRQTRRPELGDKFSSRHGQKGVVG----------------- 998

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
             I++N                                    + +   +      + ++  
Sbjct: 999  -IIVN------------------------------------QEDMPFADSGVTPDIIMNP 1021

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 +++      +L       +G       F G++ + +  +L       SG+  +  
Sbjct: 1022 HGFPSRMTVGKMLELLSGKAGVVNGSLEYGTCFGGSNVDVMGKILIDKGFSYSGKDFVTS 1081

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE     V  G IY  KL HMV DK+++RS G  +++T+QP  G+S  GG RLGEME
Sbjct: 1082 GITGESLPAYVFFGPIYYQKLKHMVQDKMHSRSRGPRAILTRQPTEGRSRDGGLRLGEME 1141

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVV---------GRTRVYESIVAGNDTFETGTPE 1345
              C+ AYGA+ +L E L + SD    D+          G  +  +S   G  T     P 
Sbjct: 1142 RDCLIAYGASQLLLERLMLSSDAHEVDICETCGLMGYSGWCQTCKS-SKGVSTM--TMPY 1198

Query: 1346 SFNVLVKEMQALGLSIDLENSRTK 1369
            +  +LV+EM ++ + + L+     
Sbjct: 1199 AAKLLVQEMLSMNVLVRLKLEDEF 1222



 Score =  184 bits (467), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 120/990 (12%), Positives = 272/990 (27%), Gaps = 185/990 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S+++F+   I    + N+        V P         LE+       P+   
Sbjct: 103 LVKQHIDSFNYFVEHEIKDIVKANK---RVTSEVDP------KFWLEYTDIRVGEPERMD 153

Query: 86  ---------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                       ++C  RD+TYA P+++ ++ +               +  ++I +G +P
Sbjct: 154 YDDRKPQNEITPNECRLRDMTYAAPIRVDIKYMRGRTI----------VARKNIAIGRMP 203

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGR 171
           +M K                         G FV+ G +++++ Q   S   +  + D  +
Sbjct: 204 IMLKSSKCRLNGKNDRQMAHMNECALDPGGYFVVNGTEKVILVQEQLSKNRVIIEADPKK 263

Query: 172 ASLSGKLLYACRIIPDQGLWMDI---EFDSKDIIHVRIDRRR----------KVPVTSFL 218
             +S  +  +  I       + +     + K   +V + + R           +P+   L
Sbjct: 264 GIVSASVTRSDCISRTSVSLLTLNSSTHERKSKSYVMLKKERISLQHNILQEALPIVIVL 323

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ S+  L           + +F      A  L +     +   +        ++ G
Sbjct: 324 KAMGIQSDHELLLLVAGSDERYQDEFSVNFEEATKLGVHTQHQALEYIGAR-----VKMG 378

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
            +  +      +   +         +   +V    ++     +YI    V          
Sbjct: 379 SRARAPGGGPQRRNYIGDALEALANIIITHVPVVGLDFRPKALYI-CFMVRRVLMAMVNP 437

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V++  +      A +   
Sbjct: 438 KLVDDRDYVGNKRLELAGQLLSLLFEDLFKKFNTDLKMNIDKVLKKPNRGMEFDAYNHMQ 497

Query: 398 FLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                        +     +  R  ++       + +   I+ + ++  + +       +
Sbjct: 498 SHGNYITIGMNRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKTRKV 557

Query: 457 DNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
                 +    G +      + +    +  +           +        ++ A+ +VS
Sbjct: 558 SGPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTYDDEEPVKKLTFVLGAEDIVS 617

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
              +         +  +   L+ +T   +          R     E   +   H+     
Sbjct: 618 MSGKEIYEKGAYVIFVNGTPLA-LTRQPKKFLNSFRKFRRMGRISEYISIFINHHSTSVH 676

Query: 572 AETSEGHNIGLVSSLTSFARVNAYGFIETPYRK----VCDGKVTNDVVYLSAMEEENRYI 627
             T EG     +  + +         +E   RK      D      + Y+   EE +  I
Sbjct: 677 IATDEGRICRPLIIVENQKPKVTKRHLEE-LRKGTMDFDDFLYKGLLEYVDCNEENDSNI 735

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A                              E    ++  P  V+   A LIP+  ++ S
Sbjct: 736 AI-----------------------RENYINEATTHLEIEPFTVLGAVAGLIPYPHHNQS 772

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R    C M +QA+                                           I  
Sbjct: 773 PRNTYQCAMGKQAIGA-----------------------------------------IAY 791

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +     +   + +Y               Q+P+VK                     L  
Sbjct: 792 NQFSRIDTLLYLMVYP--------------QQPMVK----------TRTIELIKYDKLPA 827

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD--- 864
           G+N  VA M + GY+ ED++++++              ++    +      ++   D   
Sbjct: 828 GQNATVAVMSFSGYDIEDALVLNKASCDRGFGRCQVFRKYSTQLKKYPNRSQDRIADRQV 887

Query: 865 -IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE-----EKLLRAIFG 918
                     + +   GI  VG  +N G+  + K +P   +            +  A  G
Sbjct: 888 GENGKPIAKHRILGVDGIAMVGERINAGETYLNKESPSNPNSSGMGNDYGSNDMKPAPMG 947

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
            K  D       + S        +++  R 
Sbjct: 948 YKLHDYAYIDKVMLSQTENESTVLKVQTRQ 977


>gi|154362109|gb|ABS80893.1| RNA polymerase beta subunit [Thauera butanivorans]
          Length = 234

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 135/232 (58%), Positives = 171/232 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N +GF+ETPYRKV DGKVT+ + +LSA+EE    IAQAN+ +DE G+
Sbjct: 61  IGLINSLAVYARTNRHGFLETPYRKVVDGKVTDQIDFLSAIEEGQYVIAQANAEIDEAGA 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              +LV CR  GE +L   + + ++D +P Q+VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 121 LAGDLVSCRHKGEFLLATADMVQYMDVAPGQIVSVGASLIPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP L+ E P VGTG+E  VA  SG A+ A R G+V+ VDA R+VIR  + +
Sbjct: 181 AVPWLRPEKPLVGTGIERPVAVDSGTAVQATRGGVVDYVDANRVVIRVHDDE 232


>gi|145342285|gb|ABP64839.1| RpoB [Paenibacillus amylolyticus]
 gi|145342347|gb|ABP64870.1| RpoB [Paenibacillus amylolyticus]
 gi|145342353|gb|ABP64873.1| RpoB [Paenibacillus amylolyticus]
 gi|145342367|gb|ABP64880.1| RpoB [Paenibacillus amylolyticus]
 gi|145342379|gb|ABP64886.1| RpoB [Paenibacillus amylolyticus]
 gi|145342381|gb|ABP64887.1| RpoB [Paenibacillus pabuli]
 gi|145342383|gb|ABP64888.1| RpoB [Paenibacillus amylolyticus]
 gi|145342385|gb|ABP64889.1| RpoB [Paenibacillus amylolyticus]
 gi|145342397|gb|ABP64895.1| RpoB [Paenibacillus amylolyticus]
 gi|145342405|gb|ABP64899.1| RpoB [Paenibacillus amylolyticus]
 gi|145342407|gb|ABP64900.1| RpoB [Paenibacillus amylolyticus]
 gi|145342409|gb|ABP64901.1| RpoB [Paenibacillus amylolyticus]
 gi|146217889|gb|ABQ11024.1| RNA polymerase beta subunit [Paenibacillus amylolyticus]
          Length = 232

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 86/204 (42%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV IVLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 142  TPVQIVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGAKEYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGEEFEREVTVGVMHMIKL 231



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|56553342|gb|AAV97833.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 73/172 (42%), Positives = 105/172 (61%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+    GK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSPGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G      ++D + G  V
Sbjct: 61  ATIILRALEMSSEEILDTFFDKVSVRIDKDKLMMEVVP-DRLRGETAQFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKAGLTELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|56553318|gb|AAV97821.1| RNA polymerase B subunit [Alteromonas macleodii]
          Length = 170

 Score =  235 bits (600), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 107/172 (62%), Gaps = 2/172 (1%)

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVP 213
           VSQLHRSPG+ FDHDKG+   SGK+LY  R+IP +G W+D EFD KD + VRIDRRRK+P
Sbjct: 1   VSQLHRSPGVFFDHDKGKTHSSGKVLYNARVIPYRGSWLDFEFDPKDNLFVRIDRRRKLP 60

Query: 214 VTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            T  L AL M SEEIL TF+ K+      D     +   D + G   +  ++D + G  V
Sbjct: 61  ATIILRALEMTSEEILDTFFDKVNVRIDKDKLMMEVVP-DRLRGETAAFDIIDGE-GNVV 118

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
           +E+G+++++   ++L++ G+  L + +D L G   A   VN +TGE+ + A 
Sbjct: 119 VETGRRISARHTRALEKPGLNELEVPADYLIGRVYAATYVNEDTGEVIVSAN 170


>gi|262193261|gb|ACY30633.1| RNA polymerase beta subunit [Xanthomonas axonopodis pv. axonopodis]
          Length = 241

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 145/241 (60%), Positives = 180/241 (74%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+
Sbjct: 1   TPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+C  ET EG NIGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLS
Sbjct: 61  RDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE    IAQAN+  D     TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L
Sbjct: 121 AIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAAL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           +PFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+E  VA+ SG  + A R G++EQ+
Sbjct: 181 VPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQI 240

Query: 739 D 739
           D
Sbjct: 241 D 241


>gi|52699839|gb|AAU86981.1| DNA-dependent RNA polymerase II second largest subunit [Ochrolechia
            juvenalis]
          Length = 712

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 117/832 (14%), Positives = 227/832 (27%), Gaps = 145/832 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G +R+   G ++   +R+   ++ + + +  +              + +  + + + 
Sbjct: 1    DXXGKKRLDLAGPLMAGLFRMLFKKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   GLV +L     V      E    +      +V  +   L +
Sbjct: 117  HNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMIQRSMEVLEEYEPLRS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  + +     V        I      + D  D   K         
Sbjct: 177  PNATKIFVNGVWVGVHRNPTDLVRTVQKLRRSGMISHEVSLVRDIRDREFKIFTDAGRVT 236

Query: 679  IPFLENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             P    D+        N+   ++ V  L+ +            A  +       + G+VE
Sbjct: 237  RPLFVIDNDPNSSNKGNLVLTKELVNRLEDDKDLPADMDPDEKATKTMGWDGLVKQGVVE 296

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             +DA            + +   V     +   R  Q               V+       
Sbjct: 297  YLDAEE----------EETVMIVMTPEDLDISRQLQAGYQMPETTDDPNKRVKAPMNPTA 346

Query: 797  GPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
               T      ++   +  + +P+  +N                        ++       
Sbjct: 347  HTWTHCEIHPSMILGICASIIPFPDHNQSPRN------------------TYQSAMGKQA 388

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G                       +  +             +       +   +  + A
Sbjct: 389  MGXXXXXXXXRM-----------DTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVA 437

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + 
Sbjct: 438  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDT 493

Query: 976  VILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            + L    Y +L +   +  G           K+  ++ D      R++            
Sbjct: 494  LKLKHGTYDKLXDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL----------- 542

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +K    T     E    +K+             LR VKV +   +  Q GDK A 
Sbjct: 543  ----HIKRDASTPLRTTEXGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFAS 593

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++ P  +PSRM +    E  L       G + 
Sbjct: 594  RHGQKGTIGITYRQEDMPFTSEGVVPDLIIXPHAIPSRMTIAHXIECQLSKVSSLRGFEG 653

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             +          +S L    E    +                                  
Sbjct: 654  DATPFTEVTVDSVSRLLR--EHGYQSRGFEVM---------------------------- 683

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                              +G +    G         V +G  Y  +L  MV 
Sbjct: 684  -----------------YNGHT----GR---KLVVQVFLGPTYYQRLRXMVD 711


>gi|145342299|gb|ABP64846.1| RpoB [Paenibacillus sp. FSL_H7-720]
 gi|145342369|gb|ABP64881.1| RpoB [Paenibacillus sp. FSL_H8-018]
 gi|145342371|gb|ABP64882.1| RpoB [Paenibacillus sp. FSL_H8-034]
 gi|161331453|gb|ABX60644.1| RpoB [Bacillus sp. FSL_h8466]
          Length = 232

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 112/204 (54%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+++RILP EDMPF+ DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVIARILPEEDMPFMPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A   LG    + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAAKYLGIHTATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G++I
Sbjct: 191  ----------------------------------VFD---------TMVEAGMQRNGKTI 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TG+PF+R VTVG +YM+KL
Sbjct: 208  LYDGRTGDPFEREVTVGVMYMIKL 231



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ LKN+DE GII VGAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALKNLDERGIIRVGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|80973547|gb|ABB53511.1| RNA polymerase beta subunit [Streptococcus cristatus]
 gi|80973557|gb|ABB53516.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|80973571|gb|ABB53523.1| RNA polymerase beta subunit [Streptococcus infantis ATCC 700779]
 gi|80973573|gb|ABB53524.1| RNA polymerase beta subunit [Streptococcus peroris ATCC 700780]
          Length = 226

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 98/294 (33%), Positives = 134/294 (45%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARTLGIHIATPVFDGASSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                   D   E         A +D   ++ILYDG TGEPFD  V+VG +YM+K
Sbjct: 189  -------DTVKE---------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|45120574|gb|AAO64669.2| RNA polymerase II subunit RPB2 [Phlebia radiata]
          Length = 674

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 120/809 (14%), Positives = 229/809 (28%), Gaps = 151/809 (18%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ R +    +              +    + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTRDVYRYLQKCVETHKEFNLSLAVKHNTISNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKMMSAKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  A ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +       +  +   +    +          I      +++  +  
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLAITKKH--INQLNDKTSEYKWDDLIKGGVVKLLBAXEEE 283

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
             ++I     DL+ S +G+D         +  +   +    +K              PS  
Sbjct: 284  PVMISMTPEDLENSRTGLDP--------AQNDGEFDPSARLKAPTTAHTWTHCEIHPSMV 335

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG                         +   ++     T      ++       +G    
Sbjct: 336  LG-------------------------VCASIIPFPDHTQSPRNTYQSAMGKQAMGIYLT 370

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +               +  +             +       +   +  + AI     
Sbjct: 371  NFLVRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSG 419

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    ++ R  +D  ++S   + E+ E   R+          +
Sbjct: 420  YNQEDSVIMNQSSIDRGLF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYD 478

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K   +  D      R++          ++     +  Q
Sbjct: 479  KLEDDGLIAPGTGVNGEDIIIGKXXPIPPDSEELGQRTRSHTKRDVSTPLKSTESGIIDQ 538

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VK+ V   R  Q GDK A RHG KG + 
Sbjct: 539  VLI--------------------TTNQEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIG 578

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +          
Sbjct: 579  ITYRQEDMPFTSEGITPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDV------- 631

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                          TP F     E+++ 
Sbjct: 632  ----------------------------------------------TP-FIELTVESVSQ 644

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVT 1250
             LR       G  I+Y G TG      V 
Sbjct: 645  FLRQEGYHSRGLEIMYHGHTGRKLQAQVY 673


>gi|3133339|gb|AAC38470.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVEGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDESGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|213621061|ref|ZP_03373844.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.
            enterica serovar Typhi str. E98-2068]
          Length = 90

 Score =  235 bits (599), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 66/90 (73%), Positives = 78/90 (86%)

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
            Y+YMLKLNH+V DK++ARSTGSYSLVTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQ
Sbjct: 1    YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 60

Query: 1313 EMLTIKSDDVVGRTRVYESIVAGNDTFETG 1342
            EMLT+KSDDV GRT++Y++IV GN   E G
Sbjct: 61   EMLTVKSDDVNGRTKMYKNIVDGNHQMEPG 90


>gi|3133375|gb|AAC38488.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
 gi|3133485|gb|AAC38543.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 234

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS +D DG FTE+ V  R   GE   V    +D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPIDPDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|115350032|ref|YP_764412.1| beta subunit of RNA polymerase [Stigeoclonium helveticum]
 gi|122165136|sp|Q06SF4|RPOB2_STIHE RecName: Full=DNA-directed RNA polymerase subunit beta C-terminal
            section; AltName: Full=PEP; AltName: Full=Plastid-encoded
            RNA polymerase subunit beta C-terminal section; Short=RNA
            polymerase subunit beta C-terminal section
 gi|98990246|gb|ABF60213.1| beta subunit of RNA polymerase [Stigeoclonium helveticum]
          Length = 1080

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 84/304 (27%), Positives = 138/304 (45%), Gaps = 62/304 (20%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   ++++ +++  +++  + +   +  +    G  G KK++         +P++     
Sbjct: 337  ETFDKERNFQKMSPNQSKQNWVKISIKKEWQKVGSFGKKKASKGKISFFPSFPQASLVG- 395

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                                +      RF+ K +     + +    +  V +++A KR +
Sbjct: 396  -------------------KASFFSPSRFEKKRD---ASNFLKSSCISSVHIYLAEKRKV 433

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDKMAGRHGNKGI+S+ILP +DMP+L DGTP+D+ LNPLGVPSRMNVGQI+E  LG A
Sbjct: 434  QVGDKMAGRHGNKGIISQILPRQDMPYLPDGTPIDMALNPLGVPSRMNVGQIYECLLGLA 493

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG++ +    D     + S    F  K+    + T +   +   +            
Sbjct: 494  GKHLGEQYRIQPFDEAFGPEASRSFVF-SKLYSAKTKTGQSWLFQPTN------------ 540

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                       G+  L+DG TG  FD+ +T GY YM+KL H+V 
Sbjct: 541  --------------------------PGKLKLFDGRTGNCFDQAITTGYSYMIKLVHLVD 574

Query: 1265 DKVY 1268
            +K++
Sbjct: 575  EKIH 578



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 57/110 (51%), Positives = 75/110 (68%), Gaps = 1/110 (0%)

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RS+G YSL+TQQPL G+S  GGQRLGEMEVW I+AYGAA+ L E+LTIKSDDV GR  +
Sbjct: 969  SRSSGPYSLITQQPLKGRSKHGGQRLGEMEVWAIEAYGAAFTLLELLTIKSDDVTGRLTI 1028

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            ++ ++     +  GTP SF VL+ E+QAL L I +  +   N  K   + 
Sbjct: 1029 WDYVLYKKPLY-IGTPASFKVLICELQALCLDIGIYKADKSNILKQINVS 1077



 Score =  132 bits (333), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 85/227 (37%), Positives = 142/227 (62%), Gaps = 10/227 (4%)

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y L  +QRSNQ+T +  RP+VK G+ V+  D+++D  S+  G+ ++G+N+L+A++PW GY
Sbjct: 14  YSLQTYQRSNQDTSMLHRPVVKEGEWVQAGDLLSDCASSIGGEFSIGQNILIAYLPWEGY 73

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG-LKNIDECG 880
           N+ED++LISER+V +D++TSIHIE +++       G E+IT+DI  + +   L ++D+ G
Sbjct: 74  NYEDAILISERLVYDDLYTSIHIERYDISTEKNPYGIEKITKDIVLLKDTTELNHLDKNG 133

Query: 881 IICVGAEVNPGDILVGKITP-KGESPMTPEEKLLRAIFGEK-AVDVRDTSLRVPSGVSGT 938
           I  +GA +  GDILVGKITP + +  +    +L   I G+K    +RD+SLRVP G+   
Sbjct: 134 IAQLGAWLKEGDILVGKITPTESKKEVARYVQLYNDILGKKINYAIRDSSLRVPRGLEAK 193

Query: 939 VVDVRIFN-RHGIDKNE------RSISVEREQIELLARDKDDEQVIL 978
           V+ V+ F  R    KN       +S ++       L++++ +++  L
Sbjct: 194 VIRVKTFPERKNETKNWENKIGLKSKALAFSVQHFLSKNQSNKKRTL 240


>gi|7453591|gb|AAF62902.1| RpoB [Bacillus sonorensis]
          Length = 134

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 55/149 (36%), Positives = 91/149 (61%), Gaps = 19/149 (12%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           + +  E++++P+LIE+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF
Sbjct: 1   YARISEVLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEF 50

Query: 77  VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
           + Y    PK+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P
Sbjct: 51  IDYSLGEPKYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFP 101

Query: 137 LMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
           +MT  GTF+I G +R++VS L RSP +++
Sbjct: 102 IMTDTGTFIINGAERVIVSXLVRSPSVYY 130


>gi|154362165|gb|ABS80921.1| RNA polymerase beta subunit [Ralstonia mannitolilytica]
          Length = 236

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 137/234 (58%), Positives = 176/234 (75%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV +GKVT++V YLSA+EE    +AQAN+++DEDG+
Sbjct: 61  IGLINSLALYARLNDYGFLETPYRKVENGKVTDEVHYLSAIEEGKYVVAQANATVDEDGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+A+ P VGTG+E  VA  SG A+ A R G+V+ VDA R+VIR  + +
Sbjct: 181 RQAVPCLRADKPLVGTGVERTVAVDSGTAVQATRGGLVDYVDANRVVIRVNDDE 234


>gi|154362087|gb|ABS80882.1| RNA polymerase beta subunit [Acidovorax facilis]
          Length = 234

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 137/230 (59%), Positives = 170/230 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNLLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT  + YLSA+EE    IAQAN+ LD+DG 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTEQIDYLSAIEEGKYVIAQANAVLDKDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T +LV  R  GE IL   +++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQ
Sbjct: 121 LTGDLVSAREKGESILCGADRVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
           AVP+L+ E P VGTG+E V A  SG  + A R G+V+ VDA RIVIR  +
Sbjct: 181 AVPVLRPEKPLVGTGIERVAAVDSGTVVTATRGGVVDYVDATRIVIRVND 230


>gi|123979368|gb|ABM81509.1| RNA polymerase II second largest subunit [Ramalina complanata]
          Length = 702

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 114/816 (13%), Positives = 226/816 (27%), Gaps = 143/816 (17%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L+  +R+   ++ + + +  +    +         + +  + + +     +        
Sbjct: 5    LLEGLFRMLFYKLTKDVYKYLQRCVENNKEFNLTLAVKSTTLTNGLKYSLATGNWGDQKK 64

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 65   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 120

Query: 575  SEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L    +  V   G     +      ++  +   LS       ++     
Sbjct: 121  PEGQACGLVKNLALMCYITVGTPGQPIVDFMMQRQMELLEEYEPLSNPNATKIFVNGVWV 180

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV- 690
             +    +     V        I      + D  D   K          P    + + R  
Sbjct: 181  GVHSQPAILTATVMSLRRKGLISYEVSLVRDIRDREFKIFTDAGRVCRPLFVVESNPRDQ 240

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVE 749
              G  +  +           + + M++   +          + G VE VDA       + 
Sbjct: 241  NFGNLVLTKHDVQELDHNRELISSMDAQDREDQAIGWQGLVKNGKVEYVDAEEEETIMIV 300

Query: 750  GDLDPST--SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               +          Y        +     N+R  V+     +        PS  LG    
Sbjct: 301  MTPEDLEISKHYSTYGDDALAGDDNKDDPNKRMKVRPKAIRQAWTHCEIHPSMILG---- 356

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++V                  
Sbjct: 357  ---ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDVRM---------------- 395

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 396  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 444

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R        +E   +    + + L    Y +L 
Sbjct: 445  VIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---SVVEQFEKPMRSDTLSLKHGTYDKLD 500

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D      R++          ++     +  Q   
Sbjct: 501  DDGIVSPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLL 560

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            S                         LR VKV +   +  Q GDK A RHG KG +    
Sbjct: 561  S--------------------TNSDGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 600

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 601  RQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDS 660

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 661  VSRLLR--EHGYQSRGFEVM---------------------------------------- 678

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +G +    G         V +G  Y  +L 
Sbjct: 679  -----YNGHT----GR---KLVAQVFLGPTYYQRLR 702


>gi|3133457|gb|AAC38529.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 133/231 (57%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V  G VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRRVVSGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D DG F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDADGRFVEGRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME      
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAXID 231


>gi|3133455|gb|AAC38528.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  235 bits (599), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDESGRFAEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME      
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAXID 231


>gi|55831379|gb|AAV66548.1| RNA polymerase II second largest subunit [Mallocybe dulcamara]
          Length = 639

 Score =  234 bits (598), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 110/716 (15%), Positives = 206/716 (28%), Gaps = 110/716 (15%)

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L N +R+   ++ + +    +              +  + + + +     +      
Sbjct: 2    GPLLANLFRMLFRKLTKDVYRYMQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWGDQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   A ++   F       + +  + +     +A           N 
Sbjct: 118  ETPEGQACGLVKNLALMACISVGSFSGPVIEFLEEWGLESLEE--NAHSSTTFTKVFVNG 175

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSN 688
                       LV              ++    D  +   +          P    +D  
Sbjct: 176  VWIGVHRDAANLVKTLKRLRRRDDISTEVSVVRDIREREMRVYTDAGRVCRPLFIVEDQQ 235

Query: 689  RVLMGCNM------QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             VL   ++              K E    G  +E + A+     +++      E +D  R
Sbjct: 236  LVLQKKHIKWLNNGVDDEGNEFKWEQMVKGGIIELLDAEEEETVMIS---MTPEDLDNSR 292

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            +  R ++   +                            +K G            PS  L
Sbjct: 293  LQQRGIDPHANDGEFDPAA-------------------RLKAGTHAHTWTHCEIHPSMIL 333

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 334  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 368

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 369  FLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 417

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          + 
Sbjct: 418  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDK 476

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          V   ++S ++ Y
Sbjct: 477  LEDDGFIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTR----THTRRDVSTPLKSTEIGY 532

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                 I                       + VKV V   R  Q GDK A RHG KG +  
Sbjct: 533  VDQVLI----------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGI 576

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +       
Sbjct: 577  TYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDVTPFK 632


>gi|113707347|gb|ABI36581.1| RNA polymerase II second largest subunit [Lasallia papulosa]
          Length = 710

 Score =  234 bits (598), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 123/819 (15%), Positives = 237/819 (28%), Gaps = 137/819 (16%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L   +R+   ++ R + +  +    +         + +  + + +     +        
Sbjct: 1    LLAGLFRMLFNKLTRDVSKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     +      E    +    + +V  +     +      ++     
Sbjct: 117  PEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P    D+  +  
Sbjct: 177  GVHRDPAHLVSTVQSLRRRSLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSP 236

Query: 692  MGCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
               N+   ++ +  L+ +     GT  E   AK  G   + K  G+VE VDA        
Sbjct: 237  NNGNLVLTKEHINRLEDDKDLGPGTDPEEKTAKYMGWEGLVK-QGVVEYVDAEE------ 289

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
                + +   V     ++  R  Q               V+          T      ++
Sbjct: 290  ----EETVMIVMTPEDLEISRQIQAGYTMPETTDDPNKRVKAPMNPTAHTWTHCEIHPSM 345

Query: 808  GRNMLVAFMPWHGYNFEDSM-LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
               +  + +P+  +N    + ++ E    + +                            
Sbjct: 346  ILGICASIIPFPDHNQVCYIDILCEYDTYQGLSXX----------------XXXXXXXXX 389

Query: 867  NVSEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                  L N D+    +  +             +       +   +  + AI      + 
Sbjct: 390  XXXXVFLTNFDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQ 449

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y 
Sbjct: 450  EDSVIMNQSSIDRGLF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYD 505

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   +  G           K+  ++ D                +E  QR    +K  
Sbjct: 506  KLDDDGIVAPGVRVSGEDIIIGKTAPMTQD---------------AEELGQRTKSHIKRD 550

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
              T     E+   +++             LR VKV +   +  Q GDK A RHG KG + 
Sbjct: 551  VSTPLRSTENGIVDQVLL-----TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIG 605

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +       
Sbjct: 606  ITYRSEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVT 665

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
               +S L    E    +                                           
Sbjct: 666  VDSVSRLLR--EHGYQSRGFEVM------------------------------------- 686

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                     +G +    G         V +G  Y  +L 
Sbjct: 687  --------YNGHT----GR---KLVAQVFLGPTYYQRLR 710



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 88/584 (15%), Positives = 158/584 (27%), Gaps = 90/584 (15%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 43  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 102

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   PQ 
Sbjct: 103 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQR 162

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM--- 558
             NA  V      F     +    +  + +S +   RR S +  +  + R     E    
Sbjct: 163 SPNATKV------FVNGVWVGVHRDPAHLVSTVQSLRRRSLISHEVSLVRDIRDREFKIF 216

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP------YRKVCDG 608
               R   P       P   + G+ +     +         G    P      Y      
Sbjct: 217 TDAGRVCRPLFVIDNDPKSPNNGNLVLTKEHINRLEDDKDLGPGTDPEEKTAKYMGWEGL 276

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+ A EEE   I      L+                                 
Sbjct: 277 VKQGVVEYVDAEEEETVMIVMTPEDLEISRQIQ--------------------------- 309

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
                   +     E  D     +   M                T       +   + I+
Sbjct: 310 --------AGYTMPETTDDPNKRVKAPM--------------NPTAHTWTHCEIHPSMIL 347

Query: 729 AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN----TCVNQRPLVKV 784
              A I+   D  ++    +  + D                        T  +QR     
Sbjct: 348 GICASIIPFPDHNQVCYIDILCEYDTYQGLSXXXXXXXXXXXXXXXVFLTNFDQRMDTMA 407

Query: 785 GDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                    +A   S +     +L  G+N +VA   + GYN EDS+++++  +   +F S
Sbjct: 408 NILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 467

Query: 842 IHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +   +   E     +  D   +       +D+ GI+  G  V+  DI++G
Sbjct: 468 LFYRCYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDIIIG 527

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           K  P  +      E+L +        DV        +G+   V+
Sbjct: 528 KTAPMTQDA----EELGQRTKSHIKRDVSTPLRSTENGIVDQVL 567


>gi|194277435|gb|ACF39383.1| RpoB [Streptomyces sp. FXJ52]
          Length = 255

 Score =  234 bits (598), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 138/262 (52%), Positives = 185/262 (70%), Gaps = 8/262 (3%)

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL+ SL S+ R+N +GFIETPY
Sbjct: 1   ALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPY 60

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKI 661
           RKV +G+VT+DV YL+A EE+   IAQAN++L++D  F E  V  R   GE   VP + +
Sbjct: 61  RKVVEGQVTDDVDYLTADEEDRFVIAQANATLNDDLRFAEARVLVRRRGGEVDYVPGDDV 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
           D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM RQAVPL+K+E+P VGTGME   A 
Sbjct: 121 DYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAA 180

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            +G  + A++ G+V++V A  I   + +G           YRL KF RSNQ T VNQ+ +
Sbjct: 181 DAGDVVKAEKPGVVQEVSADYITTTNDDGT-------YITYRLAKFSRSNQGTSVNQKVI 233

Query: 782 VKVGDEVRRNDIIADGPSTDLG 803
           V  GD V    ++ADGP+T+ G
Sbjct: 234 VAEGDRVIEGQVLADGPATENG 255


>gi|312204344|gb|ADQ47489.1| RNA polymerase II second largest subunit [Odontotrema phacidiellum]
          Length = 705

 Score =  234 bits (598), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 105/797 (13%), Positives = 219/797 (27%), Gaps = 119/797 (14%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + +    +              + +  + + +     +            
Sbjct: 1    LFRQLFKKLNKDVYSYLQRCVEGNKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       + ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLSRYTFAATLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L+    +      E    +    + +V  +     + +    ++      +  
Sbjct: 117  ACGLVKNLSLMCYITVGSPSEPIIEFMVQRNMEVLEEYDSTRSPDSTKIFVNGVWVGVHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
            D +     V        I      I D  D   K          P F+ ++D      G 
Sbjct: 177  DPTHLVSTVQSLRRKGMISPEVSLIRDVRDQEFKIFTDAGRVCRPLFVIDNDPKSSNKGG 236

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +  +A+     +   +   M+             K              +  ++ + + 
Sbjct: 237  LVLTKAIVNKLEDDMALPADMDPDEK---------KEKYFGWNGLMGTGAVEFLDAEEEE 287

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLV 813
            +         ++  R  Q       P   +   V+     A    T      ++   +  
Sbjct: 288  TVMIAMTPEDLEISRQVQAGYGMPEPSTDLNARVKAPVSAAQQTWTHCEIHPSMILGICA 347

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N    +  +  +V                                       
Sbjct: 348  SIIPFPDHN---HVCFNYTLVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 404

Query: 874  KNIDECG--IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                     +  +             +       +   +  + AI      +  D+ +  
Sbjct: 405  XXXXXXXXXMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMG 464

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--- 988
             S +   +    +F R  +++ +R        +E   +    E + L    Y +L +   
Sbjct: 465  QSSIDRGLF-RSLFFRSYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYEKLDDDGI 520

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  +  D      R++          ++     +  +       
Sbjct: 521  IAPGVRVSGEDIIIGKTAPIPPDAEELGQRTKLHTKRDASTPLRTTENGIVDRVLL---- 576

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                  L+ VKV     +  Q GDK A RHG KG +      ED
Sbjct: 577  ----------------TTNAEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQED 620

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   D+++NP  +PSRM +  + E  L       G +                 
Sbjct: 621  MPFSAEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------- 665

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     ++++ +LR    
Sbjct: 666  --------------------------------------ATP-FTEVTVDSVSRLLREHGY 686

Query: 1229 DESGQSILYDGLTGEPF 1245
               G  ++Y+G TG   
Sbjct: 687  QSRGFEVMYNGHTGRKL 703



 Score =  111 bits (277), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 81/583 (13%), Positives = 151/583 (25%), Gaps = 85/583 (14%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    A +  L        R+GK       +  +  +
Sbjct: 47  ATGNWGDQKKAASAKAGVSQVLSRYTFAATLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 106

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE--------F 516
               E  + Q    +  +       + S     +      N + +              F
Sbjct: 107 VCPAETPEGQACGLVKNLSLMCYITVGSPSEPIIEFMVQRNMEVLEEYDSTRSPDSTKIF 166

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEM-------RDVHPTHYGR 568
                +    +  + +S +   RR   +     + R     E        R   P     
Sbjct: 167 VNGVWVGVHRDPTHLVSTVQSLRRKGMISPEVSLIRDVRDQEFKIFTDAGRVCRPLFVID 226

Query: 569 ICPAETSEGHNIGLVSSLTSF-------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
             P  +++G  +   + +          A ++     E  Y        T  V +L A E
Sbjct: 227 NDPKSSNKGGLVLTKAIVNKLEDDMALPADMDPDEKKEK-YFGWNGLMGTGAVEFLDAEE 285

Query: 622 EENRYIAQANSSLD-------EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
           EE   IA     L+         G               +   ++     +  P  ++ I
Sbjct: 286 EETVMIAMTPEDLEISRQVQAGYGMPEPSTDLNARVKAPVSAAQQTWTHCEIHPSMILGI 345

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            AS+IPF +++                                                 
Sbjct: 346 CASIIPFPDHNHVCFNYTLVXXXXXXXXXXXXXXXXXX---------------------- 383

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                      Q+PL             
Sbjct: 384 -----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMANILYYPQKPL----------ATT 428

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                    +L  G+N +VA   + GYN EDS+++ +  +   +F S+    +    +  
Sbjct: 429 RSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMGQSSIDRGLFRSLFFRSYVEQEKRV 488

Query: 855 KLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
            +   E        +   +     + +D+ GII  G  V+  DI++GK  P    P   E
Sbjct: 489 GMSLVEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPI---PPDAE 545

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E   R     K    RD S  + +  +G V  V +       K
Sbjct: 546 ELGQRT----KLHTKRDASTPLRTTENGIVDRVLLTTNAEGLK 584


>gi|145342297|gb|ABP64845.1| RpoB [Paenibacillus sp. FSL_H7-326]
          Length = 232

 Score =  234 bits (598), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 84/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGATEHD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            L+DG TGE F+R VTVG ++M+KL
Sbjct: 208  LFDGRTGERFEREVTVGVMHMIKL 231



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEIAAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|154362085|gb|ABS80881.1| RNA polymerase beta subunit [Acidovorax delafieldii]
          Length = 234

 Score =  234 bits (598), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 138/232 (59%), Positives = 171/232 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLAEITHKRRVSALGPGGLTRERAGFEVRDVHVTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGFIETPYR+V DGKVT  + YLSA+EE    IAQAN+ LD+DG 
Sbjct: 61  IGLINSLALYARLNEYGFIETPYRRVVDGKVTEHIDYLSAIEEGKYVIAQANAQLDKDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            T ELV  R  GE IL   +++ ++D SP Q+VS+AASL+PFLE+DD+NR LMG NM RQ
Sbjct: 121 LTGELVSAREKGESILCGADRVQYMDVSPAQIVSVAASLVPFLEHDDANRALMGANMSRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           AVP+L+ E P VGTG+E V A  SG  + A R GIV+ VDA RIV+R  + +
Sbjct: 181 AVPVLRPEKPLVGTGIERVAAVDSGTVVTATRGGIVDYVDATRIVVRVNDDE 232


>gi|322801624|gb|EFZ22265.1| hypothetical protein SINV_10883 [Solenopsis invicta]
          Length = 1120

 Score =  234 bits (598), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 101/603 (16%), Positives = 184/603 (30%), Gaps = 141/603 (23%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              +    N+    + + G   +  + I           + H +E       + L      
Sbjct: 612  RMMRPVINLAAQKIEYIGTFEQIYLDICVISQEVYEGMTTH-QEISQTTIFSNLANLIPM 670

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE--K 920
             D         +   + G   +G   +           + ++P TP  + +         
Sbjct: 671  PDCNQSPRNMYQC--QMGKQTMGTPCHNWQQQSQTKLYRLQTPATPLFRPVHYDNINMDD 728

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
                 +  + V S     + D  I N+   ++     S+ + +      D +D++    R
Sbjct: 729  FAMGTNAIIAVISYTGYDMEDAMIINKSSYERGFGHGSIYKSEF----VDLNDKKSYFAR 784

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +               + P   K   V    +I    +     ++  D    + V     
Sbjct: 785  D--------------PAKPDLAKTIDVDGLPMIGIAIKEGDAYYSYYDADSAQYVIGKYK 830

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
              ET+           ++ ++    +    +R   +   + R    GDK A R G KGI+
Sbjct: 831  SAETA----------YVDNVKLCGSLGNHDIRRACITFRIPRNPIVGDKFASRAGQKGIL 880

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
            SR+ P ED+PF + G   DI+ NP G PSRM +  + E   G +    G    +    + 
Sbjct: 881  SRLYPIEDLPFTETGMVPDIIFNPHGFPSRMTIAMMIEVMAGKSAAVHGLVHDATPFRFD 940

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                       L                                                
Sbjct: 941  EENTAIDYFGKL------------------------------------------------ 952

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
              L +   +  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG    +T+
Sbjct: 953  --LELGGYNYYGTERMYSGIYGCELTANIFFGIVHYQRLRHMVSDKWQVRSTGPIDQLTR 1010

Query: 1281 QPLG-----------GKSNRGGQRLGEMEVWCIQAYGAAYVLQEM--------------- 1314
            QP+                       EME   + ++G +Y+LQ+                
Sbjct: 1011 QPIKGRRRGGGIRFG-----------EMERDALISHGCSYLLQDRLFHCSDKITTLACQK 1059

Query: 1315 --------LTIKS----DDVVGRTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLS 1360
                    LT+KS    DD   R       + G +    E   P  F  L+ ++ +  ++
Sbjct: 1060 CGSILGPELTVKSRIDDDDKKCR-------LCGEEDTVDEIEIPYIFKYLLIQLASCNIN 1112

Query: 1361 IDL 1363
            + L
Sbjct: 1113 VKL 1115



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 90/605 (14%), Positives = 201/605 (33%), Gaps = 71/605 (11%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ +       I    +    ++ Y  N+++       ++ L    +            
Sbjct: 244 MLKCLKDVTDLCIYKALLAGCEDDLYYNNSIMNMLRAVHEEGLHWHEQ---------CKA 294

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
                  + F     D + +      ++  +    D    + + ++ + K L    N K 
Sbjct: 295 YIGKMFRVKFSELPEDATDIDVCDYIVKNCVAIHLDEPADKFDLLVFMTKKLFAFSNNKC 354

Query: 452 TIDDIDNLGNRRVRSVGEMLK-------NQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            ++ +D++  +     G +           + +G+      +K   S+ +  ++  Q+++
Sbjct: 355 AVEGVDSVMMQECLMGGHLYLQVLNEKLCSWLVGVKH--HILKRAKSAGNRYTLSVQEML 412

Query: 505 NAKPVVSAVCEFFC------------------SSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           N   +   +                       SS L+ + E++N +  ++H R   A+ +
Sbjct: 413 NVTKLRCNIDAQMEYFLSTGSIRSSSGLGLTQSSGLTIVVENINRMRYMSHFR---AIHR 469

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK-- 604
           G   +     E R + P  +G ICP  T +G   GL++ LT    V  +   +       
Sbjct: 470 GAFFQEMRTTEARQLLPDAWGFICPIHTPDGAPCGLLNHLTMNCIVTKHPNAKLKAAIPT 529

Query: 605 -VCDGKVTNDVVYLSAMEEENRYIAQANSSLDE--DGSFTEELVFCRCAGEEILVP---- 657
            + D  +T   +   A + +N Y    +  L    +     ++V+     +         
Sbjct: 530 VLVDLGMTPLPI---ADDWKNSYNVMLDGKLIGLIEDKIINKVVYELRLRKIKGKEIPST 586

Query: 658 -----REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                  K +     P   +  +A+ +     + + + +       Q    +   +  V 
Sbjct: 587 LEIALVPKKNVPAQYPGLFLFTSAARMMRPVINLAAQKIEYIGTFEQIYLDICVISQEVY 646

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
            GM     + S   I +  A ++   D  +      +  +   T G   +     Q+S  
Sbjct: 647 EGMT-THQEISQTTIFSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCHNWQ--QQSQT 703

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                Q P   +   V  ++I       ++ D A+G N ++A + + GY+ ED+M+I++ 
Sbjct: 704 KLYRLQTPATPLFRPVHYDNI-------NMDDFAMGTNAIIAVISYTGYDMEDAMIINKS 756

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
                     H   ++    D         RD      +  K ID  G+  +G  +  GD
Sbjct: 757 SYERGFG---HGSIYKSEFVDLNDKKSYFARDP--AKPDLAKTIDVDGLPMIGIAIKEGD 811

Query: 893 ILVGK 897
                
Sbjct: 812 AYYSY 816



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 94/754 (12%), Positives = 217/754 (28%), Gaps = 132/754 (17%)

Query: 16  FFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF---SG 70
            FG++P+  +  +  L      S+++ L           +GL    K   P+      S 
Sbjct: 13  NFGRSPDTQNEILQSLGTPHIESFNYML----------EDGLYQNLKDNTPVYVTLPNSD 62

Query: 71  AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
             +L         P            K    +C  R +TY   +   +   +   +    
Sbjct: 63  KIVLWLDDVHIYKPAAPTNTIGLKSYKIYPSECRQRGVTYKGKIIARIGWSINGKE---- 118

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
               ++I E+   +G++P+M K                         G F+IKG++R +V
Sbjct: 119 ----QEILEKD--LGEVPIMLKSNRCHLNKMSPKELVAHGEHEQEWGGYFIIKGLER-LV 171

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV-- 212
             L  +   +    K          ++   I  + +  D    +  + +V  D   K   
Sbjct: 172 RMLIMTRRNYPIAVKRPIWKGRGEQFSDLGILLRSVRDDNSTVNNTLHYVT-DGSAKFAF 230

Query: 213 ---------PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
                    P+   L  L    +++      K + +   D   +  S  +++        
Sbjct: 231 AYKKATYYVPLILMLKCL----KDVTDLCIYKALLAGCEDDLYYNNSIMNMLRAVHEEGL 286

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---GETGEI 320
                    + +  +   S L +   +  V    + +     L    D  +     T ++
Sbjct: 287 HWHEQCKAYIGKMFRVKFSELPEDATDIDVCDYIVKNCVAIHLDEPADKFDLLVFMTKKL 346

Query: 321 YIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
           +  + +    + ++ +   E      LY+  +N         V             I + 
Sbjct: 347 FAFSNNKCAVEGVDSVMMQECLMGGHLYLQVLNEKLCSWLVGVKHH----------ILKR 396

Query: 381 MRPGDVSTFSVAESMFN----FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            +          + M N        D+      + G ++ +  L L     +  +   + 
Sbjct: 397 AKSAGNRYTLSVQEMLNVTKLRCNIDAQMEYFLSTGSIRSSSGLGLTQSSGLTIVV--EN 454

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLGLLRMERSIKERISSVDI 495
           I  ++ +   R     I         R     ++L + +  +  +         + +   
Sbjct: 455 INRMRYMSHFR----AIHRGAFFQEMRTTEARQLLPDAWGFICPIHTPDGAPCGLLNHLT 510

Query: 496 DSVMPQDLINAKPVVS--AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
            + +     NAK   +   V      + L   ++  NS + +   + +  +    + +  
Sbjct: 511 MNCIVTKHPNAKLKAAIPTVLVDLGMTPLPIADDWKNSYNVMLDGKLIGLIEDKIINKVV 570

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             + +R +            T E   +   +    +  +  +       R V +      
Sbjct: 571 YELRLRKIKGKE-----IPSTLEIALVPKKNVPAQYPGLFLFTSAARMMRPVINLAAQ-K 624

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   E+    I   +  + E                            + S   + S
Sbjct: 625 IEYIGTFEQIYLDICVISQEVYEG----------------------MTTHQEISQTTIFS 662

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
             A+LIP  + + S R +  C M +Q +      
Sbjct: 663 NLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCHN 696


>gi|52694313|emb|CAG37996.1| RNA polymerase beta subunit [Pseudomonas cichorii]
          Length = 377

 Score =  234 bits (598), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 216/333 (64%), Gaps = 13/333 (3%)

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N 
Sbjct: 50  VTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQ 109

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++     +ELV  R   E  
Sbjct: 110 YGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFT 169

Query: 655 LVPREKIDFIDASPKQVVSIAASL---IPFLENDDSNRVLMGCNMQRQAVPLL----KAE 707
           +     +   D    Q  S   S    +P           +     R   P +     + 
Sbjct: 170 VKAPADVTL-DGRFAQAGSFGRSFPDSVPRARRRQPCVDGVRTCSVRLYQPCVPTSRWSV 228

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
             +  T +    A  S   +    A +++ VDA RIV+R  + +++   +GVDIY L K+
Sbjct: 229 PAWSAT-LPVTPAFVSWLVV----AVLIDSVDASRIVVRVADDEVETGEAGVDIYNLTKY 283

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
            RSNQNTC+NQRPLV  GD V+R++I+ADGPSTD+G+LA+G+NM +AFM W+G+NFEDS+
Sbjct: 284 TRSNQNTCINQRPLVSKGDRVQRSNIMADGPSTDMGELAMGQNMRIAFMAWNGFNFEDSI 343

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +S+R+V E+ FT+IHI++   +ARDTKLGPE+
Sbjct: 344 CLSKRVVQENRFTTIHIQDMTCVARDTKLGPEK 376


>gi|153958240|gb|ABS53410.1| RpoB [Bacteriovorax sp. OC7]
          Length = 347

 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 166/350 (47%), Positives = 232/350 (66%), Gaps = 10/350 (2%)

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            A +VA   G V  VD+ RIVI+    +     SGVDIY+L+K+QR+NQNTC NQ+ LV  
Sbjct: 1    AVLVANDNGRVIFVDSNRIVIQRD--NFKDGESGVDIYKLVKYQRTNQNTCNNQKALVTE 58

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
            GD V++ D++ADGP TD GDLALG+N LVAFMPW GYN+EDS+LISE ++++DVFTS+HI
Sbjct: 59   GDIVKKGDVLADGPGTDNGDLALGQNPLVAFMPWGGYNYEDSILISEDLLAKDVFTSVHI 118

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
            E FEV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+
Sbjct: 119  EAFEVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGET 178

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++ 
Sbjct: 179  QLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVYGTVIDARVYTREGVELCARSKDIIEQET 238

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYP 1017
             LL RD+  E   +  +   ++ ++L G              +   K T ++ ++++  P
Sbjct: 239  TLLRRDERIEIKAIQTSAILKIADMLKGAKVTDVLVSEDGSAELLSKGTEITGEVLASIP 298

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
                    +Q  +++  +           + +  +  ++I K+  GD++P
Sbjct: 299  FELIGYLPLQ-AELEEKLSEYFADVRNKINRVRAKTTDEIAKLHRGDELP 347


>gi|80973551|gb|ABB53513.1| RNA polymerase beta subunit [Streptococcus minor]
          Length = 226

 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 96/286 (33%), Positives = 130/286 (45%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                              D
Sbjct: 175  ATPVFDGASADDLW---------------------------------------------D 189

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               E         A +D   ++ILYDG TGEPFD  V+VG +YM+K
Sbjct: 190  TVKE---------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|161331481|gb|ABX60658.1| RpoB [Paenibacillus sp. FSL_h8502]
          Length = 232

 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 114/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG+A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGFAAMQLGIHVATPVFDGANEYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ LKN+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALKNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|40642974|emb|CAD89599.1| RNA polymerase II, second largest subunit [Borago officinalis]
          Length = 355

 Score =  234 bits (597), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 77/415 (18%), Positives = 131/415 (31%), Gaps = 77/415 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ RE      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMETLVREDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVAGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T ++                  DE   +     +  + TS    E+   +++ 
Sbjct: 137  DVIIGKTTPINQ-----------------DEAQGQASRYTRRDHSTSMRHSENGMVDQVL 179

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +GT  
Sbjct: 180  LTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGTTP 234

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +  
Sbjct: 235  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRG 294

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 295  FETM-----------------------------------------------YNGHT---- 303

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 304  GR---RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 355



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 58/184 (31%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +  +    E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMETLVREDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V   D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDDDGLAPPGTRVAGEDVIIGKTTPINQDE---------AQGQASRYTRRDHSTSMRHSE 171

Query: 936 SGTV 939
           +G V
Sbjct: 172 NGMV 175


>gi|3133365|gb|AAC38483.1| RNA polymerase beta-subunit [Mycobacterium kansasii]
          Length = 234

 Score =  234 bits (597), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 133/231 (57%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSA G GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSAPGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVIDGLVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D +G F E  V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDAEGRFVEPRVLVRRKAGEVEYVASSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|262193257|gb|ACY30631.1| RNA polymerase beta subunit [Xanthomonas campestris pv. campestris]
          Length = 241

 Score =  234 bits (597), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 144/241 (59%), Positives = 180/241 (74%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ+LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+
Sbjct: 1   TPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+C  ET EG NIGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLS
Sbjct: 61  RDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE    IAQAN+  D     TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L
Sbjct: 121 AIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAAL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           +PFLE+DD+NR LMG NMQRQAVP L+++ P VGTG+E  VA+ SG  + A+R G++EQ+
Sbjct: 181 VPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGIERAVARDSGVTVNARRGGVIEQI 240

Query: 739 D 739
            
Sbjct: 241 T 241


>gi|192337688|gb|ACF04264.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  234 bits (596), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+ ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRIFALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|307343500|emb|CBJ18667.1| RNA polymerase B subunit [Micromonospora sp. CR39]
          Length = 193

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 89/204 (43%), Positives = 117/204 (57%), Gaps = 38/204 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 20   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 79

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 80   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 128

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I+ +L     +        
Sbjct: 129  -------------------ADESEGDTNVATPVFDGAREEEISGLLSSTLPNRDGNQLIG 169

Query: 1232 --GQSILYDGLTGEPFDRPVTVGY 1253
              G++ L+DG +GEP   P+ VGY
Sbjct: 170  ASGKAQLFDGRSGEPLPDPIAVGY 193


>gi|46019134|emb|CAE52031.1| RNA polymerase beta subunit [Bacillus licheniformis]
 gi|46019138|emb|CAE52033.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 133

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 56/155 (36%), Positives = 89/155 (57%), Gaps = 22/155 (14%)

Query: 34  KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLW 93
            +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++   
Sbjct: 1   TSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKE 50

Query: 94  RDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIV 153
           RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +R++
Sbjct: 51  RDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVI 101

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           VSQL RSP ++F    G+   +GK  +   +IP++
Sbjct: 102 VSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNR 133


>gi|189030780|gb|ABD59038.2| RNA polymerase II second largest subunit [Lepista irina]
          Length = 659

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 112/730 (15%), Positives = 224/730 (30%), Gaps = 98/730 (13%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAE  EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAEAPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +       L+ +   ++  G      +     +   + GI+E +DA   
Sbjct: 226  TDAGRVCRPLFIVENQQLALQKKHIRWLNNGYNDDGEEYKWEQL--IKGGIIELLDAEEE 283

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                +    +   +       +  Q ++       R  +K G            PS  LG
Sbjct: 284  ETVMISMTPEDLENSRLQQSGVDPQVNDAEFDPAAR--LKAGINSHTWTHCEIHPSMILG 341

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N                        ++       +G      
Sbjct: 342  -------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNF 376

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
             I               +  +             +       +   +  + AI      +
Sbjct: 377  LIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYN 425

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  ++S     + +E   +   D  + +    Y
Sbjct: 426  QEDSVIMNQSSIDRGLF-RSIYYRIYMDLEKKSGV---QXLEEFEKPLXDNTLRMKHGTY 481

Query: 984  SRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +L +   I  G           K+  +  D      R++          ++     +  
Sbjct: 482  DKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVD 541

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            Q                              + VKV V   R  Q+GDK A RHG KG +
Sbjct: 542  QVLI--------------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTI 581

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   DI++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 582  GITYRQEDMPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDL 641

Query: 1161 ANGDISPLRS 1170
                +S    
Sbjct: 642  TVESVSTFLR 651



 Score =  124 bits (310), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 85/622 (13%), Positives = 170/622 (27%), Gaps = 101/622 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 APEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N     +    K         +  L A EEE   I+     L+       
Sbjct: 246 QKKHIRW--LNNGYNDDGEEYKWEQLIKGGIIELLDAEEEETVMISMTPEDLENSRLQQS 303

Query: 643 ELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +       E          +        +  P  ++ I AS+IPF +++ S R      
Sbjct: 304 GVDPQVNDAEFDPAARLKAGINSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 363

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 364 MGKQAMGIFLTNFLI-----------------------------------------RMDT 382

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 383 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 418

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
           + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   +  
Sbjct: 419 LCYSGYNQEDSVIMNQSSIDRGLFRSIYYRIYMDLEKKSGVQXLEEFEKPLXDNTLRMKH 478

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +++ G+I  G  V   DI++GK  P         ++        +    RD S  
Sbjct: 479 GTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTP 531

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V I       K
Sbjct: 532 LKSTESGIVDQVLITTNSEGQK 553


>gi|89142761|emb|CAJ57576.1| RNA polymerase subunit B [Microbacterium keratanolyticum]
          Length = 392

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 143/288 (49%), Positives = 195/288 (67%), Gaps = 15/288 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K
Sbjct: 105 PSIEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNLG 460
           +N +L LD       +  +DI+A IK LV L     T                DDIDN G
Sbjct: 165 INQKLGLDAALTESVLTVDDIVATIKYLVRLHANVETFTGIRAGKKAEIRLATDDIDNFG 224

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 225 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 284

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 285 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNI 344

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           GL+ SL +FAR+N++GFIETPYRKV DG VT+ + YL+A EE++  +A
Sbjct: 345 GLIGSLATFARINSFGFIETPYRKVVDGVVTDQIDYLTASEEDDFVVA 392



 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 93/174 (53%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTAKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  +P I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILAEFAGFPSIEETLAKDTIVT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164


>gi|60117313|gb|AAX14428.1| DNA-directed RNA polymerase, beta/beta'' subunits [Wolbachia
           endosymbiont of Drosophila mojavensis]
          Length = 283

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 103/297 (34%), Positives = 166/297 (55%), Gaps = 29/297 (9%)

Query: 138 MTKDGTFVIKGIQRIVVSQLH--------RSPG-----IHF-DHDKGRASLSGKLLYACR 183
           MT  G F             H        RSP      ++F + DKG+   SGKL+Y+ R
Sbjct: 1   MTDKGHF-------------HHKRGGKKFRSPKCIGLLVYFLNSDKGKTYNSGKLIYSAR 47

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGD 243
            I  +G W+DIEFD KD ++ R+DR+RK+P++  L  LG+ + +IL  FY KI Y +  D
Sbjct: 48  NIHYRGSWLDIEFDVKDHLYFRVDRKRKLPISVLLKELGLSNNDILDRFYEKIKYVKHKD 107

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCL 303
            W  P    D   G ++   L+DI+ G  ++++  ++TS L K L +  +K   +  + +
Sbjct: 108 GWKVPFVP-DKYKGVRLPFDLMDIE-GNVLLKANVRITSRLAKKLYDNELKEYLVPFNSI 165

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLV 363
           CGL++AED+++  +    + AG+ I  + ++++    + +I +L +D++    YI NTL 
Sbjct: 166 CGLFLAEDLMDSASSTKILSAGESIKLEDIKKLELLSVDEISVLNIDNLFVGPYILNTLF 225

Query: 364 TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
            D+N   +DAL +IYRV+RPG+V    + E  F  LFF  + YDLS +GR+K+N  L
Sbjct: 226 LDENMSYQDALYEIYRVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 282


>gi|156547733|ref|XP_001606574.1| PREDICTED: similar to CG4033-PA, partial [Nasonia vitripennis]
          Length = 1097

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 92/532 (17%), Positives = 164/532 (30%), Gaps = 107/532 (20%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              +   +N+ V      G   +  + I       D   + H +E       + L      
Sbjct: 586  RMMRPVKNLSVNKTELIGTFEQVYLNICVTAEEADEGLTTH-QELSKTTFLSNLACLIPM 644

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEK 920
             D         +   + G   +G               + ++P TP  + +    I  ++
Sbjct: 645  PDCNQSPRNMYQC--QMGKQTMGTPCLTWQQQAETKLYRLQTPSTPLFRPVHHDNINLDE 702

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
                 +  + V S     + D  I N+   ++      + + +   L             
Sbjct: 703  FAMGTNAIVAVISYTGYDMEDAMIINKSAYERGFAHGMIYKSEFIELKE---------QS 753

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSS-DLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            + ++R        + +         T+L   D    Y +     F             L 
Sbjct: 754  DYFARDPNRADLVDKLDSDGLPNPGTILQEGDPYYSYYQVDHKTF-------------LI 800

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +Y+  ++         ++ I+    +       V + + + R    GDK A R G KGI
Sbjct: 801  GKYKGKEAAF-------VDNIKLCGSLQSSTKGKVCITLRISRNPSVGDKFASRAGQKGI 853

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
             S+  P ED+PF + G   DIV NP G PSRM +  + E   G +    G    +    +
Sbjct: 854  CSQKWPAEDLPFTETGLIPDIVFNPHGFPSRMTIAMMIEVMAGKSGAVHGLVHDATPFRF 913

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
              N                                                      E  
Sbjct: 914  SENDTA--------------------------------------------------VEYF 923

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
              +L     +  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG   ++T
Sbjct: 924  GKLLEQGGYNYYGTERIYSGIDGREMTADIFFGVVHYQRLRHMVSDKWQVRSTGPIDVLT 983

Query: 1280 QQPLGGKSNRGGQRLG-----------EMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +QP+                       EME   + ++G +++LQ+ L   SD
Sbjct: 984  RQPIK-----------GRRRGGGVRFGEMERDSLISHGCSFLLQDRLFHCSD 1024



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 98/656 (14%), Positives = 214/656 (32%), Gaps = 62/656 (9%)

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
            L+ + +   + I        +++ Y +N ++       +  L    +            
Sbjct: 221 MLKCLMNVSDKYIYNALTAGCDDDVYYKNCVLNMMRTVHEKDLHSHEQCKAY---IGKMF 277

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
               +      +D      + +  + + L  D P D  H+    +  + K L  L + K 
Sbjct: 278 RIKFYELPVNATDIEVCDFIIKYCIAIHL--DDPADKFHL----LCFMTKKLFALADNKC 331

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRL---GLLRMERSIKERISSVDIDSVMPQDLINAKP 508
            ++  D +  +     G +     +      L   RS+  R +    ++    +++NA  
Sbjct: 332 AVEGADAVMVQECLLGGHLYLQVIKEKLYSWLMGLRSVIVRRAKNVGNNFTLNEMLNALK 391

Query: 509 VVSAVCEFFC------------------SSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
                                       S+ LS + E++N +  ++H R   A+ +G   
Sbjct: 392 SCGTFDSQMENFLATGNVRSQTGLGLMQSTGLSIVAENINRMRYMSHFR---AIHRGSFF 448

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           +     E R + P  +G ICP  T +G   GL++ LT    V  +   +           
Sbjct: 449 QEMRTTEARQLLPDAWGFICPVHTPDGAPCGLLNHLTMNCIVTKHPDPKLKNAIPTILLD 508

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              +    A + +N Y    +  +       E+ +  R   +  ++   +       P  
Sbjct: 509 LGMLPMSIADDWKNSYTVVLDGRVI---GLIEDNIVGRVVDKLRVLKINE----KVPPTM 561

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
            + +        +            M R    L   +   +GT  E V       A  A 
Sbjct: 562 EIVLVPKKNVPSQYPGVFLFTGPTRMMRPVKNLSVNKTELIGT-FEQVYLNICVTAEEAD 620

Query: 731 RAGIVEQVDAIRIV---IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVG 785
                 Q  +       +  +    D + S  ++Y+    +++    C+   Q+   K+ 
Sbjct: 621 EGLTTHQELSKTTFLSNLACLIPMPDCNQSPRNMYQCQMGKQTMGTPCLTWQQQAETKLY 680

Query: 786 DEVRRNDIIA---DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                +  +       + +L + A+G N +VA + + GY+ ED+M+I++           
Sbjct: 681 RLQTPSTPLFRPVHHDNINLDEFAMGTNAIVAVISYTGYDMEDAMIINKSAYERGFA--- 737

Query: 843 HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
           H   ++    + K   +   RD      + +  +D  G+   G  +  GD          
Sbjct: 738 HGMIYKSEFIELKEQSDYFARDPN--RADLVDKLDSDGLPNPGTILQEGDPYYSYYQVDH 795

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLR--VPSGVSGTVVDVRIFNRHGIDKNERS 956
           ++       L+    G++A  V +  L   + S   G V      +R+    ++ +
Sbjct: 796 KT------FLIGKYKGKEAAFVDNIKLCGSLQSSTKGKVCITLRISRNPSVGDKFA 845



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 48/160 (30%), Gaps = 59/160 (36%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT---AFSGAAMLEFVSYEFDPP----- 84
              S+++ L           +GL  A  ++ P+    A      L       + P     
Sbjct: 9   HIDSFNYALG----------QGLTEAIDNLLPVYLTLASGDRIELRIEDVTINHPTVPSG 58

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  R  TY   +   +   +    + T  +S          +G++P+
Sbjct: 59  TIGVKNHKIYPTECRQRAATYKGKINAKIGWSINGRKQETVERS----------LGEVPI 108

Query: 138 MTKD------------------------GTFVIKGIQRIV 153
           M K                         G F+IKG +R++
Sbjct: 109 MVKSNKCHLNNMKPAQLVAVKEHEQEWGGYFIIKGHERLI 148


>gi|192337684|gb|ACF04262.1| RpoB [Vibrio parahaemolyticus]
 gi|192337686|gb|ACF04263.1| RpoB [Vibrio parahaemolyticus]
 gi|192337690|gb|ACF04265.1| RpoB [Vibrio parahaemolyticus]
 gi|192337700|gb|ACF04270.1| RpoB [Vibrio parahaemolyticus]
 gi|192337702|gb|ACF04271.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLS   +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSLFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|307343512|emb|CBJ18673.1| RNA polymerase B subunit [Micromonospora sp. SGA3]
          Length = 201

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 88/205 (42%), Positives = 116/205 (56%), Gaps = 38/205 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G  +     ++K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWSVDGDDAEWKRQLRSIN---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEPDTNVATPVFDGAREEEISGLLASTLPNRDGNQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYI 1254
              G++ L+DG +GEP   P+ VGY+
Sbjct: 177  GSGKAQLFDGRSGEPLPDPIAVGYV 201


>gi|80973521|gb|ABB53498.1| RNA polymerase beta subunit [Streptococcus pluranimalium]
          Length = 226

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 96/292 (32%), Positives = 131/292 (44%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                     A  E        A +D   +++LYDG TGEPFD  V+VG +YM
Sbjct: 189  ---------ATVEE-------AGMDSDAKTVLYDGRTGEPFDNRVSVGVMYM 224



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|62946665|gb|AAY22444.1| RNA polymerase Rpb2 domain 6 [Lymphocystis disease virus 1]
          Length = 1018

 Score =  234 bits (596), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 94/423 (22%), Positives = 158/423 (37%), Gaps = 89/423 (21%)

Query: 963  QIELLARDKDDEQ-VILDRNIYSR-LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +IE      D E     D +I +R L   L G+  V  PK  KK+      L        
Sbjct: 664  EIEKYKSKHDSELIAHPDFSIRNRDLDYSLLGKTGVLDPKLGKKNKKYRCPLCDAL---- 719

Query: 1021 WW-QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            W+    V   KV + +    + Y      ++   +  ++++     +  G  R++KV + 
Sbjct: 720  WFPAGTVLVGKVAKKLIDGVIVYRDVSLAVKADEEGYLDELLDHYTIETG--RIIKVKLR 777

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  + GDK A     KG    I   EDMPF  +G   D+++NP   PSRM +  I + 
Sbjct: 778  SSKIPEIGDKFASFTAQKGTCGMIYRQEDMPFTAEGVVPDLIINPHAFPSRMTINYILQM 837

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
              G A    GK   +                  ++   T    E   +   ++       
Sbjct: 838  CYGLAACYTGKIYDATPF---------------KRYNLTEELKELALELKLETWETTMYC 882

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +G   S+ +F                                       +G     +L
Sbjct: 883  GLTGKKFSSKIF---------------------------------------IGPCDYQRL 903

Query: 1260 NHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML---- 1315
             H+V++K+++R +G    +T QP+ G+S  GG ++GEME WC  ++GA+  L+E L    
Sbjct: 904  RHLVTNKIHSRISGPIDNLTHQPVAGRSRYGGIKVGEMEQWCKLSHGASAALKESLFDMS 963

Query: 1316 ---------TIK--SDDVVGRTRVYESIVAGNDTFETGT---PESFNVLVKEMQALGLSI 1361
                     T K  SDD       +E     +D  E      P +  +L +E+ A+G+ +
Sbjct: 964  DKYTIPVCKTCKTISDD-------FEYCRKCDDI-EIEMKNCPYTSKLLFQELMAIGIHV 1015

Query: 1362 DLE 1364
              E
Sbjct: 1016 QFE 1018



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 55/148 (37%), Gaps = 49/148 (33%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
           L      SYD FL  +I      ++ +Q            +   ++EF + +++ PK   
Sbjct: 5   LTAHHIESYDRFLFFDIPAVVARDKIIQ------------TTNFVIEFKNIQYNKPKITP 52

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT--------- 139
            +   +DLTYA+ +        +++D    +  +       I+   LPLM          
Sbjct: 53  LEAKQKDLTYAISI-------NYEIDFNGKSTIL------EIF--SLPLMLRSKLCLTNN 97

Query: 140 -------------KDGTFVIKGIQRIVV 154
                          G F++KG +R+++
Sbjct: 98  VAHQTTFELCPNDPGGYFIVKGKERVLI 125



 Score = 69.3 bits (168), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 90/547 (16%), Positives = 171/547 (31%), Gaps = 122/547 (22%)

Query: 359 RNTLVTDKNKDRKDALLDI-YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +N    +      +AL  I Y         T  V   +      D+ +  + ++ + ++ 
Sbjct: 206 KNKHTLNCKSGYYEALSTILYGHYTGNKTVTDYVPVDVKC----DNKESYVESLLKKEIF 261

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
             L   +P +V       +  +I  L  +  G+  + D D+L  +RV + G +++  ++ 
Sbjct: 262 NHLEDHSPFNV----ACHLGYMINRLAAVTAGEAALTDKDDLAYKRVDTSGTLIEFLFKG 317

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------------L 522
              +  R IK  +  +         + N   + + +   F +                 +
Sbjct: 318 LFKQYVRLIKNSLEILKNPDP-INIVKNVNVITNGLNLCFATGNWSVKKTGPPSYMRVGV 376

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ+  + N  SR++H RR        V       ++R +H +HYG ICP ET EG  +G+
Sbjct: 377 SQVLCNHNYGSRLSHLRR----LMHAVGFKGKNFKIRRLHASHYGFICPYETPEGERVGV 432

Query: 583 VSS------LTSFARVNAYGFIETPYRK----------------VCDGKVTNDVVYLSAM 620
           V +       +     N    +  PY K                V D   T   +     
Sbjct: 433 VLNTALSTAFSQGIPKNQIKPLMEPYIKNSGSFKVILNGEIVGYVDDPDQTIKFLKSVLP 492

Query: 621 EEENRYIAQANSSLDE------DGSFTEELVFCRCAGEEILVPREKIDFIDA-SPKQVVS 673
           EE + +  +    + E       G F   ++               I + +  +   +  
Sbjct: 493 EEVSVFCYRFTPKIKECHVFSDKGRFLRPVLVESKIIRVCAQEIHHIKYKELPAYSTMTD 552

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF  +  S R+    NM +QAV +       +  G +                 
Sbjct: 553 VMASVIPFYNHAPSPRIAYQSNMGKQAVGITT-----LTGGRDRYDPTF----------- 596

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + +    Y   KF       C    P+V           
Sbjct: 597 -------------YSLDYPQKALARTICYDRYKFD----IMCHGAVPIV----------- 628

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                               A     GYN EDS+++++  +   +F     + F  + + 
Sbjct: 629 --------------------AVSTMDGYNQEDSVVLNKSSIDRGLFNITCYKTFVEIEKY 668

Query: 854 TKLGPEE 860
                 E
Sbjct: 669 KSKHDSE 675


>gi|307343496|emb|CBJ18665.1| RNA polymerase B subunit [Micromonospora sp. CR36]
          Length = 193

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 89/204 (43%), Positives = 116/204 (56%), Gaps = 38/204 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 20   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 79

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 80   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 128

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 129  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 169

Query: 1232 --GQSILYDGLTGEPFDRPVTVGY 1253
              G++ L+DG +GEP   P+ VGY
Sbjct: 170  ASGKAQLFDGRSGEPLPDPIAVGY 193


>gi|192337672|gb|ACF04256.1| RpoB [Vibrio parahaemolyticus]
 gi|192337680|gb|ACF04260.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 207/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLS+  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSRFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|304322999|ref|YP_003795537.1| beta subunit of RNA polymerase [Floydiella terrestris]
 gi|270048198|gb|ACZ58493.1| beta subunit of RNA polymerase [Floydiella terrestris]
          Length = 1057

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 99/325 (30%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 951  DKNERSISVEREQIELLARDKDDEQV-----ILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             K ++  + E++Q   L +D+  ++      I +        ++L  +   S  +  +++
Sbjct: 286  MKFQKLQNKEKKQDFSLKQDERTKKRKSVNKISEEVNKKTKKKVLKTKEKKSVNEIPEET 345

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKV--QRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 +L      S   +    DE     +  + L    E      ++ F    +KI   
Sbjct: 346  GKKKQNLALPLSFSFQNKKKKNDETSLQNKKKKKLSSLNEEGPKTRKNSFFLLKKKIPQ- 404

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                  V   V++++A KR I+ GDKMAGRHGNKGIVS ILP EDMP+L DG+P+D+VLN
Sbjct: 405  --FSQKVPTFVQIYLAQKRKIRVGDKMAGRHGNKGIVSEILPREDMPYLPDGSPLDLVLN 462

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            PLGVPSRMNVGQI+E  LG+A   LG++ +    D     D S    F EK+    S T 
Sbjct: 463  PLGVPSRMNVGQIYECLLGFAGKFLGEQYRITPFDESYGPDASRSFVF-EKLYKASSQTG 521

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                +  ++                                       G+  LYDG TG+
Sbjct: 522  LSWIFKPEN--------------------------------------PGKIRLYDGRTGD 543

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVY 1268
             FD+ +TVG  Y++KL H+V DK++
Sbjct: 544  RFDQAITVGRAYIIKLVHLVDDKMH 568



 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 57/110 (51%), Positives = 77/110 (70%), Gaps = 1/110 (0%)

Query: 1269 ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV 1328
            +RS G YSL+TQQPL G+S +GGQRLGEMEVW I+ YGAA  L E++TIKSDD+VGRT V
Sbjct: 946  SRSVGPYSLITQQPLKGRSKQGGQRLGEMEVWAIEGYGAALNLLELVTIKSDDIVGRTTV 1005

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIP 1378
            ++SI+        GTP SF +L+ E+ AL L++ +  S  K   + ++I 
Sbjct: 1006 WDSIIRNKHLC-FGTPASFKLLICELNALCLNVKVYVSNKKGELEQKDIS 1054



 Score =  127 bits (318), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 86/186 (46%), Positives = 124/186 (66%), Gaps = 3/186 (1%)

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y L  +QR+NQ+T    R  V  G  V+  D++A+  ++  G+L++G+N+L+A+MPW GY
Sbjct: 8   YNLEGYQRTNQDTLSVHRTAVGEGTWVQPGDLLANCSTSVAGELSIGQNLLIAYMPWEGY 67

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE-EGLKNIDECG 880
           N+ED++LISER+VS+D+ TSIHIE++E+     K G EEITR++PN  + E  KN+D+ G
Sbjct: 68  NYEDAILISERLVSDDLHTSIHIEKYEIKVSKVKKGVEEITRNLPNSDQTEECKNLDKKG 127

Query: 881 IICVGAEVNPGDILVGKITPKGE-SPMTPEEKLLRAIFGEKA-VDVRDTSLRVPSGVSGT 938
           I+ +G  V  GDILVGK TP  E    +  EKLLR I G  +    RD+SLRVP+G    
Sbjct: 128 IVKLGTFVKEGDILVGKKTPIDEPKNRSGYEKLLRDILGHHSEPTHRDSSLRVPTGFEAK 187

Query: 939 VVDVRI 944
           V+  +I
Sbjct: 188 VIHTQI 193


>gi|80973509|gb|ABB53492.1| RNA polymerase beta subunit [Streptococcus lutetiensis]
 gi|80973611|gb|ABB53543.1| RNA polymerase beta subunit [Streptococcus equinus]
          Length = 226

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 95/294 (32%), Positives = 133/294 (45%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM+K
Sbjct: 189  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|115746590|ref|XP_782970.2| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Strongylocentrotus purpuratus]
 gi|115975796|ref|XP_001180703.1| PREDICTED: similar to Polymerase (RNA) III (DNA directed) polypeptide
            B [Strongylocentrotus purpuratus]
          Length = 830

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 99/268 (36%), Gaps = 80/268 (29%)

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP G PSRM VG++ E   G                                      
Sbjct: 625  IMNPHGFPSRMTVGKLIEFLAGK------------------------------------- 647

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                            A   +      T  F G     I   LR    +  G+  L  G+
Sbjct: 648  ----------------AGVLEGKFHYGT-AFGGDKVVDICEDLRKHGFNYLGKDFLTSGI 690

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            TGEP    +  G +Y  KL HMV DK++AR+ G  +++T+QP  G++  GG RLGEME  
Sbjct: 691  TGEPLTAYIYFGPVYYQKLKHMVLDKMHARAKGPRAVLTRQPTEGRARDGGLRLGEMERD 750

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------------NDTFETG 1342
            C+  YGA+ +L E L I SD    DV G          G               +     
Sbjct: 751  CLIGYGASMLLLERLMISSDQFQVDVCGD--------CGLIGHSGWCPYCHCSQNISSLR 802

Query: 1343 TPESFNVLVKEMQALGLSIDLENSRTKN 1370
             P +  +L +E+Q++ +   L   +   
Sbjct: 803  IPYACKLLFQELQSMNIIPRLRLKKYTE 830



 Score =  125 bits (315), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 73/600 (12%), Positives = 183/600 (30%), Gaps = 86/600 (14%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L+     S+++F+ + +              +S FP  A      L++++     P    
Sbjct: 55  LVRQHIDSFNYFINVEVFSMNFAP------LQSTFPAEALP---YLQYLNIYVGSPDVEE 105

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + +   ++ +G +P+M
Sbjct: 106 SFNITKPTSPHECRLRDMTYSAPITVDIEYT----------RGQQRVIRNNLPIGRMPIM 155

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+++G +++++ Q   S          +  +
Sbjct: 156 LRSSNCVLTGKSPAELAKLNECPLDPGGYFIVRGTEKVILIQEQLSKNRMIVEVDRKGIV 215

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
           S  +  +     ++     +    K   +++ +     +P+     A+GM+S+ EI+ T 
Sbjct: 216 SCNVTSSTH---ERKSR-TVVIVKKGKHYLKHNTFTEDIPIVVIFKAMGMESDQEIVQTI 271

Query: 233 ---------YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
                    +   +           L A   M        +    + +  ++  ++L + 
Sbjct: 272 GTEESTMVSFASNLEECHKIQVYTQLQALKYMGMKVRQRRMWGGGSKKSKVDEARELLAT 331

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    V      +  +    +   ++  +   + ++  D    K LE         
Sbjct: 332 TI--LAHIPVVQFNFRAKSIYLALMVRRVIEAQGDAVKVDDRDYYGNKRLELAGQL---- 385

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           I +L+ D                    + A  DI + MR   ++   +     +   +  
Sbjct: 386 IALLFEDLFKKFNSELKKYADQNIPRPRAAQFDIVKYMRQDQITNGLITA--ISTGNWSV 443

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+      +  +     I+         +G  ++          
Sbjct: 444 KRFKMERAGVTQVLSRLSY-----ISCLGMMTRISSQFEKTRKVSGPRSLQPSQ----WG 494

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           +   V     +  +PV     E      + 
Sbjct: 495 MLCPSDTPEGEGCGLIKNLALMTHITTDMEEAPIVKLAFNLGVEPVHLMSGEELSMKDVY 554

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            +  + N L  +   +RL    +  V RA    E   + P H  R     +  G    +V
Sbjct: 555 VVFLNGNILGVVREHKRLMRTFRL-VRRAGYISEFVSICPNHAQRCVTIASDGGRVCSIV 613



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 55/423 (13%), Positives = 131/423 (30%), Gaps = 23/423 (5%)

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
           T + ++   +   + ++  +  KG+    +TS        +  +V  + G+ Y++     
Sbjct: 190 TEKVILIQEQLSKNRMIVEVDRKGIVSCNVTSSTHERK--SRTVVIVKKGKHYLKHNTFT 247

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           ++  +  IF +   +      D                     +    I    +   +  
Sbjct: 248 EDIPIVVIFKAMGME-----SDQEIVQTIGTEESTMVSFASNLEECHKIQVYTQLQALKY 302

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA-IIKILVDLR 447
             +           S K  +     +     L            K   +A +++ +++ +
Sbjct: 303 MGMKVRQRRMWGGGSKKSKVDEARELLATTILAHIPVVQFNFRAKSIYLALMVRRVIEAQ 362

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ----DL 503
                +DD D  GN+R+   G+++   +     +    +K+            Q      
Sbjct: 363 GDAVKVDDRDYYGNKRLELAGQLIALLFEDLFKKFNSELKKYADQNIPRPRAAQFDIVKY 422

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAG 555
           +    + + +     +   S     +          RLS +              + R  
Sbjct: 423 MRQDQITNGLITAISTGNWSVKRFKMERAGVTQVLSRLSYISCLGMMTRISSQFEKTRKV 482

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
              R + P+ +G +CP++T EG   GL+ +L     +      E P  K+        V 
Sbjct: 483 SGPRSLQPSQWGMLCPSDTPEGEGCGLIKNLALMTHITTD-MEEAPIVKLAFNLGVEPVH 541

Query: 616 YLSAME--EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
            +S  E   ++ Y+   N ++       + L+             E +       ++ V+
Sbjct: 542 LMSGEELSMKDVYVVFLNGNILGVVREHKRLMRTFRLVRRAGYISEFVSICPNHAQRCVT 601

Query: 674 IAA 676
           IA+
Sbjct: 602 IAS 604


>gi|145342283|gb|ABP64838.1| RpoB [Paenibacillus borealis]
 gi|145342309|gb|ABP64851.1| RpoB [Paenibacillus borealis]
 gi|145342337|gb|ABP64865.1| RpoB [Paenibacillus borealis]
          Length = 232

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 95/287 (33%), Positives = 134/287 (46%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+         +IL G+    G         L   +  E  R           +V+
Sbjct: 16   DERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAG
Sbjct: 65   DTSLRVPHGSDGIIVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  +
Sbjct: 119  RHGNKGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHIGMAALQLGIHV 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D                                             VFD
Sbjct: 179  ATPVFDGAREND---------------------------------------------VFD 193

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                      +  A +  +G+++LYDG TGE F+R VTVG ++M+KL
Sbjct: 194  ---------TMEEAGMQRNGKTVLYDGRTGERFEREVTVGVMHMIKL 231



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+N GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|3133343|gb|AAC38472.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 234

 Score =  233 bits (595), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS +D DG FTE+ V  R   GE   V    +D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPIDTDGRFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|153958186|gb|ABS53383.1| RpoB [Bacteriovorax sp. MNZ1]
          Length = 343

 Score =  233 bits (595), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 163/344 (47%), Positives = 226/344 (65%), Gaps = 10/344 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                 ++   ++  +           + +  +  ++I K   GD
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGD 343


>gi|3133377|gb|AAC38489.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 234

 Score =  233 bits (595), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS +  DGSFTE+ V  R   GE   V    +D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPIGADGSFTEDRVMVRRKGGEVENVAPIDVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|156351040|ref|XP_001622335.1| predicted protein [Nematostella vectensis]
 gi|156208847|gb|EDO30235.1| predicted protein [Nematostella vectensis]
          Length = 185

 Score =  233 bits (595), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 93/233 (39%), Gaps = 51/233 (21%)

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD+     L    + + ++R    GDK + RHG KGI S+  P ++MPF + GT  DI+
Sbjct: 4    IGDETGDKTLSKACIKLRIQRNPIIGDKFSSRHGQKGICSQKWPVKNMPFSESGT-PDII 62

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
             NP G PSRM +G + E+  G +    G    +    +                      
Sbjct: 63   FNPHGFPSRMTIGMMIESMAGKSAALNGHVYDATPFTFSE-------------------- 102

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                          D +  +    +L  +  D  G   LY G+ 
Sbjct: 103  ------------------------------DDSAIDYFGKLLVKSGYDYFGTERLYSGID 132

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            G  F+  + +G +Y  +L HMV+DK   R+TG    +T QP+ G+  +GG R 
Sbjct: 133  GREFEADIFMGVVYYQRLRHMVADKFQVRTTGPIDALTHQPVQGRKRQGGIRF 185


>gi|194320293|gb|ACF48387.1| RNA polymerase II second largest subunit [Rhizocarpon oederi]
          Length = 696

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 111/816 (13%), Positives = 225/816 (27%), Gaps = 143/816 (17%)

Query: 468  GEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R    ++ + +   +               + +  + S +     +      
Sbjct: 1    GPLLAGLFRTLFKKLTKDVYXYLQKCVEMNREFNLTLGVKSTTLTSGLKYSLATGNWGEQ 60

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 61   KKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPA 116

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    +  +  +    S       ++   
Sbjct: 117  ETPEGQACGLVKNLALMCYITVGTPSEPIIDFMVQRNMDLLEEYEPQSYPNATKIFVNGV 176

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSN 688
               +  D +     V        I      + D  D   K          P F+  +D  
Sbjct: 177  WVGVHRDPAHLVSTVQILRRRHMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIENDPR 236

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
                G  +  +       E   +   M++   +       +K  G    V   + V+  V
Sbjct: 237  SPNRGSLVLTKEHIQKLEEDHEIAADMDADEKE-------SKFMGWEGLV--NQGVVEYV 287

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
            + + + +   V     ++  +  Q               V+          T      ++
Sbjct: 288  DAEEEETVMIVMTPADLEISKQLQQGYTLPEASDDPNRRVKAPMNPTAHTWTHCEIHPSM 347

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 348  ILGICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRM---------------- 389

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 390  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 438

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  +D+ +R      + +E   +    + + L    Y +L 
Sbjct: 439  VIMNQSSIDRGLF-RSLFYRAYVDQEKRVGM---QLVEQFEKPMRSDTLRLKHGTYDKLD 494

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   I  G           K+  +++D      R++          ++     +  Q   
Sbjct: 495  DDGIIAPGVRISGEDIIIGKTAPIAADAEELGQRTKLHVKRDVSTPLRSTESGIVDQVLL 554

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      LR VKV +   +  Q GDK A RHG KG +    
Sbjct: 555  --------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 594

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 595  RQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVDS 654

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 655  VSRLLR--EHGYQSRGFEVM---------------------------------------- 672

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +G +    G         V +G  Y  +L 
Sbjct: 673  -----YNGHT----GR---KLVAQVFLGPTYYQRLR 696


>gi|254055189|gb|ACT64194.1| RpoB [Burkholderia cepacia]
 gi|254055191|gb|ACT64195.1| RpoB [Burkholderia cepacia]
          Length = 231

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 182/231 (78%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGE+ +NQ+R GL+R+ER++KER+   + +++MP DLIN+KP+ SA+ EFF SSQL
Sbjct: 1   RVRCVGELAENQFRAGLVRVERAVKERLGQAESENLMPHDLINSKPISSAIREFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL  +A +N YGF+ETPYRKV D KVT+ + YLSA+EE    IAQAN+++DE+G+  +
Sbjct: 121 INSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGTLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R AGE ++V  ++I ++D +P Q+VS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMG 231


>gi|269912646|emb|CAY86103.1| RNA polymerase beta subunit [Gluconobacter oxydans]
          Length = 311

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 125/277 (45%), Positives = 172/277 (62%), Gaps = 28/277 (10%)

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL---------------------- 221
           IIP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL                      
Sbjct: 37  IIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYLAQREQKIAEGGDVEGL 96

Query: 222 ---GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
              GMD +EILS FY  + +++ G  W  P    D   G K+ S LVD DTGE V E+  
Sbjct: 97  DIRGMDQDEILSYFYEAVPFTRLGGEWARPFDP-DAFRGLKLLSPLVDADTGEVVAEADA 155

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           KLT+ +++ + EK  + + +    + G ++A D+VN  TGEIY EAG+ + E  L  +  
Sbjct: 156 KLTARMVRKIAEK-TRVVQVGRLDILGRFLAYDLVNENTGEIYGEAGEELTEDRLAALEE 214

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
             I ++P+L VD  ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T   AE+MF+ 
Sbjct: 215 MGITELPLLSVDG-SHGPWIRNTLAADKNSCRDEALIDIYRIMRPGEPPTKETAEAMFHG 273

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKED 435
           LFFD  +YDLS VGRVKMNMRL++D PD +R +RKED
Sbjct: 274 LFFDQGRYDLSAVGRVKMNMRLDVDAPDTLRVLRKED 310


>gi|269912606|emb|CAY86083.1| RNA polymerase beta subunit [Gluconacetobacter saccharivorans]
          Length = 259

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 110/262 (41%), Positives = 153/262 (58%), Gaps = 28/262 (10%)

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL--- 221
           FDHDKG+   SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL   
Sbjct: 1   FDHDKGKTHSSGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGA 60

Query: 222 ----------------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
                                 GMD +EIL  FY K+ +++    W     A     G K
Sbjct: 61  TSAAARAAKAAEGGDVEAMEIQGMDPDEILGYFYGKVEFNKTPKGWARRFDAE-AFRGQK 119

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
           +   L+D  TGE+V  +  KLT+ +++ + E   K + +    L G ++A D+VN  TGE
Sbjct: 120 LLEPLIDAQTGEEVAPADAKLTARMVRKIAET-TKEVLVGPAGLIGRFIASDMVNENTGE 178

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           IY EAG+ + E+ LEE+    +  +  L +D+ N   +IRNTL  DKN  R++AL DIYR
Sbjct: 179 IYAEAGEELTEQKLEELDAEGLTTLTTLAIDATN-GPWIRNTLAVDKNASREEALTDIYR 237

Query: 380 VMRPGDVSTFSVAESMFNFLFF 401
           VMRPG+  T   AE+MF+ LFF
Sbjct: 238 VMRPGEPPTPETAEAMFSGLFF 259


>gi|254055201|gb|ACT64200.1| RpoB [Pseudomonas sp. CMR5c]
          Length = 231

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 138/231 (59%), Positives = 180/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA+++++E G   +
Sbjct: 121 INSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNEKGQLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|159171907|gb|ABW96213.1| DNA-directed RNA polymerase beta subunit [Bacteriovorax stolpii]
          Length = 348

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 163/351 (46%), Positives = 230/351 (65%), Gaps = 10/351 (2%)

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            GA + AK  G V  VD+ RIVI+    +     SGVD+Y+L K+QR+NQNTC NQ+ LVK
Sbjct: 1    GAIVYAKEGGRVIFVDSNRIVIQRD--NFSEGESGVDVYKLTKYQRTNQNTCNNQKALVK 58

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD+V +  +IADGP+T LGDLALG+N+LVAFMPW GYN+EDS+LI+E +++ DVFTS+H
Sbjct: 59   EGDKVLKGMVIADGPATQLGDLALGQNVLVAFMPWGGYNYEDSILINENILARDVFTSVH 118

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IE FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE
Sbjct: 119  IESFEIEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGE 178

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            S ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D +++ R G++ + RS  +   +
Sbjct: 179  SQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDAKVYTREGVELDARSKEIIDHE 238

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEY 1016
              L+ RD+  E   +  +   ++ E+  G              +   K   ++ ++++  
Sbjct: 239  TTLIRRDERIEIKAIQTSAIQKIAEMFKGAKTTDKLISEDGTTELLGKGVAVTGEILASI 298

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            P        ++   ++  +           + +  +  ++I K+  GD++P
Sbjct: 299  PFELIGYLPLE-AALEEKLSEYFADVRNRITRVRQKANDEIAKLHKGDELP 348


>gi|145342363|gb|ABP64878.1| RpoB [Paenibacillus sp. FSL_H7-941]
          Length = 232

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALSLGIHIATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|153958212|gb|ABS53396.1| RpoB [Bacteriovorax sp. PR]
          Length = 348

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 165/350 (47%), Positives = 229/350 (65%), Gaps = 10/350 (2%)

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             VA+ S A + AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC N
Sbjct: 2    TVARDSRAILFAKHSGRVIFVDSNRIVIQRDK--FDEGQSGVDIYKLVKYQRTNQNTCNN 59

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            Q+ LVK GD V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ D
Sbjct: 60   QKALVKEGDVVSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARD 119

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            VFTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGK
Sbjct: 120  VFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGK 179

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS 
Sbjct: 180  ITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSK 239

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSS 1010
             +  ++  L+ RD+  E   +  +   ++ E+L G              +   K   L+ 
Sbjct: 240  EIIEQETTLIRRDERIEIKAIQTSSILKIAEMLKGAKTTDRLVSEDGSSELLPKGAELTG 299

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
            ++++  P        ++   ++  +           + +  +  ++I K 
Sbjct: 300  EVLASIPFELIGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKH 348


>gi|300394696|gb|ADK11886.1| DNA-directed RNA polymerase II subunit two [Aphanobasidium
            pseudotsugae]
          Length = 643

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 109/729 (14%), Positives = 208/729 (28%), Gaps = 114/729 (15%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L N +R+   ++ + +    +              +  + + + +     +   
Sbjct: 2    DLAGPLLANLFRMLFKKLTKDVYRYLQKCVESHKEFNLALAVKHQTITNGLKYSLATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H +H+G +
Sbjct: 62   GDQKKMMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNSHWGMV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   + ++  G    P  +  +      +   +A          
Sbjct: 118  CPAETPEGQACGLVKNLALMSCIS-VGSPSGPILEFLEEWGLETLE-ENAHSTTPYTKVF 175

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLEND 685
             N            LV              ++    D  +   +          P    +
Sbjct: 176  LNGVWMGVHRDPANLVKTIKRLRRRDDIPSEVSVVRDIREKELRLYTDAGRVCRPLFIVE 235

Query: 686  DSNRVLMGCNM------QRQAVPLLKAEAPFVGTGMESVVAKSSGAA--IVAKRAGIVEQ 737
            +    L+  +M      Q         E       +E + A+        +        +
Sbjct: 236  NQQLQLVKEHMTWLQDKQTPMGRPFGWEQMLRHGLIELLDAEEEETVMICMTPEDLETSR 295

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            + +    I+  E + DP+                          +K G            
Sbjct: 296  LQSSGYDIKDDEEEFDPAA------------------------RLKAGTNTHTWTHCEIH 331

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS  LG       +  + +P+  +N                        ++       +G
Sbjct: 332  PSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMG 366

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                   I               +  +             +       +   +  + AI 
Sbjct: 367  VFLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIM 415

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    ++ R  +D  ++S   + E+ E   R+       
Sbjct: 416  CYSGYNQEDSVIMNQSSIDRGLF-RSLYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKH 474

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +       I  G N         K+  +  D                +E  QR    
Sbjct: 475  GSYDKIEDDGLIAPGTNVNGEDIIIGKTAPIPPD---------------SEELGQRTRSH 519

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             +    T     E    +++              + VKV V   R  Q+GDK A RHG K
Sbjct: 520  TRRDVSTPLKSTEKGMVDQVLI-----TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQK 574

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   DIV+NP  +PSRM +G + E  L      +G +  +   
Sbjct: 575  GTIGITYRQEDMPFTAEGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPF 634

Query: 1158 DYKANGDIS 1166
                   +S
Sbjct: 635  TELTVESVS 643



 Score =  122 bits (306), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 93/623 (14%), Positives = 175/623 (28%), Gaps = 103/623 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 5   GPLLANLFRMLFKKLTKDVYRYLQKCVESH--KEFNLALAVKHQTITNGLKYSL-ATGNW 61

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++        + + +    + +  L        R GK       +  +  +    E
Sbjct: 62  GDQKKMMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNSHWGMVCPAE 121

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 122 TPEGQACGLVKNLALMSCISVGSPSGPILEFLEEWGLETLEENAHSTTPYTKVFLNGVWM 181

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC-PAETSEGHNIG 581
               +  N +  I   RR   +    V+  R   E      T  GR+C P    E   + 
Sbjct: 182 GVHRDPANLVKTIKRLRRRDDI-PSEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLQ 240

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           LV    ++ +                      +  L A EEE   I      L+     +
Sbjct: 241 LVKEHMTWLQDKQTPMGRP--FGWEQMLRHGLIELLDAEEEETVMICMTPEDLETSRLQS 298

Query: 642 EELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                     E     R             +  P  ++ I AS+IPF +++ S R     
Sbjct: 299 SGYDIKDDEEEFDPAARLKAGTNTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 358

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                                                   
Sbjct: 359 AMGKQAMGVFLTNFLI-----------------------------------------RMD 377

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
           + + +  Y       +     +  R                        +L  G+N +VA
Sbjct: 378 TMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVA 413

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            M + GYN EDS+++++  +   +F S++   +  + + + +   E            + 
Sbjct: 414 IMCYSGYNQEDSVIMNQSSIDRGLFRSLYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMK 473

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 I++ G+I  G  VN  DI++GK  P         ++        ++   RD S 
Sbjct: 474 HGSYDKIEDDGLIAPGTNVNGEDIIIGKTAPIPPDSEELGQRT-------RSHTRRDVST 526

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S   G V  V I       K
Sbjct: 527 PLKSTEKGMVDQVLITTNSEGQK 549


>gi|3133373|gb|AAC38487.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 234

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS +D DGSFTE+ V  R   GE   V    +D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPIDADGSFTEDRVMVRRKGGEVENVAPSDVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|158853040|gb|ABW82120.1| RpoB [Bacteriovorax sp. T2]
          Length = 350

 Score =  233 bits (594), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 162/347 (46%), Positives = 230/347 (66%), Gaps = 10/347 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
                 ++   ++  +           S +  +  ++I K+  GD++ 
Sbjct: 301  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRGDELS 346


>gi|75037363|gb|ABA12478.1| RNA polymerase beta subunit [Streptococcus parasanguinis ATCC 15912]
 gi|80973559|gb|ABB53517.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|80973625|gb|ABB53550.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 226

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 96/286 (33%), Positives = 131/286 (45%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DETGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                              D
Sbjct: 175  ATPVFDGASSEDLW---------------------------------------------D 189

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               E         A +D   ++ILYDG TGEPFD  V+VG +YM+K
Sbjct: 190  TVKE---------AGMDSDAKTILYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDETGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|307343504|emb|CBJ18669.1| RNA polymerase B subunit [Micromonospora sp. SG8]
          Length = 201

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 90/205 (43%), Positives = 118/205 (57%), Gaps = 38/205 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 27   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 86

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 87   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 135

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 136  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 176

Query: 1232 --GQSILYDGLTGEPFDRPVTVGYI 1254
              G++ L+DG +GEP   P+ VGY+
Sbjct: 177  RTGKAQLFDGRSGEPLPDPIAVGYV 201


>gi|3133449|gb|AAC38525.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
          Length = 234

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRD 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVEGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS  DE G FTEE V  R   GE   VP   +D++D SP+Q+
Sbjct: 121 EIRYLTADEEDRHVVAQANSPTDEKGRFTEERVLVRRKGGEVEFVPSTGVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|254055171|gb|ACT64185.1| RpoB [Pseudomonas chlororaphis]
 gi|254055173|gb|ACT64186.1| RpoB [Pseudomonas chlororaphis]
 gi|254055175|gb|ACT64187.1| RpoB [Pseudomonas chlororaphis]
 gi|254055177|gb|ACT64188.1| RpoB [Pseudomonas chlororaphis]
 gi|254055179|gb|ACT64189.1| RpoB [Pseudomonas sp. C1Phz26]
 gi|254055199|gb|ACT64199.1| RpoB [Pseudomonas sp. CMR12a]
          Length = 231

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 180/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++ G   +
Sbjct: 121 INSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKGQLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|153958275|gb|ABS53427.1| RpoB [Bacteriovorax sp. WAI19]
          Length = 351

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 163/353 (46%), Positives = 232/353 (65%), Gaps = 10/353 (2%)

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            +VAK SGA + A+ +G V  VD+ RIV++    +     SGVD+Y L+K+QR+NQNTC N
Sbjct: 2    IVAKDSGAILFAEDSGRVIFVDSNRIVLQRD--NFAEGESGVDVYELVKYQRTNQNTCCN 59

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            QR LVK GD V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++D
Sbjct: 60   QRALVKEGDIVKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQD 119

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
            +FTS+HIE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGK
Sbjct: 120  IFTSVHIESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGK 179

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS 
Sbjct: 180  ITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCSRSK 239

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSS 1010
             +   +  L+ RD+  E   +  +   ++ ++L G              +   K   ++S
Sbjct: 240  EIIESETTLIRRDERIEIKAIQTSSILKIADMLKGAKTTDKLVSEDGSSELLGKGAEVTS 299

Query: 1011 DLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            ++++  P        ++   ++  +           + +  +  + I K+  G
Sbjct: 300  EVLASIPFELIGYLPLE-ASLEERLSEYFADIRNRINRVRQKATDDIAKLHRG 351


>gi|154362179|gb|ABS80928.1| RNA polymerase beta subunit [Cupriavidus taiwanensis]
          Length = 236

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 137/234 (58%), Positives = 175/234 (74%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV D K+T++V YLSA+EE    +AQAN+++D DG+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVVDSKLTDEVDYLSAIEEGKYVVAQANATVDADGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            T+ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LTDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+RIVIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMRIVIRVNDDE 234


>gi|192337668|gb|ACF04254.1| RpoB [Vibrio parahaemolyticus]
 gi|192337670|gb|ACF04255.1| RpoB [Vibrio parahaemolyticus]
 gi|192337694|gb|ACF04267.1| RpoB [Vibrio parahaemolyticus]
 gi|192337696|gb|ACF04268.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 207/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T+ RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTYKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|192337666|gb|ACF04253.1| RpoB [Vibrio parahaemolyticus]
 gi|192337674|gb|ACF04257.1| RpoB [Vibrio parahaemolyticus]
 gi|192337676|gb|ACF04258.1| RpoB [Vibrio parahaemolyticus]
 gi|192337678|gb|ACF04259.1| RpoB [Vibrio parahaemolyticus]
 gi|192337698|gb|ACF04269.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T  RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTRKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|3133407|gb|AAC38504.1| RNA polymerase beta-subunit [Mycobacterium fortuitum]
          Length = 234

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 133/231 (57%), Positives = 177/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVH +HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG +T+
Sbjct: 61  RAGLEVRDVHSSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVITD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
            + YL+A EE+   +AQANS +D++G FTE+ V  R   GE   V   ++D++D SP+Q+
Sbjct: 121 QIDYLTADEEDRHVVAQANSPIDDNGRFTEDRVLVRRKGGEVEFVSATEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|154362163|gb|ABS80920.1| RNA polymerase beta subunit [Cupriavidus oxalaticus]
          Length = 236

 Score =  233 bits (593), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 135/234 (57%), Positives = 174/234 (74%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D DG+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDADGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            T+ELV  R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LTDELVSAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+RIVIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMRIVIRVNDDE 234


>gi|145342317|gb|ABP64855.1| RpoB [Paenibacillus sp. FSL_H7-738]
 gi|145342335|gb|ABP64864.1| RpoB [Paenibacillus sp. FSL_H7-703]
 gi|145342391|gb|ABP64892.1| RpoB [Paenibacillus sp. FSL_H8-168]
 gi|161331519|gb|ABX60677.1| RpoB [Paenibacillus sp. FSL_h8551]
          Length = 232

 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 84/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHLGMAAMRLGIHVATPVFDGAKEYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TG+ F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGDRFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|123979418|gb|ABM81534.1| RNA polymerase II second largest subunit [Buellia fimbriata]
          Length = 704

 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 115/824 (13%), Positives = 227/824 (27%), Gaps = 146/824 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    ++ + +    +    +         + A  + + +     +
Sbjct: 2    KRLDLAGPLLAGLFRTLFNKLNKDVEKYLKSCIENNKEFNLAIGVKANTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L+    V+     +    +      +   +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLSLMCYVSVGSPSDGIIDFLLQRQMESLEEYDPLTSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  + +     V        I      + D  D   K +      L P F+
Sbjct: 178  IFVNGVWVGIHRNPAHLVSAVQSLRRRHIIAHEVSLVRDIRDREFKILTDQGRVLRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAI 741
              +D      G  +  +      A+   V   M+    K            GIVE +DA 
Sbjct: 238  VENDVKSPNCGNLVLNKEHIDALAKGGDVPLDMDKDERKEMIYGWDNLIEEGIVEYIDAE 297

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +                    R  Q               V+ +        T 
Sbjct: 298  EEETVMISMSPSDLQI----------SRQYQAGYALPEADDDPNARVKASTNTKAHTWTH 347

Query: 802  LG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
                 ++   +  + +P+  +N          M  + +   + +  ++            
Sbjct: 348  CEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRMET------- 398

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  + AI    
Sbjct: 399  --------------------MAHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 438

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +      + L  
Sbjct: 439  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKR---IGLTTLETFEKPMRSNTMKLKH 494

Query: 981  NIYSRLME----ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
              Y +L +    I+ G           K+  +++D       ++  +       ++    
Sbjct: 495  GTYEKLDDGDGIIIPGARVSGEDIVIGKTAPIAADAEELGQGTKIREKRDASTPLRSTES 554

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             L  Q                             LR VKV +   +  Q GDK A RHG 
Sbjct: 555  GLVDQVLL--------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQ 594

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +  
Sbjct: 595  KGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATP 654

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
                    +S L    E    +                                      
Sbjct: 655  FTEVTVDSVSRLLR--EHGYQSRGFEVM-------------------------------- 680

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                          +G +    G         V +G  Y  +L 
Sbjct: 681  -------------YNGHT----GR---KLVAQVFLGPTYYQRLR 704


>gi|3133491|gb|AAC38546.1| RNA polymerase beta-subunit [Mycobacterium avium subsp. avium ATCC
           25291]
          Length = 234

 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 133/231 (57%), Positives = 174/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +D  G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDGKGRFAEARVLVRRKAGEVEYVPSSEVDYMDXSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NM RQAVPL+++ AP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMXRQAVPLVRSXAPLVGTGMELRAAID 231


>gi|290990263|ref|XP_002677756.1| predicted protein [Naegleria gruberi]
 gi|284091365|gb|EFC45012.1| predicted protein [Naegleria gruberi]
          Length = 1120

 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 74/340 (21%), Positives = 128/340 (37%), Gaps = 65/340 (19%)

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
            +    Y+ S    +      ++++    +   G   + K  +   R  + GDK + RHG 
Sbjct: 832  AAANTYKPSPIFYKGPCSVYVDQVLITPNYDRGGYAL-KYLLRQTRRPELGDKFSSRHGQ 890

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG+               G  VD                                 + + 
Sbjct: 891  KGVC--------------GLIVD--------------------------------QQDMP 904

Query: 1157 NDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADE 1216
             + +            + ++       +++      ++       +G       F G   
Sbjct: 905  FNEQGICP--------DMIMNPHGFPSRMTVGKMIELICGKSGVLNGKQGYGTAFGGDKV 956

Query: 1217 EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYS 1276
            E I   L       SG+ +L  G+TGE     +  G ++  +L HMV DK++ARS G   
Sbjct: 957  EDIGKGLIRHGFSYSGKDLLTSGITGETMSCYIYFGPVFYQRLKHMVLDKMHARSKGPVR 1016

Query: 1277 LVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRV---- 1328
            ++T+QPL G+S  GG RLGEME  C+  YGA+ +L E L + SD     V     +    
Sbjct: 1017 ILTRQPLEGRSKEGGLRLGEMERDCLIGYGASALLLERLMLSSDEYKVHVCEDCGMIGYM 1076

Query: 1329 -YESIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENS 1366
             Y +      +      P +F +L++E+QA+ +S  L+ S
Sbjct: 1077 GYCNFCKSKQNISLLPMPYAFKLLIQELQAMNISPKLKLS 1116



 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 114/943 (12%), Positives = 268/943 (28%), Gaps = 198/943 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L      S+++F+ ++          ++   ++   IT        +++       P+  
Sbjct: 6   LFRQHIDSFNYFINVD----------IKKIVQANSMITPDTDDKFYIKYNDIYIAKPRLD 55

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  RDLTY+  + +++        +  G +++  IK + + +G +P+M
Sbjct: 56  EGTDTIELTPQLCRLRDLTYSADIIVSVEY-----PQIVGNETL--IKHEDLSIGRMPIM 108

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRAS 173
                                      G F++KG++++ + Q   S   +  D DK +  
Sbjct: 109 LQCDRCVLCGKDDKELAKLGECPLDPGGYFIVKGVEKVCLIQEQLSKNRVIIDLDKEKQI 168

Query: 174 L---SGKLLY----ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE 226
               +G   Y       II  +        D            + +P+     A+G++S+
Sbjct: 169 TASVTGSTHYRKSKTNIIIKHE----RFYLDHNSF-------TKDIPIIMLFKAMGIESD 217

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           + +                   + +    + A   S    I  G    E   +  S  LK
Sbjct: 218 QEI----------------VQLIGSDRKYIDALGPSFEECIREGVYTSEQAIEYMSRYLK 261

Query: 287 SLKEKGVK-FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
               +  K  +  T + L  + +    V     ++ I    ++ ++ ++ +  S   D  
Sbjct: 262 LADFRKNKPKMEETREILSNIILCHIPVYKFNYKMKIVYLAIMVKRMIDALHDSANIDDK 321

Query: 346 ILYVDS--VNNNAYIRNTLVTDKNKDRKDALLDIYRVM-----RPGDVSTFSVAESMFNF 398
             Y +         +         K   +    + +       R     T  ++      
Sbjct: 322 DYYGNKRLEMAGQLLSLLFEDLFKKFNDEIKKTLEKKTGRRSRRATSTPTEDISSIFNAN 381

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL---RNGKGTIDD 455
               ++    S         R  ++       + +   IA + ++  +         +  
Sbjct: 382 SSKITEGLKNSISSGNWNVQRFKMERAGVTHVLSRLSFIAALGMMTRISSQFEKTRKVSG 441

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
              L   +   +      +     L    ++   +++ D +  + +   N       +  
Sbjct: 442 PRALQPSQWGLLCPSDTPEGEGCGLVKNLALLTHVTTDDEEEPIIRLAYNIGVEDINLIS 501

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA-RAGVEMRDVHPTHYGRICPAET 574
               +  S     +N L    H           + R      E   +      +     +
Sbjct: 502 GEELNHPSSYVVFLNGLILGIHRFPSQFTKLFRMMRRAGKIHEFVSIFKNDLHKAIYIAS 561

Query: 575 SEGHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN 631
             G        V +            +    R   D      + YL   EE N  I    
Sbjct: 562 DGGRVCRPLIIVENQKLKVTQKHLSELAEGIRTWDDFLKEGLIEYLDVNEENNSNIVFRE 621

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +                         +    +  P  ++ + A L+P+  ++ S R  
Sbjct: 622 EDIKL-----------------------ETTHFEIEPFTILGVCAGLVPYPHHNQSPRNT 658

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             C M +QA+                                           I   + +
Sbjct: 659 YQCAMGKQAMG-----------------------------------------AIAYNQFN 677

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
              +   + +Y               Q+P+VK                     L+ G+N 
Sbjct: 678 RLDTLLLLMVYP--------------QKPMVK----------TKTIELIQFEKLSGGQNA 713

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP----- 866
            +A M + GY+ ED++++++  +       I+++++    +    G E++ +  P     
Sbjct: 714 SIAVMSYSGYDIEDAVVVNKASIDRGYGRCIYLKKYVTELKRYHNGVEDVLQPPPNAQQA 773

Query: 867 ----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                   +  + +D  G+  VG  + P D+ + +   +    
Sbjct: 774 KDMDQKRLKSYQRLDFDGMCAVGERIYPNDMYINRFVAQNTQD 816


>gi|86161678|gb|ABC86974.1| RNA polymerase beta subunit [Bartonella bovis]
          Length = 244

 Score =  233 bits (593), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 163/240 (67%), Positives = 192/240 (80%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 2   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE
Sbjct: 62  NSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 121

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
            V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL
Sbjct: 122 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 181

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           ++AEAPFVGTGMES+VA+ SGAAI AKR+GIV+QVDA RIVIR+ E      +     YR
Sbjct: 182 IRAEAPFVGTGMESIVARDSGAAIGAKRSGIVDQVDATRIVIRATEDLDPSKSGVEYSYR 241


>gi|192337640|gb|ACF04240.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+ ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRIYALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGLNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|229893874|gb|ACQ90287.1| RNA polymerase B-subunit [Staphylococcus xylosus]
          Length = 257

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 148/257 (57%), Positives = 188/257 (73%), Gaps = 3/257 (1%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRK
Sbjct: 1   GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 60

Query: 605 V--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           V      +T  + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D
Sbjct: 61  VDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTVMAKEKMD 120

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME V A+ 
Sbjct: 121 YMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEHVAARD 180

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
           SGAAIVAKR G +E V++  I++R  +E D       +D Y L KF+RSN  TC NQRP+
Sbjct: 181 SGAAIVAKRKGRIEHVESNEILVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTCYNQRPI 240

Query: 782 VKVGDEVRRNDIIADGP 798
           V  GD V R +I+ADGP
Sbjct: 241 VSPGDVVTRGEILADGP 257


>gi|229893870|gb|ACQ90285.1| RNA polymerase B-subunit [Staphylococcus sp. 210]
 gi|229893872|gb|ACQ90286.1| RNA polymerase B-subunit [Staphylococcus sp. 219]
          Length = 257

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 150/257 (58%), Positives = 190/257 (73%), Gaps = 3/257 (1%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRK
Sbjct: 1   GPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 60

Query: 605 V--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           V      +T+ + YL+A EE++  +AQANS LDEDG FT++ V CR  G   ++ +EK+D
Sbjct: 61  VDLETNSITDQIDYLTADEEDSYVVAQANSKLDEDGKFTDDEVVCRFRGNNTVMAKEKMD 120

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME V A+ 
Sbjct: 121 YMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEHVAARD 180

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
           SGAAIVAKR G VE V++  I++R  +E D       +D Y L KF+RSN  TC NQRP+
Sbjct: 181 SGAAIVAKRKGRVEHVESNEILVRQLIEEDGQEYEGELDRYPLAKFKRSNTGTCYNQRPI 240

Query: 782 VKVGDEVRRNDIIADGP 798
           V  GD V + +I+ADGP
Sbjct: 241 VASGDVVTKGEILADGP 257


>gi|153958293|gb|ABS53436.1| RpoB [Bacteriovorax sp. AQ]
          Length = 343

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 163/344 (47%), Positives = 225/344 (65%), Gaps = 10/344 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRDK--FDEGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   L+ ++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIAEMLKGAKTTDRLVSEDGSSELLPKGAELTGEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                 ++   ++  +           + +  +  ++I K   GD
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGD 343


>gi|89274920|gb|ABD65901.1| RNA polymerase II second largest subunit [Piriformospora indica]
          Length = 654

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 112/723 (15%), Positives = 219/723 (30%), Gaps = 95/723 (13%)

Query: 459  LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK--PVVSAVCEF 516
             G +R+   G +L   +R+   ++ + +   +                K   + + +   
Sbjct: 1    FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYS 60

Query: 517  FCSSQL-------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              +                SQ+       S ++H RR +      + R     + R +H 
Sbjct: 61   LATGNWGDQQNAMSSKAGXSQVLNRYTYASTLSHLRRTNT----PLGREGKIAKPRQLHN 116

Query: 564  THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
            TH+G +CPAET EG   GLV +L+  A ++   +       + +  +        A+EE 
Sbjct: 117  THWGMVCPAETPEGQACGLVKNLSLMACISVGSYSAPVGEFLDEWGME-------ALEEN 169

Query: 624  NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
                AQ++    +       +   R   + +   +         P+  V           
Sbjct: 170  ----AQSDRPSTKVFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRI 225

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
              DS RV     +  +   L+  E        +   A      +       +   +    
Sbjct: 226  YTDSGRVCRPLFVVEKDKLLITPEQVARLRDEKDDPAGYRWDNLFKDGVVELLDAEEEET 285

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+  +  +   + S   +Y        +       + ++K G            PS  LG
Sbjct: 286  VMICMSPEDLDARSSGQVYHTEDMYDPSSRV----KTIIKAGSYSH----CEIHPSMILG 337

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                   +  + +P+  +N          M  + +  S+       + R   +       
Sbjct: 338  -------VCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNF----LVRMDTMANILYYP 386

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
              P  +   L+ +                             +   +  + AI      +
Sbjct: 387  QKPLATTRALEWL-------------------------KFRDLPAGQNAIVAILCYSGYN 421

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +   +    I+ R  +D  + +  +  E+ E  +RD        + +  
Sbjct: 422  QEDSVIMNQSSIDRGLF-RSIYYRSYMDMEKTAGQITLEEFEKPSRDTTLRMKHGNYDKL 480

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
                 I  G N +       K+  L  D      R+           ++     +     
Sbjct: 481  DDDGLIAPGMNVIGEDIIIGKTAPLPPDSQELGQRTDRHTRRDVSTPLKSTESGIIDHVL 540

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             +                          + VK+ V   R  Q GDK A RHG KG +  +
Sbjct: 541  ITV--------------------DGEGSKFVKIRVRSTRIPQVGDKFASRHGQKGTIGIL 580

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  DG   D+++NP  +PSRM +G + E  L       G++  +         
Sbjct: 581  YRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVE 640

Query: 1164 DIS 1166
             +S
Sbjct: 641  QVS 643


>gi|192337644|gb|ACF04242.1| RpoB [Vibrio parahaemolyticus]
 gi|192337654|gb|ACF04247.1| RpoB [Vibrio parahaemolyticus]
 gi|192337660|gb|ACF04250.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+ ALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRIFALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGLNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|46411494|gb|AAS94317.1| RNA polymerase II [Flavoparmelia caperata]
          Length = 705

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 119/786 (15%), Positives = 235/786 (29%), Gaps = 108/786 (13%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVVS 511
            DD D+ G +R+   G ++   +RL   ++ + I + +               + +  + +
Sbjct: 1    DDRDHFGKKRLDLAGPLMATLFRLLFQKLTKDIYKYLQKCVEGNREFNLTLGVKSNVLTN 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61   GLRYSLATGNWGDQKKAASAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L    +  V         +    + +       
Sbjct: 117  RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSDPIVEFMLARNMEYLEGYEP 176

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
              + +    ++      +  + S     V        +      I D  D   K      
Sbjct: 177  TRSPDATKVFVNGVWVGVHHNPSALVTSVQDLRRSSVLSHEISLIRDIRDREFKIFTDAG 236

Query: 676  ASLIP-FLENDDSNRVLMGCNMQRQAV--PLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
                P F+ ++D++    G  +  + +   L   + P V   + S         +++   
Sbjct: 237  RVCRPLFVIDNDNHSANKGNLVLTKEMINRLEDDKDPDVDEKVRSKNFFGWDGLVMSGAV 296

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
              ++  +   ++I     DL+ S      Y + +          N R   ++G       
Sbjct: 297  EFLDAEEEETVMIVMTPEDLEISRQVQAGYHVEEASAEP-----NARVKARIGAGQHTWT 351

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N                        ++    
Sbjct: 352  HCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMG 386

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G           +           +  +             +       +   +  
Sbjct: 387  KQAMGXXXXXXXXXMAT-----------MANILYYPQKPLATTRSMEFLKFRELPAGQNA 435

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   +   
Sbjct: 436  IVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMR 491

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y +L +   +  G           K+  ++ D      R++         
Sbjct: 492  SDTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTST 551

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
             ++     +  Q   S                         LR VKV +   +  Q GDK
Sbjct: 552  PLRSTENGIVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDK 591

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G
Sbjct: 592  FASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRG 651

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
             +  +          +S L                           V     +G  + T 
Sbjct: 652  FEGDATPFTEVTVDSVSRLLR---------------EHGYQSRGFEVMYNGHTGRKLVTQ 696

Query: 1210 VFDGAD 1215
            VF G  
Sbjct: 697  VFLGPT 702



 Score = 98.6 bits (244), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 81/588 (13%), Positives = 171/588 (29%), Gaps = 80/588 (13%)

Query: 375 LDIYRVMRPGDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            DIY+ ++        F++   + + +  +  +Y L   G      +         + + 
Sbjct: 31  KDIYKYLQKCVEGNREFNLTLGVKSNVLTNGLRYSL-ATGNWGDQKKAASAKAGVSQVLN 89

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R+GK       +  +  +    E  + Q    +  +     
Sbjct: 90  RYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 149

Query: 488 ERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             + +     V      N + +          A   F     +         ++ +   R
Sbjct: 150 ITVGTPSDPIVEFMLARNMEYLEGYEPTRSPDATKVFVNGVWVGVHHNPSALVTSVQDLR 209

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R S L             +RD+    +     A         + +   S  + N     E
Sbjct: 210 RSSVLS-------HEISLIRDIRDREFKIFTDAGRVCRPLFVIDNDNHSANKGNLVLTKE 262

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-VPR 658
                                          N   D+     +E V  +        V  
Sbjct: 263 -----------------------------MINRLEDDKDPDVDEKVRSKNFFGWDGLVMS 293

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-S 717
             ++F+DA  ++ V I  +      +        G +++  +          +G G    
Sbjct: 294 GAVEFLDAEEEETVMIVMTPEDLEISRQVQ---AGYHVEEASAEPNARVKARIGAGQHTW 350

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CV 776
              +   + I+   A I+   D  +    + +  +     G           +  N    
Sbjct: 351 THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXMATMANILYY 410

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA   + GYN EDS+++++  +  
Sbjct: 411 PQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDR 460

Query: 837 DVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E     +  D   +       +D+ G++  G  V+  
Sbjct: 461 GLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRVSGE 520

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 521 DIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 561


>gi|3133483|gb|AAC38542.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 133/231 (57%), Positives = 175/231 (75%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQ SQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQXSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RA +E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAVLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS +DE G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPIDESGRFAEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|145342279|gb|ABP64836.1| RpoB [Paenibacillus sp. FSL_H8-025]
          Length = 232

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHVATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G++I
Sbjct: 191  ----------------------------------VFD---------AMEEAGMQRNGKTI 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+N GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIVVDVKVFTRENGD 90


>gi|145342267|gb|ABP64830.1| RpoB [Paenibacillus sp. FSL_H7-443]
 gi|145342269|gb|ABP64831.1| RpoB [Paenibacillus sp. FSL_H8-094]
 gi|145342271|gb|ABP64832.1| RpoB [Paenibacillus sp. FSL_H7-792]
 gi|145342273|gb|ABP64833.1| RpoB [Paenibacillus sp. FSL_H8-228]
 gi|145342275|gb|ABP64834.1| RpoB [Paenibacillus sp. FSL_H8-260]
 gi|145342277|gb|ABP64835.1| RpoB [Paenibacillus sp. FSL_H8-150]
 gi|145342281|gb|ABP64837.1| RpoB [Paenibacillus sp. FSL_H8-147]
 gi|145342287|gb|ABP64840.1| RpoB [Paenibacillus sp. FSL_H8-336]
 gi|145342331|gb|ABP64862.1| RpoB [Paenibacillus sp. FSL_H8-314]
 gi|145342339|gb|ABP64866.1| RpoB [Paenibacillus sp. FSL_H7-737]
 gi|145342341|gb|ABP64867.1| RpoB [Paenibacillus sp. FSL_H8-107]
 gi|145342345|gb|ABP64869.1| RpoB [Paenibacillus sp. FSL_H7-714]
 gi|145342377|gb|ABP64885.1| RpoB [Paenibacillus sp. FSL_H8-282]
 gi|145342395|gb|ABP64894.1| RpoB [Paenibacillus sp. FSL_H8-175]
 gi|145342401|gb|ABP64897.1| RpoB [Paenibacillus sp. FSL_H8-261]
 gi|145342411|gb|ABP64902.1| RpoB [Paenibacillus sp. FSL_H8-321]
 gi|145342413|gb|ABP64903.1| RpoB [Paenibacillus sp. FSL_H7-937]
 gi|146217885|gb|ABQ11022.1| RNA polymerase beta subunit [Paenibacillus sp. FSL_H3-444]
          Length = 232

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|153958208|gb|ABS53394.1| RpoB [Bacteriovorax sp. GSL2]
          Length = 344

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 163/345 (47%), Positives = 226/345 (65%), Gaps = 10/345 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRDK--FDEGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   L+ ++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIAEMLKGAKTTDRLVSEDGSSELLPKGAELTGEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                 ++   ++  +           + +  +  ++I K   GD+
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRGDE 344


>gi|153958261|gb|ABS53420.1| RpoB [Bacteriovorax sp. T4]
          Length = 343

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 162/346 (46%), Positives = 230/346 (66%), Gaps = 10/346 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                 ++   ++  +           S +  +  ++I K+  GD++
Sbjct: 299  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRGDEL 343


>gi|192337624|gb|ACF04232.1| RpoB [Vibrio parahaemolyticus]
 gi|192337626|gb|ACF04233.1| RpoB [Vibrio parahaemolyticus]
 gi|192337628|gb|ACF04234.1| RpoB [Vibrio parahaemolyticus]
 gi|192337630|gb|ACF04235.1| RpoB [Vibrio parahaemolyticus]
 gi|192337632|gb|ACF04236.1| RpoB [Vibrio parahaemolyticus]
 gi|192337634|gb|ACF04237.1| RpoB [Vibrio parahaemolyticus]
 gi|192337636|gb|ACF04238.1| RpoB [Vibrio parahaemolyticus]
 gi|192337642|gb|ACF04241.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLS   +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSLFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGLNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|86559355|gb|ABD04085.1| RNA polymerase II second largest subunit [Clavulina sp. MB03-034]
          Length = 657

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 118/795 (14%), Positives = 222/795 (27%), Gaps = 161/795 (20%)

Query: 475  YRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R+   ++ + +   +               +    + + +     +             
Sbjct: 1    FRMVFKKLTKDVYRHLQKCVETRKEFSIGAAVKPTTISNGLKYSLATGNWGDQKKFMSAK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKPRQLHNTHWGMVCPAETPEGQA 116

Query: 580  IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
             GLV +L+  A ++  G I  P  +         +   SA +         N        
Sbjct: 117  CGLVKNLSLMACIS-VGSISAPVIEFLQEWGLESLE-ESASDHGTATKVFVNGVWIGVHR 174

Query: 640  FTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                LV              ++    D  +   +          P    ++   +L   +
Sbjct: 175  DAPSLVRTLRRLRRRDDISSEVSIVRDIRERELRIYTDAGRVCRPLFIVENQQLLLKKEH 234

Query: 696  M----QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
            +     ++++             +E + A+     ++      +E   A   V       
Sbjct: 235  IRRLNDKESMEPYTWSDLRKEGVIELLDAEEEETVMICMTPDDLEDSRANEAV------G 288

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
                    D     + Q + Q+                        PS  LG       +
Sbjct: 289  HVSGAGASDHDVAARIQSTMQS---------------HAWTHCEIHPSMILG-------I 326

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N       S R   +       +  +    +                   
Sbjct: 327  CASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVRM---------------- 364

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                     +  +             +T      +   +    AI      +  D+ +  
Sbjct: 365  -------DTMANILYYPQKPLATTRSMTYLRFRELPAGQNATVAILCYSGYNQEDSVIMN 417

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
             S +   +    ++ R   D  ++   +  E+ E   RD                  I  
Sbjct: 418  QSSIDRGLF-RSMYYRSYADAEKKVGMLPLEEFERPTRDNTLRLKHGSYEKLDDDGLIAP 476

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G   V       K+  L  D                +E  QR     +    T     E+
Sbjct: 477  GTGVVGEDIIIGKTAPLPPD---------------SEELGQRLRTHTRRDVSTPLKSTEN 521

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++     GD +     + VK+ +   R  Q GDK A RHG KG V      EDMPF
Sbjct: 522  GIVDQVVVTTNGDGL-----KFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPF 576

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   D+++NP  +PSRM +G + E  L       G++                    
Sbjct: 577  TAEGITPDLIINPHAIPSRMTIGHLIECLLSKLATLTGREGD------------------ 618

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     E+++ +LR       
Sbjct: 619  -----------------------------------ATP-FTELTVESVSQLLRQYGYQSR 642

Query: 1232 GQSILYDGLTGEPFD 1246
            G  ++Y G TG+   
Sbjct: 643  GLEVMYHGHTGKKLQ 657


>gi|153958267|gb|ABS53423.1| RpoB [Bacteriovorax sp. OC9]
          Length = 345

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 162/348 (46%), Positives = 231/348 (66%), Gaps = 10/348 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +   +   +GVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKGNGRVIFVDSNRIVIQRDK--FEEGETGVDIYELVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T +GDLALG+N+LVAFMPW GYN+EDS+L+SE ++S D+FTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHMGDLALGQNVLVAFMPWGGYNYEDSILLSEDLLSRDIFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K + ++S+++++ P   
Sbjct: 239  RRDERIEIKAIQTSAILKIAEMLNGAKTTDKLVSEDGSTELLAKGSDVTSEVLAKIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
                 ++   ++  +           S +  +  ++I K   GD++PP
Sbjct: 299  IGYLPLE-AALEERLGEYFADVRNRISRVRQKATDEIAKQHRGDELPP 345


>gi|192337638|gb|ACF04239.1| RpoB [Vibrio parahaemolyticus]
 gi|192337646|gb|ACF04243.1| RpoB [Vibrio parahaemolyticus]
 gi|192337648|gb|ACF04244.1| RpoB [Vibrio parahaemolyticus]
 gi|192337650|gb|ACF04245.1| RpoB [Vibrio parahaemolyticus]
 gi|192337652|gb|ACF04246.1| RpoB [Vibrio parahaemolyticus]
 gi|192337656|gb|ACF04248.1| RpoB [Vibrio parahaemolyticus]
 gi|192337658|gb|ACF04249.1| RpoB [Vibrio parahaemolyticus]
 gi|192337662|gb|ACF04251.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D++MPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAIMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH R +SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRHISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGLNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|80973605|gb|ABB53540.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 226

 Score =  232 bits (592), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 95/294 (32%), Positives = 133/294 (45%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEGLKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM+K
Sbjct: 189  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 56/86 (65%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EEGLK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEGLKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|161331503|gb|ABX60669.1| RpoB [Paenibacillus sp. FSL_h8537]
          Length = 232

 Score =  232 bits (591), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 84/204 (41%), Positives = 111/204 (54%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+ ++A KR I  GDKMAGRHGNKG+++RI+P EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRAYIAQKRKISEGDKMAGRHGNKGVIARIMPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV++VLNPLGVPSRMN+GQ  E HLG AC  LG    + + D     D           
Sbjct: 142  TPVEVVLNPLGVPSRMNIGQALEVHLGLACKRLGLHAATPVFDGAREND----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------AMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG +YM+KL
Sbjct: 208  LYDGRTGENFEREVTVGVMYMIKL 231



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE LKN+DE GII VGAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALKNLDERGIIRVGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|154362183|gb|ABS80930.1| RNA polymerase beta subunit [Cupriavidus gilardii]
          Length = 236

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 135/234 (57%), Positives = 173/234 (73%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV +GK+T+ V YLSA+EE    +AQAN+++D +G+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVENGKLTDQVDYLSAIEEGKYVVAQANATVDAEGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA RIVIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQATRGGVVDYVDANRIVIRVNDDE 234


>gi|145342355|gb|ABP64874.1| RpoB [Paenibacillus sp. FSL_H7-756]
 gi|145342373|gb|ABP64883.1| RpoB [Paenibacillus sp. FSL_H8-048]
 gi|145342387|gb|ABP64890.1| RpoB [Paenibacillus sp. FSL_H8-122]
 gi|145342389|gb|ABP64891.1| RpoB [Paenibacillus borealis]
 gi|145342399|gb|ABP64896.1| RpoB [Paenibacillus borealis]
 gi|146217881|gb|ABQ11020.1| RNA polymerase beta subunit [Paenibacillus sp. FSL_H3-333]
 gi|146217883|gb|ABQ11021.1| RNA polymerase beta subunit [Paenibacillus sp. FSL_H3-335]
 gi|146217891|gb|ABQ11025.1| RNA polymerase beta subunit [Paenibacillus sp. FSL_H3-469]
 gi|146217893|gb|ABQ11026.1| RNA polymerase beta subunit [Paenibacillus sp. FSL_H3-478]
          Length = 232

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 84/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHVATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+N GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|312204320|gb|ADQ47477.1| RNA polymerase II second largest subunit [Cryptodiscus pini]
          Length = 708

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 110/798 (13%), Positives = 221/798 (27%), Gaps = 115/798 (14%)

Query: 470  MLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L   +R    R+ + I    +              + +  + + +     +        
Sbjct: 1    LLAQLFRALFNRLTKDIFAYLKKCVETGKEFNLTLGVKSNTLTNGLKYSLATGNWGEQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AAQSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L     V   + G     +    + +V  +   +        ++    +
Sbjct: 117  PEGQACGLVKNLALMCNVTVGSPGDPIVDFMVQRNMEVLEEFEPMRTPNATKIFVNGVWT 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRV 690
             +  D       +      + I V    + D  D   K          P F+ ++D    
Sbjct: 177  GIHRDPVHLVRTIQSLRRRKLIDVETSLVHDIRDREFKIFTDAGRVSRPVFVIDNDERSS 236

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
              G  +  + +     +   +    E       G   +     + E +DA       +  
Sbjct: 237  SKGSLVLNREMIQKLEDDKDLDLEDEDQKRLFFGWNGLLSHGAV-EYLDAEEEETVMIAM 295

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
              +       +    +     +      +P V               PS  LG  A    
Sbjct: 296  TPEDLEISRQVQAGYEIDEGPRELSARIKPKVNPAQHT--WTHCEIHPSMILGICAS--- 350

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
             ++ F   +       +  ++                                       
Sbjct: 351  -IIPFPDHNQVMHMSHLFEAKANXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 409

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                      +                +       +   +  + AI      +  D+ + 
Sbjct: 410  XXXXXXXXXVLYYP----QKPLATTQSMEFLKFRELPAGQNAIVAISCYSGYNQEDSVIM 465

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R  +++ +R        +E   +    + + L    Y +L +  
Sbjct: 466  NQSSIDRGLF-RSLFYRSYVEQEKRVGM---SMVEQFEKPLRSDTLRLKHGTYEKLDDDG 521

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K+  ++ D      R++          ++     +         
Sbjct: 522  IIAPGVRVSGEDIIIGKTAPIAPDDEEMGQRTKLHTKRDASTPLRSTENGI--------- 572

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                     ++K+          L+ VKV +   +  Q GDK A RHG KG +      E
Sbjct: 573  ---------VDKVLV--TTNAEGLKFVKVRMRTTKIPQVGDKFASRHGQKGTIGITYRQE 621

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 622  DMPFTAEGLTPDLIINPHAIPSRMTIAHLVECLLSKVGAIRGAEGD-------------- 667

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 668  ---------------------------------------ATP-FTEVTVDSVSRLLREQG 687

Query: 1228 LDESGQSILYDGLTGEPF 1245
                G  I+Y+G +G   
Sbjct: 688  YQSRGFEIMYNGHSGRKM 705


>gi|154362167|gb|ABS80922.1| RNA polymerase beta subunit [Ralstonia pickettii]
          Length = 236

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 135/234 (57%), Positives = 175/234 (74%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A++N YGF+ETPYRKV +GK+T+ V YLSA+EE    +AQAN++LD+DG+
Sbjct: 61  IGLINSLALYAQLNDYGFLETPYRKVENGKLTDQVDYLSAIEEGKYVVAQANATLDKDGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+A+ P VGTG+E  VA  SG A+ A R G+V+ VDA R+VIR  + +
Sbjct: 181 RQAVPCLRADKPLVGTGVERTVAVDSGTAVQATRGGVVDYVDANRVVIRVNDDE 234


>gi|154362161|gb|ABS80919.1| RNA polymerase beta subunit [Cupriavidus necator]
          Length = 236

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 136/234 (58%), Positives = 174/234 (74%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV D K+T+ V YLSA+EE    +AQAN+++D DG+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVVDSKLTDQVDYLSAIEEGKYVVAQANATVDADGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            T+ELV  R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LTDELVSAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+RIVIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMRIVIRVNDDE 234


>gi|145342303|gb|ABP64848.1| RpoB [Paenibacillus sp. FSL_H7-726]
          Length = 232

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 113/204 (55%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  + + + D     D           
Sbjct: 142  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHVATPVFDGAREYD----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G++I
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTI 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            LYDG TGE F+R VTVG ++M+KL
Sbjct: 208  LYDGRTGERFEREVTVGVMHMIKL 231



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+N GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIVVDVKVFTRENGD 90


>gi|168003353|ref|XP_001754377.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162694479|gb|EDQ80827.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 401

 Score =  232 bits (591), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 85/360 (23%), Positives = 140/360 (38%), Gaps = 59/360 (16%)

Query: 1007 VLSSDLISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            +   D++ +          V+D + +   +   + +    K +L+      I+K+     
Sbjct: 77   IPDGDILRDNDGIVLIGQKVKDGDTIAAKLVITEKKQSIEKIVLKSFVSGWIDKVTK--H 134

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  ++V+V + + R    GDK   RH  KG++  IL  ED+PF KD    D+++NP 
Sbjct: 135  TSAEGNKIVRVRILLYRFPIVGDKFTSRHSQKGVIGAILSQEDLPFTKDEIVPDLIINPH 194

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +G + +  +               N+ +     S  +S     I   +  +  
Sbjct: 195  AIPSRMTMGHLLKMVMCKI-------YVLDSNNARDPMLPSKPKSRESSCIDATAFNKAY 247

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
              +                           E  I  +          +  +Y G TG P 
Sbjct: 248  RSF---------------------------EADIAKL---------SKEKMYCGTTGLPI 271

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V  G  Y   L H   DK ++ S G    +T+QP+ G+S +GG R GEME  C+ A+
Sbjct: 272  EARVATGICYYHALRHQARDKAHSISKGVIQSLTKQPVEGRSRKGGLRFGEMEKDCLIAH 331

Query: 1306 GAAYVLQEMLTIKSD--------D---VVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
            GAA +L E L   SD        D   +            G +T E   P SF +LV+E+
Sbjct: 332  GAASMLLEKLKNTSDLCEVWICHDCSTICSSNPCINC--NGRNTKEHRLPYSFKLLVQEL 389


>gi|154362185|gb|ABS80931.1| RNA polymerase beta subunit [Cupriavidus basilensis]
          Length = 236

 Score =  232 bits (591), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 134/234 (57%), Positives = 172/234 (73%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV D K+T+ V YLSA+EE    +AQAN+++D DG+
Sbjct: 61  IGLINSLALYARLNDYGFLETPYRKVVDSKLTDQVDYLSAIEEGKYVVAQANATVDADGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LVDELVSSREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E   A  SG A+ A R G+V+ VDA+R+VIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTFAVDSGTAVQAMRGGVVDYVDAMRVVIRVNDDE 234


>gi|322511118|gb|ADX06431.1| putative DNA-directed RNA polymerase II [Organic Lake phycodnavirus
            2]
          Length = 1208

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 149/1086 (13%), Positives = 325/1086 (29%), Gaps = 168/1086 (15%)

Query: 344  IPILYVDSVNNNAYIRNTLVTDKNKDRKDALL-DIYRVMRPGDVSTFSVAESMFNFLFFD 402
            I  L  D  + +  I++         R  A+  DI+R     D+    +   +F  +   
Sbjct: 149  IRTLNDDKHDFSIEIKSVSEDHSKPKRTMAIRRDIHRGHLLVDIPNVRLPIPLFIVIRA- 207

Query: 403  SDKYDLSTVGRVKMNMRLNLDTPDDVRHI-----------RKEDIIAIIKI----LVDLR 447
                 L  +    +   +  D  D+ +++                +A +      L    
Sbjct: 208  -----LGIISDKDICKCILSDLDDNEKYLELLRPSINDAGTFYTQLACLNYISVFLKHST 262

Query: 448  NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
              +      + L                      + ++I       D D+   + + +  
Sbjct: 263  VNETHNILTNYLLPHMGEMNYHAKALFLGYMTFELLKTIHGDRPLTDRDNYKFKRVESTG 322

Query: 508  PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
             ++ A+   +       +++ ++++         S      +       E  ++      
Sbjct: 323  TIMKALFTEYA----KIMKQEIHTIVEKEMYYNNSLYLDENLHEQDFNPEKSNILYLVKD 378

Query: 568  RICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
             I   +  E G          ++      G I+   R   +  +T+       ++  ++ 
Sbjct: 379  HIFNEKYIEQGFKKAFKGDWGAYGHTKRLGVIQDLNRLSYNSFLTHLRKINLEVDSSSKM 438

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
            +        + G                       +   A P +++         + + +
Sbjct: 439  VGPHLLHGSQYGYLDPVDTPDGANVGLHKHMAIMCNITRAIPNEIIYDFIKNNFDILSLE 498

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
             +  L   N  R  +  L                      I  +R GI+    +I   I+
Sbjct: 499  RSSFLQIHNHFRLFINGLWVGIVI------QDPIHFKQQFIDFRRRGIIPNTISIC--IQ 550

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL-----VKVGDEVRRND----IIADG 797
              +  +   +    + R + +   NQ    ++ P+     VK  ++V   D         
Sbjct: 551  MNDKYIFIYSDEGRLIRPLIYYEDNQVVIYDKEPIKWSNLVKTKNKVYEIDDQSKERVYL 610

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
               D  ++ +    +     + GY     + I   ++   +   I   E          G
Sbjct: 611  EYMDSSEIEMCYVSMEYKETYKGY---THLEIHPSLMFGIMGNQIIFPE-NNQLPRNLFG 666

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  + +       +  ID+ GI+          +         E      E ++ AI 
Sbjct: 667  CGQAKQAVSLYHSNFINRIDKMGIVL--NYGQKPIVRTQYFNYIHEEQHPYGENVIVAIM 724

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
               + +V D  L   S V   +     +N +             ++I +  +++     +
Sbjct: 725  CHTSYNVEDAILINESSVKRGLFKTTYYNMYETM----------DEITIAGKNEKRIDRV 774

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            L+  + +R  +     N +       ++T++    +     +           + +    
Sbjct: 775  LNHEL-TRDTKPGYNYNKLDENGLIFENTIMDDKTVVIGKVNIINNEVFDSSVLPK---- 829

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                 +     ++  F    +             ++ KV +   R    GDK   R G K
Sbjct: 830  -----KGQLGYVDKTFIYNKD-----------GRKLAKVRIREDRSPAIGDKFCSRCGQK 873

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +  ++P E+MPF K+G   DI++NP  +PSRM +GQ+ ET L   C   G    S   
Sbjct: 874  GTIGNLIPEENMPFTKNGLKPDIIINPHALPSRMTIGQLIETLLAKLCCANGMSANSTAF 933

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
              K     +  +   +    +  +    +    + +                        
Sbjct: 934  LNKGPKHENIGKHLNDLGYQSEGNEILYNGLTGEQIT----------------------- 970

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                                           + +G  Y ++L HMV DK+  R+TG   L
Sbjct: 971  -----------------------------SEIFMGPTYYMRLKHMVKDKINYRATGQRDL 1001

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV-------GRTRVYE 1330
            +T+Q   G++N GG R+GEME   + ++G +  L++ +  + DD         G   +Y 
Sbjct: 1002 MTRQTNHGRANDGGLRIGEMERDGVISHGMSAFLKDSMMKRGDDYKMAICNQSGTISIYN 1061

Query: 1331 S---------------------------IVA-GNDTFETGTPESFNVLVKEMQALGLSID 1362
                                        I   G +      P SF +L++E+  + + + 
Sbjct: 1062 KDKKHFYSLLSDGPIEYDMTEQNMNPYLITKYGKEFSVVNIPYSFKLLMQELTTMNVQMR 1121

Query: 1363 LENSRT 1368
            +  S  
Sbjct: 1122 IITSDN 1127



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 93/675 (13%), Positives = 195/675 (28%), Gaps = 97/675 (14%)

Query: 88  VDDCLWRDLTYAVPLK--ITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD---- 141
            ++C  +++TYA  +   + +   VF   + T  K+  +  E    +G  P+M K     
Sbjct: 48  PNECRLKNITYATTIYYKVDVE-YVFLTRKSTIRKTYPE--ENFYCLGSFPIMLKSKLCL 104

Query: 142 --------------------GTFVIKGIQRIVVSQLHRSPGIHF--------------DH 167
                               G F+I G +++++ Q      I +                
Sbjct: 105 LNKLNKDVCYQLGECRHDYGGYFIIDGKEKVIIPQEKFGDNIIYIRTLNDDKHDFSIEIK 164

Query: 168 DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE 227
                    K   A R    +G  +       DI +VR+     +P+   + ALG+ S++
Sbjct: 165 SVSEDHSKPKRTMAIRRDIHRGHLLV------DIPNVRLP----IPLFIVIRALGIISDK 214

Query: 228 -----ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI-ESGKKLT 281
                ILS       Y    +     ++ A          + + +      + E+   LT
Sbjct: 215 DICKCILSDLDDNEKY---LELLRPSINDAGTFYTQLACLNYISVFLKHSTVNETHNILT 271

Query: 282 SGLLKSLKE--KGVKFL---GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL--- 333
           + LL  + E     K L    +T + L  ++    + + +  +           K+L   
Sbjct: 272 NYLLPHMGEMNYHAKALFLGYMTFELLKTIHGDRPLTDRDNYKFKRVESTGTIMKALFTE 331

Query: 334 -EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
             +I   EI  I    +   N+     N    D N ++ + L  +   +           
Sbjct: 332 YAKIMKQEIHTIVEKEMYYNNSLYLDENLHEQDFNPEKSNILYLVKDHIFNEKYIEQGFK 391

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
           ++             L  +  +      +  T     ++  +    ++   +   +  G 
Sbjct: 392 KAFKGDWGAYGHTKRLGVIQDLNRLSYNSFLTHLRKINLEVDSSSKMVGPHLLHGSQYGY 451

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +D +D      V     M        + R   +        +   ++  +  +   + + 
Sbjct: 452 LDPVDTPDGANVGLHKHMAIMC---NITRAIPNEIIYDFIKNNFDILSLERSSFLQIHNH 508

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
              F     +  + +      +     R   +    ++      +      +  GR+   
Sbjct: 509 FRLFINGLWVGIVIQDPIHFKQQFIDFRRRGIIPNTISICIQMNDKYIFIYSDEGRLIRP 568

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                 N  ++         N        Y      K    + Y+ + E E  Y      
Sbjct: 569 LIYYEDNQVVIYDKEPIKWSNLVKTKNKVYEIDDQSKERVYLEYMDSSEIEMCY------ 622

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                       V                  ++  P  +  I  + I F EN+   R L 
Sbjct: 623 ------------VSMEYKETYKGY-----THLEIHPSLMFGIMGNQIIFPENNQLPRNLF 665

Query: 693 GCNMQRQAVPLLKAE 707
           GC   +QAV L  + 
Sbjct: 666 GCGQAKQAVSLYHSN 680


>gi|192337664|gb|ACF04252.1| RpoB [Vibrio parahaemolyticus]
 gi|192337682|gb|ACF04261.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLSQ  +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +T  RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG +IGL++SL++FAR N 
Sbjct: 121 VTRKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPSIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|254055193|gb|ACT64196.1| RpoB [Pectobacterium carotovorum]
          Length = 231

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 141/231 (61%), Positives = 188/231 (81%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQL
Sbjct: 1   RIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL+ +A+ N YGF+ETPYR+V +  VT+++ YLSA+EE N  IAQAN++LDE+G F +
Sbjct: 121 INSLSVYAQTNEYGFLETPYRRVRENVVTDEIHYLSAIEEGNFVIAQANTNLDEEGRFID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV CR  GE  L  R++++++D S +Q+VS+ ASLIPFLE+DD+NR LMG
Sbjct: 181 ELVTCRNKGESSLFSRDQVEYMDVSTQQIVSVGASLIPFLEHDDANRALMG 231


>gi|153958252|gb|ABS53416.1| RpoB [Bacteriovorax sp. OC1]
          Length = 345

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 164/348 (47%), Positives = 232/348 (66%), Gaps = 10/348 (2%)

Query: 723  SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            SGA + AK  G V  VD+ RIV++  +   +   SGVDIY L+K+QR+NQ+TC NQ+ LV
Sbjct: 1    SGAVLFAKDDGKVIFVDSNRIVLQRNK--FEDGESGVDIYSLVKYQRTNQSTCNNQKALV 58

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
            K GD VR+ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+
Sbjct: 59   KEGDIVRKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSV 118

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
            HIE FEV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKG
Sbjct: 119  HIEAFEVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKG 178

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
            E+ ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  +
Sbjct: 179  ETQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQ 238

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISE 1015
            +  LL RD+  E   +  +   ++ E+L G              +  +K   ++ +++++
Sbjct: 239  ETTLLRRDERIEIKAIQTSAILKIAEMLKGAKTTDKLVSEDGSTELLQKGADITGEVLAQ 298

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
             P        +Q  +++  +           + +  +  ++I K+  G
Sbjct: 299  IPFELIGYLPLQ-AELEERLSEYFADIRNRINRVRQKTTDEIAKLHRG 345


>gi|312204354|gb|ADQ47494.1| RNA polymerase II second largest subunit [Gyalecta fagicola]
          Length = 708

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 114/805 (14%), Positives = 226/805 (28%), Gaps = 124/805 (15%)

Query: 472  KNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
               +R+   ++ + + +  +              + +  + + +     +          
Sbjct: 1    AGLFRMLFNKLTKDVYQYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAA 60

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET E
Sbjct: 61   SSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPE 116

Query: 577  GHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            G   GLV +L     +      E    +    + +V  +            ++       
Sbjct: 117  GQACGLVKNLALMCYITVGSPSEPIVEFMIQRNMEVLEEYDPTRNPHATKVFVNGVWVGT 176

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND-DSNRVLM 692
              D +     V        I      I D  D   K          P    D D      
Sbjct: 177  HRDPAHLVSTVQTLRRQNMISSEVSLIRDIRDREFKIFTDAGRVCRPLFVIDTDKKSPNR 236

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV--DAIRIVIRSVEG 750
            G  +  + +     +   +   M+    K       A+  G    V   A+  +    E 
Sbjct: 237  GSLVLTKELVNKLEDDHQLPDDMDPDEKK-------ARYFGWAGLVANGAVEFLDAEEEE 289

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR---NDIIADGPSTDLGDLAL 807
             +  + +  D+    + Q        +  P+ +V  ++            PS  LG    
Sbjct: 290  TVMIAMTPEDLEVSKQLQAGYTLPEQSADPIARVKSKISAKNTWTHCEIHPSMILG---- 345

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N    +  S R                                   
Sbjct: 346  ---ICASIIPFPDHNQVGHLESSCRCRDSREXXXXXXXX-XXXXXXXXXXXXXXXXXXXX 401

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                            +             +       +   +  + AI      +  D+
Sbjct: 402  XXXXXXXXXXXXXXSNILYYPQKPLATTRSMEYLKFRQLPAGQNAIVAIACYSGYNQEDS 461

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  +++ +R        +E   +    E + +    Y +L 
Sbjct: 462  VIMNQSSIDRGLF-RSLFYRSYVEQEKRVGI---SLVEQFEKPMRSETLRVKHGTYEKLD 517

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D      R+++         ++     +      
Sbjct: 518  DDGIVAPGVRVSGEDIIIGKTAPIAPDSEELGQRTKFHTKRDASTPLRSTENGI------ 571

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                        ++K+          L+ VKV +   +  Q GDK A RHG KG +    
Sbjct: 572  ------------VDKVLM--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 617

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  DG   D+++NP  +PSRM +  + E  L       G +             
Sbjct: 618  RQEDMPFSADGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLCGAEGD----------- 666

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     ++++ +LR
Sbjct: 667  ------------------------------------------ATP-FTEITVDSVSKLLR 683

Query: 1225 MADLDESGQSILYDGLTGEPFDRPV 1249
                   G  I+Y+G +G      V
Sbjct: 684  DQGYQSRGFEIMYNGHSGRKLVAQV 708


>gi|40642972|emb|CAD89598.1| RNA polymerase II, second largest subunit [Borago officinalis]
          Length = 355

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 74/415 (17%), Positives = 128/415 (30%), Gaps = 77/415 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D  ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDXEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVAGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                  +T ++                  DE   +     +  + TS    E+   +++ 
Sbjct: 137  DVIIGXTTPINQ-----------------DEAQGQASRYTRRDHSTSMRHSENGMVDQVL 179

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 180  LTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 234

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +  
Sbjct: 235  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRG 294

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 295  FETM-----------------------------------------------YNGHT---- 303

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 304  GR---RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 355



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 57/184 (30%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDXEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V   D+++G  TP  +           A         RD S  +    
Sbjct: 121 LDDDGLAPPGTRVAGEDVIIGXTTPINQDE---------AQGQASRYTRRDHSTSMRHSE 171

Query: 936 SGTV 939
           +G V
Sbjct: 172 NGMV 175


>gi|94410902|gb|ABF18572.1| RNA polymerase II second largest subunit [Agrocybe erebia]
          Length = 641

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 112/714 (15%), Positives = 217/714 (30%), Gaps = 90/714 (12%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   + ++  G I  P  +  +      +       EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMSCIS-VGTISAPVIEFLEEWGLESL-------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + + A + +  +G +       R A   +   ++     D SP+  V            
Sbjct: 169  AHSSTAFTKVFVNGVWIG---VHRDAANLVKTLKKLRRKDDISPEVSVVRDIREKELRVY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +       ++     +   G      +      + K   I         
Sbjct: 226  TDAGRVCRPLFIVEXQRLAIQKRHIRWXRNGFNDDGEEF-KWEHLVKGGVIELLDAEEEE 284

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSN-QNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
             +      LD   S +    +  F++ +  +   +    +K              PS  L
Sbjct: 285  TVMIAMEPLDLENSRLQQQGVDPFEKKDIDSEDFDISARLKAPTHTHTWTHCEIHPSMIL 344

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N                        ++       +G     
Sbjct: 345  G-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTN 379

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              I               +  +             +       +   +  + AI      
Sbjct: 380  FLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 428

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+          + 
Sbjct: 429  NQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRLKHGTYDK 487

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                  I  G           K+  +  D      R++          ++     +  Q 
Sbjct: 488  LEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQV 547

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                                         + VKV V   R  Q GDK A RHG KG +  
Sbjct: 548  LI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGI 587

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
                EDMPF  +G   D+++NP  +PSRM +G + E  L      +GK+  +  
Sbjct: 588  TYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKGATLIGKEGDATP 641



 Score =  122 bits (305), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 86/627 (13%), Positives = 173/627 (27%), Gaps = 107/627 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + ++    +             NA    +    F     +
Sbjct: 126 TPEGQACGLVKNLALMSCISVGTISAPVIEFLEEWGLESLEENAHSSTAFTKVFVNGVWI 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  +   RR   +            +   V+        P    E   + +
Sbjct: 186 GVHRDAANLVKTLKKLRRKDDISPEVSVVRDIREKELRVYTDAGRVCRPLFIVEXQRLAI 245

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 + R       E    K         +  L A EEE   IA     L E+    +
Sbjct: 246 QKRHIRWXRNGFNDDGEE--FKWEHLVKGGVIELLDAEEEETVMIAMEPLDL-ENSRLQQ 302

Query: 643 ELVFCRCAGEEI------------LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           + V      +                        +  P  ++ I AS+IPF +++ S R 
Sbjct: 303 QGVDPFEKKDIDSEDFDISARLKAPTHTHTWTHCEIHPSMILGICASIIPFPDHNQSPRN 362

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                                               
Sbjct: 363 TYQSAMGKQAMGIYLTNFLI---------------------------------------- 382

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               + + +  Y       +     +  R                        +L  G+N
Sbjct: 383 -RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQN 417

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDI 865
            +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        + 
Sbjct: 418 AIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENT 477

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +++ G+I  G  V   DI++GK  P         ++        +    R
Sbjct: 478 LRLKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRR 530

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           D S  + S  SG V  V I       K
Sbjct: 531 DVSTPLKSTESGIVDQVLITTNSEGQK 557


>gi|192337692|gb|ACF04266.1| RpoB [Vibrio parahaemolyticus]
          Length = 269

 Score =  231 bits (590), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 159/269 (59%), Positives = 206/269 (76%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           K N  +  +   +   + + DII ++K L+ +RNGKG +DDID+LGNRR+RSVGEM +NQ
Sbjct: 1   KFNSSIGREDAQEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQ 60

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +R+GL+R+ER++KER+S  D+D+VMPQDLINAKP+ +AV EFF SSQLS   +  N LS 
Sbjct: 61  FRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSPFMDQNNPLSE 120

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FAR N 
Sbjct: 121 VTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNE 180

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT++V YLSA+EE    IAQAN+ L+EDG+F +EL+  R  GE  
Sbjct: 181 YGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESG 240

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE 683
           L PRE   ++D +  QVVSIAASLIPFLE
Sbjct: 241 LHPREHAQYMDVATNQVVSIAASLIPFLE 269


>gi|300394672|gb|ADK11874.1| DNA-directed RNA polymerase II subunit two [Athelia arachnoidea]
          Length = 671

 Score =  231 bits (590), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 123/801 (15%), Positives = 233/801 (29%), Gaps = 146/801 (18%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
             L N +R+   ++ + +    +              +  + + + +     +        
Sbjct: 1    FLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   SMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L   + ++           + +  + +         EEN +     + +
Sbjct: 117  PEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSTTPCTKV 168

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              +G +       R     +   ++     D SP+  V             D+ RV    
Sbjct: 169  FVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPL 225

Query: 695  NMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             +   Q + L K    ++  G +    +     +V  ++GIVE +DA       +    +
Sbjct: 226  FIVENQQLALQKKHVHWLNQGYDDSDEEFKWEQLV--KSGIVELLDAEEEETVMISMTPE 283

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               +       +    ++ +     R  +K G            PS  LG       +  
Sbjct: 284  DLENSRLQLSGVDPTANDGDFDPAAR--LKAGTNTHTWTHCEIHPSMILG-------ICA 334

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N                        ++       +G       I        
Sbjct: 335  SIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM------ 370

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 371  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQS 425

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V   +    I+ R  +D  ++S   + E+ E   R+          +          G 
Sbjct: 426  SVDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKIEDDGLFAPGT 484

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+                      +E  QR     +    T     E+  
Sbjct: 485  GVSGEDIIIGKTAPYPF---------------QSEECGQRTRTHTRRDVSTPLKSTENGI 529

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++              + VKV V   R  Q GDK A RHG  G V      ED PF  
Sbjct: 530  VDQVLI-----TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQTGTVGITYRQEDTPFTA 584

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +G + E  L      +G +                      
Sbjct: 585  EGIVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGD-------------------- 624

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     E++++ LR       G 
Sbjct: 625  ---------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGL 650

Query: 1234 SILYDGLTGEPFDRPVTVGYI 1254
             ++Y G +G      V +G  
Sbjct: 651  EVMYHGHSGRKLQAQVYLGPT 671



 Score =  119 bits (297), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 86/620 (13%), Positives = 173/620 (27%), Gaps = 101/620 (16%)

Query: 357 YIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           ++ N       K  KD    + + +       F+++ ++ +    +  KY L   G    
Sbjct: 1   FLANLFRMLFRKLTKDVYRYLQKCV--ETHKEFNLSLAVKHQTITNGLKYSL-ATGNWGD 57

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEML 471
             +         + + +    + +  L        R GK       +  +  +    E  
Sbjct: 58  QKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETP 117

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQ 524
           + Q    +  +       + S+    +             NA         F     +  
Sbjct: 118 EGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWMGV 177

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N +  I   RR   +            +   ++        P    E   + L  
Sbjct: 178 HRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQK 237

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
               +  +N          K      +  V  L A EEE   I+     L+        +
Sbjct: 238 KHVHW--LNQGYDDSDEEFKWEQLVKSGIVELLDAEEEETVMISMTPEDLENSRLQLSGV 295

Query: 645 VFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                 G+     R             +  P  ++ I AS+IPF +++ S R      M 
Sbjct: 296 DPTANDGDFDPAARLKAGTNTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 355

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                                                   + +
Sbjct: 356 KQAMGIFLTNFLI-----------------------------------------RMDTMA 374

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +  Y       +     +  R                        +L  G+N +VA + 
Sbjct: 375 NILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAILC 410

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEG 872
           + GYN EDS+++++  V   +F SI+   +  + + + +   E        +   +    
Sbjct: 411 YSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGT 470

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              I++ G+   G  V+  DI++GK  P         ++        +    RD S  + 
Sbjct: 471 YDKIEDDGLFAPGTGVSGEDIIIGKTAPYPFQSEECGQRT-------RTHTRRDVSTPLK 523

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           S  +G V  V I       K
Sbjct: 524 STENGIVDQVLITTNSEGQK 543


>gi|161331449|gb|ABX60642.1| RpoB [Bacillus firmus]
          Length = 232

 Score =  231 bits (590), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 83/207 (40%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVASPVFDGAREEDVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                     A  E        A +    
Sbjct: 193  -----------------------------------------ATIEE-------AGMARDA 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            +++LYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  KTVLYDGRSGEPFDNRVSVGVMYMIKL 231



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|254055169|gb|ACT64184.1| RpoB [Pseudomonas chlororaphis]
          Length = 231

 Score =  231 bits (590), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 137/231 (59%), Positives = 179/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMNQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++ G   +
Sbjct: 121 INSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKGQLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|32455007|gb|AAP83183.1| RpoB [Streptococcus infantarius]
          Length = 231

 Score =  231 bits (590), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 94/292 (32%), Positives = 131/292 (44%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 6    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 58

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 59   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 107

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 108  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 167

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 168  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 189

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM
Sbjct: 190  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYM 225



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/87 (64%), Positives = 67/87 (77%)

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +V
Sbjct: 1   IPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREV 60

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RDTSLRVP G  G V DV+IF R   D
Sbjct: 61  RDTSLRVPHGGDGVVRDVKIFTRANGD 87


>gi|300394738|gb|ADK11907.1| DNA-directed RNA polymerase II subunit two [Athelia sp. L-10567]
          Length = 654

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 111/715 (15%), Positives = 215/715 (30%), Gaps = 92/715 (12%)

Query: 472  KNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
             N +R+   ++ + +    +              +  + + + +     +          
Sbjct: 6    ANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLATGNWGDQKKSM 65

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET E
Sbjct: 66   SSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPE 121

Query: 577  GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
            G   GLV +L   + ++           + +  + +         EEN +     + +  
Sbjct: 122  GQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSTTPCTKVFV 173

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +G +       R     +   ++     D SP+  V             D+ RV     +
Sbjct: 174  NGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFI 230

Query: 697  QR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
               Q + L K    ++  G +    +     +V  ++GI+E +DA       +    +  
Sbjct: 231  VENQQLALQKKHVHWINRGYDDNEEEFKWEQLV--KSGIIELLDAEEEETVMISMTPEDL 288

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
             +     +L     +  +   +    +K G            PS  LG       +  + 
Sbjct: 289  ENSRL--QLSGVDTTANDGEFDPAARLKAGTNTHTWTHCEIHPSMILG-------ICASI 339

Query: 816  MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            +P+  +N                        ++       +G       I          
Sbjct: 340  IPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM-------- 373

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S V
Sbjct: 374  ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSV 430

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   R+          +       I  G   
Sbjct: 431  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAPGTGV 489

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 490  SGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------- 538

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 539  ---------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTVGITYRQEDMPFTAEG 589

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               DI++NP  +PSRM +G + E  L      +G +  +          +S    
Sbjct: 590  IVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGDATPFTDLTVESVSSFLR 644



 Score =  122 bits (306), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 84/610 (13%), Positives = 170/610 (27%), Gaps = 98/610 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
            +   N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 2   GSSSANLFRMLFRKLTKDVYRYLQKCVETH--KEFNLSLAVKHQTITNGLKYSL-ATGNW 58

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 59  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 118

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 119 TPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESLEENAHSTTPCTKVFVNGVWM 178

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 179 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLAL 238

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                 +  +N          K      +  +  L A EEE   I+     L+       
Sbjct: 239 QKKHVHW--INRGYDDNEEEFKWEQLVKSGIIELLDAEEEETVMISMTPEDLENSRLQLS 296

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +      GE     R             +  P  ++ I AS+IPF +++ S R      
Sbjct: 297 GVDTTANDGEFDPAARLKAGTNTHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 356

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                                                   +
Sbjct: 357 MGKQAMGIFLTNFLI-----------------------------------------RMDT 375

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            + +  Y       +     +  R                        +L  G+N +VA 
Sbjct: 376 MANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIVAI 411

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
           + + GYN EDS+++++  V   +F SI+   +  + + + +   E        +   +  
Sbjct: 412 LCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKH 471

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                I++ G+I  G  V+  DI++GK  P         E+L +        DV      
Sbjct: 472 GTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKS 527

Query: 931 VPSGVSGTVV 940
             +G+   V+
Sbjct: 528 TENGIVDQVL 537


>gi|117675883|emb|CAL69212.1| RNA polymerase subunit B [Leifsonia poae]
          Length = 392

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 139/282 (49%), Positives = 194/282 (68%), Gaps = 15/282 (5%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    +++AL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +
Sbjct: 111 EKDAILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGI 170

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLGNRRVRSV 467
           D P     +   DIIA IK LV L + +                 +DDID+ GNRR+R+V
Sbjct: 171 DAPLSDSVLTVSDIIATIKYLVSLHDNQTTFSGVRDGKAVEIRLDVDDIDHFGNRRIRAV 230

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 231 GELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMD 290

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL 
Sbjct: 291 QNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA 350

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           SFAR+N++GFIETPYR+V  GKVT  + YL+A EE++  +AQ
Sbjct: 351 SFARINSFGFIETPYRRVVKGKVTETIDYLTASEEDDFVVAQ 392



 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/173 (39%), Positives = 94/173 (54%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTFVI G +R+VVSQL RSPG++F+    +   S K +Y+ RIIP +G 
Sbjct: 1   FMGDFPLMTEKGTFVINGTERVVVSQLVRSPGVYFERTPEKT--SDKDIYSARIIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEILS F  +  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILSEFKGFQSIELTLEKDAILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EEALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163


>gi|154362171|gb|ABS80924.1| RNA polymerase beta subunit [Ralstonia solanacearum]
          Length = 236

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 133/234 (56%), Positives = 174/234 (74%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +A++N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D+DG+
Sbjct: 61  IGLINSLALYAQLNDYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDKDGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LVDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+A+ P VGTG+E  VA  SG A+ A R G+V+ VDA R+VIR  + +
Sbjct: 181 RQAVPCLRADKPLVGTGVERTVAVDSGTAVQATRGGLVDYVDANRVVIRVNDDE 234


>gi|46277251|gb|AAS86816.1| RNA polymerase II second largest subunit [Cycas revoluta]
          Length = 567

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 89/508 (17%), Positives = 152/508 (29%), Gaps = 85/508 (16%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN          Y       I   ++    
Sbjct: 143  LVAKGFIEYVDTEEEETTMISMTISDLVNARNSPSTSSSIVKY---THCEIHPSLILGVC 199

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 200  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 256

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        +F R   D+ +R  +
Sbjct: 257  EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFYRSYRDEEKRMGT 315

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+     R+          +          G           K+T ++         
Sbjct: 316  LVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPITQ-------- 367

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     DE   +     K    TS    E    +++      D +     R VKV +
Sbjct: 368  ---------DEAGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRM 413

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 414  RSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIE 473

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+  +         +IS         +                      
Sbjct: 474  CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM---------------- 517

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                                            +G +    G         + +G  Y  +
Sbjct: 518  -------------------------------YNGHT----GR---RLSAMIFLGPTYYQR 539

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
            L HMV DK+++R  G   ++T+QP  G+
Sbjct: 540  LKHMVDDKIHSRGRGPVQILTRQPAEGR 567



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 75/482 (15%), Positives = 143/482 (29%), Gaps = 97/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHRDPDLLVKTLRQLRRQVDVNTEVGVVRDIRLSELR-LYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      +      E+P     D      + Y+   EEE   I+              
Sbjct: 123 KKS-----DIRTLQQRESPEEGWHDLVAKGFIEYVDTEEEETTMISM----------TIS 167

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R +         K    +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 168 DLVNARNSPSTSSSIV-KYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 226

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 227 IYVTNYQL--------------------RMDTLAYV------------------------ 242

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 243 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 281

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 282 QEDSVIMNQSSIDRGFFRSLFYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLD 341

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           A         RD S  +    SG
Sbjct: 342 DDGLAPPGTRVSGEDVIIGKTTPITQDE---------AGGQAARYTKRDQSTSLRHSESG 392

Query: 938 TV 939
            V
Sbjct: 393 MV 394


>gi|89090014|gb|ABD46533.2| RNA polymerase II second largest subunit [Dacrymyces sp. FPL8953]
          Length = 676

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 118/810 (14%), Positives = 214/810 (26%), Gaps = 156/810 (19%)

Query: 476  RLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------ 521
            R+   R+ + +    +              +    + + +     +              
Sbjct: 1    RMLFRRLTKDVYRYMQKCVETHREFNINAAVKPATITNGLKYSLATGNWGDQKKFMQAKA 60

Query: 522  -LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R       R +H TH+G +CPAET EG   
Sbjct: 61   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIARPRQLHNTHWGMVCPAETPEGQAC 116

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGK----VTNDVVYLSAMEEENRYIAQANSSLDE 636
            GLV +L   A ++     +     + +             L+A      ++      +  
Sbjct: 117  GLVKNLALMACISVGTLSQPVVEFLEEWGLEPLGERTDEPLTAT---KVFVNGVWMGIHR 173

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
            D       V      + I      + D  +   +          P F+ N+ +  +++  
Sbjct: 174  DPQHLVNTVRTLRRSDGISSEISVVRDIRERELRLYTDAGRVCRPLFIVNEQTQNLVISK 233

Query: 695  NMQRQAVPLLKA-EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
                      K  E   V          +SG           E +DA       +     
Sbjct: 234  REINWLHAREKPGEKDKVYG---WSQLVTSGMV---------ELLDAEEEETVMIAMTPQ 281

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                            + +N  V  +  V               PS  LG       +  
Sbjct: 282  DLDQSKTKRGTGYVSNNPENAAVRIKSTVH----HEHWSHCEIHPSMILG-------ICA 330

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N       S R   +       +  +    +                     
Sbjct: 331  SIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNFQVRM------------------ 366

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 367  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQS 421

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R   D  + +  V  E+ E   RD          +       +  G 
Sbjct: 422  SIDRGLF-RSIYYRSYTDMEKTTGIVPVEEFEKPHRDTTVRMKHGTYDKLEADGLVAPGI 480

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  L  D      R++          ++     +  Q   S +      
Sbjct: 481  GINGEDIIIGKTAPLPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLISTNE----- 535

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             ++ VKV +   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 536  ---------------SGVKFVKVRIRSTRIPQIGDKFASRHGQKGTIGMTYRQEDMPFAG 580

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +G + E  L      +G +  +          +S L     
Sbjct: 581  NGITPDIIINPHAIPSRMTIGHLVECLLSKLATLIGNEGDATPFTDLTVESVSSLLR--- 637

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
               G G     +                                              G 
Sbjct: 638  ---GKGYQQRGLEVM-----------------------------------------YHGH 653

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +    G         V +G  Y  +L HMV
Sbjct: 654  T----GR---KLQAQVYLGPTYYQRLKHMV 676


>gi|80973541|gb|ABB53508.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733185|gb|ACX48603.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|260733187|gb|ACX48604.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|260733189|gb|ACX48605.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|260733197|gb|ACX48609.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|260733227|gb|ACX48624.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|260733241|gb|ACX48631.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 226

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 95/286 (33%), Positives = 128/286 (44%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                              D
Sbjct: 175  ATPVFDGASADDLW---------------------------------------------D 189

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               E           +D   ++ILYDG TGEPFD  V+VG +YM+K
Sbjct: 190  TVREA---------GMDSDAKTILYDGRTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|153958192|gb|ABS53386.1| RpoB [Bacteriovorax sp. MNZ2]
          Length = 342

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 162/343 (47%), Positives = 225/343 (65%), Gaps = 10/343 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 ++   ++  +           + +  +  ++I K   G
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHRG 342


>gi|113707351|gb|ABI36583.1| RNA polymerase II second largest subunit [Usnea sphacelata]
          Length = 710

 Score =  231 bits (589), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 114/766 (14%), Positives = 220/766 (28%), Gaps = 86/766 (11%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + + +  +    +         + +  + + +     +            
Sbjct: 1    LFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGNWGDQKKAASV 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +    + +V  +   L++      ++      +  
Sbjct: 117  ACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVWVGVHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D +     V        I      + D  D   K          P    D+  R     N
Sbjct: 177  DPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGN 236

Query: 696  MQRQAVPLL---KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            +      +L        +  T  +       G   + K  G+VE VDA       +    
Sbjct: 237  LVLTKDHVLKLEMDRENWATTEPDVREETDMGWQGLVKE-GVVEYVDAEEEETIMIVMTP 295

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +       +        +N    +N+R    +             PS  LG       + 
Sbjct: 296  EDLEISRQLQAGYVMPEANPEE-LNKRVKAPMNPTAHTWTHCEIHPSMILG-------IC 347

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          +  +        +                      V    
Sbjct: 348  ASIIPFPDHNQ---------VSFDTWMIGYSTDTIXXXXXXXXXXXXXXXXXXXXVFLTN 398

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
             +      +  +             +       +   +  + AI    + +  D+ +   
Sbjct: 399  YQQR-MDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSSYNQEDSVIMNQ 457

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---I 989
            S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +
Sbjct: 458  SSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLV 513

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  ++ D      R++          ++     +  Q   S    
Sbjct: 514  APGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---- 569

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                 LR VKV +   +  Q GDK A RHG KG +      EDM
Sbjct: 570  ----------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDM 613

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   D+++NP  +PSRM +  + E  L       G +  +          +S L 
Sbjct: 614  PFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLL 673

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                      V     +G  + T VF G  
Sbjct: 674  R---------------EHGYQSRGFEVMYNGHTGRKLVTQVFLGPT 704



 Score =  102 bits (254), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 80/611 (13%), Positives = 159/611 (26%), Gaps = 90/611 (14%)

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
            NK  KD    + + +       F++  ++ +    +  +Y L   G      +      
Sbjct: 6   FNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNWGDQKKAASVKA 62

Query: 426 DDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
              + + +    + +  L        R+GK       +  +  +    E  + Q    + 
Sbjct: 63  GVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVK 122

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSL 532
            +       + +     V      N + +         +A   F     +    +  + +
Sbjct: 123 NLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVWVGVHRDPAHLV 182

Query: 533 SRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVS 584
             + + RR   +  +  + R     E        R   P       P  ++ G+ +    
Sbjct: 183 GTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGNLVLTKD 242

Query: 585 SLTSFAR------VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            +                  E              V Y+ A EEE   I      L+   
Sbjct: 243 HVLKLEMDRENWATTEPDVREETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLEISR 302

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                 V      E                              E +   +  M      
Sbjct: 303 QLQAGYVMPEANPE------------------------------ELNKRVKAPMNPTAHT 332

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                         T  E   +   G            QV     +I      +      
Sbjct: 333 W-------------THCEIHPSMILGICASIIPFPDHNQVSFDTWMIGYSTDTIXXXXXX 379

Query: 759 VDIYRLMKFQRSNQNT--CVNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLV 813
                                QR              +A   S +     +L  G+N +V
Sbjct: 380 XXXXXXXXXXXXXXVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIV 439

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNV 868
           A   +  YN EDS+++++  +   +F S+    +    +   +   E     +  D   +
Sbjct: 440 AIACYSSYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKL 499

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G++  G  V+  DI++GK  P         ++        K    RDTS
Sbjct: 500 KHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTS 552

Query: 929 LRVPSGVSGTV 939
             + S  +G V
Sbjct: 553 TPLRSTENGIV 563


>gi|153958257|gb|ABS53418.1| RpoB [Bacteriovorax sp. MIA1]
          Length = 341

 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 162/344 (47%), Positives = 228/344 (66%), Gaps = 10/344 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                 ++   ++  +           S +  +  ++I K+  GD
Sbjct: 299  IGYLPLE-AALEERLSEYFADIRNRISRVRQKATDEIAKLHRGD 341


>gi|3133453|gb|AAC38527.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 132/231 (57%), Positives = 173/231 (74%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V  G VT+
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRRVVSGVVTD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A EE+   +AQANS L     F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEEDRHVVAQANSPLAGASHFAEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|154362175|gb|ABS80926.1| RNA polymerase beta subunit [Cupriavidus pauculus]
 gi|154362177|gb|ABS80927.1| RNA polymerase beta subunit [Cupriavidus pauculus]
          Length = 236

 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 133/234 (56%), Positives = 173/234 (73%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D +G+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDAEGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R+VIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMRVVIRVNDDE 234


>gi|153958263|gb|ABS53421.1| RpoB [Bacteriovorax sp. T8]
          Length = 341

 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 162/344 (47%), Positives = 228/344 (66%), Gaps = 10/344 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                 ++   ++  +           S +  +  ++I K+  GD
Sbjct: 299  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRGD 341


>gi|145342351|gb|ABP64872.1| RpoB [Bacillus megaterium]
 gi|161331507|gb|ABX60671.1| RpoB [Bacillus megaterium]
          Length = 232

 Score =  231 bits (589), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 83/207 (40%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHVASPVFDGAREEDVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                     A  E        A +    
Sbjct: 193  -----------------------------------------ATIEE-------AGMSRDA 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            +++LYDG TGEPFD  V+VG +YM+KL
Sbjct: 205  KTVLYDGRTGEPFDNRVSVGIMYMIKL 231



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIILDVKVFNREDGD 90


>gi|80973567|gb|ABB53521.1| RNA polymerase beta subunit [Streptococcus lutetiensis]
 gi|80973607|gb|ABB53541.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 226

 Score =  231 bits (589), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 94/292 (32%), Positives = 131/292 (44%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   D  +E         A +    +++LYDG TGEPFD  V+VG +YM
Sbjct: 189  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGVMYM 224



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|156627835|gb|ABU88905.1| RNA polymerase II second largest subunit [Psilopezia deligata]
          Length = 801

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 121/833 (14%), Positives = 247/833 (29%), Gaps = 110/833 (13%)

Query: 346  ILYVDSVNNNAYIRNT--LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
            +   D +N+  Y RN   ++       ++A +   R +    +     ++          
Sbjct: 59   VSDEDILNHVCYDRNDTEMLEMMKPCIEEAFVIQDREIALDYIGKRGNSQ---GSNKEKR 115

Query: 404  DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             +Y    + +  +         +     +   +  ++  L+     +  +DD D+ G +R
Sbjct: 116  IRYARDILQKELLPHISQQ---EGNETRKAFFLGYMVHRLLQCALERREVDDRDHFGKKR 172

Query: 464  VRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +   G +L   +R    ++ + + + +               + +  + S +     +  
Sbjct: 173  LDLAGPLLAQLFRTLWKQLTKEVYKYLEKCVEGGKEFNLNLAVKSNTITSGLKYSLATGN 232

Query: 522  -------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                         +SQ+       S ++H RR +      + R     + R +H TH+G 
Sbjct: 233  WASQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGL 288

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +CPAET EG   GLV +L   + +              + +   +     +      ++ 
Sbjct: 289  VCPAETPEGQACGLVKNLALMSYIT------------RNMEPLEEYEPQRSPNATKIFVN 336

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LEND 685
                 +  D       V        I      I D  D   K          P   +END
Sbjct: 337  GVWVGIHRDPLHLVRTVQRLRRTGVISHEVSVIRDIRDREFKIFTDAGRVCRPLFVIEND 396

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             ++       +Q++ +  L+ +        E         ++ A     VE +DA     
Sbjct: 397  PTSERRGQLVLQKEHIERLEDDHGLPE---EERFGWKGLLSVGA-----VEYLDAEEEET 448

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    +       +    +           + P+                PS  LG  
Sbjct: 449  VMIVMTPEDLELSRQVQAGYEIAEETDMAKRVKAPI---NPATHTWTHCEIHPSMILG-- 503

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N       S R   +       +  F    ++            
Sbjct: 504  -----ICASIIPFPDHNQ------SPRNTYQSAMGKQAMGVFLTNFQERM---------- 542

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                           +  +             +       +   +  + AI      +  
Sbjct: 543  -------------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQE 589

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R  +D+ +R      E+ E   R           +    
Sbjct: 590  DSVIMNQSSIDRGLF-RSLFYRCYLDQEKRVGMQIVEEFEKPQRSTTLRLKXGTYDKLDE 648

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K++ +S D                DE  QR     K    T 
Sbjct: 649  DGLVAPGVRVSGEDIIIGKTSPISPD---------------TDEMGQRQKYHTKRDVSTP 693

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E+   +++             ++ VKV +   +  Q GDK A RHG KG +     
Sbjct: 694  LRSTENGIVDQVVF-----TTNSEGMKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 748

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 749  MEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFT 801



 Score =  127 bits (319), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 109/772 (14%), Positives = 209/772 (27%), Gaps = 120/772 (15%)

Query: 203 HVRIDRRRKVPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ID    +P+     ALG+   E+IL+        ++  +     +  A ++   +++
Sbjct: 42  YIKID----IPIVIVFRALGVVSDEDILNHVCYDRNDTEMLEMMKPCIEEAFVIQDREIA 97

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
              +      Q     K++                      +    +   I   E  E  
Sbjct: 98  LDYIGKRGNSQGSNKEKRIRYAR-----------------DILQKELLPHISQQEGNE-T 139

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
            +A  +            E R++                 L        K    ++Y+ +
Sbjct: 140 RKAFFLGYMVHRLLQCALERREVDDRDHFGKKRLDLAGPLLAQLFRTLWKQLTKEVYKYL 199

Query: 382 RPGDV--STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                    F++  ++ +       KY L   G      +         + + +    + 
Sbjct: 200 EKCVEGGKEFNLNLAVKSNTITSGLKYSL-ATGNWASQKKAASSKAGVSQVLNRYTFAST 258

Query: 440 IKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           +  L        R+GK       +  +  +    E  + Q    +  +        +   
Sbjct: 259 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYITRNMEP 318

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARAR 553
           ++   PQ   NA  +      F     +    + ++ +  +   RR   +  +  V R  
Sbjct: 319 LEEYEPQRSPNATKI------FVNGVWVGIHRDPLHLVRTVQRLRRTGVISHEVSVIRDI 372

Query: 554 AGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              E        R   P       P     G  +     +      + +G  E       
Sbjct: 373 RDREFKIFTDAGRVCRPLFVIENDPTSERRGQLVLQKEHIERLE--DDHGLPEEERFGWK 430

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSL------DEDGSFTEELVFCRCAGEEILVPREK 660
                  V YL A EEE   I      L             EE    +     I      
Sbjct: 431 GLLSVGAVEYLDAEEEETVMIVMTPEDLELSRQVQAGYEIAEETDMAKRVKAPINPATHT 490

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 491 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NFQER 541

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             + A I+                            +       +KF+            
Sbjct: 542 MDTMANILY---------------------YPQKPLATTRSMEFLKFRELPAGQNAIVAI 580

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           L   G   + + +I +  S D G         + +  +        M I E         
Sbjct: 581 LCYSG-YNQEDSVIMNQSSIDRGLFRS-----LFYRCYLDQEKRVGMQIVE--------- 625

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
                EFE   R T             +       +DE G++  G  V+  DI++GK +P
Sbjct: 626 -----EFEKPQRST----------TLRLKXGTYDKLDEDGLVAPGVRVSGEDIIIGKTSP 670

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    ++       +K    RD S  + S  +G V  V         K
Sbjct: 671 ISPDTDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVVFTTNSEGMK 715


>gi|143024655|gb|ABO93151.1| RNA polymerase beta subunit [Enterobacter pulveris]
          Length = 227

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 140/227 (61%), Positives = 181/227 (79%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR V DG VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   ++
Sbjct: 121 PYRLVRDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRAD 227


>gi|171909273|gb|ACB58226.1| RpoB [Tatumella saanichensis]
 gi|171909275|gb|ACB58227.1| RpoB [Tatumella ptyseos]
 gi|171909277|gb|ACB58228.1| RpoB [Tatumella ptyseos]
 gi|171909279|gb|ACB58229.1| RpoB [Tatumella ptyseos]
 gi|171909281|gb|ACB58230.1| RpoB [Tatumella ptyseos]
          Length = 226

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 139/226 (61%), Positives = 184/226 (81%)

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
           RSVGEM +NQ+R+GL+R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ
Sbjct: 1   RSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQ 60

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 61  FMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIN 120

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +A+ N YGF+ETPYR+V D +VT+++ YLSA+EE N  IAQAN++LD+DG F ++L
Sbjct: 121 SLSVYAQTNEYGFLETPYRRVVDSQVTDEIHYLSAIEEGNFVIAQANTNLDDDGRFVDDL 180

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           V CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR 
Sbjct: 181 VTCRNKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRA 226


>gi|153958315|gb|ABS53446.1| RpoB [Bacteriovorax sp. T3]
          Length = 344

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 162/345 (46%), Positives = 229/345 (66%), Gaps = 10/345 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                 ++   ++  +           S +  +  ++I K+  GD+
Sbjct: 301  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRGDE 344


>gi|22086611|gb|AAM90691.1|AF403009_1 RNA polymerase beta subunit [Rickettsia honei]
          Length = 262

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 167/262 (63%), Positives = 209/262 (79%), Gaps = 2/262 (0%)

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
              +N +GFI++PY +V DG VT++VVYLSA+EE    I QANS +++DG    E + CR
Sbjct: 2   MLPINKHGFIQSPYIRVKDGCVTDEVVYLSAIEEGTYKIGQANSKINKDGKLQGEFINCR 61

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
              G  ++V   ++DF D +P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K +
Sbjct: 62  VEGGNFVMVEPYEVDFTDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKTD 121

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
           APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E      +  VDIY L+KF
Sbjct: 122 APFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLE-QKVDGSPSVDIYNLLKF 180

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           Q+SN NTC+NQ+PLVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+PW+GYNFEDS+
Sbjct: 181 QKSNHNTCINQKPLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLPWNGYNFEDSI 240

Query: 828 LISERMVSEDVFTSIHIEEFEV 849
           LISER+V EDVFTSIHIEEFEV
Sbjct: 241 LISERIVKEDVFTSIHIEEFEV 262


>gi|56694362|gb|AAW22921.1| RNA polymerase II second largest subunit [Pseudotsuga menziesii]
          Length = 554

 Score =  231 bits (588), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 83/501 (16%), Positives = 148/501 (29%), Gaps = 84/501 (16%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            + V   +      S  + DL   RN                  I   ++     + I   
Sbjct: 138  EYVDTEEEETTMISMTINDLVSARNNPAEAYSHTYT----HCEIHPSLILGVCASIIPFP 193

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +     R+T             V+   L+      +  V        +    +       
Sbjct: 194  DHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQ 250

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +      + AI      +  D+ +   S +        +F R   D+ +R  ++ +E+  
Sbjct: 251  LPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKRMGTLVKEEFG 309

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               R+          +          G           K+T ++ +              
Sbjct: 310  CPNRENTLNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQE-------------- 355

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               E   +    ++    TS    E    +++      D +     R VKV +   R  Q
Sbjct: 356  ---ETSGQQQRYIRRDQSTSLRHSESGMVDQVLLTTNQDGL-----RFVKVRMRSVRIPQ 407

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G   
Sbjct: 408  IGDKFSSRHGQKGTVGMTYTQEDMPWTSEGITPDIIVNPHAIPSRMTIGQLIECIMGKVA 467

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +GK+  +          IS         +                             
Sbjct: 468  AHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM----------------------- 504

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                     +G +    G         + +G  Y  +L HMV D
Sbjct: 505  ------------------------YNGHT----GR---KLSAMIFLGPTYYQRLKHMVDD 533

Query: 1266 KVYARSTGSYSLVTQQPLGGK 1286
            K+++R  G   ++T+QP  G+
Sbjct: 534  KIHSRGRGPVQILTRQPAEGR 554



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 71/452 (15%), Positives = 131/452 (28%), Gaps = 98/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + +A   F     +    +    +  +   RR   +    GV R 
Sbjct: 22  EEWSTENFEEISPAVIPTATKIFVNGCWVGIHRDPELLVKTLRQLRRQVDVNPEVGVVRD 81

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S      +       T      D     
Sbjct: 82  IRLKELR-LYTDYGRCSRPLFVVEKQRLSIKKS-----DITRLQERTTTEEGWHDLVTRG 135

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R                +  P  ++
Sbjct: 136 FIEYVDTEEEETTMISM----------TINDLVSARNNP--AEAYSHTYTHCEIHPSLIL 183

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 184 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 223

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 224 DTLAYV-----------------------------------LYYPQKPLV---------- 238

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 239 TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 298

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +  N+       +D+ G+   G  V+  D+++GK TP  +   +
Sbjct: 299 RMGTLVKEEFGCPNRENTLNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQEETS 358

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                      ++    RD S  +    SG V
Sbjct: 359 ---------GQQQRYIRRDQSTSLRHSESGMV 381


>gi|3133319|gb|AAC38460.1| RNA polymerase beta-subunit [Mycobacterium gordonae]
          Length = 234

 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 134/231 (58%), Positives = 176/231 (76%), Gaps = 1/231 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R 
Sbjct: 1   QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++
Sbjct: 61  RAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSD 120

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQV 671
           ++ YL+A E +   +AQANS +DE G F E  V  R   GE   VP  ++D++D SP+Q+
Sbjct: 121 EIHYLTADEGDPHVVAQANSPIDESGRFAEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQM 180

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           VS+A ++IPFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME   A  
Sbjct: 181 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAID 231


>gi|307343472|emb|CBJ18653.1| RNA polymerase B subunit [Micromonospora sp. GUI28]
          Length = 204

 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 88/204 (43%), Positives = 115/204 (56%), Gaps = 38/204 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPVEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVP RMN+GQ+ ETHLGW     G  ++    D+K                 
Sbjct: 91   VDIVLNPLGVPGRMNIGQVLETHLGWVAK-TGWNVEGDDADWKRALRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AAEAEPDTNVATPVFDGAREEEISGLLASTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVGY 1253
              G++ L+DG +GEP   P+ VGY
Sbjct: 181  SSGKAQLFDGRSGEPLPDPIAVGY 204


>gi|255018493|ref|ZP_05290619.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL F2-515]
          Length = 252

 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 147/252 (58%), Positives = 192/252 (76%), Gaps = 2/252 (0%)

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
           DII+ I    +L +G G  DDID+LGNRR+RSVGE+L+NQ+R+GL RMER ++ER+S  D
Sbjct: 1   DIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQD 60

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
           + ++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG GG+ R RA
Sbjct: 61  MTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGPGGLTRERA 120

Query: 555 GVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTN 612
           G E+RDVH +HYGR+CP ET EG NIGL++SL+SFA+VN +GFIETPYR+V     +VT+
Sbjct: 121 GYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKVNKFGFIETPYRRVDPETNRVTD 180

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + YL+A EE+N  +AQANS LDE G+FTEE V  R   E + V +E+ID++D SPKQVV
Sbjct: 181 KIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFRSENLAVEKERIDYMDVSPKQVV 240

Query: 673 SIAASLIPFLEN 684
           S+A + IPFLEN
Sbjct: 241 SVATACIPFLEN 252


>gi|117675873|emb|CAL69207.1| RNA polymerase subunit B [Mycetocola saprophilus]
 gi|117675875|emb|CAL69208.1| RNA polymerase subunit B [Mycetocola lacteus]
          Length = 390

 Score =  231 bits (588), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 143/281 (50%), Positives = 195/281 (69%), Gaps = 15/281 (5%)

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D    + DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR K+N +L L
Sbjct: 110 EKDSIVSKDDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINKKLGL 169

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNLGNRRVRSV 467
           + P     +  EDI++ IK LV L  G+                  DDIDN GNRR+R+V
Sbjct: 170 EAPLTDSVLTVEDIVSTIKYLVRLHAGETHFTGVRKGAPAEIRIDTDDIDNFGNRRIRAV 229

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 230 GELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMD 289

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL 
Sbjct: 290 QNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA 349

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           SFAR+NA+GFIETPYR+V DG VT ++ YL+AMEE++  +A
Sbjct: 350 SFARINAFGFIETPYRRVVDGVVTENIDYLTAMEEDDFVVA 390



 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/172 (37%), Positives = 93/172 (54%), Gaps = 6/172 (3%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K LY+ R+IP +G W
Sbjct: 1   MGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERTPEKN--SDKDLYSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SE+I S F  Y  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDIASEFAGYESIALTLEKDSIVSKD 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGIT 299
            A   +         V  +    ++++    +    L K  + K  K LG+ 
Sbjct: 119 DALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINKKLGLE 170


>gi|94469433|gb|ABF20207.1| RNA polymerase II second largest subunit [Schizophyllum radiatum]
          Length = 667

 Score =  231 bits (588), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 118/731 (16%), Positives = 207/731 (28%), Gaps = 103/731 (14%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   +M + +    +              I    +   +    
Sbjct: 1    GKKRLDLAGPLLAGLFRMLFRKMTKDVYRYLQKCVESNKDFNLNLAIKHHTISQGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQXKAGAAKAGVSQVLNRYTYASTLSHLRRCN----XPLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L+  A ++  G I  P            +   +   E  
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSXMACIS-VGSIXAPVIDFLQEWNLESLEENARSSEAT 175

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                  N           +LV                   D S +  V            
Sbjct: 176  FTKVFVNGVWMGVHRDPAKLVETIRRLRRKD---------DISQEVSVVRDIREKELRVY 226

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ RV     +      LL+       T         S       + GI+E +DA    
Sbjct: 227  TDAGRVCRPLFIVENQSLLLEKHHXHALT---QGAKWDSLV-----KQGIIELLDAEEEX 278

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +    +   +          Q++ +   +    +                PS  LG 
Sbjct: 279  TVMIAMTPEDLENSRMTPEERAAQQAEEEIDMTATKVAHTMANTHTWTHCEIHPSMILGX 338

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLGPEEIT 862
                     + +P               M  +   +F +  I                  
Sbjct: 339  -------CASIIPXXXXXXSPRNTYQSAMGKQAMGIFLTNFI------------------ 373

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                         +    +  +             +       +   +  + AI      
Sbjct: 374  -------------LRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 420

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    I+ R   D  +   SV     E   +   D  + +    
Sbjct: 421  NQEDSVIMNQSSIDRGLF-RSIYYRGYTDMEK--KSVGMMPTEEFEKPSRDNTLRMKHGT 477

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L +   I  G           K+  +  D                +E  QR     +
Sbjct: 478  YDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPD---------------SEELGQRTKNHTR 522

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                T     E    +++      D       ++++V V   R  Q GDK A RHG KG 
Sbjct: 523  RDVSTPLKSTESGIIDQVLLTTNED-----GKKLIRVRVRSTRIPQIGDKFASRHGQKGT 577

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            +      EDMPF   G   DIV+NP  +PSRM +G + E  L      +G +  +     
Sbjct: 578  IGITYRQEDMPFTAQGIVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTD 637

Query: 1160 KANGDISPLRS 1170
                 +S   +
Sbjct: 638  LTVEAVSKSLA 648


>gi|153958248|gb|ABS53414.1| RpoB [Bacteriovorax sp. VEN]
          Length = 344

 Score =  231 bits (588), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 163/347 (46%), Positives = 232/347 (66%), Gaps = 10/347 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIV++  +   +   SGVDIY L+K+QR+NQ+TC NQ+ LVK GD 
Sbjct: 1    FAKDDGKVIFVDSNRIVLQRNK--FEDGESGVDIYSLVKYQRTNQSTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            VR+ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+HIE F
Sbjct: 59   VRKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSVHIEAF 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLL 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +  +K   ++ +++++ P   
Sbjct: 239  RRDERIEIKAIQTSAILKIAEMLKGAKTTDKLVSEDGSTELLQKGADITGEVLAQIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
                 +Q  +++  +           + +  +  ++I K+  GD++P
Sbjct: 299  IGYLPLQ-AELEERLSEYFADIRNRINRVRQKTTDEIAKLHRGDELP 344


>gi|32455005|gb|AAP83182.1| RpoB [Streptococcus gallolyticus]
          Length = 239

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 135/311 (43%), Gaps = 72/311 (23%)

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            E S++      E   +D  DE  I+      +  +IL G+    G K       L   + 
Sbjct: 1    EESLAEIPNVGEEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIF 59

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             +  R           +V+     +    +     +      KI     GD++  GV  +
Sbjct: 60   GDKSR-----------EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNML 102

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+
Sbjct: 103  VRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNI 162

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLG A   LG  I + + D   + D+                            
Sbjct: 163  GQVMELHLGMAARNLGIHIATPVFDGATSEDLWDTVREAGMDSDAK-------------- 208

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                          T ++DG                           TGEPFD  V+VG 
Sbjct: 209  --------------TVLYDG--------------------------RTGEPFDNRVSVGI 228

Query: 1254 IYMLKLNHMVS 1264
            +YM+KL+HMV 
Sbjct: 229  MYMIKLHHMVD 239



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/93 (62%), Positives = 70/93 (75%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EE   +IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG
Sbjct: 1   EESLAEIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  DKSREVRDTSLRVPHGGDGVVRDVKIFTRANGD 93


>gi|154362169|gb|ABS80923.1| RNA polymerase beta subunit [Cupriavidus metallidurans]
 gi|154362173|gb|ABS80925.1| RNA polymerase beta subunit [Burkholderia sp. CIP 104848]
          Length = 236

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 133/234 (56%), Positives = 173/234 (73%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D +G+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDAEGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R+VIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQATRGGVVDYVDAMRVVIRVNDDE 234


>gi|121703239|ref|XP_001269884.1| DNA-directed rna polymerase III subunit [Aspergillus clavatus NRRL 1]
 gi|119398027|gb|EAW08458.1| DNA-directed rna polymerase III subunit [Aspergillus clavatus NRRL 1]
          Length = 1246

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 90/516 (17%), Positives = 168/516 (32%), Gaps = 98/516 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +   +  + A+      D+ D  +    
Sbjct: 811  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGQNAMVAVMSYSGYDIEDALVLNKG 870

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F R  +   +   +  ++++       ++   I    +         G+
Sbjct: 871  SVDRGFGRCQVF-RKYVTNLKSYSNGTKDRLNPPT--YENGAPIRKHALLESDGLAAVGE 927

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST          P          D           + Y     + +  +
Sbjct: 928  QVNAGEVYINKST----------PDQSHMSGIGSDAGRPIQYTPTPMTY----KLHDPAY 973

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+        +     ++VKV V   R  + GDK +                      
Sbjct: 974  IDKV-----MYSVQENENQLVKVLVRQTRRPEVGDKFS---------------------- 1006

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
                           SR                  G+K    I   +A+   + L    +
Sbjct: 1007 ---------------SR-----------------HGQKGVVGIIADQADMPFTDLGINPD 1034

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             ++       +++      ++       +G       F G   E  +  L     +  G+
Sbjct: 1035 IIMNPHGFPSRMTVGKMLELVAGKAGVLAGHHGYGTCFGGTPVEETSRTLIAHGFNYGGK 1094

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L  G+TGE     V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1095 EYLTSGITGEALPFYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1154

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1155 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1211

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                  P +  +L++E+ ++ ++  L+       +K
Sbjct: 1212 ---MTIPYAAKLLIQELMSMNVTARLKLDDEFPESK 1244



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 91/743 (12%), Positives = 207/743 (27%), Gaps = 128/743 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ +           L+   +S   I +       ++F       P   
Sbjct: 138 LVKQHIDSYNYFIEVQ----------LKKIVESSSTIRSDIDHNFYIKFTDIYVGSPCRA 187

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+ +    I          +  + +  + + 
Sbjct: 188 DEPQDASLDAFPSSVSPHECRLRDTTYAAPILVDFEYI----------RGRQRVIRRGVS 237

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 238 IGRMPIMLRSSKCVLANKTPSEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 297

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      II             KD ++V+ +     +P+   L
Sbjct: 298 TDPKKEIVQASVTSSSNERKSKSYII-----------LKKDKLYVKHNVLNEDIPIVILL 346

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
            A+G+ +E+ +      +    + DF      +  L  G       +D       I   +
Sbjct: 347 RAMGIHTEQEMLLLVAGVDSLYQDDFAINFEDSIKL--GIYTQQQALDWIGARIKINRKQ 404

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYV--AEDIVNGETGEIYIEAGDVIDEKSLEEI 336
                       + +  + I+   +  +        V      + +   D       + +
Sbjct: 405 MSYRRTHIQEAVEAIASVIISHIEVKNMNFRPKAVYVAHMARRVLMAKNDPSLVDDRDYL 464

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            +  +                +         K   D  ++I +V+   + +    A S+ 
Sbjct: 465 GNKRLEL----------AGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRAEAFDAWSVM 514

Query: 397 NFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           +       +     +     +  R  ++       + +   IA + ++  + +       
Sbjct: 515 SMHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRK 574

Query: 456 IDNLGNRRVRSVGEML-KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           +      +    G +   +        + +++         D   P   +        + 
Sbjct: 575 VSGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPIKNLVFMLGAEDIL 634

Query: 515 EFFCSSQLSQ---LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRIC 570
                 QL         +N        R    L     + R     E   ++  H+    
Sbjct: 635 -ALGGKQLYTPGSYTISINGTPIALTRRPKFFLNAFRRLRRMGRISEFVSIYINHHQCAV 693

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYI 627
              T +G     +  + +   +     +E       +  D      V YL   EE +  I
Sbjct: 694 HIATDDGRICRPLIVVENGKSLVTGEHLEKLRDGTMQFDDFLAQGLVEYLDVNEENDSLI 753

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A     +                        +    ++  P  V+   A LIP+  ++ S
Sbjct: 754 AIYEDRIT-----------------------DTTTHLEIEPFTVLGAVAGLIPYPHHNQS 790

Query: 688 NRVLMGCNMQRQAVPLLKAEAPF 710
            R    C M +QA+  + +    
Sbjct: 791 PRNTYQCAMGKQAIGAIASNQFL 813


>gi|307343470|emb|CBJ18652.1| RNA polymerase B subunit [Micromonospora sp. GUI27]
          Length = 203

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 88/203 (43%), Positives = 115/203 (56%), Gaps = 38/203 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++     +K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDASWKKQLRSIG---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A++ +    V+TPVFDGA EE I  +L     +        
Sbjct: 140  -------------------ADESEGDTNVATPVFDGAREEEIAGLLSSTLPNRDGNQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVG 1252
              G++ L+DG +GEP   P+ VG
Sbjct: 181  ASGKAQLFDGRSGEPLPDPIAVG 203


>gi|262193259|gb|ACY30632.1| RNA polymerase beta subunit [Xanthomonas axonopodis pv. citri]
          Length = 241

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 144/241 (59%), Positives = 179/241 (74%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ LINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+
Sbjct: 1   TPQKLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGR+C  ET EG NIGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLS
Sbjct: 61  RDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLS 120

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A+EE    IAQAN+  D     TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L
Sbjct: 121 AIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAAL 180

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           +PFLE+DD+NR LMG NMQRQAVP L+++ P VGTG++  VA+ SG  + A R G++EQ+
Sbjct: 181 VPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGIKRAVARDSGVTVNALRGGVIEQI 240

Query: 739 D 739
           D
Sbjct: 241 D 241


>gi|254055149|gb|ACT64174.1| RpoB [Pseudomonas sp. R11-23-07]
 gi|254055151|gb|ACT64175.1| RpoB [Pseudomonas sp. R11-45-07]
 gi|254055153|gb|ACT64176.1| RpoB [Pseudomonas sp. R2-7-07]
 gi|254055155|gb|ACT64177.1| RpoB [Pseudomonas sp. R4-35-07]
 gi|254055157|gb|ACT64178.1| RpoB [Pseudomonas sp. R4-34-07]
 gi|254055159|gb|ACT64179.1| RpoB [Pseudomonas sp. R14-24-07]
 gi|254055161|gb|ACT64180.1| RpoB [Pseudomonas sp. R5-89-07]
 gi|254055163|gb|ACT64181.1| RpoB [Pseudomonas sp. R5-90-07]
 gi|254055165|gb|ACT64182.1| RpoB [Pseudomonas sp. L1-11-07]
          Length = 231

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 136/231 (58%), Positives = 179/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++     +
Sbjct: 121 INSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|307343452|emb|CBJ18643.1| RNA polymerase B subunit [Micromonospora sp. GUI3]
          Length = 203

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 89/203 (43%), Positives = 116/203 (57%), Gaps = 38/203 (18%)

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
               + GD++PPGV  +V+V+VA KR IQ GDK+AGRHGNKG++S+ILP EDMPFL+DGTP
Sbjct: 31   FSREDGDELPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVISKILPIEDMPFLEDGTP 90

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
            VDIVLNPLGVPSRMN+GQ+ ETHLGW     G K++    D+K                 
Sbjct: 91   VDIVLNPLGVPSRMNIGQVLETHLGWVAK-TGWKVEGDDADWKRQLRSID---------- 139

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES------ 1231
                               A + +    V+TPVFDGA EE I+ +L     +        
Sbjct: 140  -------------------AHESEGDTNVATPVFDGAREEEISGLLESTLPNRDGKQLIG 180

Query: 1232 --GQSILYDGLTGEPFDRPVTVG 1252
              G++ L+DG +GEP   P+ VG
Sbjct: 181  RTGKAQLFDGRSGEPLPDPIAVG 203


>gi|269912616|emb|CAY86088.1| RNA polymerase beta subunit [Gluconacetobacter xylinus]
          Length = 264

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 121/267 (45%), Positives = 160/267 (59%), Gaps = 28/267 (10%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------- 221
           SGK L+A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL             
Sbjct: 1   SGKFLFAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGAASEAARAAKA 60

Query: 222 ------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                       GMD +EILS FY K+ +++    W     A D   G K+   L+D  T
Sbjct: 61  AEGGDVESMEIQGMDPDEILSYFYGKVEFTKTEKGWARRFDA-DAFRGQKLLEPLIDAQT 119

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE+V     KLT+ +++ + E   K + +    L G ++A DIVN  TGEIY EAGD + 
Sbjct: 120 GEEVAPVDAKLTARMVRKIAET-TKEVLVGPAGLIGRFIASDIVNEHTGEIYAEAGDELT 178

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E+ LEE+    +  +  L VD+ N   +IRNTL  DKN  R++AL DIYRVMRPG+  T 
Sbjct: 179 EQKLEELEGEGLTTLTTLAVDAAN-GPWIRNTLAVDKNASREEALTDIYRVMRPGEPPTP 237

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKM 416
             AE+MF+ LFFD D+YDLS VGRVKM
Sbjct: 238 ETAEAMFSGLFFDPDRYDLSAVGRVKM 264


>gi|56694356|gb|AAW22918.1| RNA polymerase II second largest subunit [Sequoiadendron giganteum]
          Length = 549

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 78/462 (16%), Positives = 140/462 (30%), Gaps = 80/462 (17%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 168  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 224

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 225  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 283

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R+ ++ +E+     R+          +          G           K
Sbjct: 284  FFRSYRDEEKRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 343

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  D+   +  +  K    TS    E    +++      D
Sbjct: 344  TTPIAQ-----------------DDSAGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 386

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 387  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 441

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 442  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 499

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 500  ---------------------------------------------YNGHT----GR---K 507

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                + +G  Y  +L HMV DK+++R  G   ++T+QP  G+
Sbjct: 508  LSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGR 549



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 69/453 (15%), Positives = 131/453 (28%), Gaps = 102/453 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +    GV R 
Sbjct: 19  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 78

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVT 611
               E+R ++  +     P    E   + +     +  + +   G+ E            
Sbjct: 79  IRLRELR-LYTDYGRCSRPLFVVENQRLKIRKQDINNLQASREDGWHEL--------ITQ 129

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+              +LV  R   E            +  P  +
Sbjct: 130 GCIEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLI 177

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                           R
Sbjct: 178 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------R 217

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 218 MDTLAYV-----------------------------------LYYPQKPLV--------- 233

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N +VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 234 -TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 292

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E        +   +       +D+ G+   G  V+  D+++GK TP  +   
Sbjct: 293 KRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD- 351

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   +         RD S  +    SG V
Sbjct: 352 --------SAGQVSKYTKRDQSTSLRHSESGMV 376


>gi|145342295|gb|ABP64844.1| RpoB [Bacillus sp. FSL_H7-308]
          Length = 232

 Score =  230 bits (587), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/207 (40%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++ PGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 79   LDVKVFNREDGDELAPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D        
Sbjct: 139  PDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAARNLGLHMASPVFDGATEED-------- 190

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                 V+D  +E           +    
Sbjct: 191  -------------------------------------VWDTIEEA---------GMASDA 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            +++LYDG TGEPFD  V+VG +YMLKL
Sbjct: 205  KTVLYDGRTGEPFDTRVSVGVMYMLKL 231



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE LKN+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALKNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|312204324|gb|ADQ47479.1| RNA polymerase II second largest subunit [Cyanodermella viridula]
          Length = 714

 Score =  230 bits (586), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 120/809 (14%), Positives = 227/809 (28%), Gaps = 124/809 (15%)

Query: 474  QYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    R+ + +    +              + +  + + +     +            
Sbjct: 1    LFRTLYRRLTQDVAKYLQKCVETAREFNLAIGVKSTTLTNGLKYSLATGNWGDQKNAAKA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTSFARVNAYG----FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
              GLV +L+    V+        + T +    + ++  +     + +    ++      +
Sbjct: 117  ACGLVKNLSLMCYVSVGNVQAAPLITEFMGSRNMQLLEEYEGRMSNQVTKVFVNGVWVGV 176

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
              + +     V        I      + D  D   K        + P    DD+      
Sbjct: 177  HNEPTHLVREVMALRRQGVIDTETSLVRDIRDKEFKIFTDAGRVMRPLFVVDDNQNSSNR 236

Query: 694  CNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSV 748
             N+   ++ +  L+ +            A+         + G VE +DA      +I   
Sbjct: 237  GNLVLTKEMIQKLEEDKEMSDELSPEERAERYYGWTGLLKDGAVEYIDAEEEETAMIVMT 296

Query: 749  EGDLDPSTSGVDIY-RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
              +L  S+  +  Y              +   P+   G            P+  LG    
Sbjct: 297  PEELLASSQRLAGYAEPDANLNEPHARYMP--PI---GTVAHTWTHCEIHPAMILG---- 347

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P   +                                              
Sbjct: 348  ---ICASIIPXPDHXXXXXXXXXXXXXXXXXXXXXXXXX-XXXXXXXXXXXXXXXXXXXX 403

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                            +             +       +   +  + AI      +  D+
Sbjct: 404  XXXXXXXXXXXXXXXNILYYPQKPLAXTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDS 463

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  ++  +R      E IE   +    + + L    Y +L 
Sbjct: 464  VIMNQSSIDRGLF-RSLFYRAYVESEKRVGLSSTETIE---KPLRHQTLRLKHGTYDKLD 519

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D               + E  QR     K    T
Sbjct: 520  DDGIVAPGVRVSGEDIIIGKTAPMNVD---------------ESEMGQRTKIMSKRDAST 564

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E+   +K+      D       +  KV +   +  Q GDK A RHG KG +    
Sbjct: 565  PLRSTENGIVDKVLVTTNAD-----GAKFCKVRMRTTKVPQIGDKFASRHGQKGTIGITY 619

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +  + E  L       G +             
Sbjct: 620  RMEDMPFSSEGIVPDLIINPHAIPSRMTIAHLVECLLSKVGALTGMEGD----------- 668

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     + I++MLR
Sbjct: 669  ------------------------------------------ATP-FTSVTVDQISTMLR 685

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGY 1253
             A     G  ++Y G TG+     V +G 
Sbjct: 686  EAGYQSRGFEVMYHGHTGKKLRGQVFLGP 714



 Score =  104 bits (258), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 79/607 (13%), Positives = 158/607 (26%), Gaps = 87/607 (14%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL- 446
            F++A  + +    +  KY L   G                + + +    + +  L    
Sbjct: 26  EFNLAIGVKSTTLTNGLKYSL-ATGNWGDQKNAAKAKAGVSQVLNRYTFASTLSHLRRTN 84

Query: 447 ----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
               R+GK       +  +  +    E  + Q    +  +       + +V    ++ + 
Sbjct: 85  TPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGNVQAAPLITEF 144

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNS---LSRITHTRRLSALGQGGVARARAGVEMR 559
           + +    +    E   S+Q++++  +       +  TH  R     +           +R
Sbjct: 145 MGSRNMQLLEEYEGRMSNQVTKVFVNGVWVGVHNEPTHLVREVMALRRQGVIDTETSLVR 204

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND------ 613
           D+    +     A         +  +  S  R N     E   +   D +++++      
Sbjct: 205 DIRDKEFKIFTDAGRVMRPLFVVDDNQNSSNRGNLVLTKEMIQKLEEDKEMSDELSPEER 264

Query: 614 ---------------VVYLSAMEEENRYIAQANSSLDEDGSFT--------EELVFCRCA 650
                          V Y+ A EEE   I      L                        
Sbjct: 265 AERYYGWTGLLKDGAVEYIDAEEEETAMIVMTPEELLASSQRLAGYAEPDANLNEPHARY 324

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
              I          +  P  ++ I AS+IP  ++                          
Sbjct: 325 MPPIGTVAHTWTHCEIHPAMILGICASIIPXPDHXXXXXXXXXXXXXXXXXXXXXXXXXX 384

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                                                                       
Sbjct: 385 XX---------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 417

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q+PL                      +L  G+N +VA   + GYN EDS++++
Sbjct: 418 XNILYYPQKPL----------AXTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMN 467

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEEGLKNIDECGIICVG 885
           +  +   +F S+    +    +   L   E            +       +D+ GI+  G
Sbjct: 468 QSSIDRGLFRSLFYRAYVESEKRVGLSSTETIEKPLRHQTLRLKHGTYDKLDDDGIVAPG 527

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             V+  DI++GK  P         ++        K +  RD S  + S  +G V  V + 
Sbjct: 528 VRVSGEDIIIGKTAPMNVDESEMGQRT-------KIMSKRDASTPLRSTENGIVDKVLVT 580

Query: 946 NRHGIDK 952
                 K
Sbjct: 581 TNADGAK 587


>gi|154362181|gb|ABS80929.1| RNA polymerase beta subunit [Cupriavidus gilardii]
          Length = 236

 Score =  230 bits (586), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 134/234 (57%), Positives = 172/234 (73%), Gaps = 2/234 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV +GK+T+ V YLSA+EE    +AQAN+++D +G+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVENGKLTDQVDYLSAIEEGKYVVAQANATVDAEGN 120

Query: 640 FTEELVFCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
             +ELV  R     E  LV  +++ +ID +P Q+VS AASL+PFLE+DD+NR L G NMQ
Sbjct: 121 LIDELVSAREGSERETRLVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALKGANMQ 180

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           RQAVP L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA RIVIR  + +
Sbjct: 181 RQAVPCLRPDKPLVGTGIERTVAVDSGTAVQATRGGVVDYVDANRIVIRVNDDE 234


>gi|153958269|gb|ABS53424.1| RpoB [Bacteriovorax sp. HA5]
          Length = 345

 Score =  230 bits (586), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 159/346 (45%), Positives = 228/346 (65%), Gaps = 10/346 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+ +G V  VD+ RIV++  +   +   SGVD+Y L+K+QR+NQNTC NQR LVK GD 
Sbjct: 3    FAEESGRVIFVDSNRIVLQRDK--FEEGESGVDVYELVKYQRTNQNTCCNQRALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDIFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +   +  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCSRSKEIIESETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   ++S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIAEMLNGAKTTDKLVSEDGSTELLAKGAEVTSEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                 ++   ++  +           + +  +  + I K+  GD++
Sbjct: 301  IGYLPLE-ASLEERLSEYFADIRNRINRVRQKATDDIAKLHRGDEL 345


>gi|153958222|gb|ABS53401.1| RpoB [Bacteriovorax sp. PS52B]
          Length = 352

 Score =  230 bits (586), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 10/354 (2%)

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E VVA+ S A + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT 
Sbjct: 2    ERVVARDSRAVLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTS 59

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             NQ+ LVK GD V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE +++
Sbjct: 60   NNQKALVKEGDIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLA 119

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +D+FTS+HIE FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILV
Sbjct: 120  QDIFTSVHIEAFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILV 179

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   R
Sbjct: 180  GKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCAR 239

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVL 1008
            S  +  ++  LL RD+  E   +  +   ++ E+L G              +   K   +
Sbjct: 240  SKEIIEQETTLLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEV 299

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            + + +S  P        +Q  +++  +           + +  +  ++I K+  
Sbjct: 300  TYENLSAIPFELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHR 352


>gi|123979406|gb|ABM81528.1| RNA polymerase II second largest subunit [Hypogymnia physodes]
          Length = 667

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 111/732 (15%), Positives = 212/732 (28%), Gaps = 90/732 (12%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
             ++      +  D +     V        I      + D  D   K          P   
Sbjct: 178  IFVNGVWVGVHRDSAHLVGTVQNLRRRGLISHEVSLVRDKRDREFKVFTDAGRVCRPLFV 237

Query: 684  NDDSNRVLMGCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             D+  R     N+         L      +  T  +       G   + K  G+VE VDA
Sbjct: 238  IDNDPRSSNRGNLVLTKEHVQELELDRENWATTEPDVREEADMGWQGLVKE-GVVEYVDA 296

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +       +        +N +  +N+R    +             PS 
Sbjct: 297  EEEETIMIVMTPEDLEISRQLQAGFAMPEANPDE-LNKRVKAPMNPTAHTWTHCEIHPSM 355

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +                      
Sbjct: 356  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMGXXXXXXXXXXXXXXXXXXXXX 408

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                                         +   +  + A     
Sbjct: 409  XXXXXXXXXXX-----------------------------XXXXELPAGQNAIGANACYS 439

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L  
Sbjct: 440  GYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKH 495

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K+  ++ D      R++          ++     
Sbjct: 496  GTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENG 555

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q   S                         LR VKV +   +  Q GDK A RHG K
Sbjct: 556  IVDQVLLS--------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 595

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 596  GTIGITYRQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPF 655

Query: 1158 DYKANGDISPLR 1169
                   +S L 
Sbjct: 656  TEVTVDSVSRLL 667



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 50/383 (13%), Positives = 108/383 (28%), Gaps = 38/383 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + +      NK  KD    + + +       F++  ++ +    +  +Y L   G  
Sbjct: 8   GPLLASLFRGTFNKLTKDVYKYLQKCVENN--KEFNMTLAVKSTHLTNGLRYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     V      N + +         +A   F     
Sbjct: 125 TPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATKIFVNGVW 184

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +  + + RR   +  +  + R +   E        R   P       P  
Sbjct: 185 VGVHRDSAHLVGTVQNLRRRGLISHEVSLVRDKRDREFKVFTDAGRVCRPLFVIDNDPRS 244

Query: 574 TSEGHNIGLVSSLTSF--ARVNA----YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           ++ G+ +     +      R N         E              V Y+ A EEE   I
Sbjct: 245 SNRGNLVLTKEHVQELELDRENWATTEPDVREEADMGWQGLVKEGVVEYVDAEEEETIMI 304

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EKIDFIDASPKQVVSIAASLI 679
                 L+                +E+                  +  P  ++ I AS+I
Sbjct: 305 VMTPEDLEISRQLQAGFAMPEANPDELNKRVKAPMNPTAHTWTHCEIHPSMILGICASII 364

Query: 680 PFLENDDSNRVLMGCNMQRQAVP 702
           PF +++ S R      M +QA+ 
Sbjct: 365 PFPDHNQSPRNTYQSAMGKQAMG 387


>gi|153958218|gb|ABS53399.1| RpoB [Bacteriovorax sp. PS21S]
          Length = 351

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 167/354 (47%), Positives = 230/354 (64%), Gaps = 10/354 (2%)

Query: 716  ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
            E VVA+ S A + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT 
Sbjct: 1    ERVVARDSRAVLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTS 58

Query: 776  VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             NQ+ LVK GD V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE +++
Sbjct: 59   NNQKALVKEGDIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLA 118

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            +D+FTS+HIE FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILV
Sbjct: 119  QDIFTSVHIEAFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILV 178

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            GKITPKGE+ ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   R
Sbjct: 179  GKITPKGETQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCAR 238

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVL 1008
            S  +  ++  LL RD+  E   +  +   ++ E+L G              +   K   +
Sbjct: 239  SKEIIEQETTLLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEV 298

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            + + +S  P        +Q  +++  +           + +  +  ++I K+  
Sbjct: 299  TYENLSAIPFELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHR 351


>gi|153958285|gb|ABS53432.1| RpoB [Bacteriovorax sp. GSL4A]
 gi|153958287|gb|ABS53433.1| RpoB [Bacteriovorax sp. GSL4D]
          Length = 338

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 161/341 (47%), Positives = 225/341 (65%), Gaps = 10/341 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKHSGRVIFVDSNRIVIQRNK--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 59   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+ ++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGAELTGEVLASVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
               F ++   ++  +           + +  +  ++I K+ 
Sbjct: 299  IGYFPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKLH 338


>gi|40643899|emb|CAD89688.1| RNA polymerase II, second largest subunit [Ilex x meserveae]
          Length = 356

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/421 (17%), Positives = 130/421 (30%), Gaps = 77/421 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 13   YQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACHSGYNQEDSLIMNQS 72

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ ++  ++ +E      ++          +          G 
Sbjct: 73   SIDRGFF-RSIFFRSYRDEEKKMGTLVKEDFGCPNKEDTMGMRHGSYDRLDDDGFAPPGT 131

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                       +T ++                  D+   +     +  + TS    E   
Sbjct: 132  KVSGDDVIIGXTTPIAQ-----------------DDAQGQASRYTRRDHSTSLRHSEHGI 174

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG  G V      ED+P+  
Sbjct: 175  VDQVLLTTNADGL-----RFVKVRMRSVRLPQIGDKFSSRHGQXGTVGMTYNQEDLPWTI 229

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS       
Sbjct: 230  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCG 289

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
              +     T                                                +G 
Sbjct: 290  YQMRGFETT-----------------------------------------------YNGH 302

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +    G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 303  T----GR---QIPAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 355

Query: 1294 L 1294
             
Sbjct: 356  F 356



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 57/184 (30%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                      L  G N +VA     G
Sbjct: 11  TNYQLRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACHSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +    F SI    +    +      +E        D   +       
Sbjct: 61  YNQEDSLIMNQSSIDRGFFRSIFFRSYRDEEKKMGTLVKEDFGCPNKEDTMGMRHGSYDR 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G    G +V+  D+++G  TP  +           A         RD S  +    
Sbjct: 121 LDDDGFAPPGTKVSGDDVIIGXTTPIAQDD---------AQGQASRYTRRDHSTSLRHSE 171

Query: 936 SGTV 939
            G V
Sbjct: 172 HGIV 175


>gi|71725905|gb|AAZ39071.1| DNA-directed RNA polymerase beta [Exiguobacterium sibiricum]
          Length = 359

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 162/258 (62%), Positives = 204/258 (79%), Gaps = 1/258 (0%)

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLD 753
           NMQRQAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +
Sbjct: 1   NMQRQAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGN 60

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                +D Y++ KF RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV
Sbjct: 61  IVQGELDRYKIQKFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLV 120

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            FM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L
Sbjct: 121 GFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDAL 180

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           KN+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP 
Sbjct: 181 KNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPH 240

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G ++DV+IF+R   D
Sbjct: 241 GGDGIILDVKIFDRDNGD 258



 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 71/218 (32%), Positives = 109/218 (50%), Gaps = 4/218 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 142  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 201

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 202  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 261

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++S ILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 262  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISCILPEEDMPYMPDGTPIDIMLNPLGV 321

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            PSRMN+GQ+ E HLG A   LG K+ S + D     D+
Sbjct: 322  PSRMNIGQLLELHLGMAARQLGIKVASPVFDGAREEDV 359


>gi|312204314|gb|ADQ47474.1| RNA polymerase II second largest subunit [Cryptodiscus foveolaris]
          Length = 704

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 111/796 (13%), Positives = 219/796 (27%), Gaps = 115/796 (14%)

Query: 471  LKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
                +R    R+ + I   +               + +  + + +     +         
Sbjct: 2    FGELFRTLYARLTKDIFNYLKKCVETGKEFNLTLGVKSNTLTNGLKYSLATGNWGEQKKA 61

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 62   SSSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 117

Query: 576  EGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     +   + G     +    + +V  +   +        ++    + 
Sbjct: 118  EGQACGLVKNLALMCNITVGSPGDPIIDFMVQRNMEVLEEFEPMRTPNATKIFVNGTWTG 177

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVL 691
            +  D       +      + I V    + D  D   K          P F+ ++D     
Sbjct: 178  IHRDPIHLVRTIQSLRRRKLIDVETSLVHDIRDREFKIFTDAGRVSRPVFVIDNDDRSTS 237

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             G  +  + +     +   +    E       G       +G VE +DA       +   
Sbjct: 238  KGNLVLTREMIQKLDDDKDLDLDDEEQKKHFFG-WNGLLTSGAVEYLDAEEEETVMIAMT 296

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
             +       +    +     +      +P V               PS  LG       +
Sbjct: 297  PEDLEISRQVQAGYEIDEGPRELSARIKPKVNPTQHT--WTHCEIHPSMILG-------I 347

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N       S   +                                     
Sbjct: 348  CASIIPFPDHNQVRQT-YSLFSLQAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 406

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                                              +   +  + AI      +  D+ +  
Sbjct: 407  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXLKFRELPAGQNAIVAIACYSGYNQEDSVIFN 466

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--- 988
             S +   +    +F R  +++ +R   +     E   +    + + L    Y +L +   
Sbjct: 467  QSSIDRGLF-RSLFYRTYVEQEKR---IGMSLAEQFEKPLRSDTLRLKHGTYEKLDDDGI 522

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  ++ D      R++          ++     +          
Sbjct: 523  IAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRSTENGIV--------- 573

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                  +K+      D +     + VKV +   +  Q GDK A RHG KG        ED
Sbjct: 574  ------DKVLLTTNADGL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTCGITYRQED 622

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   D+++NP  +PSRM +  + E  L       G +                 
Sbjct: 623  MPFTAEGLTPDLIINPHAIPSRMTIAHLVECLLSKVGAIRGAEGD--------------- 667

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     ++++ +LR    
Sbjct: 668  --------------------------------------ATP-FTEVTVDSVSRLLREQGY 688

Query: 1229 DESGQSILYDGLTGEP 1244
               G  I+Y+G +G+ 
Sbjct: 689  QSRGFEIMYNGHSGKK 704


>gi|153958289|gb|ABS53434.1| RpoB [Bacteriovorax sp. GSL4C]
          Length = 339

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 161/341 (47%), Positives = 224/341 (65%), Gaps = 10/341 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 2    FAKHSGRVIFVDSNRIVIQRNK--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 59

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 60   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 119

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 120  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 179

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 180  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 239

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+ ++++  P   
Sbjct: 240  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGAELTGEVLASVPFEL 299

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
               F ++   ++  +           + +  +  ++I K  
Sbjct: 300  IGYFPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHH 339


>gi|575403|emb|CAA51302.1| RNA-polymerase beta subunit [Streptomyces griseus]
          Length = 177

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 62/166 (37%), Positives = 90/166 (54%), Gaps = 20/166 (12%)

Query: 13  VRKFFGKNPEIIDIPDLIEVQKASYDHFLM-----------MNIAPDERPNEGLQAAFKS 61
           +R  F K  E +++P+L+ +Q  S+D  L            ++   D     GL+  F+ 
Sbjct: 21  LRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALDSGQDVPTKSGLEEIFEE 80

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  FSG+  L F  + F+PPK  +D+C  RD T+A PL +T                
Sbjct: 81  LSPIEDFSGSMSLTFRDHRFEPPKNSIDECKERDFTFAAPLFVTAEFT---------NNE 131

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDH 167
             +IK Q+++MGD PLMT  GTFVI G +R+VVSQL RSPG++FD 
Sbjct: 132 TGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDS 177


>gi|153958234|gb|ABS53407.1| RpoB [Bacteriovorax sp. NZ7]
          Length = 340

 Score =  229 bits (585), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 166/343 (48%), Positives = 225/343 (65%), Gaps = 10/343 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +       SGVDIY+L K+QR+NQNTC NQ+ LV  GD 
Sbjct: 1    FAKENGKVIFVDSNRIVIQRDK--FADGESGVDIYKLTKYQRTNQNTCNNQKALVTEGDL 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE +++ED+FTS+HIE F
Sbjct: 59   VKKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISENLLAEDIFTSVHIEAF 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E  ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  ETEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +   +  LL
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIETETTLL 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K T L+S++++  P   
Sbjct: 239  RRDERIEIKSIQTSAILKIGDMLKGATTTDKLVSEDGSTELLAKGTSLTSEVLAGVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 +Q E ++  +           + +  +  ++I K+  G
Sbjct: 299  IGYLPLQPE-LEEKLSEYFADIRNRINRVRQKTTDEIAKLHRG 340


>gi|111278811|gb|ABH09103.1| RNA polymerase II second largest subunit [Exophiala pisciphila]
          Length = 688

 Score =  229 bits (584), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 123/757 (16%), Positives = 222/757 (29%), Gaps = 130/757 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +A     + R     + R +H TH+G +CPAET EG   
Sbjct: 53   GVSQVLNRYTFASTLSHLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC 108

Query: 581  GLVSSLTSF--ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDE 636
            GLV +L+    A  +        Y      +   D       +    ++        L +
Sbjct: 109  GLVKNLSLMSLATNSYETGPLLSYILSKHVEPLEDWEPRLNPQATKIFVDGVWFAVVLRD 168

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGC 694
                 ++L   R  G          D  +   K        + P    END S+      
Sbjct: 169  PKRLVDDLRKLRRKGVFDPHVSLIWDIREKEFKVSGDSGRLVRPLFVVENDPSSENRGNL 228

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             + ++ +  L         G+E      +        +G++E +DA       +    + 
Sbjct: 229  VLSKEHIGKLDDAVYQHQNGIEFSEEHPAYGWRELTSSGVIEYMDAEEEETAMIIMTPEA 288

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              +      +        +      PL+               PS  LG       +  +
Sbjct: 289  L-ADSKARSMGMIIEQENDPLRRNDPLLNPHSHTL--THCELHPSMILG-------VCAS 338

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N          M  + +   I +  F+           E   +I    ++ L 
Sbjct: 339  IIPFPDHNQSPXXXXXXXMGKQAMG--IFLTNFDQ--------RMETMANILYYPQKPLA 388

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                                   +       +   +  + AI      +  D+ +   S 
Sbjct: 389  R-------------------TMAMDYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 429

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D  +   ++    +E   +    + + L    Y ++ E   +  
Sbjct: 430  IDRGLF-RSLFYRAYSDSEK---AIGHSVMEQFEKPTRSDTLRLKHGTYDKIDEDGIVAP 485

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D                +E  QR  + +K    T     E 
Sbjct: 486  GVRVSGEDIIMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTES 530

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++              R  KV V   +  Q GDK A RHG KG +      EDMPF
Sbjct: 531  GIVDQVML-----TTTAEGNRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRHEDMPF 585

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             ++G   DI++NP  +PSRM +  + E  L       G +  +          +S L   
Sbjct: 586  TREGIVPDIIINPHAIPSRMTIAHLIECQLSKVASLRGDEGDATPFTKVTVTQVSDLLRR 645

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
            +                                                          +
Sbjct: 646  MGYQSRGFEVM-----------------------------------------------YN 658

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
            G +    G         V +G  Y  +L HMV DK++
Sbjct: 659  GHT----GR---KLVAQVFLGPTYYQRLRHMVDDKIH 688



 Score =  116 bits (290), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 85/606 (14%), Positives = 159/606 (26%), Gaps = 109/606 (17%)

Query: 375 LDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            D YR MR   + +      + F               G      +L+       + + +
Sbjct: 1   KDFYRYMRKRVEANQPINIMAGFKHPIITQGLKYSLATGNWGDQKKLDKAKAGVSQVLNR 60

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R GK       +  +       E  + Q    +  +      
Sbjct: 61  YTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQACGLVKNLSLMSLA 120

Query: 489 RISSVDIDSVM---------PQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             S      +           +D        +             L +    +  +   R
Sbjct: 121 TNSYETGPLLSYILSKHVEPLEDWEPRLNPQATKIFVDGVWFAVVLRDPKRLVDDLRKLR 180

Query: 540 RLSALGQGGVARARAGVEM--------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA- 590
           R                +         R V P       P+  + G+ +     +     
Sbjct: 181 RKGVFDPHVSLIWDIREKEFKVSGDSGRLVRPLFVVENDPSSENRGNLVLSKEHIGKLDD 240

Query: 591 -----RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI-----AQANSSLDEDGSF 640
                +       E P     +   +  + Y+ A EEE   I     A A+S     G  
Sbjct: 241 AVYQHQNGIEFSEEHPAYGWRELTSSGVIEYMDAEEEETAMIIMTPEALADSKARSMGMI 300

Query: 641 TE-ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            E E    R     +      +   +  P  ++ + AS+IPF +++ S        M +Q
Sbjct: 301 IEQENDPLRRNDPLLNPHSHTLTHCELHPSMILGVCASIIPFPDHNQSPXXXXXXXMGKQ 360

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           A+ +                                                   + + +
Sbjct: 361 AMGIFLTNF-----------------------------------------DQRMETMANI 379

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
             Y      R+     +                           +L  G+N +VA   + 
Sbjct: 380 LYYPQKPLARTMAMDYL------------------------RFRELPAGQNAIVAIACYS 415

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLK 874
           GYN EDS+++++  +   +F S+    +    +       E        D   +      
Sbjct: 416 GYNQEDSVIMNQSSIDRGLFRSLFYRAYSDSEKAIGHSVMEQFEKPTRSDTLRLKHGTYD 475

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            IDE GI+  G  V+  DI++GK  P         E+L +        DV        SG
Sbjct: 476 KIDEDGIVAPGVRVSGEDIIMGKTAPMAPDA----EELGQRQKQHIKRDVSTPLRSTESG 531

Query: 935 VSGTVV 940
           +   V+
Sbjct: 532 IVDQVM 537


>gi|71725914|gb|AAZ39075.1| DNA-directed RNA polymerase beta [Exiguobacterium acetylicum]
          Length = 359

 Score =  229 bits (584), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 168/309 (54%), Positives = 221/309 (71%), Gaps = 2/309 (0%)

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLD 753
            NMQRQAVPLL  E+P VGTGME V AK SGAA+VAK AGI E+V A  I++R + E D +
Sbjct: 1    NMQRQAVPLLNPESPIVGTGMEYVSAKDSGAAVVAKHAGIAERVTAREILVRRTTEVDGN 60

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                 +D Y++ KF RSNQ TC NQ+P++K GD V + +I+ADGPS D G+LALGRN+LV
Sbjct: 61   IVEGELDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLV 120

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             FM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L
Sbjct: 121  GFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDAL 180

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP 
Sbjct: 181  KNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPH 240

Query: 934  GVSGTVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            G  G ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  
Sbjct: 241  GGDGIILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPE 300

Query: 993  QNAVSGPKG 1001
            ++    P G
Sbjct: 301  EDMPYMPDG 309



 Score =  187 bits (476), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 72/218 (33%), Positives = 110/218 (50%), Gaps = 4/218 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 142  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 201

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 202  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 261

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 262  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 321

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            PSRMN+GQ+ E HLG A   LG K+ S + D     D+
Sbjct: 322  PSRMNIGQLLELHLGMAARQLGIKVASPVFDGAREEDV 359


>gi|117675891|emb|CAL69216.1| RNA polymerase subunit B [Frigoribacterium faeni]
          Length = 391

 Score =  229 bits (584), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 141/296 (47%), Positives = 198/296 (66%), Gaps = 15/296 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            +     A I  TL  D    +++AL DIYR +RPG+      A ++ +  +F+  +YDL
Sbjct: 96  TEKFKGFASIEATLEKDAILTKEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDL 155

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TI 453
           + VGR K+N +L +D P     +  +DI+A IK LV L   +                 +
Sbjct: 156 AKVGRYKINRKLGIDAPLGDSVLTVDDIVATIKYLVSLHAEQKTIDGTRDGQAVELRLDV 215

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+
Sbjct: 216 DDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAI 275

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP E
Sbjct: 276 KEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIE 335

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           T EG NIGL+ SL SFAR+N++GFIETPYR+V  G V+  + YL+A EE++  +AQ
Sbjct: 336 TPEGPNIGLIGSLASFARINSFGFIETPYRRVVKGNVSTTIDYLTASEEDDFVVAQ 391



 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 64/172 (37%), Positives = 91/172 (52%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+    +   S K +Y+ R+IP +G W
Sbjct: 1   MGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERASDKT--SDKDIYSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SEEI   F  +  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEITEKFKGFASIEATLEKDAILTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 162


>gi|325118125|emb|CBZ53676.1| DNA-directed RNA polymerase,related [Neospora caninum Liverpool]
          Length = 1366

 Score =  229 bits (584), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 76/395 (19%), Positives = 130/395 (32%), Gaps = 81/395 (20%)

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRS-QWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
             G  +           V   +L+ E       +      E V   ++     Y  S +  
Sbjct: 1034 KGAVSRRFEALEDDGVVRVGELLEEDQVYVHKFSPTNTREHVSDPLQLDNAFYAPSFARY 1093

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +    + +E++   D       R  KV +   R  + GDK +                  
Sbjct: 1094 KTVVPSYVERVICTD--NSDGCRTYKVIMRQTRLPELGDKFS------------------ 1133

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
                               SR                  G+K    +     +   +   
Sbjct: 1134 -------------------SR-----------------HGQKGVVGLIAPAEDLPFAESG 1157

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
               + ++       +++      ++      + G       F G   + +  +L      
Sbjct: 1158 WCPDLIMNPHGFPSRMTVGKMMELIAGKSALQIGACQYGTAFGGVSVDTLAEILASHGFH 1217

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNR 1289
             SG+  L  G+TGE     V  G IY  KL HMV DK++AR  G   L+T+QP  G++  
Sbjct: 1218 YSGKEYLTSGITGEALQTYVFAGPIYYQKLKHMVQDKIHARGRGPRQLLTRQPTEGRAKE 1277

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA--------------- 1334
            GG RLGEME  C+ AYG++ +L E L + SD       V+E+ V                
Sbjct: 1278 GGLRLGEMERDCLVAYGSSALLMERLMLSSD-------VFEACVCATCGLMGYEGWCPYC 1330

Query: 1335 --GNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
              G +      P +  +L +E+ ++ +   L    
Sbjct: 1331 KTGKNVAPIRMPYACKLLFQELMSMNVCPRLHIKE 1365



 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 129/971 (13%), Positives = 275/971 (28%), Gaps = 194/971 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
            L+     SY+ F+   +    R         KS         +  +EF++     P++  
Sbjct: 203  LVHQHIESYNFFVTTELQNILRAPS--NRLVKS-----DIDPSFFIEFLNISVGTPRYEE 255

Query: 87   -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                       C  R++TYA P+ +              +K  + I+ +++ +G +P+M 
Sbjct: 256  GMILQRLTPRICRTREITYAAPVFVDAEY----------SKGDEIIRRKNVEIGSIPVML 305

Query: 140  ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLS 175
                                      G F++KG +++++ Q   S          +    
Sbjct: 306  RSQVCVLHGKDPAAIQKLGECPFDPGGYFIVKGTEKVLLMQEQLSKNRIIVETDMK-HNV 364

Query: 176  GKLLYACRIIP-DQGLWMDIEFDSKDIIHVR----IDRRRKVPVTSFLMALGMDSE-EIL 229
               + +       +   +       + +++R    +D    +P    L A+G +++ EI+
Sbjct: 365  CATVTSATAESKSRTAVVL----KNNKLYLRHNSFLD---DLPACIVLRAMGTETDQEIM 417

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
                     S                    VS SL D  T   + +              
Sbjct: 418  QMIGAGASLS----------DVTGNTAQEAVSLSLQDCHTENVLTQY------------- 454

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNG-ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
                + L      +     A+        G +  E        +   I  +    + +L+
Sbjct: 455  ----QALLWVGSRIRPKMQAKGFFTPVSRGPLLSERSGGGSRSAKSVIDEA----VDVLH 506

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
               +++     N              L I RV+   +  +    +  +     +     L
Sbjct: 507  RVVLSHIETTGNDFRAKSRFLC----LMIRRVLDAANDPSLMDDKDYYGNKRLELAGQLL 562

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDI--IAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            S +                   + +              L++     D   NL    +  
Sbjct: 563  SLLFEDLFKRFCTHVKKQADYALSRYHQARGGAAGGGSRLKDEVPYPDCFRNLPTDIITR 622

Query: 467  VGE--MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
              +  +    + +   RMER                                   S +SQ
Sbjct: 623  GMQTALSTGNWTIKRFRMER-----------------------------------SGVSQ 647

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            +   ++ ++ +    R+++       + R     R + P+ +G +CP +T EG + GLV 
Sbjct: 648  VLSRLSYIATLGMMTRINS----QFEKGRKVSGPRALQPSQWGMLCPCDTPEGESCGLVK 703

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQANSSLDEDGSFTE 642
            +L     V       TP   +       D   +S  E  +   Y+   N SL        
Sbjct: 704  NLALVTHVTTDEDP-TPIASLAFCLGVEDADAISGEELHDRGTYLVMLNGSLLGVHRRPR 762

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQR 698
            +L+             E +        + V IA+       P +  D     L+  +M +
Sbjct: 763  QLMKNIRLLRRHGEVGEFVSVHVNEAHKTVYIASDGGRLCRPLIVVDRGRPRLLPEHMAQ 822

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAA--------IVAKRAGIVEQVDAIRIVIRSVEG 750
                 +        + +E +                I A+   +      +  V+  +  
Sbjct: 823  LENGEMCFMDLLRSSILEWIDVNEENNLLIALREEDITAESTHLEIDPLTLLGVVAGLIA 882

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV--GDEVRRNDIIADGPS---TDLGDL 805
              + + S  + Y+    +++      NQ           V     +    +        L
Sbjct: 883  FPNHNQSPRNTYQCAMGKQAMGAIAYNQFNRCDTLLYLLVYPQKPLCKSRTLDLVHFEQL 942

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
              G+N  VA M + GY+ ED+++++   V         +  + V  +    G  + T   
Sbjct: 943  PAGQNASVAIMSFSGYDIEDAIVLNRGAVDRGFGRCFALRRYSVELKKYFNGSVDRTFPP 1002

Query: 866  PN-------------------------------VSEEGLKNIDECGIICVGAEVNPGDIL 894
            P                                      + +++ G++ VG  +    + 
Sbjct: 1003 PVAQGPGQRSRSAALAPGGFPRKVSPAMASGKGAVSRRFEALEDDGVVRVGELLEEDQVY 1062

Query: 895  VGKITPKGESP 905
            V K +P     
Sbjct: 1063 VHKFSPTNTRE 1073


>gi|256014694|gb|ACU56895.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
 gi|256014696|gb|ACU56896.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 203

 Score =  229 bits (584), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 83/209 (39%), Positives = 111/209 (53%), Gaps = 40/209 (19%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 27   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 87   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 131

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 132  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 174

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            +D  G++ L+DG +GEPF  PVTVGY+Y+
Sbjct: 175  VDGDGKARLFDGRSGEPFPYPVTVGYMYI 203


>gi|78100236|gb|ABB20919.1| RNA polymerase II second largest subunit [Hydnum albomagnum]
          Length = 664

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 111/717 (15%), Positives = 205/717 (28%), Gaps = 93/717 (12%)

Query: 470  MLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            +L + +R+   ++ + +   +               + +  + + +     +        
Sbjct: 1    LLASLFRMLFRKLTKDVYRHLQKCVETHKDFNISIAVKSNTITNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   SMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKPRQLHNTHWGMVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L+  A ++  G +  P  +         +   +A    +      N   
Sbjct: 117  PEGQACGLVKNLSLMACIS-VGSLSAPVIEFLQEWGLESLE-ENANAHGSATKVFVNGVW 174

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                     LV                   D S +  +             D+ RV    
Sbjct: 175  MGVHRDAPNLVKTLRRLRRKD---------DISSEVSIVRDIREKELRLYTDAGRVCRPL 225

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +      LLK E       +               + G++E +DA       +    D 
Sbjct: 226  FIVENQQLLLKKEHV---NMLNDKNRTDPYKWTHLVKDGVIELLDAEEEETVMICMTPDD 282

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              +                         +    V    +   G S    D+A+     + 
Sbjct: 283  LENS------------------------RTNQAVAAGYVSNAGAS--DHDVAVRVRSTMT 316

Query: 815  FMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
               W       SM+  I   ++            ++       +G       +       
Sbjct: 317  AHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRM----- 371

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +    AI      +  D+ +   
Sbjct: 372  ------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQ 425

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +   +    ++ R   D  ++   +  E+ E   RD                  I  G
Sbjct: 426  SSIDRGLF-RSMYYRSYTDAEKKVGVLPLEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPG 484

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  L  D                +E  QR     +    T     E+ 
Sbjct: 485  TGVAGEDIIIGKTAPLPPD---------------SEELGQRMRTHTRRDVSTPLKSTENG 529

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     + VK+ +   R  Q GDK A RHG KG V      EDMPF 
Sbjct: 530  IVDQVLVTTNQDGL-----KFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFT 584

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
             +G   DI++NP  +PSRM +G + E  L      +G +  +          +S L 
Sbjct: 585  AEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLL 641


>gi|258562144|gb|ACV81794.1| RNA polymerase II second largest subunit [Tremella mesenterica]
          Length = 650

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 105/657 (15%), Positives = 201/657 (30%), Gaps = 76/657 (11%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 51   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQAC 106

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++   +       + +  + +   Y SA +    ++      +  +  +
Sbjct: 107  GLVKNLALMSYISVGSYSAPVMEFLEEWGLEDQSEYHSAPDATKVFVNGVWMGIHREAPY 166

Query: 641  TEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
              E +     G ++      + D  +   +          P    +  ++ L        
Sbjct: 167  LHENLLNMRRGGQLKHEVSIVRDIREKELRLFTDAGRICRPLFIVNKEDQTLKLKRRHID 226

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             +  +  +      G  +             + G+VE +DA       +    +   +  
Sbjct: 227  RLDSISDQNAVPMEGFTAWEELL--------KDGVVEYIDAEEEETILIAMTSEDLENAR 278

Query: 760  DIYRLMKFQRSNQNTC---VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +    +  RS         +    VK  +  +    +   PS  LG       +  + +
Sbjct: 279  TVSGKEELVRSRAAHSLEGFDPAARVKSSNWAKTYTHMEIHPSMILG-------VCASII 331

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  +                            +
Sbjct: 332  PFPDHNQ------SPRNTYQSAMGKQAMGIYLTN-----------------------YQL 362

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +     S +   +  + AI      +  D+ +   S + 
Sbjct: 363  RMDTMANILYYPQKPLATTRSMEYLKFSELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 422

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQ 993
              +    ++ R   D  +     + E  E   R++         + Y++L     I    
Sbjct: 423  RGLF-RSLYYRAYTDTEKNVGMQKVETFEKPDRNETLRMKHGSSDRYAKLDFDGLISPAT 481

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
            N         K+  +  +      RSQ  Q       ++   + +  Q            
Sbjct: 482  NVNGEDIIIGKTAPIPPESEELGQRSQLHQKRDVSTPLKSTEQGVVDQ------------ 529

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VK+ V   R  Q GDK A RHG KG V      EDMPF  
Sbjct: 530  --------VMITTNGEGLKFVKIRVRSTRVPQIGDKFASRHGQKGTVGITYRQEDMPFTA 581

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +G   DI++NP  +PSRM +G + E  L       G    +          +S L  
Sbjct: 582  EGITPDIIINPHAIPSRMTIGHLVECLLSKLSTLTGNTGDATPFTDLTVESVSRLLR 638


>gi|312618483|gb|ADR00359.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618485|gb|ADR00360.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618487|gb|ADR00361.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618489|gb|ADR00362.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618491|gb|ADR00363.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618493|gb|ADR00364.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618495|gb|ADR00365.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618499|gb|ADR00367.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618501|gb|ADR00368.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618503|gb|ADR00369.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618505|gb|ADR00370.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618509|gb|ADR00372.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618511|gb|ADR00373.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618515|gb|ADR00375.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618519|gb|ADR00377.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
          Length = 217

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 137/216 (63%), Positives = 168/216 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR 
Sbjct: 121 NSNLDEEGRFIEDLVTCRNKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRA 180

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 LMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 216


>gi|71725907|gb|AAZ39072.1| DNA-directed RNA polymerase beta [Exiguobacterium undae]
          Length = 358

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 167/309 (54%), Positives = 221/309 (71%), Gaps = 2/309 (0%)

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLD 753
            NMQRQAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +
Sbjct: 1    NMQRQAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGN 60

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                 +D Y++ KF RSNQ TC NQ+P++K GD V + +I+ADGPS D G+LALGRN+LV
Sbjct: 61   IVQGELDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLV 120

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             FM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L
Sbjct: 121  GFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDAL 180

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP 
Sbjct: 181  KNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPH 240

Query: 934  GVSGTVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            G  G ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  
Sbjct: 241  GGDGIILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPE 300

Query: 993  QNAVSGPKG 1001
            ++    P G
Sbjct: 301  EDMPYMPDG 309



 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/217 (32%), Positives = 108/217 (49%), Gaps = 4/217 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 142  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 201

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 202  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 261

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 262  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 321

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            PSRMN+GQ+ E  LG A   LG K+ S + D     D
Sbjct: 322  PSRMNIGQLLELPLGMAARQLGIKVASPVFDGAREED 358


>gi|185179225|gb|ACC77625.1| RpoB [Mycobacterium abscessus]
          Length = 204

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/209 (40%), Positives = 109/209 (52%), Gaps = 40/209 (19%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 28   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDG 87

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LN  GVP RMN+GQI ETHLGW     G  I+                      
Sbjct: 88   TPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIEGEPEWAAN-------------- 132

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +        +    +TPVFDGA EE +  +L            
Sbjct: 133  -----------------LPADLTSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 175

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            +D  G++ L+DG +GEPF  PVTVGY+Y+
Sbjct: 176  VDGDGKARLFDGRSGEPFPYPVTVGYMYI 204


>gi|30141069|gb|AAP21845.1| RNA polymerase beta subunit [Enterococcus casseliflavus]
 gi|30141075|gb|AAP21848.1| RNA polymerase beta subunit [Enterococcus gallinarum]
          Length = 232

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 94/295 (31%), Positives = 131/295 (44%), Gaps = 72/295 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 9    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 62   -----EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D  ++ D+                                       
Sbjct: 171  ARQLGIHVATPVFDGASDEDVW-------------------------------------- 192

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                     A           A +    +++LYDG TGEPFD  ++VG +YM+KL
Sbjct: 193  ---------ATVAE-------AGMASDAKTVLYDGRTGEPFDGRISVGVMYMIKL 231



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGGGIVHDVKIFTREAGD 90


>gi|153958236|gb|ABS53408.1| RpoB [Bacteriovorax sp. MB2]
          Length = 339

 Score =  229 bits (584), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 163/342 (47%), Positives = 226/342 (66%), Gaps = 10/342 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNTC NQ+ LV  GD V
Sbjct: 1    AEDNGRVIFVDSNRIVIQRDK--FKDGESGVDIYKLVKYQRTNQNTCNNQKALVTEGDIV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ D++ADGP TD GDLALG+N LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE FE
Sbjct: 59   KKGDVLADGPGTDNGDLALGQNPLVAFMPWGGYNYEDSILISEDLLAKDVFTSVHIEAFE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRVPSSVYGTVIDARVYTREGVELCARSKDIIEQETTLLR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ E+L G              +   K T ++ ++++  P    
Sbjct: 239  RDERIEIKAIQTSAILKIAEMLNGAKITDVLVSEDGSAELLSKGTEITGEILASIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                +Q  +++  +           + +  +  ++I K+  G
Sbjct: 299  GYLPLQ-AELEEKLSEFFADVRNKINRVRAKTTDEIAKLHRG 339


>gi|117675869|emb|CAL69205.1| RNA polymerase subunit B [Okibacterium fritillariae]
          Length = 389

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 150/350 (42%), Positives = 216/350 (61%), Gaps = 33/350 (9%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I      G+ +        T  ++++A  +  E+ +EE        I +        
Sbjct: 58  EFEIDKRDQVGVRIDRKRKQSVT--VFLKALGLTTEEIMEEF--KGFESIEL-------- 105

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                 TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR 
Sbjct: 106 ------TLEKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRY 159

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L +D P     +  EDI+A IK LV L + +                 +DDID+ 
Sbjct: 160 KINRKLGIDAPLSDSVLTVEDIVATIKYLVRLHSNETTYSGVRDGKGVDIRLDVDDIDHF 219

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNR +R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 220 GNRPIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 279

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 280 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 339

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           IGL+ SL SFAR+NA+GFIETPYR+V DG+VT ++ YL+A EE++  +AQ
Sbjct: 340 IGLIGSLASFARINAFGFIETPYRRVVDGEVTTNIDYLTASEEDDFVVAQ 389



 Score =  204 bits (519), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 61/170 (35%), Positives = 91/170 (53%), Gaps = 13/170 (7%)

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W++
Sbjct: 1   DFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAWLE 58

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSA 251
            E D +D + VRIDR+RK  VT FL ALG+ +EEI+  F  +  I  +   D       A
Sbjct: 59  FEIDKRDQVGVRIDRKRKQSVTVFLKALGLTTEEIMEEFKGFESIELTLEKDTILTKEDA 118

Query: 252 ADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 LRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 160


>gi|168809726|gb|ACA29582.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
 gi|168809730|gb|ACA29584.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 211

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 90/268 (33%), Positives = 122/268 (45%), Gaps = 60/268 (22%)

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G     G     K T      +S   R     F  +  +V+     +    +     
Sbjct: 3    IRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRD 62

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
            +      KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P ED
Sbjct: 63   V------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVED 116

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+   
Sbjct: 117  MPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDLW-- 174

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                       D  +E         A +
Sbjct: 175  -------------------------------------------DTVNE---------AGM 182

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                +++LYDG TGEPFD  V+VG +YM
Sbjct: 183  ASDAKTVLYDGRTGEPFDNRVSVGVMYM 210



 Score = 68.9 bits (167), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/72 (63%), Positives = 55/72 (76%)

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V
Sbjct: 1   GIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVV 60

Query: 940 VDVRIFNRHGID 951
            DV+IF R   D
Sbjct: 61  RDVKIFTRANGD 72


>gi|153958184|gb|ABS53382.1| RpoB [Bacteriovorax sp. MNZ3]
          Length = 341

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 161/342 (47%), Positives = 224/342 (65%), Gaps = 10/342 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                 ++   ++  +           + +  +  ++I K   
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKHHR 341


>gi|153958303|gb|ABS53441.1| RpoB [Bacteriovorax sp. T9]
          Length = 342

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 161/343 (46%), Positives = 227/343 (66%), Gaps = 10/343 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 ++   ++  +           S +  +  ++I K+  G
Sbjct: 301  IGYLPLE-AALEERLSEYFADIRNRISRVRQKATDEIAKLHRG 342


>gi|153958305|gb|ABS53442.1| RpoB [Bacteriovorax sp. T5]
 gi|153958308|gb|ABS53443.1| RpoB [Bacteriovorax sp. T1]
          Length = 342

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 161/343 (46%), Positives = 227/343 (66%), Gaps = 10/343 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+  G V  VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAEDNGKVIFVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   R+ ++L G              +   K T ++S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 ++   ++  +           S +  +  ++I K+  G
Sbjct: 301  IGYLPLE-ATLEERLSEYFADIRNRISRVRQKATDEIAKLHRG 342


>gi|89142785|emb|CAJ57588.1| RNA polymerase subunit B [Microbacterium schleiferi]
          Length = 391

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 144/288 (50%), Positives = 197/288 (68%), Gaps = 15/288 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 104 DSIEETLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L L  P     +  +DI+A IK LV L  G                  +DDIDN G
Sbjct: 164 INQKLGLSGPLSDSVLTVDDIVATIKYLVRLHRGDESFEGVRSGKHATIRLDVDDIDNFG 223

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 224 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 283

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 284 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 343

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           GL+ SL SFAR+NA+GFIETPYRKV  G+VT+ + YL+A EE++  +A
Sbjct: 344 GLIGSLASFARINAFGFIETPYRKVVAGRVTDQIDYLTAAEEDDFVVA 391



 Score =  203 bits (517), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 64/173 (36%), Positives = 90/173 (52%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G 
Sbjct: 1   FMGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARIIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F  +  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFAGFDSIEETLSKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163


>gi|254055167|gb|ACT64183.1| RpoB [Pseudomonas fluorescens]
          Length = 231

 Score =  229 bits (583), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 135/231 (58%), Positives = 178/231 (77%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           RVR VGEM +NQ+R+GL+R+ER++KER+S  + + +MPQDLINAKPV +AV EFF SSQL
Sbjct: 1   RVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAVKEFFGSSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS ITH RR+ ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSEITHKRRVFALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           ++SL ++AR N YGF+E+PYR V +G VT+++V+LSA+EE +  IAQA++++++     +
Sbjct: 121 INSLAAYARTNQYGFLESPYRVVKEGLVTDEIVFLSAIEEADHVIAQASATMNDKKVLID 180

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LMG
Sbjct: 181 ELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMG 231


>gi|89145185|emb|CAJ57565.1| RNA polymerase subunit B [Microbacterium aerolatum]
          Length = 390

 Score =  229 bits (583), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 144/286 (50%), Positives = 196/286 (68%), Gaps = 15/286 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 105 PSIEETLAKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 164

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDIDNLG 460
           +N +L L  P D   +  EDI+A IK LV L  G               +   DDIDN G
Sbjct: 165 INQKLGLGQPLDSSVLTVEDIVATIKYLVRLHRGDETFEGLRSGKKAEIRIATDDIDNFG 224

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 225 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 284

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 285 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNI 344

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GL+ SL +FAR+N++GFIETPYR+V DG VT+D+ YL+A EE +  
Sbjct: 345 GLIGSLATFARINSFGFIETPYRRVVDGVVTDDIDYLTAAEENDFV 390



 Score =  202 bits (515), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 66/174 (37%), Positives = 93/174 (53%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTSKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALGM SEEIL+ F  +P I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGMTSEEILAEFSGFPSIEETLAKDTILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 164


>gi|153958238|gb|ABS53409.1| RpoB [Bacteriovorax sp. GSL23]
          Length = 342

 Score =  228 bits (582), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 163/344 (47%), Positives = 227/344 (65%), Gaps = 10/344 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNTC NQ+ LV  GD V
Sbjct: 2    AEDNGRVIFVDSNRIVIQRDK--FKDGESGVDIYKLVKYQRTNQNTCNNQKALVTEGDIV 59

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ D++ADGP TD GDLALG+N LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE FE
Sbjct: 60   KKGDVLADGPGTDNGDLALGQNPLVAFMPWGGYNYEDSILISEDLLAKDVFTSVHIEAFE 119

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++P
Sbjct: 120  VEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLSP 179

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL 
Sbjct: 180  EEKLLKAIFGDKAGDVKDTSLRVPSSVYGTVIDARVYTREGVELCARSKDIIEQETTLLR 239

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQW 1021
            RD+      +  +   ++ E+L G              +   K T ++ ++++  P    
Sbjct: 240  RDERIGIKAIQTSAILKIAEMLNGAKITDVLVSEDGSAELLSKGTEITGEILASIPFELI 299

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                +Q  +++  +           + +  +  ++I K+  GD+
Sbjct: 300  GYLPLQ-AELEEKLSEFFADVRNKINRVRAKTTDEIAKLHRGDE 342


>gi|126143413|gb|ABN80115.1| RNA polymerase beta-subunit [Prevotella marshii DSM 16973]
          Length = 125

 Score =  228 bits (582), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 76/178 (42%), Positives = 90/178 (50%), Gaps = 54/178 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN+GQIFE  LG A    G+K+                              
Sbjct: 1    NPLGVPSRMNLGQIFEAILGAA----GRKLN----------------------------- 27

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                 V  +TP+FDGA  E ++     A L     + LYDG TG
Sbjct: 28   ---------------------VKFATPIFDGAKLEDLSEWTEKAGLPHLCSTHLYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            E FD+P TVG  Y LKL HMV DK+++RS G YSL+TQQPLGGK+  GGQR GEMEVW
Sbjct: 67   EQFDQPATVGVTYFLKLGHMVEDKMHSRSIGPYSLITQQPLGGKAQFGGQRFGEMEVW 124


>gi|124490810|gb|ABN12775.1| RNA polymerase beta subunit [Bartonella sp. RN26-BBJ]
          Length = 216

 Score =  228 bits (582), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 154/216 (71%), Positives = 179/216 (82%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF SSQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET 
Sbjct: 1   FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 60

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD
Sbjct: 61  EGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTKEVIYLSAMEEAKHYVAQANSSLD 120

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +G F EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG N
Sbjct: 121 SEGRFIEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSN 180

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           MQRQAVPL++AEAPFVGTGMESVVA+ SGAA+ AKR
Sbjct: 181 MQRQAVPLVRAEAPFVGTGMESVVARDSGAAVSAKR 216


>gi|71725912|gb|AAZ39074.1| DNA-directed RNA polymerase beta [Exiguobacterium undae]
          Length = 359

 Score =  228 bits (582), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 166/309 (53%), Positives = 220/309 (71%), Gaps = 2/309 (0%)

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLD 753
            NMQRQAVP L  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +
Sbjct: 1    NMQRQAVPFLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGN 60

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                 +D Y++ KF RSNQ TC NQ+P++K GD V + +I+ADGPS D G+LALGRN+LV
Sbjct: 61   IVQGELDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLV 120

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             FM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L
Sbjct: 121  GFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDAL 180

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            KN+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP 
Sbjct: 181  KNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPH 240

Query: 934  GVSGTVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            G  G ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  
Sbjct: 241  GGDGIILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPE 300

Query: 993  QNAVSGPKG 1001
            ++    P G
Sbjct: 301  EDMPYMPDG 309



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 72/218 (33%), Positives = 110/218 (50%), Gaps = 4/218 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 142  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 201

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 202  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 261

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 262  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 321

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            PSRMN+GQ+ E HLG A   LG K+ S + D     D+
Sbjct: 322  PSRMNIGQLLELHLGMAARQLGIKVASPVFDGAREEDV 359


>gi|153958299|gb|ABS53439.1| RpoB [Bacteriovorax sp. JS5]
          Length = 344

 Score =  228 bits (582), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 160/345 (46%), Positives = 228/345 (66%), Gaps = 10/345 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +   +   +GVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKGNGRVIFVDSNRIVIQRDK--FEEGETGVDIYELVKYQRTNQNTCNNQKALVKEGDI 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T +GDLALG+N+LVAFMPW GYN+EDS+L+SE ++S D+FTS+HIE +
Sbjct: 61   VKKGDVLADGPGTHMGDLALGQNVLVAFMPWGGYNYEDSILLSEDLLSRDIFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K + ++S+++++ P   
Sbjct: 241  RRDERIEIKAIQTSAILKIAEMLNGAKTTDKLVSEDGSTELLAKGSDVTSEVLAKIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                 ++   ++  +           S +  +  ++I K   GD+
Sbjct: 301  IGYLPLE-AALEERLGEYFADVRNRISRVRQKATDEIAKQHRGDE 344


>gi|153958220|gb|ABS53400.1| RpoB [Bacteriovorax sp. PS23S]
          Length = 346

 Score =  228 bits (582), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 165/349 (47%), Positives = 228/349 (65%), Gaps = 10/349 (2%)

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
            A+ SGA + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+
Sbjct: 1    ARDSGAVLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQK 58

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
             LVK GD V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+F
Sbjct: 59   ALVKEGDIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIF 118

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
            TS+HIE FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKIT
Sbjct: 119  TSVHIEAFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKIT 178

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
            PKGE+ ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +
Sbjct: 179  PKGETQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEI 238

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDL 1012
              ++  LL RD+  E   +  +   ++ E+L G              +   K   ++ + 
Sbjct: 239  IEQETTLLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYEN 298

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
            +S  P        +Q  +++  +           + +  +  ++I K+ 
Sbjct: 299  LSAIPFELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLH 346


>gi|194320291|gb|ACF48386.1| RNA polymerase II second largest subunit [Melanelixia fuliginosa]
          Length = 683

 Score =  228 bits (581), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 108/723 (14%), Positives = 217/723 (30%), Gaps = 94/723 (13%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + +    +    +         + +  + + +     +            
Sbjct: 3    LFRGTFNKLTKDVYRYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGNWGDQKKAASV 62

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 63   KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 118

Query: 579  NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L     +      E    +      +V  +   L++      ++      +  
Sbjct: 119  ACGLVKNLALMCYITVGTPSEPIVDFMIQRSMEVLEEYEPLNSPNATKIFVNGVWVGVHR 178

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            D +     V        I      + D  D   K          P    D+  R     N
Sbjct: 179  DPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGN 238

Query: 696  MQ--RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            +   ++ V  L+ +     T    V  +++       + G+VE VDA            +
Sbjct: 239  LVLTKEHVQKLELDRENWATTEPDVREEANMGWQGLVKEGVVEYVDAEE----------E 288

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRN 810
             +   V     ++  R  Q       Q P  ++   V+          T      ++   
Sbjct: 289  ETIMIVMTPEDLEISRQLQAGYALPEQNPD-ELNKRVKAPMNPTAHTWTHCEIHPSMILG 347

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +  + +P+  +N          M  + +   + +  ++                      
Sbjct: 348  ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM------------------- 386

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                      +  +             +       +   +  + AI      +  D+ + 
Sbjct: 387  --------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 438

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 439  NQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDG 494

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++          ++     +  Q   S  
Sbjct: 495  LVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS-- 552

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                                   LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 553  ------------------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 594

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          +S 
Sbjct: 595  DMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSR 654

Query: 1168 LRS 1170
            L  
Sbjct: 655  LLR 657



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 80/579 (13%), Positives = 153/579 (26%), Gaps = 100/579 (17%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K      G  ++  R    +      R          I     
Sbjct: 41  TNGLRYSLATGNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 100

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E       + S   ++   P +
Sbjct: 101 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRSMEVLEEYEPLN 160

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM--- 558
             NA  +      F     +    +  + +  + + RR   +  +  + R     E    
Sbjct: 161 SPNATKI------FVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVF 214

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA------RVNAYGFIETPYRKVCDG 608
               R   P       P  ++ G+ +     +                  E         
Sbjct: 215 TDAGRVCRPLFVIDNDPRSSNRGNLVLTKEHVQKLELDRENWATTEPDVREEANMGWQGL 274

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--------EK 660
                V Y+ A EEE   I      L+                +E+              
Sbjct: 275 VKEGVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYALPEQNPDELNKRVKAPMNPTAHT 334

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 335 WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---------NYQQR 385

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
             + A I+      +    ++  +          +   +  Y              NQ  
Sbjct: 386 MDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE- 433

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                             S  +   ++ R +  +       + E  + +S          
Sbjct: 434 -----------------DSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS---------- 466

Query: 841 SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
              +E+FE   R           D   +       +D+ G++  G  V+  DI++GK  P
Sbjct: 467 --VVEQFEKPMR----------SDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAP 514

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                    ++        K    RDTS  + S  +G V
Sbjct: 515 IAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 546


>gi|153958196|gb|ABS53388.1| RpoB [Bacteriovorax sp. MANZ2]
          Length = 337

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 161/339 (47%), Positives = 224/339 (66%), Gaps = 10/339 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 2    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 59

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 60   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 119

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 120  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 179

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 180  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 239

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 240  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 299

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                 ++   ++  +           + +  +  ++I K
Sbjct: 300  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAK 337


>gi|113707345|gb|ABI36580.1| RNA polymerase II second largest subunit [Lasallia pustulata]
          Length = 709

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 120/817 (14%), Positives = 233/817 (28%), Gaps = 135/817 (16%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L   +R+   ++ + + +  +    +         + +  + + +     +         
Sbjct: 1    LAGLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWGDQKKA 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   ASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     +      E    +    + +V  +     +      ++      
Sbjct: 117  EGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQRSPNATKVFVNGVWVG 176

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  D +     V        I      + D  D   K          P    D+  +   
Sbjct: 177  VHRDPAHLVSTVQSLRRRALISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNDPKSPN 236

Query: 693  GCNMQ--RQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
              N+   ++ +  L+ +      T  +   AK  G      R G+VE VDA         
Sbjct: 237  NGNLVLTKEHINRLEDDKDLGPDTDPDEKTAKYMG-WEGLVRQGVVEYVDAEE------- 288

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
               + +   V     ++  R  Q               V+          T      ++ 
Sbjct: 289  ---EETVMIVMTPEDLEISRQIQAGYTMPETTDDPNKRVKAPMNPTAHTWTHCEIHPSMI 345

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N    +  S  +   D +  +                          
Sbjct: 346  LGICASIIPFPDHN---QVCYSGFLYENDTYQGL------------SXXXXXXXXXXXXX 390

Query: 869  SEEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                L N D+    +  +             +       +   +  + AI      +  D
Sbjct: 391  XXVFLTNFDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 450

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   D+ +R   +    +E   +    + + +    Y +L
Sbjct: 451  SVIMNQSSIDRGLF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSDTLKVKHGTYEKL 506

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  ++ D                +E  QR    +K    
Sbjct: 507  DDDGIVAPGVRVSGEDVIIGKTAPIAPD---------------AEELGQRTKSHIKRDVS 551

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
            T     E    +++             LR VKV +   +  Q GDK A RHG KG +   
Sbjct: 552  TPLRSTESGIVDQVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 606

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
               EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +         
Sbjct: 607  YRSEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVD 666

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
             +S L    E    +                                             
Sbjct: 667  SVSRLLR--EHGYQSRGFEVM--------------------------------------- 685

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                   +G +    G         V +G  Y  +L 
Sbjct: 686  ------YNGHT----GR---KLVAQVFLGPTYYQRLR 709



 Score =  111 bits (277), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 88/584 (15%), Positives = 157/584 (26%), Gaps = 90/584 (15%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  S+    + D  K   S  G  ++  R    +      R          I     
Sbjct: 42  TNGLKYSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQ 101

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   PQ 
Sbjct: 102 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPQR 161

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM--- 558
             NA  V      F     +    +  + +S +   RR + +  +  + R     E    
Sbjct: 162 SPNATKV------FVNGVWVGVHRDPAHLVSTVQSLRRRALISHEVSLVRDIRDREFKIF 215

Query: 559 ----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP------YRKVCDG 608
               R   P       P   + G+ +     +         G    P      Y      
Sbjct: 216 TDAGRVCRPLFVIDNDPKSPNNGNLVLTKEHINRLEDDKDLGPDTDPDEKTAKYMGWEGL 275

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
                V Y+ A EEE   I      L+                                 
Sbjct: 276 VRQGVVEYVDAEEEETVMIVMTPEDLEISRQIQ--------------------------- 308

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV 728
                   +     E  D     +   M                T       +   + I+
Sbjct: 309 --------AGYTMPETTDDPNKRVKAPM--------------NPTAHTWTHCEIHPSMIL 346

Query: 729 AKRAGIVEQVDAIRIVI----RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
              A I+   D  ++         +     S                  T  +QR     
Sbjct: 347 GICASIIPFPDHNQVCYSGFLYENDTYQGLSXXXXXXXXXXXXXXXVFLTNFDQRMDTMA 406

Query: 785 GDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                    +A   S +     +L  G+N +VA   + GYN EDS+++++  +   +F S
Sbjct: 407 NILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 466

Query: 842 IHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +   +   E     +  D   V     + +D+ GI+  G  V+  D+++G
Sbjct: 467 LFYRCYTDQEKRIGMSVVEQFEKPMRSDTLKVKHGTYEKLDDDGIVAPGVRVSGEDVIIG 526

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           K  P         E+L +        DV        SG+   V+
Sbjct: 527 KTAPIAPDA----EELGQRTKSHIKRDVSTPLRSTESGIVDQVL 566


>gi|312618507|gb|ADR00371.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
          Length = 217

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 136/216 (62%), Positives = 168/216 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFL++DD+NR 
Sbjct: 121 NSNLDEEGRFIEDLVTCRNKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLKHDDANRA 180

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
           LMG NMQRQAVP L+A+ P VGTGME  VA  SG  
Sbjct: 181 LMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVT 216


>gi|294471026|gb|ADE80774.1| RNA polymerase beta subunit [Lactococcus lactis subsp. cremoris]
          Length = 151

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 65/173 (37%), Positives = 95/173 (54%), Gaps = 22/173 (12%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
             E+I +P+LIEVQ  SY +FL          +EGL   FK +FPI  F+G   LEFV Y
Sbjct: 1   IKEVIGLPNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDNFAGTMELEFVGY 50

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
           E   PK+ V++    D  Y+ P+ +T RL+          K   ++K Q ++ GD PLMT
Sbjct: 51  EMKTPKYTVEEARAHDANYSAPIYVTFRLV---------NKETGELKTQEVFFGDFPLMT 101

Query: 140 KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           + GTF+  G +R++VSQL RSPG +F     +   +G   +    IP++G W+
Sbjct: 102 EMGTFINNGSERLIVSQLVRSPGSYFH---LKTDKNGLESFGHTTIPNRGAWL 151


>gi|67515354|gb|AAY68206.1| RNA polymerase IV second largest subunit [Solanum lycopersicum]
          Length = 1123

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 88/239 (36%), Gaps = 55/239 (23%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                 G    V V +   R    GDK +  HG KG++  +   E+ PF   G   DIV+N
Sbjct: 940  SANDEGKNFAV-VSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVIN 998

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P   PSR   GQ+ E  LG   + LG                                  
Sbjct: 999  PHAFPSRQTPGQLLEAALGK-GIALG---------------------------------- 1023

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                               G   +TP F     +AI   L+       G   +Y+G TGE
Sbjct: 1024 ------------------GGQKYATP-FSTLSVDAIMEQLQGRGFTRWGNERVYNGRTGE 1064

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                 + +G  +  +L HM  DKV  R+TG    +T+QP+  +   GG + GEME  C+
Sbjct: 1065 MVHSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCL 1123



 Score =  129 bits (325), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 128/984 (13%), Positives = 274/984 (27%), Gaps = 245/984 (24%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGA-------AMLEFV 77
           I  Q  SY+ F+          N G+Q  F SV  I        S         A ++F 
Sbjct: 78  ISHQINSYNDFI----------NYGIQRVFDSVGEIHVEPGYDPSKRGDGDWKHASVKFG 127

Query: 78  SYEFDPPKFD-----------------VDDCLWRDLTYAVPLKI-------TLRLIVFDV 113
               + PKF                        +++TY+  + +       T +L+  D 
Sbjct: 128 KVTLERPKFWAGEKFSVGGGKEYLDLLPRHARLQNMTYSARIMVETHVQVYTKKLVRSDK 187

Query: 114 DEFTGAKSIKDIKE----QSIYMGDLPLMTKD------------------GTFVIKGIQR 151
            +    + +    E    + + +G +P+M                     G F+ KG ++
Sbjct: 188 FKTGVDRFVDKEWEVEGKRDVLIGRIPVMVNSELCWMNGVDKLDCEFDHGGYFIAKGAEK 247

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEF--DSKDIIHVRIDRR 209
             ++Q                    K L+      +   WM      + +  +++++   
Sbjct: 248 TFIAQEQLC---------------LKRLWVS----NNPTWMVGYRPGEKRKRVYIKLTET 288

Query: 210 RK------------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
            K                  +P+     ALG+ S+ E+++     I      D     + 
Sbjct: 289 LKLEHIKGGEKALSVYILAEMPIWVLFFALGVSSDREVVNLIDVDIE-----DTTIVNIL 343

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCL 303
            A +    K              ++   K      +   E+ +                 
Sbjct: 344 VASIHEADKNCEDFRKGKKALAYVDRLIKNCKFPPQESVEECINAYLFPNLSGFKQKARF 403

Query: 304 CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNT 361
            G  V   +++   G   ++  D    K LE       R++   I + +     A  R+ 
Sbjct: 404 LGYMVKC-LLHSFIGRRKVDNRDDFRNKRLELAGELLERELRAHIKHAERRMVKAMQRDL 462

Query: 362 L---VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF------DSDKYDLSTVG 412
                    +   DA +    + R      +         +         ++   ++   
Sbjct: 463 YGDRQVQPIEHYLDASIITNGLSRAFSTGHWCHPYKRMERVSGVVATLRRTNPLQMTADM 522

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           R             D R+        +  +        G + ++ ++G      +   L+
Sbjct: 523 RKSRQQVTYTGKVGDARYPHPSHWGKLCFLSTPDGENCGLVKNLASMGLVSTIILKPFLE 582

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
             +R G+ ++       +                               +   E+    +
Sbjct: 583 TLFRCGMQKLVDDCSTSLHGKQK-------------------VLLDGEWVGVCEDSALFV 623

Query: 533 SRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           S++   RR + +  Q  V R     E+R              +  G  +  +  +++  +
Sbjct: 624 SKLRRKRRRNEVPHQVEVKRDELQGEVR------------IFSDPGRILRPLLVVSNLKK 671

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
           + A    +  ++ + D      +  +   EEE+   A           +  E +      
Sbjct: 672 IKALKGGDYGFQSLLDN---GIIELIGPEEEEDCRTA-----------WGVEYILKADKE 717

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                P  K    +     ++ ++  +IPF  +D + RVL                    
Sbjct: 718 N----PPAKYTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSE---------------- 757

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                    K S  AI         +VD                                
Sbjct: 758 ---------KHSQQAIGFSTVNPNNRVDTNT----------------------------- 779

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH---GYNFEDSML 828
                 QRPL +                  +       N   A +  +   GYN EDS++
Sbjct: 780 HQLYYPQRPLFRTMLADSLGKPKCAQYQKGMLPRPEYFNGQCAIVAVNVHLGYNQEDSLV 839

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI------PNVSEEGLKNIDECGII 882
           ++   +   +F S H+  ++    + +   +++  +              + ++D+ G  
Sbjct: 840 MNRASLERGMFRSEHVRSYKAEVDNKEAMAKKLKIEDSVNFGKTQSKIGRVDSLDDDGFP 899

Query: 883 CVGAEVNPGDILVGKITPKGESPM 906
            +GA +  GDI++GK +  G    
Sbjct: 900 FIGANLQSGDIIIGKFSESGADHS 923


>gi|153958182|gb|ABS53381.1| RpoB [Bacteriovorax sp. SAN1]
          Length = 336

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 161/339 (47%), Positives = 224/339 (66%), Gaps = 10/339 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V
Sbjct: 1    AKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDVV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +E
Sbjct: 59   SKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESYE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+ 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLIR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ ++L G              +   K   L+S++++  P    
Sbjct: 239  RDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                ++   ++  +           + +  +  ++I K 
Sbjct: 299  GYLPLE-PALEERLSEYFADVRNRINRVRQKANDEIAKH 336


>gi|106734117|gb|ABF82545.1| DNA-directed RNA polymerase III [Exiguobacterium sp. Glc31or]
          Length = 346

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 155/259 (59%), Positives = 204/259 (78%), Gaps = 1/259 (0%)

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLL+ ++P +GTGME V AK SGAAI+AK  G+VE+V A  I++R       
Sbjct: 1   SNMQRQAVPLLQPDSPIIGTGMEYVSAKDSGAAIIAKFPGVVERVTAREILVRRTSDVNG 60

Query: 754 PSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              SG +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++
Sbjct: 61  SEVSGDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVV 120

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
           VAFM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ 
Sbjct: 121 VAFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDA 180

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
           L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP
Sbjct: 181 LRNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVP 240

Query: 933 SGVSGTVVDVRIFNRHGID 951
           +G  G ++DV++F+R   D
Sbjct: 241 NGGDGIILDVKVFDRENGD 259



 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 82/292 (28%), Positives = 127/292 (43%), Gaps = 17/292 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 65   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 123

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 124  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 182

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 183  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 242

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 243  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 289

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GNKG++SRILP EDMP++ DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A  
Sbjct: 290  GNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAK 341


>gi|56694348|gb|AAW22914.1| RNA polymerase II second largest subunit [Cunninghamia lanceolata]
          Length = 550

 Score =  228 bits (581), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 78/462 (16%), Positives = 139/462 (30%), Gaps = 80/462 (17%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 169  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 225

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 226  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 284

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 285  FFRSYRDEEKRMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 344

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  D+   +  +  K    TS    E    +++      D
Sbjct: 345  TTPIAQ-----------------DDSGGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 387

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 388  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 442

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 443  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 500

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 501  ---------------------------------------------YNGHT----GR---K 508

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                + +G  Y  +L HMV DK+++R  G   ++T+QP  G+
Sbjct: 509  LSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGR 550



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 63/451 (13%), Positives = 123/451 (27%), Gaps = 98/451 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S    + I+   + ++   F     +    +    +  +   RR   +         
Sbjct: 20  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNP------- 72

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
               +RD+                    + +      +V+      +      +      
Sbjct: 73  EVGVVRDIRLRELRLYTDYGRCSRPLFVVENQRLKIRKVDINNLQASREDGWHELVTQGC 132

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E            +  P  ++ 
Sbjct: 133 IEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLILG 180

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                           R  
Sbjct: 181 VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMD 220

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  V                                       Q+PLV           
Sbjct: 221 TLAYV-----------------------------------LYYPQKPLV----------T 235

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N +VA   + GYN EDS+++++  +    F S+    +    + 
Sbjct: 236 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKR 295

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                +E        +   +       +D+ G+   G  V+  D+++GK TP  +     
Sbjct: 296 MGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD--- 352

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 +         RD S  +    SG V
Sbjct: 353 ------SGGQVSKYTKRDQSTSLRHSESGMV 377


>gi|153958301|gb|ABS53440.1| RpoB [Bacteriovorax sp. MED2]
          Length = 344

 Score =  228 bits (581), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 161/343 (46%), Positives = 225/343 (65%), Gaps = 10/343 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V
Sbjct: 5    AKADGKVIFVDSNRIVIQRDK--FQEGESGVDIYKLIKYQRTNQNTCNNQKALVKEGDTV 62

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+E +++ DVFTS+HIE FE
Sbjct: 63   KKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILITENLLARDVFTSVHIESFE 122

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSE+ L ++DE GII VGA + PGDILVGKITPKGE+ ++P
Sbjct: 123  VEARDTKLGKEEITRDIPNVSEDALADLDEAGIIRVGAIIKPGDILVGKITPKGETQLSP 182

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D +++ R G++ + RS  +  ++  L+ 
Sbjct: 183  EEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDAKVYTREGVELDARSKEIIDQETTLIR 242

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +  +++ ++L G              +   K   +++D +   P    
Sbjct: 243  RDERIEIKAIQNSAITQIAKLLKGATTTDKLVSEDGSTELLAKGVEVTADTLKGIPFELI 302

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                +Q E ++  +           + +  +  ++I  +  GD
Sbjct: 303  GYLPLQPE-LEEKLSEYFADIRNRINRVRTKANDEIAMLHRGD 344


>gi|312204374|gb|ADQ47504.1| RNA polymerase II second largest subunit [Stictis populorum]
          Length = 710

 Score =  228 bits (580), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 111/805 (13%), Positives = 222/805 (27%), Gaps = 121/805 (15%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            +   +R    ++ +      +              + +  + + +     +         
Sbjct: 1    MAXLFRNLFTKLNKXXXXYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGEQKKA 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   MSAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLVCPAETP 116

Query: 576  EGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L    +  V +       +    + +V  +   + +      ++      
Sbjct: 117  EGQACGLVKNLALMCYITVGSPSGPIVDFMVQRNMEVLEEYDPVRSPNATKVFVNGVWVG 176

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  D S    ++        +      I D  D   K          P L  D+  R   
Sbjct: 177  VHRDPSHLVSVMQILRRKNILSYETSLIRDIRDREFKIFSDAGRVCRPLLVVDNDPRSAN 236

Query: 693  GCNMQ--RQAVPLLKAEAPFVG--TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
              N+   ++ V  L+ +       T  E          ++  ++G VE +DA       +
Sbjct: 237  KGNLVLTKELVNKLEDDRELPADLTKEEREERHFGWNGLM--QSGAVEFLDAEEEETVMI 294

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLAL 807
                +               R  Q       P       V+    +     T      ++
Sbjct: 295  IMSPEDLEV----------SRQVQAGYAPPEPSEDPNARVKGKVNLTQHSWTHCEIHPSM 344

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P   +N                                             
Sbjct: 345  ILGVCASIIPXPDHNQXXXXXXXXXXXXXXXXXXXXXXX-XXXXXXXXXXXXXXXXXXXX 403

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 404  XXXXXXXXXXXXXMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 463

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  +++ +R        +E   +    + + L    Y +L 
Sbjct: 464  VIMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPMRSDTLRLKHGTYEKLD 519

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +  D      R++          ++     +      
Sbjct: 520  DDGIVAPGVRVSGEDIIIGKTAPIPPDSEEMGQRTKLHTKRDASTPLRSTESGI------ 573

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                        ++K+          L+ VKV     +  Q GDK+A RHG KG +    
Sbjct: 574  ------------VDKVLL--TTNAEGLKFVKVRTRTTKLPQIGDKLASRHGQKGTIGITY 619

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +  + E  L       G +             
Sbjct: 620  RMEDMPFSAEGVTPDIIINPHAIPSRMTIAHLVECQLSKVSCLRGFEGD----------- 668

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     ++++ +LR
Sbjct: 669  ------------------------------------------ATP-FTEVTVDSVSRLLR 685

Query: 1225 MADLDESGQSILYDGLTGEPFDRPV 1249
                   G  ++Y+G TG      V
Sbjct: 686  EHGYQSRGFEVMYNGHTGRKLTAQV 710


>gi|300394766|gb|ADK11921.1| DNA-directed RNA polymerase II subunit two [Plicaturopsis crispa]
          Length = 629

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 113/710 (15%), Positives = 219/710 (30%), Gaps = 101/710 (14%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   ++ + +    +              +  + + + +    
Sbjct: 1    GKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETKKEFNLALAVKHQTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L   A ++   +       + +  + +         EEN
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EEN 168

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             + +   + +  +G +       R     +   ++     D SP+  V            
Sbjct: 169  AHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
             D+ RV     +      +L+ +   ++G GM+          +       +   +    
Sbjct: 226  TDAGRVCRPLFIVENQQLILQKKHVNWLGQGMDDNGEPYKWEQLXKGGIVELLDAEEEET 285

Query: 744  VIRSVEGDLDPST----SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            V+ S+      ++    SG+D +   +F  +           +K G            PS
Sbjct: 286  VMISMTPQDLDTSRLQSSGIDPHNDEEFDPAA---------RLKAGINAHTWTHCEIHPS 336

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG  A       + +P+  +N                        ++       +G  
Sbjct: 337  MILGVAA-------SIIPFPDHNQSPRN------------------TYQSAMGKQAMGIF 371

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                 I               +  +             +       +   +  + AI   
Sbjct: 372  LTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCY 420

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+         
Sbjct: 421  SGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPVRENTLRMKHGT 479

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G           K+  +  D      R++          ++     + 
Sbjct: 480  YDKIEDDGLIAPGTGVTGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIV 539

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q GDK A RHG KG 
Sbjct: 540  DQVLI--------------------TTNSEGQKFVKVRVRSSRIPQIGDKFASRHGQKGT 579

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +      EDMPF  +G   DI++NP  +PSRM +G + E  L      +G
Sbjct: 580  IGITYRQEDMPFTSEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIG 629



 Score =  118 bits (296), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 85/613 (13%), Positives = 167/613 (27%), Gaps = 105/613 (17%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F++A ++ +    +  KY L   G  
Sbjct: 9   GPLLANLFRMLFRKLTKDVYRYLQKCVETK--KEFNLALAVKHQTITNGLKYSL-ATGNW 65

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 66  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 125

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 126 TPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 185

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +            +   ++        P    E   + L
Sbjct: 186 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLIL 245

Query: 583 VSSLTSFARVNAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
                    VN  G          K         V  L A EEE   I+     L +   
Sbjct: 246 QKK-----HVNWLGQGMDDNGEPYKWEQLXKGGIVELLDAEEEETVMISMTPQDL-DTSR 299

Query: 640 FTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                +      E          +        +  P  ++ +AAS+IPF +++ S R   
Sbjct: 300 LQSSGIDPHNDEEFDPAARLKAGINAHTWTHCEIHPSMILGVAASIIPFPDHNQSPRNTY 359

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
              M +QA+ +                                                 
Sbjct: 360 QSAMGKQAMGIFLTNFLI-----------------------------------------R 378

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
             + + +  Y       +     +  R                        +L  G+N +
Sbjct: 379 MDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAI 414

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPN 867
           VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        +   
Sbjct: 415 VAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPVRENTLR 474

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       I++ G+I  G  V   DI++GK  P         E+L +        DV   
Sbjct: 475 MKHGTYDKIEDDGLIAPGTGVTGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTP 530

Query: 928 SLRVPSGVSGTVV 940
                +G+   V+
Sbjct: 531 LKSTENGIVDQVL 543


>gi|221508871|gb|EEE34440.1| DNA-directed RNA polymerase III subunit, putative [Toxoplasma gondii
            VEG]
          Length = 1324

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 75/392 (19%), Positives = 130/392 (33%), Gaps = 84/392 (21%)

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
              A+      +   +L  D +  +  S         + +Q +       +   K+++   
Sbjct: 999  FEALEDDGVVRVGELLEEDQVYVHKFSPTNTREHVSDPLQLDNSLYAPSFARYKTVVPS- 1057

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                +E++   D       R  KV +   R  + GDK +                     
Sbjct: 1058 ---YVERVVCTD--NSDGCRTYKVMMRQTRLPELGDKFS--------------------- 1091

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
                            SR                  G+K    +     +   +      
Sbjct: 1092 ----------------SR-----------------HGQKGVVGLIAPAEDLPFAESGWCP 1118

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            + ++       +++      ++      + G       F G   E +  +L       SG
Sbjct: 1119 DLIMNPHGFPSRMTVGKMMELIAGKSALQVGACQYGTAFGGVGVETLGEILAAHGFHYSG 1178

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L  G+TGE     V  G IY  KL HMV DK++AR  G   L+T+QP  G++  GG 
Sbjct: 1179 KEYLTSGITGEALQTYVFAGPIYYQKLKHMVQDKIHARGRGPRQLLTRQPTEGRAKEGGL 1238

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA-----------------G 1335
            RLGEME  C+ AYG++ +L E L + SD       V+E+ V                  G
Sbjct: 1239 RLGEMERDCLVAYGSSALLMERLMLSSD-------VFEASVCSTCGLMGYEGWCPYCKSG 1291

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                    P +  +L +E+ ++ +   L    
Sbjct: 1292 KHVAPIRMPYACKLLFQELMSMNVCPRLHIKE 1323



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 116/1019 (11%), Positives = 267/1019 (26%), Gaps = 260/1019 (25%)

Query: 17   FGKNPEIIDIPD-------------LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +     +  +PD             L+     SY+ F+   +    R         KS  
Sbjct: 143  YASGKPVCTVPDKWRLLPAFFAAKGLVHQHIESYNFFVDTELQNILRAPS--NRLVKS-- 198

Query: 64   PITAFSGAAMLEFVSYEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVD 114
                   +  +EF++     P++             C  R++TYA P+ +          
Sbjct: 199  ---DVDPSFFIEFLNISVGTPRYEEGMILQRLTPRICRTREITYAAPVFVDAEY------ 249

Query: 115  EFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQ 150
                +K  + I+ + + +G +P+M                           G F++KG +
Sbjct: 250  ----SKGDEIIRRKHVEIGSIPVMLRSRVCVLHGKDPQTLQRLGECPFDPGGYFIVKGTE 305

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP-DQGLWMDIEFDSKDIIHVR---- 205
            ++++ Q   S          +       + +       +   +       + +++R    
Sbjct: 306  KVLLMQEQLSKNRIIVETDMK-HNVCATVTSATAESKSRTAVVL----KNNKLYLRHNSF 360

Query: 206  IDRRRKVPVTSFLMALGMDSE-EILSTFY--------------PKIVYSQRG--DFWCFP 248
            +D    +P    L A+G +++ EI+                    +  S +         
Sbjct: 361  LD---DLPACIVLRAMGTETDQEIMQMIGAGGALADVTGNTAQEAVSLSLQDCHTENVLT 417

Query: 249  LSAADLMVGAKVSSSLVDI-------------------DTGEQVIESGKKLTSGLLKSLK 289
               A L VG+++   +                       + + V++    +   ++ S  
Sbjct: 418  QQQALLWVGSRIRPKMQAKGFFTPVARGALLSERGGAGRSAKSVVDEAVDVLHRVVLSHI 477

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
            E         +  L    +   +++  +    ++  D    K LE            L+ 
Sbjct: 478  ETTGSDFRAKTRFL--CLMIRRVLDAASDPSLMDDKDYYGNKRLELAGQLLSLLFEDLFK 535

Query: 350  DSVNNNAYIRNTLVTDKNK----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                +     +  ++  ++           + +          P D+ T  +  ++    
Sbjct: 536  RFCTHVKKQADYALSRYHQARGGAGGLGSRKDEVPYPDCFRNLPTDIITRGMQTALSTGN 595

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +         T+ R +M           + +I    ++  I    +          +   
Sbjct: 596  W---------TIKRFRMERSGVSQVLSRLSYIATLGMMTRINSQFEKGRKVSGPRALQPS 646

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +                 + +++         +   P   +    +     +    
Sbjct: 647  QWGMLCPCDTPEGESCG-----LVKNLALVTHVTTDEDPTPISSLAFC-LGVEDADAISG 700

Query: 520  SQLS---QLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
             +L         +N      H R R        + R     E   VH     +     + 
Sbjct: 701  EELHDRGTYLVMLNGALLGVHRRPRQLMKNIRLLRRHGEVGEFVSVHVNEAHKTVYIASD 760

Query: 576  EGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             G     +  + S            +E       D   ++ + ++   EE N  IA    
Sbjct: 761  GGRLCRPLIVVDSGRPRLLPTHMAQLENGEMCFMDLLRSSILEWIDVNEENNLLIALREE 820

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +                         +   ++  P  ++ + A LI F  ++ S R   
Sbjct: 821  DITA-----------------------ETTHLEIDPLTLLGVVAGLIAFPNHNQSPRNTY 857

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             C M +QA+                                           I   + + 
Sbjct: 858  QCAMGKQAMGA-----------------------------------------IAYNQFNR 876

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              +   + +Y               Q+PL K                     L  G+N  
Sbjct: 877  CDTLLYLLVYP--------------QKPLCKS----------RTLDLVHFEQLPAGQNAS 912

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
            VA M + GY+ ED+++++   V         +  + V  +    G  + T   P      
Sbjct: 913  VAIMSFSGYDIEDAIVLNRGAVDRGFGRCFALRRYSVELKKYFNGSTDRTFPPPVAQASG 972

Query: 868  ---------------------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                                       + +++ G++ VG  +    + V K +P     
Sbjct: 973  PGSGKAASGLHRKSFFPGGRGAVSRRFEALEDDGVVRVGELLEEDQVYVHKFSPTNTRE 1031


>gi|221488368|gb|EEE26582.1| DNA-directed RNA polymerase III subunit, putative [Toxoplasma gondii
            GT1]
          Length = 1328

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 75/392 (19%), Positives = 130/392 (33%), Gaps = 84/392 (21%)

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
              A+      +   +L  D +  +  S         + +Q +       +   K+++   
Sbjct: 1003 FEALEDDGVVRVGELLEEDQVYVHKFSPTNTREHVSDPLQLDNSLYAPSFARYKTVVPS- 1061

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                +E++   D       R  KV +   R  + GDK +                     
Sbjct: 1062 ---YVERVVCTD--NSDGCRTYKVMMRQTRLPELGDKFS--------------------- 1095

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
                            SR                  G+K    +     +   +      
Sbjct: 1096 ----------------SR-----------------HGQKGVVGLIAPAEDLPFAESGWCP 1122

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            + ++       +++      ++      + G       F G   E +  +L       SG
Sbjct: 1123 DLIMNPHGFPSRMTVGKMMELIAGKSALQVGACQYGTAFGGVGVETLGEILAAHGFHYSG 1182

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L  G+TGE     V  G IY  KL HMV DK++AR  G   L+T+QP  G++  GG 
Sbjct: 1183 KEYLTSGITGEALQTYVFAGPIYYQKLKHMVQDKIHARGRGPRQLLTRQPTEGRAKEGGL 1242

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA-----------------G 1335
            RLGEME  C+ AYG++ +L E L + SD       V+E+ V                  G
Sbjct: 1243 RLGEMERDCLVAYGSSALLMERLMLSSD-------VFEASVCSTCGLMGYEGWCPYCKSG 1295

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                    P +  +L +E+ ++ +   L    
Sbjct: 1296 KHVAPIRMPYACKLLFQELMSMNVCPRLHIKE 1327



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 116/1019 (11%), Positives = 267/1019 (26%), Gaps = 260/1019 (25%)

Query: 17   FGKNPEIIDIPD-------------LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +     +  +PD             L+     SY+ F+   +    R         KS  
Sbjct: 147  YASGKPVCTVPDKWRLLPAFFAAKGLVHQHIESYNFFVDTELQNILRAPS--NRLVKS-- 202

Query: 64   PITAFSGAAMLEFVSYEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVD 114
                   +  +EF++     P++             C  R++TYA P+ +          
Sbjct: 203  ---DVDPSFFIEFLNISVGTPRYEEGMILQRLTPRICRTREITYAAPVFVDAEY------ 253

Query: 115  EFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQ 150
                +K  + I+ + + +G +P+M                           G F++KG +
Sbjct: 254  ----SKGDEIIRRKHVEIGSIPVMLRSRVCVLHGKDPQTLQRLGECPFDPGGYFIVKGTE 309

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP-DQGLWMDIEFDSKDIIHVR---- 205
            ++++ Q   S          +       + +       +   +       + +++R    
Sbjct: 310  KVLLMQEQLSKNRIIVETDMK-HNVCATVTSATAESKSRTAVVL----KNNKLYLRHNSF 364

Query: 206  IDRRRKVPVTSFLMALGMDSE-EILSTFY--------------PKIVYSQRG--DFWCFP 248
            +D    +P    L A+G +++ EI+                    +  S +         
Sbjct: 365  LD---DLPACIVLRAMGTETDQEIMQMIGAGGALADVTGNTAQEAVSLSLQDCHTENVLT 421

Query: 249  LSAADLMVGAKVSSSLVDI-------------------DTGEQVIESGKKLTSGLLKSLK 289
               A L VG+++   +                       + + V++    +   ++ S  
Sbjct: 422  QQQALLWVGSRIRPKMQAKGFFTPVARGALLSERGGAGRSAKSVVDEAVDVLHRVVLSHI 481

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
            E         +  L    +   +++  +    ++  D    K LE            L+ 
Sbjct: 482  ETTGSDFRAKTRFL--CLMIRRVLDAASDPSLMDDKDYYGNKRLELAGQLLSLLFEDLFK 539

Query: 350  DSVNNNAYIRNTLVTDKNK----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                +     +  ++  ++           + +          P D+ T  +  ++    
Sbjct: 540  RFCTHVKKQADYALSRYHQARGGAGGLGSRKDEVPYPDCFRNLPTDIITRGMQTALSTGN 599

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +         T+ R +M           + +I    ++  I    +          +   
Sbjct: 600  W---------TIKRFRMERSGVSQVLSRLSYIATLGMMTRINSQFEKGRKVSGPRALQPS 650

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +                 + +++         +   P   +    +     +    
Sbjct: 651  QWGMLCPCDTPEGESCG-----LVKNLALVTHVTTDEDPTPISSLAFC-LGVEDADAISG 704

Query: 520  SQLS---QLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
             +L         +N      H R R        + R     E   VH     +     + 
Sbjct: 705  EELHDRGTYLVMLNGALLGVHRRPRQLMKNIRLLRRHGEVGEFVSVHVNEAHKTVYIASD 764

Query: 576  EGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             G     +  + S            +E       D   ++ + ++   EE N  IA    
Sbjct: 765  GGRLCRPLIVVDSGRPRLLPTHMAQLENGEMCFMDLLRSSILEWIDVNEENNLLIALREE 824

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +                         +   ++  P  ++ + A LI F  ++ S R   
Sbjct: 825  DITA-----------------------ETTHLEIDPLTLLGVVAGLIAFPNHNQSPRNTY 861

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             C M +QA+                                           I   + + 
Sbjct: 862  QCAMGKQAMGA-----------------------------------------IAYNQFNR 880

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              +   + +Y               Q+PL K                     L  G+N  
Sbjct: 881  CDTLLYLLVYP--------------QKPLCKS----------RTLDLVHFEQLPAGQNAS 916

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
            VA M + GY+ ED+++++   V         +  + V  +    G  + T   P      
Sbjct: 917  VAIMSFSGYDIEDAIVLNRGAVDRGFGRCFALRRYSVELKKYFNGSTDRTFPPPVAQASG 976

Query: 868  ---------------------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                                       + +++ G++ VG  +    + V K +P     
Sbjct: 977  PGSGKAASGLHRKSFFPGGRGAVSRRFEALEDDGVVRVGELLEEDQVYVHKFSPTNTRE 1035


>gi|237833217|ref|XP_002365906.1| DNA-directed RNA polymerase III subunit, putative [Toxoplasma gondii
            ME49]
 gi|211963570|gb|EEA98765.1| DNA-directed RNA polymerase III subunit, putative [Toxoplasma gondii
            ME49]
          Length = 1332

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 75/392 (19%), Positives = 130/392 (33%), Gaps = 84/392 (21%)

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
              A+      +   +L  D +  +  S         + +Q +       +   K+++   
Sbjct: 1007 FEALEDDGVVRVGELLEEDQVYVHKFSPTNTREHVSDPLQLDNSLYAPSFARYKTVVPS- 1065

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                +E++   D       R  KV +   R  + GDK +                     
Sbjct: 1066 ---YVERVVCTD--NSDGCRTYKVMMRQTRLPELGDKFS--------------------- 1099

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
                            SR                  G+K    +     +   +      
Sbjct: 1100 ----------------SR-----------------HGQKGVVGLIAPAEDLPFAESGWCP 1126

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
            + ++       +++      ++      + G       F G   E +  +L       SG
Sbjct: 1127 DLIMNPHGFPSRMTVGKMMELIAGKSALQVGACQYGTAFGGVGVETLGEILAAHGFHYSG 1186

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            +  L  G+TGE     V  G IY  KL HMV DK++AR  G   L+T+QP  G++  GG 
Sbjct: 1187 KEYLTSGITGEALQTYVFAGPIYYQKLKHMVQDKIHARGRGPRQLLTRQPTEGRAKEGGL 1246

Query: 1293 RLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA-----------------G 1335
            RLGEME  C+ AYG++ +L E L + SD       V+E+ V                  G
Sbjct: 1247 RLGEMERDCLVAYGSSALLMERLMLSSD-------VFEASVCSTCGLMGYEGWCPYCKSG 1299

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
                    P +  +L +E+ ++ +   L    
Sbjct: 1300 KHVAPIRMPYACKLLFQELMSMNVCPRLHIKE 1331



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 116/1019 (11%), Positives = 267/1019 (26%), Gaps = 260/1019 (25%)

Query: 17   FGKNPEIIDIPD-------------LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
            +     +  +PD             L+     SY+ F+   +    R         KS  
Sbjct: 151  YASGKPVCTVPDKWRLLPAFFAAKGLVHQHIESYNFFVDTELQNILRAPS--NRLVKS-- 206

Query: 64   PITAFSGAAMLEFVSYEFDPPKF---------DVDDCLWRDLTYAVPLKITLRLIVFDVD 114
                   +  +EF++     P++             C  R++TYA P+ +          
Sbjct: 207  ---DVDPSFFIEFLNISVGTPRYEEGMILQRLTPRICRTREITYAAPVFVDAEY------ 257

Query: 115  EFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQ 150
                +K  + I+ + + +G +P+M                           G F++KG +
Sbjct: 258  ----SKGDEIIRRKHVEIGSIPVMLRSRVCVLHGKDPQTLQRLGECPFDPGGYFIVKGTE 313

Query: 151  RIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP-DQGLWMDIEFDSKDIIHVR---- 205
            ++++ Q   S          +       + +       +   +       + +++R    
Sbjct: 314  KVLLMQEQLSKNRIIVETDMK-HNVCATVTSATAESKSRTAVVL----KNNKLYLRHNSF 368

Query: 206  IDRRRKVPVTSFLMALGMDSE-EILSTFY--------------PKIVYSQRG--DFWCFP 248
            +D    +P    L A+G +++ EI+                    +  S +         
Sbjct: 369  LD---DLPACIVLRAMGTETDQEIMQMIGAGGALADVTGNTAQEAVSLSLQDCHTENVLT 425

Query: 249  LSAADLMVGAKVSSSLVDI-------------------DTGEQVIESGKKLTSGLLKSLK 289
               A L VG+++   +                       + + V++    +   ++ S  
Sbjct: 426  QQQALLWVGSRIRPKMQAKGFFTPVARGALLSERGGAGRSAKSVVDEAVDVLHRVVLSHI 485

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
            E         +  L    +   +++  +    ++  D    K LE            L+ 
Sbjct: 486  ETTGSDFRAKTRFL--CLMIRRVLDAASDPSLMDDKDYYGNKRLELAGQLLSLLFEDLFK 543

Query: 350  DSVNNNAYIRNTLVTDKNK----------DRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                +     +  ++  ++           + +          P D+ T  +  ++    
Sbjct: 544  RFCTHVKKQADYALSRYHQARGGAGGLGSRKDEVPYPDCFRNLPTDIITRGMQTALSTGN 603

Query: 400  FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
            +         T+ R +M           + +I    ++  I    +          +   
Sbjct: 604  W---------TIKRFRMERSGVSQVLSRLSYIATLGMMTRINSQFEKGRKVSGPRALQPS 654

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                +                 + +++         +   P   +    +     +    
Sbjct: 655  QWGMLCPCDTPEGESCG-----LVKNLALVTHVTTDEDPTPISSLAFC-LGVEDADAISG 708

Query: 520  SQLS---QLEEHVNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
             +L         +N      H R R        + R     E   VH     +     + 
Sbjct: 709  EELHDRGTYLVMLNGALLGVHRRPRQLMKNIRLLRRHGEVGEFVSVHVNEAHKTVYIASD 768

Query: 576  EGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             G     +  + S            +E       D   ++ + ++   EE N  IA    
Sbjct: 769  GGRLCRPLIVVDSGRPRLLPTHMAQLENGEMCFMDLLRSSILEWIDVNEENNLLIALREE 828

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +                         +   ++  P  ++ + A LI F  ++ S R   
Sbjct: 829  DITA-----------------------ETTHLEIDPLTLLGVVAGLIAFPNHNQSPRNTY 865

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
             C M +QA+                                           I   + + 
Sbjct: 866  QCAMGKQAMGA-----------------------------------------IAYNQFNR 884

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              +   + +Y               Q+PL K                     L  G+N  
Sbjct: 885  CDTLLYLLVYP--------------QKPLCKS----------RTLDLVHFEQLPAGQNAS 920

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----- 867
            VA M + GY+ ED+++++   V         +  + V  +    G  + T   P      
Sbjct: 921  VAIMSFSGYDIEDAIVLNRGAVDRGFGRCFALRRYSVELKKYFNGSTDRTFPPPVAQASG 980

Query: 868  ---------------------VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                                       + +++ G++ VG  +    + V K +P     
Sbjct: 981  PGSGKAASGLHRKSFFPGGRGAVSRRFEALEDDGVVRVGELLEEDQVYVHKFSPTNTRE 1039


>gi|56694346|gb|AAW22913.1| RNA polymerase II second largest subunit [Taxus brevifolia]
          Length = 549

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 79/462 (17%), Positives = 139/462 (30%), Gaps = 80/462 (17%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 168  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 224

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 225  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 283

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 284  FFRSYRDEEKRMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 343

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  DE   +  +  K    TS    E    +++      D
Sbjct: 344  TTPIAQ-----------------DEAGGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 386

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 387  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 441

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 442  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 499

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 500  ---------------------------------------------YNGHT----GR---K 507

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
                + +G  Y  +L HMV DK+++R  G   ++T+QP  G+
Sbjct: 508  LSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGR 549



 Score =  116 bits (291), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 70/452 (15%), Positives = 129/452 (28%), Gaps = 100/452 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +    GV R 
Sbjct: 19  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVKTLRQLRRQVDVNPEVGVVRD 78

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +       A +N             +     
Sbjct: 79  IRLRELR-LYTDYGRCSRPLFVVENQRLKIKK-----ADINNLQASRED--GWHELVTQG 130

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E            +  P  ++
Sbjct: 131 FIEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLIL 178

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 179 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 218

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 219 DTLAYV-----------------------------------LYYPQKPLV---------- 233

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 234 TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 293

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 294 RMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE-- 351

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  A         RD S  +    SG V
Sbjct: 352 -------AGGQVSKYTKRDQSTSLRHSESGMV 376


>gi|67515350|gb|AAY68204.1| RNA polymerase IV second largest subunit [Selaginella erythropus]
          Length = 593

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 73/348 (20%), Positives = 122/348 (35%), Gaps = 89/348 (25%)

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             ++    S LE  + +++              R V V +   R  Q GDK +  HG KG+
Sbjct: 311  NKFVDKMSNLEQAWVDQV----VCSMGEEQDQRHVNVRLRESRCPQVGDKFSSMHGQKGV 366

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
            V  +L  ED+ F + G   D+++NP   PSR  + Q+ E+ +G     +G  +      +
Sbjct: 367  VGMMLSQEDLLFTQQGIVPDVIINPHAFPSRQTLAQMLESLVGKTAA-MGLCLGDTPFTH 425

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
                 ++   +                                       V+ G      
Sbjct: 426  LRAEQLAQKLAKRGFQKWGQDR----------------------------VYSGCT---- 453

Query: 1220 NSMLRMADLDESGQSILYDGL-TGEPFDRPVTVGYIYMLKLNHMVSDKVYAR-STGSYSL 1277
                               G  TG       T G  +  +LNH+  DK+  R   G    
Sbjct: 454  -------------------GRMTG----AMATFGLTFYQRLNHLSRDKMKCRGGNGPVHP 490

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVG---RTRVYE 1330
            +T QP+  +  +GG + GEME  C+ A+GA+  +QE L + SD     V     R   + 
Sbjct: 491  LTHQPVKDRRRQGGTKFGEMERDCLVAHGASATVQERLFLVSDKSLVHVCANCCRLASFN 550

Query: 1331 SIVAGNDTFETG--------------TPESFNVLVKEMQALGLSIDLE 1364
            S        + G               P +  +L  E+QA+G+ +  Z
Sbjct: 551  S------QQQPGCLFCKRXQRPVAVEMPYACKLLRMELQAMGVDMRFZ 592



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 67/188 (35%), Gaps = 26/188 (13%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN- 771
           T +E   A   G +     A ++  +D      R            + +Y      R   
Sbjct: 141 THLEMHPASFLGLS-----ASVIPFLDHNHSS-RVTHQAQKHGKQAIGVYACDNLSRMEP 194

Query: 772 -QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
             +    Q+PLV           +A   +     L  G N +VA   + G+N EDS++++
Sbjct: 195 TAHLYYPQKPLVHS--------WLAQHLTCP--XLTNGTNCVVAVASYGGFNQEDSLIVN 244

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           +  V   +F S H    +                          ++D  G+  +GA++  
Sbjct: 245 QASVDRGLFRSTHFFVKKASLDSKSSQH--------FGKSSDSASLDSDGLPYIGAKMTA 296

Query: 891 GDILVGKI 898
           GD+++G++
Sbjct: 297 GDVVIGRM 304


>gi|295798047|emb|CBL86576.1| RNA polymerase beta subunit [Streptococcus sp. 682-03]
          Length = 234

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 95/299 (31%), Positives = 132/299 (44%), Gaps = 72/299 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 8    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 60

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 61   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 109

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 110  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 169

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D  ++ D+                                       
Sbjct: 170  ARNLGIHVATPVFDGASSEDLWDTVREAGMDSDAK------------------------- 204

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               T ++DG                           TGEPFD  V+VG +YM+KL+HMV
Sbjct: 205  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIKLHHMV 234



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 1   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 89


>gi|34582093|gb|AAQ76001.1| RpoB [Stevia rebaudiana]
          Length = 367

 Score =  228 bits (580), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 132/353 (37%), Positives = 202/353 (57%), Gaps = 2/353 (0%)

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              F   + +L  +GR  MN RLNLD P +   +   DI+A    L+ ++ G GT+DD++
Sbjct: 4   QKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMN 63

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCE 515
           +L N+R+RSV ++L+ Q+ L L+R+E   +     +     +  PQ+L+N+ P+      
Sbjct: 64  HLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKV 123

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF    LSQ+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TS
Sbjct: 124 FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTS 183

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG N+GL+ SL   AR+  +G +E+P+ K+ +      ++YLS   +E   +A  NS   
Sbjct: 184 EGINVGLIGSLAIHARIGRWGSLESPFYKISERSKGAQMLYLSPGRDEYYMVAAGNSLAL 243

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
             G   E++V  R   E + +  E++        Q  SI ASLIPF+E++D+NR LM  N
Sbjct: 244 NQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFAFQYFSIGASLIPFIEHNDANRALMSSN 303

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           MQRQAVPL ++E   VGTG+E   A  SGA  +A+  G +   D  +I++   
Sbjct: 304 MQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIFYTDTDKILLSGN 356


>gi|295016201|emb|CBG98938.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
          Length = 238

 Score =  228 bits (580), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 141/238 (59%), Positives = 181/238 (76%), Gaps = 2/238 (0%)

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
           GL RMER ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH
Sbjct: 1   GLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTH 60

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 61  KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 120

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 121 IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 180

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+PFVGT
Sbjct: 181 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGT 238


>gi|313611133|gb|EFR85971.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL F2-208]
          Length = 260

 Score =  227 bits (579), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 75/259 (28%), Positives = 127/259 (49%), Gaps = 22/259 (8%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R++VSQL RSPG++F+   G+   +GK  +   +IP++G W
Sbjct: 1   MGDFPLMTEMGTFIINGAERVIVSQLVRSPGVYFN---GKLDKNGKKGFGSTVIPNRGAW 57

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
           ++ E D+KD++HVRIDR RK+PVT  L ALG  S+ EI+             +      +
Sbjct: 58  LEYETDAKDVVHVRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRNTLEKDNTDNA 117

Query: 251 AADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGVKFLGIT--------SD 301
              L+           +  GE   +++ + L        K   +  +G           +
Sbjct: 118 EKALL------EIYERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRYKINKKLXXKN 171

Query: 302 CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF---HSEIRDIPILYVDSVNNNAYI 358
            L    +AE +V+ ETGEI    GD++D ++L++I     + +    +   D V  ++ +
Sbjct: 172 RLFNQTLAETLVDPETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRPTDGVMEDSVL 231

Query: 359 RNTLVTDKNKDRKDALLDI 377
             ++      D +  +  I
Sbjct: 232 VQSIKIYAPNDDEKEINII 250



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/83 (37%), Positives = 48/83 (57%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D + +N Y+RNTL  D   + + ALL+IY  +RPG+  T   A S+    FFD  +YDL
Sbjct: 96  IDLIGDNDYLRNTLEKDNTDNAEKALLEIYERLRPGEPPTVDNARSLLVSRFFDPKRYDL 155

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           ++VGR K+N +L        + +
Sbjct: 156 ASVGRYKINKKLXXKNRLFNQTL 178


>gi|153958242|gb|ABS53411.1| RpoB [Bacteriovorax sp. GSL4]
          Length = 339

 Score =  227 bits (579), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 161/341 (47%), Positives = 224/341 (65%), Gaps = 10/341 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            A+  G V  VD+ RIVI+          SGVDIY+L+K+QR+NQNTC NQ+ LV  GD V
Sbjct: 2    AEDNGRVIFVDSNRIVIQRD--SFKDGESGVDIYKLVKYQRTNQNTCNNQKALVTEGDIV 59

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            ++ D++ADGP TD GDLALG+N LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE FE
Sbjct: 60   KKGDVLADGPGTDNGDLALGQNPLVAFMPWGGYNYEDSILISEDLLAKDVFTSVHIEAFE 119

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++P
Sbjct: 120  VEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLSP 179

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL 
Sbjct: 180  EEKLLKAIFGDKAGDVKDTSLRVPSSVYGTVIDARVYTREGVELCARSKDIIEQETTLLR 239

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ ++L G              +   K T ++ ++++  P    
Sbjct: 240  RDERIEIKAIQTSAILKIADMLKGAKITDVLVTEDGSAELLSKGTEITGEVLASIPFELI 299

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                +Q  +++  +           + +  +  ++I K+  
Sbjct: 300  GYLPLQ-AELEEKLSEYFADVRNKINRVRAKTTDEIAKLHR 339


>gi|313635039|gb|EFS01402.1| DNA-directed RNA polymerase subunit beta [Listeria seeligeri FSL
            N1-067]
          Length = 125

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 59/102 (57%), Positives = 74/102 (72%)

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGND 1337
            VTQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G  
Sbjct: 1    VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGES 60

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
              E G PESF VL+KE+Q+LG+ + + ++  K     +   D
Sbjct: 61   VPEPGVPESFKVLIKELQSLGMDVKMLSADEKEIEMRDMDDD 102


>gi|327198729|emb|CCA61430.1| unnamed protein product [Diadromus pulchellus ascovirus 4a]
          Length = 1034

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 120/310 (38%), Gaps = 73/310 (23%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            +KV +   +  + GDK       KG    +L  EDMPF   G   D+++NP  +PSRM +
Sbjct: 779  IKVSILQVKVPEIGDKFCSGMAQKGTCGMMLNQEDMPFTSSGMTPDLIINPHCLPSRMTI 838

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
             Q+  +    A    G                              +     S +    +
Sbjct: 839  NQLMSSVCSKARCVTG-----------------------------DASFADGSPFSGTDL 869

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
            +  A Q                       L+     E G   LY+G TG+     + +G 
Sbjct: 870  VERAAQV----------------------LKQNGYSEDGTETLYNGFTGKKLHAKIFMGP 907

Query: 1254 IYMLKLNHMVSDKV----YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            +Y  +L H+VS+K+    +   T + + +T+QPL G++N GG R+GEME  C+  +G   
Sbjct: 908  VYQHRLTHLVSNKIFSSVH---TNAKNKLTRQPLNGRANDGGLRIGEMEKDCLLRHGVVK 964

Query: 1310 VLQEMLTIKSD----DVVGRTRVYESIV-----------AGNDTFETGTPESFNVLVKEM 1354
               E L   SD     +    + Y  +V              +      P +  +L +E+
Sbjct: 965  FSNERLLDLSDKHVVHICNDCKSYYHVVATKNSRLCTKCKSVNVSSVSIPYAAKLLTQEL 1024

Query: 1355 QALGLSIDLE 1364
            +++GLSI +E
Sbjct: 1025 ESIGLSITME 1034



 Score = 98.2 bits (243), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 77/512 (15%), Positives = 168/512 (32%), Gaps = 46/512 (8%)

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           ++   +   T  +   +    +  +++ +V    G  + DDI +L  +RV   G + ++ 
Sbjct: 252 QLFPHMGHSTNLEKTVL----LCKMLRKMVLCDAGIVSEDDIGDLAFKRVDMAGVLCQDL 307

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
           +++   +  +SI +  +     +++       K +       F +      +     L  
Sbjct: 308 FKMLWKQFIKSIIKESNKRKFSNLISTINYKKKNIGLNFQYCFSTGTWGIKKNAYKKLGV 367

Query: 535 ITHTRRLSALG---------QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
               +   +              +++    V +R +HP+    +CP ET EG ++G   S
Sbjct: 368 SEFAQYKVSNLTNLGLLRKFNIPISKKDKNVNIRMMHPSSIFFVCPFETPEGSSVGTKLS 427

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS---LDEDGSFTE 642
           L + A V+    ++T    V D   + ++V    + +  + I   N       ED     
Sbjct: 428 LAASATVS----LDTNTVLVTDMFHSRNIV--DPVLDYTKTIVSVNGCYIGHVEDWEAFV 481

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL-IPFLENDDSNRVLMGCNMQRQAV 701
             V    A E +      + + +      +   +   +  L   +  R ++  + +    
Sbjct: 482 ASVELMRADEVLARDVS-VSYDEFINVVEIWCDSGRLVRPLLVTEKLRAIVDKSEEVSID 540

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
              +     V    E                    +  +    I         +   V  
Sbjct: 541 TWERTGVLVVRDAAELNKKYI--------NDVWDMKTFSDYTEIDPSLSMGVVAGQIVFS 592

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRN------DIIADGPST-------DLGDLALG 808
                 +    +  + Q   V VG   R +      D +    +T          D+  G
Sbjct: 593 NHTQSPRVCYMSNMIKQAMGVVVGHPTRLDATTYTLDHVQRPLNTTRMAELLGTNDVPNG 652

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
            N +VA   + G+N EDS+++++  V   +F +          ++     E +       
Sbjct: 653 VNAVVAVACYTGFNQEDSIILNKSAVDRGLFRATCRRTIVSEIKNMPSFEEIVCIPPKEK 712

Query: 869 S-EEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                   +   G+I VG  VN GD+++GK  
Sbjct: 713 RLFMNYSKLGSNGVIRVGQYVNKGDVVIGKTM 744



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 49/167 (29%), Gaps = 55/167 (32%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP----- 84
           +  Q   ++ FL+           G+Q        I      ++++  +  F+ P     
Sbjct: 19  VGHQINGFNDFLL----------YGIQKVLDDEPNI--HVDGSVVDITNATFEKPARNKT 66

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT----- 139
                      LTY   + + +       D     K         + +  +P+M      
Sbjct: 67  PLTPAMARELSLTYDCNVFVDV-----FRDGQFLEK---------VLLFSIPVMVGSVAC 112

Query: 140 -------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDH 167
                              + G FVI G +RI+  Q+ R+    F H
Sbjct: 113 NLHGMTPDEKLRNGELIDDQGGYFVINGKERIITGQMKRAYNKIFCH 159


>gi|229893866|gb|ACQ90283.1| RNA polymerase B-subunit [Staphylococcus sp. 168]
 gi|229893868|gb|ACQ90284.1| RNA polymerase B-subunit [Staphylococcus sp. 196]
          Length = 257

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 150/257 (58%), Positives = 190/257 (73%), Gaps = 3/257 (1%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRK
Sbjct: 1   GPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRK 60

Query: 605 V--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
           V     +VT+ + YL+A EE++  +AQANS LDE G F E+ V CR  G+    P+E++D
Sbjct: 61  VNIETNQVTSRIDYLTADEEDSYVVAQANSVLDETGKFVEDEVLCRFRGDNTTKPKERMD 120

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPFVGTGME V A+ 
Sbjct: 121 YMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVTARD 180

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSV-EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
           SGAAIVAK  G VE V+A  I++R + E +     + +D Y L KF+RSN  TC NQRP+
Sbjct: 181 SGAAIVAKYKGRVEHVEAKEILVRRIVEENGKEIETELDRYPLSKFKRSNSGTCYNQRPI 240

Query: 782 VKVGDEVRRNDIIADGP 798
           +  GD V + +I+ADGP
Sbjct: 241 ISAGDVVTKGEILADGP 257


>gi|176838246|emb|CAQ00123.1| RNA polymerase beta subunit [Streptococcus porci]
 gi|176838248|emb|CAQ00124.1| RNA polymerase beta subunit [Streptococcus porci]
          Length = 234

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 95/299 (31%), Positives = 132/299 (44%), Gaps = 72/299 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 8    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 60

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 61   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 109

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 110  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 169

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 170  ARNLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 199

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                       +    ++L        G        TGEPFD  V+VG +YM+KL+HMV
Sbjct: 200  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLHHMV 234



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 1   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  EVRDTSLRVPHGGDGIVRDVKIFTRANGD 89


>gi|55140709|gb|AAQ01541.2| RNA polymerase II second largest subunit [Crepidotus cf. applanatus
            PBM 717]
          Length = 688

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 110/826 (13%), Positives = 218/826 (26%), Gaps = 165/826 (19%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 2    KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKDFNVAFAVKHQTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H    
Sbjct: 62   GNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PIGREGKIAKPRQLHNXXX 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
                 AET EG   GLV +L   + ++   F       + +  + +     +A       
Sbjct: 118  XXXXXAETPEGQACGLVKNLALMSCISVGSFSGPVIEFLEEWGLESLEE--NAHSSTPFT 175

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI----DFIDASPKQVVSIAASLIPFL 682
                N            LV              ++    D  +   +          P  
Sbjct: 176  KVFVNGVWIGVHRDAANLVKTLKRLRRRDDISTEVSVVRDIREREMRVYTDAGRVCRPLF 235

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAE------APFVGTG-MESVVAKSSGAAIVAKRAGIV 735
              +D  ++++     R     +  E         V TG +E + A+     +++     +
Sbjct: 236  IVED-QQLVLQKKHIRWLNNGVDDEGQEFKWEQLVKTGVIELLDAEEEETVMISMTPEDL 294

Query: 736  EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            E     +  I     +                              +K G          
Sbjct: 295  ENSRLQQRGIDPQANNDGEYDPAA---------------------RLKAGTHAHTWTHCE 333

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N                        ++    +  
Sbjct: 334  IHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGEQA 368

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            +G       I               +  +             +       +   +  + A
Sbjct: 369  MGIYLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVA 417

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+     
Sbjct: 418  ILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRM 476

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +       I  G           K+  +  D      R++          ++   
Sbjct: 477  KHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTE 536

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +  Q                              + VKV V   R  Q GDK A RHG
Sbjct: 537  SGIVDQVLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHG 576

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  + 
Sbjct: 577  QKGTIGITYRQEDMPFTAEGIVPDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDAT 636

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                         ++     + LR       G+ +         
Sbjct: 637  PFT-------------------------DLTVESVSTFLRQKGYQSRGLEIM-------- 663

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                            G +       G+     V +G  Y  +L H
Sbjct: 664  --------------YHGHT-------GKKLQAQVYLGPTYYQRLKH 688



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 94/624 (15%), Positives = 170/624 (27%), Gaps = 104/624 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+VA ++ +    +  KY L   G  
Sbjct: 8   GPLLANLFRMLFRKLTKDVYRYLQKCVETH--KDFNVAFAVKHQTITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +          E
Sbjct: 65  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPIGREGKIAKPRQLHNXXXXXXXXAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA         F     +
Sbjct: 125 TPEGQACGLVKNLALMSCISVGSFSGPVIEFLEEWGLESLEENAHSSTPFTKVFVNGVWI 184

Query: 523 SQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
               +  N +  +   RR   +  +  V R     EMR V+        P    E     
Sbjct: 185 GVHRDAANLVKTLKRLRRRDDISTEVSVVRDIREREMR-VYTDAGRVCRPLFIVEDQ--Q 241

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           LV        +N     E    K      T  +  L A EEE   I+     L+      
Sbjct: 242 LVLQKKHIRWLNNGVDDEGQEFKWEQLVKTGVIELLDAEEEETVMISMTPEDLENSRLQQ 301

Query: 642 EELVFCRCAGEEIL--------VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             +        E                   +  P  ++ I AS+IPF +++ S R    
Sbjct: 302 RGIDPQANNDGEYDPAARLKAGTHAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQ 361

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M  QA+ +                                                  
Sbjct: 362 SAMGEQAMGIYLTNFLI-----------------------------------------RM 380

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            + + +  Y       +     +  R                        +L  G+N +V
Sbjct: 381 DTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQNAIV 416

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNV 868
           A + + GYN EDS+++++  +   +F SI+   +  + + + +   E            +
Sbjct: 417 AILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRM 476

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +++ G+I  G  V   DI++GK  P         ++        +    RD S
Sbjct: 477 KHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVS 529

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  SG V  V I       K
Sbjct: 530 TPLKSTESGIVDQVLITTNSEGQK 553


>gi|153958291|gb|ABS53435.1| RpoB [Bacteriovorax sp. GSL4E]
          Length = 335

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 160/337 (47%), Positives = 223/337 (66%), Gaps = 10/337 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKHSGRVIFVDSNRIVIQRNK--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 59   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+ ++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGAELTGEVLASVPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
               F ++   ++  +           + +  +  ++I
Sbjct: 299  IGYFPLE-PALEERLSEYFADVRNRINRVRQKANDEI 334


>gi|307168561|gb|EFN61619.1| DNA-directed RNA polymerase I subunit RPA2 [Camponotus floridanus]
          Length = 1075

 Score =  227 bits (579), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 91/523 (17%), Positives = 159/523 (30%), Gaps = 115/523 (21%)

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            D         +   G   +G      +     +   L+         V   ++ +     
Sbjct: 627  DCNQSPRNMYQCQMGKQTMGTPCYNWQQQSQTKLYRLQTPAAPLFRPVHYDNINMDDYAM 686

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIEL---LARDKDDEQVILDRNIYSRLMEILCGQ 993
            GT   + + +  G D  E ++ + +   E           E V L               
Sbjct: 687  GTNAIIAVISYTGYDM-EDAMVINKASYERGFGYGTVYKSEFVDLKD----------KKS 735

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                 P   +    L  D +     S              N   +  +Y+++++      
Sbjct: 736  YFACDPDKPELGKTLDIDGLPIIGASIKEGDPYYCFYDADNANYVVGRYKSTENTY---- 791

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
               I+ ++          R   +   + R    GDK A R G KGI+SR+ P ED+PF +
Sbjct: 792  ---IDNVKLCGSFNTQDPRRACITFRIPRNPIVGDKFASRAGQKGILSRLYPAEDLPFTE 848

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
             G   DI+ NP G PSRM +  + E   G +    G    +    +            L 
Sbjct: 849  TGMVPDIIFNPHGFPSRMTIAMMIEVMAGKSAAVHGLVHDATPFKFDEENTAIDYFGRL- 907

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                                             L +   +  G 
Sbjct: 908  -------------------------------------------------LELGGYNYYGT 918

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLG--------- 1284
              +Y G+ G   +  +  G ++  +L HMVSDK   RSTG    +T+QP+          
Sbjct: 919  ERMYSGIYGCEMEASIFFGMVHYQRLRHMVSDKWQVRSTGPIDQLTRQPIKGRRRGGGVR 978

Query: 1285 --GKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTRVYESIVAG 1335
                         EME   + ++G +Y+LQ+ L   SD +        G     E I+  
Sbjct: 979  FG-----------EMERDALISHGCSYLLQDRLFHCSDKMTSLACQKCGSILGPELIMNS 1027

Query: 1336 ---------------NDTFETGTPESFNVLVKEMQALGLSIDL 1363
                           ++  E   P  F  L+ ++ +  +++ L
Sbjct: 1028 THEEDDKRCRLCGEEDNVNEIEIPYIFRFLLIQLASCNINVKL 1070



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 81/427 (18%), Positives = 149/427 (34%), Gaps = 33/427 (7%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           ++  +K      +ID+ M   L       S+      +S L+ + E++N +  ++H R  
Sbjct: 363 LQEMLKITKFRSNIDAQMEYFLATGSIRSSSSIGLMQNSGLTVVVENINRMRYMSHFR-- 420

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
            A+ +G   +     E+R + P  +G ICP  T +G   GL++ LT    V  +      
Sbjct: 421 -AIHRGAFFQGMRTTEVRRLLPDAWGFICPIHTPDGAPCGLLNHLTMNCIVTKHPDPNLK 479

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE--DGSFTEELVFCRCAG-------- 651
                       +    A   EN Y    +  +    +     ++V+             
Sbjct: 480 AAIPGILIELGMIPLSIADNWENSYTVMLDGKVIGLIENKIINKVVYRLRLLKIKGQEIP 539

Query: 652 ---EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  LVP+ K+           +    + P +        L+G   Q      +  E 
Sbjct: 540 STLEIALVPKRKVPSQYPGLFLFTNATRMMRPVINLAVQQIELIGTFEQIYMDICVLPEE 599

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            + G      V   S   I +  A ++   D  +      +  +   T G   Y     Q
Sbjct: 600 AYPGLTTHQEV---SQTTIFSNLAKLIPLPDCNQSPRNMYQCQMGKQTMGTPCYNWQ--Q 654

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           +S       Q P   +   V  ++I       ++ D A+G N ++A + + GY+ ED+M+
Sbjct: 655 QSQTKLYRLQTPAAPLFRPVHYDNI-------NMDDYAMGTNAIIAVISYTGYDMEDAMV 707

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           I++             +   V  +D K        D P +     K +D  G+  +GA +
Sbjct: 708 INKASYERGFGYGTVYKSEFVDLKDKKSYF-ACDPDKPELG----KTLDIDGLPIIGASI 762

Query: 889 NPGDILV 895
             GD   
Sbjct: 763 KEGDPYY 769



 Score = 59.3 bits (142), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 58/179 (32%), Gaps = 62/179 (34%)

Query: 16  FFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI--TAFSG- 70
            FGK PE  +  +  L      S+++ L           +GLQ   K+  P+  T  +G 
Sbjct: 18  DFGKPPEKQNRLLQSLGAPHIDSFNYML----------EDGLQGI-KNDSPVYLTLPNGD 66

Query: 71  AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTG 118
             +L     +   P            K    +   R  TY   + + L+  +   ++   
Sbjct: 67  KVVLWLDDVQIHKPTVPSGTIGVKNYKVYPTESRQRGTTYKGKIIVKLKWSINGKEQEAL 126

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
                        +G +P+M K                         G F+++GI+R++
Sbjct: 127 ESD----------LGGIPIMLKSNRCHLNKMSPKELVAHGEHEQEWGGYFIVRGIERLI 175


>gi|140084148|gb|ABO84923.1| RpoB [Paenibacillus amylolyticus]
          Length = 225

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 83/200 (41%), Positives = 109/200 (54%), Gaps = 54/200 (27%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 80   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 139

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV IVLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 140  TPVQIVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGAKEYD----------- 188

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 189  ----------------------------------VFD---------TMEEAGMQRNGKTV 205

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            LYDG TGE F+R VTVG ++
Sbjct: 206  LYDGRTGEEFEREVTVGVMH 225



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/88 (65%), Positives = 70/88 (79%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +
Sbjct: 1   DIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKARE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G  G VVDV++F R   D
Sbjct: 61  VRDTSLRVPHGTDGIVVDVKVFTRENGD 88


>gi|283481648|emb|CAZ69764.1| putative DNA-directed RNA polymerase II subunit precursor [Emiliania
            huxleyi virus 99B1]
          Length = 1507

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/285 (25%), Positives = 109/285 (38%), Gaps = 75/285 (26%)

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG+    +P  D P   DG   DI++NP  +PSRM +G + E  L       G+
Sbjct: 1266 SSRHGQKGVCGVTMPAADFPCTADGVAPDIIINPHAIPSRMTIGMLMEMVLSKVACYEGE 1325

Query: 1151 KIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPV 1210
                                                                     TP 
Sbjct: 1326 TQDG-----------------------------------------------------TP- 1331

Query: 1211 FDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
            F G + E I   L    +   G  +LY+G++GE  +  + +   Y  +L HMV DK +AR
Sbjct: 1332 FTGNNIELIADRLETHGMQRYGNEMLYNGMSGEILESMIFIAPCYYQRLKHMVVDKSHAR 1391

Query: 1271 STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVV------- 1323
            + G+  L+T+ P  G+S  GG R+GEME   I ++GA  V ++ L  +SD          
Sbjct: 1392 NRGAQQLLTRAPTEGRSRDGGLRIGEMEKDSIISHGAGDVAKDRLFEQSDIFECVACEKC 1451

Query: 1324 ---GRTRVYESIVA-----------GNDTFETGTPESFNVLVKEM 1354
                R    ++ V            G     T  P S  +L++E+
Sbjct: 1452 GHFAREGTDDTSVKNSGMWCEHCKTGEHCTHTQLPYSMKLLIQEL 1496



 Score =  129 bits (323), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 135/971 (13%), Positives = 284/971 (29%), Gaps = 195/971 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM--LEFVSYEFDPP--- 84
           +  Q  SYDHF+   +       EG       +  + + SG     + F +   + P   
Sbjct: 23  VAHQIESYDHFIENQLPYIIS--EG-----SDISYMHS-SGKVSHHVHFTNPSVNRPAIQ 74

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE--QSIYMGDL 135
                           R LTY+  + + +   + D    T +      ++  +++ +  +
Sbjct: 75  ESDGFYKPITPHIARLRGLTYSSTVVVDV---IHDRINHTVSPPTLINRKVFRNVIIAQI 131

Query: 136 PLMT---------------------------KDGTFVIKGIQRIVVSQ-LHRSPGIH-FD 166
           P+M                              G F+I G ++ ++ Q   R+  +  F 
Sbjct: 132 PVMVRSKLCYLADVSENDLSADAKKHECKVDPGGYFIISGNEKTLIPQTKIRTNHVFIFP 191

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMD----IEFDSKDIIHVRID-RRRKVP-------V 214
              G         Y   +       +     I  +  DI +  +     K+P       V
Sbjct: 192 SKHGEKHK-----YTAEVRSCHEAKLRSTSTIYMNINDISNGEVPVITCKLPFLKSNLSV 246

Query: 215 TSFLMALGM-DSEEILSTFYPKIVYSQ--------RGDFWCFPLSAADLMVGAKVSSSLV 265
                 LG   +++I++        ++              +   A    VG  V+S   
Sbjct: 247 FILFRMLGAESTDDIINYIGNIPKDTEAILRIMLDSDTKQNYSRDAIMDWVGRNVTSDTT 306

Query: 266 DIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG 325
                 +       +TS L   +                G  +   +      E+  +  
Sbjct: 307 RATKESREKYIDHIITSELAPHMGLVNNPETNKKKMIFIGHMIQRLMSVATGQEVVDDRD 366

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
           D I++     I  +      +L      N     +T +  + +  ++A  ++  ++    
Sbjct: 367 DFINK----RIDSAGALLALLLRQHHRGNAMQGLSTQLRKQVESPREATFNVGEIVSHKK 422

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPD-----DVRHIRKEDIIAII 440
           + T  +  +     +  S     +  G+  +   L   T         +           
Sbjct: 423 I-TSGLKFAFATGTWGISRGGGTANGGQTGVVQILPRLTTMATLGASRKINTPIAREGRT 481

Query: 441 KILVDLR-NGKGTIDDIDNLGNRRVRSVGEM-LKNQYRLGLLRMERSIKERISSVDIDSV 498
                L  +  G +   D    +    V  + +  + R+G      +I        ID  
Sbjct: 482 AGPRMLHPSSWGLVCCSDTPEGQACGLVSNLAMTTRIRIGAPMQPIAILLMTLDHTIDIS 541

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
                   + +  A+         +   + +  ++    + R         + + +    
Sbjct: 542 TATSHE--RYIGYALHVNGTIVGYAITIDQIKEIATQMRSLRRHGNLPFDCSISISNDNS 599

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             V+  H   + P    + ++  +  ++ + A V           K         + Y+ 
Sbjct: 600 LFVNSDHGALLRPLIIRDRYHDFVCMAMQNPAVVPN---------KYTRMLREGIIEYID 650

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           + E+ N  +A  ++ +++D                      +   I+  P  +  I  S 
Sbjct: 651 SAEQTNMRVAIHHTDIEQD----------------------EYTHIEIHPALLTGICVSQ 688

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R+       +QA+ L                         A+R   V  V
Sbjct: 689 IPFCDHNQSPRIAYQAAQCKQAIGLYTTN--------------------FAERLDTVGHV 728

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            A                                     Q+PLV       R + +    
Sbjct: 729 LAT-----------------------------------PQKPLV-----TTRLEELLGTS 748

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
               G +      +VA M + G+N +DS+L+++  +   +FTS          + T    
Sbjct: 749 VVRSGAVP-----IVAIMCYSGFNQDDSVLLNQSSIDRGLFTSFAYHTIRDEEKGTGADI 803

Query: 859 E--EITRDIP---NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
           E  E  ++IP    + E     ID+ G+  +G     GD+L+GK+         P+E  +
Sbjct: 804 ERFENPKNIPGCSGMKEADYSKIDDKGMPIIGKTFYNGDVLIGKVVSMSLLQADPKEGEV 863

Query: 914 RAIFGEKAVDV 924
           R         V
Sbjct: 864 RRDTKRDRSHV 874


>gi|52699864|gb|AAU86993.1| DNA-dependent RNA polymerase II second largest subunit [Pyrenula
            pseudobufonia]
          Length = 707

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 128/832 (15%), Positives = 237/832 (28%), Gaps = 159/832 (19%)

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G ++ N +R    ++ +  +   +        +  +    A  + + +     +      
Sbjct: 1    GPLMSNLFRTQFQKLVKDFQRYMQKQVESDRDINLKVGFKASIITNGLKYSLATGNWGEQ 60

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +A     + R     + R +H TH+G ICPA
Sbjct: 61   KKVIKSKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKMAKPRQLHNTHWGFICPA 116

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   + V            + +  +     ++  +E+    ++   +
Sbjct: 117  ETPEGQACGLVKNLALMSAVTTGSKNFAADELLTNYILQKR--HVEPLEDWEPSMSPTAT 174

Query: 633  SLDEDGSF-----------TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
             +  +G +            E     R   +   +     D  D   +     A  + P 
Sbjct: 175  KIFLNGVWFAVVKEEPRFLVEHFRNLRRKKQLPEMTALVWDIRDREFRINTEAARIVRPL 234

Query: 682  --LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKRAGIVEQV 738
              +E+D +        + ++ V  L         G      A  +         GIVE V
Sbjct: 235  FVIESDPAMPNKGELILTKEHVARLMRTRENRQMGRPIEEYADDALDWSDLVHQGIVEWV 294

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            DA       +    D      + Y        +++      PL+               P
Sbjct: 295  DAEEEETIMIVMSADELVMSRE-YHAGYELADSEDPLARVAPLLNP--YAHTFTHCEIHP 351

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N       S R   +       +  F           
Sbjct: 352  SMILG-------VCASIIPFPDHNQ------SPRNTYQXXXXXQAMGVFLTNFDQ----R 394

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             E   +I    ++ L                        +       +   +  + AI  
Sbjct: 395  METMANILYYPQKPLA-------------------TTSSMEHLRFRELPAGQNAIVAIAC 435

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +     +  +   +      V  + +E   +    + + L
Sbjct: 436  YSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQE----KQVGHQVLEKFEKPSRADTLRL 491

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             R  Y ++ E   +  G           K+  ++ D                +E  QR  
Sbjct: 492  KRGTYDKIDEDGIVAPGVRVSGEDIILGKTAPMAPD---------------SEELGQRTK 536

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              +K          E    +++              R  KV V   +  Q GDK A RHG
Sbjct: 537  AHVKRDASVQLRSTESGIVDQVLL-----TTTNEGSRFAKVRVRTTKIPQIGDKFASRHG 591

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF KDG   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 592  QKGTIGITYRQEDMPFTKDGVVPDLIINPHAIPSRMTIAHLIECQLSKLASLTGAEGDAT 651

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     IS                                                 
Sbjct: 652  PFTTVTVSQISDRLREFG------------------------------------------ 669

Query: 1216 EEAINSMLRMADLD--ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                         +   +G +    G         + +G  Y  +L HMV D
Sbjct: 670  -------FHSRGFEVMYNGHT----GR---KLMAQIFLGPTYYQRLRHMVDD 707



 Score =  102 bits (253), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 88/617 (14%), Positives = 181/617 (29%), Gaps = 58/617 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N   T   K  KD    + + +        ++       +  +  KY L   G  
Sbjct: 1   GPLMSNLFRTQFQKLVKDFQRYMQKQVESDR--DINLKVGFKASIITNGLKYSL-ATGNW 57

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               ++        + + +    + +  L        R+GK       +  +       E
Sbjct: 58  GEQKKVIKSKAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKMAKPRQLHNTHWGFICPAE 117

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI---DSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
             + Q    +  +         S +    + +    L           E   S   +++ 
Sbjct: 118 TPEGQACGLVKNLALMSAVTTGSKNFAADELLTNYILQKRHVEPLEDWEPSMSPTATKIF 177

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
            +    + +    R        + R +   EM  +      R     T     +  +  +
Sbjct: 178 LNGVWFAVVKEEPRFLVEHFRNLRRKKQLPEMTALVWDIRDREFRINTEAARIVRPLFVI 237

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            S   +   G +      V     T +   +    EE    A   S L   G        
Sbjct: 238 ESDPAMPNKGELILTKEHVARLMRTRENRQMGRPIEEYADDALDWSDLVHQG-------- 289

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                         ++++DA  ++ + I  S    + + + +    G  +     PL + 
Sbjct: 290 -------------IVEWVDAEEEETIMIVMSADELVMSREYH---AGYELADSEDPLARV 333

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLM 765
                         +   + I+   A I+   D  +    + +        GV       
Sbjct: 334 APLLNPYAHTFTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQXXXXXQAMGVFLTNFDQ 393

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           + +         Q+PL             +        +L  G+N +VA   + GYN ED
Sbjct: 394 RMETMANILYYPQKPL----------ATTSSMEHLRFRELPAGQNAIVAIACYSGYNQED 443

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    ++   +       E        D   +       IDE G
Sbjct: 444 SVIMNQSSIDRGLFRSLFYRTYQDQEKQVGHQVLEKFEKPSRADTLRLKRGTYDKIDEDG 503

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  DI++GK  P         ++        KA   RD S+++ S  SG V 
Sbjct: 504 IVAPGVRVSGEDIILGKTAPMAPDSEELGQRT-------KAHVKRDASVQLRSTESGIVD 556

Query: 941 DVRIFNRHGIDKNERSI 957
            V +   +   +  +  
Sbjct: 557 QVLLTTTNEGSRFAKVR 573


>gi|153958244|gb|ABS53412.1| RpoB [Bacteriovorax sp. OC3]
          Length = 342

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 161/345 (46%), Positives = 229/345 (66%), Gaps = 10/345 (2%)

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + AK  G V  VD+ RIV++  +   +   SGVDIY L+K+QR+NQ+TC NQ+ LVK G
Sbjct: 1    VLFAKDDGKVIFVDSNRIVLQRNK--FEDGESGVDIYSLVKYQRTNQSTCNNQKALVKEG 58

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D VR+ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+HIE
Sbjct: 59   DIVRKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSVHIE 118

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             FEV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ 
Sbjct: 119  AFEVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQ 178

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  
Sbjct: 179  LSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETT 238

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPR 1018
            LL RD+  E   +  +   ++ E+L G              +  +K   ++ +++++ P 
Sbjct: 239  LLRRDERIEIKAIQTSAILKIAEMLKGAKTTDKLVSEDGSTELLQKGADITGEVLAQIPF 298

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                   +Q  +++  +           + +  +  ++I K+  G
Sbjct: 299  ELIGYLPLQ-AELEERLSEYFADIRNRINRVRQKTTDEIAKLHRG 342


>gi|161016859|emb|CAO81744.1| RNA polymerase beta subunit [Streptococcus plurextorum]
 gi|161016861|emb|CAO81745.1| RNA polymerase beta subunit [Streptococcus plurextorum]
          Length = 234

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 99/299 (33%), Positives = 133/299 (44%), Gaps = 72/299 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 8    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 60

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +   S +      KI     GD++P GV  +V+VF+A KR I
Sbjct: 61   -----EVRDTSLRVPHGGDGVVSDV------KIFTRANGDELPSGVNILVRVFIAQKRKI 109

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 110  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 169

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 170  ARNLGIHIATPVFDGATSEDLWSTVEEAGMDSDAK------------------------- 204

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               T ++DG                           TGEPFD  V+VG +YM+KL+HMV
Sbjct: 205  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIKLHHMV 234



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 1   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  EVRDTSLRVPHGGDGVVSDVKIFTRANGD 89


>gi|153958214|gb|ABS53397.1| RpoB [Bacteriovorax sp. PS93S]
          Length = 345

 Score =  227 bits (578), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 163/348 (46%), Positives = 227/348 (65%), Gaps = 10/348 (2%)

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK G
Sbjct: 1    VLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEG 58

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE
Sbjct: 59   DIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIE 118

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ 
Sbjct: 119  AFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQ 178

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  
Sbjct: 179  LSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETT 238

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPR 1018
            LL RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P 
Sbjct: 239  LLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPF 298

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
                   +Q  +++  +           + +  +  ++I K+  GD++
Sbjct: 299  ELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHRGDEL 345


>gi|153958281|gb|ABS53430.1| RpoB [Bacteriovorax sp. GSL37]
          Length = 339

 Score =  226 bits (577), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 161/342 (47%), Positives = 226/342 (66%), Gaps = 10/342 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK AG V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNTC NQ+ LVK GD V
Sbjct: 1    AKDAGKVIFVDSNRIVIQRDK--AGEGDSGVDIYKLVKYQRTNQNTCNNQKALVKEGDRV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+E ++++DVFTS+HIE +E
Sbjct: 59   TKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINEELLAQDVFTSVHIESYE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGES ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGESQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV++ +++ R G++ + RS  +   +  L+ 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVINAKVYTREGVELDSRSKEIIDHETTLIR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ ++L G              +   K + ++S+ ++  P    
Sbjct: 239  RDERIEIKAIQTSAILKIADMLSGATTTDKLVSEDGTTELLAKGSAITSEALAAIPFELV 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                ++ E ++  +           + +  +  ++I  +  G
Sbjct: 299  GYLPLKPE-LEEKLGEYFADVRNRINRVRQKANDEIAMLHRG 339


>gi|153958310|gb|ABS53444.1| RpoB [Bacteriovorax sp. MIA3]
          Length = 337

 Score =  226 bits (577), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 158/334 (47%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
             VD+ RIV++    + +   SGVDIY L+K+QR+NQNTC NQ+ LVK GD V++ D++AD
Sbjct: 7    FVDSNRIVVQRD--NFEEGQSGVDIYHLVKYQRTNQNTCNNQKALVKEGDIVKKGDVLAD 64

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            GP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++DVFTS+HIE +EV ARDTKL
Sbjct: 65   GPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDVFTSVHIESYEVEARDTKL 124

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++PEEKLL+AI
Sbjct: 125  GKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLSPEEKLLKAI 184

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
            FG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+ RD+  E  
Sbjct: 185  FGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVEICSRSKDIIEQETTLIRRDERIEIK 244

Query: 977  ILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             +  +   R+ ++L G              +   K T ++S++++  P        ++  
Sbjct: 245  AIQTSSILRIADMLKGAKTTDKLVSEDGSTELLAKGTEVTSEVLAGVPFELIGYLPLE-A 303

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
             ++  +           S +  +  ++I K+  G
Sbjct: 304  ALEERLSEYFADIRNRISRVRQKATDEIAKLHRG 337


>gi|71725909|gb|AAZ39073.1| DNA-directed RNA polymerase beta [Exiguobacterium aurantiacum]
          Length = 359

 Score =  226 bits (577), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 155/258 (60%), Positives = 205/258 (79%), Gaps = 1/258 (0%)

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPLL+ ++P +GTGME V AK SGAAI+AK  G+VE+V A  I++R        
Sbjct: 1   NMQRQAVPLLQPDSPIIGTGMEYVSAKDSGAAIIAKYPGVVERVTAREILVRRTSDVNGS 60

Query: 755 STSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             SG +D Y+L K+ RSNQ TC NQ+P++  GD+V + +I+ADGPS D+G+LALGRN++V
Sbjct: 61  MVSGDLDRYKLQKYVRSNQGTCYNQKPIIAAGDQVEKGEILADGPSMDMGELALGRNVVV 120

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
           AFM W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L
Sbjct: 121 AFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDAL 180

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+
Sbjct: 181 RNLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPN 240

Query: 934 GVSGTVVDVRIFNRHGID 951
           G  G ++DV++F+R   D
Sbjct: 241 GGDGIILDVKVFDRENGD 258



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 72/218 (33%), Positives = 113/218 (51%), Gaps = 4/218 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 142  KDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLDDRGIIRIGAEVKDGDIL 201

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++       +  +      K+   + GD++ 
Sbjct: 202  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDGIILDVKVFDRENGDELS 261

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 262  PGVNQMVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 321

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            PSRMN+GQ+ E HLG A   LG K+ + + D     D+
Sbjct: 322  PSRMNIGQVLELHLGMAAKKLGIKVATPVFDGAREEDV 359


>gi|140084112|gb|ABO84905.1| RpoB [Paenibacillus sp. FSL_F4-199]
 gi|140084122|gb|ABO84910.1| RpoB [Paenibacillus sp. FSL_F4-129]
          Length = 227

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 83/201 (41%), Positives = 110/201 (54%), Gaps = 54/201 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 80   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 139

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 140  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 188

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 189  ----------------------------------VFD---------TMEEAGMQRNGKTV 205

Query: 1236 LYDGLTGEPFDRPVTVGYIYM 1256
            LYDG TGE F+R VTVG ++M
Sbjct: 206  LYDGRTGERFEREVTVGVMHM 226



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/88 (64%), Positives = 70/88 (79%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +
Sbjct: 1   DIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKARE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  VRDTSLRVPHGSDGIIVDVKVFTRENGD 88


>gi|52699845|gb|AAU86984.1| DNA-dependent RNA polymerase II second largest subunit [Penicillium
            freii]
          Length = 705

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 134/828 (16%), Positives = 244/828 (29%), Gaps = 150/828 (18%)

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
            R+   G +L + +R    R+ + ++   +        +     I A  +   +     + 
Sbjct: 1    RLDLXGPLLASLFRTLFTRVTKDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATG 60

Query: 521  Q-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
                          +SQ+       S ++H RR +      + R     + R +H TH+G
Sbjct: 61   NWGEQKKAATTKAGVSQVLSRYTFASSLSHLRRTNT----PIGRDGKIAKPRQLHNTHWG 116

Query: 568  RICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENR 625
             +CPAET EG   GLV +L     +      E    +    + +V  +            
Sbjct: 117  LVCPAETPEGQACGLVKNLALMCYITVGTPAEPIVDFMIQRNMEVLEEFEPQVTPNATKV 176

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN 684
            ++      +  D S     +        I      I D  +   K          P    
Sbjct: 177  FVNGVWVGIHRDPSHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVI 236

Query: 685  DDSNRVLM--GCNMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            D+  +     G  + +  +  L+++       G E    +  G      R+G VE VDA 
Sbjct: 237  DNDPKSENSGGLVLNKDHIRKLESDKDLPTDLGPEERREQYFG-WDGLVRSGAVEYVDAE 295

Query: 742  RI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 +I     DL+ S      Y L + +  + N  V  R ++               P
Sbjct: 296  EEETIMIVMTPEDLEISRQLQAGYALPEDETGDPNKRV--RSILS--QRAHTWTHCEIHP 351

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  +                      
Sbjct: 352  SMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAXXXXX----------XNFSQR 394

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
             E   +I    ++ L                        +       +   +  + AI  
Sbjct: 395  METMANILYYPQKPLA-------------------TTRSMEFLRFRELPAGQNAIVAIAT 435

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +     +  +   +      V  + +E   +    + + +
Sbjct: 436  YSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTE----KMVGLQVVERFEKPMRIDTLGM 491

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
             +  Y +L E   +  G           K+  L++D                +E  QR  
Sbjct: 492  RKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAAD---------------AEELGQRTK 536

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K+   T     E+   +++      DD+     + VKV +   +  Q GDK A RHG
Sbjct: 537  AHTKIDVSTPLRSTENGIVDQVLISTGNDDL-----KFVKVRMRTTKIPQIGDKFASRHG 591

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 592  QKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDAT 651

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                     +S L    E    +                                F+G  
Sbjct: 652  PFTDVTVDSVSRLLR--EHGYQSRGFEVM--------------------------FNGHT 683

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                                   G         V +G  Y  +L HMV
Sbjct: 684  -----------------------GR---KMVAQVFLGPTYYQRLRHMV 705



 Score =  102 bits (253), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 77/576 (13%), Positives = 161/576 (27%), Gaps = 68/576 (11%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   +  G  ++  R    +      R          I     
Sbjct: 50  TGGLKYALATGNWGEQKKAATTKAGVSQVLSRYTFASSLSHLRRTNTPIGRDGKIAKPRQ 109

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E       + +   ++   PQ 
Sbjct: 110 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPAEPIVDFMIQRNMEVLEEFEPQV 169

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
             NA  V      F     +    +  + ++ + + RR + +             +RD+ 
Sbjct: 170 TPNATKV------FVNGVWVGIHRDPSHLVTTMQNLRRRNMIS-------HEVSLIRDIR 216

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
              +                         ++     E     V +      +        
Sbjct: 217 EREFKIFTDTGRVCRPLFV----------IDNDPKSENSGGLVLNKDHIRKLE------- 259

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                  ++  L  D    E            LV    ++++DA  ++ + I  +     
Sbjct: 260 -------SDKDLPTDLGPEERREQYFGWD--GLVRSGAVEYVDAEEEETIMIVMTPEDLE 310

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
            +                 P  +  +            +   + I+   A I+   D  +
Sbjct: 311 ISRQLQ-AGYALPEDETGDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQ 369

Query: 743 IVIRSVEGDLDPSTSGVDIYRL-MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
               + +  +              + +         Q+PL                    
Sbjct: 370 SPRNTYQSAMGKQAXXXXXXNFSQRMETMANILYYPQKPL----------ATTRSMEFLR 419

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE- 860
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E 
Sbjct: 420 FRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVVER 479

Query: 861 ----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
               +  D   + +     +DE GI+  G  V+  DI++GK  P         ++     
Sbjct: 480 FEKPMRIDTLGMRKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAADAEELGQRT---- 535

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              KA    D S  + S  +G V  V I   +   K
Sbjct: 536 ---KAHTKIDVSTPLRSTENGIVDQVLISTGNDDLK 568


>gi|254055197|gb|ACT64198.1| RpoB [Streptomyces cinnamonensis]
          Length = 232

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 132/232 (56%), Positives = 179/232 (77%), Gaps = 1/232 (0%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+++ EFF +SQL
Sbjct: 1   RLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N LS +TH RRLSALG GG++R RAG E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+ RVNA+GF+ETPYRKV +G+VT+DV YL+A EE+   IAQAN+ L +D  F E
Sbjct: 121 IGSLASYGRVNAFGFVETPYRKVVEGQVTDDVDYLTADEEDRFVIAQANAPLTDDLHFAE 180

Query: 643 ELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             V  R   GE   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG
Sbjct: 181 ARVLIRRRGGEIDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMG 232


>gi|157781311|gb|ABV72010.1| RNA polymerase beta subunit [Enterococcus casseliflavus]
 gi|157781313|gb|ABV72011.1| RNA polymerase beta subunit [Enterococcus casseliflavus]
 gi|157781315|gb|ABV72012.1| RNA polymerase beta subunit [Enterococcus gallinarum]
 gi|157781317|gb|ABV72013.1| RNA polymerase beta subunit [Enterococcus gallinarum]
          Length = 226

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 93/294 (31%), Positives = 130/294 (44%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 58   -----EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D  ++ D+                                       
Sbjct: 167  ARQLGIHVATPVFDGASDEDVW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                     A           A +    +++LYDG TGEPFD  ++VG +YM+K
Sbjct: 189  ---------ATVAE-------AGMASDAKTVLYDGRTGEPFDGRISVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|153958190|gb|ABS53385.1| RpoB [Bacteriovorax sp. MNZ5]
          Length = 335

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 160/337 (47%), Positives = 223/337 (66%), Gaps = 10/337 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 59   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                 ++   ++  +           + +  +  ++I
Sbjct: 299  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEI 334


>gi|153958230|gb|ABS53405.1| RpoB [Bacteriovorax sp. IH11]
          Length = 346

 Score =  226 bits (577), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 163/349 (46%), Positives = 226/349 (64%), Gaps = 10/349 (2%)

Query: 721  KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
            + S A + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ 
Sbjct: 1    RDSRAVLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKA 58

Query: 781  LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
            LVK GD V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FT
Sbjct: 59   LVKEGDIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFT 118

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            S+HIE FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITP
Sbjct: 119  SVHIEAFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITP 178

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
            KGE+ ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  + 
Sbjct: 179  KGETQLSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEII 238

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLI 1013
             ++  LL RD+  E   +  +   ++ E+L G              +   K   ++ + +
Sbjct: 239  EQETTLLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENL 298

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
            S  P        +Q  +++  +           + +  +  ++I K+  
Sbjct: 299  SAIPFELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHR 346


>gi|153958277|gb|ABS53428.1| RpoB [Bacteriovorax sp. COCO1A]
          Length = 340

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 157/343 (45%), Positives = 224/343 (65%), Gaps = 10/343 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+ +G V  VD+ RIV++    +     SGVD+Y L+K+QR+NQNTC NQR LVK GD 
Sbjct: 1    FAEDSGRVIFVDSNRIVLQRD--NFAEGESGVDVYELVKYQRTNQNTCCNQRALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDIFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +   +  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCSRSKEIIESETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   ++S++++  P   
Sbjct: 239  RRDERIEIKAIQTSSILKIADMLKGAKTTDKLVSEDGSSELLGKGAEVTSEVLASIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                 ++   ++  +           + +  +  + I K+  G
Sbjct: 299  IGYLPLE-ASLEERLSEYFADIRNRINRVRQKATDDIAKLHRG 340


>gi|153958194|gb|ABS53387.1| RpoB [Bacteriovorax sp. MANZ1]
          Length = 337

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 160/337 (47%), Positives = 223/337 (66%), Gaps = 10/337 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK +G V  VD+ RIVI+  +   D   SGVDIY+L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 3    FAKHSGRVIFVDSNRIVIQRNQ--FDDGQSGVDIYKLVKYQRTNQNTCNNQKALVKEGDV 60

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V +  +IADGP T LGDLALG+N+LVAFMPW GYN+EDS+LI+ER+++ DVFTS+HIE +
Sbjct: 61   VSKGMVIADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILINERLLARDVFTSVHIESY 120

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 121  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 180

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 181  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 240

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAV-------SGPKGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   L+S++++  P   
Sbjct: 241  RRDERIEIKAIQTSSILKIADMLKGTKTTDRLVSEDGSTELLPKGADLTSEVLASIPFEL 300

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                 ++   ++  +           + +  +  ++I
Sbjct: 301  IGYLPLE-PALEERLSEYFADVRNRINRVRQKANDEI 336


>gi|117675901|emb|CAL69221.1| RNA polymerase subunit B [Curtobacterium albidum]
          Length = 391

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 149/377 (39%), Positives = 225/377 (59%), Gaps = 22/377 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++      I S  +    G ++  +I   +   + I+    
Sbjct: 19  ERVVVSQLVRSPGVYFERQQEKTSDKDIYSARIIPSRGAWLEFEIDKRDQVGVRIDRKRK 78

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                  +       +I     +     A I +TL  D    +++AL DIYR +RPG+  
Sbjct: 79  QSVTVFLKALGLTSEEIM----EEFQGFASIESTLEKDAVLTKEEALKDIYRKLRPGEQV 134

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+  +YDL+ VGR K++ +L +D P     +  +DI+  IK LV L 
Sbjct: 135 AAEAARALLDNFYFNPKRYDLAKVGRYKLDRKLGIDAPLSDSVLSVQDIVRTIKYLVSLH 194

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             K                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 195 AEKTTLDGVRDGEPVQLRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 254

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 255 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 314

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N++GFIETPYR+V +G+VT 
Sbjct: 315 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFIETPYRRVVNGQVTT 374

Query: 613 DVVYLSAMEEENRYIAQ 629
            + YL+A EE++  +AQ
Sbjct: 375 QIDYLTASEEDDFVVAQ 391



 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 65/172 (37%), Positives = 93/172 (54%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G W
Sbjct: 1   MGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARIIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMEEFQGFASIESTLEKDAVLTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 162


>gi|110734396|gb|ABG88853.1| RNA polymerase II second largest subunit [Rhamphospora nymphaeae]
          Length = 645

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 115/717 (16%), Positives = 218/717 (30%), Gaps = 92/717 (12%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L   +R+   ++ R I   +     +         + +  + + +    
Sbjct: 1    GKKRLDLAGPLLTGLFRMLFRKLTRDIYRHLQKCVEEQRDFHLTSAVKSSTITNGLKYSL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGDQKKFMQAKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            H+G +CPAET EG   GLV +L+  + ++  G    P  +  +    +++V     + + 
Sbjct: 117  HWGMVCPAETPEGQACGLVKNLSLMSMIS-VGSPSAPIIEFLEEFGLDNLVDTQVSDSKA 175

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
              +      +   G+  + +   R       +  E     D   K+              
Sbjct: 176  TKVFVNGVWVGTHGNPAQLVEILRDLRRRDDITTEVSLVHDIREKE----------LRLY 225

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
             D+ RV+    +       LK +   V    E      S     A     + Q   I  +
Sbjct: 226  TDAGRVMRPLFIVDPDDKTLKIKPYHVNWLNEGQKDDGS-----AFGWTQLVQEGVIEYL 280

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                E  +    S  D+    ++Q++     +NQ                A         
Sbjct: 281  DAEEEETVMICMSPRDLELSREYQQNPD-FFLNQ----------------AADEGPKDRT 323

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              L      A   W       +M+  I   ++            ++       +G     
Sbjct: 324  ETLVSPHTFAPNTWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTN 383

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                              +  +             +       +   +  + AI      
Sbjct: 384  FQTRM-----------DTMANILYYPQKPLATTMSMEHLRFRELPAGQNAIVAILCYSGY 432

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    ++ R  +D  ++   V+   +E   +      + L R  
Sbjct: 433  NQEDSVIMNQSAIDRGLF-RSLYYRTYMDMEKKVGVVD---VETFEKPMRHTTIRLKRGT 488

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y ++ +      G           K+T L  D      RS+          V   ++S +
Sbjct: 489  YDKIDDDGLCAPGTRVSGEDIIIGKTTPLPPDSEELGLRSK----THSKRDVSTPLKSTE 544

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
                    +                       + VKV V   R  Q GDK A RHG KG 
Sbjct: 545  AGIVDQVLV----------------TTNADGNKFVKVRVRSTRVPQVGDKFASRHGQKGT 588

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            +      EDMPF   G   DI++NP  +PSRM +G + E  L       G++  +  
Sbjct: 589  IGITYRQEDMPFSVQGITPDIIINPHAIPSRMTIGHLVECLLSKVSTLSGQEGDATP 645



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/361 (11%), Positives = 95/361 (26%), Gaps = 28/361 (7%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR ++    +   F +  ++ +    +  KY L   G      +         + + +
Sbjct: 26  DIYRHLQKCVEEQRDFHLTSAVKSSTITNGLKYSL-ATGNWGDQKKFMQAKAGVSQVLNR 84

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 85  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSMI 144

Query: 489 RISSVDIDSVMPQDLINAKPVVSA-------VCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +   +      +V            F     +         +  +   RR 
Sbjct: 145 SVGSPSAPIIEFLEEFGLDNLVDTQVSDSKATKVFVNGVWVGTHGNPAQLVEILRDLRRR 204

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +            +   ++      + P    +  +  L         +N     +  
Sbjct: 205 DDITTEVSLVHDIREKELRLYTDAGRVMRPLFIVDPDDKTLKIKPYHVNWLNEGQKDDGS 264

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE-------------LVFCR 648
                       + YL A EEE   I  +   L+    + +                   
Sbjct: 265 AFGWTQLVQEGVIEYLDAEEEETVMICMSPRDLELSREYQQNPDFFLNQAADEGPKDRTE 324

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                           +  P  ++ I AS+IPF +++ S R      M +QA+ +     
Sbjct: 325 TLVSPHTFAPNTWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNF 384

Query: 709 P 709
            
Sbjct: 385 Q 385


>gi|261888210|gb|ACY06065.1| beta subunit of RNA polymerase [Volvox carteri f. nagariensis]
          Length = 707

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 144/412 (34%), Positives = 225/412 (54%), Gaps = 44/412 (10%)

Query: 378 YRVMRPGDVSTFSVAESM--------FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           Y+ +   ++ +      +            F +   YDL  +GR+  N +LNL    ++ 
Sbjct: 285 YKDLNYSELISLKKTIELKSEQGRKWIFNKFMNPRTYDLGKIGRLNFNNKLNLAISSNIT 344

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK-- 487
            +  +D +A    L+ +  G   +DDID+L NRRVR+ GE+++ Q  +GL+R+E++I+  
Sbjct: 345 TLTAQDFLAATNNLILVSKGMRELDDIDHLKNRRVRTAGELIQMQIGVGLVRLEKTIREK 404

Query: 488 --------------------------------ERISSVDIDSVMPQDLINAKPVVSAVCE 515
                                             +S      +   +++N KP   A+ E
Sbjct: 405 MSLVLITNQSKKKKDFFKKTKNKKEKRIRGQMHCLSLASSRELTINNIMNTKPFNGALRE 464

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +S LSQ  + +N L+ +TH RRLS++G GGV R  A + +R +HP+HYGRICP ET 
Sbjct: 465 FFGTSPLSQFMDQINPLAELTHKRRLSSMGPGGVTRDSATLAIRGIHPSHYGRICPVETP 524

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSS 633
           EG N GLV+SLT++ARVN+ G+IETP+ +V  G+V     + + SA +EE   +  A+  
Sbjct: 525 EGKNTGLVNSLTAYARVNSQGYIETPFYRVYKGQVQKKKGLFFFSAKQEEKIKLGAADLY 584

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             + G   +  +  R   +   + R +I ++  +P Q++SIA SLIPF E+DD+NR LMG
Sbjct: 585 TSDIGFLPKASIPVRIVEDFTKIARNEIQYVGVAPIQMISIATSLIPFFEHDDANRALMG 644

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            NMQRQAVP+LK + P VGTG+E+     SG  + AK +GIV    + +I+I
Sbjct: 645 SNMQRQAVPILKPQRPIVGTGLEARAVSDSGHVVTAKYSGIVTYTSSKKIII 696


>gi|56694368|gb|AAW22924.1| RNA polymerase II second largest subunit [Drimys winteri]
          Length = 565

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 81/486 (16%), Positives = 149/486 (30%), Gaps = 83/486 (17%)

Query: 804  DLALGRNMLVAFMPWHGYNFED---SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             +++  N LV+     G  + +      I   ++     + I   +     R+T      
Sbjct: 160  MISMTINDLVSARLNRGVAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 219

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                   V+   L+      +  V        +    +       +      + AI    
Sbjct: 220  KQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 276

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +        +F R   D+ ++  ++ +E      R+          
Sbjct: 277  GYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSY 335

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +          G           K+T ++                  DE   +     + 
Sbjct: 336  DKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ-----------------DESQGQASRYTRR 378

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             + TS    E    +++      D +     R VKV +   R  Q GDK + RHG KG V
Sbjct: 379  DHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRVPQIGDKFSSRHGQKGTV 433

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +      
Sbjct: 434  GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 493

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               +IS         +                                            
Sbjct: 494  TVDNISKALHKCGYQMRGFETM-------------------------------------- 515

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
                      +G +    G         + +G  Y  +L HMV DK+++R  G   ++T+
Sbjct: 516  ---------YNGHT----GR---KLSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTR 559

Query: 1281 QPLGGK 1286
            QP  G+
Sbjct: 560  QPAEGR 565



 Score =  117 bits (292), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 74/482 (15%), Positives = 139/482 (28%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 3   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 62

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 63  IHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                    + A    ET      D      + Y+   EEE   I+              
Sbjct: 122 RKK-----DIRALQQRETQEEGWHDLVAKGFIEYVDTEEEETTMISM----------TIN 166

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R          E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 167 DLVSARLNRGV--AYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 224

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 225 IYVTNYQL--------------------RMDTLAYV------------------------ 240

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 241 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 279

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 280 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 339

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           +         RD S  +    SG
Sbjct: 340 DDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLRHSESG 390

Query: 938 TV 939
            V
Sbjct: 391 MV 392


>gi|59043057|gb|AAW83881.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043067|gb|AAW83886.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043111|gb|AAW83908.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043145|gb|AAW83925.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  226 bits (576), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 132/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|153958271|gb|ABS53425.1| RpoB [Bacteriovorax sp. HA2]
          Length = 342

 Score =  226 bits (575), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 159/345 (46%), Positives = 227/345 (65%), Gaps = 10/345 (2%)

Query: 724  GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
            GA + A+ +G V  VD+ RIV++  +   +   SGVD+Y L+K+QR+NQNTC NQR LVK
Sbjct: 1    GAILFAEESGRVIFVDSNRIVLQRDK--FEEGESGVDVYELVKYQRTNQNTCCNQRALVK 58

Query: 784  VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
             GD V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+H
Sbjct: 59   EGDIVKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDIFTSVH 118

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            IE +EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE
Sbjct: 119  IESYEVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGE 178

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
            + ++PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +   +
Sbjct: 179  TQLSPEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCSRSKEIIESE 238

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEY 1016
              L+ RD+  E   +  +   ++ E+L G              +   K   ++S++++  
Sbjct: 239  TTLIRRDERIEIKAIQTSSILKIAEMLNGAKTTDKLVSEDGSTELLAKGAEVTSEVLASI 298

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
            P        ++   ++  +           + +  +  + I K+ 
Sbjct: 299  PFELIGYLPLE-ASLEERLSEYFADIRNRINRVRQKATDDIAKLH 342


>gi|28279989|gb|AAH44796.1| Polr3b protein [Mus musculus]
          Length = 205

 Score =  226 bits (575), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 63/262 (24%), Positives = 97/262 (37%), Gaps = 78/262 (29%)

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            G PSRM VG++ E   G                                           
Sbjct: 5    GFPSRMTVGKLIELLAGK------------------------------------------ 22

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                       A          T  F G+  + +   L     +  G+  +  G+TGEP 
Sbjct: 23   -----------AGVLDGRFHYGT-AFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPL 70

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  +  G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+  Y
Sbjct: 71   EAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGY 130

Query: 1306 GAAYVLQEMLTIKSDDVVGRTRVYESIVAGN-----------------DTFETGTPESFN 1348
            GA+ +L E L I SD        +E  V G                         P +  
Sbjct: 131  GASMLLLERLMISSD-------AFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACK 183

Query: 1349 VLVKEMQALGLSIDLENSRTKN 1370
            +L +E+Q++ +   L+ ++   
Sbjct: 184  LLFQELQSMNIIPRLKLAKYNE 205


>gi|59043101|gb|AAW83903.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  226 bits (575), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 130/228 (57%), Positives = 168/228 (73%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF  SQL Q  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGPSQLPQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|153958283|gb|ABS53431.1| RpoB [Bacteriovorax sp. JS8]
          Length = 343

 Score =  226 bits (575), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 163/346 (47%), Positives = 225/346 (65%), Gaps = 10/346 (2%)

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK G
Sbjct: 1    VLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEG 58

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE
Sbjct: 59   DIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIE 118

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ 
Sbjct: 119  AFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQ 178

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  
Sbjct: 179  LSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETT 238

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPR 1018
            LL RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P 
Sbjct: 239  LLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPF 298

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                   +Q  +++  +           + +  +  ++I K+  GD
Sbjct: 299  ELIGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHRGD 343


>gi|124487781|gb|ABN11976.1| putative RNA polymerase I 135 kDa subunit [Maconellicoccus hirsutus]
          Length = 274

 Score =  225 bits (574), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/306 (22%), Positives = 104/306 (33%), Gaps = 76/306 (24%)

Query: 1028 DEKVQRNVESLKVQYE-TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
            D+      + +   Y     +  E+ F + +       D    V +   V + + R    
Sbjct: 25   DDFYYSYYDPIMQAYSLGKFTGKEEAFVDAVRLCGDFYDDKSSVRK-ACVILRISRNPSV 83

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A R G KGI S     ED+PF + G   DIV NP G PSRM +  + E   G    
Sbjct: 84   GDKFASRAGQKGIFSLAYKPEDLPFTESGLVPDIVFNPHGFPSRMTIAMMIECMAGKTAS 143

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G    +    Y                                               
Sbjct: 144  IHGLVHDASPFQYDE--------------------------------------------- 158

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                 D    +    +L+    +  G  I+Y G+ G      +  G ++  +L HMVSDK
Sbjct: 159  -----DKTAIDYFGELLQAGGYNYYGDEIMYSGVDGTEMPASIFFGVVHYQRLRHMVSDK 213

Query: 1267 VYARSTGSYSLVTQQPL------------GGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
               R+TG   ++T+QPL                        EME   + ++GA ++LQ+ 
Sbjct: 214  WQVRNTGPVDILTRQPLKGRKRGGGGRVG------------EMERDALISHGAPFLLQDR 261

Query: 1315 LTIKSD 1320
             T  SD
Sbjct: 262  FTDCSD 267


>gi|330038580|ref|XP_003239637.1| DNA-directed RNA polymerase I 135K chain [Cryptomonas paramecium]
 gi|327206561|gb|AEA38739.1| DNA-directed RNA polymerase I 135K chain [Cryptomonas paramecium]
          Length = 1102

 Score =  225 bits (574), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 85/343 (24%), Positives = 123/343 (35%), Gaps = 73/343 (21%)

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
                S+  D ++  + +          +   +K  +  +R   +GDK A RHG KG+ S 
Sbjct: 816  NQRISVYYDSYEKSVIECLKLTLKKEKINCTIK--LRARRKPNTGDKFASRHGQKGVFSM 873

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
              PC DMPF + G   DI+ NP G PSRM +G I E+  G      G    S        
Sbjct: 874  NCPCIDMPFSEIGIVPDIIFNPHGFPSRMTIGVIVESLAGKVSCLNGFFYDSSPFCLNKK 933

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                       + T  F           
Sbjct: 934  ------------------------------------------HLETYCF--------GEK 943

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            LR +     G  I Y G TGEP    V  G I+  +L HMV+DK         + +T+QP
Sbjct: 944  LRESGFKFYGNEIFYSGYTGEPLKIEVYNGIIHYQRLKHMVNDKFQVSEISPRNSITRQP 1003

Query: 1283 LGGKSNRGG-QRLGEMEVWCIQAYGAAYVLQEMLTIKSD-----------DVVGRTRVYE 1330
            + GK   GG  R GEME   +  +G+ ++L + L + SD           D+     VY+
Sbjct: 1004 IKGK-KFGGSIRFGEMERDVLLGHGSTFLLHDRLQLSSDLHSIKINMKTCDMFSLKPVYK 1062

Query: 1331 SIVA-----GNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             I         + F    P +   L  E+  L +  +L  S  
Sbjct: 1063 KIHDRTFFSNKNAF---LPYASKFLATELLVLNIKFNLVPSDG 1102



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 101/733 (13%), Positives = 213/733 (29%), Gaps = 120/733 (16%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP------ 84
           ++   S+++              GL + F     I +     +++        P      
Sbjct: 21  KLHLESFNY---AMTQGLFLIISGLSSYFLDF--IFS-KYKIVIQITGLYVSKPYSLKKE 74

Query: 85  -KFD--VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
            K+      C     +Y         L +F ++     K+        I +G +P+M K 
Sbjct: 75  IKYKVIPRQCKETKSSYKGDF-----LSIFHINHRKERKNFL------IRIGKIPIMVKS 123

Query: 142 ------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                                   G F++ G ++I+   L   P  +F H   R +   K
Sbjct: 124 LKCNLFNANSRQMVEIDEENLEMGGYFIVNGAEKIIRPLLV--PKRNFIHVVSRIANLKK 181

Query: 178 -LLYACRIIPDQGLWMDIEFDSK---------DIIHVRIDRRR---KVPVTSFLMAL-GM 223
             LY       +   +D   +SK           IHVRI  ++    +P+   L +L  +
Sbjct: 182 HKLYTSLSCSFRS--VDKIQNSKTFHLHYLISGNIHVRIVFKKHEFFIPIVILLKSLIDI 239

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL--T 281
             ++++  F                 +   ++   + + S  +I   ++V+    K+  T
Sbjct: 240 SDKKLIDIFGYFD--------LGNKYTRQRILTMIREAYSYCNISKRKEVLNFMGKILKT 291

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGL----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           +     L    +  + ++      L        D++     ++         E + + I 
Sbjct: 292 AFDFDFLTNSEISEVFLSKYLFIHLGSEYKSKFDLLLLMVQKLLYAYKGNYSENNYDSIE 351

Query: 338 HSEIRDIPILYVDSVNN--NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
             E+     LY+  +       I N  +    K+ K  L  +        +    +  S 
Sbjct: 352 SQELLLPGHLYLIYLRERFENSIYNYFLNKIKKENKYTLKYLKNSFNLVTIDIEKLVSS- 410

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
              + F+  +  +   G      RLN       R +     I     L+  +        
Sbjct: 411 -GNICFNFKEELIQLSGLSVSVERLNFG-----RFLSYFRNIHKGNFLLQSKKNTSRKIF 464

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                   +  V         +        I    +S++        + N    +    +
Sbjct: 465 P--HSWGYICPVHTSDGLLCGISNYLSFSVIFNSSNSIEKKKFKKYLIRNGFDEIEHTQK 522

Query: 516 FFCS----SQLSQLEEHVNSLSRITHTRRLSALGQGGVA-RARAGVEMRDVHPTHYGRIC 570
            F       +L    E++  L  I    R   + + G+  ++   +  R +    +   C
Sbjct: 523 PFIPILLDGKLLGFCENL-KLEWIIDKIRCEKISRLGIIPKSMEILYNRRIFTKGFFSSC 581

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
              + E   +  V         N Y   +  +      +           E+E   I   
Sbjct: 582 SFLSEENRLLRPVL-------CNNYVHTKNFFFSKKANQFNFQ------TEKELELIGPN 628

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
              L        E    R               ++     ++S+ A+L PF + + S R 
Sbjct: 629 EQFLLNIQFLENENKENRKKFFW--------THLEIDSSIILSLVAALTPFSDLNQSPRN 680

Query: 691 LMGCNMQRQAVPL 703
              C M +Q++ +
Sbjct: 681 TYQCQMFKQSIGV 693


>gi|59043049|gb|AAW83877.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  225 bits (574), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF  SQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGPSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|256077165|ref|XP_002574878.1| DNA-directed RNA polymerase I subunit [Schistosoma mansoni]
 gi|238660094|emb|CAZ31111.1| DNA-directed RNA polymerase I subunit, putative [Schistosoma mansoni]
          Length = 1155

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 99/249 (39%), Gaps = 51/249 (20%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLG 1126
             G      + + + R    GDK + RHG KGI S ++ CE+MP+   +G   D++ NP G
Sbjct: 854  NGSWSCATITLRLPRQPDIGDKYSSRHGQKGINSLLIQCEEMPWSTTNGLIPDLIFNPHG 913

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
             P+RM +G + E   G +    G  I +    +                           
Sbjct: 914  FPTRMTMGMMIEFLAGKSAALTGNLIDATPFQWSE------------------------- 948

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                     D    E    +L     +  G   +  G TG   +
Sbjct: 949  -------------------------DSPPYEDYCQILTDCGFNHWGTETMMSGSTGRQLE 983

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + VG +Y  +L HMV+DK   R+ G +  + +QP+ G+   GG RLGEME  C+ ++G
Sbjct: 984  AQIYVGVVYYQRLRHMVADKYQVRAEGRFDPILRQPIKGRKVGGGIRLGEMERDCLLSHG 1043

Query: 1307 AAYVLQEML 1315
              + LQ+ L
Sbjct: 1044 LVFSLQDRL 1052



 Score = 50.8 bits (120), Expect = 0.002,   Method: Composition-based stats.
 Identities = 33/159 (20%), Positives = 52/159 (32%), Gaps = 54/159 (33%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFV--SYEFDPPK- 85
           L  V   S+D F+           EGL    K + P+   SG+ ++EF     E  PP  
Sbjct: 4   LSRVHTGSFDFFV----------KEGLSRLVKHLQPLEFNSGSDVVEFKIQFIEVAPPVD 53

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C    LTY   LK+++R+ V                   +  G LP+M
Sbjct: 54  SDNRSTLLYPSECRRSGLTYGGELKLSVRVSVNGSPLGVL----------DVPCGVLPIM 103

Query: 139 TKD------------------------GTFVIKGIQRIV 153
                                      G F++ G +R++
Sbjct: 104 VMSRACNLSSLPRSQFYLHGEEFKEIGGYFIVHGKERVL 142


>gi|123979366|gb|ABM81508.1| RNA polymerase II second largest subunit [Pyxine sorediata]
          Length = 704

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 119/822 (14%), Positives = 227/822 (27%), Gaps = 142/822 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R    ++ + +    +    +         + +  + + +     +
Sbjct: 2    KRLDLAGPLLAGPFRTLFNKLNKDVEKYLKNCIENNREFNLTLGVKSTTITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKASSSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     V+     E    +      +   +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYVSVGTPSEGIVEFLLSRQMEPLEEYDPLASPHATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +    +     V        I      I D  D   K +      L P F+
Sbjct: 178  IFVNGVWVGIHRSPAHLVLAVQSLRRRHVIEHEVSLIRDIRDREFKILTDQGRVLRPLFV 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAI 741
              +D+     G  +  +           V   M+    +            G+VE VDA 
Sbjct: 238  IENDAKEQNYGNLVLTKEHVERLEADRDVPLDMDKEEREQLTFGWHGLINEGVVEYVDAE 297

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                  +            I         N     N+R    +             PS  
Sbjct: 298  EEETIMIVMTPYDLNVSRQIQAGYVLPEEND-ENPNRRVKAPINPTAHTWTHCEIHPSMI 356

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            LG       +  + +P+  +N                        ++       +G    
Sbjct: 357  LG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGVFLT 391

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
              D    +           +  +             +       +   +  + AI     
Sbjct: 392  NFDQRMET-----------MSHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG 440

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    +F R   D+ ++   +    +E   +    + + L   
Sbjct: 441  YNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKK---IGMYTMEQFEKPLRSDTLKLKHG 496

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   I+ G           K+  ++ D      R++          ++     L
Sbjct: 497  TYEKLDDDGIIIPGARVSGEDIIIGKTAPIAPDAEELGQRTKLHNKRDASTPLRSTESGL 556

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q   + +                       LR VKV +   +  Q GDK A RHG KG
Sbjct: 557  VDQVLLTVN--------------------SEGLRFVKVRMRTTKIPQIGDKFASRHGQKG 596

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 597  TIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFT 656

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                  +S L    E    +                                        
Sbjct: 657  DVTVDSVSRLLR--EHGYQSRGFEVM---------------------------------- 680

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                        +G +    G         V +G  Y  +L 
Sbjct: 681  -----------YNGHT----GR---KLVAQVFLGPTYYQRLR 704



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 83/561 (14%), Positives = 173/561 (30%), Gaps = 62/561 (11%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + +  K   S  G  ++  R    +      R          I    
Sbjct: 51  ITNGLKYSLATGNWGEQKKASSSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPR 110

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +      ++KN   +  + +    +  +  +    + P +  
Sbjct: 111 QLHNTHWGLVCPAETPEGQACG---LVKNLALMCYVSVGTPSEGIVEFLLSRQMEPLEEY 167

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +      A   F     +       + +  +   RR   +             +RD+   
Sbjct: 168 DPLASPHATKIFVNGVWVGIHRSPAHLVLAVQSLRRRHVI-------EHEVSLIRDIRDR 220

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +  +    T +G  +  +  + + A+   YG +      V   +   DV  L   +EE 
Sbjct: 221 EFKIL----TDQGRVLRPLFVIENDAKEQNYGNLVLTKEHVERLEADRDV-PLDMDKEER 275

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +      L  +G                      ++++DA  ++ + I  +      +
Sbjct: 276 EQLTFGWHGLINEG---------------------VVEYVDAEEEETIMIVMTPYDLNVS 314

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
                       +    P  + +AP   T       +   + I+   A I+   D  +  
Sbjct: 315 RQIQ-AGYVLPEENDENPNRRVKAPINPTAHTWTHCEIHPSMILGICASIIPFPDHNQSP 373

Query: 745 IRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
             + +  +     GV       + +  +      Q+PL                      
Sbjct: 374 RNTYQSAMGKQAMGVFLTNFDQRMETMSHILYYPQKPL----------ATTRSMEFLKFR 423

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT- 862
           +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E   
Sbjct: 424 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKKIGMYTMEQFE 483

Query: 863 ----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                D   +     + +D+ GII  GA V+  DI++GK  P         ++       
Sbjct: 484 KPLRSDTLKLKHGTYEKLDDDGIIIPGARVSGEDIIIGKTAPIAPDAEELGQRT------ 537

Query: 919 EKAVDVRDTSLRVPSGVSGTV 939
            K  + RD S  + S  SG V
Sbjct: 538 -KLHNKRDASTPLRSTESGLV 557


>gi|117675897|emb|CAL69219.1| RNA polymerase subunit B [Curtobacterium flaccumfaciens pv. betae]
          Length = 390

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 151/375 (40%), Positives = 225/375 (60%), Gaps = 22/375 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++     GI S  +    G ++  +I   +   + I+    
Sbjct: 20  ERVVVSQLVRSPGVYFERQQEKTSDKGIYSARIIPSRGAWLEFEIDKRDQVGVRIDRKRK 79

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                  +       +I     D     A I +TL  D    +++AL DIYR +RPG+  
Sbjct: 80  QSVTVFLKALGLTSEEIM----DEFQGFASIESTLEKDAVLTKEEALKDIYRKLRPGEQV 135

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+  +YDL+ VGR K+N +L +D P     +  +DI+A IK LV L 
Sbjct: 136 AAEAARALLDNFYFNPKRYDLAKVGRYKVNRKLGMDAPLSDSVLTVKDIVATIKYLVSLH 195

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 196 AERTTIDGVRDGEPVQLRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 255

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 256 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 315

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N++GFIETPYR+V DG+VT 
Sbjct: 316 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFIETPYRRVVDGEVTK 375

Query: 613 DVVYLSAMEEENRYI 627
            + YL+A EE++  +
Sbjct: 376 TIDYLTASEEDDFVV 390



 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/173 (37%), Positives = 94/173 (54%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G 
Sbjct: 1   FMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKGIYSARIIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMDEFQGFASIESTLEKDAVLTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EEALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163


>gi|258562152|gb|ACV81798.1| RNA polymerase II second largest subunit [Piriformospora indica]
          Length = 619

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 106/646 (16%), Positives = 200/646 (30%), Gaps = 80/646 (12%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 35   GVSQVLNRYTYASTLSHLRRTNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 90

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L+  A ++   +       + +  +        A+EE     AQ++    +    
Sbjct: 91   GLVKNLSLMACISVGSYSAPVGEFLDEWGME-------ALEEN----AQSDRPSTKVFLN 139

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
               +   R   + +   +         P+  V             DS RV     +  + 
Sbjct: 140  GVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRIYTDSGRVCRPLFVVEKD 199

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
              L+  E        +   A      +       +   +    V+  +  +   + S   
Sbjct: 200  KLLITPEQVARLRDEKDDPAGYRWDNLFKDGVVELLDAEEEETVMICMSPEDLDARSSGQ 259

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
            +Y        +       + ++K G            PS  LG       +  + +P+  
Sbjct: 260  VYHTEDMYDPSSRV----KTIIKAGSYSH----CEIHPSMILG-------VCASIVPFPD 304

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N          M  + +  S+       + R   +         P  +   L+ +    
Sbjct: 305  HNQSPRNTYQSAMGKQAMGISLSNF----LVRMDTMANILYYPQKPLATTRALEWL---- 356

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                                     +   +  + AI      +  D+ +   S +   + 
Sbjct: 357  ---------------------KFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 395

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+ R  +D  + +  +  E+ E  +RD        + +       I  G N +    
Sbjct: 396  -RSIYYRSYMDMEKTAGQITLEEFEKPSRDTTLRMKHGNYDKLDDDGLIAPGMNVIGEDI 454

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L  D      R+           ++     +      +               
Sbjct: 455  IIGKTAPLPPDSQELGQRTDRHTRRDVSTPLKSTESGIIDHVLITV-------------- 500

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VK+ V   R  Q GDK A RHG KG +  +   EDMPF  DG   D+
Sbjct: 501  ------DGEGSKFVKIRVRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDL 554

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            ++NP  +PSRM +G + E  L       G++  +          +S
Sbjct: 555  IINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVS 600


>gi|117675893|emb|CAL69217.1| RNA polymerase subunit B [Curtobacterium flaccumfaciens pv.
           poinsettiae]
          Length = 391

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 152/377 (40%), Positives = 226/377 (59%), Gaps = 22/377 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++      I S  +    G ++  +I   +   + I+    
Sbjct: 19  ERVVVSQLVRSPGVYFERQQEKTSDKDIYSARIIPSRGAWLEFEIDKRDQVGVRIDRKRK 78

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                  +       +I     D     A I +TL  D    +++AL DIYR +RPG+  
Sbjct: 79  QSVTVFLKALGLTSEEIM----DEFQGFASIESTLEKDAVLTKEEALKDIYRKLRPGEQV 134

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+S +YDL+ VGR K+N +L +D P     +  +DI+A IK LV L 
Sbjct: 135 AAEAARALLDNFYFNSKRYDLAKVGRYKVNRKLGMDAPLSDSVLTVKDIVATIKYLVSLH 194

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 195 AERTTIDGIRDGEPVQLRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 254

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 255 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 314

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N++GFIETPYR+V DG+VT 
Sbjct: 315 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFIETPYRRVVDGEVTK 374

Query: 613 DVVYLSAMEEENRYIAQ 629
            + YL+A EE++  + Q
Sbjct: 375 TIDYLTASEEDDFVVRQ 391



 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/172 (37%), Positives = 93/172 (54%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G W
Sbjct: 1   MGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARIIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMDEFQGFASIESTLEKDAVLTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EALKDI--------YRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 162


>gi|328792060|ref|XP_001120416.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 [Apis
            mellifera]
          Length = 1122

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/351 (19%), Positives = 114/351 (32%), Gaps = 96/351 (27%)

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                +    ++ ++    +   + R   +   + R    GDK A R G KGI S+    E
Sbjct: 828  KYHGKEDAYVDTVKLCGTLHNHIPRRACITFRIPRNPSVGDKFASRAGQKGICSQKWSAE 887

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            D+PF + G   DIV NP G PSRM +  + E   G +    G    +    +        
Sbjct: 888  DLPFTETGLIPDIVFNPHGFPSRMTIAMMIELMAGKSAAIHGLVHDATSFRFNE------ 941

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                        D    E    +L    
Sbjct: 942  --------------------------------------------DETAVEYFGKLLERGG 957

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
             +  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG   ++T+QP+    
Sbjct: 958  YNYYGTERMYSGIDGREMTADIFFGVVHYQRLRHMVSDKWQVRSTGPIDVLTRQPIK--- 1014

Query: 1288 NRGGQRLG-----------EMEVWCIQAYGAAYVLQEMLTIKSDDVV------------- 1323
                               EME   + ++G +++LQ+ L   SD                
Sbjct: 1015 --------GRRRGGGVRFGEMERDSLISHGCSFLLQDRLFHCSDKTTTLVCQKCGTLLGP 1066

Query: 1324 ---------GRTRVYESIVAGND--TFETGTPESFNVLVKEMQALGLSIDL 1363
                     G        + G++    E   P  F  LV ++ +  +++ L
Sbjct: 1067 IMEMALNASGLGNKLRCRLCGDNESVREIDIPYIFRYLVTQLTSCNINVKL 1117



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 82/576 (14%), Positives = 187/576 (32%), Gaps = 64/576 (11%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
            + ++    I ++ R             F      +D      + +  + + LN      
Sbjct: 287 NNHEECKAYIGKMFR----------IKFFELPEDATDIDVCDFIIKHCIAIHLNNPLD-- 334

Query: 428 VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY------------ 475
               +   +  + K L  L N K  ++  D++  +     G +                 
Sbjct: 335 ----KFYLLAFMTKKLFALANNKCAVEGADSVMMQECLLGGHLYLQVLKEKLYSWLTNLK 390

Query: 476 -------RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF----FCSSQLSQ 524
                  R    R   +++E ++ +   + +   + N     +           ++ L+ 
Sbjct: 391 MSILKRARSAGNRYTLNVQEMLNIMKYGNSLESQMENFLSTGNLRSSTGLGLMQNTGLTI 450

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           + E++N +  ++H R   A+ +G   +     E R + P  +G ICP  T +G   GL++
Sbjct: 451 VAENINRMRYMSHFR---AIHRGSFFQEMRTTEARQLLPDAWGFICPVHTPDGAPCGLLN 507

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            LT    +  +   +              +    A   +N YI   +  L       ++ 
Sbjct: 508 HLTMNCIITKHPDAKLKANIPIILMDLGMIPLSIADNWKNSYIVMLDGKLI---GLIDDN 564

Query: 645 VFCRC--AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +  R       + +  +++ ++            +  P L             M R  + 
Sbjct: 565 IIARVTDKLRLLKIKGQEVPYMMEIALVPKKTVPAQYPGL-----YLFTSPARMMRPIMN 619

Query: 703 LLKAEAPFVGTG--MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           L      ++GT   +   +  +   A     +       A    + S+    D + S  +
Sbjct: 620 LAAKNIEYIGTFEQIYLDICVTPEEAYEGLTSHQELSKTAFLSNLASLIPMPDYNQSPRN 679

Query: 761 IYRLMKFQRSNQNTCVN--QRPLVKVGDEVRRNDIIA---DGPSTDLGDLALGRNMLVAF 815
           +Y+    +++    C     +   K+         +         +L D A+G N +VA 
Sbjct: 680 MYQCQMSKQTMGTPCHTWQLQSETKLYRLQTPATPLFRPVHHDKINLDDFAMGTNAIVAV 739

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           + + GY+ ED+M+I++           H   ++    D K       R+      E ++ 
Sbjct: 740 ISYTGYDMEDAMIINKAAYDRGFA---HGMIYKSEFIDLKDQKSYFARNPD--KSELVEK 794

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           +D  G+   G  ++ GD+          + +T +  
Sbjct: 795 LDIDGLPLPGTIISEGDVYYCYYDADQSTYITGKYH 830



 Score = 68.9 bits (167), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 111/770 (14%), Positives = 221/770 (28%), Gaps = 164/770 (21%)

Query: 15  KFFGKNPEIIDIPDLIE----VQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP---ITA 67
           K FGK PE  +   L++        S+++ L           +GL  A K   P   I  
Sbjct: 12  KNFGKPPEKQNP--LLQRLGAPHIDSFNYML----------EDGLCKAVKDN-PHVYIHL 58

Query: 68  FSG-AAMLEFVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
            +     L       D P            K    +C  R  +Y   + + L   + D  
Sbjct: 59  PNKDKVALWIDDVSIDQPSVPSGIIGIKTHKIYPTECRQRGCSYKGKITVKLGWSINDKL 118

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQ 150
           + T A+           +G++P+M K                         G FVIKG++
Sbjct: 119 QETLARD----------LGEIPIMIKSNRCHLNKMNPKDLILHGEHEQEWGGYFVIKGLE 168

Query: 151 RIV-----------VSQLHRSP-----------GIHFDHDKGRASLSGKLLYACRIIPDQ 188
           RI+           ++ + RS            G+     +   + +   L+        
Sbjct: 169 RIIRMLLMTRRNYPIA-IKRSGWKTRGIQFSDLGLFLRSVRDDNTTANNTLHYVT----D 223

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFP 248
           G    + F  K +++        VP+   L  L +D  +I    Y  +      D +   
Sbjct: 224 GS-AKLMFSHKKVLYY-------VPLILILKCL-VDVSDI--FIYNVLTAGCEYDLYYKG 272

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYV 308
                L   A     L + +  +  I    ++       L E          D +    +
Sbjct: 273 CILNMLR--AVHEQGLNNHEECKAYIGKMFRI---KFFELPEDATDIDVC--DFIIKHCI 325

Query: 309 AEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIR 359
           A  + N           T +++  A +    +  + +   E      LY+  +    Y  
Sbjct: 326 AIHLNNPLDKFYLLAFMTKKLFALANNKCAVEGADSVMMQECLLGGHLYLQVLKEKLYSW 385

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
            T +             I +  R          + M N + + +     S +        
Sbjct: 386 LTNLKMS----------ILKRARSAGNRYTLNVQEMLNIMKYGNSLE--SQMENFLSTGN 433

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY-RLG 478
           L   T   +       I+A     +   +    I         R     ++L + +  + 
Sbjct: 434 LRSSTGLGLMQNTGLTIVAENINRMRYMSHFRAIHRGSFFQEMRTTEARQLLPDAWGFIC 493

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVS--AVCEFFCSSQLSQLEEHVNSLSRIT 536
            +         + +    + +     +AK   +   +        LS  +   NS   + 
Sbjct: 494 PVHTPDGAPCGLLNHLTMNCIITKHPDAKLKANIPIILMDLGMIPLSIADNWKNSYIVML 553

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             + +  +    +AR    + +  +              +G  +  +  +    +     
Sbjct: 554 DGKLIGLIDDNIIARVTDKLRLLKI--------------KGQEVPYMMEIALVPKKTVPA 599

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                Y      ++   ++ L+A   E  YI         +  + +  V    A E +  
Sbjct: 600 QYPGLYLFTSPARMMRPIMNLAAKNIE--YIGTF------EQIYLDICVTPEEAYEGLT- 650

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                   + S    +S  ASLIP  + + S R +  C M +Q +     
Sbjct: 651 -----SHQELSKTAFLSNLASLIPMPDYNQSPRNMYQCQMSKQTMGTPCH 695


>gi|148628042|gb|ABQ97026.1| RNA polymerase II second largest subunit [Arthroderma ciferrii]
          Length = 703

 Score =  225 bits (574), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 129/821 (15%), Positives = 240/821 (29%), Gaps = 140/821 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+  +R+ + + +  +        +     + A  +   +     +
Sbjct: 2    KRLDLAGPLLANLFRVLFMRLTKDLYKYVQRCVETGRQLYLNIGVKASTLSGGLKYALAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKAASSKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     +      E    +    + +V  +     +     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  D +     V        I      + D  D   K          P F+
Sbjct: 178  VFVNGVWVGVHRDPAHLVGTVQSLRRRNMISHEVSLVWDIRDREFKIFTDAGRVCRPLFV 237

Query: 683  ENDDSNRVLMGC-NMQRQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
             ++D      G   + ++ +  L+A+         E    +  G   + K +G+VE VDA
Sbjct: 238  VDNDPKSENSGSLVLIKEHIHKLEADKELPPDLDPEERRERHFGWDGLVK-SGVVEYVDA 296

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                   +    +   +    Y+          T  N+R    +  +          PS 
Sbjct: 297  EEEETIMIVMTPEDLEAS-KQYQAGYGMPEEDTTDRNRRVKSNLSQKAHTWTHCEIHPSM 355

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N               VF +                  E
Sbjct: 356  ILG-------ICASIIPFPDHNQSPRNTYQSAXXXXXVFLTNF------------EQRME 396

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               +I    ++ L                        +       +   +  + AI    
Sbjct: 397  TMANILYYPQKPLA-------------------TTRSMEFLKFRELPAGQNAIVAIACYS 437

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D  +       E+ E   R           
Sbjct: 438  GYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEKMIGLTVVERFEKPMRSDTLRMKHGTC 496

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       +  G           K++ L+ +                +E  QR  +  K+
Sbjct: 497  DKVDDDGIVSPGVRVSGEDIIIGKTSPLAPE---------------AEELGQRTKQHTKL 541

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E    +++      DD+     + VKV +   +  Q GDK A RHG KG +
Sbjct: 542  DVSTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTI 596

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF ++G   D+V+NP  +PSRM +  + E  L       G +  +      
Sbjct: 597  GITYRHEDMPFTREGVTPDLVINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTDV 656

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +S L    E    +                                          
Sbjct: 657  TVDSVSSLLR--EHGYQSRGFEVM------------------------------------ 678

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                      +G +    G         V +G  Y  +L H
Sbjct: 679  ---------YNGHT----GR---KLVAQVFLGPTYYQRLRH 703


>gi|59043079|gb|AAW83892.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  225 bits (573), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF S QLSQ  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSPQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|117675871|emb|CAL69206.1| RNA polymerase subunit B [Cryobacterium psychrophilum]
          Length = 388

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 149/373 (39%), Positives = 223/373 (59%), Gaps = 22/373 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++      I S  +    G ++  +I   +  ++ +     
Sbjct: 20  ERVVVSQLVRSPGVYFDRQQEKTSDKDIYSARVIPSRGAWLEFEI--DKRDQVGVRIDRK 77

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +     +    +    IL  +       I  TL  D    +++AL DIYR +RPG+  
Sbjct: 78  RKQSVTVFLKALGLSSEEIL--EEFKGFPSIELTLEKDNILTKEEALKDIYRKLRPGEQV 135

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  FF+S +YDL+ VGR K+N +L L+ P     +  +DI+A IK LV L 
Sbjct: 136 AAEAARALLDNFFFNSKRYDLAKVGRYKINRKLGLEAPLSDSVLTLQDILATIKYLVSLH 195

Query: 448 NGKGTIDDID---------------NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           + + TI  +                + GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 196 DNRSTIVGLRDGKTTDINIDIDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 255

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 256 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRD 315

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+NA+GFIETPYR+V + KVT 
Sbjct: 316 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINAFGFIETPYRRVVNNKVTE 375

Query: 613 DVVYLSAMEEENR 625
            + YL+A EE++ 
Sbjct: 376 TIDYLTASEEDDF 388



 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 68/173 (39%), Positives = 94/173 (54%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTFVI G +R+VVSQL RSPG++FD  + +   S K +Y+ R+IP +G 
Sbjct: 1   FMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFDRQQEKT--SDKDIYSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  +P I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEEILEEFKGFPSIELTLEKDNILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EEALKDI--------YRKLRPGEQVAAEAARALLDNFFFNSKRYDLAKVGRYK 163


>gi|52699900|gb|AAU87011.1| DNA-dependent RNA polymerase II second largest subunit [Thelocarpon
            laureri]
          Length = 715

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 127/835 (15%), Positives = 228/835 (27%), Gaps = 142/835 (17%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D  G  R+   G +L   +R+   ++   + +  +              + A  + + + 
Sbjct: 1    DXXGXXRLDLAGPLLAXLFRMLFNKLTXDVYKYLQKCVESNREFNLXLGVKASTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R  
Sbjct: 61   YSLATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQX 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSA 619
            H TH+G +CPAET EG   G V +L     +      E    +       +  + +   +
Sbjct: 117  HNTHWGLVCPAETPEGQACGXVKNLALMCYITVGSPSEPLVXFMVARGMXILEEYIPSKS 176

Query: 620  MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASL 678
                  ++      +  +     + V        I      I D  D   +         
Sbjct: 177  PNATKIFVNGVWVGVHNNPXRXADTVSEVRKQHSIPPEVSMIRDIRDREFRISSDAGRVC 236

Query: 679  IP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
             P F+  +D      G     +    L      +    E    + +        AG+VE 
Sbjct: 237  RPLFVIENDPXEEXYGQLRLTKEHVXLXDNXANIEAXTEXEREEKTFGWKGLVDAGVVEY 296

Query: 738  VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            VDA      ++   + P    +       +Q    NT   +R    +             
Sbjct: 297  VDAEEEE--TIMIVMTPEDLEIXRQLXAGYQXPEXNTSSXKRVKAPLNXTAHTWTHXXIH 354

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            PS   G       +  +  P+  +N          M  +                   +G
Sbjct: 355  PSMIXG-------ICASIXPFPDHNQSPRNTXQSAMGKQ------------------AMG 389

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                                      +             +       +   +  + AI 
Sbjct: 390  XXXXXXXXXXXXXXX-----------ILYYPQKPXATTRSMEFLKXRELPAGQNAIVAIA 438

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S     +    +F R   D+ +R   +    IE   +    + + 
Sbjct: 439  CYSGYNQEDSVIMNQSSXDRGLF-RSLFYRAYTDQEKR---IGMSTIEQFEKPMRGDTLX 494

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            L    Y +L +   I  G           K+  ++ D                +E  QR 
Sbjct: 495  LKXGTYDKLDDDGIIAPGVRVSGEDVIIGKTAPIAPD---------------AEELGQRT 539

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +K    T     E    +++             LR V V +   +  Q GD  A RH
Sbjct: 540  KXHVKRDVSTPLRSTESGXVDQVLL-----TTNAEGLRXVXVRMRTTKVPQXGDXFASRH 594

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +GT  D+++NP  +PSRM +  +    L       G +  +
Sbjct: 595  GQKGTIGITYRQEDMPFTSEGTIPDLIINPHAIPSRMTIAHLIXCQLSKVASLKGYEGDA 654

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                      +S L S  E    +                                    
Sbjct: 655  TPFTDVTVDSVSGLLS--EHGYQSRGFEVM------------------------------ 682

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYA 1269
                            +G +    G         V +G  Y  +L HMV D + A
Sbjct: 683  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLRHMVDDXIXA 715



 Score = 53.9 bits (128), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/381 (11%), Positives = 88/381 (23%), Gaps = 36/381 (9%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +        NK   D    + + +       F++   +      +  KY L   G  
Sbjct: 12  GPLLAXLFRMLFNKLTXDVYKYLQKCVESNR--EFNLXLGVKASTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQXHNTHWGLVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV--------CEFFCSSQ 521
             + Q    +  +       + S     V          +   +          F     
Sbjct: 129 TPEGQACGXVKNLALMCYITVGSPSEPLVXFMVARGMXILEEYIPSKSPNATKIFVNGVW 188

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDV-------HPTHYGRICPAE 573
           +            ++  R+  ++     + R     E R          P       P E
Sbjct: 189 VGVHNNPXRXADTVSEVRKQHSIPPEVSMIRDIRDREFRISSDAGRVCRPLFVIENDPXE 248

Query: 574 TSEGHNIGLVSSLTSF-----ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
              G        +                 E              V Y+ A EEE   I 
Sbjct: 249 EXYGQLRLTKEHVXLXDNXANIEAXTEXEREEKTFGWKGLVDAGVVEYVDAEEEETIMIV 308

Query: 629 QANSSLDEDGS-------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                L+                   +     +             P  +  I AS+ PF
Sbjct: 309 MTPEDLEIXRQLXAGYQXPEXNTSSXKRVKAPLNXTAHTWTHXXIHPSMIXGICASIXPF 368

Query: 682 LENDDSNRVLMGCNMQRQAVP 702
            +++ S R      M +QA+ 
Sbjct: 369 PDHNQSPRNTXQSAMGKQAMG 389


>gi|45120570|gb|AAO64659.2| RNA polymerase II subunit RPB2 [Gautieria otthii]
          Length = 856

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 112/865 (12%), Positives = 236/865 (27%), Gaps = 148/865 (17%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
            +Y    + +  +      +  +  +         ++  L+     +  +DD D+ G +R+
Sbjct: 123  RYAQEILQKEMLPHIAMSEGAESKK---AYFFGYMVHRLLLAALERRELDDRDHFGKKRL 179

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L + +R+   ++ + +    +              +    + + +     +   
Sbjct: 180  DLAGPLLASLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAVKPNTITNGLKYSLATGNW 239

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +                           
Sbjct: 240  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPXXXXXXXXXXXXXX----XXXXXXX 295

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
                  EG   GLV +L   A ++           + +  + +         EEN + A 
Sbjct: 296  XXXXXXEGQACGLVKNLALMACISVGSPSPPVIEFLEEWGLESL--------EENAHSAT 347

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 348  PCTKVFVNGVWLG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGR 404

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            V     +       L+ +                    +          D      +  +
Sbjct: 405  VCRPLFIVENQQLALQKK-------------------HIKWLQQGYRDDDPAHGQYKWDD 445

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                     +D           +   ++  P       +++  +  +    +    A  +
Sbjct: 446  MVKGGIIELLD-------AEEEETVMISMTPEDLENSRLQQQGVQTNTNDGEFDPAARLK 498

Query: 810  NMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
            +++ A   W       SM+  I   ++            ++       +G       I  
Sbjct: 499  SVMHAH-TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLIRM 557

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 558  -----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDS 606

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    ++ R  +D  + S   + E+     RD          +      
Sbjct: 607  VIMNQSSIDRGLF-RSMYYRSYMDMEKTSGIHQLEEFTKPTRDTTLRMKHGTYDKLEDDG 665

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K+  + ++                +E  Q+     +    T   
Sbjct: 666  LIAPGTGVRGEDIIIGKTAPIPAE---------------SEELGQKTSSHTRRDVSTPLK 710

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E    +++      D       R VKV V   R  Q GDK A RHG KG +      E
Sbjct: 711  STESGIVDQVLITTGSD-----GQRFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQE 765

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   DI++NP  +PSRM +G + E  L      +G +                
Sbjct: 766  DMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD-------------- 811

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     E+++++LR   
Sbjct: 812  ---------------------------------------ATP-FTELTVESVSTLLRKQG 831

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVG 1252
                G  ++Y G TG      + +G
Sbjct: 832  YHSRGLEVMYHGHTGRKLQAQIYLG 856



 Score =  137 bits (346), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 111/809 (13%), Positives = 229/809 (28%), Gaps = 109/809 (13%)

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-VPVTSFL 218
           SP       +      GK +   ++          E  S ++I   I   +  +P+    
Sbjct: 3   SPINFLAEIRSAVEKGGKTVSTFQVKMFHRSQ---EKSSGNVIKATIPYIKTDIPIWVVF 59

Query: 219 MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
            ALG+ S+ +IL      +  +Q  +     +    ++    V+   +        +   
Sbjct: 60  RALGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDRDVALDFIGNRGTTIGLSRD 119

Query: 278 KKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           ++L     + L+++ +  + ++           G  V   ++        ++  D   +K
Sbjct: 120 RRLRYAQ-EILQKEMLPHIAMSEGAESKKAYFFGYMVHRLLL-AALERRELDDRDHFGKK 177

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            L+           +L+   + +   Y++  + T K  +   A+          +  T  
Sbjct: 178 RLDLAGPLLASLFRMLFRKLTKDVYRYLQKCVETHKEFNLNLAV--------KPNTITNG 229

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK 450
           +  S+    + D  K   S  G  ++  R    +       R                  
Sbjct: 230 LKYSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLS-HLRRCNTPXXXXXXXXXXXXXX 288

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
                              ++KN   +  + +       I  ++   +      NA    
Sbjct: 289 XXXXXXXXXXXXXEGQACGLVKNLALMACISVGSPSPPVIEFLEEWGLE-SLEENAHSAT 347

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
                F     L    +  N +  I   RR   +                ++        
Sbjct: 348 PCTKVFVNGVWLGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCR 407

Query: 571 PAETSEG-HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           P    E          +    +            K  D      +  L A EEE   I+ 
Sbjct: 408 PLFIVENQQLALQKKHIKWLQQGYRDDDPAHGQYKWDDMVKGGIIELLDAEEEETVMISM 467

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFL 682
               L+      + +      GE          +        +  P  ++ I AS+IPF 
Sbjct: 468 TPEDLENSRLQQQGVQTNTNDGEFDPAARLKSVMHAHTWTHCEIHPSMILGICASIIPFP 527

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +                                       
Sbjct: 528 DHNQSPRNTYQSAMGKQAMGIYLTNFLI-------------------------------- 555

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                       + + +  Y       +     +  R                       
Sbjct: 556 ---------RMDTMANILYYPQKPLATTRSMEYLKFR----------------------- 583

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEI 861
            +L  G+N +VA + + GYN EDS+++++  +   +F S++   +  M + + +   EE 
Sbjct: 584 -ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDMEKTSGIHQLEEF 642

Query: 862 TRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           T+        +       +++ G+I  G  V   DI++GK  P         +K      
Sbjct: 643 TKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPAESEELGQKT----- 697

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              +   RD S  + S  SG V  V I  
Sbjct: 698 --SSHTRRDVSTPLKSTESGIVDQVLITT 724


>gi|94983666|gb|ABF50559.1| RNA polymerase beta subunit [Bosea eneae]
          Length = 149

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 85/152 (55%), Positives = 103/152 (67%), Gaps = 3/152 (1%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLGK+I   I+ Y+   D   LR+  +
Sbjct: 1    DGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGKQIGKAIDAYRKAHDSKALRASFD 60

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V       E I+  DD  ++ + +  + GVP++TPVF+GA E  I  +L  A L  SGQ
Sbjct: 61   AVYEDN---EIIASMDDAELIEMGQNLRRGVPIATPVFNGAKESDIERLLEQAGLHSSGQ 117

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            S LYDG TGEPFDR VT+GYIYMLKL+H+V D
Sbjct: 118  STLYDGRTGEPFDRKVTMGYIYMLKLHHLVDD 149


>gi|3133447|gb|AAC38524.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
          Length = 217

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 131/217 (60%), Positives = 170/217 (78%), Gaps = 1/217 (0%)

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RD
Sbjct: 1   QTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRD 60

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A 
Sbjct: 61  VHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTAD 120

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   +AQANS +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++I
Sbjct: 121 EEDRHVVAQANSPVDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMI 180

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           PFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGME
Sbjct: 181 PFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGME 217


>gi|68131836|gb|AAY85196.1| RNA polymerase II second largest subunit [Chimonanthus praecox]
          Length = 906

 Score =  225 bits (573), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 125/825 (15%), Positives = 252/825 (30%), Gaps = 118/825 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTKEKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEILQKEMLPHVGTGEYCETKK---AYYFGYIIHRLLLCAIGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK V S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTVTSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTFASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAAHPILEFLEEWSTEN-------FEEISPAVIPQATK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + + + R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPDLLVKTLRLLRRRV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+                K        +           +  I  V+ + +
Sbjct: 523  LFIVEKQRLLI--------------KKKDIRVLQQRETQEEGWHDLVAKGFIEYVDTEEE 568

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 569  ETTMISMTISDLVSARLNPEEAYS-----------DTYTHCEIHPSLILG-------VCA 610

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 611  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 643

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 644  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 701

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 702  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGT 760

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K++ ++                  DE   +     +  + TS    E   
Sbjct: 761  RVSGEDVIIGKTSPIAQ-----------------DESQGQTSRYTRRDHSTSLRHSESGM 803

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 804  VDQVLLTTNADGL-----RFVKVRMRSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTL 858

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 859  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 903



 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 120/907 (13%), Positives = 257/907 (28%), Gaps = 164/907 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +           + + +E   +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCE--EVTETQEFTKVFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAENQNRPPSSMFVRMLSRASSKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTKEKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                K + +K +     T +                  + + A     E   +   +  
Sbjct: 237 --KYAKEILQKEMLPHVGTGEYCETKKAYYFGYIIHR--LLLCAIGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTVTSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTFASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAAHPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRLLRRRVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + +         +      ET      D      + Y+   EEE   I+         
Sbjct: 529 QRLLIKKK-----DIRVLQQRETQEEGWHDLVAKGFIEYVDTEEEETTMISM-------- 575

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 576 --TISDLVSARLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 631

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 632 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 652

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 653 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIAC 686

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 687 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGS 746

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK +P  +           +         RD S  + 
Sbjct: 747 YDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDE---------SQGQTSRYTRRDHSTSLR 797

Query: 933 SGVSGTV 939
              SG V
Sbjct: 798 HSESGMV 804


>gi|258562134|gb|ACV81789.1| RNA polymerase II second largest subunit [Tephrocybe rancida]
          Length = 622

 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 107/639 (16%), Positives = 199/639 (31%), Gaps = 78/639 (12%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 59   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 114

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   + ++   +       + +  + +         EEN + +   + +  +G +
Sbjct: 115  GLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSSTPCTKVFVNGVW 166

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                   R     +   ++     D SP+  V             D+ RV     +    
Sbjct: 167  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQ 223

Query: 701  VPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
               L+ +   ++  GM+         ++V  + G+VE +DA       +    +   +  
Sbjct: 224  QLTLEKKHIRWLQNGMDDDQKAYKWESLV--KGGVVELLDAEEEETVMISMTPEDLETSR 281

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +       N   +    +K G            PS  LG       +  + +P+ 
Sbjct: 282  LQQSGV---NPAANDDFDPAARLKAGINSHTWTHCEIHPSMILG-------ICASIIPFP 331

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N                        ++       +G       I              
Sbjct: 332  DHNQSPR------------------XTYQSAMGKQAMGIFLTNFLIRM-----------D 362

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 363  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 422

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                I+ R  +D  ++S   + E+ E  ARD          +       I  G       
Sbjct: 423  F-RSIYYRSYMDLEKKSGIQQLEEFEKPARDSTLRMKHGTYDKLEDDGLIAPGTGVAGED 481

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  D      R++          ++     +  Q                  
Sbjct: 482  IIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI--------------- 526

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                        + VKV V   R  Q+GDK A RHG KG +      EDMPF  +G   D
Sbjct: 527  -----TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGITYRQEDMPFTAEGIVPD 581

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I++NP  +PSRM +G + E  L      +G +  +    
Sbjct: 582  IIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT 620



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 87/604 (14%), Positives = 169/604 (27%), Gaps = 102/604 (16%)

Query: 375 LDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            D+YR ++        F++A ++ +    +  KY L   G      +         + + 
Sbjct: 7   KDVYRYLQKCVETHKEFNLALAVKHQTITNGLKYSL-ATGNWGDQKKSMSAKAGVSQVLN 65

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    + +  L        R GK       +  +  +    E  + Q    +  +     
Sbjct: 66  RYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSC 125

Query: 488 ERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
             + S     +             NA         F     +    +  N +  I   RR
Sbjct: 126 ISVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRR 185

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
              +            +   ++        P    E   + L      + + N     + 
Sbjct: 186 KDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLTLEKKHIRWLQ-NGMDDDQK 244

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL----- 655
            Y K         V  L A EEE   I+     L E     +  V      +        
Sbjct: 245 AY-KWESLVKGGVVELLDAEEEETVMISMTPEDL-ETSRLQQSGVNPAANDDFDPAARLK 302

Query: 656 --VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
             +        +  P  ++ I AS+IPF +++ S R      M +QA+ +          
Sbjct: 303 AGINSHTWTHCEIHPSMILGICASIIPFPDHNQSPRXTYQSAMGKQAMGIFLTNFLI--- 359

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                                                    + + +  Y       +   
Sbjct: 360 --------------------------------------RMDTMANILYYPQKPLATTRSM 381

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
             +  R                        +L  G+N +VA + + GYN EDS+++++  
Sbjct: 382 EYLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSS 417

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEV 888
           +   +F SI+   +  + + + +   E            +       +++ G+I  G  V
Sbjct: 418 IDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPARDSTLRMKHGTYDKLEDDGLIAPGTGV 477

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DI++GK  P         ++        +    RD S  + S  SG V  V I    
Sbjct: 478 AGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNS 530

Query: 949 GIDK 952
              K
Sbjct: 531 EGQK 534


>gi|56694370|gb|AAW22925.1| RNA polymerase II second largest subunit [Asarum caudatum]
          Length = 565

 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 80/506 (15%), Positives = 146/506 (28%), Gaps = 84/506 (16%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 140  HDLVAKGFIEYVDTEEEETTMISMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 199

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+   L+      +  V        +    +  
Sbjct: 200  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEH 256

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 257  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 315

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R+          +          G           K+T ++           
Sbjct: 316  KEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---------- 365

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE   +     +  + T+    E    +++      D +     R VKV +  
Sbjct: 366  -------DESQGQASRYTRRDHSTALRHSESGMVDQVLLTTNADGL-----RFVKVRMRS 413

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 414  VRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 473

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+  +          IS         +                        
Sbjct: 474  MGKVAAHMGKEGDATPFTDVTVDSISRALHKCGYQMRGFETM------------------ 515

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                          +G +    G         + +G  Y  +L 
Sbjct: 516  -----------------------------YNGHT----GR---RLTAMIFLGPTYYQRLK 539

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGK 1286
            HMV DK+++R  G   ++T+QP  G+
Sbjct: 540  HMVDDKIHSRGRGPVQILTRQPAEGR 565



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 75/482 (15%), Positives = 140/482 (29%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 3   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 62

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 63  IHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                    + A    ET      D      + Y+   EEE   I+              
Sbjct: 122 KKK-----DIRALQQRETHEEGWHDLVAKGFIEYVDTEEEETTMISM----------TIN 166

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 167 DLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 224

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 225 IYVTNYQL--------------------RMDTLAYV------------------------ 240

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 241 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 279

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 280 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 339

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           +         RD S  +    SG
Sbjct: 340 DDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTALRHSESG 390

Query: 938 TV 939
            V
Sbjct: 391 MV 392


>gi|153958246|gb|ABS53413.1| RpoB [Bacteriovorax sp. SF1]
          Length = 341

 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 160/344 (46%), Positives = 228/344 (66%), Gaps = 10/344 (2%)

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + AK  G V  VD+ RIV++  +   +   SGVDIY L+K+QR+NQ+TC NQ+ LVK G
Sbjct: 1    VLFAKDDGKVIFVDSNRIVLQRNK--FEDGESGVDIYSLVKYQRTNQSTCNNQKALVKEG 58

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D VR+ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+HIE
Sbjct: 59   DIVRKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSVHIE 118

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             FEV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ 
Sbjct: 119  AFEVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQ 178

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  
Sbjct: 179  LSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETT 238

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPR 1018
            LL RD+  E   +  +   ++ E+L G              +  +K   ++ +++++ P 
Sbjct: 239  LLRRDERIEIKAIQTSAILKIAEMLKGAKTTDKLVSEDGSTELLQKGADITGEVLAQIPF 298

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                   +Q  +++  +           + +  +  ++I K+  
Sbjct: 299  ELIGYLPLQ-AELEERLSEYFADIRNRINRVRQKTTDEIAKLHR 341


>gi|94983662|gb|ABF50557.1| RNA polymerase beta subunit [Bosea sp. CRIB-10]
          Length = 149

 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 85/152 (55%), Positives = 103/152 (67%), Gaps = 3/152 (1%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLGK+I   I+ Y+   D   LR+  +
Sbjct: 1    DGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGKQIGKAIDAYRKAHDSKALRASFD 60

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V       E I+  DD  ++ + +  + GVP++TPVF+GA E  I  +L  A L  SGQ
Sbjct: 61   AVYEDN---EIIASMDDAELIEMGQNLRRGVPIATPVFNGAKETDIERLLEQAGLHSSGQ 117

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            S LYDG TGEPFDR VT+GYIYMLKL+H+V D
Sbjct: 118  STLYDGRTGEPFDRKVTMGYIYMLKLHHLVDD 149


>gi|117675903|emb|CAL69222.1| RNA polymerase subunit B [Curtobacterium herbarum]
          Length = 388

 Score =  224 bits (572), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 147/376 (39%), Positives = 224/376 (59%), Gaps = 22/376 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+     ++      I S  +    G ++  +I   +   + I+    
Sbjct: 15  ERVVVSQLVRSPGVYFERAQEKTSDKDIYSARIIPSRGAWLEFEIDKRDQVGVRIDRKRK 74

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                  +       +I     +     A + +TL  D    +++AL DIYR +RPG+  
Sbjct: 75  QSVTVFLKALGLTSEEIM----EEFQGFASMESTLEKDAVLTKEEALKDIYRKLRPGEQV 130

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+S +YDL+ VGR K++ +L +D P     +  +DI+A IK LV L 
Sbjct: 131 AAEAARALLDNFYFNSKRYDLAKVGRYKLDRKLGIDAPLSDAVLTVQDIVATIKYLVSLH 190

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             +                 +DDID+ GNRR+R+ GE+++NQ R GL RMER ++ER+++
Sbjct: 191 AERTTMDGVRDGEPVQLRLDVDDIDHFGNRRIRAAGELIQNQVRTGLSRMERVVRERMTT 250

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 251 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 310

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N++GFIETPYR+V +G+VT 
Sbjct: 311 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFIETPYRRVVNGEVTK 370

Query: 613 DVVYLSAMEEENRYIA 628
            + YL+A EE++  +A
Sbjct: 371 TIDYLTASEEDDFVVA 386



 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 61/168 (36%), Positives = 90/168 (53%), Gaps = 13/168 (7%)

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G W++ E
Sbjct: 1   PLMTERGTFIINGTERVVVSQLVRSPGVYFERAQEKT--SDKDIYSARIIPSRGAWLEFE 58

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAAD 253
            D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  +  +   D       A  
Sbjct: 59  IDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMEEFQGFASMESTLEKDAVLTKEEALK 118

Query: 254 LMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 DI--------YRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 158


>gi|59043083|gb|AAW83894.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043121|gb|AAW83913.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++H RRLSA G GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSASGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|207109467|ref|ZP_03243629.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
            HPKX_438_CA4C1]
          Length = 185

 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 81/185 (43%), Positives = 113/185 (61%), Gaps = 6/185 (3%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            MP GV++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P  DMP+  DG PVDIVLNPL
Sbjct: 1    MPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPL 60

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK- 1184
            GVPSRMN+GQI E HLG      GK+I  ++ D K       LR+ + ++    +  +  
Sbjct: 61   GVPSRMNIGQILEMHLGLVGKEFGKQIARMLED-KTKDFAKELRAKMLEIANAINEKDPL 119

Query: 1185 ----ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                + +  D+ +L  A+ W  GV ++ PVF+G  +E    +  +A +   G+  LYDG 
Sbjct: 120  TIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGR 179

Query: 1241 TGEPF 1245
            TGE  
Sbjct: 180  TGEKM 184


>gi|106734119|gb|ABF82546.1| DNA-directed RNA polymerase III [Exiguobacterium sp. Indian Stream]
          Length = 337

 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 164/305 (53%), Positives = 218/305 (71%), Gaps = 2/305 (0%)

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTS 757
            QAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +    
Sbjct: 1    QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQG 60

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +D Y++ KF RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV FM 
Sbjct: 61   ELDRYKIQKFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLVGFMT 120

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D
Sbjct: 121  WDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLD 180

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            + GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 181  DRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240

Query: 938  TVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  ++  
Sbjct: 241  IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMP 300

Query: 997  SGPKG 1001
              P G
Sbjct: 301  YMPDG 305



 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 59/186 (31%), Positives = 93/186 (50%), Gaps = 4/186 (2%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 138  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 197

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 198  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 257

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 258  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 317

Query: 1128 PSRMNV 1133
            PSRMN+
Sbjct: 318  PSRMNI 323


>gi|59043063|gb|AAW83884.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 133/228 (58%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ     N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMNQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ETSEG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETSEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|117675899|emb|CAL69220.1| RNA polymerase subunit B [Curtobacterium citreum]
          Length = 391

 Score =  224 bits (572), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 148/376 (39%), Positives = 224/376 (59%), Gaps = 22/376 (5%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+    +++      I S  +    G ++  +I   +   + I+    
Sbjct: 18  ERVVVSQLVRSPGVYFERQQEKTSDKDIYSARIIPSRGAWLEFEIDKRDQVGVRIDRKRK 77

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                  +       +I     +     A I +TL  D    +++AL DIYR +RPG+  
Sbjct: 78  QSVTVFLKALGLTSEEIM----EEFQGFASIESTLEKDAVLTKEEALKDIYRKLRPGEQV 133

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+  +YDL+ VGR K++ +L +D P     +  +DI+  IK LV L 
Sbjct: 134 AAEAARALLDNFYFNPKRYDLAKVGRYKLDRKLGIDAPLSDSVLSVQDIVRTIKYLVSLH 193

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
             K                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 194 AEKTTLDGVRDGEPVQLRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 253

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 254 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 313

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SF R+N++GFIETPYR+V +G+VT 
Sbjct: 314 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFGRINSFGFIETPYRRVVNGQVTT 373

Query: 613 DVVYLSAMEEENRYIA 628
            + YL+A EE++  +A
Sbjct: 374 QIDYLTASEEDDFVVA 389



 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 64/171 (37%), Positives = 92/171 (53%), Gaps = 13/171 (7%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G W+
Sbjct: 1   GDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARIIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  I  +   D       
Sbjct: 59  EFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMEEFQGFASIESTLEKDAVLTKEE 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
           A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 ALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 161


>gi|149238948|ref|XP_001525350.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Lodderomyces
            elongisporus NRRL YB-4239]
 gi|146450843|gb|EDK45099.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Lodderomyces
            elongisporus NRRL YB-4239]
          Length = 1157

 Score =  224 bits (571), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 75/311 (24%), Positives = 119/311 (38%), Gaps = 64/311 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  +VKV +   R  + GDK +                                   
Sbjct: 899  SDNDQALVKVLLRQTRRPELGDKFS----------------------------------- 923

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR         H      G+  + + L      +  ISP          +     K+ 
Sbjct: 924  --SR---------HGQKGVCGIIVQHEDLPF---NDDGISPDIIMNPHGFPSRMTVGKMI 969

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
            +        +    + G       F G+  E ++ +L       SG+ +LY G+TGE   
Sbjct: 970  ELISGKAGVLNGSLEYGTC-----FGGSKLEDMSKILVSKGFSYSGKDMLYSGITGECLQ 1024

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1025 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1084

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRV--YES---IVAG-NDTFETGTPESFNVLVKEMQA 1356
            A+ +L E L I SD    DV  +  +  Y S      G  +  +   P +  +L +E+ +
Sbjct: 1085 ASQLLLERLMISSDAFEVDVCNKCGLMGYNSWCTTCKGSENIIKMTIPYAAKLLFQELLS 1144

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 1145 MNIAPRLRLGD 1155



 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 129/1001 (12%), Positives = 272/1001 (27%), Gaps = 205/1001 (20%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K         L++    S+++F+  ++    + N         V P         +++
Sbjct: 47  FLKIKG------LVKQHLDSFNYFVDTDLKKILKANS---LVLSDVDP------DFYVKY 91

Query: 77  VSYEFD----------PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
           +                      +C  RDLTY+ P+ + +             +  K I+
Sbjct: 92  LDIRVGHKSTSAPGTKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIR 141

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
              + +G +P+M                           G FV+ G +++++ Q   S  
Sbjct: 142 HNDLEIGRMPVMLRSNKCMLDGLDERQMAQVDECPLDPGGYFVVNGTEKVILVQEQLSKN 201

Query: 163 IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV---------- 212
                   +  +    + +               + K   +V I +  K+          
Sbjct: 202 RIIVEADDKKGIVQASVTSST------------HERKSKTYV-ITKNGKIYLKHNSIGED 248

Query: 213 -PVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
            P+   L A G+ S+ EIL        + Q  D +      A  +       +L+ +   
Sbjct: 249 VPIVIVLKAAGITSDLEILQLVCGSNPHYQ--DLFVVNFEEAARLEVFTQQQALLYLGKR 306

Query: 271 EQVIESGKKLTSGLLKSLKEK---------GVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
            + I          L+   E           V  L           +A  +V        
Sbjct: 307 VKTIRRAGAPKLSQLQEGIEAIATTIVAHLTVSNLQFKEKAFYMAMMARRVVMAMHNPKM 366

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRV 380
           ++  D +  K LE            L+    ++     + ++   ++  + DALL I   
Sbjct: 367 VDDRDYVGNKRLELAGQLMSLLFEDLFKKFNSDFKANIDKILKKPSRTTEFDALLSINIH 426

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAII 440
                           +   +   ++ +   G   +  RL+  +   +            
Sbjct: 427 SNN----ITMGLNRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSR 482

Query: 441 KI--LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSV 498
           K+     L+  +  +    +        + + L     +     E  IK+   ++  +S+
Sbjct: 483 KVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITTDDEELPIKKLCIALGCESI 542

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           +  D      V      F   + +      V  ++   H RR   +            + 
Sbjct: 543 LGLDSSTL-HVDGNFGVFLNGTLIGATRFPVKFVNDFRHLRRAGKVSAFISIYTNTHHQA 601

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
             +         P    E +   +        +      +     +  D      V YL 
Sbjct: 602 VHLATDGGRICRPLIIVEKNKSKV--------QSEHLKKLLRGEWQFDDFLREGLVEYLD 653

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EE +  IA     +  + + T                   +  ++  P  V+   A L
Sbjct: 654 VNEENDSLIALYEKDIGSNANAT-------------------VTHLEIEPFTVLGAVAGL 694

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IP+  ++ S R    C M +QA+                                     
Sbjct: 695 IPYPHHNQSPRNTYQCAMGKQAIGA----------------------------------- 719

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                 I   +     +     +Y               Q+P+VK               
Sbjct: 720 ------IAYNQFKRIDTLLYFMVYP--------------QQPMVK----------TKTIE 749

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE-------EFEVMA 851
             +   L  G+N  VA M + GY+ ED++++++  +         +        ++    
Sbjct: 750 LINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSLDRGFGRCQVVRKNTVQLKKYPNHT 809

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
           +D   G      + P    +    +   G+  VG+ +  G +   K  P      T    
Sbjct: 810 KDILSGMRVDENNEPIFPHQA---LGPDGLGEVGSRIENGQVFANKFVPTNSGESTFAGG 866

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           + +    E   +               V+     N   + K
Sbjct: 867 MQQQPQAESHREAAQYYKGPEPSYVDQVMMSVSDNDQALVK 907


>gi|157781307|gb|ABV72008.1| RNA polymerase beta subunit [Enterococcus dispar]
          Length = 226

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 80/206 (38%), Positives = 107/206 (51%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP+L
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPYL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+       
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGANDEDVW------ 188

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                     A  +        A +    
Sbjct: 189  -----------------------------------------ATVKE-------AGMASDA 200

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            +++LYDG TGEPFD  ++VG +YM+K
Sbjct: 201  KTVLYDGRTGEPFDGRISVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|106734123|gb|ABF82548.1| DNA-directed RNA polymerase III [Exiguobacterium sp. M37]
          Length = 340

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 154/254 (60%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ ++P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG
Sbjct: 1   QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSG 60

Query: 759 -VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM 
Sbjct: 61  DLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMT 120

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D
Sbjct: 121 WDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLD 180

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G
Sbjct: 181 DRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 240

Query: 938 TVVDVRIFNRHGID 951
            ++DV++F+R   D
Sbjct: 241 IILDVKVFDRENGD 254



 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 85/295 (28%), Positives = 129/295 (43%), Gaps = 17/295 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 60   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 118

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 119  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 177

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 178  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 237

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 238  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 284

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            GNKG++SRILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG
Sbjct: 285  GNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLG 339


>gi|94983660|gb|ABF50556.1| RNA polymerase beta subunit [Bosea sp. CRIB-12]
          Length = 149

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 84/152 (55%), Positives = 105/152 (69%), Gaps = 3/152 (1%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLGK+I   ++ YK + D   L++  +
Sbjct: 1    DGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGKQISQALDAYKKSHDFKALKAQFD 60

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V       E I+  D++ ++ + +  + GVPV+TPVF+GA E  I  +L  A L  SGQ
Sbjct: 61   AVYEDN---EIIASMDENELVEMGQNLRRGVPVATPVFNGAKEADIERLLEQAGLHSSGQ 117

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            S LYDG TGEPFDR VT+GYIYMLKL+H+V D
Sbjct: 118  STLYDGRTGEPFDRKVTMGYIYMLKLHHLVDD 149


>gi|153958273|gb|ABS53426.1| RpoB [Bacteriovorax sp. PR3]
          Length = 342

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 156/342 (45%), Positives = 223/342 (65%), Gaps = 10/342 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             A+ +G V  VD+ RIV++    +     SGVD+Y L+K+QR+NQNTC NQR LVK GD 
Sbjct: 4    FAEDSGRVIFVDSNRIVLQRD--NFAEGESGVDVYELVKYQRTNQNTCCNQRALVKEGDI 61

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T LGDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE +
Sbjct: 62   VKKGDVLADGPGTHLGDLALGQNVLVAFMPWGGYNYEDSILISEDLLAQDIFTSVHIESY 121

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 122  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 181

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +   +  L+
Sbjct: 182  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCSRSKEIIESETTLI 241

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ ++L G              +   K   ++S++++  P   
Sbjct: 242  RRDERIEIKAIQTSSILKIADMLKGAKTTDKLVSEDGSTELLGKGAEVTSEVLASIPFEL 301

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                 ++   ++  +           + +  +  + I K+  
Sbjct: 302  IGYLPLE-ASLEERLSEYFADIRNRINRVRQKATDDIAKLHR 342


>gi|315277598|ref|ZP_07869516.1| DNA-directed RNA polymerase subunit beta [Listeria marthii FSL
            S4-120]
 gi|313615683|gb|EFR88981.1| DNA-directed RNA polymerase subunit beta [Listeria marthii FSL
            S4-120]
          Length = 124

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 57/101 (56%), Positives = 73/101 (72%)

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDT 1338
            TQQPLGGK+  GGQR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G   
Sbjct: 1    TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESV 60

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPD 1379
             E G PESF VL+KE+Q+LG+ + + ++  +     +   D
Sbjct: 61   PEPGVPESFKVLIKELQSLGMDVKMLSADEEEIEMRDMDDD 101


>gi|153958265|gb|ABS53422.1| RpoB [Bacteriovorax sp. OC8]
          Length = 339

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 158/342 (46%), Positives = 225/342 (65%), Gaps = 10/342 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +   +   +GVDIY L+K+QR+NQNTC NQ+ LVK GD 
Sbjct: 1    FAKGNGRVIFVDSNRIVIQRDK--FEEGETGVDIYELVKYQRTNQNTCNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP T +GDLALG+N+LVAFMPW GYN+EDS+L+SE ++S D+FTS+HIE +
Sbjct: 59   VKKGDVLADGPGTHMGDLALGQNVLVAFMPWGGYNYEDSILLSEDLLSRDIFTSVHIESY 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GII VGA + PGDILVGKITPKGE+ ++
Sbjct: 119  EVEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRVGAIIKPGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLR PS V GTV+D +++ R G++   RS  +  ++  L+
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRAPSSVRGTVIDAKVYTREGVELCARSKEIIEQETTLI 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K + ++S+++++ P   
Sbjct: 239  RRDERIEIKAIQTSAILKIAEMLNGAKTTDKLVSEDGSTELLAKGSDVTSEVLAKIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                 ++   ++  +           S +  +  ++I K   
Sbjct: 299  IGYLPLE-AALEERLGEYFADVRNRISRVRQKATDEIAKQHR 339


>gi|190694718|gb|ACE88924.1| RpoB [Streptococcus pyogenes]
          Length = 239

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 139/239 (58%), Positives = 178/239 (74%), Gaps = 2/239 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSA
Sbjct: 1   RNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYR
Sbjct: 61  LGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYR 120

Query: 604 KVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV    G+VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R  G         +
Sbjct: 121 KVDRATGRVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVV 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           DF+D SPKQVV++A + IPFLENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A
Sbjct: 181 DFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAA 239


>gi|59043061|gb|AAW83883.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N L  ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLFELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|66854091|gb|AAY57354.1| RpoB [Prevotella corporis]
          Length = 125

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 73/179 (40%), Positives = 88/179 (49%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN+GQIFE         LG   ++L                           
Sbjct: 1    NPMGVPSRMNLGQIFE-------AILGAAGRNL--------------------------- 26

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                GV  +TP+FDGA  + +      A L     + +YDG TG
Sbjct: 27   --------------------GVKFATPIFDGAKLDDLKEWTDKAGLPNMCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   ERFDQPATVGVTYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|59043077|gb|AAW83891.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043107|gb|AAW83906.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043159|gb|AAW83932.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (571), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 132/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ     N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMVQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|106734115|gb|ABF82544.1| DNA-directed RNA polymerase III [Exiguobacterium sp. Colorado Road]
          Length = 340

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 154/254 (60%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ ++P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG
Sbjct: 1   QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSG 60

Query: 759 -VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM 
Sbjct: 61  DLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMT 120

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D
Sbjct: 121 WDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLD 180

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G
Sbjct: 181 DRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 240

Query: 938 TVVDVRIFNRHGID 951
            ++DV++F+R   D
Sbjct: 241 IILDVKVFDRENGD 254



 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 84/294 (28%), Positives = 128/294 (43%), Gaps = 17/294 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 60   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 118

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 119  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 177

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 178  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 237

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 238  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 284

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            GNKG++SRILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 285  GNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKL 338


>gi|157781327|gb|ABV72018.1| RNA polymerase beta subunit [Enterococcus pallens]
          Length = 226

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 80/206 (38%), Positives = 109/206 (52%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP+L
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPYL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D  ++          
Sbjct: 135  PDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAARSLGIHVATPVFDGASD---------- 184

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T V++   E         A +    
Sbjct: 185  -----------------------------------TDVWETVRE---------AGMAGDA 200

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            +++LYDG TGEPFD  ++VG +YM+K
Sbjct: 201  KTVLYDGRTGEPFDNRISVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV+ GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|15079139|ref|NP_149891.1| 428L [Invertebrate iridescent virus 6]
 gi|82012001|sp|Q91F97|RPB2_IIV6 RecName: Full=Probable DNA-directed RNA polymerase II subunit RPB2
            homolog
 gi|15042508|gb|AAK82288.1|AF303741_429 428L [Invertebrate iridescent virus 6]
          Length = 1193

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 127/327 (38%), Gaps = 65/327 (19%)

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+          + + K+ +A ++  + GDK       KG V  IL   DMPF++DG+  
Sbjct: 913  KVDRIIRTSKKGILMFKIVIAQQKRPEIGDKFCSAMAQKGTVGMILEEVDMPFMEDGSIP 972

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK-IKSLINDYKANGDISPLRSFLEKVIG 1177
            D+++NP  +PSRM + QI  + +G  C    +    +      +                
Sbjct: 973  DMIINPHCLPSRMTINQIMASIMGKTCCAKNETFGDASPFQESSLEKPQD---------- 1022

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                                    A+   L     + +G   + 
Sbjct: 1023 -------------------------------------KIHALCKELEECGYNYNGTETMM 1045

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR-STG-SYSLVTQQPLGGKSNRGGQRLG 1295
             G  G+     +  G +Y  +L HMVSDK+++R ST      +T+QPL G++N GG R+G
Sbjct: 1046 CGWNGKKLRAEIFFGPVYYHRLTHMVSDKIFSRASTNQKRHAITRQPLNGRANEGGLRIG 1105

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVA-----------GNDTFE 1340
            EME  C+  +G +  L E +  +SD    ++    + Y  +V            G D  +
Sbjct: 1106 EMEKDCMLVHGISKFLHEKMFDQSDKFIINLCVPCKSYFKVVKTQNGFFCSGCNGIDIVK 1165

Query: 1341 TGTPESFNVLVKEMQALGLSIDLENSR 1367
               P +  +  +E+ A+G  ++ +   
Sbjct: 1166 FNCPFAAKLFFQELTAMGQKLEFKVKN 1192



 Score =  140 bits (352), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 128/973 (13%), Positives = 283/973 (29%), Gaps = 162/973 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS----VFPITA----------FSGAAML 74
           L++ Q  ++DHF+  +I         +   F         I             S   ML
Sbjct: 38  LVKHQLETFDHFIFHDIKTIIDDEASI--IFNGKRSLSSQIKNGAVEEGYNRKESEKIML 95

Query: 75  EFVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITL-RLIVFDVDEFTGAKSIK 123
           +F +     P               +   + +TY   + + +   ++ D +E    K ++
Sbjct: 96  KFENVFVAKPTITNDDTTVRPLYPAEARQKMITYDSFVFVDVLEYVLRDEEEILVNKHLR 155

Query: 124 DIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHR 159
                 + +  +P+M                           G F+I G +R+++ QL  
Sbjct: 156 ------VQIAKIPIMLRSSTCNLYNCTPQERIELGEGIEDPGGYFIINGNERVLIGQL-- 207

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
                            +  Y  R I  +  + +                   P+T  + 
Sbjct: 208 -----------------RNAYN-RSICFRNKFSE-------------------PLTCDMR 230

Query: 220 ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           ++   SEE        ++   R +            +    +  L+   T   +      
Sbjct: 231 SM---SEE----TGHSVLIQLRLNDSPISQKRNLKKLDKNGTIDLIISQTKTPI---PIS 280

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
               +LK      +KFL    + L   Y+ + +     G I+       D+  +E     
Sbjct: 281 FVFRVLKVATIDKLKFLIGDEEEL-DKYLIKIVEETSDGGIF-------DDMEIEISQED 332

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +  +      +      +I   +                        ST      +   +
Sbjct: 333 DFNEENEESTEKKKITQFIEQDMFPHLGVS-----------------STHEEKAILLGKM 375

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                  + +++   K   R N +T    +  +            + R     +   +  
Sbjct: 376 VRKLLLVNETSINANKFAQRANDETNKTNKTNKMYYTQEDRDNYSNKRVETAGVLCFELF 435

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                R +   +         R+E  +  + + +           N   V          
Sbjct: 436 RMLYKRFIKSNINQL--EKRNRVEMDVISKNAFITTGLHFSFSTGNW-GVQKNNYIRTGV 492

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           +Q+ Q    V+  +  ++ RR        + +     ++R +HP+     CP+ET EG  
Sbjct: 493 AQIPQ--NKVSFGAFFSYLRRFVI----PMGKEGKNTKIRQIHPSSIFFACPSETPEGQF 546

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           +G+  + +  A V+           +         V+  ++EE  +++++ +      G 
Sbjct: 547 VGITLNFSMLAEVSIRTSSVVIKEIIEASHQAFKHVHEISLEENKQFLSKLSIIFVNGGI 606

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDAS-------PKQVVSIAASLIPFLENDDSNRVLM 692
                   +   +   +  +     D S        +  +S  A        +  +    
Sbjct: 607 CGLTSKPQQLLSDVRDLKLKHCLKYDVSAVFIPELKEVHISSDAGRFIRPVLNLQSIKTN 666

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV-----DAIRIVIRS 747
           G  M       L+          E   ++ +       R   V          +  V+ +
Sbjct: 667 GNVMWNSFQNCLENGHVVYKDAYEIEQSQIAINLQDLSRYPTVYDSMEIHASCMLGVMAA 726

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ---RPLVKVGDEVRRNDIIADGPSTD-LG 803
                + + S    Y+    +++  N   +        +V D V+R  +       +   
Sbjct: 727 QIPFAEHTQSPRLCYQSSMAKQAIGNIPSHHVKSDNTTRVMDYVQRPLVTTQIAEMNRFN 786

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           D   G N +VA   + G+N EDS+++++  +   +F  +  +   V  R   +  +    
Sbjct: 787 DFPNGLNAMVAVAIYTGFNQEDSIILNKASIDRGMFHVVTYKTIIVEERKIGVNEKICMP 846

Query: 864 DIPNVSEEGLKNIDEC------GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                       +++       G++ V + V   D+LVGK+  K     T +E     I 
Sbjct: 847 VASVRRMNNYSLLEDNPESPYFGVVKVKSFVKRNDVLVGKVITKISKDGTRQETDHSTIV 906

Query: 918 GEKAVDVRDTSLR 930
                   D  +R
Sbjct: 907 SISEEGKVDRIIR 919


>gi|106734113|gb|ABF82543.1| DNA-directed RNA polymerase III [Exiguobacterium sp. AT4]
          Length = 339

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 154/254 (60%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ ++P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG
Sbjct: 1   QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSG 60

Query: 759 -VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM 
Sbjct: 61  DLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMT 120

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D
Sbjct: 121 WDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLD 180

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G
Sbjct: 181 DRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 240

Query: 938 TVVDVRIFNRHGID 951
            ++DV++F+R   D
Sbjct: 241 IILDVKVFDRENGD 254



 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 84/294 (28%), Positives = 128/294 (43%), Gaps = 17/294 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 60   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 118

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 119  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 177

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 178  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 237

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 238  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 284

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            GNKG++SRILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   L
Sbjct: 285  GNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKL 338


>gi|106734111|gb|ABF82542.1| DNA-directed RNA polymerase III [Exiguobacterium sp. AT1b]
          Length = 339

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 154/254 (60%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ ++P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG
Sbjct: 1   QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSG 60

Query: 759 -VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM 
Sbjct: 61  DLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMT 120

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D
Sbjct: 121 WDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLD 180

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G
Sbjct: 181 DRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 240

Query: 938 TVVDVRIFNRHGID 951
            ++DV++F+R   D
Sbjct: 241 IILDVKVFDRENGD 254



 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 80/286 (27%), Positives = 124/286 (43%), Gaps = 17/286 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 60   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 118

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 119  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 177

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 178  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 237

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 238  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 284

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            GNKG++SRILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E H
Sbjct: 285  GNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELH 330


>gi|322784943|gb|EFZ11714.1| hypothetical protein SINV_06174 [Solenopsis invicta]
          Length = 1123

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 95/583 (16%), Positives = 184/583 (31%), Gaps = 95/583 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D+    + L+A            + I+E  +       I         R+T     
Sbjct: 618  IEYLDVNEENDSLIACTESEINEDTTHLEIAEFAILGVCAGLIPYPHHNQSPRNTYQCAM 677

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               + I ++ E     ID   ++   A      +    I       +   E  + A+   
Sbjct: 678  -GKQAIGSIGENQRTRIDT--VMYNLAYSQRPIVKTRAIELINYDKLPAGENAIVAVMSY 734

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               D+ D  +   + +        ++        + +    +++I   + D + ++ +  
Sbjct: 735  SGYDIEDALIFNKASIDRGYGRCLVYRNAKCTLKKYANQT-QDRIMGPSIDANTKKPLSK 793

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
              I         G+   +      KS    S+ I                         +
Sbjct: 794  HEILDSDGIAAPGELVENKTVMVNKSVPAPSENIGPVRSGNV---------------QTQ 838

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             +Y  ++   +      +EK+    +       +VK+ +   R  + GDK +        
Sbjct: 839  TEYRNAEIQYKGLVPAYVEKVMISKNAEDAF--LVKLLLRQTRRPEIGDKFS-------- 888

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                                         SR                  G+K    +   
Sbjct: 889  -----------------------------SR-----------------HGQKGVIGLIVE 902

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            + +   +      + ++       +++      VL       +G       F GA  E +
Sbjct: 903  QEDMPFNDYGMCPDIIMNPHGFPSRMTVGKLIEVLAGKAGVVNGKFQDATAFGGAKVEDL 962

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
               L     +  G+   Y+G+TG P    +  G +Y  KL HMV DK++AR+ G   ++T
Sbjct: 963  CEELAKNGYNYLGKDFFYNGMTGRPLIGYIYSGPVYYQKLKHMVQDKIHARARGPRVVLT 1022

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG 1335
            +QP  G++  GG RLGEME  C+  YGA+ +L E L I SD    DV       +  + G
Sbjct: 1023 RQPTEGRAREGGLRLGEMERDCLIGYGASMLLIERLMISSDAFKVDVCN-----KCGLIG 1077

Query: 1336 ND-----------TFETGTPESFNVLVKEMQALGLSIDLENSR 1367
             +                 P +  +L +E+Q++ +   L    
Sbjct: 1078 YNNWCQRCQSSSSVSTITMPYACKLLFQELQSMNVVPRLSLKE 1120



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 97/767 (12%), Positives = 236/767 (30%), Gaps = 163/767 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    SY++F+   I    + NE +Q         +       L++++ +   PK   
Sbjct: 16  LVKQHIDSYNYFINEEIKNIVKANEKIQ---------SDEDPHFYLKYLNIQVGRPKLQD 66

Query: 87  ----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                        +C  RDL Y+ P+++ +  +  + D   G    +  K+  + +G +P
Sbjct: 67  SCTLNRDYDTTPHECRLRDLNYSAPIEVEIEYVRNNPDNKEGGGKQRTWKK--VVIGMMP 124

Query: 137 LMT------------------------KDGTFVIKGIQRIVVS--QLHRSPGIHFDHDKG 170
           +M                           G F+I G +++++   Q+ R           
Sbjct: 125 IMLRSSNCVLTKKSESQLAKLNECPHDPGGYFIINGQEKVILIQEQMVR----------- 173

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDII-----HVRIDRRRK-------------- 211
                           ++   + +E D+KD +         D++ K              
Sbjct: 174 ----------------NR---IVLEVDNKDCVVAACNSFTHDKKTKTNVVGKSGKYYLRH 214

Query: 212 ------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSL 264
                 + +T    A+G+ S+ EI+     +  Y            AA L    +   ++
Sbjct: 215 NMFQDDILITIIFKAMGIVSDLEIMQMVGTQDKY--------LDKFAASLEECQREDLNI 266

Query: 265 VDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEA 324
              +   + + S +K T   +   +        I ++ L  + V +     +   + +  
Sbjct: 267 FSQNQALKYLNSKRKQTRFHVPKSRVADEMKDAIATNILSHVPVIDFNFRPKALYLALMI 326

Query: 325 GD----VIDEKSLEEIFHSEIRDIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
                   D   +++  +   + +        +++ D      +    +        K A
Sbjct: 327 RRVINAQSDRSLIDDKDYYGNKRLELAGSLLALMFEDLFKRFNWELKQIADKNIPKIKAA 386

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
             DI + MR  D+ T  +A ++ +  +         T+ R +M           + +I  
Sbjct: 387 AFDIAKHMRH-DLITNGLAFAISSGNW---------TIKRFRMERHGVTQVLSRLSYISA 436

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
             ++  +    +          +       +    +  + +    +  +           
Sbjct: 437 LGMMTRVHSQFEKTRKVSGPRSLQGSQWG-MLCPNDTPEGEACGLVKNLALMAHITTEVP 495

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +   +     +  + + +   E      +  +  +      + + +RL    +  + RA 
Sbjct: 496 EKPLIDLMRNLGVEDIYTLAGEELTKEGVYTVFVNGIMAGIVQNHKRLVKQFRL-LRRAG 554

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV---CDGKV 610
                  ++  H  +     +  G        +     +     I+   R +    D   
Sbjct: 555 YINSFVSIYTQHRHKCIQVSSDGGRLCRPCIIVKHGKSLVKPKHIKDLERNITTFEDFLY 614

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + YL   EE +  IA   S ++ED                          ++ +   
Sbjct: 615 DGLIEYLDVNEENDSLIACTESEINED-----------------------TTHLEIAEFA 651

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL-KAEAPFVGTGME 716
           ++ + A LIP+  ++ S R    C M +QA+  + + +   + T M 
Sbjct: 652 ILGVCAGLIPYPHHNQSPRNTYQCAMGKQAIGSIGENQRTRIDTVMY 698



 Score =  117 bits (293), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 74/517 (14%), Positives = 163/517 (31%), Gaps = 45/517 (8%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
           +   +  +I+ +++ ++ +  IDD D  GN+R+   G +L   +     R    +K+   
Sbjct: 318 KALYLALMIRRVINAQSDRSLIDDKDYYGNKRLELAGSLLALMFEDLFKRFNWELKQIAD 377

Query: 492 SVDID----SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                    +      +    + + +     S   +     +          RLS +   
Sbjct: 378 KNIPKIKAAAFDIAKHMRHDLITNGLAFAISSGNWTIKRFRMERHGVTQVLSRLSYISAL 437

Query: 548 GVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           G+         + R     R +  + +G +CP +T EG   GLV +L   A +      +
Sbjct: 438 GMMTRVHSQFEKTRKVSGPRSLQGSQWGMLCPNDTPEGEACGLVKNLALMAHITTEVPEK 497

Query: 600 TPYRKVCDGKVTNDVVYLSAMEE---ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                + +  V +  +Y  A EE   E  Y    N  +       + LV           
Sbjct: 498 PLIDLMRNLGVED--IYTLAGEELTKEGVYTVFVNGIMAGIVQNHKRLVKQFRLLRRAGY 555

Query: 657 PREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
               +        + + +++       P +       ++   +++     +   E     
Sbjct: 556 INSFVSIYTQHRHKCIQVSSDGGRLCRPCIIVKHGKSLVKPKHIKDLERNITTFEDFLYD 615

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV---------EGDLDPSTSGVDIYR 763
             +E +       +++A         D   + I                  + S  + Y+
Sbjct: 616 GLIEYLDVNEENDSLIA-CTESEINEDTTHLEIAEFAILGVCAGLIPYPHHNQSPRNTYQ 674

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD-----GPSTDLGDLALGRNMLVAFMPW 818
               +++  +   NQR  +                       +   L  G N +VA M +
Sbjct: 675 CAMGKQAIGSIGENQRTRIDTVMYNLAYSQRPIVKTRAIELINYDKLPAGENAIVAVMSY 734

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIE-------EFEVMARDTKLGPEEITRDIPNVSEE 871
            GY+ ED+++ ++  +       +          ++    +D  +GP         +S+ 
Sbjct: 735 SGYDIEDALIFNKASIDRGYGRCLVYRNAKCTLKKYANQTQDRIMGPSIDANTKKPLSKH 794

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            +  +D  GI   G  V    ++V K  P     + P
Sbjct: 795 EI--LDSDGIAAPGELVENKTVMVNKSVPAPSENIGP 829


>gi|123979416|gb|ABM81533.1| RNA polymerase II second largest subunit [Buellia dialyta]
          Length = 706

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 116/826 (14%), Positives = 229/826 (27%), Gaps = 148/826 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L + +R    ++ + +    +              + +  + + +     +
Sbjct: 2    KRLDLAGPLLASLFRTLFNKLNKDVEKYLKACIESNKEFNLTIAVKSNTISNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     V+          +      +   +   L++     
Sbjct: 118  GLVCPAETPEGQACGLVKNLALMCNVSVGTPSGGLADFLNERGMETLEEYDPLTSPHATK 177

Query: 625  RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
             ++      +  +       V        I      + D  D   K +      L P F+
Sbjct: 178  IFLNGVWVGVHRNPGHLFNAVMKLRRTHVIKDEVSLVRDIRDREFKILFDAGRVLRPLFV 237

Query: 683  ENDDSNRVLMGC-NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDA 740
              +D      G   +Q+  +  L+ +       M+    +            G+VE VDA
Sbjct: 238  VENDLKNSNYGNLVLQKHHIAKLELDRDIAPLDMDKDEREKVIYGWQGLLHEGVVEYVDA 297

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR--PLVKVGDEVRRNDIIADGP 798
                   +            +         ++N    +R  PL   G            P
Sbjct: 298  DEEETIMIVMTPWDLNVSRQVQAGYALPERDENNPNARRTAPLNPTG---HTWTHCEIHP 354

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N          M  + +   + +  ++          
Sbjct: 355  SMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYDQRMET----- 400

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                  +  +             +       +   +  + AI  
Sbjct: 401  ----------------------MAHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAC 438

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R   D  +    +    +E   +      + L
Sbjct: 439  YSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDVEK---QIGLNTLESFEKPMRMNTMKL 494

Query: 979  DRNIYSRLME----ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                Y +L +    I+ G           K+  +++D       ++  +       ++  
Sbjct: 495  KHGTYEKLDDGDGIIVPGCRVSGEDIIIGKTAPIAADAEELGQGTKIREKRDVSTPLRST 554

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               L  Q                              R VKV +   +  Q GDK A RH
Sbjct: 555  ESGLVDQVLL--------------------TTNAEGRRFVKVRMRTTKIPQIGDKFASRH 594

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 595  GQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGGA 654

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     ++S L    E    +                                    
Sbjct: 655  TPFTDVTVDNVSKLLR--EHGYQSRGFEVM------------------------------ 682

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +G +    G         V +G  Y  +L 
Sbjct: 683  ---------------YNGHT----GR---KLVAQVFLGPTYYQRLR 706



 Score =  110 bits (274), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 88/624 (14%), Positives = 178/624 (28%), Gaps = 109/624 (17%)

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L+    N         +    +  K+  L I       +  +  +  S+    + +  K 
Sbjct: 14  LFRTLFNKLNKDVEKYLKACIESNKEFNLTIAVK---SNTISNGLKYSLATGNWGEQKKA 70

Query: 407 DLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRV 464
             S  G  ++  R    +      R          I     L N    +         + 
Sbjct: 71  ASSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 130

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQ 524
             + + L     + +      + + ++   ++++   D + +               +  
Sbjct: 131 CGLVKNLALMCNVSVGTPSGGLADFLNERGMETLEEYDPLTSPHATKIF---LNGVWVGV 187

Query: 525 LEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAETSE 576
                +  + +   RR   +  +  + R     E        R + P          ++ 
Sbjct: 188 HRNPGHLFNAVMKLRRTHVIKDEVSLVRDIRDREFKILFDAGRVLRPLFVVENDLKNSNY 247

Query: 577 GHNIGL---VSSLTSFARVNAYGFIETPYRKVCDGKV----TNDVVYLSAMEEENRYIAQ 629
           G+ +     ++ L     +      +    KV  G         V Y+ A EEE   I  
Sbjct: 248 GNLVLQKHHIAKLELDRDIAPLDMDKDEREKVIYGWQGLLHEGVVEYVDADEEETIMIVM 307

Query: 630 ANSSLDEDGSFT--------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
               L+              +E          +          +  P  ++ I AS+IPF
Sbjct: 308 TPWDLNVSRQVQAGYALPERDENNPNARRTAPLNPTGHTWTHCEIHPSMILGICASIIPF 367

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
            +++ S R      M +QA+                                        
Sbjct: 368 PDHNQSPRNTYQSAMGKQAMG--------------------------------------- 388

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
             V  +       + + +  Y               Q+PL                    
Sbjct: 389 --VFLTNYDQRMETMAHILYYP--------------QKPL----------ATTRSMEFLK 422

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE- 860
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +  + +   L   E 
Sbjct: 423 FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDVEKQIGLNTLES 482

Query: 861 ----ITRDIPNVSEEGLKNIDE-CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               +  +   +     + +D+  GII  G  V+  DI++GK  P         +     
Sbjct: 483 FEKPMRMNTMKLKHGTYEKLDDGDGIIVPGCRVSGEDIIIGKTAPIAADAEELGQ----- 537

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
             G K  + RD S  + S  SG V
Sbjct: 538 --GTKIREKRDVSTPLRSTESGLV 559


>gi|59043069|gb|AAW83887.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043147|gb|AAW83926.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043149|gb|AAW83927.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 132/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  E  N LS ++H RRLSA+G GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMEQHNPLSELSHKRRLSAVGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|106734109|gb|ABF82541.1| DNA-directed RNA polymerase III [Exiguobacterium sp. A19]
          Length = 336

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 164/305 (53%), Positives = 218/305 (71%), Gaps = 2/305 (0%)

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTS 757
            QAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +    
Sbjct: 1    QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQG 60

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +D Y++ KF RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV FM 
Sbjct: 61   ELDRYKIQKFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLVGFMT 120

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D
Sbjct: 121  WDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLD 180

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            + GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 181  DRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240

Query: 938  TVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  ++  
Sbjct: 241  IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMP 300

Query: 997  SGPKG 1001
              P G
Sbjct: 301  YMPDG 305



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 59/186 (31%), Positives = 93/186 (50%), Gaps = 4/186 (2%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 138  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 197

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 198  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 257

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 258  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 317

Query: 1128 PSRMNV 1133
            PSRMN+
Sbjct: 318  PSRMNI 323


>gi|140084126|gb|ABO84912.1| RpoB [Viridibacillus arenosi]
          Length = 238

 Score =  224 bits (571), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 83/211 (39%), Positives = 110/211 (52%), Gaps = 54/211 (25%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 82   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFL 141

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 142  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGVHMATPVFDGANEEDVW------ 195

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G  +                          
Sbjct: 196  -------------------ETMEEAGMNRDGKTI-------------------------- 210

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               LYDG +GEPFD  V+VG +YM+KL HMV
Sbjct: 211  ---LYDGRSGEPFDNRVSVGVMYMIKLAHMV 238



 Score = 88.6 bits (218), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 64/93 (68%), Positives = 76/93 (81%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV EE L+N+DE GII +GAEV+ GDILVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEEALRNLDERGIIRIGAEVHDGDILVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 61  EKAREVRDTSLRVPHGAGGIVLDVKVFNREDGD 93


>gi|68131850|gb|AAY85203.1| RNA polymerase II second largest subunit [Dicentra formosa]
          Length = 873

 Score =  224 bits (570), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 122/911 (13%), Positives = 262/911 (28%), Gaps = 171/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +             ++ K+  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCEEVTETQEFKK--VFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSSMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTKEKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +GI   C          +      + + A     E   +   +  
Sbjct: 237 KYAR-EILQKEMLPHVGIGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  +   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQSTKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPELLVKTLRALRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L      +  G+         D      + Y+   EEE   I+     
Sbjct: 529 QRLLIKKRDIRALQLRESPDEGGW--------HDLVAKGYIEYVDTEEEETTMISM---- 576

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +LV  R   E      E     +  P  ++ + AS+IPF +++ S R    
Sbjct: 577 ------TINDLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 628

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                           R   +  V               
Sbjct: 629 SAMGKQAMGIYVTNYQL--------------------RMDTLAYV--------------- 653

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 654 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 683

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 684 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGM 743

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           +         RD S
Sbjct: 744 RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHS 794

Query: 929 LRVPSGVSGTV 939
             +    SG V
Sbjct: 795 TSLRHSESGMV 805



 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 117/794 (14%), Positives = 235/794 (29%), Gaps = 117/794 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTKEKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  REILQKEMLPHVGIGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +   ++ 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQSTK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPELLVKTLRALRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K          E   +   G        G +E VD        +   ++
Sbjct: 523  LFIVEKQRLLIKKRDIRALQLRE---SPDEGGWHDLVAKGYIEYVDTEEEETTMISMTIN 579

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
               S                                        PS  LG       +  
Sbjct: 580  DLVSARLNPEEA---------------------YSETYTHCEIHPSLILG-------VCA 611

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 612  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 644

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 645  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 702

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 703  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGT 761

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++                  DE   +     +  + TS    E   
Sbjct: 762  RVSGEDVIIGKTTPIAQ-----------------DESQGQASRYTRRDHSTSLRHSESGM 804

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 805  VDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 859

Query: 1114 DGTPVDIVLNPLGV 1127
            +G   DI++NP  +
Sbjct: 860  EGITPDIIVNPHAI 873


>gi|157781345|gb|ABV72027.1| RNA polymerase beta subunit [Enterococcus casseliflavus]
          Length = 226

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 92/292 (31%), Positives = 128/292 (43%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 58   -----EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D  ++ D+                                       
Sbjct: 167  ARQLGIHVATPVFDGASDEDVW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                     A           A +    +++LYDG TGEPFD  ++VG +YM
Sbjct: 189  ---------ATVAE-------AGMASDAKTVLYDGRTGEPFDGRISVGVMYM 224



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|106734107|gb|ABF82540.1| DNA-directed RNA polymerase III [Exiguobacterium sp. A1]
          Length = 337

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 164/305 (53%), Positives = 218/305 (71%), Gaps = 2/305 (0%)

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTS 757
            QAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +    
Sbjct: 1    QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQG 60

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +D Y++ KF RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV FM 
Sbjct: 61   ELDRYKIQKFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLVGFMT 120

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D
Sbjct: 121  WDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLD 180

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            + GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 181  DRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240

Query: 938  TVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  ++  
Sbjct: 241  IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMP 300

Query: 997  SGPKG 1001
              P G
Sbjct: 301  YMPDG 305



 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/193 (32%), Positives = 98/193 (50%), Gaps = 4/193 (2%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 138  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 197

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 198  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 257

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 258  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 317

Query: 1128 PSRMNVGQIFETH 1140
            PSRMN+GQ+ E H
Sbjct: 318  PSRMNIGQLLELH 330


>gi|59043081|gb|AAW83893.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLS   +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSLFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|30142153|gb|AAP13996.1| RNA polymerase subunit B [Serratia rubidaea]
          Length = 219

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 138/219 (63%), Positives = 177/219 (80%)

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR
Sbjct: 1   RVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRR 60

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
           +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ET
Sbjct: 61  ISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLET 120

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           PYR+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R++
Sbjct: 121 PYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDDGRFVEDLVTCRSKGESSLFSRDQ 180

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQR+
Sbjct: 181 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRR 219


>gi|106734103|gb|ABF82538.1| DNA-directed RNA polymerase III [Exiguobacterium sp. India Orange]
          Length = 342

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 154/254 (60%), Positives = 200/254 (78%), Gaps = 1/254 (0%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPLL+ ++P VGTGME V AK SGAAIVAK  G+VE+V A  I+IR          SG
Sbjct: 2   QAVPLLQPDSPIVGTGMEYVSAKDSGAAIVAKHPGVVERVTAREILIRRTSDVNGSEVSG 61

Query: 759 -VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            +D Y+L K+ RSNQ TC NQ+P++  GD V + +I+ADGPS D+G+LALGRN++VAFM 
Sbjct: 62  DLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPSMDMGELALGRNVVVAFMT 121

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
           W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ L+N+D
Sbjct: 122 WDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALRNLD 181

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP+G  G
Sbjct: 182 DRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNGGDG 241

Query: 938 TVVDVRIFNRHGID 951
            ++DV++F+R   D
Sbjct: 242 IILDVKVFDRENGD 255



 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 86/297 (28%), Positives = 130/297 (43%), Gaps = 17/297 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  +    V        ++  II  G  V  G+IL    +      +     ++ A 
Sbjct: 61   GDLDRYKLQKYVRSNQGTCYNQKPIIAAGDRVEKGEILADGPS-MDMGELALGRNVVVAF 119

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     V   V    I       ++  +     E    +    DD   
Sbjct: 120  MTWDGYNYEDAIIMSERLVKDDV-YTSIHIEEYESESRDTKLGPEEITRDIPNVGDDALR 178

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD--LISEYPRSQWWQFAVQDEKVQRN 1034
             LD     R+   +   + + G    K  T L+++  L+      +  +      +V   
Sbjct: 179  NLDDRGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPNG 238

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
             + +                 K+   + GD++ PGV ++V+V++  KR I  GDKMAGRH
Sbjct: 239  GDGI-------------ILDVKVFDRENGDELSPGVNQMVRVYIVQKRKIHEGDKMAGRH 285

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GNKG++SRILP EDMP++ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG K
Sbjct: 286  GNKGVISRILPEEDMPYMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAAKKLGIK 342


>gi|59043051|gb|AAW83878.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043073|gb|AAW83889.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043095|gb|AAW83900.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043097|gb|AAW83901.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043099|gb|AAW83902.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043103|gb|AAW83904.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043115|gb|AAW83910.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043119|gb|AAW83912.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043153|gb|AAW83929.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043155|gb|AAW83930.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043157|gb|AAW83931.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043169|gb|AAW83937.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  224 bits (570), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|3133459|gb|AAC38530.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
          Length = 215

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 128/213 (60%), Positives = 167/213 (78%), Gaps = 1/213 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVHP+
Sbjct: 2   NIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPS 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A EE+ 
Sbjct: 62  HYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTADEEDR 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             +AQANS +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE
Sbjct: 122 HVVAQANSPVDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLE 181

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
           +DD+NR LMG NMQRQAVPL+++EAP VGTGME
Sbjct: 182 HDDANRALMGANMQRQAVPLVRSEAPLVGTGME 214


>gi|167042832|gb|ABZ07549.1| putative RNA polymerase Rpb2, domain 6 [uncultured marine
            microorganism HF4000_ANIW137J11]
          Length = 1231

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 100/254 (39%), Gaps = 54/254 (21%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 R+ ++ V  +R  + GDK A RHG K                            G
Sbjct: 969  SENGSRIARIRVRDQRIPELGDKFASRHGQK----------------------------G 1000

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            V     +G I                             +    F + +I   +   +++
Sbjct: 1001 V-----IGHIV---------------------PPEGMPFTASGIFPDLIINPHAIPSRMT 1034

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G  +    F G  E+ +   L       SG+  LYDG TG   D
Sbjct: 1035 IAHVLEMVGGKLGAMNGKFIDGSAFSGDKEDDLRDELASLGFKHSGRESLYDGQTGRRID 1094

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              + +G IY  KL+HMVS K++ARS G   L+T+QP  G++  GG R GEME  C+  +G
Sbjct: 1095 ADIFIGVIYYQKLHHMVSGKLHARSRGPMQLLTRQPTEGRARMGGLRFGEMERDCLIGHG 1154

Query: 1307 AAYVLQEMLTIKSD 1320
            A+ V+++ L  +SD
Sbjct: 1155 ASMVIKDRLLDESD 1168



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 169/1003 (16%), Positives = 325/1003 (32%), Gaps = 175/1003 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV--FPITAFSGAAMLEFVSYEF----- 81
           L+  Q  S++ FL              Q    ++      +  G+  LE    E      
Sbjct: 102 LVNHQLGSFNDFLPHAGNRAAWM----QRVVNNITVGSDESMRGSVRLELGDLEVVVKLG 157

Query: 82  ----DPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE 127
                 P                   R+LTYA P+ +   +I  +++  +  + I     
Sbjct: 158 EVRMGQPMVVEANGSQSMSTPMMARLRNLTYAAPVFLGFSVIEEEMEIESSEEEI----- 212

Query: 128 QSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPD 187
                G +P+M K    +           LHR         + +   S K  Y  R+ P 
Sbjct: 213 -----GMMPVMVKSA--LCN---------LHR---------ESKYLRS-KPEYEARLGP- 245

Query: 188 QGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCF 247
                D  F   D  +  I              L M+ E+        IV        C 
Sbjct: 246 -----DESFS--DEAYAAI--------------LQMEQEDPEDPGGYFIVNGTERVLVCL 284

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLY 307
              A + ++  + +      +  +      +   +  +   K+ G+  + I         
Sbjct: 285 EDLAPNRVMVEREARYQRQTEYAKV-FSQREGFRALTMVEKKKDGILHVSIPV------- 336

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKN 367
                     G   +     +  +S ++I  +   D     +   N     R+  V    
Sbjct: 337 -------ASGGVPLVVLMMALGMESADDIMGAITSDEATRNLVLANIEGIHRDEQV---- 385

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL-NLDTPD 426
              ++AL  + R    G                  S +Y    +  +  N  L +L T  
Sbjct: 386 YTTEEALEYLERRFAAGQ-----------------SKEYRRKRINYIIDNTLLPHLSTSL 428

Query: 427 DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG-------- 478
           +VR+ +   +  + + +++L  G    DD D+  N+R++  G +++  +R G        
Sbjct: 429 EVRYKKALFLGRMAREVLELATGTRQPDDKDHYANKRLKLAGNLMEELFRAGLQALLNDM 488

Query: 479 LLRMERSIKERISSVDIDSVMPQDLIN-AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
             +MERS  +R       ++    L N     ++        + +SQL +   +++ ++H
Sbjct: 489 KYQMERSYSKRKEKRVKHAIRRDVLTNKIMHAMATGNWIGGRAGVSQLLDRTCNMATLSH 548

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY-- 595
            RR+ +     + R++   + RD+H T +GR+CP ET EG N GLV +L     V+    
Sbjct: 549 LRRVIS----PLTRSQPHFQARDLHSTQFGRLCPNETPEGQNCGLVKNLALMIDVSENLP 604

Query: 596 -GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
            G +    R++ D +    +       +E       N  L    +    LV         
Sbjct: 605 AGEVLETLREL-DMQPLEKL-------QEGWGKVYFNGDLAGCTAEPRNLVEKLRGLRRQ 656

Query: 655 LVPREKIDFIDASPKQVVSIAA-----SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
                 ++         V + +          L + ++   L   ++ R     L     
Sbjct: 657 ARLSHTVNVRHDESLNDVLVNSDPGRIRRPLLLVHRNNKLALRRKHLDRLEAGKLTWNDL 716

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                +E + A+     ++A     +++              +             ++  
Sbjct: 717 IDLGLVEYIDAEEEEDCLIALGETDLKRNRKTHAYTHMEVDPMVILGVATSNVPFPEYNS 776

Query: 770 SNQNTC---------------VNQRPLVKVGDEVRRNDIIADGPSTDLGDL---ALGRNM 811
           S + T                   RP  +          +    +     L     G+NM
Sbjct: 777 SPRCTMGAGMSKQSLGMGQSNYRLRPDTRGHLLHYTQKPMVQTEAMKHNTLLTRPAGQNM 836

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-RDIPNV-- 868
           +VA M +HGYN ED+++ +   +   +  S  +  +    R    G E+      P V  
Sbjct: 837 VVAVMSYHGYNMEDALIFNRGSIDRGLGRSTFMRSYFSEERRYPGGQEDRFIIPDPEVRG 896

Query: 869 --SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
             SEE   N+++ G+I    E+   ++L+GK +P        +    +         VR+
Sbjct: 897 ARSEEAYFNLEDDGLIYPEVELRGREVLIGKTSPPRFLSEPTDFMTPQR--------VRE 948

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           +SL V  G  GTV  V +       +  R    ++   EL  +
Sbjct: 949 SSLTVRHGEKGTVDSVMLSESENGSRIARIRVRDQRIPELGDK 991


>gi|154362079|gb|ABS80878.1| RNA polymerase beta subunit [Brevundimonas diminuta]
          Length = 233

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 147/229 (64%), Positives = 180/229 (78%), Gaps = 1/229 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL + ARVN YGFIE+PYR+V +GK T++VVY+SAMEE    IAQAN  L +DG 
Sbjct: 61  IGLINSLATHARVNKYGFIESPYRRVVEGKATDEVVYISAMEEGKHVIAQANIDL-KDGE 119

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             EELV  R  G+  L+ +E +D +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQ
Sbjct: 120 IVEELVPGRINGDSQLLTKETVDMMDVSPKQVVSVAAALIPFLENDDANRALMGANMQRQ 179

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           AVPL++++AP VGTGME+VVA  SGA ++A+R G+VEQ+D  RIV+R+ 
Sbjct: 180 AVPLVQSDAPLVGTGMEAVVAVDSGAVVIARRDGVVEQIDGTRIVVRAT 228


>gi|94983664|gb|ABF50558.1| RNA polymerase beta subunit [Bosea sp. CRIB-13]
          Length = 149

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 83/152 (54%), Positives = 105/152 (69%), Gaps = 3/152 (1%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            DGT  DIVLNPLGVPSRMNVGQI ETHLGWA  GLGK+I   ++ YK + D   L++  +
Sbjct: 1    DGTHADIVLNPLGVPSRMNVGQILETHLGWAAAGLGKQISKALDAYKKSHDFKALKAEFD 60

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             V       E ++  D++ ++ + +  + GVPV+TPVF+GA E  I  +L  A L  SGQ
Sbjct: 61   AVYEDN---EIVASMDENELVEMGQNLRRGVPVATPVFNGAKEADIERLLEQAGLHSSGQ 117

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            S LYDG TGEPFDR VT+GYIYMLKL+H+V D
Sbjct: 118  STLYDGRTGEPFDRKVTMGYIYMLKLHHLVDD 149


>gi|153958250|gb|ABS53415.1| RpoB [Bacteriovorax sp. AO]
          Length = 337

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 160/340 (47%), Positives = 227/340 (66%), Gaps = 10/340 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK  G V  VD+ RIV++  +   +   SGVDIY L+K+QR+NQ+TC NQ+ LVK GD V
Sbjct: 1    AKDDGKVIFVDSNRIVLQRNK--FEDGESGVDIYSLVKYQRTNQSTCNNQKALVKEGDIV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
            R+ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+HIE FE
Sbjct: 59   RKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSVHIEAFE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLLR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ E+L G              +  +K   ++ +++++ P    
Sbjct: 239  RDERIEIKAIQTSAILKIAEMLKGAKTTDKLVSEDGSTELLQKGADITGEVLAQIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                +Q  +++  +           + +  +  ++I K+ 
Sbjct: 299  GYLPLQ-AELEERLSEYFADIRNRINRVRQKTTDEIAKLH 337


>gi|25144348|ref|NP_498192.2| hypothetical protein F09F7.3 [Caenorhabditis elegans]
 gi|20451233|gb|AAA50695.2| Hypothetical protein F09F7.3 [Caenorhabditis elegans]
          Length = 1154

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 84/504 (16%), Positives = 164/504 (32%), Gaps = 80/504 (15%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              I+ +        +    I       +      + A+      D+ D  +   + +   
Sbjct: 719  DSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRG 778

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 ++ +H     ++  +   +++   A D +  + I       +   +  G   +  
Sbjct: 779  YGRCLVY-KHVKGTAKKYPNQTFDRLLGPALDPNTRKPIFKHKNLDQEGIVFAGARIMPK 837

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K   + S        +      +   +V          Y+      +    +  E
Sbjct: 838  QTIINKHMPVVSGESGPGASASANTIGIAGRQV---------DYKDVSITYKTPTPSYAE 888

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++    +       + KV +   R  + GDK +                           
Sbjct: 889  RVLLTYNEDEA--HLFKVLLRQTRRPELGDKFS--------------------------- 919

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
                      SR                  G+K    +   + +   + L    + ++  
Sbjct: 920  ----------SR-----------------HGQKGVCGLIAQQEDMPFNDLGMVPDMIMNP 952

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
              +  +++      +L       +G       F G   + +   L     +  G+ +L  
Sbjct: 953  HGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTS 1012

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TG+P    +  G IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG RLGEME
Sbjct: 1013 GITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEME 1072

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPES 1346
              C+ AYGA+ +L E L + SD    DV     V  S   G                P +
Sbjct: 1073 RDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGS--KGWCQKCRSSKSMANIKIPYA 1130

Query: 1347 FNVLVKEMQALGLSIDLENSRTKN 1370
              +L +E+Q++ +   L+ +R   
Sbjct: 1131 CKLLFQELQSMNIVPRLDLARYTE 1154



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 123/961 (12%), Positives = 274/961 (28%), Gaps = 178/961 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+DHF+   I      N+ +          +  +    L+++      P    
Sbjct: 41  LVKQHLVSFDHFVQEEIRSIMLSNQKIT---------SDANPNFYLKYLDIRIGKPSSEE 91

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  RD+TY+ P+ + +             +  + + ++ + +G +P+
Sbjct: 92  GLNMTHDKITPQECRLRDMTYSAPISVDIEYT----------RGNQRVFKKDLIIGRMPI 141

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G FV+KG +++++ Q   S             
Sbjct: 142 MLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQLSKNRI-----MVGR 196

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EI 228
            S K L  C ++     +          K    VR ++    VPV+    A+G++S+ +I
Sbjct: 197 NSSKEL-QCEVLSSTSERKSK-TYVTMKKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDI 254

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +ST   +  Y             A +    +  + +       +    G    + +    
Sbjct: 255 VSTIGHEEKYVSAFAQTLEESINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLT 314

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
             K  + +   S+ +   ++A    N +   IY+        ++  E+  + + D     
Sbjct: 315 PPKEHEAVDFLSNSMI-THIACPDGNFKMKAIYLGLMTRRLIQT--ELGENGLDDRDFYG 371

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
              +     + + L  D  K     L  I        ++               +   + 
Sbjct: 372 NKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQDMITNTIVNA 431

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
            + G   +  R  ++     + + +   I+ + ++  + +       +      R     
Sbjct: 432 MSTGNWII-KRFRMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKV---SGPRSLQPS 487

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
           +                + + ++ +   +    +    + ++++  E   +   S + + 
Sbjct: 488 QWGMLCPSDTPEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGVEDLHNVHFSHVNKP 547

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N+L  +      +A+    V +A   +    +                        L  
Sbjct: 548 ENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCR 607

Query: 589 FARVNAYG----------FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
              +   G           ++       D      V YL   E  +  IA     +    
Sbjct: 608 PYIIVKNGTPMLTQAHVQELKEGKMIFEDFVDDGIVEYLDVNEMNDALIAVYGREIGP-- 665

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                +   ++  P  ++ + A LIP+  ++ S R    C M +
Sbjct: 666 ---------------------ETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGK 704

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+  +                  S                                   
Sbjct: 705 QAMGTI---------AYNQQKRIDS----------------------------------- 720

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                           C  QRPLVK                T+   L  G N ++A M +
Sbjct: 721 -----------IMYLLCYPQRPLVKS----------KTIELTNFEKLPAGANGIIAVMSY 759

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEEGL 873
            GY+ ED++++++  +       +  +  +  A+       +                  
Sbjct: 760 SGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTFDRLLGPALDPNTRKPIFKH 819

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV--DVRDTSLRV 931
           KN+D+ GI+  GA + P   ++ K  P       P         G      D +D S+  
Sbjct: 820 KNLDQEGIVFAGARIMPKQTIINKHMPVVSGESGPGASASANTIGIAGRQVDYKDVSITY 879

Query: 932 P 932
            
Sbjct: 880 K 880


>gi|154277042|ref|XP_001539366.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Ajellomyces
            capsulatus NAm1]
 gi|150414439|gb|EDN09804.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Ajellomyces
            capsulatus NAm1]
          Length = 1186

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 90/518 (17%), Positives = 167/518 (32%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +    A+      D+ D  +  
Sbjct: 748  NNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLN 807

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V       ++F R      +   +  +++++   R         +  +  R   +L 
Sbjct: 808  KGSVDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------ENGVPIRKHALLD 857

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
                 +  +      V  + +  E   S        D             Y  S    + 
Sbjct: 858  NDGLAAVGEKVNHGEVYINKVTPENALSS--GITGSDAGRPIA-------YIPSPQTYKL 908

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               + I+K+           +++KV     R  + GDK +                    
Sbjct: 909  PDPSYIDKVMI--SATEAENQLIKVQTRQTRVPEVGDKFS-------------------- 946

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    I    A+   S L   
Sbjct: 947  -----------------SR-----------------HGQKGVVGIIAEHADMPFSDLGIV 972

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++       +++      ++       SG       F G+  E ++++L        
Sbjct: 973  PDIIMNPHGFPSRMTVGKMLELIAGKAGILSGQFGYGTAFGGSPVEEMSAILVDHGFSYG 1032

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGEP    V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG
Sbjct: 1033 GKDYLTSGITGEPLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGG 1092

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1093 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK- 1151

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1152 -----MAIPYAAKLLVQELFSMNVVARLKLADEFPEER 1184



 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 91/751 (12%), Positives = 198/751 (26%), Gaps = 133/751 (17%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K         L++    SY++F+ + +    + +    A  +S            + F
Sbjct: 78  FLKIKG------LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRF 122

Query: 77  VSYEFDPPK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                  P+                  ++C  RD+TYA P+ +    +          + 
Sbjct: 123 HDIYLGNPRRADEEQDSKFDLASTITPNECRLRDMTYAAPILVDFEYV----------RG 172

Query: 122 IKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQL 157
            + +K     +G +P+M                           G F++ G +++++ Q 
Sbjct: 173 RQRVKRNGTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQE 232

Query: 158 HRSPG-IHFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-R 208
             S   +  + D  +        S S +      II             KD I++R +  
Sbjct: 233 QLSKNRVIVETDLKKDIVQASVTSSSNERKSKSYII-----------LKKDRIYMRHNVL 281

Query: 209 RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDI 267
              VP+   L A+G+ S++ +      I  + + DF      +  L +     +   +  
Sbjct: 282 SEDVPIVILLKAMGIQSDKEMLLLVAGIDSTFQEDFAINFEESVKLGIYTQHQALEYIGS 341

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                   +   +T         + +  + I+   +  L                 A   
Sbjct: 342 RIKINRKPNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMA 393

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                 +           +           +         K + D  ++I +V++    +
Sbjct: 394 RRVLMAKHDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRT 453

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKIL 443
               A  +         +     +     +++        V H    +     + ++  +
Sbjct: 454 EQFDAYGVVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRI 513

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
                    +     L   +   +      +     L    ++   I++ D +  + + +
Sbjct: 514 SSQFEKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEQPVRKLI 573

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVH 562
                                    +N        R    L     + R     E   V 
Sbjct: 574 FALGAEDVQTVGGRELHGQGAYIIFLNGSPIALTRRPKFFLNSFRRLRRTGRVSEFISVF 633

Query: 563 PTHYGRICPAETSEGHNI-GLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSA 619
             H+       T +G     L+      +     G   T +  V      V        A
Sbjct: 634 INHHQNAVHVATDDGRICRPLIIVEDGKSNERDDGNSTTSWLMVSWSIWIVMRKTTSYIA 693

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
           + EE+R  A                   R           ++ F    P         LI
Sbjct: 694 VYEEDRLRA-------------------RRIW-----KSNRLPFSALWP--------GLI 721

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           P+  ++ S R    C M +QA+  +      
Sbjct: 722 PYPHHNQSPRNTYQCAMGKQAIGAIANNQFL 752



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 89/652 (13%), Positives = 200/652 (30%), Gaps = 67/652 (10%)

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
           + K   ++ +  D +   +            I ++A  +  +K +  +       +  + 
Sbjct: 260 ERKSKSYIILKKDRIYMRHNVLSEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 310

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                + A      V      +  AL  I   ++             F     +  +  +
Sbjct: 311 STFQEDFAINFEESVKLGIYTQHQALEYIGSRIKINRKPNS------FGITRRNHVQEAI 364

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 365 EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 421

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQ 521
           ++L   +     + +  IK  I  V    V  +          +   +   +     +  
Sbjct: 422 QLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNRAISTGN 481

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAE 573
            S     +          RLS +   G+         + R     R + P+ +G +CP++
Sbjct: 482 WSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPSQFGMLCPSD 541

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN---RYIAQA 630
           T EG   GLV +L     +      E P RK+       DV  +   E        I   
Sbjct: 542 TPEGEACGLVKNLALMTHITTN-DEEQPVRKLIFALGAEDVQTVGGRELHGQGAYIIFLN 600

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREK---IDFIDASPKQVVSIAASLIPFLENDDS 687
            S +         L   R       V       I+    +            P +  +D 
Sbjct: 601 GSPIALTRRPKFFLNSFRRLRRTGRVSEFISVFINHHQNAVHVATDDGRICRPLIIVEDG 660

Query: 688 N-------RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA------IVAKRAGI 734
                          M   ++ ++  +        E    ++            A   G+
Sbjct: 661 KSNERDDGNSTTSWLMVSWSIWIVMRKTTSYIAVYEEDRLRARRIWKSNRLPFSALWPGL 720

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSG-VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
           +      +    + +  +     G +   + ++           Q+P+VK          
Sbjct: 721 IPYPHHNQSPRNTYQCAMGKQAIGAIANNQFLRIDSLLYTMVYPQKPMVK---------- 770

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G++  VA M + GY+ ED++++++  V           ++    + 
Sbjct: 771 TRTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSTNLKS 830

Query: 854 TKLGPEEITRDIPN---VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
              G ++  +       V       +D  G+  VG +VN G++ + K+TP+ 
Sbjct: 831 YSNGTKDKLKGPDRENGVPIRKHALLDNDGLAAVGEKVNHGEVYINKVTPEN 882


>gi|240276965|gb|EER40475.1| DNA-directed RNA polymerase III [Ajellomyces capsulatus H143]
          Length = 1227

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 151/1102 (13%), Positives = 318/1102 (28%), Gaps = 185/1102 (16%)

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            + K   ++ +  D +   +            I ++A  +  +K +  +       +  + 
Sbjct: 292  ERKSKSYIILKKDRIYMRHNVLSEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 342

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + A      V      +  AL  I   ++             F     +  +  +
Sbjct: 343  STFQEDFAINFEESVKLSIYTQHQALEYIGSRIKINRKPNS------FGITRRNHVQEAI 396

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 397  EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 453

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            ++L   +           K +         + +  +  +   +        + ++Q    
Sbjct: 454  QLLALLFEDLFK------KFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNR 507

Query: 529  VNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              S    +  R R+   G   V    + +    +      +        G      S   
Sbjct: 508  AISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMLTRISSQFEKTRKVSGPRALQPSQFG 567

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                 +           V +  +   +   +  EEE          +   G+   + V  
Sbjct: 568  MLCPSDTPEGEACG--LVKNLALMTHIT--TNDEEE-----PVRKLIFALGAEDVQTVGG 618

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R    +       I F++ SP     IA +  P    +   R+     +       +   
Sbjct: 619  RELHGQGAY----IIFLNGSP-----IALTRRPKFFLNSFRRLRRTGRVSEFISVFINHH 669

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V     +   +     I+ +          +R++        D    G+  Y     
Sbjct: 670  QNAVHVA--TDDGRICRPLIIVEDGKSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLDC-- 725

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                 N   +    V   D  +    +   P T LG +A         +P+  +N     
Sbjct: 726  -----NEENDSYIAVYEEDITQSTTHLEIEPFTILGAVA-------GLIPYPHHNQSPRN 773

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
                 M  + +                                   + +    ++     
Sbjct: 774  TYQCAMGKQAIGV-----------------------------IANNQFLRIDSLLYTMVY 804

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                 +    I       +   +    A+      D+ D  +     V       ++F R
Sbjct: 805  PQKPMVKTRTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVF-R 863

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
                  +   +  +++++   R         +  +  R   +L      +  +      V
Sbjct: 864  KYSTNLKSYSNGTKDKLKGPDR---------ENGVPIRKHALLDNDGLAAVGEKVNYGEV 914

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + +  E   S        D             Y  S    +    + I+K+       
Sbjct: 915  YINKVTPENALSS--GITGSDAGRPIA-------YIPSPQTYKLPDPSYIDKVMI--SAT 963

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                +++KV     R  + GDK +                                    
Sbjct: 964  EAENQLIKVQTRQTRVPEVGDKFS------------------------------------ 987

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
             SR                  G+K    I    A+   S L    + ++       +++ 
Sbjct: 988  -SR-----------------HGQKGVVGIIAEHADMPFSDLGIVPDIIMNPHGFPSRMTV 1029

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                 ++       SG       F G+  E ++++L        G+  L  G+TGEP   
Sbjct: 1030 GKMLELIAGKAGILSGQFGYGTAFGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLPA 1089

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+ AYG 
Sbjct: 1090 YVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGT 1149

Query: 1308 AYVLQEMLTIKSD----DV------------VGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            + +L E L I SD    DV              R +    +V          P +  +LV
Sbjct: 1150 SQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK------MVIPYAAKLLV 1203

Query: 1352 KEMQALGLSIDLENSRTKNSAK 1373
            +E+ ++ +   L+ +      +
Sbjct: 1204 QELFSMNVVARLKLADEFPEER 1225



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 88/752 (11%), Positives = 207/752 (27%), Gaps = 126/752 (16%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K         L++    SY++F+ + +    + +    A  +S            + F
Sbjct: 110 FLKIKG------LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRF 154

Query: 77  VSYEFDPPK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                  P+                  ++C  RD+TYA P+ +    +          + 
Sbjct: 155 HDIYLGNPRRADEEQDSKFDLASTITPNECRLRDMTYAAPILVDFEYV----------RG 204

Query: 122 IKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQL 157
            + +K     +G +P+M                           G F++ G +++++ Q 
Sbjct: 205 RQRVKRNGTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQE 264

Query: 158 HRSPG-IHFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-R 208
             S   +  + D  +        S S +      II             KD I++R +  
Sbjct: 265 QLSKNRVIVETDLKKEIVQASVTSSSNERKSKSYII-----------LKKDRIYMRHNVL 313

Query: 209 RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDI 267
              VP+   L A+G+ S++ +      I  + + DF      +  L +     +   +  
Sbjct: 314 SEDVPIVILLKAMGIQSDKEMLLLVAGIDSTFQEDFAINFEESVKLSIYTQHQALEYIGS 373

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                   +   +T         + +  + I+   +  L                 A   
Sbjct: 374 RIKINRKPNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMA 425

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                 +           +           +         K + D  ++I +V++    +
Sbjct: 426 RRVLMAKHDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRT 485

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
               A  +         +     +     +  R  ++       + +   IA + +L  +
Sbjct: 486 EQFDAYGVVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMLTRI 545

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
            +       +      +    G +      + +    +  +        +  +       
Sbjct: 546 SSQFEKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLI 605

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
             + A+ V +             +  + + ++ +T   +        + R     E   V
Sbjct: 606 FALGAEDVQTVGGRELHGQGAYIIFLNGSPIA-LTRRPKFFLNSFRRLRRTGRVSEFISV 664

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
              H+       T +G     +  +              +     +  D      V YL 
Sbjct: 665 FINHHQNAVHVATDDGRICRPLIIVEDGKSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLD 724

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EE + YIA     + +                           ++  P  ++   A L
Sbjct: 725 CNEENDSYIAVYEEDITQS-----------------------TTHLEIEPFTILGAVAGL 761

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           IP+  ++ S R    C M +QA+ ++      
Sbjct: 762 IPYPHHNQSPRNTYQCAMGKQAIGVIANNQFL 793


>gi|59043113|gb|AAW83909.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  223 bits (569), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLS+  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSKFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|46277267|gb|AAS86824.1| RNA polymerase II second largest subunit [Eschscholzia californica]
          Length = 559

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 108/704 (15%), Positives = 201/704 (28%), Gaps = 149/704 (21%)

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            + R +H +H+G +CPAET EG   GLV +L     +            + +    N    
Sbjct: 4    KPRQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVGSAAHPILEFLEEWSTEN---- 59

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
                EE +  +   ++ +  +G +           + +   R ++   D + +  V    
Sbjct: 60   ---FEEISPAVIPQSTKIFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDI 113

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             L       D  R      +  +   L+K +        E   +   G        G +E
Sbjct: 114  HLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIQALQLRE---SPEEGGWHDLVAKGFIE 170

Query: 737  QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD-EVRRNDIIA 795
             VD        +   ++   S                        V   +          
Sbjct: 171  YVDTEEEETTMISMTINDLVSA----------------------RVNPKEAYSETYTHCE 208

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N          M  + +   I++  ++       
Sbjct: 209  IHPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------- 252

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                                +    +  V        +    +       +      + A
Sbjct: 253  --------------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVA 292

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +        +F R   D+ ++  ++ +E      R+     
Sbjct: 293  IACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGM 351

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +          G           K+T ++                  D+   +  
Sbjct: 352  RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ-----------------DDSQGQAS 394

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               +  + TS    E    +++      D +     R VKV +   R  Q GDK + RHG
Sbjct: 395  RYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHG 449

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+    
Sbjct: 450  QKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-- 507

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP F    
Sbjct: 508  ---------------------------------------------------ATP-FTDVT 515

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 516  VDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 559


>gi|161331517|gb|ABX60676.1| RpoB [Paenibacillus sp. FSL_h8548]
          Length = 227

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 81/200 (40%), Positives = 107/200 (53%), Gaps = 54/200 (27%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+ ++A KR I  GDKMAGRHGNKG+++RI+P EDMPFL DG
Sbjct: 82   KVFTRENGDELPPGVNQLVRAYIAQKRKISEGDKMAGRHGNKGVIARIMPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV++VLNPLGVPSRMN+GQ  E HLG AC  LG    + + D     D           
Sbjct: 142  TPVEVVLNPLGVPSRMNIGQALEVHLGMACKHLGIHAATPVFDGAREND----------- 190

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 191  ----------------------------------VFD---------TMEEAGMQRNGKTV 207

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            LYDG TGE F+R VTVG +Y
Sbjct: 208  LYDGRTGENFEREVTVGVMY 227



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII VGAE+  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRVGAEIGAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G VVDV++F R   D
Sbjct: 62  EVRDTSLRVPHGTDGIVVDVKVFTRENGD 90


>gi|59043087|gb|AAW83896.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043127|gb|AAW83916.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++  RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSSKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|157781303|gb|ABV72006.1| RNA polymerase beta subunit [Enterococcus cecorum]
          Length = 226

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 84/206 (40%), Positives = 109/206 (52%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D  ++ D+       
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGASDEDVW------ 188

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                     A           ADL +  
Sbjct: 189  -----------------------------------------ATVRE-------ADLAKDA 200

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            ++ILYDG TGEPFD  ++VG +YM+K
Sbjct: 201  KTILYDGRTGEPFDGRISVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|106734101|gb|ABF82537.1| DNA-directed RNA polymerase III [Exiguobacterium sp. TC38]
 gi|106734105|gb|ABF82539.1| DNA-directed RNA polymerase III [Exiguobacterium sp. 5138]
          Length = 339

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 164/305 (53%), Positives = 218/305 (71%), Gaps = 2/305 (0%)

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTS 757
            QAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +    
Sbjct: 1    QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQG 60

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +D Y++ KF RSNQ TC NQ+P++KVGD V + +I+ADGPS D G+LALGRN+LV FM 
Sbjct: 61   ELDRYKIQKFIRSNQGTCYNQKPIIKVGDPVDKGEILADGPSMDGGELALGRNVLVGFMT 120

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D
Sbjct: 121  WDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLD 180

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            + GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 181  DRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240

Query: 938  TVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  ++  
Sbjct: 241  IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMP 300

Query: 997  SGPKG 1001
              P G
Sbjct: 301  YMPDG 305



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 67/201 (33%), Positives = 102/201 (50%), Gaps = 4/201 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 138  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 197

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 198  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 257

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 258  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 317

Query: 1128 PSRMNVGQIFETHLGWACVGL 1148
            PSRMN+GQ+ E HLG A   L
Sbjct: 318  PSRMNIGQLLELHLGMAARQL 338


>gi|325094900|gb|EGC48210.1| DNA-directed RNA polymerase III [Ajellomyces capsulatus H88]
          Length = 1227

 Score =  223 bits (569), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 151/1102 (13%), Positives = 318/1102 (28%), Gaps = 185/1102 (16%)

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            + K   ++ +  D +   +            I ++A  +  +K +  +       +  + 
Sbjct: 292  ERKSKSYIILKKDRIYMRHNVLSEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 342

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + A      V      +  AL  I   ++             F     +  +  +
Sbjct: 343  STFQEDFAINFEESVKLGICTQHQALEYIGSRIKINRKPNS------FGITRRNHVQEAI 396

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 397  EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 453

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
            ++L   +           K +         + +  +  +   +        + ++Q    
Sbjct: 454  QLLALLFEDLFK------KFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNR 507

Query: 529  VNSLSRITHTR-RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
              S    +  R R+   G   V    + +    +      +        G      S   
Sbjct: 508  AISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMLTRISSQFEKTRKVSGPRALQPSQFG 567

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
                 +           V +  +   +   +  EEE          +   G+   + V  
Sbjct: 568  MLCPSDTPEGEACG--LVKNLALMTHIT--TNDEEE-----PVRKLIFALGAEDVQTVGG 618

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
            R    +       I F++ SP     IA +  P    +   R+     +       +   
Sbjct: 619  RELHGQGAY----IIFLNGSP-----IALTRRPKFFLNSFRRLRRTGRVSEFISVFINHH 669

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
               V     +   +     I+ +          +R++        D    G+  Y     
Sbjct: 670  QNAVHVA--TDDGRICRPLIIVEDGKSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLDC-- 725

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                 N   +    V   D  +    +   P T LG +A         +P+  +N     
Sbjct: 726  -----NEENDSYIAVYEEDITQSTTHLEIEPFTILGAVA-------GLIPYPHHNQSPRN 773

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
                 M  + +                                   + +    ++     
Sbjct: 774  TYQCAMGKQAIGV-----------------------------IANNQFLRIDSLLYTMVY 804

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                 +    I       +   +    A+      D+ D  +     V       ++F R
Sbjct: 805  PQKPMVKTRTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVF-R 863

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
                  +   +  +++++   R         +  +  R   +L      +  +      V
Sbjct: 864  KYSTNLKSYSNGTKDKLKGPDR---------ENGVPIRKHALLDNDGLAAVGEKVNYGEV 914

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              + +  E   S        D             Y  S    +    + I+K+       
Sbjct: 915  YINKVTPENALSS--GITGSDAGRPIA-------YIPSPQTYKLPDPSYIDKVMI--SAT 963

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                +++KV     R  + GDK +                                    
Sbjct: 964  EAENQLIKVQTRQTRVPEVGDKFS------------------------------------ 987

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
             SR                  G+K    I    A+   S L    + ++       +++ 
Sbjct: 988  -SR-----------------HGQKGVVGIIAEHADMPFSDLGIVPDIIMNPHGFPSRMTV 1029

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                 ++       SG       F G+  E ++++L        G+  L  G+TGEP   
Sbjct: 1030 GKMLELIAGKAGILSGQFGYGTAFGGSPVEEMSAILVDHGFSYGGKDYLTSGITGEPLPA 1089

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+ AYG 
Sbjct: 1090 YVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGT 1149

Query: 1308 AYVLQEMLTIKSD----DV------------VGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            + +L E L I SD    DV              R +    +V          P +  +LV
Sbjct: 1150 SQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK------MVIPYAAKLLV 1203

Query: 1352 KEMQALGLSIDLENSRTKNSAK 1373
            +E+ ++ +   L+ +      +
Sbjct: 1204 QELFSMNVVARLKLADEFPEER 1225



 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 88/752 (11%), Positives = 207/752 (27%), Gaps = 126/752 (16%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K         L++    SY++F+ + +    + +    A  +S            + F
Sbjct: 110 FLKIKG------LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRF 154

Query: 77  VSYEFDPPK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                  P+                  ++C  RD+TYA P+ +    +          + 
Sbjct: 155 HDIYLGNPRRADEEQDSKFDLASTITPNECRLRDMTYAAPILVDFEYV----------RG 204

Query: 122 IKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQL 157
            + +K     +G +P+M                           G F++ G +++++ Q 
Sbjct: 205 RQRVKRNGTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQE 264

Query: 158 HRSPG-IHFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-R 208
             S   +  + D  +        S S +      II             KD I++R +  
Sbjct: 265 QLSKNRVIVETDLKKEIVQASVTSSSNERKSKSYII-----------LKKDRIYMRHNVL 313

Query: 209 RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDI 267
              VP+   L A+G+ S++ +      I  + + DF      +  L +     +   +  
Sbjct: 314 SEDVPIVILLKAMGIQSDKEMLLLVAGIDSTFQEDFAINFEESVKLGICTQHQALEYIGS 373

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                   +   +T         + +  + I+   +  L                 A   
Sbjct: 374 RIKINRKPNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMA 425

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                 +           +           +         K + D  ++I +V++    +
Sbjct: 426 RRVLMAKHDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRT 485

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
               A  +         +     +     +  R  ++       + +   IA + +L  +
Sbjct: 486 EQFDAYGVVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMLTRI 545

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
            +       +      +    G +      + +    +  +        +  +       
Sbjct: 546 SSQFEKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLI 605

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
             + A+ V +             +  + + ++ +T   +        + R     E   V
Sbjct: 606 FALGAEDVQTVGGRELHGQGAYIIFLNGSPIA-LTRRPKFFLNSFRRLRRTGRVSEFISV 664

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
              H+       T +G     +  +              +     +  D      V YL 
Sbjct: 665 FINHHQNAVHVATDDGRICRPLIIVEDGKSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLD 724

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EE + YIA     + +                           ++  P  ++   A L
Sbjct: 725 CNEENDSYIAVYEEDITQS-----------------------TTHLEIEPFTILGAVAGL 761

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           IP+  ++ S R    C M +QA+ ++      
Sbjct: 762 IPYPHHNQSPRNTYQCAMGKQAIGVIANNQFL 793


>gi|143024653|gb|ABO93150.1| RNA polymerase beta subunit [Enterobacter pulveris]
          Length = 220

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 135/219 (61%), Positives = 173/219 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRAD 220


>gi|52699886|gb|AAU87004.1| DNA-dependent RNA polymerase II second largest subunit [Stictis
            radiata]
          Length = 703

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 108/804 (13%), Positives = 214/804 (26%), Gaps = 129/804 (16%)

Query: 468  GEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G ++ + +R     + + + +  +              + +  + + +     +      
Sbjct: 2    GPLMASLFRQLFGHLTKDVYKYLQRCVEAGKEFNLTLGVKSTLLTNGLKYSLATGNWGEQ 61

Query: 522  ---------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
                     +SQ+       S ++H RR +      + R     + R +H TH+G +CPA
Sbjct: 62   KKAMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLVCPA 117

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
            ET EG   GLV +L     +      E    +    + +V  +     +      ++   
Sbjct: 118  ETPEGQACGLVKNLAMMCYITVGSPSEPIIDFMVQRNMEVLEEYEPTRSPNSTKVFVNGV 177

Query: 631  NSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN-DDSN 688
               +  D +     V        I      I D  D   K          P L   +D  
Sbjct: 178  WVGVHRDPAHLVSTVQLLRRKNLISYEVSLIRDIRDREFKIFTDAGRVCRPLLVIDNDPK 237

Query: 689  RVLMGCNMQ-RQAVPLLKAEAPFVG--TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                G  M  ++ V  L+ +       T  E          ++A               +
Sbjct: 238  SSNKGNLMLTKELVNKLEDDRDLPPDLTKEERAERYFGWNGLLA------------SGAV 285

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-D 804
              ++ + + +   V     ++  R  Q       P       V+    ++    T     
Sbjct: 286  EFLDAEEEETVMIVMTPEDLEISRQVQAGYAAPEPSSDPNARVKGKVNLSQHMWTHCEIH 345

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
             ++   +  + +P+                                              
Sbjct: 346  PSMILGVCASIIPFPDQXXXXXXXXXXXXXXXXXXX---------XXXXXXXXXXXXXXX 396

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
                            +  +             +       +   +  + AI      + 
Sbjct: 397  XXXXXXXXXXXXRXDTMSNILYYPQKPXATTRSMEXLKFRELPAGQNAIVAIACYSGYNQ 456

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +        +F R  +   +R        +E   +    + + L    Y 
Sbjct: 457  EDSVIMNQSXIDRGFF-RSLFYRAYVXXEKRVGM---SLVEQFEKPMRSDTLRLKHGTYX 512

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   +  G           K+  ++ D      R++           +     +   
Sbjct: 513  KLDDDGIVAPGVRVSGEDIIIGKTAPMAPDTEEMGQRTKMHTKRDASTPXRSTENGIVDX 572

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                         L+ VKV     +  Q GDKMA RHG KG V 
Sbjct: 573  VLL--------------------TTNAEGLKFVKVRTRTTKIPQIGDKMASRHGQKGTVG 612

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                 EDMPF  +G   D+++NP  +PSRM +  + E  L       G +          
Sbjct: 613  ITYRMEDMPFSSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------- 664

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
                                                         +TP F     ++++ 
Sbjct: 665  ---------------------------------------------ATP-FTEVTVDSVSR 678

Query: 1222 MLRMADLDESGQSILYDGLTGEPF 1245
            +LR       G  ++Y+G TG   
Sbjct: 679  LLREHGYQSRGFEVMYNGHTGRKL 702



 Score =  102 bits (255), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 76/618 (12%), Positives = 157/618 (25%), Gaps = 92/618 (14%)

Query: 375 LDIYRVM-RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
            D+Y+ + R  +                 +        G      +         + + +
Sbjct: 18  KDVYKYLQRCVEAGKEFNLTLGVKSTLLTNGLKYSLATGNWGEQKKAMSSKAGVSQVLNR 77

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 78  YTFASTLSHLRRTNTPIGRDGKIAKPRQLHCTHWGLVCPAETPEGQACGLVKNLAMMCYI 137

Query: 489 RISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
            + S     +      N + +         ++   F     +    +  + +S +   RR
Sbjct: 138 TVGSPSEPIIDFMVQRNMEVLEEYEPTRSPNSTKVFVNGVWVGVHRDPAHLVSTVQLLRR 197

Query: 541 LSALG-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGH---NIGLVSSLTSF 589
            + +  +  + R     E        R   P       P  +++G+      LV+ L   
Sbjct: 198 KNLISYEVSLIRDIRDREFKIFTDAGRVCRPLLVIDNDPKSSNKGNLMLTKELVNKLEDD 257

Query: 590 ARVNAYGFIETPYRKVCDGKVT---NDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL-- 644
             +      E    +            V +L A EEE   I      L+           
Sbjct: 258 RDLPPDLTKEERAERYFGWNGLLASGAVEFLDAEEEETVMIVMTPEDLEISRQVQAGYAA 317

Query: 645 -----VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                        ++ + +      +  P  ++ + AS+IPF +                
Sbjct: 318 PEPSSDPNARVKGKVNLSQHMWTHCEIHPSMILGVCASIIPFPDQXXXXXXXXXXXXXXX 377

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                                                                       
Sbjct: 378 XXXXXXXXXXX-----------------------------------XXXXXXXXXXXXXX 402

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +    +      Q+P                       +L  G+N +VA   + 
Sbjct: 403 XXXXXXRXDTMSNILYYPQKPX----------ATTRSMEXLKFRELPAGQNAIVAIACYS 452

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLK 874
           GYN EDS+++++  +    F S+    +    +   +   E     +  D   +      
Sbjct: 453 GYNQEDSVIMNQSXIDRGFFRSLFYRAYVXXEKRVGMSLVEQFEKPMRSDTLRLKHGTYX 512

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +D+ GI+  G  V+  DI++GK  P         ++        K    RD S    S 
Sbjct: 513 KLDDDGIVAPGVRVSGEDIIIGKTAPMAPDTEEMGQRT-------KMHTKRDASTPXRST 565

Query: 935 VSGTVVDVRIFNRHGIDK 952
            +G V  V +       K
Sbjct: 566 ENGIVDXVLLTTNAEGLK 583


>gi|68490742|ref|XP_710813.1| hypothetical protein CaO19.13269 [Candida albicans SC5314]
 gi|68490765|ref|XP_710802.1| hypothetical protein CaO19.5847 [Candida albicans SC5314]
 gi|46432047|gb|EAK91554.1| hypothetical protein CaO19.5847 [Candida albicans SC5314]
 gi|46432059|gb|EAK91565.1| hypothetical protein CaO19.13269 [Candida albicans SC5314]
 gi|238879996|gb|EEQ43634.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Candida albicans
            WO-1]
          Length = 1157

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 90/501 (17%), Positives = 178/501 (35%), Gaps = 70/501 (13%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTP--EEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             G   +GA        +  +      P  P  + K +  I  +K    ++ ++ V S   
Sbjct: 713  MGKQAIGAIAYNQFRRIDTLLYFMVYPQQPMVKTKTIELIEYDKLPAGQNATVAVMSYSG 772

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D  + N+  +D+      V R+    L +  +  Q IL         + +    A+
Sbjct: 773  YDIEDALVLNKASLDRGFGRCQVVRKNTVQLKKYPNHTQDILAGMRVDENNKPIFQHQAL 832

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                  +  + + +  +  +        +       +  +     +  + +  +    + 
Sbjct: 833  GPDGLGEVGSRIFNGQV--FANKCVPTNSGDSTLGAQQEQRAAESHREAPAFYKGPEPSY 890

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I+++     +      ++KV +   R  + GDK +                         
Sbjct: 891  IDQVMM--SVSDNDQALIKVLLRQTRRPELGDKFS------------------------- 923

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
                        SR                  G+K    I   + +   +      + ++
Sbjct: 924  ------------SR-----------------HGQKGVCGIIVQQEDLPFNDSGISPDIIM 954

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                   +++      ++       +G       F G+  E ++ +L       SG+ +L
Sbjct: 955  NPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILIEKGFSYSGKDML 1014

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y G+TGE     +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGE
Sbjct: 1015 YSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGE 1074

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRV--YESIVA----GNDTFETGTPES 1346
            ME  C+ AYGA+ +L E L I SD    DV  +  +  Y S         +  +   P +
Sbjct: 1075 MERDCVIAYGASQLLLERLMISSDAFEVDVCNKCGLMGYNSWCTTCKSSENVIKMTIPYA 1134

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ ++  L    
Sbjct: 1135 AKLLFQELLSMNIAPRLRLGD 1155



 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 128/975 (13%), Positives = 274/975 (28%), Gaps = 178/975 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    SY++F+ +++    + NE        V P         ++++           
Sbjct: 54  LVKQHLDSYNYFVDVDLKKIIKANE---LVLSDVDP------EFYVKYLDIRVGHKSTSK 104

Query: 84  P-----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           P          +C  RDLTY+ P+ + +             +  K I+   + +G +P+M
Sbjct: 105 PGVKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIRHNDLEIGRMPVM 154

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+ G +++++ Q   S          +  +
Sbjct: 155 LRSNKCMLEGMSEATMAQVEECPLDPGGYFVVNGTEKVILVQEQLSKNRIIVEADEKKGI 214

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++           D I+++ +     +P+   L A G+ S+ EIL   
Sbjct: 215 VQASVTSST--HERKSK-TYVITKNDKIYLKHNSISEDIPIVIILKAAGIVSDLEILQLV 271

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK- 291
                  Q  D +      A  +       +L  +    + I          L+   E  
Sbjct: 272 CGSDSNYQ--DLFVVNFEEAARLEVFTQQQALYYVGKRVKTIRRAGAPKLSQLQEGIEAI 329

Query: 292 --------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                    V  L      L    +A  +V        ++  D +  K LE         
Sbjct: 330 ATTIIAHLTVSDLQFREKALYIATMARRVVMAMHNPKMVDDRDYVGNKRLELAGQLMSLL 389

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              L+    ++     + ++   ++  + DALL I                   +   + 
Sbjct: 390 FEDLFKKFNSDFKANIDKVLKKPSRTSEFDALLSINIHSNN----ITMGLNRAISTGNWS 445

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G   +  RL+  +   +            K+     L+  +  +    +  
Sbjct: 446 LKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTP 505

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +     E  +K+   ++  + +   D        +        +
Sbjct: 506 EGEACGLVKNLALMTHITTDDEEAPVKKLCIALGCEPIFALDSATLHVDGNFGVY-LNGT 564

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +      V  +    H RR+  +            +   +         P    E    
Sbjct: 565 LIGTTRFPVKFVHDFRHLRRVGKVSAFISIYTNTHHQAVHIATDGGRICRPLIIVENGKS 624

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            + +   +      + F         D      V YL   EE +  IA            
Sbjct: 625 KVTAEHLAKLINQEWSF--------DDFLTHGLVEYLDVNEENDSLIA------------ 664

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                      +    P   +  ++  P  V+   A LIP+  ++ S R    C M +QA
Sbjct: 665 -------LYEDDITANPGAIVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQA 717

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +                                           I   +     +     
Sbjct: 718 IGA-----------------------------------------IAYNQFRRIDTLLYFM 736

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +Y               Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 737 VYP--------------QQPMVK----------TKTIELIEYDKLPAGQNATVAVMSYSG 772

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNI 876
           Y+ ED++++++  +         + +  V  +      ++    +  D  N      + +
Sbjct: 773 YDIEDALVLNKASLDRGFGRCQVVRKNTVQLKKYPNHTQDILAGMRVDENNKPIFQHQAL 832

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
              G+  VG+ +  G +   K  P      T     L A   ++A +    +     G  
Sbjct: 833 GPDGLGEVGSRIFNGQVFANKCVPTNSGDST-----LGAQQEQRAAESHREAPAFYKGPE 887

Query: 937 GTVVDVRIFNRHGID 951
            + +D  + +    D
Sbjct: 888 PSYIDQVMMSVSDND 902


>gi|168010053|ref|XP_001757719.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162690995|gb|EDQ77359.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 533

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 91/401 (22%), Positives = 144/401 (35%), Gaps = 71/401 (17%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF--AVQDEKVQ 1032
              +L + I S   EIL   N      G    + L +  +   P     +    + D+K  
Sbjct: 171  MKVLRKTIASAKREILSWTNHPKEVSGLLLESQLDATTLDSNPTCSTERILATLDDDKKV 230

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV--KV------FVAMKRPI 1084
            + +  +  ++  +   L           +        V R +  ++       +   R  
Sbjct: 231  KMLSLMICRFIETILSLRQEDDRDCLSFKCVHTPADIVRRCIEKRINKLNQQKIKSNR-- 288

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
               DK   RH  KG++  IL  ED+PF KDG   D+++NP  +PSRM +G + E  +   
Sbjct: 289  ---DKFTSRHSQKGVIGAILSQEDLPFTKDGIVPDLIINPHAIPSRMTMGHLLEMVMCKI 345

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                        N+ +     S  RS     I   +  +    +                
Sbjct: 346  -------YVLDSNNARDPTLPSKPRSRESSCIDATAFNKAYRSF---------------- 382

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                       E  I  +          +  +Y G TG P +  V  G  Y   L H   
Sbjct: 383  -----------EVDIAKL---------SKEKMYCGTTGLPIEARVATGICYYHALRHQAR 422

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD---- 1320
            DK ++ S G    +T+QP+ G+S +GG R GEME  C+ A+GAA +L E L   SD    
Sbjct: 423  DKAHSISKGVIQSLTKQPVEGRSRKGGLRFGEMEKDCLIAHGAASMLLEKLKNTSDLCEV 482

Query: 1321 -------DVVGRTRVYESIVAGNDTFETGTPESFNVLVKEM 1354
                    +            G +T E   P SF +L +E+
Sbjct: 483  WICHGCSTICSSNPCVNC--NGRNTKEHHLPYSFKLLAQEL 521


>gi|111610540|gb|ABH11666.1| RNA polymerase II second largest subunit [Ustilago tritici]
          Length = 635

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 116/708 (16%), Positives = 220/708 (31%), Gaps = 91/708 (12%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +R+   ++ R +   +     +      Q  + +  + + + 
Sbjct: 1    DHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHIQAAVKSSTITNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMQAKAGVSQVLNRFAFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  A V            + +  + + V    A  
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHA 176

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            +  +     N           +LV                   D S +  V         
Sbjct: 177  KATKIFV--NGVWMGTHDDPAQLVDTLRDLRRKD---------DISHEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D++RVL    +       L  +   V   G                + G++E +DA
Sbjct: 226  RIYTDASRVLRPVFIVNPHDMTLLIKKRHVEMIGQTIPQTGEEFRWTHLVQEGVIEYLDA 285

Query: 741  IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                    E  +    S  D+ +  +++  N    +N          ++    IA    T
Sbjct: 286  E------EEESVLICMSTTDLEQSREYKARNGQINLNSA---DPSARLKSIHTIAPDTWT 336

Query: 801  DLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                  A+   +  + +P+  +N     +    M  +    +I I     ++R   +   
Sbjct: 337  HCEIHPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQ----AIGIPISNFISRADSMNHI 392

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                  P  +   ++++                             +   +  + AI   
Sbjct: 393  LYYPQKPLGTTRSMEHL-------------------------RFRELPAGQNAIVAIMCY 427

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    ++ R  + + ++   ++ E+ E   RD         
Sbjct: 428  SGYNQEDSVIMNQSSIDRGLF-RSLYYRGYMAEEKKVGVMQLEEFEKPHRDTTIRMKHGT 486

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +          G           K+  L  D      RS+          ++     + 
Sbjct: 487  YDKIDADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRSKLHTKKDASISLKSTENGII 546

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q+GDK A RHG KG 
Sbjct: 547  DQVLL--------------------TTNSHGNKFVKVRVRNSRVPQTGDKFASRHGQKGT 586

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            +      EDMPF  +G   DI++NP  +PSRM +G + E  L      
Sbjct: 587  IGITYRQEDMPFSTEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAAL 634


>gi|59043093|gb|AAW83899.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 132/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL++SL+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINSLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|52699892|gb|AAU87007.1| DNA-dependent RNA polymerase II second largest subunit [Hamigera
            avellanea]
          Length = 693

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 123/811 (15%), Positives = 232/811 (28%), Gaps = 139/811 (17%)

Query: 460  GNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFF 517
            G +R+   G +L N +R+   R+ R ++   +        +     I A  +   +    
Sbjct: 1    GKKRLDLAGPLLANLFRVLFTRVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYAL 60

Query: 518  CSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
             +               +SQ+       S ++H RR +      + R     + R +H T
Sbjct: 61   ATGNWGEQKKAASSKAGVSQVLSRYTYASTLSHLRRTNT----PIGRDGKIAKPRQLHNT 116

Query: 565  HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE 622
            H+G +CPAET EG   GLV +L     +      E    +    + +V  +         
Sbjct: 117  HWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVTPNA 176

Query: 623  ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP- 680
               ++      +  D +     +        I      I D  D   K          P 
Sbjct: 177  TKVFVNGVWVGIHRDPAHLVNTMNSLRRRNMISHEVSLIRDIRDREFKIFTDAGRVCRPL 236

Query: 681  FLENDDSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQV 738
            F+ ++D      G  +  ++ +  L+A+         E    +  G   + K +G+VE V
Sbjct: 237  FVIDNDPKSENCGSLVLNKEHIRKLEADKELPPDLDPEERRERYFGWDGLVK-SGVVEYV 295

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
            DA       +    +       +      +    +     R ++    +          P
Sbjct: 296  DAEEEETIMIVMTPEDLEISKQLQAGYTLEDETNDPNKRVRSILS--QKAHTWTHCEIHP 353

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N                        +           
Sbjct: 354  SMILG-------VCASIIPFPDHNQSPRN------------------TYXXXXXXXXXXX 388

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                                     +             +       +   +  + AI  
Sbjct: 389  XXXXXXXXXXXXX-----------XILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIAT 437

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    +F R   D  +       E+ E   R         
Sbjct: 438  YSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYADTEKMVGLQVVERFEKPMRIDTLGMRKG 496

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
              +       +  G           K+  L++D                +E  QR     
Sbjct: 497  TYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAAD---------------AEELGQRTKAHT 541

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K+   T     E+   +++      DD+     + VKV +   +  Q GDK A RHG KG
Sbjct: 542  KIDVSTPLRSTENGIVDQVLISTGNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKG 596

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +       
Sbjct: 597  TIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD----- 651

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                            +TP F     ++
Sbjct: 652  ------------------------------------------------ATP-FTDVTVDS 662

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            ++ +LR       G  ++++G  G      V
Sbjct: 663  VSRLLREHGYQSRGFEVMFNGHXGRKMVAQV 693



 Score = 99.4 bits (246), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 84/578 (14%), Positives = 161/578 (27%), Gaps = 73/578 (12%)

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVD 445
           T  +  ++    + +  K   S  G  ++  R    +      R          I     
Sbjct: 53  TGGLKYALATGNWGEQKKAASSKAGVSQVLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQ 112

Query: 446 LRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQD 502
           L N   G +   +    +    V  +    Y       E  I    + +   ++   PQ 
Sbjct: 113 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEFEPQV 172

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
             NA  V      F     +    +  + ++ +   RR + +             +RD+ 
Sbjct: 173 TPNATKV------FVNGVWVGIHRDPAHLVNTMNSLRRRNMIS-------HEVSLIRDIR 219

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
              +     A                   ++     E     V + +    +        
Sbjct: 220 DREFKIFTDAGRVCRPLFV----------IDNDPKSENCGSLVLNKEHIRKLE------- 262

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                  A+  L  D    E     R  G + LV    ++++DA  ++ + I  +     
Sbjct: 263 -------ADKELPPDLDPEERR--ERYFGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLE 313

Query: 683 ENDD---SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            +        +    N   + V  + ++     T  E   +   G            Q  
Sbjct: 314 ISKQLQAGYTLEDETNDPNKRVRSILSQKAHTWTHCEIHPSMILGVCASIIPFPDHNQSP 373

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                                 Q+PL                  
Sbjct: 374 RNT----YXXXXXXXXXXXXXXXXXXXXXXXXXILYYPQKPL----------ATTRSMEF 419

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   
Sbjct: 420 LRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVV 479

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  D   + +     +DE GI+  G  V+  DI++GK  P         ++   
Sbjct: 480 ERFEKPMRIDTLGMRKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPLAADAEELGQRT-- 537

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                KA    D S  + S  +G V  V I   +   K
Sbjct: 538 -----KAHTKIDVSTPLRSTENGIVDQVLISTGNDDLK 570


>gi|106734121|gb|ABF82547.1| DNA-directed RNA polymerase III [Exiguobacterium oxidotolerans]
          Length = 339

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 163/305 (53%), Positives = 217/305 (71%), Gaps = 2/305 (0%)

Query: 699  QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR-SVEGDLDPSTS 757
            QAVPLL  E+P VGTGME V AK SGAA+VAK +GI E+V A  I++R + E D +    
Sbjct: 1    QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIVQG 60

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +D Y++ KF RSNQ TC NQ+P++K GD V + +I+ADGPS D G+LALGRN+LV FM 
Sbjct: 61   ELDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMT 120

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            W GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV ++ LKN+D
Sbjct: 121  WDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLD 180

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
            + GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G
Sbjct: 181  DRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240

Query: 938  TVVDVRIFNR-HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
             ++DV+IF+R +G + +     + R  I    +  + +++         +  IL  ++  
Sbjct: 241  IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMP 300

Query: 997  SGPKG 1001
              P G
Sbjct: 301  YMPDG 305



 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 66/202 (32%), Positives = 101/202 (50%), Gaps = 4/202 (1%)

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG---FKKSTVL 1008
            K++   S+  E+ E  +RD       + R+I +   + L   +     +     K   +L
Sbjct: 138  KDDVYTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDIL 197

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR-FKNKIEKIQWGDDMP 1067
               +  +       +  +           ++          +      KI     GD++ 
Sbjct: 198  VGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELS 257

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            PGV ++++ ++  KR I  GDKMAGRHGNKG++SRILP EDMP++ DGTP+DI+LNPLGV
Sbjct: 258  PGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGV 317

Query: 1128 PSRMNVGQIFETHLGWACVGLG 1149
            PSRMN+GQ+ E HLG A     
Sbjct: 318  PSRMNIGQLLELHLGMAARHSN 339


>gi|56694328|gb|AAW22904.1| RNA polymerase II second largest subunit [Ephedra distachya]
          Length = 551

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/470 (16%), Positives = 136/470 (28%), Gaps = 82/470 (17%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                        I   ++     + I   +     R+T             V+   L+  
Sbjct: 164  EEAYTTTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 222

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 223  --DTLAYVLYYPQXPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 280

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   +F R   D+ ++  S+ +E     +R+          +          G    
Sbjct: 281  RGFF-RSLFFRSYRDEEKKMGSLVKEDFGRPSRENTAGMRHGSYDKLDEDGLAPPGTRVS 339

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++ +                        ES+  +Y         R    
Sbjct: 340  GEDVIIGKTTPVTQE------------------------ESMGGRYTRRDQSTSMRHSES 375

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                Q         LR VK+ +   R  Q GDK + RHG KG V      EDMP+  +G 
Sbjct: 376  GMVDQVLLTTNQDGLRFVKIRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGV 435

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +
Sbjct: 436  SPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQM 495

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                                                  +G +  
Sbjct: 496  RGFETM-----------------------------------------------YNGHT-- 506

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
              G         + +G  Y  +L HMV DK+++R  G   ++T+QP  G+
Sbjct: 507  --GR---RLPAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGR 551



 Score =  110 bits (276), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 73/452 (16%), Positives = 129/452 (28%), Gaps = 100/452 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + +A   F     +         ++ +   RR   +    GV R 
Sbjct: 21  EEWSTESFEEISPAVIPTATKVFVNGCWVGIHRNPDQLVNTLRQLRRQVDVNPEVGVVRD 80

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    +  N  L+       R+      +       D     
Sbjct: 81  IPLKELR-LYTDYGRCSRPLFVVK--NQRLLIRKPDIIRLQERTSSDEG---WHDLVARG 134

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   EE           +  P  ++
Sbjct: 135 FIEYVDTEEEETTMISM----------TINDLVQARRHPEEAYT--TTYTHCEIHPSLIL 182

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 183 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 222

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q PLV          
Sbjct: 223 DTLAYV-----------------------------------LYYPQXPLV---------- 237

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 238 TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 297

Query: 853 DTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +DE G+   G  V+  D+++GK TP  +    
Sbjct: 298 KMGSLVKEDFGRPSRENTAGMRHGSYDKLDEDGLAPPGTRVSGEDVIIGKTTPVTQEESM 357

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                            RD S  +    SG V
Sbjct: 358 GG-----------RYTRRDQSTSMRHSESGMV 378


>gi|56681221|gb|AAW21247.1| RNA polymerase beta subunit [Streptococcus vestibularis ATCC 49124]
          Length = 185

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 83/201 (41%), Positives = 106/201 (52%), Gaps = 54/201 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 38   KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 97

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+          
Sbjct: 98   TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW--------- 148

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                                D   E           +D   ++I
Sbjct: 149  ------------------------------------DTVREA---------GMDSDAKTI 163

Query: 1236 LYDGLTGEPFDRPVTVGYIYM 1256
            LYDG TGEPFD  V+VG +YM
Sbjct: 164  LYDGRTGEPFDNRVSVGVLYM 184


>gi|3133487|gb|AAC38544.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
          Length = 216

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 130/216 (60%), Positives = 169/216 (78%), Gaps = 1/216 (0%)

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
           Q LIN +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RD
Sbjct: 1   QTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRD 60

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A 
Sbjct: 61  VHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTAD 120

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLI 679
           EE+   +AQANS +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++I
Sbjct: 121 EEDRHVVAQANSPVDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMI 180

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           PFLE+DD+NR LMG NMQRQAVPL+++EAP VGTGM
Sbjct: 181 PFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGM 216


>gi|59043053|gb|AAW83879.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043055|gb|AAW83880.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043059|gb|AAW83882.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043065|gb|AAW83885.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043085|gb|AAW83895.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043131|gb|AAW83918.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043133|gb|AAW83919.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043135|gb|AAW83920.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043137|gb|AAW83921.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043139|gb|AAW83922.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043141|gb|AAW83923.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043143|gb|AAW83924.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  223 bits (568), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|241958746|ref|XP_002422092.1| DNA-directed RNA polymerase III subunit, putative [Candida
            dubliniensis CD36]
 gi|223645437|emb|CAX40093.1| DNA-directed RNA polymerase III subunit, putative [Candida
            dubliniensis CD36]
          Length = 1157

 Score =  223 bits (567), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 89/501 (17%), Positives = 178/501 (35%), Gaps = 70/501 (13%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTP--EEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             G   +GA        +  +      P  P  + K +  I  +K    ++ ++ V S   
Sbjct: 713  MGKQAIGAIAYNQFRRIDTLLYFMVYPQQPMVKTKTIELIEYDKLPAGQNATVAVMSYSG 772

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              + D  + N+  +D+      V R+    L +  +  Q IL         + +    A+
Sbjct: 773  YDIEDALVLNKASLDRGFGRCQVVRKNTVQLKKYPNHTQDILAGMRVDENNKPIFPHQAL 832

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                  +  + + +  +  +        +       +  +     +  + +  +    + 
Sbjct: 833  GPDGLGEVGSRIFNGQV--FANKCVPTNSGDSTLGAQQEQRTAESHREAPAFYKGPEPSY 890

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            I+++     +      ++KV +   R  + GDK +                         
Sbjct: 891  IDQVMM--SVSDNDQALIKVLLRQTRRPELGDKFS------------------------- 923

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
                        SR                  G+K    I   + +   +      + ++
Sbjct: 924  ------------SR-----------------HGQKGVCGIIVQQEDLPFNDSGISPDIIM 954

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                   +++      ++       +G       F G+  E ++ +L       SG+ +L
Sbjct: 955  NPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFSYSGKDML 1014

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y G+TGE     +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGE
Sbjct: 1015 YSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGE 1074

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRV--YESIVA----GNDTFETGTPES 1346
            ME  C+ AYGA+ +L E L I SD    DV  +  +  Y +         +  +   P +
Sbjct: 1075 MERDCVIAYGASQLLLERLMISSDAFEVDVCNKCGLMGYNNWCTTCKSSENVIKMTIPYA 1134

Query: 1347 FNVLVKEMQALGLSIDLENSR 1367
              +L +E+ ++ ++  L    
Sbjct: 1135 AKLLFQELLSMNIAPRLRLGD 1155



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 126/978 (12%), Positives = 270/978 (27%), Gaps = 184/978 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    SY++F+ +++    + NE        V P         ++++           
Sbjct: 54  LVKQHLDSYNYFVDVDLKKIIKANE---LVLSDVDP------EFYVKYLDIRVGHKSTSK 104

Query: 84  P-----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           P          +C  RDLTY+ P+ + +             +  K I+   + +G +P+M
Sbjct: 105 PGVKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIRHNDLEIGRMPVM 154

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+ G +++++ Q   S          +  +
Sbjct: 155 LRSNKCMLEGMSEATMAQVEECPLDPGGYFVVNGTEKVILVQEQLSKNRIIVEADEKKGI 214

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++           D I+++ +     +P+   L A G+ S+ EIL   
Sbjct: 215 VQASVTSST--HERKSK-TYVITKNDKIYLKHNSISEDIPIVIILKAAGIVSDLEILQLV 271

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK- 291
                  Q  D +      A  +       +L  +    + I          L+   E  
Sbjct: 272 CGSDPNYQ--DLFVVNFEEAARLEVFTQQQALYYVGKRVKTIRRAGAPKLSQLQEGIEAI 329

Query: 292 --------GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
                    V  L      L    +A  +V        ++  D +  K LE         
Sbjct: 330 ATTIIAHLTVSDLQFKEKALYIATMARRVVMAMHNPKMVDDRDYVGNKRLELAGQLMSLL 389

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              L+    ++     + ++   ++  + DALL I                   +   + 
Sbjct: 390 FEDLFKKFNSDFKANIDKVLKKPSRTSEFDALLSINIHSNN----ITMGLNRAISTGNWS 445

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G   +  RL+  +   +            K+     L+  +  +    +  
Sbjct: 446 LKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTP 505

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +     E  +K+    +  + +   D        +        +
Sbjct: 506 EGEACGLVKNLALMTHITTDDEEAPVKKLCIVLGCEPIFALDSATLHVEGNFGVY-LNGT 564

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +      V  +    H RR   +            +   +         P    E    
Sbjct: 565 LIGTTRFPVKFVHDFRHLRRNGKVSAFISIYTNTHHQAVHIATDGGRICRPLIIVENGKS 624

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            + +   +      + F         D      V YL   EE +  IA     +  +   
Sbjct: 625 KVTAEHLAKLINQEWSF--------DDFLKHGLVEYLDVNEENDSLIALYEDDITANPGA 676

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                               +  ++  P  V+   A LIP+  ++ S R    C M +QA
Sbjct: 677 V-------------------VTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQA 717

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +                                           I   +     +     
Sbjct: 718 IGA-----------------------------------------IAYNQFRRIDTLLYFM 736

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +Y               Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 737 VYP--------------QQPMVK----------TKTIELIEYDKLPAGQNATVAVMSYSG 772

Query: 821 YNFEDSMLISERMVSEDVFTSIHIE-------EFEVMARDTKLGPEEITRDIPNVSEEGL 873
           Y+ ED++++++  +         +        ++    +D   G      + P    +  
Sbjct: 773 YDIEDALVLNKASLDRGFGRCQVVRKNTVQLKKYPNHTQDILAGMRVDENNKPIFPHQA- 831

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +   G+  VG+ +  G +   K  P      T     L A   ++  +    +     
Sbjct: 832 --LGPDGLGEVGSRIFNGQVFANKCVPTNSGDST-----LGAQQEQRTAESHREAPAFYK 884

Query: 934 GVSGTVVDVRIFNRHGID 951
           G   + +D  + +    D
Sbjct: 885 GPEPSYIDQVMMSVSDND 902


>gi|117675895|emb|CAL69218.1| RNA polymerase subunit B [Curtobacterium flaccumfaciens pv.
           flaccumfaciens]
          Length = 390

 Score =  223 bits (567), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 138/294 (46%), Positives = 199/294 (67%), Gaps = 15/294 (5%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
           +D     A I +TL  D    +++AL DIYR +RPG+      A ++ +  +F+  +YDL
Sbjct: 97  MDEFQGFASIESTLEKDAVLTKEEALKDIYRKLRPGEQGAAEAARALLDNFYFNPKRYDL 156

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TI 453
           + VGR K+N +L +D P     +  +DI+A IK LV L   +                 +
Sbjct: 157 AKVGRYKVNRKLGMDAPLSDSVLTVKDIVATIKYLVSLHAERTTIDGVRDGEPVQLRLDV 216

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
           DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ P+ LIN +PVV+A+
Sbjct: 217 DDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPRTLINVRPVVAAI 276

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP E
Sbjct: 277 KEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIE 336

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           T EG NIGL+ SL SF R+N++GFIETPYR+V +G+VT  + YL+A EE++  +
Sbjct: 337 TPEGPNIGLIGSLASFGRINSFGFIETPYRRVVNGEVTKTIDYLTASEEDDFVV 390



 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 64/173 (36%), Positives = 92/173 (53%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  +     S K +Y+ RIIP +G 
Sbjct: 1   FMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERQQETT--SDKDIYSARIIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEI+  F  +  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEIMDEFQGFASIESTLEKDAVLTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQ-VIESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQ   E+ + L      + K   +  +G   
Sbjct: 119 EEALKDI--------YRKLRPGEQGAAEAARALLDNFYFNPKRYDLAKVGRYK 163


>gi|190407518|gb|EDV10785.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Saccharomyces
            cerevisiae RM11-1a]
          Length = 881

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 89/491 (18%), Positives = 163/491 (33%), Gaps = 87/491 (17%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             L+           T E      +   +   V   S          V++    +R     
Sbjct: 458  YLMTYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRC 517

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              R  +        + +   +    +   +          Q+   GP G     V     
Sbjct: 518  ETRRKTT------TVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPDGL--GEVGMKVQ 569

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   ++       D     NV  ++ QY  +  I      + I+++     +      
Sbjct: 570  SGQIYINKSVPTNSADAPNPNNVN-VQTQYREAPVIYRGPEPSHIDQVMM--SVSDNDQA 626

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +   R  + GDK +                                     SR  
Sbjct: 627  LIKVLLRQNRRPELGDKFS-------------------------------------SR-- 647

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                            G+K    I   + +   +      + ++       +++      
Sbjct: 648  ---------------HGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKMIE 692

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE     +  G
Sbjct: 693  LISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFG 752

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L 
Sbjct: 753  PIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLL 812

Query: 1313 EMLTIKSD----DVVGR------------TRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            E L I SD    DV  +             +  E+I+          P +  +L +E+ +
Sbjct: 813  ERLMISSDAFEVDVCDKCGLMGYSGWCTTCKSAENIIK------MTIPYAAKLLFQELLS 866

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 867  MNIAPRLRLED 877



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 81/694 (11%), Positives = 188/694 (27%), Gaps = 115/694 (16%)

Query: 285 LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI--R 342
           +K+++ + +  L    + +    +A   V             ++  + +  +++ ++   
Sbjct: 41  VKTMRRQKLTILQEGIEAIATTVIAHLTVEALDFREKALYIAMMTRRVVMAMYNPKMIDD 100

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              +           I         K   D  L I +V++  + +    A    N    +
Sbjct: 101 RDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALLSINVHSNN 160

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                   +     +++        V H    +     + ++  +         +     
Sbjct: 161 ITSGLNRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRA 220

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L   +   +      +     L    ++   I++ D +  + +       +         
Sbjct: 221 LQPSQFGMLCTADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCY---VLGVEDITLID 277

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           S+ L        + + I   R  +        + R     E   ++   +       T  
Sbjct: 278 SASLHLNYGVYLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVHIATDG 337

Query: 577 GHNI-GLVSSLTSFARVNAYG--FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           G     L+      +RV       +        D      V YL   EE + YIA     
Sbjct: 338 GRICRPLIIVSDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLDVNEENDSYIAL---- 393

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                 + +++V                  ++  P  ++   A LIP+  ++ S R    
Sbjct: 394 ------YEKDIVPSM-------------THLEIEPFTILGAVAGLIPYPHHNQSPRNTYQ 434

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+                                           I   +    
Sbjct: 435 CAMGKQAIGA-----------------------------------------IAYNQFKRI 453

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +   +  Y               Q+P+VK                 D   L  G+N  V
Sbjct: 454 DTLLYLMTYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATV 489

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVS 869
           A M + GY+ ED++++++  +           +   + +      ++    +  D     
Sbjct: 490 AVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKRYANHTQDIIGGMRVDENGDP 549

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP---------MTPEEKLLRAIFGEK 920
               +++   G+  VG +V  G I + K  P   +           T   +      G +
Sbjct: 550 IWQHQSLGPDGLGEVGMKVQSGQIYINKSVPTNSADAPNPNNVNVQTQYREAPVIYRGPE 609

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
              +    + V       +  +   NR     ++
Sbjct: 610 PSHIDQVMMSVSDNDQALIKVLLRQNRRPELGDK 643


>gi|157781337|gb|ABV72023.1| RNA polymerase beta subunit [Enterococcus asini]
          Length = 226

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 93/292 (31%), Positives = 128/292 (43%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 58   -----EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D   + D+                                       
Sbjct: 167  ARQLGIHVATPVFDGATDEDVW-------------------------------------- 188

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                     A  +        A +    ++ILYDG TGEPFD  ++VG +YM
Sbjct: 189  ---------ATVKE-------AGMASDAKTILYDGRTGEPFDGRISVGVMYM 224



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|59043125|gb|AAW83915.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++  RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSLKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|32455013|gb|AAP83186.1| RpoB [Streptococcus lutetiensis]
          Length = 220

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 92/289 (31%), Positives = 128/289 (44%), Gaps = 72/289 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 4    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 56

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 57   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 105

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 106  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 165

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 166  ARNLGIHIATPVFDGATSEDLW-------------------------------------- 187

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                   D  +E         A +    +++LYDG TGEPFD  V+VG 
Sbjct: 188  -------DTVNE---------AGMASDAKTVLYDGRTGEPFDNRVSVGV 220



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 54/85 (63%), Positives = 65/85 (76%)

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           NV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRD
Sbjct: 1   NVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRD 60

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGID 951
           TSLRVP G  G V DV+IF R   D
Sbjct: 61  TSLRVPHGGDGVVRDVKIFTRANGD 85


>gi|327133535|gb|AEA29772.1| RNA polymerase subunit B [Acinetobacter sp. 10N2]
          Length = 203

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 88/206 (42%), Positives = 121/206 (58%), Gaps = 4/206 (1%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F
Sbjct: 1    QMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKF 60

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K  K   GD++  GVL+VVKV++A KR IQ GDKMAGRHGNKG+VS ILP EDMP   
Sbjct: 61   AEKKRKFSTGDELTTGVLKVVKVYLAEKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDA 120

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR FL 
Sbjct: 121  NGVPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLH 177

Query: 1174 KVIGT-GSHTEKISDYDDDSVLRVAE 1198
            K+    G   E++    DD VL +A 
Sbjct: 178  KIYNKVGGEQEELETLTDDEVLILAG 203


>gi|59043105|gb|AAW83905.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 130/228 (57%), Positives = 169/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF  SQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGPSQLSQFMDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|270690778|ref|ZP_06222896.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
           HK1212]
 gi|270316104|gb|EFA28109.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
           HK1212]
          Length = 160

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 67/163 (41%), Positives = 98/163 (60%), Gaps = 3/163 (1%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
           HRSPG+ FD DKG+   SGK+LY  RIIP +G W+D EFD KD +  RIDRRRK+P T  
Sbjct: 1   HRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFARIDRRRKLPATII 60

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
           L ALG  +EEIL+ F+ KI +   GD     L    L  G   S  +     G+  +E G
Sbjct: 61  LRALGYTTEEILNLFFDKITFEIAGDKLLMTLVPERL-RGETASFDIE--ANGKVYVERG 117

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEI 320
           +++T+  +K+L++  +  + + S+ + G   ++D V+ E+GEI
Sbjct: 118 RRITARHIKALEKDNISQVVVPSEYILGKVASKDYVDLESGEI 160


>gi|154499233|ref|ZP_02037611.1| hypothetical protein BACCAP_03228 [Bacteroides capillosus ATCC 29799]
 gi|150272073|gb|EDM99299.1| hypothetical protein BACCAP_03228 [Bacteroides capillosus ATCC 29799]
          Length = 1237

 Score =  222 bits (566), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 88/255 (34%), Positives = 127/255 (49%), Gaps = 30/255 (11%)

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
             +++GDKMAGRH NKG  S I    +MP   +G  +DI+LNP GVPSRMN+GQ FE +LG
Sbjct: 918  RLRTGDKMAGRHSNKGTASIIRKNSEMPCFMNGRQLDILLNPCGVPSRMNIGQNFEAYLG 977

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
            +    L   ++S   +    GDI  L  ++  +    +     S+Y         +  + 
Sbjct: 978  FIAYLLDVYVESDPFNGATKGDIKLLMRYVWDLANNENAKSVCSNYPMLPSTLHEQAIR- 1036

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD-LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                          EAI      A   +  G + L++  TG+  + PVT G  YMLKL H
Sbjct: 1037 ------------RHEAIRDW---AGCFNPDGTAYLWNPATGKCLENPVTFGVPYMLKLEH 1081

Query: 1262 MVSDKVYARSTG----SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE---- 1313
             V+ K +AR+ G     YS +++QP  G +  GGQ++GEME+  + AYGA   L E    
Sbjct: 1082 EVNHKFHARA-GMLEEDYSQISKQPTEGSARGGGQKMGEMELCALAAYGATDFLYETCNS 1140

Query: 1314 MLTIKSDDVVGRTRV 1328
            M    SD+V+ R   
Sbjct: 1141 M----SDNVLDRVNT 1151



 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 156/931 (16%), Positives = 317/931 (34%), Gaps = 134/931 (14%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV---------FPITA-FSGAAMLEFVS 78
           L+E QK SY  +L   I  D      L    + +         F +   + G        
Sbjct: 25  LLEYQKESYQKYLTETIYSDMEY---LLQVMRELLQVSQVDAEFRVGDLYCGNYK----- 76

Query: 79  YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                     ++   +  +Y  P+     +         GA    ++    ++   +P M
Sbjct: 77  ----------NEVKKKSPSYY-PVYAKFTI--------DGAVFPNEV---EVF--RIPAM 112

Query: 139 TKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDS 198
            +DG     G +R+++ Q+  +  + +  DK   S++          P +   + + FD 
Sbjct: 113 DEDGILNFNGDRRVLLMQMVAAERVSYAADKQTVSITT---------PRRN--ISLMFDG 161

Query: 199 KDIIHVRIDRRRKVPVTSFLMALG------------MDSEEILSTF-------YPKIVYS 239
              + ++   R K+P+   + A                S  ILS F          I   
Sbjct: 162 TKDVTIKYGPRNKIPMHKLIRAYNAKEKVYDDPSKLFTSAYILSAFATDSAATDEAIEDE 221

Query: 240 QRGDFWCFPLSAADLMVGAKV----SSSLVDIDTGEQV------IESGKKLTSGLLKSLK 289
                     S  D  +G        +  +D   G  +       E+G+++   +L  + 
Sbjct: 222 LDKLNIYATYSGDDYALGKTRDALNEALSLDRARGRILSRPVGPFEAGRRVDDEVLHYIH 281

Query: 290 EKGVKFLGITSD-CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS------EIR 342
              +  + + +   + G  + +++V       ++ AG   + +  E +            
Sbjct: 282 LHCINEIYVKAIPDVVGYTLTQELVIS-----FVPAGTHNNSRLQEALPEFADYSAIPQD 336

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
               +++ S           + D      D        +R           ++     + 
Sbjct: 337 SQVCIFMSSKETLTKEDVQFLYDVGAHHVDCKRPGSAPIRATFEEEVIGNYTVRLGDIYG 396

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG--TIDDIDNLG 460
            +                      D+ H+   D++A+  +   ++       + D D   
Sbjct: 397 HNIPAGRFHDEWVCFYNNPKFERTDMDHLNTHDLMALYSLCAFIKKNPEENFLLDKDFGL 456

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ-DLINAKPVVSAVCEFFCS 519
            ++V +  E+  N  R  L    +     IS     +++ +        +          
Sbjct: 457 LKKVLAANELFSNAMREVLPDFVKHYSVSISRAISQNLLTEGKFAGLSDMWKKYLWDKNY 516

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             ++     +  +++  H           +  +    +MR +    YGRICP ET  G  
Sbjct: 517 LDIANTINPIAVVAQTNHL-------VSDLHTSEIPEKMRLLSMGFYGRICPYETPSGKK 569

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN------DVVYLSAMEEENRYIAQANSS 633
           +G+ ++    AR+   G + TPYR+V             ++ Y+ A EE    I    S 
Sbjct: 570 LGITNTKAIGARI-KDGILTTPYRRVLKNSNGEIESISQEITYMDAQEEAQFRIGDLLSL 628

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKID-----FIDASPKQVVSIAASLIPFLENDDSN 688
             +   +    V  R       V  E +D     +++A  +Q +S  A+LIPF  +DD+ 
Sbjct: 629 KKDGYRYLNTKVMARVPAPNNQVTVESVDAYTLDYVNAYCEQHLSPTAALIPFAGSDDAV 688

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG-AAIVAKRAGIVEQVDAIRIVIRS 747
           RV    NM +Q++ +  ++ P V T M       S    I AK+ G VEQ+   ++ +  
Sbjct: 689 RVTYATNMLKQSILVQGSQIPRVFTSMYRRCFNHSNTYVIRAKKDGWVEQIPMGKLQLTY 748

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G ++     ++I       +S      +    VK GD  ++ D++ D      G  + 
Sbjct: 749 DDGTIED----IEICETSVTNQSVNFLNFH----VKEGDHFKKGDVLVDSAIAREGIYSP 800

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
           G N+  A++   GYN+ED++ +SE   ++ +  S       +  +  +         I  
Sbjct: 801 GVNLFAAYL-ADGYNYEDAVELSEYAANQFISISTETITHRMHRQSNES--------IRV 851

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            +E   + I E G+I   +  +  D      
Sbjct: 852 GTEYCYRFIPENGVIAKVSRQSKSDARCHSK 882


>gi|164661167|ref|XP_001731706.1| hypothetical protein MGL_0974 [Malassezia globosa CBS 7966]
 gi|159105607|gb|EDP44492.1| hypothetical protein MGL_0974 [Malassezia globosa CBS 7966]
          Length = 1131

 Score =  222 bits (565), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/509 (14%), Positives = 156/509 (30%), Gaps = 105/509 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +  + A+      D+ D  +   + +   
Sbjct: 706  DTLLYLMVYPQKPMVSTKTIELIGYDKLPAGQNAMVAVMSFSGYDIEDALVMNCASLDRG 765

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++  +      + +        +    +  +     +          L        
Sbjct: 766  FGRCQVMRKQSTVLRKYANGTFDRLADAPVNEHGEPLRRFE---------ALEADGISGA 816

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
             +  +   V  +  I              ++     + +  + Y+ +    +   +  I+
Sbjct: 817  GERLEPGDVYINKQIP----------TNANDNSAGTMLNSAITYKNAPLSYKSPVEGYID 866

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++   D        +VK  +   R  + GDK +                           
Sbjct: 867  QVLISD--TDSDQTLVKSLIRQTRRPELGDKFS--------------------------- 897

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
                      SR                  G+K    +   +A+   +      + ++  
Sbjct: 898  ----------SR-----------------HGQKGVIGLIVPQADMPFNDQGICPDIIMNP 930

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 +++      ++        G       F G+  E ++ +L        G+  +  
Sbjct: 931  HGFPSRMTVGKMIELVSGKAGVLRGTQEYGTAFGGSKVEDMSRILVEHGYHYGGKEYMTS 990

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGEP +  V  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME
Sbjct: 991  GMTGEPLEAYVYFGPIYYQKLKHMVMDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEME 1050

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIV------------AG--------NDT 1338
              C+  YGA  +L E L + SD          + V             G           
Sbjct: 1051 RDCLIGYGATQLLLERLMVSSD----------AFVVNACEECGLLGYNGYCGYCKSSKHV 1100

Query: 1339 FETGTPESFNVLVKEMQALGLSIDLENSR 1367
             +   P +  +L +E+ A+ +   L    
Sbjct: 1101 VKLTVPYATKLLFQELMAMQVVPRLVLEE 1129



 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 112/947 (11%), Positives = 270/947 (28%), Gaps = 179/947 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S+++F+ +++    R NE        + P         L++ +     P+   
Sbjct: 34  LVKQHIDSFNYFVDVDLKNILRANE---RVTSDIDP------KFYLKYTNITVGHPERAD 84

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+  + + +             +  K ++ +++ +G LP+M
Sbjct: 85  PDAIDRSITPHECRLRDITYSAFIYVDIEYT----------RGGKIVRRKNVPIGRLPIM 134

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+KG +++++ Q   S            + 
Sbjct: 135 LRSNKCWLAGQDEATLARMNECPLDPGGYFVVKGTEKVILVQEQLSKNRIIVE-----AD 189

Query: 175 SGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EIL 229
           S K +    +      +     +      +I+V+ +     +P+     A+G+ S+ EIL
Sbjct: 190 SRKEVVQASVTSSTHERKSKSYVLT-KHGLIYVKHNSLNEDIPIVVVFRAMGIQSDKEIL 248

Query: 230 STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKS 287
                +              +A   +   + +   +           G + T+    L+ 
Sbjct: 249 QLVAGQDETYAELFSINLERAAKLGIFTRQQALDYMGARVKIMRRGVGMRRTASDEALEV 308

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
           L    +  + +              +      + +    ++DE  +++  +   + + + 
Sbjct: 309 LATVIMAHVPVEQGDFRNKT---MYIATMVRRVLV---CMVDESKVDDRDYVGNKRLEL- 361

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                     +         K   D   +I +V++  + ++   A + F +         
Sbjct: 362 ------AGQLLALLFEDLFKKFNFDLKTNIDKVLKKPNRTSEFDAYNQFFYHGDYITAGF 415

Query: 408 LSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           +  +     +++        V H    +     + ++  +         +     L   +
Sbjct: 416 VRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKTRKVSGPRALQPSQ 475

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
              +      +     L    ++   I++   ++ + +           +       Q S
Sbjct: 476 WGMLCPSDTPEGEACGLVKNLALMTHITTDVDEAPIVRLCYALGLEDINLLTGAELYQPS 535

Query: 524 QLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                +N             + Q   + RA    E   ++   + +     +  G     
Sbjct: 536 TYIVFLNGNVVGVTLTPHRFVAQFRRLRRAGLISEFVGIYTNTHHQTVNIASDGGRICRP 595

Query: 583 VSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           +  + +            ++       D      V YL   EE +  IA           
Sbjct: 596 MIIVENGRPQVTSEHIRQLQAGTMTFDDFLRRGLVEYLDVNEENDSNIAL---------- 645

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                                   ++     ++   A LIP+  ++ S R    C M +Q
Sbjct: 646 -------------FEHSIGPSTTHLEIECFTLLGACAGLIPYPHHNQSPRNTYQCAMGKQ 692

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
           A+                                           I   + +   +   +
Sbjct: 693 AIGA-----------------------------------------IGYNQLNRIDTLLYL 711

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
            +Y               Q+P+V                      L  G+N +VA M + 
Sbjct: 712 MVYP--------------QKPMVS----------TKTIELIGYDKLPAGQNAMVAVMSFS 747

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE----GLKN 875
           GY+ ED+++++   +         + +   + R    G  +   D P           + 
Sbjct: 748 GYDIEDALVMNCASLDRGFGRCQVMRKQSTVLRKYANGTFDRLADAPVNEHGEPLRRFEA 807

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           ++  GI   G  + PGD+ + K  P   +  +    L  AI  + A 
Sbjct: 808 LEADGISGAGERLEPGDVYINKQIPTNANDNSAGTMLNSAITYKNAP 854


>gi|300394762|gb|ADK11919.1| DNA-directed RNA polymerase II subunit two [Tapinella atrotomentosa]
          Length = 650

 Score =  222 bits (565), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 105/651 (16%), Positives = 199/651 (30%), Gaps = 76/651 (11%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 59   GVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 114

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++   +       + +  + +         EEN + +   + +  +G +
Sbjct: 115  GLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSSTPCTKVFVNGVW 166

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR-Q 699
                   R     +   ++     D SP+  V             D+ RV     +   Q
Sbjct: 167  MG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQ 223

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             + L K    ++  G  +   +      + K   I    DA       +    +   +  
Sbjct: 224  QLALKKKHVKWLSRGYRNDETEEYKWEHLVKGGIIELL-DAEEEETVMISMTPEDLENSR 282

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                 +    ++ +     R  +K              PS  LG       +  + +P+ 
Sbjct: 283  LQQAGVDPHANDGDFDPAAR--LKASTNAHTWTHCEIHPSMILG-------ICASIIPFP 333

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N                        ++       +G       I              
Sbjct: 334  DHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM-----------D 364

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 365  TMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 424

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                I+ R  +D  ++S   + E+ E   RD          +       I  G       
Sbjct: 425  F-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVTGED 483

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  D      R++          ++     +  Q      ++   F+     
Sbjct: 484  IIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ-----VLISTNFE----- 533

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                        + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 534  ----------GQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVPD 583

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +++NP  +PSRM +G + E  L      +G +  +          +S    
Sbjct: 584  LIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTELTVEAVSAFLR 634



 Score =  120 bits (301), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 84/603 (13%), Positives = 167/603 (27%), Gaps = 100/603 (16%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           D+YR ++        F+++ ++ +    +  KY L   G      +         + + +
Sbjct: 8   DVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSL-ATGNWGDQKKSMSSKAGVSQVLNR 66

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R GK       +  +  +    E  + Q    +  +      
Sbjct: 67  YTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACI 126

Query: 489 RISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +             NA         F     +    +  N +  I   RR 
Sbjct: 127 SVGSYSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRK 186

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +            +   ++        P    E   + L      +         ET 
Sbjct: 187 DDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALKKKHVKWLSRGYRND-ETE 245

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR--- 658
             K         +  L A EEE   I+     L+        +      G+     R   
Sbjct: 246 EYKWEHLVKGGIIELLDAEEEETVMISMTPEDLENSRLQQAGVDPHANDGDFDPAARLKA 305

Query: 659 ----EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
                     +  P  ++ I AS+IPF +++ S R      M +QA+ +           
Sbjct: 306 STNAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI---- 361

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                                                   + + +  Y       +    
Sbjct: 362 -------------------------------------RMDTMANILYYPQKPLATTRSME 384

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
            +  R                        +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 385 YLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 420

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F SI+   +  + + + +   E            +       +++ G+I  G  V 
Sbjct: 421 DRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVT 480

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        +    RD S  + S  +G V  V I     
Sbjct: 481 GEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLISTNFE 533

Query: 950 IDK 952
             K
Sbjct: 534 GQK 536


>gi|68131890|gb|AAY85223.1| RNA polymerase II second largest subunit [Nelumbo nucifera]
          Length = 865

 Score =  222 bits (565), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 124/904 (13%), Positives = 261/904 (28%), Gaps = 163/904 (18%)

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD-------- 141
              R+LTY+ PL + +   V           + + +E   +++G +P+M +         
Sbjct: 2   ARLRNLTYSAPLYVDVTKRVIKKGHDCE--EVTETQEFAKVFIGKVPIMLRSSYCTLYQN 59

Query: 142 ----------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRI 184
                           G F+I G ++++++Q   S   ++      +     K  Y   +
Sbjct: 60  SEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYVAEV 115

Query: 185 IPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMALGMD 224
                   + +      + VR+  R                   R ++P+     ALG  
Sbjct: 116 R----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFV 171

Query: 225 SE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           ++ +IL         +Q  +     L  A ++   +V+   +        +   K++   
Sbjct: 172 ADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRIKYA 231

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + L+++ +  +G+   C          +      + + A     E   +   +  +  
Sbjct: 232 K-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRAEDDRDHYGNKRLDL 287

Query: 344 I-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
             P+L          +   +     K   +      +        T  +  S+    +  
Sbjct: 288 AGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 347

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
           ++           +N      T   +R +         +     L N    +        
Sbjct: 348 ANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAETPE 407

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F     
Sbjct: 408 GQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCW 464

Query: 522 LSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           +         +  +   RR   +  + GV R     E+R ++  +     P    E   +
Sbjct: 465 VGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRL 523

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            L+      A        E       D      + Y+   EEE   I+            
Sbjct: 524 -LIKKKDIRALQQRESSEEGG---WHDLVAKGFIEYVDTEEEETTMISM----------T 569

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
             +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA
Sbjct: 570 INDLVTARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 627

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           + +                           R   +  V                      
Sbjct: 628 MGIYVTNYQL--------------------RMDTLAYV---------------------- 645

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+PLV                      L  G N +VA   + G
Sbjct: 646 -------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSG 682

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 683 YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPSRENTMGMRHGSYDK 742

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           +         RD S  +    
Sbjct: 743 LDDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------SQGQSSRYTRRDHSTSLRHSE 793

Query: 936 SGTV 939
           SG V
Sbjct: 794 SGMV 797



 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 117/794 (14%), Positives = 239/794 (30%), Gaps = 117/794 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 175  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 231

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 232  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 288

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 289  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 348

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 349  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 404

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 405  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 457

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 458  IFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 514

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K +            +   G        G +E VD             +
Sbjct: 515  LFIVEKQRLLIKKKDIRALQ---QRESSEEGGWHDLVAKGFIEYVDTEE----------E 561

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 562  ETTMISMTINDLVTARLNPEEAYS-----------ETYTHCEIHPSLILG-------VCA 603

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 604  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 636

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 637  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 694

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E     +R+          +          G 
Sbjct: 695  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPSRENTMGMRHGSYDKLDDDGLAPPGT 753

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++                  D+   ++    +  + TS    E   
Sbjct: 754  RVSGEDVIIGKTTPIAQ-----------------DDSQGQSSRYTRRDHSTSLRHSESGM 796

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 797  VDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 851

Query: 1114 DGTPVDIVLNPLGV 1127
            +G   DI++NP  +
Sbjct: 852  EGITPDIIVNPHAI 865


>gi|91082339|ref|XP_966549.1| PREDICTED: similar to RNA polymerase III 128kD subunit CG8344-PA
            [Tribolium castaneum]
 gi|270007487|gb|EFA03935.1| hypothetical protein TcasGA2_TC014075 [Tribolium castaneum]
          Length = 1122

 Score =  221 bits (564), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 71/333 (21%), Positives = 124/333 (37%), Gaps = 68/333 (20%)

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y+ +     +   + IEK+    +     +  +K+ +   R  + GDK +          
Sbjct: 840  YKDTPICYRNNEPSYIEKVLVSTNEEDTTI--IKILLRQTRRPEIGDKFS---------- 887

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                                       SR                  G+K    +   + 
Sbjct: 888  ---------------------------SR-----------------HGQKGVVGLVVEQE 903

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +   +      + ++    +  +++      +L        G       F G+    +  
Sbjct: 904  DMPFNEYGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLVEGKFHYGTAFGGSKVNDVCE 963

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L     +  G+   Y G+TGEP +  +  G +Y  KL HMV DK++AR  G  +++T+Q
Sbjct: 964  ELAKHGFNYQGKDFFYSGITGEPLEAYIYSGPVYYQKLKHMVQDKIHARGRGPRAVLTRQ 1023

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV---VGRTRVY----E 1330
            P  G+S  GG RLGEME  C+  YGA+ +L E L + SD    DV    GR   Y     
Sbjct: 1024 PTEGRSRDGGLRLGEMERDCLIGYGASMMLIERLMVSSDQCEVDVCNLCGRLG-YCGWCN 1082

Query: 1331 SIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            S  +  +      P +  +L+ E+QA+ ++  L
Sbjct: 1083 SCKSSREVSSITMPYACKLLLTELQAMNITARL 1115



 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 107/937 (11%), Positives = 246/937 (26%), Gaps = 196/937 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S+++F+ ++I      N  L         +        +++ +     P    
Sbjct: 32  LVKQHIDSFNYFINVDIKKIVEANNKL---------VCDADPLFYVKYTNVYVGRPDVDE 82

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + + +  + +G +P+M
Sbjct: 83  GFNISKPTTPHECRLRDMTYSAPISVDIEYT----------RGTQRVSKAGLMIGRMPIM 132

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHD------ 168
                                      G FV+KG +++++ Q   S       +      
Sbjct: 133 LRSSNCVLTNKSEYELAKMNECPLDPGGYFVVKGQEKVILIQEQLSKNRMIVEESKFGVQ 192

Query: 169 ---KGRAS---LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALG 222
                          ++                     +          VPV+    AL 
Sbjct: 193 CAVTSSTHEKKSRTNVVCKAN---------KYYLGHNSL-------TDLVPVSIIFKALD 236

Query: 223 MDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLT 281
           + S+ EI      +       D      +  +       +        G +++      +
Sbjct: 237 VTSDKEICELIGVE-------DISKLTPTLEECHTLKIYTQLGALKHIGSKLVAKRYVTS 289

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
           +  +K+  ++         D L    +A   V      +      V+ ++ +E     + 
Sbjct: 290 ASKMKTPVDE-------ARDVLATTVLAHVPVENYNFRMKAIYLGVMVKRVIEAQSDKKF 342

Query: 342 RDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
            D    Y +  +     + + +  D  K     L  I     P   +T            
Sbjct: 343 MDDKDYYGNKRLELAGSLLSLMFEDVFKRFNWELKSIAEKTIPKIRATQFDVVKYMRSDL 402

Query: 401 FDSDKYDLSTVGRV--KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
             +      + G    K      L     +  +     + ++  +         +    +
Sbjct: 403 ITNCLVYAISTGNWTIKRFRMERLGVTQVLSRLSYISALGMMTRVNSQFEKTRKVSGPRS 462

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           L   +   +      +     L    ++   I++   +  + +   NA  V   +     
Sbjct: 463 LQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTDVDEYPLIRLANNAGVVDINMSSGMS 522

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGG-VARARAGVEMRDVHPTHYGRICPAETSEG 577
                     +N     T       +     + R+        ++P    R     +  G
Sbjct: 523 IHSPETFFVFLNGNILGTIRNYKKLIHTFRMLRRSGLISGYVSIYPNFLHRCIYISSDGG 582

Query: 578 HNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                   +         N    +E   R   D      + +L   EE + +IA     +
Sbjct: 583 RLCRPYIIVERGRPLVTQNHIIELEKGIRSFEDFLHDGLIEFLDVNEENDSFIACYEKDI 642

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                                   +    ++ +   ++ + A L+P+  ++ S R    C
Sbjct: 643 T-----------------------DLTTHLEIATFTLLGVCAGLVPYPHHNQSPRNTYQC 679

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+  +         G                                        
Sbjct: 680 AMGKQAMGTI---------GYNQKNRMD-------------------------------- 698

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                             +    Q P+VK                T+   L  G+N  +A
Sbjct: 699 --------------TLLYSLVYPQAPMVK----------TKSIELTNFDKLPAGQNATIA 734

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVS 869
            M + GY+ ED+++I++  +       +  +  + + +       +           N  
Sbjct: 735 VMSYSGYDIEDALIINKASIDRGFGRCLVYKNSKCVMKRYANQTFDRIQGPLIDTTTNAP 794

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
                 +D  GI+  G  V+   +LV K  P   +  
Sbjct: 795 MWKHAVLDMDGIVAPGESVDNKQVLVNKSVPTVSAVP 831


>gi|308497698|ref|XP_003111036.1| hypothetical protein CRE_04747 [Caenorhabditis remanei]
 gi|308242916|gb|EFO86868.1| hypothetical protein CRE_04747 [Caenorhabditis remanei]
          Length = 1154

 Score =  221 bits (564), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 84/504 (16%), Positives = 163/504 (32%), Gaps = 80/504 (15%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              I+ +        +    I       +      + A+      D+ D  +   + +   
Sbjct: 719  DSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRG 778

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 ++ +H      +  +   +++   A D +    I       +   +  G   +  
Sbjct: 779  YGRCLVY-KHVKGTVRKYPNQTFDRLLGPALDPNTRLPISKHKNLDQEGIVFAGARILPK 837

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K   + S      P +      +   +V          Y+      +    +  E
Sbjct: 838  QTIINKHMPVVSGESGPGPSASANTIGIAGRQV---------DYKDVSISYKTPTPSYAE 888

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++    +       ++KV +   R  + GDK +                           
Sbjct: 889  RVLLTYNEDEA--HLIKVLLRQTRRPELGDKFS--------------------------- 919

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
                      SR                  G+K    +   + +   + L    + ++  
Sbjct: 920  ----------SR-----------------HGQKGVCGLIAQQEDMPFNDLGMVPDMIMNP 952

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
              +  +++      +L       +G       F G   + +   L     +  G+ +L  
Sbjct: 953  HGYPSRMTVGKLMELLSGKAGVMNGTYHYGTAFGGDQVKDVCEELAARGYNYMGKDMLTS 1012

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TG+     +  G IY  KL HMV DK++AR+ G  + +T+QP  G+S  GG RLGEME
Sbjct: 1013 GITGQSLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEME 1072

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPES 1346
              C+ AYGA+ +L E L + SD    DV     V  S   G                P +
Sbjct: 1073 RDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGS--KGWCQKCRSSKSMANIKIPYA 1130

Query: 1347 FNVLVKEMQALGLSIDLENSRTKN 1370
              +L +E+Q++ +   L+ +R   
Sbjct: 1131 CKLLFQELQSMNIVPRLDLARYTE 1154



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 133/967 (13%), Positives = 287/967 (29%), Gaps = 190/967 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+DHF+ + I    + N+ +          +  +    L+++      P    
Sbjct: 41  LVKQHLVSFDHFVNIEIRNIMQSNQKIT---------SDANPNFYLKYLDIRVGNPSSEE 91

Query: 85  -------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                  K    +C  RD+TY+ P+ + +             +  + + ++ + +G +P+
Sbjct: 92  GLNMTHDKITPQECRLRDMTYSAPISVDIEYT----------RGNQRVFKKDLIIGRMPI 141

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G FV+KG +++++ Q   S       ++    
Sbjct: 142 MLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQLS------KNRIMVG 195

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EI 228
            +      C ++     +          K    VR ++    VPV+    A+G++S+ +I
Sbjct: 196 RNSSKELQCEVLSSTSERKSK-TYVTMKKGKYSVRHNQLTDDVPVSIIFKAMGVESDYDI 254

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +ST   +  Y             A +    +  + +       +    G    + +    
Sbjct: 255 VSTIGHEEKYVSAFAQTLEECINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLT 314

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAG------DVIDEKSLEEIFHSEIR 342
             K  + +   S+ +   ++A    N +   IY+           + E  L++      +
Sbjct: 315 PPKEHEAVDFLSNSMI-THIACPDGNFKMKAIYLGLMTRRLIQTELGENELDDRDFYGNK 373

Query: 343 DIP-------ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
            +        +L+ D           +  +       A LDI + MR  D+ T ++  +M
Sbjct: 374 RLELAGSLLALLFEDVFKRFNSELKRIADNALMKTMAAPLDIVKHMRQ-DMITNTIVNAM 432

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI---RKEDIIAIIKILVDLRNGKGT 452
            +   +   ++ +  +G  ++  RL+  +   +        E    +        +  G 
Sbjct: 433 -STGNWIIKRFRMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGM 491

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +   D         V  +    +       +  ++  ++S   D          KP  + 
Sbjct: 492 LCPSDTPEGEACGLVKNLALISHITTDSDEKPVLRLLLNSGVEDLHNVHFSHVNKPENTL 551

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           +  F     +    +    +  +   RR   L +         +  R V  +  G     
Sbjct: 552 I--FLNGVLIGTAVDPERVVRAVRDLRRSGLLSE--FVSVSRSITNRSVFISSDG----- 602

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
                  I + +      + +    ++   R   D      V YL   E  +  IA    
Sbjct: 603 GRLCRPYIIVKNGKPMLTQ-DHVQQLKEGKRIFEDFVDDGIVEYLDVNEMNDALIAVYEK 661

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +                         +   ++  P  ++ + A LIP+  ++ S R   
Sbjct: 662 EIGP-----------------------ETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTY 698

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
            C M +QA+  +                  S                             
Sbjct: 699 QCAMGKQAMGTI---------AYNQQKRIDS----------------------------- 720

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                                 C  QRPLVK                T+   L  G N +
Sbjct: 721 -----------------IMYLLCYPQRPLVKS----------KTIELTNFEKLPAGANGI 753

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPN 867
           +A M + GY+ ED++++++  +       +  +  +   R       +            
Sbjct: 754 IAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTVRKYPNQTFDRLLGPALDPNTR 813

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV--DVR 925
           +     KN+D+ GI+  GA + P   ++ K  P       P         G      D +
Sbjct: 814 LPISKHKNLDQEGIVFAGARILPKQTIINKHMPVVSGESGPGPSASANTIGIAGRQVDYK 873

Query: 926 DTSLRVP 932
           D S+   
Sbjct: 874 DVSISYK 880


>gi|3133451|gb|AAC38526.1| RNA polymerase beta-subunit [Mycobacterium chelonae]
          Length = 213

 Score =  221 bits (564), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 127/212 (59%), Positives = 166/212 (78%), Gaps = 1/212 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG+ R RAG+E+RDVHP+
Sbjct: 2   NIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLTRDRAGLEVRDVHPS 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV +G VT+++ YL+A EE+ 
Sbjct: 62  HYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVSEGVVTDEIHYLTADEEDR 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             +AQANS +D DG FTE+ +  R   GE   V   ++D++D SP+Q+VS+A ++IPFLE
Sbjct: 122 HVVAQANSPVDADGRFTEDKILVRRKGGEVEFVSATEVDYMDVSPRQMVSVATAMIPFLE 181

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           +DD+NR LMG NMQRQAVPL+++EAP VGTGM
Sbjct: 182 HDDANRALMGANMQRQAVPLVRSEAPLVGTGM 213


>gi|59043123|gb|AAW83914.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  221 bits (564), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 168/228 (73%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ     N LS ++H  RLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMNQHNPLSELSHKHRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|317025401|ref|XP_001388998.2| DNA-directed RNA polymerase III subunit RET1 [Aspergillus niger CBS
            513.88]
          Length = 1226

 Score =  221 bits (564), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 87/514 (16%), Positives = 170/514 (33%), Gaps = 97/514 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +   +  + A+      D+ D  +    
Sbjct: 790  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGQNAIVAVMSYSGYDIEDALVLNKG 849

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F R  +   +   +  ++++       +++  I    +         G+
Sbjct: 850  SVDRGFGRCQVF-RKYVTNLKSYSNGTKDRLSGPT--YENDAPIRKHALLESDGLAAVGE 906

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST           +S    F   D     +     + Y     + +  +
Sbjct: 907  QVNAGEVYINKSTP---------DQSMSSGFPNSDAGRPVSYMPTPMTY----KLPDPAY 953

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+        +     ++VKV     R  + GDK +                      
Sbjct: 954  IDKV-----MVSVTENENQLVKVLTRQTRRPEVGDKFS---------------------- 986

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
                           SR                  G+K    I   +A+   +      +
Sbjct: 987  ---------------SR-----------------HGQKGVVGIIADQADMPFTDTGINPD 1014

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             ++       +++      ++       +G       F G+  + ++ +L        G+
Sbjct: 1015 IIMNPHGFPSRMTVGKMLELVAGKAGVLAGQHGYGTCFGGSPVQEMSQILIDNGFSYGGK 1074

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L  G+TGE     V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1075 DYLTSGITGEALPFYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1134

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1135 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1191

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1192 ---MAIPYAAKLLIQELMSMNVTARLKLDDEFPE 1222



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 90/741 (12%), Positives = 207/741 (27%), Gaps = 123/741 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F +     P+  
Sbjct: 116 LVKQHIDSYNYLVEVQ----------LKKIVESSSTIRSDVDHTFYIKFTNIYLGFPRRA 165

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    +          +  + +  + + 
Sbjct: 166 DEPQDARADFTYSTVSPQECRLRDTTYAAPIQVDFEYV----------RGRQRVMRKGVA 215

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 216 IGRMPVMLRSSKCVLANKTPAEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 275

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 276 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLSEDIPIVILL 324

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ +++ +      +    + DF      A  L +   + +   +            
Sbjct: 325 KAMGIHTDKEMLLLVAGVDKVYQEDFAINFEEAIKLGIYTQQQALDWIGARI-------- 376

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
            K+      S +   V+        +   ++    +N     +Y+ A         +   
Sbjct: 377 -KINRKQSPSYRRTHVQEAVEAIASVIISHIEVKNMNFRPKAVYV-AHMARRVLMAKNDA 434

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V+   + +    A S+  
Sbjct: 435 SLVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRAEAFDAYSVIT 494

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTI 453
                  +     +     +++        V H    +     + ++  +         +
Sbjct: 495 MHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKV 554

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                L   +   +      +     L    ++   I++ D +  +   +          
Sbjct: 555 SGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPVRNLIFMLGAEDIQT 614

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPA 572
                          +N        R    L     + R     E   ++  H+ R    
Sbjct: 615 VGGKELYGPGCYTISINGTPTALTRRPKYFLDAFRRLRRMGRISEFVSIYINHHQRAVHV 674

Query: 573 ETSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            T +G     L+      +RVN      +     +  D      V YL   EE +  I+ 
Sbjct: 675 ATDDGRICRPLIVVENGKSRVNAQHLEKLRNGTMQFDDFLAQGLVEYLDVNEENDSLISI 734

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +                        E    ++  P  V+   A LIP+  ++ S R
Sbjct: 735 YEKDIT-----------------------ETTTHLEIEPFTVLGAVAGLIPYPHHNQSPR 771

Query: 690 VLMGCNMQRQAVPLLKAEAPF 710
               C M +QA+  + +    
Sbjct: 772 NTYQCAMGKQAIGAIASNQFL 792


>gi|119182523|ref|XP_001242390.1| hypothetical protein CIMG_06286 [Coccidioides immitis RS]
          Length = 1233

 Score =  221 bits (564), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 93/518 (17%), Positives = 169/518 (32%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +    A+      D+ D  +  
Sbjct: 795  NNQFLRIDSLLYTMVYPQKPMVKTRTIELVKYDKLPAGQSATVAVMSYSGYDIEDALVLN 854

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V       ++F ++  +    S   +     LL  D+ D   I    +         
Sbjct: 855  KGSVDRGFGRCQVFRKYSANLKSYSNGTKDR---LLGPDRQDGVPIRKHALLDNDGLAAV 911

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G+   SG     K+T    + +S             D           + Y  S    + 
Sbjct: 912  GEKVSSGEVYINKATP--ENALSS-------GITGSD-------AGGPIAYIPSPQTYKL 955

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               + I+K+        G  +++KV     R  + GDK +                    
Sbjct: 956  PDPSYIDKVMI--STTEGENQLLKVQTRQTRRPEVGDKFS-------------------- 993

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    I   +A+   +     
Sbjct: 994  -----------------SR-----------------HGQKGVVGIIAEQADMPFTDQGIV 1019

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++       +++      ++       SG       F G+  E ++++L     +  
Sbjct: 1020 PDIIMNPHGFPSRMTVGKMLELVAGKAGILSGQFGYGTAFGGSPVEEMSAILISKGFNYG 1079

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGE     V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG
Sbjct: 1080 GKDYLTSGITGEALPAYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGG 1139

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1140 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK- 1198

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1199 -----MVIPYAAKLLVQELFSMNVVARLKLADEFPEER 1231



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 89/742 (11%), Positives = 210/742 (28%), Gaps = 122/742 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 120 LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGSPRRAD 170

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                            ++C  RD+TYA P+ +    +          +  + +K     
Sbjct: 171 EEQSEDARFKIESTVTPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTA 220

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   +  +
Sbjct: 221 IGRMPVMLRSSKCVLSKKSPREMYLLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVE 280

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      +I             KD I++R +     +PV   L
Sbjct: 281 TDPKKEIVQASVTSSSNERKSKSYVI-----------LKKDRIYLRHNVLSDDIPVVILL 329

Query: 219 MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ S+ E+L          Q      F  S    +   + +   +          +G
Sbjct: 330 KAMGIQSDKEMLLLVAGVDSVYQEDFAINFEESIKLGIYTQQQALEYLGSHIKITRKPNG 389

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
                        + +  + I+   +  +                 A         +   
Sbjct: 390 FGGGRRNYIQEAVEAIASVIISHVQVENMNFRPKA--------LYVAHMARRVLMAKHDS 441

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V++    +    A S+  
Sbjct: 442 SLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAFSVVA 501

Query: 398 FLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                  +     +     +  R  ++       + +   I+ + ++  + +       +
Sbjct: 502 IHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYISALGMMTRISSQFEKTRKV 561

Query: 457 DNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
                 +    G +      + +    +  +        +  +         + A+ V +
Sbjct: 562 SGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLVFALGAEDVQA 621

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                F       +  + + ++ +T   +        + R     E   V+  H+     
Sbjct: 622 VGGREFYGQGAYIIFLNGSPIA-LTRRPKHFLNSFRRLRRMGRVSEFVSVYINHHQSAVH 680

Query: 572 AETSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             T +G     L+      ++V     G +     +  D      V YL   EE + YIA
Sbjct: 681 IATDDGRICRPLIIVENQKSKVTDLHLGMLRNGTMEFDDFLAQGLVEYLDVNEENDSYIA 740

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              + ++E+                          ++  P  ++   A LIP+  ++ S 
Sbjct: 741 VYENEINEN-----------------------TTHLEIEPFTILGAVAGLIPYPHHNQSP 777

Query: 689 RVLMGCNMQRQAVPLLKAEAPF 710
           R    C M +QA+  +      
Sbjct: 778 RNTYQCAMGKQAIGAIANNQFL 799


>gi|68131852|gb|AAY85204.1| RNA polymerase II second largest subunit [Dillenia suffruticosa]
          Length = 868

 Score =  221 bits (564), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 121/902 (13%), Positives = 260/902 (28%), Gaps = 158/902 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCEEVTETQDFAK--VFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  + 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAFV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR--------------RRKVPVTSFLMALGMDSE 226
             +        + +      + VR+  R              R ++P+     ALG  ++
Sbjct: 121 AEVR----SMAESQNRPPSSMFVRMLSRTSAKGYIRATLPYIRTEIPIIIVFRALGFVAD 176

Query: 227 -EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
            +IL         +Q  +     L  A ++   +V+   +        +   K++     
Sbjct: 177 KDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRIKYAK- 235

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI- 344
           + L+++ +  +G+   C          +      + + A     E   +   +  +    
Sbjct: 236 EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKRLDLAG 292

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           P+L          +   +     K   +      +        T  +  S+    +  ++
Sbjct: 293 PLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKPITSGLKYSLATGNWGQAN 352

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
                      +N      T   +R +         +     L N    +         +
Sbjct: 353 AAGTRAGVSQVLNRLTYSSTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAETPEGQ 412

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 413 ACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 469

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++  +     P    E   + L
Sbjct: 470 IHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRL-L 527

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +      A        E       D      + Y+   EEE   I+              
Sbjct: 528 IKKKDIRALQQRESPEEGG---WHDLVAKGFIEYVDTEEEETTMISM----------TIN 574

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 575 DLVSARLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 632

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 633 IYVTNYQL--------------------RMDTLAYV------------------------ 648

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 649 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINSIVAIACYSGYN 687

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 688 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLD 747

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK +P  +           A         RD S  +    SG
Sbjct: 748 DDGLAPPGTRVSGEDVIIGKTSPIAQDD---------AQGVSSRYTRRDHSTSLRHSESG 798

Query: 938 TV 939
            V
Sbjct: 799 MV 800



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 116/795 (14%), Positives = 238/795 (29%), Gaps = 119/795 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 178  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 234

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 235  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 291

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AKP+ S +     +      
Sbjct: 292  GPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKPITSGLKYSLATGNWGQA 351

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 352  NAAGTRAGVSQVLNRLTYSSTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 407

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 408  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 460

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 461  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 517

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                K   A    +        D   +  I  V+ + 
Sbjct: 518  LFIVEKQRLLI--------------KKKDIRALQQRESPEEGGWHDLVAKGFIEYVDTEE 563

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 564  EETTMISMTINDLVSARLNPEEAYS-----------DTYTHCEIHPSLILG-------VC 605

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 606  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 639

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 640  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINSIVAIACYSGYNQEDSVIMNQ 696

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 697  SSIDRGFF-RSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 755

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K++ ++                  D+    +    +  + TS    E  
Sbjct: 756  TRVSGEDVIIGKTSPIAQ-----------------DDAQGVSSRYTRRDHSTSLRHSESG 798

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 799  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 853

Query: 1113 KDGTPVDIVLNPLGV 1127
             +G   DI++NP  +
Sbjct: 854  VEGITPDIIVNPHAI 868


>gi|294471040|gb|ADE80781.1| RNA polymerase beta subunit [Lactococcus lactis]
          Length = 144

 Score =  221 bits (563), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 63/166 (37%), Positives = 91/166 (54%), Gaps = 22/166 (13%)

Query: 27  PDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF 86
           P+LIEVQ  SY +FL          +EGL   FK +FPI  F+G   LEFV YE   PK+
Sbjct: 1   PNLIEVQTLSYKNFL----------DEGLANVFKEMFPIDNFAGTMELEFVGYEMKTPKY 50

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVI 146
            V++    D  Y+ P+ +T RL+          K   ++K Q ++ GD PLMT+ GTF+ 
Sbjct: 51  TVEEARAHDANYSAPIYVTFRLV---------NKETGELKTQEVFFGDFPLMTEMGTFIN 101

Query: 147 KGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
            G +R++VSQL RSPG +F     +   +G   +    IP++G W+
Sbjct: 102 NGSERLIVSQLVRSPGSYFH---LKTDKNGLESFGHTTIPNRGAWL 144


>gi|134055102|emb|CAK43742.1| unnamed protein product [Aspergillus niger]
          Length = 1225

 Score =  221 bits (563), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 87/514 (16%), Positives = 170/514 (33%), Gaps = 97/514 (18%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            + +    I+ +        +    I       +   +  + A+      D+ D  +    
Sbjct: 789  QFLRIDSILYLMVYPQKPMVKSRTIELTKYDQLPAGQNAIVAVMSYSGYDIEDALVLNKG 848

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V       ++F R  +   +   +  ++++       +++  I    +         G+
Sbjct: 849  SVDRGFGRCQVF-RKYVTNLKSYSNGTKDRLSGPT--YENDAPIRKHALLESDGLAAVGE 905

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G     KST           +S    F   D     +     + Y     + +  +
Sbjct: 906  QVNAGEVYINKSTP---------DQSMSSGFPNSDAGRPVSYMPTPMTY----KLPDPAY 952

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +K+        +     ++VKV     R  + GDK +                      
Sbjct: 953  IDKV-----MVSVTENENQLVKVLTRQTRRPEVGDKFS---------------------- 985

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
                           SR                  G+K    I   +A+   +      +
Sbjct: 986  ---------------SR-----------------HGQKGVVGIIADQADMPFTDTGINPD 1013

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
             ++       +++      ++       +G       F G+  + ++ +L        G+
Sbjct: 1014 IIMNPHGFPSRMTVGKMLELVAGKAGVLAGQHGYGTCFGGSPVQEMSQILIDNGFSYGGK 1073

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              L  G+TGE     V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG R
Sbjct: 1074 DYLTSGITGEALPFYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGGLR 1133

Query: 1294 LGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAGND 1337
            LGEME  C+ AYG + +L E L I SD    DV              R +   S+V    
Sbjct: 1134 LGEMERDCLIAYGTSQLLLERLMISSDRHEIDVCEQCGFMGYLNWCQRCKSSRSVVK--- 1190

Query: 1338 TFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                  P +  +L++E+ ++ ++  L+       
Sbjct: 1191 ---MAIPYAAKLLIQELMSMNVTARLKLDDEFPE 1221



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 90/741 (12%), Positives = 207/741 (27%), Gaps = 123/741 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++ + +           L+   +S   I +       ++F +     P+  
Sbjct: 115 LVKQHIDSYNYLVEVQ----------LKKIVESSSTIRSDVDHTFYIKFTNIYLGFPRRA 164

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                             +C  RD TYA P+++    +          +  + +  + + 
Sbjct: 165 DEPQDARADFTYSTVSPQECRLRDTTYAAPIQVDFEYV----------RGRQRVMRKGVA 214

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   I  +
Sbjct: 215 IGRMPVMLRSSKCVLANKTPAEMTVLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVE 274

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      I              KD ++V+ +     +P+   L
Sbjct: 275 TDPKKEIVQASVTSSSNERKSKSYI-----------VLKKDKLYVKHNVLSEDIPIVILL 323

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ +++ +      +    + DF      A  L +   + +   +            
Sbjct: 324 KAMGIHTDKEMLLLVAGVDKVYQEDFAINFEEAIKLGIYTQQQALDWIGARI-------- 375

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
            K+      S +   V+        +   ++    +N     +Y+ A         +   
Sbjct: 376 -KINRKQSPSYRRTHVQEAVEAIASVIISHIEVKNMNFRPKAVYV-AHMARRVLMAKNDA 433

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V+   + +    A S+  
Sbjct: 434 SLVDDRDYLGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLNKRNRAEAFDAYSVIT 493

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTI 453
                  +     +     +++        V H    +     + ++  +         +
Sbjct: 494 MHSNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKV 553

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                L   +   +      +     L    ++   I++ D +  +   +          
Sbjct: 554 SGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPVRNLIFMLGAEDIQT 613

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPA 572
                          +N        R    L     + R     E   ++  H+ R    
Sbjct: 614 VGGKELYGPGCYTISINGTPTALTRRPKYFLDAFRRLRRMGRISEFVSIYINHHQRAVHV 673

Query: 573 ETSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            T +G     L+      +RVN      +     +  D      V YL   EE +  I+ 
Sbjct: 674 ATDDGRICRPLIVVENGKSRVNAQHLEKLRNGTMQFDDFLAQGLVEYLDVNEENDSLISI 733

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               +                        E    ++  P  V+   A LIP+  ++ S R
Sbjct: 734 YEKDIT-----------------------ETTTHLEIEPFTVLGAVAGLIPYPHHNQSPR 770

Query: 690 VLMGCNMQRQAVPLLKAEAPF 710
               C M +QA+  + +    
Sbjct: 771 NTYQCAMGKQAIGAIASNQFL 791


>gi|154362083|gb|ABS80880.1| RNA polymerase beta subunit [Brevundimonas bacteroides]
          Length = 233

 Score =  221 bits (563), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 145/229 (63%), Positives = 174/229 (75%), Gaps = 1/229 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL + ARVN YGFIE+PYR+V DG  T +VVY+SAMEE    IAQAN    EDG 
Sbjct: 61  IGLINSLATHARVNKYGFIESPYRRVKDGVATEEVVYISAMEEVKYTIAQANVE-AEDGQ 119

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E+LV  R AGE  L+  + +D +D SPKQVVS+AA+L+PFLENDD+NR L+G NMQRQ
Sbjct: 120 IVEDLVPGRMAGESQLLEPDAVDKMDVSPKQVVSVAAALVPFLENDDANRALLGANMQRQ 179

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           AVPL   +AP VGTGME+VVA  SGA ++A+R G+VEQ+D  RIV+R+ 
Sbjct: 180 AVPLGCLDAPLVGTGMEAVVAVDSGAVVIARRDGVVEQIDGTRIVVRAT 228


>gi|190347676|gb|EDK39998.2| DNA-directed RNA polymerase III 130 kDa polypeptide [Meyerozyma
            guilliermondii ATCC 6260]
          Length = 1156

 Score =  221 bits (563), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/311 (21%), Positives = 119/311 (38%), Gaps = 64/311 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++KV +   R  + GDK +                                   
Sbjct: 898  SDNDQTLIKVLLRQTRRPELGDKFS----------------------------------- 922

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR                  G+K    I   + +   +      + ++       +++
Sbjct: 923  --SR-----------------HGQKGVCGIIVQQEDLPFNDDGIVPDIIMNPHGFPSRMT 963

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE   
Sbjct: 964  VGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSEILVKNGFNYSGKDMLYSGITGECLQ 1023

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1024 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1083

Query: 1307 AAYVLQEMLTIKSD----DVV------GRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+ +L E L + SD    DV       G      S  +  +  +   P +  +L +E+ +
Sbjct: 1084 ASQLLLERLMLSSDAFEVDVCNNCGLMGYNSWCTSCKSSENVIKMTIPYAAKLLFQELLS 1143

Query: 1357 LGLSIDLENSR 1367
            + ++  L+   
Sbjct: 1144 MNIAPRLKLDD 1154



 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 128/986 (12%), Positives = 270/986 (27%), Gaps = 199/986 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
           L++    S++ F+ +++    + NE        V P         L+++           
Sbjct: 52  LVKQHLDSFNFFVDVDLKKIVQANE---LVLSDVDP------DFYLKYLDIRVGHKSTSS 102

Query: 83  ----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 103 PGTKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIMHKDLEIGRMPIM 152

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F++ G +++++ Q   S          +  +
Sbjct: 153 LKSNKCILDGINDHQMAKLDECPIDPGGYFIVNGTEKVILIQEQLSKNRIIVEADEKKGI 212

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV-----------PVTSFLMALGM 223
               + +               + K   +V I +  K+           P+   L A G+
Sbjct: 213 VQASVTSST------------HERKSKTYV-ITKNEKIYLKHNSIGEDVPIVIILKAAGI 259

Query: 224 DSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
            S+ EIL          Q      F  +A   +   + + + V             KL+ 
Sbjct: 260 TSDLEILQLVCGSNPQYQDLFAVNFEEAARLEVFTQQQALNYVGKRVKTVRRAGAPKLSQ 319

Query: 283 GL--LKSLKEKGVKFLGIT-----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
               ++++    +  + +         L    +A  ++        ++  D +  K LE 
Sbjct: 320 LQEGIEAIATTIIAHITVDDLQFREKALYIAMMARRVLMTMHNPKMVDDRDYVGNKRLEL 379

Query: 336 IFHSEIRDIPILYVDSVNN-NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                      L+    ++  A I   L         DALL I                 
Sbjct: 380 AGQLMSLLFEDLFKKFNSDFKANIDKILKKPSRASEFDALLSINIHSNN----ITMGMNR 435

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID 454
             +   +   ++ +   G   +  R           +     + ++  +         + 
Sbjct: 436 AISTGNWSLKRFKMERAGVTHVLSR-----------LSYISALGMMTRISSQFEKSRKVS 484

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
               L   +   +      +     L    ++   I++ D +  +               
Sbjct: 485 GPRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTDDEEEPIRSVCFALGCEDILEV 544

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAE 573
           +            ++N     T       +G    + R+        +H   +       
Sbjct: 545 DSATLHADGNFGIYLNGTIIGTTRFPAQFVGNFRALRRSGKVSPFISIHTNTHQNAVQIA 604

Query: 574 TSEGHNIGLVSSLTSFARVN----AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
           T  G     +  + S  + N        +        D      V YL   EE + +IA 
Sbjct: 605 TDGGRVCRPLIIVDSKNKANVKAVHLKKLMAGEWVFEDFIKHGLVEYLDVNEENDSFIAL 664

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               L+ + +                     I  ++  P  V+   A LIP+  ++ S R
Sbjct: 665 YERDLEANQN---------------------ITHLEIEPFTVLGAVAGLIPYPHHNQSPR 703

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
               C M +QA+                                           I   +
Sbjct: 704 NTYQCAMGKQAIGA-----------------------------------------IAYNQ 722

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                +   + +Y               Q+P+VK                 D   L  G+
Sbjct: 723 FRRIDTLLYLMVYP--------------QQPMVK----------TKTIELIDYDKLPAGQ 758

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDI 865
           N  VA M + GY+ ED++++++  +         + +  V  +      ++    +  D 
Sbjct: 759 NATVAVMSYSGYDIEDALVLNKASIDRGFGRCQVLRKNTVNLKRYPNHTKDVVSGMRVDE 818

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                    ++   G+  VG +V  G + V K  P   S               ++    
Sbjct: 819 QGEPIFPHASLGPDGLGEVGMKVENGQVYVNKCVPTNASESVLGANEPHHQQNVESHRET 878

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
               R P     + +D  + +    D
Sbjct: 879 PAYYRGP---EPSYIDQVMMSVSDND 901


>gi|146414794|ref|XP_001483367.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Meyerozyma
            guilliermondii ATCC 6260]
          Length = 1156

 Score =  221 bits (563), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/311 (21%), Positives = 119/311 (38%), Gaps = 64/311 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++KV +   R  + GDK +                                   
Sbjct: 898  SDNDQTLIKVLLRQTRRPELGDKFS----------------------------------- 922

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR                  G+K    I   + +   +      + ++       +++
Sbjct: 923  --SR-----------------HGQKGVCGIIVQQEDLPFNDDGIVPDIIMNPHGFPSRMT 963

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE   
Sbjct: 964  VGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSEILVKNGFNYSGKDMLYSGITGECLQ 1023

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1024 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1083

Query: 1307 AAYVLQEMLTIKSD----DVV------GRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            A+ +L E L + SD    DV       G      S  +  +  +   P +  +L +E+ +
Sbjct: 1084 ASQLLLERLMLSSDAFEVDVCNNCGLMGYNSWCTSCKSSENVIKMTIPYAAKLLFQELLS 1143

Query: 1357 LGLSIDLENSR 1367
            + ++  L+   
Sbjct: 1144 MNIAPRLKLDD 1154



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 118/978 (12%), Positives = 270/978 (27%), Gaps = 183/978 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
           L++    S++ F+ +++    + NE        V P         L+++           
Sbjct: 52  LVKQHLDSFNFFVDVDLKKIVQANE---LVLSDVDP------DFYLKYLDIRVGHKSTSS 102

Query: 83  ----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 103 PGTKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIMHKDLEIGRMPIM 152

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
            K                         G F++ G +++++ Q   S          +  +
Sbjct: 153 LKSNKCILDGINDHQMAKLDECPIDPGGYFIVNGTEKVILIQEQLSKNRIIVEADEKKGI 212

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV-----------PVTSFLMALGM 223
               + +               + K   +V I +  K+           P+   L A G+
Sbjct: 213 VQASVTSST------------HERKSKTYV-ITKNEKIYLKHNSIGEDVPIVIILKAAGI 259

Query: 224 DSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
            S+ EIL          Q      F  +A   +   + + + V     + V  +G    S
Sbjct: 260 TSDLEILQLVCGSNPQYQDLFAVNFEEAARLEVFTQQQALNYVGKRV-KTVRRAGAPKLS 318

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
            L + ++      +   +            +      + +      + K +++  +   +
Sbjct: 319 QLQEGIEAIATTIIAHITVDDLQFREKALYIAMMARRVLMTMH---NPKMVDDRDYVGNK 375

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
            + +           +     +D   +    L    R +    + + ++  +        
Sbjct: 376 RLELAGQLMSLLFEDLFKKFNSDFKANIDKILKKPSRALEFDALLSINIHSNNITMGMNR 435

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           +      ++ R KM           + +I    ++  I    +          +      
Sbjct: 436 AISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFG 495

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            +    +  + +    +  +           +    +    +  + ++        +   
Sbjct: 496 -MLCTSDTPEGEACGLVKNLALMTHITTDDEEEPIRLVCFALGCEDILEVDSATLHADG- 553

Query: 523 SQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
                ++N     T       +G    + R+        +H   +       T  G    
Sbjct: 554 -NFGIYLNGTIIGTTRFPAQFVGNFRALRRSGKVSPFISIHTNTHQNAVQIATDGGRVCR 612

Query: 582 LVSSLTSFARVN----AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +  + S  + N        +        D      V YL   EE + +IA     L+ +
Sbjct: 613 PLIIVDSKNKANVKAVHLKKLMAGEWVFEDFIKHGLVEYLDVNEENDSFIALYERDLEAN 672

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            +                     I  ++  P  V+   A LIP+  ++ S R    C M 
Sbjct: 673 QN---------------------ITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMG 711

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+                                           I   +     +  
Sbjct: 712 KQAIGA-----------------------------------------IAYNQFRRIDTLL 730

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            + +Y               Q+P+VK                 D   L  G+N  VA M 
Sbjct: 731 YLMVYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMS 766

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGL 873
           + GY+ ED++++++  +         + +  V  +      ++    +  D         
Sbjct: 767 YSGYDIEDALVLNKASIDRGFGRCQVLRKNTVNLKRYPNHTKDVVSGMRVDEQGEPIFPH 826

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
            ++   G+  VG +V  G + V K  P   S               ++        R P 
Sbjct: 827 ASLGPDGLGEVGMKVENGQVYVNKCVPTNASESVLGANEPHHQQNVESHRETPAYYRGP- 885

Query: 934 GVSGTVVDVRIFNRHGID 951
               + +D  + +    D
Sbjct: 886 --EPSYIDQVMMSVSDND 901


>gi|327133515|gb|AEA29762.1| RNA polymerase subunit B [Acinetobacter sp. 13NS1]
          Length = 182

 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 83/184 (45%), Positives = 116/184 (63%), Gaps = 3/184 (1%)

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F  K
Sbjct: 1    NGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKFAEK 60

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G 
Sbjct: 61   KRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGV 120

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   K    I+ LR FL+K+ 
Sbjct: 121  PVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLDKIY 177

Query: 1177 GTGS 1180
              G 
Sbjct: 178  NKGG 181


>gi|56694378|gb|AAW22929.1| RNA polymerase II second largest subunit [Musa velutina]
          Length = 561

 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 76/492 (15%), Positives = 145/492 (29%), Gaps = 91/492 (18%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDT 854
              T    +   +N   A+   +       S++  +   ++            ++      
Sbjct: 158  SMTINDLVNARQNPEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 217

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G          V+   L+      +  V        +    +       +      + 
Sbjct: 218  AMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 266

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +   + +   S +        +F R   D+ ++  ++ +E      R+    
Sbjct: 267  AIACYSGYNQEVSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMG 325

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                             G           K++ +                  QD+   + 
Sbjct: 326  MRHGSYEKLDDDGLAPPGTRVSGEDVIIGKTSPI-----------------PQDDAQGQA 368

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                +  + TS    E    +++      D +     R VKV +   R  Q GDK + RH
Sbjct: 369  SRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRH 423

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 424  GQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 483

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS         +                                      
Sbjct: 484  TPFTDVTVDNISKALHKCGYQMRGFETM-------------------------------- 511

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                            +G +    G         + +G  Y  +L HMV DK+++R  G 
Sbjct: 512  ---------------YNGHT----GR---KLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 549

Query: 1275 YSLVTQQPLGGK 1286
              ++T+QP  G+
Sbjct: 550  VQILTRQPAEGR 561



 Score =  118 bits (296), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 74/476 (15%), Positives = 141/476 (29%), Gaps = 98/476 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++  S    + I+   +  +   F     +       
Sbjct: 5   LVKNLALMVYITVGSAAHPILEFLEEWSTENFEEISPAVIPQSTKIFVNGCWVGIHRNPD 64

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + GV R     E+R ++  +     P    E   + +      
Sbjct: 65  LLVKTLRQLRRQIDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKK--- 120

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
              + A    ETP     D      + Y+   EEE   I+              +LV  R
Sbjct: 121 --DIRALQQRETPEEGWHDLVSKGFIEYIDTEEEETTMISM----------TINDLVNAR 168

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 169 QNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 226

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                                 R   +  V                              
Sbjct: 227 QL--------------------RMDTLAYV------------------------------ 236

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PLV                      L  G N +VA   + GYN E S++
Sbjct: 237 -----LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEVSVI 281

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIIC 883
           +++  +    F S+    +    +      +E        +   +     + +D+ G+  
Sbjct: 282 MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYEKLDDDGLAP 341

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  D+++GK +P  +           A         RD S  +    SG V
Sbjct: 342 PGTRVSGEDVIIGKTSPIPQDD---------AQGQASRYTRRDHSTSLRHSESGMV 388


>gi|154362081|gb|ABS80879.1| RNA polymerase beta subunit [Brevundimonas intermedia]
          Length = 233

 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 145/229 (63%), Positives = 176/229 (76%), Gaps = 1/229 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL + ARVN YGFIE+PYR+V DG+ T +VVY+SAMEE    IAQAN    EDG 
Sbjct: 61  IGLINSLATHARVNKYGFIESPYRRVKDGQATGEVVYISAMEEVKYTIAQANVE-AEDGK 119

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E+LV  R  GE +L+ +E++D +D SPKQVVS+AA+L+PFLENDD+NR L+G NMQRQ
Sbjct: 120 LVEDLVSGRADGETLLLEQERVDKMDVSPKQVVSVAAALVPFLENDDANRALLGANMQRQ 179

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           AVPL   +AP VGTGME+ VA  SGA +VA+R G+VEQ+D  RIV+R+ 
Sbjct: 180 AVPLGCLDAPLVGTGMEARVAVDSGAVVVARRDGVVEQIDGTRIVVRAT 228


>gi|66854095|gb|AAY57356.1| RpoB [Prevotella disiens]
          Length = 125

 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 73/179 (40%), Positives = 87/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN+GQIFE         LG   ++L                           
Sbjct: 1    NPMGVPSRMNLGQIFE-------AILGAAGRNL--------------------------- 26

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                G+  +TP+FDGA  E +      A L       +YDG TG
Sbjct: 27   --------------------GIKFATPIFDGAKLEDLKEWTDKAGLPPMCSRYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   ERFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|148628036|gb|ABQ97023.1| RNA polymerase II second largest subunit [Exophiala salmonis]
          Length = 676

 Score =  221 bits (563), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 117/745 (15%), Positives = 219/745 (29%), Gaps = 130/745 (17%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +A     + R     + R +H TH+G +CPAET EG   
Sbjct: 53   GVSQVLNRYTFASTLSHLRRTNA----PIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC 108

Query: 581  GLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI--AQANSSLDE 636
            GLV +L+  + V  +        Y      +   D       +    ++        L +
Sbjct: 109  GLVKNLSLLSMVTNSYETGPLLKYIMSKHVEPLEDWEPRLNPQATKVFVDGVWFAVVLRD 168

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGC 694
                 ++L   R  G          D  D   K        + P    END S+      
Sbjct: 169  PKRLVDDLRKLRRKGIFDPHVSLIWDIRDKEFKVSGDSGRLVRPLFVVENDPSSDNRGNL 228

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             + ++ +  L         G +          +    +G++E +DA       +    + 
Sbjct: 229  VLNKEHIAKLDNTTYLREGGYQFNDEVRPYGWMDLLSSGVIEYMDAEEEETAMIIMTPEA 288

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              +      +        +      PL+               PS  LG       +  +
Sbjct: 289  L-ADSKARSMGMVIEQENDPLRRNDPLLNP--YSHTFTHCELHPSMILG-------VCAS 338

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                                     E   +I    ++ L 
Sbjct: 339  IIPFPDHNQSPRXXXXXXXXXXXXXXXX----------XXXXXRMETMANILYYPQKPLA 388

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                                   +       +   +  + AI      +  D+ +   S 
Sbjct: 389  -------------------TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 429

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +     +  +     +    +    +E   +    + + +    Y ++ +   +  
Sbjct: 430  IDRGLFRSLFYRTYT----DSEKMIGLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVSP 485

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K++ L+ +                +E  QR  +  K+   T     E 
Sbjct: 486  GVRVSGEDIIIGKTSPLAPE---------------AEELGQRTKQHTKLDVSTPLRSTES 530

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               +++      DD+     + VKV +   +  Q GDK A RHG KG +      EDMPF
Sbjct: 531  GIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRHEDMPF 585

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             ++G   D+V+NP  +PSRM +  + E  L       G +                    
Sbjct: 586  TREGVTPDLVINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD------------------ 627

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++S+LR       
Sbjct: 628  -----------------------------------ATP-FTDVTVDSVSSLLREHGYQSR 651

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYM 1256
            G  ++Y+G TG      V +G  Y 
Sbjct: 652  GFEVMYNGHTGRKLVAQVFLGPTYY 676



 Score =  105 bits (263), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 87/595 (14%), Positives = 175/595 (29%), Gaps = 62/595 (10%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           KD    + + +  G           F               G      +L+       + 
Sbjct: 1   KDFYRYMQKRVEAGQPINIMAG---FKHPIITQGLKYSLATGNWGDQKKLDKAKAGVSQV 57

Query: 431 IRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
           + +    + +  L        R GK       +  +       E  + Q   GL++    
Sbjct: 58  LNRYTFASTLSHLRRTNAPIGREGKIAKPRQLHNTHWGYVCPAETPEGQAC-GLVKNLSL 116

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +    +S +   ++   +      +                + V     +   +R     
Sbjct: 117 LSMVTNSYETGPLLKYIMSKHVEPLEDWEPRLNPQATKVFVDGVWFAVVLRDPKR----- 171

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              +      +  + +   H   I      E    G              G +  P   V
Sbjct: 172 ---LVDDLRKLRRKGIFDPHVSLIWDIRDKEFKVSG------------DSGRLVRPLFVV 216

Query: 606 CDGKVTNDVVYLSAMEEENRYIA--QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            +   +++   L   +E   +IA     + L E G    + V      + +      I++
Sbjct: 217 ENDPSSDNRGNLVLNKE---HIAKLDNTTYLREGGYQFNDEVRPYGWMDLL--SSGVIEY 271

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           +DA  ++   I  +        DS    MG  ++++  PL + +             +  
Sbjct: 272 MDAEEEETAMIIMTPEALA---DSKARSMGMVIEQENDPLRRNDPLLNPYSHTFTHCELH 328

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLV 782
            + I+   A I+   D  +                           +  N     Q+PL 
Sbjct: 329 PSMILGVCASIIPFPDHNQSPRXXXXXXXXXXXXXXXXXXXXXRMETMANILYYPQKPL- 387

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA   + GYN EDS+++++  +   +F S+
Sbjct: 388 ---------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 438

Query: 843 HIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               +    +   L   E     +  D   +       +D+ GI+  G  V+  DI++GK
Sbjct: 439 FYRTYTDSEKMIGLTVVERFEKPMRSDTLRMKHGTYDKVDDDGIVSPGVRVSGEDIIIGK 498

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +P     + PE + L     +      D S  + S  SG V  V +   +   K
Sbjct: 499 TSP-----LAPEAEELGQRTKQH--TKLDVSTPLRSTESGIVDQVLVSTSNDDLK 546


>gi|225554621|gb|EEH02917.1| DNA-directed RNA polymerase III polypeptide [Ajellomyces capsulatus
            G186AR]
          Length = 1227

 Score =  221 bits (563), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 90/518 (17%), Positives = 167/518 (32%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +    A+      D+ D  +  
Sbjct: 789  NNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLN 848

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V       ++F R      +   +  +++++   R         +  +  R   +L 
Sbjct: 849  KGSVDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------ENGVPIRKHALLD 898

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
                 +  +      V  + +  E   S        D             Y  S    + 
Sbjct: 899  NDGLAAVGEKVNHGEVYINKVTPENALSS--GITGSDAGRPIA-------YIPSPQTYKL 949

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               + I+K+           +++KV     R  + GDK +                    
Sbjct: 950  PDPSYIDKVMI--SATEAENQLIKVQTRQTRVPEVGDKFS-------------------- 987

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    I    A+   S L   
Sbjct: 988  -----------------SR-----------------HGQKGVVGIIAEHADMPFSDLGIV 1013

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++       +++      ++       SG       F G+  E ++++L        
Sbjct: 1014 PDIIMNPHGFPSRMTVGKMLELIAGKAGILSGQFGYGTAFGGSPVEEMSAILVDHGFSYG 1073

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGEP    V +G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG
Sbjct: 1074 GKDYLTSGITGEPLPAYVFMGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGG 1133

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1134 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK- 1192

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1193 -----MVIPYAAKLLVQELFSMNVVARLKLADEFPEER 1225



 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 89/751 (11%), Positives = 200/751 (26%), Gaps = 124/751 (16%)

Query: 17  FGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF 76
           F K         L++    SY++F+ + +    + +    A  +S            + F
Sbjct: 110 FLKIKG------LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRF 154

Query: 77  VSYEFDPPK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
                  P+                  ++C  RD+TYA P+ +    +          + 
Sbjct: 155 HDIYLGNPRRADEEQDSKFDLASTITPNECRLRDMTYAAPILVDFEYV----------RG 204

Query: 122 IKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQL 157
            + +K     +G +P+M                           G F++ G +++++ Q 
Sbjct: 205 RQRVKRNGTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQE 264

Query: 158 HRSPG-IHFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-R 208
             S   +  + D  +        S S +      II             KD I++R +  
Sbjct: 265 QLSKNRVIVETDLKKEIVQASVTSSSNERKSKSYII-----------LKKDRIYMRHNVL 313

Query: 209 RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDI 267
              VP+   L A+G+ S++ +      I  + + DF      +  L +     +   +  
Sbjct: 314 SEDVPIVILLKAMGIQSDKEMLLLVAGIDSTFQEDFAINFEESVKLGIYTQHQALEYIGS 373

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
                   +   +T         + +  + I+   +  L                 A   
Sbjct: 374 RIKINRKPNSFGITRRNHVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMA 425

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
                 +           +           +         K + D  ++I +V++    +
Sbjct: 426 RRVLMAKHDPSLVDDRDYVGNKRLELAGQLLALLFEDLFKKFQFDIKMNIDKVLKKPVRT 485

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKIL 443
               A  +         +     +     +++        V H    +     + ++  +
Sbjct: 486 EQFDAYGVVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRI 545

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
                    +     L   +   +      +     L    ++   I++ D +  + + +
Sbjct: 546 SSQFEKTRKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLI 605

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVH 562
                                    +N        R    L     + R     E   V 
Sbjct: 606 FALGAEDVQTVGGRELHGQGAYIIFLNGSPIALTRRPKFFLNSFRRLRRTGRVSEFISVF 665

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             H+       T +G     +  +              +     +  D      V YL  
Sbjct: 666 INHHQNAVHVATDDGRICRPLIIVEDGKSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLDC 725

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            EE + YIA     + +                           ++  P  ++   A LI
Sbjct: 726 NEENDSYIAVYEEDITQS-----------------------TTHLEIEPFTILGAVAGLI 762

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           P+  ++ S R    C M +QA+  +      
Sbjct: 763 PYPHHNQSPRNTYQCAMGKQAIGAIANNQFL 793



 Score =  130 bits (327), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 88/651 (13%), Positives = 205/651 (31%), Gaps = 56/651 (8%)

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
           + K   ++ +  D +   +            I ++A  +  +K +  +       +  + 
Sbjct: 292 ERKSKSYIILKKDRIYMRHNVLSEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 342

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                + A      V      +  AL  I   ++             F     +  +  +
Sbjct: 343 STFQEDFAINFEESVKLGIYTQHQALEYIGSRIKINRKPNS------FGITRRNHVQEAI 396

Query: 409 STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
             +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 397 EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 453

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQ 521
           ++L   +     + +  IK  I  V    V  +          +   +   +     +  
Sbjct: 454 QLLALLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNRAISTGN 513

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAE 573
            S     +          RLS +   G+         + R     R + P+ +G +CP++
Sbjct: 514 WSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPSQFGMLCPSD 573

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN---RYIAQA 630
           T EG   GLV +L     +      E P RK+       DV  +   E        I   
Sbjct: 574 TPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGRELHGQGAYIIFLN 632

Query: 631 NSSL---DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            S +        F       R  G         I+    +            P +  +D 
Sbjct: 633 GSPIALTRRPKFFLNSFRRLRRTGRVSEFISVFINHHQNAVHVATDDGRICRPLIIVEDG 692

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV--- 744
              +   +++      ++ +       +E +       + +A     + Q      +   
Sbjct: 693 KSKVTNRHLRLLRNGTMEFDDFLAHGLVEYLDCNEENDSYIAVYEEDITQSTTHLEIEPF 752

Query: 745 -----IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ----RPLVKVGDEVRRNDIIA 795
                +  +      + S  + Y+    +++      NQ      L+      ++  +  
Sbjct: 753 TILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIANNQFLRIDSLLYTMVYPQKPMVKT 812

Query: 796 DG-PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                     L  G++  VA M + GY+ ED++++++  V           ++    +  
Sbjct: 813 RTIELIKYDKLPAGQSATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYSTNLKSY 872

Query: 855 KLGPEEITRDIPN---VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             G ++  +       V       +D  G+  VG +VN G++ + K+TP+ 
Sbjct: 873 SNGTKDKLKGPDRENGVPIRKHALLDNDGLAAVGEKVNHGEVYINKVTPEN 923


>gi|153958297|gb|ABS53438.1| RpoB [Bacteriovorax sp. ISRE]
          Length = 331

 Score =  221 bits (563), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 161/339 (47%), Positives = 222/339 (65%), Gaps = 17/339 (5%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIV++  +       SGVDIY L+K+QR+NQ+TC NQ+ LVK GD 
Sbjct: 2    FAKEDGKVIFVDSNRIVLQRDK--FADGESGVDIYSLVKYQRTNQSTCNNQKALVKEGDI 59

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V++ D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ D+FTS+HIE F
Sbjct: 60   VKKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILITEDLLARDIFTSVHIEAF 119

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            EV ARDTKLG EEITRDIPNVSEE LK++DE GI+ VGA + PGDILVGKITPKGE+ ++
Sbjct: 120  EVEARDTKLGKEEITRDIPNVSEESLKDLDEAGIVRVGAIIKPGDILVGKITPKGETQLS 179

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL
Sbjct: 180  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLL 239

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   ++ ++++  P   
Sbjct: 240  RRDERIEIKAIQTSSILKIAEMLKGAKTTDKLISEDGSTELLPKGADITGEVLASIPFEL 299

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                 +Q E        L+ +     + + +R     +K
Sbjct: 300  IGYLPLQAE--------LEEKLSEYFADIRNRINRVRQK 330


>gi|18104644|gb|AAL59633.1| RpoB [Bacillus subtilis]
 gi|18104646|gb|AAL59634.1| RpoB [Bacillus subtilis]
 gi|18104648|gb|AAL59635.1| RpoB [Bacillus subtilis]
 gi|18104650|gb|AAL59636.1| RpoB [Bacillus subtilis]
 gi|18104652|gb|AAL59637.1| RpoB [Bacillus subtilis]
 gi|18104654|gb|AAL59638.1| RpoB [Bacillus subtilis]
 gi|18104656|gb|AAL59639.1| RpoB [Bacillus subtilis]
 gi|18104658|gb|AAL59640.1| RpoB [Bacillus subtilis]
 gi|18104660|gb|AAL59641.1| RpoB [Bacillus subtilis]
 gi|18104662|gb|AAL59642.1| RpoB [Bacillus subtilis]
 gi|18104664|gb|AAL59643.1| RpoB [Bacillus subtilis]
 gi|18104666|gb|AAL59644.1| RpoB [Bacillus subtilis]
          Length = 117

 Score =  221 bits (563), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 53/129 (41%), Positives = 86/129 (66%), Gaps = 12/129 (9%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTF 144
           K+ V++   RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF
Sbjct: 1   KYPVEESKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTF 51

Query: 145 VIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           +I G +R++VSQL RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++V
Sbjct: 52  IINGAERVIVSQLVRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYV 108

Query: 205 RIDRRRKVP 213
           RIDR RK+P
Sbjct: 109 RIDRTRKLP 117


>gi|146217879|gb|ABQ11019.1| RNA polymerase beta subunit [Paenibacillus borealis]
          Length = 225

 Score =  221 bits (563), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 92/281 (32%), Positives = 128/281 (45%), Gaps = 71/281 (25%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+         +IL G+    G         L   +  E  R           +V+
Sbjct: 16   DERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      K+   + GD++PPGV ++V+V++A KR I  GDKMAG
Sbjct: 65   DTSLRVPHGSDGIIVDV------KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+V+RILP EDMPFL DGTPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  +
Sbjct: 119  RHGNKGVVARILPEEDMPFLPDGTPVQVVLNPLGVPSRMNIGQVLEVHIGMAALQLGIHV 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D                                             VFD
Sbjct: 179  ATPVFDGAREND---------------------------------------------VFD 193

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                      +  A +  +G+++LYDG TGE F+R VTVG 
Sbjct: 194  ---------TMEEAGMQRNGKTVLYDGRTGERFEREVTVGV 225



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAE+N GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEINAGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 62  EVRDTSLRVPHGSDGIIVDVKVFTRENGD 90


>gi|327133543|gb|AEA29776.1| RNA polymerase subunit B [Acinetobacter sp. 17N2]
          Length = 204

 Score =  221 bits (562), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 86/203 (42%), Positives = 119/203 (58%), Gaps = 4/203 (1%)

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L      +G    K+   L+ D +S+       +    DE +   +  ++   +   + +
Sbjct: 5    LLNDQMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEI 64

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +++F  K  K+  GD++  GVL+VVKV++A KR IQ GDKMAGRHGNKG+VS ILP EDM
Sbjct: 65   DEKFAEKKRKLSTGDELTTGVLKVVKVYLAEKRRIQPGDKMAGRHGNKGVVSNILPVEDM 124

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P   +G PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR
Sbjct: 125  PHDANGVPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELR 181

Query: 1170 SFLEKVIGT-GSHTEKISDYDDD 1191
             FL K+    G   E++    DD
Sbjct: 182  EFLHKIYNKVGGEQEELETLTDD 204


>gi|68131824|gb|AAY85190.1| RNA polymerase II second largest subunit [Aextoxicon punctatum]
          Length = 873

 Score =  221 bits (562), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 124/907 (13%), Positives = 260/907 (28%), Gaps = 163/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDCEEVTETQDFTK--VFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNHQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWXMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L+      A        E       D      + Y+   EEE   I+         
Sbjct: 529 QRL-LIKKKDIQALQQRESHEEGG---WHDLVAKGFIEYVDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +L+  R   E      E     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 577 --TINDLITARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 633 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISC 687

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 688 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGS 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +           A         RD S  + 
Sbjct: 748 YDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRRDHSTSLR 798

Query: 933 SGVSGTV 939
              SG V
Sbjct: 799 HSESGMV 805



 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 128/822 (15%), Positives = 244/822 (29%), Gaps = 134/822 (16%)

Query: 320  IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            ++   G V D+  LE I +       +  +      A++              AL  I +
Sbjct: 172  VFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNHQV--------ALDYIGK 223

Query: 380  VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
                  V+          +      K  L  VG             +     +      I
Sbjct: 224  RGSTVGVTRE----KRIKYAKEILQKEMLPHVG-----------VGEYCETKKAYYFGYI 268

Query: 440  IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK--ERISSVDIDS 497
            I  L+    G+   DD D+ GN+R+   G +L   +R+   ++ R ++   +    +   
Sbjct: 269  IHRLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKD 328

Query: 498  VMPQDLINAKPVVSAVCEFFCSSQ------------LSQLEEHVNSLSRITHTRRLSALG 545
            V  Q  I AK + S +     +              +SQ+   +   S ++H RRL++  
Sbjct: 329  VNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-- 386

Query: 546  QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
               + R     + R +H +H+  +CPAET EG   GLV +L     +            +
Sbjct: 387  --PIGREGKLAKPRQLHNSHWXMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFL 444

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             +    N        EE +  +    + +  +G +           + +   R ++   D
Sbjct: 445  EEWSTEN-------FEEISPAVIPQATKIFVNGCWVGIHRNPDLLVKTLRQLRRQV---D 494

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             + +  V     L       D  R      +  +   L+K +            +   G 
Sbjct: 495  VNTEVGVIRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIQALQ---QRESHEEGG 551

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                   G +E VD             + +T        +   R N     +        
Sbjct: 552  WHDLVAKGFIEYVDTEE----------EETTMISMTINDLITARLNPEEAYS-------- 593

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                        PS  LG       +  + +P+  +N          M  + +   I++ 
Sbjct: 594  ---ETYTHCEIHPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVT 641

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             ++                           +    +  V        +    +       
Sbjct: 642  NYQ---------------------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQ 674

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +      + AI      +  D+ +   S +        +F R   D+ ++  ++ +E   
Sbjct: 675  LPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFG 733

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               R+          +          G           K+T +S                
Sbjct: 734  RPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--------------- 778

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              D+   +     +  + TS    E    +++      D +     R VKV +   R  Q
Sbjct: 779  --DDAQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQ 831

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
             GDK + RHG KG V      EDMP+  +G   DI++NP  +
Sbjct: 832  IGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 873


>gi|153958216|gb|ABS53398.1| RpoB [Bacteriovorax sp. PS12B]
 gi|153958226|gb|ABS53403.1| RpoB [Bacteriovorax sp. PS91S]
 gi|153958232|gb|ABS53406.1| RpoB [Bacteriovorax sp. JS7]
          Length = 340

 Score =  221 bits (562), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 161/342 (47%), Positives = 222/342 (64%), Gaps = 10/342 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK GD 
Sbjct: 2    FAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEGDI 59

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE F
Sbjct: 60   VVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIEAF 119

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ ++
Sbjct: 120  EIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQLS 179

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL
Sbjct: 180  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLL 239

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P   
Sbjct: 240  RRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPFEL 299

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
                 +Q  +++  +           + +  +  ++I K+  
Sbjct: 300  IGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLHR 340


>gi|59043117|gb|AAW83911.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043161|gb|AAW83933.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043163|gb|AAW83934.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043165|gb|AAW83935.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|59043167|gb|AAW83936.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 237

 Score =  221 bits (562), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 131/228 (57%), Positives = 170/228 (74%), Gaps = 2/228 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFIDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPANIVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  SGAA++A+
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPQAPYVGTGMEYQAAHDSGAAVIAQ 231


>gi|111278805|gb|ABH09100.1| RNA polymerase II second largest subunit [Staurothele frustulenta]
          Length = 705

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 127/826 (15%), Positives = 234/826 (28%), Gaps = 148/826 (17%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G ++ N +RL   ++ER      +        +  +  +    + + +     +
Sbjct: 2    KRLDLAGPLMANLFRLQFQKVERDFFRYMQKQVESDREINIKVGLKPNIITNGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +A     + R     + R +H TH+
Sbjct: 62   GNWGDQKKASQAKAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARV--NAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            G +CPAET EG   GLV +L     V  +        Y      +   D     + +   
Sbjct: 118  GYVCPAETPEGQACGLVKNLALMTMVTNSHNTAPLQEYIMNQGVEPLEDWEPRLSPQATK 177

Query: 625  RYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             ++        + +     ++    R             D  D   K        + P  
Sbjct: 178  VFLNGVWFAVVIKDPKHLVDQFKGLRRKCSLDPQISLVWDIRDKEFKISGDAGRIIRPLF 237

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG----MESVVAKSSGAAIVAKRAGIVEQV 738
              +         N+    V + K +   V T     ++       G      + G+VE +
Sbjct: 238  AVETDPSSDNNGNLVLNKVHIQKLDNTVVNTVAQLPIDQWPEPPFG-WKDLLKEGVVEYL 296

Query: 739  DAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
            DA      +I     DL+ S +    Y   +             P          +    
Sbjct: 297  DAEEEETAMIIMTPEDLNTSEAKHMGYTTEETDDPLARYDPLLNP------HAHTSTHCE 350

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N              + + S        +     
Sbjct: 351  IHPSMILG-------VCASIIPFPDHNQSP----------RNTYQSAXXXXXXXVFLTNF 393

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                E   +I    ++ L                        +       +   +  + A
Sbjct: 394  DQRMETMSNILYYPQKPLAR-------------------TMSMEYLKFRELPAGQNAIVA 434

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +   +    +F R   D+ +       EQ E   R+     
Sbjct: 435  IACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYQDQEKVVGHNVVEQFEKPTRNDTLRM 493

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +       +  GQ          K+  ++ D                +E  QR  
Sbjct: 494  KHGTYDKIDTDGIVQVGQRVCGEDIIIGKTAPMAPD---------------AEELGQRQK 538

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
            + LK    T     E    +++     GD       + VKV V   +  Q GDK A RHG
Sbjct: 539  QHLKRDVSTPLRSTESGIIDQVLVTTSGD-----GQKFVKVRVRTTKIPQIGDKFASRHG 593

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  + 
Sbjct: 594  QKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDAT 653

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                    ++S +   +                                           
Sbjct: 654  PFTKVTVTNVSNILRSMGYQSRGFEVM--------------------------------- 680

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           +G +    G         + +G  Y  +L H
Sbjct: 681  --------------YNGHT----GR---KLVAQIFLGPTYYQRLRH 705



 Score =  116 bits (291), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 92/639 (14%), Positives = 177/639 (27%), Gaps = 117/639 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +         V   +   +  +  KY L   G  
Sbjct: 8   GPLMANLFRLQFQKVERDFFRYMQKQVESDREINIKVG--LKPNIITNGLKYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               + +       + + +    + +  L        R+GK       +  +       E
Sbjct: 65  GDQKKASQAKAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGYVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKE---------RISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
             + Q    +  +               +   ++      +D        +         
Sbjct: 125 TPEGQACGLVKNLALMTMVTNSHNTAPLQEYIMNQGVEPLEDWEPRLSPQATKVFLNGVW 184

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQ--------GGVARARAGVEMRDVHPTHYGRICPA 572
               +++  + + +    RR  +L                 +G   R + P       P+
Sbjct: 185 FAVVIKDPKHLVDQFKGLRRKCSLDPQISLVWDIRDKEFKISGDAGRIIRPLFAVETDPS 244

Query: 573 ETSEGHNIGLVSSLTSF--------ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
             + G+ +     +           A++    + E P+    D      V YL A EEE 
Sbjct: 245 SDNNGNLVLNKVHIQKLDNTVVNTVAQLPIDQWPEPPF-GWKDLLKEGVVEYLDAEEEET 303

Query: 625 RYIAQANSSLD-----EDGSFTEELVFCRCAGEEILVPR-EKIDFIDASPKQVVSIAASL 678
             I      L+       G  TEE        + +L P        +  P  ++ + AS+
Sbjct: 304 AMIIMTPEDLNTSEAKHMGYTTEETDDPLARYDPLLNPHAHTSTHCEIHPSMILGVCASI 363

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPF +++ S R             +                                   
Sbjct: 364 IPFPDHNQSPRNTYQSAXXXXXXXVFLTNF------------------------------ 393

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                           + S +  Y      R+     +  R                   
Sbjct: 394 -----------DQRMETMSNILYYPQKPLARTMSMEYLKFR------------------- 423

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                +L  G+N +VA   + GYN EDS+++++  +   +F S+    ++   +      
Sbjct: 424 -----ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKVVGHNV 478

Query: 859 EEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            E        D   +       ID  GI+ VG  V   DI++GK  P     M P+ + L
Sbjct: 479 VEQFEKPTRNDTLRMKHGTYDKIDTDGIVQVGQRVCGEDIIIGKTAP-----MAPDAEEL 533

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                +     RD S  + S  SG +  V +       K
Sbjct: 534 GQRQKQHLK--RDVSTPLRSTESGIIDQVLVTTSGDGQK 570


>gi|312204362|gb|ADQ47498.1| RNA polymerase II second largest subunit [Porina lectissima]
          Length = 604

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 115/712 (16%), Positives = 207/712 (29%), Gaps = 127/712 (17%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRK 604
              + R     + R +H TH+G +C AETSEG   G V +L     +      E    +  
Sbjct: 4    TPIGRDGKIAKPRQLHNTHWGXVCXAETSEGQACGPVKNLALMCYITVGSPSEPIDEFMI 63

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
              + +V  +            ++      +  D +     V        I      + D 
Sbjct: 64   QRNMEVLEEFEPTRTPNATKVFVNGVWVGVHRDPTHLVSTVQSLRRSNYISSEVSLVRDI 123

Query: 664  IDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             D   K          P F+ ++D      G  +  ++      +   +   M+      
Sbjct: 124  RDREFKIFTYAGRVCRPLFVIDNDPKSANKGSLVLTKSKIKKLEDDKDLPADMDRDRKAE 183

Query: 723  SGAAIVAK-RAGIVEQVDAIRI---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                     + GIVE +DA      +I     DL+ S      Y + +    N N     
Sbjct: 184  VYYGWNGLVKDGIVEFLDAEEEETVMIAMTPEDLEISRQVQAGYAMPEPDPDNPNA---- 239

Query: 779  RPLVK--VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
               VK  V  + +        PS  LG       +  + +P+  +N       S R    
Sbjct: 240  --RVKAPVRQQQQTWTHCEIHPSMILG-------ICASIIPFPDHNQXXXXXXSPRN--- 287

Query: 837  DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                      ++    +  +G                                       
Sbjct: 288  ---------TYQSAMGNQAMGXXXXXXXXXXXXXXXXX-----------XYPQKPLATTR 327

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R 
Sbjct: 328  SMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYVEQEKR- 385

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLI 1013
              +    +E   +    E + +    Y +L +   I  G           K+  ++ D  
Sbjct: 386  --IGMSLVERFEKPLRTETLRVKHGTYEKLDDDGIIAPGTRVSGEDIIIGKTAPIAPDAE 443

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                R++                  K    T     E+   +K+      D +     + 
Sbjct: 444  ELGQRTKLHT---------------KRDASTPLRSTENGIVDKVLLTTNADGL-----KF 483

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   +  Q GDK A RHG KG +      EDMPF   G   D+++NP  +PSRM +
Sbjct: 484  VKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSSQGITPDLIINPHAIPSRMTI 543

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
              + E  +       G +                                          
Sbjct: 544  AHLIECQISKVASLQGLEGD---------------------------------------- 563

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                         +TP F     ++I+ +LR +     G  I+Y+G TG   
Sbjct: 564  -------------ATP-FTTITVDSISRLLRQSGYQSRGFEIMYNGHTGRKL 601



 Score = 99.0 bits (245), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 85/549 (15%), Positives = 147/549 (26%), Gaps = 92/549 (16%)

Query: 429 RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRME--RS 485
           R          I     L N   G +   +    +    V  +    Y       E    
Sbjct: 1   RTNTPIGRDGKIAKPRQLHNTHWGXVCXAETSEGQACGPVKNLALMCYITVGSPSEPIDE 60

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
              + +   ++   P    NA  V      F     +    +  + +S +   RR + + 
Sbjct: 61  FMIQRNMEVLEEFEPTRTPNATKV------FVNGVWVGVHRDPTHLVSTVQSLRRSNYIS 114

Query: 546 -QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSF-------A 590
            +  + R     E        R   P       P   ++G  +   S +          A
Sbjct: 115 SEVSLVRDIRDREFKIFTYAGRVCRPLFVIDNDPKSANKGSLVLTKSKIKKLEDDKDLPA 174

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            ++     E  Y           V +L A EEE   IA     L                
Sbjct: 175 DMDRDRKAE-VYYGWNGLVKDGIVEFLDAEEEETVMIAMTPEDL---------------- 217

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                         + S +     A   +P  + D+ N  +     Q+Q           
Sbjct: 218 --------------EISRQVQAGYA---MPEPDPDNPNARVKAPVRQQQQT--------- 251

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR--SVEGDLDPSTSGVDIYRLMKFQ 768
             T  E   +   G            Q        R        + +             
Sbjct: 252 -WTHCEIHPSMILGICASIIPFPDHNQXXXXXXSPRNTYQSAMGNQAMGXXXXXXXXXXX 310

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PL                      +L  G+N +VA   + GYN EDS++
Sbjct: 311 XXXXXXXYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVI 360

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++  +   +F S+    +    +   +   E        +   V     + +D+ GII 
Sbjct: 361 MNQSSIDRGLFRSLFYRTYVEQEKRIGMSLVERFEKPLRTETLRVKHGTYEKLDDDGIIA 420

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            G  V+  DI++GK  P         ++        K    RD S  + S  +G V  V 
Sbjct: 421 PGTRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHTKRDASTPLRSTENGIVDKVL 473

Query: 944 IFNRHGIDK 952
           +       K
Sbjct: 474 LTTNADGLK 482


>gi|304334229|gb|ADM25192.1| RNA polymerase beta subunit [Cupriavidus sp. mapud8.1]
 gi|304334231|gb|ADM25193.1| RNA polymerase beta subunit [Cupriavidus sp. tpud27.6]
 gi|304334279|gb|ADM25217.1| RNA polymerase beta subunit [Cupriavidus sp. pp2.49]
          Length = 219

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 127/219 (57%), Positives = 164/219 (74%), Gaps = 2/219 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L  +AR+N YGF+ETPYRKV D K+T++V YLSA+EE    +AQAN+++D DG+ T+ELV
Sbjct: 61  LALYARLNEYGFLETPYRKVVDSKLTDEVDYLSAIEEGKYVVAQANATVDADGNLTDELV 120

Query: 646 FCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 SAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPC 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R
Sbjct: 181 LRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMR 219


>gi|93278297|gb|ABF06604.1| RNA polymerase II second largest subunit [Conocybe apala]
          Length = 629

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 106/706 (15%), Positives = 213/706 (30%), Gaps = 94/706 (13%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +  + + + + 
Sbjct: 1    DHFGKKRLDLAGPLLSNLFRMLFRKLTKDVYRYLQKCVETRKEFNISLAVKHQTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   + ++      T    + +  + +      +  
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMSYISVGSTSATVIEFLQEWGLESLEDNAHSNV 176

Query: 622  EENRYIAQA-NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
               +         +  +     +++       +I      +  I     ++ + A  +  
Sbjct: 177  PCTKVFVNGVWMGIHRNAENLMKILRRLRRRSQINFEVSMVRDIREREVRIYADAGRVCR 236

Query: 681  FLENDDSNRVLMGCNMQRQAVPLLK-AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
             L    + R++M  +  R     +   + P+  T +           I+       E+  
Sbjct: 237  PLFLVKNQRLVMRKHHVRWLSDKVNVFDQPYSFTSLLQKG-------ILELLDAEEEETV 289

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
             I +    +E     S          +F  +           +K    V+        PS
Sbjct: 290  MICMTPEDLEASRAKSLGMQMESNEAEFDPA---------TRLKAPTNVQSWTHCEIHPS 340

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
              LG       +  + +P+  +N          M  + +   I +  F V          
Sbjct: 341  MILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--IFLTNFLVRM-------- 383

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
                                 +  +             +       +   +  + AI   
Sbjct: 384  -------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCY 424

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   R+         
Sbjct: 425  SGYNQEDSVIMNQSSIDRGLFRX-IYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGT 483

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +       I  G           K+  +  D      R++          ++     + 
Sbjct: 484  YDKIEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIV 543

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q GDK A RHG KG 
Sbjct: 544  DQVLI--------------------TTNSEGHKFVKVRVRSTRIPQIGDKFASRHGQKGT 583

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
            +      EDMPF  +G   D+++NP  +PSRM +G + E  L    
Sbjct: 584  IGITYRQEDMPFTNEGIVPDLIINPHAIPSRMTIGHLVECLLSKVA 629



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 86/605 (14%), Positives = 159/605 (26%), Gaps = 88/605 (14%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLSNLFRMLFRKLTKDVYRYLQKCV--ETRKEFNISLAVKHQTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S     +             NA   V     F     +
Sbjct: 129 TPEGQACGLVKNLALMSYISVGSTSATVIEFLQEWGLESLEDNAHSNVPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                  N +  +   RR S +                ++        P       N  L
Sbjct: 189 GIHRNAENLMKILRRLRRRSQINFEVSMVRDIREREVRIYADAGRVCRPL--FLVKNQRL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           V        ++    +               +  L A EEE   I      L+   + + 
Sbjct: 247 VMRKHHVRWLSDKVNVFDQPYSFTSLLQKGILELLDAEEEETVMICMTPEDLEASRAKSL 306

Query: 643 ELVFCRCAGEEILVPREK-------IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +       E     R K           +  P  ++ I AS+IPF +++ S R      
Sbjct: 307 GMQMESNEAEFDPATRLKAPTNVQSWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 366

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +              +V   + A I+                           
Sbjct: 367 MGKQAMGIFLT---------NFLVRMDTMANILY---------------------YPQKP 396

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
            +       +KF+            L   G   + + +I +  S D G            
Sbjct: 397 LATTRSMEYLKFRELPAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRXIYY----- 450

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
                 + E    I +            +EEFE   R+T             +       
Sbjct: 451 --RSYMDLEKKSGIQQ------------LEEFEKPTRET----------TLRMKHGTYDK 486

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           I++ G+I  G  V   DI++GK  P         E+L +        DV        SG+
Sbjct: 487 IEDDGLIAPGTGVRGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTESGI 542

Query: 936 SGTVV 940
              V+
Sbjct: 543 VDQVL 547


>gi|327133513|gb|AEA29761.1| RNA polymerase subunit B [Acinetobacter sp. 11NS4]
          Length = 178

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 82/181 (45%), Positives = 115/181 (63%), Gaps = 3/181 (1%)

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F  K
Sbjct: 1    NGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKFAEK 60

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
              K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G 
Sbjct: 61   KRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGV 120

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   K    I+ LR FL+K+ 
Sbjct: 121  PVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLDKIY 177

Query: 1177 G 1177
             
Sbjct: 178  N 178


>gi|294471032|gb|ADE80777.1| RNA polymerase beta subunit [Lactococcus piscium]
          Length = 150

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/172 (36%), Positives = 94/172 (54%), Gaps = 22/172 (12%)

Query: 22  EIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEF 81
           E++D+P+LIE+Q  SY  FL          ++ L   FK + PI  F+G   LEFV YE 
Sbjct: 1   EVLDLPNLIEIQTDSYQLFL----------DQSLADVFKEMLPIDNFAGTKDLEFVGYEM 50

Query: 82  DPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD 141
             PK+ +++    D  Y+ PL +T RL+          K   ++K Q ++ GD P+MT+ 
Sbjct: 51  KAPKYTIEEARAHDANYSAPLFVTFRLV---------DKESGELKTQEVFFGDFPIMTEM 101

Query: 142 GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           GTF++ G +RI+VSQL RSPG +F     +   S    Y    IP++G W++
Sbjct: 102 GTFIVNGAERIIVSQLVRSPGTYFHPKVDK---SSVESYGHTTIPNRGAWLE 150


>gi|78100228|gb|ABB20915.1| RNA polymerase II second largest subunit [Cintractia sorghi-vulgaris]
          Length = 676

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 117/805 (14%), Positives = 235/805 (29%), Gaps = 147/805 (18%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
            + +   G ++ N +R+   ++ R +   +     +      Q  + +  + + +     +
Sbjct: 2    KSIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHIQAAVKSSTITNGLRYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMQAKAGVSQVLNRFAFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  A V            + +  + + V    A  +  + 
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHAKATKI 177

Query: 627  IAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                    + D+ G   + L   R   +         D  +   +     +  L P    
Sbjct: 178  FVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIV 237

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
            +      M   ++++ V ++    P  G           G          +E +DA    
Sbjct: 238  N---PNDMTLFIKKRHVNMIGQPVPLTGEEFGWSHLVQEGV---------IEYLDAEEEE 285

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +           + Y+    Q +  +   + R                  P+  LG 
Sbjct: 286  SALICMSTTDLEQSRE-YQARNGQINLHSADPSARLKSPHYIAPNTWTHCEIHPAMVLG- 343

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N     + +                         +G + ++  
Sbjct: 344  ------ICASIIPFPDHNQSPRNVYA-------------------------MGKQAVSIP 372

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
            I N             ++ +             +       +   +  + AI      + 
Sbjct: 373  ISNFLTRA------DSMMHILCYPQKPLGTTRSMEHLKFRELPAGQNGVIAIMCYSGYNQ 426

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +   +    ++ R  + + ++   ++ E+ E  +RD          +   
Sbjct: 427  EDSVIMNQSSIDRGLF-RSLYYRGYVAEEKKVGVMQLEEFEKPSRDTTIRMKHGTYDKID 485

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                   G           K+  L  D      RS+          ++     +  Q   
Sbjct: 486  ADGFCAPGTRVSGDDVIIGKTAPLPPDSEELGMRSKLHTKKDASISLKSTENGIIDQVLL 545

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            + +   ++F     +                         Q+GDK A RHG KG +    
Sbjct: 546  TTNSHGNKFVKVRVRNVRV--------------------PQTGDKFASRHGQKGTIGITY 585

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +G + E  L       G++             
Sbjct: 586  RQEDMPFSAEGITPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGD----------- 634

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     EA++S+LR
Sbjct: 635  ------------------------------------------ATP-FTELTVEAVSSILR 651

Query: 1225 MADLDESGQSILYDGLTGEPFDRPV 1249
                   G  ++Y G TG      V
Sbjct: 652  GLGYQSRGLEVMYHGHTGRKLQAQV 676



 Score =  100 bits (248), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 80/624 (12%), Positives = 180/624 (28%), Gaps = 104/624 (16%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +   +   F +  ++ +    +  +Y L   G  
Sbjct: 8   GPLMANLFRMLFRKVTRDVYRHLQKCV--EEHREFHIQAAVKSSTITNGLRYSL-ATGNW 64

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 65  GDQKKAMQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAE 124

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI------DSVMPQDLINAKPVVSAVCEFF-CSSQL 522
             + Q    +  +       + +         +      L++ +   +   + F     +
Sbjct: 125 TPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHAKATKIFVNGVWM 184

Query: 523 SQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
              ++    +  +   RR   +  +  V R     E+R ++      + P      +++ 
Sbjct: 185 GTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELR-IYTDASRVLRPVFIVNPNDMT 243

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L         +     +               + YL A EEE+  I  + + L++   + 
Sbjct: 244 LFIKKRHVNMIGQPVPLTGEEFGWSHLVQEGVIEYLDAEEEESALICMSTTDLEQSREYQ 303

Query: 642 EEL--------VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                                 +        +  P  V+ I AS+IPF +++ S R +  
Sbjct: 304 ARNGQINLHSADPSARLKSPHYIAPNTWTHCEIHPAMVLGICASIIPFPDHNQSPRNVYA 363

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QAV +  +                                               
Sbjct: 364 --MGKQAVSIPISNFL-----------------------------------------TRA 380

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            S   +  Y       +     +  R                + P+   G +A+      
Sbjct: 381 DSMMHILCYPQKPLGTTRSMEHLKFR----------------ELPAGQNGVIAIMCY--- 421

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNV 868
                 GYN EDS+++++  +   +F S++   +    +   +   E            +
Sbjct: 422 -----SGYNQEDSVIMNQSSIDRGLFRSLYYRGYVAEEKKVGVMQLEEFEKPSRDTTIRM 476

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  ID  G    G  V+  D+++GK  P    P   EE  +R+    K    +D S
Sbjct: 477 KHGTYDKIDADGFCAPGTRVSGDDVIIGKTAP---LPPDSEELGMRS----KLHTKKDAS 529

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
           + + S  +G +  V +      +K
Sbjct: 530 ISLKSTENGIIDQVLLTTNSHGNK 553


>gi|260945433|ref|XP_002617014.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Clavispora
            lusitaniae ATCC 42720]
 gi|238848868|gb|EEQ38332.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Clavispora
            lusitaniae ATCC 42720]
          Length = 1159

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 117/316 (37%), Gaps = 74/316 (23%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++KV +   R  + GDK +                                   
Sbjct: 901  SDNDQALIKVLLRQTRRPELGDKFS----------------------------------- 925

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR                  G+K    I     +   + +    + ++       +++
Sbjct: 926  --SR-----------------HGQKGVCGIIVQHEDMPFNDMGISPDIIMNPHGFPSRMT 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE   
Sbjct: 967  VGKMIELISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDKGFNYSGKDMLYSGITGECLQ 1026

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++ARS G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1027 AYIFFGPIYYQKLKHMVLDKMHARSRGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1086

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRVYESIVAG-----------NDTFETGTPESFNVLV 1351
            A+ +L E L I SD    DV          + G               +   P +  +L 
Sbjct: 1087 ASQLLLERLMISSDAFEVDVCN-----NCGLMGYSSWCSTCKSSEHVIKMTIPYAAKLLF 1141

Query: 1352 KEMQALGLSIDLENSR 1367
            +E+ ++ ++  L+   
Sbjct: 1142 QELLSMNIAPRLKLGD 1157



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 132/997 (13%), Positives = 272/997 (27%), Gaps = 220/997 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
           L++    S+++F+ +++    R NE        V P         L+++           
Sbjct: 54  LVKQHLDSFNYFVDVDLKKIIRANE---LVLSDVDP------QFYLKYLDIRVGHKSSSA 104

Query: 83  ----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 105 PGTKEVIMAPHECRLRDLTYSAPIYVDVEYT----------RGRKIIMHKDLEIGRMPIM 154

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++ G +++++ Q   S          + ++
Sbjct: 155 LRSNKCVLDGIDEHQMAVFEECPIDPGGYFIVNGTEKVILIQEQLSKNRIIVEADEKKAI 214

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV-----------PVTSFLMALGM 223
               + +               + K   +V I +  K+           P+   L A G+
Sbjct: 215 VQASVTSST------------HERKSKTYV-ISKNEKIYLKHNSIAEDVPIVVVLKAAGI 261

Query: 224 DSE-EILSTFYP---------KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQV 273
            S+ EIL               I + +      F    A L +G +V +           
Sbjct: 262 VSDMEILQLVCGANSQYQDLFAINFEEAAKLEIFTQQQALLYIGKRVKTVRRAGAPKLSQ 321

Query: 274 IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
           ++ G  + +     +    V  L      L    +A  ++        ++  D +  K L
Sbjct: 322 LQEG--IEAIATTVIAHLTVSDLNFREKALYIAIMARKVLMTMHNPSMVDDRDYVGNKRL 379

Query: 334 EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVA 392
           E            L+     +     + ++   ++  + DALL I               
Sbjct: 380 ELAGQLMSLLFEDLFKKFNTDFKANIDKILKKPSRTSEFDALLSINIHSNN----ITMGM 435

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK-- 450
               +   +   ++ +   G   +  RL+  +   +            K+          
Sbjct: 436 NRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQ 495

Query: 451 -GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   D         V  +      +     E  IK     +  + +   D       
Sbjct: 496 FGMLCTSDTPEGEACGLVKNLALMT-HITTDDEEEPIKRLCFILGCEDIYSIDSATIYTE 554

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
            +       +   +        +  +   RR        + R+    E   +    +   
Sbjct: 555 GNYGVFLNGTMVGTTRFP----VKFVKDFRR--------LRRSGKVSEFISIFTNSHQAA 602

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK--------VCDGKVTNDVVYLSAME 621
               T  G     +  +     V     +E  + K          D      V YL   E
Sbjct: 603 VHIATDGGRVCRPLIIVD---EVTGQPRVEAHHLKKLLSGDWVFDDFLKYGLVEYLDVNE 659

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E +  IA     + E+                   P  +   ++  P  V+   A LIP+
Sbjct: 660 ENDSLIALYEKDMAEN-------------------PHLRFTHLEIEPFTVLGAVAGLIPY 700

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             ++ S R    C M +QA+                                        
Sbjct: 701 PHHNQSPRNTYQCAMGKQAIGA-------------------------------------- 722

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              I   +     +     +Y               Q+P+VK                 +
Sbjct: 723 ---IAYNQFRRIDTLLYFMVYP--------------QQPMVKS----------KTIELIE 755

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE-------FEVMARDT 854
              L  G+N  VA M + GY+ ED++++++  +         + +       +    +D 
Sbjct: 756 YDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCQVVRKNTIVLKRYPNHTKDI 815

Query: 855 KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             G        P  +      +   G+  VG  +  G +   K  P         E +L 
Sbjct: 816 VAGMRVDENGDPIFAHNA---LGPDGLGEVGMRIENGQVYANKQVPTNA-----GESVLG 867

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
                ++ +    +     G   + VD  + +    D
Sbjct: 868 DHNQPQSAESHRETPAYYRGPEPSYVDQVMMSVSDND 904


>gi|323302937|gb|EGA56741.1| Ret1p [Saccharomyces cerevisiae FostersB]
          Length = 1149

 Score =  220 bits (561), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 89/491 (18%), Positives = 163/491 (33%), Gaps = 87/491 (17%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             L+           T E      +   +   V   S          V++    +R     
Sbjct: 726  YLMTYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRC 785

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              R  +        + +   +    +   +          Q+   GP G     V     
Sbjct: 786  ETRRKTT------TVLKRYANHTQDIIGGMRVDENGXPIWQHQSLGPDGL--GEVGMKVQ 837

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   ++       D     NV  ++ QY  +  I      + I+++     +      
Sbjct: 838  SGQIYINKSVPTNSADAPNPNNVN-VQTQYREAPVIYRGPEPSHIDQVMM--SVSDNDQA 894

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +   R  + GDK +                                     SR  
Sbjct: 895  LIKVLLRQNRRPELGDKFS-------------------------------------SR-- 915

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                            G+K    I   + +   +      + ++       +++      
Sbjct: 916  ---------------HGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKMIE 960

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE     +  G
Sbjct: 961  LISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L 
Sbjct: 1021 PIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLL 1080

Query: 1313 EMLTIKSD----DVVGR------------TRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            E L I SD    DV  +             +  E+I+          P +  +L +E+ +
Sbjct: 1081 ERLMISSDAFEVDVCDKCGLMGYSGWCTTCKSAENIIK------MTIPYAAKLLFQELLS 1134

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 1135 MNIAPRLRLED 1145



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 118/984 (11%), Positives = 276/984 (28%), Gaps = 187/984 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L++    S+++F+  ++    + N   Q     V P         L++V           
Sbjct: 57  LVKQHLDSFNYFVDTDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGKKSSSS 107

Query: 88  -------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT- 139
                    +C  RD+TY+ P+ + +             +    I  + + +G +P+M  
Sbjct: 108 TKDYLTPPHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKDVEIGRMPIMLR 157

Query: 140 -----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F++ G +++++ Q   S          +  +  
Sbjct: 158 SNKCILYDADESKMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKGIVQ 217

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYP 234
             + +     ++             I+++ +    ++P+   L A G+ S+ EI+     
Sbjct: 218 ASVTSST--HERKSK-TYVITKNGKIYLKHNSIAEEIPIAIVLKACGILSDLEIMQLVCG 274

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
                Q         S+   +   + +   +        +++ ++    +L+   E    
Sbjct: 275 NDSSYQDIFAVNLEESSKLDIYTQQQALEYIGAK-----VKTMRRQKLTILQEGIEAIAT 329

Query: 295 FL--GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            +   +T + L     A  I       +        + K +++  +   + + +      
Sbjct: 330 TVIAHLTVEALDFREKALYIAMMTRRVVMAM----YNPKMIDDRDYVGNKRLEL------ 379

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I         K   D  L I +V++  + +    A    N    +        + 
Sbjct: 380 -AGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALLSINVHSNNITSGLNRAIS 438

Query: 413 RVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               +++        V H    +     + ++  +         +     L   +   + 
Sbjct: 439 TGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLC 498

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                +     L    ++   I++ D +  + +       +         S+ L      
Sbjct: 499 TADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCY---VLGVEDITLIDSASLHLNYGV 555

Query: 529 VNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI-GLVSS 585
             + + I   R  +        + R     E   ++   +       T  G     L+  
Sbjct: 556 YLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVHIATDGGRICRPLIIV 615

Query: 586 LTSFARVNAYG--FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
               +RV       +        D      V YL   EE + YIA           + ++
Sbjct: 616 SDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLDVNEENDSYIAL----------YEKD 665

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V                  ++  P  ++   A LIP+  ++ S R    C M +QA+  
Sbjct: 666 IVPSM-------------THLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIG- 711

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                    I   +     +   +  Y 
Sbjct: 712 ----------------------------------------AIAYNQFKRIDTLLYLMTYP 731

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+P+VK                 D   L  G+N  VA M + GY+ 
Sbjct: 732 --------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDI 767

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDEC 879
           ED++++++  +           +   + +      ++    +  D         +++   
Sbjct: 768 EDALVLNKSSIDRGFGRCETRRKTTTVLKRYANHTQDIIGGMRVDENGXPIWQHQSLGPD 827

Query: 880 GIICVGAEVNPGDILVGKITPKGESP---------MTPEEKLLRAIFGEKAVDVRDTSLR 930
           G+  VG +V  G I + K  P   +           T   +      G +   +    + 
Sbjct: 828 GLGEVGMKVQSGQIYINKSVPTNSADAPNPNNVNVQTQYREAPVIYRGPEPSHIDQVMMS 887

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNE 954
           V       +  +   NR     ++
Sbjct: 888 VSDNDQALIKVLLRQNRRPELGDK 911


>gi|303319249|ref|XP_003069624.1| DNA-directed RNA polymerase III, putative [Coccidioides posadasii
            C735 delta SOWgp]
 gi|240109310|gb|EER27479.1| DNA-directed RNA polymerase III, putative [Coccidioides posadasii
            C735 delta SOWgp]
 gi|320040958|gb|EFW22891.1| DNA-directed RNA polymerase 3 subunit RPC2 [Coccidioides posadasii
            str. Silveira]
          Length = 1197

 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 93/518 (17%), Positives = 169/518 (32%), Gaps = 97/518 (18%)

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
              + +    ++          +    I       +   +    A+      D+ D  +  
Sbjct: 759  NNQFLRIDSLLYTMVYPQKPMVKTRTIELVKYDKLPAGQSATVAVMSYSGYDIEDALVLN 818

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
               V       ++F ++  +    S   +     LL  D+ D   I    +         
Sbjct: 819  KGSVDRGFGRCQVFRKYSANLKSYSNGTKDR---LLGPDRQDGVPIRKHALLDNDGLAAV 875

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G+   SG     K+T    + +S             D           + Y  S    + 
Sbjct: 876  GEKVSSGEVYINKATP--ENALSS-------GITGSD-------AGGPIAYIPSPQTYKL 919

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               + I+K+        G  +++KV     R  + GDK +                    
Sbjct: 920  PDPSYIDKVMI--STTEGENQLLKVQTRQTRRPEVGDKFS-------------------- 957

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    I   +A+   +     
Sbjct: 958  -----------------SR-----------------HGQKGVVGIIAEQADMPFTDQGIV 983

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
             + ++       +++      ++       SG       F G+  E ++++L     +  
Sbjct: 984  PDIIMNPHGFPSRMTVGKMLELVAGKAGILSGQFGYGTAFGGSPVEEMSAILISKGFNYG 1043

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            G+  L  G+TGE     V  G IY  KL HMV DK+++R+ G  +++T+QP  G+S  GG
Sbjct: 1044 GKDYLTSGITGEALPAYVFTGPIYYQKLKHMVQDKMHSRARGPRAILTRQPTEGRSRDGG 1103

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV------------VGRTRVYESIVAG 1335
             RLGEME  C+ AYG + +L E L I SD    DV              R +    +V  
Sbjct: 1104 LRLGEMERDCLIAYGTSQLLLERLMISSDRHEVDVCENCGFMGYLGWCQRCKTSRGVVK- 1162

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
                    P +  +LV+E+ ++ +   L+ +      +
Sbjct: 1163 -----MVIPYAAKLLVQELFSMNVVARLKLADEFPEER 1195



 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 89/742 (11%), Positives = 210/742 (28%), Gaps = 122/742 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    SY++F+ + +    + +    A  +S            + F       P+   
Sbjct: 84  LVKQHIDSYNYFVEVQLKKIVQAS----AEIRS-----DVDPNFYIRFHDIYLGSPRRAD 134

Query: 86  --------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
                            ++C  RD+TYA P+ +    +          +  + +K     
Sbjct: 135 EEQSEDARFKIESTVTPNECRLRDMTYAAPILVDFEYV----------RGRQRVKRNGTA 184

Query: 132 MGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFD 166
           +G +P+M                           G F++ G +++++ Q   S   +  +
Sbjct: 185 IGRMPVMLRSSKCVLSKKSPREMYLLHECPLDPGGYFIVNGTEKVILVQEQLSKNRVIVE 244

Query: 167 HDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFL 218
            D  +        S S +      +I             KD I++R +     +PV   L
Sbjct: 245 TDPKKEIVQASVTSSSNERKSKSYVI-----------LKKDRIYLRHNVLSDDIPVVILL 293

Query: 219 MALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESG 277
            A+G+ S+ E+L          Q      F  S    +   + +   +          +G
Sbjct: 294 KAMGIQSDKEMLLLVAGVDSVYQEDFAINFEESIKLGIYTQQQALEYLGSHIKITRKPNG 353

Query: 278 KKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
                        + +  + I+   +  +                 A         +   
Sbjct: 354 FGGGRRNYIQEAVEAIASVIISHVQVENMNFRPKA--------LYVAHMARRVLMAKHDS 405

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                   +           +         K   D  ++I +V++    +    A S+  
Sbjct: 406 SLVDDRDYVGNKRLELAGQLLALLFEDLFKKFCFDIKMNIDKVLKKPVRTEAFDAFSVVA 465

Query: 398 FLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
                  +     +     +  R  ++       + +   I+ + ++  + +       +
Sbjct: 466 IHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYISALGMMTRISSQFEKTRKV 525

Query: 457 DNLGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVS 511
                 +    G +      + +    +  +        +  +         + A+ V +
Sbjct: 526 SGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLVFALGAEDVQA 585

Query: 512 AVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP 571
                F       +  + + ++ +T   +        + R     E   V+  H+     
Sbjct: 586 VGGREFYGQGAYIIFLNGSPIA-LTRRPKHFLNSFRRLRRMGRVSEFVSVYINHHQSAVH 644

Query: 572 AETSEGHNI-GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             T +G     L+      ++V     G +     +  D      V YL   EE + YIA
Sbjct: 645 IATDDGRICRPLIIVENQKSKVTDLHLGMLRNGTMEFDDFLAQGLVEYLDVNEENDSYIA 704

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              + ++E+                          ++  P  ++   A LIP+  ++ S 
Sbjct: 705 VYENEINEN-----------------------TTHLEIEPFTILGAVAGLIPYPHHNQSP 741

Query: 689 RVLMGCNMQRQAVPLLKAEAPF 710
           R    C M +QA+  +      
Sbjct: 742 RNTYQCAMGKQAIGAIANNQFL 763


>gi|126132998|ref|XP_001383024.1| DNA-directed RNA polymerase III [Scheffersomyces stipitis CBS 6054]
 gi|126094849|gb|ABN64995.1| DNA-directed RNA polymerase III [Scheffersomyces stipitis CBS 6054]
          Length = 1155

 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 118/311 (37%), Gaps = 64/311 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++KV +   R  + GDK +                                   
Sbjct: 897  SDNDQALIKVLLRQTRRPELGDKFS----------------------------------- 921

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR                  G+K    I   + +   +      + ++       +++
Sbjct: 922  --SR-----------------HGQKGVCGIIVQQEDLPFNDDGISPDIIMNPHGFPSRMT 962

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G       F G+  E ++ +L       SG+ +LY G+TGE   
Sbjct: 963  VGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFSYSGKDMLYSGITGECLQ 1022

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1023 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1082

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRV--YESIVAG----NDTFETGTPESFNVLVKEMQA 1356
            A+ +L E L I SD    DV  +  +  Y S            +   P +  +L +E+ +
Sbjct: 1083 ASQLLLERLMISSDAFEVDVCNKCGLMGYNSWCTTCKSFEHVIKMTIPYAAKLLFQELLS 1142

Query: 1357 LGLSIDLENSR 1367
            + ++  L+   
Sbjct: 1143 MNIAPRLKLGD 1153



 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 127/937 (13%), Positives = 261/937 (27%), Gaps = 189/937 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD------ 82
           L++    S+++F+ +++    R NE        V P         L+++           
Sbjct: 54  LVKQHLDSFNYFVDVDLKKIIRANE---LVLSDVDP------EFYLKYLDIRVGHKSSSA 104

Query: 83  ----PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 105 PGTKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIMHKDLEIGRMPVM 154

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+ G +++++ Q   S          +  +
Sbjct: 155 LRSNKCILDGINDKQMAKFDECPLDPGGYFVVNGTEKVILVQEQLSKNRIIVEADEKKGI 214

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++           D I+++ +     +P+   L A G+ S+ EIL   
Sbjct: 215 VQASVTSST--HERKSK-TYVITKNDKIYLKHNSISEDIPIVIVLKAAGITSDLEILQLV 271

Query: 233 YPK---------IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
                       + + +      F    A   VG +V +          V++ G  + + 
Sbjct: 272 CGSDPQYQDLFVVNFEEAAKLEVFTQQQALNYVGKRVKTIRRAGAAKLSVLQEG--IEAI 329

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
               +    V  L      L    +A  +V        ++  D +  K LE         
Sbjct: 330 ATTVIAHITVADLQFREKALYIATMARRVVMTMHNPKMVDDRDYVGNKRLELAGQLMSLL 389

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              L+    ++     + ++   ++  + DALL I                   +   + 
Sbjct: 390 FEDLFKKFNSDFKANIDKILKKPSRTSEFDALLSINIHSNN----ITMGLNRAISTGNWS 445

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK---GTIDDIDNL 459
             ++ +   G   +  RL+  +   +            K+           G +   D  
Sbjct: 446 LKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTSDTP 505

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
                  V  +      +     E  I++    +  ++++  D        +       +
Sbjct: 506 EGEACGLVKNLALMT-HITTDDEEAPIRKLCYVLGCENILGIDSATLHSQGNFGIYLNGT 564

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
                +         +T  RR        + R     E   ++   +       T  G  
Sbjct: 565 ----LIGTSRFPSKFVTDFRR--------LRRTGKISEFVSIYTNTHQTAVHIATDGGRI 612

Query: 580 IGL---VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                 V +     +      +        D      V YL   EE +  IA        
Sbjct: 613 CRPLIIVKNNEPMVKAEHLLKLRQGEWAFDDFLSHGLVEYLDVNEENDSLIA-------- 664

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                          E+ L P + +  ++  P  V+   A LIP+  ++ S R    C M
Sbjct: 665 -------------LYEKDLDPSQPVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAM 711

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                           I   +     + 
Sbjct: 712 GKQAIGA-----------------------------------------IAYNQFRRIDTL 730

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               +Y               Q+P+VK                 D   L  G+N  VA M
Sbjct: 731 LYFMVYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVM 766

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEE-------FEVMARDTKLGPEEITRDIPNVS 869
            + GY+ ED++++++  +         + +       +    +D   G        P   
Sbjct: 767 SYSGYDIEDALVLNKSSIDRGFGRCQVVRKNTIQLKRYPNHTKDIVSGMRVDEDGEPIFP 826

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
            +    +   G+  +GA V  G +   K  P      
Sbjct: 827 HKA---LGPDGLGEIGARVENGQVYANKFVPTNAGES 860


>gi|153958228|gb|ABS53404.1| RpoB [Bacteriovorax sp. JS10]
          Length = 338

 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 161/341 (47%), Positives = 222/341 (65%), Gaps = 10/341 (2%)

Query: 728  VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
             AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK GD 
Sbjct: 1    FAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEGDI 58

Query: 788  VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE F
Sbjct: 59   VVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIEAF 118

Query: 848  EVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
            E+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ ++
Sbjct: 119  EIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQLS 178

Query: 908  PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELL 967
            PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL
Sbjct: 179  PEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLL 238

Query: 968  ARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQ 1020
             RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P   
Sbjct: 239  RRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPFEL 298

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                 +Q  +++  +           + +  +  ++I K+ 
Sbjct: 299  IGYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLH 338


>gi|158252952|gb|ABW23960.1| RNA polymerase beta subunit [Pantoea terrea]
 gi|158252966|gb|ABW23967.1| RNA polymerase beta subunit [Pantoea terrea]
 gi|158253036|gb|ABW24002.1| RNA polymerase beta subunit [Tatumella ptyseos]
 gi|169667021|gb|ACA64041.1| RpoB [Pantoea terrea]
 gi|169667023|gb|ACA64042.1| RpoB [Pantoea terrea]
          Length = 212

 Score =  220 bits (560), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LD+DG F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDDDGRFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|66517310|ref|XP_625037.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2 isoform 1
            [Apis mellifera]
          Length = 1134

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 83/480 (17%), Positives = 158/480 (32%), Gaps = 92/480 (19%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +    A+      D+ D  +   + +        ++ R+     +R  +   
Sbjct: 730  NFDKLPAGQNATIAVMSYSGYDIEDALILNKASIDRGFGRCLVY-RNAKCTLKRYANQTY 788

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            ++I     D + ++ +    I         G+   +      KS+               
Sbjct: 789  DRIMGPLIDANTKKSVWKHEIIDSDGIAAPGEMVENRKVMVNKSSP-------------- 834

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
               A     V       + +Y+    + +      IEK+    +       ++K+ +   
Sbjct: 835  ---AANIGPVNSGNVQTQTEYKDVPVVFKGPVPAYIEKVMISSNAEDAF--LIKLLLRQT 889

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  + GDK +                                     SR           
Sbjct: 890  RRPEIGDKFS-------------------------------------SR----------- 901

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                   G+K    +   + +   +      + ++       +++      +L       
Sbjct: 902  ------HGQKGVVGLIVEQEDMPFNDYGICPDMIMNPHGFPSRMTVGKLIELLAGKAGVI 955

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             G       F G+  E + + L     +  G+   Y G+TGEP    +  G +Y  KL H
Sbjct: 956  KGEFHYGTAFGGSKVEDVCAELVKHGFNYLGKDFFYSGITGEPLQAYIYSGPVYYQKLKH 1015

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK++AR+ G  +++T+QP GG++  GG RLGEME  C+  YGA+ +L E L I SD 
Sbjct: 1016 MVQDKMHARARGPRAVLTRQPTGGRAKEGGLRLGEMERDCLIGYGASMMLIERLMISSDA 1075

Query: 1321 ---DVVGR--TRVYESIVAG--------NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               DV  +     Y     G        +       P +  +L +E+Q++ +   L    
Sbjct: 1076 FDIDVCNKCGLMAYS----GWCHSCRSSSCVSTISMPYACKLLFQELQSMNIVPRLTLKN 1131



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 118/946 (12%), Positives = 270/946 (28%), Gaps = 226/946 (23%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++    S+++F+ + I    + NE          P+        +++++     P    
Sbjct: 41  LVKQHIDSFNYFINVEIKKIVKANE---KVLSDADPL------FYVKYLNVHVGLPDVEE 91

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RDL Y+ P+ + +  I          +  + I + ++ +G +P+M
Sbjct: 92  GFNVTRSTTPHECRLRDLNYSAPITVDIEYI----------RGHQPIIKNNLLIGRMPIM 141

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++ G +++++ Q                  
Sbjct: 142 LRSSNCVLTGKSHFELAKMNECPHDPGGYFIVNGQEKVILIQEQ---------------- 185

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDII-----HVRIDRRRK------------------ 211
               +   RII        +E DSK  I      V  +R+ K                  
Sbjct: 186 ----MLRNRII--------LEEDSKGCIVASCNSVTHERKTKTNIVGRAGRYYMRHNIFQ 233

Query: 212 --VPVTSFLMALGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
             +PVT    A+G+   +EI+     +  + ++           ++    +    L +  
Sbjct: 234 DDIPVTIIFKAMGIVSDQEIMQLIGTEEEFMKKFAPSLEECHVLNVFAQNQALRFLSNKR 293

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGI------TSDCLCGLYVAEDIVNGETGEIYI 322
             ++       +T  +  +L    +  + +             L + + +     G++  
Sbjct: 294 KQKRFSVIKSSITDEMKDALATNILSHVPVIDFNFKMKATYIALMIRKVMKAQSDGKLVD 353

Query: 323 EAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
           +     +++            + +++ D      +    +        K A  DI + MR
Sbjct: 354 DRDYYGNKRL-----ELAGSLLSLMFEDLFKRFNWELKQIADKNIPKIKAAQFDIVKHMR 408

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
             D  T  +A ++ +  +         T+ R KM           + +I    ++  +  
Sbjct: 409 Q-DQITNGLAFAISSGNW---------TIKRFKMERHGVTQVLSRLSYISALGMMTRVNS 458

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
             +          +       +    +  + +    +  +           +   +    
Sbjct: 459 QFEKTRKVSGPRSLQPSQWG-MLCPSDTPEGEGCGLVKNLALMTHITTEIDEEPIIRLAF 517

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            +  + V     E   +  +  +  + N L  + + +RL  + +  + R         ++
Sbjct: 518 NLGVENVNILGGEEINNKNVYMVFLNGNILGIVKNYQRLVNVFRL-LRRKGLINGFVSIY 576

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSA 619
             H  R     +  G        + +     +      +E   R   D      + YL  
Sbjct: 577 TQHQHRCIQISSDGGRLCRPYIIVQNGDPLVQEEHVKLLEQGIRSFEDFLQDGLIEYLDV 636

Query: 620 MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            EE +  IA   S ++                       EK   ++  P  ++ + A L+
Sbjct: 637 NEENDSSIAFNESHIN-----------------------EKTTHLEIEPFTLLGVCAGLV 673

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           P+  ++ S R    C M +QA+  +         G                         
Sbjct: 674 PYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRID----------------- 707

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                                            N    Q P+VK                
Sbjct: 708 -----------------------------TLMYNLVYPQTPMVKS----------RTIEL 728

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
            +   L  G+N  +A M + GY+ ED++++++  +       +     +   +       
Sbjct: 729 INFDKLPAGQNATIAVMSYSGYDIEDALILNKASIDRGFGRCLVYRNAKCTLKRYANQTY 788

Query: 860 EITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           +             S    + ID  GI   G  V    ++V K +P
Sbjct: 789 DRIMGPLIDANTKKSVWKHEIIDSDGIAAPGEMVENRKVMVNKSSP 834


>gi|288188620|gb|ADC42769.1| RNA polymerase beta subunit [Pantoea allii]
          Length = 212

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D SP
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|224797497|gb|ACN62778.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
            simulans]
          Length = 373

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 147/318 (46%), Positives = 215/318 (67%), Gaps = 8/318 (2%)

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            NDD+NR LMG NMQRQA+PL+   +P+VGTG+E   A+ SG AIV++  G ++ VDA RI
Sbjct: 1    NDDANRALMGANMQRQAIPLISPNSPYVGTGVEYAAARDSGLAIVSQYDGSIDYVDATRI 60

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            V+++ E        G+  Y L  F RSNQ T +   PLVK G +V +  ++ADGPS D G
Sbjct: 61   VLKTKE--------GLKNYNLDTFVRSNQGTSLTHVPLVKQGQKVEKGQVLADGPSIDKG 112

Query: 804  DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            +LALG+N++VAF  W+GYN+ED++++SER+VSEDVFTSIHIEE+ +  R TK G EEITR
Sbjct: 113  ELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVFTSIHIEEYTIERRQTKQGGEEITR 172

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
            +IPN+SE   K +D+ G++ +G EV PGDILVGK+TPKG++ ++PE+KLL+AIFGEK+ +
Sbjct: 173  EIPNISENARKFLDDDGLVIIGTEVKPGDILVGKVTPKGQTQLSPEDKLLQAIFGEKSKN 232

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
            V+D SLRVP+G  G +  ++ F R   + +   + V +  I    + ++ +++       
Sbjct: 233  VKDNSLRVPNGGEGIIQAIKRFPREKYELSVDVLEVIKIYIVQKRKIQEGDKMAGRHGNK 292

Query: 984  SRLMEILCGQNAVSGPKG 1001
              + +IL  ++      G
Sbjct: 293  GVISKILPLEDMPHMEDG 310



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 81/293 (27%), Positives = 135/293 (46%), Gaps = 14/293 (4%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++  G +V  G +L    +   +  +   + ++ A       +  D  +     VS  V 
Sbjct: 90   LVKQGQKVEKGQVLADGPS-IDKGELALGQNVVVAFTTWNGYNYEDAIIVSERLVSEDVF 148

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                   + I++ +     E    E+    ++  + + D  +      ++ G     G  
Sbjct: 149  TSIHIEEYTIERRQTKQGGEEITREIPNISENARKFLDDDGL------VIIGTEVKPGDI 202

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T      +S   +     F  + + V+ N   +    E     ++   + K E  
Sbjct: 203  LVGKVTPKGQTQLSPEDKLLQAIFGEKSKNVKDNSLRVPNGGEGIIQAIKRFPREKYE-- 260

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +   VL V+K+++  KR IQ GDKMAGRHGNKG++S+ILP EDMP ++DGTP+DI
Sbjct: 261  -----LSVDVLEVIKIYIVQKRKIQEGDKMAGRHGNKGVISKILPLEDMPHMEDGTPIDI 315

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +LNPLGVPSRMN+GQ+ E HLG A   LG+K+ + + D   N ++  +     
Sbjct: 316  MLNPLGVPSRMNIGQVLEIHLGMAAKKLGQKVSTPVFDGMTNEELIEIMEKAN 368


>gi|126143375|gb|ABN80112.1| RNA polymerase beta-subunit [Prevotella nanceiensis]
 gi|126143386|gb|ABN80113.1| RNA polymerase beta-subunit [Prevotella nanceiensis]
          Length = 126

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 72/180 (40%), Positives = 88/180 (48%), Gaps = 54/180 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN               LG+  ++++                          
Sbjct: 1    NPLGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA  E ++     A L     + LYDG TG
Sbjct: 21   --------------AAGKKLGVKFATPIFDGAKLEDLSEWTEKAGLPHLCSTHLYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW +
Sbjct: 67   EQFDQPATVGVTYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAL 126


>gi|37784150|gb|AAO83544.1| DNA-directed RNA polymerase beta subunit [Hydrogenobacter
            hydrogenophilus]
          Length = 286

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 128/286 (44%), Positives = 180/286 (62%), Gaps = 7/286 (2%)

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
            GYNFED+++ISER+V EDVFTSIHIEE EV AR+TK+G EEITR IP V E  L ++DE 
Sbjct: 1    GYNFEDAIVISERLVKEDVFTSIHIEELEVEARETKIGYEEITRSIPGVPERALAHLDEF 60

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            GI+ +G  V PGDILVGK+TPKGE  +TPEEKLL+AIFGEK+ DV+DTSLR P GV G V
Sbjct: 61   GIVRIGTYVKPGDILVGKVTPKGEQQLTPEEKLLQAIFGEKSRDVKDTSLRCPPGVEGVV 120

Query: 940  VDVRIFNRH-GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            VDV++F R  G  +N  +  VER++ E L  + + ++ +L     S +  ++ G+     
Sbjct: 121  VDVQVFARKVGERRNYLAEHVERQEKENLRNELEKKKRLLVEGRNSVIKSLVLGRETSKD 180

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFA------VQDEKVQRNVESLKVQYETSKSILEDR 1052
                KK+    + +  +                  D+++   +  ++ + +    +LE  
Sbjct: 181  ITIKKKTYKAGTKVDEKTFEVLLNYIVAKPENLFDDKELCEKINQVRERTKAQVELLERI 240

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            ++ K E I    ++P GV+ +VKV++A KR I+ GDKMAGRHGNKG
Sbjct: 241  YREKEESIGKRSELPAGVIALVKVYIAQKRKIKVGDKMAGRHGNKG 286


>gi|68131860|gb|AAY85208.1| RNA polymerase II second largest subunit [Euptelea polyandra]
          Length = 874

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 121/911 (13%), Positives = 261/911 (28%), Gaps = 170/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +           + + +E   +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCE--EVTETQEFTKVFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 GEVR----SMAESQNRPPSSMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L      +  G+         D      + Y+   EEE   I+     
Sbjct: 529 QRLLIKKKDIRALQQRESPDDGGW--------HDLVAKGFIEYVDTEEEETTMISM---- 576

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +L+  R   E      E     +  P  ++ + AS+IPF +++ S R    
Sbjct: 577 ------TINDLITARINPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 628

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +                           R   +  V               
Sbjct: 629 SAMGKQAMGIYVTNYQL--------------------RMDTLAYV--------------- 653

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 654 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 683

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 684 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGM 743

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +                     RD S
Sbjct: 744 RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQEES--------QGQASSRYTRRDHS 795

Query: 929 LRVPSGVSGTV 939
             +    SG V
Sbjct: 796 TSLRHSESGMV 806



 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 118/794 (14%), Positives = 238/794 (29%), Gaps = 116/794 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  +   L+K +            +   G        G +E VD             +
Sbjct: 523  LFIVEKQRLLIKKKDIRALQ---QRESPDDGGWHDLVAKGFIEYVDTEE----------E 569

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
             +T        +   R N     +                    PS  LG       +  
Sbjct: 570  ETTMISMTINDLITARINPEEAYS-----------ETYTHCEIHPSLILG-------VCA 611

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   I++  ++                         
Sbjct: 612  SIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------- 644

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 645  --LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 702

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ ++  ++ +E      R+          +          G 
Sbjct: 703  SIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGT 761

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T                  A ++ + Q +    +  + TS    E   
Sbjct: 762  RVSGEDVIIGKTTP----------------IAQEESQGQASSRYTRRDHSTSLRHSESGM 805

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 806  VDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 860

Query: 1114 DGTPVDIVLNPLGV 1127
            +G   DI++NP  +
Sbjct: 861  EGITPDIIVNPHAI 874


>gi|153958224|gb|ABS53402.1| RpoB [Bacteriovorax sp. PS22S]
          Length = 337

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 161/340 (47%), Positives = 222/340 (65%), Gaps = 10/340 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK GD V
Sbjct: 1    AKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEGDIV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE FE
Sbjct: 59   VKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIEAFE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            + ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ ++P
Sbjct: 119  IEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  LL 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETTLLR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P    
Sbjct: 239  RDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                +Q  +++  +           + +  +  ++I K+ 
Sbjct: 299  GYLPLQ-AELEEKLSEYFADIRNRINRVRQKTTDEIAKLH 337


>gi|172383|gb|AAB59324.1| RNA polymerase III [Saccharomyces cerevisiae]
          Length = 1149

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 89/491 (18%), Positives = 163/491 (33%), Gaps = 87/491 (17%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             L+           T E      +   +   V   S          V++    +R     
Sbjct: 726  YLMTYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRC 785

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              R  +        + +   +    +   +          Q+   GP G     V     
Sbjct: 786  ETRRKTT------TVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPDGL--GEVGMKVQ 837

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   ++       D     NV  ++ QY  +  I      + I+++     +      
Sbjct: 838  SGQIYINKSVPTNSADAPNPNNVN-VQTQYREAPVIYRGPEPSHIDQVMM--SVSDNDQA 894

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +   R  + GDK +                                     SR  
Sbjct: 895  LIKVLLRQNRRPELGDKFS-------------------------------------SR-- 915

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                            G+K    I   + +   +      + ++       +++      
Sbjct: 916  ---------------HGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKMIE 960

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE     +  G
Sbjct: 961  LISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L 
Sbjct: 1021 PIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLL 1080

Query: 1313 EMLTIKSD----DVVGR------------TRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            E L I SD    DV  +             +  E+I+          P +  +L +E+ +
Sbjct: 1081 ERLMISSDAFEVDVCDKCGLMGYSGWCTTCKSAENIIK------MTIPYAAKLLFQELLS 1134

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 1135 MNIAPRLRLED 1145



 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 118/984 (11%), Positives = 276/984 (28%), Gaps = 187/984 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L++    S+++F+  ++    + N   Q     V P         L++V           
Sbjct: 57  LVKQHLDSFNYFVDTDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGKKSSSS 107

Query: 88  -------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT- 139
                    +C  RD+TY+ P+ + +             +    I  + + +G +P+M  
Sbjct: 108 TKDYLTPPHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKDVEIGRMPIMLR 157

Query: 140 -----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F++ G +++++ Q   S          +  +  
Sbjct: 158 SNKCILYDADESKMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKEGIVQ 217

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYP 234
             + +     ++             I+++ +    ++P+   L A G+ S+ EI+     
Sbjct: 218 ASVTSST--HERKSK-TYVITKNGKIYLKHNSIAEEIPIAIVLKACGILSDLEIMQLVCG 274

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
                Q         S+   +   + +   +        +++ ++    +L+   E    
Sbjct: 275 NDSSYQDIFAVNLEESSKLDIYTQQQALEYIGAK-----VKTMRRQKLTILQEGIEAIAT 329

Query: 295 FL--GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            +   +T + L     A  I       +        + K +++  +   + + +      
Sbjct: 330 TVIAHLTVEALDFREKALYIAMMTRRVVMAM----YNPKMIDDRDYVGNKRLEL------ 379

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I         K   D  L I +V++  + +    A    N    +        + 
Sbjct: 380 -AGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALLSINVHSNNITSGLNRAIS 438

Query: 413 RVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               +++        V H    +     + ++  +         +     L   +   + 
Sbjct: 439 TGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLC 498

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                +     L    ++   I++ D +  + +       +         S+ L      
Sbjct: 499 TADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCY---VLGVEDITLIDSASLHLNYGV 555

Query: 529 VNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI-GLVSS 585
             + + I   R  +        + R     E   ++   +       T  G     L+  
Sbjct: 556 YLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVHIATDGGRICRPLIIV 615

Query: 586 LTSFARVNAYG--FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
               +RV       +        D      V YL   EE + YIA           + ++
Sbjct: 616 SDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLDVNEENDSYIAL----------YEKD 665

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V                  ++  P  ++   A LIP+  ++ S R    C M +QA+  
Sbjct: 666 IVPSM-------------THLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIG- 711

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                    I   +     +   +  Y 
Sbjct: 712 ----------------------------------------AIAYNQFKRIDTLLYLMTYP 731

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+P+VK                 D   L  G+N  VA M + GY+ 
Sbjct: 732 --------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDI 767

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDEC 879
           ED++++++  +           +   + +      ++    +  D         +++   
Sbjct: 768 EDALVLNKSSIDRGFGRCETRRKTTTVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPD 827

Query: 880 GIICVGAEVNPGDILVGKITPKGESP---------MTPEEKLLRAIFGEKAVDVRDTSLR 930
           G+  VG +V  G I + K  P   +           T   +      G +   +    + 
Sbjct: 828 GLGEVGMKVQSGQIYINKSVPTNSADAPNPNNVNVQTQYREAPVIYRGPEPSHIDQVMMS 887

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNE 954
           V       +  +   NR     ++
Sbjct: 888 VSDNDQALIKVLLRQNRRPELGDK 911


>gi|6324781|ref|NP_014850.1| Ret1p [Saccharomyces cerevisiae S288c]
 gi|2507350|sp|P22276|RPC2_YEAST RecName: Full=DNA-directed RNA polymerase III subunit RPC2; Short=RNA
            polymerase III subunit C2; AltName: Full=C128; AltName:
            Full=DNA-directed RNA polymerase III 130 kDa polypeptide
 gi|1420485|emb|CAA99422.1| RPC128 [Saccharomyces cerevisiae]
 gi|151945297|gb|EDN63540.1| RNA polymerase C [Saccharomyces cerevisiae YJM789]
 gi|256269629|gb|EEU04911.1| Ret1p [Saccharomyces cerevisiae JAY291]
 gi|259149688|emb|CAY86492.1| Ret1p [Saccharomyces cerevisiae EC1118]
 gi|285815086|tpg|DAA10979.1| TPA: Ret1p [Saccharomyces cerevisiae S288c]
          Length = 1149

 Score =  220 bits (560), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 89/491 (18%), Positives = 163/491 (33%), Gaps = 87/491 (17%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             L+           T E      +   +   V   S          V++    +R     
Sbjct: 726  YLMTYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRC 785

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              R  +        + +   +    +   +          Q+   GP G     V     
Sbjct: 786  ETRRKTT------TVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPDGL--GEVGMKVQ 837

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +   ++       D     NV  ++ QY  +  I      + I+++     +      
Sbjct: 838  SGQIYINKSVPTNSADAPNPNNVN-VQTQYREAPVIYRGPEPSHIDQVMM--SVSDNDQA 894

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            ++KV +   R  + GDK +                                     SR  
Sbjct: 895  LIKVLLRQNRRPELGDKFS-------------------------------------SR-- 915

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                            G+K    I   + +   +      + ++       +++      
Sbjct: 916  ---------------HGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKMIE 960

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE     +  G
Sbjct: 961  LISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFG 1020

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L 
Sbjct: 1021 PIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLL 1080

Query: 1313 EMLTIKSD----DVVGR------------TRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            E L I SD    DV  +             +  E+I+          P +  +L +E+ +
Sbjct: 1081 ERLMISSDAFEVDVCDKCGLMGYSGWCTTCKSAENIIK------MTIPYAAKLLFQELLS 1134

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 1135 MNIAPRLRLED 1145



 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 118/984 (11%), Positives = 276/984 (28%), Gaps = 187/984 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L++    S+++F+  ++    + N   Q     V P         L++V           
Sbjct: 57  LVKQHLDSFNYFVDTDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGKKSSSS 107

Query: 88  -------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT- 139
                    +C  RD+TY+ P+ + +             +    I  + + +G +P+M  
Sbjct: 108 TKDYLTPPHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKDVEIGRMPIMLR 157

Query: 140 -----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F++ G +++++ Q   S          +  +  
Sbjct: 158 SNKCILYDADESKMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKGIVQ 217

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYP 234
             + +     ++             I+++ +    ++P+   L A G+ S+ EI+     
Sbjct: 218 ASVTSST--HERKSK-TYVITKNGKIYLKHNSIAEEIPIAIVLKACGILSDLEIMQLVCG 274

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
                Q         S+   +   + +   +        +++ ++    +L+   E    
Sbjct: 275 NDSSYQDIFAVNLEESSKLDIYTQQQALEYIGAK-----VKTMRRQKLTILQEGIEAIAT 329

Query: 295 FL--GITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSV 352
            +   +T + L     A  I       +        + K +++  +   + + +      
Sbjct: 330 TVIAHLTVEALDFREKALYIAMMTRRVVMAM----YNPKMIDDRDYVGNKRLEL------ 379

Query: 353 NNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I         K   D  L I +V++  + +    A    N    +        + 
Sbjct: 380 -AGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALLSINVHSNNITSGLNRAIS 438

Query: 413 RVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               +++        V H    +     + ++  +         +     L   +   + 
Sbjct: 439 TGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLC 498

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                +     L    ++   I++ D +  + +       +         S+ L      
Sbjct: 499 TADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCY---VLGVEDITLIDSASLHLNYGV 555

Query: 529 VNSLSRITHTRRLSAL--GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI-GLVSS 585
             + + I   R  +        + R     E   ++   +       T  G     L+  
Sbjct: 556 YLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVHIATDGGRICRPLIIV 615

Query: 586 LTSFARVNAYG--FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
               +RV       +        D      V YL   EE + YIA           + ++
Sbjct: 616 SDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLDVNEENDSYIAL----------YEKD 665

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           +V                  ++  P  ++   A LIP+  ++ S R    C M +QA+  
Sbjct: 666 IVPSM-------------THLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIG- 711

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                    I   +     +   +  Y 
Sbjct: 712 ----------------------------------------AIAYNQFKRIDTLLYLMTYP 731

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+P+VK                 D   L  G+N  VA M + GY+ 
Sbjct: 732 --------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDI 767

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDEC 879
           ED++++++  +           +   + +      ++    +  D         +++   
Sbjct: 768 EDALVLNKSSIDRGFGRCETRRKTTTVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPD 827

Query: 880 GIICVGAEVNPGDILVGKITPKGESP---------MTPEEKLLRAIFGEKAVDVRDTSLR 930
           G+  VG +V  G I + K  P   +           T   +      G +   +    + 
Sbjct: 828 GLGEVGMKVQSGQIYINKSVPTNSADAPNPNNVNVQTQYREAPVIYRGPEPSHIDQVMMS 887

Query: 931 VPSGVSGTVVDVRIFNRHGIDKNE 954
           V       +  +   NR     ++
Sbjct: 888 VSDNDQALIKVLLRQNRRPELGDK 911


>gi|269912628|emb|CAY86094.1| RNA polymerase beta subunit [Gluconobacter cerinus]
          Length = 250

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 108/253 (42%), Positives = 151/253 (59%), Gaps = 28/253 (11%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------- 221
           SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL             
Sbjct: 1   SGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYIAQREEKI 60

Query: 222 ------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                       GMD +EILS FY  + +++ GD W  P    D   G K+ S LVD DT
Sbjct: 61  AEGGDVEGLDIRGMDQDEILSYFYDMVTFTRMGDGWARPFEP-DAFRGQKLLSPLVDADT 119

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE V E+  KLT+ +++ + EK  + + +    + G Y+A D++N  TGEIY EAG+ + 
Sbjct: 120 GEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDVLGCYLAHDLINENTGEIYGEAGEELT 178

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E  L  +    I ++P L +D  ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T 
Sbjct: 179 EDRLAALEELGITELPTLSIDG-SHGPWIRNTLSVDKNTSRDEALIDIYRIMRPGEPPTK 237

Query: 390 SVAESMFNFLFFD 402
             AE+MF  LFFD
Sbjct: 238 ETAEAMFRGLFFD 250


>gi|158252866|gb|ABW23917.1| RNA polymerase beta subunit [Erwinia sp. BCC003]
          Length = 212

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD+DG F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDDGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|284162088|ref|YP_003400711.1| RNA polymerase Rpb2 domain 6 [Archaeoglobus profundus DSM 5631]
 gi|284012085|gb|ADB58038.1| RNA polymerase Rpb2 domain 6 [Archaeoglobus profundus DSM 5631]
          Length = 603

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 99/612 (16%), Positives = 200/612 (32%), Gaps = 101/612 (16%)

Query: 779  RPLVKVGD--EVRRNDIIADGP----STDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +PLV   D  +++R +I           +  D     N  +A            + +   
Sbjct: 70   KPLVTEKDIEKLKRGEITFYDLVKQGKIEFLDAEEEENAYIAVNEEDLTPEHTHLELDPS 129

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            +++     SI   E+    R+T      + +    +    L    +     +        
Sbjct: 130  LIAGICLGSIPYPEYNASPRNTMGAA--MIKQSLGLPYSSLHWRTDTRG-HLMHYPQIPI 186

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            +                +  + A+   +  ++ D  +   + V   +     F R    +
Sbjct: 187  VTTDTQKEIRFDERPAGQNFVVAVLSYEGYNIEDAIILNKASVDRGLARTHFF-RTYEAE 245

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
              R    + ++ E+   D  D +        +   + L       GP             
Sbjct: 246  ELRYPGGQEDRFEIPPSDVADYRGA--EAYKNLDEDGLIFPETEVGPDDVLIGRTSPPRF 303

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + E       Q   +     R+ E         K I++  F                  +
Sbjct: 304  LEEPTLGISPQKRRESSITMRSNE---------KGIVDAVFL----------MQSESGSK 344

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            + KV V   R  +         G+K                               SR  
Sbjct: 345  LAKVRVRDLRIPEI--------GDK-----------------------------FASR-- 365

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                            G+K    +   + +   +      + +I   +   +++      
Sbjct: 366  ---------------HGQKGVVGLIVPEEDMPWTESGIVPDMIINPHAIPSRMTVGHILE 410

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            ++        G  V   +F G  E+ +  +L+      +G+ ++YDG+TG+ F+  + VG
Sbjct: 411  MIGGKVGCLEGRRVDGTIFHGEKEKDLREVLKKYGFVHTGKEVMYDGITGKRFEVDIFVG 470

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             IY  KL HMV++K++ARS G   ++T+QP  G++ +GG RLGEME   +  +GAA +L+
Sbjct: 471  VIYYQKLYHMVANKIHARSRGPVQILTRQPTEGRARKGGLRLGEMERDVLIGHGAALLLK 530

Query: 1313 EMLTIKSDDV-------VGRTRVYE-------SIVAGN--DTFETGTPESFNVLVKEMQA 1356
            + L  +SD V        G    Y+         V  +    ++     +F +L+ E+++
Sbjct: 531  DRLLEESDKVEVWVCAKCGHVATYDYRRNTAYCHVCEDDSHVYKVEMSYAFKLLLDELKS 590

Query: 1357 LGLSIDLENSRT 1368
            + ++  L     
Sbjct: 591  MLIAPRLILGDK 602



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 63/351 (17%), Positives = 105/351 (29%), Gaps = 101/351 (28%)

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           D      + +L A EEEN YIA     L  +                          ++ 
Sbjct: 90  DLVKQGKIEFLDAEEEENAYIAVNEEDLTPEH-----------------------THLEL 126

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
            P  +  I    IP+ E + S R  MG  M +Q++ L  +   +                
Sbjct: 127 DPSLIAGICLGSIPYPEYNASPRNTMGAAMIKQSLGLPYSSLHW---------------- 170

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
                                       +   +  Y               Q P+V    
Sbjct: 171 -------------------------RTDTRGHLMHYP--------------QIPIV---- 187

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +   G+N +VA + + GYN ED++++++  V   +  +     
Sbjct: 188 ------TTDTQKEIRFDERPAGQNFVVAVLSYEGYNIEDAIILNKASVDRGLARTHFFRT 241

Query: 847 FEVMARDTKLGPEEITRDIP-----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +E        G E+     P         E  KN+DE G+I    EV P D+L+G+ +P 
Sbjct: 242 YEAEELRYPGGQEDRFEIPPSDVADYRGAEAYKNLDEDGLIFPETEVGPDDVLIGRTSPP 301

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                           G      R++S+ + S   G V  V +       K
Sbjct: 302 RFLEEPT--------LGISPQKRRESSITMRSNEKGIVDAVFLMQSESGSK 344


>gi|157704384|gb|ABV68883.1| RpoB [Candidatus Liberibacter asiaticus]
          Length = 141

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 140/140 (100%), Positives = 140/140 (100%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTK 140
           SIKDIKEQSIYMGDLPLMTK
Sbjct: 121 SIKDIKEQSIYMGDLPLMTK 140


>gi|304334223|gb|ADM25189.1| RNA polymerase beta subunit [Cupriavidus sp. tpig.6a]
 gi|304334225|gb|ADM25190.1| RNA polymerase beta subunit [Cupriavidus sp. tpud28.1]
 gi|304334227|gb|ADM25191.1| RNA polymerase beta subunit [Cupriavidus sp. mapud4.3]
 gi|304334241|gb|ADM25198.1| RNA polymerase beta subunit [Cupriavidus sp. tpud31.3]
 gi|304334263|gb|ADM25209.1| RNA polymerase beta subunit [Cupriavidus sp. ip2.14]
 gi|304334271|gb|ADM25213.1| RNA polymerase beta subunit [Cupriavidus sp. mip15]
 gi|304334273|gb|ADM25214.1| RNA polymerase beta subunit [Cupriavidus sp. ip2.89]
 gi|304334275|gb|ADM25215.1| RNA polymerase beta subunit [Cupriavidus sp. mip2]
 gi|304334287|gb|ADM25221.1| RNA polymerase beta subunit [Cupriavidus sp. myp8]
 gi|304334289|gb|ADM25222.1| RNA polymerase beta subunit [Cupriavidus sp. mym10]
          Length = 219

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 126/219 (57%), Positives = 163/219 (74%), Gaps = 2/219 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D DG+ T+ELV
Sbjct: 61  LALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDADGNLTDELV 120

Query: 646 FCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 SAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPC 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R
Sbjct: 181 LRPDKPLVGTGIERTVAVDSGTAVQAMRGGVVDYVDAMR 219


>gi|327133517|gb|AEA29763.1| RNA polymerase subunit B [Acinetobacter sp. 13N3]
          Length = 200

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 87/203 (42%), Positives = 122/203 (60%), Gaps = 4/203 (1%)

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F 
Sbjct: 1    MSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKFA 60

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K+  GD++  GVL+VVKV++A KR IQ GDKMAGRHGNKG+VS ILP EDMP   +
Sbjct: 61   EKKRKLSTGDELTTGVLKVVKVYLAEKRHIQPGDKMAGRHGNKGVVSNILPVEDMPHDAN 120

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR FL+K
Sbjct: 121  GVPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLDK 177

Query: 1175 VIGT-GSHTEKISDYDDDSVLRV 1196
            +    G   E++    DD VL +
Sbjct: 178  IYNKGGGEQEELETLTDDEVLIL 200


>gi|258562150|gb|ACV81797.1| RNA polymerase II second largest subunit [Sebacina incrustans]
          Length = 581

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 104/637 (16%), Positives = 190/637 (29%), Gaps = 101/637 (15%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 36   GVSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQAC 91

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV +L   A ++   +       + +  + +         EEN   A   + +  +G +
Sbjct: 92   GLVKNLALMACISVGSYSAPVGEFLDEWGLESL--------EENAQAATPCTKVFVNGVW 143

Query: 641  ----------TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                         L   R   +         D  +   +          P    +D   +
Sbjct: 144  MGVHRDPAALVRTLKKLRRNEDLNPEVSVVRDIREKELRIYTDSGRVCRPLFVVNDGKLL 203

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            +   ++ + A       +  +  G+  ++       ++                      
Sbjct: 204  IQKEHVMKIAEKQGYGWSDLIHDGVIELLDAEEEETVM--------------------IC 243

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                           ++          QR  VK   +          PS  LG       
Sbjct: 244  MSPEDLEAARTQADTQYHTEIAAPDPAQR--VKTVIKAHAWSHCEIHPSMILG------- 294

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            +  + +P+  +N          M  + +  S+             L   E   +I    +
Sbjct: 295  VCASIIPFPDHNQSPRNTYQSAMGKQAMGVSL----------SNFLLRMETMANILYYPQ 344

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            + L                        +       +   +  + AI      +  D+ + 
Sbjct: 345  KPLA-------------------TTRALEYLKFRELPAGQNAIVAILCYSGYNQEDSVIM 385

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
              S +   +    I+ +  +D  + +  +  E+ E  +R+        + +       I 
Sbjct: 386  NQSSIDRGLF-RSIYYKSYMDVEKTTGQIILEEFEKPSRENTLRMKHGNYDKLDDDGIIA 444

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G N +       K+  L                   +E  QR     +    T     E
Sbjct: 445  PGTNVIGEDILIGKTAPLPE---------------GSEELGQRKSTHTRRDVSTPLKSTE 489

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                + +        +     R VK+ V   R  Q GDK A RHG KG +      EDMP
Sbjct: 490  SGIVDHVIV-----SLNADGHRFVKIRVRSTRVPQIGDKFASRHGQKGTIGVTYRQEDMP 544

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            F  DG   D+V+NP  +PSRM +G + E  L      
Sbjct: 545  FTADGITPDLVINPHAIPSRMTIGHLVECLLSKVATL 581


>gi|194304390|gb|ACF41630.1| RNA polymerase beta subunit [Enterobacter cowanii]
 gi|194304392|gb|ACF41631.1| RNA polymerase beta subunit [Enterobacter cowanii]
 gi|194304394|gb|ACF41632.1| RNA polymerase beta subunit [Enterobacter cowanii]
 gi|194304396|gb|ACF41633.1| RNA polymerase beta subunit [Enterobacter cowanii]
 gi|194304398|gb|ACF41634.1| RNA polymerase beta subunit [Enterobacter cowanii]
          Length = 212

 Score =  219 bits (559), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F E+LV CR  GE  L   +++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFAEDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|158253032|gb|ABW24000.1| RNA polymerase beta subunit [Pantoea vagans]
          Length = 212

 Score =  219 bits (558), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD++R LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDAHRALMGANMQRQ 212


>gi|68131834|gb|AAY85195.1| RNA polymerase II second largest subunit [Callistemon subulatus]
          Length = 952

 Score =  219 bits (558), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 123/907 (13%), Positives = 266/907 (29%), Gaps = 162/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + + + V             +D+  Q +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVSMRVIKKGHDGEELTEPQDL--QKVFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVEEYCETKKAYYFGYIIH---RLLLCALGRRAEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N +  +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLPHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++       + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPVVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +    +    +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + +        ++   G  +       D      + Y+   EEE   I+         
Sbjct: 529 QRLLIKKKDIHALQLREGGPDDVG---WHDLVAKGFIEYIDTEEEETTMISM-------- 577

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 578 --TINDLVQARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 633

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +      F                    R   +  V                   
Sbjct: 634 KQAMGIYVTNYQF--------------------RMDTLAYV------------------- 654

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 655 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIAC 688

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 689 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGS 748

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +           A         RD S+ + 
Sbjct: 749 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------AQGQASRYSRRDHSISLR 799

Query: 933 SGVSGTV 939
              +G V
Sbjct: 800 HSETGIV 806



 Score =  201 bits (511), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 76/482 (15%), Positives = 130/482 (26%), Gaps = 84/482 (17%)

Query: 782  VKVGDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            V   D V +  I      +  +T +                          I   ++   
Sbjct: 551  VGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLNPEEAYSETYTHCEIHPSLILGV 610

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              + I   +     R+T             V+    +      +  V        +    
Sbjct: 611  CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRA 667

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +      + AI      +  D+ +   S +        +F R   D+ ++  
Sbjct: 668  MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMG 726

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
            ++ +E      R           +          G           K+T ++ D      
Sbjct: 727  TLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQD------ 780

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                            + +    +Y      +  R        Q         LR VKV 
Sbjct: 781  ----------------DAQGQASRYSRRDHSISLRHSETGIVDQVLLTTNADGLRFVKVR 824

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ 
Sbjct: 825  VRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLI 884

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  +G     +GK+                                              
Sbjct: 885  ECIMGKVAAHMGKEGD-------------------------------------------- 900

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYML 1257
                     +TP F     + I+  L        G   +Y+G TG      + +G  Y  
Sbjct: 901  ---------ATP-FTDVTVDNISKALHRCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQ 950

Query: 1258 KL 1259
            +L
Sbjct: 951  RL 952


>gi|145342329|gb|ABP64861.1| RpoB [Viridibacillus arenosi]
 gi|145342359|gb|ABP64876.1| RpoB [Viridibacillus arenosi]
          Length = 232

 Score =  219 bits (558), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 81/207 (39%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGVHMATPVFDGANEEDVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G                             
Sbjct: 193  -------------------ETMEEAGMNRDG----------------------------- 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            ++ILYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  KTILYDGRSGEPFDNRVSVGVMYMIKL 231



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+DE GII +GAEV+ GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDERGIIRIGAEVHDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 90


>gi|256858907|gb|ACV31763.1| RpoB [Corynebacterium pseudotuberculosis]
          Length = 148

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 68/176 (38%), Positives = 95/176 (53%), Gaps = 36/176 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G KI       +   +   L++  E +              
Sbjct: 1    RMNIGQVLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP---------- 44

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                        +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +
Sbjct: 45   ------------AGSLTATPVFDGATNEEVAGLLTNSRPNRDGDVMVDANGKAQLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 93   GEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 148


>gi|158252948|gb|ABW23958.1| RNA polymerase beta subunit [Pantoea punctata]
 gi|158252950|gb|ABW23959.1| RNA polymerase beta subunit [Pantoea punctata]
 gi|158252964|gb|ABW23966.1| RNA polymerase beta subunit [Pantoea punctata]
 gi|158252968|gb|ABW23968.1| RNA polymerase beta subunit [Pantoea punctata]
 gi|158252970|gb|ABW23969.1| RNA polymerase beta subunit [Pantoea punctata]
 gi|158252974|gb|ABW23971.1| RNA polymerase beta subunit [Pantoea punctata]
          Length = 212

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LD+DG F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDDDGQFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|304334219|gb|ADM25187.1| RNA polymerase beta subunit [Cupriavidus sp. mapud10.1]
 gi|304334221|gb|ADM25188.1| RNA polymerase beta subunit [Cupriavidus sp. mapud3.4]
 gi|304334233|gb|ADM25194.1| RNA polymerase beta subunit [Cupriavidus sp. mapud3.2]
 gi|304334235|gb|ADM25195.1| RNA polymerase beta subunit [Cupriavidus sp. tpud23.3]
 gi|304334237|gb|ADM25196.1| RNA polymerase beta subunit [Cupriavidus sp. mapud10.5]
 gi|304334239|gb|ADM25197.1| RNA polymerase beta subunit [Cupriavidus sp. tpud17.3]
 gi|304334251|gb|ADM25203.1| RNA polymerase beta subunit [Cupriavidus sp. cmp2]
 gi|304334257|gb|ADM25206.1| RNA polymerase beta subunit [Cupriavidus sp. cmp52]
 gi|304334259|gb|ADM25207.1| RNA polymerase beta subunit [Cupriavidus sp. cmp60]
 gi|304334261|gb|ADM25208.1| RNA polymerase beta subunit [Cupriavidus sp. cmp57]
 gi|304334265|gb|ADM25210.1| RNA polymerase beta subunit [Cupriavidus sp. ip2.35]
 gi|304334267|gb|ADM25211.1| RNA polymerase beta subunit [Cupriavidus sp. pp2.22]
 gi|304334269|gb|ADM25212.1| RNA polymerase beta subunit [Cupriavidus sp. pp2.75]
 gi|304334277|gb|ADM25216.1| RNA polymerase beta subunit [Cupriavidus sp. pp2.43]
 gi|304334281|gb|ADM25218.1| RNA polymerase beta subunit [Cupriavidus sp. mpp1.6]
 gi|304334283|gb|ADM25219.1| RNA polymerase beta subunit [Cupriavidus sp. mpp2.10]
 gi|304334285|gb|ADM25220.1| RNA polymerase beta subunit [Cupriavidus sp. mpp2.18]
 gi|304334291|gb|ADM25223.1| RNA polymerase beta subunit [Cupriavidus sp. mpp1.16]
 gi|304334293|gb|ADM25224.1| RNA polymerase beta subunit [Cupriavidus sp. mpp2.1]
 gi|304334295|gb|ADM25225.1| RNA polymerase beta subunit [Cupriavidus sp. mpp1.13]
 gi|304334297|gb|ADM25226.1| RNA polymerase beta subunit [Cupriavidus sp. mpp1.1]
 gi|304334299|gb|ADM25227.1| RNA polymerase beta subunit [Cupriavidus sp. mpp2.26]
          Length = 219

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 126/219 (57%), Positives = 163/219 (74%), Gaps = 2/219 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D DG+ T+ELV
Sbjct: 61  LALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDADGNLTDELV 120

Query: 646 FCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 SAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPC 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R
Sbjct: 181 LRPDKPLVGTGIERTVAVDSGTAVQAMRGGLVDYVDAMR 219


>gi|302307227|ref|NP_983821.2| ADL275Cp [Ashbya gossypii ATCC 10895]
 gi|299788898|gb|AAS51645.2| ADL275Cp [Ashbya gossypii ATCC 10895]
          Length = 1141

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 72/352 (20%), Positives = 131/352 (37%), Gaps = 76/352 (21%)

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +  ++ QY  +  I      + I+++     +      ++KV +   R  + GDK +   
Sbjct: 851  LNQVQSQYREAPIIYRAPEPSHIDQVMM--SVSDNDQALIKVLLRQNRRPELGDKFS--- 905

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
                                              SR                  G+K   
Sbjct: 906  ----------------------------------SR-----------------HGQKGVC 914

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             I   + +   +      + ++       +++      ++       +G       F G+
Sbjct: 915  GIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMLELVSGKAGVLNGTLEYGTCFGGS 974

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                ++ +L     + SG+ +LY G+TGE     V  G IY  KL HMV DK++AR+ G 
Sbjct: 975  QLADMSEILVNNGFNYSGKDMLYSGITGECLQAYVFFGPIYYQKLKHMVLDKMHARARGP 1034

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE 1330
             +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD    DV       +
Sbjct: 1035 RAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMLSSDAFEVDVCN-----K 1089

Query: 1331 SIVAG-----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
              + G               +   P +  +L +E+ ++ ++  L+      S
Sbjct: 1090 CGLMGYSGWCTSCKSAEHIIKMTIPYAAKLLFQELLSMNIAPRLKLEDVFQS 1141



 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 112/924 (12%), Positives = 263/924 (28%), Gaps = 173/924 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP----P 84
           L++    S+++F+ +++    + NE        V P         L++V           
Sbjct: 53  LVKQHLDSFNYFVDVDLKKIIKANE---MVLSDVDP------EFYLKYVDIRVGRRSNSS 103

Query: 85  KFD---VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT-- 139
           K D     +C  RD+TY+ P+ + +             +    +  + + +G +P+M   
Sbjct: 104 KIDMTPPHECRLRDMTYSAPIFVDIEYT----------RGRSIVLHKDVEIGKMPIMLRS 153

Query: 140 ----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK 177
                                   G F++ G +++++ Q   S          + ++   
Sbjct: 154 NKCILNGASEEVMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKAIVQA 213

Query: 178 LLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPK 235
            + +     ++     +     D I+++ +    +VP+   L A G+ S+ EI+      
Sbjct: 214 SVTSST--HERKSKTYVVT-KNDKIYLKHNSIAEEVPIVIVLKACGIVSDLEIMQLVCGN 270

Query: 236 IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKF 295
               Q      F  ++   +   + +   +                   +K+++ + +  
Sbjct: 271 DSSYQDIFAINFEEASKMNIYTQQQALEYIGTK----------------VKTIRRQKLTV 314

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN- 354
           L    + +    +A   V             ++  + +  I + ++ D      +     
Sbjct: 315 LQEGIEAIATTVIAHLTVEALDFREKALYVAMMTRRVIMAIHNPKMVDDRDYVGNKRLEL 374

Query: 355 -NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
               +         K   D    I +V++  + +    A    N    +        +  
Sbjct: 375 AGQLMSLLFEDLFKKFNNDFKASIDKVLKKPNRAEMYDALLSINVHSNNITSGLNRAIST 434

Query: 414 VKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
              +++        V H    +     + ++  +         +     L   +   +  
Sbjct: 435 GNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCT 494

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
               +     L    ++   I++ D +  +             + +         +  + 
Sbjct: 495 SDTPEGEACGLVKNLALMTHITTDDEEEPIKNLCYLLGVEDITLLDSASIHLNYGVYLNG 554

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL--- 586
             +       R     +  + R     E   ++   + +     T  G     +  +   
Sbjct: 555 TIIGTTRFPARFVNQFRL-LRRTGKVSEFISIYTNSHQKAVHIATDGGRICRPLIIVRNG 613

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            S         +     +  D      V YL   EE + YIA     ++E          
Sbjct: 614 KSMVTAGHLRRLLEGELQFDDFLKLGLVEYLDVNEENDSYIALYEKDIEEG--------- 664

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                            ++  P  V+   A LIP+  ++ S R    C M +QA+     
Sbjct: 665 --------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA--- 707

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                                                 I   +     +   + IY    
Sbjct: 708 --------------------------------------IAYNQFKRIDTLLYLMIYP--- 726

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+P+VK                 D   L  G+N  VA M + GY+ ED+
Sbjct: 727 -----------QQPMVKS----------KTIELIDYDKLPAGQNATVAVMSYSGYDIEDA 765

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDECGII 882
           ++I++  +          ++   + +      ++    +  D         +++   G+ 
Sbjct: 766 LVINKSSIDRGFGRCETRKKTTTILKRYPNHTQDIIGGMRVDENGEPIWQHQSLGPDGLG 825

Query: 883 CVGAEVNPGDILVGKITPKGESPM 906
            VG +V  G I + K  P   S  
Sbjct: 826 EVGMKVTSGQIYINKSIPTNASDS 849


>gi|11499471|ref|NP_070712.1| DNA-directed RNA polymerase subunit B' [Archaeoglobus fulgidus DSM
            4304]
 gi|3122770|sp|O28392|RPOB1_ARCFU RecName: Full=DNA-directed RNA polymerase subunit B'
 gi|2648657|gb|AAB89366.1| DNA-directed RNA polymerase, subunit B' (rpoB1) [Archaeoglobus
            fulgidus DSM 4304]
          Length = 604

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 94/616 (15%), Positives = 195/616 (31%), Gaps = 108/616 (17%)

Query: 779  RPLVKVG--DEVRRNDIIADGPS----TDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +PLV     +++++ ++  +        +  D     N  VA            + +   
Sbjct: 70   KPLVTPEHIEKIKKGELTIEDLVRQGLIEYLDAEEEENAYVAVYEHELTPEHTHLELDPS 129

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            ++      SI   E     R+T      + +    +    L    +      G  +    
Sbjct: 130  LIVGICTGSIPYAEHNASPRNTMGAA--MIKQSLGIPYSNLAWRTDTR----GHLMQHPQ 183

Query: 893  ILVGKITPKGE---SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
            + +     + E         +  + A+   +  ++ D  +     V    +    F R  
Sbjct: 184  VPIVTTDTQVEIKFDERPAGQNFVVAVLSYEGYNIEDALIMNKGSVERG-LGRSFFYRTY 242

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
              +  R    + ++ E+   D                   + G           +  ++ 
Sbjct: 243  ESEEMRYPGGQEDKFEIPGAD-------------------ISGFRGAEAYAHLDEDGLIF 283

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP- 1068
             +   E              +       L +  +  +        N+   +     M   
Sbjct: 284  PET--EVGPDDVLIGRTSPPRFLEEPTELGISPQKRRETSVTMRSNEKGVVDAVFLMQSE 341

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
            G  ++ KV V   R  +         G+K                               
Sbjct: 342  GGSKLAKVRVRDLRIPEL--------GDK-----------------------------FA 364

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SR                  G+K    +   + +   +      + +I   +   +++  
Sbjct: 365  SR-----------------HGQKGVVGLLVPEEDMPFTESGIVPDLIINPHAIPSRMTVG 407

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                ++        G  V   +F G  EE + + L+      +G+ ++YDG+TG  +   
Sbjct: 408  HVLEMIGGKVGSLEGRRVDGSLFHGESEEDLRATLKKYGFSHTGKEVMYDGITGRRYLVD 467

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + VG IY  KL HMVS K++ARS G   ++T+QP  G++ +GG R GEME   +  +GAA
Sbjct: 468  IFVGVIYYQKLYHMVSSKIHARSRGPVQVLTRQPTEGRARKGGLRFGEMERDVLIGHGAA 527

Query: 1309 YVLQEMLTIKSDD----VVG-----------RTRVYESIVAGN-DTFETGTPESFNVLVK 1352
             +L++ L  +SD     V G           R   Y  I     +  +     +F +L+ 
Sbjct: 528  LLLKDRLLEESDKVEVWVCGNCGHVATYDYRRNTAYCHICDDESNIHKVEMSYAFKLLLD 587

Query: 1353 EMQALGLSIDLENSRT 1368
            E++++ ++  +     
Sbjct: 588  ELKSMMIAPRIILGDK 603



 Score = 43.9 bits (102), Expect = 0.22,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 41/113 (36%), Gaps = 23/113 (20%)

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           I+     + D      + YL A EEEN Y+A     L  +                    
Sbjct: 81  IKKGELTIEDLVRQGLIEYLDAEEEENAYVAVYEHELTPEH------------------- 121

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                 ++  P  +V I    IP+ E++ S R  MG  M +Q++ +  +   +
Sbjct: 122 ----THLELDPSLIVGICTGSIPYAEHNASPRNTMGAAMIKQSLGIPYSNLAW 170


>gi|140084094|gb|ABO84896.1| RpoB [Bacillus licheniformis]
          Length = 228

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 81/211 (38%), Positives = 106/211 (50%), Gaps = 54/211 (25%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 72   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 131

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 132  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDVWETLEEA 191

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 192  GMSRDAK----------------------------TVLYDG------------------- 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    TGEPFD  V+VG +YM+KL HMV
Sbjct: 205  -------RTGEPFDNRVSVGIMYMIKLAHMV 228



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 52/83 (62%), Positives = 65/83 (78%)

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTS
Sbjct: 1   GEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTS 60

Query: 929 LRVPSGVSGTVVDVRIFNRHGID 951
           LRVP G  G ++DV++FNR   D
Sbjct: 61  LRVPHGGGGIILDVKVFNREDGD 83


>gi|30141083|gb|AAP21852.1| RNA polymerase beta subunit [Streptococcus acidominimus]
          Length = 232

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARNLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 200

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGADGVVRDVKIFTRANGD 90


>gi|158252982|gb|ABW23975.1| RNA polymerase beta subunit [Pantoea anthophila]
 gi|158252984|gb|ABW23976.1| RNA polymerase beta subunit [Pantoea anthophila]
          Length = 212

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LDE+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDENGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|330934625|ref|XP_003304626.1| hypothetical protein PTT_17275 [Pyrenophora teres f. teres 0-1]
 gi|311318641|gb|EFQ87258.1| hypothetical protein PTT_17275 [Pyrenophora teres f. teres 0-1]
          Length = 1214

 Score =  219 bits (558), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 70/420 (16%), Positives = 135/420 (32%), Gaps = 78/420 (18%)

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             + +    +          R+       +  S     K         I            
Sbjct: 859  QVMKKHVTQLKTYANGTSDRINAGALDTDNKSHQAIGKDGIAQVGARIEAGDAYLLKSIP 918

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            +               Y+      ++   + I+K           + ++K+     R  +
Sbjct: 919  LDTAG------PATNTYKDKPEKYKNPDFSYIDK--ACVTENEAGVTLIKLLFRQTRRPE 970

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK +                                     SR               
Sbjct: 971  LGDKFS-------------------------------------SR--------------- 978

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G+K  + +   + +   +      + ++       +++      +L       +G  
Sbjct: 979  --HGQKGTTGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMMELLSGKAGVLNGTL 1036

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                 F G+  E ++ +L       +G+  L  G+TGE        G IY  KL HMV D
Sbjct: 1037 EYGTAFGGSTVEDMSKILVDKGFSYTGKDYLTSGITGEAHQFYTFFGPIYYQKLKHMVQD 1096

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----D 1321
            K+++R+ G  +++T+QP  G++  GG RLGEME  C+ AYGA+ +L E L + SD    D
Sbjct: 1097 KMHSRARGPRAILTRQPTEGRARDGGLRLGEMERDCLIAYGASQLLLERLMLSSDAHTVD 1156

Query: 1322 VV---------GRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
            V          G  ++ ES        +   P +  +L++E+ ++ + + +         
Sbjct: 1157 VCEKCGQMGYSGYCKLCES---EKAVRKITMPYAAKLLIQELGSMNVKVTIGLEDEFPRD 1213



 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 131/984 (13%), Positives = 277/984 (28%), Gaps = 202/984 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV-FPITAFSGAAMLEFVSYEFDPP--- 84
           L++    SY+HF+ +           L+   K+  F  + F    +LE+       P   
Sbjct: 120 LVKQHVDSYNHFVDVE----------LKKIIKANRFVRSDFDPKFLLEYTDIRVLSPNRQ 169

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                         ++C  RD+TYA P+ + +             +    +K   I +G 
Sbjct: 170 EEDDLEHHRSTITPNECRLRDMTYAAPIVVDI----------IYTRGNAKVKRTGIKIGR 219

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHR---------SP 161
           +P+M K                         G F+ +G +++++ Q            + 
Sbjct: 220 MPIMLKSNKCVLADKSDREMAVMDECPLDPGGYFITRGQEKVILVQEQLNKNRVIVESAK 279

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMA 220
           GI                Y   +I             K ++++R +    ++P+   + A
Sbjct: 280 GIMQASVTSSTHERRTKTY---VI-----------QKKGLMYLRHNTLSEEIPIVFVMKA 325

Query: 221 LGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG+   +EIL     +    Q      F   A + +   + +   +           G  
Sbjct: 326 LGVASDKEILVMIAGEDSAYQDNFSTNFEACAKEKIFTQERALEYIGHRVRLVKKPLGTS 385

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                    +   ++ +   S+ +   +V  +  N     +Y+ A          +    
Sbjct: 386 RN-------RNYHLEAIECLSNVVLP-HVPVEGTNYRPKALYV-ALMARRVLMAMQNPKL 436

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +       +   +         +   D  L I +V++    +    A S F+  
Sbjct: 437 VDDRDYVGNKRLELSGQMLSLLFEDHFKRFNHDFKLSIDKVLKKPIRAQEFDAFSHFSVH 496

Query: 400 FFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                      +     +  R  +D       + +   IA + ++  + +       +  
Sbjct: 497 KNHITMGVERAIATGNWSLKRFKMDRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 556

Query: 459 LGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
               +    G +      + +    +  +           D        ++ A+ + S  
Sbjct: 557 PRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTEDDDDPVRKIVFMLGAQDICSLT 616

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            E   +  +  L  +   ++ IT   +        + R     E   +H  H        
Sbjct: 617 GEDIHAEGVYSLCLNGTPIA-ITDRPKQFLNSFRQLRRMGRVSEFTSIHIDHDHCEVHIA 675

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRK--------VCDGKVTNDVVYLSAMEEENR 625
           T EG     +  +      N    + + Y K          D      V YL   EE + 
Sbjct: 676 TDEGRICRPMIIVE-----NQRSKVTSRYLKALRKGTLDFEDFLTRGLVEYLDTNEENDT 730

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA   + +++                           ++  P  ++   A LIP+  ++
Sbjct: 731 NIALKETDINQ-----------------------HTTHLEIEPFTILGAVAGLIPYPHHN 767

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R    C M +QA+                                           I
Sbjct: 768 QSPRNTYQCAMGKQAIGA-----------------------------------------I 786

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              + +   +   + +Y               Q+P+VK                T    L
Sbjct: 787 AYNQFNRIDTLLYLMVYP--------------QQPMVK----------TRTIELTKYDKL 822

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD- 864
             G+N  VA M + GY+ ED++++++            +++     +    G  +     
Sbjct: 823 PAGQNATVAVMSYSGYDIEDALILNKASCDRGFGRCQVMKKHVTQLKTYANGTSDRINAG 882

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             +   +  + I + GI  VGA +  GD  + K  P   +               K  D 
Sbjct: 883 ALDTDNKSHQAIGKDGIAQVGARIEAGDAYLLKSIPLDTAGPATNTY-KDKPEKYKNPDF 941

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRH 948
                   +     V  +++  R 
Sbjct: 942 SYIDKACVTENEAGVTLIKLLFRQ 965


>gi|145342289|gb|ABP64841.1| RpoB [Bacillus sp. FSL_H7-170]
          Length = 232

 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 92/287 (32%), Positives = 129/287 (44%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R      +++     
Sbjct: 16   DERGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGA 74

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              +                    K+   + GD++PPGV ++V+ ++  KR I+ GDKMAG
Sbjct: 75   GGI----------------VLDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 119  RHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRYLGIHM 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+                            +  A   + G         
Sbjct: 179  ATPVFDGANEEDVW-------------------------ETMEEAGMDRDG--------- 204

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                                ++ILYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  --------------------KTILYDGRSGEPFDNRVSVGVMYMIKL 231



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 90


>gi|158252864|gb|ABW23916.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252868|gb|ABW23918.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252870|gb|ABW23919.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252872|gb|ABW23920.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252874|gb|ABW23921.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252876|gb|ABW23922.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252878|gb|ABW23923.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252880|gb|ABW23924.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252886|gb|ABW23927.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252888|gb|ABW23928.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252890|gb|ABW23929.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252894|gb|ABW23931.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252896|gb|ABW23932.1| RNA polymerase beta subunit [Pantoea vagans]
 gi|158252898|gb|ABW23933.1| RNA polymerase beta subunit [Pantoea deleyi]
 gi|158252930|gb|ABW23949.1| RNA polymerase beta subunit [Pantoea vagans]
          Length = 212

 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|273067966|gb|ACZ97547.1| DNA-directed RNA polymerase subunit beta [Lactobacillus reuteri]
          Length = 222

 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 135/222 (60%), Positives = 168/222 (75%), Gaps = 2/222 (0%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           +ER+S  D D+V PQ LIN +PVV+++ EFF SSQLSQ  +  N L  +TH RRLSALG 
Sbjct: 1   RERMSIQDPDTVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRLSALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV- 605
           GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+S+ARVN YGFIETPYR+V 
Sbjct: 61  GGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINSLSSYARVNKYGFIETPYRRVS 120

Query: 606 -CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D KVT+ + YL+A EE+N  IAQAN+ L++DGSF ++ V  R   + I    E ID++
Sbjct: 121 WKDHKVTDKIDYLTADEEDNFIIAQANTPLNDDGSFVDDQVMARDKDDYIETSVENIDYM 180

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           D SPKQVVS+A++ IPFLENDDSNR LMG NMQRQAVPL+  
Sbjct: 181 DVSPKQVVSVASACIPFLENDDSNRALMGANMQRQAVPLINP 222


>gi|161331497|gb|ABX60666.1| RpoB [Bacillus sp. FSL_h8526]
          Length = 232

 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 81/207 (39%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARYLGVHMATPVFDGANEDDVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G                             
Sbjct: 193  -------------------ETMEEAGMNRDG----------------------------- 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            ++ILYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  KTILYDGRSGEPFDSRVSVGIMYMIKL 231



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R IPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RXIPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|183232813|ref|XP_654890.2| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide
            [Entamoeba histolytica HM-1:IMSS]
 gi|169801863|gb|EAL49502.2| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Entamoeba histolytica HM-1:IMSS]
          Length = 1122

 Score =  219 bits (557), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 85/577 (14%), Positives = 180/577 (31%), Gaps = 97/577 (16%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D+    N  +A            + I    +   V   I         R+T     
Sbjct: 625  IEYLDVNEENNSYIAINENEINEHTTHLEIDPLSILGVVAGLIPYPHHNQSPRNTYQCAM 684

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               + I  +     K +D   ++ +        +    I       +   +  + A+   
Sbjct: 685  -GKQAIGTIGYNQFKRVDT--LLYLLYYPQIPMVKTKTIDMINFDKLPAGQNAMVAVMSY 741

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               D+ D S+   + +        ++ +      +         +     +++  +    
Sbjct: 742  SGYDIEDASILNKASIDRGYGRCFVYRKAECVIKKYKNGACDRVVCPTDEERELPK---- 797

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                    + L      S        ++  +  +            ++D++         
Sbjct: 798  -------YKSLDFDGVCSPGSILNPGSIYLNKQVPLNTIGTLTTDTIKDDE--------- 841

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
              Y       +    + ++++    +    +   VK+ +   R  + GDK +        
Sbjct: 842  --YRREVLTYKGPVPSYVDQVLITSNEEEPL--KVKISLRTSRRPELGDKFS-------- 889

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                                         SR                  G+K  + +   
Sbjct: 890  -----------------------------SR-----------------HGQKGVTGLIVN 903

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            + +   +      + ++       +++      ++        G       F G   + +
Sbjct: 904  QEDMPFTNTGICPDVIMNPHGFPSRMTVGKLLELVSGKAGLMDGSFKYGTAFGGDKLDDM 963

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            + +L  A     G+  LY G+TG+     + +G +Y  KL HMV DK++AR+ G  S +T
Sbjct: 964  SKILIEAGYSYDGKEELYSGITGKALHAYIFIGPVYYQKLKHMVLDKMHARARGPKSSLT 1023

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----------DVVGRT--- 1326
            +QP  G+S  GG RLGEME  C+  YGA  +L E L   SD           ++G +   
Sbjct: 1024 RQPTEGRSRDGGLRLGEMERDCLIGYGATNLLLERLMYSSDAFKVCVCKKCGLIGHSGYC 1083

Query: 1327 RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            +  ES +   +      P +  +L +EMQ++ +   L
Sbjct: 1084 KFCESSLYCTNV---TMPYACKLLFQEMQSMNVVPRL 1117



 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 136/915 (14%), Positives = 284/915 (31%), Gaps = 162/915 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           L+     S+++F+          +E ++   K+   IT        L+++  + D P   
Sbjct: 36  LVRQHIDSFNYFI----------DEEIKQIVKANDKITCDADPRFYLKYLDVKVDTPCVE 85

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK------------ 126
                      +C  RD++Y  P+   ++    D   F    +I  +             
Sbjct: 86  VDYKKESITPQECRLRDISYTAPILANIQYTR-DNKIFRKTVTIGYMPIMLQSKHCVLYN 144

Query: 127 ---EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
              E+ I  G+ P M   G F++KG++R+++SQ   S          +  LS  +  A  
Sbjct: 145 NTFEEFIRHGECP-MDPGGYFIVKGVERVILSQEQMSKNRILIETTTQGFLSASVTSATH 203

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIVYS-Q 240
            +  +     + +  K  ++++ +     +P+   + A+GM+S+ E L            
Sbjct: 204 EVKSR----TVVYLKKGKLYLKHNSLTEDLPIMIVIKAMGMESDMEFLQFVGNHYTSKMI 259

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                C      +     +   + + I TG++   S +         L    +  + +  
Sbjct: 260 NSIEECKAKDVLNQREALRYIGNHLKIYTGQKGYISKRPKIEEARDVLANLVLPHIEVNR 319

Query: 301 DCLCGLYVAEDIVN------GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                  +   ++        ETGE+  +  D    K +E            L+     +
Sbjct: 320 YNFKTKIIYIALMVNWILKADETGEL--DDKDYYGNKRMELAGQLMSLLFEDLFKQFNTD 377

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              ++N       K  +    DI + + P  + T  +  S+ +   +   ++++   G  
Sbjct: 378 ---LQNAANKGLTKKSRSETFDIIKCISPHRI-TQGLIHSL-STGNWVLKRFNMDRAGIT 432

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           ++  R           +     + ++  L         +    +L   +   V      +
Sbjct: 433 QVLSR-----------LSYISALGMMTRLNSHFEKTRKVSGPRSLQGSQWGMVCPSDTPE 481

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                L    S+   +++   D  +   L N     + +      +  S     +N    
Sbjct: 482 GESCGLVKNFSLLTEVTTDSNDEAIVTMLFNLGVEDANLISGDEVNAPSSYLVFLNGQLL 541

Query: 535 ITHTRRLSALGQGGVARAR-AGVEMRDVHPTHYGRICPAETSEGHNIG---LVSSLTSFA 590
             H   +  L Q  + R      +   +H     R     +  G       +V +  S  
Sbjct: 542 GIHQNPIHFLKQCRLLRRHGRLGKKVSLHLNEMQRSINISSDGGRVCRPLIVVENCKSKI 601

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                  I   ++ + D      + YL   EE N YIA   + ++               
Sbjct: 602 GPKEIRDIVEGFKSIEDCLKEGLIEYLDVNEENNSYIAINENEIN--------------- 646

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   E    ++  P  ++ + A LIP+  ++ S R    C M +QA+         
Sbjct: 647 --------EHTTHLEIDPLSILGVVAGLIPYPHHNQSPRNTYQCAMGKQAIGT------- 691

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                                             I   +     +   +  Y        
Sbjct: 692 ----------------------------------IGYNQFKRVDTLLYLLYYP------- 710

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q P+VK                 +   L  G+N +VA M + GY+ ED+ +++
Sbjct: 711 -------QIPMVK----------TKTIDMINFDKLPAGQNAMVAVMSYSGYDIEDASILN 753

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE--GLKNIDECGIICVGAEV 888
           +  +           + E + +  K G  +      +   E    K++D  G+   G+ +
Sbjct: 754 KASIDRGYGRCFVYRKAECVIKKYKNGACDRVVCPTDEERELPKYKSLDFDGVCSPGSIL 813

Query: 889 NPGDILVGKITPKGE 903
           NPG I + K  P   
Sbjct: 814 NPGSIYLNKQVPLNT 828


>gi|30141095|gb|AAP21857.1| RNA polymerase beta subunit [Streptococcus mitis]
          Length = 232

 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARTLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 200

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGADGVVRDVKIFTRANGD 90


>gi|158252994|gb|ABW23981.1| RNA polymerase beta subunit [Pantoea dispersa]
 gi|158252996|gb|ABW23982.1| RNA polymerase beta subunit [Pantoea dispersa]
 gi|158253024|gb|ABW23996.1| RNA polymerase beta subunit [Pantoea dispersa]
 gi|158253044|gb|ABW24006.1| RNA polymerase beta subunit [Pantoea eucrina]
 gi|158253062|gb|ABW24015.1| RNA polymerase beta subunit [Pantoea eucrina]
          Length = 212

 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|158252882|gb|ABW23925.1| RNA polymerase beta subunit [Pantoea eucalypti]
 gi|158252884|gb|ABW23926.1| RNA polymerase beta subunit [Pantoea eucalypti]
 gi|158252908|gb|ABW23938.1| RNA polymerase beta subunit [Pantoea eucalypti]
 gi|158252910|gb|ABW23939.1| RNA polymerase beta subunit [Pantoea eucalypti]
 gi|158252912|gb|ABW23940.1| RNA polymerase beta subunit [Pantoea eucalypti]
 gi|158252954|gb|ABW23961.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158252978|gb|ABW23973.1| RNA polymerase beta subunit [Pantoea agglomerans pv. gypsophilae]
 gi|158252980|gb|ABW23974.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158252986|gb|ABW23977.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158252988|gb|ABW23978.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158252990|gb|ABW23979.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158253004|gb|ABW23986.1| RNA polymerase beta subunit [Pantoea agglomerans]
 gi|158253028|gb|ABW23998.1| RNA polymerase beta subunit [Pantoea agglomerans]
          Length = 212

 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQIVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|154362077|gb|ABS80877.1| RNA polymerase beta subunit [Brevundimonas vesicularis]
          Length = 233

 Score =  219 bits (557), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 144/229 (62%), Positives = 176/229 (76%), Gaps = 1/229 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL + AR N YGFIE+PYR+V DG+    VVY+SAMEE    IAQAN  L ++G 
Sbjct: 61  IGLINSLATHARANKYGFIESPYRRVKDGQAAGQVVYISAMEEVKYTIAQANIEL-KNGQ 119

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
             E+LV  R  GE  L+ ++ +D +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQ
Sbjct: 120 IVEDLVPGRINGESQLLNKDAVDMMDVSPKQVVSVAAALIPFLENDDANRALMGANMQRQ 179

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           AVPL++++AP VGTGME+VVA  SGA +VA+R G+VEQ+D  RIV+R+ 
Sbjct: 180 AVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRAT 228


>gi|158252962|gb|ABW23965.1| RNA polymerase beta subunit [Pantoea citrea]
          Length = 212

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDDNGLFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|52694297|emb|CAG37988.1| RNA polymerase beta subunit [Pseudomonas mendocina]
          Length = 382

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 137/228 (60%), Positives = 175/228 (76%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              ++G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 152 PERQEGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 211

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 212 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVNDDEV 271

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+ADGPSTD+G+LALG+NM 
Sbjct: 272 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVSRGDIMADGPSTDMGELALGQNMR 331

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEE
Sbjct: 332 VAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEE 379


>gi|52694165|emb|CAG30612.1| DNA-directed RNA polymerase beta chain [Pseudomonas mendocina]
          Length = 381

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 137/228 (60%), Positives = 175/228 (76%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              ++G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 151 PERQEGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 210

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 211 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVNDDEV 270

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+ADGPSTD+G+LALG+NM 
Sbjct: 271 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVSRGDIMADGPSTDMGELALGQNMR 330

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           VAFMPW+G+NFEDS+ +SER+V ED FT+IHI+E   +ARDTKLGPEE
Sbjct: 331 VAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEE 378


>gi|315936488|gb|ADU55872.1| RNA polymerase beta subunit [Erwinia papayae]
 gi|315936490|gb|ADU55873.1| RNA polymerase beta subunit [Erwinia mallotivora]
 gi|315936492|gb|ADU55874.1| RNA polymerase beta subunit [Erwinia mallotivora]
 gi|315936494|gb|ADU55875.1| RNA polymerase beta subunit [Erwinia tracheiphila]
 gi|315936496|gb|ADU55876.1| RNA polymerase beta subunit [Erwinia tracheiphila]
 gi|315936502|gb|ADU55879.1| RNA polymerase beta subunit [Erwinia tasmaniensis]
 gi|315936504|gb|ADU55880.1| RNA polymerase beta subunit [Erwinia amylovora]
 gi|315936506|gb|ADU55881.1| RNA polymerase beta subunit [Erwinia pyrifoliae DSM 12163]
          Length = 212

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|126143416|gb|ABN80116.1| RNA polymerase beta-subunit [Prevotella shahii]
          Length = 126

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 70/180 (38%), Positives = 87/180 (48%), Gaps = 54/180 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN               LG+  ++++     N                    
Sbjct: 1    NPLGVPSRMN---------------LGQIFEAILGAAGTNL------------------- 26

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                GV  +TP+FDGA  E ++     A L     + L+DG TG
Sbjct: 27   --------------------GVKFATPIFDGAKLEDLSEWTDKAGLPHLCSTYLFDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW +
Sbjct: 67   EKFDQPATVGVTYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAL 126


>gi|199580777|gb|ACH89090.1| RNA polymerase subunit beta [Staphylococcus sciuri subsp. carnaticus]
 gi|199580779|gb|ACH89091.1| RNA polymerase subunit beta [Staphylococcus sciuri subsp. rodentium]
 gi|199580781|gb|ACH89092.1| RNA polymerase subunit beta [Staphylococcus sciuri subsp. sciuri]
 gi|199580789|gb|ACH89096.1| RNA polymerase subunit beta [Staphylococcus vitulinus]
          Length = 231

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 80/206 (38%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++SRILP EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISRILPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  V+VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRVSVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDNALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|140084104|gb|ABO84901.1| RpoB [Bacillus licheniformis]
          Length = 239

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 81/211 (38%), Positives = 106/211 (50%), Gaps = 54/211 (25%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 83   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 142

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 143  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDVWETLEEA 202

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 203  GMSRDAK----------------------------TVLYDG------------------- 215

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    TGEPFD  V+VG +YM+KL HMV
Sbjct: 216  -------RTGEPFDNRVSVGIMYMIKLAHMV 239



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 63/94 (67%), Positives = 75/94 (79%)

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEITRDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIF
Sbjct: 1   PEEITRDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIF 60

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  GEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 94


>gi|161331505|gb|ABX60670.1| RpoB [Bacillus massiliensis]
          Length = 232

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 81/207 (39%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRYLGIHMATPVFDGANEADVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G                             
Sbjct: 193  -------------------ETMEEAGMNRDG----------------------------- 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            ++ILYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  KTILYDGRSGEPFDNRVSVGIMYMIKL 231



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/87 (63%), Positives = 69/87 (79%)

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA +V
Sbjct: 4   IPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREV 63

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RDTSLRVP G  G ++DV++FNR   D
Sbjct: 64  RDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|158253064|gb|ABW24016.1| RNA polymerase beta subunit [Erwinia toletana]
          Length = 212

 Score =  218 bits (556), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQIVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|56681225|gb|AAW21249.1| RNA polymerase beta subunit [Streptococcus vestibularis]
          Length = 230

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 7    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 59

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 60   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 108

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 109  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 168

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 169  ARNLGIHIATPVFDGASSEDLWDTVREAGM------------------------------ 198

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 199  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 230



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/88 (62%), Positives = 68/88 (77%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           ++PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +
Sbjct: 1   ELPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSRE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  VRDTSLRVPHGGDGVVRDVKIFTRANGD 88


>gi|261333952|emb|CBH16946.1| RNA polymerase I second largest subunit,putative [Trypanosoma brucei
            gambiense DAL972]
          Length = 1545

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 102/311 (32%), Gaps = 70/311 (22%)

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +F   D               T     +      +  +       P     V V   + R
Sbjct: 1216 RFEYIDPLTNEKTYEYTRHQITKWRHFDKGEDAWVHSVIPLTYDGPDP-TSVLVLFRIPR 1274

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            P   GDK + RHG KG +   +   D+PF  +DG   DI++NP   PSRM VG + E   
Sbjct: 1275 PPVIGDKFSSRHGQKGTLPLDIRSHDLPFSTRDGITPDIIINPHAFPSRMTVGMVLEMMG 1334

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                   G+               S                                   
Sbjct: 1335 AKLGCIQGRLCDHSAWSVIDEQPRSA---------------------------------- 1360

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           + I   L     +  G+  L DG+TGE  +  V VG     +L H
Sbjct: 1361 ---------------KTIGDALEALGYNRYGREKLIDGITGEEIEAEVLVGISGYQRLRH 1405

Query: 1262 MVSDKVYARS------------TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            MVSDK  AR+            TG       QP+ G+   GG R+GEME   + ++G A 
Sbjct: 1406 MVSDKWQARARTDSHTHRAVTKTG-------QPVKGRKRHGGVRVGEMERDALLSHGVAE 1458

Query: 1310 VLQEMLTIKSD 1320
            V+ + L   SD
Sbjct: 1459 VVIDRLLHVSD 1469


>gi|30141060|gb|AAP21841.1| RNA polymerase beta subunit [Streptococcus salivarius]
          Length = 232

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARNLGIHIATPVFDGASSEDLWDTVREAGM------------------------------ 200

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   RELPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|19913065|emb|CAD26832.1| RNA polymerase I second largest subunit [Trypanosoma brucei brucei]
          Length = 1596

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 102/311 (32%), Gaps = 70/311 (22%)

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +F   D               T     +      +  +       P     V V   + R
Sbjct: 1267 RFEYIDPLTNEKTYEYTRHQITKWRHFDKGEDAWVHSVIPLTYDGPDP-TSVLVLFRIPR 1325

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            P   GDK + RHG KG +   +   D+PF  +DG   DI++NP   PSRM VG + E   
Sbjct: 1326 PPVIGDKFSSRHGQKGTLPLDIRSHDLPFSTRDGITPDIIINPHAFPSRMTVGMVLEMMG 1385

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                   G+               S                                   
Sbjct: 1386 AKLGCIQGRLCDHSAWSVIDEQPRSA---------------------------------- 1411

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           + I   L     +  G+  L DG+TGE  +  V VG     +L H
Sbjct: 1412 ---------------KTIGDALEALGYNRYGREKLIDGITGEEIEAEVLVGISGYQRLRH 1456

Query: 1262 MVSDKVYARS------------TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            MVSDK  AR+            TG       QP+ G+   GG R+GEME   + ++G A 
Sbjct: 1457 MVSDKWQARARTDSHTHRAVTKTG-------QPVKGRKRHGGVRVGEMERDALLSHGVAE 1509

Query: 1310 VLQEMLTIKSD 1320
            V+ + L   SD
Sbjct: 1510 VVIDRLLHVSD 1520


>gi|71754481|ref|XP_828155.1| RNA polymerase I second largest subunit [Trypanosoma brucei TREU927]
 gi|70833541|gb|EAN79043.1| RNA polymerase I second largest subunit [Trypanosoma brucei]
          Length = 1596

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 102/311 (32%), Gaps = 70/311 (22%)

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            +F   D               T     +      +  +       P     V V   + R
Sbjct: 1267 RFEYIDPLTNEKTYEYTRHQITKWRHFDKGEDAWVHSVIPLTYDGPDP-TSVLVLFRIPR 1325

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            P   GDK + RHG KG +   +   D+PF  +DG   DI++NP   PSRM VG + E   
Sbjct: 1326 PPVIGDKFSSRHGQKGTLPLDIRSHDLPFSTRDGITPDIIINPHAFPSRMTVGMVLEMMG 1385

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                   G+               S                                   
Sbjct: 1386 AKLGCIQGRLCDHSAWSVIDEQPRSA---------------------------------- 1411

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                           + I   L     +  G+  L DG+TGE  +  V VG     +L H
Sbjct: 1412 ---------------KTIGDALEALGYNRYGREKLIDGITGEEIEAEVLVGISGYQRLRH 1456

Query: 1262 MVSDKVYARS------------TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
            MVSDK  AR+            TG       QP+ G+   GG R+GEME   + ++G A 
Sbjct: 1457 MVSDKWQARARTDSHTHRAVTKTG-------QPVKGRKRHGGVRVGEMERDALLSHGVAE 1509

Query: 1310 VLQEMLTIKSD 1320
            V+ + L   SD
Sbjct: 1510 VVIDRLLHVSD 1520


>gi|294953589|ref|XP_002787839.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Perkinsus marinus ATCC 50983]
 gi|239902863|gb|EER19635.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Perkinsus marinus ATCC 50983]
          Length = 1159

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 110/307 (35%), Gaps = 67/307 (21%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ K      R  + GDK +                                     SR 
Sbjct: 906  KIFKCITRQTRRPELGDKFS-------------------------------------SR- 927

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                             G+K    +   + +          + ++       +++     
Sbjct: 928  ----------------HGQKGVVGLIVNQEDMPFGEKGWCPDLIMNPHGFPSRMTVGKLL 971

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
              +        G       F G  +E +   L       S +  +  G+TGE  +  + V
Sbjct: 972  ECVSGKAGVLDGERSYGTAFGGTTKEHMTQSLIRHGFHPSAKEYITSGVTGEALECYIFV 1031

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IY  KL HMV DK++ARSTG  + +T+QP  G++  GG RLGEME  C+ AYGA+ +L
Sbjct: 1032 GPIYYQKLKHMVMDKIHARSTGPVNQLTRQPTEGRAKDGGLRLGEMERDCLVAYGASNLL 1091

Query: 1312 QEMLTIKSD----DVVGRTRVYESIVAG--------NDTFETGTPESFNVLVKEMQALGL 1359
             E L + SD     V  R  +  S   G         +  +   P +  +L +E+QA+ +
Sbjct: 1092 LERLMLSSDVFTASVCRRCGLL-SYQNGTCKLCGTSENIVDIRMPYACKLLFQELQAMNV 1150

Query: 1360 SIDLENS 1366
               L+  
Sbjct: 1151 CPRLKVE 1157



 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 92/752 (12%), Positives = 198/752 (26%), Gaps = 146/752 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L++    S+++F+   I               S   IT        LE+       P + 
Sbjct: 45  LVKQHIDSFNYFVTTEIKDIVLAE--------SNRRITSDVDPNWFLEYHDVRVGAPSYR 96

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                       C  RD+TYA  + + +  +          +  + +++  + +G LP+M
Sbjct: 97  GVLQHVQTTPMMCRIRDMTYASDILVDISYV----------RGREVVRKNGVCVGRLPIM 146

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F+IKG +++++ Q   S              
Sbjct: 147 LRSKLCRLHDATTEQMERMQECPHDPGGYFIIKGTEKVLLMQEQLS-------------- 192

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI------DRRRK----------------- 211
                   RII        +E D K ++   +      ++ R                  
Sbjct: 193 ------NNRII--------VEMDPKKLVQAVVTSSTADNKSRTVVCFKSELSGLFVKHSA 238

Query: 212 ----VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
               +P    L A+GM+S++ +             D     L  A          +L  +
Sbjct: 239 FTELIPAVIMLRAMGMESDQEIVQMVGTEKCHV--DGMILSLQDAHATGVFSQQQALEYL 296

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
               ++        S      K    K L  +  C     +    ++  +    ++  D 
Sbjct: 297 GNKLKIRMYADGSFSSAFDQDKGGATKPLDFSGKCRFLCLMMRRALDARSDSTLLDDRDY 356

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
              K LE            L+           +  +T   +    A      V       
Sbjct: 357 YGNKRLELAGQLIALLFEDLFKSMNTEIKKSVDMRLTKFFQQTSSARAGRSTVGLDSGYP 416

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                  + +       +     +     N  R  +D     + + +   IA +  +  +
Sbjct: 417 DV-----LRDIDSERITRGMNRAISSGNWNIKRFRIDRSGVSQVLSRFSFIAALGAMTRV 471

Query: 447 RNGKGTIDD---IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           ++             L   +   +      +     L    S+   +++ D +  + +  
Sbjct: 472 KSQFEKSRKLAGPRALQPSQWGMLCPSDTPEGEQCGLIKALSLLAHVTTPDEEGPIRRLC 531

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG-VARARAGVEMRDVH 562
            +     +A            +   +N      H R  + +     + R     E   ++
Sbjct: 532 YSLGVEDAAGLTGEELHSAGTITVFLNGALLGVHRRPQTFMSDMRTLRRRGKIGEFVSIY 591

Query: 563 PTHYGRICPAETSEGHNIG----LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
                R     T  G        +               + +   +  D      + ++ 
Sbjct: 592 EHEAQRAIIIATDGGRLCRPLIVVKKGKPMLKPEVHLRKLRSGELRFTDFLRLGIIEWVD 651

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
             EE N YIA     +                         +   ++  P  ++   A L
Sbjct: 652 VNEENNSYIAINPEDVTM-----------------------ESTHLEIEPLTLLGAVAGL 688

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +P+  ++ S R    C M +QA+  +      
Sbjct: 689 VPYPHHNQSPRNTYQCAMGKQAMGNIACNQHL 720


>gi|30141064|gb|AAP21843.1| RNA polymerase beta subunit [Streptococcus suis]
          Length = 231

 Score =  218 bits (556), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 126/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 15   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 63

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 64   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 117

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 118  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 177

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 178  ATPVFDGASSEDLWSTVKEAGM-------------------------------------- 199

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 200  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 231



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 1   REIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  EVRDTSLRVPHGADGVVRDVKIFTRANGD 89


>gi|68131914|gb|AAY85235.1| RNA polymerase II second largest subunit [Tetracentron sinense]
          Length = 951

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 119/907 (13%), Positives = 261/907 (28%), Gaps = 163/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKE-QSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +           + + +E   +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCE--EVTETQEFTKVFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSGMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCAIGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L+      A        E       D      + Y+   EEE   I+         
Sbjct: 529 QRL-LIKKKDIRALQQRESPEEGG---WHDLVAKGYIEYVDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +L+  +   E      +     +  P  ++ + AS+IPF +++ + R      M 
Sbjct: 577 --TINDLITAKLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQTPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 633 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIAC 687

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 688 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGS 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +           +         RD S  + 
Sbjct: 748 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLR 798

Query: 933 SGVSGTV 939
              SG V
Sbjct: 799 HSESGMV 805



 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 79/485 (16%), Positives = 143/485 (29%), Gaps = 94/485 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSMLI--SERMV 834
            LV  G  + V   +      S  + DL   + N   A+   +       S+++     ++
Sbjct: 555  LVAKGYIEYVDTEEEETTMISMTINDLITAKLNPEEAYSDTYTHCEIHPSLILGVCASII 614

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 615  PFPDHNQTPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 663

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 664  TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 722

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +  ++ +E      R+          +          G           K+T ++     
Sbjct: 723  KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---- 778

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE   +     +  + TS    E    +++      D +     R V
Sbjct: 779  -------------DESQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFV 820

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 821  KVRMRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIG 880

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+                                           
Sbjct: 881  QLIECIMGKVAAHMGKEGD----------------------------------------- 899

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                        +TP F     + I+  L        G   +Y+G TG      + +G  
Sbjct: 900  ------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPT 946

Query: 1255 YMLKL 1259
            Y  +L
Sbjct: 947  YYQRL 951


>gi|117675889|emb|CAL69215.1| RNA polymerase subunit B [Rathayibacter tritici]
          Length = 362

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 65/175 (37%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G
Sbjct: 1   VFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEQFAGYESIELTLEKDNILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              A   +         V  +    ++++    +    L K  + K  + LGI  
Sbjct: 119 KEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIDK 173



 Score =  194 bits (493), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 137/354 (38%), Positives = 202/354 (57%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 11  EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 70

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +       I  TL  D    ++DAL DIYR
Sbjct: 71  VGVRIDRKRKQSVTVFLKALGLTSEEIL--EQFAGYESIELTLEKDNILTKEDALRDIYR 128

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+S +YDL+ VGR K+N +L +D       +  EDIIA 
Sbjct: 129 KLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIDKALSDSVLTVEDIIAT 188

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L +G+                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 189 IKYLVALHDGRTALPGVRDGESVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 248

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 249 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 308

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 309 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 362


>gi|3133349|gb|AAC38475.1| RNA polymerase beta-subunit [Mycobacterium avium]
          Length = 208

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 125/208 (60%), Positives = 163/208 (78%), Gaps = 1/208 (0%)

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
           +PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HY
Sbjct: 1   RPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHY 60

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           GR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG VT+++ YL+A EE+   
Sbjct: 61  GRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVTDEIHYLTADEEDRHV 120

Query: 627 IAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           +AQANS +D+ G F E  V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+D
Sbjct: 121 VAQANSPIDDKGRFAEARVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHD 180

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           D+NR LMG NMQRQAVPL+++EAP VGT
Sbjct: 181 DANRALMGANMQRQAVPLVRSEAPLVGT 208


>gi|290794225|gb|ADD64434.1| RNA polymerase beta subunit [Streptococcus salivarius]
          Length = 226

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 3    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 55

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 56   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 104

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 105  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 164

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 165  ARNLGIHIATPVFDGASSEDLWDTVREAGM------------------------------ 194

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 195  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 226



 Score = 79.7 bits (195), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 53/84 (63%), Positives = 64/84 (76%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDT
Sbjct: 1   VGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDT 60

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SLRVP G  G V DV+IF R   D
Sbjct: 61  SLRVPHGGDGVVRDVKIFTRANGD 84


>gi|320581721|gb|EFW95940.1| DNA-directed RNA polymerase III [Pichia angusta DL-1]
          Length = 1138

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 84/505 (16%), Positives = 166/505 (32%), Gaps = 95/505 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I       +   +    A+      D+ D  +   + +   
Sbjct: 711  DTLLYLMCYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKASIDRG 770

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                ++  R      +R  +  ++ +  +   K+D + I              G    SG
Sbjct: 771  FGRCQVL-RKTTAVLKRYPNHSKDILAGMRV-KEDGKPIFQHEALGPDGLAEVGVEVQSG 828

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K            P +           + +       Q+  +         + ++
Sbjct: 829  QTYINK----------CVPTNATESVVGGQPTINQQ-----QQHRETPVNYRAPVSSVVD 873

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++     +      ++KV +   R  + GDK +                           
Sbjct: 874  QVMM--SVSDNDQALIKVLLRQTRRPELGDKFS--------------------------- 904

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
                      SR                  G+K    I   + +   +      + ++  
Sbjct: 905  ----------SR-----------------HGQKGVCGIIVQQEDMPFNDDGISPDIIMNP 937

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                 +++      ++        G       F G+  E ++ +L     + SG+ +LY 
Sbjct: 938  HGFPSRMTVGKMLELVSGKAGVLDGSLQYGTCFGGSKLEDMSQILIDKGFNYSGKDMLYS 997

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+TGE     +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME
Sbjct: 998  GITGEALQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEME 1057

Query: 1299 VWCIQAYGAAYVLQEMLTIKSD----DVV------GRT------RVYESIVAGNDTFETG 1342
              C+ AYGA+ +L E L + SD    DV       G        +  E +V         
Sbjct: 1058 RDCVIAYGASQLLLERLMLSSDAFDVDVCNSCGLMGYNSWCPSCKTSEGVVK------MT 1111

Query: 1343 TPESFNVLVKEMQALGLSIDLENSR 1367
             P +  +L +E+ ++ ++  L+ + 
Sbjct: 1112 IPYAAKLLFQELISMNIAPRLKMAD 1136



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 129/971 (13%), Positives = 273/971 (28%), Gaps = 185/971 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    S++ F+  ++    + NE        V P         L+++           
Sbjct: 39  LVKQHLDSFNFFVDTDLKKIIQANE---KVLSDVDP------EFYLKYLDIRVGYKSGGN 89

Query: 84  PKFD-----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           P          +C  RDLTY+ P+ + +             +  K I  + + +G +P+M
Sbjct: 90  PNETEVLLPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIIHRDLEIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++ G +++++ Q   S          + ++
Sbjct: 140 LRSNKCILNGKNEAQMAYLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKNI 199

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++     +     D I+++ +    ++P+   L A G+ S+ EIL   
Sbjct: 200 VQASVTSST--HERKSKTYVVT-KNDKIYLKHNSISEEIPIVIVLKAAGLVSDLEILQLV 256

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKE-- 290
                  Q      F  +A   +   K +   +        +++ ++L +  L  L+E  
Sbjct: 257 CGNDSVYQDLFAVNFEEAAKLGIYSQKEALEYIGRK-----VKTIRRLNAPKLSILQEGI 311

Query: 291 ----------KGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                       V+ L      L    +   ++        ++  D +  K LE      
Sbjct: 312 EAIATTVIAHITVENLDFKEKALYIAIMTRRVIMAMHNPKLVDDRDYVGNKRLELAGQLM 371

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 L+    N+     + ++   ++  + DALL I   +   +++T        +  
Sbjct: 372 SLLFEDLFKKFNNDFKANLDKILKKPSRVSEFDALLHIN--IHSSNITT--GLNRAISTG 427

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGK---GTIDDI 456
            +   ++ +   G   +  RL+  +   +            K+           G +   
Sbjct: 428 NWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTS 487

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D         V  +      +     E  IK+    +  + +   D        +     
Sbjct: 488 DTPEGEACGLVKNLALMT-HITTDDEEDPIKKLCYILGAEDISVIDSSTLHNNGTFGVH- 545

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
              + +         +S+  H RR   L                +         P    E
Sbjct: 546 LNGTLIGTTRFPNVFVSKFRHLRRTGKLSAFVSIFTNVHQSAVHIAADGGRICRPLIIVE 605

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                + +      R   + F         D      V YL   EE +  IA     +  
Sbjct: 606 NGKAKVTAEHLKRLRDGEWSF--------DDFLTNGLVEYLDVNEENDSLIALYEKDITG 657

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                                      ++  P  V+   A LIP+  ++ S R    C M
Sbjct: 658 S-----------------------TTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAM 694

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+                                           I   +     + 
Sbjct: 695 GKQAIGA-----------------------------------------IAYNQFRRIDTL 713

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
             +  Y               Q+P+VK                 D   L  G+N  VA M
Sbjct: 714 LYLMCYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVM 749

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN- 875
            + GY+ ED++++++  +         + +   + +      ++I   +    +      
Sbjct: 750 SYSGYDIEDALVLNKASIDRGFGRCQVLRKTTAVLKRYPNHSKDILAGMRVKEDGKPIFQ 809

Query: 876 ---IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +   G+  VG EV  G   + K  P   +      +       +      +    V 
Sbjct: 810 HEALGPDGLAEVGVEVQSGQTYINKCVPTNATESVVGGQPTINQQQQHRETPVNYRAPVS 869

Query: 933 SGVSGTVVDVR 943
           S V   ++ V 
Sbjct: 870 SVVDQVMMSVS 880


>gi|304334243|gb|ADM25199.1| RNA polymerase beta subunit [Cupriavidus sp. amp6]
 gi|304334245|gb|ADM25200.1| RNA polymerase beta subunit [Cupriavidus sp. amp18]
 gi|304334247|gb|ADM25201.1| RNA polymerase beta subunit [Cupriavidus sp. amp34]
 gi|304334249|gb|ADM25202.1| RNA polymerase beta subunit [Cupriavidus sp. amp45]
 gi|304334253|gb|ADM25204.1| RNA polymerase beta subunit [Cupriavidus sp. cmp29]
 gi|304334255|gb|ADM25205.1| RNA polymerase beta subunit [Cupriavidus sp. cmp36]
          Length = 219

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 125/219 (57%), Positives = 163/219 (74%), Gaps = 2/219 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D +G+ T+ELV
Sbjct: 61  LALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDAEGNLTDELV 120

Query: 646 FCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 SAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPC 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R
Sbjct: 181 LRPDKPLVGTGIERTVAVDSGTAVQAMRGGLVDYVDAMR 219


>gi|30141062|gb|AAP21842.1| RNA polymerase beta subunit [Streptococcus sanguinis]
          Length = 232

 Score =  218 bits (555), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 126/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSEDLWDTVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGADGVVRDVKIFTRANGD 90


>gi|226374585|gb|ACO52463.1| RpoB [Corynebacterium sp. CD443]
 gi|226374587|gb|ACO52464.1| RpoB [Corynebacterium sp. CD450]
 gi|256858901|gb|ACV31760.1| RpoB [Corynebacterium diphtheriae]
 gi|256858905|gb|ACV31762.1| RpoB [Corynebacterium diphtheriae]
          Length = 148

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/176 (38%), Positives = 96/176 (54%), Gaps = 36/176 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G KI +     +   +   L++  E +              
Sbjct: 1    RMNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP---------- 44

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                        +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 45   ------------AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 93   GEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 148


>gi|140084110|gb|ABO84904.1| RpoB [Bacillus licheniformis]
          Length = 238

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 81/211 (38%), Positives = 106/211 (50%), Gaps = 54/211 (25%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 82   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 141

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 142  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDVWETLEEA 201

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 202  GMSRDAK----------------------------TVLYDG------------------- 214

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    TGEPFD  V+VG +YM+KL HMV
Sbjct: 215  -------RTGEPFDNRVSVGIMYMIKLAHMV 238



 Score = 89.4 bits (220), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 62/93 (66%), Positives = 75/93 (80%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 61  EKAREVRDTSLRVPHGGGGIILDVKVFNREDGD 93


>gi|294715529|gb|ADF30858.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
 gi|294715531|gb|ADF30859.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
 gi|294715533|gb|ADF30860.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
 gi|294715535|gb|ADF30861.1| DNA-directed RNA polymerase beta subunit [Acinetobacter baumannii]
          Length = 151

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 82/154 (53%), Positives = 109/154 (70%), Gaps = 4/154 (2%)

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               +G PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG KI+ ++ + +    +  LR 
Sbjct: 1    HDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT---VLELRE 57

Query: 1171 FLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
            FL+K+    G   E +    D+ +L +A   ++GVP++TPVFDGA+E  I  +L +AD+ 
Sbjct: 58   FLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPLATPVFDGAEESQIKDLLELADIS 117

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
             +GQ++L+DG TGE FDRPVTVGY+YMLKLNH+V
Sbjct: 118  RTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLV 151


>gi|169597943|ref|XP_001792395.1| hypothetical protein SNOG_01766 [Phaeosphaeria nodorum SN15]
 gi|160707624|gb|EAT91415.2| hypothetical protein SNOG_01766 [Phaeosphaeria nodorum SN15]
          Length = 1443

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/344 (19%), Positives = 123/344 (35%), Gaps = 72/344 (20%)

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            Y+      +    + I+K+            ++K+     R  + GDK +          
Sbjct: 1158 YKDKPEKYKLPDCSYIDKV--CITENEAGTTLIKILNRQTRRPELGDKFS---------- 1205

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                                       SR                  G+K  + +   + 
Sbjct: 1206 ---------------------------SR-----------------HGQKGTTGLIVQQE 1221

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +   +      + ++       +++      +L       +G       F G+  E +  
Sbjct: 1222 DMPFNDQGINPDIIMNPHGFPSRMTVGKMMELLSGKAGVLNGTLEYGTAFGGSRVEDMAD 1281

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L       +G+  L  G+TGE        G IY  KL HMV DK++AR+ G  +++T+Q
Sbjct: 1282 ILVSKGFSYTGKDYLTSGITGEAHQFYTFFGPIYYQKLKHMVQDKMHARARGPRAILTRQ 1341

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV---------GRTRV 1328
            P  G++  GG RLGEME  C+ AYGA+ +L E L I SD    DV          G  ++
Sbjct: 1342 PTEGRARDGGLRLGEMERDCLIAYGASQLLLERLMISSDAHNVDVCEKCGQMGYSGYCKL 1401

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
             ES            P +  +L++E+ ++ + + +  +      
Sbjct: 1402 CES---EKAVRRITMPYAAKLLIQELGSMNVKVTIGLADEFPRE 1442



 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 136/980 (13%), Positives = 278/980 (28%), Gaps = 194/980 (19%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV-FPITAFSGAAMLEFVSYEFDPP--- 84
            L++    SY+HF+ +           L+   K+  F  + F    +LE+       P   
Sbjct: 349  LVKQHVDSYNHFVDVE----------LKKIIKANRFVRSDFDPKFLLEYTDIRVLSPNRQ 398

Query: 85   ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          ++C  RD+TYA P+ + +             +    +K   I +G 
Sbjct: 399  EEDDLDNHRSTVTPNECRLRDMTYAAPIVVDI----------VYTRGSAKVKRTGIKIGR 448

Query: 135  LPLMTKD------------------------GTFVIKGIQRIVVSQLHR---------SP 161
            +P+M K                         G F+ +G +++++ Q            + 
Sbjct: 449  MPIMLKSNKCVLAAKNDREMAVMDECPLDPGGYFITRGQEKVILVQEQLNKNRVIVESAK 508

Query: 162  GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMA 220
            GI                Y   +I             K ++ +R +    +VP+   L A
Sbjct: 509  GIMQASVTSSTHERRTKTY---VI-----------QKKGLMFLRHNTLSEEVPIVFVLKA 554

Query: 221  LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
            LG+ S+ EIL          Q      F   A + +   + +   +           G  
Sbjct: 555  LGVHSDKEILLMIAGTDAAYQDSFAINFEACAREGIHTQEKALEYIGHRVRLVKKPLGTS 614

Query: 280  LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                    ++   ++ +   ++ +   +V  +  N     +Y+ A          +    
Sbjct: 615  -------RMRNYHLEAIECLANVVLP-HVPVEGTNYRPKALYV-ALMARRVLMAMQDPKL 665

Query: 340  EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                  +       +   +         +   D  L I +V++  + +    A S F+  
Sbjct: 666  VDDRDYVGNKRLELSGQMLSLLFEDHFKRFNHDFKLSIDKVLKKQNRAQEFDAFSHFSVH 725

Query: 400  FFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                       +     +  R  +D       + +   IA + ++  + +       +  
Sbjct: 726  KNHITMGIERAIATGNWSLKRFKMDRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 785

Query: 459  LGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                +    G +      + +    +  +           +        L+ A+ + S  
Sbjct: 786  PRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTEDDEDPVRKIIFLLGAEEICSQT 845

Query: 514  CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
             E      +  +  +   ++     +R        + R     E   +H  H        
Sbjct: 846  GEEIHREGVYSVCLNGTPIAITDIPKRF-LNSFRKLRRMGRISEFTSIHINHDFCEVHVA 904

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRK----VCDGKVTNDVVYLSAMEEENRYIAQ 629
            T EG     +  + +  R    G      RK      D      V YL   EE +  IA 
Sbjct: 905  TDEGRICRPMIVVENQ-RSKVTGRYLKALRKGTMEFEDFLTRGLVEYLDTNEENDTNIAL 963

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +++                           ++  P  ++   A LIP+  ++ S R
Sbjct: 964  KETDINQ-----------------------HTTHLEIEPFTILGAVAGLIPYPHHNQSPR 1000

Query: 690  VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                C M +QA+                                           I   +
Sbjct: 1001 NTYQCAMGKQAIGA-----------------------------------------IAYNQ 1019

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
                 +   + +Y               Q P+VK                T    L  G+
Sbjct: 1020 FSRIDTILYLMVYP--------------QEPMVK----------TRTIELTKYDKLPAGQ 1055

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-IPNV 868
            N  VA M + GY+ ED++++++            +++     +    G  +        V
Sbjct: 1056 NATVAVMSYSGYDIEDALILNKASCDRGFGRCQVMKKVSHQLKSYANGTSDRINAGALKV 1115

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
             +   + I + GI  VGA +N GD  + K  P+ ++   P           K  D     
Sbjct: 1116 DDPTHQAIGQDGIAQVGARINQGDAFLLKAIPQ-DTAGPPSTTYKDKPEKYKLPDCSYID 1174

Query: 929  LRVPSGVSGTVVDVRIFNRH 948
                +        ++I NR 
Sbjct: 1175 KVCITENEAGTTLIKILNRQ 1194


>gi|60101377|gb|AAX13757.1| RNA polymerase beta subunit [Streptococcus massiliensis]
          Length = 232

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 126/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSDDLWDTVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGADGVVRDVKIFTRANGD 90


>gi|256858903|gb|ACV31761.1| RpoB [Corynebacterium diphtheriae]
          Length = 148

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/176 (38%), Positives = 97/176 (55%), Gaps = 36/176 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G KI +     +   +   L++  E +              
Sbjct: 1    RMNIGQVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYD------------ 42

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                      + +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 43   ----------FPAGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 93   GEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 148


>gi|62947922|gb|AAY22958.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 223

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 126/220 (57%), Positives = 162/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV    G VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQ+NS L+E G F E +V  R  G     P +++D++D SPKQVV++A + IPFL
Sbjct: 124 DEYIVAQSNSKLNEKGGFAEPIVMGRHRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|219513972|gb|ABW24001.2| RNA polymerase beta subunit [Erwinia rhapontici]
          Length = 212

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVREG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFNRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +Q VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQSVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|50310217|ref|XP_455128.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644264|emb|CAG97835.1| KLLA0F01078p [Kluyveromyces lactis]
          Length = 1142

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 73/352 (20%), Positives = 133/352 (37%), Gaps = 78/352 (22%)

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +   + QY+ +  +      + I+++     +      ++KV +   R  + GDK +   
Sbjct: 852  LTQTQAQYKETPVVYRAPEPSHIDQVMM--SVSDNDQALIKVLLRQNRRPELGDKFS--- 906

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
                                              SR                  G+K   
Sbjct: 907  ----------------------------------SR-----------------HGQKGVC 915

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             I   + +   +      + ++       +++      ++       +G       F G+
Sbjct: 916  GIIVKQEDLPFNDQGVVPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGTLEYGTCFGGS 975

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              E ++ +L     + SG+ +LY G+TGE     +  G IY  KL HMV DK++AR+ G 
Sbjct: 976  KLEDMSKILVDNGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGP 1035

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV------G 1324
             +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L + SD    DV       G
Sbjct: 1036 RAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMLSSDAFEVDVCEKCGLMG 1095

Query: 1325 RT------RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
             +      +  E +V          P +  +L +E+ A+ ++  L+      
Sbjct: 1096 YSGWCTSCKTAEHVVK------MTIPYAAKLLFQELLAMNIAPRLKLGDVFE 1141



 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 113/924 (12%), Positives = 269/924 (29%), Gaps = 173/924 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L++    S+++F+ +++    + NE +      V P         L+++       K + 
Sbjct: 54  LVKQHLDSFNYFVDVDLKKIIKANEVI---LSDVDP------EFYLKYIDIRVGY-KHNG 103

Query: 88  -------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT- 139
                    +C  RD+TY+ P+ + +             +    +  + + +G +P+M  
Sbjct: 104 NKAIMTPPHECRLRDMTYSTPIFVDIEYT----------RGRSIVLHRDVEIGRMPIMLR 153

Query: 140 -----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F++ G +++++ Q   S          + ++  
Sbjct: 154 SNKCILDGAAENDMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKNIVQ 213

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYP 234
             + +     ++     +     D I+++ +    +VP+   L A G+ S+ EI+     
Sbjct: 214 ASVTSST--HERKSKTYVVT-KNDKIYLKHNSIAEEVPIVVVLKACGVVSDLEIMQLVCG 270

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK-KLTSGLLKSLKEKGV 293
                Q  D +   L  A  +       +L  I T  + +   K  +    ++++    +
Sbjct: 271 NDSSYQ--DIFAVNLEEAAELKIYTQQQALEFIGTKVKTVRRQKLSILQEGIEAIATTVI 328

Query: 294 KFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVN 353
             L + +       +    +   T  + +   +       + + +  +            
Sbjct: 329 AHLTVEALDFREKAL---YIAMMTRRVVMAIDNPKMVDDRDYVGNKRLEL---------- 375

Query: 354 NNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
               +         K   D   +I +V++  + +    A    N    +        +  
Sbjct: 376 AGQLMSLLFEDLFKKFNNDFKANIDKVLKKPNRAEMYDALLTINVHSNNITTGMNRAIST 435

Query: 414 VKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
              +++        V H    +     + ++  +         +     L   +   +  
Sbjct: 436 GNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCT 495

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
               +     L    ++   I++ D +  + +          ++ +         +  + 
Sbjct: 496 SDTPEGEACGLVKNLALMTHITTDDEEEPIKRICYLLGVEDISLIDSASIHLNYGVYLNG 555

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL---VSSL 586
             +       +  +  +  + R     E   ++   + +     T  G        VS+ 
Sbjct: 556 TIIGTTRFPTKFVSQFRC-LRRTGRASEFISIYTNTHQKAVHIATDGGRICRPLIIVSNG 614

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            S    +    +     +  D      V YL   EE + +IA     L E+         
Sbjct: 615 QSSVTADHLRSLLAGKLQFDDFLKLGLVEYLDVNEENDSFIALYEKDLSEN--------- 665

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                         I  ++     V+   A LIP+  ++ S R    C M +QA+     
Sbjct: 666 --------------ITHLEIESFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA--- 708

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                                                 I   +     +   + IY    
Sbjct: 709 --------------------------------------IAYNQFKRIDTLLYLMIYP--- 727

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+P+VK                 D   L  G+N  VA M + GY+ ED+
Sbjct: 728 -----------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDIEDA 766

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDECGII 882
           +++++  +           +   + +      ++    +  D         + +   G+ 
Sbjct: 767 LVLNKASIDRGFGRCETRRKNTTVLKRYPNHTQDIIGGMRVDENGEPIWQHQALGPDGLG 826

Query: 883 CVGAEVNPGDILVGKITPKGESPM 906
            VG +V  G I V K  P   S  
Sbjct: 827 EVGMKVESGQIYVNKSVPTNASDS 850


>gi|22086599|gb|AAM90687.1|AF403005_1 RNA polymerase beta subunit [Rickettsia slovaca]
          Length = 266

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 161/264 (60%), Positives = 206/264 (78%), Gaps = 2/264 (0%)

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           N GL +S+ ++A +N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG
Sbjct: 1   NFGLTNSMATYATINKHGFIESPYRRVKDGCVTDEVVYLSAIEEGKYKIGQANSKINKDG 60

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               E + CR   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQ
Sbjct: 61  KLQGEFINCRVEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQ 120

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           RQAVPL+K +APFVGTG+E VVAK SGA+++A   GIVEQVD+ RIVIR++E      + 
Sbjct: 121 RQAVPLIKTDAPFVGTGVEGVVAKDSGASVLALHDGIVEQVDSNRIVIRTLE-QKVDGSP 179

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
            VDIY L+KFQ+SN NTC+ Q  LVKVG  V++NDIIADGPSTD G++ALGRN+LVAF+ 
Sbjct: 180 SVDIYNLLKFQKSNHNTCITQMRLVKVGHYVKKNDIIADGPSTDNGEIALGRNVLVAFLR 239

Query: 818 WHGYNFEDSMLISERMVSEDVFTS 841
           W+G NFEDS+LIS R+V EDV+TS
Sbjct: 240 WNGSNFEDSILISGRIVKEDVYTS 263


>gi|158253046|gb|ABW24007.1| RNA polymerase beta subunit [Pantoea eucrina]
          Length = 212

 Score =  218 bits (555), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGGNMQRQ 212


>gi|68076367|ref|XP_680103.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56500986|emb|CAH95536.1| hypothetical protein PB000108.01.0 [Plasmodium berghei]
          Length = 446

 Score =  218 bits (555), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 86/498 (17%), Positives = 167/498 (33%), Gaps = 91/498 (18%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER-- 955
            I       +   +  + ++      D+ D  +   S +           +H I+  +   
Sbjct: 13   IEFINFEKLPAGQNAIVSVMSFCGYDIEDAIVMNKSSIDRGFGRCMSLRKHFIELKKYFN 72

Query: 956  -----------SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
                       SIS +++  +   ++ +D       +    +   L   +++        
Sbjct: 73   GSNDIVLPSPLSISKQQQMQKKYGKESNDNLANAKEDPKKTINSELKKYHSLDADGVVSI 132

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              +L    +     S         + V+   +     ++ S+   +  + + ++KI +  
Sbjct: 133  GYLLKEGQVYVNKYSPIN----VKDHVKDISKLDLNDFKLSEVKYKSVYPSYVDKIIF-- 186

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                  L++ K+ +   R  + GDK +                                 
Sbjct: 187  TENGEGLKIYKIIMRQSRLPELGDKFS--------------------------------- 213

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
                SR                  G+K    +   + +   +      + ++       +
Sbjct: 214  ----SR-----------------HGQKGVVGLLVNQEDMPFTESGICPDLIMNPHGFPSR 252

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            ++      ++        G      +F G   E    +L     + S + +LY GLTGEP
Sbjct: 253  MTVGKLLELVSSKSAVLDGEYKYGSIFSGTPFEEAAEVLFRYGFNWSCKELLYSGLTGEP 312

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
             +  + +G IY  KL HMV DK++ARS G   L+T+QP  G+S  GG RLGEME  C+ A
Sbjct: 313  LETYIFMGPIYYQKLKHMVQDKIHARSRGPRQLLTRQPTEGRSKEGGLRLGEMERDCLIA 372

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------------NDTFETGTPESFNVL 1350
            YG + +L E L + SD V      Y     G              +       P +  +L
Sbjct: 373  YGVSNLLLERLMLSSD-VC---DTYICEDCGMMGYDLCCTFCKKYDKNVVVKMPYACKLL 428

Query: 1351 VKEMQALGLSIDLENSRT 1368
             +E+Q + +   +    T
Sbjct: 429  FQELQTMNVFPKIIVKET 446


>gi|226897622|gb|ACO90260.1| RNA polymerase beta subunit gene [Bacillus aquimaris]
          Length = 277

 Score =  218 bits (555), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 148/252 (58%), Positives = 194/252 (76%), Gaps = 1/252 (0%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG-DLDPSTSGV 759
           + L+  E+P VGTGME V AK SGAA++ K  GIVE+V+A ++ +R V+  D       +
Sbjct: 2   MTLMNPESPIVGTGMEHVSAKDSGAAVICKYEGIVEKVEAKQVWVRRVKEIDGQEVKGDL 61

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
           D YR+ KF RSNQ TC NQRP+V  GD V + +I+ADGPS + G+LALGRN++V FM W 
Sbjct: 62  DKYRMQKFIRSNQGTCYNQRPIVSEGDRVVKGEILADGPSMEKGELALGRNVMVGFMTWD 121

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           GYN+ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE 
Sbjct: 122 GYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDER 181

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +V+DTSLRVP G  G +
Sbjct: 182 GIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVQDTSLRVPHGGGGII 241

Query: 940 VDVRIFNRHGID 951
           +DV++FNR   D
Sbjct: 242 LDVKVFNREDGD 253



 Score = 43.5 bits (101), Expect = 0.28,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 77/231 (33%), Gaps = 13/231 (5%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R    +        ++  I+  G  V  G+IL    +   +  +     ++   
Sbjct: 59   GDLDKYRMQKFIRSNQGTCYNQRPIVSEGDRVVKGEILADGPS-MEKGELALGRNVMVGF 117

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +     +S  +V   ++    I++ E      +   E + RD  +   
Sbjct: 118  MTWDGYNYEDAII-----MSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGE 172

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               RN+  R   I  G     G     K T      ++   R     F  +  +VQ    
Sbjct: 173  DALRNLDER-GIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVQDTSL 231

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
             +                 K+   + GD++PPG  ++V+V++  KR +  G
Sbjct: 232  RVPHGGGGII------LDVKVFNREDGDELPPGKNQLVRVYIVQKRKVSDG 276


>gi|199580747|gb|ACH89075.1| RNA polymerase subunit beta [Staphylococcus kloosii]
          Length = 231

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDSALKNLDDRGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|158253050|gb|ABW24009.1| RNA polymerase beta subunit [Pantoea brenneri]
 gi|158253054|gb|ABW24011.1| RNA polymerase beta subunit [Pantoea conspicua]
          Length = 212

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+SLD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANASLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|68131878|gb|AAY85217.1| RNA polymerase II second largest subunit [Homalocladium
           platycladum]
          Length = 875

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 121/911 (13%), Positives = 261/911 (28%), Gaps = 169/911 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTK--VFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YHNSEKDLTELGECPLDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAENQNRPPSTMFVRMLSRAGAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTKEKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAR-EILQKEMLPHVGVGEYCETKKAYYFGYIVH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K          +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDQGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N +  +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPTGREGKLAKPRQLHNSQWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +   + + L     + +      I E +     ++   ++ I+   +  A   F  
Sbjct: 413 TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWSTENF--EEEISPAVIPQAAKIFVN 470

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +    +    +  +   RR   +  + GV R     E+R ++  +     P    + 
Sbjct: 471 GCWVGIHRDPDLLVKTLRQLRRRVDVNTEVGVVRDIHLKELR-IYTDYGRCSRPLFIVDK 529

Query: 578 H----NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
                    + +L         G+         D      + Y+   EEE   I+     
Sbjct: 530 QRLLIKKRDIRALQLRETPEDGGW--------HDLVAKGFIEYIDTEEEETTMISM---- 577

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                    +L+  R   E      E     +  P  ++ + AS+IPF +++ S R    
Sbjct: 578 ------TINDLITARVNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 629

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QA+ +      F                    R   +  V               
Sbjct: 630 SAMGKQAMGIYVTNYQF--------------------RMDTLAYV--------------- 654

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                                   Q+PLV                      L  G N +V
Sbjct: 655 --------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIV 684

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 685 AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGM 744

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G +V+  D+++GK TP                        RD S
Sbjct: 745 RHGSYDKLDDDGLAPPGTKVSGEDVIIGKTTPLAPDE--------AQGPNAARYTRRDHS 796

Query: 929 LRVPSGVSGTV 939
           + +    +G V
Sbjct: 797 ISLRHSENGIV 807



 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 116/795 (14%), Positives = 228/795 (28%), Gaps = 117/795 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       +          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGATVGVTKEKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         I+  L+    G+   DD D+ GN+R+   
Sbjct: 240  REILQKEMLPHVGVGEYCETKK---AYYFGYIVHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +        V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRGYVQKCVDQGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++       R     + R +H + +G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNSPT----GREGKLAKPRQLHNSQWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWSTENF------EEEISPAVIPQAAK 466

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 467  IFVNGCWVGIHRDPDLLVKTLRQLRRRV---DVNTEVGVVRDIHLKELRIYTDYGRCSRP 523

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                +   A  + +        D   +  I  ++ + 
Sbjct: 524  LFIVDKQRLLI--------------KKRDIRALQLRETPEDGGWHDLVAKGFIEYIDTEE 569

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 570  EETTMISMTINDLITARVNPEEAYS-----------ETYTHCEIHPSLILG-------VC 611

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +     I       R   L         P V+   
Sbjct: 612  ASIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRA 667

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
            ++++                             +      + AI      +  D+ +   
Sbjct: 668  MEHL-------------------------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 702

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R           +          G
Sbjct: 703  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPG 761

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T L+ D                             +Y      +  R
Sbjct: 762  TKVSGEDVIIGKTTPLAPDEAQGPN---------------------AARYTRRDHSISLR 800

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                    Q         LR VKV V   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 801  HSENGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 860

Query: 1113 KDGTPVDIVLNPLGV 1127
             +G   DI++NP  +
Sbjct: 861  VEGITPDIIVNPHAI 875


>gi|315936508|gb|ADU55882.1| RNA polymerase beta subunit [Erwinia persicina]
 gi|315936510|gb|ADU55883.1| RNA polymerase beta subunit [Erwinia persicina]
          Length = 212

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVREG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFNRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|168218636|emb|CAP45846.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 53/136 (38%), Positives = 81/136 (59%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP ++F 
Sbjct: 102 RVIVSQLVRSPSVYFS 117


>gi|217030931|gb|ACJ74066.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639565|gb|ADG21997.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639567|gb|ADG21998.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639569|gb|ADG21999.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639571|gb|ADG22000.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639573|gb|ADG22001.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|295639575|gb|ADG22002.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|315936498|gb|ADU55877.1| RNA polymerase beta subunit [Erwinia psidii]
 gi|315936500|gb|ADU55878.1| RNA polymerase beta subunit [Erwinia psidii]
          Length = 212

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVREG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|58758743|gb|AAW81770.1| RNA polymerase II second largest subunit [Fibulorhizoctonia sp.
            LA082103L]
          Length = 576

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 110/701 (15%), Positives = 201/701 (28%), Gaps = 127/701 (18%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   + ++           + +  + +         EEN + +   +
Sbjct: 2    ETPEGQACGLVKNLALMSCISVGSLSAPVIEFLEEWGLESL--------EENAHSSTPCT 53

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +G +       R     +   ++     D SP+  V             D+ RV  
Sbjct: 54   KVFVNGVWMG---VHRDPANLVXTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCR 110

Query: 693  GCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               +   Q + L K    ++  G +    +     +V  ++GIVE +DA       +   
Sbjct: 111  PLFIVENQQLALQKKHVHWINRGYDDAEEEFKWEQLV--KSGIVELLDAEEEETVMISMT 168

Query: 752  LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
             +   +       +    ++ +     R  +K G            PS  LG       +
Sbjct: 169  PEDLENSRLQLSGVDPTVNDGDFDPAAR--LKAGTNAHTWTHCEIHPSMILG-------I 219

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N                        ++       +G       I      
Sbjct: 220  CASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM---- 257

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                     +  +             +       +   +  + AI      +  D+ +  
Sbjct: 258  -------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMN 310

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILC 991
             S V   +    I+ R  +D  ++S   + E+ E   R+          +       I  
Sbjct: 311  QSSVDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAP 369

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  +  D      R++          ++     +  Q          
Sbjct: 370  GTGVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI------- 422

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                                + VKV V   R  Q+GDK A RHG KG V      EDMPF
Sbjct: 423  -------------TTNSEGQKFVKVRVRATRIPQTGDKFASRHGQKGTVGITYRQEDMPF 469

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   DI++NP  +PSRM +G + E  L      +G +  +                 
Sbjct: 470  TAEGIVPDIIINPHAIPSRMTIGHLIECLLSKVATLIGNEGDATPFT------------- 516

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                         ++     + LR       G+ V                         
Sbjct: 517  ------------DLTVESVSAFLRQKGYQSRGLEVM----------------------YH 542

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
            G      G         V +G  Y  +L HMV DK+++R+ 
Sbjct: 543  GH----SGR---KLQAQVYLGPTYYQRLKHMVDDKIHSRAR 576



 Score =  112 bits (279), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 68/449 (15%), Positives = 128/449 (28%), Gaps = 83/449 (18%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR   +            +   ++ 
Sbjct: 44  ENAHSSTPCTKVFVNGVWMGVHRDPANLVXTIKKLRRKDDISPEVSVVRDIREKELRLYT 103

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                  P    E   + L      +  +N          K      +  V  L A EEE
Sbjct: 104 DAGRVCRPLFIVENQQLALQKKHVHW--INRGYDDAEEEFKWEQLVKSGIVELLDAEEEE 161

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAA 676
              I+     L+        +      G+     R             +  P  ++ I A
Sbjct: 162 TVMISMTPEDLENSRLQLSGVDPTVNDGDFDPAARLKAGTNAHTWTHCEIHPSMILGICA 221

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 222 SIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI-------------------------- 255

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y       +     +  R                 
Sbjct: 256 ---------------RMDTMANILYYPQKPLATTRSMEYLKFR----------------- 283

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA + + GYN EDS+++++  V   +F SI+   +  + + + +
Sbjct: 284 -------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGI 336

Query: 857 GPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        +   +       I++ G+I  G  V+  DI++GK  P         E+
Sbjct: 337 QQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEE 392

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           L +        DV        +G+   V+
Sbjct: 393 LGQRTRTHTRRDVSTPLKSTENGIVDQVL 421


>gi|30141056|gb|AAP21839.1| RNA polymerase beta subunit [Streptococcus mutans]
          Length = 232

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 93/296 (31%), Positives = 128/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGVVCDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 171  ARNLGIHIATPVFDGATSDDLWETVKEAGMDSDAK------------------------- 205

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               T ++DG                           TGEPFD  V+VG +YM+KL+
Sbjct: 206  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVCDVKIFTRANGD 90


>gi|161331459|gb|ABX60647.1| RpoB [Bacillus sp. FSL_h8473]
          Length = 232

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 82/207 (39%), Positives = 109/207 (52%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRYLGIHMASPVFDGANEADVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G                             
Sbjct: 193  -------------------ETMEEAGMNRDG----------------------------- 204

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            ++ILYDG +GEPFD  V+VG +YM+KL
Sbjct: 205  KTILYDGRSGEPFDSRVSVGIMYMIKL 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|304334217|gb|ADM25186.1| RNA polymerase beta subunit [Cupriavidus sp. pp2.3]
          Length = 219

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 125/219 (57%), Positives = 162/219 (73%), Gaps = 2/219 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT YGR+CP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTQYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L  +AR+N YGF+ETPYRKV + K+T+ V YLSA+EE    +AQAN+++D DG+ T+ELV
Sbjct: 61  LALYARLNEYGFLETPYRKVENSKLTDQVDYLSAIEEGKYVVAQANATVDADGNLTDELV 120

Query: 646 FCRCA--GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             R     E  +V  +++ +ID +P Q+VS AASL+PFLE+DD+NR LMG NMQRQAVP 
Sbjct: 121 SAREGSERETRMVTPDRVQYIDVAPSQIVSAAASLVPFLEHDDANRALMGANMQRQAVPC 180

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           L+ + P VGTG+E  VA  SG A+ A R G+V+ VDA+R
Sbjct: 181 LRPDKPLVGTGIERTVAVDSGTAVQAMRGGLVDYVDAMR 219


>gi|115606119|gb|ABJ16034.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606121|gb|ABJ16035.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  218 bits (554), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 132/259 (50%), Positives = 186/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVCLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|199580713|gb|ACH89058.1| RNA polymerase subunit beta [Staphylococcus carnosus subsp. utilis]
          Length = 231

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREDGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGLHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV+E  LKN+DE GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVAESALKNLDERGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 91


>gi|217030923|gb|ACJ74062.1| RNA polymerase beta subunit [Pectobacterium cypripedii]
          Length = 212

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNFVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDEVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|199580735|gb|ACH89069.1| RNA polymerase subunit beta [Staphylococcus gallinarum]
          Length = 231

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|50295201|gb|AAT72973.1| RpoB [Streptococcus thermophilus]
          Length = 232

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARNLGIYIATPVFDGASSEDLWDTVREAGM------------------------------ 200

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                       +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNVSEE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   RELPNVSEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|217030925|gb|ACJ74063.1| RNA polymerase beta subunit [Pectobacterium cypripedii]
 gi|217030927|gb|ACJ74064.1| RNA polymerase beta subunit [Pectobacterium cypripedii]
 gi|217030929|gb|ACJ74065.1| RNA polymerase beta subunit [Pectobacterium cypripedii]
          Length = 212

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNFVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|199580759|gb|ACH89081.1| RNA polymerase subunit beta [Staphylococcus pasteuri]
          Length = 231

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 62/89 (69%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+DE GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDERGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580733|gb|ACH89068.1| RNA polymerase subunit beta [Staphylococcus fleurettii]
          Length = 231

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 80/206 (38%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++SRILP EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISRILPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  V+VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRVSVGVMYML 231



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GII VGAEV  GDILVGK+TPKG   +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDNALKNLDDRGIIYVGAEVKDGDILVGKVTPKGVKELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|158252976|gb|ABW23972.1| RNA polymerase beta subunit [Pantoea terrea]
          Length = 212

 Score =  218 bits (554), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LD+DG F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDDDGRFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEQDDANRALMGANMQRQ 212


>gi|312985630|gb|ADR31276.1| RNA polymerase II [Fusarium sporotrichioides]
          Length = 612

 Score =  218 bits (554), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 108/723 (14%), Positives = 198/723 (27%), Gaps = 130/723 (17%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + R     + R +H TH+G +CPAET EG   GLV +L+    V+     E     + 
Sbjct: 3    TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 607  D--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
            +   +V  +            ++  +   +  D       V        +      + D 
Sbjct: 63   NRGMEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLVRDI 122

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--------------QRQAVPLLKAEAP 709
             D   K        + P       +    G N               Q QA P       
Sbjct: 123  RDREFKIFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAQPPSDPSEK 182

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                G+    A     A   + A I        + I   +   + + +  +    ++ ++
Sbjct: 183  IGWEGLIRSGAVEYLDAEEEETAMICM--TPEDLEIYREQKQDEINLTEEEKQAKLEAEK 240

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
              Q    N+R   KV             PS  LG       +  + +P+  +N       
Sbjct: 241  REQEEERNKRLKTKVNPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTY 293

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +     +  +                                 +  +     
Sbjct: 294  QSAMGKQAMG--FFLTNYSRRM---------------------------DTMANILYYPQ 324

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    +       +   +  + AI      +  D+ +   S +   +    +F R  
Sbjct: 325  KPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSY 383

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             D+ ++      E  E   +           +       +  G           K+  + 
Sbjct: 384  SDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID 443

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +      R+Q  Q       ++     +  Q   + +                      
Sbjct: 444  QENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA--------------------D 483

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PS
Sbjct: 484  NVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPS 543

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 544  RMTIAHLIECLLSKVSTLEGMEGD------------------------------------ 567

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++ +LR       G  ++Y+G TG      V
Sbjct: 568  -----------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLRAQV 609

Query: 1250 TVG 1252
              G
Sbjct: 610  FFG 612



 Score =  102 bits (253), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 74/540 (13%), Positives = 151/540 (27%), Gaps = 76/540 (14%)

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I ++  +A  + L +     G +   +    +    V  +    Y       E  I+  I
Sbjct: 5   IGRDGKLAKPRQLHNTH--WGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +       + ++    +   +       S      +      S +   R+     +  + 
Sbjct: 63  NRG---MEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLV 119

Query: 551 RARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVNAYGFIE 599
           R     E + +       + P  T           ++G  +     +   A+  A    +
Sbjct: 120 RDIRDREFK-IFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAQPPSD 178

Query: 600 TPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
              +        +  V YL A EEE   I      L+      ++ +             
Sbjct: 179 PSEKIGWEGLIRSGAVEYLDAEEEETAMICMTPEDLEIYREQKQDEIN------------ 226

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                                   E +   ++      Q +             T M   
Sbjct: 227 ----------------------LTEEEKQAKLEAEKREQEEERNKRLKTKVNPTTHM-YT 263

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVN 777
             +   + I+   A I+   D  +    + +  +     G        +           
Sbjct: 264 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRMDTMANILYYP 323

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PL                      +L  G+N +VA   + GYN EDS+++++  +   
Sbjct: 324 QKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 373

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +   L   E+           +       +DE GI+  G  V+  D
Sbjct: 374 LFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGED 433

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P  +       +        +    RD S  + S  +G V  V +       K
Sbjct: 434 IIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNADNVK 486


>gi|46142986|gb|AAS80336.1| RNA polymerase II [Gibberella moniliformis]
          Length = 973

 Score =  218 bits (554), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 117/776 (15%), Positives = 229/776 (29%), Gaps = 97/776 (12%)

Query: 396  FNFLFFDSDKYDLSTVGRVKMNMRL-------NLDTPDDVRHIRKEDIIAIIKILVDLRN 448
            F     + D+  L    RV++   +       ++   +     +   +  ++  L+    
Sbjct: 264  FIGKRGNRDQASLGREKRVRVAKDILQKETLPHISQSEGSETRKAFFLGYMVHKLLQCAL 323

Query: 449  GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINA 506
            G+   DD D+ G +R+   G +L   +R  + R+   +    +       +      I  
Sbjct: 324  GRREPDDRDHFGKKRLDLAGPLLAKLFRGIIRRINTELSNYLKRCVESNRNFNLTVAIKP 383

Query: 507  KPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
              + + +     +               +SQ+       S ++H RR +      + R  
Sbjct: 384  STLSNGLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRRTNT----PIGRDG 439

Query: 554  AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVT 611
               + R +H TH+G +CPAET EG   GLV +L+    V+     E     + +   +V 
Sbjct: 440  KLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMINRGMEVV 499

Query: 612  NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQ 670
             +            ++  +   +  D       V        +      + D  D   K 
Sbjct: 500  EEYEPTRYPHATKIFVNGSWVGVHADPKHLVNQVLDTRRKSYVQFEVSLVRDIRDREFKI 559

Query: 671  VVSIAASLIPFL---ENDDSNRVLMGCNMQ--RQAVPLLKAEAPFVGTGMESVVAKSSGA 725
                   + P     + DD    +    +   ++ V  L  E        E         
Sbjct: 560  FSDAGRVMRPVFTVHQEDDYENNITKGQLVLTKEHVNRLAQEQAEPPANPEDKFGWD--- 616

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKV 784
                 R G VE +DA       +    +      +      + ++  Q    N+R   KV
Sbjct: 617  --GLIREGAVEYLDAEEEETAMICMTPEDLELYREQKNDEAEAEKREQEEDRNKRLKTKV 674

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                         PS  LG       +  + +P+  +N          M  + +     +
Sbjct: 675  NPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--FFL 725

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              +                                 +  +             +      
Sbjct: 726  TNYSRRM---------------------------DTMANILYYPQKPLATTRSMEFLKFR 758

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E  
Sbjct: 759  ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTEIF 817

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +           +       +  G           K+  +  +      R+Q  Q 
Sbjct: 818  EKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTQSHQR 877

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                  ++     +  Q   + +                       ++ VKV V   +  
Sbjct: 878  RDISTPLRSTENGIVDQVILTVNA--------------------DNVKYVKVRVRTTKIP 917

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  
Sbjct: 918  QIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPSRMTIAHLIECL 973



 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 125/965 (12%), Positives = 258/965 (26%), Gaps = 177/965 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLR------------LIVFDVDEFTGAKSIKD----------- 124
             +C  R+LTYA P  + +             L   D ++    K   +           
Sbjct: 18  PYECRDRNLTYAAPTYLKITKKVSVAVDKEVPLHEMDDEQQAEYKRTGENPTKLVWEVEE 77

Query: 125 ----IKEQS-----IYMGDLPLMTKD------------------------GTFVIKGIQR 151
               IK +      I++G +P+M K                         G FVI G ++
Sbjct: 78  DAGSIKAEDEPSEMIFIGKMPIMVKSKICHLSSHSDEDLFMLNECPYDQGGYFVINGSEK 137

Query: 152 IVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDSKDIIHVRIDRR 209
           ++++Q  RS          + +      Y   I    ++G  +      K  ++ + D  
Sbjct: 138 VLIAQE-RSAANI--VQVFKKAQPSPFTYTAEIRSALEKGSRLISSLTMK--LYGKGDSA 192

Query: 210 R----------------KVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAA 252
           R                 +PV     ALG +  E+IL+        SQ  +     +  A
Sbjct: 193 RGGFGQTIQATLPFVKADLPVAIVFRALGVVSDEDILNHICYDRNDSQMLEMLRPCIEEA 252

Query: 253 DLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS-LKEKGVKFLGITSDCLCGLYVAED 311
             +   +V+   +           G++    + K  L+++ +  +  +            
Sbjct: 253 FCVQDREVALDFIGKRGNRDQASLGREKRVRVAKDILQKETLPHISQSEGSETRKAFFLG 312

Query: 312 IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  +  +  +   +  D     +         P+L          I   L     +  +
Sbjct: 313 YMVHKLLQCALGRREPDDRDHFGK--KRLDLAGPLLAKLFRGIIRRINTELSNYLKRCVE 370

Query: 372 DALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--R 429
                   V       +  +  S+    + D  K   ST G  ++  R    +      R
Sbjct: 371 SNRNFNLTVAIKPSTLSNGLKYSLATGNWGDQKKAASSTAGVSQVLNRYTFASTLSHLRR 430

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                     +     L N    +         +   + + L     + +      + E 
Sbjct: 431 TNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEF 490

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + +  ++ V   +                 S +    +  + ++++  TRR S +     
Sbjct: 491 MINRGMEVVEEYEPTRYPHATKIF---VNGSWVGVHADPKHLVNQVLDTRRKSYVQFEVS 547

Query: 550 ARARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVN-AYGF 597
                      +       + P  T           ++G  +     +   A+       
Sbjct: 548 LVRDIRDREFKIFSDAGRVMRPVFTVHQEDDYENNITKGQLVLTKEHVNRLAQEQAEPPA 607

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
                           V YL A EEE   I      L+       +        +E    
Sbjct: 608 NPEDKFGWDGLIREGAVEYLDAEEEETAMICMTPEDLELYREQKNDEAEAEKREQEEDRN 667

Query: 658 R----------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           +                +  P  ++ I AS+IPF +++ S R      M +QA+      
Sbjct: 668 KRLKTKVNPTTHMYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTN 727

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                          + A I+      +    ++  +          +   +  Y     
Sbjct: 728 YS---------RRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG--- 775

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                    NQ                    S  +   ++ R +  +       + E  +
Sbjct: 776 --------YNQE------------------DSVIMNQSSIDRGLFRSLFFRSYSDQEKKV 809

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
            ++   + E  F                            +       +DE GI+  G  
Sbjct: 810 GLNYTEIFEKPFQQT----------------------TLRMKHGTYDKLDEDGIVAPGVR 847

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+  DI++GK  P  +       +        ++   RD S  + S  +G V  V +   
Sbjct: 848 VSGEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVN 900

Query: 948 HGIDK 952
               K
Sbjct: 901 ADNVK 905


>gi|169667027|gb|ACA64044.1| RpoB [Tatumella morbirosei]
          Length = 212

 Score =  218 bits (554), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N L  ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLDEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDENGQFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS  ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSGGASLIPFLEHDDANRALMGANMQRQ 212


>gi|30141092|gb|AAP21856.1| RNA polymerase beta subunit [Streptococcus equi]
          Length = 232

 Score =  218 bits (554), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 93/296 (31%), Positives = 128/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 171  ARNLGIHIATPVFDGATSEDLWETVREAGMDSDAK------------------------- 205

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               T ++DG                           TGEPFD  V+VG +YM+KL+
Sbjct: 206  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGIVRDVKIFTRANGD 90


>gi|199580697|gb|ACH89050.1| RNA polymerase subunit beta [Staphylococcus arlettae]
          Length = 231

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLAPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDNALKNLDDRGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|312985628|gb|ADR31275.1| RNA polymerase II [Fusarium sporotrichioides]
          Length = 612

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 108/723 (14%), Positives = 198/723 (27%), Gaps = 130/723 (17%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + R     + R +H TH+G +CPAET EG   GLV +L+    V+     E     + 
Sbjct: 3    TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 607  D--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
            +   +V  +            ++  +   +  D       V        +      + D 
Sbjct: 63   NRGMEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLVRDI 122

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--------------QRQAVPLLKAEAP 709
             D   K        + P       +    G N               Q QA P       
Sbjct: 123  RDREFKIFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAQPPSDPSEK 182

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                G+    A     A   + A I        + I   +   + + +  +    ++ ++
Sbjct: 183  IGWEGLIRSGAVEYLDAEEEETAMICM--TPEDLEIYREQKQDEINLTEEERQAKLEAEK 240

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
              Q    N+R   KV             PS  LG       +  + +P+  +N       
Sbjct: 241  REQEEERNKRLKTKVNPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTY 293

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +     +  +                                 +  +     
Sbjct: 294  QSAMGKQAMG--FFLTNYSRRM---------------------------DTMANILYYPQ 324

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    +       +   +  + AI      +  D+ +   S +   +    +F R  
Sbjct: 325  KPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSY 383

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             D+ ++      E  E   +           +       +  G           K+  + 
Sbjct: 384  SDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID 443

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +      R+Q  Q       ++     +  Q   + +                      
Sbjct: 444  QENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA--------------------D 483

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PS
Sbjct: 484  NVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPS 543

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 544  RMTIAHLIECLLSKVSTLEGMEGD------------------------------------ 567

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++ +LR       G  ++Y+G TG      V
Sbjct: 568  -----------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLRAQV 609

Query: 1250 TVG 1252
              G
Sbjct: 610  FFG 612



 Score =  102 bits (254), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 73/540 (13%), Positives = 153/540 (28%), Gaps = 76/540 (14%)

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I ++  +A  + L +     G +   +    +    V  +    Y       E  I+  I
Sbjct: 5   IGRDGKLAKPRQLHNTH--WGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +       + ++    +   +       S      +      S +   R+     +  + 
Sbjct: 63  NRG---MEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLV 119

Query: 551 RARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVNAYGFIE 599
           R     E + +       + P  T           ++G  +     +   A+  A    +
Sbjct: 120 RDIRDREFK-IFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAQPPSD 178

Query: 600 TPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
              +        +  V YL A EEE   I      L+      ++ +             
Sbjct: 179 PSEKIGWEGLIRSGAVEYLDAEEEETAMICMTPEDLEIYREQKQDEIN------------ 226

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                                  L  ++    L     +++     + +     T     
Sbjct: 227 -----------------------LTEEERQAKLEAEKREQEEERNKRLKTKVNPTTHMYT 263

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVN 777
             +   + I+   A I+   D  +    + +  +     G        +           
Sbjct: 264 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRMDTMANILYYP 323

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PL                      +L  G+N +VA   + GYN EDS+++++  +   
Sbjct: 324 QKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 373

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +   L   E+           +       +DE GI+  G  V+  D
Sbjct: 374 LFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGED 433

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P  +       +        +    RD S  + S  +G V  V +       K
Sbjct: 434 IIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNADNVK 486


>gi|115383163|gb|ABI96802.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 202

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 80/204 (39%), Positives = 106/204 (51%), Gaps = 40/204 (19%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 31   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 90

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 91   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 135

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR--------MAD 1227
                             +    +   +    +TPVFDGA EE +  +L            
Sbjct: 136  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDGEVM 178

Query: 1228 LDESGQSILYDGLTGEPFDRPVTV 1251
            +D  G++ L+DG +GEPF  PVTV
Sbjct: 179  VDGDGKARLFDGRSGEPFPYPVTV 202


>gi|158253066|gb|ABW24017.1| RNA polymerase beta subunit [Erwinia billingiae]
          Length = 212

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVREG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQIVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|158253042|gb|ABW24005.1| RNA polymerase beta subunit [Pantoea septica]
          Length = 212

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANAQLDEEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|126143400|gb|ABN80114.1| RNA polymerase beta-subunit [Prevotella nanceiensis]
          Length = 125

 Score =  217 bits (553), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 72/179 (40%), Positives = 87/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN               LG+  ++++                          
Sbjct: 1    NPLGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA  E ++     A L     + LYDG TG
Sbjct: 21   --------------AAGKKLGVKFATPIFDGAKLEDLSEWTEKAGLPHLCSTHLYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EQFDQPATVGVTYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|158253030|gb|ABW23999.1| RNA polymerase beta subunit [Pantoea vagans]
          Length = 212

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHP HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPRHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|68131876|gb|AAY85216.1| RNA polymerase II second largest subunit [Hibbertia scandens]
          Length = 873

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 121/907 (13%), Positives = 260/907 (28%), Gaps = 163/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   +             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRIIKKGHDCEEVTETQDFAK--VFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYVRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYSSTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L+      A        +       D      + Y+   EEE   I+         
Sbjct: 529 QRL-LIKKKDIRALQQRESPEDGG---WHDLVAKGFIEYVDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 577 --TINDLVTARLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 633 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINSIVAIAC 687

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 688 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGS 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK +P  +           A         RD S  + 
Sbjct: 748 YDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDD---------AQGVSSRYTRRDHSTSLR 798

Query: 933 SGVSGTV 939
              SG V
Sbjct: 799 HSESGMV 805



 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 115/795 (14%), Positives = 237/795 (29%), Gaps = 119/795 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYSSTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                K   A    +        D   +  I  V+ + 
Sbjct: 523  LFIVEKQRLLI--------------KKKDIRALQQRESPEDGGWHDLVAKGFIEYVDTEE 568

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N     +                    PS  LG       + 
Sbjct: 569  EETTMISMTINDLVTARLNPEEAYS-----------DTYTHCEIHPSLILG-------VC 610

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 611  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 644

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 645  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINSIVAIACYSGYNQEDSVIMNQ 701

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 702  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 760

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K++ ++                  D+    +    +  + TS    E  
Sbjct: 761  TRVSGEDVIIGKTSPIAQ-----------------DDAQGVSSRYTRRDHSTSLRHSESG 803

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 804  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 858

Query: 1113 KDGTPVDIVLNPLGV 1127
             +G   DI++NP  +
Sbjct: 859  VEGITPDIIVNPHAI 873


>gi|117675865|emb|CAL69203.1| RNA polymerase subunit B [Subtercola frigoramans]
          Length = 362

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/176 (38%), Positives = 97/176 (55%), Gaps = 6/176 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R+VVSQL RSPG++FD    +   S K +Y+ RIIP +G
Sbjct: 1   VFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFDRQLEKT--SDKDIYSARIIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEQFKGYSSIEATLEKDSILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSD 301
              A   +         V  +    ++++    +    L K  + K  + LG+ S+
Sbjct: 119 KEEALKDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGLESE 174



 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 133/354 (37%), Positives = 200/354 (56%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  D        +DI +                +  +
Sbjct: 11  EKGTFIINGTERVVVSQLVRSPGVYFDRQLEKTSDKDIYSARIIPSRGAWLEFEIDKRDQ 70

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     + I  TL  D    +++AL DIYR
Sbjct: 71  VGVRIDRKRKQSVTVFLKALGLTSEEIL--EQFKGYSSIEATLEKDSILTKEEALKDIYR 128

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+S +YDL+ VGR K+N +L L++      +  EDIIA 
Sbjct: 129 KLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGLESELSNSVLTNEDIIAT 188

Query: 440 IKILVDLRNGKGTIDDID---------------NLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   + T+  +                + GNRR+R+VGE+++NQ R GL RMER
Sbjct: 189 IKYLVALHENQTTLPGVRAGKKVDIRLDIDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 248

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 249 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 308

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 309 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 362


>gi|312985608|gb|ADR31265.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985610|gb|ADR31266.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985612|gb|ADR31267.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985614|gb|ADR31268.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985616|gb|ADR31269.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985618|gb|ADR31270.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985620|gb|ADR31271.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985622|gb|ADR31272.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985624|gb|ADR31273.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985632|gb|ADR31277.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985634|gb|ADR31278.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985638|gb|ADR31280.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985640|gb|ADR31281.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985642|gb|ADR31282.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985644|gb|ADR31283.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985646|gb|ADR31284.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985648|gb|ADR31285.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985650|gb|ADR31286.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985652|gb|ADR31287.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985654|gb|ADR31288.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985656|gb|ADR31289.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985658|gb|ADR31290.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985660|gb|ADR31291.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985662|gb|ADR31292.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985664|gb|ADR31293.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985666|gb|ADR31294.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985668|gb|ADR31295.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985670|gb|ADR31296.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985672|gb|ADR31297.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985674|gb|ADR31298.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985676|gb|ADR31299.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985678|gb|ADR31300.1| RNA polymerase II [Fusarium sp. YM-2010]
 gi|312985680|gb|ADR31301.1| RNA polymerase II [Fusarium sporotrichioides]
 gi|312985682|gb|ADR31302.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985684|gb|ADR31303.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985686|gb|ADR31304.1| RNA polymerase II [Fusarium langsethiae]
 gi|312985688|gb|ADR31305.1| RNA polymerase II [Fusarium langsethiae]
          Length = 612

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 108/723 (14%), Positives = 198/723 (27%), Gaps = 130/723 (17%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + R     + R +H TH+G +CPAET EG   GLV +L+    V+     E     + 
Sbjct: 3    TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 607  D--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
            +   +V  +            ++  +   +  D       V        +      + D 
Sbjct: 63   NRGMEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLVRDI 122

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--------------QRQAVPLLKAEAP 709
             D   K        + P       +    G N               Q QA P       
Sbjct: 123  RDREFKIFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAEPPSDPSEK 182

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                G+    A     A   + A I        + I   +   + + +  +    ++ ++
Sbjct: 183  IGWEGLIRSGAVEYLDAEEEETAMICM--TPEDLEIYREQKQDEINLTEEEKQAKLEAEK 240

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
              Q    N+R   KV             PS  LG       +  + +P+  +N       
Sbjct: 241  REQEEERNKRLKTKVNPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTY 293

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +     +  +                                 +  +     
Sbjct: 294  QSAMGKQAMG--FFLTNYSRRM---------------------------DTMANILYYPQ 324

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    +       +   +  + AI      +  D+ +   S +   +    +F R  
Sbjct: 325  KPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSY 383

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             D+ ++      E  E   +           +       +  G           K+  + 
Sbjct: 384  SDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID 443

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +      R+Q  Q       ++     +  Q   + +                      
Sbjct: 444  QENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA--------------------D 483

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PS
Sbjct: 484  NVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPS 543

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 544  RMTIAHLIECLLSKVSTLEGMEGD------------------------------------ 567

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++ +LR       G  ++Y+G TG      V
Sbjct: 568  -----------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLRAQV 609

Query: 1250 TVG 1252
              G
Sbjct: 610  FFG 612



 Score =  101 bits (252), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 74/540 (13%), Positives = 151/540 (27%), Gaps = 76/540 (14%)

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I ++  +A  + L +     G +   +    +    V  +    Y       E  I+  I
Sbjct: 5   IGRDGKLAKPRQLHNTH--WGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +       + ++    +   +       S      +      S +   R+     +  + 
Sbjct: 63  NRG---MEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLV 119

Query: 551 RARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVNAYGFIE 599
           R     E + +       + P  T           ++G  +     +   A+  A    +
Sbjct: 120 RDIRDREFK-IFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAQEQAEPPSD 178

Query: 600 TPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
              +        +  V YL A EEE   I      L+      ++ +             
Sbjct: 179 PSEKIGWEGLIRSGAVEYLDAEEEETAMICMTPEDLEIYREQKQDEIN------------ 226

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                                   E +   ++      Q +             T M   
Sbjct: 227 ----------------------LTEEEKQAKLEAEKREQEEERNKRLKTKVNPTTHM-YT 263

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVN 777
             +   + I+   A I+   D  +    + +  +     G        +           
Sbjct: 264 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRMDTMANILYYP 323

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PL                      +L  G+N +VA   + GYN EDS+++++  +   
Sbjct: 324 QKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 373

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +   L   E+           +       +DE GI+  G  V+  D
Sbjct: 374 LFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGED 433

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P  +       +        +    RD S  + S  +G V  V +       K
Sbjct: 434 IIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNADNVK 486


>gi|255721739|ref|XP_002545804.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Candida
            tropicalis MYA-3404]
 gi|240136293|gb|EER35846.1| DNA-directed RNA polymerase III 130 kDa polypeptide [Candida
            tropicalis MYA-3404]
          Length = 1159

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 118/311 (37%), Gaps = 64/311 (20%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                  ++KV +   R  + GDK +                                   
Sbjct: 901  SDNDQALIKVLLRQTRRPELGDKFS----------------------------------- 925

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
              SR                  G+K    I   + +   +      + ++       +++
Sbjct: 926  --SR-----------------HGQKGVCGIIVQQEDMPFNDYGISPDIIMNPHGFPSRMT 966

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  ++       +G       F G+  E ++ +L       SG+ +L  G+TGE   
Sbjct: 967  VGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFSYSGKDMLQSGITGECLQ 1026

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYG 1306
              +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AYG
Sbjct: 1027 AYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYG 1086

Query: 1307 AAYVLQEMLTIKSD----DVVGRTRV--YES----IVAGNDTFETGTPESFNVLVKEMQA 1356
            A+ +L E L I SD    DV  +  +  Y +      +  +  +   P +  +L +E+ +
Sbjct: 1087 ASQLLLERLMISSDAFEVDVCNKCGLMGYNNWCTTCQSSENVIKMTIPYAAKLLFQELLS 1146

Query: 1357 LGLSIDLENSR 1367
            + ++  L    
Sbjct: 1147 MNIAPRLRLGD 1157



 Score =  185 bits (470), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 125/978 (12%), Positives = 279/978 (28%), Gaps = 183/978 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFD-----P 83
           L++    SY++F+ +++    + NE        V P         ++++           
Sbjct: 55  LVKQHLDSYNYFVDVDLKKIIKANE---LVLSDVDP------EFYVKYLDIRVGHKSTAK 105

Query: 84  P-----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
           P          +C  RDLTY+ P+ + +             +  K I+   + +G +P+M
Sbjct: 106 PGVKEVILPPHECRLRDLTYSAPIYVDVEYT----------RGRKIIRHNDLEIGRMPVM 155

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G FV+ G +++++ Q   S          + ++
Sbjct: 156 LRSNKCMLEGMSEASMAQVEECPLDPGGYFVVNGTEKVILVQEQLSKNRIIVEADEKKAI 215

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
               + +     ++           D I+++ +     +P+   L A G+ S+ EIL   
Sbjct: 216 VQASVTSST--HERKSK-TYVITKNDKIYLKHNSVSEDIPIVIILKAAGITSDLEILQLV 272

Query: 233 YPK---------IVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
                       + + +      F    A L VG +V +           ++ G +  + 
Sbjct: 273 CGTDPNYQDLFVVNFEEAAKLEVFTQQQALLYVGKRVKTIRRAGAPKLSQLQEGIEAIAT 332

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  +    V  L      L    +A  +V        ++  D +  K LE         
Sbjct: 333 TI--VAHLTVSDLQFREKALYIATMARRVVMAMHNPKMVDDRDYVGNKRLELAGQLMSLL 390

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRK-DALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
              L+    ++     + ++   ++  + DALL I                   +   + 
Sbjct: 391 FEDLFKKFNSDFKANIDKVLKKPSRTSEFDALLSINIHSNN----ITMGLNRAISTGNWS 446

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G   +  RL+  +   +            K+     L+  +  +    +  
Sbjct: 447 LKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTP 506

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +     E  +K+   ++  + +   D        +       + 
Sbjct: 507 EGEACGLVKNLALMTHITTDDEEAPVKKLCIALGCEPIYALDSATLHSEGNFGVYLNGTL 566

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +        ++   H RR   +            +   +         P    E    
Sbjct: 567 IGTTRFPQK-FVNDFRHLRRNGKVSAFISIYTNTHHQAVHIATDGGRICRPLIIVENGES 625

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            + +   +         +        D      V YL   EE +  IA     ++ +   
Sbjct: 626 KVTAEHLA--------KLLNQEWSFDDFLKHGLVEYLDVNEENDSLIALYEEDINAN--- 674

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                               +  ++  P  V+   A LIP+  ++ S R    C M +QA
Sbjct: 675 ----------------SSTTVTHMEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQA 718

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +                                           I   +     +     
Sbjct: 719 IGA-----------------------------------------IAYNQFRRIDTLLYFM 737

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
           +Y               Q+P+VK                 D   L  G+N  VA M + G
Sbjct: 738 VYP--------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSG 773

Query: 821 YNFEDSMLISERMVSEDVFTSIHIE-------EFEVMARDTKLGPEEITRDIPNVSEEGL 873
           Y+ ED++++++  +         +        ++    +D   G      + P    +  
Sbjct: 774 YDIEDALVLNKSSLDRGFGRCQVVRKNTVQLKKYPNHTQDILSGMRVDENNNPIFPHQA- 832

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +   G+  VG+ ++ G +   K  P      + E  L      ++ +D    +     
Sbjct: 833 --LGPDGLGEVGSRIHNGQVFANKCVPTN----SGESALGGPQQDDRQMDRHREAPAFYK 886

Query: 934 GVSGTVVDVRIFNRHGID 951
           G   + +D  + +    D
Sbjct: 887 GPEPSYIDQVMMSVSDND 904


>gi|30141085|gb|AAP21853.1| RNA polymerase beta subunit [Streptococcus agalactiae ATCC 13813]
          Length = 232

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 91/288 (31%), Positives = 126/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 179  ATPVFDGASSEDLWETVQEAGMDSDAK----------------------------TVLYD 210

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            G                           TGEPFD  V+VG +YM+KL+
Sbjct: 211  G--------------------------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/89 (61%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|218513317|ref|ZP_03510157.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli 8C-3]
          Length = 208

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 148/207 (71%), Positives = 173/207 (83%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  + VN LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NI
Sbjct: 1   QLSQFMDQVNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL +FARVN YGFIE+PYR++ DGKVTNDV+YLSAMEE   Y+AQAN+ ++ DGSF
Sbjct: 61  GLINSLATFARVNKYGFIESPYRRIVDGKVTNDVLYLSAMEEAKYYVAQANAEMNPDGSF 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
            +E V CR AGE +L PR+ ++ +D SPKQVVS+AA+LIPFLENDD+NR LMG NMQRQA
Sbjct: 121 VDEFVVCRHAGEVMLAPRDSMNLMDVSPKQVVSVAAALIPFLENDDANRALMGSNMQRQA 180

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAI 727
           VPLL+AEAPFVGTGME VVA+ SGAAI
Sbjct: 181 VPLLRAEAPFVGTGMEPVVARDSGAAI 207


>gi|158253038|gb|ABW24003.1| RNA polymerase beta subunit [Pantoea septica]
 gi|158253040|gb|ABW24004.1| RNA polymerase beta subunit [Pantoea septica]
          Length = 212

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANAQLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|269912644|emb|CAY86102.1| RNA polymerase beta subunit [Gluconobacter oxydans]
          Length = 250

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 108/253 (42%), Positives = 152/253 (60%), Gaps = 28/253 (11%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------- 221
           SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL             
Sbjct: 1   SGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYLAQREQKI 60

Query: 222 ------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                       GMD +EILS FY  + +++ G  W  P    D   G K+ S LVD DT
Sbjct: 61  AEGGDVEGLDIRGMDQDEILSYFYEAVPFTRLGGEWARPFDP-DAFRGLKLLSPLVDADT 119

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE V E+  KLT+ +++ + EK  + + +    + G ++A D+VN  TGEIY EAG+ + 
Sbjct: 120 GEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDILGRFLAYDLVNENTGEIYGEAGEELT 178

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E  L  +    I ++P+L VD  ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T 
Sbjct: 179 EDRLAALEEMGITELPLLSVDG-SHGPWIRNTLAADKNSCRDEALIDIYRIMRPGEPPTK 237

Query: 390 SVAESMFNFLFFD 402
             AE+MF+ LFFD
Sbjct: 238 ETAEAMFHGLFFD 250


>gi|199580785|gb|ACH89094.1| RNA polymerase subunit beta [Staphylococcus succinus subsp. casei]
 gi|199580787|gb|ACH89095.1| RNA polymerase subunit beta [Staphylococcus succinus subsp. succinus]
          Length = 231

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 107/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  ++ D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GII VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580711|gb|ACH89057.1| RNA polymerase subunit beta [Staphylococcus carnosus subsp. carnosus]
 gi|199580763|gb|ACH89083.1| RNA polymerase subunit beta [Staphylococcus piscifermentans]
 gi|199580783|gb|ACH89093.1| RNA polymerase subunit beta [Staphylococcus simulans]
          Length = 231

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREDGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV+E  LKN+DE GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVAESALKNLDERGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 91


>gi|158252892|gb|ABW23930.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158252900|gb|ABW23934.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252902|gb|ABW23935.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158252904|gb|ABW23936.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252914|gb|ABW23941.1| RNA polymerase beta subunit [Pantoea sp. LMG 24202]
 gi|158252916|gb|ABW23942.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252920|gb|ABW23944.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252922|gb|ABW23945.1| RNA polymerase beta subunit [Pantoea sp. LMG 24203]
 gi|158252926|gb|ABW23947.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252928|gb|ABW23948.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252932|gb|ABW23950.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252936|gb|ABW23952.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252938|gb|ABW23953.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252944|gb|ABW23956.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252946|gb|ABW23957.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252958|gb|ABW23963.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252960|gb|ABW23964.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252998|gb|ABW23983.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158253000|gb|ABW23984.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158253002|gb|ABW23985.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158253006|gb|ABW23987.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158253010|gb|ABW23989.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158253012|gb|ABW23990.1| RNA polymerase beta subunit [Pantoea stewartii subsp. indologenes]
 gi|158253016|gb|ABW23992.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|288188618|gb|ADC42768.1| RNA polymerase beta subunit [Pantoea allii]
 gi|288188622|gb|ADC42770.1| RNA polymerase beta subunit [Pantoea allii]
 gi|288188624|gb|ADC42771.1| RNA polymerase beta subunit [Pantoea allii]
 gi|288188626|gb|ADC42772.1| RNA polymerase beta subunit [Pantoea allii]
          Length = 212

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|158252972|gb|ABW23970.1| RNA polymerase beta subunit [Pantoea punctata]
          Length = 212

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LD+DG F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDDDGQFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEPDDANRALMGANMQRQ 212


>gi|30141090|gb|AAP21855.1| RNA polymerase beta subunit [Streptococcus dysgalactiae]
          Length = 232

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 93/296 (31%), Positives = 129/296 (43%), Gaps = 72/296 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 171  ARNLGIHIATPVFDGASSEDLWDTVREAGMDSDAK------------------------- 205

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               T ++DG                           TGEPFD  V+VG +YM+KL+
Sbjct: 206  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGIVRDVKIFTRANGD 90


>gi|312216855|emb|CBX96804.1| similar to DNA-directed rna polymerase III subunit [Leptosphaeria
            maculans]
          Length = 1257

 Score =  217 bits (553), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/345 (20%), Positives = 125/345 (36%), Gaps = 79/345 (22%)

Query: 1051 DRFKNKIEKIQWGD---------DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            + +K+K EK +  D                 ++K+ +   R  + GDK +          
Sbjct: 970  NIYKDKPEKYKMPDCSYVDKACITENEAGTTLIKLLMRQTRRPELGDKFS---------- 1019

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                                       SR                  G+K  + +   + 
Sbjct: 1020 ---------------------------SR-----------------HGQKGTTGLIVQQE 1035

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +   +      + ++       +++      +L        G       F G+  E ++ 
Sbjct: 1036 DMPFNDQGINPDIIMNPHGFPSRMTVGKMMELLSGKAGVLRGTLEYGTAFGGSRVEDMSQ 1095

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            +L       +G+  L  G+TGE        G IY  KL HMV DK+++R+ G  +++T+Q
Sbjct: 1096 VLVENGFSYTGKDYLTSGITGEAHQFYTFFGPIYYQKLKHMVQDKMHSRARGPRAILTRQ 1155

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV---------GRTRV 1328
            P  G++  GG RLGEME  C+ AYGA+ +L E L I SD    DV          G  ++
Sbjct: 1156 PTEGRARDGGLRLGEMERDCLIAYGASQLLLERLMISSDAHDVDVCEKCGQMGYSGYCKL 1215

Query: 1329 YESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAK 1373
             ES            P +  +L++E+ ++ + + +         +
Sbjct: 1216 CES---EKAIRRITMPYAAKLLIQELGSMNVKVTIGLEDEFPREE 1257



 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 133/939 (14%), Positives = 271/939 (28%), Gaps = 201/939 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV-FPITAFSGAAMLEFVSYEFDPP--- 84
           L++    SY+HF+ +           L+   K+  F  + F    +LE+V      P   
Sbjct: 163 LVKQHVDSYNHFVDVE----------LKKIIKANRFVRSDFDPKFLLEYVDIRILSPNRQ 212

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                         ++C  RD+TYA P+ + +             +    +K   I +G 
Sbjct: 213 EEDDLDHHRSTITPNECRLRDMTYAAPIVVDI----------IYTRGNAKVKRTGIRIGR 262

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHR---------SP 161
           +P+M K                         G F+ +G +++++ Q            + 
Sbjct: 263 MPIMLKSSKCVLAGKSDREMAVMEECPLDPGGYFITRGQEKVILVQEQLNKNRVIVESAK 322

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMA 220
           GI                Y   +I             K ++ +R +    +VP+   L A
Sbjct: 323 GIMQASVTSSTHERRTKTY---VI-----------QKKGLMFLRHNTLSEEVPIVFALKA 368

Query: 221 LGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG+ S+ EIL          Q  D +     A           +L  I    ++++    
Sbjct: 369 LGVHSDKEILLMVAGDDSAYQ--DNFAINFEACAREKIHTQEKALEYIGHRVRLVKK--- 423

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                   ++   ++ +   S+ +   +V  +  N     +YI A          +    
Sbjct: 424 --PLGASRMRNYHLEAIECLSNVVLP-HVPVEGTNYRPKALYI-ALMARRVLMAMQDPKL 479

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +       +   +         +   D  L I +V++  + +    A + F+  
Sbjct: 480 VDDRDYVGNKRLELSGQMLSLLFEDHFKRFNHDFKLSIDKVLKKQNRAQEFDAFTHFSVH 539

Query: 400 FFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                      +     +  R  +D       + +   IA + ++  + +       +  
Sbjct: 540 KSQITMGIERAIATGNWSLKRFKMDRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 599

Query: 459 LGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
               +    G +      + +    +  +           +        L+ A+ + S  
Sbjct: 600 PRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTEDDEEPVRKIIFLLGAEDICSQT 659

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            E   S  +  +  +   ++     +R        + R     E   +H  H        
Sbjct: 660 GEEIHSEGIYSVCLNGTPIAVTDTPKRF-LNSFRKLRRMGRISEFTSIHINHDFCEVHVA 718

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRK--------VCDGKVTNDVVYLSAMEEENR 625
           T EG     +  +      N +  + + Y K          D      V YL   EE + 
Sbjct: 719 TDEGRICRPMIVVE-----NQHSKVTSRYLKALRKGTMEFEDFLTRGLVEYLDTNEENDT 773

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA     +++                           ++  P  ++   A LIP+  ++
Sbjct: 774 NIALKEEDINQ-----------------------HTTHLEIEPFTILGAVAGLIPYPHHN 810

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            S R    C M +QA+                                           I
Sbjct: 811 QSPRNTYQCAMGKQAIGA-----------------------------------------I 829

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              + +   +   + +Y               Q+P+VK                T    L
Sbjct: 830 AYNQFNRIDTLLYLMVYP--------------QQPMVK----------TRTIELTKYDKL 865

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             G+N  VA M + GY+ ED++++++            +++     +    G  +     
Sbjct: 866 PAGQNATVAVMSYSGYDIEDALILNKASCDRGFGRCQVLKKHVTPLKTYANGTSDRINAG 925

Query: 866 PNVSEE-GLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              SE    + I   GI  VGA +  GD  + K  P+  
Sbjct: 926 ALNSENPSHQAIGLDGIAQVGARIEAGDAFLLKSIPQDT 964


>gi|312204330|gb|ADQ47482.1| RNA polymerase II second largest subunit [Gyalecta geoica]
          Length = 691

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 104/721 (14%), Positives = 205/721 (28%), Gaps = 61/721 (8%)

Query: 473  NQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------- 521
              +R+   ++ + + +  +              + +  + + +     +           
Sbjct: 1    GLFRMLFNKLTKDVXQYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAAS 60

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 61   AKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 116

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L     +      E    +    + +V  +            ++      + 
Sbjct: 117  QACGLVKNLALMCYITVGSPSEPIVEFMVQRNMEVLEEYEPTRNPHSTKVFVNGVWVGVH 176

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMG 693
             D +     V        I      I D  D   K          P F+  +D   V  G
Sbjct: 177  RDPAHLVSTVQTLRRQNMISFEVSLIRDIRDREFKIFTDAGRVCRPLFVIENDKKSVNKG 236

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  + +     +   +   M+    K       AK  G    V      +  ++ + +
Sbjct: 237  YLVLSKELIGKLEDDRELPQDMDPDERK-------AKYFGWAGLV--ANGAVEFLDAEEE 287

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNML 812
             +         ++  R+ Q       P   +   V+          T      ++   + 
Sbjct: 288  ETVMIAMTPEDLEISRAVQAGYELPEPSADLNARVKAPVSARGHTWTHCEIHPSMILGIC 347

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N     L                                            
Sbjct: 348  ASIIPFPDHNQVRRSLXXXXXXXXXXXXXXXXXX-XXXXXXXXXXXXXXXXXXXXXXXXX 406

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                                             +   +  + AI      +  D+ +   
Sbjct: 407  XXXXXXXXXXXXXXXXXXXXXXXXXXXFLKFRQLPAGQNAIVAIACYSGYNQEDSVIMNQ 466

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---I 989
            S +   +    +F R  +++ +R        +E   +    E +      Y +L +   I
Sbjct: 467  SSIDRGLF-RSLFYRSYMEQEKRVGI---SLVEQFEKPLRSETLRFKHGTYDKLDDDGII 522

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  LS D      R+++         ++     +           
Sbjct: 523  APGVRVSGEDIIIGKTAPLSQDAEELGQRTKFHTKRDASTPLRSTESGI----------- 571

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                   ++K+          L+ VKV +   +  Q GDK A RHG KG +      EDM
Sbjct: 572  -------VDKVLM--TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDM 622

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  DG   D+++NP  +PSRM +  + E  L       G +  +          +S L 
Sbjct: 623  PFSTDGIAPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEITVDQVSRLL 682

Query: 1170 S 1170
             
Sbjct: 683  R 683



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 50/370 (13%), Positives = 97/370 (26%), Gaps = 49/370 (13%)

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                NK  KD    + + +  G    F++   + +    +  KY L   G      +  
Sbjct: 3   FRMLFNKLTKDVXQYLQKCVESG--KEFNLTLGVKSTTLTNGLKYSL-ATGNWGDQKKAA 59

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                  + + +    + +  L        R+GK       +  +  +    E  + Q  
Sbjct: 60  SAKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 119

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEH 528
             +  +       + S     V      N + +          +   F     +    + 
Sbjct: 120 GLVKNLALMCYITVGSPSEPIVEFMVQRNMEVLEEYEPTRNPHSTKVFVNGVWVGVHRDP 179

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            + +S +   RR + +                +         P    E     +      
Sbjct: 180 AHLVSTVQTLRRQNMISFEVSLIRDIRDREFKIFTDAGRVCRPLFVIENDKKSVNKGYLV 239

Query: 589 FARVNAYGFIETPYRKVCDGKVTND---------------VVYLSAMEEENRYIA----- 628
            ++    G +E       D                     V +L A EEE   IA     
Sbjct: 240 LSK-ELIGKLEDDRELPQDMDPDERKAKYFGWAGLVANGAVEFLDAEEEETVMIAMTPED 298

Query: 629 -------QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                  QA   L E  +     V        +          +  P  ++ I AS+IPF
Sbjct: 299 LEISRAVQAGYELPEPSADLNARVKA-----PVSARGHTWTHCEIHPSMILGICASIIPF 353

Query: 682 LENDDSNRVL 691
            +++   R L
Sbjct: 354 PDHNQVRRSL 363


>gi|199580755|gb|ACH89079.1| RNA polymerase subunit beta [Staphylococcus muscae]
          Length = 231

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGMTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|327133519|gb|AEA29764.1| RNA polymerase subunit B [Acinetobacter sp. 12NS2]
          Length = 179

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 81/182 (44%), Positives = 113/182 (62%), Gaps = 3/182 (1%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G    K+   L+ D++S+       +    DE +   +  ++   +   + ++++F  
Sbjct: 1    SNGGGTTKRGDQLTEDILSQLKMVDLLEIPPSDEGIAERLTQIQTYLKEKSAEIDEKFAE 60

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP    G
Sbjct: 61   KKRKLSTGDELTTGVLKVVKVYLAVKRHIQPGDKMAGRHGNKGVVSNILPVEDMPHDASG 120

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR FL K+
Sbjct: 121  VPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLHKI 177

Query: 1176 IG 1177
              
Sbjct: 178  YN 179


>gi|312204304|gb|ADQ47469.1| RNA polymerase II second largest subunit [Carestiella socia]
          Length = 701

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 105/795 (13%), Positives = 212/795 (26%), Gaps = 119/795 (14%)

Query: 470  MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
            ++    R    ++ + +    +              + A  + + +     +        
Sbjct: 1    LMAGCSRNLFNKLNKDVYXYLQKCVESGKEFNLNLGVKASTLTNGLKYSLATGNWGDQKK 60

Query: 522  -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                   +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61   AMSSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLVCPAET 116

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
             EG   GLV +L+    V      E    +    + +V  +   + +      ++     
Sbjct: 117  PEGQACGLVKNLSLMCYVTVGQPSEPLIDFMVQRNMEVLEEYDPMRSPNATKVFVNGVWV 176

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +  D +     V        I      + D  D   K          P L  DD  +  
Sbjct: 177  GVHRDPAHLVSTVKMLRRKSLISWEISLVRDIRDREFKIFTDAGRVCRPLLVIDDDPKSP 236

Query: 692  MGCNMQ--RQAVPLLKAEAPFVG--TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
               N+   ++ V  L+ +       T  E          I+                +  
Sbjct: 237  NKGNLVLTKELVNKLEDDKDLPLDLTKDERAERYFGWDGIM------------KAGAVEF 284

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            ++ + + +   +     ++  R  Q       P       V+    +     T       
Sbjct: 285  LDAEEEETVMIIMTPEDLEISRQVQAGYAPPEPNPDPNARVKGTVNLTQHQWTHCEIHPS 344

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                  A +                                                   
Sbjct: 345  MILEXCASIIPFPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 404

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 405  XXXXXXXXXXXXXMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 464

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  +++ +R        +E   +    + + L    Y +L 
Sbjct: 465  VIMNQSSIDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPMRSDTLRLKHGTYEKLD 520

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  +  D      R++          ++     +      
Sbjct: 521  DDGIVAPGVRVSGEDIIIGKTAPIPPDSEEMGQRTKLHTKRDASTPLRSTESGI------ 574

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                        ++K+          L+ VKV     +  Q GDK+A RHG KG +    
Sbjct: 575  ------------VDKVLL--TTNAEGLKFVKVRTRTTKIPQIGDKLASRHGQKGTIGITY 620

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   DI++NP  +PSRM +  + E  L       G +             
Sbjct: 621  RMEDMPFSAEGVTPDIIINPHAIPSRMTIAHLVECQLSKVSSLRGFEGD----------- 669

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
                                                      +TP F     ++++ +LR
Sbjct: 670  ------------------------------------------ATP-FTDVTVDSVSRLLR 686

Query: 1225 MADLDESGQSILYDG 1239
                   G  ++Y+G
Sbjct: 687  EHGYQSRGFEVMYNG 701



 Score =  108 bits (269), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 89/636 (13%), Positives = 171/636 (26%), Gaps = 90/636 (14%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +        NK  KD    + + +  G    F++   +      +  KY L   G     
Sbjct: 2   MAGCSRNLFNKLNKDVYXYLQKCVESG--KEFNLNLGVKASTLTNGLKYSL-ATGNWGDQ 58

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLK 472
            +         + + +    + +  L        R+GK       +  +  +    E  +
Sbjct: 59  KKAMSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHCTHWGLVCPAETPE 118

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQ 524
            Q    +  +       +       +      N + +         +A   F     +  
Sbjct: 119 GQACGLVKNLSLMCYVTVGQPSEPLIDFMVQRNMEVLEEYDPMRSPNATKVFVNGVWVGV 178

Query: 525 LEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRIC--------PAETS 575
             +  + +S +   RR S +  +  + R     E +    T  GR+C          ++ 
Sbjct: 179 HRDPAHLVSTVKMLRRKSLISWEISLVRDIRDREFK--IFTDAGRVCRPLLVIDDDPKSP 236

Query: 576 EGHNIGLVSSLTSFARVNAYGFIE-------TPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
              N+ L   L +    +    ++         Y           V +L A EEE   I 
Sbjct: 237 NKGNLVLTKELVNKLEDDKDLPLDLTKDERAERYFGWDGIMKAGAVEFLDAEEEETVMII 296

Query: 629 QANSSLDEDGSFTEELVFCRCAGE-------EILVPREKIDFIDASPKQVVSIAASLIPF 681
                L+                +        + + + +    +  P  ++   AS+IPF
Sbjct: 297 MTPEDLEISRQVQAGYAPPEPNPDPNARVKGTVNLTQHQWTHCEIHPSMILEXCASIIPF 356

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                                                                       
Sbjct: 357 PXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX---------------------------XX 389

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                                        +      Q+PL                    
Sbjct: 390 XXXXXXXXXXXXXXXXXXXXXXXXXXXXMSNILYYPQKPL----------ATTRSMEFLK 439

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE- 860
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E 
Sbjct: 440 FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKRVGMSLVEQ 499

Query: 861 ----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
               +  D   +     + +D+ GI+  G  V+  DI++GK  P    P   EE   R  
Sbjct: 500 FEKPMRSDTLRLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPI---PPDSEEMGQRT- 555

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              K    RD S  + S  SG V  V +       K
Sbjct: 556 ---KLHTKRDASTPLRSTESGIVDKVLLTTNAEGLK 588


>gi|312618481|gb|ADR00358.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618497|gb|ADR00366.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618513|gb|ADR00374.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
 gi|312618517|gb|ADR00376.1| RNA polymerase beta subunit [Gibbsiella quercinecans]
          Length = 212

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 134/211 (63%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVTDEINYLSAIEEGNFVIAQANSNLDEEGRFIEDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|269913233|emb|CAY86043.1| RNA polymerase beta subunit [Asaia bogorensis]
          Length = 243

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 144/246 (58%), Gaps = 28/246 (11%)

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------- 221
           SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL             
Sbjct: 1   SGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGEHSIAARAAKA 60

Query: 222 ------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
                       GMD +EIL+ FY  + +++    W  P        G K+   L D DT
Sbjct: 61  AEGGDVEALGIRGMDQDEILAYFYGTVPFTRMPKGWARPFDPE-AFRGMKLLEPLYDADT 119

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
           GE V E+  KLT+ + + + E   K + +    L G ++A+D+VN  TGEIY EAG+ + 
Sbjct: 120 GEVVAEADAKLTARMCRKIAET-TKDVLVGRADLLGRFIAQDLVNENTGEIYAEAGEELT 178

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E  LE +  S + ++P+L VDS ++  +IRNTL  DKN  R +AL+DIYR+MRPG+  T 
Sbjct: 179 EARLEALEESGVTELPMLAVDS-SHGPWIRNTLAVDKNNRRDEALIDIYRIMRPGEPPTP 237

Query: 390 SVAESM 395
             AE+M
Sbjct: 238 ETAEAM 243


>gi|62947920|gb|AAY22957.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 223

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 131/220 (59%), Positives = 163/220 (74%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYRKV    G+VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYRKVDRATGRVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F EE+V  R  G         +DF+D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVVDFVDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|140084132|gb|ABO84915.1| RpoB [Bacillus pumilus]
          Length = 238

 Score =  217 bits (552), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 81/211 (38%), Positives = 106/211 (50%), Gaps = 54/211 (25%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 82   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 141

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 142  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 201

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 202  GMSRDAK----------------------------TVLYDG------------------- 214

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                    TGEPFD  V+VG +YM+KL HMV
Sbjct: 215  -------RTGEPFDNRVSVGIMYMIKLAHMV 238



 Score = 88.6 bits (218), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 61/93 (65%), Positives = 74/93 (79%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITRDIPNV E+ L+N+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFG
Sbjct: 1   EEITRDIPNVGEDALRNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           EKA +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 61  EKAREVRDTSLRVPHGGGGIIHDVKVFNREDGD 93


>gi|327133547|gb|AEA29778.1| RNA polymerase subunit B [Acinetobacter sp. 14N1]
          Length = 204

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 85/203 (41%), Positives = 120/203 (59%), Gaps = 4/203 (1%)

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L      +G    K+   L+ D +S+       +    DE +   +  ++   +   + +
Sbjct: 5    LLNDQMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEI 64

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +++F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDM
Sbjct: 65   DEKFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDM 124

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P   +G PVD+VLNPLGV SRMNVG I ETHLG A  GLG++I  ++   K    I+ LR
Sbjct: 125  PHDANGVPVDVVLNPLGVSSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELR 181

Query: 1170 SFLEKVIGT-GSHTEKISDYDDD 1191
             FL+K+    G   E++    DD
Sbjct: 182  EFLDKIYNKVGGEQEELETLTDD 204


>gi|89274916|gb|ABD65899.1| RNA polymerase II second largest subunit [Peniophora nuda]
          Length = 561

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/395 (17%), Positives = 117/395 (29%), Gaps = 75/395 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 242  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 301

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G     G
Sbjct: 302  LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLHMKHGTYDKLEDDGMIAPGTGVNGG 360

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L  D      R++          ++     +  Q                 
Sbjct: 361  DIIIGKTAPLPVDSEELGQRNRLHTRRDVSTPLKSTESGIVDQVLI-------------- 406

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VK+ V   R  Q+GDK A RHG KG +      EDMPF  +G   
Sbjct: 407  ------TTNHEGQKFVKIRVRSTRIPQTGDKFASRHGQKGTIGITYRQEDMPFTSEGIVP 460

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      +G +  +                        
Sbjct: 461  DIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-------------------- 500

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  ++     + LR       G+ +                         G +    
Sbjct: 501  -----DLTVESVSTFLRQQGYHSRGLEIM----------------------YHGHT---- 529

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
               G      V +G  Y  +L HMV DK++AR+ G
Sbjct: 530  ---GRKLQAQVYLGPTYYQRLKHMVDDKIHARARG 561



 Score = 98.6 bits (244), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 71/443 (16%), Positives = 132/443 (29%), Gaps = 75/443 (16%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           F     +    +  N +S +   RR   +                ++        P    
Sbjct: 41  FVNGVWVGVHRDPTNLISTLKRLRRKDDVHPEVSIVRDIRERELRIYTDPGRVCRPLFVV 100

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E  ++ +      +           P+R       T  +  L A EEE   I+ +N  L+
Sbjct: 101 EDGSLVIEKKHVQWVSQGHTDDPNEPFR-WSQLIKTGVIEMLDAEEEETVMISMSNEDLE 159

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                 + L                    D +P  +    +S +                
Sbjct: 160 ARKLEAQGLD----------------THEDTNPDSMHFDPSSRL---------------- 187

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
                   L A  P + T  E                 I+   D  +    + +  +   
Sbjct: 188 ------KPLSAMRPHLFTHCE-------------IHPSIIPFPDHNQSPRNTYQSAMGKQ 228

Query: 756 TSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             G+     L++           Q+PL                      +L  G+N +VA
Sbjct: 229 AMGIYLTNFLVRMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVA 278

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVS 869
            + + GYN EDS+++++  +   +F SI+   +  + + + +   E           ++ 
Sbjct: 279 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLHMK 338

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +++ G+I  G  VN GDI++GK  P         ++        +    RD S 
Sbjct: 339 HGTYDKLEDDGMIAPGTGVNGGDIIIGKTAPLPVDSEELGQR-------NRLHTRRDVST 391

Query: 930 RVPSGVSGTVVDVRIFNRHGIDK 952
            + S  SG V  V I   H   K
Sbjct: 392 PLKSTESGIVDQVLITTNHEGQK 414


>gi|115606113|gb|ABJ16031.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606115|gb|ABJ16032.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606117|gb|ABJ16033.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 132/259 (50%), Positives = 186/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|62947912|gb|AAY22953.1| RNA polymerase beta subunit [Streptococcus sanguinis]
          Length = 223

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 125/220 (56%), Positives = 161/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF SSQLSQ  +  N LS ++H RRL ALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSHKRRLFALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDREAGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+E+G F E +V  R  G     P +++D++D SPKQVV++A + IPFL
Sbjct: 124 DEFIVAQANSKLNEEGGFAEPIVMGRHQGNNQEFPSDQVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|68300794|gb|AAY89340.1| RNA polymerase II second largest subunit [Berberidopsis beckleri]
          Length = 873

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 122/907 (13%), Positives = 260/907 (28%), Gaps = 163/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDCEEVTETQDFTK--VFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 GEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L+      A        +       D      + Y+   EEE   I+         
Sbjct: 529 QRL-LIKKKDIQALQQRESHEDGG---WHDLVAKGFIEYVDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +L+  +   E      E     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 577 --TINDLISAKLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 633 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAITC 687

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 688 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGS 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +           A         RD S  + 
Sbjct: 748 YDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRRDHSTSLR 798

Query: 933 SGVSGTV 939
              SG V
Sbjct: 799 HSESGMV 805



 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 116/795 (14%), Positives = 237/795 (29%), Gaps = 119/795 (14%)

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
             +       +    ++       ++A +   + +    +       S          KY 
Sbjct: 183  DILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGSTVGVTREKRIKYA 239

Query: 408  LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
               + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 240  KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLA 296

Query: 468  GEMLKNQYRLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
            G +L   +R+   ++ R ++   +    +   V  Q  I AK + S +     +      
Sbjct: 297  GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 356

Query: 522  --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                    +SQ+   +   S ++H RRL++     + R     + R +H +H+G +CPAE
Sbjct: 357  NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            T EG   GLV +L     +            + +    N        EE +  +    + 
Sbjct: 413  TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQATK 465

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  +G +           + +   R ++   D + +  V     L       D  R    
Sbjct: 466  IFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSRP 522

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIVIRSVEGDL 752
              +  +   L+                K   A    +        D   +  I  V+ + 
Sbjct: 523  LFIVEKQRLLI--------------KKKDIQALQQRESHEDGGWHDLVAKGFIEYVDTEE 568

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   + N     +                    PS  LG       + 
Sbjct: 569  EETTMISMTINDLISAKLNPEEAYS-----------ETYTHCEIHPSLILG-------VC 610

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 611  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 644

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 645  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAITCYSGYNQEDSVIMNQ 701

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      R+          +          G
Sbjct: 702  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPG 760

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T +S                  D+   +     +  + TS    E  
Sbjct: 761  TRVSGEDVIIGKTTPISQ-----------------DDAQGQASRYTRRDHSTSLRHSESG 803

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 804  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 858

Query: 1113 KDGTPVDIVLNPLGV 1127
             +G   DI++NP  +
Sbjct: 859  VEGITPDIIVNPHAI 873


>gi|213399748|gb|ACJ46649.1| RpoB [Prevotella sp. 8400706]
 gi|213399750|gb|ACJ46650.1| RpoB [Prevotella veroralis]
          Length = 126

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 70/180 (38%), Positives = 86/180 (47%), Gaps = 54/180 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NPLGVPSRMN               LG+  ++++                          
Sbjct: 1    NPLGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA    +      A L     + +YDG TG
Sbjct: 21   --------------AAGRKLGVKFATPIFDGAKLSDLKEWTDKAGLPNLCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW +
Sbjct: 67   EKFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWAL 126


>gi|158252942|gb|ABW23955.1| RNA polymerase beta subunit [Pantoea vagans]
          Length = 212

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEQDDANRALMGANMQRQ 212


>gi|50292925|ref|XP_448895.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528208|emb|CAG61865.1| unnamed protein product [Candida glabrata]
          Length = 1133

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 117/319 (36%), Gaps = 70/319 (21%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                   ++KV +   R  + GDK +                                  
Sbjct: 872  TSDNDQDLIKVLLRQNRRPELGDKFS---------------------------------- 897

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
               SR                  G+K    I   + +   +      + ++       ++
Sbjct: 898  ---SR-----------------HGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRM 937

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
            +      ++       +G       F G+  E ++ +L     + SG+ +LY G+TGE  
Sbjct: 938  TVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECL 997

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               +  G IY  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  C+ AY
Sbjct: 998  QAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAY 1057

Query: 1306 GAAYVLQEMLTIKSD----DVV---------GRTRVYESIVAGNDTFETGTPESFNVLVK 1352
            GA+ +L E L I SD    DV          G     +S        +   P +  +L +
Sbjct: 1058 GASQLLLERLMISSDAFEVDVCSNCGLMGYSGWCSTCKS---AEHIIKMTIPYAAKLLFQ 1114

Query: 1353 EMQALGLSIDLENSRTKNS 1371
            E+ A+ ++  L        
Sbjct: 1115 ELLAMNIAPRLRLEDIFQE 1133



 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 111/925 (12%), Positives = 259/925 (28%), Gaps = 176/925 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP----P 84
           L++    S+++F+ +++    + N   Q     V P         L++V          P
Sbjct: 45  LVKQHLDSFNYFVDVDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGQRSGSP 95

Query: 85  KFD----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT- 139
             D      +C  RD+TY+ P+ + +             +    I  +++ +G +P+M  
Sbjct: 96  HKDQLVPPHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKNVEIGRMPIMLR 145

Query: 140 -----------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSG 176
                                    G F++ G +++++ Q   S          +  +  
Sbjct: 146 SNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKDIVQ 205

Query: 177 KLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYP 234
             + +     ++     +       I+++ +    +VP+   L A G+ S+ EI+     
Sbjct: 206 ASVTSST--HERKSKTYVVT-KNGKIYLKHNSIAEEVPIVIVLKAAGIISDLEIMQLVCG 262

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVK 294
                Q         +A   +   + +   +                   +K+++ + + 
Sbjct: 263 NDSSYQDIFSVNLEEAAKLNICTQQQALEYIGAK----------------VKTMRRQKLT 306

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
            L    + +    +A   V              +  + +  + + ++ D      +    
Sbjct: 307 ILQEGIEAIATTIIAHLTVEALDFREKALYIATMTRRVVMAMHNPKMVDDRDYVGNKRLE 366

Query: 355 --NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG 412
                I         K   D  L I +V++  + +    A    N    +        + 
Sbjct: 367 LAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALLSINVHSNNITSGLNRAIS 426

Query: 413 RVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
               +++        V H    +     + ++  +         +     L   +   + 
Sbjct: 427 TGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLC 486

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEH 528
                +     L    ++   I++ D +  + +          ++ +            +
Sbjct: 487 TADTPEGEACGLVKNLALMTHITTDDEEEPIRKLCYVLGVEPISLLDSASLH--LNYGVY 544

Query: 529 VNSLSRITHTRRLSALGQGG-VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
           +N     T     + + +   + R     E   ++   +       T  G     +  + 
Sbjct: 545 LNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVK 604

Query: 588 S---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                        + +      D      V YL   EE + YIA     +  D       
Sbjct: 605 DGKSMVEAEHLKRLLSGELVFDDFLKLGLVEYLDVNEENDSYIALYEKDITHD------- 657

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                           I  ++  P  V+   A LIP+  ++ S R    C M +QA+   
Sbjct: 658 ----------------ITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGA- 700

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
                                                   I   +     +   + IY  
Sbjct: 701 ----------------------------------------IAYNQFKRIDTLLYLMIYP- 719

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                        Q+P+VK                 D   L  G+N  VA M + GY+ E
Sbjct: 720 -------------QQPMVK----------TKTIELIDYDKLPAGQNATVAVMSYSGYDIE 756

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN----IDECG 880
           D++++++  +           +   + +      ++    +              +   G
Sbjct: 757 DALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDALCGMRVDENGEAIWQHESLGPDG 816

Query: 881 IICVGAEVNPGDILVGKITPKGESP 905
           +  VG ++  G I + K  P   S 
Sbjct: 817 LGEVGLKIRSGQIYINKSVPVQSSD 841


>gi|158253048|gb|ABW24008.1| RNA polymerase beta subunit [Pantoea eucrina]
          Length = 212

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 170/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MP+D+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDALMPRDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|312985626|gb|ADR31274.1| RNA polymerase II [Fusarium armeniacum]
 gi|312985636|gb|ADR31279.1| RNA polymerase II [Fusarium armeniacum]
 gi|312985690|gb|ADR31306.1| RNA polymerase II [Fusarium armeniacum]
          Length = 612

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 107/723 (14%), Positives = 198/723 (27%), Gaps = 130/723 (17%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
              + R     + R +H TH+G +CPAET EG   GLV +L+    V+     E     + 
Sbjct: 3    TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 607  D--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
            +   +V  +            ++  +   +  D       V        +      + D 
Sbjct: 63   NRGMEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLVRDI 122

Query: 664  IDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--------------QRQAVPLLKAEAP 709
             D   K        + P       +    G N               + QA P       
Sbjct: 123  RDREFKIFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAREQAQPPSDPSEK 182

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                G+    A     A   + A I        + I   +   + + +  +    ++ ++
Sbjct: 183  IGWEGLIRSGAVEYLDAEEEETAMICM--TPEDLEIYREQKQDEINLTEEEKQAKLEAEK 240

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
              Q    N+R   KV             PS  LG       +  + +P+  +N       
Sbjct: 241  REQEEERNKRLKTKVNPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTY 293

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
               M  + +     +  +                                 +  +     
Sbjct: 294  QSAMGKQAMG--FFLTNYSRRM---------------------------DTMANILYYPQ 324

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                    +       +   +  + AI      +  D+ +   S +   +    +F R  
Sbjct: 325  KPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSY 383

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
             D+ ++      E  E   +           +       +  G           K+  + 
Sbjct: 384  SDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID 443

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
             +      R+Q  Q       ++     +  Q   + +                      
Sbjct: 444  QENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA--------------------D 483

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PS
Sbjct: 484  NVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPS 543

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +  + E  L       G +                                      
Sbjct: 544  RMTIAHLIECLLSKVSTLEGMEGD------------------------------------ 567

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                             +TP F     ++++ +LR       G  ++Y+G TG      V
Sbjct: 568  -----------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLRAQV 609

Query: 1250 TVG 1252
              G
Sbjct: 610  FFG 612



 Score =  102 bits (253), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 75/540 (13%), Positives = 151/540 (27%), Gaps = 76/540 (14%)

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERI 490
           I ++  +A  + L +     G +   +    +    V  +    Y       E  I+  I
Sbjct: 5   IGRDGKLAKPRQLHNTH--WGLVCPAETPEGQACGLVKNLSLMCYVSVGSPAEPLIEFMI 62

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
           +       + ++    +   +       S      +      S +   R+     +  + 
Sbjct: 63  NRG---MEVVEEYEPTRYPHATKVFVNGSWVGVHPDPRGLVNSVLDTRRKSYVQFEVSLV 119

Query: 551 RARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVNAYGFIE 599
           R     E + +       + P  T           ++G  +     +   AR  A    +
Sbjct: 120 RDIRDREFK-IFSDAGRVMRPVFTVQQEDDYETGINKGQLVLTKDLVNKIAREQAQPPSD 178

Query: 600 TPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
              +        +  V YL A EEE   I      L+      ++ +             
Sbjct: 179 PSEKIGWEGLIRSGAVEYLDAEEEETAMICMTPEDLEIYREQKQDEIN------------ 226

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
                                   E +   ++      Q +             T M   
Sbjct: 227 ----------------------LTEEEKQAKLEAEKREQEEERNKRLKTKVNPTTHM-YT 263

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVN 777
             +   + I+   A I+   D  +    + +  +     G        +           
Sbjct: 264 HCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRMDTMANILYYP 323

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PL                      +L  G+N +VA   + GYN EDS+++++  +   
Sbjct: 324 QKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 373

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +F S+    +    +   L   E+           +       +DE GI+  G  V+  D
Sbjct: 374 LFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGED 433

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           I++GK  P  +       +        +    RD S  + S  +G V  V +       K
Sbjct: 434 IIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNADNVK 486


>gi|117675881|emb|CAL69211.1| RNA polymerase subunit B [Agromyces cerinus subsp. nitratus]
          Length = 362

 Score =  216 bits (551), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 67/174 (38%), Positives = 93/174 (53%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K +Y+ R+IP +G
Sbjct: 1   VFMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFERTPEKT--SDKDIYSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEEFAGYESIALTLEKDNILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEEALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164



 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 131/341 (38%), Positives = 197/341 (57%), Gaps = 21/341 (6%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S         +   +K +    +      G ++  +I   +  ++ +       +  
Sbjct: 28  LVRSPGVYFERTPEKTSDKDIYSARVIPSR--GAWLEFEI--DKRDQVGVRIDRKRKQSV 83

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +    +    IL  +       I  TL  D    +++AL DIYR +RPG+      A
Sbjct: 84  TVFLKALGLTSEEIL--EEFAGYESIALTLEKDNILTKEEALKDIYRKLRPGEQVAAEAA 141

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
            ++ +  +F+  +YDL+ VGR K+N +L L+ P     +  +DI+A IK LV L + +  
Sbjct: 142 RALLDNFYFNPKRYDLAKVGRYKINNKLGLEAPLTDSVLTVQDIVATIKYLVALHDERTT 201

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI++
Sbjct: 202 LPGRRAGKAVDLRLDVDDIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEA 261

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE
Sbjct: 262 ITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVE 321

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           +RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 322 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 362


>gi|158252918|gb|ABW23943.1| RNA polymerase beta subunit [Pantoea ananatis]
          Length = 212

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPF E+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFREHDDANRALMGANMQRQ 212


>gi|153958295|gb|ABS53437.1| RpoB [Bacteriovorax sp. PS82B]
          Length = 329

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 159/332 (47%), Positives = 217/332 (65%), Gaps = 10/332 (3%)

Query: 726  AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
             + AK  G V  VD+ RIVI+  +       SGVDIY+L+K+QR+NQNT  NQ+ LVK G
Sbjct: 1    VLFAKEDGRVIFVDSNRIVIQRNK--FKDGESGVDIYKLVKYQRTNQNTSNNQKALVKEG 58

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            D V + D++ADGP TD GDLALG+N+LVAFMPW GYN+EDS+LISE ++++D+FTS+HIE
Sbjct: 59   DIVVKGDVLADGPGTDNGDLALGQNVLVAFMPWGGYNYEDSILISEELLAQDIFTSVHIE 118

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             FE+ ARDTKLG EEITRDIPNVSEE LK++DE GII VGA +  GDILVGKITPKGE+ 
Sbjct: 119  AFEIEARDTKLGKEEITRDIPNVSEESLKDLDEAGIIRVGAIIKSGDILVGKITPKGETQ 178

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            ++PEEKLL+AIFG+KA DV+DTSLRVPS V GTV+D R++ R G++   RS  +  ++  
Sbjct: 179  LSPEEKLLKAIFGDKAGDVKDTSLRVPSSVRGTVIDARVYTREGVELCARSKEIIEQETT 238

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPR 1018
            LL RD+  E   +  +   ++ E+L G              +   K   ++ + +S  P 
Sbjct: 239  LLRRDERIEIKAIQTSAILKIAEMLKGAKTSDKLVSEDGSTELLAKGAEVTYENLSAIPF 298

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
                   +Q  +++  +           + + 
Sbjct: 299  ELIGYLPLQ-AELEEKLSEYFADIRNRINRVR 329


>gi|327133529|gb|AEA29769.1| RNA polymerase subunit B [Acinetobacter sp. 10NS6]
          Length = 191

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 81/189 (42%), Positives = 112/189 (59%), Gaps = 3/189 (1%)

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
            L      +G    K+   L+ D +S+       +    DE +   +  ++   +   + +
Sbjct: 5    LLNDQMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPADEGIAERLTQIQTYLKEKSAEI 64

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            +++F  K  K   GD++  GVL+VVKV++A KR I  GDKMAGRHGNKG+VS ILP EDM
Sbjct: 65   DEKFAEKKRKFSTGDELTTGVLKVVKVYLAEKRRIPPGDKMAGRHGNKGVVSNILPVEDM 124

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P   +G PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR
Sbjct: 125  PHDANGVPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELR 181

Query: 1170 SFLEKVIGT 1178
             FL+K+   
Sbjct: 182  EFLDKIYNK 190


>gi|168218600|emb|CAP45828.1| DNA-directed RNA polymerase subunit beta [Bacillus sonorensis]
 gi|168218602|emb|CAP45829.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218604|emb|CAP45830.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218606|emb|CAP45831.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218610|emb|CAP45833.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218618|emb|CAP45837.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218620|emb|CAP45838.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218630|emb|CAP45843.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 52/136 (38%), Positives = 81/136 (59%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|169667025|gb|ACA64043.1| RpoB [Tatumella morbirosei]
          Length = 212

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N L  ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLDEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D 
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDS 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT+++ YLSA+EE N  IAQAN++LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 QVTDEIHYLSAIEEGNFVIAQANTNLDENGQFVDDLVTCRNKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEGDDANRALMGANMQRQ 212


>gi|62947904|gb|AAY22949.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
          Length = 223

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 126/220 (57%), Positives = 163/220 (74%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV    G VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+E+G F E +V  R  G     P +++D++D SPKQVV++A + IPFL
Sbjct: 124 DEYIVAQANSKLNEEGGFAEPIVMGRHRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|158253052|gb|ABW24010.1| RNA polymerase beta subunit [Pantoea brenneri]
          Length = 212

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+SLD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANASLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASL PFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLNPFLEHDDANRALMGANMQRQ 212


>gi|30141099|gb|AAP21859.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 232

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 125/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSDDLWETVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/89 (61%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G +G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGAGVVRDVKIFTRANGD 90


>gi|60101385|gb|AAX13761.1| RNA polymerase beta subunit [Streptococcus gordonii]
          Length = 227

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 91/287 (31%), Positives = 125/287 (43%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 175  ATPVFDGASSDDLWDTVREAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            G                           TGEPFD  V+VG +YM+KL
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIKL 227



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 53/85 (62%), Positives = 65/85 (76%)

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           NV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRD
Sbjct: 2   NVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRD 61

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGID 951
           TSLRVP G  G V DV+IF R   D
Sbjct: 62  TSLRVPHGADGVVRDVKIFTRANGD 86


>gi|30141088|gb|AAP21854.1| RNA polymerase beta subunit [Streptococcus constellatus]
          Length = 232

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 125/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSDDLWDTVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
               +    ++L        G        TGEPFD  V+VG +YM+KL+
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/89 (61%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G +G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGAGVVRDVKIFTRANGD 90


>gi|320101550|ref|YP_004177142.1| DNA-directed RNA polymerase subunit B' ;DNA-directed RNA polymerase
            subunit B' [Desulfurococcus mucosus DSM 2162]
 gi|319753902|gb|ADV65660.1| DNA-directed RNA polymerase, subunit B' ;DNA-directed RNA polymerase,
            subunit B' [Desulfurococcus mucosus DSM 2162]
          Length = 1165

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 125/333 (37%), Gaps = 72/333 (21%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            R + K         M     +++KV V   R  +         G+K              
Sbjct: 881  RHEEKGVVDTVLITMDSEGNKLIKVRVRDLRIPEL--------GDK-------------- 918

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
                             SR                  G+K    +   + +   +     
Sbjct: 919  ---------------FASR-----------------HGQKGVVGLLVPQYDMPFTEEGVV 946

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDGADEEAINSMLRMADLDE 1230
             + +I   +   +++       +        G    +TP F     E +  +++      
Sbjct: 947  PDLIINPHAFPSRMTVAQLMESIAGKAAALEGRTFDATP-FYKTPIEELQVIIKRHGYSP 1005

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
            +G+  +YDG TGE  D PV +G +Y  KL+HMVSDK++AR+ G   ++T+QP  G+S  G
Sbjct: 1006 TGEEAMYDGRTGELLDAPVFIGVVYYQKLHHMVSDKMHARARGPVQILTRQPTEGRSRAG 1065

Query: 1291 GQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG------RTR-VYESIVAGN 1336
            G R GEMEV C+  +G+A +L+E +T +SD          G      R +  Y   V   
Sbjct: 1066 GLRWGEMEVDCLVGHGSAMLLKEAMTDRSDSTIIYVCELCGSMGWYDRNKGKYMCPVHKE 1125

Query: 1337 D-TFET-GTPESFNVLVKEMQALGLSIDLENSR 1367
                +      +F +L++E+ +LG+   L    
Sbjct: 1126 RGVLKPVEVSYAFKLLLQELMSLGIRPRLITGE 1158



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 167/1010 (16%), Positives = 312/1010 (30%), Gaps = 229/1010 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L+     SY+ FL   +         +   F+ +  I   +    +    Y  D PK+  
Sbjct: 26  LVRQHLDSYERFLKELLPS-------ILEEFREI-RI---AEKTRIVIEKYRVDEPKWTS 74

Query: 88  ---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  R+LTYA P+ +T+R+                 +EQ + + DLP+M
Sbjct: 75  IEGIEESKSPMECRLRNLTYATPVYVTVRI----------EDESGYTREQELKLMDLPVM 124

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHR-SPGIHFD---HDKG 170
            K                         G F+I G ++++V+Q    S  I  D       
Sbjct: 125 LKSSIDPLSKLTPEELVAMGEDPRDPGGYFIINGSEKVIVAQEDLASNNIIVDAMPEGSS 184

Query: 171 RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EIL 229
              ++ K+    R    +   + IE     + +    +  K P    ++ALG+ SE EIL
Sbjct: 185 VTHVA-KVTSVAR---GRRSQLVIERRKDGVFYASF-QGHKFPAVMLMVALGLASEAEIL 239

Query: 230 ----------STFYPKIVYSQR-----------------GDFWCFPLSAADLMVGAKVSS 262
                     +   P I+  Q                       +     +  +    S 
Sbjct: 240 YATSLKPEVHNHLLPSIIQIQEVLPKLEIPEGASEEEVERLKEEYRRRVVEEALDFIASK 299

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
            ++     E+++ + + L   LL  +         +      G  ++  I      E+Y+
Sbjct: 300 FIIGKPREERILRAQRLLDERLLPHIGTDPSPETRLRKAVFIGQMISRII------ELYL 353

Query: 323 EAGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRV 380
                 D+     + +  +      +L    +  +  I+  +     K RK   +D+  V
Sbjct: 354 GYRSPDDKDHYRNKRLKLAGDMLATLLRAAIMGFSREIKEGVEKQLAKTRK---VDLKMV 410

Query: 381 MRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL-----------DTPDDVR 429
            +P  + T  +  +M    +          + R  M   L+                + R
Sbjct: 411 FKPS-IITDRLLHAMATGNWPGGRTGVSQLLDRTNMLSTLSHLRRVVSPLARGQPHFEAR 469

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS-VGEMLKNQYRLGLLRM---ERS 485
            +       +           G + ++  + N  V     E+    YR+G++ +      
Sbjct: 470 ELHGTQWGRMCPFETPEGANIGLVKNLALMTNVSVGVDDKEIELLLYRIGVVPLVSINTG 529

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS-QLEEHVNSLSRITHTRRLSAL 544
            K     +DI        +      S   + F + +L             I   RR   +
Sbjct: 530 DKSYKGILDIIREDVSAAVELSEKYSGWSKVFLNGKLVGYHRNGEELARAIRELRRKGKI 589

Query: 545 -GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
             +  VA   +G     V  T  GRI          I + +      R      +E    
Sbjct: 590 SSEVNVAHINSGYVDEVVVNTDPGRIR------RPLIVVENGKPKLTR-EHVKMLEEGRL 642

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
              D      + YL   EEEN YIA    S+  +                          
Sbjct: 643 GFEDLVKQGIIEYLDPDEEENAYIALEPGSVGAEH-----------------------TH 679

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           ++     ++ I AS+IP+ E++ S R +    M +Q++ L                    
Sbjct: 680 MEIWIPAILGITASIIPYPEHNQSPRNMYQSAMAKQSLGLY------------------- 720

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                  +       +      Y               Q+PLV 
Sbjct: 721 ----------------------AANFQRRMDTRGHFLHYP--------------QKPLV- 743

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
              + R  D+          +   G+NM+VA + + GYN ED++++++  V   +  S  
Sbjct: 744 ---QTRAMDV------IGYNERPAGQNMVVAVLTYTGYNMEDALILNKSSVDRGLARSTF 794

Query: 844 IEEFEVMARDTKLG-PEEITRDIP----NVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  +      G  +EIT           ++  + ++E GI+     V  GD+L+GKI
Sbjct: 795 FRLYTTVEYKYPGGIQDEITIPSTNIRGYRGQKAYEKLEEDGIVAPETPVTGGDVLIGKI 854

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           +P       P     +       +  +DTS+ +       VVD  +    
Sbjct: 855 SP-------PRFLSAQEYEVGSTLTRQDTSVVMRH-EEKGVVDTVLITMD 896


>gi|223954139|gb|ACN30236.1| RpoB [Corynebacterium stationis]
          Length = 149

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 66/177 (37%), Positives = 102/177 (57%), Gaps = 36/177 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +     +   +   L++  +++    + +       
Sbjct: 1    RMNIGQVLELHLGWLA-HTGWKVDT-----EDPKNAELLKTLPQELYDVPADSLT----- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------LDESGQSILYDGLT 1241
                             +TPVFDGA  E I+ +L  +         +DE G+++L+DG +
Sbjct: 50   -----------------ATPVFDGATNEEISRLLASSKPNRDGDVMIDEDGKTVLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            GEP+  P++VGY+YMLKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 93   GEPYQYPISVGYMYMLKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 149


>gi|161347193|gb|ABX65300.1| RNA polymerase beta subunit [Bartonella vinsonii subsp. berkhoffii]
          Length = 219

 Score =  216 bits (550), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 157/216 (72%), Positives = 182/216 (84%)

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN 
Sbjct: 1   ITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNK 60

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE +
Sbjct: 61  YGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVL 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
           + PR  +D +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTG
Sbjct: 121 MAPRNHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTG 180

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           MESVVA+ SGAA+ AKR GIV+QVDA RIVIR+ E 
Sbjct: 181 MESVVARDSGAAVSAKRGGIVDQVDATRIVIRATED 216


>gi|158252992|gb|ABW23980.1| RNA polymerase beta subunit [Pantoea dispersa]
          Length = 212

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 132/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLERDDANRALMGANMQRQ 212


>gi|199580727|gb|ACH89065.1| RNA polymerase subunit beta [Staphylococcus equorum subsp. equorum]
 gi|199580729|gb|ACH89066.1| RNA polymerase subunit beta [Staphylococcus equorum subsp. linens]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 107/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+++P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKLVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  ++ D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGASDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDSALKNLDDRGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580717|gb|ACH89060.1| RNA polymerase subunit beta [Staphylococcus cohnii subsp. cohnii]
 gi|199580719|gb|ACH89061.1| RNA polymerase subunit beta [Staphylococcus cohnii subsp.
            urealyticus]
 gi|199580757|gb|ACH89080.1| RNA polymerase subunit beta [Staphylococcus nepalensis]
 gi|199580769|gb|ACH89086.1| RNA polymerase subunit beta [Staphylococcus saprophyticus subsp.
            bovis]
 gi|199580771|gb|ACH89087.1| RNA polymerase subunit beta [Staphylococcus saprophyticus subsp.
            saprophyticus]
 gi|199580793|gb|ACH89098.1| RNA polymerase subunit beta [Staphylococcus xylosus]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 107/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+++P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKLVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  ++ D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 72/89 (80%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEVN GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDSALKNLDDRGIVYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|157870530|ref|XP_001683815.1| RNA polymerase I second largest subunit [Leishmania major strain
            Friedlin]
 gi|68126882|emb|CAJ04831.1| putative RNA polymerase I second largest subunit [Leishmania major
            strain Friedlin]
          Length = 1616

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 70/299 (23%), Positives = 106/299 (35%), Gaps = 56/299 (18%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D    + V      + T     +      ++++       P     V +   + RP   G
Sbjct: 1290 DPFTNKAVYEYTRHHATKWRHFDKGEDAWVQQVIPLVYSGPDP-TSVLMIFRIPRPPTVG 1348

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            DK + RHG KG +   +   D+PF    G   D+++NP   PSRM VG + E        
Sbjct: 1349 DKFSSRHGQKGTLPLHIRSHDLPFATASGITPDVIINPHAFPSRMTVGMVLEIMTAKVGA 1408

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+ I +                                                    
Sbjct: 1409 IEGRFIDNSAWSTVDEQPRVA--------------------------------------- 1429

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                      E I   L  A  +  G+  L DG++GE     V +G     +L HMVSDK
Sbjct: 1430 ----------ELIGEALVKAGYNRYGREHLIDGISGEEMKADVFMGICGYQRLRHMVSDK 1479

Query: 1267 VYARSTGS---YSLVTQ--QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              AR+      Y  VT+  QP+ G+   GG R+GEME   + ++G + V+ + L   SD
Sbjct: 1480 WQARARTDAHTYRAVTKTGQPVKGRKRHGGVRVGEMERDGLLSHGISEVVVDRLLHVSD 1538


>gi|199580767|gb|ACH89085.1| RNA polymerase subunit beta [Staphylococcus saccharolyticus]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHIASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580731|gb|ACH89067.1| RNA polymerase subunit beta [Staphylococcus felis]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|66854083|gb|AAY57350.1| RpoB [Prevotella massiliensis]
          Length = 125

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 71/179 (39%), Positives = 87/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA  E ++     A L     + LYDG TG
Sbjct: 21   --------------AAGRKLGVKFATPIFDGAKLEDLSEWTDKAGLPRLCSTYLYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EQFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|62947914|gb|AAY22954.1| RNA polymerase beta subunit [Streptococcus equinus]
          Length = 223

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 128/220 (58%), Positives = 160/220 (72%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS ++  RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSDKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+++  +N YGFI+TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSTYGHLNKYGFIQTPYRKVDRTTGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F EE+V  R  G     P   +DF+D SPKQVV++A + IPFL
Sbjct: 124 DEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFPSNIVDFVDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+   AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPHAPYVGTGMEYQAAHD 223


>gi|199580709|gb|ACH89056.1| RNA polymerase subunit beta [Staphylococcus caprae]
 gi|199580725|gb|ACH89064.1| RNA polymerase subunit beta [Staphylococcus epidermidis]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580705|gb|ACH89054.1| RNA polymerase subunit beta [Staphylococcus capitis subsp. capitis]
 gi|199580707|gb|ACH89055.1| RNA polymerase subunit beta [Staphylococcus capitis subsp.
            urealyticus]
 gi|199580751|gb|ACH89077.1| RNA polymerase subunit beta [Staphylococcus lugdunensis]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|62947924|gb|AAY22959.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 223

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 125/220 (56%), Positives = 162/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAIKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV    G VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVDREKGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQ+NS L+E G F E +V  R  G     P +++D++D SPKQVV++A + IPFL
Sbjct: 124 DEYIVAQSNSKLNEKGGFAEPIVMGRHRGNNQEFPSDQVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|199580791|gb|ACH89097.1| RNA polymerase subunit beta [Staphylococcus warneri]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+DE GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDERGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|322492356|emb|CBZ27630.1| RNA polymerase I second largest subunit,putative [Leishmania mexicana
            MHOM/GT/2001/U1103]
          Length = 1615

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 70/299 (23%), Positives = 106/299 (35%), Gaps = 56/299 (18%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D    ++V      + T     +      ++++       P     V +   + RP   G
Sbjct: 1289 DPFTNKSVYEYTRHHATKWRHFDKGEDAWVQQVIPLVYSGPDP-TSVLMIFRIPRPPTVG 1347

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            DK + RHG KG +   +   D+PF    G   D+++NP   PSRM VG + E        
Sbjct: 1348 DKFSSRHGQKGTLPLHIRSHDLPFATASGITPDVIINPHAFPSRMTVGMVLEIMTAKVGA 1407

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+ I                                                      
Sbjct: 1408 IEGRFIDHSAWSTVDEQPRVA--------------------------------------- 1428

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                      E I   L  A  +  G+  L DG++GE     V +G     +L HMVSDK
Sbjct: 1429 ----------ELIGEALVKAGYNRYGREHLIDGISGEEMKADVFMGICGYQRLRHMVSDK 1478

Query: 1267 VYARSTGS---YSLVTQ--QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              AR+      Y  VT+  QP+ G+   GG R+GEME   + ++G + V+ + L   SD
Sbjct: 1479 WQARARTDAHTYRAVTKTGQPVKGRKRHGGVRVGEMERDGLLSHGISEVVVDRLLHVSD 1537


>gi|80973499|gb|ABB53487.1| RNA polymerase beta subunit [Streptococcus devriesei]
          Length = 226

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLTAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVCDV------KIFTRANGDELQSGVNTLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARSLGIHIATPVFDGATSDDLWETVKEAGMAADAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/86 (65%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  +T EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLTAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVCDVKIFTRANGD 86


>gi|30141101|gb|AAP21860.1| RNA polymerase beta subunit [Streptococcus agalactiae]
          Length = 232

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 91/288 (31%), Positives = 126/288 (43%), Gaps = 71/288 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 179  ATPVFDGASSEDLWETVQEAGMDSDAK----------------------------TVLYD 210

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
            G                           TGEPFD  V+VG +YM+KL+
Sbjct: 211  G--------------------------HTGEPFDNRVSVGVMYMIKLH 232



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 55/89 (61%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|199580749|gb|ACH89076.1| RNA polymerase subunit beta [Staphylococcus lentus]
          Length = 231

 Score =  216 bits (549), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++SRILP EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHEGDKMCGRHGNKGVISRILPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+D++LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDLMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  V+VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRVSVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVS+  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSDNALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580745|gb|ACH89074.1| RNA polymerase subunit beta [Staphylococcus intermedius]
 gi|199580765|gb|ACH89084.1| RNA polymerase subunit beta [Staphylococcus pseudintermedius]
          Length = 231

 Score =  215 bits (548), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|160331424|ref|XP_001712419.1| rpa2 [Hemiselmis andersenii]
 gi|159765867|gb|ABW98094.1| rpa2 [Hemiselmis andersenii]
          Length = 1129

 Score =  215 bits (548), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 96/467 (20%), Positives = 147/467 (31%), Gaps = 67/467 (14%)

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG-ESPMTPEEKLL 913
                E    +I +V        D         +       VG                LL
Sbjct: 664  GTHSEIEASNILSVIAGATPFSDLNQSPRNMYQCQMSKQSVGTPFYTFWRRDDIKSFFLL 723

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
                      +    L++ +  +G    V +    G D  E ++ + +  IE       +
Sbjct: 724  NPQVPICRNKIIQDGLQMDAFPNGFNSVVSVITYTGFDM-EDAMIINKSSIERGFAS-SN 781

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                 D +I   L++           +   K+  L        P+  W+    ++E    
Sbjct: 782  VYNCFDLDIKPSLLKKSNFFKKKKTEENVLKTGDLLKKGAPLVPKESWYSIHKKNEAFFC 841

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               S K   +  K   +      IEK                + +  +R    GDK A R
Sbjct: 842  YNSSEKAIIDQIKIFSDIENNQNIEKNS--------------IKIRSRRRPLVGDKFASR 887

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG+ S +    D+PF   G   +I+ NP G PSRM +G I E+ +G      G    
Sbjct: 888  HGQKGVFSYLYSSIDLPFTDLGMNPEIIFNPHGFPSRMTIGVILESMIGKIGALDGVFHD 947

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +    +  N                                                   
Sbjct: 948  TTPFRFGQNR-------------------------------------------------- 957

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
            A        LR +     G  I Y G +GEPF   V +G +   +L HMV DK    + G
Sbjct: 958  AAIYHFGEKLRKSGFQFYGNEIFYSGYSGEPFSIDVFLGIVNYQRLRHMVLDKYQISNQG 1017

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              + +T+QP+ GK   G  R GEME   I   G  ++L + L   SD
Sbjct: 1018 PKNSLTRQPIKGKKIGGSIRFGEMERDAILGQGCVFLLHDRLQTSSD 1064



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 100/742 (13%), Positives = 211/742 (28%), Gaps = 116/742 (15%)

Query: 29  LIEVQKASYDH-------FLMMNIAPDERPNEGLQAAFK----SVFPITAFSGAAMLEFV 77
           L  +   S++        FL          ++      +     +F I        L+  
Sbjct: 14  LTRIHIDSFNFAISQGFFFLKFFSNNILIQDK--LKILRHFTLEIFGIHLSLPNFFLKNK 71

Query: 78  SYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY-MGDLP 136
                  K     C    + Y+            D      +   K  K   IY +G++P
Sbjct: 72  KI-----KKIPRQCRELKINYSG-----------DFLLGISSVFGKHGKFSFIYKIGNIP 115

Query: 137 LMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRA 172
           +M K                         G F+I G+++++   +     I F   +   
Sbjct: 116 IMVKSLKCNLYQQKKKQLIEMDEEEIEMGGYFIINGMEKMIRLLIVPKKNISFTLSRLTN 175

Query: 173 SLSGKL--LYACRIIP------DQGLWMDIEFDSKDIIHVRIDRRRK---VPVTSFLMAL 221
           +  G L    +C           + L +         IH RI  ++K   +PV   + +L
Sbjct: 176 TSRGNLCTTLSCSFRSVDRLQTSRTLHLHYLT--NGSIHARIIVQKKEFFIPVIMLIKSL 233

Query: 222 GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL- 280
              S+        KI  S    F         +M   K +    D+ T   V+E   K+ 
Sbjct: 234 MPISD-------KKIFESLTKTFSKDKFYRIRIMAMIKDAHETCDLKTQISVLEFLGKVF 286

Query: 281 -TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
            TS    ++  K +    + +  L  L   ++        +  +   V  + S+E+   S
Sbjct: 287 KTSLQTNTIDAKSIGEKFLFNHILIHLGEDKEAKVKLLLFMINKLLSVQKKISIEDNPDS 346

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +L    +      +     +    +K+   +I         S      + F   
Sbjct: 347 LSSQEFLLPGHLIMVYFKEKFESSLNFIFSQKEFEQNISNNFNKEGKSFQKQFCTDFLSK 406

Query: 400 FFDSDKYDLSTVGRV-----KMNMRLNLDTPDDV--------RHIRKEDIIAIIKILVDL 446
            F +    L+ +        K N  L+  +   V        R +     I   K   +L
Sbjct: 407 AFMTTGKGLAQIISTGSYVSKFNHELSQTSGLSVSIERINFGRFLSYFRSIHRGKFFFEL 466

Query: 447 RNGKGTIDDIDNLG-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
           +N  G      + G     +    ++  +L +     L+ +   +            +P+
Sbjct: 467 KNTSGRKLLPQSWGFLCPVHTPDGALCGILNHTASSVLVSLSNPLNCDFFKKYFFRYLPK 526

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           + +  K + S++            +    S      T ++S LG+  +      +   + 
Sbjct: 527 NFLKEKKISSSIFMIDGKILGFIPKFFFKSFVDKLRTEKVSVLGKISLGCEIFSISRFNR 586

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
             +     C   + +G  +  V   +   +     F +   +   +     +++      
Sbjct: 587 KCSFPS--CILLSQDGRPLRPVKWFSFKKKKKFSVFKKKNEKDFLNYCSEIEII------ 638

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                                  +                   +     ++S+ A   PF
Sbjct: 639 --------------GTLEQCFLNIDNLDYQSSFFTKNMVGTHSEIEASNILSVIAGATPF 684

Query: 682 LENDDSNRVLMGCNMQRQAVPL 703
            + + S R +  C M +Q+V  
Sbjct: 685 SDLNQSPRNMYQCQMSKQSVGT 706


>gi|199580737|gb|ACH89070.1| RNA polymerase subunit beta [Staphylococcus haemolyticus]
          Length = 231

 Score =  215 bits (548), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|312985692|gb|ADR31307.1| RNA polymerase II [Gibberella zeae]
          Length = 612

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 105/724 (14%), Positives = 196/724 (27%), Gaps = 132/724 (18%)

Query: 547  GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRK 604
              + R     + R +H TH+G +CPAET EG   GLV +L+    V+     E    +  
Sbjct: 3    TPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPGEPLIDFMV 62

Query: 605  VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DF 663
                +V  +            ++  +   +  +       V        +      + D 
Sbjct: 63   SRGMEVVEEYEPTRYPHATKVFVNGSWVGVHPEPRALVNSVLETRRKSYLQFEVSLVRDI 122

Query: 664  IDASPKQVVSIAASLIPFLENDDS--------------NRVLMGCNMQRQAVPLLKAEAP 709
             D   K        + P                      + L+    Q QA P       
Sbjct: 123  RDREFKIFSDAGRVMRPVFTVQQEDDYETGLTKGQLVLTKDLVNKIAQEQAEPPSDPSER 182

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQV-DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                G+    A      I A+             + I   +   + + +  +    ++ +
Sbjct: 183  IGWQGLIRSGAVE---YIDAEEEETAMICMTPEDLEIYREQKRDEVNLTEEEKQAKLEAE 239

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            +  Q    N+R   KV             PS  LG       +  + +P+  +N      
Sbjct: 240  KREQEEERNKRLKTKVNPTTHMYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNT 292

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
                M  + +     +  +                                 +  +    
Sbjct: 293  YQSAMGKQAMG--FFLTNYSRRM---------------------------DTMANILYYP 323

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     +       +   +  + AI      +  D+ +   S +   +    +F R 
Sbjct: 324  QKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRS 382

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              D+ ++      E  E   +           +       +  G           K+  +
Sbjct: 383  YSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPI 442

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +      R+Q  Q       ++     +  Q   + +                     
Sbjct: 443  DQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA-------------------- 482

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +P
Sbjct: 483  DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIP 542

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +  + E  L       G +                                     
Sbjct: 543  SRMTIAHLIECLLSKVSTLEGMEGD----------------------------------- 567

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                              +TP F     ++++ +LR       G  ++Y+G TG      
Sbjct: 568  ------------------ATP-FTDVTVDSVSDILRKHGYQSRGFEVMYNGHTGRKLRAQ 608

Query: 1249 VTVG 1252
            V  G
Sbjct: 609  VFFG 612



 Score =  100 bits (250), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 72/541 (13%), Positives = 146/541 (26%), Gaps = 73/541 (13%)

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
                     +     L N    +         +   + + L     + +      + + 
Sbjct: 1   TNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPGEPLIDF 60

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
           + S  ++  + ++    +   +       S      E      S +   R+     +  +
Sbjct: 61  MVSRGME--VVEEYEPTRYPHATKVFVNGSWVGVHPEPRALVNSVLETRRKSYLQFEVSL 118

Query: 550 ARARAGVEMRDVHPTHYGRICPAET-----------SEGHNIGLVSSLTSFARVNAYGFI 598
            R     E + +       + P  T           ++G  +     +   A+  A    
Sbjct: 119 VRDIRDREFK-IFSDAGRVMRPVFTVQQEDDYETGLTKGQLVLTKDLVNKIAQEQAEPPS 177

Query: 599 ETPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +   R        +  V Y+ A EEE   I      L+       + V            
Sbjct: 178 DPSERIGWQGLIRSGAVEYIDAEEEETAMICMTPEDLEIYREQKRDEVN----------- 226

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                                    E +   ++      Q +             T M  
Sbjct: 227 -----------------------LTEEEKQAKLEAEKREQEEERNKRLKTKVNPTTHM-Y 262

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCV 776
              +   + I+   A I+   D  +    + +  +     G        +          
Sbjct: 263 THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGFFLTNYSRRMDTMANILYY 322

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA   + GYN EDS+++++  +  
Sbjct: 323 PQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDR 372

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   L   EI           +       +DE GI+  G  V+  
Sbjct: 373 GLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 432

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P  +       +        +    RD S  + S  +G V  V +       
Sbjct: 433 DIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNADNV 485

Query: 952 K 952
           K
Sbjct: 486 K 486


>gi|199580773|gb|ACH89088.1| RNA polymerase subunit beta [Staphylococcus schleiferi subsp.
            coagulans]
 gi|199580775|gb|ACH89089.1| RNA polymerase subunit beta [Staphylococcus schleiferi subsp.
            schleiferi]
          Length = 231

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|111278813|gb|ABH09104.1| RNA polymerase II second largest subunit [Ramichloridium anceps]
          Length = 681

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 123/739 (16%), Positives = 227/739 (30%), Gaps = 99/739 (13%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP--VVSAVCEFFCS 519
            +R+   G ++ N +RL   +  +     +            +   K   + S +     +
Sbjct: 2    KRLDLAGPLMTNLFRLQFDKATKDFYRYMQKRVEAGQPINIMAGFKHPIITSGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +A     + R     + R +H TH+
Sbjct: 62   GNWGDQKKLDKAKAGVSQVLSRYTFASTLSHLRRTNA----PIGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + V            + +  +T +V    A+E+    
Sbjct: 118  GYVCPAETPEGQACGLVKNLSLMSMVTNSYETGP----LVNYIMTKNVE---ALEDWEPR 170

Query: 627  IAQANSSLDEDGSFTEELV--------FCRCAGEEILVPREKIDFIDASPKQVVSIAAS- 677
            +    + +  DG +   ++          R    + +         D   K+      S 
Sbjct: 171  LNPQATKVFVDGVWFAVVLRDPKRLVDDLRKLRRKAIFDPHVSLVWDIREKEFKISGDSG 230

Query: 678  ----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                 +  +E D S+  L    + ++ +  L   A    +G E          +    +G
Sbjct: 231  RIVRPLFVVETDRSSENLGNLVLNKEHITKLDQTAYLKESGFEWSDDVKPYGWMNLLESG 290

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE VDA       +    +        +  M+ +  +     N  PL+           
Sbjct: 291  VVEYVDAEEEETAMIIMTPEALADSKARWLGMEIENEDDPLRRN-DPLLNPHSHTF--TH 347

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 348  CEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLT 390

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E   +I    ++ L                        +       +   +  +
Sbjct: 391  NFDQRMETMANILYYPQKPLAR-------------------TMAMDYLKFRELPAGQNAI 431

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +    +F R   D  +       EQ E   R    
Sbjct: 432  VAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYQDSEKSVGHSVMEQFEKPTRADTL 490

Query: 974  EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
                   +       I  G           K+  ++ D                +E  QR
Sbjct: 491  RLKHGTYDKIEEDGLIAPGVRVSGEDIIMGKTAPMAPD---------------AEELGQR 535

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
              + +K    T     E    +++              R  KV V + +  Q GDK A R
Sbjct: 536  QKQHVKRDVSTPLRSTESGIVDQVML-----TTTSEGHRFAKVRVRVTKVPQIGDKFASR 590

Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            HG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  
Sbjct: 591  HGQKGTIGITYRMEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGD 650

Query: 1154 SLINDYKANGDISPLRSFL 1172
            +          IS +   +
Sbjct: 651  ATPFTKVTVTQISDILRRM 669


>gi|115606111|gb|ABJ16030.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 185/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSA G GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSAPGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|158253056|gb|ABW24012.1| RNA polymerase beta subunit [Pantoea brenneri]
          Length = 212

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+SLD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANASLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEQDDANRALMGANMQRQ 212


>gi|226897654|gb|ACO90276.1| RNA polymerase beta subunit gene [Bacillus sp. CU040510-015]
          Length = 272

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 150/249 (60%), Positives = 190/249 (76%), Gaps = 1/249 (0%)

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIY 762
           ++ EAP V TGME V  K SGAA++ K  GIVE V+A  + +R     D       +D Y
Sbjct: 1   MQPEAPVVRTGMEYVSGKDSGAAVICKHEGIVEHVEAREVWVRRINVVDGQEVKGDLDKY 60

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           R++KF RSNQ TC NQRP+V VG+ V + +I+ADGPS +LG+LALGRN+LVAFM W GYN
Sbjct: 61  RMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPSMELGELALGRNVLVAFMTWDGYN 120

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           +ED++++SER+V +DV+TSIHIEE+E  +RDTKLGPEEITRDIPNV E+ L+N+DE GII
Sbjct: 121 YEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRNLDERGII 180

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRVP G  G V+DV
Sbjct: 181 RTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDV 240

Query: 943 RIFNRHGID 951
           ++FNR   D
Sbjct: 241 KVFNREDGD 249



 Score = 47.4 bits (111), Expect = 0.017,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 72/236 (30%), Gaps = 23/236 (9%)

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
            G  +  R +  +        ++  I+ VG  V  G+IL    +      +     +L A 
Sbjct: 55   GDLDKYRMLKFIRSNQGTCYNQRPIVAVGNRVTKGEILADGPS-MELGELALGRNVLVAF 113

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER--EQIELLARDKD-- 972
                  +  D  +     V   V        +  +  +  +  E     I  +  D    
Sbjct: 114  MTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESESRDTKLGPEEITRDIPNVGEDALRN 173

Query: 973  -DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             DE+ I+      +  ++L G+    G         L   +  E  R             
Sbjct: 174  LDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR------------- 220

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
                E                   K+   + GD++PPGV ++V+V++  KR    G
Sbjct: 221  ----EVRDTSLRVPHGGGGIVLDVKVFNREDGDELPPGVNQLVRVYIVQKRKFSEG 272


>gi|199580761|gb|ACH89082.1| RNA polymerase subunit beta [Staphylococcus pettenkoferi]
          Length = 231

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+DE GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDERGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|327133533|gb|AEA29771.1| RNA polymerase subunit B [Acinetobacter sp. 10N4]
          Length = 180

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 81/183 (44%), Positives = 112/183 (61%), Gaps = 3/183 (1%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F
Sbjct: 1    QVSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKF 60

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K  K+  GD++  GVL+VVKV++A KR IQ GDKMAGRHGNKG+VS ILP EDMP   
Sbjct: 61   AEKKRKLSTGDELTTGVLKVVKVYLAEKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDA 120

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G PVD+VLNPLGV SRMNVGQI ETHLG A  GLG++I  ++   K    I+ LR FL 
Sbjct: 121  NGVPVDVVLNPLGVSSRMNVGQILETHLGLAAKGLGEQIDKML---KQQRTIAELREFLH 177

Query: 1174 KVI 1176
            K+ 
Sbjct: 178  KIY 180


>gi|158253018|gb|ABW23993.1| RNA polymerase beta subunit [Pantoea stewartii subsp. stewartii]
          Length = 212

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 169/211 (80%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR++ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRLIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEHDDANRALMGANMQRQ 212


>gi|199580699|gb|ACH89051.1| RNA polymerase subunit beta [Staphylococcus aureus subsp. anaerobius]
 gi|199580701|gb|ACH89052.1| RNA polymerase subunit beta [Staphylococcus aureus subsp. aureus]
          Length = 231

 Score =  215 bits (548), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSESALKNLDDRGIVYIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|199580715|gb|ACH89059.1| RNA polymerase subunit beta [Staphylococcus chromogenes]
 gi|199580743|gb|ACH89073.1| RNA polymerase subunit beta [Staphylococcus hyicus]
          Length = 231

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREDGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 91


>gi|149602544|ref|XP_001521110.1| PREDICTED: similar to RNA polymerase II 140 kDa subunit, partial
           [Ornithorhynchus anatinus]
          Length = 951

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 128/907 (14%), Positives = 262/907 (28%), Gaps = 193/907 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI------TAFSG------AAMLEF 76
           L+  Q  S+D F+ M++          Q   +   PI         +G        +L+F
Sbjct: 39  LVRQQLDSFDEFIQMSV----------QRIVEDAPPIDLQAEAQHATGEVEEPPRYLLKF 88

Query: 77  VSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK 126
                  P              ++   R+LTY+ PL + +   V    E          +
Sbjct: 89  EQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQL-----QTQ 143

Query: 127 EQSIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG 162
            Q  ++G +P+M                           G F+I G ++++++Q   +  
Sbjct: 144 HQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATN 203

Query: 163 -IH-FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR-----RK---- 211
            ++ F     + + +G+    CR        ++        I V +  R     +K    
Sbjct: 204 TVYVFAKKDSKYAYTGE----CR------SCLENSSRPTSTIWVSMLARGGQGAKKSAIG 253

Query: 212 -------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
                        VP+     ALG  S+ +IL          +  +     L  A ++  
Sbjct: 254 QRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQE 313

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
             V+ + +     +  +   K++     + L+++ +  +G++  C          +    
Sbjct: 314 QNVALNFIGSRGAKPGVTKEKRIKYAK-EVLQKEMLPHVGVSDFCETKKAYFLGYMVH-- 370

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
             + + A    +    +   +  +    P+L          +   +     K        
Sbjct: 371 -RLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDF 429

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKE 434
              +     + +  +  S+    + D  K   +  G  ++  RL   +      R     
Sbjct: 430 NLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPI 489

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
                +     L N    +                ++KN   +  + +       +  ++
Sbjct: 490 GRDGKLAKPRQLHNTLWGMVCPAETPEGHAVG---LVKNLALMAYISVGSQPSPILEFLE 546

Query: 495 IDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARA 554
             S+   + I+   +  A   F     +   ++    ++ +   RR   +    V+  R 
Sbjct: 547 EWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRD 606

Query: 555 GVEMRDVHPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
             E      T  GRIC P    E   + L         ++     E       D   +  
Sbjct: 607 IREREIRIYTDAGRICRPLLIVEKQKLLLKKR-----HIDQLKEREYNNYSWQDLVASGV 661

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           V Y+  +EEE   +A     L E G                +         +  P  ++ 
Sbjct: 662 VEYIDTLEEETVMLAMTPDDLQEKG----------------VAYCSTYTHCEIHPSMILG 705

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 706 VCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHV----------------------- 742

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + V  Y               Q+PLV           
Sbjct: 743 ------------------RMDTLAHVLYYP--------------QKPLV----------T 760

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G N +VA   + GYN EDS++++   V    F  +    ++     
Sbjct: 761 TRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRCVFYRSYKEQESK 820

Query: 854 TKLGPEE 860
                EE
Sbjct: 821 KGFDQEE 827


>gi|158253058|gb|ABW24013.1| RNA polymerase beta subunit [Pantoea eucrina]
          Length = 212

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++S + +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSFSVYAQTNEYGFLETPYRRVVDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KV++++ YLSA+EE N  IAQAN++L +DGSF ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 KVSDEIHYLSAIEEGNYVIAQANTNLADDGSFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLERDDANRALMGANMQRQ 212


>gi|110669598|gb|ABG81894.1| RNA polymerase II second largest subunit [Monascus purpureus]
          Length = 700

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 130/824 (15%), Positives = 239/824 (29%), Gaps = 152/824 (18%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R+   R+ R ++   +        +     I A  +   +     +   
Sbjct: 2    DLAGPLLAYLFRVLFTRVTRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNW 61

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 62   GEQKKAASSKAGVSQVLSRYTYSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 117

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     ++     E    +    + +V  +   L        ++
Sbjct: 118  CPAETPEGQACGLVKNLALMCYISVGTPSEPIIEFMIQRNMEVLEEFEPLGTPNATKVFV 177

Query: 628  AQANSSLDEDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP-FLEND 685
                  +  D +     ++  R  G          D  +   K          P F+ ++
Sbjct: 178  NGVWVGIHRDPAHLVNTMLSLRRRGMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDN 237

Query: 686  DSNRVLMGCNMQ-RQAVPLLKAEAPFV-GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            D      G  +  ++ +  L+ +         E    +  G   + K +G+VE VDA   
Sbjct: 238  DPKSENCGSLVLNKEHIRKLEQDKELPPDLDPEERRERYFGWDGLVK-SGVVEYVDAEEE 296

Query: 744  ---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               +I     DL+ S      Y L      N+      R +V               PS 
Sbjct: 297  ETIMIVMTPEDLEISKQLQAGYTLPDENDPNKRV----RFIVS--QRAHTWTHCEIHPSM 350

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+   N                                     E
Sbjct: 351  ILG-------VCASIIPFPDDNQSPRXXXXXXXXXXXXXV----------FLTNFDQRME 393

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
               +I    ++ L                        +       +   +  + AI    
Sbjct: 394  TMANILYYPQKPLA-------------------TTRSMEFLRFRELPAGQNAIVAIACYS 434

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R   D  +    +    +E   +    + + + +
Sbjct: 435  GYNQEDSVIMNQSSIDRGLF-RSLFYRTYTDSEK---MIGLTVVERFEKPMRTDTLGMRK 490

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L +   I  G           K+  L+ +                +E  QR    
Sbjct: 491  GTYDKLDDDGIIAPGVRVSGEDIIIGKTAPLAPE---------------AEELGQRTKAH 535

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             K+   T     E    +++      DD+     + VKV +   +  Q GDK A RHG K
Sbjct: 536  TKLDASTPLRSTESGIVDQVLVSTSNDDL-----KFVKVRMRTTKIPQIGDKFASRHGQK 590

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 591  GTIGITYRQEDMPFTREGLTPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPF 650

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                   +S L    E    +                                       
Sbjct: 651  TDVTVDSVSRLLR--EHGYQSRGFEVM--------------------------------- 675

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                         +G +    G         + +G  Y  +L H
Sbjct: 676  ------------YNGHT----GR---KLVAQIFLGPTYYQRLRH 700



 Score =  105 bits (261), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 77/575 (13%), Positives = 150/575 (26%), Gaps = 98/575 (17%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R+GK       +  +  +
Sbjct: 57  ATGNWGEQKKAASSKAGVSQVLSRYTYSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 116

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEF 516
               E  + Q    +  +       + +     +      N + +         +A   F
Sbjct: 117 VCPAETPEGQACGLVKNLALMCYISVGTPSEPIIEFMIQRNMEVLEEFEPLGTPNATKVF 176

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGR 568
                +    +  + ++ +   RR   +  +  + R     E        R   P     
Sbjct: 177 VNGVWVGIHRDPAHLVNTMLSLRRRGMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVD 236

Query: 569 ICPAETSEGHNIGLVSSLTSFARVN------AYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
             P   + G  +     +    +                Y        +  V Y+ A EE
Sbjct: 237 NDPKSENCGSLVLNKEHIRKLEQDKELPPDLDPEERRERYFGWDGLVKSGVVEYVDAEEE 296

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   I      L+                                         +     
Sbjct: 297 ETIMIVMTPEDLEISKQLQ-----------------------------------AGYTLP 321

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           + +D N+           V  + ++     T  E   +   G              D   
Sbjct: 322 DENDPNKR----------VRFIVSQRAHTWTHCEIHPSMILGVCASIIPFPD----DNQS 367

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                                  + +         Q+PL                     
Sbjct: 368 PRXXXXXXXXXXXXXVFLTNFDQRMETMANILYYPQKPL----------ATTRSMEFLRF 417

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-- 860
            +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E  
Sbjct: 418 RELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVERF 477

Query: 861 ---ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
              +  D   + +     +D+ GII  G  V+  DI++GK  P     + PE + L    
Sbjct: 478 EKPMRTDTLGMRKGTYDKLDDDGIIAPGVRVSGEDIIIGKTAP-----LAPEAEELGQR- 531

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             KA    D S  + S  SG V  V +   +   K
Sbjct: 532 -TKAHTKLDASTPLRSTESGIVDQVLVSTSNDDLK 565


>gi|115606097|gb|ABJ16023.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 185/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQ SQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQPSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|199580739|gb|ACH89071.1| RNA polymerase subunit beta [Staphylococcus hominis subsp. hominis]
 gi|199580741|gb|ACH89072.1| RNA polymerase subunit beta [Staphylococcus hominis subsp.
            novobiosepticus]
          Length = 231

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIIYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|168218622|emb|CAP45839.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 52/136 (38%), Positives = 81/136 (59%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|199580795|gb|ACH89099.1| RNA polymerase subunit beta [Staphylococcus massiliensis]
          Length = 231

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKYLGIHVASPVFDGANDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|56759090|gb|AAW27685.1| SJCHGC09486 protein [Schistosoma japonicum]
          Length = 204

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 95/258 (36%), Gaps = 85/258 (32%)

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +G + E   G      G+                                        
Sbjct: 1    MTIGHLIECLQGKVSANKGEIGD------------------------------------- 23

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                            +TP  D  +   I+ +L+      +G  I+Y+G TG   +  + 
Sbjct: 24   ----------------ATPFNDAVNVRKISLLLQEYGYQHTGNEIMYNGFTGRKLNSQIF 67

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G  Y  +L HMV DK+++RS G   ++ +QP+ G+S  GG R GEME  C  A+GAA  
Sbjct: 68   LGPTYYQRLKHMVDDKIHSRSRGPVQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQF 127

Query: 1311 LQEMLTIKSD-------DVVG-------RTRVYE----------SIVAGNDTFETGTPES 1346
            L+E L   SD       ++ G       R + YE          S+V          P +
Sbjct: 128  LRERLFFASDPYQVYVCNLCGLIAIAHQRNKTYECRSCKNTTQISLVK--------LPYA 179

Query: 1347 FNVLVKEMQALGLSIDLE 1364
              +L +E+ ++ ++  + 
Sbjct: 180  CKLLFQELMSMSIAPRMM 197


>gi|62947906|gb|AAY22950.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 223

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 127/220 (57%), Positives = 161/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N L  ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLFELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGAVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E+ V  R  G     P E +D++D SPKQVV++A + IPFL
Sbjct: 124 DEFTVAQANSRLNEDGTFAEKTVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|327133527|gb|AEA29768.1| RNA polymerase subunit B [Acinetobacter sp. 11N1]
          Length = 162

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 75/162 (46%), Positives = 105/162 (64%)

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F 
Sbjct: 1    MSNGGGTTKRGDQLTEDKLSQLEMVDLLEIPPSDEGIAERLTQIQTYLKEKSAEIDEKFA 60

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +
Sbjct: 61   EKKRKLSTGDELTTGVLKVVKVYLAVKRHIQPGDKMAGRHGNKGVVSNILPVEDMPHDAN 120

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++
Sbjct: 121  GVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKML 162


>gi|199580753|gb|ACH89078.1| RNA polymerase subunit beta [Staphylococcus lutrae]
          Length = 231

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 106/206 (51%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREDGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D  ++ D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 91


>gi|80973575|gb|ABB53525.1| RNA polymerase beta subunit [Streptococcus ratti]
          Length = 226

 Score =  215 bits (547), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLTAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVCDV------KIFTRANGDELQSGVNTLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARSLGIHIATPVFDGATSDDLWETVKEAGMASDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/86 (65%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  +T EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLTAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVCDVKIFTRANGD 86


>gi|115606109|gb|ABJ16029.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  215 bits (547), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 132/259 (50%), Positives = 185/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ   
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMV 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|83282218|ref|XP_729674.1| DNA-directed RNA polymerase, subunit beta [Plasmodium yoelii yoelii
            str. 17XNL]
 gi|23488130|gb|EAA21239.1| DNA-directed RNA polymerase, beta subunit, putative [Plasmodium
            yoelii yoelii]
          Length = 1323

 Score =  215 bits (547), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 84/501 (16%), Positives = 168/501 (33%), Gaps = 97/501 (19%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER-- 955
            I       +   +  + ++      D+ D  +   S +           +H I+  +   
Sbjct: 890  IEFINFEKLPAGQNAIVSVMSFCGYDIEDAIVMNKSSIDRGFGRCMSLRKHFIELKKYFN 949

Query: 956  -----------SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
                       SIS +++  +   ++ +D       +    +   L   +++        
Sbjct: 950  GSNDIVLPSPLSISKQQQMQKKTGKESNDNLANTKEDPRKTINSELKKYHSLDADGVVSI 1009

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
              +L    +     S         + V+   +     ++ S+   +  + + ++KI +  
Sbjct: 1010 GYLLKEGQVYVNKYSPIN----VKDHVKDMSKLDLNDFKLSEVKYKSVYPSYVDKIIF-- 1063

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                  L++ K+ +   R  + GDK +                                 
Sbjct: 1064 TENGEGLKIYKIIMRQSRLPELGDKFS--------------------------------- 1090

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
                SR                  G+K    +   + +   +      + ++       +
Sbjct: 1091 ----SR-----------------HGQKGVVGLLVNQEDMPFTESGICPDLIMNPHGFPSR 1129

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            ++      ++        G      +F G   E    +L     + S + +LY GLTGEP
Sbjct: 1130 MTVGKLLELVSSKSAVLDGEYKYGSIFSGTPFEEAAEVLFRYGFNWSCKELLYSGLTGEP 1189

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
             +  + +G IY  KL HMV DK++ARS G   L+T+QP  G+S  GG RLGEME  C+ A
Sbjct: 1190 LETYIFMGPIYYQKLKHMVQDKIHARSRGPRQLLTRQPTEGRSKEGGLRLGEMERDCLIA 1249

Query: 1305 YGAAYVLQEMLTIKSDDVVGRTRVYESIV-----------------AGNDTFETGTPESF 1347
            YG + +L E L + SD       V ++ +                   +       P + 
Sbjct: 1250 YGVSNLLLERLMLSSD-------VCDAYICEDCGMMGYDSCCTFCKKYDKNVVVKMPYAC 1302

Query: 1348 NVLVKEMQALGLSIDLENSRT 1368
             +L +E+Q + +   +    T
Sbjct: 1303 KLLFQELQTMNVFPKIIVKET 1323



 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 127/979 (12%), Positives = 277/979 (28%), Gaps = 218/979 (22%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
            L++    SY++F+   I              KS            LEF+      P    
Sbjct: 168  LVKQHIESYNYFIKREIKTIMNATT--NKIIKS-----DIDEHFYLEFLDISVGRPSIEE 220

Query: 87   -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                       C  RDLTY+ P+ + +  I          K    + + ++ +G LP+M 
Sbjct: 221  NMIESNLTPQICRQRDLTYSAPIYVDVEYI----------KGNSIVTKNNVEIGRLPVML 270

Query: 140  ------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR---- 171
                                      G F++KG +R+++ Q   S          +    
Sbjct: 271  RSDICVLNNKNENELMKLGECPYDPGGYFIVKGTERVLLMQEQLSKNRIIVEMDIKHNIC 330

Query: 172  -ASLSGKLLYACR-IIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEE- 227
                S       R  I  +           + ++++ +     + V   L A+G +S++ 
Sbjct: 331  ATITSTTAESKSRCAIVYK----------NNKLYLKHNSFTEDIGVCIILRAMGYESDQE 380

Query: 228  --------------ILSTFYP--KIVYSQRGDFWCF---PLSAADLMVGAKVSSSLVDID 268
                          IL + Y           D   +    +    L  G   S     + 
Sbjct: 381  IFQMIGSHKMYLNGILLSLYDLYTENIKTNLDALLYIGKKIRPRLLAKGFFSSMKEKQVK 440

Query: 269  TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
              + +IE G    S +L S  ++  K+          L +   +++    +  ++  D  
Sbjct: 441  NEKDIIEEGLDFLSRVLLSHIQQKSKYDFRNKARCICLMI-RRVLDSANNKNELDDKDYY 499

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
              K LE            LY           +  ++   +   ++ L     +   +  +
Sbjct: 500  GNKRLELAGQLISLLFEDLYKRFYFTLKKQIDQTLSKYMQSSYNSKLKNNSSIGGNNNFS 559

Query: 389  FSVAESMFNFLFFDSD-KYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
             +    +F  L  D   +   + +     N  R  ++     + + +   IA I ++  L
Sbjct: 560  DNSYPDVFRNLPKDIITRGMQTAISTGNWNIKRFKMEKSGVSQVLSRLSFIACIGMMTRL 619

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEML----KNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
             +       +      +    G +           GL++    +    +  D +  + + 
Sbjct: 620  NSQFEKGRKVSGPRALQPSQWGVLCPCDTPEGESCGLVKNLALMTHVTNDNDNNENLIEI 679

Query: 503  LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG-VARARAGVEMRDV 561
            L       S         +       +N +    H +    + +   + R     E   +
Sbjct: 680  LYTLGVEDSDSLTGEEMYKEGVFFVVLNGILLGVHRKPHKFMKRIRCLRRFGKIGEFVSI 739

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
            +           T  G     +  + +       +    +E+      D   ++ + ++ 
Sbjct: 740  YDNFLHNAIYISTDGGRLCRPLIIVENGKSKLLNSHIKALESGEINFFDLLKSSVIEWID 799

Query: 619  AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
              E+ N  IA     ++ +                          ++  P  ++ + A L
Sbjct: 800  VNEQNNLLIALNEKDINLN-----------------------TTHLEIDPLTILGVVAGL 836

Query: 679  IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
            IP+  ++ S R    C M +QA+                                     
Sbjct: 837  IPYPNHNQSPRNTYQCAMGKQAIGS----------------------------------- 861

Query: 739  DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                  I   +     +   + IY               Q+PLVK               
Sbjct: 862  ------IGYNQFIRCDTLLYLLIYP--------------QKPLVKS----------KTIE 891

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG- 857
              +   L  G+N +V+ M + GY+ ED++++++  +       + + +  +  +    G 
Sbjct: 892  FINFEKLPAGQNAIVSVMSFCGYDIEDAIVMNKSSIDRGFGRCMSLRKHFIELKKYFNGS 951

Query: 858  -------------------------------PEEITRDIPNVSEEGLKNIDECGIICVGA 886
                                            +E  R   N   +   ++D  G++ +G 
Sbjct: 952  NDIVLPSPLSISKQQQMQKKTGKESNDNLANTKEDPRKTINSELKKYHSLDADGVVSIGY 1011

Query: 887  EVNPGDILVGKITPKGESP 905
             +  G + V K +P     
Sbjct: 1012 LLKEGQVYVNKYSPINVKD 1030


>gi|322815538|gb|EFZ24178.1| RNA polymerase I second largest subunit, putative [Trypanosoma cruzi]
          Length = 756

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 67/258 (25%), Positives = 96/258 (37%), Gaps = 69/258 (26%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVG 1134
            V   + RP   GDK + RHG KG +   +   D+PF  +DG   DI++NP   PSRM VG
Sbjct: 479  VVFRIPRPPAIGDKFSSRHGQKGTLPLHIRAYDLPFSTRDGITPDIIINPHAFPSRMTVG 538

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E          G+               S                            
Sbjct: 539  MVLEMMGAKLGSIQGRFCDHSAWSVVDERPRSA--------------------------- 571

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                  E I   L+ A  +  G+  L DG++GE  +  V +G  
Sbjct: 572  ----------------------EVIGDALQKAGYNRYGREKLIDGISGEEMEADVFMGIS 609

Query: 1255 YMLKLNHMVSDKVYARS------------TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
               +L HMV+DK  AR+            TG       QP+ G+   GG R+GEME   +
Sbjct: 610  GYQRLRHMVNDKWQARARTDAHTHRAVTKTG-------QPVKGRKRHGGVRVGEMERDGL 662

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             ++G+A V+ + L   SD
Sbjct: 663  LSHGSAEVVLDRLLHVSD 680


>gi|52699790|gb|AAU86957.1| DNA-dependent RNA polymerase II second largest subunit [Biatoridium
            monasteriense]
          Length = 692

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 122/814 (14%), Positives = 233/814 (28%), Gaps = 147/814 (18%)

Query: 472  KNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
             N +R    ++ R I++  +    +         + A  V + +     +          
Sbjct: 1    ANLFRTLFTKLTRDIQKYLQKCVENSREFNLTLGVKASTVTNGLKYSLATGNWGEQKKAM 60

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET E
Sbjct: 61   SSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPE 116

Query: 577  GHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            G   GLV +L     ++     E    +      +V  +     +      ++      +
Sbjct: 117  GQACGLVKNLALMCYISVGTPSEPIIDFMASRAMEVLEEYEPQRSPNATKVFVNGVWVGV 176

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVL 691
              D +     V               I D  D   K        + P    E++ S+   
Sbjct: 177  HRDPAHLVAAVQETRRKNITSHEVSLIRDIRDREFKIFTDAGRVMRPLFVVESNPSHPEY 236

Query: 692  MGCNMQRQAVPLLKAEAPF--VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
                ++++ +  L+ +       T  E          +V    GI+E VDA      ++ 
Sbjct: 237  GRLALKKEHIMKLEDDKELDPSLTAEEREELYFGWKGLVT--NGIIEYVDAEEEE--TIM 292

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
              + P    +   R    +  + N   N+R    +             PS  LG      
Sbjct: 293  IVMTPEDLEISRQRQEGIEVPDDNPDPNRRVKAPLNPTAHTWTHCEIHPSMILG------ 346

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N                        ++               D     
Sbjct: 347  -ICASIIPFPDHNQSPXN------------------TYQXXMGXXXXXXXXXXYDQRM-- 385

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 386  ---------DTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVI 436

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME- 988
               S +   +    +F R   D+ +   SV    +E   +    + + L    Y +L + 
Sbjct: 437  MNQSSIDRGLF-RSLFYRSYTDQEK---SVGMHTLEQFEKPTRSDTLKLKHGTYDKLDDD 492

Query: 989  --ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              I  G           K+  ++ D      R++                 +K    T  
Sbjct: 493  GIIAPGVRVSGEDMIIGKTAPIAPDAEELGQRTKL---------------HIKRDVSTPL 537

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
               E    +++      D +     R VKV +   +  Q GDK A RHG KG +      
Sbjct: 538  RSTESGIVDQVLISTNSDGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQ 592

Query: 1107 EDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
            EDMPF ++G   D+++NP  +PSRM +  + E  L       G +  +          +S
Sbjct: 593  EDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVSALKGFEGDATPFTEVTVDSVS 652

Query: 1167 PLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMA 1226
             L    ++   +                                                
Sbjct: 653  KLLR--DEGYQSRGLEVM------------------------------------------ 668

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                +G +    G         V +G  Y  +L 
Sbjct: 669  ---YNGHT----GR---KLVAQVFLGPTYYQRLR 692



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 90/585 (15%), Positives = 157/585 (26%), Gaps = 97/585 (16%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + +  K   S  G  ++  R    +      R          I    
Sbjct: 40  VTNGLKYSLATGNWGEQKKAMSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPR 99

Query: 445 DLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS--SVDIDSVMPQ 501
            L N   G +   +    +    V  +    Y       E  I    S     ++   PQ
Sbjct: 100 QLHNTHWGLVCPAETPEGQACGLVKNLALMCYISVGTPSEPIIDFMASRAMEVLEEYEPQ 159

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-- 558
              NA  V      F     +    +  + ++ +  TRR +    +  + R     E   
Sbjct: 160 RSPNATKV------FVNGVWVGVHRDPAHLVAAVQETRRKNITSHEVSLIRDIRDREFKI 213

Query: 559 -----RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF------IETPYRKVCD 607
                R + P       P+    G        +                  E  Y     
Sbjct: 214 FTDAGRVMRPLFVVESNPSHPEYGRLALKKEHIMKLEDDKELDPSLTAEEREELYFGWKG 273

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 + Y+ A EEE   I      L                 E     +E I+  D +
Sbjct: 274 LVTNGIIEYVDAEEEETIMIVMTPEDL-----------------EISRQRQEGIEVPDDN 316

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P     + A                                P   T       +   + I
Sbjct: 317 PDPNRRVKA--------------------------------PLNPTAHTWTHCEIHPSMI 344

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDL-DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +              +    +      Q+PL     
Sbjct: 345 LGICASIIPFPDHNQSPXNTYQXXMGXXXXXXXXXXYDQRMDTMSNILYYPQKPL----- 399

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +VA   + GYN EDS+++++  +   +F S+    
Sbjct: 400 -----ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 454

Query: 847 FEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        D   +       +D+ GII  G  V+  D+++GK  P 
Sbjct: 455 YTDQEKSVGMHTLEQFEKPTRSDTLKLKHGTYDKLDDDGIIAPGVRVSGEDMIIGKTAPI 514

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                   ++        K    RD S  + S  SG V  V I  
Sbjct: 515 APDAEELGQRT-------KLHIKRDVSTPLRSTESGIVDQVLIST 552


>gi|158253060|gb|ABW24014.1| RNA polymerase beta subunit [Pantoea septica]
          Length = 212

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 131/211 (62%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LDE+G F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANAQLDEEGHFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLERDDANRALMGANMQRQ 212


>gi|323652571|gb|ADO15382.2| RNA polymerase beta subunit [Xanthomonas sacchari]
          Length = 204

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 121/204 (59%), Positives = 150/204 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV DG++T++V YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVYARTNQYGFLETPYRKVVDGQITDEVEYLSAIEENEYVIAQANALHDAKSR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+ R LMG NMQRQ
Sbjct: 121 LTEQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDAYRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
            VP L+A+ P VGTG+E  VA+ S
Sbjct: 181 GVPTLRAQKPLVGTGIERAVARDS 204


>gi|115606059|gb|ABJ16004.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606061|gb|ABJ16005.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606063|gb|ABJ16006.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606065|gb|ABJ16007.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606067|gb|ABJ16008.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606069|gb|ABJ16009.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606071|gb|ABJ16010.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606073|gb|ABJ16011.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606075|gb|ABJ16012.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606077|gb|ABJ16013.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606079|gb|ABJ16014.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606081|gb|ABJ16015.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606083|gb|ABJ16016.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606085|gb|ABJ16017.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606087|gb|ABJ16018.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606089|gb|ABJ16019.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606091|gb|ABJ16020.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 185/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLLALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|254055195|gb|ACT64197.1| RpoB [Brevibacterium iodinum]
          Length = 234

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 131/234 (55%), Positives = 178/234 (76%), Gaps = 3/234 (1%)

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQL
Sbjct: 1   RIRAVGELIENQIRTGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQL 60

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N L+ +TH RRLSALG GG++R RA +E+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 61  SQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAAMEVRDVHPSHYGRMCPIETPEGPNIGL 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           + SL S+AR+N +GFIETPYRKV DG VT++  YL+A +E    IAQAN+ L +D  F E
Sbjct: 121 IGSLASYARINPFGFIETPYRKVVDGVVTDETQYLTADDELEFNIAQANAPLTDDQRFAE 180

Query: 643 ELVFCRCA---GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             V  R     GE  LV  ++IDF+D S +Q+VS+A++LIPFLE+DD+NR LMG
Sbjct: 181 VEVLARPKGGGGEAELVQHDQIDFMDVSARQMVSVASALIPFLEHDDANRALMG 234


>gi|145342325|gb|ABP64859.1| RpoB [Bacillus sp. FSL_H7-590]
 gi|146217875|gb|ABQ11017.1| RNA polymerase beta subunit [Bacillus sp. FSL_H3-288]
 gi|161331477|gb|ABX60656.1| RpoB [Bacillus macroides]
          Length = 232

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 91/287 (31%), Positives = 127/287 (44%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      R  +IL G+    G         L   +  E  R      +++     
Sbjct: 16   DERGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKARE-VRDTSLRVPHGA 74

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              +                    K+   + GD++PPGV ++V+ ++  KR I+ GDKMAG
Sbjct: 75   GGI----------------ILDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPF+ DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 119  RHGNKGVISRILPEEDMPFMPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRYLGVHM 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+                            +  A   + G  +      
Sbjct: 179  ATPVFDGANEEDVW-------------------------ETMEEAGMNRDGKTI------ 207

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                                   LYDG +GEPFD  V+VG +YM+KL
Sbjct: 208  -----------------------LYDGRSGEPFDNRVSVGIMYMIKL 231



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|158252924|gb|ABW23946.1| RNA polymerase beta subunit [Pantoea sp. LMG 24248]
 gi|158252934|gb|ABW23951.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158252940|gb|ABW23954.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158253014|gb|ABW23991.1| RNA polymerase beta subunit [Pantoea ananatis]
 gi|158253026|gb|ABW23997.1| RNA polymerase beta subunit [Pantoea ananatis]
          Length = 212

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEQDDANRALMGANMQRQ 212


>gi|37956400|gb|AAP15372.1| RNA polymerase beta subunit [Desulfuromusa kysingii]
          Length = 211

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 132/210 (62%), Positives = 166/210 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+DS+MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQDVDSLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N YGF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEYGFVETPYRIVKDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT ++ Y SA+EEE   IAQAN+ +DE+G F  +LV  R  GE +L+P ++ID +D SP
Sbjct: 122 QVTTEIKYFSALEEEGHAIAQANAPIDENGVFVNDLVNVRQTGEFLLLPPDQIDLMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           KQ+VS+AA+LIPFLENDD+NR LMG NMQR
Sbjct: 182 KQIVSVAAALIPFLENDDANRALMGSNMQR 211


>gi|2736127|gb|AAB94064.1| RPB140 [Marchantia polymorpha]
          Length = 555

 Score =  214 bits (546), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 117/703 (16%), Positives = 203/703 (28%), Gaps = 148/703 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   A +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMAHITVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +   ++ +  +G +             +   R ++   D +P+  V     L       
Sbjct: 54   AVIPQSTKIFVNGCWVGIHRDPELLVRTLRQLRRQV---DVNPEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+K              A  SG        G +E VD      
Sbjct: 111  DYGRCSRPLFIVEKQRLLIKKSDVRALQ---LKEASESG-WHELVAKGFIEYVDTEE--- 163

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                   + +T        +   R+N     +           +        PS  LG  
Sbjct: 164  -------EETTMISMTISDLVNARNNPEEAYS-----------KTYTHCEIHPSMILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +     I       R   L         
Sbjct: 204  -----VCGSIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQLRMDTLAYVLYYPQK 254

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            P V+ + + ++                             +      + AI      +  
Sbjct: 255  PLVTTQAMAHL-------------------------HFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        IF R   D+ ++  ++ +E+ E   R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSIFYRSYRDEEKKQGTLVKEEFERPNRENTTGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T L                  QDE   +     K    T 
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTTPL-----------------PQDETGSQAQRYTKRDQSTC 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK+ V   R  Q GDK + RHG KG V     
Sbjct: 392  LRHSESGMIDQVLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+ ++G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 447  QEDMPWTQEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S                                                        +R 
Sbjct: 507  SKALHKCGY-----------------------------------------------QMRG 519

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             ++  +G +    G         + +G  Y  +L HMV DK++
Sbjct: 520  FEVMYNGHT----GR---RLYAHIFLGPTYYQRLKHMVDDKIH 555



 Score =  120 bits (302), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 72/482 (14%), Positives = 139/482 (28%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  +   F     + 
Sbjct: 11  EGQACGLVKNLALMAHITVGSAANPILEFLEEWSTENFEEISPAVIPQSTKIFVNGCWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +    GV R     E+R ++  +     P    E   + +
Sbjct: 71  IHRDPELLVRTLRQLRRQVDVNPEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 129

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      V A    E       +      + Y+   EEE   I+              
Sbjct: 130 KKS-----DVRALQLKEASESGWHELVAKGFIEYVDTEEEETTMISM----------TIS 174

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      +     +  P  ++ +  S+IPF +++ S R      M +QA+ 
Sbjct: 175 DLVNARNNPE--EAYSKTYTHCEIHPSMILGVCGSIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 233 IYVTNYQL--------------------RMDTLAYV------------------------ 248

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 249 -----------LYYPQKPLV----------TTQAMAHLHFRQLPAGINAIVAIACYSGYN 287

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F SI    +    +      +E        +   +       +D
Sbjct: 288 QEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKQGTLVKEEFERPNRENTTGMRHGSYDKLD 347

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +                +    RD S  +    SG
Sbjct: 348 DDGLAPPGTRVSGEDVIIGKTTPLPQDE---------TGSQAQRYTKRDQSTCLRHSESG 398

Query: 938 TV 939
            +
Sbjct: 399 MI 400


>gi|111278807|gb|ABH09101.1| RNA polymerase II second largest subunit [Capronia pilosella]
          Length = 689

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 124/743 (16%), Positives = 228/743 (30%), Gaps = 91/743 (12%)

Query: 454  DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP--VVS 511
            DD D+LG +R+   G ++ N +RL   +  +     +      +     +   K   + S
Sbjct: 1    DDRDHLGKKRLDLAGPLMTNLFRLQFDKATKDFYRYMQKRVESNQPINIMAGFKHPIITS 60

Query: 512  AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
             +     +               +SQ+       S ++H RR +A     + R     + 
Sbjct: 61   GLKYSLATGNWGDQKKLDKAKAGVSQVLSRYTFASTLSHLRRTNA----PIGREGKIAKP 116

Query: 559  RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVY 616
            R +H TH+G +CPAET EG   GLV +L+  + V           Y      +   D   
Sbjct: 117  RQLHNTHWGYVCPAETPEGQACGLVKNLSLMSMVTNTYETGPLLNYILTKHVEALEDWEP 176

Query: 617  LSAMEEENRYI--AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
                +    ++        L +     ++L   R  G          D  D   K     
Sbjct: 177  RLNPQATKVFVDGVWFAVVLRDPKRLVDDLRKLRRKGVFDSQVSLVWDIRDKEFKISGDS 236

Query: 675  AASLIPFL--ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
               + P    E D ++  L    + +  +  L   A     G +               +
Sbjct: 237  GRIVRPLFIVETDRASENLGNLVLNKDHISKLDQTAYLKEGGFQWTDEIRPYGWNDLLES 296

Query: 733  GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            G+VE +DA       +    +  +     +  M+ +  +     N  PL+          
Sbjct: 297  GVVEYLDAEEEETAMIIMTPEALSDSKAKWLGMEIENEDDPLRRN-XPLLNPHSHTF--T 353

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N          M  + +              
Sbjct: 354  HCEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FL 396

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                   E   +I    ++ L                        +       +   +  
Sbjct: 397  TNFDQRMETMANILYYPQKPLAR-------------------TMAMDYLKFRELPAGQNA 437

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +     +  +     +   SV    +E   +   
Sbjct: 438  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQ----DSEKSVGHSVMEQFEKPTR 493

Query: 973  DEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDE 1029
             + + L    Y ++ E   +  G           K+  ++ D                +E
Sbjct: 494  TDTLRLKHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPD---------------AEE 538

Query: 1030 KVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDK 1089
              QR  + +K    T     E    +++      D       R  KV V   +  Q GDK
Sbjct: 539  LGQRQKQHIKRDVSTPLRSTESGIVDQVMLTTTND-----GHRFAKVRVRTTKTPQIGDK 593

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G
Sbjct: 594  FASRHGQKGTIGITYRTEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRG 653

Query: 1150 KKIKSLINDYKANGDISPLRSFL 1172
             +  +          +S L   +
Sbjct: 654  DEGDATPFTKVTVTQVSDLLRRM 676


>gi|88976120|gb|ABD59034.1| RNA polymerase II second largest subunit [Clitocybe candicans]
          Length = 563

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 73/458 (15%), Positives = 127/458 (27%), Gaps = 88/458 (19%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             W       SM+  I   ++            ++       +G       I         
Sbjct: 192  TWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLIRM------- 244

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 245  ----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 300

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    I+ R  +D  ++S   + E+ E   RD          +       I  G  
Sbjct: 301  IDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPVRDNTLRMKHGTYDKLEDDGLIAPGTG 359

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +  D      R++          ++     +  Q             
Sbjct: 360  VAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI---------- 409

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                             + VKV V   R  Q+GDK A RHG KG +      EDMPF  +
Sbjct: 410  ----------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHGQKGTIGITYRQEDMPFTAE 459

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  +PSRM +G + E  L      +G +  +                    
Sbjct: 460  GIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT---------------- 503

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                      ++     + LR       G+ V                         G +
Sbjct: 504  ---------DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGHT 532

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                   G      V +G  Y  +L HMV DK+++R+ 
Sbjct: 533  -------GRKLQAQVYLGPTYYQRLKHMVDDKIHSRAR 563



 Score =  111 bits (277), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 67/461 (14%), Positives = 128/461 (27%), Gaps = 86/461 (18%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR   +            +   ++ 
Sbjct: 31  ENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYT 90

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                  P    E   + L      +  +N     +    K         +  L A EEE
Sbjct: 91  DAGRVCRPLFIVENQQLALQKKHVKW--LNNGYNDDGEEYKWEQLVKGGIIELLDAEEEE 148

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAA 676
              I+     L+                +          +        +  P  ++ I A
Sbjct: 149 TVMISMTPEDLENSRLQQSGADPHAQDADFDPAARLKAGINSHTWTHCEIHPSMILGICA 208

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 209 SIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI-------------------------- 242

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y       +     +  R                 
Sbjct: 243 ---------------RMDTMANILYYPQKPLATTRSMEYLKFR----------------- 270

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +
Sbjct: 271 -------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGI 323

Query: 857 GPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        +   +       +++ G+I  G  V   DI++GK  P         ++
Sbjct: 324 QQLEEFEKPVRDNTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQR 383

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   +    RD S  + S  SG V  V I       K
Sbjct: 384 T-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 417


>gi|113707355|gb|ABI36585.1| RNA polymerase II second largest subunit [Buellia frigida]
          Length = 673

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 109/724 (15%), Positives = 211/724 (29%), Gaps = 76/724 (10%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            L   +R    ++ + ++   +    +         + +  + + +     +         
Sbjct: 1    LAGLFRTLFNKLNKDVERYLKNCIENNREFNITLGVKSNHITNGLKYALATGNWGEQKKA 60

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET 
Sbjct: 61   ASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETP 116

Query: 576  EGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L     V+    IE    +      +   +   +++ +    ++      
Sbjct: 117  EGQACGLVKNLALMCYVSVGSPIEGIVDFLYQRQMEPLEEYDPITSPKATKIFLNGVWVG 176

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  + +     V        I      + D  D   K +      L P    +   R  +
Sbjct: 177  VHRNPASLVSAVQALRRRHIIEHEVSLVRDIRDKEFKILTDAGRVLRPLFVVETDPRSEI 236

Query: 693  GCNMQ---RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRSV 748
               +    +Q +  L+ +   +   M+    +            G+VE VDA      +V
Sbjct: 237  CGELVLNKQQHIEKLEQDKDEIPKDMDRDDREKLTFGWQGLINEGVVEYVDADEEE--TV 294

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
               + P+   +       +    ++   N R  V               PS  LG     
Sbjct: 295  MISMTPTDLSISRQLQAGYAVQEEDDDPNARVRVAPNPTAHTWTHCETHPSMILG----- 349

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N   S                H                         
Sbjct: 350  --ICASIIPFPDHNQVWS-----------RSXKCHRANLCTSXXXXXXXXXXXXXXXXXX 396

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                                         +       +   +  + AI      +  D+ 
Sbjct: 397  XXXXXXXXXXX---XXXXXXXXXXXXXXSMEXLKFRELPAGQNAIVAIACYSGYNQEDSV 453

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S     +    +F R   D+  R   +    +E   +      + L    Y +L +
Sbjct: 454  IMNQSSXDRGLF-RSLFYRSYSDQESR---IGMNIVECFEKPMRSNTMKLKHGTYDKLDD 509

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I+ G           K+  +++D       +++         ++     L  Q    
Sbjct: 510  DGIIIPGYRVSGEDIIIGKTAPITADAEELGQGAKYQDKRDASTPLRSTESGLVDQVLL- 568

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                     LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 569  -------------------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 609

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          +
Sbjct: 610  QEDMPFTSEGVIPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGLEGDATPXTDVTVDXV 669

Query: 1166 SPLR 1169
            S L 
Sbjct: 670  SRLL 673



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 73/582 (12%), Positives = 134/582 (23%), Gaps = 80/582 (13%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             +  T  +  ++    + +  K   S  G  ++  R    +      R          I
Sbjct: 37  KSNHITNGLKYALATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKI 96

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +         +      ++KN   +  + +   I+  +  +    + P
Sbjct: 97  AKPRQLHNTHWGLVCPAETPEGQACG---LVKNLALMCYVSVGSPIEGIVDFLYQRQMEP 153

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM- 558
            +  +      A   F     +       + +S +   RR   +  +  + R     E  
Sbjct: 154 LEEYDPITSPKATKIFLNGVWVGVHRNPASLVSAVQALRRRHIIEHEVSLVRDIRDKEFK 213

Query: 559 ------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR--------K 604
                 R + P       P     G  +            +     +   R         
Sbjct: 214 ILTDAGRVLRPLFVVETDPRSEICGELVLNKQQHIEKLEQDKDEIPKDMDRDDREKLTFG 273

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS-------FTEELVFCRCAGEEILVP 657
                    V Y+ A EEE   I+   + L              E+              
Sbjct: 274 WQGLINEGVVEYVDADEEETVMISMTPTDLSISRQLQAGYAVQEEDDDPNARVRVAPNPT 333

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P  ++ I AS+IPF +++        C+                      
Sbjct: 334 AHTWTHCETHPSMILGICASIIPFPDHNQVWSRSXKCHRANLCTSXXXXXXXXXX----- 388

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
                                                          +KF+         
Sbjct: 389 ----------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSMEXLKFRELPAGQNAI 438

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
                  G             S  +   +  R +  +       + E  + ++     E 
Sbjct: 439 VAIACYSG--------YNQEDSVIMNQSSXDRGLFRSLFYRSYSDQESRIGMNIVECFEK 490

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
              S             K G  +   D               GII  G  V+  DI++GK
Sbjct: 491 PMRS--------NTMKLKHGTYDKLDD--------------DGIIIPGYRVSGEDIIIGK 528

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             P         +       G K  D RD S  + S  SG V
Sbjct: 529 TAPITADAEELGQ-------GAKYQDKRDASTPLRSTESGLV 563


>gi|328704219|ref|XP_001948731.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like
            [Acyrthosiphon pisum]
          Length = 1121

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 88/258 (34%), Gaps = 76/258 (29%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + V ++R    GDK A R G KGI S+  P ED+PF + G   DIV NP G PSRM +  
Sbjct: 858  ITVRVQRNPTVGDKFASRAGQKGIFSKGWPAEDLPFTESGMVPDIVFNPHGFPSRMTIAM 917

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E   G +    G    +    Y                                    
Sbjct: 918  MIECMAGKSAAVHGVVHDATPFKYSEEDTAID---------------------------- 949

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F G        +L     +  G   +Y G+ G      +  G ++
Sbjct: 950  ---------------FFG-------KLLEAGGYNYFGTEQMYSGVDGRAMKASIFFGVVH 987

Query: 1256 MLKLNHMVSDKVYARSTGSYSLVTQQP-------------LGGKSNRGGQRLGEMEVWCI 1302
              +L HMVSDK   RSTG    VT+QP                          EME   +
Sbjct: 988  YQRLRHMVSDKWQVRSTGPVDAVTKQPVKGRKRGGGGRVG-------------EMERDAL 1034

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             ++G  +++Q+     SD
Sbjct: 1035 ISHGTPFLMQDRFMDCSD 1052



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 107/785 (13%), Positives = 231/785 (29%), Gaps = 158/785 (20%)

Query: 15  KFFGKNPEIID--IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGA 71
             +GK P+  +  + +L      S+++ +           EGL  A   + P+     G 
Sbjct: 12  VDYGKPPDSQNQILQELGTPHIDSFNYMI----------EEGLNLAISDLLPVEFDTKGK 61

Query: 72  A--MLEFVSYEFDPPK------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFT 117
               L  +      P+                +C  R  TY+  L+I L   + DV++  
Sbjct: 62  YRVKLTLLEATIHQPRVPTGSLGVKSHSIYPLECRQRHGTYSGRLEIKLSWRINDVEQMI 121

Query: 118 GAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
             + I  +          P+M K                         G F++KG +R  
Sbjct: 122 IDRDIGQV----------PIMLKSKLCHLEKMSPKQLVKLGEHQDEWGGYFIVKGKER-- 169

Query: 154 VSQLHR---SPGIHFDHDKGRASLSGKLLYACRI-IPDQGLWMDIEFDSKDIIHVR---- 205
              L R       +F     R +   K  +   I I  + +  D+   + ++ ++     
Sbjct: 170 ---LVRLLLGTRRNFPTAVQRNTWKNKDQFFSDIGILIRCVKDDLTTVTNNLHYLTNGTA 226

Query: 206 ---IDRRRKV---PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAK 259
              I  +++V   P+   +  L   S+E +                       DL     
Sbjct: 227 KLMIPIKKRVFYAPIFLIMRCLTNSSDEFI-------------FRHIIKGHEDDLYFIRS 273

Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
           V   +  +       +   K   G+L   +   +       +    +  +  +++  T  
Sbjct: 274 VMEMMRSLHESNIHCQEDAKEYIGILFRPRFYELPEWKTNKEVCDHMLRSYVLIHLNT-- 331

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL-LDIY 378
                    D   L+ +     +   +     +   A        D    ++  L   +Y
Sbjct: 332 ---------DFDKLKLLVFMLQKLFSVAQNKCLIEGA--------DGIMMQELMLGGHLY 374

Query: 379 RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIA 438
             +    + T+    ++        D+    ++G +   +R         R    E  + 
Sbjct: 375 LKILKEKLQTW---LNLVKINLLKVDQGGQPSIGDMMTALR---------RCDLIEHAMT 422

Query: 439 IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISSVDID 496
                 +L +  G     D    + +  + E +     +   R     +I E + + +  
Sbjct: 423 NFFATGNLNSQSGLGMQQD----KGLTILVENISRMRYMAHFRAVHRGAIFESMRTTEPR 478

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT-RRLSALGQGGVARARAG 555
            ++P       PV +          L+ L +       I+    R        +    A 
Sbjct: 479 RLLPDAWGFICPVHTPDGTPCGL--LNHLTKSCIVTKSISRKVLRDIPKVLVSLGMCEAS 536

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            + +D++             +G  IG V    +   +     + T   K      T ++V
Sbjct: 537 YKPQDINIGF----VYNVILDGRIIGYVPETLTALFI---RKLRTLKVKGKQIPETTEIV 589

Query: 616 YLSAMEEE------NRYIAQANSSLDEDGSFTE----------ELVFCRCAGEEILVPRE 659
           +L   EE         ++   N+ +       +          E V+   +  E  +   
Sbjct: 590 WLQKKEENILGQFPGLFLFTGNARMMRPVFNLDLEQIELIGTFEQVYLDISISEDEIRPN 649

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF-VGTGMESV 718
              + + +    +S  A LIP  + + S R +  C M +Q +            T +  +
Sbjct: 650 ITSYREVTKTDFLSHLACLIPLPDYNQSPRNMYQCQMGKQTMGTACHNWHLQSETKLYRI 709

Query: 719 VAKSS 723
            + +S
Sbjct: 710 QSPAS 714


>gi|115398832|ref|XP_001215005.1| DNA-directed RNA polymerase I polypeptide 2 [Aspergillus terreus
            NIH2624]
 gi|114191888|gb|EAU33588.1| DNA-directed RNA polymerase I polypeptide 2 [Aspergillus terreus
            NIH2624]
          Length = 1205

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 85/480 (17%), Positives = 147/480 (30%), Gaps = 101/480 (21%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E    +I ++        D         +       +G      +     +   L+ 
Sbjct: 696  THIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGTPGTAIDYRTDNKLYRLQT 755

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI-------------SVERE 962
                        +  + +  +GT   V I +  G D ++  I             ++ + 
Sbjct: 756  GQTPIVRPPLYNAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGHGTIYKT 815

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG--PKGFKKSTVLSSDLISEYPRSQ 1020
            +I  L  D  D +    R   ++L     G    +       +         + E     
Sbjct: 816  KIHSL--DDKDSRRGRSRREITKLFGFAPGGEIKAEWRNSLDEDGLPHIGARVREGSLVA 873

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
             W     D      V    + +       E+ + + I  +     + P   + + V   +
Sbjct: 874  AWHTVRYDAATDSYVNVDGITHFIKYKDAEEGYIDSIRVMGAETGVEP--CQSISVKYRV 931

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG                                M + Q+ E+ 
Sbjct: 932  PRKPVIGDKFSSRHGQKG--------------------------------MTIAQMIESM 959

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +                                         
Sbjct: 960  AGKAGALHGHPQDSTPFQFSEENT------------------------------------ 983

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +T  F           LR A  +  G   LY G+TG+ F   + +G ++  +L 
Sbjct: 984  ------ATDYF--------GEQLRKAGYNYYGNEPLYSGITGKEFAADIFIGVVHYQRLR 1029

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG  + +T QP+ G++  GG R+GEME   + A+GAA++LQ+ L   SD
Sbjct: 1030 HMVNDKFQVRTTGPVNSLTGQPVKGRAKGGGIRVGEMERDSLIAHGAAFILQDRLMNCSD 1089



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 83/536 (15%), Positives = 160/536 (29%), Gaps = 66/536 (12%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           +V +    N +  +   + + + I+ +I+ L  L  G    D+ D + N+ +   G    
Sbjct: 359 KVVLPHLGNQNVTETQDYDKFKMIMFMIRKLYALVAGDCAPDNPDAVSNQEILLGGFLYG 418

Query: 469 ----EMLKNQYRLG------LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               E L+   R                K    + + D +      + + + SA+  F  
Sbjct: 419 MILKERLEEWVRSFGPILRDWSNRNNGAKFTDPAFERDFLSKIVKRSNENLGSALEYFLS 478

Query: 519 SSQL--------------SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           +  L              + + E +N    I+H R    + +G          +R + P 
Sbjct: 479 TGNLVSPTGLDLQQASGYTVMAEKINFYRFISHFR---MIHRGSFFAQLKTTTVRKLLPE 535

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
            +G +CP  T +G   GL++ L     ++      +   K+           +S  E   
Sbjct: 536 SWGFLCPVHTPDGAPCGLLNHLAHKCLISTSDIDVSHLPKLLVQLGVRSESSVSLDESVP 595

Query: 625 RYI--AQANSSLDEDGSFTEELVFCRCAGEEILVPRE-KIDFIDASP-------KQVVSI 674
             I          +      + +      E   VP+E +I ++  S              
Sbjct: 596 VQIDGRIVGYCSPKQARVVADTLRYWKVMEMHNVPKELEIGYVPNSNGGQYPGIYIFSQA 655

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF--VGTGMESVVAKSSGAAIVAKRA 732
           A    P           +G   Q         E     V T +E                
Sbjct: 656 ARMFRPVKYLLLDKLDYVGPFEQPFLEIACLPEDLIPGVSTHIEFTPTNILSIVANMTPF 715

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
               Q        +  +  +    + +D     K  R        Q P+V+         
Sbjct: 716 SDYNQSPRNMYQCQMSKQTMGTPGTAIDYRTDNKLYRLQTG----QTPIVRP-------- 763

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 +  L +   G N +VA + + GY+ +D+M+I++             +       
Sbjct: 764 --PLYNAYGLDNFPNGTNAVVAIISYTGYDMDDAMIINKSSHERGFGHGTIYKTKIHSLD 821

Query: 853 DTKLGPEEITRDIPNV---------SEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           D         R+I  +           E   ++DE G+  +GA V  G ++    T
Sbjct: 822 DKDSRRGRSRREITKLFGFAPGGEIKAEWRNSLDEDGLPHIGARVREGSLVAAWHT 877



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 104/707 (14%), Positives = 199/707 (28%), Gaps = 109/707 (15%)

Query: 46  APDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKIT 105
               R N  ++  F     I   S        +           +C  R  TY   L+  
Sbjct: 91  PKRNRLNVRIREVFLDRPAIP-PSNKFTTRNRNIY-------PSECRERHATYRGKLRAR 142

Query: 106 LRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTK------------------------D 141
           L   V + D       ++ ++E    +G +P+M +                         
Sbjct: 143 LEYQVNNGD------WVESVRE----LGQVPIMLRTNRCHLEKATPEELVQHKEESEELG 192

Query: 142 GTFVIKGIQRIVVSQLHRS--------PGIHFDHDKGRA-SLSGKLLYACR-IIPDQGLW 191
           G F++ G ++     L R         P         +      K     R + PDQ   
Sbjct: 193 GYFIVNGNEK-----LIRMLVVGKRNFPMAIIRGSFVKRGHTYTKYGIQIRSVRPDQTSQ 247

Query: 192 ---MDIEFDSKDIIHVRIDRRRK---VPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
              +    D    +  R   R+    +PV   L AL +++ +     +  +V +   +  
Sbjct: 248 TNVLHYLSDGN--VTFRFSWRKNEYLIPVMMILKAL-VETND--REIFEGLVGNASSEGI 302

Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD---C 302
                        +V   L           S  +        L EK    LG+ SD    
Sbjct: 303 NNTFVTD------RVELLLRTYKGYNVHTRSSCRAY------LGEKFKPVLGVPSDMSNE 350

Query: 303 LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
             G      +V    G          ++   E   + + + I  +        A      
Sbjct: 351 DAGTEFLRKVVLPHLG----------NQNVTETQDYDKFKMIMFMIRKLYALVAGDCAPD 400

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
             D   +++  L      M   +     V              +     G    +     
Sbjct: 401 NPDAVSNQEILLGGFLYGMILKERLEEWV-----RSFGPILRDWSNRNNGAKFTDPAFER 455

Query: 423 DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
           D    +     E++ + ++  +   N   +   +D         + E +     +   RM
Sbjct: 456 DFLSKIVKRSNENLGSALEYFLSTGN-LVSPTGLDLQQASGYTVMAEKINFYRFISHFRM 514

Query: 483 ER--SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC-SSQLSQLEEHVNSLSRITHTR 539
               S   ++ +  +  ++P+      PV +         + L+       S   ++H  
Sbjct: 515 IHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHLAHKCLISTSDIDVSHLP 574

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS--SLTSFARVNAYGF 597
           +   L Q GV    +      V     GRI    + +   +   +          N    
Sbjct: 575 K--LLVQLGVRSESSVSLDESVPVQIDGRIVGYCSPKQARVVADTLRYWKVMEMHNVPKE 632

Query: 598 IETPYRKVCDGKVTNDVVYLS-AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
           +E  Y    +G     +   S A              LD  G F +  +   C  E   +
Sbjct: 633 LEIGYVPNSNGGQYPGIYIFSQAARMFRPVKYLLLDKLDYVGPFEQPFLEIACLPE--DL 690

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                  I+ +P  ++SI A++ PF + + S R +  C M +Q +  
Sbjct: 691 IPGVSTHIEFTPTNILSIVANMTPFSDYNQSPRNMYQCQMSKQTMGT 737


>gi|158253008|gb|ABW23988.1| RNA polymerase beta subunit [Pantoea ananatis]
          Length = 212

 Score =  214 bits (546), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLERDDANRALMGANMQRQ 212


>gi|62947910|gb|AAY22952.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 223

 Score =  214 bits (545), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 127/220 (57%), Positives = 162/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLS   +  N LS ++H RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSLFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A + IPFL
Sbjct: 124 DEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|138248516|gb|ABO72619.1| RNA polymerase B-subunit [Staphylococcus epidermidis]
          Length = 228

 Score =  214 bits (545), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 133/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D+
Sbjct: 122 DLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPF 228


>gi|218090029|emb|CAP57924.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|218090031|emb|CAP57925.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|218090033|emb|CAP57926.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
          Length = 228

 Score =  214 bits (545), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 132/228 (57%), Positives = 172/228 (75%), Gaps = 2/228 (0%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSA
Sbjct: 1   RVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 61  LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 120

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +EK+
Sbjct: 121 KVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKM 180

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+P
Sbjct: 181 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESP 228


>gi|117675867|emb|CAL69204.1| RNA polymerase subunit B [Subtercola boreus]
          Length = 361

 Score =  214 bits (545), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 67/175 (38%), Positives = 95/175 (54%), Gaps = 6/175 (3%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R+VVSQL RSPG++FD    +   S K +Y+ R+IP +G 
Sbjct: 1   FMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFDRQLEKT--SDKDIYSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEQFKGYSSIEATLEKDSILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITSD 301
             A   +         V  +    ++++         L K  + K  + LGI S+
Sbjct: 119 EEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIESE 173



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 131/354 (37%), Positives = 198/354 (55%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  D        +DI +                +  +
Sbjct: 10  EKGTFIINGTERVVVSQLVRSPGVYFDRQLEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 69

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     + I  TL  D    +++AL DIYR
Sbjct: 70  VGVRIDRKRKQSVTVFLKALGLTSEEIL--EQFKGYSSIEATLEKDSILTKEEALKDIYR 127

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +++      +  EDIIA 
Sbjct: 128 KLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIESELSNSVLTNEDIIAT 187

Query: 440 IKILVDLRNGKGTIDDID---------------NLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   + T+                   + GNRR+R+VGE+++NQ R GL RMER
Sbjct: 188 IKYLVALHENQTTLPGTRGGKSVDIRLDIDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 247

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 248 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 307

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 308 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 361


>gi|161331495|gb|ABX60665.1| RpoB [Bacillus sp. FSL_h8524]
          Length = 231

 Score =  214 bits (545), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 107/207 (51%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I+ GDKMAGRHGNKG++SRILP EDMPF+
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKIRVGDKMAGRHGNKGVISRILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARYLGVHMATPVFDGANEDDVW------ 192

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G  +                          
Sbjct: 193  -------------------ETMEEAGMNRDGKTI-------------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               LYDG +GEPFD  V+VG +YM+KL
Sbjct: 208  ---LYDGRSGEPFDSRVSVGIMYMIKL 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|168218612|emb|CAP45834.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218614|emb|CAP45835.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 80/136 (58%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+  ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDHDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|312204372|gb|ADQ47503.1| RNA polymerase II second largest subunit [Stictis mollis]
          Length = 692

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 99/659 (15%), Positives = 190/659 (28%), Gaps = 48/659 (7%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 62   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLVCPAETPEGQAC 117

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L+    +      E    +    + +V  +     +      ++      +  + 
Sbjct: 118  GLVKNLSLMCYITVGSPSEPIVEFMVQRNMEVLEEYEPTKSPNATKVFVNGVWVGVHREP 177

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            +     +        I      I D  D   K          P    D+  +     N+ 
Sbjct: 178  AHLVRTMQHLRRKNLISYEVSLIRDIRDREFKIFTDAGRVCRPLFVVDNDPKSANKGNLV 237

Query: 698  --RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
              ++ +  L+ +        E   A+         + G VE VDA            + +
Sbjct: 238  LTKEIINRLEDDKDLPADLTEDEKAEKFFGWNGLLQNGAVEFVDAEE----------EET 287

Query: 756  TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVA 814
               +     ++  R  Q       P       V+    +     T      +    +  +
Sbjct: 288  VLIIMTPEDLEVSRQVQAGYAPPEPSDDPNARVKGKVNLTQHAWTHCEIHPSXILGVCAS 347

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                                                    
Sbjct: 348  IIPFPDHNQSPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 407

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                     +             +       +   +  + AI      +  D+++   S 
Sbjct: 408  XXXXXXXXXL-YYPQKPLATTRSMEFLKFRELPAGQXAIVAIACYSGYNQEDSTIMNQSS 466

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R  +++ +R        +E   +    + + L    Y +L +   +  
Sbjct: 467  IDRGLF-RSLFYRAYVEQEKRVGM---SLVEQFEKPMRADTLRLKHGTYEKLDDDGLVAP 522

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  +  D      R++          ++     L             
Sbjct: 523  GVRVSGEDIIIGKTAPIPPDSEEMGQRTKLHTKRDASTPLRSTESGL------------- 569

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                 ++K+          L+ VKV     +  Q GDK A RHG KG +      EDMPF
Sbjct: 570  -----VDKVML--TTNAEGLKFVKVRTRTTKLPQIGDKFASRHGQKGTIGITYRMEDMPF 622

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
              +G   DI++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 623  SAEGVVPDIIVNPHAIPSRMTIAHLVECQLSKVSSLRGFEGDATPFTDVTVDSVSRLLR 681


>gi|56681223|gb|AAW21248.1| RNA polymerase beta subunit [Streptococcus thermophilus]
          Length = 231

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 90/287 (31%), Positives = 125/287 (43%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 16   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 65   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 119  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYI 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 179  ATPVFDGASSEDLWDTVREAGM-------------------------------------- 200

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +    ++L        G        TGEPFD  V+VG +YM+KL
Sbjct: 201  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIKL 231



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNVSEE LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   RELPNVSEEALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGVVRDVKIFTRANGD 90


>gi|40643888|emb|CAD88887.1| DNA-directed RNA polymerase subunit B [Fagonia lahovarii]
          Length = 484

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 50/211 (23%), Positives = 76/211 (36%), Gaps = 54/211 (25%)

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK + RHG KG +      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G
Sbjct: 328  IPQIGDKFSSRHGQKGTIGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECVMG 387

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                 +GK+            +IS         +                          
Sbjct: 388  KVAAHMGKEGDXTPFTDVTVDNISKALHKCGYQMRGFETM-------------------- 427

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                        +G +    G         + +G  Y  +L HM
Sbjct: 428  ---------------------------YNGHT----GR---RLTAMIFLGPTYYQRLKHM 453

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            V DK+++R  G   ++T+QP  G+S  GG R
Sbjct: 454  VDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 484



 Score = 99.4 bits (246), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 57/340 (16%), Positives = 98/340 (28%), Gaps = 91/340 (26%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + Y+   EEE   I+              +L+  R   E      E     
Sbjct: 51  WHDLVAKGFIEYIDTEEEETTMISM----------TINDLIQARQNPE--EAYSETYTHC 98

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ + AS+IPF +++ S R      M +QA+ +      F              
Sbjct: 99  EIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF-------------- 144

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                 R   +  V                                       Q+PLV  
Sbjct: 145 ------RMDTLAYV-----------------------------------LYYPQKPLVX- 162

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               L  G N  VA   + GYN EDS+++++  +    F S+  
Sbjct: 163 ---------TRAMEHLHFRQLPAGINAXVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFF 213

Query: 845 EEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             +    +      +E        +   +     + +D  G+   G  V+  D+++GK T
Sbjct: 214 RSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYEKLDGDGLAPPGTRVSGEDVIIGKTT 273

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           P              A         RD S+ +    +G V
Sbjct: 274 PISXE---------XAQGAAARXTRRDHSISLRHSETGIV 304


>gi|138248522|gb|ABO72622.1| RNA polymerase B-subunit [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 228

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 133/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DSV PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSVTPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS+LDE+G F  + V CR  G   ++ +EK+D+
Sbjct: 122 DLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFIADEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPF 228


>gi|138248528|gb|ABO72625.1| RNA polymerase B-subunit [Staphylococcus schleiferi subsp.
           schleiferi]
 gi|138248530|gb|ABO72626.1| RNA polymerase B-subunit [Staphylococcus schleiferi subsp.
           coagulans]
          Length = 228

 Score =  214 bits (545), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 132/227 (58%), Positives = 172/227 (75%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +EK+D+
Sbjct: 122 DLETNTITDRIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E+PF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPF 228


>gi|115606103|gb|ABJ16026.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  214 bits (545), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 186/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +T+ RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTYKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVAYVPSSEVDYMD 260


>gi|138248524|gb|ABO72623.1| RNA polymerase B-subunit [Staphylococcus warneri]
          Length = 228

 Score =  214 bits (545), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 133/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D+
Sbjct: 122 DLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPF 228


>gi|117675879|emb|CAL69210.1| RNA polymerase subunit B [Agromyces cerinus subsp. cerinus]
          Length = 353

 Score =  214 bits (545), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K +Y+ R+IP +G 
Sbjct: 1   FMGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFERTPEKT--SDKDIYSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEEFAGYESIALTLEKDNILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EEALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163



 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 126/333 (37%), Positives = 190/333 (57%), Gaps = 21/333 (6%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S         +   +K +    +      G ++  +I   +  ++ +       +  
Sbjct: 27  LVRSPGVYFERTPEKTSDKDIYSARVIPSR--GAWLEFEI--DKRDQVGVRIDRKRKQSV 82

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +    +    IL  +       I  TL  D    +++AL DIYR +RPG+      A
Sbjct: 83  TVFLKALGLTSEEIL--EEFAGYESIALTLEKDNILTKEEALKDIYRKLRPGEQVAAEAA 140

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
            ++ +  +F+  +YDL+ VGR K+N +L L+ P     +  +DI+A IK LV L + +  
Sbjct: 141 RALLDNFYFNPKRYDLAKVGRYKINNKLGLEAPLTDSVLTVQDIVATIKYLVALHDERTT 200

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI++
Sbjct: 201 LPGRRAGKAVELRLDVDDIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEA 260

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE
Sbjct: 261 ITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVE 320

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           +RDVHP+HYGR+CP ET EG NIGL+ SL SFA
Sbjct: 321 VRDVHPSHYGRMCPIETPEGPNIGLIGSLASFA 353


>gi|199580723|gb|ACH89063.1| RNA polymerase subunit beta [Staphylococcus delphini]
          Length = 231

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREEGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG IYML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVIYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|62947916|gb|AAY22955.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 223

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 127/220 (57%), Positives = 163/220 (74%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P E +D++D SPKQVV++A + IPFL
Sbjct: 124 DEFTVAQANSRLNEDGTFAEKIVMGRHQGVNQEYPAEVVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPKAPYVGTGMEYQAAHD 223


>gi|145342349|gb|ABP64871.1| RpoB [Oceanobacillus chironomi]
          Length = 232

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               +I   + GD++ PGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMPF+
Sbjct: 79   LDVRIFNREDGDELSPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISKILPEEDMPFM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+FE HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVFELHLGMAARLLGIHVASPVFDGATEEDVYETLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                                            ++L         
Sbjct: 199  GMA-----------------------------------------RDAKTIL--------- 208

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                YDG TGE FD  V+VG +YM+KL
Sbjct: 209  ----YDGRTGEAFDNRVSVGVMYMIKL 231



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 61/89 (68%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE LKN+DE GI+ VGAEV  GDILVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALKNLDEQGIVRVGAEVTDGDILVGKVTPKGVTELSAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DVRIFNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIILDVRIFNREDGD 90


>gi|138248520|gb|ABO72621.1| RNA polymerase B-subunit [Staphylococcus hominis]
          Length = 228

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 133/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D+
Sbjct: 122 DIDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPF 228


>gi|80973553|gb|ABB53514.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|157429507|gb|ABV56820.1| RNA polymerase beta subunit [Streptococcus pseudopneumoniae ATCC
            BAA-960]
          Length = 226

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 91/294 (30%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARTLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 196

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                       +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|138248532|gb|ABO72627.1| RNA polymerase B-subunit [Staphylococcus lugdunensis]
          Length = 228

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 132/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D+
Sbjct: 122 DIDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPF 228


>gi|199580703|gb|ACH89053.1| RNA polymerase subunit beta [Staphylococcus auricularis]
          Length = 231

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 75/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+++P EDMP+
Sbjct: 80   LDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKLVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DG P+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDEDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG +YML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMYML 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNVSE  LKN+D+ GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREEGD 91


>gi|80973613|gb|ABB53544.1| RNA polymerase beta subunit [Streptococcus gallinaceus]
          Length = 226

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSEDLWSTVKEAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 65/86 (75%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+ +DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRQLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|80973569|gb|ABB53522.1| RNA polymerase beta subunit [Streptococcus cristatus ATCC 51100]
          Length = 226

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 91/294 (30%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARNLGIHIATPVFDGASSEDLWSTVREAGM------------------------------ 196

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                       +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|47156951|gb|AAT12334.1| DNA-directed RNA polymerase III subunit 2 130KDa subunit [Antonospora
            locustae]
          Length = 1014

 Score =  214 bits (544), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 75/411 (18%), Positives = 147/411 (35%), Gaps = 71/411 (17%)

Query: 970  DKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS--TVLSSDLISEYPRSQWWQFAVQ 1027
            D +D  +I    +          ++     K +       +S    S+  R    +    
Sbjct: 662  DIEDALIINKGALDRGFGRCEVYRSYKHSLKRYSNGMCDRISGSKHSDGVRGPGERVFDG 721

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D  V +   +    ++ S  + ++   + ++K+            +VK  +   R  + G
Sbjct: 722  DFFVYKESPTEDADFKFSGELYKNLSPSVVDKVIVARSGEDQF--MVKTCLRQVRQPEVG 779

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK +                                     SR                 
Sbjct: 780  DKFS-------------------------------------SR----------------- 785

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G+K    +   + +   S      + ++       +++      ++       +G    
Sbjct: 786  HGQKGVIGLVVPETDLPFSEDGQVPDIIMNPHGFPSRMTVGKIIELISGKAAVFTGRQSD 845

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              VF     E ++ +L        G+    +G+TG+ ++  V  G +Y  +L HMV+DK+
Sbjct: 846  ATVFREDITEDLSHILIKHGYSYCGKDTFTNGITGDVYEGYVFFGPVYYQRLKHMVADKM 905

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------- 1320
            +ARS G  +++T+QP  GKS  GG RLGEME  C+  YGA+ +L E L I SD       
Sbjct: 906  HARSRGPRAMLTRQPTEGKSREGGLRLGEMERDCLIGYGASAILCERLMISSDVFRAYIC 965

Query: 1321 DVVGRTRVYESIV----AGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
               G   VY+++      G+       P +  +L +E+ ++ +   ++  +
Sbjct: 966  HRCG-IIVYKNMCTLCKRGDPVP-VDMPYACKLLFQELMSMNILPRIKLQK 1014



 Score =  135 bits (340), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 88/665 (13%), Positives = 193/665 (29%), Gaps = 115/665 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
            ++C  RDLTY   + + +             K  K I ++++++G +P+M +       
Sbjct: 8   PEECRLRDLTYCGNIYVDIEYT----------KHRKVIIKKNVFIGKVPIMLRSMLCHLE 57

Query: 142 -----------------------GTFVIKGIQRIVVSQLHRS----------PGIHFDHD 168
                                  G F++KG++R+++ Q   S           G  F   
Sbjct: 58  EKRDDCETVRETYGHRECPLDMGGYFIVKGVERVILIQEQLSKNRIIADIDNKGCKFTSV 117

Query: 169 KGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEI 228
                   K      I+  + L++      K+ +         VP    L ALGM S+  
Sbjct: 118 TSSTH--DKKSKTSIILKKRLLYL------KNNVF-----TDSVPAVIVLKALGMVSDCE 164

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           ++ F       Q G        + +  +   V + L  +D     I    +    + +  
Sbjct: 165 IAEF-----VGQEGALLEMLEPSLEHALQTGVHTQLQALD----FISKLTRPRQNVSRID 215

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
           + + + +  +  +      +  D ++     I + A  +      E    S      +  
Sbjct: 216 EARTILYEVVLPN------IPNDGIDMRRKAITV-AIMIRVLLQAELNMISMDDIDFLGN 268

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                    +         +   +    I +V+     +    A +  N          +
Sbjct: 269 KRFELAGNLLSILFEDTFLRFNSELKKSIDKVLSKSQRTQDLDALTFLNLQVNLISNSFV 328

Query: 409 STVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
             +        R  ++     + + +   IA+I  +  +++       I   G R + + 
Sbjct: 329 RAISTGNWTVRRFRMERAGVTQVLSRLSYIAMIGSMAKIQSQFEKTRKI--SGPRSLHTS 386

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
              +              +K      +I + +PQ  +  + +       F +        
Sbjct: 387 SWGMLCPADTPEGESCGLVKNLAILAEITTDVPQSDV-EQLLFQLGVRDFRTCSGIDFYS 445

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP-------AETSEGHNI 580
             + L  +  T          + R    +  R V                   T  G   
Sbjct: 446 KHSYLIFLNGTIVGICYNNNTLVRKFVEMRRRGVVSQFVSVYKNDEKRTISIATDGGRIC 505

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDG---KVTNDVVYLSAMEEENRYIAQANSSLDED 637
             +  + +  ++  +  +E   R+  +         V +L   EE N  IA   S++   
Sbjct: 506 RPLIIVENGRQMLEHEDLELLRRRYKNPDDLFKEGKVEFLDVNEENNTKIALRESNICRS 565

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                                     ++     ++   A LIP+  ++ S R    C M 
Sbjct: 566 -----------------------TTHLEICEYSILGCVAGLIPYPHHNQSPRNTYQCAMG 602

Query: 698 RQAVP 702
           +QA+ 
Sbjct: 603 KQAMG 607



 Score =  119 bits (299), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 121/774 (15%), Positives = 249/774 (32%), Gaps = 95/774 (12%)

Query: 211 KVPVTSFLMALGMDSEE-------ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           KVP    L ++    EE       +  T+  +      G ++        +++  ++S +
Sbjct: 44  KVP--IMLRSMLCHLEEKRDDCETVRETYGHRECPLDMGGYFIVKGVERVILIQEQLSKN 101

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +  D    +   G K TS    +  +K    + +    L          +     I ++
Sbjct: 102 RIIAD----IDNKGCKFTSVTSSTHDKKSKTSIILKKRLLYLKN--NVFTDSVPAVIVLK 155

Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRP 383
           A  ++ +  + E    E   + +L               +      +  AL  I ++ RP
Sbjct: 156 ALGMVSDCEIAEFVGQEGALLEMLEPSL--------EHALQTGVHTQLQALDFISKLTRP 207

Query: 384 GDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKIL 443
                                    + +  V +    N       + I    +  +I++L
Sbjct: 208 --------------RQNVSRIDEARTILYEVVLPNIPNDGIDMRRKAIT---VAIMIRVL 250

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD- 502
           +       ++DDID LGN+R    G +L   +    LR    +K+ I  V   S   QD 
Sbjct: 251 LQAELNMISMDDIDFLGNKRFELAGNLLSILFEDTFLRFNSELKKSIDKVLSKSQRTQDL 310

Query: 503 ------LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG-------- 548
                  +    + ++      +   +     +          RLS +   G        
Sbjct: 311 DALTFLNLQVNLISNSFVRAISTGNWTVRRFRMERAGVTQVLSRLSYIAMIGSMAKIQSQ 370

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY---GFIETPYRK- 604
             + R     R +H + +G +CPA+T EG + GLV +L   A +        +E    + 
Sbjct: 371 FEKTRKISGPRSLHTSSWGMLCPADTPEGESCGLVKNLAILAEITTDVPQSDVEQLLFQL 430

Query: 605 -VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
            V D +  + + + S    ++ Y+   N ++         LV          V  + +  
Sbjct: 431 GVRDFRTCSGIDFYS----KHSYLIFLNGTIVGICYNNNTLVRKFVEMRRRGVVSQFVSV 486

Query: 664 IDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
                K+ +SIA        P +  ++  ++L   +++         +  F    +E + 
Sbjct: 487 YKNDEKRTISIATDGGRICRPLIIVENGRQMLEHEDLELLRRRYKNPDDLFKEGKVEFLD 546

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSV--------EGDLDPSTSGVDIYRLMKFQRSN 771
                   +A R   + +      +                  + S  + Y+    +++ 
Sbjct: 547 VNEENNTKIALRESNICRSTTHLEICEYSILGCVAGLIPYPHHNQSPRNTYQCAMGKQAM 606

Query: 772 QNTCVNQ--RPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDS 826
               +NQ  R    +   V     +     TD      L  G+N +VA M + GY+ ED+
Sbjct: 607 GFVALNQYRRFDTLLNLLVYPQKPLVSTKITDIVNFEKLPAGQNGMVAVMAYAGYDIEDA 666

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           ++I++  +            ++   +    G  +      +            G+   G 
Sbjct: 667 LIINKGALDRGFGRCEVYRSYKHSLKRYSNGMCDRISGSKH----------SDGVRGPGE 716

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            V  GD  V K +P  ++      K    ++   +  V D  +   SG    +V
Sbjct: 717 RVFDGDFFVYKESPTEDAD----FKFSGELYKNLSPSVVDKVIVARSGEDQFMV 766


>gi|154338984|ref|XP_001565714.1| RNA polymerase I second largest subunit [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1567

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 108/299 (36%), Gaps = 56/299 (18%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D    +++      + T     +      ++++       P     V +   + RP   G
Sbjct: 1241 DPFTNKSIYEYTRHHATKWRHFDKGEDAWVQQVIPLVYSGPDP-TSVLMIFRIPRPPTVG 1299

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            DK + RHG KG +   +   D+PF    G   D+++NP   PSRM VG + E        
Sbjct: 1300 DKFSSRHGQKGTLPLHISSHDLPFSTTSGITPDVIINPHAFPSRMTVGMMLEIMTAKVGA 1359

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+ I +       +                                            
Sbjct: 1360 IEGRFIDNSAWSTVDDQPRVA--------------------------------------- 1380

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                      E I   L  A  +  G+  L DG++GE     V +G     +L HMVSDK
Sbjct: 1381 ----------ELIGDALVKAGYNRYGREHLIDGISGEEMKADVFMGICGYQRLRHMVSDK 1430

Query: 1267 VYARSTGS---YSLVTQ--QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              AR+      Y  VT+  QP+ G+   GG R+GEME   + ++G + V+ + L   SD
Sbjct: 1431 WQARARTDAHTYRAVTKTGQPVKGRKRHGGVRVGEMERDGLLSHGISEVVVDRLLHVSD 1489


>gi|115606099|gb|ABJ16024.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
 gi|115606101|gb|ABJ16025.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 186/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +T+ RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTYKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|115606095|gb|ABJ16022.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 130/259 (50%), Positives = 184/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ S +
Sbjct: 122 QNNPLSGLTHKRRLLALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSPS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|242006406|ref|XP_002424041.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Pediculus humanus corporis]
 gi|212507347|gb|EEB11303.1| DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide,
            putative [Pediculus humanus corporis]
          Length = 1137

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 133/978 (13%), Positives = 286/978 (29%), Gaps = 165/978 (16%)

Query: 405  KYDLSTVGRVKMNMRLNLDTPDDVRHI--RKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
            K  +   G +  N  L      D R +  + + +  +++ ++          D+D+ GN+
Sbjct: 306  KNVVDDAGDILANTILAHVDVLDFRCMCEKTQYLGLMVRRILQAETDPRFYTDLDHYGNK 365

Query: 463  RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            R+   G ML   +   L R    +K        D ++P+       +V  + + F ++  
Sbjct: 366  RLELAGAMLGLLFEDFLKRYNLELKMI-----ADKMIPKIKAAQFDIVKHLRQDFITNGF 420

Query: 523  SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
            S      N   +     R+   G   V    + +    +               G     
Sbjct: 421  SNAISTGNWTIKRF---RMHTQGVTQVLSRLSYISAFGMMTRVNSHFEKTRKVSGPRSLH 477

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             +        +           V +  +   +  LS+     + IAQ    +       E
Sbjct: 478  ATQWGMLCPSDTPEGEACG--LVKNLALMCHISTLSSELPIKQ-IAQLCGIIPPMRMNME 534

Query: 643  ELVFCRCAGEEILVPREKIDF-IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +++        +      I +      K++  I  S         S   L          
Sbjct: 535  QILAPDTFMVFLNGSLLGITYEPKKLCKKLRKIRRSGKLNPFVSISLHALHRTVYIFSDS 594

Query: 702  PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
              L      +  G+  +                 + +D +   +       + + S + +
Sbjct: 595  GRLCRPYIIIENGVPLITKSDLNDL----ERKFKKFIDFLDDGVIEYMDVNEENDSLIAL 650

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y                       D   ++  +   P T LG       +  + +P+   
Sbjct: 651  YEK---------------------DITPKHTHLEIAPFTLLG-------VCASIIPYPHN 682

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N          M  + +    + +E  +                               +
Sbjct: 683  NQSPRNTYQCAMGKQAMGAIGYNQENRIDT-----------------------------L 713

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +          ++   +       +   +  +  +      D+ D  +   + +      
Sbjct: 714  LYNMVYTQKPMVITKPMVMVNYDKLPAGQNAIVCVMSYSGYDIEDALIINKASLERGYGR 773

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
             ++F R+     +R      ++I+    D +  + +    +         G+  ++    
Sbjct: 774  CQVF-RNTKCVLKRYADGTSDRIQGPLVDAETRKPLWKHGVLDTDGIGAPGEKILNRQVL 832

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              KS    S+  +     +                     Y  +    +    + I+K+ 
Sbjct: 833  INKSVPSRSNTSNVPIFGE-------------------RDYIDTPVDYKGLEHSYIDKVL 873

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
               +       ++K+ +   R  + GDK +                              
Sbjct: 874  ISTNSDDD--SLIKIKLRQTRIPEIGDKFS------------------------------ 901

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
                   SR                  G+K    +   + N   +      + ++     
Sbjct: 902  -------SR-----------------HGQKGVVGLIVEQENMPFNESGICPDVIMNPHGF 937

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
              +++      +L       +G       F G+    +   L     +  G+ ILY G+T
Sbjct: 938  PSRMTVGKLIELLAGKAGVVTGKHHYGTAFGGSTVSEVQEELVKNKFNYEGKDILYSGIT 997

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEP +  V  G ++  +L HMV DK++AR+ G  +++T+QP  G++  GG RLGEME  C
Sbjct: 998  GEPMEVYVYSGPVFYQRLKHMVQDKIHARARGPRAVLTRQPTEGRAADGGLRLGEMERDC 1057

Query: 1302 IQAYGAAYVLQEMLTIKSD----DVVGRTR----VYESIVAG----NDTFETGTPESFNV 1349
            + AYGA+ ++ E L I SD    DV          Y     G     +      P +  +
Sbjct: 1058 LIAYGASSMISERLMISSDAFQCDVC--NECGLIAYSKWCHGCKSSKEISTIKLPYATKL 1115

Query: 1350 LVKEMQALGLSIDLENSR 1367
            L +E++++ +   L    
Sbjct: 1116 LFQELRSMNIVPRLSLKN 1133



 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 140/1009 (13%), Positives = 281/1009 (27%), Gaps = 214/1009 (21%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
            PE + I  L++    S+++F+ ++I      N   Q     V P         L+++  
Sbjct: 31  VPEFLKIKGLVKQHTDSFNYFIKVDIKKIVEAN---QYVRSDVDP------NFYLKYLDV 81

Query: 80  EFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
           E   P+              +C  RD+TY+ P+ +T+             +  + I ++ 
Sbjct: 82  EVGVPEIEEGLDVKRASTPQECRLRDMTYSAPITVTIEYT----------RGNERIIKKD 131

Query: 130 IYMGDLPLMT------------------------KDGTFVIKGIQRIVVS--QLHR---- 159
           + +G +P+M                           G F++KG +R+++   QL +    
Sbjct: 132 LIIGRIPIMLQSANCVLYGKDEYELSKLNECPLDPGGYFIVKGQERVILIREQLLKNSLV 191

Query: 160 ----SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPV 214
               S G    H         K      II             KD  ++R +     +P+
Sbjct: 192 VEKDSKGNPCAHVMSSTHE--KKSKTNIII------------KKDKFYLRHNAFSDDIPL 237

Query: 215 TSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAA------------DLMVGAKVSS 262
                  G++S+     F+  +   Q       P                   +G K   
Sbjct: 238 AVIYKGFGVESD---IEFFMSVGIEQEYHEKLIPSMEECHKLNICTQTQALRYIGNKTKV 294

Query: 263 SLVDIDTG---EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
                 +G   + V++    + +  + +  +              GL V   I+  ET  
Sbjct: 295 KRSLPGSGGKPKNVVDDAGDILANTILAHVDVLDFRCMCEKTQYLGLMV-RRILQAETDP 353

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
            +    D    K LE         + +L+ D +         +        K A  DI +
Sbjct: 354 RFYTDLDHYGNKRLELAGA----MLGLLFEDFLKRYNLELKMIADKMIPKIKAAQFDIVK 409

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +R   ++                 +     V +V   +          R     +    
Sbjct: 410 HLRQDFITNGFSNAISTGNWTIKRFRMHTQGVTQVLSRLSYISAFGMMTRVNSHFEKTRK 469

Query: 440 IKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +     L   +  +    +        + + L     +  L  E  IK+         ++
Sbjct: 470 VSGPRSLHATQWGMLCPSDTPEGEACGLVKNLALMCHISTLSSELPIKQIAQLC---GII 526

Query: 500 PQDLINAKPV--VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           P   +N + +        F   S L    E      ++   RR   L         A   
Sbjct: 527 PPMRMNMEQILAPDTFMVFLNGSLLGITYEPKKLCKKLRKIRRSGKLNPFVSISLHALHR 586

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
              +         P    E                +    +E  ++K  D      + Y+
Sbjct: 587 TVYIFSDSGRLCRPYIIIENG--------VPLITKSDLNDLERKFKKFIDFLDDGVIEYM 638

Query: 618 SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
              EE +  IA     +                             ++ +P  ++ + AS
Sbjct: 639 DVNEENDSLIALYEKDITPKH-----------------------THLEIAPFTLLGVCAS 675

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
           +IP+  N+ S R    C M +QA+  +         G                       
Sbjct: 676 IIPYPHNNQSPRNTYQCAMGKQAMGAI---------GYNQENRID--------------- 711

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
                                              N    Q+P+V          I    
Sbjct: 712 -------------------------------TLLYNMVYTQKPMV----------ITKPM 730

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
              +   L  G+N +V  M + GY+ ED+++I++  +             + + +    G
Sbjct: 731 VMVNYDKLPAGQNAIVCVMSYSGYDIEDALIINKASLERGYGRCQVFRNTKCVLKRYADG 790

Query: 858 PEEITRDIPNVSE-----EGLKNIDECGIICVGAEVNPGDILVGKITPKGES----PMTP 908
             +  +     +E          +D  GI   G ++    +L+ K  P   +    P+  
Sbjct: 791 TSDRIQGPLVDAETRKPLWKHGVLDTDGIGAPGEKILNRQVLINKSVPSRSNTSNVPIFG 850

Query: 909 EEKLLRAIFGEKA--VDVRDTSLRVPSGVSGTVVDVRI-FNRHGIDKNE 954
           E   +      K       D  L   +    +++ +++   R     ++
Sbjct: 851 ERDYIDTPVDYKGLEHSYIDKVLISTNSDDDSLIKIKLRQTRIPEIGDK 899


>gi|308156029|gb|ADO15384.1| RNA polymerase beta subunit [Xanthomonas translucens pv.
           translucens]
          Length = 204

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV DG++T+DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVYARTNQYGFLETPYRKVVDGQITDDVEYLSAIEENEYVIAQANALHDSKSR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+A+ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRAQKPLVGTGIERAVARDS 204


>gi|78099512|gb|ABB20870.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099514|gb|ABB20871.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099516|gb|ABB20872.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099518|gb|ABB20873.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099520|gb|ABB20874.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099522|gb|ABB20875.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099524|gb|ABB20876.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099526|gb|ABB20877.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099528|gb|ABB20878.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099530|gb|ABB20879.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099532|gb|ABB20880.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099534|gb|ABB20881.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099536|gb|ABB20882.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099538|gb|ABB20883.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099540|gb|ABB20884.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099542|gb|ABB20885.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099544|gb|ABB20886.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099546|gb|ABB20887.1| RNA polymerase subunit B [Acinetobacter baumannii]
 gi|78099550|gb|ABB20889.1| RNA polymerase subunit B [Acinetobacter baumannii]
          Length = 149

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 81/152 (53%), Positives = 107/152 (70%), Gaps = 4/152 (2%)

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  G
Sbjct: 1    DKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKG 60

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            LG KI+ ++ + +    +  LR FL+K+    G   E +    D+ +L +A   ++GVP+
Sbjct: 61   LGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDEEILALAGNLRAGVPL 117

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYD 1238
            +TPVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 118  ATPVFDGAEESQIKDLLELADISRTGQTVLFD 149


>gi|115606107|gb|ABJ16028.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 184/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQ SQ   
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQPSQFMG 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|294471030|gb|ADE80776.1| RNA polymerase beta subunit [Lactococcus lactis subsp. lactis]
          Length = 142

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 63/164 (38%), Positives = 90/164 (54%), Gaps = 22/164 (13%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
           +LIEVQ  SY +FL          +EGL   FK +FPI  F+G   LEFV YE   PK+ 
Sbjct: 1   NLIEVQTLSYKNFL----------DEGLANVFKEMFPIDNFAGTMELEFVGYEMKTPKYT 50

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIK 147
           V++    D  Y+ P+ +T RL+          K   ++K Q ++ GD PLMT+ GTF+  
Sbjct: 51  VEEARAHDANYSAPIYVTFRLV---------NKETGELKTQEVFFGDFPLMTEMGTFINN 101

Query: 148 GIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           G +R++VSQL RSPG +F     +A  +G   +    IP++G W
Sbjct: 102 GSERLIVSQLVRSPGSYFH---LKADKNGLESFGHTTIPNRGAW 142


>gi|80973523|gb|ABB53499.1| RNA polymerase beta subunit [Streptococcus sinensis]
 gi|148357836|gb|ABQ59245.1| RNA polymerase beta subunit [Streptococcus sinensis]
          Length = 226

 Score =  213 bits (543), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 123/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                               
Sbjct: 175  ATPVFDGASAEDLWDTVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|327133539|gb|AEA29774.1| RNA polymerase subunit B [Acinetobacter sp. 9N1]
          Length = 183

 Score =  213 bits (543), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 74/178 (41%), Positives = 108/178 (60%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F
Sbjct: 1    QMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIPPSDEGIAERLTQIQTYLKEKSAEIDEKF 60

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAG HGNKG+VS ILP EDMP   
Sbjct: 61   AEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGPHGNKGVVSNILPVEDMPHDA 120

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +G PVD+VLNPLGVPSRMNVGQI ETHLG A  GLG++I  ++   +   ++    + 
Sbjct: 121  NGVPVDVVLNPLGVPSRMNVGQILETHLGLAAKGLGEQIDKMLKQQRTIAELREFLTK 178


>gi|115606093|gb|ABJ16021.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  213 bits (543), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 185/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMD 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +T  RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTDKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|80973581|gb|ABB53528.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|80973587|gb|ABB53531.1| RNA polymerase beta subunit [Streptococcus gordonii]
          Length = 226

 Score =  213 bits (543), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 175  ATPVFDGASSDDLWDTVREAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|138248518|gb|ABO72620.1| RNA polymerase B-subunit [Staphylococcus haemolyticus]
 gi|138248526|gb|ABO72624.1| RNA polymerase B-subunit [Staphylococcus capitis]
          Length = 228

 Score =  213 bits (543), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 133/227 (58%), Positives = 173/227 (76%), Gaps = 2/227 (0%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           ++ER+S  D DS+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG
Sbjct: 2   VRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALG 61

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV
Sbjct: 62  PGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKV 121

Query: 606 --CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
                 +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D+
Sbjct: 122 DLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDY 181

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           +D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAPF
Sbjct: 182 MDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEAPF 228


>gi|80973549|gb|ABB53512.1| RNA polymerase beta subunit [Streptococcus halichoeri]
          Length = 226

 Score =  213 bits (543), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWETVQEAGMDADAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|158252956|gb|ABW23962.1| RNA polymerase beta subunit [Pantoea ananatis LMG 20103]
          Length = 212

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 130/211 (61%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS  ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSGGASLIPFLEQDDANRALMGANMQRQ 212


>gi|80973579|gb|ABB53527.1| RNA polymerase beta subunit [Streptococcus porcinus]
          Length = 226

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  +  D+    +                                  
Sbjct: 167  ARNLGIHIATPVFDGASAEDLWETVAEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|80973561|gb|ABB53518.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 226

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 91/294 (30%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGADGVVRDV------KIFTRVNGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARTLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 196

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                       +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRVNGD 86


>gi|66854101|gb|AAY57359.1| RpoB [Prevotella nigrescens]
          Length = 125

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/179 (39%), Positives = 87/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A  +K GV  STP+FDGA  E +      A L     + +YDG TG
Sbjct: 21   --------------AAGYKLGVKFSTPIFDGAKLEDLKEWTDKAGLPPMCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   ERFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|66854089|gb|AAY57353.1| RpoB [Prevotella buccae ATCC 33574]
          Length = 125

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 70/179 (39%), Positives = 85/179 (47%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA    +      A L     + LYDG TG
Sbjct: 21   --------------AAGKKLGVKFATPIFDGAKLADLQEWTDKAGLPRLCSTHLYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EQFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|80973593|gb|ABB53534.1| RNA polymerase beta subunit [Streptococcus iniae]
          Length = 226

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  +  D+    +                                  
Sbjct: 167  ARNLGIHIATPVFDGASAEDLWDTVAEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|158252906|gb|ABW23937.1| RNA polymerase beta subunit [Pantoea agglomerans pv. betae]
          Length = 212

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ     N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMYQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 LVSDEIHYLSAIEEGNYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +Q+VS+ ASLIPFLE+DD+NR LMG NMQRQ
Sbjct: 182 QQIVSVGASLIPFLESDDANRALMGANMQRQ 212


>gi|322499619|emb|CBZ34693.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 1616

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 106/299 (35%), Gaps = 56/299 (18%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D    ++V      + T     +      ++++       P     V +   + RP   G
Sbjct: 1290 DPFTNKSVYEYTRHHATKWRHFDKGEDAWVQQVIPLVYSGPDP-TSVLMIFRIPRPPTVG 1348

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            DK + RHG KG +   +   ++PF    G   D+++NP   PSRM VG + E        
Sbjct: 1349 DKFSSRHGQKGTLPLHIRSHNLPFATASGITPDVIINPHAFPSRMTVGMVLEIMTAKVGA 1408

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+ I                                                      
Sbjct: 1409 IEGRFIDHSAWSTVDEQPRVA--------------------------------------- 1429

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                      E I   L  A  +  G+  L DG++GE     V +G     +L HMVSDK
Sbjct: 1430 ----------ELIGEALVKAGYNRYGREHLIDGISGEEMKADVFMGICGYQRLRHMVSDK 1479

Query: 1267 VYARSTGS---YSLVTQ--QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              AR+      Y  VT+  QP+ G+   GG R+GEME   + ++G + V+ + L   SD
Sbjct: 1480 WQARARTDAHTYRAVTKTGQPVKGRKRHGGVRVGEMERDGLLSHGISEVVVDRLLHVSD 1538


>gi|146088594|ref|XP_001466094.1| RNA polymerase I second largest subunit [Leishmania infantum JPCM5]
 gi|134070196|emb|CAM68531.1| putative RNA polymerase I second largest subunit [Leishmania infantum
            JPCM5]
          Length = 1616

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 106/299 (35%), Gaps = 56/299 (18%)

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
            D    ++V      + T     +      ++++       P     V +   + RP   G
Sbjct: 1290 DPFTNKSVYEYTRHHATKWRHFDKGEDAWVQQVIPLVYSGPDP-TSVLMIFRIPRPPTVG 1348

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            DK + RHG KG +   +   ++PF    G   D+++NP   PSRM VG + E        
Sbjct: 1349 DKFSSRHGQKGTLPLHIRSHNLPFATASGITPDVIINPHAFPSRMTVGMVLEIMTAKVGA 1408

Query: 1147 GLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
              G+ I                                                      
Sbjct: 1409 IEGRFIDHSAWSTVDEQPRVA--------------------------------------- 1429

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
                      E I   L  A  +  G+  L DG++GE     V +G     +L HMVSDK
Sbjct: 1430 ----------ELIGEALVKAGYNRYGREHLIDGISGEEMKADVFMGICGYQRLRHMVSDK 1479

Query: 1267 VYARSTGS---YSLVTQ--QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
              AR+      Y  VT+  QP+ G+   GG R+GEME   + ++G + V+ + L   SD
Sbjct: 1480 WQARARTDAHTYRAVTKTGQPVKGRKRHGGVRVGEMERDGLLSHGISEVVVDRLLHVSD 1538


>gi|60101383|gb|AAX13760.1| RNA polymerase beta subunit [Streptococcus gordonii]
          Length = 227

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 13   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 61

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 62   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 115

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 116  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 175

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 176  ATPVFDGASSDDLWDTVREAGMDSDAK----------------------------TVLYD 207

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 208  G--------------------------RTGEPFDNRVSVGVMYMIK 227



 Score = 84.4 bits (207), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/87 (63%), Positives = 67/87 (77%)

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +V
Sbjct: 1   IPNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREV 60

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RDTSLRVP G  G V DV+IF R   D
Sbjct: 61  RDTSLRVPHGADGVVRDVKIFTRANGD 87


>gi|80973577|gb|ABB53526.1| RNA polymerase beta subunit [Streptococcus criceti]
          Length = 226

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 125/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGAGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWETVEEAGMASDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 79.7 bits (195), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 54/85 (63%), Positives = 66/85 (77%)

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
           NV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRD
Sbjct: 2   NVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRD 61

Query: 927 TSLRVPSGVSGTVVDVRIFNRHGID 951
           TSLRVP G +G V DV+IF R   D
Sbjct: 62  TSLRVPHGGAGIVRDVKIFTRANGD 86


>gi|115382722|gb|ABI95382.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum intermedium
           LMG 3301]
          Length = 214

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 124/215 (57%), Positives = 156/215 (72%), Gaps = 1/215 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD EEILSTFY  + Y++ GD W  P SA D   G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRIPYSA-DRFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S L+D DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y+AED+VN  TGEIY
Sbjct: 60  SDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLLDTGETEINVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           RPG+  T   AE+MF+ LFFD+++YDLS VGRVKM
Sbjct: 180 RPGEPPTMDSAEAMFSSLFFDAERYDLSAVGRVKM 214


>gi|62947918|gb|AAY22956.1| RNA polymerase beta subunit [Streptococcus mitis]
          Length = 223

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 126/220 (57%), Positives = 162/220 (73%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGF++TPYRKV      VTN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFVQTPYRKVDRETGVVTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG+F E++V  R  G     P   +D++D SPKQVV++A + IPFL
Sbjct: 124 DEFTVAQANSRLNEDGTFAEKVVMGRHQGVNQEYPANVVDYMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+  +AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLINPKAPYVGTGMEYQAAHD 223


>gi|308156001|gb|ADO15370.1| RNA polymerase beta subunit [Xanthomonas albilineans]
          Length = 204

 Score =  213 bits (542), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTTETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DG++T++V YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVVDGQITDEVEYLSAIEENEYVIAQANALHDAKNR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+A+ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRAQKPLVGTGIERAVARDS 204


>gi|168218592|emb|CAP45824.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218594|emb|CAP45825.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218596|emb|CAP45826.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218598|emb|CAP45827.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218608|emb|CAP45832.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
 gi|168218628|emb|CAP45842.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 121

 Score =  213 bits (541), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 52/136 (38%), Positives = 80/136 (58%), Gaps = 18/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL            GL+  FK++ PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFLGWR---------GLERCFKTISPIEDFTGNLSLEFIDYSLGEPKYPVEE 51

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 52  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 102

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 103 RVIVSQLVRSPSVYYS 118


>gi|158253022|gb|ABW23995.1| RNA polymerase beta subunit [Pantoea stewartii subsp. stewartii]
          Length = 212

 Score =  213 bits (541), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 129/211 (61%), Positives = 168/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR++ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRLIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE DD+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLEQDDANRALMGANMQRQ 212


>gi|80973501|gb|ABB53488.1| RNA polymerase beta subunit [Streptococcus didelphis]
          Length = 226

 Score =  213 bits (541), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D     D+    +                                  
Sbjct: 167  ARNLGIHIATPVFDGATAEDLWETVTEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|327133537|gb|AEA29773.1| RNA polymerase subunit B [Acinetobacter sp. 9N6]
          Length = 175

 Score =  213 bits (541), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/174 (41%), Positives = 105/174 (60%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F  
Sbjct: 1    SNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKFAE 60

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K  K   GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +G
Sbjct: 61   KKRKFSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANG 120

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
             PVD+VL PLGVPSRMNVG I ETHLG A  GLG++I  ++   +   ++    
Sbjct: 121  VPVDVVLTPLGVPSRMNVGHILETHLGLAAKGLGEQIDKMLKQQRTIAELREFL 174


>gi|80973513|gb|ABB53494.1| RNA polymerase beta subunit [Streptococcus orisratti]
          Length = 226

 Score =  213 bits (541), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSDDLWSTVQEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|46451692|gb|AAS97969.1| RNA polymerase II [Cladonia caroliniana]
          Length = 642

 Score =  213 bits (541), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 104/703 (14%), Positives = 208/703 (29%), Gaps = 86/703 (12%)

Query: 465  RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
               G +L   +R    ++ + + +  +    +         + +  + + +     +   
Sbjct: 1    DLAGPLLAGLFRTLFHKLTKDVYKYLQKCVENNKDFNMALAVKSTHITNGLRYSLATGNW 60

Query: 522  ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                        +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 61   GDQKKAAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLV 116

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
            CPAET EG   GLV +L     +      E    +    + +V  +   LS+      ++
Sbjct: 117  CPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNATKIFV 176

Query: 628  AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LEN 684
                  +  D +     V        I      I D  D   K          P   +EN
Sbjct: 177  NGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIEN 236

Query: 685  DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
            + ++       + +Q +  L+ +   +           S     AK             V
Sbjct: 237  NPASPNRGNLVLTKQMLEQLEQDKQDLAA---RAAGGDSDDTDKAKLGWYRL---INNGV 290

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            +  V+ + + +   V     +   +  Q   V                +  D     +  
Sbjct: 291  VEYVDAEEEETIMIVMTPEDLLISQQXQQGFV----------------LPEDTSHYIIER 334

Query: 805  LALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            +    N   A           SM+  I   ++       +    F+       +G     
Sbjct: 335  VKATPNPTCAQRETAICEIHPSMILGICASIIPFPDHNQLPRNTFQXXMGKQAMGVFLTN 394

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             ++               +  +             +       +   +  + AI      
Sbjct: 395  YNVRM-----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGY 443

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +   +    +F R   D+ +R   +    +E   +    + + L    
Sbjct: 444  NQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGT 499

Query: 983  YSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
            Y +L +   +  G           K+  ++ D      R++          ++     + 
Sbjct: 500  YDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDSEELGQRTKLHVKRDASTPLRSTENGIV 559

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q   S                         LR  KV +   +  Q GDK A RHG KG 
Sbjct: 560  DQVVLS--------------------TNADGLRFAKVRMRTTKIPQIGDKFASRHGQKGT 599

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
            +      EDMPF  +G   D+++NP  +P RM +  + E  L 
Sbjct: 600  IGITYRQEDMPFTSEGVVPDLIINPHAIPFRMTIAHLIECQLS 642



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 84/630 (13%), Positives = 174/630 (27%), Gaps = 119/630 (18%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              +     T  +K  KD    + + +       F++A ++ +    +  +Y L   G  
Sbjct: 4   GPLLAGLFRTLFHKLTKDVYKYLQKCVENN--KDFNMALAVKSTHITNGLRYSL-ATGNW 60

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 61  GDQKKAAQSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAE 120

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQ 521
             + Q    +  +       + +     +      N + +         +A   F     
Sbjct: 121 TPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLSSPNATKIFVNGVW 180

Query: 522 LSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM-------RDVHPTHYGRICPAE 573
           +    +  + +S + + RR   +  +  + R     E        R   P       PA 
Sbjct: 181 VGVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIENNPAS 240

Query: 574 TSEGHNIGLVSSLTSFARV--------------NAYGFIETPYRKVCDGKVTNDVVYLSA 619
            + G+ +     L    +               +        YR + +G     V Y+ A
Sbjct: 241 PNRGNLVLTKQMLEQLEQDKQDLAARAAGGDSDDTDKAKLGWYRLINNGV----VEYVDA 296

Query: 620 MEEENRYIAQANSSLDEDGSFTEELV----FCRCAGEEILVPRE------KIDFIDASPK 669
            EEE   I      L       +  V          E +           +    +  P 
Sbjct: 297 EEEETIMIVMTPEDLLISQQXQQGFVLPEDTSHYIIERVKATPNPTCAQRETAICEIHPS 356

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IPF +++   R      M +QA+ +                   + A I+ 
Sbjct: 357 MILGICASIIPFPDHNQLPRNTFQXXMGKQAMGVFLTNYNV---------RMDTMANILY 407

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                +    ++  +          +   +  Y              NQ           
Sbjct: 408 YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSG-----------YNQE---------- 446

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                    S  +   ++ R +  +       + E  + +S             +E+FE 
Sbjct: 447 --------DSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMS------------VVEQFEK 486

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
             R           D   +       +D+ GI+  G  V+  DI++GK  P         
Sbjct: 487 PMR----------SDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDSEELG 536

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           ++        K    RD S  + S  +G V
Sbjct: 537 QRT-------KLHVKRDASTPLRSTENGIV 559


>gi|323652573|gb|ADO15383.2| RNA polymerase beta subunit [Xanthomonas theicola]
          Length = 204

 Score =  213 bits (541), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 122/204 (59%), Positives = 151/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +    LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNTPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV DG++T++V YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVYARTNQYGFLETPYRKVVDGQITDEVEYLSAIEENEYVIAQANALHDAKSR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+A+ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRAQKPLVGTGIERAVARDS 204


>gi|56694324|gb|AAW22902.1| RNA polymerase II second largest subunit [Zamia integrifolia]
          Length = 556

 Score =  213 bits (541), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 106/697 (15%), Positives = 195/697 (27%), Gaps = 145/697 (20%)

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L     +            + +   T +   +S     N  
Sbjct: 1    GMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWS-TENFEEISPAVIPNAT 59

Query: 627  IAQANSSLDEDGSFTEELV-FCRCAGEEILVPREKIDFIDA---SPKQVVSIAASLIPFL 682
                N          + LV   R    ++ V  E     D      +          P  
Sbjct: 60   KIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRDIRLSELRXYTXYGRCSRPLF 119

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
              ++   ++   +++R                   + +     ++      +       +
Sbjct: 120  IVENQXLLIKKSDIRRLQQRXQLP-----------LPSPDDETSVRGWHELV------TK 162

Query: 743  IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
              I  V+ + + +T        +   R +     N   +VK              PS  L
Sbjct: 163  GFIEYVDTEEEETTMISMTINDLVNARKSPP---NATSIVKY-------THCEIHPSLIL 212

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
            G       +  + +P+  +N          M  + +   I++  ++              
Sbjct: 213  G-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ-------------- 249

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
                         +    +  V        +    +       +      + AI      
Sbjct: 250  -------------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGY 296

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
            +  D+ +   S +        +F R   D+ +R  ++ +E+     R+          + 
Sbjct: 297  NQEDSVIMNQSSIDRGFF-RSLFYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDK 355

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
                     G           K+T ++                  DE   +     K   
Sbjct: 356  LDDDGLAPPGTRVSGEDVIIGKTTPVTQ-----------------DESGGQAARYTKRDQ 398

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             TS         +++      D +     R VKV +   R  Q GDK + RHG KG V  
Sbjct: 399  STSLRHSXSGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGM 453

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+           
Sbjct: 454  TYCQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD--------- 504

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
                                                        +TP F     + I+  
Sbjct: 505  --------------------------------------------ATP-FTDVTVDNISKA 519

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            L        G   +Y+G TG      + +G  Y  +L
Sbjct: 520  LHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRL 556



 Score =  118 bits (295), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 78/488 (15%), Positives = 144/488 (29%), Gaps = 99/488 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 10  EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVG 69

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRI-CPAETSEGH--- 578
              +    +  +   RR   +  + GV R     E+R    T YGR   P    E     
Sbjct: 70  IHRDPDLLVKTLRQLRRQVDVNTEVGVVRDIRLSELRX--YTXYGRCSRPLFIVENQXLL 127

Query: 579 -NIGLVSSLTSFARVNAYGFI-ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
                +  L    ++       ET  R   +      + Y+   EEE   I+        
Sbjct: 128 IKKSDIRRLQQRXQLPLPSPDDETSVRGWHELVTKGFIEYVDTEEEETTMISM------- 180

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                 +LV  R +         K    +  P  ++ + AS+IPF +++ S R      M
Sbjct: 181 ---TINDLVNARKSPPNATSIV-KYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAM 236

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +QA+ +                           R   +  V                  
Sbjct: 237 GKQAMGIYVTNYQL--------------------RMDTLAYV------------------ 258

Query: 757 SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                                Q+PLV                      L  G N +VA  
Sbjct: 259 -----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIA 291

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEE 871
            + GYN EDS+++++  +    F S+    +    +      +E        +   +   
Sbjct: 292 CYSGYNQEDSVIMNQSSIDRGFFRSLFYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHG 351

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G+   G  V+  D+++GK TP  +           +         RD S  +
Sbjct: 352 SYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQDE---------SGGQAARYTKRDQSTSL 402

Query: 932 PSGVSGTV 939
               SG V
Sbjct: 403 RHSXSGMV 410


>gi|51103929|gb|AAT96670.1| RpoB [Corynebacterium sp. CCUG 32360]
          Length = 146

 Score =  213 bits (541), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 89/174 (51%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G  +    +D      +  L   L  V              
Sbjct: 1    RMNIGQVLEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT-------- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNEEIAGLLANSKPNRDGDVMVDENGKTTLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPFKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|80973603|gb|ABB53539.1| RNA polymerase beta subunit [Streptococcus gallolyticus subsp.
            gallolyticus]
          Length = 226

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E  ++D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEASKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWDTVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGIMYMIK 226



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 65/86 (75%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE  K++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEASKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|115382726|gb|ABI95384.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum
           gallinifaecis]
          Length = 214

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 128/215 (59%), Positives = 157/215 (73%), Gaps = 1/215 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD EEILSTFY  + YS+ GD W  P S      G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEEILSTFYNTVTYSRDGDNWRIPYSVE-RFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S LVD DTGE V+E+GKKLT+   K L EKG+KF+  T D L G Y+AEDIVN ETGEIY
Sbjct: 60  SDLVDADTGEVVLEAGKKLTARSAKQLAEKGLKFIKATEDDLFGSYLAEDIVNYETGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  + + +I +L +D VN  AYIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLLDTGVDEINVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKM 416
           RPG+  T   AE+MF+ LFFDS++YDLS VGRVKM
Sbjct: 180 RPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKM 214


>gi|78099548|gb|ABB20888.1| RNA polymerase subunit B [Acinetobacter baumannii]
          Length = 149

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 81/152 (53%), Positives = 107/152 (70%), Gaps = 4/152 (2%)

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DKMAGRHGNKG+VS ILP EDMP   +G PVDIVLNPLGVPSRMNVGQI ETHLG A  G
Sbjct: 1    DKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKG 60

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGT-GSHTEKISDYDDDSVLRVAEQWKSGVPV 1206
            LG KI+ ++ + +    +  LR FL+K+    G   E +    DD +L ++   ++GVP+
Sbjct: 61   LGDKIEKMLKEQRT---VLELREFLDKIYNKVGGEQEDLDSLTDDEILALSGNLRAGVPL 117

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYD 1238
            +TPVFDGA+E  I  +L +AD+  +GQ++L+D
Sbjct: 118  ATPVFDGAEESQIKDLLELADISRTGQTVLFD 149


>gi|80973591|gb|ABB53533.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 226

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRTNGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARNLGIHIATPVFDGASSEDLWDTVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRTNGD 86


>gi|80973531|gb|ABB53503.1| RNA polymerase beta subunit [Streptococcus agalactiae]
 gi|80973533|gb|ABB53504.1| RNA polymerase beta subunit [Streptococcus agalactiae]
 gi|80973535|gb|ABB53505.1| RNA polymerase beta subunit [Streptococcus agalactiae]
 gi|80973537|gb|ABB53506.1| RNA polymerase beta subunit [Streptococcus agalactiae]
 gi|80973539|gb|ABB53507.1| RNA polymerase beta subunit [Streptococcus agalactiae]
          Length = 226

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 175  ATPVFDGASSEDLWETVQEAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDSLRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|254584222|ref|XP_002497679.1| ZYRO0F11066p [Zygosaccharomyces rouxii]
 gi|238940572|emb|CAR28746.1| ZYRO0F11066p [Zygosaccharomyces rouxii]
          Length = 1143

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 72/347 (20%), Positives = 126/347 (36%), Gaps = 74/347 (21%)

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
            +   + QY  +  I      + I+++     +      ++KV +   R  + GDK +   
Sbjct: 853  LTQTQSQYRETPVIYRAPEPSHIDQVMM--SVSDNDQALIKVLLRQNRRPELGDKFS--- 907

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
                                              SR                  G+K   
Sbjct: 908  ----------------------------------SR-----------------HGQKGVC 916

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             I   + +   S      + ++       +++      ++       +G       F G+
Sbjct: 917  GIIVQQEDMPFSDQGVVPDIIMNPHGFPSRMTVGKMIELISGKAGVMNGSLEYGTCFGGS 976

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              E ++ +L     + SG+ +LY G+TGE     +  G IY  KL HMV DK++AR+ G 
Sbjct: 977  KLEDMSQILVDNGFNYSGKDMLYSGVTGECLQAYIFFGPIYYQKLKHMVLDKMHARARGP 1036

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
             +++T+QP  G+S  GG RLGEME  C+ AYGA+ +L E L   SD       V E    
Sbjct: 1037 RAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMTSSDAFE--VEVCEK--C 1092

Query: 1335 G--------------NDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
            G                  +   P +  +L +E+ ++ ++  L    
Sbjct: 1093 GLMGYSGWCTTCRSAEHINKMSIPYAAKLLFQELLSMNIAPRLRLED 1139



 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 110/926 (11%), Positives = 263/926 (28%), Gaps = 178/926 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDP----- 83
           L++    S+++F+ +++    + N   Q     V P         L++V           
Sbjct: 54  LVKQHLDSFNYFVDVDLKKIIKAN---QLILSDVDP------EFYLKYVDIRVGQRSNAS 104

Query: 84  ------PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                 P     +C  RD+TY+ P+ + +             +    I  + + +G +P+
Sbjct: 105 SKDYLTP---PHECRLRDMTYSAPIYVDIEYT----------RGRNIIMHKDVEIGRMPI 151

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F++ G +++++ Q   S          + +
Sbjct: 152 MLRSNKCILHNSDEKTMARLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKA 211

Query: 174 LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILST 231
           +    + +     ++     +     D I+++ +    +VP+   L A G+ S+ E++  
Sbjct: 212 IVQASVTSST--HERKSKTYVVT-KNDKIYLKHNSIAEEVPIVVVLKACGIVSDLEVMQL 268

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
                   Q         ++   +   + +   +         +    L  G ++++   
Sbjct: 269 VCGNDSSYQDIFAVNLEEASKLGLYTQQQALEYIGSKVKTVRRQKLSVLQEG-IEAIATT 327

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +  L + +       +    +   T  + +   +       + + +  +          
Sbjct: 328 VIAHLTVAALDFREKAL---YIAMMTRRVVMAMQNYKMVDDRDYVGNKRLEL-------- 376

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                 I         K   D    I +V++  + +    A    N    +        +
Sbjct: 377 --AGQLISLLFEDLFKKFNNDFKASIDKVLKKPNRAMEYDALLSINVHSNNITSGLSRAI 434

Query: 412 GRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
                +++        V H    +     + ++  +         +     L   +   +
Sbjct: 435 STGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGML 494

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
                 +     L    ++   I++ D +  + +           + +            
Sbjct: 495 CTADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCFILGVEDITLIDSASLH--LHYGV 552

Query: 528 HVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL---V 583
           ++N     T    +  + Q   + R+    E   ++   + +     T  G        V
Sbjct: 553 YLNGTLIGTTKFPVKFVSQFRNLRRSGKISEFISIYTNSHHKAVHIATDGGRICRPLIIV 612

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           S+  S         +        D      V YL   EE + +IA     +         
Sbjct: 613 SNGKSRVTSEHLKELLEGRLVFDDFLKLGLVEYLDVNEENDSFIALYEQDIAP------- 665

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                           +I  ++  P  V+   A LIP+  ++ S R    C M +QA+  
Sbjct: 666 ----------------EITHMEIEPFTVLGACAGLIPYPHHNQSPRNTYQCAMGKQAIGA 709

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                                    I   +     +   + IY 
Sbjct: 710 -----------------------------------------IAYNQFKRIDTLLYLMIYP 728

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+P+VK                 D   L  G+N  VA M + GY+ 
Sbjct: 729 --------------QQPMVK----------TKTIELIDYDKLPAGQNATVAIMSYSGYDI 764

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE----ITRDIPNVSEEGLKNIDEC 879
           ED++++++  +           +   + +      ++    +  +         K++   
Sbjct: 765 EDALVLNKSSIDRGFGRCETRRKTTAVLKRYPNHTQDIIGGMRVNENGEPIWQHKSLGPD 824

Query: 880 GIICVGAEVNPGDILVGKITPKGESP 905
           G+  VG +++ G I + K  P   S 
Sbjct: 825 GLGEVGMKLDSGQIYINKSVPTNASE 850


>gi|62947908|gb|AAY22951.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 223

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 126/220 (57%), Positives = 160/220 (72%), Gaps = 2/220 (0%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           N +PV +A+ EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+RDVH T
Sbjct: 4   NIRPVTAAIKEFFGSSQLSQFIDQHNPLSELSYKRRLSALGPGGLTRDRAGYEVRDVHYT 63

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEE 622
           HYGR+CP ET EG NIGL+++L+S+  +N YGFI+TPYRKV       TN++V+L+A EE
Sbjct: 64  HYGRMCPIETPEGPNIGLINNLSSYGHLNKYGFIQTPYRKVNRETGLLTNEIVWLTADEE 123

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           +   +AQANS L+EDG F E +V  R  G     P +++DF+D SPKQVV++A + IPFL
Sbjct: 124 DEFIVAQANSKLNEDGRFAEAIVMGRHQGNNQEFPSDQVDFMDVSPKQVVAVATACIPFL 183

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
           ENDDSNR LMG NMQRQAVPL+   AP+VGTGME   A  
Sbjct: 184 ENDDSNRALMGANMQRQAVPLIDPHAPYVGTGMEYQAAHD 223


>gi|145342343|gb|ABP64868.1| RpoB [Paenibacillus amylolyticus]
 gi|145342403|gb|ABP64898.1| RpoB [Paenibacillus amylolyticus]
          Length = 209

 Score =  212 bits (540), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 79/192 (41%), Positives = 103/192 (53%), Gaps = 54/192 (28%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 72   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 131

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV IVLNPLGVPSRMN+GQ+ E HLG A + LG  + + + D     D           
Sbjct: 132  TPVQIVLNPLGVPSRMNIGQVLEVHLGMAAMQLGIHVATPVFDGAKEYD----------- 180

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 181  ----------------------------------VFD---------TMEEAGMQRNGKTV 197

Query: 1236 LYDGLTGEPFDR 1247
            LYDG TGE F+R
Sbjct: 198  LYDGRTGEEFER 209



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/80 (63%), Positives = 63/80 (78%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRV
Sbjct: 1   ALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRV 60

Query: 932 PSGVSGTVVDVRIFNRHGID 951
           P G  G VVDV++F R   D
Sbjct: 61  PHGTDGIVVDVKVFTRENGD 80


>gi|115382732|gb|ABI95387.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum
           pseudintermedium]
 gi|115382734|gb|ABI95388.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum
           pseudintermedium]
 gi|115382736|gb|ABI95389.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum
           pseudintermedium]
          Length = 212

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 122/213 (57%), Positives = 154/213 (72%), Gaps = 1/213 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD E+ILSTFY  + Y++ GD W  P SA D   G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEDILSTFYKTVTYTRDGDNWRIPYSA-DRFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S L+D DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y+AED+VN  TGEIY
Sbjct: 60  SDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  +   +I +L +D VN  AYIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLLDTGETEIKVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           RPG+  T   AE+MFN LFFD+++YDLS VGRV
Sbjct: 180 RPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRV 212


>gi|145408655|gb|ABP68348.1| ribosomal polymerase B2 [Beauveria bassiana]
          Length = 204

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 87/187 (46%), Gaps = 34/187 (18%)

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +TP F     ++++ +LR       G  I+Y+G TG+     V  G  Y  +L HMV DK
Sbjct: 22   ATP-FTDVTVDSVSDLLRKHGYQSRGFEIMYNGHTGKKLRAQVFFGPTYYQRLRHMVDDK 80

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD------ 1320
            ++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GAA  L+E L   SD      
Sbjct: 81   IHARARGPVQIMTRQPVEGRARDGGLRFGEMERDCMIAHGAAAFLKERLFEVSDAFRVHI 140

Query: 1321 -DVVG------------------RTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSI 1361
             ++ G                  + +            +   P +  +L +E+Q++ ++ 
Sbjct: 141  CEICGLMTPIANLSKQSFECRPCKNKT--------KIAQIHIPYAAKLLFQELQSMNIAA 192

Query: 1362 DLENSRT 1368
             +   R+
Sbjct: 193  RMFTDRS 199


>gi|80973503|gb|ABB53489.1| RNA polymerase beta subunit [Streptococcus entericus]
          Length = 226

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 90/284 (31%), Positives = 123/284 (43%), Gaps = 71/284 (25%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEVGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++P GV ++V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELPSGVNKLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAAKNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D   + D+                                          T ++D
Sbjct: 175  ATPVFDGATSEDLWSTVKEAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            G                           TGEPFD  V+VG +YM
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYM 224



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 56/111 (50%), Positives = 77/111 (69%), Gaps = 7/111 (6%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDEVGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           DTSLRVP G  G V DV+IF R        G++K  R    ++ +I++  +
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGDELPSGVNKLVRVYIAQKRKIKVGDK 111


>gi|80973525|gb|ABB53500.1| RNA polymerase beta subunit [Streptococcus uberis]
          Length = 226

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 123/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+    +                                          
Sbjct: 175  ATPVFDGATAEDLWDTVAEAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|80973583|gb|ABB53529.1| RNA polymerase beta subunit [Streptococcus canis]
 gi|80973589|gb|ABB53532.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|80973629|gb|ABB53552.1| RNA polymerase beta subunit [Streptococcus dysgalactiae subsp.
            equisimilis]
          Length = 226

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 127/294 (43%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARNLGIHIATPVFDGASSEDLWDTVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|80973565|gb|ABB53520.1| RNA polymerase beta subunit [Streptococcus equi subsp. zooepidemicus]
          Length = 226

 Score =  212 bits (540), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWETVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|194293716|gb|ACF39954.1| RNA polymerase beta subunit [Candidatus Liberibacter solanacearum]
          Length = 141

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 125/140 (89%), Positives = 130/140 (92%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAK VVFNGLGR RKFFGK PEIIDIPDLIEVQ+ASYD FLMMN +P+ERPNEGLQAAFK
Sbjct: 1   MAKDVVFNGLGRARKFFGKIPEIIDIPDLIEVQRASYDQFLMMNSSPEERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEF SYEFD PKFDVDDCL RDLTYA PLKI LRLIVFD+DEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFESYEFDSPKFDVDDCLRRDLTYAAPLKIILRLIVFDIDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDLPLMTK 140
           SIKDIKEQSIYMGD+PLMTK
Sbjct: 121 SIKDIKEQSIYMGDVPLMTK 140


>gi|80973497|gb|ABB53486.1| RNA polymerase beta subunit [Streptococcus alactolyticus]
          Length = 226

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSDDLWDTVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGIMYMIK 226



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|66854093|gb|AAY57355.1| RpoB [Prevotella denticola]
 gi|66854099|gb|AAY57358.1| RpoB [Prevotella melaninogenica ATCC 25845]
          Length = 125

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 69/179 (38%), Positives = 85/179 (47%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA    +      A L     + +YDG TG
Sbjct: 21   --------------AAGRKLGVKFATPIFDGAKLSDLKEWTDKAGLPNLCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EKFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|80973595|gb|ABB53535.1| RNA polymerase beta subunit [Streptococcus pasteurianus]
 gi|80973601|gb|ABB53538.1| RNA polymerase beta subunit [Streptococcus gallolyticus subsp.
            gallolyticus]
 gi|80973615|gb|ABB53545.1| RNA polymerase beta subunit [Streptococcus macedonicus]
 gi|80973617|gb|ABB53546.1| RNA polymerase beta subunit [Streptococcus pasteurianus]
 gi|80973619|gb|ABB53547.1| RNA polymerase beta subunit [Streptococcus gallolyticus subsp.
            gallolyticus]
          Length = 226

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWDTVREAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGIMYMIK 226



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|46277287|gb|AAS86834.1| RNA polymerase II second largest subunit [Camellia japonica]
          Length = 559

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 112/704 (15%), Positives = 199/704 (28%), Gaps = 149/704 (21%)

Query: 557  EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
            + R +H + +G +CPAET EG   GLV +L     +   G    P  +  +   T +   
Sbjct: 4    KPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT-VGSXAYPILEFLEEWGTENFEE 62

Query: 617  LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            +S        I QA + +  +G +       R     +   R     +D + +  V    
Sbjct: 63   ISP-----AVIPQA-TKIFVNGCWVG---IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDI 113

Query: 677  SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
             L       D  R      +  +   L+                K   +    +      
Sbjct: 114  RLKELRIYTDYGRCSRPLFIVEKQRLLI--------------KKKDIQSLQQRETPEDGG 159

Query: 737  QVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D   +  I  ++ + + +T        +   R N     +                  
Sbjct: 160  WHDLVAKGYIEYIDTEEEETTMISMTINDLITARLNPEEAYS-----------ETYTHCE 208

Query: 796  DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              PS  LG       +  + +P+  +N          M  + +     I       R   
Sbjct: 209  IHPSLILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDT 257

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            L         P V+   ++++                             +      + A
Sbjct: 258  LAYVLYYPQKPLVTTRAMEHL-------------------------HFRQLPAGINAIVA 292

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
            I      +  D+ +   S +        +F R   D+ ++  ++ +E      R      
Sbjct: 293  IACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGCPDRANTMGM 351

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
                 +          G           K+T ++ +                 +      
Sbjct: 352  RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQE-----------------DAQGPAA 394

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
               K  + TS    E    +++      D +     R VKV V   R  Q GDK + RHG
Sbjct: 395  RYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHG 449

Query: 1096 NKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             KG V      EDMP+  +G   DI++ P  +PSRM +GQ+ E  +G     +GK+    
Sbjct: 450  QKGTVGMTYTQEDMPWTMEGITPDIIVYPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-- 507

Query: 1156 INDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                                               +TP F    
Sbjct: 508  ---------------------------------------------------ATP-FTDVT 515

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 516  VDNISKALHKCGYQMRGFETMYNGHTGRRLPAMIFLGPTYYQRL 559


>gi|46277285|gb|AAS86833.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum]
          Length = 549

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 80/488 (16%), Positives = 137/488 (28%), Gaps = 84/488 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 142  HDLVAKGFIEYIDTEEEETTMISMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 201

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 202  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 258

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 259  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 317

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T ++           
Sbjct: 318  KEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVVIGKTTPIAQ---------- 367

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE         +  + TS    E    +++      D +     R VKV V  
Sbjct: 368  -------DEAQGPAARYTRRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 415

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 416  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECI 475

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 476  MGKVAAHMGKEGD----------------------------------------------- 488

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +TP F     + I+  L        G     BG TG      + +G  Y  +L 
Sbjct: 489  ------ATP-FTDVTVDNISKALHKCGYQCVGSRPCTBGHTGRRLTSMIFLGPTYYQRLK 541

Query: 1261 HMVSDKVY 1268
            HMV DK++
Sbjct: 542  HMVDDKIH 549



 Score =  108 bits (269), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 74/482 (15%), Positives = 140/482 (29%), Gaps = 97/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + L
Sbjct: 64  IHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRL-L 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +      A        +       D      + Y+   EEE   I+              
Sbjct: 122 IKRKDIQALQQRETPEDGG---WHDLVAKGFIEYIDTEEEETTMISM----------TIN 168

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 169 DLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 226

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +      F                    R   +  V                        
Sbjct: 227 IYVTNYQF--------------------RMDTLAYV------------------------ 242

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 243 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 281

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 282 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLD 341

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           A         RD S  +    +G
Sbjct: 342 DDGLAPPGTRVSGEDVVIGKTTPIAQDE---------AQGPAARYTRRDHSTSLRHSETG 392

Query: 938 TV 939
            V
Sbjct: 393 MV 394


>gi|75037200|gb|ABA12476.1| RNA polymerase beta subunit [Streptococcus australis ATCC 700641]
          Length = 226

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSEDLWDTVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|323652569|gb|ADO15378.2| RNA polymerase beta subunit [Xanthomonas hyacinthi]
          Length = 204

 Score =  212 bits (539), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 123/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SKLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV DG++T+DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVYARTNQYGFLETPYRKVVDGQITDDVEYLSAIEENEYVIAQANALHDAKSR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VSIAA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRYQGESLLKPPAEVHFMDVSPMQTVSIAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+A+ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRAQKPLVGTGIERAVARDS 204


>gi|80973505|gb|ABB53490.1| RNA polymerase beta subunit [Streptococcus hyointestinalis]
          Length = 226

 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 175  ATPVFDGASSEDLWDTVREAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 65/86 (75%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK +DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKELDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|115382730|gb|ABI95386.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum lupini]
 gi|115382738|gb|ABI95390.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi
           ATCC 49188]
          Length = 213

 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 121/214 (56%), Positives = 154/214 (71%), Gaps = 1/214 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD E+ILSTFY  + Y++ GD W  P SA D   G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEDILSTFYKTVTYTRDGDNWRIPYSA-DRFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S L+D DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y+AED+VN  TGEIY
Sbjct: 60  SDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  +   +I +L +D +N   YIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLIDTGETEINVLDIDHINIGGYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           RPG+  T   AE+MFN LFFD+++YDLS VGRVK
Sbjct: 180 RPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRVK 213


>gi|224797601|gb|ACN62830.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           tenebrosa]
          Length = 276

 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 143/264 (54%), Positives = 190/264 (71%), Gaps = 8/264 (3%)

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQA+PLLK + P VGTG+E  VA+ SG A+VA   GIV+ VD+  I+I
Sbjct: 1   DANRALMGANMQRQAIPLLKPQTPIVGTGVEYAVARDSGLAVVANLPGIVQYVDSNEIII 60

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +S +         V  Y L +F+RSNQ T V   PLVK GD V  N I+ADGPS   G+L
Sbjct: 61  KSKDE--------VTTYELSRFERSNQGTSVTHIPLVKAGDVVEANQILADGPSMKDGEL 112

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           ALG+N+++AFM WHGYN+ED+++ISER+V +DV+TS+HIEE+ +  R TK G EEIT +I
Sbjct: 113 ALGQNVIIAFMTWHGYNYEDAIIISERLVKDDVYTSMHIEEYNLECRKTKQGKEEITPEI 172

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PN SE+  + +D+ GI+ +G EV  GDILVGK+TPKG++  T EEKLL AIFGEK+ +V+
Sbjct: 173 PNTSEQSRRYLDDEGIVLIGTEVKEGDILVGKVTPKGQTQSTAEEKLLAAIFGEKSRNVK 232

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHG 949
           D SLRVP+G +G V  ++ + R  
Sbjct: 233 DNSLRVPNGGAGIVQGIKRYKRED 256


>gi|14587117|gb|AAK70487.1|AF387737_1 RNA polymerase II subunit 2 [Blepharisma japonicum]
          Length = 203

 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 87/256 (33%), Gaps = 75/256 (29%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RM +G + E          G++                                      
Sbjct: 2    RMTIGHLIECLASKVACLRGEEGDG----------------------------------- 26

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                              TP F     E I+  L        G  ++Y+G TG      +
Sbjct: 27   ------------------TP-FQSVTVEDISRDLHALGYQLRGNEVMYNGHTGNRLASQI 67

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
              G  Y  +L HMV DK+++R+ G    +T+QP  G+S  GG R GEME  C+ ++GAA 
Sbjct: 68   FFGPTYYQRLKHMVDDKIHSRARGQVQSLTRQPTEGRSRDGGLRFGEMERDCMISHGAAR 127

Query: 1310 VLQEMLTIKSDDVVGRTRVYE-----SIV--------------AGNDTFETGTPESFNVL 1350
             L+E L   SD    R  V E     +I                     +   P +  +L
Sbjct: 128  FLKERLFEASD--AYRVHVCENCGLFAIANLDRNMFQCKQCKNKNTRISQIFIPYACKLL 185

Query: 1351 VKEMQALGLSIDLENS 1366
             +E+ A+ ++  L  S
Sbjct: 186  FQELMAMHIAPRLHTS 201


>gi|80973585|gb|ABB53530.1| RNA polymerase beta subunit [Streptococcus sobrinus]
          Length = 226

 Score =  212 bits (539), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 92/294 (31%), Positives = 125/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGAGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWETVEEAGMDGDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGIVRDVKIFTRANGD 86


>gi|115606105|gb|ABJ16027.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 260

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 131/259 (50%), Positives = 184/259 (71%), Gaps = 13/259 (5%)

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSV 467
           L++  P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+V
Sbjct: 2   LHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTV 61

Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
           GE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQ SQ   
Sbjct: 62  GELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQPSQFMY 121

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+
Sbjct: 122 QNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLS 181

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS +D DG F E  V  
Sbjct: 182 VYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLV 241

Query: 648 RCA-GEEILVPREKIDFID 665
           R   GE   VP  ++D++D
Sbjct: 242 RRKAGEVEYVPSSEVDYMD 260


>gi|83305715|dbj|BAE53692.1| RNA polymerase beta subunit [Nocardia farcinica]
          Length = 257

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 133/255 (52%), Positives = 179/255 (70%), Gaps = 13/255 (5%)

Query: 424 TPDDVRHIRKEDIIAIIKILVDLRNG------------KGTIDDIDNLGNRRVRSVGEML 471
            P     + KEDI+  I+ LV L  G               +DDID+ GNRR+R+VGE++
Sbjct: 3   EPVTGSVLTKEDIVTTIEYLVRLHAGDKTMTAPGGVEVPVEVDDIDHFGNRRLRTVGELI 62

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNS 531
           +NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N 
Sbjct: 63  QNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNP 122

Query: 532 LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +AR
Sbjct: 123 LSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYAR 182

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC-A 650
           VN +GFIETPYRKV DG+VT++VVYL+A EE+    AQANS +  DG F E+ V CR   
Sbjct: 183 VNPFGFIETPYRKVVDGRVTDEVVYLTADEEDRHVRAQANSPVGPDGRFLEDRVLCRRGN 242

Query: 651 GEEILVPREKIDFID 665
            E   V   ++DF+D
Sbjct: 243 EEMEYVAATEVDFMD 257


>gi|308156021|gb|ADO15380.1| RNA polymerase beta subunit [Xanthomonas oryzae pv. oryzae]
 gi|323652575|gb|ADO15385.2| RNA polymerase beta subunit [Xanthomonas vasicola]
 gi|326909323|gb|AEA11036.1| RNA polymerase beta subunit [Xanthomonas euvesicatoria]
 gi|326909325|gb|AEA11037.1| RNA polymerase beta subunit [Xanthomonas perforans]
          Length = 204

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|199580721|gb|ACH89062.1| RNA polymerase subunit beta [Staphylococcus condimenti]
          Length = 231

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 76/206 (36%), Positives = 105/206 (50%), Gaps = 55/206 (26%)

Query: 1053 FKNKIEKIQWGDD-MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
               K+   + GDD + PGV ++V+V++  KR I  GDKM GRHGNKG++S+I+P EDMP+
Sbjct: 80   LDVKVFNREDGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D   + D+      
Sbjct: 140  LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWST--- 196

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                  +  A   + G                            
Sbjct: 197  ----------------------IEEAGMARDG---------------------------- 206

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
             +++LYDG TGEPFD  ++VG + ML
Sbjct: 207  -KTVLYDGRTGEPFDNRISVGVMNML 231



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 60/89 (67%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV+E  LKN+DE GI+ VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 3   RDIPNVAESALKNLDERGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 62

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 63  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 91


>gi|269912612|emb|CAY86086.1| RNA polymerase beta subunit [Gluconacetobacter sacchari]
          Length = 242

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 103/242 (42%), Positives = 142/242 (58%), Gaps = 28/242 (11%)

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL------------------ 221
           +A R+IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                  
Sbjct: 1   FAARVIPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGEASAAARAAKIAEGGD 60

Query: 222 -------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
                  GMD++EIL  FY ++V+++    W  P  A     G K+   LVD  +GE V 
Sbjct: 61  VDALEIRGMDADEILGYFYNQVVFTKTPKGWARPFDAE-SFRGMKLLEPLVDAQSGEVVA 119

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
           E+  KLT+ +++ + E   K + + +  L G YVA D+VN ETGEIY EAG+ + E  LE
Sbjct: 120 EADAKLTARMVRKIAET-TKEVLVGAAGLVGRYVAHDLVNPETGEIYAEAGEELTEARLE 178

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
            +  + +  +P L +D+ N   +IRNTL  DKN  R DAL DIYRVMRPG+  T   AE+
Sbjct: 179 AMEAAGVDRLPTLAIDAAN-GPWIRNTLAVDKNGSRDDALTDIYRVMRPGEPPTPETAEA 237

Query: 395 MF 396
           MF
Sbjct: 238 MF 239


>gi|80973563|gb|ABB53519.1| RNA polymerase beta subunit [Streptococcus suis]
          Length = 226

 Score =  211 bits (538), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 88/284 (30%), Positives = 122/284 (42%), Gaps = 71/284 (25%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSEDLWSTVKEAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
               +    ++L        G        TGEPFD  V+VG +YM
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYM 224



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|169248084|gb|ACA51825.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248094|gb|ACA51830.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248096|gb|ACA51831.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248100|gb|ACA51833.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248104|gb|ACA51835.1| RNA polymerase beta subunit [Aliivibrio salmonicida]
          Length = 151

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 77/154 (50%), Positives = 107/154 (69%), Gaps = 5/154 (3%)

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   ++   R+FL+KV   G
Sbjct: 1    IVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQELHKFRNFLQKVYDLG 57

Query: 1180 SHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
               +   I+   DD V  + +  + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+
Sbjct: 58   ETRQEVDIAALSDDEVRTLVKNLRGGLPIATPIFDGAPESSIKELLKLVDLPESGQLKLF 117

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARS 151


>gi|169248082|gb|ACA51824.1| RNA polymerase beta subunit [Aliivibrio fischeri]
          Length = 151

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 78/154 (50%), Positives = 107/154 (69%), Gaps = 5/154 (3%)

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E H+G A  G+G KI  ++   K   ++   R+FL+KV   G
Sbjct: 1    IVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKINQML---KEQQELHKFRNFLQKVYDLG 57

Query: 1180 SHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
               +   I+   DD V  + +  + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+
Sbjct: 58   ETRQEVDIAALSDDEVRTLIKNLRGGLPIATPIFDGAPEASIKELLKLVDLPESGQLKLF 117

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARS 151


>gi|66854087|gb|AAY57352.1| RpoB [Prevotella bivia DSM 20514]
          Length = 125

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 70/179 (39%), Positives = 86/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA  E +      A L     + +YDG TG
Sbjct: 21   --------------AAGRKLGVKFATPIFDGAKLEDLKEWTDKAGLPNLCSTHIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   ERFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|71659679|ref|XP_821560.1| RNA polymerase I second largest subunit [Trypanosoma cruzi strain CL
            Brener]
 gi|70886943|gb|EAN99709.1| RNA polymerase I second largest subunit, putative [Trypanosoma cruzi]
          Length = 1591

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 67/258 (25%), Positives = 96/258 (37%), Gaps = 69/258 (26%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF-LKDGTPVDIVLNPLGVPSRMNVG 1134
            V   + RP   GDK + RHG KG +   +   D+PF  +DG   DI++NP   PSRM VG
Sbjct: 1314 VVFRIPRPTAIGDKFSSRHGQKGTLPLHIRAYDLPFSTRDGITPDIIINPHAFPSRMTVG 1373

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E          G+               S                            
Sbjct: 1374 MVLEMMGAKLGAIQGRFCDHSAWSVVDERPRSA--------------------------- 1406

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                  E I   L+ A  +  G+  L DG++GE  +  V +G  
Sbjct: 1407 ----------------------EVIGDALQKAGYNRYGREKLIDGISGEEMEADVFMGIS 1444

Query: 1255 YMLKLNHMVSDKVYARS------------TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
               +L HMV+DK  AR+            TG       QP+ G+   GG R+GEME   +
Sbjct: 1445 GYQRLRHMVNDKWQARARTDAHTHRAVTKTG-------QPVKGRKRHGGVRVGEMERDGL 1497

Query: 1303 QAYGAAYVLQEMLTIKSD 1320
             ++G+A V+ + L   SD
Sbjct: 1498 LSHGSAEVVLDRLLHVSD 1515


>gi|66854103|gb|AAY57360.1| RpoB [Prevotella oris]
          Length = 125

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 69/179 (38%), Positives = 85/179 (47%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K G   +TP+FDGA  E +      A L     + +YDG TG
Sbjct: 21   --------------AAGQKLGCKFATPIFDGAKLEDLKEWTDKAGLPNLCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EKFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|80973621|gb|ABB53548.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 226

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 122/286 (42%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                          T ++D
Sbjct: 175  ATPVFDGASADDLWDTVREAGMDNDAK----------------------------TILYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+N+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|308156019|gb|ADO15379.1| RNA polymerase beta subunit [Xanthomonas melonis]
          Length = 204

 Score =  211 bits (538), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 125/204 (61%), Positives = 154/204 (75%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D  G+
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|260733193|gb|ACX48607.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733201|gb|ACX48611.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733239|gb|ACX48630.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 226

 Score =  211 bits (537), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 122/286 (42%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                               
Sbjct: 175  ATPVFDGASADDLWDTVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|117675909|emb|CAL69225.1| RNA polymerase subunit B [Clavibacter michiganensis subsp.
           insidiosus]
          Length = 360

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 63/175 (36%), Positives = 94/175 (53%), Gaps = 6/175 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G
Sbjct: 1   VFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F     I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKGVASIELTLEKDSILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              A   +         V  +    ++++         L K  + K  + LGI  
Sbjct: 119 KEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDK 173



 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 132/352 (37%), Positives = 198/352 (56%), Gaps = 32/352 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 11  EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 70

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     A I  TL  D    +++AL DIYR
Sbjct: 71  VGVRIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYR 128

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A 
Sbjct: 129 KLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILAT 188

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 189 IKYLVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 248

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 249 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 308

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +G
Sbjct: 309 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFG 360


>gi|75037275|gb|ABA12477.1| RNA polymerase beta subunit [Streptococcus downei MFe28]
          Length = 226

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 93/294 (31%), Positives = 122/294 (41%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+         +IL G+    G K       L   +  +  R     F
Sbjct: 5    EEALKDL-DEMGIIRIGAEVEEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTF 63

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                      V  +                 KI     GD++  GV  +V+V++A KR I
Sbjct: 64   LRVPHGGAGIVRDV-----------------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 167  ARNLGIHIATPVFDGATSEDLWETVEEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVEEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DT LRVP G +G V DV+IF R   D
Sbjct: 61  DTFLRVPHGGAGIVRDVKIFTRANGD 86


>gi|115382728|gb|ABI95385.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum tritici]
          Length = 212

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 122/213 (57%), Positives = 153/213 (71%), Gaps = 1/213 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD EEILSTFY  + YS+ GD W  P SA D   G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYSRDGDNWRIPYSA-DRFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S L+D DTGE V+E+GKKLT+   K L EKG+K +  T D L G Y+AED+VN  TGEIY
Sbjct: 60  SDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  +   +I +L +D +N   YIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLIDTGETEINVLDIDHINIGGYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           RPG+  T   AE+MFN LFFD+++YDLS VGRV
Sbjct: 180 RPGEPPTMDSAEAMFNSLFFDAERYDLSAVGRV 212


>gi|80973517|gb|ABB53496.1| RNA polymerase beta subunit [Streptococcus parauberis]
          Length = 226

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 122/286 (42%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+                                          T ++D
Sbjct: 175  ATPVFDGATADDLWETVIEAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|80973543|gb|ABB53509.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733191|gb|ACX48606.1| RNA polymerase beta subunit [Streptococcus sp. 5402857]
 gi|260733205|gb|ACX48613.1| RNA polymerase beta subunit [Streptococcus sp. 6401233]
 gi|260733211|gb|ACX48616.1| RNA polymerase beta subunit [Streptococcus sp. 6401638]
 gi|260733213|gb|ACX48617.1| RNA polymerase beta subunit [Streptococcus constellatus]
 gi|260733217|gb|ACX48619.1| RNA polymerase beta subunit [Streptococcus sp. 6402538]
 gi|260733219|gb|ACX48620.1| RNA polymerase beta subunit [Streptococcus constellatus]
 gi|260733223|gb|ACX48622.1| RNA polymerase beta subunit [Streptococcus sp. 7401233]
 gi|260733233|gb|ACX48627.1| RNA polymerase beta subunit [Streptococcus sp. 7402928]
 gi|260733235|gb|ACX48628.1| RNA polymerase beta subunit [Streptococcus sp. 7403049]
 gi|260733237|gb|ACX48629.1| RNA polymerase beta subunit [Streptococcus sp. 8400103]
          Length = 226

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 123/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSDDLWDTVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|169248088|gb|ACA51827.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248092|gb|ACA51829.1| RNA polymerase beta subunit [Aliivibrio logei]
          Length = 151

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 76/154 (49%), Positives = 105/154 (68%), Gaps = 5/154 (3%)

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI--G 1177
            IVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   ++   R+FL+KV   G
Sbjct: 1    IVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQELHKFRNFLQKVYDLG 57

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                   I+   DD V  + +  + G+P++TP+FDGA E +I  +L++ DL  SGQ  L+
Sbjct: 58   DTRQEVDIAALSDDEVRTLVKNLRGGLPIATPIFDGAPESSIKELLQLVDLPASGQLKLF 117

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARS 151


>gi|80973545|gb|ABB53510.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733183|gb|ACX48602.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733195|gb|ACX48608.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733199|gb|ACX48610.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733203|gb|ACX48612.1| RNA polymerase beta subunit [Streptococcus sp. 6400988]
 gi|260733207|gb|ACX48614.1| RNA polymerase beta subunit [Streptococcus sp. 6401499]
 gi|260733209|gb|ACX48615.1| RNA polymerase beta subunit [Streptococcus sp. 6401637]
 gi|260733215|gb|ACX48618.1| RNA polymerase beta subunit [Streptococcus sp. 6402381]
 gi|260733221|gb|ACX48621.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733225|gb|ACX48623.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733229|gb|ACX48625.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|260733231|gb|ACX48626.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 226

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 123/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSDDLWETVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|80973527|gb|ABB53501.1| RNA polymerase beta subunit [Streptococcus urinalis 2285-97]
          Length = 226

 Score =  211 bits (537), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 88/276 (31%), Positives = 118/276 (42%), Gaps = 60/276 (21%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
               +  I  G     G     K T      +S   R     F  +  +V+     +    
Sbjct: 11   LDEMGIIRIGAEVSEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGG 70

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR
Sbjct: 71   DGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSR 124

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   +
Sbjct: 125  IVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATS 184

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             D+                                          T ++DG         
Sbjct: 185  EDLWETVQEAGMDSDAK----------------------------TVLYDG--------- 207

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                              TGEPFD  V+VG +YM+K
Sbjct: 208  -----------------RTGEPFDNRVSVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV+ GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVSEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|80973597|gb|ABB53536.1| RNA polymerase beta subunit [Streptococcus constellatus subsp.
            constellatus]
 gi|80973599|gb|ABB53537.1| RNA polymerase beta subunit [Streptococcus constellatus subsp.
            constellatus]
          Length = 226

 Score =  211 bits (537), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 123/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +          +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGAGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSDDLWDTVREAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               +    ++L        G        TGEPFD  V+VG +YM+K
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMIK 226



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 52/86 (60%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV ++ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGKDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G +G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGAGVVRDVKIFTRANGD 86


>gi|117675905|emb|CAL69223.1| RNA polymerase subunit B [Clavibacter michiganensis subsp.
           tessellarius]
          Length = 363

 Score =  211 bits (537), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 63/175 (36%), Positives = 94/175 (53%), Gaps = 6/175 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G
Sbjct: 1   VFMGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F     I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKGVASIELTLEKDSILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              A   +         V  +    ++++         L K  + K  + LGI  
Sbjct: 119 KEEALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDK 173



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 134/355 (37%), Positives = 201/355 (56%), Gaps = 32/355 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 11  EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 70

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     A I  TL  D    +++AL DIYR
Sbjct: 71  VGVRIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYR 128

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A 
Sbjct: 129 KLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILAT 188

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 189 IKYLVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 248

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 249 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 308

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI+
Sbjct: 309 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFID 363


>gi|80973623|gb|ABB53549.1| RNA polymerase beta subunit [Streptococcus oligofermentans]
          Length = 226

 Score =  211 bits (537), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 88/284 (30%), Positives = 122/284 (42%), Gaps = 71/284 (25%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 175  ATPVFDGASSEDLWSTVKEAGM-------------------------------------- 196

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
               +    ++L        G        TGEPFD  V+VG +YM
Sbjct: 197  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYM 224



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|80973609|gb|ABB53542.1| RNA polymerase beta subunit [Streptococcus agalactiae]
          Length = 226

 Score =  211 bits (536), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 175  ATPVFDGASSEDLWETVQEAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 207  G--------------------------HTGEPFDNRVSVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ L+++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDALRDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGVVRDVKIFTRANGD 86


>gi|60101381|gb|AAX13759.1| RNA polymerase beta subunit [Streptococcus ferus]
          Length = 228

 Score =  211 bits (536), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 90/286 (31%), Positives = 124/286 (43%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 14   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 62

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 63   DTSLRVPHGGDGVVCDV------KIFTRDNGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 116

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 117  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 176

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                          T ++D
Sbjct: 177  ATPVFDGASSEDLWETVREAGMDSDAK----------------------------TVLYD 208

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEPFD  V+VG +YM+K
Sbjct: 209  G--------------------------RTGEPFDNRVSVGVMYMIK 228



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/88 (64%), Positives = 68/88 (77%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNV EE LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +
Sbjct: 1   EIPNVGEEALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSRE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  VRDTSLRVPHGGDGVVCDVKIFTRDNGD 88


>gi|295099851|emb|CBK88940.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [Eubacterium cylindroides T2-87]
          Length = 155

 Score =  211 bits (536), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 52/164 (31%), Positives = 87/164 (53%), Gaps = 15/164 (9%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           A  +V  G    R+ + K    +++P+L+E+Q  S+  F            +G+Q  F+ 
Sbjct: 6   AYRIVSCGKKSTRRDYSKVSGKLELPNLVEIQTDSFKWFTR----------QGIQEVFEE 55

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           ++PI  +     L F+ Y FD PK++ +  ++R+  YA PL   + L + D +       
Sbjct: 56  IYPIENYGKNIKLNFIRYHFDEPKYNAEQSMYRECNYAAPLYAEMELEITDPETGELV-- 113

Query: 122 IKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHF 165
               K + +Y+GD PLMT+ GTF+I G +R++VSQ+ RSPG  F
Sbjct: 114 ---TKNEEVYLGDFPLMTETGTFIINGAERVIVSQIVRSPGALF 154


>gi|80973555|gb|ABB53515.1| RNA polymerase beta subunit [Streptococcus mitis]
          Length = 226

 Score =  211 bits (536), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 90/292 (30%), Positives = 125/292 (42%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EDSLKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGADGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D  ++ D+                                       
Sbjct: 167  ARTLGIHIATPVFDGASSEDLWSTVKEAGM------------------------------ 196

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                       +    ++L        G        TGEPFD  V+VG +YM
Sbjct: 197  -----------DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYM 224



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEDSLKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGADGVVRDVKIFTRANGD 86


>gi|168218616|emb|CAP45836.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 121

 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 79/136 (58%), Gaps = 18/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL            GL+  FK++ PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFLGWR---------GLERCFKTISPIEDFTGNLSLEFIDYSLGEPKYPVEE 51

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+  ++MGD P+MT  GTF+I G +
Sbjct: 52  SKERDVTYSAPLRVKVRLI---------NKETGEVKDHDVFMGDFPIMTDTGTFIINGAE 102

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 103 RVIVSQLVRSPSVYYS 118


>gi|168218634|emb|CAP45845.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 80/136 (58%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EG +  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGSREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|115382724|gb|ABI95383.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum
           grignonense]
          Length = 212

 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 122/213 (57%), Positives = 153/213 (71%), Gaps = 1/213 (0%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++ RIDRRRK+P T+ LMALGMD EEILSTFY  + YS+ GD W  P S      G K+ 
Sbjct: 1   VYARIDRRRKLPATTLLMALGMDGEEILSTFYNTVTYSRDGDNWRIPYSVE-RFKGMKII 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
           S L+D DTGE V+E+GKKLT+   K L EKG+KF+  T D L G Y+AED VN  TGEIY
Sbjct: 60  SDLIDADTGEVVLEAGKKLTARSAKQLAEKGLKFIKATEDDLFGSYLAEDTVNYATGEIY 119

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           +EAGD IDEK L+ +  + + +I +L +D +N  AYIRNTL  DKN+ R++AL DIYRVM
Sbjct: 120 LEAGDEIDEKVLKTLLDTGVDEINVLDIDHINIGAYIRNTLAVDKNESRQEALFDIYRVM 179

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
           RPG+  T   AE+MF+ LFFDS++YDLS VGRV
Sbjct: 180 RPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRV 212


>gi|168218638|emb|CAP45847.1| DNA-directed RNA polymerase subunit beta [Bacillus atrophaeus]
          Length = 120

 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 79/136 (58%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ + LI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVPLI---------NKETGEVKDQDVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RS  ++F 
Sbjct: 102 RVIVSQLVRSASVYFS 117


>gi|89145112|emb|CAJ57564.1| RNA polymerase subunit B [Agromyces albus]
          Length = 343

 Score =  211 bits (536), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 67/172 (38%), Positives = 91/172 (52%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT  GTFVI G +R+VVSQL RSPG++F+    +   S K +Y+ R+IP +G W
Sbjct: 1   MGDFPLMTPKGTFVINGTERVVVSQLVRSPGVYFERTPEKT--SDKDIYSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILEEFAGYESIAITLEKDNILTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EALKDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 162



 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 183/324 (56%), Gaps = 21/324 (6%)

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKS 332
           ++ S         +   +K +    +      G ++  +I   +  ++ +       +  
Sbjct: 26  LVRSPGVYFERTPEKTSDKDIYSARVIPSR--GAWLEFEI--DKRDQVGVRIDRKRKQSV 81

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
              +    +    IL  +       I  TL  D    +++AL DIYR +RPG+      A
Sbjct: 82  TVFLKALGLTSEEIL--EEFAGYESIAITLEKDNILTKEEALKDIYRKLRPGEQVAAEAA 139

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG- 451
            ++ +  +F+  +YDL+ VGR K+N +L L+ P     +  +DI+A IK LV L + +  
Sbjct: 140 RALLDNFYFNPKRYDLAKVGRYKINNKLGLEAPLTDSVLTVQDIVATIKYLVALHDERTT 199

Query: 452 --------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                          +DDIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI++
Sbjct: 200 LAGRRGGKAVELRLDVDDIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEA 259

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE
Sbjct: 260 ITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVE 319

Query: 558 MRDVHPTHYGRICPAETSEGHNIG 581
           +RDVHP+HYGR+CP ET EG NIG
Sbjct: 320 VRDVHPSHYGRMCPIETPEGPNIG 343


>gi|308156003|gb|ADO15371.1| RNA polymerase beta subunit [Xanthomonas arboricola pv. juglandis]
 gi|308156005|gb|ADO15372.1| RNA polymerase beta subunit [Xanthomonas bromi]
 gi|308156007|gb|ADO15373.1| RNA polymerase beta subunit [Xanthomonas cassavae]
 gi|308156009|gb|ADO15374.1| RNA polymerase beta subunit [Xanthomonas codiaei]
 gi|308156023|gb|ADO15381.1| RNA polymerase beta subunit [Xanthomonas pisi]
 gi|308156033|gb|ADO15386.1| RNA polymerase beta subunit [Xanthomonas vesicatoria]
 gi|326909327|gb|AEA11038.1| RNA polymerase beta subunit [Xanthomonas gardneri]
          Length = 204

 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|66854097|gb|AAY57357.1| RpoB [Prevotella intermedia]
          Length = 125

 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 57/99 (57%), Positives = 67/99 (67%)

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            GV  +TP+FDGA  E +      A L     + +YDG TGE FD+P TVG  Y LKL HM
Sbjct: 27   GVKFATPIFDGAKLEDLKEWTDKAGLPPMCSTYIYDGETGERFDQPATVGITYFLKLGHM 86

Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            V DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 87   VEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|68072695|ref|XP_678261.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56498673|emb|CAH95237.1| hypothetical protein PB001188.00.0 [Plasmodium berghei]
          Length = 209

 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 97/262 (37%), Gaps = 70/262 (26%)

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            ++P  VP  M++  + E   G      G                                
Sbjct: 1    MDPHAVPYSMSIEHLVECLAGKVAAIEG-------------------------------- 28

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                 G   +TP F     + I+  L     ++ G  ILY+G  
Sbjct: 29   ---------------------GEGDATP-FSKITVQEISERLHRLGYEKYGNDILYNGHN 66

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            G+     + +G  +  +L HMV DK++ARS G  +++T+QP  G+S  GG R GEME  C
Sbjct: 67   GKMLTSKIFIGPTFYQRLKHMVEDKIHARSRGPLTMITRQPTEGRSRDGGLRFGEMERDC 126

Query: 1302 IQAYGAAYVLQEMLTIKSD-------DVVG-------RTRVYESIVAG--NDTFETGTPE 1345
            + ++G+A +L+E L  +SD       D  G           YE  +     +  +   P 
Sbjct: 127  MISHGSAKMLKERLFEESDAYRVHVCDTCGLCCVADINKNAYECTICNSKTNISQIYIPY 186

Query: 1346 SFNVLVKEMQALGLSIDLENSR 1367
            +  +L +E+  + +   L    
Sbjct: 187  ACKLLFQELMTMAIYPKLVLED 208


>gi|308156013|gb|ADO15376.1| RNA polymerase beta subunit [Xanthomonas fragariae]
          Length = 204

 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 152/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDVKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|140084130|gb|ABO84914.1| RpoB [Paenibacillus sp. FSL_F4-152]
          Length = 225

 Score =  210 bits (535), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 79/194 (40%), Positives = 104/194 (53%), Gaps = 54/194 (27%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 86   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 145

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 146  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 194

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 195  ----------------------------------VFD---------TMEEAGMQRNGKTV 211

Query: 1236 LYDGLTGEPFDRPV 1249
            LYDG TGE F+R V
Sbjct: 212  LYDGRTGERFEREV 225



 Score = 89.4 bits (220), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 63/94 (67%), Positives = 76/94 (80%)

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           PEEITRDIPNV EE L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIF
Sbjct: 1   PEEITRDIPNVGEEALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIF 60

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           GEKA +VRDTSLRVP G  G +VDV++F R   D
Sbjct: 61  GEKAREVRDTSLRVPHGSDGIIVDVKVFTRENGD 94


>gi|158253020|gb|ABW23994.1| RNA polymerase beta subunit [Pantoea stewartii subsp. stewartii]
          Length = 212

 Score =  210 bits (534), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 128/211 (60%), Positives = 167/211 (79%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR++ DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRLIDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            V++++ YLSA+EE N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S 
Sbjct: 122 VVSDEIHYLSAIEEGNYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVST 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           +QVVS+ ASLIPFLE  D+NR LMG NMQRQ
Sbjct: 182 QQVVSVGASLIPFLETHDANRALMGANMQRQ 212


>gi|80973511|gb|ABB53493.1| RNA polymerase beta subunit [Streptococcus macacae NCTC 11558]
          Length = 226

 Score =  210 bits (534), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 93/294 (31%), Positives = 126/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 5    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    E     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 58   -----EVRDTSLRVPHGGEGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               L   I + + D   + D+    S                                  
Sbjct: 167  ARTLDIHIATPVFDGATSEDLWETVSEAGMDSDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 202  ---TVLYDG--------------------------RTGEPFDNRVSVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGEGVVRDVKIFTRANGD 86


>gi|157429503|gb|ABV56818.1| RNA polymerase beta subunit [Streptococcus castoreus]
          Length = 226

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 88/276 (31%), Positives = 119/276 (43%), Gaps = 60/276 (21%)

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
               +  I  G     G     K T      +S   R     F  +  +V+     +    
Sbjct: 11   LDGMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGG 70

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR
Sbjct: 71   DGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSR 124

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
            I+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++
Sbjct: 125  IVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASS 184

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             D+                                          T ++DG         
Sbjct: 185  EDLWETVREAGMDSDAK----------------------------TVLYDG--------- 207

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                              TGEPFD  V+VG +YM+K
Sbjct: 208  -----------------RTGEPFDNRVSVGVMYMIK 226



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 65/86 (75%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++D  GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVGEEALKDLDGMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|145342293|gb|ABP64843.1| RpoB [Bacillus clausii]
          Length = 232

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 93/287 (32%), Positives = 124/287 (43%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE+ I+      +  +IL G+    G         L   +  E  R           +V+
Sbjct: 16   DERGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR-----------EVR 64

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                      +            KI   + GD++PPGV ++V+V++  KR I  GDKMAG
Sbjct: 65   DTSLRAPHGGDGIV------LDVKIFNREDGDELPPGVNQLVRVYIVQKRKINQGDKMAG 118

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG++SRILP EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 119  RHGNKGVISRILPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARKLGIHV 178

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             S + D  +  D+                                          T ++D
Sbjct: 179  ASPVFDGASEEDVWGTLEEAGMARDGK----------------------------TILYD 210

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
            G                           TGEPFD  V+VG +YM+KL
Sbjct: 211  G--------------------------RTGEPFDNRVSVGIMYMIKL 231



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLR P G  G V+DV+IFNR   D
Sbjct: 62  EVRDTSLRAPHGGDGIVLDVKIFNREDGD 90


>gi|308156011|gb|ADO15375.1| RNA polymerase beta subunit [Xanthomonas cucurbitae]
          Length = 204

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 124/204 (60%), Positives = 151/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD NR LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDPNRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|51103937|gb|AAT96674.1| RpoB [Corynebacterium sp. 3301750]
          Length = 146

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 89/174 (51%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G  +    +D      +  L   L  V              
Sbjct: 1    RMNIGQVLEIHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYDVPADSLT-------- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNEEIAGLLANSKPNRDGDVMVDENGKTRLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|51103931|gb|AAT96671.1| RpoB [Corynebacterium sp. 25850]
 gi|51103933|gb|AAT96672.1| RpoB [Corynebacterium sp. 59614]
          Length = 148

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/174 (39%), Positives = 91/174 (52%), Gaps = 34/174 (19%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +   D K    +  L   L  V              
Sbjct: 1    RMNIGQVLEVHLGWLAKA-GWKVDTESQDPKIQKMLETLPEELYDVPADSLT-------- 51

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA    ++ +LR +  +  G        +S L DG +
Sbjct: 52   -----------------ATPVFDGASNAELSGLLRSSLPNRDGERQVDDFGKSNLIDGRS 94

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 95   GEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 148


>gi|169248086|gb|ACA51826.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248090|gb|ACA51828.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248098|gb|ACA51832.1| RNA polymerase beta subunit [Aliivibrio logei]
 gi|169248102|gb|ACA51834.1| RNA polymerase beta subunit [Aliivibrio logei]
          Length = 151

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/154 (49%), Positives = 106/154 (68%), Gaps = 5/154 (3%)

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   ++   R+FL+KV   G
Sbjct: 1    IVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQELHKFRNFLQKVYDLG 57

Query: 1180 SHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
               +   I+   DD V  + +  + G+P++TP+FDGA E +I  +L++ DL  SGQ  L+
Sbjct: 58   ETRQEVDIAALSDDEVRTLVKNLRGGLPIATPIFDGAPESSIKELLQLVDLPVSGQLKLF 117

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARS 151


>gi|117675863|emb|CAL69202.1| RNA polymerase subunit B [Agreia bicolorata]
          Length = 361

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/173 (38%), Positives = 96/173 (55%), Gaps = 6/173 (3%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ RIIP +G 
Sbjct: 1   FMGDFPLMTERGTFIINGTERVVVSQLVRSPGVYFERAQEKT--SDKDIYSSRIIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SEEILS F  Y  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEEILSEFKGYASIEATLEKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGIT 299
             A   +         V  +    ++++    +    L K  + K  + LGI 
Sbjct: 119 EEALKDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIE 171



 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 136/346 (39%), Positives = 203/346 (58%), Gaps = 22/346 (6%)

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC---GLYVAEDIVNGETGEIYIEAGDV 327
           E+V+ S    + G+     ++      I S  +    G ++  +I   +  ++ +     
Sbjct: 20  ERVVVSQLVRSPGVYFERAQEKTSDKDIYSSRIIPSRGAWLEFEI--DKRDQVGVRIDRK 77

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
             +     +    +    IL        A I  TL  D    +++AL DIYR +RPG+  
Sbjct: 78  RKQSVTVFLKALGLTSEEIL--SEFKGYASIEATLEKDTILTKEEALKDIYRKLRPGEQV 135

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
               A ++ +  +F+S +YDL+ VGR K+N +L +++      +  EDIIA IK LV L 
Sbjct: 136 AAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIESALSNSVLTVEDIIATIKYLVALH 195

Query: 448 NGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
           + +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER ++ER+++
Sbjct: 196 DNQTTIPGTREGKKVDIRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTT 255

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R 
Sbjct: 256 QDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRE 315

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 316 RAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 361


>gi|51103939|gb|AAT96675.1| RpoB [Corynebacterium sp. 89349]
          Length = 148

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 66/174 (37%), Positives = 90/174 (51%), Gaps = 34/174 (19%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLG      G K+     D      +  L   L  V              
Sbjct: 1    RMNIGQVLEVHLGMLAKS-GWKVDPESQDPAVKAMLETLPEDLYDVPADSR--------- 50

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                            V+TPVFDG   E ++ ++R +  +  G        +S L DG T
Sbjct: 51   ----------------VATPVFDGTTNEELSGLMRSSRPNRDGDQMVNEFGKSTLIDGRT 94

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF +P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 95   GEPFQQPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 148


>gi|169248106|gb|ACA51836.1| RNA polymerase beta subunit [Aliivibrio wodanis]
 gi|169248108|gb|ACA51837.1| RNA polymerase beta subunit [Aliivibrio wodanis]
          Length = 151

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 77/154 (50%), Positives = 107/154 (69%), Gaps = 5/154 (3%)

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            IVLNPLGVPSRMN+GQI E H+G A  G+G K+  ++   K   ++   R+FL+KV   G
Sbjct: 1    IVLNPLGVPSRMNIGQILEVHMGLAAKGVGDKLNQML---KEQQELHKFRNFLQKVYDLG 57

Query: 1180 SHTE--KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
               +   I+   DD V  + +  + G+P++TP+FDGA E +I  +L++ DL ESGQ  L+
Sbjct: 58   ETRQEVDIAALSDDEVRTLIKNLRGGLPIATPIFDGAPEASIKELLKLVDLPESGQLKLF 117

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
            DG TG+ F+RPVTVGY+YMLKLNH+V DK++ARS
Sbjct: 118  DGRTGDEFERPVTVGYMYMLKLNHLVDDKMHARS 151


>gi|66854085|gb|AAY57351.1| RpoB [Prevotella albensis]
          Length = 125

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/179 (37%), Positives = 86/179 (48%), Gaps = 54/179 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K GV  +TP+FDGA  + +      A L     + +YDG TG
Sbjct: 21   --------------AAGKKLGVKFATPIFDGAKLKDLQEWTDKAGLPRLCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            E FD+P T+G  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW 
Sbjct: 67   EKFDQPATIGMTYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWA 125


>gi|161331443|gb|ABX60639.1| RpoB [Bacillus firmus]
          Length = 232

 Score =  210 bits (534), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 79/207 (38%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVASPVFDGAREEDVWSTIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMARDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGVMYMIKL 231



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|255950612|ref|XP_002566073.1| Pc22g21780 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211593090|emb|CAP99466.1| Pc22g21780 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 1208

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 97/585 (16%), Positives = 181/585 (30%), Gaps = 97/585 (16%)

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +  D+    +  +A       N    + I    V   V   I         R+T      
Sbjct: 703  EYLDVNEENDSYIAIYEKDITNTHTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAM- 761

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              + I  ++    + ID   I+ +        +    I       +   +    A+    
Sbjct: 762  GKQAIGAIASNQFQRIDS--ILYLMVYPQKPMVKSRTIELTKYDQLPAGQNATVAVMSYS 819

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              D+ D  +     V       ++F ++           +           ++   I   
Sbjct: 820  GYDIEDALVLNKGSVDRGFGRCQVFRKYVTTLKSYPNGAKDSLRAPT---FENGAPIRKH 876

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
             +         G+   +G     K T    + +               +    +V    +
Sbjct: 877  ALLESDGLAAVGEMVNNGETYINKVTPRVQNSLG----------FSGPDIGGGDVLEAPM 926

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             Y     + +  + +K+           G  +++KV     R  + GDK +         
Sbjct: 927  NY----KLPDPSYIDKVLV-----SATEGETQLIKVLTRQTRRPEVGDKFS--------- 968

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                                        SR                  G+K    I   +
Sbjct: 969  ----------------------------SR-----------------HGQKGVVGIIADQ 983

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
            A+   S      + ++       +++      ++       SG       F G+  + ++
Sbjct: 984  ADMPFSDQGINPDIIMNPHGFPSRMTVGKMLELVAGKAGVLSGQHGYGTCFGGSPVQEMS 1043

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQ 1280
             +L        G+  L  G+TGEP    V  G IY  KL HMV DK+++R+ G  + +T+
Sbjct: 1044 QILIDKGFSYGGKDYLTSGITGEPLPFYVFTGPIYYQKLKHMVQDKMHSRAKGPTATLTR 1103

Query: 1281 QPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRV----------YE 1330
            QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    R  V          Y 
Sbjct: 1104 QPTEGRSRNGGLRLGEMERDCLIAYGTSQLLLERLMISSD----RHEVDICEKCGFMGYL 1159

Query: 1331 SIVAG----NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
            +   G        +   P +  +L++E+ ++ ++  L+       
Sbjct: 1160 NWCPGCKSSRSVVKMVIPYAAKLLIQELMSMNVTARLKLDDEFPE 1204



 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 131/996 (13%), Positives = 297/996 (29%), Gaps = 215/996 (21%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI-TAFSGAAMLEFVSYEFDPPK-- 85
           L++    SY++F+ + +          +   +S   I +       ++F       P+  
Sbjct: 101 LVKQHIDSYNYFVEVQM----------KKIVESSSTIRSDVDHNFYIKFTDIYVASPRRA 150

Query: 86  -------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
                            +C  RD TYA P+ +    +          +  + +  +++ +
Sbjct: 151 DEQGDGGLDFESTITPQECRLRDTTYAAPILVDFEYV----------RGRQRVIRRAVPI 200

Query: 133 GDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDH 167
           G +P+M                           G FV+ G +++++ Q   S   I  + 
Sbjct: 201 GRIPMMLRSSKCVLSNKTPAQMSVLNECPLDPGGYFVVNGTEKVILVQEQLSKNRIIVET 260

Query: 168 DKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTSFLM 219
           D  +        S S +      I+             K  ++V+ +     +P+   L 
Sbjct: 261 DPKKDIVQASVTSSSNERKSKSYIVS-----------KKGRLYVKHNVLNEDIPIVILLK 309

Query: 220 ALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL----------MVGAKVSSSLVDIDT 269
           A+G+ +++ +           + DF      A ++           +G ++  +      
Sbjct: 310 AMGIHTDKEMMQMVTGDDALYQDDFAINFEEAINVDVYTQQQALDWIGCRIKINRKQAAY 369

Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVID 329
            +  ++   +  + ++  +    VK +      +   ++A  ++  ++    ++  D + 
Sbjct: 370 RKTHVQEAVEAIASVI--ISHIEVKDMNFRPKAIYVAHMARRVLMAKSDPALVDDRDYLG 427

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
            K LE            L+                   K   D  ++I +V+   + +  
Sbjct: 428 NKRLELAGQMLALLFEDLF------------------KKFCFDIKMNIDKVLNKRNRAEQ 469

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
             A ++         +     +     +  R  ++       + +   IA + ++  + +
Sbjct: 470 FDAWTIVTMHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISS 529

Query: 449 GKGTIDDIDNLGNRRVRSVGEML-KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
                  +      +    G +   +        + +++         D   P   +   
Sbjct: 530 QFEKTRKVSGPRALQPSQFGMLCPADTPEGEACGLVKNLALMTHITTNDEEGPVRNLIFM 589

Query: 508 PVVSAVCEFFCSSQLSQ--LEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPT 564
             V  +         ++      +N        R  S L     + R     E   ++  
Sbjct: 590 LGVEDISSVGGQQLYARGAYTISINGTPTGLTRRPKSFLNAFRRLRRMGRVSEFVSIYIN 649

Query: 565 HYGRICPAETSEGHNIG---LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
           H+ R     T +G       +V +  S         +     +  D      V YL   E
Sbjct: 650 HHQRAVHVATDDGRICRPLIVVENGKSLVGAQHLEKLRDGKMEFDDFLAQGLVEYLDVNE 709

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E + YIA     +                             ++  P  V+   A LIP+
Sbjct: 710 ENDSYIAIYEKDITNTH-----------------------THLEIEPFTVLGAVAGLIPY 746

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             ++ S R    C M +Q                          AI A  +   +++D+I
Sbjct: 747 PHHNQSPRNTYQCAMGKQ--------------------------AIGAIASNQFQRIDSI 780

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
             ++                                Q+P+VK                T 
Sbjct: 781 LYLMVY-----------------------------PQKPMVKS----------RTIELTK 801

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
              L  G+N  VA M + GY+ ED++++++  V           ++    +    G ++ 
Sbjct: 802 YDQLPAGQNATVAVMSYSGYDIEDALVLNKGSVDRGFGRCQVFRKYVTTLKSYPNGAKDS 861

Query: 862 TRDIPNVSEEGLKN---IDECGIICVGAEVNPGDILVGKITPKGES------PMTPEEKL 912
            R     +   ++    ++  G+  VG  VN G+  + K+TP+ ++      P      +
Sbjct: 862 LRAPTFENGAPIRKHALLESDGLAAVGEMVNNGETYINKVTPRVQNSLGFSGPDIGGGDV 921

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           L A    K  D       + S   G    +++  R 
Sbjct: 922 LEAPMNYKLPDPSYIDKVLVSATEGETQLIKVLTRQ 957


>gi|30141103|gb|AAP21861.1| RNA polymerase beta subunit [Enterococcus avium]
          Length = 231

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 78   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 137

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 138  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQ----------- 186

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D  V     + +      T ++DG                   
Sbjct: 187  -----------------DSDVWETVREARMAADAKTVLYDG------------------- 210

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  ++VG +YM+KL
Sbjct: 211  -------RTGEPFDNRISVGVMYMIKL 230



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LKN+DE GII +GAEV+ GD+LVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 1   REIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  EVRDTSLRVPHGGGGIVHDVKIFTREAGD 89


>gi|326909321|gb|AEA11035.1| RNA polymerase beta subunit [Xanthomonas cynarae]
          Length = 204

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 123/204 (60%), Positives = 151/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSDVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+ R LMG NMQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDAYRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|300394716|gb|ADK11896.1| DNA-directed RNA polymerase II subunit two [Leptosporomyces
            raunkiaeri]
          Length = 669

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 114/804 (14%), Positives = 215/804 (26%), Gaps = 161/804 (20%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN- 530
             +R+   ++ + +    +              +  + + + +     +            
Sbjct: 1    LFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYPLATGNGGDQRSPCLQ 60

Query: 531  -----SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH-----YGRICPAETSEGHNI 580
                   S +T  RR   + +        G   R  +P H      GR  PAET EG   
Sbjct: 61   KLVYLRCSSVTRMRRHYLILRR--CNRHLGERARLQNPRHCTILTGGRCVPAETPEGQAC 118

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            GLV++L   A ++  G +  P  +  +      +   +A           N         
Sbjct: 119  GLVTNLALMACIS-VGSLSAPVIEFLEEWGLESLE-ENAHSSTPCTKVFVNGVWMGVHRD 176

Query: 641  TEELVFCRCA-GEEILVPREKIDFIDASPKQ---VVSIAASLIPFLENDDSNRVLMGCNM 696
               LV        +  +  E     D   K+            P    ++    L   ++
Sbjct: 177  PANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHI 236

Query: 697  Q------RQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
            +      R            V  G+ E + A+     +++      E ++  R+ +  V+
Sbjct: 237  KWLNQGFRDGDEEEFKWEQLVKGGIIELLDAEEEETVMIS---MTPEDLENSRLQLAGVD 293

Query: 750  GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
              ++                            +K G +          PS  LG      
Sbjct: 294  SQMNDGEFDPAA-------------------RLKAGTDAHTWTHCEIHPSMILG------ 328

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  + +P+  +N                        ++       +G       I    
Sbjct: 329  -ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM-- 367

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                       +  +             +       +   +  + AI      +  D+ +
Sbjct: 368  ---------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVI 418

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI 989
               S +   +    I+ R  +D   +S   + E+ E   R+          +       I
Sbjct: 419  MNQSSIDRGLF-RSIYYRSYMDLERKSGVQQLEEFEKPTRENTLRMKHGTYDKIEDDGLI 477

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G N         K+  +  D      R++          ++     +  Q        
Sbjct: 478  APGTNVSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI----- 532

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
                                  + VKV V   R  Q GDK A RHG KG +      EDM
Sbjct: 533  ---------------TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGITYRQEDM 577

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   DI++NP  +PSRM +G + E  L      +G +                  
Sbjct: 578  PFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------- 621

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                 +TP F     E++++ LR     
Sbjct: 622  -------------------------------------ATP-FTDLTVESVSTFLRQKGYQ 643

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGY 1253
              G  ++Y G +G      V +G 
Sbjct: 644  SRGLEVMYHGHSGRKLQAQVYLGP 667


>gi|323652567|gb|ADO15377.2| RNA polymerase beta subunit [Xanthomonas hortorum pv. hederae]
          Length = 204

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 123/203 (60%), Positives = 151/203 (74%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG NI
Sbjct: 2   QLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNI 61

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D     
Sbjct: 62  GLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNML 121

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
           TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG NMQRQA
Sbjct: 122 TEQFVPCRFQGESLLKPPAEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQA 181

Query: 701 VPLLKAEAPFVGTGMESVVAKSS 723
           VP L+++ P VGTG+E  VA+ S
Sbjct: 182 VPTLRSQKPLVGTGIERAVARDS 204


>gi|146217873|gb|ABQ11016.1| RNA polymerase beta subunit [Bacillus licheniformis]
          Length = 232

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARRLGLHVASPVFDGAREEDVWETLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGIMYMIKL 231



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIILDVKVFNREDGD 90


>gi|304561746|gb|ADM43735.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 325

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 113/350 (32%), Positives = 172/350 (49%), Gaps = 35/350 (10%)

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
           SPG+ ++    +    GK L +  +IP++G W++ E DS DI++VRIDR RKVPVT  L 
Sbjct: 1   SPGVLYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDIVYVRIDRTRKVPVTVLLR 57

Query: 220 ALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESG 277
           ALG  ++ +IL     +       D          L+   K       +  GE   +ES 
Sbjct: 58  ALGYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK------RLRPGEPPTVESA 111

Query: 278 KKLTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAEDIVNGETGEIYIEAGDVID 329
           K L   L    K   +  +G             +  L  A+ IVN  TGEI +E G+ I 
Sbjct: 112 KSLLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKKIVNPVTGEILVEEGEKIS 171

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           ++  EEI +  I  + +L    V     I N              +DI +   P DVS  
Sbjct: 172 KEKAEEIQNCGINVVEVLVEGKVVR--VIGNNT------------VDINKYPMPYDVSNL 217

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           ++ E++   L    +  D  +     +N   N       ++I K+DIIA I   ++L +G
Sbjct: 218 NIKEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNITKDDIIATISYQLNLTHG 275

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
            G+IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++  D++ + 
Sbjct: 276 IGSIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMTIQDVNEIT 325


>gi|50295199|gb|AAT72972.1| RpoB [Streptococcus thermophilus]
          Length = 218

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 89/287 (31%), Positives = 124/287 (43%), Gaps = 71/287 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 2    DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 50

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 51   DTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 104

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 105  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIYI 164

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  ++ D+                                               
Sbjct: 165  ATPVFDGASSEDLWDTVREAGM-------------------------------------- 186

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +    ++L        G        TGEPFD  V+VG +YM+ L
Sbjct: 187  ---DSDAKTIL------YDG-------RTGEPFDNRVSVGVMYMINL 217



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 48/76 (63%), Positives = 58/76 (76%)

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G 
Sbjct: 1   LDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGG 60

Query: 936 SGTVVDVRIFNRHGID 951
            G V DV+IF R   D
Sbjct: 61  DGVVRDVKIFTRANGD 76


>gi|326909329|gb|AEA11039.1| RNA polymerase beta subunit [Xanthomonas dyei pv. dysoxyli]
          Length = 204

 Score =  209 bits (533), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 123/204 (60%), Positives = 151/204 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+NR LMG  MQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGAFMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AVP L+++ P VGTG+E  VA+ S
Sbjct: 181 AVPTLRSQKPLVGTGIERAVARDS 204


>gi|46277249|gb|AAS86815.1| RNA polymerase II second largest subunit [Selaginella densa]
          Length = 547

 Score =  209 bits (532), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 110/696 (15%), Positives = 186/696 (26%), Gaps = 149/696 (21%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   A +   G    P     +   T +   +S     N      N 
Sbjct: 1    ETPEGQACGLVKNLALMAYIT-VGSAANPILVFLEEWSTENFEEISPAAIPNSTKIFVNG 59

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            S        + LV         +         D + +  V     L       D  R   
Sbjct: 60   SWVGIHREPDNLVKTLRQLRRQV---------DVNTEVGVVRDTRLKELRLYTDYGRCSR 110

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  +   L+                         +           +  I  V+ + 
Sbjct: 111  PLFIVEKQRLLI--------------KKSDIRTLQQKEAGENGWHDLVTKGFIEFVDTEE 156

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R N             GD           PS  LG       + 
Sbjct: 157  EETTMISMTINDLVNARLN------------PGDAYSTYTHCEIHPSMILG-------VC 197

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 198  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 231

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 232  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 288

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        IF R   D+  +  ++ +E+ E  +RD   +                 G
Sbjct: 289  SSIDRGFF-RSIFYRSYRDEERKQGTLVKEEFEKPSRDSTKDMRHGSYEKLDDDGITPPG 347

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T L                   DE   +     K    TS    E  
Sbjct: 348  TRVSGEDVIIGKTTPLGQ-----------------DETGAQAQRYTKRDQSTSLRHSESG 390

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VK+ V   R  Q GDK + RHG KG V      EDMPF 
Sbjct: 391  MVDQVLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPFT 445

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS      
Sbjct: 446  QEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAALMGKEGDATPFTDVTVDNISKALHKC 505

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
               +                                                      +G
Sbjct: 506  GYQMRGFETM-----------------------------------------------YNG 518

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             +    G         + +G  Y  +L HMV DK++
Sbjct: 519  HT----GR---KLSAMIFIGPTYYQRLKHMVDDKIH 547



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 53/329 (16%), Positives = 103/329 (31%), Gaps = 37/329 (11%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + ++   F   S + 
Sbjct: 4   EGQACGLVKNLALMAYITVGSAANPILVFLEEWSTENFEEISPAAIPNSTKIFVNGSWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              E  N +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHREPDNLVKTLRQLRRQVDVNTEVGVVRDTRLKELR-LYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      +      E       D      + ++   EEE   I+              
Sbjct: 123 KKS-----DIRTLQQKEAGENGWHDLVTKGFIEFVDTEEEETTMISM----------TIN 167

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R    +           +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 168 DLVNARLNPGDAY---STYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 224

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 225 IYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 284

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 285 IMNQSSIDRGFFRSIFYRSYRDEERKQGT 313


>gi|145342357|gb|ABP64875.1| RpoB [Paenibacillus sp. FSL_H8-101]
          Length = 209

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/192 (40%), Positives = 103/192 (53%), Gaps = 54/192 (28%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+   + GD++PPGV ++V+V++A KR I  GDKMAGRHGNKG+V+RILP EDMPFL DG
Sbjct: 72   KVFTRENGDELPPGVNQLVRVYIAQKRKISEGDKMAGRHGNKGVVARILPEEDMPFLPDG 131

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPV +VLNPLGVPSRMN+GQ+ E H+G A + LG  I + + D     D           
Sbjct: 132  TPVQVVLNPLGVPSRMNIGQVLEVHIGMAALRLGIHIATPVFDGAREYD----------- 180

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                              VFD          +  A +  +G+++
Sbjct: 181  ----------------------------------VFD---------TMEEAGMQRNGKTV 197

Query: 1236 LYDGLTGEPFDR 1247
            LYDG TGE F+R
Sbjct: 198  LYDGRTGERFER 209



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 50/80 (62%), Positives = 63/80 (78%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L+N+DE GII +GAE++ GDILVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLRV
Sbjct: 1   ALRNLDERGIIRIGAEISAGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRV 60

Query: 932 PSGVSGTVVDVRIFNRHGID 951
           P G  G +VDV++F R   D
Sbjct: 61  PHGSDGIIVDVKVFTRENGD 80


>gi|168068028|ref|XP_001785899.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162662437|gb|EDQ49293.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 449

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 79/365 (21%), Positives = 135/365 (36%), Gaps = 69/365 (18%)

Query: 1007 VLSSDLISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
            +L  D++ +          V+D + +       + +    K +L+     +++K+     
Sbjct: 132  ILDGDILRDNDGIVLIDQQVKDGDTIAAKFIITEKKQSIEKIVLKSFVSGRVDKVTK--H 189

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  ++V+V + + +    GDK   RH  KG++  I+  ED+ F KDG   D+++NP 
Sbjct: 190  TSVEGNKIVRVRILLYKFPIVGDKFTSRHSQKGVIGAIMSQEDLLFTKDGIAPDLIINPH 249

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +  + E  +                          +               K 
Sbjct: 250  AIPSRMTMDHLLEMVMCK------------------------IYVLDSNNARDPILPSKP 285

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
               +   +         G       F+G            A      +  +Y G TG P 
Sbjct: 286  KSRESSCIDATTFNKAYGS------FEGDT----------AKFS---KQKMYCGTTGLPI 326

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            +  V +G  Y   L H   DK ++ S G    +T+QP+ G+S +GG R G+ME  C+ A+
Sbjct: 327  EARVAIGICYYDVLRHQARDKAHSISKGVIQSLTKQPVEGQSRKGGLRFGKMEKDCLIAH 386

Query: 1306 GAAYVLQEMLTIKSD--------DVVGRTRVYESIVAGNDTFETG--------TPESFNV 1349
            GAA +L E L   SD        D         +I +GN               P SF +
Sbjct: 387  GAASMLLEKLKNTSDLCEVWICHDCS-------TIYSGNPCINCNRRNTKEYRLPYSFKL 439

Query: 1350 LVKEM 1354
              +E+
Sbjct: 440  QTQEL 444


>gi|256809231|gb|ACV30716.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
          Length = 167

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 99/167 (59%), Positives = 121/167 (72%), Gaps = 1/167 (0%)

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD EEILST
Sbjct: 1   THSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILST 60

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY  + YS+ GD W  P SA D   G K+ S L+D DTGE V+E+GKKLT+   K L EK
Sbjct: 61  FYKTVTYSRDGDNWRIPYSA-DRFKGMKIISDLIDADTGEVVLEAGKKLTARSAKQLAEK 119

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           G+K +  T D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  
Sbjct: 120 GLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLID 166


>gi|80973519|gb|ABB53497.1| RNA polymerase beta subunit [Streptococcus phocae]
          Length = 226

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 89/284 (31%), Positives = 121/284 (42%), Gaps = 71/284 (25%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  +IL G+    G K       L   +  +  R           +V+
Sbjct: 12   DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI     GD++  GV  +V+V++A KR I+ GDKMAG
Sbjct: 61   DTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I
Sbjct: 115  RHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D  +  D+                                          T ++D
Sbjct: 175  ATPVFDGASAEDLWDTVREAGMDSDAK----------------------------TVLYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            G                           TGEPFD  V+VG +YM
Sbjct: 207  G--------------------------RTGEPFDNRVSVGVMYM 224



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/86 (65%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNVSE+ LKN+DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VR
Sbjct: 1   PNVSEDALKNLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVRDVKIFTRANGD 86


>gi|256809121|gb|ACV30661.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809123|gb|ACV30662.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809125|gb|ACV30663.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809127|gb|ACV30664.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809129|gb|ACV30665.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809131|gb|ACV30666.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809133|gb|ACV30667.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809135|gb|ACV30668.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi
           ATCC 49188]
 gi|256809137|gb|ACV30669.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809139|gb|ACV30670.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809141|gb|ACV30671.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809143|gb|ACV30672.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809145|gb|ACV30673.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809147|gb|ACV30674.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809149|gb|ACV30675.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809151|gb|ACV30676.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809153|gb|ACV30677.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809155|gb|ACV30678.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809157|gb|ACV30679.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809159|gb|ACV30680.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809161|gb|ACV30681.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809163|gb|ACV30682.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809165|gb|ACV30683.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809167|gb|ACV30684.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809169|gb|ACV30685.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809171|gb|ACV30686.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809173|gb|ACV30687.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809175|gb|ACV30688.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809177|gb|ACV30689.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809179|gb|ACV30690.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809181|gb|ACV30691.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809183|gb|ACV30692.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809185|gb|ACV30693.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809187|gb|ACV30694.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809189|gb|ACV30695.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809193|gb|ACV30697.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809195|gb|ACV30698.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809197|gb|ACV30699.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809199|gb|ACV30700.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809201|gb|ACV30701.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809203|gb|ACV30702.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809205|gb|ACV30703.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809207|gb|ACV30704.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809209|gb|ACV30705.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809211|gb|ACV30706.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809213|gb|ACV30707.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum lupini]
 gi|256809215|gb|ACV30708.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809217|gb|ACV30709.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809219|gb|ACV30710.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809221|gb|ACV30711.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809223|gb|ACV30712.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809225|gb|ACV30713.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809227|gb|ACV30714.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809229|gb|ACV30715.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809233|gb|ACV30717.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum cytisi]
 gi|256809237|gb|ACV30719.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809239|gb|ACV30720.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809241|gb|ACV30721.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809243|gb|ACV30722.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809245|gb|ACV30723.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809247|gb|ACV30724.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809249|gb|ACV30725.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809251|gb|ACV30726.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809253|gb|ACV30727.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809255|gb|ACV30728.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809257|gb|ACV30729.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
 gi|256809259|gb|ACV30730.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
          Length = 167

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 97/167 (58%), Positives = 121/167 (72%), Gaps = 1/167 (0%)

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD E+ILST
Sbjct: 1   THSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEDILST 60

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY  + Y++ GD W  P SA D   G K+ S L+D DTGE V+E+GKKLT+   K L EK
Sbjct: 61  FYKTVTYTRDGDNWRIPYSA-DRFKGMKIISDLIDADTGEVVLEAGKKLTARSAKQLAEK 119

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           G+K +  T D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  
Sbjct: 120 GLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLID 166


>gi|323514491|gb|ADX89816.1| RNA polymerase beta subunit [Enterobacter asburiae]
          Length = 215

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 132/215 (61%), Positives = 166/215 (77%)

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           GF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE  L
Sbjct: 1   GFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSKGESSL 60

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
             R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGM
Sbjct: 61  FSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGM 120

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E  VA  SG   VAKR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC
Sbjct: 121 ERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTC 180

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +NQ P V +G+ V R D++ADGPSTDLG+LALG+N
Sbjct: 181 INQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 215


>gi|161331511|gb|ABX60673.1| RpoB [Bacillus sp. FSL_h8543]
          Length = 232

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMP++
Sbjct: 79   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYM 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARSLGIHVASPVFDGATEEDVWETIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGVMYMIKL 231



 Score = 85.1 bits (209), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII  GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRTGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVHDVKVFNREDGD 90


>gi|30141071|gb|AAP21846.1| RNA polymerase beta subunit [Enterococcus faecalis]
          Length = 232

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 79   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 186

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 187  ----------------TDEDVWETVREAGMASDAKTVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  ++VG +YM+KL
Sbjct: 212  -------RTGEPFDNRISVGVMYMIKL 231



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGGGIVHDVKIFTREAGD 90


>gi|46277376|gb|AAS86878.1| DNA-dependent RNA polymerase II [Peziza varia]
 gi|46277380|gb|AAS86880.1| DNA-dependent RNA polymerase II [Peziza varia]
          Length = 563

 Score =  209 bits (532), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 102/681 (14%), Positives = 181/681 (26%), Gaps = 122/681 (17%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     E    +    + +V  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
              F    +        I      I D  +   K          P    D+         +
Sbjct: 62   PGFIVRTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGEL 121

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              Q   + K E     T  E      SG        G+VE +DA       +    +   
Sbjct: 122  VLQKHHIEKLEDDKDITDEEQRYGW-SGL----IGEGVVEYIDAEEEETVMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            +    +   + Q         QR    V             PS  LG       +  + +
Sbjct: 177  TSRQFHAGYEIQTEVDPA---QRVKASVNKYAHTWTHCEIHPSMILG-------ICASII 226

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  F    R+                       
Sbjct: 227  PFPDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM--------------------- 259

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 260  --DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 317

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +    +F R  +D+ +R      E+ E   R           +       +  G    
Sbjct: 318  RGLF-RSLFYRTYMDQEKRVGMNVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVS 376

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+  +S ++     R+++         ++     +  Q               
Sbjct: 377  GEDIIIGKTAPISPNMEELGQRTKFHTKRDVSTPLRSTENGIVDQ--------------- 421

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 422  -----VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGV 476

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +  + E  L       G +                         
Sbjct: 477  VPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------------- 513

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     ++++ +LR       G  I+
Sbjct: 514  ------------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEIM 542

Query: 1237 YDGLTGEPFDRPVTVGYIYML 1257
            Y+G TG      V +G  Y  
Sbjct: 543  YNGHTGRKLVVQVFLGPTYYQ 563



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 75/482 (15%), Positives = 131/482 (27%), Gaps = 88/482 (18%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 25  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 78

Query: 545 G-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           G +  + +     E        R   P       PA    G  +     +          
Sbjct: 79  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKDIT 138

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCA 650
             E  Y           V Y+ A EEE   I      L+    F        E+   +  
Sbjct: 139 DEEQRY-GWSGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQTEVDPAQRV 197

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
              +          +  P  ++ I AS+IPF +++ S R      M +QA+ +       
Sbjct: 198 KASVNKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---- 253

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                       + A I+                                    +KF+  
Sbjct: 254 -----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFREL 287

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                     L   G   + + +I +  S D G                  + E  + ++
Sbjct: 288 PAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLFY-------RTYMDQEKRVGMN 339

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                        +EEFE   R           +   +       +DE G++  G  V+ 
Sbjct: 340 ------------VVEEFEKPTR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSG 377

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P      +P  + L      K    RD S  + S  +G V  V +      
Sbjct: 378 EDIIIGKTAPI-----SPNMEELGQR--TKFHTKRDVSTPLRSTENGIVDQVMVTTNQEG 430

Query: 951 DK 952
            K
Sbjct: 431 LK 432


>gi|53854334|gb|AAU95612.1| RNA polymerase beta subunit [Neisseria meningitidis]
          Length = 207

 Score =  209 bits (531), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 122/207 (58%), Positives = 159/207 (76%)

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG 545
           +KER++  + +++MP DLINAKPV +A+ EFF SSQLSQ  +  N LS +TH RR+SALG
Sbjct: 1   VKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSEVTHKRRVSALG 60

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
            GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPYR+V
Sbjct: 61  PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFLETPYRRV 120

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
            DGKVT ++ YLSA+EE    IAQAN+ LD DG+   +LV CR  GE I+   +++ ++D
Sbjct: 121 IDGKVTEEIDYLSAIEEGRYVIAQANADLDSDGNLIGDLVTCREKGETIMATPDRVQYMD 180

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  QVVS+AASLIPFLE+DD+NR LM
Sbjct: 181 VATGQVVSVAASLIPFLEHDDANRALM 207


>gi|328876497|gb|EGG24860.1| RNA polymerase III [Dictyostelium fasciculatum]
          Length = 203

 Score =  209 bits (531), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 93/260 (35%), Gaps = 72/260 (27%)

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP G PSRM +        G     L  K   +   +                      
Sbjct: 1    MNPHGFPSRMTI--------GKMIELLAGKAGVVSGKFGYGTC----------------- 35

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                         F G   E ++ +L        G+  +  G+T
Sbjct: 36   -----------------------------FGGDKVEDLSKVLISKGFSYGGKDYVTSGVT 66

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEP    +  G I+  KL HMV DK++AR+ G    +T+QP  G++  GG RLGEME  C
Sbjct: 67   GEPLQCFIFFGPIFYQKLKHMVMDKMHARARGPTVTLTRQPTEGRARGGGLRLGEMERDC 126

Query: 1302 IQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--------------NDTFETGTPESF 1347
            +  YGA+ ++ E L I SD    R  VY     G                      P + 
Sbjct: 127  LIGYGASALIMERLMISSD----RFTVYACKECGFLGYEGWCQYCKSTLQVSTLQIPYAC 182

Query: 1348 NVLVKEMQALGLSIDLENSR 1367
             +L +E+QA+ +   L+   
Sbjct: 183  KLLFQELQAMNIVPKLKLVD 202


>gi|148628034|gb|ABQ97022.1| RNA polymerase II second largest subunit [Capronia munkii]
          Length = 681

 Score =  209 bits (531), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 121/742 (16%), Positives = 229/742 (30%), Gaps = 105/742 (14%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP--VVSAVCEFFCS 519
            +R+   G ++ N +RL   +  +     +            +   K   + S +     +
Sbjct: 2    KRLDLAGPLMTNLFRLQFDKATKDFYRYMQKRVESGQPINIMAGFKHPIITSGLKYSLAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +A     + R     + R +H TH+
Sbjct: 62   GNWGDQKKLDKAKAGVSQVLSRYTFSSTLSHLRRTNA----PIGREGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + V            + +  +T  V    A+E+    
Sbjct: 118  GYVCPAETPEGQACGLVKNLSLMSMVTNSYETGP----LLNYVMTKHVE---ALEDWEPR 170

Query: 627  IAQANSSLDEDGSF-------TEELVFCRCAGEEILVPREKIDF-IDASPKQVVSIAAS- 677
            +    + +  DG +        + LV          V    +    D   K+      S 
Sbjct: 171  LNPRATKIFVDGVWFAVVLRDPKRLVDDLRKLRRKGVFDSHVSLVWDIREKEFKISGDSG 230

Query: 678  ----LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
                 +  +E D S+  L    + ++ +  L   A    +G +               +G
Sbjct: 231  RIVRPLFVVETDRSSENLGNLVLNKEHINKLDQTAYLKESGFQWTDEIRPYGWTDLLESG 290

Query: 734  IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +VE +DA       +    +        +  M+ +  +     N  PL+           
Sbjct: 291  VVEYLDAEEEETAMICMTPEALADSKARWLGMEIENEDDPLRRN-DPLLNPHAHTF--TH 347

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                PS  LG       +  + +P+  +N          M  + +               
Sbjct: 348  CEIHPSMILG-------VCASIIPFPDHNQSPRNTYQSAMGKQAMGV----------FLT 390

Query: 854  TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
                  E   +I    ++ L                        +       +   +  +
Sbjct: 391  NFDQRMETMANILYYPQKPLAR-------------------TMAMDYLKFRELPAGQNAI 431

Query: 914  RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
             AI      +  D+ +   S +   +     +  +     +   SV    +E   +    
Sbjct: 432  VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQ----DSEKSVGHSVVEQFEKPTRS 487

Query: 974  EQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
            + + L    Y ++ E   +  G           K+  ++ D                +E 
Sbjct: 488  DTLRLKHGTYDKIDEDGIVAPGVRVSGEDIIMGKTAPMAPD---------------AEEL 532

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
             QR  + +K    T     E    +++              R  KV V   +  Q GDK 
Sbjct: 533  GQRLKQHIKRDVSTPLRSTESGIVDQVML-----TTTAEGHRFAKVRVRTTKVPQIGDKF 587

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E  L       G 
Sbjct: 588  ASRHGQKGTIGITYRHEDMPFTREGIVPDLIINPHAIPSRMTIAHLIECQLSKVATLRGD 647

Query: 1151 KIKSLINDYKANGDISPLRSFL 1172
            +  +          +S L   +
Sbjct: 648  EGDATPFTKVTVTQVSELLRTM 669


>gi|51103945|gb|AAT96678.1| RpoB [Corynebacterium sp. 110960]
          Length = 146

 Score =  208 bits (530), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 63/174 (36%), Positives = 91/174 (52%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G  +                            + E +    
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWNVDV----------------------NDPKNAELLKMLP 37

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
            ++     A+        +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +
Sbjct: 38   EELYDVPADSLT-----ATPVFDGATNEEISRLLASSKPNRDGDVLVDEHGKARLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|161331465|gb|ABX60650.1| RpoB [Bacillus sp. FSL_h8483]
 gi|161331467|gb|ABX60651.1| RpoB [Bacillus sp. FSL_h8484]
          Length = 232

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 105/207 (50%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++ PGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELSPGVNQLVRAYIVQKRKISVGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARLLGVHMASPVFDGANEEDVWNT---- 194

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G    T ++DG                   
Sbjct: 195  ---------------------MEEAGLNRDG---KTTLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGVMYMIKL 231



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 90


>gi|153958279|gb|ABS53429.1| RpoB [Bacteriovorax sp. IP]
          Length = 339

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 157/342 (45%), Positives = 223/342 (65%), Gaps = 10/342 (2%)

Query: 729  AKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
            +  AG V  VD+ RIVI+  +   +   SGVDIY+L+K+ R+NQNTC NQ+ LVK GD V
Sbjct: 1    SDHAGRVIFVDSNRIVIQRDQ--FEEGQSGVDIYKLLKYSRTNQNTCSNQKALVKEGDIV 58

Query: 789  RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
             +  +IADGP T +GDLALG+N+LVAFMPW GYN+EDS+LI+E +++ DVFTS+HIE FE
Sbjct: 59   TKGMVIADGPGTHMGDLALGQNVLVAFMPWGGYNYEDSILINEGLLARDVFTSVHIESFE 118

Query: 849  VMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
            V ARDTKLG EEITRDIPNVSEE LK++DE GII +GA + PGDILVGKITPKGE+ ++P
Sbjct: 119  VEARDTKLGKEEITRDIPNVSEEALKDLDEAGIIRIGAIIKPGDILVGKITPKGETQLSP 178

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
            EEKLL+AIFG+KA DV+DTSLRV S V GTV+D +++ R G++   RS  +  ++  L+ 
Sbjct: 179  EEKLLKAIFGDKAGDVKDTSLRVSSSVRGTVIDAKVYTREGVELCARSKDIIDQESTLIR 238

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGP-------KGFKKSTVLSSDLISEYPRSQW 1021
            RD+  E   +  +   ++ ++L G              +   K   L+S++++  P    
Sbjct: 239  RDERIEIKAIQTSSIMKIADMLGGAKTTDKLVSEDGSTELLGKGVELTSEVLASIPFELI 298

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
                ++   ++  +           + +  +  ++I K+  G
Sbjct: 299  GYLPLE-ASLEEQLGEYFADVRNRINRVRTKSNDEIAKLHRG 339


>gi|40644545|emb|CAD88975.1| DNA-directed RNA polymerase subunit B [Myrtus communis]
          Length = 572

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 74/484 (15%), Positives = 130/484 (26%), Gaps = 79/484 (16%)

Query: 798  PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
             +T +                          I   ++     + I   +     R+T   
Sbjct: 162  ETTMISMTINDLVQARLXXEXAYSETYTHCEIHPSLILGVCASIIPFPDHNQSXRNTYQS 221

Query: 858  PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                      V+    +      +  V        +    +       +      + AI 
Sbjct: 222  AMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIA 278

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +        +F R   D+ ++  ++ +E      R        
Sbjct: 279  CYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRH 337

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
               +          G           K+T ++         S+                 
Sbjct: 338  GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAXXXXXXGXASR----------------- 380

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
                Y      +  R        Q         LR VKV V   R  Q GDK + RHG K
Sbjct: 381  ----YSRRDHSISLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQK 436

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G V      EDMP+  +G   DI++NP  +PSRM +GQ+    +G     +GK+  +   
Sbjct: 437  GTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIXCIMGKVAAHMGKEGDATPF 496

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                  +IS         +                                         
Sbjct: 497  TDVTVDNISKALHKCGYQMRGFETM----------------------------------- 521

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                         +G +    G         + +G  Y  +L HMV DK+++R  G   +
Sbjct: 522  ------------YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 562

Query: 1278 VTQQ 1281
            +T+Q
Sbjct: 563  LTRQ 566



 Score =  106 bits (265), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 71/482 (14%), Positives = 139/482 (28%), Gaps = 95/482 (19%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 6   EGQACGLVKNLALMVYVTVGSAAYPILEFLEEWGTENFEEISPVVIPQATKIFVNGCWVG 65

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 66  IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 124

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                   +    G  +       +      + Y+   EEE   I+              
Sbjct: 125 KKKDIHALQQREEGPDDVG---WHNLVAKGFIEYIDTEEEETTMISM----------TIN 171

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 172 DLVQARLXXE--XAYSETYTHCEIHPSLILGVCASIIPFPDHNQSXRNTYQSAMGKQAMG 229

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +      F                    R   +  V                        
Sbjct: 230 IYVTNYQF--------------------RMDTLAYV------------------------ 245

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 246 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 284

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 285 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLD 344

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP                        RD S+ +    +G
Sbjct: 345 DDGLAPPGTRVSGEDVIIGKTTPIAXXXXXXGXA--------SRYSRRDHSISLRHSETG 396

Query: 938 TV 939
            V
Sbjct: 397 IV 398


>gi|51103921|gb|AAT96666.1| RpoB [Corynebacterium pseudogenitalium]
          Length = 146

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 94/174 (54%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G KI +     +   +   L+   E++      +       
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWKIDT-----EDPANADLLKKLPEELYDVPPESLT----- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPYMYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|134141849|gb|ABO61289.1| RpoB [Klebsiella variicola]
          Length = 197

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 125/195 (64%), Positives = 155/195 (79%)

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT 564
           NAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPT
Sbjct: 2   NAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT 61

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N
Sbjct: 62  HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGN 121

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+
Sbjct: 122 YVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEH 181

Query: 685 DDSNRVLMGCNMQRQ 699
           DD+NR LMG NMQRQ
Sbjct: 182 DDANRALMGANMQRQ 196


>gi|68131844|gb|AAY85200.1| RNA polymerase II second largest subunit [Coriaria sarmentosa]
          Length = 952

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 119/907 (13%), Positives = 261/907 (28%), Gaps = 162/907 (17%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTK--VFIGKVPIMLRSSYCTL 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  + 
Sbjct: 65  FQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAFV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 AEVR----SMAESQNRPPSTMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFADTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEFCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N +  +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++       + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +    E    +  +   RR   +  + GV R     E+R ++  +     P    E 
Sbjct: 470 GCWVGIHREPDMLVKTLRRLRRRVDVNTEVGVVRDIRLRELR-IYTDYGRCSRPLFIVEK 528

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             + L+      A        +       D      + Y+   EEE   I+         
Sbjct: 529 QRL-LIRKKDIHALQQRESPEDGG---WHDLVSKGFIEYIDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +LV  R + E      +     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 577 --TIRDLVQARNSPE--EAYSDNYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +      F                    R   +  V                   
Sbjct: 633 KQAMGIYVTNYQF--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G   +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGIYAIVAIAC 687

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + GYN EDS+++++  +    F S+    +    +      +E        +   +    
Sbjct: 688 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGS 747

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +                      D S+ + 
Sbjct: 748 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE--------AQGQAAARYTRSDHSISLR 799

Query: 933 SGVSGTV 939
              +G V
Sbjct: 800 HSETGIV 806



 Score =  204 bits (518), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 80/481 (16%), Positives = 133/481 (27%), Gaps = 85/481 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + +   +      S  + DL   RN           +      I   ++    
Sbjct: 555  LVSKGFIEYIDTEEEETTMISMTIRDLVQARNSP----EEAYSDNYTHCEIHPSLILGVC 610

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+    +      +  V        +    +
Sbjct: 611  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAM 667

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        +F R   D+ ++  +
Sbjct: 668  EHLHFRQLPAGIYAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGT 726

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E      R           +          G           K+T ++ D       
Sbjct: 727  LVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQD------- 779

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                                  +Y  S   +  R        Q         LR VKV V
Sbjct: 780  --------------EAQGQAAARYTRSDHSISLRHSETGIVDQVLLTTNADGLRFVKVRV 825

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 826  RSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIE 885

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+                                               
Sbjct: 886  CIMGKVAAHMGKEGD--------------------------------------------- 900

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     + I+  L        G   +Y+G TG      + +G  Y  +
Sbjct: 901  --------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRQLSAMIFLGPTYYQR 951

Query: 1259 L 1259
            L
Sbjct: 952  L 952


>gi|145342313|gb|ABP64853.1| RpoB [Bacillus subtilis]
 gi|145342315|gb|ABP64854.1| RpoB [Bacillus subtilis]
 gi|161331489|gb|ABX60662.1| RpoB [Bacillus amyloliquefaciens]
          Length = 232

 Score =  208 bits (530), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 79   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGIMYMIKL 231



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIIHDVKVFNREDGD 90


>gi|145342291|gb|ABP64842.1| RpoB [Bacillus pumilus]
 gi|145342307|gb|ABP64850.1| RpoB [Bacillus pumilus]
 gi|145342319|gb|ABP64856.1| RpoB [Bacillus pumilus]
 gi|145342321|gb|ABP64857.1| RpoB [Bacillus pumilus]
 gi|145342323|gb|ABP64858.1| RpoB [Bacillus pumilus]
 gi|145342327|gb|ABP64860.1| RpoB [Bacillus pumilus]
 gi|145342393|gb|ABP64893.1| RpoB [Bacillus pumilus]
 gi|146217887|gb|ABQ11023.1| RNA polymerase beta subunit [Bacillus pumilus]
 gi|161331451|gb|ABX60643.1| RpoB [Bacillus pumilus]
 gi|161331455|gb|ABX60645.1| RpoB [Bacillus pumilus]
 gi|161331475|gb|ABX60655.1| RpoB [Bacillus pumilus]
 gi|161331479|gb|ABX60657.1| RpoB [Bacillus pumilus]
 gi|161331485|gb|ABX60660.1| RpoB [Bacillus pumilus]
 gi|161331487|gb|ABX60661.1| RpoB [Bacillus pumilus]
 gi|161331493|gb|ABX60664.1| RpoB [Bacillus pumilus]
          Length = 232

 Score =  208 bits (529), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 79   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGIMYMIKL 231



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 57/89 (64%), Positives = 70/89 (78%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIIHDVKVFNREDGD 90


>gi|161331491|gb|ABX60663.1| RpoB [Bacillus pumilus]
          Length = 232

 Score =  208 bits (529), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++S+ILP EDMP+L
Sbjct: 79   HDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E H+G A   LG  I S + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGIMYMIKL 231



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R IPNV E+ L+N+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RYIPNVGEDALRNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G + DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIIHDVKVFNREDGD 90


>gi|300394708|gb|ADK11892.1| DNA-directed RNA polymerase II subunit two [Hydnomerulius pinastri]
          Length = 358

 Score =  208 bits (529), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 71/444 (15%), Positives = 123/444 (27%), Gaps = 88/444 (19%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  +   ++            ++       +G       +          
Sbjct: 1    WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S V
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSV 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD          +       I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 169  SGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  IVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E++++ LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            +Y G TG+     V +G  Y  +L
Sbjct: 335  MYHGHTGKKLQAQVYLGPTYYQRL 358



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 90/285 (31%), Gaps = 74/285 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ + AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  V   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       I++ G+I  G  V+  DI++
Sbjct: 116 SIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           GK  P         E+L +        DV        +G+   V+
Sbjct: 176 GKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 216


>gi|256809235|gb|ACV30718.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
          Length = 167

 Score =  208 bits (529), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 96/167 (57%), Positives = 121/167 (72%), Gaps = 1/167 (0%)

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD E+ILST
Sbjct: 1   THSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEDILST 60

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY  + Y++ GD W   L +AD   G K+ S L+D DTGE V+E+GKKLT+   K L EK
Sbjct: 61  FYKTVTYTRDGDNWRI-LYSADRFKGMKIISDLIDADTGEVVLEAGKKLTARSAKQLAEK 119

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
           G+K +  T D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  
Sbjct: 120 GLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLID 166


>gi|66854105|gb|AAY57361.1| RpoB [Prevotella oulorum]
          Length = 124

 Score =  208 bits (529), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 69/178 (38%), Positives = 86/178 (48%), Gaps = 54/178 (30%)

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP+GVPSRMN               LG+  ++++                          
Sbjct: 1    NPMGVPSRMN---------------LGQIFEAILG------------------------- 20

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                          A   K G   +TP+FDGA  E + +    A L     + +YDG TG
Sbjct: 21   --------------AAGQKLGCKFATPIFDGAKLEDLKAWTDKAGLPNLCSTYIYDGETG 66

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            E FD+P TVG  Y LKL HMV DK++ARS G YSL+TQQPLGGK+  GGQR GEMEVW
Sbjct: 67   EKFDQPATVGITYFLKLGHMVEDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVW 124


>gi|145342311|gb|ABP64852.1| RpoB [Bacillus sp. FSL_H7-431]
          Length = 232

 Score =  208 bits (528), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 79/207 (38%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVASPVFDGAREEDVWSTIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMARDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGVMYMIKL 231



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GI+ VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIVRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|51103943|gb|AAT96677.1| RpoB [Corynebacterium sp. 2300500]
          Length = 146

 Score =  208 bits (528), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 62/174 (35%), Positives = 90/174 (51%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G  I                              +  +   
Sbjct: 1    RMNIGQVLEVHLGWLAAA-GWHID---------------------------PEDVKNAKL 32

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
             +++        +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +
Sbjct: 33   LETLPEELYDVPAGSLTATPVFDGATNEELAGLLANSLPNRDGDVMVDENGKAQLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPFPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|2736123|gb|AAB94062.1| RPB140 [Aristolochia gigantea]
          Length = 555

 Score =  208 bits (528), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 115/703 (16%), Positives = 191/703 (27%), Gaps = 148/703 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L   A +   G   TP     +     D   +SA      
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMAYIT-VGSATTPITAFLEEWGMEDFGEISAAVIPQA 59

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                 N          E LV                  +D + +  V    SL       
Sbjct: 60   TKVFLNGCWVGIHRNPELLVKTLRQLR---------RRVDVNTEVGVVRDVSLKELRVYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +      L+K             +   S     ++  G    V   +  +
Sbjct: 111  DYGRCSRPLFIVENQRLLIK------------KMDILSLQQRESEEEGWHSLV--EKGYV 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              ++ + + +T        + F R N                          PS  LG  
Sbjct: 157  EYIDTEEEETTMISMTIADLAFARENPEEAY-----------CTTYTHCEIHPSMILGVS 205

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            A       + +P+  +N          M  + +     +       R             
Sbjct: 206  A-------SIIPFPDHNQSPRNTYQSAMGKQAMG----MYVTNYQLRMDTQAYVLYYPQK 254

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            P V+    +++                             +      + AI      +  
Sbjct: 255  PLVTTHATEHL-------------------------HFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ +R  ++ +E+     R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKRMGTLVQEEFGRPNRENTMGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K++ +  + +      Q  +F  +D  +              
Sbjct: 349  DGFAPPGTRISGDDVIIGKTSPIPQEELPG----QLSKFTKRDHSIS------------- 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                  R        Q         LR  K+ V   R +Q GDK + RHG KG V     
Sbjct: 392  -----LRHSESGVVDQVLYTTNAEGLRFTKIRVRSVRILQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  DG   DI++NP  +PSRM +GQ+ E  +G     +GK+  +          I
Sbjct: 447  QEDMPWTIDGITPDIIVNPHAIPSRMTIGQLIECVMGKVAAEVGKEGDATPFTEVTVDGI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                           G       +M   
Sbjct: 507  CKRLHEC----------------------------------------GFQMRGFETM--- 523

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                 +G +    G         + VG  Y  +L HMV DK++
Sbjct: 524  ----YNGHT----GR---RLPAMIFVGPTYYQRLKHMVDDKIH 555



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 74/489 (15%), Positives = 142/489 (29%), Gaps = 98/489 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +     + ++   +     I+A  +  A   F     + 
Sbjct: 11  EGQACGLVKNLALMAYITVGSATTPITAFLEEWGMEDFGEISAAVIPQATKVFLNGCWVG 70

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R  +  E+R V+  +     P    E   + L
Sbjct: 71  IHRNPELLVKTLRQLRRRVDVNTEVGVVRDVSLKELR-VYTDYGRCSRPLFIVENQRL-L 128

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           +  +   +        E  +  V  G     V Y+   EEE   I+   + L       E
Sbjct: 129 IKKMDILSLQQRESEEEGWHSLVEKGY----VEYIDTEEEETTMISMTIADLAFARENPE 184

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           E                     +  P  ++ ++AS+IPF +++ S R      M +QA+ 
Sbjct: 185 E------------AYCTTYTHCEIHPSMILGVSASIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R      V                        
Sbjct: 233 MYVTNYQL--------------------RMDTQAYV------------------------ 248

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 249 -----------LYYPQKPLV----------TTHATEHLHFRQLPAGINAIVAIACYSGYN 287

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 288 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKRMGTLVQEEFGRPNRENTMGMRHGSYDKLD 347

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G    G  ++  D+++GK +P  +  +                  RD S+ +    SG
Sbjct: 348 DDGFAPPGTRISGDDVIIGKTSPIPQEEL---------PGQLSKFTKRDHSISLRHSESG 398

Query: 938 TVVDVRIFN 946
            V  V    
Sbjct: 399 VVDQVLYTT 407


>gi|270585805|ref|ZP_06221388.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            HK1212]
 gi|270318541|gb|EFA29617.1| DNA-directed RNA polymerase, beta subunit [Haemophilus influenzae
            HK1212]
          Length = 151

 Score =  208 bits (528), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 77/151 (50%), Positives = 107/151 (70%)

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
             +  R++W +  + DE+ Q  +E L  QYE  +   E + + K +KI  GDD+ PGVL+V
Sbjct: 1    DKVERTKWLEQTIADEEKQNQLEQLAEQYEELRKEFEHKLEVKRKKIIKGDDLAPGVLKV 60

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV++A+KR IQ GDKMAGRHGNKG++S+I P EDMP+ ++G PV+IVLNPLGVPSRMN+
Sbjct: 61   VKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVEIVLNPLGVPSRMNI 120

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            GQI ETHLG A  G+G +I +++   +    
Sbjct: 121  GQILETHLGLAAKGIGDQINAMLKQKQEVEK 151


>gi|218937982|gb|ACL13132.1| RNA polymerase II second largest subunit [Arthonia caesia]
          Length = 685

 Score =  208 bits (528), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 111/807 (13%), Positives = 214/807 (26%), Gaps = 143/807 (17%)

Query: 474  QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + I +  +              I    +   +     +            
Sbjct: 3    LFRSNFQKLTKDIYKYLQRCVETNREFNLAMAIKPNTITQGLRYSLATGNWGDQKKAAKA 62

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       + ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 63   KAGVSQVLSRYTFAAALSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 118

Query: 579  NIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L+    V+     E     +      +  +            ++      +  
Sbjct: 119  ACGLVKNLSLMCYVSVGTPGEPLLEFMSSLAMDLLEEYDPKHNPNATKIFLNGVWVGVSY 178

Query: 637  DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN--DDSNRVLMGC 694
            D       +        +      +  I     ++ S A  ++  L    +D      G 
Sbjct: 179  DPQHLVRRLQELRRNGTLRYEITLVHDIREREFKIFSDAGRVMRPLYVIENDPRSANCGN 238

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
                     L      +   +ES+  + SG      + G    VD    VI  ++ + + 
Sbjct: 239  ---------LVFNRSHLDKLVESMNPEFSGD-----KYGWSSLVD--EGVIEFLDAEEEE 282

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            S   +     +   R  Q     Q P               D             N    
Sbjct: 283  SALIIMSPNDLAELRERQ-EFGTQAP-------------APDDDDLTKRVKPKIENPH-- 326

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             + +       SM++              I  F++                  ++    +
Sbjct: 327  GLSYTHCEIHPSMILGVCAS---------IIPFQITIXXXXXXXXXXXXXXIFLTNYAQR 377

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 378  M---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSS 434

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    +F R  +D  +R      E+ E   R+          +       +  G  
Sbjct: 435  IDRGLF-RSLFYRTYMDNQKRIGINTTEEFEKPQRNTTLRMRQGTYDKLDDDGFVAPGVR 493

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L++D      R++          ++     +  Q             
Sbjct: 494  ISGDDIIIGKTAPLAADAEESGMRTKMHTRRDISMPLRGTEAGIVDQVV----------- 542

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            LR +KV     +  Q GDK A RHG KG +      EDMPF  +
Sbjct: 543  ----------LTSSEGLRFIKVRTRTTKTPQIGDKFASRHGQKGTIGITYRQEDMPFTAE 592

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G++  +          +S L    E+
Sbjct: 593  GVVPDLIINPHAIPSRMTIAHLIECLLSKLATLSGREGDATPFTGLTVELVSKLLR--ER 650

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                                                    +G +
Sbjct: 651  GYQGRGFEVM---------------------------------------------YNGHT 665

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G         + +G  Y  +L H
Sbjct: 666  ----GR---KLRAQIFLGPTYYQRLRH 685



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 60/442 (13%), Positives = 113/442 (25%), Gaps = 49/442 (11%)

Query: 375 LDIYRVM-RPGDV-STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            DIY+ + R  +    F++A ++         +Y L   G      +         + + 
Sbjct: 13  KDIYKYLQRCVETNREFNLAMAIKPNTITQGLRYSL-ATGNWGDQKKAAKAKAGVSQVLS 71

Query: 433 KEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK 487
           +    A +  L        R+GK       +  +  +    E  + Q    +  +     
Sbjct: 72  RYTFAAALSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 131

Query: 488 ERISSVDI--------------DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
             + +                 +   P+   NA  +         S     L   +  L 
Sbjct: 132 VSVGTPGEPLLEFMSSLAMDLLEEYDPKHNPNATKIFLNGVWVGVSYDPQHLVRRLQELR 191

Query: 534 RITHTRRLSALGQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
           R    R    L      R         R + P +     P   + G+ +   S L     
Sbjct: 192 RNGTLRYEITLVHDIREREFKIFSDAGRVMRPLYVIENDPRSANCGNLVFNRSHLDKLVE 251

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT---------- 641
            +                    + +L A EEE+  I  + + L E               
Sbjct: 252 -SMNPEFSGDKYGWSSLVDEGVIEFLDAEEEESALIIMSPNDLAELRERQEFGTQAPAPD 310

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF-------------LENDDSN 688
           ++ +  R   +            +  P  ++ + AS+IPF                    
Sbjct: 311 DDDLTKRVKPKIENPHGLSYTHCEIHPSMILGVCASIIPFQITIXXXXXXXXXXXXXXIF 370

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
                  M   A  L   + P   T  ME +  +   A   A  A            +  
Sbjct: 371 LTNYAQRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIM 430

Query: 748 VEGDLDPSTSGVDIYRLMKFQR 769
            +  +D        YR     +
Sbjct: 431 NQSSIDRGLFRSLFYRTYMDNQ 452


>gi|256809191|gb|ACV30696.1| DNA-dependent RNA polymerase beta subunit [Ochrobactrum anthropi]
          Length = 167

 Score =  208 bits (528), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 96/167 (57%), Positives = 120/167 (71%), Gaps = 1/167 (0%)

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST 231
              SGKLL+A R+IP +G W+DIEFDSKDI++ RIDRRRK+P T+ LMALGMD E+ILST
Sbjct: 1   THSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEDILST 60

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           FY  + Y++ GD W  P SA D   G K+ S L+D DTGE V+E+GKKLT+   K L EK
Sbjct: 61  FYKTVTYTRDGDNWRIPYSA-DRFKGMKIISDLIDADTGEVVLEAGKKLTARSAKQLAEK 119

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            +K +  T D L G Y+AED+VN  TGEIY+EAGD IDEK L+ +  
Sbjct: 120 SLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLID 166


>gi|161331463|gb|ABX60649.1| RpoB [Bacillus cereus]
          Length = 230

 Score =  208 bits (528), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 77   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 136

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 137  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 196

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 197  GMANDAK----------------------------TILYDG------------------- 209

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 210  -------RTGEPFDNRVSVGVMYMIKL 229



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 57/88 (64%), Positives = 70/88 (79%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           DIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +
Sbjct: 1   DIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKARE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 61  VRDTSLRVPHGGGGIILDVKVFNREDGD 88


>gi|30141073|gb|AAP21847.1| RNA polymerase beta subunit [Enterococcus faecium]
          Length = 232

 Score =  207 bits (527), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 79   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 186

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 187  ----------------SDEDVWETVREAGMASDAKTVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDGRVSVGVMYMIKL 231



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGGGIVHDVKIFTREAGD 90


>gi|145342301|gb|ABP64847.1| RpoB [Bacillus cereus]
 gi|145342305|gb|ABP64849.1| RpoB [Bacillus cereus]
 gi|145342333|gb|ABP64863.1| RpoB [Bacillus weihenstephanensis]
 gi|145342361|gb|ABP64877.1| RpoB [Bacillus weihenstephanensis]
 gi|145342365|gb|ABP64879.1| RpoB [Bacillus cereus]
 gi|145342375|gb|ABP64884.1| RpoB [Bacillus weihenstephanensis]
 gi|161331457|gb|ABX60646.1| RpoB [Bacillus cereus]
 gi|161331461|gb|ABX60648.1| RpoB [Bacillus sp. FSL_h8481]
 gi|161331469|gb|ABX60652.1| RpoB [Bacillus weihenstephanensis]
 gi|161331473|gb|ABX60654.1| RpoB [Bacillus weihenstephanensis]
 gi|161331513|gb|ABX60674.1| RpoB [Bacillus sp. FSL_h8546]
          Length = 232

 Score =  207 bits (527), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMANDAK----------------------------TILYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGVMYMIKL 231



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIILDVKVFNREDGD 90


>gi|30141077|gb|AAP21849.1| RNA polymerase beta subunit [Enterococcus saccharolyticus]
          Length = 232

 Score =  207 bits (527), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 81/207 (39%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 79   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 186

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             DD V     +        T ++DG                   
Sbjct: 187  ----------------SDDDVWETVREAGMARDAKTVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  ++VG +YM+KL
Sbjct: 212  -------RTGEPFDGRISVGVMYMIKL 231



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA 
Sbjct: 2   REIPNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGGGIVHDVKIFTREAGD 90


>gi|46277281|gb|AAS86831.1| RNA polymerase II second largest subunit [Arceuthobium campylopodum]
          Length = 584

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 111/735 (15%), Positives = 209/735 (28%), Gaps = 151/735 (20%)

Query: 525  LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
            +   +   S ++H RRL++     + R     + R +H + +G + PAET EG   GLV 
Sbjct: 1    VLNRLTYASTLSHLRRLNS----PIGREGKLPKPRQLHNSQWGMMXPAETPEGQACGLVK 56

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            +L     +            + +    N        EE +  +   ++ +  +G +    
Sbjct: 57   NLALMVYITVGSAAYPILEFLEEWGTEN-------FEEISPAVIPQSTKIFVNGCWVG-- 107

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
               R     +   R     +D + +  V     L       D  R      +  +   L+
Sbjct: 108  -IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDICLKELRLYTDYGRCSRPLFIVDEQRLLI 166

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            K +            A   G        G +E +D        +   ++   +G      
Sbjct: 167  KKKDIQALQ---QRDASEEGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVNGRLNLDD 223

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                                    +        PS  LG       +  + +P+  +N  
Sbjct: 224  A---------------------YSKTYTHCEIHPSLILG-------VCASIIPFPDHNQS 255

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +     I       R   L         P V+   ++++        
Sbjct: 256  PRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHL-------- 303

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                                 +      + AI      +  D+ +   S +        +
Sbjct: 304  -----------------HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 345

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ ++  ++ +E      R           +          G           K
Sbjct: 346  FFRSYRDEEKKMGTLIKEDFGRPNRTDTMGMRHGSYDKLDDDGLAPPGTKVTGENVIIGK 405

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            ++ ++                  DE  +++    K  + TS    E+   +++      D
Sbjct: 406  TSPIAP-----------------DESQEQSFRYTKRDHSTSLRHSENGVVDQVLLTTNAD 448

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV V   R  Q GDK + RHG KG +      EDMP+  +G   DI++NP
Sbjct: 449  GL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWTVEGITPDIIVNP 503

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM + Q+ E  +G     +GK+  +         +IS                  
Sbjct: 504  HAIPSRMTIAQLIECIMGKVAAHMGKEGDATPFTDVTVDNISQALHKCGY---------- 553

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                   +M   +      +Y+G TG  
Sbjct: 554  ---------------------------------------QMHGFET-----MYNGHTGRK 569

Query: 1245 FDRPVTVGYIYMLKL 1259
                + +G  Y  +L
Sbjct: 570  LTSMIFIGPTYYQRL 584


>gi|283132441|dbj|BAI63626.1| rpoB protein [Corynebacterium propinquum]
          Length = 147

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 66/175 (37%), Positives = 94/175 (53%), Gaps = 36/175 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+    ND +    I  L   L  V              
Sbjct: 1    RMNIGQVLEIHLGWLAHA-GWKVD--PNDPQNEELIKTLPKELYDVPANSLT-------- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  E ++ +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGASNEEVSGLLANSRPNRDGNVMVDRHGKARLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            GEPF+ P++VGY+Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR GE
Sbjct: 93   GEPFEHPISVGYMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 147


>gi|46277374|gb|AAS86877.1| DNA-dependent RNA polymerase II [Peziza arvernensis]
          Length = 563

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 101/681 (14%), Positives = 181/681 (26%), Gaps = 122/681 (17%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     E    +    + +V  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
              F    +        I      I D  +   K          P    D+         +
Sbjct: 62   PGFIVRTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGEL 121

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              Q   + K E     T  E      SG        G+VE +DA       +    +   
Sbjct: 122  VLQKHHIEKLEDDKDITDEEQRYGW-SGL----IGEGVVEYIDAEEEETVMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            +    +   + Q+        QR    V             PS  LG       +  + +
Sbjct: 177  TSRQFHAGYEIQQEVDPA---QRVKASVNKYAHTWTHCEIHPSMILG-------ICASII 226

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  F    R+                       
Sbjct: 227  PFPDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM--------------------- 259

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 260  --DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 317

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +    +F R  +D+ +R      E+     R           +       +  G    
Sbjct: 318  RGLF-RSLFYRTYMDQEKRVGMNVVEEFGKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVS 376

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+  +S ++     R+++         ++     +  Q               
Sbjct: 377  GEDIIIGKTAPISPNMEELGQRTKFHTRRDVSTPLRSTENGIVDQ--------------- 421

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 422  -----VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGV 476

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +  + E  L       G +                         
Sbjct: 477  VPDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------------- 513

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     ++++ +LR       G  I+
Sbjct: 514  ------------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEIM 542

Query: 1237 YDGLTGEPFDRPVTVGYIYML 1257
            Y+G TG      V +G  Y  
Sbjct: 543  YNGHTGRKLVVQVFLGPTYYQ 563



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 74/482 (15%), Positives = 131/482 (27%), Gaps = 88/482 (18%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 25  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 78

Query: 545 G-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           G +  + +     E        R   P       PA    G  +     +          
Sbjct: 79  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKDIT 138

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCA 650
             E  Y           V Y+ A EEE   I      L+    F       +E+   +  
Sbjct: 139 DEEQRY-GWSGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEVDPAQRV 197

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
              +          +  P  ++ I AS+IPF +++ S R      M +QA+ +       
Sbjct: 198 KASVNKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---- 253

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                       + A I+                                    +KF+  
Sbjct: 254 -----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFREL 287

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                     L   G   + + +I +  S D G                  + E  + ++
Sbjct: 288 PAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLFY-------RTYMDQEKRVGMN 339

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                        +EEF    R           +   +       +DE G++  G  V+ 
Sbjct: 340 ------------VVEEFGKPTR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSG 377

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P      +P  + L      K    RD S  + S  +G V  V +      
Sbjct: 378 EDIIIGKTAPI-----SPNMEELGQR--TKFHTRRDVSTPLRSTENGIVDQVMVTTNQEG 430

Query: 951 DK 952
            K
Sbjct: 431 LK 432


>gi|51103925|gb|AAT96668.1| RpoB [Corynebacterium sp. CCUG 18436]
 gi|51103927|gb|AAT96669.1| RpoB [Corynebacterium sp. CCUG 18437]
          Length = 146

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 62/174 (35%), Positives = 95/174 (54%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +     +   +   L++  E++    +++       
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWKVDT-----EDPKNAELLKTLPEELYDVPANSLT----- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA    I  +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|161331447|gb|ABX60641.1| RpoB [Bacillus thuringiensis]
          Length = 231

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 78   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 137

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 138  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 197

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 198  GMANDAK----------------------------TILYDG------------------- 210

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 211  -------RTGEPFDNRVSVGVMYMIKL 230



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 1   RDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 60

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 61  EVRDTSLRVPHGGGGIILDVKVFNREDGD 89


>gi|30141066|gb|AAP21844.1| RNA polymerase beta subunit [Granulicatella adiacens]
          Length = 231

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/204 (38%), Positives = 103/204 (50%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++     GD++ PGV ++V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL DG
Sbjct: 82   RVFTRAAGDELAPGVNKLVRVYIVQKRKINEGDKMAGRHGNKGVVSRIMPEEDMPFLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+    +     
Sbjct: 142  TPVDIMLNPLGVPSRMNIGQVLELHLGMAARELGIYIATPVFDGAQDEDVWGTVAEAGMA 201

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 202  RDAK----------------------------TILYDG---------------------- 211

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
                 TGEPFD  V+VG +YM+KL
Sbjct: 212  ----RTGEPFDNRVSVGVMYMIKL 231



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 62/114 (54%), Positives = 78/114 (68%), Gaps = 7/114 (6%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E+ LKN+D  GII +GAEV  GDILVGK+TPKG +  +PEE+LL AIFGEKA 
Sbjct: 2   REIPNVGEDALKNLDADGIIRIGAEVKDGDILVGKVTPKGLTEQSPEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNR-------HGIDKNERSISVEREQIELLAR 969
           +VRDTSLRVP G  G V DVR+F R        G++K  R   V++ +I    +
Sbjct: 62  EVRDTSLRVPHGGGGIVRDVRVFTRAAGDELAPGVNKLVRVYIVQKRKINEGDK 115


>gi|157781357|gb|ABV72033.1| RNA polymerase beta subunit [Enterococcus hermanniensis]
          Length = 226

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQ----------- 183

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D  V     + +      T ++DG                   
Sbjct: 184  -----------------DSDVWETVREARMAADAKTVLYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDNRISVGVMYMIK 226



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|30141079|gb|AAP21850.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 232

 Score =  207 bits (527), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/204 (38%), Positives = 103/204 (50%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 82   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 141

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 142  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDVWSTVAEAGMA 201

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 202  KDAK----------------------------TVLYDG---------------------- 211

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
                 TGEPFD  V+VG +YM+KL
Sbjct: 212  ----RTGEPFDSRVSVGVMYMIKL 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/87 (64%), Positives = 65/87 (74%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R+IPNV E  L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ 
Sbjct: 2   REIPNVGENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSK 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           +VRDTSLRVP G  G V DV+IF R  
Sbjct: 62  EVRDTSLRVPHGADGVVADVKIFKRED 88


>gi|157781301|gb|ABV72005.1| RNA polymerase beta subunit [Enterococcus avium]
 gi|157781323|gb|ABV72016.1| RNA polymerase beta subunit [Enterococcus malodoratus]
 gi|157781353|gb|ABV72031.1| RNA polymerase beta subunit [Enterococcus raffinosus]
          Length = 226

 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQ----------- 183

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D  V     + +      T ++DG                   
Sbjct: 184  -----------------DSDVWETVREARMAADAKTVLYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDNRISVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV+ GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|51103923|gb|AAT96667.1| RpoB [Corynebacterium tuberculostearicum]
          Length = 146

 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 62/174 (35%), Positives = 94/174 (54%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +     +   +   L++  E++    + +       
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWKVDT-----EDPKNAELLKTLPEELYDVPADSLT----- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA    I  +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|283132437|dbj|BAI63624.1| rpoB protein [Corynebacterium pseudodiphtheriticum]
 gi|283132439|dbj|BAI63625.1| rpoB protein [Corynebacterium jeikeium]
          Length = 147

 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 66/175 (37%), Positives = 94/175 (53%), Gaps = 36/175 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+    ND +    I  L   L  V              
Sbjct: 1    RMNIGQVLEIHLGWLAHA-GWKVD--PNDPQNEELIKTLPKELYDVPAHSLT-------- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  E ++ +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGASNEEVSGLLANSRPNRDGNVMVDRHGKARLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            GEPF+ P++VGY+Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR GE
Sbjct: 93   GEPFEHPISVGYMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 147


>gi|161331445|gb|ABX60640.1| RpoB [Bacillus psychrodurans]
 gi|161331471|gb|ABX60653.1| RpoB [Bacillus psychrodurans]
 gi|161331499|gb|ABX60667.1| RpoB [Bacillus psychrodurans]
          Length = 232

 Score =  207 bits (526), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 80/207 (38%), Positives = 105/207 (50%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++ PGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELSPGVNQLVRAYIVQKRKISVGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASKLLGVHMASPVFDGANEEDVWNT---- 194

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                 +  A   + G    T ++DG                   
Sbjct: 195  ---------------------MEEAGLNRDG---KTILYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGVMYMIKL 231



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII +GAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRIGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIVLDVKVFNREDGD 90


>gi|157781339|gb|ABV72024.1| RNA polymerase beta subunit [Enterococcus canis]
          Length = 226

 Score =  207 bits (526), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 88/286 (30%), Positives = 120/286 (41%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  ++L G+    G         L   +  E  R           +V+
Sbjct: 12   DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR-----------EVR 60

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
                 +    +     +      KI   + GD++ PGV  +V+V++  KR I  GDKMAG
Sbjct: 61   DTSLRVPHGGDGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 115  RHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHV 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D     D+                                          T ++D
Sbjct: 175  ATPVFDGANEEDVWSTVQEAGLARDAK----------------------------TILYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           TGEP D  V+VG +YM+K
Sbjct: 207  G--------------------------RTGEPMDNRVSVGVMYMIK 226



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGDGIVHDVKIFTREAGD 86


>gi|304561482|gb|ADM43603.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 323

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 111/348 (31%), Positives = 171/348 (49%), Gaps = 35/348 (10%)

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL 221
           G++++    +    GK L +  +IP++G W++ E DS DI++VRIDR RKVPVT  L AL
Sbjct: 1   GVYYEQQFDKF---GKKLISATVIPNRGAWLEYEEDSNDIVYVRIDRTRKVPVTVLLRAL 57

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKK 279
           G  ++ +IL     +       D          L+   K       +  GE   +ES K 
Sbjct: 58  GYSTDIQILDLLGEEEKLKATLDKDTTKSEEEALIEIYK------RLRPGEPPTVESAKS 111

Query: 280 LTSGLLKSLKEKGVKFLGITSD--------CLCGLYVAEDIVNGETGEIYIEAGDVIDEK 331
           L   L    K   +  +G             +  L  A+ IVN  TGEI +E G+ I ++
Sbjct: 112 LLYALFFDAKRYDLAKVGRYKFNKKLALKTRIVNLKSAKKIVNPVTGEILVEEGEKISKE 171

Query: 332 SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
             EEI +  I  + +L    V     I N              +DI +   P DVS  ++
Sbjct: 172 KAEEIQNCGINVVEVLVEGKVVR--VIGNNT------------VDINKYPMPYDVSNLNI 217

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG 451
            E++   L    +  D  +     +N   N       ++I K+DIIA I   ++L +G G
Sbjct: 218 KEAV--NLSILKEILDNFSDEEAVINEIKNRMDELVPKNITKDDIIATISYQLNLTHGIG 275

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVM 499
           +IDDID+LGNRR+RSVGE+L+NQ+R+GL R+ER +KER++  D++ + 
Sbjct: 276 SIDDIDHLGNRRLRSVGELLQNQFRIGLARLERVVKERMTIQDVNEIT 323


>gi|94548941|gb|ABF38968.1| RNA polymerase beta subunit [Candidatus Liberibacter asiaticus]
          Length = 135

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 135/135 (100%), Positives = 135/135 (100%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK
Sbjct: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120
           SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK
Sbjct: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK 120

Query: 121 SIKDIKEQSIYMGDL 135
           SIKDIKEQSIYMGDL
Sbjct: 121 SIKDIKEQSIYMGDL 135


>gi|326909319|gb|AEA11034.1| RNA polymerase beta subunit [Xanthomonas axonopodis pv. alfalfae]
          Length = 204

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 120/204 (58%), Positives = 149/204 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  FAR N YGF+ETPYRKV DGKV++DV YLSA+EE    IAQAN+  D    
Sbjct: 61  IGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNM 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            TE+ V CR  GE +L P  ++ F+D SP Q VS+AA+L+PFLE+DD+ R LMG +MQRQ
Sbjct: 121 LTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDAYRALMGAHMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAKSS 723
           AV  L+++   VGTG+E  VA+ S
Sbjct: 181 AVATLRSQMRLVGTGIERAVARYS 204


>gi|17225284|gb|AAL37335.1| RNA polymerase B-subunit [Staphylococcus aureus]
          Length = 203

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 123/203 (60%), Positives = 155/203 (76%), Gaps = 2/203 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G
Sbjct: 61  GLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENG 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQR
Sbjct: 121 RFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQR 180

Query: 699 QAVPLLKAEAPFVGTGMESVVAK 721
           QAVPL+  EAPFVGTGME V A+
Sbjct: 181 QAVPLMNPEAPFVGTGMEHVAAR 203


>gi|17225282|gb|AAL37334.1| RNA polymerase B-subunit [Staphylococcus caprae]
          Length = 203

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 123/203 (60%), Positives = 155/203 (76%), Gaps = 2/203 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G
Sbjct: 61  GLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENG 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQR
Sbjct: 121 RFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQR 180

Query: 699 QAVPLLKAEAPFVGTGMESVVAK 721
           QAVPL+  EAPFVGTGME V A+
Sbjct: 181 QAVPLMNPEAPFVGTGMEHVAAR 203


>gi|140084098|gb|ABO84898.1| RpoB [Bacillus weihenstephanensis]
          Length = 231

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMANDAK----------------------------TILYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    TGEPFD  V+VG +YM+KL
Sbjct: 212  -------RTGEPFDNRVSVGVMYMIKL 231



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 58/90 (64%), Positives = 71/90 (78%)

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
            RDIPNV E+ L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA
Sbjct: 1   YRDIPNVGEDALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKA 60

Query: 922 VDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 61  REVRDTSLRVPHGGGGIILDVKVFNREDGD 90


>gi|21436697|emb|CAD34024.1| RNA polymerase beta-subunit [Enterobacteriaceae bacterium
           CF01Ent-1]
          Length = 199

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 124/198 (62%), Positives = 158/198 (79%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LD++  F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 122 IHYLSAIEEGNYVIAQANSNLDDENHFEEDLVTCRSRGESSLFSRDQVDYMDVSTQQVVS 181

Query: 674 IAASLIPFLENDDSNRVL 691
           + ASLIPFLE+DD+NR L
Sbjct: 182 VGASLIPFLEHDDANRAL 199


>gi|71841601|gb|AAZ43091.1| RNA polymerase II second largest subunit [Gunnera chilensis]
          Length = 534

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/481 (16%), Positives = 143/481 (29%), Gaps = 86/481 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + +   +      S  + +LA  RN+         Y       I   ++    
Sbjct: 138  LVSKGFIEYIDTEEEETTMISMTIQELANVRNVQQ----EAFYGLHTHCEIHPSLILGVC 193

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 194  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 250

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        +F R   D+ ++  +
Sbjct: 251  EHLHFRELPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGT 309

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E      RD          +          G           K+T ++         
Sbjct: 310  LVKEDFGRPNRDNTMGMRHGSYDKLDEDGLAPPGTRVAGEDVIIGKTTPIAQ-------- 361

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     D+   +     +  + TS    E    +++      D +     R VKV +
Sbjct: 362  ---------DDTQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRM 407

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 408  RSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIE 467

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +G++                                               
Sbjct: 468  CIMGKVAAHMGQEGD--------------------------------------------- 482

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     ++I+  L        G   +Y+G TG      + +G  Y  +
Sbjct: 483  --------ATP-FTEVTVDSISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQR 533

Query: 1259 L 1259
            L
Sbjct: 534  L 534



 Score =  112 bits (280), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 72/476 (15%), Positives = 134/476 (28%), Gaps = 97/476 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++  S    + I+   +  +   F     +       
Sbjct: 4   LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPESTKIFVNGCWVGIHRNPE 63

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + G+ R     E+R    T YGR             L+     
Sbjct: 64  LLVKTLRQLRRQVDVNTEVGIIRDIRLKELR--LYTDYGRCSRPLFIVDKQRLLIKKKDI 121

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A                D      + Y+   EEE   I+     L    +  +E  +  
Sbjct: 122 RA---LQQRENPDEMGWHDLVSKGFIEYIDTEEEETTMISMTIQELANVRNVQQEAFYGL 178

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                           +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 179 H------------THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 226

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                                 R   +  V                              
Sbjct: 227 QL--------------------RMDTLAYV------------------------------ 236

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PLV                     +L  G N +VA   + GYN EDS++
Sbjct: 237 -----LYYPQKPLV----------TTRAMEHLHFRELPAGINAIVAIACYSGYNQEDSVI 281

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIIC 883
           +++  +    F S+    +    +      +E        +   +       +DE G+  
Sbjct: 282 MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRDNTMGMRHGSYDKLDEDGLAP 341

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V   D+++GK TP  +                     RD S  +    SG V
Sbjct: 342 PGTRVAGEDVIIGKTTPIAQDD---------TQGQASRYTRRDHSTSLRHSESGMV 388


>gi|161331439|gb|ABX60637.1| RpoB [Bacillus badius]
          Length = 232

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 78/207 (37%), Positives = 103/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+V++  KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D     D+       
Sbjct: 139  PDGTPIDIMLNPLGVPSRMNIGQVMELHLGMAARYLGLHVATPVFDGATEDDVWETIEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMSRDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGIMYMIKL 231



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+DE GII +GAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDERGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|157781349|gb|ABV72029.1| RNA polymerase beta subunit [Enterococcus faecalis]
          Length = 226

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 182

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 183  ----------------TDEDVWETVREAGMASDAKTVLYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDNRISVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|120561267|gb|ABM27018.1| RNA polymerase II second largest subunit [Entophlyctis
            confervae-glomeratae]
          Length = 886

 Score =  206 bits (525), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 128/974 (13%), Positives = 260/974 (26%), Gaps = 149/974 (15%)

Query: 303  LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTL 362
            L    +A     G  G++   +   I       I    +  +    +       +  + +
Sbjct: 47   LFIKMLAPKGGKGTLGQVIRTSLPYIKADIPIIIVFRALGIVTDRDILEHVCYDFNDHQM 106

Query: 363  VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL 422
            +       ++A +   + +    +        +         +Y    + +  +     +
Sbjct: 107  LELLKPSVEEAFVIQDKEVALDFIGVRGTQMGV---SKDKRIRYATDILTKEMLPH---V 160

Query: 423  DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRM 482
                  +  +      +I  L+     +  +DD D+ G +R+   G +L + +R    ++
Sbjct: 161  SMESHHQTRKAFFFGYMIHRLLLAALERRPLDDRDHFGRKRLDLAGPLLSSLFRTLFRKL 220

Query: 483  ERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEE 527
               +      +            + +  +   +     +               +SQ+  
Sbjct: 221  TTDVSRYTKKIVETGGEFNLAMALKSATITKGLQYSLATGNWGDQKKFMSAKAGVSQVLN 280

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                 S ++H RRL+      + R     + R +H TH+G +CPAET EG   GLV +L+
Sbjct: 281  RYTYASTLSHLRRLNT----PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLS 336

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
              + ++  G                 +  +             N          E LV  
Sbjct: 337  LMSHIS-VGNDAKIVLPYLGEFGMETLEDIQPSMLPKATKVFLNGQWLGIHHEPETLVKT 395

Query: 648  RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
                        ++  +     + V +       +      +      + +     L+ +
Sbjct: 396  LRDLRRSADISTELSIVRDVSDKEVRLQTDYGRIMRPLLIVKEDYHLAITKGMARDLRPD 455

Query: 708  APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
                 + +      SSGA          E +D        +  D++             F
Sbjct: 456  VETGASALVWGDLLSSGAV---------EYLDTEEEETVMIAMDVEDVKRVRTERYGEVF 506

Query: 768  QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
             R  Q+     +         RR       PS  LG       +  + +P+  +N     
Sbjct: 507  VRPPQDITARLK---SKAAYARRFTHCEIHPSMILG-------ICASIIPFPDHNQSPRN 556

Query: 828  LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
                 M  + +   I +  ++                           +    +  +   
Sbjct: 557  TYQSAMGKQAMG--IFLTNYQ---------------------------LRMDTMANILFY 587

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
                      +       +   +  + AI      +  D+ +   S +   +    ++ R
Sbjct: 588  PQKPLATTRAMQFMHFRELPAGQNAIVAISTYSGYNQEDSLIMNQSSIDRGLF-RSMYYR 646

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              +D  ++   ++ E IE   R+          +       I  G           K+  
Sbjct: 647  VYMDTEKKIGMIDSETIEKPDREDCLRLKHGSYHKIDSDGLIAPGTRVSGEDIIIGKTVP 706

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +  D      R+           ++     +  Q   + +    +F     +        
Sbjct: 707  IKEDSSEMGQRTAAHTKRDASTPMKSTENGIVDQVMLTTNEAGYKFVKVRVRSVRV---- 762

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                             Q GDK A RHG KG V      EDMPF  +G   D+V+NP  +
Sbjct: 763  ----------------PQMGDKFASRHGQKGTVGITYRMEDMPFSGEGLSPDLVVNPHAI 806

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E  L       G +  +          IS                     
Sbjct: 807  PSRMTIGHLVECLLSKLSTFTGIEGDASPFTDVTVDQISKS------------------- 847

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                  L      K G  V                        +G +    G        
Sbjct: 848  ------LESFGYQKRGFEVL----------------------YNGHT----GR---KLQA 872

Query: 1248 PVTVGYIYMLKLNH 1261
             V  G  Y  +L H
Sbjct: 873  QVYFGPTYYQRLKH 886



 Score =  110 bits (274), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 100/769 (13%), Positives = 226/769 (29%), Gaps = 107/769 (13%)

Query: 203 HVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           +++ D    +P+     ALG+ ++ +IL          Q  +     +  A ++   +V+
Sbjct: 71  YIKAD----IPIIIVFRALGIVTDRDILEHVCYDFNDHQMLELLKPSVEEAFVIQDKEVA 126

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNG 315
              + +   +  +   K++       L ++ +  + +            G  +   ++  
Sbjct: 127 LDFIGVRGTQMGVSKDKRIRYAT-DILTKEMLPHVSMESHHQTRKAFFFGYMIHRLLL-A 184

Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDAL 374
                 ++  D    K L+            L+   + + + Y +  + T    +   AL
Sbjct: 185 ALERRPLDDRDHFGRKRLDLAGPLLSSLFRTLFRKLTTDVSRYTKKIVETGGEFNLAMAL 244

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVG-RVKMNMRLNLDTPDDVRHI-R 432
                        T  +  S+    + D  K+  +  G    +N      T   +R +  
Sbjct: 245 KSAT--------ITKGLQYSLATGNWGDQKKFMSAKAGVSQVLNRYTYASTLSHLRRLNT 296

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS 492
                  +     L N    +         +   + + L     + +    + +   +  
Sbjct: 297 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSHISVGNDAKIVLPYLGE 356

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVAR 551
             ++++   + I    +  A   F     L    E    +  +   RR + +  +  + R
Sbjct: 357 FGMETL---EDIQPSMLPKATKVFLNGQWLGIHHEPETLVKTLRDLRRSADISTELSIVR 413

Query: 552 ARAGVEMRDVHPTHYGRICPAETS-EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
             +  E+R +   +   + P     E +++ +   +    R +             D   
Sbjct: 414 DVSDKEVR-LQTDYGRIMRPLLIVKEDYHLAITKGMARDLRPDVETGASA--LVWGDLLS 470

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL------VPREKIDFI 664
           +  V YL   EEE   IA     +    +     VF R   +             +    
Sbjct: 471 SGAVEYLDTEEEETVMIAMDVEDVKRVRTERYGEVFVRPPQDITARLKSKAAYARRFTHC 530

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ I AS+IPF +++ S R      M +QA+ +                     
Sbjct: 531 EIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNYQL-------------- 576

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         + + +  Y       +     ++ R     
Sbjct: 577 ---------------------------RMDTMANILFYPQKPLATTRAMQFMHFR----- 604

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
             E+          ST  G            +  +  + +  +  S       ++  +++
Sbjct: 605 --ELPAGQNAIVAISTYSG------YNQEDSLIMNQSSIDRGLFRS-------MYYRVYM 649

Query: 845 EEFEVMARDTKLGPEEITR-DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           +  + +        E+  R D   +       ID  G+I  G  V+  DI++GK  P  E
Sbjct: 650 DTEKKIGMIDSETIEKPDREDCLRLKHGSYHKIDSDGLIAPGTRVSGEDIIIGKTVPIKE 709

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 ++         A   RD S  + S  +G V  V +       K
Sbjct: 710 DSSEMGQRT-------AAHTKRDASTPMKSTENGIVDQVMLTTNEAGYK 751


>gi|46277358|gb|AAS86869.1| DNA-dependent RNA polymerase II [Peziza vesiculosa]
          Length = 563

 Score =  206 bits (524), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 97/681 (14%), Positives = 180/681 (26%), Gaps = 122/681 (17%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     E    +    + +V  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
              F    +        I      I D  +   K          P    D+         +
Sbjct: 62   PGFIVRTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASSRRGEL 121

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
              Q   + K E     T  +                G+VE +DA       +    +   
Sbjct: 122  VLQKHHIEKLEDDKDITEEDQRYG-----WQGLIGEGVVEYIDAEEEETVMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            +    +   + Q+        QR    V             PS  LG       +  + +
Sbjct: 177  TSRQFHAGYEIQQEIDPA---QRVKASVNKYAHTWTHCEIHPSMILG-------ICASII 226

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  F    R+                       
Sbjct: 227  PFPDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM--------------------- 259

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 260  --DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 317

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +    +F R  +D+ +R      E+ E   R           +       +  G    
Sbjct: 318  RGLF-RSLFFRTYMDQEKRVGMNVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVS 376

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+  ++ ++     R+++         ++     +  Q               
Sbjct: 377  GEDIIIGKTAPIAPNMEELGQRTKFHTKRDVSTPLRSTENGIVDQ--------------- 421

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 422  -----VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGI 476

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM +  + E  L       G +                         
Sbjct: 477  VPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------------- 513

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     ++++ +LR       G  I+
Sbjct: 514  ------------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEIM 542

Query: 1237 YDGLTGEPFDRPVTVGYIYML 1257
            Y+G TG      V +G  Y  
Sbjct: 543  YNGHTGRKLVVQVFLGPTYYQ 563



 Score = 75.9 bits (185), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 66/481 (13%), Positives = 125/481 (25%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 25  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +S    + L          +    
Sbjct: 79  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASSRRGELVLQKHHIEKLEDDKDIT 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E              V Y+ A EEE   I      L+    F       +E+   +   
Sbjct: 139 EEDQRYGWQGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEIDPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +          +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 199 ASVNKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT----- 253

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                      + A I+                                    +KF+   
Sbjct: 254 ----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFRELP 288

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                    L   G             S  +   ++ R +  +       + E  + ++ 
Sbjct: 289 AGQNAIVAILCYSG--------YNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRVGMN- 339

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                       +EEFE   R           +   +       +D+ G++  G  V+  
Sbjct: 340 -----------VVEEFEKPTR----------GNTLRLKHGTYDKLDDDGLVAPGVRVSGE 378

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P   +     ++        K    RD S  + S  +G V  V +       
Sbjct: 379 DIIIGKTAPIAPNMEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 431

Query: 952 K 952
           K
Sbjct: 432 K 432


>gi|30141081|gb|AAP21851.1| RNA polymerase beta subunit [Gemella morbillorum]
          Length = 229

 Score =  206 bits (524), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/204 (37%), Positives = 102/204 (50%), Gaps = 54/204 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++  GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 80   KIFKREDGAELANGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 139

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 140  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGANDDDVWATIAEAGMA 199

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 200  KDAK----------------------------TVLYDG---------------------- 209

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
                 TGEPFD  V+VG +YM+KL
Sbjct: 210  ----RTGEPFDSRVSVGVMYMIKL 229



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 64/86 (74%)

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +IPNV E  L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +
Sbjct: 1   EIPNVGENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKE 60

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHG 949
           VRDTSLRVP G  G V DV+IF R  
Sbjct: 61  VRDTSLRVPHGADGVVADVKIFKRED 86


>gi|161331509|gb|ABX60672.1| RpoB [Sporosarcina sp. FSL_h8542]
          Length = 232

 Score =  206 bits (524), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 79/207 (38%), Positives = 102/207 (49%), Gaps = 54/207 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMPFL
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISVGDKMAGRHGNKGVISRILPEEDMPFL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMASRTLGIHMASPVFDGANEADVWDTMEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMNRDGK----------------------------TTLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                    +GEPFD  V+VG +YM+KL
Sbjct: 212  -------RSGEPFDNRVSVGIMYMIKL 231



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 59/89 (66%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV EE L+N+D+ GII VGAEV  GDILVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEEALRNLDDRGIIRVGAEVRDGDILVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G ++DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGAGGIILDVKVFNREDGD 90


>gi|110554875|gb|ABG75544.1| RpoB [Klebsiella pneumoniae]
          Length = 195

 Score =  206 bits (524), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 123/194 (63%), Positives = 156/194 (80%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R R
Sbjct: 2   DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRER 61

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
           AG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT++
Sbjct: 62  AGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE 121

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS
Sbjct: 122 IHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 181

Query: 674 IAASLIPFLENDDS 687
           + ASLIPFLE+DD+
Sbjct: 182 VGASLIPFLEHDDA 195


>gi|300244849|gb|ADJ93857.1| RNA polymerase B subunit [Staphylococcus sp. 361]
          Length = 237

 Score =  206 bits (524), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 137/236 (58%), Positives = 174/236 (73%), Gaps = 3/236 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T  + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++P+E
Sbjct: 62  YRKVDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTVMPKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E+PFVGTGME V 
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPESPFVGTGMEHVA 181

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRS-VEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           A+ SGAAIVAKR G VE V++  +++R  +E D       +D Y L KF+RSN  T
Sbjct: 182 ARDSGAAIVAKRKGRVEHVESNEVLVRQLIEEDGQEYEGELDRYPLAKFKRSNTGT 237


>gi|258576889|ref|XP_002542626.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Uncinocarpus
            reesii 1704]
 gi|237902892|gb|EEP77293.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Uncinocarpus
            reesii 1704]
          Length = 153

 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 47/201 (23%), Positives = 76/201 (37%), Gaps = 61/201 (30%)

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E  L       G +                                       
Sbjct: 1    MTIAHLIECQLSKVSSLRGYEGD------------------------------------- 23

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                            +TP F     ++++ +LR       G  ++Y+G TG      + 
Sbjct: 24   ----------------ATP-FTDVTVDSVSGLLREHGYQSRGFEVMYNGHTGRKLVAQIF 66

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
            +G  Y  +L HMV DK++AR+ G   ++T+QP+ G++  GG R GEME  C+ A+GA+  
Sbjct: 67   LGPTYYQRLRHMVDDKIHARARGPTQILTRQPVEGRARDGGLRFGEMERDCMIAHGASAF 126

Query: 1311 LQEMLTIKSD-------DVVG 1324
            L+E L   SD       D+ G
Sbjct: 127  LKERLFDVSDPFRVHICDICG 147


>gi|32455009|gb|AAP83184.1| RpoB [Streptococcus macedonicus]
          Length = 230

 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 90/291 (30%), Positives = 123/291 (42%), Gaps = 72/291 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 12   EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 64

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 65   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 113

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 114  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 173

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 174  ARNLGIHIATPVFDGATSEDLWDTVREAGMDSDAK------------------------- 208

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
               T ++DG                           TGEPFD  V+VG +Y
Sbjct: 209  ---TVLYDG--------------------------RTGEPFDNRVSVGIMY 230



 Score = 87.4 bits (215), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 61/93 (65%), Positives = 73/93 (78%)

Query: 859 EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
           EEITR+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG
Sbjct: 1   EEITREIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFG 60

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 61  DKSREVRDTSLRVPHGGDGVVRDVKIFTRANGD 93


>gi|45330863|gb|AAS57792.1| RNA polymerase II second largest subunit [Calocera cornea]
          Length = 631

 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 105/697 (15%), Positives = 202/697 (28%), Gaps = 93/697 (13%)

Query: 482  MERSIKERISSVDIDSVMPQDLINAKP-----VVSAVCEFFCSS--QLSQLEEHVNSLSR 534
            M++ +K         ++ P  + N              + F  +   +SQ+       S 
Sbjct: 15   MQKCVKTHHEFNINAAIKPTTITNKSQYSLATNNWDDQKKFMQTKANISQVLNQYTFTST 74

Query: 535  ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
            ++H ++ +              + + +H TH+G +CPAET EG   GLV +L   A ++ 
Sbjct: 75   LSHLQQTNTPINHD----SKITQPQQLHNTHWGMVCPAETPEGQACGLVKNLALMACISV 130

Query: 595  YGFIETPYRKVCDGKVTNDVV----YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                +     + +  +          L+A      ++      +  D       V     
Sbjct: 131  GSLSQPVVEFLEEWGLEPLGERSEGPLTAT---KVFVNGVWMGIHRDPQHLVNTVRTLRR 187

Query: 651  GEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEA 708
             + I      + D  +   +          P F+ N+ +  +++              + 
Sbjct: 188  SDGISNEISVVRDIRERELRLYTDAGRVCRPLFIVNEQTQNLVITKREINYLQQGRVDDD 247

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              V T    +V+            G+VE +DA       +    +   +           
Sbjct: 248  GHVFT-YNQLVSN-----------GMVELLDAEEEETVMIAMTPEDLEASKTKRGTGYIS 295

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
               QN  V  + +V               PS  LG       +  + +P+  +N      
Sbjct: 296  NEPQNAAVRIKSIVH----HEHWSHCEIHPSMILG-------ICASIIPFPDHNQ----- 339

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
             S R   +       +  +    +                            +  +    
Sbjct: 340  -SPRNTYQSAMGKQAMGIYLTNFQVRM-----------------------DTMANILYYP 375

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     +       +   +  + AI      +  D+ +   S +   +    I+ R 
Sbjct: 376  QKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRS 434

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
              D  + +  V  E+ E   RD          +       +  G           K+  L
Sbjct: 435  YTDMEKTTGIVPVEEFEKPHRDTTVRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPL 494

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              D      R++          ++     +  Q   S +                     
Sbjct: 495  PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLISTNE-------------------- 534

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              ++ VKV +   R  Q GDK A RHG KG +      EDMPF  +G   DIV+NP  +P
Sbjct: 535  SGVKFVKVRIRSTRIPQIGDKFASRHGQKGTIGMTYRQEDMPFAANGVTPDIVINPHAIP 594

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            SRM +G + E         +G +  +          +
Sbjct: 595  SRMTIGHLVECLXSKLXTLIGNEGDATPFTDLTVESV 631


>gi|117675911|emb|CAL69226.1| RNA polymerase subunit B [Clavibacter michiganensis subsp.
           michiganensis]
          Length = 360

 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/173 (36%), Positives = 92/173 (53%), Gaps = 6/173 (3%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W
Sbjct: 1   MGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F     I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKGVASIELTLEKDSILTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
            A   +         V  +    ++++         L K  + K  + LGI  
Sbjct: 119 EALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDK 171



 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 133/354 (37%), Positives = 199/354 (56%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 9   EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 68

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     A I  TL  D    +++AL DIYR
Sbjct: 69  VGVRIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYR 126

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A 
Sbjct: 127 KLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILAT 186

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 187 IKYLVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 246

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 247 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 306

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+C  ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 307 GPGGLSRERAGVEVRDVHPSHYGRMCTIETPEGPNIGLIGSLESFARINPFGFI 360


>gi|56694338|gb|AAW22909.1| RNA polymerase II second largest subunit [Podocarpus coriaceus]
          Length = 514

 Score =  206 bits (523), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 67/386 (17%), Positives = 118/386 (30%), Gaps = 77/386 (19%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 206  YQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 265

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        +F R   D+ +R  ++ +E+     R+          +          G 
Sbjct: 266  SIDRGFF-RSLFFRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGT 324

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T +S +                 E   +  +  +    TS    E   
Sbjct: 325  RVSGEDVIIGKTTPVSQE-----------------ESGNQISKYTRRDQSTSLRHSESGM 367

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 368  VDQVLLTTNQDGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTV 422

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 423  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 462

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++I+  L        G 
Sbjct: 463  ---------------------------------ATP-FTDVTVDSISKALHKCGYQMRGF 488

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +Y+G TG   +  + +G  Y  +L
Sbjct: 489  ETMYNGHTGRKLNAMIFLGPTYYQRL 514



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 65/451 (14%), Positives = 121/451 (26%), Gaps = 98/451 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S    + I+   + +A   F     +    +    +  +   RR   +         
Sbjct: 11  EEWSTENFEEISPAVIPTATKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNP------- 63

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
               +RD+                    +        + +     + P     D      
Sbjct: 64  EVGVVRDIRLRELRLYTDYGRCSRPLFVVKKQRLIIKKRDINELWQNPEDGWHDLITKGF 123

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E            +  P  ++ 
Sbjct: 124 IEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPXLILG 171

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+                             R  
Sbjct: 172 VCASIIPFPDHNQSPRNTYQSAMGKQAMGXYVTNYQL--------------------RMD 211

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  V                                       Q+PLV           
Sbjct: 212 TLAYV-----------------------------------LYYPQKPLV----------T 226

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N +VA   + GYN EDS+++++  +    F S+    +    + 
Sbjct: 227 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKR 286

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                +E        +   +       +D+ G+   G  V+  D+++GK TP  +     
Sbjct: 287 MGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVSQEE--- 343

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 +         RD S  +    SG V
Sbjct: 344 ------SGNQISKYTRRDQSTSLRHSESGMV 368


>gi|17225286|gb|AAL37336.1| RNA polymerase B-subunit [Staphylococcus haemolyticus]
          Length = 202

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 123/202 (60%), Positives = 154/202 (76%), Gaps = 2/202 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GL++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G
Sbjct: 61  GLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENG 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQR
Sbjct: 121 RFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQR 180

Query: 699 QAVPLLKAEAPFVGTGMESVVA 720
           QAVPL+  EAPFVGTGME V A
Sbjct: 181 QAVPLMNTEAPFVGTGMEHVAA 202


>gi|117675913|emb|CAL69227.1| RNA polymerase subunit B [Clavibacter michiganensis subsp.
           nebraskensis]
          Length = 360

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 63/173 (36%), Positives = 91/173 (52%), Gaps = 6/173 (3%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W
Sbjct: 1   MGDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F     I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKGVASIELTLEKDSILTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
            A   +         V       ++++         L K  + K  + LGI  
Sbjct: 119 EALKDIYRKLRPGEQVAAGAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDK 171



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 134/354 (37%), Positives = 200/354 (56%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 9   EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 68

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     A I  TL  D    +++AL DIYR
Sbjct: 69  VGVRIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYR 126

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A 
Sbjct: 127 KLRPGEQVAAGAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILAT 186

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 187 IKYLVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 246

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 247 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 306

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 307 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 360


>gi|194320248|gb|ACF48361.1| DNA-dependent RNA polymerase II second largest subunit [Phlyctis
            argena]
          Length = 317

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 66/393 (16%), Positives = 121/393 (30%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE       +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNFDERLDNSANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R  +++ +R   +    +E   +    E + L    Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFYRSYVEQEKR---IGMSLVETFEKPLRSETLRLKHGTYEKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G           K+  ++ D      R++          ++     +         
Sbjct: 119  IISPGIRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRSTENGI--------- 169

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                     ++K+          L+ VKV +   +  Q GDK A RHG KG +      E
Sbjct: 170  ---------VDKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFSAEGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G  ++Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 18  YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 67

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +     + +D+ GII  G  V+
Sbjct: 68  DRGLFRSLFYRSYVEQEKRIGMSLVETFEKPLRSETLRLKHGTYEKLDDDGIISPGIRVS 127

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 128 GEDIIIGKTAPIAPDAEELGQRT-------KLHTKRDASTPLRSTENGIVDKVLLTTNAE 180

Query: 950 IDK 952
             K
Sbjct: 181 GLK 183


>gi|56694332|gb|AAW22906.1| RNA polymerase II second largest subunit [Agathis australis]
          Length = 514

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 80/485 (16%), Positives = 145/485 (29%), Gaps = 94/485 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV  G  + V   +      S  + DL   R N   A+   +       S++  +   ++
Sbjct: 118  LVNKGFIEYVDTEEEETTMISMTINDLVNARINPEDAYSHTYTHCEIHPSLILGVCASII 177

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 178  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQXPLVT 226

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 227  TRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 285

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R  ++ +E+     R+          +          G           K+T ++     
Sbjct: 286  RMGTLVKEEFGRPNRENTTGMRHGSYDKLDEDGLAPPGTRVSGEDVIIGKTTPITQ---- 341

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE+  +     +    TS    E    +++      D +     R V
Sbjct: 342  -------------DEQGGQLSRFSRRDQSTSLRHSESGMVDQVLLTTNQDGL-----RFV 383

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            K+ +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 384  KIRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIG 443

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+                                           
Sbjct: 444  QLIECIMGKVAAHMGKEGD----------------------------------------- 462

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                        +TP F     ++I+  L        G   +Y+G TG      + +G  
Sbjct: 463  ------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRKLSAMIFLGPT 509

Query: 1255 YMLKL 1259
            Y  +L
Sbjct: 510  YYQRL 514



 Score =  115 bits (288), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 71/430 (16%), Positives = 122/430 (28%), Gaps = 100/430 (23%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAET 574
           F     +    +    +  +   RR   +    GV R     E+R ++  +     P   
Sbjct: 33  FVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRDIRLRELR-LYTDYGRCSRPLFV 91

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            E   + +     +  R N     E  +  V  G     + Y+   EEE   I+      
Sbjct: 92  VENQRLKIKKKDINELRQNPE---EGWHELVNKGF----IEYVDTEEEETTMISM----- 139

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                   +LV  R   E            +  P  ++ + AS+IPF +++ S R     
Sbjct: 140 -----TINDLVNARINPE--DAYSHTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQS 192

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M +QA+ +                           R   +  V                
Sbjct: 193 AMGKQAMGIYVTNYQL--------------------RMDTLAYV---------------- 216

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                                  Q PLV                      L  G N +VA
Sbjct: 217 -------------------LYYPQXPLV----------TTRAMEHLHFRQLPAGINAIVA 247

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVS 869
              + GYN EDS+++++  +    F S+    +    +      +E        +   + 
Sbjct: 248 ISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKRMGTLVKEEFGRPNRENTTGMR 307

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +DE G+   G  V+  D+++GK TP  +                     RD S 
Sbjct: 308 HGSYDKLDEDGLAPPGTRVSGEDVIIGKTTPITQDEQG---------GQLSRFSRRDQST 358

Query: 930 RVPSGVSGTV 939
            +    SG V
Sbjct: 359 SLRHSESGMV 368


>gi|40643891|emb|CAD89360.1| RNA polymerase II, second largest subunit [Hypericum canariense]
          Length = 134

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 70/187 (37%), Gaps = 54/187 (28%)

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 2    EGICPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 41

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+  L        G 
Sbjct: 42   ---------------------------------ATP-FTDVTVDNISKALHKCGYQMRGF 67

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              +Y+G TG      + +G  Y  +L HMV DK+++R  G   ++T+QP  G S  GG R
Sbjct: 68   ETMYNGHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGXSRDGGLR 127

Query: 1294 LGEMEVW 1300
             GEME  
Sbjct: 128  FGEMERD 134


>gi|70938226|ref|XP_739815.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56517090|emb|CAH81649.1| hypothetical protein PC000741.04.0 [Plasmodium chabaudi chabaudi]
          Length = 195

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 105/236 (44%), Gaps = 41/236 (17%)

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            Q GDK+  RHG+KG++S I    DMP+L +    D+ ++ +G+PSR+N+GQI E   G  
Sbjct: 1    QLGDKICNRHGHKGVISYINDINDMPYLNNKIQPDLFVSAIGIPSRINIGQILEGIYGLN 60

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
             + L  +     N      +         K   + +       Y+ +             
Sbjct: 61   SLYLNNRYIISNNLNNNYYNNYINSFNYYKYNYSNNFEFNKISYNYN------------- 107

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                                        +  L +  TG      V +  IY  KL HMV 
Sbjct: 108  ----------------------------KYFLKNPFTGHLIHNSVCLNNIYYYKLIHMVK 139

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            DK+  R  G YS +TQQP+ G + +GGQR GEMEVW ++A+GA+++ +E  T KSD
Sbjct: 140  DKLRYRFIGLYSELTQQPIKGNTKQGGQRFGEMEVWALEAFGASFLFKEFFTYKSD 195


>gi|258562154|gb|ACV81799.1| RNA polymerase II second largest subunit [Exobasidium vaccinii]
          Length = 583

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 95/627 (15%), Positives = 188/627 (29%), Gaps = 87/627 (13%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 37   GVSQVLNRYTYASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQAC 92

Query: 581  GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDG 638
            GLV +L+  + ++           + +  + + V    A  +  +         + D   
Sbjct: 93   GLVKNLSLMSMISVGSPSGPIIEFLEEYGLDSLVDMQIADAKATKVFVNGVWMGTCDAPA 152

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM-GCNMQ 697
               + L   R   +  +      D  +   +          P    +  ++ L       
Sbjct: 153  GLVDTLRDLRRKDDISIEVSVVHDIREKELRLYTDAGRVQRPLFIVNPEDKTLYVKPKHV 212

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                   + +    G G                            ++    E  +    S
Sbjct: 213  EWVNNQERPDGQPYGWGQLVRDGLI-------------------ELLDAEEEETVMICMS 253

Query: 758  GVDIYRLMKFQRSNQNTCVNQRP---LVKVGDEVRR-NDIIADGPSTDLGDLALGRNMLV 813
              D+     +  +  +  ++  P   LV V   +          P+  LG       +  
Sbjct: 254  PQDLESSRMYNENPDSVKLSGDPTARLVSVQTYMPATWTHCEIHPAMILG-------VCA 306

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N     +    M  + +   +++  +++                        
Sbjct: 307  SIIPFPDHNQSPRNVYQSAMGKQAMG--VYLTNYQMRM---------------------- 342

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 343  -----DTMANILYYPQKPLATTHSMQYLKFRELPAGQNAIVAILCYSGYNQEDSVIMSQS 397

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    ++ R  +D  +++  +  E+ E  +R+          +          G 
Sbjct: 398  AIDRGLF-RSLYYRTHMDMEKKTGMILLEEFEKPSRETAVRLKHGTYDKIDADGFCAPGT 456

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T L  D      RS+          ++     +  Q   S        
Sbjct: 457  RVSGEDIIIGKTTPLPPDSEELGLRSKLHTKKDVSXPLKSTENGIVDQVLVS-------- 508

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                              + VKV +   R  Q+GDK A RHG KG V      EDMPF  
Sbjct: 509  ------------TNAEGNKFVKVRIRSTRIPQTGDKFASRHGQKGTVGITYRQEDMPFTV 556

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETH 1140
            +G   DI++NP  +PSRM +G + E  
Sbjct: 557  EGVTPDIIINPHAIPSRMTIGHLVECL 583



 Score =  107 bits (266), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 88/588 (14%), Positives = 170/588 (28%), Gaps = 97/588 (16%)

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-- 446
           F++  ++ +    +  KY L   G      +         + + +    + +  L     
Sbjct: 1   FTLQAAVKSSTITNGLKYSL-ATGNWGDQKKFMQAKAGVSQVLNRYTYASTLSHLRRCNT 59

Query: 447 ---RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD------IDS 497
              R+GK       +  +  +    E  + Q    +  +       + S        ++ 
Sbjct: 60  PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSMISVGSPSGPIIEFLEE 119

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
                L++ +   +   + F +       +    L       R        V+      E
Sbjct: 120 YGLDSLVDMQIADAKATKVFVNGVWMGTCDAPAGLVDTLRDLRRKDDISIEVSVVHDIRE 179

Query: 558 MRDVHPTHYGRI-CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
                 T  GR+  P       +  L         VN     +              +  
Sbjct: 180 KELRLYTDAGRVQRPLFIVNPEDKTLYVKPKHVEWVNNQERPDGQPYGWGQLVRDGLIEL 239

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCR-------CAGEEILVPREKIDFIDASPK 669
           L A EEE   I  +   L+    + E     +                       +  P 
Sbjct: 240 LDAEEEETVMICMSPQDLESSRMYNENPDSVKLSGDPTARLVSVQTYMPATWTHCEIHPA 299

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R +    M +QA+ +                          
Sbjct: 300 MILGVCASIIPFPDHNQSPRNVYQSAMGKQAMGVYLTNYQM------------------- 340

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       ++    +  R          
Sbjct: 341 ----------------------RMDTMANILYYPQKPLATTHSMQYLKFR---------- 368

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++S+  +   +F S++      
Sbjct: 369 --------------ELPAGQNAIVAILCYSGYNQEDSVIMSQSAIDRGLFRSLYYRTHMD 414

Query: 850 MARDTKLG-PEEITRDIP----NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           M + T +   EE  +        +       ID  G    G  V+  DI++GK TP    
Sbjct: 415 MEKKTGMILLEEFEKPSRETAVRLKHGTYDKIDADGFCAPGTRVSGEDIIIGKTTP---L 471

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           P   EE  LR+    K    +D S  + S  +G V  V +      +K
Sbjct: 472 PPDSEELGLRS----KLHTKKDVSXPLKSTENGIVDQVLVSTNAEGNK 515


>gi|88976165|gb|ABD59040.1| RNA polymerase II second largest subunit [Megacollybia platyphylla]
          Length = 558

 Score =  205 bits (522), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 111/684 (16%), Positives = 195/684 (28%), Gaps = 126/684 (18%)

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +CPAET EG   GLV +L   A ++   +       + +  + +         EEN   A
Sbjct: 1    VCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENANTA 52

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
              ++ +  +G +       R     +   ++     D SP+  V             D+ 
Sbjct: 53   -VSTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAG 108

Query: 689  RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            RV     +      +LK +     T  E+   K         + GI+E +DA       +
Sbjct: 109  RVCRPLFIVEDQNLVLKKKHVRWLTAGEND-DKDEYKWEHLVKGGIIELLDAEEEETVMI 167

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +   +       +    ++       R  +K G            PS  LG     
Sbjct: 168  SMTPEDLENSRLQQAGIDPHANDGEFDPAAR--LKAGINAHTWTHCEIHPSMILG----- 220

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G       I   
Sbjct: 221  --ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIFLTNFLIRM- 259

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 260  ----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 309

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    I+ R  +D  ++S   + E+ E  +R           +       
Sbjct: 310  IMNQSSIDRGLF-RSIYYRSYMDLEKKSGIAQLEEFEKPSRQNTLRMKHGTYDKLDDDGL 368

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G   V       K+  +  D      R++          ++     +  Q       
Sbjct: 369  IAPGTGVVGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI---- 424

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   + VKV V   R  Q GDK A RHG KG +      ED
Sbjct: 425  ----------------TTNSEGQKFVKVRVRSIRIPQIGDKFASRHGQKGTIGITYRQED 468

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  +PSRM +G + E  L      +G +                 
Sbjct: 469  MPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------- 513

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                                                  +TP F     E+++S LR    
Sbjct: 514  --------------------------------------ATP-FTDLTVESVSSYLRTKGY 534

Query: 1229 DESGQSILYDGLTGEPFDRPVTVG 1252
               G  ++Y G TG      V +G
Sbjct: 535  QSRGLEVMYHGHTGRKLQAQVYLG 558



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 72/463 (15%), Positives = 134/463 (28%), Gaps = 88/463 (19%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           F     +    +  N +  I   RR   +            +   ++        P    
Sbjct: 58  FVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIV 117

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E  N+ L      +  + A    +    K         +  L A EEE   I+     L+
Sbjct: 118 EDQNLVLKKKHVRW--LTAGENDDKDEYKWEHLVKGGIIELLDAEEEETVMISMTPEDLE 175

Query: 636 EDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                   +      GE          +        +  P  ++ I AS+IPF +++ S 
Sbjct: 176 NSRLQQAGIDPHANDGEFDPAARLKAGINAHTWTHCEIHPSMILGICASIIPFPDHNQSP 235

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                                             
Sbjct: 236 RNTYQSAMGKQAMGIFLTNFLI-------------------------------------- 257

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                 + + +  Y       +     +  R                        +L  G
Sbjct: 258 ---RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAG 290

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----- 863
           +N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E        
Sbjct: 291 QNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIAQLEEFEKPSRQ 350

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+I  G  V   DI++GK  P         ++        +   
Sbjct: 351 NTLRMKHGTYDKLDDDGLIAPGTGVVGEDIIIGKTAPIPPDSEELGQRT-------RTHT 403

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDK--NERSISVEREQI 964
            RD S  + S  +G V  V I       K    R  S+   QI
Sbjct: 404 RRDVSTPLKSTENGIVDQVLITTNSEGQKFVKVRVRSIRIPQI 446


>gi|157781331|gb|ABV72020.1| RNA polymerase beta subunit [Tetragenococcus solitarius]
          Length = 226

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 93/294 (31%), Positives = 125/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      R  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIVRVGAEVRDGDLLVGKVTPKGVTELSAEERLLHAIFGEKARE-VRDT 62

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +++       +                    KI   + GD++ PGV  +V+V++  KR I
Sbjct: 63   SLRVPHGGGGI----------------IHDVKIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D                               DD V    E+     
Sbjct: 167  ARQLGIHVATPVFDGA----------------------------SDDDVWETVEEAGLAK 198

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 199  DAKTVLYDG--------------------------RTGEPFDGRVSVGVMYMIK 226



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GI+ VGAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIVRVGAEVRDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G + DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIIHDVKIFTREAGD 86


>gi|327133523|gb|AEA29766.1| RNA polymerase subunit B [Acinetobacter sp. 11NS3]
          Length = 162

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 73/162 (45%), Positives = 101/162 (62%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F
Sbjct: 1    QMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIQPSDEGIAERLTQIQTYLKEKSAEIDEKF 60

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K  K+  GD++  GVL+VVKV++A KR IQ GDKMAGRHGNKG+VS ILP E MP   
Sbjct: 61   AEKKRKLSTGDELTTGVLKVVKVYLAEKRHIQPGDKMAGRHGNKGVVSNILPVEHMPHDA 120

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            +G PVD+VLNPLGV SRMNVGQI ETHLG A  GLG++I  +
Sbjct: 121  NGVPVDVVLNPLGVSSRMNVGQILETHLGLAAKGLGEQIDKM 162


>gi|68131884|gb|AAY85220.1| RNA polymerase II second largest subunit [Berberis nervosa]
          Length = 540

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 81/484 (16%), Positives = 143/484 (29%), Gaps = 92/484 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFMPWHGYNFEDSML--ISERMVS 835
            LV  G  + V   +      S  + DL   R N    +  +       S++  +   ++ 
Sbjct: 144  LVAKGYIEYVDTEEEETTMISMTIDDLVNARTNPNETYQLYTHCEIHPSLILGVCASIIP 203

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                       ++       +G          V+   L+      +  V        +  
Sbjct: 204  FPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVTT 252

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S +        +F R   D+ ++
Sbjct: 253  RAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKK 311

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
              ++ +E      R+          +          G           K+T ++ D    
Sbjct: 312  MGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAPDETQG 371

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
               SQ+                 K  + TS    E    +++      D +     R VK
Sbjct: 372  GVASQY----------------TKRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVK 410

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ
Sbjct: 411  VRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQ 470

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  +G     +GK+                                            
Sbjct: 471  LIECIMGKVAAHMGKEGD------------------------------------------ 488

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                       +TP F     + I+  L        G   +Y+G TG      + +G  Y
Sbjct: 489  -----------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTY 536

Query: 1256 MLKL 1259
              +L
Sbjct: 537  YQRL 540



 Score =  112 bits (281), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 72/486 (14%), Positives = 142/486 (29%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPSVIPTAHKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
                   +  +   RR   +  + G+ R  +  E+R ++  +     P    E      
Sbjct: 64  IHRNPELLVKTLRQLRRQVDVNTEVGIIRDFSLKELR-LYTDYGRCSRPLFIVENQRLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L     ++  G+         D      + Y+   EEE   I+          
Sbjct: 123 KKKDIRALQQRESLDEGGWH--------DLVAKGYIEYVDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
              ++LV  R    E     +     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TIDDLVNARTNPNETY---QLYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 221

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +                           R   +  V                    
Sbjct: 222 QAMGIYVTNYQL--------------------RMDTLAYV-------------------- 241

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 242 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 276

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 277 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSY 336

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP                        RD S  +  
Sbjct: 337 DKLDDDGLAPPGTRVSGEDVIIGKTTPIAPDETQGGVA--------SQYTKRDHSTSLRH 388

Query: 934 GVSGTV 939
             SG V
Sbjct: 389 SESGMV 394


>gi|168218626|emb|CAP45841.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 79/136 (58%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+  ++MGD P+MT  GTF+I G  
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDHDVFMGDFPIMTDTGTFIISGAD 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|168218624|emb|CAP45840.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 50/136 (36%), Positives = 78/136 (57%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F  + PI   +G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFXDISPIEDXTGNLSLEFIDYSLGDPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+  ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDHDVFMGDFPIMTDTGTFIISGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|168218590|emb|CAP45823.1| DNA-directed RNA polymerase subunit beta [Bacillus mojavensis]
          Length = 120

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 51/136 (37%), Positives = 79/136 (58%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY  FL          +EGL+  F+ +  I  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYQWFL----------DEGLREMFQDISQIEDFTGNLSLEFIDYSLGEPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+  ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKDNGEVKDPRVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP ++F 
Sbjct: 102 RVIVSQLVRSPSVYFS 117


>gi|157781309|gb|ABV72009.1| RNA polymerase beta subunit [Enterococcus durans]
 gi|157781347|gb|ABV72028.1| RNA polymerase beta subunit [Enterococcus durans]
          Length = 226

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 91/294 (30%), Positives = 125/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +          +      KI   + GD++ PGV  +V+V++  KR I
Sbjct: 58   -----EVRDTSLRVPHGGGGIVHDV------KIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D                               D+ V     +     
Sbjct: 167  ARQLGIHVATPVFDGA----------------------------SDEDVWETVREAGMAS 198

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  V+VG +YM+K
Sbjct: 199  DAKTVLYDG--------------------------RTGEPFDGRVSVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|89142757|emb|CAJ57574.1| RNA polymerase subunit B [Microbacterium hominis]
          Length = 362

 Score =  205 bits (521), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEDILAEFAGYESIADTLSKDTILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164



 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 129/259 (49%), Positives = 175/259 (67%), Gaps = 15/259 (5%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              I +TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR 
Sbjct: 104 YESIADTLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRY 163

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L LD P     +  +DI+A IK LV L NG                  +DDIDN 
Sbjct: 164 KINQKLGLDKPLSDSVLTVDDIVATIKYLVALHNGDTTIPGVRGGQAAEIRLDVDDIDNF 223

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 224 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 283

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 284 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 343

Query: 580 IGLVSSLTSFARVNAYGFI 598
           IGL+ SL SFAR+N +GFI
Sbjct: 344 IGLIGSLASFARINPFGFI 362


>gi|89142749|emb|CAJ57570.1| RNA polymerase subunit B [Microbacterium dextranolyticum]
          Length = 352

 Score =  205 bits (521), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 62/175 (35%), Positives = 93/175 (53%), Gaps = 6/175 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEDILNEFAGYESIADTLSKDTILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              A   +         V  +    ++++    +    L K  + K  + LG+  
Sbjct: 119 KEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINQKLGLDK 173



 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 121/252 (48%), Positives = 166/252 (65%), Gaps = 15/252 (5%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +       I +TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+
Sbjct: 99  NEFAGYESIADTLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLA 158

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L LD P     +  +DI+A IK LV L  G                  +D
Sbjct: 159 KVGRYKINQKLGLDKPLSDSVLTVDDIVATIKYLVALHRGDESIPGIRNGEAAEIRLDVD 218

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ 
Sbjct: 219 DIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIK 278

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET
Sbjct: 279 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIET 338

Query: 575 SEGHNIGLVSSL 586
            EG NIGL+ SL
Sbjct: 339 PEGPNIGLIGSL 350


>gi|56694316|gb|AAW22898.1| RNA polymerase II second largest subunit [Encephalartos barteri]
          Length = 527

 Score =  205 bits (521), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 84/481 (17%), Positives = 139/481 (28%), Gaps = 85/481 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN          Y       I   ++    
Sbjct: 130  LVTKGFIEYVDTEEEETTMISMTISDLVNARNSPPTAASIVKY---THCEIHPSLILGVC 186

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V             +
Sbjct: 187  XSIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLXTTRAM 243

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        +F R   D+ +R  +
Sbjct: 244  EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFYRSYRDEEKRMGT 302

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+     R+          +          G           K+T ++         
Sbjct: 303  LVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQ-------- 354

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     DE   +     K    TS    E    +++      D +     R VKV +
Sbjct: 355  ---------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRM 400

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 401  RSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIE 460

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+                                               
Sbjct: 461  CIMGKVAAHMGKEGD--------------------------------------------- 475

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     + I+  L        G   +Y+G TG      + +G  Y  +
Sbjct: 476  --------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQR 526

Query: 1259 L 1259
            L
Sbjct: 527  L 527



 Score =  113 bits (283), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 68/457 (14%), Positives = 127/457 (27%), Gaps = 97/457 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   + +A   F     +    +    +  +   RR   +  + GV R 
Sbjct: 11  EEWSTENFEEISPAVIPNATKIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRD 70

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGH----NIGLVSSLTSFARVNAYGFI-ETPYRKVCD 607
               E+R ++  +     P    E          +  L    ++       E   R   +
Sbjct: 71  IRLSELR-LYTDYGRCSRPLFIVENQRLLIKKPDIRRLQQRDQLPPPSPDDENTVRGWHE 129

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 + Y+   EEE   I+   S L                         K    +  
Sbjct: 130 LVTKGFIEYVDTEEEETTMISMTISDL-----------VNARNSPPTAASIVKYTHCEIH 178

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P  ++ +  S+IPF +++ S R      M +QA+ +                        
Sbjct: 179 PSLILGVCXSIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL----------------- 221

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
              R   +  V                                       Q+PL      
Sbjct: 222 ---RMDTLAYV-----------------------------------LYYPQKPL------ 237

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                            L  G N +VA   + GYN EDS+++++  +    F S+    +
Sbjct: 238 ----XTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFYRSY 293

Query: 848 EVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
               +      +E        +   +       +D+ G+   G  V+  D+++GK TP  
Sbjct: 294 RDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVT 353

Query: 903 ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           +           +         RD S  +    SG V
Sbjct: 354 QDE---------SGGQAARYTKRDQSTSLRHSESGMV 381


>gi|46277326|gb|AAS86853.1| DNA-dependent RNA polymerase II [Iodowynnea auriformis]
          Length = 556

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 94/675 (13%), Positives = 188/675 (27%), Gaps = 124/675 (18%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L ++  V         +    + +V  +     +      ++      +  D SF    +
Sbjct: 3    LMAYVSVGTPAGPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPSFIVRTI 62

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    I      I  I     ++ + A      +  ++ND ++       +Q+  + 
Sbjct: 63   QKLRRQGHISAEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIN 122

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ +        E    +   A ++A   G+VE +DA       +    +   +    +
Sbjct: 123  KLQDDYEI-----EDESQRYGWAGLMA--DGVVEYIDAEEEETVMIVMTPEDLETSRQFH 175

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
               + Q+        QR    V             PS  LG       +  + +P+  +N
Sbjct: 176  AGYEIQQEVDPA---QRVKSAVNKFAHTWTHCEIHPSMILG-------ICASIIPFPDHN 225

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                   S R   +       +  F    R+                           + 
Sbjct: 226  Q------SPRNTYQSAMGKQAMGVFLTNYRERM-----------------------DTMA 256

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 257  NILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-R 315

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +F R  +D+ +R      E+ E  +R           +       +  G          
Sbjct: 316  SLFFRTYMDQEKRIGMSVVEEFEKPSRGNTLRLKHGTYDKLDEDGLVAPGVRVSGEDIII 375

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+  ++ +      R+++         ++     +  Q                     
Sbjct: 376  GKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ--------------------V 415

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                    L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++
Sbjct: 416  MVTTNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGIVPDLII 475

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +  + E  +       G +                               
Sbjct: 476  NPHAIPSRMTIAHLIECLISKVSSLRGYEGD----------------------------- 506

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    +TP F     ++I+ +LR       G  ++Y+G TG
Sbjct: 507  ------------------------ATP-FTDVTVDSISKLLREHGYQSRGFEVMYNGHTG 541

Query: 1243 EPFDRPVTVGYIYML 1257
                  V +G  Y  
Sbjct: 542  RKLVAQVFLGPTYYQ 556



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 66/481 (13%), Positives = 126/481 (26%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 18  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPSFIVRTIQKLRRQGHI 71

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
                           +         P         +     + L     +  + +    
Sbjct: 72  SAEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHINKLQDDYEIE 131

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E+             V Y+ A EEE   I      L+    F       +E+   +   
Sbjct: 132 DESQRYGWAGLMADGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEVDPAQRVK 191

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +          +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 192 SAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT----- 246

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                      + A I+                                    +KF+   
Sbjct: 247 ----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFRELP 281

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                    L   G             S  +   ++ R +  +       + E  + +S 
Sbjct: 282 AGQNAIVAILCYSG--------YNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMS- 332

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                       +EEFE  +R           +   +       +DE G++  G  V+  
Sbjct: 333 -----------VVEEFEKPSR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSGE 371

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P   +     ++        K    RD S  + S  +G V  V +       
Sbjct: 372 DIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNSEGL 424

Query: 952 K 952
           K
Sbjct: 425 K 425


>gi|37956410|gb|AAP15376.1| RNA polymerase beta subunit [Geobacter humireducens]
          Length = 211

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 123/210 (58%), Positives = 164/210 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVKEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT++V + SA+EEE   IAQAN+ +DE G F  + +  R +GE +LV R++++ +D +P
Sbjct: 122 KVTDEVRFFSALEEEGHAIAQANADVDETGRFVADYISARKSGEFVLVGRDELELMDVAP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            Q+VS+A SLIPFLENDD+NR LMG NMQR
Sbjct: 182 MQLVSVAGSLIPFLENDDANRALMGSNMQR 211


>gi|157781319|gb|ABV72014.1| RNA polymerase beta subunit [Enterococcus gilvus]
 gi|157781355|gb|ABV72032.1| RNA polymerase beta subunit [Enterococcus pseudoavium]
          Length = 226

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 77/206 (37%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMP+L
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPYL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQ----------- 183

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D  V     + +      T ++DG                   
Sbjct: 184  -----------------DSDVWETVRESRMAADAKTVLYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDNRISVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 67/86 (77%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV+ GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|193247967|emb|CAQ68301.1| RNA polymerase B-subunit [Staphylococcus lugdunensis]
          Length = 210

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 121/209 (57%), Positives = 158/209 (75%), Gaps = 2/209 (0%)

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
            D +S+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R 
Sbjct: 1   PDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRE 60

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKV 610
           RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +
Sbjct: 61  RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDTNAI 120

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQ
Sbjct: 121 TDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 180

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           VVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 181 VVSAATACIPFLENDDSNRALMGANMQRQ 209


>gi|51103935|gb|AAT96673.1| RpoB [Corynebacterium sp. 110393]
          Length = 146

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 93/174 (53%), Gaps = 36/174 (20%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+    ND +    I  L   L  V              
Sbjct: 1    RMNIGQVLEIHLGWLAHA-GWKVD--PNDPQNEQLIKTLPKELYDVPANSLT-------- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA  + ++ +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGASNDEVSGLLANSRPNRDGDVMVDRHGKARLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF+ P++VGY+Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   GEPFEHPISVGYMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 146


>gi|327133525|gb|AEA29767.1| RNA polymerase subunit B [Acinetobacter sp. 11N2]
          Length = 163

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 72/162 (44%), Positives = 103/162 (63%)

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
              +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F 
Sbjct: 1    MSNGGGTTKRGDQLTEDKLSQLEMVDLLEIPPSDEGIAERLTQIQTYLKEKSAEIDEKFA 60

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
             K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   +
Sbjct: 61   EKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDAN 120

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            G PVD+VL P+GV SRMNVGQI ETHLG A  GLG++I  ++
Sbjct: 121  GVPVDVVLTPVGVLSRMNVGQILETHLGLAAKGLGEQIDKML 162


>gi|157781351|gb|ABV72030.1| RNA polymerase beta subunit [Enterococcus mundtii]
          Length = 226

 Score =  204 bits (520), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 182

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 183  ----------------SDEDVWETVREAGMASDAKTVLYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  V+VG +YM+K
Sbjct: 208  -------RTGEPFDGRVSVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|157781305|gb|ABV72007.1| RNA polymerase beta subunit [Enterococcus columbae]
          Length = 226

 Score =  204 bits (520), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 78/206 (37%), Positives = 101/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+       
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGARDADVWETVREA 194

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 195  GLARDAK----------------------------TILYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDGRISVGVMYMIK 226



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|89142747|emb|CAJ57569.1| RNA polymerase subunit B [Microbacterium chocolatum]
          Length = 363

 Score =  204 bits (520), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G
Sbjct: 2   VFMGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARIIPSRG 59

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  +  I  +   D    
Sbjct: 60  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDILAEFAGFDSIEETLSKDTILS 119

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 120 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 165



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 128/258 (49%), Positives = 173/258 (67%), Gaps = 15/258 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 106 DSIEETLSKDTILSKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 165

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L L  P     +  EDI+A IK LV L  G                  +DDIDN G
Sbjct: 166 INQKLGLTGPLSDSVLTVEDIVATIKYLVRLHRGDTTFDGTRAGKPAEIRLDVDDIDNFG 225

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 226 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 285

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 286 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 345

Query: 581 GLVSSLTSFARVNAYGFI 598
           GL+ SL SFAR+N +GFI
Sbjct: 346 GLIGSLASFARINPFGFI 363


>gi|157781329|gb|ABV72019.1| RNA polymerase beta subunit [Enterococcus ratti]
 gi|157781335|gb|ABV72022.1| RNA polymerase beta subunit [Enterococcus villorum]
          Length = 226

 Score =  204 bits (520), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 182

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 183  ----------------SDEDVWETVREAGMASDAKTILYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  V+VG +YM+K
Sbjct: 208  -------RTGEPFDGRVSVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|157781321|gb|ABV72015.1| RNA polymerase beta subunit [Enterococcus hirae]
 gi|157781343|gb|ABV72026.1| RNA polymerase beta subunit [Enterococcus hirae]
          Length = 226

 Score =  204 bits (520), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 182

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 183  ----------------SDEDVWETVREAGMASDAKTILYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  V+VG +YM+K
Sbjct: 208  -------RTGEPFDGRVSVGVMYMIK 226



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/86 (61%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++D+ GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDKMGIIRIGAEVQDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|193247965|emb|CAQ68300.1| RNA polymerase B-subunit [Staphylococcus lugdunensis]
          Length = 212

 Score =  204 bits (520), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 124/210 (59%), Positives = 161/210 (76%), Gaps = 2/210 (0%)

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGV 556
           S+ PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +
Sbjct: 1   SITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQM 60

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDV 614
           E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ +
Sbjct: 61  EVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDTNAITDQI 120

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS 
Sbjct: 121 DYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSA 180

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           A + IPFLENDDSNR LMG NMQRQAVPL+
Sbjct: 181 ATACIPFLENDDSNRALMGANMQRQAVPLM 210


>gi|157781359|gb|ABV72034.1| RNA polymerase beta subunit [Enterococcus italicus DSM 15952]
          Length = 226

 Score =  204 bits (519), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 79/206 (38%), Positives = 102/206 (49%), Gaps = 54/206 (26%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               KI   + GD++ PGV  +V+V++  KR I  GDKMAGRHGNKG+VSRI+P EDMPFL
Sbjct: 75   HDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFL 134

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D              
Sbjct: 135  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGA------------ 182

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                             D+ V     +        T ++DG                   
Sbjct: 183  ----------------SDEDVWETVREAGMAKDAKTILYDG------------------- 207

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    TGEPFD  ++VG +YM+K
Sbjct: 208  -------RTGEPFDGRISVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/86 (63%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVEDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|218884686|ref|YP_002429068.1| DNA-directed RNA polymerase subunit B [Desulfurococcus kamchatkensis
            1221n]
 gi|218766302|gb|ACL11701.1| DNA-directed RNA polymerase, subunit B [Desulfurococcus kamchatkensis
            1221n]
          Length = 1149

 Score =  204 bits (519), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 82/401 (20%), Positives = 140/401 (34%), Gaps = 76/401 (18%)

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLI----SEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
            EI      V G +G K    L  D I    ++          V   +     E       
Sbjct: 797  EITIPSTNVRGYRGQKAYEKLEEDGIVAPETQVSGGDVLIGKVSPPRFLSTQEYEVGGLT 856

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
               + +  R + K         M     +++KV V   R  +         G+K      
Sbjct: 857  RQDTSIVMRHEEKGIVDTVLITMDSEGNKLIKVRVRDLRIPEL--------GDK------ 902

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
                                     SR         H     +GL      +    +   
Sbjct: 903  -----------------------FASR---------HGQKGVLGLLLPQYDMPFTEEG-- 928

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPV-STPVFDGADEEAINSM 1222
             ++P          +     ++ +        +  +   G P   TP+      E +  +
Sbjct: 929  -VTPDLIINPHAFPSRMTVAQLMESIAGKAAALEGRIIDGTPFYKTPI------EDLQII 981

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQP 1282
            LR      +G+  +YDG TGE    PV +G +Y  KL+HM SDK++AR+ G   ++T+QP
Sbjct: 982  LRRHGYPYTGEEAMYDGRTGELIKTPVFIGIVYYQKLHHMASDKIHARARGPVQILTRQP 1041

Query: 1283 LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG------RTR-V 1328
              G+S  GG R GEMEV C+  +G+A +L+E +T +SD          G      R +  
Sbjct: 1042 TEGRSRAGGLRWGEMEVDCLIGHGSALLLKEAMTDRSDSTIIYVCELCGSMGWYDRNKGK 1101

Query: 1329 YESIVAGND-TFET-GTPESFNVLVKEMQALGLSIDLENSR 1367
            +   +       +      +F +L++E+ ++G+   L    
Sbjct: 1102 FVCPIHKEKGVLKPVEVSYAFKLLLQELMSMGIRPRLLIED 1142



 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 157/972 (16%), Positives = 296/972 (30%), Gaps = 220/972 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L+     SY+ F+   +         +   FK +  I   +    L    Y  D PK+  
Sbjct: 10  LVRQHLDSYERFIKEILPS-------ILEEFKEI--I--ITNKIKLVIEKYRIDSPKWTS 58

Query: 88  ---------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  R+LTYA P+ +++R+                 +EQ + + DLP+M
Sbjct: 59  VEGIEESKTPMECRLRNLTYATPIYVSVRI----------EDESGYTREQELKLMDLPVM 108

Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHR-SPGIHFD--HDKGR 171
            K                         G F+I G ++++V+Q    S  I  D   +   
Sbjct: 109 LKSSIDPLSKLTPQELIENGEDPRDPGGYFIINGSEKVIVAQEDLASNNIIVDVMQEGSS 168

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE----- 226
            +   K+    R    +   + IE     + +    +  K P    ++ALG+ SE     
Sbjct: 169 VTHVAKVTSVSR---GRRSQLIIERRKDGVFYASF-QGHKFPALILMIALGLASEAEMLY 224

Query: 227 ------EI-----------------LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
                 EI                 L           R     +     +  +    S  
Sbjct: 225 STSLKPEIQTYLLPSILQVQEILPKLEIPEGASEEEVRRLKEEYRRKVIEEALDFIASKF 284

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
           ++     E+++ + + L   LL  +         +      G  ++  I      E+ + 
Sbjct: 285 IIGRPREERILRAERLLDERLLPHIGIDSSPETRLKKAVFIGQMISRII------ELQLG 338

Query: 324 AGDVIDEKSL--EEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
             +  D+     + +  +      +L    +     I+  +     K +K   +D+  V 
Sbjct: 339 YREPDDKDHYRNKRLKLAGDMLAVLLRAAMMGFAREIKEGIEKQLAKTKK---IDLKMVF 395

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNL-----------DTPDDVRH 430
           +P  + T  +  +M    +          + R  M   L+                + R 
Sbjct: 396 KPS-IITDRIQHAMATGNWPGGRTGVSQLLDRTNMLSTLSHLRRVVSPLARGQPHFEARE 454

Query: 431 IRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS-VGEMLKNQYRLGLLRMER----S 485
           +       +           G + ++  + N  V     E+    YR+G++ +       
Sbjct: 455 LHGTQWGRMCPFETPEGANIGLVKNLALMTNVSVGIDDKEIEALLYRIGVVPIVSTRTID 514

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS-QLEEHVNSLSRITHTRRLSAL 544
            K     +D+ S             S  C+ F + +L    ++       I   RR   +
Sbjct: 515 GKIHKGLIDMISEDVSKASEISEKYSGWCKVFLNGKLIGYHKDGEELARTIRSLRRSGKI 574

Query: 545 -GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
             +  VA          V  T  GRI          I + + +    R      +     
Sbjct: 575 SSEVNVAYIGNKYIKEVVVNTDSGRIR------RPLIVIENGVPKLTR-EHVKLLSEGKL 627

Query: 604 KVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDF 663
              D      V YL   EEEN YIA   S +  +                          
Sbjct: 628 TFEDLVKQGIVEYLDPDEEENAYIALQPSDVTAEH-----------------------TH 664

Query: 664 IDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSS 723
           ++     ++ I AS+IP+ E++ S R +    M +Q++ L                    
Sbjct: 665 LEIWIPAILGITASIIPYPEHNQSPRNMYQSAMAKQSLGLY------------------- 705

Query: 724 GAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVK 783
                                  +       +      Y               QRPLV+
Sbjct: 706 ----------------------AANFQRRMDTRGHFLHYP--------------QRPLVE 729

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +   G+NM+VA + + GYN ED+++++   V   +  S  
Sbjct: 730 TRM----------MNVIGYNERPAGQNMVVAVLTYTGYNMEDALIMNRSSVERGLARSTF 779

Query: 844 IEEFEVMARDTKLG-PEEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  +      G  +EIT    NV     ++  + ++E GI+    +V+ GD+L+GK+
Sbjct: 780 FRLYTTVEYKYPGGIQDEITIPSTNVRGYRGQKAYEKLEEDGIVAPETQVSGGDVLIGKV 839

Query: 899 TPKGESPMTPEE 910
           +P         E
Sbjct: 840 SPPRFLSTQEYE 851


>gi|168218632|emb|CAP45844.1| DNA-directed RNA polymerase subunit beta [Bacillus licheniformis]
          Length = 120

 Score =  204 bits (519), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 48/136 (35%), Positives = 78/136 (57%), Gaps = 19/136 (13%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDVDD 90
           E+Q +SY              + GL+  ++ + PI  F+G   LEF+ Y    PK+ V++
Sbjct: 1   EIQTSSYHW----------CLDSGLRDMYQDISPIEDFTGNLSLEFIDYSLGEPKYPVEE 50

Query: 91  CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQ 150
              RD+TY+ PL++ +RLI          K   ++K+Q ++MGD P+MT  GTF+I G +
Sbjct: 51  SKERDVTYSAPLRVKVRLI---------NKETGEVKDQEVFMGDFPIMTDTGTFIINGAE 101

Query: 151 RIVVSQLHRSPGIHFD 166
           R++VSQL RSP +++ 
Sbjct: 102 RVIVSQLVRSPSVYYS 117


>gi|168002663|ref|XP_001754033.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162695009|gb|EDQ81355.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 472

 Score =  204 bits (519), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 85/363 (23%), Positives = 141/363 (38%), Gaps = 69/363 (19%)

Query: 1009 SSDLISEYPRSQWWQFAVQD-EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
              D++ +          V+D + +   +   + +    K +L+      ++K+       
Sbjct: 150  DGDILRDNDGIILVGQQVKDGDTIAAKLVITEKKQSIEKIVLKSFVSRWVDKVTK--HTS 207

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++V+V + + R    G K   RH  KGI+  IL  ED+ F KD    D+++NP  +
Sbjct: 208  VEGNKIVRVRILLYRFPIVGHKFTSRHSQKGIIGAILSQEDLSFTKDEIAPDLIINPHVI 267

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +G + E  +                                       +    ++
Sbjct: 268  PSRMTMGHLLEMVMYKI------------------------------------YVLDSNN 291

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              D  +    +  +S    +T VF+ A           AD+ +  +  +Y G T  P + 
Sbjct: 292  ARDPMLSSKPKSRESSCIDAT-VFNRAHRS------FEADIAKLCKEKMYCGATRLPIEA 344

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGA 1307
             V  G  Y   L H   DK ++ S G    +T+QP+ G+S +GG R GEME   + A+G 
Sbjct: 345  IVATGICYYHVLRHQARDKAHSISKGVIQSLTKQPVEGRSRKGGLRFGEMEKDYLIAHGV 404

Query: 1308 AYVLQEMLTIKSDDVVGRTRVYE---------------SI-VAGNDTFETGTPESFNVLV 1351
            A +L E L   SD       +YE               SI   G +T E   P SF +L 
Sbjct: 405  ASMLFEKLKNTSD-------LYEIWIYHDCSMICSSSPSINCNGRNTKEHRLPYSFKLLA 457

Query: 1352 KEM 1354
            +E+
Sbjct: 458  QEL 460


>gi|17225288|gb|AAL37337.1| RNA polymerase B-subunit [Staphylococcus haemolyticus]
          Length = 202

 Score =  204 bits (519), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 122/202 (60%), Positives = 154/202 (76%), Gaps = 2/202 (0%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIG
Sbjct: 1   LSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L++SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G 
Sbjct: 61  LINSLSSYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           F ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 FLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 180

Query: 700 AVPLLKAEAPFVGTGMESVVAK 721
           AVPL+  EAPFVGTGME V A+
Sbjct: 181 AVPLMNTEAPFVGTGMEHVAAR 202


>gi|157781341|gb|ABV72025.1| RNA polymerase beta subunit [Enterococcus haemoperoxidus]
          Length = 226

 Score =  204 bits (518), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 90/294 (30%), Positives = 125/294 (42%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKARE-VRDT 62

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +++       +                    KI   + GD++ PGV  +V+V++  KR I
Sbjct: 63   SLRVPHGGGGI----------------VHDVKIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTP+D++LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  NEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPIDVMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D                              +DD V     +     
Sbjct: 167  ARQLGIHIATPVFDGA----------------------------NDDDVWETVREAGMAR 198

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  ++VG +YM+K
Sbjct: 199  DAKTVLYDG--------------------------RTGEPFDNRISVGVMYMIK 226



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|111283850|gb|ABH09217.1| RNA polymerase II second largest subunit [Rhodotorula mucilaginosa]
          Length = 356

 Score =  204 bits (518), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 67/380 (17%), Positives = 118/380 (31%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 52   DTMANILYYPQKPLATTRSMEYLHFRELPAGQNAVVAILCYSGYNQEDSVIMNQSSIDRG 111

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  +D+ ++S +++ E+ E   RD                  +  G+     
Sbjct: 112  LF-RSLYYRSYMDQEKKSGTIQLEEFEKPTRDTTLRLKHGTYEKLDGDGLVGLGERVSGE 170

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  + +D                +E  QR     K    T     E+   +++ 
Sbjct: 171  DIIIGKTAPIPTD---------------SEEMGQRLKTHTKRDVSTPLKSTENGLVDQVL 215

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VK+ V   R  + GDK A RHG KG +      EDMPF  +G   
Sbjct: 216  L-----TTNSEGLKFVKIRVRSTRIPEIGDKFASRHGQKGTIGITYRHEDMPFSAEGITP 270

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  L       G +                           
Sbjct: 271  DLIINPHAIPSRMTIGHLVECLLSKLSTITGNEGD------------------------- 305

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     EAI+ +LR       G  ++Y+
Sbjct: 306  ----------------------------ATP-FSEVTVEAISDLLRQYGYHSRGLEVMYN 336

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V +G  Y  +
Sbjct: 337  GHTGRKLQAQVYLGPTYYQR 356



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/405 (13%), Positives = 117/405 (28%), Gaps = 81/405 (20%)

Query: 662  DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                  
Sbjct: 1    THCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQV----------- 49

Query: 722  SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
                                             + + +  Y       +     ++ R  
Sbjct: 50   ------------------------------RMDTMANILYYPQKPLATTRSMEYLHFR-- 77

Query: 782  VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                  +L  G+N +VA + + GYN EDS+++++  +   +F S
Sbjct: 78   ----------------------ELPAGQNAVVAILCYSGYNQEDSVIMNQSSIDRGLFRS 115

Query: 842  IHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
            ++   +    + +     E            +     + +D  G++ +G  V+  DI++G
Sbjct: 116  LYYRSYMDQEKKSGTIQLEEFEKPTRDTTLRLKHGTYEKLDGDGLVGLGERVSGEDIIIG 175

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            K  P      T  E++ + +      DV        +G+   V+           K    
Sbjct: 176  KTAPI----PTDSEEMGQRLKTHTKRDVSTPLKSTENGLVDQVLLTTNSEGLKFVKIRVR 231

Query: 957  ISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
             +   E  +  A     +  I     +  +     G             + ++   + E 
Sbjct: 232  STRIPEIGDKFASRHGQKGTIGITYRHEDMPFSAEGITPDLIINPHAIPSRMTIGHLVEC 291

Query: 1017 PRSQWWQFAVQ-------DEKVQRNVESLKVQYETSKSILEDRFK 1054
              S+               E     +  L  QY      LE  + 
Sbjct: 292  LLSKLSTITGNEGDATPFSEVTVEAISDLLRQYGYHSRGLEVMYN 336


>gi|56694302|gb|AAW22891.1| RNA polymerase II second largest subunit [Cryptogramma crispa]
          Length = 537

 Score =  204 bits (518), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 74/443 (16%), Positives = 130/443 (29%), Gaps = 80/443 (18%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                 +      I   M+     + I   +     R+T             V+   L+  
Sbjct: 175  EEAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 233

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 234  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSID 291

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   IF R   D+ ++  ++ +E+ E   R+          +          G    
Sbjct: 292  RGFF-RSIFYRSYRDEEKKQGTLVKEEFERPIREHTQGMRHGSYDKXDDDGLAPPGTRVS 350

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++                  D+   +     K    T     E    ++
Sbjct: 351  GEDVIIGKTTPIAQ-----------------DDTGTQAQRYSKRDQSTCLRHSESGMVDQ 393

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ ++G 
Sbjct: 394  VLLTTNADGL-----RXVKIRVXSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGI 448

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +GQ+ E  +G     +GK+                         
Sbjct: 449  TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD----------------------- 485

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     + I+  L        G   +
Sbjct: 486  ------------------------------ATP-FTDVTVDNISKALHKCGYQXRGFETM 514

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKL 1259
            Y+G TG   +  + +G  Y  +L
Sbjct: 515  YNGHTGRRLNAMIFLGPTYYQRL 537



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 55/329 (16%), Positives = 104/329 (31%), Gaps = 36/329 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 2   EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 61

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 62  IHRDPELLVRTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S      + A    ET      D      + Y+   EEE   I+             +
Sbjct: 121 KKS-----DIRALQQKETTEPGWYDLVTKGFIEYVDTEEEETTMISM----------TIQ 165

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 166 DLVNARLHPE--EAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 223

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 224 IYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 283

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 284 IMNQSSIDRGFFRSIFYRSYRDEEKKQGT 312


>gi|148689460|gb|EDL21407.1| polymerase (RNA) III (DNA directed) polypeptide B [Mus musculus]
          Length = 1102

 Score =  204 bits (518), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 50/165 (30%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
               +   L     +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  
Sbjct: 938  VTDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPR 997

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYE- 1330
            +++T+QP  G+S  GG RLGEME  C+  YGA+ +L E L I SD    DV G+  +   
Sbjct: 998  AVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY 1057

Query: 1331 ----SIVAGN-DTFETGTPESFNVLVKEMQALGLSIDLENSRTKN 1370
                     +        P +  +L +E+Q++ +   L+ ++   
Sbjct: 1058 SGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLAKYNE 1102



 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 116/941 (12%), Positives = 259/941 (27%), Gaps = 235/941 (24%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 80  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 130

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 131 SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 180

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 181 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 239

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 240 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 296

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS---GLLKSLK 289
             +                A +    +V             +   + + +     +    
Sbjct: 297 GTEEHVMAAFGPSLEECQKAQIFTQMQVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRD 356

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
             G K L      L G  ++                                    +L+ 
Sbjct: 357 YYGNKRL-----ELAGQLLS------------------------------------LLFE 375

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           D           +       ++ A  D+ + MR   ++   V     +   +   ++ + 
Sbjct: 376 DLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSLKRFKMD 433

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             G  ++  RL+  +   +            K    ++N                     
Sbjct: 434 RQGVTQVLSRLSYISALGMMTRISSQFEKTRKACGLVKN--------------------- 472

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
                       +           D   +     +  + V     E      +  +  + 
Sbjct: 473 ------------LALMTHITTDMEDGPIIKLAGNLGVEDVNLLCGEELSYPNVFLVFLNG 520

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL--VSSLT 587
           N L  I   ++L +  +  + RA    E   +      R     +  G       +    
Sbjct: 521 NILGVIRDHKKLVSTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKKQ 579

Query: 588 SFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             A  N     +   YR   D    + V YL   EE +  IA                  
Sbjct: 580 KPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------------- 622

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
                       +    ++  P  ++ + A LIP+  ++ S R    C M +QA+  +  
Sbjct: 623 ------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI-- 674

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
                  G        +   ++A                                     
Sbjct: 675 -------GYNQRNRIDTLMYLLA------------------------------------- 690

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+P+VK                 D   L  G+N  VA M + GY+ ED+
Sbjct: 691 ---------YPQKPMVK----------TKTIELIDFEKLPAGQNATVAVMSYSGYDIEDA 731

Query: 827 MLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGI 881
           +++++  +       +  +  +    R T    +++   + + +          +D  GI
Sbjct: 732 LVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGI 791

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
              G +V    +LV K  P           + +    +   
Sbjct: 792 CSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 832



 Score =  151 bits (381), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 59/325 (18%), Positives = 105/325 (32%), Gaps = 29/325 (8%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 687  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 746

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 747  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 805

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 806  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 848

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 849  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 906

Query: 1123 NPLGVPSRMNVGQIFETHLGWA---CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            NP G PSRM V  +      WA   C   GKK    +        +    ++L K   T 
Sbjct: 907  NPHGFPSRMTVSYL------WAFQGCCSEGKKRAVSLVTDVCEDLVRHGYNYLGKDYVTS 960

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGV 1204
              T +  +          ++ K  V
Sbjct: 961  GITGEPLEAYIYFGPVYYQKLKHMV 985


>gi|117675907|emb|CAL69224.1| RNA polymerase subunit B [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 359

 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 62/172 (36%), Positives = 91/172 (52%), Gaps = 6/172 (3%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PLMT+ GTF+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W+
Sbjct: 1   GDFPLMTEKGTFIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F     I  +   D       
Sbjct: 59  EFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFKGVASIELTLEKDSILTKEE 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
           A   +         V  +    ++++         L K  + K  + LGI  
Sbjct: 119 ALKDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDK 170



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 134/354 (37%), Positives = 200/354 (56%), Gaps = 32/354 (9%)

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---------------GETGE 319
           E G  + +G  + +  + V+  G+  +        +DI +                +  +
Sbjct: 8   EKGTFIINGTERVVVSQLVRSPGVYFERQQEKTSDKDIYSARVIPSRGAWLEFEIDKRDQ 67

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + +       +     +    +    IL  +     A I  TL  D    +++AL DIYR
Sbjct: 68  VGVRIDRKRKQSVTVFLKALGLTSEQIL--EEFKGVASIELTLEKDSILTKEEALKDIYR 125

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAI 439
            +RPG+      A ++ +  +F+  +YDL+ VGR K+N +L +D       +  EDI+A 
Sbjct: 126 KLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKINRKLGIDKQLTDSVLTVEDILAT 185

Query: 440 IKILVDLRNGKG---------------TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER 484
           IK LV L   +                 +DDID+ GNRR+R+VGE+++NQ R GL RMER
Sbjct: 186 IKYLVSLHANETKMNGTRDGKPVELRLDVDDIDHFGNRRIRAVGELIQNQVRTGLSRMER 245

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
            ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L+ +TH RRLSAL
Sbjct: 246 VVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQLSQFMDQNNPLAGLTHKRRLSAL 305

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           G GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL+ SL SFAR+N +GFI
Sbjct: 306 GPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASFARINPFGFI 359


>gi|56694330|gb|AAW22905.1| RNA polymerase II second largest subunit [Welwitschia mirabilis]
          Length = 553

 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 109/703 (15%), Positives = 192/703 (27%), Gaps = 150/703 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +   T +   +S     N 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSSANPILEFLEEW-GTENFEEVSPSNIPNA 59

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
                 N        + E LV         +         D +P+  V     L       
Sbjct: 60   TKIFVNGCWVGIHRYPETLVKTLKQLRRQV---------DVNPEVGVVRDIPLRELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+  +   +    E +        +VAK  G +E VD      
Sbjct: 111  DYGRCSRPLFVVEKQQLLI--KKSHIIRLQERMSPDEGWHDLVAK--GFIEYVDTE---- 162

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               E     S +  D+ +  K      +       +                        
Sbjct: 163  --EEETTMISMTITDLVQARKNPLEAYSHTYTHCEI----------------------HP 198

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
            +L   +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 199  SLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ +R  ++ +E+    +RD          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKRMGTLVKEEFGRPSRDNTAGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T  + D                        E+   +Y   
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTTPTNQD------------------------ENAGGRYTRR 384

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                  R        Q         LR VK+ +   R  Q GDK + RHG KG V     
Sbjct: 385  DQSTSMRHSESGMVDQVLLTTNQDGLRFVKIRMRSVRIPQIGDKFSSRHGQKGTVGMTYC 444

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 445  QEDMPWTIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNI 504

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 505  SKALHKCGYQMRGFETM------------------------------------------- 521

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                 +G +    G         + +G  Y  +L HMV DK++
Sbjct: 522  ----YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDDKIH 553



 Score =  117 bits (292), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 75/496 (15%), Positives = 140/496 (28%), Gaps = 104/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  S    +  ++       + ++   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSSANPILEFLEEWGTENFEEVSPSNI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGR 568
            +A   F     +         +  +   RR   +    GV R     E+R ++  +   
Sbjct: 57  PNATKIFVNGCWVGIHRYPETLVKTLKQLRRQVDVNPEVGVVRDIPLRELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +  S     +        +P     D      + Y+   EEE   I+
Sbjct: 116 SRPLFVVEKQQLLIKKSHIIRLQ-----ERMSPDEGWHDLVAKGFIEYVDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R     +          +  P  ++ + AS+IPF +++ S 
Sbjct: 171 M----------TITDLVQARKNP--LEAYSHTYTHCEIHPSLILGVCASIIPFPDHNQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 248

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 249 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 273

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITRDIPN 867
            N +VA   + GYN EDS+++++  +    F S+    +    +    L  EE  R   +
Sbjct: 274 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKRMGTLVKEEFGRPSRD 333

Query: 868 ----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
               +       +D+ G+   G  V+  D+++GK TP  +                    
Sbjct: 334 NTAGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPTNQDENAGG-----------RYT 382

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 383 RRDQSTSMRHSESGMV 398


>gi|111154412|gb|ABH07420.1| RNA polymerase II second largest subunit [Pyrgillus javanicus]
          Length = 692

 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 124/815 (15%), Positives = 233/815 (28%), Gaps = 147/815 (18%)

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
            E+ + Q++  +   +R +++++ +    ++      N             +         
Sbjct: 1    ELFRTQFQKVVKDFQRYMQKQVENGQEINLRVGFKPNIITNGLKYSLATGNWGEQKKANK 60

Query: 522  ----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
                +SQ+       S ++H RR +A     + R     + R +H TH+G ICPAET EG
Sbjct: 61   NTAGVSQVLSRYTFASTLSHLRRTNA----PIGRDGKIAKPRQLHNTHWGFICPAETPEG 116

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY----LSAMEEENRYIAQANSS 633
               GLV +L   + V   G  +   + + + +    +      L+    +        + 
Sbjct: 117  QACGLVKNLALMSAVTTGGPSQPIMKYLLEKRHVEPLEDWEPQLTPHATKIFINGVWFAV 176

Query: 634  LDEDGSF-TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL--ENDDSNRV 690
            + E+  F  E     R       +     D  D   +        + P    E++ ++  
Sbjct: 177  IKEEPRFLVEHFRELRRKTHLPDMTALVWDIRDREFRINTDAGRIVRPLFVVESNPAHPN 236

Query: 691  LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                 + +  V  L A             A+ +G  I        E  D +R  I     
Sbjct: 237  KGYLVLNKSHVARLSAT----------REARMAGRPIEEYEQEPFEWPDLVREGIIDWVD 286

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
              +  T                        +V   DE+  + I   G S    +  L R 
Sbjct: 287  AEEEETL----------------------MIVMSPDELENSRIHHSGYSLPPAEDPLERV 324

Query: 811  MLVAFM---PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
              +       +       SM++          T+                          
Sbjct: 325  APLLNPYAHTFTHCEIHPSMILGVCASIIPSPTTTXXXXXXXXXXXXXXXXXXXXXXXXX 384

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
              E          +  +         +   +       +   +  + AI      +  D+
Sbjct: 385  XMET---------MANILYYPQKPLAITSSMEYLRFRDLPAGQNAIVAIACYSGYNQEDS 435

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +     +  +   +      V    +E   +    + + L R  Y ++ 
Sbjct: 436  VIMNQSSIDRGLFRSLFYRTYQDQE----KQVGHSVLEKFEKPTRADTLRLKRGTYEKID 491

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            E   +  G           K+  ++ D                +E  QR  + +K    T
Sbjct: 492  EDGIVAPGVRVSGEDIIMGKTAPMAPD---------------AEELGQRTKQHVKRDVST 536

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E+   +++      D       + VKV V   +  Q GDK A RHG KG +    
Sbjct: 537  PLRSTENGIVDQVLVTSTQDAT-----KFVKVRVRTTKVPQIGDKFASRHGQKGTIGITY 591

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF +DG   DI++NP  +PSRM +  + E  L       G++  +          
Sbjct: 592  RQEDMPFSRDGVVPDIIINPHAIPSRMTIAHLIECQLSKLASLTGQEGDATPFTAVTVTA 651

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S          G  S   ++                                       
Sbjct: 652  VSQRLRE----YGFQSRGFEVM-------------------------------------- 669

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +G +    G         V  G  Y  +L
Sbjct: 670  -----YNGHT----GR---KLVAQVFFGPTYYQRL 692



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 93/606 (15%), Positives = 161/606 (26%), Gaps = 60/606 (9%)

Query: 360 NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
               T   K  KD    + + +  G      V       +  +  KY L   G      +
Sbjct: 1   ELFRTQFQKVVKDFQRYMQKQVENGQEINLRVGFK--PNIITNGLKYSL-ATGNWGEQKK 57

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
            N +T    + + +    + +  L        R+GK       +  +       E  + Q
Sbjct: 58  ANKNTAGVSQVLSRYTFASTLSHLRRTNAPIGRDGKIAKPRQLHNTHWGFICPAETPEGQ 117

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
               +  +               +           +                      + 
Sbjct: 118 ACGLVKNLALMSAVTTGGPSQPIMKYLLEKRHVEPLEDWEPQLTPHATKIFIN-GVWFAV 176

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           I    R        + R     +M  +      R     T  G  +        F   + 
Sbjct: 177 IKEEPRFLVEHFRELRRKTHLPDMTALVWDIRDREFRINTDAGRIVRP-----LFVVESN 231

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
                  Y  +    V      LSA  E               G   EE           
Sbjct: 232 PAHPNKGYLVLNKSHVAR----LSATREARM-----------AGRPIEEYEQEPFEW-PD 275

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLE---NDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           LV    ID++DA  ++ + I  S         +     +    +   +  PLL   A   
Sbjct: 276 LVREGIIDWVDAEEEETLMIVMSPDELENSRIHHSGYSLPPAEDPLERVAPLLNPYAH-T 334

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
            T  E   +   G       +                                   +   
Sbjct: 335 FTHCEIHPSMILGVCASIIPSPT----TTXXXXXXXXXXXXXXXXXXXXXXXXXXMETMA 390

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL           I +        DL  G+N +VA   + GYN EDS+++++
Sbjct: 391 NILYYPQKPL----------AITSSMEYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQ 440

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    ++   +       E        D   +     + IDE GI+  G 
Sbjct: 441 SSIDRGLFRSLFYRTYQDQEKQVGHSVLEKFEKPTRADTLRLKRGTYEKIDEDGIVAPGV 500

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  DI++GK  P     M P+ + L     +     RD S  + S  +G V  V + +
Sbjct: 501 RVSGEDIIMGKTAP-----MAPDAEELGQRTKQHVK--RDVSTPLRSTENGIVDQVLVTS 553

Query: 947 RHGIDK 952
                K
Sbjct: 554 TQDATK 559


>gi|507769|gb|AAA19557.1| RNA polymerase beta subunit [Candidatus Liberibacter africanus]
          Length = 147

 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 121/129 (93%), Positives = 124/129 (96%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           RKFFGKNPEIIDIPDLIEVQKASYD FLMMN AP++RPNEGLQAAFKSVFPI AFSGAAM
Sbjct: 18  RKFFGKNPEIIDIPDLIEVQKASYDQFLMMNTAPEDRPNEGLQAAFKSVFPIKAFSGAAM 77

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           LEFVSYEFDPPKFDVDDCL RDLTYAVPLKI LRLIVFDVDEFTGAKSIKDIKEQSIYMG
Sbjct: 78  LEFVSYEFDPPKFDVDDCLRRDLTYAVPLKIILRLIVFDVDEFTGAKSIKDIKEQSIYMG 137

Query: 134 DLPLMTKDG 142
           D+PLMTKDG
Sbjct: 138 DVPLMTKDG 146


>gi|89142789|emb|CAJ57590.1| RNA polymerase subunit B [Microbacterium testaceum]
          Length = 362

 Score =  203 bits (517), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 61/175 (34%), Positives = 93/175 (53%), Gaps = 6/175 (3%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTNKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  +  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDILAEFSGFDSIEETLSKDTILT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              A   +         V  +    ++++    +    L K  + K  + LG+  
Sbjct: 119 KEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINQKLGLDK 173



 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 129/258 (50%), Positives = 173/258 (67%), Gaps = 15/258 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR K
Sbjct: 105 DSIEETLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 164

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L LD P     +  +DI+A IK LV L  G                   DDIDN G
Sbjct: 165 INQKLGLDKPLSDSVLTVDDIVATIKYLVRLHRGDVTFDGVRGGKAAEIRLDTDDIDNFG 224

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 225 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 284

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 285 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 344

Query: 581 GLVSSLTSFARVNAYGFI 598
           GL+ SL SFAR+N +GFI
Sbjct: 345 GLIGSLASFARINPFGFI 362


>gi|68300792|gb|AAY89339.1| RNA polymerase II second largest subunit [Berberidopsis corallina]
          Length = 853

 Score =  203 bits (517), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 121/909 (13%), Positives = 257/909 (28%), Gaps = 187/909 (20%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDCEEVTETQDFTK--VFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     K  Y 
Sbjct: 65  YQNSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNKYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 GEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q  +     L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRPEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERI---SSVDIDSVMPQDLINAKPVVSAVCE 515
               +   + + L     + +      I E +   S+ + + + P  +  A  +    C 
Sbjct: 413 TPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCW 472

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              ++++                         GV R     E+R ++  +     P    
Sbjct: 473 VDVNTEV-------------------------GVIRDIRLKELR-LYTDYGRCSRPLFIV 506

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           E   + L+      A        +       D      + Y+   EEE   I+       
Sbjct: 507 EKQRL-LIKKKDIQALQQRESHEDGG---WHDLVAKGFIEYVDTEEEETTMISM------ 556

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
                  +L+  +   E      E     +  P  ++ + AS+IPF +++ S R      
Sbjct: 557 ----TINDLITAKLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 610

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +                           R   +  V                 
Sbjct: 611 MGKQAMGIYVTNYQL--------------------RMDTLAYV----------------- 633

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                                 Q+PLV                      L  G N +VA 
Sbjct: 634 ------------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAI 665

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSE 870
             + GYN EDS+++++  +    F S+    +    +      +E        +   +  
Sbjct: 666 TCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRH 725

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +D+ G+   G  V+  D+++GK TP  +           A         RD S  
Sbjct: 726 GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRRDHSTS 776

Query: 931 VPSGVSGTV 939
           +    SG V
Sbjct: 777 LRHSESGMV 785



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/353 (15%), Positives = 107/353 (30%), Gaps = 40/353 (11%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSMLI--SERMV 834
            LV  G  + V   +      S  + DL   + N   A+   +       S+++     ++
Sbjct: 535  LVAKGFIEYVDTEEEETTMISMTINDLITAKLNPEEAYSETYTHCEIHPSLILGVCASII 594

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 595  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 643

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 644  TRAMEHLHFRQLPAGINAIVAITCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 702

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +  ++ +E      R+          +          G           K+T +S     
Sbjct: 703  KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ---- 758

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         D+   +     +  + TS    E    +++      D +     R V
Sbjct: 759  -------------DDAQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFV 800

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +
Sbjct: 801  KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 853


>gi|1173149|sp|P41187|RPOB_LIBAF RecName: Full=DNA-directed RNA polymerase subunit beta; Short=RNAP
           subunit beta; AltName: Full=RNA polymerase subunit beta;
           AltName: Full=Transcriptase subunit beta
          Length = 146

 Score =  203 bits (517), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 121/129 (93%), Positives = 124/129 (96%)

Query: 14  RKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAM 73
           RKFFGKNPEIIDIPDLIEVQKASYD FLMMN AP++RPNEGLQAAFKSVFPI AFSGAAM
Sbjct: 18  RKFFGKNPEIIDIPDLIEVQKASYDQFLMMNTAPEDRPNEGLQAAFKSVFPIKAFSGAAM 77

Query: 74  LEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMG 133
           LEFVSYEFDPPKFDVDDCL RDLTYAVPLKI LRLIVFDVDEFTGAKSIKDIKEQSIYMG
Sbjct: 78  LEFVSYEFDPPKFDVDDCLRRDLTYAVPLKIILRLIVFDVDEFTGAKSIKDIKEQSIYMG 137

Query: 134 DLPLMTKDG 142
           D+PLMTKDG
Sbjct: 138 DVPLMTKDG 146


>gi|46277269|gb|AAS86825.1| RNA polymerase II second largest subunit [Platanus orientalis]
          Length = 536

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 75/479 (15%), Positives = 135/479 (28%), Gaps = 84/479 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 138  HDLVAKGYIEYVDTEEEETTMISMTINDLVTARLNPEEAYSETYTHCEIHPSLILGVCAS 197

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+   L+      +  V        +    +  
Sbjct: 198  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEH 254

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 255  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 313

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R+          +          G           K+T ++ +         
Sbjct: 314  KEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQE--------- 364

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                    E   +     +  + TS    E    +++      D +     R VKV +  
Sbjct: 365  --------EPQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRS 411

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 412  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 471

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 472  MGKVAAHMGKEGD----------------------------------------------- 484

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 485  ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLSAMIFLGPTYYQRL 536



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 73/482 (15%), Positives = 139/482 (28%), Gaps = 101/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   ++ +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHRNPELLVNTLRKLRRQVDVNTEVGVIRDIHLKELR-LYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                   +    G+         D      + Y+   EEE   I+              
Sbjct: 123 KKKDIRALQQRDGGWH--------DLVAKGYIEYVDTEEEETTMISM----------TIN 164

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 165 DLVTARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 222

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 223 IYVTNYQL--------------------RMDTLAYV------------------------ 238

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 239 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 277

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 278 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 337

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +                     RD S  +    SG
Sbjct: 338 DDGLAPPGTRVSGEDVIIGKTTPIAQEEP---------QGQASRYTRRDHSTSLRHSESG 388

Query: 938 TV 939
            V
Sbjct: 389 MV 390


>gi|37956405|gb|AAP15374.1| RNA polymerase beta subunit [Desulfuromonas acetexigens]
          Length = 208

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 128/207 (61%), Positives = 160/207 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  ++DS+MP DLIN+KPV + V EFF SSQLSQ  +  N LS ITH RRLSALG GG
Sbjct: 2   RMSLQEVDSLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRLVKDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT +V Y SA+EEE   IAQAN+ L+ED +F  EL+  R  GE +L+ RE I+ +D SP
Sbjct: 122 VVTTEVKYFSALEEEGHAIAQANAMLNEDCTFVNELINARKNGEFMLMNREDIELMDVSP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCN 695
            Q+VS+AA+LIPFLENDD+NR LMG N
Sbjct: 182 XQLVSVAAALIPFLENDDANRALMGSN 208


>gi|56694290|gb|AAW22885.1| RNA polymerase II second largest subunit [Equisetum hyemale]
          Length = 539

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 103/687 (14%), Positives = 189/687 (27%), Gaps = 149/687 (21%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   + +            + +    N        EE +  +    +
Sbjct: 2    ETPEGQACGLVKNLALMSYITVGSAANPILEFLEEWSTEN-------FEEISPAVIPQAT 54

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +G +           + +   R ++   D + +  V     L       D  R   
Sbjct: 55   KIFVNGCWVGIHRDPELLVKTLRQLRRQV---DVNTEVGVVRDIILKELRLXTDYGRCSR 111

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +      L+K              +  SG                 +  I  V+ + 
Sbjct: 112  PLFIVENQRLLIKKSDIRALQ---QRDSSDSGW-----------YDLVAKGFIEYVDTEE 157

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            + +T        +   R+N     +                    PS  LG       + 
Sbjct: 158  EETTMISMTISDVVNARNNPEEAYS-----------DTYTHCEIHPSMILG-------VC 199

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 200  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 233

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 234  ---LRXDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQ 290

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        IF R   D+ ++  ++ +E+ E   RD  +       +          G
Sbjct: 291  SSIDRGFF-RSIFYRSYRDEEKKQGTLVKEEFERPNRDNTNGMRHGSYDKLDDDGLAPPG 349

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T L  D   +  R                            + L   
Sbjct: 350  TRVSGEDVIIGKTTPLPXDDSGQVQRYTK---------------------RDQSTCLRHS 388

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                I+++          LR VK+ V   R  Q GDK + RHG  G V      EDMP+ 
Sbjct: 389  ESGMIDQVLL--TTNADGLRFVKIRVRSVRIPQIGDKFSSRHGQXGTVGMTYTQEDMPWS 446

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 447  QEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 487

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     ++I+  L        G
Sbjct: 488  ----------------------------------ATP-FTDVTVDSISKALHKCGYQMRG 512

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +Y+G TG      + +G  Y  +L
Sbjct: 513  FETMYNGHTGRRLSAMIFLGPTYYQRL 539



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 54/329 (16%), Positives = 101/329 (30%), Gaps = 36/329 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 5   EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 64

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R +   +     P    E   + +
Sbjct: 65  IHRDPELLVKTLRQLRRQVDVNTEVGVVRDIILKELR-LXTDYGRCSRPLFIVENQRLLI 123

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S    A           Y  V  G     + Y+   EEE   I+              
Sbjct: 124 KKS-DIRALQQRDSSDSGWYDLVAKGF----IEYVDTEEEETTMISM----------TIS 168

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           ++V  R   E      +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 169 DVVNARNNPE--EAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 226

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 227 IYVTNYQLRXDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSV 286

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 287 IMNQSSIDRGFFRSIFYRSYRDEEKKQGT 315


>gi|157781325|gb|ABV72017.1| RNA polymerase beta subunit [Enterococcus moraviensis]
          Length = 226

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 91/292 (31%), Positives = 120/292 (41%), Gaps = 72/292 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAR------ 57

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                       E                   KI   + GD++ PGV  +V+V++  KR I
Sbjct: 58   -----------EVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMPFL DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D                              +DD V     +     
Sbjct: 167  ARQLGIHIATPVFDGA----------------------------NDDDVWETVREAGMAS 198

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
               T ++DG                           TGEPFD  ++VG +YM
Sbjct: 199  DAKTVLYDG--------------------------RTGEPFDNRISVGVMYM 224



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|83415493|gb|ABC17954.1| RNA polymerase II second largest subunit [Phycomyces blakesleeanus]
          Length = 801

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 106/715 (14%), Positives = 207/715 (28%), Gaps = 93/715 (13%)

Query: 427  DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI 486
                 +      +I  L+     +  +DD D+ G +R+   G ++   +RL   ++ + +
Sbjct: 165  KTETRKSYFFGYMIHRLLLAALERRELDDRDHYGKKRMDLAGPLMAGLFRLLFKKLTKDV 224

Query: 487  --KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNS 531
                +              + +  + + +     +               +SQ+      
Sbjct: 225  AKYLQKCIESSREFNLTLAVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVLNRYTF 284

Query: 532  LSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
             S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L   + 
Sbjct: 285  ASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSY 340

Query: 592  VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
            ++  G   TP     +     ++  LSA    +      N           ELV    + 
Sbjct: 341  IS-VGSAATPLIMFLEEWAMENLEELSANNIPDATKVFVNGVWIGVHRDPGELVNSLKSM 399

Query: 652  EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
               +         D SP+  +             D+ R      + +     L  +    
Sbjct: 400  RRSV---------DISPEVSIVRDIREKELRMYTDAGRCCRPLFLVQDQQLRLTRDHL-- 448

Query: 712  GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                     + S         GIVE VDA       +    +         +     +  
Sbjct: 449  ---SRLQDPEDSYRWQDMISDGIVEYVDADEEETAMICMTPEDLVEARMAAQFGAPLQEE 505

Query: 772  QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            ++     +   + G            PS  LG       +  + +P+  +N         
Sbjct: 506  RDLASRVKS--QTGAYSHTWTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQS 556

Query: 832  RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
             M  + +   +++  ++                                +  +       
Sbjct: 557  AMGKQAMG--VYLTNYQTRM---------------------------DTMANILYYPQKP 587

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
                  +       +   +  + AI      +  D+ +   S +   +    +F R  +D
Sbjct: 588  LTTTRSMEFLRFRELPAGQNAVVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYMD 646

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSD 1011
              +++  +  E+ E   RD                  I  G           K+  + ++
Sbjct: 647  AEKKAGMMFMEEFEKPTRDSTLRLKHGTYEKLEEDGLIAPGTRVSGDDIIIGKTAPIPAE 706

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                  R+Q          ++     +  Q                             L
Sbjct: 707  SEELGQRTQTHNKHDASTPLRSTETGIVDQVML--------------------TTNQDGL 746

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
            + VKV V   R  Q GDK A RHG KG +      ED PF  +G   D+++NP  
Sbjct: 747  KFVKVRVRSTRVPQMGDKFASRHGQKGTIGMTYRQEDFPFSAEGITPDLIINPHA 801



 Score =  111 bits (278), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 110/844 (13%), Positives = 239/844 (28%), Gaps = 137/844 (16%)

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII--PDQGLWMDIEFDSKDI--IHV 204
            ++++++Q   +    +   K        + Y   I   P++G         K+   +++
Sbjct: 1   SEKVLIAQERMATNTVYVFAKA---PPSNVQYTAEIRSQPEKGS--------KNASPLYI 49

Query: 205 RI-----DR--------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDF 244
           ++     DR              R  +P+     ALG  ++ ++L          +  + 
Sbjct: 50  KMMRASTDRGGTGQCIRATLPYIRSDIPIVIVFRALGQVADRDVLEHICYDRNDYEMLEM 109

Query: 245 WCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT----- 299
               +  A ++    V+   +    G  V  + ++ T    + L+++ +  +G       
Sbjct: 110 LKPSIEEAFVIQDQDVALDFIGKR-GTTVGATRERRTKYATEILQKELLPHVGTAYKTET 168

Query: 300 -SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYI 358
                 G  +   ++        ++  D   +K ++           +L+         +
Sbjct: 169 RKSYFFGYMIHRLLL-AALERRELDDRDHYGKKRMDLAGPLMAGLFRLLFKK-------L 220

Query: 359 RNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
              +     K  + +      +    +  T  +  S+    + D  K   +  G  ++  
Sbjct: 221 TKDVAKYLQKCIESSREFNLTLAVKSNTITNGLKYSLATGNWGDQKKAMQARAGVSQVLN 280

Query: 419 RLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
           R    +      R          I     L N    +         +   + + L     
Sbjct: 281 RYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSY 340

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           + +      +   +    ++++      N   +  A   F     +    +    ++ + 
Sbjct: 341 ISVGSAATPLIMFLEEWAMENLEELSANN---IPDATKVFVNGVWIGVHRDPGELVNSLK 397

Query: 537 HTRRLSALGQG-GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
             RR   +     + R     E+R    T  GR C         +       +   ++  
Sbjct: 398 SMRRSVDISPEVSIVRDIREKELRM--YTDAGRCC----RPLFLVQDQQLRLTRDHLSRL 451

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT-------EELVFCR 648
              E  YR   D      V Y+ A EEE   I      L E            EE     
Sbjct: 452 QDPEDSYR-WQDMISDGIVEYVDADEEETAMICMTPEDLVEARMAAQFGAPLQEERDLAS 510

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
               +           +  P  ++ I AS+IPF +++ S R      M +QA+ +     
Sbjct: 511 RVKSQTGAYSHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLT-- 568

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
                         + A I+      +    ++  +          +   +  Y      
Sbjct: 569 -------NYQTRMDTMANILYYPQKPLTTTRSMEFLRFRELPAGQNAVVAILCYSG---- 617

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                   NQ                    S  +   ++ R +  +       + E    
Sbjct: 618 -------YNQE------------------DSVIMNQSSIDRGLFRSLFFRTYMDAEKKAG 652

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           +            + +EEFE   RD+             +     + ++E G+I  G  V
Sbjct: 653 M------------MFMEEFEKPTRDS----------TLRLKHGTYEKLEEDGLIAPGTRV 690

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           +  DI++GK  P        E + L            D S  + S  +G V  V +    
Sbjct: 691 SGDDIIIGKTAPI-----PAESEELGQRTQTHNKH--DASTPLRSTETGIVDQVMLTTNQ 743

Query: 949 GIDK 952
              K
Sbjct: 744 DGLK 747


>gi|46277324|gb|AAS86852.1| DNA-dependent RNA polymerase II [Hydnotryopsis sp. Trappe 17231]
          Length = 557

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 96/678 (14%), Positives = 186/678 (27%), Gaps = 126/678 (18%)

Query: 585  SLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +L   + V+     E    +    + +V  +     +      ++      +  D  F  
Sbjct: 1    NLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIV 60

Query: 643  ELVFCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGCNMQRQ 699
              +        I      I  I     ++ + A      +  ++ND ++       +Q+ 
Sbjct: 61   RTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKY 120

Query: 700  AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
             +  L+ +      G+E          I     G+VE +DA       +    +   +  
Sbjct: 121  HIEKLEDDKD----GVEEEQRYGWQGLIS---EGVVEYIDAEEEETVMIVMTPEDLETSR 173

Query: 760  DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
              +   + Q+        QR    V             PS  LG       +  + +P+ 
Sbjct: 174  QFHAGYEIQQEVDPA---QRVKAAVNKYAHTWTHCEIHPSMILG-------ICASIIPFP 223

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
             +N       S R   +       +  F    R+                          
Sbjct: 224  DHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM-----------------------D 254

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  +             +       +   +  + AI      +  D+ +   S +   +
Sbjct: 255  TMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGL 314

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R  +D+ +R      E+ E   R           +       +  G       
Sbjct: 315  F-RSLFYRTYMDQEKRIGMNVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVSGED 373

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +S +      R+++         ++     +  Q                  
Sbjct: 374  IIIGKTAPISPNTEELGQRTKFHTKRDVSTPLRSTENGIVDQ------------------ 415

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 416  --VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVPD 473

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 474  LIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------------- 507

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     ++++ +LR       G  I+Y+G
Sbjct: 508  ---------------------------ATP-FTDVTVDSVSKLLREHGYQSRGFEIMYNG 539

Query: 1240 LTGEPFDRPVTVGYIYML 1257
             TG      V +G  Y  
Sbjct: 540  HTGRKLVVQVFLGPTYYQ 557



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 71/481 (14%), Positives = 127/481 (26%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 19  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 72

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +  G 
Sbjct: 73  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKYHIEKLEDDKDGV 132

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E              V Y+ A EEE   I      L+    F       +E+   +   
Sbjct: 133 EEEQRYGWQGLISEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEVDPAQRVK 192

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +          +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 193 AAVNKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT----- 247

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                      + A I+                                    +KF+   
Sbjct: 248 ----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFRELP 282

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                    L   G   + + +I +  S D G                  + E  + ++ 
Sbjct: 283 AGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLFY-------RTYMDQEKRIGMN- 333

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                       +EEFE   R           +   +       +DE G++  G  V+  
Sbjct: 334 -----------VVEEFEKPTR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSGE 372

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P      +P  + L      K    RD S  + S  +G V  V +       
Sbjct: 373 DIIIGKTAPI-----SPNTEELGQR--TKFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 425

Query: 952 K 952
           K
Sbjct: 426 K 426


>gi|89142777|emb|CAJ57584.1| RNA polymerase subunit B [Microbacterium oxydans]
          Length = 363

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 2   VFMGDFPLQTDKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 59

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D    
Sbjct: 60  AWLEFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVT 119

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 120 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 165



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 125/256 (48%), Positives = 171/256 (66%), Gaps = 16/256 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 108 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 167

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P     +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 168 HKLGLDQPLTSSVLTVEDIVATIKYLVRLHAGTEETFTGIRGGKKAEIRLATDDIDNFGN 227

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 228 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 287

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 288 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 347

Query: 582 LVSSLTSFARVNAYGF 597
           L+ +L +FAR+N +GF
Sbjct: 348 LIGALATFARINPFGF 363


>gi|194320271|gb|ACF48374.1| DNA-dependent RNA polymerase II second largest subunit [Aspicilia
            cinerea]
          Length = 317

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 69/393 (17%), Positives = 122/393 (31%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNFDERMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R  +D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFYRAYVDQEKR---IGMATVEQFEKPMRSDTLRLKHGTYDKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  +  D      R++                 +K    T   
Sbjct: 119  LVAPGVRVSGEDVIIGKTAPIQPDAEELGQRTKL---------------HIKRDASTPLR 163

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 164  TTENGIVDKVLL-----TTNSEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G  ++Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 27/161 (16%), Positives = 57/161 (35%), Gaps = 15/161 (9%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNFDERMDTMSNILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYTG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYVDQEKRIGMATVEQFEKPMRSDTLRLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           +D+ G++  G  V+  D+++GK  P         ++    I
Sbjct: 114 LDDDGLVAPGVRVSGEDVIIGKTAPIQPDAEELGQRTKLHI 154


>gi|89142773|emb|CAJ57582.1| RNA polymerase subunit B [Microbacterium luteolum]
          Length = 364

 Score =  203 bits (516), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 2   VFMGDFPLQTDKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 59

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D    
Sbjct: 60  AWLEFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVT 119

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 120 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 165



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 126/257 (49%), Positives = 173/257 (67%), Gaps = 16/257 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 108 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 167

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 168 HKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFTGIRGGKKAEIRLATDDIDNFGN 227

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 228 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 287

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 288 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 347

Query: 582 LVSSLTSFARVNAYGFI 598
           L+ +L +FAR+N +GFI
Sbjct: 348 LIGALATFARINPFGFI 364


>gi|22217989|emb|CAC86922.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|22217991|emb|CAC86923.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|22217999|emb|CAC86927.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|22218003|emb|CAC86929.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 207

 Score =  202 bits (515), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 125/207 (60%), Positives = 155/207 (74%), Gaps = 2/207 (0%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS ++H RRLSALG GG+ R RAG E+
Sbjct: 1   TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSHKRRLSALGPGGLTRDRAGYEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYRKV    G+VTN++V+
Sbjct: 61  RDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYRKVDRATGRVTNEIVW 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F EE+V  R  G         +DF+D SPKQVV++A 
Sbjct: 121 LTADEEDEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVVDFVDVSPKQVVAVAT 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPL 703
           + IPFLENDDSNR LMG NMQRQAVPL
Sbjct: 181 ACIPFLENDDSNRALMGANMQRQAVPL 207


>gi|89142775|emb|CAJ57583.1| RNA polymerase subunit B [Microbacterium maritypicum]
          Length = 363

 Score =  202 bits (515), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTDKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164



 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 126/257 (49%), Positives = 173/257 (67%), Gaps = 16/257 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 107 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 166

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 167 HKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFTGIRGGKKAEIRLATDDIDNFGN 226

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 227 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 286

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 287 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 346

Query: 582 LVSSLTSFARVNAYGFI 598
           L+ +L +FAR+N +GFI
Sbjct: 347 LIGALATFARINPFGFI 363


>gi|37956393|gb|AAP15369.1| RNA polymerase beta subunit [Geobacter bemidjiensis Bem]
          Length = 211

 Score =  202 bits (515), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 121/208 (58%), Positives = 164/208 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVSEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT++V + SA+EEE   IAQAN+ +D+DG F  + +  R +GE +LV R++++ +D +P
Sbjct: 122 KVTDEVRFFSALEEEGHAIAQANAEIDKDGRFAADYISARKSGEFVLVGRDELELMDVAP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNM 696
            Q+VS+AASLIPFLENDD+NR LMG N+
Sbjct: 182 MQLVSVAASLIPFLENDDANRALMGSNI 209


>gi|162568922|gb|ABY19387.1| RNA polymerase beta subunit [Klebsiella alba]
          Length = 198

 Score =  202 bits (515), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 123/197 (62%), Positives = 157/197 (79%)

Query: 488 ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
           +R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG G
Sbjct: 1   QRLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPG 60

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV D
Sbjct: 61  GLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTD 120

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           G VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S
Sbjct: 121 GVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVS 180

Query: 668 PKQVVSIAASLIPFLEN 684
            +QVVS+ ASLIPFLE+
Sbjct: 181 TQQVVSVGASLIPFLEH 197


>gi|298239786|gb|ADI70692.1| DNA-directed RNA polymerase beta subunit [Solimonas soli]
          Length = 184

 Score =  202 bits (515), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 112/183 (61%), Positives = 135/183 (73%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 2   EFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 61

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL  +AR N YGF+ET YRKV DGKVT+ V YLSA+EE    IAQAN+ L
Sbjct: 62  PEGPNIGLINSLACYARTNEYGFLETAYRKVVDGKVTDQVEYLSAIEEGRYVIAQANAEL 121

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           D    F  +LV  R   E  L   +KI ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG 
Sbjct: 122 DAKNHFKGDLVSVRFQNEFTLTAPDKIQYMDVSPRQIVSVAAALIPFLEHDDANRALMGP 181

Query: 695 NMQ 697
           NMQ
Sbjct: 182 NMQ 184


>gi|157429505|gb|ABV56819.1| RNA polymerase beta subunit [Streptococcus marimammalium]
          Length = 219

 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 79/257 (30%), Positives = 114/257 (44%), Gaps = 60/257 (23%)

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
             K+  +L   +  +  +     F  +  +V+     +    +     +      +I    
Sbjct: 23   VKEGDILVGKVTPKGEKDLSADFGDKSREVRDTSLRVPHGGDGVVRDV------RIFTRA 76

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  GV  +V+V++A KR ++ GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+
Sbjct: 77   NGDELQSGVNMLVRVYIAQKRKVKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIM 136

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            LNPLGVPSRMN+GQ+ E HLG A   L   + + + D     D+                
Sbjct: 137  LNPLGVPSRMNIGQVMELHLGMAARSLDVHMATPVFDGATAEDLWETVKEAGMDSDAK-- 194

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                      T ++DG                           T
Sbjct: 195  --------------------------TVLYDG--------------------------RT 202

Query: 1242 GEPFDRPVTVGYIYMLK 1258
            GEPFD  V+VG +YM+K
Sbjct: 203  GEPFDNRVSVGVMYMIK 219



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 49/86 (56%), Positives = 60/86 (69%), Gaps = 7/86 (8%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV EE LK++DE G++ +GAEV  GDILVGK+TPKGE  ++       A FG+K+ +VR
Sbjct: 1   PNVGEEALKDLDEMGVVRIGAEVKEGDILVGKVTPKGEKDLS-------ADFGDKSREVR 53

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DVRIF R   D
Sbjct: 54  DTSLRVPHGGDGVVRDVRIFTRANGD 79


>gi|300394718|gb|ADK11897.1| DNA-directed RNA polymerase II subunit two [Leucogyrophana arizonica]
          Length = 405

 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 69/443 (15%), Positives = 120/443 (27%), Gaps = 88/443 (19%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             W       SM+  +   ++            ++       +G       +         
Sbjct: 49   TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM------- 101

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 102  ----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 157

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            V   +    I+ R  +D  ++S   + E+ E   RD          +       I  G  
Sbjct: 158  VDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTG 216

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +  D      R++          ++     +  Q             
Sbjct: 217  VSGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI---------- 266

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                             + VKV V   R  Q GDK A RHG KG +      EDMPF  +
Sbjct: 267  ----------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAE 316

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  +PSRM +G + E  L      +G +                       
Sbjct: 317  GIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD--------------------- 355

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP F     E++++ LR       G  
Sbjct: 356  --------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLE 382

Query: 1235 ILYDGLTGEPFDRPVTVGYIYML 1257
            ++Y G TG      + +G  Y  
Sbjct: 383  VMYHGHTGRKLQAQIYLGPTYYQ 405



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 50/332 (15%), Positives = 100/332 (30%), Gaps = 81/332 (24%)

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVS 673
           EEE   I      L+     +  +       +          +        +  P  ++ 
Sbjct: 3   EEETVMIYMIPEDLENSRLQSAGIDPRANDEDYDPAARLKAGINAHTWTHCEIHPSMILG 62

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                              
Sbjct: 63  VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV----------------------- 99

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
                                + + +  Y       +     +  R              
Sbjct: 100 ------------------RMDTMANILYYPQKPLATTRSMEYLKFR-------------- 127

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA + + GYN EDS+++++  V   +F SI+   +  + + 
Sbjct: 128 ----------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKK 177

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
           + +   E            +       I++ G+I  G  V+  DI++GK  P        
Sbjct: 178 SGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIIIGKTAPI----PPD 233

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            E+L +        DV        +G+   V+
Sbjct: 234 SEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 265


>gi|89142771|emb|CAJ57581.1| RNA polymerase subunit B [Microbacterium laevaniformans]
          Length = 361

 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 64/173 (36%), Positives = 91/173 (52%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G 
Sbjct: 1   FMGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  Y  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEDILAEFAGYESIADTLSKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163



 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 129/259 (49%), Positives = 175/259 (67%), Gaps = 15/259 (5%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              I +TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR 
Sbjct: 103 YESIADTLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRY 162

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L LD P     +  +DI+A IK LV L NG                  +DDIDN 
Sbjct: 163 KINQKLGLDKPLSDSVLTVDDIVATIKYLVALHNGDASIPGVRNGQAAEIRLDVDDIDNF 222

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 223 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 282

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 283 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 342

Query: 580 IGLVSSLTSFARVNAYGFI 598
           IGL+ SL SFAR+N +GFI
Sbjct: 343 IGLIGSLASFARINPFGFI 361


>gi|166865102|gb|ABZ01810.1| RNA polymerase beta-subunit [Serratia nematodiphila]
          Length = 203

 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 127/203 (62%), Positives = 161/203 (79%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
           KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG 
Sbjct: 1   KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGP 60

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V 
Sbjct: 61  GGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVR 120

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
           DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D 
Sbjct: 121 DGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDV 180

Query: 667 SPKQVVSIAASLIPFLENDDSNR 689
           S +QVVS+ ASLIPFLE+D  NR
Sbjct: 181 STQQVVSVGASLIPFLEHDAPNR 203


>gi|56694308|gb|AAW22894.1| RNA polymerase II second largest subunit [Marsilea quadrifolia]
          Length = 539

 Score =  202 bits (514), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 68/386 (17%), Positives = 116/386 (30%), Gaps = 77/386 (19%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D  +   S
Sbjct: 231  YQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDXVIMNQS 290

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +        IF R   D+ ++  ++ +E+ E  +R+          +          G 
Sbjct: 291  SIDRGFF-RSIFYRSYRDEEKKQGTLVKEEFERPSRENTSGMRHGSYDKLDDDGLAPPGT 349

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++                  DE   +     K    T     E   
Sbjct: 350  RVSGEDVIIGKTTPVAQ-----------------DETGTQAQRYTKRDQSTCLRHSESGM 392

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
             +++      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ +
Sbjct: 393  XDQVLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQ 447

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 448  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------- 487

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP  D    + I+  L        G 
Sbjct: 488  ---------------------------------ATPXTD-VTVDNISKALHKCGYQMRGF 513

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKL 1259
              +Y+G TG      + +G  Y  +L
Sbjct: 514  ETMYNGHTGRRLTAMIFLGPTYYQRL 539



 Score =  102 bits (255), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 56/400 (14%), Positives = 103/400 (25%), Gaps = 46/400 (11%)

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG   GLV +L   + +            + +   T +   +S            N 
Sbjct: 1   ETPEGQACGLVKNLALMSYITVGSAANPILEFLEEWS-TENXEEISPAVITQATKIFVNG 59

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKI------DFIDASPKQVVSIAASLIPFLENDD 686
                    + LV         +    ++         +          +  +  +EN  
Sbjct: 60  CWVGIHRNPDLLVRTLRQLRRQVDVNTEVGVVRDFSLKELRLYTDYGRCSRPLFIVENQR 119

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGM-------ESVVAKSS---GAAIVAKRAGIVE 736
                      +Q           V  G        E      S      + A+      
Sbjct: 120 LVIKKSDIRDLQQRESSESGWYDLVTKGFIEYVDTEEEETTMISXTIQDLVNARLHPEEA 179

Query: 737 QVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             D      I                      + + Q+    Q   + V +   R D +A
Sbjct: 180 YSDXYTHCEIHPSMIXXXXXXXXXXXXHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLA 239

Query: 796 DGPST--------------DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                  L  G N +VA   + GYN ED +++++  +    F S
Sbjct: 240 YVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDXVIMNQSSIDRGFFRS 299

Query: 842 IHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           I    +    +      +E        +   +       +D+ G+   G  V+  D+++G
Sbjct: 300 IFYRSYRDEEKKQGTLVKEEFERPSRENTSGMRHGSYDKLDDDGLAPPGTRVSGEDVIIG 359

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           K TP  +                +    RD S  +    S
Sbjct: 360 KTTPVAQDE---------TGTQAQRYTKRDQSTCLRHSES 390


>gi|520511|gb|AAA50226.1| RNA polymerase II, second largest subunit [Crassostrea gigas]
          Length = 859

 Score =  202 bits (514), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 60/384 (15%), Positives = 113/384 (29%), Gaps = 66/384 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGE--SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
             G+      V    +  G + P+    +  + E    R +       V   S    +   
Sbjct: 540  MGVYITNFHVRMDTLAHGLLYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQED 599

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +++     R            + E  + L     D++ I ++     +  +       
Sbjct: 600  SVIINASAIERGFFRSFFFRSYKDSESKKGL-----DQEEIFEKPTRENVQGMRQAVYDK 654

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                G      + S  I            +     +  +E    ++    + +  R    
Sbjct: 655  LDEDG------IISPGIRVSGDDVLIGKTLTLPANEDELEGTTKRFTKRDASVFMRRSET 708

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                Q    +     +  K+ V   +  Q GDK A RHG KG        EDMPF  +G 
Sbjct: 709  GIIDQVMITLNQEGYKFCKIRVRTVKTPQIGDKFASRHGQKGTCGITYRQEDMPFTCEGI 768

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  VPSRM +G + E   G      G+   +   +                  
Sbjct: 769  TPDIIINPHAVPSRMTIGHLIECLQGKVAANKGEIGDATPFN------------------ 810

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                               D  + + ++++L      + G  +L
Sbjct: 811  -----------------------------------DAVNVQKVSNLLHQYGYHQRGNEVL 835

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLN 1260
            ++G TG   +  + +G  Y  +L 
Sbjct: 836  FNGFTGRKLNAQIFLGPTYYQRLK 859



 Score =  147 bits (372), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 110/682 (16%), Positives = 221/682 (32%), Gaps = 64/682 (9%)

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDI 377
           G+  I     I ++    I    +  +    +       +    ++        +A +  
Sbjct: 60  GQRIIGILPYIKQEIPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ 119

Query: 378 YRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
            + +    + +      +         KY    + +  +      D  +  +      + 
Sbjct: 120 EQNVALNFIGSRGARPGV---TKEKRIKYAREILQKEMLPHVGVSDFCETKK---AYFLG 173

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID- 496
            ++  L+    G+  +DD D+ GN+R+   G +L   +R     + + ++          
Sbjct: 174 YMVHRLLLAAIGRREVDDRDHYGNKRLDLAGPLLAFLFRGLFRNLMKEVRLYAQKFIDRG 233

Query: 497 -SVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLS 542
                +  I  + +   +     +               +SQ+   +   S ++H RRL+
Sbjct: 234 KDFNLELAIKTRIITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLN 293

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           +     + R       R +H T +G ICPAET EG  +GLV +L   A ++         
Sbjct: 294 S----PIGRDGKLARPRQLHNTQWGMICPAETPEGSAVGLVKNLALMAYISVGSQPSPIL 349

Query: 603 RKVCDGKVTN-DVVYLSAMEEENRYIAQAN--SSLDEDGSFTEELVFCRCAGEEILVPRE 659
             + +  + N + V  SA+++  +            +       L   R   + I+    
Sbjct: 350 EFLEEWSMENLEEVSPSAIQDATKIFVNGCWVGIHRDPEQLMNTLRKLRREMDIIVSEVS 409

Query: 660 KI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM--QRQAVPLLKAEAPFVGTG-M 715
            I D  D   +          P L  ++   +L   ++   +Q      +    V +G +
Sbjct: 410 MIRDIRDREIRIYTDAGRICRPLLIVENQKLLLKQSHIKQLKQREYNNYSWQDLVASGVV 469

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVD------AIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           E +      + ++A     +   D           I         ++           + 
Sbjct: 470 EYIDPLEEESIMLAMTPDDLSDKDVQYCSTYTHCEIHPAMILGVCASIIPFPDHNQSPRN 529

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADG--------------PSTDLGDLALGRNMLVAF 815
           + Q+    Q   V + +   R D +A G                    +L  G N +VA 
Sbjct: 530 TYQSAMGKQAMGVYITNFHVRMDTLAHGLLYPQKPLVTTRSMEYLRFRELPAGINSIVAI 589

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
             + GYN EDS++I+   +    F S     ++       L  EEI       ++  + +
Sbjct: 590 ASYTGYNQEDSVIINASAIERGFFRSFFFRSYKDSESKKGLDQEEIFEKPTRENVQGMRQ 649

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +DE GII  G  V+  D+L+GK      +    E          K    RD S+ 
Sbjct: 650 AVYDKLDEDGIISPGIRVSGDDVLIGKTLTLPANEDELEGTT-------KRFTKRDASVF 702

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           +    +G +  V I       K
Sbjct: 703 MRRSETGIIDQVMITLNQEGYK 724



 Score =  100 bits (249), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 67/509 (13%), Positives = 152/509 (29%), Gaps = 43/509 (8%)

Query: 212 VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG 270
           +P+     ALG  S+ +IL          +  +     L  A ++    V+ + +     
Sbjct: 74  IPIIIVFRALGFVSDRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGA 133

Query: 271 EQVIESGKKLTSGLLKSLKEKGVKFLGIT------SDCLCGLYVAEDIVNGETGEIYIEA 324
              +   K++     + L+++ +  +G++           G  V   ++    G   ++ 
Sbjct: 134 RPGVTKEKRIKYAR-EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLL-AAIGRREVDD 191

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
            D    K L+            L+ + +          +        +       +    
Sbjct: 192 RDHYGNKRLDLAGPLLAFLFRGLFRNLMKEVRLYAQKFIDRGKDFNLE-------LAIKT 244

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKI 442
            + T  +  S+    + D  K   +  G  ++  RL   +      R          +  
Sbjct: 245 RIITDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAR 304

Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
              L N +  +                ++KN   +  + +       +  ++  S+   +
Sbjct: 305 PRQLHNTQWGMICPAETPEGSAVG---LVKNLALMAYISVGSQPSPILEFLEEWSMENLE 361

Query: 503 LINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVH 562
            ++   +  A   F     +    +    ++ +   RR   +    V+  R   +     
Sbjct: 362 EVSPSAIQDATKIFVNGCWVGIHRDPEQLMNTLRKLRREMDIIVSEVSMIRDIRDREIRI 421

Query: 563 PTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            T  GRIC P    E   +     L   + +      E       D   +  V Y+  +E
Sbjct: 422 YTDAGRICRPLLIVENQKL-----LLKQSHIKQLKQREYNNYSWQDLVASGVVEYIDPLE 476

Query: 622 EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           EE+  +A     L +                            +  P  ++ + AS+IPF
Sbjct: 477 EESIMLAMTPDDLSDKDVQ----------------YCSTYTHCEIHPAMILGVCASIIPF 520

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            +++ S R      M +QA+ +       
Sbjct: 521 PDHNQSPRNTYQSAMGKQAMGVYITNFHV 549


>gi|194320180|gb|ACF48318.1| DNA-dependent RNA polymerase II second largest subunit [Loxospora
            cismonica]
 gi|194320183|gb|ACF48320.1| DNA-dependent RNA polymerase II second largest subunit [Loxospora
            ochrophaea]
          Length = 317

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 65/385 (16%), Positives = 118/385 (30%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   ++ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 71   LF-RSLFYRTYPEQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGVIAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
              G     K+  ++ D      R++                 +K    T     E    +
Sbjct: 127  SGGDIIIGKTAPIAPDAEELGQRTKL---------------HIKRDASTPLRSTESGIVD 171

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 172  RVLM-----STNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSGLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 67/191 (35%), Gaps = 22/191 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYEERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRTYPEQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+I  G  V+ GDI++GK  P         ++        K    RD S  + S  
Sbjct: 114 LDDDGVIAPGVRVSGGDIIIGKTAPIAPDAEELGQRT-------KLHIKRDASTPLRSTE 166

Query: 936 SGTVVDVRIFN 946
           SG V  V +  
Sbjct: 167 SGIVDRVLMST 177


>gi|89142781|emb|CAJ57586.1| RNA polymerase subunit B [Microbacterium resistens]
          Length = 347

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 66/173 (38%), Positives = 92/173 (53%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G 
Sbjct: 1   FMGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALGM SEEIL+ F  +P I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGMSSEEILAEFAGFPSIEETLAKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163



 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 118/244 (48%), Positives = 160/244 (65%), Gaps = 15/244 (6%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K
Sbjct: 104 PSIEETLAKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 163

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT---------------IDDIDNLG 460
           +N +L LD P     +  +DI+  IK LV L  G  T                DDIDN G
Sbjct: 164 INQKLGLDQPLSDSVLTVKDIVETIKYLVRLHAGVETFEGIRGGKTTEIRLATDDIDNFG 223

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 224 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 283

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 284 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNI 343

Query: 581 GLVS 584
           GL+ 
Sbjct: 344 GLIG 347


>gi|148616252|gb|ABQ96886.1| RNA polymerase beta subunit [Bartonella sp. LEV]
          Length = 198

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 143/198 (72%), Positives = 167/198 (84%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 1   GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 60

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +
Sbjct: 61  IIDGKVTKEVIYLSAMEESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLM 120

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SG
Sbjct: 121 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSG 180

Query: 725 AAIVAKRAGIVEQVDAIR 742
           AAI AKR GIV+QVDA+R
Sbjct: 181 AAIGAKRGGIVDQVDAMR 198


>gi|46277263|gb|AAS86822.1| RNA polymerase II second largest subunit [Liriodendron tulipifera]
          Length = 539

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 73/440 (16%), Positives = 128/440 (29%), Gaps = 80/440 (18%)

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
                     I   ++     + I   +     R+T             V+   L+     
Sbjct: 180  YSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---D 236

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  V        +    +       +      + AI      +  D+ +   S +    
Sbjct: 237  TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGF 296

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D+ ++  ++ +E      R+          +          G       
Sbjct: 297  F-RSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGED 355

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T ++                  DE   +     +  + TS    E    +++  
Sbjct: 356  VIIGKTTPIAQ-----------------DESQGQASRYTRRDHSTSLRHSESGMVDQVLL 398

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                D +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   D
Sbjct: 399  TTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPD 453

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +GQ+ E  +G   V +GK+                            
Sbjct: 454  IIVNPHAIPSRMTIGQLIECIMGKVAVHMGKEGD-------------------------- 487

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     + I+  L        G   +Y+G
Sbjct: 488  ---------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNG 519

Query: 1240 LTGEPFDRPVTVGYIYMLKL 1259
             TG      + +G  Y  +L
Sbjct: 520  HTGRRLTAMIFLGPTYYQRL 539



 Score =  117 bits (293), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 73/482 (15%), Positives = 140/482 (29%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                    + +    ET      D      + Y+   EEE   I+              
Sbjct: 123 KKK-----HIRSLQQRETQDEGWHDLVAKGFIEYVDTEEEETTMISM----------TIS 167

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   +      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 168 DLVSARLNPD--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 225

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 226 IYVTNYQL--------------------RMDTLAYV------------------------ 241

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 242 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYN 280

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 281 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPNRENTMGMRHGSYDKLD 340

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           +         RD S  +    SG
Sbjct: 341 DDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLRHSESG 391

Query: 938 TV 939
            V
Sbjct: 392 MV 393


>gi|308194107|gb|ADO16471.1| RNA polymerase beta subunit [Gemella haemolysans]
          Length = 220

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 76/201 (37%), Positives = 100/201 (49%), Gaps = 54/201 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 74   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 133

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 134  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDVWSTVAEAGMA 193

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 194  KDAK----------------------------TVLYDG---------------------- 203

Query: 1236 LYDGLTGEPFDRPVTVGYIYM 1256
                 TGEPFD  V+VG +YM
Sbjct: 204  ----RTGEPFDSRVSVGVMYM 220



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/80 (63%), Positives = 59/80 (73%)

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
           E  L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSL
Sbjct: 1   ENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSL 60

Query: 930 RVPSGVSGTVVDVRIFNRHG 949
           RVP G  G V DV+IF R  
Sbjct: 61  RVPHGADGVVADVKIFKRED 80


>gi|157781361|gb|ABV72035.1| RNA polymerase beta subunit [Enterococcus phoeniculicola]
          Length = 226

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 87/294 (29%), Positives = 123/294 (41%), Gaps = 72/294 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  ++L G+    G         L   +  E  R      
Sbjct: 5    EDALKDL-DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKARE-VRDT 62

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
            +++       +                    KI   + GD++ PGV  +V+V++  KR I
Sbjct: 63   SLRVPHGGGGI----------------VHDVKIFTREAGDELSPGVNMLVRVYIVQKRKI 106

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
              GDKMAGRHGNKG+VSRI+P EDMP+L DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 107  HEGDKMAGRHGNKGVVSRIMPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMA 166

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  + + + D   + D+                                       
Sbjct: 167  ARQLGIHVATPVFDGATDDDVWETVREAGMAKDAK------------------------- 201

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               T ++DG                           TGEPFD  ++VG +YM+K
Sbjct: 202  ---TILYDG--------------------------RTGEPFDGRISVGVMYMIK 226



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LK++DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKDLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G V DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIVHDVKIFTREAGD 86


>gi|194320147|gb|ACF48296.1| DNA-dependent RNA polymerase II second largest subunit [Bacidia
            rubella]
          Length = 317

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 63/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R        +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKRVGM---SVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +++D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAADAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNSDGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLQGCEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTDVTVDSVSKLLRDHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 66/184 (35%), Gaps = 22/184 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      DL  G+N +VA   + G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRDLPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         ++        K    RDTS  + S  
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAADAEELGQRT-------KLHVKRDTSTPLRSTE 166

Query: 936 SGTV 939
           +G V
Sbjct: 167 NGIV 170


>gi|66806019|ref|XP_636731.1| RNA polymerase III, second largest subunit [Dictyostelium discoideum
            AX4]
 gi|74852634|sp|Q54IZ9|RPC2_DICDI RecName: Full=DNA-directed RNA polymerase III subunit rpc2; Short=RNA
            polymerase III subunit C2; AltName: Full=DNA-directed RNA
            polymerase III subunit B; Contains: RecName: Full=Ddi
            rpc2 intein
 gi|60465151|gb|EAL63250.1| RNA polymerase III, second largest subunit [Dictyostelium discoideum
            AX4]
          Length = 1608

 Score =  202 bits (513), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 93/464 (20%), Positives = 157/464 (33%), Gaps = 80/464 (17%)

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
             K     + ++ V S     + D  + N+  +D+      V ++Q+  + +  +D    +
Sbjct: 1211 YKLPAGHNATVAVMSYSGYDIEDALVMNKASLDRGFGRCIVLKKQVTSIKKHGNDTSDRI 1270

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                 + L +   G     G    K   +     I     S                 + 
Sbjct: 1271 FPPTPNDLRQPKYGLLDSDGIA--KPGELAQKGQILVNKYSPLNTIDATPNPELIPDSAY 1328

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            K  Y   K      F +K+  +  GDD       ++K+ +   R  + GDK +       
Sbjct: 1329 KSSYMGYKYD-NPAFIDKVL-LTSGDDEQL----LIKMLMRSTRRPELGDKFS------- 1375

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                                          SR                  G+K    I  
Sbjct: 1376 ------------------------------SR-----------------HGQKGVCGIIV 1388

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             + +   S L    + ++       +++      +L       SG       F G   E 
Sbjct: 1389 KQEDMPFSDLGICPDIIMNPHGFPSRMTIGKMIELLAGKAGVLSGKFGFGTCFGGDRVEN 1448

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I+ +L        G+  +  G+TGEP    +  G I+  KL HMV DK++AR+ G    +
Sbjct: 1449 ISKVLISKGFSYGGKDYVTSGVTGEPLACFIFFGPIFYQKLKHMVMDKMHARARGPTVTL 1508

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG--- 1335
            T+QP  G++  GG RLGEME  C+  YGA+ ++ E L I SD    R  VY     G   
Sbjct: 1509 TRQPTEGRARGGGLRLGEMERDCLIGYGASALIMERLMISSD----RFTVYACKNCGFLG 1564

Query: 1336 -----------NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                        D      P +  +L +E+QA+ +   L+   +
Sbjct: 1565 YEGYCQYCKSSVDISTIQIPYACKLLFQELQAMNIVPRLKLVDS 1608



 Score =  104 bits (258), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/514 (11%), Positives = 148/514 (28%), Gaps = 57/514 (11%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L++    S++ F+ + +    + NE L A             +  + F       P    
Sbjct: 52  LVKQHIDSFNFFINVEMKKIVKANERLTAE---------NDPSYFVRFTDINVGSPTSTE 102

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI------------- 125
                       C  RD+TY+ P+ + +               I +I             
Sbjct: 103 DNLDSVQLTPQRCRLRDMTYSAPIFVNIEYTRNKQIISKRDVHIGNIPIMLRSSNCVLSK 162

Query: 126 --KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
              EQ   +G+ P M   G F+++G ++++++    S          +   S  +  +  
Sbjct: 163 KTPEQMAALGECP-MDPGGYFIVRGQEKVILNHEQLSKNRIIIEMDSKGLPSASVTSSTH 221

Query: 184 IIPDQ-GLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
               + G+ +       + ++++ +     +PV   L  +G+++++ ++           
Sbjct: 222 ERKSRTGVTL-----KNEKLYLKHNTFGEDIPVAIVLKGMGVETDQEMAQLVGSDDVFLN 276

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTG---EQVIESGKKLTSGLLKSLKEKGVKFLGI 298
                        +  A  +   +               KK  S   + +   GV    +
Sbjct: 277 AITPSLEECQKCGVHTAAQALDYLGSRIKVFRRPYGVQNKKTKSEEARDIL-AGVVLNHV 335

Query: 299 TSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR----DIPILYVDSVNN 354
                    +    ++     I + + D       +   +  I      I +L+ D    
Sbjct: 336 PVRR-YNFRLKVIYLSLMIRRIIMASKDKSCLDDKDYYGNKRIELSGQLISLLFEDCFKK 394

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                   V         A       +   D  T     +  +   ++  ++ +   G  
Sbjct: 395 FQSELKKSVDQAIAKANRAENLDLPKLIRTDTITNGFTHA-ISSGQWNLKRFRMERSGVS 453

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---NGKGTIDDIDNLGNRRVRSVGEML 471
           ++  RL+  +   +    +       K+        +  G +   D            ++
Sbjct: 454 QVLSRLSYISCMGMMTRIQSQFEKTRKVAGPRSLQPSQWGMLCPSDTPEGEACLHPDTII 513

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
                 G  +  R +K+  S + +D +  +    
Sbjct: 514 TM--SNGQQKPIRQLKDGDSIITLDPITMEAHST 545



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 57/366 (15%), Positives = 118/366 (32%), Gaps = 22/366 (6%)

Query: 578  HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQANSSLD 635
            HN GLV +    + V          R   +  V + ++ ++  E    N Y+   N  + 
Sbjct: 968  HNCGLVKNFALMSHVTTDDSEGPLLRLAYNLGVQD-ILLVTGEELNSRNAYLVLLNGQII 1026

Query: 636  EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVL 691
               +  +  V            RE +       +Q +S+A        P +  DD    L
Sbjct: 1027 GIHNSPDYFVTTLRKMRRAGRIREFVSICKNKAQQTISVACDGGRLCRPVIIVDDQRPRL 1086

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA--------GIVEQVDAIRI 743
               +++     L   +       +E +       + +A R          +  +   +  
Sbjct: 1087 TQEHIEDLKDGLRTFDDFIREGIIEYLDVNEENDSFLAWREAAIQPWTTHLEIEPFTMLG 1146

Query: 744  VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV--GDEVRRNDIIADGPSTD 801
             +  +      + S  + Y+    +++      NQ   +       V     +    + D
Sbjct: 1147 CVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQLTRIDTLLYLLVHTQRPLCQTRTID 1206

Query: 802  LG---DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            L     L  G N  VA M + GY+ ED++++++  +       I +++     +      
Sbjct: 1207 LLNWYKLPAGHNATVAVMSYSGYDIEDALVMNKASLDRGFGRCIVLKKQVTSIKKHGNDT 1266

Query: 859  EEITRDIPN--VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
             +         + +     +D  GI   G     G ILV K +P      TP  +L+   
Sbjct: 1267 SDRIFPPTPNDLRQPKYGLLDSDGIAKPGELAQKGQILVNKYSPLNTIDATPNPELIPDS 1326

Query: 917  FGEKAV 922
              + + 
Sbjct: 1327 AYKSSY 1332



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/212 (15%), Positives = 75/212 (35%), Gaps = 15/212 (7%)

Query: 394 SMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR--HIRKEDIIAIIKILVDLRNGKG 451
            +F   +   +K   S   R  +   +    P       ++   +  +I+ ++     K 
Sbjct: 305 KVFRRPYGVQNKKTKSEEARDILAGVVLNHVPVRRYNFRLKVIYLSLMIRRIIMASKDKS 364

Query: 452 TIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE-----RISSVDIDSVMPQDLINA 506
            +DD D  GN+R+   G+++   +     + +  +K+        +   +++    LI  
Sbjct: 365 CLDDKDYYGNKRIELSGQLISLLFEDCFKKFQSELKKSVDQAIAKANRAENLDLPKLIRT 424

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAGVEM 558
             + +       S Q +     +          RLS +         Q    + R     
Sbjct: 425 DTITNGFTHAISSGQWNLKRFRMERSGVSQVLSRLSYISCMGMMTRIQSQFEKTRKVAGP 484

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
           R + P+ +G +CP++T EG       ++ + +
Sbjct: 485 RSLQPSQWGMLCPSDTPEGEACLHPDTIITMS 516



 Score = 39.7 bits (91), Expect = 3.9,   Method: Composition-based stats.
 Identities = 20/135 (14%), Positives = 41/135 (30%), Gaps = 24/135 (17%)

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            C         I +        +      ++   R   D      + YL   EE + ++A 
Sbjct: 1067 CDGGRLCRPVIIVDDQRPRLTQ-EHIEDLKDGLRTFDDFIREGIIEYLDVNEENDSFLAW 1125

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              +++                             ++  P  ++   A LIP+  ++ S R
Sbjct: 1126 REAAIQPW-----------------------TTHLEIEPFTMLGCVAGLIPYPHHNQSPR 1162

Query: 690  VLMGCNMQRQAVPLL 704
                C M +QA+  +
Sbjct: 1163 NTYQCAMGKQAIGAI 1177


>gi|56694352|gb|AAW22916.1| RNA polymerase II second largest subunit [Juniperus communis]
          Length = 514

 Score =  202 bits (513), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 72/435 (16%), Positives = 127/435 (29%), Gaps = 80/435 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 160  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 216

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      +  I         D+ +   S +        +
Sbjct: 217  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVXISCYSGXXQEDSVIMNQSSIDRGFF-RSL 275

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R+ ++ +E+     R+          +          G           K
Sbjct: 276  FFRSYRDEEKRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 335

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  D+   +  +  K    TS    E    +++      D
Sbjct: 336  TTPIAQ-----------------DDTAGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 378

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 379  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 433

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+                                 
Sbjct: 434  HAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------------- 462

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                  +TP F     + I+  L        G   +Y+G TG  
Sbjct: 463  ----------------------ATP-FTDVTVDXISKALHKCGYQMRGFETMYNGHTGRK 499

Query: 1245 FDRPVTVGYIYMLKL 1259
                + +G  Y  +L
Sbjct: 500  LSAMIXLGPTYYQRL 514



 Score =  109 bits (272), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 65/452 (14%), Positives = 125/452 (27%), Gaps = 100/452 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +    GV R 
Sbjct: 11  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 70

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S       +      +      +     
Sbjct: 71  IRLRELR-LYTDYGRCSRPLFVVENQRLKIKKS-------DXNNLQASREEGWHELITQG 122

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E            +  P  ++
Sbjct: 123 CIEYVDTEEEETTMISM----------TIXDLVNARINPE--DAYSHTYTHCEIHPSLIL 170

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 171 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 210

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 211 DTLAYV-----------------------------------LYYPQKPLV---------- 225

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +V    + G   EDS+++++  +    F S+    +    +
Sbjct: 226 TTRAMEHLHFRQLPAGINAIVXISCYSGXXQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 285

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 286 RAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD-- 343

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                            RD S  +    SG V
Sbjct: 344 -------TAGQVSKYTKRDQSTSLRHSESGMV 368


>gi|22217995|emb|CAC86925.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|22217997|emb|CAC86926.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 207

 Score =  202 bits (513), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 124/207 (59%), Positives = 154/207 (74%), Gaps = 2/207 (0%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N L  ++H RRLSALG GG+ R RAG E+
Sbjct: 1   TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLLELSHKRRLSALGPGGLTRDRAGYEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYRKV    G+VTN++V+
Sbjct: 61  RDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYRKVDRATGRVTNEIVW 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F EE+V  R  G         +DF+D SPKQVV++A 
Sbjct: 121 LTADEEDEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVVDFVDVSPKQVVAVAT 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPL 703
           + IPFLENDDSNR LMG NMQRQAVPL
Sbjct: 181 ACIPFLENDDSNRALMGANMQRQAVPL 207


>gi|46277277|gb|AAS86829.1| RNA polymerase II second largest subunit [Astilbe chinensis]
          Length = 540

 Score =  202 bits (513), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 76/479 (15%), Positives = 135/479 (28%), Gaps = 84/479 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                    +     I   ++     +
Sbjct: 142  HDLVAKGFIEYVDTEEEETTMISMTINDLVSARLNPEEAYSEYYTHCEIHPSLILGVCAS 201

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 202  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 258

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 259  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 317

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R+          +          G           K++ ++           
Sbjct: 318  KEDFGRPNRNDTMNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQ---------- 367

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE   +     K  + TS    E    +++      D +     R VKV V  
Sbjct: 368  -------DESQGQASRYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 415

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 416  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 475

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 476  MGKVAAHMGKEGD----------------------------------------------- 488

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 489  ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 540



 Score =  110 bits (276), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 74/486 (15%), Positives = 141/486 (29%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPEATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
              +    +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 64  IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L         G+         D      + Y+   EEE   I+          
Sbjct: 123 KKKDIQALQQRETPEDGGWH--------DLVAKGFIEYVDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLVSARLNPE--EAYSEYYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        D  N+     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRNDTMNMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK +P  +           +         RD S  +  
Sbjct: 338 DKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDE---------SQGQASRYTKRDHSTSLRH 388

Query: 934 GVSGTV 939
             +G V
Sbjct: 389 SETGMV 394


>gi|194320235|gb|ACF48353.1| DNA-dependent RNA polymerase II second largest subunit [Sphaerophorus
            globosus]
          Length = 317

 Score =  201 bits (512), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 68/382 (17%), Positives = 117/382 (30%), Gaps = 75/382 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R      EQ+E   R    +      +       +  G      
Sbjct: 71   LF-RSLFYRSYTDQEKRVGMSVVEQLEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGE 129

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +S D                +E  QR  +  K    T     E+   +++ 
Sbjct: 130  DIIIGKTAPISPD---------------AEELGQRTKQHTKRNTSTPLRSTENGIVDQVL 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 175  LSTNSDGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 229

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 230  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 264

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  I+Y+
Sbjct: 265  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEIMYN 295

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TG+     V +G  Y  +L 
Sbjct: 296  GHTGQKLRAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 70/172 (40%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRVGMSVVEQLEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P      +P+ + L     +     R+TS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPI-----SPDAEELGQRTKQH--TKRNTSTPLRSTENGIV 170


>gi|294942350|ref|XP_002783487.1| DNA-directed RNA polymerase, beta subunit, putative [Perkinsus
            marinus ATCC 50983]
 gi|239895970|gb|EER15283.1| DNA-directed RNA polymerase, beta subunit, putative [Perkinsus
            marinus ATCC 50983]
          Length = 255

 Score =  201 bits (512), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 57/249 (22%), Positives = 90/249 (36%), Gaps = 54/249 (21%)

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            ++ K      R  + GDK +                                     SR 
Sbjct: 40   KIFKCITRQTRRPELGDKFS-------------------------------------SR- 61

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                             G+K    +   + +          + ++       +++     
Sbjct: 62   ----------------HGQKGVVGLIVNQEDMPFGEKGWCPDLIMNPHGFPSRMTVGKLL 105

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
              +        G       F G  +E +   L       S +  +  G+TGE  +  + V
Sbjct: 106  ECVSGKAGVLDGERSYGTAFGGTTKEHMTQSLIRHGFHPSAKEYITSGVTGEALECYIFV 165

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G IY  KL HMV DK++ARSTG  + +T+QP  G++  GG RLGEME  C+ AYGA+ +L
Sbjct: 166  GPIYYQKLKHMVMDKIHARSTGPVNQLTRQPTEGRAKDGGLRLGEMERDCLVAYGASNLL 225

Query: 1312 QEMLTIKSD 1320
             E L + SD
Sbjct: 226  LERLMLSSD 234


>gi|2736121|gb|AAB94061.1| RPB140 [Magnolia virginiana]
          Length = 555

 Score =  201 bits (512), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 101/706 (14%), Positives = 186/706 (26%), Gaps = 154/706 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISA 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +  +G +           + + + R +I   D + +  V     L       
Sbjct: 54   AVIPQATKIFVNGCWVGIHRNPDLLVKTLRLLRRRI---DVNTEVGVIRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  Q   L+                               + + A++   
Sbjct: 111  DYGRCSRPLFIVDQQRLLI-----------------------------KKKHIHALQQRE 141

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
               EG  D    G   Y                             +      +      
Sbjct: 142  TQEEGWHDLVAKGFIEYVDP-----------------------EEEETTMISMTISDLIS 178

Query: 806  ALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
            A           +       S++  +   ++            ++       +G      
Sbjct: 179  ARHNPEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG------ 232

Query: 864  DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
                V+   L+      +  V        +    +       +      + AI      +
Sbjct: 233  --IYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYN 287

Query: 924  VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIY 983
              D+ +   S +        +F R   D+ ++  ++ +E      R+          +  
Sbjct: 288  QEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRESTMGMRHGSYDKL 346

Query: 984  SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL-KVQY 1042
                    G           K                     +  + VQ  V    +  +
Sbjct: 347  DDDGLAPPGTRVSGEDVIIGK------------------TIPIAQDDVQGQVTRYTRRDH 388

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             TS    E    +++      D +     R VKV +   R  Q GDK + RHG KG V  
Sbjct: 389  STSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGM 443

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +        
Sbjct: 444  TYTQEDMPWTPEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTV 503

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSM 1222
             +IS         +                                              
Sbjct: 504  DNISKALHKCGYQMRGFETM---------------------------------------- 523

Query: 1223 LRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                    +G +    G         + +G  Y  +L HMV DK++
Sbjct: 524  -------YNGHT----GR---RLPAMIFLGPTYYQRLKHMVDDKIH 555



 Score =  117 bits (292), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 78/496 (15%), Positives = 138/496 (27%), Gaps = 102/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+A  +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAANPILEFLEEWSTENFEEISAAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             A   F     +         +  +   RR   +  + GV R     E+R    T YGR
Sbjct: 57  PQATKIFVNGCWVGIHRNPDLLVKTLRLLRRRIDVNTEVGVIRDIRLKELR--LYTDYGR 114

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                        L+      A        ET      D      + Y+   EEE   I+
Sbjct: 115 CSRPLFIVDQQRLLIKKKHIHA----LQQRETQEEGWHDLVAKGFIEYVDPEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +L+  R   E      E     +  P  ++ + AS+IPF +++ S 
Sbjct: 171 M----------TISDLISARHNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 248

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 249 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 273

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 274 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRE 333

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
               +       +D+ G+   G  V+  D+++GK  P  +  +                 
Sbjct: 334 STMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTIPIAQDDV---------QGQVTRYT 384

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 385 RRDHSTSLRHSESGMV 400


>gi|80973627|gb|ABB53551.1| RNA polymerase beta subunit [Gemella morbillorum]
          Length = 226

 Score =  201 bits (512), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 75/201 (37%), Positives = 99/201 (49%), Gaps = 54/201 (26%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++  GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 78   KIFKREDGAELANGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 137

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 138  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGANDDDVWATIAEAGMA 197

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 198  KDAK----------------------------TVLYDG---------------------- 207

Query: 1236 LYDGLTGEPFDRPVTVGYIYM 1256
                 TGEPFD  V+VG +YM
Sbjct: 208  ----RTGEPFDSRVSVGVMYM 224



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 54/84 (64%), Positives = 62/84 (73%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E  L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VR
Sbjct: 1   PNVGENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHG 949
           DTSLRVP G  G V DV+IF R  
Sbjct: 61  DTSLRVPHGADGVVADVKIFKRED 84


>gi|156105527|gb|ABQ96887.2| RNA polymerase beta subunit [Bartonella sp. HMD]
          Length = 198

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 141/198 (71%), Positives = 167/198 (84%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 1   GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 60

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G F+EE V CR AGE ++ P + +D +
Sbjct: 61  IIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFSEEFVVCRHAGEVLMAPHDHVDLM 120

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SG
Sbjct: 121 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLIRAEAPFVGTGMESIVARDSG 180

Query: 725 AAIVAKRAGIVEQVDAIR 742
           AAI AKR GIV+QVDA R
Sbjct: 181 AAIGAKRGGIVDQVDATR 198


>gi|194320220|gb|ACF48343.1| DNA-dependent RNA polymerase II second largest subunit [Psora
            rubiformis]
          Length = 317

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 65/381 (17%), Positives = 114/381 (29%), Gaps = 75/381 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R      EQ E   R    +      +       +  G      
Sbjct: 71   LF-RSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGE 129

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +S D      R++                 +K    T     E+   +++ 
Sbjct: 130  DIIIGKTAPISPDAEELGQRTKL---------------HIKRDTSTPLRSTENGIVDQVL 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 175  LSTNSDGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 229

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 230  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 264

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 265  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYN 295

Query: 1239 GLTGEPFDRPVTVGYIYMLKL 1259
            G TG      V +G  Y  +L
Sbjct: 296  GHTGRKLVAQVFLGPTYYQRL 316



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ G++  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPISPDAEELGQRT-------KLHIKRDTSTPLRSTENGIV 170


>gi|22217993|emb|CAC86924.1| RNA polymerase beta subunit [Streptococcus pyogenes]
 gi|22218001|emb|CAC86928.1| RNA polymerase beta subunit [Streptococcus pyogenes]
          Length = 209

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 124/208 (59%), Positives = 156/208 (75%), Gaps = 2/208 (0%)

Query: 499 MPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSALG GG+ R RAG E+
Sbjct: 1   TPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSALGPGGLTRDRAGYEV 60

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD--GKVTNDVVY 616
           RDVH THYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYRKV    G+VTN++V+
Sbjct: 61  RDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYRKVDRATGRVTNEIVW 120

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           L+A EE+   +AQANS L+EDG+F EE+V  R  G         +DF+D SPKQVV++A 
Sbjct: 121 LTADEEDEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVVDFVDVSPKQVVAVAT 180

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           + IPFLENDDSNR LMG NMQRQAVPL+
Sbjct: 181 ACIPFLENDDSNRALMGANMQRQAVPLI 208


>gi|193599220|ref|XP_001950634.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC2
            [Acyrthosiphon pisum]
          Length = 1112

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 72/394 (18%), Positives = 145/394 (36%), Gaps = 78/394 (19%)

Query: 984  SRLMEILCGQNAVSGPKG-FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE----SL 1038
            +++M+ + G    +  K    K   L +D I+   +  + +    ++   + +       
Sbjct: 768  NQMMDSIQGPIIDNATKKPIYKHRALENDGIAAIGQPVFDKQVTINKATPKTITVEDVGG 827

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
               ++ +    +    + ++K+            ++K      R  + GDK +       
Sbjct: 828  DRGFKETPLYYKGYDPSYVDKVMI---TSNSDCFLIKENFRQPRRPEIGDKFS------- 877

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
                                          SR                  G+K    +  
Sbjct: 878  ------------------------------SR-----------------HGQKGVVGLIV 890

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             + +   + +    + ++       +++      +L        G       F GA    
Sbjct: 891  DQEDMPFNEVGICPDLIMNPHGFPSRMTVGKLIELLAGKAGVLEGKFQDGSAFGGATVTD 950

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            I++ L+  + +  G+ +LY G+ G P +  +  G ++  +L HMV+DK++ARS G   L+
Sbjct: 951  ISNELQKHNYNYLGKDVLYCGIDGRPMEAYIYSGPVFYQRLKHMVADKIHARSRGPRVLL 1010

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV---------GR 1325
            T+QP  G+S  GG R+GEME  C+ AYGA+ ++ E L + SD    DV          G 
Sbjct: 1011 TRQPTEGRSKDGGLRMGEMERDCLIAYGASMLIIERLMLSSDVVEMDVCKLCGLFSYSGW 1070

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
              + +     N       P +  +L +E+QA+ +
Sbjct: 1071 CHMCQ---KSNSVCRIKMPYACKLLFQELQAMSI 1101



 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 118/1000 (11%), Positives = 275/1000 (27%), Gaps = 201/1000 (20%)

Query: 20  NPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
             E ++   L      S++ F+  ++    + N     A +S            L F + 
Sbjct: 12  VKEYLETRGLYSHHINSFNAFIDSDLKKIIQQNH----AVRS-----DADPNFYLHFKNV 62

Query: 80  EFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               P+              +C  RDLTY  P+ + +  +            +K +++  
Sbjct: 63  TVGHPQVDDGFNVTRNVTPQECRLRDLTYCAPIYVDIEYV---------KSGMKYLRKGF 113

Query: 130 IYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHF 165
           I +G LP+M +                         G F++KG +++++ Q   +     
Sbjct: 114 I-IGRLPIMLRSNRCCLYQKSDAELAKMKECIYDSGGYFIVKGTEKVILMQEQPAKNKIL 172

Query: 166 DHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMD 224
             +K    +    + +  +  D+    +I F  K++I+V  +     +P   F+ ALG+ 
Sbjct: 173 V-EKDSNGVPTVQVMSSTV--DKKSKTNIIF-KKNLIYVCHNALEENIPFVIFMKALGVC 228

Query: 225 SEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD--IDTGEQVIESGKKLT 281
           S++ IL     +     +        S  ++    +    + D     G    +   ++ 
Sbjct: 229 SDQLILQMVGTEFAIMNQMYPCFLEGSKLNIYTQKQALRFIGDRIKKMGFSSEDYDSRVI 288

Query: 282 SGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE----EIF 337
           + +   L    +  + +T+      ++     +     +     +     S +    +  
Sbjct: 289 TEVHDFLSTVILAHIPVTN---TNYHMKAIYTSIMVRRLIFSLSNPDLFDSKDYYGNKCL 345

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                 + +L+ D+     +   ++        K    DI + +R  D  T ++  ++  
Sbjct: 346 DLPGSFLSLLFDDTFKRFTFELKSVADKNIPKVKATPFDIIKYIR-TDTITNALVFAIQT 404

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
             +         ++ R +M           + ++    ++  +    +          + 
Sbjct: 405 GNW---------SIKRFRMERHGVTQVLTRLSYLSAIGMMTRVNSQFEKSRKVSGPRSLQ 455

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                 +             GL++    +    +  + D  + Q  +N       +    
Sbjct: 456 PSQFGMLCPSDTPEGEAC--GLIKNISLLAHVTTESEDDDAVLQLALNLGVEPVGLYSVD 513

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +        N           + +G             R      + +      SE 
Sbjct: 514 DLHEDYMYLIIFNG----------NIIGSTNKCIDFVDKFRRCRRKGIFSKFISIYISER 563

Query: 578 HNIGLVSS----LTSFARVNAYGF----------IETPYRKVCDGKVTNDVVYLSAMEEE 623
           H    ++S    L     V   G           ++  Y    D    + + ++   EE 
Sbjct: 564 HKCIYINSGDGRLCRPYLVVENGQPLLTNAHIDDLKRGYCTFQDFIDQSLIEFIDVDEEN 623

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IA     +                         +   ++ +P  ++ I AS+IPF  
Sbjct: 624 NCLIAYNEEKIVP-----------------------ETTHMEMAPFSILGICASVIPFPH 660

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R    C M +QA+                                          
Sbjct: 661 HNQSPRNTYQCAMGKQAIGT---------------------------------------- 680

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
            I         +      Y  +    S     +N        D++           +  G
Sbjct: 681 -IALNYQHRIDTLQYNLWYTHIPMVHSKAVPMIN-------YDKLPAGQNATIAVMSYSG 732

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE--- 860
                            Y+ ED++++++  V             +   R       +   
Sbjct: 733 -----------------YDIEDAIILNKASVDRGFGRGGTFRNSKCFLRHYPNQMMDSIQ 775

Query: 861 --ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK--LLRAI 916
             I  +         + ++  GI  +G  V    + + K TPK  +              
Sbjct: 776 GPIIDNATKKPIYKHRALENDGIAAIGQPVFDKQVTINKATPKTITVEDVGGDRGFKETP 835

Query: 917 FGEKAVD--VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
              K  D    D  +   +     + +     R     ++
Sbjct: 836 LYYKGYDPSYVDKVMITSNSDCFLIKENFRQPRRPEIGDK 875


>gi|29825367|gb|AAO92263.1| RpoB [Kluyvera sp. 2002-86274]
          Length = 201

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 124/200 (62%), Positives = 160/200 (80%)

Query: 480 LRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
           +R+ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH R
Sbjct: 2   VRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKR 61

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
           R+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+E
Sbjct: 62  RISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLE 121

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           TPYRKV DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  L  R+
Sbjct: 122 TPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRD 181

Query: 660 KIDFIDASPKQVVSIAASLI 679
           ++D++D S +QVVS+ ASLI
Sbjct: 182 QVDYMDVSTQQVVSVGASLI 201


>gi|89142791|emb|CAJ57591.1| RNA polymerase subunit B [Microbacterium thalassium]
          Length = 357

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 63/173 (36%), Positives = 91/173 (52%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G 
Sbjct: 1   FMGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  +  I  +   D     
Sbjct: 59  WLEFEVDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDILAEFAGFDSIEETLSKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 126/254 (49%), Positives = 171/254 (67%), Gaps = 15/254 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 104 DSIEETLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L L+ P D   +  EDI+A IK LV L  G                  +DDIDN G
Sbjct: 164 INQKLGLELPIDASVLTVEDIVATIKYLVRLHRGDVTFEGSRGGKTTEIRLDVDDIDNFG 223

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 224 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 283

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 284 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 343

Query: 581 GLVSSLTSFARVNA 594
           GL+ SL SFAR+N 
Sbjct: 344 GLIGSLASFARINP 357


>gi|22086614|gb|AAM90692.1|AF403010_1 RNA polymerase beta subunit [Rickettsia martinet]
          Length = 284

 Score =  201 bits (511), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 158/271 (58%), Positives = 201/271 (74%), Gaps = 4/271 (1%)

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A +N +GFIE+PYR+V DG VT++VVYLSA+EE    I QANS +++DG    E + C
Sbjct: 1   TYATINKHGFIESPYRRVKDGYVTDEVVYLSAIEEGKYKIGQANSKINKDGKLQGEFINC 60

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKA 706
           R   G  ++V   ++DFID +P QVVS+AASLIPFLENDD+NR LMG NMQRQAVPL+K 
Sbjct: 61  RVEGGNFVMVEPYEVDFIDVTPMQVVSVAASLIPFLENDDANRALMGSNMQRQAVPLIKT 120

Query: 707 EAPFVGTGME--SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           +APFVGTG+E  S +     +  +    GI EQVD+ RIVIR++E  +D S   +    L
Sbjct: 121 DAPFVGTGVEGGSSLKILEPSVPLHLHDGICEQVDSNRIVIRTLEQKVDGSPVRLIFITL 180

Query: 765 MKFQR-SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
            K ++  N NTC+NQ+PLVKVG  V++NDIIADGP      L LGRN+LVAF+PW+GYNF
Sbjct: 181 PKIRKNHNHNTCINQKPLVKVGHYVKKNDIIADGPVRITVKLLLGRNVLVAFLPWNGYNF 240

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
           EDS+LISER+V EDVFTSIHIEEFEV+ARDT
Sbjct: 241 EDSILISERIVKEDVFTSIHIEEFEVIARDT 271


>gi|193201742|gb|ACF16035.1| RNA polymerase beta subunit [Streptococcus equi subsp. zooepidemicus]
 gi|193201744|gb|ACF16036.1| RNA polymerase beta subunit [Streptococcus equi subsp. zooepidemicus]
 gi|193201746|gb|ACF16037.1| RNA polymerase beta subunit [Streptococcus equi subsp. zooepidemicus]
          Length = 219

 Score =  201 bits (511), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 89/289 (30%), Positives = 121/289 (41%), Gaps = 72/289 (24%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 3    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 55

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 56   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 104

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 105  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 164

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
               LG  I + + D   + D+                                       
Sbjct: 165  ARNLGIHIATPVFDGATSEDLWETVREAGMDSDAK------------------------- 199

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
               T ++DG                           TGEPFD  V+VG 
Sbjct: 200  ---TVLYDG--------------------------RTGEPFDNRVSVGV 219



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 53/84 (63%), Positives = 64/84 (76%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           V EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDT
Sbjct: 1   VGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDT 60

Query: 928 SLRVPSGVSGTVVDVRIFNRHGID 951
           SLRVP G  G V DV+IF R   D
Sbjct: 61  SLRVPHGGDGIVRDVKIFTRANGD 84


>gi|298239782|gb|ADI70690.1| DNA-directed RNA polymerase beta subunit [Solimonas sp. NAA16]
          Length = 184

 Score =  201 bits (511), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 108/183 (59%), Positives = 134/183 (73%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 2   EFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 61

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL  +AR N YGF+ET YRKV DG V++ V YLSA+EE    IAQAN+ L
Sbjct: 62  PEGPNIGLINSLACYARTNEYGFLETAYRKVTDGVVSDQVDYLSAIEEGRYVIAQANAEL 121

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           D    F  +LV  R   E  +   +K+ ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG 
Sbjct: 122 DAGNRFKTDLVSVRFQNEFTMTAPDKVQYMDVSPRQIVSVAAALIPFLEHDDANRALMGP 181

Query: 695 NMQ 697
           NMQ
Sbjct: 182 NMQ 184


>gi|56694342|gb|AAW22911.1| RNA polymerase II second largest subunit [Sciadopitys verticillata]
          Length = 514

 Score =  201 bits (511), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 78/485 (16%), Positives = 142/485 (29%), Gaps = 94/485 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV  G  + V   +      S  +  L   R N   A+   +        ++  +   ++
Sbjct: 118  LVAXGYIEYVDTEEEETTMISMTINXLVNARINPHDAYSHTYTHCEIHPXLILGVCASII 177

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 178  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 226

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 227  TRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 285

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R  ++ +E+     R+          +          G           K++ ++     
Sbjct: 286  RMGTLVKEEFGRPNRENTQNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQ---- 341

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE   +     +    TS    E    +++      D +     R V
Sbjct: 342  -------------DESGGQANRYTRRDQSTSLRHSESGMVDQVLLTTNQDGL-----RFV 383

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 384  KVRMRSVRIPQIGDKFSSRHGXKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIG 443

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+                                           
Sbjct: 444  QLIECIMGKVAAHMGKEGD----------------------------------------- 462

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                        +TP F     ++I+  L        G   +Y+G TG      + +G  
Sbjct: 463  ------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRKLSAMIFLGPT 509

Query: 1255 YMLKL 1259
            Y  +L
Sbjct: 510  YYQRL 514



 Score =  117 bits (293), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 71/453 (15%), Positives = 130/453 (28%), Gaps = 102/453 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   +  +   F     +    +    +  +   RR   +    GV R 
Sbjct: 11  EEWSTENFEEISPAAIPQSTKIFVNGCWVGIHRDPDLLVRTLRQLRRQIDVNPEVGVVRD 70

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVT 611
               E+R ++  +     P    E   + +  S  +  R N   G+ E            
Sbjct: 71  IRLRELR-LYTDYGRCSRPLFVVENQRLRIKKSDINNLRANPXDGWHELV--------AX 121

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   I+               LV  R                +  P  +
Sbjct: 122 GYIEYVDTEEEETTMISM----------TINXLVNARINPH--DAYSHTYTHCEIHPXLI 169

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + + AS+IPF +++ S R      M +QA+ +                           R
Sbjct: 170 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------R 209

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
              +  V                                       Q+PLV         
Sbjct: 210 MDTLAYV-----------------------------------LYYPQKPLV--------- 225

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
                        L  G N +VA   + GYN EDS+++++  +    F S+    +    
Sbjct: 226 -TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 284

Query: 852 RDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +      +E        +  N+       +D+ G+   G  V+  D+++GK +P  +   
Sbjct: 285 KRMGTLVKEEFGRPNRENTQNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDE- 343

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                   +         RD S  +    SG V
Sbjct: 344 --------SGGQANRYTRRDQSTSLRHSESGMV 368


>gi|157781333|gb|ABV72021.1| RNA polymerase beta subunit [Enterococcus sulfureus]
          Length = 226

 Score =  201 bits (511), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 87/286 (30%), Positives = 121/286 (42%), Gaps = 71/286 (24%)

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
            DE  I+      +  ++L G+    G         L   +  E  R      +++     
Sbjct: 12   DEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKARE-VRDTSLRVPHGG 70

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
              +                    KI   + GD++ PGV  +V+V++  KR I  GDKMAG
Sbjct: 71   GGI----------------IHDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAG 114

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHGNKG+VSRI+P EDMPFL DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  +
Sbjct: 115  RHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHV 174

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
             + + D                               D+ V     +        T ++D
Sbjct: 175  ATPVFDGA----------------------------SDEDVWETVREAGMARDAKTILYD 206

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
            G                           +GEPFD  ++VG +YM+K
Sbjct: 207  G--------------------------RSGEPFDGRISVGVMYMIK 226



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 54/86 (62%), Positives = 66/86 (76%)

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
           PNV E+ LKN+DE GII +GAEV  GD+LVGK+TPKG + ++ EE+LL AIFGEKA +VR
Sbjct: 1   PNVGEDALKNLDEMGIIRIGAEVKDGDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVR 60

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGID 951
           DTSLRVP G  G + DV+IF R   D
Sbjct: 61  DTSLRVPHGGGGIIHDVKIFTREAGD 86


>gi|47156741|gb|AAT12267.1| RNA polymerase II second largest subunit [Diapensia lapponica]
          Length = 541

 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 99/687 (14%), Positives = 190/687 (27%), Gaps = 147/687 (21%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L     +            + +    N        EE +  +    +
Sbjct: 2    ETPEGQACGLVKNLALMVYITVGSAAHPILEFLEEWSTEN-------FEEISPAVIPQAT 54

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             +  +GS+           + +   R ++   D + +  V     L       D  R   
Sbjct: 55   KIFVNGSWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYTDYGRCSR 111

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  +   L++ +                G        G +E VD        +   +
Sbjct: 112  PLFIVEKQRLLIRKKDILALQ---QRETPEEGGWHDLVGKGFIEYVDTEEEETTMISMTI 168

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                S                              +  +D +++  +      +L   + 
Sbjct: 169  KDLVSA----------------------------RINPDDALSETFTHCEIHPSLILGVC 200

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 201  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 234

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        ++   +       +        AI      +  D+ +   
Sbjct: 235  ---LRMDTLAYVLYYPQKPLVITRAMEHLHFRQLPAGINATVAIACYSGYNQEDSLIMNQ 291

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ ++  ++ +E      RD          +          G
Sbjct: 292  SSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGCPNRDNTMGMRHGSYDKLDDDGLAPPG 350

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T ++                  D+   +N    +  + TS    E  
Sbjct: 351  TRVSGEDVIIGKTTPIAP-----------------DDATGQNSRYTRRDHSTSLRHSESG 393

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++      D +     R VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 394  MVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 448

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                     
Sbjct: 449  IEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------- 489

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                              +TP F     + I+  L        G
Sbjct: 490  ----------------------------------ATP-FTEVTVDNISKALHKCGYQMRG 514

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKL 1259
               +Y+G TG      + +G  Y  +L
Sbjct: 515  FETMYNGHTGRQLTSMIFLGPTYYQRL 541


>gi|269912610|emb|CAY86085.1| RNA polymerase beta subunit [Gluconacetobacter sacchari]
          Length = 236

 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 100/237 (42%), Positives = 138/237 (58%), Gaps = 28/237 (11%)

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------------------- 221
           IP +G W+D EFDSKD+I+VRIDR+RK+PVT+ L AL                       
Sbjct: 1   IPYRGSWLDFEFDSKDLIYVRIDRKRKLPVTTLLYALEGEASAAARAAKIAEGGDVDALE 60

Query: 222 --GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
             GMD++EIL  FY ++V+++    W  P  A     G K+   LVD  +G+ V E+  K
Sbjct: 61  IRGMDADEILGYFYNQVVFTKTPKGWARPFDAE-SFRGMKLLEPLVDAQSGDVVAEADAK 119

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           LT+ +++ + E   K + + +  L G YVA D+VN ETGEIY EAG+ + E  LE +  +
Sbjct: 120 LTARMVRKIAET-TKEVLVGAAGLVGRYVAHDLVNPETGEIYAEAGEELTEARLEAMEAA 178

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMF 396
            +  +P L +D+ N   +IRNTL  DKN  R DAL DIYRVMRPG+  T   AE+MF
Sbjct: 179 GVDRLPTLAIDAAN-GPWIRNTLAVDKNGSRDDALTDIYRVMRPGEPPTPETAEAMF 234


>gi|89142787|emb|CAJ57589.1| RNA polymerase subunit B [Microbacterium terregens]
          Length = 354

 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 91/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G
Sbjct: 1   VFMGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDRTPDKT--SDKDIVSARIIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL  F  +  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEQILEEFAGFDSIDETLAKDTILS 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 164



 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 125/250 (50%), Positives = 166/250 (66%), Gaps = 15/250 (6%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR K
Sbjct: 105 DSIDETLAKDTILSKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 164

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L LD P     +   DI+A IK LV L  G                  IDDIDN G
Sbjct: 165 INQKLGLDAPLSDSVLTVADIVATIKYLVRLHRGDTTFNGLRGGKPAEIRMDIDDIDNFG 224

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 225 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 284

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 285 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 344

Query: 581 GLVSSLTSFA 590
           GL+ SL SFA
Sbjct: 345 GLIGSLASFA 354


>gi|37956436|gb|AAP15387.1| RNA polymerase beta subunit [Geobacter thiogenes]
          Length = 213

 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 120/208 (57%), Positives = 163/208 (78%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF++TPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVKTPYRVVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT++V + SA+EEE   IAQAN+ +DE G F  + +  R +GE +LV R++++ +D +P
Sbjct: 122 RVTDEVRFFSALEEEGHAIAQANAEIDETGRFAADYISARKSGEFVLVGRDELELMDVAP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNM 696
            Q+VS+AASLIPFLENDD+NR LMG N+
Sbjct: 182 MQLVSVAASLIPFLENDDANRALMGSNI 209


>gi|89142783|emb|CAJ57587.1| RNA polymerase subunit B [Microbacterium saperdae]
          Length = 364

 Score =  201 bits (510), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 92/174 (52%), Gaps = 13/174 (7%)

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQG 189
           ++MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G
Sbjct: 1   VFMGDFPLQTGKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRG 58

Query: 190 LWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCF 247
            W++ E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D    
Sbjct: 59  AWLEFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVT 118

Query: 248 PLSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
              A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 KEDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 164



 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 126/258 (48%), Positives = 174/258 (67%), Gaps = 16/258 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 107 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 166

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 167 QKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFSGIRSGKKADIRLATDDIDNFGN 226

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 227 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 286

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 287 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 346

Query: 582 LVSSLTSFARVNAYGFIE 599
           L+ +L +FAR+N +GFI+
Sbjct: 347 LIGALATFARINPFGFID 364


>gi|194320226|gb|ACF48347.1| DNA-dependent RNA polymerase II second largest subunit [Tephromela
            atra]
          Length = 317

 Score =  201 bits (510), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 64/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S V   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSVDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNADGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTGEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSKLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            V   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SVDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|194320215|gb|ACF48340.1| DNA-dependent RNA polymerase II second largest subunit
            [Protoblastenia calva]
          Length = 317

 Score =  201 bits (510), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 64/382 (16%), Positives = 111/382 (29%), Gaps = 75/382 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R      EQ E   R    +      +       +  G      
Sbjct: 71   LF-RSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGE 129

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +S+D      R++          ++     +  Q   S             
Sbjct: 130  DIIIGKTAPISADAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS------------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 177  -------TNSDGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 229

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 230  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 264

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 265  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYN 295

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TG      V +G  Y  +L 
Sbjct: 296  GHTGRKLVAQVFLGPTYYQRLR 317



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPISADAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|56694374|gb|AAW22927.1| RNA polymerase II second largest subunit [Dianthus sp. UWG]
          Length = 540

 Score =  201 bits (510), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 76/479 (15%), Positives = 128/479 (26%), Gaps = 84/479 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 142  HDLVAKGFIEYIDTEEEETTMISMTINDLVSARLNPEESYSGTYTHCEIHPSLILGVCAS 201

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 202  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 258

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 259  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 317

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T LS +         
Sbjct: 318  KEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPLSPEEAQGP---- 373

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                                +Y      +  R        Q         LR VKV V  
Sbjct: 374  ------------------AARYSRKDHSISLRHSESGIVDQVLLTTNADGLRFVKVRVRS 415

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 416  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 475

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 476  MGKVAAHVGKEGD----------------------------------------------- 488

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +TP F     + I+  L+       G   +Y+G TG      + +G  Y  +L
Sbjct: 489  ------ATP-FTDVTVDNISKALQKCGYQMRGFETMYNGHTGRKLSAMIFLGPTYYQRL 540



 Score =  114 bits (286), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 78/486 (16%), Positives = 146/486 (30%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWSTENFEEISPAVIPQATKIFVNGGWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
              +    +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 64  IHRDPDLLVKTLRELRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L         G+         D      + Y+   EEE   I+          
Sbjct: 123 KKKDIRALQQRETPEDGGWH--------DLVAKGFIEYIDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R   EE           +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLVSARLNPEESY--SGTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP     ++PEE    A         +D S+ +  
Sbjct: 338 DKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSRKDHSISLRH 388

Query: 934 GVSGTV 939
             SG V
Sbjct: 389 SESGIV 394


>gi|2736117|gb|AAB94059.1| RPB140 [Hordeum vulgare]
          Length = 555

 Score =  200 bits (509), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 104/703 (14%), Positives = 195/703 (27%), Gaps = 148/703 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWGTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +  +G +           + +   R +I   D + +  V     L       
Sbjct: 54   AVIPQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQI---DVNTEVGVVRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +      L+                K   A    +           +  I
Sbjct: 111  DYGRCSRPLFIVENQRLLI--------------KKKHIRALQQRETPDEGWHDLVAKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              ++ + + +T      R ++  R N     +                    PS  LG  
Sbjct: 157  EYIDTEEEETTMISMTIRDLETSRHNPGEAYS-----------ETYTHCEIHPSLILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLLFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ ++  ++ +E+     R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEEFGRPNRENTMGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K++ +                  QD+   +     K  + TS
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTSPI-----------------PQDDAQGQATRYSKRDHSTS 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VKV +   R  Q GDK + RHG KG V     
Sbjct: 392  LRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +          I
Sbjct: 447  QEDMPWTIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDHI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 507  SKALHKCGYQMRGFETM------------------------------------------- 523

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                 +G +    G         + +G  Y  +L HMV DK++
Sbjct: 524  ----YNGHT----GR---KLTAMIFLGPTYYQRLKHMVDDKIH 555



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 73/496 (14%), Positives = 138/496 (27%), Gaps = 102/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++       + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAANPILEFLEEWGTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             A   F     +         +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQAAKIFVNGCWVGIHRNPDLLVKTLRRLRRQIDVNTEVGVVRDIRLKELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +         + A    ETP     D      + Y+   EEE   I+
Sbjct: 116 SRPLFIVENQRLLIKKK-----HIRALQQRETPDEGWHDLVAKGFIEYIDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                L+                       E     +  P  ++ + AS+IPF +++ S 
Sbjct: 171 MTIRDLETS------------RHNPGEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 248

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 249 -------------------------LYYPQKPLV----------TTRAMEHLLFRQLPAG 273

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 274 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEEFGRPNRE 333

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK +P  +           A        
Sbjct: 334 NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIPQDD---------AQGQATRYS 384

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 385 KRDHSTSLRHSESGMV 400


>gi|298239784|gb|ADI70691.1| DNA-directed RNA polymerase beta subunit [Sinobacter flavus]
          Length = 184

 Score =  200 bits (509), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 110/183 (60%), Positives = 137/183 (74%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET
Sbjct: 2   EFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIET 61

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL  +AR N YGF+ET YRKV DGKVT++V YLSA+EE    IAQANS L
Sbjct: 62  PEGPNIGLINSLACYARTNEYGFLETAYRKVVDGKVTDEVEYLSAIEEGRYVIAQANSEL 121

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +    FT +LV  R   E  ++  +K+ ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG 
Sbjct: 122 NAKNEFTADLVSVRFQNEFTMMTGDKVQYMDVSPRQIVSVAAALIPFLEHDDANRALMGP 181

Query: 695 NMQ 697
           NMQ
Sbjct: 182 NMQ 184


>gi|194320279|gb|ACF48379.1| DNA-dependent RNA polymerase II second largest subunit [Phyllobaeis
            erythrella]
          Length = 317

 Score =  200 bits (509), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/393 (17%), Positives = 122/393 (31%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFFRTYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYEKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++                 +K    T   
Sbjct: 119  IVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL---------------HIKRDVSTPLR 163

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 164  TTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRME 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++I+ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSISRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G  ++Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 65/185 (35%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFFRTYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRTTENGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDKVL 174


>gi|194320243|gb|ACF48358.1| DNA-dependent RNA polymerase II second largest subunit [Sticta
            beauvoisii]
          Length = 317

 Score =  200 bits (509), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMAVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMAVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 174


>gi|40644582|emb|CAD89877.1| RNA polymerase II, second largest subunit [Philadelphus sp. Oxelman
            2326]
          Length = 320

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 68/381 (17%), Positives = 113/381 (29%), Gaps = 78/381 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T ++ D                  + Q      K  + TS    E    +++ 
Sbjct: 137  DVIIGKTTPITQD------------------ESQGQARYTKRDHSTSLRHSETGMVDQVL 178

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 179  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 233

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 234  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------- 268

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+  L        G   +Y+
Sbjct: 269  ----------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYN 299

Query: 1239 GLTGEPFDRPVTVGYIYMLKL 1259
            G TG      + +G  Y  +L
Sbjct: 300  GHTGRRLTAMIFLGPTYYQRL 320



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 60/184 (32%), Gaps = 25/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +              G+     RD S  +    
Sbjct: 121 LDDDGLAPPGTRVSGEDVIIGKTTPITQDES----------QGQARYTKRDHSTSLRHSE 170

Query: 936 SGTV 939
           +G V
Sbjct: 171 TGMV 174


>gi|40643996|emb|CAD91515.1| RNA polymerase II second largest subunit [Hedera helix]
          Length = 541

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/465 (15%), Positives = 128/465 (27%), Gaps = 90/465 (19%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDT 854
              T    L+   N   A+   +       S+++     ++            ++      
Sbjct: 164  SMTINDLLSARVNPEEAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 223

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G                       +  V        +    +       +      + 
Sbjct: 224  AMGIYVTNFQFRM-----------DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 272

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +        IF R   D+ ++  ++ +E      R     
Sbjct: 273  AIACYSGYNQEDSVIMNQSSIDRGFF-RSIFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 331

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T                  A  D + Q  
Sbjct: 332  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP----------------IAQDDAQGQAA 375

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                +  + TS    E    +++      D +     R VKV V   R    GDK + RH
Sbjct: 376  SRYTRRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSXRIPXIGDKFSSRH 430

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+   
Sbjct: 431  GQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD- 489

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP F   
Sbjct: 490  ----------------------------------------------------ATP-FTDV 496

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 497  TVDNISRALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 541



 Score =  107 bits (267), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 71/486 (14%), Positives = 141/486 (29%), Gaps = 104/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYVTVGSAAYPILEFLEEWGTENFEEISPAVITQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    +   + +
Sbjct: 64  IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVKNQRLLI 122

Query: 583 ----VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L         G+         D      + Y+   EEE   I+          
Sbjct: 123 RKKDIQALQQRESPEDGGWH--------DLVAKGFIEYIDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +L+  R   E      +     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLLSARVNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNFQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +    F SI    +    +      +E        +   +     
Sbjct: 278 SGYNQEDSVIMNQSSIDRGFFRSIFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP  +                     RD S  +  
Sbjct: 338 DKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD--------AQGQAASRYTRRDHSTSLRH 389

Query: 934 GVSGTV 939
             +G V
Sbjct: 390 SETGMV 395


>gi|46277279|gb|AAS86830.1| RPB140 [Liquidambar acalycina]
          Length = 540

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 77/479 (16%), Positives = 132/479 (27%), Gaps = 84/479 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 142  HDLVAKGFIEYVDTEEEETTMISMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 201

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 202  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 258

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S V        +F R   D+ ++  ++ 
Sbjct: 259  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSVDRGFF-RSLFFRSYRDEEKKMGTLV 317

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R                      G           K+T ++           
Sbjct: 318  KEDFGRPNRADTMGMRHGSYEKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---------- 367

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE   +     +  + TS    E    +++      D +     R VKV V  
Sbjct: 368  -------DESQGQASRYTRRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 415

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 416  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 475

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 476  MGKVAAHMGKEGD----------------------------------------------- 488

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 489  ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 540



 Score =  112 bits (281), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 75/486 (15%), Positives = 142/486 (29%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
              +    +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 64  IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVERQRLLI 122

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L      +  G+         D      + Y+   EEE   I+          
Sbjct: 123 KKKDIQALQQRETPDDGGWH--------DLVAKGFIEYVDTEEEETTMISM--------- 165

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 166 -TINDLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 222

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 223 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 242

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 243 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 277

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  V    F S+    +    +      +E        D   +     
Sbjct: 278 SGYNQEDSVIMNQSSVDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRADTMGMRHGSY 337

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           + +D+ G+   G  V+  D+++GK TP  +           +         RD S  +  
Sbjct: 338 EKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLRH 388

Query: 934 GVSGTV 939
             +G V
Sbjct: 389 SETGMV 394


>gi|194320177|gb|ACF48316.1| DNA-dependent RNA polymerase II second largest subunit [Lecidea
            laboriosa]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLRSTENGIVDQALL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGRTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 40/172 (23%), Positives = 68/172 (39%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P        EE  LR     K    RD S  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIA---PDAEELGLRT----KLHMKRDVSTPLRSTENGIV 170


>gi|194320206|gb|ACF48334.1| DNA-dependent RNA polymerase II second largest subunit [Porpidia
            albocaerulescens]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACCSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMNVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG+     V +G  Y  +L 
Sbjct: 293  MYNGHTGKKLVAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 66/184 (35%), Gaps = 22/184 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA     G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACCSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMNVVEEFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P        EE  LR     K    RD S  + S  
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIA---PDAEELGLRT----KLHMKRDVSTPLRSTE 166

Query: 936 SGTV 939
           +G V
Sbjct: 167 NGIV 170


>gi|194320282|gb|ACF48381.1| DNA-dependent RNA polymerase II second largest subunit [Phyllobaeis
            imbricata]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/393 (18%), Positives = 122/393 (31%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNYDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFFRTYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYEKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++                 +K    T   
Sbjct: 119  IVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL---------------HIKRDVSTPLR 163

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 164  TTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRME 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++I+ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSISRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G  I+Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEIMYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 65/185 (35%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFFRTYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRTTENGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDKVL 174


>gi|194320144|gb|ACF48294.1| DNA-dependent RNA polymerase II second largest subunit [Boreoplaca
            ultrafrigida]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 174


>gi|115636808|ref|XP_001193648.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
            purpuratus]
 gi|115652210|ref|XP_001180537.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
            purpuratus]
          Length = 263

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 48/208 (23%), Positives = 76/208 (36%), Gaps = 50/208 (24%)

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
            G+D+   V +   + + ++R    GDK + RHG KG+ S+  P EDMPF + G   DI+ 
Sbjct: 29   GNDLGNQVCQRAFIQLRIQRNPIIGDKFSSRHGQKGVCSQRWPTEDMPFTESGMTPDILF 88

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP G PSRM +G + E+  G +    G    +    +                       
Sbjct: 89   NPHGFPSRMTIGMMIESMAGKSASLHGLCHDATPFTFSEEQPA----------------- 131

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                              +    +L     +  G   +Y G +G
Sbjct: 132  ---------------------------------VDYFGKLLTAGGYNYYGTERMYSGTSG 158

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYAR 1270
               +  + +G +Y  +L HMVSDK   R
Sbjct: 159  VELEADIFIGVVYYQRLRHMVSDKFQTR 186


>gi|194320229|gb|ACF48349.1| DNA-dependent RNA polymerase II second largest subunit [Tephromela
            atra]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 63/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNADGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTGEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSKLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|194320209|gb|ACF48336.1| DNA-dependent RNA polymerase II second largest subunit [Porpidia
            speirea]
          Length = 317

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMSVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 40/172 (23%), Positives = 68/172 (39%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRIGMSVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P        EE  LR     K    RD S  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIA---PDAEELGLRT----KLHMKRDVSTPLRSTENGIV 170


>gi|46122499|ref|XP_385803.1| hypothetical protein FG05627.1 [Gibberella zeae PH-1]
          Length = 1201

 Score =  200 bits (508), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 96/300 (32%), Gaps = 80/300 (26%)

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W            N++ +           E+ F   +  I       P  L+ V +   +
Sbjct: 859  WHTVTPDYNGKLVNLDGITHY--EKYKDSEEGFIETVRLIGAESGNEP--LQTVSIKFRI 914

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK + RHG KG+ S+  P  D+PF +                           
Sbjct: 915  PRSPIVGDKFSSRHGQKGVASQKWPTMDLPFSET-------------------------- 948

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
             G A    G    S    +                                         
Sbjct: 949  AGKAGALHGLAQDSTPFKFDEENTAG---------------------------------- 974

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                            +     L  A  +  G   +Y G+TGE     + +G +Y  +L 
Sbjct: 975  ----------------DYFGHQLMKAGYNYHGNEPMYSGITGEELQADIYIGVVYYQRLR 1018

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            HMV+DK   R+TG     T QP+ G+   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1019 HMVNDKYQVRTTGPVVPTTGQPIKGRKRGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1078



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 114/899 (12%), Positives = 245/899 (27%), Gaps = 183/899 (20%)

Query: 66  TAFSGAAMLEFVSYEFDPPKFDV------------DDCLWRDLTYAVPLKITLRLIVFDV 113
           +       + +       P+                +C  R +TY   L  TL   +   
Sbjct: 81  SDGKNILTVRYKDVFLQKPQVPPSNKLARNRQVFPAECRERHVTYRGRLSATLEYRINGG 140

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGI 149
           D     +            G +P+M K                         G FV+ GI
Sbjct: 141 DPVEFTRE----------FGQVPVMIKSNRCHLEGNSPALLVERKEESEELGGYFVVNGI 190

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH------ 203
           ++ ++  L  +           +  +    Y    I  + +  D E    +++H      
Sbjct: 191 EK-IIRMLQLNKRNFPMAINRPSFQNRGPGYTPYGIILRAVRPD-ETSQTNVLHYLNDGN 248

Query: 204 --VRIDRRRK---VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
              R   R+    VPV   L AL   ++ EI             G+ +        L+  
Sbjct: 249 MTFRFSWRKNEYLVPVMMILKALVETNDREIFEGLVGPAGSKAAGNTFLTD-RIELLLRT 307

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS---DCLCGLYVAEDIVN 314
            K  +     DT   + E  + +               LG+     +   G      IV 
Sbjct: 308 YKSYNLYSKSDTRAFLGEKFRVV---------------LGVPDTMTNYEVGTEFLRKIVL 352

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDAL 374
              G + +       E+   E +   +  I  LY       A      V ++       L
Sbjct: 353 VHLGNVDV------TEEQDNEKYKLILFMIRKLYALVAGECAVDNPDAVQNQEILLGGFL 406

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKE 434
                  R  +  + +V  SM ++   +      S   R +    +     +++      
Sbjct: 407 YGQILKERFDEFLSVNVRGSMRDYFRRNPGIPFTSEEFRKEFPNNIFRKANENLG----- 461

Query: 435 DIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--SIKERISS 492
           + +       +L++  G    +D         V E L     +   RM    +   ++ +
Sbjct: 462 NALEYFMSTGNLQSQSG----LDLQQTAGFTVVAEKLNFTRFISHFRMVHRGAFFAQLKT 517

Query: 493 VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARA 552
             +  ++P+      PV                    +    + H  R  ++    +  +
Sbjct: 518 TAVRKLLPESWGFMCPV---------------HTPDGSPCGLLNHLARKCSITTDYLDVS 562

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR--KVCDGKV 610
                  ++       +  A T E   + +   +  +        I   +R  KV     
Sbjct: 563 HIATLAAELG---VVDVSSASTDENVVVMMDGKILGYCTPKESVRIADCFRYWKVEGTHG 619

Query: 611 TN---DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                ++ Y+      +                       R       +P +K D+    
Sbjct: 620 VPLQLEIGYVPPSRGGSY------------PGVYLTSTPARMVRPVKYLPLQKEDW--VG 665

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           P +   ++ +++P                        +       T +E          I
Sbjct: 666 PYEQPYMSIAVVP------------------------QEIESGKSTHVEFDP-----TNI 696

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE 787
           ++  A +    D  +   +  +  +    +        K  +        Q P+V+    
Sbjct: 697 LSILANMTPFSDFNQSPCQMAKQTMGTPGTASVYRTDNKSYQIQTG----QTPIVRA--- 749

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                      +    +   G N +VA + + GY+ +D+M++++             +  
Sbjct: 750 -------PLHNTYGFDNFPNGFNAVVAVISYTGYDMDDAMILNKSAHERGFGHGTIYKTK 802

Query: 848 EVMARDTKLGPEEI-------TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           ++  +D                    +VS      +D+ G+  VG  +  GD++    T
Sbjct: 803 KISLKDDSRTKATKSVTKAFGFAPHSHVSAHHQGMLDDDGLPHVGRLIQEGDVICAWHT 861


>gi|3002941|gb|AAC08961.1| RNA polymerase II second largest subunit [Nymphaea odorata]
          Length = 555

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 101/703 (14%), Positives = 195/703 (27%), Gaps = 148/703 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +  +G +           + +   R ++   D + +  V     L       
Sbjct: 54   AVIPQATKIFVNGCWVGIHRNPELLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+                K   A  + +           +  I
Sbjct: 111  DYGRCSRPLFIVEKQRLLI--------------KKKDIRALQLRETQEEGWHDLVAKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              ++ + + +T        +   R N     +                    PS  LG  
Sbjct: 157  EYIDTEEEETTMISMTISDLVSARLNPEEAYS-----------ETYTHCEIHPSLILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ ++  ++ +E      R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K++ +S                  D+   +     +  + TS
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTSPISQ-----------------DDSQGQASRYTRRDHSTS 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VKV +   R  Q GDK + RHG KG V     
Sbjct: 392  LRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYC 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 447  QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 507  SKALHKCGYQMRGFETM------------------------------------------- 523

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                 +G +    G         + +G  Y  +L HMV DK++
Sbjct: 524  ----YNGHT----GR---RLSAMIFLGPTYYQRLKHMVDDKIH 555



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 75/496 (15%), Positives = 141/496 (28%), Gaps = 102/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAANPILEFLEEWSTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             A   F     +         +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQATKIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +         + A    ET      D      + Y+   EEE   I+
Sbjct: 116 SRPLFIVEKQRLLIKKK-----DIRALQLRETQEEGWHDLVAKGFIEYIDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R   E      E     +  P  ++ + AS+IPF +++ S 
Sbjct: 171 M----------TISDLVSARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 248

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 249 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 273

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 274 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRE 333

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK +P  +           +        
Sbjct: 334 NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPISQDD---------SQGQASRYT 384

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 385 RRDHSTSLRHSESGMV 400


>gi|50299763|emb|CAH04349.1| RNA polymerase, subunit B [Enterobacter radicincitans]
          Length = 185

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 114/185 (61%), Positives = 144/185 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           N++L E+G F ++LV CR  GE  L   +++D++D S +QVVS+ ASLIPFLE+DD+NR 
Sbjct: 121 NTNLTEEGRFVDDLVTCRSKGESSLFSADQVDYMDVSTQQVVSVGASLIPFLEHDDANRA 180

Query: 691 LMGCN 695
           LMG N
Sbjct: 181 LMGAN 185


>gi|46277298|gb|AAS86839.1| DNA-dependent RNA polymerase II [Ascobolus carbonarius]
          Length = 555

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 89/675 (13%), Positives = 174/675 (25%), Gaps = 123/675 (18%)

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL S+  +         +    + +   +     +      ++      +  D +     
Sbjct: 2    SLMSYITIGQPSDPIVEFMSQRNMEALEEYEPTRSPNATKIFVNGVWVGVHRDPAQLVST 61

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            V        I      I  I     ++ + A  +   L   ++                +
Sbjct: 62   VQSLRRTGVISPEISLIRDIRDREFKIFTDAGRVCRPLYVVETTDDNGRQGELALQKHHI 121

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            +         +E              R G+VE +DA       +    +           
Sbjct: 122  EKLEDDKDLSLEERYGWD-----GLLRDGVVEYIDAEEEETVMITMSPEDLEISRQ---- 172

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
                             V+ G  V     +A          +   N       W      
Sbjct: 173  -----------------VQAGYHVEAEQDLAKRI-----KASASMNTH----TWTHCEIH 206

Query: 825  DSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
             SM+  +   ++            ++       +G                       + 
Sbjct: 207  PSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFPERM-----------DTMA 255

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 256  NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-R 314

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +F R  +D+ +R      E+ E   R +         +       +  G          
Sbjct: 315  SLFYRAYLDQEKRVGMSVVEEFEKPQRSETLRLKHGTYDKLDDDGLVAPGVRISGEDIII 374

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+  ++ D      R+++         ++     +                  ++K+  
Sbjct: 375  GKTAPIAPDSEELGQRTKYHTKRDVSTPLRSTENGI------------------VDKVML 416

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                    L+ VKV +   +  Q GDK A RHG KG +     CEDMPF  +G   D+++
Sbjct: 417  --TTNASGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRCEDMPFTTEGVVPDLII 474

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +  + E  L       G +                               
Sbjct: 475  NPHAIPSRMTIAHLIECQLSKVASLRGFEGD----------------------------- 505

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    +TP F     ++++S+LR A     G  I+Y+G TG
Sbjct: 506  ------------------------ATP-FTEVTVDSVSSLLRDAGYQSRGFEIMYNGHTG 540

Query: 1243 EPFDRPVTVGYIYML 1257
                  V  G  Y  
Sbjct: 541  RKLVAQVFFGPTYYQ 555



 Score =  102 bits (254), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 66/486 (13%), Positives = 132/486 (27%), Gaps = 97/486 (19%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +S +   RR   +
Sbjct: 18  EFMSQRNMEALEEYEPTRSPNATKI------FVNGVWVGVHRDPAQLVSTVQSLRRTGVI 71

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSE-------GHNIGLVSSLTSFARVNAYGF 597
                           +         P    E          + L          +    
Sbjct: 72  SPEISLIRDIRDREFKIFTDAGRVCRPLYVVETTDDNGRQGELALQKHHIEKLEDDKDLS 131

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG------SFTEELVFCRCAG 651
           +E  Y           V Y+ A EEE   I  +   L+             E    +   
Sbjct: 132 LEERY-GWDGLLRDGVVEYIDAEEEETVMITMSPEDLEISRQVQAGYHVEAEQDLAKRIK 190

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
               +        +  P  ++ + AS+IPF +++ S R      M +QA+ +     P  
Sbjct: 191 ASASMNTHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFP-- 248

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                                                  +   + + +  Y       + 
Sbjct: 249 ---------------------------------------ERMDTMANILYYPQKPLATTR 269

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
               +  R                        +L  G+N +VA   + GYN EDS+++++
Sbjct: 270 SMEYLKFR------------------------ELPAGQNAIVAIAVYSGYNQEDSVIMNQ 305

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   +   E        +   +       +D+ G++  G 
Sbjct: 306 SSIDRGLFRSLFYRAYLDQEKRVGMSVVEEFEKPQRSETLRLKHGTYDKLDDDGLVAPGV 365

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++  DI++GK  P         ++        K    RD S  + S  +G V  V +  
Sbjct: 366 RISGEDIIIGKTAPIAPDSEELGQRT-------KYHTKRDVSTPLRSTENGIVDKVMLTT 418

Query: 947 RHGIDK 952
                K
Sbjct: 419 NASGLK 424


>gi|309753162|gb|ADO85604.1| DNA-dependent RNA polymerase II [Morchella elata]
 gi|309753164|gb|ADO85605.1| DNA-dependent RNA polymerase II [Morchella elata]
          Length = 312

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/382 (16%), Positives = 112/382 (29%), Gaps = 75/382 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 66   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 124

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 125  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 171  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 260  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TG      V +G  Y  +L 
Sbjct: 291  GYTGRKLVCQVFLGPTYYQRLR 312



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 68/192 (35%), Gaps = 22/192 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA + + GYN ED
Sbjct: 4   RMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 53

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        +   +       +DE G
Sbjct: 54  SVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDG 113

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         ++       +K    RD S  + S  +G V 
Sbjct: 114 LVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVD 166

Query: 941 DVRIFNRHGIDK 952
            V +       K
Sbjct: 167 QVMLTTNAEGLK 178


>gi|17225280|gb|AAL37333.1| RNA polymerase B-subunit [Staphylococcus warneri]
          Length = 197

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 117/196 (59%), Positives = 149/196 (76%), Gaps = 2/196 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           +SL+S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F 
Sbjct: 61  NSLSSYARVNEFGFIETPYRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFI 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
           ++ V CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAV
Sbjct: 121 DDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAV 180

Query: 702 PLLKAEAPFVGTGMES 717
           PL+  EAPFVGTGM+ 
Sbjct: 181 PLMNPEAPFVGTGMDH 196


>gi|46277308|gb|AAS86844.1| DNA-dependent RNA polymerase II [Marcelleina persoonii]
          Length = 561

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 89/684 (13%), Positives = 182/684 (26%), Gaps = 130/684 (19%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     +    +    + ++  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGTPADPIIEFMLQRNMEMLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                   +        I      I D  D   K          P    D++         
Sbjct: 62   PVHLVRTIQNLRRNNVIGHEVSLIQDIRDREFKIFTDAGRICRPLFVIDNNP---TSARR 118

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                +     E             +   + +VA   G+VE +DA       +    +   
Sbjct: 119  GELVLRKEHIEKLEYDKDQPDEDLRYGWSGLVA--DGVVEYIDAEEEETIMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                +    + Q+            VK              PS  LG       +  + +
Sbjct: 177  ISRQVQAGYEIQKDADTGK-----RVKANSTAHTWTHCEIHPSMILG-------ICASII 224

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +   + +  +                             
Sbjct: 225  PFPDHNQSPRNTYQSAMGKQAMG--VFLTNYSERM------------------------- 257

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 258  --DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 315

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R   D+ ++   +    +E   +      + L    Y +L +   +  G 
Sbjct: 316  RGLF-RSLFFRSYTDQEKK---IGNSVLEQFEKPTRGNTLRLKHGTYDKLDDDGLVAPGV 371

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  ++ +      R+++         ++     +  Q   + +      
Sbjct: 372  RISGEDIIIGKTAPIAPNTEELGQRTKYHTKRDASTPLRSTENGIVDQVLITVN------ 425

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  
Sbjct: 426  --------------GEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTC 471

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 472  EGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------- 511

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++++ +LR       G 
Sbjct: 512  ---------------------------------ATP-FTEVTVDSVSKLLREMGYQSRGF 537

Query: 1234 SILYDGLTGEPFDRPVTVGYIYML 1257
             ++Y+G TG      V +G  Y  
Sbjct: 538  EVMYNGHTGRKLVAQVFLGPTYYQ 561



 Score = 58.9 bits (141), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 60/206 (29%), Gaps = 13/206 (6%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM-------RDVHPTHYG 567
           F     +    + V+ +  I + RR + +G +  + +     E        R   P    
Sbjct: 50  FVNGVWVGIHRDPVHLVRTIQNLRRNNVIGHEVSLIQDIRDREFKIFTDAGRICRPLFVI 109

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              P     G  +     +      +     E              V Y+ A EEE   I
Sbjct: 110 DNNPTSARRGELVLRKEHIEKLEY-DKDQPDEDLRYGWSGLVADGVVEYIDAEEEETIMI 168

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR----EKIDFIDASPKQVVSIAASLIPFLE 683
                 L+            + A     V            +  P  ++ I AS+IPF +
Sbjct: 169 VMTPEDLEISRQVQAGYEIQKDADTGKRVKANSTAHTWTHCEIHPSMILGICASIIPFPD 228

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAP 709
           ++ S R      M +QA+ +      
Sbjct: 229 HNQSPRNTYQSAMGKQAMGVFLTNYS 254


>gi|46277255|gb|AAS86818.1| RNA polymerase II second largest subunit [Gnetum gnemon]
          Length = 546

 Score =  199 bits (507), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 106/696 (15%), Positives = 191/696 (27%), Gaps = 150/696 (21%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L     +            + +   T +   +S     N      N 
Sbjct: 1    ETPEGQACGLVKNLALMVYITVGSSANPILEFLEEW-GTENFEEVSPSNIPNATKIFVNG 59

Query: 633  SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                   + E LV         +         D +P+  V     L       D  R   
Sbjct: 60   CWVGIHRYPETLVKTLKQLRRQV---------DVNPEVGVVRDIPLRELRLYTDYGRCSR 110

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  +   L+K     +    E V  +     +VAK  G +E VD         E   
Sbjct: 111  PLFVVEKQQLLIKKAD--IIRLQERVSPEEGWHDLVAK--GFIEYVDTE------EEETT 160

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
              S +  D+ +  K  +   +       +                        +L   + 
Sbjct: 161  MISMTITDLVQSRKNPKEAYSNTYTHCEI----------------------HPSLILGVC 198

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   I++  ++                        
Sbjct: 199  ASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ------------------------ 232

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
               +    +  V        +    +       +      + AI      +  D+ +   
Sbjct: 233  ---LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQ 289

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +        +F R   D+ +R  ++ +E+    +RD          +          G
Sbjct: 290  SSIDRGFF-RSLFFRSYRDEEKRMGTLIKEEFGRPSRDNTSGMRHGSYDKLDDDGLAPPG 348

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+T ++ D  +    ++  Q           V+ + +            
Sbjct: 349  TRVSGEDIIIGKTTPINQDENAGGKFTRRDQSTSLRHSESGMVDQVLL------------ 396

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              LR VKV +   R  Q GDK + RHG KG V      EDMP+ 
Sbjct: 397  ------------TTNQDGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWT 444

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS      
Sbjct: 445  IEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKC 504

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
               +                                                      +G
Sbjct: 505  GYQMRGFETM-----------------------------------------------YNG 517

Query: 1233 QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             +    G         + +G  Y  +L HMV DK++
Sbjct: 518  HT----GR---RLSAMIFLGPTYYQRLKHMVDDKIH 546


>gi|124127043|gb|ABM92264.1| RpoB [Bartonella henselae]
 gi|124127047|gb|ABM92266.1| RpoB [Bartonella henselae]
          Length = 198

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 139/198 (70%), Positives = 168/198 (84%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 1   GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 60

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +
Sbjct: 61  IIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLM 120

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SG
Sbjct: 121 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSG 180

Query: 725 AAIVAKRAGIVEQVDAIR 742
           AA+ A+R+GIV+QVDA R
Sbjct: 181 AAVAARRSGIVDQVDATR 198


>gi|89142763|emb|CAJ57577.1| RNA polymerase subunit B [Microbacterium ketosireducens]
          Length = 360

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 63/172 (36%), Positives = 90/172 (52%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G W
Sbjct: 1   MGDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARIIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT F+ ALG+ SE+IL+ F  +  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFMKALGLSSEDILNEFAGFDSIEETLSKDTVLTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 DALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 162



 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 125/264 (47%), Positives = 173/264 (65%), Gaps = 15/264 (5%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +       I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+
Sbjct: 97  NEFAGFDSIEETLSKDTVLTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLA 156

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L L++      +  +DI+  IK LV L  G                  +D
Sbjct: 157 KVGRYKINQKLGLESELGESVLTVKDIVETIKYLVRLHRGDTVFEGVRGGKAAEIRLDVD 216

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ 
Sbjct: 217 DIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIK 276

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET
Sbjct: 277 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIET 336

Query: 575 SEGHNIGLVSSLTSFARVNAYGFI 598
            EG NIGL+ SL SFAR+N +GFI
Sbjct: 337 PEGPNIGLIGSLASFARINPFGFI 360


>gi|56694354|gb|AAW22917.1| RNA polymerase II second largest subunit [Thuja plicata]
          Length = 514

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 72/435 (16%), Positives = 128/435 (29%), Gaps = 80/435 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 160  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 216

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 217  LYYPQXPLVTTRAMEHLHFXQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 275

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R+ ++ +E+     R+          +          G           K
Sbjct: 276  FFRSYRDEEKRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 335

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  D+   +  +  K    TS    E    +++      D
Sbjct: 336  TTPIAQ-----------------DDSAGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 378

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK   RHG KG V      E MP+  +G   DI++NP
Sbjct: 379  GL-----RFVKVRMRSVRIPQIGDKFXSRHGQKGTVGMTYTQEXMPWXVEGITPDIIVNP 433

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+                                 
Sbjct: 434  HAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------------- 462

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                  +TP F     ++I+  L        G   +Y+G TG  
Sbjct: 463  ----------------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRK 499

Query: 1245 FDRPVTVGYIYMLKL 1259
                + +G  Y  +L
Sbjct: 500  LSAMIFLGPTYYQRL 514



 Score =  112 bits (279), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 64/452 (14%), Positives = 125/452 (27%), Gaps = 100/452 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S    + I+   + ++   F     +    +    +  +   RR   +         
Sbjct: 11  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 70

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-YGFIETPYRKVCDGKVTN 612
             +    ++  +     P    E   + +  +     + +   G+ E             
Sbjct: 71  IRLRXLRLYTDYGRCSRPLFVVENQRLKIKKAHIDHLQSSREDGWHEL--------ITQG 122

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E            +  P  ++
Sbjct: 123 CIEYVDTEEEETTMISM----------TIXDLVNARTNPE--DAYSHTYTHCEIHPSLIL 170

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 171 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 210

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q PLV          
Sbjct: 211 DTLAYV-----------------------------------LYYPQXPLV---------- 225

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 226 TTRAMEHLHFXQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 285

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 286 RAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD-- 343

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  +         RD S  +    SG V
Sbjct: 344 -------SAGQVSKYTKRDQSTSLRHSESGMV 368


>gi|226287945|gb|EEH43458.1| DNA-directed RNA polymerase III subunit RPC2 [Paracoccidioides
            brasiliensis Pb18]
          Length = 1209

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 128/897 (14%), Positives = 259/897 (28%), Gaps = 149/897 (16%)

Query: 289  KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
            + K   ++ +  + +   +   +        I ++A  +  +K +  +       +  + 
Sbjct: 312  ERKSKSYIILKKERIYVRHNVLNEDVPI--VILLKAMGIQSDKEMLLL-------VAGID 362

Query: 349  VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                 + A      V      +  AL  I   ++             F  +  +  +  +
Sbjct: 363  STYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRKPNN------FGVIRRNYVQEAI 416

Query: 409  STVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG 468
              +  V ++  +  +     + +    +  + + ++  ++    +DD D +GN+R+   G
Sbjct: 417  EAISSVIISHVVVENLNFRPKAL---YVAHMARRVLMAKHDPSLVDDRDYVGNKRLELAG 473

Query: 469  EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQ 521
            ++L   +     + +  IK  I  V    V  +          +   +   +     +  
Sbjct: 474  QLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYGVVAIHGNHITQGMNRAISTGN 533

Query: 522  LSQLEEHVNSLSRITHTRRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAE 573
             S     +          RLS +   G+         + R     R + P+ +G +CP++
Sbjct: 534  WSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSGPRALQPSQFGMLCPSD 593

Query: 574  TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQAN 631
            T EG   GLV +L     +      E P RK+       DV  +   E   +  YI   N
Sbjct: 594  TPEGEACGLVKNLALMTHITTN-DEEEPVRKLIFALGAEDVQTVGGRELHGQGAYIVFLN 652

Query: 632  SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDS 687
             S        +  +             E I       ++ V IA        P +  +D 
Sbjct: 653  GSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRAVHIATDDGRICRPLIIVEDG 712

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
             +  +  +  R                ME     + G           E +D        
Sbjct: 713  -KSKVQAHHLR----------ALRSGSMEFDDFLAHGLV---------EYLDCNE----- 747

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                   + S + +Y                       D V     +   P T LG +A 
Sbjct: 748  ------ENDSNIAVYED---------------------DIVDSTTHLEIEPFTILGAVA- 779

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
                    +P+  +N          M  + +                             
Sbjct: 780  ------GLIPYPHHNQSPRNTYQCAMGKQAIGA--------------------------- 806

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                  + +    ++          +    I       +   +    A+      D+ D 
Sbjct: 807  --IANNQFLRIDSLLYTMVYPQKPMVKTRTIELIKYDRLPAGQAATVAVMSYSGYDIEDA 864

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +     +       ++F R      +   +  +++++   R         +  +  R  
Sbjct: 865  LVLNKGSIDRGFGRCQVF-RKYSTNLKSYSNGTKDKLKGPDR---------ENGLPVRKH 914

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +L      +  +      V  + +  E   S        D             Y  S  
Sbjct: 915  ALLDNDGLAAVGEKVNHGEVYINKVTPENALSS--GITGSDAGRPIT-------YIPSPQ 965

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              +    + I+K+           +++KV     R  + GDK + RHG KG+V  I    
Sbjct: 966  TYKLPDPSYIDKVMISS--TEAENQLIKVQTRQTRRPEVGDKFSSRHGQKGVVGIIAEQA 1023

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            DMPF   G   DI++NP G PSRM VG++ E   G A +  G+              
Sbjct: 1024 DMPFSDLGIVPDIIMNPHGFPSRMTVGKMLELVAGKAGILSGQFSYGTAFGGSPLRK 1080



 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 87/744 (11%), Positives = 205/744 (27%), Gaps = 114/744 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA-----MLEFVSYEFDP 83
           L++    SY++F+ + +    + +  +++     F I + +  +     +  F       
Sbjct: 122 LVKQHIDSYNYFVEVQLKKIVQASAEIRSDVDPNFYIRSSAKTSHSVFRVFRFHDIYLGT 181

Query: 84  PK---------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
           P+                  ++C  RD+TYA P+ +    +          +  + +K  
Sbjct: 182 PRRADEEQDSNFNAASTITPNECRLRDMTYASPILVDFEYV----------RGRQRVKRN 231

Query: 129 SIYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPG-I 163
              +G +P+M                           G F++ G +++++ Q   S   +
Sbjct: 232 GTAIGRMPVMLRSSKCVLSNKSEAEMQLLQECPLDPGGYFIVNGTEKVILVQEQLSKNRV 291

Query: 164 HFDHDKGR-------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVT 215
             + D  +        S S +      II             K+ I+VR +     VP+ 
Sbjct: 292 IVETDLKKEIVQASVTSSSNERKSKSYII-----------LKKERIYVRHNVLNEDVPIV 340

Query: 216 SFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL-MVGAKVSSSLVDIDTGEQVI 274
             L A+G+ S++ +      I  + + DF      A  L +     +   +         
Sbjct: 341 ILLKAMGIQSDKEMLLLVAGIDSTYQEDFAINFEEAVKLGIYTQHQALEYIGSRIKINRK 400

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLE 334
            +   +          + +  + I+   +  L                 A         +
Sbjct: 401 PNNFGVIRRNYVQEAIEAISSVIISHVVVENLNFRPKA--------LYVAHMARRVLMAK 452

Query: 335 EIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAES 394
                      +           +         K + D  ++I +V++    +    A  
Sbjct: 453 HDPSLVDDRDYVGNKRLELAGQLLSLLFEDLFKKFQFDIKMNIDKVLKKPVRTEQFDAYG 512

Query: 395 MFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH----IRKEDIIAIIKILVDLRNGK 450
           +         +     +     +++        V H    +     + ++  +       
Sbjct: 513 VVAIHGNHITQGMNRAISTGNWSLKRFRMERAGVTHVLSRLSYIAALGMMTRISSQFEKT 572

Query: 451 GTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV 510
             +     L   +   +      +     L    ++   I++ D +  + + +       
Sbjct: 573 RKVSGPRALQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTNDEEEPVRKLIFALGAED 632

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYGRI 569
                             +N        R    L     + R     E   V   H+ R 
Sbjct: 633 VQTVGGRELHGQGAYIVFLNGSPIALTRRPKFFLHSFRRLRRTGRVSEFISVFINHHQRA 692

Query: 570 CPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
               T +G     +  +       + +    + +   +  D      V YL   EE +  
Sbjct: 693 VHIATDDGRICRPLIIVEDGKSKVQAHHLRALRSGSMEFDDFLAHGLVEYLDCNEENDSN 752

Query: 627 IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           IA     +                        +    ++  P  ++   A LIP+  ++ 
Sbjct: 753 IAVYEDDI-----------------------VDSTTHLEIEPFTILGAVAGLIPYPHHNQ 789

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPF 710
           S R    C M +QA+  +      
Sbjct: 790 SPRNTYQCAMGKQAIGAIANNQFL 813



 Score =  121 bits (304), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 34/121 (28%), Positives = 56/121 (46%), Gaps = 29/121 (23%)

Query: 1265 DKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG 1324
            DK+++R+ G  +++T+QP  G+S  GG RLGEME  C+ AYG + +L E L I SD    
Sbjct: 1104 DKMHSRARGPRAILTRQPTEGRSRDGGLRLGEMERDCLIAYGTSQLLLERLMISSD---- 1159

Query: 1325 RTRVYESIVAGNDTFETGTPESF------------NVLVKEMQALGLSIDLENSRTKNSA 1372
                          +E    ES              +LV+E+ ++ +   L+ +      
Sbjct: 1160 -------------QYEVDVCESCGFMGYSGWCQRSKLLVQELFSMNVVARLKLADEFPED 1206

Query: 1373 K 1373
            +
Sbjct: 1207 R 1207


>gi|56694286|gb|AAW22883.1| RNA polymerase II second largest subunit [Botrychium virginianum]
          Length = 488

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 83/480 (17%), Positives = 141/480 (29%), Gaps = 86/480 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN           +      I   M+    
Sbjct: 93   LVAKGFIEYVDTEEEETTMISMTISDLVNARNHP----EEAYSDTYTHCEIHPSMILGVC 148

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 149  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 205

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        IF R   D+ ++  +
Sbjct: 206  EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSIDRGFF-RSIFYRSYRDEEKKQGT 264

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+ E   R+          +          G           K+T +          
Sbjct: 265  LVKEEFERPNRETTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPV---------- 314

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                    QD+   +     K    T     E    +++      D +     R VKV +
Sbjct: 315  -------PQDDSGTQAQRFTKRDQXTCLRHSESGMVDQVLLTTNADGL-----RFVKVRM 362

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+ ++G   DI++NP  +PSRM +GQ+ E
Sbjct: 363  RXIRVPQIGDKFSXRHGQKGTVGMTYTQEDMPWTQEGITPDIIVNPHAIPSRMTIGQLIE 422

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+                                               
Sbjct: 423  CIMGKVAAHMGKEGD--------------------------------------------- 437

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     + I+  L        G   +Y+G TG   +  + +G  Y  +
Sbjct: 438  --------ATP-FTDVTVDNISKALHRCGYQMRGFETMYNGHTGRRLNAMIFLGPTYYQR 488



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 49/277 (17%), Positives = 86/277 (31%), Gaps = 36/277 (12%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAET 574
           F     +    +    +  +   RR   +  + GV R     E+R ++  +     P   
Sbjct: 6   FVNGCWVGIHRDPELLVRTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFI 64

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            E   + +  S      + A    E+      D      + Y+   EEE   I+      
Sbjct: 65  VENQRLLIKKS-----DIRALQQKESTESGWYDLVAKGFIEYVDTEEEETTMISM----- 114

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                   +LV  R   E      +     +  P  ++ + AS+IPF +++ S R     
Sbjct: 115 -----TISDLVNARNHPE--EAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 167

Query: 695 NMQRQAVP----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
            M +QA+                 L   + P V T  ME +  +   A I A  A     
Sbjct: 168 AMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYS 227

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                  +   +  +D        YR  + +   Q T
Sbjct: 228 GYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKQGT 264


>gi|119710058|gb|ABL96277.1| RNA polymerase II second largest subunit [Lepraria incana]
          Length = 317

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMAVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQALLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR  KV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 177  ----------TNADGLRFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 15/149 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMAVVEEFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGES 904
           +D+ GI+  G  V+  DI++GK  P    
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAPD 142


>gi|124127045|gb|ABM92265.1| RpoB [Bartonella vinsonii subsp. berkhoffii]
          Length = 198

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 143/198 (72%), Positives = 167/198 (84%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK
Sbjct: 1   GPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRK 60

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           + DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR  +D +
Sbjct: 61  IIDGKVTTEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRNHVDLM 120

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMESVVA+ SG
Sbjct: 121 DVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESVVARDSG 180

Query: 725 AAIVAKRAGIVEQVDAIR 742
           AA+ AKR GIV+QVDA R
Sbjct: 181 AAVSAKRGGIVDQVDATR 198


>gi|194320171|gb|ACF48312.1| DNA-dependent RNA polymerase II second largest subunit [Hypocenomyce
            scalaris]
          Length = 317

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 62/380 (16%), Positives = 113/380 (29%), Gaps = 81/380 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 16   ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 74

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G        
Sbjct: 75   LFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDI 131

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D      R++          ++     +  Q                   
Sbjct: 132  IIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTESGIVDQVLL---------------- 175

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 176  ----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDL 231

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 232  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 264

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 265  --------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGH 297

Query: 1241 TGEPFDRPVTVGYIYMLKLN 1260
            TG      V +G  Y  +L 
Sbjct: 298  TGRKLVAQVFLGPTYYQRLR 317



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 36/173 (20%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YEQRMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        SG+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTESGIVDQVL 174


>gi|194320159|gb|ACF48304.1| DNA-dependent RNA polymerase II second largest subunit [Polychidium
            muscicola]
          Length = 312

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 66   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMKSDTLKLKHGTYDKLDDDGIVPPGVRV 121

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 122  TGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ---------TTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 222  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 260  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 288  MYNGHTGRKLVAQVFLGPTYYQRLR 312



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 1   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 60

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 61  SIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMKSDTLKLKHGTYDKLDDDGIVPPGVR 120

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V   DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 121 VTGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 169


>gi|194320268|gb|ACF48373.1| DNA-dependent RNA polymerase II second largest subunit [Ochrolechia
            yasudae]
          Length = 317

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 70/393 (17%), Positives = 121/393 (30%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNFDERMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L E  
Sbjct: 63   NQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDEDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++                 +K    T   
Sbjct: 119  IVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKL---------------HIKRDASTPLR 163

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 164  TTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G   +Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEAMYNGHTGRKLVVQVFLGPTYYQRLR 317



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 30/161 (18%), Positives = 57/161 (35%), Gaps = 15/161 (9%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNFDERMDTMSNILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           +DE GI+  G  V+  DI++GK  P         ++    I
Sbjct: 114 LDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHI 154


>gi|56694336|gb|AAW22908.1| RNA polymerase II second largest subunit [Dacrydium cupressinum]
          Length = 498

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 72/432 (16%), Positives = 128/432 (29%), Gaps = 80/432 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 147  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 203

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 204  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 262

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 263  FFRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 322

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T +S +                 E   +  +  +    TS    E    +++      D
Sbjct: 323  TTPVSQE-----------------ESGNQISKYTRRDQSTSLRHSESGMVDQVLLTTNQD 365

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 366  GL-----RFVKVRMRSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 420

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+                                 
Sbjct: 421  HAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------------- 449

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                  +TP F     ++I+  L        G   +Y+G TG  
Sbjct: 450  ----------------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRK 486

Query: 1245 FDRPVTVGYIYM 1256
             +  + +G  Y 
Sbjct: 487  LNAMIFLGPTYY 498



 Score =  114 bits (284), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 63/436 (14%), Positives = 117/436 (26%), Gaps = 98/436 (22%)

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + +A   F     +    +    +  +   RR   +             +RD+       
Sbjct: 13  IPTATKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNP-------EVGVVRDIRLRELRL 65

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                        +        + +     + P     D      + Y+   EEE   I+
Sbjct: 66  YTDYGRCSRPLFVVKKQRLIIKKRDINELWQNPEDGWHDLITKGFIEYVDTXEEETTMIS 125

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R   E            +  P  ++ + AS+IPF +++ S 
Sbjct: 126 M----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLILGVCASIIPFPDHNQSP 173

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 174 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 203

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 204 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 228

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 229 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKRMGTLVKEEFGRPNRE 288

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK TP  +           +        
Sbjct: 289 NTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVSQEE---------SGNQISKYT 339

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 340 RRDQSTSLRHSESGMV 355


>gi|40642976|emb|CAD90163.1| DNA-directed RNA polymerase II largest subunit [Convolvulus arvensis]
          Length = 321

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 68/381 (17%), Positives = 113/381 (29%), Gaps = 77/381 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDEDGLAPPGTRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T LS +                 +   +     K  + TS    E    +++ 
Sbjct: 137  DVIIGKTTPLSQE-----------------DAQGQAARYTKRDHSTSLRHSETGMVDQVL 179

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 180  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 234

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 235  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------- 269

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+  L        G   +Y+
Sbjct: 270  ----------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYN 300

Query: 1239 GLTGEPFDRPVTVGYIYMLKL 1259
            G TG      + +G  Y  +L
Sbjct: 301  GHTGRRLTAMIFLGPTYYQRL 321



 Score = 85.9 bits (211), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 59/184 (32%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDEDGLAPPGTRVSGEDVIIGKTTPLSQED---------AQGQAARYTKRDHSTSLRHSE 171

Query: 936 SGTV 939
           +G V
Sbjct: 172 TGMV 175


>gi|2500625|sp|P70700|RPA2_MOUSE RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2; AltName: Full=DNA-directed RNA
            polymerase I 135 kDa polypeptide; Short=RPA135
 gi|1621594|gb|AAC52850.1| second largest subunit of RNA polymerase I [Mus musculus]
          Length = 1135

 Score =  199 bits (506), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 86/413 (20%), Positives = 142/413 (34%), Gaps = 88/413 (21%)

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            ++  +  +          P   +    L  D +         +    D        +   
Sbjct: 780  DLSEKFKQGEDNLVFGVKPGDPRVMQKLDDDGLPSIGA----KLEYGDPYYSYLNLNTGE 835

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             +       E+   + I+     +DM  G  + + + V + R    GDK A RHG K   
Sbjct: 836  GFVVYYKSKENCVVDNIKVCS--NDMGSGKFKCICITVRIPRNPTIGDKFASRHGQK--- 890

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                                     G+ SR+           W    +      ++ D  
Sbjct: 891  -------------------------GILSRL-----------WPAEDMPFTESGMMPDIL 914

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGAD--EE 1217
             N    P R  +  +I              +S+   +         +TP +F   +   E
Sbjct: 915  FNPHGFPSRMTIGMLI--------------ESMAGKSAALHGLCHDATPFIFSEENSALE 960

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
                ML+ A  +  G   LY G++G   +  + +G +Y  +L HMVSDK   R+TG+   
Sbjct: 961  YFGEMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDK 1020

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV---VG------ 1324
            VT QPLGG++ +GG R GEME   + A+G +++L + L   SD     V    G      
Sbjct: 1021 VTNQPLGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVECGSLLSPL 1080

Query: 1325 -----------RTRVYESIVAG--NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                       R R Y   V G  +       P  F   V E+ A+ + + L+
Sbjct: 1081 LEKPPPSWSAMRNRKYNCTVCGRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 91/664 (13%), Positives = 219/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFRNSVSQMLRIVIEEGCHSQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y         +N  + +    +    +      + + L  L  G+  
Sbjct: 305 GECFRVKLSLPDWYPNVEAAEFLLNQGICIHLQSN--TDKFYLRCLMTRKLFALARGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V S G++           + + +  +     ++ +    +  + +    
Sbjct: 363 DDNPDSLVNQEVLSPGQLFLMFLKEKMENWLVSIKIVLDKRAQKANVSINNENLMKIFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N L  ++H R    + +G    
Sbjct: 423 GTELTRPFEYLLATGNLRSKTGLGFLEDSGLCVVADKLNFLRYLSHFR---CVHRGAAFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V   +G   +    +C   V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKFGDTASIPALLCGLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           +   +      +          V           E+ + P  ++  I 
Sbjct: 540 TGADTAPCRPYSDCYPVLLDGVMVGWVDKDLAPEVADTLRRFKVLREKRIPPWMEVALIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  R  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGREELIGTMEQLFMNVAIFEDEVFGGISTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQNRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRP----------CMYDFYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G + +   +       ++ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKFKQGEDNLVFGVKPGDPRVMQKLDDDGLPSIGAKLEYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S  + SG    +       R+    
Sbjct: 826 YSYL-----NLNTGEGFVVYYKSKENCVVDNIKVCSNDMGSGKFKCICITVRIPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 49/163 (30%), Gaps = 57/163 (34%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK 85
           DL      S+++             EGL  A +++ P           L  V     PP 
Sbjct: 37  DLTRAHVDSFNY----------AALEGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPS 86

Query: 86  F-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  R  TY   L   +   V  V         K I +Q  ++G 
Sbjct: 87  VPKGTICKDLNVYPAECRGRKSTYRGRLTADISWAVNGVP--------KGIIKQ--FLGY 136

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV 153
           +P+M K                         G F+I GI++++
Sbjct: 137 VPIMVKSKLCNLYNLPPRVLIEHHEEAEEMGGYFIINGIEKVI 179


>gi|194320238|gb|ACF48355.1| DNA-dependent RNA polymerase II second largest subunit [Lepraria
            lobificans]
          Length = 317

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMAVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR  KV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 177  ----------TNADGLRFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 15/149 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMAVVEEFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGES 904
           +D+ GI+  G  V+  DI++GK  P    
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAPD 142


>gi|194320223|gb|ACF48345.1| DNA-dependent RNA polymerase II second largest subunit [Squamarina
            cartilaginea]
          Length = 317

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 63/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGVAVVEEFEKPMRSDTLKLKHGTYDKLDEDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR  KV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 177  ----------TNADGLRFAKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 54/149 (36%), Gaps = 15/149 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGVAVVEEFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGES 904
           +DE GI+  G  V+  DI++GK  P    
Sbjct: 114 LDEDGIVAPGVRVSGEDIIIGKTAPIAPD 142


>gi|40641904|emb|CAD88602.1| RNA polymerase II second largest subunit [Alangium platanifolium]
          Length = 540

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 75/479 (15%), Positives = 133/479 (27%), Gaps = 84/479 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 142  HDLVAKGFIEYIDTEEEETTMISMTINDLVSARINPEEAYSETYTHCEIHPSLILGVCAS 201

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 202  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 258

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 259  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 317

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T ++           
Sbjct: 318  KEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---------- 367

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+   +     +  + TS    E    +++      D +     R VKV V  
Sbjct: 368  -------DDSQGQASRYSRRDHSTSLRHSETGIVDQVLLTTNADGL-----RFVKVRVRS 415

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 416  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 475

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+                                                 
Sbjct: 476  MGKVAAHMGKEGD----------------------------------------------- 488

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                  +TP F     + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 489  ------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTSMIFLGPTYYQRL 540



 Score =  109 bits (272), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 74/483 (15%), Positives = 141/483 (29%), Gaps = 99/483 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 4   EGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVG 63

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 64  IHRDPDMLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 122

Query: 583 VSSLTSFARVNAYGFIETPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
                    +      ETP      D      + Y+   EEE   I+             
Sbjct: 123 KKK-----DIQMLQQRETPEEGGWHDLVAKGFIEYIDTEEEETTMISM----------TI 167

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
            +LV  R   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+
Sbjct: 168 NDLVSARINPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 225

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            +      F                    R   +  V                       
Sbjct: 226 GIYVTNYQF--------------------RMDTLAYV----------------------- 242

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
                           Q+PLV                      L  G N +VA   + GY
Sbjct: 243 ------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGY 280

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNI 876
           N EDS+++++  +    F S+    +    +      +E        +   +       +
Sbjct: 281 NQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKL 340

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D+ G+   G  V+  D+++GK TP  +           +         RD S  +    +
Sbjct: 341 DDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------SQGQASRYSRRDHSTSLRHSET 391

Query: 937 GTV 939
           G V
Sbjct: 392 GIV 394


>gi|194320141|gb|ACF48292.1| DNA-dependent RNA polymerase II second largest subunit [Squamarina
            gypsacea]
          Length = 317

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGVAVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR  KV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 177  ----------TNADGLRFAKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 54/149 (36%), Gaps = 15/149 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGVAVVEEFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGES 904
           +D+ GI+  G  V+  DI++GK  P    
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPIAPD 142


>gi|300394764|gb|ADK11920.1| DNA-directed RNA polymerase II subunit two [Pseudoclitocybe
            cyathiformis]
          Length = 569

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 105/695 (15%), Positives = 189/695 (27%), Gaps = 127/695 (18%)

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
            CPAET EG   GLV +L   A ++   +       + +  + +         EEN + + 
Sbjct: 1    CPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESL--------EENAHSST 52

Query: 630  ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
              + +  +G +       R     +   ++     D SP+  V             D+ R
Sbjct: 53   PCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGR 109

Query: 690  VLMGCNMQR-QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
            V     +   Q + L K    ++  G                + GI+E +DA       +
Sbjct: 110  VCRPLFIVENQQLALQKKHVRWLNNGFNEDG--DEYKWEQLIKGGIIELLDAEEEETVMI 167

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                +   +       +     + +     R  +K G            PS  LG     
Sbjct: 168  SMTPEDLETSRLQQSGVDPHTDDGDFDPAAR--LKAGINAHTWTHCEIHPSMILG----- 220

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G       I   
Sbjct: 221  --ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYLTNFLIRM- 259

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 260  ----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSV 309

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    I+ R  +D  ++S   + E+ E   RD          +       
Sbjct: 310  IMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPLRDNTLRMKHGTYDKLEDDGL 368

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            I  G           K+  +  D      R++          ++     +  Q       
Sbjct: 369  IAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI---- 424

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                   + VKV V   R  Q+GDK A RH  KG +      ED
Sbjct: 425  ----------------TTNSEGQKFVKVRVRSTRIPQTGDKFASRHXQKGTIGITYRQED 468

Query: 1109 MPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            MPF  +G   DI++NP  +PSRM +G + E  L      +G +  +          +S  
Sbjct: 469  MPFTAEGIVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTX 528

Query: 1169 RSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADL 1228
                +K   +                                                  
Sbjct: 529  LR--QKGYQSRGLEVMF------------------------------------------- 543

Query: 1229 DESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               G +    G         V +G  Y  +L HMV
Sbjct: 544  --HGHT----GR---KLQAQVYLGPTYYQRLKHMV 569



 Score =  112 bits (281), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 68/461 (14%), Positives = 130/461 (28%), Gaps = 86/461 (18%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR   +            +   ++ 
Sbjct: 46  ENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYT 105

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                  P    E   + L      +  +N     +    K         +  L A EEE
Sbjct: 106 DAGRVCRPLFIVENQQLALQKKHVRW--LNNGFNEDGDEYKWEQLIKGGIIELLDAEEEE 163

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAA 676
              I+     L+        +      G+          +        +  P  ++ I A
Sbjct: 164 TVMISMTPEDLETSRLQQSGVDPHTDDGDFDPAARLKAGINAHTWTHCEIHPSMILGICA 223

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 224 SIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI-------------------------- 257

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y       +     +  R                 
Sbjct: 258 ---------------RMDTMANILYYPQKPLATTRSMEYLKFR----------------- 285

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +
Sbjct: 286 -------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGI 338

Query: 857 GPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        +   +       +++ G+I  G  V   DI++GK  P         ++
Sbjct: 339 QQLEEFEKPLRDNTLRMKHGTYDKLEDDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQR 398

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   +    RD S  + S  SG V  V I       K
Sbjct: 399 T-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 432


>gi|56694358|gb|AAW22919.1| RNA polymerase II second largest subunit [Metasequoia
            glyptostroboides]
          Length = 533

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 72/444 (16%), Positives = 129/444 (29%), Gaps = 80/444 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 170  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 226

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 227  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 285

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R+ ++ +E+     R+          +          G           K
Sbjct: 286  FFRSYRDEEKRAGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 345

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  D+   +  +  K    TS    E    +++      D
Sbjct: 346  TTPIAQ-----------------DDSAGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 388

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 389  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 443

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 444  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 501

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 502  ---------------------------------------------YNGHT----GR---K 509

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVY 1268
                + +G  Y  +L HMV DK++
Sbjct: 510  LSAMIFLGPTYYQRLKHMVDDKIH 533



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 63/451 (13%), Positives = 123/451 (27%), Gaps = 98/451 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S    + I+   + ++   F     +    +    +  +   RR   +         
Sbjct: 21  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNP------- 73

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
               +RD+                    + +      +V+      +      +      
Sbjct: 74  EVGVVRDIRLRELRLYTDYGRCSRPLFVVDNQRLKIRKVDINNLQASREDGWHELVTQGC 133

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E            +  P  ++ 
Sbjct: 134 IEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLILG 181

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
           + AS+IPF +++ S R      M +QA+ +                           R  
Sbjct: 182 VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMD 221

Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
            +  V                                       Q+PLV           
Sbjct: 222 TLAYV-----------------------------------LYYPQKPLV----------T 236

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G N +VA   + GYN EDS+++++  +    F S+    +    + 
Sbjct: 237 TRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKR 296

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                +E        +   +       +D+ G+   G  V+  D+++GK TP  +     
Sbjct: 297 AGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDD--- 353

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                 +         RD S  +    SG V
Sbjct: 354 ------SAGQVSKYTKRDQSTSLRHSESGMV 378


>gi|89142767|emb|CAJ57579.1| RNA polymerase subunit B [Microbacterium lacticum]
          Length = 359

 Score =  199 bits (505), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 63/171 (36%), Positives = 89/171 (52%), Gaps = 13/171 (7%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W+
Sbjct: 1   GDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  Y  I  +   D       
Sbjct: 59  EFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEDILNEFAGYESIEDTLSKDTILTKED 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
           A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 ALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 161



 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 129/264 (48%), Positives = 175/264 (66%), Gaps = 15/264 (5%)

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
           +       I +TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+
Sbjct: 96  NEFAGYESIEDTLSKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLA 155

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TID 454
            VGR K+N +L LD P     +  EDI+A IK LV L  G                  +D
Sbjct: 156 KVGRYKINQKLGLDKPLSDSVLTVEDIVATIKYLVALHRGDASIPGVRAGKPAEIRLDVD 215

Query: 455 DIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVC 514
           DIDN GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ 
Sbjct: 216 DIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIK 275

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF +SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET
Sbjct: 276 EFFGTSQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIET 335

Query: 575 SEGHNIGLVSSLTSFARVNAYGFI 598
            EG NIGL+ SL SFAR+N +GFI
Sbjct: 336 PEGPNIGLIGSLASFARINPFGFI 359


>gi|89274938|gb|ABD65910.1| RNA polymerase II second largest subunit [Malassezia pachydermatis]
          Length = 693

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/389 (16%), Positives = 108/389 (27%), Gaps = 75/389 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 380  DTMANILYYPQKPLATTRAMEHLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSAIDRG 439

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R   D  ++   +  E+ E   R+                  +  G      
Sbjct: 440  LF-RSLYYRTFQDMEKKVGVITMEEFEKPTRETAIRLKHGTYEKLDIDGLVPPGTRVSGE 498

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L  D                DE   R+    K    T     E    +++ 
Sbjct: 499  DIIIGKTAPLPPD---------------SDELGMRSKTHTKKDVSTPMKSTESGIIDQVL 543

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                G        + VKV V   R  Q GDK A RHG KG +      ED+PF  +G   
Sbjct: 544  ITTNG-----EGAKFVKVRVRSTRVPQVGDKFASRHGQKGTIGITYRQEDLPFTAEGITP 598

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L       G++  +          +S +   L      
Sbjct: 599  DIIINPHAIPSRMTIGHLVECLLSKVATLSGQEGDATPFTDLTVKGVSDILFSLGYQSRG 658

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 659  LEVM-----------------------------------------------YNGHT---- 667

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            G         V +G  Y  +L HMV DK+
Sbjct: 668  GR---KLQAQVYLGPTYYQRLKHMVDDKI 693



 Score =  135 bits (339), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 89/562 (15%), Positives = 171/562 (30%), Gaps = 82/562 (14%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G +L   +R+   ++ R I    +    D      Q  +    + + +     +
Sbjct: 2   KRLDLAGPLLSGLFRMLFRKVTRDIYRHLQRCVEDQKEFHLQAAVRHATITNGLRYSLAT 61

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62  GNWGDQKKAMQSKAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           G +CPAET EG   GLV +L+  + ++           + +  + + V   +A  +  + 
Sbjct: 118 GMVCPAETPEGQACGLVKNLSLMSNISVGTPSAPIVEFLEEFGLNSLVDMQAADPKATKV 177

Query: 627 IAQAN--SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                   + D+ G   + L   R   +         D  +   +        L P    
Sbjct: 178 FVNGVWLGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIREKELRIYTDAGRMLRPLFIV 237

Query: 685 DDSNRVLMGCNM----QRQAVPLLKAEAPFVGTG----------------MESVVAKSSG 724
           D  +  L+                      V +G                M     + S 
Sbjct: 238 DQQDMTLLIKRHHVEALNDESGEGWDWTRLVQSGVIEYLDTEEEETVLICMSPTDLEQSR 297

Query: 725 AAIVAKRAGIVEQVDA---------------IRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
               +    + +  DA                   I                        
Sbjct: 298 EYKASNGHMLPDTSDATRRLRSAHTFAPDIWTHCEIHPAXXXXXXXXXXXXXXXXXXXXX 357

Query: 770 SNQNTCVNQRPLV-----------KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAF 815
                   Q   V                      +A   + +     +L  G+N +VA 
Sbjct: 358 XXXXXMGKQAMGVFLTNYQIRMDTMANILYYPQKPLATTRAMEHLRFRELPAGQNAIVAI 417

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSE 870
           + + GYN EDS+++++  +   +F S++   F+ M +    +  EE  +        +  
Sbjct: 418 LCYSGYNQEDSVIMNQSAIDRGLFRSLYYRTFQDMEKKVGVITMEEFEKPTRETAIRLKH 477

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              + +D  G++  G  V+  DI++GK  P     + P+   L      K    +D S  
Sbjct: 478 GTYEKLDIDGLVPPGTRVSGEDIIIGKTAP-----LPPDSDELG--MRSKTHTKKDVSTP 530

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG +  V I       K
Sbjct: 531 MKSTESGIIDQVLITTNGEGAK 552


>gi|291419546|gb|ADE05286.1| RNA polymerase II second largest subunit [Laurera megasperma]
          Length = 315

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 63/391 (16%), Positives = 118/391 (30%), Gaps = 83/391 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNFDERMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R  +++ +R        +E   +    E +      Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFYRAYVEQEKRVGM---SAVENFEKPLRSETLRPKHGTYEKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R+   +       ++     +         
Sbjct: 119  LVAPGVRVSGEDIIIGKTAPIALDSEELGQRTMLHKKRDVSTPLRSTENGI--------- 169

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                     ++K+          L+ VKV +   +  Q GDK A RHG KG +      E
Sbjct: 170  ---------VDKVLL--TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQE 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   DI++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTAEGITPDIIINPHAIPSRMTIAHLVECQLSKVSSLRGAEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 265  ---------------------------------------ATP-FTAVTVDSVSRLLRDQG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                G  ++Y+G TG      +  G  Y  +
Sbjct: 285  YQSRGFEVMYNGHTGRKLRAQIFFGPTYYQR 315



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 33/185 (17%), Positives = 64/185 (34%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNFDERMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +         + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKRVGMSAVENFEKPLRSETLRPKHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G++  G  V+  DI++GK  P         E+L +     K  DV        +G+
Sbjct: 114 LDDDGLVAPGVRVSGEDIIIGKTAPIALDS----EELGQRTMLHKKRDVSTPLRSTENGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDKVL 174


>gi|282598422|gb|ADA83441.1| RNA polymerase beta subunit [Corynebacterium sp. NML93-0607]
          Length = 143

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 64/172 (37%), Positives = 86/172 (50%), Gaps = 37/172 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPKNAALLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L     +  G        ++ LYDG +GEP+ 
Sbjct: 45   ------------ATPVFDGASNEEIAGLLANTKPNRDGDVMVDGQGKTRLYDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G ME
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG-ME 143


>gi|315936253|gb|ADU55800.1| RNA polymerase beta subunit [Bartonella clarridgeiae]
          Length = 195

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 139/193 (72%), Positives = 163/193 (84%)

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ D
Sbjct: 2   GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIVD 61

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           G+VT +V+YLSAMEE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D S
Sbjct: 62  GRVTKEVIYLSAMEESKHYVAQANSSLDVEGRFTEEFVVCRHAGEVLMAPRDHIDLMDVS 121

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME++VA  SGAAI
Sbjct: 122 PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAIVACDSGAAI 181

Query: 728 VAKRAGIVEQVDA 740
            AKR GIV+QVDA
Sbjct: 182 GAKRGGIVDQVDA 194


>gi|56694360|gb|AAW22920.1| RNA polymerase II second largest subunit [Larix occidentalis]
          Length = 534

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 78/483 (16%), Positives = 137/483 (28%), Gaps = 84/483 (17%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            + V   +      S  + DL   RN                  I   ++     + I   
Sbjct: 136  EYVDTEEEETTMISMTINDLVSARNNPAEAYSHTYT----HCEIHPSLILGVCASIIPFP 191

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
            +     R+T             V+   L+      +  V        +    +       
Sbjct: 192  DHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQ 248

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +      + AI      +  D+ +   S +        +F R   D+ +R  ++ +E+  
Sbjct: 249  LPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKRMGTLVKEEFG 307

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               R+          +          G           K+T ++ +              
Sbjct: 308  CPNRENTLNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVAQE-------------- 353

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
               E   +    +K    TS    E    +++      D +     R VKV +   R  Q
Sbjct: 354  ---ETTGQQQRYIKRDQSTSLRHSESGMVDQVLLTTNQDGL-----RFVKVRMRSVRIPQ 405

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G   
Sbjct: 406  IGDKFSSRHGQKGTVGMTYTQEDMPWTSEGITPDIIVNPHAIPSRMTIGQLIECIMGKVA 465

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
              +GK+  +          IS         +                             
Sbjct: 466  AHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM----------------------- 502

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                     +G +    G         + +G  Y  +L HMV D
Sbjct: 503  ------------------------YNGHT----GR---KLSAMIFLGPTYYQRLKHMVDD 531

Query: 1266 KVY 1268
            K++
Sbjct: 532  KIH 534



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 73/452 (16%), Positives = 133/452 (29%), Gaps = 98/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + +A   F     +    +    +  +   RR   +    GV R 
Sbjct: 20  EEWSTENFEEISPAVIPTATKIFVNGCWVGIHRDPELLVKTLRQLRRQVDVNPEVGVVRD 79

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S      +N      +P     D     
Sbjct: 80  IRLKELR-LYTDYGRCSRPLFVVEKQRLSIKKS-----DINRLQERTSPDEGWHDLVTRG 133

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R                +  P  ++
Sbjct: 134 FIEYVDTEEEETTMISM----------TINDLVSARNNP--AEAYSHTYTHCEIHPSLIL 181

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 182 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 221

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 222 DTLAYV-----------------------------------LYYPQKPLV---------- 236

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 237 TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 296

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +  N+       +D+ G+   G  V+  D+++GK TP  +   T
Sbjct: 297 RMGTLVKEEFGCPNRENTLNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVAQEETT 356

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                      ++    RD S  +    SG V
Sbjct: 357 ---------GQQQRYIKRDQSTSLRHSESGMV 379


>gi|143024657|gb|ABO93152.1| RNA polymerase beta subunit [Enterobacter pulveris]
          Length = 195

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 117/194 (60%), Positives = 151/194 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG
Sbjct: 2   RLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            VT+++ YLSA+EE N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S 
Sbjct: 122 VVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 181

Query: 669 KQVVSIAASLIPFL 682
           +QVVS+ ASLIPFL
Sbjct: 182 QQVVSVGASLIPFL 195


>gi|194320174|gb|ACF48314.1| DNA-dependent RNA polymerase II second largest subunit [Lecidea
            silacea]
          Length = 317

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 63/385 (16%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L   IY +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSAVEEFEKPMRSDTLKLKHGIYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGLRTKLHMKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/172 (23%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YGQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSAVEEFEKPMRSDTLKLKHGIYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P        EE  LR     K    RD S  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIA---PDAEELGLRT----KLHMKRDVSTPLRSTENGIV 170


>gi|194320245|gb|ACF48359.1| DNA-dependent RNA polymerase II second largest subunit [Fuscopannaria
            ignobilis]
          Length = 317

 Score =  198 bits (504), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 61/385 (15%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      + +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQIFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 174


>gi|40643897|emb|CAD89687.1| RNA polymerase II, second largest subunit [Ilex x meserveae]
          Length = 322

 Score =  198 bits (503), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 68/382 (17%), Positives = 113/382 (29%), Gaps = 77/382 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLFYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 IF R   D+ ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSIFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T ++                  D+   +     K  + TS    E    +++ 
Sbjct: 137  DVIIGKTTPIAQ-----------------DDAQGQASRYTKRDHSTSLRHSETGIVDQVL 179

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 180  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGVTP 234

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 235  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------------------- 269

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+  L        G   +Y+
Sbjct: 270  ----------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYN 300

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TG      + +G  Y  +L 
Sbjct: 301  GHTGRRLTSMIFLGPTYYQRLK 322



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 59/184 (32%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLFYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F SI    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSIFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------AQGQASRYTKRDHSTSLRHSE 171

Query: 936 SGTV 939
           +G V
Sbjct: 172 TGIV 175


>gi|194320191|gb|ACF48325.1| DNA-dependent RNA polymerase II second largest subunit [Fuscopannaria
            mediterranea]
          Length = 317

 Score =  198 bits (503), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDIITGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI+ GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIITGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 174


>gi|330793440|ref|XP_003284792.1| RNA polymerase III, second largest subunit [Dictyostelium purpureum]
 gi|325085286|gb|EGC38696.1| RNA polymerase III, second largest subunit [Dictyostelium purpureum]
          Length = 1586

 Score =  198 bits (503), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 89/457 (19%), Positives = 157/457 (34%), Gaps = 80/457 (17%)

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            + ++ V S     + D  + N+  +D+      V ++Q+  + +  +D    +       
Sbjct: 1196 NATVAVMSYSGYDIEDALVMNKASLDRGFGRCIVLKKQVTSIKKHGNDTSDRIFPPTPDN 1255

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
            L +         G     +       L+++Y        A   E +     + K  Y   
Sbjct: 1256 LRQSKFALLDSDGIAKPGELAQKGQILVNKYSPMNTVDPAPNPELIPD--SAYKSSYMGY 1313

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
            K      F +K+  +  GD        ++K+ +   R  + GDK +              
Sbjct: 1314 KYE-NPAFIDKVL-LTNGD----DDQLLIKLLMRSTRRPELGDKFS-------------- 1353

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
                                   SR                  G+K    I   + +   
Sbjct: 1354 -----------------------SR-----------------HGQKGVCGIIVKQEDMPF 1373

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S L    + ++       +++      +L       SG       F G     I+ +L  
Sbjct: 1374 SDLGICPDIIMNPHGFPSRMTIGKMIELLAGKAAVLSGKFGYGTCFGGDRVANISKVLIS 1433

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGG 1285
                  G+  +  G+TGEP    +  G I+  KL HMV DK++AR+ G    +T+QP  G
Sbjct: 1434 KGFSYGGKDYVTSGVTGEPLACFIFFGPIFYQKLKHMVMDKMHARARGPTVTLTRQPTEG 1493

Query: 1286 KSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAG---------- 1335
            ++  GG RLGEME  C+  YGA+ ++ E L I SD    R  VY     G          
Sbjct: 1494 RARGGGLRLGEMERDCLIGYGASALIMERLMISSD----RFTVYCCKKCGFLGYEGYCQY 1549

Query: 1336 ----NDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
                 +      P +  +L +E+QA+ +   L+   +
Sbjct: 1550 CKSSVNVSTIQIPYACKLLFQELQAMNIVPRLKLIDS 1586



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 59/534 (11%), Positives = 154/534 (28%), Gaps = 62/534 (11%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L++    S++ F+ + +    + NE L             S    ++FV      P    
Sbjct: 54  LVKQHIDSFNFFVNVEMKKIVKANERLTTE-------QDPS--FFVKFVDIRVGSPISTE 104

Query: 88  ----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK----------- 126
                        C  RD+TY+ P+ + +               I +I            
Sbjct: 105 NDDFDSSQQTPQKCRLRDMTYSAPILVDIEYTRGKTVIGKKDVHIGNIPIMLRSSNCVLA 164

Query: 127 ----EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
               EQ   +G+ P M   G F+++G+++++++    S       ++       K L + 
Sbjct: 165 NKTHEQMALLGECP-MDPGGYFIVRGVEKVILNHEQLS------KNRIIIETDSKHLPSA 217

Query: 183 RIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVY 238
           ++      +     I     + ++++ +     +PV   L  +G+++++ ++        
Sbjct: 218 QVTSSTHERKSRTTI-TLKNEKLYLKHNTFGEDIPVAIVLKGMGVETDQEMAQLVGSDDV 276

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTG---EQVIESGKKLTSGLLKSLKEKGVKF 295
                       +   +     +   +               KK  S   + +   GV  
Sbjct: 277 FLDAIAPSLEECSKCGVHTQAQALDYLGSRIKVFRRPYGVQTKKTKSEEARDIL-AGVVL 335

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR----DIPILYVDS 351
             +         +    ++     I + + D       +   +  I      I +L+ D 
Sbjct: 336 NHVPVRR-YNFRLKVIYISLMIRRIIMASKDKGCLDDKDYYGNKRIELSGQLISLLFEDV 394

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
                      +         A    +  +   D  T     +  +   ++  ++ +   
Sbjct: 395 FKKFLSELKKSIDQAIAKPNRAEPFDFPKLIRTDTITNGFTHA-ISSGQWNLKRFRMERS 453

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR---NGKGTIDDIDNLGNRRVRSVG 468
           G  ++  RL+  +   +    +       K+        +  G +   D           
Sbjct: 454 GVSQVLSRLSYISCLGMMTRIQSQFEKTRKVAGPRSLQPSQWGMLCPSDTPEGEACLDPN 513

Query: 469 EMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
            ++  Q   G  ++ + + +    + +D +  +                   QL
Sbjct: 514 TII--QLSNGKSKLIKELVDGDEIITVDPITMEQHTTRIYSHFIKKSKDYGKQL 565



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 67/481 (13%), Positives = 148/481 (30%), Gaps = 40/481 (8%)

Query: 481  RMERSIKERISSVDIDSVMPQDL-INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTR 539
             +E SI  + +   +  V   +   NAK   + +      + L+      +  S+++  R
Sbjct: 831  EIENSIIIQENQDIMKFVNIFNFKYNAKENTNLIQIREYLNYLNYQNMKHSQHSQLSTER 890

Query: 540  RLSALGQGGVARARAGV------EMRDVHPTHYGRICPAETSEG-----------HNIGL 582
             +         + R          +  ++   Y  I    T              HN GL
Sbjct: 891  IIDFNSYFKKLKVRNNCLAILIDRIEPLNFEQYPEISDFTTESDYHSMISNGFITHNCGL 950

Query: 583  VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME--EENRYIAQANSSLDEDGSF 640
            V +      V          R   +  V + ++ ++  E    N ++   N  +    + 
Sbjct: 951  VKNFALMTHVTTDDPEGPLLRLAFNLGVQD-ILLVTGEELNSRNAFLVLLNGQIIGIHNS 1009

Query: 641  TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNM 696
             +  V            RE +     + +Q ++IA        P +  D+    L   ++
Sbjct: 1010 PDYFVNTLRKMRRAGRIREFVSICKNAAQQTINIACDGGRLCRPLIIVDNRVPRLKQEHI 1069

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI--------VIRSV 748
            +     L   +       +E +       + +A R   ++                +  +
Sbjct: 1070 EDLKDGLRTFDDFIKEGIIEYLDVNEENDSYLAWRELAIKPHTTHLEIEPFTMLGCVAGL 1129

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV--GDEVRRNDIIADGPSTDLGDL- 805
                  + S  + Y+    +++      NQ   +       V     +    + +L    
Sbjct: 1130 IPYPHHNQSPRNTYQCAMGKQAIGAIAYNQLTRIDTLLYLLVHPQRPLCQTRTIELLQWF 1189

Query: 806  --ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
                G N  VA M + GY+ ED++++++  +       I +++     +       +   
Sbjct: 1190 RLPAGHNATVAVMSYSGYDIEDALVMNKASLDRGFGRCIVLKKQVTSIKKHGNDTSDRIF 1249

Query: 864  DI--PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                 N+ +     +D  GI   G     G ILV K +P       P  +L+     + +
Sbjct: 1250 PPTPDNLRQSKFALLDSDGIAKPGELAQKGQILVNKYSPMNTVDPAPNPELIPDSAYKSS 1309

Query: 922  V 922
             
Sbjct: 1310 Y 1310



 Score = 56.2 bits (134), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 46/370 (12%), Positives = 116/370 (31%), Gaps = 35/370 (9%)

Query: 284 LLKSLKEKGVKFLGITSDCLC----GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +++ +++  +    ++ + +       ++    V   T E        +  + L    ++
Sbjct: 186 IVRGVEKVILNHEQLSKNRIIIETDSKHLPSAQVTSSTHERKSRTTITLKNEKLYLKHNT 245

Query: 340 EIRDIPI--------LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSV 391
              DIP+        +  D         + +  D      +         +   +     
Sbjct: 246 FGEDIPVAIVLKGMGVETDQEMAQLVGSDDVFLDAIAPSLEECSKCGVHTQAQALDYLGS 305

Query: 392 AESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR--HIRKEDIIAIIKILVDLRNG 449
              +F   +    K   S   R  +   +    P       ++   I  +I+ ++     
Sbjct: 306 RIKVFRRPYGVQTKKTKSEEARDILAGVVLNHVPVRRYNFRLKVIYISLMIRRIIMASKD 365

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISS-----VDIDSVMPQDLI 504
           KG +DD D  GN+R+   G+++   +     +    +K+ I          +      LI
Sbjct: 366 KGCLDDKDYYGNKRIELSGQLISLLFEDVFKKFLSELKKSIDQAIAKPNRAEPFDFPKLI 425

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG--------QGGVARARAGV 556
               + +       S Q +     +          RLS +         Q    + R   
Sbjct: 426 RTDTITNGFTHAISSGQWNLKRFRMERSGVSQVLSRLSYISCLGMMTRIQSQFEKTRKVA 485

Query: 557 EMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVY 616
             R + P+ +G +CP++T EG      +++   +  N    +      + +    ++++ 
Sbjct: 486 GPRSLQPSQWGMLCPSDTPEGEACLDPNTIIQLS--NGKSKL------IKELVDGDEIIT 537

Query: 617 LSAMEEENRY 626
           +  +  E   
Sbjct: 538 VDPITMEQHT 547



 Score = 42.8 bits (99), Expect = 0.49,   Method: Composition-based stats.
 Identities = 53/478 (11%), Positives = 128/478 (26%), Gaps = 51/478 (10%)

Query: 228  ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            I+       VY  +       L   +     K+++ L+  +     I +  ++       
Sbjct: 728  IIDFIGTSFVYFIK------SLLQLEKGWIEKLNNQLITQEFLSSFISNPNRIHFN--FE 779

Query: 288  LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
            L E     L +                    EI+           L    +     I I 
Sbjct: 780  LNENNQFKLLLNYKQQQQQQPQPQQQPQPNNEIFNIKLLNQLLNQLNIQSNEIENSIIIQ 839

Query: 348  YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
                +     I N     K       + +    +   ++     ++     +   +  + 
Sbjct: 840  ENQDIMKFVNIFNFKYNAKENTNLIQIREYLNYLNYQNMKHSQHSQLSTERIIDFNSYFK 899

Query: 408  LSTVGRVKMNMRLNLDTPDD-VRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
               V    + + ++   P +  ++    D          + NG  T +       +    
Sbjct: 900  KLKVRNNCLAILIDRIEPLNFEQYPEISDFTTESDYHSMISNGFITHNC---GLVKNFAL 956

Query: 467  VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
            +  +  +     LLR+  ++  +   +     +         +   +     S       
Sbjct: 957  MTHVTTDDPEGPLLRLAFNLGVQDILLVTGEELNSRNAFLVLLNGQIIGIHNS------- 1009

Query: 527  EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
                 ++ +   RR   + +       A  +  ++        C         I + + +
Sbjct: 1010 -PDYFVNTLRKMRRAGRIREFVSICKNAAQQTINI-------ACDGGRLCRPLIIVDNRV 1061

Query: 587  TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                +      ++   R   D      + YL   EE + Y+A                  
Sbjct: 1062 PRLKQ-EHIEDLKDGLRTFDDFIKEGIIEYLDVNEENDSYLA------------------ 1102

Query: 647  CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                  E+ +       ++  P  ++   A LIP+  ++ S R    C M +QA+  +
Sbjct: 1103 ----WRELAIKPH-TTHLEIEPFTMLGCVAGLIPYPHHNQSPRNTYQCAMGKQAIGAI 1155


>gi|89145191|emb|CAJ57568.1| RNA polymerase subunit B [Microbacterium aurum]
          Length = 361

 Score =  198 bits (503), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 129/257 (50%), Positives = 174/257 (67%), Gaps = 15/257 (5%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I +TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 105 IEDTLSKDTILTQEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 164

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLGNR 462
            +L LD P     +  +DI+A IK LV L  G                  +DDIDN GNR
Sbjct: 165 QKLGLDKPLSDSVLTVDDIVATIKYLVALHRGDASIPGVRNGEAAEIRLDVDDIDNFGNR 224

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQL
Sbjct: 225 RIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQL 284

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N L+ +TH RRLSALG GG+ R RAGVE+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 285 SQFMDQNNPLAGLTHKRRLSALGPGGLCRERAGVEVRDVHPSHYGRMCPIETPEGPNIGL 344

Query: 583 VSSLTSFARVNAYGFIE 599
           + SL SFAR+N +GFIE
Sbjct: 345 IGSLASFARINPFGFIE 361



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 61/172 (35%), Positives = 88/172 (51%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PL T  GTF+I G +R+VV QL RSPG++FD    +     K + + R+IP +G W
Sbjct: 1   MGDFPLQTGKGTFIINGTERVVVCQLVRSPGVYFDKTPDKT--CDKDIVSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SE+IL+ F  +  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLSSEDILAEFAGFYSIEDTLSKDTILTQE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 DALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 162


>gi|123979386|gb|ABM81518.1| RNA polymerase II second largest subunit [Solorina crocea]
          Length = 701

 Score =  198 bits (503), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 112/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 395  DTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 454

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G   
Sbjct: 455  LF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRTDTLKLKHGTYDKLDEDGIVAPGVRV 510

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 511  SGEDMIIGKTAPIPPDAEELGQRTKLHIKRDVSTPLRSTENGIVDQVLL----------- 559

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 560  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 610

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L       G +                        
Sbjct: 611  VVPDIIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD---------------------- 648

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +L+       G  +
Sbjct: 649  -------------------------------ATP-FTEVTVDSVSKILQAHGYQSRGFEV 676

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+  TG      V +G  Y  +L 
Sbjct: 677  MYNAHTGHKLVAQVFLGPTYYQRLR 701



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 390 YDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 449

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +DE GI+  G  
Sbjct: 450 SIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRTDTLKLKHGTYDKLDEDGIVAPGVR 509

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  D+++GK  P         E+L +        DV        +G+   V+
Sbjct: 510 VSGEDMIIGKTAPI----PPDAEELGQRTKLHIKRDVSTPLRSTENGIVDQVL 558



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 92/279 (32%), Gaps = 23/279 (8%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G +L   +R+   ++ + + +  +    +         + +  + + +     +
Sbjct: 2   KRLDLAGPLLAGLFRMLFNKLTKDVYKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLAT 61

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62  GNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
           G +CPAET EG   GLV +L     +      E    +    + +V  +   L +     
Sbjct: 118 GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFMIQRNMEVLEEYEPLRSPNATK 177

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FL 682
            ++      +  D +     V     G  I      + D  D   K          P F+
Sbjct: 178 VFVNGVWVGVHRDPAHLVSNVQDLRGGHVISHEVSLVRDIRDREFKIFTDAGRVCRPLFV 237

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            ++DS     G  +  +       E   +   M+    +
Sbjct: 238 IDNDSKSPSFGNLVLTKEHVNRLEEDKELAASMDPEEQE 276


>gi|32455011|gb|AAP83185.1| RpoB [Streptococcus pasteurianus]
          Length = 229

 Score =  198 bits (503), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 77/201 (38%), Positives = 106/201 (52%), Gaps = 18/201 (8%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 17   EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 69

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 70   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 118

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 119  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 178

Query: 1145 CVGLGKKIKSLINDYKANGDI 1165
               LG  I + + D   + D+
Sbjct: 179  ARNLGIHIATPVFDGATSEDL 199



 Score = 90.5 bits (223), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 63/96 (65%), Positives = 75/96 (78%)

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
            GPEEITR+IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL A
Sbjct: 3   WGPEEITREIPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHA 62

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           IFG+K+ +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 63  IFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRANGD 98



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 45/107 (42%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 123  KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 182

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            G+ ++TPVFDGA  E +   +R A +D   +++LYDG TGEPFD  V
Sbjct: 183  GIHIATPVFDGATSEDLWDTVREAGMDSDAKTVLYDGRTGEPFDNRV 229


>gi|37956434|gb|AAP15386.1| RNA polymerase beta subunit [Geobacter grbiciae]
          Length = 210

 Score =  198 bits (503), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 118/203 (58%), Positives = 157/203 (77%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQEVENLMPHDLINSKPVSAEVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V +G
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRIVSEG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           KVT +V + SA+EEE   IAQAN+ +D DG F  + V  R +GE +LV R++++ +D +P
Sbjct: 122 KVTAEVKFFSALEEEGHAIAQANAEMDADGRFVNDYVSARKSGEFLLVHRDELELMDVAP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVL 691
            Q+VS+A SLIPFLENDD+NR L
Sbjct: 182 MQLVSVATSLIPFLENDDANRAL 204


>gi|194320150|gb|ACF48298.1| DNA-dependent RNA polymerase II second largest subunit [Bacidina
            arnoldiana]
          Length = 314

 Score =  198 bits (503), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 59/382 (15%), Positives = 107/382 (28%), Gaps = 75/382 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLGTTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++  +   E+ E   R           +       +  G      
Sbjct: 68   LF-RSLFYRAYTDQEKKVGANTVEEFEKPMRSTTLRMKQATYDKLDDDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D      RS+          ++     +  Q                 
Sbjct: 127  DIIIGKTAPITADHNELGQRSKLHAKRDVSTPLRSTENGIVDQ----------------- 169

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR  KV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 170  ---VMVSTNSDGLRFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L                                     
Sbjct: 227  DLIINPHAIPSRMTIAHLIECQLSKVSA-------------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                  +     +TP F     + ++ +LR       G  ++Y+
Sbjct: 255  ---------------------LRGCEGDATP-FTEVTVDKVSRLLREHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G TG      V +G  Y  +L 
Sbjct: 293  GHTGRKLVAQVFLGPTYYQRLR 314



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/191 (18%), Positives = 63/191 (32%), Gaps = 22/191 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNFNTXMDTMANILYYPQKPL----------GTTRSMEFLRFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +       E            + +     
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKKVGANTVEEFEKPMRSTTLRMKQATYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         ++        K    RD S  + S  
Sbjct: 111 LDDDGIVAPGVRVSGEDIIIGKTAPITADHNELGQR-------SKLHAKRDVSTPLRSTE 163

Query: 936 SGTVVDVRIFN 946
           +G V  V +  
Sbjct: 164 NGIVDQVMVST 174


>gi|92111215|gb|ABE73463.1| DNA-directed RNA polymerase beta chain [Chlamydophila pneumoniae]
          Length = 229

 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 73/214 (34%), Positives = 117/214 (54%), Gaps = 8/214 (3%)

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK-------KSTVLSSDLISEY 1016
            ++ L +   ++   L      +L  +L  + A +     +       +  +   + I   
Sbjct: 1    LKDLQKGYKNQVATLKTEYREKLGALLLNEKAPAAIIHRRTAEIVVHEGLLFDQETIERI 60

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD-DMPPGVLRVVK 1075
             +       + + ++   ++ L   YET+   LE  +K ++E I+ GD D+  GV+R VK
Sbjct: 61   EQEDLVDLLMPNCEMYEVLKGLLSDYETALQRLEINYKTEVEHIREGDADLDHGVIRQVK 120

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V+VA KR +Q GDKMAGRHGNKG+VS+I+P  DMP+L +G  V ++LNPLGVPSRMN+GQ
Sbjct: 121  VYVASKRKLQVGDKMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNLGQ 180

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            + ETHLG+A    G  +K+ + +      I  + 
Sbjct: 181  VLETHLGYAAKTAGIYVKTPVFEGFPEQRIWDMM 214



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 35/96 (36%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K        +A+         ++ ++       +++               +
Sbjct: 134  KMAGRHGNKGVVSKIVPEADMPYLSNGETVQMILNPLGVPSRMNLGQVLETHLGYAAKTA 193

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
            G+ V TPVF+G  E+ I  M+    L E G+S LYD
Sbjct: 194  GIYVKTPVFEGFPEQRIWDMMIEQGLPEDGKSFLYD 229


>gi|330982601|gb|EGH80704.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 459

 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 112/207 (54%), Positives = 154/207 (74%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            + G+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR+N YGF+++PYR 
Sbjct: 252 LEIGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARINQYGFLKSPYRV 311

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V +G VT ++V+LSA+EE +  IAQA++++++     +ELV  R   E  +     +  +
Sbjct: 312 VKEGLVTEEIVFLSAIEEADHVIAQASAAMNDKQELIDELVAVRHLNEFTVKAPADVTLM 371

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA+ SG
Sbjct: 372 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSG 431

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGD 751
             +VA+R G+++ VDA RIV+R  + +
Sbjct: 432 VCVVARRGGVIDSVDASRIVVRVADDE 458


>gi|83305713|dbj|BAE53691.1| RNA polymerase beta subunit [Nocardia farcinica]
          Length = 227

 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 113/214 (52%), Positives = 161/214 (75%), Gaps = 1/214 (0%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
           +DDID+ GNRRVR+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ L+N +PVV+A
Sbjct: 14  VDDIDHFGNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQSLMNIRPVVAA 73

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N L+ +T+ RRLSALG GG++R RAG+E+RDVH +HYGR+CP 
Sbjct: 74  MKEFFGTSQLSQFMDQRNPLASLTNKRRLSALGPGGLSRERAGLEVRDVHYSHYGRMCPI 133

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL+  L+ +ARVN +GF+ETPYR+V DG+VT++V YL+A EE+   +AQAN 
Sbjct: 134 ETPEGPNIGLMGYLSVYARVNPFGFVETPYRRVVDGRVTDEVDYLTADEEDRHVVAQANE 193

Query: 633 SLDEDGSFTEELVFCRCAG-EEILVPREKIDFID 665
            LD +G F    +  R    E  LV    +D++D
Sbjct: 194 PLDAEGRFLAARIPVRRKNSEVELVDSAAVDYMD 227


>gi|66876501|gb|AAY58041.1| RpoB [Cuscuta europaea]
          Length = 473

 Score =  197 bits (502), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 126/414 (30%), Positives = 210/414 (50%), Gaps = 7/414 (1%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   D+  +  ++    
Sbjct: 61  ISVYTGTIISDWGGRSELEIDRKARIWARVSRKKKISILVLSSAMGLDLKKIIENACYPE 120

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN--FLFFDSDKYDLSTV 411
            ++   +     K   +K+A+L  Y+   PG        E +       F   + +L  +
Sbjct: 121 IFLSFLSDKDKKKIGSKKNAILKFYKK-SPGVGGDLLGYEYLCKELQKKFFHQRCELGQL 179

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 180 GRRNMNRRLNLDIPQNNTFLVPRDILAAADHLIALKFGMGTLDDMNHLQNKRIRSVADLL 239

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R E  +K  I       +   PQ+L+ + P+ +    FF    LSQ+ +  
Sbjct: 240 QDQFGLALVRFENVVKSTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDQT 299

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I H R+ S LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 300 NPLTQIVHARKFSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 359

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           AR+  +G +E+P  ++ +      ++YLS   +E   +A  NS         +++V  R 
Sbjct: 360 ARIGRWGSLESPLFEISERSTRVRMLYLSPGRDEYYMVAAGNSLALNQNIQEDQVVPARY 419

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
             E + +  E++        Q  SI ASLIPF+E++D+NR LM  NMQRQAVPL
Sbjct: 420 CQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPL 473



 Score =  127 bits (320), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 41/120 (34%), Positives = 71/120 (59%), Gaps = 4/120 (3%)

Query: 125 IKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRI 184
           ++EQ I++G +PLM   G+F++ GI RIV++Q+ +SPGI++  +     +S   +Y   I
Sbjct: 12  MQEQIIFLGSIPLMNSLGSFIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGTI 68

Query: 185 IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILST-FYPKIVYSQRGD 243
           I D G   ++E D K  I  R+ R++K+ +     A+G+D ++I+    YP+I  S   D
Sbjct: 69  ISDWGGRSELEIDRKARIWARVSRKKKISILVLSSAMGLDLKKIIENACYPEIFLSFLSD 128


>gi|46277304|gb|AAS86842.1| DNA-dependent RNA polymerase II [Ascobolus crenulatus]
          Length = 538

 Score =  197 bits (502), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 70/446 (15%), Positives = 129/446 (28%), Gaps = 94/446 (21%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             W       SM+  +   ++            ++       +G                 
Sbjct: 182  TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFPERM------- 234

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 235  ----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSS 290

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R  +D+ +R        +E   +    E + L    Y +L E   +  
Sbjct: 291  IDRGLF-RSLFYRAYLDQEKRVGM---SVVEEFEKPHRSETLRLKHGTYDKLDEDGLVAP 346

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D      R+++         ++     +             
Sbjct: 347  GVRISGEDIIIGKTAPIAPDSEELGQRTKYHTKRDVSTPLRSTENGI------------- 393

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                 ++K+          L+ VKV +   +  Q GDK A RHG KG +     CEDMPF
Sbjct: 394  -----VDKVML--TTNASGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRCEDMPF 446

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G   D+++NP  +PSRM +  + E  L       G +                    
Sbjct: 447  TTEGVVPDLIINPHAIPSRMTIAHLIECQLSKVASLRGFEGD------------------ 488

Query: 1172 LEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES 1231
                                               +TP F     ++++S+LR A     
Sbjct: 489  -----------------------------------ATP-FTEVTVDSVSSLLRDAGYQSR 512

Query: 1232 GQSILYDGLTGEPFDRPVTVGYIYML 1257
            G  I+Y+G TG      V  G  Y  
Sbjct: 513  GFEIMYNGHTGRKLVAQVFFGPTYYQ 538



 Score =  101 bits (252), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 67/485 (13%), Positives = 132/485 (27%), Gaps = 95/485 (19%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +S +   RR   +
Sbjct: 1   EFMSQRNMEALEEYEPTRSPNATKI------FVNGVWVGVHRDPAQLVSTVQSLRRTGVI 54

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSE-----GHNIGLVSSLTSFARVNAYGFIE 599
                           +         P    E     G    L        ++     + 
Sbjct: 55  SAEISLVRDIRDREFKIFTDAGRVCRPLYVVETTDDNGRQGELALQKHHIEKLEDDKDLP 114

Query: 600 TPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG------SFTEELVFCRCAGE 652
              R           V Y+ A EEE   I  +   L+             E    +    
Sbjct: 115 PEERYGWDGLLRDGVVEYIDAEEEETVMITMSPEDLEISRQVQAGYHVEAEQDLAKRIKA 174

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
              +        +  P  ++ + AS+IPF +++ S R      M +QA+ +     P   
Sbjct: 175 SSSMNTHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFP--- 231

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                                                 +   + + +  Y       +  
Sbjct: 232 --------------------------------------ERMDTMANILYYPQKPLATTRS 253

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
              +  R                        +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 254 MEYLKFR------------------------ELPAGQNAIVAIAVYSGYNQEDSVIMNQS 289

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        +   +       +DE G++  G  
Sbjct: 290 SIDRGLFRSLFYRAYLDQEKRVGMSVVEEFEKPHRSETLRLKHGTYDKLDEDGLVAPGVR 349

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           ++  DI++GK  P         ++        K    RD S  + S  +G V  V +   
Sbjct: 350 ISGEDIIIGKTAPIAPDSEELGQRT-------KYHTKRDVSTPLRSTENGIVDKVMLTTN 402

Query: 948 HGIDK 952
               K
Sbjct: 403 ASGLK 407


>gi|38614338|gb|AAH60656.1| Polymerase (RNA) I polypeptide B [Mus musculus]
          Length = 1135

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 123/330 (37%), Gaps = 82/330 (24%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +DM  G  + + + V + R    GDK A RHG K                          
Sbjct: 857  NDMGSGKFKCICITVRIPRNPTIGDKFASRHGQK-------------------------- 890

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
              G+ SR+           W    +      ++ D   N    P R  +  +I       
Sbjct: 891  --GILSRL-----------WPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLI------- 930

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGL 1240
                   +S+   +         +TP +F   +   E    ML+ A  +  G   LY G+
Sbjct: 931  -------ESMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGI 983

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +G   +  + +G +Y  +L HMVSDK   R+TG+   VT QPLGG++ +GG R GEME  
Sbjct: 984  SGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPLGGRNVQGGIRFGEMERD 1043

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVG------------------------RTRVYESIVAG- 1335
             + A+G +++L + L   SD  V                         R R Y   V G 
Sbjct: 1044 ALLAHGTSFLLHDRLFNCSDRSVAHMCVECGSLLSPLLEKPPPSWSAMRNRKYNCTVCGR 1103

Query: 1336 -NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             +       P  F   V E+ A+ + + L+
Sbjct: 1104 SDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 90/664 (13%), Positives = 220/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFRNSVSQMLRIVIEEGCHSQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y         +N  + +    +    +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLSLPDWYPNVEAAEFLLNQCICIHLQSN--TDKFYLLCLMTRKLFALARGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V S G++           + + +  +     ++ +    +  + +    
Sbjct: 363 DDNPDSLVNQEVFSPGQLFLMFLKEKMENWLVSIKIVLDKRAQKANVSINNENLMKIFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N L  ++H R    + +G    
Sbjct: 423 GTELTRPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFLRYLSHFR---CVHRGAAFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V   + +  +    +C   V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKFVYTASIPALLCGLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           +   +      +          V           E+ + P  ++  I 
Sbjct: 540 TPVDTAPCRPYSDCYPVLLDGVMVGWVDKDLAPEVADTLRRFKVLREKRIPPWMEVALIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  R  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGREELIGTMEQLFMNVAIFEDEVFGGISTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQNRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRP----------CMYDFYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G + +   +       ++ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKFKQGEDNLVFGVKPGDPRVMQKLDDDGLPFIGAKLEYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S  + SG    +       R+    
Sbjct: 826 YSYL-----NLNTGEGFVVYYKSKENCVVDNIKVCSNDMGSGKFKCICITVRIPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 49/163 (30%), Gaps = 57/163 (34%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK 85
           DL      S+++             EGL  A +++ P           L  V     PP 
Sbjct: 37  DLTRAHVDSFNY----------AALEGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPS 86

Query: 86  F-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  R  TY   L   +   V  V         K I +Q  ++G 
Sbjct: 87  VPKGTICKDLNVYPAECRGRKSTYRGRLTADISWAVNGVP--------KGIIKQ--FLGY 136

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV 153
           +P+M K                         G F+I GI++++
Sbjct: 137 VPIMVKSKLCNLYNLPPRVLIEHHEEAEEMGGYFIINGIEKVI 179


>gi|224967092|ref|NP_033112.2| DNA-directed RNA polymerase I subunit RPA2 [Mus musculus]
 gi|74137985|dbj|BAE25401.1| unnamed protein product [Mus musculus]
 gi|74194733|dbj|BAE25971.1| unnamed protein product [Mus musculus]
 gi|123230106|emb|CAM18667.1| RNA polymerase 1-2 [Mus musculus]
 gi|123284570|emb|CAM27884.1| RNA polymerase 1-2 [Mus musculus]
 gi|148696280|gb|EDL28227.1| RNA polymerase 1-2 [Mus musculus]
          Length = 1135

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 123/330 (37%), Gaps = 82/330 (24%)

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            +DM  G  + + + V + R    GDK A RHG K                          
Sbjct: 857  NDMGSGKFKCICITVRIPRNPTIGDKFASRHGQK-------------------------- 890

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
              G+ SR+           W    +      ++ D   N    P R  +  +I       
Sbjct: 891  --GILSRL-----------WPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLI------- 930

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGL 1240
                   +S+   +         +TP +F   +   E    ML+ A  +  G   LY G+
Sbjct: 931  -------ESMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGI 983

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            +G   +  + +G +Y  +L HMVSDK   R+TG+   VT QPLGG++ +GG R GEME  
Sbjct: 984  SGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPLGGRNVQGGIRFGEMERD 1043

Query: 1301 CIQAYGAAYVLQEMLTIKSDDVVG------------------------RTRVYESIVAG- 1335
             + A+G +++L + L   SD  V                         R R Y   V G 
Sbjct: 1044 ALLAHGTSFLLHDRLFNCSDRSVAHMCVECGSLLSPLLEKPPPSWSAMRNRKYNCTVCGR 1103

Query: 1336 -NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
             +       P  F   V E+ A+ + + L+
Sbjct: 1104 SDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 90/664 (13%), Positives = 220/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +     +++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEEDSFFRNSVSQMLRIVIEEGCHSQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y         +N  + +    +    +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLSLPDWYPNVEAAEFLLNQCICIHLQSN--TDKFYLLCLMTRKLFALARGECM 362

Query: 453 IDDIDNLGNRRVRSVGEML-------KNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            D+ D+L N+ V S G++           + + +  +     ++ +    +  + +    
Sbjct: 363 DDNPDSLVNQEVLSPGQLFLMFLKEKMENWLVSIKIVLDKRAQKANVSINNENLMKIFSM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N L  ++H R    + +G    
Sbjct: 423 GTELTRPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFLRYLSHFR---CVHRGAAFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V   + +  +    +C   V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKFVYTASIPALLCGLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           +   +      +          V           E+ + P  ++  I 
Sbjct: 540 TPVDTAPCRPYSDCYPVLLDGVMVGWVDKDLAPEVADTLRRFKVLREKRIPPWMEVALIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  R  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGREELIGTMEQLFMNVAIFEDEVFGGISTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQNRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRP----------CMYDFYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G + +   +       ++ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKFKQGEDNLVFGVKPGDPRVMQKLDDDGLPFIGAKLEYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S  + SG    +       R+    
Sbjct: 826 YSYL-----NLNTGEGFVVYYKSKENCVVDNIKVCSNDMGSGKFKCICITVRIPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 49/163 (30%), Gaps = 57/163 (34%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK 85
           DL      S+++             EGL  A +++ P           L  V     PP 
Sbjct: 37  DLTRAHVDSFNY----------AALEGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPS 86

Query: 86  F-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                          +C  R  TY   L   +   V  V         K I +Q  ++G 
Sbjct: 87  VPKGTICKDLNVYPAECRGRKSTYRGRLTADISWAVNGVP--------KGIIKQ--FLGY 136

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV 153
           +P+M K                         G F+I GI++++
Sbjct: 137 VPIMVKSKLCNLYNLPPRVLIEHHEEAEEMGGYFIINGIEKVI 179


>gi|194320265|gb|ACF48371.1| DNA-dependent RNA polymerase II second largest subunit [Ochrolechia
            trochophora]
          Length = 317

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 69/393 (17%), Positives = 121/393 (30%), Gaps = 83/393 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 3    LTNFDERMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 62

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 63   NQSSIDRGLF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDG 118

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  ++ D      R++                 +K    T   
Sbjct: 119  IVAPGVRVSGEDIIIGKTAPMAPDAEELGQRTKL---------------HIKRDASTPLR 163

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 164  TTENGIVDKVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 218

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 219  DMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 264

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 265  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 284

Query: 1228 LDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                G   +Y+G TG      V +G  Y  +L 
Sbjct: 285  YQSRGFEAMYNGHTGRKLVVQVFLGPTYYQRLR 317



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 57/161 (35%), Gaps = 15/161 (9%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNFDERMDTMSNILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           +D+ GI+  G  V+  DI++GK  P         ++    I
Sbjct: 114 LDDDGIVAPGVRVSGEDIIIGKTAPMAPDAEELGQRTKLHI 154


>gi|46277306|gb|AAS86843.1| DNA-dependent RNA polymerase II [Marcelleina persoonii]
          Length = 560

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 89/683 (13%), Positives = 182/683 (26%), Gaps = 130/683 (19%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     +    +    + ++  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGTPADPIIEFMLQRNMEMLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                   +        I      I D  D   K          P    D++         
Sbjct: 62   PVHLVRTIQNLRRNNVIGHEVSLIQDIRDREFKIFTDAGRICRPLFVIDNNP---TSARR 118

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
                +     E             +   + +VA   G+VE +DA       +    +   
Sbjct: 119  GELVLRKEHIEKLEYDKDQPDEDLRYGWSGLVA--DGVVEYIDAEEEETIMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                +    + Q+            VK              PS  LG       +  + +
Sbjct: 177  ISRQVQAGYEIQKDADTGK-----RVKANSTAHTWTHCEIHPSMILG-------ICASII 224

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +   + +  +                             
Sbjct: 225  PFPDHNQSPRNTYQSAMGKQAMG--VFLTNYSERM------------------------- 257

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 258  --DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 315

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R   D+ ++   +    +E   +      + L    Y +L +   +  G 
Sbjct: 316  RGLF-RSLFFRSYTDQEKK---IGNSVLEQFEKPTRGNTLRLKHGTYDKLDDDGLVAPGV 371

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  ++ +      R+++         ++     +  Q   + +      
Sbjct: 372  RISGEDIIIGKTAPIAPNTEELGQRTKYHTKRDASTPLRSTENGIVDQVLITVN------ 425

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  
Sbjct: 426  --------------GEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTC 471

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +  + E  L       G +                      
Sbjct: 472  EGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------- 511

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     ++++ +LR       G 
Sbjct: 512  ---------------------------------ATP-FTEVTVDSVSKLLREMGYQSRGF 537

Query: 1234 SILYDGLTGEPFDRPVTVGYIYM 1256
             ++Y+G TG      V +G  Y 
Sbjct: 538  EVMYNGHTGRKLVAQVFLGPTYY 560



 Score = 58.9 bits (141), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 60/206 (29%), Gaps = 13/206 (6%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM-------RDVHPTHYG 567
           F     +    + V+ +  I + RR + +G +  + +     E        R   P    
Sbjct: 50  FVNGVWVGIHRDPVHLVRTIQNLRRNNVIGHEVSLIQDIRDREFKIFTDAGRICRPLFVI 109

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              P     G  +     +      +     E              V Y+ A EEE   I
Sbjct: 110 DNNPTSARRGELVLRKEHIEKLEY-DKDQPDEDLRYGWSGLVADGVVEYIDAEEEETIMI 168

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPR----EKIDFIDASPKQVVSIAASLIPFLE 683
                 L+            + A     V            +  P  ++ I AS+IPF +
Sbjct: 169 VMTPEDLEISRQVQAGYEIQKDADTGKRVKANSTAHTWTHCEIHPSMILGICASIIPFPD 228

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAP 709
           ++ S R      M +QA+ +      
Sbjct: 229 HNQSPRNTYQSAMGKQAMGVFLTNYS 254


>gi|194320212|gb|ACF48338.1| DNA-dependent RNA polymerase II second largest subunit [Lecidoma
            demissum]
          Length = 317

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 62/385 (16%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 127  SGEDMIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 176  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFASEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  D+++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDMIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 174


>gi|153842038|ref|ZP_01993464.1| DNA-directed RNA polymerase beta chain [Vibrio parahaemolyticus
           AQ3810]
 gi|149745419|gb|EDM56670.1| DNA-directed RNA polymerase beta chain [Vibrio parahaemolyticus
           AQ3810]
          Length = 285

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 127/229 (55%), Gaps = 3/229 (1%)

Query: 202 IHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           ++VRIDRRRK+P +  L ALG  +EEIL  F+ K+ +  +       L   D + G   S
Sbjct: 1   LYVRIDRRRKLPASIILRALGKSTEEILDIFFEKVNFEVKDQTLLMELVP-DRLRGETAS 59

Query: 262 SSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIY 321
             +     G+  +E G+++T+  ++ L++ GV  + +  + + G   ++D +N  TGEI 
Sbjct: 60  FDIES--NGKVYVEQGRRVTARHIRQLEKDGVDHIEVPVEYIVGKVASKDYINEATGEII 117

Query: 322 IEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM 381
           + A   I  ++L  +  +  + + +L+ + +++  ++  TL  D   DR  AL++IYR+M
Sbjct: 118 VNANQEISLEALANLSQAGHKALEVLFTNDLDHGPFMSETLRIDSTVDRISALVEIYRMM 177

Query: 382 RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRH 430
           RPG+  T   AE++F  LFF  ++YDLSTVGR+K N  +  +   +   
Sbjct: 178 RPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGREDAQEQGT 226


>gi|126632268|emb|CAM54067.1| RNA Polymerase beta subunit [Streptococcus equi subsp. ruminatorum]
          Length = 211

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 77/203 (37%), Positives = 106/203 (52%), Gaps = 18/203 (8%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 9    EEALKDL-DEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 61

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 62   -----EVRDTSLRVPHGGDGIVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 110

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSRI+P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 111  KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 170

Query: 1145 CVGLGKKIKSLINDYKANGDISP 1167
               LG  I + + D   + D+  
Sbjct: 171  ARNLGIHIATPVFDGATSEDLWE 193



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/89 (62%), Positives = 69/89 (77%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           R++PNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ 
Sbjct: 2   REVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V DV+IF R   D
Sbjct: 62  EVRDTSLRVPHGGDGIVRDVKIFTRANGD 90



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 115  KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 174

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
            G+ ++TPVFDGA  E +   +R A +D   +++LYDG
Sbjct: 175  GIHIATPVFDGATSEDLWETVREAGMDSDAKTVLYDG 211


>gi|289610731|emb|CBI60188.1| unnamed protein product [Sordaria macrospora]
          Length = 69

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 53/68 (77%), Positives = 59/68 (86%)

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            VTVG IYMLKL+H+V DK++ARS G YSLVTQQPLGGK+  GGQR GEMEVW +QAYGAA
Sbjct: 2    VTVGIIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALQAYGAA 61

Query: 1309 YVLQEMLT 1316
            Y LQEMLT
Sbjct: 62   YTLQEMLT 69


>gi|46277291|gb|AAS86836.1| RNA polymerase II second largest subunit [Teucrium fruticans]
          Length = 336

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/390 (18%), Positives = 113/390 (28%), Gaps = 78/390 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTP-------EEKLLRAIFGEKAVDVRDTSLRV 931
             G   +G  V      +  +      P  P       E    R +       V       
Sbjct: 16   MGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSG 75

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEI-L 990
             +     +++    +R             R       RD++ +   L +  + R      
Sbjct: 76   YNQEDSVIMNQSSIDRGFF----------RSLFFRSYRDEEKKMGTLVKEDFGRPDRASC 125

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL-KVQYETSKSIL 1049
             G    S  K            +S           +  +  Q       K  + TS    
Sbjct: 126  MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAPDDAQGQAARYTKRDHSTSLRHS 185

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E    +++      D +     R VKV V   R  Q GDK + RHG KG V      EDM
Sbjct: 186  ETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDM 240

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                  
Sbjct: 241  PWTLEGITPDIIVNPHAIPSRMTIGQLIECVMGKVAAHMGKEGD---------------- 284

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                                                 +TP F     + I+  L      
Sbjct: 285  -------------------------------------ATP-FTDVTVDNISRALHKCGYQ 306

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
              G   +Y+G TG      + +G  Y  +L
Sbjct: 307  MRGFETMYNGHTGRRLTAMIFLGPTYYQRL 336



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 64/207 (30%), Gaps = 25/207 (12%)

Query: 739 DAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           D  +    + +  +     G+       +           Q+PLV               
Sbjct: 3   DHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLV----------TTRAM 52

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                  L  G N +VA   + GYN EDS+++++  +    F S+    +    +     
Sbjct: 53  EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTL 112

Query: 858 PEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
            +E            +       +D+ G+   G  V+  D+++GK +P            
Sbjct: 113 VKEDFGRPDRASCMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAPDD------- 165

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             A         RD S  +    +G V
Sbjct: 166 --AQGQAARYTKRDHSTSLRHSETGMV 190


>gi|311697793|gb|ADQ00199.1| DNA-directed RNA polymerase beta chain [Neptuniibacter sp.
           antisso-13]
          Length = 184

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 107/183 (58%), Positives = 142/183 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +A+ EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL +FAR N YGF+ETPYR+V D KVT+++ YLSA+EE    IAQA
Sbjct: 61  PIETPEGPNIGLINSLATFARTNDYGFLETPYRRVVDSKVTDELDYLSAIEENTFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           ++++D++G   +++V  R   E  ++  EK+ ++D SP+QVVS+AASLIPFLE+DD+NR 
Sbjct: 121 SATMDDEGRLVDDMVTVRHLNETTVMAPEKVQYMDVSPRQVVSVAASLIPFLEHDDANRA 180

Query: 691 LMG 693
           LMG
Sbjct: 181 LMG 183


>gi|56694340|gb|AAW22910.1| RNA polymerase II second largest subunit [Saxegothaea conspicua]
          Length = 526

 Score =  197 bits (501), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/444 (16%), Positives = 128/444 (28%), Gaps = 80/444 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 163  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DXLAYV 219

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 220  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 278

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 279  FFRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 338

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T +S +                 E   +  +  +    TS    E    +++      D
Sbjct: 339  TTPVSQE-----------------ESGNQISKYTRRDQSTSLRHSESGMVDQVLLTTNQD 381

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 382  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 436

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 437  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 494

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 495  ---------------------------------------------YNGHT----GR---K 502

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVY 1268
                + +G  Y  +L HMV DK++
Sbjct: 503  LSAMIFLGPTYYQRLKHMVDDKIH 526



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/217 (13%), Positives = 61/217 (28%), Gaps = 19/217 (8%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
           +  S    + I+   + +A   F     +    +    +  +   RR   +         
Sbjct: 14  EEWSTENFEEISPAVIPTATKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNP------- 66

Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
               +RD+                    +        + +     + P     D      
Sbjct: 67  EVGVVRDIRLRELRLYTDYGRCSRPLFVVKKQRLIIKKRDINELWQNPEDGWHDLITKGF 126

Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           + Y+   EEE   I+              +LV  R   E            +  P  ++ 
Sbjct: 127 IEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLILG 174

Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           + AS+IPF +++ S R      M +QA+ +       
Sbjct: 175 VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL 211


>gi|89142759|emb|CAJ57575.1| RNA polymerase subunit B [Microbacterium imperiale]
          Length = 361

 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 62/173 (35%), Positives = 91/173 (52%), Gaps = 13/173 (7%)

Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
           +MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G 
Sbjct: 1   FMGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGA 58

Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFP 248
           W++ E D +D + VRIDR+RK  VT FL ALG+ SE+I++ F  +  I  +   D     
Sbjct: 59  WLEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDIMAEFAGFDSIEETLAKDTILTK 118

Query: 249 LSAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 EDALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 129/258 (50%), Positives = 173/258 (67%), Gaps = 15/258 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR K
Sbjct: 104 DSIEETLAKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 163

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L LDTP +   +   DI+A IK LV L  G                   DDIDN G
Sbjct: 164 INQKLGLDTPIEESVLTVADIVATIKYLVRLHRGDATFDGVRDGKAVEIRLDTDDIDNFG 223

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE ++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 224 NRRIRAVGERIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 283

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 284 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 343

Query: 581 GLVSSLTSFARVNAYGFI 598
           GL+ SL SFAR+N +GFI
Sbjct: 344 GLIGSLASFARINPFGFI 361


>gi|269964271|ref|ZP_06178547.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269830993|gb|EEZ85176.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 224

 Score =  197 bits (500), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 117/237 (49%), Positives = 165/237 (69%), Gaps = 13/237 (5%)

Query: 811  MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSE 870
            M +AFMPW+GYNFEDS+L+SER+V ED FT+IHI+E   +ARDTKLG EEIT DIPNV E
Sbjct: 1    MRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGE 60

Query: 871  EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
              L  +DE GI+ +GAEV  GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLR
Sbjct: 61   SALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLR 120

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEIL 990
            VP+ VSGT++DV++F R G++K++R++ +E+ Q++   +D  +E  IL+  + +R+  +L
Sbjct: 121  VPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVRAVL 180

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
                              S   +    R +W +  ++D+ +Q  +E L  Q++ +KS
Sbjct: 181  IDGG-------------YSEAKLDTTDRKKWLELTLEDDALQSQLEQLAEQWDETKS 224


>gi|218193010|gb|EEC75437.1| hypothetical protein OsI_11967 [Oryza sativa Indica Group]
          Length = 1117

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 56/170 (32%), Positives = 84/170 (49%), Gaps = 16/170 (9%)

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              E I+  L       +G+ +LY G+ G P    V +G IY  KL HMV DK++AR++G 
Sbjct: 948  KVEDISRTLVKHGFSYNGKDLLYSGILGHPCQAYVFMGPIYYQKLKHMVLDKMHARASGP 1007

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTR 1327
              L+T+QP  G+S  GG RLGEME  C+ AYGA+ ++ E L I SD          G   
Sbjct: 1008 RVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFERLLISSDPYQVQVCRKCGLLG 1067

Query: 1328 VYESIVA---------GNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             Y   +          G +  +   P +  +L +E+QA+ +   L+ +  
Sbjct: 1068 YYNHKLKASYCSMCKNGENMAKMRMPYACKLLFQELQAMNVVPRLKLTEG 1117



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 47/286 (16%), Positives = 90/286 (31%), Gaps = 22/286 (7%)

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I  +E   +D          +I  ++  GL   D   ++ +        +    I   G 
Sbjct: 674  IALYEHEDQDDVQRSSITHIEIEPLTILGLFRADS--LLYLLVYAQRPLLTTKTIELVGY 731

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              +   +    A+      D+ D  +   S +           ++ + K +       ++
Sbjct: 732  DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIAMKKYTVTKEK-YEGGYSDR 790

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            I    RDKD   +  +            G    +      K T  ++   S    +    
Sbjct: 791  IVKPQRDKDGALLKQNMRALDEDGFAAPGLIIRNHDIYVNKQTPRNTKRDSGAHLTD--- 847

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                              Y+ S ++ +          +           ++K  +   R 
Sbjct: 848  ----------------RDYKDSPAVYKGVDGETTVVDRVMLCSDTDEKLIIKCIIRHTRR 891

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             + GDK + RHG KG+   I+  ED PF + G   D+++NP G PS
Sbjct: 892  PEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPS 937



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 83/647 (12%), Positives = 182/647 (28%), Gaps = 129/647 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML---EFVSYEFDPP- 84
           L++    S+++F+           +G++   K+   I        +   ++ S     P 
Sbjct: 111 LVKEHIDSFNYFIT----------KGIRNIVKANNRIE-ARNNPSIFLRQYNSVRVGVPS 159

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   K     C   D TY+ P+   +   V    E     +          +G LP
Sbjct: 160 VQVQYIAEKITPHFCRLTDRTYSAPVLADIEYTVGKQYELKRKPNFI--------IGYLP 211

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDHDKG 170
           +M                           G F++KG +++++ Q   S    I     KG
Sbjct: 212 IMLRSHACVLNGKDEAELARYGECPLDPGGYFIVKGTEKVILIQEQLSKNRIIIDTDSKG 271

Query: 171 RA----SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDS 225
           R     + S   + +  +I          F  K+ I++++++  + +P+   + A+GM+S
Sbjct: 272 RVIASVTSSTHEIKSKTVI----------FMEKEKIYLQLNQFTKPIPIIVVMKAMGMES 321

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           ++ ++    +        +      A + +   K +   +D                   
Sbjct: 322 DQEVAQMVGRDPRYGDLLYPSIQECAFERIYTLKQALQYMDDKV---------------- 365

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
                 G +  G +   L  ++VA   V             +     L  +  +      
Sbjct: 366 -MYPGAGNQKEGRSKSILRDVFVAHVPVESGN----FRPKCIYTAVMLRRMMDA------ 414

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           IL  D+ ++  Y+ N                  + +         + E +F  +  ++ +
Sbjct: 415 ILNADTFDDKDYVGN------------------KRLELSGQLISLLFEDLFKTMNSNAVE 456

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
               T  ++  +  L+L        I      AI         G   I           +
Sbjct: 457 LMNKTSEKIHSSP-LDLSLHIKENIITHGLERAI-------STGNWDIKRFRMHRKGVSQ 508

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            +  +        + R+    ++   +    ++ P    +      ++            
Sbjct: 509 VLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQCYSLGVEDLSLLSGEEIHASGSF 568

Query: 526 EEHVNSLSRITHTRRLS-ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
               N L    H +    A     + R+    E   +            +  G     + 
Sbjct: 569 LVMFNGLILGKHRQPQRFANAMRKLRRSGIIGEFVSIFVNEKQHCIHIASDGGRVCRPLI 628

Query: 585 SLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                    + +    +    R   D      + YL   EE N  IA
Sbjct: 629 IADKGIPRVKEHHMKQLRDGIRSFDDFLRDGLIEYLDVNEENNALIA 675


>gi|283132435|dbj|BAI63623.1| rpoB protein [Corynebacterium striatum]
          Length = 142

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/170 (36%), Positives = 90/170 (52%), Gaps = 36/170 (21%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+           +   L++  E++              
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWKVDV-----DDPANAELLKTLPEELYDVP---------- 44

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                        +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 45   ------------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   GEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 142


>gi|222625092|gb|EEE59224.1| hypothetical protein OsJ_11195 [Oryza sativa Japonica Group]
          Length = 1115

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 56/170 (32%), Positives = 84/170 (49%), Gaps = 16/170 (9%)

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
              E I+  L       +G+ +LY G+ G P    V +G IY  KL HMV DK++AR++G 
Sbjct: 946  KVEDISRTLVKHGFSYNGKDLLYSGILGHPCQAYVFMGPIYYQKLKHMVLDKMHARASGP 1005

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VGRTR 1327
              L+T+QP  G+S  GG RLGEME  C+ AYGA+ ++ E L I SD          G   
Sbjct: 1006 RVLLTRQPTEGRSRDGGLRLGEMERDCLIAYGASMLIFERLLISSDPYQVQVCRKCGLLG 1065

Query: 1328 VYESIVA---------GNDTFETGTPESFNVLVKEMQALGLSIDLENSRT 1368
             Y   +          G +  +   P +  +L +E+QA+ +   L+ +  
Sbjct: 1066 YYNHKLKASYCSMCKNGENMAKMRMPYACKLLFQELQAMNVVPRLKLTEG 1115



 Score =  119 bits (298), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 47/286 (16%), Positives = 90/286 (31%), Gaps = 22/286 (7%)

Query: 844  IEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
            I  +E   +D          +I  ++  GL   D   ++ +        +    I   G 
Sbjct: 672  IALYEHEDQDDVQRSSITHIEIEPLTILGLFRADS--LLYLLVYAQRPLLTTKTIELVGY 729

Query: 904  SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQ 963
              +   +    A+      D+ D  +   S +           ++ + K +       ++
Sbjct: 730  DKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIAMKKYTVTKEK-YEGGYSDR 788

Query: 964  IELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQ 1023
            I    RDKD   +  +            G    +      K T  ++   S    +    
Sbjct: 789  IVKPQRDKDGALLKQNMRALDEDGFAAPGLIIRNHDIYVNKQTPRNTKRDSGAHLTD--- 845

Query: 1024 FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRP 1083
                              Y+ S ++ +          +           ++K  +   R 
Sbjct: 846  ----------------RDYKDSPAVYKGVDGETTVVDRVMLCSDTDEKLIIKCIIRHTRR 889

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             + GDK + RHG KG+   I+  ED PF + G   D+++NP G PS
Sbjct: 890  PEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPS 935



 Score =  118 bits (296), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 83/647 (12%), Positives = 182/647 (28%), Gaps = 129/647 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML---EFVSYEFDPP- 84
           L++    S+++F+           +G++   K+   I        +   ++ S     P 
Sbjct: 109 LVKEHIDSFNYFIT----------KGIRNIVKANNRIE-ARNNPSIFLRQYNSVRVGVPS 157

Query: 85  --------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLP 136
                   K     C   D TY+ P+   +   V    E     +          +G LP
Sbjct: 158 VQVQYIAEKITPHFCRLTDRTYSAPVLADIEYTVGKQYELKRKPNFI--------IGYLP 209

Query: 137 LMT------------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDHDKG 170
           +M                           G F++KG +++++ Q   S    I     KG
Sbjct: 210 IMLRSHACVLNGKDEAELARYGECPLDPGGYFIVKGTEKVILIQEQLSKNRIIIDTDSKG 269

Query: 171 RA----SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDS 225
           R     + S   + +  +I          F  K+ I++++++  + +P+   + A+GM+S
Sbjct: 270 RVIASVTSSTHEIKSKTVI----------FMEKEKIYLQLNQFTKPIPIIVVMKAMGMES 319

Query: 226 EEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLL 285
           ++ ++    +        +      A + +   K +   +D                   
Sbjct: 320 DQEVAQMVGRDPRYGDLLYPSIQECAFERIYTQKQALQYMDDKV---------------- 363

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
                 G +  G +   L  ++VA   V             +     L  +  +      
Sbjct: 364 -MYPGAGNQKEGRSKSILRDVFVAHVPVESGN----FRPKCIYTAVMLRRMMDA------ 412

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           IL  D+ ++  Y+ N                  + +         + E +F  +  ++ +
Sbjct: 413 ILNADTFDDKDYVGN------------------KRLELSGQLISLLFEDLFKTMNSNAVE 454

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
               T  ++  +  L+L        I      AI         G   I           +
Sbjct: 455 LMNKTSEKIHSSP-LDLSLHIKENIITHGLERAI-------STGNWDIKRFRMHRKGVSQ 506

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQL 525
            +  +        + R+    ++   +    ++ P    +      ++            
Sbjct: 507 VLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQCYSLGVEDLSLLSGEEIHASGSF 566

Query: 526 EEHVNSLSRITHTRRLS-ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
               N L    H +    A     + R+    E   +            +  G     + 
Sbjct: 567 LVMFNGLILGKHRQPQRFANAMRKLRRSGIIGEFVSIFVNEKQHCIHIASDGGRVCRPLI 626

Query: 585 SLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                    + +    +    R   D      + YL   EE N  IA
Sbjct: 627 IADKGIPRVKEHHMKQLRDGIRSFDDFLRDGLIEYLDVNEENNALIA 673


>gi|282598428|gb|ADA83444.1| RNA polymerase beta subunit [Corynebacterium sp. NML97-0186]
          Length = 141

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 64/169 (37%), Positives = 88/169 (52%), Gaps = 36/169 (21%)

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ ETHLGW     G  +    +D K    +  L   L  V                  
Sbjct: 1    GQVLETHLGWLAAA-GWHVD--PDDPKNEELLKTLPEDLYDV------------------ 39

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPF 1245
                    +G   +TPVFDGA    I  +L+ +  +  G        ++ L+DG +GEPF
Sbjct: 40   -------PAGSLTATPVFDGASNTEIAGLLQNSLPNRDGDVMVDGDGKTRLFDGRSGEPF 92

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
              PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   QYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 141


>gi|89142765|emb|CAJ57578.1| RNA polymerase subunit B [Microbacterium kitamiense]
          Length = 359

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/171 (36%), Positives = 89/171 (52%), Gaps = 13/171 (7%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G W+
Sbjct: 1   GDFPLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARIIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VRIDR+RK  VT FL ALG+ S++IL+ F  +  I  +   D       
Sbjct: 59  EFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSDDILAEFAGFDSIEETLSKDTILSKED 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
           A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 ALRDI--------YRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 161



 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 129/258 (50%), Positives = 173/258 (67%), Gaps = 15/258 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR K
Sbjct: 102 DSIEETLSKDTILSKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 161

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L L  P     +  EDI+A IK LV L  G                  +DDIDN G
Sbjct: 162 INQKLGLTGPLSDSVLTVEDIVATIKYLVRLHRGDTTFDGTRAGKPAEIRLDVDDIDNFG 221

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 222 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 281

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 282 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 341

Query: 581 GLVSSLTSFARVNAYGFI 598
           GL+ SL SFAR+N +GFI
Sbjct: 342 GLIGSLASFARINPFGFI 359


>gi|67942356|gb|AAY83378.1| DNA-dependent RNA polymerase II [Strobiloscypha keliae]
          Length = 571

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 103/695 (14%), Positives = 201/695 (28%), Gaps = 139/695 (20%)

Query: 569  ICPAETSEGHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            +CPAET EG   GLV +L   + ++    G     +    + ++  +     +      +
Sbjct: 5    VCPAETPEGQACGLVKNLALMSYISIGTPGQPIAEFLAQRNMEMLEEYEPQRSPNATKIF 64

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LE 683
            +      +  D     + +        I      I D  D   K          P   ++
Sbjct: 65   VNGTWVGVHRDPLQLTKALQEVRRKAIIAHEVSVIRDIRDREFKIFTDAGRVCRPLFVID 124

Query: 684  NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
            N+ ++       +++  V  L+ ++    +  E              R G VE VDA   
Sbjct: 125  NNPASERRGQLVLRKDHVERLEQDSQLPES--ERFG------WKGLLREGAVEYVDAEEE 176

Query: 744  ---VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
               +I     DL+ +      Y + +    N+      +P                 PS 
Sbjct: 177  ETIMIVMTPEDLELARQVAQGYEVEEETDPNKRVKAPIKPNTHQY------THCEIHPSM 230

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   + +  F             
Sbjct: 231  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFSERM--------- 272

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                                +  +             +       +   +  +  I    
Sbjct: 273  ------------------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYS 314

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    +F R  +D+ +R   +  + +E   +      + L  
Sbjct: 315  GYNQEDSVIMNQSSIDRGLF-RSLFYRSYMDQEKR---IGMQVVEEFEKPLRTNTLKLKH 370

Query: 981  NIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
              Y +L E   +  G           K+  ++ D      R ++         ++     
Sbjct: 371  GTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDADEMGQRQKYHTKRDVSTPLRSTENG 430

Query: 1038 LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
            +  Q                             L+ VKV +   +  Q GDK A RHG K
Sbjct: 431  IVDQVML--------------------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQK 470

Query: 1098 GIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G +      EDMPF  +G   D+++NP  +PSRM +  + E  L       G +      
Sbjct: 471  GTIGITYRSEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---- 526

Query: 1158 DYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEE 1217
                                                             +TP F     +
Sbjct: 527  -------------------------------------------------ATP-FTDVTVD 536

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
            +++++LR       G  ++Y+G TG+     V +G
Sbjct: 537  SVSTLLRQEGYQSRGFEVMYNGYTGKKMVAQVFLG 571



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 69/526 (13%), Positives = 142/526 (26%), Gaps = 100/526 (19%)

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           L  G    +  +      V+++  M           +   + +R   + ++   PQ   N
Sbjct: 1   LGFGVCPAETPEGQACGLVKNLALMSYISIGTPGQPIAEFLAQRNMEM-LEEYEPQRSPN 59

Query: 506 AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEM------ 558
           A  +      F   + +    + +     +   RR + +  +  V R     E       
Sbjct: 60  ATKI------FVNGTWVGVHRDPLQLTKALQEVRRKAIIAHEVSVIRDIRDREFKIFTDA 113

Query: 559 -RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
            R   P       PA    G  +     +    + +     E+             V Y+
Sbjct: 114 GRVCRPLFVIDNNPASERRGQLVLRKDHVERLEQDSQ--LPESERFGWKGLLREGAVEYV 171

Query: 618 SAMEEENRYIAQANSSLD------EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
            A EEE   I      L+      +     EE    +     I     +    +  P  +
Sbjct: 172 DAEEEETIMIVMTPEDLELARQVAQGYEVEEETDPNKRVKAPIKPNTHQYTHCEIHPSMI 231

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           + I AS+IPF +++ S R      M +QA+ +                            
Sbjct: 232 LGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFS---------------------- 269

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
                              +   + + +  Y       +     +  R            
Sbjct: 270 -------------------ERMDTMANILYYPQKPLATTRSMEYLKFR------------ 298

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
             +  G +  +G +          +  +  + +  +  S           +    +    
Sbjct: 299 -ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRS-----------LFYRSYMDQE 346

Query: 852 RDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
           +   +   E        +   +       +DE G++  G  V+  DI++GK  P      
Sbjct: 347 KRIGMQVVEEFEKPLRTNTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDAD 406

Query: 907 TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              ++       +K    RD S  + S  +G V  V +       K
Sbjct: 407 EMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 445


>gi|51103941|gb|AAT96676.1| RpoB [Corynebacterium sp. 31595]
          Length = 142

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 65/174 (37%), Positives = 85/174 (48%), Gaps = 40/174 (22%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G  I+   +  K   D                         
Sbjct: 1    RMNIGQVLEVHLGWLAKS-GWAIEGDPDWAKRIPDD------------------------ 35

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                     +      ++TPVFDGA  E I  +L     D  G        ++ L+DG +
Sbjct: 36   -------LREVPPNSLLATPVFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRS 88

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            GEPF  PV VG  YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 89   GEPFKYPVCVGEKYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 142


>gi|194320251|gb|ACF48363.1| DNA-dependent RNA polymerase II second largest subunit [Umbilicaria
            aprina]
 gi|194320256|gb|ACF48366.1| DNA-dependent RNA polymerase II second largest subunit [Umbilicaria
            rigida]
          Length = 317

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/385 (17%), Positives = 119/385 (30%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 127  SGEDIIIGKTAPIAPD---------------AEELGQRTKSHVKRDVSTPLRSTENGIVD 171

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 172  QVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRCYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKSHVKRDVSTPLRSTENGIVDQVL 174


>gi|194320254|gb|ACF48365.1| DNA-dependent RNA polymerase II second largest subunit [Umbilicaria
            arctica]
          Length = 317

 Score =  196 bits (499), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/385 (17%), Positives = 118/385 (30%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                 E  QR    +K    T     E+   +
Sbjct: 127  SGEDIIIGKTAPIAPD---------------AGELGQRTKSHVKRDVSTPLRSTENGIVD 171

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 172  QVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 293  MYNGHTGRKLVAQVFLGPTYYQRLR 317



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRCYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P          +L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----GELGQRTKSHVKRDVSTPLRSTENGIVDQVL 174


>gi|198446953|emb|CAP08295.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
 gi|206720919|emb|CAP08297.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
 gi|206720921|emb|CAP08298.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
 gi|206720923|emb|CAP08299.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
 gi|206720925|emb|CAP08300.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
          Length = 179

 Score =  196 bits (498), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 111/179 (62%), Positives = 139/179 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV  GKVT+ V YLSA++E    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYARLNEYGFLETPYRKVARGKVTDTVEYLSAIDEGRYVIAQANATVAEDGA 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            T+ELV  R  GE  +V  E++ ++D +P Q+VS+AASLIPFLE+DD+NR LMG NMQR
Sbjct: 121 LTDELVSVREMGETRMVAPEQVQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQR 179


>gi|88769946|gb|ABD51462.1| F2R [Squirrel poxvirus]
          Length = 1165

 Score =  196 bits (498), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/431 (18%), Positives = 142/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 705  DNGIHLVYPERPIVISKALETSKIAVNCFGHHVMIALMSYRGINQEDGIIIKRQFVERGG 764

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 765  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVRLNAFLESG 811

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y++    ++    +K++          
Sbjct: 812  DAIARNISSRTLEDDFVVDNQISFDISERYTDMYKSRVERVQVDLTDKVK---------- 861

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    +MP+ +DGT  D+++N   + 
Sbjct: 862  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADESEMPYTEDGTRPDVIINSTSIF 916

Query: 1129 SRMNVGQIFETHL--GWACVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L   +A      + ++            +     F  K  G       
Sbjct: 917  SRKTLSMLVEVILTSAYAAKPYNNQGENRPVCFPSSNETGLDVYLDFARKCHGHEHPE-- 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                         A EE I             +  L+D  T EP
Sbjct: 975  -----------------------------ASEEEIED-------RVYCERTLFDPETDEP 998

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            ++  V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG + GEME  CI A
Sbjct: 999  YEAKVFFGPLYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCIIA 1058

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1059 HGAANTITEIL 1069



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 91/683 (13%), Positives = 202/683 (29%), Gaps = 53/683 (7%)

Query: 317 TGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLD 376
           +G +   A   I    +  I +        +     N+  Y              D+   
Sbjct: 210 SGCVISSAKTFITVNVVLLIQYLANLSFDFI----RNSLTYDMPAEAAYLVNAIVDSAPA 265

Query: 377 IYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDI 436
            Y      D  T+S    +                    +         D    ++   +
Sbjct: 266 AYAKQNDNDADTYSYVHELIEAEHAKQRSTMTLDEFHYDLMHNFLPHMQDSPNQLKGLYL 325

Query: 437 IAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDID 496
           +++++  +          D D++   RV + G   +      L     +I+  I +   +
Sbjct: 326 LSLLRKFIFCIFHTSRYPDRDSMACHRVLTYGSYFETLANDELENYISNIRTDIMNNHKN 385

Query: 497 SVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------ 550
                 +             F      + ++   S     H   +  +            
Sbjct: 386 RGTC-AVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRSVGYYPDQ 444

Query: 551 -RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSF-----ARVNAYGFIETPYR 603
            +      +R  HP+ Y   CP++  E G  +GLVS L+        RV  Y  +     
Sbjct: 445 VKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLSVLTAITNIRVTDYVELNRRIC 504

Query: 604 KVCDGKVTNDVVYLS---AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           +       +D+ Y     A+  EN  IA  N ++ ++                + V    
Sbjct: 505 EYVRSYPRDDISYFETGFAVTVENALIASLNPAIVDEFVRDFRRRKRVGFFGNLEVGITL 564

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSN------RVLMGCNMQRQAVPLLKAEAPFVGTG 714
           +       +  +     + PFL  +D           +  ++       ++ E P V   
Sbjct: 565 VRDHMNEVRINIGGGRLIRPFLVVEDGELVMDVVNADLEASIDSMTFSDIQREFPHVMEM 624

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-----EGDLDPSTSGVDIYR------ 763
           ++      S     A+R   +   +  R  +        +G +  S  G++         
Sbjct: 625 VDVEQFTFSNVCESARRFRTLPPEERRRYDLCDFPTEFRDGYVASSLVGINHNSGPRAIL 684

Query: 764 -LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPSTDLGDL---ALGRNMLVAFMPW 818
              + +++      + R  +  G   V     I    + +   +     G ++++A M +
Sbjct: 685 GCAQAKQAISCLSSDIRNKIDNGIHLVYPERPIVISKALETSKIAVNCFGHHVMIALMSY 744

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            G N ED ++I  + V       I  ++ +V        P E   +   V       +D 
Sbjct: 745 RGINQEDGIIIKRQFVERGGLDIITAKKHQVEI------PLENFNNKERVKSTAYSKLDS 798

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            G++ + A +  GD +   I+ +        +  +     E+  D+  + +         
Sbjct: 799 NGLVRLNAFLESGDAIARNISSRTLEDDFVVDNQISFDISERYTDMYKSRVER----VQV 854

Query: 939 VVDVRIFNRHGIDKNERSISVER 961
            +  ++  R    K  R +  ++
Sbjct: 855 DLTDKVKVRVLTMKERRPVLGDK 877


>gi|83414421|dbj|BAE54001.1| RNA polymerase beta subunit [Streptococcus pseudopneumoniae]
 gi|193873286|gb|ACF23333.1| RpoB [Streptococcus pseudopneumoniae]
          Length = 172

 Score =  196 bits (498), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERFLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+ L AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERFLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWSTVKEAG 172


>gi|308194111|gb|ADO16473.1| RNA polymerase beta subunit [Gemella haemolysans]
          Length = 216

 Score =  196 bits (498), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 74/199 (37%), Positives = 98/199 (49%), Gaps = 54/199 (27%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 72   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 131

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 132  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDVWSTVAEAGMA 191

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 192  KDAK----------------------------TVLYDG---------------------- 201

Query: 1236 LYDGLTGEPFDRPVTVGYI 1254
                 TGEPFD  V+VG +
Sbjct: 202  ----RTGEPFDSRVSVGVM 216



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 50/78 (64%), Positives = 58/78 (74%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRV
Sbjct: 1   ALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRV 60

Query: 932 PSGVSGTVVDVRIFNRHG 949
           P G  G V DV+IF R  
Sbjct: 61  PHGADGVVADVKIFKRED 78


>gi|89888205|gb|ABD78646.1| DNA-directed RNA polymerase beta subunit [Achromobacter
           xylosoxidans]
          Length = 281

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 104/281 (37%), Positives = 163/281 (58%), Gaps = 3/281 (1%)

Query: 223 MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
           M  E IL+ F+    +  + +       A     G      + D  +G+ ++E  K++ +
Sbjct: 1   MTPESILANFFDFDNFELKSEGAMMEFVAE-RWKGEMARFDISD-RSGKVIVEKDKRINA 58

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIR 342
             L+ L   G++ + +  D L G  +A++IV+ +TGE+   A D I E  L  +  + + 
Sbjct: 59  KHLRDLAAGGIQRISVPEDFLYGRVLAKNIVDPDTGEVIANANDEITESVLGALRAASVH 118

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
           DI  LY + ++   YI  TL TD+  D+  A + IYR+MRPG+  T    E++F  LF+ 
Sbjct: 119 DIQTLYTNDLDRGPYISQTLRTDETADQMAARVAIYRMMRPGEPPTEEAVEALFQRLFYS 178

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPD-DVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
            + YDLS VGR+K+N RL           +  EDI+  IK+LV+LRNG+G IDDID+LGN
Sbjct: 179 EETYDLSRVGRMKVNSRLGRGEDTSGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGN 238

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           RRVR VGE+ +NQ+R GL+R+ER++KER+   + +++MP D
Sbjct: 239 RRVRCVGELAENQFRAGLVRVERAVKERLGQAETENLMPHD 279


>gi|89145187|emb|CAJ57566.1| RNA polymerase subunit B [Microbacterium arborescens]
          Length = 360

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 63/172 (36%), Positives = 90/172 (52%), Gaps = 13/172 (7%)

Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
           MGD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W
Sbjct: 1   MGDFPLQTGKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAW 58

Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPL 249
           ++ E D +D + VRIDR+RK  VT FL ALG+ SE+I++ F  Y  I  +   D      
Sbjct: 59  LEFEIDKRDQVGVRIDRKRKQSVTVFLKALGLTSEDIMAEFAGYDSIEETLAKDTILTKE 118

Query: 250 SAADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 DALRDI--------YRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRYK 162



 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 129/259 (49%), Positives = 174/259 (67%), Gaps = 15/259 (5%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F++ +YDL+ VGR 
Sbjct: 102 YDSIEETLAKDTILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNAKRYDLAKVGRY 161

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L LDTP +   +   DI+A IK LV L  G                   DDIDN 
Sbjct: 162 KINQKLGLDTPIEESVLTVADIVATIKYLVRLHRGDATFEGVRDGKPAEIRLDTDDIDNF 221

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 222 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 281

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 282 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 341

Query: 580 IGLVSSLTSFARVNAYGFI 598
           IGL+ SL SFAR+N +GFI
Sbjct: 342 IGLIGSLASFARINPFGFI 360


>gi|206720917|emb|CAP08296.1| RNA polymerase beta subunit [Candidatus Glomeribacter gigasporarum]
          Length = 179

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 110/179 (61%), Positives = 138/179 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR+N YGF+ETPYRKV  GKVT+ V YLSA++E    IAQAN+++ EDG+
Sbjct: 61  IGLINSLALYARINEYGFLETPYRKVVHGKVTDTVEYLSAIDEGRYVIAQANAAVAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            T+ELV  R  GE  +V  E++ ++D +P Q+VS+AASLIP LE+DD+NR LMG NMQR
Sbjct: 121 LTDELVSVREMGETRMVAPEQVQYMDVAPSQIVSVAASLIPLLEHDDANRALMGSNMQR 179


>gi|315936249|gb|ADU55798.1| RNA polymerase beta subunit [Bartonella henselae]
          Length = 195

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 136/194 (70%), Positives = 165/194 (85%)

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
           G+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ D
Sbjct: 2   GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIID 61

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           GKVT +V+YLSAMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D S
Sbjct: 62  GKVTTEVIYLSAMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMDVS 121

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGAA+
Sbjct: 122 PKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGAAV 181

Query: 728 VAKRAGIVEQVDAI 741
            A+R+GIV+QVDA 
Sbjct: 182 AARRSGIVDQVDAT 195


>gi|83414565|dbj|BAE54073.1| RNA polymerase beta subunit [Streptococcus sanguinis]
          Length = 172

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 38.5 bits (88), Expect = 7.7,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 28/85 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +  A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVLEAG 172


>gi|83414427|dbj|BAE54004.1| RNA polymerase beta subunit [Streptococcus cristatus]
 gi|83414595|dbj|BAE54088.1| RNA polymerase beta subunit [Streptococcus cristatus]
 gi|83414597|dbj|BAE54089.1| RNA polymerase beta subunit [Streptococcus cristatus]
          Length = 172

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.3 bits (90), Expect = 5.6,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S +R A 
Sbjct: 148  GIHIATPVFDGASSEDLWSTVREAG 172


>gi|312204366|gb|ADQ47500.1| RNA polymerase II second largest subunit [Schizoxylon albescens]
          Length = 728

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 62/379 (16%), Positives = 115/379 (30%), Gaps = 81/379 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 428  ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 486

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +++ +R        +E   +    + + L    Y +L +   +  G        
Sbjct: 487  LFYRAYVEQEKRVGM---SLVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRVSGEDI 543

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  D      R++          ++     +                  ++K+
Sbjct: 544  IIGKTAPIPPDSEEMGQRTKLHTKRDSSTPLRSTESGI------------------VDKV 585

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV     +  Q GDK+A RHG KG +      EDMPF  +G   DI
Sbjct: 586  LL--TTNAEGLKFVKVRTRTTKIPQIGDKIASRHGQKGTIGITYRMEDMPFSAEGVTPDI 643

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 644  IINPHAIPSRMTIAHLVECQLSKVSSLRGFEGD--------------------------- 676

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++I+ +LR       G  ++Y+G 
Sbjct: 677  --------------------------ATP-FTEVTVDSISRLLREHGYQSRGFEVMYNGH 709

Query: 1241 TGEPFDRPVTVGYIYMLKL 1259
            TG      V +G  Y  +L
Sbjct: 710  TGRKLTTXVFLGPTYYQRL 728



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/183 (22%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 430 YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 479

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +       +D+ GI+  G  V+
Sbjct: 480 DRGLFRSLFYRAYVEQEKRVGMSLVEQFEKPMRSDTLRLKHGTYDKLDDDGIVAPGVRVS 539

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P    P   EE   R     K    RD+S  + S  SG V  V +     
Sbjct: 540 GEDIIIGKTAPI---PPDSEEMGQRT----KLHTKRDSSTPLRSTESGIVDKVLLTTNAE 592

Query: 950 IDK 952
             K
Sbjct: 593 GLK 595



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 84/261 (32%), Gaps = 24/261 (9%)

Query: 470 MLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
           ++ + +R    ++ + + +  +              + +  + + +     +        
Sbjct: 1   LMASLFRGLFNKLNKDVFKYLQKCIESGKEFNLALGVKSNTMTNGLKYSLATGNWGDQKK 60

Query: 522 -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                  +SQ+       S ++H RR +      + R     + R +H +H+G +CPAET
Sbjct: 61  AMQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCSHWGLVCPAET 116

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            EG   GLV +L+    +      E    +    + +V  +     +      ++     
Sbjct: 117 PEGQACGLVKNLSLMCYITVGSPSEPIIDFMVQRNMEVLEEYDQTRSPNATKVFVNGVWV 176

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +  D +     V        I      I D  D   K          P L  DD  +  
Sbjct: 177 GVHRDPAHLVNTVKLLRRKNLISYEVSLIRDIRDREFKIFTDAGRVCRPLLVIDDDPKSP 236

Query: 692 MGCNMQ--RQAVPLLKAEAPF 710
              N+   ++ V  L+ +   
Sbjct: 237 NMGNLVLTKEIVNKLEDDRDL 257


>gi|56694322|gb|AAW22901.1| RNA polymerase II second largest subunit [Stangeria eriopus]
          Length = 538

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 80/490 (16%), Positives = 139/490 (28%), Gaps = 85/490 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S     +A   N   +              I   ++    
Sbjct: 132  LVNQGFIEYVDTEEEETTMISM---TIADLVNARNSPPTASSIVKYTHCEIHXSLILGVC 188

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 189  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 245

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        +F R   D+ +R  +
Sbjct: 246  EHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFYRSYRDEEKRMGT 304

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+     R+          +          G           K+T ++         
Sbjct: 305  LIKEEFGRPNRENTIGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQ-------- 356

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                     DE   +     K    TS    E    +++      D +     R VKV +
Sbjct: 357  ---------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRM 402

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 403  RSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIE 462

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+  +         +IS         +                      
Sbjct: 463  CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM---------------- 506

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                                            +G +    G         + +G  Y  +
Sbjct: 507  -------------------------------YNGHT----GR---RLSAMIFLGPTYYQR 528

Query: 1259 LNHMVSDKVY 1268
            L HMV DK++
Sbjct: 529  LKHMVDDKIH 538



 Score =  109 bits (273), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 67/458 (14%), Positives = 127/458 (27%), Gaps = 98/458 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +  + GV R 
Sbjct: 12  EEWSTENFEEISPAVIPNSTKIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRD 71

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGH----NIGLVSSLTSFARVNAYGFIETPY--RKVC 606
               E+R ++  +     P    E          +  L    ++      E     R   
Sbjct: 72  IRLSELR-LYTDYGRCSRPLFIVENQRLLIKKPDIIRLQQRDQLPPPDPEEEXPPARGWP 130

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDA 666
                  + Y+   EEE   I+   + L                         K    + 
Sbjct: 131 ALVNQGFIEYVDTEEEETTMISMTIADL-----------VNARNSPPTASSIVKYTHCEI 179

Query: 667 SPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA 726
               ++ + AS+IPF +++ S R      M +QA+ +                       
Sbjct: 180 HXSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL---------------- 223

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGD 786
               R   +  V                                       Q+PLV    
Sbjct: 224 ----RMDTLAYV-----------------------------------LYYPQKPLV---- 240

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                             L  G N +VA   + GYN EDS+++++  +    F S+    
Sbjct: 241 ------TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFYRS 294

Query: 847 FEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +      +E        +   +       +D+ G+   G  V+  D+++GK TP 
Sbjct: 295 YRDEEKRMGTLIKEEFGRPNRENTIGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPV 354

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            +           +         RD S  +    SG V
Sbjct: 355 TQDE---------SGGQAARYTKRDQSTSLRHSESGMV 383


>gi|194320165|gb|ACF48308.1| DNA-dependent RNA polymerase II second largest subunit [Lecanora
            contractula]
          Length = 317

 Score =  196 bits (497), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 61/377 (16%), Positives = 114/377 (30%), Gaps = 83/377 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR----- 947
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 15   NILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIMNQSSIDRGLFRG 74

Query: 948  -HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +++   +    +E   +    E + L    Y +L +   +  G           
Sbjct: 75   LFYRAYSDQEKQIGHSILEQFEKPMRSETLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIG 134

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D                +E  QR     K    T     E+   +++      
Sbjct: 135  KTAPITAD---------------AEELGQRTKAHTKRDISTPLRSTENGIVDQVLMSTNA 179

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +     R  KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 180  DGL-----RFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIIN 234

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 235  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 264

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  ++Y+G TG 
Sbjct: 265  -----------------------ATP-FTEVTVDSVSRLLRENGYHSRGFEVMYNGHTGR 300

Query: 1244 PFDRPVTVGYIYMLKLN 1260
                 V +   Y  +L 
Sbjct: 301  KLVAQVFLXPTYYQRLR 317



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 67/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F  +    +    +       E     +  +   +       +D+ G++  G  
Sbjct: 66  SIDRGLFRGLFYRAYSDQEKQIGHSILEQFEKPMRSETLKLKHGTYDKLDDDGLVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V +  
Sbjct: 126 VSGEDIIIGKTAPITADAEELGQRT-------KAHTKRDISTPLRSTENGIVDQVLMST 177


>gi|83414513|dbj|BAE54047.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|193873144|gb|ACF23262.1| RpoB [Streptococcus oralis]
 gi|193873150|gb|ACF23265.1| RpoB [Streptococcus oralis]
          Length = 172

 Score =  196 bits (497), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 64/110 (58%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I   + D  ++ D+
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIAPPVFDGASSEDL 164



 Score = 48.1 bits (113), Expect = 0.011,   Method: Composition-based stats.
 Identities = 34/63 (53%), Positives = 42/63 (66%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             G+ILV K+TPKGE  ++ E+ LL A  G+K+  VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGNILVSKVTPKGEIDLSTEDTLLLATLGDKSRQVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|246880791|gb|ACS95103.1| beta subunit of RNA polymerase fragment 1 [Dunaliella salina]
          Length = 916

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 88/472 (18%), Positives = 159/472 (33%), Gaps = 63/472 (13%)

Query: 28  DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPK 85
           D + VQ+ S+   L           +GL   F    PIT         F    Y    P+
Sbjct: 10  DFVTVQRQSFFELL----------EKGLIEEFAKRNPITNGRKDYSFFFYPEYYILTRPE 59

Query: 86  FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFV 145
           +   + + ++ +Y   L + +++           K  K I  + +Y+G++PLMTK G F+
Sbjct: 60  YKPHEAILKNKSYTSKLFVPVQIT---------NKKHKQIVLKWVYIGNIPLMTKRGHFI 110

Query: 146 IKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK-----------------------LLYAC 182
           + G  R++V+Q+ RSPGI++           K                         + C
Sbjct: 111 LNGAARVIVNQILRSPGIYYQQKIYENYEDNKGSKSNAQDDETGEGSSLQPVNTYKRFYC 170

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYP--KIVYSQ 240
            +I  +G W+ IE D +  I  ++ +  K+P+  FL+A+G+  + IL +     K++ + 
Sbjct: 171 DLICMRGSWLRIEMDKEKNIWAQMKKGPKIPIYWFLLAMGLSEKVILKSIMDPQKVLGNL 230

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
             +     LS  +        S++   +T +   E  K L            +K   I +
Sbjct: 231 ERNKAVPKLSKKNKKDLTTARSAMQADETLKSTGEDKKNL-----------EIKQDLIVA 279

Query: 301 DCLCGLYVAED-----IVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           D L       D         ET E    A          E   + +  I  +   S  +N
Sbjct: 280 DSLNESNSQTDKTTKLFWPEETREGTKGALTGFPHDLKNEGEENSLNKINEVNFVSEFSN 339

Query: 356 AYIRNTLV-TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             ++N  +  D  K  K       +      +     A      L     K    +  + 
Sbjct: 340 KSVKNDFIEEDNEKAIKTNASTSSKKQNYPYLKNTPEAWQAIYTLLHSKTKISNVSKTKD 399

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
           K + +      D  R   + D           ++        D     R+  
Sbjct: 400 KSDQKDTKGVSDIARSAIRADETLKSARTDKNQDSIIKETFGDTKFPGRLGL 451



 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 116/261 (44%), Positives = 168/261 (64%), Gaps = 2/261 (0%)

Query: 487 KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQ 546
            ++  S  +  +    +IN K   SA+ EFF +S LSQ  + +N L+ +TH RRLS++G 
Sbjct: 654 SKKDISQQLKGLTSSSIINNKAFNSAIREFFGTSPLSQFMDQINPLAELTHKRRLSSMGP 713

Query: 547 GGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
           GGV R  A + +R +HPTHYGRICP ET EG N GLV+S+T++ARVN+ G +E+P+ KV 
Sbjct: 714 GGVTRDTATLAIRGIHPTHYGRICPIETPEGKNTGLVNSMTTYARVNSSGILESPFYKVY 773

Query: 607 DGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
            G+V  +  + YL+A +EE   +A A+  +   G   + ++  R A     + R  + +I
Sbjct: 774 KGQVQKNTGMYYLNAEQEEKIKLAAADLYVSPIGFLPKAMIPARIAETFTKISRSSVQYI 833

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
             SP Q++SIAASLIPFLE+DD+NR LMG NMQRQAVPL++ E P VGTG+E      SG
Sbjct: 834 GVSPLQMISIAASLIPFLEHDDANRALMGSNMQRQAVPLIRHERPIVGTGLEGRAVSDSG 893

Query: 725 AAIVAKRAGIVEQVDAIRIVI 745
             I ++ +G+V  V A +I++
Sbjct: 894 HVIQSRYSGLVTYVSAKKIIV 914


>gi|83414417|dbj|BAE53999.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414439|dbj|BAE54010.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414441|dbj|BAE54011.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414443|dbj|BAE54012.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414445|dbj|BAE54013.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414447|dbj|BAE54014.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414449|dbj|BAE54015.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414451|dbj|BAE54016.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414453|dbj|BAE54017.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414455|dbj|BAE54018.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414457|dbj|BAE54019.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414459|dbj|BAE54020.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414461|dbj|BAE54021.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414463|dbj|BAE54022.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414465|dbj|BAE54023.1| RNA polymerase beta subunit [Streptococcus mitis]
 gi|83414467|dbj|BAE54024.1| RNA polymerase beta subunit [Streptococcus pseudopneumoniae]
 gi|83414515|dbj|BAE54048.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414517|dbj|BAE54049.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414519|dbj|BAE54050.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414523|dbj|BAE54052.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414527|dbj|BAE54054.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414529|dbj|BAE54055.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414531|dbj|BAE54056.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414535|dbj|BAE54058.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414543|dbj|BAE54062.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|193873090|gb|ACF23235.1| RpoB [Streptococcus mitis]
 gi|193873094|gb|ACF23237.1| RpoB [Streptococcus mitis]
 gi|193873096|gb|ACF23238.1| RpoB [Streptococcus mitis]
 gi|193873098|gb|ACF23239.1| RpoB [Streptococcus mitis]
 gi|193873100|gb|ACF23240.1| RpoB [Streptococcus mitis]
 gi|193873102|gb|ACF23241.1| RpoB [Streptococcus mitis]
 gi|193873104|gb|ACF23242.1| RpoB [Streptococcus mitis]
 gi|193873106|gb|ACF23243.1| RpoB [Streptococcus mitis]
 gi|193873108|gb|ACF23244.1| RpoB [Streptococcus mitis]
 gi|193873110|gb|ACF23245.1| RpoB [Streptococcus infantis]
 gi|193873114|gb|ACF23247.1| RpoB [Streptococcus mitis]
 gi|193873118|gb|ACF23249.1| RpoB [Streptococcus infantis]
 gi|193873120|gb|ACF23250.1| RpoB [Streptococcus mitis]
 gi|193873124|gb|ACF23252.1| RpoB [Streptococcus mitis]
 gi|193873126|gb|ACF23253.1| RpoB [Streptococcus mitis]
 gi|193873128|gb|ACF23254.1| RpoB [Streptococcus mitis]
 gi|193873132|gb|ACF23256.1| RpoB [Streptococcus mitis]
 gi|193873136|gb|ACF23258.1| RpoB [Streptococcus mitis]
 gi|193873140|gb|ACF23260.1| RpoB [Streptococcus infantis]
 gi|193873142|gb|ACF23261.1| RpoB [Streptococcus oralis]
 gi|193873166|gb|ACF23273.1| RpoB [Streptococcus oralis]
 gi|193873176|gb|ACF23278.1| RpoB [Streptococcus oralis]
 gi|193873188|gb|ACF23284.1| RpoB [Streptococcus pneumoniae]
 gi|193873206|gb|ACF23293.1| RpoB [Streptococcus sp. SK597]
 gi|193873208|gb|ACF23294.1| RpoB [Streptococcus mitis]
 gi|193873210|gb|ACF23295.1| RpoB [Streptococcus mitis]
 gi|193873212|gb|ACF23296.1| RpoB [Streptococcus mitis]
 gi|193873214|gb|ACF23297.1| RpoB [Streptococcus mitis]
 gi|193873216|gb|ACF23298.1| RpoB [Streptococcus mitis]
 gi|193873218|gb|ACF23299.1| RpoB [Streptococcus mitis]
 gi|193873220|gb|ACF23300.1| RpoB [Streptococcus mitis]
 gi|193873222|gb|ACF23301.1| RpoB [Streptococcus mitis]
 gi|193873224|gb|ACF23302.1| RpoB [Streptococcus mitis]
 gi|193873226|gb|ACF23303.1| RpoB [Streptococcus mitis]
 gi|193873228|gb|ACF23304.1| RpoB [Streptococcus mitis]
 gi|193873230|gb|ACF23305.1| RpoB [Streptococcus mitis]
 gi|193873232|gb|ACF23306.1| RpoB [Streptococcus mitis]
 gi|193873234|gb|ACF23307.1| RpoB [Streptococcus mitis]
 gi|193873236|gb|ACF23308.1| RpoB [Streptococcus mitis]
 gi|193873238|gb|ACF23309.1| RpoB [Streptococcus mitis]
 gi|193873240|gb|ACF23310.1| RpoB [Streptococcus mitis]
 gi|193873244|gb|ACF23312.1| RpoB [Streptococcus mitis]
 gi|193873246|gb|ACF23313.1| RpoB [Streptococcus infantis]
 gi|193873248|gb|ACF23314.1| RpoB [Streptococcus mitis]
 gi|193873250|gb|ACF23315.1| RpoB [Streptococcus mitis]
 gi|193873252|gb|ACF23316.1| RpoB [Streptococcus mitis]
 gi|193873254|gb|ACF23317.1| RpoB [Streptococcus infantis]
 gi|193873256|gb|ACF23318.1| RpoB [Streptococcus infantis]
 gi|193873258|gb|ACF23319.1| RpoB [Streptococcus mitis]
 gi|193873260|gb|ACF23320.1| RpoB [Streptococcus mitis]
 gi|193873262|gb|ACF23321.1| RpoB [Streptococcus mitis]
 gi|193873264|gb|ACF23322.1| RpoB [Streptococcus mitis]
 gi|193873266|gb|ACF23323.1| RpoB [Streptococcus pseudopneumoniae]
 gi|193873270|gb|ACF23325.1| RpoB [Streptococcus infantis]
 gi|193873272|gb|ACF23326.1| RpoB [Streptococcus infantis]
 gi|193873274|gb|ACF23327.1| RpoB [Streptococcus mitis]
 gi|193873284|gb|ACF23332.1| RpoB [Streptococcus pseudopneumoniae ATCC BAA-960]
 gi|193873288|gb|ACF23334.1| RpoB [Streptococcus infantis]
 gi|193873290|gb|ACF23335.1| RpoB [Streptococcus infantis]
 gi|193873294|gb|ACF23337.1| RpoB [Streptococcus oralis]
 gi|193873298|gb|ACF23339.1| RpoB [Streptococcus oralis]
 gi|193873304|gb|ACF23342.1| RpoB [Streptococcus mitis]
 gi|193873306|gb|ACF23343.1| RpoB [Streptococcus mitis]
 gi|193873308|gb|ACF23344.1| RpoB [Streptococcus mitis]
 gi|193873310|gb|ACF23345.1| RpoB [Streptococcus mitis]
 gi|193873312|gb|ACF23346.1| RpoB [Streptococcus mitis]
 gi|193873314|gb|ACF23347.1| RpoB [Streptococcus mitis]
 gi|193873318|gb|ACF23349.1| RpoB [Streptococcus oralis]
 gi|193873320|gb|ACF23350.1| RpoB [Streptococcus mitis]
 gi|193873322|gb|ACF23351.1| RpoB [Streptococcus mitis]
          Length = 172

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.1 bits (92), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWSTVKEAG 172


>gi|66876483|gb|AAY58030.1| RpoB [Cuscuta japonica]
          Length = 468

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 120/413 (29%), Positives = 210/413 (50%), Gaps = 7/413 (1%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 57  ISVYTGTIISDWGGRSELEIDKKARIWARVSRKQKISILVLSSAMGSNLREIIENVCYPE 116

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
             +      +K K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 117 ILLSFLRDKEKKKIGSKENAILEFYKKFACVGGDPLFSESLCKELQNKFF-QQRCELGRI 175

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RL+LD P +   +   DI+     L+ L+ G GT+DD+++L N+R+RSV ++L
Sbjct: 176 GRRNMNRRLHLDIPQNNTFLLPRDILEATDHLIGLKFGMGTLDDMNHLQNKRIRSVADLL 235

Query: 472 KNQYRLGLLRMERSIKERI--SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++Q+ L L+R+E +++  I  +        PQ+L+ +  + +    FF    LSQ+ +  
Sbjct: 236 QDQFGLALVRLENAVQGTIGGAIRHKRIPTPQNLVTSTLLTTTYESFFGLHPLSQVLDGT 295

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L++I   R++S+LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+ SL   
Sbjct: 296 NPLTQIVQARKVSSLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLIGSLAIH 355

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            R+  +G +E P+ ++ D      V++LS   +E   +A  NS         +++V  R 
Sbjct: 356 VRIGNWGSLERPFYEISDRLTGVRVLHLSPGRDEYYMVAAGNSLALNQDIQEDQVVPARY 415

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
             E + +  E+++     P Q  SI ASLIPF+E++D+NR LM  NMQRQAVP
Sbjct: 416 RQEFLTIAWEQVNLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVP 468



 Score =  126 bits (317), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 100/239 (41%), Gaps = 10/239 (4%)

Query: 120 KSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
           K+  D++EQ+I++G +P+M   GT ++ GI RIV++Q+ +SPGI++  +      +G  +
Sbjct: 3   KASTDMQEQTIFIGSIPIMNSLGTSIVNGIYRIVINQILQSPGIYYRSELD---PNGISV 59

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVY 238
           Y   II D G   ++E D K  I  R+ R++K+ +     A+G +  EI+    YP+I+ 
Sbjct: 60  YTGTIISDWGGRSELEIDKKARIWARVSRKQKISILVLSSAMGSNLREIIENVCYPEILL 119

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
           S   D     + + +  +                     K+L +   +   E G      
Sbjct: 120 SFLRDKEKKKIGSKENAILEFYKKFACVGGDPLFSESLCKELQNKFFQQRCELGRIGRRN 179

Query: 299 TSDCL------CGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            +  L         ++    +   T  +      +     +  + +  IR +  L  D 
Sbjct: 180 MNRRLHLDIPQNNTFLLPRDILEATDHLIGLKFGMGTLDDMNHLQNKRIRSVADLLQDQ 238


>gi|56694326|gb|AAW22903.1| RNA polymerase II second largest subunit [Dioon edule]
          Length = 538

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 73/444 (16%), Positives = 128/444 (28%), Gaps = 80/444 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 175  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 231

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 232  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 290

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 291  FYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 350

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  DE   +     K    TS    E    +++      D
Sbjct: 351  TTPVTQ-----------------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNAD 393

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 394  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNP 448

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +         +IS         +        
Sbjct: 449  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM-- 506

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 507  ---------------------------------------------YNGHT----GR---R 514

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVY 1268
                + +G  Y  +L HMV DK++
Sbjct: 515  LSAMIFLGPTYYQRLKHMVDDKIH 538



 Score =  114 bits (284), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 71/452 (15%), Positives = 131/452 (28%), Gaps = 96/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   + +A   F     +    +    +  +   RR   +  + GV R 
Sbjct: 22  EEWSTENFEEISPAVIPNATKIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRD 81

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S     +          +  V  G    
Sbjct: 82  IRLSELR-LYTDYGRCSRPLFIVENQRLLIKKSDIRRLQQRDNLPPPGWHELVTKGF--- 137

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R           K    +  P  ++
Sbjct: 138 -IEYVDTEEEETTMISM----------TIYDLVNAR-NSPPTAASIVKYTHCEIHPSLIL 185

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 186 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 225

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 226 DTLAYV-----------------------------------LYYPQKPLV---------- 240

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 241 TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFYRSYRDEEK 300

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 301 RMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQDE-- 358

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  +         RD S  +    SG V
Sbjct: 359 -------SGGQAARYTKRDQSTSLRHSESGMV 383


>gi|264658141|emb|CBH32070.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 53/101 (52%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 11   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 70

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 71   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 111


>gi|40644041|emb|CAD92463.1| RNA polymerase II [Evolvulus sp. Stefanovic s.n.]
          Length = 270

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 67/347 (19%), Positives = 109/347 (31%), Gaps = 77/347 (22%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R   
Sbjct: 1    IVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGKPDRSNT 59

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+T +S                  D+   
Sbjct: 60   MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DDAQG 102

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            ++    K  + TS    E    +++      D +     R VKV V   R  Q GDK + 
Sbjct: 103  QSARYTKRDHSTSLRHSETGMVDQVLMTTNADGL-----RFVKVRVRSVRIPQIGDKFSS 157

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+ 
Sbjct: 158  RHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 217

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                                                                  +TP F 
Sbjct: 218  D-----------------------------------------------------ATP-FT 223

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                + I+  L        G   +Y+G TG      + +G  Y  +L
Sbjct: 224  DVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRL 270



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 14/140 (10%)

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIP 866
           +VA   + GYN EDS+++++  +    F S+    +    +      +E        +  
Sbjct: 1   IVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGKPDRSNTM 60

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +       +D+ G+   G  V+  D+++GK TP  +           A         RD
Sbjct: 61  GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQSARYTKRD 111

Query: 927 TSLRVPSGVSGTVVDVRIFN 946
            S  +    +G V  V +  
Sbjct: 112 HSTSLRHSETGMVDQVLMTT 131


>gi|83414553|dbj|BAE54067.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 172

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGLAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGLAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|193873242|gb|ACF23311.1| RpoB [Streptococcus mitis]
          Length = 172

 Score =  195 bits (496), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVIRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G + DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVIRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWSTVKEAG 172


>gi|83414429|dbj|BAE54005.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414577|dbj|BAE54079.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414579|dbj|BAE54080.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414581|dbj|BAE54081.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414583|dbj|BAE54082.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414585|dbj|BAE54083.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414587|dbj|BAE54084.1| RNA polymerase beta subunit [Streptococcus gordonii]
 gi|83414591|dbj|BAE54086.1| RNA polymerase beta subunit [Streptococcus gordonii]
          Length = 172

 Score =  195 bits (496), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.3 bits (90), Expect = 4.4,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  + +   +R A 
Sbjct: 148  GIHIATPVFDGASSDDLWDTVREAG 172


>gi|46277259|gb|AAS86820.1| RNA polymerase II second largest subunit [Trochodendron aralioides]
          Length = 547

 Score =  195 bits (496), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 78/494 (15%), Positives = 144/494 (29%), Gaps = 94/494 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV  G  + V   +      S  + DL   + N   A+   +       S++  +   ++
Sbjct: 142  LVAKGYIEYVDTEEEETTMISMTINDLITAKVNPEEAYSETYTHCEIHPSLILGVCASII 201

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 202  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 250

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 251  TRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 309

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +  ++ +E      R+          +          G           K+T ++     
Sbjct: 310  KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---- 365

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE   +     +  + TS    E    +++      D +     R V
Sbjct: 366  -------------DESQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFV 407

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 408  KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTAEGITPDIIVNPHAIPSRMTIG 467

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+  +         +IS         +                  
Sbjct: 468  QLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------ 515

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                +G +    G         + +G  
Sbjct: 516  -----------------------------------YNGHT----GR---RLTAMIFLGPT 533

Query: 1255 YMLKLNHMVSDKVY 1268
            Y  +L HMV DK++
Sbjct: 534  YYQRLKHMVDDKIH 547



 Score =  113 bits (282), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 73/482 (15%), Positives = 142/482 (29%), Gaps = 98/482 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 3   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVG 62

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
                   +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 63  IHRNPEFLVKTLRQLRRRVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 121

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                    + A    E+P     D      + Y+   EEE   I+              
Sbjct: 122 KKK-----DIQALQQRESPEGGWHDLVAKGYIEYVDTEEEETTMISM----------TIN 166

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +L+  +   E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 167 DLITAKVNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 224

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           +                           R   +  V                        
Sbjct: 225 IYVTNYQL--------------------RMDTLAYV------------------------ 240

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                          Q+PLV                      L  G N +VA   + GYN
Sbjct: 241 -----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSGYN 279

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 280 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 339

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           +         RD S  +    SG
Sbjct: 340 DDGLAPPGTRVSGEDVIIGKTTPIAQDE---------SQGQASRYTRRDHSTSLRHSESG 390

Query: 938 TV 939
            V
Sbjct: 391 MV 392


>gi|83414415|dbj|BAE53998.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414557|dbj|BAE54069.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414561|dbj|BAE54071.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414563|dbj|BAE54072.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414567|dbj|BAE54074.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414569|dbj|BAE54075.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414571|dbj|BAE54076.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414573|dbj|BAE54077.1| RNA polymerase beta subunit [Streptococcus sanguinis]
 gi|83414575|dbj|BAE54078.1| RNA polymerase beta subunit [Streptococcus sanguinis]
          Length = 172

 Score =  195 bits (496), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 3.4,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +R A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVREAG 172


>gi|83414533|dbj|BAE54057.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 172

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 70/168 (41%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ ++
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEEL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.3 bits (90), Expect = 4.8,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S ++ A 
Sbjct: 148  GIHIATPVFDGASSEELWSTVKEAG 172


>gi|2736125|gb|AAB94063.1| RPB140 [Ginkgo biloba]
          Length = 555

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 101/702 (14%), Positives = 193/702 (27%), Gaps = 148/702 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +  + + +  +G +           + +   R ++   D + +  V     L       
Sbjct: 54   AVIPSATKIFVNGCWVGIHRDPDLLVKTLRQLRRQV---DVNTEVGVVRDIRLRELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+                    A    +           +  I
Sbjct: 111  DYGRCSRPLFIVEKQRLLI--------------KKADIRALQQREGPEEGWHDLVAKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              V+ + + +T        +   R+N     +                    PS  LG  
Sbjct: 157  EYVDTEEEETTMISMTISDLVTARNNPEEAYSH-----------TYTHCEIHPSLILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  ++          M  + +     I       R   L         
Sbjct: 204  -----VCASIIPFPDHDQSPRNTYQSAMGKQAMG----IYVTNYQLRMDTLAFVLYYPQK 254

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
            P V+   ++++                             +      + AI      +  
Sbjct: 255  PLVTTRAMEHL-------------------------HFRQLPAGINAIVAISCYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
             + +   S +        +F R   D+ +R  ++ +E+     R+          +    
Sbjct: 290  GSVIMNQSSIDRGFF-RSLFYRAYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K++ +S          Q  ++  +D+                
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTSPISRMK----QGGQVARYTKRDQSTS------------- 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VK+ +   R  Q GDK + RHG KG V     
Sbjct: 392  LRHSESGMVDQVLLTTNADGL-----RFVKIRMRSVRIPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 447  QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNI 506

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
            S         +                                                 
Sbjct: 507  SKALHKCGYQMRGFETM------------------------------------------- 523

Query: 1226 ADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                 +G +    G         + +G  Y  +L HMV DK+
Sbjct: 524  ----YNGHT----GR---KLSAMIFLGPTYYQRLKHMVDDKI 554



 Score = 65.9 bits (159), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 82/262 (31%), Gaps = 23/262 (8%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAANPILEFLEEWSTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
            SA   F     +    +    +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PSATKIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRDIRLRELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +       A + A    E P     D      + Y+   EEE   I+
Sbjct: 116 SRPLFIVEKQRLLIKK-----ADIRALQQREGPEEGWHDLVAKGFIEYVDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R   E            +  P  ++ + AS+IPF ++D S 
Sbjct: 171 M----------TISDLVTARNNPE--EAYSHTYTHCEIHPSLILGVCASIIPFPDHDQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPF 710
           R      M +QA+ +       
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL 240


>gi|83414433|dbj|BAE54007.1| RNA polymerase beta subunit [Streptococcus sinensis]
          Length = 172

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 70/168 (41%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  +  ++
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEEL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +R A 
Sbjct: 148  GIHIATPVFDGASAEELWDTVREAG 172


>gi|193873158|gb|ACF23269.1| RpoB [Streptococcus oralis]
          Length = 172

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWETVKEA 171



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWETVKEAG 172


>gi|193873122|gb|ACF23251.1| RpoB [Streptococcus mitis]
          Length = 172

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGTSSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|67515346|gb|AAY68202.1| RNA polymerase IV second largest subunit [Lycopodium sp. JL-2005]
          Length = 510

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 86/237 (36%), Gaps = 54/237 (22%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
            M     +  +V +   R  Q GDK +  HG KGI+  +   ED+PF ++G   DI++NP 
Sbjct: 328  MDEDGKKHARVRLRESRMPQVGDKFSSMHGQKGILGMVFNQEDLPFTQEGIVPDIIINPH 387

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
              PSR  +GQ+ E+ LG A      +  +  +   +   ++ L                 
Sbjct: 388  AFPSRQTLGQMLESVLGKAVANGCCQNDATPSSSISVESLTDLLH--------------- 432

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                +          ++G  +   +F G                                
Sbjct: 433  RSGYERWGKECMCNGRTGHMLKARIFMG-------------------------------- 460

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
                     +  +L HM  DK+  R TG    +++QP+  +   GG + GEME  C+
Sbjct: 461  -------PTFYQRLIHMAQDKLKWRRTGPVHPLSRQPVADRKRHGGVKFGEMERDCL 510



 Score = 60.1 bits (144), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 57/378 (15%), Positives = 114/378 (30%), Gaps = 43/378 (11%)

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
           +  G+ + P   V   +      ++S   E  R        +  D       +       
Sbjct: 2   SWKGWHQNPETLVETLRKLRRCGHISXEVEIARDPIYKEVKIYTDSGRILRPLLXVDKQH 61

Query: 653 EILVPREKIDFIDASPKQVVS--IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
            ++  +          +      +   ++  L  D+    L+  N++   V         
Sbjct: 62  LLITKKHIAKAKALKSESAFKFLLQEGVVELLGVDEEEEALVALNVEXLEVS--NKRHSV 119

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
             T  E   +   G            Q      V++  +     +          +   S
Sbjct: 120 HYTHCELHPSFILGLGASVIPFPNHNQSS---RVMQQAQKHGKXAIGFYCSNFKSRSDTS 176

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           +      Q+ LV+     R + ++     T+      G+N +VA   + GYN EDS++++
Sbjct: 177 SHLLYYPQKQLVRT----RASALLERPEFTN------GQNAIVAIACYSGYNQEDSIIMN 226

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP------NVSEEGLKNIDECGIICV 884
           +  +   ++ ++H   F     D     +E  R            +     +D  G   +
Sbjct: 227 QSSIERGLYRTMHYHTF---HFDIPANVDEEFRKPSASDVGGTRYQGSNDKLDNEGFPYI 283

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GA ++  DI+ GK+T    S                     D S+R+     G V  V +
Sbjct: 284 GAALSSPDIVAGKVTSVPNSSRL-----------------SDRSVRLKHTEMGRVDRVVL 326

Query: 945 FNRHGIDKNERSISVERE 962
                  K+ R    E  
Sbjct: 327 SMDEDGKKHARVRLRESR 344


>gi|83414423|dbj|BAE54002.1| RNA polymerase beta subunit [Streptococcus infantis]
 gi|83414469|dbj|BAE54025.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414473|dbj|BAE54027.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414475|dbj|BAE54028.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414477|dbj|BAE54029.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414479|dbj|BAE54030.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414481|dbj|BAE54031.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414483|dbj|BAE54032.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414487|dbj|BAE54034.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414489|dbj|BAE54035.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414491|dbj|BAE54036.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414493|dbj|BAE54037.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414497|dbj|BAE54039.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414499|dbj|BAE54040.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414501|dbj|BAE54041.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414503|dbj|BAE54042.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414505|dbj|BAE54043.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414509|dbj|BAE54045.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414511|dbj|BAE54046.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414521|dbj|BAE54051.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414537|dbj|BAE54059.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414539|dbj|BAE54060.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414541|dbj|BAE54061.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414545|dbj|BAE54063.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414547|dbj|BAE54064.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414549|dbj|BAE54065.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414551|dbj|BAE54066.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414555|dbj|BAE54068.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|83414559|dbj|BAE54070.1| RNA polymerase beta subunit [Streptococcus sanguinis SK36]
 gi|83414599|dbj|BAE54090.1| RNA polymerase beta subunit [Streptococcus infantis]
 gi|193873092|gb|ACF23236.1| RpoB [Streptococcus oralis]
 gi|193873134|gb|ACF23257.1| RpoB [Streptococcus mitis]
 gi|193873138|gb|ACF23259.1| RpoB [Streptococcus infantis]
 gi|193873146|gb|ACF23263.1| RpoB [Streptococcus oralis]
 gi|193873148|gb|ACF23264.1| RpoB [Streptococcus oralis]
 gi|193873154|gb|ACF23267.1| RpoB [Streptococcus oralis]
 gi|193873156|gb|ACF23268.1| RpoB [Streptococcus oralis]
 gi|193873160|gb|ACF23270.1| RpoB [Streptococcus oralis]
 gi|193873162|gb|ACF23271.1| RpoB [Streptococcus oralis ATCC 35037]
 gi|193873164|gb|ACF23272.1| RpoB [Streptococcus oralis]
 gi|193873168|gb|ACF23274.1| RpoB [Streptococcus oralis]
 gi|193873170|gb|ACF23275.1| RpoB [Streptococcus oralis]
 gi|193873172|gb|ACF23276.1| RpoB [Streptococcus oralis]
 gi|193873174|gb|ACF23277.1| RpoB [Streptococcus oralis]
 gi|193873268|gb|ACF23324.1| RpoB [Streptococcus infantis ATCC 700779]
 gi|193873276|gb|ACF23328.1| RpoB [Streptococcus infantis]
 gi|193873282|gb|ACF23331.1| RpoB [Streptococcus oralis]
 gi|193873292|gb|ACF23336.1| RpoB [Streptococcus oralis]
 gi|193873296|gb|ACF23338.1| RpoB [Streptococcus oralis]
 gi|193873300|gb|ACF23340.1| RpoB [Streptococcus oralis]
 gi|193873302|gb|ACF23341.1| RpoB [Streptococcus oralis]
          Length = 172

 Score =  195 bits (495), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.4 bits (93), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|83414525|dbj|BAE54053.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|193873152|gb|ACF23266.1| RpoB [Streptococcus oralis]
          Length = 172

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 94/175 (53%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T       S   R     F  +  +V      +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDFSAEERLLHAIFGDKSREVSDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 45/63 (71%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE   + EE+LL AIFG+K+ +V DTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDFSAEERLLHAIFGDKSREVSDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|145581380|gb|ABP87788.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|145581382|gb|ABP87789.1| RNA polymerase beta subunit [Klebsiella oxytoca]
          Length = 180

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 114/179 (63%), Positives = 142/179 (79%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET
Sbjct: 2   EFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 61

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+L
Sbjct: 62  PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNL 121

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+NR LMG
Sbjct: 122 DDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 180


>gi|193873130|gb|ACF23255.1| RpoB [Streptococcus mitis]
 gi|193873178|gb|ACF23279.1| RpoB [Streptococcus pneumoniae]
 gi|193873180|gb|ACF23280.1| RpoB [Streptococcus pneumoniae]
 gi|193873182|gb|ACF23281.1| RpoB [Streptococcus pneumoniae]
 gi|193873184|gb|ACF23282.1| RpoB [Streptococcus pneumoniae]
 gi|193873186|gb|ACF23283.1| RpoB [Streptococcus pneumoniae]
 gi|193873190|gb|ACF23285.1| RpoB [Streptococcus pneumoniae]
 gi|193873192|gb|ACF23286.1| RpoB [Streptococcus pneumoniae]
 gi|193873194|gb|ACF23287.1| RpoB [Streptococcus pneumoniae]
 gi|193873196|gb|ACF23288.1| RpoB [Streptococcus pneumoniae]
 gi|193873198|gb|ACF23289.1| RpoB [Streptococcus pneumoniae]
 gi|193873200|gb|ACF23290.1| RpoB [Streptococcus pneumoniae]
 gi|193873202|gb|ACF23291.1| RpoB [Streptococcus pneumoniae]
 gi|193873204|gb|ACF23292.1| RpoB [Streptococcus pneumoniae]
 gi|193873278|gb|ACF23329.1| RpoB [Streptococcus pneumoniae]
 gi|193873280|gb|ACF23330.1| RpoB [Streptococcus pneumoniae]
 gi|193873324|gb|ACF23352.1| RpoB [Streptococcus pneumoniae]
          Length = 172

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRVNGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDL 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRV 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 30/85 (35%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E + S ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWSTVKEAG 172


>gi|46277362|gb|AAS86871.1| DNA-dependent RNA polymerase II [Peziza whitei]
          Length = 554

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 91/675 (13%), Positives = 182/675 (26%), Gaps = 126/675 (18%)

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL S+  V         +    + +V  +     +      ++      +  D  F    
Sbjct: 2    SLMSYVSVGTPSQPIVDFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRT 61

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            +        I      I  I     ++ + A  +   L   D              +   
Sbjct: 62   IQKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVD--NDPTSARRGELVLQKH 119

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
              E   +   +E    +     ++    G+VE +DA            + +   V     
Sbjct: 120  HIERLEIDRDLEDETQRYGWQGLLT--DGVVEYIDAEE----------EETVMIVMTPED 167

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYNF 823
            ++  R        Q+P V     V+          T      ++   +  + +P+  +N 
Sbjct: 168  LETSRQFHAGYEIQQP-VDPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQ 226

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                                        R+T                   +      +  
Sbjct: 227  SP--------------------------RNTXXXXXXXXXXXXXXXXXXXRM---DTMAN 257

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 258  ILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RS 316

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G        
Sbjct: 317  LFFRTYMDQEKR---IGMAVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDI 373

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ +      R+++         ++     +  Q                   
Sbjct: 374  IIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ------------------- 414

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 415  -VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVPDL 473

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 474  IINPHAIPSRMTIAHLIECLLSKVSSLRGYEGD--------------------------- 506

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++++LR       G  I+Y+G 
Sbjct: 507  --------------------------ATP-FTDVTVDSVSTLLREHGYQSRGFEIMYNGH 539

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG      V +G  Y
Sbjct: 540  TGRKMVAQVFLGPTY 554



 Score = 92.8 bits (229), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 67/441 (15%), Positives = 132/441 (29%), Gaps = 35/441 (7%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S  +       N    +       +     +      V    +H      +   +     
Sbjct: 13  SQPIVDFMMQRNM-EVLEEYEPSRSPNATKIFVNGVWV---GIHRDPGFIVRTIQKLRRQ 68

Query: 579 -NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +IG   SL    R   +       R      V ++    SA   E          L+ D
Sbjct: 69  GHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDN-DPTSARRGELVLQKHHIERLEID 127

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +E    R   + +L     +++IDA  ++ V I  +      +   +    G  +Q
Sbjct: 128 RDLEDE--TQRYGWQGLLTDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGYEIQ 181

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +   P  + +             +   + I+   A I+   D  +    +          
Sbjct: 182 QPVDPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTXXXXXXXXXX 241

Query: 758 GVDIYRLM-KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                    +           Q+PL                      +L  G+N +VA M
Sbjct: 242 XXXXXXXXXRMDTMANILYYPQKPL----------GTTRSMEFLKFRELPAGQNAIVAIM 291

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
            + GYN EDS+++++  +   +F S+    +    +   +   E        +   +   
Sbjct: 292 CYSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMAVVEEFEKPTRGNTLRLKHG 351

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S  +
Sbjct: 352 TYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPL 404

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            S  +G V  V +       K
Sbjct: 405 RSTENGIVDQVMVTTNQEGLK 425


>gi|83414507|dbj|BAE54044.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 172

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVLRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G + DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVLRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|300394742|gb|ADK11909.1| DNA-directed RNA polymerase II subunit two [Podoserpula pusio]
          Length = 359

 Score =  195 bits (495), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 68/443 (15%), Positives = 119/443 (26%), Gaps = 88/443 (19%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  I   ++            ++       +G       I          
Sbjct: 1    WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLIRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMLYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   R+          +       I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 169  AGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  IVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++  LR          +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSKFLRQKGYQSRALEV 334

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLK 1258
            +Y G TG      + +G  Y  +
Sbjct: 335  MYKGHTGRRLQAQLPLGPTYYQR 357



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 90/285 (31%), Gaps = 74/285 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMLYLKFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E        +   +       I++ G+I  G  V   DI++
Sbjct: 116 SIYYRSYMDLEKKSGIQQLEEFEKPTRENTLRMKHGTYDKIEDDGLIAPGTGVAGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           GK  P         E+L +        DV        +G+   V+
Sbjct: 176 GKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 216


>gi|56694292|gb|AAW22886.1| RNA polymerase II second largest subunit [Isoetes sp. JZ73]
          Length = 536

 Score =  194 bits (494), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 100/684 (14%), Positives = 184/684 (26%), Gaps = 148/684 (21%)

Query: 575  SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
             EG   GLV +L   A +            + +    N        EE +  +   ++ +
Sbjct: 1    PEGQACGLVKNLALMAYITVGSAANPILVFLEEWSTEN-------FEEISPAVIPQSTKI 53

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
              +G +           + +   R ++   D + +  V     L       D  R     
Sbjct: 54   FVNGCWVGIHRDPEHLVKTLRQLRRQV---DVNTEVGVVRDIRLKELRLYTDYGRCSRPL 110

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +  +   L+                K   +    + +         +  I  V+ + + 
Sbjct: 111  FIVEKQRLLI--------------KKKDIRSLQQKESSENGWYDLVQKGFIEYVDTEEEE 156

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            +T        +   R+N     +                    PS  LG       +  +
Sbjct: 157  TTMISMTISDLVNARNNPEEAYS-----------ETYTHCEIHPSMILG-------VXGS 198

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+   N          M  + +   I++  ++                          
Sbjct: 199  IIPFPDXNQSPRNTYQSAMGKQAMG--IYVTNYQ-------------------------- 230

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
             +    +  V        +    +       +      + AI      +  D+ +   S 
Sbjct: 231  -LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSS 289

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +        IF R   ++  +  S+ +E+ E   R+          +          G  
Sbjct: 290  IDRGFF-RSIFYRSYREEEXKQGSLVKEEFERPNRENTLGMRHGSYDKLDDDGLAPPGTR 348

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L                  QDE   +     K    T     E    
Sbjct: 349  VSGEDVIIGKTVPL-----------------PQDETGTQAQRYTKRDQSTPLRHSESGMI 391

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +++      D +     R VK  V   R  Q GDK + RHG KG V      EDMP+  +
Sbjct: 392  DQVLLTTNADGL-----RFVKTRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTME 446

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   DI++NP  + SRM +GQ+ E  +G     +GK+                       
Sbjct: 447  GITPDIIVNPHAIXSRMTIGQLIECIMGKVAAHMGKEGD--------------------- 485

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP F     + I+  L        G  
Sbjct: 486  --------------------------------ATP-FTDVTVDNISRALHKCGYQMRGFE 512

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLK 1258
             +Y+G TG P    + +G  Y  +
Sbjct: 513  RMYNGHTGRPLSAMIFLGPTYYQR 536


>gi|83414671|dbj|BAE54126.1| RNA polymerase beta subunit [Streptococcus mutans]
          Length = 172

 Score =  194 bits (494), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 95/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERFLHAIFGDKSREVRDTSLRVPHGGDGVVCDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSDDLWETVKEA 171



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+ L AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERFLHAIFGDKSREVRDTSLRVPHGGDGVVCDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/85 (14%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  + +   ++ A 
Sbjct: 148  GIHIATPVFDGATSDDLWETVKEAG 172


>gi|126165873|gb|ABN80330.1| RNA polymerase B [Staphylococcus croceolyticus]
          Length = 199

 Score =  194 bits (494), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 114/199 (57%), Positives = 150/199 (75%), Gaps = 2/199 (1%)

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           + PQ LIN +PV++++ EFF SSQLSQ  +  N L+ +TH RRLSALG GG+ R RA +E
Sbjct: 1   ITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQME 60

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV--CDGKVTNDVV 615
           +RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +T+ + 
Sbjct: 61  VRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQID 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
           YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQVVS A
Sbjct: 121 YLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAA 180

Query: 676 ASLIPFLENDDSNRVLMGC 694
            + IPFLENDDSNR LMG 
Sbjct: 181 TACIPFLENDDSNRALMGA 199


>gi|284431197|gb|ADB84360.1| RNA polymerase beta subunit [Aeromonas tecta]
          Length = 182

 Score =  194 bits (494), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 107/181 (59%), Positives = 139/181 (76%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN+
Sbjct: 62  ETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANA 121

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           +  E+G   +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR LM
Sbjct: 122 ATSEEGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRALM 181

Query: 693 G 693
           G
Sbjct: 182 G 182


>gi|301129140|emb|CAX51310.2| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 119

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 19   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 78

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 79   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 119


>gi|224419496|emb|CAX51329.1| RNA polymerase beta subunit [Corynebacterium freneyi]
          Length = 127

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 27   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 86

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 87   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 127


>gi|224419494|emb|CAX51328.1| RNA polymerase beta subunit [Corynebacterium freneyi]
          Length = 120

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 20   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 79

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 80   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 120


>gi|224419484|emb|CAX51323.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 122

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 22   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 81

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 82   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 122


>gi|224419482|emb|CAX51322.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 115

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 15   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 74

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 75   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 115


>gi|224419478|emb|CAX51320.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 120

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 20   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 79

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 80   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 120


>gi|224419474|emb|CAX51318.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 124

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 24   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 83

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 84   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 124


>gi|224419472|emb|CAX51317.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 112

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 12   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 71

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 72   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 112


>gi|224419468|emb|CAX51315.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 103

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 3    VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 62

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 63   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 103


>gi|224419464|emb|CAX51313.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 110

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 10   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 69

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 70   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 110


>gi|224419462|emb|CAX51312.1| RNA polymerase beta subunit [Corynebacterium xerosis]
 gi|224419470|emb|CAX51316.1| RNA polymerase beta subunit [Corynebacterium xerosis]
 gi|224419480|emb|CAX51321.1| RNA polymerase beta subunit [Corynebacterium xerosis]
 gi|224419486|emb|CAX51324.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 123

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 23   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 82

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 83   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 123


>gi|224419460|emb|CAX51311.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 127

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 27   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 86

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 87   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 127


>gi|224419500|emb|CAX51331.1| RNA polymerase beta subunit [Corynebacterium freneyi]
 gi|224419502|emb|CAX51332.1| RNA polymerase beta subunit [Corynebacterium freneyi]
          Length = 119

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 19   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 78

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 79   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 119


>gi|167382955|ref|XP_001733337.1| DNA-directed RNA polymerase III subunit RPC2 [Entamoeba dispar
            SAW760]
 gi|165901325|gb|EDR27409.1| DNA-directed RNA polymerase III subunit RPC2, putative [Entamoeba
            dispar SAW760]
          Length = 1115

 Score =  194 bits (494), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 73/512 (14%), Positives = 156/512 (30%), Gaps = 81/512 (15%)

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
             +  D+    N  +A            + I    +   V   I         R+T     
Sbjct: 644  IEYLDVNEENNSYIAISENEINEHTTHLEIDPLSILGVVAGLIPYPHHNQSPRNTYQCAM 703

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
               + I  +     K ID   ++ +        +    I       +   +  + A+   
Sbjct: 704  -GKQAIGTIGYNQFKRIDT--LLYLLYYPQIPMVKTKTIDMINFDKLPAGQNAMVAVMSY 760

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               D+ D S+   + +        ++ +      +         +     +++  +    
Sbjct: 761  SGYDIEDASILNKASIDRGYGRCFVYRKAECVIKKYKNGACDRVVCPTDEERELPK---- 816

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
                    + L      S        ++  +  +            ++D++         
Sbjct: 817  -------YKSLDFDGVCSPGSILNPGSIYLNKQVPINTVGTLTTDTIKDDE--------- 860

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
              Y       +    + ++++    +    +   VK+ +   R  + GDK +        
Sbjct: 861  --YRREVLTYKGPVPSYVDQVLITSNEEEPL--KVKISLRTSRRPELGDKFS-------- 908

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
                                         SR                  G+K  + +   
Sbjct: 909  -----------------------------SR-----------------HGQKGVTGLIVN 922

Query: 1160 KANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAI 1219
            + +   +      + ++       +++      ++        G       F G   + +
Sbjct: 923  QEDMPFTNTGICPDVIMNPHGFPSRMTVGKLLELVSGKAGLMDGSFKYGTAFGGDKLDDM 982

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            + +L  A     G+  LY G+TG+  +  + +G +Y  KL HMV DK++AR+ G  S +T
Sbjct: 983  SKILIEAGYSYDGKEELYSGITGKALNAYIFIGPVYYQKLKHMVLDKMHARARGPKSSLT 1042

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            +QP  G+S  GG RLGEME  C+  YGA  +L
Sbjct: 1043 RQPTEGRSRDGGLRLGEMERDCLIGYGATNLL 1074



 Score =  188 bits (478), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 137/915 (14%), Positives = 286/915 (31%), Gaps = 162/915 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           L+     S+++F+          +E ++   K+   IT        L+++  + D P   
Sbjct: 55  LVRQHIDSFNYFI----------DEEIKQIVKANDKITCDADPTFYLKYLDVKVDTPCVE 104

Query: 86  -------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIK------------ 126
                      +C  RD++Y  P+   ++    D   F    +I  +             
Sbjct: 105 VDYKKESITPQECRLRDISYTAPILANIQYTR-DKKIFRKTVTIGYMPIMLQSKHCVLYN 163

Query: 127 ---EQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
              E+ I  G+ P M   G F++KG++R+++SQ   S          +  LS  +  A  
Sbjct: 164 NTFEEFIRHGECP-MDPGGYFIVKGVERVILSQEQMSKNRILIETTTQGFLSASVTSATH 222

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTFYPKIVYS-Q 240
            +  +     + +  K  ++++ +     +P+   + A+GM+S+ E L            
Sbjct: 223 EVKSR----TVVYLKKGKLYLKHNSLTEDLPIMIVIKAMGMESDMEFLQFVGNHYTSKMI 278

Query: 241 RGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS 300
                C      +     +   + + I TG++   S +         L    +  + +  
Sbjct: 279 NSIEECKTKDVLNQREALRYIGNHLKIYTGQKGYISKRPKIEEARDVLANLVLPHIEVNR 338

Query: 301 DCLCGLYVAEDIVN------GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
                  +   ++        ETGE+  +  D    K +E            L+     +
Sbjct: 339 YNFKTKIIYLALMVNWILKADETGEL--DDKDYYGNKRMELAGQLMSLLFEDLFKQFNTD 396

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              ++N       K  +    DI + + P  + T  +  S+ +   +   ++++   G  
Sbjct: 397 ---LQNAANKGLTKKSRSETFDIIKCISPHRI-TQGLIHSL-STGNWVLKRFNMDRAGIT 451

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
           ++  R           +     + ++  L         +    +L   +   V      +
Sbjct: 452 QVLSR-----------LSYISALGMMTRLNSHFEKTRKVSGPRSLQGSQWGMVCPSDTPE 500

Query: 475 YRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSR 534
                L    S+   +++   D  +   L N     + +      + LS     +N    
Sbjct: 501 GESCGLVKNFSLLTEVTTDSDDQAIVTMLFNLGVEDANLISGDEVNALSSYLVFLNGQLL 560

Query: 535 ITHTRRLSALGQGGVARAR-AGVEMRDVHPTHYGRICPAETSEGHNIG---LVSSLTSFA 590
             H   +  L Q  + R      +   +H     R     +  G       +V +  S  
Sbjct: 561 GIHQNPIHFLKQCRLLRRHGRLGKKVSLHLNEMQRSINISSDGGRVCRPLIVVENCKSKI 620

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                  I   ++ + D      + YL   EE N YIA + + ++               
Sbjct: 621 GPKEIRDIVEGFKSIEDCLKEGLIEYLDVNEENNSYIAISENEIN--------------- 665

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                   E    ++  P  ++ + A LIP+  ++ S R    C M +QA+         
Sbjct: 666 --------EHTTHLEIDPLSILGVVAGLIPYPHHNQSPRNTYQCAMGKQAIGT------- 710

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                                             I   +     +   +  Y        
Sbjct: 711 ----------------------------------IGYNQFKRIDTLLYLLYYP------- 729

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q P+VK                 +   L  G+N +VA M + GY+ ED+ +++
Sbjct: 730 -------QIPMVK----------TKTIDMINFDKLPAGQNAMVAVMSYSGYDIEDASILN 772

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE--GLKNIDECGIICVGAEV 888
           +  +           + E + +  K G  +      +   E    K++D  G+   G+ +
Sbjct: 773 KASIDRGYGRCFVYRKAECVIKKYKNGACDRVVCPTDEERELPKYKSLDFDGVCSPGSIL 832

Query: 889 NPGDILVGKITPKGE 903
           NPG I + K  P   
Sbjct: 833 NPGSIYLNKQVPINT 847


>gi|83414485|dbj|BAE54033.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 172

 Score =  194 bits (493), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/177 (39%), Positives = 95/177 (53%), Gaps = 6/177 (3%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K T      +S   R     F  +  +V+     +    +     +      
Sbjct: 1    KGSDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------ 54

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 54.3 bits (129), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KGSDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|46277318|gb|AAS86849.1| DNA-dependent RNA polymerase II [Pachyella adnata]
          Length = 549

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 59/376 (15%), Positives = 107/376 (28%), Gaps = 75/376 (19%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 249  ANILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 307

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R  +D+ +R      E+ E   R           +       +  G         
Sbjct: 308  RSLFFRTYMDQEKRVGMAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGEDII 367

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  ++ +      R+++         ++     +  Q                    
Sbjct: 368  IGKTAPIAPNTEELGQRTKFHTKRDVSTPLRSTESGIVDQVML----------------- 410

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 411  ---TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGIVPDII 467

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G +                              
Sbjct: 468  INPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------------- 499

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     ++++ +LR       G  ++Y+G T
Sbjct: 500  -------------------------ATP-FTDVTVDSVSGLLREHGYQSRGFEVMYNGHT 533

Query: 1242 GEPFDRPVTVGYIYML 1257
            G      V +G  Y  
Sbjct: 534  GRKLVVQVFLGPTYYQ 549



 Score = 90.1 bits (222), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 71/476 (14%), Positives = 122/476 (25%), Gaps = 74/476 (15%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
              ++ +   ++   P    NA  +             + +  ++  L R  H     +L
Sbjct: 9   DFMKQRNMEVLEEYEPSRHPNATKIFVNGVWVGIHRDPNFIVRNIQKLRRQNHIGHEVSL 68

Query: 545 GQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            Q    R         R   P       PA T  G  +   S +                
Sbjct: 69  IQDVRNREFKIFTDAGRICRPLFVVDNDPASTRRGELVLQKSHIEKLEYDKELPKDSELK 128

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                      V Y+ A EEE   I      LD    +           +     R+ ++
Sbjct: 129 YGWQGLINEGVVEYVDAEEEETIMIMMTPEELDLSRQYHAGYEIQAEPMDLAARVRQPVN 188

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                                            M                        + 
Sbjct: 189 KH-----------------------------ATM--------------------WTHCEI 199

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPL 781
             A I+   A I+   D  +                              N     Q+PL
Sbjct: 200 HPAMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXANILYYPQKPL 259

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                 +L  G+N +VA   + GYN EDS+++++  +   +F S
Sbjct: 260 ----------GTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 309

Query: 842 IHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +   +   E        +   +       +DE G++  G  VN  DI++G
Sbjct: 310 LFFRTYMDQEKRVGMAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGEDIIIG 369

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K  P   +     ++        K    RD S  + S  SG V  V +       K
Sbjct: 370 KTAPIAPNTEELGQRT-------KFHTKRDVSTPLRSTESGIVDQVMLTTNQEGLK 418


>gi|89142753|emb|CAJ57572.1| RNA polymerase subunit B [Microbacterium flavescens]
          Length = 358

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 129/256 (50%), Positives = 173/256 (67%), Gaps = 15/256 (5%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 103 IEETLSKDTILSKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 162

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLGNR 462
            +L LD P     +  +DI+A IK LV L  G                  IDDIDN GNR
Sbjct: 163 QKLGLDKPLTDSVLTVDDIVATIKYLVRLHRGDVTFDGIRGGKPAEIRLDIDDIDNFGNR 222

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
           R+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQL
Sbjct: 223 RIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQL 282

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
           SQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIGL
Sbjct: 283 SQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNIGL 342

Query: 583 VSSLTSFARVNAYGFI 598
           + SL SFAR+N +GFI
Sbjct: 343 IGSLASFARINPFGFI 358



 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 57/163 (34%), Positives = 84/163 (51%), Gaps = 13/163 (7%)

Query: 141 DGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKD 200
            GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W++ E D +D
Sbjct: 8   QGTFIINGTERVVVSQLVRSPGVYFDRTPDKT--SDKDIVSARVIPSRGAWLEFEIDKRD 65

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGA 258
            + VRIDR+RK  VT FL ALG+ SE+IL+ F  +  I  +   D       A   +   
Sbjct: 66  QVGVRIDRKRKQSVTVFLKALGLTSEDILAEFAGFESIEETLSKDTILSKEDALRDI--- 122

Query: 259 KVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
                   +  GEQV  E+ + L      + K   +  +G   
Sbjct: 123 -----YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 160


>gi|89142755|emb|CAJ57573.1| RNA polymerase subunit B [Microbacterium foliorum]
          Length = 360

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 127/258 (49%), Positives = 175/258 (67%), Gaps = 16/258 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 103 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 162

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG----------------KGTIDDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                +   DDIDN GN
Sbjct: 163 HKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFPGIRSGKKADIRIATDDIDNFGN 222

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 223 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 282

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 283 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 342

Query: 582 LVSSLTSFARVNAYGFIE 599
           L+ +L +FAR+N +GFIE
Sbjct: 343 LIGALATFARINPFGFIE 360



 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 77/282 (27%), Positives = 122/282 (43%), Gaps = 30/282 (10%)

Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
           D PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W++
Sbjct: 1   DFPLQTDKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAWLE 58

Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSA 251
            E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D       A
Sbjct: 59  FEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILTEFAGYTSIEETLAKDTIVTKEDA 118

Query: 252 ADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
              +           +  GEQV  E+ + L      + K   +  +G             
Sbjct: 119 LRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK---------- 160

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDR 370
             +N + G   ++        ++E+I  + I+ +  L+  +      IR+    D     
Sbjct: 161 --INHKLG---LDQPLNSSVLTVEDIV-ATIKYLVRLHAGTEETFPGIRSGKKADIRIAT 214

Query: 371 KDALLDIYRVMRP-GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            D      R +R  G++    V   +        ++     +
Sbjct: 215 DDIDNFGNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDI 256


>gi|83414677|dbj|BAE54129.1| RNA polymerase beta subunit [Streptococcus salivarius]
 gi|83414679|dbj|BAE54130.1| RNA polymerase beta subunit [Streptococcus salivarius]
          Length = 172

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.7 bits (91), Expect = 3.5,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +R A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVREAG 172


>gi|40644998|emb|CAD89358.1| RNA polymerase II, second largest subunit [Vitis piasezkii]
          Length = 551

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 79/494 (15%), Positives = 144/494 (29%), Gaps = 94/494 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV  G  + V   +      S  + DL   R N   A+   +       S++  +   ++
Sbjct: 146  LVSKGFIEYVDTEEEETTMISMTINDLISARLNPEEAYSETYTHCEIHPSLILGVCASII 205

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 206  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 254

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 255  TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 313

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            +  ++ +E      R+          +          G           K+T +S     
Sbjct: 314  KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ---- 369

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         D+   +     +  + TS    E    +++      D +     R V
Sbjct: 370  -------------DDSQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFV 411

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 412  KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIG 471

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+  +         +IS         +                  
Sbjct: 472  QLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------ 519

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                +G +    G         + +G  
Sbjct: 520  -----------------------------------YNGHT----GR---RLTAMIFLGPT 537

Query: 1255 YMLKLNHMVSDKVY 1268
            Y  +L HMV DK++
Sbjct: 538  YYQRLKHMVDDKIH 551



 Score =  114 bits (284), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 72/486 (14%), Positives = 139/486 (28%), Gaps = 105/486 (21%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  +   F     + 
Sbjct: 6   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQSTKIFVNGCWVG 65

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
                   +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 66  IHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 124

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L         G+         D      + Y+   EEE   I+          
Sbjct: 125 KKRDIRALQLRESPEDGGWH--------DLVSKGFIEYVDTEEEETTMISM--------- 167

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +L+  R   E      E     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 168 -TINDLISARLNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 224

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +                           R   +  V                    
Sbjct: 225 QAMGIYVTNYQL--------------------RMDTLAYV-------------------- 244

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 245 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 279

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 280 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSY 339

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP  +           +         RD S  +  
Sbjct: 340 DKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------SQGQASRYTRRDHSTSLRH 390

Query: 934 GVSGTV 939
             SG V
Sbjct: 391 SESGMV 396


>gi|83414665|dbj|BAE54123.1| RNA polymerase beta subunit [Streptococcus gallolyticus subsp.
            gallolyticus]
          Length = 172

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDL 164



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.1 bits (92), Expect = 2.6,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +R A 
Sbjct: 148  GIHIATPVFDGATSEDLWDTVREAG 172


>gi|56694334|gb|AAW22907.1| RNA polymerase II second largest subunit [Araucaria araucana]
          Length = 523

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 78/494 (15%), Positives = 143/494 (28%), Gaps = 94/494 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGR-NMLVAFM-PWHGYNFEDSML--ISERMV 834
            LV  G  + V   +      S  + DL   R N   A+   +       S++  +   ++
Sbjct: 118  LVNKGFIEYVDTEEEEXTMISMTINDLVNARTNPEDAYSHTYTHCEIHPSLILGVCASII 177

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +           + 
Sbjct: 178  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYXLYYPQKPLVT 226

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 227  TRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEK 285

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R  ++ +E+     R+          +          G           K+T ++     
Sbjct: 286  RMGTLVKEEFGRPNRENTXGXRHGSXDKLDEDGLAPPGTRVSGEDVIIGKTTPITQ---- 341

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE+  +     +    TS    E    +++      D +     R V
Sbjct: 342  -------------DEQGGQLSRFSRRDQSTSLRHSESGMVDQVLLTTNQDGL-----RFV 383

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            K+ +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 384  KIRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIG 443

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+  +          IS         +                  
Sbjct: 444  QLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM------------ 491

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                +G +    G         + +G  
Sbjct: 492  -----------------------------------YNGHT----GR---KLSAMIFLGPT 509

Query: 1255 YMLKLNHMVSDKVY 1268
            Y  +L HMV DK++
Sbjct: 510  YYQRLKHMVDDKIH 523



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/281 (15%), Positives = 82/281 (29%), Gaps = 23/281 (8%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + +A   F     +    +    +  +   RR   +    GV R 
Sbjct: 11  EEWSTENFEEISPAVIPTATKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 70

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +     +  R N     E  +  V  G    
Sbjct: 71  IRLRELR-LYTDYGRCSRPLFVVENQRLKIKKKDINELRQNPE---EGWHELVNKGF--- 123

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E            +  P  ++
Sbjct: 124 -IEYVDTEEEEXTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLIL 170

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG--TGMESVVAKSSGAAIVAK 730
            + AS+IPF +++ S R      M +QA+ +                   +       A 
Sbjct: 171 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYXLYYPQKPLVTTRAM 230

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                 Q+ A    I ++      +     I       R  
Sbjct: 231 EHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGF 271


>gi|269978596|gb|ACZ55980.1| RNA polymerase II [Fusarium sp. NRRL 36351]
 gi|269978599|gb|ACZ55982.1| RNA polymerase II [Fusarium armeniacum]
 gi|269978638|gb|ACZ56008.1| RNA polymerase II [Fusarium sporotrichioides]
          Length = 312

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 66/197 (33%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   L   E+           +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P  +       +        +    RD S  + S  
Sbjct: 111 LDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTE 163

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 164 NGIVDQVILTVNADNVK 180


>gi|83414673|dbj|BAE54127.1| RNA polymerase beta subunit [Streptococcus mutans]
 gi|83414675|dbj|BAE54128.1| RNA polymerase beta subunit [Streptococcus mutans]
          Length = 172

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 95/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVCDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSDDLWETVKEA 171



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVCDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/85 (14%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  + +   ++ A 
Sbjct: 148  GIHIATPVFDGATSDDLWETVKEAG 172


>gi|282598430|gb|ADA83445.1| RNA polymerase beta subunit [Corynebacterium sp. NML98-0116]
          Length = 140

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 83/168 (49%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D      +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEPF 
Sbjct: 45   ------------ATPVFDGATNEEIAGLLANSKPNRDGDVMVDENGKTTLFDGRSGEPFK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|83414657|dbj|BAE54119.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 172

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 64/110 (58%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  +  D+
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASANDL 164



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|312204302|gb|ADQ47468.1| RNA polymerase II second largest subunit [Bryodiscus arctoalpinus]
          Length = 718

 Score =  194 bits (493), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 61/377 (16%), Positives = 115/377 (30%), Gaps = 81/377 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 420  MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 479

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +++ +R   +    +E   +    + + L    Y +L +   I  G     
Sbjct: 480  -RSLFYRAYVEQEKR---IGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVSG 535

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D      R++          ++     +                  +
Sbjct: 536  EDIIIGKTAPIAPDDEELGQRTKLHTKRDASTPLRSTESGI------------------V 577

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+          L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G  
Sbjct: 578  DKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFSSEGIV 635

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             DI++NP  +PSRM +  + E  L       G +                          
Sbjct: 636  PDIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------ 671

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  ++Y
Sbjct: 672  -----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMY 701

Query: 1238 DGLTGEPFDRPVTVGYI 1254
            +G TG      V +G  
Sbjct: 702  NGHTGRKLVAQVFLGPT 718



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 425 YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 474

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +     + +D+ GII  G  V+
Sbjct: 475 DRGLFRSLFYRAYVEQEKRIGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVS 534

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  SG V  V +     
Sbjct: 535 GEDIIIGKTAPIAPDDEELGQRT-------KLHTKRDASTPLRSTESGIVDKVLLTTNAE 587

Query: 950 IDK 952
             K
Sbjct: 588 GLK 590



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 81/264 (30%), Gaps = 23/264 (8%)

Query: 474 QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
            +R    ++ + + +  +              + +  + + +     +            
Sbjct: 1   LFRNLFTKLTKDVYKYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 60

Query: 522 ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61  KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579 NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
             GLV +L     +      E    +    + +V  +     +      ++      +  
Sbjct: 117 ACGLVKNLALMCYITVGSPSEPIIEFMVQRNMEVLEEYEPTRSPNSTKVFVNGVWVGVHR 176

Query: 637 DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
           D +     V        I      I D  D   K          P F+ ++DS     G 
Sbjct: 177 DPAHLVSTVQSLRRRNMISPEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDSKSANKGG 236

Query: 695 NMQRQAVPLLKAEAPFVGTGMESV 718
            +  +       +   +   +E  
Sbjct: 237 LVLTKETVNKLEDDKELPADLEEE 260


>gi|83414637|dbj|BAE54109.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 172

 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/112 (57%), Positives = 82/112 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+  
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWE 166



 Score = 55.1 bits (131), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEESLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|38229278|ref|NP_938371.1| 116R [Yaba monkey tumor virus]
 gi|38000549|gb|AAR07472.1| 116R [Yaba monkey tumor virus]
          Length = 1164

 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 77/431 (17%), Positives = 142/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDV--RDTSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V     S +  +   G ++  +  +R G
Sbjct: 711  DNGIHLIYPERPIVLSKALETSKIAVNCFGQHVMIALMSYKGMNQEDGIIIKKQFVDRGG 770

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 771  LDI-------------ITAKKHQVEIPLENFNNKERVKSTSYSKLDSNGLVKLNAFLENG 817

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y++    ++    +K++          
Sbjct: 818  DAIARNISSKTLEDDFVNDNQISFDISERYTDMYKSRVERVQVDLTDKVK---------- 867

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    D+P+  +G   D+++N   + 
Sbjct: 868  -----VRVLTMKERKPILGDKFTSRTSQKGTVAFIADEADLPYDDNGIKPDVIINSTSIF 922

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A         ++ + +         I     F +K   +      
Sbjct: 923  SRKTLSMLVEVILTSAYASKPYNNNEQNRPICFPSSNETSIDTYLEFAKKCYKSVYANLN 982

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
             ++ DD                                            ILYD  T  P
Sbjct: 983  ENEIDDKVFCEK--------------------------------------ILYDPETDVP 1004

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1005 YKSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1064

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1065 HGAANTITEIL 1075



 Score = 59.7 bits (143), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 82/584 (14%), Positives = 178/584 (30%), Gaps = 47/584 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y     +        ++  ++ + +   D+ T+     + +  +            + +
Sbjct: 253 SYDMPNEIIYLVNSLIESTKELIKGISDFDLDTYIN--DLVSSEYTKQKSQLQYDEFKYE 310

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         +    ++   +I++++  +          D D++   RV + G+  +   
Sbjct: 311 MINNFLPHMYNSPNQLKGFYVISLLRKFIYCIYFTYRYPDRDSMVCHRVLTYGKYFEILA 370

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +IK  + +   +       I+           F      + ++   S    
Sbjct: 371 HDELENYIGNIKTDMINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 429

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
            H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 430 PHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 489

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E    K        D+ Y      +  EN  IA  N     D  
Sbjct: 490 VLTSITNICTNEYLDLEKKIYKYIKSFSYEDISYFKTGYYITLENSLIASLNPEKVYDFV 549

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                         + V    +       +  +     + PFL  DD   V+     + +
Sbjct: 550 NDFRRKKRMGFFGNLEVGITLVQDHMNEIRINIGGGRLIRPFLVIDDGELVMDTVVERLK 609

Query: 700 AVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV 759
                   +  +      V          +     V++  ++    R      D  +   
Sbjct: 610 EKIEDFTFSDILKEFPNVVEMVDIEQFTFSNVCESVQKFKSLSKTERFKYHLCDFPSEFR 669

Query: 760 DIYRLMKFQRSNQN----------------TCVNQRPLVKVGD-----EVRRNDIIADGP 798
           D Y        N N                +C++     K+ +        R  +++   
Sbjct: 670 DGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVLSKAL 729

Query: 799 STDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            T    +   G+++++A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 730 ETSKIAVNCFGQHVMIALMSYKGMNQEDGIIIKKQFVDRGGLDIITAKKHQVEI------ 783

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           P E   +   V       +D  G++ + A +  GD +   I+ K
Sbjct: 784 PLENFNNKERVKSTSYSKLDSNGLVKLNAFLENGDAIARNISSK 827


>gi|281324443|gb|ADA60287.1| RNA polymerase beta subunit [Helicobacter pullorum NCTC 12824]
          Length = 237

 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 123/233 (52%), Positives = 173/233 (74%), Gaps = 2/233 (0%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVV 510
           IDD D+LGNRR+R++GE+L N+  LGL++M+++I++++S++    + +MP DLIN+K + 
Sbjct: 1   IDDRDHLGNRRIRAIGELLANELHLGLVKMQKAIRDKLSTISSGLEELMPHDLINSKMIT 60

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
             + EFF   QLSQ  +  N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRIC
Sbjct: 61  GTILEFFTGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRIC 120

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL+++L+++A+VN  GFIE PYRKV D KVT+++VYL+A +EE   IA A
Sbjct: 121 PIETPEGQNIGLINTLSTYAKVNELGFIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPA 180

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           ++ L  D    E+++  R  GE IL+   K++ ID SP+ VV +AASLIPFLE
Sbjct: 181 STVLTNDNVIKEDIIEVRKDGEIILMESSKVELIDLSPRMVVGVAASLIPFLE 233


>gi|168809720|gb|ACA29579.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 186

 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/199 (37%), Positives = 104/199 (52%), Gaps = 18/199 (9%)

Query: 965  ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQF 1024
            E   +D  DE  I+      +  +IL G+    G K       L   +  +  R      
Sbjct: 6    EEPLKDL-DETGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSR------ 58

Query: 1025 AVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPI 1084
                 +V+     +    +     +      KI     GD++  GV  +V+V++A KR I
Sbjct: 59   -----EVRDTSLRVPHGGDGVVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKI 107

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            + GDKMAGRHGNKG+VSR++P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A
Sbjct: 108  KVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMA 167

Query: 1145 CVGLGKKIKSLINDYKANG 1163
               LG  I + + D   + 
Sbjct: 168  ARNLGIHIATPVFDGATSE 186



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 56/87 (64%), Positives = 67/87 (77%)

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
           IPNV EE LK++DE GII +GAEV  GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +V
Sbjct: 1   IPNVGEEPLKDLDETGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREV 60

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID 951
           RDTSLRVP G  G V DV+IF R   D
Sbjct: 61  RDTSLRVPHGGDGVVRDVKIFTRANGD 87


>gi|83414471|dbj|BAE54026.1| RNA polymerase beta subunit [Streptococcus oralis]
 gi|193873316|gb|ACF23348.1| RpoB [Streptococcus oralis]
          Length = 172

 Score =  194 bits (493), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/175 (40%), Positives = 95/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S         F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEEGLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEEGLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.8 bits (94), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|83414419|dbj|BAE54000.1| RNA polymerase beta subunit [Streptococcus australis]
          Length = 172

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/168 (42%), Positives = 96/168 (57%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|83414431|dbj|BAE54006.1| RNA polymerase beta subunit [Streptococcus peroris]
          Length = 172

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P +DMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVQDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARTLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 40.4 bits (93), Expect = 1.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 29/85 (34%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRIVPVQDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARTL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   ++ A 
Sbjct: 148  GIHIATPVFDGASSEDLWDTVKEAG 172


>gi|196122267|gb|ACG69790.1| RNA polymerase beta subunit [Capsicum frutescens]
          Length = 147

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/185 (37%), Positives = 95/185 (51%), Gaps = 39/185 (21%)

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            I+S+ILP +DMP+L+DG  VD+V NPLGVPSRMNVGQIFE  LG A   L +  +    D
Sbjct: 2    IISKILPRQDMPYLQDGRSVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFD 61

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
             +   + S    F E    +   +                           VF+      
Sbjct: 62   ERYEQEASRKLVFSELYEASKQTSNPW------------------------VFE------ 91

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
                      +  G+S ++DG TG PF++PV +G  Y+LKL H V DK++ RS+G Y+LV
Sbjct: 92   ---------PEYPGKSRIFDGRTGNPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALV 142

Query: 1279 TQQPL 1283
            TQQPL
Sbjct: 143  TQQPL 147


>gi|40643905|emb|CAD89691.1| RNA polymerase II, second largest subunit [Escallonia sp. Oxelman
            2340]
          Length = 508

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 72/474 (15%), Positives = 131/474 (27%), Gaps = 91/474 (19%)

Query: 798  PSTDLGDLALGRNMLVAFM-PWHGYNFEDSMLI--SERMVSEDVFTSIHIEEFEVMARDT 854
              T    ++   N   A+   +       S+++     ++            ++      
Sbjct: 101  SMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 160

Query: 855  KLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
             +G                       +  V        +    +       +      + 
Sbjct: 161  AMGIYVTNFQFRM-----------DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIV 209

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S V        +F R   D+ ++  ++ +E      R     
Sbjct: 210  AIACYSGYNQEDSVIMNQSSVDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 268

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
                  +          G           K+T ++                  D+   + 
Sbjct: 269  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ-----------------DDAQGQA 311

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
                K  + TS    E    +++      D +     R VKV V   R  Q GDK + RH
Sbjct: 312  SRYSKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRH 366

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 367  GQKGTVGMTYTQEDMPWTAEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 426

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                     +IS         +                                      
Sbjct: 427  TPFTDVTVDNISKALHKCGYQMRGFETM-------------------------------- 454

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                            +G +    G         + +G  Y  +L HMV DK++
Sbjct: 455  ---------------YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDDKIH 486



 Score =  110 bits (274), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 71/408 (17%), Positives = 115/408 (28%), Gaps = 94/408 (23%)

Query: 540 RLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS--SLTSFARVNAYGF 597
           R S L    V        +RD+                    +     L   A + A   
Sbjct: 10  RRSVLESPLVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVNKQRLLIKKADIQALQQ 69

Query: 598 IETPYRK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
            ETP      D      + Y+   EEE   I+              +LV  R   E    
Sbjct: 70  RETPEDGGWHDLVAKGYIEYIDTEEEETTMISM----------TINDLVSARLNPE--EA 117

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
             E     +  P  ++ + AS+IPF +++ S R      M +QA+ +      F      
Sbjct: 118 YSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNFQF------ 171

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                         R   +  V                                      
Sbjct: 172 --------------RMDTLAYV-----------------------------------LYY 182

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PLV                      L  G N +VA   + GYN EDS+++++  V  
Sbjct: 183 PQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSVDR 232

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPG 891
             F S+    +    +      +E        +   +       +D+ G+   G  V+  
Sbjct: 233 GFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGE 292

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           D+++GK TP  +           A         RD S  +    +G V
Sbjct: 293 DVIIGKTTPIAQDD---------AQGQASRYSKRDHSTSLRHSETGMV 331


>gi|83414425|dbj|BAE54003.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
 gi|83414601|dbj|BAE54091.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
 gi|83414603|dbj|BAE54092.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
 gi|83414605|dbj|BAE54093.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
 gi|83414607|dbj|BAE54094.1| RNA polymerase beta subunit [Streptococcus cristatus]
 gi|83414611|dbj|BAE54096.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
 gi|83414613|dbj|BAE54097.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
          Length = 172

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|67582937|ref|XP_664954.1| DNA-directed RNA polymerase, beta subunit [Cryptosporidium hominis
            TU502]
 gi|54655176|gb|EAL34724.1| DNA-directed RNA polymerase, beta subunit [Cryptosporidium hominis]
          Length = 344

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 65/395 (16%), Positives = 115/395 (29%), Gaps = 69/395 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +             I       +   +    A+      D+ D  +   + V   
Sbjct: 18   DSVLYLLVYPQKPLCKTRTIEMINFEQLPAGQNSSVAVMSFAGYDIEDAIVMNKASVDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +  R          ++E +++     ++    +                   +  
Sbjct: 78   FARCFVMKR---------QTIELQKLPNGLSERVVRPISGALGNTGNRRFSFKNDGILDN 128

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                     +S D I     S         +  Q ++      Y+ S    +    + I+
Sbjct: 129  DGVCNVGVQVSEDDIIVNKMSPINTREYVGDPSQFDLSE----YKPSPVKYKGPTSSYID 184

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++           ++ KV     R  + GDK + RHG KG+V  I+  ED+PF + G   
Sbjct: 185  RVIL--TENADGNQIYKVITRQTRRPELGDKFSSRHGQKGVVGLIISQEDLPFSETGWCP 242

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM VG++ E     A V  G              + +            
Sbjct: 243  DLIMNPHGFPSRMTVGKLLELISSKASVLDGNYRYGTAFGGTPLEESAKCLVEHGFHYSG 302

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
              +                                                 SG +    
Sbjct: 303  KEYL-----------------------------------------------TSGTT---- 311

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
               GE  +  + VG IY  KL HMV DK++AR  G
Sbjct: 312  ---GEAIEAYIFVGPIYYQKLKHMVLDKMHARRKG 343


>gi|89888212|gb|ABD78649.1| DNA-directed RNA polymerase beta subunit [Bordetella hinzii]
          Length = 280

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 100/280 (35%), Positives = 164/280 (58%), Gaps = 3/280 (1%)

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             E IL+ F+    +  + +             G      + D  +G+ ++E  K++ + 
Sbjct: 1   TPESILAHFFDFDNFELKSEGAMMEFVPE-RWKGEMARFDISD-RSGKVIVEKDKRINAK 58

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            L+ L   G++ + +  + L G  +A+++V+ +TGE+   A D I E  L  +  +++ D
Sbjct: 59  HLRDLANGGIQRISVPEEFLYGRVLAKNVVDADTGEVIAHANDEITESVLAAMRAAKVLD 118

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           +  LY + ++   YI  TL TD+  D+  A + IYR+MRPG+  T    E++F  LF+  
Sbjct: 119 LQTLYTNDLDRGPYISQTLRTDETADQTAARVAIYRMMRPGEPPTEEAVEALFQRLFYSE 178

Query: 404 DKYDLSTVGRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           + YDLS VGR+K+N RL   D  +    +  EDI+  IK+LV+LRNG+G IDDID+LGNR
Sbjct: 179 ETYDLSRVGRMKVNSRLGRGDDANGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNR 238

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQD 502
           RVR VGE+ +NQ+R GL+R+ER++KER+   + +++MP D
Sbjct: 239 RVRCVGELAENQFRAGLVRVERAVKERLGQAETENLMPHD 278


>gi|312458557|gb|ADQ89212.1| DNA-directed RNA polymerase beta subunit [Corynebacterium
            diphtheriae]
          Length = 141

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 62/169 (36%), Positives = 90/169 (53%), Gaps = 36/169 (21%)

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLGW     G KI +     +   +   L++  E +                 
Sbjct: 1    IGQVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP------------- 41

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEP 1244
                     +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP
Sbjct: 42   ---------AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSGEP 92

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            F  PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   FPYPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 141


>gi|119644218|gb|ABL85613.1| RNA polymerase II second largest subunit [Rinodina tephraspis]
          Length = 718

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 65/388 (16%), Positives = 111/388 (28%), Gaps = 81/388 (20%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 409  HILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-R 467

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R   D+ +R   +    +E   +    + + L    Y +L E   I+ G       
Sbjct: 468  SLFYRSYTDQEKR---IGANVLEQFEKPMRADTLKLKHGTYDKLDEDGIIIPGARVSGED 524

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  ++ D      R++          ++     L  Q                  
Sbjct: 525  IIIGKTAPIAPDAEEMGQRTKLHTKRDASTPLRSTESGLVDQVLL--------------- 569

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 570  -----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPD 624

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +  +          +S L    E    + 
Sbjct: 625  LIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSRLLR--EHGYQSR 682

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                               +G +    G
Sbjct: 683  GFEVM---------------------------------------------YNGHT----G 693

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                     V +G  Y  +L HMV DK+
Sbjct: 694  R---KLVAQVFLGPTYYQRLRHMVDDKI 718



 Score = 93.2 bits (230), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 79/606 (13%), Positives = 154/606 (25%), Gaps = 68/606 (11%)

Query: 345 PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSD 404
           P+L          +   +        ++    I  +       T  +  S+    + +  
Sbjct: 16  PLLAGLFRTLFNKLTKDVEKYLKMCIENNKEFILTLGVKSSTLTNGLKYSLATGNWGEQK 75

Query: 405 KYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           K   S  G  ++  R    +      R          I     L N    +         
Sbjct: 76  KAASSKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEG 135

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKE---RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +   + + L     + +      I     +     ++   P    NA  +      F   
Sbjct: 136 QACGLVKNLALMCHISVGTPSDGIVPFLLQRQMESLEEYEPHTSPNATKI------FVNG 189

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
             +       + ++ +   RR   L             +RD+    +  +          
Sbjct: 190 VWVGVHRNPAHLVNAVQTLRRKHVLEPEVSL-------IRDIRDREFRILTDQGRVLRPL 242

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVC-DGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             + + + S    N        + KV  +    +D+V     +E    +    + L  +G
Sbjct: 243 FVVDNGVKSPNCGNL------VFNKVHSNRLDADDLVPYDMDKEVRENMIFGWNGLINEG 296

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                 ++++DA  ++ V I  +                     
Sbjct: 297 ---------------------VVEYVDAEEEETVMIVMTRANXXXXXXXXXXXXXXXXXX 335

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                                                                   +   
Sbjct: 336 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGKQAMGV 395

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                  + +  +      Q+PL                      +L  G+N +VA   +
Sbjct: 396 FLTNYEQRMETMSHILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACY 445

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +   +F S+    +    +       E        D   +     
Sbjct: 446 SGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGANVLEQFEKPMRADTLKLKHGTY 505

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +DE GII  GA V+  DI++GK  P        EE   R     K    RD S  + S
Sbjct: 506 DKLDEDGIIIPGARVSGEDIIIGKTAPIA---PDAEEMGQRT----KLHTKRDASTPLRS 558

Query: 934 GVSGTV 939
             SG V
Sbjct: 559 TESGLV 564



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 89/262 (33%), Gaps = 22/262 (8%)

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVS 511
           DD D+ G +R+   G +L   +R    ++ + +    ++   +    +    + +  + +
Sbjct: 1   DDRDHFGKKRLDLAGPLLAGLFRTLFNKLTKDVEKYLKMCIENNKEFILTLGVKSSTLTN 60

Query: 512 AVCEFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
            +     +               +SQ+       S ++H RR +      + R     + 
Sbjct: 61  GLKYSLATGNWGEQKKAASSKAGVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKP 116

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE--TPYRKVCDGKVTNDVVY 616
           R +H TH+G +CPAET EG   GLV +L     ++     +   P+      +   +   
Sbjct: 117 RQLHNTHWGLVCPAETPEGQACGLVKNLALMCHISVGTPSDGIVPFLLQRQMESLEEYEP 176

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIA 675
            ++      ++      +  + +     V        +      I D  D   + +    
Sbjct: 177 HTSPNATKIFVNGVWVGVHRNPAHLVNAVQTLRRKHVLEPEVSLIRDIRDREFRILTDQG 236

Query: 676 ASLIPFLENDDSNRVLMGCNMQ 697
             L P    D+  +     N+ 
Sbjct: 237 RVLRPLFVVDNGVKSPNCGNLV 258


>gi|83414635|dbj|BAE54108.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414655|dbj|BAE54118.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|83414659|dbj|BAE54120.1| RNA polymerase beta subunit [Streptococcus intermedius]
 gi|219564707|dbj|BAH03890.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 172

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/110 (58%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  +  D+
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASADDL 164



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|294886741|ref|XP_002771830.1| DNA-directed RNA polymerase II subunit, putative [Perkinsus marinus
            ATCC 50983]
 gi|239875630|gb|EER03646.1| DNA-directed RNA polymerase II subunit, putative [Perkinsus marinus
            ATCC 50983]
          Length = 196

 Score =  194 bits (492), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 45/165 (27%), Positives = 75/165 (45%), Gaps = 15/165 (9%)

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG 1273
                 I + L        G+ ++Y+G TG      + +G  Y  +L HMV DK+++R+ G
Sbjct: 27   VTVHEIMARLHELGFQRQGREVMYNGHTGLRLPAKIFIGPTYYQRLKHMVEDKIHSRARG 86

Query: 1274 SYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD-------DVVGRT 1326
               ++T+QP+ G+   GG R GEME  C+ ++GAA  L+E L   SD       D  G  
Sbjct: 87   PMQMLTRQPMEGRGREGGLRFGEMERDCMISHGAAKFLKERLFDISDAYRVHVCDNCGMF 146

Query: 1327 RV-------YESIV-AGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
             +       YE      +   +   P +  +L +E+  + +   L
Sbjct: 147  AIANLYKNHYECRACKNSTISQVHIPYACKLLFQELMTMSIMPKL 191


>gi|256014680|gb|ACU56888.1| RNA polymerase beta subunit [Mycobacterium salmoniphilum]
          Length = 180

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/184 (38%), Positives = 94/184 (51%), Gaps = 33/184 (17%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DG
Sbjct: 27   RVFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDG 86

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LN  GVP RMN+GQI ETHLGW     G  I+      +               
Sbjct: 87   TPVDVILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN-------------- 131

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                             +    +   +    +TPVFDGA EE +  +L     +  G  +
Sbjct: 132  -----------------LPEDLQSAPADTRTATPVFDGAREEELTGLLSSTLPNRDG-EV 173

Query: 1236 LYDG 1239
            + DG
Sbjct: 174  MVDG 177


>gi|269978620|gb|ACZ55996.1| RNA polymerase II [Fusarium kyushuense]
 gi|269978629|gb|ACZ56002.1| RNA polymerase II [Fusarium poae]
 gi|269978632|gb|ACZ56004.1| RNA polymerase II [Gibberella pulicaris]
 gi|269978641|gb|ACZ56010.1| RNA polymerase II [Fusarium venenatum]
          Length = 312

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 66/197 (33%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   L   EI           +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P  +       +        +    RD S  + S  
Sbjct: 111 LDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTE 163

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 164 NGIVDQVILTVNADNVK 180


>gi|83414617|dbj|BAE54099.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414621|dbj|BAE54101.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414623|dbj|BAE54102.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414625|dbj|BAE54103.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414627|dbj|BAE54104.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414629|dbj|BAE54105.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414631|dbj|BAE54106.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414639|dbj|BAE54110.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414641|dbj|BAE54111.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414643|dbj|BAE54112.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414645|dbj|BAE54113.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 172

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/112 (57%), Positives = 82/112 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+  
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDLWE 166



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|40644039|emb|CAD92460.1| RNA polymerase II [Escallonia sp. Oxelman 2340]
          Length = 543

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 76/488 (15%), Positives = 134/488 (27%), Gaps = 84/488 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 136  HDLVAKGYIEYIDTEEEETTMISMTINDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 195

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 196  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNFQFRM---DTLAYVLYYPQKPLVTTRAMEH 252

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S V        +F R   D+ ++  ++ 
Sbjct: 253  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSVDRGFF-RSLFFRSYRDEEKKMGTLV 311

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T ++           
Sbjct: 312  KEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---------- 361

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   D+   +     K  + TS    E    +++      D +     R VKV V  
Sbjct: 362  -------DDAQGQASRYSKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRS 409

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 410  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTAEGITPDIIVNPHAIPSRMTIGQLIECI 469

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+  +         +IS         +                        
Sbjct: 470  MGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------------ 511

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                          +G +    G         + +G  Y  +L 
Sbjct: 512  -----------------------------YNGHT----GR---RLTAMIFLGPTYYQRLK 535

Query: 1261 HMVSDKVY 1268
            HMV DK++
Sbjct: 536  HMVDDKIH 543



 Score =  107 bits (267), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 77/476 (16%), Positives = 138/476 (28%), Gaps = 97/476 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++       + I+   +  A   F     +    +  
Sbjct: 4   LVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPPATKIFVNGCWVGIHRDPD 63

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + GV R     E+R    T YGR             L+     
Sbjct: 64  MLVRTLRKLRRRXDVNTEVGVVRDIRLKELR--IYTDYGRCSRPLFIVNKQRLLIKKADI 121

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A        +       D      + Y+   EEE   I+              +LV  R
Sbjct: 122 QALQQRETPEDGG---WHDLVAKGYIEYIDTEEEETTMISM----------TINDLVSAR 168

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E      E     +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 169 LNPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNF 226

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            F                    R   +  V                              
Sbjct: 227 QF--------------------RMDTLAYV------------------------------ 236

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PLV                      L  G N +VA   + GYN EDS++
Sbjct: 237 -----LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVI 281

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++  V    F S+    +    +      +E        +   +       +D+ G+  
Sbjct: 282 MNQSSVDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAP 341

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  D+++GK TP  +           A         RD S  +    +G V
Sbjct: 342 PGTRVSGEDVIIGKTTPIAQDD---------AQGQASRYSKRDHSTSLRHSETGMV 388


>gi|56694344|gb|AAW22912.1| RNA polymerase II second largest subunit [Torreya californica]
          Length = 514

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 73/435 (16%), Positives = 127/435 (29%), Gaps = 80/435 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 160  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 216

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI         D+ +   S +        +
Sbjct: 217  LYYPQKPLVTTRAMEHLHFRQLPAGIXAIVAIACYSGYXQEDSVIMNQSSIDRGFF-RSL 275

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 276  FFRSYRDEEKRMGTLVKEEFGRPNRENTXGMRHGSYDKLDDDGLAPPGTRVSGXDVIIGK 335

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  DE   +  +  K    TS    E    +++      D
Sbjct: 336  TTPIAQ-----------------DESGGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 378

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 379  GL-----RFVKVRMRSVRIPQIGDKFSXRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 433

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +G + E  +G     +GK+                                 
Sbjct: 434  HAIPSRMTIGXLIECIMGKVAAHMGKEGD------------------------------- 462

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                  +TP F     ++I+  L        G   +Y+G TG  
Sbjct: 463  ----------------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRK 499

Query: 1245 FDRPVTVGYIYMLKL 1259
                + +G  Y  +L
Sbjct: 500  LSAMIFLGPTYYQRL 514



 Score =  109 bits (271), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 65/437 (14%), Positives = 122/437 (27%), Gaps = 100/437 (22%)

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEMRDVHPTHYG 567
           + ++   F     +    +    +  +   RR   +    GV R     E+R ++  +  
Sbjct: 26  IPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRDIRLRELR-LYTDYGR 84

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              P    E   + +       A +N             +      + Y+   EEE   I
Sbjct: 85  CSRPLFVVENQRLKIKK-----ADINNLQASRED--GWHELVTQGFIEYVDTEEEETTMI 137

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           +              +LV  R   E            +  P  ++ + AS+IPF +++ S
Sbjct: 138 SM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLILGVCASIIPFPDHNQS 185

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            R      M +QA+ +                           R   +  V         
Sbjct: 186 PRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV--------- 216

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
                                         Q+PLV                      L  
Sbjct: 217 --------------------------LYYPQKPLV----------TTRAMEHLHFRQLPA 240

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----IT 862
           G   +VA   + GY  EDS+++++  +    F S+    +    +      +E       
Sbjct: 241 GIXAIVAIACYSGYXQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKRMGTLVKEEFGRPNR 300

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +   +       +D+ G+   G  V+  D+++GK TP  +           +       
Sbjct: 301 ENTXGMRHGSYDKLDDDGLAPPGTRVSGXDVIIGKTTPIAQDE---------SGGQVSKY 351

Query: 923 DVRDTSLRVPSGVSGTV 939
             RD S  +    SG V
Sbjct: 352 TKRDQSTSLRHSESGMV 368


>gi|83414633|dbj|BAE54107.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 172

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 63/110 (57%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  +  ++
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASADNL 164



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|83414435|dbj|BAE54008.1| RNA polymerase beta subunit [Streptococcus constellatus subsp.
            pharyngis]
 gi|83414647|dbj|BAE54114.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414649|dbj|BAE54115.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414651|dbj|BAE54116.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414653|dbj|BAE54117.1| RNA polymerase beta subunit [Streptococcus anginosus]
 gi|83414661|dbj|BAE54121.1| RNA polymerase beta subunit [Streptococcus constellatus]
          Length = 172

 Score =  193 bits (491), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/110 (58%), Positives = 82/110 (74%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDL 164



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|83414615|dbj|BAE54098.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
          Length = 172

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/175 (40%), Positives = 96/175 (54%), Gaps = 6/175 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHITTPVFDGASSEDLWDTVKEA 171



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|117675887|emb|CAL69214.1| RNA polymerase subunit B [Rathayibacter iranicus]
          Length = 347

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 192/318 (60%), Gaps = 33/318 (10%)

Query: 295 FLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNN 354
              I      G+ +        T  ++++A  +  E+ LE+   +    I +        
Sbjct: 48  EFEIDKRDQVGVRIDRKRKQSVT--VFLKALGLTSEEILEQF--AGYESIEL-------- 95

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
                 TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR 
Sbjct: 96  ------TLEKDNILTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRY 149

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNL 459
           K+N +L +D       +  EDIIA IK LV L +G+                 +DDID+ 
Sbjct: 150 KINRKLGIDKALSDSVLTVEDIIATIKYLVALHDGRTTLPGVRDGGAVDLRLDVDDIDHF 209

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 210 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 269

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 270 SQLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPN 329

Query: 580 IGLVSSLTSFARVNAYGF 597
           IGL+ SL SFAR+N +GF
Sbjct: 330 IGLIGSLASFARINPFGF 347



 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 6/161 (3%)

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I G +R+VVSQL RSPG++F+  + +   S K +Y+ R+IP +G W++ E D +D + 
Sbjct: 1   FIINGTERVVVSQLVRSPGVYFERQQEKT--SDKDIYSARVIPSRGAWLEFEIDKRDQVG 58

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVS 261
           VRIDR+RK  VT FL ALG+ SEEIL  F  Y  I  +   D       A   +      
Sbjct: 59  VRIDRKRKQSVTVFLKALGLTSEEILEQFAGYESIELTLEKDNILTKEDALRDIYRKLRP 118

Query: 262 SSLVDIDTGEQVIESGKKLTSG--LLKSLKEKGVKFLGITS 300
              V  +    ++++    +    L K  + K  + LGI  
Sbjct: 119 GEQVAAEAARALLDNFYFNSKRYDLAKVGRYKINRKLGIDK 159


>gi|92090856|gb|ABE73204.1| RNA polymerase II second largest subunit [Resinicium bicolor]
          Length = 551

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 70/376 (18%), Positives = 111/376 (29%), Gaps = 75/376 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 251  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 310

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  +D  ++S   + E+ E   R+          +       I  G N    
Sbjct: 311  LF-RSMYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGTNVRGE 369

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     K    T     E    +++ 
Sbjct: 370  DIIIGKTAPIPPD---------------SEELGQRTRTHTKRDVSTPLKSTESGIVDQVL 414

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D       + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 415  ITTNHD-----GQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 469

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIV+NP  +PSRM +G + E  L      +G +                           
Sbjct: 470  DIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 504

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++  LR       G  I+Y 
Sbjct: 505  ----------------------------ATP-FTDLTVESVSKFLRQRGYQSRGLEIMYH 535

Query: 1239 GLTGEPFDRPVTVGYI 1254
            G TG      V +G  
Sbjct: 536  GHTGRKLQAQVYLGPT 551



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 51/327 (15%), Positives = 98/327 (29%), Gaps = 26/327 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
                 G   ++        E + V    I+++DA  ++ V I   + P    +   +  
Sbjct: 117 IRWLNQGHRDDDPDKAPYKWESL-VKGGVIEYLDAEEEETVMIC--MTPEDLENSRLQAQ 173

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                         A    V         +   + I+                       
Sbjct: 174 GIDPHAHDGDFDPAARLKAVQNAHSFTHCEIHPSMILGXXXXXXXXXXXXXXXXXXXXXX 233

Query: 752 LDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
                 G+      ++           Q+PL                      +L  G+N
Sbjct: 234 XXKQAMGIYLTNFQVRMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQN 283

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----I 865
            +VA + + GYN EDS+++++  +   +F S++   +  + + + +   E          
Sbjct: 284 AIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYMDLEKKSGVQQLEEFEKPTRETT 343

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       I++ G+I  G  V   DI++GK  P         ++        +    R
Sbjct: 344 LRMKHGTYDKIEDDGLIAPGTNVRGEDIIIGKTAPIPPDSEELGQRT-------RTHTKR 396

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           D S  + S  SG V  V I   H   K
Sbjct: 397 DVSTPLKSTESGIVDQVLITTNHDGQK 423



 Score = 42.0 bits (97), Expect = 0.74,   Method: Composition-based stats.
 Identities = 34/288 (11%), Positives = 61/288 (21%), Gaps = 25/288 (8%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA   V     F     +    +  N +  +   RR   +            +   ++ 
Sbjct: 34  ENAHSTVPLTKVFVNGIWMGVHRDPGNLVRTLKKLRRKDDVSSEVSIVRDIREKELRLYT 93

Query: 564 THYGRICPAETSEGH-NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
                  P    E          +    + +     +    K         + YL A EE
Sbjct: 94  DAGRVCRPLFIVEDQQLALQKKHIRWLNQGHRDDDPDKAPYKWESLVKGGVIEYLDAEEE 153

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIA 675
           E   I      L+      + +      G+     R             +  P  ++   
Sbjct: 154 ETVMICMTPEDLENSRLQAQGIDPHAHDGDFDPAARLKAVQNAHSFTHCEIHPSMILGXX 213

Query: 676 ASLIPFLEN----------------DDSNRVLMGCNMQRQAVPLLKAEAPFVGT-GMESV 718
                                               M   A  L   + P   T  ME +
Sbjct: 214 XXXXXXXXXXXXXXXXXXXXXXKQAMGIYLTNFQVRMDTMANILYYPQKPLATTRSMEYL 273

Query: 719 VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
             +   A   A  A +          +   +  +D        YR   
Sbjct: 274 KFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYM 321


>gi|269978608|gb|ACZ55988.1| RNA polymerase II [Fusarium camptoceras]
 gi|269978617|gb|ACZ55994.1| RNA polymerase II [Fusarium equiseti]
 gi|269978623|gb|ACZ55998.1| RNA polymerase II [Fusarium longipes]
 gi|269978626|gb|ACZ56000.1| RNA polymerase II [Fusarium incarnatum]
 gi|269978635|gb|ACZ56006.1| RNA polymerase II [Fusarium sp. FRC R-06979]
          Length = 312

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 67/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   L   EI           +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P  +       +        ++   RD S  + S  
Sbjct: 111 LDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTE 163

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 164 NGIVDQVILTVNADNVK 180


>gi|42794991|gb|AAS45851.1| RpoB [Morganella morganii]
          Length = 178

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 108/178 (60%), Positives = 136/178 (76%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL+ +A+ N YGF+ETPYR V D  VT+++ YLSA+EE N  IAQAN+ LD+
Sbjct: 61  GPNIGLINSLSVYAQTNEYGFLETPYRLVRDDVVTDEIHYLSAIEEGNFIIAQANTVLDD 120

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DG F +EL+ CR  GE  L  R+++ ++D S +QVVS+ ASLIPFLE+DD+NR LMG 
Sbjct: 121 DGHFVDELITCRNKGESSLFSRDQVQYMDVSTQQVVSVGASLIPFLEHDDANRALMGA 178


>gi|83414593|dbj|BAE54087.1| RNA polymerase beta subunit [Streptococcus australis]
          Length = 172

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/181 (39%), Positives = 101/181 (55%), Gaps = 17/181 (9%)

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +  +IL G+    G K       L   ++ +  R           +V+     +    + 
Sbjct: 1    KEGDILVGKVTPKGEKDLSAEERLLHAILGDKSR-----------EVRDTSLRVPHGGDG 49

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                +      KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+
Sbjct: 50   VVRDV------KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIV 103

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
            P EDMP+L DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D
Sbjct: 104  PVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSED 163

Query: 1165 I 1165
            +
Sbjct: 164  L 164



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AI G+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAILGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|83414437|dbj|BAE54009.1| RNA polymerase beta subunit [Streptococcus lutetiensis]
 gi|83414667|dbj|BAE54124.1| RNA polymerase beta subunit [Streptococcus lutetiensis]
 gi|83414669|dbj|BAE54125.1| RNA polymerase beta subunit [Streptococcus lutetiensis]
          Length = 172

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 70/168 (41%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D   + D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGATSEDL 164



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63



 Score = 39.3 bits (90), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 28/85 (32%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K          +    P  + ++ ++       +++      +         
Sbjct: 88   KMAGRHGNKGVVSRVVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNL 147

Query: 1203 GVPVSTPVFDGADEEAINSMLRMAD 1227
            G+ ++TPVFDGA  E +   +  A 
Sbjct: 148  GIHIATPVFDGATSEDLWDTVNEAG 172


>gi|162605772|ref|XP_001713401.1| DNA-directed RNA polymerase I 135K chain [Guillardia theta]
 gi|13794333|gb|AAK39710.1|AF083031_67 DNA-directed RNA polymerase I 135K chain [Guillardia theta]
          Length = 1109

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 68/256 (26%), Positives = 100/256 (39%), Gaps = 61/256 (23%)

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            V + +  KR    GDK A RHG KGI+S     E++PF + G   DI+ NP G PSRM +
Sbjct: 851  VMIRLKSKRKPIEGDKFASRHGQKGILSFKYEVENLPFSETGIIPDILFNPHGFPSRMTI 910

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            G + E+  G +    G    S       N + S +     +  G   + +          
Sbjct: 911  GMVIESLSGKSGALNGNFNDSSPFTSFLNCNKSYIFGEFLRENGFEFYGK---------- 960

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
              +      G+P+ T VF                                       VG 
Sbjct: 961  -EMFYSGFVGLPLQTDVF---------------------------------------VGV 980

Query: 1254 IYMLKLNHMVSDKVY-----ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            I+  +L HM+ DK       AR+      +T+QP+ G+   G  RLGEME   +  +G  
Sbjct: 981  IHYQRLKHMILDKFQVSNNSARNH-----LTRQPIKGRKLGGSIRLGEMERDALLGHGCI 1035

Query: 1309 YVLQEMLTIKSDDVVG 1324
            ++L E    KS D+ G
Sbjct: 1036 FLLHEK-MQKSSDLHG 1050



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 83/729 (11%), Positives = 192/729 (26%), Gaps = 100/729 (13%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD- 87
           L+++   SY+  ++       R    +   FK      +F G   ++F       P +  
Sbjct: 12  LLKIHLNSYNQ-IISQGFYFLRQKYFITKNFKEYN---SFKGLTSIDF---YLSNPIYQF 64

Query: 88  --------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                           +TY     I++ +   + +     K            GD P+M 
Sbjct: 65  GTLIHKILPRQSKELKITYQGEFIISINIQNNEKNFNLVYKE-----------GDFPIMI 113

Query: 140 KD------------------------GTFVIKGIQRIVVSQLHRSPGI-----HFDHDKG 170
           K                         G F+  G ++     L R   +      F   K 
Sbjct: 114 KSLKCNLFGLKPHQLTEIDEEEFENGGYFITNGTEK-----LIRLIIVPRRNYIFTSSKI 168

Query: 171 RASLSGKLL--YACRIIP------DQGLWMDIEFDSKDIIHVRIDRRRK--VPVTSFLMA 220
             +L GK    +AC I         +   +    +   I+   I R ++   PV   L A
Sbjct: 169 SNTLRGKNFSSFACSIRCVNRYGLSRTFHLHYLTNGS-ILCRFIIRNQEFFFPVVIILKA 227

Query: 221 L-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           +  +   EI       +  +         L +                  G+      KK
Sbjct: 228 IKDVSDTEIFKDITNNLHDNNMFKEVAIKLISDSYNYIKSNFRDNYLEYIGKLFKIFEKK 287

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
           +    L++ K             L    +   + N    +  +    +          + 
Sbjct: 288 IHLNNLETGKN------------LIENNLFIHVENDMNQKYLLLIYMIQKLIKSRMGLNL 335

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 I + + + +   I + L    + +     +D +  +    +    +   +F+  
Sbjct: 336 GENPDSIEFQEILLSGNLIGSILEKKLSANFDLIKIDEFMNIENSPIRKTKLIMKVFSNF 395

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNL 459
                      +    + + +N + P         +     + L   R+    I      
Sbjct: 396 SVGIRYL----ISSGNVPLIVNFEIPQTSGFNISIERNNYSRFLSFFRS----IHRGKYF 447

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
              +  S  +++ + +                   +       ++N    ++ +  F   
Sbjct: 448 TTLKTTSGRKLMPSNWGYLCPIHTPDGSLCGILNHLTISSITSVVNPIERINFLKYFKKH 507

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICP-AETSEGH 578
             +       N  S I    ++         +     ++R    + +G      E     
Sbjct: 508 KTIFDRLSFKNRTSIILLDGKIIGFSTEIFLKWFTD-KIRCEKVSDFGIFSNSIEIVCLK 566

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           N  +++          Y       R V      ++    ++  E +         L    
Sbjct: 567 NENILNLFELKI----YSSEARLLRPVRWNSFNSNFNKTNSKNESSFTYNFHTIELIGSL 622

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
             +   +      ++  +        +     + SI     PF + + S R +  C M +
Sbjct: 623 EQSYLNIHQSIFTKKGEI-CLLYTHYEIDNLNIFSIVPGCTPFFDMNQSPRNMYQCQMAK 681

Query: 699 QAVPLLKAE 707
           Q++ +    
Sbjct: 682 QSIGIPFHN 690


>gi|117675877|emb|CAL69209.1| RNA polymerase subunit B [Agrococcus jenensis]
          Length = 360

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/171 (37%), Positives = 89/171 (52%), Gaps = 13/171 (7%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W+
Sbjct: 1   GDFPLQTGKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D       
Sbjct: 59  EFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVTKED 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
           A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 ALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 161



 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 126/257 (49%), Positives = 173/257 (67%), Gaps = 16/257 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 104 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 163

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 164 QKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFSGIRSGKKADIRLATDDIDNFGN 223

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 224 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 283

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 284 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 343

Query: 582 LVSSLTSFARVNAYGFI 598
           L+ +L +FAR+N +GFI
Sbjct: 344 LIGALATFARINPFGFI 360


>gi|89142779|emb|CAJ57585.1| RNA polymerase subunit B [Microbacterium phyllosphaerae]
          Length = 355

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/171 (37%), Positives = 89/171 (52%), Gaps = 13/171 (7%)

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWM 192
           GD PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W+
Sbjct: 1   GDFPLQTGKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAWL 58

Query: 193 DIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLS 250
           + E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D       
Sbjct: 59  EFEIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVTKED 118

Query: 251 AADLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
           A   +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 ALRDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 161



 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 121/252 (48%), Positives = 168/252 (66%), Gaps = 16/252 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 104 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 163

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG----------------KGTIDDIDNLGN 461
            +L LD P     +  +DI+A IK LV L  G                +   DDIDN GN
Sbjct: 164 HKLGLDAPLTDSVLTVQDIVATIKYLVRLHAGTEETFPGIRSGKKAEIRIATDDIDNFGN 223

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 224 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 283

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NIG
Sbjct: 284 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPNIG 343

Query: 582 LVSSLTSFARVN 593
           L+ +L +FAR+ 
Sbjct: 344 LIGALATFARIT 355


>gi|40644651|emb|CAD90165.1| DNA-directed RNA polymerase II largest subunit [Mimulus guttatus]
          Length = 179

 Score =  193 bits (491), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 46/194 (23%), Positives = 69/194 (35%), Gaps = 54/194 (27%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VK+ +   R  Q GDK + RHG KG +      EDMP+  +G   DI++NP 
Sbjct: 40   TNADGLRFVKIRMRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWSIEGITPDIIVNPH 99

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 100  AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 127

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     ++I+  L        G   +Y+G TG   
Sbjct: 128  ---------------------ATP-FTDVTVDSISKALHKCGYQMRGFETMYNGHTGRQL 165

Query: 1246 DRPVTVGYIYMLKL 1259
               + +G  Y  +L
Sbjct: 166  TAMIFLGPTYYQRL 179


>gi|116326824|ref|YP_803361.1| RNA polymerase subunit [Trichoplusia ni ascovirus 2c]
 gi|102231832|gb|ABF70655.1| RNA polymerase subunit [Trichoplusia ni ascovirus 2c]
          Length = 1160

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 80/427 (18%), Positives = 136/427 (31%), Gaps = 106/427 (24%)

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
            + +I      +  G    +  +       + + +       +  +     + +  +   +
Sbjct: 792  EDSIIINKSALDRGMFNATQRREITVDLRIGTIVDDMCKPPEDLRIRANYDNIGEDGLPI 851

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGD------DMPPGVLRVVKVFVAMKRP-------IQ 1085
                      L  +        +  D          GV++ VK+  +  R        + 
Sbjct: 852  MGSIIKKGDALLGKVSTDRNTSRREDTSIIARMQDEGVVKSVKIDGSSVRIRLEVVLDVM 911

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
             GDK       KG    ILP  DMPF+ D G   DI++N   +PSRM V QI  +  G  
Sbjct: 912  IGDKFCSAMAQKGTCGMILPDIDMPFVADSGMIPDILVNVHSMPSRMTVNQIMASMAGKL 971

Query: 1145 CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGV 1204
                 + I         N  +                                       
Sbjct: 972  ACITARNIDGSPFQLDVNDVLF-------------------------------------- 993

Query: 1205 PVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
                          +   L     D+ G   + +GLTGE F  P+ +G +Y L+   +V 
Sbjct: 994  -------------DLCEQLAEVKYDKDGCETMCNGLTGEMFSCPIFIGVVYYLRPVQLVR 1040

Query: 1265 DKV----------YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE- 1313
             K+          +         +T+QPL G+++ GG R+GEME   +  +G+   LQE 
Sbjct: 1041 HKIFSSTTTTMRNH---------LTRQPLNGRAHEGGLRVGEMEKDDLLRHGSINFLQER 1091

Query: 1314 MLTIKSD--------------DVVGRTRVYESIV--AGNDTF--ETGTPESFNVLVKEMQ 1355
            MLT+ SD               V  R+    S V              P +  +  + +Q
Sbjct: 1092 MLTL-SDKHIMMICTICGSESHVALRSD--GSFVCLRCKQLMVNPITIPYAAKLFFQYLQ 1148

Query: 1356 ALGLSID 1362
             +GL + 
Sbjct: 1149 GVGLGVK 1155



 Score = 44.3 bits (103), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/155 (13%), Positives = 44/155 (28%), Gaps = 58/155 (37%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF------ 86
           Q  S+  FL             ++       P+    G  ++ F +  F  P +      
Sbjct: 24  QLDSFTSFLDN-----------IRTVLHDEPPLV--IGGEVIRFENVTFLTPSYLVNGIS 70

Query: 87  ---DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT---- 139
                     + L Y   + + +      ++E TG +         + +  LP M     
Sbjct: 71  KTLYPSIARMKGLNYEFTMCVDV------INETTGVRDNG------VELCQLPCMVGSEM 118

Query: 140 --------------------KDGTFVIKGIQRIVV 154
                                 G F+  G++R+++
Sbjct: 119 CNLKGMSDAELLTHGEILGIPGGYFIHNGVERVLI 153


>gi|83414609|dbj|BAE54095.1| RNA polymerase beta subunit [Streptococcus parasanguinis]
          Length = 172

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/117 (54%), Positives = 82/117 (70%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+       
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVKEA 171



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 46/63 (73%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
              DILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KGSDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|282598442|gb|ADA83451.1| RNA polymerase beta subunit [Corynebacterium sp. NML94-0380]
          Length = 140

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 61/168 (36%), Positives = 84/168 (50%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D      +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L  +  +  G        +++L+DG +GEPF 
Sbjct: 45   ------------ATPVFDGASNEEIAGLLANSKPNRDGDVMVDGDGKTVLFDGRSGEPFK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|189194954|ref|XP_001933815.1| DNA-directed RNA polymerase III subunit RPC2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
 gi|187979694|gb|EDU46320.1| DNA-directed RNA polymerase III subunit RPC2 [Pyrenophora
            tritici-repentis Pt-1C-BFP]
          Length = 1167

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 65/407 (15%), Positives = 127/407 (31%), Gaps = 76/407 (18%)

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
             + +    +          R+       +  +     K         I            
Sbjct: 836  QVMKKHVTQLKTYANGTSDRINAGALDPDNKNHQAIGKDGIAQVGARIEAGDAYLLKSIP 895

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
            V       N       Y+      ++   + I+K     +   GV  ++K+     R  +
Sbjct: 896  VDTAGPPSN------TYKDKPEKYKNPDYSYIDK-TCVTENEAGV-TLIKLLFRQTRRPE 947

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK +                                     SR               
Sbjct: 948  LGDKFS-------------------------------------SR--------------- 955

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G+K  + +   + +   +      + ++       +++      +L       +G  
Sbjct: 956  --HGQKGTTGLIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMMELLSGKAGVLNGTL 1013

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                 F G+  E ++ +L       +G+  L  G+TGE        G IY  KL HMV D
Sbjct: 1014 EYGTAFGGSTVEDMSKILVDKGFSYTGKDYLTSGITGEAHQFYTFFGPIYYQKLKHMVQD 1073

Query: 1266 KVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGR 1325
            K+++R+ G  +++T+QP  G++  GG RLGEME  C+ AYG                 G 
Sbjct: 1074 KMHSRARGPRAILTRQPTEGRARDGGLRLGEMERDCLIAYGGQM-----------GYSGY 1122

Query: 1326 TRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSA 1372
             ++ ES        +   P +  +L++E+ ++ + + +         
Sbjct: 1123 CKLCES---EKAVRKITMPYAAKLLIQELGSMNIKVTIGLEDEFPRD 1166



 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 100/757 (13%), Positives = 218/757 (28%), Gaps = 135/757 (17%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFK-SVFPITAFSGAAMLEFVSYEFDPP--- 84
           L++    SY+HF+ +           L+   K + F  + F    +LE+       P   
Sbjct: 113 LVKQHVDSYNHFVDVE----------LKKIIKVNRFVRSDFDPKFLLEYTDIRVLAPNRQ 162

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                         ++C  RD+TYA P+ + +             +    +K   I +G 
Sbjct: 163 EEDDLDHHKSTVTPNECRLRDMTYAAPIVVDI----------IYTRGNAKVKRTGIKIGR 212

Query: 135 LPLMTKD------------------------GTFVIKGIQRIVVSQLHR---------SP 161
           +P+M K                         G F+ +G +++++ Q            + 
Sbjct: 213 MPIMLKSNKCVLAGKNDNDMAVMGECPLDPGGYFITRGQEKVILVQEQLNKNRVIVESAK 272

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMA 220
           GI                Y   +I             K ++++R +    ++P+   + A
Sbjct: 273 GIMQASVTSSTHERRTKTY---VI-----------QKKGLMYLRHNTLSEEIPIVFVMKA 318

Query: 221 LGM-DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKK 279
           LG+   +EIL+    +    Q      F   A + +   + +   +           G  
Sbjct: 319 LGVASDKEILTMVAGEDSAYQDNFSINFEACAKEEIFTQERALEYIGHRVRLVKKPLGTS 378

Query: 280 LTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHS 339
                    +   ++ +   S+ +   +V  +  N     +Y+ A          +    
Sbjct: 379 RN-------RNYHLEAIECLSNVVLP-HVPVEGTNYRPKALYV-ALMARRVLMAMQNPKL 429

Query: 340 EIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
                 +       +   +         +   D  L I +V++    +    A S F+  
Sbjct: 430 VDDRDYVGNKRLELSGQMLSLLFEDHFKRFNHDFKLSIDKVLKKPVRAQEFDAFSHFSVH 489

Query: 400 FFDSDKYDLSTVGRVKMN-MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
                      +     +  R  +D       + +   IA + ++  + +       +  
Sbjct: 490 KNHITMGVERAIATGNWSLKRFKMDRAGVTHVLSRLSYIAALGMMTRISSQFEKTRKVSG 549

Query: 459 LGNRRVRSVGEML-----KNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
               +    G +      + +    +  +           D        ++ A+ + S  
Sbjct: 550 PRALQPSQFGMLCTSDTPEGEACGLVKNLALMTHITTEDDDDPVRKIVFMLGAQDICSLT 609

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
            E   +  +  L  +   ++ +T   +       G+ R     E   +H  H        
Sbjct: 610 GEDIHAEGVYSLCLNGTPIA-VTDRPKHFLNSFRGLRRMGRVSEFTSIHIDHDHCEVHIA 668

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRK--------VCDGKVTNDVVYLSAMEEENR 625
           T EG     +  +      N    + + Y K          D      V YL   EE + 
Sbjct: 669 TDEGRICRPMIIVE-----NQRSKVTSRYLKALRKGTLDFEDFLTRGLVEYLDTNEENDT 723

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA   + +++                           ++  P  ++   A LIP+  ++
Sbjct: 724 NIALKETDINQ-----------------------HTTHLEIEPFTILGAVAGLIPYPHHN 760

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
            S R    C M      ++  + P V T    +    
Sbjct: 761 QSPRNTYQCAMDTLLYLMVYPQQPMVKTRTIELTKYD 797


>gi|30025574|gb|AAP04348.1| RpoB [Serratia rubidaea]
          Length = 191

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 117/191 (61%), Positives = 152/191 (79%)

Query: 482 MERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
           +ER++KER+S  D+D++MPQD+INAKP+ +AV EFF SSQLSQ  +  N LS ITH RR+
Sbjct: 1   VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRI 60

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETP
Sbjct: 61  SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETP 120

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR+V DG VT+++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++
Sbjct: 121 YRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDDGRFVEDLVTCRSKGESSLFSRDQV 180

Query: 662 DFIDASPKQVV 672
           D++D S +QVV
Sbjct: 181 DYMDVSTQQVV 191


>gi|282598424|gb|ADA83442.1| RNA polymerase beta subunit [Corynebacterium sp. NML93-0481]
          Length = 140

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/168 (35%), Positives = 83/168 (49%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D      +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L     +  G        +++L+DG +GEPF 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANTKPNRDGDVMVDGDGKTVLFDGRSGEPFK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|194320156|gb|ACF48302.1| DNA-dependent RNA polymerase II second largest subunit [Peltigera sp.
            AFTOL 1838]
          Length = 332

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 61/384 (15%), Positives = 112/384 (29%), Gaps = 81/384 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 27   DTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 86

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 87   LF-RSLFYRSYTDQEKR---IGMSIVEQFEKPMRTDTLRLKHGTYEKLDDDGIVAPGVRV 142

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 143  SGEDMIIGKTAPIPPDSEELGQRTKMHIKRDASTPLRSTENGIVDQVLL----------- 191

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 192  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 242

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 243  VVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD---------------------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 281  -------------------------------ATP-FTEVTVDSVSKILRAHGYQSRGFEV 308

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
            +Y+  TG      V +G  Y  +L
Sbjct: 309  MYNAHTGHKLMAQVFLGPTYYQRL 332



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 73/193 (37%), Gaps = 17/193 (8%)

Query: 757 SGVDIYRLMKFQRSNQNT--CVNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNM 811
           S  + Y+    +++        +QR              +A   S +     +L  G+N 
Sbjct: 1   SPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNA 60

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIP 866
           +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D  
Sbjct: 61  IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPMRTDTL 120

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +     + +D+ GI+  G  V+  D+++GK  P         ++        K    RD
Sbjct: 121 RLKHGTYEKLDDDGIVAPGVRVSGEDMIIGKTAPIPPDSEELGQRT-------KMHIKRD 173

Query: 927 TSLRVPSGVSGTV 939
            S  + S  +G V
Sbjct: 174 ASTPLRSTENGIV 186


>gi|225382140|gb|ACN89283.1| DNA-directed RNA polymerase beta chain [Actinobacillus minor]
 gi|225382142|gb|ACN89284.1| DNA-directed RNA polymerase beta chain [Actinobacillus minor]
          Length = 187

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 116/186 (62%), Positives = 142/186 (76%), Gaps = 1/186 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS
Sbjct: 62  ETPEGPNIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANS 121

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +LDE+  FT+  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 122 NLDENFRFTDTYVTCRGEHGESGLYKPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 181

Query: 692 MGCNMQ 697
           MG NMQ
Sbjct: 182 MGPNMQ 187


>gi|269978605|gb|ACZ55986.1| RNA polymerase II [Fusarium boothii]
 gi|269978614|gb|ACZ55992.1| RNA polymerase II [Fusarium culmorum]
          Length = 312

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSDILRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 66/197 (33%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   L   EI           +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P  +       +        +    RD S  + S  
Sbjct: 111 LDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTE 163

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 164 NGIVDQVILTVNADNVK 180


>gi|151573507|gb|ABS18002.1| RNA polymerase II [Fusarium napiforme]
 gi|151573606|gb|ABS18067.1| RNA polymerase II [Gibberella moniliformis]
          Length = 299

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 106/372 (28%), Gaps = 75/372 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVTVGYIYMLK 1258
              V  G  Y  +
Sbjct: 288  AQVFFGPTYYQR 299



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|224419490|emb|CAX51326.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 119

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 8/101 (7%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 19   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLMDGRSGEPFPFPVSVGYMYML 78

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEME
Sbjct: 79   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 119


>gi|22086617|gb|AAM90693.1|AF403011_1 RNA polymerase beta subunit [Neorickettsia helminthoeca]
          Length = 155

 Score =  193 bits (490), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 73/152 (48%), Positives = 96/152 (63%), Gaps = 5/152 (3%)

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI-GTGSHTEKI 1185
            VPSRMNVGQI ETHLGWA   LGKK+  L+       +   L+S L ++          +
Sbjct: 1    VPSRMNVGQILETHLGWAVNNLGKKVSKLL----DENNFPELKSLLFEIYKNDKKMMAIL 56

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                DD VL  ++  + G+PV+  VF+G   + I  +L +A  D SGQ +LYDG+TGE F
Sbjct: 57   KGMSDDEVLHYSQSLRKGIPVAASVFEGPKTDEIERLLILAGKDPSGQEVLYDGVTGEQF 116

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            DR VTVG  YMLKL+H+V+DK++ARS GSYSL
Sbjct: 117  DRKVTVGCKYMLKLHHLVNDKIHARSIGSYSL 148


>gi|89888191|gb|ABD78640.1| DNA-directed RNA polymerase beta subunit [Bordetella trematum]
          Length = 282

 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 166/283 (58%), Gaps = 3/283 (1%)

Query: 224 DSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
           D E IL+ F+    +  + +             G      + D  +G+ ++E  K++ + 
Sbjct: 1   DPEAILAHFFDFDNFELKSEGAMMEFVPE-RWKGEMARFDITD-RSGKVIVEKDKRINAK 58

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            L+ L   G++ + +  + L G  +A+++V+ +TGE+   A + I E  L  +  +++ D
Sbjct: 59  HLRDLAAAGIQRISVPEEFLYGRVLAKNVVDADTGELIAHANEEITESVLANMRAAKVLD 118

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           +  LY + ++   YI  TL TD   D+  A + IYR+MRPG+  T    E++F  LF+  
Sbjct: 119 LQALYTNDLDRGPYISQTLRTDDTADQTAARVAIYRMMRPGEPPTEEAVEALFQRLFYSD 178

Query: 404 DKYDLSTVGRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNR 462
           + YDLS VGR+K+N RL   D       +  EDI+  IK+LV+LRNG+G IDDID+LGNR
Sbjct: 179 ETYDLSRVGRMKVNSRLGRGDDASGPMTLTDEDILETIKVLVELRNGRGQIDDIDHLGNR 238

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
           RVR VGE+ +NQ+R GL+R+ER++KER+   + +++MP DLIN
Sbjct: 239 RVRCVGELAENQFRAGLVRVERAVKERLGQAETENLMPHDLIN 281


>gi|46277368|gb|AAS86874.1| DNA-dependent RNA polymerase II [Peziza michelii]
          Length = 548

 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 60/382 (15%), Positives = 113/382 (29%), Gaps = 81/382 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 245  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 304

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G   
Sbjct: 305  LF-RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRV 360

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ +      R+++         ++     +  Q              
Sbjct: 361  SGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------- 406

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 407  ------VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGLTYRNEDMPFTSEG 460

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 461  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD---------------------- 498

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  I
Sbjct: 499  -------------------------------ATP-FTDVTVDSVSKLLREHGYQSRGFEI 526

Query: 1236 LYDGLTGEPFDRPVTVGYIYML 1257
            +Y+G TG      V +G  Y  
Sbjct: 527  MYNGHTGRKLVAQVFLGPTYYQ 548



 Score = 92.4 bits (228), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 66/474 (13%), Positives = 133/474 (28%), Gaps = 72/474 (15%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F   + +    +    +  I   RR   +
Sbjct: 10  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGTWVGIHRDPGFIVRTIQKLRRQGHI 63

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
           G               +         P                    V+           
Sbjct: 64  GSEVSLIQDIRNREFKIFTDAGRICRPLFV-----------------VDNDPASPRRGEL 106

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
           V        + Y    E+E                        R   + ++     +++I
Sbjct: 107 VLQKHHVQKLEYDRDTEDE----------------------SQRYGWQGLMTDG-VVEYI 143

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           DA  ++ V I  +      +   +    G  +Q +A P  + +A            +   
Sbjct: 144 DAEEEETVMIVMTPEDLETSRQFH---AGYEIQTEADPAQRVKASVNKFAHTWTHCEIHP 200

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPLVK 783
           A I+   A I+   D  +                       +   +  N     Q+PL  
Sbjct: 201 AMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXNYRERMDTMANILYYPQKPL-- 258

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +L  G+N +VA + + GYN EDS+++++  +   +F S+ 
Sbjct: 259 --------GTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLF 310

Query: 844 IEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +    +   +   E        +   +       +D+ G++  G  V+  DI++GK 
Sbjct: 311 FRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKT 370

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P   +     ++        K    RD S  + S  +G V  V +       K
Sbjct: 371 APIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 417


>gi|89145189|emb|CAJ57567.1| RNA polymerase subunit B [Microbacterium aurantiacum]
          Length = 357

 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 129/259 (49%), Positives = 174/259 (67%), Gaps = 15/259 (5%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
             I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+S +YDL+ VGR K
Sbjct: 99  DSIEETLSKDTILSKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 158

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKG---------------TIDDIDNLG 460
           +N +L L  P     +  EDI+A IK LV L  G                  +DDIDN G
Sbjct: 159 INQKLGLTGPLSDSVLTVEDIVATIKYLVRLHRGDTTFDGTRAGKPAEIRLDVDDIDNFG 218

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           NRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +S
Sbjct: 219 NRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTS 278

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N L+ +TH RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG NI
Sbjct: 279 QLSQFMDQNNPLAGLTHKRRLSALGPGGLSRERAGVEVRDVHPSHYGRMCPIETPEGPNI 338

Query: 581 GLVSSLTSFARVNAYGFIE 599
           GL+ SL SFAR+N +GFI+
Sbjct: 339 GLIGSLASFARINPFGFID 357



 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 87/168 (51%), Gaps = 13/168 (7%)

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIE 195
           PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + RIIP +G W++ E
Sbjct: 1   PLQTDKGTFIINGTERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARIIPSRGAWLEFE 58

Query: 196 FDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAAD 253
            D +D + VRIDR+RK  VT FL ALG+ S++IL+ F  +  I  +   D       A  
Sbjct: 59  IDKRDQVGVRIDRKRKQSVTVFLKALGLTSDDILAEFAGFDSIEETLSKDTILSKEDALR 118

Query: 254 LMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
            +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 DI--------YRKLRPGEQVAAEAARALLDNFYFNSKRYDLAKVGRYK 158


>gi|46277354|gb|AAS86867.1| DNA-dependent RNA polymerase II [Peziza succosa]
          Length = 561

 Score =  192 bits (489), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 89/681 (13%), Positives = 177/681 (25%), Gaps = 126/681 (18%)

Query: 580  IGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+          +    + +V  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGTPAGPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGTWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGC 694
              F    +        I      I  I     ++ + A      +  ++ND ++      
Sbjct: 62   PGFIVRTIQKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGEL 121

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +Q+  +  L+ +      G                  G+VE +DA       +    + 
Sbjct: 122  VLQKFHIEKLEDDREIEDEGQRY-------GWQGLMTDGVVEYIDAEEEETVMIVMTPED 174

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              +    +   + Q         QR    V             P+  LG       +  +
Sbjct: 175  LETSRQFHAGYEIQ---HEADPAQRVKAAVNKFAHTWTHCEIHPAMILG-------ICAS 224

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N                                                    
Sbjct: 225  IIPFPDHNQSPXXX-----------------------------XXXXXXXXXXXXXXXXY 255

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 256  RERMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 315

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    +F R  +D+ +R      E+ E   R           +       +  G  
Sbjct: 316  IDRGLF-RSLFYRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVR 374

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  ++ +      R+++         ++     +  Q             
Sbjct: 375  VSGEDIIIGKTAPIAPNQEELGQRTKFHTKRDTSTPLRSTENGIVDQ------------- 421

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +
Sbjct: 422  -------VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSE 474

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +  + E  L       G +                       
Sbjct: 475  GVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------- 513

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                                            +TP F     ++++ +LR       G  
Sbjct: 514  --------------------------------ATP-FTDVTVDSVSKLLREHGYQSRGFE 540

Query: 1235 ILYDGLTGEPFDRPVTVGYIY 1255
            ++Y+G TG      V +G  Y
Sbjct: 541  VMYNGHTGRKLVAQVFLGPTY 561



 Score = 52.4 bits (124), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 43/314 (13%), Positives = 75/314 (23%), Gaps = 36/314 (11%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F   + +    +    +  I   RR   +
Sbjct: 25  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGTWVGIHRDPGFIVRTIQKLRRQGHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 79  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKFHIEKLEDDREIE 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E              V Y+ A EEE   I      L+    F        E    +   
Sbjct: 139 DEGQRYGWQGLMTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQHEADPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN----------------RVLMGCN 695
             +          +  P  ++ I AS+IPF +++ S                        
Sbjct: 199 AAVNKFAHTWTHCEIHPAMILGICASIIPFPDHNQSPXXXXXXXXXXXXXXXXXXXYRER 258

Query: 696 MQRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           M   A  L   + P   T  ME +  +   A   A  A +          +   +  +D 
Sbjct: 259 MDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 318

Query: 755 STSGVDIYRLMKFQ 768
                  YR    Q
Sbjct: 319 GLFRSLFYRTYMDQ 332


>gi|46277314|gb|AAS86847.1| DNA-dependent RNA polymerase II [Pachyella babingtonii]
          Length = 551

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 92/671 (13%), Positives = 183/671 (27%), Gaps = 128/671 (19%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V +       +    + +V  +     +      ++      +  D  F    +
Sbjct: 3    LMSYVSVGSPSEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTI 62

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    I      +  I     ++ + A      +  ++ND ++       +Q+  + 
Sbjct: 63   QKLRRQNHIGHEVSLVQDIRNREFKIFTDAGRICRPLFVIDNDPTSPRRGELVLQKYHIE 122

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ +   +  G                  G+VE +DA       +    +   +    +
Sbjct: 123  KLEDDKEALEEGASRYG------WDGLISEGVVEYIDAEEEETAMIVMTPEDLETSRQFH 176

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
                F   N N    QR    V             PS  LG       +  + +P+  +N
Sbjct: 177  AG--FAIHNDNVDPAQRVKAAVNKFAHMWTHCEIHPSMILG-------ICASIIPFPDHN 227

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                   S R   +       +  F    R+                           + 
Sbjct: 228  Q------SPRNTYQSAMGKQAMGVFLTNYRERM-----------------------DTMA 258

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 259  NILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-R 317

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R  +D+ +R        IE   +      + L    Y +L +   +  G       
Sbjct: 318  SLFYRTYMDQEKRVGI---SVIEKFEKPSRSNTLRLKHGTYDKLDDDGLVAPGIRVSGED 374

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  ++ +      R+++         ++     +                     
Sbjct: 375  IIIGKTAPIAPNTEEMGQRTKFHTKRDTSTPLRSTESGIVD------------------- 415

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 416  -TVMITTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGIVPD 474

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 475  LIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------------- 508

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     ++++ +LR       G  ++Y+G
Sbjct: 509  ---------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEVMYNG 540

Query: 1240 LTGEPFDRPVT 1250
             TG      V 
Sbjct: 541  HTGRKLVAQVF 551


>gi|282598444|gb|ADA83452.1| RNA polymerase beta subunit [Corynebacterium sp. NML98-0058]
          Length = 140

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 62/168 (36%), Positives = 85/168 (50%), Gaps = 36/168 (21%)

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLGW     G  +    +D      +  L   L  V                  
Sbjct: 1    GQVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT------------ 45

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPF 1245
                         +TPVFDGA  E I  +L  +  +  G        +++L+DG +GEPF
Sbjct: 46   -------------ATPVFDGASNEEIAGLLANSKPNRDGDVMVDGDGKTVLFDGRSGEPF 92

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   KYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 140


>gi|170037347|ref|XP_001846520.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167880429|gb|EDS43812.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 928

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 121/1002 (12%), Positives = 286/1002 (28%), Gaps = 198/1002 (19%)

Query: 15  KFFGKNPEIID-----IPDLIEV------QKASYDHFLMMNIAPDERPNEGLQAAFKSVF 63
           K   K  + ++     +P  +++         S+++F+ ++I    R N       KS  
Sbjct: 13  KNLKKVQKTLEDKWKLVPAFLQIKGLVKQHIDSFNYFINVDIKNIVRAN----DEVKS-- 66

Query: 64  PITAFSGAAMLEFVSYEFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDV 113
                     L++++     P               +C  RD+TYA P+ + +       
Sbjct: 67  ---DADPCFYLKYLNVAIGMPDVEEGFNNTKSTTPHECRLRDMTYAAPITVDIEYT---- 119

Query: 114 DEFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGI 149
                 +  + +    + +G +P+M                           G FVI+G 
Sbjct: 120 ------RGTQRVVRNGLLIGRMPIMLRSSNCVLSGKSEYELSKVNECPLDPGGYFVIRGT 173

Query: 150 QRIVVSQLHRSPGIHFDHDKG-----RASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHV 204
           +++++ Q   S       D       + + S     +  I+                 ++
Sbjct: 174 EKVILIQEQVSWNKMLTEDYNNVIQCQVTSSTHEKKSRTIL----------LSKHGKYYL 223

Query: 205 RIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSS 263
           + +    ++PV     A+G+ S++ +         +Q+        +A   +   + +  
Sbjct: 224 KHNSMTEEIPVAIIFKAMGIASDQEIMQLVGIDTETQKRLAPSLLEAANHKVYTQQRALE 283

Query: 264 LVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIE 323
            +           G KL +    +   K         D L    +A   VN    ++   
Sbjct: 284 YM-----------GSKLIAKRFTTAATKYKTTADEARDLLATTILAHVPVNNFNFQVKAI 332

Query: 324 AGDVIDEK-SLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMR 382
              ++  +    E+  S + D        +     + + +  D  K     L  I     
Sbjct: 333 YVALMIRRVMAAELDRSAVDDRDYYGNKRLELAGSLLSLMFEDLFKRFNWELKMIADKNI 392

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI 442
           P   +               +      + G   +  R  ++     + + +   I+ + +
Sbjct: 393 PKIKAAQFDIVKHMRAALISTGLETAISTGNWTI-KRFKMERAGVTQVLSRLSYISALGM 451

Query: 443 LVDLRNGKGTIDDIDNLG-----NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
           +  + +       +            +    +  + +    +  +           +   
Sbjct: 452 MTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEEPV 511

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +        + +     E   + ++  +  + N L      +RL  + +  + R      
Sbjct: 512 IRLAYNSGVEDIRLLGGETINNPKVFMVFINGNILGVTIMYKRLVEVFRM-MRRKGLIGS 570

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDV 614
              +H +   R     T  G        + +     +      ++   RK  D      +
Sbjct: 571 FVSIHTSFSQRCVYIHTDGGRLCRPYIIVQNGQPLVKQEHIEQLKVGLRKFDDFLHDGLI 630

Query: 615 VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI 674
            YL   EE + +IA                       +E+ +  EK   ++  P  ++ +
Sbjct: 631 EYLDVNEENDSFIA----------------------YQELDIDPEKTTHLEIEPFTLLGV 668

Query: 675 AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
            A L+P+  ++ S R    C M +QA+ ++         G                    
Sbjct: 669 CAGLVPYPHHNQSPRNTYQCAMGKQAMGII---------GYNQKNRID------------ 707

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
                                                 N    Q P+V+           
Sbjct: 708 ----------------------------------TLMYNIVYPQTPMVRS---------- 723

Query: 795 ADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT 854
                T+   L  G+N  VA M + GY+ ED++++++  +       +  +  +   +  
Sbjct: 724 RTIELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTIKRY 783

Query: 855 KLGPEEITRDIPNVS-----EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
                +        S         + +D  GII  G +V+    +V K  P  +S    E
Sbjct: 784 SNQTFDRIMGPMKDSLTNKIIFRHECLDTDGIISPGEKVSSKQTMVNKEMPAVKSINPIE 843

Query: 910 EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
               +   G++ +      +         +  V +   +  +
Sbjct: 844 ----QKESGQQPIAYSGVPITYKGTEPSYIEKVMVSTNNDEE 881



 Score =  105 bits (262), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 88/682 (12%), Positives = 178/682 (26%), Gaps = 120/682 (17%)

Query: 432  RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
            +   +  +I+ ++     +  +DD D  GN+R+   G +L   +     R    +K    
Sbjct: 330  KAIYVALMIRRVMAAELDRSAVDDRDYYGNKRLELAGSLLSLMFEDLFKRFNWELKMIAD 389

Query: 492  SVDIDSVMPQ----DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG 547
                     Q      + A  + + +     +   +     +          RLS +   
Sbjct: 390  KNIPKIKAAQFDIVKHMRAALISTGLETAISTGNWTIKRFKMERAGVTQVLSRLSYISAL 449

Query: 548  GVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE 599
            G+         + R     R + P+ +G +CP++T EG   GLV +L     +      E
Sbjct: 450  GMMTRVNSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITTEVDEE 509

Query: 600  TPYRKVCDGKVTNDVVYLSAMEEENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVP 657
               R   +  V  D+  L      N  +     N ++       + LV          + 
Sbjct: 510  PVIRLAYNSGV-EDIRLLGGETINNPKVFMVFINGNILGVTIMYKRLVEVFRMMRRKGLI 568

Query: 658  REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
               +    +  ++ V I         + D  R              L      V  G   
Sbjct: 569  GSFVSIHTSFSQRCVYI---------HTDGGR--------------LCRPYIIVQNGQPL 605

Query: 718  VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            V  +      V  R       D +   +   E +                          
Sbjct: 606  VKQEHIEQLKVGLRKFDDFLHDGLIEYLDVNEENDS------------------------ 641

Query: 778  QRPLVKVGDEVRRNDIIADGPSTDLGDLALGR--NMLVAFMPWHGYNFEDSMLISERMVS 835
                      +   ++  D   T   ++       +    +P+  +N          M  
Sbjct: 642  ---------FIAYQELDIDPEKTTHLEIEPFTLLGVCAGLVPYPHHNQSPRNTYQCAMGK 692

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            + +     I  +    R   L    +    P V                           
Sbjct: 693  QAMG----IIGYNQKNRIDTLMYNIVYPQTPMVRSRT----------------------- 725

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              I       +   +    A+      D+ D  +   + +        ++        +R
Sbjct: 726  --IELTNFDKLPAGQNATVAVMSYSGYDIEDALILNKASIDRGYGRCLVYKNSKCTI-KR 782

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
              +   ++I    +D    ++I           I  G+   S      K       +   
Sbjct: 783  YSNQTFDRIMGPMKDSLTNKIIFRHECLDTDGIISPGEKVSSKQTMVNKEMPAVKSI--- 839

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        +   Q+      + Y       +    + IEK+    +       +VK
Sbjct: 840  ------------NPIEQKESGQQPIAYSGVPITYKGTEPSYIEKVMVSTNNDEEF--LVK 885

Query: 1076 VFVAMKRPIQSGDKMAGRHGNK 1097
            + +   R  + GDK + RHG K
Sbjct: 886  ILLRQTRRPEIGDKFSSRHGQK 907


>gi|46277366|gb|AAS86873.1| DNA-dependent RNA polymerase II [Peziza howsei]
          Length = 562

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 94/678 (13%), Positives = 178/678 (26%), Gaps = 120/678 (17%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     E    +    + +V  +     +      ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
              F    +        I      I  I     ++ + A  +   L   D+          
Sbjct: 62   PGFIVRTIQKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNEPASG----- 116

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRSVEGDLDPST 756
            R+   +L+                 S          G+VE +DA       +    +   
Sbjct: 117  RKGELVLQKHHIEKLEDDRDNPDPDSKYGWSGLIGEGVVEYIDAEEEETVMIVMTPEDLE 176

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
            +    +               + P+ K G            PS  LG       +  + +
Sbjct: 177  TSRQYHAGYDIAPEVDPAQRVKAPMNKSGSA-HTWTHCEIHPSMILG-------ICASII 228

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R           +  F    R+                       
Sbjct: 229  PFPDHNQ------SPRNTYXXAMGKQAMGXFLTNYRERM--------------------- 261

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  + AI      +  D+ +   S + 
Sbjct: 262  --DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 319

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +    +F R  +D+ +R      E+ E   R           +       +  G    
Sbjct: 320  RGLF-RSLFFRTYMDQEKRVGMNVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVS 378

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+  ++ +      R+++         ++     +  Q               
Sbjct: 379  GEDIIIGKTAPIAPNQDELGQRTKYHTKRDVSTPLRSTENGIVDQ--------------- 423

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 424  -----VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGV 478

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM +  + E  L       G +                         
Sbjct: 479  VPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD----------------------- 515

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     ++++ +LR       G  I+
Sbjct: 516  ------------------------------ATP-FTDVTVDSVSKLLREHGYQSRGFEIM 544

Query: 1237 YDGLTGEPFDRPVTVGYI 1254
            Y+G TG      V +G  
Sbjct: 545  YNGHTGRKLVVQVFLGPT 562


>gi|281485720|gb|ADA70456.1| RNA polymerase beta subunit [Corynebacterium sp. ATCC 43833]
          Length = 141

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 61/169 (36%), Positives = 89/169 (52%), Gaps = 36/169 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G KI       +   +   L++  E++                   
Sbjct: 1    QVLEVHLGWLAAA-GWKID-----PEDPKNAELLKTLPEELYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF 
Sbjct: 40   -------AGSLTATPVFDGASNEELAGLLGNSLPNRDGDVMVDENGKAQLFDGRSGEPFP 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
             PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   YPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 141


>gi|256575369|gb|ACU87652.1| RpoB [Gallibacterium anatis]
 gi|270357551|gb|ACZ81008.1| RpoB [Gallibacterium anatis]
          Length = 190

 Score =  192 bits (489), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 113/187 (60%), Positives = 142/187 (75%), Gaps = 1/187 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 3   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPI 62

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS
Sbjct: 63  ETPEGPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANS 122

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +LDE+  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 123 NLDENFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRAL 182

Query: 692 MGCNMQR 698
           MG NMQ+
Sbjct: 183 MGPNMQQ 189


>gi|256575364|gb|ACU87650.1| RpoB [Gallibacterium anatis]
          Length = 187

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 113/186 (60%), Positives = 141/186 (75%), Gaps = 1/186 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 2   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS
Sbjct: 62  ETPEGPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANS 121

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +LDE+  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 122 NLDENFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRAL 181

Query: 692 MGCNMQ 697
           MG NMQ
Sbjct: 182 MGPNMQ 187


>gi|46277364|gb|AAS86872.1| DNA-dependent RNA polymerase II [Peziza ampelina]
          Length = 549

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 59/379 (15%), Positives = 109/379 (28%), Gaps = 75/379 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 246  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 305

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R           +       +  G      
Sbjct: 306  LF-RSLFYRTYMDQEKRVGMNVVEEFEKPQRGNTLRLKHGTYDKLDDDGLVAPGVRVSGE 364

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ ++     R+++         ++     +  Q                 
Sbjct: 365  DIIIGKTAPIAPNMEELGQRTKFHTKRDVSTPLRSTENGIVDQ----------------- 407

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 408  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVP 464

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 465  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 499

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  I+Y+
Sbjct: 500  ----------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEIMYN 530

Query: 1239 GLTGEPFDRPVTVGYIYML 1257
            G TG      V +G  Y  
Sbjct: 531  GHTGRKLVVQVFLGPTYYQ 549



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 63/481 (13%), Positives = 121/481 (25%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 11  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 64

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 65  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKENQ 124

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            E              V Y+ A EEE   I      L+    F                 
Sbjct: 125 DEDTRYGWSGLIGDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQ---------- 174

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P Q V  + +                                        
Sbjct: 175 ------TEVDPAQRVKASVNKY----------------------------------AHTW 194

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CV 776
              +   + I+   A I+   D  +                       +   +  N    
Sbjct: 195 THCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXXRERMDTMANILYY 254

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA + + GYN EDS+++++  +  
Sbjct: 255 PQKPL----------GTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 304

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E        +   +       +D+ G++  G  V+  
Sbjct: 305 GLFRSLFYRTYMDQEKRVGMNVVEEFEKPQRGNTLRLKHGTYDKLDDDGLVAPGVRVSGE 364

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P   +     ++        K    RD S  + S  +G V  V +       
Sbjct: 365 DIIIGKTAPIAPNMEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 417

Query: 952 K 952
           K
Sbjct: 418 K 418


>gi|303391303|ref|XP_003073881.1| DNA-directed RNA polymerase III subunit 2 [Encephalitozoon
            intestinalis ATCC 50506]
 gi|303303030|gb|ADM12521.1| DNA-directed RNA polymerase III subunit 2 [Encephalitozoon
            intestinalis ATCC 50506]
          Length = 1110

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/415 (17%), Positives = 139/415 (33%), Gaps = 88/415 (21%)

Query: 978  LDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVES 1037
            ++  +      I  G   V   K         S+ +S+       +  + D+ + +  + 
Sbjct: 758  IEDALVLNKTSIERGLFRVEVYKTITTLLKKHSNGLSDILGPNPKESVLDDDGLGKPGKM 817

Query: 1038 LKVQ--YETSKSILEDRFKNKIEKIQWGDD--------MPPGVLRVVKVFVAMKRPIQSG 1087
            ++    Y    S +E  +K    K+  GD                ++K  +   RP + G
Sbjct: 818  IRDGTVYVNKMSPVEGVYK-FTGKVHRGDPAYIDKVLITKSQDQILIKTMLRQTRPPEIG 876

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            DK +                                     SR                 
Sbjct: 877  DKFS-------------------------------------SR----------------- 882

Query: 1148 LGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVS 1207
             G+K    +   + +   +      + ++       +++      ++       SG  + 
Sbjct: 883  HGQKGVVGLIVGQEDMPFNDQGISPDIIMNPHGFPSRMTVGKIIELISGKAGVLSGQILD 942

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            +  F     E    +L       SG+     G TG P    +  G ++  +L HMV+DK+
Sbjct: 943  STAFKENSVEQTCELLAKHGFSYSGKDCFTSGTTGAPLTAYIFFGPVFYQRLKHMVADKI 1002

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTR 1327
            + R+ G  +++T+QP  G+S  GG +LGEME  C+  YGA+ ++ E L I SD       
Sbjct: 1003 HMRARGPRAILTRQPTEGRSKDGGLKLGEMERDCLIGYGASSLIIERLMISSD------- 1055

Query: 1328 VYESIV----------------AGNDTFETGTPESFNVLVKEMQALGLSIDLENS 1366
            ++E+ V                      +   P +  +L +E+ ++ +   L   
Sbjct: 1056 MFEAYVCKPCGVLAFKGCCVACKNTKPAKIKMPYACKLLFQELISMNILPRLHIE 1110



 Score =  125 bits (313), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 107/759 (14%), Positives = 227/759 (29%), Gaps = 156/759 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK--- 85
           L+     SYD+F+   I    R N+       S            L+++      P    
Sbjct: 19  LVRQHIESYDYFVDHEIKALVRANQ----IVDS-----DIDHTFYLKYLDIRVGMPSIEE 69

Query: 86  ----FD--VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
               +D    +C  RD+TY+  + + +  +          ++ + I ++ I +G +P+M 
Sbjct: 70  NMVNYDVFPIECRLRDMTYSANIYVDIEYV----------RNRQIIVKRDICIGKMPVML 119

Query: 140 KD----------------------------------GTFVIKGIQRIVVSQLHRSPGIHF 165
           +                                   G F+I+GI+R+++ Q   S     
Sbjct: 120 RSSRCHLRKEAKGIIESNKTRDRKIRESQECPLDVGGYFIIRGIERVILIQEQLSKNRII 179

Query: 166 DHDKGR------ASLSG--KLLYACRIIPDQGLWMDIEFDSKDIIHVRID-RRRKVPVTS 216
                +       S +   K   +  I               D  +++      ++P   
Sbjct: 180 IESGPKGLFASVTSSTDEHKSKTSVTI-------------KDDCYYLKSSMFNEEIPAII 226

Query: 217 FLMALGMDSEEIL-----STFYPKIV--YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
            + ALG+  ++ +       ++  IV  + +      F    A L +   +     D   
Sbjct: 227 AMKALGLTQDKEIAECIGKEYFEIIVPSFGECISKEVFTKDQALLYMSNYIKLKPEDNRI 286

Query: 270 GEQVIESGKKLTSGLLKS---LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
            E +    +K+   +      L++KG+ ++ +    L    +     +        +   
Sbjct: 287 EEVLTILSEKVLPNVQTEGCNLRKKGI-YIALMIRRLVQTKLNILKED--------DKDF 337

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           V +++         I         +      I   L         DAL  +       ++
Sbjct: 338 VGNKRFELAGQLLSILFEDTFKRFNFELKKSIDKILSKRSRAQEFDALTFLN---LQANM 394

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD- 445
            T +++ +  +   ++  ++ +   G   +  R +  +   +            K+    
Sbjct: 395 ITSTLSRA-ISTGNWNLKRFRMERSGVTHVLSRHSYISALGMMTKINSHFEKTRKVSGPR 453

Query: 446 --LRNGKGTIDDIDNLGNRRVRSVGE--MLKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
               +  G +  +D         V    +L         R    +  R+  VDI+SV  +
Sbjct: 454 SLHTSSWGMLCPVDTPEGESCGLVKNLALLAEITTNSDTRPVLDLMFRLGVVDINSVYTR 513

Query: 502 DLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
           ++         +   F +  +  +      L       R   L    V+  R   E    
Sbjct: 514 EIHQ-----KDMFSVFLNGDIVGITNKAGFLIEQFRLNRRKGLIGKFVSIYRVPAEKVIH 568

Query: 562 HPTHYGRICP---AETSEGHNIGLVSSL--TSFARVNAYGFIE--------TPYRKVCDG 608
             +  GR+C           N  ++S+        +N    IE          Y K    
Sbjct: 569 VASDNGRVCRPLVVIDKGRINQMIISNQVDKYLEALNISEKIEMGSERSFFDCYLKYKSF 628

Query: 609 KVTND---VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
               +   V YL   EE +  +A     +                        E+   ++
Sbjct: 629 SDLLEEGFVEYLDVNEENDCLVALRPEDI-----------------------VEETTHLE 665

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            S   ++   A L+PF  ++ S R    C M +QA+  +
Sbjct: 666 ISEFAILGYVAGLVPFPHHNQSPRNTYQCAMGKQAIGHI 704



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 87/591 (14%), Positives = 195/591 (32%), Gaps = 63/591 (10%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF-DSDKYDLSTVGRVKMNMRLNLDTPD 426
           K+  + ++  +      +V T   A    +       +   +  V  +     L     +
Sbjct: 245 KEYFEIIVPSFGECISKEVFTKDQALLYMSNYIKLKPEDNRIEEVLTILSEKVLPNVQTE 304

Query: 427 DVRHIRKEDIIA-IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERS 485
                +K   IA +I+ LV  +      DD D +GN+R    G++L   +     R    
Sbjct: 305 GCNLRKKGIYIALMIRRLVQTKLNILKEDDKDFVGNKRFELAGQLLSILFEDTFKRFNFE 364

Query: 486 IKERISSVDIDSVMPQDLI-------NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
           +K+ I  +       Q+          A  + S +     +   +     +         
Sbjct: 365 LKKSIDKILSKRSRAQEFDALTFLNLQANMITSTLSRAISTGNWNLKRFRMERSGVTHVL 424

Query: 539 RRLSALGQGGVA--------RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            R S +   G+         + R     R +H + +G +CP +T EG + GLV +L   A
Sbjct: 425 SRHSYISALGMMTKINSHFEKTRKVSGPRSLHTSSWGMLCPVDTPEGESCGLVKNLALLA 484

Query: 591 RVNAYGFIETPYRKVCDGKVTN-DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            +            +    V + + VY   + +++ +    N  +    +    L+    
Sbjct: 485 EITTNSDTRPVLDLMFRLGVVDINSVYTREIHQKDMFSVFLNGDIVGITNKAGFLIEQFR 544

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAAS----LIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                 +  + +       ++V+ +A+       P +  D      M  + Q        
Sbjct: 545 LNRRKGLIGKFVSIYRVPAEKVIHVASDNGRVCRPLVVIDKGRINQMIISNQVDKYLEAL 604

Query: 706 AEAPFVGTG-----------------------MESVVAKSSGAAIVAKRAGIVEQVD--- 739
             +  +  G                       +E +        +VA R   + +     
Sbjct: 605 NISEKIEMGSERSFFDCYLKYKSFSDLLEEGFVEYLDVNEENDCLVALRPEDIVEETTHL 664

Query: 740 -----AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR----PLVKVGDEVRR 790
                AI   +  +      + S  + Y+    +++  +  +N +    P++       R
Sbjct: 665 EISEFAILGYVAGLVPFPHHNQSPRNTYQCAMGKQAIGHISLNVKKRFDPVILQLTYTHR 724

Query: 791 NDIIADGPS-TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
             +        +  ++  G+N +VA M + GY+ ED++++++  +   +F     +    
Sbjct: 725 PMVSTKILDLINYNEIPAGQNAMVAVMSYSGYDIEDALVLNKTSIERGLFRVEVYKTITT 784

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
           + +    G  +I    P  S      +D+ G+   G  +  G + V K++P
Sbjct: 785 LLKKHSNGLSDILGPNPKESV-----LDDDGLGKPGKMIRDGTVYVNKMSP 830


>gi|281485722|gb|ADA70457.1| RNA polymerase beta subunit [Corynebacterium sp. NML93-0612]
          Length = 144

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 58/169 (34%), Positives = 85/169 (50%), Gaps = 36/169 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  I                              +  +    +++ 
Sbjct: 1    QVLEVHLGWLAAA-GWHID---------------------------PEDVKNAKLLETLP 32

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF 
Sbjct: 33   EELYDVPAGSLTATPVFDGATNEELAGLLANSLPNRDGDVMVDENGKAQLFDGRSGEPFP 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
             PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 93   YPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 141


>gi|83414495|dbj|BAE54038.1| RNA polymerase beta subunit [Streptococcus oralis]
          Length = 172

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/173 (41%), Positives = 96/173 (55%), Gaps = 6/173 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+     
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAPRTLGIHIATPVFDGASSEDLWDTVK 169



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|67942338|gb|AAY83369.1| DNA-dependent RNA polymerase II [Donadinia sp. mh669]
          Length = 561

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 91/677 (13%), Positives = 177/677 (26%), Gaps = 119/677 (17%)

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L   + +      E    Y    + +   +     +      ++      +  D 
Sbjct: 1    GLVKNLALMSYITVGTPSEPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDP 60

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                  V        +      I D  D   K          P    ++         + 
Sbjct: 61   MHLVRNVQEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLV 120

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
             Q   + K E        E        + ++    G+VE VDA       +    +    
Sbjct: 121  LQKEHIEKLEEDHNLDEDEPQRQPYGWSGLL--GDGVVEYVDAEEEETIMIVMTPEDLEV 178

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               + +  + +         + P   V     +       PS  LG       +  + +P
Sbjct: 179  AQQVRQGYELEEETDPNKRVKAP---VNPNASQYTHCEIHPSMILG-------ICASIIP 228

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +   + +  F                              
Sbjct: 229  FPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM-------------------------- 260

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  +  I      +  D+ +   S +  
Sbjct: 261  -DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDR 319

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +    +F R  +D+ +R      E+ E   R    +      +       +  G     
Sbjct: 320  GLF-RSLFYRSYMDQEKRIGMQVVEEFEKPQRTNTLKLKHGTYDKLDEDGLVAPGVRVSG 378

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D+     R ++         ++     +  Q                
Sbjct: 379  EDIIIGKTAPIAPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML------------- 425

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 426  -------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIV 478

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +                          
Sbjct: 479  PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGMEGD------------------------ 514

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++S+LR       G  ++Y
Sbjct: 515  -----------------------------ATP-FTDVTVDSVSSLLRAEGYQSRGFEVMY 544

Query: 1238 DGLTGEPFDRPVTVGYI 1254
            +G TG      V +G  
Sbjct: 545  NGHTGRKLVAQVFLGPT 561



 Score = 94.8 bits (234), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 71/471 (15%), Positives = 146/471 (30%), Gaps = 71/471 (15%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 27  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG--- 77

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                    +RD+    +     A                   VN     E   + V   
Sbjct: 78  ----HEVSVIRDIRDREFKIFTDAGRVCRPLFV----------VNNDTTSERRGQLVLQK 123

Query: 609 KVTNDVVYLSAMEEENRYIAQ-ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           +    +     ++E+         S L  DG                      ++++DA 
Sbjct: 124 EHIEKLEEDHNLDEDEPQRQPYGWSGLLGDG---------------------VVEYVDAE 162

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            ++ + I  +         + +V  G  ++ +  P  + +AP      +    +   + I
Sbjct: 163 EEETIMIVMTPEDLEV---AQQVRQGYELEEETDPNKRVKAPVNPNASQYTHCEIHPSMI 219

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +     GV       +           Q+PL     
Sbjct: 220 LGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAERMDTMANILYYPQKPL----- 274

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +V  M + GYN EDS+++++  +   +F S+    
Sbjct: 275 -----ATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 329

Query: 847 FEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        +   +       +DE G++  G  V+  DI++GK  P 
Sbjct: 330 YMDQEKRIGMQVVEEFEKPQRTNTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPI 389

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++       +K    RD S  + S  +G V  V +       K
Sbjct: 390 APDVDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 433


>gi|94410940|gb|ABF18588.1| RNA polymerase II second largest subunit [Inocephalus sp. GD-b]
          Length = 546

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 96/618 (15%), Positives = 181/618 (29%), Gaps = 105/618 (16%)

Query: 570  CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR---- 625
            CPAET EG   GLV +L   A ++   +       + +         L ++EE       
Sbjct: 1    CPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWG-------LESLEENAHSQTP 53

Query: 626  ----YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
                ++      +  D +   + +      ++I      +  I     ++ + A  +   
Sbjct: 54   CTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRP 113

Query: 682  LENDDSNRVLMGCNMQRQ------AVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGI 734
            L   DS ++ +     +                  V  G+ E + A+     ++A     
Sbjct: 114  LFIVDSQQLTLQKKHVKWLAEGFNEEGEEYKWDNLVKGGIVELLDAEEEETVMIAMTPED 173

Query: 735  VEQVDAIRIVI--RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
            +E     +  I   + +G+ DP+                          +K G       
Sbjct: 174  LENSRLQQSGIDPAANDGEFDPAA------------------------RLKAGTNSHTWT 209

Query: 793  IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                 PS  LG       +  + +P+  +N                        ++    
Sbjct: 210  HCEIHPSMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMG 244

Query: 853  DTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
               +G       I               +  +             +       +   +  
Sbjct: 245  KQAMGIFLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNA 293

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +   +    I+ R  +D  ++S   + E+ E  +R+  
Sbjct: 294  IVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPSRENT 352

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +       I  G           K+  +  D                +E  Q
Sbjct: 353  LRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPD---------------SEELGQ 397

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            R     +    T     E    +++      D       + VKV V   R  Q GDK A 
Sbjct: 398  RTRTHTRRDVSTPLKSTESGMVDQVLITTNSD-----GQKFVKVRVRSTRIPQIGDKFAS 452

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG +      EDMPF  +G   D+++NP  +PSRM +G + E  L      +G + 
Sbjct: 453  RHGQKGTIGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEG 512

Query: 1153 KSLINDYKANGDISPLRS 1170
             +          +S    
Sbjct: 513  DATPFTDLTVESVSTFLR 530



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 70/461 (15%), Positives = 128/461 (27%), Gaps = 86/461 (18%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR   +            +   ++ 
Sbjct: 46  ENAHSQTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYT 105

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                  P    +   + L      +         E    K  +      V  L A EEE
Sbjct: 106 DAGRVCRPLFIVDSQQLTLQKKHVKWLA--EGFNEEGEEYKWDNLVKGGIVELLDAEEEE 163

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIAA 676
              IA     L+        +      GE                   +  P  ++ I A
Sbjct: 164 TVMIAMTPEDLENSRLQQSGIDPAANDGEFDPAARLKAGTNSHTWTHCEIHPSMILGICA 223

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           S+IPF +++ S R      M +QA+ +                                 
Sbjct: 224 SIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLI-------------------------- 257

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                             + + +  Y       +     +  R                 
Sbjct: 258 ---------------RMDTMANILYYPQKPLATTRSMEYLRFR----------------- 285

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + +
Sbjct: 286 -------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGI 338

Query: 857 GPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        +   +       +++ G+I  G  V   DI++GK  P         ++
Sbjct: 339 QQLEEFEKPSRENTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQR 398

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   +    RD S  + S  SG V  V I       K
Sbjct: 399 T-------RTHTRRDVSTPLKSTESGMVDQVLITTNSDGQK 432


>gi|282598438|gb|ADA83449.1| RNA polymerase beta subunit [Corynebacterium sp. NML99-0020]
 gi|282598440|gb|ADA83450.1| RNA polymerase beta subunit [Corynebacterium sp. NML00-0156]
          Length = 140

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 61/168 (36%), Positives = 83/168 (49%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPKNAALLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L     +  G        ++ LYDG +GEP+ 
Sbjct: 45   ------------ATPVFDGASNEEIAGLLANTKPNRDGDVMVDGQGKTRLYDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|253778916|emb|CAY90193.1| RNA polymerase subunit B [Acinetobacter sp. G13]
          Length = 287

 Score =  192 bits (488), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/142 (52%), Positives = 100/142 (70%), Gaps = 4/142 (2%)

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
             PVDIVLNPLGVPSRMNVGQI ETHLG A  GLG +I  ++ + +    +  LR FL+K+
Sbjct: 149  VPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDQIDKMMKEQRT---VLELRDFLDKI 205

Query: 1176 IGT-GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                G   E +    D+ +L+++   ++GVP++TPVFDGA+E  I  +L++A L  +GQ+
Sbjct: 206  YNKVGGEQEDLDSLTDEEILKLSGNLRAGVPLATPVFDGAEEGQIKELLQLAGLSSTGQT 265

Query: 1235 ILYDGLTGEPFDRPVTVGYIYM 1256
            +LYDG TGE FDRPVTVGY+YM
Sbjct: 266  VLYDGRTGERFDRPVTVGYMYM 287


>gi|269978602|gb|ACZ55984.1| RNA polymerase II [Fusarium avenaceum]
          Length = 312

 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DIIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSDLLRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/185 (20%), Positives = 69/185 (37%), Gaps = 15/185 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            ++R              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 3   YSRRMDTMANILYYPQKPLATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 62

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   L   EI           +       +DE GI+  G  
Sbjct: 63  SIDRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVR 122

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+  DI++GK  P  +       +        ++   RD S  + S  +G V  V +   
Sbjct: 123 VSGEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVN 175

Query: 948 HGIDK 952
               K
Sbjct: 176 ADNVK 180


>gi|56694318|gb|AAW22899.1| RNA polymerase II second largest subunit [Macrozamia moorei]
          Length = 523

 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 80/495 (16%), Positives = 144/495 (29%), Gaps = 95/495 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNML---VAFMPWHGYNFEDSML--ISERM 833
            LV  G  + V   +      S  + DL   RN      + + +       S++  +   +
Sbjct: 117  LVTKGFIEYVDTEEEETTMISMTISDLVNARNSPPTAASIVKYTHCEIHPSLILGVCASI 176

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            +            ++       +G          V+   L+      +  V        +
Sbjct: 177  IPFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLV 225

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
                +       +      + AI      +  D+ +   S +        +F R   D+ 
Sbjct: 226  TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFYRSYRDEE 284

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +R  ++ +E+     R+          +          G           K+T ++    
Sbjct: 285  KRMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEXVIIGKTTPVTQ--- 341

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                          DE   +     K    TS    E    +++      D +     R 
Sbjct: 342  --------------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RF 382

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +
Sbjct: 383  VKVRMXSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNPHAIPSRMTI 442

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E  +G     +GK+  +         +IS         +                 
Sbjct: 443  GQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMXGFETM----------- 491

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                                 +G +    G         + +G 
Sbjct: 492  ------------------------------------YNGHT----GR---RLSAMIFLGP 508

Query: 1254 IYMLKLNHMVSDKVY 1268
             Y  +L HMV DK++
Sbjct: 509  TYYQRLKHMVDDKIH 523



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 67/442 (15%), Positives = 123/442 (27%), Gaps = 97/442 (21%)

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYG 567
           + +A   F     +    +    +  +   RR   +  + GV R     E+R ++  +  
Sbjct: 13  IPNATKIFVNGCWVGIHRDPDLLVKTLRQLRRQVDVNTEVGVVRDIRLSELR-LYTDYGR 71

Query: 568 RICPAETSEGH----NIGLVSSLTSFARVNAYGFI-ETPYRKVCDGKVTNDVVYLSAMEE 622
              P    E          +  L    ++       E   R   +      + Y+   EE
Sbjct: 72  CSRPLFIVENQRLLIKKPDIRRLQQRDQLPPPSPDDENTVRGWHELVTKGFIEYVDTEEE 131

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E   I+   S L                         K    +  P  ++ + AS+IPF 
Sbjct: 132 ETTMISMTISDL-----------VNARNSPPTAASIVKYTHCEIHPSLILGVCASIIPFP 180

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +                           R   +  V    
Sbjct: 181 DHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---- 216

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
                                              Q+PLV                    
Sbjct: 217 -------------------------------LYYPQKPLV----------TTRAMEHLHF 235

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-- 860
             L  G N +VA   + GYN EDS+++++  +    F S+    +    +      +E  
Sbjct: 236 RQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFYRSYRDEEKRMGTLVKEEF 295

Query: 861 ---ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                 +   +       +D+ G+   G  V+   +++GK TP  +           +  
Sbjct: 296 GRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEXVIIGKTTPVTQDE---------SGG 346

Query: 918 GEKAVDVRDTSLRVPSGVSGTV 939
                  RD S  +    SG V
Sbjct: 347 QAARYTKRDQSTSLRHSESGMV 368


>gi|256575362|gb|ACU87649.1| RpoB [Gallibacterium anatis]
          Length = 188

 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 113/186 (60%), Positives = 141/186 (75%), Gaps = 1/186 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 3   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPI 62

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS
Sbjct: 63  ETPEGPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANS 122

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +LDE+  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 123 NLDENFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRAL 182

Query: 692 MGCNMQ 697
           MG NMQ
Sbjct: 183 MGPNMQ 188


>gi|330785430|gb|AEC46521.1| RNA polymerase II second largest subunit [Sigridea californica]
 gi|330785432|gb|AEC46522.1| RNA polymerase II second largest subunit [Sigridea californica]
          Length = 307

 Score =  192 bits (488), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 63/377 (16%), Positives = 105/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQEDSVIVNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E+ E  A+                   +  G      
Sbjct: 64   LF-RSLFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEEDGFVAPGTRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++   + +                E  QR  E  K          E    +K+ 
Sbjct: 123  DVIIGKTSPFQAPM------------QEGSEGGQRTKEHTKRDVSAPLRSTEAGIVDKVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSNGIVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVSSLTGHEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+S+L        G  ++Y+
Sbjct: 260  ----------------------------ATP-FTEVTVSEISSLLAENGYQRRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG   +  V +G  Y
Sbjct: 291  GHTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 67/197 (34%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      DL  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  +   +V         + ++E 
Sbjct: 51  DSVIVNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  D+++GK +P         E   R        DV        +G+   V
Sbjct: 111 GFVAPGTRVSGEDVIIGKTSPFQAPMQEGSEGGQRTKE-HTKRDVSAPLRSTEAGIVDKV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTTEGRRSVKVRTRT 186


>gi|40644557|emb|CAD89597.1| RNA polymerase II, second largest subunit [Senecio vulgaris]
          Length = 325

 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 63/381 (16%), Positives = 107/381 (28%), Gaps = 73/381 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVGGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T                  A  D    +     +  + TS    E    +++ 
Sbjct: 137  DVIIGKTTP----------------IAQDDAAQGQASRYTRRDHSTSLRHSETGMVDQVL 180

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 181  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 235

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +          +  +   L      
Sbjct: 236  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVSFVDNISRAL------ 289

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                 G   +Y+
Sbjct: 290  ---------------------------------------------HKCGYQMRGFETMYN 304

Query: 1239 GLTGEPFDRPVTVGYIYMLKL 1259
            G TG      + +G  Y  +L
Sbjct: 305  GHTGRRLPAMIFLGPTYYQRL 325



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 58/184 (31%), Gaps = 23/184 (12%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNFQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V   D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDDDGLAPPGTRVGGEDVIIGKTTPIAQDD--------AAQGQASRYTRRDHSTSLRHSE 172

Query: 936 SGTV 939
           +G V
Sbjct: 173 TGMV 176


>gi|125560304|gb|EAZ05752.1| hypothetical protein OsI_27986 [Oryza sativa Indica Group]
          Length = 1347

 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 89/432 (20%), Positives = 136/432 (31%), Gaps = 95/432 (21%)

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
            I ++ I  RL      +N   G    KK  V S D+          Q    ++ +   V 
Sbjct: 967  IENKEITKRLKH---KENINFGKTPSKKGLVDSLDIDGLPYIGASLQ---SNDIIIGKVS 1020

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
                 +       E     K+      D           V +   R  + GDK A  HG 
Sbjct: 1021 DCGEDHSIKLLHTEKGIVEKVVLSATDDGTNSAF-----VTLRQTRSPRIGDKFASMHGQ 1075

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
            KG++  +   E+ PF   G   DIV+NP G P+R   GQ+ E  LG      G    +  
Sbjct: 1076 KGVIGFLDSQENFPFTHQGIVPDIVINPHGFPTRQTPGQLLEAALGKGIALGGATRYATP 1135

Query: 1157 NDYKANGDISPLRS-----FLEKVIGTGSHTEKISDYDDDS--VLRVAEQWKSGVPV--S 1207
                +   I+         FL   +      + +  ++     VL V    +   P   +
Sbjct: 1136 FTSPSVEVITEQLHNKFDWFLFMKVEELEMFQMLLHFNPGQGWVLEVGRGERDQRPHRRA 1195

Query: 1208 TPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
              V  G     +   L  A     GQ  +     G P                       
Sbjct: 1196 CGV-AGVHRADV---LPAAPPHGRGQGQV----PGTP----------------------- 1224

Query: 1268 YARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DV- 1322
             AR       +T+QP+  +   GG + GEME  C+ A+GAA  L E L + SD     V 
Sbjct: 1225 -AR-CNP---LTRQPVEDRRRYGGVKFGEMERDCLLAHGAAANLHERLFLLSDVSRLHVC 1279

Query: 1323 -------------------VGRTRVYESIVAG---------NDTFETGTPESFNVLVKEM 1354
                                GR       V G          +      P    +L +E+
Sbjct: 1280 RRCQRAAVVVSPAVAADGGCGRK------VRGPYCRFCRSAEEVVRVSVPYGAKILYQEL 1333

Query: 1355 QALGLSIDLENS 1366
             ++G+ +  +  
Sbjct: 1334 FSMGICLKFDTE 1345



 Score =  141 bits (356), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 132/946 (13%), Positives = 264/946 (27%), Gaps = 221/946 (23%)

Query: 29   LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA------AMLEFV 77
            L+  Q  SY+ F+            GLQ  F S     V P    S        A ++F 
Sbjct: 235  LVSHQINSYNDFVS----------HGLQKMFDSLDEVTVEPDYDPSKKVGPWRHATIKFG 284

Query: 78   SYEFDPPKFDVDDC--------------LWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
              E + P F VD+C                + +TY+  +K+ + + V+ + +   AK+ +
Sbjct: 285  RVELEEPVFWVDNCDLDVETLKLKPKHARLQKMTYSSKMKVEMTVQVYSLHKSDKAKTGE 344

Query: 124  D--------IKE-QSIYMGDLPLMTK------DGTFVIKGIQRIVVSQLHRSPGIHFDHD 168
            D        +KE + + +G LP+M         G F+IKG++++ V++  R         
Sbjct: 345  DPYIQRKHIMKETKWVTIGKLPVMESECEYDFGGYFLIKGMEKVFVAEEQRC-------- 396

Query: 169  KGRASLSGKLLYACRIIPDQGLWMDIE------FDSKDIIHVRIDRRRK----------V 212
              R  ++    +       Q   +  E        S D         RK          +
Sbjct: 397  LSRIWINDSPTWEA---CYQRSQIRRENISIKPVQSNDGF-------RKVINLYFLGATI 446

Query: 213  PVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE- 271
            P+     ALG+ S+                                K +  ++DI   + 
Sbjct: 447  PIWIMFFALGVSSD--------------------------------KEAFDIIDIQECDA 474

Query: 272  ---QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
                +I +    +    +  + +G     I        +  +   +   G          
Sbjct: 475  SMANIISATITESHEQCEGFQREGRASEYIDKLIRNTKFPPKGSFDEYIGRHMFPDVSGN 534

Query: 329  DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
              K+L            +L   S N  +  R+      NK    A   + R +    +  
Sbjct: 535  RSKAL----FLGYMVRCLLLASSGNRKSDNRDDFR---NKRLDLACELLQRELWVHIMHA 587

Query: 389  FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK--EDIIAIIKILVDL 446
                  +                      +   L+                    I+  L
Sbjct: 588  QKRMVKVMQRHLSGDGDLQPLECYVHASIVTNGLNRAFSTGSWCHPFNKRERCSGIIATL 647

Query: 447  RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER-SIKERISSVDIDSVMPQDLIN 505
            R         D    R+  +      +     L R              +D ++ Q++  
Sbjct: 648  RRTNPLQMMSDMRKTRQWVAYAGKAGDARYPCLAREPSVDALVSCGMKKLDELLLQEISG 707

Query: 506  AKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
               +      F   + +    + V  +  +   RR   +      +     +   +    
Sbjct: 708  KDRI------FLNGNLVGVCADSVEFVLHLRSMRRRKQIDAQVEIKRDKQNKEVRIFSDP 761

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
               + P    E       +      R N             +    N +  +   EEE+ 
Sbjct: 762  GRILRPLLIVE-------NLRNIMNRKNGS-------YSFQELMDQNIIELIGVEEEEDI 807

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
              A     L                              +  P  ++ ++ S+IPF  +D
Sbjct: 808  RCAYGIRHLFAGDEEKN---------------FSFYTHCELDPSFLLGLSCSIIPFANHD 852

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             + R+LM      Q         P                                    
Sbjct: 853  TAKRILMQAEKISQQAIGYSTTNPL----------------------------------- 877

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
                     + S    Y      ++    C+ +R      D    +      P    G  
Sbjct: 878  -----FRVDTHSHQLYYPQRPLFKTVAADCLGKR------DYTSGSKHDFARPEYFNG-- 924

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
               +N +V+     G+N EDS++++   +   +F + H + ++    + ++      ++ 
Sbjct: 925  ---QNAIVSISVHQGFNQEDSLVLNRASLERGMFRTQHFKSYKAPIENKEITKRLKHKEN 981

Query: 866  PNV-----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
             N       +  + ++D  G+  +GA +   DI++GK++  GE   
Sbjct: 982  INFGKTPSKKGLVDSLDIDGLPYIGASLQSNDIIIGKVSDCGEDHS 1027


>gi|330785428|gb|AEC46520.1| RNA polymerase II second largest subunit [Sigridea californica]
          Length = 300

 Score =  192 bits (487), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 62/372 (16%), Positives = 106/372 (28%), Gaps = 81/372 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + +    + +   +   V        +     +V+    +R     
Sbjct: 1    NILYYPQKPLATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQEDSVIVNQSSIDRGLFRS 60

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 61   LFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEEDGFVAPGTRVSGEDVIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++   + +                E  QR  E  K          E    +K+      
Sbjct: 121  KTSPFQAPM------------QEGSEGGQRTKEHTKRDVSAPLRSTEAGIVDKVL----- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 164  -VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSNGIVPDLIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 223  PHAIPSRMTIAHLIECLLSKVSSLTGHEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+S+L        G  ++Y+G TG 
Sbjct: 253  -----------------------ATP-FTEVTVSEISSLLAENGYQRRGFEVMYNGHTGR 288

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 289  KLNAQVFLGPTY 300



 Score = 78.6 bits (192), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQEDSVIVNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +   +V         + ++E G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEEDGFVAPGTRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK +P         E   R        DV        +G+   V+      R  
Sbjct: 114 GEDVIIGKTSPFQAPMQEGSEGGQRTKE-HTKRDVSAPLRSTEAGIVDKVLVTTTEGRRS 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRT 179


>gi|296280551|gb|ADH04623.1| RNA polymerase beta subunit [Moraxella sp. CI24]
          Length = 187

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 109/185 (58%), Positives = 138/185 (74%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 3   VKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPI 62

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL  +A+ N +GF+ETPY KV DGKV++++ YLSA+EE    IAQA+S
Sbjct: 63  ETPEGPNIGLINSLAVYAKTNEFGFLETPYLKVIDGKVSDEIEYLSAIEEVGTVIAQADS 122

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +DE+G  TE+ V  R  GE + +  +K+  +D SP+QVVS+AASLIPFLE+DD+NR   
Sbjct: 123 PIDENGRLTEDYVSVRNYGEFVRMSPDKVTHMDVSPRQVVSVAASLIPFLEHDDANRAXX 182

Query: 693 GCNMQ 697
           G NMQ
Sbjct: 183 GPNMQ 187


>gi|83414663|dbj|BAE54122.1| RNA polymerase beta subunit [Streptococcus constellatus]
          Length = 172

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 64/110 (58%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I  GDKMAGRHGNKG+VSRI+P EDMP+L DG
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIPVGDKMAGRHGNKGVVSRIVPVEDMPYLPDG 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDRASSDDL 164



 Score = 51.6 bits (122), Expect = 0.001,   Method: Composition-based stats.
 Identities = 38/63 (60%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             G ILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGHILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|114646703|ref|XP_001161478.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide B
           isoform 1 [Pan troglodytes]
          Length = 995

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 116/947 (12%), Positives = 274/947 (28%), Gaps = 183/947 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 39  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 89

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 90  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 139

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 140 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 198

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSE-EILSTF 232
            G  + +     ++    ++    +   ++R +     +P+     A+G++S+ EI+   
Sbjct: 199 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 255

Query: 233 YPKIVY---------SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
             +              +       + A   +        +      +  IE  ++L + 
Sbjct: 256 GTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGGPKKTKIEEARELLAS 315

Query: 284 LLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            +  L    VK     + C+    +   ++  +      +     +++          + 
Sbjct: 316 TI--LTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNKRL-----ELAGQL 368

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           + +L+ D           +       ++ A  D+ + MR   ++   V     +   +  
Sbjct: 369 LSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNA--ISTGNWSL 426

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
            ++ +   G  ++  RL+  +   +            K+                     
Sbjct: 427 KRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQ---------PSQWG 477

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +    +  + +    +  +           D   V     +  + V     E      + 
Sbjct: 478 MLCPSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVF 537

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL- 582
            +  + N L  I   ++L    +  + RA    E   +      R     +  G      
Sbjct: 538 LVFLNGNILGVIRDHKKLVNTFRL-MRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPY 596

Query: 583 -VSSLTSFARVN-AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
            +      A  N     +   YR   D    + V YL   EE +  IA            
Sbjct: 597 IIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIAL----------- 645

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                             +    ++  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 646 ------------YEHTINKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQA 693

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +  +         G        +   ++A                               
Sbjct: 694 MGTI---------GYNQRNRIDTLMYLLA------------------------------- 713

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                            Q+P+VK                 +   L  G+N  VA M + G
Sbjct: 714 ---------------YPQKPMVK----------TKTIELIEFEKLPAGQNATVAVMSYSG 748

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKN---- 875
           Y+ ED++++++  +       +  +  +    R T    +++   + + +          
Sbjct: 749 YDIEDALVLNKASLDRGFGRCLVYKNAKCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEI 808

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           +D  GI   G +V    +LV K  P           + +    +   
Sbjct: 809 LDADGICSPGEKVENKQVLVNKSMPTVTQIPLEGSNVPQQPQYKDVP 855



 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 54/299 (18%), Positives = 96/299 (32%), Gaps = 20/299 (6%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 710  YLLAYPQKPMVKTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 769

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 770  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 828

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 829  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 871

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 872  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 929

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            NP G PSRM VG++ E   G A V  G+             D+               +
Sbjct: 930  NPHGFPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLVRHGYNYLGKDY 988


>gi|282598426|gb|ADA83443.1| RNA polymerase beta subunit [Corynebacterium sp. NML96-0244]
          Length = 140

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 59/168 (35%), Positives = 86/168 (51%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+           +   L+   E++      +            
Sbjct: 1    QVLEVHLGWLAHA-GWKVDV-----DDPANADLLKKLPEELYDVPPESLT---------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I+ +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGASNEEISRLLASSKPNRDGDVMVDEHGKARLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|56694350|gb|AAW22915.1| RNA polymerase II second largest subunit [Cephalotaxus fortunei]
          Length = 533

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 73/443 (16%), Positives = 127/443 (28%), Gaps = 80/443 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 171  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 227

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 228  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSL 286

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ +R  ++ +E+     R+          +          G           K
Sbjct: 287  FFRSYRDEEKRMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 346

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++                  DE   +  +  K    TS    E    +++      D
Sbjct: 347  TTPIAQ-----------------DESGGQVSKYTKRDQSTSLRHSESGMVDQVLLTTNQD 389

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 390  GL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 444

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +          IS         +        
Sbjct: 445  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDSISKALHKCGYQMRGFETM-- 502

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 503  ---------------------------------------------YNGHT----GR---K 510

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKV 1267
                + +G  Y  +L HMV DK+
Sbjct: 511  LSAMIFLGPTYYQRLKHMVDDKI 533



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 68/452 (15%), Positives = 129/452 (28%), Gaps = 100/452 (22%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARA 552
           +  S    + I+   + ++   F     +    +    +  +   RR   +    GV R 
Sbjct: 22  EEWSTENFEEISPAAIPTSTKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNPEVGVVRD 81

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +         V+      +      +     
Sbjct: 82  IRLRELR-LYTDYGRCSRPLFVVENQRLKIKK-------VDINNLQASREDGWHELVTQG 133

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E            +  P  ++
Sbjct: 134 FIEYVDTEEEETTMISM----------TINDLVNARTNPE--DAYSHTYTHCEIHPSLIL 181

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 182 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 221

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 222 DTLAYV-----------------------------------LYYPQKPLV---------- 236

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 237 TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 296

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 297 RMGTLVKEEFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE-- 354

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                  +         RD S  +    SG V
Sbjct: 355 -------SGGQVSKYTKRDQSTSLRHSESGMV 379


>gi|10434547|dbj|BAB14296.1| unnamed protein product [Homo sapiens]
          Length = 714

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 175/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 217  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 275

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V           D 
Sbjct: 276  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVTSYTGYDMEDA 335

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 336  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 385

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 386  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 443

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 444  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 475

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 476  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 510

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 511  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 570

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 571  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 630

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 631  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 690

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 691  VPYVFRYFVAELAAMNIKVKLD 712



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 73/456 (16%), Positives = 151/456 (33%), Gaps = 41/456 (8%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S L  + + +N +  ++H R    + +G          +R + P  +G +CP  T +G  
Sbjct: 30  SGLCVVADKLNFIRYLSHFR---CVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEP 86

Query: 580 IGLVSSLTSFARVNAYGFIETPY-RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GL++ LT+   V             +C+  VT           E   +      +    
Sbjct: 87  CGLMNHLTAVCEVVTQFVYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDGVMVGWVD 146

Query: 639 SFTEELVFCRCAG-----EEILVPREKIDFIDASPKQVVSI--------AASLIPFLEND 685
                 +           E+ + P  ++  I  + K  +             + P     
Sbjct: 147 KDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLA 206

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                L+G   Q      +  +  F G      +   S  +++A     +   D  +   
Sbjct: 207 LGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPR 263

Query: 746 RSVEGDLDPSTSG--VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
              +  +   T G  +  Y+     +  +     Q PLV+                 D+ 
Sbjct: 264 NMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMD 312

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEIT 862
           +  +G N +VA   + GY+ ED+M++++          S++  EF  ++   K G   + 
Sbjct: 313 NYPIGTNAIVAVTSYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLV 372

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK-- 920
             I       L+ +D+ G+  +GA++  GD     +     +  T E  ++     E   
Sbjct: 373 FGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCV 427

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             +++  S    SG    V       R+    ++ +
Sbjct: 428 VDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 463


>gi|310750818|gb|ADP09202.1| RpoB' [Natrialba sp. Aidin-3]
          Length = 173

 Score =  192 bits (487), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 49/196 (25%), Positives = 77/196 (39%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTENGVVPDLIVNPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   +                       
Sbjct: 91   PSRMTVGHILEMIGGKLGAMEGRRVDGTPFLGEDESE----------------------- 127

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                         + G+  +                     + +G+  +Y G+TGE  + 
Sbjct: 128  ------------LRDGLEDA-------------------GFNSAGKETMYSGVTGEKIEA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGIIFYQKLYHMV 172


>gi|108708689|gb|ABF96484.1| DNA-directed RNA polymerase III 130 kDa polypeptide, putative,
            expressed [Oryza sativa Japonica Group]
          Length = 1039

 Score =  191 bits (486), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 65/384 (16%), Positives = 114/384 (29%), Gaps = 69/384 (17%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ +        +    I   G   +   +    A+      D+ D  +   S +   
Sbjct: 719  DSLLYLLVYAQRPLLTTKTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRG 778

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                    ++ + K +       ++I    RDKD   +  +            G    + 
Sbjct: 779  FGRCIAMKKYTVTKEK-YEGGYSDRIVKPQRDKDGALLKQNMRALDEDGFAAPGLIIRNH 837

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K T  ++   S    +                      Y+ S ++ +        
Sbjct: 838  DIYVNKQTPRNTKRDSGAHLTD-------------------RDYKDSPAVYKGVDGETTV 878

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
              +           ++K  +   R  + GDK + RHG KG+   I+  ED PF + G   
Sbjct: 879  VDRVMLCSDTDEKLIIKCIIRHTRRPEVGDKFSSRHGQKGVCGTIVQQEDFPFSERGICP 938

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP G PSRM +G++ E   G A V  G+          +                 
Sbjct: 939  DLIMNPHGFPSRMTIGKMIELLGGKAGVSCGQFHYGSAFGEPSGNAD------------- 985

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                  E I+  L       +G+ +LY 
Sbjct: 986  ------------------------------------KVEDISRTLVKHGFSYNGKDLLYS 1009

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+ G P    V +G IY  KL HM
Sbjct: 1010 GILGHPCQAYVFMGPIYYQKLKHM 1033



 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 105/725 (14%), Positives = 221/725 (30%), Gaps = 113/725 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-AAMLEFVSYEFDPP--- 84
           L++    S+++F+           +G++   K+   I A +  +  L + S     P   
Sbjct: 50  LVKEHIDSFNYFIT----------KGIRNIVKANNRIEARNNPSIFLRYNSVRVGVPSVQ 99

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                 K     C   D TY+ P+   +   V    E     +          +G LP+M
Sbjct: 100 VQYIAEKITPHFCRLTDRTYSAPVLADIEYTVGKQYELKRKPNFI--------IGYLPIM 151

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPG--IHFDHDKGR- 171
                                      G F++KG +++++ Q   S    I     KGR 
Sbjct: 152 LRSHACVLNGKDEAELARYGECPLDPGGYFIVKGTEKVILIQEQLSKNRIIIDTDSKGRV 211

Query: 172 ---ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEE 227
               + S   + +  +I          F  K+ I++++++  + +P+   + A+GM+S++
Sbjct: 212 IASVTSSTHEIKSKTVI----------FMEKEKIYLQLNQFTKPIPIIVVMKAMGMESDQ 261

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKS 287
            ++    +        +      A + +   K +   +D         +G +        
Sbjct: 262 EVAQMVGRDPRYGDLLYPSIQECAFERIYTQKQALQYMDDKVMYP--GAGNQKEGRSKSI 319

Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEK-----SLEEIFHSEIR 342
           L++  V  + + S       +   ++     +  + A    D+       LE        
Sbjct: 320 LRDVFVAHVPVESGNFRPKCIYTAVMLRRMMDAILNADTFDDKDYVGNKRLELSGQLISL 379

Query: 343 DIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
               L+    +N   + N      +    D  L I       +       E   +   +D
Sbjct: 380 LFEDLFKTMNSNAVELMNKTSEKIHSSPLDLSLHI------KENIITHGLERAISTGNWD 433

Query: 403 SDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLG 460
             ++ +   G  ++  RL+                   K      L+  +  +    +  
Sbjct: 434 IKRFRMHRKGVSQVLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTP 493

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
                 + + L     +   + E  +     S+ ++ +            S +   F   
Sbjct: 494 EGEACGLTKNLALLTHVTTDQEEGPLMNLCYSLGVEDLSLLSGEEIHASGSFLV-MFNGL 552

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHN 579
            L +  +     + +   RR   +G+          +   +H  +  GR+C         
Sbjct: 553 ILGKHRQPQRFANAMRKLRRSGIIGE--FVSIFVNEKQHCIHIASDGGRVCRPLIIADKG 610

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I  V              +    R   D      + YL   EE N  IA           
Sbjct: 611 IPRVKEHH-------MKQLRDGIRSFDDFLRDGLIEYLDVNEENNALIA----------- 652

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                       ++  V R  I  I+  P  ++ + A LIP+  ++ S R    C M +Q
Sbjct: 653 -------LYEHEDQDDVQRSSITHIEIEPLTILGVVAGLIPYPHHNQSPRNTYQCAMGKQ 705

Query: 700 AVPLL 704
           A+  +
Sbjct: 706 AMGNI 710


>gi|269978611|gb|ACZ55990.1| RNA polymerase II [Fusarium cerealis]
          Length = 312

 Score =  191 bits (486), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 58/380 (15%), Positives = 108/380 (28%), Gaps = 75/380 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E   +           +       +  G      
Sbjct: 68   LF-RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+Q  Q       ++     +  Q   + +           
Sbjct: 127  DIIIGKTAPIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA---------- 176

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 177  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 227  DVIINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------- 261

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 262  ----------------------------ATP-FTDVTVDSVSDILRKHGYQSRGFEVMYN 292

Query: 1239 GLTGEPFDRPVTVGYIYMLK 1258
            G TG      V  G  Y  +
Sbjct: 293  GHTGRKLRAQVFFGPTYYQR 312



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 66/197 (33%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA   + G
Sbjct: 1   TNYSRRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   L   EI           +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P  +       +        +    RD S  + S  
Sbjct: 111 LDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTE 163

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 164 NGIVDQVILTVNADNVK 180


>gi|3002819|gb|AAC08937.1| RPB140 [Chloranthus spicatus]
          Length = 533

 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 75/488 (15%), Positives = 136/488 (27%), Gaps = 84/488 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 126  HDLVAKGFIEYVDTEEEETTMISMTISDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 185

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+   L+      +  V        +    +  
Sbjct: 186  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEH 242

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 243  LHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 301

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R+          +          G           K+T ++           
Sbjct: 302  KEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQ---------- 351

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                   DE   +     +  + TS    E    +++      D +     R VKV +  
Sbjct: 352  -------DETQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRS 399

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 400  VRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 459

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+  +         +IS         +                        
Sbjct: 460  MGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------------ 501

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                          +G +    G         + +G  Y  +L 
Sbjct: 502  -----------------------------YNGHT----GR---KLTAMIFLGPTYYQRLK 525

Query: 1261 HMVSDKVY 1268
            HMV DK++
Sbjct: 526  HMVDDKIH 533



 Score =  115 bits (289), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 73/452 (16%), Positives = 129/452 (28%), Gaps = 98/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   +  A   F     +         +  +   RR   +  + GV R 
Sbjct: 19  EEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRD 78

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +         + A    ET      D     
Sbjct: 79  IRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKK-----DIRALQQRETQEEGWHDLVAKG 132

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E      E     +  P  ++
Sbjct: 133 FIEYVDTEEEETTMISM----------TISDLVSARLNPE--EAYSETYTHCEIHPSLIL 180

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 181 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 220

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 221 DTLAYV-----------------------------------LYYPQKPLV---------- 235

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 236 TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 295

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +    
Sbjct: 296 KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDE-- 353

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                            RD S  +    SG V
Sbjct: 354 -------TQGQASRYTRRDHSTSLRHSESGMV 378


>gi|225572595|gb|ACN93883.1| RpoB [Gallibacterium anatis]
 gi|225729824|gb|ACO24827.1| RpoB [Gallibacterium anatis]
          Length = 188

 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 113/186 (60%), Positives = 140/186 (75%), Gaps = 1/186 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP 
Sbjct: 3   VKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPI 62

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS
Sbjct: 63  ETPEGPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANS 122

Query: 633 SLDEDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +LDE+  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA LIPFLE+DD+NR L
Sbjct: 123 NLDENFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAVLIPFLEHDDANRAL 182

Query: 692 MGCNMQ 697
           MG NMQ
Sbjct: 183 MGSNMQ 188


>gi|161331515|gb|ABX60675.1| RpoB [Bacillus sp. FSL_h8547]
          Length = 223

 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 74/199 (37%), Positives = 95/199 (47%), Gaps = 54/199 (27%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 79   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 138

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  + S + D     D+       
Sbjct: 139  PDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARKLGMHVASPVFDGAREEDVWSTLEEA 198

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 199  GMARDAK----------------------------TVLYDG------------------- 211

Query: 1233 QSILYDGLTGEPFDRPVTV 1251
                    TGEPFD  V+V
Sbjct: 212  -------RTGEPFDNRVSV 223



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 58/89 (65%), Positives = 71/89 (79%)

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
           RDIPNV E+ L+N+D+ GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA 
Sbjct: 2   RDIPNVGEDALRNLDDRGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAR 61

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           +VRDTSLRVP G  G V+DV++FNR   D
Sbjct: 62  EVRDTSLRVPHGGGGIVLDVKVFNREDGD 90


>gi|300394680|gb|ADK11878.1| DNA-directed RNA polymerase II subunit two [Amylocorticium
            subsulphureum]
          Length = 344

 Score =  191 bits (486), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 63/377 (16%), Positives = 105/377 (27%), Gaps = 75/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 43   DTMANILYYPQKPLATTRSMLYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 102

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + EQ E   RD                  I  G      
Sbjct: 103  LF-RSIYYRSYMDLEKKSGIQQLEQFEKPTRDNTLRMKHGTYEKLEDDGLIAPGTGVAGE 161

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 162  DIIIGKTAPIPPDSEELGQRTRTHSRRDVSTPLKSTENGIVDQVLI-------------- 207

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 208  ------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVP 261

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  L      +G +                           
Sbjct: 262  DLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 296

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++  L        G  +++ 
Sbjct: 297  ----------------------------ATP-FTDLTVESVSKFLLQKGYQSRGLEVMHH 327

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 328  GHTGRKLQAQVYLGPTY 344



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/220 (17%), Positives = 80/220 (36%), Gaps = 20/220 (9%)

Query: 727 IVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVG 785
           I+     I+   D  +    + +  +     G+     L++           Q+PL    
Sbjct: 1   ILGICPSIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRMDTMANILYYPQKPL---- 56

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                             +L  G+N +VA + + GYN EDS+++++  +   +F SI+  
Sbjct: 57  ------ATTRSMLYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYR 110

Query: 846 EFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +  + + + +   E        +   +     + +++ G+I  G  V   DI++GK  P
Sbjct: 111 SYMDLEKKSGIQQLEQFEKPTRDNTLRMKHGTYEKLEDDGLIAPGTGVAGEDIIIGKTAP 170

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                    E+L +        DV        +G+   V+
Sbjct: 171 I----PPDSEELGQRTRTHSRRDVSTPLKSTENGIVDQVL 206


>gi|308194105|gb|ADO16470.1| RNA polymerase beta subunit [Gemella haemolysans]
          Length = 207

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 74/197 (37%), Positives = 97/197 (49%), Gaps = 54/197 (27%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 65   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 124

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+    +     
Sbjct: 125  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDVWSTVAEAGMA 184

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                            T ++DG                      
Sbjct: 185  KDAK----------------------------TVLYDG---------------------- 194

Query: 1236 LYDGLTGEPFDRPVTVG 1252
                 TGEPFD  V+VG
Sbjct: 195  ----RTGEPFDSRVSVG 207



 Score = 69.3 bits (168), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 47/71 (66%), Positives = 53/71 (74%)

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRVP G  G 
Sbjct: 1   RGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRVPHGADGV 60

Query: 939 VVDVRIFNRHG 949
           V DV+IF R  
Sbjct: 61  VADVKIFKRED 71


>gi|224419504|emb|CAX51333.1| RNA polymerase beta subunit [Corynebacterium freneyi]
          Length = 122

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 54/100 (54%), Positives = 72/100 (72%), Gaps = 8/100 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 23   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 82

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 83   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 122


>gi|224419498|emb|CAX51330.1| RNA polymerase beta subunit [Corynebacterium freneyi]
          Length = 126

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 54/100 (54%), Positives = 72/100 (72%), Gaps = 8/100 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 27   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 86

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 87   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 126


>gi|224419492|emb|CAX51327.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 121

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 54/100 (54%), Positives = 72/100 (72%), Gaps = 8/100 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 22   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 81

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 82   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 121


>gi|224419488|emb|CAX51325.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 113

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 54/100 (54%), Positives = 72/100 (72%), Gaps = 8/100 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 14   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 73

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GEM
Sbjct: 74   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEM 113


>gi|40642970|emb|CAD88979.1| DNA-directed RNA polymerase subunit B [Cornus kousa]
          Length = 317

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 66/387 (17%), Positives = 106/387 (27%), Gaps = 82/387 (21%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  V        +    +       +      + AI      +  D+ +   S
Sbjct: 13   YQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQS 72

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             V        +F R   D+ ++  ++ +E      R           +          G 
Sbjct: 73   SVDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGT 131

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T ++ D                           + Q            
Sbjct: 132  RVSGEDVIIGKTTPIAQD-------------------------DAQGQASRYTKRDHSTS 166

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                E            LR VKV V   R  Q GDK + RHG KG V      EDMP+  
Sbjct: 167  LRHSETGTVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGXVGMTYTQEDMPWTV 226

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   DI++NP  +PSRM +GQ+ E  +G     +GK+                      
Sbjct: 227  EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHVGKEGD-------------------- 266

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP  D    + I+  L        G 
Sbjct: 267  ---------------------------------ATPFTD---VDNISKALHKCGYQMRGF 290

Query: 1234 SILYDGLTGEPFDRPVTVGYIYMLKLN 1260
              +Y+G TG      + +G  Y  +L 
Sbjct: 291  ETMYNGHTGRKLTAMIFLGPTYYQRLK 317



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 62/185 (33%), Gaps = 24/185 (12%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQLRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  V    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSVDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDDDGLAPPGTRVSGEDVIIGKTTPIAQDD---------AQGQASRYTKRDHSTSLRHSE 171

Query: 936 SGTVV 940
           +GTV+
Sbjct: 172 TGTVL 176


>gi|37956425|gb|AAP15382.1| RNA polymerase beta subunit [Pelobacter massiliensis]
          Length = 211

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 116/210 (55%), Positives = 156/210 (74%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           R+S  +++++MP DLIN+KPV + V EFF SSQLSQ  +  N LS +TH RRLSALG GG
Sbjct: 2   RMSLQEVENLMPHDLINSKPVSAVVKEFFGSSQLSQFMDQTNPLSEVTHKRRLSALGPGG 61

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
           + R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N +GF+ETPYR V DG
Sbjct: 62  LTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEHGFVETPYRVVRDG 121

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
           +VT++V + SA+EEE   IAQAN+ +DE G F  + +  R +GE +LV R++++ +D +P
Sbjct: 122 RVTDEVRFFSALEEEGHAIAQANAEIDETGRFAADYISARKSGEFVLVGRDELELMDVAP 181

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            Q+VS+AASLIPFLE           NMQR
Sbjct: 182 MQLVSVAASLIPFLEKTTQTARSWARNMQR 211


>gi|327239541|gb|AEA39620.1| RpoB [Corynebacterium striatum]
 gi|327239547|gb|AEA39623.1| RpoB [Corynebacterium striatum]
          Length = 140

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 87/168 (51%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+           +   L++  E++                   
Sbjct: 1    QVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 40   -------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|114579614|ref|XP_001144922.1| PREDICTED: RNA polymerase I polypeptide B isoform 3 [Pan troglodytes]
          Length = 912

 Score =  191 bits (485), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 415  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 473

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 474  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 533

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 534  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 583

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 584  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 641

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 642  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 673

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 674  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 708

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 709  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 768

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 769  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 828

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 829  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 888

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 889  VPYVFRYFVAELAAMNIKVKLD 910



 Score = 90.5 bits (223), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 30  LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 81

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 82  GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 139

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 140 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 199

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 200 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 256

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 257 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 316

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 317 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 376

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 377 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 436

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 437 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPILTYQDRSDNKLYRLQ- 492

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 493 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 542

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 543 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 602

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 603 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 657

Query: 953 NERS 956
           ++ +
Sbjct: 658 DKFA 661


>gi|312204340|gb|ADQ47487.1| RNA polymerase II second largest subunit [Odontotrema cassiopes]
          Length = 297

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 115/375 (30%), Gaps = 81/375 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +++ +R   + R  +E   +    + + L    Y +L +   I  G      
Sbjct: 60   RSLFYRAYVEQEKR---IGRSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +                  ++
Sbjct: 117  DIIIGKTAPIAPDDEELGQRTKLHTKRDASTPLRSTESGI------------------VD 158

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+          L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 159  KVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFSSEGIVP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DIIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 252  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYN 282

Query: 1239 GLTGEPFDRPVTVGY 1253
            G TG      V +G 
Sbjct: 283  GHTGRKLVAQVFLGP 297



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E     +  D   +     + +D+ GII  G  V+
Sbjct: 55  DRGLFRSLFYRAYVEQEKRIGRSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  SG V  V +     
Sbjct: 115 GEDIIIGKTAPIAPDDEELGQRT-------KLHTKRDASTPLRSTESGIVDKVLLTTNAE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|89142769|emb|CAJ57580.1| RNA polymerase subunit B [Microbacterium liquefaciens]
          Length = 358

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 125/257 (48%), Positives = 172/257 (66%), Gaps = 16/257 (6%)

Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           I  TL  D    ++DAL DIYR +RPG+      A ++ +  +F+  +YDL+ VGR K+N
Sbjct: 102 IEETLAKDTIVTKEDALRDIYRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYKIN 161

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTI----------------DDIDNLGN 461
            +L LD P +   +  EDI+A IK LV L  G                    DDIDN GN
Sbjct: 162 HKLGLDQPLNSSVLTVEDIVATIKYLVRLHAGTEETFTGIRGGKKAEIRLATDDIDNFGN 221

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
           RR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +SQ
Sbjct: 222 RRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGTSQ 281

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET E  NIG
Sbjct: 282 LSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPESPNIG 341

Query: 582 LVSSLTSFARVNAYGFI 598
           L+ +L +FAR+N +GFI
Sbjct: 342 LIGALATFARINPFGFI 358



 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/169 (36%), Positives = 87/169 (51%), Gaps = 13/169 (7%)

Query: 135 LPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
            PL T  GTF+I G +R+VVSQL RSPG++FD    +   S K + + R+IP +G W++ 
Sbjct: 1   FPLQTDKGTFIINGSERVVVSQLVRSPGVYFDKTPDKT--SDKDIVSARVIPSRGAWLEF 58

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAA 252
           E D +D + VR+DR+RK  VT FL ALGM SEEIL+ F  Y  I  +   D       A 
Sbjct: 59  EIDKRDQVGVRVDRKRKQSVTVFLKALGMTSEEILAEFAGYTSIEETLAKDTIVTKEDAL 118

Query: 253 DLMVGAKVSSSLVDIDTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             +           +  GEQV  E+ + L      + K   +  +G   
Sbjct: 119 RDI--------YRKLRPGEQVAAEAARALLDNFYFNPKRYDLAKVGRYK 159


>gi|193873112|gb|ACF23246.1| RpoB [Streptococcus mitis]
          Length = 172

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 70/168 (41%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E  LG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELPLGMAARTLGIHIATPVFDGTSSEDL 164



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|114579608|ref|XP_001145162.1| PREDICTED: RNA polymerase I polypeptide B isoform 6 [Pan troglodytes]
          Length = 1070

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 573  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 631

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 632  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 691

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 692  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 741

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 742  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 799

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 800  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 831

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 832  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 866

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 867  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 926

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 927  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 986

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 987  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 1046

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1047 VPYVFRYFVAELAAMNIKVKLD 1068



 Score = 90.5 bits (223), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 188 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 239

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 240 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 297

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 298 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 357

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 358 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 414

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 415 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 474

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 475 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 534

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 535 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 594

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 595 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPILTYQDRSDNKLYRLQ- 650

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 651 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 700

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 701 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 760

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 761 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 815

Query: 953 NERS 956
           ++ +
Sbjct: 816 DKFA 819



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 92/673 (13%), Positives = 188/673 (27%), Gaps = 133/673 (19%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------ 141
             +C  R  TY   L   +   V  +         K I +Q  ++G +P+M K       
Sbjct: 35  PAECRGRRSTYRGKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLR 84

Query: 142 ------------------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLY 180
                             G F+I GI++++   L    R+  I     K +    G   Y
Sbjct: 85  NLPPQALIEHHEEAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQY 143

Query: 181 ACRIIPDQGL---------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSE 226
              +   +           +++      + I+      RK    +P+   L AL      
Sbjct: 144 GVSMHCVREEHSAVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDY 197

Query: 227 EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
           +I    + +++  +  D +     +  L                  V+E G      +L 
Sbjct: 198 QI----FQELIKGKEDDSFLRNSVSQMLR----------------IVMEEGCLTQKQVLN 237

Query: 287 SLKEKGVKFLGITS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVID 329
            L E     L +          + L    +   + +           T +++  A     
Sbjct: 238 YLGECFRVKLNVPDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECM 297

Query: 330 EKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF 389
           E + + + + E+     L++  +          +       K A     +      ++T 
Sbjct: 298 EDNPDSLVNQEVLTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTD 349

Query: 390 SVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG 449
           ++ +     +        L   G ++    L L     +  +   D +  I+ L   R  
Sbjct: 350 NLMKIFTMGIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR-- 405

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
              +    +    R  +V  +L   +                  +   +M       + V
Sbjct: 406 --CVHRGADFAKMRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVV 456

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
              V      + L  L   V  +    H R  S      +     G   +D+ P     +
Sbjct: 457 TQFVYTASIPALLCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSL 513

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
              +      I     +               +      ++   V  L   +EE      
Sbjct: 514 RHFKVLREKRIPPWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE------ 567

Query: 630 ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
               L          V          V   +    +  P  ++S+ A+ IPF +++ S R
Sbjct: 568 ----LIGTMEQIFMNVAIFEDEVFAGVTTHQ----ELFPHSLLSVIANFIPFSDHNQSPR 619

Query: 690 VLMGCNMQRQAVP 702
            +  C M +Q + 
Sbjct: 620 NMYQCQMGKQTMG 632


>gi|17975048|ref|NP_536562.1| A25R [Monkeypox virus Zaire-96-I-16]
 gi|56404925|sp|Q8V4V3|RPO2_MONPV RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|17529915|gb|AAL40593.1|AF380138_135 A25R [Monkeypox virus Zaire-96-I-16]
          Length = 1164

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 146/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSTKPYNNKGENRPVCFPSSNETSIDAYMQFAKQCYEYSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P++  V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYESKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|327239537|gb|AEA39618.1| RpoB [Corynebacterium striatum]
          Length = 141

 Score =  191 bits (485), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 61/169 (36%), Positives = 89/169 (52%), Gaps = 36/169 (21%)

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +GQ+ E HLGW     G K+           +   L++  E++                 
Sbjct: 1    LGQVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP------------- 41

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEP 1244
                     +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP
Sbjct: 42   ---------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEP 92

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 141


>gi|56404712|sp|O57230|RPO2_VACCA RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|2772787|gb|AAB96526.1| RNA polymerase subunit rpo132 [Vaccinia virus]
 gi|47088464|gb|AAT10534.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus]
          Length = 1156

 Score =  191 bits (484), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 702  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 761

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 762  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAIA-------RN 814

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 815  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 858

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 859  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 911

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 912  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 971

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 972  LSDEELSDKIFCEK--------------------------------------ILYDPETD 993

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 994  KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1053

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1054 IAHGAANTITEVL 1066


>gi|68449013|gb|AAY97135.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
 gi|68449215|gb|AAY97336.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
 gi|300872759|gb|ADK39161.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 146/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSTKPYNNKGENRPVCFPSSNETSIDAYMQFAKQCYEYSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P++  V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYESKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|323395|gb|AAA42920.1| rpo132 RNA polymerase (early and late) [Cowpox virus]
          Length = 1156

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 702  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 761

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 762  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 814

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 815  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 858

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 859  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 911

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 912  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 971

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 972  LSDEELSDKIFCEK--------------------------------------ILYDPETD 993

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 994  KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1053

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1054 IAHGAANTITEVL 1066


>gi|56404808|sp|Q6RZF8|RPO2_RABPU RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|44971496|gb|AAS49846.1| RPXV133 [Rabbitpox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAIA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|51342296|gb|AAU01340.1| MPXV-WRAIR130 [Monkeypox virus]
 gi|58220600|gb|AAW67888.1| MPXV-SL-130 [Monkeypox virus]
 gi|59858936|gb|AAX09231.1| MPXV-COP-130 [Monkeypox virus]
 gi|68448812|gb|AAY96935.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
 gi|68449414|gb|AAY97534.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
 gi|68449614|gb|AAY97733.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 146/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSTKPYNNKGENRPVCFPSSNETSIDAYMQFAKQCYEYSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P++  V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYESKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|113195323|ref|YP_717453.1| DNA-dependent RNA polymerase subunit rpo132 [Taterapox virus]
 gi|71024918|gb|AAZ17442.1| RNA polymerase subunit 132 [Taterapox virus]
 gi|90660599|gb|ABD97712.1| DNA-dependent RNA polymerase subunit rpo132 [Taterapox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNNGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|151573164|gb|ABS17774.1| RNA polymerase II [Fusarium sp. NRRL 43523]
 gi|151573176|gb|ABS17782.1| RNA polymerase II [Fusarium sp. NRRL 43538]
          Length = 297

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 58/370 (15%), Positives = 103/370 (27%), Gaps = 75/370 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVGYIYM 1256
              V  G  Y 
Sbjct: 288  AQVFFGPTYY 297



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|20178520|ref|NP_619941.1| Rpo132 or CPXV157 protein [Cowpox virus]
 gi|133382|sp|P17474|RPO2_CWPXB RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|20153138|gb|AAM13599.1|AF482758_150 Rpo132 or CPXV157 protein [Cowpox virus]
 gi|323394|gb|AAA42919.1| rpo132 RNA polymerase (late) [Cowpox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|327239553|gb|AEA39626.1| RpoB [Corynebacterium striatum]
          Length = 140

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/168 (36%), Positives = 88/168 (52%), Gaps = 36/168 (21%)

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E HLGW     G K+           +   L++  E++                  
Sbjct: 1    GQVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP-------------- 40

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPF 1245
                    +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP+
Sbjct: 41   --------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEPY 92

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
              PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   KYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 140


>gi|33469941|ref|NP_061887.2| DNA-directed RNA polymerase I subunit RPA2 isoform 1 [Homo sapiens]
 gi|92090637|sp|Q9H9Y6|RPA2_HUMAN RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA
            polymerase I subunit 2; AltName: Full=DNA-directed RNA
            polymerase I 135 kDa polypeptide; Short=RPA135
 gi|62420281|gb|AAX81999.1| unknown [Homo sapiens]
 gi|119593998|gb|EAW73592.1| polymerase (RNA) I polypeptide B, 128kDa, isoform CRA_c [Homo
            sapiens]
          Length = 1135

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 806

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 807  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 864

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 865  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 896

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 897  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 931

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 932  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 991

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 992  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 1051

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 1052 FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 1111

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1112 VPYVFRYFVAELAAMNIKVKLD 1133



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 215/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 599

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 62.4 bits (150), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 100/721 (13%), Positives = 200/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++       +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMRIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +D+ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +               +      ++   V  L+  +EE          L       
Sbjct: 591 PWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V        +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|323098742|gb|ADX22979.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
          Length = 1164

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A            + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSTKPYNNKGXXRPVCFXSSNETSIDAYMQFAKQCYEYSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P++  V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYESKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|114579598|ref|XP_515692.2| PREDICTED: RNA polymerase I polypeptide B isoform 9 [Pan troglodytes]
 gi|114579600|ref|XP_001145399.1| PREDICTED: RNA polymerase I polypeptide B isoform 8 [Pan troglodytes]
          Length = 1135

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 806

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 807  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 864

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 865  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 896

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 897  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 931

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 932  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 991

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 992  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 1051

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 1052 FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 1111

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1112 VPYVFRYFVAELAAMNIKVKLD 1133



 Score = 90.1 bits (222), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 422

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPILTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 100/721 (13%), Positives = 201/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCLTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++ +     +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMKIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +D+ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +               +      ++   V  L   +EE          L       
Sbjct: 591 PWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V   +    +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVTTHQ----ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|119640583|gb|ABL85485.1| RNA polymerase II second largest subunit [Lecanactis abietina]
 gi|330785346|gb|AEC46479.1| RNA polymerase II second largest subunit [Lecanactis luteola]
          Length = 307

 Score =  191 bits (484), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  + +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPM------------QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSSITGREGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L  A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSDISELLEFAGYQSRGFEMMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  + +G  Y
Sbjct: 293  TGRKLNAQIFLGPTY 307



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 71/196 (36%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                  + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|149727186|ref|XP_001495511.1| PREDICTED: similar to RNA polymerase I polypeptide B isoform 1 [Equus
            caballus]
          Length = 1135

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 105/558 (18%), Positives = 180/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F +I I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNIAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            G            +   L+                + +   GT   V + +  G D  + 
Sbjct: 697  GFPLLTYRDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             I  +       A     +   +D  +  ++ +          P   +    L  D +  
Sbjct: 757  MIVNKASWERGFAHGSVYKSEFID--LSEKIKQGDDSLVFGVKPGDPRIVQKLDDDGLPF 814

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                   Q    D        +    +       E+   + I+     +D   G  + + 
Sbjct: 815  IGA----QLQYGDPYYSYLNLNTGESFVMYYKSKENCIVDNIKVCS--NDTGSGKFKCIC 868

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + + + R    GDK A RHG K                            G+ SR+    
Sbjct: 869  ITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL---- 896

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                   W    +      ++ D   N    P R  +  +I              +S+  
Sbjct: 897  -------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------ESMAG 935

Query: 1196 VAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  + +G
Sbjct: 936  KSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGVELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 97/673 (14%), Positives = 217/673 (32%), Gaps = 90/673 (13%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    ++++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFFRNSVSQMLRIVTEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y  +       N  + +         +   +  + + L  L  G+  
Sbjct: 305 GERFRVKLNLPDWYPDAQAAEFLFNQCICIH--LKSNTEKFYVLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGL------LRMERSIKERISSVDIDSVMPQDLIN- 505
            ++ D+L N+ V + G++     +  +      +++    K + + V I++     + N 
Sbjct: 363 EENPDSLVNQEVLTPGQLFLMFLKEKMEAWLVSIKIALDKKAQKTDVSINTDNLMKIFNL 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GTDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV------------------- 592
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAICEVVTQFAYTASVPALLCSLGV 539

Query: 593 -NAYGFIETPY---RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
               G    PY     V    V    V     +E    IA +   L       E+ +   
Sbjct: 540 TPVDGAPHRPYSECYPVLLDGVMVGWV----DKELAPSIADS---LRHFKVLREKRIPP- 591

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
              E  L+P      +        +    + P    +     L+G   Q      +  + 
Sbjct: 592 -WMEVALIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGREELIGTMEQIFMNIAIFEDE 650

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMK 766
            F G      +   S  +++A     +   D  +      +  +   T G  +  YR   
Sbjct: 651 VFAGVTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYRDRS 707

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +  +     Q PLV+                 D+ +  +G N +VA + + GY+ ED+
Sbjct: 708 DNKLYRLQ-TPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 827 MLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           M++++          S++  EF  ++   K G + +   +       ++ +D+ G+  +G
Sbjct: 757 MIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDDSLVFGVKPGDPRIVQKLDDDGLPFIG 816

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           A++  GD     +     +  T E  ++   +       +++  S    SG    +    
Sbjct: 817 AQLQYGDPYYSYL-----NLNTGESFVMYYKSKENCIVDNIKVCSNDTGSGKFKCICITM 871

Query: 944 IFNRHGIDKNERS 956
              R+    ++ +
Sbjct: 872 RVPRNPTIGDKFA 884



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 98/712 (13%), Positives = 191/712 (26%), Gaps = 128/712 (17%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK-----------FDVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPTVPKGSICKDLSIYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWSVNGIP--------KGIIKQ--FLGYVPIMVKSKLCNLYNLPPRALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIALTRPKWKTRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + ++      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFVY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V E G      +L  L E+    L +
Sbjct: 271 GKEDDSFFRNSVSQMLR----------------IVTEEGCSTQKQVLNYLGERFRVKLNL 314

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +   +    T + Y+         +L +    E     ++  +
Sbjct: 315 PDWYPDAQAAEFLFNQCICIHL-KSNTEKFYVLCLMTRKLFALAKGECMEENPDSLVNQE 373

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         L            + + +  +  DVS  +        L  D  K     
Sbjct: 374 VLTPGQLFLMFLKEKMEAWLVSIKIALDKKAQKTDVSINTDNLMKIFNLGTDLTKPFEYL 433

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +    +  +  L    D       D +  I+ L   R     +    +    R  +V  +
Sbjct: 434 LATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRL 489

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                  +   +M       + V          + L  L   V 
Sbjct: 490 LPESWGFLC-------PVHTPDGEPCGLMNHLTAICEVVTQFAYTASVPALLCSLG--VT 540

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +    H R  S      +     G   +++ P+    +   +      I     +    
Sbjct: 541 PVDGAPH-RPYSECYPVLLDGVMVGWVDKELAPSIADSLRHFKVLREKRIPPWMEVALIP 599

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                      +      ++   V  L    EE          L          +     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGREE----------LIGTMEQIFMNIAIFED 649

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                V        +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 650 EVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 697


>gi|114579604|ref|XP_001145082.1| PREDICTED: hypothetical protein isoform 5 [Pan troglodytes]
          Length = 1079

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 641  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 701  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 750

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 751  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 808

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 809  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 840

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 841  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 875

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 876  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 935

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 936  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 995

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 996  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 1055

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1056 VPYVFRYFVAELAAMNIKVKLD 1077



 Score = 90.1 bits (222), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 249 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 307 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 366

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 483

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 484 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 543

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 544 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 603

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 604 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPILTYQDRSDNKLYRLQ- 659

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 660 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 709

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 710 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 769

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 770 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 824

Query: 953 NERS 956
           ++ +
Sbjct: 825 DKFA 828



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 86/642 (13%), Positives = 179/642 (27%), Gaps = 125/642 (19%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
               K I +Q  ++G +P+M K                         G F+I GI++++ 
Sbjct: 67  NGISKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVI- 123

Query: 155 SQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL---------WMDIEFDSKDII 202
             L    R+  I     K +    G   Y   +   +           +++      + I
Sbjct: 124 RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHSAVNMNLHYLENGTVMLNFI 183

Query: 203 HVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           +      RK    +P+   L AL      +I    + +++  +  D +     +  L   
Sbjct: 184 Y------RKELFFLPLGFALKALVSFSDYQI----FQELIKGKEDDSFLRNSVSQMLR-- 231

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVA 309
                          V+E G      +L  L E     L +          + L    + 
Sbjct: 232 --------------IVMEEGCLTQKQVLNYLGECFRVKLNVPDWYPNEQAAEFLFNQCIC 277

Query: 310 EDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             + +           T +++  A     E + + + + E+     L++  +        
Sbjct: 278 IHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEK----- 332

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             +       K A     +      ++T ++ +     +        L   G ++    L
Sbjct: 333 --LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMKIFTMGIDLTKPFEYLFATGNLRSKTGL 389

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            L     +  +   D +  I+ L   R     +    +    R  +V  +L   +     
Sbjct: 390 GLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRLLPESWGFLC- 442

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
                        +   +M       + V   V      + L  L   V  +    H R 
Sbjct: 443 ------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLG--VTPIDGAPH-RS 493

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            S      +     G   +D+ P     +   +      I     +              
Sbjct: 494 YSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTGKPSLYPG 553

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            +      ++   V  L   +EE          L          V          V   +
Sbjct: 554 LFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQIFMNVAIFEDEVFAGVTTHQ 603

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
               +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 604 ----ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 641


>gi|212286172|ref|NP_001131076.1| DNA-directed RNA polymerase I subunit RPA2 isoform 2 [Homo sapiens]
 gi|119593996|gb|EAW73590.1| polymerase (RNA) I polypeptide B, 128kDa, isoform CRA_a [Homo
            sapiens]
          Length = 1079

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 641  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 701  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 750

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 751  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 808

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 809  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 840

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 841  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 875

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 876  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 935

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 936  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 995

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 996  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 1055

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1056 VPYVFRYFVAELAAMNIKVKLD 1077



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 215/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 249 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 307 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 366

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 483

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 484 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 543

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 544 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 603

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 604 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 659

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 660 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 709

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 710 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 769

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 770 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 824

Query: 953 NERS 956
           ++ +
Sbjct: 825 DKFA 828



 Score = 47.8 bits (112), Expect = 0.016,   Method: Composition-based stats.
 Identities = 86/642 (13%), Positives = 178/642 (27%), Gaps = 125/642 (19%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
               K I +Q  ++G +P+M K                         G F+I GI++++ 
Sbjct: 67  NGISKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVI- 123

Query: 155 SQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL---------WMDIEFDSKDII 202
             L    R+  I     K +    G   Y   +   +           +++      + I
Sbjct: 124 RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHSAVNMNLHYLENGTVMLNFI 183

Query: 203 HVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVG 257
           +      RK    +P+   L AL      +I    + +++  +  D +     +  L   
Sbjct: 184 Y------RKELFFLPLGFALKALVSFSDYQI----FQELIKGKEDDSFLRNSVSQMLR-- 231

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVA 309
                          V+E G      +L  L E     L +          + L    + 
Sbjct: 232 --------------IVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAAEFLFNQCIC 277

Query: 310 EDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRN 360
             + +           T +++  A     E + + + + E+     L++  +        
Sbjct: 278 IHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEK----- 332

Query: 361 TLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRL 420
             +       K A     +      ++T ++       +        L   G ++    L
Sbjct: 333 --LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMRIFTMGIDLTKPFEYLFATGNLRSKTGL 389

Query: 421 NLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
            L     +  +   D +  I+ L   R     +    +    R  +V  +L   +     
Sbjct: 390 GLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRLLPESWGFLC- 442

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
                        +   +M       + V   V      + L  L   V  +    H R 
Sbjct: 443 ------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLG--VTPIDGAPH-RS 493

Query: 541 LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIET 600
            S      +     G   +D+ P     +   +      I     +              
Sbjct: 494 YSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTGKPSLYPG 553

Query: 601 PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
            +      ++   V  L+  +EE          L          V          V    
Sbjct: 554 LFLFTTPCRLVRPVQNLALGKEE----------LIGTMEQIFMNVAIFEDEVFAGVT--- 600

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
               +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 601 -THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 641


>gi|225194776|gb|ACN81896.1| DNA-dependent RNA polymerase subunit rpo132 [Skunkpox virus]
          Length = 1164

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 139/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 770  LDI-------------VTAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 816

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V+D ++  +V E     Y++    ++    +K++          
Sbjct: 817  DAMARNISSRTLEDDFVRDNQISFDVSERYTDMYKSRVERVQVELTDKVK---------- 866

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 867  -----VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTSIF 921

Query: 1129 SRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A        K ++            I     F ++     +    
Sbjct: 922  SRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPQLS 981

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D                                            ILYD  T +P
Sbjct: 982  DEELSDKIFCEK--------------------------------------ILYDPETDKP 1003

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1004 YASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1063

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1064 HGAANTITEVL 1074



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 80/600 (13%), Positives = 179/600 (29%), Gaps = 76/600 (12%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           + +M         D    ++   +I++++  V          D D++   R+ + G+  +
Sbjct: 308 KYEMLHNFLPHMNDTPDQLKGFYMISLLRKFVYCIYYTSRYPDRDSMVCHRILTYGKYFE 367

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                 L     +I+  I +   +      +         +   F S    + ++   S 
Sbjct: 368 TLAHDELENYIGNIRNDIMNNHKNRGT-YAVNIHVLTTPGLNHAFSSLLSGKFKKSDGSY 426

Query: 533 SRITHTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVS 584
               H   +  +             +      +R  HP+ Y   CP++  E G+ +GLVS
Sbjct: 427 RTHPHYSWMQNISIPRSVGFYPDQVKISKMFSVRKYHPSQYLYFCPSDVPERGNQVGLVS 486

Query: 585 SLTSFARVNA-----YGFIETPYRKVCDGKVTNDVVYL---SAMEEENRYIAQANSSLDE 636
            L+  + +       Y  +E            +D+ Y      +  EN  +A  N ++  
Sbjct: 487 QLSVLSSITNILTSEYLDLEKKICAYIRSYYKDDISYFETGYPITIENALVASLNPNIVC 546

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN-----RVL 691
           +                + +    +       +  +     + PFL  D+          
Sbjct: 547 EFVTDFRRRKRMGLFGNLEIGITLVRDHMNEIRINIGAGRLVRPFLVVDNGELMMDACPD 606

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA-------------------IVAKRA 732
           +   +       ++ E P V   ++      S                            
Sbjct: 607 LESRLDDMTFSDIQKEFPHVIEMVDIEQFTFSNVCESVQKFRMLSKEEKKLYDLCDFPAE 666

Query: 733 GIVEQVDAIRIVIRSVEGDL--------DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                V +  + I    G            + S +      K           +RP+V  
Sbjct: 667 FRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIH-LMYPERPIV-- 723

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                   I     ++ +     G+++ +A M + G N ED ++I ++ +       +  
Sbjct: 724 --------ISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGGLDIVTA 775

Query: 845 EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           ++ +V        P E   +   V       ++  G++ + A +  GD        +  S
Sbjct: 776 KKHQVEI------PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDA-----MARNIS 824

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
             T E+  +R    + + DV +    +       V   +  ++  R    K  R I  ++
Sbjct: 825 SRTLEDDFVRD--NQISFDVSERYTDMYKSRVERVQVELTDKVKVRVLTMKERRPILGDK 882


>gi|1143635|emb|CAA53897.1| unnamed protein product [Variola virus]
 gi|5830689|emb|CAB54728.1| A25R protein [Variola minor virus]
 gi|94483775|gb|ABF22892.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94484388|gb|ABF23502.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94485793|gb|ABF24900.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94487413|gb|ABF26512.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94488022|gb|ABF27118.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94490032|gb|ABF29118.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
          Length = 1164

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LTEKELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|22164733|ref|NP_671646.1| EVM127 [Ectromelia virus]
 gi|56404906|sp|Q8JL90|RPO2_ECTVM RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|22123874|gb|AAM92432.1|AF523264_128 EVM127 [Ectromelia virus]
          Length = 1164

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNNGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPQ 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LTDDELSDKVFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|145307864|gb|ABP57238.1| RNA polymerase II second largest subunit [Conidiobolus obscurus]
          Length = 307

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/382 (15%), Positives = 113/382 (29%), Gaps = 75/382 (19%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 1    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 60

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D+ +++  VE E  E  +                    I  G 
Sbjct: 61   SIDRGLF-RSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGT 119

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+T + +D      R +          ++     +  +   + +      
Sbjct: 120  RVSGDDIIIGKTTPVPADSEELGQRLRGHTKKDVSTPLKSTETGIVDRVMLTINQ----- 174

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             +R  KV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 175  ---------------EGMRFAKVRVRSTRVPQIGDKFASRHGQKGTIGMTYRHEDMPFSA 219

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            +G   D+++NP  +PSRM +G + E  +G      G +                      
Sbjct: 220  EGIVPDLIINPHAIPSRMTIGHMVECLVGKVGTLDGSEGD-------------------- 259

Query: 1174 KVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQ 1233
                                             +TP F     + I+ +L      + G 
Sbjct: 260  ---------------------------------ATP-FTDVTVDGISHLLERFGYQKRGF 285

Query: 1234 SILYDGLTGEPFDRPVTVGYIY 1255
             ++Y+G TG+     + +G  Y
Sbjct: 286  EVMYNGHTGKKLTAQIYLGPTY 307



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 4   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 53

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + T L   E            +     + +++ G
Sbjct: 54  SVIMNQSSIDRGLFRSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDG 113

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK TP         E+L + + G    DV        +G+   V+
Sbjct: 114 LIAPGTRVSGDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGIVDRVM 169


>gi|320172584|gb|ADW24175.1| RNA polymerase II second largest subunit [Gloeophyllum protractum]
          Length = 350

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 66/435 (15%), Positives = 117/435 (26%), Gaps = 88/435 (20%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  +   ++            ++       +G       +          
Sbjct: 1    WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD          +       I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 169  NGEDIIIGKTAPIPPDSEELGQRTRLHTRRDVSTALKSTESGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  ITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E++++ LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      + 
Sbjct: 335  MYHGHTGRKLQAQIY 349



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 48/297 (16%), Positives = 93/297 (31%), Gaps = 77/297 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ + AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLRFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       +++ G+I  G  VN  DI++
Sbjct: 116 SIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 176 GKTAPIPPDSEELGQRT-------RLHTRRDVSTALKSTESGIVDQVLITTNSEGQK 225


>gi|145687748|gb|ABP88851.1| DNA-dependent RNA polymerase subunit rpo132 [Cowpox virus]
          Length = 1164

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|41023473|emb|CAE52727.1| A24R RPO132 orthologue [Fowlpox virus isolate HP-438/Munich]
          Length = 1157

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/431 (18%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDV--RDTSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V     S +  +   G VV      R G
Sbjct: 702  DNGIHLLYPERPIVLSKATETSKIAINCFGQHVLVALMSYKGMNQEDGIVVKREFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  I +     R+      +  ++G           
Sbjct: 762  LDI-------------VTAKKHQVEIPIENFKNRERINSTAYSKLDINGLVRLNAFLEPG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y +    ++    +K++          
Sbjct: 809  DAIAKNISSRTLDDDFVADNQISFDISEKYTDMYMSRVERVQVDLTDKVK---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG ++ I    ++P+ K+G   DI++N   + 
Sbjct: 859  -----VRVLTMKERRPIMGDKFTSRTSQKGTIAYIASESELPYDKNGVTPDIIINSTSIY 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A          K + +        DI     F  K   +      
Sbjct: 914  SRKTISMLIEMILTSAYSVKPYNNNGKNRPICFPSSNETDIEYYIEFARKCYQSAIPDLD 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              + +++                                          SILYD  T +P
Sbjct: 974  KDELENEVYCE--------------------------------------SILYDPETDKP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G +Y L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YKTKVFMGPLYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 56.2 bits (134), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 90/665 (13%), Positives = 208/665 (31%), Gaps = 57/665 (8%)

Query: 341 IRDIPILYVDSVNNNAYIRN---TLVTDKNKDRKDALLDIYR-VMRPGDVSTFSVAESMF 396
           +  I ++      +  YI+N     +  +     +A+++  + ++   D +     ES+ 
Sbjct: 223 VNVIVLIKFLINQDLNYIKNNLTYGMPLETIYLINAIIESSKTILEAEDFNINDYIESLI 282

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              F            R  +         +    ++   ++ +++  +          D 
Sbjct: 283 ESEFQKQRSITSIDDFRYDLMYNFLPHMVNSSDQLKGFYLLGLLRKFIYCIYHTSRYPDR 342

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D++   RV + G   +      L     +IK  I++   +     ++             
Sbjct: 343 DSMVCHRVLTYGRYFEILANDELENYITNIKNDITNSHKNK-GVCNVSIHVLTTPGFNHA 401

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRI 569
           F      + ++   S     H   +  +             +      +R  HP+ Y   
Sbjct: 402 FSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAFF 461

Query: 570 CPAETSE-GHNIGLVSSLTSF-----ARVNAYGFIETPYRKVCDGKVTNDVVYL---SAM 620
           CP++  E G  +GL+S L+        R   Y  ++    K       ND+ Y      +
Sbjct: 462 CPSDVPERGPQVGLISQLSVLTSVSNIRTTEYIDLKNAIMKYIYTYDKNDISYFQTGHII 521

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             EN  +A  N  L +      +        + + +    +       +  +     + P
Sbjct: 522 TIENDLVAAINPELVDKFVDDFKFRKRVNYFDNLEIGISNVKDHMNEIRINIGSGRLIRP 581

Query: 681 FLEN------DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           FL         D+    +   +       ++ E P V   ++      S       +   
Sbjct: 582 FLVVYKGELVMDTIGEELEKRIDTITFSDIQKEYPHVIEMLDLEQFVFSNVCESVSKFRE 641

Query: 735 VEQVDAIRIVIRSVEGDL------------DPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
           +   D           +             + ++    I    + +++      + R  +
Sbjct: 642 LSDEDKKLYDYCDFPNEFRDGYVASTLVGINHNSGPRAILGCAQAKQAISCLSSDLRNKI 701

Query: 783 KVGDEVRRND-IIADGPSTDLGDLAL---GRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
             G  +   +  I    +T+   +A+   G+++LVA M + G N ED +++    +    
Sbjct: 702 DNGIHLLYPERPIVLSKATETSKIAINCFGQHVLVALMSYKGMNQEDGIVVKREFIERGG 761

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  ++ +V        P E  ++   ++      +D  G++ + A + PGD +   I
Sbjct: 762 LDIVTAKKHQVEI------PIENFKNRERINSTAYSKLDINGLVRLNAFLEPGDAIAKNI 815

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD--VRIFNRHGIDKNERS 956
           + +        +  +     EK  D         S V    VD   ++  R    K  R 
Sbjct: 816 SSRTLDDDFVADNQISFDISEKYTD------MYMSRVERVQVDLTDKVKVRVLTMKERRP 869

Query: 957 ISVER 961
           I  ++
Sbjct: 870 IMGDK 874


>gi|89142751|emb|CAJ57571.1| RNA polymerase subunit B [Microbacterium esteraromaticum]
          Length = 342

 Score =  190 bits (483), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 124/259 (47%), Positives = 172/259 (66%), Gaps = 15/259 (5%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              I  TL  D    ++DAL DIYR +RPG+      A S+ +  +F+  +YDL+ VGR 
Sbjct: 84  YPSIEETLAKDTILTQEDALRDIYRKLRPGEQVAAEAARSLLDNFYFNPKRYDLAKVGRY 143

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNG---------------KGTIDDIDNL 459
           K+N +L L  P     +  +DI+A IK LV +  G               +   DDIDN 
Sbjct: 144 KINQKLGLAAPLTDSVLTVDDIVATIKYLVRVHRGDETFEGIRGGKKTEIRIATDDIDNF 203

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R GL RMER ++ER+++ DI+++ PQ LIN +PVV+A+ EFF +
Sbjct: 204 GNRRIRAVGELIQNQVRTGLSRMERVVRERMTTQDIEAITPQTLINVRPVVAAIKEFFGT 263

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N L+ +T+ RRLSALG GG++R RAGVE+RDVHP+HYGR+CP ET EG N
Sbjct: 264 SQLSQFMDQNNPLAGLTNKRRLSALGPGGLSRDRAGVEVRDVHPSHYGRMCPIETPEGPN 323

Query: 580 IGLVSSLTSFARVNAYGFI 598
           IGL+ +L +FAR+N +GFI
Sbjct: 324 IGLIGALATFARINPFGFI 342



 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/154 (35%), Positives = 78/154 (50%), Gaps = 13/154 (8%)

Query: 150 QRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR 209
           +R+VVSQL RSPG++FD    +   S K +   R+IP +G W++ E D +D + VRIDR+
Sbjct: 1   ERVVVSQLVRSPGVYFDKTPDKT--SDKDIVTARVIPSRGAWLEFEIDKRDQVGVRIDRK 58

Query: 210 RKVPVTSFLMALGMDSEEILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
           RK  VT FL ALGM SE+IL+ F  YP I  +   D       A   +           +
Sbjct: 59  RKQSVTVFLKALGMSSEQILAEFAGYPSIEETLAKDTILTQEDALRDI--------YRKL 110

Query: 268 DTGEQV-IESGKKLTSGLLKSLKEKGVKFLGITS 300
             GEQV  E+ + L      + K   +  +G   
Sbjct: 111 RPGEQVAAEAARSLLDNFYFNPKRYDLAKVGRYK 144


>gi|300394710|gb|ADK11893.1| DNA-directed RNA polymerase II subunit two [Jaapia argillacea]
          Length = 352

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/375 (18%), Positives = 110/375 (29%), Gaps = 75/375 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 53   DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 112

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E  E   RD          +       I  G      
Sbjct: 113  LF-RSIYYRSYMDIEKKSGVQQLEMFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGE 171

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     +    T+    E    +++ 
Sbjct: 172  DIIIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTALKSTESGIVDQVL 216

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 217  I-----TTNSEGQKFVKVRVRATRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 271

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIV+NP  +PSRM +G + E  L      +G +                           
Sbjct: 272  DIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 306

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E++++ LR       G  ++Y 
Sbjct: 307  ----------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYH 337

Query: 1239 GLTGEPFDRPVTVGY 1253
            G TG      V +G 
Sbjct: 338  GHTGRKLQAQVYLGP 352



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 89/242 (36%), Gaps = 23/242 (9%)

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTC 775
               +   + I+   A I+   D  +    + +  +     G+     L++         
Sbjct: 1   WTHLEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRMDTMANILY 60

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+PL                      +L  G+N +VA + + GYN EDS+++++  + 
Sbjct: 61  YPQKPL----------ATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSID 110

Query: 836 EDVFTSIHIEEFEVMARDTK----LGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNP 890
             +F SI+   +  + + +        E+ TRD    +       +++ G+I  G  VN 
Sbjct: 111 RGLFRSIYYRSYMDIEKKSGVQQLEMFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNG 170

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P         ++        ++   RD S  + S  SG V  V I      
Sbjct: 171 EDIIIGKTAPIPPDSEELGQRT-------RSHTRRDVSTALKSTESGIVDQVLITTNSEG 223

Query: 951 DK 952
            K
Sbjct: 224 QK 225


>gi|56694376|gb|AAW22928.1| RNA polymerase II second largest subunit [Acorus gramineus]
          Length = 536

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 100/684 (14%), Positives = 188/684 (27%), Gaps = 148/684 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     V            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYVTVGSAANPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +    + +  +G +           + +   R ++   D + +  V     L       
Sbjct: 54   AVIPQATKIFVNGCWVGIHRNPDLLVKTLRQLRRQV---DVNTEVGVIRDIRLKELRLYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
            D  R      +  +   L+                +   A    +           +  I
Sbjct: 111  DYGRCSRPLFIVEKQRLLI--------------KKRHIRALQQRETQEEGWHELVTKGFI 156

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              ++ + + +T        +   R N     +                    PS  LG  
Sbjct: 157  EYIDTEEEETTMISMTINDLINARQNPEEAYS-----------SMYTHCEIHPSLILG-- 203

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   I++  ++                 
Sbjct: 204  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMG--IYVTNYQ----------------- 239

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                      +    +  V        +    +       +      + AI      +  
Sbjct: 240  ----------LRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 289

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +        +F R   D+ ++  ++ +E      R+          +    
Sbjct: 290  DSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDD 348

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
                  G           K+T ++ +                 E   +     K  + TS
Sbjct: 349  DGLAPPGTRVSGEDVIIGKTTPIAQE-----------------EAQGQASRYTKRDHSTS 391

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E    +++      D +     R VKV +   R  Q GDK + RHG KG V     
Sbjct: 392  LRHSESGMVDQVLLTTNADGL-----RFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYT 446

Query: 1106 CEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+              
Sbjct: 447  QEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD------------ 494

Query: 1166 SPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRM 1225
                                                     +TP F     + I+  L  
Sbjct: 495  -----------------------------------------ATP-FTDVTVDNISKALHK 512

Query: 1226 ADLDESGQSILYDGLTGEPFDRPV 1249
                  G   +Y+G TG      +
Sbjct: 513  CGYQMRGFETMYNGHTGRKLTAMI 536



 Score =  120 bits (301), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 74/496 (14%), Positives = 140/496 (28%), Gaps = 102/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYVT----VGSAANPILEFLEEWSTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             A   F     +         +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQATKIFVNGCWVGIHRNPDLLVKTLRQLRRQVDVNTEVGVIRDIRLKELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +         + A    ET      +      + Y+   EEE   I+
Sbjct: 116 SRPLFIVEKQRLLIKKR-----HIRALQQRETQEEGWHELVTKGFIEYIDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +L+  R   E            +  P  ++ + AS+IPF +++ S 
Sbjct: 171 M----------TINDLINARQNPE--EAYSSMYTHCEIHPSLILGVCASIIPFPDHNQSP 218

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 219 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 248

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 249 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 273

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 274 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRE 333

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK TP  +           A        
Sbjct: 334 NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQEE---------AQGQASRYT 384

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 385 KRDHSTSLRHSESGMV 400


>gi|303325242|gb|ADM14346.1| RNA polymerase subunit B [uncultured Mycobacterium sp.]
          Length = 136

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/167 (40%), Positives = 87/167 (52%), Gaps = 32/167 (19%)

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      DD+P GV  +V+V+VA KR I  GDK+AGRHGNKG++ +ILP EDMPFL DGT
Sbjct: 1    VFSRDDDDDLPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGT 60

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
            PVDI+LN  GVP RMN+GQI ETHLGW     G  I+      +                
Sbjct: 61   PVDIILNTHGVPRRMNIGQILETHLGWVAK-TGWNIEGNPEWAQN--------------- 104

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
                            +    +   +    +TPVFDGA EE +  +L
Sbjct: 105  ----------------LPEDLQSAPADTRTATPVFDGAREEELTGLL 135


>gi|221039778|dbj|BAH11652.1| unnamed protein product [Homo sapiens]
          Length = 996

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 499  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 557

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 558  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 617

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 618  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 667

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 668  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 725

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 726  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 757

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 758  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 792

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 793  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 852

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 853  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 912

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 913  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 972

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 973  VPYVFRYFVAELAAMNIKVKLD 994



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 215/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 114 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 165

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 166 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 223

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 224 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 283

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 284 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 340

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 341 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 400

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 401 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 460

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 461 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 520

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 521 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 576

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 577 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 626

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 627 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 686

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 687 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 741

Query: 953 NERS 956
           ++ +
Sbjct: 742 DKFA 745



 Score = 42.0 bits (97), Expect = 0.68,   Method: Composition-based stats.
 Identities = 79/596 (13%), Positives = 166/596 (27%), Gaps = 99/596 (16%)

Query: 141 DGTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL------- 190
            G F+I GI++++   L    R+  I     K +    G   Y   +   +         
Sbjct: 28  GGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHSAVNMN 86

Query: 191 --WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVYSQRGD 243
             +++      + I+      RK    +P+   L AL      +I    + +++  +  D
Sbjct: 87  LHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIKGKEDD 136

Query: 244 FWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITS--- 300
            +     +  L                  V+E G      +L  L E     L +     
Sbjct: 137 SFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNVPDWYP 180

Query: 301 -----DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
                + L    +   + +           T +++  A     E + + + + E+     
Sbjct: 181 NEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQ 240

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L++  +          +       K A     +      ++T ++       +       
Sbjct: 241 LFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMRIFTMGIDLTKPFE 292

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
            L   G ++    L L     +  +   D +  I+ L   R     +    +    R  +
Sbjct: 293 YLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAKMRTTT 346

Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
           V  +L   +                  +   +M       + V   V      + L  L 
Sbjct: 347 VRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLG 399

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
             V  +    H R  S      +     G   +D+ P     +   +      I     +
Sbjct: 400 --VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEV 456

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
                          +      ++   V  L+  +EE          L          V 
Sbjct: 457 VLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEE----------LIGTMEQIFMNVA 506

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    V        +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 507 IFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 558


>gi|9634859|ref|NP_039152.1| RNA polymerase subunit, RPO132 [Fowlpox virus]
 gi|18203059|sp|Q9J544|RPO2_FOWPN RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|7271687|gb|AAF44533.1|AF198100_180 ORF FPV189 RNA polymerase subunit, RPO132 [Fowlpox virus]
          Length = 1161

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 78/431 (18%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDV--RDTSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V     S +  +   G VV      R G
Sbjct: 702  DNGIHLLYPERPIVLSKATETSKIAINCFGQHVLVALMSYKGMNQEDGIVVKREFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  I +     R+      +  ++G           
Sbjct: 762  LDI-------------VTAKKHQVEIPIENFKNRERINSTAYSKLDINGLVRLNAFLEPG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y +    ++    +K++          
Sbjct: 809  DAIAKNISSRTLDDDFVADNQISFDISEKYTDMYMSRVERVQVDLTDKVK---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG ++ I    ++P+ K+G   DI++N   + 
Sbjct: 859  -----VRVLTMKERRPIMGDKFTSRTSQKGTIAYIASESELPYDKNGVTPDIIINSTSIY 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A          K + +        DI     F  K   +      
Sbjct: 914  SRKTISMLIEMILTSAYSVKPYNNNGKNRPICFPSSNETDIEYYIEFARKCYQSAIPDLD 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              + +++                                          SILYD  T +P
Sbjct: 974  KDELENEVYCE--------------------------------------SILYDPETDKP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G +Y L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YKTKVFMGPLYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 94/684 (13%), Positives = 207/684 (30%), Gaps = 63/684 (9%)

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIY--------- 378
           +D   LE  + S  +    + V  +      ++      N      L  IY         
Sbjct: 204 MDLSQLENCYISSAKTFITVNVIVLIKFLINQDLNYIKNNLTYGMPLETIYLINAIIESS 263

Query: 379 -RVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDII 437
             ++   D +     ES+    F            R  +         +    ++   ++
Sbjct: 264 KTILEAEDFNINDYIESLIESEFQKQRSITSIDDFRYDLMYNFLPHMVNSSDQLKGFYLL 323

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
            +++  +          D D++   RV + G   +      L     +IK  I++   + 
Sbjct: 324 GLLRKFIYCIYHTSRYPDRDSMVCHRVLTYGRYFEILANDELENYITNIKNDITNSHKNK 383

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA------- 550
               ++             F      + ++   S     H   +  +             
Sbjct: 384 -GVCNVSIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRSVGYYPDQV 442

Query: 551 RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSF-----ARVNAYGFIETPYRK 604
           +      +R  HP+ Y   CP++  E G  +GL+S L+        R   Y  ++    K
Sbjct: 443 KISKMFSVRKYHPSQYAFFCPSDVPERGPQVGLISQLSVLTSVSNIRTTEYIDLKNAIMK 502

Query: 605 VCDGKVTNDVVYL---SAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
                  ND+ Y      +  EN  +A  N  L +      +        + + +    +
Sbjct: 503 YIYTYDKNDISYFQTGHIITIENDLVAAINPELVDKFVDDFKFRKRVNYFDNLEIGISNV 562

Query: 662 DFIDASPKQVVSIAASLIPFLEN------DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
                  +  +     + PFL         D+    +   +       ++ E P V   +
Sbjct: 563 KDHMNEIRINIGSGRLIRPFLVVYKGELVMDTIGEELEKRIDTITFSDIQKEYPHVIEML 622

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL------------DPSTSGVDIYR 763
           +      S       +   +   D           +             + ++    I  
Sbjct: 623 DLEQFVFSNVCESVSKFRELSDEDKKLYDYCDFPNEFRDGYVASTLVGINHNSGPRAILG 682

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRND-IIADGPSTDLGDLAL---GRNMLVAFMPWH 819
             + +++      + R  +  G  +   +  I    +T+   +A+   G+++LVA M + 
Sbjct: 683 CAQAKQAISCLSSDLRNKIDNGIHLLYPERPIVLSKATETSKIAINCFGQHVLVALMSYK 742

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
           G N ED +++    +       +  ++ +V        P E  ++   ++      +D  
Sbjct: 743 GMNQEDGIVVKREFIERGGLDIVTAKKHQVEI------PIENFKNRERINSTAYSKLDIN 796

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++ + A + PGD +   I+ +        +  +     EK  D         S V    
Sbjct: 797 GLVRLNAFLEPGDAIAKNISSRTLDDDFVADNQISFDISEKYTD------MYMSRVERVQ 850

Query: 940 VD--VRIFNRHGIDKNERSISVER 961
           VD   ++  R    K  R I  ++
Sbjct: 851 VDLTDKVKVRVLTMKERRPIMGDK 874


>gi|3002939|gb|AAC08960.1| RNA polymerase II second largest subunit [Peperomia caperata]
          Length = 554

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 76/493 (15%), Positives = 142/493 (28%), Gaps = 93/493 (18%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAF-MPWHGYNFEDSML--ISERMVS 835
            LV  G  + V   +      S  + DL   R    A+   +       S++  +   ++ 
Sbjct: 150  LVSKGFIEYVDTEEEETTMISMTINDLVQARRSKDAYSTTYTHCEIHPSLILGVCASIIP 209

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                       ++       +G          V+   L+      +  V        +  
Sbjct: 210  FPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVTT 258

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S +        +F R   D+ ++
Sbjct: 259  RAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKK 317

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
              ++ +E      R+          +          G           K++ ++      
Sbjct: 318  MGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQ----- 372

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                        DE   +     +  + TS    E    +++      D +     R VK
Sbjct: 373  ------------DESQGQASRYNRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVK 415

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            V +   R  Q GDK + RHG KG V      EDMP+  +G   DI++N   +PSRM +GQ
Sbjct: 416  VRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTAEGITPDIIVNQHAIPSRMTIGQ 475

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  +G     +GK+  +         +IS         +                   
Sbjct: 476  LIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------- 522

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                                               +G +    G         + +G  Y
Sbjct: 523  ----------------------------------YNGHT----GR---RLSAMIFLGPTY 541

Query: 1256 MLKLNHMVSDKVY 1268
              +L HMV DK++
Sbjct: 542  YQRLKHMVDDKIH 554



 Score =  118 bits (295), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 72/496 (14%), Positives = 141/496 (28%), Gaps = 103/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAANPILEFLEEWSTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             A   F     +         +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQATKIFVNGCWVGIHRNPDLLVKTLRQLRRQIDVNTEVGVIRDIRLKELR-LYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E   + +         + A    ET             + Y+   EEE   I+
Sbjct: 116 SRPLFIVENQKLLIKKR-----DIQALQQRETQEEGWHFLVSKGFIEYVDTEEEETTMIS 170

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R + +            +  P  ++ + AS+IPF +++ S 
Sbjct: 171 M----------TINDLVQARRSKD---AYSTTYTHCEIHPSLILGVCASIIPFPDHNQSP 217

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +                           R   +  V          
Sbjct: 218 RNTYQSAMGKQAMGIYVTNYQL--------------------RMDTLAYV---------- 247

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 248 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 272

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITR 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 273 INAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRE 332

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G  V+  D+++GK +P  +           +       +
Sbjct: 333 NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTSPIAQDE---------SQGQASRYN 383

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S  +    SG V
Sbjct: 384 RRDHSTSLRHSESGMV 399


>gi|114579610|ref|XP_001144997.1| PREDICTED: RNA polymerase I polypeptide B isoform 4 [Pan troglodytes]
 gi|114579612|ref|XP_001145239.1| PREDICTED: RNA polymerase I polypeptide B isoform 7 [Pan troglodytes]
          Length = 996

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 499  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 557

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 558  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 617

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 618  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 667

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 668  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 725

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 726  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 757

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 758  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 792

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 793  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 852

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 853  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 912

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 913  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 972

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 973  VPYVFRYFVAELAAMNIKVKLD 994



 Score = 89.7 bits (221), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 95/662 (14%), Positives = 221/662 (33%), Gaps = 68/662 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 114 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 165

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 166 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 223

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 224 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 283

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 284 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 340

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 341 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 400

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 401 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 460

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 461 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 520

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
            +   S  +++A      +   + R + +   G        +  Y+     +  +     
Sbjct: 521 ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMG-KQTMGFPILTYQDRSDNKLYRLQ-TP 578

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++      
Sbjct: 579 QSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERG 628

Query: 838 V-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
               S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD    
Sbjct: 629 FAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYS 688

Query: 897 KITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
            +     +  T E  ++     E     +++  S    SG    V       R+    ++
Sbjct: 689 YL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDK 743

Query: 955 RS 956
            +
Sbjct: 744 FA 745



 Score = 38.1 bits (87), Expect = 9.7,   Method: Composition-based stats.
 Identities = 5/13 (38%), Positives = 10/13 (76%)

Query: 141 DGTFVIKGIQRIV 153
            G F+I GI++++
Sbjct: 28  GGYFIINGIEKVI 40


>gi|56404863|sp|Q80DV1|RPO2_CWPXG RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|30519517|emb|CAD90692.1| A25R protein [Cowpox virus]
          Length = 1164

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYTSKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|282598446|gb|ADA83453.1| RNA polymerase beta subunit [Corynebacterium sp. NML09-0341]
          Length = 139

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 84/167 (50%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D      +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L  +  +  G        +++L+DG +GEPF 
Sbjct: 45   ------------ATPVFDGASNEEIAGLLANSKPNRDGDVMVDGDGKTVLFDGRSGEPFK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|157939739|ref|YP_001497111.1| RNA polymerase subunit rpo132 [Tanapox virus]
 gi|146746455|gb|ABQ43591.1| RNA polymerase subunit rpo132 [Tanapox virus]
          Length = 1165

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/431 (17%), Positives = 139/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 711  DNGIHLIYPERPIVLSKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGG 770

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 771  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVKLNAFLENG 817

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y++    ++    +K++          
Sbjct: 818  DAIARNISSKTLEDDFVNDNQISFDISERYTDMYKSRVERVQVDLTDKVK---------- 867

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    D+P+  +G   DI++N   + 
Sbjct: 868  -----VRVLTMKERRPILGDKFTSRTSQKGTVAFIADETDLPYDDEGIKPDIIINSTSIF 922

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A         ++ + +         I     F ++          
Sbjct: 923  SRKTLSMLVEVILTAAYASKPYNNNEQNRPICFPSSNETSIDTYLDFAKQCYECVYPNLD 982

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
             ++ D+                                            ILYD  T  P
Sbjct: 983  KNEIDNKVFCEK--------------------------------------ILYDPETDVP 1004

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1005 YKSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1064

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1065 HGAANTITEVL 1075



 Score = 57.0 bits (136), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 86/648 (13%), Positives = 203/648 (31%), Gaps = 59/648 (9%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + +        ++  ++ + +   ++  +     +  +    S         + +
Sbjct: 253 SYDMPSEIIYLVNSLIESTKELIKNISDFNLDNYINDLVLSEYTKQKSQLQYEEF--KYE 310

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   II +++  +          D D++   RV + G+  +   
Sbjct: 311 MINNFLPHMYDSPNQLKGFYIILLLRKFIYCIYFTSRYPDRDSMVCHRVLTYGKYFEILA 370

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +IK  I +   +       I+           F      + ++   S    
Sbjct: 371 HDELENYIGNIKTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 429

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
            H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 430 PHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 489

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-DGSFT 641
               +     N Y  +E             D+ Y     E   YI   NS +   +    
Sbjct: 490 VLTSITNICTNEYLELEKKIYSYIKSFNYEDISYF----ETGYYITLENSLVASLNPEKV 545

Query: 642 EELVFCRCAGE------EILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNR 689
            + V      +       + +    +       +  +     + PFL  D      D+  
Sbjct: 546 YDFVNDFRRKKRIGYFGNLEIGITLVQDHMNEIRINIGGGRLIRPFLVIDNGELVMDTVI 605

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV- 748
             +   ++      +  E P V   ++      S      ++   + + + ++  +    
Sbjct: 606 KDLEEKIEDFTFSDILKEFPHVVEMVDIEQFTFSNVCESVQKFKSLSKAERVKYHLCDFP 665

Query: 749 ----EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGD---EVRRNDII 794
               +G +  S  G++            + +++      + R  +  G       R  ++
Sbjct: 666 SEFRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVL 725

Query: 795 ADGPSTDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +    T    +   G+++++A M + G N ED ++I ++ V       I  ++ +V    
Sbjct: 726 SKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI-- 783

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               P E   +   V       +D  G++ + A +  GD +   I+ K        +  +
Sbjct: 784 ----PLENFNNKERVKSTAYSKLDSNGLVKLNAFLENGDAIARNISSKTLEDDFVNDNQI 839

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                E+  D+  + +          +  ++  R    K  R I  ++
Sbjct: 840 SFDISERYTDMYKSRVER----VQVDLTDKVKVRVLTMKERRPILGDK 883


>gi|225194758|gb|ACN81887.1| DNA-dependent RNA polymerase subunit rpo132 [Raccoonpox virus]
          Length = 1164

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 76/431 (17%), Positives = 148/431 (34%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFVQRGG 769

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D     ++ ++ Q+E+   + ++++  +  N YS+L          +G           
Sbjct: 770  LD----IVTAKKHQVEIPLENFNNKER-VKSNAYSKLES--------NGLVRLNAFLESG 816

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V+D ++  +V E     Y++    ++    +K++          
Sbjct: 817  DAMARNISSRTLEDDFVRDNQISFDVSERYTDMYKSRVERVQVELTDKVK---------- 866

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 867  -----VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTSIF 921

Query: 1129 SRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A        K ++            I     F ++     +    
Sbjct: 922  SRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPQLS 981

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D                                            ILYD  T +P
Sbjct: 982  DEELSDKIFCEK--------------------------------------ILYDPETDKP 1003

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1004 YTSKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1063

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1064 HGAANTITEVL 1074


>gi|146746611|gb|ABQ43746.1| RNA polymerase subunit rpo132 [Tanapox virus]
          Length = 1165

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/431 (17%), Positives = 139/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 711  DNGIHLIYPERPIVLSKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGG 770

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 771  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVKLNAFLENG 817

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y++    ++    +K++          
Sbjct: 818  DAIARNISSKTLEDDFVNDNQISFDISERYTDMYKSRVERVQVDLTDKVK---------- 867

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    D+P+  +G   DI++N   + 
Sbjct: 868  -----VRVLTMKERRPILGDKFTSRTSQKGTVAFIADETDLPYDDEGIKPDIIINSTSIF 922

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A         ++ + +         I     F ++          
Sbjct: 923  SRKTLSMLVEVILTAAYASKPYNNNEQNRPICFPSSNETSIDTYLDFAKQCYECVYPNLD 982

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
             ++ D+                                            ILYD  T  P
Sbjct: 983  KNEIDNKVFCEK--------------------------------------ILYDPETDVP 1004

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1005 YKSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1064

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1065 HGAANTITEVL 1075



 Score = 56.6 bits (135), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 86/648 (13%), Positives = 203/648 (31%), Gaps = 59/648 (9%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + +        ++  ++ + +   ++  +     +  +    S         + +
Sbjct: 253 SYDMPSEIIYLVNSLIESTKELIKNISDFNLDNYINDLVLSEYTKQKSQLQYEEF--KYE 310

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   II +++  +          D D++   RV + G+  +   
Sbjct: 311 MINNFLPHMYDSPNQLKGFYIILLLRKFIYCIYFTSRYPDRDSMVCHRVLTYGKYFEILA 370

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +IK  I +   +       I+           F      + ++   S    
Sbjct: 371 HDELENYIGNIKTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 429

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
            H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 430 PHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 489

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-DGSFT 641
               +     N Y  +E             D+ Y     E   YI   NS +   +    
Sbjct: 490 VLTSITNICTNEYLELEKKIYSYIKSFNYEDISYF----ETGYYITLENSLVASLNPEKV 545

Query: 642 EELVFCRCAGE------EILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNR 689
            + V      +       + +    +       +  +     + PFL  D      D+  
Sbjct: 546 YDFVNDFRRKKRIGYFGNLEIGITLVQDHMNEIRINIGGGRLIRPFLVIDNGELVMDTVI 605

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV- 748
             +   ++      +  E P V   ++      S      ++   + + + ++  +    
Sbjct: 606 KDLEEKIEDFTFSDILKEFPHVVEMVDIEQFTFSNVCESVQKFKSLSKAERVKYHLCDFP 665

Query: 749 ----EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGD---EVRRNDII 794
               +G +  S  G++            + +++      + R  +  G       R  ++
Sbjct: 666 SEFRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVL 725

Query: 795 ADGPSTDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +    T    +   G+++++A M + G N ED ++I ++ V       I  ++ +V    
Sbjct: 726 SKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI-- 783

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               P E   +   V       +D  G++ + A +  GD +   I+ K        +  +
Sbjct: 784 ----PLENFNNKERVKSTAYSKLDSNGLVKLNAFLENGDAIARNISSKTLEDDFVNDNQI 839

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                E+  D+  + +          +  ++  R    K  R I  ++
Sbjct: 840 SFDISERYTDMYKSRVER----VQVDLTDKVKVRVLTMKERRPILGDK 883


>gi|9627649|ref|NP_042172.1| hypothetical protein VARVgp128 [Variola virus]
 gi|298286900|sp|P33811|RPO2_VAR67 RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|297307|emb|CAA49069.1| A24R [Variola virus]
 gi|745248|prf||2015436EU A24R gene
          Length = 1164

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHLNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LTEKELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|40644549|emb|CAD89106.1| RNA polymerase II, second largest subunit [Tephrosia purpurea]
          Length = 550

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/449 (15%), Positives = 122/449 (27%), Gaps = 80/449 (17%)

Query: 820  GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDEC 879
              +      I   ++     + I   +     R+T             V+    +     
Sbjct: 180  YSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---D 236

Query: 880  GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             +  V        +    +       +      + AI      +  D+ +   S +    
Sbjct: 237  TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGF 296

Query: 940  VDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGP 999
                +F R   D+ ++  ++ +E      R           +          G       
Sbjct: 297  F-RSLFFRSYRDEEKKMGTLVKEDFCRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGED 355

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+T +S                      Q   +    +Y      +  R       
Sbjct: 356  VIIGKTTPIS----------------------QEEAQGQASRYTRRDHSISLRHSETGIV 393

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
             Q         LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   D
Sbjct: 394  DQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPD 453

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            I++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +   
Sbjct: 454  IIVNPHAIPSRMTIGQLIECVMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGF 513

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                               +G +    G
Sbjct: 514  ETM-----------------------------------------------YNGHT----G 522

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                     + +G  Y  +L HMV DK++
Sbjct: 523  R---RLTSMIFLGPTYYQRLKHMVDDKIH 548



 Score =  100 bits (249), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 63/403 (15%), Positives = 111/403 (27%), Gaps = 47/403 (11%)

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG   GLV +L     +            + +   T +   +S            N  
Sbjct: 1   TPEGQACGLVKNLAXMVYITVGSAASPILEFLEEW-GTENFEEISPAVIPQATKIFVNGC 59

Query: 634 LDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPK---QVVSIAASLIPFLENDDSNR 689
                   + LV         + V  E     D   K             P    D    
Sbjct: 60  WLGIHRDPDMLVKTLRNLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVDKQRL 119

Query: 690 VLMGCNM---QRQAVPLLKAEAPFVGTGM-------ESVVAKSS---GAAIVAKRAGIVE 736
           ++   ++   Q++  P        V  G        E      S      I A+      
Sbjct: 120 LIKKKDIIALQQRESPEEGGWHDLVSKGFIEYIDTEEEETTMISMTINDLIQARLNPGEA 179

Query: 737 QVDA-IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
             D      I         ++           + + Q+    Q   + V +   R D +A
Sbjct: 180 YSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLA 239

Query: 796 DGPST--------------DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                  L  G N +VA   + GYN EDS+++++  +    F S
Sbjct: 240 YVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS 299

Query: 842 IHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +      +E        +   +       +D+ G+   G  V+  D+++G
Sbjct: 300 LFFRSYRDEEKKMGTLVKEDFCRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIG 359

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           K TP  +           A         RD S+ +    +G V
Sbjct: 360 KTTPISQEE---------AQGQASRYTRRDHSISLRHSETGIV 393


>gi|12085099|ref|NP_073501.1| 116R protein [Yaba-like disease virus]
 gi|12056275|emb|CAC21354.1| 116R protein [Yaba-like disease virus]
          Length = 1165

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/431 (17%), Positives = 138/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 711  DNGIHLIYPERPIVLSKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGG 770

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 771  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVKLNAFLENG 817

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y++    ++    +K++          
Sbjct: 818  DAIARNISSKTLEDDFVNDNQISFDISERYTDMYKSRVERVQVDLTDKVK---------- 867

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    D+P+  +G   DI++N   + 
Sbjct: 868  -----VRVLTMKERRPILGDKFTSRTSQKGTVAFIADETDLPYDDEGIKPDIIINSTSIF 922

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A         ++ + +         I     F ++          
Sbjct: 923  SRKTLSMLVEVILTAAYASKPYNNNEQNRPICFPSSNETSIDTYLDFAKQCYECVYPNLD 982

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              + D+                                            ILYD  T  P
Sbjct: 983  KDEIDNKVFCEK--------------------------------------ILYDPETDVP 1004

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1005 YKSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1064

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1065 HGAANTITEVL 1075



 Score = 57.0 bits (136), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 86/648 (13%), Positives = 203/648 (31%), Gaps = 59/648 (9%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + +        ++  ++ + +   ++  +     +  +    S         + +
Sbjct: 253 SYDMPSEIIYLVNSLIESTKELIKDISDFNLDNYINDLVLSEYTKQKSQLQYEEF--KYE 310

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   II +++  +          D D++   RV + G+  +   
Sbjct: 311 MINNFLPHMYDSPNQLKGFYIILLLRKFIYCIYFTSRYPDRDSMVCHRVLTYGKYFEILA 370

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +IK  I +   +       I+           F      + ++   S    
Sbjct: 371 HDELENYIGNIKTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 429

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
            H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 430 PHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 489

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE-DGSFT 641
               +     N Y  +E             D+ Y     E   YI   NS +   +    
Sbjct: 490 VLTSITNICTNEYLELEKKIYSYIKSFNYEDISYF----ETGYYITLENSLVASLNPEKV 545

Query: 642 EELVFCRCAGE------EILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNR 689
            + V      +       + +    +       +  +     + PFL  D      D+  
Sbjct: 546 YDFVNDFRRKKRIGYFGNLEIGITLVQDHMNEIRINIGGGRLIRPFLVIDNGELVMDTVI 605

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV- 748
             +   ++      +  E P V   ++      S      ++   + + + ++  +    
Sbjct: 606 KDLEEKIEDFTFSDILKEFPHVVEMVDIEQFTFSNVCESVQKFKSLSKAERVKYHLCDFP 665

Query: 749 ----EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGD---EVRRNDII 794
               +G +  S  G++            + +++      + R  +  G       R  ++
Sbjct: 666 SEFRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVL 725

Query: 795 ADGPSTDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
           +    T    +   G+++++A M + G N ED ++I ++ V       I  ++ +V    
Sbjct: 726 SKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI-- 783

Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
               P E   +   V       +D  G++ + A +  GD +   I+ K        +  +
Sbjct: 784 ----PLENFNNKERVKSTAYSKLDSNGLVKLNAFLENGDAIARNISSKTLEDDFVNDNQI 839

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                E+  D+  + +          +  ++  R    K  R I  ++
Sbjct: 840 SFDISERYTDMYKSRVER----VQVDLTDKVKVRVLTMKERRPILGDK 883


>gi|94487211|gb|ABF26311.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94490237|gb|ABF29322.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109724172|gb|ABG43298.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109725190|gb|ABG44311.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109725395|gb|ABG44515.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109725598|gb|ABG44717.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109726005|gb|ABG45122.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109726615|gb|ABG45729.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
          Length = 1164

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHLNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LTEKELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|439046|gb|AAA60876.1| homolog of vaccinia virus CDS A24R (RNA polymerase, 132 kDa subunit);
            putative [Variola major virus]
 gi|94483980|gb|ABF23096.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94484183|gb|ABF23298.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94484592|gb|ABF23705.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94484790|gb|ABF23902.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94484988|gb|ABF24099.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94485186|gb|ABF24296.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94485388|gb|ABF24497.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94485591|gb|ABF24699.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94485996|gb|ABF25102.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94486197|gb|ABF25302.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94486400|gb|ABF25504.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94486603|gb|ABF25706.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94486805|gb|ABF25907.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94487008|gb|ABF26109.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94487617|gb|ABF26715.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94487818|gb|ABF26915.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94488225|gb|ABF27320.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94488425|gb|ABF27519.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94488625|gb|ABF27718.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94488826|gb|ABF27918.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94489027|gb|ABF28118.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94489226|gb|ABF28316.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94489426|gb|ABF28515.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94489628|gb|ABF28716.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|94489828|gb|ABF28915.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109724376|gb|ABG43501.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109724578|gb|ABG43702.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109724783|gb|ABG43906.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109724986|gb|ABG44108.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109725802|gb|ABG44920.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109726209|gb|ABG45325.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
 gi|109726412|gb|ABG45527.1| DNA-dependent RNA polymerase subunit rpo132 [Variola virus]
          Length = 1164

 Score =  190 bits (482), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHLNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LTEKELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|310750836|gb|ADP09211.1| RpoB' [Halococcus saccharolyticus]
          Length = 173

 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 76/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDQRIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEDEEELRGSLEEHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I+Y G+TGE  D 
Sbjct: 137  -----------------------FD-----------------SSGKEIMYSGVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGTIFYQKLYHMV 172


>gi|39644698|gb|AAH04882.4| POLR1B protein [Homo sapiens]
          Length = 582

 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 85   EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 143

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 144  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 203

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 204  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 253

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 254  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 311

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 312  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 343

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 344  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 378

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 379  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 438

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 439  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 498

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 499  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 558

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 559  VPYVFRYFVAELAAMNIKVKLD 580



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 96/273 (35%), Gaps = 20/273 (7%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
               L+G   Q      +  +  F G      +   S  +++A      +   + R + +
Sbjct: 76  GKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 135

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              G        +  Y+     +  +     Q PLV+                 D+ +  
Sbjct: 136 CQMG-KQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYP 183

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDI 865
           +G N +VA + + GY+ ED+M++++          S++  EF  ++   K G   +   I
Sbjct: 184 IGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGI 243

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVD 923
                  L+ +D+ G+  +GA++  GD     +     +  T E  ++     E     +
Sbjct: 244 KPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDN 298

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           ++  S    SG    V       R+    ++ +
Sbjct: 299 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 331


>gi|205363457|gb|ACI04158.1| RpoB [Corynebacterium stationis]
 gi|205363459|gb|ACI04159.1| RpoB [Corynebacterium stationis]
          Length = 140

 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 58/168 (34%), Positives = 93/168 (55%), Gaps = 36/168 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+ +     +   +   L++  +++    + +            
Sbjct: 1    QVLELHLGWLA-HTGWKVDT-----EDPKNAELLKTLPQELYDVPADSLT---------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFD 1246
                        +TPVFDGA  E I+ +L  +         +DE G+++L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNEEISRLLASSKPNRDGDVMIDEDGKTVLFDGRSGEPYQ 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             P++VGY+YMLKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 93   YPISVGYMYMLKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 140


>gi|67678361|gb|AAH96748.1| POLR1B protein [Homo sapiens]
          Length = 594

 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 176/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 97   EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 155

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 156  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 215

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 216  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQE 265

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 266  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 323

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 324  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 355

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 356  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 390

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 391  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 450

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 451  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 510

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 511  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 570

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 571  VPYVFRYFVAELAAMNIKVKLD 592



 Score = 62.4 bits (150), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 96/273 (35%), Gaps = 20/273 (7%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
               L+G   Q      +  +  F G      +   S  +++A      +   + R + +
Sbjct: 88  GKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 147

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              G        +  Y+     +  +     Q PLV+                 D+ +  
Sbjct: 148 CQMG-KQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYP 195

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDI 865
           +G N +VA + + GY+ ED+M++++          S++  EF  ++   K G   +   I
Sbjct: 196 IGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGI 255

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVD 923
                  L+ +D+ G+  +GA++  GD     +     +  T E  ++     E     +
Sbjct: 256 KPGDPRVLQELDDDGLPFIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDN 310

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           ++  S    SG    V       R+    ++ +
Sbjct: 311 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 343


>gi|151573555|gb|ABS18034.1| RNA polymerase II [Gibberella thapsina]
          Length = 297

 Score =  189 bits (481), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 59/370 (15%), Positives = 105/370 (28%), Gaps = 75/370 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVTVGYIYM 1256
              V  G  Y 
Sbjct: 288  AQVFFGPTYY 297



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|161331501|gb|ABX60668.1| RpoB [Bacillus sp. FSL_h8534]
          Length = 215

 Score =  189 bits (481), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/199 (36%), Positives = 95/199 (47%), Gaps = 54/199 (27%)

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
               K+   + GD++PPGV ++V+ ++  KR I  GDKMAGRHGNKG++SRILP EDMP+L
Sbjct: 71   LDVKVFNREDGDELPPGVNQLVRAYIVQKRKISEGDKMAGRHGNKGVISRILPEEDMPYL 130

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DGTP+DI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D     D+       
Sbjct: 131  PDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAARYLGIHIATPVFDGAREEDVWGTIEEA 190

Query: 1173 EKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG 1232
                                               T ++DG                   
Sbjct: 191  GMANDAK----------------------------TILYDG------------------- 203

Query: 1233 QSILYDGLTGEPFDRPVTV 1251
                    TGEPFD  V+V
Sbjct: 204  -------RTGEPFDNRVSV 215



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/81 (62%), Positives = 64/81 (79%)

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
           + L+N+DE GII VGAEV  GD+LVGK+TPKG + +T EE+LL AIFGEKA +VRDTSLR
Sbjct: 2   DALRNLDERGIIRVGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLR 61

Query: 931 VPSGVSGTVVDVRIFNRHGID 951
           VP G  G ++DV++FNR   D
Sbjct: 62  VPHGGGGIILDVKVFNREDGD 82


>gi|151573113|gb|ABS17740.1| RNA polymerase II [Fusarium sp. NRRL 43486]
 gi|151573179|gb|ABS17784.1| RNA polymerase II [Fusarium sp. NRRL 43541]
          Length = 297

 Score =  189 bits (481), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 58/370 (15%), Positives = 103/370 (27%), Gaps = 75/370 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVGYIYM 1256
              V  G  Y 
Sbjct: 288  AQVFFGPTYY 297



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|330785286|gb|AEC46449.1| RNA polymerase II second largest subunit [Sparria cerebriformis]
 gi|330785288|gb|AEC46450.1| RNA polymerase II second largest subunit [Sparria cerebriformis]
 gi|330785290|gb|AEC46451.1| RNA polymerase II second largest subunit [Sparria cerebriformis]
 gi|330785292|gb|AEC46452.1| RNA polymerase II second largest subunit [Sparria cerebriformis]
          Length = 307

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 61/377 (16%), Positives = 103/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFSELPAGQNAIVAISCYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     F R  I+K++       E+ E  A+                   +  G      
Sbjct: 64   LF-RSFFYRTYIEKSKAVGFNGIEEFEKPAKQLTMRTRPGTYEKLDDDGFVAPGVRVSGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T  +  +       Q  +   + +       +     +               
Sbjct: 123  DIIIGKTTPFTEAMSENAEGGQRTKVHNRRDISSPLRSTEAGIIDRVL------------ 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTSVEGNRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGMVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM V  + E  L       G +                           
Sbjct: 225  DIIINPHAIPSRMTVAHLIECLLSKVSATNGLEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+++L  A     G  ++++
Sbjct: 260  ----------------------------ATP-FTDVTVSEISNLLSNAGYQSRGLEVMHN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 291  GYTGRKLMAQVYLGPTY 307



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 44/196 (22%), Positives = 80/196 (40%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFSELPAGQNAIVAISCYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S     +   ++     G EE  +    +         + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEKSKAVGFNGIEEFEKPAKQLTMRTRPGTYEKLDDDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK TP  E+     E   R     K  + RD S  + S  +G +  V + +  G
Sbjct: 121 GDDIIIGKTTPFTEAMSENAEGGQRT----KVHNRRDISSPLRSTEAGIIDRVLVTSVEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 NRSVKVRTRTTKVPQI 192


>gi|88854214|gb|ABD52632.1| DNA-directed RNA polymerase subunit rpo132 [Vaccinia virus]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAIA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|160858027|emb|CAM58315.1| RNA polymerase subunit rpo132 [Vaccinia virus Ankara]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAIA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|218284158|ref|ZP_03489952.1| hypothetical protein EUBIFOR_02557 [Eubacterium biforme DSM 3989]
 gi|218215357|gb|EEC88895.1| hypothetical protein EUBIFOR_02557 [Eubacterium biforme DSM 3989]
          Length = 193

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 114/195 (58%), Positives = 143/195 (73%), Gaps = 3/195 (1%)

Query: 515 EFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
           EFF SSQLSQ  +  N L+ +T+ RR+SALG GG++R RA  E+RDVH +HYGRICP ET
Sbjct: 1   EFFSSSQLSQFMDQQNPLAELTNKRRISALGPGGISRDRASFEVRDVHNSHYGRICPIET 60

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVC-DGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG NIGL+++LT++AR+N YGFI+TPYRKV  DG V+ D VYLSA EE +  IAQAN  
Sbjct: 61  PEGPNIGLINNLTTYARINEYGFIQTPYRKVNADGTVSEDTVYLSADEEADYVIAQANEV 120

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
              DG    E V  R AGE I+  RE+++  D SPKQ+VS+A + +PFLENDD++R LMG
Sbjct: 121 --RDGHLVNERVVARKAGETIIADREEVELADVSPKQIVSVATACVPFLENDDASRALMG 178

Query: 694 CNMQRQAVPLLKAEA 708
            NMQRQAVPLL   +
Sbjct: 179 ANMQRQAVPLLVPHS 193


>gi|148628044|gb|ABQ97027.1| RNA polymerase II second largest subunit [Ceramothyrium carniolicum]
          Length = 325

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 68/391 (17%), Positives = 119/391 (30%), Gaps = 81/391 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 13   MANILYYPQKPLARTMAMEYLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLF 72

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +    +    +E   +    + + L    Y +L E   +  G     
Sbjct: 73   -RSLFYRAYQDQEK---MIGHAVVEQFEKPTRSDTLRLKHGTYDKLDEDGIVAPGVRVSG 128

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR  + +K    T     E    +++
Sbjct: 129  EDIIMGKTAPMAPD---------------AEELGQRMKQHIKRDVSTPLRSAESGVIDQV 173

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       +  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 174  LLTTTGD-----GCKFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGIV 228

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +  +          IS           
Sbjct: 229  PDLIINPHAIPSRMTIAHLIECLLSKVGALRGDEGDATPFTKVTVTQISS---------- 278

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                           +L      + G  V                        +G +   
Sbjct: 279  ---------------ILENMGYQRRGFEVM----------------------YNGHT--- 298

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
             G         V +G  Y  +L HMV DK++
Sbjct: 299  -GR---KLVAQVFLGPTYYQRLRHMVDDKIH 325



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/173 (21%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   + +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMETMANILYYPQKPLARTMAMEYLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    ++   +       E        D   +       +DE GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYQDQEKMIGHAVVEQFEKPTRSDTLRLKHGTYDKLDEDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L + +      DV        SGV   V+
Sbjct: 126 VSGEDIIMGKTAPMAPDA----EELGQRMKQHIKRDVSTPLRSAESGVIDQVL 174


>gi|167412662|gb|ABZ80096.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus GLV-1h68]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|56404962|sp|Q9JF79|RPO2_VACCT RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|6969808|gb|AAF34020.1| TA25R [Vaccinia virus Tian Tan]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 76/434 (17%), Positives = 143/434 (32%), Gaps = 79/434 (18%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAIA--------- 820

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDD 1065
                                +D ++  +V E     Y++    ++    +K++       
Sbjct: 821  -------RNISSRTLEDDFARDNQISFDVPEKYTDMYKSRVERVQVELTDKVK------- 866

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                    V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N  
Sbjct: 867  --------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINST 918

Query: 1126 GVPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSH 1181
             + SR  +  + E  L  A        K ++            I     F ++     + 
Sbjct: 919  SIFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNP 978

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                 +  D                                            ILYD  T
Sbjct: 979  KLSDEELSDKIFCEK--------------------------------------ILYDPET 1000

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
             +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C
Sbjct: 1001 DKPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDC 1060

Query: 1302 IQAYGAAYVLQEML 1315
            + A+GAA  + E+L
Sbjct: 1061 LIAHGAANTITEVL 1074


>gi|308194109|gb|ADO16472.1| RNA polymerase beta subunit [Gemella haemolysans]
          Length = 210

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 62/110 (56%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 72   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 131

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+
Sbjct: 132  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDV 181



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 50/78 (64%), Positives = 58/78 (74%)

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
            L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTSLRV
Sbjct: 1   ALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTSLRV 60

Query: 932 PSGVSGTVVDVRIFNRHG 949
           P G  G V DV+IF R  
Sbjct: 61  PHGADGVVADVKIFKRED 78



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 47/106 (44%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K        + +    P  + ++ ++       +++      +       + 
Sbjct: 105  KMAGRHGNKGVISNILPEEDMPYLPDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQL 164

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            G+ V+TPVFDGA +E + S +  A + +  +++LYDG TGEPFD  
Sbjct: 165  GIHVATPVFDGATDEDVWSTVAEAGMAKDAKTVLYDGRTGEPFDSR 210


>gi|49522875|gb|AAH73857.1| POLR1B protein [Homo sapiens]
          Length = 560

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 101/562 (17%), Positives = 174/562 (30%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 63   EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 121

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 122  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 181

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 182  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 231

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 232  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 289

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 290  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 321

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I + +           
Sbjct: 322  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAA------ 364

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                           +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 365  --------LHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 416

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 417  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 476

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 477  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 536

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 537  VPYVFRYFVAELAAMNIKVKLD 558



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 96/273 (35%), Gaps = 20/273 (7%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
               L+G   Q      +  +  F G      +   S  +++A      +   + R + +
Sbjct: 54  GKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 113

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              G        +  Y+     +  +     Q PLV+                 D+ +  
Sbjct: 114 CQMG-KQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYP 161

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDI 865
           +G N +VA + + GY+ ED+M++++          S++  EF  ++   K G   +   I
Sbjct: 162 IGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGI 221

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVD 923
                  L+ +D+ G+  +GA++  GD     +     +  T E  ++     E     +
Sbjct: 222 KPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDN 276

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           ++  S    SG    V       R+    ++ +
Sbjct: 277 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 309


>gi|83405170|gb|AAI10834.1| POLR1B protein [Homo sapiens]
          Length = 952

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 101/562 (17%), Positives = 174/562 (30%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 455  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 513

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 514  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 573

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 574  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 623

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 624  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 681

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 682  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 713

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I + +           
Sbjct: 714  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAA------ 756

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                           +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 757  --------LHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 808

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 809  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 868

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 869  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 928

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 929  VPYVFRYFVAELAAMNIKVKLD 950



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/273 (16%), Positives = 96/273 (35%), Gaps = 20/273 (7%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
               L+G   Q      +  +  F G      +   S  +++A      +   + R + +
Sbjct: 446 GKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 505

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
              G        +  Y+     +  +     Q PLV+                 D+ +  
Sbjct: 506 CQMG-KQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYP 553

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDI 865
           +G N +VA + + GY+ ED+M++++          S++  EF  ++   K G   +   I
Sbjct: 554 IGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGI 613

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVD 923
                  L+ +D+ G+  +GA++  GD     +     +  T E  ++     E     +
Sbjct: 614 KPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDN 668

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           ++  S    SG    V       R+    ++ +
Sbjct: 669 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 701



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 44/138 (31%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179


>gi|56713532|gb|AAW23572.1| DNA-directed RNA polymerase subunit [Vaccinia virus]
 gi|56713816|gb|AAW23854.1| DNA-directed RNA polymerase subunit [Vaccinia virus]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|71024920|gb|AAZ17443.1| RNA polymerase subunit 132 [Cowpox virus]
 gi|90660381|gb|ABD97495.1| DNA-dependent RNA polymerase subunit rpo132 [Cowpox virus]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|282598436|gb|ADA83448.1| RNA polymerase beta subunit [Corynebacterium sp. NML92-0415]
          Length = 139

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 83/167 (49%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPKNAALLETLPEHLYDVPPESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I  +L     +  G        ++ LYDG +GEP+ 
Sbjct: 45   ------------ATPVFDGASNEEIAGLLANTKPNRDGDVMVDGQGKTRLYDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|213053796|gb|ACJ39203.1| RpoB [Corynebacterium ureicelerivorans]
          Length = 139

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 60/167 (35%), Positives = 84/167 (50%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEIHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPADSLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANSKPNRDGDVMVDENGKTTLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|66275941|ref|YP_233026.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus]
 gi|56405099|sp|P68694|RPO2_VACCC RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|56405100|sp|Q76ZP7|RPO2_VACCV RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|335496|gb|AAA48148.1| putative A24R [Vaccinia virus Copenhagen]
 gi|335801|gb|AAA72882.1| RNA polymerase subunit rpo132 [Vaccinia virus]
 gi|29692250|gb|AAO89423.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus WR]
 gi|38349011|gb|AAR17987.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus]
 gi|88900762|gb|ABD57674.1| VACV140 [Vaccinia virus]
          Length = 1164

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|310750816|gb|ADP09201.1| RpoB' [Haloarcula sp. shark2]
 gi|310750820|gb|ADP09203.1| RpoB' [Haloarcula sp. Safaga-17]
 gi|310750822|gb|ADP09204.1| RpoB' [Haloarcula sp. Toen-14]
 gi|310750828|gb|ADP09207.1| RpoB' [Haloarcula argentinensis]
 gi|310750830|gb|ADP09208.1| RpoB' [Haloarcula quadrata]
 gi|310750832|gb|ADP09209.1| RpoB' [Haloarcula sinaiiensis ATCC 33800]
          Length = 173

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 75/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEDELRGSLEEHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+  +Y G+TGE  D 
Sbjct: 137  -----------------------FD-----------------SSGKETMYSGVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGDIFYQKLYHMV 172


>gi|310750804|gb|ADP09195.1| RpoB' [Haloarcula aidinensis]
 gi|310750806|gb|ADP09196.1| RpoB' [Haloarcula sp. Aidin-11]
 gi|310750808|gb|ADP09197.1| RpoB' [Haloarcula sp. Aidin-2]
 gi|310750810|gb|ADP09198.1| RpoB' [Haloarcula sp. Aidin-5]
 gi|310750812|gb|ADP09199.1| RpoB' [Haloarcula sp. NG5]
 gi|310750814|gb|ADP09200.1| RpoB' [Haloarcula sp. port]
 gi|310750824|gb|ADP09205.1| RpoB' [Haloarcula sp. Toen-15]
          Length = 173

 Score =  189 bits (480), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 75/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEELRGSLEEHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+  +Y G+TGE  D 
Sbjct: 137  -----------------------FD-----------------SSGKETMYSGVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGDIFYQKLYHMV 172


>gi|56694372|gb|AAW22926.1| RNA polymerase II second largest subunit [Illicium anisatum]
          Length = 539

 Score =  189 bits (479), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/444 (15%), Positives = 127/444 (28%), Gaps = 81/444 (18%)

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                I   ++     + I   +     R+T             V+   L+      +  V
Sbjct: 177  THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYV 233

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                    +    +       +      + AI      +  D+ +   S +        +
Sbjct: 234  LYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSL 292

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R   D+ ++  ++ +E      R+          +          G           K
Sbjct: 293  FFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 352

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +T ++ D   +  R                    +  + T     E    +++      D
Sbjct: 353  TTPIAQDEQGQASRYT------------------RRDHSTCLRHSESGMIDQVLLTTNAD 394

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
             +     R VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP
Sbjct: 395  GL-----RFVKVRMRSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 449

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +GQ+ E  +G     +GK+  +         +IS         +        
Sbjct: 450  HAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM-- 507

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                                          +G +    G     
Sbjct: 508  ---------------------------------------------YNGHT----GR---R 515

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVY 1268
                + +G  Y  +L HMV DK++
Sbjct: 516  LSAMIFLGPTYYQRLKHMVDDKIH 539



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 52/362 (14%), Positives = 106/362 (29%), Gaps = 32/362 (8%)

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             F      G    P   V   +     V ++      R I      L  D       +F
Sbjct: 46  KIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLF 105

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVS---IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                  ++  ++          +      +A   I +++ ++    ++   +       
Sbjct: 106 IVEKQRLLIKKKDIRALQQRETPEEGWHDLVAKGFIEYVDTEEEETTMISMTISDLVTAR 165

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IY 762
           L  E     T       +   + I+   A I+   D  +    + +  +     G+    
Sbjct: 166 LNPEEAISET---YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTN 222

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             ++           Q+PLV                      L  G N +VA   + GYN
Sbjct: 223 YQLRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSGYN 272

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 273 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 332

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +                     RD S  +    SG
Sbjct: 333 DDGLAPPGTRVSGEDVIIGKTTPIAQDEQ----------GQASRYTRRDHSTCLRHSESG 382

Query: 938 TV 939
            +
Sbjct: 383 MI 384


>gi|308194113|gb|ADO16474.1| RNA polymerase beta subunit [Gemella haemolysans]
          Length = 213

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 62/110 (56%), Positives = 81/110 (73%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI K + G ++P GV  +V+VF+  KR I+ GDKMAGRHGNKG++S ILP EDMP+L DG
Sbjct: 75   KIFKREDGAELPNGVNELVRVFIVQKRKIRVGDKMAGRHGNKGVISNILPEEDMPYLPDG 134

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            TPVD++LNPLGVPSRMN+GQ+ E HLG A   LG  + + + D   + D+
Sbjct: 135  TPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQLGIHVATPVFDGATDEDV 184



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 51/81 (62%), Positives = 59/81 (72%)

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
            E  L+N+D  GII +GAEV  GDILVGK+TPKG +  TPEEKLL AIFG K+ +VRDTS
Sbjct: 1   GENALRNLDARGIIRIGAEVKDGDILVGKVTPKGLTEQTPEEKLLYAIFGAKSKEVRDTS 60

Query: 929 LRVPSGVSGTVVDVRIFNRHG 949
           LRVP G  G V DV+IF R  
Sbjct: 61  LRVPHGADGVVADVKIFKRED 81



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 47/106 (44%)

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G K        + +    P  + ++ ++       +++      +       + 
Sbjct: 108  KMAGRHGNKGVISNILPEEDMPYLPDGTPVDVMLNPLGVPSRMNIGQVLELHLGMAAKQL 167

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            G+ V+TPVFDGA +E + S +  A + +  +++LYDG TGEPFD  
Sbjct: 168  GIHVATPVFDGATDEDVWSTVAEAGMAKDAKTVLYDGRTGEPFDSR 213


>gi|67942366|gb|AAY83383.1| DNA-dependent RNA polymerase II [Chorioactis geaster]
          Length = 559

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 94/682 (13%), Positives = 179/682 (26%), Gaps = 129/682 (18%)

Query: 577  GHNIGLVSSLTS--FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            G   GLV +L    +  V         Y    + +   +     +      ++      +
Sbjct: 1    GQACGLVKNLALMSYITVGTPSDPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGI 60

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
              D       V        +      I D  D   K          P    ++       
Sbjct: 61   HRDPMHLVRNVQEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERR 120

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
              +  Q   + + E          +              GIVE VDA       +    +
Sbjct: 121  GQLVLQKEHIQRLEQDA------ELPPDERWGWDGLLDEGIVEYVDAEEEETIMIVMTPE 174

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   + +              + P+        +       PS  LG       +  
Sbjct: 175  DLEIAQQVRQGYVLDEETDQHKRVKAPI---NPNTHQYTHCEIHPSMILG-------ICA 224

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   + +  F                          
Sbjct: 225  SIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFSERM---------------------- 260

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  +  I      +  D+ +   S
Sbjct: 261  -----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQS 315

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R   D+ +R   +    +E   + +    + L    Y +L +   + 
Sbjct: 316  SIDRGLF-RSLFYRSYTDQEKR---IGMMVVEEFEKPQRSNTLRLKHGTYEKLDDDGLVA 371

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D                DE  QR     K    T     E
Sbjct: 372  PGVRVSGEDIIIGKTAPIAPD---------------ADEMGQRQKFHTKRDVSTPLRSTE 416

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
            +   +++             L+  KV +   +  Q GDK A RHG KG +      EDMP
Sbjct: 417  NGIVDQVLL-----TTNAEGLKFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMP 471

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F  +G   D+++NP  +PSRM +  + E  L       G +                   
Sbjct: 472  FTCEGIIPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGMEGD----------------- 514

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     ++++++LR      
Sbjct: 515  ------------------------------------ATP-FTDVTVDSVSNLLREEGYQS 537

Query: 1231 SGQSILYDGLTGEPFDRPVTVG 1252
             G  ++Y+G TG+     V +G
Sbjct: 538  RGFEVMYNGHTGKKMVAQVFLG 559



 Score =  109 bits (272), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 77/487 (15%), Positives = 149/487 (30%), Gaps = 97/487 (19%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 31  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG-HE 83

Query: 549 VARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           V+  R   +      T  GR+C        +T+      LV       R+     +    
Sbjct: 84  VSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEQDAELPPDE 143

Query: 603 RK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLD-----EDGSFTEELVFCRCAGEEILV 656
           R           V Y+ A EEE   I      L+       G   +E        +  + 
Sbjct: 144 RWGWDGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAQQVRQGYVLDEETDQHKRVKAPIN 203

Query: 657 PR-EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           P   +    +  P  ++ I AS+IPF +++ S R      M +QA+ +            
Sbjct: 204 PNTHQYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFS------ 257

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                              +   + + +  Y       +     
Sbjct: 258 -----------------------------------ERMDTMANILYYPQKPLATTRSMEY 282

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +  R                        +L  G+N +V  M + GYN EDS+++++  + 
Sbjct: 283 LKFR------------------------ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSID 318

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
             +F S+    +    +   +   E        +   +     + +D+ G++  G  V+ 
Sbjct: 319 RGLFRSLFYRSYTDQEKRIGMMVVEEFEKPQRSNTLRLKHGTYEKLDDDGLVAPGVRVSG 378

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P         ++       +K    RD S  + S  +G V  V +      
Sbjct: 379 EDIIIGKTAPIAPDADEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVLLTTNAEG 431

Query: 951 DKNERSI 957
            K  +  
Sbjct: 432 LKFAKVR 438


>gi|317408993|gb|ADV17878.1| RNA polymerase II second largest subunit [Gloeophyllum striatum]
          Length = 349

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 69/435 (15%), Positives = 121/435 (27%), Gaps = 88/435 (20%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  +   ++            ++       +G       +          
Sbjct: 1    WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   R+          +       I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D                +E  QR     +    T+    E    +
Sbjct: 169  NGDDIIIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTALKSTESGIVD 213

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 214  QVLI-----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  ITPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E++++ LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      V 
Sbjct: 335  MYHGHTGRKLQAQVY 349



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 49/297 (16%), Positives = 94/297 (31%), Gaps = 77/297 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ + AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLRFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       I++ G+I  G  VN  DI++
Sbjct: 116 SIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGLIAPGTGVNGDDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        ++   RD S  + S  SG V  V I       K
Sbjct: 176 GKTAPIPPDSEELGQRT-------RSHTRRDVSTALKSTESGIVDQVLITTNSEGQK 225


>gi|312458551|gb|ADQ89209.1| DNA-directed RNA polymerase beta subunit [Corynebacterium
            diphtheriae]
          Length = 139

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 88/167 (52%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G KI +     +   +   L++  E +                   
Sbjct: 1    QVLEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEPF 
Sbjct: 40   -------AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSGEPFP 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPVSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|310750826|gb|ADP09206.1| RpoB' [Haloarcula hispanica ATCC 33960]
          Length = 173

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 75/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIINPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEELRGSLEDHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+  +Y G+TGE  D 
Sbjct: 137  -----------------------FD-----------------SSGKETMYSGVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGDIFYQKLYHMV 172


>gi|300394704|gb|ADK11890.1| DNA-directed RNA polymerase II subunit two [Coniophora prasinoides]
          Length = 352

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 67/435 (15%), Positives = 117/435 (26%), Gaps = 88/435 (20%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  I   ++            ++       +G       +          
Sbjct: 1    WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD          +       I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q              
Sbjct: 169  SGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  IVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E++++ LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      + 
Sbjct: 335  MYHGHTGRKLQAQIY 349



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 90/285 (31%), Gaps = 74/285 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       I++ G+I  G  V+  DI++
Sbjct: 116 SIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           GK  P         E+L +        DV        +G+   V+
Sbjct: 176 GKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 216


>gi|37551589|gb|AAQ93241.1| DNA-dependent RNA polymerase subunit rpo132 [Vaccinia virus]
          Length = 1164

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RDK +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDKSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|193873116|gb|ACF23248.1| RpoB [Streptococcus mitis]
          Length = 172

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 69/168 (41%), Positives = 94/168 (55%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E  LG A   LG  I + + D  ++  +
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMEPPLGLAARSLGIPIATPVFDGTSSEKL 164



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGADGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|114579606|ref|XP_001144853.1| PREDICTED: RNA polymerase I polypeptide B isoform 2 [Pan troglodytes]
          Length = 952

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 101/562 (17%), Positives = 174/562 (30%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 455  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 513

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 514  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 573

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 574  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 623

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 624  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 681

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 682  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 713

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I + +           
Sbjct: 714  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAA------ 756

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                           +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 757  --------LHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 808

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 809  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 868

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 869  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVS 928

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 929  VPYVFRYFVAELAAMNIKVKLD 950



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 100/289 (34%), Gaps = 20/289 (6%)

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             +    + P    +     L+G   Q      +  +  F G      +   S  +++A 
Sbjct: 430 FTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIAN 489

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                +   + R + +   G        +  Y+     +  +     Q PLV+       
Sbjct: 490 FIPFSDHNQSPRNMYQCQMG-KQTMGFPILTYQDRSDNKLYRLQ-TPQSPLVRPSMY--- 544

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEV 849
                     D+ +  +G N +VA + + GY+ ED+M++++          S++  EF  
Sbjct: 545 -------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFID 597

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           ++   K G   +   I       L+ +D+ G+  +GA++  GD     +     +  T E
Sbjct: 598 LSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGE 652

Query: 910 EKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             ++     E     +++  S    SG    V       R+    ++ +
Sbjct: 653 SFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 701



 Score = 57.8 bits (138), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 44/138 (31%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179


>gi|40643907|emb|CAD89692.1| RNA polymerase II, second largest subunit [Escallonia sp. Oxelman
            2340]
          Length = 321

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 68/389 (17%), Positives = 105/389 (26%), Gaps = 76/389 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTP-------EEKLLRAIFGEKAVDVRDTSLRV 931
             G   +G  V      +  +      P  P       E    R +       V       
Sbjct: 1    MGKQAMGIYVTNYQTRMDTLAYVLYYPQKPLVTTRALEHLHFRQLPAGINAIVAIACYSG 60

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL-DRNIYSRLMEIL 990
             +     +++    +R             R       RD++ +   L   +      +  
Sbjct: 61   YNQEDSVIMNQSAIDRGFF----------RSLFYCPYRDEEKKMGTLVKEDFGCPHRDNT 110

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G    S  K            +S              E  Q  V     +Y        
Sbjct: 111  MGMRHGSYDKLDNDGLAPPGSRVSGDDVIIGKTTPFNQEDAQGQVS----RYTRRDHSTS 166

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
             R        Q         L+ VKV +   R  Q GDK + RHG KG V      EDMP
Sbjct: 167  LRHSESGTVDQVLLTTNADGLKFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMP 226

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +  +G   DI++N   +PSRM +GQ+ E  +G     +G +                   
Sbjct: 227  WTIEGINPDIIVNLHAIPSRMTIGQLIECIMGKVAAQMGXEGD----------------- 269

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
                                                +TP F     + I+  L       
Sbjct: 270  ------------------------------------ATP-FTDVTVDNISKALHKCGYQM 292

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
             G   +Y+G TG      + +G  Y  +L
Sbjct: 293  RGFETMYNGHTGRRMTAMIFLGPTYYQRL 321



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 63/197 (31%), Gaps = 24/197 (12%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQTRMDTLAYVLYYPQKPLV----------TTRALEHLHFRQLPAGINAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSAIDRGFFRSLFYCPYRDEEKKMGTLVKEDFGCPHRDNTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  G+   G+ V+  D+++GK TP  +           A         RD S  +    
Sbjct: 121 LDNDGLAPPGSRVSGDDVIIGKTTPFNQED---------AQGQVSRYTRRDHSTSLRHSE 171

Query: 936 SGTVVDVRIFNRHGIDK 952
           SGTV  V +       K
Sbjct: 172 SGTVDQVLLTTNADGLK 188


>gi|119640677|gb|ABL85532.1| RNA polymerase II second largest subunit [Roccellina inaequabilis]
 gi|119640681|gb|ABL85534.1| RNA polymerase II second largest subunit [Roccellina lutosa]
 gi|330785344|gb|AEC46478.1| RNA polymerase II second largest subunit [Roccellina inaequabilis]
          Length = 307

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R    E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPLKAETMRTRHGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLQFAGYQSRGFEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFMGPTY 307



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPLKAETMRTRHGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|213053800|gb|ACJ39205.1| RpoB [Corynebacterium ureicelerivorans]
 gi|213053804|gb|ACJ39207.1| RpoB [Corynebacterium ureicelerivorans]
          Length = 139

 Score =  189 bits (479), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/167 (35%), Positives = 84/167 (50%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEIHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPADSLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANSKPNRDGDVMVDENGKTTLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|37956388|gb|AAP15367.1| RNA polymerase beta subunit [Geopsychrobacter electrodiphilus]
          Length = 179

 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 110/176 (62%), Positives = 135/176 (76%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRMSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N YGF+ETPYR V DGKVT D+ Y SA+EEE   IAQAN+ LD  G FT E
Sbjct: 61  ASLSTYARINEYGFVETPYRLVKDGKVTTDIKYFSALEEEKHAIAQANAPLDTKGKFTNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           LV  R  GE +L+P  ++  +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQ Q
Sbjct: 121 LVNVRKDGEFMLLPPAEVSLMDVSPKQIVSVAAALIPFLENDDANRALMGSNMQSQ 176


>gi|18640376|ref|NP_570532.1| CMLV142 [Camelpox virus]
 gi|56404839|sp|Q775Q3|RPO2_CAMPS RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|56404918|sp|Q8V2N1|RPO2_CAMPM RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide
 gi|18483052|gb|AAL73849.1|AF438165_139 RNA polymerase subunit RPO132 [Camelpox virus M-96]
 gi|19718108|gb|AAG37633.1| CMP141R [Camelpox virus CMS]
          Length = 1164

 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A          + + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSVKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYGSKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|190714321|emb|CAQ64502.1| DNA dependant RNA polymerase [Mycobacterium tuberculosis]
 gi|190714340|emb|CAQ64506.1| DNA dependant RNA polymerase [Mycobacterium tuberculosis]
          Length = 175

 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 101/174 (58%), Positives = 133/174 (76%), Gaps = 1/174 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 2   IKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS
Sbjct: 62  ETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANS 121

Query: 633 SLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +D DG F E  V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+D
Sbjct: 122 PIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHD 175


>gi|323098545|gb|ADX22783.1| DNA-dependent RNA polymerase subunit rpo132 [Monkeypox virus]
          Length = 1164

 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 78/433 (18%), Positives = 144/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E     A            + +         I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVIXTAAYSTKPYNNKGXXRPVCFXSSNETSIDAYMQFAKQCYEYSNPK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSEEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P++  V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYESKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|119644276|gb|ABL85616.1| RNA polymerase II second largest subunit [uncultured Ascomycota]
          Length = 326

 Score =  188 bits (478), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 62/392 (15%), Positives = 112/392 (28%), Gaps = 81/392 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 13   DIMANILYYPQKPLATTQSMEFLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 72

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +   ++ + L    Y +L E   +  G   
Sbjct: 73   LF-RSLFYRSYTDQEKR---IGMNVVEQFEKPYRNDTLKLKHGTYDKLDEDGIVAPGVRV 128

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 129  SGEDIIIGKTAPIAPDAEELGQRTKAHSKRDASTPLRSTENGIVDQVLI----------- 177

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 178  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREG 228

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    +  
Sbjct: 229  IVPDLIINPHAIPSRMTIAHLIECQLSKVASLSGYEGDATPFTEVTVDSVSRLLR--DNG 286

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                                                     G + 
Sbjct: 287  YQSRGFEIM---------------------------------------------YHGHT- 300

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
               G         V +G  Y  +L HMV DK+
Sbjct: 301  ---GR---KLVAQVFLGPTYYQRLRHMVDDKI 326



 Score = 88.6 bits (218), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 41/181 (22%), Positives = 70/181 (38%), Gaps = 15/181 (8%)

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLIS 830
              +QR  +           +A   S +     DL  G+N +VA + + GYN EDS++++
Sbjct: 6   MNFDQRMDIMANILYYPQKPLATTQSMEFLKFRDLPAGQNAIVAILCYSGYNQEDSVIMN 65

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVG 885
           +  +   +F S+    +    +   +   E        D   +       +DE GI+  G
Sbjct: 66  QSSIDRGLFRSLFYRSYTDQEKRIGMNVVEQFEKPYRNDTLKLKHGTYDKLDEDGIVAPG 125

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I 
Sbjct: 126 VRVSGEDIIIGKTAPIAPDAEELGQRT-------KAHSKRDASTPLRSTENGIVDQVLIT 178

Query: 946 N 946
            
Sbjct: 179 T 179


>gi|61611841|gb|AAX47237.1| RpoB [Aeromonas simiae]
          Length = 172

 Score =  188 bits (478), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVNDGVITDEVEYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|149727190|ref|XP_001495532.1| PREDICTED: similar to RNA polymerase I polypeptide B isoform 2 [Equus
            caballus]
          Length = 952

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 104/558 (18%), Positives = 178/558 (31%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F +I I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 455  EQIFMNIAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 513

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            G            +   L+                + +   GT   V + +  G D  + 
Sbjct: 514  GFPLLTYRDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 573

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             I  +       A     +   +D  +  ++ +          P   +    L  D +  
Sbjct: 574  MIVNKASWERGFAHGSVYKSEFID--LSEKIKQGDDSLVFGVKPGDPRIVQKLDDDGLPF 631

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                   Q    D        +    +       E+   + I+     +D   G  + + 
Sbjct: 632  IGA----QLQYGDPYYSYLNLNTGESFVMYYKSKENCIVDNIKVCS--NDTGSGKFKCIC 685

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + + + R    GDK A RHG K                            G+ SR+    
Sbjct: 686  ITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL---- 713

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                   W    +      ++ D   N    P R  +  +I + +               
Sbjct: 714  -------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAA---------- 756

Query: 1196 VAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                       +TP +F   +   E    ML+ A  +  G   LY G++G   +  + +G
Sbjct: 757  ----LHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGVELEADIFIG 812

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 813  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 872

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 873  DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCNRSDTIDTVSVPYV 932

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 933  FRYFVAELAAMNIKVKLD 950



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/138 (19%), Positives = 43/138 (31%), Gaps = 47/138 (34%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPK-----------FDVDDCLWRDLTYA 99
           EGL  A +++ P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLSHAVQAIPPFEFAFKDERISLTIVDAVISPPTVPKGSICKDLSIYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWSVNGIP--------KGIIKQ--FLGYVPIMVKSKLCNLYNLPPRALIEHHE 161

Query: 142 ------GTFVIKGIQRIV 153
                 G F+I GI++++
Sbjct: 162 EAEEMGGYFIINGIEKVI 179



 Score = 62.4 bits (150), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/289 (14%), Positives = 101/289 (34%), Gaps = 20/289 (6%)

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             +    + P    +     L+G   Q      +  +  F G      +   S  +++A 
Sbjct: 430 FTTPCRLVRPVQNLELGREELIGTMEQIFMNIAIFEDEVFAGVTTHQELFPHSLLSVIAN 489

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                +   + R + +   G        +  YR     +  +     Q PLV+       
Sbjct: 490 FIPFSDHNQSPRNMYQCQMG-KQTMGFPLLTYRDRSDNKLYRLQ-TPQSPLVRPYMY--- 544

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEV 849
                     D+ +  +G N +VA + + GY+ ED+M++++          S++  EF  
Sbjct: 545 -------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFID 597

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           ++   K G + +   +       ++ +D+ G+  +GA++  GD     +     +  T E
Sbjct: 598 LSEKIKQGDDSLVFGVKPGDPRIVQKLDDDGLPFIGAQLQYGDPYYSYL-----NLNTGE 652

Query: 910 EKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             ++   +       +++  S    SG    +       R+    ++ +
Sbjct: 653 SFVMYYKSKENCIVDNIKVCSNDTGSGKFKCICITMRVPRNPTIGDKFA 701


>gi|46277328|gb|AAS86854.1| DNA-dependent RNA polymerase II [Peziza depressa]
          Length = 561

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 92/682 (13%), Positives = 188/682 (27%), Gaps = 136/682 (19%)

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL S+  V         +    + +V  +     +      ++      +  D  F    
Sbjct: 7    SLMSYVSVGTPSQPIVDFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRT 66

Query: 645  VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP--FLENDDSNRVLMGCNMQRQAVP 702
            +        I      I  I     ++ + A  +    F+ ++D      G  + ++   
Sbjct: 67   IQKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHI 126

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKR----AGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                      T +E              +     G+VE +DA       +    +   + 
Sbjct: 127  ----------TKLEDDRDNDDETQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETS 176

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
               +   + Q++       QR    V             PS  LG       +  + +P+
Sbjct: 177  RQFHAGYEIQQTLDPA---QRVKGAVNKFAHTWTHCEIHPSMILG-------ICASIIPF 226

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N       S R   +       +  F    R+                         
Sbjct: 227  PDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM----------------------- 257

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 258  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 317

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G   
Sbjct: 318  LF-RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRV 373

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ +      R+++         ++     +  Q              
Sbjct: 374  SGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------- 419

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 420  ------VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEG 473

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  +                                       
Sbjct: 474  VVPDLIINPHAIPSRMTIAHLI-------------------------------------- 495

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                           + +L      +     +TP F     ++++++LR       G  +
Sbjct: 496  ---------------ECLLSKVSSLRGFEGDATP-FTDVTVDSVSTLLREHGYQSRGFEV 539

Query: 1236 LYDGLTGEPFDRPVTVGYIYML 1257
            +Y+G TG      V +G  Y  
Sbjct: 540  MYNGHTGRKMVAQVFLGPTYYQ 561



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 66/481 (13%), Positives = 127/481 (26%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 23  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 76

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L     +    +    
Sbjct: 77  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHITKLEDDRDND 136

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            ET             V Y+ A EEE   I      L+    F       + L   +   
Sbjct: 137 DETQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQTLDPAQRVK 196

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +          +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 197 GAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT----- 251

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                      + A I+      +    ++  +          +   +  Y         
Sbjct: 252 ----NYRERMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSG------- 300

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                NQ                    S  +   ++ R +  +       + E  + +S 
Sbjct: 301 ----YNQE------------------DSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMS- 337

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                       +EEFE   R           +   +       +D+ G++  G  V+  
Sbjct: 338 -----------VVEEFEKPTR----------GNTLRLKHGTYDKLDDDGLVAPGVRVSGE 376

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P   +     ++        K    RD S  + S  +G V  V +       
Sbjct: 377 DIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 429

Query: 952 K 952
           K
Sbjct: 430 K 430


>gi|300394720|gb|ADK11898.1| DNA-directed RNA polymerase II subunit two [Cristinia sp. FP-100305]
          Length = 350

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/435 (16%), Positives = 118/435 (27%), Gaps = 88/435 (20%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  I   ++            ++       +G       I          
Sbjct: 1    WTQCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFLIRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD                  I  G N 
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYEKLESDGLIAPGTNV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            +       K+  +  D      R++          ++     +  Q              
Sbjct: 169  LGEDIIIGKTAPIPPDSEELGQRTRLHTRRDVSTPLKSTERGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q+GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSSRIPQTGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  IVPDIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++  LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSQFLRSKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      V 
Sbjct: 335  MYHGHTGRKLQAQVY 349


>gi|225194740|gb|ACN81878.1| DNA-dependent RNA polymerase subunit rpo132 [Volepox virus]
          Length = 1164

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 75/431 (17%), Positives = 146/431 (33%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFVQRGG 769

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D     ++ ++ Q+E+   + ++++  +  N YS+L          +G           
Sbjct: 770  LD----IVTAKKHQVEIPLENFNNKER-VKSNAYSKLES--------NGLVRLNAFLESG 816

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V+D ++  +V E     Y++    ++    +K++          
Sbjct: 817  DAMARNISSRTLEDDFVRDNQISFDVSERYTDMYKSRVERVQVELTDKVK---------- 866

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 867  -----VRVLTMKERRPILGDKFTTRTSQKGTVAYIADETELPYDENGITPDVIINSTSIF 921

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A          + + +         I     F  +     +    
Sbjct: 922  SRKTISMLIEVILTAAYSSKPYNNKGENRPVCFPSSNETSIDTYMQFARQCYEHSNPQLS 981

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D                                            ILYD  T  P
Sbjct: 982  DEELSDKIFCEK--------------------------------------ILYDPETDRP 1003

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1004 YTSKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1063

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1064 HGAANTITEVL 1074


>gi|151573155|gb|ABS17768.1| RNA polymerase II [Fusarium sp. NRRL 43516]
          Length = 296

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 103/369 (27%), Gaps = 75/369 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVGYIY 1255
              V  G  Y
Sbjct: 288  AQVFFGPTY 296



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|111184331|gb|ABH08251.1| HSPV145 [Horsepox virus]
          Length = 1164

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 79/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RD+ +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDRSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHLNSK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|61611813|gb|AAX47223.1| RpoB [Aeromonas schubertii]
          Length = 172

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 100/172 (58%), Positives = 131/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N  S +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPQSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVEYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|40644547|emb|CAD88888.1| DNA-directed RNA polymerase subunit B [Gymnosporia arbutifolia]
          Length = 459

 Score =  188 bits (477), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/468 (15%), Positives = 127/468 (27%), Gaps = 83/468 (17%)

Query: 804  DLALGRNMLV---AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             + +  N LV                  I   ++     + I   +     R+T      
Sbjct: 72   MIPMTINDLVQARVNPEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 131

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                   V+    +      +  V        +    +       +      + AI    
Sbjct: 132  KQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 188

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S V        +F R   D+ ++  ++ +E      R           
Sbjct: 189  GYNQEDSVIMNQSSVDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSY 247

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +          G           K+T ++                      Q + +    
Sbjct: 248  DKLDDDGLAPPGTRVSGEDVIIGKTTPIT----------------------QEDAQGQGS 285

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
            +Y      +  R        Q         LR VKV V   R  Q GDK + RHG KG V
Sbjct: 286  RYTRRDHSISLRHSETGMVDQVLLTTNADGLRSVKVRVRSVRIPQIGDKFSSRHGQKGTV 345

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +      
Sbjct: 346  GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECLMGKVAAHMGKEGDATPFTDV 405

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
               +IS         +                                            
Sbjct: 406  TVDNISKALHKCGYQMRGFETM-------------------------------------- 427

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                      +G +    G         + +G  Y  +L HMV DK++
Sbjct: 428  ---------YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDDKIH 459



 Score = 48.5 bits (114), Expect = 0.008,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 53/160 (33%), Gaps = 17/160 (10%)

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
           R     E+R ++  +     P    E   + L+      A        E  + ++     
Sbjct: 2   RDIRLKELR-IYTDYGRCSRPLFIVEKQRL-LIKKKDIHALQQRESLEEDAWHELIK--- 56

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
              + Y+   +EE   I               +LV  R   E      E     +  P  
Sbjct: 57  KGFIEYIDTEKEETTMIPM----------TINDLVQARVNPE--EAYSETYTHCEIHPSL 104

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
           ++ + AS+IPF +++ S R      M +QA+ +      F
Sbjct: 105 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF 144


>gi|37956390|gb|AAP15368.1| RNA polymerase beta subunit [Geopsychrobacter electrodiphilus]
          Length = 179

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 110/176 (62%), Positives = 135/176 (76%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRMSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N YGF+ETPYR V DGKVT D+ Y SA+EEE   IAQAN+ LD  G FT E
Sbjct: 61  ASLSTYARINEYGFVETPYRLVKDGKVTTDIKYFSALEEEKHAIAQANAPLDTKGKFTNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           LV  R  GE +L+P  ++  +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQ Q
Sbjct: 121 LVNVRKDGEFMLLPPAEVSLMDVSPKQIVSVAAALIPFLENDDANRALMGSNMQGQ 176


>gi|320172586|gb|ADW24176.1| RNA polymerase II second largest subunit [Gloeophyllum sepiarium]
          Length = 341

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 65/372 (17%), Positives = 109/372 (29%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 45   DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 104

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   R+          +       I  G      
Sbjct: 105  LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGFIAPGTGVNGD 163

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     +    T+    E    +++ 
Sbjct: 164  DIIIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTALKSTESGIVDQVL 208

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 209  I-----TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 263

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      +G +                           
Sbjct: 264  DIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 298

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E++++ LR       G  ++Y 
Sbjct: 299  ----------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYH 329

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 330  GHTGRKLQAQVY 341



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 84/234 (35%), Gaps = 23/234 (9%)

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVK 783
           + I+   A I+   D  +    + +  +     G+     L++           Q+PL  
Sbjct: 1   SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRMDTMANILYYPQKPL-- 58

Query: 784 VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIH 843
                               +L  G+N +VA + + GYN EDS+++++  +   +F SI+
Sbjct: 59  --------ATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIY 110

Query: 844 IEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  + + + +   E            +       I++ G I  G  VN  DI++GK 
Sbjct: 111 YRSYMDLEKKSGVQQLEEFEKPTRETTLRMKHGTYDKIEDDGFIAPGTGVNGDDIIIGKT 170

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            P         ++        ++   RD S  + S  SG V  V I       K
Sbjct: 171 APIPPDSEELGQRT-------RSHTRRDVSTALKSTESGIVDQVLITTNSEGQK 217


>gi|310750842|gb|ADP09214.1| RpoB' [Halorhabdus utahensis DSM 12940]
          Length = 173

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 54/196 (27%), Positives = 75/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KGIV  I P EDMPF + G   D+++NP  +
Sbjct: 31   EDGSKLSKVKVRDERIPELGDKFASRHGQKGIVGHIAPQEDMPFTEQGVVPDLIINPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   D+                      
Sbjct: 91   PSRMTVGHILEMIGGKVGALEGRRVDGTAFTGEDEEDLRDSLEDHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ ++Y G+TGE  + 
Sbjct: 137  -----------------------FD-----------------SSGKEVMYSGITGEKVEA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGNIFYQKLYHMV 172


>gi|154152065|ref|NP_001093762.1| DNA-directed RNA polymerase I subunit RPA2 [Bos taurus]
 gi|151553633|gb|AAI48065.1| POLR1B protein [Bos taurus]
 gi|296482453|gb|DAA24568.1| DNA-directed RNA polymerase I subunit RPA2 [Bos taurus]
          Length = 1135

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 101/558 (18%), Positives = 179/558 (32%), Gaps = 91/558 (16%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV+A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVLAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
            G      +     +   L+                + +   GT   V + +  G D  + 
Sbjct: 697  GFPLLTFQDRSDNKLYRLQTPQSPLVRPYMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
             I  +       A     +   +D  +  R+ +          P   +    L +D +  
Sbjct: 757  MIVNKASWERGFAHGSVYKSEFID--LSERIKQGDDSLVFGVKPGDPRVLQKLDNDGLPF 814

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                  +             E   + Y++ ++ + D  K         +D   G  + V 
Sbjct: 815  IGAQLKYGDPYYSYLNLNTGEGFVMYYKSKENCIVDNIK------VCSNDTGTGKFKCVC 868

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + + + R    GDK A RHG K                            G+ SR+    
Sbjct: 869  ITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL---- 896

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
                            ++ +                       G  +        +S+  
Sbjct: 897  --------------WPVEDMPFTESGMVPDIL-------FNPHGFPSRMTIGMLIESMAG 935

Query: 1196 VAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
             +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  + +G
Sbjct: 936  KSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNYYGTERLYSGISGLELEADIFIG 995

Query: 1253 YIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQ 1312
             +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +++L 
Sbjct: 996  VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLH 1055

Query: 1313 EMLTIKSD----DV---VG-----------------RTRVYESIVAG--NDTFETGTPES 1346
            + L   SD     V    G                 R R Y   +    +       P  
Sbjct: 1056 DRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSALRNRKYICALCNRSDTIDTISLPYV 1115

Query: 1347 FNVLVKEMQALGLSIDLE 1364
            F   V E+ A+ + + L+
Sbjct: 1116 FRYFVAELAAMNIKVKLD 1133



 Score = 88.6 bits (218), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 93/671 (13%), Positives = 210/671 (31%), Gaps = 86/671 (12%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    ++++ RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFFRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GERFRVKLSLPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLK-------NQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            ++ D+L N+ V + G++           + + +        ++ +       + +    
Sbjct: 363 EENPDSLMNQEVLTPGQLFLMFLKEKLEAWLVSIKIAIDKKSQKTNVSLNSENLMKIFSL 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +         +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLLATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIE------------ 599
                 +R + P  +G +CP  T +G   GL++ LT+   V                   
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAICEVVTQSVYTASIPALLCNLGV 539

Query: 600 -----TPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGE 652
                TP+R   +      + V+   A +E    IA   +          E        E
Sbjct: 540 TPVDGTPHRPYSECYPVLLDGVMIGWADKE----IAPGIADSLRHFKVLREKRIPP-WME 594

Query: 653 EILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
             L+P      +        +    + P    +     L+G   Q      +  +    G
Sbjct: 595 VALIPMTGKPSLYPGLYLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVLAG 654

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
                 +   S  +++A     +   D  +      +  +   T G   + L+ FQ  + 
Sbjct: 655 VTTHQELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMG---FPLLTFQDRSD 708

Query: 773 NTCV----NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           N        Q PLV+                 D+ +  +G N +VA + + GY+ ED+M+
Sbjct: 709 NKLYRLQTPQSPLVRPYMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMI 758

Query: 829 ISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
           +++          S++  EF  ++   K G + +   +       L+ +D  G+  +GA+
Sbjct: 759 VNKASWERGFAHGSVYKSEFIDLSERIKQGDDSLVFGVKPGDPRVLQKLDNDGLPFIGAQ 818

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLR--AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
           +  GD     +     +  T E  ++   +       +++  S    +G    V      
Sbjct: 819 LKYGDPYYSYL-----NLNTGEGFVMYYKSKENCIVDNIKVCSNDTGTGKFKCVCITMRV 873

Query: 946 NRHGIDKNERS 956
            R+    ++ +
Sbjct: 874 PRNPTIGDKFA 884



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 103/712 (14%), Positives = 198/712 (27%), Gaps = 128/712 (17%)

Query: 53  EGLQAAFKSVFPITAF--SGAAMLEFVSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A ++V P           L  V     PP                +C  R  TY 
Sbjct: 52  EGLSHAVQAVPPFEFAFKDERICLTIVDAVISPPAVPKGSICKELNVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K + +Q  ++G +P+M K                   
Sbjct: 112 GKLTADISWSVNGI--------SKGVIKQ--FLGYVPIMVKSKLCNLYNLPPKALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K ++   G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMVRPKWKSRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E+    L +
Sbjct: 271 GKEDDSFFRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGERFRVKLSL 314

Query: 299 TS--------DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVD 350
                     + L    +   +    T + Y+         +L +    E     ++  +
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHL-KSNTEKFYMLCLMTRKLFALAKGECMEENPDSLMNQE 373

Query: 351 SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLST 410
            +         L            + I +  +  +VS  S        L  D  K     
Sbjct: 374 VLTPGQLFLMFLKEKLEAWLVSIKIAIDKKSQKTNVSLNSENLMKIFSLGIDLTKPFEYL 433

Query: 411 VGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           +    +  +  L    D       D +  I+ L   R     +    +    R  +V  +
Sbjct: 434 LATGNLRSKTGLGFLQDSGLCVVADKLNFIRYLSHFR----CVHRGADFAKMRTTTVRRL 489

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           L   +                  +   +M       + V  +V      + L  L   V 
Sbjct: 490 LPESWGFLC-------PVHTPDGEPCGLMNHLTAICEVVTQSVYTASIPALLCNLG--VT 540

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +    H R  S      +     G   +++ P     +   +      I     +    
Sbjct: 541 PVDGTPH-RPYSECYPVLLDGVMIGWADKEIAPGIADSLRHFKVLREKRIPPWMEVALIP 599

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
                      Y      ++   V  L   +EE   I            F +E++     
Sbjct: 600 MTGKPSLYPGLYLFTTPCRLVRPVQNLELGKEE--LIGTMEQIFMNVAIFEDEVLAG--- 654

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                         +  P  ++S+ A+ IPF +++ S R +  C M +Q + 
Sbjct: 655 ---------VTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG 697


>gi|327239539|gb|AEA39619.1| RpoB [Corynebacterium striatum]
 gi|327239543|gb|AEA39621.1| RpoB [Corynebacterium striatum]
          Length = 139

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 60/167 (35%), Positives = 87/167 (52%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+           +   L++  E++                   
Sbjct: 1    QVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 40   -------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|327133545|gb|AEA29777.1| RNA polymerase subunit B [Acinetobacter sp. 14N2]
          Length = 124

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 73/127 (57%), Positives = 90/127 (70%), Gaps = 3/127 (2%)

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
            +F  K  K+  GD++  GVL+VVKV++A+KR IQ GDKMAG HGNKG+VS ILP EDMP 
Sbjct: 1    KFAEKKRKLSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGPHGNKGVVSNILPVEDMPH 60

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
              +G PVD+VLNPLGVPSRMNVG I ETHLG A  GLG++I  ++   K    I+ LR F
Sbjct: 61   DANGVPVDVVLNPLGVPSRMNVGHILETHLGLAAKGLGEQIDKML---KQQRTIAELREF 117

Query: 1172 LEKVIGT 1178
            L K+   
Sbjct: 118  LHKIYNK 124


>gi|151573572|gb|ABS18045.1| RNA polymerase II [Fusarium sp. NRRL 28014]
          Length = 295

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 103/369 (27%), Gaps = 75/369 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 61   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 120

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 121  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 163  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 221  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 247

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 248  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 286

Query: 1247 RPVTVGYIY 1255
              V  G  Y
Sbjct: 287  AQVFFGPTY 295



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 51  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 111 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 163

Query: 950 IDK 952
             K
Sbjct: 164 NVK 166


>gi|218683109|gb|ACL00599.1| RNA polymerase beta subunit [Aeromonas schubertii]
          Length = 172

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVEYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|83414923|dbj|BAE54252.1| b subunit of the RNA polymerase gene [Streptococcus vestibularis]
          Length = 172

 Score =  188 bits (477), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/168 (41%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+  DKMAGRHGNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVRDKMAGRHGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVLEPHLGMAARNLGIHIATPVFDGASSEDL 164



 Score = 55.5 bits (132), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|90819804|gb|ABD98614.1| VACV-DUKE-152 [Vaccinia virus]
          Length = 1164

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 80/433 (18%), Positives = 145/433 (33%), Gaps = 77/433 (17%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 710  DNGIHLMYPERPIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGG 769

Query: 950  IDK---NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            +D     +  + +  E      RDK +    L+ N   RL   L   +A++         
Sbjct: 770  LDIVTAKKHQVEIPLENFNNKERDKSNAYSKLESNGLVRLNAFLESGDAMA-------RN 822

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
            + S  L  ++ R     F V         E     Y++    ++    +K++        
Sbjct: 823  ISSRTLEDDFARDNQISFDVS--------EKYTDMYKSRVERVQVELTDKVK-------- 866

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                   V+V    +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   
Sbjct: 867  -------VRVLTMKERRPILGDKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTS 919

Query: 1127 VPSRMNVGQIFETHLGWA--CVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHT 1182
            + SR  +  + E  L  A        K ++            I     F ++     +  
Sbjct: 920  IFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNETSIDTYMQFAKQCYEHLNSK 979

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                +  D                                            ILYD  T 
Sbjct: 980  LSDEELSDKIFCEK--------------------------------------ILYDPETD 1001

Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
            +P+   V  G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+
Sbjct: 1002 KPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCL 1061

Query: 1303 QAYGAAYVLQEML 1315
             A+GAA  + E+L
Sbjct: 1062 IAHGAANTITEVL 1074


>gi|10433976|dbj|BAB14082.1| unnamed protein product [Homo sapiens]
          Length = 1079

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 102/562 (18%), Positives = 177/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 582  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 640

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 641  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 700

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 701  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 750

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 751  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 808

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V++ + + R    GDK A RHG K                            G+ SR+
Sbjct: 809  KCVRITMRVPRNPTIGDKFASRHGRK----------------------------GILSRL 840

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 841  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 875

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 876  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 935

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 936  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 995

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 996  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 1055

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 1056 VPYVFRYFVAELAAMNIKVKLD 1077



 Score = 87.8 bits (216), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 97/664 (14%), Positives = 216/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 197 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 248

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 249 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 306

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 307 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 366

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 367 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 423

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 424 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 483

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 484 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 543

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 544 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 603

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 604 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 659

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 660 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 709

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 710 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 769

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 770 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVRITMRVPRNPTIG 824

Query: 953 NERS 956
           ++ +
Sbjct: 825 DKFA 828



 Score = 43.9 bits (102), Expect = 0.23,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 26/59 (44%)

Query: 119 AKSIKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIV 153
               K I +Q  ++G +P+M K                         G F+I GI++++
Sbjct: 67  NGISKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVI 123


>gi|189031174|gb|ACD74761.1| RpoB [Gallibacterium anatis]
          Length = 180

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 108/180 (60%), Positives = 136/180 (75%), Gaps = 1/180 (0%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET 
Sbjct: 1   FFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETP 60

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           EG NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LD
Sbjct: 61  EGPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLD 120

Query: 636 EDGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           E+  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR LMG 
Sbjct: 121 ENFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRALMGS 180


>gi|119640705|gb|ABL85546.1| RNA polymerase II second largest subunit [Syncesia leprobola]
          Length = 307

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 108/376 (28%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R    E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPLRSETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V  G  Y
Sbjct: 292  HTGRKLNAQVFFGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPLRSETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|330785274|gb|AEC46443.1| RNA polymerase II second largest subunit [Lecanographa lyncea]
 gi|330785276|gb|AEC46444.1| RNA polymerase II second largest subunit [Lecanographa lyncea]
          Length = 307

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 59/377 (15%), Positives = 107/377 (28%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQENA------------EGGARLKEHSKRDISAPLRSTEAGIIDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 291  GHTGRKLVSQVFLGPTY 307



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 67/189 (35%), Gaps = 13/189 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P        E     A   E +       LR        ++D  +     
Sbjct: 121 GEDIIIGKTSPLAG--PMQENAEGGARLKEHSKRDISAPLR---STEAGIIDQVLVTTTD 175

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 176 GKKSVKVRT 184


>gi|283132445|dbj|BAI63628.1| rpoB protein [Corynebacterium amycolatum]
          Length = 105

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 51/99 (51%), Positives = 71/99 (71%), Gaps = 8/99 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 7    VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 66

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GE
Sbjct: 67   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 105


>gi|264658153|emb|CBH32067.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 51/99 (51%), Positives = 71/99 (71%), Gaps = 8/99 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 13   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 72

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GE
Sbjct: 73   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 111


>gi|46277372|gb|AAS86876.1| DNA-dependent RNA polymerase II [Peziza echinispora]
          Length = 541

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 94/651 (14%), Positives = 168/651 (25%), Gaps = 120/651 (18%)

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             +    + +V  +     +      ++      +  D  F    +        I      
Sbjct: 10   DFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTIQKLRRQNHIGHEVSL 69

Query: 661  I-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            I D  +   K          P    D+         +  Q   + K E     T  E   
Sbjct: 70   IQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKEITDEEQRY 129

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
               SG        G+VE +DA       +    +   +    +   + Q         QR
Sbjct: 130  GW-SGL----IGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQTEVDPA---QR 181

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                V             PS  LG       +  + +P+  +N       S R   +   
Sbjct: 182  VKASVNKYAHTWTHCEIHPSMILG-------ICASIIPFPDHNQ------SPRNTYQSAM 228

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                +  F    R+                           +  +             + 
Sbjct: 229  GKQAMGVFLTNYRERM-----------------------DTMANILYYPQKPLGTTRSME 265

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R    
Sbjct: 266  FLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYMDQEKRVGMN 324

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              E+ E   R           +       +  G           K+  +S ++     R+
Sbjct: 325  VVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPISPNMEELGQRT 384

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +          ++     +  Q                             L+ VKV + 
Sbjct: 385  KXHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFVKVRMR 424

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + E 
Sbjct: 425  TTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVPDIIINPHAIPSRMTIAHLIEC 484

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             L       G +                                                
Sbjct: 485  QLSKVSSLRGFEGD---------------------------------------------- 498

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                   +TP F     ++++ +LR       G  I+Y+G TG      V 
Sbjct: 499  -------ATP-FTDVTVDSVSRLLREHGYQSRGFEIMYNGHTGRKLVVQVF 541



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 75/482 (15%), Positives = 131/482 (27%), Gaps = 88/482 (18%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 10  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 63

Query: 545 G-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           G +  + +     E        R   P       PA    G  +     +          
Sbjct: 64  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKEIT 123

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCA 650
             E  Y           V Y+ A EEE   I      L+    F        E+   +  
Sbjct: 124 DEEQRY-GWSGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQTEVDPAQRV 182

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
              +          +  P  ++ I AS+IPF +++ S R      M +QA+ +       
Sbjct: 183 KASVNKYAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT---- 238

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
                       + A I+                                    +KF+  
Sbjct: 239 -----NYRERMDTMANILY---------------------YPQKPLGTTRSMEFLKFREL 272

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                     L   G   + + +I +  S D G                  + E  + ++
Sbjct: 273 PAGQNAIVAILCYSG-YNQEDSVIMNQSSIDRGLFRSLFY-------RTYMDQEKRVGMN 324

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
                        +EEFE   R           +   +       +DE G++  G  V+ 
Sbjct: 325 ------------VVEEFEKPTR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSG 362

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P      +P  + L      K    RD S  + S  +G V  V +      
Sbjct: 363 EDIIIGKTAPI-----SPNMEELGQR--TKXHTKRDVSTPLRSTENGIVDQVMVTTNQEG 415

Query: 951 DK 952
            K
Sbjct: 416 LK 417


>gi|90568540|gb|ABD94216.1| RNA polymerase beta subunit [Aeromonas molluscorum]
 gi|90568542|gb|ABD94217.1| RNA polymerase beta subunit [Aeromonas molluscorum]
 gi|90568544|gb|ABD94218.1| RNA polymerase beta subunit [Aeromonas molluscorum]
 gi|90568546|gb|ABD94219.1| RNA polymerase beta subunit [Aeromonas molluscorum]
 gi|90568548|gb|ABD94220.1| RNA polymerase beta subunit [Aeromonas molluscorum]
          Length = 172

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGLITDEVDYLSAIEEGKYVIAQANAAASEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|9629061|ref|NP_044080.1| MC129R [Molluscum contagiosum virus subtype 1]
 gi|1492072|gb|AAC55257.1| MC129R [Molluscum contagiosum virus subtype 1]
          Length = 1165

 Score =  187 bits (476), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 77/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++      R G
Sbjct: 711  DNGIHLLFPERPIVLSKAVETSKIAVNCFGQHVLIALMSYKGINQEDGIILKREFVQRGG 770

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 771  LDI-------------VTAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVKLNAFLEPG 817

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y +    ++    +K++          
Sbjct: 818  DAVARNISSRTLEDEFVDDNQISFDIAERYTDMYPSRVERVQVDLTDKVK---------- 867

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ +    ++P+  DG   DI++N   + 
Sbjct: 868  -----VRVLTIKERRPVLGDKFTSRTSQKGTVAYLADEAELPYDDDGLTPDIIVNSTSIY 922

Query: 1129 SRMNVGQIFETHL--GWACVGLG--KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L   +A        + + +         I    +F  K   +      
Sbjct: 923  SRKTISMLVEIMLTAAYAAKPYNNQDQNRPICFPSSNETSIETYLAFARKCYES------ 976

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                     VF    E  + + L         +  LYD  T EP
Sbjct: 977  -------------------------VFPELRETELQARL-------FCEKTLYDPETDEP 1004

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1005 YAAAVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIA 1064

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1065 HGAANTITEIL 1075



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 95/652 (14%), Positives = 201/652 (30%), Gaps = 60/652 (9%)

Query: 356 AYIRNTLVTDK---NKDRKDALLDIYRVMRPGDV---STFSVAESMFNFLFFDSDKYDLS 409
            +IRN+L  D         +AL++  R +   +        VAE +            L 
Sbjct: 246 DFIRNSLAYDMPPEAVYLVNALVESTRRLAAAEDDFDVAEYVAELIEAEHAKQRSPAKLE 305

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                 +   L        +      +  + K L          D  D++   R+ + G+
Sbjct: 306 DFRYDMLQNFLPHMLHSGNQLKGLYLLSLLRKFLFCTFFPSRYPDR-DSMICHRILTYGK 364

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             +      L     +IK  + +   +       I+           F      + ++  
Sbjct: 365 YFETLANDELENYINNIKTDLFNNHKNRGTCTVNIHV-LTTPGFNHAFSGLLSGKFKKTD 423

Query: 530 NSLSRITHTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSEGH---- 578
            S     H   +  +             +      +R  HP+ Y   CP++  E      
Sbjct: 424 GSYRTHPHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYVYFCPSDVPERGPQVG 483

Query: 579 --NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS---AMEEENRYIAQANSS 633
             +   V S  +  R + Y  +E   R+        ++ +      +  EN  +A  N  
Sbjct: 484 LVSQLSVLSYVTNIRTDEYLALEQRIREYVYSYPQVNISFFETGFPLTIENALVAVLNPH 543

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN------DDS 687
           L +D     +        E + +    +       +  +     + PFL         D+
Sbjct: 544 LVDDFVADFKTRKRLNFFENMELGITLVKDHMNEVRVNIGSGRLVRPFLVVHQGVLVMDT 603

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG--------IVEQVD 739
               +   M+      ++ E P V   ++      S     A R          + + VD
Sbjct: 604 VGAELDARMETMTFSDIQREYPHVLELVDVEQFTFSNVCESAARFRALPEAERRLYDYVD 663

Query: 740 AIRI----VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV---RRND 792
                    + S    ++ ++    I    + +++      + R  +  G  +    R  
Sbjct: 664 FPAEFRDGYVASTLVGVNHNSGPRAILGCAQAKQAISCLSSDLRNKIDNGIHLLFPERPI 723

Query: 793 IIADGPSTDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMA 851
           +++    T    +   G+++L+A M + G N ED +++    V       +  ++ +V  
Sbjct: 724 VLSKAVETSKIAVNCFGQHVLIALMSYKGINQEDGIILKREFVQRGGLDIVTAKKHQVEI 783

Query: 852 RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                 P E   +   V       +D  G++ + A + PGD +   I+ +       ++ 
Sbjct: 784 ------PLENFNNKERVKSTAYSKLDSNGLVKLNAFLEPGDAVARNISSRTLEDEFVDDN 837

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVD--VRIFNRHGIDKNERSISVER 961
            +     E+  D        PS V    VD   ++  R    K  R +  ++
Sbjct: 838 QISFDIAERYTD------MYPSRVERVQVDLTDKVKVRVLTIKERRPVLGDK 883


>gi|123979412|gb|ABM81531.1| RNA polymerase II second largest subunit [Platismatia glauca]
          Length = 358

 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 61/385 (15%), Positives = 115/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 52   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 111

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 112  LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRV 167

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 168  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 218  ----------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 267

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  +                                       
Sbjct: 268  MVPDLIINPHAIPSRMTIAHLI-------------------------------------- 289

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                           + +L      +     +TP F     ++++ +LR       G  +
Sbjct: 290  ---------------ECLLSKVSSLRGFEGDATP-FTEVTVDSVSRLLREHGYQSRGFEV 333

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V +G  Y  +L 
Sbjct: 334  MYNGHTGRKLVTQVFLGPTYYQRLR 358



 Score = 89.4 bits (220), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 79/228 (34%), Gaps = 23/228 (10%)

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCV 776
              +   + I+   A I+   D  +    + +  +     GV       +          
Sbjct: 1   THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYY 60

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA   + GYN EDS+++++  +  
Sbjct: 61  PQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDR 110

Query: 837 DVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E     +  D   +       +D+ G++  G  V+  
Sbjct: 111 GLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGE 170

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 171 DIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 211


>gi|189031172|gb|ACD74760.1| RpoB [Gallibacterium anatis]
          Length = 179

 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 107/179 (59%), Positives = 135/179 (75%), Gaps = 1/179 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE
Sbjct: 61  GPNIGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDE 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +  FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR LMG 
Sbjct: 121 NFRFTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRALMGS 179


>gi|55583682|gb|AAV53360.1| RNA polymerase II second largest subunit [Dacryopinax spathularia]
          Length = 534

 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 87/587 (14%), Positives = 152/587 (25%), Gaps = 120/587 (20%)

Query: 666  ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             S +  V             D+ RV     +  +    L      +G   E       G 
Sbjct: 65   ISSEISVVRDIRERELRLYTDAGRVCRPLFIVNEQTQNLVISKREIGWLQERRD--DLGQ 122

Query: 726  AIVAKRAGIVEQV---DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
                 +      V   DA       +    +   +              QN  V  + +V
Sbjct: 123  PYGWSQLVTSGMVELLDAEEEETVMIAMTPEDLEASKTKRGTGYISNEPQNAAVRIKSIV 182

Query: 783  KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                           PS  LG       +  + +P+  +N       S R   +      
Sbjct: 183  H----HEHWTHCEIHPSMILG-------ICASIIPFPDHNQ------SPRNTYQSAMGKQ 225

Query: 843  HIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKG 902
             +  +    +                            +  +             +    
Sbjct: 226  AMGIYLTNFQVRM-----------------------DTMANILYYPQKPLATTRSMEYLK 262

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    I+ R   D  + +  V  E
Sbjct: 263  FRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYTDMEKTTGIVPVE 321

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            + E   RD          +       +  G           K+  L  D      R++  
Sbjct: 322  EFEKPHRDTTVRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPLPPDSEELGQRTRTH 381

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                    ++     +  Q   S +                       ++ VKV +   R
Sbjct: 382  TRRDVSTPLKSTENGIVDQVLISTNE--------------------SGVKFVKVRIRSTR 421

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L 
Sbjct: 422  IPQIGDKFASRHGQKGTIGMTYRQEDMPFAANGITPDIIINPHAIPSRMTIGHLVECLLS 481

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                 +G +                                                   
Sbjct: 482  KLATLIGNEGD------------------------------------------------- 492

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                +TP F     E+++++LR     + G  ++Y G TG      V
Sbjct: 493  ----ATP-FTDLTVESVSALLRGKGYQQRGLEVMYHGHTGRKLQAQV 534



 Score =  100 bits (248), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 64/435 (14%), Positives = 123/435 (28%), Gaps = 79/435 (18%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           F     +    +  + ++ +   RR   +                ++        P    
Sbjct: 37  FVNGVWMGIHRDPQHLVNTVRTMRRSDGISSEISVVRDIRERELRLYTDAGRVCRPLFIV 96

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                 LV S      +                  +  V  L A EEE   IA     L+
Sbjct: 97  NEQTQNLVISKREIGWLQERRDDLGQPYGWSQLVTSGMVELLDAEEEETVMIAMTPEDLE 156

Query: 636 EDG-----SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
                    +            + +V  E     +  P  ++ I AS+IPF +++ S R 
Sbjct: 157 ASKTKRGTGYISNEPQNAAVRIKSIVHHEHWTHCEIHPSMILGICASIIPFPDHNQSPRN 216

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                M +QA+ +                                               
Sbjct: 217 TYQSAMGKQAMGIYLTNFQV---------------------------------------- 236

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
               + + +  Y       +     +  R                        +L  G+N
Sbjct: 237 -RMDTMANILYYPQKPLATTRSMEYLKFR------------------------ELPAGQN 271

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----I 865
            +VA + + GYN EDS+++++  +   +F SI+   +  M + T + P E          
Sbjct: 272 AIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYTDMEKTTGIVPVEEFEKPHRDTT 331

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       ++  G++  G  +N  DI++GK  P         E+L +        DV 
Sbjct: 332 VRMKHGTYDKLEADGLVAPGIGINGEDIIIGKTAPL----PPDSEELGQRTRTHTRRDVS 387

Query: 926 DTSLRVPSGVSGTVV 940
                  +G+   V+
Sbjct: 388 TPLKSTENGIVDQVL 402


>gi|307148852|gb|ADN38251.1| RpoB [Mycobacterium tuberculosis]
          Length = 186

 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 108/183 (59%), Positives = 148/183 (80%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 3   TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 62

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +T  RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 63  IKEFFGTSQLSQFMDQNNPLSGLTGKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 122

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V++ +VYL+A EE+   +AQANS
Sbjct: 123 ETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDGIVYLTADEEDRHVVAQANS 182

Query: 633 SLD 635
            +D
Sbjct: 183 PID 185


>gi|45593172|gb|AAS68148.1| RNA polymerase beta subunit [Pelobacter carbinolicus DSM 2380]
          Length = 173

 Score =  187 bits (476), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 110/173 (63%), Positives = 134/173 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V  GKVTN++ Y SA+EE    IAQAN+ LD+DG F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRIVEQGKVTNEIRYFSALEEGGHAIAQANAPLDDDGRFLNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           LV  R  GE +L+ RE+I  +D SPKQ+VS+AASLIPFLENDD+NR LMG NM
Sbjct: 121 LVNARQNGEFVLIQREEIGLMDVSPKQLVSVAASLIPFLENDDANRALMGSNM 173


>gi|301134640|gb|ADK63754.1| m114R [Myxoma virus]
          Length = 1155

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 137/431 (31%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G +V  +   R G
Sbjct: 702  DNGIHLLYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 762  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 809  DAIARNISSRTLEDDFVQDNQISFDIADRYTDMYKSRVERVQVDLTDKVK---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 859  -----VRVLTMKERRPILGDKFTSRTSQKGTVAYIADENELPYDENGIKPDVIINSTSIF 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          K + +         I    +F ++          
Sbjct: 914  SRKTVSMLIEVILTAAYASKPYNNDGKNRPICFPSSNETTIDTYLNFAKQCHTHTYPDAS 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                +D                                             LYD  T  P
Sbjct: 974  DEVINDKIFCDK--------------------------------------TLYDPETDTP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YTAKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 53.2 bits (126), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 85/644 (13%), Positives = 197/644 (30%), Gaps = 56/644 (8%)

Query: 360 NTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  + D+     +A+++  +       +    +    +F                + +M 
Sbjct: 245 SYDMPDEIIYLVNAVIESTKHFVDSINEFDIDTYINDLFIEEHTKQKSQVSLDEFKHEML 304

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                   +    ++   II++++  +          D D++   RV + G+  +     
Sbjct: 305 YNFLPHMTNTPNQLKGFYIISLLRKFIYCIYYTSRYPDRDSMICHRVLTYGKYFEILAHD 364

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            L     +IK      +  +     +             F      + ++   S     H
Sbjct: 365 ELENYIGNIK-TDIINNHKNRGTHSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPH 423

Query: 538 TRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSF 589
              +  +             +      +R  HP+ Y   CP++  E G+ +G+VS L+  
Sbjct: 424 YSWMQNISIPRSVGFYPEQVKISKMFSVRKYHPSQYAYFCPSDVPERGNQVGMVSQLSVL 483

Query: 590 ARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE------ENRYIAQANSSLDEDGSFT 641
             V      E     RK+C+   + DV  +S  E       EN  IA  N  L       
Sbjct: 484 TSVTNICTNEYLDLERKICEYVRSYDVKDISYFETGYYVTLENALIASLNPDLTHAFVRD 543

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                       + +    +       +  +S    + PFL  +    ++         +
Sbjct: 544 FRRKKREGYFNSLEIGITHVADHMNEIRINISSGRLIRPFLVIESGELIMDTVPELADKL 603

Query: 702 PLL-----KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
             +     + E P V   ++      S      ++   + + + ++  +     +     
Sbjct: 604 DDMTFSDVQREYPHVIEMVDIEQFTFSNVCESVQKFRSLPKSEKVKYQLCDFPSEFRDGY 663

Query: 756 --TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND-------------IIADGPST 800
             +S V I      +         Q       D   + D             I     ++
Sbjct: 664 VASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLLYPERPIVISKALETS 723

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +     G+++ +A M + G N ED +++ ++ +       I  ++ +V        P E
Sbjct: 724 KIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGGLDIITAKKHQVEI------PLE 777

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              +   V       ++  G++ + A +  GD +      +  S  T E+  ++    + 
Sbjct: 778 NFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQD--NQI 830

Query: 921 AVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
           + D+ D    +       V   +  ++  R    K  R I  ++
Sbjct: 831 SFDIADRYTDMYKSRVERVQVDLTDKVKVRVLTMKERRPILGDK 874


>gi|62637502|ref|YP_227500.1| RNA polymerase subunit RPO132 [Deerpox virus W-848-83]
 gi|115503362|gb|ABI99280.1| RNA polymerase subunit RPO132 [Deerpox virus W-848-83]
          Length = 1155

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/431 (16%), Positives = 138/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +  +R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKRQFVDRGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVHDNQISFDISDRYTDMYKSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG ++ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERKPILGDKFTSRTSQKGTIAYIADESELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A          K + +         I     F +K   T      
Sbjct: 915  SRKTLSMLVEVILTSAYACKPYNNSGKNRPICFPSSNETTIDTYLDFAKKCYETIYPDLT 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D                                            +LYD  T  P
Sbjct: 975  EDELTDKVFCDK--------------------------------------VLYDPETDRP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YMSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEIL 1067



 Score = 61.6 bits (148), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 79/568 (13%), Positives = 179/568 (31%), Gaps = 47/568 (8%)

Query: 372 DALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           +A+++  +    +  D         +    +            + +M         D   
Sbjct: 257 NAIIENTKEFITKNNDFDIDLYINELILDEYNKQKSQLSIEEFKYEMIYNFLPHMNDTPN 316

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            ++   II++++  +          D D++   RV + G+  +      L     +IK  
Sbjct: 317 QLKGFYIISLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILAHDELENYIGNIKN- 375

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
               +  +     +             F      + ++   S     H   +  +     
Sbjct: 376 DIINNHKNRGVYSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRS 435

Query: 550 A-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARV-----NAYG 596
                   +      +R  HP+ Y   CP++  E G  +GLVS L+    +     N Y 
Sbjct: 436 VGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLSVLTSITNICTNEYL 495

Query: 597 FIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            +E    +       ND+ Y      +  EN  IA  N  L +               + 
Sbjct: 496 ELEKKICQYIRSYDINDISYFETGYYITLENSLIASLNPKLVDKFVIDFRRKKRMGYFDN 555

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL------MGCNMQRQAVPLLKAE 707
           + +    +       +  +     + PFL  DD N ++      +   M+      ++ E
Sbjct: 556 LEIGITLVRDHMNEIRINIGGGRLVRPFLVIDDGNLIMDDIMDNLESKMEDMTFSDIQKE 615

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-----EGDLDPSTSGVDIY 762
            P V   ++      S      ++   + + + I+  +        +G +  S  G++  
Sbjct: 616 FPHVIEMVDIEQFTFSNVCESVQKFRTLPKNERIKFHLCDFPAEFRDGYVASSLVGINHN 675

Query: 763 R-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPSTDLGDL---ALGRNM 811
                     + +++      + R  +  G   +     I    + +   +     G+++
Sbjct: 676 SGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKALETSKIAVNCFGQHV 735

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            +A M + G N ED ++I  + V       I  ++ +V        P E   +   V   
Sbjct: 736 TIALMSYKGINQEDGIIIKRQFVDRGGLDIITAKKHQVEI------PLENFNNKERVKST 789

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKIT 899
               ++  G++ + A +  GD +   I+
Sbjct: 790 AYSKLESNGLVRLNAFLESGDAIARNIS 817


>gi|61611787|gb|AAX47210.1| RpoB [Aeromonas eucrenophila]
 gi|61611791|gb|AAX47212.1| RpoB [Aeromonas eucrenophila]
 gi|61611809|gb|AAX47221.1| RpoB [Aeromonas encheleia]
 gi|61611811|gb|AAX47222.1| RpoB [Aeromonas encheleia]
 gi|61611821|gb|AAX47227.1| RpoB [Aeromonas encheleia]
          Length = 172

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATSEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|145307913|gb|ABP57260.1| RNA polymerase II second largest subunit [Batkoa major]
          Length = 302

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 60/376 (15%), Positives = 110/376 (29%), Gaps = 75/376 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D+ +++  VE E  E  +                    I  G      
Sbjct: 62   LF-RSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGTRVSGD 120

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T + +D      R +          ++     +  +   + +           
Sbjct: 121  DIIIGKTTPVPADSEELGQRLRGHTKKDVSTPLKSTETGIVDRVMLTINQ---------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ----------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAEGIVP 220

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  +G      G +                           
Sbjct: 221  DLIINPHAIPSRMTIGHMVECLVGKVGTMDGSEGD------------------------- 255

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L      + G  ++Y+
Sbjct: 256  ----------------------------ATP-FTDVTVDGISKLLARFGYQKRGFEVMYN 286

Query: 1239 GLTGEPFDRPVTVGYI 1254
            G TG+     +  G  
Sbjct: 287  GHTGKKLTAQIYFGPT 302



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/179 (21%), Positives = 68/179 (37%), Gaps = 19/179 (10%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PLV                     +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGI 881
           +++++  +   +F SI+   +    + T L   E            +     + +++ G+
Sbjct: 51  VIMNQSSIDRGLFRSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGL 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I  G  V+  DI++GK TP         E+L + + G    DV        +G+   V+
Sbjct: 111 IAPGTRVSGDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGIVDRVM 165


>gi|61611737|gb|AAX47185.1| RpoB [Aeromonas hydrophila]
 gi|61611739|gb|AAX47186.1| RpoB [Aeromonas hydrophila]
 gi|61611741|gb|AAX47187.1| RpoB [Aeromonas hydrophila]
 gi|61611743|gb|AAX47188.1| RpoB [Aeromonas hydrophila]
 gi|61611745|gb|AAX47189.1| RpoB [Aeromonas bestiarum]
 gi|61611747|gb|AAX47190.1| RpoB [Aeromonas bestiarum]
 gi|61611749|gb|AAX47191.1| RpoB [Aeromonas bestiarum]
 gi|61611751|gb|AAX47192.1| RpoB [Aeromonas salmonicida]
 gi|61611753|gb|AAX47193.1| RpoB [Aeromonas salmonicida]
 gi|61611755|gb|AAX47194.1| RpoB [Aeromonas salmonicida]
 gi|61611757|gb|AAX47195.1| RpoB [Aeromonas salmonicida]
 gi|61611759|gb|AAX47196.1| RpoB [Aeromonas caviae]
 gi|61611761|gb|AAX47197.1| RpoB [Aeromonas caviae]
 gi|61611763|gb|AAX47198.1| RpoB [Aeromonas caviae]
 gi|61611765|gb|AAX47199.1| RpoB [Aeromonas caviae]
 gi|61611767|gb|AAX47200.1| RpoB [Aeromonas caviae]
 gi|61611769|gb|AAX47201.1| RpoB [Aeromonas caviae]
 gi|61611771|gb|AAX47202.1| RpoB [Aeromonas media]
 gi|61611773|gb|AAX47203.1| RpoB [Aeromonas media]
 gi|61611775|gb|AAX47204.1| RpoB [Aeromonas media]
 gi|61611777|gb|AAX47205.1| RpoB [Aeromonas media]
 gi|61611779|gb|AAX47206.1| RpoB [Aeromonas media]
 gi|61611781|gb|AAX47207.1| RpoB [Aeromonas media]
 gi|61611783|gb|AAX47208.1| RpoB [Aeromonas media]
 gi|61611785|gb|AAX47209.1| RpoB [Aeromonas media]
 gi|61611793|gb|AAX47213.1| RpoB [Aeromonas sobria]
 gi|61611795|gb|AAX47214.1| RpoB [Aeromonas veronii]
 gi|61611797|gb|AAX47215.1| RpoB [Aeromonas jandaei]
 gi|61611799|gb|AAX47216.1| RpoB [Aeromonas veronii bv. veronii]
 gi|61611801|gb|AAX47217.1| RpoB [Aeromonas veronii]
 gi|61611803|gb|AAX47218.1| RpoB [Aeromonas veronii]
 gi|61611805|gb|AAX47219.1| RpoB [Aeromonas veronii]
 gi|61611807|gb|AAX47220.1| RpoB [Aeromonas veronii]
 gi|61611815|gb|AAX47224.1| RpoB [Aeromonas sp. 'CDC 2478-85']
 gi|61611817|gb|AAX47225.1| RpoB [Aeromonas enteropelogenes]
 gi|61611819|gb|AAX47226.1| RpoB [Aeromonas allosaccharophila]
 gi|61611823|gb|AAX47228.1| RpoB [Aeromonas encheleia]
 gi|61611825|gb|AAX47229.1| RpoB [Aeromonas encheleia]
 gi|61611827|gb|AAX47230.1| RpoB [Aeromonas encheleia]
 gi|61611829|gb|AAX47231.1| RpoB [Aeromonas encheleia]
 gi|61611831|gb|AAX47232.1| RpoB [Aeromonas popoffii]
 gi|61611833|gb|AAX47233.1| RpoB [Aeromonas popoffii]
 gi|61611835|gb|AAX47234.1| RpoB [Aeromonas popoffii]
 gi|61611837|gb|AAX47235.1| RpoB [Aeromonas popoffii]
 gi|61611839|gb|AAX47236.1| RpoB [Aeromonas veronii]
 gi|90568550|gb|ABD94221.1| RNA polymerase beta subunit [Aeromonas salmonicida subsp.
           achromogenes]
 gi|90568554|gb|ABD94223.1| RNA polymerase beta subunit [Aeromonas salmonicida subsp.
           masoucida]
 gi|90568558|gb|ABD94225.1| RNA polymerase beta subunit [Aeromonas hydrophila subsp. dhakensis]
 gi|90568560|gb|ABD94226.1| RNA polymerase beta subunit [Aeromonas hydrophila subsp. ranae]
 gi|90568562|gb|ABD94227.1| RNA polymerase beta subunit [Aeromonas hydrophila subsp.
           anaerogenes]
 gi|157142163|gb|ABV24351.1| RNA polymerase beta subunit [Aeromonas bivalvium]
 gi|199601430|emb|CAR66082.1| RNA polymerase beta subunit [Aeromonas aquariorum]
 gi|320202793|emb|CBZ01769.1| RNA polymerase beta subunit [Aeromonas sp. P2G1]
 gi|320202795|emb|CBZ01770.1| RNA polymerase beta subunit [Aeromonas sp. P1A11]
 gi|320202797|emb|CBZ01771.1| RNA polymerase beta subunit [Aeromonas sp. P1D3]
          Length = 172

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|40556201|ref|NP_955286.1| CNPV263 RNA polymerase subunit RPO132 [Canarypox virus]
 gi|40234026|gb|AAR83609.1| CNPV263 RNA polymerase subunit RPO132 [Canarypox virus]
          Length = 1157

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 79/430 (18%), Positives = 152/430 (35%), Gaps = 71/430 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDV--RDTSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V     S +  +   G ++      R G
Sbjct: 702  DNGIHLLFPERPIVLSKATETSKIAINCFGQHVFVALMSYKGMNQEDGIIIKKEFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D     ++ ++ Q+E+   + ++ + I     YS+L      +       G   +  +S
Sbjct: 762  LD----IVTAKKHQVEIPVENFNNRERI-KSTAYSKLRSNGLVRLNAFLEAGDAIARNIS 816

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            S  + +       +F   ++      E     Y++    ++    +K++           
Sbjct: 817  SRTLDD-------EFVADNQISFDISEKYTDMYKSRVERVQVDLTDKVK----------- 858

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
                V+V    +R    GDK   R   KG ++ I P  ++P+ K+G   DI++N   + S
Sbjct: 859  ----VRVLTMKERRPIMGDKFTSRTSQKGTIAYIAPESELPYDKNGLTPDIIINSTSIYS 914

Query: 1130 RMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
            R  +  + E  L  A          + + +        DI     F  K           
Sbjct: 915  RKTISMLVEMILTSAYSVKPYNNNGQNRPICFPSSNETDIEEYVEFARKCYQHAMPNLSK 974

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
             + +++                                          S+LYD  T +P+
Sbjct: 975  EELENEVYCE--------------------------------------SVLYDPETDKPY 996

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
               V +G +Y L+L H+  DK   R  G  + + +Q   G+   GG + GEME  CI A+
Sbjct: 997  KTKVFMGPLYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCIIAH 1056

Query: 1306 GAAYVLQEML 1315
            GAA  + E+L
Sbjct: 1057 GAANTITEIL 1066



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 86/663 (12%), Positives = 199/663 (30%), Gaps = 53/663 (7%)

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNK---DRKDALLDIYR-VMRPGDVSTFSVAESMF 396
           +  I ++      +  +I+N L  D  K      +A+++  + ++   D + +   +++ 
Sbjct: 223 VNIIILIKYLINQDLDFIKNNLSYDMPKETIYLIEAIIESTKTILDTEDFNMYEYIDNLI 282

Query: 397 NFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDI 456
              F            R ++         +    ++   I+ +++  +          D 
Sbjct: 283 EIEFQKQRSITKIEDFRYELMHNFLPHMVNSSDQLKGFYILGLLRKFIYCIYYTSRYPDR 342

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D++   RV + G   +      L     +IK    + +  S     +             
Sbjct: 343 DSMVCHRVLTYGRYFEILANDELENYVTNIKN-DITNNHKSKGICSVSIHVLTTPGFNHA 401

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRI 569
           F      + ++   S     H   +  +             +      +R  HP+ Y   
Sbjct: 402 FSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAFF 461

Query: 570 CPAETSE-GHNIGLVSSLTSF-----ARVNAYGFIETPYRKVCDGKVTNDVVYL---SAM 620
           CP++  E G  +GL+S L+        R   Y  ++    +       ND+ Y      +
Sbjct: 462 CPSDVPERGPQVGLISQLSVLTSVSNIRTTEYIDLKEKIMEYVYSYDKNDMSYFETGHII 521

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             EN  +A  N  L +      +          + +    +       +  +     + P
Sbjct: 522 TIENDLVAAINPELVDKFVDVFKFKKRENYFGNLEIGISNVKDHMNEIRINIGSGRLIRP 581

Query: 681 FLE------NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGI 734
           FL         D+    +   +       ++ E P V   ++      S       +   
Sbjct: 582 FLVVYKGELVMDTVSEELDQRLNTITFSDIQREYPHVIEMLDLEQFVFSNVCESVSKFRQ 641

Query: 735 VEQVDAIRIVIRSVEGDLDPS---TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
           +   D           +       ++ V I      +         Q       D   + 
Sbjct: 642 LNDEDKKLYDYCDFPNEFRDGYVASTLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKI 701

Query: 792 D----------IIADGPSTDLGDLAL---GRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
           D           I    +T+   +A+   G+++ VA M + G N ED ++I +  +    
Sbjct: 702 DNGIHLLFPERPIVLSKATETSKIAINCFGQHVFVALMSYKGMNQEDGIIIKKEFIERGG 761

Query: 839 FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
              +  ++ +V        P E   +   +       +   G++ + A +  GD +   I
Sbjct: 762 LDIVTAKKHQVEI------PVENFNNRERIKSTAYSKLRSNGLVRLNAFLEAGDAIARNI 815

Query: 899 TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
           + +        +  +     EK  D+  + +          +  ++  R    K  R I 
Sbjct: 816 SSRTLDDEFVADNQISFDISEKYTDMYKSRVER----VQVDLTDKVKVRVLTMKERRPIM 871

Query: 959 VER 961
            ++
Sbjct: 872 GDK 874


>gi|300394700|gb|ADK11888.1| DNA-directed RNA polymerase II subunit two [Chroogomphus helveticus]
          Length = 334

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 63/385 (16%), Positives = 103/385 (26%), Gaps = 74/385 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 24   DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 83

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G      
Sbjct: 84   LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGE 142

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 143  DIIIGKTAPIPPDNEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI-------------- 188

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 189  ------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVP 242

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DIV+NP  +PSRM +G + E  L      +G +  +          +S      +K   +
Sbjct: 243  DIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLR--QKGYQS 300

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                SG+     
Sbjct: 301  RGLEVMYHG-----------------------------------------HPSGK----- 314

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMV 1263
                      V VG  Y  +  HMV
Sbjct: 315  -----KLQAQVYVGPTYYQRPKHMV 334



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L++           Q+PL                      +L  G+N +VA + + G
Sbjct: 17  TNFLVRMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 66

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +  + + + +   E            +       
Sbjct: 67  YNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDK 126

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           I++ G+I  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 127 IEDDGLIAPGTGVSGEDIIIGKTAPI----PPDNEELGQRTRTHTRRDVSTPLKSTENGI 182

Query: 936 SGTVV 940
              V+
Sbjct: 183 VDQVL 187


>gi|47156743|gb|AAT12268.1| RNA polymerase II second largest subunit [Diapensia lapponica]
          Length = 530

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/462 (15%), Positives = 129/462 (27%), Gaps = 93/462 (20%)

Query: 794  IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMA 851
            +         +     N    F  +       S++  +   ++            ++   
Sbjct: 160  MTINELVSNREHPEDSN----FGIYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAM 215

Query: 852  RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
                +G          V+    +      +  V        +    +       +     
Sbjct: 216  GKQAMG--------IYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEHLHFRELPAGIN 264

Query: 912  LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDK 971
             + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R  
Sbjct: 265  AIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRAN 323

Query: 972  DDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
                     +          G           K+T ++ D     P  ++          
Sbjct: 324  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDDSQGGPGGRY---------- 373

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                   K  + TS    E    +++      D +     R VKV V   R  Q GDK +
Sbjct: 374  ------TKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFS 422

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+
Sbjct: 423  SRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE 482

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
                                                                   +TP F
Sbjct: 483  GD-----------------------------------------------------ATP-F 488

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                 + I+  L        G   +Y+G TG      + +G 
Sbjct: 489  TEVTVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGP 530



 Score =  105 bits (261), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 72/476 (15%), Positives = 138/476 (28%), Gaps = 96/476 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++       + I+   +  A   F          +  
Sbjct: 5   LVKNLALMVYVTVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWAGIHRDPD 64

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + GV R     E+R ++  +     P    E     L+     
Sbjct: 65  MLVKTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQ-QLLIKKKDI 122

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            A        E       D      + Y+   EEE   I+   + L  +    E+  F  
Sbjct: 123 RALQQRETPEEGG---WHDLVAKGFIEYIDTEEEETTLISMTINELVSNREHPEDSNFGI 179

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                           +  P  ++ + AS+IPF +++ S R      M +QA+ +     
Sbjct: 180 Y------------THCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 227

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
            F                    R   +  V                              
Sbjct: 228 QF--------------------RMDTLAYV------------------------------ 237

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
                    Q+PLV                     +L  G N +VA   + GYN EDS++
Sbjct: 238 -----LYYPQKPLV----------TTRAMEHLHFRELPAGINAIVAIACYSGYNQEDSVI 282

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIIC 883
           +++  +    F S+    +    +      +E        +   +       +D+ G+  
Sbjct: 283 MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAP 342

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  D+++GK TP  +                     RD S  +    +G V
Sbjct: 343 PGTRVSGEDVIIGKTTPIAQDDSQGGPGG--------RYTKRDHSTSLRHSETGMV 390


>gi|37956430|gb|AAP15384.1| RNA polymerase beta subunit [Desulfuromusa sp. S1]
          Length = 179

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 108/176 (61%), Positives = 137/176 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N YGF+ETPYR V  GKV+ ++ Y SA+EEE   IAQAN+ +D++G F  E
Sbjct: 61  TSLSTYARINEYGFVETPYRIVNGGKVSTEIKYFSALEEEGHAIAQANAPIDDNGVFINE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           LV  R  GE +L+P ++ID +D SPKQ+VS+AA+LIPFLENDD+NR LMG NMQ Q
Sbjct: 121 LVNVRKNGEFLLLPPDQIDLMDVSPKQIVSVAAALIPFLENDDANRALMGSNMQGQ 176


>gi|241614087|ref|XP_002407492.1| RNA polymerase III, putative [Ixodes scapularis]
 gi|215502825|gb|EEC12319.1| RNA polymerase III, putative [Ixodes scapularis]
          Length = 1141

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/266 (20%), Positives = 94/266 (35%), Gaps = 56/266 (21%)

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
            ++      +      +EK+    +       ++K+ +   R  + GDK +          
Sbjct: 859  HKEVPVAYKGLEPVHVEKVLISSNTEEAF--LIKLLLRQTRRPEIGDKFS---------- 906

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKA 1161
                                       SR                  G+K    +   + 
Sbjct: 907  ---------------------------SR-----------------HGQKGVVGLIAQQE 922

Query: 1162 NGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINS 1221
            +   S      + ++       +++      +L       +G       F G+  + +  
Sbjct: 923  DMPFSDQGVCPDLIMNPHGFPSRMTVGKLIELLAGKAGVLNGKFHYGTAFGGSKVQDVGE 982

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
             L     +  G+  L  G+TGEP    +  G IY  KL HMV DKV+AR+ G  +++T+Q
Sbjct: 983  ELIRRGFNYRGKDCLTSGITGEPLSAYIYFGPIYYQKLKHMVMDKVHARARGPRAVLTRQ 1042

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGA 1307
            P  G+S  GG RLGEME  C+  +GA
Sbjct: 1043 PTEGRSRDGGLRLGEMERDCLIGHGA 1068



 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 121/1003 (12%), Positives = 277/1003 (27%), Gaps = 209/1003 (20%)

Query: 26  IPDLIEVQ------KASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSY 79
           +P  + VQ        S++HF+ + I    R NE +          +       L+++  
Sbjct: 37  LPAFLSVQGLVRHHIDSFNHFINVEIKEIVRANEKIT---------SDADPQFYLKYLDI 87

Query: 80  EFDPPKF----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQS 129
               P               +C  RD+TY+ P+ + +             +  + +    
Sbjct: 88  HIGKPDVEENCVASKATTPHECRLRDMTYSAPITVDIEYT----------RGTQRVVRGD 137

Query: 130 IYMGDLPLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHF 165
             +G +P+M                           G FV+ G++R+++ Q   S     
Sbjct: 138 FPIGRMPIMLRSANCILADKTHFQMSQMNECPYDPGGYFVVNGVERVILMQEQLSKNRMI 197

Query: 166 DHDKGR------ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLM 219
             +  +       + S     +     + G      +   +           +P+     
Sbjct: 198 VEEDRKGGLMCQVTSSTHERKSRT---NVGTKHGRYYLKHNCF------TEDIPIAIVFK 248

Query: 220 ALGMDSEE-----------ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDID 268
            +G++S++           ILSTF P +    R   +    +   L    K         
Sbjct: 249 GMGLESDQEIVQMIGSADSILSTFAPSLEECHRSQVFTQTQALRYLGGKLKHRRMFFAGG 308

Query: 269 TGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
             +  ++  + + +  + +          + +  L    +   ++  +T    I+  D  
Sbjct: 309 PRKTPVDDARDILATTVLAHVPVEHYNFRVKAMYLA--LMIRRVIEAQTNREMIDDRDYY 366

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
             K LE            L+         + +  +      + D +  + + +    + +
Sbjct: 367 GNKRLELAGSLLSLLFEDLFKRFNTELKLVADKTIPKVRATQFDVVKYVRQDLITNGLVS 426

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                   +   +   ++ +  +G  ++  R           +     + ++  +     
Sbjct: 427 S------ISTGNWTVKRFKMERIGVTQVLTR-----------LSYISALGMMTRVNSQFE 469

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +    +L   +   +      +     L    ++   I++   ++ + + L+N   
Sbjct: 470 KTRKVSGPRSLQPSQFGMLCPSDTPEGEACGLVKNLALMTHITTDLEEAPIVRLLLNLGV 529

Query: 509 VVSAVCEFFCSSQLSQLEEHVN-SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
               +      S  S     +N  +  + H           + R+    E   +H +   
Sbjct: 530 EDVHLLNGEELSDPSVYLVFLNGGIIGVVHNHARLLRTLRLLRRSGHLSEFVSLHSSRVQ 589

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR---KVCDGKVTNDVVYLSAMEEEN 624
           R        G        +     +     +E   R      D      V +L   EE +
Sbjct: 590 RCVNISADGGRMCRPYIVVEGGRPLVTAAHLEDLTRGLLFFNDFVRRGLVEFLDVNEEND 649

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            YIA     +                         +   ++  P  ++ + A LIP+  +
Sbjct: 650 SYIALRECDIGP-----------------------ETTHLEIEPFTLLGVCAGLIPYPHH 686

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           + S R    C M +QA+                                           
Sbjct: 687 NQSPRNTYQCAMGKQAMGT----------------------------------------- 705

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
           I   + +   S   + +Y                RP+VK                    D
Sbjct: 706 IALNQRNRIDSLLYLLVYP--------------HRPMVK----------TKTIELIHFED 741

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR- 863
           +  G+N  VA M + GY+ ED+++++   +             +   +       +    
Sbjct: 742 IPAGQNATVAVMSYSGYDIEDAIVMNRSSIDRGFGRCQVCRHQKCTLKRYANQSHDRVMG 801

Query: 864 ----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES------PMTPEEK-- 911
                         + +D  GI   G  +    +LV K  P   S        +P E   
Sbjct: 802 PLVDSTTMKPIWKHEPLDTDGIARPGDRIENRQVLVNKWVPSASSVGAQPGQPSPPEHKE 861

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           +  A  G + V V    +   +  +  +  +    R     ++
Sbjct: 862 VPVAYKGLEPVHVEKVLISSNTEEAFLIKLLLRQTRRPEIGDK 904


>gi|330785248|gb|AEC46430.1| RNA polymerase II second largest subunit [Lecanographa cf. farinosa
            Ertz 14042]
 gi|330785270|gb|AEC46441.1| RNA polymerase II second largest subunit [Lecanographa hypothallina]
 gi|330785272|gb|AEC46442.1| RNA polymerase II second largest subunit [Lecanographa hypothallina]
          Length = 307

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 58/377 (15%), Positives = 107/377 (28%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQDNA------------EGGARLKEHSKRDISAPLRSTEAGIIDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      + +G  Y
Sbjct: 291  GHTGRKLVSQIFLGPTY 307



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTSPLAGPMQDNAEGGAR----LKEHSKRDISAPLRSTEAGIIDQVLVTTTDG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KKSVKVRTRTTKVPQI 192


>gi|320172582|gb|ADW24174.1| RNA polymerase II second largest subunit [Gloeophyllum carbonarium]
          Length = 461

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 64/372 (17%), Positives = 109/372 (29%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 165  DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 224

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G      
Sbjct: 225  LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGE 283

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     +    T+    E    +++ 
Sbjct: 284  DIIIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTALKSTESGIVDQVL 328

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 329  I-----TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 383

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  L      +G +                           
Sbjct: 384  DVIINPHAIPSRMTIGHLVECLLSKVATLIGNEGD------------------------- 418

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E++++ LR       G  ++Y 
Sbjct: 419  ----------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYY 449

Query: 1239 GLTGEPFDRPVT 1250
            G TG      + 
Sbjct: 450  GHTGRKLQAQIY 461



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 93/265 (35%), Gaps = 28/265 (10%)

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            +++R   PL +       T  E   +   G       A I+   D  +    + +  + 
Sbjct: 95  SHLRRCNTPLGREGKIAXXTHCEIHPSMILGVC-----ASIIPFPDHNQSPRNTYQSAMG 149

Query: 754 PSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
               G+     L++           Q+PL                      +L  G+N +
Sbjct: 150 KQAMGIYLTNFLVRMDTMANILYYPQKPL----------ATTRSMEYLRFRELPAGQNAI 199

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPN 867
           VA + + GYN EDS+++++  +   +F SI+   +  + + + +   E            
Sbjct: 200 VAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLR 259

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +++ G+I  G  VN  DI++GK  P         ++        ++   RD 
Sbjct: 260 MKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRT-------RSHTRRDV 312

Query: 928 SLRVPSGVSGTVVDVRIFNRHGIDK 952
           S  + S  SG V  V I       K
Sbjct: 313 STALKSTESGIVDQVLITTNSEGQK 337



 Score = 44.3 bits (103), Expect = 0.16,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
           D+ G +R+   G +L N +R+   ++ + +    +              +    + + + 
Sbjct: 1   DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHNTITNGLK 60

Query: 515 EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
               +               +SQ+       S ++H RR +     G     A     ++
Sbjct: 61  YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT--PLGREGKIAXXTHCEI 118

Query: 562 HPTHYGRIC-PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           HP+    +C        HN    ++  S     A G   T +  +       +++Y 
Sbjct: 119 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNF--LVRMDTMANILYY 173


>gi|330785258|gb|AEC46435.1| RNA polymerase II second largest subunit [Lecanographa dimelaenoides]
          Length = 307

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 58/377 (15%), Positives = 107/377 (28%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFERPTKQNTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQENA------------EGGARLKEHSKRDISAPLRSTEAGIIDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      + +G  Y
Sbjct: 291  GHTGRKLVSQIFLGPTY 307



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 67/189 (35%), Gaps = 13/189 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFERPTKQNTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P        E     A   E +       LR        ++D  +     
Sbjct: 121 GEDIIIGKTSPLAG--PMQENAEGGARLKEHSKRDISAPLR---STEAGIIDQVLVTTTD 175

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 176 GKKSVKVRT 184


>gi|213053798|gb|ACJ39204.1| RpoB [Corynebacterium ureicelerivorans]
          Length = 139

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 59/167 (35%), Positives = 85/167 (50%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEIHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPADSLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L  +  +  G        +++L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANSKPNRDGDVMVDENGKTMLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|15150555|ref|NP_150550.1| LSDV116 RNA polymerase subunit [Lumpy skin disease virus NI-2490]
 gi|15149127|gb|AAK85077.1| LSDV116 RNA polymerase subunit [Lumpy skin disease virus NI-2490]
 gi|22595651|gb|AAN02684.1| RNA polymerase subunit [Lumpy skin disease virus NW-LW]
          Length = 1156

 Score =  187 bits (475), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYQSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADETELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          + + +         I     F ++       +  
Sbjct: 915  SRKTVSMLIEVILTSAYASKPYNNDGQNRPICFPSSNETSIDTYLDFAKRCHRDRYPSLS 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D +D                                           +ILYD  T +P
Sbjct: 975  DDDINDKMFCD--------------------------------------TILYDPETDKP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   + +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YSSKIFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEVL 1067



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 86/645 (13%), Positives = 206/645 (31%), Gaps = 53/645 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + ++       ++  ++ + +   D+ T+     +    +       +    + +
Sbjct: 245 SYDMPSEISYLVNTIIESTKELIKTINDFDIDTYIN--DLIISEYNKQKSQLILEEFKHE 302

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   I+++++  +          D D++   RV + G+  +   
Sbjct: 303 MINNFLPHMNDTPNQLKGFYIMSLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 362

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +I+  I +   +       I+           F      + ++   S    
Sbjct: 363 HDELENYIGNIRTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 421

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
           +H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 422 SHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 481

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E            ND+ Y      +  EN  IA  N +L +D  
Sbjct: 482 VLTSITNICTNEYLELEKKICNYIRSYNHNDISYFETGYYITLENSLIACLNPNLVDDFV 541

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNRVLMG 693
                         + +    ++      +  +     + PFL  D      D     + 
Sbjct: 542 IDFRRKKRMNYFGNLEIGITLVNDHMNEIRINIGGGRLIRPFLVIDNGNLIMDEIFSELE 601

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----V 748
             +       ++ E P V   ++      S      ++   + + +  +  +        
Sbjct: 602 FKIDDMTFSDIQKEFPHVIEIVDIEQFTFSNVCESVQKFRALPKSEKCKYHLCDFPAEFK 661

Query: 749 EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPST 800
           +G +  S  G++            + +++      + R  +  G   +     I    + 
Sbjct: 662 DGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKAL 721

Query: 801 DLGDL---ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +   +     G+++ +A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 722 ETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI------ 775

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++   
Sbjct: 776 PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQDNQ 830

Query: 918 GEKAVDVRDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVER 961
               +  R T +         V +  ++  R    K  R +  ++
Sbjct: 831 ISFDISDRYTDMYQSRVERVQVDLTDKVKVRVLTMKERRPVLGDK 875



 Score = 38.5 bits (88), Expect = 8.6,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 15/99 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVFPITAFSGAAMLEFVSYEFDPPKF 86
           +  Q  SY +F+          N  LQ      +++      +   ++E  + +  PP++
Sbjct: 23  LHFQYKSYSNFI----------NYRLQEILSVKRTLLSFKNDTEKIIIEIDNIKVTPPEY 72

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
                  +  +Y     +T  + ++         +I  I
Sbjct: 73  SPIIASIKGKSYDA--LVTFTVHIYKEVMTKDGTTITKI 109


>gi|90568552|gb|ABD94222.1| RNA polymerase beta subunit [Aeromonas salmonicida subsp. smithia]
          Length = 172

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 133/172 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  NSLS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNSLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|292661207|gb|ADE35219.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661209|gb|ADE35220.1| RNA polymerase II [Morchella sp. Mel-18]
 gi|292661211|gb|ADE35221.1| RNA polymerase II [Morchella sp. Mel-13]
 gi|292661213|gb|ADE35222.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661215|gb|ADE35223.1| RNA polymerase II [Morchella sp. Mel-24]
 gi|292661217|gb|ADE35224.1| RNA polymerase II [Morchella sp. Mel-21]
 gi|292661219|gb|ADE35225.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661221|gb|ADE35226.1| RNA polymerase II [Morchella sp. Mel-12]
 gi|292661223|gb|ADE35227.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|292661225|gb|ADE35228.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|292661227|gb|ADE35229.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661229|gb|ADE35230.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661231|gb|ADE35231.1| RNA polymerase II [Morchella sp. Mel-23]
 gi|292661237|gb|ADE35234.1| RNA polymerase II [Morchella sp. Mel-16]
 gi|292661239|gb|ADE35235.1| RNA polymerase II [Morchella sp. Mel-16]
 gi|292661241|gb|ADE35236.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|292661245|gb|ADE35238.1| RNA polymerase II [Morchella sp. Mel-12]
 gi|292661247|gb|ADE35239.1| RNA polymerase II [Morchella sp. Mel-12]
 gi|292661259|gb|ADE35245.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661263|gb|ADE35247.1| RNA polymerase II [Morchella sp. Mel-13]
 gi|292661265|gb|ADE35248.1| RNA polymerase II [Morchella sp. Mel-16]
 gi|292661267|gb|ADE35249.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661269|gb|ADE35250.1| RNA polymerase II [Morchella sp. Mel-23]
 gi|292661273|gb|ADE35252.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|292661275|gb|ADE35253.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|292661277|gb|ADE35254.1| RNA polymerase II [Morchella sp. Mel-12]
 gi|292661279|gb|ADE35255.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|292661281|gb|ADE35256.1| RNA polymerase II [Morchella sp. Mel-14]
 gi|292661285|gb|ADE35258.1| RNA polymerase II [Morchella sp. Mel-14]
 gi|292661293|gb|ADE35262.1| RNA polymerase II [Morchella sp. Mel-13]
          Length = 301

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 62/379 (16%), Positives = 114/379 (30%), Gaps = 81/379 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 166  ---------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++++LR       G  +
Sbjct: 255  -------------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEV 282

Query: 1236 LYDGLTGEPFDRPVTVGYI 1254
            +Y+G TG      V +G  
Sbjct: 283  MYNGYTGRKLVCQVFLGPT 301



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|259018543|gb|ACV89781.1| RNA polymerase B beta subunit [Haemophilus parainfluenzae]
 gi|259018545|gb|ACV89782.1| RNA polymerase B beta subunit [Haemophilus parainfluenzae]
          Length = 178

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 109/178 (61%), Positives = 136/178 (76%), Gaps = 1/178 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE
Sbjct: 61  GPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDE 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +  FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 121 NNRFTDAFVTARGERGESGLYKPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 178


>gi|52694375|emb|CAG38027.1| RNA polymerase beta subunit [Pseudomonas aeruginosa]
          Length = 364

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 102/178 (57%), Positives = 131/178 (73%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAG 555
           + +MPQDLINAKPV +A+ EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG
Sbjct: 1   EGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAG 60

Query: 556 VEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVV 615
            E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+PYR V D  VT+++V
Sbjct: 61  FEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIV 120

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
           +LSA+EE +  IAQA+++L+E G   +ELV  R   E  +   E +  +D SPKQVV 
Sbjct: 121 FLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVF 178


>gi|148912993|ref|YP_001293307.1| hypothetical protein GTPV_gp111 [Goatpox virus Pellor]
          Length = 1156

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYQSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADETELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          + + +         I     F ++       +  
Sbjct: 915  SRKTVSMLIEVILTSAYASKPYNNDGQNRPICFPSSNETSIDTYLDFAKRCHRDRYPSLS 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D +D                                           +ILYD  T +P
Sbjct: 975  DDDINDKMFCD--------------------------------------TILYDPETDKP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   + +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YSSKIFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEVL 1067



 Score = 65.9 bits (159), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 86/645 (13%), Positives = 206/645 (31%), Gaps = 53/645 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + ++       ++  ++ + +   D+ T+     +    +       +    + +
Sbjct: 245 SYDMPSEISYLVNTIIESTKELIKTINDFDIDTYIN--DLIISEYNKQKSQLMLEEFKHE 302

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   I+++++  +          D D++   RV + G+  +   
Sbjct: 303 MINNFLPHMNDTPNQLKGFYIMSLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 362

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +I+  I +   +       I+           F      + ++   S    
Sbjct: 363 HDELENYIGNIRTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 421

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
           +H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 422 SHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 481

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E            ND+ Y      +  EN  IA  N +L +D  
Sbjct: 482 VLTSITNICTNEYLELEKKICNYIRSYNHNDISYFETGYYITLENSLIASLNPNLVDDFV 541

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNRVLMG 693
                         + +    ++      +  +     + PFL  D      D     + 
Sbjct: 542 IDFRRKKRMNYFGNLEIGITLVNDHMNEIRINIGGGRLIRPFLVIDNGNLIMDEISSELE 601

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----V 748
             +       ++ E P V   ++      S      ++   + + +  +  +        
Sbjct: 602 FKIDDMTFSDIQKEFPHVIEIVDIEQFTFSNVCESVQKFRALPKSEKCKYHLCDFPAEFK 661

Query: 749 EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPST 800
           +G +  S  G++            + +++      + R  +  G   +     I    + 
Sbjct: 662 DGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKAL 721

Query: 801 DLGDL---ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +   +     G+++ +A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 722 ETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI------ 775

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++   
Sbjct: 776 PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQDNQ 830

Query: 918 GEKAVDVRDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVER 961
               +  R T +         V +  ++  R    K  R +  ++
Sbjct: 831 ISFDISDRYTDMYQSRVERVQVDLTDKVKVRVLTMKERRPVLGDK 875



 Score = 39.7 bits (91), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 15/99 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVFPITAFSGAAMLEFVSYEFDPPKF 86
           +  Q  SY +F+          N  LQ      +++      +   ++E  + +  PP++
Sbjct: 23  LHFQYKSYSNFI----------NYRLQEILSVKRTILSFKNDTEKIIIEIDNIKVTPPEY 72

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
                  +  +Y     +T  + ++         +I  I
Sbjct: 73  SPIIASIKGKSYDA--LVTFTVNIYKEVMTKDGTTITKI 109


>gi|22595809|gb|AAN02841.1| RNA polymerase subunit [lumpy skin disease virus]
          Length = 1156

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYQSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADETELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          + + +         I     F ++       +  
Sbjct: 915  SRKTVSMLIEVILTSAYASKPYNNDGQNRPICFPSSNETSIDTYLDFAKRCHRDRYPSLS 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D +D                                           +ILYD  T +P
Sbjct: 975  DDDINDKMFCD--------------------------------------TILYDPETDKP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   + +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YSSKIFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEVL 1067



 Score = 67.0 bits (162), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 86/645 (13%), Positives = 206/645 (31%), Gaps = 53/645 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + ++       ++  ++ + +   D+ T+     +    +       +    + +
Sbjct: 245 SYDMPSEISYLVNTIIESTKELIKTINDFDIDTYIN--DLIISEYNKQKSQLILEEFKHE 302

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   I+++++  +          D D++   RV + G+  +   
Sbjct: 303 MINNFLPHMNDTPNQLKGFYIMSLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 362

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +I+  I +   +       I+           F      + ++   S    
Sbjct: 363 HDELENYIGNIRTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 421

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
           +H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 422 SHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYVYFCPSDVPERGPQVGLVSQLS 481

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E            ND+ Y      +  EN  IA  N +L +D  
Sbjct: 482 VLTSITNICTNEYLELEKKICNYIRSYNHNDISYFETGYYITLENSLIASLNPNLVDDFV 541

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNRVLMG 693
                         + +    ++      +  +     + PFL  D      D     + 
Sbjct: 542 IDFRRKKRMNYFGNLEIGITLVNDHMNEIRINIGGGRLIRPFLVIDNGNLIMDEIFSELE 601

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----V 748
             +       ++ E P V   ++      S      ++   + + +  +  +        
Sbjct: 602 FKIDDMTFSDIQKEFPHVIEIVDIEQFTFSNVCESVQKFRALPKSEKCKYHLCDFPAEFK 661

Query: 749 EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPST 800
           +G +  S  G++            + +++      + R  +  G   +     I    + 
Sbjct: 662 DGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKAL 721

Query: 801 DLGDL---ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +   +     G+++ +A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 722 ETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI------ 775

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++   
Sbjct: 776 PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQDNQ 830

Query: 918 GEKAVDVRDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVER 961
               +  R T +         V +  ++  R    K  R +  ++
Sbjct: 831 ISFDISDRYTDMYQSRVERVQVDLTDKVKVRVLTMKERRPVLGDK 875



 Score = 38.5 bits (88), Expect = 8.6,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 15/99 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVFPITAFSGAAMLEFVSYEFDPPKF 86
           +  Q  SY +F+          N  LQ      +++      +   ++E  + +  PP++
Sbjct: 23  LHFQYKSYSNFI----------NYRLQEILSVKRTLLSFKNDTEKIIIEIDNIKVTPPEY 72

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
                  +  +Y     +T  + ++         +I  I
Sbjct: 73  SPIIASIKGKSYDA--LVTFTVHIYKEVMTKDGTTITKI 109


>gi|310750850|gb|ADP09218.1| RpoB' [Haloterrigena sp. GSL-11]
          Length = 173

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 52/196 (26%), Positives = 75/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+VLNP  +
Sbjct: 31   EDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVLNPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG I E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHILEMIGGKLGSMEGRRVDGTPFLGEDEDELRQGLEDAG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD A                 G+  +Y G++GE  + 
Sbjct: 137  -----------------------FDSA-----------------GKETMYSGISGEKIEA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGVIFYQKLYHMV 172


>gi|94410942|gb|ABF18589.1| RNA polymerase II second largest subunit [Inocybe mutata]
          Length = 563

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 101/699 (14%), Positives = 182/699 (26%), Gaps = 149/699 (21%)

Query: 573  ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            ET EG   GLV +L   A ++   F       + +  + +     +A           N 
Sbjct: 2    ETPEGQACGLVKNLALMACISVGSFSGPVIEFLEEWGLESLEE--NAHSSTPFTKVFVNG 59

Query: 633  SLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                       LV      R   +         D  +   +          P    +D  
Sbjct: 60   VWIGVHRDAANLVKTLKRLRRRDDISTEISVVRDIREREMRVYTDAGRVCRPLFIVEDQQ 119

Query: 689  RVLMGCNM------QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
             VL   ++        +     K E    G  +E + ++     +++     +E     +
Sbjct: 120  LVLQKKHVRWLNNGVDEEGQEFKWEQMIKGGIIELLDSEEEETVMISMTPEDLENSRLQQ 179

Query: 743  IVI--RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
              I   + +G+ DP+                          +K G            PS 
Sbjct: 180  RGIDPHANDGEFDPAA------------------------RLKAGTHAHTWTHCEIHPSM 215

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N                        ++       +G   
Sbjct: 216  ILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGIYL 250

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                I               +  +             +       +   +  + AI    
Sbjct: 251  TNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 299

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    I+ R  +D  ++S   + E+ E   RD          
Sbjct: 300  GYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTY 358

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       I  G           K+  +  D      R++          V   ++S + 
Sbjct: 359  DKLEDDGFIAPGTGVCGEDIIIGKTAPIPPDSEELGQRTR----THTRRDVSTPLKSTEK 414

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
                   I                       + VKV V   R  Q GDK A RHG KG +
Sbjct: 415  GTVDQVLI----------------TTNSEGQKFVKVRVRSIRIPQIGDKFASRHGQKGTI 458

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                  EDMPF  +G   D+++NP  +PSRM +G + E  L      +G +  +      
Sbjct: 459  GITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-- 516

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                                    ++     + LR       G+ V              
Sbjct: 517  -----------------------DLTVESVSTFLRQRGYQSRGLEVM------------- 540

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKL 1259
                       G +       G      V +G  Y  +L
Sbjct: 541  ---------YHGHT-------GRKLQAQVYLGPTYYQRL 563



 Score =  112 bits (279), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 79/476 (16%), Positives = 136/476 (28%), Gaps = 90/476 (18%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVH 562
            NA         F     +    +  N +  +   RR   +  +  V R     EMR V+
Sbjct: 44  ENAHSSTPFTKVFVNGVWIGVHRDAANLVKTLKRLRRRDDISTEISVVRDIREREMR-VY 102

Query: 563 PTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEE 622
                   P    E     LV        +N     E    K         +  L + EE
Sbjct: 103 TDAGRVCRPLFIVEDQ--QLVLQKKHVRWLNNGVDEEGQEFKWEQMIKGGIIELLDSEEE 160

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPKQVVSIA 675
           E   I+     L+        +      GE                   +  P  ++ I 
Sbjct: 161 ETVMISMTPEDLENSRLQQRGIDPHANDGEFDPAARLKAGTHAHTWTHCEIHPSMILGIC 220

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
           AS+IPF +++ S R      M +QA+ +                                
Sbjct: 221 ASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI------------------------- 255

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
                              + + +  Y       +     +  R                
Sbjct: 256 ----------------RMDTMANILYYPQKPLATTRSMEYLKFR---------------- 283

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  + + + 
Sbjct: 284 --------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSG 335

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +   E            +       +++ G I  G  V   DI++GK  P         +
Sbjct: 336 VQQLEEFEKPTRDTTLRMKHGTYDKLEDDGFIAPGTGVCGEDIIIGKTAPIPPDSEELGQ 395

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK--NERSISVEREQI 964
           +        +    RD S  + S   GTV  V I       K    R  S+   QI
Sbjct: 396 RT-------RTHTRRDVSTPLKSTEKGTVDQVLITTNSEGQKFVKVRVRSIRIPQI 444


>gi|21492568|ref|NP_659688.1| RNA polymerase subunit RPO132 [Sheeppox virus]
          Length = 1156

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYQSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADETELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          + + +         I     F ++       +  
Sbjct: 915  SRKTVSMLIEVILTSAYASKPYNNDGQNRPICFPSSNETSIDTYLDFAKRCHRDRYPSLS 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D +D                                           +ILYD  T +P
Sbjct: 975  DDDINDKMFCD--------------------------------------TILYDPETDKP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   + +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YSSKIFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEVL 1067



 Score = 66.3 bits (160), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 86/645 (13%), Positives = 206/645 (31%), Gaps = 53/645 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + ++       ++  ++ + +   D+ T+     +    +       +    + +
Sbjct: 245 SYDMPSEISYLVNTIIESTKELIKTINDFDIDTYIN--DLIISEYNKQKSQLILEEFKHE 302

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   I+++++  +          D D++   RV + G+  +   
Sbjct: 303 MINNFLPHMNDTPNQLKGFYIMSLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 362

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +I+  I +   +       I+           F      + ++   S    
Sbjct: 363 HDELENYIGNIRTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 421

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
           +H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 422 SHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 481

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E            ND+ Y      +  EN  IA  N +L +D  
Sbjct: 482 VLTSITNICTNEYLELEKKICNYIRSYNHNDISYFETGYYITLENSLIASLNPNLVDDFV 541

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNRVLMG 693
                         + +    ++      +  +     + PFL  D      D     + 
Sbjct: 542 IDFRRKKRMNFFGNLEIGITLVNDHMNEIRINIGGGRLIRPFLVIDNGNLIMDEIFSELE 601

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----V 748
             +       ++ E P V   ++      S      ++   + + +  +  +        
Sbjct: 602 FKIDDMTFSDIQKEFPHVIEIVDIEQFTFSNVCESVQKFRALPKSEKYKYHLCDFPAEFK 661

Query: 749 EGDLDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPST 800
           +G +  S  G++            + +++      + R  +  G   +     I    + 
Sbjct: 662 DGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKAL 721

Query: 801 DLGDL---ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
           +   +     G+++ +A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 722 ETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI------ 775

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++   
Sbjct: 776 PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQDNQ 830

Query: 918 GEKAVDVRDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVER 961
               +  R T +         V +  ++  R    K  R +  ++
Sbjct: 831 ISFDISDRYTDMYQSRVERVQVDLTDKVKVRVLTMKERRPVLGDK 875



 Score = 38.5 bits (88), Expect = 8.7,   Method: Composition-based stats.
 Identities = 14/99 (14%), Positives = 34/99 (34%), Gaps = 15/99 (15%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAF---KSVFPITAFSGAAMLEFVSYEFDPPKF 86
           +  Q  SY +F+          N  LQ      +++      +   ++E  + +  PP++
Sbjct: 23  LHFQYKSYSNFI----------NYRLQEILSVKRTLLSFKNDTEKIIIEIDNIKVTPPEY 72

Query: 87  DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
                  +  +Y     +T  + ++         +I  I
Sbjct: 73  SPIIASIKGKSYDA--LVTFTVHIYKEVMTKDGTTITKI 109


>gi|330785302|gb|AEC46457.1| RNA polymerase II second largest subunit [Dimidiographa loandensis]
          Length = 307

 Score =  187 bits (474), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 106/372 (28%), Gaps = 81/372 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLSTTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L +   +  G           
Sbjct: 68   LFYRTYIEQQQAVGFNSLEEFEKPSKQLTMRTRPGTYDKLDDDGFVAPGVRVSGEDIIVG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +       Q  +   + +       +     +                    
Sbjct: 128  KTAPFQAPMQESAEGGQRNKQHTKRDVSCPLRSTEAGIIDRVL----------------- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L   C   G +                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVCSTTGLEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     + I+++LR A   + G  ++Y+G TG 
Sbjct: 260  -----------------------ATP-FTDVTVQGISNLLRNAGYHQRGFEVMYNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
                 V +G  Y
Sbjct: 296  KLMAQVFLGPTY 307



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 72/206 (34%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   NRMDTMANILYYPQKPL----------STTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  +    +           +D+ 
Sbjct: 51  DSVIMNQSAIDRGLFRSLFYRTYIEQQQAVGFNSLEEFEKPSKQLTMRTRPGTYDKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI+VGK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GFVAPGVRVSGEDIIVGKTAPFQAPMQESAEGGQR----NKQHTKRDVSCPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V +    G    + R+ + +  QI
Sbjct: 167 DRVLVTTTEGRRSVKVRTRTTKVPQI 192


>gi|49175464|gb|AAT52058.1| RNA polymerase II subunit [Lecanactis abietina]
          Length = 300

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 60/374 (16%), Positives = 106/374 (28%), Gaps = 79/374 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 3    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 62

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  + +      Y +L +   +  G        
Sbjct: 63   FYRTYI----EQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVSGEDI 118

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 119  IIGKTAPFQAPM------------QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 164

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 165  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 220

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 221  IINPHAIPSRMTIAHLIECLLSKVSSITGREGD--------------------------- 253

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L  A     G  ++Y+G 
Sbjct: 254  --------------------------ATP-FTDITVSDISELLEFAGYQSRGFEMMYNGH 286

Query: 1241 TGEPFDRPVTVGYI 1254
            TG   +  +  G  
Sbjct: 287  TGRKLNAQIFXGPT 300



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 69/196 (35%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                  + +D+ G +  G  V+
Sbjct: 55  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 115 GEDIIIGKTAPFQAPMQENSEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 170

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 171 KRSVKVRTRTTKVPQI 186


>gi|151573578|gb|ABS18049.1| RNA polymerase II [Fusarium sp. NRRL 28017]
          Length = 296

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 103/369 (27%), Gaps = 75/369 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVGYIY 1255
              V  G  Y
Sbjct: 288  AQVFFGPTY 296



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|190714323|emb|CAQ64503.1| DNA dependant RNA polymerase [Mycobacterium tuberculosis]
 gi|190714342|emb|CAQ64507.1| DNA dependant RNA polymerase [Mycobacterium tuberculosis]
          Length = 175

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 101/174 (58%), Positives = 132/174 (75%), Gaps = 1/174 (0%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 2   IKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 61

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL  SL+ +ARVN +GFIETPYRKV DG V++++VYL+A EE+   +AQANS
Sbjct: 62  ETPEGPNIGLFGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANS 121

Query: 633 SLDEDGSFTEELVFCRCA-GEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +D DG F E  V  R   GE   VP  ++D++D SP+Q+VS+A ++IPFLE+D
Sbjct: 122 PIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHD 175


>gi|119640703|gb|ABL85545.1| RNA polymerase II second largest subunit [Syncesia farinacea]
 gi|330785434|gb|AEC46523.1| RNA polymerase II second largest subunit [Syncesia glyphysoides]
 gi|330785446|gb|AEC46529.1| RNA polymerase II second largest subunit [Syncesia madagascariensis]
 gi|330785448|gb|AEC46530.1| RNA polymerase II second largest subunit [Syncesia myrticola]
 gi|330785450|gb|AEC46531.1| RNA polymerase II second largest subunit [Syncesia myrticola]
          Length = 307

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLEFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|292661295|gb|ADE35263.1| RNA polymerase II [Morchella sp. Mel-11]
          Length = 301

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/379 (16%), Positives = 114/379 (30%), Gaps = 81/379 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 166  ---------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++++LR       G  +
Sbjct: 255  -------------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEV 282

Query: 1236 LYDGLTGEPFDRPVTVGYI 1254
            +Y+G TG      V +G  
Sbjct: 283  MYNGYTGRKLVCQVFLGPT 301



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|330785440|gb|AEC46526.1| RNA polymerase II second largest subunit [Syncesia leprobola]
          Length = 307

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 109/376 (28%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R    E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPLRSETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPLRSETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|241898907|gb|ACS71537.1| RNA polymerase II subunit [Spathularia velutipes]
          Length = 614

 Score =  187 bits (474), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 104/679 (15%), Positives = 200/679 (29%), Gaps = 89/679 (13%)

Query: 475  YRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R    R+   + +  +              + +  + + +     +             
Sbjct: 1    FRXLWKRLTGDVXKYLQTCVEKQSEFNLTLAVKSSTITNGLKYSLATGNWGDQKKAASST 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 116

Query: 580  IGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L+   +  V         +       V  +   L +      ++      +   
Sbjct: 117  CGLVKNLSLMCYVTVGTPSDPIVEFMIQRGMDVLEEYEPLRSPNSTKVFVNGVWVGVHNQ 176

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFL--ENDDSNRVLMGC 694
             +     V        I      I D  D   K          P    E ++ N      
Sbjct: 177  PARLVRNVQGLRRQHLISHEVSLIRDIRDREFKVFTDAGRVCRPLFIVETNEDNPNKGNL 236

Query: 695  NMQRQAVPLLKAEAPF-VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             + +  +  L+ +    +   +E               +G+VE VDA       +    +
Sbjct: 237  VLNKDHIKKLEDDQAMPLQMALEVKNKHGYFGFNGLLDSGVVEYVDAEEEETIMIVMTPE 296

Query: 754  PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   I   ++ Q+ + +  +N+R    V             PS  LG       +  
Sbjct: 297  DLEISRQIQAGLE-QQPDDSGDLNKRVKAPVNPTAHIWTHCEIHPSMILG-------ICA 348

Query: 814  AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            + +P+  +N          M  + +   + +  ++                         
Sbjct: 349  SIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM---------------------- 384

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
                   +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 385  -----DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIMXQS 439

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R   D+ +R        IE   +    + + L    Y +L E   + 
Sbjct: 440  SIDRGLF-RSLFYRAYTDQEKRVGM---ATIESFEKPNRSDTIRLKTATYDKLDEDGIVS 495

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +  Q         
Sbjct: 496  PGVRVSGEDIIIGKTAPIAPDAEELGQRTKAHTKRDASTPLRSTENGIVDQVLL------ 549

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                LR VKV +   +  Q GDK A RHG KG V      EDMP
Sbjct: 550  --------------TTNADGLRFVKVRMRTTKXPQIGDKFASRHGQKGTVGITYRQEDMP 595

Query: 1111 FLKDGTPVDIVLNPLGVPS 1129
            F ++G   DI++NP  +PS
Sbjct: 596  FTREGIVPDIIINPHAIPS 614


>gi|330785214|gb|AEC46413.1| RNA polymerase II second largest subunit [Fulvophyton subseriale]
 gi|330785216|gb|AEC46414.1| RNA polymerase II second largest subunit [Fulvophyton subseriale]
          Length = 307

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 60/372 (16%), Positives = 105/372 (28%), Gaps = 81/372 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEFMKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 68   LFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDEDGFVAPGVRVSGEDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                +  QR  E  K          E    +++      
Sbjct: 128  KTAPFQAPM------------QENSDGGQRTKEHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTDGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSATSAMEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +LR A     G  ++Y+G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSGISGLLREAGYQSRGFEVMYNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  + +G  Y
Sbjct: 296  KLNAQIFLGPTY 307



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 64/197 (32%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      DL  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRDLPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       E                    +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P  ++PM       +        DV        +G+   V
Sbjct: 111 GFVAPGVRVSGEDIIIGKTAPF-QAPMQENSDGGQRTKEHTKRDVSAPLRSTEAGIIDRV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTTDGRRSVKVRTRT 186


>gi|259018555|gb|ACV89787.1| RNA polymerase B beta subunit [Haemophilus influenzae-murium]
 gi|259018557|gb|ACV89788.1| RNA polymerase B beta subunit [Actinobacillus muris]
          Length = 178

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 110/178 (61%), Positives = 135/178 (75%), Gaps = 1/178 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE N  IAQANS+LD 
Sbjct: 61  GPNIGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGNFVIAQANSNLDA 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D  FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 121 DFRFTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 178


>gi|119640691|gb|ABL85539.1| RNA polymerase II second largest subunit [Roccella portentosa]
 gi|119640693|gb|ABL85540.1| RNA polymerase II second largest subunit [Roccella portentosa]
 gi|119640695|gb|ABL85541.1| RNA polymerase II second largest subunit [Roccella portentosa]
          Length = 307

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/375 (17%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMTEN------------SEGGQRTKDHKKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F      +I+ +L  A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSSISELLEFAGYQSRGFEMMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 71/187 (37%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++PMT   +  +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPF-QAPMTENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|304561492|gb|ADM43608.1| DNA-directed RNA polymerase beta subunit [Thermoanaerobacter
           uzonensis]
          Length = 297

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 102/313 (32%), Positives = 150/313 (47%), Gaps = 32/313 (10%)

Query: 176 GKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYP 234
           GK L +  +IP++G W++ E DS DI++VRIDR RKVPVT  L ALG  ++ +IL     
Sbjct: 5   GKKLISATVIPNRGAWLEYEEDSNDIVYVRIDRTRKVPVTVLLRALGYSTDIQILDLLGE 64

Query: 235 KIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLKEKGV 293
           +       D          L+   K       +  GE   +ES K L   L    K   +
Sbjct: 65  EEKLKATLDKDTTKSEEEALIEIYK------RLRPGEPPTVESAKSLLYALFFDAKRYDL 118

Query: 294 KFLGITSD--------CLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
             +G             +  L  A+ IVN  TGEI +E G+ I ++  EEI +  I  + 
Sbjct: 119 AKVGRYKFNKKLALKTRIVNLKSAKKIVNPVTGEILVEEGEKISKEKAEEIQNCGINVVE 178

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L    V     I N              +DI +   P DVS  ++ E++   L    + 
Sbjct: 179 VLVEGKVVR--VIGNNT------------VDINKYPMPYDVSNLNIKEAV--NLSILKEI 222

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            D  +     +N   N       ++I K+DIIA I   ++L +G G+IDDID+LGNRR+R
Sbjct: 223 LDNFSDEEAVINEIKNRMDELVPKNITKDDIIATISYQLNLTHGIGSIDDIDHLGNRRLR 282

Query: 466 SVGEMLKNQYRLG 478
           SVGE+L+NQ+R+G
Sbjct: 283 SVGELLQNQFRIG 295


>gi|9633750|ref|NP_051828.1| m114R [Myxoma virus]
 gi|6523969|gb|AAF15002.1|AF170726_118 m114R [Myxoma virus]
          Length = 1155

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 136/431 (31%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G +V  +   R G
Sbjct: 702  DNGIHLLYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 762  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K+           
Sbjct: 809  DAIARNISSRTLEDDFVQDNQISFDIADRYTDMYKSRVERVQVDLTDKVX---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 859  -----VRVLTMKERRPILGDKFTSRTSQKGTVAYIADENELPYDENGIKPDVIINSTSIF 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          K + +         I    +F ++          
Sbjct: 914  SRKTVSMLIEVILTAAYASKPYNNDGKNRPICFPSSNETTIDTYLNFAKQCHTHTYPDAS 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                +D                                             LYD  T  P
Sbjct: 974  DEVINDKIFCDK--------------------------------------TLYDPETDTP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YTAKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRXGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 85/644 (13%), Positives = 197/644 (30%), Gaps = 56/644 (8%)

Query: 360 NTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  + D+     +A+++  +       +    +    +F                + +M 
Sbjct: 245 SYDMPDEIIYLVNAVIESTKHFVDSINEFDIDTYINDLFIEEHTKQKSQVSLDEFKHEML 304

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                   +    ++   II++++  +          D D++   RV + G+  +     
Sbjct: 305 YNFLPHMTNTPNQLKGFYIISLLRKFIYCIYYTSRYPDRDSMICHRVLTYGKYFEILAHD 364

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            L     +IK      +  +     +             F      + ++   S     H
Sbjct: 365 ELENYIGNIK-TDIINNHKNRGTHSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPH 423

Query: 538 TRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSF 589
              +  +             +      +R  HP+ Y   CP++  E G+ +G+VS L+  
Sbjct: 424 YSWMQNISIPRSVGFYPEQVKISKMFSVRKYHPSQYAYFCPSDVPERGNQVGMVSQLSVL 483

Query: 590 ARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE------ENRYIAQANSSLDEDGSFT 641
             V      E     RK+C+   + DV  +S  E       EN  IA  N  L       
Sbjct: 484 TSVTNICTNEYLDLERKICEYVRSYDVKDISYFETGYYVTLENALIASLNPDLTHAFVRD 543

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                       + +    +       +  +S    + PFL  +    ++         +
Sbjct: 544 FRRKKREGYFNSLEIGITHVADHMNEIRINISSGRLIRPFLVIESGELIMDTVPELADKL 603

Query: 702 PLL-----KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
             +     + E P V   ++      S      ++   + + + ++  +     +     
Sbjct: 604 DDMTFSDVQREYPHVIEMVDIEQFTFSNVCESVQKFRSLPKSEKVKYQLCDFPSEFRDGY 663

Query: 756 --TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND-------------IIADGPST 800
             +S V I      +         Q       D   + D             I     ++
Sbjct: 664 VASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLLYPERPIVISKALETS 723

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +     G+++ +A M + G N ED +++ ++ +       I  ++ +V        P E
Sbjct: 724 KIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGGLDIITAKKHQVEI------PLE 777

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              +   V       ++  G++ + A +  GD +      +  S  T E+  ++    + 
Sbjct: 778 NFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQD--NQI 830

Query: 921 AVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
           + D+ D    +       V   +  ++  R    K  R I  ++
Sbjct: 831 SFDIADRYTDMYKSRVERVQVDLTDKVXVRVLTMKERRPILGDK 874


>gi|259018549|gb|ACV89784.1| RNA polymerase B beta subunit [Pasteurella pneumotropica]
 gi|259018551|gb|ACV89785.1| RNA polymerase B beta subunit [Pasteurella pneumotropica]
 gi|259018559|gb|ACV89789.1| RNA polymerase B beta subunit [Pasteurella pneumotropica]
          Length = 178

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 109/178 (61%), Positives = 135/178 (75%), Gaps = 1/178 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE
Sbjct: 61  GPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDE 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +  FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 121 NNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 178


>gi|282598434|gb|ADA83447.1| RNA polymerase beta subunit [Corynebacterium sp. NML08-0024]
          Length = 139

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/167 (35%), Positives = 84/167 (50%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEVHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPANSLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L     +  G        ++IL+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANTKPNRDGDVMVDEDGKTILFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P+++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|157142165|gb|ABV24352.1| RNA polymerase beta subunit [Aeromonas bivalvium]
 gi|218683113|gb|ACL00601.1| RNA polymerase beta subunit [Aeromonas aquariorum]
          Length = 171

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 100/171 (58%), Positives = 131/171 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR 
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRA 171


>gi|218683107|gb|ACL00598.1| RNA polymerase beta subunit [Aeromonas sp. CECT 4253]
          Length = 171

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 100/171 (58%), Positives = 131/171 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATSEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR 
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRA 171


>gi|133381|sp|P16716|RPO2_SHEVK RecName: Full=DNA-directed RNA polymerase 132 kDa polypeptide;
            AltName: Full=HM1 protein
 gi|323259|gb|AAC32897.1| ORF HM1 [sheeppox virus]
          Length = 919

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 141/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 466  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGG 525

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 526  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 572

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 573  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYQSRVERVQVDLTDKVK---------- 622

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 623  -----VRVLTMKERRPVLGDKFTSRTSQKGTVAYIADETELPYDENGIKPDVIINSTSIF 677

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          + + +         I     F ++       +  
Sbjct: 678  SRKTVSMLIEVILTSAYEVSPYNNDGQNRPICFPSSNETSIDTYLDFAKRCHRDRYPSLS 737

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D +D                                           +ILYD  T +P
Sbjct: 738  DDDINDKMFCD--------------------------------------TILYDPETDKP 759

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   + +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 760  YSSKIFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 819

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 820  HGAANTITEVL 830



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 90/645 (13%), Positives = 209/645 (32%), Gaps = 53/645 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y   + ++       ++  ++ + +   D+ T+     +    +       +    + +
Sbjct: 8   SYDMPSEISYLVNTIIESTKELIKTINDFDIDTYIN--DLIISEYNKQKSQLILEEFKHE 65

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         D    ++   I+++++  +          D D++   RV + G+  +   
Sbjct: 66  MINNFLPHMNDTPNQLKGFYIMSLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 125

Query: 476 RLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRI 535
              L     +I+  I +   +       I+           F      + ++   S    
Sbjct: 126 HDELENYIGNIRTDIINNHKNRGTYSVNIHV-LTTPGFNHAFSGLLSGKFKKTDGSYRTH 184

Query: 536 THTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLT 587
           +H   +  +             +      +R  HP+ Y   CP++  E G  +GLVS L+
Sbjct: 185 SHYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLS 244

Query: 588 SFARV-----NAYGFIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGS 639
               +     N Y  +E            ND+ Y      +  EN  IA  N +L +D  
Sbjct: 245 VLTSITNICTNEYLELEKKICNYIRSYNHNDISYFETGYYITLENSLIACLNPNLVDDFV 304

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND------DSNRVLMG 693
                         + +    ++      +  +     + PFL  D      D     + 
Sbjct: 305 IDFRRKKRMNYFGNLEIGITLVNDHMNEIRINIGGGRLIRPFLVIDNGNLIMDEIFSELE 364

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----V 748
             +       ++ E P V   ++      S      ++   + + +  +  +        
Sbjct: 365 FKIDDMTFSDIQKEFPHVIEIVDIEQFTFSNVCESVQKFRALPKSEKCKYHLCDFPAEFK 424

Query: 749 EGDLDPSTSGVDIYRLMK-----FQRSNQNTCVNQRPLVKVGD-----EVRRNDIIADGP 798
           +G +  S  G++     +      QR    +C++     K+ +        R  +I+   
Sbjct: 425 DGYVASSLVGINHNSGPRAILGCAQRKQAISCLSSDIRNKIDNGIHLIYPERPIVISKAL 484

Query: 799 STDLGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
            T    +   G+++ +A M + G N ED ++I ++ V       I  ++ +V        
Sbjct: 485 ETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFVERGGLDIITAKKHQVEI------ 538

Query: 858 PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
           P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++   
Sbjct: 539 PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQDNQ 593

Query: 918 GEKAVDVRDTSLRVPSGVSGTV-VDVRIFNRHGIDKNERSISVER 961
               +  R T +         V +  ++  R    K  R +  ++
Sbjct: 594 ISFDISDRYTDMYQSRVERVQVDLTDKVKVRVLTMKERRPVLGDK 638


>gi|330785438|gb|AEC46525.1| RNA polymerase II second largest subunit [Syncesia graphica]
          Length = 307

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYXTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYXTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|115298554|ref|YP_762407.1| 128.1 kDa DNA-directed RNA polymerase II subunit 2 [Spodoptera
            frugiperda ascovirus 1a]
 gi|114416821|emb|CAL44652.1| 128.1 kDa DNA-directed RNA polymerase II subunit 2 [Spodoptera
            frugiperda ascovirus 1a]
          Length = 1157

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/306 (22%), Positives = 103/306 (33%), Gaps = 93/306 (30%)

Query: 1085 QSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
              GDK       KGI   +L  EDMPF+ D G   DI++N   +PSRM V Q+  +  G 
Sbjct: 902  TIGDKFCSAMAQKGICGMVLAQEDMPFVPDSGMVPDIIVNSHSMPSRMTVNQMMASVAGK 961

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                  K++           D+                                      
Sbjct: 962  LACVAAKRVDGSSFQNDEYDDLL------------------------------------- 984

Query: 1204 VPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
                           +   L   + D SG   +  G TG  F   V +G +Y L+   +V
Sbjct: 985  -------------AHLCEQLSSVEFDGSGAERMCCGATGVEFPYDVFIGVVYYLRPVQLV 1031

Query: 1264 SDK-------VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
              K         AR+      +T+QPL G+++ GG R+GEME   +  +GA   L E + 
Sbjct: 1032 KHKKFSSTTTATARNR-----LTRQPLNGRAHEGGLRVGEMEKDDLLCHGAVSFLMERML 1086

Query: 1317 IKSD--------------------D---VVGRTRVYESIVAGNDTFETGTPESFNVLVKE 1353
              SD                    D   V  R +            E   P S  +L + 
Sbjct: 1087 DLSDAYTMRLCTTCGSESQVVKRNDNGYVCTRCKTLT-------VSELVLPYSAKLLHQN 1139

Query: 1354 MQALGL 1359
            +QA+G+
Sbjct: 1140 LQAIGV 1145



 Score = 45.1 bits (105), Expect = 0.097,   Method: Composition-based stats.
 Identities = 20/159 (12%), Positives = 44/159 (27%), Gaps = 59/159 (37%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++ Q+ S+  F+             +        P     G   + F +  F  P +  
Sbjct: 19  LVKAQQDSFSSFVDH-----------ISTVLHD-EPNLNVCGN-EIAFENVTFVKPSYIV 65

Query: 87  -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                         ++L Y   +++ +             K  ++  E    +  LP M 
Sbjct: 66  NGKTLVLYPTTARLQNLDYEFTVRVDV---------VNLTKGTRENIE----LCRLPSMV 112

Query: 140 ------------------------KDGTFVIKGIQRIVV 154
                                     G F+  G++R+++
Sbjct: 113 FGKMCNLHDANESVRVAKGELVGDPGGYFIHNGVERVLI 151



 Score = 41.6 bits (96), Expect = 0.94,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 47/115 (40%), Gaps = 5/115 (4%)

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE----ELVFCRCAGEEILVPR 658
           R V       D   + A++E    +A   S L  +G        EL     A    +  R
Sbjct: 620 RFVRPLLYCRDGDDVDALKE-RVMLADNASELFANGDMVHRDAIELCREHVAITTHVAKR 678

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           +++ +I+ +P  +  + A+ IPF     S R     NM RQ++ +L +     GT
Sbjct: 679 DRVSYIELNPNCMFGLLAAQIPFANYSPSPRACYKTNMARQSMGVLPSLGDRNGT 733


>gi|205363461|gb|ACI04160.1| RpoB [Corynebacterium stationis]
          Length = 139

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 58/167 (34%), Positives = 93/167 (55%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+ +     +   +   L++  +++    + +            
Sbjct: 1    QVLELHLGWLA-HTGWKVDT-----EDPKNAELLKTLPQELYDVPADSLT---------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD--------LDESGQSILYDGLTGEPFD 1246
                        +TPVFDGA  E I+ +L  +         +DE G+++L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNEEISRLLASSKPNRDGDVMIDEDGKTVLFDGRSGEPYQ 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VGY+YMLKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGYMYMLKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|170664580|gb|ACB28737.1| m114R [Myxoma virus]
 gi|170664753|gb|ACB28909.1| m114R [recombinant virus 6918VP60-T2]
          Length = 1155

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/431 (17%), Positives = 137/431 (31%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G +V  +   R G
Sbjct: 702  DNGIHLLYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 762  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 809  DAIARNISSRTLEDDFVQDNQISFDIADRYTDMYKSRVERVQVDLTDKVK---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   D+++N   + 
Sbjct: 859  -----VRVLAMKERRPILGDKFTSRTSQKGTVAYIADENELPYDENGIKPDVIINSTSIF 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          K + +         I    +F ++          
Sbjct: 914  SRKTVSMLIEVILTAAYASKPYNNDGKNRPICFPSSNETTIDTYLNFAKQCHTHTYPDAS 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                +D                                             LYD  T  P
Sbjct: 974  DEVINDKIFCDK--------------------------------------TLYDPETDTP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YTAKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 52.8 bits (125), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 85/644 (13%), Positives = 197/644 (30%), Gaps = 56/644 (8%)

Query: 360 NTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMN 417
           +  + D+     +A+++  +       +    +    +F                + +M 
Sbjct: 245 SYDMPDEIIYLVNAVIESTKHFVDSINEFDIDTYINDLFIEEHTKQKSQVSLDEFKHEML 304

Query: 418 MRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRL 477
                   +    ++   II++++  +          D D++   RV + G+  +     
Sbjct: 305 YNFLPHMTNTPNQLKGFYIISLLRKFIYCIYYTSRYPDRDSMICHRVLTYGKYFEILAHD 364

Query: 478 GLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITH 537
            L     +IK      +  +     +             F      + ++   S     H
Sbjct: 365 ELENYIGNIK-TDIINNHKNRGTHSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPH 423

Query: 538 TRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSF 589
              +  +             +      +R  HP+ Y   CP++  E G+ +G+VS L+  
Sbjct: 424 YSWMQNISIPRSVGFYPEQVKISKMFSVRKYHPSQYAYFCPSDVPERGNQVGMVSQLSVL 483

Query: 590 ARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE------ENRYIAQANSSLDEDGSFT 641
             V      E     RK+C+   + DV  +S  E       EN  IA  N  L       
Sbjct: 484 TSVTNICTNEYLDLERKICEYVRSYDVKDISYFETGYYVTLENALIASLNPDLTHAFVRD 543

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                       + +    +       +  +S    + PFL  +    ++         +
Sbjct: 544 FRRKKREGYFNSLEIGITHVADHMNEIRINISSGRLIRPFLVIESGELIMDTVPELADKL 603

Query: 702 PLL-----KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS- 755
             +     + E P V   ++      S      ++   + + + ++  +     +     
Sbjct: 604 DDMTFSDVQREYPHVIEMVDIEQFTFSNVCESVQKFRSLPKSEKVKYQLCDFPSEFRDGY 663

Query: 756 --TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND-------------IIADGPST 800
             +S V I      +         Q       D   + D             I     ++
Sbjct: 664 VASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLLYPERPIVISKALETS 723

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
            +     G+++ +A M + G N ED +++ ++ +       I  ++ +V        P E
Sbjct: 724 KIAVNCFGQHVTIALMSYKGINQEDGIIVKKQFIERGGLDIITAKKHQVEI------PLE 777

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              +   V       ++  G++ + A +  GD +      +  S  T E+  ++    + 
Sbjct: 778 NFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQD--NQI 830

Query: 921 AVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
           + D+ D    +       V   +  ++  R    K  R I  ++
Sbjct: 831 SFDIADRYTDMYKSRVERVQVDLTDKVKVRVLAMKERRPILGDK 874


>gi|45593168|gb|AAS68146.1| RNA polymerase beta subunit [Desulfuromonas palmitatis]
          Length = 173

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 108/173 (62%), Positives = 135/173 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V  GKVT ++ Y SA+EEE   IAQAN+ L+ED +F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRLVSAGKVTTEIKYFSALEEEGHAIAQANAPLNEDNTFVNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           LV  R  GE +L+ RE+I+ +D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 121 LVNARKNGEFMLMNREEIELMDVSPKQLVSVAAALIPFLENDDANRALMGSNM 173


>gi|37956419|gb|AAP15380.1| RNA polymerase beta subunit [Malonomonas rubra]
          Length = 178

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 107/176 (60%), Positives = 139/176 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 2   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V +G+VTN+V + SA+EEE   IAQAN+ +D+DG    E
Sbjct: 62  ASLSTYARINEHGFVETPYRLVREGQVTNEVKFFSALEEEGHAIAQANALMDQDGRLINE 121

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            V  R +GE +LV R++I+ +D +PKQ+VS+AA+LIPFLENDD+NR LMG NMQRQ
Sbjct: 122 YVSARKSGEFVLVQRDEIELMDVAPKQLVSVAAALIPFLENDDANRALMGSNMQRQ 177


>gi|292661255|gb|ADE35243.1| RNA polymerase II [Morchella sp. Mel-21]
          Length = 296

 Score =  186 bits (473), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/374 (16%), Positives = 113/374 (30%), Gaps = 81/374 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G        
Sbjct: 60   LFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D+     R ++         ++     +  Q                   
Sbjct: 117  IIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML---------------- 160

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+
Sbjct: 161  ----TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDL 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 249

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E+++++LR       G  ++Y+G 
Sbjct: 250  --------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGY 282

Query: 1241 TGEPFDRPVTVGYI 1254
            TG      V +G  
Sbjct: 283  TGRKLVCQVFLGPT 296



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 53  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 113 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 165

Query: 950 IDK 952
             K
Sbjct: 166 GLK 168


>gi|119640599|gb|ABL85493.1| RNA polymerase II second largest subunit [Roccella canariensis]
          Length = 307

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V  G  Y
Sbjct: 293  TGRKLNAQVFFGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|9633924|ref|NP_052003.1| gp114R [Rabbit fibroma virus]
 gi|6578643|gb|AAF17997.1|AF170722_115 gp114R [Rabbit fibroma virus]
          Length = 1155

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 76/431 (17%), Positives = 137/431 (31%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++  +   R G
Sbjct: 702  DNGIHLLYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFIERGG 761

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 762  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 808

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 809  DAIARNISSRTLEDDFVQDNQISFDIADRYTDMYKSRVERVQVDLTDKVK---------- 858

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ +DG   D+V+N   + 
Sbjct: 859  -----VRVLTMKERRPILGDKFTSRTSQKGTVAYIADENELPYDEDGIKPDVVINSTSIF 913

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A          K + +         I    +F ++          
Sbjct: 914  SRKTVSMLIEVILTAAYASKPYNNDGKNRPICFPSSNETTIDTYLNFAKQCHTHTHPYAS 973

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                DD                                             LYD  T  P
Sbjct: 974  EDIIDDKIFCNK--------------------------------------KLYDPETDTP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 996  YTAKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1056 HGAANTITEIL 1066



 Score = 52.8 bits (125), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 81/589 (13%), Positives = 183/589 (31%), Gaps = 54/589 (9%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
           + +M         +    ++   II++++  +          D D++   RV + G+  +
Sbjct: 300 KHEMLYNFLPHMTNTPNQLKGFYIISLLRKFIYCIYYTSRYPDRDSMICHRVLTYGKYFE 359

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
                 L     +IK      +  +     +             F      + ++   S 
Sbjct: 360 ILAHDELENYIGNIK-TDIINNHKNRGTHSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSY 418

Query: 533 SRITHTRRLSALGQGGVA-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVS 584
               H   +  +             +      +R  HP+ Y   CP++  E G+ +G+VS
Sbjct: 419 RTHPHYSWMQNISIPRSVGFYPEQVKISKMFSVRKYHPSQYAYFCPSDVPERGNQVGMVS 478

Query: 585 SLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEE------ENRYIAQANSSLDE 636
            L+    V      E     RK+C+   + DV  +S  E       EN  IA  N  +  
Sbjct: 479 QLSVLTSVTNICTNEYLDLERKICEYVRSYDVKDISYFETGYYITLENALIASLNPDITH 538

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                            + +    +       +  ++    + PFL  +    ++     
Sbjct: 539 TFVRDFRRKKREGYFNNLEIGITHVMDHMNEIRINIASGRLIRPFLVIESGELIMDTVPD 598

Query: 697 QRQAVPLL-----KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
               +  +     + E P V   ++      S      ++   + + + ++  +     +
Sbjct: 599 LVDKLDDMTFSDVQKEYPHVIEMVDIEQFTFSNVCESVQKFRSLPKSEKVKYQLCDFPSE 658

Query: 752 LDPS---TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND-------------IIA 795
                  +S V I      +         Q       D   + D             I  
Sbjct: 659 FRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLLYPERPIVISK 718

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
              ++ +     G+++ +A M + G N ED ++I ++ +       I  ++ +V      
Sbjct: 719 ALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKKQFIERGGLDIITAKKHQVEI---- 774

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
             P E   +   V       ++  G++ + A +  GD +      +  S  T E+  ++ 
Sbjct: 775 --PLENFNNKERVKSTAYSKLESNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQD 827

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
              + + D+ D    +       V   +  ++  R    K  R I  ++
Sbjct: 828 --NQISFDIADRYTDMYKSRVERVQVDLTDKVKVRVLTMKERRPILGDK 874


>gi|46277316|gb|AAS86848.1| DNA-dependent RNA polymerase II [Pachyella punctispora]
          Length = 555

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 58/376 (15%), Positives = 107/376 (28%), Gaps = 75/376 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 255  DTMANILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 314

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R           +       +  G      
Sbjct: 315  LF-RSLFFRTYMDQEKRVGMAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGE 373

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 374  DIIIGKTAPIAPNTEELGQRTKFHTKRDVSTPLRSTESGIVDQVML-------------- 419

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 420  ------TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGIVP 473

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 474  DIIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD------------------------- 508

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 509  ----------------------------ATP-FTDVTVDSVSGLLREHGYQSRGFEVMYN 539

Query: 1239 GLTGEPFDRPVTVGYI 1254
            G TG      V +G  
Sbjct: 540  GHTGRKLVVQVFLGPT 555



 Score = 94.0 bits (232), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 73/476 (15%), Positives = 127/476 (26%), Gaps = 74/476 (15%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
              ++ +   ++   P    NA  +             + +  ++  L R  H     +L
Sbjct: 18  DFMKQRNMEVLEEYEPSRHPNATKIFVNGVWVGIHRDPNFIVRNIQKLRRQNHIGHEVSL 77

Query: 545 GQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            Q    R         R   P       PA T  G  +   S +                
Sbjct: 78  IQDVRNREFKIFTDAGRICRPLFVVDNDPASTRRGELVLQKSHIEKLEYDKELPKDSELK 137

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                      V Y+ A EEE   I      LD    +                      
Sbjct: 138 YGWQGLINEGVVEYVDAEEEETIMIMMTPEELDLSRQYHAG------------------- 178

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +  P+ +   A    P  ++           M                        + 
Sbjct: 179 -YEIQPEPMDLAARVRQPVNKH---------ATM--------------------WTHCEI 208

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQRPL 781
             A I+   A I+   D  +                       +   +  N     Q+PL
Sbjct: 209 HPAMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXNYRERMDTMANILYYPQKPL 268

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
                                 +L  G+N +VA   + GYN EDS+++++  +   +F S
Sbjct: 269 ----------GTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 318

Query: 842 IHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
           +    +    +   +   E        +   +       +DE G++  G  VN  DI++G
Sbjct: 319 LFFRTYMDQEKRVGMAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGEDIIIG 378

Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           K  P   +     ++        K    RD S  + S  SG V  V +       K
Sbjct: 379 KTAPIAPNTEELGQRT-------KFHTKRDVSTPLRSTESGIVDQVMLTTNQEGLK 427


>gi|312204348|gb|ADQ47491.1| RNA polymerase II second largest subunit [Odontotrema sp. 1 EB-2010]
          Length = 289

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/358 (17%), Positives = 113/358 (31%), Gaps = 81/358 (22%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 10   MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKR-- 66

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +    + + L    Y +L +   I  G           K+  ++ D   
Sbjct: 67   -IGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDDEE 125

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                  ++K+          L+ V
Sbjct: 126  LGQRTKLHTKRDASTPLRSTESGI------------------VDKVLL--TTNAEGLKFV 165

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG V      EDMPF  +G   DI++NP  +PSRM + 
Sbjct: 166  KVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFSSEGIVPDIIINPHAIPSRMTIA 225

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 226  HLIECQLSKVSSLRGFEGD----------------------------------------- 244

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                        +TP F     ++++ +LR       G  I+Y+G TG      V +G
Sbjct: 245  ------------ATP-FTEVTVDSVSRLLREHGYQSRGFEIMYNGHTGRKLVAQVFLG 289



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 7   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKR 66

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  D   +     + +D+ GII  G  V+  DI++GK  P        
Sbjct: 67  IGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDDEEL 126

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++        K    RD S  + S  SG V  V +       K
Sbjct: 127 GQRT-------KLHTKRDASTPLRSTESGIVDKVLLTTNAEGLK 163


>gi|119640649|gb|ABL85518.1| RNA polymerase II second largest subunit [Roccella sinensis]
 gi|119640651|gb|ABL85519.1| RNA polymerase II second largest subunit [Roccella sinensis]
 gi|307547781|gb|ADN44504.1| RNA polymerase II second largest subunit [Roccella sinensis]
 gi|307547783|gb|ADN44505.1| RNA polymerase II second largest subunit [Roccella sinensis]
 gi|330785318|gb|AEC46465.1| RNA polymerase II second largest subunit [Roccella sinensis]
          Length = 307

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRAEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRAEVLRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640653|gb|ABL85520.1| RNA polymerase II second largest subunit [Roccella tinctoria]
          Length = 307

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFXAPMXENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFXAPMXENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|56406268|gb|AAV87517.1| RpoB [Enterobacteriaceae bacterium A2JM]
          Length = 172

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 105/172 (61%), Positives = 135/172 (78%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +A+ N YGF+ETPYR+V D  VT+++ YLSA+EE N  IAQAN++LDE+G 
Sbjct: 61  IGLINSLSVYAQTNEYGFLETPYRRVRDNVVTDEIHYLSAIEEGNFVIAQANTNLDEEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           F +ELV CR  GE  L  R++++++D S +QVVS+ ASLIPFLE+DD+NR L
Sbjct: 121 FIDELVTCRNKGESSLFSRDQVEYMDVSTQQVVSVGASLIPFLEHDDANRAL 172


>gi|61611789|gb|AAX47211.1| RpoB [Aeromonas eucrenophila]
          Length = 172

 Score =  186 bits (472), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 100/172 (58%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  E+G 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATSEEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|330785218|gb|AEC46415.1| RNA polymerase II second largest subunit [Syncesia socotrana]
          Length = 305

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 7    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 66

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 67   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 122

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 123  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 163

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 164  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 223

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 224  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 257

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 258  ---------------------------ATP-FTDITVSSISELLSFAGYQSRGFELMYNG 289

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 290  HTGRKLNAQVFLGPTY 305



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 65/195 (33%), Gaps = 16/195 (8%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
               +      Q+PL                      +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTMSNILYYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +       EE  R              + +D+ G 
Sbjct: 51  VIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGF 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +  G  V+  DI++GK  P         E   +     K  DV        +G+   V+ 
Sbjct: 111 VPPGVRVSGEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLL 169

Query: 942 VRIFNRHGIDKNERS 956
                +  +    R+
Sbjct: 170 TTTEGKRSVKVRTRT 184


>gi|307547621|gb|ADN44424.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
 gi|307547623|gb|ADN44425.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
 gi|307547625|gb|ADN44426.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
 gi|307547627|gb|ADN44427.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
 gi|307547629|gb|ADN44428.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
 gi|307547631|gb|ADN44429.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010a]
          Length = 307

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRAEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGEEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRAEVLRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|302847118|ref|XP_002955094.1| hypothetical protein VOLCADRAFT_95925 [Volvox carteri f. nagariensis]
 gi|300259622|gb|EFJ43848.1| hypothetical protein VOLCADRAFT_95925 [Volvox carteri f. nagariensis]
          Length = 1095

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 91/249 (36%), Gaps = 72/249 (28%)

Query: 1095 GNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
            G KG++S + P  DMPF    G   D+++NP   PSRM +G + E+ +       G+ + 
Sbjct: 822  GQKGVLSILWPDVDMPFCASTGIRPDLIINPHAFPSRMTIGMLVESLVSKGGALAGQFVD 881

Query: 1154 SLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDG 1213
            +                                                GV    PV   
Sbjct: 882  ASPFQR-----------------------------------------SDGVEKGNPV--- 897

Query: 1214 ADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY----A 1269
               E     L        GQ  +  G+TG+     + +G +Y  +L HMVSDK       
Sbjct: 898  ---ERWGEYLERQGFSRYGQETMISGVTGQEMPCDIFIGPVYYQRLRHMVSDKFQCPGGF 954

Query: 1270 RSTGSYSLVTQQP--LGGKSNR---------GGQRLGEMEVWCIQAYGAAYVLQEMLTIK 1318
            R+    S V + P  LG  S+          GG R GEME   + A+GAAY+  + L   
Sbjct: 955  RNV--VS-VPRSPSFLG--SSFTRSWAENFGGGIRFGEMERDSLLAHGAAYLFHDRLHAC 1009

Query: 1319 SD----DVV 1323
            SD    DV 
Sbjct: 1010 SDYHVADVC 1018



 Score = 49.3 bits (116), Expect = 0.005,   Method: Composition-based stats.
 Identities = 27/160 (16%), Positives = 46/160 (28%), Gaps = 52/160 (32%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA-AMLEFVSYEFDPPKFD 87
           L+E    SY++F+   I              KS       +G    + +     + P  +
Sbjct: 47  LVEPHVESYNYFISEGIDHVM-------ENLKSYEVTHPGTGRTMRMWWTDVRVERPVRE 99

Query: 88  ----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       DC     TY   L  T      D  E+T  +           +G +P+
Sbjct: 100 EGLKRSRRLLPRDCREGGTTYKGNLVATFNWQSGDGMEYTVERK----------LGGMPI 149

Query: 138 MTKD------------------------GTFVIKGIQRIV 153
           M +                         G F+  G++RI+
Sbjct: 150 MVRSRACWLNGLTRGELVACREEANEMGGYFICNGLERII 189


>gi|90568556|gb|ABD94224.1| RNA polymerase beta subunit [Aeromonas salmonicida subsp.
           pectinolytica]
          Length = 172

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 100/172 (58%), Positives = 131/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +EL+ CR  GE   +  ++  ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 LKDELIPCRHKGESTFMNADQSQYMDVSPQQIVSVAAALIPFLEHDDANRAL 172


>gi|259018553|gb|ACV89786.1| RNA polymerase B beta subunit [Haemophilus sp. HK445]
 gi|259018561|gb|ACV89790.1| RNA polymerase B beta subunit [Pasteurella pneumotropica]
 gi|259018563|gb|ACV89791.1| RNA polymerase B beta subunit [Pasteurella pneumotropica]
          Length = 178

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 109/178 (61%), Positives = 135/178 (75%), Gaps = 1/178 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE
Sbjct: 61  GPNIGLINSLSAFARTNDYGFLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDE 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +  FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 121 NNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 178


>gi|83414589|dbj|BAE54085.1| RNA polymerase beta subunit [Streptococcus gordonii]
          Length = 172

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/168 (41%), Positives = 95/168 (56%), Gaps = 6/168 (3%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTRKGEKDLSAEERLLHAVFRDKSREVRDTSLRVPHGADGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GD+MAGR GNKG+VSRI+P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDRMAGRPGNKGVVSRIVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
            VDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+
Sbjct: 117  VDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSDDL 164


>gi|330785210|gb|AEC46411.1| RNA polymerase II second largest subunit [Dendrographa alectoroides]
          Length = 304

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 65

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 66   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 121

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 122  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 162

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 163  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 222

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 223  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 256

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 257  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 288

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 289  HTGRKLNAQVFLGPTY 304



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 118 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKVRTRT 183


>gi|307547581|gb|ADN44404.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547583|gb|ADN44405.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547585|gb|ADN44406.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547587|gb|ADN44407.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547589|gb|ADN44408.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547591|gb|ADN44409.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547593|gb|ADN44410.1| RNA polymerase II second largest subunit [Roccella balfourii]
 gi|307547773|gb|ADN44500.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010b]
 gi|307547775|gb|ADN44501.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010b]
 gi|307547777|gb|ADN44502.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010b]
 gi|307547779|gb|ADN44503.1| RNA polymerase II second largest subunit [Roccella sp. MI-2010b]
          Length = 307

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRAEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRAEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|313639721|gb|EFS04486.1| DNA-directed RNA polymerase subunit beta [Listeria seeligeri FSL
            S4-171]
          Length = 111

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 48/88 (54%), Positives = 62/88 (70%)

Query: 1292 QRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLV 1351
            QR GEMEVW ++AYGAAY LQE+LTIKSDDVVGR + YE+IV G    E G PESF VL+
Sbjct: 1    QRFGEMEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLI 60

Query: 1352 KEMQALGLSIDLENSRTKNSAKMEEIPD 1379
            KE+Q+LG+ + + ++  K     +   D
Sbjct: 61   KELQSLGMDVKMLSADEKEIEMRDMDDD 88


>gi|330785380|gb|AEC46496.1| RNA polymerase II second largest subunit [Schismatomma dirinellum]
          Length = 307

 Score =  186 bits (472), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 64/375 (17%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + L                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPLSENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VK+     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSSITGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLQFAGYQSRGFELMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 70/187 (37%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++P++   +  +        DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPF-QAPLSENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKIRTRT 186


>gi|330785452|gb|AEC46532.1| RNA polymerase II second largest subunit [Syncesia socotrana]
          Length = 307

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|164614622|gb|ABY64537.1| RNA polymerase beta subunit [Candidatus Bartonella eldjazairii]
          Length = 207

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 134/188 (71%), Positives = 157/188 (83%)

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           VHPTHYGRICP  T EG NIGL++SL +FARVN YGF+E+PYRK+ DGKV  +V+YLSAM
Sbjct: 12  VHPTHYGRICPTATPEGPNIGLINSLATFARVNKYGFLESPYRKIIDGKVPKEVIYLSAM 71

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           EE   Y+AQANSSLD +G FTEE V CR AGE ++ PR+ ID +D SPKQ+VS+AA+LIP
Sbjct: 72  EESKHYVAQANSSLDAEGRFTEEFVVCRHAGEVLMAPRDHIDLMDVSPKQLVSVAAALIP 131

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLENDD+NR LMG NMQRQAVPLL+AEAP VGTGME+ VA  SGAAI AKR GIV+QVDA
Sbjct: 132 FLENDDANRALMGSNMQRQAVPLLRAEAPLVGTGMEAKVACDSGAAIGAKRGGIVDQVDA 191

Query: 741 IRIVIRSV 748
           +RIVIR+ 
Sbjct: 192 MRIVIRAT 199


>gi|242876436|gb|ACS94013.1| RNA polymerase beta subunit [Pasteurellaceae bacterium DD1]
 gi|242876438|gb|ACS94014.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4016]
 gi|242876440|gb|ACS94015.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4134]
 gi|242876442|gb|ACS94016.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4136]
 gi|242876444|gb|ACS94017.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4141]
 gi|242876446|gb|ACS94018.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4142]
 gi|242876448|gb|ACS94019.1| RNA polymerase beta subunit [Pasteurellaceae bacterium JF4213]
          Length = 173

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 109/173 (63%), Positives = 134/173 (77%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE N  IAQAN+SLDED  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVDGQVTEEIEYLSAIEEGNYVIAQANASLDEDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D SP+QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIQYMDVSPQQVVSVAAALIPFLEHDDANRAL 173


>gi|330785378|gb|AEC46495.1| RNA polymerase II second largest subunit [Schismatomma dirinellum]
          Length = 307

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMSENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VK+     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSSITGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLQFAGYQSRGFELMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 79.3 bits (194), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 70/187 (37%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++PM+   +  +        DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPF-QAPMSENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKIRTRT 186


>gi|124377268|emb|CAM32367.1| RpoB protein [Aeromonas sharmana]
          Length = 171

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 102/171 (59%), Positives = 132/171 (77%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL  ++R N YGF+ETPYRKV DG +T++V YLSA+EE N  IAQAN+++DE G  
Sbjct: 61  GLINSLAVYSRTNDYGFLETPYRKVIDGVITDEVDYLSAIEEGNFVIAQANANVDEHGKL 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            +EL+ CR  GE   +  ++I ++D SP+QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 KDELIPCRHKGESTFMNADQIQYMDVSPQQVVSVAAALIPFLEHDDANRAL 171


>gi|34535223|dbj|BAC87247.1| unnamed protein product [Homo sapiens]
          Length = 1135

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 104/561 (18%), Positives = 179/561 (31%), Gaps = 97/561 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G     GP+  +K       L
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGIK-PGGPRVLQK-------L 807

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 808  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 865

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A R G K                            G+ SR+ 
Sbjct: 866  CVCITMRVPRNPTIGDKFASRRGQK----------------------------GILSRL- 896

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
                      W    +      ++ D   N    P R  +  +I              +S
Sbjct: 897  ----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------ES 932

Query: 1193 VLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
            +   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  +
Sbjct: 933  MAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADI 992

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAY 1309
             +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G ++
Sbjct: 993  FIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSF 1052

Query: 1310 VLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETGT 1343
            +L + L   SD     V    G                 R R Y   +    +       
Sbjct: 1053 LLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVSV 1112

Query: 1344 PESFNVLVKEMQALGLSIDLE 1364
            P  F   V E+ A+ + + L+
Sbjct: 1113 PYVFRYFVAELAAMNIKVKLD 1133



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 215/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++      +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 422

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 599

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGGPRVLQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 62.4 bits (150), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 100/721 (13%), Positives = 200/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCSTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++       +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMRIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +D+ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +               +      ++   V  L+  +EE          L       
Sbjct: 591 PWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V        +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVT----THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|89888219|gb|ABD78652.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888226|gb|ABD78655.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888233|gb|ABD78658.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888240|gb|ABD78661.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888247|gb|ABD78664.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
 gi|89888261|gb|ABD78670.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
          Length = 269

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 97/271 (35%), Positives = 159/271 (58%), Gaps = 3/271 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F+    +  + +             G      + D  +G+ ++E  K++ +  L+ L   
Sbjct: 1   FFDFDNFELKSEGAMMEFVPE-RWKGEMARFDISD-RSGKVIVEKDKRINAKHLRDLANA 58

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           G++ + +  D L G  +A+++V+ +TGE+   A D I E  L  +  +++ D+  LY + 
Sbjct: 59  GIQRISVPEDFLFGRVLAKNVVDADTGEVIAHANDEITESVLAAMRDAKVLDLQALYTND 118

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           ++   YI  TL TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS V
Sbjct: 119 LDRGPYISQTLRTDETADQTAARVAIYRMMRPGEPPTEEAVEAVFQRLFYSEESYDLSRV 178

Query: 412 GRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           GR+K+N RL   D  +    +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+
Sbjct: 179 GRMKVNSRLGRGDDANGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGEL 238

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
            +NQ+R GL+R+ER++KER+   + +++MP 
Sbjct: 239 AENQFRAGLVRVERAVKERLGQAETENLMPH 269


>gi|330785336|gb|AEC46474.1| RNA polymerase II second largest subunit [Dendrographa conformis]
          Length = 307

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAMVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAMVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|45593165|gb|AAS68145.1| RNA polymerase beta subunit [Desulfuromusa succinoxidans]
          Length = 173

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 134/173 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N YGF+ETPYR V  GKV+ ++ Y SA+EEE   IAQAN+ +D++G F  E
Sbjct: 61  ASLSTYARINEYGFVETPYRIVNGGKVSTEIKYFSALEEEGHAIAQANAPIDDNGVFINE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           LV  R  GE +L+P ++ID +D SPKQ+VS+AA+LIPFLENDD+ R LMG NM
Sbjct: 121 LVNVRKNGEFLLLPPDQIDLMDVSPKQIVSVAAALIPFLENDDAIRALMGSNM 173


>gi|300394724|gb|ADK11900.1| DNA-directed RNA polymerase II subunit two [Leucogyrophana mollusca]
          Length = 316

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/384 (16%), Positives = 106/384 (27%), Gaps = 75/384 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 8    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G      
Sbjct: 68   LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVSGE 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  Q                 
Sbjct: 127  DIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI-------------- 172

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 173  ------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGIVP 226

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L      +G +  +                        
Sbjct: 227  DIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT-------------------- 266

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                  ++     + LR       G+ V                         G +    
Sbjct: 267  -----DLTVESVSTFLRQKGYQSRGLEVM----------------------YHGHT---- 295

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHM 1262
            G         V +G  Y  +L HM
Sbjct: 296  GR---KLQAQVYLGPTYYQRLKHM 316



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L++           Q+PL                      +L  G+N +VA + + G
Sbjct: 1   TNFLVRMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +  + + + +   E            +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           I++ G+I  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 111 IEDDGLIAPGTGVSGEDIIIGKTAPI----PPDSEELGQRTRTHTRRDVSTPLKSTENGI 166

Query: 936 SGTVV 940
              V+
Sbjct: 167 VDQVL 171


>gi|113957128|gb|ABI49099.1| RNA polymerase II second largest subunit [Crocynia pyxinoides]
          Length = 331

 Score =  186 bits (471), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/389 (16%), Positives = 107/389 (27%), Gaps = 75/389 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 18   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R      EQ E   R    +      +       +  G      
Sbjct: 78   LF-RSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +  Q   S             
Sbjct: 137  DIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS------------- 183

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 184  -------TNSDGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 236

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +  +          +S L    E    +
Sbjct: 237  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSKLLR--EHGYHS 294

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 295  RGFEVM---------------------------------------------YNGHT---- 305

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
            G         V +G  Y  +L HMV DK+
Sbjct: 306  GR---KLVAQVFLGPTYYQRLRHMVDDKI 331



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 66/184 (35%), Gaps = 22/184 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 11  TNYDVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         ++        K    RDTS  + S  
Sbjct: 121 LDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTE 173

Query: 936 SGTV 939
           +G V
Sbjct: 174 NGIV 177


>gi|119640567|gb|ABL85477.1| RNA polymerase II second largest subunit [Dendrographa alectoroides]
 gi|119640569|gb|ABL85478.1| RNA polymerase II second largest subunit [Dendrographa alectoroides
            f. parva]
 gi|330785200|gb|AEC46406.1| RNA polymerase II second largest subunit [Dendrographa leucophaea]
 gi|330785202|gb|AEC46407.1| RNA polymerase II second largest subunit [Dendrographa leucophaea]
 gi|330785204|gb|AEC46408.1| RNA polymerase II second largest subunit [Dendrographa leucophaea]
 gi|330785206|gb|AEC46409.1| RNA polymerase II second largest subunit [Dendrographa leucophaea f.
            minor]
 gi|330785208|gb|AEC46410.1| RNA polymerase II second largest subunit [Dendrographa leucophaea]
 gi|330785338|gb|AEC46475.1| RNA polymerase II second largest subunit [Dendrographa conformis]
 gi|330785362|gb|AEC46487.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785364|gb|AEC46488.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785366|gb|AEC46489.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785368|gb|AEC46490.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785370|gb|AEC46491.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785372|gb|AEC46492.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
 gi|330785374|gb|AEC46493.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
          Length = 307

 Score =  186 bits (471), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|46277356|gb|AAS86868.1| DNA-dependent RNA polymerase II [Peziza sp. PM-120-97]
          Length = 548

 Score =  186 bits (471), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 93/670 (13%), Positives = 185/670 (27%), Gaps = 130/670 (19%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V +       +    + +V  +     +      ++      +  D  F    +
Sbjct: 3    LMSYVSVGSPADPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTI 62

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    I      I  I     ++ + A      +  ++ND ++       +Q+  + 
Sbjct: 63   QKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIE 122

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
             L+ +      G E                G+VE +DA       +    +   +    +
Sbjct: 123  KLEDDKEI---GDEDQRYG----WQGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFH 175

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
               + Q+        QR    V             PS  LG       +  + +P+  +N
Sbjct: 176  AGYEIQQEVDPA---QRVKAAVNKYAHTWTHCEIHPSMILG-------ICASIIPFPDHN 225

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                   S R   +       +  F    R+                           + 
Sbjct: 226  Q------SPRNTYQSXMGKQAMGVFLTNYRERM-----------------------DTMA 256

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 257  NILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-R 315

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G       
Sbjct: 316  SLFYRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGED 372

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  ++ +      R+++         ++     +  Q                  
Sbjct: 373  IIIGKTAPIAPNQEELGQRTKFHTKRDTSTPLRSTENGIVDQ------------------ 414

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 415  --VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVPD 472

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 473  LIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------------------- 506

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     ++++ +LR       G  I+Y+G
Sbjct: 507  ---------------------------ATP-FTDVTVDSVSKLLREHGYQSRGFEIMYNG 538

Query: 1240 LTGEPFDRPV 1249
             TG      V
Sbjct: 539  HTGRKLVVQV 548


>gi|300394740|gb|ADK11908.1| DNA-directed RNA polymerase II subunit two [Paragyrodon
            sphaerosporus]
          Length = 547

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 96/603 (15%), Positives = 181/603 (30%), Gaps = 72/603 (11%)

Query: 569  ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
            +CPAET EG   GLV +L   + ++   +       + +  + +         EEN + +
Sbjct: 1    VCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESL--------EENAHSS 52

Query: 629  QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
               + +  +G +       R     +   ++     D SP+  V             D+ 
Sbjct: 53   TPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKADISPEVSVVRDIRERELRLYTDAG 109

Query: 689  RVLMGCNMQRQAVPLLKAEA-PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            RV     +       L+ +   ++  G      +      + K +GI+E +DA       
Sbjct: 110  RVCRPLFIVENQQLALQKKHIKWLNQGYRDDDGEEFKWEQLVK-SGIIELLDAEEEETVM 168

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +    +   +       +    ++ +     R  +K G             S  LG    
Sbjct: 169  ISMPPEDLENFRLQSAGINPHENDGDFDPAAR--LKAGINAHTWTHCEIHLSMILG---- 222

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N       S R   +       +  +                    
Sbjct: 223  ---VCASIIPFPDHNQ------SPRNTYQSAMGKQAMGIYLTNF---------------L 258

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            V  + + N        +             +       +   +  + AI      +  D+
Sbjct: 259  VGMDTMAN--------ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDS 310

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    I+ R  +D  ++S   + E+ E   RD          +      
Sbjct: 311  VIMNQSSIDRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDSTLRMKHGTYDKLEDDG 369

Query: 988  EILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             I  G N         K+  +  D      R++          ++     +  Q      
Sbjct: 370  LIAPGTNVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI--- 426

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
                                    + VKV V   R  Q GDK A RHG KG +      E
Sbjct: 427  -----------------TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQE 469

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+V+NP  +PSRM +G + E  L      +G +  +          +S 
Sbjct: 470  DMPFTAEGIVSDLVINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVST 529

Query: 1168 LRS 1170
               
Sbjct: 530  FLR 532



 Score =  108 bits (270), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 67/468 (14%), Positives = 130/468 (27%), Gaps = 99/468 (21%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR + +                ++ 
Sbjct: 47  ENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKADISPEVSVVRDIRERELRLYT 106

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVY 616
                  P    E   + L              ++   YR       K      +  +  
Sbjct: 107 DAGRVCRPLFIVENQQLALQKK--------HIKWLNQGYRDDDGEEFKWEQLVKSGIIEL 158

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPK 669
           L A EEE   I+     L+     +  +      G+          +        +    
Sbjct: 159 LDAEEEETVMISMPPEDLENFRLQSAGINPHENDGDFDPAARLKAGINAHTWTHCEIHLS 218

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +                          
Sbjct: 219 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------------- 259

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 260 ----------------------GMDTMANILYYPQKPLATTRSMEYLKFR---------- 287

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  
Sbjct: 288 --------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMD 333

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + + + +   E            +       +++ G+I  G  V   DI++GK  P    
Sbjct: 334 LEKKSGVQQLEEFEKPTRDSTLRMKHGTYDKLEDDGLIAPGTNVRGEDIIIGKTAPIPPD 393

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                ++        +    RD S  + S  SG V  V I       K
Sbjct: 394 SEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 434


>gi|194320194|gb|ACF48327.1| DNA-dependent RNA polymerase II second largest subunit [Bryoria
            trichodes]
          Length = 317

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 61/385 (15%), Positives = 114/385 (29%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNADGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  +                                       
Sbjct: 227  MVPDLIINPHAIPSRMTIAHLI-------------------------------------- 248

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                           + +L      +     +TP F     ++++ +LR       G  +
Sbjct: 249  ---------------ECLLSKVSSLRGFEGDATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
            +Y+G TG      V  G  Y  +L 
Sbjct: 293  MYNGHTGRKLVTQVFFGXTYYQRLR 317



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 66/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YEQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ G++  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|119640563|gb|ABL85475.1| RNA polymerase II second largest subunit [Arthonia leucopellaea]
          Length = 304

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 60/372 (16%), Positives = 106/372 (28%), Gaps = 76/372 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  +D  +R      E IE   R    +      +       +  G           
Sbjct: 68   LFYRTYVDAEKRIGINVTETIEKPFRQSTLKMRQGTYDKLDDDGLVTPGTRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++ L+ D      R++          ++     +  Q                      
Sbjct: 128  KTSPLAPDTEESGMRTKDHTKRDISTPLRGTEAGIIDQVV-------------------- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   +R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -LSTTDAMRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVGSLQGLEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     + I+ +L  A     G  ++++G TG+
Sbjct: 257  -----------------------ATP-FSPVTVDRISKLLSSAGYQSRGFEVMHNGHTGK 292

Query: 1244 PFDRPVTVGYIY 1255
                 + +G  Y
Sbjct: 293  KLVAQIFLGPTY 304



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 69/193 (35%), Gaps = 23/193 (11%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   HRMDTMMNILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +   +   E            + +     +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYVDAEKRIGINVTETIEKPFRQSTLKMRQGTYDKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++  G  V+  DI++GK +P        EE  +R     K    RD S  +  G    +
Sbjct: 111 GLVTPGTRVSGDDIIIGKTSPLA---PDTEESGMRT----KDHTKRDISTPLR-GTEAGI 162

Query: 940 VDVRIFNRHGIDK 952
           +D  + +     +
Sbjct: 163 IDQVVLSTTDAMR 175


>gi|37956408|gb|AAP15375.1| RNA polymerase beta subunit [Geobacter chapelleii]
          Length = 177

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 108/176 (61%), Positives = 139/176 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQANPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V DGK+TN+V + SA+EEE   IAQAN+ +D+DG F  +
Sbjct: 61  ASLSTYARINDHGFVETPYRIVLDGKLTNEVRFFSALEEEGHAIAQANAEVDKDGRFVND 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            V  R +GE ILV R++I+ +D +PKQ+VS+AA+LIPFLENDD+NR LMG NMQ Q
Sbjct: 121 YVSARKSGEFILVHRDEIELMDVAPKQLVSVAAALIPFLENDDANRALMGSNMQSQ 176


>gi|45593170|gb|AAS68147.1| RNA polymerase beta subunit [Desulfuromonas acetoxidans DSM 684]
          Length = 173

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 136/173 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V DG+VT+++ Y SA+EEE   IAQAN+ LD+DG F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRLVQDGRVTSEIKYFSALEEEGHAIAQANAELDDDGCFVNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           ++  R +GE +++ RE I  +D SPKQ+VS+AA+LIPFLENDD+NR LMG NM
Sbjct: 121 VINARQSGEFMMLRREDIQLMDVSPKQLVSVAAALIPFLENDDANRALMGSNM 173


>gi|119640663|gb|ABL85525.1| RNA polymerase II second largest subunit [Roccellina accedens]
 gi|119640665|gb|ABL85526.1| RNA polymerase II second largest subunit [Roccellina cerebriformis]
 gi|119640671|gb|ABL85529.1| RNA polymerase II second largest subunit [Roccellina flavida]
 gi|119640679|gb|ABL85533.1| RNA polymerase II second largest subunit [Roccellina limitata]
 gi|119640687|gb|ABL85537.1| RNA polymerase II second largest subunit [Roccellaria mollis]
 gi|119640689|gb|ABL85538.1| RNA polymerase II second largest subunit [Roccellina nigricans]
 gi|119640699|gb|ABL85543.1| RNA polymerase II second largest subunit [Roccellina terrestris]
 gi|330785326|gb|AEC46469.1| RNA polymerase II second largest subunit [Roccellina cerebriformis]
 gi|330785328|gb|AEC46470.1| RNA polymerase II second largest subunit [Roccellina cerebriformis]
 gi|330785330|gb|AEC46471.1| RNA polymerase II second largest subunit [Roccellina cerebriformis]
 gi|330785332|gb|AEC46472.1| RNA polymerase II second largest subunit [Roccellina cerebriformis]
 gi|330785340|gb|AEC46476.1| RNA polymerase II second largest subunit [Roccellina flavida]
 gi|330785348|gb|AEC46480.1| RNA polymerase II second largest subunit [Roccellina mahuiana]
 gi|330785350|gb|AEC46481.1| RNA polymerase II second largest subunit [Roccellina nigricans]
 gi|330785352|gb|AEC46482.1| RNA polymerase II second largest subunit [Roccellina terrestris]
          Length = 307

 Score =  185 bits (470), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 111/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGFEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|119640629|gb|ABL85508.1| RNA polymerase II second largest subunit [Roccella maderensis]
 gi|119640633|gb|ABL85510.1| RNA polymerase II second largest subunit [Roccella maderensis]
 gi|256808300|gb|ACV30281.1| RNA polymerase II second largest subunit [Roccella fuciformis]
          Length = 307

 Score =  185 bits (470), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGEEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|307547653|gb|ADN44440.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  185 bits (470), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVAFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVAFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640701|gb|ABL85544.1| RNA polymerase II second largest subunit [Schismatomma pericleum]
          Length = 307

 Score =  185 bits (470), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/375 (16%), Positives = 107/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   +    + +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPPRAQTMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VK+     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTDGKRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSSITGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSDISELLQFAGYQSRGLEMMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 72/196 (36%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN-----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E     P            + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPPRAQTMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTDG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKIRTRTTKVPQI 192


>gi|119640669|gb|ABL85528.1| RNA polymerase II second largest subunit [Roccella tinctoria]
          Length = 307

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 64/375 (17%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMTEN------------SEGGQRTKDHKKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F      +I+ +L  A     G  ++Y+G 
Sbjct: 260  --------------------------ATP-FTDITVSSISELLEFAGYQSRGFXMMYNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 71/187 (37%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++PMT   +  +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPF-QAPMTENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|119644296|gb|ABL85617.1| RNA polymerase II second largest subunit [uncultured Ascomycota]
          Length = 326

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 65/392 (16%), Positives = 111/392 (28%), Gaps = 81/392 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 13   DTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 72

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R        +E   +    + + +    Y +L +   I  G   
Sbjct: 73   LF-RSLFYRAYLDQEKRVGM---SVVEAFEKPIRSDTLKMKGGTYDKLDDDGIISPGARV 128

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 129  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIIDQVLL----------- 177

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV     +  Q GDK A RHG KG +      EDMPF  DG
Sbjct: 178  ---------TTNVEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSADG 228

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L       G++  +          IS L       
Sbjct: 229  LVPDIIINPHAIPSRMTIAHLIECLLSKVAALTGQEGDATPFTEVTITSISALLE----- 283

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                V     +G  ++  VF                        
Sbjct: 284  ----------QHGFQKRGFEVMYNGHTGKKLAAQVF------------------------ 309

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                           +G  Y  +L HMV DK+
Sbjct: 310  ---------------LGPTYYQRLRHMVDDKI 326



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/185 (20%), Positives = 66/185 (35%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      DL  G+N +VA   + G
Sbjct: 6   TNFNVRMDTMANVLYYPQKPL----------ATTRSMEFLKFRDLPAGQNAIVAIACYSG 55

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     I  D   +       
Sbjct: 56  YNQEDSVIMNQSSIDRGLFRSLFYRAYLDQEKRVGMSVVEAFEKPIRSDTLKMKGGTYDK 115

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GII  GA V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 116 LDDDGIISPGARVSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGI 171

Query: 936 SGTVV 940
              V+
Sbjct: 172 IDQVL 176


>gi|211956396|ref|YP_002302465.1| RNA polymerase subunit RPO132 [Deerpox virus W-1170-84]
 gi|115503191|gb|ABI99109.1| RNA polymerase subunit RPO132 [Deerpox virus W-1170-84]
          Length = 1155

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 73/431 (16%), Positives = 139/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  I P+    ++   +  +         V    +     +   G ++  +  +R G
Sbjct: 703  DNGIHLIYPERPIVISKALETSKIAVNCFGQHVTIALMSYKGINQEDGIIIKRQFVDRGG 762

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 763  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLESNGLVRLNAFLESG 809

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++       Y++    ++    +K++          
Sbjct: 810  DAIARNISSRTLEDDFVHDNQISFDISDRYTDMYKSRVERVQVDLTDKVK---------- 859

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG ++ I    ++P+ ++G   D+++N   + 
Sbjct: 860  -----VRVLTMKERKPILGDKFTSRTSQKGTIAYIADESELPYDENGIKPDVIINSTSIF 914

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A          K + +         I    +F +K   T      
Sbjct: 915  SRKTLSMLVEVILTSAYACKPYNNSGKNRPICFPSSNETTIDTYLNFAKKCYETIYPDLT 974

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              +  D                                            +LYD  T  P
Sbjct: 975  EDELTDKVFCDK--------------------------------------VLYDPETDRP 996

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 997  YMSKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRRGGGIKFGEMERDCLIA 1056

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1057 HGAANTITEVL 1067



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 78/568 (13%), Positives = 180/568 (31%), Gaps = 47/568 (8%)

Query: 372 DALLDIYRVM--RPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
           +A+++  +    +  D         +    +            + +M         D   
Sbjct: 257 NAIIENTKEFINKNNDFDIDLYINELILDEYNKQKSQLSIEEFKYEMIHNFLPHMNDTPN 316

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            ++   II++++  +          D D++   RV + G+  +      L     +IK  
Sbjct: 317 QLKGFYIISLLRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILAHDELENYIGNIKN- 375

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV 549
               +  +     +             F      + ++   S     H   +  +     
Sbjct: 376 DIINNHKNRGVYSVNIHVLTTPGFNHAFSGLLSGKFKKTDGSYRTHPHYSWMQNISIPRS 435

Query: 550 A-------RARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARV-----NAYG 596
                   +      +R  HP+ Y   CP++  E G  +GLVS L+    +     N Y 
Sbjct: 436 VGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLSVLTSITNICTNEYL 495

Query: 597 FIETPYRKVCDGKVTNDVVYLSA---MEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            +E    +       ND+ Y      +  EN  IA  N  L ++              + 
Sbjct: 496 ELEKKICQYIRSYDINDISYFETGYYITLENSLIASLNPKLVDNFVIDFRRKKRMGYFDN 555

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL------MGCNMQRQAVPLLKAE 707
           + +    +       +  +     + PFL  DD N ++      +   ++      ++ E
Sbjct: 556 LEIGITLVRDHMNEIRINIGGGRLVRPFLVIDDGNLIMDDIMDDLESKLEDMTFSDIQKE 615

Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-----EGDLDPSTSGVDIY 762
            P V   ++      S      ++   + + + I+  +        +G +  S  G++  
Sbjct: 616 FPHVIEMVDIEQFTFSNVCESVQKFRTLPKNERIKFHLCDFPAEFRDGYVASSLVGINHN 675

Query: 763 R-------LMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPSTDLGDL---ALGRNM 811
                     + +++      + R  +  G   +     I    + +   +     G+++
Sbjct: 676 SGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLIYPERPIVISKALETSKIAVNCFGQHV 735

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
            +A M + G N ED ++I  + V       I  ++ +V        P E   +   V   
Sbjct: 736 TIALMSYKGINQEDGIIIKRQFVDRGGLDIITAKKHQVEI------PLENFNNKERVKST 789

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKIT 899
               ++  G++ + A +  GD +   I+
Sbjct: 790 AYSKLESNGLVRLNAFLESGDAIARNIS 817


>gi|89888254|gb|ABD78667.1| DNA-directed RNA polymerase beta subunit [Bordetella holmesii]
          Length = 269

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 96/271 (35%), Positives = 158/271 (58%), Gaps = 3/271 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F+    +  + +             G      + D  +G+ ++E  K++ +  L+ L   
Sbjct: 1   FFDFDNFELKSEGAMMEFVPE-RWKGEMARFDISD-RSGKVIVEKDKRINAKHLRDLANA 58

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
           G++ + +  D L G  +A+++V+ +TGE+   A D I E  L  +  +++ D+  LY + 
Sbjct: 59  GIQRISVPEDFLFGRVLAKNVVDADTGEVIAHANDEITESVLAAMRDAKVLDLQALYTND 118

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           ++   YI  TL TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS +
Sbjct: 119 LDRGPYISQTLRTDETADQTAARVAIYRMMRPGEPPTEEAVEAVFQRLFYSEESYDLSRI 178

Query: 412 GRVKMNMRLNL-DTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           GR+K+N RL   D       +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+
Sbjct: 179 GRMKVNSRLGRGDDAXGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGEL 238

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQ 501
            +NQ+R GL+R+ER++KER+   + +++MP 
Sbjct: 239 AENQFRAGLVRVERAVKERLGQAETENLMPH 269


>gi|119640591|gb|ABL85489.1| RNA polymerase II second largest subunit [Roccella allorgei]
 gi|119640595|gb|ABL85491.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|119640597|gb|ABL85492.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|119640601|gb|ABL85494.1| RNA polymerase II second largest subunit [Roccella canariensis]
 gi|119640605|gb|ABL85496.1| RNA polymerase II second largest subunit [Roccella elisabethae]
 gi|119640607|gb|ABL85497.1| RNA polymerase II second largest subunit [Roccella elisabethae]
 gi|119640655|gb|ABL85521.1| RNA polymerase II second largest subunit [Roccella tinctoria]
 gi|119640657|gb|ABL85522.1| RNA polymerase II second largest subunit [Roccella tinctoria]
 gi|119640661|gb|ABL85524.1| RNA polymerase II second largest subunit [Roccella tuberculata]
 gi|256808380|gb|ACV30321.1| RNA polymerase II second largest subunit [Roccella tuberculata]
 gi|307547557|gb|ADN44392.1| RNA polymerase II second largest subunit [Roccella applanata]
 gi|307547561|gb|ADN44394.1| RNA polymerase II second largest subunit [Roccella applanata]
 gi|307547563|gb|ADN44395.1| RNA polymerase II second largest subunit [Roccella applanata]
 gi|307547565|gb|ADN44396.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547567|gb|ADN44397.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547569|gb|ADN44398.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547571|gb|ADN44399.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547573|gb|ADN44400.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547575|gb|ADN44401.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547577|gb|ADN44402.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547579|gb|ADN44403.1| RNA polymerase II second largest subunit [Roccella babingtonii]
 gi|307547595|gb|ADN44411.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547597|gb|ADN44412.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547599|gb|ADN44413.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547601|gb|ADN44414.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547603|gb|ADN44415.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547605|gb|ADN44416.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547607|gb|ADN44417.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547609|gb|ADN44418.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547611|gb|ADN44419.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547613|gb|ADN44420.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547615|gb|ADN44421.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547617|gb|ADN44422.1| RNA polymerase II second largest subunit [Roccella boryi]
 gi|307547619|gb|ADN44423.1| RNA polymerase II second largest subunit [Roccella boryi]
          Length = 307

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|50058765|gb|AAT69135.1| RNA polymerase II [Schizanthus pinnatus]
          Length = 272

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 49/203 (24%), Positives = 70/203 (34%), Gaps = 54/203 (26%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 122  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 181

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+  +         +IS         +         
Sbjct: 182  AIPSRMTIGQLIECVMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM--- 238

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                                         +G +    G    P 
Sbjct: 239  --------------------------------------------YNGHT----GR---PL 247

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVY 1268
               + +G  Y  +L HMV DK++
Sbjct: 248  TAMIFLGPTYYQRLKHMVDDKIH 270



 Score = 65.1 bits (157), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 44/124 (35%), Gaps = 14/124 (11%)

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
            N EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 1   SNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 60

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 61  LDDDGIAPPGTRVSGEDVIIGKTTPIAQDD---------AQGQATRYTKRDHSTSLRHSE 111

Query: 936 SGTV 939
           +G V
Sbjct: 112 TGMV 115


>gi|221043492|dbj|BAH13423.1| unnamed protein product [Homo sapiens]
          Length = 924

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 101/562 (17%), Positives = 175/562 (31%), Gaps = 99/562 (17%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 427  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 485

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 486  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 545

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 546  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 595

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 596  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 653

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A R G K                            G+ SR+
Sbjct: 654  KCVCITMRVPRNPTIGDKFASRRGQK----------------------------GILSRL 685

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 686  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 720

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 721  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 780

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 781  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 840

Query: 1309 YVLQEMLTIKSD----DV---VG-----------------RTRVYESIV--AGNDTFETG 1342
            ++L + L   SD     V    G                 R R Y   +    +      
Sbjct: 841  FLLHDRLFNCSDRSVAHVCVKCGSLLSPLLEKPPPSWSAMRNRKYNCTLCSRSDTIDTVS 900

Query: 1343 TPESFNVLVKEMQALGLSIDLE 1364
             P  F   V E+ A+ + + L+
Sbjct: 901  VPYVFRYFVAELAAMNIKVKLD 922



 Score = 88.6 bits (218), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 97/664 (14%), Positives = 216/664 (32%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 42  LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 93

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 94  GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 151

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDS-VMPQDLIN 505
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++  + +    
Sbjct: 152 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIFTM 211

Query: 506 AKPVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 212 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 268

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 269 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 328

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 329 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 388

Query: 666 ASPKQVVSI--------AASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            + K  +             + P          L+G   Q      +  +  F G     
Sbjct: 389 MTGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 448

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 449 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ- 504

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 505 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 554

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 555 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 614

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 615 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 669

Query: 953 NERS 956
           ++ +
Sbjct: 670 DKFA 673


>gi|207109782|ref|ZP_03243944.1| DNA-directed RNA polymerase subunit beta/beta' [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 156

 Score =  185 bits (469), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 60/157 (38%), Positives = 99/157 (63%), Gaps = 4/157 (2%)

Query: 143 TFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDII 202
           +F+I G++R+VV+QLHRSPG+ F  ++   SL+ KL+Y  +IIPD+G W+  E+DSKD++
Sbjct: 3   SFIINGVERVVVNQLHRSPGVIFKEEESSTSLN-KLIYTGQIIPDRGSWLYFEYDSKDVL 61

Query: 203 HVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSS 262
           + RI++RRKVPVT    A+    ++I+  FYP +      D +  P ++ D     ++  
Sbjct: 62  YARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLD--ANQRMEF 119

Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT 299
            L D   G+ ++ +GKKLTS  +K LKE  ++++   
Sbjct: 120 DLKDSQ-GKIILLAGKKLTSRKIKELKENHLEWVEYP 155


>gi|119640667|gb|ABL85527.1| RNA polymerase II second largest subunit [Roccellina chalybea]
 gi|330785334|gb|AEC46473.1| RNA polymerase II second largest subunit [Roccellina chalybea]
          Length = 307

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 111/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEDFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGFEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 65/187 (34%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        +         + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEDFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|310750834|gb|ADP09210.1| RpoB' [Halococcus morrhuae DSM 1307]
          Length = 173

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 52/196 (26%), Positives = 76/196 (38%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  I P EDMPF ++G   D+++NP  +
Sbjct: 31   EDGSKLSKVSVRDQRVPELGDKFASRHGQKGVVGHIAPQEDMPFTEEGVVPDLIVNPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +   ++                      
Sbjct: 91   PSRMTVGHVLEMLGGKVGSLEGRRVDGTAFTGEEEEELRSSLEEHG-------------- 136

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                   FD                  SG+ I++ G+TGE  D 
Sbjct: 137  -----------------------FD-----------------SSGKEIMHSGVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGTIFYQKLYHMV 172


>gi|119640593|gb|ABL85490.1| RNA polymerase II second largest subunit [Roccella allorgei]
          Length = 307

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 58/375 (15%), Positives = 106/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +       Q  +   + +       +     +                 
Sbjct: 125  IIGKTAPFQAPMQENAXGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-------------- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 75/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P       P ++        K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPF----QAPMQENAXGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|307547643|gb|ADN44435.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547785|gb|ADN44506.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 305

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 7    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 66

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 67   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 122

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 123  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 168

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 169  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 224

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 225  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 257

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 258  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 290

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 291  TGRKLNAQVFLGPTY 305



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 73/204 (35%), Gaps = 20/204 (9%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
               +      Q+PL                      DL  G+N +VA   + GYN EDS
Sbjct: 1   MDTMSNILYYPQKPL----------ASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +       E        ++        + +D+ G+
Sbjct: 51  VIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGL 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +  
Sbjct: 111 VPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDR 166

Query: 942 VRIFNRHGIDKNE-RSISVEREQI 964
           V +    G    + R+ + +  QI
Sbjct: 167 VLLTTTEGKRSVKVRTRTTKVPQI 190


>gi|46277296|gb|AAS86838.1| DNA-dependent RNA polymerase II [Iodophanus hyperboreus]
          Length = 552

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 61/374 (16%), Positives = 112/374 (29%), Gaps = 81/374 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 257  ILYYPQKPLGTTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RS 315

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G        
Sbjct: 316  LFFRTYMDQEKR---IGMSVVEEFEKPMRSNTLRLKHGTYDKLDDDGLVAPGIRVTGDDI 372

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  LS+D      R+++         ++     +  Q                   
Sbjct: 373  IIGKTAPLSADNPEAGQRTKFHSKRDVSTPLRSTESGIVDQ------------------- 413

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 414  -VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVPDL 472

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 473  IINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD--------------------------- 505

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 506  --------------------------ATP-FTEVTVDSVSKLLREHGYQSRGFEVMYNGH 538

Query: 1241 TGEPFDRPVTVGYI 1254
            TG      V +G  
Sbjct: 539  TGRKLVAQVFLGPT 552



 Score = 88.2 bits (217), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 47/298 (15%), Positives = 93/298 (31%), Gaps = 26/298 (8%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           I++IDA  ++ + I  +      +   +           +  +  +   F  T       
Sbjct: 147 IEYIDAEEEETIMIVMTPEDLEISRQIHAGYDVEIELEPSQRVKTSMKKFAHT---WTHC 203

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQR 779
           +   + I+   A I+   D  +                                    Q+
Sbjct: 204 EVHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXILYYPQK 263

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL                      +L  G+N +VA + + GYN EDS+++++  +   +F
Sbjct: 264 PL----------GTTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 313

Query: 840 TSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S+    +    +   +   E     +  +   +       +D+ G++  G  V   DI+
Sbjct: 314 RSLFFRTYMDQEKRIGMSVVEEFEKPMRSNTLRLKHGTYDKLDDDGLVAPGIRVTGDDII 373

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P         ++        K    RD S  + S  SG V  V +       K
Sbjct: 374 IGKTAPLSADNPEAGQRT-------KFHSKRDVSTPLRSTESGIVDQVMVTTNQEGLK 424


>gi|307547633|gb|ADN44430.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/374 (16%), Positives = 107/374 (28%), Gaps = 77/374 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--ILCGQNAVSGPKG 1001
             +  +     E+  SV    +E   + +  E +      Y +L +  ++     VSG   
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                T      + E               V   + S +        +             
Sbjct: 125  IIGKTAPFQAPLQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLL------------- 171

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D++
Sbjct: 172  ----TTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLI 227

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G++                              
Sbjct: 228  INPHAIPSRMTIAHLIECLLSKVSTVTGQEGD---------------------------- 259

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F       I+ +LR A     G  ++++G T
Sbjct: 260  -------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGHT 293

Query: 1242 GEPFDRPVTVGYIY 1255
            G   +  V +G  Y
Sbjct: 294  GRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 75/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P       P ++        K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPF----QAPLQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|283806279|dbj|BAI66378.1| RNA polymerase second largest subunit [Massarina arundinariae]
          Length = 303

 Score =  185 bits (469), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 108/375 (28%), Gaps = 81/375 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 7    YPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 65

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L E   +  G           
Sbjct: 66   RAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDEDGVVAPGVRVSGDDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + +D      ++           ++     +  Q                      
Sbjct: 123  KTAPIPTDAKELGQKTALHTKRDVSTPLRSTENGIVDQ--------------------VL 162

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF   G   DI++N
Sbjct: 163  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSQGLTPDIIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L      +G++                                
Sbjct: 223  PHAIPSRMTIAHLVECLLSKVGAVIGQEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E I+ +LR     + G  I+Y+G TG+
Sbjct: 253  -----------------------ATP-FTDVTVENISEILRNNGFQQRGFEIMYNGHTGK 288

Query: 1244 PFDRPVTVGYIYMLK 1258
                       Y  +
Sbjct: 289  KLRAQDLFRSTYYQR 303



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 63/176 (35%), Gaps = 19/176 (10%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 1   MMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIM 50

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +DE G++  
Sbjct: 51  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDEDGVVAP 110

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           G  V+  DI++GK  P      T  ++L +        DV        +G+   V+
Sbjct: 111 GVRVSGDDIIIGKTAPI----PTDAKELGQKTALHTKRDVSTPLRSTENGIVDQVL 162


>gi|119640683|gb|ABL85535.1| RNA polymerase II second largest subunit [Roccellina mahuiana]
          Length = 307

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 111/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGXEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|18640199|ref|NP_570273.1| SPV113 RNA polymerase subunit RPO132 [Swinepox virus]
 gi|18448606|gb|AAL69852.1| SPV113 RNA polymerase subunit RPO132 [Swinepox virus]
          Length = 1162

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 80/431 (18%), Positives = 142/431 (32%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +         V    +     +   G ++     NR G
Sbjct: 709  DNGIHLLYPERPIVISKALETSKIAVNCFGQHVIIALMSYKGINQEDGIIIKKEFINRGG 768

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              + A+    E  + + N   R+      +   +G           
Sbjct: 769  LDI-------------ITAKKHQVEIPLENFNNKERVKSTAYSKLDSNGLVRLNAFLESG 815

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             VQD ++  ++       Y++    ++    +K++          
Sbjct: 816  DAIARNISSRTLEDDFVQDNQISFDISDRYTDMYKSRVERVQVDLTDKVK---------- 865

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+V    +R    GDK   R   KG V+ I    ++P+ ++G   DI++N   + 
Sbjct: 866  -----VRVLTMKERRPILGDKFTSRTSQKGTVAFIANESELPYDENGIRPDIIVNSTSIF 920

Query: 1129 SRMNVGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  V  + E  L  A            + +        +I     F +K          
Sbjct: 921  SRKTVSMLIEVILTSAYASKPYNNNGYNRPVCFPSSNETNIDTYLEFAKKCHEHLYTDLS 980

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
            ISD +D                   VF                       +LYD  T  P
Sbjct: 981  ISDINDK------------------VF--------------------CNKVLYDPETDMP 1002

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A
Sbjct: 1003 YKTKVFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRRKGGGIKFGEMERDCLIA 1062

Query: 1305 YGAAYVLQEML 1315
            +GAA  + E+L
Sbjct: 1063 HGAANTITEIL 1073



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 88/644 (13%), Positives = 210/644 (32%), Gaps = 53/644 (8%)

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
           +Y     V        ++  ++ + +   D+  +     + +  +            +  
Sbjct: 253 SYDMPEEVIFLVNSIIESTKELIKSIHDFDIDIYIN--DLISSEYNKQKSQMTIEEFKYD 310

Query: 416 MNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQY 475
           M         +    ++   II++I+  +          D D++   RV + G+  +   
Sbjct: 311 MITNFLPHMNELPNQLKGFYIISLIRKFIYCIYYTSRYPDRDSMVCHRVLTYGKYFEILA 370

Query: 476 RLGLLRMERSIK--ERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
              L     +I+     +  +  +      +   P  +       S +  + +    +  
Sbjct: 371 HDELENYINNIRTDIINNHKNRGTYSVNIHVLTTPGFNHAYSGLLSGKFKKTDGSYRTHP 430

Query: 534 RITHTRRLSALGQGGV----ARARAGVEMRDVHPTHYGRICPAETSE-GHNIGLVSSLTS 588
             +  + +S     G      +      +R  HP+ Y   CP++  E G  +GLVS L+ 
Sbjct: 431 HYSWMQNISIPRSVGYYPDQVKISKMFSVRKYHPSQYAYFCPSDVPERGPQVGLVSQLSV 490

Query: 589 FARVNAYGFIETPYRK------VCDGKVTNDVVYLS--AMEEENRYIAQANSSLDEDGSF 640
              +      E  Y +      V     T+   + +  ++  EN  IA  N S+ +D   
Sbjct: 491 LTSITNICTNEYLYLEKRICEYVRSYDATDISYFETGFSITLENALIASLNPSMVDDFVS 550

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG----CNM 696
                        + +    +       +  +     + PFL  D+   ++        +
Sbjct: 551 DFRRKKRMGYFRNLEIGITLVKDHMNEIRINIGSGRLIRPFLVIDNGELIMDTLDLYSKI 610

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS-----VEGD 751
           +      ++ E P V   ++      S      ++   + + D  R  +        +G 
Sbjct: 611 EDMTFSDIQKEFPHVIEMVDIEQFIFSNVCESVQKFRTLSKSDRYRYHLCDFPAEFKDGY 670

Query: 752 LDPSTSGVDIYR-------LMKFQRSNQNTCVNQRPLVKVGD---EVRRNDIIADGPSTD 801
           +  S  G++            + +++      + R  +  G       R  +I+    T 
Sbjct: 671 VASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLLYPERPIVISKALETS 730

Query: 802 LGDL-ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +   G+++++A M + G N ED ++I +  ++      I  ++ +V        P E
Sbjct: 731 KIAVNCFGQHVIIALMSYKGINQEDGIIIKKEFINRGGLDIITAKKHQVEI------PLE 784

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
              +   V       +D  G++ + A +  GD +      +  S  T E+  ++    + 
Sbjct: 785 NFNNKERVKSTAYSKLDSNGLVRLNAFLESGDAI-----ARNISSRTLEDDFVQD--NQI 837

Query: 921 AVDVRDTSLRVPSGVSGTV---VDVRIFNRHGIDKNERSISVER 961
           + D+ D    +       V   +  ++  R    K  R I  ++
Sbjct: 838 SFDISDRYTDMYKSRVERVQVDLTDKVKVRVLTMKERRPILGDK 881


>gi|119640635|gb|ABL85511.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|119640637|gb|ABL85512.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|119640639|gb|ABL85513.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|119640641|gb|ABL85514.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547637|gb|ADN44432.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547647|gb|ADN44437.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547649|gb|ADN44438.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547651|gb|ADN44439.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547655|gb|ADN44441.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547657|gb|ADN44442.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547659|gb|ADN44443.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547661|gb|ADN44444.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547663|gb|ADN44445.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547665|gb|ADN44446.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547669|gb|ADN44448.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547679|gb|ADN44453.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547681|gb|ADN44454.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547683|gb|ADN44455.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547685|gb|ADN44456.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547687|gb|ADN44457.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547689|gb|ADN44458.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547691|gb|ADN44459.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547693|gb|ADN44460.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547695|gb|ADN44461.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547697|gb|ADN44462.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547699|gb|ADN44463.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547701|gb|ADN44464.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547703|gb|ADN44465.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547705|gb|ADN44466.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547707|gb|ADN44467.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547709|gb|ADN44468.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547711|gb|ADN44469.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547713|gb|ADN44470.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547715|gb|ADN44471.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547717|gb|ADN44472.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547719|gb|ADN44473.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547721|gb|ADN44474.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547723|gb|ADN44475.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547725|gb|ADN44476.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547727|gb|ADN44477.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547729|gb|ADN44478.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547731|gb|ADN44479.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547733|gb|ADN44480.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547735|gb|ADN44481.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547737|gb|ADN44482.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547739|gb|ADN44483.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547741|gb|ADN44484.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547743|gb|ADN44485.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547745|gb|ADN44486.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547747|gb|ADN44487.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547749|gb|ADN44488.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547751|gb|ADN44489.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547753|gb|ADN44490.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547759|gb|ADN44493.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547761|gb|ADN44494.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547763|gb|ADN44495.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547767|gb|ADN44497.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547789|gb|ADN44508.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 63/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640645|gb|ABL85516.1| RNA polymerase II second largest subunit [Roccella phycopsis]
          Length = 307

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGHEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|151573320|gb|ABS17878.1| RNA polymerase II [Fusarium sp. NRRL 43690]
          Length = 295

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 57/368 (15%), Positives = 102/368 (27%), Gaps = 75/368 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVGYI 1254
              V  G  
Sbjct: 288  AQVFFGPT 295



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|89888198|gb|ABD78643.1| DNA-directed RNA polymerase beta subunit [Bordetella petrii]
          Length = 274

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 99/275 (36%), Positives = 157/275 (57%), Gaps = 3/275 (1%)

Query: 232 FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEK 291
           F+    +  + +             G      +     G  ++E  K++ +  L+ +   
Sbjct: 1   FFDFDNFELKSEGGMIEFVPE-RWKGEMARFDI-TGRDGNVIVEKDKRINAKHLRDMANA 58

Query: 292 GVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDS 351
            ++ + +  + L G  +A++IV+ +TGE+   A D I E  L  +  + +RDI  LY + 
Sbjct: 59  NIQRVSVPEEFLYGRVLAKNIVDPDTGEVVAHANDEITESVLSALRAANVRDIQTLYTND 118

Query: 352 VNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTV 411
           ++   YI  TL TD+  D+  A + IYR+MRPG+  T    E++F  LF+  + YDLS V
Sbjct: 119 LDRGPYISQTLRTDETADQMAARVAIYRMMRPGEPPTEDAVEALFQRLFYSEETYDLSRV 178

Query: 412 GRVKMNMRLNLDTP-DDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEM 470
           GR+K+N RL           +  EDI+  IK+LV+LRNG+G IDDID+LGNRRVR VGE+
Sbjct: 179 GRMKVNSRLGRGEDITGPMTLTNEDILETIKVLVELRNGRGQIDDIDHLGNRRVRCVGEL 238

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
            +NQ+R GL+R+ER++KER+   + +++MP DLIN
Sbjct: 239 AENQFRAGLVRVERAVKERLGQAETENLMPHDLIN 273


>gi|327239549|gb|AEA39624.1| RpoB [Corynebacterium striatum]
 gi|327239551|gb|AEA39625.1| RpoB [Corynebacterium striatum]
          Length = 138

 Score =  184 bits (468), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 59/166 (35%), Positives = 86/166 (51%), Gaps = 36/166 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+           +   L++  E++                   
Sbjct: 1    QVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 40   -------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQ
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQ 138


>gi|119640673|gb|ABL85530.1| RNA polymerase II second largest subunit [Roccella hypomecha]
 gi|119640675|gb|ABL85531.1| RNA polymerase II second largest subunit [Roccella hypomecha]
 gi|330785342|gb|AEC46477.1| RNA polymerase II second largest subunit [Roccellina hypomecha]
          Length = 307

 Score =  184 bits (468), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 61/376 (16%), Positives = 111/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  S+    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSIGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VK+     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGLEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSIGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKIRTRT 186


>gi|34923332|gb|AAQ83553.1| RpoB [Pasteurella bettyae]
          Length = 173

 Score =  184 bits (467), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 107/173 (61%), Positives = 134/173 (77%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANSSLD++  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSSLDDELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D SP+QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIHYMDVSPQQVVSVAAALIPFLEHDDANRAL 173


>gi|270000437|gb|ACZ58066.1| RNA polymerase II [Fusarium sp. NRRL 44906]
 gi|270000439|gb|ACZ58067.1| RNA polymerase II [Fusarium sp. NRRL 46437]
 gi|270000441|gb|ACZ58068.1| RNA polymerase II [Fusarium sp. NRRL 46438]
 gi|270000445|gb|ACZ58070.1| RNA polymerase II [Fusarium sp. NRRL 46443]
 gi|270000449|gb|ACZ58072.1| RNA polymerase II [Fusarium sp. NRRL 46598]
          Length = 298

 Score =  184 bits (467), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 104/373 (27%), Gaps = 75/373 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  I+Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGH 285

Query: 1241 TGEPFDRPVTVGY 1253
            TG      V  G 
Sbjct: 286  TGRKLRAQVFFGP 298



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|218683111|gb|ACL00600.1| RNA polymerase beta subunit [Aeromonas tecta]
          Length = 170

 Score =  184 bits (467), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 99/170 (58%), Positives = 131/170 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  E+G 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATSEEGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANR 170


>gi|312204376|gb|ADQ47505.1| RNA polymerase II second largest subunit [Thelotrema saxatile]
          Length = 291

 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 111/369 (30%), Gaps = 81/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +++ +R        +E   +    E + L    Y +L +   I  G        
Sbjct: 60   LFYRAYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYEKLDDDGLIAPGVRVSGEDV 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D      R++          ++     +                  ++K+
Sbjct: 117  IIGKTAPIAPDTEELGQRTKLHSKRDASTPLRSTENGI------------------VDKV 158

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 159  LL--TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDL 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 249

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 250  --------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGH 282

Query: 1241 TGEPFDRPV 1249
            TG      +
Sbjct: 283  TGRKLRAQI 291



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/183 (19%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +     + +D+ G+I  G  V+
Sbjct: 53  DRGLFRSLFYRAYVEQEKRVGMSLVEQFEKPLRSETLRLKHGTYEKLDDDGLIAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 113 GEDVIIGKTAPIAPDTEELGQRT-------KLHSKRDASTPLRSTENGIVDKVLLTTNQE 165

Query: 950 IDK 952
             K
Sbjct: 166 GLK 168


>gi|46277378|gb|AAS86879.1| DNA-dependent RNA polymerase II [Peziza varia]
          Length = 551

 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 60/357 (16%), Positives = 106/357 (29%), Gaps = 75/357 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R  
Sbjct: 270  MEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYMDQEKRVG 328

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   R           +       +  G           K+  +S ++     
Sbjct: 329  MNVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPISPNMEELGQ 388

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+++         ++     +  Q                             L+ VKV 
Sbjct: 389  RTKFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFVKVR 428

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + 
Sbjct: 429  MRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVPDIIINPHAIPSRMTIAHLI 488

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 489  ECQLSKVSSLRGFEGD-------------------------------------------- 504

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                     +TP F     ++++ +LR       G  I+Y+G TG      V +G  
Sbjct: 505  ---------ATP-FTDVTVDSVSRLLREHGYQSRGFEIMYNGHTGRKLVVQVFLGPT 551



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 67/481 (13%), Positives = 121/481 (25%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR + +
Sbjct: 16  DFMLQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQNHI 69

Query: 545 G-QGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           G +  + +     E        R   P       PA    G  +     +          
Sbjct: 70  GHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDKDIT 129

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
             E  Y           V Y+ A EEE   I      L+    F                
Sbjct: 130 DEEQRY-GWSGLIGEGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQ--------- 179

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P Q V  + +                                       
Sbjct: 180 -------TEVDPAQRVKASVNKY----------------------------------AHT 198

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
               +   + I+   A I+   D  +                                  
Sbjct: 199 WTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 258

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
                                      +L  G+N +VA + + GYN EDS+++++  +  
Sbjct: 259 X---------XXXXXXXSRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDR 309

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E        +   +       +DE G++  G  V+  
Sbjct: 310 GLFRSLFYRTYMDQEKRVGMNVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVSGE 369

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P      +P  + L      K    RD S  + S  +G V  V +       
Sbjct: 370 DIIIGKTAPI-----SPNMEELGQR--TKFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 422

Query: 952 K 952
           K
Sbjct: 423 K 423


>gi|330785408|gb|AEC46510.1| RNA polymerase II second largest subunit [Fulvophyton murex]
 gi|330785410|gb|AEC46511.1| RNA polymerase II second largest subunit [Fulvophyton murex]
          Length = 307

 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 60/377 (15%), Positives = 105/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E+ E  A+           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDEDGFVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR  E  K          E    +++ 
Sbjct: 123  DIIIGKTAPFQAPMQENA------------EGGQRTKEHTKRDVSAPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L         +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVSATQAMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+ +L+ A     G  ++Y+
Sbjct: 260  ----------------------------ATP-FTEVTVSGISQLLKDAGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG   +  + +G  Y
Sbjct: 291  GYTGRKLNAQIFLGPTY 307



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 61/197 (30%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       E                    +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P         E   R        DV        +G+   V
Sbjct: 111 GFVAPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRTKE-HTKRDVSAPLRSTEAGIIDRV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTTDGRRSVKVRTRT 186


>gi|330785188|gb|AEC46400.1| RNA polymerase II second largest subunit [Arthothelium sp. Tehler
            9330]
          Length = 304

 Score =  184 bits (467), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 109/372 (29%), Gaps = 84/372 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     V++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVVMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 68   LYYRTYIEQEQTVGIQVLEEFEKPIKSQTLRMRPGTYDKLDDDGIVAPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L  ++               +E+  R     K    T     E    +++      
Sbjct: 128  KTAPLPQNV---------------EERGMRQTSHTKRDVSTPLRSTESGIVDQVL----- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVAATNALEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +LR +     G  ++Y+G TG 
Sbjct: 257  -----------------------ATP-FTDVTVENVSQLLRESGYQSRGFEVMYNGHTGR 292

Query: 1244 PFDRPVTVGYIY 1255
                 + +G  Y
Sbjct: 293  KLVAQIFLGPTY 304



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 40/187 (21%), Positives = 74/187 (39%), Gaps = 12/187 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVVMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQTVGIQVLEEFEKPIKSQTLRMRPGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++    EE+ +R        DV        SG+   V+   +  +  
Sbjct: 121 GDDIIIGKTAPLPQNV---EERGMRQTS-HTKRDVSTPLRSTESGIVDQVLLTSVDGKKN 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKIRTRT 183


>gi|103002027|gb|ABF71533.1| DNA-dependent RNA polymerase II second largest subunit [Pleopsidium
            sp. Zhurbenko 92515]
          Length = 305

 Score =  184 bits (467), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/383 (16%), Positives = 109/383 (28%), Gaps = 81/383 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 1    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 59

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D+ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 60   RSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIG 116

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R++          ++     +  Q                      
Sbjct: 117  KTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL------------------- 157

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG +      EDMPF K+G   D+++N
Sbjct: 158  -TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTKEGVVPDLIIN 216

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +  +          +S L    E    +     
Sbjct: 217  PHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKLLR--EHGYQSRGFEV 274

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                           +G +    G    
Sbjct: 275  M---------------------------------------------YNGHT----GR--- 282

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDK 1266
                 V +G  Y  +L HMV DK
Sbjct: 283  KLVAQVFLGPTYYQRLRHMVDDK 305



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 31/152 (20%), Positives = 59/152 (38%), Gaps = 9/152 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 9   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKR 68

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  D   +       +D+ GI+  G  V+  DI++GK  P        
Sbjct: 69  IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDA--- 125

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            E+L +        DV        +G+   V+
Sbjct: 126 -EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 156


>gi|158514843|gb|ABW69377.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 174

 Score =  184 bits (467), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 134/173 (77%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 2   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNI 61

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  F
Sbjct: 62  GLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRF 121

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           T+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 122 TDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRALMG 174


>gi|71025985|ref|XP_762697.1| DNA-directed RNA polymerase subunit beta [Theileria parva strain
            Muguga]
 gi|93140682|sp|Q4MY95|RPOB_THEPA RecName: Full=DNA-directed RNA polymerase subunit beta; AltName:
            Full=PEP; AltName: Full=Plastid-encoded RNA polymerase
            subunit beta; Short=RNA polymerase subunit beta
 gi|68349646|gb|EAN30414.1| DNA-directed RNA polymerase beta chain, putative [Theileria parva]
          Length = 1005

 Score =  184 bits (467), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 110/568 (19%), Positives = 204/568 (35%), Gaps = 64/568 (11%)

Query: 797  GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
            G       L L  N     M    YN  + +L ++ + S      + +  ++++  D K 
Sbjct: 484  GSKMHTQALPLIYNEHPYVMTK--YNHMNGLLFNKCITSLCEGIIVSVNNYKIIVMDDKN 541

Query: 857  GPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      NV +     +    I+ VG ++N G  ++   +    S  T     L   
Sbjct: 542  RYLHYYLYPFNVLDYN-SFVSYKPIVWVGEKINIG-KILALPSDLKHSEFTLGVNNLLNY 599

Query: 917  FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQV 976
                  +  D  +   +     ++   I      D  E  +S+ +     L      E  
Sbjct: 600  SFYNGYEHEDAIVINKN-----LIIEDILTSISFDVYEEYLSINKLDYVELTLRHLLEYN 654

Query: 977  ILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK--VQRN 1034
              +R + + +         + G     K     S   ++     +     +++K  V   
Sbjct: 655  RYNRYLINEVGVSSNQDYMLFGDILSTKIRYELSLSKNKKFFKVFKLIFKENKKLIVYTK 714

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
              ++K   E      E    +K  ++             ++ F+     I  GDK+ GRH
Sbjct: 715  PLTIKRGGEGRLIKYEILGYSKFRQLDAMYPEINVSYLTLRFFIFKIDRINIGDKLCGRH 774

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            GNKG+VS+I+   D+P+   G     + +P+G  +R+N+GQ  E   G+  +    +IK+
Sbjct: 775  GNKGVVSKIVDNIDLPYTFRGLCPYSITSPIGALARINLGQFLEGSCGYFGLNFNCRIKA 834

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
             IN Y  +            +          +  +  +   +    +             
Sbjct: 835  PINLYNYH------------LYSNMYLKNIFNSLNVYNNSYINFSIEK------------ 870

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGS 1274
                                 L D  TG        +   Y LKL H    K   R+ G 
Sbjct: 871  --------------------YLRDFKTGYQLKNFNLMLMPYFLKLMHTSKSKFQYRTVGK 910

Query: 1275 YSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVA 1334
            YS +TQQP+ GK   G Q+ GEMEVW ++++G+AY ++E+  IK++      + ++    
Sbjct: 911  YSSLTQQPVKGKRVNGSQKFGEMEVWALESHGSAYTIRELGYIKTN-----VKYFK---K 962

Query: 1335 GNDTFETGTPESFNVLVKEMQALGLSID 1362
                   G  E+F VL  E++ + ++I+
Sbjct: 963  FEHKGYKG-SETFKVLTLELKNVLININ 989



 Score =  117 bits (293), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 113/658 (17%), Positives = 243/658 (36%), Gaps = 21/658 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           L I  + L   ++  +I+N        +       +           +I  ++ + +   
Sbjct: 86  LQIKFNNLKSRFINYNIINIPKINQSGDIILNGYLRLPILYLQLATNNISYIFNEKITRT 145

Query: 356 AYIR--NTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGR 413
            +I+  N +            + I       D+ +     S  N     S   ++  V  
Sbjct: 146 YFIKIKNNIYLYIYLYDDFITVYINSYKIKNDLFSMYNNVSFKNKYINFSKIDNVIYVMN 205

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           +K N  +     D   +I       +   ++ + N    ++            + +   +
Sbjct: 206 LKNNN-IKYHIFDKTININNFVNNTMFMDILSIVNKFLNLNLKKKFIQSSNNLINKSTNS 264

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
             +    +  +S+         D ++ +  I     +    E    + +    + +N LS
Sbjct: 265 VLKTIFRQFTKSVTIFDIEKYCDKLLYKKKIFRSFNIVLFKEHLLVNPVIHYTDQLNVLS 324

Query: 534 RITHTRRLSALGQGGVA--RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR 591
            +T+  +++  G    +  + +    +R +   + G I    T +G   GL+S L +   
Sbjct: 325 YLTNKFKINIFGYSNSSNDKFKVSTNLRKIQSDYIGFINIVNTPDGDTCGLISKLANNTI 384

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQAN-SSLDEDGSFTEELVFCRCA 650
           ++ +          C+ +   +   +    +    +   N  ++ ++ +F  + +     
Sbjct: 385 LDKFKLKLIN----CNNEYFENFTKIDITSKNLYNMTSNNFINIKKNSTFKVKQIEVFKN 440

Query: 651 GEEILVPREK-IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
            E  L+  +K     + +    +SI   +IPFL N+D  R LMG  M  QA+PL+  E P
Sbjct: 441 NEFKLINFDKNKTNKNLNVFNTLSITELIIPFLFNNDPCRGLMGSKMHTQALPLIYNEHP 500

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
           +V T    +        I +   GI+  V+  +I++   +            Y L  F  
Sbjct: 501 YVMTKYNHMNGLLFNKCITSLCEGIIVSVNNYKIIVMDDKNR-------YLHYYLYPFNV 553

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
            + N+ V+ +P+V VG+++    I+A        +  LG N L+ +  ++GY  ED+++I
Sbjct: 554 LDYNSFVSYKPIVWVGEKINIGKILALPSDLKHSEFTLGVNNLLNYSFYNGYEHEDAIVI 613

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI-DECGIICVGAEV 888
           ++ ++ ED+ TSI  + +E      KL   E+T           + + +E G+      +
Sbjct: 614 NKNLIIEDILTSISFDVYEEYLSINKLDYVELTLRHLLEYNRYNRYLINEVGVSSNQDYM 673

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFG--EKAVDVRDTSLRVPSGVSGTVVDVRI 944
             GDIL  KI  +       +   +  +     K + V    L +  G  G ++   I
Sbjct: 674 LFGDILSTKIRYELSLSKNKKFFKVFKLIFKENKKLIVYTKPLTIKRGGEGRLIKYEI 731


>gi|300394732|gb|ADK11904.1| DNA-directed RNA polymerase II subunit two [Pseudomerulius aureus]
          Length = 345

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/431 (16%), Positives = 119/431 (27%), Gaps = 88/431 (20%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  I   ++            ++       +G       I          
Sbjct: 1    WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLIRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   RD                  I  G   
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTYEKLEDDGLIAPGTGV 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R++          ++     +  Q      ++   F+ 
Sbjct: 169  SGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQ-----VLISTNFE- 222

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 223  --------------GQKFVKVRVRSSRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DIV+NP  +PSRM +G + E  L      +G +                        
Sbjct: 269  IVPDIVINPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------- 306

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E++++ LR       G  +
Sbjct: 307  -------------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEV 334

Query: 1236 LYDGLTGEPFD 1246
            +Y G TG    
Sbjct: 335  MYHGHTGRKLQ 345



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 47/297 (15%), Positives = 95/297 (31%), Gaps = 77/297 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ I AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLI---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA + + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E        +   +     + +++ G+I  G  V+  DI++
Sbjct: 116 SIYYRSYMDLEKKSGVQQLEEFEKPTRDNTLRMKHGTYEKLEDDGLIAPGTGVSGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        +    RD S  + S  +G V  V I       K
Sbjct: 176 GKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLISTNFEGQK 225


>gi|293601758|gb|ADE48283.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601770|gb|ADE48289.1| RNA polymerase II [Morchella sp. Mes-3]
 gi|293601772|gb|ADE48290.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601776|gb|ADE48292.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601788|gb|ADE48298.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601790|gb|ADE48299.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601796|gb|ADE48302.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601804|gb|ADE48306.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601814|gb|ADE48311.1| RNA polymerase II [Morchella sp. Mes-3]
 gi|293601816|gb|ADE48312.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601818|gb|ADE48313.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601822|gb|ADE48315.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601824|gb|ADE48316.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601828|gb|ADE48318.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601830|gb|ADE48319.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601832|gb|ADE48320.1| RNA polymerase II [Morchella sp. Mes-3]
 gi|293601834|gb|ADE48321.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601836|gb|ADE48322.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601842|gb|ADE48325.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601844|gb|ADE48326.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601846|gb|ADE48327.1| RNA polymerase II [Morchella sp. Mes-3]
 gi|293601848|gb|ADE48328.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601850|gb|ADE48329.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601852|gb|ADE48330.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601854|gb|ADE48331.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601856|gb|ADE48332.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601860|gb|ADE48334.1| RNA polymerase II [Morchella steppicola]
          Length = 293

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 60/366 (16%), Positives = 107/366 (29%), Gaps = 75/366 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 287

Query: 1247 RPVTVG 1252
              V +G
Sbjct: 288  CQVFLG 293



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|330785444|gb|AEC46528.1| RNA polymerase II second largest subunit [Syncesia intercedens]
          Length = 307

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  + GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPRVGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVPSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLEFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|119640573|gb|ABL85480.1| RNA polymerase II second largest subunit [Dirina catalinariae]
          Length = 307

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQRPLASTHSMNYMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ +     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLKFSGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/206 (20%), Positives = 75/206 (36%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +    +      QRPL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMSNILYYPQRPL----------ASTHSMNYMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  R     +        + +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GLVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V +    G    + R+ + +  QI
Sbjct: 167 DRVLLTTTEGKRSVKVRTRTTKVPQI 192


>gi|259018547|gb|ACV89783.1| RNA polymerase B beta subunit [Haemophilus influenzae]
          Length = 178

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 108/178 (60%), Positives = 134/178 (75%), Gaps = 1/178 (0%)

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F SSQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E
Sbjct: 1   FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPE 60

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLS ++E N  IAQANS+LDE
Sbjct: 61  GPNIGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDE 120

Query: 637 DGSFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +  FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 121 NNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRALMG 178


>gi|119640609|gb|ABL85498.1| RNA polymerase II second largest subunit [Roccella fuciformis]
 gi|119640631|gb|ABL85509.1| RNA polymerase II second largest subunit [Roccella maderensis]
          Length = 307

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/372 (17%), Positives = 108/372 (29%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +     E+  SV    +E   + +  E +      Y +L +       V       
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDDDGLVPPGV------- 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               V   D+I               E  QR  +  K          E    +++      
Sbjct: 118  --RVSGEDIIIGKTAPXXXXXXXXAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 171  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G++                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSTVTGEEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +L+ A     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVFLGPTY 307



 Score = 78.6 bits (192), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPXXXXXXXXAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640685|gb|ABL85536.1| RNA polymerase II second largest subunit [Roccellaria mollis]
          Length = 307

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 111/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGFXMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|119640659|gb|ABL85523.1| RNA polymerase II second largest subunit [Roccella tuberculata]
          Length = 307

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/372 (17%), Positives = 108/372 (29%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +     E+  SV    +E   + +  E +      Y +L +       V       
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGV------- 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               V   D+I               E  QR  +  K          E    +++      
Sbjct: 118  --RVSGEDIIIGKTAPXXXXXXXXAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 171  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G++                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSTVTGQEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +L+ A     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPXXXXXXXXAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|83414619|dbj|BAE54100.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 172

 Score =  184 bits (466), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/112 (55%), Positives = 80/112 (71%)

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            KI     GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSRI+P EDMP+  D 
Sbjct: 55   KIFTRANGDELQSGVNMLVRVYIAQKRKIRVGDKMAGRHGNKGVVSRIVPLEDMPYPPDR 114

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            TPVDI+LNPLGVPSRMN+GQ+ E HLG A   LG  I + + D  ++ D+  
Sbjct: 115  TPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDEASSDDLWE 166



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 48/63 (76%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G +G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGAGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|224419506|emb|CAX51334.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 118

 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 52/98 (53%), Positives = 70/98 (71%), Gaps = 8/98 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 21   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 80

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR G
Sbjct: 81   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFG 118


>gi|293601768|gb|ADE48288.1| RNA polymerase II [Morchella sp. Mes-14]
 gi|293601778|gb|ADE48293.1| RNA polymerase II [Morchella sp. Mes-6]
 gi|293601792|gb|ADE48300.1| RNA polymerase II [Morchella sp. Mes-5]
 gi|293601798|gb|ADE48303.1| RNA polymerase II [Morchella sp. Mes-14]
 gi|293601806|gb|ADE48307.1| RNA polymerase II [Morchella sp. Mes-13]
 gi|293601840|gb|ADE48324.1| RNA polymerase II [Morchella sp. Mes-7]
 gi|293601858|gb|ADE48333.1| RNA polymerase II [Morchella sp. Mes-7]
          Length = 293

 Score =  183 bits (465), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/369 (16%), Positives = 112/369 (30%), Gaps = 81/369 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L E   +  G           
Sbjct: 62   RSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 119  KTAPITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML------------------- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 160  -TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 284

Query: 1244 PFDRPVTVG 1252
                 V +G
Sbjct: 285  KLVCQVFLG 293



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|307547769|gb|ADN44498.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 304

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/372 (17%), Positives = 108/372 (29%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 65

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +     E+  SV    +E   + +  E +      Y +L +       V       
Sbjct: 66   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGV------- 114

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               V   D+I               E  QR  +  K          E    +++      
Sbjct: 115  --RVSGEDIIIGKTAPXXXXXXXXAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 168  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G++                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVSTVTGQEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +LR A     G  ++++G TG 
Sbjct: 257  -----------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGHTGR 292

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 293  KLNAQVFLGPTY 304



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 72/196 (36%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 118 GEDIIIGKTAPXXXXXXXXAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 173

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 174 KRSVKVRTRTTKVPQI 189


>gi|119640615|gb|ABL85501.1| RNA polymerase II second largest subunit [Roccella galapagoensis]
 gi|256808276|gb|ACV30269.1| RNA polymerase II second largest subunit [Roccella albida]
          Length = 307

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 110/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLEDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A+    G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFANYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307


>gi|90192146|gb|ABD91733.1| RNA polymerase beta subunit [Klebsiella variicola]
          Length = 172

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 107/172 (62%), Positives = 134/172 (77%)

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
           + +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR
Sbjct: 1   ISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGR 60

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
           +CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IA
Sbjct: 61  VCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIA 120

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           QANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 QANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 172


>gi|330785198|gb|AEC46405.1| RNA polymerase II second largest subunit [Chrysothrix chrysophthalma]
          Length = 305

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 57/377 (15%), Positives = 102/377 (27%), Gaps = 75/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R   D  +        Q    +R           +       +  G      
Sbjct: 64   LF-RSLYYRTYNDTEKAVGINIAGQFSKPSRATTLSMKQTTYDKLDDDGIVSPGVRISGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L++D      R++          ++     +  Q                 
Sbjct: 123  DIIIGKTAPLAADAEESGMRTKLHTRRDVSTPLRGTEAGIVDQ----------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 166  ---VMITSSSEGERFVKVRTRATKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVP 222

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L         +                           
Sbjct: 223  DLIINPHAIPSRMTIAHLIECLLSKVSTMSCLEGD------------------------- 257

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F G   E I+ +L+     + G  ++Y+
Sbjct: 258  ----------------------------ATP-FTGVTVEIISKLLKDQGYQDRGFEVMYN 288

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      + +G  Y
Sbjct: 289  GHTGRKLRAQIFLGPTY 305



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 69/177 (38%), Gaps = 16/177 (9%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +   +       +       ++ +     +D+ GI+  G  ++
Sbjct: 61  DRGLFRSLYYRTYNDTEKAVGINIAGQFSKPSRATTLSMKQTTYDKLDDDGIVSPGVRIS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P        EE  +R     K    RD S  +  G    +VD  +  
Sbjct: 121 GDDIIIGKTAPLAAD---AEESGMRT----KLHTRRDVSTPLR-GTEAGIVDQVMIT 169


>gi|114579602|ref|XP_001144478.1| PREDICTED: RNA polymerase I polypeptide B isoform 1 [Pan troglodytes]
          Length = 1098

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 91/492 (18%), Positives = 158/492 (32%), Gaps = 73/492 (14%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 638  EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 697  GFPILTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 756

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G          K         
Sbjct: 757  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFG---------IKPGDPRVLQK 806

Query: 1013 ISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            + +        +    D        +    +       E+   + I+     +D   G  
Sbjct: 807  LDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKF 864

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + V + + + R    GDK A RHG K                            G+ SR+
Sbjct: 865  KCVCITMRVPRNPTIGDKFASRHGQK----------------------------GILSRL 896

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
                       W    +      ++ D   N    P R  +  +I              +
Sbjct: 897  -----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--------------E 931

Query: 1192 SVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
            S+   +         +TP +F   +   E    ML+ A  +  G   LY G++G   +  
Sbjct: 932  SMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEAD 991

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GEME   + A+G +
Sbjct: 992  IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTS 1051

Query: 1309 YVLQEMLTIKSD 1320
            ++L + L   SD
Sbjct: 1052 FLLHDRLFNCSD 1063



 Score = 90.1 bits (222), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 222/664 (33%), Gaps = 72/664 (10%)

Query: 333 LEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVA 392
           L+ +       I    +    +++++RN++        ++  L   +V+           
Sbjct: 253 LKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCLTQKQVLN--------YL 304

Query: 393 ESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGT 452
              F       D Y          N  + +         +   +  + + L  L  G+  
Sbjct: 305 GECFRVKLNVPDWYPNEQAAEFLFNQCICIH--LKSNTEKFYMLCLMTRKLFALAKGECM 362

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYR------LGLLRMERSIKERISSVDIDSVMPQDLINA 506
            D+ D+L N+ V + G++     +      L  +++    K + +SV +++     +   
Sbjct: 363 EDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMKIFTM 422

Query: 507 K-PVVSAVCEFFCS--------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
              +       F +              S L  + + +N +  ++H R    + +G    
Sbjct: 423 GIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFR---CVHRGADFA 479

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKV 610
                 +R + P  +G +CP  T +G   GL++ LT+   V             +C+  V
Sbjct: 480 KMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGV 539

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG-----EEILVPREKIDFID 665
           T           E   +      +          +           E+ + P  ++  I 
Sbjct: 540 TPIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIP 599

Query: 666 ASPKQVVSIA-------ASLIPFLENDDSNRVLMGCNMQRQAVPL-LKAEAPFVGTGMES 717
            + K  +            L+  ++N +  +  +   M++  + + +  +  F G     
Sbjct: 600 MTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQ 659

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG--VDIYRLMKFQRSNQNTC 775
            +   S  +++A     +   D  +      +  +   T G  +  Y+     +  +   
Sbjct: 660 ELFPHSLLSVIA---NFIPFSDHNQSPRNMYQCQMGKQTMGFPILTYQDRSDNKLYRLQ- 715

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q PLV+                 D+ +  +G N +VA + + GY+ ED+M++++    
Sbjct: 716 TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWE 765

Query: 836 EDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                 S++  EF  ++   K G   +   I       L+ +D+ G+  +GA++  GD  
Sbjct: 766 RGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPY 825

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +     +  T E  ++     E     +++  S    SG    V       R+    
Sbjct: 826 YSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIG 880

Query: 953 NERS 956
           ++ +
Sbjct: 881 DKFA 884



 Score = 59.3 bits (142), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 100/721 (13%), Positives = 201/721 (27%), Gaps = 146/721 (20%)

Query: 53  EGLQAAFKSVFPITAFSGAAMLEF--VSYEFDPPKF-----------DVDDCLWRDLTYA 99
           EGL  A +++ P         + F  +     PP                +C  R  TY 
Sbjct: 52  EGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYR 111

Query: 100 VPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD------------------ 141
             L   +   V  +         K I +Q  ++G +P+M K                   
Sbjct: 112 GKLTADINWAVNGI--------SKGIIKQ--FLGYVPIMVKSKLCNLRNLPPQALIEHHE 161

Query: 142 ------GTFVIKGIQRIVVSQLH---RSPGIHFDHDKGRASLSGKLLYACRIIPDQGL-- 190
                 G F+I GI++++   L    R+  I     K +    G   Y   +   +    
Sbjct: 162 EAEEMGGYFIINGIEKVI-RMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHS 220

Query: 191 -------WMDIEFDSKDIIHVRIDRRRK----VPVTSFLMAL-GMDSEEILSTFYPKIVY 238
                  +++      + I+      RK    +P+   L AL      +I    + +++ 
Sbjct: 221 AVNMNLHYLENGTVMLNFIY------RKELFFLPLGFALKALVSFSDYQI----FQELIK 270

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGI 298
            +  D +     +  L                  V+E G      +L  L E     L +
Sbjct: 271 GKEDDSFLRNSVSQMLR----------------IVMEEGCLTQKQVLNYLGECFRVKLNV 314

Query: 299 TS--------DCLCGLYVAEDIVNG---------ETGEIYIEAGDVIDEKSLEEIFHSEI 341
                     + L    +   + +           T +++  A     E + + + + E+
Sbjct: 315 PDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 374

Query: 342 RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                L++  +          +       K A     +      ++T ++ +     +  
Sbjct: 375 LTPGQLFLMFLKEK-------LEGWLVSIKIAFDKKAQKTSVS-MNTDNLMKIFTMGIDL 426

Query: 402 DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
                 L   G ++    L L     +  +   D +  I+ L   R     +    +   
Sbjct: 427 TKPFEYLFATGNLRSKTGLGLLQDSGLCVV--ADKLNFIRYLSHFR----CVHRGADFAK 480

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
            R  +V  +L   +                  +   +M       + V   V      + 
Sbjct: 481 MRTTTVRRLLPESWGFLC-------PVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPAL 533

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           L  L   V  +    H R  S      +     G   +D+ P     +   +      I 
Sbjct: 534 LCNLG--VTPIDGAPH-RSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIP 590

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
               +               +      ++   V  L   +EE          L       
Sbjct: 591 PWMEVVLIPMTGKPSLYPGLFLFTTPCRLVRPVQNLELGKEE----------LIGTMEQI 640

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
              V          V   +    +  P  ++S+ A+ IPF +++ S R +  C M +Q +
Sbjct: 641 FMNVAIFEDEVFAGVTTHQ----ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 696

Query: 702 P 702
            
Sbjct: 697 G 697


>gi|46277330|gb|AAS86855.1| DNA-dependent RNA polymerase II [Peziza badiofusca]
          Length = 541

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 88/666 (13%), Positives = 183/666 (27%), Gaps = 136/666 (20%)

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             +    + +V  +     +      ++      +  D  F    +        I      
Sbjct: 3    DFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTIQKLRRQGHIGSEVSL 62

Query: 661  IDFIDASPKQVVSIAASLIP--FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            I  I     ++ + A  +    F+ ++D      G  + ++             T +E  
Sbjct: 63   IQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHI----------TKLEDD 112

Query: 719  VAKSSGAAIVAKR----AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
                        +     G+VE +DA       +    +   +    +   + Q++    
Sbjct: 113  RDNDDETQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQTLDPA 172

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
               QR    V             PS  LG       +  + +P+  +N       S R  
Sbjct: 173  ---QRVKGAVNKFAHTWTHCEIHPSMILG-------ICASIIPFPDHNQ------SPRNT 216

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
             +       +  F    R+                           +  +          
Sbjct: 217  YQSAMGKQAMGVFLTNYRERM-----------------------DTMANILYYPQKPLGT 253

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +    +F R  +D+ +
Sbjct: 254  TRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYMDQEK 312

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSD 1011
            R   +    +E   +      + L    Y +L +   +  G           K+  ++ +
Sbjct: 313  R---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPN 369

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                  R+++         ++     +  Q                             L
Sbjct: 370  QEELGQRTKFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGL 409

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM
Sbjct: 410  KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVPDLIINPHAIPSRM 469

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +  +                                                      +
Sbjct: 470  TIAHLI-----------------------------------------------------E 476

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
             +L      +     +TP F     ++++++LR       G  ++Y+G TG      V +
Sbjct: 477  CLLSKVSSLRGFEGDATP-FTDVTVDSVSTLLREHGYQSRGFEVMYNGHTGRKMVAQVFL 535

Query: 1252 GYIYML 1257
            G  Y  
Sbjct: 536  GPTYYQ 541



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 66/481 (13%), Positives = 127/481 (26%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 3   DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 56

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L     +    +    
Sbjct: 57  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHITKLEDDRDND 116

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            ET             V Y+ A EEE   I      L+    F       + L   +   
Sbjct: 117 DETQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQTLDPAQRVK 176

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +          +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 177 GAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLT----- 231

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                      + A I+      +    ++  +          +   +  Y         
Sbjct: 232 ----NYRERMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSG------- 280

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                NQ                    S  +   ++ R +  +       + E  + +S 
Sbjct: 281 ----YNQE------------------DSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMS- 317

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
                       +EEFE   R           +   +       +D+ G++  G  V+  
Sbjct: 318 -----------VVEEFEKPTR----------GNTLRLKHGTYDKLDDDGLVAPGVRVSGE 356

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P   +     ++        K    RD S  + S  +G V  V +       
Sbjct: 357 DIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 409

Query: 952 K 952
           K
Sbjct: 410 K 410


>gi|119640571|gb|ABL85479.1| RNA polymerase II second largest subunit [Dirina paradoxa subsp.
            africana]
          Length = 307

 Score =  183 bits (465), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYMKFRELPAGQNAMVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ +     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLKFSGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 75/206 (36%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +    +      Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMSNILYYPQKPL----------ASTHSMNYMKFRELPAGQNAMVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  R     +        + +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GLVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V +    G    + R+ + +  QI
Sbjct: 167 DRVLLTTTEGKRSVKVRTRTTKVPQI 192


>gi|119640647|gb|ABL85517.1| RNA polymerase II second largest subunit [Roccella phycopsis]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/372 (17%), Positives = 107/372 (28%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +     E+  SV    +E   + +  E +      Y +L +       V       
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGV------- 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               V   D+I               E  QR  +  K          E    +++      
Sbjct: 118  --RVSGEDIIIGKTAPXXXXXXXXAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 171  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSTVTGHEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +L+ A     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPXXXXXXXXAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|307547639|gb|ADN44433.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547645|gb|ADN44436.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547667|gb|ADN44447.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547671|gb|ADN44449.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547673|gb|ADN44450.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547771|gb|ADN44499.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 63/374 (16%), Positives = 106/374 (28%), Gaps = 77/374 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--ILCGQNAVSGPKG 1001
             +  +     E+  SV    +E   + +  E +      Y +L +  ++     VSG   
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                T      + E               V   + S +        +             
Sbjct: 125  IIGKTAPFQAPLQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLL------------- 171

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D++
Sbjct: 172  ----TTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLI 227

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G++                              
Sbjct: 228  INPHAIPSRMTIAHLIECLLSKVSTVTGQEGD---------------------------- 259

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F       I+ +LR A     G  ++ +G T
Sbjct: 260  -------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMQNGHT 293

Query: 1242 GEPFDRPVTVGYIY 1255
            G   +  V +G  Y
Sbjct: 294  GRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 75/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P       P ++        K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPF----QAPLQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640603|gb|ABL85495.1| RNA polymerase II second largest subunit [Roccella decipiens]
 gi|119640621|gb|ABL85504.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|119640623|gb|ABL85505.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808278|gb|ACV30270.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808280|gb|ACV30271.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808282|gb|ACV30272.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808284|gb|ACV30273.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808286|gb|ACV30274.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808288|gb|ACV30275.1| RNA polymerase II second largest subunit [Roccella bajasurensis]
 gi|256808290|gb|ACV30276.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808292|gb|ACV30277.1| RNA polymerase II second largest subunit [Roccella decipiens]
 gi|256808294|gb|ACV30278.1| RNA polymerase II second largest subunit [Roccella decipiens]
 gi|256808296|gb|ACV30279.1| RNA polymerase II second largest subunit [Roccella decipiens]
 gi|256808298|gb|ACV30280.1| RNA polymerase II second largest subunit [Roccella decipiens]
 gi|256808302|gb|ACV30282.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808304|gb|ACV30283.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808306|gb|ACV30284.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808308|gb|ACV30285.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808310|gb|ACV30286.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808312|gb|ACV30287.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808314|gb|ACV30288.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808316|gb|ACV30289.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808318|gb|ACV30290.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808320|gb|ACV30291.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808322|gb|ACV30292.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808324|gb|ACV30293.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808326|gb|ACV30294.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808328|gb|ACV30295.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808330|gb|ACV30296.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808332|gb|ACV30297.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808334|gb|ACV30298.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808336|gb|ACV30299.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808338|gb|ACV30300.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808340|gb|ACV30301.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808342|gb|ACV30302.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808344|gb|ACV30303.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808346|gb|ACV30304.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808348|gb|ACV30305.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808350|gb|ACV30306.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808352|gb|ACV30307.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808354|gb|ACV30308.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808356|gb|ACV30309.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808358|gb|ACV30310.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808360|gb|ACV30311.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808362|gb|ACV30312.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808364|gb|ACV30313.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808366|gb|ACV30314.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808368|gb|ACV30315.1| RNA polymerase II second largest subunit [Roccella gracilis]
 gi|256808370|gb|ACV30316.1| RNA polymerase II second largest subunit [Roccella gracilis]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 110/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGEEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A+    G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFANYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|119640613|gb|ABL85500.1| RNA polymerase II second largest subunit [Roccella galapagoensis]
 gi|119640617|gb|ABL85502.1| RNA polymerase II second largest subunit [Roccella galapagoensis]
 gi|119640619|gb|ABL85503.1| RNA polymerase II second largest subunit [Roccella galapagoensis]
 gi|119640625|gb|ABL85506.1| RNA polymerase II second largest subunit [Roccella lirellina]
 gi|119640627|gb|ABL85507.1| RNA polymerase II second largest subunit [Roccella lirellina]
 gi|256808372|gb|ACV30317.1| RNA polymerase II second largest subunit [Roccella lirellina]
 gi|256808374|gb|ACV30318.1| RNA polymerase II second largest subunit [Roccella lirellina]
 gi|256808376|gb|ACV30319.1| RNA polymerase II second largest subunit [Roccella lirellina]
 gi|256808378|gb|ACV30320.1| RNA polymerase II second largest subunit [Roccella margaritifera]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 110/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A+    G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFANYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|280985755|gb|ACZ99658.1| RNA polymerase II [Fusarium redolens]
          Length = 298

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 58/373 (15%), Positives = 106/373 (28%), Gaps = 75/373 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGH 285

Query: 1241 TGEPFDRPVTVGY 1253
            TG      V  G 
Sbjct: 286  TGRKLRAQVFFGP 298



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|15208247|dbj|BAB63148.1| hypothetical protein [Macaca fascicularis]
          Length = 441

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/426 (16%), Positives = 124/426 (29%), Gaps = 65/426 (15%)

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
            E +F ++ I E EV A  T    E     + +V    +   D         +   G   +
Sbjct: 77   EQIFMNVAIFEDEVFAGVT-THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTM 135

Query: 896  GKITPKGESPMTPEEKLLRAIFG---EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            G      +     +   L+         ++         P G +  V  +        D 
Sbjct: 136  GFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDA 195

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDL 1012
               + +               E + L   I      ++ G               +   L
Sbjct: 196  MIVNKASWERGFAH-GSVYKSEFIDLSEKIKQGDSSLVFGIKPGDP--------RILQKL 246

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
              +       +    D        +    +       E+   + I+     +D   G  +
Sbjct: 247  DDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKVCS--NDTGSGKFK 304

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V + + + R    GDK A RHG KGI+SR+ P EDMPF + G   DI+ NP G PSRM 
Sbjct: 305  CVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 364

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDS 1192
            +G + E+  G +    G    +    +                                 
Sbjct: 365  IGMLIESMAGKSAALHGLCHDATPFIFSEENSALEY------------------------ 400

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                                         ML+ A  +  G   LY G++G   +  + +G
Sbjct: 401  --------------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIG 434

Query: 1253 YIYMLK 1258
             +Y  +
Sbjct: 435  VVYYQR 440



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 100/289 (34%), Gaps = 20/289 (6%)

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
             +    + P    +     L+G   Q      +  +  F G      +   S  +++A 
Sbjct: 52  FTTPCRLVRPVQNLELGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQELFPHSLLSVIAN 111

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                +   + R + +   G        +  Y+     +  +     Q PLV+       
Sbjct: 112 FIPFSDHNQSPRNMYQCQMG-KQTMGFPLLTYQDRSDNKLYRLQ-TPQSPLVRPSMY--- 166

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV-FTSIHIEEFEV 849
                     D+ +  +G N +VA + + GY+ ED+M++++          S++  EF  
Sbjct: 167 -------DYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFID 219

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           ++   K G   +   I       L+ +D+ G+  +GA++  GD     +     +  T E
Sbjct: 220 LSEKIKQGDSSLVFGIKPGDPRILQKLDDDGLPFIGAKLQYGDPYYSYL-----NLNTGE 274

Query: 910 EKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
             ++     E     +++  S    SG    V       R+    ++ +
Sbjct: 275 SFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFA 323


>gi|270000429|gb|ACZ58062.1| RNA polymerase II [Fusarium sp. NRRL 44892]
 gi|270000435|gb|ACZ58065.1| RNA polymerase II [Fusarium sp. NRRL 44904]
          Length = 298

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 104/373 (27%), Gaps = 75/373 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  I+Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGH 285

Query: 1241 TGEPFDRPVTVGY 1253
            TG      V  G 
Sbjct: 286  TGRKLRAQVFFGP 298



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|119640575|gb|ABL85481.1| RNA polymerase II second largest subunit [Dirina paradoxa subsp.
            approximata]
 gi|307547551|gb|ADN44389.1| RNA polymerase II second largest subunit [Dirina catalinariae]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ +     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLKFSGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 75/206 (36%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +    +      Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMSNILYYPQKPL----------ASTHSMNYMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  R     +        + +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GLVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V +    G    + R+ + +  QI
Sbjct: 167 DRVLLTTTEGKRSVKVRTRTTKVPQI 192


>gi|312458555|gb|ADQ89211.1| DNA-directed RNA polymerase beta subunit [Corynebacterium
            diphtheriae]
          Length = 136

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/164 (36%), Positives = 86/164 (52%), Gaps = 36/164 (21%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G KI +     +   +   L++  E +                      
Sbjct: 1    EVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP------------------ 36

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPV 1249
                +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEPF  PV
Sbjct: 37   ----AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSGEPFPYPV 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            +VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   SVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 136


>gi|256808382|gb|ACV30322.1| RNA polymerase II second largest subunit [Roccella verruculosa]
 gi|256808384|gb|ACV30323.1| RNA polymerase II second largest subunit [Roccella verruculosa]
 gi|256808386|gb|ACV30324.1| RNA polymerase II second largest subunit [Roccella verruculosa]
 gi|256808388|gb|ACV30325.1| RNA polymerase II second largest subunit [Roccella verruculosa]
 gi|256808390|gb|ACV30326.1| RNA polymerase II second largest subunit [Roccella verruculosa]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 110/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQTPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A+    G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFANYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 76/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP ++        K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPF----QTPMQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|158514855|gb|ABW69383.1| RNA polymerase beta subunit [Bibersteinia trehalosi]
          Length = 176

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 106/176 (60%), Positives = 134/176 (76%), Gaps = 1/176 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           T+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR LMG N
Sbjct: 121 TDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRALMGTN 176


>gi|119640697|gb|ABL85542.1| RNA polymerase II second largest subunit [Roccellina suffructicosa]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 63/376 (16%), Positives = 110/376 (29%), Gaps = 81/376 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +    E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHXIECLLSKVSTITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L+ A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISDLLQFAGYQSRGFEMMYNG 291

Query: 1240 LTGEPFDRPVTVGYIY 1255
             TG   +  V +G  Y
Sbjct: 292  HTGRKLNAQVFLGPTY 307



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|330785194|gb|AEC46403.1| RNA polymerase II second largest subunit [Fulvophyton stalactinum]
 gi|330785196|gb|AEC46404.1| RNA polymerase II second largest subunit [Fulvophyton stalactinum]
          Length = 307

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/377 (15%), Positives = 107/377 (28%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E+ E  A++          +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQQQAVGFNALEEFERPAKNITMRTRPGTYDKLDDDGFVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR  E  K          E    +++ 
Sbjct: 123  DIIIGKTAPFQAPMQENA------------EGGQRTKEHTKRDVSAPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VK+     +  Q GDK A RHG KG +      EDMP+  +G   
Sbjct: 171  ------VTTSDGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPYTSEGVVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L         +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVSATSAMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+++LR A     G  ++Y+
Sbjct: 260  ----------------------------ATP-FTDVTVSGISALLRDAGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG   +  + +G  Y
Sbjct: 291  GYTGRKLNAQIFLGPTY 307



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 63/197 (31%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  R                +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFERPAKNITMRTRPGTYDKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P         E   R        DV        +G+   V
Sbjct: 111 GFVAPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRTKE-HTKRDVSAPLRSTEAGIIDRV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTSDGRRSVKIRTRT 186


>gi|145307917|gb|ABP57262.1| RNA polymerase II second largest subunit [Batkoa apiculata]
          Length = 298

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/372 (16%), Positives = 111/372 (29%), Gaps = 75/372 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +        +    +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    LANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               I+ R  +D+ +++  VE E  E  +                    I  G        
Sbjct: 61   -RSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGTRVSGDDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+T + +D      R +          ++     +  +   + +             
Sbjct: 120  IIGKTTPVPADSEELGQRLRGHTKKDVSTPLKSTETGIVDRVMLTINQ------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 168  --------EGMRFAKVRVRSTRVPQIGDKFASRHGQKGTIGMTYRHEDMPFSAEGIVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +G + E  +G      G +                             
Sbjct: 220  IINPHAIPSRMTIGHMVECLVGKVGTLDGSEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+ +L      + G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDGISVLLAKFGYQKRGFEVMYNGH 285

Query: 1241 TGEPFDRPVTVG 1252
            TG+     + +G
Sbjct: 286  TGKKLTAQIYLG 297



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 68/171 (39%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F SI+   +    + T L   E            +     + +++ G+I  G  V+
Sbjct: 56  DRGLFRSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGTRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK TP         E+L + + G    DV        +G+   V+
Sbjct: 116 GDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGIVDRVM 162


>gi|194320274|gb|ACF48376.1| DNA-dependent RNA polymerase II second largest subunit [Aspicilia
            caesiocinerea]
          Length = 311

 Score =  183 bits (464), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/382 (17%), Positives = 117/382 (30%), Gaps = 83/382 (21%)

Query: 873  LKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
            L N DE    +  +             +       +   +  + AI      +  D+ + 
Sbjct: 8    LTNFDERMDTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIM 67

Query: 931  VPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME-- 988
              + +   +    +F R  +D+ +R   +    +E   +    + + L    Y +L +  
Sbjct: 68   NQNSIDRGLF-RSLFYRAYVDQEKR---IGMATVEQFEKPMRSDTLRLKHGTYDKLDDDG 123

Query: 989  -ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKS 1047
             +  G           K+  +  D      R++                 +K    T   
Sbjct: 124  LVAPGVRVSGEDVIIGKTAPIQPDAEELGQRTKL---------------HIKRDASTPLR 168

Query: 1048 ILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCE 1107
              E+   +K+             LR VKV +   +  Q GDK A RHG KG +      E
Sbjct: 169  TTENGIVDKVLL-----TTNSEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQE 223

Query: 1108 DMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            DMPF  +G   D+++NP  +PSRM +  + E  L       G +                
Sbjct: 224  DMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD-------------- 269

Query: 1168 LRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMAD 1227
                                                   +TP F     ++++ +LR   
Sbjct: 270  ---------------------------------------ATP-FTEVTVDSVSRLLREHG 289

Query: 1228 LDESGQSILYDGLTGEPFDRPV 1249
                G  ++Y+G TG      V
Sbjct: 290  YQSRGFEVMYNGHTGRKLVAQV 311



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 27/161 (16%), Positives = 57/161 (35%), Gaps = 15/161 (9%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 9   TNFDERMDTMSNILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYTG 58

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 59  YNQEDSVIMNQNSIDRGLFRSLFYRAYVDQEKRIGMATVEQFEKPMRSDTLRLKHGTYDK 118

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
           +D+ G++  G  V+  D+++GK  P         ++    I
Sbjct: 119 LDDDGLVAPGVRVSGEDVIIGKTAPIQPDAEELGQRTKLHI 159


>gi|330785404|gb|AEC46508.1| RNA polymerase II second largest subunit [Fulvophyton desertorum]
          Length = 307

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/372 (16%), Positives = 105/372 (28%), Gaps = 81/372 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 68   LFYRTYIEQQQAVGFNALEEFEKPSKQITMRTRPGTYDKLDEDGFVAPGVRVSGEDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR  E  K          E    +++      
Sbjct: 128  KTAPFQAPMQENA------------EGGQRTREHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VK+     +  Q GDK A RHG KG +      EDMPF  +G   DIV+N
Sbjct: 171  -VTTTDGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSSEGLVPDIVIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSATSAMEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +LR A     G  ++Y+G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSGISGLLRDAGYQSRGFEVMYNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  + +G  Y
Sbjct: 296  KLNAQIFLGPTY 307



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 64/197 (32%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  +    +           +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFEKPSKQITMRTRPGTYDKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P         E   R        DV        +G+   V
Sbjct: 111 GFVAPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRTRE-HTKRDVSAPLRSTEAGIIDRV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTTDGRRSVKIRTRT 186


>gi|270000431|gb|ACZ58063.1| RNA polymerase II [Fusarium sp. NRRL 44896]
          Length = 276

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 57/351 (16%), Positives = 101/351 (28%), Gaps = 75/351 (21%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 1    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 59

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +           +       +  G           K+  +  +      R+   
Sbjct: 60   VFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTTVH 119

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +      + +                       ++ VKV V   +
Sbjct: 120  QRRDISTPLRSTENGIVDSVIVTVNA--------------------DNVKYVKVRVRTTK 159

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 160  IPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLS 219

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G +                                                   
Sbjct: 220  KVSTLEGMEGD------------------------------------------------- 230

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                +TP F     ++++ +LR       G  I+Y+G TG      V  G 
Sbjct: 231  ----ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLRAQVFFGP 276



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 60/156 (38%), Gaps = 12/156 (7%)

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E+
Sbjct: 1   FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEV 60

Query: 862 TRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      +       +DE GI+  G  V+  DI++GK  P  +       +     
Sbjct: 61  FEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT---- 116

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   RD S  + S  +G V  V +       K
Sbjct: 117 ---TVHQRRDISTPLRSTENGIVDSVIVTVNADNVK 149


>gi|291170442|gb|ADD82430.1| RNA polymerase II second largest subunit [Dothideomycetes sp. AN13]
          Length = 324

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/395 (15%), Positives = 111/395 (28%), Gaps = 81/395 (20%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             N+    ++ V             +       +   +  + AI      +  D+ +   S
Sbjct: 8    YNLRMDTMVNVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 67

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    +F R  +D+ +R        +E   +    + + L    Y +L     + 
Sbjct: 68   SIDRGLF-RSLFYRSYLDQEKRVGM---SVVESFEKPMRSDTLRLKHGTYDKLDHDGIVA 123

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  ++ D      R++          ++     +  Q         
Sbjct: 124  PGVRVSGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRSTENGIVDQVIL------ 177

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                L+ VKV     +  Q GDK A RHG KG +      EDMP
Sbjct: 178  --------------TTNTEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMP 223

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            F ++G   D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 224  FTREGLTPDLIINPHAIPSRMTIAHLIECLLSKVGALKGCEGDATPFTDVTVSSVSRLLR 283

Query: 1171 FLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDE 1230
              E    +                                                    
Sbjct: 284  --EHGYQSRGFEVM---------------------------------------------Y 296

Query: 1231 SGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
            +G +    G         V +G  Y  +L HMV D
Sbjct: 297  NGHT----GR---KLVAQVFLGPTYYQRLRHMVDD 324



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/173 (20%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            N R    V         +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 8   YNLRMDTMVNVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 67

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D  GI+  G  
Sbjct: 68  SIDRGLFRSLFYRSYLDQEKRVGMSVVESFEKPMRSDTLRLKHGTYDKLDHDGIVAPGVR 127

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 128 VSGEDIIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRSTENGIVDQVI 176


>gi|37956427|gb|AAP15383.1| RNA polymerase beta subunit [Pelobacter propionicus]
          Length = 183

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 105/175 (60%), Positives = 136/175 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V +GKVT +V + SA+EEE   IAQAN+ +D DG F  +
Sbjct: 61  ASLSTYARINEHGFVETPYRIVSEGKVTAEVKFFSALEEEGHAIAQANAEMDADGRFVND 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            V  R +GE +LV R++++ +D +P Q+VS+AASLIPFLENDD+NR LMG NMQR
Sbjct: 121 YVSARKSGEFLLVHRDELELMDVAPMQLVSVAASLIPFLENDDANRALMGSNMQR 175


>gi|34923298|gb|AAQ83536.1| RpoB [Mannheimia sp. P373]
 gi|34980321|gb|AAO41853.1| RNA polymerase beta subunit [Mannheimia haemolytica]
 gi|38373318|gb|AAR19023.1| RpoB [Mannheimia glucosida]
 gi|110294711|gb|ABG66789.1| RpoB [Mannheimia sp. P224]
          Length = 172

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 133/172 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 172


>gi|270000453|gb|ACZ58074.1| RNA polymerase II [Fusarium sp. NRRL 52680]
 gi|270000455|gb|ACZ58075.1| RNA polymerase II [Fusarium sp. NRRL 52832]
          Length = 297

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 57/372 (15%), Positives = 104/372 (27%), Gaps = 75/372 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  I+Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGH 285

Query: 1241 TGEPFDRPVTVG 1252
            TG      V  G
Sbjct: 286  TGRKLRAQVFFG 297



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|67942344|gb|AAY83372.1| DNA-dependent RNA polymerase II [Sarcoscypha occidentalis]
          Length = 542

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 92/662 (13%), Positives = 172/662 (25%), Gaps = 128/662 (19%)

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +  V   G     Y      +   +            +I      +  D      +V   
Sbjct: 2    YISVGTPGTPIVEYLAQRGMEFLEEYEPQRFPNATKVFINGVWVGVHRDPIGLTRVVQDV 61

Query: 649  CAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKA 706
                 +      I D  D   K          P F  ++D      G  M R+       
Sbjct: 62   RRKGIVSHEASVIRDIRDREFKIFTDAGRVCRPLFTIDNDPTSERRGQLMLRKEHIRRLQ 121

Query: 707  EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
            E        E          + A   G ++ VDA       +    +      ++    +
Sbjct: 122  EDALAD---EDDQRFGWDGLLKA---GAIQYVDAEEEETIMIVMTPEDLELAREVQEGYE 175

Query: 767  FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
             +         + P+      V +       PS  LG       +  + +P+  +N    
Sbjct: 176  IEEDPDPMKRVKAPI---PPHVPQYTHCEIHPSMILG-------ICASIIPFPDHNQ--- 222

Query: 827  MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
               S R   +       +  +     +                           +  +  
Sbjct: 223  ---SPRNTYQSAMGKQAMGVYLTNFAERM-----------------------DTMANILY 256

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  +  I      +  D+ +   S +   +    +F 
Sbjct: 257  YPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 315

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L +   +  G           
Sbjct: 316  RTYMDQEKR---IGMQVVEEFEKPMRGNTLRLKHGTYDKLDDDGLVAPGVRVTGEDIIIG 372

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +S D      R ++         ++     +  Q   S                  
Sbjct: 373  KTAPISPDADEMGQRQKYHTKRDVSTPLRSTESGIVDQVMLS------------------ 414

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   DI++N
Sbjct: 415  --TNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDIIIN 472

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L                                          
Sbjct: 473  PHAIPSRMTIAHLIECLLSKLST------------------------------------- 495

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                             +     +TP F      +++ MLR       G  ++Y+G TG+
Sbjct: 496  ----------------LRGAEGDATP-FTDVTVRSVSEMLRDHGYQSRGFEVMYNGHTGK 538

Query: 1244 PF 1245
              
Sbjct: 539  KL 540


>gi|37956421|gb|AAP15381.1| RNA polymerase beta subunit [Pelobacter acetylenicus]
          Length = 177

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 112/176 (63%), Positives = 136/176 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           QL +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QLMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V +GKVTN++ Y S  EE    IAQAN+ LDE+G F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRVVRNGKVTNEIRYFSRPEEGGHAIAQANAPLDEEGRFVNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           LV  R  GE +L+ RE+I  +D SPKQ+VS+AASLIPFLENDD+NR LMG NMQ Q
Sbjct: 121 LVNARQNGEFVLIQREEIGLMDVSPKQLVSVAASLIPFLENDDANRALMGSNMQGQ 176


>gi|38373322|gb|AAR19025.1| RpoB [Mannheimia ruminalis]
          Length = 172

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSDLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 172


>gi|6693814|gb|AAF24993.1|AF129446_1 RpoB [Klebsiella pneumoniae subsp. rhinoscleromatis]
 gi|4098391|gb|AAD09613.1| RNA polymerase beta-subunit [Klebsiella pneumoniae]
 gi|90192150|gb|ABD91735.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192154|gb|ABD91737.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192156|gb|ABD91738.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192162|gb|ABD91741.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192166|gb|ABD91743.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192176|gb|ABD91748.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192182|gb|ABD91751.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192186|gb|ABD91753.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192190|gb|ABD91755.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192196|gb|ABD91758.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 170

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV +G VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|153805631|ref|YP_001382216.1| RNA polymerase beta chain [Leptosira terrestris]
 gi|160175219|sp|A6YGD9|RPOB1_LEPTE RecName: Full=DNA-directed RNA polymerase subunit beta N-terminal
           section; AltName: Full=PEP; AltName:
           Full=Plastid-encoded RNA polymerase subunit beta
           N-terminal section; Short=RNA polymerase subunit beta
           N-terminal section
 gi|134270162|gb|ABO69351.1| RNA polymerase beta chain [Leptosira terrestris]
          Length = 1142

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 79/403 (19%), Positives = 140/403 (34%), Gaps = 74/403 (18%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
             F    + + I +L+E+Q+ S++  L +          GL+     +  I   +    L
Sbjct: 1   MEFSVKNKNLLIQNLVEIQQQSFNELLCV----------GLKRQLLQLNFIENKTRNIKL 50

Query: 75  EF--VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
            F   +Y+F  P+    + + +  T+A  L I +             ++   I    + +
Sbjct: 51  IFHAKNYKFILPEITPKEAVLKSKTFASALFIPVEY-----------RAKNSIGLYWVLL 99

Query: 133 GDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFD------------HDKGRASLSGKLLY 180
           G LP MTK G F+I G+ R+V++Q+ RSPG+++                  +  S   ++
Sbjct: 100 GHLPFMTKRGHFIINGVPRVVLNQMVRSPGLYYKTTANPQNVSNQVSINDSSHTS--PVF 157

Query: 181 ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFY------- 233
              IIP++G W+ +E D K  I +R+ R  K+P+  FL ALG D   I    Y       
Sbjct: 158 YSDIIPNRGTWLRLEIDRKKNIWIRMKRVDKIPMMLFLQALGYDLHCIEKLLYSRKFLNC 217

Query: 234 ----------PKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIES------G 277
                           ++            L     +     DI      IE       G
Sbjct: 218 DYLLNTDHPADSNSALKKIKVEIEQQKVLKLAALEALDDDDPDIAKQLDYIEKTTTPEMG 277

Query: 278 KKLTSGLLKSLKEKGVKFLG-----------ITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           K        +     +  +G           I SD      + E  +   T E+   A  
Sbjct: 278 KDFLFQSFFNPASYDLSPIGRFQLNKKLNLSIPSDY---TVLTEFDIYFATKELIKRATT 334

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKD 369
           + +   ++ +    IR    L    +          + DK  +
Sbjct: 335 MSNSDDIDHLQTRRIRSCGELLEIQLGEGIERLQKTIIDKINN 377



 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 127/383 (33%), Positives = 193/383 (50%), Gaps = 11/383 (2%)

Query: 376  DIYRVMRPGDVST---FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
            +IYR +    V +    +V +S          K +   + R      L  D        +
Sbjct: 755  EIYRQLNRRFVRSRLQLNVLKSELTNSHSQLIKANNDPIDRELSIQILKQDVQKSNPFNK 814

Query: 433  KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER--I 490
            K            L   +    ++ +        +   L +          + IK +   
Sbjct: 815  KGIYNQRFINKKFLDTSQFIDQELLHFLKTHKIFLDRQLTSLKTKQQNEKLKFIKWKKLR 874

Query: 491  SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVA 550
            +  +      Q+LI    +  A+ E F  + LSQ  + +N LS ITH RR+S++G GGV 
Sbjct: 875  NFKNALKNPIQNLITTNAINGALQELFGLNPLSQFMDQINPLSEITHKRRISSMGPGGVN 934

Query: 551  RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKV 610
            R  A +++R +HPTHYGRICP ET EGHN GLV+S T +AR+N YGF+ETP+ KV  G++
Sbjct: 935  RDNASMDVRSIHPTHYGRICPIETPEGHNAGLVNSPTIYARINNYGFLETPFFKVNSGQI 994

Query: 611  TNDVVYLSAMEEENRYIAQANSS------LDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
                 YL+A +E+   ++  + S      L    +  E  V  R   +   +   +I+FI
Sbjct: 995  QAKAFYLNAQKEQKFKVSPPDLSCSELQFLPLGPTKIESEVPMRKDFKFQRMAATQIEFI 1054

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
              SP Q++S+A SLIPFLE+DD+NR LMG NMQRQAVPLL AE P VGTG+E  V   S 
Sbjct: 1055 GISPLQMISVATSLIPFLEHDDANRALMGSNMQRQAVPLLIAERPVVGTGLEGRVIADSS 1114

Query: 725  AAIVAKRAGIVEQVDAIRIVIRS 747
              +  K++G++  V   ++++++
Sbjct: 1115 YIMQTKQSGVISYVSNEQVIVQT 1137



 Score = 63.6 bits (153), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/147 (27%), Positives = 72/147 (48%), Gaps = 1/147 (0%)

Query: 371 KDALLDIYRVMRPGDVST-FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
            D   DI + +   + +T   + +      FF+   YDLS +GR ++N +LNL  P D  
Sbjct: 255 DDDDPDIAKQLDYIEKTTTPEMGKDFLFQSFFNPASYDLSPIGRFQLNKKLNLSIPSDYT 314

Query: 430 HIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKER 489
            + + DI    K L+         DDID+L  RR+RS GE+L+ Q   G+ R++++I ++
Sbjct: 315 VLTEFDIYFATKELIKRATTMSNSDDIDHLQTRRIRSCGELLEIQLGEGIERLQKTIIDK 374

Query: 490 ISSVDIDSVMPQDLINAKPVVSAVCEF 516
           I++ ++           +   S++   
Sbjct: 375 INNTNLKKFAKHSSTYKRGTSSSIYRQ 401


>gi|256808274|gb|ACV30268.1| RNA polymerase II second largest subunit [Dirina ceratoniae]
 gi|307547553|gb|ADN44390.1| RNA polymerase II second largest subunit [Dirina ceratoniae]
          Length = 307

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTITGDEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ +     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDITVSNISELLKFSGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 75/206 (36%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +    +      Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMSNILYYPQKPL----------ASTHSMNYMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  R     +        + +D+ 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFERPRKGEVLRTRPGTYEKLDDD 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G++  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GLVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V +    G    + R+ + +  QI
Sbjct: 167 DRVLLTTTEGKRSVKVRTRTTKVPQI 192


>gi|213053802|gb|ACJ39206.1| RpoB [Corynebacterium ureicelerivorans]
          Length = 139

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 57/167 (34%), Positives = 83/167 (49%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  LGW     G  +    +D K    +  L   L  V                   
Sbjct: 1    QVLEVPLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPAESLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  + I  +L     +  G        +++L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNDEIAGLLANTKPNRDGDVMVDGNGKTVLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P+++GY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISIGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|145307872|gb|ABP57241.1| RNA polymerase II second largest subunit [Conidiobolus
            pseudapiculatus]
          Length = 301

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/374 (16%), Positives = 111/374 (29%), Gaps = 75/374 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D+ +++  VE E  E  +                    I  G      
Sbjct: 63   LF-RSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGTRVSGD 121

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T + +D      R +          ++     +  +   + +           
Sbjct: 122  DIIIGKTTPVPADSEELGQRLRGHTKKDVSTPLKSTETGIVDRVMLTINQ---------- 171

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 172  ----------EGMRFAKVRVRSTRVPQIGDKFASRHGQKGTIGMTYRHEDMPFSAEGIVP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  +G      G +                           
Sbjct: 222  DLIINPHAIPSRMTIGHMVECLVGKVGTLDGSEGD------------------------- 256

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L      + G  ++Y+
Sbjct: 257  ----------------------------ATP-FTDVTVDGISVLLAKFGYQKRGFEVMYN 287

Query: 1239 GLTGEPFDRPVTVG 1252
            G TG+     + +G
Sbjct: 288  GHTGKKLTAQIYLG 301



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + T L   E            +     + +++ G
Sbjct: 51  SVIMNQSSIDRGLFRSIYYRTYLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK TP         E+L + + G    DV        +G+   V+
Sbjct: 111 LIAPGTRVSGDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGIVDRVM 166


>gi|56694310|gb|AAW22895.1| RNA polymerase II second largest subunit [Polystichum lonchitis]
          Length = 527

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/433 (16%), Positives = 123/433 (28%), Gaps = 80/433 (18%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                 +      I   M+     + I   +     R+T             V+   L+  
Sbjct: 175  EEAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 233

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 234  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSID 291

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   IF R   D+ ++  ++ +E+ E   R+                     G    
Sbjct: 292  RGFF-RSIFYRSYRDEEKKQGTLVKEEFERPIRENTQGMRHGSYGKLDDDGLAPPGTRVS 350

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++                  D+   +     K    T     E    ++
Sbjct: 351  GEDVIIGKTTPIAQ-----------------DDTGTQAQRYSKRDQSTCLRHSESGMVDQ 393

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ ++G 
Sbjct: 394  VLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGI 448

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +GQ+ E  +G     +GK+                         
Sbjct: 449  TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD----------------------- 485

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     + I+  L        G   +
Sbjct: 486  ------------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETM 514

Query: 1237 YDGLTGEPFDRPV 1249
            Y G TG   +  +
Sbjct: 515  YXGHTGRRLNAMI 527



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 55/329 (16%), Positives = 103/329 (31%), Gaps = 36/329 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   +  A   F     + 
Sbjct: 2   EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVG 61

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 62  IHRDPELLVRTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLI 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S    A           Y  V  G     + Y+   EEE   I+             +
Sbjct: 121 KKS-DIRALQQKESAEPGWYDLVTKGF----IEYVDTEEEETTMISM----------TIQ 165

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 166 DLVNARLHPE--EAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 223

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 224 IYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 283

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
              +  +D        YR  + +   Q T
Sbjct: 284 IMNQSSIDRGFFRSIFYRSYRDEEKKQGT 312


>gi|330785176|gb|AEC46394.1| RNA polymerase II second largest subunit [Arthonia pruinata]
          Length = 304

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 108/372 (29%), Gaps = 84/372 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     V++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVVMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 68   LYYRTYIEQEQTVGIQVLEEFEKPIKSQTLRMRPGTYDKLDDDGIVAPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L   +               +E+  R     K    T     E    +++      
Sbjct: 128  KTAPLPQGV---------------EERGMRQTAHTKRDVSTPLRGTESGIVDQVL----- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVAATNALEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +LR +     G  ++Y+G TG 
Sbjct: 257  -----------------------ATP-FTDVTVENVSQLLRESGYQSRGFEVMYNGHTGR 292

Query: 1244 PFDRPVTVGYIY 1255
                 + +G  Y
Sbjct: 293  KLVAQIFLGPTY 304



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/184 (23%), Positives = 74/184 (40%), Gaps = 16/184 (8%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVVMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQTVGIQVLEEFEKPIKSQTLRMRPGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +     EE+ +R    + A   RD S  +  G    +VD  +     
Sbjct: 121 GDDIIIGKTAPLPQGV---EERGMR----QTAHTKRDVSTPLR-GTESGIVDQVLLTSVD 172

Query: 950 IDKN 953
             KN
Sbjct: 173 GKKN 176


>gi|4098395|gb|AAD09615.1| RNA polymerase beta-subunit [Proteus mirabilis]
          Length = 170

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 104/170 (61%), Positives = 129/170 (75%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVENNAVTDEIHYLSAIEEGNFIIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS LD+DG F EELV CR  GE  L  R+++ ++D S +QVVS+ ASLIP
Sbjct: 121 NSVLDDDGHFVEELVTCRHKGESSLFSRDQVQYMDVSTQQVVSVGASLIP 170


>gi|330785414|gb|AEC46513.1| RNA polymerase II second largest subunit [Fulvophyton rostratum]
 gi|330785416|gb|AEC46514.1| RNA polymerase II second largest subunit [Fulvophyton rostratum]
 gi|330785418|gb|AEC46515.1| RNA polymerase II second largest subunit [Fulvophyton rostratum]
          Length = 307

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 106/372 (28%), Gaps = 81/372 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 68   LFYRTYIEQQQAVGFNALEEFEKPAKQVTMRTRPGTYEKLDEDGFVPPGVRVSGEDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR  E  K          E    +++      
Sbjct: 128  KTAPFQAPMQENA------------EGGQRTKEHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -ITTTDGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSATSAMEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+++L+ A     G  ++Y+G TG 
Sbjct: 260  -----------------------ATP-FTEVTVSGISNLLKEAGYQSRGFEVMYNGYTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  + +G  Y
Sbjct: 296  KLNAQIFLGPTY 307



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/206 (20%), Positives = 73/206 (35%), Gaps = 20/206 (9%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       EE  +    V         + +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFEKPAKQVTMRTRPGTYEKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +
Sbjct: 111 GFVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KEHTKRDVSAPLRSTEAGII 166

Query: 940 VDVRIFNRHGIDKNE-RSISVEREQI 964
             V I    G    + R+ + +  QI
Sbjct: 167 DRVLITTTDGRRSVKIRTRTTKVPQI 192


>gi|45593174|gb|AAS68149.1| RNA polymerase beta subunit [Geobacter sulfurreducens PCA]
          Length = 173

 Score =  182 bits (463), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 135/173 (78%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V DGKVT+DV + SA+EEE   IAQAN+ +D DG F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRIVQDGKVTSDVKFFSALEEEGHAIAQANAEMDADGRFVNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            V  R +GE +LV R++++ +D +P Q+VS+AASLIPFLENDD+NR LMG NM
Sbjct: 121 YVSARKSGEFLLVHRDELELMDVAPMQLVSVAASLIPFLENDDANRALMGSNM 173


>gi|151573633|gb|ABS18085.1| RNA polymerase II [Gibberella thapsina]
          Length = 294

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 58/367 (15%), Positives = 104/367 (28%), Gaps = 75/367 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVTVGY 1253
              V  G 
Sbjct: 288  AQVFFGP 294



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|312204338|gb|ADQ47486.1| RNA polymerase II second largest subunit [Myriotrema olivaceum]
          Length = 291

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 108/369 (29%), Gaps = 81/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +++ +R        +E   +    E + L    Y +L +   I  G        
Sbjct: 60   LFYRAYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYEKLDDDGLIAPGVRVSGEDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D      R++          ++     +  +                   
Sbjct: 117  IIGKTAPIAPDTEELGQRTKLHTKRDASTPLRSTENGIVDRVLL---------------- 160

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 161  ----TTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDL 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 249

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 250  --------------------------ATP-FTEVTVDSVSRLLRDQGYQSRGFEVMYNGH 282

Query: 1241 TGEPFDRPV 1249
            TG      V
Sbjct: 283  TGRKLRAQV 291



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +     + +D+ G+I  G  V+
Sbjct: 53  DRGLFRSLFYRAYVEQEKRVGMSLVEQFEKPLRSETLRLKHGTYEKLDDDGLIAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 113 GEDIIIGKTAPIAPDTEELGQRT-------KLHTKRDASTPLRSTENGIVDRVLLTTNQE 165

Query: 950 IDK 952
             K
Sbjct: 166 GLK 168


>gi|119644079|gb|ABL85605.1| RNA polymerase II second largest subunit [Parmotrema austrosinense]
          Length = 710

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/392 (16%), Positives = 112/392 (28%), Gaps = 81/392 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 397  DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 456

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 457  LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRV 512

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 513  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 562

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK+A RHG KG +      EDMPF  +G
Sbjct: 563  ----------TNAEGLRFVKVRMRTTKIPQIGDKLASRHGQKGTIGITYRQEDMPFTSEG 612

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSR  +  + E  L       G +  +          +S L       
Sbjct: 613  MVPDLIINPHAIPSRKTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLR----- 667

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                V     +G  + T VF                        
Sbjct: 668  ----------EHGYQSRGFEVMYNGHTGKKLVTQVF------------------------ 693

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                           +G  Y  +L HMV DK+
Sbjct: 694  ---------------LGPTYYQRLRHMVDDKI 710



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/254 (15%), Positives = 83/254 (32%), Gaps = 22/254 (8%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 1   KRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 60

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61  GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
           G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 117 GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 176

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 236

Query: 684 NDDSNRVLMGCNMQ 697
            D+  R     N+ 
Sbjct: 237 IDNDPRSSNRGNLV 250



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 66/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 392 YEQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 451

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ G++  G  
Sbjct: 452 SIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVR 511

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 512 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 556


>gi|46411498|gb|AAS94319.1| RNA polymerase II [Parmotrema tinctorum]
          Length = 712

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/392 (16%), Positives = 112/392 (28%), Gaps = 81/392 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 399  DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 458

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 459  LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVRV 514

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 515  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 564

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK+A RHG KG +      EDMPF  +G
Sbjct: 565  ----------TNAEGLRFVKVRMRTTKIPQIGDKLASRHGQKGTIGITYRQEDMPFTSEG 614

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSR  +  + E  L       G +  +          +S L       
Sbjct: 615  MVPDLIINPHAIPSRKTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLR----- 669

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                V     +G  + T VF                        
Sbjct: 670  ----------EHGYQSRGFEVMYNGHTGKKLVTQVF------------------------ 695

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKV 1267
                           +G  Y  +L HMV DK+
Sbjct: 696  ---------------LGPTYYQRLRHMVDDKI 712



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/254 (15%), Positives = 83/254 (32%), Gaps = 22/254 (8%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 1   KRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 60

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61  GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
           G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 117 GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 176

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 236

Query: 684 NDDSNRVLMGCNMQ 697
            D+  R     N+ 
Sbjct: 237 IDNDPRSSNRGNLV 250



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 66/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 394 YEQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 453

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ G++  G  
Sbjct: 454 SIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLRLKHGTYDKLDDDGLVAPGVR 513

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 514 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 558


>gi|950068|emb|CAA83716.1| DNA-directed RNA polymerase (beta) [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 345

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 112/238 (47%), Gaps = 22/238 (9%)

Query: 108 LIVFDVDEFTGAKSIKDI---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIH 164
           LI  D+ E      I ++   K   +++GD PLMT+ GTF+I G Q+++VSQL RSPG +
Sbjct: 109 LIQIDIIEDKKTSLICNVSIYKSGEVFLGDFPLMTEAGTFIINGSQKVIVSQLVRSPGAY 168

Query: 165 FDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDI-------IHVRIDRRRKVPVTSF 217
           F+ +      +G+++Y   IIP +G W++ E DSK I       ++V+ID+ RK   TS 
Sbjct: 169 FNKEL--NRKTGEMIYFADIIPSRGTWLEYETDSKKIGSDAINPLYVKIDKSRKTTATSL 226

Query: 218 LMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ-VIES 276
           L+A G+  ++IL+ F    V  +        +    +    +V      I  GE    E 
Sbjct: 227 LLAFGISKDDILNIFDNDEVLVETLQQDSI-IGDFKIDWLNQVQEIYKKIRQGETATSEG 285

Query: 277 GKKLTSGLLKSLKEKGVKFLGI--------TSDCLCGLYVAEDIVNGETGEIYIEAGD 326
             K  + +L   ++  +   G           + +    +AEDI++     +  +  +
Sbjct: 286 ASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNRILNKVIAEDILDANNNVLIAKDTE 343



 Score = 45.5 bits (106), Expect = 0.065,   Method: Composition-based stats.
 Identities = 30/138 (21%), Positives = 58/138 (42%), Gaps = 1/138 (0%)

Query: 306 LYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             +  D +N    +I            L     S+   + I   D V      +++++ D
Sbjct: 201 KKIGSDAINPLYVKIDKSRKTTATS-LLLAFGISKDDILNIFDNDEVLVETLQQDSIIGD 259

Query: 366 KNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTP 425
              D  + + +IY+ +R G+ +T   A    N + FD  KYDL+  GR K+  +L++   
Sbjct: 260 FKIDWLNQVQEIYKKIRQGETATSEGASKFINSILFDKRKYDLTKAGRFKLKQKLSIKNR 319

Query: 426 DDVRHIRKEDIIAIIKIL 443
              + I ++ + A   +L
Sbjct: 320 ILNKVIAEDILDANNNVL 337



 Score = 38.9 bits (89), Expect = 6.1,   Method: Composition-based stats.
 Identities = 9/39 (23%), Positives = 13/39 (33%)

Query: 81  FDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA 119
           F  P+  V         Y  P+   L+L V   +E    
Sbjct: 21  FKEPRLSVRQAREESKIYDAPIYANLKLSVNKTEEIQKE 59


>gi|38373324|gb|AAR19026.1| RpoB [Mannheimia varigena]
 gi|38373326|gb|AAR19027.1| RpoB [Mannheimia sp. NCTC 11313]
 gi|268528993|gb|ACZ06549.1| RpoB [Mannheimia varigena]
          Length = 172

 Score =  182 bits (462), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 105/172 (61%), Positives = 133/172 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 172


>gi|111283892|gb|ABH09229.1| RNA polymerase II second largest subunit [Sporisorium reilianum]
          Length = 608

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 111/685 (16%), Positives = 213/685 (31%), Gaps = 94/685 (13%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G ++ N +R+   ++ R +   +     +      Q  + +  + + + 
Sbjct: 1    DHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHIQAAVKSSTITNGLR 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKAMQAKAGVSQVLNRFAFASTLSHLRRTNT----PIGRDGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L+  A V            + +  + + V    A  
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHA 176

Query: 622  EENRYIAQA--NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI 679
            +  +         + D+ G   + L   R   +         D  +   +     +  L 
Sbjct: 177  KATKIFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLR 236

Query: 680  PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
            P    +      M   ++++ V ++    P   TG E              + G++E +D
Sbjct: 237  PVFIVN---PNDMSLLIKKRHVNMIG--QPVPQTGEEF-------GWTHLVQEGVIEYLD 284

Query: 740  AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            A        E       S  D+ +  ++Q  N    +N              D  A   S
Sbjct: 285  AE------EEESALICMSPTDLEQSREYQARNGQISLN------------SADPSARLKS 326

Query: 800  TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
                         +A   W       +M++          + I   +     R++ +G +
Sbjct: 327  PHY----------IAPSTWTHCEIHPAMVLGICA------SIIPFPDHNQSPRNSAMGKQ 370

Query: 860  EITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGE 919
             ++ +I N             +  V             +       +      + AI   
Sbjct: 371  AVSVNISNFLSRA------DSMNHVLCYPQKPLGTTRSMEHLKFRELPAGTNCIVAIMCY 424

Query: 920  KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILD 979
               +  D+ +   S +   +    ++ R  + + ++   ++ E+ E   RD         
Sbjct: 425  SGYNQEDSVIMNQSSIDRGLF-RSMYYRGYVAEEKKVGVMQLEEFEKPNRDTTIRMKHGT 483

Query: 980  RNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLK 1039
             +          G           K+  L  D      RS+          ++     + 
Sbjct: 484  YDKIDADGFCAPGTRVSGDDVIIGKTAPLPPDSEELGMRSKLHTXKDASISLKSTXNGII 543

Query: 1040 VQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             Q                              + VKV V   R  Q+GDK A RHG KG 
Sbjct: 544  DQVLL--------------------TTNSHGNKFVKVRVRNTRVPQTGDKFASRHGQKGT 583

Query: 1100 VSRILPCEDMPFLKDGTPVDIVLNP 1124
            +      EDMPF  +G   DI++NP
Sbjct: 584  IGITYRQEDMPFSAEGVTPDIIINP 608



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 86/619 (13%), Positives = 179/619 (28%), Gaps = 95/619 (15%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  +D    + + +   +   F +  ++ +    +  +Y L   G  
Sbjct: 12  GPLMANLFRMLFRKVTRDVYRHLQKCV--EEHREFHIQAAVKSSTITNGLRYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R+GK       +  +  +    E
Sbjct: 69  GDQKKAMQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDI------DSVMPQDLINAKPVVSAVCEFF-CSSQL 522
             + Q    +  +       + +         +      L++ +   +   + F     +
Sbjct: 129 TPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHAKATKIFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
              ++    +  +   RR   +  +  V R     E+R ++      + P      +++ 
Sbjct: 189 GTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELR-IYTDASRVLRPVFIVNPNDMS 247

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF- 640
           L+        +                     + YL A EEE+  I  + + L++   + 
Sbjct: 248 LLIKKRHVNMIGQPVPQTGEEFGWTHLVQEGVIEYLDAEEEESALICMSPTDLEQSREYQ 307

Query: 641 -------TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                                 +        +  P  V+ I AS+IPF +++ S R    
Sbjct: 308 ARNGQISLNSADPSARLKSPHYIAPSTWTHCEIHPAMVLGICASIIPFPDHNQSPRN--- 364

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
             M +QAV +  +        M  V+                                  
Sbjct: 365 SAMGKQAVSVNISNFLSRADSMNHVLC------------------------------YPQ 394

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                      +KF+     T      +   G   + + +I +  S D G          
Sbjct: 395 KPLGTTRSMEHLKFRELPAGTNCIVAIMCYSG-YNQEDSVIMNQSSIDRGLFRS------ 447

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
             M + GY  E+  +             + +EEFE   RDT             +     
Sbjct: 448 --MYYRGYVAEEKKV-----------GVMQLEEFEKPNRDT----------TIRMKHGTY 484

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             ID  G    G  V+  D+++GK  P    P   EE  +R+    K    +D S+ + S
Sbjct: 485 DKIDADGFCAPGTRVSGDDVIIGKTAP---LPPDSEELGMRS----KLHTXKDASISLKS 537

Query: 934 GVSGTVVDVRIFNRHGIDK 952
             +G +  V +      +K
Sbjct: 538 TXNGIIDQVLLTTNSHGNK 556


>gi|7716608|gb|AAF68454.1| RpoB [Candidatus Liberibacter africanus subsp. capensis]
          Length = 139

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 113/121 (93%), Positives = 116/121 (95%)

Query: 15  KFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAML 74
           KFFGKNPEIIDIPDLIEVQKASYD FLMMNI P++RPNEGLQAAFKSVFPI AFSGAAML
Sbjct: 19  KFFGKNPEIIDIPDLIEVQKASYDQFLMMNIRPEDRPNEGLQAAFKSVFPIKAFSGAAML 78

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
           EFVSYEFDPPKFDVDDCL RDLTYAVPLKI LRLIVFDVDEFTGAKSIKDIKEQSIYMGD
Sbjct: 79  EFVSYEFDPPKFDVDDCLRRDLTYAVPLKIILRLIVFDVDEFTGAKSIKDIKEQSIYMGD 138

Query: 135 L 135
           +
Sbjct: 139 V 139


>gi|134287220|ref|YP_001110916.1| DNA-directed RNA polymerase II [Heliothis virescens ascovirus 3e]
 gi|133722128|gb|ABO37250.1| DNA-directed RNA polymerase II [Heliothis virescens ascovirus 3e]
          Length = 1155

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 115/322 (35%), Gaps = 97/322 (30%)

Query: 1073 VVKVFVAMK----RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGV 1127
            ++K+ V            GDK       KGI   +L  EDMPF+ + G   DI++N   +
Sbjct: 885  LIKIRVEETIHHVTNQTIGDKFCSAMAQKGICGMVLNQEDMPFVANSGMTPDIIVNSHSM 944

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM V Q+  +  G       +++         +                         
Sbjct: 945  PSRMTVNQMMASVAGKLSCVAARRVDGSSFQNDEH------------------------- 979

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
              DD +  + +Q +         FDG                 SG  I+  G TG  F +
Sbjct: 980  --DDLLAHLCDQLRKVN------FDG-----------------SGAEIMCSGTTGVEFPQ 1014

Query: 1248 PVTVGYIYMLKLNHMVSDK-------VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            PV +G +Y L+   +V  K         AR+      +T+QPL G+++ GG R+GEME  
Sbjct: 1015 PVFIGVVYYLRPVQLVKHKKFSSTTTATARNR-----LTRQPLNGRAHEGGLRVGEMEKD 1069

Query: 1301 CIQAYGAAYVLQEMLTIKSD--------------------D---VVGRTRVYESIVAGND 1337
             +  +G    L E +   SD                    D   V  R +          
Sbjct: 1070 DLLCHGTVSFLMERMLNLSDAYTMRLCTVCGSESQVVKRNDHGYVCARCKTLT------- 1122

Query: 1338 TFETGTPESFNVLVKEMQALGL 1359
              E   P S  +L + +QA+G+
Sbjct: 1123 VTELVLPYSAKLLHQNLQAIGV 1144



 Score = 47.0 bits (110), Expect = 0.023,   Method: Composition-based stats.
 Identities = 25/159 (15%), Positives = 43/159 (27%), Gaps = 59/159 (37%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKF-- 86
           L++ Q  S+  F+  NI         L   F          G   L F +  F  P +  
Sbjct: 18  LVKAQLDSFASFIE-NIPNVLHDEPNL---FM--------CGN-ELRFENITFVKPSYIV 64

Query: 87  -------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                         ++L Y   ++  +                KD  E    +  LP M 
Sbjct: 65  NGKTMVLYPSTARLKNLDYEFSVRADV---------VNATLGTKDNIE----LCRLPAMV 111

Query: 140 ------------------------KDGTFVIKGIQRIVV 154
                                     G F+  G++R+++
Sbjct: 112 FGVLCNLHNAPDSKRLAKGEIMGDPGGYFIHNGVERVLI 150



 Score = 39.3 bits (90), Expect = 5.4,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 56/175 (32%), Gaps = 29/175 (16%)

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
           Q  +   R    +R +H           T                  N    IE+  R V
Sbjct: 582 QRALCVVRKLRLLRCLHHDV-SISVDGITGALEIWCDAGRFVRPLLYNRDDDIESLKRSV 640

Query: 606 CDGKVTNDV------VYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
              +  +++      V+  A+E    +IA                +    A E      +
Sbjct: 641 MYAEHADEIFNSGHMVHRDAIEIGREHIA----------------ITMHRAIE------D 678

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTG 714
            + +++ +P  +  + A+ IPF     S R     NM RQ++ +L       GTG
Sbjct: 679 NVKYVELNPNCMFGLLAAQIPFANYSPSPRACYKTNMARQSMGVLPMLNDCNGTG 733


>gi|6693812|gb|AAF24992.1|AF129445_1 RpoB [Klebsiella pneumoniae subsp. ozaenae]
 gi|4098393|gb|AAD09614.1| RNA polymerase beta-subunit [Klebsiella pneumoniae]
 gi|11526795|gb|AAG36784.1| RNA polymerase beta-subunit [Klebsiella granulomatis]
 gi|90192140|gb|ABD91730.1| RNA polymerase beta subunit [Klebsiella variicola]
 gi|90192142|gb|ABD91731.1| RNA polymerase beta subunit [Klebsiella variicola]
 gi|90192144|gb|ABD91732.1| RNA polymerase beta subunit [Klebsiella variicola]
 gi|90192148|gb|ABD91734.1| RNA polymerase beta subunit [Klebsiella variicola]
 gi|90192152|gb|ABD91736.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192158|gb|ABD91739.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192160|gb|ABD91740.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192164|gb|ABD91742.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192168|gb|ABD91744.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192170|gb|ABD91745.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192172|gb|ABD91746.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192174|gb|ABD91747.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192178|gb|ABD91749.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192180|gb|ABD91750.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192184|gb|ABD91752.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192188|gb|ABD91754.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192192|gb|ABD91756.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192194|gb|ABD91757.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192198|gb|ABD91759.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|90192200|gb|ABD91760.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|188988355|gb|ACD67722.1| RNA polymerase beta subunit [Klebsiella pneumoniae subsp.
           pneumoniae]
          Length = 170

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 107/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|119710056|gb|ABL96276.1| RNA polymerase II second largest subunit [Sphaerophorus fragilis]
          Length = 315

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/372 (16%), Positives = 106/372 (28%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 18   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R      EQ E   R    +      +       +  G      
Sbjct: 78   LF-RSLFYRSYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +S D      R++          ++     +  Q   S             
Sbjct: 137  DIIIGKTAPISPDAEELGQRTKQHTKRDTSTPLRSTENGIVDQVLLS------------- 183

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 184  -------TNSDGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 236

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 237  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 271

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  I+Y+
Sbjct: 272  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEIMYN 302

Query: 1239 GLTGEPFDRPVT 1250
            G TG+     V 
Sbjct: 303  GHTGQKLRAQVF 314



 Score = 87.4 bits (215), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 70/172 (40%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 13  YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 72

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 73  SIDRGLFRSLFYRSYTDQEKRVGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 132

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P      +P+ + L     +     RDTS  + S  +G V
Sbjct: 133 VSGEDIIIGKTAPI-----SPDAEELGQRTKQH--TKRDTSTPLRSTENGIV 177


>gi|224797603|gb|ACN62831.1| RNA polymerase beta subunit [Spiroplasma endosymbiont of Drosophila
           tenebrosa]
          Length = 225

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 124/233 (53%), Positives = 162/233 (69%), Gaps = 8/233 (3%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            L  D       V  R  G+ I+V  +++++ID SPKQ+VSIA S IPFLENDD+NR LM
Sbjct: 1   ELTPDNIIKNNNVIARSNGQNIIVGPKEVEYIDVSPKQIVSIATSCIPFLENDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQA+PLLK + P VGTG+E  VA+ SG A+VA   GIV+ VD+  I+I+S +   
Sbjct: 61  GANMQRQAIPLLKPQTPIVGTGVEYAVARDSGLAVVANLPGIVQYVDSNEIIIKSKDE-- 118

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
                 V  Y L +F+RSNQ T V   PLVK GD V  N I+ADGPS   G+LALG+N++
Sbjct: 119 ------VTTYELSRFERSNQGTSVTHIPLVKAGDVVEANQILADGPSMKDGELALGQNVI 172

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
           +AFM WHGYN+ED+++ISER+V +DV+TS+HIEE+ +  R TK G EEIT +I
Sbjct: 173 IAFMTWHGYNYEDAIIISERLVKDDVYTSMHIEEYNLECRKTKQGKEEITPEI 225


>gi|38373320|gb|AAR19024.1| RpoB [Mannheimia granulomatis]
 gi|260401062|gb|ACX37082.1| RNA polymerase beta subunit [Mannheimia granulomatis]
          Length = 172

 Score =  182 bits (462), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 105/172 (61%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSDLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRQQGESGLYKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 172


>gi|119643987|gb|ABL85599.1| RNA polymerase II second largest subunit [Candelariella reflexa]
          Length = 318

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 63/386 (16%), Positives = 112/386 (29%), Gaps = 81/386 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFINFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L +  Y +L E   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLRLKQGTYDKLDEDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHIKRDVSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF +DG
Sbjct: 177  ----------TNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRDG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +         +IS L    E+ 
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTDVTVQNISKLLH--EQG 284

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +    E  +                                                 
Sbjct: 285  YHSRGFEEMYN------------------------------------------------- 295

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNH 1261
               G TG      V +G  Y  +L H
Sbjct: 296  ---GHTGRKMVVQVFLGPTYYQRLRH 318



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 66/185 (35%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                   +  +L  G+N +VA   + G
Sbjct: 4   TNFDTRMDTMANILYYPQKPL----------ATTRSMEFINFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   + +     
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLRLKQGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE GI+  G  V+  DI++GK  P         E+L +        DV        +G+
Sbjct: 114 LDEDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRSTENGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDQVL 174


>gi|312204306|gb|ADQ47470.1| RNA polymerase II second largest subunit [Chapsa phlyctidioides]
          Length = 291

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 58/367 (15%), Positives = 110/367 (29%), Gaps = 81/367 (22%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 3    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R  +++ +R        +E   +    E + L    Y +L +   I  G        
Sbjct: 62   LFYRAYVEQEKRVGL---STVEHFEKPLRSETLRLKHGTYDKLDDDGLIAPGVRVSGEDI 118

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D      R++          ++     +                  ++K+
Sbjct: 119  IIGKTAPIAPDTEELGQRTKLHTKRDASTPLRSTENGI------------------VDKV 160

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 161  LL--TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 219  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 251

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 252  --------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGH 284

Query: 1241 TGEPFDR 1247
            TG     
Sbjct: 285  TGRKLRA 291



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E     +  +   +       +D+ G+I  G  V+
Sbjct: 55  DRGLFRSLFYRAYVEQEKRVGLSTVEHFEKPLRSETLRLKHGTYDKLDDDGLIAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPIAPDTEELGQRT-------KLHTKRDASTPLRSTENGIVDKVLLTTNQE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|151573363|gb|ABS17906.1| RNA polymerase II [Fusarium sp. NRRL 43705]
 gi|151573390|gb|ABS17924.1| RNA polymerase II [Fusarium sp. NRRL 43727]
 gi|151573396|gb|ABS17928.1| RNA polymerase II [Fusarium sp. NRRL 43729]
 gi|151573441|gb|ABS17958.1| RNA polymerase II [Fusarium sp. NRRL 43814]
 gi|151573546|gb|ABS18028.1| RNA polymerase II [Fusarium sp. NRRL 28002]
          Length = 293

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 57/366 (15%), Positives = 102/366 (27%), Gaps = 75/366 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVG 1252
              V  G
Sbjct: 288  AQVFFG 293



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|270000443|gb|ACZ58069.1| RNA polymerase II [Fusarium sp. NRRL 46440]
          Length = 298

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 57/373 (15%), Positives = 104/373 (27%), Gaps = 75/373 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  I+Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGH 285

Query: 1241 TGEPFDRPVTVGY 1253
            TG      V  G 
Sbjct: 286  TGRKLRAHVFFGP 298



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|45593176|gb|AAS68150.1| RNA polymerase beta subunit [Geobacter metallireducens]
          Length = 173

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 134/173 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V +GKVT +V + SA+EEE   IAQAN+ +D DG F  +
Sbjct: 61  ASLSTYARINEHGFVETPYRIVSEGKVTAEVKFFSALEEEGHAIAQANAEMDADGRFVND 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            V  R +GE +LV R++++ +D +P Q+VS+AASLIPFLENDD+NR LMG NM
Sbjct: 121 YVSARKSGEFLLVHRDELELMDVAPMQLVSVAASLIPFLENDDANRALMGSNM 173


>gi|307547675|gb|ADN44451.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  182 bits (461), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 63/375 (16%), Positives = 109/375 (29%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVIPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPXY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|56675894|emb|CAD98811.2| RNA polymerase II, second largest subunit [Gardenia sp. Oxelman 2319]
          Length = 545

 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 78/480 (16%), Positives = 134/480 (27%), Gaps = 85/480 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V R  I      +  +T +                   +      I   ++     +
Sbjct: 141  HDLVARGFIEYIDTEEEETTMISMTINDLVTARLNPEEAYSDTYTHCEIHPSLILGVCAS 200

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 201  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 257

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 258  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 316

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R           +          G           K+T +  D         
Sbjct: 317  KEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIHQD--------- 367

Query: 1021 WWQFAVQDEKVQRNVES--LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                   D +V   + S   K  + TS    E    +++      D +    +RV     
Sbjct: 368  -------DAQVPSALASRYTKRDHSTSLRHSETGIVDQVLLTTNADGLRFVKVRV----- 415

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMPF  +G   DI++NP  +PSRM +GQ+ E
Sbjct: 416  RSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPFTIEGITPDIIVNPHAIPSRMTIGQLIE 475

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+                                               
Sbjct: 476  CIMGKVAAHMGKEGD--------------------------------------------- 490

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                    +TP F     + I+  L        G   +Y+G TG P    + +G  Y  +
Sbjct: 491  --------ATP-FTDVTVDNISKALHKCGYQMRGFERMYNGHTGRPLTATIFLGPTYYQR 541



 Score =  109 bits (272), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 73/486 (15%), Positives = 143/486 (29%), Gaps = 102/486 (20%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++       + I+   +  A   F     + 
Sbjct: 3   PEGACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVG 62

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH---- 578
              +    +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 63  IHRDPDMLVRTLRRLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRCSRPLFIVEKQRLLI 121

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
               + +L +    +  G+ +   R          + Y+   EEE   I+          
Sbjct: 122 KKKDIQALQARESPDECGWHDLVAR--------GFIEYIDTEEEETTMISM--------- 164

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               +LV  R   E      +     +  P  ++ + AS+IPF +++ S R      M +
Sbjct: 165 -TINDLVTARLNPE--EAYSDTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 221

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+ +      F                    R   +  V                    
Sbjct: 222 QAMGIYVTNYQF--------------------RMDTLAYV-------------------- 241

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+PLV                      L  G N +VA   +
Sbjct: 242 ---------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACY 276

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 277 SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSY 336

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP  +        L            RD S  +  
Sbjct: 337 DKLDDDGLAPPGTRVSGEDVIIGKTTPIHQDDAQVPSAL------ASRYTKRDHSTSLRH 390

Query: 934 GVSGTV 939
             +G V
Sbjct: 391 SETGIV 396


>gi|330785396|gb|AEC46504.1| RNA polymerase II second largest subunit [Schizopelte californica]
 gi|330785398|gb|AEC46505.1| RNA polymerase II second largest subunit [Schizopelte californica]
          Length = 307

 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 60/380 (15%), Positives = 107/380 (28%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  ++    +E   +      +      Y +L E   +  G   
Sbjct: 64   LFRSFFYRTYV----EQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDEDGFVPPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR     K          E    +
Sbjct: 120  SGDDIIIGKTAPFQAPMADNA------------EGGQRTKMHAKRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+              R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  KVL------VTTNEGRRSVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L  A    G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKASATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYHSRGLEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      + +G  Y
Sbjct: 288  MHNGYTGRKLVAQIYLGPTY 307



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 62/199 (31%), Gaps = 16/199 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------ATTRSMEYLQFAELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       E                  + +DE G
Sbjct: 52  SVIMNQSAIDRGLFRSFFYRTYVEQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDEDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P         E   R        DV        +G+   V+
Sbjct: 112 FVPPGVRVSGDDIIIGKTAPFQAPMADNAEGGQRTKM-HAKRDVSAPLRSTEAGIVDKVL 170

Query: 941 DVRIFNRHGIDKNERSISV 959
                 R  +    R+  +
Sbjct: 171 VTTNEGRRSVKVRTRTTKI 189


>gi|292661195|gb|ADE35213.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661197|gb|ADE35214.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661199|gb|ADE35215.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661201|gb|ADE35216.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661203|gb|ADE35217.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661205|gb|ADE35218.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661233|gb|ADE35232.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661235|gb|ADE35233.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661249|gb|ADE35240.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661271|gb|ADE35251.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661283|gb|ADE35257.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661287|gb|ADE35259.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|292661289|gb|ADE35260.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661291|gb|ADE35261.1| RNA polymerase II [Morchella sp. Mel-20]
          Length = 298

 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 61/375 (16%), Positives = 112/375 (29%), Gaps = 81/375 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 166  ---------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++++LR       G  +
Sbjct: 255  -------------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEV 282

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y+G TG      V 
Sbjct: 283  MYNGYTGRKLVCQVF 297



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|193201491|gb|ACF15953.1| RNA polymerase II subunit [Lecanactis sp. Ertz 7995]
          Length = 301

 Score =  182 bits (461), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 59/370 (15%), Positives = 104/370 (28%), Gaps = 79/370 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 8    ILYYPQKPLASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  + +      Y +L     +  G        
Sbjct: 68   FYRTYI----EQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDGSVSPGVRVSGEDI 123

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 124  IIGKTAPFQAPM------------QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 169

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 170  ----VTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDL 225

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 226  IINPHAIPSRMTIAHLIECLLSKVSSITGREGD--------------------------- 258

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L  A     G  ++Y+G 
Sbjct: 259  --------------------------ATP-FTDITVSDISELLEFAGYQSRGFEMMYNGH 291

Query: 1241 TGEPFDRPVT 1250
            TG   +  + 
Sbjct: 292  TGRKLNAQIF 301



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 71/205 (34%), Gaps = 20/205 (9%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                      DL  G+N +VA   + GYN ED
Sbjct: 1   RMDTMSNILYYPQKPL----------ASTHSMNYLRFRDLPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       E                  + +D+ G
Sbjct: 51  SVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFEKPQKSQTMRTRPGTYEKLDDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P         E   R     K    RD S  + S  +G + 
Sbjct: 111 SVSPGVRVSGEDIIIGKTAPFQAPMQENSEGGQRT----KDHTKRDVSAPLRSTEAGIID 166

Query: 941 DVRIFNRHGIDKNE-RSISVEREQI 964
            V +    G    + R+ + +  QI
Sbjct: 167 RVLVTTTEGKRSVKVRTRTTKVPQI 191


>gi|10438131|dbj|BAB15175.1| unnamed protein product [Homo sapiens]
          Length = 459

 Score =  181 bits (460), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 117/324 (36%), Gaps = 59/324 (18%)

Query: 1001 GFKKSTVLSSDLISEYPRSQW-WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
            G K         + +        +    D        +    +       E+   + I+ 
Sbjct: 154  GIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMYYKSKENCVVDNIKV 213

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                +D   G  + V + + + R    GDK A RHG K                      
Sbjct: 214  CS--NDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQK---------------------- 249

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
                  G+ SR+           W    +      ++ D   N    P R  +  +I   
Sbjct: 250  ------GILSRL-----------WPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLI--- 289

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTP-VFDGAD--EEAINSMLRMADLDESGQSIL 1236
                       +S+   +         +TP +F   +   E    ML+ A  +  G   L
Sbjct: 290  -----------ESMAGKSAALHGLCHDATPFIFSEENSALEYFGEMLKAAGYNFYGTERL 338

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            Y G++G   +  + +G +Y  +L HMVSDK   R+TG+   VT QP+GG++ +GG R GE
Sbjct: 339  YSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGE 398

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSD 1320
            ME   + A+G +++L + L   SD
Sbjct: 399  MERDALLAHGTSFLLHDRLFNCSD 422



 Score = 62.0 bits (149), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 92/256 (35%), Gaps = 20/256 (7%)

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
           +  +  F G      +   S  +++A      +   + R + +   G        +  Y+
Sbjct: 5   IFEDEVFAGVTTHQELFPHSLLSVIANFIPFSDLNQSPRNMYQCQMG-KQTMGFPLLTYQ 63

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                +  +     Q PLV+                 D+ +  +G N +VA + + GY+ 
Sbjct: 64  DRSDNKLYRLQ-TPQSPLVRPSMY----------DYYDMDNYPIGTNAIVAVISYTGYDM 112

Query: 824 EDSMLISERMVSEDV-FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           ED+M++++          S++  EF  ++   K G   +   I       L+ +D+ G+ 
Sbjct: 113 EDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 172

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK--AVDVRDTSLRVPSGVSGTVV 940
            +GA++  GD     +     +  T E  ++     E     +++  S    SG    V 
Sbjct: 173 FIGAKLQYGDPYYSYL-----NLNTGESFVMYYKSKENCVVDNIKVCSNDTGSGKFKCVC 227

Query: 941 DVRIFNRHGIDKNERS 956
                 R+    ++ +
Sbjct: 228 ITMRVPRNPTIGDKFA 243


>gi|34980325|gb|AAO41855.1| RNA polymerase beta subunit [Phocoenobacter uteri]
          Length = 173

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N+YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQAN++LDE+  
Sbjct: 61  IGLINSLSVYARTNSYGFLETPYRKVIDGQVTEEIEYLSAIEEGQYVIAQANANLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTARGEHGESGLFRPEDIQYMDVSPQQMVSVAAALIPFLEHDDANRAL 173


>gi|46277310|gb|AAS86845.1| DNA-dependent RNA polymerase II [Amylascus tasmanicus]
          Length = 549

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 83/663 (12%), Positives = 180/663 (27%), Gaps = 130/663 (19%)

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             +    + +V  +     +      ++      +  D  F    +        I      
Sbjct: 11   DFMTQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTIQKLRRQGHIGSEVSL 70

Query: 661  IDFIDASPKQVVSIAASLIP--FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESV 718
            I  I     ++ + A  +    F+ ++D      G  + ++               +E  
Sbjct: 71   IQDIRNREFKIFTDAGRICRPLFIVDNDPASPRRGELVLQKHHIE----------RLEYD 120

Query: 719  VAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
                  +        + + V      +  ++ + + +   V     ++  R        Q
Sbjct: 121  REIDDESQRYGWGGLMSDGV------VEYIDAEEEETVMIVMTPEDLETSRQYHAGYEIQ 174

Query: 779  RPLVKVGDEVRRNDIIADGPSTDLG-DLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
            +  V     V+ +        T      ++   +  + +P+  +N       S R   + 
Sbjct: 175  Q-EVDPAQRVKASVSKFAHTWTHCEIHPSMILGICASIIPFPDHNQ------SPRNTYQS 227

Query: 838  VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                  +  F    R+                           +  +             
Sbjct: 228  AMGKQAMGVFLTNYRERM-----------------------DTMANILYYPQKPLGTTRS 264

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D S+ +  G     +   +F R  +D+  R  
Sbjct: 265  MEFLKFRELPAGQNAIVAIMCYSGYNQED-SVIMNQGSIDRGLFRSLFFRTYMDQERR-- 321

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +      + L    Y +L +   +  G           K+  ++ +   
Sbjct: 322  -IGMAVVEEFEKPTRSNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEE 380

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+++         ++     +  Q                             L+ V
Sbjct: 381  LGQRTKFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFV 420

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 421  KVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVPDLIINPHAIPSRMTIA 480

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             +                                                      + +L
Sbjct: 481  HLI-----------------------------------------------------ECLL 487

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                  +     +TP F     ++++ +LR       G  I+Y+G TG      V +G  
Sbjct: 488  SKVSSLRGFEGDATP-FTDVTVDSVSKLLREHGYQSRGFEIMYNGHTGRKLVVQVFLGPT 546

Query: 1255 YML 1257
            Y  
Sbjct: 547  YYQ 549


>gi|119640611|gb|ABL85499.1| RNA polymerase II second largest subunit [Roccella fuciformis]
          Length = 307

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 61/375 (16%), Positives = 107/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L     +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDNDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      E MPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEGMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGEEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +G  Y
Sbjct: 293  TGRKLNAQVFLGPTY 307



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 73/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D  G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVLRTRPGTYEKLDNDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|292661243|gb|ADE35237.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661251|gb|ADE35241.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|292661257|gb|ADE35244.1| RNA polymerase II [Morchella sp. Mel-16]
 gi|292661261|gb|ADE35246.1| RNA polymerase II [Morchella sp. Mel-17]
 gi|293601678|gb|ADE48243.1| RNA polymerase II [Morchella punctipes]
 gi|293601682|gb|ADE48245.1| RNA polymerase II [Morchella punctipes]
 gi|293601692|gb|ADE48250.1| RNA polymerase II [Morchella semilibera]
 gi|293601696|gb|ADE48252.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601698|gb|ADE48253.1| RNA polymerase II [Morchella sp. Mel-2]
 gi|293601702|gb|ADE48255.1| RNA polymerase II [Morchella sp. Mel-2]
 gi|293601718|gb|ADE48263.1| RNA polymerase II [Morchella sp. Mel-2]
 gi|293601726|gb|ADE48267.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601732|gb|ADE48270.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601734|gb|ADE48271.1| RNA polymerase II [Morchella sp. Mel-10]
 gi|293601738|gb|ADE48273.1| RNA polymerase II [Morchella punctipes]
 gi|293601740|gb|ADE48274.1| RNA polymerase II [Morchella punctipes]
 gi|293601744|gb|ADE48276.1| RNA polymerase II [Morchella sp. Mel-7]
 gi|293601748|gb|ADE48278.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601750|gb|ADE48279.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|293601752|gb|ADE48280.1| RNA polymerase II [Morchella sp. Mel-13]
 gi|293601754|gb|ADE48281.1| RNA polymerase II [Morchella sp. Mel-7]
          Length = 297

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 107/372 (28%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 255  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 285

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 286  GYTGRKLVCQVF 297



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|119640643|gb|ABL85515.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547755|gb|ADN44491.1| RNA polymerase II second largest subunit [Roccella montagnei]
 gi|307547757|gb|ADN44492.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 65/372 (17%), Positives = 107/372 (28%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             +  +     E+  SV    +E   + +  E +      Y +L +       V       
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGV------- 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
               V   D+I               E  QR  +  K          E    +++      
Sbjct: 118  --RVSGEDIIIGKTAPXXXXXXXXAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 171  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G++                                
Sbjct: 230  PHAIPSRMTIAHLIECLLSKVSTVTGQEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+ +LR A     G  ++ +G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMQNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVFLGPTY 307



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPXXXXXXXXAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|164653959|gb|ABY65348.1| RpoB [Volucribacter amazonae]
          Length = 173

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDED  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDEDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAYVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|292661253|gb|ADE35242.1| RNA polymerase II [Morchella sp. Mel-23]
          Length = 295

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 59/370 (15%), Positives = 107/370 (28%), Gaps = 75/370 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R  +D+ +R      E+ E   R    +      +       +  G        
Sbjct: 61   -RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D+     R ++         ++     +  Q                   
Sbjct: 120  IIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML---------------- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+
Sbjct: 164  ----TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E+++++LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGY 285

Query: 1241 TGEPFDRPVT 1250
            TG      V 
Sbjct: 286  TGRKLVCQVF 295



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 56  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 168

Query: 950 IDK 952
             K
Sbjct: 169 GLK 171


>gi|83415445|gb|ABC17930.1| RNA polymerase II second largest subunit [Allomyces arbuscula]
          Length = 584

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 103/668 (15%), Positives = 196/668 (29%), Gaps = 107/668 (16%)

Query: 479  LLRMERSIKERISSVDID--SVMPQDLINAKPVVSAVCEFFCSSQ-------------LS 523
              ++ + +    +              IN+  + + +     +               +S
Sbjct: 4    FQKLTKDVSRYFTVCIERGREFNLNMAINSNTITNGLRYALATGNWGDQKKFMETRAGVS 63

Query: 524  QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
            Q+       S ++H RRL+      + R     + R +H TH+G +CPAET EG   GLV
Sbjct: 64   QVLNRYTFASTLSHLRRLNT----PIGREGKLAKPRQLHNTHWGMVCPAETPEGQACGLV 119

Query: 584  SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
             +L   A ++  G    P  +  +   T ++  ++A    +      N S        + 
Sbjct: 120  KNLALMAYIS-VGSASGPILEFLEEWTTENLEEITASAIGSNTKVFVNGSWVGIHRQPDS 178

Query: 644  LV----FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
            LV      R +G+ +       D  D   +          P    ++  ++++  +   +
Sbjct: 179  LVQTLISLRRSGDIMPEVSVVRDVRDNELRIYTDAGRICRPLFIVNEQQQLVLRRDHVAR 238

Query: 700  AVPLLKAEAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
                       +  G+ E +  +     ++                +   +         
Sbjct: 239  LEVGEWGWEDLLANGIVEYLDTEEEETTMIC---------------MTPDDLAESRGDPI 283

Query: 759  VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
             D  +L K  R             K GD  ++       PS  LG       +  + +P+
Sbjct: 284  PDKSKLDKTARLKSR---------KAGDVCKQWSHCEIHPSMILG-------ICASIIPF 327

Query: 819  HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
              +N       S R   +       +  +    +                          
Sbjct: 328  PDHNQ------SPRNTYQSAMGKQAMGLYLTNFQXRM----------------------- 358

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 359  DTLANILYYPQKPLVATRSMKYLRFRELPAGQNAVVAIAVYSGYNQEDSIIMNQSSIDRG 418

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D+ ++S   + E  E   R+   +      +       +  G      
Sbjct: 419  LF-RSIYYRAYMDQEKKSGFSDVETFEKPTRETTLKLRHGSYDKIEEDGLVAPGTRVTGD 477

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L  D      R+                        TS    E    + + 
Sbjct: 478  DIIIGKTAPLPPDTSEMGART----------------TQTXKDVSTSLKSTEQGIVDHVM 521

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D       + VKV V   R  Q GDK A RHG KG V      EDMPF  DG   
Sbjct: 522  LTTNND-----GYKFVKVRVRSTRVPQMGDKFASRHGQKGTVGMTYRQEDMPFSADGVTP 576

Query: 1119 DIVLNPLG 1126
            D+++NP  
Sbjct: 577  DLIVNPHA 584


>gi|264658147|emb|CBH32066.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  181 bits (460), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 49/97 (50%), Positives = 69/97 (71%), Gaps = 8/97 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 15   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 74

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 75   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 111


>gi|56694300|gb|AAW22890.1| RNA polymerase II second largest subunit [Anemia phyllitidis]
          Length = 549

 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 85/489 (17%), Positives = 133/489 (27%), Gaps = 86/489 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN           +      I   M+    
Sbjct: 145  LVTKGFIEYVDTEEEETTMISMTISDLVNSRNHP----EEAYSDTYTHCEIHPSMILGVC 200

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 201  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 257

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        IF R   D+ ++  +
Sbjct: 258  EHLHFRHLPAGINAVVAIACYSGYNQEDSVIMNQSSVDRGFF-RSIFYRSYRDEEKKQGT 316

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+ E   R+                     G           K+T L  D       
Sbjct: 317  LVKEEFERPNREATLGMRHGSYEKLDDDGLAPPGTRVSGEDVIIGKTTPLPQDDTGS--- 373

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                                  +Y         R        Q         LR VK+ V
Sbjct: 374  -------------------QAQRYSKRDQSTCLRHSESGMIDQVLLTTNSEGLRFVKIRV 414

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+ ++G   DI++NP  +PSRM +GQ+ E
Sbjct: 415  RSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGITPDIIVNPHAIPSRMTIGQLIE 474

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+  +         +IS         +                      
Sbjct: 475  CIMGKVAAHMGKEGDATPFTDVTVDNISKALHRCGYQMRG---------------FETMY 519

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
               SG  +S  +F G                                         Y  +
Sbjct: 520  NGHSGRRLSAMIFLG---------------------------------------PTYYQR 540

Query: 1259 LNHMVSDKV 1267
              HMV DK+
Sbjct: 541  PKHMVDDKI 549



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 55/323 (17%), Positives = 103/323 (31%), Gaps = 36/323 (11%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++  S    + I+   +  A   F     +    E  
Sbjct: 12  LVKNLALMAYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVGIHREPD 71

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
             +  +   RR   +  + GV R     E+R ++  +     P    E   + +  S   
Sbjct: 72  LLVKTLRQLRRQVDVNTEVGVVRDIRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKS--- 127

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
              + A    +T      D      + Y+   EEE   I+   S L    +  EE     
Sbjct: 128 --DIRALQSKDTAEVGWHDLVTKGFIEYVDTEEEETTMISMTISDLVNSRNHPEE----- 180

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP------ 702
                     +     +  P  ++ + AS+IPF +++ S R      M +QA+       
Sbjct: 181 -------AYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 233

Query: 703 ----------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                     L   + P V T  ME +  +   A I A  A            +   +  
Sbjct: 234 QLRMDTLAYVLYYPQKPLVTTRAMEHLHFRHLPAGINAVVAIACYSGYNQEDSVIMNQSS 293

Query: 752 LDPSTSGVDIYRLMKFQRSNQNT 774
           +D        YR  + +   Q T
Sbjct: 294 VDRGFFRSIFYRSYRDEEKKQGT 316


>gi|38373292|gb|AAR19010.1| RpoB [Actinobacillus succinogenes]
          Length = 173

 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQAN++LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANANLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|327239545|gb|AEA39622.1| RpoB [Corynebacterium striatum]
          Length = 137

 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 58/165 (35%), Positives = 85/165 (51%), Gaps = 36/165 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G K+           +   L++  E++                   
Sbjct: 1    QVLEVHLGWLAHA-GWKVDV-----DDPKNAELLKTLPEELYDVP--------------- 39

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                   +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 40   -------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRSGEPYK 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   YPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 137


>gi|293601720|gb|ADE48264.1| RNA polymerase II [Morchella rufobrunnea]
          Length = 297

 Score =  181 bits (460), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 61/375 (16%), Positives = 112/375 (29%), Gaps = 81/375 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 166  ---------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++++LR       G  +
Sbjct: 255  -------------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEV 282

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y+G TG      V 
Sbjct: 283  MYNGYTGRKLVCQVF 297



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|293601688|gb|ADE48248.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601730|gb|ADE48269.1| RNA polymerase II [Morchella sp. Mel-9]
 gi|293601736|gb|ADE48272.1| RNA polymerase II [Morchella sp. Mel-10]
          Length = 294

 Score =  181 bits (459), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 61/372 (16%), Positives = 111/372 (29%), Gaps = 81/372 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G      
Sbjct: 60   RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 117  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 162

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 163  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 252  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 282

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 283  GYTGRKLVCQVF 294



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 55  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|169125453|gb|ACA48209.1| RNA polymerase II second largest subunit [Tricharina praecox]
          Length = 291

 Score =  181 bits (459), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 64/366 (17%), Positives = 112/366 (30%), Gaps = 75/366 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  +  I      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNXSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  +D+ +R      E+ E   R    +      +       +  G           
Sbjct: 60   LFYRAYMDQEKRIGMQVVEEFEKPMRGTTLKLKHGTYDKLEDDGLVAPGIRVSGEDIIIG 119

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +S+D                DE  QR     K    T     E+   +++      
Sbjct: 120  KTAPISAD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVMLTTNA 164

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +     + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   DI++N
Sbjct: 165  DGL-----KFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRSEDMPFTAEGIVPDIIIN 219

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 220  PHAIPSRMTIAHLIECQLSKVASLRGFEGD------------------------------ 249

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++S+LR +     G  ++Y+G TG+
Sbjct: 250  -----------------------ATP-FTDVTVDSVSSLLRQSGYQSRGFEVMYNGYTGK 285

Query: 1244 PFDRPV 1249
                 V
Sbjct: 286  KLVAQV 291


>gi|4098377|gb|AAD09605.1| RNA polymerase beta-subunit [Escherichia coli]
 gi|4098399|gb|AAD09617.1| RNA polymerase beta-subunit [Shigella dysenteriae]
          Length = 170

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 107/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|307547765|gb|ADN44496.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 62/374 (16%), Positives = 108/374 (28%), Gaps = 79/374 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYI 1254
            TG   +  V +G  
Sbjct: 293  TGRKLNAQVFLGPT 306



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|299849845|gb|ADJ57167.1| RNA polymerase II second largest subunit [Xylogone sphaerospora]
          Length = 322

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 67/389 (17%), Positives = 113/389 (29%), Gaps = 81/389 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQXDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               G         V  G  Y  +L HMV 
Sbjct: 300  ---GR---KLRAQVFFGPTYYQRLRHMVD 322



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 67/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN  DS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQXDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|158514837|gb|ABW69374.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 171

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 102/170 (60%), Positives = 131/170 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 2   QFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+ 
Sbjct: 62  NSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFTDT 121

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR LMG
Sbjct: 122 YVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRALMG 171


>gi|293601700|gb|ADE48254.1| RNA polymerase II [Morchella sp. Mel-5]
 gi|293601722|gb|ADE48265.1| RNA polymerase II [Morchella sp. Mel-5]
          Length = 297

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 60/372 (16%), Positives = 107/372 (28%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  I+Y+
Sbjct: 255  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEIMYN 285

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 286  GYTGRKLVCQVF 297



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|268528981|gb|ACZ06543.1| RpoB [Mannheimia varigena]
          Length = 172

 Score =  181 bits (459), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+N  L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANSAL 172


>gi|4098379|gb|AAD09606.1| RNA polymerase beta-subunit [Escherichia fergusonii ATCC 35469]
          Length = 170

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 107/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVIDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|18643363|gb|AAL76281.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
          Length = 170

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 132/170 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQL Q  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLFQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|258627697|gb|ACV85523.1| RNA polymerase beta subunit [Volucribacter sp. 31564/2sv]
          Length = 173

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAYVTARGEHGESGLYRPEEIQYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|238058452|gb|ACR39377.1| RNA polymerase beta subunit [Aeromonas hydrophila]
          Length = 167

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 96/167 (57%), Positives = 127/167 (76%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL
Sbjct: 61  SLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDEL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           + CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 IPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRAL 167


>gi|299849857|gb|ADJ57175.1| RNA polymerase II second largest subunit [Scytalidium cuboideum]
          Length = 322

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 67/389 (17%), Positives = 112/389 (28%), Gaps = 81/389 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +             +S L       
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDXTPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               G         V  G  Y  +L HMV 
Sbjct: 300  ---GR---KLKAQVFFGPTYYQRLRHMVD 322



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|4098401|gb|AAD09618.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
           serovar Shomron]
 gi|4098403|gb|AAD09619.1| RNA polymerase beta-subunit [Salmonella enterica subsp. salamae
           serovar Sofia]
 gi|4098405|gb|AAD10529.1| RNA polymerase beta-subunit [Salmonella enterica subsp. arizonae]
 gi|4098409|gb|AAD09620.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
           serovar Paratyphi A]
          Length = 170

 Score =  181 bits (459), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|156453779|gb|ABU63744.1| RpoB [Pasteurellaceae bacterium Clin29]
          Length = 173

 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTARGEHGEAGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|300123537|emb|CBK24809.2| unnamed protein product [Blastocystis hominis]
          Length = 1056

 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 85/437 (19%), Positives = 149/437 (34%), Gaps = 71/437 (16%)

Query: 888  VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            V+P +++V  + P   S +       +   G+ A+      + V S     + D  + NR
Sbjct: 654  VSPLNVMVYPMMPMVRSRVLDLLHFSQLPAGQNAM------VAVMSYSGYDIEDAVVLNR 707

Query: 948  HGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTV 1007
              ID+    + + ++Q+  L +  +    ++         + +         + +K    
Sbjct: 708  ASIDRGYGRVVISKKQVFSLKKYPNGSSDLIKGPPRREDQKNIDDHTWNRLFEPYK---- 763

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDD-- 1065
                L S+            D  V ++V      +   +  L        E   + D   
Sbjct: 764  ---ALGSDGIVESGVPIHPGDIMVNKHVPMDTGSFGADRDQLRAAPVKYKESGGYVDKVL 820

Query: 1066 --MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                     V+K  V   R  + GDK +                                
Sbjct: 821  ITTTDNEYFVIKTMVRDMRRPELGDKFS-------------------------------- 848

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
                 SR                  G+K    +   + N   S    + + ++       
Sbjct: 849  -----SR-----------------HGQKGVVGLITGQENLPFSTAGIYPDMIMNPHGFPS 886

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
            +++      +L        G      +F G D E     L     + SG+ + Y G+TGE
Sbjct: 887  RMTVGKMMELLAGKAGLWDGERKFGTIFGGTDIEDCAEELIRHGFNYSGKDLFYSGITGE 946

Query: 1244 PFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            P    +  G +Y  +L HMV DKV+AR+ G    +T QP  G+S  GG R+GEME  C+ 
Sbjct: 947  PLRAYIFTGPVYYQRLKHMVKDKVFARAKGPRMALTHQPTQGRSRDGGLRVGEMERDCLV 1006

Query: 1304 AYGAAYVLQEMLTIKSD 1320
            A+G + +L E L + SD
Sbjct: 1007 AHGTSMLLIERLLLSSD 1023



 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 118/954 (12%), Positives = 262/954 (27%), Gaps = 181/954 (18%)

Query: 66  TAFSGAAMLEFVSYEFDPP-----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           +  +    + +   E   P           K    +C  R LTY+ P+   +   + D  
Sbjct: 9   SDVNHKFFVRYEKIEVGEPMVLEDSSIINNKITPMECRKRSLTYSAPIFADIIYTLGDK- 67

Query: 115 EFTGAKSIKDIKEQSIYMGDLPLMT------------------------KDGTFVIKGIQ 150
                     I  + + +G +P+M                           G F++KG +
Sbjct: 68  ----------IIRKKVRIGQIPIMLHSCKCVLRNKSPAELAAMQECLYDPGGYFIVKGNE 117

Query: 151 RIVVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRID-R 208
           ++++S    S   +  D +     +             +        + K  ++++ +  
Sbjct: 118 KVLLSGEQMSKNRVLCDINDDGTIVVNVTSSTAE----RKSRC-YVLEKKGKLYLKHNVF 172

Query: 209 RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
            + +P+      +G++S+ EI++    +  Y      +          +G       +  
Sbjct: 173 TKDIPICIAFRCMGIESDQEIMALIGNEPKYR----TYFNQSIEEAHELGIFTQQQALKW 228

Query: 268 DTGEQVIESGKKLTSGLL-KSLKEKGVKFLGITSDCL-CGLYVAEDIVNGETGEIYIEAG 325
                 +  G+        +  +E     +      +    +     +   T E      
Sbjct: 229 VGSLVSMRKGRWSRKRSAEEEGREVFNTTILCHVPVVRYDFWPKCVYLAYMTRECL---Q 285

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
            + D   L +  +   + I             +         +    +L    RV     
Sbjct: 286 CIFDHSLLSDKDYYGNKRIETAGDLMSLLFEDLFKMYNAKVKEFVNKSLQKTTRVNAFDV 345

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
           V        +      ++ K     + R  ++ +   +    + +I     +  I+  V+
Sbjct: 346 VPVMQQFHDIITNGCVNAIKSGNWVLKRFHIDRKGVAEPVTRLSYIAAIGHMTRIRSHVE 405

Query: 446 LRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLIN 505
                     +       V         Q   GL++    +       D  ++       
Sbjct: 406 KAQKISGPRALQPSQFGMVCPSDTPEGEQC--GLVKSLTILAYITIDQDEKAL----RQV 459

Query: 506 AKPVVSAVCEFFCSSQLSQL---EEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDV 561
           A  +       F + +L         +N      H++  + + G   + R         V
Sbjct: 460 AYDLGVLDVGLFGAEELYARPASLVFLNGGLLGVHSQPQALVRGVRQLRRRGLLGAFVSV 519

Query: 562 HPTHYGRICPAETSEGHNIGLVSSLTS-----FARVNAYGFIETPYRKVCDGKVTNDVVY 616
           +     R        G     +  L       F        I      + +      + Y
Sbjct: 520 YYDRIRRCVHLSCDGGRICRPLLVLNRETGRPFLTKAHTDGIRRGTITIQELVRAGVIEY 579

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
           +   EE +  IA  +  +                             ++  P  ++ I A
Sbjct: 580 IDVNEENSCLIAVTDKDITPAH-----------------------THMEIDPVSILGIVA 616

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIP+ +++ S R    C M +QA+  +                                
Sbjct: 617 SLIPYPDHNQSPRNTYQCAMGKQAIGTVACNQ---------------------------- 648

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                       +  +D S   V +Y +M   RS            +V D +  + + A 
Sbjct: 649 ------------QQRVDVSPLNVMVYPMMPMVRS------------RVLDLLHFSQLPAG 684

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
             +             VA M + GY+ ED+++++   +       +  ++     +    
Sbjct: 685 QNAM------------VAVMSYSGYDIEDAVVLNRASIDRGYGRVVISKKQVFSLKKYPN 732

Query: 857 GPEEITRDIPNVSE-------------EGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
           G  ++ +  P   +             E  K +   GI+  G  ++PGDI+V K  P   
Sbjct: 733 GSSDLIKGPPRREDQKNIDDHTWNRLFEPYKALGSDGIVESGVPIHPGDIMVNKHVPMDT 792

Query: 904 SPMTPEEKLLRA---IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
                +   LRA    + E    V    +         +  +    R     ++
Sbjct: 793 GSFGADRDQLRAAPVKYKESGGYVDKVLITTTDNEYFVIKTMVRDMRRPELGDK 846


>gi|6693820|gb|AAF24996.1|AF129449_1 RpoB [Raoultella planticola]
 gi|6693822|gb|AAF24997.1|AF129450_1 RpoB [Raoultella planticola]
 gi|19172394|gb|AAL85882.1|AF480166_1 RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|4098373|gb|AAD09603.1| RNA polymerase beta-subunit [Citrobacter freundii]
 gi|4098375|gb|AAD09604.1| RNA polymerase beta-subunit [Enterobacter cloacae]
 gi|4098383|gb|AAD09609.1| RNA polymerase beta-subunit [Kluyvera ascorbata]
 gi|4098385|gb|AAD09610.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|4098387|gb|AAD09611.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|4098389|gb|AAD09612.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|18643359|gb|AAL76279.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|18643361|gb|AAL76280.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|18643365|gb|AAL76282.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|18643367|gb|AAL76283.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|18643369|gb|AAL76284.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|28849308|gb|AAO52820.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
 gi|46361496|gb|AAS89294.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|46361498|gb|AAS89295.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|46361500|gb|AAS89296.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|46361502|gb|AAS89297.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|46361504|gb|AAS89298.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
 gi|90192136|gb|ABD91728.1| RNA polymerase beta subunit [Raoultella planticola]
 gi|90192138|gb|ABD91729.1| RNA polymerase beta subunit [Raoultella planticola]
 gi|90192202|gb|ABD91761.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192206|gb|ABD91763.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192208|gb|ABD91764.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192210|gb|ABD91765.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192212|gb|ABD91766.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192214|gb|ABD91767.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192216|gb|ABD91768.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192220|gb|ABD91770.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192222|gb|ABD91771.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192224|gb|ABD91772.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192226|gb|ABD91773.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192228|gb|ABD91774.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|90192230|gb|ABD91775.1| RNA polymerase beta subunit [Klebsiella oxytoca]
          Length = 170

 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|293601812|gb|ADE48310.1| RNA polymerase II [Morchella sp. Mes-4]
          Length = 291

 Score =  181 bits (458), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 59/364 (16%), Positives = 105/364 (28%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  CQVF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|67942360|gb|AAY83380.1| DNA-dependent RNA polymerase II [Desmazierella acicola]
          Length = 544

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 94/666 (14%), Positives = 177/666 (26%), Gaps = 129/666 (19%)

Query: 585  SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
            SL S+  V         Y    + +   +     +      ++      +  D       
Sbjct: 2    SLMSYITVGTPSDPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDPMHLVRN 61

Query: 645  VFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVP 702
            V        +      I D  D   K          P F+ N+D+     G  + ++   
Sbjct: 62   VQEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHI 121

Query: 703  LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
                +                         GIVE VDA       +    +       + 
Sbjct: 122  QRLEDDQ-------ERDMDDRWGWTGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAAQVR 174

Query: 763  RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            +  + +         + P   V     +       PS  LG       +  + +P+  +N
Sbjct: 175  QGFQIEEETDRHKRVKAP---VNTYSHQYTHCEIHPSMILG-------ICASIIPFPDHN 224

Query: 823  FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
                      M  + +   + +  F                                 + 
Sbjct: 225  QSPRNTYQSAMGKQAMG--VFLTNFSERM---------------------------DTMA 255

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  +  I      +  D+ +   S +   +   
Sbjct: 256  NILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-R 314

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R   D+ +R   +    +E   +      + L    Y +L +   +  G       
Sbjct: 315  SLFYRSYTDQEKR---IGMMVVEEFEKPLRHNTLRLKHGTYEKLDDDGLVAPGVRVSGED 371

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  ++ D                DE  QR     K    T     E+   +++  
Sbjct: 372  IIIGKTAPIAPD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVLL 416

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       L+  KV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 417  -----TTNAEGLKFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTCEGIIPD 471

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +V+NP  +PSRM +  + E  L       G +                            
Sbjct: 472  LVINPHAIPSRMTIAHLIECQLSKVSSLRGMEGD-------------------------- 505

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F     ++++++LR       G  ++Y+G
Sbjct: 506  ---------------------------ATP-FTDVTVDSVSNLLREEGYQSRGFEVMYNG 537

Query: 1240 LTGEPF 1245
             TG+  
Sbjct: 538  HTGKKL 543



 Score =  106 bits (265), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 75/487 (15%), Positives = 145/487 (29%), Gaps = 97/487 (19%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 22  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG-HE 74

Query: 549 VARARAGVEMRDVHPTHYGRIC-------PAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           V+  R   +      T  GR+C          TSE     ++         +        
Sbjct: 75  VSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEDDQERDMDD 134

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD-----EDGSFTEELVFCRCAGE-EIL 655
                       V Y+ A EEE   I      L+       G   EE        +  + 
Sbjct: 135 RWGWTGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAAQVRQGFQIEEETDRHKRVKAPVN 194

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
               +    +  P  ++ I AS+IPF +++ S R      M +QA+ +            
Sbjct: 195 TYSHQYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFS------ 248

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                              +   + + +  Y       +     
Sbjct: 249 -----------------------------------ERMDTMANILYYPQKPLATTRSMEY 273

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +  R                        +L  G+N +V  M + GYN EDS+++++  + 
Sbjct: 274 LKFR------------------------ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSID 309

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNP 890
             +F S+    +    +   +   E        +   +     + +D+ G++  G  V+ 
Sbjct: 310 RGLFRSLFYRSYTDQEKRIGMMVVEEFEKPLRHNTLRLKHGTYEKLDDDGLVAPGVRVSG 369

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P         ++       +K    RD S  + S  +G V  V +      
Sbjct: 370 EDIIIGKTAPIAPDADEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVLLTTNAEG 422

Query: 951 DKNERSI 957
            K  +  
Sbjct: 423 LKFAKVR 429


>gi|312204332|gb|ADQ47483.1| RNA polymerase II second largest subunit [Gyalecta truncigena]
          Length = 665

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/335 (17%), Positives = 103/335 (30%), Gaps = 81/335 (24%)

Query: 918  GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVI 977
                 +  D+ +   S +   +    +F R  +++ +R        +E   +    E + 
Sbjct: 409  CYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMEQEKRVGI---SLVEQFEKPLRSETLR 464

Query: 978  LDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            +    Y +L E   I  G           K+  LS D      R ++         ++  
Sbjct: 465  VKHGTYDKLDEDGIIAPGVRVSGEDIIIGKTAPLSQDAEELGQRMKFHTKRDASTPLRST 524

Query: 1035 VESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRH 1094
               +                  ++K+          L+ VKV +   +  Q GDK A RH
Sbjct: 525  ESGI------------------VDKVLV--TTNAEGLKFVKVRMRTTKVPQIGDKFASRH 564

Query: 1095 GNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            G KG +      EDMPF  DG   D+++NP  +PSRM +  + E  L       G +   
Sbjct: 565  GQKGTIGITYRQEDMPFSTDGITPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD- 623

Query: 1155 LINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGA 1214
                                                                +TP F   
Sbjct: 624  ----------------------------------------------------ATP-FTEI 630

Query: 1215 DEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
              + ++ +LR       G  ++Y+G TG      +
Sbjct: 631  TVDQVSRLLREHGYQSRGFEVMYNGHTGRKLVAQI 665



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/142 (22%), Positives = 55/142 (38%), Gaps = 12/142 (8%)

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSE 870
             + GYN EDS+++++  +   +F S+    +    +   +   E        +   V  
Sbjct: 408 ACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMEQEKRVGISLVEQFEKPLRSETLRVKH 467

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +DE GII  G  V+  DI++GK  P  +      +++       K    RD S  
Sbjct: 468 GTYDKLDEDGIIAPGVRVSGEDIIIGKTAPLSQDAEELGQRM-------KFHTKRDASTP 520

Query: 931 VPSGVSGTVVDVRIFNRHGIDK 952
           + S  SG V  V +       K
Sbjct: 521 LRSTESGIVDKVLVTTNAEGLK 542



 Score = 58.9 bits (141), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 4/87 (4%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 32  GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 87

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCD 607
           GLV +L     +      E      C+
Sbjct: 88  GLVKNLALMCYITVGSISEPIIDLWCN 114


>gi|258627695|gb|ACV85522.1| RNA polymerase beta subunit [Volucribacter sp. B96/6]
          Length = 173

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE N  IAQAN++LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVDGQVTEEIEYLSAIEEGNYVIAQANANLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAYVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|110294725|gb|ABG66796.1| RpoB [Pasteurellaceae bacterium R46]
          Length = 173

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 133/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYKPEEIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|293601704|gb|ADE48256.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601714|gb|ADE48261.1| RNA polymerase II [Morchella sp. Mel-6]
          Length = 293

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/367 (16%), Positives = 106/367 (28%), Gaps = 75/367 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  +D+ +R      E+ E   R    +      +       +  G           
Sbjct: 61   LFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 121  KTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML------------------- 161

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 162  -TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 221  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 250

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 251  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 286

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 287  KLVCQVF 293



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 54  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 114 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 166

Query: 950 IDK 952
             K
Sbjct: 167 GLK 169


>gi|161015860|gb|ABX55931.1| RNA polymerase II subunit [Fusarium sp. NRRL 47514]
          Length = 293

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/366 (15%), Positives = 104/366 (28%), Gaps = 75/366 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVTVG 1252
              V  G
Sbjct: 288  AQVFFG 293



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|299849851|gb|ADJ57171.1| RNA polymerase II second largest subunit [Xylogone sphaerospora]
          Length = 322

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/389 (17%), Positives = 113/389 (29%), Gaps = 81/389 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               G         V  G  Y  +L HMV 
Sbjct: 300  ---GR---KLRAQVFFGPTYYQRLRHMVD 322



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|283806276|dbj|BAI66376.1| RNA polymerase second largest subunit [Massarina arundinariae]
          Length = 296

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/365 (16%), Positives = 106/365 (29%), Gaps = 81/365 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 7    YPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 65

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L E   +  G           
Sbjct: 66   RAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDEDGVVAPGVRVSGDDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + +D      ++           ++     +  Q                      
Sbjct: 123  KTAPIPTDAKELGQKTALHTKRDVSTPLRSTENGIVDQ--------------------VL 162

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF   G   DI++N
Sbjct: 163  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSQGLTPDIIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L      +G++                                
Sbjct: 223  PHAIPSRMTIAHLVECLLSKVGAVIGQEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E I+ +LR     + G  I+Y+G TG+
Sbjct: 253  -----------------------ATP-FTDVTVENISEILRNNGFQQRGFEIMYNGHTGK 288

Query: 1244 PFDRP 1248
                 
Sbjct: 289  KLRAQ 293



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 63/176 (35%), Gaps = 19/176 (10%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 1   MMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIM 50

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +DE G++  
Sbjct: 51  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDEDGVVAP 110

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           G  V+  DI++GK  P      T  ++L +        DV        +G+   V+
Sbjct: 111 GVRVSGDDIIIGKTAPI----PTDAKELGQKTALHTKRDVSTPLRSTENGIVDQVL 162


>gi|261499958|gb|ACX85232.1| RpoB [Mannheimia varigena]
 gi|261499960|gb|ACX85233.1| RpoB [Mannheimia varigena]
 gi|261499962|gb|ACX85234.1| RpoB [Mannheimia varigena]
 gi|261499964|gb|ACX85235.1| RpoB [Mannheimia varigena]
 gi|261499966|gb|ACX85236.1| RpoB [Mannheimia varigena]
 gi|261499968|gb|ACX85237.1| RpoB [Mannheimia varigena]
 gi|261499970|gb|ACX85238.1| RpoB [Mannheimia varigena]
 gi|261499972|gb|ACX85239.1| RpoB [Mannheimia varigena]
 gi|261499974|gb|ACX85240.1| RpoB [Mannheimia varigena]
 gi|261499976|gb|ACX85241.1| RpoB [Mannheimia varigena]
 gi|261499978|gb|ACX85242.1| RpoB [Mannheimia varigena]
 gi|261499980|gb|ACX85243.1| RpoB [Mannheimia varigena]
 gi|261499982|gb|ACX85244.1| RpoB [Mannheimia varigena]
 gi|261499984|gb|ACX85245.1| RpoB [Mannheimia varigena]
 gi|261499986|gb|ACX85246.1| RpoB [Mannheimia varigena]
 gi|268528991|gb|ACZ06548.1| RpoB [Mannheimia varigena]
          Length = 172

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N  S +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNRRSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 172


>gi|330785386|gb|AEC46499.1| RNA polymerase II second largest subunit [Paraschismatomma
            ochroleucum]
 gi|330785388|gb|AEC46500.1| RNA polymerase II second largest subunit [Paraschismatomma
            ochroleucum]
 gi|330785390|gb|AEC46501.1| RNA polymerase II second largest subunit [Paraschismatomma
            ochroleucum]
 gi|330785392|gb|AEC46502.1| RNA polymerase II second largest subunit [Paraschismatomma
            ochroleucum]
 gi|330785394|gb|AEC46503.1| RNA polymerase II second largest subunit [Paraschismatomma
            ochroleucum]
          Length = 307

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/377 (15%), Positives = 102/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVVMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     F R  I++ +       E+ E   +                   +  G      
Sbjct: 64   LF-RSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDEDGFVAPGVRVSGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+   +  +       Q  +   + + V   + S +                   
Sbjct: 123  DIIIGKTAPFAQPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLIDRVL----------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+ +L+ +     G  ++++
Sbjct: 260  ----------------------------ATP-FTDVTVSGISELLKGSGYQSRGLEVMHN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 291  GHTGRKLMAQVYLGPTY 307



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 63/187 (33%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVVMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       E                  + +DE G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDEDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +      E   R        DV        +G+   V+      R  
Sbjct: 121 GDDIIIGKTAPFAQPMADNAEGGQRTKM-HSKRDVSAPLRSTEAGLIDRVLVTTNEGRRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|330785240|gb|AEC46426.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
 gi|330785264|gb|AEC46438.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
 gi|330785266|gb|AEC46439.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
          Length = 307

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 107/380 (28%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   ++ +       Q  +   + + V   + S +                
Sbjct: 120  SGDDIIIGKTAPFANPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLVDRVL-------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ---------VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYQSRGLEL 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGHTGRKLMAQVFLGPTY 307



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 62/187 (33%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       E                  + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R        DV        +G+   V+      R  
Sbjct: 121 GDDIIIGKTAPFANPMADNAEGGQRTKM-HSKRDVSAPLRSTEAGLVDRVLVTTNEGRRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|293601680|gb|ADE48244.1| RNA polymerase II [Morchella sp. Mel-9]
          Length = 289

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/367 (16%), Positives = 110/367 (29%), Gaps = 81/367 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 1    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 59

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L E   +  G           
Sbjct: 60   RSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 116

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 117  KTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML------------------- 157

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 158  -TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 216

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 217  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 246

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 247  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 282

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 283  KLVCQVF 289



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA + + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 9   TRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKR 68

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   +       +DE G++  G  V+  DI++GK  P        
Sbjct: 69  IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEM 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++       +K    RD S  + S  +G V  V +       K
Sbjct: 129 GQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 165


>gi|151573149|gb|ABS17764.1| RNA polymerase II [Fusarium sp. NRRL 43511]
 gi|151573381|gb|ABS17918.1| RNA polymerase II [Fusarium sp. NRRL 43724]
 gi|151573384|gb|ABS17920.1| RNA polymerase II [Fusarium sp. NRRL 43725]
 gi|151573402|gb|ABS17932.1| RNA polymerase II [Fusarium sp. NRRL 43731]
 gi|151573417|gb|ABS17942.1| RNA polymerase II [Fusarium sp. NRRL 43736]
 gi|151573426|gb|ABS17948.1| RNA polymerase II [Fusarium sp. NRRL 43809]
 gi|151573432|gb|ABS17952.1| RNA polymerase II [Fusarium sp. NRRL 43811]
 gi|151573435|gb|ABS17954.1| RNA polymerase II [Fusarium sp. NRRL 43812]
 gi|151573438|gb|ABS17956.1| RNA polymerase II [Fusarium sp. NRRL 43813]
 gi|151573444|gb|ABS17960.1| RNA polymerase II [Fusarium sp. NRRL 43815]
 gi|151573447|gb|ABS17962.1| RNA polymerase II [Fusarium sp. NRRL 43816]
 gi|151573450|gb|ABS17964.1| RNA polymerase II [Fusarium sp. NRRL 43817]
 gi|151573456|gb|ABS17968.1| RNA polymerase II [Fusarium sp. NRRL 43819]
 gi|151573465|gb|ABS17974.1| RNA polymerase II [Fusarium sp. NRRL 43823]
 gi|151573563|gb|ABS18039.1| RNA polymerase II [Fusarium sp. FSSC_15a KOD-2010]
 gi|151573566|gb|ABS18041.1| RNA polymerase II [Fusarium sp. NRRL 28010]
 gi|151573575|gb|ABS18047.1| RNA polymerase II [Fusarium sp. NRRL 28016]
 gi|151573581|gb|ABS18051.1| RNA polymerase II [Fusarium sp. NRRL 28018]
 gi|151573859|gb|ABS18235.1| RNA polymerase II [Fusarium sp. NRRL 43805]
          Length = 293

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/366 (15%), Positives = 102/366 (27%), Gaps = 75/366 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTVG 1252
              V  G
Sbjct: 288  AQVFFG 293



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|4098381|gb|AAD09607.1| RNA polymerase beta-subunit [Hafnia alvei ATCC 13337]
          Length = 170

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGIVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|293601756|gb|ADE48282.1| RNA polymerase II [Morchella sp. Mes-5]
 gi|293601760|gb|ADE48284.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601774|gb|ADE48291.1| RNA polymerase II [Morchella sp. Mes-11]
 gi|293601782|gb|ADE48295.1| RNA polymerase II [Morchella sp. Mes-9]
 gi|293601794|gb|ADE48301.1| RNA polymerase II [Morchella sp. Mes-9]
 gi|293601802|gb|ADE48305.1| RNA polymerase II [Morchella sp. Mes-11]
 gi|293601810|gb|ADE48309.1| RNA polymerase II [Morchella sp. Mes-11]
 gi|293601820|gb|ADE48314.1| RNA polymerase II [Morchella sp. Mes-11]
          Length = 291

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/364 (16%), Positives = 105/364 (28%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  CQVF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|293601690|gb|ADE48249.1| RNA polymerase II [Morchella sp. Mel-10]
          Length = 290

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/364 (16%), Positives = 105/364 (28%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 61   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 120

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 121  PIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML--------------------TT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 161  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 221  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 247

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 248  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 286

Query: 1247 RPVT 1250
              V 
Sbjct: 287  CQVF 290



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 51  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 111 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 163

Query: 950 IDK 952
             K
Sbjct: 164 GLK 166


>gi|34923310|gb|AAQ83542.1| RpoB [Volucribacter psittacicida]
 gi|117959720|gb|ABK59831.1| RpoB [Volucribacter psittacicida]
 gi|258627693|gb|ACV85521.1| RNA polymerase beta subunit [Volucribacter sp. 62Hinz]
          Length = 173

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAYVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|145307898|gb|ABP57253.1| RNA polymerase II second largest subunit [Batkoa major]
          Length = 299

 Score =  181 bits (458), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 109/372 (29%), Gaps = 75/372 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D+ +++  VE E  E  +                    I  G      
Sbjct: 63   LF-RSIYYRTXLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDGLIAPGTRVSGD 121

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T + +D      R +          ++     +  +   + +           
Sbjct: 122  DIIIGKTTPVPADSEELGQRLRGHTKKDVSTPLKSTETGIVDRVMLTINQ---------- 171

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 172  ----------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAEGIVP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +G + E  +G      G +                           
Sbjct: 222  DLIINPHAIPSRMTIGHMVECLVGKVGTMDGSEGD------------------------- 256

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +L      + G  ++Y+
Sbjct: 257  ----------------------------ATP-FTDVTVDGISKLLARFGYQKRGFEVMYN 287

Query: 1239 GLTGEPFDRPVT 1250
            G TG+     + 
Sbjct: 288  GHTGKKLTAQIY 299



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 68/180 (37%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+        + T L   E            +     + +++ G
Sbjct: 51  SVIMNQSSIDRGLFRSIYYRTXLDQEKKTGLVEMETFEKPSYKTTLRLRHGTYEKLEDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK TP         E+L + + G    DV        +G+   V+
Sbjct: 111 LIAPGTRVSGDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGIVDRVM 166


>gi|224419476|emb|CAX51319.1| RNA polymerase beta subunit [Corynebacterium xerosis]
          Length = 113

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 51/97 (52%), Positives = 69/97 (71%), Gaps = 8/97 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 17   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLIDGRSGEPFPFPVSVGYMYML 76

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 77   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 113


>gi|293601686|gb|ADE48247.1| RNA polymerase II [Morchella tomentosa]
 gi|293601694|gb|ADE48251.1| RNA polymerase II [Morchella tomentosa]
 gi|293601708|gb|ADE48258.1| RNA polymerase II [Morchella tomentosa]
 gi|293601724|gb|ADE48266.1| RNA polymerase II [Morchella tomentosa]
 gi|293601728|gb|ADE48268.1| RNA polymerase II [Morchella tomentosa]
 gi|293601742|gb|ADE48275.1| RNA polymerase II [Morchella tomentosa]
          Length = 288

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/356 (17%), Positives = 110/356 (30%), Gaps = 81/356 (22%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R  
Sbjct: 11   MEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMDQEKR-- 67

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +  + +E   +      + L    Y +L E   +  G           K+  ++ D+  
Sbjct: 68   -IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDE 126

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R ++         ++     +  Q                             L+ V
Sbjct: 127  MGQRQKFHTKRDVSTPLRSTENGIVDQVML--------------------TTNAEGLKFV 166

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 167  KVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHAIPSRMTIA 226

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 227  HLIECQLSKVSSLRGFEGD----------------------------------------- 245

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                        +TP F     E+++++LR       G  ++Y+G TG      V 
Sbjct: 246  ------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLVCQVF 288



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA + + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 8   TRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKR 67

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   +       +DE G++  G  V+  DI++GK  P        
Sbjct: 68  IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEM 127

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++       +K    RD S  + S  +G V  V +       K
Sbjct: 128 GQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 164


>gi|291170436|gb|ADD82427.1| RNA polymerase II second largest subunit [Dothideomycetes sp. A6]
          Length = 323

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/389 (15%), Positives = 107/389 (27%), Gaps = 81/389 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 13   DTMANILYYPQKPLATTKSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMSQSSIDRG 72

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y ++ +   I  G   
Sbjct: 73   LF-RSLFYRSYTDQEKR---IGMSVVEKFEKPMRADTLRLKHGTYDKIDDDGLIAPGVRV 128

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 129  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTESGIVDQVLL----------- 177

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 178  ---------TTNSEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 228

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L   C   G +  +          IS L     + 
Sbjct: 229  LTPDLIINPHAIPSRMTIAHLIECLLSKVCSLTGLEGDATPFTDVTVDAISALLR--NQG 286

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                                                    +G + 
Sbjct: 287  YQSRGFEVM---------------------------------------------YNGHT- 300

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVS 1264
               G         V  G  Y  +L HMV 
Sbjct: 301  ---GR---KLVAQVFFGPTYYQRLRHMVD 323


>gi|31580900|dbj|BAC77552.1| RNA polymerase beta subunit [Nicotiana sylvestris]
          Length = 248

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 110/226 (48%), Gaps = 25/226 (11%)

Query: 31  EVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDPPKFDV 88
           ++Q   +  F+          ++GL         I         + FV  Y+   P    
Sbjct: 3   QIQFEGFCRFI----------DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVEPLIKE 52

Query: 89  DDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKG 148
            D ++  LTY+  L ++  LI          K+ +D++EQ+I++G++PLM   GTF++ G
Sbjct: 53  RDAVYESLTYSSELYVSAGLIW---------KNSRDMQEQTIFIGNIPLMNSLGTFIVNG 103

Query: 149 IQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR 208
           I RIV++Q+ +SPGI++  +     +S   +Y   II D G  +++E D K  I  R+ R
Sbjct: 104 IYRIVINQILQSPGIYYRSELDHNGIS---VYTGTIISDWGGRLELEIDRKARIWARVSR 160

Query: 209 RRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCFPLSAAD 253
           ++K+ +   L A+G++  EIL    YP+I  S   D     + + +
Sbjct: 161 KQKISILVLLSAMGLNLREILENVCYPEIFLSFLSDKERKKIGSKE 206


>gi|307716716|gb|ADN88411.1| RNA polymerase beta-subunit [Serratia rubidaea]
          Length = 170

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD+DG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDDGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|158514839|gb|ABW69375.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 173

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 133/173 (76%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           + +LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 1   TYKLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENF 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 RFTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|328726866|gb|AEB38716.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 136

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/164 (35%), Positives = 84/164 (51%), Gaps = 36/164 (21%)

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E HLGW     G KI       +   +   L++  E +                    
Sbjct: 1    VLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP---------------- 38

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDR 1247
                  +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  
Sbjct: 39   ------AGSLTATPVFDGATNEEVAGLLTNSRPNRDGDVMVDANGKAQLFDGRSGEPFPY 92

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   PVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 136


>gi|298104012|dbj|BAJ09331.1| RNA polymerase II second largest subunit [Dasyscyphella
            longistipitata]
          Length = 610

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 114/677 (16%), Positives = 211/677 (31%), Gaps = 95/677 (14%)

Query: 472  KNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
               +R    R+ + + + +S    +         + +  + + +     +          
Sbjct: 2    CQLFRNLFRRLTQDVYKYLSKCVSENKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAA 61

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET E
Sbjct: 62   SATAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPE 117

Query: 577  GHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            G   GLV +L    +  V         +    + +V  +   L A      ++      +
Sbjct: 118  GQACGLVKNLALMCYVTVGTPSDPIIEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVGV 177

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLM 692
              D +   + V        I      I D  D   K          P F+ ++D +    
Sbjct: 178  HRDPAHLVKTVQHLRRSHLISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDLDSANK 237

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA--IVAKRAGIVEQVDAIRI---VIRS 747
            G  +  +       +   +   M+     S+G          G+VE VDA      +I  
Sbjct: 238  GNLVLNKDHIRRLEDDQTMPANMDDEQKASAGYFGFQGLINEGVVEYVDAEEEETVMIVM 297

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
               DLD S      Y++    R +++  +N+R    +             PS  LG    
Sbjct: 298  TPEDLDISRQLQAGYQI----RPDESGDLNKRVKAPMNPTAHIWTHCEIHPSMILG---- 349

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N                        ++       +G      D   
Sbjct: 350  ---ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGVFLTNFDQRM 388

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 389  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 437

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R   +   Q+E   +    + + L    Y +L 
Sbjct: 438  VIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNQLEQFEKPYRADTLKLKHGTYDKLD 493

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            E   I  G           K+  ++ D                +E  QR     K    T
Sbjct: 494  EDGIIAPGVRVSGEDIIIGKTAPIAPD---------------AEELGQRTKAHTKRDAST 538

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                 E+   +++     GD +     R VKV +   +  Q GDK A RHG KG +    
Sbjct: 539  PLRSTENGIVDQVLITTSGDGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITY 593

Query: 1105 PCEDMPFLKDGTPVDIV 1121
              EDMPF + G   D++
Sbjct: 594  RQEDMPFTRQGIVPDLI 610


>gi|328726868|gb|AEB38717.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 136

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/164 (35%), Positives = 84/164 (51%), Gaps = 36/164 (21%)

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E HLGW     G KI       +   +   L++  E +                    
Sbjct: 1    VLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP---------------- 38

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDR 1247
                  +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  
Sbjct: 39   ------AGSLTATPVFDGATNEEVAGLLANSRPNRDGDVMVDANGKAQLFDGRSGEPFPY 92

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   PVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 136


>gi|4098411|gb|AAD10531.1| RNA polymerase beta-subunit [Yersinia enterocolitica]
          Length = 170

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 107/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDEDG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDEDGRFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|4001754|gb|AAC94960.1| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica
           serovar Typhi]
          Length = 170

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 104/170 (61%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E++V CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDVVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|330785296|gb|AEC46454.1| RNA polymerase II second largest subunit [Dictyographa arabica]
          Length = 307

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/380 (15%), Positives = 107/380 (28%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRAMEYMSFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSLFYRTYI----EQQQAVGFAALEQFEKPVKQMTLRTRPGTYEKLDDDGFVPPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   + +                +E  QR  +  +          E    +
Sbjct: 120  SGDDIIIGKTAPFNQEAADN------------EEGGQRTKQHTRRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VK+     +  Q GDK A RHG KG +      EDMPF  DG
Sbjct: 168  RVL------VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  VVPDLIINPHAIPSRMTVAHLIECLLSKVASFKGFEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F+      I+  ++       G  +
Sbjct: 260  -------------------------------ATP-FEPTTVSQISHFMQEQGYHSRGLEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +Y+G TG      + +G  Y
Sbjct: 288  MYNGYTGRKLAAQIYLGPTY 307



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 64/196 (32%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------ATTRAMEYMSFSELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       E                  + +D+ G
Sbjct: 52  SVIMNQSAIDRGLFRSLFYRTYIEQQQAVGFAALEQFEKPVKQMTLRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  +     EE   +        DV        +G+   V+
Sbjct: 112 FVPPGVRVSGDDIIIGKTAPFNQEAADNEEGG-QRTKQHTRRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKIRTRT 186


>gi|220067239|gb|ACL79828.1| RNA polymerase B subunit [Gloeocapsopsis crepidinum LEGE 06123]
          Length = 200

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 95/205 (46%), Positives = 137/205 (66%), Gaps = 6/205 (2%)

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           A EE++  +A  ++ +D++G      V  R   +      E++D++  SP Q+VS+A S+
Sbjct: 2   ADEEDDLRVAPGDTPIDDNGYILGSQVPVRYRQDWTTTTPEQVDYVAVSPVQIVSVATSM 61

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE+DD+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G +  V
Sbjct: 62  IPFLEHDDANRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGEISYV 121

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA RI +R         +     Y++ K+QRSNQ+TC+NQRPLV+ GD V    +IADG 
Sbjct: 122 DANRIRVRPD------GSGSEIEYQISKYQRSNQDTCLNQRPLVQKGDRVVAGQVIADGS 175

Query: 799 STDLGDLALGRNMLVAFMPWHGYNF 823
           +T+ G+LALG+N+++A+MPW GYN+
Sbjct: 176 ATEGGELALGQNIMIAYMPWDGYNY 200


>gi|282598432|gb|ADA83446.1| RNA polymerase beta subunit [Corynebacterium sp. NML99-0018]
          Length = 139

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 54/167 (32%), Positives = 88/167 (52%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  + +     +   +   L++  E++    + +            
Sbjct: 1    QVLELHLGWLA-HTGWTVDT-----QDPKNEELLKTLPEELYDVPAESLT---------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNEELTRLLASSKPNRDGDVMVNENGKAQLFDGRSGEPYQ 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VGY+Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGYMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|219564109|gb|ACL28238.1| RNA polymerase II second largest subunit [Hyaloscypha aureliella]
          Length = 296

 Score =  180 bits (457), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/373 (17%), Positives = 113/373 (30%), Gaps = 81/373 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G     
Sbjct: 62   -RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E+   +++
Sbjct: 118  EDIIIGKTAPIAPD---------------AEELGQRTKAHIKRDASTPLRSTENGIVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF + G  
Sbjct: 163  LI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +                          
Sbjct: 218  PDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD------------------------ 253

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  I+Y
Sbjct: 254  -----------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEIMY 283

Query: 1238 DGLTGEPFDRPVT 1250
             G TG      V 
Sbjct: 284  HGHTGRKLMAQVF 296



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 57  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 117 GEDIIIGKTAPIAPDAEELGQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 166


>gi|34923334|gb|AAQ83554.1| RpoB [Bisgaard Taxon 14]
          Length = 173

 Score =  180 bits (457), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 107/173 (61%), Positives = 133/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+E V CR   GE  L   E+ID++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDEFVTCRGEHGESGLYKPEQIDYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|38373262|gb|AAR18995.1| RpoB [Aggregatibacter actinomycetemcomitans]
 gi|38373306|gb|AAR19017.1| RpoB [Aggregatibacter aphrophilus ATCC 33389]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYKPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|6693818|gb|AAF24995.1|AF129448_1 RpoB [Raoultella terrigena]
          Length = 170

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFEEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|28849306|gb|AAO52819.1| RNA polymerase beta-subunit [Klebsiella oxytoca]
          Length = 170

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/168 (62%), Positives = 131/168 (77%)

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           V EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP 
Sbjct: 3   VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI 62

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
           ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS
Sbjct: 63  ETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANS 122

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           +LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 123 NLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|311992423|gb|ADQ26769.1| RpoB [Pasteurella sp. B]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDED  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|83415491|gb|ABC17953.1| RNA polymerase II second largest subunit [Piptocephalis corymbifera]
          Length = 622

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 101/688 (14%), Positives = 202/688 (29%), Gaps = 90/688 (13%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVV----------- 510
            +R+   G ++   +R+   ++ +  ++ +  V  +S+     +  K              
Sbjct: 2    KRMDLAGPLIAGLFRMLFRKLTKDARKYLQKVIDNSLDFNLTLAVKSNTLTSGLKYSIAT 61

Query: 511  ----SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                         + +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKAMTARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   A ++           + +  + N      +       
Sbjct: 118  GMVCPAETPEGQACGLVKNLALMAYISVGTATAPVIDFLEEWNMENLDELPPSPLSSAIT 177

Query: 627  IAQANSSLDEDGSFTEELVFCRC--AGEEILVPREKIDFIDASPKQ---VVSIAASLIPF 681
                N          + LV        ++ +V RE     D   ++      +     P 
Sbjct: 178  KIFVNGVWVGVHRDAQHLVINFKALRRKDPVVFREVSVVRDIRERELHLFTDVGRCCRPL 237

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
               +++++ L+       A+   +   P             S   + +     ++ + A+
Sbjct: 238  FVVEEASQRLILRRKHIAALQTFEPSGPL-------QGPDGSRNLVPSMTWDDLKSLGAV 290

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              +    E       S  D+     +          Q   V+ G      D +A    T 
Sbjct: 291  EFLDTEEEETCMICMSPQDLADNRLY----------QDMGVERG----PGDDLAARIRTS 336

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
               +           P         + I   ++            ++       +G    
Sbjct: 337  ---IFSHTWTHCEIPPSM------ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLT 387

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               I               +  +        +    +       +   +  + AI     
Sbjct: 388  NYQIRM-----------DTLANILYYPQKPLVTTRAMELLKFRELPAGQNAIVAIACYSG 436

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    ++ R  +D+  R  S    + E      +    +    
Sbjct: 437  YNQEDSVIMNQSSIDRGLF-RSLYFRTYMDQERRVGSATTLEEEFERPTHETTLRM-RAG 494

Query: 982  IYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
             Y +L +   I  G           K+  L  +                +E  QR     
Sbjct: 495  TYEKLEDDGLIGPGVRVTGDDIIIGKTAALPPE---------------SEEFGQRQGSHT 539

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
            +    T     E    +++             ++ VK+ V   R  Q GDK A RHG KG
Sbjct: 540  RRDLSTPLKSTEQGLVDQVLV-----TTNAEGMKFVKIRVRSTRIPQMGDKFASRHGQKG 594

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
             +      EDMPF  DG   D+++NP  
Sbjct: 595  TIGITYRTEDMPFTADGLTPDLIINPHA 622


>gi|158514851|gb|ABW69381.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 170

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 102/170 (60%), Positives = 131/170 (77%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIG
Sbjct: 1   LSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT
Sbjct: 61  LINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFT 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 DTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRAL 170


>gi|219564107|gb|ACL28237.1| RNA polymerase II second largest subunit [Hyaloscypha aureliella]
          Length = 294

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/372 (17%), Positives = 112/372 (30%), Gaps = 81/372 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G      
Sbjct: 60   RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D                +E  QR    +K    T     E+   +++ 
Sbjct: 117  DIIIGKTAPIAPD---------------AEELGQRTKAHIKRDASTPLRSTENGIVDQVL 161

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV +   +  Q GDK A RHG KG +      EDMPF + G   
Sbjct: 162  I-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIVP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  I+Y 
Sbjct: 252  ----------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEIMYH 282

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 283  GHTGRKLMAQVF 294



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 55  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 115 GEDIIIGKTAPIAPDAEELGQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 164


>gi|38373278|gb|AAR19003.1| RpoB [Actinobacillus minor NM305]
 gi|38373284|gb|AAR19006.1| RpoB [Actinobacillus porcitonsillarum]
 gi|38373286|gb|AAR19007.1| RpoB [Actinobacillus porcitonsillarum]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 132/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYKPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34923324|gb|AAQ83549.1| RpoB [Pasteurella canis]
 gi|156453771|gb|ABU63740.1| RpoB [Pasteurella canis]
 gi|156453773|gb|ABU63741.1| RpoB [Pasteurella canis]
 gi|156453775|gb|ABU63742.1| RpoB [Pasteurella canis]
 gi|156453777|gb|ABU63743.1| RpoB [Pasteurella canis]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDED  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEDLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34923304|gb|AAQ83539.1| RpoB [Bibersteinia trehalosi]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 132/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34923322|gb|AAQ83548.1| RpoB [Actinobacillus delphinicola]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 101/173 (58%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   +++ ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGEKGESGLFRPDEVQYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|2105319|gb|AAB57999.1| similar to variola A25R and vaccinia A24R [Molluscum contagiosum
            virus subtype 1]
          Length = 337

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/247 (24%), Positives = 93/247 (37%), Gaps = 42/247 (17%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             V+V    +R    GDK   R   KG V+ +    ++P+  DG   DI++N   + SR  
Sbjct: 39   KVRVLTIKERRPVLGDKFTSRTSQKGTVAYLADEAELPYDDDGLTPDIIVNSTSIYSRKT 98

Query: 1133 VGQIFETHLGWA----CVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            +  + E  L  A          + + +         I    +F  K   +          
Sbjct: 99   ISMLVEIMLTAAYAAKPYNNQDQNRPICFPSSNETSIETYLAFARKCYES---------- 148

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                 VF    E  + + L         +  LYD  T EP+   
Sbjct: 149  ---------------------VFPELRETELQARL-------FCEKTLYDPETDEPYAAA 180

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V +G IY L+L H+  DK   R  G  + + +Q   G+   GG + GEME  C+ A+GAA
Sbjct: 181  VFMGPIYYLRLRHLTQDKATVRCRGKKTKLIRQANEGRKRGGGIKFGEMERDCLIAHGAA 240

Query: 1309 YVLQEML 1315
              + E+L
Sbjct: 241  NTITEIL 247


>gi|312204328|gb|ADQ47481.1| RNA polymerase II second largest subunit [Gyalecta flotowii]
          Length = 713

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/355 (16%), Positives = 108/355 (30%), Gaps = 81/355 (22%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +    AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 437  MEFLKFRQLPAGQNAXVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMEQEKRVG 495

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    E + +    Y +L +   I  G           K+  LS D   
Sbjct: 496  I---SLVEQFEKPLRTETLRVKHGTYDKLDDDGIIAPGVRVSGEDIIIGKTAPLSQDAEE 552

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+++         ++     +                  ++K+          L+ V
Sbjct: 553  LGQRTKFHTKRDASTPLRSTESGI------------------VDKVLM--TTNAEGLKFV 592

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM + 
Sbjct: 593  KVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSTDGITPDLIINPHAIPSRMTIA 652

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 653  HLIECQLSKVSSLRGFEGD----------------------------------------- 671

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                        +TP F     + ++ +LR       G  + Y+G TG      +
Sbjct: 672  ------------ATP-FTEITVDQVSRLLREHGYQSRGFEVXYNGHTGRKLVAQI 713



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 60/164 (36%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                      L  G+N  VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 434 TRSMEFLKFRQLPAGQNAXVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYMEQEKR 493

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   V       +D+ GII  G  V+  DI++GK  P  +     
Sbjct: 494 VGISLVEQFEKPLRTETLRVKHGTYDKLDDDGIIAPGVRVSGEDIIIGKTAPLSQDAEEL 553

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++        K    RD S  + S  SG V  V +       K
Sbjct: 554 GQRT-------KFHTKRDASTPLRSTESGIVDKVLMTTNAEGLK 590



 Score = 73.6 bits (179), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/267 (14%), Positives = 80/267 (29%), Gaps = 23/267 (8%)

Query: 474 QYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
            +R+   ++ + +    +              + +  + + +     +            
Sbjct: 1   LFRMLFNKLTKDVYXYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGDQKKAASA 60

Query: 522 ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61  KAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579 NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
             GLV +L     +      E    +    + +V  +            ++      +  
Sbjct: 117 ACGLVKNLALMCYITVGSPSEPIVEFMVQRNMEVLEEYEPTRNPHSTKVFVNGVWVGVHR 176

Query: 637 DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGC 694
           D +     V        I      I D  D   K          P F+  +D      G 
Sbjct: 177 DPAHLVSTVQTLRRQNMISFEVSLIRDIRDREFKIFTDAGRVCRPLFVIENDKKSANKGY 236

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAK 721
            +  + +     +   +   M+    K
Sbjct: 237 LVLNKELIGKLEDDRELPQDMDPDERK 263


>gi|172085059|gb|ACB71409.1| RpoB [Gallibacterium melopsittaci]
 gi|172085061|gb|ACB71410.1| RpoB [Gallibacterium melopsittaci]
 gi|172085063|gb|ACB71411.1| RpoB [Gallibacterium melopsittaci]
 gi|172085065|gb|ACB71412.1| RpoB [Gallibacterium melopsittaci]
 gi|172085067|gb|ACB71413.1| RpoB [Gallibacterium melopsittaci]
 gi|172085069|gb|ACB71414.1| RpoB [Gallibacterium melopsittaci]
 gi|172085071|gb|ACB71415.1| RpoB [Gallibacterium melopsittaci]
 gi|172085073|gb|ACB71416.1| RpoB [Gallibacterium melopsittaci]
 gi|172085075|gb|ACB71417.1| RpoB [Gallibacterium melopsittaci]
 gi|172085077|gb|ACB71418.1| RpoB [Gallibacterium trehalosifermentans]
 gi|172085079|gb|ACB71419.1| RpoB [Gallibacterium trehalosifermentans]
 gi|172085083|gb|ACB71421.1| RpoB [Gallibacterium genomosp. 3]
 gi|172085085|gb|ACB71422.1| RpoB [Gallibacterium genomosp. 3]
 gi|172085087|gb|ACB71423.1| RpoB [Gallibacterium genomosp. 3]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|4098397|gb|AAD09616.1| RNA polymerase beta-subunit [Providencia stuartii]
          Length = 170

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 131/170 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDEIHYLSAIEEGNFIIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           N+ L EDGSF EEL+ CR  GE  L  R++++++D S +QVVS+ ASLIP
Sbjct: 121 NTVLAEDGSFVEELITCRNRGESSLFSRDQVEYMDVSTQQVVSVGASLIP 170


>gi|89274942|gb|ABD65912.1| RNA polymerase II second largest subunit [Pseudozyma flocculosa]
          Length = 353

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/385 (15%), Positives = 103/385 (26%), Gaps = 75/385 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              ++ V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 44   DSMMHVLCYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 103

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  + + ++   ++ E+ E   R+          +          G      
Sbjct: 104  LF-RSMYYRGYVAEEKKVGVMQLEEFEKPDRNTTIRMKHGTYDKIDADGFCAPGTRVSGD 162

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L  D      RS+          ++     +  Q                 
Sbjct: 163  DVIIGKTAPLPPDSEELGMRSKLHTKKDASISLKSTESGIIDQVLL-------------- 208

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q+G K A RHG KG +      EDMPF  +G   
Sbjct: 209  ------TTNANGNKFVKVRVRNFRVPQTGXKFASRHGQKGTIGITYRQEDMPFSAEGVTP 262

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +G + E  L       G++  +          +S +   L      
Sbjct: 263  DIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRG 322

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                 G +    
Sbjct: 323  LEVM-----------------------------------------------YHGHT---- 331

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMV 1263
            G         V +G  Y  +L HMV
Sbjct: 332  GR---KLQAQVYLGPTYYQRLKHMV 353



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 40/188 (21%), Positives = 70/188 (37%), Gaps = 22/188 (11%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                C  Q+PL                      +L  G+N +VA M + GYN EDS+++
Sbjct: 46  MMHVLCYPQKPL----------GTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIM 95

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S++   +    +   +   E            +       ID  G    
Sbjct: 96  NQSSIDRGLFRSMYYRGYVAEEKKVGVMQLEEFEKPDRNTTIRMKHGTYDKIDADGFCAP 155

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  D+++GK  P    P   EE  +R+    K    +D S+ + S  SG +  V +
Sbjct: 156 GTRVSGDDVIIGKTAP---LPPDSEELGMRS----KLHTKKDASISLKSTESGIIDQVLL 208

Query: 945 FNRHGIDK 952
                 +K
Sbjct: 209 TTNANGNK 216


>gi|34923308|gb|AAQ83541.1| RpoB [Bisgaard Taxon 7]
          Length = 173

 Score =  180 bits (456), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGSYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTARGEHGEAGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|330785406|gb|AEC46509.1| RNA polymerase II second largest subunit [Fulvophyton murex]
          Length = 305

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/375 (15%), Positives = 104/375 (27%), Gaps = 73/375 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E+ E  A+           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDEDGFVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR  E  K          E    +++ 
Sbjct: 123  DIIIGKTAPFQAPMQENA------------EGGQRTKEHTKRDVSAPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L         +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVSATQAMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+ +L+ A     G  ++Y+
Sbjct: 260  ----------------------------ATP-FTEVTVSGISQLLKDAGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPVTVGY 1253
            G TG   +  + +G 
Sbjct: 291  GYTGRKLNAQIFLGP 305



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 61/197 (30%), Gaps = 16/197 (8%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   QRMDTMANILYYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +       E                    +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFYRTYIEQQQAVGFNALEEFEKPAKQLTMRTRPGTYDKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           G +  G  V+  DI++GK  P         E   R        DV        +G+   V
Sbjct: 111 GFVAPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRTKE-HTKRDVSAPLRSTEAGIIDRV 169

Query: 940 VDVRIFNRHGIDKNERS 956
           +      R  +    R+
Sbjct: 170 LVTTTDGRRSVKVRTRT 186


>gi|46277332|gb|AAS86856.1| DNA-dependent RNA polymerase II [Peziza saniosa]
          Length = 550

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 84/669 (12%), Positives = 170/669 (25%), Gaps = 121/669 (18%)

Query: 589  FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
            +  V         +    + +V  +     +      ++      +  D  F    +   
Sbjct: 3    YVSVGTPSQPIVDFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTIQKL 62

Query: 649  CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEA 708
                 I      I  I     ++ + A  +   L   D++               L  + 
Sbjct: 63   RRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPA-------SPRRGELVLQK 115

Query: 709  PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              +    E                G+VE +DA       +    +   +    +   + Q
Sbjct: 116  HHISKLEEDREGDDRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQ 175

Query: 769  RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
            ++       QR    V             PS  LG       +  + +P+  +N      
Sbjct: 176  QTLDPA---QRVKGAVNKFAHTWTHCEIHPSMILG-------ICASIIPFPDHNQXXXXX 225

Query: 829  ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
                         +      +                               +  +    
Sbjct: 226  XXXXXXXXXXXXXLTNYRXRMDT-----------------------------MANILYYP 256

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                     +       +   +  + AI      +  D+ +   S +   +    +F R 
Sbjct: 257  QKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRT 315

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
             +D+ +R      E+ E   R           +       +  G           K+  +
Sbjct: 316  YMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPI 375

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
            + +      R+++         ++     +  Q                           
Sbjct: 376  APNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQ 415

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +P
Sbjct: 416  EGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVPDLIINPHAIP 475

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM +  +                                                    
Sbjct: 476  SRMTIAHLI--------------------------------------------------- 484

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
              + +L      +     +TP F     ++++++LR       G  I+Y+G TG      
Sbjct: 485  --ECLLSKVSSLRGFEGDATP-FTDVTVDSVSTLLREHGYQSRGFEIMYNGHTGRKMVAQ 541

Query: 1249 VTVGYIYML 1257
            V +G  Y  
Sbjct: 542  VFLGPTYYQ 550



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 61/479 (12%), Positives = 119/479 (24%), Gaps = 85/479 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 15  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 68

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL-----VSSLTSFARVNAYGFIE 599
           G               +         P    +           V      +++      +
Sbjct: 69  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHISKLEEDREGD 128

Query: 600 TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAGEE 653
             Y           V Y+ A EEE   I      L+    F       + L   +     
Sbjct: 129 DRY-GWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQTLDPAQRVKGA 187

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
           +          +  P  ++ I AS+IPF +++                            
Sbjct: 188 VNKFAHTWTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXLT------- 240

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
                    + A I+      +    ++  +          +   +  Y           
Sbjct: 241 --NYRXRMDTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSG--------- 289

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
              NQ                    S  +   ++ R +  +       + E  + +S   
Sbjct: 290 --YNQE------------------DSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMS--- 326

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
                     +EEFE   R           +   +       +DE G++  G  V+  DI
Sbjct: 327 ---------VVEEFEKPTR----------GNTLRLKHGTYDKLDEDGLVAPGVRVSGEDI 367

Query: 894 LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           ++GK  P   +     ++        K    RD S  + S  +G V  V +       K
Sbjct: 368 IIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 419


>gi|46394217|gb|AAS91532.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394219|gb|AAS91533.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394221|gb|AAS91534.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394223|gb|AAS91535.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394225|gb|AAS91536.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394227|gb|AAS91537.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394229|gb|AAS91538.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394231|gb|AAS91539.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394233|gb|AAS91540.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394235|gb|AAS91541.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394237|gb|AAS91542.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394239|gb|AAS91543.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394241|gb|AAS91544.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394243|gb|AAS91545.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394245|gb|AAS91546.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394247|gb|AAS91547.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394249|gb|AAS91548.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394251|gb|AAS91549.1| RNA polymerase beta subunit [Nicoletella semolina]
 gi|46394253|gb|AAS91550.1| RNA polymerase beta subunit [Nicoletella semolina]
          Length = 173

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|112824298|gb|ABI26086.1| second largest RNA polymerase II [Peltula umbilicata]
          Length = 292

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/366 (16%), Positives = 106/366 (28%), Gaps = 75/366 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ +R+     EQ E   R           +       I  G           
Sbjct: 61   LFYRAYTDQEKRAGMQVVEQFEKPMRSDTVRLKHGTYDKLDEDGIINPGVRVSGEDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R+++         ++     +  Q                      
Sbjct: 121  KTAPIAPDAEELGQRTKYHNKRDVSTPLRSTESGIVDQ--------------------VL 160

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 161  VTTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGIVPDLIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 221  PHAIPSRMTIAHLIECQLSKVSALKGFEGD------------------------------ 250

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++++LR       G  ++Y+G TG 
Sbjct: 251  -----------------------ATP-FTDVTVDSVSALLREHGYQSRGFEVMYNGHTGR 286

Query: 1244 PFDRPV 1249
                 +
Sbjct: 287  KLVAQI 292



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 66/177 (37%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +       +DE GII  G  V+
Sbjct: 54  DRGLFRSLFYRAYTDQEKRAGMQVVEQFEKPMRSDTVRLKHGTYDKLDEDGIINPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        K  + RD S  + S  SG V  V +  
Sbjct: 114 GEDIIIGKTAPIAPDAEELGQRT-------KYHNKRDVSTPLRSTESGIVDQVLVTT 163


>gi|313493498|gb|ADR57126.1| RNA polymerase beta subunit [Corynebacterium ulcerans]
 gi|313493500|gb|ADR57127.1| RNA polymerase beta subunit [Corynebacterium ulcerans]
 gi|313493502|gb|ADR57128.1| RNA polymerase beta subunit [Corynebacterium ulcerans]
 gi|313493506|gb|ADR57130.1| RNA polymerase beta subunit [Corynebacterium ulcerans]
          Length = 135

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 84/163 (51%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI       +   +   L++  E++                     
Sbjct: 1    LEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEELYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGATNEEVAGLLANSRPNRDGDVMVDENGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|46277265|gb|AAS86823.1| RNA polymerase II second largest subunit [Eschscholzia californica]
          Length = 539

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/484 (13%), Positives = 132/484 (27%), Gaps = 93/484 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAF-MPWHGYNFEDSMLI--SERMVS 835
            LV  G  + +   +      S  + DLA   N   A+ + +       S+++     ++ 
Sbjct: 144  LVAKGYVEYIDTEEEENTMISMTINDLASVFNPKEAYSVTYTHCEIHPSLILGVCASIIP 203

Query: 836  EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
                       ++       +G                  +    +  +        +  
Sbjct: 204  FPDHNQSPRNTYQSAMGKQAMGI-----------YATNYQLRMDTLAHILYYPQKPLVTT 252

Query: 896  GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
              +       +      + AI      +  D+ +   S +         F          
Sbjct: 253  RAMEHLHFRQLPAGMNAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLYF--------RS 304

Query: 956  SISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                E++   L+  +           +     + L                ++    +  
Sbjct: 305  YKGEEKKMGNLVKENFGRPNRENTIGMKHGSYDKLDNDGLAPPGTLVSGEDIIIGKTVQ- 363

Query: 1016 YPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVK 1075
                      VQDE   ++ +  +    TS    E    +++      D       + VK
Sbjct: 364  ---------IVQDESQGQSSQYSQRDCSTSLHHNECGVVDQVMLTTNAD-----GSKFVK 409

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
              +   R  Q GDK + RHG KG +      EDMP+  +G   DI++NP  +PSRM + Q
Sbjct: 410  TRMRSVRIPQVGDKFSSRHGQKGTIGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIAQ 469

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E  +G     +GK+  +         +IS                             
Sbjct: 470  LIECIMGKVAAHMGKEGDATPFTDVTVDNISQALHKCGY--------------------- 508

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                                        +M   +      +Y+G TG      + +G  Y
Sbjct: 509  ----------------------------QMHGFET-----MYNGHTGRKLTSMIFIGPTY 535

Query: 1256 MLKL 1259
              +L
Sbjct: 536  YQRL 539



 Score =  100 bits (248), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/388 (15%), Positives = 111/388 (28%), Gaps = 88/388 (22%)

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRK 604
            + G+ R     E+R    T YGR C       +   L+               E  +R 
Sbjct: 86  TEVGITRDTRLKELR--IYTDYGRCCRPLFIVENQRLLIKRKDIRVIQQRENPDEGGWR- 142

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      V Y+   EEEN  I+              +L       E   V        
Sbjct: 143 --DLVAKGYVEYIDTEEEENTMISM----------TINDLASVFNPKEAYSVT---YTHC 187

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ + AS+IPF +++ S R      M +QA+ +                     
Sbjct: 188 EIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYATNYQL-------------- 233

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                                         + + +  Y               Q+PLV  
Sbjct: 234 ---------------------------RMDTLAHILYYP--------------QKPLV-- 250

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               L  G N +VA   + GYN EDS+++++  +    F S++ 
Sbjct: 251 --------TTRAMEHLHFRQLPAGMNAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLYF 302

Query: 845 EEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
             ++   +      +E        +   +       +D  G+   G  V+  DI++GK  
Sbjct: 303 RSYKGEEKKMGNLVKENFGRPNRENTIGMKHGSYDKLDNDGLAPPGTLVSGEDIIIGKTV 362

Query: 900 PKGESPMTPEEKLLRAIFGEKAVDVRDT 927
              +     +           ++   + 
Sbjct: 363 QIVQDESQGQSSQYSQRDCSTSLHHNEC 390


>gi|330785278|gb|AEC46445.1| RNA polymerase II second largest subunit [Lecanographa uniseptata]
          Length = 296

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 56/369 (15%), Positives = 104/369 (28%), Gaps = 73/369 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R  I++ ++      E+ E   +           +       +  G        
Sbjct: 61   -RSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDEDGFVAPGIRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K++ L+  +                E   R  E +K          E    +++   
Sbjct: 120  IIGKTSPLAGPMQENA------------EGGARLKEHVKRDISAPLRSTEAGIIDQVL-- 165

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 166  ----VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTNEGLVPDL 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 222  IINPHAIPSRMTIAHLIECLLSKVAATDGMEGD--------------------------- 254

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      ++P F     + I+ +L  A     G  ++Y+G 
Sbjct: 255  --------------------------ASP-FTNVTVKDISKLLESAGYQSRGFEVMYNGH 287

Query: 1241 TGEPFDRPV 1249
            TG      +
Sbjct: 288  TGRKLVSQI 296



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 64/189 (33%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R        +       +DE G +  G  V+
Sbjct: 56  DRGLFRSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDEDGFVAPGIRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P        E     A   E         LR        ++D  +     
Sbjct: 116 GEDIIIGKTSPLAG--PMQENAEGGARLKEHVKRDISAPLR---STEAGIIDQVLVTTTD 170

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 171 GKKSVKVRT 179


>gi|158514847|gb|ABW69379.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 172

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 101/172 (58%), Positives = 132/172 (76%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           + +LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 1   TYKLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENF 120

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
            FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR 
Sbjct: 121 RFTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRA 172


>gi|67942342|gb|AAY83371.1| DNA-dependent RNA polymerase II [Urnula craterium]
          Length = 545

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 87/660 (13%), Positives = 170/660 (25%), Gaps = 117/660 (17%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V         Y    + +   +     +      ++      +  D       V
Sbjct: 2    LMSYITVGTPSEPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDPMHLVRNV 61

Query: 646  FCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                    +      I D  D   K          P    ++         +  Q   + 
Sbjct: 62   QEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIE 121

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            K E        E        + ++    G+VE VDA       +    +       + + 
Sbjct: 122  KLEEDHNLDEDEPQRQPYGWSGLL--GDGVVEYVDAEEEETIMIVMTPEDLEVAQQVRQG 179

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             + +         + P   V     +       PS  LG       +  + +P+  +N  
Sbjct: 180  YELEEETDPNKRVKAP---VNPNASQYTHCEIHPSMILG-------ICASIIPFPDHNQS 229

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +   + +  F                                 +  +
Sbjct: 230  PRNTYQSAMGKQAMG--VFLTNFAERM---------------------------DTMANI 260

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +       +   +  +  I      +  D+ +   S +   +    +
Sbjct: 261  LYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSL 319

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R  +D+ +R      E+ E   R    +      +       +  G           K
Sbjct: 320  FYRSYMDQEKRIGMQVVEEFEKPTRSNTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGK 379

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +  ++ D+     R ++         ++     +  Q                       
Sbjct: 380  TAPIAPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML-------------------- 419

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                  L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP
Sbjct: 420  TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDLIINP 479

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
              +PSRM +  + E  L       G +                                 
Sbjct: 480  HAIPSRMTIAHLIECQLSKVSSLRGMEGD------------------------------- 508

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                  +TP F     ++++S+LR       G  ++Y+G TG  
Sbjct: 509  ----------------------ATP-FTDVTVDSVSSLLRAEGYQSRGFEVMYNGHTGRK 545



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 70/471 (14%), Positives = 146/471 (30%), Gaps = 71/471 (15%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 21  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG--- 71

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                    +RD+    +     A                   VN     E   + V   
Sbjct: 72  ----HEVSVIRDIRDREFKIFTDAGRVCRPLFV----------VNNDTTSERRGQLVLQK 117

Query: 609 KVTNDVVYLSAMEEENRYIAQ-ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           +    +     ++E+         S L  DG                      ++++DA 
Sbjct: 118 EHIEKLEEDHNLDEDEPQRQPYGWSGLLGDG---------------------VVEYVDAE 156

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            ++ + I  +         + +V  G  ++ +  P  + +AP      +    +   + I
Sbjct: 157 EEETIMIVMTPEDLEV---AQQVRQGYELEEETDPNKRVKAPVNPNASQYTHCEIHPSMI 213

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +     GV       +           Q+PL     
Sbjct: 214 LGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAERMDTMANILYYPQKPL----- 268

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +V  M + GYN EDS+++++  +   +F S+    
Sbjct: 269 -----ATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 323

Query: 847 FEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        +   +       +D+ G++  G  V+  DI++GK  P 
Sbjct: 324 YMDQEKRIGMQVVEEFEKPTRSNTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPI 383

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++       +K    RD S  + S  +G V  V +       K
Sbjct: 384 APDVDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 427


>gi|223954141|gb|ACN30237.1| RpoB [Corynebacterium ammoniagenes]
          Length = 139

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/167 (34%), Positives = 86/167 (51%), Gaps = 36/167 (21%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  + +   D K    +  L   L  V                   
Sbjct: 1    QVLELHLGWLA-HTGWTVDT--EDPKNEELLKTLPEELYDVPADSLT------------- 44

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                        +TPVFDGA  E I+ +L  +  +  G        +++L+DG +GEP+ 
Sbjct: 45   ------------ATPVFDGATNEEISRLLASSKPNRDGDVMVDEDGKTVLFDGRSGEPYQ 92

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
             P++VG++Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 93   YPISVGFMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGGQR 139


>gi|212283805|gb|ACJ23320.1| RNA polymerase beta subunit [Staphylococcus warneri]
          Length = 179

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 107/179 (59%), Positives = 137/179 (76%), Gaps = 2/179 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            CR  G   ++ +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLM 179


>gi|4098407|gb|AAD10530.1| RNA polymerase beta-subunit [Serratia marcescens subsp. marcescens
           ATCC 13880]
 gi|307716708|gb|ADN88407.1| RNA polymerase beta-subunit [Serratia marcescens subsp. marcescens]
 gi|307716714|gb|ADN88410.1| RNA polymerase beta-subunit [Serratia odorifera]
          Length = 170

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|313493508|gb|ADR57131.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 135

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 84/163 (51%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI       +   ++  L++  E +                     
Sbjct: 1    LEVHLGWLAAA-GWKID-----PEDPANVELLKTLPEDLYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGATNEEVAGLLANSRPNRDGDVMVDANGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|152938342|gb|ABS43111.1| RNA polymerase beta subunit [Plesiomonas shigelloides]
          Length = 167

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 106/167 (63%), Positives = 132/167 (79%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVKDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDEDG F EELV CR  GE  L  ++++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDEDGRFEEELVTCRSKGESSLFSKDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG  +VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTVVAK 167


>gi|46277344|gb|AAS86862.1| DNA-dependent RNA polymerase II [Peziza ellipsospora]
          Length = 545

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/382 (15%), Positives = 114/382 (29%), Gaps = 81/382 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 242  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 301

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G   
Sbjct: 302  LF-RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRV 357

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ +      R+++         ++     +  Q              
Sbjct: 358  SGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------- 403

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 404  ------VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEG 457

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  +                                       
Sbjct: 458  VVPDLIINPHAIPSRMTIAHLI-------------------------------------- 479

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                           + +L      +     +TP F     ++++++LR       G  I
Sbjct: 480  ---------------ECLLSKVSSLRGFEGDATP-FTDVTVDSVSTLLREHGYQSRGFEI 523

Query: 1236 LYDGLTGEPFDRPVTVGYIYML 1257
            +Y+G TG      V +G  Y  
Sbjct: 524  MYNGHTGRKMVAQVFLGPTYYQ 545



 Score = 92.1 bits (227), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 51/324 (15%), Positives = 105/324 (32%), Gaps = 27/324 (8%)

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
                  ++    R   + +L     +++IDA  ++ V I  +      +   +    G 
Sbjct: 112 HHISKLEDDRDSDRYGWQGLLTDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGY 167

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            +Q+   P  + +             +   + I+   A I+   D  +            
Sbjct: 168 EIQQTLDPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXX 227

Query: 755 STSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                      +   +  N     Q+PL                      +L  G+N +V
Sbjct: 228 XXXXXXXXXYRERMDTMANILYYPQKPL----------GTTRSMEFLKFRELPAGQNAIV 277

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A M + GYN EDS+++++  +   +F S+    +    +   +   E        +   +
Sbjct: 278 AIMCYSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLRL 337

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S
Sbjct: 338 KHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDVS 390

Query: 929 LRVPSGVSGTVVDVRIFNRHGIDK 952
             + S  +G V  V +       K
Sbjct: 391 TPLRSTENGIVDQVMVTTNQEGLK 414


>gi|2736119|gb|AAB94060.1| RPB140 [Spinacia oleracea]
          Length = 556

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 104/704 (14%), Positives = 193/704 (27%), Gaps = 149/704 (21%)

Query: 566  YGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR 625
            +G +CPAET EG   GLV +L     +            + +    N        EE + 
Sbjct: 1    WGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWSTEN-------FEEISP 53

Query: 626  YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
             +   ++ +  +G +           + +   R ++   D + +  V     L       
Sbjct: 54   AVIPQSTKIFVNGCWVGIHRDPELLVKTLRQLRRRV---DVNTEVGVVRDIRLKELRIYT 110

Query: 686  DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA-IRIV 744
            D  R      +  +   L+                K   A    +        D   +  
Sbjct: 111  DYGRCSRPLFIVEKQSLLI--------------KKKDIRALQQRENPEDGGWHDLVAKGY 156

Query: 745  IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            I  ++ + + +T        +   R N     +                    PS  LG 
Sbjct: 157  IEYIDTEGEETTMISMTINDLVTARINPEEAYS-----------ETYTHCEIHPSLILG- 204

Query: 805  LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
                  +  + +P+  +N          M  + +     I       R   L        
Sbjct: 205  ------VCASIIPFPDHNQSPRNTYQSAMGKQAMG----IYVTNYQFRMDTLAYVLYYPQ 254

Query: 865  IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
             P V+   ++++                             +      + AI      + 
Sbjct: 255  KPLVTTRAMEHL-------------------------HFRQLPAGINAIVAIACYSGYNQ 289

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
             D+ +   S +        +F R   D+ ++  ++++E      R           +   
Sbjct: 290  EDSVIMNQSAIDRGFF-RSLFFRSYRDEEKKMGTLDKEDFGRPDRSNTMGMRHGSYDKLD 348

Query: 985  RLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
                   G           K+T L+                  DE    +    +  +  
Sbjct: 349  DDGLAPPGTRCAGEDVIIGKTTPLAP-----------------DEATGPSARYSRRDHSI 391

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
            S    E    +++      D +    +RV        R  Q GDK + RHG KG V    
Sbjct: 392  SLRHSETGMVDQVLPTTNADGLRFVKVRV-----RSVRVPQIGDKFSSRHGQKGTVGMTY 446

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +
Sbjct: 447  TQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDN 506

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            IS         +                                                
Sbjct: 507  ISKALHKCGYQMRGFETM------------------------------------------ 524

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVY 1268
                  +G +    G         + +G  Y  +L HMV DK++
Sbjct: 525  -----YNGHT----GR---KLTAMIFLGPTYYQRLKHMVDDKIH 556



 Score =  108 bits (270), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 73/496 (14%), Positives = 140/496 (28%), Gaps = 101/496 (20%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV 509
            G +   +    +    V  +    Y      +  +    +  ++  S    + I+   +
Sbjct: 1   WGMMCPAETPEGQACGLVKNLALMVYIT----VGSAAYPILEFLEEWSTENFEEISPAVI 56

Query: 510 VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGR 568
             +   F     +    +    +  +   RR   +  + GV R     E+R ++  +   
Sbjct: 57  PQSTKIFVNGCWVGIHRDPELLVKTLRQLRRRVDVNTEVGVVRDIRLKELR-IYTDYGRC 115

Query: 569 ICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
             P    E  ++ L+      A        +       D      + Y+    EE   I+
Sbjct: 116 SRPLFIVEKQSL-LIKKKDIRALQQRENPEDGG---WHDLVAKGYIEYIDTEGEETTMIS 171

Query: 629 QANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
                         +LV  R   E      E     +  P  ++ + AS+IPF +++ S 
Sbjct: 172 M----------TINDLVTARINPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSP 219

Query: 689 RVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV 748
           R      M +QA+ +      F                    R   +  V          
Sbjct: 220 RNTYQSAMGKQAMGIYVTNYQF--------------------RMDTLAYV---------- 249

Query: 749 EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
                                        Q+PLV                      L  G
Sbjct: 250 -------------------------LYYPQKPLV----------TTRAMEHLHFRQLPAG 274

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----R 863
            N +VA   + GYN EDS+++++  +    F S+    +    +      +E        
Sbjct: 275 INAIVAIACYSGYNQEDSVIMNQSAIDRGFFRSLFFRSYRDEEKKMGTLDKEDFGRPDRS 334

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +       +D+ G+   G      D+++GK TP              A        
Sbjct: 335 NTMGMRHGSYDKLDDDGLAPPGTRCAGEDVIIGKTTPLAPDE---------ATGPSARYS 385

Query: 924 VRDTSLRVPSGVSGTV 939
            RD S+ +    +G V
Sbjct: 386 RRDHSISLRHSETGMV 401


>gi|330785238|gb|AEC46425.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
          Length = 307

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 106/380 (27%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   ++ +       Q  +   + + V   + S +                
Sbjct: 120  SGDDIIIGKTAPFANPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLVDRVL-------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ---------VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L  +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLXGSGYQSRGLEL 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGHTGRKLMAQVFLGPTY 307



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 62/187 (33%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       E                  + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R        DV        +G+   V+      R  
Sbjct: 121 GDDIIIGKTAPFANPMADNAEGGQRTKM-HSKRDVSAPLRSTEAGLVDRVLVTTNEGRRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|46361506|gb|AAS89299.1| RNA polymerase beta-subunit [Raoultella ornithinolytica]
          Length = 170

 Score =  179 bits (455), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 132/170 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EF  SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFCGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFNRDQVDYMDVSTQQVVSVGASLIP 170


>gi|219564113|gb|ACL28240.1| RNA polymerase II second largest subunit [Hyaloscypha vitreola]
          Length = 299

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/375 (17%), Positives = 113/375 (30%), Gaps = 81/375 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 63   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 118

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 119  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVD 163

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 164  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 218

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 219  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD---------------------- 256

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  I
Sbjct: 257  -------------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEI 284

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      V 
Sbjct: 285  MYHGHTGRKLMAQVF 299



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 66/186 (35%), Gaps = 22/186 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        D   +       +D+ G
Sbjct: 51  SVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  DI++GK  P         ++        KA   RD S  + S  +G V 
Sbjct: 111 IVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVD 163

Query: 941 DVRIFN 946
            V I  
Sbjct: 164 QVLITT 169


>gi|193201505|gb|ACF15960.1| RNA polymerase II subunit [Opegrapha celtidicola]
          Length = 293

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/367 (16%), Positives = 109/367 (29%), Gaps = 75/367 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  I++ ++      E+ E   +       +   +       +  G           
Sbjct: 60   LFYRTYIEQEQKIGFNNLEEFEKPVKQYTTRMRMGTYDKLDEDGFVAPGVRVSGEDIIIG 119

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++ L+                   E +Q N E      E +K  +    ++    I   
Sbjct: 120  KTSPLA-------------------EPMQENAEGGARLREHTKRDISAPLRSTEAGIIDR 160

Query: 1064 DDMPP-GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +      + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++
Sbjct: 161  VLLTTVEGRKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGLVPDLII 220

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +  + E  L       G +                               
Sbjct: 221  NPHAIPSRMTIAHLIECLLSKVAAVDGLEGD----------------------------- 251

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    +TP F     + I+S+L+ +     G  ++Y+G TG
Sbjct: 252  ------------------------ATP-FTPVTVQDISSLLKHSGYQSRGFEVMYNGHTG 286

Query: 1243 EPFDRPV 1249
                  V
Sbjct: 287  RKLVSQV 293



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 68/187 (36%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  + +      +       +DE G +  G  V+
Sbjct: 53  DRGLFRSLFYRTYIEQEQKIGFNNLEEFEKPVKQYTTRMRMGTYDKLDEDGFVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P  E      E   R +      D+        +G+   V+   +  R  
Sbjct: 113 GEDIIIGKTSPLAEPMQENAEGGAR-LREHTKRDISAPLRSTEAGIIDRVLLTTVEGRKS 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKVRTRT 178


>gi|212283803|gb|ACJ23319.1| RNA polymerase beta subunit [Staphylococcus hyicus]
          Length = 179

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 107/179 (59%), Positives = 136/179 (75%), Gaps = 2/179 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ +
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
            CR  G    + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL
Sbjct: 121 VCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLL 179


>gi|119640585|gb|ABL85486.1| RNA polymerase II second largest subunit [Sclerophyton californicum]
 gi|330785220|gb|AEC46416.1| RNA polymerase II second largest subunit [Schizopelte parishii]
 gi|330785222|gb|AEC46417.1| RNA polymerase II second largest subunit [Schizopelte parishii]
 gi|330785282|gb|AEC46447.1| RNA polymerase II second largest subunit [Schizopelte crustosa]
 gi|330785284|gb|AEC46448.1| RNA polymerase II second largest subunit [Schizopelte crustosa]
          Length = 307

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/380 (15%), Positives = 106/380 (27%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  ++    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR     K          E    +
Sbjct: 120  SGDDIIIGKTAPFQAPMADNA------------EGGQRTKMHAKRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  RVL------VTTNEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYQSRGLEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGYTGRKLVAQVYLGPTY 307



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 61/196 (31%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------ATTRSMEYLQFAELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       E                  + +D+ G
Sbjct: 52  SVIMNQSAIDRGLFRSFFYRTYIEQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P         E   R        DV        +G+   V+
Sbjct: 112 FVAPGVRVSGDDIIIGKTAPFQAPMADNAEGGQRTKM-HAKRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTNEGRRSVKVRTRT 186


>gi|330785304|gb|AEC46458.1| RNA polymerase II second largest subunit [Opegrapha medusulina]
          Length = 307

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/379 (15%), Positives = 114/379 (30%), Gaps = 77/379 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLKFAELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--ILCGQNAV 996
            +    ++  +     E    + ++ ++   +      +      Y +L E  ++     V
Sbjct: 64   LFRSFLYRTYI----EAQKYIRKDVMDQFEKPVRQLTLRTRPGTYEKLDEDGLVAPGVRV 119

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
            SG       T    + ++E         A Q   V   + S +        + ++     
Sbjct: 120  SGDDIIIGKTAPFEEGMAENSEGGHRHKAHQKRDVSIPLRSTEAGIVDRVLVCQNE---- 175

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                          LR VKV     +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 176  -------------NLRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGL 222

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM V  + E  L       G +                         
Sbjct: 223  VPDLIINPHAIPSRMTVAHLIECLLSKVSATQGMEGD----------------------- 259

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F       I+ +L+ +     G  ++
Sbjct: 260  ------------------------------ATP-FTDVTVSEISKLLKDSGYQSRGFELM 288

Query: 1237 YDGLTGEPFDRPVTVGYIY 1255
            ++G TG   +  + +G  Y
Sbjct: 289  HNGHTGRKLNAQIFLGPTY 307



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 67/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFAELPAGQNAIVAIACYSGYNQEDSIIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +  +    +                  + +DE G++  G  V+
Sbjct: 61  DRGLFRSFLYRTYIEAQKYIRKDVMDQFEKPVRQLTLRTRPGTYEKLDEDGLVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  E      E   R     +  DV        +G+   V+  +  N   
Sbjct: 121 GDDIIIGKTAPFEEGMAENSEGGHRHKA-HQKRDVSIPLRSTEAGIVDRVLVCQNENLRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRA 186


>gi|34923312|gb|AAQ83543.1| RpoB [Gallibacterium anatis]
 gi|34923314|gb|AAQ83544.1| RpoB [Gallibacterium genomosp. 1]
          Length = 173

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEEIQYMDISTQQIVSVAAALIPFLEHDDANRAL 173


>gi|313465586|gb|ADR51583.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313465588|gb|ADR51584.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313465590|gb|ADR51585.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313465592|gb|ADR51586.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313465594|gb|ADR51587.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313465598|gb|ADR51589.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 135

 Score =  179 bits (455), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 83/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI       +   +   L++  E +                     
Sbjct: 1    LEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGATNEEVAGLLTNSRPNRDGDVMVDANGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|313465596|gb|ADR51588.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
 gi|313493510|gb|ADR57132.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 135

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 83/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI       +   +   L++  E +                     
Sbjct: 1    LEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGATNEEVAGLLANSRPNRDGDVMVDANGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|297500375|gb|ADI43624.1| RNA polymerase beta subunit [Agrobacterium sp. LMG63]
 gi|297500377|gb|ADI43625.1| RNA polymerase beta subunit [Agrobacterium sp. LMG99]
 gi|297500379|gb|ADI43626.1| RNA polymerase beta subunit [Agrobacterium sp. LMG109]
 gi|297500381|gb|ADI43627.1| RNA polymerase beta subunit [Agrobacterium sp. LMG229]
 gi|297500383|gb|ADI43628.1| RNA polymerase beta subunit [Agrobacterium sp. LMG253]
 gi|297500387|gb|ADI43630.1| RNA polymerase beta subunit [Agrobacterium sp. LMG341]
 gi|297500399|gb|ADI43636.1| RNA polymerase beta subunit [Agrobacterium sp. LMG29]
          Length = 178

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 145/179 (81%), Positives = 163/179 (91%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME VVA+ SGAAI A+R G+V+QVDA RIVIR+ E  LDPS SGVDIYRLMK
Sbjct: 1   EAPFVGTGMEPVVARDSGAAIGARRGGVVDQVDATRIVIRATED-LDPSKSGVDIYRLMK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD V + DI+ADGPSTDLGDLALGRN+LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVTVGDFVNKGDILADGPSTDLGDLALGRNVLVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+V++DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILLSERIVADDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|312204298|gb|ADQ47466.1| RNA polymerase II second largest subunit [Belonia herculana]
          Length = 289

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 56/362 (15%), Positives = 107/362 (29%), Gaps = 81/362 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R        +E   +    E + +    Y +L +   I  G           
Sbjct: 62   RVYTEQEKRVGI---SLVEQFEKPLRSETLRVKHGTYEKLDDDGLIAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R+++         ++     +                  ++K+   
Sbjct: 119  KTAPIAPDSEEMGQRTKFHTKRDASTPLRSTESGI------------------VDKVMV- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+  KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 160  -TTNAEGLKFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGITPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  +       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECLISKVASLSGCEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++  LR       G  I+Y+G TG 
Sbjct: 249  -----------------------ATP-FTDITVDSVSDALRKHGYQSRGFEIMYNGHTGR 284

Query: 1244 PF 1245
              
Sbjct: 285  KL 286



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 63/169 (37%), Gaps = 12/169 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 11  TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRVYTEQEKR 70

Query: 854 TKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   V     + +D+ G+I  G  V+  DI++GK  P        
Sbjct: 71  VGISLVEQFEKPLRSETLRVKHGTYEKLDDDGLIAPGVRVSGEDIIIGKTAPIAPDSEEM 130

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            ++        K    RD S  + S  SG V  V +       K  +  
Sbjct: 131 GQRT-------KFHTKRDASTPLRSTESGIVDKVMVTTNAEGLKFAKVR 172


>gi|307547677|gb|ADN44452.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 307

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/375 (16%), Positives = 108/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG   +  V +   Y
Sbjct: 293  TGRKLNAQVFLXPTY 307



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|305662316|gb|ADM62269.1| RNA-polymerase beta-subunit [Bisgaardia hudsonensis]
 gi|305662318|gb|ADM62270.1| RNA-polymerase beta-subunit [Bisgaardia hudsonensis]
 gi|305662320|gb|ADM62271.1| RNA-polymerase beta-subunit [Bisgaardia hudsonensis]
 gi|305662322|gb|ADM62272.1| RNA-polymerase beta-subunit [Bisgaardia hudsonensis]
 gi|305662324|gb|ADM62273.1| RNA-polymerase beta-subunit [Bisgaardia hudsonensis]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 101/173 (58%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   ++I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGEHGESGLYRPDEIHYMDVSTQQIVSVAAALIPFLEHDDANRAL 173


>gi|328726870|gb|AEB38718.1| RNA polymerase beta subunit [Corynebacterium pseudotuberculosis]
          Length = 136

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/164 (35%), Positives = 84/164 (51%), Gaps = 36/164 (21%)

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + E HLGW     G KI       +   +   L++  E +                    
Sbjct: 1    VLEVHLGWLAAA-GWKID-----PEDPANAELLKTLPEDLYDVP---------------- 38

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDR 1247
                  +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  
Sbjct: 39   ------AGSLTATPVFDGATNEQVAGLLANSRPNRDGDVMVDANGKAQLFDGRSGEPFPY 92

Query: 1248 PVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   PVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 136


>gi|307716710|gb|ADN88408.1| RNA polymerase beta-subunit [Serratia ficaria]
          Length = 170

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|172085089|gb|ACB71424.1| RpoB [Gallibacterium salpingitidis]
 gi|172085091|gb|ACB71425.1| RpoB [Gallibacterium salpingitidis]
 gi|172085093|gb|ACB71426.1| RpoB [Gallibacterium group V]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIQYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|42560438|gb|AAS20391.1| DNA-directed RNA polymerase beta subunit [Enterococcus faecium]
          Length = 209

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 112/209 (53%), Positives = 154/209 (73%), Gaps = 2/209 (0%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLK 472
             ++N+  N      V+ +R  DIIA +   ++L  G G +DDID+LGNRR+RSVGE+L+
Sbjct: 1   EREVNVIGNGYPEAAVKTVRPADIIASMSYFLNLMEGIGNVDDIDHLGNRRIRSVGELLQ 60

Query: 473 NQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSL 532
           NQ+R+GL RMER ++ER+S  D +++ PQ LIN +PVV+++ EFF SSQLSQ  +  N L
Sbjct: 61  NQFRIGLARMERVVRERMSIQDTETLTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPL 120

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
             +TH RRLSALG GG+ R RAG E+RDVH +HYGR+CP ET EG NIGL++SL+S+A+V
Sbjct: 121 GELTHKRRLSALGPGGLTRDRAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKV 180

Query: 593 NAYGFIETPYRKVCDG--KVTNDVVYLSA 619
           N +GFIETPYR+V     +VT+ + YL+A
Sbjct: 181 NKFGFIETPYRRVDRETGRVTDQIDYLTA 209


>gi|38373282|gb|AAR19005.1| RpoB [Actinobacillus porcinus]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAYVTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|312204308|gb|ADQ47471.1| RNA polymerase II second largest subunit [Chapsa pulchra]
          Length = 288

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/361 (16%), Positives = 109/361 (30%), Gaps = 81/361 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +++ +R        +E   +    E + L    Y +L +   I  G           
Sbjct: 61   RAYVEQEKRVGM---SLVEQFEKPLRSETLRLKHGTYDKLDDDGLIAPGVRVSGEDIIIG 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R++          ++     +                  ++K+   
Sbjct: 118  KTAPIAPDTEELGQRTKMHTKRDASTPLRSTENGI------------------VDKVLL- 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 159  -TTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDLIIN 217

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 218  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 247

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  ++Y+G TG 
Sbjct: 248  -----------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGR 283

Query: 1244 P 1244
             
Sbjct: 284  K 284



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +D+ G+I  G  V+
Sbjct: 51  DRGLFRSLFYRAYVEQEKRVGMSLVEQFEKPLRSETLRLKHGTYDKLDDDGLIAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 111 GEDIIIGKTAPIAPDTEELGQRT-------KMHTKRDASTPLRSTENGIVDKVLLTTNQE 163

Query: 950 IDK 952
             K
Sbjct: 164 GLK 166


>gi|299849860|gb|ADJ57177.1| RNA polymerase II second largest subunit [Scytalidium cuboideum]
          Length = 321

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/388 (17%), Positives = 113/388 (29%), Gaps = 81/388 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               G         V  G  Y  +L HMV
Sbjct: 300  ---GR---KLKAQVFFGPTYYQRLRHMV 321



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|4001756|gb|AAC94961.1| RNA polymerase beta-subunit [Yersinia pestis]
          Length = 170

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 105/170 (61%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  RE++D++D S +Q+VS+ ASLIP
Sbjct: 121 NSNLDDEGRFLEDLVTCRSKGESSLFSREQVDYMDVSTQQIVSVGASLIP 170


>gi|305662326|gb|ADM62274.1| RNA-polymerase beta-subunit [Bisgaardia genomosp. 1]
 gi|305662328|gb|ADM62275.1| RNA-polymerase beta-subunit [Bisgaardia genomosp. 1]
 gi|305662330|gb|ADM62276.1| RNA-polymerase beta-subunit [Bisgaardia genomosp. 1]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|38373260|gb|AAR18994.1| RpoB [Aggregatibacter actinomycetemcomitans]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+N  L
Sbjct: 121 FTDAFVTCRGEHGESGLYKPEEIHYMDVSTQQVVSVAAALIPFLEHDDANPAL 173


>gi|312204334|gb|ADQ47484.1| RNA polymerase II second largest subunit [Gyalidea fritzei]
          Length = 295

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/368 (16%), Positives = 115/368 (31%), Gaps = 74/368 (20%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R  +++ +R  +   + +E   +    E + L +  Y +L               
Sbjct: 60   RSLFYRTYVEQEKRVGA---QLVEQFEKPLRSETLRLKQGTYEKL----------DDDGL 106

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKV-QRNVESLKVQYETSKSILEDRFKNKIEKI 1060
                T +S + I     +   Q +  + ++ QR     K    T     E+   +++   
Sbjct: 107  IAPGTRVSGEDIIIGKTAPLVQDSNTNSEMGQRTKLHTKRDASTPLRSTENGIVDRVLL- 165

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      L+ VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 166  ----TTNSEALKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGITPDL 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 222  IINPHAIPSRMTIAHLVECQLSKVSSLRGFEGD--------------------------- 254

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+++LR       G  ++Y+G 
Sbjct: 255  --------------------------ATP-FTDVTVQGISALLREHGYQSRGFEVMYNGH 287

Query: 1241 TGEPFDRP 1248
            TG+     
Sbjct: 288  TGKKLKGQ 295



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 68/183 (37%), Gaps = 19/183 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------GTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        +   + +   + +D+ G+I  G  V+
Sbjct: 55  DRGLFRSLFYRTYVEQEKRVGAQLVEQFEKPLRSETLRLKQGTYEKLDDDGLIAPGTRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +   T  E   R     K    RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPLVQDSNTNSEMGQRT----KLHTKRDASTPLRSTENGIVDRVLLTTNSE 170

Query: 950 IDK 952
             K
Sbjct: 171 ALK 173


>gi|168419749|gb|ACA23842.1| RNA polymerase II [Fusarium falciforme]
          Length = 291

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKCVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|268528977|gb|ACZ06541.1| RpoB [Mannheimia varigena]
 gi|268528979|gb|ACZ06542.1| RpoB [Mannheimia varigena]
 gi|268528983|gb|ACZ06544.1| RpoB [Mannheimia varigena]
 gi|268528985|gb|ACZ06545.1| RpoB [Mannheimia varigena]
 gi|268528997|gb|ACZ06551.1| RpoB [Mannheimia varigena]
 gi|268528999|gb|ACZ06552.1| RpoB [Mannheimia varigena]
 gi|268529001|gb|ACZ06553.1| RpoB [Mannheimia varigena]
          Length = 172

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/172 (59%), Positives = 133/172 (77%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNRLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+D+++R L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDNADRAL 172


>gi|34980323|gb|AAO41854.1| RNA polymerase beta subunit [Lonepinella koalarum]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 129/173 (74%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34923306|gb|AAQ83540.1| RpoB [Actinobacillus muris]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE N  IAQANS+LD D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGNFVIAQANSNLDADFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|293601684|gb|ADE48246.1| RNA polymerase II [Morchella rufobrunnea]
          Length = 296

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/374 (16%), Positives = 112/374 (29%), Gaps = 81/374 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 166  ---------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E+++++LR       G  +
Sbjct: 255  -------------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEV 282

Query: 1236 LYDGLTGEPFDRPV 1249
            +Y+G TG      V
Sbjct: 283  MYNGYTGRKLVCQV 296



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|172085081|gb|ACB71420.1| RpoB [Gallibacterium genomosp. 3]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVINGQVTEEIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|307716718|gb|ADN88412.1| RNA polymerase beta-subunit [Pectobacterium carotovorum subsp.
           carotovorum]
          Length = 170

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 102/170 (60%), Positives = 132/170 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +  VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRENVVTDEIHYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           N++LDE+G F +ELV CR  GE  L  R++++++D S +QVVS+ ASLIP
Sbjct: 121 NTNLDEEGRFIDELVTCRNKGESSLFSRDQVEYMDVSTQQVVSVGASLIP 170


>gi|158514845|gb|ABW69378.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 169

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 101/169 (59%), Positives = 130/169 (76%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIG
Sbjct: 1   LSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT
Sbjct: 61  LINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFT 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           +  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+NR 
Sbjct: 121 DTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDANRA 169


>gi|55831375|gb|AAV66546.1| RNA polymerase II second largest subunit [Lactarius deceptivus]
          Length = 557

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/447 (14%), Positives = 121/447 (27%), Gaps = 88/447 (19%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             W       SM+  I   ++            ++       +G       +         
Sbjct: 197  EWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM------- 249

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 250  ----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 305

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    I+ R  +D  +RS     E+ E   R+          +       +  G  
Sbjct: 306  IDRGLF-RSIYYRSYMDLEKRSGVTPLEEFEKPTRETTLRMKHGTYDKLEDDGLVAPGTG 364

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  L  +                +E  QR     +    T     E+   
Sbjct: 365  VTGEDIIIGKTAPLPPE---------------NEELGQRTRTHSRRDVSTPLKSTENGIV 409

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            +++      D       + VK+ V   R  Q GDK A RHG KG +      EDMPF  +
Sbjct: 410  DQVLITTNSD-----GQKFVKIRVRSPRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCE 464

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEK 1174
            G   D+++NP  +PSRM +G + E  L      +G +  +                    
Sbjct: 465  GITPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT---------------- 508

Query: 1175 VIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQS 1234
                      ++     + LR       G+ V                         G +
Sbjct: 509  ---------DLTVESVSTFLRQQGYQSRGLEVM----------------------YHGHT 537

Query: 1235 ILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
                G         + +G  Y  +L H
Sbjct: 538  ----GR---KLQAQIYLGPTYYQRLKH 557



 Score =  112 bits (279), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 71/468 (15%), Positives = 132/468 (28%), Gaps = 93/468 (19%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  +   RR   +                ++ 
Sbjct: 29  ENAHSSTLTTKVFVNGVWMGVHRDPTNLIETLKKLRRKDDVHPEVSIVRDIRERELRLYT 88

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                  P    E     LV        +N     +    K      +  +  L A EEE
Sbjct: 89  DPGRVCRPLFIVEAQ--QLVLQKKHVRWLNQGTTDDGEDFKWQHLTKSGVIEMLDAEEEE 146

Query: 624 NRYIAQANSSLD--------------EDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
              I      L+               D +  +     R           +    +  P 
Sbjct: 147 TVMICMTPEDLEAPRLQGRGAQSGSKSDTNDADFDPAARLKPTLGKSAPHEWTHCEIHPS 206

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ I AS+IPF +++ S R      M +QA+ +                          
Sbjct: 207 MILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------------- 247

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 248 ----------------------RMDTMANILYYPQKPLATTRSMEYLKFR---------- 275

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  
Sbjct: 276 --------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMD 321

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + + + + P E            +       +++ G++  G  V   DI++GK  P    
Sbjct: 322 LEKRSGVTPLEEFEKPTRETTLRMKHGTYDKLEDDGLVAPGTGVTGEDIIIGKTAP---- 377

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            + PE + L       +   RD S  + S  +G V  V I       K
Sbjct: 378 -LPPENEELGQRTRTHSR--RDVSTPLKSTENGIVDQVLITTNSDGQK 422


>gi|293601706|gb|ADE48257.1| RNA polymerase II [Morchella semilibera]
          Length = 293

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/371 (16%), Positives = 111/371 (29%), Gaps = 81/371 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G      
Sbjct: 60   RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 117  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 162

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 163  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 252  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 282

Query: 1239 GLTGEPFDRPV 1249
            G TG      V
Sbjct: 283  GYTGRKLVCQV 293



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 55  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|168419440|gb|ACA23636.1| RNA polymerase II [Fusarium sp. NRRL 28550]
 gi|168419680|gb|ACA23796.1| RNA polymerase II [Fusarium sp. NRRL 32838]
          Length = 291

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENHDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENHDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|330785262|gb|AEC46437.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
          Length = 307

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 107/380 (28%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   ++ +       Q  +   + + V   + S +                
Sbjct: 120  SGDDIIIGKTAPFANPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLVDRVL-------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ---------VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYQSRGLXL 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGHTGRKLMAQVFLGPTY 307



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 62/187 (33%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       E                  + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R        DV        +G+   V+      R  
Sbjct: 121 GDDIIIGKTAPFANPMADNAEGGQRTKM-HSKRDVSAPLRSTEAGLVDRVLVTTNEGRRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|154090285|emb|CAL25597.1| DNA-directed RNA polymerase beta chain [Bartonella henselae]
 gi|154090287|emb|CAL25598.1| DNA-directed RNA polymerase beta chain [Bartonella henselae]
          Length = 169

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 121/169 (71%), Positives = 145/169 (85%)

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLS
Sbjct: 1   RDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLS 60

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           AMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+L
Sbjct: 61  AMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAAL 120

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           IPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGAA+
Sbjct: 121 IPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGAAV 169


>gi|45593163|gb|AAS68144.1| RNA polymerase beta subunit [Geobacter pelophilus]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 100/173 (57%), Positives = 134/173 (77%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG+ R R G E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLTRERDGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V DG+VT++V + SA+EEE   IAQAN+ +DE G F  +
Sbjct: 61  ASLSTYARINEHGFVETPYRVVRDGRVTDEVRFFSALEEEGHAIAQANAEIDETGRFAAD 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            +  R +GE +LV R++++ +D +P Q+VS+AASLIPFLENDD+NR LMG N+
Sbjct: 121 YISARKSGEFVLVGRDELELMDVAPMQLVSVAASLIPFLENDDANRALMGSNI 173


>gi|330785212|gb|AEC46412.1| RNA polymerase II second largest subunit [Dolichocarpus chilensis]
          Length = 307

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/380 (15%), Positives = 112/380 (29%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   + ++ AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLNFSELPAGQNVIVAIACYSGYNQEDSIIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    ++  +     E+  +V    ++   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFLYRTYI----EQQKAVGFNALDEFEKPIKTHTLRTRPGTYEKLDDDGFVEPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR+ +  +          E    +
Sbjct: 120  SGDDIIIGKTAPFQNAMQDNA------------EGGQRHKQHTRRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+              R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  KVL------VSNTEGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+++L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSEISNLLKGSGYQSRGLEL 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG   +  V +G  Y
Sbjct: 288  MHNGHTGRKLNAQVYLGPTY 307



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 67/196 (34%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                   +  +L  G+N++VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------ATTRSMEYLNFSELPAGQNVIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECG 880
           S+++++  +   +F S     +    +       +E  + I            + +D+ G
Sbjct: 52  SIIMNQSAIDRGLFRSFLYRTYIEQQKAVGFNALDEFEKPIKTHTLRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P   +     E   R        DV        +G+   V+
Sbjct: 112 FVEPGVRVSGDDIIIGKTAPFQNAMQDNAEGGQRHK-QHTRRDVSAPLRSTEAGIVDKVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VSNTEGRRTVKVRTRA 186


>gi|38373344|gb|AAR19036.1| RpoB [Pasteurella testudinis]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDENSR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTCRGEHGESGLYKADEIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|156453781|gb|ABU63745.1| RpoB [Pasteurellaceae bacterium Clin7]
 gi|156453785|gb|ABU63747.1| RpoB [Pasteurellaceae bacterium Clin51]
 gi|156453787|gb|ABU63748.1| RpoB [Pasteurellaceae bacterium Clin103]
 gi|156453789|gb|ABU63749.1| RpoB [Pasteurellaceae bacterium Clin107]
 gi|156453791|gb|ABU63750.1| RpoB [Pasteurellaceae bacterium Clin109]
 gi|156453793|gb|ABU63751.1| RpoB [Pasteurellaceae bacterium Clin175]
 gi|156453795|gb|ABU63752.1| RpoB [Pasteurellaceae bacterium Clin216]
 gi|156453797|gb|ABU63753.1| RpoB [Pasteurellaceae bacterium Clin217]
 gi|156453799|gb|ABU63754.1| RpoB [Pasteurellaceae bacterium Clin829]
 gi|309385662|gb|ADO66684.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385664|gb|ADO66685.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385666|gb|ADO66686.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385668|gb|ADO66687.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385670|gb|ADO66688.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385672|gb|ADO66689.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385674|gb|ADO66690.1| RNA polymerase beta subunit [Necropsobacter rosorum]
 gi|309385676|gb|ADO66691.1| RNA polymerase beta subunit [Necropsobacter rosorum]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVINGQVTEEIEYLSAIEEGKYVIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEYGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|38373274|gb|AAR19001.1| RpoB [Actinobacillus hominis]
          Length = 173

 Score =  179 bits (454), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDEEFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR    E  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHSESGLYKPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|259141805|emb|CBF38192.1| RNA polymerase beta subunit [Corynebacterium hansenii]
          Length = 115

 Score =  179 bits (453), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 51/97 (52%), Positives = 69/97 (71%), Gaps = 8/97 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  D  G        ++ L DG +GEPF  PV+VGY+YML
Sbjct: 19   VATPVFDGAENEELAGLLASSRPDRDGDVLVNADGKAQLMDGRSGEPFPFPVSVGYMYML 78

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 79   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 115


>gi|312204318|gb|ADQ47476.1| RNA polymerase II second largest subunit [Cryptodiscus pallidus]
          Length = 708

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 57/351 (16%), Positives = 109/351 (31%), Gaps = 81/351 (23%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 433  MEFLKFRELPAGQNAIVAISCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYVEQEKRVG 491

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    + + L    Y +L +   I  G           K+  ++ D   
Sbjct: 492  M---SMVEQFEKPLRSDTLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDDEE 548

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                  ++K+          L+ V
Sbjct: 549  MGQRTKLHTKRDASTPLRSTENGI------------------VDKVLV--TTNAEGLKFV 588

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 589  KVRMRTTKIPQVGDKFASRHGQKGTIGITYRQEDMPFTAEGLTPDLIINPHAIPSRMTIA 648

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 649  HLVECLLSKVGAIRGAEGD----------------------------------------- 667

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                        +TP F     ++++ +LR       G  I+Y+G +G   
Sbjct: 668  ------------ATP-FTEVTVDSVSRLLREQGYQSRGFEIMYNGHSGRKM 705



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 421 YYPQKPL----------ATTQSMEFLKFRELPAGQNAIVAISCYSGYNQEDSVIMNQSSI 470

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +     + +D+ GII  G  V+
Sbjct: 471 DRGLFRSLFYRSYVEQEKRVGMSMVEQFEKPLRSDTLRLKHGTYEKLDDDGIIAPGVRVS 530

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 531 GEDIIIGKTAPIAPDDEEMGQRT-------KLHTKRDASTPLRSTENGIVDKVLVTTNAE 583

Query: 950 IDK 952
             K
Sbjct: 584 GLK 586



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 63/176 (35%), Gaps = 7/176 (3%)

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
            ++ +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 58  STAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 113

Query: 578 HNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
              GLV +L     V   + G     +    + +V  +   +        ++    + + 
Sbjct: 114 QACGLVKNLALMCNVTVGSPGDPIVDFMVQRNMEVLEEFEPMRTPNATKIFVNGVWTGIH 173

Query: 636 EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV 690
            D       +      + I V    + D  D   K          P    DD+ R 
Sbjct: 174 RDPVHLVRTIQSLRRRKLIDVETSLVHDIRDREFKIFTDAGRVSRPVFVIDDAERS 229


>gi|293601946|gb|ADE48235.1| RNA polymerase II [Verpa sp. M203]
          Length = 290

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/366 (16%), Positives = 110/366 (30%), Gaps = 81/366 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNPEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L E   +  G           
Sbjct: 62   RSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 119  KTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML------------------- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 160  -TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 284

Query: 1244 PFDRPV 1249
                 V
Sbjct: 285  KLVCQV 290



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNPEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|219564105|gb|ACL28236.1| RNA polymerase II second largest subunit [Hyaloscypha albohyalina
            var. spiralis]
          Length = 290

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/367 (17%), Positives = 111/367 (30%), Gaps = 81/367 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D+ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 61   RAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIG 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D                +E  QR    +K    T     E+   +++      
Sbjct: 118  KTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVDQVLI---- 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV +   +  Q GDK A RHG KG +      EDMPF + G   D+++N
Sbjct: 159  -TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIVPDLIIN 217

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 218  PHAIPSRMTIAHLIECQLSKVSTLRGLEGD------------------------------ 247

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  I+Y G TG 
Sbjct: 248  -----------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEIMYHGHTGR 283

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 284  KLMAQVF 290



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 51  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 111 GEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 160


>gi|156453747|gb|ABU63728.1| RpoB [Pasteurella multocida]
 gi|156453749|gb|ABU63729.1| RpoB [Pasteurella multocida]
 gi|156453751|gb|ABU63730.1| RpoB [Pasteurella multocida]
 gi|156453753|gb|ABU63731.1| RpoB [Pasteurella multocida]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG  G+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPSGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|219564103|gb|ACL28235.1| RNA polymerase II second largest subunit [fungal sp. M339]
          Length = 285

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/356 (17%), Positives = 111/356 (31%), Gaps = 81/356 (22%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 8    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 64

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +    + + L    Y +L +   +  G           K+  ++ D   
Sbjct: 65   -IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPD--- 120

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         +E  QR    +K    T     E+   +++             LR V
Sbjct: 121  ------------AEELGQRTKAHVKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFV 163

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF + G   D+++NP  +PSRM + 
Sbjct: 164  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIVPDLIINPHAIPSRMTIA 223

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 224  HLIECQLSKVSTLRGLEGD----------------------------------------- 242

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                        +TP F     ++++ +LR       G  I+Y G TG      V 
Sbjct: 243  ------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEIMYHGHTGRKLMAQVF 285



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 61/158 (38%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 5   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 64

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +       +D+ GI+  G  V+  DI++GK  P        
Sbjct: 65  IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEEL 124

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        KA   RD S  + S  +G V  V I  
Sbjct: 125 GQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 155


>gi|151573453|gb|ABS17966.1| RNA polymerase II [Fusarium sp. NRRL 43818]
          Length = 292

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 101/365 (27%), Gaps = 75/365 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVTV 1251
              V  
Sbjct: 288  AQVFF 292



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|330785230|gb|AEC46421.1| RNA polymerase II second largest subunit [Ingaderia pulcherrima]
 gi|330785232|gb|AEC46422.1| RNA polymerase II second largest subunit [Ingaderia pulcherrima]
 gi|330785234|gb|AEC46423.1| RNA polymerase II second largest subunit [Ingaderia pulcherrima]
 gi|330785236|gb|AEC46424.1| RNA polymerase II second largest subunit [Ingaderia pulcherrima]
          Length = 307

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/377 (15%), Positives = 104/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANVLYYPQKPLATTRSMEFLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     F R  I++ +       E+ E   +                   +  G      
Sbjct: 64   LF-RSFFYRTYIEQQKSVGFNALEEFEKPQKQLTMRTRPGTYEKLDEDGFVAPGVRVSGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+   ++ +                E  QR     K          E    +++ 
Sbjct: 123  DIIIGKTAPFANPMADNA------------EGGQRTKAHTKRDVSAPLRTTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKRCVKVRTRTTKIPQIGDKFASRHGQKGTIGITYGQEDMPFTVEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L         +                           
Sbjct: 225  DLIINPHAIPSRMTVAHLIECLLSKVSATHTLEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F      A++ +L+ +   + G  ++++
Sbjct: 260  ----------------------------ATP-FTDVTVSAVSDLLQESGYQKRGFEVMHN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      + +G  Y
Sbjct: 291  GHTGRKLVAQIFLGPTY 307



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 69/190 (36%), Gaps = 9/190 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANVLYYPQKPLATTRSMEFLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       EE  +    +         + +DE G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKSVGFNALEEFEKPQKQLTMRTRPGTYEKLDEDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +PM    +  +        DV        +G+   V+      +  
Sbjct: 121 GDDIIIGKTAPF-ANPMADNAEGGQRTKAHTKRDVSAPLRTTEAGIIDRVLVTTTDGKRC 179

Query: 950 IDKNERSISV 959
           +    R+  +
Sbjct: 180 VKVRTRTTKI 189


>gi|34923326|gb|AAQ83550.1| RpoB [Bisgaard Taxon 5]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|38373264|gb|AAR18996.1| RpoB [Actinobacillus capsulatus]
 gi|38373266|gb|AAR18997.1| RpoB [Actinobacillus capsulatus]
 gi|38373268|gb|AAR18998.1| RpoB [Actinobacillus capsulatus]
 gi|38373270|gb|AAR18999.1| RpoB [Actinobacillus equuli subsp. haemolyticus]
 gi|38373272|gb|AAR19000.1| RpoB [Actinobacillus equuli subsp. equuli]
 gi|38373294|gb|AAR19011.1| RpoB [Actinobacillus suis ATCC 33415]
 gi|38373300|gb|AAR19014.1| RpoB [Actinobacillus ureae ATCC 25976]
 gi|110294685|gb|ABG66776.1| RpoB [Actinobacillus sp. CCUG 23125]
 gi|110294687|gb|ABG66777.1| RpoB [Actinobacillus sp. CCUG 26442]
 gi|110294689|gb|ABG66778.1| RpoB [Actinobacillus capsulatus]
 gi|110294691|gb|ABG66779.1| RpoB [Actinobacillus capsulatus]
 gi|110294693|gb|ABG66780.1| RpoB [Actinobacillus capsulatus]
 gi|110294695|gb|ABG66781.1| RpoB [Actinobacillus capsulatus]
 gi|110294697|gb|ABG66782.1| RpoB [Actinobacillus capsulatus]
 gi|110294699|gb|ABG66783.1| RpoB [Actinobacillus capsulatus]
 gi|110294701|gb|ABG66784.1| RpoB [Actinobacillus capsulatus]
 gi|110294703|gb|ABG66785.1| RpoB [Actinobacillus capsulatus]
 gi|110294705|gb|ABG66786.1| RpoB [Actinobacillus capsulatus]
 gi|110294707|gb|ABG66787.1| RpoB [Actinobacillus capsulatus]
 gi|110294709|gb|ABG66788.1| RpoB [Actinobacillus capsulatus]
 gi|110294713|gb|ABG66790.1| RpoB [Actinobacillus suis]
 gi|110294715|gb|ABG66791.1| RpoB [Actinobacillus capsulatus]
 gi|110294717|gb|ABG66792.1| RpoB [Actinobacillus capsulatus]
 gi|110294719|gb|ABG66793.1| RpoB [Actinobacillus capsulatus]
 gi|110294721|gb|ABG66794.1| RpoB [Actinobacillus capsulatus]
 gi|110294723|gb|ABG66795.1| RpoB [Actinobacillus capsulatus]
 gi|110294727|gb|ABG66797.1| RpoB [Actinobacillus suis]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 132/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDEEFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYKPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|198279383|emb|CAP04726.1| RNA polymerase beta subunit [Pinus gerardiana]
          Length = 288

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 109/260 (41%), Positives = 160/260 (61%), Gaps = 10/260 (3%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA+              
Sbjct: 1   MQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSI 52

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+
Sbjct: 53  NGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAY 112

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L++
Sbjct: 113 MPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRH 172

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +DE G++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P 
Sbjct: 173 LDENGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPI 232

Query: 934 GVSGTVVDVRIFNRHGIDKN 953
           G  G V+DVR  NR     +
Sbjct: 233 GGKGRVIDVRWINRVDDSGD 252



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 79   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 137

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 138  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 191

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 192  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 249

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 250  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILP 288


>gi|305662332|gb|ADM62277.1| RNA-polymerase beta-subunit [Chelonobacter oris]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 106/173 (61%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDED  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDEDSR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRAEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|189397230|gb|ACD93411.1| RNA polymerase beta subunit [Mycoplasma zalophi]
          Length = 235

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 121/241 (50%), Positives = 167/241 (69%), Gaps = 8/241 (3%)

Query: 560 DVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLS 618
           DVH THYGRICP ET EG NIGL+ ++ S+A+++ YGFI+TPY KV DG V  ND+ YL+
Sbjct: 1   DVHSTHYGRICPIETPEGPNIGLILNMASYAKIDDYGFIQTPYFKVNDGVVDFNDIRYLT 60

Query: 619 AMEEENRYIAQANSSLDED-GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           A+EE N   AQ++ +++E+ G   +E V  R   E I + +++ID+I  + +Q+ SI+AS
Sbjct: 61  AIEEINFTFAQSSININEETGEILDERVMSRKNNEYIELDKKEIDYIGVTSRQMTSISAS 120

Query: 678 LIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQ 737
            IPFLENDD+NR LMG NMQRQAVPL+K EAP V TG+E+ +A+ S + + A + GIV  
Sbjct: 121 AIPFLENDDANRALMGSNMQRQAVPLIKPEAPLVATGVEADIARFSASNVRATKDGIVTY 180

Query: 738 VDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
           VDA  I I+S +           IY L  F+RSNQ T ++Q+PLVKVG E++  D++ DG
Sbjct: 181 VDANEIRIQSDDEKKPS------IYFLRTFERSNQGTVIHQKPLVKVGQEIKAGDLLTDG 234

Query: 798 P 798
           P
Sbjct: 235 P 235


>gi|34980317|gb|AAO41851.1| RNA polymerase beta subunit [Actinobacillus lignieresii]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 132/173 (76%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYKPEEIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|292606618|gb|ADE34125.1| RNA polymerase II second largest subunit [Dothideomycetes sp. TRN
            142]
          Length = 290

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/362 (17%), Positives = 103/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 4    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      EQ E   R           +       I  G           K+ 
Sbjct: 63   RAYLDQEKRVGMSVVEQFEKPVRSDTLRMKHGTYDKIEDDGIIAPGTRVSGDDVIIGKTA 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D      R++          ++     +  Q                         
Sbjct: 123  PIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVVL--------------------TT 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV     +  Q GDK A RHG KG +      EDMPF  DG   DIV+NP  
Sbjct: 163  NTEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGLTPDIVINPHA 222

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G++                                   
Sbjct: 223  IPSRMTIAHLVECLLSKVGALTGQEGD--------------------------------- 249

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F      +I+ +L+  D  + G  ++Y+G TG+   
Sbjct: 250  --------------------ATP-FTDVTVTSISDILKDYDFQQRGFEVMYNGHTGKKLA 288

Query: 1247 RP 1248
              
Sbjct: 289  AQ 290



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       I++ GII  G  V+
Sbjct: 53  DRGLFRSLFYRAYLDQEKRVGMSVVEQFEKPVRSDTLRMKHGTYDKIEDDGIIAPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             D+++GK  P         E+L +        DV        +G+   VV
Sbjct: 113 GDDVIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVV 159


>gi|293601838|gb|ADE48323.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601862|gb|ADE48193.1| RNA polymerase II [Morchella sp. Mes-12]
 gi|293601864|gb|ADE48194.1| RNA polymerase II [Morchella sp. Mes-3]
 gi|293601874|gb|ADE48199.1| RNA polymerase II [Morchella sp. Mes-2]
 gi|293601876|gb|ADE48200.1| RNA polymerase II [Morchella sp. Mes-4]
 gi|293601886|gb|ADE48205.1| RNA polymerase II [Morchella sp. Mes-10]
 gi|293601892|gb|ADE48208.1| RNA polymerase II [Morchella steppicola]
          Length = 290

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/363 (16%), Positives = 105/363 (28%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 287

Query: 1247 RPV 1249
              V
Sbjct: 288  CQV 290



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|34980319|gb|AAO41852.1| RNA polymerase beta subunit [Pasteurella multocida]
 gi|38373332|gb|AAR19030.1| RpoB [Pasteurella dagmatis ATCC 43325]
 gi|38373338|gb|AAR19033.1| RpoB [Pasteurella multocida subsp. gallicida]
 gi|38373340|gb|AAR19034.1| RpoB [Pasteurella multocida subsp. septica]
 gi|38373342|gb|AAR19035.1| RpoB [Pasteurella stomatis]
 gi|56406209|gb|AAV87488.1| RpoB [Pasteurella multocida subsp. septica]
 gi|56406225|gb|AAV87496.1| RpoB [Bisgaard Taxon 46]
 gi|156453719|gb|ABU63714.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453721|gb|ABU63715.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453723|gb|ABU63716.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453727|gb|ABU63718.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453729|gb|ABU63719.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453731|gb|ABU63720.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453733|gb|ABU63721.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453735|gb|ABU63722.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|156453737|gb|ABU63723.1| RpoB [Pasteurella multocida]
 gi|156453739|gb|ABU63724.1| RpoB [Pasteurella multocida]
 gi|156453741|gb|ABU63725.1| RpoB [Pasteurella multocida]
 gi|156453743|gb|ABU63726.1| RpoB [Pasteurella multocida]
 gi|156453745|gb|ABU63727.1| RpoB [Pasteurella multocida]
 gi|156453755|gb|ABU63732.1| RpoB [Pasteurella multocida]
 gi|156453757|gb|ABU63733.1| RpoB [Pasteurella multocida]
 gi|156453759|gb|ABU63734.1| RpoB [Pasteurella multocida subsp. septica]
 gi|156453761|gb|ABU63735.1| RpoB [Pasteurella multocida subsp. septica]
 gi|156453763|gb|ABU63736.1| RpoB [Pasteurella multocida subsp. septica]
 gi|156453765|gb|ABU63737.1| RpoB [Pasteurella multocida subsp. septica]
 gi|156453767|gb|ABU63738.1| RpoB [Pasteurella multocida subsp. septica]
 gi|156453769|gb|ABU63739.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992387|gb|ADQ26751.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992389|gb|ADQ26752.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992391|gb|ADQ26753.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992393|gb|ADQ26754.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992395|gb|ADQ26755.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992397|gb|ADQ26756.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992399|gb|ADQ26757.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992401|gb|ADQ26758.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992403|gb|ADQ26759.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992405|gb|ADQ26760.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992407|gb|ADQ26761.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992409|gb|ADQ26762.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992411|gb|ADQ26763.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992413|gb|ADQ26764.1| RpoB [Pasteurella multocida subsp. multocida]
 gi|311992415|gb|ADQ26765.1| RpoB [Pasteurella multocida]
 gi|311992417|gb|ADQ26766.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992419|gb|ADQ26767.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992421|gb|ADQ26768.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992425|gb|ADQ26770.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992427|gb|ADQ26771.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992429|gb|ADQ26772.1| RpoB [Pasteurella multocida]
 gi|311992431|gb|ADQ26773.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992433|gb|ADQ26774.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992435|gb|ADQ26775.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992437|gb|ADQ26776.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992439|gb|ADQ26777.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992441|gb|ADQ26778.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992443|gb|ADQ26779.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992445|gb|ADQ26780.1| RpoB [Pasteurella multocida subsp. septica]
 gi|311992447|gb|ADQ26781.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|162532566|gb|ABY16689.1| RNA polymerase beta subunit [Aeromonas enteropelogenes]
          Length = 170

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 99/170 (58%), Positives = 131/170 (77%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            + LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   RHPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR
Sbjct: 61  YSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
             GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR LMG  MQ+
Sbjct: 121 HKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRALMGTTMQQ 170


>gi|110816116|gb|ABG91768.1| putative DNA-directed RNA polymerase beta subunit [Arcanobacterium
            pyogenes]
          Length = 102

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 50/97 (51%), Positives = 69/97 (71%), Gaps = 1/97 (1%)

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
            G+ +++PVFDGA EE +   L  A +    +++LYDG TGEPFD  V+VG +YM+KL HM
Sbjct: 4    GIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHM 63

Query: 1263 VSDKVYARSTGS-YSLVTQQPLGGKSNRGGQRLGEME 1298
            V DK++ARSTG  Y+ + ++ L GK+  GGQR GEME
Sbjct: 64   VDDKLHARSTGPYYTCIRRRHLAGKAQFGGQRFGEME 100


>gi|307716712|gb|ADN88409.1| RNA polymerase beta-subunit [Serratia fonticola]
          Length = 170

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 106/170 (62%), Positives = 133/170 (78%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDEEGRFEEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|257137635|ref|ZP_05585897.1| DNA-directed RNA polymerase subunit beta [Burkholderia
           thailandensis E264]
          Length = 137

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 50/129 (38%), Positives = 74/129 (57%), Gaps = 1/129 (0%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               F    R+RK F K   +  +P L+  Q  S+  FL  ++ P +R +EGLQAAF SV
Sbjct: 1   MQYSFTEKKRIRKSFAKRSIVHQVPFLLATQLESFSTFLQADVLPAQRKSEGLQAAFTSV 60

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G A LEFVSY    P F++ +C  R LTY   L+  +RL++ D +  +    +
Sbjct: 61  FPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRLVLLDKESPS-KPVV 119

Query: 123 KDIKEQSIY 131
           K++KEQ +Y
Sbjct: 120 KEVKEQEVY 128


>gi|258590807|emb|CBE67081.1| RNA polymerase beta subunit [Arcanobacterium abortisuis]
          Length = 135

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/163 (37%), Positives = 82/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE HLGW                    D S  R+  E+                  +   
Sbjct: 1    FELHLGWVAK--------------QGWDASAARAAGEEWA--------------VRLPER 32

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
            A +      V+TPVFDG   + +N +L   + +  G        ++ L+DG TGEPF  P
Sbjct: 33   AVKAGPDRTVATPVFDGVRSDELNGLLANTNPNRDGDRLVDGAGKARLFDGRTGEPFPDP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|34923316|gb|AAQ83545.1| RpoB [Pasteurella pneumotropica]
 gi|34923318|gb|AAQ83546.1| RpoB [Bisgaard Taxon 17]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSAFARTNDYGFLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|312204364|gb|ADQ47499.1| RNA polymerase II second largest subunit [Sagiolechia protuberans]
          Length = 292

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 60/367 (16%), Positives = 110/367 (29%), Gaps = 81/367 (22%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +     S +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTQSMEYLKFSKLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +++ +R   +    +E   +    E + +    Y +L +   I  G      
Sbjct: 60   RSLFYRSYVEQEKR---IGMSLVEAFEKPLRSETLKVKHGTYEKLDDDGIIAPGIRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R++          ++     +                  ++
Sbjct: 117  DIIIGKTAPIEPNAEEMGQRTKLHTKRDASTPLRSTENGI------------------VD 158

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 159  KVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLTP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DIIINPHAIPSRMTIAHLIECQLSKVACLRGLEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     + I+ +LR       G  I+Y+
Sbjct: 252  ----------------------------ATP-FTDITVDGISGVLREQGYHSRGFEIMYN 282

Query: 1239 GLTGEPF 1245
            G TG   
Sbjct: 283  GHTGRKL 289



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                       L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTQSMEYLKFSKLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   V     + +D+ GII  G  V+
Sbjct: 55  DRGLFRSLFYRSYVEQEKRIGMSLVEAFEKPLRSETLKVKHGTYEKLDDDGIIAPGIRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P        EE   R     K    RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPI---EPNAEEMGQRT----KLHTKRDASTPLRSTENGIVDKVLLTTNAE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|38373290|gb|AAR19009.1| RpoB [Actinobacillus seminis]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEFGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|313611136|gb|EFR85972.1| DNA-directed RNA polymerase subunit beta [Listeria monocytogenes
           FSL F2-208]
          Length = 116

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 45/131 (34%), Positives = 71/131 (54%), Gaps = 19/131 (14%)

Query: 2   AKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS 61
           +   V  G  R R+ F +  E++++P+LIE+Q ASY  FL          +EGL+  F+ 
Sbjct: 5   SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFL----------DEGLREMFRD 54

Query: 62  VFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKS 121
           + PI  F+G   LEF+ Y+   PK+ V++   RD  YA PL++ LRLI          K 
Sbjct: 55  ISPIEDFAGNLSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLI---------NKE 105

Query: 122 IKDIKEQSIYM 132
             ++K+Q ++M
Sbjct: 106 TGEVKDQEVFM 116


>gi|34923320|gb|AAQ83547.1| RpoB [Pasteurella caballi]
 gi|38373280|gb|AAR19004.1| RpoB [Actinobacillus rossii]
 gi|81251241|gb|ABB69965.1| RpoB [Actinobacillus rossii]
 gi|81251243|gb|ABB69966.1| RpoB [Actinobacillus rossii]
 gi|81251245|gb|ABB69967.1| RpoB [Actinobacillus rossii]
 gi|81251247|gb|ABB69968.1| RpoB [Actinobacillus rossii]
 gi|81251249|gb|ABB69969.1| RpoB [Actinobacillus rossii]
 gi|81251251|gb|ABB69970.1| RpoB [Actinobacillus rossii]
 gi|81251253|gb|ABB69971.1| RpoB [Actinobacillus rossii]
 gi|81251255|gb|ABB69972.1| RpoB [Actinobacillus rossii]
 gi|81251257|gb|ABB69973.1| RpoB [Actinobacillus rossii]
 gi|81251261|gb|ABB69975.1| RpoB [Actinobacillus rossii]
 gi|81251263|gb|ABB69976.1| RpoB [Actinobacillus rossii]
 gi|81251267|gb|ABB69978.1| RpoB [Actinobacillus rossii]
 gi|81251269|gb|ABB69979.1| RpoB [Actinobacillus rossii]
 gi|81251271|gb|ABB69980.1| RpoB [Actinobacillus rossii]
 gi|81251273|gb|ABB69981.1| RpoB [Actinobacillus rossii]
 gi|81251275|gb|ABB69982.1| RpoB [Actinobacillus rossii]
 gi|81251277|gb|ABB69983.1| RpoB [Actinobacillus rossii]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 129/173 (74%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|56406211|gb|AAV87489.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 173

 Score =  179 bits (453), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEESKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|293601894|gb|ADE48209.1| RNA polymerase II [Morchella sp. Mel-10]
 gi|293601898|gb|ADE48211.1| RNA polymerase II [Morchella sp. Mel-6]
 gi|293601900|gb|ADE48212.1| RNA polymerase II [Morchella sp. Mel-2]
 gi|293601902|gb|ADE48213.1| RNA polymerase II [Morchella sp. Mel-8]
 gi|293601904|gb|ADE48214.1| RNA polymerase II [Morchella sp. Mel-9]
 gi|293601906|gb|ADE48215.1| RNA polymerase II [Morchella punctipes]
 gi|293601908|gb|ADE48216.1| RNA polymerase II [Morchella sp. Mel-7]
 gi|293601910|gb|ADE48217.1| RNA polymerase II [Morchella semilibera]
 gi|293601912|gb|ADE48218.1| RNA polymerase II [Morchella tomentosa]
 gi|293601914|gb|ADE48219.1| RNA polymerase II [Morchella sp. Mel-18]
 gi|293601916|gb|ADE48220.1| RNA polymerase II [Morchella sp. Mel-13]
 gi|293601918|gb|ADE48221.1| RNA polymerase II [Morchella sp. Mel-24]
 gi|293601920|gb|ADE48222.1| RNA polymerase II [Morchella sp. Mel-16]
 gi|293601922|gb|ADE48223.1| RNA polymerase II [Morchella sp. Mel-20]
 gi|293601924|gb|ADE48224.1| RNA polymerase II [Morchella sp. Mel-21]
 gi|293601926|gb|ADE48225.1| RNA polymerase II [Morchella sp. Mel-15]
 gi|293601928|gb|ADE48226.1| RNA polymerase II [Morchella sp. Mel-17]
 gi|293601930|gb|ADE48227.1| RNA polymerase II [Morchella sp. Mel-23]
 gi|293601932|gb|ADE48228.1| RNA polymerase II [Morchella sp. Mel-22]
 gi|293601934|gb|ADE48229.1| RNA polymerase II [Morchella sp. Mel-12]
 gi|293601936|gb|ADE48230.1| RNA polymerase II [Morchella sp. Mel-14]
 gi|293601938|gb|ADE48231.1| RNA polymerase II [Morchella sp. Mel-19]
 gi|293601944|gb|ADE48234.1| RNA polymerase II [Verpa cf. conica M22]
 gi|293601948|gb|ADE48236.1| RNA polymerase II [Verpa cf. conica M503]
 gi|293601950|gb|ADE48237.1| RNA polymerase II [Verpa sp. M90]
 gi|293601952|gb|ADE48238.1| RNA polymerase II [Verpa bohemica]
 gi|293601954|gb|ADE48239.1| RNA polymerase II [Verpa sp. M499]
 gi|293601956|gb|ADE48240.1| RNA polymerase II [Disciotis venosa]
 gi|293601958|gb|ADE48241.1| RNA polymerase II [Disciotis sp. M95]
          Length = 290

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/366 (16%), Positives = 110/366 (30%), Gaps = 81/366 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L E   +  G           
Sbjct: 62   RSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 119  KTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML------------------- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 160  -TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 284

Query: 1244 PFDRPV 1249
                 V
Sbjct: 285  KLVCQV 290



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|293601766|gb|ADE48287.1| RNA polymerase II [Morchella sp. Mes-16]
 gi|293601780|gb|ADE48294.1| RNA polymerase II [Morchella sp. Mes-16]
 gi|293601826|gb|ADE48317.1| RNA polymerase II [Morchella sp. Mes-11]
 gi|293601866|gb|ADE48195.1| RNA polymerase II [Morchella sp. Mes-14]
 gi|293601868|gb|ADE48196.1| RNA polymerase II [Morchella sp. Mes-16]
 gi|293601870|gb|ADE48197.1| RNA polymerase II [Morchella sp. Mes-11]
 gi|293601872|gb|ADE48198.1| RNA polymerase II [Morchella sp. Mes-7]
 gi|293601878|gb|ADE48201.1| RNA polymerase II [Morchella sp. Mes-9]
 gi|293601880|gb|ADE48202.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601882|gb|ADE48203.1| RNA polymerase II [Morchella sp. Mes-5]
 gi|293601884|gb|ADE48204.1| RNA polymerase II [Morchella sp. Mes-6]
 gi|293601888|gb|ADE48206.1| RNA polymerase II [Morchella sp. Mes-13]
 gi|293601890|gb|ADE48207.1| RNA polymerase II [Morchella sp. Mes-15]
          Length = 290

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 59/363 (16%), Positives = 105/363 (28%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKLV 287

Query: 1247 RPV 1249
              V
Sbjct: 288  CQV 290



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|81251265|gb|ABB69977.1| RpoB [Actinobacillus rossii]
          Length = 173

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 128/173 (73%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+ R L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEHDDAXRAL 173


>gi|116634271|emb|CAL25599.1| DNA-directed RNA polymerase beta chain [Bartonella henselae]
          Length = 169

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 121/169 (71%), Positives = 145/169 (85%)

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLS
Sbjct: 1   RDVHPTHYGRICPIETLEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLS 60

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           AMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+L
Sbjct: 61  AMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAAL 120

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           IPFLENDD+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+ SGAA+
Sbjct: 121 IPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGAAV 169


>gi|258590813|emb|CBE67084.1| RNA polymerase beta subunit [Arcanobacterium bonasi]
          Length = 135

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 59/163 (36%), Positives = 83/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE HLGW                    D +  R   E+                  +   
Sbjct: 1    FELHLGWVAKH--------------GWDATEARKAGEEWA--------------MRLPEN 32

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
            A + + G  V+TPVFDG + + +  +L +   +  G        ++ L+DG TG+PF  P
Sbjct: 33   AIEAEPGRTVATPVFDGVEADELKGLLSVTKPNRDGERMVDDTGKARLFDGRTGDPFPDP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|123979362|gb|ABM81506.1| RNA polymerase II second largest subunit [Pertusaria amara]
          Length = 688

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 56/294 (19%), Positives = 91/294 (30%), Gaps = 77/294 (26%)

Query: 964  IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E   +    + + L    Y +L E   +  G           K+  ++ D      R++
Sbjct: 469  VEQFEKPMRSDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRTK 528

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                             +K    T     E+   +K+             LR VKV    
Sbjct: 529  L---------------HVKRDVSTPLRSTENGIVDKVLL-----TTNAEGLRFVKVRTRT 568

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  
Sbjct: 569  TKVPQIGDKFASRHGQKGTIGITYRMEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQ 628

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            L       G +                                                 
Sbjct: 629  LSKVSSLRGFEGD----------------------------------------------- 641

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                  +TP F     ++++ +LR       G  ++Y+G TG      V +G  
Sbjct: 642  ------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPT 688



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 54/375 (14%), Positives = 118/375 (31%), Gaps = 35/375 (9%)

Query: 470 MLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------ 521
           ++   +R    ++ + +    +              + +  + + +     +        
Sbjct: 1   LMAGLFRNLFKKLTKDVFKYLQKCVESNREFNLTLGVKSTTLTNGLKYSLATGNWGDQKK 60

Query: 522 -------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAET 574
                  +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET
Sbjct: 61  AAQSKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAET 116

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANS 632
            EG   GLV +L+    V      E    +    + +V  +   L +      ++     
Sbjct: 117 PEGQACGLVKNLSLMCCVTVGSPSEPIIDFMIQRNMEVLEEYEPLRSPNATKIFVNGVWV 176

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRV 690
            +  D +     V        I      + D  D   K          P F+ ++D+   
Sbjct: 177 GIHRDPAHLVNTVQTLRRRGMISSEVSLVRDIRDREFKIFTDAGRVCRPLFVVDNDAKSS 236

Query: 691 LMGCNMQ-RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVE 749
             G  +  ++ V  L+ +            A+ +       + G+VE +DA         
Sbjct: 237 NKGSLVLTKELVNKLEDDKDLPDDMDPDEKAEKTMGWDGLVKRGVVEYLDAEE------- 289

Query: 750 GDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG-DLALG 808
              + +   V     ++  R  Q       P+ +    V+          T      ++ 
Sbjct: 290 ---EETVMIVMTPEDLEISRQIQAGYQMPEPVDEPNKRVKAPLNRTAHTWTHCEIHPSMI 346

Query: 809 RNMLVAFMPWHGYNF 823
             +  + +P+  +N 
Sbjct: 347 LGICASIIPFPDHNQ 361



 Score = 43.9 bits (102), Expect = 0.20,   Method: Composition-based stats.
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 4/80 (5%)

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           +  D   +       +DE GI+  G  V+  DI++GK  P         E+L +      
Sbjct: 476 MRSDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHV 531

Query: 921 AVDVRDTSLRVPSGVSGTVV 940
             DV        +G+   V+
Sbjct: 532 KRDVSTPLRSTENGIVDKVL 551


>gi|282598450|gb|ADA83455.1| RNA polymerase beta subunit [Corynebacterium sp. NML95-0358]
          Length = 137

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 79/168 (47%), Gaps = 40/168 (23%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  I+   +  K   D                              
Sbjct: 1    QVLEVHLGWLAKS-GWAIEGDPDWAKRIPDD----------------------------- 30

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                +      ++TPVFDGA  E I  +L     D  G        ++ L+DG +GEPF 
Sbjct: 31   --LREVPPNSLLATPVFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFK 88

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             PV VG  YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 89   YPVCVGEKYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 136


>gi|282598448|gb|ADA83454.1| RNA polymerase beta subunit [Corynebacterium sp. NML94-0264]
 gi|282598452|gb|ADA83456.1| RNA polymerase beta subunit [Corynebacterium sp. NML96-0085]
 gi|282598454|gb|ADA83457.1| RNA polymerase beta subunit [Corynebacterium sp. NML00-0179]
          Length = 136

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 79/168 (47%), Gaps = 40/168 (23%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E HLGW     G  I+   +  K   D                              
Sbjct: 1    QVLEVHLGWLAKS-GWAIEGDPDWAKRIPDD----------------------------- 30

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFD 1246
                +      ++TPVFDGA  E I  +L     D  G        ++ L+DG +GEPF 
Sbjct: 31   --LREVPPNSLLATPVFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFK 88

Query: 1247 RPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRL 1294
             PV VG  YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR 
Sbjct: 89   YPVCVGEKYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRF 136


>gi|34923328|gb|AAQ83551.1| RpoB [Pasteurella aerogenes]
 gi|38373328|gb|AAR19028.1| RpoB [Pasteurella aerogenes]
          Length = 173

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEYGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|258590819|emb|CBE67087.1| RNA polymerase beta subunit [Arcanobacterium phocae]
 gi|258590821|emb|CBE67088.1| RNA polymerase beta subunit [Arcanobacterium phocae]
          Length = 135

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 50/107 (46%), Positives = 69/107 (64%), Gaps = 8/107 (7%)

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEP 1244
            +   A   K    V+TPVFDG +   +  +L   + +  G        ++ L+DG TG+P
Sbjct: 29   LPEHAVVGKRDGRVATPVFDGVESGELRGLLENTNPNRDGDRLIGASGKARLFDGRTGDP 88

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            F  PV+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 89   FPEPVSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|193201511|gb|ACF15963.1| RNA polymerase II subunit [Opegrapha longissima]
          Length = 298

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 56/367 (15%), Positives = 103/367 (28%), Gaps = 81/367 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 3    NILYYPQKPLATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 62

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L +   +  G           
Sbjct: 63   LFYRTYIEQQQAVGFNSLEEFEKPSKQLTMRTRPGTYDKLDDDGFVAPGVRVSGEDIIVG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +       Q  +   + +       +     +                    
Sbjct: 123  KTAPFQAPMQESAEGGQRNKQHTKRDVSCPLRSTEAGIIDRVL----------------- 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 166  -VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGLVPDLIIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L   C   G +                                
Sbjct: 225  PHAIPSRMTIAHLIECLLSKVCSTTGLEGD------------------------------ 254

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     + I+++LR A   + G  ++Y+G TG 
Sbjct: 255  -----------------------ATP-FTDVTVQGISNLLRNAGYHQRGFEVMYNGHTGR 290

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 291  KLMAQVF 297



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 72/196 (36%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFMKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +    +           +D+ G +  G  V+
Sbjct: 56  DRGLFRSLFYRTYIEQQQAVGFNSLEEFEKPSKQLTMRTRPGTYDKLDDDGFVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI+VGK  P       P ++        K    RD S  + S  +G +  V +    G
Sbjct: 116 GEDIIVGKTAPF----QAPMQESAEGGQRNKQHTKRDVSCPLRSTEAGIIDRVLVTTTEG 171

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 172 RRSVKVRTRTTKVPQI 187


>gi|293601940|gb|ADE48232.1| RNA polymerase II [Morchella sp. Mel-11]
 gi|293601942|gb|ADE48233.1| RNA polymerase II [Morchella rufobrunnea]
          Length = 290

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/366 (16%), Positives = 110/366 (30%), Gaps = 81/366 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +  + +E   +      + L    Y +L E   +  G           
Sbjct: 62   RSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D+     R ++         ++     +  Q                      
Sbjct: 119  KTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML------------------- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++N
Sbjct: 160  -TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E+++++LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGR 284

Query: 1244 PFDRPV 1249
                 V
Sbjct: 285  KLVCQV 290



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|219563993|gb|ACL28180.1| RNA polymerase II second largest subunit [Cyathicula microspora]
          Length = 302

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/375 (16%), Positives = 108/375 (28%), Gaps = 81/375 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 66   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLKHGTYDKLDDDGIVAPGVRV 121

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 122  SGEDIIIGKTAPMAPDAEELGQRTKAHTKRDASTPLRSTENGIVDQVLI----------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 171  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTRQG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 222  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  I
Sbjct: 260  -------------------------------ATP-FTEVTVDSVSKLLRAHGYQSRGFEI 287

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      V 
Sbjct: 288  MYHGHTGRKMMAQVF 302



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 66/186 (35%), Gaps = 22/186 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 4   RMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 53

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        D   +       +D+ G
Sbjct: 54  SVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPYRSDTLKLKHGTYDKLDDDG 113

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  DI++GK  P         ++        KA   RD S  + S  +G V 
Sbjct: 114 IVAPGVRVSGEDIIIGKTAPMAPDAEELGQRT-------KAHTKRDASTPLRSTENGIVD 166

Query: 941 DVRIFN 946
            V I  
Sbjct: 167 QVLITT 172


>gi|38373288|gb|AAR19008.1| RpoB [Actinobacillus scotiae]
          Length = 173

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 129/173 (74%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LD+D  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDDDFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGEKGESGLYRPEDIQYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|46277320|gb|AAS86850.1| DNA-dependent RNA polymerase II [Pachyella violaceonigra]
          Length = 547

 Score =  178 bits (452), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 57/352 (16%), Positives = 103/352 (29%), Gaps = 75/352 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R  
Sbjct: 271  MEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYMDQEKRVG 329

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   R           +       +  G           K+  ++ +      
Sbjct: 330  MAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGEDIIIGKTAPIAPNTEELGQ 389

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+++         ++     +  Q                             L+ VKV 
Sbjct: 390  RTKFHTKRDVSTPLRSTESGIVDQVML--------------------TTNQEGLKFVKVR 429

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + 
Sbjct: 430  MRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGIVPDIIINPHAIPSRMTIAHLI 489

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 490  ECQLSKVSSLXGYEGD-------------------------------------------- 505

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                     +TP F     ++++ +LR       G  ++Y+G TG      V
Sbjct: 506  ---------ATP-FTDVTVDSVSGLLREHGYQSRGFEVMYNGHTGRKLVVQV 547



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 69/475 (14%), Positives = 119/475 (25%), Gaps = 72/475 (15%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
              ++ +   ++   P    NA  +             + +  ++  L R  H     +L
Sbjct: 15  DFMKQRNMEVLEEYEPSRHPNATKIFVNGVWVGIHRDPNFIVRNIQKLRRQNHIGHEVSL 74

Query: 545 GQGGVARARAGVEM--RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
            Q    R         R   P       PA T  G  +   S +                
Sbjct: 75  IQDVRNREFKIFTDAGRICRPLFVVDNDPASTRRGELVLQKSHIEKLEYDKELPKDSELK 134

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                      V Y+ A EEE                     +      EE+ + R+   
Sbjct: 135 YGWQGLINEGVVEYVDAEEEET--------------------IMIMMTPEELDLSRQYHA 174

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
             +   + +   A    P  ++                            T  E   A  
Sbjct: 175 GYEIQAEPMDLAARVRQPVNKHATMW------------------------THCEIHPAMI 210

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            G            Q                                          PL 
Sbjct: 211 LGICASIIPFPDHNQS----PRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLYYPXXPL- 265

Query: 783 KVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSI 842
                                +L  G+N +VA   + GYN EDS+++++  +   +F S+
Sbjct: 266 ---------GTTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 316

Query: 843 HIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
               +    +   +   E        +   +       +DE G++  G  VN  DI++GK
Sbjct: 317 FFRTYMDQEKRVGMAVVEEFEKPNRQNTLRLKHGTYDKLDEDGLVAPGIRVNGEDIIIGK 376

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             P   +     ++        K    RD S  + S  SG V  V +       K
Sbjct: 377 TAPIAPNTEELGQRT-------KFHTKRDVSTPLRSTESGIVDQVMLTTNQEGLK 424


>gi|38373334|gb|AAR19031.1| RpoB [Pasteurella langaaensis]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 129/173 (74%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYIIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34980305|gb|AAO41845.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980309|gb|AAO41847.1| RNA polymerase beta subunit [Histophilus somni]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD +  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDGELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|34923300|gb|AAQ83537.1| RpoB [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|38373296|gb|AAR19012.1| RpoB [Actinobacillus genomosp. 1]
 gi|38373298|gb|AAR19013.1| RpoB [Actinobacillus genomosp. 1]
 gi|38373302|gb|AAR19015.1| RpoB [Actinobacillus genomosp. 2]
 gi|38373348|gb|AAR19038.1| RpoB [Actinobacillus arthritidis]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 105/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYKPEDIHYMDISTQQVVSVAAALIPFLEHDDANRAL 173


>gi|330785260|gb|AEC46436.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
          Length = 307

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 107/380 (28%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   ++ +       Q  +   + + V   + S +                
Sbjct: 120  SGDDIIIGKTAPFANPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLVDRVL-------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ---------VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYQSRGLEL 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGHTGRKLMAQVFLGXTY 307



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 62/187 (33%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       E                  + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R        DV        +G+   V+      R  
Sbjct: 121 GDDIIIGKTAPFANPMADNAEGGQRTKM-HSKRDVSAPLRSTEAGLVDRVLVTTNEGRRT 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|203285481|gb|ACH97331.1| RNA polymerase II subunit [Thozetella sp. RJ-2008]
          Length = 297

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 59/374 (15%), Positives = 105/374 (28%), Gaps = 81/374 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +         +   +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTMANILYYPQKPLGITRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D  +R        +E   +    E + + R  Y +L +   +  G   
Sbjct: 62   LF-RSLFFRSYTDCEKRVGI---NVVEQFEKPSRQEVLRVKRGTYDKLEDDGLVAPGIRV 117

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K++ + ++      R+           ++     +                 
Sbjct: 118  SGEDIIIGKTSPIDTNNQELGQRTASHTKRDSSTPLRSTESGIIDSVIL----------- 166

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV V   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 167  ---------TTNQDGLRYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTAEG 217

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L       G +                        
Sbjct: 218  ITPDIIINPHAIPSRMTIAHLIECLLSKVATLKGFEGD---------------------- 255

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     + ++ +LR       G   
Sbjct: 256  -------------------------------ATP-FTDVTVDVVSKLLREQGYQSRGFEG 283

Query: 1236 LYDGLTGEPFDRPV 1249
            ++ G TG      V
Sbjct: 284  MFHGHTGRKLRSQV 297


>gi|38373308|gb|AAR19018.1| RpoB [Haemophilus felis]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVINGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|40643895|emb|CAD89520.1| RNA polymerase II second largest subunit [Davidia involucrata]
          Length = 135

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 46/185 (24%), Positives = 63/185 (34%), Gaps = 54/185 (29%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 5    TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 64

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 65   AIPSRMTIGQLIECIMGKVAAHMGKEGD-------------------------------- 92

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                 +TP F     + I+  L        G   +Y+G TG   
Sbjct: 93   ---------------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRL 130

Query: 1246 DRPVT 1250
               + 
Sbjct: 131  TSMIF 135


>gi|34923302|gb|AAQ83538.1| RpoB [Haemophilus parasuis]
 gi|38373276|gb|AAR19002.1| RpoB [Actinobacillus indolicus]
 gi|38373316|gb|AAR19022.1| RpoB [Haemophilus parasuis]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|268528973|gb|ACZ06539.1| RpoB [Mannheimia varigena]
 gi|268528975|gb|ACZ06540.1| RpoB [Mannheimia varigena]
 gi|268528987|gb|ACZ06546.1| RpoB [Mannheimia varigena]
 gi|268528989|gb|ACZ06547.1| RpoB [Mannheimia varigena]
 gi|268528995|gb|ACZ06550.1| RpoB [Mannheimia varigena]
          Length = 172

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 132/172 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N  S +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNRRSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+D+++R L
Sbjct: 121 FTDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDNADRAL 172


>gi|34980301|gb|AAO41843.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980303|gb|AAO41844.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980307|gb|AAO41846.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980311|gb|AAO41848.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980313|gb|AAO41849.1| RNA polymerase beta subunit [Histophilus somni]
 gi|34980315|gb|AAO41850.1| RNA polymerase beta subunit [Histophilus somni]
          Length = 173

 Score =  178 bits (452), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD +  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDNELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|297500273|gb|ADI43573.1| RNA polymerase beta subunit [Agrobacterium sp. T37]
 gi|297500277|gb|ADI43575.1| RNA polymerase beta subunit [Agrobacterium sp. H100]
 gi|297500339|gb|ADI43606.1| RNA polymerase beta subunit [Agrobacterium sp. CCUG50385B]
          Length = 178

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDAISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|300394758|gb|ADK11917.1| DNA-directed RNA polymerase II subunit two [Serpula similis]
          Length = 512

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 55/356 (15%), Positives = 101/356 (28%), Gaps = 34/356 (9%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             W       SM+  +   ++            ++       +G       +         
Sbjct: 189  TWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM------- 241

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 242  ----DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 297

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    I+ R  +D  ++S   + E+ E   RD          +       I  G  
Sbjct: 298  IDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRDNTLRMKHGTYDKIEDDGLIAPGTG 356

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +  D      R++          ++     +  Q             
Sbjct: 357  VRGDDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI---------- 406

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                             + VKV V   R  Q GDK A RHG KG +      EDMPF  +
Sbjct: 407  ----------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTAE 456

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            G   D+++NP  +PSRM +G + E  L      +G +  +          +S    
Sbjct: 457  GIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLR 512



 Score =  106 bits (264), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 66/456 (14%), Positives = 127/456 (27%), Gaps = 96/456 (21%)

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            NA         F     +    +  N +  I   RR   +                ++ 
Sbjct: 27  ENAHSSTPCTKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYT 86

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR-------KVCDGKVTNDVVY 616
                  P    E   + L              ++   YR       K         V  
Sbjct: 87  DAGRVCRPLFIVENQQLILQKK--------HIKWLNQGYRDDDGEEFKWEQLVKGGIVEL 138

Query: 617 LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL-------VPREKIDFIDASPK 669
           L A EEE   I+     L+     +  +      G+          +        +  P 
Sbjct: 139 LDAEEEETVMISMTPEDLENSRLQSAGIDPHANDGDYDPAARLKAGINAHTWTHCEIHPS 198

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
            ++ + AS+IPF +++ S R      M +QA+ +                          
Sbjct: 199 MILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV------------------- 239

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
                                    + + +  Y       +     +  R          
Sbjct: 240 ----------------------RMDTMANILYYPQKPLATTRSMEYLKFR---------- 267

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  
Sbjct: 268 --------------ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMD 313

Query: 850 MARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + + + +   E        +   +       I++ G+I  G  V   DI++GK  P    
Sbjct: 314 LEKKSGIQQLEEFEKPTRDNTLRMKHGTYDKIEDDGLIAPGTGVRGDDIIIGKTAPI--- 370

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
                E+L +        DV        +G+   V+
Sbjct: 371 -PPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVL 405


>gi|297500373|gb|ADI43623.1| RNA polymerase beta subunit [Agrobacterium sp. AGR8]
          Length = 178

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDVISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|146335200|gb|ABQ23340.1| RNA polymerase beta subunit [Corynebacterium timonense]
          Length = 135

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 78/163 (47%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G  +    +D      +  L   L  V                     
Sbjct: 1    LEVHLGWLAKA-GWTVN--PDDPANAKLLETLPEHLYDVPAESLT--------------- 42

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                      +TPVFDGA  E I  +L     +  G        ++ L+DG +GEPF  P
Sbjct: 43   ----------ATPVFDGATNEEIAGLLANTKPNRDGDVMVDGNGKARLFDGRSGEPFKYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|330785308|gb|AEC46460.1| RNA polymerase II second largest subunit [Dictyographa varians]
          Length = 307

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 58/380 (15%), Positives = 106/380 (27%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQRPLATTRPMEYMNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  +V    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSLFYRTYI----EQQQAVGFAALEQFEKPVKQMTLRTRPGTYEKLDDDGFVPPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+   S +                +E  QR  +  +          E    +
Sbjct: 120  SGDDIIIGKTAPFSQEAAEN------------EEGGQRTKQHTRRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VK+     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  RVL------VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  VVPDLIVNPHAIPSRMTVAHLIECLLSKVSTFNGSEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+  L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTETTVSQISGFLKDSGFQSRGLEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +Y+G TG      + +   Y
Sbjct: 288  MYNGHTGRKLAAQIFLXPTY 307



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 65/196 (33%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           QRPL                   +  +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQRPL----------ATTRPMEYMNFSELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       E                  + +D+ G
Sbjct: 52  SIIMNQSAIDRGLFRSLFYRTYIEQQQAVGFAALEQFEKPVKQMTLRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  +     EE   +        DV        +G+   V+
Sbjct: 112 FVPPGVRVSGDDIIIGKTAPFSQEAAENEEGG-QRTKQHTRRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKIRTRT 186


>gi|293601896|gb|ADE48210.1| RNA polymerase II [Morchella sp. Mel-5]
          Length = 290

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 60/363 (16%), Positives = 105/363 (28%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     E+++++LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEIMYNGYTGRKLV 287

Query: 1247 RPV 1249
              V
Sbjct: 288  CQV 290



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|264658145|emb|CBH32072.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 109

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 49/96 (51%), Positives = 69/96 (71%), Gaps = 8/96 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 14   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 73

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 74   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 109


>gi|264658143|emb|CBH32071.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
 gi|264658157|emb|CBH32075.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 49/96 (51%), Positives = 69/96 (71%), Gaps = 8/96 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 16   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 75

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 76   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 111


>gi|158514841|gb|ABW69376.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 169

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 130/168 (77%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 2   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNI 61

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  F
Sbjct: 62  GLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEESNNIIAQANSNLDENFRF 121

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
           T+  V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE+DD+N
Sbjct: 122 TDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLEHDDAN 169


>gi|258590823|emb|CBE67089.1| RNA polymerase beta subunit [Arcanobacterium pluranimalium]
          Length = 135

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 53/95 (55%), Positives = 69/95 (72%), Gaps = 8/95 (8%)

Query: 1205 PVSTPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
            PV+TPVFDG   + +  +L            +DESG++ L+DG TGEPF  PV+VGY+YM
Sbjct: 41   PVATPVFDGVLSDELKGLLGNTLPNRDGDRMVDESGKARLFDGRTGEPFPEPVSVGYMYM 100

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            LKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 101  LKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|258590809|emb|CBE67082.1| RNA polymerase beta subunit [Arcanobacterium bernardiae]
          Length = 135

 Score =  178 bits (451), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 78/163 (47%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE HLGW      +   +             L     K     +                
Sbjct: 1    FELHLGWVAK---QGWDATAAREAGEEWAVRLPERAVKAGPDRT---------------- 41

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                     V+TPVFDG   + +N +L   + +  G        ++ L+DG TGEPF  P
Sbjct: 42   ---------VATPVFDGVLSDELNGLLANTNPNRDGDRMVDAAGKARLFDGRTGEPFPDP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|81251279|gb|ABB69984.1| RpoB [Actinobacillus rossii]
          Length = 173

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 128/173 (73%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS  TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEXTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|293601712|gb|ADE48260.1| RNA polymerase II [Morchella punctipes]
          Length = 294

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 58/367 (15%), Positives = 106/367 (28%), Gaps = 75/367 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 255  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 285

Query: 1239 GLTGEPF 1245
            G TG   
Sbjct: 286  GYTGRKL 292



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|38373336|gb|AAR19032.1| RpoB [Pasteurella mairii]
 gi|81251281|gb|ABB69985.1| RpoB [Pasteurella mairii]
 gi|81251283|gb|ABB69986.1| RpoB [Pasteurella mairii]
 gi|81251285|gb|ABB69987.1| RpoB [Pasteurella mairii]
 gi|81251287|gb|ABB69988.1| RpoB [Pasteurella mairii]
 gi|81251289|gb|ABB69989.1| RpoB [Pasteurella mairii]
 gi|81251291|gb|ABB69990.1| RpoB [Pasteurella mairii]
          Length = 173

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD +  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDNELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEFGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|151573167|gb|ABS17776.1| RNA polymerase II [Fusarium sp. NRRL 43527]
 gi|151573170|gb|ABS17778.1| RNA polymerase II [Fusarium sp. NRRL 43529]
 gi|151573173|gb|ABS17780.1| RNA polymerase II [Fusarium sp. NRRL 43536]
 gi|151573393|gb|ABS17926.1| RNA polymerase II [Fusarium sp. NRRL 43728]
 gi|161015854|gb|ABX55927.1| RNA polymerase II subunit [Fusarium sp. NRRL 47512]
 gi|168419266|gb|ACA23520.1| RNA polymerase II [Fusarium sp. NRRL 22098]
 gi|168419275|gb|ACA23526.1| RNA polymerase II [Fusarium sp. NRRL 22153]
 gi|168419290|gb|ACA23536.1| RNA polymerase II [Neocosmospora vasinfecta]
 gi|168419332|gb|ACA23564.1| RNA polymerase II [Fusarium sp. NRRL 22436]
 gi|168419335|gb|ACA23566.1| RNA polymerase II [Neocosmospora vasinfecta]
 gi|168419350|gb|ACA23576.1| RNA polymerase II [Fusarium sp. FSSC_20a KOD-2010]
 gi|168419359|gb|ACA23582.1| RNA polymerase II [Fusarium sp. NRRL 22640]
 gi|168419362|gb|ACA23584.1| RNA polymerase II [Fusarium sp. NRRL 22641]
 gi|168419368|gb|ACA23588.1| RNA polymerase II [Fusarium sp. NRRL 22645]
 gi|168419371|gb|ACA23590.1| RNA polymerase II [Fusarium sp. NRRL 22661]
 gi|168419377|gb|ACA23594.1| RNA polymerase II [Fusarium sp. NRRL 22779]
 gi|168419380|gb|ACA23596.1| RNA polymerase II [Fusarium falciforme]
 gi|168419389|gb|ACA23602.1| RNA polymerase II [Fusarium sp. NRRL 22791]
 gi|168419401|gb|ACA23610.1| RNA polymerase II [Fusarium falciforme]
 gi|168419404|gb|ACA23612.1| RNA polymerase II [Fusarium sp. NRRL 25388]
 gi|168419407|gb|ACA23614.1| RNA polymerase II [Fusarium sp. NRRL 25391]
 gi|168419413|gb|ACA23618.1| RNA polymerase II [Fusarium falciforme]
 gi|168419419|gb|ACA23622.1| RNA polymerase II [Fusarium falciforme]
 gi|168419422|gb|ACA23624.1| RNA polymerase II [Fusarium falciforme]
 gi|168419434|gb|ACA23632.1| RNA polymerase II [Fusarium falciforme]
 gi|168419437|gb|ACA23634.1| RNA polymerase II [Fusarium falciforme]
 gi|168419446|gb|ACA23640.1| RNA polymerase II [Fusarium falciforme]
 gi|168419449|gb|ACA23642.1| RNA polymerase II [Fusarium falciforme]
 gi|168419452|gb|ACA23644.1| RNA polymerase II [Fusarium falciforme]
 gi|168419455|gb|ACA23646.1| RNA polymerase II [Fusarium sp. NRRL 28561]
 gi|168419458|gb|ACA23648.1| RNA polymerase II [Fusarium falciforme]
 gi|168419461|gb|ACA23650.1| RNA polymerase II [Fusarium falciforme]
 gi|168419464|gb|ACA23652.1| RNA polymerase II [Fusarium falciforme]
 gi|168419467|gb|ACA23654.1| RNA polymerase II [Fusarium sp. NRRL 28679]
 gi|168419479|gb|ACA23662.1| RNA polymerase II [Fusarium falciforme]
 gi|168419482|gb|ACA23664.1| RNA polymerase II [Fusarium falciforme]
 gi|168419485|gb|ACA23666.1| RNA polymerase II [Fusarium sp. NRRL 31165]
 gi|168419488|gb|ACA23668.1| RNA polymerase II [Fusarium sp. NRRL 31168]
 gi|168419506|gb|ACA23680.1| RNA polymerase II [Fusarium falciforme]
 gi|168419509|gb|ACA23682.1| RNA polymerase II [Fusarium falciforme]
 gi|168419515|gb|ACA23686.1| RNA polymerase II [Fusarium falciforme]
 gi|168419518|gb|ACA23688.1| RNA polymerase II [Fusarium falciforme]
 gi|168419521|gb|ACA23690.1| RNA polymerase II [Fusarium sp. NRRL 32316]
 gi|168419530|gb|ACA23696.1| RNA polymerase II [Fusarium falciforme]
 gi|168419533|gb|ACA23698.1| RNA polymerase II [Fusarium falciforme]
 gi|168419536|gb|ACA23700.1| RNA polymerase II [Fusarium falciforme]
 gi|168419539|gb|ACA23702.1| RNA polymerase II [Fusarium falciforme]
 gi|168419545|gb|ACA23706.1| RNA polymerase II [Fusarium falciforme]
 gi|168419548|gb|ACA23708.1| RNA polymerase II [Fusarium sp. NRRL 32484]
 gi|168419551|gb|ACA23710.1| RNA polymerase II [Fusarium sp. NRRL 32492]
 gi|168419554|gb|ACA23712.1| RNA polymerase II [Fusarium falciforme]
 gi|168419557|gb|ACA23714.1| RNA polymerase II [Fusarium falciforme]
 gi|168419560|gb|ACA23716.1| RNA polymerase II [Fusarium falciforme]
 gi|168419563|gb|ACA23718.1| RNA polymerase II [Fusarium falciforme]
 gi|168419566|gb|ACA23720.1| RNA polymerase II [Fusarium falciforme]
 gi|168419569|gb|ACA23722.1| RNA polymerase II [Fusarium falciforme]
 gi|168419572|gb|ACA23724.1| RNA polymerase II [Fusarium falciforme]
 gi|168419575|gb|ACA23726.1| RNA polymerase II [Fusarium falciforme]
 gi|168419578|gb|ACA23728.1| RNA polymerase II [Fusarium falciforme]
 gi|168419584|gb|ACA23732.1| RNA polymerase II [Fusarium sp. NRRL 32707]
 gi|168419587|gb|ACA23734.1| RNA polymerase II [Fusarium sp. NRRL 32710]
 gi|168419590|gb|ACA23736.1| RNA polymerase II [Fusarium sp. NRRL 32711]
 gi|168419593|gb|ACA23738.1| RNA polymerase II [Fusarium falciforme]
 gi|168419596|gb|ACA23740.1| RNA polymerase II [Fusarium falciforme]
 gi|168419599|gb|ACA23742.1| RNA polymerase II [Fusarium falciforme]
 gi|168419602|gb|ACA23744.1| RNA polymerase II [Fusarium falciforme]
 gi|168419605|gb|ACA23746.1| RNA polymerase II [Fusarium falciforme]
 gi|168419608|gb|ACA23748.1| RNA polymerase II [Fusarium falciforme]
 gi|168419611|gb|ACA23750.1| RNA polymerase II [Fusarium falciforme]
 gi|168419617|gb|ACA23754.1| RNA polymerase II [Fusarium sp. NRRL 32737]
 gi|168419620|gb|ACA23756.1| RNA polymerase II [Fusarium falciforme]
 gi|168419623|gb|ACA23758.1| RNA polymerase II [Fusarium sp. NRRL 32741]
 gi|168419626|gb|ACA23760.1| RNA polymerase II [Fusarium falciforme]
 gi|168419629|gb|ACA23762.1| RNA polymerase II [Fusarium falciforme]
 gi|168419632|gb|ACA23764.1| RNA polymerase II [Fusarium sp. NRRL 32751]
 gi|168419635|gb|ACA23766.1| RNA polymerase II [Fusarium falciforme]
 gi|168419641|gb|ACA23770.1| RNA polymerase II [Fusarium falciforme]
 gi|168419647|gb|ACA23774.1| RNA polymerase II [Fusarium falciforme]
 gi|168419650|gb|ACA23776.1| RNA polymerase II [Fusarium sp. NRRL 32780]
 gi|168419656|gb|ACA23780.1| RNA polymerase II [Fusarium falciforme]
 gi|168419659|gb|ACA23782.1| RNA polymerase II [Fusarium sp. NRRL 32791]
 gi|168419668|gb|ACA23788.1| RNA polymerase II [Fusarium falciforme]
 gi|168419671|gb|ACA23790.1| RNA polymerase II [Fusarium sp. NRRL 32810]
 gi|168419677|gb|ACA23794.1| RNA polymerase II [Fusarium falciforme]
 gi|168419689|gb|ACA23802.1| RNA polymerase II [Fusarium sp. NRRL 32858]
 gi|168419692|gb|ACA23804.1| RNA polymerase II [Fusarium sp. NRRL 32862]
 gi|168419695|gb|ACA23806.1| RNA polymerase II [Fusarium falciforme]
 gi|168419698|gb|ACA23808.1| RNA polymerase II [Fusarium falciforme]
 gi|168419701|gb|ACA23810.1| RNA polymerase II [Fusarium sp. NRRL 32959]
 gi|168419707|gb|ACA23814.1| RNA polymerase II [Neocosmospora vasinfecta]
 gi|168419716|gb|ACA23820.1| RNA polymerase II [Fusarium sp. NRRL 43649]
 gi|168419722|gb|ACA23824.1| RNA polymerase II [Fusarium falciforme]
 gi|168419725|gb|ACA23826.1| RNA polymerase II [Fusarium falciforme]
 gi|168419728|gb|ACA23828.1| RNA polymerase II [Fusarium falciforme]
 gi|168419731|gb|ACA23830.1| RNA polymerase II [Fusarium falciforme]
 gi|168419734|gb|ACA23832.1| RNA polymerase II [Fusarium falciforme]
 gi|168419737|gb|ACA23834.1| RNA polymerase II [Fusarium falciforme]
 gi|168419740|gb|ACA23836.1| RNA polymerase II [Fusarium falciforme]
 gi|168419743|gb|ACA23838.1| RNA polymerase II [Fusarium falciforme]
 gi|168419746|gb|ACA23840.1| RNA polymerase II [Fusarium falciforme]
 gi|168419752|gb|ACA23844.1| RNA polymerase II [Fusarium sp. NRRL 46693]
 gi|168419755|gb|ACA23846.1| RNA polymerase II [Fusarium sp. NRRL 46694]
 gi|168419758|gb|ACA23848.1| RNA polymerase II [Fusarium falciforme]
 gi|168419761|gb|ACA23850.1| RNA polymerase II [Fusarium sp. NRRL 46696]
 gi|168419764|gb|ACA23852.1| RNA polymerase II [Fusarium sp. NRRL 46697]
 gi|168419767|gb|ACA23854.1| RNA polymerase II [Fusarium sp. NRRL 46698]
 gi|168419770|gb|ACA23856.1| RNA polymerase II [Fusarium sp. NRRL 46699]
 gi|168419773|gb|ACA23858.1| RNA polymerase II [Fusarium sp. NRRL 46700]
 gi|168419776|gb|ACA23860.1| RNA polymerase II [Fusarium sp. NRRL 46701]
 gi|168419779|gb|ACA23862.1| RNA polymerase II [Fusarium sp. NRRL 46702]
 gi|168419782|gb|ACA23864.1| RNA polymerase II [Fusarium sp. FSSC_34a KOD-2010]
 gi|215789634|gb|ACJ69876.1| RNA polymerase II [Fusarium sp. NRRL 28036]
 gi|215789661|gb|ACJ69894.1| RNA polymerase II [Fusarium sp. NRRL 32341]
 gi|215789667|gb|ACJ69898.1| RNA polymerase II [Fusarium sp. NRRL 32504]
 gi|215789673|gb|ACJ69902.1| RNA polymerase II [Fusarium falciforme]
 gi|215789676|gb|ACJ69904.1| RNA polymerase II [Fusarium falciforme]
 gi|215789679|gb|ACJ69906.1| RNA polymerase II [Fusarium sp. NRRL 32795]
 gi|215789685|gb|ACJ69910.1| RNA polymerase II [Fusarium sp. NRRL 32829]
 gi|215789688|gb|ACJ69912.1| RNA polymerase II [Fusarium sp. NRRL 32843]
 gi|215789691|gb|ACJ69914.1| RNA polymerase II [Fusarium sp. NRRL 32851]
 gi|215789703|gb|ACJ69922.1| RNA polymerase II [Fusarium sp. NRRL 32762]
 gi|215789706|gb|ACJ69924.1| RNA polymerase II [Fusarium sp. NRRL 32749]
 gi|215789709|gb|ACJ69926.1| RNA polymerase II [Fusarium sp. NRRL 32812]
 gi|280985759|gb|ACZ99660.1| RNA polymerase II [Fusarium sp. NRRL 44924]
 gi|280985761|gb|ACZ99661.1| RNA polymerase II [Fusarium sp. NRRL 44932]
 gi|280985763|gb|ACZ99662.1| RNA polymerase II [Fusarium sp. NRRL 44936]
 gi|280985765|gb|ACZ99663.1| RNA polymerase II [Fusarium sp. NRRL 44944]
 gi|280985769|gb|ACZ99665.1| RNA polymerase II [Fusarium sp. NRRL 46489]
 gi|280985775|gb|ACZ99668.1| RNA polymerase II [Fusarium sp. NRRL 46672]
 gi|280985779|gb|ACZ99670.1| RNA polymerase II [Fusarium sp. NRRL 46678]
          Length = 291

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|297500253|gb|ADI43563.1| RNA polymerase beta subunit [Agrobacterium sp. AGR13]
 gi|297500291|gb|ADI43582.1| RNA polymerase beta subunit [Agrobacterium sp. RTP8]
 gi|297500295|gb|ADI43584.1| RNA polymerase beta subunit [Agrobacterium sp. AB35-9]
 gi|297500297|gb|ADI43585.1| RNA polymerase beta subunit [Agrobacterium sp. B10-2]
 gi|297500333|gb|ADI43603.1| RNA polymerase beta subunit [Agrobacterium sp. AGR36]
          Length = 178

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 144/179 (80%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME VVA+ SGAAI A+R GIV+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPVVARDSGAAIAARRGGIVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDAISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|297500313|gb|ADI43593.1| RNA polymerase beta subunit [Agrobacterium sp. AGR28]
 gi|297500315|gb|ADI43594.1| RNA polymerase beta subunit [Agrobacterium sp. AGR29]
 gi|297500317|gb|ADI43595.1| RNA polymerase beta subunit [Agrobacterium sp. AGR30]
          Length = 178

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVAVGDLISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|168419269|gb|ACA23522.1| RNA polymerase II [Fusarium sp. NRRL 22101]
          Length = 291

 Score =  178 bits (451), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 63/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + G N EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|156453725|gb|ABU63717.1| RpoB [Pasteurella multocida subsp. multocida]
          Length = 173

 Score =  178 bits (451), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  + CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFITCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|56406193|gb|AAV87480.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 173

 Score =  178 bits (451), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR +
Sbjct: 121 FTDAFVTCRGEHGESDLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAV 173


>gi|152938338|gb|ABS43109.1| RNA polymerase beta subunit [Proteus mirabilis]
          Length = 167

 Score =  178 bits (451), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 102/167 (61%), Positives = 126/167 (75%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V +  VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRVVENNAVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS LD+DG F EELV CR  GE  L  R+++ ++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFIIAQANSVLDDDGHFVEELVTCRHKGESSLFSRDQVQYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+ + P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRGDKPLVGTGMERAVAVDSGVTAVAK 167


>gi|297500299|gb|ADI43586.1| RNA polymerase beta subunit [Agrobacterium sp. CFBP2414]
 gi|297500345|gb|ADI43609.1| RNA polymerase beta subunit [Agrobacterium sp. LMG306]
          Length = 178

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATEE-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVAVGDLISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|156453783|gb|ABU63746.1| RpoB [Pasteurellaceae bacterium Clin8]
          Length = 172

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 103/172 (59%), Positives = 130/172 (75%), Gaps = 1/172 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNDYGFLETPYRKVINGQVTEEIEYLSAIEEGKYVIAQANSNLDENLRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           T+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 TDAFVTCRGEYGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 172


>gi|193201489|gb|ACF15952.1| RNA polymerase II subunit [Erythrodecton granulatum]
          Length = 296

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 59/369 (15%), Positives = 103/369 (27%), Gaps = 73/369 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMQFMRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R  I++ +      +E  E   ++                  +  G        
Sbjct: 61   -RSLFYRTYIEQQQAVGFNAQEDFEKPPKNLTMRTRPGTYEKLDDDSFVAPGVRVSGDDV 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + L                E  QR  + +K          E    +++   
Sbjct: 120  IIGKTAPFQAPLAEGA------------EGGQRTKDHVKRDVSAPLRSTEAGIIDRVL-- 165

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 166  ----LTTTDGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDL 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 222  IINPHAIPSRMTIAHLIECLLSKVSSATGLEGD--------------------------- 254

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++Y+G 
Sbjct: 255  --------------------------ATP-FTDVTVSGISDLLRDAGYQSRGFEMMYNGH 287

Query: 1241 TGEPFDRPV 1249
            TG   +  +
Sbjct: 288  TGRKLNAQI 296


>gi|68123863|emb|CAI65896.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123867|emb|CAI65898.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123871|emb|CAI65900.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123877|emb|CAI65903.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
          Length = 167

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 105/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV +G VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|46277386|gb|AAS86883.1| DNA-dependent RNA polymerase II [Terfezia claveryi]
          Length = 548

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 58/379 (15%), Positives = 113/379 (29%), Gaps = 81/379 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 248  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 307

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G   
Sbjct: 308  LF-RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRV 363

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ +      R+++         ++     +  Q              
Sbjct: 364  SGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------- 409

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 410  ------VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAEG 463

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+V+NP  +PSRM +  + E                                     
Sbjct: 464  IVPDLVINPHAIPSRMTIAHLIEC------------------------------------ 487

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                             +L      +     +TP F     ++++++LR       G  +
Sbjct: 488  -----------------LLSKVSSLRGFEGDATP-FTDVTVDSVSTLLREHGYQSRGFEV 529

Query: 1236 LYDGLTGEPFDRPVTVGYI 1254
            +Y+G TG      V +G  
Sbjct: 530  MYNGHTGRKMVAQVFLGPT 548



 Score = 92.4 bits (228), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 49/298 (16%), Positives = 99/298 (33%), Gaps = 26/298 (8%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +++IDA  ++ V I  +      +   +    G  +Q+   P  + +             
Sbjct: 143 VEYIDAEEEETVMIVMTPEDLETSRQFH---AGYEIQQTLDPAQRVKGAVNKFAHTWTHC 199

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQR 779
           +   + I+   A I+   D  +                       +   +  N     Q+
Sbjct: 200 EIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXYRERMDTMANILYYPQK 259

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL                      +L  G+N +VA M + GYN EDS+++++  +   +F
Sbjct: 260 PL----------GTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF 309

Query: 840 TSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S+    +    +   +   E        +   +       +D+ G++  G  V+  DI+
Sbjct: 310 RSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDII 369

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P   +     ++        K    RD S  + S  +G V  V +       K
Sbjct: 370 IGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 420


>gi|34923330|gb|AAQ83552.1| RpoB [Avibacterium gallinarum]
 gi|38373330|gb|AAR19029.1| RpoB [Avibacterium avium]
 gi|164653957|gb|ABY65347.1| RpoB [Avibacterium paragallinarum]
 gi|300086685|gb|ADJ67684.1| RpoB [Avibacterium endocarditidis]
          Length = 173

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 102/173 (58%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD++  
Sbjct: 61  IGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTCRGEHGESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRAL 173


>gi|162532587|gb|ABY16691.1| RNA polymerase beta subunit [Aeromonas veronii bv. sobria]
          Length = 164

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 96/164 (58%), Positives = 125/164 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ ++R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG 
Sbjct: 61  IGLINSLSVYSRTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGR 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             +EL+ CR  GE   +  ++I ++D SP+Q+VS+AA+LIPFLE
Sbjct: 121 LKDELIPCRHKGESTFMNADQIQYMDVSPQQIVSVAAALIPFLE 164


>gi|297500323|gb|ADI43598.1| RNA polymerase beta subunit [Agrobacterium sp. RTH4]
          Length = 178

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDNISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|283105205|gb|ADB11060.1| RpoB [Corynebacterium accolens]
          Length = 131

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 47/95 (49%), Positives = 67/95 (70%), Gaps = 8/95 (8%)

Query: 1207 STPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            +TPVFDGA    I  +L  +  +  G        ++ L+DG +GEP+  P++VGY+YMLK
Sbjct: 37   ATPVFDGATNHEIERLLASSRPNRDGDVLVNEHGKATLFDGRSGEPYKYPISVGYMYMLK 96

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQR 1293
            L+H+V +K++ARSTG YS++TQQPLGGK+  GGQR
Sbjct: 97   LHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQR 131


>gi|299849848|gb|ADJ57169.1| RNA polymerase II second largest subunit [Xylogone sphaerospora]
          Length = 321

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 67/388 (17%), Positives = 113/388 (29%), Gaps = 81/388 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQXDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVXMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               G         V  G  Y  +L HMV
Sbjct: 300  ---GR---KLRAQVFFGPTYYQRLRHMV 321



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 67/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN  DS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQXDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|119640587|gb|ABL85487.1| RNA polymerase II second largest subunit [Camanchaca corallina]
 gi|119640589|gb|ABL85488.1| RNA polymerase II second largest subunit [Pentagenella fragillima]
 gi|330785310|gb|AEC46461.1| RNA polymerase II second largest subunit [Pentagenella sp. Tehler
            8916]
          Length = 307

 Score =  177 bits (450), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 59/372 (15%), Positives = 104/372 (27%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   + ++ AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLNFSELPAGQNVIVAIACYSGYNQEDSIVMNQSAIDRGLF-RS 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               R  I++ +       ++ E   +                   +  G           
Sbjct: 68   FLYRTYIEQQKAVGFNALDEFEKPNKGATMRTRPGTYEKLDEDGFVEPGIRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR+ +  K          E    +K+      
Sbjct: 128  KTAPFQNPMADNA------------EGGQRHKQHTKRDVSAPLRSTEAGIVDKVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTEGRRSVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 230  PHAIPSRMTVAHLIECLLSKVSATQGLEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+++L+ +     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSEISNLLKGSGYQSRGLELMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
                 V +G  Y
Sbjct: 296  KLMAQVYLGPTY 307



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 70/196 (35%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                   +  +L  G+N++VA   + GYN ED
Sbjct: 2   RMDTMSNILYYPQKPL----------ATTRSMEYLNFSELPAGQNVIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       +E  +              + +DE G
Sbjct: 52  SIVMNQSAIDRGLFRSFLYRTYIEQQKAVGFNALDEFEKPNKGATMRTRPGTYEKLDEDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  ++PM    +  +        DV        +G+   V+
Sbjct: 112 FVEPGIRVSGDDIIIGKTAPF-QNPMADNAEGGQRHKQHTKRDVSAPLRSTEAGIVDKVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKVRTRA 186


>gi|151573158|gb|ABS17770.1| RNA polymerase II [Fusarium sp. NRRL 43520]
          Length = 292

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 57/365 (15%), Positives = 103/365 (28%), Gaps = 75/365 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVTV 1251
              V  
Sbjct: 288  AQVFF 292



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|297500235|gb|ADI43554.1| RNA polymerase beta subunit [Agrobacterium sp. AGR2]
 gi|297500237|gb|ADI43555.1| RNA polymerase beta subunit [Agrobacterium sp. AGR3]
 gi|297500239|gb|ADI43556.1| RNA polymerase beta subunit [Agrobacterium sp. AGR4]
 gi|297500241|gb|ADI43557.1| RNA polymerase beta subunit [Agrobacterium sp. AGR5]
 gi|297500243|gb|ADI43558.1| RNA polymerase beta subunit [Agrobacterium sp. AGR6]
 gi|297500245|gb|ADI43559.1| RNA polymerase beta subunit [Agrobacterium sp. AGR7]
 gi|297500247|gb|ADI43560.1| RNA polymerase beta subunit [Agrobacterium sp. AGR9]
 gi|297500249|gb|ADI43561.1| RNA polymerase beta subunit [Agrobacterium sp. AGR10]
 gi|297500251|gb|ADI43562.1| RNA polymerase beta subunit [Agrobacterium sp. AGR11]
 gi|297500255|gb|ADI43564.1| RNA polymerase beta subunit [Agrobacterium sp. AGR14]
 gi|297500257|gb|ADI43565.1| RNA polymerase beta subunit [Agrobacterium sp. AGR15]
 gi|297500259|gb|ADI43566.1| RNA polymerase beta subunit [Agrobacterium sp. AGR16]
 gi|297500261|gb|ADI43567.1| RNA polymerase beta subunit [Agrobacterium sp. AGR17]
 gi|297500263|gb|ADI43568.1| RNA polymerase beta subunit [Agrobacterium sp. AGR18]
 gi|297500265|gb|ADI43569.1| RNA polymerase beta subunit [Agrobacterium sp. AGR19]
 gi|297500267|gb|ADI43570.1| RNA polymerase beta subunit [Agrobacterium sp. AGR20]
 gi|297500301|gb|ADI43587.1| RNA polymerase beta subunit [Agrobacterium sp. AGR21B]
 gi|297500303|gb|ADI43588.1| RNA polymerase beta subunit [Agrobacterium sp. AGR23]
 gi|297500305|gb|ADI43589.1| RNA polymerase beta subunit [Agrobacterium sp. AGR24]
 gi|297500307|gb|ADI43590.1| RNA polymerase beta subunit [Agrobacterium sp. AGR25]
 gi|297500309|gb|ADI43591.1| RNA polymerase beta subunit [Agrobacterium sp. AGR26]
 gi|297500311|gb|ADI43592.1| RNA polymerase beta subunit [Agrobacterium sp. AGR27]
 gi|297500319|gb|ADI43596.1| RNA polymerase beta subunit [Agrobacterium sp. AGR32]
 gi|297500321|gb|ADI43597.1| RNA polymerase beta subunit [Agrobacterium sp. AGR33]
 gi|297500331|gb|ADI43602.1| RNA polymerase beta subunit [Agrobacterium sp. AGR21A]
 gi|297500335|gb|ADI43604.1| RNA polymerase beta subunit [Agrobacterium sp. AGR37]
 gi|297500337|gb|ADI43605.1| RNA polymerase beta subunit [Agrobacterium sp. CCUG12509]
 gi|297500341|gb|ADI43607.1| RNA polymerase beta subunit [Agrobacterium sp. AGR39]
 gi|297500347|gb|ADI43610.1| RNA polymerase beta subunit [Agrobacterium sp. LMG361T1]
 gi|297500349|gb|ADI43611.1| RNA polymerase beta subunit [Agrobacterium sp. LMG378]
 gi|297500351|gb|ADI43612.1| RNA polymerase beta subunit [Agrobacterium sp. LMG399]
 gi|297500355|gb|ADI43614.1| RNA polymerase beta subunit [Agrobacterium sp. CCUG48648]
 gi|297500357|gb|ADI43615.1| RNA polymerase beta subunit [Agrobacterium sp. CCUG49619]
 gi|297500365|gb|ADI43619.1| RNA polymerase beta subunit [Agrobacterium sp. AGR1]
 gi|297500367|gb|ADI43620.1| RNA polymerase beta subunit [Agrobacterium sp. AGR12]
 gi|297500369|gb|ADI43621.1| RNA polymerase beta subunit [Agrobacterium sp. AGR35]
 gi|297500371|gb|ADI43622.1| RNA polymerase beta subunit [Agrobacterium sp. AGR38]
 gi|297500391|gb|ADI43632.1| RNA polymerase beta subunit [Agrobacterium sp. AGR34]
 gi|297500393|gb|ADI43633.1| RNA polymerase beta subunit [Agrobacterium sp. AGR40]
 gi|297500395|gb|ADI43634.1| RNA polymerase beta subunit [Agrobacterium sp. AGR41]
 gi|297500397|gb|ADI43635.1| RNA polymerase beta subunit [Agrobacterium sp. AGR43]
 gi|297500405|gb|ADI43639.1| RNA polymerase beta subunit [Agrobacterium sp. LMG355]
          Length = 178

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDIISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|158514857|gb|ABW69384.1| RNA polymerase beta subunit [Bibersteinia trehalosi]
          Length = 172

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 130/172 (75%), Gaps = 1/172 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  
Sbjct: 61  SLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTY 120

Query: 645 VFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR LMG N
Sbjct: 121 VTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRALMGTN 172


>gi|168419293|gb|ACA23538.1| RNA polymerase II [Fusarium sp. NRRL 22178]
          Length = 291

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 57/364 (15%), Positives = 102/364 (28%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 63/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + G N EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|68123865|emb|CAI65897.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123869|emb|CAI65899.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123873|emb|CAI65901.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|68123875|emb|CAI65902.1| RNA polymerase, beta subunit [Klebsiella pneumoniae]
 gi|152938300|gb|ABS43090.1| RNA polymerase beta subunit [Klebsiella pneumoniae subsp.
           pneumoniae]
          Length = 167

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 106/167 (63%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|119640577|gb|ABL85482.1| RNA polymerase II second largest subunit [Hubbsia langei]
          Length = 307

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 105/372 (28%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   + ++ AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLNFSELPAGQNVIVAIACYSGYNQEDSIIMNQSAIDRGLF-RS 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               R  I++ +       ++ E   +                   +  G           
Sbjct: 68   FLYRTYIEQQKAVGFNALDEFEKPNKATTMRTRPGTYEKLDYDGFVEPGIRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR+ +  K          E    +K+      
Sbjct: 128  KTAPFQNPMADNA------------EGGQRHKQHTKRDVSAPLRSTEAGIVDKVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTEGRRSVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 230  PHAIPSRMTVAHLIECLLSKVSATQGLEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+++L+ +     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSEISNLLKGSGYQSRGLELMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  + +G  Y
Sbjct: 296  KLNAQIYLGPTY 307



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 69/196 (35%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                   +  +L  G+N++VA   + GYN ED
Sbjct: 2   RMDTMSNILYYPQKPL----------ATTRSMEYLNFSELPAGQNVIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       +E  +              + +D  G
Sbjct: 52  SIIMNQSAIDRGLFRSFLYRTYIEQQKAVGFNALDEFEKPNKATTMRTRPGTYEKLDYDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  ++PM    +  +        DV        +G+   V+
Sbjct: 112 FVEPGIRVSGDDIIIGKTAPF-QNPMADNAEGGQRHKQHTKRDVSAPLRSTEAGIVDKVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKVRTRA 186


>gi|56406217|gb|AAV87492.1| RpoB [Bisgaard Taxon 45]
          Length = 172

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 130/172 (75%), Gaps = 1/172 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           T+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 TDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 172


>gi|260586438|gb|ACX46108.1| RNA polymerase beta subunit [Corynebacterium sp. 1145]
 gi|260586440|gb|ACX46109.1| RNA polymerase beta subunit [Corynebacterium sp. 1146]
 gi|260586442|gb|ACX46110.1| RNA polymerase beta subunit [Corynebacterium sp. 1147]
 gi|260586444|gb|ACX46111.1| RNA polymerase beta subunit [Corynebacterium sp. 1148]
 gi|260586446|gb|ACX46112.1| RNA polymerase beta subunit [Corynebacterium sp. 1149]
 gi|260586448|gb|ACX46113.1| RNA polymerase beta subunit [Corynebacterium sp. 1150]
          Length = 134

 Score =  177 bits (450), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 58/162 (35%), Positives = 80/162 (49%), Gaps = 36/162 (22%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G  +    +D      +  L   L  V                      
Sbjct: 1    EVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT---------------- 41

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPV 1249
                     +TPVFDGA  E I  +L  +  +  G        +++L+DG +GEPF  PV
Sbjct: 42   ---------ATPVFDGASNEEIAGLLANSKPNRDGDVMVDGDGKTVLFDGRSGEPFKYPV 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            +VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   SVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 134


>gi|68445670|dbj|BAE02829.1| RNA polymerase beta subunit [Nocardia asteroides]
          Length = 171

 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/171 (56%), Positives = 128/171 (74%), Gaps = 1/171 (0%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PVV+A+ EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYG
Sbjct: 1   PVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL+ SL+ +ARVN +GFIETPYR+V DGKVT++V YL+A EE+    
Sbjct: 61  RMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRRVVDGKVTDEVKYLTADEEDRYVR 120

Query: 628 AQANSSLDEDGSFTEELVFCRC-AGEEILVPREKIDFIDASPKQVVSIAAS 677
           AQANS +D +G F E+ V  R    E   V   ++D++D SP+Q+VS+A +
Sbjct: 121 AQANSPVDAEGRFIEDRVLVRRAGEEVEFVNPSQVDYMDISPRQMVSVATA 171


>gi|38373310|gb|AAR19019.1| RpoB [Haemophilus haemoglobinophilus]
          Length = 173

 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGLN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|38373312|gb|AAR19020.1| RpoB [Haemophilus parainfluenzae ATCC 33392]
          Length = 173

 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL++FAR N YGF+ETPYRKV  G+VT ++ YLSA++E N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSAFARTNDYGFLETPYRKVVYGQVTEEIEYLSAIDEANYIIAQANSNLDENNR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGERGESGLYKPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|283459387|gb|ADB22385.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
          Length = 540

 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 92/309 (29%), Gaps = 74/309 (23%)

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ R  +D  ++S   + E+ E  +RD          +       I  G   V     
Sbjct: 306  RSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGTGVVGEDII 365

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  D      R++          ++     +  Q                    
Sbjct: 366  IGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------------- 408

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 409  ---TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDII 465

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L      +G +                              
Sbjct: 466  INPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------------- 497

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     E++++ LR       G  ++Y G T
Sbjct: 498  -------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEVMYHGHT 531

Query: 1242 GEPFDRPVT 1250
            G      V 
Sbjct: 532  GRKLQAQVY 540



 Score = 47.0 bits (110), Expect = 0.024,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             V   +F S++   +  + + + +   E        +   +       ++  G+I  G 
Sbjct: 298 SSVDRGLFRSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGT 357

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V   DI++GK  P         ++        +    RD S  + S  +G V  V I  
Sbjct: 358 GVVGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITT 410

Query: 947 RHGIDK 952
            H   K
Sbjct: 411 NHEGQK 416


>gi|270000447|gb|ACZ58071.1| RNA polymerase II [Fusarium sp. NRRL 46596]
          Length = 295

 Score =  177 bits (450), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 56/370 (15%), Positives = 103/370 (27%), Gaps = 75/370 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  I+Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGH 285

Query: 1241 TGEPFDRPVT 1250
            TG      V 
Sbjct: 286  TGRKLRAQVF 295



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|320172592|gb|ADW24179.1| RNA polymerase II second largest subunit [Neolentinus adhaerens]
          Length = 327

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 94/292 (32%), Gaps = 21/292 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 39   DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 98

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G      
Sbjct: 99   LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVTGD 157

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     +    T+    E+   +++ 
Sbjct: 158  DIIIGKTAPIPPD---------------SEELGQRTRSHTRRDVSTAMKSTENGIVDQVL 202

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 203  I-----TTNSEGQKFVKVRVRATRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 257

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            DI++NP  +PSRM +G + E  L      +G +  +          +S    
Sbjct: 258  DIIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSAFLR 309



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 81/228 (35%), Gaps = 23/228 (10%)

Query: 731 RAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
            A I+   D  +    + +  +     G+     L++           Q+PL        
Sbjct: 1   CASIIPFPDHNQSPRNTYQSTMGKQAMGIYLTNFLVRMDTMANILYYPQKPL-------- 52

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
                         +L  G+N +VA + + GYN EDS+++++  +   +F SI+   +  
Sbjct: 53  --ATTRSMEYLRFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMD 110

Query: 850 MARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
           + + + +   E            +       +++ G+I  G  V   DI++GK  P    
Sbjct: 111 LEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVTGDDIIIGKTAPIPPD 170

Query: 905 PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                ++        ++   RD S  + S  +G V  V I       K
Sbjct: 171 SEELGQRT-------RSHTRRDVSTAMKSTENGIVDQVLITTNSEGQK 211


>gi|330785382|gb|AEC46497.1| RNA polymerase II second largest subunit [Schismatomma dirinellum]
          Length = 278

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/354 (17%), Positives = 105/354 (29%), Gaps = 79/354 (22%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + AI      +  D+ +   S +   +     +  +     E+  SV  
Sbjct: 1    RFXDLPXGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSLFYRTYI----EQQQSVGF 56

Query: 962  EQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              +E   R +  E +      Y +L +   +  G           K+    + +      
Sbjct: 57   NALEEFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMSENA-- 114

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                      E  QR  +  K          E    +++              R VK+  
Sbjct: 115  ----------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL------LTTTEGKRSVKIRT 158

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + E
Sbjct: 159  RTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSRMTIAHLIE 218

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              L       G +                                               
Sbjct: 219  CLLSKVSSITGHEGD--------------------------------------------- 233

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVG 1252
                    +TP F       I+ +L+ A     G  ++Y+G TG   +  V +G
Sbjct: 234  --------ATP-FTDITVSNISELLQFAGYQSRGFELMYNGHTGRKLNAQVFLG 278



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/161 (20%), Positives = 64/161 (39%), Gaps = 6/161 (3%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-E 859
              DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       E
Sbjct: 1   RFXDLPXGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSLFYRTYIEQQQSVGFNALE 60

Query: 860 EITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           E  R              + +D+ G +  G  V+  DI++GK  P  ++PM+   +  + 
Sbjct: 61  EFERPRRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPF-QAPMSENAEGGQR 119

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                  DV        +G+   V+      +  +    R+
Sbjct: 120 TKDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKIRTRT 160


>gi|94421197|gb|ABF18825.1| RNA polymerase beta subunit [Bartonella vinsonii subsp. vinsonii]
          Length = 166

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 114/166 (68%), Positives = 135/166 (81%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE
Sbjct: 61  NSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRFTEE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
            V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD+NR
Sbjct: 121 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANR 166


>gi|293601786|gb|ADE48297.1| RNA polymerase II [Morchella sp. Mes-4]
          Length = 289

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/359 (16%), Positives = 104/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     E+++++LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKL 286



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|152938340|gb|ABS43110.1| RNA polymerase beta subunit [Hafnia alvei ATCC 13337]
 gi|209943960|gb|ACI96287.1| RNA polymerase beta-subunit [Obesumbacterium proteus]
 gi|219814328|gb|ACL36448.1| RNA polymerase beta subunit [Obesumbacterium proteus]
 gi|219814332|gb|ACL36450.1| RNA polymerase beta subunit [Obesumbacterium proteus]
          Length = 167

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 104/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGIVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDDEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|258590825|emb|CBE67090.1| RNA polymerase beta subunit [Arcanobacterium pyogenes]
 gi|258590827|emb|CBE67091.1| RNA polymerase beta subunit [Arcanobacterium pyogenes]
 gi|258590829|emb|CBE67092.1| RNA polymerase beta subunit [Arcanobacterium pyogenes]
 gi|258590831|emb|CBE67093.1| RNA polymerase beta subunit [Arcanobacterium pyogenes]
          Length = 135

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 82/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE HLGW                                 G  +  E+ +    +  ++ 
Sbjct: 1    FELHLGWVAK------------------------QGWDASGPRAAGEEWALRLPEDAVKA 36

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
            A +      V+TPVFDG   + +  +L   + +  G        ++ L+DG TGEPF  P
Sbjct: 37   AGERT----VATPVFDGVQSDELRGLLGHTNPNRDGERMVDETGKARLFDGRTGEPFPDP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|219564045|gb|ACL28206.1| RNA polymerase II second largest subunit [fungal sp. M171]
          Length = 300

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/374 (17%), Positives = 113/374 (30%), Gaps = 81/374 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 65   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 120

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 121  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVD 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 166  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 220

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 221  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD---------------------- 258

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  I
Sbjct: 259  -------------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEI 286

Query: 1236 LYDGLTGEPFDRPV 1249
            +Y G TG      V
Sbjct: 287  MYHGHTGRKLMAQV 300



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 67/177 (37%), Gaps = 15/177 (8%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 61

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 62  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 121

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 122 GEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 171


>gi|297500269|gb|ADI43571.1| RNA polymerase beta subunit [Agrobacterium sp. A6]
 gi|297500271|gb|ADI43572.1| RNA polymerase beta subunit [Agrobacterium sp. R10]
 gi|297500275|gb|ADI43574.1| RNA polymerase beta subunit [Agrobacterium sp. 181]
 gi|297500279|gb|ADI43576.1| RNA polymerase beta subunit [Agrobacterium sp. RTG2]
 gi|297500281|gb|ADI43577.1| RNA polymerase beta subunit [Agrobacterium sp. RTB1]
 gi|297500283|gb|ADI43578.1| RNA polymerase beta subunit [Agrobacterium sp. RTE4]
 gi|297500285|gb|ADI43579.1| RNA polymerase beta subunit [Agrobacterium sp. RTB7]
 gi|297500287|gb|ADI43580.1| RNA polymerase beta subunit [Agrobacterium sp. RTB8]
 gi|297500289|gb|ADI43581.1| RNA polymerase beta subunit [Agrobacterium sp. RTA10]
 gi|297500293|gb|ADI43583.1| RNA polymerase beta subunit [Agrobacterium sp. RTP1]
 gi|297500325|gb|ADI43599.1| RNA polymerase beta subunit [Agrobacterium sp. RTB12]
 gi|297500327|gb|ADI43600.1| RNA polymerase beta subunit [Agrobacterium sp. RTP7]
 gi|297500329|gb|ADI43601.1| RNA polymerase beta subunit [Agrobacterium sp. RTP2]
 gi|297500343|gb|ADI43608.1| RNA polymerase beta subunit [Agrobacterium sp. LMG197]
 gi|297500353|gb|ADI43613.1| RNA polymerase beta subunit [Agrobacterium sp. LMG90]
 gi|297500359|gb|ADI43616.1| RNA polymerase beta subunit [Agrobacterium sp. LMG142]
 gi|297500361|gb|ADI43617.1| RNA polymerase beta subunit [Agrobacterium sp. LMG227]
 gi|297500363|gb|ADI43618.1| RNA polymerase beta subunit [Agrobacterium sp. LMG232]
 gi|297500385|gb|ADI43629.1| RNA polymerase beta subunit [Agrobacterium sp. LMG303]
 gi|297500401|gb|ADI43637.1| RNA polymerase beta subunit [Agrobacterium sp. LMG167]
 gi|297500403|gb|ADI43638.1| RNA polymerase beta subunit [Agrobacterium sp. LMG175]
          Length = 178

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 142/179 (79%), Positives = 159/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIAARRGGVVDQVDATRIVIRATEE-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVAVGDIISKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|158514853|gb|ABW69382.1| RNA polymerase beta subunit [Bibersteinia trehalosi]
          Length = 172

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 130/172 (75%), Gaps = 1/172 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNLLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  
Sbjct: 61  SLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTY 120

Query: 645 VFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR LMG N
Sbjct: 121 VTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRALMGTN 172


>gi|152938330|gb|ABS43105.1| RNA polymerase beta subunit [Escherichia fergusonii ATCC 35469]
          Length = 167

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 106/167 (63%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVIDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|280985767|gb|ACZ99664.1| RNA polymerase II [Fusarium sp. NRRL 44938]
          Length = 276

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 56/348 (16%), Positives = 100/348 (28%), Gaps = 75/348 (21%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 4    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 62

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +           +       +  G           K+  +  +      R+   
Sbjct: 63   VFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTTVH 122

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +      + +                       ++ VKV V   +
Sbjct: 123  QRRDISTPLRSTENGIVDSVIVTVNA--------------------DNVKYVKVRVRTTK 162

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 163  IPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLS 222

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G +                                                   
Sbjct: 223  KVSTLEGMEGD------------------------------------------------- 233

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                +TP F     ++++ +LR       G  I+Y+G TG      V 
Sbjct: 234  ----ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLRAQVF 276



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 60/157 (38%), Gaps = 12/157 (7%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E
Sbjct: 3   KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTE 62

Query: 861 ITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           +           +       +DE GI+  G  V+  DI++GK  P  +       +    
Sbjct: 63  VFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT--- 119

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    RD S  + S  +G V  V +       K
Sbjct: 120 ----TVHQRRDISTPLRSTENGIVDSVIVTVNADNVK 152


>gi|293601762|gb|ADE48285.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601764|gb|ADE48286.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601784|gb|ADE48296.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601800|gb|ADE48304.1| RNA polymerase II [Morchella sp. Mes-8]
 gi|293601808|gb|ADE48308.1| RNA polymerase II [Morchella sp. Mes-8]
          Length = 288

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/359 (16%), Positives = 104/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  +D+ +R      E+ E   R    +      +       +  G           K+ 
Sbjct: 62   RSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D+     R ++         ++     +  Q                         
Sbjct: 122  PITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML--------------------TT 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   D+++NP  
Sbjct: 162  NAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVPDLIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECQLSKVSSLRGFEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     E+++++LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYNGYTGRKL 286



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 52  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P      TP+   +     +K    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTENGIVDQVMLTTNAE 164

Query: 950 IDK 952
             K
Sbjct: 165 GLK 167


>gi|152938352|gb|ABS43116.1| RNA polymerase beta subunit [Cedecea davisae DSM 4568]
          Length = 167

 Score =  177 bits (449), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/167 (61%), Positives = 130/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGIVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++LDE+G F ++LV CR  GE  L   +++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|251830062|gb|ACT21442.1| RNA polymerase beta subunit [Corynebacterium sp. 3010]
 gi|260586452|gb|ACX46115.1| RNA polymerase beta subunit [Corynebacterium sp. 1152]
          Length = 131

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 48/120 (40%), Positives = 73/120 (60%), Gaps = 8/120 (6%)

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG------- 1232
            +  +  +    +++             +TPVFDGA  E I  +L  +  +  G       
Sbjct: 12   NPDDPANAKLLETLPEHLYDVPPESLTATPVFDGASNEEIAGLLANSKPNRDGDVMVDGD 71

Query: 1233 -QSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
             +++L+DG +GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 72   GKTVLFDGRSGEPFKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 131


>gi|168419311|gb|ACA23550.1| RNA polymerase II [Fusarium ambrosium]
          Length = 291

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 63/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + G N EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|193201529|gb|ACF15972.1| RNA polymerase II subunit [Opegrapha viridis]
          Length = 300

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 57/371 (15%), Positives = 105/371 (28%), Gaps = 73/371 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTMANVLYYPQKPLATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++  R      E+ E   R    +    + +       +  G      
Sbjct: 63   LF-RSLFYRTYIEQESRVGFENVEEFEKPDRLSTTKMRHGNYDKLDPDGLVAPGIRVSGD 121

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++                   +  +     +   + + +   + L       I+
Sbjct: 122  DVIIGKTSP---------------HVTLMQDNADGGIRRPEHRKDDRSTPLRSTEAGIID 166

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            ++           + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 167  RVL---MTSTDGKKAVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGLVP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 224  DLIINPHAIPSRMTIAHLIECLLSKVAATRGSEGD------------------------- 258

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+++L  A     G  I+++
Sbjct: 259  ----------------------------ATP-FTSVTVGDISNLLHEAGYQSRGYEIMHN 289

Query: 1239 GLTGEPFDRPV 1249
            G TG      V
Sbjct: 290  GHTGRKLRAQV 300



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/192 (19%), Positives = 68/192 (35%), Gaps = 20/192 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTMANVLYYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEEITRD----IPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    + E  +R      EE  +        +       +D  G
Sbjct: 51  SVIMNQSAIDRGLFRSLFYRTYIEQESRVGFENVEEFEKPDRLSTTKMRHGNYDKLDPDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  D+++GK +P         +  +R    E   D R T LR        ++
Sbjct: 111 LVAPGIRVSGDDVIIGKTSPHVTLMQDNADGGIRRP--EHRKDDRSTPLR---STEAGII 165

Query: 941 DVRIFNRHGIDK 952
           D  +       K
Sbjct: 166 DRVLMTSTDGKK 177


>gi|309385724|gb|ADO66707.1| RNA polymerase beta subunit [Pasteurellaceae bacterium P625]
          Length = 172

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/172 (59%), Positives = 129/172 (75%), Gaps = 1/172 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD +  F
Sbjct: 61  GLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDAELRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           T+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 TDAFVTCRGEYGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 172


>gi|280985773|gb|ACZ99667.1| RNA polymerase II [Fusarium sp. NRRL 46643]
          Length = 291

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AHVF 291



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|42794993|gb|AAS45852.1| RpoB [Proteus vulgaris]
          Length = 165

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 97/162 (59%), Positives = 123/162 (75%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQANS LD+D  F EELV
Sbjct: 61  LSVYAQTNEYGFLETPYRVVENNAVTDEIHYLSAIEEGNFIIAQANSVLDDDNHFVEELV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            CR  GE  L  R+++ ++D S +QVVS+ ASLIPFLE+DD+
Sbjct: 121 TCRHRGESSLFSRDQVQYMDVSTQQVVSVGASLIPFLEHDDA 162


>gi|258590811|emb|CBE67083.1| RNA polymerase beta subunit [Arcanobacterium bialowiezense]
          Length = 135

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/163 (35%), Positives = 82/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
            FE HLGW                    D +  R   E+                  +   
Sbjct: 1    FELHLGWVAKH--------------GWDATEAREAGEEWA--------------VRLPEN 32

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
            A +  +   V+TPVFDG   + +  +L + + +  G        ++ L+DG TG+PF  P
Sbjct: 33   AVKADAERTVATPVFDGVQSDELKGLLGVTNPNRDGDRLVDETGKARLFDGRTGDPFPEP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|152938350|gb|ABS43115.1| RNA polymerase beta subunit [Erwinia amylovora]
          Length = 167

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 102/167 (61%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++LD++G F ++LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLDDEGHFVDDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|52694399|emb|CAG38039.1| RNA polymerase beta subunit [Pseudomonas mendocina]
          Length = 335

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 109/189 (57%), Positives = 142/189 (75%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              ++G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 147 PERQEGQLIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALM 206

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 207 GSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVNDDEV 266

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+ADGPSTD+G+LALG+NM 
Sbjct: 267 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVSRGDIMADGPSTDMGELALGQNMR 326

Query: 813 VAFMPWHGY 821
           VAF+PW+G+
Sbjct: 327 VAFIPWNGF 335


>gi|209943958|gb|ACI96286.1| RNA polymerase beta-subunit [Escherichia blattae DSM 4481]
          Length = 167

 Score =  177 bits (448), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 104/167 (62%), Positives = 129/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPYR V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYARTNEYGFLETPYRLVRDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV  R  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDEEGHFVEDLVTARNKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+++ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRSDKPLVGTGMERAVAVDSGVTAVAK 167


>gi|312204296|gb|ADQ47465.1| RNA polymerase II second largest subunit [Absconditella sp. SW048]
          Length = 292

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/367 (15%), Positives = 111/367 (30%), Gaps = 81/367 (22%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    AXILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +++ +R   +    +E   +    + + L    Y +L +   I  G      
Sbjct: 60   RSLFYRAYVEQEKR---IGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +                  ++
Sbjct: 117  DIIIGKTAPIAPDAEELGQRTKMHTKRDASTPLRSTESGI------------------VD 158

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 159  KVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSGEGITP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 252  ----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYN 282

Query: 1239 GLTGEPF 1245
            G TG   
Sbjct: 283  GHTGRKL 289



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +     + +D+ GII  G  V+
Sbjct: 55  DRGLFRSLFYRAYVEQEKRIGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIIAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  SG V  V +     
Sbjct: 115 GEDIIIGKTAPIAPDAEELGQRT-------KMHTKRDASTPLRSTESGIVDKVLLTTNAE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|152938328|gb|ABS43104.1| RNA polymerase beta subunit [Escherichia coli DSM 30083]
 gi|194394772|gb|ACF60020.1| RNA polymerase beta subunit [Enterobacter sp. ECC_10]
          Length = 167

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 106/167 (63%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|224126291|ref|XP_002198858.1| PREDICTED: hypothetical protein, partial [Taeniopygia guttata]
          Length = 127

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 45/181 (24%), Positives = 67/181 (37%), Gaps = 54/181 (29%)

Query: 1099 IVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +   I+P EDMPF   G   DI++NP G PSRM VG++ E   G                
Sbjct: 1    VCGLIVPQEDMPFCDTGICPDIIMNPHGFPSRMTVGKLIELLAGK--------------- 45

Query: 1159 YKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEA 1218
                                                  A          T  F G+  + 
Sbjct: 46   --------------------------------------AGVLDGRFHYGT-AFGGSKVKD 66

Query: 1219 INSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
            +   L     +  G+  +  G+TGEP +  +  G +Y  KL HMV DK++AR+ G  +++
Sbjct: 67   VCEDLIRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVL 126

Query: 1279 T 1279
            T
Sbjct: 127  T 127


>gi|152938334|gb|ABS43107.1| RNA polymerase beta subunit [Brenneria salicis ATCC 15712]
          Length = 167

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 102/167 (61%), Positives = 130/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V D  VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDNVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++LDE+G F +ELV CR  GE  L  R++++++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVEYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|6693816|gb|AAF24994.1|AF129447_1 RpoB [Raoultella ornithinolytica]
          Length = 172

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 102/167 (61%), Positives = 129/167 (77%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF SSQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+  S
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGGS 167


>gi|290558680|gb|ADD37835.1| DNA-directed RNA polymerase beta chain [Bartonella henselae]
          Length = 169

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 120/169 (71%), Positives = 144/169 (85%)

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           RDVHPTHYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLS
Sbjct: 1   RDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLS 60

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           AMEE   Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+L
Sbjct: 61  AMEESKHYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAAL 120

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
           IPFLENDD+NR LMG NMQ QAVPL++AEAPFVGTGMES+VA+ SGAA+
Sbjct: 121 IPFLENDDANRALMGSNMQHQAVPLVRAEAPFVGTGMESIVARDSGAAV 169


>gi|330785312|gb|AEC46462.1| RNA polymerase II second largest subunit [Roccellographa
            circumscripta]
          Length = 296

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/366 (15%), Positives = 104/366 (28%), Gaps = 81/366 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + +    R +   +   V        +     +++    +R     
Sbjct: 3    NILYYPQKPLATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 62

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 63   LFYRSYIEQQQPVGFNALETFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRVSGEDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR  E  +          E    +++      
Sbjct: 123  KTAPFQAPMQDNA------------EGGQRTKEHTRRDVSCPLRSTEAGIIDRVL----- 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 166  -VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGICPDLIIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 225  PHAIPSRMTIAHLIECLLSKVATTQGCEGD------------------------------ 254

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F      +I+S+L  A     G  ++Y+G TG 
Sbjct: 255  -----------------------ATP-FTPVTVSSISSILESAGYQRRGFEVMYNGHTGR 290

Query: 1244 PFDRPV 1249
              +  +
Sbjct: 291  KLNAQI 296



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 69/196 (35%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                   +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                    +DE G +  G  V+
Sbjct: 56  DRGLFRSLFYRSYIEQQQPVGFNALETFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 116 GEDIIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIIDRVLVTTTEG 171

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 172 RRSVKIRTRTTKVPQI 187


>gi|219564115|gb|ACL28241.1| RNA polymerase II second largest subunit [Hymenoscyphus fructigenus]
          Length = 300

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/375 (15%), Positives = 105/375 (28%), Gaps = 81/375 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R        +E   +    + + L +  Y +L +   +  G   
Sbjct: 64   LF-RSLFYRAYTDQEKRVGM---NVVEQFEKPFRSDTLKLKQGTYDKLDDDGIVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +         R++          ++     +  Q              
Sbjct: 120  SGEDIIIGKTAPMPEASEELGQRTKAHTKRDASTPLRSTENGIVDQVLI----------- 168

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 169  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTCQG 219

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 220  IVPDLIINPHAIPSRMTIAHLIECQLSKVGTLRGLEGD---------------------- 257

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  I
Sbjct: 258  -------------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEI 285

Query: 1236 LYDGLTGEPFDRPVT 1250
            +Y G TG      V 
Sbjct: 286  MYHGHTGRKMMAQVF 300



 Score = 87.4 bits (215), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 15/177 (8%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   + +     +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLFYRAYTDQEKRVGMNVVEQFEKPFRSDTLKLKQGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P  E+     ++        KA   RD S  + S  +G V  V I  
Sbjct: 121 GEDIIIGKTAPMPEASEELGQRT-------KAHTKRDASTPLRSTENGIVDQVLITT 170


>gi|209943962|gb|ACI96288.1| RNA polymerase beta-subunit [Enterobacteriaceae bacterium 521]
 gi|219814330|gb|ACL36449.1| RNA polymerase beta subunit [Enterobacteriaceae bacterium Am-4]
          Length = 167

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/167 (62%), Positives = 130/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +AR N YGF+ETPYR V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYARTNEYGFLETPYRLVRDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDEEGHFEEDLVTCRNKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+++ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRSDKPLVGTGMERAVAVDSGVTAVAK 167


>gi|330785280|gb|AEC46446.1| RNA polymerase II second largest subunit [Schizopelte crustosa]
          Length = 307

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/380 (15%), Positives = 106/380 (27%), Gaps = 79/380 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLXTTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +     +  +     E+  ++    +E   +      +      Y +L +   +  G   
Sbjct: 64   LFRSFFYRTYI----EQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDDDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR     K          E    +
Sbjct: 120  SGDDIIIGKTAPFQAPMADNA------------EGGQRTKMHAKRDVSAPLRSTEAGIVD 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  RVL------VTTNEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 222  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 259

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+ +L+ +     G  +
Sbjct: 260  -------------------------------ATP-FTDVTVSGISDLLKGSGYQSRGLEV 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +++G TG      V +G  Y
Sbjct: 288  MHNGYTGRKLVAQVYLGXTY 307



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 61/196 (31%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------XTTRSMEYLQFAELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       E                  + +D+ G
Sbjct: 52  SVIMNQSAIDRGLFRSFFYRTYIEQQKAIGFNALEEFEKPNKAMTMRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P         E   R        DV        +G+   V+
Sbjct: 112 FVAPGVRVSGDDIIIGKTAPFQAPMADNAEGGQRTKM-HAKRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTNEGRRSVKVRTRT 186


>gi|312204312|gb|ADQ47473.1| RNA polymerase II second largest subunit [Coenogonium pineti]
          Length = 693

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/348 (17%), Positives = 108/348 (31%), Gaps = 81/348 (23%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +   
Sbjct: 424  MEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYVEQEK--- 479

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +  E +E   +    E + L    Y +L +   I  G           K+  + S+   
Sbjct: 480  HLGMEVVEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPMRSNDEE 539

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++                  K    T+    E    +K+             L+ V
Sbjct: 540  LGQRTKLHT---------------KRDASTALRSTESGIVDKVLI-----TTNAEGLKFV 579

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV     +  Q GDK A RHG KG +      EDMPF   G   D+++NP  +PSRM + 
Sbjct: 580  KVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSALGITPDLIINPHAIPSRMTIA 639

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 640  HLIECQLSKVSSLRGFEGD----------------------------------------- 658

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                        +TP F     ++++ +LR       G  ++Y+G TG
Sbjct: 659  ------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTG 693



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 63/162 (38%), Gaps = 12/162 (7%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 423 SMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYVEQEKHLG 482

Query: 856 LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +   E        +   +     + +D+ GII  G  V+  DI++GK  P   +     +
Sbjct: 483 MEVVEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPMRSNDEELGQ 542

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +        K    RD S  + S  SG V  V I       K
Sbjct: 543 RT-------KLHTKRDASTALRSTESGIVDKVLITTNAEGLK 577



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 6/98 (6%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            ++Q+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 45  GVAQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 100

Query: 581 GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVY 616
           GLV +L     +      E    +       V  +   
Sbjct: 101 GLVKNLALMCYITVGTPSEPIIEFMVQRQMDVLEEYEP 138


>gi|67942340|gb|AAY83370.1| DNA-dependent RNA polymerase II [Galiella rufa]
          Length = 531

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 85/644 (13%), Positives = 171/644 (26%), Gaps = 123/644 (19%)

Query: 606  CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFI 664
             + +   +     +      ++      +  D       V        +      I D  
Sbjct: 4    HNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDPMHLVRNVQEVRRKGIVGHEVSVIRDIR 63

Query: 665  DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
            D   K          P    ++         +  Q   + K E        E   A    
Sbjct: 64   DREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIEKLEEDHNLDEDEPQKAPYGW 123

Query: 725  AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
            + ++    G+VE VDA       +    +       + +  + +         + P   V
Sbjct: 124  SGLL--GDGVVEYVDAEEEETIMIVMTPEDLEVAQQVRQGYELEEETDPNKRVKAP---V 178

Query: 785  GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                 +       PS  LG       +  + +P+  +N          M  + +   + +
Sbjct: 179  NPNASQYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFL 229

Query: 845  EEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGES 904
              F                                 +  +             +      
Sbjct: 230  TNFAERM---------------------------DTMANILYYPQKPLATTRSMEYLKFR 262

Query: 905  PMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQI 964
             +   +  +  I      +  D+ +   S +   +    +F R  +D+ +R   +  + +
Sbjct: 263  ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMDQEKR---IGMQVV 318

Query: 965  ELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E   +      + L    Y +L +   +  G           K+  ++ D+     R ++
Sbjct: 319  EEFEKPTRSNTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQRQKY 378

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                     ++     +  Q                             L+ VKV +   
Sbjct: 379  HTKRDVSTPLRSTENGIVDQVML--------------------TTNAEGLKFVKVRMRTT 418

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L
Sbjct: 419  KIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDLIINPHAIPSRMTIAHLIECQL 478

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                   G +                                                  
Sbjct: 479  SKVSSLRGMEGD------------------------------------------------ 490

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                 +TP F     ++++S+LR       G  ++Y+G TG   
Sbjct: 491  -----ATP-FTDVTVDSVSSLLRAEGYQSRGFEVMYNGHTGRKL 528



 Score = 96.3 bits (238), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 71/471 (15%), Positives = 147/471 (31%), Gaps = 71/471 (15%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 3   QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG--- 53

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                    +RD+    +     A                   VN     E   + V   
Sbjct: 54  ----HEVSVIRDIRDREFKIFTDAGRVCRPLFV----------VNNDTTSERRGQLVLQK 99

Query: 609 KVTNDVVYLSAMEEENRYIAQ-ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           +    +     ++E+    A    S L  DG                      ++++DA 
Sbjct: 100 EHIEKLEEDHNLDEDEPQKAPYGWSGLLGDG---------------------VVEYVDAE 138

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            ++ + I  +         + +V  G  ++ +  P  + +AP      +    +   + I
Sbjct: 139 EEETIMIVMTPEDLEV---AQQVRQGYELEEETDPNKRVKAPVNPNASQYTHCEIHPSMI 195

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +     GV       +           Q+PL     
Sbjct: 196 LGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAERMDTMANILYYPQKPL----- 250

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +V  M + GYN EDS+++++  +   +F S+    
Sbjct: 251 -----ATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 305

Query: 847 FEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        +   +       +D+ G++  G  V+  DI++GK  P 
Sbjct: 306 YMDQEKRIGMQVVEEFEKPTRSNTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPI 365

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++       +K    RD S  + S  +G V  V +       K
Sbjct: 366 APDVDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 409


>gi|151573853|gb|ABS18231.1| RNA polymerase II [Fusarium sp. NRRL 43803]
 gi|161015857|gb|ABX55929.1| RNA polymerase II subunit [Fusarium sp. NRRL 47513]
 gi|168419260|gb|ACA23516.1| RNA polymerase II [Fusarium ambrosium]
 gi|168419272|gb|ACA23524.1| RNA polymerase II [Fusarium sp. NRRL 22141]
 gi|168419278|gb|ACA23528.1| RNA polymerase II [Fusarium sp. NRRL 22157]
 gi|168419281|gb|ACA23530.1| RNA polymerase II [Fusarium sp. NRRL 22161]
 gi|168419284|gb|ACA23532.1| RNA polymerase II [Fusarium sp. NRRL 22162]
 gi|168419287|gb|ACA23534.1| RNA polymerase II [Fusarium sp. NRRL 22163]
 gi|168419296|gb|ACA23540.1| RNA polymerase II [Fusarium sp. NRRL 22230]
 gi|168419302|gb|ACA23544.1| RNA polymerase II [Fusarium sp. NRRL 22278]
 gi|168419308|gb|ACA23548.1| RNA polymerase II [Fusarium ambrosium]
 gi|168419317|gb|ACA23554.1| RNA polymerase II [Fusarium sp. NRRL 22389]
 gi|168419326|gb|ACA23560.1| RNA polymerase II [Fusarium sp. NRRL 22400]
 gi|168419347|gb|ACA23574.1| RNA polymerase II [Fusarium sp. NRRL 22586]
 gi|168419353|gb|ACA23578.1| RNA polymerase II [Fusarium sp. FSSC_14a KOD-2010]
 gi|168419365|gb|ACA23586.1| RNA polymerase II [Fusarium sp. NRRL 22642]
 gi|168419383|gb|ACA23598.1| RNA polymerase II [Fusarium sp. NRRL 22782]
 gi|168419386|gb|ACA23600.1| RNA polymerase II [Fusarium sp. NRRL 22783]
 gi|168419392|gb|ACA23604.1| RNA polymerase II [Fusarium sp. NRRL 22792]
 gi|168419395|gb|ACA23606.1| RNA polymerase II [Fusarium sp. NRRL 22820]
 gi|168419410|gb|ACA23616.1| RNA polymerase II [Fusarium sp. NRRL 25392]
 gi|168419416|gb|ACA23620.1| RNA polymerase II [Fusarium sp. NRRL 25726]
 gi|168419428|gb|ACA23628.1| RNA polymerase II [Fusarium sp. NRRL 28542]
 gi|168419431|gb|ACA23630.1| RNA polymerase II [Fusarium sp. FSSC_1a KOD-2010]
 gi|168419443|gb|ACA23638.1| RNA polymerase II [Fusarium sp. NRRL 28553]
 gi|168419476|gb|ACA23660.1| RNA polymerase II [Fusarium sp. FSSC_18a KOD-2010]
 gi|168419491|gb|ACA23670.1| RNA polymerase II [Fusarium sp. FSSC_25a KOD-2010]
 gi|168419500|gb|ACA23676.1| RNA polymerase II [Fusarium sp. NRRL 32301]
 gi|168419503|gb|ACA23678.1| RNA polymerase II [Fusarium sp. NRRL 32304]
 gi|168419512|gb|ACA23684.1| RNA polymerase II [Fusarium sp. FSSC_12d KOD-2010]
 gi|168419524|gb|ACA23692.1| RNA polymerase II [Fusarium sp. NRRL 32317]
 gi|168419527|gb|ACA23694.1| RNA polymerase II [Fusarium sp. NRRL 32323]
 gi|168419542|gb|ACA23704.1| RNA polymerase II [Fusarium sp. FSSC_28a KOD-2010]
 gi|168419581|gb|ACA23730.1| RNA polymerase II [Fusarium sp. NRRL 32705]
 gi|168419614|gb|ACA23752.1| RNA polymerase II [Fusarium sp. NRRL 32736]
 gi|168419638|gb|ACA23768.1| RNA polymerase II [Fusarium sp. FSSC_9a KOD-2010]
 gi|168419644|gb|ACA23772.1| RNA polymerase II [Fusarium sp. NRRL 32770]
 gi|168419653|gb|ACA23778.1| RNA polymerase II [Fusarium sp. NRRL 32785]
 gi|168419665|gb|ACA23786.1| RNA polymerase II [Fusarium sp. NRRL 32794]
 gi|168419674|gb|ACA23792.1| RNA polymerase II [Fusarium sp. NRRL 32821]
 gi|168419683|gb|ACA23798.1| RNA polymerase II [Fusarium sp. NRRL 32849]
 gi|168419686|gb|ACA23800.1| RNA polymerase II [Fusarium sp. NRRL 32856]
 gi|168419704|gb|ACA23812.1| RNA polymerase II [Fusarium lichenicola]
 gi|168419710|gb|ACA23816.1| RNA polymerase II [Fusarium sp. FSSC_27a KOD-2010]
 gi|168419713|gb|ACA23818.1| RNA polymerase II [Fusarium sp. NRRL 37640]
 gi|168419719|gb|ACA23822.1| RNA polymerase II [Fusarium sp. NRRL 45880]
 gi|168419785|gb|ACA23866.1| RNA polymerase II [Fusarium sp. NRRL 46704]
 gi|168419788|gb|ACA23868.1| RNA polymerase II [Fusarium sp. NRRL 46705]
 gi|168419791|gb|ACA23870.1| RNA polymerase II [Fusarium sp. NRRL 46706]
 gi|168419794|gb|ACA23872.1| RNA polymerase II [Fusarium sp. FSSC_35a KOD-2010]
 gi|168419797|gb|ACA23874.1| RNA polymerase II [Fusarium sp. NRRL 46708]
 gi|215789619|gb|ACJ69866.1| RNA polymerase II [Fusarium sp. NRRL 22142]
 gi|215789622|gb|ACJ69868.1| RNA polymerase II [Fusarium sp. NRRL 22277]
 gi|215789625|gb|ACJ69870.1| RNA polymerase II [Fusarium sp. NRRL 22402]
 gi|215789628|gb|ACJ69872.1| RNA polymerase II [Fusarium sp. NRRL 22834]
 gi|215789631|gb|ACJ69874.1| RNA polymerase II [Fusarium sp. NRRL 22939]
 gi|215789637|gb|ACJ69878.1| RNA polymerase II [Fusarium sp. NRRL 28545]
 gi|215789652|gb|ACJ69888.1| RNA polymerase II [Fusarium sp. NRRL 32172]
 gi|215789655|gb|ACJ69890.1| RNA polymerase II [Fusarium sp. NRRL 32303]
 gi|215789658|gb|ACJ69892.1| RNA polymerase II [Fusarium sp. NRRL 32334]
 gi|215789664|gb|ACJ69896.1| RNA polymerase II [Fusarium sp. NRRL 32344]
 gi|215789670|gb|ACJ69900.1| RNA polymerase II [Fusarium sp. NRRL 32704]
 gi|215789682|gb|ACJ69908.1| RNA polymerase II [Fusarium sp. NRRL 32806]
 gi|215789694|gb|ACJ69916.1| RNA polymerase II [Fusarium sp. NRRL 34095]
 gi|215789700|gb|ACJ69920.1| RNA polymerase II [Fusarium sp. NRRL 37626]
 gi|215789712|gb|ACJ69928.1| RNA polymerase II [Fusarium sp. NRRL 32846]
 gi|215789715|gb|ACJ69930.1| RNA polymerase II [Fusarium sp. NRRL 46237]
 gi|280985771|gb|ACZ99666.1| RNA polymerase II [Fusarium sp. NRRL 46615]
 gi|280985777|gb|ACZ99669.1| RNA polymerase II [Fusarium sp. NRRL 46676]
          Length = 291

 Score =  177 bits (448), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|316978998|gb|EFV61866.1| DNA-directed RNA polymerase III subunit RPC2 [Trichinella spiralis]
          Length = 1302

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/356 (18%), Positives = 119/356 (33%), Gaps = 77/356 (21%)

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
             ++    +     +   E++    ++      ++KV +   R  + GDK +         
Sbjct: 990  DFKEEPLVWTGAAEAYAERVLLTSNLDN--QCLIKVLLRQTRRPELGDKFS--------- 1038

Query: 1101 SRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                                        SR                  G+K    +   +
Sbjct: 1039 ----------------------------SR-----------------HGQKGVVGLIVQQ 1053

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
             +   S      + ++    +  +++      ++       +G P     F G   E I 
Sbjct: 1054 EDMPFSSEGIVPDLIMNPHGYPSRMTVGKLLELINGKGGTFTGTPRYGTAFSGDKIEEIA 1113

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVT------VGY--IYML-KLNHMVSDKVYARS 1271
              L     +  G+ +L  G         V        G   +Y+L KL HMV DK++AR 
Sbjct: 1114 KDLMQHGFNYLGKDVLISG---------VFRLIQMQFGCDEVYLLQKLKHMVLDKIHARG 1164

Query: 1272 TGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES 1331
             G    +T+QP  G+S  GG RLGEME  C  AYGA+ +L E L + SD      ++Y  
Sbjct: 1165 KGPMENLTRQPTEGRSRDGGLRLGEMERDCFIAYGASAILVERLMVSSDAFEATFQLYNM 1224

Query: 1332 IVAGND---TFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFNKCE 1384
                           P +  +L +E+QA+ +   ++          +   +  K E
Sbjct: 1225 CQNCKSSQALATVCMPYACKLLFQELQAMNVMPQMKLRDGNLPRSFKTTMEPRKQE 1280



 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 135/928 (14%), Positives = 262/928 (28%), Gaps = 183/928 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPK-- 85
           LI     S+D+F+             ++   K+   +      +  ++++      PK  
Sbjct: 191 LINQHIDSFDYFINSE----------IKEIVKANNMVRCNADPSFYIKYIDIRVGLPKAE 240

Query: 86  --------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI------------ 125
                       +C  RD+TYA P+ + +               I  +            
Sbjct: 241 EADCLQTSVTPHECRLRDITYAAPIFVDIEYTRGKEKVLRKNFQIGRMPIMLRSSRCVLK 300

Query: 126 ---KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYAC 182
              +++ I M + PL    G F+I+G +R+V+ Q   S          +       +   
Sbjct: 301 GKNEKELIKMNECPL-DPGGYFIIRGTERVVLIQEQMSKNRMLVA-MDKTDEISCGVLTM 358

Query: 183 RIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEILSTFYPKIVYSQR 241
             I  +G         KDI  +R +R    + +     A+G     ILS    + +    
Sbjct: 359 THIS-RGK--TYVVYKKDIFFMRNNRLTEDISMAIIFRAMG-----ILS---EREMLHLV 407

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSD 301
                  L   + +            D    +I  G ++        K   V    +   
Sbjct: 408 SGEQDSCLVFLNTLQDLHKREIFTQKDVIVALIFVGNRIKGNTFFIAKNSTVSKDELALS 467

Query: 302 CL---CGLYVAEDIVNGETGEIYIEAGDVID------EKSLEEIFHSEIRDIP------- 345
            L      +V     N +   IY+             + ++++  +   + +        
Sbjct: 468 FLTDVICAHVPSSAGNMKLKAIYMGLMIQRIIQVMLGKATVDDPDYYGNKRLELAGSLLA 527

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
           +L+ D         + L     +  + AL D  + + P D+ T  +  ++    +    +
Sbjct: 528 LLFEDLFKRFNQEISLLTDRTIQRLRTALFDFVKHI-PKDLITNGLLNAIATGNWVI-RR 585

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLGNRR 463
           Y +   G  ++  R++      +            K+     L+  +  +    +     
Sbjct: 586 YRMDRHGVTQILSRMSYIAMLGMMTRINSQFEHTRKMGGPRSLQPSQWGMLCPADTPEGE 645

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
              + + L     +     E  +K+   ++ ++ V            ++   F       
Sbjct: 646 PCGLIKSLALLSHITTDSEELPVKKAFCNLGVEDVNYLSTEVLLHPSTSFV-FLNGVLFG 704

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG--RICPAETSEGHNIG 581
              + V   + + + RR   L            E R ++ +  G     P    E     
Sbjct: 705 ITRDVVQLYNSLRYMRRHGFLN--KFVNLFLNEEQRTLYVSCDGGRICRPYIIVENGKSL 762

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L               +    R + D      + YL   EEE+  IA  +S +       
Sbjct: 763 LQHHHLR--------ELACGKRNLEDFFKDGLIEYLDVSEEESALIAVYDSEIT------ 808

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAV 701
                            EK   ++  P  +  + A LIP+  ++ S R    C M +QA+
Sbjct: 809 -----------------EKTTHLEIEPFTLFGVCAGLIPYPNHNQSPRNTYQCAMGKQAM 851

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
            +                                         I   +     S     +
Sbjct: 852 GI-----------------------------------------IAYNQSIRMDSLLYGLV 870

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
           Y               QRPLVK                 +   L  G+N +VA M + G+
Sbjct: 871 YP--------------QRPLVK----------TKTIELINFECLPAGQNAIVAVMSYSGF 906

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
                                 ++ +  M  D  LGP                 +D  GI
Sbjct: 907 ----------GRCHVYRSNKCFVKSYSNMDSDRILGPLVDV--TTGKPVFRHMALDAEGI 954

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPE 909
           +  G  V  G +LV K+ P+       E
Sbjct: 955 VKPGNVVKIGQVLVNKVAPRSALLNEEE 982


>gi|46277338|gb|AAS86859.1| DNA-dependent RNA polymerase II [Plicaria anthracina]
          Length = 551

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 88/676 (13%), Positives = 181/676 (26%), Gaps = 132/676 (19%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V         +    + +V  +     +      ++      +  D  F    +
Sbjct: 1    LMSYVSVGTPSQPIVDFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTI 60

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP--FLENDDSNRVLMGCNMQRQAVPL 703
                    I      I  I     ++ + A  +    F+ ++D      G  + ++    
Sbjct: 61   QKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPTSPRRGELVLQKHHIE 120

Query: 704  LKAEAPFVG--TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
               +   +   T         S   +        E +DA       +    +   +    
Sbjct: 121  KLEDDREIDDETQRYGWQGLLSDGVV--------EYIDAEEEETVMIVMTPEDLETSRQF 172

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            +   + Q+        QR    V             PS  LG       +  + +P+  +
Sbjct: 173  HAGYEIQQEADPA---QRVKGAVNKFAHTWTHCEIHPSMILG-------ICASIIPFPDH 222

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N       S R   +       +  F    R+                           +
Sbjct: 223  NQ------SPRNTYQSAMGKQAMGVFLTNYRERM-----------------------DTM 253

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +     +   +  
Sbjct: 254  ANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQHSIDRGLF- 312

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G      
Sbjct: 313  RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGE 369

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 370  DIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ----------------- 412

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 413  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVP 469

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  +                                          
Sbjct: 470  DLIINPHAIPSRMTIAHLI----------------------------------------- 488

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                        + +L      +     +TP F     ++++ +LR       G  I+Y+
Sbjct: 489  ------------ECLLSKVSSLRGFEGDATP-FTDVTVDSVSKLLREHGYQSRGFEIMYN 535

Query: 1239 GLTGEPFDRPVTVGYI 1254
            G TG      V +G  
Sbjct: 536  GHTGRKIVCQVFLGPT 551


>gi|38373314|gb|AAR19021.1| RpoB [Haemophilus parasuis]
          Length = 173

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 103/173 (59%), Positives = 131/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGSGGLTRERAGFEVRDVHTTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENFR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|330785252|gb|AEC46432.1| RNA polymerase II second largest subunit [Lecanographa atropunctata]
          Length = 293

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 54/358 (15%), Positives = 101/358 (28%), Gaps = 67/358 (18%)

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
            ++           + E    R +   +   V        +     +++    +R      
Sbjct: 1    ILYYPQKPLXXTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS- 59

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF-KKSTVLSSDL 1012
                   R  IE   +   +     ++   +    +  G        GF      +S + 
Sbjct: 60   ----LFYRSYIEQEQKVGFNSLEEFEKPTKATTTRMRPGTYDKLDDDGFVAPGIRVSGED 115

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVES-LKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            I     +        + +    ++   K    +     E    +++              
Sbjct: 116  IIIGKTAPLIGPMQDNAEGGARLKQHTKRDISSPLRSTEAGIVDQVL------VTSTDGR 169

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM
Sbjct: 170  KSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDLIINPHAIPSRM 229

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +  + E  L       G +                                        
Sbjct: 230  TIAHLIECLLSKVAATDGMEGD-------------------------------------- 251

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                           ++P F     + I+++L  A     G  I+Y+G TG      +
Sbjct: 252  ---------------ASP-FTSVTVKDISALLEGAGYQSRGFEIMYNGHTGRKLVSQI 293



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------XXTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIP----NVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +        +       +D+ G +  G  V+
Sbjct: 53  DRGLFRSLFYRSYIEQEQKVGFNSLEEFEKPTKATTTRMRPGTYDKLDDDGFVAPGIRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R +      D+        +G+   V+      R  
Sbjct: 113 GEDIIIGKTAPLIGPMQDNAEGGAR-LKQHTKRDISSPLRSTEAGIVDQVLVTSTDGRKS 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKVRTRT 178


>gi|168419338|gb|ACA23568.1| RNA polymerase II [Fusarium sp. NRRL 22570]
 gi|168419425|gb|ACA23626.1| RNA polymerase II [Fusarium sp. FSSC_26a KOD-2010]
 gi|168419662|gb|ACA23784.1| RNA polymerase II [Fusarium sp. NRRL 32792]
          Length = 291

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 63/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + G N EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|152938344|gb|ABS43112.1| RNA polymerase beta subunit [Salmonella bongori]
          Length = 167

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 104/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|56694320|gb|AAW22900.1| RNA polymerase II second largest subunit [Microcycas calocoma]
          Length = 545

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/487 (15%), Positives = 138/487 (28%), Gaps = 94/487 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVA--FMPWHGYNFEDSMLI--SERMV 834
            LV  G  + V   +      S  + DL   RN   A   + +       S+++     ++
Sbjct: 147  LVTKGFIEYVDTEEEETTMISMTINDLVNARNSPTATSIVKYTHCEIHPSLILGVCASII 206

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
                        ++       +G          V+   L+      +  V        + 
Sbjct: 207  PFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYPQKPLVT 255

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +      + AI      +  D+ +   S +        +F R   D+ +
Sbjct: 256  TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFYRSYRDEEK 314

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLIS 1014
            R  ++ +E+     R+          +          G           K+T ++     
Sbjct: 315  RMGTLVKEEFGRPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPVTQ---- 370

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         DE   +     K    TS    E    +++      D +     R V
Sbjct: 371  -------------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RFV 412

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +G
Sbjct: 413  KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNPHAIPSRMTIG 472

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
            Q+ E  +G     +GK+  +         +IS         +                  
Sbjct: 473  QLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------ 520

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                                +G +    G         + +G  
Sbjct: 521  -----------------------------------YNGHT----GR---RLSAMIFLGPT 538

Query: 1255 YMLKLNH 1261
            Y  +L H
Sbjct: 539  YYQRLKH 545



 Score =  117 bits (294), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 73/481 (15%), Positives = 142/481 (29%), Gaps = 98/481 (20%)

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           ++KN   +  + +  +    +  ++  S    + I+   + +A   F     +    +  
Sbjct: 4   LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVGIHRDPD 63

Query: 530 NSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGH----NIGLVS 584
             +      RR   +  + GV R     E+R ++  +     P    E          + 
Sbjct: 64  LLVKTXRQLRRQVDVNTEVGVVRDIRLSELR-LYTDYGRCSRPLFIVENQRLLIKKPDIR 122

Query: 585 SLTSFARVNAYGFI-ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L    ++       E   R   +      + Y+   EEE   I+              +
Sbjct: 123 RLQQRDQLPPPSPDDENSVRGWHELVTKGFIEYVDTEEEETTMISM----------TIND 172

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
           LV  R +     +   K    +  P  ++ + AS+IPF +++ S R      M +QA+ +
Sbjct: 173 LVNARNSPTATSIV--KYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGI 230

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
                                      R   +  V                         
Sbjct: 231 YVTNYQL--------------------RMDTLAYV------------------------- 245

Query: 764 LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
                         Q+PLV                      L  G N +VA   + GYN 
Sbjct: 246 ----------LYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQ 285

Query: 824 EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDE 878
           EDS+++++  +    F S+    +    +      +E        +   +       +D+
Sbjct: 286 EDSVIMNQSSIDRGFFRSLFYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGSYDKLDD 345

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
            G+   G  V+  D+++GK TP  +           +         RD S  +    SG 
Sbjct: 346 DGLAPPGTRVSGEDVIIGKTTPVTQDE---------SGGQAARYTKRDQSTSLRHSESGM 396

Query: 939 V 939
           V
Sbjct: 397 V 397


>gi|292606621|gb|ADE34127.1| RNA polymerase II second largest subunit [Dothideomycetes sp. TRN
            153]
          Length = 291

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/369 (17%), Positives = 110/369 (29%), Gaps = 81/369 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R      EQ E     + D   +     Y +L +   I  G      
Sbjct: 60   RSLFYRAYLDQEKRVGMSVVEQFEKP--IRSDTLRM-KHGTYEKLEDDGIIAPGTRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +  Q                 
Sbjct: 117  DVIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVVL-------------- 162

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDMPF  DG   
Sbjct: 163  ------TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGLTP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G++                           
Sbjct: 217  DIIINPHAIPSRMTIAHLVECLLSKVGALTGQEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F      +I+ +L+  D  + G  ++Y+
Sbjct: 252  ----------------------------ATP-FTDVTITSISEILKQYDFQQRGFEVMYN 282

Query: 1239 GLTGEPFDR 1247
            G TG+  + 
Sbjct: 283  GHTGKKLNA 291



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/298 (15%), Positives = 96/298 (32%), Gaps = 28/298 (9%)

Query: 775  CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
               Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5    YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835  SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               +F S+    +    +   +   E        D   +     + +++ GII  G  V+
Sbjct: 55   DRGLFRSLFYRAYLDQEKRVGMSVVEQFEKPIRSDTLRMKHGTYEKLEDDGIIAPGTRVS 114

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
              D+++GK  P         E+L +        DV        +G+   VV +       
Sbjct: 115  GEDVIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVV-LTTNTEGL 169

Query: 950  IDKNERSISVEREQI-ELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVL 1008
                 R+ + +  QI +  A     +  I        +     G             + +
Sbjct: 170  RFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGLTPDIIINPHAIPSRM 229

Query: 1009 SSDLISEYPRSQWWQFAVQD-------EKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
            +   + E   S+      Q+       +    ++  +  QY+  +   E  +     K
Sbjct: 230  TIAHLVECLLSKVGALTGQEGDATPFTDVTITSISEILKQYDFQQRGFEVMYNGHTGK 287


>gi|152938306|gb|ABS43093.1| RNA polymerase beta subunit [Citrobacter braakii]
 gi|152938310|gb|ABS43095.1| RNA polymerase beta subunit [Enterobacter aerogenes]
 gi|152938312|gb|ABS43096.1| RNA polymerase beta subunit [Enterobacter asburiae]
 gi|152938314|gb|ABS43097.1| RNA polymerase beta subunit [Enterobacter cloacae subsp. cloacae]
 gi|152938322|gb|ABS43101.1| RNA polymerase beta subunit [Kluyvera ascorbata]
 gi|152938332|gb|ABS43106.1| RNA polymerase beta subunit [Klebsiella oxytoca]
 gi|152938346|gb|ABS43113.1| RNA polymerase beta subunit [Citrobacter freundii]
 gi|194394768|gb|ACF60018.1| RNA polymerase beta subunit [Enterobacter cloacae]
 gi|194394770|gb|ACF60019.1| RNA polymerase beta subunit [Enterobacter sp. ECC_1]
 gi|194394774|gb|ACF60021.1| RNA polymerase beta subunit [Enterobacter sp. ECC_100]
 gi|194394776|gb|ACF60022.1| RNA polymerase beta subunit [Enterobacter sp. ECC_101]
 gi|194394778|gb|ACF60023.1| RNA polymerase beta subunit [Enterobacter sp. ECC_102]
 gi|194394780|gb|ACF60024.1| RNA polymerase beta subunit [Enterobacter sp. ECC_103]
 gi|194394782|gb|ACF60025.1| RNA polymerase beta subunit [Enterobacter sp. ECC_104]
 gi|194394784|gb|ACF60026.1| RNA polymerase beta subunit [Enterobacter sp. ECC_105]
 gi|194394786|gb|ACF60027.1| RNA polymerase beta subunit [Enterobacter sp. ECC_106]
 gi|194394788|gb|ACF60028.1| RNA polymerase beta subunit [Enterobacter sp. ECC_107]
 gi|194394790|gb|ACF60029.1| RNA polymerase beta subunit [Enterobacter sp. ECC_108]
 gi|194394792|gb|ACF60030.1| RNA polymerase beta subunit [Enterobacter sp. ECC_109]
 gi|194394794|gb|ACF60031.1| RNA polymerase beta subunit [Enterobacter sp. ECC_11]
 gi|194394796|gb|ACF60032.1| RNA polymerase beta subunit [Enterobacter sp. ECC_110]
 gi|194394798|gb|ACF60033.1| RNA polymerase beta subunit [Enterobacter sp. ECC_111]
 gi|194394800|gb|ACF60034.1| RNA polymerase beta subunit [Enterobacter sp. ECC_112]
 gi|194394802|gb|ACF60035.1| RNA polymerase beta subunit [Enterobacter sp. ECC_113]
 gi|194394804|gb|ACF60036.1| RNA polymerase beta subunit [Enterobacter sp. ECC_114]
 gi|194394806|gb|ACF60037.1| RNA polymerase beta subunit [Enterobacter sp. ECC_115]
 gi|194394808|gb|ACF60038.1| RNA polymerase beta subunit [Enterobacter sp. ECC_116]
 gi|194394810|gb|ACF60039.1| RNA polymerase beta subunit [Enterobacter sp. ECC_117]
 gi|194394812|gb|ACF60040.1| RNA polymerase beta subunit [Enterobacter sp. ECC_118]
 gi|194394814|gb|ACF60041.1| RNA polymerase beta subunit [Enterobacter sp. ECC_119]
 gi|194394816|gb|ACF60042.1| RNA polymerase beta subunit [Enterobacter sp. ECC_12]
 gi|194394818|gb|ACF60043.1| RNA polymerase beta subunit [Enterobacter sp. ECC_120]
 gi|194394820|gb|ACF60044.1| RNA polymerase beta subunit [Enterobacter sp. ECC_121]
 gi|194394822|gb|ACF60045.1| RNA polymerase beta subunit [Enterobacter sp. ECC_122]
 gi|194394824|gb|ACF60046.1| RNA polymerase beta subunit [Enterobacter sp. ECC_123]
 gi|194394826|gb|ACF60047.1| RNA polymerase beta subunit [Enterobacter sp. ECC_124]
 gi|194394828|gb|ACF60048.1| RNA polymerase beta subunit [Enterobacter sp. ECC_125]
 gi|194394830|gb|ACF60049.1| RNA polymerase beta subunit [Enterobacter sp. ECC_126]
 gi|194394832|gb|ACF60050.1| RNA polymerase beta subunit [Enterobacter sp. ECC_127]
 gi|194394834|gb|ACF60051.1| RNA polymerase beta subunit [Enterobacter sp. ECC_128]
 gi|194394836|gb|ACF60052.1| RNA polymerase beta subunit [Enterobacter sp. ECC_129]
 gi|194394838|gb|ACF60053.1| RNA polymerase beta subunit [Enterobacter sp. ECC_13]
 gi|194394840|gb|ACF60054.1| RNA polymerase beta subunit [Enterobacter sp. ECC_130]
 gi|194394842|gb|ACF60055.1| RNA polymerase beta subunit [Enterobacter sp. ECC_131]
 gi|194394844|gb|ACF60056.1| RNA polymerase beta subunit [Enterobacter sp. ECC_132]
 gi|194394846|gb|ACF60057.1| RNA polymerase beta subunit [Enterobacter sp. ECC_133]
 gi|194394848|gb|ACF60058.1| RNA polymerase beta subunit [Enterobacter sp. ECC_134]
 gi|194394850|gb|ACF60059.1| RNA polymerase beta subunit [Enterobacter sp. ECC_135]
 gi|194394852|gb|ACF60060.1| RNA polymerase beta subunit [Enterobacter sp. ECC_136]
 gi|194394854|gb|ACF60061.1| RNA polymerase beta subunit [Enterobacter sp. ECC_137]
 gi|194394856|gb|ACF60062.1| RNA polymerase beta subunit [Enterobacter sp. ECC_138]
 gi|194394858|gb|ACF60063.1| RNA polymerase beta subunit [Enterobacter sp. ECC_139]
 gi|194394860|gb|ACF60064.1| RNA polymerase beta subunit [Enterobacter sp. ECC_14]
 gi|194394862|gb|ACF60065.1| RNA polymerase beta subunit [Enterobacter sp. ECC_140]
 gi|194394864|gb|ACF60066.1| RNA polymerase beta subunit [Enterobacter sp. ECC_141]
 gi|194394866|gb|ACF60067.1| RNA polymerase beta subunit [Enterobacter sp. ECC_142]
 gi|194394868|gb|ACF60068.1| RNA polymerase beta subunit [Enterobacter sp. ECC_143]
 gi|194394870|gb|ACF60069.1| RNA polymerase beta subunit [Enterobacter sp. ECC_144]
 gi|194394872|gb|ACF60070.1| RNA polymerase beta subunit [Enterobacter sp. ECC_145]
 gi|194394874|gb|ACF60071.1| RNA polymerase beta subunit [Enterobacter sp. ECC_146]
 gi|194394876|gb|ACF60072.1| RNA polymerase beta subunit [Enterobacter sp. ECC_147]
 gi|194394878|gb|ACF60073.1| RNA polymerase beta subunit [Enterobacter sp. ECC_148]
 gi|194394880|gb|ACF60074.1| RNA polymerase beta subunit [Enterobacter sp. ECC_149]
 gi|194394882|gb|ACF60075.1| RNA polymerase beta subunit [Enterobacter sp. ECC_15]
 gi|194394884|gb|ACF60076.1| RNA polymerase beta subunit [Enterobacter sp. ECC_150]
 gi|194394886|gb|ACF60077.1| RNA polymerase beta subunit [Enterobacter sp. ECC_151]
 gi|194394888|gb|ACF60078.1| RNA polymerase beta subunit [Enterobacter sp. ECC_152]
 gi|194394890|gb|ACF60079.1| RNA polymerase beta subunit [Enterobacter sp. ECC_153]
 gi|194394892|gb|ACF60080.1| RNA polymerase beta subunit [Enterobacter sp. ECC_154]
 gi|194394894|gb|ACF60081.1| RNA polymerase beta subunit [Enterobacter sp. ECC_155]
 gi|194394896|gb|ACF60082.1| RNA polymerase beta subunit [Enterobacter sp. ECC_156]
 gi|194394898|gb|ACF60083.1| RNA polymerase beta subunit [Enterobacter sp. ECC_16]
 gi|194394900|gb|ACF60084.1| RNA polymerase beta subunit [Enterobacter sp. ECC_17]
 gi|194394902|gb|ACF60085.1| RNA polymerase beta subunit [Enterobacter sp. ECC_18]
 gi|194394904|gb|ACF60086.1| RNA polymerase beta subunit [Enterobacter sp. ECC_19]
 gi|194394906|gb|ACF60087.1| RNA polymerase beta subunit [Enterobacter sp. ECC_2]
 gi|194394908|gb|ACF60088.1| RNA polymerase beta subunit [Enterobacter sp. ECC_20]
 gi|194394910|gb|ACF60089.1| RNA polymerase beta subunit [Enterobacter sp. ECC_21]
 gi|194394912|gb|ACF60090.1| RNA polymerase beta subunit [Enterobacter sp. ECC_22]
 gi|194394914|gb|ACF60091.1| RNA polymerase beta subunit [Enterobacter sp. ECC_23]
 gi|194394916|gb|ACF60092.1| RNA polymerase beta subunit [Enterobacter sp. ECC_24]
 gi|194394918|gb|ACF60093.1| RNA polymerase beta subunit [Enterobacter sp. ECC_25]
 gi|194394920|gb|ACF60094.1| RNA polymerase beta subunit [Enterobacter sp. ECC_26]
 gi|194394922|gb|ACF60095.1| RNA polymerase beta subunit [Enterobacter sp. ECC_27]
 gi|194394924|gb|ACF60096.1| RNA polymerase beta subunit [Enterobacter sp. ECC_28]
 gi|194394926|gb|ACF60097.1| RNA polymerase beta subunit [Enterobacter sp. ECC_29]
 gi|194394928|gb|ACF60098.1| RNA polymerase beta subunit [Enterobacter sp. ECC_3]
 gi|194394930|gb|ACF60099.1| RNA polymerase beta subunit [Enterobacter sp. ECC_30]
 gi|194394932|gb|ACF60100.1| RNA polymerase beta subunit [Enterobacter sp. ECC_31]
 gi|194394934|gb|ACF60101.1| RNA polymerase beta subunit [Enterobacter sp. ECC_32]
 gi|194394936|gb|ACF60102.1| RNA polymerase beta subunit [Enterobacter sp. ECC_33]
 gi|194394938|gb|ACF60103.1| RNA polymerase beta subunit [Enterobacter sp. ECC_34]
 gi|194394940|gb|ACF60104.1| RNA polymerase beta subunit [Enterobacter sp. ECC_35]
 gi|194394942|gb|ACF60105.1| RNA polymerase beta subunit [Enterobacter sp. ECC_36]
 gi|194394944|gb|ACF60106.1| RNA polymerase beta subunit [Enterobacter sp. ECC_37]
 gi|194394946|gb|ACF60107.1| RNA polymerase beta subunit [Enterobacter sp. ECC_38]
 gi|194394948|gb|ACF60108.1| RNA polymerase beta subunit [Enterobacter sp. ECC_39]
 gi|194394950|gb|ACF60109.1| RNA polymerase beta subunit [Enterobacter sp. ECC_4]
 gi|194394952|gb|ACF60110.1| RNA polymerase beta subunit [Enterobacter sp. ECC_40]
 gi|194394954|gb|ACF60111.1| RNA polymerase beta subunit [Enterobacter sp. ECC_41]
 gi|194394956|gb|ACF60112.1| RNA polymerase beta subunit [Enterobacter sp. ECC_42]
 gi|194394958|gb|ACF60113.1| RNA polymerase beta subunit [Enterobacter sp. ECC_43]
 gi|194394960|gb|ACF60114.1| RNA polymerase beta subunit [Enterobacter sp. ECC_44]
 gi|194394962|gb|ACF60115.1| RNA polymerase beta subunit [Enterobacter sp. ECC_45]
 gi|194394964|gb|ACF60116.1| RNA polymerase beta subunit [Enterobacter sp. ECC_46]
 gi|194394966|gb|ACF60117.1| RNA polymerase beta subunit [Enterobacter sp. ECC_47]
 gi|194394968|gb|ACF60118.1| RNA polymerase beta subunit [Enterobacter sp. ECC_48]
 gi|194394970|gb|ACF60119.1| RNA polymerase beta subunit [Enterobacter sp. ECC_49]
 gi|194394972|gb|ACF60120.1| RNA polymerase beta subunit [Enterobacter sp. ECC_5]
 gi|194394974|gb|ACF60121.1| RNA polymerase beta subunit [Enterobacter sp. ECC_50]
 gi|194394976|gb|ACF60122.1| RNA polymerase beta subunit [Enterobacter sp. ECC_51]
 gi|194394978|gb|ACF60123.1| RNA polymerase beta subunit [Enterobacter sp. ECC_52]
 gi|194394980|gb|ACF60124.1| RNA polymerase beta subunit [Enterobacter sp. ECC_53]
 gi|194394982|gb|ACF60125.1| RNA polymerase beta subunit [Enterobacter sp. ECC_54]
 gi|194394984|gb|ACF60126.1| RNA polymerase beta subunit [Enterobacter sp. ECC_55]
 gi|194394986|gb|ACF60127.1| RNA polymerase beta subunit [Enterobacter sp. ECC_56]
 gi|194394988|gb|ACF60128.1| RNA polymerase beta subunit [Enterobacter sp. ECC_57]
 gi|194394990|gb|ACF60129.1| RNA polymerase beta subunit [Enterobacter sp. ECC_58]
 gi|194394992|gb|ACF60130.1| RNA polymerase beta subunit [Enterobacter sp. ECC_59]
 gi|194394994|gb|ACF60131.1| RNA polymerase beta subunit [Enterobacter sp. ECC_6]
 gi|194394996|gb|ACF60132.1| RNA polymerase beta subunit [Enterobacter sp. ECC_60]
 gi|194394998|gb|ACF60133.1| RNA polymerase beta subunit [Enterobacter sp. ECC_61]
 gi|194395000|gb|ACF60134.1| RNA polymerase beta subunit [Enterobacter sp. ECC_62]
 gi|194395002|gb|ACF60135.1| RNA polymerase beta subunit [Enterobacter sp. ECC_63]
 gi|194395004|gb|ACF60136.1| RNA polymerase beta subunit [Enterobacter sp. ECC_64]
 gi|194395006|gb|ACF60137.1| RNA polymerase beta subunit [Enterobacter sp. ECC_65]
 gi|194395008|gb|ACF60138.1| RNA polymerase beta subunit [Enterobacter sp. ECC_66]
 gi|194395010|gb|ACF60139.1| RNA polymerase beta subunit [Enterobacter sp. ECC_67]
 gi|194395012|gb|ACF60140.1| RNA polymerase beta subunit [Enterobacter sp. ECC_68]
 gi|194395014|gb|ACF60141.1| RNA polymerase beta subunit [Enterobacter sp. ECC_69]
 gi|194395016|gb|ACF60142.1| RNA polymerase beta subunit [Enterobacter sp. ECC_7]
 gi|194395018|gb|ACF60143.1| RNA polymerase beta subunit [Enterobacter sp. ECC_70]
 gi|194395020|gb|ACF60144.1| RNA polymerase beta subunit [Enterobacter sp. ECC_71]
 gi|194395022|gb|ACF60145.1| RNA polymerase beta subunit [Enterobacter sp. ECC_72]
 gi|194395024|gb|ACF60146.1| RNA polymerase beta subunit [Enterobacter sp. ECC_73]
 gi|194395026|gb|ACF60147.1| RNA polymerase beta subunit [Enterobacter sp. ECC_74]
 gi|194395028|gb|ACF60148.1| RNA polymerase beta subunit [Enterobacter sp. ECC_75]
 gi|194395030|gb|ACF60149.1| RNA polymerase beta subunit [Enterobacter sp. ECC_76]
 gi|194395032|gb|ACF60150.1| RNA polymerase beta subunit [Enterobacter sp. ECC_77]
 gi|194395034|gb|ACF60151.1| RNA polymerase beta subunit [Enterobacter sp. ECC_78]
 gi|194395036|gb|ACF60152.1| RNA polymerase beta subunit [Enterobacter sp. ECC_79]
 gi|194395038|gb|ACF60153.1| RNA polymerase beta subunit [Enterobacter sp. ECC_8]
 gi|194395040|gb|ACF60154.1| RNA polymerase beta subunit [Enterobacter sp. ECC_80]
 gi|194395042|gb|ACF60155.1| RNA polymerase beta subunit [Enterobacter sp. ECC_81]
 gi|194395044|gb|ACF60156.1| RNA polymerase beta subunit [Enterobacter sp. ECC_82]
 gi|194395046|gb|ACF60157.1| RNA polymerase beta subunit [Enterobacter sp. ECC_83]
 gi|194395048|gb|ACF60158.1| RNA polymerase beta subunit [Enterobacter sp. ECC_84]
 gi|194395050|gb|ACF60159.1| RNA polymerase beta subunit [Enterobacter sp. ECC_85]
 gi|194395052|gb|ACF60160.1| RNA polymerase beta subunit [Enterobacter sp. ECC_86]
 gi|194395054|gb|ACF60161.1| RNA polymerase beta subunit [Enterobacter sp. ECC_87]
 gi|194395056|gb|ACF60162.1| RNA polymerase beta subunit [Enterobacter sp. ECC_88]
 gi|194395058|gb|ACF60163.1| RNA polymerase beta subunit [Enterobacter sp. ECC_89]
 gi|194395060|gb|ACF60164.1| RNA polymerase beta subunit [Enterobacter sp. ECC_9]
 gi|194395062|gb|ACF60165.1| RNA polymerase beta subunit [Enterobacter sp. ECC_90]
 gi|194395064|gb|ACF60166.1| RNA polymerase beta subunit [Enterobacter sp. ECC_91]
 gi|194395066|gb|ACF60167.1| RNA polymerase beta subunit [Enterobacter sp. ECC_92]
 gi|194395068|gb|ACF60168.1| RNA polymerase beta subunit [Enterobacter sp. ECC_93]
 gi|194395070|gb|ACF60169.1| RNA polymerase beta subunit [Enterobacter sp. ECC_94]
 gi|194395072|gb|ACF60170.1| RNA polymerase beta subunit [Enterobacter sp. ECC_95]
 gi|194395074|gb|ACF60171.1| RNA polymerase beta subunit [Enterobacter sp. ECC_96]
 gi|194395076|gb|ACF60172.1| RNA polymerase beta subunit [Enterobacter sp. ECC_97]
 gi|194395078|gb|ACF60173.1| RNA polymerase beta subunit [Enterobacter sp. ECC_98]
 gi|194395080|gb|ACF60174.1| RNA polymerase beta subunit [Enterobacter sp. ECC_99]
          Length = 167

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|312458553|gb|ADQ89210.1| DNA-directed RNA polymerase beta subunit [Corynebacterium
            diphtheriae]
          Length = 134

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/162 (35%), Positives = 84/162 (51%), Gaps = 36/162 (22%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G KI +     +   +   L++  E +                      
Sbjct: 1    EVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP------------------ 36

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPV 1249
                +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +GEPF  PV
Sbjct: 37   ----AGSLTATPVFDGATNEEIAGLLGNSRPNRDGDVMVDENGKATLFDGRSGEPFPYPV 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            +VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   SVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 134


>gi|294998753|gb|ADF58093.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998756|gb|ADF58095.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998759|gb|ADF58097.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998765|gb|ADF58101.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998777|gb|ADF58109.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998796|gb|ADF58121.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998799|gb|ADF58123.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998802|gb|ADF58125.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998805|gb|ADF58127.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998808|gb|ADF58129.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998811|gb|ADF58131.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998814|gb|ADF58133.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
 gi|294998817|gb|ADF58135.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            ferulae]
          Length = 243

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 92/309 (29%), Gaps = 74/309 (23%)

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ R  +D  ++S   + E+ E  +RD          +       I  G   V     
Sbjct: 9    RSMYYRSYMDLEKKSGVQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGTGVVGEDII 68

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  D      R++          ++     +  Q                    
Sbjct: 69   IGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------------- 111

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 112  ---TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDII 168

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L      +G +                              
Sbjct: 169  INPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------------- 200

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     E++++ LR       G  ++Y G T
Sbjct: 201  -------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEVMYHGHT 234

Query: 1242 GEPFDRPVT 1250
            G      V 
Sbjct: 235  GRKLQAQVY 243



 Score = 46.6 bits (109), Expect = 0.033,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             V   +F S++   +  + + + +   E        +   +       ++  G+I  G 
Sbjct: 1   SSVDRGLFRSMYYRSYMDLEKKSGVQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGT 60

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V   DI++GK  P         ++        +    RD S  + S  +G V  V I  
Sbjct: 61  GVVGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITT 113

Query: 947 RHGIDK 952
            H   K
Sbjct: 114 NHEGQK 119


>gi|152938302|gb|ABS43091.1| RNA polymerase beta subunit [Citrobacter amalonaticus]
 gi|152938308|gb|ABS43094.1| RNA polymerase beta subunit [Citrobacter rodentium]
          Length = 167

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 105/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFVIAQANSNLDDDGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|38373304|gb|AAR19016.1| RpoB [Haemophilus aegyptius ATCC 11116]
          Length = 173

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 104/173 (60%), Positives = 130/173 (75%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL++FAR N YGF+ETPYRKV DG+VT ++ YLS ++E N  IAQANS+LDE+  
Sbjct: 61  IGLINSLSAFARTNDYGFLETPYRKVVDGQVTEEIEYLSVIDEANYIIAQANSNLDENNR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 173


>gi|145640491|ref|ZP_01796075.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
           R3021]
 gi|145275077|gb|EDK14939.1| DNA-directed RNA polymerase beta subunit [Haemophilus influenzae
           22.4-21]
          Length = 128

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 50/132 (37%), Positives = 83/132 (62%), Gaps = 6/132 (4%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
            G  ++   R+RK FGK P+++++P L+ +Q  S+D F+  +        +GL+AAF+SV
Sbjct: 1   MGYSYSEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQKD----PEGQQGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI 122
           FPI + +G   L++V Y  + P+FDV +C  R  TYA  L++ LRL+ +D    + ++++
Sbjct: 57  FPIVSNNGYTELQYVDYRLEEPEFDVRECQIRGSTYAAGLRVKLRLVSYDK--ESSSRAV 114

Query: 123 KDIKEQSIYMGD 134
           KDIKE  +YMG 
Sbjct: 115 KDIKENEVYMGK 126


>gi|258590815|emb|CBE67085.1| RNA polymerase beta subunit [Arcanobacterium haemolyticum DSM 20595]
          Length = 135

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 50/107 (46%), Positives = 70/107 (65%), Gaps = 8/107 (7%)

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEP 1244
            +   A   K+   V+TPVFDG +   +  +L    ++  G        ++ L+DG TG+P
Sbjct: 29   LPENAVVGKAQGRVATPVFDGVESNELRGLLENTTVNRDGDRLIGASGKAQLFDGRTGDP 88

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            F  PV+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 89   FPEPVSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|56406195|gb|AAV87481.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 172

 Score =  176 bits (447), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 102/171 (59%), Positives = 130/171 (76%), Gaps = 1/171 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR
Sbjct: 121 FTDAFVTCRGEHGESDLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANR 171


>gi|168419344|gb|ACA23572.1| RNA polymerase II [Fusarium sp. NRRL 22579]
          Length = 291

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  AQVF 291



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/183 (19%), Positives = 63/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + G N EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGXNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|215400980|gb|ACJ66348.1| RNA polymerase beta subunit [Corynebacterium sp. 3105]
          Length = 135

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 57/163 (34%), Positives = 84/163 (51%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI +     +   +   L++  E +                     
Sbjct: 1    LEVHLGWLAAA-GWKIDT-----EDPANAELLKTLPEDLYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGASNEELAGLLANSRPNRDGDVMVNADGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|152938304|gb|ABS43092.1| RNA polymerase beta subunit [Buttiauxella agrestis]
          Length = 167

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 101/167 (60%), Positives = 130/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +G VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVVEGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++LDE+G F ++LV CR  GE  L   +++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|330785254|gb|AEC46433.1| RNA polymerase II second largest subunit [Lecanographa dialeuca]
          Length = 301

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/371 (15%), Positives = 104/371 (28%), Gaps = 73/371 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFEKPTKQTTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQENA------------EGGARLKEHSKRDISAPLRSTEAGIVDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPV 1249
            G TG      +
Sbjct: 291  GHTGRKLVSQI 301



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 67/189 (35%), Gaps = 13/189 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFEKPTKQTTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P        E     A   E +       LR        +VD  +     
Sbjct: 121 GEDIIIGKTSPLAG--PMQENAEGGARLKEHSKRDISAPLR---STEAGIVDQVLVTTTD 175

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 176 GKKSVKVRT 184


>gi|46277302|gb|AAS86841.1| DNA-dependent RNA polymerase II [Scabropezia flavovirens]
          Length = 558

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/377 (15%), Positives = 109/377 (28%), Gaps = 75/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D S+ +  G    
Sbjct: 257  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQED-SVIMNQGSIDR 315

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
             +   +F R  +D+ +R      E+ E   R           +       +  G      
Sbjct: 316  GLFRSLFYRTYMDQEKRVGMDVVEEFERPTRSNTLRLKHGTYDKLDDDGLVAPGVRVSGE 375

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ ++ +      R+++         ++     +  Q                 
Sbjct: 376  DIIIGKTSPIAPNQEELGQRTRFHTKRDVSTPLRSTENGIVDQ----------------- 418

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 419  ---VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVP 475

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  +                                          
Sbjct: 476  DLIINPHAIPSRMTIAHLI----------------------------------------- 494

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                        + +L      +     +TP F     ++++ +LR       G  I+Y+
Sbjct: 495  ------------ECLLSKVSSLRGFEGDATP-FTDVTVDSVSKLLREHGYQSRGFEIMYN 541

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 542  GHTGRKLVAQVFLGPTY 558



 Score = 97.1 bits (240), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 64/481 (13%), Positives = 122/481 (25%), Gaps = 86/481 (17%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 22  DFMTQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 75

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 76  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIEKLEDDRELD 135

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
            E+             V Y+ A EEE   I      L+    F                 
Sbjct: 136 DESHRYGWAGLMSDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQ---------- 185

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
                  +  P Q V  + S                                        
Sbjct: 186 ------QEVDPAQRVKASVSKF----------------------------------AHTW 205

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CV 776
              +   + I+   A I+   D  +                       +   +  N    
Sbjct: 206 THCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXFNHYRERMDTMANILYY 265

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA M + GYN EDS+++++  +  
Sbjct: 266 PQKPL----------GTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQGSIDR 315

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E        +   +       +D+ G++  G  V+  
Sbjct: 316 GLFRSLFYRTYMDQEKRVGMDVVEEFERPTRSNTLRLKHGTYDKLDDDGLVAPGVRVSGE 375

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK +P   +     ++        +    RD S  + S  +G V  V +       
Sbjct: 376 DIIIGKTSPIAPNQEELGQRT-------RFHTKRDVSTPLRSTENGIVDQVMVTTNQEGL 428

Query: 952 K 952
           K
Sbjct: 429 K 429


>gi|119640579|gb|ABL85483.1| RNA polymerase II second largest subunit [Ingaderia friabillima]
 gi|330785224|gb|AEC46418.1| RNA polymerase II second largest subunit [Pentagenella gracillima]
 gi|330785226|gb|AEC46419.1| RNA polymerase II second largest subunit [Pentagenella gracillima]
 gi|330785228|gb|AEC46420.1| RNA polymerase II second largest subunit [Pentagenella gracillima]
          Length = 307

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 105/372 (28%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   + ++ AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLNFSELPAGQNVIVAIACYSGYNQEDSIIMNQSAIDRGLF-RS 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               R  I++ +       ++ E   +                   +  G           
Sbjct: 68   FLYRTYIEQQKAVGFNSLDEFEKPNKATTMRTRPGTYEKLDYDGFVEPGIRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR+ +  K          E    +++      
Sbjct: 128  KTAPFQNPMADNA------------EGGQRHKQHTKRDVSAPLRSTEAGIVDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTEGRRSVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 230  PHAIPSRMTVAHLIECLLSKVSATQGLEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+++L+ +     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSEISNLLKGSGYQSRGLELMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVYLGPTY 307



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 69/196 (35%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                   +  +L  G+N++VA   + GYN ED
Sbjct: 2   RMDTMSNILYYPQKPL----------ATTRSMEYLNFSELPAGQNVIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       +E  +              + +D  G
Sbjct: 52  SIIMNQSAIDRGLFRSFLYRTYIEQQKAVGFNSLDEFEKPNKATTMRTRPGTYEKLDYDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  ++PM    +  +        DV        +G+   V+
Sbjct: 112 FVEPGIRVSGDDIIIGKTAPF-QNPMADNAEGGQRHKQHTKRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKVRTRA 186


>gi|56675892|emb|CAD89518.2| RNA polymerase II second largest subunit [Tephrosia purpurea]
          Length = 423

 Score =  176 bits (446), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/466 (15%), Positives = 135/466 (28%), Gaps = 88/466 (18%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +            +      +      I   ++     +
Sbjct: 37   HDLVSKGFIEYIDTEEEETTMISMTINDLVQGRLYPEDAYSDTYTHCEIHPSLILGVCAS 96

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+    +      +  V        +    +  
Sbjct: 97   IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRM---DTLAYVLYYPQKPLVTTRAMEH 153

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 154  LHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 212

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILC---GQNAVSGPKGFKKSTVLSSDLISEYP 1017
            +E      R  +     +    Y +L +      G           K+T +S +      
Sbjct: 213  KEDFGRPDR-ANTMVRGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQE------ 265

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       E   +++   +  +  S    E    +++      D +     R VKV 
Sbjct: 266  -----------EAQGQSLRYTRRDHSISLRHSETGIVDQVLLTTNADGL-----RFVKVR 309

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ 
Sbjct: 310  VRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLI 369

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  +G     +GK+                                              
Sbjct: 370  ECIMGRVAAHMGKEGD-------------------------------------------- 385

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                     +TP F     + I+  L        G   +Y+G TG 
Sbjct: 386  ---------ATP-FTDVTVDNISKALHKCGYQMXGFETMYNGHTGR 421



 Score =  102 bits (255), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 57/342 (16%), Positives = 100/342 (29%), Gaps = 93/342 (27%)

Query: 605 VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFI 664
             D      + Y+   EEE   I+              +LV  R   E      +     
Sbjct: 36  WHDLVSKGFIEYIDTEEEETTMISM----------TINDLVQGRLYPE--DAYSDTYTHC 83

Query: 665 DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSG 724
           +  P  ++ + AS+IPF +++ S R      M +QA+ +      F              
Sbjct: 84  EIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQF-------------- 129

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKV 784
                 R   +  V                                       Q+PLV  
Sbjct: 130 ------RMDTLAYV-----------------------------------LYYPQKPLV-- 146

Query: 785 GDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHI 844
                               L  G N +VA   + GYN EDS+++++  +    F S+  
Sbjct: 147 --------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFF 198

Query: 845 EEFEVMARDTKLGPEEITR-------DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
             +    +      +E           +  +       +D+ G+   G  V+  D+++GK
Sbjct: 199 RSYRDEEKKMGTLVKEDFGRPDRANTMVRGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGK 258

Query: 898 ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            TP  +           A         RD S+ +    +G V
Sbjct: 259 TTPISQEE---------AQGQSLRYTRRDHSISLRHSETGIV 291


>gi|168419305|gb|ACA23546.1| RNA polymerase II [Nectria atrofusca]
          Length = 291

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/364 (15%), Positives = 102/364 (28%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVAPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
              V 
Sbjct: 288  SQVF 291



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|56694304|gb|AAW22892.1| RNA polymerase II second largest subunit [Dicksonia antarctica]
          Length = 525

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 70/445 (15%), Positives = 125/445 (28%), Gaps = 80/445 (17%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                 +      I   M+     + I   +     R+T             V+   L+  
Sbjct: 161  EEAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 219

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S V 
Sbjct: 220  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSVD 277

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   IF R   D+ ++  ++ +E+ E   R+          +          G    
Sbjct: 278  RGFF-RSIFYRSYRDEEKKQGTLVKEEFERPNRENTSGMRHGSYDKLDDDGLAPPGTRVS 336

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++                  D+   +     K    T     E    ++
Sbjct: 337  GEDVIIGKTTPIAQ-----------------DDTGSQAQRYSKRDQSTCLRHSESGMVDQ 379

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ ++G 
Sbjct: 380  VLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGI 434

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +
Sbjct: 435  TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQM 494

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                                                  +G +  
Sbjct: 495  RGFETM-----------------------------------------------YNGHT-- 505

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G      +  + +G  Y  +L H
Sbjct: 506  --GR---RLNAMIFLGPTYYQRLKH 525



 Score = 62.0 bits (149), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 54/299 (18%), Positives = 94/299 (31%), Gaps = 36/299 (12%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   +  A   F     +    E    +  +   RR   +  + GV R 
Sbjct: 18  EEWSTENFEEISPAVIPQATKIFVNGCWVGIHREPELLVRTLRQLRRQVDVNTEVGVVRD 77

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S      + A    ET      D     
Sbjct: 78  IRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKS-----DIRALQQKETTEAGWYDLVTKG 131

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+             ++LV  R   E      +     +  P  ++
Sbjct: 132 FIEYVDTEEEETTMISM----------TIQDLVNARLHPE--EAYSDTYTHCEIHPSMIL 179

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GM 715
            + AS+IPF +++ S R      M +QA+                 L   + P V T  M
Sbjct: 180 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAM 239

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E +  +   A I A  A            +   +  +D        YR  + +   Q T
Sbjct: 240 EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSVDRGFFRSIFYRSYRDEEKKQGT 298


>gi|281324365|gb|ADA60248.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324385|gb|ADA60258.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324389|gb|ADA60260.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324393|gb|ADA60262.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324395|gb|ADA60263.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324409|gb|ADA60270.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|281324415|gb|ADA60273.1| RNA polymerase beta subunit [Helicobacter fennelliae]
          Length = 217

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 113/217 (52%), Positives = 158/217 (72%), Gaps = 2/217 (0%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVV 510
           IDD DNLGNRR+R++GE+L N+   GL++M+++IK++++++    D++MP DLINAK + 
Sbjct: 1   IDDRDNLGNRRIRAIGELLANELHSGLVKMQKAIKDKLTTMSGSFDAIMPHDLINAKMIT 60

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           S + EFF   QLSQ  +  N LS ITH RRLSALG+GG+ + R G E RDVHPTHYGRIC
Sbjct: 61  STIIEFFTGGQLSQFMDQTNPLSEITHKRRLSALGEGGLVKERVGFEARDVHPTHYGRIC 120

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++++++F  VN  GFIE PYRKV +GKVT+++VYL+A +E+ + IA A
Sbjct: 121 PIETPEGQNIGLINTISTFTLVNDLGFIEAPYRKVVNGKVTDEIVYLTATQEDGKVIAPA 180

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           ++ LD+D    + L+  RC GE  L   E ++ ID S
Sbjct: 181 STQLDKDNKIIDSLIETRCGGEITLRKTEDVELIDLS 217


>gi|152938326|gb|ABS43103.1| RNA polymerase beta subunit [Pectobacterium wasabiae]
          Length = 167

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 101/167 (60%), Positives = 130/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V +  VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRENVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++LDE+G F +ELV CR  GE  L  R++++++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFVIAQANTNLDEEGRFIDELVTCRNKGESSLFSRDQVEYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|330785300|gb|AEC46456.1| RNA polymerase II second largest subunit [Dimidiographa graphidiza]
          Length = 296

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/369 (15%), Positives = 104/369 (28%), Gaps = 73/369 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R  I++ +       E+ E  A+           +       +  G        
Sbjct: 61   -RSLFYRTYIEQQQAVGFNSLEEFEKPAKQLTMRTRPGTYDKLDEDGFVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +K+   
Sbjct: 120  IIGKTAPFQAAMQENA------------EGGQRTRQHTKRDVSXPLRSTEAGIVDKVL-- 165

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 166  ----VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDL 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 222  IINPHAIPSRMTIAHLIECLLSKVSATAGMEGD--------------------------- 254

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+++L      + G  ++Y+G 
Sbjct: 255  --------------------------ATP-FTDVTVQNISNLLSEKGYQQRGFEVMYNGH 287

Query: 1241 TGEPFDRPV 1249
            TG   +  +
Sbjct: 288  TGRKLNAQI 296



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 61/187 (32%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                    +DE G +  G  V+
Sbjct: 56  DRGLFRSLFYRTYIEQQQAVGFNSLEEFEKPAKQLTMRTRPGTYDKLDEDGFVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +     E   +        DV        +G+   V+      R  
Sbjct: 116 GEDIIIGKTAPFQAAMQENAEGG-QRTRQHTKRDVSXPLRSTEAGIVDKVLVTTTEGRRS 174

Query: 950 IDKNERS 956
           +    R+
Sbjct: 175 VKVRTRT 181


>gi|269912636|emb|CAY86098.1| RNA polymerase beta subunit [Gluconobacter frateurii]
          Length = 187

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 76/189 (40%), Positives = 107/189 (56%), Gaps = 27/189 (14%)

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------- 221
             SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL           
Sbjct: 1   HSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYIAQRDR 60

Query: 222 --------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
                         GMD +EILS FY  + +++ GD W  P        G K+ S LVD 
Sbjct: 61  KIAEGGDVEGLDIRGMDQDEILSYFYDMVPFTRMGDGWARPFEPE-AFRGQKLLSPLVDA 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           DTGE V E+  KLT+ +++ + EK  + + +    + G Y+A D+VN  TGEIY EAG+ 
Sbjct: 120 DTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDVLGRYLAYDLVNEHTGEIYGEAGEE 178

Query: 328 IDEKSLEEI 336
           + E  L  +
Sbjct: 179 LTEDRLVAL 187


>gi|198279497|emb|CAP04783.1| RNA polymerase beta subunit [Equisetum palustre]
          Length = 274

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 167/251 (66%), Gaps = 9/251 (3%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL K E   VGTG+E   A  SG+ + ++R G +  +D  +I +   E      
Sbjct: 1   MQRQAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDGEKITLFVDEETSINK 60

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+
Sbjct: 61  -------NLLSYERSNNNTCMNQKPLLCKNKFLRQGQIIADGASTVGGELALGRNILVAY 113

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER++ EDVFTS HIE +E+    T  GPE++TR+IP+++   L++
Sbjct: 114 MPWEGYNFEDAILISERLIYEDVFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRH 173

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +DE G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP 
Sbjct: 174 LDENGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPV 233

Query: 934 GVSGTVVDVRI 944
           GV G V+D+R 
Sbjct: 234 GVKGRVIDIRW 244


>gi|330785250|gb|AEC46431.1| RNA polymerase II second largest subunit [Lecanographa cf. farinosa
            Ertz 14053]
          Length = 301

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/371 (15%), Positives = 104/371 (28%), Gaps = 73/371 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQDNA------------EGGARLKEHSKRDISAPLRSTEAGIIDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPFDRPV 1249
            G TG      +
Sbjct: 291  GHTGRKLVSQI 301



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFERPTKQTTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTSPLAGPMQDNAEGGAR----LKEHSKRDISAPLRSTEAGIIDQVLVTTTDG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KKSVKVRTRTTKVPQI 192


>gi|169260876|gb|ACA52150.1| RpoB [Chelonobacter oris]
          Length = 171

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 104/171 (60%), Positives = 128/171 (74%), Gaps = 1/171 (0%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIG
Sbjct: 1   LSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDED  FT
Sbjct: 61  LINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDEDSRFT 120

Query: 642 EELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +  V CR   GE  L   E I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 DAFVTCRGEHGESGLYRAEDIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 171


>gi|90192218|gb|ABD91769.1| RNA polymerase beta subunit [Klebsiella oxytoca]
          Length = 170

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 102/170 (60%), Positives = 130/170 (76%)

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           +AV EFF  +  SQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+C
Sbjct: 1   AAVKEFFGFTSWSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 60

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQA
Sbjct: 61  PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 120

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           NS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 NSNLDDEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 170


>gi|293627812|gb|ADE58437.1| RNA polymerase beta-subunit [Bartonella quintana]
 gi|293627814|gb|ADE58438.1| RNA polymerase beta-subunit [Bartonella quintana]
 gi|293627816|gb|ADE58439.1| RNA polymerase beta-subunit [Bartonella quintana]
          Length = 169

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 134/169 (79%), Positives = 159/169 (94%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           DLGDLALGRN+LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV ARDTKLGPEE
Sbjct: 1   DLGDLALGRNVLVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEVAARDTKLGPEE 60

Query: 861 ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
           ITRDIPNV+EE L+N+DE GII +GAEV PGDILVGKITPKGESPMTPEEKLLRAIFGEK
Sbjct: 61  ITRDIPNVAEESLRNLDEAGIIYIGAEVQPGDILVGKITPKGESPMTPEEKLLRAIFGEK 120

Query: 921 AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
           A DVRDTS+R+P G  GTVV+VR+FNRHG++K+ER++++ERE+IE LA+
Sbjct: 121 ASDVRDTSMRMPPGAFGTVVEVRVFNRHGVEKDERAMAIEREEIERLAK 169


>gi|152938348|gb|ABS43114.1| RNA polymerase beta subunit [Pantoea agglomerans]
          Length = 167

 Score =  176 bits (446), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 100/167 (59%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG V++++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVIDGLVSDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN+ LD++G+F ++LV CR  GE  L  R+++D++D S +Q+VS+ ASLIPFLE
Sbjct: 61  NYVIAQANAPLDDNGAFVDDLVTCRSKGESSLFSRDQVDYMDVSTQQIVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|152938318|gb|ABS43099.1| RNA polymerase beta subunit [Serratia liquefaciens]
          Length = 167

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 105/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGLVTDEINYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LDEDG F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFVIAQANSNLDEDGRFIEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA+
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAR 167


>gi|45120527|gb|AAS55049.1| RNA polymerase II second largest subunit [Heterobasidion annosum]
          Length = 235

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 89/256 (34%), Gaps = 21/256 (8%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S V   +    I+ R  +D  ++S   + E
Sbjct: 1    FRELPAGQSAIVAILCYSGYNQEDSVIMNQSSVDRGLF-RSIYYRSYMDLEKKSGVQQLE 59

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
            + E   RD          +       I  G           K+  + +D           
Sbjct: 60   EFEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVAGEDIIIGKTAPIPAD----------- 108

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
                 +E  QR     +    T     E    +++      D       + VKV V   R
Sbjct: 109  ----SEELGQRLRTHTRRDVSTPLKSTESGIVDQVLITTNSD-----GQKFVKVRVRSTR 159

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +G + E  L 
Sbjct: 160  IPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIGHLVECLLS 219

Query: 1143 WACVGLGKKIKSLIND 1158
                 +G +  +    
Sbjct: 220  KVATLIGNEGDATPFT 235



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/156 (23%), Positives = 64/156 (41%), Gaps = 12/156 (7%)

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +L  G++ +VA + + GYN EDS+++++  V   +F SI+   +  + + + +   E 
Sbjct: 1   FRELPAGQSAIVAILCYSGYNQEDSVIMNQSSVDRGLFRSIYYRSYMDLEKKSGVQQLEE 60

Query: 862 TRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                      +       I++ G+I  G  V   DI++GK  P         ++L    
Sbjct: 61  FEKPTRDTTLRMKHGTYDKIEDDGLIAPGTGVAGEDIIIGKTAPIPADSEELGQRL---- 116

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
              +    RD S  + S  SG V  V I       K
Sbjct: 117 ---RTHTRRDVSTPLKSTESGIVDQVLITTNSDGQK 149


>gi|294998741|gb|ADF58085.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998744|gb|ADF58087.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998747|gb|ADF58089.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998750|gb|ADF58091.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998762|gb|ADF58099.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            elaeoselini]
 gi|294998768|gb|ADF58103.1| RNA polymerase II second largest subunit [Pleurotus nebrodensis]
 gi|294998771|gb|ADF58105.1| RNA polymerase II second largest subunit [Pleurotus nebrodensis]
 gi|294998780|gb|ADF58111.1| RNA polymerase II second largest subunit [Pleurotus ostreatus]
 gi|294998790|gb|ADF58117.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998793|gb|ADF58119.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
 gi|294998820|gb|ADF58137.1| RNA polymerase II second largest subunit [Pleurotus eryngii var.
            eryngii]
          Length = 243

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 92/309 (29%), Gaps = 74/309 (23%)

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ R  +D  ++S   + E+ E  +RD          +       I  G   V     
Sbjct: 9    RSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGTGVVGEDII 68

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  D      R++          ++     +  Q                    
Sbjct: 69   IGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------------- 111

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 112  ---TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDII 168

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L      +G +                              
Sbjct: 169  INPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------------- 200

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     E++++ LR       G  ++Y G T
Sbjct: 201  -------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEVMYHGHT 234

Query: 1242 GEPFDRPVT 1250
            G      V 
Sbjct: 235  GRKLQAQVY 243



 Score = 46.6 bits (109), Expect = 0.032,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             V   +F S++   +  + + + +   E        +   +       ++  G+I  G 
Sbjct: 1   SSVDRGLFRSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGT 60

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V   DI++GK  P         ++        +    RD S  + S  +G V  V I  
Sbjct: 61  GVVGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITT 113

Query: 947 RHGIDK 952
            H   K
Sbjct: 114 NHEGQK 119


>gi|159576880|dbj|BAF92763.1| RpoB [Corynebacterium macginleyi]
 gi|159576882|dbj|BAF92764.1| RpoB [Corynebacterium macginleyi]
          Length = 135

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 54/163 (33%), Positives = 84/163 (51%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G K+ +     +   +   L++  E++    + +              
Sbjct: 1    LELHLGWLAHA-GWKVDT-----EDPANAELLKTLPEELYDVPADSLT------------ 42

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                      +TPVFDGA    I  +L  +  +  G        ++ L+DG +GEP+  P
Sbjct: 43   ----------ATPVFDGATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRSGEPYKYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            ++VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   ISVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|151573152|gb|ABS17766.1| RNA polymerase II [Fusarium sp. NRRL 43512]
 gi|151573540|gb|ABS18024.1| RNA polymerase II [Fusarium sp. NRRL 28000]
 gi|151573543|gb|ABS18026.1| RNA polymerase II [Fusarium sp. NRRL 28001]
 gi|151573862|gb|ABS18237.1| RNA polymerase II [Fusarium sp. NRRL 43806]
          Length = 290

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/363 (15%), Positives = 101/363 (27%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPV 1249
              V
Sbjct: 288  AQV 290



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|152938320|gb|ABS43100.1| RNA polymerase beta subunit [Edwardsiella tarda]
          Length = 167

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 104/167 (62%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGIVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQANS+LD++G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFVIAQANSNLDDEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTSVAK 167


>gi|330785436|gb|AEC46524.1| RNA polymerase II second largest subunit [Syncesia glyphysoides]
          Length = 301

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/370 (16%), Positives = 107/370 (28%), Gaps = 81/370 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 125  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 165

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 166  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 225

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 226  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 259

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 260  ---------------------------ATP-FTDITVSSISELLEFAGYQSRGFELMYNG 291

Query: 1240 LTGEPFDRPV 1249
             TG   +  V
Sbjct: 292  HTGRKLNAQV 301



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 9/187 (4%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 121 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 179

Query: 950 IDKNERS 956
           +    R+
Sbjct: 180 VKVRTRT 186


>gi|164430474|gb|ABY55554.1| RNA polymerase beta subunit [Bartonella durdenii]
          Length = 170

 Score =  176 bits (445), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 113/167 (67%), Positives = 133/167 (79%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             SQ  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NI
Sbjct: 2   NYSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNI 61

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G F
Sbjct: 62  GLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDAEGRF 121

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           TEE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLENDD 
Sbjct: 122 TEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDC 168


>gi|112824222|gb|ABI26084.1| second largest RNA polymerase II [Peltula auriculata]
          Length = 291

 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/369 (16%), Positives = 111/369 (30%), Gaps = 81/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R   D+ ++      + IE   +    + V L    Y +L E   I  G        
Sbjct: 60   LFYRSYTDQEKKVGI---QFIEQFEKPMRSDTVRLKHGTYDKLDEDGIINPGVRVSGEDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D      R+++         ++     +  Q                   
Sbjct: 117  IIGKTAPIAPDAEELGQRTKYHNKRDVSTPLRSTESGIVDQ------------------- 157

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      LR VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+
Sbjct: 158  -VLVTTNAEGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGIVPDL 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVSALKGFEGD--------------------------- 249

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++++LR       G  ++Y+G 
Sbjct: 250  --------------------------ATP-FTDVTVDSVSALLREHGYQSRGFEVMYNGH 282

Query: 1241 TGEPFDRPV 1249
            TG      +
Sbjct: 283  TGRKLVAQI 291



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 66/177 (37%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +       +DE GII  G  V+
Sbjct: 53  DRGLFRSLFYRSYTDQEKKVGIQFIEQFEKPMRSDTVRLKHGTYDKLDEDGIINPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        K  + RD S  + S  SG V  V +  
Sbjct: 113 GEDIIIGKTAPIAPDAEELGQRT-------KYHNKRDVSTPLRSTESGIVDQVLVTT 162


>gi|168419329|gb|ACA23562.1| RNA polymerase II [Fusarium sp. NRRL 22412]
          Length = 291

 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
                
Sbjct: 288  AQCF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|46277346|gb|AAS86863.1| DNA-dependent RNA polymerase II [Peziza bananincola]
          Length = 555

 Score =  176 bits (445), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/350 (16%), Positives = 106/350 (30%), Gaps = 81/350 (23%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R   +   
Sbjct: 284  FRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYMDQEKR---IGMS 339

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E   +      + L    Y +L +   +  G           K+  ++ +      R+
Sbjct: 340  VVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT 399

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            ++         ++     +  Q                             L+ VKV + 
Sbjct: 400  KFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFVKVRMR 439

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  +G   D+ +NP  +PSRM +  + E 
Sbjct: 440  TTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVPDLSINPHAIPSRMTIAHLIEC 499

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             L       G +                                                
Sbjct: 500  LLSKVSSLRGYEGD---------------------------------------------- 513

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                   +TP F     ++++ +LR       G  I+Y+G TG      V
Sbjct: 514  -------ATP-FTDVTVDSVSKLLREHGYQSRGFEIMYNGHTGRKLVAQV 555



 Score = 85.5 bits (210), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 64/440 (14%), Positives = 129/440 (29%), Gaps = 33/440 (7%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S  +       N    +       +     +      V    +H      +   +     
Sbjct: 20  SQPIVDFMMQRNM-EVLEEYEPSRSPNATKIFVNGVWV---GIHRDPGFIVRTIQKLRRQ 75

Query: 579 -NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +IG   SL    R   +       R      V ++    S    E     Q    L++D
Sbjct: 76  GHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDN-DPSSPRRGELALQKQHIEKLEDD 134

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +E    R   + +L     +++IDA  ++ V I  +      +   +    G  +Q
Sbjct: 135 REIDDE--TQRYGWQGLLSDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGYEIQ 188

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           ++  P  + +             +   + I+   A I+   D  +    +          
Sbjct: 189 QELDPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRXTYXSAXXXXXX 248

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                                                         +L  G+N +VA M 
Sbjct: 249 XXXXXXXXXXXXXXXXXXXX---------XXXXXXXXXXXXXXXFRELPAGQNAIVAIMC 299

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    +    +   +   E        +   +    
Sbjct: 300 YSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGT 359

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S  + 
Sbjct: 360 YDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLR 412

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           S  +G V  V +       K
Sbjct: 413 STENGIVDQVMVTTNQEGLK 432



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/223 (14%), Positives = 57/223 (25%), Gaps = 19/223 (8%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 25  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPA-------ETSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 79  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPSSPRRGELALQKQHIEKLEDDREID 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            ET             V Y+ A EEE   I      L+    F       +EL   +   
Sbjct: 139 DETQRYGWQGLLSDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQELDPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             +          +  P  ++ I AS+IPF +++ S R     
Sbjct: 199 GAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPRXTYXS 241


>gi|297500389|gb|ADI43631.1| RNA polymerase beta subunit [Agrobacterium sp. LMG8750]
          Length = 178

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 141/179 (78%), Positives = 158/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+ SGAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARDSGAAIGARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMP +GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVAVGDILNKGDIIADGPSTDLGDLALGRNALVAFMPGNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +G
Sbjct: 120 ILMSERIVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALRNLDEAGIVYIG 178


>gi|115531811|ref|YP_784337.1| RNA polymerase subunit RPO132 [Crocodilepox virus]
 gi|115521164|gb|ABJ09038.1| RNA polymerase subunit RPO132 [Crocodilepox virus]
          Length = 1149

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 76/431 (17%), Positives = 147/431 (34%), Gaps = 73/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP--SGVSGTVVDVRIFNRHG 949
            D  +  + P+    ++   +  +  F      V    +     +   G V+      R G
Sbjct: 707  DNGIHLLFPERPVVLSKALETSKIAFNCFGHHVVIALMSYKGINQEDGIVIKREFVERGG 766

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D     I+ ++ Q+E+   + ++++  +    YS+L          +G           
Sbjct: 767  LD----IITAKKIQVEIPLENFNNQES-VKSTAYSKL--------DCNGLVRINSFLEHG 813

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESL-KVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++  +    Y +    ++  F +K+           
Sbjct: 814  DSIAKNISSRNLEDEFVTDNQISFDISEIYTEIYSSRVERVQANFTDKV----------- 862

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ I   +D+P+ +DG   DI++N   + 
Sbjct: 863  ----RVRALTIKERKPIMGDKFTSRTSQKGTVAYIEDEKDLPYDEDGISPDIIVNSTSIY 918

Query: 1129 SRMNVGQIFETHL--GWACVGLGKKIKSLI--NDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L   +A      + ++           DIS    F ++   +      
Sbjct: 919  SRKTISMLIEIILTAAYAAKPFNNRGQNRPVCFPSSNETDISTYLQFAKECYRSVRPDLS 978

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                +D +                                           LY+  T   
Sbjct: 979  DPALEDLAYCER--------------------------------------TLYEPETDRT 1000

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            +   V +G IY L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ A
Sbjct: 1001 YSAKVLMGPIYYLRLRHLTLDKATVRCRGKKTKLIRQANEGRKKGGGIKVGEMERDCLIA 1060

Query: 1305 YGAAYVLQEML 1315
            +GA   + E+L
Sbjct: 1061 HGATNTITEIL 1071


>gi|320172578|gb|ADW24172.1| RNA polymerase II second largest subunit [Boreostereum radiatum]
          Length = 316

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 93/292 (31%), Gaps = 21/292 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 28   DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAIMCYSGYNQEDSVITNQSAIDRG 87

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D  ++S   + E+ E   RD          +       I  G      
Sbjct: 88   LF-RSIYYRSYMDLEKKSGVQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVNGE 146

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D                +E  QR     +    T+    E    +++ 
Sbjct: 147  DIIIGKTAPIPPD---------------SEELGQRTRTHTRRDVSTALKSTESGIVDQVL 191

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 192  I-----TTNSEGQKFVKVRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 246

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            DI++NP  +PSRM +G + E  L      +G +  +          +S    
Sbjct: 247  DIIINPHAIPSRMTIGHLVEALLSKVATLIGNEGDATPFTDLTVESVSSFLR 298



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 76/207 (36%), Gaps = 17/207 (8%)

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDEVRRNDIIADGPSTD---LGDLALGRN 810
            S  + Y+    +++      N   R              +A   S +     +L  G+N
Sbjct: 1   QSPRNTYQSAMGKQAMGINLTNFLVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQN 60

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----I 865
            +VA M + GYN EDS++ ++  +   +F SI+   +  + + + +   E          
Sbjct: 61  AIVAIMCYSGYNQEDSVITNQSAIDRGLFRSIYYRSYMDLEKKSGVQQLEEFEKPTRDTT 120

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +++ G+I  G  VN  DI++GK  P         ++        +    R
Sbjct: 121 LRMKHGTYDKLEDDGLIAPGTGVNGEDIIIGKTAPIPPDSEELGQRT-------RTHTRR 173

Query: 926 DTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           D S  + S  SG V  V I       K
Sbjct: 174 DVSTALKSTESGIVDQVLITTNSEGQK 200


>gi|152938336|gb|ABS43108.1| RNA polymerase beta subunit [Providencia stuartii]
          Length = 167

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 104/167 (62%), Positives = 129/167 (77%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDGIVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN+ L EDGSF EEL+ CR  GE  L  R++++++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFIIAQANTVLAEDGSFVEELITCRNRGESSLFSRDQVEYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|212960917|gb|ACJ38678.1| RNA polymerase beta subunit [Corynebacterium tuscaniense]
          Length = 134

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/162 (35%), Positives = 81/162 (50%), Gaps = 36/162 (22%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G  +    +D K    +  L   L  V                      
Sbjct: 1    EVHLGWLAKA-GWTVN--PDDPKNAKLLETLPEHLYDVPAESLT---------------- 41

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLR--------MADLDESGQSILYDGLTGEPFDRPV 1249
                     +TPVFDGA  + I  +L            +D  G+++L+DG +GEPF  P+
Sbjct: 42   ---------ATPVFDGATNDEIAGLLANTLPYRDGDVMVDADGKTVLFDGRSGEPFKYPI 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            +VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   SVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 134


>gi|56406219|gb|AAV87493.1| RpoB [Bisgaard Taxon 45]
          Length = 171

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 101/170 (59%), Positives = 129/170 (75%), Gaps = 1/170 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
           T+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR
Sbjct: 121 TDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANR 170


>gi|113707357|gb|ABI36586.1| RNA polymerase II second largest subunit [Roccellographa cretacea]
          Length = 668

 Score =  175 bits (444), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 43/196 (21%), Positives = 63/196 (32%), Gaps = 54/196 (27%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  R VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++NP 
Sbjct: 527  TTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGVAPDLIINPH 586

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +  + E  L       G +  +          IS                   
Sbjct: 587  AIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS------------------ 628

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                   +L  A   + G  V                             +Y+G TG   
Sbjct: 629  -------ILESAGYQRRGFEV-----------------------------MYNGHTGRKL 652

Query: 1246 DRPVTVGYIYMLKLNH 1261
            +  + +G  Y  +L H
Sbjct: 653  NAQIFLGPTYYQRLRH 668



 Score =  114 bits (285), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 78/501 (15%), Positives = 158/501 (31%), Gaps = 66/501 (13%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +SQ+       S ++H RR +      + R     + R +H TH+G +CP+ET EG   
Sbjct: 56  GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPSETPEGQAC 111

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVT--NDVVYLSAMEEENRYIAQANSSLDEDG 638
           GLV +L+    V+     +  +  +         +     A      ++        +D 
Sbjct: 112 GLVKNLSLMCYVSVGSPHDVLFDFLISQGTELIEEYEPRRAPNATKVFVNGVWIGTHQDP 171

Query: 639 SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
           ++    +        I      + D  +   K        + P ++  +D  +V  G  +
Sbjct: 172 AYLTGQILGIRRNGTIPFEVSIVRDIREREFKIFTDAGRVMRPLYIVENDPRKVNYGSLV 231

Query: 697 QRQAVPLLKAEAPFVG-----------------------------------TGMESVVAK 721
             +       ++  V                                    + M  +   
Sbjct: 232 ITRGHTARLKKSLEVHNNEYSTEEDKAFWEYRFRDILSEGMVEFLDAEEEESAMIQMFPS 291

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSV---EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ 778
             G  I A       +        ++      ++ PS        ++ F   NQ+  +  
Sbjct: 292 DIGQDINAPVETDFSEPVRKNTRSKTTLHTHCEIHPSMILGICASIIPFPDHNQSPRLQY 351

Query: 779 RPLVKVGDEVRRNDIIADGPSTDL---------GDLALGRNMLVAFMPWHGYNFEDSMLI 829
           + L   G    ++ +++   S            G            +   GYN EDS+++
Sbjct: 352 QFLTSHGHN-GKHPLLSSKTSCHNTISAIYEFQGATCWSEYHRCYSVLXXGYNQEDSVIM 410

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +       EE  + +  +           +DE G +  
Sbjct: 411 NQSSIDRGLFRSLFYRSYIEQQQPVGFNALEEFEKPVKQMTMRTRPGTYDKLDEDGFVAP 470

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  D+++GK  P         E   R     K    RD S  + S  +G +  V +
Sbjct: 471 GVRVSGEDVIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIIDRVLL 526

Query: 945 FNRHGIDKNE-RSISVEREQI 964
               G    + R+ + +  QI
Sbjct: 527 TTTEGRRSVKIRTRTTKVPQI 547



 Score = 59.7 bits (143), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 53/350 (15%), Positives = 95/350 (27%), Gaps = 31/350 (8%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDD 427
           +  ++       V    ++ T  +  S+    + D  K   S  G  ++  R    +   
Sbjct: 12  RCVENNKEFNMDVAVKTNIITNGLRYSLATGNWGDQKKAAQSKAGVSQVLNRYTFASTLS 71

Query: 428 V--RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG---LLRM 482
              R          I     L N    +         +   + + L     +       +
Sbjct: 72  HLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPSETPEGQACGLVKNLSLMCYVSVGSPHDV 131

Query: 483 ERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                    +  I+   P+   NA  V      F     +   ++      +I   RR  
Sbjct: 132 LFDFLISQGTELIEEYEPRRAPNATKV------FVNGVWIGTHQDPAYLTGQILGIRRNG 185

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSE---------------GHNIGLVSSLT 587
            +                +       + P    E               GH   L  SL 
Sbjct: 186 TIPFEVSIVRDIREREFKIFTDAGRVMRPLYIVENDPRKVNYGSLVITRGHTARLKKSLE 245

Query: 588 SFARVNAYGFIETP---YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
                N Y   E       +  D      V +L A EEE+  I    S + +D +   E 
Sbjct: 246 VH--NNEYSTEEDKAFWEYRFRDILSEGMVEFLDAEEEESAMIQMFPSDIGQDINAPVET 303

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
            F     +            +  P  ++ I AS+IPF +++ S R+    
Sbjct: 304 DFSEPVRKNTRSKTTLHTHCEIHPSMILGICASIIPFPDHNQSPRLQYQF 353


>gi|313493504|gb|ADR57129.1| RNA polymerase beta subunit [Corynebacterium ulcerans]
          Length = 135

 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/163 (34%), Positives = 83/163 (50%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HL W     G KI       +   +   L++  E++                     
Sbjct: 1    LEVHLCWLAAA-GWKID-----PEDPANAELLKTLPEELYDVP----------------- 37

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L+DG +GEPF  P
Sbjct: 38   -----AGSLTATPVFDGATNEEVAGLLANSRPNRDGDVMVDENGKAQLFDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|291419548|gb|ADE05287.1| RNA polymerase II second largest subunit [Trypethelium nitidiusculum]
          Length = 329

 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/359 (15%), Positives = 106/359 (29%), Gaps = 40/359 (11%)

Query: 817  PWHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +       +M+  I   ++            ++       +G                 
Sbjct: 4    SYTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVMLTNFSSRM------- 56

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  ++ V             +       +   +  + AI      +  D+ +   S 
Sbjct: 57   ----DTMVNVLYYPQKPLATTHSMKYLNFQELPAGQNAIVAIACYSGYNQEDSVIMNQSS 112

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +    +F R   D+ +R   +    +E   +    + + L R  Y +L     I  
Sbjct: 113  IDRGLF-RSLFYRSYTDQEKR---IGSTVLEEFEKPMRSDTLRLKRGTYDKLDNDGIISP 168

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++ D+     R++          ++     +  Q          
Sbjct: 169  GVRVSGEDIIIGKTAPIAPDVEELGQRTKLHTKRDVSTPLRSTENGIVDQVVL------- 221

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                               L+ VKV     +  Q GDK A RHG KG +      EDMPF
Sbjct: 222  -------------TTNTEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPF 268

Query: 1112 LKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               G   D+++NP  +PSRM +  + E  L       G +  +         DIS +R 
Sbjct: 269  TSQGITPDLIINPHAIPSRMTIAHLVECLLSKLGSLTGNEGDATPFSPITVSDISMMRR 327


>gi|292606625|gb|ADE34129.1| RNA polymerase II second largest subunit [Dothideomycetes sp. TRN
            267]
          Length = 289

 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 60/367 (16%), Positives = 107/367 (29%), Gaps = 81/367 (22%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANVLYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +    +E   +    + + +    Y +L +   I  G      
Sbjct: 60   RSLFFRAYLDQEKR---IGMSVVENFEKPVRSDTLRMKGGSYEKLDDDGIISPGSRVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +  Q                 
Sbjct: 117  DIIIGKTAPMAPDQEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL-------------- 162

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV     +  Q GDK A RHG KG +      EDMPF  DG   
Sbjct: 163  ------TTNVEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCDGLVP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G++                           
Sbjct: 217  DIIINPHAIPSRMTIAHLIECLLSKVGALTGQEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       ++ +L      + G  I+Y+
Sbjct: 252  ----------------------------ATP-FTDVTITNVSEILEGHGFQKRGFEIMYN 282

Query: 1239 GLTGEPF 1245
            G TG+  
Sbjct: 283  GHTGKKL 289



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 64/171 (37%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +     + +D+ GII  G+ V+
Sbjct: 55  DRGLFRSLFFRAYLDQEKRIGMSVVENFEKPVRSDTLRMKGGSYEKLDDDGIISPGSRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 115 GEDIIIGKTAPMAPDQ----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 161


>gi|219564111|gb|ACL28239.1| RNA polymerase II second largest subunit [Hyaloscypha fuckelii]
          Length = 294

 Score =  175 bits (444), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 63/371 (16%), Positives = 112/371 (30%), Gaps = 81/371 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G     
Sbjct: 62   -RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E+   +++
Sbjct: 118  EDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF + G  
Sbjct: 163  LI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +                          
Sbjct: 218  PDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGD------------------------ 253

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  I+Y
Sbjct: 254  -----------------------------ATP-FTEVTVDSVSKLLRDHGYQSRGFEIMY 283

Query: 1238 DGLTGEPFDRP 1248
             G TG      
Sbjct: 284  HGHTGRKLMAR 294



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 57  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 117 GEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 166


>gi|294998783|gb|ADF58113.1| RNA polymerase II second largest subunit [Pleurotus ostreatus]
          Length = 243

 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 91/309 (29%), Gaps = 74/309 (23%)

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ R  +D  ++S   + E+ E  +RD          +       I  G   V     
Sbjct: 9    RSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGTGVVGEDII 68

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+     D      R++          ++     +  Q                    
Sbjct: 69   IGKTAPXPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------------- 111

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 112  ---TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDII 168

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L      +G +                              
Sbjct: 169  INPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------------- 200

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     E++++ LR       G  ++Y G T
Sbjct: 201  -------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEVMYHGHT 234

Query: 1242 GEPFDRPVT 1250
            G      V 
Sbjct: 235  GRKLQAQVY 243



 Score = 46.6 bits (109), Expect = 0.030,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             V   +F S++   +  + + + +   E        +   +       ++  G+I  G 
Sbjct: 1   SSVDRGLFRSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGT 60

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V   DI++GK  P         ++        +    RD S  + S  +G V  V I  
Sbjct: 61  GVVGEDIIIGKTAPXPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITT 113

Query: 947 RHGIDK 952
            H   K
Sbjct: 114 NHEGQK 119


>gi|152938316|gb|ABS43098.1| RNA polymerase beta subunit [Morganella morganii subsp. morganii]
          Length = 167

 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 101/167 (60%), Positives = 127/167 (76%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR V D  VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRLVRDDVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN+ LD+DG F +EL+ CR  GE  L  R+++ ++D S +QVVS+ ASLIPFLE
Sbjct: 61  NFIIAQANTVLDDDGHFVDELITCRNKGESSLFSRDQVQYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|269912638|emb|CAY86099.1| RNA polymerase beta subunit [Gluconobacter frateurii]
          Length = 184

 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 76/186 (40%), Positives = 106/186 (56%), Gaps = 27/186 (14%)

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------- 221
             SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL           
Sbjct: 1   HSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYIAQRDR 60

Query: 222 --------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
                         GMD +EILS FY  + +++ GD W  P        G K+ S LVD 
Sbjct: 61  KIAEGGDVEGLDIRGMDQDEILSYFYDMVPFTRMGDGWARPFEPE-AFRGQKLLSPLVDA 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           DTGE V E+  KLT+ +++ + EK  + + +    + G Y+A D+VN  TGEIY EAG+ 
Sbjct: 120 DTGEVVAEADAKLTARMVRKIAEK-TRVVQVGRLDVLGRYLAYDLVNEHTGEIYGEAGEE 178

Query: 328 IDEKSL 333
           + E  L
Sbjct: 179 LTEDRL 184


>gi|330785190|gb|AEC46401.1| RNA polymerase II second largest subunit [Arthothelium galapagoense]
          Length = 304

 Score =  175 bits (443), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 56/377 (14%), Positives = 102/377 (27%), Gaps = 76/377 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  I++ +   S   E+ E   + +         +       +  G      
Sbjct: 64   LF-RSLYYRTYIEQEQSVSSQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L+++      R            ++     +  Q                 
Sbjct: 123  DIIIGKTAPLAANAEERGARLSTHTKRDVSTPLRSTEAGIVDQVL--------------- 167

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VK+     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 168  ------LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLIP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L         +  +         ++S L          
Sbjct: 222  DIIINPHAIPSRMTIAHLIECLLSKVAATSAYEGDATPFTDVTVENVSELL--------- 272

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                 WKSG                            G  ++Y+
Sbjct: 273  ---------------------WKSG------------------------YQSRGFEVMYN 287

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 288  GHTGRKLVAQVFLGPTY 304



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 71/187 (37%), Gaps = 12/187 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARD-TKLGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +  +    EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQSVSSQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 121 GEDIIIGKTAPLAANAEERGARL----STHTKRDVSTPLRSTEAGIVDQVLLTSVDGKKN 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKIRTRT 183


>gi|330785246|gb|AEC46429.1| RNA polymerase II second largest subunit [Dendrographa latebrarum]
          Length = 294

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/370 (16%), Positives = 107/370 (28%), Gaps = 81/370 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 62   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 117

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 118  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 158

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 159  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 218

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 219  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 252

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 253  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 284

Query: 1240 LTGEPFDRPV 1249
             TG   +  V
Sbjct: 285  HTGRKLNAQV 294



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 114 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRT 179


>gi|119640581|gb|ABL85484.1| RNA polymerase II second largest subunit [Ingaderia gracillima]
          Length = 307

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 104/372 (27%), Gaps = 73/372 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   + ++ AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLNFSELPAGQNVIVAIACYSGYNQEDSIIMNQSAIDRGLF-RS 67

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
               R  I++ +       +  E   +                   +  G           
Sbjct: 68   FLYRTYIEQQKAVGFNSLDDFEKPNKATTMRTRPGTYEKLDYDGFVEPGIRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR+ +  K          E    +++      
Sbjct: 128  KTAPFQNPMADNA------------EGGQRHKQHTKRDVSAPLRSTEAGIVDRVL----- 170

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 171  -VTTTEGRRSVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDLIIN 229

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 230  PHAIPSRMTVAHLIECLLSKVSATQGLEGD------------------------------ 259

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+++L+ +     G  ++++G TG 
Sbjct: 260  -----------------------ATP-FTDVTVSEISNLLKGSGYQSRGLELMHNGHTGR 295

Query: 1244 PFDRPVTVGYIY 1255
              +  V +G  Y
Sbjct: 296  KLNAQVYLGPTY 307



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 67/196 (34%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                   +  +L  G+N++VA   + GYN ED
Sbjct: 2   RMDTMSNILYYPQKPL----------ATTRSMEYLNFSELPAGQNVIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +       +                  + +D  G
Sbjct: 52  SIIMNQSAIDRGLFRSFLYRTYIEQQKAVGFNSLDDFEKPNKATTMRTRPGTYEKLDYDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P  ++PM    +  +        DV        +G+   V+
Sbjct: 112 FVEPGIRVSGDDIIIGKTAPF-QNPMADNAEGGQRHKQHTKRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VTTTEGRRSVKVRTRA 186


>gi|38373346|gb|AAR19037.1| RpoB [Avibacterium volantium]
          Length = 173

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 101/173 (58%), Positives = 129/173 (74%), Gaps = 1/173 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDV  THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVQATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD++  
Sbjct: 61  IGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           FT+  V CR   GE  L   E+I ++D S +Q+VS+AA+LIPFLE+DD+NR L
Sbjct: 121 FTDTFVTCRGEHGESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRAL 173


>gi|168419314|gb|ACA23552.1| RNA polymerase II [Fusarium sp. NRRL 22387]
          Length = 291

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTMHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
                
Sbjct: 288  AQCF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TMHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|312204370|gb|ADQ47502.1| RNA polymerase II second largest subunit [Stictis confusa]
          Length = 723

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 57/351 (16%), Positives = 108/351 (30%), Gaps = 81/351 (23%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 451  MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVG 509

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    + + L    Y +L +   +  G           K+  +  D   
Sbjct: 510  M---SLVEQFEKPMRSDTLRLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPIPPDSEE 566

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                  ++K+          L+ V
Sbjct: 567  MGQRTKLHTKRDASTPLRSTESGI------------------VDKVLL--TTNAEGLKFV 606

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV     +  Q GDK+A RHG KG +      EDMPF  +G   DI++NP  +PSRM + 
Sbjct: 607  KVRTRTTKLPQIGDKLASRHGQKGTIGITYRMEDMPFSAEGVTPDIIINPHAIPSRMTIA 666

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 667  HLVECQLSKVSCLRGFEGD----------------------------------------- 685

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                        +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 686  ------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKL 723



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 39/164 (23%), Positives = 65/164 (39%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 448 TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKR 507

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  D   +     + +D+ GI+  G  V+  DI++GK  P    P   
Sbjct: 508 VGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPI---PPDS 564

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           EE   R     K    RD S  + S  SG V  V +       K
Sbjct: 565 EEMGQRT----KLHTKRDASTPLRSTESGIVDKVLLTTNAEGLK 604



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 77/239 (32%), Gaps = 22/239 (9%)

Query: 465 RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
              G ++ + +R    ++ + + +  +              + +  + + +     +   
Sbjct: 1   DLXGPLMASLFRNLFTKLNKDVYKYLQKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNW 60

Query: 522 ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                       +SQ+       S ++H RR +      + R     + R +H TH+G +
Sbjct: 61  GKQKKAMSAKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHCTHWGLV 116

Query: 570 CPAETSEGHNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           CPAET EG   GLV +L    +  V +       +    + +V  +   + +      ++
Sbjct: 117 CPAETPEGQACGLVKNLALMCYITVGSPSGPIVDFMVQRNMEVLEEYDPVRSPNATKVFV 176

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND 685
                 +  D S    ++        +      I D  D   K          P L  D
Sbjct: 177 NGVWVGVHRDPSHLVSVMQILRRKNILSYETSLIRDIRDREXKIXSDAGRVCRPXLVVD 235


>gi|151573501|gb|ABS17998.1| RNA polymerase II [Fusarium concolor]
          Length = 290

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 57/363 (15%), Positives = 103/363 (28%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEMFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPV 1249
              V
Sbjct: 288  AQV 290



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEMFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|41057537|ref|NP_958010.1| ORF101 RNA polymerase subunit RPO132 [Bovine papular stomatitis
            virus]
 gi|41018853|gb|AAR98458.1| ORF101 RNA polymerase subunit RPO132 [Bovine papular stomatitis
            virus]
          Length = 1161

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 78/435 (17%), Positives = 142/435 (32%), Gaps = 70/435 (16%)

Query: 886  AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             +V+ G  L+    P   S      K+    FG     V   S +  +   G ++  +  
Sbjct: 697  NKVDNGIHLMNAERPIVLSKALETSKIADNCFGNHV-TVALMSFKGMNQEDGIILKRQFA 755

Query: 946  NRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKS 1005
             R G+D              L  +    E  + + N   R+      +  V+G       
Sbjct: 756  ERGGLDI-------------LTCKKYQVEIPLENFNNRERVRSSAYSKIDVNGVVRLNAF 802

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
                  +             V D ++  ++ E     Y      ++    +K++      
Sbjct: 803  LEQGDAIARNVSSRTLDDDFVADNQISFDIAERYSDIYPARVERVQADLTDKVK------ 856

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                     V+     +R    GDK   R   KG V+ +    ++P+ +DG   D+++N 
Sbjct: 857  ---------VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDEDGITPDVIINS 907

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGS 1180
              + SR  +  + E  L  A              +        D      F  +      
Sbjct: 908  TSIFSRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALAH 967

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
               ++ D + +S +                                        +LYD  
Sbjct: 968  PDARLDDPEVESRIFCER------------------------------------VLYDPE 991

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            T EPF   +  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  
Sbjct: 992  TDEPFAARIFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERD 1051

Query: 1301 CIQAYGAAYVLQEML 1315
            C+ ++GAA+ + E+L
Sbjct: 1052 CMISHGAAFTVSEIL 1066


>gi|330785244|gb|AEC46428.1| RNA polymerase II second largest subunit [Dendrographa latebrarum]
          Length = 296

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/370 (16%), Positives = 107/370 (28%), Gaps = 81/370 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 4    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 63

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 64   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 120  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 160

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 161  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 220

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 221  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 254

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 255  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 286

Query: 1240 LTGEPFDRPV 1249
             TG   +  V
Sbjct: 287  HTGRKLNAQV 296



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 56  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 116 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 174

Query: 950 IDKNERS 956
           +    R+
Sbjct: 175 VKVRTRT 181


>gi|330785256|gb|AEC46434.1| RNA polymerase II second largest subunit [Lecanographa dialeuca]
          Length = 299

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/367 (15%), Positives = 103/367 (28%), Gaps = 73/367 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ ++      E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRTYIEQEQKVGFNSVEEFEKPTKQTTTRMRPGTYDKLDDDGFVAPGIRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K++ L+  +                E   R  E  K          E    +++ 
Sbjct: 123  DIIIGKTSPLAGPMQENA------------EGGARLKEHSKRDISAPLRSTEAGIVDQVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTDGKKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        ++P F     + I+S+L  +     G  ++Y+
Sbjct: 260  ----------------------------ASP-FTNVTVKDISSLLERSGYQSRGFEVMYN 290

Query: 1239 GLTGEPF 1245
            G TG   
Sbjct: 291  GHTGRKL 297



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 67/189 (35%), Gaps = 13/189 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +        +       +D+ G +  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKVGFNSVEEFEKPTKQTTTRMRPGTYDKLDDDGFVAPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK +P        E     A   E +       LR        +VD  +     
Sbjct: 121 GEDIIIGKTSPLAG--PMQENAEGGARLKEHSKRDISAPLR---STEAGIVDQVLVTTTD 175

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 176 GKKSVKVRT 184


>gi|264658149|emb|CBH32073.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  175 bits (443), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 48/95 (50%), Positives = 68/95 (71%), Gaps = 8/95 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 17   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 76

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQ 1292
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GGQ
Sbjct: 77   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQ 111


>gi|56694314|gb|AAW22897.1| RNA polymerase II second largest subunit [Ceratozamia miqueliana]
          Length = 552

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 77/490 (15%), Positives = 137/490 (27%), Gaps = 95/490 (19%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNML---VAFMPWHGYNFEDSMLI--SERM 833
            LV  G  + V   +      S  + DL   RN      + + +       S+++     +
Sbjct: 151  LVTKGFIEYVDTEEEETTMISMTISDLVNARNSPPTATSIVKYTHCEIHPSLILGVCASI 210

Query: 834  VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
            +            ++       +G          V+   L+      +  V        +
Sbjct: 211  IPFPDHNQSPRNTYQSAMGKQAMG--------IYVTNYQLRM---DTLAYVLYYXXKPLV 259

Query: 894  LVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
                +       +      + AI      +  D+ +   S          +F R   D+ 
Sbjct: 260  TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSXDRGFF-RSLFYRSYRDEE 318

Query: 954  ERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLI 1013
            +R  ++ +E+     R+                     G           K+T ++    
Sbjct: 319  KRMGTLVKEEFGRPNRENTTGMRHGSYXKLDDDGLAPPGTRVSGEDVIIGKTTPVTQ--- 375

Query: 1014 SEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV 1073
                          DE   +     K    TS    E    +++      D +     R 
Sbjct: 376  --------------DESGGQAARYTKRDQSTSLRHSESGMVDQVLLTTNADGL-----RF 416

Query: 1074 VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNV 1133
            VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +P RM +
Sbjct: 417  VKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYCQEDMPWTVEGITPDIIVNPHAIPXRMTI 476

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSV 1193
            GQ+ E  +G     +GK+  +         +IS         +                 
Sbjct: 477  GQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM----------- 525

Query: 1194 LRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGY 1253
                                                 +G +    G         + +G 
Sbjct: 526  ------------------------------------YNGHT----GR---RLSAMIFLGP 542

Query: 1254 IYMLKLNHMV 1263
             Y  +L HMV
Sbjct: 543  TYYQRLKHMV 552



 Score =  113 bits (282), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 71/487 (14%), Positives = 136/487 (27%), Gaps = 97/487 (19%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 2   EGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVG 61

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG----H 578
              +    +  +   RR   +  + GV R     E+R ++  +     P    E      
Sbjct: 62  IHRDPELLVKTLRQLRRQVDVNTEVGVVRDIRLSELR-LYTDYGRCSRPLFIVEDXRLLI 120

Query: 579 NIGLVSSLTSFAR-VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
               +  L    +        E   R   +      + Y+   EEE   I+   S L   
Sbjct: 121 KKPDIRRLQQRDQLPPPXPDDENTVRGWHELVTKGFIEYVDTEEEETTMISMTISDL--- 177

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                                 K    +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 178 --------VNARNSPPTATSIVKYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 229

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 230 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 250

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                                +PLV                      L  G N +VA   
Sbjct: 251 ----------------LYYXXKPLV----------TTRAMEHLHFRQLPAGINAIVAIAC 284

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEG 872
           + GYN EDS+++++       F S+    +    +      +E        +   +    
Sbjct: 285 YSGYNQEDSVIMNQSSXDRGFFRSLFYRSYRDEEKRMGTLVKEEFGRPNRENTTGMRHGS 344

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G+   G  V+  D+++GK TP  +           +         RD S  + 
Sbjct: 345 YXKLDDDGLAPPGTRVSGEDVIIGKTTPVTQDE---------SGGQAARYTKRDQSTSLR 395

Query: 933 SGVSGTV 939
              SG V
Sbjct: 396 HSESGMV 402


>gi|118201872|gb|ABK79750.1| RNA polymerase subunit B [Roseobacter denitrificans]
 gi|118201876|gb|ABK79751.1| RNA polymerase subunit B [Roseobacter litoralis]
          Length = 163

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV +  VT++V Y+SA EE    +AQAN+ LDEDG F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVENRMVTDEVQYMSATEEMRHTVAQANAQLDEDGRFKNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPSENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|294998774|gb|ADF58107.1| RNA polymerase II second largest subunit [Pleurotus nebrodensis]
          Length = 243

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 91/309 (29%), Gaps = 74/309 (23%)

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              ++ R  +D  ++S   + E+ E  +RD          +       I  G   V     
Sbjct: 9    RSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGTGVVGEDII 68

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  D      R++          ++     +  Q                    
Sbjct: 69   IGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTENGIVDQVLI----------------- 111

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      + VK+ V   R  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 112  ---TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDII 168

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +G + E  L      +G +                              
Sbjct: 169  INPHAIPSRMTIGHLVECLLSKVATLIGNEGD---------------------------- 200

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     E++++ LR       G   +Y G T
Sbjct: 201  -------------------------ATP-FTDLTVESVSAFLRQKGYQSRGLEXMYHGHT 234

Query: 1242 GEPFDRPVT 1250
            G      V 
Sbjct: 235  GRKLQAQVY 243



 Score = 46.6 bits (109), Expect = 0.032,   Method: Composition-based stats.
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGA 886
             V   +F S++   +  + + + +   E        +   +       ++  G+I  G 
Sbjct: 1   SSVDRGLFRSMYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHGTYDKLENDGLIAPGT 60

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V   DI++GK  P         ++        +    RD S  + S  +G V  V I  
Sbjct: 61  GVVGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTENGIVDQVLITT 113

Query: 947 RHGIDK 952
            H   K
Sbjct: 114 NHEGQK 119


>gi|119640565|gb|ABL85476.1| RNA polymerase II second largest subunit [Combea mollusca]
          Length = 307

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 56/375 (14%), Positives = 106/375 (28%), Gaps = 79/375 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFRSF 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            ++  +     E+   V    ++   +    + +      Y +L +   +  G        
Sbjct: 69   LYRTYI----EQQKVVGFNDLDEFEKPVKAQTMRTRPGTYEKLDDDGFVEPGVRVSGDDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +       Q  +   +   V   + S +                     
Sbjct: 125  IIGKTAPFQNAMQDNAEGGQRNEL-HKRRDVSAPLRSTEAGIVDRVL------------- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 171  ----VSNSEGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGVTYCQEDMPFTAEGLVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM V  + E  L       G +                             
Sbjct: 227  IINPHAIPSRMTVAHLIECLLSKVAATQGLEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+++L+ +     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSEISNLLKGSGYQSRGLELMHNGH 292

Query: 1241 TGEPFDRPVTVGYIY 1255
            TG      + +G  Y
Sbjct: 293  TGRKLMAQIYLGPTY 307



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 67/196 (34%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                   +  +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMSNILYYPQKPL----------ATTRSMEYLNFSELPAGQNAIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMAR-----DTKLGPEEITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S     +    +     D     + +            + +D+ G
Sbjct: 52  SIIMNQSAIDRGLFRSFLYRTYIEQQKVVGFNDLDEFEKPVKAQTMRTRPGTYEKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P   +     E   R     K  DV        +G+   V+
Sbjct: 112 FVEPGVRVSGDDIIIGKTAPFQNAMQDNAEGGQRNEL-HKRRDVSAPLRSTEAGIVDRVL 170

Query: 941 DVRIFNRHGIDKNERS 956
                 R  +    R+
Sbjct: 171 VSNSEGRRTVKVRTRA 186


>gi|56694294|gb|AAW22887.1| RNA polymerase II second largest subunit [Lycopodium annotinum]
          Length = 533

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 79/481 (16%), Positives = 131/481 (27%), Gaps = 86/481 (17%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN           +      I   ++    
Sbjct: 137  LVSKGFIEYVDTEEEETTMISMTISDLVNARNNPN----EAYSDTYTHCEIHPSLILGVC 192

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 193  GSIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 249

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S V        IF R   D+ ++  +
Sbjct: 250  EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSVDRGFF-RSIFYRSYRDEEKKQGT 308

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+ E   R+          +          G           K+T L  D       
Sbjct: 309  LVKEEFERPNRENTTGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPLPQD------- 361

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                              +   +Y         R        Q         LR VKV V
Sbjct: 362  ---------------ETGTQAQRYTKRDQSTCLRHSESGMIDQXVLTTNADGLRFVKVRV 406

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+ ++G   DI++NP  +PSRM +GQ+ E
Sbjct: 407  RSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGIXPDIIVNPHAIPSRMTIGQLIE 466

Query: 1139 THLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAE 1198
              +G     +GK+  +         +IS         +                      
Sbjct: 467  CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM---------------- 510

Query: 1199 QWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLK 1258
                                            +G +    G      +  + +G  Y  +
Sbjct: 511  -------------------------------YNGHT----GR---RLNAMIFIGPTYYQR 532

Query: 1259 L 1259
            L
Sbjct: 533  L 533



 Score =  100 bits (250), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 52/381 (13%), Positives = 107/381 (28%), Gaps = 31/381 (8%)

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            E     +  S   F      G    P   V   +     V ++      R I      L
Sbjct: 36  EEISPAVIPQSTKIFVNGCWVGIHRNPEHLVNTLRQLRRQVDVNTEVGVXRDIRLKELRL 95

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS---IAASLIPFLENDDSNRVL 691
             D       +F       ++              +      ++   I +++ ++    +
Sbjct: 96  YTDYGRCSRPLFIVEKQRLLIKKSHIRALQQKESPEGGWFELVSKGFIEYVDTEEEETTM 155

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           +   +             +  T       +   + I+     I+   D  +    + +  
Sbjct: 156 ISMTISDLVNARNNPNEAYSDT---YTHCEIHPSLILGVCGSIIPFPDHNQSPRNTYQSA 212

Query: 752 LDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +     G+      ++           Q+PLV                      L  G N
Sbjct: 213 MGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGIN 262

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDI 865
            +VA   + GYN EDS+++++  V    F SI    +    +      +E        + 
Sbjct: 263 AVVAIACYSGYNQEDSVIMNQSSVDRGFFRSIFYRSYRDEEKKQGTLVKEEFERPNRENT 322

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G+   G  V+  D+++GK TP  +                +    R
Sbjct: 323 TGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPLPQDE---------TGTQAQRYTKR 373

Query: 926 DTSLRVPSGVSGTVVDVRIFN 946
           D S  +    SG +    +  
Sbjct: 374 DQSTCLRHSESGMIDQXVLTT 394


>gi|151573161|gb|ABS17772.1| RNA polymerase II [Fusarium sp. NRRL 43521]
 gi|151573182|gb|ABS17786.1| RNA polymerase II [Fusarium sacchari]
 gi|151573399|gb|ABS17930.1| RNA polymerase II [Fusarium sp. NRRL 43730]
 gi|151573408|gb|ABS17936.1| RNA polymerase II [Fusarium sp. NRRL 43733]
 gi|151573420|gb|ABS17944.1| RNA polymerase II [Fusarium sp. NRRL 43807]
 gi|151573459|gb|ABS17970.1| RNA polymerase II [Fusarium sp. NRRL 43821]
 gi|151573462|gb|ABS17972.1| RNA polymerase II [Fusarium sp. NRRL 43822]
 gi|151573549|gb|ABS18030.1| RNA polymerase II [Gibberella fujikuroi]
 gi|151573594|gb|ABS18059.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573720|gb|ABS18143.1| RNA polymerase II [Gibberella moniliformis]
          Length = 290

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 57/363 (15%), Positives = 103/363 (28%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RPV 1249
              V
Sbjct: 288  AQV 290



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|330785184|gb|AEC46398.1| RNA polymerase II second largest subunit [Sparria endlicheri]
          Length = 303

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 58/372 (15%), Positives = 99/372 (26%), Gaps = 73/372 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     F R  I+K++       E+ E   +                   +  G      
Sbjct: 64   LF-RSFFYRTYIEKSKAVGFNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRISGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+   +  +                E  QR     +          E    +++ 
Sbjct: 123  DIIIGKTAPFAEPMAENA------------EGGQRTKSHARRDISAPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------LTSVEGNRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +                           
Sbjct: 225  DLIINPHAIPSRMTVAHLIECLLSKLSATQGLEGD------------------------- 259

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I++ L+       G  ++++
Sbjct: 260  ----------------------------ATP-FTDVTVSIISNELKALGYQSRGLEVMHN 290

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 291  GHTGRKLMAQVF 302



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 77/196 (39%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +   ++     G EE  +              + +D+ G +  G  ++
Sbjct: 61  DRGLFRSFFYRTYIEKSKAVGFNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRIS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  E      E   R     K+   RD S  + S  +G +  V + +  G
Sbjct: 121 GDDIIIGKTAPFAEPMAENAEGGQRT----KSHARRDISAPLRSTEAGIIDRVLLTSVEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 NRSVKVRTRTTKVPQI 192


>gi|255348256|gb|ACU09429.1| RNA polymerase beta subunit [Mycobacterium tuberculosis H37Rv]
          Length = 114

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 47/117 (40%), Positives = 73/117 (62%), Gaps = 16/117 (13%)

Query: 83  PPKFD-----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPL 137
            P+FD     VD+C  +D+TYA PL +T   I           +  +IK Q+++MGD P+
Sbjct: 3   RPRFDEGQAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIKSQTVFMGDFPM 53

Query: 138 MTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           MT+ GTF+I G +R+VVSQL RSPG++FD    +   + KLL++ ++IP +G W++ 
Sbjct: 54  MTEKGTFIINGTERVVVSQLVRSPGVYFDETIDK--STEKLLHSVKVIPSRGAWLEF 108


>gi|151573569|gb|ABS18043.1| RNA polymerase II [Fusarium sp. NRRL 28011]
          Length = 288

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 56/363 (15%), Positives = 101/363 (27%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 1    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 59

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 60   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 119

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 120  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 162  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 219

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 220  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 246

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 247  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 285

Query: 1247 RPV 1249
              V
Sbjct: 286  AQV 288



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 34/164 (20%), Positives = 60/164 (36%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 9   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 68

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E+           +       +DE GI+  G  V+  DI++GK  P  +     
Sbjct: 69  VGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDL 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +             RD S  + S  +G V  V +       K
Sbjct: 129 GTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNADNVK 165


>gi|220172200|gb|ACL79864.1| RNA polymerase beta subunit [Corynebacterium ulcerans BR-AD22]
          Length = 148

 Score =  174 bits (442), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 60/166 (36%), Positives = 80/166 (48%), Gaps = 23/166 (13%)

Query: 1134 GQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG---TGSHTEKISDYDD 1190
            GQ+ E HLGW     G KI     D      +  L   L  V G   +            
Sbjct: 1    GQVLEVHLGWLAAA-GWKID--PEDPANAELLKTLPEELYDVPGWFCSPLTPSVRQALPT 57

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
              +L      +S    +T            S         + +  L+DG +GEPF  PV+
Sbjct: 58   RKLLVFVANSRSKSATAT------------SWWTK-----TARHSLFDGRSGEPFPYPVS 100

Query: 1251 VGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGE 1296
            VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GGQR GE
Sbjct: 101  VGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 146


>gi|300394730|gb|ADK11903.1| DNA-directed RNA polymerase II subunit two [Pisolithus arhizus]
          Length = 321

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 55/352 (15%), Positives = 103/352 (29%), Gaps = 34/352 (9%)

Query: 818  WHGYNFEDSML--ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
            W       SM+  +   ++            ++       +G       +          
Sbjct: 1    WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLVRM-------- 52

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
                 +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 53   ---DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSI 109

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D  ++S   + E+ E   R+          +       I  G  A
Sbjct: 110  DRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLIAPGIRA 168

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
            +       K+  +  D      R++          ++     +  Q              
Sbjct: 169  LGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIVDQVLI----------- 217

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VKV V   R  Q GDK A RHG KG +      +DMPF  +G
Sbjct: 218  ---------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIGITYRQDDMPFTAEG 268

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
               D+++NP  +PSRM +G + E  L      LG +  +          +S 
Sbjct: 269  ITPDLIINPHAIPSRMTIGHLVECLLSKVATLLGNEGDATPFTELTVESVST 320



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/297 (15%), Positives = 91/297 (30%), Gaps = 77/297 (25%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
               +  P  ++ + AS+IPF +++ S R      M +QA+ +                 
Sbjct: 1   WTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNFLV---------- 50

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP 780
                                             + + +  Y       +     +  R 
Sbjct: 51  -------------------------------RMDTMANILYYPQKPLATTRSMEYLKFR- 78

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
                                  +L  G+N +VA M + GYN EDS+++++  +   +F 
Sbjct: 79  -----------------------ELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFR 115

Query: 841 SIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           SI+   +  + + + +   E            +       +++ G+I  G      DI++
Sbjct: 116 SIYYRSYMDLEKKSGIQQLEEFEKPTRETTLRMKHGTYDKLEDDGLIAPGIRALGEDIII 175

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P         ++        +    RD S  + S  SG V  V I       K
Sbjct: 176 GKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTESGIVDQVLITTNSEGQK 225


>gi|198279495|emb|CAP04782.1| RNA polymerase beta subunit [Equisetum sylvaticum]
          Length = 268

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 118/251 (47%), Positives = 169/251 (67%), Gaps = 9/251 (3%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL K E   VGTG+E   A  SG+ + ++R G +  +D+ +I +   E      
Sbjct: 1   MQRQAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDSEKITLFVDEETSINK 60

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+
Sbjct: 61  -------NLLSYERSNNNTCMNQKPLLYKDKFLRQGQIIADGASTVGGELALGRNILVAY 113

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER++ ED+FTS HIE +E+    T LGPE++TR+IP+++   L++
Sbjct: 114 MPWEGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSLGPEKLTREIPHLNNHILRH 173

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPS 933
           +DE G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP 
Sbjct: 174 LDENGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPV 233

Query: 934 GVSGTVVDVRI 944
           GV G V+D+R 
Sbjct: 234 GVKGRVIDIRW 244


>gi|193201475|gb|ACF15945.1| RNA polymerase II subunit [Cryptothecia candida]
          Length = 302

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 54/367 (14%), Positives = 102/367 (27%), Gaps = 84/367 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    YILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 68   LYYRTYIEQEQTVGVQILEEFEKPIKSQTLRMRNGTYDKLDDDGIVAPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L++++     R            ++     +  Q                      
Sbjct: 128  KTAPLAANVEERGARLSTHTKRDVSTPLRSTEAGIIDQVL-------------------- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMP   +G   DI++N
Sbjct: 168  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPLTAEGLVPDIIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVAATSAYEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +LR +   + G  ++Y G TG 
Sbjct: 257  -----------------------ATP-FTDVTVENVSELLRKSGYQQRGFEVMYSGHTGR 292

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 293  KLVAQVF 299



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 69/184 (37%), Gaps = 16/184 (8%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMAYILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQTVGVQILEEFEKPIKSQTLRMRNGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L            RD S  + S     ++D  +     
Sbjct: 121 GDDIIIGKTAPLAANVEERGARL-------STHTKRDVSTPLRS-TEAGIIDQVLLTSVD 172

Query: 950 IDKN 953
             KN
Sbjct: 173 GKKN 176


>gi|77745521|gb|ABB02658.1| RNA polymerase beta subunit [Bartonella bacilliformis]
          Length = 166

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 115/164 (70%), Positives = 133/164 (81%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL +FARV+ YGFIE+PYRK+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE
Sbjct: 61  NSLATFARVDKYGFIESPYRKITDGKVTTEVVYLSAMEEAKHYVAQANSSLDSEGRFTEE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            V CR AGE ++VPR+ ID +D SPKQ+VS+AASLIPFLENDD 
Sbjct: 121 FVVCRHAGEVLMVPRDHIDLMDVSPKQLVSVAASLIPFLENDDG 164


>gi|198279381|emb|CAP04725.1| RNA polymerase beta subunit [Pinus ayacahuite]
          Length = 285

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 106/257 (41%), Positives = 157/257 (61%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL + E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGK 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+ GRHGNKGI+S ILP
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVPGRHGNKGIISIILP 285


>gi|307547559|gb|ADN44393.1| RNA polymerase II second largest subunit [Roccella applanata]
          Length = 298

 Score =  174 bits (442), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 60/369 (16%), Positives = 106/369 (28%), Gaps = 79/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 65

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 66   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 121

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 122  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 168  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 223

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 224  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 256

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ A     G  ++++G 
Sbjct: 257  --------------------------ATP-FTDVTVSNISELLKFAGYQSRGFEMMHNGH 289

Query: 1241 TGEPFDRPV 1249
            TG   +  V
Sbjct: 290  TGRKLNAQV 298



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 72/196 (36%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 118 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 173

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 174 KRSVKVRTRTTKVPQI 189


>gi|193201497|gb|ACF15956.1| RNA polymerase II subunit [Opegrapha bicolor]
          Length = 294

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 56/370 (15%), Positives = 106/370 (28%), Gaps = 79/370 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +N++ I       E   +      + +  N Y +L +   +  G        
Sbjct: 61   FYRTYNESENDKGI----NNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVSGDDV 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+  +                E   R     +          E    +K+   
Sbjct: 117  IIGKTEALAEPM------------RQGAEGGARLPTHERRDCSAPLRSTEAGIIDKVV-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----VTLSESKKSVKVRTRTTKVPQVGDKFASRHGQKGTIGITYRQEDMPFTSEGLTPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 219  IINPHAIPSRMTIAHLIECLLSKVAAVXGMEGD--------------------------- 251

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+ +L+ +   + G  ++Y+G 
Sbjct: 252  --------------------------ATP-FTPVTVQDISDLLQNSGYQKRGFEVMYNGH 284

Query: 1241 TGEPFDRPVT 1250
            TG+     + 
Sbjct: 285  TGQKLRAQMF 294



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 66/189 (34%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +     D  +   E           ++       +D+ G +  G  V+
Sbjct: 53  DRGLFRSLFYRTYNESENDKGINNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK     E      E   R        + RD S  + S     ++D  +     
Sbjct: 113 GDDVIIGKTEALAEPMRQGAEGGARLP----THERRDCSAPLRS-TEAGIIDKVVVTLSE 167

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 168 SKKSVKVRT 176


>gi|118426172|gb|ABK90985.1| RpoB [Mycoplasma cottewii]
          Length = 208

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 114/215 (53%), Positives = 156/215 (72%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   ++ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMARIDEIDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+PFVGTG+E   A+ SG A+VAK  GIV+ VD+  I I+          SG+  Y L 
Sbjct: 61  PESPFVGTGIEFEAARDSGEAVVAKEDGIVKYVDSKMISIQ--------GQSGIKTYTLS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSN  T + Q P+VK GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DFERSNNGTSLTQAPIVKKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERVVMDDRFTSIHIDEYTIEVRNTKQGLEE 207


>gi|169836340|ref|ZP_02869528.1| DNA-directed RNA polymerase beta chain [candidate division TM7
            single-cell isolate TM7a]
          Length = 178

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 56/112 (50%), Positives = 79/112 (70%)

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
            + GDD+  GV +++++++A KR I  GDKM+GRHGNKG++SR+LP EDMP L+DGTP+D+
Sbjct: 37   ENGDDLKAGVNKLIRIYIAEKRKIMVGDKMSGRHGNKGVISRVLPIEDMPHLEDGTPIDV 96

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             LNPLGVPSRMN+GQ+ E HLG A   + K I + + D  +  D+       
Sbjct: 97   CLNPLGVPSRMNIGQVLEVHLGLAIGDIDKYIATPVFDGASEDDVKNYLEEA 148


>gi|56406199|gb|AAV87483.1| RpoB [Pasteurella multocida subsp. multocida]
          Length = 169

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 99/169 (58%), Positives = 127/169 (75%), Gaps = 1/169 (0%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+ 
Sbjct: 61  NSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDA 120

Query: 644 LVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 169


>gi|168419320|gb|ACA23556.1| RNA polymerase II [Fusarium sp. NRRL 22395]
          Length = 291

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
                
Sbjct: 288  AQCF 291



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|190694716|gb|ACE88923.1| RpoB [Streptococcus pyogenes]
          Length = 189

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 104/189 (55%), Positives = 136/189 (71%), Gaps = 2/189 (1%)

Query: 484 RSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSA 543
           R+++ER+S  D D + PQ +IN +PV +AV EFF SSQLSQ  +  N LS +++ RRLSA
Sbjct: 1   RNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPLSELSNKRRLSA 60

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+++L+SF  +N YGFI+TPYR
Sbjct: 61  LGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHLNKYGFIQTPYR 120

Query: 604 KVCD--GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV    G VTN++V+L+A EE+   +AQANS L+EDG+F EE+V  R  G         +
Sbjct: 121 KVDRATGTVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGRHQGNNQEFSASVV 180

Query: 662 DFIDASPKQ 670
           DF+D SPKQ
Sbjct: 181 DFVDVSPKQ 189


>gi|299849863|gb|ADJ57179.1| RNA polymerase II second largest subunit [Scytalidium cuboideum]
          Length = 323

 Score =  174 bits (441), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 66/388 (17%), Positives = 111/388 (28%), Gaps = 81/388 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKXLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +P RM +  + E  L       G +             +S L       
Sbjct: 228  IVPDLIINPHAIPXRMTIAHLIECQLSKVSTLRGLEGDXTPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               G         V  G  Y  +L HMV
Sbjct: 300  ---GR---KLKAQVFFGPTYYQRLRHMV 321



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKXLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|198279319|emb|CAP04695.1| RNA polymerase beta subunit [Pinus koraiensis]
          Length = 281

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 103/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPJ + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 2   VPJFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTV 53

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 54  RTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 114 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 173

Query: 881 IICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G 
Sbjct: 174 LVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGR 233

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 234 VIDVRWINRVDDSGD 248



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/221 (23%), Positives = 85/221 (38%), Gaps = 14/221 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 75   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 133

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 134  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 187

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 188  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 245

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S 
Sbjct: 246  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISI 281


>gi|215400978|gb|ACJ66347.1| RNA polymerase beta subunit [Corynebacterium sp. 2396]
          Length = 137

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/163 (36%), Positives = 81/163 (49%), Gaps = 34/163 (20%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G K+ +   D K    +  L S L  V                     
Sbjct: 1    LEVHLGWLAKA-GWKVDTDSEDPKIQKMLETLPSELYDVPADSLT--------------- 44

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                      +TPVFDGA    ++ +LR +  +  G        ++ L DG +GEPF  P
Sbjct: 45   ----------ATPVFDGASNAELSGLLRSSLPNRDGIRLVDDFGKAQLMDGRSGEPFPYP 94

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V VGY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 95   VAVGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 137


>gi|198279489|emb|CAP04859.1| RNA polymerase beta subunit [Equisetum variegatum]
          Length = 274

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 166/251 (66%), Gaps = 9/251 (3%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL KAE   VGTG+E  +A  SG+ + ++R G V  +D+ RI +   E      
Sbjct: 1   MQRQAVPLSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDSERITLFVDEETSINK 60

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L+ ++RSN NTC+NQ+PLV     +R+  +IADG ST  G+LALG+N+LVA+
Sbjct: 61  -------NLLSYERSNNNTCMNQKPLVSKDQFLRQGQVIADGASTVGGELALGKNILVAY 113

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L++
Sbjct: 114 MPWEGYNFEDATLISERLIYEDIFTSFHIERHEINVAFTGQGPEKLTREIPHLNNHILRH 173

Query: 876 IDECGIICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           + E G++ +G+ V  GD+LVGK+TP    E+   PE KLL+AIFG    + R+T L+VP 
Sbjct: 174 LGENGLVKLGSWVEAGDVLVGKLTPLEYLETLGAPEGKLLQAIFGTDVTNARETCLKVPV 233

Query: 934 GVSGTVVDVRI 944
           G  G V+D++ 
Sbjct: 234 GFKGRVIDIKW 244


>gi|229258312|gb|ACQ45458.1| RpoB [Corynebacterium macginleyi]
          Length = 134

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 54/162 (33%), Positives = 84/162 (51%), Gaps = 36/162 (22%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G K+ +     +   +   L++  E++    + +               
Sbjct: 1    ELHLGWLAHA-GWKVDT-----EDPANAELLKTLPEELYDVPADSLT------------- 41

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPV 1249
                     +TPVFDGA    I  +L  +  +  G        ++ L+DG +GEP+  P+
Sbjct: 42   ---------ATPVFDGATNHEIERLLASSRPNRDGDVLVDEHGKATLFDGRSGEPYKYPI 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            +VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   SVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 134


>gi|118201858|gb|ABK79742.1| RNA polymerase subunit B [Oceanicola batsensis]
          Length = 163

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 129/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR+V +G+VT++V Y+SA EE    +AQAN++LDE+G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRRVENGQVTDEVKYMSATEEMRHTVAQANANLDENGKFVNDLVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +GE  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGEYTLAPNETVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|298529417|ref|ZP_07016820.1| RNA polymerase Rpb2 domain 6 [Desulfonatronospira thiodismutans
            ASO3-1]
 gi|298510853|gb|EFI34756.1| RNA polymerase Rpb2 domain 6 [Desulfonatronospira thiodismutans
            ASO3-1]
          Length = 1518

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 135/326 (41%), Gaps = 77/326 (23%)

Query: 1006 TVLSSDLISEYPRSQWWQFAVQDEK---VQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             V S D+++ +   +W   +   ++   V    E L V+          RF+  +  ++ 
Sbjct: 433  EVKSGDVLAAFYPVRWNHDSRSKKRQIVVNTLAEPLLVRVPDHVQGKLVRFE--VVCLET 490

Query: 1063 GD-DMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG----- 1115
             D  +P  + R+ V + +   RP++ GDK+ GRHGNKG++SRILP  +MP+  D      
Sbjct: 491  SDLPLPRHITRMAVHMEIEESRPLEPGDKIMGRHGNKGVISRILPDREMPYFLDSMHGIT 550

Query: 1116 ---------------TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYK 1160
                           T V+++LNPLGV  RMN GQ+ E H G A   + ++++   N   
Sbjct: 551  DLRSSSHFHGEEQAHTHVEVILNPLGVIGRMNTGQLLECHTGLAMRCIPERMEFYQNSGM 610

Query: 1161 ANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN 1220
                +         +             D+    R+  + ++G  V T            
Sbjct: 611  PFSSV--------DIESLRQDLLSTKIVDETGKARLFWRDEAGNHVQT------------ 650

Query: 1221 SMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTG---SYSL 1277
                       G + +              +G  Y++KL+HM  DK +    G      +
Sbjct: 651  -----------GHASM--------------IGVQYLMKLDHMARDKFHV--CGKKPPRCM 683

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            +T QP+ G+S  GG RLGEME WCI 
Sbjct: 684  ITNQPVKGRSRGGGLRLGEMENWCII 709



 Score = 43.5 bits (101), Expect = 0.24,   Method: Composition-based stats.
 Identities = 51/279 (18%), Positives = 96/279 (34%), Gaps = 40/279 (14%)

Query: 623 ENRYIAQANSSLDE--DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           ++  +A   + L E   G               I    E  +  +  P+    I     P
Sbjct: 199 DHFPLADTTNKLAETAQGRQVSAKSLRCHRKTMIGSKPED-NVRNLLPEHTGMICPVETP 257

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                +S  + +  ++ R+A P L ++        E+      G          +     
Sbjct: 258 -----ESESIGLVMHLARKARPELWSQDAA---FNENDQRSEEGILKTPDPDNFLGYSAC 309

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ--RPLVKVGDEVRRNDIIADGP 798
           +   I+  +       +          +   Q   + Q   PL++ G      ++   G 
Sbjct: 310 MVPYIQHTDPTRAMMGA----------KNMKQALSLTQGEAPLIRTG---HEEEVFGRGE 356

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                D+ +GRN+LVA++PW+G+N+ED ++IS     + +    H           K GP
Sbjct: 357 --HDLDMDIGRNLLVAYLPWYGFNYEDGIVISRSAAEKFLSVKKH-----------KFGP 403

Query: 859 EEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
                +  P   +   + +D  G+   G EV  GD+L  
Sbjct: 404 YFCPGNYRPANPDSKWRKLDRDGLAPQGQEVKSGDVLAA 442


>gi|118426174|gb|ABK90986.1| RpoB [Mycoplasma yeatsii]
          Length = 208

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 114/215 (53%), Positives = 156/215 (72%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   ++ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMARIDEIDYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+PFVGTG+E   A+ SG A+VAK  GIV+ VD+  I I+          SG+  Y L 
Sbjct: 61  PESPFVGTGIEFEAARDSGEAVVAKEDGIVKYVDSKMISIQ--------GESGIKTYTLS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSN  T + Q P+VK GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DFERSNNGTSLTQAPIVKKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERVVMDDRFTSIHIDEYTIEVRNTKQGLEE 207


>gi|258590817|emb|CBE67086.1| RNA polymerase beta subunit [Arcanobacterium hippocoleae]
          Length = 135

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 51/107 (47%), Positives = 69/107 (64%), Gaps = 8/107 (7%)

Query: 1193 VLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEP 1244
            +   A +      V+TPVFDG   + +N +L     +  G        ++ L+DG TGEP
Sbjct: 29   LPENAVKTDGRQNVATPVFDGVLSDELNGLLGCTLPNRDGDHMVNGAGKARLFDGRTGEP 88

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            F  PV+VGY+YMLKL+H+V DK++ARSTG YS+VTQQPLGGK+  GG
Sbjct: 89   FPEPVSVGYMYMLKLHHLVDDKIHARSTGPYSMVTQQPLGGKAQFGG 135


>gi|219564053|gb|ACL28210.1| RNA polymerase II second largest subunit [fungal sp. M179]
          Length = 287

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/357 (16%), Positives = 105/357 (29%), Gaps = 81/357 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 9    YPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 67

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 68   RAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIG 124

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D      ++           ++     +  Q                      
Sbjct: 125  KTAPIAADAQEMGQKTSLHTKRDVSTPLRSTENGIVDQ--------------------VL 164

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF +DG   D+V+N
Sbjct: 165  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRDGLTPDLVIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G++                                
Sbjct: 225  PHAIPSRMTIAHLVECLLSKVGAITGREGD------------------------------ 254

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                   +TP F     + I+ +L  A   + G  I+Y+G 
Sbjct: 255  -----------------------ATP-FTDVTVDQISELLEEAGYQKRGLEIMYNGH 287



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 63/184 (34%), Gaps = 22/184 (11%)

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
           +         Q+PL                      +L  G+N +VA   + GYN EDS+
Sbjct: 1   ETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSV 50

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGII 882
           ++++  +   +F S+    +    +   +   E        D   +       +D+ G++
Sbjct: 51  IMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVV 110

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             G  V+  DI++GK  P         +K             RD S  + S  +G V  V
Sbjct: 111 APGVRVSGDDIIIGKTAPIAADAQEMGQKT-------SLHTKRDVSTPLRSTENGIVDQV 163

Query: 943 RIFN 946
               
Sbjct: 164 LFTT 167


>gi|193201473|gb|ACF15944.1| RNA polymerase II subunit [Chiodecton natalense]
          Length = 282

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/354 (16%), Positives = 100/354 (28%), Gaps = 79/354 (22%)

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     +  +     E
Sbjct: 4    THSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----E 59

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPKGFKKSTVLSSD 1011
            +  SV    +E   +    + +      Y +L     +  G           K+    + 
Sbjct: 60   QQQSVGFNSLEEFEKPLRSQTMRTRPGTYEKLDVDGFVPPGVRVSGEDIIIGKTAPFQAP 119

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +                E  QR  +  K          E    +++              
Sbjct: 120  M------------QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL------LTTTEGK 161

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM
Sbjct: 162  RSVKVRTRTIKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGIVPDLIINPHAIPSRM 221

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +  + E  L       G +                                        
Sbjct: 222  TIAHLIECLLSKVSSITGHEGD-------------------------------------- 243

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                           +TP F       I+ +L+ A     G  ++Y+G TG   
Sbjct: 244  ---------------ATP-FTDITVSDISELLQFAGYQRRGFELMYNGHTGRKL 281



 Score = 75.9 bits (185), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 65/177 (36%), Gaps = 10/177 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 4   THSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQS 63

Query: 854 TKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 E                  + +D  G +  G  V+  DI++GK  P        
Sbjct: 64  VGFNSLEEFEKPLRSQTMRTRPGTYEKLDVDGFVPPGVRVSGEDIIIGKTAPFQAPMQEN 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQI 964
            E   R     K    RD S  + S  +G +  V +    G    + R+ +++  QI
Sbjct: 124 SEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRTIKVPQI 176


>gi|308387849|pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
           Transcription-Repair Coupling Factor Rna Polymerase
           Interacting Domain With The Thermus Aquaticus Rna
           Polymerase Beta1 Domain
 gi|308387850|pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
           Transcription-Repair Coupling Factor Rna Polymerase
           Interacting Domain With The Thermus Aquaticus Rna
           Polymerase Beta1 Domain
 gi|308387851|pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
           Transcription-Repair Coupling Factor Rna Polymerase
           Interacting Domain With The Thermus Aquaticus Rna
           Polymerase Beta1 Domain
 gi|308387852|pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
           Transcription-Repair Coupling Factor Rna Polymerase
           Interacting Domain With The Thermus Aquaticus Rna
           Polymerase Beta1 Domain
          Length = 188

 Score =  174 bits (441), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 55/134 (41%), Positives = 76/134 (56%), Gaps = 13/134 (9%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS---GAAMLEFVSYEFD 82
           +P L E+Q  SY   L  ++ P++R N G+QAAFK  FPI       G  +L+F+ Y   
Sbjct: 1   MP-LTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIG 59

Query: 83  PPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDG 142
            P F  D+C  +DLTY  PL   L+LI  D            IKE  +++G LPLMT+DG
Sbjct: 60  DPPFSQDECREKDLTYQAPLYARLQLIHKD---------TGLIKEDEVFLGHLPLMTEDG 110

Query: 143 TFVIKGIQRIVVSQ 156
           +F+I G  R++VSQ
Sbjct: 111 SFIINGADRVIVSQ 124



 Score = 48.5 bits (114), Expect = 0.008,   Method: Composition-based stats.
 Identities = 46/201 (22%), Positives = 89/201 (44%), Gaps = 15/201 (7%)

Query: 326 DVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGD 385
             + E  +E    +   D+P    ++V   A  + T   ++    K  L+  +   R GD
Sbjct: 1   MPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGD 60

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVD 445
                      +        Y      R+++  +           + KED + +  + + 
Sbjct: 61  PPFSQ------DECREKDLTYQAPLYARLQLIHK--------DTGLIKEDEVFLGHLPLM 106

Query: 446 LRNGKGTIDDIDNLGNRRV-RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
             +G   I+  D +   +  R+VGE++ +Q+R+GL R+ R ++ER+     D++ P  L+
Sbjct: 107 TEDGSFIINGADRVIVSQGGRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKLV 166

Query: 505 NAKPVVSAVCEFFCSSQLSQL 525
           N++P+ +A+ EFF  SQLSQ 
Sbjct: 167 NSRPLEAALREFFSRSQLSQF 187


>gi|307547635|gb|ADN44431.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 298

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/369 (16%), Positives = 106/369 (28%), Gaps = 79/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 65

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 66   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 121

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 122  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 168  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 223

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 224  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 256

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 257  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 289

Query: 1241 TGEPFDRPV 1249
            TG   +  V
Sbjct: 290  TGRKLNAQV 298



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 72/196 (36%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 118 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 173

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 174 KRSVKVRTRTTKVPQI 189


>gi|118201888|gb|ABK79757.1| RNA polymerase subunit B [Silicibacter lacuscaerulensis ITI-1157]
          Length = 163

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 108/162 (66%), Positives = 129/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V DG+VT++V Y+SA EE    +AQAN++LDE+G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDGQVTDEVHYMSATEEMRHTVAQANATLDENGKFINDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGDYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|168419299|gb|ACA23542.1| RNA polymerase II [Fusarium phaseoli]
 gi|168419341|gb|ACA23570.1| RNA polymerase II [Fusarium sp. NRRL 22574]
 gi|168419374|gb|ACA23592.1| RNA polymerase II [Fusarium brasiliense]
 gi|168419398|gb|ACA23608.1| RNA polymerase II [Fusarium virguliforme]
 gi|168419470|gb|ACA23656.1| RNA polymerase II [Fusarium tucumaniae]
 gi|168419473|gb|ACA23658.1| RNA polymerase II [Fusarium cuneirostrum]
 gi|168419494|gb|ACA23672.1| RNA polymerase II [Fusarium brasiliense]
 gi|168419497|gb|ACA23674.1| RNA polymerase II [Fusarium sp. NRRL 31949]
 gi|215789640|gb|ACJ69880.1| RNA polymerase II [Fusarium virguliforme]
 gi|215789643|gb|ACJ69882.1| RNA polymerase II [Fusarium tucumaniae]
 gi|215789646|gb|ACJ69884.1| RNA polymerase II [Fusarium phaseoli]
 gi|215789649|gb|ACJ69886.1| RNA polymerase II [Fusarium cuneirostrum]
 gi|215789697|gb|ACJ69918.1| RNA polymerase II [Fusarium sp. NRRL 36877]
 gi|270000457|gb|ACZ58076.1| RNA polymerase II [Fusarium virguliforme]
 gi|270000459|gb|ACZ58077.1| RNA polymerase II [Fusarium tucumaniae]
          Length = 291

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 101/364 (27%), Gaps = 75/364 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RPVT 1250
                
Sbjct: 288  AQCF 291



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|67942348|gb|AAY83374.1| DNA-dependent RNA polymerase II [Sarcoscypha austriaca]
          Length = 317

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/369 (15%), Positives = 108/369 (29%), Gaps = 81/369 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  +  I      +  D+ +   S +   
Sbjct: 27   DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRG 86

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L +   +  G   
Sbjct: 87   LF-RSLFYRTYMDQEKR---IGMQVVEEFEKPMRGNTLRLKHGTYDKLDDDGLVAPGVRV 142

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +S D      R ++         ++     +  Q   S          
Sbjct: 143  TGEDIIIGKTAPISPDADEMGQRQKYHTKRDVSTPLRSTESGIVDQVMLS---------- 192

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 193  ----------TNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGIAYRQEDMPFTCEG 242

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L                                  
Sbjct: 243  IVPDIIINPHAIPSRMTIAHLIECLLSKLST----------------------------- 273

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                     +     +TP F      +++ MLR       G  +
Sbjct: 274  ------------------------LRGAEGDATP-FTDVTVRSVSEMLRDHGYQSRGFEV 308

Query: 1236 LYDGLTGEP 1244
            +Y+G TG+ 
Sbjct: 309  MYNGHTGKK 317



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 67/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +V  M + G
Sbjct: 20  TNFAERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVGIMCYSG 69

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  +   +       
Sbjct: 70  YNQEDSVIMNQSSIDRGLFRSLFYRTYMDQEKRIGMQVVEEFEKPMRGNTLRLKHGTYDK 129

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G++  G  V   DI++GK  P         ++       +K    RD S  + S  
Sbjct: 130 LDDDGLVAPGVRVTGEDIIIGKTAPISPDADEMGQR-------QKYHTKRDVSTPLRSTE 182

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG V  V +       K
Sbjct: 183 SGIVDQVMLSTNSEGLK 199


>gi|281324363|gb|ADA60247.1| RNA polymerase beta subunit [Helicobacter fennelliae]
          Length = 217

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 112/217 (51%), Positives = 158/217 (72%), Gaps = 2/217 (0%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD--IDSVMPQDLINAKPVV 510
           IDD DNLGNRR+R++GE+L N+   GL++M+++IK++++++    D++MP DLINAK + 
Sbjct: 1   IDDRDNLGNRRIRAIGELLANELHSGLVKMQKAIKDKLTTMSGSFDAIMPHDLINAKMIT 60

Query: 511 SAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRIC 570
           S + EFF   QLSQ  +  N LS IT+ RRLSALG+GG+ + R G E RDVHPTHYGRIC
Sbjct: 61  STIIEFFTGGQLSQFMDQTNPLSEITNKRRLSALGEGGLVKERVGFEARDVHPTHYGRIC 120

Query: 571 PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQA 630
           P ET EG NIGL++++++F  VN  GFIE PYRKV +GKVT+++VYL+A +E+ + IA A
Sbjct: 121 PIETPEGQNIGLINTISTFTLVNDLGFIEAPYRKVVNGKVTDEIVYLTATQEDGKVIAPA 180

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           ++ LD+D    + L+  RC GE  L   E ++ ID S
Sbjct: 181 STQLDKDNKIIDSLIETRCGGEITLRKTEDVELIDLS 217


>gi|330785306|gb|AEC46459.1| RNA polymerase II second largest subunit [Alyxoria subelevata]
          Length = 294

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 55/369 (14%), Positives = 106/369 (28%), Gaps = 79/369 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRAMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSAIDRGLFRSL 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   ++++ I       E   +      + +  N Y +L +   +  G        
Sbjct: 62   FYRTYNESESDKGI----NNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVSGDDV 117

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+  +                E   R     +          E    +K+   
Sbjct: 118  IIGKTEALAEPM------------RQGAEGGARLPTHERRDCSAPLRSTEAGIIDKVV-- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 164  ----VTLSESKKSVKVRTRTTKVPQVGDKFASRHGQKGTIGITYRQEDMPFTAEGLTPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+ +L+ +   + G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTPVTVQDISDLLQNSGYQKRGFEVMYNGH 285

Query: 1241 TGEPFDRPV 1249
            TG+     +
Sbjct: 286  TGQKLRAQI 294



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 66/189 (34%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSAI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +     D  +   E           ++       +D+ G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYNESESDKGINNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK     E      E   R        + RD S  + S     ++D  +     
Sbjct: 114 GDDVIIGKTEALAEPMRQGAEGGARLP----THERRDCSAPLRS-TEAGIIDKVVVTLSE 168

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 169 SKKSVKVRT 177


>gi|193201531|gb|ACF15973.1| RNA polymerase II subunit [Opegrapha cf. viridis Ertz 7807]
          Length = 280

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/351 (17%), Positives = 103/351 (29%), Gaps = 73/351 (20%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  I++  ++ 
Sbjct: 3    MEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF-RSLFYRTYIEQESKTA 61

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E  AR    +      +          G           K+   S+ +     
Sbjct: 62   FDSSEDFEKPARGVTTKMKSGTYDKIEDDGFPAPGTRVAGNDVIIGKTVPYSTPMQEGA- 120

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       E   R  E  K     +    E    +K+              + VKV 
Sbjct: 121  -----------EGGARRKEHTKADSSITLRSTESGIIDKVL------VSSTDGRKSVKVR 163

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                +    GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + 
Sbjct: 164  TRTTKIPTIGDKFASRHGQKGTIGITYTQEDMPFTSEGLVPDLIINPHAIPSRMTIAHLI 223

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L     G G + +                                            
Sbjct: 224  ECLLSKVAAGTGNEGE-------------------------------------------- 239

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                     +TP F     E I+++L+ A     G  ++Y+G TG      
Sbjct: 240  ---------ATP-FADITVEDISNLLKNAGYQSRGYEVMYNGYTGRKLRAQ 280



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 61/164 (37%), Gaps = 9/164 (5%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +      T 
Sbjct: 2   SMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSLFYRTYIEQESKTA 61

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
               E            +       I++ G    G  V   D+++GK  P      TP +
Sbjct: 62  FDSSEDFEKPARGVTTKMKSGTYDKIEDDGFPAPGTRVAGNDVIIGKTVP----YSTPMQ 117

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
           +        K     D+S+ + S  SG +  V + +  G    +
Sbjct: 118 EGAEGGARRKEHTKADSSITLRSTESGIIDKVLVSSTDGRKSVK 161


>gi|112824163|gb|ABI26082.1| second largest RNA polymerase II [Lichinella iodopulchra]
          Length = 286

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/352 (17%), Positives = 106/352 (30%), Gaps = 75/352 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 10   MEFLKFRELPAGQNAIVAIAVYSGYNQEDSVVMNQSSIDRGLF-RSLFYRAYTDQEKRLG 68

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                EQ E   R           +       I  G           K+  ++ D      
Sbjct: 69   MQVVEQFEKPMRSDTLRLKHGTYDKLDEDGIIAPGVRISGEDIIIGKTAPIAPD------ 122

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                      +E  QR    +K    T     E    +++      D +     R  KV 
Sbjct: 123  ---------AEELGQRTKFHIKRDVSTPLRSTETGIVDQVLVATNSDGL-----RFTKVR 168

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + 
Sbjct: 169  MRSTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGIVPDLIINPHAIPSRMTIAHLI 228

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 229  ECQLSKVSSLKGFEGD-------------------------------------------- 244

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                     +TP F     ++++ +LR       G  ++++G TG      V
Sbjct: 245  ---------ATP-FTDVTVDSVSKLLREHGYQSRGFEVMFNGHTGRKLVAQV 286



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/158 (21%), Positives = 61/158 (38%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 7   TRSMEFLKFRELPAGQNAIVAIAVYSGYNQEDSVVMNQSSIDRGLFRSLFYRAYTDQEKR 66

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  D   +       +DE GII  G  ++  DI++GK  P        
Sbjct: 67  LGMQVVEQFEKPMRSDTLRLKHGTYDKLDEDGIIAPGVRISGEDIIIGKTAPIAPDAEEL 126

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        K    RD S  + S  +G V  V +  
Sbjct: 127 GQRT-------KFHIKRDVSTPLRSTETGIVDQVLVAT 157


>gi|118201874|gb|ABK79749.1| RNA polymerase subunit B [Roseivivax halotolerans]
          Length = 163

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 108/162 (66%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V DG VT++V Y+SA EE    IAQAN+ LDE+G F  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRLVKDGTVTDEVRYMSATEEMRHTIAQANALLDENGRFINELVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPAENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|56694364|gb|AAW22922.1| RNA polymerase II second largest subunit [Amborella trichopoda]
          Length = 516

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 71/482 (14%), Positives = 131/482 (27%), Gaps = 84/482 (17%)

Query: 785  GDEVRRNDI----IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
             D V +  I      +  +T +                          I   ++     +
Sbjct: 115  HDLVAKGFIEYVDTEEEETTMISMTISDLVSARLNPEEAYSETYTHCEIHPSLILGVCAS 174

Query: 841  SIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
             I   +     R+T             V+   L+      +  V        +    +  
Sbjct: 175  IIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAMEH 231

Query: 901  KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVE 960
                 +      + AI      +  D+ +   S +        +F R   D+ ++  ++ 
Sbjct: 232  LHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLV 290

Query: 961  REQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQ 1020
            +E      R+          +          G           K+T ++ +         
Sbjct: 291  KEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPITQE--------- 341

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
                    E   +     +  + TS    E    +++      D +     R VKV +  
Sbjct: 342  --------EMQGQASRYTRRDHSTSLRHSESGMVDQVLLTTNADGL-----RFVKVRMRS 388

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  
Sbjct: 389  VRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECI 448

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQW 1200
            +G     +GK+  +         +IS         +                        
Sbjct: 449  MGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETM------------------ 490

Query: 1201 KSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                                          +G +    G         + +G  Y  +L 
Sbjct: 491  -----------------------------YNGHT----GR---RLSAMIFLGPTYYQRLK 514

Query: 1261 HM 1262
            HM
Sbjct: 515  HM 516



 Score =  115 bits (287), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 75/452 (16%), Positives = 132/452 (29%), Gaps = 98/452 (21%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   +  A   F     +         +  +   RR   +  + GV R 
Sbjct: 8   EEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRD 67

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S      + A    E+P     D     
Sbjct: 68  IRLKELR-LYTDYGRCSRPLFIVEKQRLLIKKS-----DIRALQQRESPDEGWHDLVAKG 121

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E      E     +  P  ++
Sbjct: 122 FIEYVDTEEEETTMISM----------TISDLVSARLNPE--EAYSETYTHCEIHPSLIL 169

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRA 732
            + AS+IPF +++ S R      M +QA+ +                           R 
Sbjct: 170 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQL--------------------RM 209

Query: 733 GIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRND 792
             +  V                                       Q+PLV          
Sbjct: 210 DTLAYV-----------------------------------LYYPQKPLV---------- 224

Query: 793 IIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMAR 852
                       L  G N +VA   + GYN EDS+++++  +    F S+    +    +
Sbjct: 225 TTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK 284

Query: 853 DTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMT 907
                 +E        +   +       +D+ G+   G  V+  D+++GK TP  +  M 
Sbjct: 285 KMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPITQEEM- 343

Query: 908 PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
                            RD S  +    SG V
Sbjct: 344 --------QGQASRYTRRDHSTSLRHSESGMV 367


>gi|298162096|gb|ADI59496.1| RNA polymerase II beta subunit [Fusarium cf. lateritium NRRL 13622]
 gi|298162120|gb|ADI59512.1| RNA polymerase II beta subunit [Fusarium cf. lateritium NRRL 37021]
          Length = 289

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/365 (15%), Positives = 108/365 (29%), Gaps = 81/365 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D+ ++         E+  +    + + +    Y +L E   +  G           
Sbjct: 62   RSYSDQEKKVGLNY---TEVFEKPFQQQTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+Q  Q       ++     +  Q   + +                
Sbjct: 119  KTAPIDQENQDLGARTQAHQRRDISTPLRSTENGIVDQVILTVNA--------------- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 164  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVDSVSDLLRKHGYQSRGFEVMYNGHTGR 284

Query: 1244 PFDRP 1248
                 
Sbjct: 285  KLRAQ 289



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQQTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +A   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGART-------QAHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|270000433|gb|ACZ58064.1| RNA polymerase II [Fusarium sp. NRRL 44903]
          Length = 290

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 55/365 (15%), Positives = 101/365 (27%), Gaps = 75/365 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ ++      E  E   +           +       +  G           
Sbjct: 60   LFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIG 119

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+   Q       ++     +      + +                
Sbjct: 120  KTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA--------------- 164

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 165  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIIN 219

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 220  PHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------------ 249

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  I+Y+G TG 
Sbjct: 250  -----------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGR 285

Query: 1244 PFDRP 1248
                 
Sbjct: 286  KLRAQ 290



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 53  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 113 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 165

Query: 950 IDK 952
             K
Sbjct: 166 NVK 168


>gi|198279357|emb|CAP04713.1| RNA polymerase beta subunit [Pinus monticola]
          Length = 282

 Score =  174 bits (440), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 102/254 (40%), Positives = 154/254 (60%), Gaps = 10/254 (3%)

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PJ + E    GTG+E   A  SG+  +A + G +E +DA+                    
Sbjct: 1   PJFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVR 52

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GY
Sbjct: 53  TESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGY 112

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G+
Sbjct: 113 NFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGL 172

Query: 882 ICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V
Sbjct: 173 VMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRV 232

Query: 940 VDVRIFNRHGIDKN 953
           +DVR  NR     +
Sbjct: 233 IDVRWINRVDDSGD 246



 Score = 85.9 bits (211), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 73   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 131

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 132  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 185

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 186  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 243

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 244  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXILP 282


>gi|151573387|gb|ABS17922.1| RNA polymerase II [Fusarium sp. NRRL 43726]
          Length = 290

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/363 (15%), Positives = 100/363 (27%), Gaps = 75/363 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSNEGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G   +Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFENMYNGHTGRKLR 287

Query: 1247 RPV 1249
              V
Sbjct: 288  AQV 290



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|194320259|gb|ACF48368.1| DNA-dependent RNA polymerase II second largest subunit [Umbilicaria
            spodochroa]
          Length = 303

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/370 (16%), Positives = 113/370 (30%), Gaps = 81/370 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRCYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 127  SGEDIIIGKTAPIAPD---------------AEELGQRTKSHVKRDVSTPLRSTENGIVD 171

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 172  QVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 264

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 265  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 292

Query: 1236 LYDGLTGEPF 1245
            +Y+G TG   
Sbjct: 293  MYNGHTGRKL 302



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRCYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 126 VSGEDIIIGKTAPIAPDA----EELGQRTKSHVKRDVSTPLRSTENGIVDQVL 174


>gi|299849854|gb|ADJ57173.1| RNA polymerase II second largest subunit [Scytalidium cuboideum]
          Length = 321

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/388 (17%), Positives = 111/388 (28%), Gaps = 81/388 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVRV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +P RM +  + E  L       G +             +S L       
Sbjct: 228  IVPDLIINPHAIPXRMTIAHLIECQLSKVSTLRGLEGDXTPFTEVTVDSVSKL------- 280

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                              LR       G  +                         G + 
Sbjct: 281  ------------------LRAHGYQSRGFEIM----------------------YHGHT- 299

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
               G         V  G  Y  +L HMV
Sbjct: 300  ---GR---KLKAXVFFGPTYYQRLRHMV 321



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 40/179 (22%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNXEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  G  
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRADTLKLKHGTYDKLDDDGIIAPGVR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|118201848|gb|ABK79737.1| RNA polymerase subunit B [Loktanella salsilacus]
          Length = 163

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 112/162 (69%), Positives = 130/162 (80%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DGKVT+DV Y+SA EE    +AQAN++L+EDGSF  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGKVTDDVSYMSATEEMRHTVAQANANLNEDGSFGNELVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 NGDYTLSPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|151573678|gb|ABS18115.1| RNA polymerase II [Fusarium sp. NRRL 43584]
 gi|151573681|gb|ABS18117.1| RNA polymerase II [Fusarium sp. NRRL 43585]
 gi|151573684|gb|ABS18119.1| RNA polymerase II [Fusarium sp. NRRL 43586]
          Length = 289

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 100/362 (27%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118426170|gb|ABK90984.1| RpoB [Mycoplasma putrefaciens]
          Length = 208

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 155/215 (72%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   ++I++ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMARVDEIEYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P VGTG+E   A+ SG AIVAK  GIV+ VD+  I ++          SG+  Y L 
Sbjct: 61  PESPIVGTGIEFEAARDSGEAIVAKEDGIVKYVDSKMISVQ--------GESGIKTYTLS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSN  T + Q P+V+ GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DFERSNNGTSLTQSPIVRKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERVVIDDRFTSIHIDEYTLEVRNTKQGLEE 207


>gi|118201880|gb|ABK79753.1| RNA polymerase subunit B [Roseovarius tolerans]
          Length = 163

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 108/162 (66%), Positives = 130/162 (80%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG+VT++V Y+SA EE    +AQAN++LD+ G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGQVTDEVQYMSATEEMRHTVAQANANLDDAGKFVNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +GE +L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGEYMLAPREHVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|330785360|gb|AEC46486.1| RNA polymerase II second largest subunit [Dendrographa franciscana]
          Length = 276

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/353 (17%), Positives = 105/353 (29%), Gaps = 81/353 (22%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +   +  + AI      +  D+ +   S +   +     +  +     E+  SV  
Sbjct: 1    RFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----EQQQSVGF 56

Query: 962  EQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
              +E   R +  E +      Y +L +   +  G           K+    + +      
Sbjct: 57   NALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPM------ 110

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRV-VKVF 1077
                         Q N E  +   +  K  +    ++    I     +     +  VKV 
Sbjct: 111  -------------QENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVR 157

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + 
Sbjct: 158  TRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSRMTIAHLI 217

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 218  ECLLSKVSTITGHEGD-------------------------------------------- 233

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                     +TP F      +I+ +L  A     G  ++Y+G TG   +  V 
Sbjct: 234  ---------ATP-FTDITVSSISDLLSFAGYQSRGLELMYNGHTGRKLNAQVF 276



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/161 (19%), Positives = 60/161 (37%), Gaps = 6/161 (3%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-E 859
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       E
Sbjct: 1   RFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALE 60

Query: 860 EITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           E  R              + +D+ G +  G  V+  DI++GK  P         E   + 
Sbjct: 61  EFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMQENSEGG-QR 119

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
               K  DV        +G+   V+      +  +    R+
Sbjct: 120 TKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRT 160


>gi|198279445|emb|CAP04757.1| RNA polymerase beta subunit [Pinus cembroides]
          Length = 283

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 103/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE +TR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERVTREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERVTREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILP 283


>gi|198279417|emb|CAP04743.1| RNA polymerase beta subunit [Pinus maximartinezii]
          Length = 283

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 2   VPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTV 53

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 54  RTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 114 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 173

Query: 881 IICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G 
Sbjct: 174 LVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGR 233

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 234 VIDVRWINRVDDSGD 248



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/223 (24%), Positives = 87/223 (39%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 75   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 133

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 134  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 187

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 188  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 245

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S IL
Sbjct: 246  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIIL 283


>gi|118426168|gb|ABK90983.1| RpoB [Mycoplasma putrefaciens KS1]
          Length = 208

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 155/215 (72%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   ++I++ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMARFDEIEYIDVSPKQIVSVATSAIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P VGTG+E   A+ SG AIVAK  GIV+ VD+  I ++          SG+  Y L 
Sbjct: 61  PESPIVGTGIEFEAARDSGEAIVAKEDGIVKYVDSKMISVQ--------GESGIKTYTLS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            F+RSN  T + Q P+V+ GD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DFERSNNGTSLTQSPIVRKGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERVVIDDRFTSIHIDEYTLEVRNTKQGLEE 207


>gi|298162123|gb|ADI59514.1| RNA polymerase II beta subunit [Fusarium sp. NRRL 54149]
 gi|298162126|gb|ADI59516.1| RNA polymerase II beta subunit [Fusarium sp. NRRL 54150]
 gi|298162129|gb|ADI59518.1| RNA polymerase II beta subunit [Fusarium sp. NRRL 54152]
 gi|298162132|gb|ADI59520.1| RNA polymerase II beta subunit [Fusarium sp. NRRL 54154]
 gi|298162135|gb|ADI59522.1| RNA polymerase II beta subunit [Fusarium sp. NRRL 54155]
          Length = 289

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/362 (15%), Positives = 102/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQVHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QVHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118201844|gb|ABK79735.1| RNA polymerase subunit B [Loktanella fryxellensis]
          Length = 163

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 112/162 (69%), Positives = 129/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DGKVT+DV Y+SA EE    +AQAN+ L+EDGSF  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGKVTDDVQYMSATEEMRHTVAQANADLNEDGSFGNELVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 NGDYTLSPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|292606612|gb|ADE34122.1| RNA polymerase II second largest subunit [Dothideomycetes sp. TRN 77]
          Length = 287

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/365 (16%), Positives = 105/365 (28%), Gaps = 81/365 (22%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R        +E   +    + + +    Y +L +   I  G      
Sbjct: 60   RSLFYRAYMDQEKRVGM---SVVENFEKPIRADTLKMKHGTYDKLDDDGIISPGARVSGE 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +  Q                 
Sbjct: 117  DIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL-------------- 162

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV     +  Q GDK A RHG KG +      EDMPF  DG   
Sbjct: 163  ------TTNVEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADGLTP 216

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +                           
Sbjct: 217  DIIINPHAIPSRMTIAHLIECLLSKVACLQGMEGD------------------------- 251

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       +++ML      + G  ++Y+
Sbjct: 252  ----------------------------ATP-FTDVTITHLSTMLEERGFQKRGFEVMYN 282

Query: 1239 GLTGE 1243
            G TG 
Sbjct: 283  GHTGR 287



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 37/171 (21%), Positives = 63/171 (36%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSAI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GII  GA V+
Sbjct: 55  DRGLFRSLFYRAYMDQEKRVGMSVVENFEKPIRADTLKMKHGTYDKLDDDGIISPGARVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 115 GEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 161


>gi|67942368|gb|AAY83384.1| DNA-dependent RNA polymerase II [Chorioactis geaster]
          Length = 519

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 68/464 (14%), Positives = 128/464 (27%), Gaps = 88/464 (18%)

Query: 786  DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
            + V   +           DL + + +   ++     +           V   +  + H  
Sbjct: 144  EYVDAEEEETIMIVMTPEDLEIAQQVRQGYVLDEETDQHKR-------VKAPINPNTHQY 196

Query: 846  EFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
                +     LG        P+ ++          +  +             +       
Sbjct: 197  THCEIHPSMILGICASIIPFPDHNQRM------DTMANILYYPQKPLATTRSMEYLKFRE 250

Query: 906  MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIE 965
            +   +  +  I      +  D+ +   S +   +    +F R   D+ +R   +  E+ E
Sbjct: 251  LPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRIGMMVVEEFE 309

Query: 966  LLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
               R                   +  G           K+  ++ D              
Sbjct: 310  KPQRSNTLRLKHGTYEKLDDDGLVAPGVRVSGEDIIIGKTAPIAPD-------------- 355

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
              DE  QR     K    T     E+   +++             L+  KV +   +  Q
Sbjct: 356  -ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVLL-----TTNAEGLKFAKVRMRTTKIPQ 409

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM    + E  L    
Sbjct: 410  IGDKFASRHGQKGTIGITYRSEDMPFTCEGIIPDLIINPHAIPSRMTXAHLIECQLSKVS 469

Query: 1146 VGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVP 1205
               G +                                                      
Sbjct: 470  SLRGMEGD---------------------------------------------------- 477

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
             +TP F     ++++++LR       G  ++Y+G TG+     V
Sbjct: 478  -ATP-FTDVTVDSVSNLLREEGYQSRGFEVMYNGHTGKKMVAQV 519



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 51/301 (16%), Positives = 89/301 (29%), Gaps = 29/301 (9%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 18  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG-HE 70

Query: 549 VARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           V+  R   +      T  GR+C        +T+      LV       R+     +    
Sbjct: 71  VSVIRDIRDREFKIFTXAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEQDADLPPDE 130

Query: 603 RK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLD-----EDGSFTEELVFCRCAGEEILV 656
           R           V Y+ A EEE   I      L+       G   +E        +  + 
Sbjct: 131 RWGWDGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAQQVRQGYVLDEETDQHKRVKAPIN 190

Query: 657 PR-EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT-G 714
           P   +    +  P  ++ I AS+IPF +++          M   A  L   + P   T  
Sbjct: 191 PNTHQYTHCEIHPSMILGICASIIPFPDHNQ--------RMDTMANILYYPQKPLATTRS 242

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           ME +  +   A   A    +          +   +  +D        YR    Q      
Sbjct: 243 MEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGM 302

Query: 775 C 775
            
Sbjct: 303 M 303


>gi|193201515|gb|ACF15965.1| RNA polymerase II subunit [Opegrapha ochrocheila]
          Length = 292

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/368 (15%), Positives = 105/368 (28%), Gaps = 79/368 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +N++ I       E   +      + +  N Y +L +   +  G        
Sbjct: 61   FYRTYNESENDKGI----NNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVSGDDV 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+  +                E   R     +          E    +K+   
Sbjct: 117  IIGKTEALAEPM------------RQGAEGGARLPTHERRDCSAPLRSTEAGIIDKVV-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----VTLSESKKSVKVRTRTTKVPQVGDKFASRHGQKGTIGITYRQEDMPFTSEGLTPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 219  IINPHAIPSRMTIAHLIECLLSKVAAVDGMEGD--------------------------- 251

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     + I+ +L+ +   + G  ++Y+G 
Sbjct: 252  --------------------------ATP-FTPVTVQDISDLLQNSGYQKRGFEVMYNGH 284

Query: 1241 TGEPFDRP 1248
            TG+     
Sbjct: 285  TGQKLRAQ 292



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 66/189 (34%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +     D  +   E           ++       +D+ G +  G  V+
Sbjct: 53  DRGLFRSLFYRTYNESENDKGINNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK     E      E   R        + RD S  + S     ++D  +     
Sbjct: 113 GDDVIIGKTEALAEPMRQGAEGGARLP----THERRDCSAPLRS-TEAGIIDKVVVTLSE 167

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 168 SKKSVKVRT 176


>gi|56406201|gb|AAV87484.1| RpoB [Pasteurella multocida subsp. multocida]
          Length = 169

 Score =  173 bits (439), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 99/169 (58%), Positives = 127/169 (75%), Gaps = 1/169 (0%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNQLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+ 
Sbjct: 61  NSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDA 120

Query: 644 LVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 FVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 169


>gi|56406221|gb|AAV87494.1| RpoB [Bisgaard Taxon 45]
          Length = 169

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 99/169 (58%), Positives = 127/169 (75%), Gaps = 1/169 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQ SQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQXSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD+
Sbjct: 121 FTDSFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDA 169


>gi|46277382|gb|AAS86881.1| DNA-dependent RNA polymerase II [Peziza exogelatinosa]
          Length = 516

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 81/583 (13%), Positives = 162/583 (27%), Gaps = 73/583 (12%)

Query: 580  IGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L   + V+     E    +    + +V  +            ++      +  D
Sbjct: 2    CGLVKNLALMSYVSVGSPAEPIIDFMLQRNMEVLEEYEPAQTPNATKIFVNGVWVGIHRD 61

Query: 638  GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGC 694
             +F    +        I      I  I     ++ + A      +  ++ND ++      
Sbjct: 62   PNFIVRTIQKLRRQNHIGHEVSLIQDIRGREFKIFTDAGRICRPLFVVDNDPASPRRGEL 121

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
             +Q+  +  L+ +               S   +        E +DA       +    + 
Sbjct: 122  VLQKHHIEKLEDDKDLEPDQRYGWAGLISDGVV--------EYIDAEEEETIMIVMTPED 173

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
              +    +   + Q         QR    V             PS  LG       +  +
Sbjct: 174  LETSRQFHAGYEIQTEVDPA---QRVKAAVNKYAHTWTHCEIHPSMILG-------ICAS 223

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
             +P+  +N       S R   +       +  F    R+                     
Sbjct: 224  IIPFPDHNQ------SPRNTYQSAMGKQAMGVFLTNYRERM------------------- 258

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 259  ----DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSS 314

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQN 994
            +   +    +F R  +D+ +R      E+ E   R           +       +  G  
Sbjct: 315  IDRGLF-RSLFFRTYMDQEKRVGMNVVEEFEKPQRGNTLRLKHGTYDKLDDDGLVAPGVR 373

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +S ++     R+++         ++     +  Q             
Sbjct: 374  VSGEDIIIGKTAPISPNMEELGQRTKFHTKRDVSTPLRSTENGIVDQ------------- 420

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
                            L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +
Sbjct: 421  -------VMVTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTAE 473

Query: 1115 GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            G   D+++NP  +PSRM +  + E  L       G +  +   
Sbjct: 474  GVVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPF 516


>gi|118201870|gb|ABK79748.1| RNA polymerase subunit B [Roseivivax halodurans]
          Length = 163

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 127/162 (78%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V DG+VT++V Y+SA EE    +AQAN+SLDE+G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRIVKDGQVTDEVHYMSATEEMRHTVAQANASLDENGRFVNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+ ASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPNETVDLIDVSPKQLVSVGASLIPFLENDDANRAL 163


>gi|118201846|gb|ABK79736.1| RNA polymerase subunit B [Loktanella hongkongensis]
          Length = 163

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 110/162 (67%), Positives = 131/162 (80%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG+VT++V YLSA EE    +AQAN+SLDE+G FT +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGQVTDEVNYLSATEEMRHTVAQANASLDENGKFTNDLVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+ +L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYMLAPSESVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|118201832|gb|ABK79729.1| RNA polymerase subunit B [Antarctobacter heliothermus]
          Length = 163

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 125/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D  VT++V Y+SA EE    +AQAN+ LDE+G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDRHVTDEVHYMSATEEMRHTVAQANAKLDENGRFENDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P + +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPSDNVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|297500407|gb|ADI43640.1| RNA polymerase beta subunit [Agrobacterium sp. LMG17935]
          Length = 178

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 141/179 (78%), Positives = 158/179 (88%), Gaps = 1/179 (0%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           EAPFVGTGME +VA+  GAAI A+R G+V+QVDA RIVIR+ E  LD   SGVDIYRL K
Sbjct: 1   EAPFVGTGMEPIVARELGAAIAARRGGVVDQVDATRIVIRATED-LDAGKSGVDIYRLQK 59

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           FQRSNQNTCVNQRPLV VGD + + DIIADGPSTDLGDLALGRN LVAFMPW+GYN+EDS
Sbjct: 60  FQRSNQNTCVNQRPLVSVGDILNKGDIIADGPSTDLGDLALGRNALVAFMPWNGYNYEDS 119

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +L+SER+VS+DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +G
Sbjct: 120 ILMSERIVSDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 178


>gi|260609517|gb|ACX47131.1| RNA polymerase beta subunit [Corynebacterium freiburgense]
          Length = 135

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 55/163 (33%), Positives = 78/163 (47%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI +                                    D +   
Sbjct: 1    LEVHLGWLAAA-GWKIDT---------------------------ENPEMQGLMDMLPEE 32

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +  G        ++ L DG +GEPF  P
Sbjct: 33   LYDVPAGSLTATPVFDGATNEELAGLLANSRPNRDGDVLVDGDGKAKLIDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V++GY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSIGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|308800510|ref|XP_003075036.1| RNA polymerase III, second largest subunit (ISS) [Ostreococcus tauri]
 gi|116061590|emb|CAL52308.1| RNA polymerase III, second largest subunit (ISS) [Ostreococcus tauri]
          Length = 1128

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 45/202 (22%), Positives = 67/202 (33%), Gaps = 53/202 (26%)

Query: 1066 MPPGVLRVVK---VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK-DGTPVDIV 1121
                  + VK   +     R    GDK + RHG KG++S + P EDMPF +  G   D++
Sbjct: 845  TTQKGNQNVKRAAITFRYDRNPVIGDKFSSRHGQKGVLSFLWPEEDMPFCERTGVRPDVI 904

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP   PSRM +G + E+    A         +              R            
Sbjct: 905  INPHAFPSRMTIGMLVESLASKAGAMAAVFADATPFKRDKKYSSPAERY----------- 953

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                                   S+LR    +  G   + +G T
Sbjct: 954  --------------------------------------GSLLREHGYNFCGNESMINGYT 975

Query: 1242 GEPFDRPVTVGYIYMLKLNHMV 1263
            GE F   + +G +Y  +L HMV
Sbjct: 976  GESFSVDIFIGIVYYQRLRHMV 997



 Score = 39.7 bits (91), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/117 (17%), Positives = 35/117 (29%), Gaps = 53/117 (45%)

Query: 87  DVDDCLWRDLTYAVPLKITL--RLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
               C     TY   + ++   RL   D            ++ + + +G  P+M +    
Sbjct: 101 TPRSCREVGETYKTSMSVSYCWRLQGNDA-----------MQRRVVQLGQCPVMVQSNVC 149

Query: 142 ---------------------GTFVIKGIQ---RIVVSQ-------------LHRSP 161
                                G F+I GI+   R+++ Q             L RSP
Sbjct: 150 SLARLCPAELVAFGEEANEAGGYFIINGIERMIRMIIMQRRHHILGLRRRAFLKRSP 206


>gi|118201882|gb|ABK79754.1| RNA polymerase subunit B [Ruegeria atlantica]
          Length = 163

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 127/162 (78%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D +VT++V Y+SA EE    +AQAN++LD DG F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDAEVTDEVHYMSATEEMRHTVAQANATLDADGKFINDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|118201906|gb|ABK79766.1| RNA polymerase subunit B [Thalassobius gelatinovorus]
          Length = 163

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 108/162 (66%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D KVT++V Y+SA EE    +AQAN++LDEDG F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVTDAKVTDEVHYMSATEEMRHTVAQANATLDEDGKFINDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|193201485|gb|ACF15950.1| RNA polymerase II subunit [Enterographa crassa]
          Length = 282

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/348 (16%), Positives = 101/348 (29%), Gaps = 73/348 (20%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  I+  +   
Sbjct: 7    MQFMRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYIEHEQAVG 65

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
               +E+ E  A++                  +  G           K++   + L     
Sbjct: 66   FNSQEEFEKPAKNLTMRTRPGTYEKLEDDGFVAPGVRVSGDDVIIGKTSPFQAPLAEG-- 123

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       E  QR  + +K          E    +++              R VKV 
Sbjct: 124  ----------SEGGQRTRDHVKRDVSAPLRSTEAGIIDRVL------ITTTDGRRNVKVR 167

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + 
Sbjct: 168  TRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTSEGLVPDIIINPHAIPSRMTIAHLI 227

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 228  ECLLSKVSAATGLEGD-------------------------------------------- 243

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                     +TP F      +I+  L+ A     G  ++Y+G +G   
Sbjct: 244  ---------ATP-FTDITVSSISDXLQDAGYQSRGFEVMYNGHSGRKL 281


>gi|198279379|emb|CAP04724.1| RNA polymerase beta subunit [Pinus lambertiana]
          Length = 281

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 54/222 (24%), Positives = 86/222 (38%), Gaps = 14/222 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S I
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISII 281


>gi|91981474|gb|ABE68079.1| RNA polymerase subunit B [Pseudomonas sp. CHA0]
 gi|91981494|gb|ABE68089.1| RNA polymerase subunit B [Pseudomonas sp. Pf-5]
 gi|91981504|gb|ABE68094.1| RNA polymerase subunit B [Pseudomonas sp. PF]
 gi|117573514|gb|ABK40933.1| RNA polymerase subunit B [Pseudomonas sp. C6-23]
          Length = 160

 Score =  173 bits (438), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 91/160 (56%), Positives = 120/160 (75%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 160


>gi|298162117|gb|ADI59510.1| RNA polymerase II beta subunit [Nectria desmazierii]
          Length = 289

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 56/362 (15%), Positives = 101/362 (27%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSDLLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|198279491|emb|CAP04780.1| RNA polymerase beta subunit [Equisetum palustre]
 gi|198279501|emb|CAP04785.1| RNA polymerase beta subunit [Equisetum palustre]
          Length = 260

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 115/248 (46%), Positives = 164/248 (66%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL K E   VGTG+E   A  SG+ + ++R G +  +D  +I +   E         
Sbjct: 1   QAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDGEKITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLLCKNKFLRQGQIIADGASTVGGELALGRNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER++ EDVFTS HIE +E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDAILISERLIYEDVFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP GV 
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPVGVK 233

Query: 937 GTVVDVRI 944
           G V+D+R 
Sbjct: 234 GRVIDIRW 241


>gi|118426136|gb|ABK90967.1| RpoB [Mycoplasma mycoides subsp. capri LC]
 gi|118426138|gb|ABK90968.1| RpoB [Mycoplasma mycoides subsp. capri]
 gi|118426144|gb|ABK90971.1| RpoB [Mycoplasma mycoides subsp. capri]
 gi|118426146|gb|ABK90972.1| RpoB [Mycoplasma mycoides subsp. capri]
          Length = 208

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 112/215 (52%), Positives = 153/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|288804206|gb|ADC53872.1| RNA-polymerase RPO132 [Pseudocowpox virus]
          Length = 1161

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 72/431 (16%), Positives = 136/431 (31%), Gaps = 71/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMYAERPIVVSKALETSKIADNCFGNHVTIALMSFRGMNQEDGIILKKQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDIYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGVTPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A              +        D      F  +          
Sbjct: 912  SRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALAHPDAA 971

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D + +S +                                        +LYD  T EP
Sbjct: 972  PDDPEVESRVFCER------------------------------------VLYDPETDEP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ +
Sbjct: 996  FAARVFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMIS 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA+ + E+L
Sbjct: 1056 HGAAFTVSEIL 1066


>gi|193201501|gb|ACF15958.1| RNA polymerase II subunit [Opegrapha calcarea]
          Length = 294

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 54/366 (14%), Positives = 103/366 (28%), Gaps = 84/366 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 4    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 63

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 64   LYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 123

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+S+      R+           ++     +  Q                      
Sbjct: 124  KTAPLASNAEERGMRATQHTKRDVSTPLRSTEAGIIDQVL-------------------- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 164  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 223  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 253  -----------------------ATP-FTDITVEMVSEILEKSGYQKRGFEVMYNGHTGR 288

Query: 1244 PFDRPV 1249
                 V
Sbjct: 289  KLMAQV 294



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 57  DRGLFRSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +    EE+ +RA       DV        +G+   V+   +  +  
Sbjct: 117 GDDIIIGKTAPLASN---AEERGMRAT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKN 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKIRTRT 179


>gi|162956008|gb|ABY25369.1| RNA polymerase beta subunit [Bartonella volans]
          Length = 162

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 111/162 (68%), Positives = 131/162 (80%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE   Y+AQANSSLD +G FTEE
Sbjct: 61  NSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEND
Sbjct: 121 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEND 162


>gi|198279525|emb|CAP04797.1| RNA polymerase beta subunit [Equisetum sylvaticum]
 gi|198279573|emb|CAP04799.1| RNA polymerase beta subunit [Equisetum x fontqueri]
          Length = 271

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL K E   VGTG+E   A  SG+ + ++R G +  +DA +I +   E         
Sbjct: 1   QAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDAEKITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLLCKNKFLRQGQIIADGASTVGGELALGRNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER++ ED+FTS HIE +E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP GV 
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPVGVK 233

Query: 937 GTVVDVRI 944
           G V+D+R 
Sbjct: 234 GRVIDIRW 241


>gi|260181569|gb|ACX35461.1| RNA polymerase beta subunit [Corynebacterium sp. 1170]
          Length = 135

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/163 (33%), Positives = 81/163 (49%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G KI +   + +   D+                           +   
Sbjct: 1    LEVHLGWLAAA-GWKIDTENPEMQELMDM---------------------------LPEE 32

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDES--------GQSILYDGLTGEPFDRP 1248
                 +G   +TPVFDGA  E +  +L  +  +          G++ L DG +GEPF  P
Sbjct: 33   LYDVPAGSLTATPVFDGATNEELAGLLASSRPNRDGDVLVDGNGKANLIDGRSGEPFPYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V++GY+Y+LKL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSIGYMYILKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|40644543|emb|CAD88886.1| DNA-directed RNA polymerase subunit B [Stellaria media]
          Length = 302

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 65/365 (17%), Positives = 103/365 (28%), Gaps = 80/365 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 18   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 78   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGE 136

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T LSS+                             +Y      +  R     E
Sbjct: 137  DVIIGKTTPLSSEEAQGP----------------------AARYSRKDHSISLRHS---E 171

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 172  SGIVDQTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 231

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+                           
Sbjct: 232  DIIVNPHAIPSRMTIGQLIECIMGKVAAHVGKEGD------------------------- 266

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F      +I+  L+       G   +Y+
Sbjct: 267  ----------------------------ATP-FTDVTVRSISRALQKCGYQMRGFETMYN 297

Query: 1239 GLTGE 1243
            G TG 
Sbjct: 298  GHTGR 302



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 59/184 (32%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 11  TNYQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP              A         +D S+ +    
Sbjct: 121 LDDDGLAPPGTRVSGEDVIIGKTTPLSSEE---------AQGPAARYSRKDHSISLRHSE 171

Query: 936 SGTV 939
           SG V
Sbjct: 172 SGIV 175


>gi|151573471|gb|ABS17978.1| RNA polymerase II [Fusarium sp. NRRL 43874]
          Length = 286

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 100/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  I+Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|253756997|gb|ACT35302.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 171

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 95/171 (55%), Positives = 127/171 (74%), Gaps = 1/171 (0%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N L  +TH RRLSALG GG++R
Sbjct: 1   TQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLLGLTHKRRLSALGPGGLSR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG+E+RD+HP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V+
Sbjct: 61  ERAGLEVRDLHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVS 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKI 661
           +++VYL+A EE+   +AQANS +D DG F E  V  R   GE   VP  ++
Sbjct: 121 DEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEV 171


>gi|118201868|gb|ABK79747.1| RNA polymerase subunit B [Roseisalinus antarcticus]
          Length = 163

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D  VT++V Y+SA EE    +AQAN++LD+ G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDAHVTDEVHYMSATEEMRHTVAQANATLDDAGHFMNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +GE  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGEYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|118426130|gb|ABK90964.1| RpoB [Mycoplasma mycoides subsp. capri LC]
 gi|118426132|gb|ABK90965.1| RpoB [Mycoplasma mycoides subsp. capri LC]
 gi|118426134|gb|ABK90966.1| RpoB [Mycoplasma mycoides subsp. capri LC]
          Length = 208

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 113/215 (52%), Positives = 153/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|118426148|gb|ABK90973.1| RpoB [Mycoplasma capricolum subsp. capricolum]
 gi|118426150|gb|ABK90974.1| RpoB [Mycoplasma capricolum subsp. capricolum]
 gi|118426154|gb|ABK90976.1| RpoB [Mycoplasma capricolum subsp. capricolum]
          Length = 208

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 112/215 (52%), Positives = 152/215 (70%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|152938324|gb|ABS43102.1| RNA polymerase beta subunit [Pantoea stewartii subsp. stewartii]
          Length = 167

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 100/167 (59%), Positives = 131/167 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR++ DG V++++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRLIDGVVSDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++L E+G+F ++LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLSEEGAFVDDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK 730
           +DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAK
Sbjct: 121 HDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 167


>gi|330785242|gb|AEC46427.1| RNA polymerase II second largest subunit [Dendrographa latebrarum]
          Length = 289

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/366 (16%), Positives = 105/366 (28%), Gaps = 81/366 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +     + 
Sbjct: 1    YPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYR 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
             +     E+  SV    +E   R +  E +      Y +L +   +  G           
Sbjct: 61   TYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIG 116

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                   Q N E  +   +  K  +    ++    I   
Sbjct: 117  KTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGIIDR 157

Query: 1064 DDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++
Sbjct: 158  VLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLII 217

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +  + E  L       G +                               
Sbjct: 218  NPHAIPSRMTIAHLIECLLSKVSTITGHEGD----------------------------- 248

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    +TP F      +I+ +L  A     G  ++Y+G TG
Sbjct: 249  ------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNGHTG 283

Query: 1243 EPFDRP 1248
               +  
Sbjct: 284  RKLNAQ 289



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/168 (19%), Positives = 60/168 (35%), Gaps = 6/168 (3%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 9   THSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQS 68

Query: 854 TKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 EE  R              + +D+ G +  G  V+  DI++GK  P        
Sbjct: 69  VGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMQEN 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            E   +     K  DV        +G+   V+      +  +    R+
Sbjct: 129 SEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRT 175


>gi|298162111|gb|ADI59506.1| RNA polymerase II beta subunit [Gibberella xylarioides]
          Length = 289

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 102/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV +   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRIRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|219564119|gb|ACL28243.1| RNA polymerase II second largest subunit [Lasiosphaeria ovina]
          Length = 287

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/295 (20%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D  +R      EQ E    ++ D    L    Y +L        G   
Sbjct: 61   IF-RSLFFRSYTDCEKRVGINIVEQFEKP--NRSDTLR-LKHGTYDKLDADGITAPGIRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K++ +++D                 E  QR V+ +K    T     E    +
Sbjct: 117  SGEDIIIGKTSPINAD---------------NAELGQRQVQHVKRDASTPLRSTESGIID 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      D +     R VKV V   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 162  QVILTTNQDGL-----RYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTAEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               DI++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  ITPDIIINPHAIPSRMTIAHLIECLLSKVATLKGLEGDATPFTDVTVDSVSELLR 271



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 63/170 (37%), Gaps = 22/170 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D  GI   G  V+
Sbjct: 58  DRGIFRSLFFRSYTDCEKRVGINIVEQFEKPNRSDTLRLKHGTYDKLDADGITAPGIRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             DI++GK +P         ++ ++ +        RD S  + S  SG +
Sbjct: 118 GEDIIIGKTSPINADNAELGQRQVQHVK-------RDASTPLRSTESGII 160


>gi|162532585|gb|ABY16690.1| RNA polymerase beta subunit [Aeromonas veronii]
          Length = 162

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 126/162 (77%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ ++
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYS 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R N YGF+ETPYRKV DG +T++V YLSA+EE    IAQAN++  EDG   +EL+ CR  
Sbjct: 61  RTNEYGFLETPYRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHK 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
           GE   +  ++I ++D SP+Q+VS+AA+LIPFLE+DD+NR L+
Sbjct: 121 GESTFMNADQIQYMDVSPQQIVSVAAALIPFLEHDDANRALI 162


>gi|118426176|gb|ABK90987.1| RpoB [Mycoplasma sp. 8756-C13]
          Length = 208

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 153/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG A+VAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAVVAKEDAIVKYVDSKTI--------ITDGESGIRTYVLS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q PLV+VGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPLVRVGDMVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERVVMDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|118426160|gb|ABK90979.1| RpoB [Mycoplasma leachii PG50]
 gi|118426162|gb|ABK90980.1| RpoB [Mycoplasma leachii]
 gi|118426164|gb|ABK90981.1| RpoB [Mycoplasma leachii]
 gi|118426166|gb|ABK90982.1| RpoB [Mycoplasma leachii]
          Length = 208

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 112/215 (52%), Positives = 152/215 (70%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMARVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|168419323|gb|ACA23558.1| RNA polymerase II [Fusarium sp. NRRL 22396]
          Length = 288

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/361 (15%), Positives = 100/361 (27%), Gaps = 75/361 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 R 1247
             
Sbjct: 288  A 288



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|151573791|gb|ABS18190.1| RNA polymerase II [Fusarium sp. NRRL 43627]
 gi|151573794|gb|ABS18192.1| RNA polymerase II [Fusarium sp. NRRL 43628]
 gi|151573797|gb|ABS18194.1| RNA polymerase II [Fusarium sp. FCSC_1b KOD-2010]
 gi|151573799|gb|ABS18195.1| RNA polymerase II [Fusarium sp. NRRL 43630]
 gi|151573802|gb|ABS18197.1| RNA polymerase II [Fusarium sp. FCSC_3a KOD-2010]
 gi|151573808|gb|ABS18201.1| RNA polymerase II [Fusarium sp. NRRL 43633]
 gi|151573811|gb|ABS18203.1| RNA polymerase II [Fusarium sp. NRRL 43634]
          Length = 289

 Score =  172 bits (437), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 56/362 (15%), Positives = 102/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|126644104|gb|ABO25867.1| second largest RNA polymerase subunit [Arthonia radiata]
          Length = 302

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 52/374 (13%), Positives = 101/374 (27%), Gaps = 76/374 (20%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTMANILYYPPKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    ++ R  I++ +       E+ E   + +         +       +  G   
Sbjct: 61   DRGLF-RSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  L+++      R            ++     +  Q              
Sbjct: 120  SGDDIIIGKTAPLAANAEERGMRGTQHTKRDVSTPLRSTEAGIIDQVL------------ 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                            + VK+     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  ---------LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEG 218

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L         +                        
Sbjct: 219  LVPDIIINPHAIPSRMTIAHLIECLLSKVAATNAYEGD---------------------- 256

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     E ++ +L  +   + G  +
Sbjct: 257  -------------------------------ATP-FTDITVEMVSEILEKSGYQKRGFEV 284

Query: 1236 LYDGLTGEPFDRPV 1249
            +Y+G TG      V
Sbjct: 285  MYNGHTGRKLMAQV 298



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 67/168 (39%), Gaps = 9/168 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S++   +    + 
Sbjct: 20  TRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYIEQEQS 79

Query: 854 TK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 EE  + I      +       +D+ GI+  G  V+  DI++GK  P   +    
Sbjct: 80  VGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPLAAN---A 136

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           EE+ +R        DV        +G+   V+   +  +  +    R+
Sbjct: 137 EERGMRGT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKNVKIRTRT 183


>gi|193201503|gb|ACF15959.1| RNA polymerase II subunit [Opegrapha calcarea]
          Length = 292

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 54/366 (14%), Positives = 103/366 (28%), Gaps = 84/366 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 2    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 61

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 62   LYYRTYIEQEQSVGVQVLEGFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 121

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+S+      R+           ++     +  Q                      
Sbjct: 122  KTAPLASNAEERGMRATQHTKRDVSTPLRSTEAGIIDQVL-------------------- 161

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 162  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 221  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 250

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 251  -----------------------ATP-FTDITVEMVSEILEKSGYQKRGFEVMYNGHTGR 286

Query: 1244 PFDRPV 1249
                 V
Sbjct: 287  KLMAQV 292



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 72/187 (38%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTK----LGPEEITR-DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +        G E+  +     +       +D+ GI+  G  V+
Sbjct: 55  DRGLFRSLYYRTYIEQEQSVGVQVLEGFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +    EE+ +RA       DV        +G+   V+   +  +  
Sbjct: 115 GDDIIIGKTAPLASN---AEERGMRAT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKN 170

Query: 950 IDKNERS 956
           +    R+
Sbjct: 171 VKIRTRT 177


>gi|322517862|gb|ADX06848.1| RNA polymerase II [Fusarium falciforme]
          Length = 287

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 100/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  I+Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118426128|gb|ABK90963.1| RpoB [Mycoplasma mycoides subsp. capri LC]
          Length = 208

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 113/215 (52%), Positives = 154/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L+
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILL 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|118426140|gb|ABK90969.1| RpoB [Mycoplasma mycoides subsp. capri]
          Length = 208

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 112/215 (52%), Positives = 153/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDIVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|198279449|emb|CAP04759.1| RNA polymerase beta subunit [Pinus rzedowskii]
          Length = 284

 Score =  172 bits (436), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 105/257 (40%), Positives = 155/257 (60%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL        GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFXPXKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGK 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/223 (24%), Positives = 87/223 (39%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S IL
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIIL 284


>gi|167393760|ref|XP_001740696.1| DNA-directed RNA polymerase I subunit RPA2 [Entamoeba dispar SAW760]
 gi|165895066|gb|EDR22870.1| DNA-directed RNA polymerase I subunit RPA2, putative [Entamoeba
            dispar SAW760]
          Length = 1106

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 97/636 (15%), Positives = 179/636 (28%), Gaps = 133/636 (20%)

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y     Q       +N  P    G  +R     A G   ++G        +       G 
Sbjct: 577  YCDGYLQDGYHALYLNNLP----GQMIRPVIHRATGNIVNIGPYEQVFLDIKCGDSIEGM 632

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N  +   IS       + T           R+                    +       
Sbjct: 633  NNAEYEEISALNSLSLLATLTPFCHMNQSPRNMYQCQMAKQTMGIPALSNKYR---SDTK 689

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +               + P G +        + A+      D+ D  +   S +      
Sbjct: 690  LLWLHYPQRSICQCALMEPFGFNEYPTGANAIVAVISYTGYDMEDALIIKKSAIERGFGH 749

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                +++   K +     E+ ++                                    G
Sbjct: 750  ---GSQYKAYKVDFEKEGEKNEM----------------------------------FSG 772

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
               S  +  + + +    +  +   ++  +  +++ +  + +    + E  +   + +I 
Sbjct: 773  ITSSGEIFDEHLDDDGLPRPGEI-FENSPIYSHIDKITGKIKGKVLMGERGYIESV-RIV 830

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
             GD++  G+ + V V V   R    GDK +                              
Sbjct: 831  GGDNIDSGLQKAV-VRVRYNRTPVIGDKFS------------------------------ 859

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
                   SR         H     + L  + K +                   +      
Sbjct: 860  -------SR---------HGQKGTLSLHYQEKDMPFTESGMTPDI-------IINPHAFP 896

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPV-FDGAD--EEAINSMLRMADLDESGQSILYD 1238
            +        +S+       K     +TP  FD  +   +     L     +  G   LY 
Sbjct: 897  SRMTIAMLVESMASKVGALKGEYQDATPFKFDEENTAVDYFGKQLLKYGYNYYGSEPLYS 956

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
            G+ G      + +G +Y  +L H V DK   RSTG  S+VT QP+ G+   GG R GEME
Sbjct: 957  GIYGNELQSDIYIGVVYYQRLVHQVKDKYQVRSTGPISIVTHQPIKGRKRGGGIRFGEME 1016

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDV-------VG------RTRVYE----------SIVAG 1335
               + A+G + ++ + L   SD          G      R++ Y+          SIV  
Sbjct: 1017 RDSLVAHGTSMLVHDRLFECSDKCYHYVCTKCGSICTIKRSKEYDKMICQSCGPTSIVK- 1075

Query: 1336 NDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS 1371
                +   P  F  L  E+ A+  ++ L     +NS
Sbjct: 1076 ----KIQIPYVFRYLAAELSAM--NVRLNLKVDRNS 1105



 Score = 70.9 bits (172), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 64/446 (14%), Positives = 145/446 (32%), Gaps = 27/446 (6%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++  S   E +N     +H     ++ +G          +R + P  +G +CP  T +G 
Sbjct: 430 TNGFSITAERLNHSRFTSH---FVSVHRGAFYTTMKTTSIRKLVPEAWGFMCPVHTPDGA 486

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++      R+NA        + +       ++  +S    +   I      +  +G
Sbjct: 487 PCGLLNHFAVSCRINARKHPLPEQKIIDLCT---ELGMVSTQFMKLPSI---YIPVLLNG 540

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               ++           +  E+  +    P  +                    +   M R
Sbjct: 541 KVIGKVSPHEINSFVQQLRYERAIYNPKIPNTLEIGYCDGYLQDGYHALYLNNLPGQMIR 600

Query: 699 QAVPLLKAEAPFVGTGMESVVAKS--SGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDP 754
             +   +A    V  G    V      G +I        E++ A     ++ ++      
Sbjct: 601 PVIH--RATGNIVNIGPYEQVFLDIKCGDSIEGMNNAEYEEISALNSLSLLATLTPFCHM 658

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRP-----LVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           + S  ++Y+    +++     ++ +      L+ +    R     A        +   G 
Sbjct: 659 NQSPRNMYQCQMAKQTMGIPALSNKYRSDTKLLWLHYPQRSICQCALMEPFGFNEYPTGA 718

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N +VA + + GY+ ED+++I +  +          + ++V          E+   I +  
Sbjct: 719 NAIVAVISYTGYDMEDALIIKKSAIERGFGHGSQYKAYKVDFEKEGE-KNEMFSGITSSG 777

Query: 870 EEGLKNIDECGIICVGAEVNPG------DILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           E   +++D+ G+   G            D + GKI  K         + +R + G+    
Sbjct: 778 EIFDEHLDDDGLPRPGEIFENSPIYSHIDKITGKIKGKVLMGERGYIESVRIVGGDNIDS 837

Query: 924 VRDTSLRVPSGVSGTVVDVRIFNRHG 949
               ++         V+  +  +RHG
Sbjct: 838 GLQKAVVRVRYNRTPVIGDKFSSRHG 863



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 86/739 (11%), Positives = 200/739 (27%), Gaps = 147/739 (19%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD----- 87
              S+++FL             L+   K        +    L       + P+++     
Sbjct: 18  HTESFNYFLEKGKEDI------LKYMKKYKIIKKDSTELMELSCTGISIEKPRYNGLPLF 71

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM--------- 138
              C    LTY+  +++T+ +           K  +  K   +  G++P+M         
Sbjct: 72  PYMCRSAALTYSGKIRLTITI-----------KENETSKTIEVDGGEIPIMVGTSKCWIG 120

Query: 139 ----TK-------------DGTFVIKGIQR---------------IVVSQLHR----SPG 162
               T               G F+I GI+R               ++     R    + G
Sbjct: 121 SEYITPEERINIREDPHEIGGYFIINGIERYLRMIVYAKANHPLAVI-----RPSWTNKG 175

Query: 163 IHFDHD--------KGRASLSGKLLY--ACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV 212
            HF           +   +L+  L +    ++       +   F  ++           +
Sbjct: 176 AHFTKYGIIIRCMREDITTLTNTLHFLDNGKVT------LRFIFKKQEFF---------I 220

Query: 213 PVTSFLMAL-GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE 271
           PV   L    GM   EI        + +                      + L   +   
Sbjct: 221 PVVLLLRVYGGMSDREIFELI---TMNNYENSNLVNAAEMLVRRENGSPLNGLNTPEQVL 277

Query: 272 QVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---GETGEIYIEAGDVI 328
             I S  +L     + + +  +    +   CL  L    +  +       +++      I
Sbjct: 278 SYIGSKFRLIMDSTEGVNDIELGKRVLEEFCLVHLSSYSEKSDLLIFMLQKLFALVHGEI 337

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
           DE+ ++      +     LY   +                    A L I + ++     +
Sbjct: 338 DEEGVDTPMSQGVLLPGHLYQTVIKEE----------IQNILSKARLFILKDLKDVKKGS 387

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                     +  +  K   + +            +  D++      I A         +
Sbjct: 388 KITERVYLQRILSNVAKSFGTRIKSFISTGNFETSSTTDLQQTNGFSITAERLNHSRFTS 447

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
              ++         +  S+ +++   +              +  V      P  L+N   
Sbjct: 448 HFVSVHRGAFYTTMKTTSIRKLVPEAWG------------FMCPVHTPDGAPCGLLNHFA 495

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARARAGVEMRDVHPTHY 566
           V   +          ++ +    L  ++    +  S      +     G        +  
Sbjct: 496 VSCRINARKHPLPEQKIIDLCTELGMVSTQFMKLPSIYIPVLLNGKVIGKVSPHEINSFV 555

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--AMEEEN 624
            ++          I     +         G+++  Y  +          YL+    +   
Sbjct: 556 QQLRYERAIYNPKIPNTLEIGYC-----DGYLQDGYHAL----------YLNNLPGQMIR 600

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             I +A  ++   G + +  +  +C      +   +  + + S    +S+ A+L PF   
Sbjct: 601 PVIHRATGNIVNIGPYEQVFLDIKCGDSIEGMNNAE--YEEISALNSLSLLATLTPFCHM 658

Query: 685 DDSNRVLMGCNMQRQAVPL 703
           + S R +  C M +Q + +
Sbjct: 659 NQSPRNMYQCQMAKQTMGI 677


>gi|330785442|gb|AEC46527.1| RNA polymerase II second largest subunit [Syncesia myrticola]
          Length = 292

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 60/366 (16%), Positives = 105/366 (28%), Gaps = 81/366 (22%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 4    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 63

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 64   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 120  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 160

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 161  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 220

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 221  LIINPHAIPSRMTIAHLIECLLSKVSSITGHEGD-------------------------- 254

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 255  ---------------------------ATP-FTDITVSSISELLEFAGYQSRGFELMYNG 286

Query: 1240 LTGEPF 1245
             TG   
Sbjct: 287  HTGRKL 292



 Score = 76.7 bits (187), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 56  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 116 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 174

Query: 950 IDKNERS 956
           +    R+
Sbjct: 175 VKVRTRT 181


>gi|198279325|emb|CAP04697.1| RNA polymerase beta subunit [Pinus taeda]
          Length = 285

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 107/257 (41%), Positives = 158/257 (61%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL + E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 285


>gi|118201866|gb|ABK79746.1| RNA polymerase subunit B [Phaeobacter gallaeciensis]
          Length = 163

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 107/162 (66%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V + KVT++V Y+SA EE    +AQAN++LDEDG F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVNEAKVTDEVHYMSATEEMRHTVAQANATLDEDGKFINDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|5714728|gb|AAD48050.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|5714731|gb|AAD48053.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|12225106|gb|AAG47864.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|12225112|gb|AAG47867.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 166

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 102/164 (62%), Positives = 128/164 (78%)

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV +G VT+++ YLSA+EE N  I
Sbjct: 1   RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVI 60

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+
Sbjct: 61  AQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDA 120

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR
Sbjct: 121 NRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR 164


>gi|151573405|gb|ABS17934.1| RNA polymerase II [Fusarium sp. NRRL 43732]
 gi|151573522|gb|ABS18012.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573537|gb|ABS18022.1| RNA polymerase II [Fusarium nygamai]
 gi|151573699|gb|ABS18129.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573702|gb|ABS18131.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573705|gb|ABS18133.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573708|gb|ABS18135.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573711|gb|ABS18137.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573714|gb|ABS18139.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573717|gb|ABS18141.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573723|gb|ABS18145.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573726|gb|ABS18147.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573729|gb|ABS18149.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573734|gb|ABS18152.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573737|gb|ABS18154.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573740|gb|ABS18156.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573743|gb|ABS18158.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573746|gb|ABS18160.1| RNA polymerase II [Gibberella intermedia]
 gi|151573749|gb|ABS18162.1| RNA polymerase II [Gibberella fujikuroi]
 gi|151573752|gb|ABS18164.1| RNA polymerase II [Gibberella intermedia]
 gi|151573755|gb|ABS18166.1| RNA polymerase II [Gibberella fujikuroi]
 gi|151573758|gb|ABS18168.1| RNA polymerase II [Gibberella intermedia]
 gi|151573761|gb|ABS18170.1| RNA polymerase II [Gibberella intermedia]
 gi|151573764|gb|ABS18172.1| RNA polymerase II [Gibberella intermedia]
 gi|151573767|gb|ABS18174.1| RNA polymerase II [Gibberella intermedia]
 gi|151573770|gb|ABS18176.1| RNA polymerase II [Gibberella intermedia]
 gi|151573773|gb|ABS18178.1| RNA polymerase II [Gibberella intermedia]
 gi|151573776|gb|ABS18180.1| RNA polymerase II [Fusarium sp. NRRL 43619]
 gi|151573785|gb|ABS18186.1| RNA polymerase II [Fusarium sp. NRRL 43624]
 gi|151573788|gb|ABS18188.1| RNA polymerase II [Fusarium sp. NRRL 43625]
 gi|151573814|gb|ABS18205.1| RNA polymerase II [Fusarium sp. FIESC_13a KOD-2010]
 gi|151573829|gb|ABS18215.1| RNA polymerase II [Fusarium sp. FIESC_1a KOD-2010]
 gi|298162099|gb|ADI59498.1| RNA polymerase II beta subunit [Gibberella moniliformis]
 gi|298162102|gb|ADI59500.1| RNA polymerase II beta subunit [Gibberella intermedia]
 gi|298162105|gb|ADI59502.1| RNA polymerase II beta subunit [Fusarium mangiferae]
 gi|298162108|gb|ADI59504.1| RNA polymerase II beta subunit [Gibberella circinata]
 gi|298162114|gb|ADI59508.1| RNA polymerase II beta subunit [Fusarium commune]
          Length = 289

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 56/362 (15%), Positives = 102/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|151573477|gb|ABS17982.1| RNA polymerase II [Fusarium sp. NRRL 43876]
          Length = 281

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 55/348 (15%), Positives = 100/348 (28%), Gaps = 75/348 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ ++  
Sbjct: 8    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVG 66

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E   +           +       +  G           K+  +  +      
Sbjct: 67   LNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGT 126

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+   Q       ++     +      + +                       ++ VKV 
Sbjct: 127  RTTVHQRRDISTPLRSTENGIVDSVIVTVNA--------------------DNVKYVKVR 166

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + 
Sbjct: 167  VRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLI 226

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 227  ECLLSKVSTLEGMEGD-------------------------------------------- 242

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                     +TP F     ++++ +LR       G  I+Y+G TG   
Sbjct: 243  ---------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKL 280



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 34/164 (20%), Positives = 60/164 (36%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 5   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 64

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E+           +       +DE GI+  G  V+  DI++GK  P  +     
Sbjct: 65  VGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDL 124

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +             RD S  + S  +G V  V +       K
Sbjct: 125 GTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNADNVK 161


>gi|151573675|gb|ABS18113.1| RNA polymerase II [Fusarium sp. NRRL 43583]
 gi|151573690|gb|ABS18123.1| RNA polymerase II [Fusarium sp. NRRL 43589]
 gi|151573693|gb|ABS18125.1| RNA polymerase II [Fusarium sp. NRRL 43590]
 gi|151573696|gb|ABS18127.1| RNA polymerase II [Fusarium sp. NRRL 43591]
          Length = 289

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 100/362 (27%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|111278803|gb|ABH09099.1| RNA polymerase II second largest subunit [Endocarpon pallidulum]
          Length = 318

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/378 (16%), Positives = 105/378 (27%), Gaps = 75/378 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 16   ILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 74

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   +  +       EQ E   R           +       I  GQ          
Sbjct: 75   LFYRTYQESEKVVGHNIVEQFEKPTRSDTLRMKHGTYDKIDVDGLIEVGQRVSGEDIIIG 134

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D                +E  QR  + LK    T     E    +++     G
Sbjct: 135  KTAPMAPD---------------AEELGQRQKQHLKRDVSTPLRSTESGIVDQVLVTTSG 179

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D       + VKV V   +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 180  D-----GQKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVVPDLIIN 234

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +  +         ++S +   +           
Sbjct: 235  PHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTNVSNILRSMGYQSRGFEVM- 293

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                           +G +    G    
Sbjct: 294  ----------------------------------------------YNGHT----GR--- 300

Query: 1244 PFDRPVTVGYIYMLKLNH 1261
                 V +G  Y  +L H
Sbjct: 301  KLVAQVFLGPTYYQRLRH 318


>gi|162605726|ref|XP_001713378.1| second-largest subunit of RNA polymerase III [Guillardia theta]
 gi|13794310|gb|AAK39687.1|AF083031_44 second-largest subunit of RNA polymerase III [Guillardia theta]
          Length = 1049

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/375 (17%), Positives = 128/375 (34%), Gaps = 75/375 (20%)

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
             S  +GF K+  L    I         Q   +     + V     +   +   +    K 
Sbjct: 731  SSVERGFFKTAFLRKTKIEISSFRHLTQLFSKVNHNNKEVFEFLNKSNNNNQKITSNLKY 790

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                +     +    L + K  +   R  + GDK +                        
Sbjct: 791  SDNLVVVKYGLD---LTLAKFLIRECRNPEIGDKFS------------------------ 823

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
                         SR                  G+K        + +   S      + +
Sbjct: 824  -------------SR-----------------HGQKGICGFIKPQQDMPFSEKGICPDII 853

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
            +       +++      ++       SG      +F   +   I   LR      +G+  
Sbjct: 854  MNPHGFPSRMTIGKTIEIILSKSGCISGKFKDGSIFKKININTIVKSLRSFGFVSNGEDF 913

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +Y+G+TG   +  +  G ++  +L HMV DK+++R+TG  S +T QP+ G+S  GG R G
Sbjct: 914  MYNGITGNLINNQIYSGIVFYQRLKHMVKDKIHSRATGIKSKLTYQPVEGRSKGGGLRFG 973

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYES-------IVA----GNDTFETGTP 1344
            EME  C+ ++GA+ +  + L + SD        YE+       I+       +      P
Sbjct: 974  EMERDCLISFGASELALDRLLLNSD-------CYEAKFDKNSGIIHTSNSNTNVVAVKIP 1026

Query: 1345 ESFNVLVKEMQALGL 1359
             +  +L++E+Q++ +
Sbjct: 1027 YACKLLLQELQSMNI 1041



 Score =  110 bits (274), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 94/730 (12%), Positives = 221/730 (30%), Gaps = 117/730 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV-FPITAFSGAAMLEFVSYEFDPPKF- 86
           LI  Q  SY+  +             L +  K +   I  ++    ++F++       F 
Sbjct: 12  LIWQQIESYNKLINYQ----------LISILKKIENEIWNYNSFLEIKFINTSMSIGTFF 61

Query: 87  --------DVDDCLWRDLTYAVPLKITL-------------RLIVFDVDEFTGAKSIKDI 125
                          +D TY++ +   L              LI          + I   
Sbjct: 62  EKNIGNTVTPFHSRIKDTTYSIDIYSDLFIRINNKKKFINNNLIFKIPLMLKCNRCILYG 121

Query: 126 KEQSIYM--GDLPLMTKDGTFVIKGIQRIVVSQ----LHRSPGIHFDHDKGRASLSGKLL 179
           K++  Y+   + PL    G F+IKG +++++ Q    L+R        +K ++       
Sbjct: 122 KKEDFYIKINECPL-DPGGYFIIKGTEKVILIQEKLVLNR-----IGIEKDKSGN----- 170

Query: 180 YACRIIPD---QGLWMDIEFDSKDIIHVRIDRRRK-----VPVTSFLMALGMDSE-EILS 230
           +   +I     +          ++ I+ R     K     +P+   L A G ++  +I+ 
Sbjct: 171 FYSYVISSYKKRNTK-SFIIIKENKIYFR----NKIFIEDIPIFIILKAFGFENNLDIID 225

Query: 231 T----FYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLK 286
                F   + YS         ++    +        +  I+T +      +     L  
Sbjct: 226 LIGYEFESTLFYSLTESLKIGFVNQFQSVCYLMQKLDIRFIETNKITFFYNESNYQILDH 285

Query: 287 SLKEKGVKFLGITSDC---LCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
            L    V    ++ +    +    +   ++        +++ D    K LE         
Sbjct: 286 ILSHIIVNKNPVSQNLEKGIFMTMMIRKLLYALQIPDLLDSKDYYGNKRLELSGDLVEIL 345

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
           +  L   S   +         + N+        IY      D  ++ +  +     +   
Sbjct: 346 LEDLLHKSWIESKKFIEKKKIEVNET-------IYHHFIKSDFISYGIENAFITGNWKI- 397

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
           +KY +   G  ++  RL+  +   +      +     K +              +    R
Sbjct: 398 NKYGIDKNGITQILSRLSFMSSFSMLLKTSSNFEKTRKSISPRNL---------HPTQWR 448

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                +  + +    +  +  ++   IS  + D  + +                  + L+
Sbjct: 449 FICTSDTPEGESCGLIKNL--ALLSHISIQENDYFLAKVCNILGVDSKLSSIKTIKNYLN 506

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
             +  +N      H      L     + R+        ++     ++    + +G     
Sbjct: 507 MTKIFLNQKLIGFHQFPSKFLFCFRNMRRSNLIESSVSIYWDSTMKLIWILSDKGRLCRP 566

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTND---VVYLSAMEEENRYIAQANSSLDEDGS 639
           +  + +    +    ++   +K+ +  +      + Y+ + EE N  IA           
Sbjct: 567 LYIIENGILKSKKKHLKLYSKKIINWNILTKFGFIEYIDSNEENNTIIA----------- 615

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
                       + +     +   ++ S   ++ I+ASLIPF +++ S R    C+M +Q
Sbjct: 616 ------------DSLKAINFRSSHLEISEGNILGISASLIPFSDHNQSPRNTYQCSMGKQ 663

Query: 700 AVPLLKAEAP 709
           +   L     
Sbjct: 664 SASFLGFNQN 673


>gi|56406191|gb|AAV87479.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 167

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 99/167 (59%), Positives = 126/167 (75%), Gaps = 1/167 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+D
Sbjct: 121 FTDAFVTCRGEHGESDLYRPDEIHYMDVSTQQVVSVAAALIPFLEHD 167


>gi|293601710|gb|ADE48259.1| RNA polymerase II [Morchella sp. Mel-10]
          Length = 288

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 57/363 (15%), Positives = 105/363 (28%), Gaps = 75/363 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     E+++++LR       G  ++Y+
Sbjct: 255  ----------------------------ATP-FTDVTVESVSTLLRQNGYQSRGFEVMYN 285

Query: 1239 GLT 1241
            G T
Sbjct: 286  GYT 288



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|280985735|gb|ACZ99648.1| RNA polymerase II [Fusarium sp. NRRL 46670]
          Length = 291

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 104/365 (28%), Gaps = 75/365 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGH 285

Query: 1241 TGEPF 1245
            TG   
Sbjct: 286  TGRKL 290



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|151573832|gb|ABS18217.1| RNA polymerase II [Fusarium sp. NRRL 43641]
          Length = 286

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|5714727|gb|AAD48049.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|5714729|gb|AAD48051.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|5714730|gb|AAD48052.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|5714732|gb|AAD48054.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|5714733|gb|AAD48055.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|12225104|gb|AAG47863.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|12225108|gb|AAG47865.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
 gi|12225110|gb|AAG47866.1| RNA polymerase beta subunit [Klebsiella pneumoniae]
          Length = 166

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 103/164 (62%), Positives = 128/164 (78%)

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
           R+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  I
Sbjct: 1   RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVI 60

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           AQANS+LDE+G F E+LV CR  GE  L  R+++D++D S +QVVS+ ASLIPFLE+DD+
Sbjct: 61  AQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDA 120

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR
Sbjct: 121 NRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR 164


>gi|330785180|gb|AEC46396.1| RNA polymerase II second largest subunit [Sparria endlicheri]
          Length = 294

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/366 (15%), Positives = 98/366 (26%), Gaps = 73/366 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
             F R  I+K++       E+ E   +                   +  G           
Sbjct: 61   FFYRTYIEKSKAVGFNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRISGDDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+   +  +                E  QR     +          E    +++      
Sbjct: 121  KTAPFAEPMAENA------------EGGQRTKSHARRDISAPLRSTEAGIIDRVL----- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 164  -LTSVEGNRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM V  + E  L       G +                                
Sbjct: 223  PHAIPSRMTVAHLIECLLSKLSATQGLEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I++ L+       G  ++++G TG 
Sbjct: 253  -----------------------ATP-FTDVTVSIISNELKALGYQSRGLEVMHNGHTGR 288

Query: 1244 PFDRPV 1249
                 V
Sbjct: 289  KLMAQV 294



 Score = 74.3 bits (181), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 75/196 (38%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 53

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +   ++     G EE  +              + +D+ G +  G  ++
Sbjct: 54  DRGLFRSFFYRTYIEKSKAVGFNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRIS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  E      E   R     K+   RD S  + S  +G +  V + +  G
Sbjct: 114 GDDIIIGKTAPFAEPMAENAEGGQRT----KSHARRDISAPLRSTEAGIIDRVLLTSVEG 169

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 170 NRSVKVRTRTTKVPQI 185


>gi|118426126|gb|ABK90962.1| RpoB [Mycoplasma mycoides subsp. mycoides SC]
 gi|290566360|gb|ADD39558.1| DNA-dependent RNA polymerase beta-subunit [Mycoplasma capricolum
           subsp. capripneumoniae M1601]
          Length = 208

 Score =  172 bits (436), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 112/215 (52%), Positives = 152/215 (70%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTS HI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSTHIDEYTLEVRNTKQGQEE 207


>gi|306413154|gb|ADM86675.1| RNA polymerase II beta subunit [Fusarium lateritium]
          Length = 287

 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/362 (16%), Positives = 108/362 (29%), Gaps = 81/362 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D+ ++         E+  +    + + +    Y +L E   +  G           
Sbjct: 62   RSYSDQEKKVGLNY---TEVFEKPFQQQTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+Q  Q       ++     +  Q   + +                
Sbjct: 119  KTAPIDQENQDLGTRTQAHQRRDISTPLRSTENGIVDQVIMTVNA--------------- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 164  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 219  PHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------------ 248

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     ++++ +LR       G  ++Y+G TG 
Sbjct: 249  -----------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGR 284

Query: 1244 PF 1245
              
Sbjct: 285  KL 286



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQQTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +A   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QAHQRRDISTPLRSTENGIVDQVIMTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118201860|gb|ABK79743.1| RNA polymerase subunit B [Oceanicola granulosus]
          Length = 163

 Score =  172 bits (435), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D +VT++V Y+SA EE    +AQAN++LD+ G+F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDAQVTDEVHYMSATEEMRHTVAQANATLDDAGNFLNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +GE  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGEYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|306413163|gb|ADM86681.1| RNA polymerase II beta subunit [Fusarium sporotrichioides]
          Length = 287

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|197941928|gb|ACH78569.1| RNA polymerase subunit [Picea mariana]
          Length = 281

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 102/253 (40%), Positives = 152/253 (60%), Gaps = 10/253 (3%)

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L + E    GTG+E   A  SG+  +A + G +E +DA+                     
Sbjct: 1   LFQPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRT 52

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYN
Sbjct: 53  ELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYN 112

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           FED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++
Sbjct: 113 FEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLV 172

Query: 883 CVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +G+ +  GD+LVGK+TP+        PE +LL+ IFG +    R+  LR P G  G V+
Sbjct: 173 MLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVI 232

Query: 941 DVRIFNRHGIDKN 953
           DVR  NR     +
Sbjct: 233 DVRWINRVDDSGD 245



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 72   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 130

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 131  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 184

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 185  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 242

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 243  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 281


>gi|118201862|gb|ABK79744.1| RNA polymerase subunit B [Octadecabacter antarcticus]
 gi|118201864|gb|ABK79745.1| RNA polymerase subunit B [Octadecabacter arcticus]
          Length = 163

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 105/162 (64%), Positives = 125/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V DG VT++V Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVTDGVVTDEVHYMSATEEMRHTVAQANANLDENMRFVNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE  L P E ++ ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 NGEYTLAPSENVNLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|168419263|gb|ACA23518.1| RNA polymerase II [Nectria illudens]
 gi|168419356|gb|ACA23580.1| RNA polymerase II [Fusarium sp. NRRL 22632]
          Length = 289

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 100/362 (27%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  I+Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|280985717|gb|ACZ99639.1| RNA polymerase II [Fusarium equiseti]
 gi|280985719|gb|ACZ99640.1| RNA polymerase II [Fusarium equiseti]
 gi|280985721|gb|ACZ99641.1| RNA polymerase II [Fusarium sp. NRRL 44925]
 gi|280985725|gb|ACZ99643.1| RNA polymerase II [Fusarium sp. NRRL 46658]
 gi|280985727|gb|ACZ99644.1| RNA polymerase II [Fusarium sp. NRRL 46660]
 gi|280985729|gb|ACZ99645.1| RNA polymerase II [Fusarium sp. NRRL 46666]
 gi|280985731|gb|ACZ99646.1| RNA polymerase II [Fusarium sp. NRRL 46668]
 gi|280985733|gb|ACZ99647.1| RNA polymerase II [Fusarium sp. NRRL 46669]
 gi|280985737|gb|ACZ99649.1| RNA polymerase II [Fusarium sp. NRRL 46671]
 gi|280985739|gb|ACZ99650.1| RNA polymerase II [Fusarium sp. NRRL 46680]
          Length = 291

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 104/365 (28%), Gaps = 75/365 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGH 285

Query: 1241 TGEPF 1245
            TG   
Sbjct: 286  TGRKL 290



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|46488902|gb|AAS99654.1| RNA polymerase II [Xanthoparmelia conspersa]
          Length = 713

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 57/338 (16%), Positives = 102/338 (30%), Gaps = 42/338 (12%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 415  MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 474

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G     
Sbjct: 475  -RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSG 530

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D      R++          ++     +  Q   S            
Sbjct: 531  EDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS------------ 578

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 579  --------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMV 630

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +  +          +S L         
Sbjct: 631  PDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLR------- 683

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                              V     +G  + T VF G  
Sbjct: 684  --------EHGYQSRGFEVMYNGHTGRKLVTQVFFGPT 713



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 35/170 (20%), Positives = 64/170 (37%), Gaps = 22/170 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 420 YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 469

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +       +D+ G++  G  V+
Sbjct: 470 DRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVS 529

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 530 GEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 572



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/280 (13%), Positives = 85/280 (30%), Gaps = 23/280 (8%)

Query: 465 RSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ- 521
              G +L + +R    ++ + + +  +    +         + +  + + +     +   
Sbjct: 2   ELAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLPVKSTHLTNGLSYSLATGNW 61

Query: 522 ------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRI 569
                       +SQ+       S ++H  R +      +       + R +H TH+G +
Sbjct: 62  GDQKKADCVKAGVSQVLNRYTFASTLSHLLRTNT----PIGXDGKIAKPRQLHNTHWGLV 117

Query: 570 CPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYI 627
           CPAET EG   GLV +L     +      E    +    + +   +   L++      ++
Sbjct: 118 CPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEXLEEYEPLNSPNATKIFV 177

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLEND 685
                 +  D +     V        I      + D  D   K          P F+ ++
Sbjct: 178 NGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDN 237

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
           D      G  +  +           +G     ++    G 
Sbjct: 238 DPKSSNRGNLVLTKEHRPTLEMDREIGLRPNLMLESDMGW 277


>gi|330785186|gb|AEC46399.1| RNA polymerase II second largest subunit [Arthonia zwackhii]
          Length = 294

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/367 (15%), Positives = 106/367 (28%), Gaps = 84/367 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 3    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 62

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 63   LYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+               A  +E+  R  +  K    T     E    +++      
Sbjct: 123  KTAPLA---------------ATAEERGSRLSQHTKRDVSTPLRSTEAGIIDQVL----- 162

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 163  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 221

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 222  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 251

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 252  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTGR 287

Query: 1244 PFDRPVT 1250
                   
Sbjct: 288  KLMAQCF 294



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 66/187 (35%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +   +   E            +       +D+ GI+  G  V+
Sbjct: 56  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 116 GDDIIIGKTAPLAATAEERGSRL----SQHTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKIRTRT 178


>gi|294721630|gb|ADF32965.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 292

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 57/366 (15%), Positives = 104/366 (28%), Gaps = 75/366 (20%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             V             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 2    HVLYYPQKPLATTRSMEFLXFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-R 60

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +F R  ID+ ++    + E+     R           +       I  G          
Sbjct: 61   SLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVSGDDVII 120

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K   ++ D      R++                    +Y    + L       ++ +  
Sbjct: 121  GKVAPIAPDADELGQRTK------------------AHEYRDVSTPLRSTENGIVDCVAL 162

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                    L+ VK+     +  Q GDK A RHG KG +      EDMPF ++G   D+++
Sbjct: 163  --TTNAENLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLII 220

Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
            NP  +PSRM +  + E  L       G++                               
Sbjct: 221  NPHAIPSRMTIAHLIECLLSKVGAIKGQEGD----------------------------- 251

Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                    +TP F     + I+ +L        G  ++Y+G TG
Sbjct: 252  ------------------------ATP-FTDVTVQNISDLLIQHGYQSRGFEVMYNGHTG 286

Query: 1243 EPFDRP 1248
            +     
Sbjct: 287  QKLRAQ 292



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 67/186 (36%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 2   HVLYYPQKPL----------ATTRSMEFLXFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 51

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   +   E            +       +D+ G+I  G 
Sbjct: 52  SSIDRGLFRSLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGV 111

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK+ P         ++        KA + RD S  + S  +G V  V +  
Sbjct: 112 RVSGDDVIIGKVAPIAPDADELGQRT-------KAHEYRDVSTPLRSTENGIVDCVALTT 164

Query: 947 RHGIDK 952
                K
Sbjct: 165 NAENLK 170


>gi|289183866|ref|YP_003457407.1| RNA-polymerase RPO132 [Pseudocowpox virus]
 gi|288804338|gb|ADC54003.1| RNA-polymerase RPO132 [Pseudocowpox virus]
          Length = 1161

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 73/427 (17%), Positives = 139/427 (32%), Gaps = 63/427 (14%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMYAERPIVVSKALETSKIADNCFGNHVTIALMSFRGMNQEDGIILKRQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDIYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGVTPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SR  +  + E  L            +    +K   +    R               I   
Sbjct: 912  SRKTLSMLMEVIL------------TTAYGHKPFAEDGSNRPICFPSTNETDFDTYIEFA 959

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                 L   E  +      + VF                     + +L+D  T EPF   
Sbjct: 960  RRCYALSHPEAAEDDPEFESRVF--------------------CERVLFDPETDEPFAAR 999

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAA 1308
            V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ ++GAA
Sbjct: 1000 VFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMISHGAA 1059

Query: 1309 YVLQEML 1315
            + + E+L
Sbjct: 1060 FTVSEIL 1066


>gi|118201854|gb|ABK79740.1| RNA polymerase subunit B [Nereida ignava]
          Length = 163

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 105/162 (64%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG+VT++V Y+SA EE    +AQAN++LDE G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGQVTDEVQYMSATEEMRHTVAQANANLDEGGKFVNDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P + ++ ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPSDSVNLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|325073788|gb|ADY76841.1| PP245 [Orf virus]
          Length = 1161

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 70/431 (16%), Positives = 135/431 (31%), Gaps = 71/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMFAERPIVVSKALETSKIADNCFGHHVTIALMSFRGMNQEDGIILKRQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDMYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGIAPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A              +        D      F  +          
Sbjct: 912  SRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALSHPEAA 971

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D + +  +                                        +L+D  T EP
Sbjct: 972  ADDPEFERRVFCER------------------------------------VLFDPETDEP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ +
Sbjct: 996  FAARVFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMIS 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA+ + E+L
Sbjct: 1056 HGAAFTVAEIL 1066


>gi|258576891|ref|XP_002542627.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Uncinocarpus
           reesii 1704]
 gi|237902893|gb|EEP77294.1| DNA-directed RNA polymerase II 138 kDa polypeptide [Uncinocarpus
           reesii 1704]
          Length = 884

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 104/786 (13%), Positives = 229/786 (29%), Gaps = 157/786 (19%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG-----AAMLEFVSYEFDP 83
           L+  Q  S+D F+   +  +    +G     +++ P              L+F +     
Sbjct: 38  LVSQQLDSFDEFISTTMQ-ELVEEQGQVTLDQTIAPEEDDPDPVLVRRYELKFGTVMLAR 96

Query: 84  PKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSI----------- 122
           P               +   R+LTYA PL + +   V +  E + A+             
Sbjct: 97  PSMTEGDGATSIMLPQEARLRNLTYASPLYLGITKKVAEGRERSLAERDEDEEPEEKGDE 156

Query: 123 ------------------KDIKEQSIYMGDLPLMTKD----------------------- 141
                              +  E++I++G +P+M K                        
Sbjct: 157 ERRARGTYLQWAPRALPEDEEGEENIFIGKMPIMLKSKYCILKDLGEHALYNWNECPYDS 216

Query: 142 -GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIP--DQGLWMDIEFDS 198
            G F+I G ++++++Q  RS G        + +      +   I    ++G  +  +   
Sbjct: 217 GGYFIINGSEKVLIAQE-RSAGNI--VQVFKKAPPSPTPFVAEIRSAVEKGSRILSQLSI 273

Query: 199 KDIIHVRIDRRR--------------K--VPVTSFLMALG-MDSEEILSTFYPKIVYSQR 241
           K  +  + D  +              K  +P+     ALG +  E+IL+        +  
Sbjct: 274 K--LFAKGDSSKGGFGPTIRSTLPYIKTDIPIVVVFRALGVVSDEDILNHICYDRNDTPM 331

Query: 242 GDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-- 299
            +     +    ++   +V+   +          + +K        ++++ +  +  +  
Sbjct: 332 LEMLKPCIEEGFVIQDREVALDFISKRGSSPTSMNHEKRVRYARDIIQKEFLPHISQSEG 391

Query: 300 ----SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
                    G  V + ++    G   ++  D   +K L+           +L++    + 
Sbjct: 392 SETRKAFFLGYMVHK-LLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDL 450

Query: 356 AYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVK 415
                  V    +      +    +       T  +  ++    + +  K   S  G  +
Sbjct: 451 YKYVQRCVETNRQLYLKIGVKASTL-------TGGLKYALATGNWGEQKKAASSKAGVSQ 503

Query: 416 MNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLK 472
           +  R    +      R          I     L N   G +   +    +    V  +  
Sbjct: 504 VLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 563

Query: 473 NQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
             Y       E  I    + +   ++   PQ   N+  +      F     +    +  +
Sbjct: 564 MCYITVGTPSEPIIDFMIQRNMEVLEEFEPQVSPNSTKI------FVNGVWVGVHRDASH 617

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            +S +   RR + +                   +H   +  A+                A
Sbjct: 618 LVSTVQSLRRRNLI-------------------SHEVSLLEAD------------KEIPA 646

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----- 645
            ++A    E  Y        +  V Y+ A EEE   I      L+    +    +     
Sbjct: 647 DLDAEERRER-YYGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEASKQYRAGYIPEEDT 705

Query: 646 --FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
               R    ++          +  P  ++ I AS+IPF +++ S R      M +QA+ +
Sbjct: 706 SDPNRRVKSKLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGV 765

Query: 704 LKAEAP 709
                 
Sbjct: 766 FLTNFD 771



 Score =  136 bits (343), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 108/735 (14%), Positives = 219/735 (29%), Gaps = 110/735 (14%)

Query: 211 KVPVTSFLMALGMDSEEILSTFYPKIVYS------QRGDFWCFPLSAADLMVGAKVSSSL 264
           K+P    L         IL       +Y+        G ++    S   L+   + + ++
Sbjct: 186 KMP--IMLK----SKYCILKDLGEHALYNWNECPYDSGGYFIINGSEKVLIAQERSAGNI 239

Query: 265 VDIDTGEQ------------VIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDI 312
           V +                  +E G ++ S L   L  KG    G     +    +    
Sbjct: 240 VQVFKKAPPSPTPFVAEIRSAVEKGSRILSQLSIKLFAKGDSSKGGFGPTIRST-LPYIK 298

Query: 313 VNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKD 372
            +     ++   G V DE  L  I +       +  +       ++         +DR+ 
Sbjct: 299 TDIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFV--------IQDREV 350

Query: 373 ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIR 432
           AL  I +    G   T    E    +      K  L  +              +     +
Sbjct: 351 ALDFISKR---GSSPTSMNHEKRVRYARDIIQKEFLPHI-----------SQSEGSETRK 396

Query: 433 KEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RI 490
              +  ++  L+    G+  +DD D+ G +R+   G +L N +R+  +R+ + + +  + 
Sbjct: 397 AFFLGYMVHKLLQCALGRRDVDDRDHFGKKRLDLAGPLLANLFRVLFMRLTKDLYKYVQR 456

Query: 491 SSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRITH 537
                  +  +  + A  +   +     +               +SQ+       S ++H
Sbjct: 457 CVETNRQLYLKIGVKASTLTGGLKYALATGNWGEQKKAASSKAGVSQVLNRYTYASTLSH 516

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RR +      + R     + R +H TH+G +CPAET EG   GLV +L     +     
Sbjct: 517 LRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTP 572

Query: 598 IET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
            E    +    + +V  +     +      ++      +  D S     V        I 
Sbjct: 573 SEPIIDFMIQRNMEVLEEFEPQVSPNSTKIFVNGVWVGVHRDASHLVSTVQSLRRRNLIS 632

Query: 656 VP----------REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ-------- 697
                          +D  +   +            +E  D+        +         
Sbjct: 633 HEVSLLEADKEIPADLDAEERRERYYGWDGLVKSGVVEYVDAEEEETIMIVMTPEDLEAS 692

Query: 698 RQAVPLLKAE-----------APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +Q       E           +            +   + I+   A I+   D  +    
Sbjct: 693 KQYRAGYIPEEDTSDPNRRVKSKLSQKAHTWTHCEIHPSMILGICASIIPFPDHNQSPRN 752

Query: 747 SVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           + +  +     GV       + +         Q+PL                      +L
Sbjct: 753 TYQSAMGKQAMGVFLTNFDQRMETMANILYYPQKPL----------ATTRSMEFLKFREL 802

Query: 806 ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
             G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E  R  
Sbjct: 803 PAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYTDSEKMIGLTVVE--RFE 860

Query: 866 PNVSEEGLKNIDECG 880
             +  + L+     G
Sbjct: 861 KPMRSDTLRMKHGTG 875


>gi|197941922|gb|ACH78566.1| RNA polymerase subunit [Picea glauca]
          Length = 280

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 102/253 (40%), Positives = 152/253 (60%), Gaps = 10/253 (3%)

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L + E    GTG+E   A  SG+  +A + G +E +DA+                     
Sbjct: 1   LFQPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRT 52

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
            L+ +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYN
Sbjct: 53  ELVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYN 112

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           FED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++
Sbjct: 113 FEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLV 172

Query: 883 CVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +G+ +  GD+LVGK+TP+        PE +LL+ IFG +    R+  LR P G  G V+
Sbjct: 173 MLGSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVI 232

Query: 941 DVRIFNRHGIDKN 953
           DVR  NR     +
Sbjct: 233 DVRWINRVDDSGD 245



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/223 (23%), Positives = 86/223 (38%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 72   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 130

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 131  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 184

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 185  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 242

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +L
Sbjct: 243  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVL 280


>gi|118426142|gb|ABK90970.1| RpoB [Mycoplasma mycoides subsp. capri]
          Length = 208

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 153/215 (71%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL++
Sbjct: 1   VSRFNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIR 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD +++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVIKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|146335198|gb|ABQ23339.1| RNA polymerase beta subunit [Corynebacterium massiliense]
          Length = 135

 Score =  172 bits (435), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/163 (34%), Positives = 84/163 (51%), Gaps = 36/163 (22%)

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E HLGW     G K+ +   D +    +  L   L  V                     
Sbjct: 1    LELHLGWLAKA-GWKVDT--EDPRNEEILKTLPEELYDVPPNSLA--------------- 42

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRP 1248
                      +TPVFDGA  E ++++LR +  +  G        ++ L+DG +GEP+  P
Sbjct: 43   ----------ATPVFDGATNEELSALLRSSKPNRDGDVLVDENGKATLFDGRSGEPYMYP 92

Query: 1249 VTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            V+VGY+Y+LKL+H++ +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 93   VSVGYMYILKLHHLIDEKIHARSTGPYSMITQQPLGGKAQFGG 135


>gi|67942354|gb|AAY83377.1| DNA-dependent RNA polymerase II [Neournula pouchetii]
          Length = 540

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 88/596 (14%), Positives = 158/596 (26%), Gaps = 69/596 (11%)

Query: 576  EGHNIGLVS--SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV   SL S+  V         Y    + +   +     +      ++      
Sbjct: 1    EGQACGLVKLLSLMSYITVGTPSDPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVG 60

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +  D       V        +      I D  D   K          P    ++      
Sbjct: 61   IHRDPMHLVRNVQEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSER 120

Query: 693  GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
               +  Q   + + E          +              G+VE VDA       +    
Sbjct: 121  RGQLVLQKEHIQRLEQDA------ELEPDDRWGWDGLLNEGVVEYVDAEEEETIMIVMTP 174

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +       + +  + +         + P   V     +       PS  LG       + 
Sbjct: 175  EDLEIAAQVRQGFQIEEDADRHKRVKAP---VNSNTHQYTHCEIHPSMILG-------IC 224

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   + +  F                         
Sbjct: 225  ASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM--------------------- 261

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +  +  I      +  D+ +   
Sbjct: 262  ------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQ 315

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +   +    +F R   D+ +R   +  E+ E   R           +       +  G
Sbjct: 316  SSIDRGLF-RSLFYRSYTDQEKRVGMMVVEEFEKPQRSNTLRLKHGTYDKIDDDGLVAPG 374

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +S D                DE  QR     K    T     E+ 
Sbjct: 375  VRVSGEDIIIGKTAPISPD---------------ADEMGQRQKFHTKRDVSTPLRSTENG 419

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
              +++             L+  KV +   +  Q GDK A RHG KG +      EDMPF 
Sbjct: 420  IVDQVLL-----TTNAEGLKFAKVRMRTTKVPQIGDKFASRHGQKGTIGITYRMEDMPFT 474

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
             +G   D+V+NP  +PSRM +  + E  L       G +  +          +S L
Sbjct: 475  CEGIIPDLVINPHAIPSRMTIAHLIECQLSKVSSLRGMEGDATPFTDVTVDSVSSL 530



 Score = 94.8 bits (234), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 76/482 (15%), Positives = 140/482 (29%), Gaps = 87/482 (18%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 32  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG-HE 84

Query: 549 VARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           V+  R   +      T  GR+C        +T+      LV       R+     +E   
Sbjct: 85  VSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEQDAELEPDD 144

Query: 603 RK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           R           V Y+ A EEE   I      L+         V      EE     +++
Sbjct: 145 RWGWDGLLNEGVVEYVDAEEEETIMIVMTPEDLE-----IAAQVRQGFQIEEDADRHKRV 199

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
                S                                                     +
Sbjct: 200 KAPVNSNTHQ---------------------------------------------YTHCE 214

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRP 780
              + I+   A I+   D  +    + +  +     GV       +           Q+P
Sbjct: 215 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAERMDTMANILYYPQKP 274

Query: 781 LVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFT 840
           L                      +L  G+N +V  M + GYN EDS+++++  +   +F 
Sbjct: 275 L----------ATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFR 324

Query: 841 SIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           S+    +    +   +   E        +   +       ID+ G++  G  V+  DI++
Sbjct: 325 SLFYRSYTDQEKRVGMMVVEEFEKPQRSNTLRLKHGTYDKIDDDGLVAPGVRVSGEDIII 384

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNER 955
           GK  P      +P+   +     +K    RD S  + S  +G V  V +       K  +
Sbjct: 385 GKTAPI-----SPDADEMGQR--QKFHTKRDVSTPLRSTENGIVDQVLLTTNAEGLKFAK 437

Query: 956 SI 957
             
Sbjct: 438 VR 439


>gi|264658155|emb|CBH32068.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 111

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 67/94 (71%), Gaps = 8/94 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 18   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 77

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 78   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 111


>gi|264658151|emb|CBH32074.1| RNA polymerase beta subunit [Corynebacterium amycolatum]
          Length = 110

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 67/94 (71%), Gaps = 8/94 (8%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYML 1257
            V+TPVFDGA+ E +  +L  +  +  G        ++ L+DG +GE F  PV+VGY+YML
Sbjct: 17   VATPVFDGAENEELAGLLASSRPNRDGEVLVNADGKATLFDGRSGEKFPFPVSVGYMYML 76

Query: 1258 KLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            KL+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 77   KLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 110


>gi|41057164|ref|NP_957878.1| ORF101 RNA polymerase subunit RPO132 [Orf virus]
 gi|41018721|gb|AAR98326.1| ORF101 RNA polymerase subunit RPO132 [Orf virus]
          Length = 1161

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 70/431 (16%), Positives = 135/431 (31%), Gaps = 71/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMFAERPIVVSKALETSKIADNCFGHHVTIALMSFRGMNQEDGIILKRQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDIYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGIAPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A              +        D      F  +          
Sbjct: 912  SRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALSHPEAA 971

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D + +  +                                        +L+D  T EP
Sbjct: 972  ADDPEFEHRVFCER------------------------------------VLFDPETDEP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ +
Sbjct: 996  FAARVFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMIS 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA+ + E+L
Sbjct: 1056 HGAAFTVAEIL 1066


>gi|118426152|gb|ABK90975.1| RpoB [Mycoplasma capricolum subsp. capricolum]
          Length = 208

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 152/215 (70%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG +IVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGESIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SER+V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSERIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|74230813|gb|ABA00618.1| RNA polymerase RPO132 [Orf virus]
          Length = 1161

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 70/431 (16%), Positives = 135/431 (31%), Gaps = 71/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMFAERPIVVSKALETSKIADNCFGHHVTIALMSFRGMNQEDGIILKRQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDIYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGIAPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A              +        D      F  +          
Sbjct: 912  SRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALSHPEAA 971

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D + +  +                                        +L+D  T EP
Sbjct: 972  ADDPEFEHRVFCER------------------------------------VLFDPETDEP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ +
Sbjct: 996  FAARVFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMIS 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA+ + E+L
Sbjct: 1056 HGAAFTVAEIL 1066


>gi|151573856|gb|ABS18233.1| RNA polymerase II [Fusarium oxysporum]
          Length = 288

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 56/361 (15%), Positives = 102/361 (28%), Gaps = 75/361 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G  ++Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKLR 287

Query: 1247 R 1247
             
Sbjct: 288  A 288



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|41018588|gb|AAR98196.1| ORF101 RNA polymerase subunit RPO132 [Orf virus]
          Length = 1161

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 70/431 (16%), Positives = 135/431 (31%), Gaps = 71/431 (16%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD--TSLRVPSGVSGTVVDVRIFNRHG 949
            D  +  +  +    ++   +  +         V     S R  +   G ++  +   R G
Sbjct: 700  DNGIHLMFAERPIVVSKALETSKIADNCFGHHVTIALMSFRGMNQEDGIILKRQFAERGG 759

Query: 950  IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLS 1009
            +D              L  +    E  + + N   R+      +  V+G           
Sbjct: 760  LDI-------------LTCKKYQVEIPLENFNNRERVRSAAYSKIDVNGVVRLNAFLEQG 806

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNV-ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
              +             V D ++  ++ E     Y      ++    +K++          
Sbjct: 807  DAIARNVSSRTLDDDFVADNQISFDIAERYSDIYAARVERVQADLTDKVK---------- 856

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
                 V+     +R    GDK   R   KG V+ +    ++P+ ++G   D+++N   + 
Sbjct: 857  -----VRALTVRERRAILGDKFTTRTSQKGTVAYVADETELPYDENGIAPDVIINSTSIF 911

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKS----LINDYKANGDISPLRSFLEKVIGTGSHTEK 1184
            SR  +  + E  L  A              +        D      F  +          
Sbjct: 912  SRKTLSMLMEVILTTAYGHKPFAEDGSNRPICFPSTNETDFETYIEFARRCYALSHPEAA 971

Query: 1185 ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
              D + +  +                                        +L+D  T EP
Sbjct: 972  ADDPEFEHRVFCER------------------------------------VLFDPETDEP 995

Query: 1245 FDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQA 1304
            F   V  G +Y L+L H+  DK   R  G  + + +Q   G+   GG ++GEME  C+ +
Sbjct: 996  FAARVFFGPLYYLRLRHLTLDKATVRCRGRKTKLIRQANEGRRRGGGIKIGEMERDCMIS 1055

Query: 1305 YGAAYVLQEML 1315
            +GAA+ + E+L
Sbjct: 1056 HGAAFTVAEIL 1066


>gi|17225234|gb|AAL37310.1| RNA polymerase B-subunit [Staphylococcus epidermidis]
          Length = 172

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|197941920|gb|ACH78565.1| RNA polymerase subunit [Picea glauca]
 gi|197941924|gb|ACH78567.1| RNA polymerase subunit [Picea glauca]
          Length = 280

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 101/251 (40%), Positives = 151/251 (60%), Gaps = 10/251 (3%)

Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
           + E    GTG+E   A  SG+  +A + G +E +DA+                      L
Sbjct: 2   QPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTEL 53

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
           + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFE
Sbjct: 54  VIYQRSNTNTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFE 113

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
           D++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +
Sbjct: 114 DAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVML 173

Query: 885 GAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
           G+ +  GD+LVGK+TP+        PE +LL+ IFG +    R+  LR P G  G V+DV
Sbjct: 174 GSWIETGDVLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDV 233

Query: 943 RIFNRHGIDKN 953
           R  NR     +
Sbjct: 234 RWINRVDDSGD 244



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 280


>gi|17225242|gb|AAL37314.1| RNA polymerase B-subunit [Staphylococcus hyicus]
          Length = 172

 Score =  171 bits (434), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 131/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDLETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPE 172


>gi|306413166|gb|ADM86683.1| RNA polymerase II beta subunit [Fusarium concolor]
          Length = 287

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEMFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEMFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118201896|gb|ABK79761.1| RNA polymerase subunit B [Sulfitobacter delicatus]
 gi|118201898|gb|ABK79762.1| RNA polymerase subunit B [Sulfitobacter dubius]
          Length = 163

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 105/162 (64%), Positives = 125/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D  VT++V Y+SA EE    +AQAN++LDE+  F  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDSTVTDEVHYMSATEEMRHTVAQANANLDENMKFVNELVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPTENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|312204300|gb|ADQ47467.1| RNA polymerase II second largest subunit [Belonia russula]
          Length = 705

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 56/347 (16%), Positives = 108/347 (31%), Gaps = 81/347 (23%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 437  MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKRVG 495

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    E + +    Y +L +   I  G           K+  ++ D   
Sbjct: 496  I---SLVEQFEKPMRSETLRVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEE 552

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+++         ++     +                  ++K+          L+ V
Sbjct: 553  LGQRTKFHTKRDASTPLRSTENGI------------------VDKVLM--TTNAEGLKFV 592

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMP   DG   D+++NP  +PSRM + 
Sbjct: 593  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPLSADGITPDLIINPHAIPSRMTIA 652

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E  L       G +                                           
Sbjct: 653  HLIECQLSKVSSLRGYEGD----------------------------------------- 671

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                        +TP F     ++++ +LR       G  ++Y+G T
Sbjct: 672  ------------ATP-FTEVTVDSVSRLLREHGYQSRGFELMYNGHT 705



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 434 TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKR 493

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  +   V     + +D+ GII  G  V+  DI++GK  P        
Sbjct: 494 VGISLVEQFEKPMRSETLRVKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDSEEL 553

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++        K    RD S  + S  +G V  V +       K
Sbjct: 554 GQRT-------KFHTKRDASTPLRSTENGIVDKVLMTTNAEGLK 590



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 66/195 (33%), Gaps = 9/195 (4%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 63  GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 118

Query: 581 GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GLV +L     +      E    +    + +V  +   +        ++      +  D 
Sbjct: 119 GLVKNLALMCYITVGSPSEPIVEFMVQRNMEVLEEYEPIRNPHSTKVFVNGVWVGVHRDP 178

Query: 639 SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMGCN 695
           +     V        I      I D  D   K          P   ++ND  +       
Sbjct: 179 AHLVSTVQTLRRQNMISSEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNDKKSPNKGSLV 238

Query: 696 MQRQAVPLLKAEAPF 710
           + ++ V  L+ +   
Sbjct: 239 LTKELVGKLEDDREL 253



 Score = 40.1 bits (92), Expect = 2.6,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 65/249 (26%), Gaps = 31/249 (12%)

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRV 464
             G      +         + + +    + +  L        R+GK       +  +  +
Sbjct: 47  ATGNWGDQKKAASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGL 106

Query: 465 RSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEF 516
               E  + Q    +  +       + S     V      N + +          +   F
Sbjct: 107 VCPAETPEGQACGLVKNLALMCYITVGSPSEPIVEFMVQRNMEVLEEYEPIRNPHSTKVF 166

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETS 575
                +    +  + +S +   RR + +  +  + R     E +    T  GR+C     
Sbjct: 167 VNGVWVGVHRDPAHLVSTVQTLRRQNMISSEVSLIRDIRDREFK--IFTDAGRVCRPLFV 224

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND---------------VVYLSAM 620
             ++    +  +        G +E       D                     V +L A 
Sbjct: 225 IDNDKKSPNKGSLVLTKELVGKLEDDRELPADMDPDEKKARYFGWAGLVANGAVEFLDAE 284

Query: 621 EEENRYIAQ 629
           EEE   IA 
Sbjct: 285 EEETVMIAM 293


>gi|218547417|sp|P0C8K3|RPB2_ASFM2 RecName: Full=DNA-directed RNA polymerase subunit 2
          Length = 1242

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 96/257 (37%), Gaps = 72/257 (28%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYAR----STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
              +L   V  D    R    S G    +T QPL GK + GG RLGEME W + A GA   
Sbjct: 1108 HQRLQKFVLDD----RYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA--- 1160

Query: 1311 LQEMLTI--KS-DDVVG 1324
               M TI  KS DD  G
Sbjct: 1161 ---MQTIIEKSHDDSDG 1174



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 83/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + S+ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNSASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHSTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----AGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T      +       E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMLRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNKACYKAAEARKKGDKDWEKHKIPFIQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSITELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|198279479|emb|CAP04774.1| RNA polymerase beta subunit [Pinus aristata]
          Length = 276

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 103/255 (40%), Positives = 154/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL +      GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFRPXKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 51/217 (23%), Positives = 82/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 276


>gi|118201890|gb|ABK79758.1| RNA polymerase subunit B [Ruegeria pomeroyi]
          Length = 163

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 107/162 (66%), Positives = 127/162 (78%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V  G+VT++V Y+SA EE    +AQAN++LDE+G F  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKGGQVTDEVHYMSATEEMRHTVAQANATLDENGKFVNELVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGDYTLAPMESVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|218547418|sp|P0C8K4|RPB2_ASFP4 RecName: Full=DNA-directed RNA polymerase subunit 2
 gi|218547419|sp|P0C8K5|RPB2_ASFWA RecName: Full=DNA-directed RNA polymerase subunit 2
          Length = 1242

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 96/257 (37%), Gaps = 72/257 (28%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYAR----STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
              +L   V  D    R    S G    +T QPL GK + GG RLGEME W + A GA   
Sbjct: 1108 HQRLQKFVLDD----RYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA--- 1160

Query: 1311 LQEMLTI--KS-DDVVG 1324
               M TI  KS DD  G
Sbjct: 1161 ---MQTIIEKSHDDSDG 1174



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 82/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----AGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T      +       E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMLRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKGDKDWEKHKIPFVQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSIIELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|151573414|gb|ABS17940.1| RNA polymerase II [Fusarium sp. NRRL 43735]
 gi|151573817|gb|ABS18207.1| RNA polymerase II [Fusarium sp. NRRL 43636]
 gi|151573820|gb|ABS18209.1| RNA polymerase II [Fusarium sp. NRRL 43637]
 gi|151573823|gb|ABS18211.1| RNA polymerase II [Fusarium sp. NRRL 43638]
 gi|151573826|gb|ABS18213.1| RNA polymerase II [Fusarium sp. FIESC_19a KOD-2010]
          Length = 286

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|67942336|gb|AAY83368.1| DNA-dependent RNA polymerase II [Plectania nannfeldtii]
          Length = 541

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 78/586 (13%), Positives = 154/586 (26%), Gaps = 63/586 (10%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V         Y    + +   +     +      ++      +  D       V
Sbjct: 2    LMSYITVGTPSEPIVDYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDPMHLVRNV 61

Query: 646  FCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                    +      I D  D   K          P    ++         +  Q   + 
Sbjct: 62   QEVRRKGIVGHEVSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIE 121

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            K E        E        + ++    G+VE VDA       +    +       + + 
Sbjct: 122  KLEEDHNLDEDEPQRQPYGWSGLL--GDGVVEYVDAEEEETIMIVMTPEDLEVAQQVRQG 179

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             + +         + P   V     +       PS  LG       +  + +P+  +N  
Sbjct: 180  YELEEETDPNKRVKAP---VNPNASQYTHCEIHPSMILG-------ICASIIPFPDHNQS 229

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                    M  + +   + +  F                                 +  +
Sbjct: 230  PRNTYQSAMGKQAMG--VFLTNFAERM---------------------------DTMANI 260

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +       +   +  +  I      +  D+ +   S +   +    +
Sbjct: 261  LYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSL 319

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKK 1004
            F R  +D+ +R      E+ E   R    +      +       +  G           K
Sbjct: 320  FYRSYMDQEKRIGMQVVEEFEKPQRTNTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGK 379

Query: 1005 STVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGD 1064
            +  ++ D+     R ++         ++     +  Q                       
Sbjct: 380  TAPIAPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML-------------------- 419

Query: 1065 DMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNP 1124
                  L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP
Sbjct: 420  TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGIVPDLIINP 479

Query: 1125 LGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
              +PSRM +  + E  L       G +  +          +S L  
Sbjct: 480  HAIPSRMTIAHLIECQLSKVSSLRGMEGDATPFTDVTVDSVSSLLR 525



 Score = 94.4 bits (233), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 71/471 (15%), Positives = 146/471 (30%), Gaps = 71/471 (15%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 21  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG--- 71

Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG 608
                    +RD+    +     A                   VN     E   + V   
Sbjct: 72  ----HEVSVIRDIRDREFKIFTDAGRVCRPLFV----------VNNDTTSERRGQLVLQK 117

Query: 609 KVTNDVVYLSAMEEENRYIAQ-ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
           +    +     ++E+         S L  DG                      ++++DA 
Sbjct: 118 EHIEKLEEDHNLDEDEPQRQPYGWSGLLGDG---------------------VVEYVDAE 156

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
            ++ + I  +         + +V  G  ++ +  P  + +AP      +    +   + I
Sbjct: 157 EEETIMIVMTPEDLEV---AQQVRQGYELEEETDPNKRVKAPVNPNASQYTHCEIHPSMI 213

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +     GV       +           Q+PL     
Sbjct: 214 LGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAERMDTMANILYYPQKPL----- 268

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +V  M + GYN EDS+++++  +   +F S+    
Sbjct: 269 -----ATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 323

Query: 847 FEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        +   +       +DE G++  G  V+  DI++GK  P 
Sbjct: 324 YMDQEKRIGMQVVEEFEKPQRTNTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPI 383

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++       +K    RD S  + S  +G V  V +       K
Sbjct: 384 APDVDEMGQR-------QKYHTKRDVSTPLRSTENGIVDQVMLTTNAEGLK 427


>gi|218547416|sp|P0C8K2|RPB2_ASFK5 RecName: Full=DNA-directed RNA polymerase subunit 2
          Length = 1242

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 96/257 (37%), Gaps = 72/257 (28%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYAR----STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
              +L   V  D    R    S G    +T QPL GK + GG RLGEME W + A GA   
Sbjct: 1108 HQRLQKFVLDD----RYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA--- 1160

Query: 1311 LQEMLTI--KS-DDVVG 1324
               M TI  KS DD  G
Sbjct: 1161 ---MQTIIEKSHDDSDG 1174



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 81/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHSTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----AGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T      +       E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMLRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNEACYKAAEARKKGNKDWEKHKISFVQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKAILAGTLTLEDLVAQGICEFITPEEAENCLVAFSITELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   +I  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQSILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|198279339|emb|CAP04704.1| RNA polymerase beta subunit [Pinus flexilis]
          Length = 280

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 101/250 (40%), Positives = 151/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S ILP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISIILP 280


>gi|303398738|emb|CBW46719.1| EP1242L [African swine fever virus Georgia 2007/1]
          Length = 1242

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 75/257 (29%), Positives = 96/257 (37%), Gaps = 72/257 (28%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYAR----STGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYV 1310
              +L   V  D    R    S G    +T QPL GK + GG RLGEME W + A GA   
Sbjct: 1108 HQRLQKFVLDD----RYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA--- 1160

Query: 1311 LQEMLTI--KS-DDVVG 1324
               M TI  KS DD  G
Sbjct: 1161 ---MQTIIEKSHDDSDG 1174



 Score = 65.1 bits (157), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 82/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC----AGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T      +       E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMLRREGKVVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKGDKDWEKHKIPFIQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTPQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSIIELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|198279473|emb|CAP04771.1| RNA polymerase beta subunit [Pinus mugo]
          Length = 275

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 106/257 (41%), Positives = 156/257 (60%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVP    E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPXFXPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T+ GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTRQGPERITREIPHLDAHLLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 62.4 bits (150), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 48/214 (22%), Positives = 77/214 (35%), Gaps = 14/214 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+        ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTRQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             GD+        V V+++ KR IQ GDK+AGRHG
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHG 275


>gi|151573480|gb|ABS17984.1| RNA polymerase II [Fusarium sp. NRRL 43877]
 gi|151573636|gb|ABS18087.1| RNA polymerase II [Fusarium sp. FSSC_16b KOD-2010]
 gi|151573687|gb|ABS18121.1| RNA polymerase II [Fusarium sp. NRRL 43588]
          Length = 286

 Score =  171 bits (434), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 100/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  I+Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|193201463|gb|ACF15939.1| RNA polymerase II subunit [Arthonia cinnabarina]
          Length = 293

 Score =  171 bits (433), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 53/366 (14%), Positives = 101/366 (27%), Gaps = 84/366 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 3    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 62

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 63   LYYRTYIEQEQTVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L++       R            ++     +  Q                      
Sbjct: 123  KTAPLAATTEERGARLTQHTKRDVSTPLRSTEAGIIDQVL-------------------- 162

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 163  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 221

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 222  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 251

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 252  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTGR 287

Query: 1244 PFDRPV 1249
                 V
Sbjct: 288  KLMAQV 293



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 69/187 (36%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 56  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L +        DV        +G+   V+   +  +  
Sbjct: 116 GDDIIIGKTAPLAATTEERGARLTQ----HTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKIRTRT 178


>gi|117573516|gb|ABK40934.1| RNA polymerase subunit B [Pseudomonas sp. C6-2]
          Length = 160

 Score =  171 bits (433), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 90/160 (56%), Positives = 120/160 (75%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+D++
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDNA 160


>gi|17225244|gb|AAL37315.1| RNA polymerase B-subunit [Staphylococcus simulans]
          Length = 172

 Score =  171 bits (433), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 105/172 (61%), Positives = 131/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F +E + CR  G    
Sbjct: 61  IETPYRKVDHEKNAVTDQIDYLTADEEDSYVVAQANSRLDDEGRFLDEEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + REK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MDREKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|151573586|gb|ABS18054.1| RNA polymerase II [Lecanicillium lecanii]
          Length = 286

 Score =  171 bits (433), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 101/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E               +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDPETQDLGTRTTAHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  I+Y+G TG+  
Sbjct: 249  --------------------ATP-FTDVTVDSVSDLLRKHGYQSRGFEIMYNGHTGKKL 286



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P       PE + L       A   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPID-----PETQDLGTR--TTAHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|118201838|gb|ABK79732.1| RNA polymerase subunit B [Ketogulonicigenium robustum]
          Length = 163

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 111/162 (68%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DGKVT+DV Y+SA EE    IAQAN+ LD +G F EELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGKVTDDVQYMSATEEMRHTIAQANAHLDAEGRFVEELVDTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+  L  RE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGDYTLATRETVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|17225262|gb|AAL37324.1| RNA polymerase B-subunit [Staphylococcus schleiferi]
          Length = 172

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 131/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDLETNTITDRIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPE 172


>gi|151573558|gb|ABS18036.1| RNA polymerase II [Gibberella thapsina]
 gi|280985743|gb|ACZ99652.1| RNA polymerase II [Fusarium sp. NRRL 53091]
 gi|280985745|gb|ACZ99653.1| RNA polymerase II [Fusarium sp. NRRL 53092]
          Length = 285

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 1    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 59

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 60   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 119

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 120  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 161

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 162  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 219

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 220  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 246

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 247  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 284



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 62/164 (37%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 9   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 68

Query: 854 TKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   EI           +       +DE GI+  G  V+  DI++GK  P  +     
Sbjct: 69  VGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDL 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +        ++   RD S  + S  +G V  V +       K
Sbjct: 129 GTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNADNVK 165


>gi|162849436|emb|CAN10401.1| RNA polymerase subunit 2 [African swine fever virus OURT 88/3]
 gi|291289497|emb|CBH29154.1| BA71V-EP1242L [African swine fever virus E75]
          Length = 1242

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 96/253 (37%), Gaps = 64/253 (25%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
              +L   V  D+    S G    +T QPL GK + GG RLGEME W + A GA      M
Sbjct: 1108 HQRLQKFVLDDRYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA------M 1161

Query: 1315 LTI--KS-DDVVG 1324
             TI  KS DD  G
Sbjct: 1162 QTIIEKSHDDSDG 1174



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 82/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL----VFCRCAGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T        +     E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMFRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKGDKDWEKHKIPFIQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSIIELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|151573552|gb|ABS18032.1| RNA polymerase II [Gibberella intermedia]
 gi|306413157|gb|ADM86677.1| RNA polymerase II beta subunit [Fusarium oxysporum]
 gi|306413172|gb|ADM86687.1| RNA polymerase II beta subunit [Fusarium ananatum]
 gi|306413175|gb|ADM86689.1| RNA polymerase II beta subunit [Fusarium acutatum]
 gi|306413181|gb|ADM86693.1| RNA polymerase II beta subunit [Fusarium subglutinans]
          Length = 287

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 56/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|9628161|ref|NP_042747.1| RNA polymerase subunit 2 [African swine fever virus]
 gi|1173143|sp|P42487|RPO2_ASFB7 RecName: Full=DNA-directed RNA polymerase subunit 2
 gi|311528|emb|CAA79698.1| putative RNA polymerase second largest subunit [African swine fever
            virus]
 gi|780423|gb|AAA65283.1| RNA polymerase subunit 2 [African swine fever virus]
 gi|1097443|prf||2113434BD RNA polymerase:SUBUNIT=2
          Length = 1242

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 96/253 (37%), Gaps = 64/253 (25%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSERLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
              +L   V  D+    S G    +T QPL GK + GG RLGEME W + A GA      M
Sbjct: 1108 HQRLQKFVLDDRYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA------M 1161

Query: 1315 LTI--KS-DDVVG 1324
             TI  KS DD  G
Sbjct: 1162 QTIIEKSHDDSDG 1174



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 82/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL----VFCRCAGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T        +     E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMFRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKGDKDWEKHKIPFIQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSIIELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|67623921|ref|XP_668243.1| DNA-directed RNA polymerase II second largest chain
           [Cryptosporidium hominis TU502]
 gi|54659429|gb|EAL38006.1| DNA-directed RNA polymerase (EC 2.7.7.6) II second largest chain
           [Cryptosporidium hominis]
          Length = 733

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 100/741 (13%), Positives = 216/741 (29%), Gaps = 123/741 (16%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-------------AFSGAAMLE 75
           L+  Q  S++ F+M            LQ       PI                    +L+
Sbjct: 34  LVNQQLESFNDFIMYK----------LQEIVDEHPPIIITPQSQYRPDEQIDTKVRYVLK 83

Query: 76  FVSYEFDPPKFD----------VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
           F       P  +           ++   R+LTY+ P+ +     V+ +++      + + 
Sbjct: 84  FGQLSLSRPSVEEREGVARGLWPNEARLRNLTYSSPVFVDAEQKVYKLEDDGSETLVYET 143

Query: 126 KEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSP 161
               + +  +P+M +                         G F+I G+++++V Q  R  
Sbjct: 144 VYSRLPLAKIPIMLRSEYCWTHNISERELQSAGECVYDQGGYFIINGMEKVLVGQE-RMA 202

Query: 162 GIHFDHDKGRASLSGKLLYACRIIPDQ-GLWMDIEFDSK---------DII----HVRID 207
              F +   ++  S K  +   I  ++ G+     F  K          I+    ++R D
Sbjct: 203 NN-FVYLFQKSQPS-KYTWIAEIRSNREGMQATSGFSVKLRGSDGNQGQIVATLPYIRTD 260

Query: 208 RRRKVPVTSFLMALG-MDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
               +P+     ALG +  ++ILS        +Q        L          V    + 
Sbjct: 261 ----IPIAILFRALGVLSDKDILSRCVYDFNDTQMLALLRPSLEETFEFFSQDVCLDFIG 316

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKG-VKFLGIT------SDCLCGLYVAEDIVNGETGE 319
                  + + ++      K L EK  +  +G+T           G  V +  + G  G 
Sbjct: 317 KRG--PTVGAAREKRIQYAKELFEKELLPHVGVTSGSESRKAYFIGYMVHKLCL-GALGR 373

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           +  +  D   +K L+             +   + +   +    + +  +       D+  
Sbjct: 374 VPEDDRDHFGKKRLDLAGPLVAASFGQCFRKMMKDVRRLLQRNIDNGKE------FDVAG 427

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDII 437
           V+R     T ++        +       +   G  ++  RL   +      R        
Sbjct: 428 VIRSASYITQTIQYQFATGNWGKDKDGKIIRTGVSQVLSRLTFTSALSYLRRLNTPLGRE 487

Query: 438 AIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDS 497
                   L N    +                ++KN   +  + +        + +D   
Sbjct: 488 GKFAKPRQLHNTHWGMICPAETPEGHSVG---LVKNLALMCEISVGYRPYAIRTFLDEWG 544

Query: 498 VMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVE 557
           +   D I  + +   +  F   + +   ++  +S+S +   RR   +             
Sbjct: 545 MDSIDEIPPEGIKRKIKVFLNGNWVGCFDDSEDSISNLRMIRRSGEIPYETSIVLDVVNR 604

Query: 558 MRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI------ETPYRKVCDGKVT 611
              +       + P           +      + +N           E       D   T
Sbjct: 605 EVKLFTDSGRSMRPLYIVGEDGDLKIKKSHINSLLNENPSFDEKMEDEKHDYTWDDLVNT 664

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             + Y+   EEE   IA   + L  D  +                        +  P  +
Sbjct: 665 GIIEYIDCEEEETSMIAMFINDLRIDRGY-----------------CSTYTHCEIHPSLI 707

Query: 672 VSIAASLIPFLENDDSNRVLM 692
           + + AS+IPF +++ S++  +
Sbjct: 708 LGVCASIIPFPDHNQSSKKCL 728



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 60/375 (16%), Positives = 125/375 (33%), Gaps = 39/375 (10%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---E 488
           +   I  ++  L     G+   DD D+ G +R+   G ++   +     +M + ++   +
Sbjct: 355 KAYFIGYMVHKLCLGALGRVPEDDRDHFGKKRLDLAGPLVAASFGQCFRKMMKDVRRLLQ 414

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
           R      +  +   + +A  +   +   F +               +SQ+   +   S +
Sbjct: 415 RNIDNGKEFDVAGVIRSASYITQTIQYQFATGNWGKDKDGKIIRTGVSQVLSRLTFTSAL 474

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           ++ RRL+      + R     + R +H TH+G ICPAET EGH++GLV +L     ++  
Sbjct: 475 SYLRRLNT----PLGREGKFAKPRQLHNTHWGMICPAETPEGHSVGLVKNLALMCEIS-V 529

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL----DEDGSFTEELVFCRCAG 651
           G+     R   D    + +  +     + +     N +     D+       L   R +G
Sbjct: 530 GYRPYAIRTFLDEWGMDSIDEIPPEGIKRKIKVFLNGNWVGCFDDSEDSISNLRMIRRSG 589

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFL-------------ENDDSNRVLMGCNMQR 698
           E        +D ++   K       S+ P                 +         + + 
Sbjct: 590 EIPYETSIVLDVVNREVKLFTDSGRSMRPLYIVGEDGDLKIKKSHINSLLNENPSFDEKM 649

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           +           V TG+   +        +        ++D           ++ PS   
Sbjct: 650 EDEKHDYTWDDLVNTGIIEYIDCEEEETSMIAMFINDLRIDRGYCS-TYTHCEIHPSLIL 708

Query: 759 VDIYRLMKFQRSNQN 773
                ++ F   NQ+
Sbjct: 709 GVCASIIPFPDHNQS 723


>gi|330785322|gb|AEC46467.1| RNA polymerase II second largest subunit [Reichlingia leopoldii]
          Length = 291

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 106/365 (29%), Gaps = 84/365 (23%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 1    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 60

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 61   LYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+               A  +E+  R  +  K    T     E    +++      
Sbjct: 121  KTAPLA---------------ATAEERGSRLSQHTKRDVSTPLRSTEAGIIDQVL----- 160

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 161  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 219

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 220  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 249

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 250  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTGR 285

Query: 1244 PFDRP 1248
                 
Sbjct: 286  KLMAQ 290



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 66/187 (35%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +   +   E            +       +D+ GI+  G  V+
Sbjct: 54  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 114 GDDIIIGKTAPLAATAEERGSRL----SQHTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 169

Query: 950 IDKNERS 956
           +    R+
Sbjct: 170 VKIRTRT 176


>gi|197941934|gb|ACH78572.1| RNA polymerase subunit [Pinus strobus]
 gi|197941936|gb|ACH78573.1| RNA polymerase subunit [Pinus strobus]
 gi|197941938|gb|ACH78574.1| RNA polymerase subunit [Pinus strobus]
          Length = 280

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 101/250 (40%), Positives = 151/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILP 280


>gi|198279409|emb|CAP04739.1| RNA polymerase beta subunit [Pinus douglasiana]
          Length = 281

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 106/257 (41%), Positives = 157/257 (61%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL +      GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPXKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 84/220 (38%), Gaps = 14/220 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIIS 281


>gi|198279317|emb|CAP04694.1| RNA polymerase beta subunit [Pinus brutia]
          Length = 276

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 72.0 bits (175), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 81/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 276


>gi|151573474|gb|ABS17980.1| RNA polymerase II [Fusarium sp. NRRL 43875]
          Length = 287

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 100/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G  I+Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|17225236|gb|AAL37311.1| RNA polymerase B-subunit [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 172

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F  + V CR  G   +
Sbjct: 61  IETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFIADEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|219564075|gb|ACL28221.1| RNA polymerase II second largest subunit [fungal sp. M218]
          Length = 284

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 101/359 (28%), Gaps = 75/359 (20%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              V             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R  +D+ +R      EQ E   R +  +      +       +  G         
Sbjct: 60   RSLFYRAYLDQEKRVGMSVVEQFEKPQRAETMKMKQGTYDKLDDDGLVAPGARVSGEDIL 119

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  ++ D      R++          ++     +  Q                    
Sbjct: 120  IGKTAPIAPDAEELGQRTKMHVKRDASTPLRSTENGIVDQVLL----------------- 162

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     L+ VK+     +  Q GDK A RHG KG +      EDMPF  +G   DI+
Sbjct: 163  ---TTNTEGLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDII 219

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G++                              
Sbjct: 220  INPHAIPSRMTIAHLIECLLSKVAALTGQEGD---------------------------- 251

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                     +TP F      +++ +L      + G  ++Y+G 
Sbjct: 252  -------------------------ATP-FTDVTITSVSELLERHGFQKRGFEVMYNGH 284



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   + +     +D+ G++  GA V+
Sbjct: 55  DRGLFRSLFYRAYLDQEKRVGMSVVEQFEKPQRAETMKMKQGTYDKLDDDGLVAPGARVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DIL+GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 115 GEDILIGKTAPIAPDAEELGQRT-------KMHVKRDASTPLRSTENGIVDQVLLTTNTE 167

Query: 950 IDK 952
             K
Sbjct: 168 GLK 170


>gi|198279447|emb|CAP04758.1| RNA polymerase beta subunit [Pinus maximinoi]
          Length = 285

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 107/257 (41%), Positives = 158/257 (61%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL + E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 285


>gi|118201850|gb|ABK79738.1| RNA polymerase subunit B [Loktanella vestfoldensis]
          Length = 163

 Score =  171 bits (433), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 110/162 (67%), Positives = 129/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DGKVT+DV Y+SA EE    +AQAN+S++ DGSF  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGKVTDDVQYMSATEEMRHTVAQANASMNPDGSFRNDLVSTRV 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 NGDYTLAPRENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|297528029|gb|ADI46059.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-31]
 gi|297528031|gb|ADI46060.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-27]
 gi|297528033|gb|ADI46061.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-10]
 gi|297528035|gb|ADI46062.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-27]
 gi|297528037|gb|ADI46063.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-26]
 gi|297528039|gb|ADI46064.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-26]
 gi|297528041|gb|ADI46065.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528043|gb|ADI46066.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-26]
 gi|297528045|gb|ADI46067.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528047|gb|ADI46068.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528049|gb|ADI46069.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528051|gb|ADI46070.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-29]
 gi|297528053|gb|ADI46071.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-26]
 gi|297528057|gb|ADI46073.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528059|gb|ADI46074.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-9]
 gi|297528061|gb|ADI46075.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528063|gb|ADI46076.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528065|gb|ADI46077.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528067|gb|ADI46078.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528069|gb|ADI46079.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528071|gb|ADI46080.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528073|gb|ADI46081.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528075|gb|ADI46082.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528079|gb|ADI46084.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528081|gb|ADI46085.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-30]
 gi|297528083|gb|ADI46086.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528085|gb|ADI46087.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528087|gb|ADI46088.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528089|gb|ADI46089.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-2]
 gi|297528091|gb|ADI46090.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-8]
 gi|297528093|gb|ADI46091.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-31]
 gi|297528095|gb|ADI46092.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-31]
 gi|297528097|gb|ADI46093.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-27]
 gi|297528099|gb|ADI46094.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-31]
 gi|297528101|gb|ADI46095.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-3]
 gi|297528103|gb|ADI46096.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-3]
 gi|297528105|gb|ADI46097.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-3]
 gi|297528111|gb|ADI46100.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528113|gb|ADI46101.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-10]
 gi|297528115|gb|ADI46102.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528117|gb|ADI46103.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528119|gb|ADI46104.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528121|gb|ADI46105.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528123|gb|ADI46106.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
 gi|297528125|gb|ADI46107.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-27]
 gi|297528127|gb|ADI46108.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-8]
 gi|297528129|gb|ADI46109.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528131|gb|ADI46110.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528133|gb|ADI46111.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-29]
 gi|297528135|gb|ADI46112.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-20]
 gi|297528137|gb|ADI46113.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-8]
 gi|297528141|gb|ADI46115.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-29]
 gi|297528143|gb|ADI46116.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-10]
 gi|297528147|gb|ADI46118.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-7]
          Length = 318

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 58/386 (15%), Positives = 107/386 (27%), Gaps = 81/386 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 71   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 176  ---------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    +  
Sbjct: 227  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVESVSTLLR--QNG 284

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +       + Y                                               
Sbjct: 285  YQSRGFEVMYNGYT---------------------------------------------- 298

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNH 1261
               G         V +G  Y  +L H
Sbjct: 299  ---GR---KLVCQVFLGPTYYQRLRH 318



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 68/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA + + G
Sbjct: 4   TNFAERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G++  G  V+  DI++GK  P         ++       +K    RD S  + S  
Sbjct: 114 LDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTE 166

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 167 NGIVDQVMLTTNAEGLK 183


>gi|162849263|emb|CAN10153.1| RNA polymerase subunit 2 [African swine fever virus Benin 97/1]
          Length = 1242

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 96/253 (37%), Gaps = 64/253 (25%)

Query: 1076 VFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQ 1135
            + +  +R +  GDKM+ R GNKGI +  LP  DMPF +DG   D+++NP   PSRM  GQ
Sbjct: 982  MRLRYERNLNIGDKMSSRSGNKGIAALALPTSDMPFTEDGLQPDLIVNPHSHPSRMTNGQ 1041

Query: 1136 IFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLR 1195
            + ET +G A    G               +S   +                         
Sbjct: 1042 MIETTVGLANALQGVVTDGTAFLPINVQLLSKRLAQEGLRFNGCQKM------------- 1088

Query: 1196 VAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIY 1255
                           F+G                           TGE FD  + +G  Y
Sbjct: 1089 ---------------FNG--------------------------QTGEYFDAAIFIGPTY 1107

Query: 1256 MLKLNHMV-SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
              +L   V  D+    S G    +T QPL GK + GG RLGEME W + A GA      M
Sbjct: 1108 HQRLQKFVLDDRYAVASYGPTDALTGQPLDGKRSHGGLRLGEMEHWVLTAQGA------M 1161

Query: 1315 LTI--KS-DDVVG 1324
             TI  KS DD  G
Sbjct: 1162 QTIIEKSHDDSDG 1174



 Score = 66.3 bits (160), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 82/526 (15%), Positives = 175/526 (33%), Gaps = 58/526 (11%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + ++ D++  M Q +I+    +        +   +Q  E  N L+ I+  R ++      
Sbjct: 472 KNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTN 531

Query: 549 VARARAGVEM-RDVHPTHYGRICPAETSE-GHNIGLVSSLTSFARVNAYGFIETPYRKVC 606
            ++     +M R VH ++ G IC A++++ G  +G+   L   A V   G + +  +++ 
Sbjct: 532 ASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLL 591

Query: 607 DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL----VFCRCAGEEILVPREKID 662
                  +  +S  +   + +A+   + +  G  T        +     E  +V      
Sbjct: 592 SDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMFRREGKIVHPHTTI 651

Query: 663 FID---ASPKQVVSIAASLIPFLENDD------------------------------SNR 689
           + D      +  + +     P L  D+                                 
Sbjct: 652 YWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKGDKDWEKHKIPFIQN 711

Query: 690 VLMGCNMQRQAVPLLKAEAPFVGTGM-ESVVAKSSGAAIVA--------------KRAGI 734
                 M +  +         V  G+ E +  + +   +VA              +R   
Sbjct: 712 TRFTSQMAKDILAGTLTLEDLVAQGICEFITPEEAENCLVAFSIIELRKHKHDVTRRFTH 771

Query: 735 VEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDII 794
           V+   AI  +   V    + +      Y   + +++    C +    V +    +  + +
Sbjct: 772 VDVPQAILGLAALVSPYANCTQPARVTYETNQGRQTGGWYCFSWPYRVDMNRFFQFYNEM 831

Query: 795 ADGPSTDLGD-LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
               +      +  G N +VA+M + GYN EDS+++S+  +    F      E +V    
Sbjct: 832 PLVKTIAHNYVIPNGLNTIVAYMIYGGYNQEDSVIVSQSFIDRGGFAGTFYREEKVELES 891

Query: 854 TKLGPEEITRDI-PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEK 911
                 +    I  N+           G + VG  V  GDI++GK+   +GE     +  
Sbjct: 892 DIESFGKPDPLITKNLKPGANYEKLVDGFVPVGTVVKKGDIIIGKVAKIRGEKDELNKYI 951

Query: 912 LLRAIFGEKAVDVRDTSLRVP-SGVSGTVVDVRIFNRHGIDKNERS 956
               ++G     V D  +R          +    + R+    ++ S
Sbjct: 952 DRSVMYGFDEPAVVDAVMRPHGPNDEIFGLMRLRYERNLNIGDKMS 997


>gi|123979414|gb|ABM81532.1| RNA polymerase II second largest subunit [Usnea strigosa]
          Length = 697

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 57/340 (16%), Positives = 102/340 (30%), Gaps = 42/340 (12%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 397  DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 456

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 457  LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRV 512

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 513  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 562

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 563  ----------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 612

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 613  MVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLR----- 667

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                V     +G  + T VF G  
Sbjct: 668  ----------EHGYQSRGFEVMYNGHTGRKLVTQVFLGPT 697



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 86/264 (32%), Gaps = 22/264 (8%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            R+   G +L + +R    ++ + + +  +    +         + +  + + +     +
Sbjct: 1   ERLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSLAT 60

Query: 520 SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                          +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 61  GNWGDQKKAASVKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHW 116

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEEN 624
           G +CPAET EG   GLV +L     +      E    +    + +V  +   L++     
Sbjct: 117 GLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMIQRNMEVLEEYEPLNSPNATK 176

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLE 683
            ++      +  D +     V        I      + D  D   K          P   
Sbjct: 177 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFV 236

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAE 707
            D+  R     ++      +LK E
Sbjct: 237 IDNDPRSSNRGHLVLTKDHVLKLE 260



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 35/178 (19%), Positives = 64/178 (35%), Gaps = 22/178 (12%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PL                      +L  G+N +VA   + GYN EDS
Sbjct: 396 MDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 445

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +   +   E     +  D   +       +D+ G+
Sbjct: 446 VIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGL 505

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           +  G  V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 506 VAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 556


>gi|198279457|emb|CAP04763.1| RNA polymerase beta subunit [Pinus pinea]
          Length = 281

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 107/257 (41%), Positives = 156/257 (60%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL   E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFXPEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGK 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 84/220 (38%), Gaps = 14/220 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIIS 281


>gi|81251259|gb|ABB69974.1| RpoB [Actinobacillus rossii]
          Length = 166

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 98/166 (59%), Positives = 123/166 (74%), Gaps = 1/166 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDENLR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
           FT+  V  R   GE  L   E I ++D S +QVVS+AA+LIPFLE+
Sbjct: 121 FTDTFVTARGEHGESGLYRPEDIHYMDVSTQQVVSVAAALIPFLEH 166


>gi|198279435|emb|CAP04752.1| RNA polymerase beta subunit [Pinus hartwegii]
          Length = 283

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL   E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFXPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 283


>gi|17225240|gb|AAL37313.1| RNA polymerase B-subunit [Staphylococcus hominis subsp. hominis]
          Length = 172

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|330785384|gb|AEC46498.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
          Length = 294

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 60/366 (16%), Positives = 105/366 (28%), Gaps = 81/366 (22%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 65

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 66   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 121

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 122  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 162

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 163  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 222

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +                            
Sbjct: 223  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGD-------------------------- 256

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                       +TP F      +I+ +L  A     G  ++Y+G
Sbjct: 257  ---------------------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNG 288

Query: 1240 LTGEPF 1245
             TG   
Sbjct: 289  HTGRKL 294



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 64/187 (34%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 118 GEDIIIGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKVRTRT 183


>gi|198279443|emb|CAP04756.1| RNA polymerase beta subunit [Pinus devoniana]
          Length = 281

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 107/257 (41%), Positives = 158/257 (61%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL + E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 78.2 bits (191), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 84/220 (38%), Gaps = 14/220 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIIS 281


>gi|17225256|gb|AAL37321.1| RNA polymerase B-subunit [Staphylococcus xylosus]
          Length = 172

 Score =  171 bits (433), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 131/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T  + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|193201467|gb|ACF15941.1| RNA polymerase II subunit [Arthonia radiata]
          Length = 278

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 52/352 (14%), Positives = 98/352 (27%), Gaps = 76/352 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    ++ R  I++ +   
Sbjct: 3    MEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLYYRTYIEQEQSVG 61

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   + +         +       +  G           K+  L+++      
Sbjct: 62   VQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPLAANAEERGM 121

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R            ++     +  Q                              + VK+ 
Sbjct: 122  RGTQHTKRDVSTPLRSTEAGIIDQVL---------------------LTSVDGKKNVKIR 160

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM +  + 
Sbjct: 161  TRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIAHLI 220

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L         +                                              
Sbjct: 221  ECLLSKVAATNAYEGD-------------------------------------------- 236

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPV 1249
                     +TP F     E ++ +L  +   + G  ++Y+G TG      V
Sbjct: 237  ---------ATP-FTDITVEMVSEILEKSGYQKRGFEVMYNGHTGRKLMAQV 278



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/166 (20%), Positives = 67/166 (40%), Gaps = 9/166 (5%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S++   +    +   
Sbjct: 2   SMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYIEQEQSVG 61

Query: 856 -LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
               EE  + I      +       +D+ GI+  G  V+  DI++GK  P   +    EE
Sbjct: 62  VQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPLAAN---AEE 118

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           + +R        DV        +G+   V+   +  +  +    R+
Sbjct: 119 RGMRGT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKNVKIRTRT 163


>gi|151573651|gb|ABS18097.1| RNA polymerase II [Fusarium sp. NRRL 36168]
          Length = 289

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 100/362 (27%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     ++++ +LR       G   +Y+G TG    
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFENMYNGHTGRKLR 287

Query: 1247 RP 1248
              
Sbjct: 288  AQ 289



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|297528107|gb|ADI46098.1| DNA-dependent RNA polymerase II [Morchella sp. Mes-8]
 gi|297528109|gb|ADI46099.1| DNA-dependent RNA polymerase II [Morchella sp. Mes-17]
 gi|297528149|gb|ADI46119.1| DNA-dependent RNA polymerase II [Morchella sp. Mes-17]
 gi|297528151|gb|ADI46120.1| DNA-dependent RNA polymerase II [Morchella sp. Mes-17]
          Length = 318

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/383 (14%), Positives = 102/383 (26%), Gaps = 75/383 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 71   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 129

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 130  DIIIGKTAPITPDVDEMGQRQKYHTKRDVSTPLRSTENGIVDQVML-------------- 175

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 176  ------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 229

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +  +          +S L    +    +
Sbjct: 230  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVESVSTLLR--QNGYQS 287

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                   + Y                                                  
Sbjct: 288  RGFEVMYNGYT------------------------------------------------- 298

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNH 1261
            G         V +G  Y  +L H
Sbjct: 299  GR---KLVCQVFLGPTYYQRLRH 318



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 70/197 (35%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA + + G
Sbjct: 4   TNFSERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G++  G  V+  DI++GK  P      TP+   +     +K    RD S  + S  
Sbjct: 114 LDEDGLVAPGVRVSGEDIIIGKTAPI-----TPDVDEMGQR--QKYHTKRDVSTPLRSTE 166

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 167 NGIVDQVMLTTNAEGLK 183


>gi|297528055|gb|ADI46072.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-25]
 gi|297528077|gb|ADI46083.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-25]
 gi|297528139|gb|ADI46114.1| DNA-dependent RNA polymerase II [Morchella sp. Mel-25]
          Length = 318

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/386 (15%), Positives = 107/386 (27%), Gaps = 81/386 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L E   +  G   
Sbjct: 71   LF-RSLFYRSYMDQEKR---IGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D+     R ++         ++     +  Q              
Sbjct: 127  SGEDIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML----------- 175

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G
Sbjct: 176  ---------TTNAEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTVGITYRQEDMPFTCEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    +  
Sbjct: 227  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVESVSTLLR--QNG 284

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +       + Y                                               
Sbjct: 285  YQSRGFEVMYNGYT---------------------------------------------- 298

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNH 1261
               G         V +G  Y  +L H
Sbjct: 299  ---GR---KLVCQVFLGPTYYQRLRH 318



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 68/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +VA + + G
Sbjct: 4   TNFAERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        +   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +DE G++  G  V+  DI++GK  P         ++       +K    RD S  + S  
Sbjct: 114 LDEDGLVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTE 166

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 167 NGIVDQVMLTTNAEGLK 183


>gi|294721613|gb|ADF32954.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 289

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/361 (15%), Positives = 103/361 (28%), Gaps = 75/361 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 4    YPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  ID+ ++    + E+     R           +       I  G           K  
Sbjct: 63   RSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVSGDDVIIGKVA 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D      R++                    +Y    + L       ++ +      
Sbjct: 123  PIAPDADELGQRTK------------------AHEYRDVSTPLRSTENGIVDCVAL--TT 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VK+     +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  
Sbjct: 163  NAENLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHA 222

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G++                                   
Sbjct: 223  IPSRMTIAHLIECLLSKVGAIKGQEGD--------------------------------- 249

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     + I+ +L        G  ++Y+G TG+   
Sbjct: 250  --------------------ATP-FTDVTVQNISDLLIQHGYQSRGFEVMYNGHTGQKLR 288

Query: 1247 R 1247
             
Sbjct: 289  A 289



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E            +       +D+ G+I  G  V+
Sbjct: 53  DRGLFRSLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK+ P         ++        KA + RD S  + S  +G V  V +     
Sbjct: 113 GDDVIIGKVAPIAPDADELGQRT-------KAHEYRDVSTPLRSTENGIVDCVALTTNAE 165

Query: 950 IDK 952
             K
Sbjct: 166 NLK 168


>gi|299561914|gb|ADJ37004.1| RNA polymerase II beta subunit [Fusarium tricinctum]
 gi|299561917|gb|ADJ37006.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561920|gb|ADJ37008.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561923|gb|ADJ37010.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561927|gb|ADJ37012.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561930|gb|ADJ37014.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561933|gb|ADJ37016.1| RNA polymerase II beta subunit [Fusarium acuminatum]
 gi|299561939|gb|ADJ37020.1| RNA polymerase II beta subunit [Fusarium acuminatum]
          Length = 291

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 104/365 (28%), Gaps = 75/365 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     ++++ +LR       G  ++Y+G 
Sbjct: 253  --------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGH 285

Query: 1241 TGEPF 1245
            TG   
Sbjct: 286  TGRKL 290



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|310750844|gb|ADP09215.1| RpoB' [Halorubrum sp. TP009]
 gi|310750846|gb|ADP09216.1| RpoB' [Halorubrum coriense]
 gi|310750848|gb|ADP09217.1| RpoB' [Halorubrum distributum]
          Length = 173

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 53/196 (27%), Positives = 73/196 (37%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF ++G   D+V+NP  +
Sbjct: 31   EDGSKLSKVKVRDQRVPELGDKFASRHGQKGVVGHLAPQEDMPFTEEGVVPDLVMNPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G ++       +       LR  LE+     S  E +  
Sbjct: 91   PSRMTVGHVLEMLGGKVGSLRGSRVDGTPFQGEDE---EELRGQLEEYGFESSGKEVMYS 147

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                                               G+TGE  D 
Sbjct: 148  ---------------------------------------------------GVTGEKIDA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGTIFYHKLYHMV 172


>gi|330785324|gb|AEC46468.1| RNA polymerase II second largest subunit [Reichlingia leopoldii]
          Length = 298

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 106/365 (29%), Gaps = 84/365 (23%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 68   LYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+               A  +E+  R  +  K    T     E    +++      
Sbjct: 128  KTAPLA---------------ATAEERGSRLSQHTKRDVSTPLRSTEAGIIDQVL----- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 256

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 257  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTGR 292

Query: 1244 PFDRP 1248
                 
Sbjct: 293  KLMAQ 297



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 68/187 (36%), Gaps = 12/187 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +   +   E            +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 121 GDDIIIGKTAPLAATAEERGSRL----SQHTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKIRTRT 183


>gi|223154|prf||0601198A polymerase beta,RNA
          Length = 253

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/211 (30%), Positives = 103/211 (48%), Gaps = 43/211 (20%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 69  MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEED----PEGQYGLEAAFRSV 124

Query: 63  FPITAFS-----GAAMLEFVSYEFDPP----KFDVDDCLWRDL--TYAVPLKITLRLIVF 111
           FPI A +                   P     FDV++  WRDL  T     ++ LRL+++
Sbjct: 125 FPIQATAVIPSCNNVT---------TPWRTGFFDVEE-PWRDLFRT----ARVKLRLVIY 170

Query: 112 DVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQ--LHRSPGIHFDHDK 169
           + +   G  ++KDIKEQ +YMG++PLM  +GTFVI G +R++V    + R+    F   K
Sbjct: 171 EREAPEG--TVKDIKEQEVYMGEIPLMADNGTFVINGTERVIVPSCTVVRASS--FTPTK 226

Query: 170 GR----ASLSGKLLYACRIIPDQGLWMDIEF 196
            +           + +  +      W+D EF
Sbjct: 227 VKPTLRVKCCTTRVSSLTV----DSWLDFEF 253


>gi|118201842|gb|ABK79734.1| RNA polymerase subunit B [Leisingera methylohalidivorans DSM 14336]
          Length = 163

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V +G+VT++V Y+SA EE    +AQAN++LDE G F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVNEGQVTDEVHYMSATEEMRHTVAQANATLDEGGKFINDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L PRE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPRESVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|299561936|gb|ADJ37018.1| RNA polymerase II beta subunit [Fusarium acuminatum]
          Length = 290

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/364 (15%), Positives = 103/364 (28%), Gaps = 75/364 (20%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R   D+ ++      E  E   +           +       +  G         
Sbjct: 60   RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDII 119

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  +      R+Q  Q       ++     +  Q   + +              
Sbjct: 120  IGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------- 166

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI+
Sbjct: 167  -------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDII 219

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSH 1181
            +NP  +PSRM +  + E  L       G +                              
Sbjct: 220  INPHAIPSRMTIAHLIECLLSKVSTLEGMEGD---------------------------- 251

Query: 1182 TEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLT 1241
                                     +TP F     ++++ +LR       G  ++Y+G T
Sbjct: 252  -------------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHT 285

Query: 1242 GEPF 1245
            G   
Sbjct: 286  GRKL 289



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 55  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 167

Query: 950 IDK 952
             K
Sbjct: 168 NVK 170


>gi|118201884|gb|ABK79755.1| RNA polymerase subunit B [Sagittula stellata]
          Length = 163

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 109/162 (67%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V DG VT++V Y+SA EE    +AQAN+SLDE+G FT E+V  R 
Sbjct: 62  ARVNKYGFIETPYRVVTDGVVTDEVHYMSATEEMRHTVAQANASLDENGKFTNEMVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGDYTLAPSETVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|330785400|gb|AEC46506.1| RNA polymerase II second largest subunit [Sclerophyton elegans]
          Length = 294

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 54/366 (14%), Positives = 99/366 (27%), Gaps = 79/366 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                   +   +       +   +  + AI      +  D+ +   S +   +     + 
Sbjct: 3    YPQKPLAVTRAMDYMQFKELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYR 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPKGFK 1003
             +     E+  +V    +E   +      +      Y +L     +  G           
Sbjct: 63   TYI----EQQGTVGFNTLEEFEKPAKQNTMRTRPGTYEKLDIDGFVPPGVRVSGDDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +       Q  +   + +       +     +                    
Sbjct: 119  KTAPFQAPMQENAEGGQRNKQHTRRDCSAPLRSTEAGIIDRVL----------------- 161

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 162  -VTNTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYGQEDMPFTTDGLVPDLIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 221  PHAIPSRMTIAHLIECLLSKVAATKGMEGD------------------------------ 250

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F       I+S+L+ +     G  ++++G TG 
Sbjct: 251  -----------------------ATP-FTNVTVSDISSLLKESGYQSRGFEMMHNGHTGR 286

Query: 1244 PFDRPV 1249
                 V
Sbjct: 287  KLMAQV 292



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 70/196 (35%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL           +          +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------AVTRAMDYMQFKELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +            E        +         + +D  G +  G  V+
Sbjct: 52  DRGLFRSLFYRTYIEQQGTVGFNTLEEFEKPAKQNTMRTRPGTYEKLDIDGFVPPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V + N  G
Sbjct: 112 GDDIIIGKTAPFQAPMQENAEGGQR----NKQHTRRDCSAPLRSTEAGIIDRVLVTNTEG 167

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 168 KRSVKVRTRTTKVPQI 183


>gi|91981476|gb|ABE68080.1| RNA polymerase subunit B [Pseudomonas sp. CM1'A2]
 gi|91981478|gb|ABE68081.1| RNA polymerase subunit B [Pseudomonas sp. F113]
 gi|91981480|gb|ABE68082.1| RNA polymerase subunit B [Pseudomonas sp. F96.27]
 gi|91981482|gb|ABE68083.1| RNA polymerase subunit B [Pseudomonas sp. K93.2]
 gi|91981484|gb|ABE68084.1| RNA polymerase subunit B [Pseudomonas sp. K94.31]
 gi|91981486|gb|ABE68085.1| RNA polymerase subunit B [Pseudomonas sp. K94.37]
 gi|91981488|gb|ABE68086.1| RNA polymerase subunit B [Pseudomonas sp. P12]
 gi|91981490|gb|ABE68087.1| RNA polymerase subunit B [Pseudomonas sp. P97.30]
 gi|91981502|gb|ABE68093.1| RNA polymerase subunit B [Pseudomonas sp. Q65c-80]
 gi|91981522|gb|ABE68103.1| RNA polymerase subunit B [Pseudomonas sp. TM1A3]
 gi|91981524|gb|ABE68104.1| RNA polymerase subunit B [Pseudomonas sp. C*1A1]
 gi|91981534|gb|ABE68109.1| RNA polymerase subunit B [Pseudomonas sp. P96.25]
 gi|117573512|gb|ABK40932.1| RNA polymerase subunit B [Pseudomonas sp. C6-16]
 gi|117573518|gb|ABK40935.1| RNA polymerase subunit B [Pseudomonas sp. C6-9]
 gi|117573522|gb|ABK40937.1| RNA polymerase subunit B [Pseudomonas sp. S7-29]
 gi|117573524|gb|ABK40938.1| RNA polymerase subunit B [Pseudomonas sp. S7-42]
 gi|117573526|gb|ABK40939.1| RNA polymerase subunit B [Pseudomonas sp. S7-46]
 gi|117573528|gb|ABK40940.1| RNA polymerase subunit B [Pseudomonas sp. S7-52]
 gi|117573534|gb|ABK40943.1| RNA polymerase subunit B [Pseudomonas sp. S8-151]
 gi|117573536|gb|ABK40944.1| RNA polymerase subunit B [Pseudomonas sp. C6-11]
 gi|117573538|gb|ABK40945.1| RNA polymerase subunit B [Pseudomonas sp. F96.26]
 gi|117573542|gb|ABK40947.1| RNA polymerase subunit B [Pseudomonas sp. K94.38]
 gi|117573546|gb|ABK40949.1| RNA polymerase subunit B [Pseudomonas sp. P97.27]
          Length = 160

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 90/160 (56%), Positives = 119/160 (74%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 160


>gi|198279493|emb|CAP04781.1| RNA polymerase beta subunit [Equisetum variegatum]
          Length = 263

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 114/248 (45%), Positives = 163/248 (65%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL KAE   VGTG+E  +A  SG+ + ++R G V  +D+ RI +   E         
Sbjct: 1   QAVPLSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDSERITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PLV     +R+  +IADG ST  G+LALG+N+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLVSKDQFLRQGQVIADGASTVGGELALGKNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++ E
Sbjct: 114 EGYNFEDATLISERLIYEDIFTSFHIERHEINVAFTGQGPEKLTREIPHLNNHILRHLGE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP    E+   PE KLL+AIFG    + R+T L+VP G  
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEYLETLGAPEGKLLQAIFGTDVTNARETCLKVPVGFK 233

Query: 937 GTVVDVRI 944
           G V+D++ 
Sbjct: 234 GRVIDIKW 241


>gi|91981492|gb|ABE68088.1| RNA polymerase subunit B [Pseudomonas sp. P97.38]
 gi|91981496|gb|ABE68090.1| RNA polymerase subunit B [Pseudomonas sp. PILH1]
 gi|91981500|gb|ABE68092.1| RNA polymerase subunit B [Pseudomonas sp. Q37-87]
 gi|117573500|gb|ABK40926.1| RNA polymerase subunit B [Pseudomonas sp. C10-186]
 gi|117573502|gb|ABK40927.1| RNA polymerase subunit B [Pseudomonas sp. C10-189]
 gi|117573504|gb|ABK40928.1| RNA polymerase subunit B [Pseudomonas sp. C10-190]
 gi|117573506|gb|ABK40929.1| RNA polymerase subunit B [Pseudomonas sp. C10-197]
 gi|117573508|gb|ABK40930.1| RNA polymerase subunit B [Pseudomonas sp. C10-204]
 gi|117573510|gb|ABK40931.1| RNA polymerase subunit B [Pseudomonas sp. C10-205]
 gi|117573520|gb|ABK40936.1| RNA polymerase subunit B [Pseudomonas sp. P97.39]
 gi|117573530|gb|ABK40941.1| RNA polymerase subunit B [Pseudomonas sp. S8-110]
 gi|117573532|gb|ABK40942.1| RNA polymerase subunit B [Pseudomonas sp. S8-130]
 gi|117573540|gb|ABK40946.1| RNA polymerase subunit B [Pseudomonas sp. K93.52]
 gi|117573544|gb|ABK40948.1| RNA polymerase subunit B [Pseudomonas sp. P97.1]
 gi|117573548|gb|ABK40950.1| RNA polymerase subunit B [Pseudomonas sp. Q86-87]
          Length = 160

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 90/160 (56%), Positives = 119/160 (74%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 160


>gi|219564073|gb|ACL28220.1| RNA polymerase II second largest subunit [fungal sp. M202]
          Length = 287

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/365 (15%), Positives = 105/365 (28%), Gaps = 81/365 (22%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAISTYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R        +E   +    E + + +  Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYLDQEKRVGM---SVVEQFEKPTRAETMKMKQGTYDKLDDDGLVAPGARV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 117  SGEDILIGKTAPIAPDAEELGQRTKLHVKRDASTPLRSTENGIVDQVLL----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VK+     +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 166  ---------TTNTEGLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSAG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L       G++                        
Sbjct: 217  LVPDIIINPHAIPSRMTIAHLIECLLSKVAALTGQEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F      +I+ +L      + G  +
Sbjct: 255  -------------------------------ATP-FTDVTITSISQLLEAHGFQKRGFEV 282

Query: 1236 LYDGL 1240
            +Y+G 
Sbjct: 283  MYNGH 287



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAISTYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   + +     +D+ G++  GA V+
Sbjct: 58  DRGLFRSLFYRAYLDQEKRVGMSVVEQFEKPTRAETMKMKQGTYDKLDDDGLVAPGARVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DIL+GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 118 GEDILIGKTAPIAPDAEELGQRT-------KLHVKRDASTPLRSTENGIVDQVLLTTNTE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|198279485|emb|CAP04777.1| RNA polymerase beta subunit [Pinus rigida]
          Length = 276

 Score =  171 bits (432), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 106/257 (41%), Positives = 156/257 (60%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL        GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFXPXKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 50/215 (23%), Positives = 79/215 (36%), Gaps = 14/215 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             GD+        V V+++ KR IQ GDK+AGRHGN
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGN 276


>gi|306413178|gb|ADM86691.1| RNA polymerase II beta subunit [Fusarium sp. FTSC_grp2 KOD-2010]
          Length = 287

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/343 (16%), Positives = 101/343 (29%), Gaps = 75/343 (21%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 19   FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 77

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +           +       +  G           K+  +  +      R+Q  
Sbjct: 78   IFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTQSH 137

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +  Q   + +                       ++ VKV V   +
Sbjct: 138  QRRDISTPLRSTENGIVDQVILTVNA--------------------DNVKYVKVRVRTTK 177

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 178  IPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPSRMTIAHLIECLLS 237

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G +                                                   
Sbjct: 238  KVSTLEGMEGD------------------------------------------------- 248

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 249  ----ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 286



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEHLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|193201479|gb|ACF15947.1| RNA polymerase II subunit [Dendrographa leucophaea]
          Length = 282

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/355 (16%), Positives = 104/355 (29%), Gaps = 81/355 (22%)

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     +  +     E
Sbjct: 4    THSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----E 59

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSD 1011
            +  SV    +E   R +  E +      Y +L +   +  G           K+    + 
Sbjct: 60   QQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAP 119

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +                   Q N E  +   +  K  +    ++    I     +     
Sbjct: 120  M-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEG 160

Query: 1072 RV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
            +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSR
Sbjct: 161  KRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSR 220

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E  L       G +                                       
Sbjct: 221  MTIAHLIECLLSKVSTITGHEGD------------------------------------- 243

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                            +TP F      +I+ +L  A     G  ++Y+G TG   
Sbjct: 244  ----------------ATP-FTDITVSSISDLLSFAGYQSRGFELMYNGHTGRKL 281



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/168 (19%), Positives = 60/168 (35%), Gaps = 6/168 (3%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 4   THSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQS 63

Query: 854 TKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 EE  R              + +D+ G +  G  V+  DI++GK  P        
Sbjct: 64  VGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMQEN 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            E   +     K  DV        +G+   V+      +  +    R+
Sbjct: 124 SEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRT 170


>gi|118201900|gb|ABK79763.1| RNA polymerase subunit B [Sulfitobacter mediterraneus]
          Length = 163

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 103/162 (63%), Positives = 124/162 (76%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D  VT++V Y+SA EE    +AQAN++LD +  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDSVVTDEVHYMSATEEMRHTVAQANANLDGNMKFVNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPSENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|17225260|gb|AAL37323.1| RNA polymerase B-subunit [Staphylococcus capitis subsp. capitis]
          Length = 172

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 132/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTE 172


>gi|151573423|gb|ABS17946.1| RNA polymerase II [Fusarium sp. NRRL 43808]
 gi|151573429|gb|ABS17950.1| RNA polymerase II [Fusarium sp. NRRL 43810]
          Length = 285

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/358 (15%), Positives = 102/358 (28%), Gaps = 75/358 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEP 1244
                                +TP F     ++++ +LR       G  ++Y+G TG  
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRK 285



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|89274924|gb|ABD65903.1| RNA polymerase II second largest subunit [Hydnellum geogenium]
          Length = 600

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 98/675 (14%), Positives = 194/675 (28%), Gaps = 90/675 (13%)

Query: 457  DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVC 514
            D+ G +R+   G +L N +R+   ++ + +    +              +    + + + 
Sbjct: 1    DHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVEAHKEFNLSLAVKHNTITNGLK 60

Query: 515  EFFCSSQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
                +               +SQ+       S ++H RR +      + R     + R +
Sbjct: 61   YSLATGNWGDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQL 116

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H TH+G +CPAET EG   GLV +L   A ++           + +  + +         
Sbjct: 117  HNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESL-------- 168

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            EEN + +   + +  +G +       R     +   ++     D SP+  V         
Sbjct: 169  EENAHSSTPCTKVFVNGVWMG---VHRDPANLVKTIKKLRRKDDISPEVSVVRDIREREL 225

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
                D+ RV     +       L+ +       +E +     G   + +     + V   
Sbjct: 226  RLYTDAGRVCRPLFIVENQQLALRKK------HIEWLNR---GQDDMGEEFKWDQLVKG- 275

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
              VI  ++ + + +         ++  R           L   G E   ND   D  +  
Sbjct: 276  -GVIELLDAEEEETVMICMTPEELENSR-----------LQSQGMEPHENDSEFDPSARL 323

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
                A          P         + +   ++            ++       +G    
Sbjct: 324  RATSAAHTWTHCEIHPSM------ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYLT 377

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
               +               +  +             +       +   +  + AI     
Sbjct: 378  NFLVRM-----------DTMANILYYPQKPLATTRSMEYLRFRELPAGQNAIVAIMCYSG 426

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +  D+ +   S +   +    I+ R  +D  ++S   + E+ E  +RD           
Sbjct: 427  YNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPSRDTTLRMKHGTYE 485

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
                   I  G           K+  +  D      R++          ++     +  Q
Sbjct: 486  KLEEDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGIIDQ 545

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                          + VKV V   R  Q GDK A RHG KG + 
Sbjct: 546  VLI--------------------TTNSEGQKFVKVRVRSTRIPQIGDKFASRHGQKGTIG 585

Query: 1102 RILPCEDMPFLKDGT 1116
                 EDMPF  +G 
Sbjct: 586  ITYRQEDMPFTAEGI 600



 Score = 87.4 bits (215), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 85/617 (13%), Positives = 164/617 (26%), Gaps = 91/617 (14%)

Query: 355 NAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
              + N       K  KD    + + +       F+++ ++ +    +  KY L   G  
Sbjct: 12  GPLLANLFRMLFRKLTKDVYRYLQKCVEAH--KEFNLSLAVKHNTITNGLKYSL-ATGNW 68

Query: 415 KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGE 469
               +         + + +    + +  L        R GK       +  +  +    E
Sbjct: 69  GDQKKSMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 128

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMP-------QDLINAKPVVSAVCEFFCSSQL 522
             + Q    +  +       + S+    +             NA         F     +
Sbjct: 129 TPEGQACGLVKNLALMACISVGSLSAPVIEFLEEWGLESLEENAHSSTPCTKVFVNGVWM 188

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
               +  N +  I   RR   +                ++        P    E  N  L
Sbjct: 189 GVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE--NQQL 246

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
                    +N          K         +  L A EEE   I      L+     ++
Sbjct: 247 ALRKKHIEWLNRGQDDMGEEFKWDQLVKGGVIELLDAEEEETVMICMTPEELENSRLQSQ 306

Query: 643 ELVFCRCAGEEILVPR-------EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +       E     R             +  P  ++ + AS+IPF +++ S R      
Sbjct: 307 GMEPHENDSEFDPSARLRATSAAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA 366

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           M +QA+ +              +V   + A I+      +    ++  +          +
Sbjct: 367 MGKQAMGIYLT---------NFLVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNA 417

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
              +  Y              NQ                    S  +   ++ R +  + 
Sbjct: 418 IVAIMCYSG-----------YNQE------------------DSVIMNQSSIDRGLFRSI 448

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
                 + E    I +            +EEFE  +RDT             +     + 
Sbjct: 449 YYRSYMDLEKKSGIQQ------------LEEFEKPSRDT----------TLRMKHGTYEK 486

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           ++E G+I  G  V   DI++GK  P         ++        +    RD S  + S  
Sbjct: 487 LEEDGLIAPGTGVAGEDIIIGKTAPIPPDSEELGQRT-------RTHTRRDVSTPLKSTE 539

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG +  V I       K
Sbjct: 540 SGIIDQVLITTNSEGQK 556


>gi|158288277|ref|XP_310152.4| AGAP009539-PA [Anopheles gambiae str. PEST]
 gi|157019172|gb|EAA05843.4| AGAP009539-PA [Anopheles gambiae str. PEST]
          Length = 1152

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 92/597 (15%), Positives = 167/597 (27%), Gaps = 106/597 (17%)

Query: 803  GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              +   +N+L       G   +  M I           + H  E    +  + L      
Sbjct: 625  RMMRPVKNLLCGKTELIGSFEQVYMDICVTPEEAYPQLTTH-AELAKTSFMSNLAQLIPM 683

Query: 863  RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
             D         +   + G   +G   +  D        + ++P TP              
Sbjct: 684  PDCNQSPRNMYQC--QMGKQTMGTPCHNWDKQCIAKMYRLQTPATPLF--------RPVH 733

Query: 923  DVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNI 982
                       G +  V  +        D    + +            K +   +   + 
Sbjct: 734  HDNIALDNYAMGTNAIVAVISYTGYDMEDAMIINKAAFERGFAAGNIYKHEYVELTGDSF 793

Query: 983  YSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQY 1042
            ++R  +       +       K   L+      Y               Q   E++    
Sbjct: 794  FARNPKDATLNPFLDNDGLPFKGAQLTKGT-PLYCYFDVNDHTYHVVSYQGYEEAIVDNV 852

Query: 1043 ETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
            +     L    ++    I  G  M     +++  +  + R            G+K     
Sbjct: 853  K-----LGAPLQDAGRGIGRG-GMAIVTKQLILTY-RVPRNPSV--------GDK----- 892

Query: 1103 ILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKAN 1162
                                      SR                  G+K     +    +
Sbjct: 893  ------------------------FASR-----------------AGQKGICSQHWPAID 911

Query: 1163 GDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG-VPVSTPVFDGADEEAI-- 1219
               +      + +        +++       +        G V  +TP        AI  
Sbjct: 912  LPFTESGMIPDIIFNPHGFPSRMTIAMMIETMAGKTAACQGLVHDATPFRYDESNTAIDY 971

Query: 1220 -NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLV 1278
               +L  +  D  G   +Y G+ G      +  G ++  +L HMVSDK   RSTG    +
Sbjct: 972  FGRLLEQSGYDYYGTERMYSGVDGREMKVDIFFGVVHYQRLRHMVSDKWQVRSTGPIDQL 1031

Query: 1279 TQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVG----RTRVY----E 1330
            T QP  G+S  GG R GEME   + ++GA+++LQ+ L   SD VV     R        +
Sbjct: 1032 THQPNKGRSRGGGVRFGEMERDGLISHGASFLLQDRLVHGSDKVVALVCRRCGTLIGPID 1091

Query: 1331 SIVA------------------GNDTFETG---TPESFNVLVKEMQALGLSIDLENS 1366
            S+                      D  E G    P  F  LV ++ ++ +++ L+ S
Sbjct: 1092 SVTKRLADNSNQLQHVPATCRLCEDDKEIGHVEIPYIFKFLVSQLTSMNINVKLQLS 1148



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 133/942 (14%), Positives = 275/942 (29%), Gaps = 203/942 (21%)

Query: 19  KNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFSG-AAMLE 75
           K  EI+   +L      S+++ L          +EG++     + P      +G    L 
Sbjct: 27  KQNEILA--NLGRPHIDSFNYML----------DEGIEDVLSRLVPVCFEMANGSRIKLR 74

Query: 76  FVSYEFDPP------------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
                  PP            +    +C  +  TYA     T+ L  +++D    +   +
Sbjct: 75  ITDISIAPPTVPMMLVEVAEKRVFPSECRQKSDTYAG--MCTITL-NWELDGMPQSPLTR 131

Query: 124 DIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHR 159
           +       MG +P+M +                         G FV++G ++     L R
Sbjct: 132 E-------MGRIPIMLRSNACNLANATPEELVARGEHEDEWGGYFVVRGNEK-----LIR 179

Query: 160 SPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVT-SFL 218
                         +S +  Y   I  ++  W             R DR +    T  F+
Sbjct: 180 ------------MLISTRRNYP--IAVNRNTW-------------R-DRGKDFSATGVFI 211

Query: 219 MALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGK 278
                                             +     +     +   T + +I   +
Sbjct: 212 RC------------------------------VREDQYSTRNVLHYLTNGTAKLMISVSR 241

Query: 279 KLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH 338
            L+   +  + +        + + +     A D  +       +     +  ++L     
Sbjct: 242 ALSFIPVMMILKALGD---RSDNEIYKKLTACDESDQYYKRCIMAMLRDLHAENLHSSQE 298

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                  +L    ++      N      ++     LL    ++           E  FN 
Sbjct: 299 CRSYMGMLLRRRLMDI-----NLPAWYSDEQAGHFLLQHCVLI------HLDSVEDKFNL 347

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDN 458
           L     K      GR  +              + +E ++        LR     +  +  
Sbjct: 348 LVHMVHKLYAVVQGRHAVESL--------DGTMMQEILLGGHIYQGLLREM--CLSTMQY 397

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
           +    ++   +       +    + +++K         ++       AK     + +   
Sbjct: 398 VRINLMKLCPDRTSPM--VTTHELAQALKNVAGFQHPFTMFLATGNLAKATEMGLMQ--- 452

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S+ L  + E++N +  ++H R   A+ +G         E R + P  +G ICP  T +G 
Sbjct: 453 STGLVIIAENINRMRYMSHFR---AVHRGSYFLTMRTTEARQLLPDAWGFICPVHTPDGE 509

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT-----------NDVVYLSAMEEENRYI 627
             GL++ +TS   V+     E     V +   T           +   + +   ++   +
Sbjct: 510 PCGLLNHMTSDCTVSVTQDPE----LVANIPATLVSLGMQPFGGDAGSFGTLSHDDGYVV 565

Query: 628 ------------AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
                       A A+  + +      E        E   VP  +           V  A
Sbjct: 566 MLEGKMLGMLARATASQVVQKLRLLKIEGKTIPNQTEIAFVPAREGGQYPGLFL-FVGPA 624

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV 735
             + P          L+G   Q      +  E  +      + +AK+S  + +A+   + 
Sbjct: 625 RMMRPVKNLLCGKTELIGSFEQVYMDICVTPEEAYPQLTTHAELAKTSFMSNLAQLIPMP 684

Query: 736 EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIA 795
              D  +      +  +   T G   +   K  +        Q P   +   V  ++I  
Sbjct: 685 ---DCNQSPRNMYQCQMGKQTMGTPCHNWDK--QCIAKMYRLQTPATPLFRPVHHDNIAL 739

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
           D  +        G N +VA + + GY+ ED+M+I++       F + +I + E +     
Sbjct: 740 DNYAM-------GTNAIVAVISYTGYDMEDAMIINKAAFERG-FAAGNIYKHEYVELTGD 791

Query: 856 LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
                  +D           +D  G+   GA++  G  L   
Sbjct: 792 SFFARNPKD-----ATLNPFLDNDGLPFKGAQLTKGTPLYCY 828


>gi|118201852|gb|ABK79739.1| RNA polymerase subunit B [Marinovum algicola]
          Length = 163

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V +G VT++V Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRVVKEGTVTDEVHYMSATEEMRHTVAQANANLDENMKFVNDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPNENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|118201840|gb|ABK79733.1| RNA polymerase subunit B [Ketogulonicigenium vulgare]
          Length = 163

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 109/162 (67%), Positives = 129/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV +GKVT+DV Y+SA EE    IAQAN+ LD++G F +ELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVEGKVTDDVQYMSATEEMRHTIAQANAILDDEGRFVDELVDTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+  L  RE +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGDYTLATRETVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|14971093|gb|AAK74111.1| RNA polymerase beta subunit [Bacillus subtilis]
          Length = 259

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 117/305 (38%), Gaps = 56/305 (18%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EIL             D      S   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI  E G +
Sbjct: 112 NAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQI 171

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +D ++L++             V     N      L  +      +  L   ++  P D  
Sbjct: 172 LDRRTLDK-------------VLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD-- 216

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                                   G   +N+  N    +++++I   DII+ I    +L 
Sbjct: 217 ----------------------QEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLL 254

Query: 448 NGKGT 452
           +G G 
Sbjct: 255 HGVGD 259


>gi|284799232|gb|ADB93972.1| RNA polymerase II second largest subunit [Quintaria lignatilis]
          Length = 613

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 101/677 (14%), Positives = 200/677 (29%), Gaps = 95/677 (14%)

Query: 471  LKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------- 521
              N +R+  L+M + + +  +    +      Q  + A  + + +     +         
Sbjct: 5    CCNLFRILFLKMTKDVYKYLQKCVENSQEFNIQMAVKASLITNGLKYSLATGNWGDQKKA 64

Query: 522  ------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                  +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET 
Sbjct: 65   ASAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETP 120

Query: 576  EGHNIGLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
            EG   GLV +L+    V+        T +    +  V  +   +        ++      
Sbjct: 121  EGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMDVLEEYDPMINPTATKVFVNGVWVG 180

Query: 634  LDEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEND-DSNRVL 691
            +    S    +V        +      I D  D   K        + P    + D+ +  
Sbjct: 181  VHSQPSQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLYVVETDARKPN 240

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIV----EQVDAIRIVIRS 747
             G  +  +A      E   V T    +  + + A     R  I     E +DA       
Sbjct: 241  RGSLVLTRAHLEKLEEDKHVDTS--GLNDEDTAAVTFGWRGLIHSGVVEYLDAEEEETAM 298

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQ-RPLVKVGDEVRRNDIIADGPSTDLGDLA 806
            +    +      D+ + +    + +N    + +P  K    ++        PS  LG   
Sbjct: 299  IVMTPEDLEEHRDLMQGIPQPEAPENEQYKRIKP--KPNPSIKTYTHCEIHPSMILG--- 353

Query: 807  LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
                +  + +P+  +N          M  + +  ++      +                 
Sbjct: 354  ----ICASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNYALRMETMMN------------ 397

Query: 867  NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
                             V             +       +   +  + AI      +  D
Sbjct: 398  -----------------VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQED 440

Query: 927  TSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
            + +   S +   +    +F R   ++ +R   +    +E   +    + + L    Y +L
Sbjct: 441  SVIMNQSSIDRGIF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRSDTLRLKGGTYDKL 496

Query: 987  ME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYE 1043
             +   +  G           K+  + +D      ++           ++     +  Q  
Sbjct: 497  DDDGVVAPGVRVSGEDIIIGKTAPIPTDAKELGQKTSLHTKRDVSTPLRTTENGIVDQ-- 554

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
                                       LR VKV     +  Q GDK A RHG KG +   
Sbjct: 555  ------------------VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGVT 596

Query: 1104 LPCEDMPFLKDGTPVDI 1120
               EDMPF ++G   D+
Sbjct: 597  YRQEDMPFTREGLTPDL 613



 Score =  108 bits (270), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 84/615 (13%), Positives = 184/615 (29%), Gaps = 69/615 (11%)

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
            + S      IL++        +   +     K  +++     ++     + T  +  S+
Sbjct: 1   CWTSCCNLFRILFLK-------MTKDVYKYLQKCVENSQEFNIQMAVKASLITNGLKYSL 53

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTI 453
               + D  K   +  G  ++  R    +      R          +     L N    +
Sbjct: 54  ATGNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNTHWGL 113

Query: 454 DDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAV 513
                    +   + + L     + +      I + +S  ++D +   D +         
Sbjct: 114 VCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMDVLEEYDPMINPTATKVF 173

Query: 514 CEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                   +    +    +S +   RR   L             +RD+      R     
Sbjct: 174 ---VNGVWVGVHSQPSQLVSVVQELRRNGTLSY-------EMSLIRDIR----DREFKIF 219

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T  G  +  +  + + AR    G +      V        +      EE+          
Sbjct: 220 TDAGRVMRPLYVVETDARKPNRGSL------VLTRAHLEKL------EEDKH-------- 259

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +D  G   E+           L+    ++++DA  ++   I  +     E+ D  + +  
Sbjct: 260 VDTSGLNDEDTAAVTFGWR-GLIHSGVVEYLDAEEEETAMIVMTPEDLEEHRDLMQGIPQ 318

Query: 694 CN--MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
                  Q   +     P + T       +   + I+   A I+   D  +    + +  
Sbjct: 319 PEAPENEQYKRIKPKPNPSIKT---YTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSA 375

Query: 752 LDPSTSGV-DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
           +     GV      ++ +         Q+PL                      +L  G+N
Sbjct: 376 MGKQAMGVALTNYALRMETMMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQN 425

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDI 865
            +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D 
Sbjct: 426 AIVAIACYSGYNQEDSVIMNQSSIDRGIFRSLFYRAYTEQEKRIGVNVLEQFEKPTRSDT 485

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G++  G  V+  DI++GK  P      T  ++L +        DV 
Sbjct: 486 LRLKGGTYDKLDDDGVVAPGVRVSGEDIIIGKTAPI----PTDAKELGQKTSLHTKRDVS 541

Query: 926 DTSLRVPSGVSGTVV 940
                  +G+   V+
Sbjct: 542 TPLRTTENGIVDQVL 556


>gi|91981532|gb|ABE68108.1| RNA polymerase subunit B [Pseudomonas sp. P97.26]
          Length = 160

 Score =  170 bits (431), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 91/160 (56%), Positives = 120/160 (75%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++    T+ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLTDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDA 160


>gi|198279407|emb|CAP04738.1| RNA polymerase beta subunit [Pinus caribaea]
          Length = 283

 Score =  170 bits (431), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP  + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPXFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 283


>gi|118201856|gb|ABK79741.1| RNA polymerase subunit B [Oceanibulbus indolifex]
          Length = 163

 Score =  170 bits (431), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 125/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V D  VT++V Y+SA EE    +AQAN++LDE+  F  E+V  R 
Sbjct: 62  ARVNKYGFIETPYRVVKDSIVTDEVHYMSATEEMRHTVAQANANLDENMKFVNEMVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPTENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|9501919|gb|AAF87945.1|AF177294_1 RNA polymerase beta-subunit [Mycobacterium tuberculosis]
          Length = 111

 Score =  170 bits (431), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 46/119 (38%), Positives = 72/119 (60%), Gaps = 16/119 (13%)

Query: 81  FDPPKFD-----VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
           F  P+FD     VD+C  +D+TYA PL +T   I           +  +IK Q+++MGD 
Sbjct: 1   FSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFI---------NNNTGEIKSQTVFMGDF 51

Query: 136 PLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDI 194
           P+MT+ GTF+I G +R+V SQL RSPG++FD    +   + K L++ ++IP +G W++ 
Sbjct: 52  PMMTEKGTFIINGTERVVFSQLVRSPGVYFDETIDK--STDKTLHSVKVIPSRGAWLEF 108


>gi|306413187|gb|ADM86697.1| RNA polymerase II beta subunit [Fusarium dimerum]
          Length = 287

 Score =  170 bits (431), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 99/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQESQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSNEGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G   +Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFENMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQESQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|193201507|gb|ACF15961.1| RNA polymerase II subunit [Opegrapha filicina]
          Length = 298

 Score =  170 bits (431), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/371 (14%), Positives = 100/371 (26%), Gaps = 73/371 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +                   + +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTQSAKYLKFADLPAGQNAIVAIACYSGYNQEDSLIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       ++ E   +                   +  G      
Sbjct: 61   LF-RSLFYRTYIEQQKAVGFNALDEFEKPVKQLTMRTRPGTYEKLDDDGFVPPGIRVSGD 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                +  QR  E  +          E    +++ 
Sbjct: 120  DIIIGKTAPFQAPM------------QDNSDGGQRKQEHTRRDVSAPLRSTEAGIIDRVL 167

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 168  ------VTNTEGRRSVKVRTRATKIPQIGDKFASRHGQKGTIGVTYGQEDMPFTAEGIVP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +                           
Sbjct: 222  DLIINPHAIPSRMTVAHLIECLLSKLAACHGMEGD------------------------- 256

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F       I+ ML++      G  ++++
Sbjct: 257  ----------------------------ATP-FTEITVSQISEMLKLTGYHTRGFEVMHN 287

Query: 1239 GLTGEPFDRPV 1249
            G TG      +
Sbjct: 288  GHTGRKLMAQI 298



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/190 (18%), Positives = 69/190 (36%), Gaps = 16/190 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTQSAKYLKFADLPAGQNAIVAIACYSGYNQEDSLIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       +E  + +  +         + +D+ G +  G  V+
Sbjct: 58  DRGLFRSLFYRTYIEQQKAVGFNALDEFEKPVKQLTMRTRPGTYEKLDDDGFVPPGIRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++PM       +        DV        +G+   V+      R  
Sbjct: 118 GDDIIIGKTAPF-QAPMQDNSDGGQRKQEHTRRDVSAPLRSTEAGIIDRVLVTNTEGRRS 176

Query: 950 IDKNERSISV 959
           +    R+  +
Sbjct: 177 VKVRTRATKI 186


>gi|198279509|emb|CAP04789.1| RNA polymerase beta subunit [Equisetum x dycei]
          Length = 271

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 114/248 (45%), Positives = 165/248 (66%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL K E   VGTG+E   A  SG+ + ++R G +  +D+ +I +   E         
Sbjct: 1   QAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDSEKITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLLCKDKFLRQGQIIADGASTVGGELALGRNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER++ ED+FTS HIE +E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP GV 
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPVGVK 233

Query: 937 GTVVDVRI 944
           G V+D+R 
Sbjct: 234 GRVIDIRW 241


>gi|306413184|gb|ADM86695.1| RNA polymerase II beta subunit [Fusarium penzigii]
          Length = 287

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 99/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSNEGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G   +Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFENMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|17225246|gb|AAL37316.1| RNA polymerase B-subunit [Staphylococcus felis]
          Length = 172

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 103/172 (59%), Positives = 132/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV     K+T+ + YL+A EE++  +AQAN+ LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDLETNKITDQIDYLTADEEDSYVVAQANARLDEEGRFLDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 172


>gi|280985741|gb|ACZ99651.1| RNA polymerase II [Fusarium sp. NRRL 53075]
          Length = 273

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 56/343 (16%), Positives = 101/343 (29%), Gaps = 75/343 (21%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 5    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 63

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E   +           +       +  G           K+  +  +      R+Q  
Sbjct: 64   IFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRTQSH 123

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +  Q   + +                       ++ VKV V   +
Sbjct: 124  QRRDISTPLRSTENGIVDQVILTVNA--------------------DNVKYVKVRVRTTK 163

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 164  IPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHAIPSRMTIAHLIECLLS 223

Query: 1143 WACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKS 1202
                  G +                                                   
Sbjct: 224  KVSTLEGMEGD------------------------------------------------- 234

Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                +TP F     ++++ +LR       G  ++Y+G TG   
Sbjct: 235  ----ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGRKL 272



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 62/160 (38%), Gaps = 12/160 (7%)

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L 
Sbjct: 1   EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLN 60

Query: 858 PEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             EI           +       +DE GI+  G  V+  DI++GK  P  +       + 
Sbjct: 61  YTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQENQDLGTRT 120

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                  ++   RD S  + S  +G V  V +       K
Sbjct: 121 -------QSHQRRDISTPLRSTENGIVDQVILTVNADNVK 153


>gi|193201487|gb|ACF15951.1| RNA polymerase II subunit [Enterographa hutchinsiae]
          Length = 294

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/366 (16%), Positives = 105/366 (28%), Gaps = 73/366 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMQFMRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  I++ +      +E+ E  A++                  +  G           
Sbjct: 61   LFYRTYIEQEQTVGFNAQEEFEKPAKNLTMRTRPGTYEKLDDDGFVSPGVRVSGDDVIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + L                E  QR  + +K          E    +++      
Sbjct: 121  KTAPFQAPLAEG------------SEGGQRTRDHVKRDVSAPLRSTEAGIIDRVL----- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D V+N
Sbjct: 164  -ITTADGKRNVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDPVIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 223  PHAIPSRMTIAHLIECLLSKVSSTTGLEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F      +I+++L+ A     G  ++Y+G +G 
Sbjct: 253  -----------------------ATP-FTDITVSSISALLQDAGYQSRGLEMMYNGHSGR 288

Query: 1244 PFDRPV 1249
              +  +
Sbjct: 289  KLNAQI 294



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 66/187 (35%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMQFMRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +      +E                  + +D+ G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQEQTVGFNAQEEFEKPAKNLTMRTRPGTYEKLDDDGFVSPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  ++P+    +  +        DV        +G+   V+      +  
Sbjct: 114 GDDVIIGKTAPF-QAPLAEGSEGGQRTRDHVKRDVSAPLRSTEAGIIDRVLITTADGKRN 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRT 179


>gi|198279395|emb|CAP04732.1| RNA polymerase beta subunit [Pinus radiata]
          Length = 276

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 105/255 (41%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL   E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFXPEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 81/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 276


>gi|193201495|gb|ACF15955.1| RNA polymerase II subunit [Opegrapha atra]
          Length = 291

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/365 (15%), Positives = 105/365 (28%), Gaps = 76/365 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               ++ R  I++ +       E+ E   + +         +       +  G        
Sbjct: 61   -RSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+S+                +E+  R  E  K    T     E    +++   
Sbjct: 120  IIGKTAPLASN---------------AEERGMRATEHTKRDVSTPLRSTEAGIIDQVL-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L         +                             
Sbjct: 219  IINPHAIPSRMTIAHLIECLLSKVAATNAYEGD--------------------------- 251

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F     E ++ +L  +   + G  ++Y+G 
Sbjct: 252  --------------------------ATP-FTDITVEMVSEILEKSGYQKRGFEVMYNGH 284

Query: 1241 TGEPF 1245
            TG   
Sbjct: 285  TGRKL 289



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 56  DRGLFRSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +    EE+ +RA       DV        +G+   V+   +  +  
Sbjct: 116 GDDIIIGKTAPLASN---AEERGMRATE-HTKRDVSTPLRSTEAGIIDQVLLTSVDGKKN 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKIRTRT 178


>gi|40643911|emb|CAD89878.1| RNA polymerase II, second largest subunit [Doronicum orientale]
          Length = 326

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/383 (16%), Positives = 106/383 (27%), Gaps = 76/383 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 20   DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRG 79

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
                 +F R   D+ ++  ++ +E      R           +          G      
Sbjct: 80   FF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVGGE 138

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T                  A  D    +     +  + TS    E    +++ 
Sbjct: 139  DVIIGKTTP----------------IAQDDAAQGQASRYTRRDHSTSLRHSETGMVDQVL 182

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV V   R  Q GDK + RHG KG V      EDMP+  +G   
Sbjct: 183  LTTNADGL-----RFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 237

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +         +IS         +  
Sbjct: 238  DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISRALHKCGYQMRG 297

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 298  FETM-----------------------------------------------YNGHT---- 306

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNH 1261
            G         + +G  Y  +L H
Sbjct: 307  GR---RLPAMIFLGPTYYQRLKH 326



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 58/184 (31%), Gaps = 23/184 (12%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PLV                      L  G N +VA   + G
Sbjct: 13  TNFQFRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSG 62

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 63  YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 122

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V   D+++GK TP  +           A         RD S  +    
Sbjct: 123 LDDDGLAPPGTRVGGEDVIIGKTTPIAQDD--------AAQGQASRYTRRDHSTSLRHSE 174

Query: 936 SGTV 939
           +G V
Sbjct: 175 TGMV 178


>gi|118201886|gb|ABK79756.1| RNA polymerase subunit B [Salipiger mucosus]
          Length = 163

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 105/162 (64%), Positives = 127/162 (78%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR V + +VT++V Y+SA EE    +AQAN+SLD +G FT E+V  R 
Sbjct: 62  ARVNKYGFIETPYRVVKESQVTDEVHYMSATEEMRHTVAQANASLDAEGKFTNEMVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L PRE +D ID SPKQ+VS+ ASLIPFLENDD+NR L
Sbjct: 122 SGDYTLAPRESVDLIDVSPKQLVSVGASLIPFLENDDANRAL 163


>gi|198279335|emb|CAP04702.1| RNA polymerase beta subunit [Pinus massoniana]
          Length = 283

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 154/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP  + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPXFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK++GRHGNKGI+S +LP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVSGRHGNKGIISXVLP 283


>gi|198279323|emb|CAP04696.1| RNA polymerase beta subunit [Pinus yunnanensis]
 gi|198279329|emb|CAP04699.1| RNA polymerase beta subunit [Pinus tabuliformis]
          Length = 283

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 154/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP  + E    GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPXFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPKIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 283


>gi|145307868|gb|ABP57239.1| RNA polymerase II second largest subunit [Batkoa gigantea]
          Length = 299

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/374 (16%), Positives = 110/374 (29%), Gaps = 75/374 (20%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D+ +++   E E  E  +                    I  G   
Sbjct: 61   DRGLF-RSIYYRTYLDQEKKTGLQEVETFEKPSHKTTLRLRHGTYEKLEDDGLIAPGTRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+T + +D                +E  QR     K    T     E    +
Sbjct: 120  SGDDIIIGKTTPVPAD---------------SEELGQRLRGHTKKDVSTPLKSTETGXVD 164

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++        +    +R  KV V   R  Q GDK A RHG KG +       DMPF  +G
Sbjct: 165  RVML-----TINQEGMRFAKVRVXSTRIPQIGDKFASRHGQKGTIGMTYRHXDMPFXAEG 219

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++ P  +PSRM +G + E  +G      G +                        
Sbjct: 220  IVPDLIIXPHAIPSRMTIGHMVECLVGKVGTLDGSEGD---------------------- 257

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     + I+ +L      + G  +
Sbjct: 258  -------------------------------ATP-FTDVTVDGISKLLSXFGYQKRGFEV 285

Query: 1236 LYDGLTGEPFDRPV 1249
            +Y+G TG+     +
Sbjct: 286  MYNGHTGKKLTAQI 299



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + T L   E       +    +     + +++ G
Sbjct: 52  SVIMNQSSIDRGLFRSIYYRTYLDQEKKTGLQEVETFEKPSHKTTLRLRHGTYEKLEDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK TP         E+L + + G    DV        +G    V+
Sbjct: 112 LIAPGTRVSGDDIIIGKTTPVPADS----EELGQRLRGHTKKDVSTPLKSTETGXVDRVM 167


>gi|17225238|gb|AAL37312.1| RNA polymerase B-subunit [Staphylococcus arlettae]
          Length = 172

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 133/172 (77%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLATNSITDQIDYLTADEEDSYVVAQANSNLDENGKFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNRE 172


>gi|302848540|ref|XP_002955802.1| hypothetical protein VOLCADRAFT_66175 [Volvox carteri f. nagariensis]
 gi|300258995|gb|EFJ43227.1| hypothetical protein VOLCADRAFT_66175 [Volvox carteri f. nagariensis]
          Length = 1154

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 39/79 (49%), Positives = 53/79 (67%)

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWC 1301
            GEP +  + +G +Y  KL HMV DK++AR+ G   ++T+QP  G+S  GG RLGEME  C
Sbjct: 1008 GEPLEAYIFMGPVYYQKLKHMVLDKMHARARGPRVVLTRQPTEGRSRDGGLRLGEMERDC 1067

Query: 1302 IQAYGAAYVLQEMLTIKSD 1320
            + AYGA+ +L E L I SD
Sbjct: 1068 LIAYGASMLLLERLMISSD 1086



 Score =  155 bits (391), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 123/949 (12%), Positives = 275/949 (28%), Gaps = 197/949 (20%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-AFSGAAMLEFVSYEFDPPKF- 86
           L++    S++ FL          N  L+    +   +T        L++ +     P   
Sbjct: 50  LVKQHLDSFN-FL---------LNSELRKIVAANEKVTCDTDPNFYLKYTNIYVGSPSMD 99

Query: 87  --------DVDDCLWRDLTYAVPLKITLRLIV-FDVDEFTGAKSIKDIKEQSIYMGDLPL 137
                       C  RD TY+ P+ + +      ++    G   +       + +G +PL
Sbjct: 100 EDMVQVGTTPQQCRLRDATYSAPITVDIEYTRGKEIVVKRGRGGVGA-----VCIGRMPL 154

Query: 138 MT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRAS 173
           M                           G F+++G +++++ Q   S             
Sbjct: 155 MLRCDRCVLYGKNEAQLAQLGECPLDPGGYFIVRGTEKVILIQEQLSKNRIIVD----TD 210

Query: 174 LSGKLLYACRIIPD---QGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEIL 229
             G+++    +      +    +I F SK  I+++ +  +  V +   L A+G +S++ +
Sbjct: 211 SHGEVI--ASVTSSTHERKSKTNIVF-SKGKIYLKHNAFQDDVNIMVVLKAMGCESDQEV 267

Query: 230 ------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSG 283
                   F  +    + G      L     M       + +      +V E+   L + 
Sbjct: 268 VQAVVGGGFGVRAASGRDGGLDAKSLGVFTQMQALDYLGTRLRKRRKSKVDEARDVLANV 327

Query: 284 LL------KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIF 337
           +L      +      + ++ +    +    +    ++           D    K LE   
Sbjct: 328 VLCHVPVPRYQFAHKIAYVAVMMRRMLYAVLDPACID---------DRDYYGNKRLELAG 378

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
                    L+    ++   I+    +  +K  +    D+ + +R  D  T+ +  ++ +
Sbjct: 379 ALMSLLFEDLFKRLNSD---IKRQADSVLSKANRATQFDVAKAIR-TDTITYGLESAL-S 433

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
              +   ++ +   G  ++  RL+      +            K          +     
Sbjct: 434 SGNWIIKRFRMERKGVTQVLSRLSFIAAMGMMTRMTSQFEKTRK---------VSGPRAL 484

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
           +     +    +  + +    +  +           ++       ++  +P+ S      
Sbjct: 485 HPSQWGMLCPADTPEGESCGLVKNLALMTHVTTDEEEVSICRLLVMLGTEPITSLAPAEM 544

Query: 518 CSSQLSQLEEHVNSLSRITHTRRLSALGQ-GGVARARAGVEMRDVHPTHYGRICPAETSE 576
                + +  + N +    H R    + +   + RA    E   VH       C      
Sbjct: 545 HGQGGALVFLNGNLVGV--HRRPHRLVKEVRELRRAGHLGEFVHVHLQQ--DACYVSADG 600

Query: 577 GHNIGLVSSLTS---FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           G     +    +     R      + +      D      V YL   EE    IA     
Sbjct: 601 GRVCRPLIICDAGVPRVRQEHITKLRSGEWTFPDFLRRGLVEYLDVNEENVSLIA----- 655

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           L E                      +    ++  P  ++ + + LIPF  ++ S R    
Sbjct: 656 LYEKDCN------------------KMTTHLEIEPFTIMGVVSGLIPFPHHNQSPRNTYQ 697

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           C M +QA+                                           I   +    
Sbjct: 698 CAMGKQAMGN-----------------------------------------IAYNQLSRM 716

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
            +   + +Y               QRPL+                      L  G+N  V
Sbjct: 717 DTLLYLLVYP--------------QRPLL----------TTRTIELVGFDKLGAGQNASV 752

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDT-KLGPEEITRDIPNVSEEG 872
           A M + GY+ ED++++++  +       I ++++    R       + I   +P   ++ 
Sbjct: 753 AVMSYSGYDIEDAIVMNKYSLDRGFGRCIVLKKYGCSLRKYANRSHDRIVAPLPAPGQKS 812

Query: 873 ----LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIF 917
                + +D  GI  VG  + PGD+ +    P       P   +  + +
Sbjct: 813 VQSRFRLLDRDGIASVGDYILPGDVYINMQRPSNTRDPLPASNMPDSFY 861


>gi|113707361|gb|ABI36588.1| RNA polymerase II second largest subunit [Schismatomma decolorans]
          Length = 693

 Score =  170 bits (430), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 62/382 (16%), Positives = 106/382 (27%), Gaps = 81/382 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 389  ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 448

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   R +  E +      Y +L +   +  G        
Sbjct: 449  FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDI 504

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                   Q N E  +   +  K  +    ++    I
Sbjct: 505  IIGKTAPFQAPM-------------------QENSEGGQRTKDHKKRDVSAPLRSTEAGI 545

Query: 1061 QWGDDMPPGVLRV-VKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                 +     +  VKV     +  Q GDK A RHG KG +      EDMPF  DG   D
Sbjct: 546  IDRVLLTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPD 605

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTG 1179
            +++NP  +PSRM +  + E  L       G +  +          IS L SF        
Sbjct: 606  LIINPHAIPSRMTIAHLIECLLSKVSTITGHEGDATPFTDITVSSISDLLSFAGYQSRGF 665

Query: 1180 SHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                                            L  +G +    G
Sbjct: 666  E-----------------------------------------------LMYNGHT----G 674

Query: 1240 LTGEPFDRPVTVGYIYMLKLNH 1261
                  +  V +G  Y  +L H
Sbjct: 675  R---KLNAQVFLGPTYYQRLRH 693



 Score = 93.2 bits (230), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 86/581 (14%), Positives = 164/581 (28%), Gaps = 58/581 (9%)

Query: 383 PGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAII 440
             +V T  +  S+    + +  K   +  G  ++  R    +      R          I
Sbjct: 37  KTNVVTNGLRYSLATGNWGEQKKAMQTKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKI 96

Query: 441 KILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMP 500
                L N    +         +   + + L     + + +    I E +   D++   P
Sbjct: 97  AKPRQLHNTHWGLVCPSETPEGQACGLVKNLSLMCTVSVGKPGEPISEFLFGKDME---P 153

Query: 501 QDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRD 560
            +    +   +A   F     L            +  TRR   L             +RD
Sbjct: 154 VEDYEPQKAPNATKIFLNGVWLGTHNNPRVLEEAVFATRRGGDLDA-------EISIVRD 206

Query: 561 VHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAM 620
           +    +       T  G  +  +  + +  R +  G +      V D +    +      
Sbjct: 207 IREREFKIF----TDAGRVMRPLLVVNNDPRSSKNGQL------VLDFQHLEKL------ 250

Query: 621 EEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
                     +  +  D +  E        G   LV    I+F+DA  ++   I  S+  
Sbjct: 251 --------SGDQDIRNDLNLAEADKKKLFYGFRGLVADGVIEFLDAEEEESAMILMSVAH 302

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
                D +R  +     R  +    A    + T  E   +   G       + I  Q   
Sbjct: 303 LPGAQDPSRQKVYKLGDRIEMKPSSAAN--IFTHCEIHPSMILGIC----ASIIPSQTTT 356

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
                                    +    +      Q+PL                   
Sbjct: 357 XXXXXXXXXXXXXXXXXVFLTNFAQRMDTMSNILYYPQKPL----------ASTHSMNYL 406

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-E 859
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       E
Sbjct: 407 RFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALE 466

Query: 860 EITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
           E  R              + +D+ G +  G  V+  DI++GK  P         E   R 
Sbjct: 467 EFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMQENSEGGQRT 526

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
               K  DV        +G+   V+      +  +    R+
Sbjct: 527 KD-HKKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRT 566



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 79/237 (33%), Gaps = 22/237 (9%)

Query: 472 KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
            + +R    RM R +    ++   +         +    V + +     +          
Sbjct: 2   GHLFRQLFQRMSRDVFRHLQLCVENNKQFSMDVAVKTNVVTNGLRYSLATGNWGEQKKAM 61

Query: 522 -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                +SQ+       S ++H RR +      + R     + R +H TH+G +CP+ET E
Sbjct: 62  QTKAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPSETPE 117

Query: 577 GHNIGLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           G   GLV +L+    V+    G   + +    D +   D     A      ++       
Sbjct: 118 GQACGLVKNLSLMCTVSVGKPGEPISEFLFGKDMEPVEDYEPQKAPNATKIFLNGVWLGT 177

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV 690
             +    EE VF    G ++      + D  +   K        + P L  ++  R 
Sbjct: 178 HNNPRVLEEAVFATRRGGDLDAEISIVRDIREREFKIFTDAGRVMRPLLVVNNDPRS 234


>gi|306413190|gb|ADM86699.1| RNA polymerase II beta subunit [Fusarium delphinoides]
 gi|306413193|gb|ADM86701.1| RNA polymerase II beta subunit [Fusarium sp. FDSC_grp5 KOD-2010]
 gi|306413196|gb|ADM86703.1| RNA polymerase II beta subunit [Fusarium sp. FDSC_grp2 KOD-2010]
          Length = 287

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/359 (15%), Positives = 100/359 (27%), Gaps = 75/359 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                +TP F     ++++ +LR       G   +Y+G TG   
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFENMYNGHTGRKL 286



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|219564071|gb|ACL28219.1| RNA polymerase II second largest subunit [fungal sp. M198]
          Length = 287

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/362 (16%), Positives = 101/362 (27%), Gaps = 75/362 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      EQ E   R +  +      +       +  G      
Sbjct: 61   LF-RSLFYRAYLDQEKRVGMAVVEQFEKPNRSETLKMKAGTYDKLDDDGLVSPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++          ++     +  Q                 
Sbjct: 120  DMIIGKTAPIAPDAEELGQRTKLHIKRDASTPLRSTENGIIDQVLL-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        LR VKV     +  Q GDK A RHG KG +      EDM F  DG   
Sbjct: 166  ------TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMAFTSDGLTP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G++                           
Sbjct: 220  DIIINPHAIPSRMTIAHLIECLLSKVAALTGQEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F      +I+ +L      + G  ++Y+
Sbjct: 255  ----------------------------ATP-FTDVTITSISQLLEEHGFQKRGFEVMYN 285

Query: 1239 GL 1240
            G 
Sbjct: 286  GH 287



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 62/170 (36%), Gaps = 22/170 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +D+ G++  G  V+
Sbjct: 58  DRGLFRSLFYRAYLDQEKRVGMAVVEQFEKPNRSETLKMKAGTYDKLDDDGLVSPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK  P         ++        K    RD S  + S  +G +
Sbjct: 118 GEDMIIGKTAPIAPDAEELGQRT-------KLHIKRDASTPLRSTENGII 160


>gi|194320135|gb|ACF48288.1| DNA-dependent RNA polymerase II second largest subunit [Lecanora
            polytropa]
          Length = 316

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/384 (15%), Positives = 109/384 (28%), Gaps = 81/384 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 10   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIMNQSSIDRG 69

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +    +    +E   +    E + L    Y +L +   +  G   
Sbjct: 70   LF-RSLFYRAYSDQEK---QIGHSVLEQFEKPMRSETLKLKHGTYDKLDDDGLVAPGVRV 125

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +++D                +E  QR     K    T     E+   +
Sbjct: 126  SGEDIIIGKTAPITAD---------------AEELGQRTKAHTKRDISTPLRSTENGIVD 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++      D +     R  KV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  QVLMSTNADGL-----RFAKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 225

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    E  
Sbjct: 226  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSRLLR--ENG 283

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                                                    +G + 
Sbjct: 284  YHSRGFEVM---------------------------------------------YNGHT- 297

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKL 1259
                  G      V +G  Y  +L
Sbjct: 298  ------GRKLVAQVFLGPTYYQRL 315



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 68/179 (37%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 5   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDSVIMNQS 64

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +       E     +  +   +       +D+ G++  G  
Sbjct: 65  SIDRGLFRSLFYRAYSDQEKQIGHSVLEQFEKPMRSETLKLKHGTYDKLDDDGLVAPGVR 124

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V +  
Sbjct: 125 VSGEDIIIGKTAPITADAEELGQRT-------KAHTKRDISTPLRSTENGIVDQVLMST 176


>gi|219564121|gb|ACL28244.1| RNA polymerase II second largest subunit [Placynthiella icmalea]
          Length = 287

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/362 (16%), Positives = 106/362 (29%), Gaps = 75/362 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      EQ E   R           +       +  G      
Sbjct: 61   LF-RSLFYRTYMDQEKRVGLSVVEQFEKPMRSDTLRLKHGTYDKLDEDGIVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R++                 +K    T     E+   +++ 
Sbjct: 120  DIIIGKTAPIAPDAEELGQRTKL---------------HIKRDASTPLRSTENGIVDRVL 164

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 165  MTTNQDGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +                           
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------- 254

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                        +TP F     ++++ +LR       G  ++Y+
Sbjct: 255  ----------------------------ATP-FTDVTVDSVSRLLREHGYQSRGFEVMYN 285

Query: 1239 GL 1240
            G 
Sbjct: 286  GH 287



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 65/180 (36%), Gaps = 22/180 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E     +  D   +       +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRTYMDQEKRVGLSVVEQFEKPMRSDTLRLKHGTYDKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KLHIKRDASTPLRSTENGIVDRVLMTTNQD 170


>gi|198279477|emb|CAP04773.1| RNA polymerase beta subunit [Pinus thunbergii]
          Length = 285

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 106/257 (41%), Positives = 156/257 (60%), Gaps = 10/257 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL +      GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPXKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPKIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  
Sbjct: 173 NGLVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGR 232

Query: 937 GTVVDVRIFNRHGIDKN 953
           G V+DVR  NR     +
Sbjct: 233 GRVIDVRWINRVDDSGD 249



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 76   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 134

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 135  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 188

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 189  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 246

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 247  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 285


>gi|118426156|gb|ABK90977.1| RpoB [Mycoplasma capricolum subsp. capripneumoniae]
 gi|118426158|gb|ABK90978.1| RpoB [Mycoplasma capricolum subsp. capripneumoniae]
          Length = 208

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 111/215 (51%), Positives = 151/215 (70%), Gaps = 8/215 (3%)

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
             R  G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LMG NMQRQAVPL+K
Sbjct: 1   VSRFNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALMGANMQRQAVPLIK 60

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E+P V TG+E   A+ SG AIVAK   IV+ VD+  I        +    SG+  Y L 
Sbjct: 61  PESPIVATGIEFEAARDSGEAIVAKEDAIVKYVDSKTI--------ITDGESGIRTYILS 112

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            ++RSN  T + Q P+VKVGD V++ +IIADGPS D G+LA+G+N++VAF  ++GYNFED
Sbjct: 113 DYERSNNGTSLTQSPIVKVGDVVKKGEIIADGPSMDQGELAIGQNVVVAFSTYNGYNFED 172

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
           ++++SE +V +D FTSIHI+E+ +  R+TK G EE
Sbjct: 173 AIVMSEIIVIDDRFTSIHIDEYTLEVRNTKQGQEE 207


>gi|198279511|emb|CAP04790.1| RNA polymerase beta subunit [Equisetum arvense]
 gi|198279513|emb|CAP04791.1| RNA polymerase beta subunit [Equisetum arvense]
          Length = 271

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 114/248 (45%), Positives = 164/248 (66%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL K E   VGTG+E   A  SG+ + ++R G +  +D  +I +   E         
Sbjct: 1   QAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDGEKITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLLCKDKFLRQGQIIADGASTVGGELALGRNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER++ ED+FTS HIE +E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG + ++ R+T L+VP GV 
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEFLDSLGAPEGKLLQAIFGTEVINARETCLKVPVGVK 233

Query: 937 GTVVDVRI 944
           G V+D+R 
Sbjct: 234 GRVIDIRW 241


>gi|260593951|gb|ACX46270.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593953|gb|ACX46271.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKNV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|40644724|emb|CAD92664.1| RNA polymerase II [Solanum lycopersicum]
          Length = 342

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/412 (15%), Positives = 122/412 (29%), Gaps = 77/412 (18%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V        +    +       +      + AI      +  D+ +   S +   
Sbjct: 8    DTLAYVLYYPQKPXVTXRAMEHLHFXQLPAGINAIVAITCYSGYNQEDSVIMNQSSIDRG 67

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++  ++ +E      R+        + +          G      
Sbjct: 68   LF-RSLFFRSYRDEEKKMGTLVKEDFGRPDREHTMGMRHGNYDKLEDDGFAPPGTRVSGD 126

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+T +S                  DE   ++    +  + TS    E    +++ 
Sbjct: 127  DVIIGKTTPISQ-----------------DEAQGQSARYTRKDHSTSLRHSETGIVDQVL 169

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VK+ +   R  Q GDK + RHG KG +      EDMP+  +G   
Sbjct: 170  LTTNADGL-----RFVKIRMRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWSAEGITP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +GQ+ E  +G     +GK+  +          IS            
Sbjct: 225  DIIVNPHAIPSRMTIGQLVECIMGKVAAHIGKEGDATPFTDVTVDSISRTLH-------- 276

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                   +               +G  +   +F G         +    +   G+     
Sbjct: 277  -------NCGYQMRGFERMYNGHTGRVLPAMIFLGPTYYQRLKHMVDDKIHSRGR----- 324

Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRG 1290
                         G +                      ++T+QP  G+S  G
Sbjct: 325  -------------GPV---------------------QILTRQPAEGRSRDG 342



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 30/184 (16%), Positives = 57/184 (30%), Gaps = 24/184 (13%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+P V                      L  G N +VA   + G
Sbjct: 1   TNYQFRMDTLAYVLYYPQKPXV----------TXRAMEHLHFXQLPAGINAIVAITCYSG 50

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +      +E            +       
Sbjct: 51  YNQEDSVIMNQSSIDRGLFRSLFFRSYRDEEKKMGTLVKEDFGRPDREHTMGMRHGNYDK 110

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G    G  V+  D+++GK TP  +           A         +D S  +    
Sbjct: 111 LEDDGFAPPGTRVSGDDVIIGKTTPISQDE---------AQGQSARYTRKDHSTSLRHSE 161

Query: 936 SGTV 939
           +G V
Sbjct: 162 TGIV 165


>gi|17225258|gb|AAL37322.1| RNA polymerase B-subunit [Staphylococcus muscae]
          Length = 172

 Score =  169 bits (429), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 104/172 (60%), Positives = 131/172 (76%), Gaps = 2/172 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGLNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPE 172


>gi|151573411|gb|ABS17938.1| RNA polymerase II [Fusarium sp. NRRL 43734]
          Length = 284

 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 56/357 (15%), Positives = 102/357 (28%), Gaps = 75/357 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                +TP F     ++++ +LR       G  ++Y+G TG 
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEVMYNGHTGR 284



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|219564007|gb|ACL28187.1| RNA polymerase II second largest subunit [fungal sp. M24]
          Length = 285

 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 54/363 (14%), Positives = 109/363 (30%), Gaps = 81/363 (22%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R  +++ +R        +E   +    + + L    Y +L +   +  G     
Sbjct: 61   -RSLFYRAYVEQEKRVGM---SLVEQFEKPMRSDTLRLKHGTYEKLDDDGMVAPGVRVSG 116

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D      R++          ++     +                  +
Sbjct: 117  EDIIIGKTAPIAPDAEELGQRTKLHTKRDASTPLRSTENGI------------------V 158

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
            +K+          L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 159  DKVLL--TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGIT 216

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +                          
Sbjct: 217  PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD------------------------ 252

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                         +TP F     ++++ +LR       G  ++Y
Sbjct: 253  -----------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEVMY 282

Query: 1238 DGL 1240
            +G 
Sbjct: 283  NGH 285



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +     + +D+ G++  G  V+
Sbjct: 56  DRGLFRSLFYRAYVEQEKRVGMSLVEQFEKPMRSDTLRLKHGTYEKLDDDGMVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++        K    RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIAPDAEELGQRT-------KLHTKRDASTPLRSTENGIVDKVLLTTNAE 168

Query: 950 IDK 952
             K
Sbjct: 169 GLK 171


>gi|56406223|gb|AAV87495.1| RpoB [Bisgaard Taxon 45]
          Length = 167

 Score =  169 bits (429), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 97/166 (58%), Positives = 125/166 (75%), Gaps = 1/166 (0%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRF 120

Query: 641 TEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           T+  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE++
Sbjct: 121 TDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHE 166


>gi|151573468|gb|ABS17976.1| RNA polymerase II [Fusarium sp. NRRL 43873]
          Length = 284

 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 55/357 (15%), Positives = 100/357 (28%), Gaps = 75/357 (21%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +                                   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------------- 248

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                +TP F     ++++ +LR       G  I+Y+G TG 
Sbjct: 249  --------------------ATP-FTDVTVDSVSELLRKHGYQSRGFEIMYNGHTGR 284



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|46277352|gb|AAS86866.1| DNA-dependent RNA polymerase II [Peziza natrophila]
          Length = 531

 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 84/589 (14%), Positives = 160/589 (27%), Gaps = 72/589 (12%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V +       +    + +V  +     +      ++      +  D  F    +
Sbjct: 3    LMSYVSVGSPADPIIDFMLQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTI 62

Query: 646  FCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
                    I      I D  +   K          P    D+         +  Q   + 
Sbjct: 63   QKLRRQNHIGHEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIE 122

Query: 705  KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
            K E     T  E                G+VE +DA       +    +   +    +  
Sbjct: 123  KLEDDKDITDDEQRYG-----WQGLISDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAG 177

Query: 765  MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
             + Q+        QR    V             PS  LG       +  + +P+  +N  
Sbjct: 178  YEIQQEIDPA---QRVKAAVNKYAHTWTHCEIHPSMILG-------ICASIIPFPDHNQ- 226

Query: 825  DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
                 S R   +       +  F    R+                           +  +
Sbjct: 227  -----SPRNTYQSAMGKQAMGXFLTNYRERM-----------------------DTMANI 258

Query: 885  GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
                         +       +   +  + AI      +  D+ +   S +   +    +
Sbjct: 259  LYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF-RSL 317

Query: 945  FNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKG 1001
            F R  +D+ +R   +    +E   +      + L    Y +L +   +  G         
Sbjct: 318  FFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDII 374

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  ++ +      R+++         ++     +  Q                    
Sbjct: 375  IGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------------- 414

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D++
Sbjct: 415  VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVPDLI 474

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            +NP  +PSRM +  + E  L       G +             +S L  
Sbjct: 475  INPHAIPSRMTIAHLIECQLSKVSSLXGFEXXXXPFTDVTVDSVSKLLR 523


>gi|70952223|ref|XP_745294.1| DNA-directed RNA polymerase, beta subunit [Plasmodium chabaudi
            chabaudi]
 gi|56525572|emb|CAH82099.1| DNA-directed RNA polymerase, beta subunit, putative [Plasmodium
            chabaudi chabaudi]
          Length = 1218

 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 123/949 (12%), Positives = 280/949 (29%), Gaps = 36/949 (3%)

Query: 230  STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLK 289
            +  Y KI    + +     +   + +    + +++ + +  E+         + + +++ 
Sbjct: 291  NYIYNKIKLGIKNENAIKYI--ENYINSIFLKNNINEKEVFEKYNLKYIGKYANVSRTIF 348

Query: 290  EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
                         +    V   +      E +     +  +  L +       +   L  
Sbjct: 349  RYYEGNNYKKGKSIIKYCVLPHL--QSNSEKFETVCLMFKQLVLSKFKLINTVNKDSLEY 406

Query: 350  DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
             SV   + + + ++ ++  +    +  +Y       +        +     +   K  + 
Sbjct: 407  HSVTTCSGLLSNILKERILNCFYRMQMVYARSLHKFLEKKYEMFKLNVKQIYLRYKEMIL 466

Query: 410  TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
                     +++L+   D     K        +   +   K       N   +   SV  
Sbjct: 467  HELSEDHFNQISLNNNVDTLENNKALTSENDHLNSKMDATKKLRLMFMNEKEKLFASVDG 526

Query: 470  MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
             L+  +        R   E   +    S     L     + S    +   S  + L + +
Sbjct: 527  YLREMFSDT-----RIFVENSKAFTAASFSVSYLFKTGNITSDHIHYQQRSGWAILADEI 581

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
            N+L  +T+ R   A+ +G   +    +  R +    +G ICP  T +G   GL++ L+ +
Sbjct: 582  NNLRLLTNFR---AIHRGSFFQDVKVLSPRKLLGESWGFICPVHTPDGSPCGLLNHLSQY 638

Query: 590  ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
              +      E     +    +    + ++  E    +    N ++        + V    
Sbjct: 639  CCIYNVASNEPHKFNIK-MYLKKIGININLDETSGIHTIYENQTIP----IIVDSVPITY 693

Query: 650  AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
              E     +  +  +  +    +    S    + + +   ++    +      +++    
Sbjct: 694  ISENDF--KRTVYKLKYAKNHNLYNLKSHFEIIAHLNEPSMMDSIIINTCTGRIIRPLLN 751

Query: 710  FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
                 +E +       +I      I++   A +I+ +        S +     + M  + 
Sbjct: 752  LKMKCIEFIPGYQPYVSIAVNYDDIIKNNLARKILKKKENIVNLNSINNTKNTKKMTLKE 811

Query: 770  SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                    +  + K G+    ++I+               ++L     +  +  E     
Sbjct: 812  QYHFFTNKKHNMEKEGENYNESEIVRKEKKKISKSKNKILDILENKKQYQFHEDEYISSS 871

Query: 830  SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG--------------LKN 875
                 SE    S             +    +I   IP   E                   
Sbjct: 872  DYETSSESDKYSDDNMSSTTYIDSDENLNLDIYEQIPQKFEYMELKQTSFLSFLASLTPF 931

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
             D         +       +G  +       T +   +        V        + +  
Sbjct: 932  SDHNQSPRNIYQCQMLKQTMGIQSLNMFYTFTNKIYRMITPQFPLVVTRDYELYGIDNFP 991

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
            SGT   V I    G D  +  I  +      + R    +  I+D    +   + + G N 
Sbjct: 992  SGTNAVVAILAYTGYDMEDALIINKASSDRGMFRTHIYKTEIIDLYKKTDSPDFVLGNNI 1051

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                        +         +        +  +       +  + E +   + +    
Sbjct: 1052 RYTTNSLSSKNNMREHKGKFLNKDGLPCVNQKMVENNPLYSYINKKNELTTYEIFNYGDY 1111

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
             ++ +    +      +V  + +   RP   GDK A RHG KG+VSR+ P EDMPF + G
Sbjct: 1112 YVDCV---SNSQSSNNQVAIIRLRTTRPPLVGDKFASRHGQKGVVSRLFPHEDMPFSESG 1168

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
               D++ NP G+PSRM +G + E+  G A    GK+I +          
Sbjct: 1169 IVPDVIFNPHGIPSRMTIGMLIESICGKAASIYGKRIDATPFRKYTKQK 1217


>gi|198279487|emb|CAP04779.1| RNA polymerase beta subunit [Equisetum scirpoides]
          Length = 263

 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 115/248 (46%), Positives = 162/248 (65%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL KAE   VGTG+E  +A  SG+ + A+R G V  +D  RI +   E         
Sbjct: 1   QAVPLSKAEKCIVGTGLEGQIALDSGSCVTAEREGKVIYIDGERITLFVDEEISINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ+PLV     +R+  +IADG ST  G+LALG+N+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCMNQKPLVCKDKFLRQGQLIADGASTVGGELALGKNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDATLISERLIYEDIFTSFHIERHEINVSFTSQGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG +  + R+T L+VP G  
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLEYLDSLGAPEGKLLQAIFGTEVTNARETCLKVPVGFK 233

Query: 937 GTVVDVRI 944
           G V+D++ 
Sbjct: 234 GRVIDIKW 241


>gi|194320199|gb|ACF48330.1| DNA-dependent RNA polymerase II second largest subunit [Imshaugia
            aleurites]
          Length = 317

 Score =  169 bits (428), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/340 (17%), Positives = 102/340 (30%), Gaps = 42/340 (12%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 227  MVPDIIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDPVSRLLR----- 281

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                V     +G  + T VF G  
Sbjct: 282  ----------EHGYQSRGFEVMYNGHTGRKLVTQVFLGPT 311



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 66/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
             QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FEQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ G++  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|294721619|gb|ADF32958.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 289

 Score =  169 bits (428), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 56/361 (15%), Positives = 101/361 (27%), Gaps = 75/361 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +    AI         D+ +   S +   +    +F 
Sbjct: 4    YPQKPLATTRSMEFLXFRELPAGQNAXVAIACYSGYXQEDSVIMNQSSIDRGLF-RSLFY 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  ID+ ++    + E+     R           +       I  G           K  
Sbjct: 63   RSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVSGDDVIIGKVA 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D      R++                    +Y    + L       ++ +      
Sbjct: 123  PIAPDADELGQRTK------------------AHEYRDVSTPLRSTENGIVDCVAL--TT 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VK+     +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  
Sbjct: 163  NAENLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHA 222

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G++                                   
Sbjct: 223  IPSRMTIAHLIECLLSKVGAIKGQEGD--------------------------------- 249

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     + I+ +L        G  ++Y+G TG+   
Sbjct: 250  --------------------ATP-FTDVTVQNISDLLIQHGYQSRGFEVMYNGHTGQKLR 288

Query: 1247 R 1247
             
Sbjct: 289  A 289



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 35/183 (19%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N  VA   + GY  EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLXFRELPAGQNAXVAIACYSGYXQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E            +       +D+ G+I  G  V+
Sbjct: 53  DRGLFRSLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK+ P         ++        KA + RD S  + S  +G V  V +     
Sbjct: 113 GDDVIIGKVAPIAPDADELGQRT-------KAHEYRDVSTPLRSTENGIVDCVALTTNAE 165

Query: 950 IDK 952
             K
Sbjct: 166 NLK 168


>gi|219564043|gb|ACL28205.1| RNA polymerase II second largest subunit [fungal sp. M169]
          Length = 287

 Score =  169 bits (428), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 53/292 (18%), Positives = 94/292 (32%), Gaps = 21/292 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  +  I      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYTGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRAYMDQEKRIGMQVVEEFEKPTRGSTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D                DE  QR     K    T     E+   +++ 
Sbjct: 120  DIIIGKTAPITAD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVM 164

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 165  LTTNADGL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            DI++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 220  DIIINPHAIPSRMTIAHLIECQLSKVASLRGFEGDATPFTDVTVDSVSSLLR 271



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +V  M + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVGIMCYTGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E            +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRAYMDQEKRIGMQVVEEFEKPTRGSTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPITADADEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAD 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|198279367|emb|CAP04718.1| RNA polymerase beta subunit [Pinus hartwegii var. rudis]
          Length = 279

 Score =  169 bits (428), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 2   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 53

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 54  IYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 113

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 114 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 173

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 174 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 233

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 234 WINRVDDSGD 243



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 70   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 128

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 129  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 182

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 183  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 240

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 241  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 279


>gi|312204326|gb|ADQ47480.1| RNA polymerase II second largest subunit [Graphis scripta]
          Length = 502

 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 50/276 (18%), Positives = 95/276 (34%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 245  MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYVEQEKR-- 301

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +    E + +    Y +L +   I  G           K+  ++ D   
Sbjct: 302  -IGISAVESFEKPLRSETMKMKHGTYEKLDDDGIIAPGTRVSGEDVIIGKTAPMAPDNEE 360

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                  ++K+          L+ V
Sbjct: 361  LGQRTKLHTKRDASTPLRSTENGI------------------VDKVLL--TTNQEGLKFV 400

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  +PSRM + 
Sbjct: 401  KVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITPDIIINPHAIPSRMTIA 460

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 461  HLIECQLSKVSSLRGAEGDATPFTAVTVDSVSRLLR 496



 Score = 90.1 bits (222), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 53/366 (14%), Positives = 94/366 (25%), Gaps = 56/366 (15%)

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-------CAG 651
           +  Y           V YL A EEE   IA     L+                       
Sbjct: 77  KEKYXGWEGLIKAGAVEYLDAEEEETVMIAMTPEDLEISRQVQAGYAPPEPSSDPNARVK 136

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
             +    +     +  P  ++ I AS+IP  +++                          
Sbjct: 137 APVNPAAQTWTHCEIHPSXILGICASIIPXPDHNXXXXXXXXXXXXXXXXXXXXXXXXXX 196

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                                                                       
Sbjct: 197 X---------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 229

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 230 XXXXXPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 279

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   +   E        +   +     + +D+ GII  G 
Sbjct: 280 SSIDRGLFRSLFYRAYVEQEKRIGISAVESFEKPLRSETMKMKHGTYEKLDDDGIIAPGT 339

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK  P         ++        K    RD S  + S  +G V  V +  
Sbjct: 340 RVSGEDVIIGKTAPMAPDNEELGQRT-------KLHTKRDASTPLRSTENGIVDKVLLTT 392

Query: 947 RHGIDK 952
                K
Sbjct: 393 NQEGLK 398


>gi|213622760|ref|ZP_03375543.1| DNA-directed RNA polymerase subunit beta [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 103

 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 42/107 (39%), Positives = 66/107 (61%), Gaps = 4/107 (3%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FGK P+++D+P L+ +Q  S+  F+  +         GL+AAF+SV
Sbjct: 1   MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD----PEGQYGLEAAFRSV 56

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           FPI ++SG + L++VSY    P FDV +C  R +TY+ PL++ LRL+
Sbjct: 57  FPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLV 103


>gi|193201499|gb|ACF15957.1| RNA polymerase II subunit [Opegrapha calcarea]
          Length = 285

 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 53/358 (14%), Positives = 100/358 (27%), Gaps = 84/358 (23%)

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
                   +  + E    R +   +   V        +     +++    +R         
Sbjct: 1    YPQKXLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYR 60

Query: 957  ISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTV 1007
              +E+EQ      +E   +    + + +    Y +L +   +  G           K+  
Sbjct: 61   TYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIGKTAP 120

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            L+S+      R+           ++     +  Q                          
Sbjct: 121  LASNAEERGMRATQHTKRDVSTPLRSTEAGIIDQVL---------------------LTS 159

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +
Sbjct: 160  VDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIINPHAI 219

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM +  + E  L         +                                    
Sbjct: 220  PSRMTIAHLIECLLSKVAATNAYEGD---------------------------------- 245

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                               +TP F     E ++ +L  +   + G  ++Y+G TG   
Sbjct: 246  -------------------ATP-FTDITVEMVSEILEKSGYQKRGFEVMYNGHTGRKL 283



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 68/168 (40%), Gaps = 9/168 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S++   +    + 
Sbjct: 9   TRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYIEQEQS 68

Query: 854 TK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 EE  + I      +       +D+ GI+  G  V+  DI++GK  P   +    
Sbjct: 69  VGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPLASN---A 125

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
           EE+ +RA       DV        +G+   V+   +  +  +    R+
Sbjct: 126 EERGMRAT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKNVKIRTRT 172


>gi|67473159|ref|XP_652347.1| DNA-directed RNA polymerase subunit [Entamoeba histolytica HM-1:IMSS]
 gi|56469186|gb|EAL46961.1| DNA-directed RNA polymerase subunit, putative [Entamoeba histolytica
            HM-1:IMSS]
          Length = 1106

 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 98/645 (15%), Positives = 188/645 (29%), Gaps = 157/645 (24%)

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            Y     Q       +N  P    G  +R     A G   ++G        +       G 
Sbjct: 577  YCDGYLQDGYHALYLNDLP----GQMIRPVIHRATGNIVNIGPYEQVFLDIKCGDSIEGM 632

Query: 822  NFEDSMLISE--------RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL 873
            N  +   IS          +             ++       +G   ++      S+  L
Sbjct: 633  NNAEYEEISALNSLSLLATLTPFCHMNQSPRNMYQCQMAKQTMGIPALSN--KYRSDTKL 690

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +                     + P G +        + A+      D+ D  +   S
Sbjct: 691  LWL---------HYPQRSICQCALMEPFGFNEYPTGANAVVAVISYTGYDMEDALIIKKS 741

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +          +++   K +     E+ +                              
Sbjct: 742  AIERGFGH---GSQYKAYKVDFEKEGEKNE------------------------------ 768

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWW---QFAVQDEKVQRNVESLKVQYETSKSILE 1050
                        T  S ++  E+             ++  +  +++ +  + +    + E
Sbjct: 769  --------MFSGTTSSGEVFDEHLDDDGLPRPGEVFENSPIYSHIDKITGKIKGKVLMGE 820

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
              +   + +I  GD++  G+ + V V V   R    GDK +                   
Sbjct: 821  RGYIESV-RIVGGDNIDSGLQKAV-VRVRYNRTPVIGDKFS------------------- 859

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
                              SR                  G+K    ++  + +   +    
Sbjct: 860  ------------------SR-----------------HGQKGTLSVHYQEKDMPFTESGM 884

Query: 1171 FLEKVIGTGSHTEKIS-DYDDDSVLRVAEQWKSGVPVSTPV-FDGAD--EEAINSMLRMA 1226
              + +I   +   +++     +S+       K     +TP  FD  +   +     L   
Sbjct: 885  TPDIIINPHAFPSRMTIAMLVESMASKVGALKGEYQDATPFKFDEENSAVDYFGKQLLKY 944

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
              +  G   LY G+ G      + +G +Y  +L H V DK   RSTG  S+VT QP+ G+
Sbjct: 945  GYNYYGSEPLYSGIYGNELQSDIYIGIVYYQRLVHQVKDKYQVRSTGPISIVTHQPIKGR 1004

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV-------VG------RTRVYE--- 1330
               GG R GEME   + A+G A ++ + L   SD          G      R++ Y+   
Sbjct: 1005 KRGGGIRFGEMERDSLVAHGTAMLVHDRLFECSDKCYHYVCTKCGSICTIKRSKEYDKMV 1064

Query: 1331 -------SIVAGNDTFETGTPESFNVLVKEMQALG--LSIDLENS 1366
                   SIV      +   P  F  L  E+ A+   L++ ++ +
Sbjct: 1065 CQSCGPTSIVK-----KIQIPYVFRYLAAELSAMNVRLNLRVDRN 1104



 Score = 68.9 bits (167), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 55/389 (14%), Positives = 127/389 (32%), Gaps = 22/389 (5%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++  S   E +N     +H     ++ +G          +R + P  +G +CP  T +G 
Sbjct: 430 TNGFSITAERLNHSRFTSH---FVSVHRGAFYTTMKTTSIRKLVPEAWGFMCPVHTPDGA 486

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
             GL++      R+NA        + +       ++  +S    +   I      +  +G
Sbjct: 487 PCGLLNHFAVSCRINARKHPLPDQQIIDLCT---ELGMVSTQFMKLPSI---YIPVLLNG 540

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
               ++           +  E+  +    P  +                    +   M R
Sbjct: 541 KVIGKVSPHEINSFVQQLRYERAVYNPKIPNTLEIGYCDGYLQDGYHALYLNDLPGQMIR 600

Query: 699 QAVPLLKAEAPFVGTGMESVVAKS--SGAAIVAKRAGIVEQVDA--IRIVIRSVEGDLDP 754
             +   +A    V  G    V      G +I        E++ A     ++ ++      
Sbjct: 601 PVIH--RATGNIVNIGPYEQVFLDIKCGDSIEGMNNAEYEEISALNSLSLLATLTPFCHM 658

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRP-----LVKVGDEVRRNDIIADGPSTDLGDLALGR 809
           + S  ++Y+    +++     ++ +      L+ +    R     A        +   G 
Sbjct: 659 NQSPRNMYQCQMAKQTMGIPALSNKYRSDTKLLWLHYPQRSICQCALMEPFGFNEYPTGA 718

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
           N +VA + + GY+ ED+++I +  +          + ++V          E+     +  
Sbjct: 719 NAVVAVISYTGYDMEDALIIKKSAIERGFGHGSQYKAYKVDFEKEGE-KNEMFSGTTSSG 777

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKI 898
           E   +++D+ G+   G EV     +   I
Sbjct: 778 EVFDEHLDDDGLPRPG-EVFENSPIYSHI 805



 Score = 68.6 bits (166), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 96/730 (13%), Positives = 205/730 (28%), Gaps = 129/730 (17%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD----- 87
              S+++FL             L+   K        +    L       + P ++     
Sbjct: 18  HTESFNYFLEKGKEDI------LKYMKKYKIIKKDSTELMELSCTGISIEKPTYNGLPLF 71

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM--------- 138
              C    LTY+  +K+T+ +   D +           K   +  G++P+M         
Sbjct: 72  PYMCRSAALTYSGRIKLTITIKENDSN-----------KTIEVDGGEIPIMVGSSKCWIG 120

Query: 139 ----TK-------------DGTFVIKGIQ---RIVVSQLHRSPGIHFDHDKGRASLS--G 176
               T               G F+I GI+   R++V           +H       S   
Sbjct: 121 SEYTTPEERINIREDPHEIGGYFIINGIERYLRMIV-------YAKPNHPLAVTRPSWTN 173

Query: 177 K----LLYACRIIPDQGLWMDIEFDSKDIIHV----RIDRR---RK----VPVTSFLMAL 221
           K      Y   I   +    D      + +H     ++  R   +K    +PV   L   
Sbjct: 174 KGAHFTKYGIIIRCMR----DDITTLTNTLHFLDNGKVSLRFIFKKQEFFIPVVLLLRVY 229

Query: 222 -GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
            GM   EI   F    + +                      + L   +     I S  +L
Sbjct: 230 GGMSDREI---FQLITMNNYENSNLVNAAEMLVRRENGSPLNGLNSPEQVLTYIGSKFRL 286

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN---GETGEIYIEAGDVIDEKSLEEIF 337
                + + +  +    +   CL  L    +  +       +++      IDE+ ++   
Sbjct: 287 IMDGTEGVNDTELGKRVLDEFCLVHLSSYAEKSDLLIFMLQKLFALVHGEIDEEGVDTPM 346

Query: 338 HSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
              +     LY   +     I+N L          A L I + ++     +    +    
Sbjct: 347 SQGVLLPGHLYQTVIKEE--IQNVLSK--------ARLFILKDLKDVKKGSKVTEKIYLQ 396

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDID 457
                + K   + +           +T  D++      I A         +   ++    
Sbjct: 397 RALSSAAKSFGTRIKSFISTGNFETNTTTDLQQTNGFSITAERLNHSRFTSHFVSVHRGA 456

Query: 458 NLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFF 517
                +  S+ +++   +              +  V      P  L+N   V   +    
Sbjct: 457 FYTTMKTTSIRKLVPEAWG------------FMCPVHTPDGAPCGLLNHFAVSCRINARK 504

Query: 518 CSSQLSQLEEHVNSLSRITH--TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                 Q+ +    L  ++    +  S      +     G        +   ++      
Sbjct: 505 HPLPDQQIIDLCTELGMVSTQFMKLPSIYIPVLLNGKVIGKVSPHEINSFVQQLRYERAV 564

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--AMEEENRYIAQANSS 633
               I     +         G+++  Y  +          YL+    +     I +A  +
Sbjct: 565 YNPKIPNTLEIGYC-----DGYLQDGYHAL----------YLNDLPGQMIRPVIHRATGN 609

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +   G + +  +  +C      +   +  + + S    +S+ A+L PF   + S R +  
Sbjct: 610 IVNIGPYEQVFLDIKCGDSIEGMNNAE--YEEISALNSLSLLATLTPFCHMNQSPRNMYQ 667

Query: 694 CNMQRQAVPL 703
           C M +Q + +
Sbjct: 668 CQMAKQTMGI 677


>gi|260593927|gb|ACX46258.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593929|gb|ACX46259.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593931|gb|ACX46260.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593933|gb|ACX46261.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593955|gb|ACX46272.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593959|gb|ACX46274.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593961|gb|ACX46275.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594035|gb|ACX46312.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594037|gb|ACX46313.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594039|gb|ACX46314.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594041|gb|ACX46315.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  169 bits (427), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|197941940|gb|ACH78575.1| RNA polymerase subunit [Pinus sylvestris]
 gi|197941942|gb|ACH78576.1| RNA polymerase subunit [Pinus sylvestris]
 gi|197941944|gb|ACH78577.1| RNA polymerase subunit [Pinus sylvestris]
          Length = 281

 Score =  169 bits (427), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 103/253 (40%), Positives = 153/253 (60%), Gaps = 10/253 (3%)

Query: 703 LLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIY 762
           L + E    GTG+E   A  SG+  +A + G +E +DA+                     
Sbjct: 1   LFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRT 52

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYN
Sbjct: 53  ESVIYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYN 112

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGII 882
           FED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++
Sbjct: 113 FEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLV 172

Query: 883 CVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+
Sbjct: 173 MLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVI 232

Query: 941 DVRIFNRHGIDKN 953
           DVR  NR     +
Sbjct: 233 DVRWINRVDDSGD 245



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 72   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 130

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 131  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 184

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 185  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 242

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK++GRHGNKGI+S +LP
Sbjct: 243  SGDNAE-----TVHVYISQKRKIQVGDKVSGRHGNKGIISIVLP 281


>gi|198279401|emb|CAP04735.1| RNA polymerase beta subunit [Pinus brutia var. pityusa]
          Length = 280

 Score =  169 bits (427), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 151/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 280


>gi|260594045|gb|ACX46317.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  169 bits (427), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|198279411|emb|CAP04740.1| RNA polymerase beta subunit [Pinus herrerae]
          Length = 283

 Score =  169 bits (427), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 104/255 (40%), Positives = 155/255 (60%), Gaps = 10/255 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL +      GTG+E   A  SG+  +A + G +E +DA+                   
Sbjct: 1   VPLFRPXKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTV 52

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW G
Sbjct: 53  RTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G
Sbjct: 113 YNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENG 172

Query: 881 IICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G 
Sbjct: 173 LVMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGR 232

Query: 939 VVDVRIFNRHGIDKN 953
           V+DVR  NR     +
Sbjct: 233 VIDVRWINRVDDSGD 247



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 74   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 132

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 133  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 186

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 187  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 244

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 245  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 283


>gi|329568271|gb|EGG50086.1| hypothetical protein HMPREF9520_03541 [Enterococcus faecalis
           TX1467]
          Length = 108

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 42/114 (36%), Positives = 61/114 (53%), Gaps = 10/114 (8%)

Query: 1   MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
           +A  VV  G  R R+ F +  E++++P+LIE+Q  SY  FL          +EGL+  F+
Sbjct: 4   LAGHVVKYGKHRERRSFARISEVLELPNLIEIQTDSYQWFL----------DEGLREMFE 53

Query: 61  SVFPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
            + PI  F G   LEFV YE   PK+ V++    D  Y+ PL +TLRL   +  
Sbjct: 54  DILPIDDFQGNLSLEFVDYELKEPKYTVEEARAHDANYSAPLHVTLRLTNRETG 107


>gi|56406207|gb|AAV87487.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 166

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 96/164 (58%), Positives = 123/164 (75%), Gaps = 1/164 (0%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIG
Sbjct: 3   LSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIG 62

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT
Sbjct: 63  LINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFT 122

Query: 642 EELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
           +  V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+
Sbjct: 123 DAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEH 166


>gi|198279465|emb|CAP04767.1| RNA polymerase beta subunit [Pinus pumila]
          Length = 276

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 101/249 (40%), Positives = 151/249 (60%), Gaps = 10/249 (4%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E    GTG+E   A  SG+  +A + G +E +DA+                       + 
Sbjct: 1   EKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVI 52

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED+
Sbjct: 53  YQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDA 112

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+
Sbjct: 113 ILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGS 172

Query: 887 EVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR 
Sbjct: 173 WIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRW 232

Query: 945 FNRHGIDKN 953
            NR     +
Sbjct: 233 INRVDDSGD 241



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 54/223 (24%), Positives = 86/223 (38%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 68   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 126

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 127  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 180

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 181  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 238

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S IL
Sbjct: 239  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISIIL 276


>gi|198279515|emb|CAP04792.1| RNA polymerase beta subunit [Equisetum giganteum]
          Length = 268

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 115/248 (46%), Positives = 161/248 (64%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL KAE   VGTG+E  +A  SG+ + ++R G V  +D  RI +   E         
Sbjct: 1   QAVPLSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDGQRITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDATLISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG +  + R+T L+VP G  
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLDYLDTLGAPEGKLLQAIFGTELTNARETCLKVPVGFK 233

Query: 937 GTVVDVRI 944
           G V+D++ 
Sbjct: 234 GRVIDIKW 241


>gi|330785298|gb|AEC46455.1| RNA polymerase II second largest subunit [Lecanographa brattiae]
          Length = 307

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 55/365 (15%), Positives = 98/365 (26%), Gaps = 67/365 (18%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 67

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG-FKKSTVLSSD 1011
                    R  IE   +   +     ++      + +  G        G       +S +
Sbjct: 68   -----LFYRTYIEQEQKLGFNSLEEFEKPTRHNTVRMRPGSYDKLDEDGFISPGIRVSGE 122

Query: 1012 LISEYPRSQWWQ-FAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGV 1070
             +     S   +      E   R  E  K          E  + + +             
Sbjct: 123  DVIIGKTSPLREPMQQGAEGGARLKEHTKRDVSAPLRSTEAGYIDTV------SISTTDG 176

Query: 1071 LRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSR 1130
             + VKV     +  Q GDK A RHG KG +      EDMPF   G   D+++NP  +PSR
Sbjct: 177  KKSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSQGIIPDLIINPHAIPSR 236

Query: 1131 MNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDD 1190
            M +  + E  L       G++  +      +  +IS     L                  
Sbjct: 237  MTIAHLIECLLSKVACLQGQEGDATPFTETSVREISDALQALG----------------- 279

Query: 1191 DSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVT 1250
                                             +          I+Y+G TG      + 
Sbjct: 280  --------------------------------FQKRGF-----EIMYNGHTGRKLRSQIX 302

Query: 1251 VGYIY 1255
            +G  Y
Sbjct: 303  LGPXY 307



 Score = 85.1 bits (209), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 44/196 (22%), Positives = 76/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPN----VSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +   +    +       +DE G I  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQEQKLGFNSLEEFEKPTRHNTVRMRPGSYDKLDEDGFISPGIRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK +P  E      E   R     K    RD S  + S  +G +  V I    G
Sbjct: 121 GEDVIIGKTSPLREPMQQGAEGGAR----LKEHTKRDVSAPLRSTEAGYIDTVSISTTDG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KKSVKVRTRTTKVPQI 192


>gi|304633241|gb|ADM46125.1| RpoB [Mannheimia caviae]
          Length = 164

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 96/160 (60%), Positives = 122/160 (76%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 1   QLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  F
Sbjct: 61  GLINSLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFRF 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           T+  V CR  GE  L   E++ ++D S +QVVS+AA+LIP
Sbjct: 121 TDTYVTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIP 160


>gi|70930328|ref|XP_737090.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56512187|emb|CAH84997.1| hypothetical protein PC301357.00.0 [Plasmodium chabaudi chabaudi]
          Length = 145

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 39/146 (26%), Positives = 67/146 (45%), Gaps = 20/146 (13%)

Query: 1240 LTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEV 1299
              G      + +G  +  +L HMV DK++ARS G  +++T+QP  G+S  GG R GEME 
Sbjct: 1    HNGRMLKSKIFIGPTFYQRLKHMVEDKIHARSRGPLTMITRQPTEGRSRDGGLRFGEMER 60

Query: 1300 WCIQAYGAAYVLQEMLTIKSD----------------DVVGRTRVYESIVAG--NDTFET 1341
             C+ ++G+A +L+E L  +SD                D+      YE  +     +  + 
Sbjct: 61   DCMISHGSAKMLKERLFEESDAYRVHVCDNCGLSCVADIN--KNAYECTICNSKTNISQI 118

Query: 1342 GTPESFNVLVKEMQALGLSIDLENSR 1367
              P +  +L +E+  + +   L    
Sbjct: 119  YIPYACKLLFQELMTMAIYPKLVLED 144


>gi|330785420|gb|AEC46516.1| RNA polymerase II second largest subunit [Paraingaderia placodioidea]
 gi|330785422|gb|AEC46517.1| RNA polymerase II second largest subunit [Paraingaderia placodioidea]
 gi|330785424|gb|AEC46518.1| RNA polymerase II second largest subunit [Paraingaderia placodioidea]
          Length = 307

 Score =  168 bits (426), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 61/378 (16%), Positives = 104/378 (27%), Gaps = 75/378 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLANTRSMEFLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     +  +     E+   V    +E   +      +      Y +L            
Sbjct: 64   LFRSFFYRTYI----EQQKQVGFNALEEFEKPNKQMTMRTRPGTYEKL----------DD 109

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN-KI 1057
                   T +S D I         + A     +  N E  +     +K  +    ++ + 
Sbjct: 110  DGFVAPGTRVSGDDII------IGKIAPFQAPMAENAEGGQRTKVHTKRDISSPLRSTEA 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
              +           R VKV     +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 164  GIVDRVLVTTNEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTVEGLV 223

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             DI++NP  +PSRM V  + E  L       G +  +          IS L         
Sbjct: 224  PDIIINPHAIPSRMTVAHLIECLLSKVSATQGLEGDATPFTDVTVSAISDLLR------- 276

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
                                              DG                  G  +++
Sbjct: 277  ----------------------------------DG-------------GYQSRGMELMH 289

Query: 1238 DGLTGEPFDRPVTVGYIY 1255
            +G TG      + +G  Y
Sbjct: 290  NGHTGRKLMAQIFLGPTY 307



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/196 (21%), Positives = 75/196 (38%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A+  S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLANTRSMEFLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       EE  +    +         + +D+ G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEQQKQVGFNALEEFEKPNKQMTMRTRPGTYEKLDDDGFVAPGTRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GKI P         E   R     K    RD S  + S  +G V  V +    G
Sbjct: 121 GDDIIIGKIAPFQAPMAENAEGGQRT----KVHTKRDISSPLRSTEAGIVDRVLVTTNEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 RRSVKVRTRTTKVPQI 192


>gi|330785426|gb|AEC46519.1| RNA polymerase II second largest subunit [Sigridea californica]
          Length = 285

 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 57/357 (15%), Positives = 99/357 (27%), Gaps = 81/357 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + +    + +   +   V        +     +V+    +R     
Sbjct: 1    NILYYPQKPLATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQEDSVIVNQSSIDRGLFRS 60

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 61   LFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEEDGFVAPGTRVSGEDVIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++   + +                E  QR  E  K          E    +K+      
Sbjct: 121  KTSPFQAPM------------QEGSEGGQRTKEHTKRDVSAPLRSTEAGIVDKVL----- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 164  -VTTTEGRRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSNGIVPDLIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 223  PHAIPSRMTIAHLIECLLSKVSSLTGHEGD------------------------------ 252

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                   +TP F       I+S+L        G  ++Y+G 
Sbjct: 253  -----------------------ATP-FTEVTVSEISSLLAENGYQRRGFEVMYNGH 285



 Score = 78.6 bits (192), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 66/187 (35%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTQSMKYMRFQDLPAGQNAIVAIACYSGYNQEDSVIVNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  +   +V         + ++E G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPAKHVTMRTRPGTYEKLEEDGFVAPGTRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK +P         E   R        DV        +G+   V+      R  
Sbjct: 114 GEDVIIGKTSPFQAPMQEGSEGGQRTKE-HTKRDVSAPLRSTEAGIVDKVLVTTTEGRRS 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRT 179


>gi|193201481|gb|ACF15948.1| RNA polymerase II subunit [Enterographa anguinella]
          Length = 298

 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 53/370 (14%), Positives = 100/370 (27%), Gaps = 73/370 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +     + +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEWLKFAELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
                  R  I++ +       ++ E   +                   +  G        
Sbjct: 61   -RSFLYRTYIEQQKAVGFNALDEFEKPVKQLTMRTRPGTYEKLDEDGFVAPGIRVSGDDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +       Q  +               + Q     + L       ++++
Sbjct: 120  IIGKTAPFQNPMADNAEGGQRTK---------------QHQRRDVSAPLRSTESGIVDRV 164

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 165  LV---TTTEGRRSVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDL 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM V  + E  L       G +                             
Sbjct: 222  IINPHAIPSRMTVAHLIECLLSKVSATSGLEGD--------------------------- 254

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +L+ +     G  ++++G 
Sbjct: 255  --------------------------ATP-FTDVTVSEISQLLKGSGYQSRGFELMHNGH 287

Query: 1241 TGEPFDRPVT 1250
            TG      V 
Sbjct: 288  TGRKLMAQVY 297



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 69/187 (36%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEWLKFAELPAGQNAIVAIACYSGYNQEDSIIMNQSAI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S     +    +       +E  + +  +         + +DE G +  G  V+
Sbjct: 56  DRGLFRSFLYRTYIEQQKAVGFNALDEFEKPVKQLTMRTRPGTYEKLDEDGFVAPGIRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  ++PM    +  +     +  DV        SG+   V+      R  
Sbjct: 116 GDDIIIGKTAPF-QNPMADNAEGGQRTKQHQRRDVSAPLRSTESGIVDRVLVTTTEGRRS 174

Query: 950 IDKNERS 956
           +    R+
Sbjct: 175 VKVRTRA 181


>gi|330785412|gb|AEC46512.1| RNA polymerase II second largest subunit [Roccellographa muriformis]
          Length = 307

 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/377 (15%), Positives = 103/377 (27%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSLQFMNFRELPAGQNTIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E+ E   +           +       +  G      
Sbjct: 64   LF-RSLFYRSYIEQQQPVGFNAMEEFEKPVKSMTMRTRPGTYDKLDEDGFVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +               +E  QR  E  K          E    +++ 
Sbjct: 123  DIIIGKTAPFQAPMRDN------------EEGGQRTKEHTKRDVSCPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VK+     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGITP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +  +          IS            
Sbjct: 225  DLIINPHAIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS----------- 273

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                          +L  A   + G  V                             +Y+
Sbjct: 274  --------------ILESAGYQRRGFEV-----------------------------MYN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG   +  + +G  Y
Sbjct: 291  GHTGRKLNAQIFLGPTY 307



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 71/196 (36%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPS---TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S    +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSLQFMNFRELPAGQNTIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                    +DE G +  G  V+
Sbjct: 61  DRGLFRSLFYRSYIEQQQPVGFNAMEEFEKPVKSMTMRTRPGTYDKLDEDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P        EE   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMRDNEEGGQRT----KEHTKRDVSCPLRSTEAGIIDRVLVTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 RRSVKIRTRTTKVPQI 192


>gi|307547787|gb|ADN44507.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 297

 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 60/365 (16%), Positives = 104/365 (28%), Gaps = 79/365 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 9    ILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 68

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +     E+  SV    +E   + +  E +      Y +L +   +  G        
Sbjct: 69   FYRTYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDI 124

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  K          E    +++   
Sbjct: 125  IIGKTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL-- 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 171  ----LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDL 226

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G++                             
Sbjct: 227  IINPHAIPSRMTIAHLIECLLSKVSTVTGQEGD--------------------------- 259

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+ +LR A     G  ++++G 
Sbjct: 260  --------------------------ATP-FTDVTVSNISELLRFAGYQSRGFEMMHNGH 292

Query: 1241 TGEPF 1245
            TG   
Sbjct: 293  TGRXL 297



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMSNILYYPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        ++        + +D+ G++  G  V+
Sbjct: 61  DRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|118201892|gb|ABK79759.1| RNA polymerase subunit B [Sulfitobacter guttiformis]
          Length = 163

 Score =  168 bits (426), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG V+++V Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVKDGIVSDEVQYMSATEEMRHTVAQANANLDENMKFVNDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P   +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPSMNVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|117573498|gb|ABK40925.1| RNA polymerase subunit B [Pseudomonas sp. C10-181]
          Length = 160

 Score =  168 bits (425), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 89/159 (55%), Positives = 118/159 (74%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           R   E  +   E +  +D SPKQVVS+AASLIPFLE+D+
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDN 159


>gi|193201533|gb|ACF15974.1| RNA polymerase II subunit [Opegrapha vulgata]
          Length = 293

 Score =  168 bits (425), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 58/368 (15%), Positives = 105/368 (28%), Gaps = 79/368 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFRSF 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            ++  +   +N  +     +Q+E   +      +      Y +L +   +  G        
Sbjct: 62   LYRTYIEQQNVSA----SQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVSGDDI 117

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  +          E    +K+   
Sbjct: 118  IIGKTAPFPAPMQDNA------------EGGQRTKQHTRRDVSAPLRSTEAGIVDKVL-- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 164  ----VSNVDGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM V  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTVAHLIECLLSKVSATQGLEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP F       I+S+L+ +     G  ++++G 
Sbjct: 253  --------------------------ATP-FTDVTVSEISSLLKGSGYQSRGLELMHNGH 285

Query: 1241 TGEPFDRP 1248
            TG      
Sbjct: 286  TGRKLMAQ 293



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 62/187 (33%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                   +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +      +     E                  + +D+ G +  G  V+
Sbjct: 54  DRGLFRSFLYRTYIEQQNVSASQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +        DV        +G+   V+   +  R  
Sbjct: 114 GDDIIIGKTAPFPAPMQDNAEGG-QRTKQHTRRDVSAPLRSTEAGIVDKVLVSNVDGRRT 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRA 179


>gi|17225248|gb|AAL37317.1| RNA polymerase B-subunit [Staphylococcus vitulinus]
 gi|17225252|gb|AAL37319.1| RNA polymerase B-subunit [Staphylococcus sciuri subsp. sciuri]
 gi|17225268|gb|AAL37327.1| RNA polymerase B-subunit [Staphylococcus auricularis]
 gi|60687397|gb|AAX35725.1| RNA polymerase subunit B [Staphylococcus sciuri]
          Length = 169

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 103/168 (61%), Positives = 130/168 (77%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV     +VT+ + YL+A EE++  +AQANS LDE G F ++ V CR  G+    P+E
Sbjct: 62  YRKVNIETNQVTDRIDYLTADEEDSYVVAQANSVLDETGKFVDDEVLCRFRGDNTTKPKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           ++D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 RMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|219564089|gb|ACL28228.1| RNA polymerase II second largest subunit [fungal sp. M258]
          Length = 273

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 53/276 (19%), Positives = 92/276 (33%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 10   MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 66

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    IE   +   ++ + L    Y +L E   +  G           K++ ++ D   
Sbjct: 67   -IGMNVIEQFEKPFREDTLKLKHGTYEKLDEDGIVAPGVRVSGEDIIIGKTSPIAPDAEE 125

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +  Q                             LR V
Sbjct: 126  LGQRTKAHTKRDASTPLRSTENGIVDQVLI--------------------TTNAEGLRFV 165

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF   G   DI++NP  +PSRM + 
Sbjct: 166  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTVQGIVPDIIINPHAIPSRMTIA 225

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 226  HLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 261



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 7   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 66

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +     + +DE GI+  G  V+  DI++GK +P        
Sbjct: 67  IGMNVIEQFEKPFREDTLKLKHGTYEKLDEDGIVAPGVRVSGEDIIIGKTSPIAPDAEEL 126

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 GQRT-------KAHTKRDASTPLRSTENGIVDQVLITT 157


>gi|330785174|gb|AEC46393.1| RNA polymerase II second largest subunit [Arthonia cinnabarina]
          Length = 304

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 51/372 (13%), Positives = 99/372 (26%), Gaps = 84/372 (22%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 8    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 67

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 68   LYYRTYIEQEQAVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+++      R            ++     +  Q                      
Sbjct: 128  KTAPLAANAEERGARLTQHTKRDVSTPLRSTEAGIVDQVL-------------------- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +  +          +S +               
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVAATNAYEGDATPFTEITVEMVSDILE------------- 273

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                 S  +          ++Y+G TG 
Sbjct: 274  ------------------------------------KSGYQKRGF-----EVMYNGHTGR 292

Query: 1244 PFDRPVTVGYIY 1255
                 V +G  Y
Sbjct: 293  KLMAQVFLGPTY 304



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 71/187 (37%), Gaps = 12/187 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQAVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L +        DV        +G+   V+   +  +  
Sbjct: 121 GDDIIIGKTAPLAANAEERGARLTQ----HTKRDVSTPLRSTEAGIVDQVLLTSVDGKKN 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKIRTRT 183


>gi|194320168|gb|ACF48310.1| DNA-dependent RNA polymerase II second largest subunit [Lecidella
            elaeochroma]
          Length = 317

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 59/385 (15%), Positives = 106/385 (27%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQEPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    E + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRAYTDQEKR---IGMNVLEQFEKPMRSETLKLKHGTYDKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPMAGDAEELGQRTKAHTKRDTSTPLRSTENGIVDQVLMS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNADGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    E  
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTDVTVDSVSSLLR--ENG 284

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                                                    +G + 
Sbjct: 285  YQSRGFEVM---------------------------------------------YNGHT- 298

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
               G         V +G  Y  +L 
Sbjct: 299  ---GR---KLVAQVFLGPTYYQRLR 317



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/179 (21%), Positives = 71/179 (39%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR            + +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMDTMANILYYPQEPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  +   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRIGMNVLEQFEKPMRSETLKLKHGTYDKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RDTS  + S  +G V  V +  
Sbjct: 126 VSGEDIIIGKTAPMAGDAEELGQRT-------KAHTKRDTSTPLRSTENGIVDQVLMST 177


>gi|56406203|gb|AAV87485.1| RpoB [Pasteurella multocida subsp. multocida]
          Length = 172

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 96/167 (57%), Positives = 124/167 (74%), Gaps = 1/167 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
           + +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 6   VMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLIN 65

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  
Sbjct: 66  SLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAF 125

Query: 645 VFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE+DD   V
Sbjct: 126 VTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDRTCV 172


>gi|260593957|gb|ACX46273.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++ +++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADPVIAQASAPMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|253756999|gb|ACT35303.1| DNA-directed RNA polymerase beta subunit [Mycobacterium
           tuberculosis]
          Length = 171

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 95/171 (55%), Positives = 125/171 (73%), Gaps = 1/171 (0%)

Query: 492 SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVAR 551
           + D++++ PQ LIN +PVV+A+ EFF + Q SQ     N LS +TH RRLSALG GG++R
Sbjct: 1   TQDVEAITPQTLINIRPVVAAIKEFFGTRQPSQFMVQNNPLSGLTHKRRLSALGPGGLSR 60

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            RAG+E+RDVHP+HYGR+CP ET EG NIGL+ SL+ +ARVN +GFIETPYRKV DG V+
Sbjct: 61  ERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVS 120

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA-GEEILVPREKI 661
           +++VYL+A EE+   +AQANS +D DG F E  V  R   GE   VP  ++
Sbjct: 121 DEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEV 171


>gi|260593945|gb|ACX46267.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594005|gb|ACX46297.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594017|gb|ACX46303.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594029|gb|ACX46309.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++ L ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINFLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|198279481|emb|CAP04775.1| RNA polymerase beta subunit [Pinus sabiniana]
          Length = 274

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 103/254 (40%), Positives = 153/254 (60%), Gaps = 10/254 (3%)

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           P  + E    GTG+E   A  SG+  +A + G +E +DA+                    
Sbjct: 1   PXFRPEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVR 52

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
              + +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GY
Sbjct: 53  TESVIYQRSNTNTCTHQKPQICQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGY 112

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G+
Sbjct: 113 NFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGL 172

Query: 882 ICVGAEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V
Sbjct: 173 VMLGSWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRV 232

Query: 940 VDVRIFNRHGIDKN 953
           +DVR  NR     +
Sbjct: 233 IDVRWINRVDDSGD 246



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 52/216 (24%), Positives = 81/216 (37%), Gaps = 14/216 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            IC G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 73   ICQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 131

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 132  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 185

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 186  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 243

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             GD+        V V+++ KR IQ GDK+AGRHGNK
Sbjct: 244  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNK 274


>gi|198279527|emb|CAP04798.1| RNA polymerase beta subunit [Equisetum variegatum]
          Length = 269

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 111/246 (45%), Positives = 160/246 (65%), Gaps = 9/246 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP  KAE   VGTG+E  +A  SG+ + ++R G V  +D+ RI +   E           
Sbjct: 1   VPXSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDSERITLFVDEETSINK----- 55

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+ ++RSN NTC+NQ+PLV     +R+  +IADG ST  G+LALG+N+LVA+MPW G
Sbjct: 56  --NLLSYERSNNNTCMNQKPLVSKDQFLRQGQVIADGASTVGGELALGKNILVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++ E G
Sbjct: 114 YNFEDATLISERLIYEDIFTSFHIERHEINVAFTGQGPEKLTREIPHLNNHILRHLGENG 173

Query: 881 IICVGAEVNPGDILVGKITPKG--ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ V  GD+LVGK+TP    E+   PE KLL+AIFG    + R+T L+VP G  G 
Sbjct: 174 LVKLGSWVEAGDVLVGKLTPLEYLETLGAPEGKLLQAIFGTDVTNARETCLKVPVGFKGR 233

Query: 939 VVDVRI 944
           V+D++ 
Sbjct: 234 VIDIKW 239


>gi|198279341|emb|CAP04705.1| RNA polymerase beta subunit [Pinus taiwanensis]
          Length = 280

 Score =  168 bits (425), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 150/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG   +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGXVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPKIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGLEVSTARENCLRAPIGGRGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTIEESLCTPEGRLLQTIFGLEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 280


>gi|198279475|emb|CAP04772.1| RNA polymerase beta subunit [Pinus parviflora]
          Length = 267

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 100/246 (40%), Positives = 150/246 (60%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 51/217 (23%), Positives = 82/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 267


>gi|260594071|gb|ACX46330.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMNQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAVYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|198279505|emb|CAP04787.1| RNA polymerase beta subunit [Equisetum hyemale]
          Length = 271

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 114/248 (45%), Positives = 159/248 (64%), Gaps = 9/248 (3%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVP  KAE   VGTG+E  +A  SG+ + ++R G V  +D  RI +   E         
Sbjct: 1   QAVPXSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDGQRITLFVDEETSINK--- 57

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                L+ ++RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW
Sbjct: 58  ----NLLSYERSNNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPW 113

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE
Sbjct: 114 EGYNFEDATLISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDE 173

Query: 879 CGIICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
            G++ +G+ V  GD+LVGK+TP         PE KLL+AIFG    + R+T L+VP G  
Sbjct: 174 NGLVKLGSWVEAGDVLVGKLTPLDYLDTLGAPEGKLLQAIFGTDVTNARETCLKVPVGFK 233

Query: 937 GTVVDVRI 944
           G V+D++ 
Sbjct: 234 GRVIDIKW 241


>gi|118201904|gb|ABK79765.1| RNA polymerase subunit B [Thalassobacter stenotrophicus]
          Length = 163

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG+VT++V Y+SA EE    +AQAN+ LD++  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGQVTDEVSYMSATEEMRHTVAQANAQLDDEMRFKNDLVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AG+ +L  R+ +D ID SPKQ+VS+AA+LIPFLENDD+NR L
Sbjct: 122 AGDYMLQSRDNVDLIDVSPKQLVSVAAALIPFLENDDANRAL 163


>gi|17225254|gb|AAL37320.1| RNA polymerase B-subunit [Staphylococcus equorum]
          Length = 169

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 102/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V CR  G   ++ +E
Sbjct: 62  YRKVDLETHSITDQIDYLTADEEDSYVVAQANSVLDENGRFVEDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|283806282|dbj|BAI66380.1| RNA polymerase second largest subunit [Ophiosphaerella sasicola]
          Length = 271

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 55/286 (19%), Positives = 95/286 (33%), Gaps = 27/286 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   + +   +    +F 
Sbjct: 10   YPQKPLGTTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQTSIDRGLF-RSLFY 68

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 69   RAYTEQEKR---IGVNVLEQFEKPTRADTMRLKAGTYDKLDDDGVVAPGVRVSGDDIIIG 125

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + SD                 E  Q+ V   K    T     E+   +++      
Sbjct: 126  KTAPIPSD---------------AKELGQKTVLHTKRDVSTPLRSTENGIVDQVLF---- 166

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF +DG   DI++N
Sbjct: 167  -TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRDGLTPDIIIN 225

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            P  +PSRM +  + E  L       G +  +          +S L 
Sbjct: 226  PHAIPSRMTIAHLVECLLSKVGAINGCEGDATPFTDVTVDQVSNLL 271



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 63/179 (35%), Gaps = 19/179 (10%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PL                      +L  G+N +VA   + GYN EDS
Sbjct: 1   MPSMMNVLYYPQKPL----------GTTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +   +   E        D   +       +D+ G+
Sbjct: 51  VIMNQTSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTMRLKAGTYDKLDDDGV 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +  G  V+  DI++GK  P      +  ++L +        DV        +G+   V+
Sbjct: 111 VAPGVRVSGDDIIIGKTAPI----PSDAKELGQKTVLHTKRDVSTPLRSTENGIVDQVL 165


>gi|90192204|gb|ABD91762.1| RNA polymerase beta subunit [Klebsiella oxytoca]
          Length = 156

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 95/156 (60%), Positives = 121/156 (77%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 1   FMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE N  IAQANS+LD++G F E+L
Sbjct: 61  SLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDL 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           V CR  GE  L  R+++D++D S +QVVS+ ASLIP
Sbjct: 121 VTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIP 156


>gi|330785294|gb|AEC46453.1| RNA polymerase II second largest subunit [Llimonaea flexuosa]
          Length = 307

 Score =  168 bits (425), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 60/377 (15%), Positives = 99/377 (26%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     + +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLQFNELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +     F R  I+  +       E+ E   +                   +  G      
Sbjct: 64   LF-RSFFYRTYIEIQKTVGFNALEEFEKPNKQMTMRTRPGTYEKLDEDGFVAPGVRVSGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR     K    T     E    +++ 
Sbjct: 123  DVIVGKTAPFQAPMAENA------------EGGQRTKTHTKRDVSTPLRSTEAGIIDRVL 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ------VTTNEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTVEGLVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM V  + E  L       G +  +          IS L          
Sbjct: 225  DLIINPHAIPSRMTVAHLIECLLSKVAATQGLEGDATPFTDVTVSAISDLL--------- 275

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                 W SG                            G  ++++
Sbjct: 276  ---------------------WDSGYH------------------------SRGFEMMHN 290

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      + +G  Y
Sbjct: 291  GHTGRKLAAQIFLGPTY 307



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 74/196 (37%), Gaps = 13/196 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEFLQFNELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 60

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECGIICVGAEVN 889
              +F S     +  + +       EE  +    +         + +DE G +  G  V+
Sbjct: 61  DRGLFRSFFYRTYIEIQKTVGFNALEEFEKPNKQMTMRTRPGTYEKLDEDGFVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D++VGK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 121 GDDVIVGKTAPFQAPMAENAEGGQRT----KTHTKRDVSTPLRSTEAGIIDRVLVTTNEG 176

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 177 KRSVKVRTRTTKVPQI 192


>gi|198279419|emb|CAP04744.1| RNA polymerase beta subunit [Pinus montezumae]
          Length = 278

 Score =  167 bits (424), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 1   PEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 52

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 53  IYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 112

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 113 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 172

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 173 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 232

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 233 WINRVDDSGD 242



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 69   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 127

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 128  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 181

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 182  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 239

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 240  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 278


>gi|197941930|gb|ACH78570.1| RNA polymerase subunit [Pinus banksiana]
 gi|197941932|gb|ACH78571.1| RNA polymerase subunit [Pinus banksiana]
          Length = 280

 Score =  167 bits (424), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPKIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 280


>gi|118201836|gb|ABK79731.1| RNA polymerase subunit B [Jannaschia rubra]
          Length = 163

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 102/162 (62%), Positives = 127/162 (78%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DG+V+++V Y+SA EE    +AQAN+ L +D  F  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVIDGQVSDEVQYMSATEEMRHTVAQANAQLTDDMRFENELVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+ +L  R+ +D ID SPKQ+VS+AA+LIPFLENDD+NR L
Sbjct: 122 SGDYMLQSRDNVDLIDVSPKQLVSVAAALIPFLENDDANRAL 163


>gi|193201525|gb|ACF15970.1| RNA polymerase II subunit [Opegrapha viridistellata]
          Length = 282

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 57/346 (16%), Positives = 97/346 (28%), Gaps = 73/346 (21%)

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                + +   +  + AI      +  D+ +   S +   +     F R  I++ +     
Sbjct: 9    YLKFADLPAGQNAIVAIACYSGYNQEDSLIMNQSSIDRGLF-RSFFYRTYIEQQKAVGFN 67

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              ++ E   +                   +  G           K+    + L       
Sbjct: 68   ALDEFEKPVKQLTMRTKTGTYEKLDDDGFVPPGIRVSGDDIIIGKTAPFQAPL------- 120

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                 A   +  QR  E  +          E    +++              R VKV   
Sbjct: 121  -----ADSSDGGQRKQEHTRRDVSAPLRSTEAGIVDRVL------VTNTEGRRSVKVRTR 169

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM V  + E 
Sbjct: 170  ATKIPQIGDKFASRHGQKGTIGVTYCQEDMPFTAEGIVPDLIINPHAIPSRMTVAHLIEC 229

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             L       G +                                                
Sbjct: 230  LLSKLGACHGMEGD---------------------------------------------- 243

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                   +TP F       I+ ML++      G  ++++G TG   
Sbjct: 244  -------ATP-FTEITVSQISEMLKLTGYHTRGFELMHNGHTGRKL 281



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/166 (18%), Positives = 64/166 (38%), Gaps = 6/166 (3%)

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                DL  G+N +VA   + GYN EDS+++++  +   +F S     +    +      
Sbjct: 9   YLKFADLPAGQNAIVAIACYSGYNQEDSLIMNQSSIDRGLFRSFFYRTYIEQQKAVGFNA 68

Query: 859 -EEITRDIPNV----SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
            +E  + +  +         + +D+ G +  G  V+  DI++GK  P  ++P+       
Sbjct: 69  LDEFEKPVKQLTMRTKTGTYEKLDDDGFVPPGIRVSGDDIIIGKTAPF-QAPLADSSDGG 127

Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
           +        DV        +G+   V+      R  +    R+  +
Sbjct: 128 QRKQEHTRRDVSAPLRSTEAGIVDRVLVTNTEGRRSVKVRTRATKI 173


>gi|198279423|emb|CAP04746.1| RNA polymerase beta subunit [Pinus oocarpa]
          Length = 274

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 1   PEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 52

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 53  IYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 112

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 113 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 172

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 173 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 232

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 233 WINRVDDSGD 242



 Score = 78.2 bits (191), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 84/220 (38%), Gaps = 14/220 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 69   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 127

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 128  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 181

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 182  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 239

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S
Sbjct: 240  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIIS 274


>gi|198279421|emb|CAP04745.1| RNA polymerase beta subunit [Pinus oocarpa]
          Length = 275

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 1   PEKXIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 52

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 53  IYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 112

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 113 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLG 172

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 173 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 232

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 233 WINRVDDSGD 242



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 53/221 (23%), Positives = 83/221 (37%), Gaps = 14/221 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 69   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 127

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 128  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 181

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 182  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 239

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSR 1102
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S 
Sbjct: 240  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISI 275


>gi|198279349|emb|CAP04709.1| RNA polymerase beta subunit [Pinus virginiana]
          Length = 273

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 102/250 (40%), Positives = 152/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
            E    GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPKIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 64.3 bits (155), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 79/217 (36%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+ GRHG KG
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVXGRHGXKG 273


>gi|260594031|gb|ACX46310.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (424), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 88/158 (55%), Positives = 116/158 (73%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITHTRR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQTNPLSEITHTRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260593939|gb|ACX46264.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593963|gb|ACX46276.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593975|gb|ACX46282.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594011|gb|ACX46300.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594091|gb|ACX46340.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|118201878|gb|ABK79752.1| RNA polymerase subunit B [Roseovarius nubinhibens]
          Length = 163

 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 106/162 (65%), Positives = 128/162 (79%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHATHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYR+V DG+VT++V Y+SA EE+   +AQAN+++DE G F  E+V  R 
Sbjct: 62  ARVNKYGFIETPYRRVVDGQVTDNVQYMSATEEQRHVVAQANANIDETGRFVNEMVNTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           AGE  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 AGEYTLSPIENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|198279397|emb|CAP04733.1| RNA polymerase beta subunit [Pinus sylvestris]
          Length = 280

 Score =  167 bits (424), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 101/250 (40%), Positives = 150/250 (60%), Gaps = 10/250 (4%)

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                 GTG+E   A  SG+  +A + G +E +DA+                       +
Sbjct: 3   PXKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESV 54

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
            +QRSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED
Sbjct: 55  IYQRSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFED 114

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           ++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G
Sbjct: 115 AILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLG 174

Query: 886 AEVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
           + +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR
Sbjct: 175 SWIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVR 234

Query: 944 IFNRHGIDKN 953
             NR     +
Sbjct: 235 WINRVDDSGD 244



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 71   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 129

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 130  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 183

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 184  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 241

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK++GRHGNKGI+S +LP
Sbjct: 242  SGDNAE-----TVHVYISQKRKIQVGDKVSGRHGNKGIISXVLP 280


>gi|300086683|gb|ADJ67683.1| RpoB [Avibacterium sp. CCUG 18551]
          Length = 164

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 96/164 (58%), Positives = 122/164 (74%), Gaps = 1/164 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL  +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LD++  
Sbjct: 61  IGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           FT+  V CR   GE  L   E+I ++D S +Q+VS+AA+LIPFL
Sbjct: 121 FTDTFVTCRGEHGESGLYRPEEIHYMDVSTQQIVSVAAALIPFL 164


>gi|67942346|gb|AAY83373.1| DNA-dependent RNA polymerase II [Sarcoscypha austriaca]
          Length = 526

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/365 (15%), Positives = 105/365 (28%), Gaps = 81/365 (22%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  +  I      +  D+ +   S +   
Sbjct: 240  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRG 299

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L +   +  G   
Sbjct: 300  LF-RSLFYRTYMDQEKR---IGMQVVEEFEKPMRGNTLRLKHGTYDKLDDDGLVAPGVRV 355

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +S D      R ++         ++     +  Q   S          
Sbjct: 356  TGEDIIIGKTAPISPDADEMGQRQKYHTKRDVSTPLRSTESGIVDQVMLS---------- 405

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 406  ----------TNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEG 455

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               DI++NP  +PSRM +  + E  L                                  
Sbjct: 456  IVPDIIINPHAIPSRMTIAHLIECLLSKLST----------------------------- 486

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                     +     +TP F      +++ MLR       G  +
Sbjct: 487  ------------------------LRGAEGDATP-FTDVTVRSVSEMLRDHGYQSRGFEV 521

Query: 1236 LYDGL 1240
            +Y+G 
Sbjct: 522  MYNGH 526



 Score = 84.7 bits (208), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 67/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +           Q+PL                      +L  G+N +V  M + G
Sbjct: 233 TNFAERMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVGIMCYSG 282

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  +   +       
Sbjct: 283 YNQEDSVIMNQSSIDRGLFRSLFYRTYMDQEKRIGMQVVEEFEKPMRGNTLRLKHGTYDK 342

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G++  G  V   DI++GK  P         ++       +K    RD S  + S  
Sbjct: 343 LDDDGLVAPGVRVTGEDIIIGKTAPISPDADEMGQR-------QKYHTKRDVSTPLRSTE 395

Query: 936 SGTVVDVRIFNRHGIDK 952
           SG V  V +       K
Sbjct: 396 SGIVDQVMLSTNSEGLK 412


>gi|293601716|gb|ADE48262.1| RNA polymerase II [Morchella sp. Mel-7]
 gi|293601746|gb|ADE48277.1| RNA polymerase II [Morchella sp. Mel-7]
          Length = 286

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/292 (16%), Positives = 90/292 (30%), Gaps = 21/292 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVESVSTLLR 271



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|330785178|gb|AEC46395.1| RNA polymerase II second largest subunit [Arthonia radiata]
          Length = 304

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 50/377 (13%), Positives = 97/377 (25%), Gaps = 76/377 (20%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    ++ R  I++ +       E+ E   + +         +       +  G      
Sbjct: 64   LF-RSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGD 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  L+++      R            ++     +  Q                 
Sbjct: 123  DIIIGKTAPLAANAEERGMRGTQHTKRDVSTPLRSTEAGIIDQVL--------------- 167

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         + VK+     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 168  ------LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L         +  +          +S +          
Sbjct: 222  DIIINPHAIPSRMTIAHLIECLLSKVAATNAYEGDATPFTDITVEMVSEILE-------- 273

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                      S  +          ++Y+
Sbjct: 274  -----------------------------------------KSGYQKRGF-----EVMYN 287

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG      V +G  Y
Sbjct: 288  GHTGRKLMAQVFLGPTY 304



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 73/187 (39%), Gaps = 12/187 (6%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   QRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 60

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 61  DRGLFRSLYYRTYIEQEQSVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 120

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +    EE+ +R        DV        +G+   V+   +  +  
Sbjct: 121 GDDIIIGKTAPLAAN---AEERGMRGT-QHTKRDVSTPLRSTEAGIIDQVLLTSVDGKKN 176

Query: 950 IDKNERS 956
           +    R+
Sbjct: 177 VKIRTRT 183


>gi|283806273|dbj|BAI66374.1| RNA polymerase second largest subunit [Katumotoa bambusicola]
          Length = 303

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/367 (16%), Positives = 105/367 (28%), Gaps = 81/367 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 7    YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 65

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 66   RAYTEQEKR---IGVNVLEQFEKPTRADTMRLKAGTYDKLDDDGVVAPGVRVSGDDIIIG 122

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + SD                 E  Q+ +   K    T     E+   +++      
Sbjct: 123  KTAPIPSD---------------AKELGQKTILHTKRDVSTPLRSTENGIVDQVLF---- 163

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF +DG   DI++N
Sbjct: 164  -TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRDGLTPDIIIN 222

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +  +          +S L               
Sbjct: 223  PHAIPSRMTIAHLVECLLSKVGAINASEGDATPFMDITVDQVSNLLEAAN---------- 272

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                    +   L      I+Y+G TG+
Sbjct: 273  ---------------------------------------FQKRGL-----EIMYNGHTGK 288

Query: 1244 PFDRPVT 1250
                 V 
Sbjct: 289  KMRAQVF 295



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 63/182 (34%), Gaps = 22/182 (12%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 1   MMNVLYYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIM 50

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +D+ G++  
Sbjct: 51  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTMRLKAGTYDKLDDDGVVAP 110

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  DI++GK  P         +K +           RD S  + S  +G V  V  
Sbjct: 111 GVRVSGDDIIIGKTAPIPSDAKELGQKTI-------LHTKRDVSTPLRSTENGIVDQVLF 163

Query: 945 FN 946
             
Sbjct: 164 TT 165


>gi|194320287|gb|ACF48384.1| RNA polymerase II second largest subunit [Alectoria ochroleuca]
          Length = 311

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/340 (16%), Positives = 102/340 (30%), Gaps = 42/340 (12%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 65   LF-RSLFYRAYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRV 120

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 121  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  ----------TNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 220

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L       
Sbjct: 221  MVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLR----- 275

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                                +     +G  + T VF G  
Sbjct: 276  ----------EHGYQSRGFEIMYNGHTGRKLVTQVFLGPT 305



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 66/170 (38%), Gaps = 15/170 (8%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           QR              +A   S +     +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   QRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 61

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E     +  D   +       +D+ G++  G  V+
Sbjct: 62  DRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVS 121

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 122 GEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 164


>gi|260594061|gb|ACX46325.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594067|gb|ACX46328.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594073|gb|ACX46331.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594075|gb|ACX46332.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594077|gb|ACX46333.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594079|gb|ACX46334.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594081|gb|ACX46335.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMNQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|1008044|dbj|BAA02417.1| rpoB protein [Oryza sativa Japonica Group]
          Length = 193

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 58/206 (28%), Positives = 98/206 (47%), Gaps = 26/206 (12%)

Query: 26  IPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSG--AAMLEFVSYEFDP 83
           IP   ++Q   +  F+          N+GL    +    I       +  L    Y+   
Sbjct: 12  IPGFSQIQFEGFCRFI----------NQGLAEELEKFPTIKDPDHGISFQLFAKGYQLLE 61

Query: 84  PKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGT 143
           P     D ++  LTY+  L ++ RLI              D+++Q+IY+G++P+M   GT
Sbjct: 62  PSIKERDAVYESLTYSSELYVSARLIFGF-----------DVQKQTIYIGNIPIMNSLGT 110

Query: 144 FVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH 203
           F+I GI RIV++Q+  SPGI++  +     +S   +Y   II D G   ++  D K+ I 
Sbjct: 111 FIINGIYRIVINQILLSPGIYYRSELDHKGIS---IYTGTIISDWGGRSELAIDKKERIW 167

Query: 204 VRIDRRRKVPVTSFLMALGMDSEEIL 229
            R+ R++K+ V     A+G + +EIL
Sbjct: 168 ARVSRKQKISVLVLSSAMGSNLKEIL 193


>gi|260593937|gb|ACX46263.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  +T+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALLTDEIVFLSAIEEADHVIAQASATMNDKRV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|193201471|gb|ACF15943.1| RNA polymerase II subunit [Arthonia sp. Ertz 9090]
          Length = 290

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/362 (14%), Positives = 100/362 (27%), Gaps = 84/362 (23%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 2    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 61

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 62   LYYRTYIEQEQTVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 121

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L++       R            ++     +  Q                      
Sbjct: 122  KTAPLAAAAEERGARLSQHTKRDVSTPLRSTEAGIIDQVL-------------------- 161

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 162  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 221  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 250

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 251  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTGR 286

Query: 1244 PF 1245
              
Sbjct: 287  KL 288



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 68/187 (36%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 54

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ GI+  G  V+
Sbjct: 55  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 115 GDDIIIGKTAPLAAAAEERGARL----SQHTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 170

Query: 950 IDKNERS 956
           +    R+
Sbjct: 171 VKIRTRT 177


>gi|169125448|gb|ACA48206.1| RNA polymerase II second largest subunit [Melastiza cornubiensis]
          Length = 481

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 51/280 (18%), Positives = 91/280 (32%), Gaps = 21/280 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  +  I      +  D+ +   S +   
Sbjct: 217  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYTGYNQEDSVIMNQSSIDRG 276

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 277  LF-RSLFYRAYMDQEKRIGMQVVEEFEKPTRGTTLKLKHGTYDKLDEDGLVAPGVRVSGE 335

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +++D                DE  QR     K    T     E+   +++ 
Sbjct: 336  DIIIGKTAPITAD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVM 380

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     + VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 381  LTTNADGL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTCEGIVP 435

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            DI++NP  +PSRM +  + E  L       G +  +    
Sbjct: 436  DIIINPHAIPSRMTIAHLIECQLSKVASLRGFEGDATPFT 475



 Score =  111 bits (278), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 67/454 (14%), Positives = 127/454 (27%), Gaps = 89/454 (19%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE-- 573
           F     +    + ++ +  +   RR  ++                +         P    
Sbjct: 8   FLNGVWIGIHRDPLHLVRLVQELRRRGSISHEVSVIRDIRDREFKIFTDAGRVCRPLFVI 67

Query: 574 ----TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQ 629
               T E     +++              E              V Y+ A EEE   I  
Sbjct: 68  DNDPTHERRGQLVLTKEHVMQLEEDQELPEEQRFGWKGLLECGAVEYVDAEEEETIMIVM 127

Query: 630 ------ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
                  +  + +     EE    +     I     +    +  P  ++ I AS+IPF +
Sbjct: 128 TPEDLEVSRQVQQGYELAEETDPNKRVKTPINKNTNQYTHCEIHPSMILGICASIIPFPD 187

Query: 684 NDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI 743
           ++ S R      M +QA+ +                         A+R   +  +     
Sbjct: 188 HNQSPRNTYQSAMGKQAMGVFLTN--------------------FAERMDTMANI----- 222

Query: 744 VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLG 803
                                             Q+PL                      
Sbjct: 223 ------------------------------LYYPQKPL----------ATTRSMEYLKFR 242

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           +L  G+N +V  M + GYN EDS+++++  +   +F S+    +    +   +   E   
Sbjct: 243 ELPAGQNAIVGIMCYTGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRIGMQVVEEFE 302

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                    +       +DE G++  G  V+  DI++GK  P         ++       
Sbjct: 303 KPTRGTTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAPITADADEMGQR------- 355

Query: 919 EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +K    RD S  + S  +G V  V +       K
Sbjct: 356 QKFHTKRDVSTPLRSTENGIVDQVMLTTNADGLK 389


>gi|126023277|gb|ABN71267.1| RNA polymerase beta subunit [Paenibacillus larvae]
          Length = 266

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 74/312 (23%), Positives = 124/312 (39%), Gaps = 57/312 (18%)

Query: 157 LHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTS 216
           L RSP ++ +    +   +GK  +   +IP++G W+++E D+KDII+VRIDR RK+PVT 
Sbjct: 1   LVRSPSVYCN---TKVDKNGKKAFTATVIPNRGAWLELETDAKDIIYVRIDRTRKIPVTV 57

Query: 217 FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVI 274
            L ALG  ++ EIL             D      +   L+           +  GE   +
Sbjct: 58  LLRALGFGTDAEILDLLGDDEYIRNTLDKDNTDSTDKALI------EIYERLRPGEPPTL 111

Query: 275 ESGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           ++ + L        K           +       + L    +AE +V+ ETGEI  EAG 
Sbjct: 112 DNARSLLYARFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVHPETGEIIAEAGQ 171

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
           ++D + L+EI            +  +      +   V +   +     +    V  P + 
Sbjct: 172 LVDRRLLDEI------------LPCLEEGVGFKEYSVPNGVLESDHIPMQTIDVFSPIE- 218

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                                   V +V  N  +      +V++I   DII+ I   ++L
Sbjct: 219 ---------------------DGKVVKVISNGVI----DKNVKNITPADIISSINYFINL 253

Query: 447 RNGKGTIDDIDN 458
            +G G  DDID+
Sbjct: 254 LHGIGNTDDIDH 265


>gi|193201477|gb|ACF15946.1| RNA polymerase II subunit [Cryptothecia sp. Ertz 8472]
          Length = 296

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 53/370 (14%), Positives = 98/370 (26%), Gaps = 76/370 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLATTRSMEYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               ++ R  I++ +   S   E+ E   + +         +       +  G        
Sbjct: 62   -RSLYYRTYIEQEQSVSSQIVEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGEDI 120

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L ++      R            ++     +  Q                   
Sbjct: 121  IIGKTAPLPANAEERGARLSSHTKRDVSTPLRSTEAGIVDQVL----------------- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 164  ----LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L         +  +         ++S L            
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVAATSAYEGDATPFTDVTVENVSELL----------- 268

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                               WKSG                            G  ++Y+G 
Sbjct: 269  -------------------WKSG------------------------YQSRGFEVMYNGH 285

Query: 1241 TGEPFDRPVT 1250
            TG      V 
Sbjct: 286  TGRKMVAQVF 295



 Score = 80.1 bits (196), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 69/187 (36%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARD-TKLGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +  +    EE  + I      +       +D+ GI+  G  V+
Sbjct: 57  DRGLFRSLYYRTYIEQEQSVSSQIVEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 117 GEDIIIGKTAPLPANAEERGARL----SSHTKRDVSTPLRSTEAGIVDQVLLTSVDGKKN 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKIRTRT 179


>gi|193201465|gb|ACF15940.1| RNA polymerase II subunit [Arthonia didyma]
          Length = 289

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/362 (14%), Positives = 104/362 (28%), Gaps = 82/362 (22%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +     + 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYR 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
             +   +     +V  + +E   +    + + +    Y +L +   +  G           
Sbjct: 63   TYINQE----QAVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGVVAPGVRVSGDDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+                 ++E+  R  +  K          E    +++      
Sbjct: 119  KTAPLA---------------PTEEERGARLSQHTKRDVSIPLRSTEAGIVDQVL----- 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 159  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGVVPDLIIN 217

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 218  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 247

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 248  -----------------------ATP-FTDITVEMVSDILEKSGYQKRGLEVMYNGHTGR 283

Query: 1244 PF 1245
              
Sbjct: 284  KL 285



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 68/187 (36%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTK-LGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +       EE  + I      +       +D+ G++  G  V+
Sbjct: 52  DRGLFRSLYYRTYINQEQAVGVQVLEEFEKPIKSQTLRMRHGTYDKLDDDGVVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 112 GDDIIIGKTAPLAPTEEERGARL----SQHTKRDVSIPLRSTEAGIVDQVLLTSVDGKKN 167

Query: 950 IDKNERS 956
           +    R+
Sbjct: 168 VKIRTRT 174


>gi|118201894|gb|ABK79760.1| RNA polymerase subunit B [Sulfitobacter brevis]
          Length = 163

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 103/162 (63%), Positives = 124/162 (76%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV  G V+++V Y+SA EE    +AQAN+ LDE+  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVSGGVVSDEVQYMSATEEMRHTVAQANAHLDENMKFVNDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P   +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPSTSVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|193201509|gb|ACF15962.1| RNA polymerase II subunit [Opegrapha lithyrga]
          Length = 298

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 58/370 (15%), Positives = 106/370 (28%), Gaps = 79/370 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +     S +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTMANILYYPQKPLATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    ++  +   +N  +     +Q+E   +      +      Y +L +   +  G   
Sbjct: 63   LFRSFLYRTYIEQQNVST----SQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRV 118

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR  +  +          E    +
Sbjct: 119  SGDDIIIGKTAPFPAPMQDNA------------EGGQRTKQHTRRDVSAPLRSTEAGIVD 166

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            K+              R VKV     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 167  KVL------VSNVEGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEG 220

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM V  + E  L       G +                        
Sbjct: 221  LVPDLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGD---------------------- 258

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F       I+S+L+ +     G  +
Sbjct: 259  -------------------------------ATP-FTDVTVSEISSLLKGSGYQSRGLEL 286

Query: 1236 LYDGLTGEPF 1245
            +++G TG   
Sbjct: 287  MHNGHTGRKL 296



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 67/196 (34%), Gaps = 16/196 (8%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                   +  +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTMANILYYPQKPL----------ATTRSMEYLNFSELPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEF-EVMARDTKLGPEEITRDIPNV----SEEGLKNIDECG 880
           S+++++  +   +F S     + E     T    E   + +  +         + +D+ G
Sbjct: 51  SIIMNQSAIDRGLFRSFLYRTYIEQQNVSTSQQLETFEKPVKQLTMRTRPGTYEKLDDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  DI++GK  P         E   +        DV        +G+   V+
Sbjct: 111 FVSPGVRVSGDDIIIGKTAPFPAPMQDNAEGG-QRTKQHTRRDVSAPLRSTEAGIVDKVL 169

Query: 941 DVRIFNRHGIDKNERS 956
              +  R  +    R+
Sbjct: 170 VSNVEGRRTVKVRTRA 185


>gi|291170440|gb|ADD82429.1| RNA polymerase II second largest subunit [Davidiellaceae sp. AN1]
          Length = 322

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/393 (16%), Positives = 117/393 (29%), Gaps = 83/393 (21%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             N+    +  V             +       +   +  + AI      +  D+ +   S
Sbjct: 9    YNVXMDTMANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 68

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR-DKDDEQVILDRNIYSRLME---I 989
             +   +    +F R  +D+ ++   +    +E   + ++ D   +  +  Y +L     I
Sbjct: 69   SIDRGLF-RSLFFRAYLDQEKK---IGMSVMESFEKPNRGDTLRM-KQGTYDKLDSDGII 123

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K   ++ D      R++                 +K    T     
Sbjct: 124  TPGSRVSGDDIIIGKVAPIAPDAEELGQRTKL---------------HVKRDVSTPLRST 168

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E+   +++      D +     + VKV     +  Q GDK A RHG KG +      EDM
Sbjct: 169  ENGIIDQVLLTTNSDGL-----KFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDM 223

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            PF  +G   DI++NP  +PSRM +  + E  L       G++  +          IS + 
Sbjct: 224  PFTSEGIIPDIIINPHAIPSRMTIAHLIECLLSKVGALRGQEGDATPFTDVTLTTISHIL 283

Query: 1170 SFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLD 1229
                K  G                  V     +G  ++  +F                  
Sbjct: 284  ----KDYGFQQRG-----------FEVMYNGHTGKKLAAQIF------------------ 310

Query: 1230 ESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
                                 +G  Y  +L HM
Sbjct: 311  ---------------------LGPTYYQRLRHM 322



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 65/186 (34%), Gaps = 19/186 (10%)

Query: 760 DIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH 819
                +            Q+PL                      +L  G+N +VA   + 
Sbjct: 6   MTNYNVXMDTMANVLYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYS 55

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLK 874
           GYN EDS+++++  +   +F S+    +    +   +   E        D   + +    
Sbjct: 56  GYNQEDSVIMNQSSIDRGLFRSLFFRAYLDQEKKIGMSVMESFEKPNRGDTLRMKQGTYD 115

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            +D  GII  G+ V+  DI++GK+ P         E+L +        DV        +G
Sbjct: 116 KLDSDGIITPGSRVSGDDIIIGKVAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENG 171

Query: 935 VSGTVV 940
           +   V+
Sbjct: 172 IIDQVL 177


>gi|17225276|gb|AAL37331.1| RNA polymerase B-subunit [Staphylococcus cohnii subsp. cohnii]
          Length = 169

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLETNSITDQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|312074084|ref|XP_003139811.1| hypothetical protein LOAG_04226 [Loa loa]
 gi|307765023|gb|EFO24257.1| hypothetical protein LOAG_04226 [Loa loa]
          Length = 222

 Score =  167 bits (423), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 84/262 (32%), Gaps = 85/262 (32%)

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVL 1194
             + E+  G A    G    S    +                                   
Sbjct: 1    MMIESMAGKAGAMHGSTYDSSPFVFNEKKTA----------------------------- 31

Query: 1195 RVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYI 1254
                                  +    +L  A  +  G   +Y G+ G   +  +  G +
Sbjct: 32   ---------------------IDHFGQLLVRAGYNYYGNETMYSGVDGREMEVQIFFGIV 70

Query: 1255 YMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
            Y  +L HM++DK   RSTG    VT QP+ G+   GG R GEME   + A+GAA+ LQ+ 
Sbjct: 71   YYQRLRHMIADKFQVRSTGPTDPVTLQPVKGRKKGGGIRFGEMERDAMIAHGAAFTLQDR 130

Query: 1315 LTIKSD----DVVGR----------TRVY------ESIV-------------AGNDTFET 1341
            L   SD     +  R          +++       E+ V               ++    
Sbjct: 131  LFNCSDRDIAHICARCGSMISTLRCSKMLPEHRNSENSVLNYSEREMCLLCGKDDEVCPV 190

Query: 1342 GTPESFNVLVKEMQALGLSIDL 1363
              P  F  LV E+ A+  ++ L
Sbjct: 191  EVPRVFRYLVAELAAM--NVRL 210


>gi|118201902|gb|ABK79764.1| RNA polymerase subunit B [Sulfitobacter pontiacus]
          Length = 163

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL +F
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHATHYGRMCPIETPEGPNIGLINSLATF 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV +G V++DV Y+SA EE    +AQAN++LDE+  F  +LV  R 
Sbjct: 62  ARVNKYGFIETPYRKVTNGVVSDDVQYMSATEEMRHTVAQANANLDENMKFVNDLVSTRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L P E +D ID SPKQ+VS+AASLIPFLENDD+NR L
Sbjct: 122 SGDYTLSPSENVDLIDVSPKQLVSVAASLIPFLENDDANRAL 163


>gi|323701068|gb|ADY00196.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701070|gb|ADY00197.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701072|gb|ADY00198.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701074|gb|ADY00199.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701076|gb|ADY00200.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701078|gb|ADY00201.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701080|gb|ADY00202.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701082|gb|ADY00203.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701084|gb|ADY00204.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701086|gb|ADY00205.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701088|gb|ADY00206.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701090|gb|ADY00207.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
 gi|323701092|gb|ADY00208.1| ribosomal polymerase subunit beta [Staphylococcus agnetis]
          Length = 169

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 128/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +E
Sbjct: 62  YRKVDLETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPLL  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPE 169


>gi|17225278|gb|AAL37332.1| RNA polymerase B-subunit [Staphylococcus aureus subsp. anaerobius]
          Length = 169

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|283806264|dbj|BAI66368.1| RNA polymerase second largest subunit [Astrosphaeriella aggregata]
          Length = 304

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 88/284 (30%), Gaps = 27/284 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +      L AI      +  D+ +   S +   +    +F 
Sbjct: 10   YPQKPLATTRSMEYLRFQELPAGHSALXAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 68

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 69   RAYTEQEKR---IGVNVLEQFEKPTRGDTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIG 125

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  D      ++           +++    +  Q                      
Sbjct: 126  KTAPIPPDAKELGQKTALHTKRDVSTPLRQTENGIVDQ--------------------VL 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 166  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVTPDLIIN 225

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            P  +PSRM +  + E  L       G +  +          IS 
Sbjct: 226  PHAIPSRMTIAHLVECLLSKVGALRGCEGDATPFTDVTVESISS 269



 Score = 78.6 bits (192), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 61/179 (34%), Gaps = 19/179 (10%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           F          Q+PL                      +L  G + L A   + GYN EDS
Sbjct: 1   FTAGPGVLYYPQKPL----------ATTRSMEYLRFQELPAGHSALXAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +   +   E        D   +       +D+ G+
Sbjct: 51  VIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRGDTLRLKGGTYDKLDDDGV 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +  G  V+  DI++GK  P          +L +        DV     +  +G+   V+
Sbjct: 111 VAPGVRVSGDDIIIGKTAPIPPDAK----ELGQKTALHTKRDVSTPLRQTENGIVDQVL 165


>gi|198279521|emb|CAP04795.1| RNA polymerase beta subunit [Equisetum ramosissimum]
          Length = 265

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 112/245 (45%), Positives = 157/245 (64%), Gaps = 9/245 (3%)

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL KAE   VGTG+E  +A  SG+ + ++R G V  +D  RI +   E            
Sbjct: 1   PLSKAEKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDGQRITLFVDEETSINK------ 54

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ ++RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW GY
Sbjct: 55  -NLLSYERSNNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPWEGY 113

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G+
Sbjct: 114 NFEDATLISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDENGL 173

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GD+LVGK+TP         PE KLL+AIFG    + R+T L+VP G  G V
Sbjct: 174 VKLGSWVEAGDVLVGKLTPLDYLDTLGAPEGKLLQAIFGTDVTNARETCLKVPVGFKGRV 233

Query: 940 VDVRI 944
           +D++ 
Sbjct: 234 IDIKW 238


>gi|68131856|gb|AAY85206.1| RNA polymerase II second largest subunit [Embothrium coccineum]
          Length = 706

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 105/799 (13%), Positives = 223/799 (27%), Gaps = 149/799 (18%)

Query: 88  VDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQSIYMGDLPLMTKD----- 141
                 R+LTY+ PL + +   V             +D  +  +++G +P+M +      
Sbjct: 7   PKAARLRNLTYSAPLYVDVTKRVIKKGHDCEEVTETQDFAK--VFIGKVPIMLRSSYCTV 64

Query: 142 -------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRASLSGKLLYA 181
                              G F+I G ++++++Q   S   ++      +     +  Y 
Sbjct: 65  YQNSEKDLTELGECPFDQGGYFIINGSEKVLIAQEKMSTNHVY----VFKKRQPNRYAYV 120

Query: 182 CRIIPDQGLWMDIEFDSKDIIHVRI-DR-------------------RRKVPVTSFLMAL 221
             +        + +      + VR+  R                   R ++P+     AL
Sbjct: 121 GEVR----SMAESQNRPPSSMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRAL 176

Query: 222 GMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKL 280
           G  ++ +IL         +Q        L  A ++   +V+   +        +   K++
Sbjct: 177 GFVADKDILEHICYDFSDTQMMGLLRPSLEEAFVIQNQQVALDYIGKRGSTVGVTREKRI 236

Query: 281 TSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSE 340
                + L+++ +  +G+   C          +      + + A     E   +   +  
Sbjct: 237 KYAK-EILQKEMLPHVGVGEYCETKKAYYFGYIIH---RLLLCALGRRAEDDRDHYGNKR 292

Query: 341 IRDI-PILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFL 399
           +    P+L          +   +     K   +      +        T  +  S+    
Sbjct: 293 LDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGN 352

Query: 400 FFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI-RKEDIIAIIKILVDLRNGKGTIDDIDN 458
           +  ++           +N      T   +R +         +     L N    +     
Sbjct: 353 WGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMMCPAE 412

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
               +      ++KN   +  + +  +    +  ++  S    + I+   +  A   F  
Sbjct: 413 TPEGQACG---LVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVN 469

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
              +         +  +   RR   +  + GV R     E+R    T YGR         
Sbjct: 470 GCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELR--LYTDYGRCSRPLFIVD 527

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
               L+      A        +       D      + Y+   EEE   I+         
Sbjct: 528 KQRLLIKKKDVRALQQRESPDDGG---WHDLVAKGFIEYIDTEEEETTMISM-------- 576

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                +L+  R   E      E     +  P  ++ + AS+IPF +++ S R      M 
Sbjct: 577 --TINDLISARLHPE--EAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMG 632

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           +QA+ +                           R   +  V                   
Sbjct: 633 KQAMGIYVTNYQL--------------------RMDTLAYV------------------- 653

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                               Q+PLV                      L  G N +VA   
Sbjct: 654 ----------------LYYPQKPLV----------TTRAMEHLHFRQLPAGINSIVAIAC 687

Query: 818 WHGYNFEDSMLISERMVSE 836
           + GYN EDS+++++  +  
Sbjct: 688 YSGYNQEDSVIMNQSSIDR 706


>gi|321453922|gb|EFX65117.1| hypothetical protein DAPPUDRAFT_333503 [Daphnia pulex]
          Length = 1153

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 86/256 (33%), Gaps = 56/256 (21%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              +  V +   + R  Q GDK A R G KG    I   +                     
Sbjct: 868  SGMNKVTITFRIPRNPQIGDKFASRAGQKG----ICSQQ--------------------- 902

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
                          W    L      +I D   N    P R  +  +I   +        
Sbjct: 903  --------------WLAEDLPWTESGMIPDIVFNPHGFPSRMTIAMMIECMAGKSAA--- 945

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAIN---SMLRMADLDESGQSILYDGLTGEPF 1245
                           V  +TP        AI     +L  A     G   LY G+ G   
Sbjct: 946  -----------VHGLVHDATPFRFSEKNTAIEYHGKLLEEAGYSYYGTEKLYSGIDGREM 994

Query: 1246 DRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAY 1305
            D  +  G ++  +L HMVSDK   RS G+   VT QP+ G+   GG R GEME   + ++
Sbjct: 995  DADIFFGVVHYQRLRHMVSDKFQVRSVGAIDHVTLQPIKGRKRGGGVRFGEMERDGLVSH 1054

Query: 1306 GAAYVLQEMLTIKSDD 1321
            GA Y+L + L   SD 
Sbjct: 1055 GALYLLYDRLFHCSDH 1070



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 77/574 (13%), Positives = 181/574 (31%), Gaps = 35/574 (6%)

Query: 339 SEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNF 398
                I ++     +   Y    +     ++ +    D+ +      V  F +  S+   
Sbjct: 284 YYKDRIVLMLRQLQDEGLYTHEHVRNFIGRNFRAKFTDLPKWYTDEQVCKFLLENSVLFH 343

Query: 399 LFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR--HIRKEDIIAIIKILVDLRNGKGTIDDI 456
           L  + DK++L      K+          +     + +E  +     L  +++   +   +
Sbjct: 344 LKDNKDKFNLLVFMARKLFAFAYGKCALEGMDPVMMQEISLPGHLYLQLVKDRLASWLTV 403

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
                + V    E +   + L    M  ++     S  IDS +           +A    
Sbjct: 404 ----VKYVILKRERMTKNFVLTSSEMGIALS---KSGKIDSAIENVFATGNLPGTADLGM 456

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
             ++ LS + E++N +  ++H R   A+ +G V       E+R + P  +G +CP  T +
Sbjct: 457 NQNTGLSIMAENINHMRYMSHFR---AVHRGAVFMDSRSSEVRQLKPDAWGFLCPVHTPD 513

Query: 577 GHNIGLVSSLTSFARV---NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           G   GL++ L++   V                       + ++ +   E    + +    
Sbjct: 514 GSPCGLLNHLSATCHVVNTTQDTSGIPTLLVALGMTPVEETIHNNNYSECYVVMLEGRVL 573

Query: 634 LDEDGSFTEELVFCRCA---------GEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
                      V               + + +           P   +  A++ +     
Sbjct: 574 GRVGDRSATRFVDKLRMLKVRGAENVPKTLEIAFVPRTLNGQYPGIYLFTASARMMRPVY 633

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           + +   +       Q    +         G+     + S  + ++  A ++   D  +  
Sbjct: 634 NIAAGTVELVGTFEQVYLNICVTEDENENGI-FTHQELSETSFLSNLACLIPLPDFNQSP 692

Query: 745 IRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
               +  +   T G  ++      ++N      Q P              A     ++ D
Sbjct: 693 RNMYQCQMGKQTMGTPVHNWRF--QTNSKLYRLQTP-------TTPLFRPAHWDRINMDD 743

Query: 805 LALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD 864
            A+G N +VA + + GY+ ED+M+I+   +              +  ++   G     + 
Sbjct: 744 FAMGTNAIVAVISYTGYDMEDAMVINRASLQRGFAHGQVYTSKVIDLKEIGKGNSRYFKR 803

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
            P  +++  + +DE G+   G  +   D     +
Sbjct: 804 DPA-NDDLKEFLDEDGLPYPGILLQERDPYYCYL 836



 Score = 64.3 bits (155), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 97/714 (13%), Positives = 200/714 (28%), Gaps = 121/714 (16%)

Query: 54  GLQAAFKSVFPITAFSGA---AMLEFVSYEFDPPKFD-------------VDDCLWRDLT 97
           GL+ A   + P+           L+        P                  +C  R+ T
Sbjct: 51  GLKKAALDMLPVEFEMKNQLKIKLKINKISIYKPTVGDDVVPPPKIPETFPKECRMRNST 110

Query: 98  YAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD---------------- 141
           Y   L + +   +    E      +   +     +G++P+M +                 
Sbjct: 111 YKGKLFVQVGWSISKTPEGPLIAQVPFER----CLGEIPVMIQSELCNLSGLSPKELVSK 166

Query: 142 --------GTFVIKGIQRIV--VS----------Q---------LHRSPGIHFDHDKGRA 172
                   G FV+KG +RI+  +S          Q         L    G+     K   
Sbjct: 167 GEHEQEWGGYFVVKGHERILRMISATRKNYPMTVQRDVWKRRGKLFTDKGVFIRCVKEDM 226

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF 232
           + +  +L+    + +  + +   F  K I++V        P+   L AL   ++   S  
Sbjct: 227 TATNNVLHY---LSNGTMRLMFNF--KKILYV-------FPLMLVLKALINCTD---SYI 271

Query: 233 YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKG 292
           Y ++V    GD +        L    +             +  + +   + L K   ++ 
Sbjct: 272 YEQLVQGLEGDIYYKDRIVLML-RQLQDEGLYTHEHVRNFIGRNFRAKFTDLPKWYTDEQ 330

Query: 293 VKFLGITSDCLCGLYVAEDIVN---GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYV 349
           V    + +  L  L   +D  N       +++  A      + ++ +   EI     LY+
Sbjct: 331 VCKFLLENSVLFHLKDNKDKFNLLVFMARKLFAFAYGKCALEGMDPVMMQEISLPGHLYL 390

Query: 350 DSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLS 409
             V +      T+V      R+       R+ +   +++  +  ++      DS   ++ 
Sbjct: 391 QLVKDRLASWLTVVKYVILKRE-------RMTKNFVLTSSEMGIALSKSGKIDSAIENVF 443

Query: 410 TVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGE 469
             G +     L ++    +      + I  ++ +   R        +D+    R   V +
Sbjct: 444 ATGNLPGTADLGMNQNTGLSI--MAENINHMRYMSHFRAVHRGAVFMDS----RSSEVRQ 497

Query: 470 MLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHV 529
           +  + +                      ++         V +        + L  L    
Sbjct: 498 LKPDAWGFLC-------PVHTPDGSPCGLLNHLSATCHVVNTTQDTSGIPTLLVALGM-- 548

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
             +    H    S      +     G            ++   +     N+     +  F
Sbjct: 549 TPVEETIHNNNYSECYVVMLEGRVLGRVGDRSATRFVDKLRMLKVRGAENVPKTLEIA-F 607

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
                 G     Y      ++   V            IA     L      T E V+   
Sbjct: 608 VPRTLNGQYPGIYLFTASARMMRPV----------YNIAAGTVELVG----TFEQVYLNI 653

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
              E           + S    +S  A LIP  + + S R +  C M +Q +  
Sbjct: 654 CVTEDENENGIFTHQELSETSFLSNLACLIPLPDFNQSPRNMYQCQMGKQTMGT 707


>gi|17225270|gb|AAL37328.1| RNA polymerase B-subunit [Staphylococcus gallinarum]
          Length = 169

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 102/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V CR  G   ++ +E
Sbjct: 62  YRKVDIETQSITDQIDYLTADEEDSYVVAQANSVLDENGRFVEDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|1742933|emb|CAA64391.1| DNA-directed RNA polymerase I [Agaricus bisporus]
          Length = 114

 Score =  167 bits (422), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 61/112 (54%), Gaps = 3/112 (2%)

Query: 1207 STPVFDGADEEAI---NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMV 1263
            +TP      + AI      L  A  +  G   +Y G+TG+ F   + +G +Y  +L HMV
Sbjct: 3    ATPFKFSEKDTAIDYFGKQLSAAGYNYYGNEPMYSGITGQEFAADIYIGVVYYQRLRHMV 62

Query: 1264 SDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEML 1315
             DK   R+TG    +T+QP+ G+   GG R GEME   + A+GA+++LQ+ L
Sbjct: 63   LDKFQVRTTGPVDPITRQPVKGRKRAGGIRFGEMERDALIAHGASFLLQDRL 114


>gi|219564069|gb|ACL28218.1| RNA polymerase II second largest subunit [fungal sp. M195]
          Length = 277

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 52/292 (17%), Positives = 97/292 (33%), Gaps = 27/292 (9%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 3    ILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 62

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +      +    +E   +    + + L    Y ++ E   I  G        
Sbjct: 63   FYRTYQDQE----KMIGHSVLEQFEKPMRSDTLRLKHGTYDKIDEDGVIAPGVRVSGEDI 118

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D                +E+ QR  + +K    T     E    +++   
Sbjct: 119  IIGKTAPMAPD---------------SEEQGQRQKQHIKRDVSTPLRSTESGIVDQVMLT 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 164  TTGD-----GSRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVVPDI 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            ++NP  +PSRM +  + E  L       G +  +         ++S +   +
Sbjct: 219  IINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTNVSRILRSM 270


>gi|290760030|gb|ADD54492.1| RNA polymerase II second largest subunit [Ascocratera manglicola]
          Length = 644

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 49/287 (17%), Positives = 90/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 347  YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 405

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 406  RAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIG 462

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  D      ++           +++    +  Q                      
Sbjct: 463  KTAPIPPDAKELGQKTALHTKRDVSTPLRQTENGIVDQ--------------------VL 502

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 503  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVTPDLIIN 562

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          IS L  
Sbjct: 563  PHAIPSRMTIAHLVECLLSKVGALRGCEGDATPFTDVTVESISKLLR 609



 Score =  139 bits (351), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 87/512 (16%), Positives = 170/512 (33%), Gaps = 58/512 (11%)

Query: 477 LGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ------------- 521
           +  L++ + I +  +    +      Q  + A  + + +     +               
Sbjct: 1   ILFLKLTKDIYKYLQKCVENNQEFNVQMAVKASVITNGLKYSLATGNWGDQKKAASAKAG 60

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG   G
Sbjct: 61  VSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG 116

Query: 582 LVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           LV +L+    V+        T +    + ++  +    ++      ++      +    S
Sbjct: 117 LVKNLSLMCYVSVGTESTPITDFMSQRNMEILEEYDPQTSPNATKVFVNGVWVGVHSQPS 176

Query: 640 FTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQ 697
               +V        +      I D  D   K        + P F+   D  +  +G  + 
Sbjct: 177 QLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVETDPRKPNVGSLVL 236

Query: 698 RQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRSVEGDLDPS 755
            +       E   + T GM    A++           GI+E +DA       +    +  
Sbjct: 237 NKTHIQKLEEDKSIDTSGMSDEDAQALKYGWRGLINDGIIEYLDAEEEETAMIIMTPEDL 296

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST--------------- 800
               ++   M      Q+     +P  +  D VR        PS                
Sbjct: 297 DDHRNLRSGMPIPDGXQDRHKRIKP--RPSDSVRMYTACEIHPSMIXDDVLYYPQKPLAT 354

Query: 801 -------DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 355 TRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKR 414

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +       +D+ G++  G  V+  DI++GK  P        
Sbjct: 415 IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPPDAK-- 472

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             +L +        DV     +  +G+   V+
Sbjct: 473 --ELGQKTALHTKRDVSTPLRQTENGIVDQVL 502


>gi|299849820|gb|ADJ57151.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849823|gb|ADJ57153.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849826|gb|ADJ57155.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849829|gb|ADJ57157.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849832|gb|ADJ57159.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849838|gb|ADJ57163.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
          Length = 285

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGARV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 282



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 69/179 (38%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  GA 
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGAR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|219564099|gb|ACL28233.1| RNA polymerase II second largest subunit [fungal sp. M295]
          Length = 286

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/293 (18%), Positives = 97/293 (33%), Gaps = 27/293 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G     
Sbjct: 62   -RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E+   +++
Sbjct: 118  EDIIIGKTAPIAPD---------------AEELGQRTKAHIKRDASTPLRSTENGIVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF   G  
Sbjct: 163  LI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTVQGIV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 218  PDLIINPHAIPSRMTIAHLIECQLSKVGTLRGLEGDATPFTEVTVDSVSKLLR 270



 Score = 84.4 bits (207), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +DE GI+  G  V+
Sbjct: 57  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 117 GEDIIIGKTAPIAPDAEELGQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 166


>gi|197941926|gb|ACH78568.1| RNA polymerase subunit [Picea mariana]
          Length = 266

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 100/245 (40%), Positives = 149/245 (60%), Gaps = 10/245 (4%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            GTG+E   A  SG+  +A + G +E +DA+                      L+ +QRS
Sbjct: 1   AGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTELVIYQRS 52

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LIS
Sbjct: 53  NTNTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILIS 112

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  
Sbjct: 113 ERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIET 172

Query: 891 GDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           GD+LVGK+TP+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR 
Sbjct: 173 GDVLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRV 232

Query: 949 GIDKN 953
               +
Sbjct: 233 DDSGD 237



 Score = 71.6 bits (174), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 81/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 64   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 122

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 123  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 176

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 177  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 234

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 235  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 266


>gi|198279523|emb|CAP04796.1| RNA polymerase beta subunit [Equisetum scirpoides]
          Length = 265

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 112/246 (45%), Positives = 159/246 (64%), Gaps = 9/246 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP  KAE   VGTG+E  +A  SG+ + A+R G V  +D  RI +   E           
Sbjct: 1   VPXSKAEKCIVGTGLEGQIALDSGSCVTAEREGKVIYIDGERITLFVDEEISINK----- 55

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+ ++RSN NTC+NQ+PLV     +R+  +IADG ST  G+LALG+N+LVA+MPW G
Sbjct: 56  --NLLSYERSNNNTCMNQKPLVCKDKFLRQGQLIADGASTVGGELALGKNILVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G
Sbjct: 114 YNFEDATLISERLIYEDIFTSFHIERHEINVSFTSQGPEKLTREIPHLNNHILRHLDENG 173

Query: 881 IICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
           ++ +G+ V  GD+LVGK+TP         PE KLL+AIFG +  + R+T L+VP G  G 
Sbjct: 174 LVKLGSWVEAGDVLVGKLTPLEYLDSLGAPEGKLLQAIFGTEVTNARETCLKVPVGFKGR 233

Query: 939 VVDVRI 944
           V+D++ 
Sbjct: 234 VIDIKW 239


>gi|260593993|gb|ACX46291.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLS+  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSRFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260594069|gb|ACX46329.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++  +
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKA 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260593941|gb|ACX46265.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593943|gb|ACX46266.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593947|gb|ACX46268.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593965|gb|ACX46277.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593967|gb|ACX46278.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593979|gb|ACX46284.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593989|gb|ACX46289.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593999|gb|ACX46294.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594003|gb|ACX46296.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594007|gb|ACX46298.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594009|gb|ACX46299.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594013|gb|ACX46301.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594015|gb|ACX46302.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594019|gb|ACX46304.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594025|gb|ACX46307.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594027|gb|ACX46308.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594057|gb|ACX46323.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594083|gb|ACX46336.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594085|gb|ACX46337.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594089|gb|ACX46339.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594095|gb|ACX46342.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594097|gb|ACX46343.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594099|gb|ACX46344.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594117|gb|ACX46353.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594119|gb|ACX46354.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594121|gb|ACX46355.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594123|gb|ACX46356.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594129|gb|ACX46359.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260594059|gb|ACX46324.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594063|gb|ACX46326.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL +SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLFNSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|219564091|gb|ACL28229.1| RNA polymerase II second largest subunit [fungal sp. M283]
          Length = 287

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 97/295 (32%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHIKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTVQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVGTLRGLEGDATPFTEVTVDSVSKLLR 271



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 167


>gi|198279393|emb|CAP04731.1| RNA polymerase beta subunit [Pinus bungeana]
          Length = 259

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 100/244 (40%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 50.8 bits (120), Expect = 0.001,   Method: Composition-based stats.
 Identities = 44/211 (20%), Positives = 75/211 (35%), Gaps = 14/211 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
             GD+        V V+++ KR IQ GDK+ G
Sbjct: 234  SGDNAE-----TVHVYISQKRKIQVGDKVXG 259


>gi|299849835|gb|ADJ57161.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
          Length = 285

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 97/295 (32%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D  +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDXEKR---IGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGARV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 282



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 69/179 (38%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  GA 
Sbjct: 67  SIDRGLFRSLFYRAYTDXEKRIGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGAR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|118201834|gb|ABK79730.1| RNA polymerase subunit B [Jannaschia helgolandensis]
          Length = 163

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 104/162 (64%), Positives = 126/162 (77%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++
Sbjct: 2   NPLSEVTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRMCPIETPEGPNIGLINSLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ARVN YGFIETPYRKV DGK+T+DV Y+SA EE    +AQAN+ L +D  F  ELV  R 
Sbjct: 62  ARVNKYGFIETPYRKVVDGKITDDVQYMSATEEMRHTVAQANAQLTDDMKFQNELVSTRQ 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           +G+  L  R+ +D ID SPKQ+VS+AA+LIPFLENDD+NR L
Sbjct: 122 SGDYKLQSRDNVDLIDVSPKQLVSVAAALIPFLENDDANRAL 163


>gi|158514849|gb|ABW69380.1| RNA polymerase beta subunit [Mannheimia haemolytica]
          Length = 161

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 95/159 (59%), Positives = 121/159 (76%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++
Sbjct: 3   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLIN 62

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETP+RKV DG+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  
Sbjct: 63  SLSVYARTNNYGFLETPFRKVVDGQVTEEIEYLSAIEESNNIIAQANSNLDENFRFTDTY 122

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           V CR  GE  L   E++ ++D S +QVVS+AA+LIPFLE
Sbjct: 123 VTCRQQGESGLFKPEEVQYMDISTQQVVSVAAALIPFLE 161


>gi|17225264|gb|AAL37325.1| RNA polymerase B-subunit [Staphylococcus warneri]
          Length = 169

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|219564037|gb|ACL28202.1| RNA polymerase II second largest subunit [fungal sp. M157]
          Length = 287

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/365 (16%), Positives = 111/365 (30%), Gaps = 81/365 (22%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   + +    V +    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYVDQEKR---IGMAVVEQFEKPERRNTVRVKHGTYEKLDEDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ DL               +E  QR    +K    T     E    +
Sbjct: 117  SGEDIIIGKTAPMAPDL---------------EELGQRTTSHIKRDVSTPLRSTESGLVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTHQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 255  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 282

Query: 1236 LYDGL 1240
            +++G 
Sbjct: 283  MFNGH 287



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/171 (21%), Positives = 64/171 (37%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E       R+   V     + +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRSYVDQEKRIGMAVVEQFEKPERRNTVRVKHGTYEKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        SG+   V+
Sbjct: 118 GEDIIIGKTAPMAPDL----EELGQRTTSHIKRDVSTPLRSTESGLVDQVL 164


>gi|219564021|gb|ACL28194.1| RNA polymerase II second largest subunit [fungal sp. M125]
          Length = 277

 Score =  167 bits (422), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 50/295 (16%), Positives = 96/295 (32%), Gaps = 27/295 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      + +  +E   +    + + L    Y ++ +   +  G     
Sbjct: 62   RSLFYRTYQDQE----KQIGQNVLEQFEKPNRTDTLRLKHGTYDKIDDDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E    +++
Sbjct: 118  EDIIMGKTAPMAPD---------------AEELGQRQKHHIKRDVSTPLRSTESGVVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 163  MLTTTGD-----GNRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             DI++NP  +PSRM +  + E  L       G +  +          +S +   +
Sbjct: 218  PDIIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQVSDILRRM 272



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 39/180 (21%), Positives = 65/180 (36%), Gaps = 23/180 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL +                    +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPLAR----------TMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    ++   +       E        D   +       ID+ GI+  G  V+
Sbjct: 57  DRGLFRSLFYRTYQDQEKQIGQNVLEQFEKPNRTDTLRLKHGTYDKIDDDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P     M P+ + L             T LR        VVD  +    G
Sbjct: 117 GEDIIMGKTAP-----MAPDAEELGQRQKHHIKRDVSTPLR---STESGVVDQVMLTTTG 168


>gi|330785182|gb|AEC46397.1| RNA polymerase II second largest subunit [Sparria endlicheri]
          Length = 282

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/345 (16%), Positives = 96/345 (27%), Gaps = 73/345 (21%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +     S +   +  + AI      +  D+ +   S +   +     F R  I+K++   
Sbjct: 11   MEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLF-RSFFYRTYIEKSKAVG 69

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   +                   +  G           K+   +  +     
Sbjct: 70   FNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRISGDDIIIGKTAPFAEPMAENA- 128

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
                       E  QR     +          E    +++              R VKV 
Sbjct: 129  -----------EGGQRTKSHARRDISAPLRSTEAGIIDRVL------LTSVEGNRSVKVR 171

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
                +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM V  + 
Sbjct: 172  TRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIINPHAIPSRMTVAHLI 231

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E  L       G +                                              
Sbjct: 232  ECLLSKLSATQGLEGD-------------------------------------------- 247

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                     +TP F       I++ L+       G  ++++G TG
Sbjct: 248  ---------ATP-FTDVTVSIISNELKALGYQSRGLEVMHNGHTG 282



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 71/177 (40%), Gaps = 10/177 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S     +   ++ 
Sbjct: 8   TRSMEYLQFSELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSFFYRTYIEKSKA 67

Query: 854 TK-LGPEEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
               G EE  +              + +D+ G +  G  ++  DI++GK  P  E     
Sbjct: 68  VGFNGLEEFEKPVKSTTMRTRPGTYEKLDDDGFVPPGVRISGDDIIIGKTAPFAEPMAEN 127

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQI 964
            E   R     K+   RD S  + S  +G +  V + +  G    + R+ + +  QI
Sbjct: 128 AEGGQRT----KSHARRDISAPLRSTEAGIIDRVLLTSVEGNRSVKVRTRTTKVPQI 180


>gi|312204310|gb|ADQ47472.1| RNA polymerase II second largest subunit [Coccomycetella
            richardsonii]
          Length = 259

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 50/271 (18%), Positives = 89/271 (32%), Gaps = 27/271 (9%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R  +++ +R       
Sbjct: 2    FRELPAGQNAIVAIACYSGYNQEDSVIMGQSSIDRGLF-RSLFFRSYVEQEKRVGM---S 57

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E   +    E + L    Y +L E   I  G           K+  ++ D      R+
Sbjct: 58   LVEQFEKPLRSETLRLKHGTYEKLDEDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRT 117

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +          ++     +  +                             L+ VKV   
Sbjct: 118  KLHTKRDASTPLRTTENGIVDRVLL--------------------TTNAEGLKFVKVRTR 157

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E 
Sbjct: 158  TTKVPQIGDKFASRHGQKGTIGMTYRQEDMPFSAEGIVPDLIINPHAIPSRMTIAHLIEC 217

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             L       G +  +          +S L  
Sbjct: 218  QLSKVSSLRGFEGDATPFTEVTVDSVSRLLR 248



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 61/157 (38%), Gaps = 12/157 (7%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++ +  +   +F S+    +    +   +   E
Sbjct: 1   KFRELPAGQNAIVAIACYSGYNQEDSVIMGQSSIDRGLFRSLFFRSYVEQEKRVGMSLVE 60

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   +   +     + +DE GII  G  V+  DI++GK  P         ++    
Sbjct: 61  QFEKPLRSETLRLKHGTYEKLDEDGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRT--- 117

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
               K    RD S  + +  +G V  V +       K
Sbjct: 118 ----KLHTKRDASTPLRTTENGIVDRVLLTTNAEGLK 150


>gi|46277350|gb|AAS86865.1| DNA-dependent RNA polymerase II [Peziza subisabellina]
          Length = 550

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/372 (15%), Positives = 109/372 (29%), Gaps = 81/372 (21%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 257  ANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF- 315

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G      
Sbjct: 316  RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGE 372

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 373  DIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ----------------- 415

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 416  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVP 472

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  +                                          
Sbjct: 473  DLIINPHAIPSRMTIAHLI----------------------------------------- 491

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                        + +L      +     +TP F     ++++ +LR       G  I+Y+
Sbjct: 492  ------------ECLLSKVSSLRGYEGDATP-FTDVTVDSVSKLLREHGYQSRGFEIMYN 538

Query: 1239 GLTGEPFDRPVT 1250
            G TG      V 
Sbjct: 539  GHTGRKLVAQVF 550



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 65/441 (14%), Positives = 128/441 (29%), Gaps = 35/441 (7%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S  +       N    +       +     +      V    +H      +   +     
Sbjct: 14  SQPIVDFMMQRNM-EVLEEYEPSRSPNATKIFVNGVWV---GIHRDPGFIVRTIQKLRRQ 69

Query: 579 -NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +IG   SL    R   +       R      V ++    S    E     Q    L++D
Sbjct: 70  GHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDN-DPSSPRRGELALQKQHIEKLEDD 128

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +E    R   + +L     +++IDA  ++ V I  +      +   +    G  +Q
Sbjct: 129 REIDDE--TQRYGWQGLLSDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGYEIQ 182

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           ++  P  + +             +   + I+                             
Sbjct: 183 QELDPAQRVKGAVNKFAHTWTHCEIHPSMILGICXXXXXXXXXXXXXXXXXXXXXXXXXX 242

Query: 758 GVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                          N     Q+PL                      +L  G+N +VA M
Sbjct: 243 XXXXXXXXXXXXXXANILYYPQKPL----------GTTRSMEFLKFRELPAGQNAIVAIM 292

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
            + GYN EDS+++++  +   +F S+    +    +   +   E        +   +   
Sbjct: 293 CYSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHG 352

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S  +
Sbjct: 353 TYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPL 405

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            S  +G V  V +       K
Sbjct: 406 RSTENGIVDQVMVTTNQEGLK 426



 Score = 38.5 bits (88), Expect = 8.7,   Method: Composition-based stats.
 Identities = 25/204 (12%), Positives = 46/204 (22%), Gaps = 19/204 (9%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 19  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 72

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPA-------ETSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 73  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPSSPRRGELALQKQHIEKLEDDREID 132

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            ET             V Y+ A EEE   I      L+    F       +EL   +   
Sbjct: 133 DETQRYGWQGLLSDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQELDPAQRVK 192

Query: 652 EEILVPREKIDFIDASPKQVVSIA 675
             +          +  P  ++ I 
Sbjct: 193 GAVNKFAHTWTHCEIHPSMILGIC 216


>gi|229428545|gb|ACQ65687.1| RNA polymerase II second largest subunit [Opegrapha varia]
          Length = 710

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/385 (16%), Positives = 108/385 (28%), Gaps = 83/385 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 405  MANILYYPQKPLARTMAMDYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 464

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLAR-DKDDEQVILDRNIYSRLME---ILCGQNAV 996
                +  +   +      V  E  E   + ++ D   +     Y ++ E   I+ G    
Sbjct: 465  RSLFYRTYQSQE----KLVGPENFERFEKPNRSDTLRM-KHGTYDKIDEDGIIIPGLRVS 519

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K   L++D                +E  QR     K     +    E    ++
Sbjct: 520  GEDIIMGKVAPLAAD---------------TEELGQRTKTQTKRDASITLRSTESGVIDQ 564

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D       R  KV V   +  Q GDK A RHG KG +      EDMPF + G 
Sbjct: 565  VMLTTTND-----GHRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGI 619

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              D+++NP  +PSRM +  + E  L       G +  +          IS          
Sbjct: 620  VPDLIINPHAIPSRMTIAHLVECQLSKVATLKGDEGDATPFTKVTVTQIS---------- 669

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                            +LR       G  V                        +G +  
Sbjct: 670  ---------------EILRSQGYQSRGFEVM----------------------YNGHT-- 690

Query: 1237 YDGLTGEPFDRPVTVGYIYMLKLNH 1261
              G         V +G  Y  +L H
Sbjct: 691  --GR---KLVAQVFLGPTYYQRLRH 710



 Score = 94.4 bits (233), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 85/595 (14%), Positives = 157/595 (26%), Gaps = 86/595 (14%)

Query: 386 VSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKIL 443
           + T  +  S+    + +  K   +  G  ++  R    +      R          I   
Sbjct: 33  IITNGLRYSLATGNWGEQKKAQQTKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKP 92

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
             L N    +         +      ++KN   +  + +    +     ++   + P + 
Sbjct: 93  RQLHNTHWGLVCPAETPEGQACG---LVKNLALMCYVSVGSPGEPFYEYLNDQGMEPIED 149

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQG-GVARARAGVEM---- 558
             A+   +A   F   + +         ++ +   RR  ++     + R     E     
Sbjct: 150 YEARRFPNATKIFLNGTWIGVSRNPGPLVADMQTLRRAGSMSPEVSLVRDIREREFKIFT 209

Query: 559 ---RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA-------------YGFIETPY 602
              R + P       P   + G+     S +      N              +   +   
Sbjct: 210 DAGRVMRPLFVVDTDPKSRNNGNLAIDSSHIQRLEDWNQEKGNFTRAQLEDEHAEDDLGM 269

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
                   T  + YL A EEE+  I    S L   G         +   E    P  K  
Sbjct: 270 FGWSQLVKTGVIEYLDAEEEESAMIIMDPSQL---GQNKAPKEEVKEGEEGRTAPPSK-- 324

Query: 663 FIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS 722
                                                  P   +      T  E   +  
Sbjct: 325 --------------------------------------GPAQLSRNVHTYTHCEINPSMI 346

Query: 723 SGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV 782
            G    A                                            T  +QR   
Sbjct: 347 LGVC--ASIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVFLTNFDQRMET 404

Query: 783 KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
                      +A   + D     +L  G+N +VA   + GYN EDS+++++  +   +F
Sbjct: 405 MANILYYPQKPLARTMAMDYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 464

Query: 840 TSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S+    ++   +       E        D   +       IDE GII  G  V+  DI+
Sbjct: 465 RSLFYRTYQSQEKLVGPENFERFEKPNRSDTLRMKHGTYDKIDEDGIIIPGLRVSGEDII 524

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           +GK+ P         ++        K    RD S+ + S  SG +  V +   + 
Sbjct: 525 MGKVAPLAADTEELGQRT-------KTQTKRDASITLRSTESGVIDQVMLTTTND 572


>gi|17225250|gb|AAL37318.1| RNA polymerase B-subunit [Staphylococcus carnosus subsp. carnosus]
          Length = 169

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 102/168 (60%), Positives = 128/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V CR  G   ++ R+
Sbjct: 62  YRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFISEEVVCRFRGNNTMMDRD 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|82706475|gb|ABB89615.1| RNA polymerase II second largest subunit [Scutellinia scutellata]
          Length = 538

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 100/609 (16%), Positives = 172/609 (28%), Gaps = 87/609 (14%)

Query: 528  HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
                 S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L 
Sbjct: 7    RYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLA 62

Query: 588  S--FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
               +  V   G+    +    + +   +     +      ++      +  D      LV
Sbjct: 63   LMSYITVGTPGYPLVNFMAEQNMEYLEEYEPQRSPNATKIFLNGVWIGVHRDPLHLVRLV 122

Query: 646  FCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD-------SNRVLMGCNMQ 697
                    I      I D  D   K          P    D+          VL   ++ 
Sbjct: 123  QELRRRGSISHEVSVIRDIRDREFKIFTDAGRVCRPLFVIDNDPTHESRGQLVLTKEHIM 182

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
            +        E    G           GA          E VDA       +    +    
Sbjct: 183  QLDEDGDLPEEERFG----WKGLLECGAV---------EYVDAEEEETIMIVMTPEDLEI 229

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               + +  +    N      + P+ K      +       PS  LG       +  + +P
Sbjct: 230  TRQVQQGYELVEDNDPNKRVKAPINK---NTSQYTHCEIHPSMILG-------ICASIIP 279

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +   + +  F                              
Sbjct: 280  FPDHNQSPRNTYQSAMGKQAMG--VFLTNFSERM-------------------------- 311

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  +  I      +  D+ +   S +  
Sbjct: 312  -DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDR 370

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVS 997
             +    +F R  +D+ +R      E+ E   R    +              I  G     
Sbjct: 371  GLF-RSLFYRAYMDQEKRIGMTVVEEFEKPTRGTTLKLKHGTYEKLDDDGLIAPGVRVSG 429

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  +S+D                DE  QR     K    T     E+   +++
Sbjct: 430  EDIIIGKTAPISAD---------------ADEMGQRQKCHTKRDVSTPLRSTENGIVDQV 474

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                  D +     + VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 475  MLTTNADGL-----KFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRSEDMPFTSEGIV 529

Query: 1118 VDIVLNPLG 1126
             DI++NP  
Sbjct: 530  PDIIINPHA 538


>gi|4972801|gb|AAD34796.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            pullorum]
          Length = 176

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 47/102 (46%), Positives = 64/102 (62%), Gaps = 6/102 (5%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTIKSDDV GR + Y++I  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDVEGRVKAYKAITRGESVKESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRT---KNSAKMEEI---PDFNKCEL 1385
            L KE+Q+L L +++             ++E     DFN  +L
Sbjct: 61   LTKELQSLALDVNVFAKNKEGVNEPILIKEDNRPSDFNAFQL 102


>gi|298501289|ref|ZP_07011086.1| DNA-directed RNA polymerase subunit beta [Vibrio cholerae MAK 757]
 gi|297539980|gb|EFH76044.1| DNA-directed RNA polymerase subunit beta [Vibrio cholerae MAK 757]
          Length = 142

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 44/112 (39%), Positives = 70/112 (62%), Gaps = 4/112 (3%)

Query: 3   KGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSV 62
               +    R+RK FG  P+++DIP L+ +Q  S++ F+  +         GL+AAF+SV
Sbjct: 35  MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQD----PEGQYGLEAAFRSV 90

Query: 63  FPITAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVD 114
           FPI +++G + L++VSY    P FDV +C  R +TY+ PL++ LRL++FD D
Sbjct: 91  FPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKD 142


>gi|14971087|gb|AAK74108.1| RNA polymerase beta subunit [Bacillus sp. Bsp. AX16]
 gi|14971089|gb|AAK74109.1| RNA polymerase beta subunit [Bacillus sp. Bsp. N52]
          Length = 259

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 115/305 (37%), Gaps = 56/305 (18%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI              D      S   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITDLIGENEYLRNTLDKDNTENSDKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI  E G +
Sbjct: 112 NAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQI 171

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +D ++L++             V     N      L  +      +  L   ++  P D  
Sbjct: 172 LDRRTLDK-------------VLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD-- 216

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                                   G   +N+  N    + +++I   DII+ I    +L 
Sbjct: 217 ----------------------AEGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLL 254

Query: 448 NGKGT 452
           +G G 
Sbjct: 255 HGVGD 259


>gi|198279455|emb|CAP04762.1| RNA polymerase beta subunit [Pinus canariensis]
          Length = 275

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 150/247 (60%), Gaps = 10/247 (4%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              GTG+E   A  SG+  +A + G +E +DA+                       + +Q
Sbjct: 1   CIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQ 52

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++L
Sbjct: 53  RSNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAIL 112

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +
Sbjct: 113 ISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWI 172

Query: 889 NPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  N
Sbjct: 173 ETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWIN 232

Query: 947 RHGIDKN 953
           R     +
Sbjct: 233 RVDDSGD 239



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 86/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 66   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 124

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 125  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 178

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 179  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 236

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S +LP
Sbjct: 237  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISIVLP 275


>gi|312204358|gb|ADQ47496.1| RNA polymerase II second largest subunit [Porina byssophila]
          Length = 687

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 88/252 (34%), Gaps = 27/252 (10%)

Query: 910  EKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLAR 969
            +  + AI      +  D+ +   S +   +    +F R  +++ +R        +E   +
Sbjct: 455  QNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRTYMEQEKRVGM---SLVERFEK 510

Query: 970  DKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAV 1026
                E + L R  Y +L +   I  G           K+  ++ D      R++      
Sbjct: 511  PLRTETLRLKRGTYEKLDDDGIIAPGTRVSGEDIIIGKTAPIAPDAEELGQRTKLHTKRD 570

Query: 1027 QDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQS 1086
                ++     +                  ++K+          L  VKV +   +  Q 
Sbjct: 571  ASTPLRSTENGI------------------VDKVML--TTNAEGLPFVKVRMRTTKVPQI 610

Query: 1087 GDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            GDK A RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E  +     
Sbjct: 611  GDKFASRHGQKGTIGITYRQEDMPFSSQGITPDLIINPHAIPSRMTIAHLIECQISKVAS 670

Query: 1147 GLGKKIKSLIND 1158
              G +  +    
Sbjct: 671  LSGFEGDATPFT 682



 Score = 75.9 bits (185), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 31/143 (21%), Positives = 58/143 (40%), Gaps = 12/143 (8%)

Query: 809 RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR----- 863
           +N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E        
Sbjct: 455 QNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYMEQEKRVGMSLVERFEKPLRT 514

Query: 864 DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVD 923
           +   +     + +D+ GII  G  V+  DI++GK  P         ++        K   
Sbjct: 515 ETLRLKRGTYEKLDDDGIIAPGTRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHT 567

Query: 924 VRDTSLRVPSGVSGTVVDVRIFN 946
            RD S  + S  +G V  V +  
Sbjct: 568 KRDASTPLRSTENGIVDKVMLTT 590



 Score = 75.1 bits (183), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 61/176 (34%), Gaps = 7/176 (3%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           ++ +SQ+       + ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 63  TAGVSQVLSRYTFAATLSHLRRTNT----PLGREGKIAKPRQLHNTHWGLVCPAETPEGQ 118

Query: 579 NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
             GLV +L     +      E    +    + +V  +     A      ++      +  
Sbjct: 119 ACGLVKNLALMCYITVGSPSEPIVEFMIQRNMEVLEEFEPTRAPHSTKVFVNGVWVGVHR 178

Query: 637 DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           D +    ++        I      + D  D   K          P    D+S R  
Sbjct: 179 DPTHLVGVMQTLRRSGTISPEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNSPRST 234


>gi|198279517|emb|CAP04793.1| RNA polymerase beta subunit [Equisetum giganteum]
          Length = 265

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 108/240 (45%), Positives = 154/240 (64%), Gaps = 9/240 (3%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E   VGTG+E  +A  SG+ + ++R G V  +D  RI +   E              L+ 
Sbjct: 3   EKCIVGTGLEGQIALDSGSCVTSEREGKVIYIDGERITLFVDEETSINK-------NLLS 55

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           ++RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW GYNFED+
Sbjct: 56  YERSNNNTCINQTPLVCKDKFIRQGQIIADGASTVGGELALGKNILVAYMPWEGYNFEDA 115

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
            LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G++ +G+
Sbjct: 116 TLISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDENGLVKLGS 175

Query: 887 EVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            V  GD+LVGK+TP         PE KLL+AIFG +  + R+T L+VP G  G V+D++ 
Sbjct: 176 WVEAGDVLVGKLTPLEYLDTLGAPEGKLLQAIFGTEVTNARETCLKVPVGFKGRVIDIKW 235


>gi|260593987|gb|ACX46288.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITNKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|219564083|gb|ACL28225.1| RNA polymerase II second largest subunit [fungal sp. M224]
          Length = 264

 Score =  166 bits (421), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/341 (16%), Positives = 103/341 (30%), Gaps = 81/341 (23%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +     +  +   +      +   
Sbjct: 2    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQE----KQIGHN 57

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E   +   ++ + L    Y ++ +   +  G           K+  ++ D        
Sbjct: 58   VLEQFEKPSRNDTLRLKHGTYDKIDDDGIVAPGVRVSGEDIIMGKTAPMAPD-------- 109

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    +E  QR    +K    T     E    +++     GD       R  KV V 
Sbjct: 110  -------AEELGQRQKHHIKRDVSTPLRSTESGVVDQVMLTTTGD-----GNRFAKVRVR 157

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM +  + E 
Sbjct: 158  TTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVVPDLIINPHAIPSRMTIAHLIEC 217

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             L       G +                                                
Sbjct: 218  QLSKVATLRGDEGD---------------------------------------------- 231

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                   +TP F       ++ +LR       G  ++Y+G 
Sbjct: 232  -------ATP-FTKVTVTQVSDILRRMGYQSRGFEVMYNGH 264



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/154 (23%), Positives = 60/154 (38%), Gaps = 13/154 (8%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    ++   +       E
Sbjct: 1   KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKQIGHNVLE 60

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   D   +       ID+ GI+  G  V+  DI++GK  P     M P+ + L  
Sbjct: 61  QFEKPSRNDTLRLKHGTYDKIDDDGIVAPGVRVSGEDIIMGKTAP-----MAPDAEELGQ 115

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
                      T LR        VVD  +    G
Sbjct: 116 RQKHHIKRDVSTPLR---STESGVVDQVMLTTTG 146


>gi|198279439|emb|CAP04754.1| RNA polymerase beta subunit [Pinus ayacahuite]
          Length = 272

 Score =  166 bits (420), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 100/244 (40%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 86.3 bits (212), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 234  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIILP 272


>gi|260586450|gb|ACX46114.1| RNA polymerase beta subunit [Corynebacterium sp. 1151]
          Length = 130

 Score =  166 bits (420), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/158 (35%), Positives = 78/158 (49%), Gaps = 36/158 (22%)

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVA 1197
            E HLGW     G  +    +D      +  L   L  V                      
Sbjct: 1    EVHLGWLAHA-GWTVN--PDDPANAKLLETLPEHLYDVPPESLT---------------- 41

Query: 1198 EQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPV 1249
                     +TPVFDGA  E I  +L  +  +  G        +++L+DG +GEPF  PV
Sbjct: 42   ---------ATPVFDGASNEEIAGLLANSKPNRDGDVMVDGDGKTVLFDGRSGEPFKYPV 92

Query: 1250 TVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKS 1287
            +VGY+YMLKL+H+V +K++ARSTG YS++TQQPLGGK+
Sbjct: 93   SVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKA 130


>gi|299849811|gb|ADJ57145.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
          Length = 285

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRSDTLKLKHGXYDKLDDDGIIAPGARV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 282



 Score = 87.1 bits (214), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 69/179 (38%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  GA 
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRSDTLKLKHGXYDKLDDDGIIAPGAR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|21307734|gb|AAK63184.1| RNA polymerase beta subunit RpoB [Staphylococcus lentus]
          Length = 169

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 102/168 (60%), Positives = 130/168 (77%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV     +VT+ + YL+A EE++  +AQANS LDE G F ++ V CR  G+    P+E
Sbjct: 62  YRKVNIETNQVTDRIDYLTADEEDSYVVAQANSVLDETGRFVDDEVLCRFRGDNTTKPKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           ++D++D SPKQVVS  ++ IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 RMDYMDVSPKQVVSAPSACIPFLENDDSNRALMGANMQRQAVPLMNPE 169


>gi|198279355|emb|CAP04712.1| RNA polymerase beta subunit [Pinus culminicola]
          Length = 271

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 99/244 (40%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE +TR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERVTREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 54/223 (24%), Positives = 86/223 (38%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERVTREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+ GRHGNKGI+S IL
Sbjct: 234  SGDNAE-----TVXVYISQKRKIQVGDKVXGRHGNKGIISIIL 271


>gi|299013261|gb|ADJ00223.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013263|gb|ADJ00224.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013265|gb|ADJ00225.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013269|gb|ADJ00227.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013271|gb|ADJ00228.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013273|gb|ADJ00229.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013275|gb|ADJ00230.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013277|gb|ADJ00231.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013279|gb|ADJ00232.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013281|gb|ADJ00233.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013283|gb|ADJ00234.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013285|gb|ADJ00235.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013287|gb|ADJ00236.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013289|gb|ADJ00237.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013291|gb|ADJ00238.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013293|gb|ADJ00239.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013295|gb|ADJ00240.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013297|gb|ADJ00241.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013299|gb|ADJ00242.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013301|gb|ADJ00243.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013303|gb|ADJ00244.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013305|gb|ADJ00245.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013307|gb|ADJ00246.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013309|gb|ADJ00247.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013311|gb|ADJ00248.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013313|gb|ADJ00249.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013315|gb|ADJ00250.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013317|gb|ADJ00251.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
 gi|299013319|gb|ADJ00252.1| DNA-dependent RNA polymerase II subunit [Eutypa lata var. aceri]
 gi|299013321|gb|ADJ00253.1| DNA-dependent RNA polymerase II subunit [Eutypa petrakii var.
            petrakii]
 gi|299013323|gb|ADJ00254.1| DNA-dependent RNA polymerase II subunit [Eutypa lata var. aceri]
 gi|299013325|gb|ADJ00255.1| DNA-dependent RNA polymerase II subunit [Eutypa laevata]
 gi|299013327|gb|ADJ00256.1| DNA-dependent RNA polymerase II subunit [Eutypa cf. laevata DSA600]
          Length = 274

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/287 (18%), Positives = 92/287 (32%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D  +R   +    IE   +    + + L +  Y +L +   I  G           
Sbjct: 62   RSYSDCEKR---IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++ ++ +      R++          ++     +                         
Sbjct: 119  KTSPINPENEEMGQRTKVHVKRDASTPLRSTESGIIDS--------------------VV 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 159  VTTNADGLRYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGITPDIIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 219  PHAIPSRMTIAHLIECLLSKVSTLKGMEGDATPFTDVTVDSVSNLLR 265



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 11  TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDCEKR 70

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   + +     +D+ GII  G  V+  DI++GK +P       P
Sbjct: 71  IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPIN-----P 125

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           E + +           RD S  + S  SG +  V +  
Sbjct: 126 ENEEMGQRTKVHVK--RDASTPLRSTESGIIDSVVVTT 161


>gi|169125446|gb|ACA48205.1| RNA polymerase II second largest subunit [Eleutherascus lectardii]
          Length = 530

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 87/581 (14%), Positives = 164/581 (28%), Gaps = 73/581 (12%)

Query: 595  YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
             G     +    + ++  +     +      ++      +  +      LV        I
Sbjct: 3    PGDPLKSFFSEQNMEMLEEYEPQRSPNATKVFLNGTWIGIHREPLHLVRLVQGLRRDGTI 62

Query: 655  LVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVG 712
                  I D  D   K          P F+ ++D      G  +  +       E  F+ 
Sbjct: 63   SHEVSVIRDIRDREFKIFTDAGRVCRPLFVIDNDPTHERRGQLVLTKDHIERLREDQFLD 122

Query: 713  TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
               E+               G VE VDA       +    +       I    +F+  + 
Sbjct: 123  ESDENKFGWE-----GLLNCGAVEYVDAEEEETIMIVMSPEDLDMARQIQAGYEFEEESD 177

Query: 773  NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
                N+R        + +       PS  LG       +  + +P+  +N       S R
Sbjct: 178  T---NKRVKTPFNKNMNQYTHCEIHPSMILG-------ICASIIPFPDHNQ------SPR 221

Query: 833  MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
               +       +  F     +                           +  +        
Sbjct: 222  NTXQSAMGKQAMGVFLTNFAERM-----------------------DTMANILYYPQKPL 258

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                 +       +   +  +  I      +  D+ +   S +   +    +F R  +D+
Sbjct: 259  ATTRSMEYLKFRELPAGQNAIVGIMCYGGYNQEDSVIMNQSSIDRGLF-RSLFYRSYMDQ 317

Query: 953  NERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLS 1009
             +R      + +E   +    + + L    Y +L +   +  G           K+  ++
Sbjct: 318  EKRVGM---QTVEAFEKPTRADTLKLKHGTYEKLDDDGLVAPGVRVSGEDIIIGKTAPIA 374

Query: 1010 SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPG 1069
            +D                DE  QR     K    T     E    +++            
Sbjct: 375  AD---------------ADEMGQRQKFHTKRDVSTPLRSTESGIVDQVLL-----TTNAE 414

Query: 1070 VLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPS 1129
             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PS
Sbjct: 415  GLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTCEGVVPDLIINPHAIPS 474

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            RM +  + E  L       G +  +          +S L  
Sbjct: 475  RMTIAHLIECQLSKVASLRGFEGDATPFTDVTVDTVSKLLR 515



 Score = 95.1 bits (235), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 69/471 (14%), Positives = 128/471 (27%), Gaps = 87/471 (18%)

Query: 496 DSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARA 554
           +   PQ   NA  V      F   + +    E ++ +  +   RR   +  +  V R   
Sbjct: 20  EEYEPQRSPNATKV------FLNGTWIGIHREPLHLVRLVQGLRRDGTISHEVSVIRDIR 73

Query: 555 GVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCD 607
             E        R   P       P     G  +     +            +        
Sbjct: 74  DREFKIFTDAGRVCRPLFVIDNDPTHERRGQLVLTKDHIERLREDQFLDESDENKFGWEG 133

Query: 608 GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDAS 667
                 V Y+ A EEE   I  +                                  D  
Sbjct: 134 LLNCGAVEYVDAEEEETIMIVMSPE--------------------------------DLD 161

Query: 668 PKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAI 727
             + +          + +   +     NM +                      +   + I
Sbjct: 162 MARQIQAGYEFEEESDTNKRVKTPFNKNMNQ------------------YTHCEIHPSMI 203

Query: 728 VAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGD 786
           +   A I+   D  +    + +  +     GV       +           Q+PL     
Sbjct: 204 LGICASIIPFPDHNQSPRNTXQSAMGKQAMGVFLTNFAERMDTMANILYYPQKPL----- 258

Query: 787 EVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEE 846
                            +L  G+N +V  M + GYN EDS+++++  +   +F S+    
Sbjct: 259 -----ATTRSMEYLKFRELPAGQNAIVGIMCYGGYNQEDSVIMNQSSIDRGLFRSLFYRS 313

Query: 847 FEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +   +   E        D   +     + +D+ G++  G  V+  DI++GK  P 
Sbjct: 314 YMDQEKRVGMQTVEAFEKPTRADTLKLKHGTYEKLDDDGLVAPGVRVSGEDIIIGKTAPI 373

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                   ++       +K    RD S  + S  SG V  V +       K
Sbjct: 374 AADADEMGQR-------QKFHTKRDVSTPLRSTESGIVDQVLLTTNAEGLK 417


>gi|4972813|gb|AAD34801.1| DNA-directed RNA polymerase beta and beta' subunits [Wolinella
            succinogenes]
          Length = 176

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 45/102 (44%), Positives = 63/102 (61%), Gaps = 6/102 (5%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLT KSDDV GR + Y++I  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTAKSDDVEGRVKAYKAITRGEPVKESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKN------SAKMEEIPDFNKCEL 1385
            L KE+Q+L L + +     ++        + +   DFN  +L
Sbjct: 61   LTKELQSLALDVTVYGETEEDSFVPMPIKEDDRPSDFNAFQL 102


>gi|17225266|gb|AAL37326.1| RNA polymerase B-subunit [Staphylococcus haemolyticus]
          Length = 169

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTE 169


>gi|551832|gb|AAA24580.1| RNA polymerase (rpoB) [Escherichia coli]
 gi|223184|prf||0604200A polymerase binding gene,RNA
          Length = 168

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/171 (30%), Positives = 89/171 (52%), Gaps = 3/171 (1%)

Query: 195 EFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADL 254
           EFD KD + VRIDRRRK+P T  L AL   +E+IL  F+ K+++  R +     L    L
Sbjct: 1   EFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERL 60

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVN 314
             G   S  +     G+  +E G+++T+  ++ L++  VK + +  + + G  VA+D ++
Sbjct: 61  -RGETASFDIE--ANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYID 117

Query: 315 GETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD 365
             TGE+   A   +    L ++  S  + I  L+ + +++  YI  TL  D
Sbjct: 118 ESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVD 168


>gi|46277340|gb|AAS86860.1| DNA-dependent RNA polymerase II [Peziza phyllogena]
          Length = 549

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 53/337 (15%), Positives = 98/337 (29%), Gaps = 36/337 (10%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 246  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 305

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 306  LF-RSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLKLKHGTYDKLDDDGLVAPGVRVSGE 364

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 365  DIIIGKTAPIAPNQEELGQRTKFHTKRDTSTPLRSTENGIVDQ----------------- 407

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 408  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVP 464

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            DI++NP  +PSRM +  + E  L       G +  +          +S L          
Sbjct: 465  DIIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTDVTVDSVSKLLR-------- 516

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGAD 1215
                             +     +G  + T VF G  
Sbjct: 517  -------EHGYQSRGFEIMYNGHTGRKLVTQVFLGPT 546



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 69/441 (15%), Positives = 137/441 (31%), Gaps = 35/441 (7%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S+ +       N    +       +     +      V    +H      +   +     
Sbjct: 6   SAPIVDFMMQRNM-EVLEEYEPSRSPNATKIFVNGVWV---GIHRDPGFIVRTIQKLRRQ 61

Query: 579 -NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +IG   SL    R   +       R      V ++    S    E     Q    L++D
Sbjct: 62  GHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDN-DPTSPRRGELVLQKQHIEKLEDD 120

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
               +E    R   + +L     +++IDA  ++ V I  +      +   +    G ++Q
Sbjct: 121 REIDDE--TQRYGWQGLLSDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGYDIQ 174

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           ++A P  + +             +   + I+   A I+   D  +               
Sbjct: 175 QEADPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXX 234

Query: 758 GVDIYRLM-KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                    +           Q+PL                      +L  G+N +VA M
Sbjct: 235 XXXXXXXXXRMDTMANILYYPQKPL----------GTTRSMEFLKFRELPAGQNAIVAIM 284

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEE 871
            + GYN EDS+++++  +   +F S+    +    +   +   E        +   +   
Sbjct: 285 CYSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLKLKHG 344

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G++  G  V+  DI++GK  P   +     ++        K    RDTS  +
Sbjct: 345 TYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDTSTPL 397

Query: 932 PSGVSGTVVDVRIFNRHGIDK 952
            S  +G V  V +       K
Sbjct: 398 RSTENGIVDQVMVTTNQEGLK 418


>gi|294721625|gb|ADF32962.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 290

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 55/362 (15%), Positives = 102/362 (28%), Gaps = 75/362 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 4    YPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  ID+ ++    + E+     R           +       I  G           K  
Sbjct: 63   RSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVSGDDVIIGKVA 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D      R++                    +Y    + L       ++ +      
Sbjct: 123  PIAPDADELGQRTK------------------AHEYRDVSTPLRSTENGIVDCVAL--TT 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VK+     +  Q GDK A RH  KG +      EDMPF ++G   D+++NP  
Sbjct: 163  NAENLKFVKIRTRTTKVPQIGDKFASRHVQKGTIGITYRQEDMPFTREGLTPDLIINPHA 222

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G++                                   
Sbjct: 223  IPSRMTIAHLIECLLSKVGAIKGQEGD--------------------------------- 249

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                +TP F     + I+ +L        G  ++Y+G TG+   
Sbjct: 250  --------------------ATP-FTDVTVQNISDLLIQHGYQSRGFEVMYNGHTGQKLR 288

Query: 1247 RP 1248
              
Sbjct: 289  AQ 290



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E            +       +D+ G+I  G  V+
Sbjct: 53  DRGLFRSLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK+ P         ++        KA + RD S  + S  +G V  V +     
Sbjct: 113 GDDVIIGKVAPIAPDADELGQRT-------KAHEYRDVSTPLRSTENGIVDCVALTTNAE 165

Query: 950 IDK 952
             K
Sbjct: 166 NLK 168


>gi|299013331|gb|ADJ00258.1| DNA-dependent RNA polymerase II subunit [Cryptosphaeria pullmanensis]
          Length = 273

 Score =  166 bits (420), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/287 (18%), Positives = 92/287 (32%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D  +R   +    IE   +    + + L +  Y +L +   I  G           
Sbjct: 61   RSYSDCEKR---IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIG 117

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K++ ++ +      R++          ++     +                         
Sbjct: 118  KTSPINPENEEMGQRTKVHVKRDASTPLRSTESGIIDS--------------------VV 157

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 158  VTTNADGLRYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGITPDIIIN 217

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 218  PHAIPSRMTIAHLIECLLSKVSTLKGMEGDATPFTDVTVDSVSNLLR 264



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 10  TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDCEKR 69

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   + +     +D+ GII  G  V+  DI++GK +P       P
Sbjct: 70  IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPIN-----P 124

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           E + +           RD S  + S  SG +  V +  
Sbjct: 125 ENEEMGQRTKVHVK--RDASTPLRSTESGIIDSVVVTT 160


>gi|56406197|gb|AAV87482.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 162

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 121/162 (74%), Gaps = 1/162 (0%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  
Sbjct: 61  IGLINSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELR 120

Query: 640 FTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           FT+  V CR   GE  L   ++I ++D S +QVVS+AA+LIP
Sbjct: 121 FTDAFVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIP 162


>gi|219564005|gb|ACL28186.1| RNA polymerase II second largest subunit [fungal sp. M23 (TL-2008)]
          Length = 287

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/295 (17%), Positives = 93/295 (31%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANVLYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R        +E   +    + + +    Y +L E   I  G   
Sbjct: 61   LF-RSLFFRSYMDQEKRVGM---SVVECFEKPTRADTLRMKHGTYEKLDEDGIISPGARV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDVSTPLRSTENGIVDQVLL----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV     +  Q GDK A RHG KG +      EDMPF  DG
Sbjct: 166  ---------TTNVEGLKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTADG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               DI++NP  +PSRM +  + E  L       G++  +          +S +  
Sbjct: 217  LTPDIIINPHAIPSRMTIAHLIECLLSKVASLTGQEGDATPFTDVTITSVSEILK 271



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 64/171 (37%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +     + +DE GII  GA V+
Sbjct: 58  DRGLFRSLFFRSYMDQEKRVGMSVVECFEKPTRADTLRMKHGTYEKLDEDGIISPGARVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 118 GEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDQVL 164


>gi|260594001|gb|ACX46295.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++ L ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINFLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV      E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVPHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260594105|gb|ACX46347.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++S+ ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSVAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260593991|gb|ACX46290.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N +S IT  RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPVSEITCKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|219564001|gb|ACL28184.1| RNA polymerase II second largest subunit [fungal sp. M19 (TL-2008)]
          Length = 267

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 96/291 (32%), Gaps = 27/291 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  Q     +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELXQXTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDIS 1166
               D+++NP  +PSRM +  + E  L       G +  +          +S
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVS 267



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 61/171 (35%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        D         +G+   V+
Sbjct: 118 GEDIIIGKTAPIAPDA----EELXQXTKAHVKRDASTPLRSTENGIVDQVL 164


>gi|260594127|gb|ACX46358.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE    IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEAAHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260593973|gb|ACX46281.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593985|gb|ACX46287.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 115/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITYKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|319922005|gb|ADV78613.1| RNA polymerase beta subunit [x Colmanara hybrid cultivar]
 gi|319922008|gb|ADV78614.1| RNA polymerase beta subunit [x Degarmoara hybrid cultivar]
          Length = 300

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 81/268 (30%), Positives = 129/268 (48%), Gaps = 16/268 (5%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D  L     ++  +V 
Sbjct: 47   VHRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAVL-----INERLVY 100

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + +D    E  +L      R   ++ G    +G  
Sbjct: 101  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEARLLRN--LDRNGIVMLGSWIETGDI 158

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++  +S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 159  LVGKLTPQTASELSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK--- 215

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+
Sbjct: 216  ----VVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDM 271

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            V NPLGVPSRMNVGQIFE  LG A   L
Sbjct: 272  VFNPLGVPSRMNVGQIFECSLGLAGDLL 299



 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 95/234 (40%), Positives = 151/234 (64%), Gaps = 6/234 (2%)

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I+    +  +  S        L+ +QRSN+NTC++Q+  V  G  +++  I+A G +T 
Sbjct: 7   KIIYTDTQKIIFSSNGDTLSIPLVMYQRSNKNTCMHQKTQVHRGKYIKKGQILAGGVATA 66

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+LVA+MPW GYNFED++LI+ER+V ED++TS HI ++E+    T  GPE I
Sbjct: 67  GGELALGKNVLVAYMPWEGYNFEDAVLINERLVYEDIYTSFHIRKYEIQTHVTSQGPERI 126

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGE 919
           T+DIP++    L+N+D  GI+ +G+ +  GDILVGK+TP+  S +  TPE++LLRAI G 
Sbjct: 127 TKDIPHLEARLLRNLDRNGIVMLGSWIETGDILVGKLTPQTASELSYTPEDRLLRAILGI 186

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNR----HGIDKNERSISVEREQIELLAR 969
           +    ++TSLR+P G  G V+DVR  +R    +   +  R    ++ +I++  +
Sbjct: 187 QVSTSKETSLRLPIGGRGRVIDVRWIHRKVVSNSNPEKIRVYISQKREIKVGDK 240


>gi|299849841|gb|ADJ57165.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
          Length = 285

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSXIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGARV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 282



 Score = 86.7 bits (213), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 69/179 (38%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  GA 
Sbjct: 67  XIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGAR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|330785314|gb|AEC46463.1| RNA polymerase II second largest subunit [Roccellographa
            circumscripta]
          Length = 305

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/377 (15%), Positives = 101/377 (26%), Gaps = 73/377 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTMANILYYPQKPLATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  I++ +       E  E   +           +       +  G      
Sbjct: 62   LF-RSLFYRSYIEQQQPVGFNALETFEXPVKQMTMRTRPGTYDKLDEDGFVAPGVRVSGE 120

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR  E  +          E    +++ 
Sbjct: 121  DIIIGKTAPFQAPMQDNA------------EGGQRTKEHTRRDVSCPLRSTEAGIIDRVL 168

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VK+     +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 169  ------VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGICP 222

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+++NP  +PSRM +  + E  L       G +  +          IS            
Sbjct: 223  DLIINPHAIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS----------- 271

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                          +L  A   + G  V                             +Y+
Sbjct: 272  --------------ILESAGYQRRGFEV-----------------------------MYN 288

Query: 1239 GLTGEPFDRPVTVGYIY 1255
            G TG   +  + +G  Y
Sbjct: 289  GHTGRKLNAQIFLGPTY 305



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 69/204 (33%), Gaps = 20/204 (9%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PL                   +  +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTMANILYYPQKPL----------ATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +       E                    +DE G 
Sbjct: 51  VIMNQSSIDRGLFRSLFYRSYIEQQQPVGFNALETFEXPVKQMTMRTRPGTYDKLDEDGF 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +  G  V+  DI++GK  P         E   R     K    RD S  + S  +G +  
Sbjct: 111 VAPGVRVSGEDIIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIIDR 166

Query: 942 VRIFNRHGIDKNE-RSISVEREQI 964
           V +    G    + R+ + +  QI
Sbjct: 167 VLVTTTEGRRSVKIRTRTTKVPQI 190


>gi|46277342|gb|AAS86861.1| DNA-dependent RNA polymerase II [Peziza phyllogena]
          Length = 522

 Score =  166 bits (419), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 48/292 (16%), Positives = 90/292 (30%), Gaps = 21/292 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 227  DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 286

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 287  LF-RSLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLKLKHGTYDKLDDDGLVAPGVRVSGE 345

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 346  DIIIGKTAPIAPNQEELGQRTKFHTKRDTSTPLRSTENGIVDQ----------------- 388

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 389  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVP 445

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            DI++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 446  DIIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTDVTVDSVSKLLR 497



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 64/450 (14%), Positives = 119/450 (26%), Gaps = 80/450 (17%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE-- 573
           F     +    +    +  I   RR   +G               +         P    
Sbjct: 17  FVNGVWVGIHRDPGFIVRTIQKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVV 76

Query: 574 -----TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                +     + L          +     ET             V Y+ A EEE   I 
Sbjct: 77  DNDPTSPRRGELVLQKQHIEKLEDDREIDDETQRYGWQGLLSDGVVEYIDAEEEETVMIV 136

Query: 629 QANSSLDEDGSFT------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                L+    F       +E    +     +          +  P  ++ I AS+IPF 
Sbjct: 137 MTPEDLETSRQFHAGYDIQQEADPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFP 196

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIR 742
           +++ S R      M +QA+ +                   + A I+      +    ++ 
Sbjct: 197 DHNQSPRNTYQSAMGKQAMGVFLT---------NYRERMDTMANILYYPQKPLGTTRSME 247

Query: 743 IVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
            +          +   +  Y              NQ                    S  +
Sbjct: 248 FLKFRELPAGQNAIVAIMCYSG-----------YNQE------------------DSVIM 278

Query: 803 GDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT 862
              ++ R +  +       + E  + +S             +EEFE   R          
Sbjct: 279 NQSSIDRGLFRSLFFRTYMDQEKRIGMS------------VVEEFEKPTR---------- 316

Query: 863 RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            +   +       +D+ G++  G  V+  DI++GK  P   +     ++        K  
Sbjct: 317 GNTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFH 369

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             RDTS  + S  +G V  V +       K
Sbjct: 370 TKRDTSTPLRSTENGIVDQVMVTTNQEGLK 399


>gi|14971091|gb|AAK74110.1| RNA polymerase beta subunit [Bacillus sp. Bsp. V770]
          Length = 259

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 115/305 (37%), Gaps = 56/305 (18%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP ++F    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYFS---GKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI              D      S   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITDLIGENEYLRNALDKDNTENSDKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI  E G +
Sbjct: 112 NAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQI 171

Query: 328 IDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVS 387
           +D ++L++             V     N      L  +      +  L   ++  P D  
Sbjct: 172 LDRRTLDK-------------VLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTD-- 216

Query: 388 TFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLR 447
                                   G   +N+  N    + +++I   DII+ I    +L 
Sbjct: 217 ----------------------AEGEQTINVIGNAYIEEAIKNITPADIISSISYFFNLL 254

Query: 448 NGKGT 452
           +G G 
Sbjct: 255 HGVGD 259


>gi|198279387|emb|CAP04728.1| RNA polymerase beta subunit [Pinus morrisonicola]
          Length = 260

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 99/244 (40%), Positives = 149/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+       TPE +LL+ IFG +    R++ L  P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/212 (21%), Positives = 76/212 (35%), Gaps = 14/212 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L         +++ R+ N+++   
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
             GD+        V V+++ KR IQ GDK+AGR
Sbjct: 234  SGDNAE-----TVHVYISQKRKIQVGDKVAGR 260


>gi|310750838|gb|ADP09212.1| RpoB' [Haloferax denitrificans ATCC 35960]
 gi|310750840|gb|ADP09213.1| RpoB' [Haloferax volcanii]
          Length = 173

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/196 (27%), Positives = 72/196 (36%), Gaps = 54/196 (27%)

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
                ++ KV V  +R  + GDK A RHG KG+V  + P EDMPF  DG   D+VLNP  +
Sbjct: 31   EDGSKLAKVSVRDQRVPELGDKFASRHGQKGVVGHLAPQEDMPFTADGVVPDLVLNPHAL 90

Query: 1128 PSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISD 1187
            PSRM VG + E   G      G+++       +       LRS LE+     S  E +  
Sbjct: 91   PSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENE---EELRSALEERGFMSSGKEVMYS 147

Query: 1188 YDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDR 1247
                                     G   E I                          + 
Sbjct: 148  -------------------------GVTGEKI--------------------------EA 156

Query: 1248 PVTVGYIYMLKLNHMV 1263
             + VG I+  KL HMV
Sbjct: 157  EIFVGIIFYHKLYHMV 172


>gi|14971031|gb|AAK74080.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971035|gb|AAK74082.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971045|gb|AAK74087.1| RNA polymerase beta subunit [Bacillus anthracis]
          Length = 258

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGSWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|330785354|gb|AEC46483.1| RNA polymerase II second largest subunit [Roccellographa cretacea]
 gi|330785358|gb|AEC46485.1| RNA polymerase II second largest subunit [Roccellographa cretacea]
          Length = 307

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 103/380 (27%), Gaps = 73/380 (19%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +             +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTMANILYYPQKPLATTRSLQFMNFRELPAGQNTIVAIACYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    +F R  I++ +       E+ E   +           +       +  G   
Sbjct: 61   DRGLF-RSLFYRSYIEQQQPVGFNALEEFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR  E  +          E    +
Sbjct: 120  SGEDVIIGKTAPFQAPMQDNA------------EGGQRTKEHTRRDVSCPLRSTEAGIID 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VK+     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  RVL------LTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          IS         
Sbjct: 222  VAPDLIINPHAIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS-------- 273

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                             +L  A   + G  V                             
Sbjct: 274  -----------------ILESAGYQRRGFEV----------------------------- 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +Y+G TG   +  + +G  Y
Sbjct: 288  MYNGHTGRKLNAQIFLGPTY 307



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 74/205 (36%), Gaps = 20/205 (9%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                   +  +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTMANILYYPQKPL----------ATTRSLQFMNFRELPAGQNTIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       EE  + +  +           +DE G
Sbjct: 52  SVIMNQSSIDRGLFRSLFYRSYIEQQQPVGFNALEEFEKPVKQMTMRTRPGTYDKLDEDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  D+++GK  P         E   R     K    RD S  + S  +G + 
Sbjct: 112 FVAPGVRVSGEDVIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIID 167

Query: 941 DVRIFNRHGIDKNE-RSISVEREQI 964
            V +    G    + R+ + +  QI
Sbjct: 168 RVLLTTTEGRRSVKIRTRTTKVPQI 192


>gi|55650702|emb|CAF31401.1| RNA polymerase B subunit [Microcystis sp. 130]
          Length = 193

 Score =  166 bits (419), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 93/192 (48%), Positives = 129/192 (67%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + DE+G    E +  R   E      E++D++  SP Q+VS+A SLIPFLE+D
Sbjct: 2   RVAPGDVATDENGYILGETIPVRYRQEFSTTSPEQVDYVCVSPVQIVSVATSLIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  VDA RI I
Sbjct: 62  DANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSYVDANRIRI 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +  + D D        Y + K+QRSNQ+TC+NQRPLV  G++V    I+ADG +T+ G++
Sbjct: 122 KVADEDKDIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEGGEI 181

Query: 806 ALGRNMLVAFMP 817
           ALG+N+LVA+MP
Sbjct: 182 ALGQNILVAYMP 193


>gi|198279467|emb|CAP04768.1| RNA polymerase beta subunit [Pinus jeffreyi]
          Length = 264

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 150/246 (60%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 49/214 (22%), Positives = 78/214 (36%), Gaps = 14/214 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             GD+        V V+++ KR IQ GDK+AGRHG
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHG 264


>gi|197941918|gb|ACH78564.1| RNA polymerase subunit [Picea glauca]
          Length = 262

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 99/243 (40%), Positives = 148/243 (60%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                      L+ +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTELVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 65.1 bits (157), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 48/215 (22%), Positives = 79/215 (36%), Gaps = 14/215 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
             GD+        V V+++ KR IQ GDK+AGRHGN
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGN 262


>gi|297835422|ref|XP_002885593.1| hypothetical protein ARALYDRAFT_898915 [Arabidopsis lyrata subsp.
            lyrata]
 gi|297331433|gb|EFH61852.1| hypothetical protein ARALYDRAFT_898915 [Arabidopsis lyrata subsp.
            lyrata]
          Length = 505

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 76/176 (43%), Gaps = 29/176 (16%)

Query: 1216 EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSY 1275
            E+ I      A     G   +Y+G +GE     + +G  +  +L HM  DKV  R+TG  
Sbjct: 332  EQQIKPW--RAGFSRWGNERVYNGRSGEMMRSLIFMGPTFYQRLVHMSEDKVKFRNTGPV 389

Query: 1276 SLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTRVYES 1331
              +T+Q +  +   GG R GEME  C+ A+GA+  L E L   SD     +  + + Y +
Sbjct: 390  HPLTRQQVADRKRFGGIRFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYAN 449

Query: 1332 IVAGNDTFETG---------------------TPESFNVLVKEMQALGLSIDLENS 1366
            ++    T  +G                      P    +L +E+ ++G++++ +  
Sbjct: 450  VI--ERTPSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGITLNFDTK 503



 Score =  107 bits (266), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 54/266 (20%), Positives = 91/266 (34%), Gaps = 90/266 (33%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F+S     V P              A ++F
Sbjct: 44  LISHQLNSYNFFIQ----------HGLQDVFESFGDMLVEPSFDVIKKKDNDWRYATVKF 93

Query: 77  VSYEFDPPKF--DVDD-------CLWRDLTYAVPLKITLRLIVFDV-----------DEF 116
                + P F  D  +          +++TY+  +K+ +++ VF              + 
Sbjct: 94  GKVTVEKPTFFSDDKELEFLPWHARLQNMTYSARIKVNVQVEVFIKTVVKSDKFKTGQDE 153

Query: 117 TGAKSIKDIKEQSIYMGDLPLMTKD-----------------------GTFVIKGIQRIV 153
              K I ++K+Q I +G +P+M K                        G FVIKG +++ 
Sbjct: 154 YVEKKILEVKKQDILIGSIPVMVKSVLCKTSEKGKENCRKGDCAFDQGGYFVIKGAEKVF 213

Query: 154 VSQLHR---------SP-GIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSK---D 200
           ++Q            SP  + F  +  R           R I  +    +   D K    
Sbjct: 214 IAQEQMCTKRLWISNSPWTVSFRSENKRN----------RFI-VRLSENEKSEDYKKREK 262

Query: 201 IIHVRIDRRRKVPVTSFLMALGMDSE 226
           ++ V       +PV     ALG+ S+
Sbjct: 263 VLTVYFLSTE-IPVWLLFFALGVSSD 287


>gi|14971067|gb|AAK74098.1| RNA polymerase beta subunit [Bacillus mycoides]
          Length = 258

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/197 (27%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G V
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTV 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|219564025|gb|ACL28196.1| RNA polymerase II second largest subunit [fungal sp. M133]
          Length = 257

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 51/275 (18%), Positives = 92/275 (33%), Gaps = 27/275 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   V    +E   +    E + L    Y +L +   +  G           
Sbjct: 62   RTYMDQEKR---VGFHTVESFEKPSRGETIRLKHGTYDKLDDDGVVAPGVRVSGEDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R+Q                 +K    T     E+   +K+      
Sbjct: 119  KTAPIAPDAEELGQRTQL---------------HVKRDVSTPLRSTENGIVDKV-----M 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + +KV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 159  VTTNSEGNKFIKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            P  +PSRM +  + E  L       G +  +    
Sbjct: 219  PHAIPSRMTIAHLIECLLSKVGALSGNEGDATPFT 253



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 61/171 (35%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E        +   +       +D+ G++  G  V+
Sbjct: 52  DRGLFRSLFYRTYMDQEKRVGFHTVESFEKPSRGETIRLKHGTYDKLDDDGVVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 112 GEDIIIGKTAPIAPDA----EELGQRTQLHVKRDVSTPLRSTENGIVDKVM 158


>gi|219564093|gb|ACL28230.1| RNA polymerase II second largest subunit [fungal sp. M288]
          Length = 287

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 271



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|198279433|emb|CAP04751.1| RNA polymerase beta subunit [Pinus pinceana]
          Length = 271

 Score =  165 bits (418), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 99/243 (40%), Positives = 149/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 85.5 bits (210), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 88/224 (39%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S ILP
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXILP 271


>gi|260594107|gb|ACX46348.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I L++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IALINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|260594087|gb|ACX46338.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D   T+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALFTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|219564035|gb|ACL28201.1| RNA polymerase II second largest subunit [fungal sp. M149]
          Length = 287

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 55/365 (15%), Positives = 109/365 (29%), Gaps = 81/365 (22%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  V             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANVLYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   ++ ++   + +  IE   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYSEQEKK---IGKNTIETFEKPMRSDTLRLKHGTYEKLDDDGLVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                ++  Q+    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEDLGQKTQAHIKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++                 KV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 162  QVLL-----STNSEGALFCKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +                        
Sbjct: 217  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGD---------------------- 254

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                                           +TP F     ++++ +LR       G  +
Sbjct: 255  -------------------------------ATP-FTEVTVDSVSRLLREHGYQSRGFEV 282

Query: 1236 LYDGL 1240
            +Y+G 
Sbjct: 283  MYNGH 287



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 35/170 (20%), Positives = 64/170 (37%), Gaps = 22/170 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E     +  D   +     + +D+ G++  G  V+
Sbjct: 58  DRGLFRSLFYRAYSEQEKKIGKNTIETFEKPMRSDTLRLKHGTYEKLDDDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             DI++GK  P         +K        +A   RD S  + S  +G V
Sbjct: 118 GEDIIIGKTAPIAPDAEDLGQKT-------QAHIKRDASTPLRSTENGIV 160


>gi|299013267|gb|ADJ00226.1| DNA-dependent RNA polymerase II subunit [Eutypa lata]
          Length = 264

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 52/276 (18%), Positives = 92/276 (33%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D  +R  
Sbjct: 4    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDCEKR-- 60

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    IE   +    + + L +  Y +L +   I  G           K++ ++ +   
Sbjct: 61   -IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPINPENEE 119

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                                LR V
Sbjct: 120  MGQRTKVHVKRDASTPLRSTESGIIDS--------------------VVVTTNADGLRYV 159

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM + 
Sbjct: 160  KVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGITPDIIINPHAIPSRMTIA 219

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 220  HLIECLLSKVSTLKGMEGDATPFTDVTVDSVSNLLR 255



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 63/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 1   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDCEKR 60

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   + +     +D+ GII  G  V+  DI++GK +P       P
Sbjct: 61  IGINTIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPIN-----P 115

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           E + +           RD S  + S  SG +  V +  
Sbjct: 116 ENEEMGQRTKVHVK--RDASTPLRSTESGIIDSVVVTT 151


>gi|260594023|gb|ACX46306.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  V +++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVPDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|319922018|gb|ADV78618.1| RNA polymerase beta subunit [Oncidium hybrid cultivar]
          Length = 300

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 81/268 (30%), Positives = 129/268 (48%), Gaps = 16/268 (5%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D  L     ++  +V 
Sbjct: 47   VQRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAVL-----INERLVY 100

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + +D    E  +L      R   ++ G    +G  
Sbjct: 101  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEARLLRN--LDRNGIVMLGSWIETGDI 158

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++  +S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 159  LVGKLTPQTASELSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK--- 215

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+
Sbjct: 216  ----GVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDM 271

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            V NPLGVPSRMNVGQIFE  LG A   L
Sbjct: 272  VFNPLGVPSRMNVGQIFECSLGLAGDLL 299



 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 94/229 (41%), Positives = 150/229 (65%), Gaps = 6/229 (2%)

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
             +  +  S        L+ ++RSN+NTC++Q+  V+ G  +++  I+A G +T  G+LA
Sbjct: 12  DTQKIIFSSNGDTLSIPLVMYKRSNKNTCMHQKTQVQRGKYIKKGQILAGGVATAGGELA 71

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVA+MPW GYNFED++LI+ER+V ED++TS HI ++E+    T  GPE IT+DIP
Sbjct: 72  LGKNVLVAYMPWEGYNFEDAVLINERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKDIP 131

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDV 924
           ++    L+N+D  GI+ +G+ +  GDILVGK+TP+  S +  TPE++LLRAI G +    
Sbjct: 132 HLEARLLRNLDRNGIVMLGSWIETGDILVGKLTPQTASELSYTPEDRLLRAILGIQVSTS 191

Query: 925 RDTSLRVPSGVSGTVVDVRIFNRHGID----KNERSISVEREQIELLAR 969
           ++TSLR+P G  G V+DVR  +R G+     +  R    ++ +I++  +
Sbjct: 192 KETSLRLPIGGRGRVIDVRWIHRKGVSNSNPEKIRVYISQKREIKVGDK 240


>gi|260594125|gb|ACX46357.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+   RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTPERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|14971065|gb|AAK74097.1| RNA polymerase beta subunit [Bacillus cereus]
          Length = 258

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 50/191 (26%), Positives = 88/191 (46%), Gaps = 7/191 (3%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVY--SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
           L ALG  S+ EI            +   D       A   +           ++  + ++
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLL 117

Query: 275 ESGKKLTSGL-LKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSL 333
            SG        L ++    +       + L    +AE +V+ ETGEI    G ++D ++L
Sbjct: 118 VSGFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTL 177

Query: 334 EEIFHSEIRDI 344
           + I     ++I
Sbjct: 178 DRILPYLEKNI 188



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSGFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|198279331|emb|CAP04700.1| RNA polymerase beta subunit [Pinus clausa]
          Length = 275

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 101/247 (40%), Positives = 151/247 (61%), Gaps = 10/247 (4%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
              GTG+E   A  SG+  +A + G +E +DA+                       + +Q
Sbjct: 1   CIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQ 52

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++L
Sbjct: 53  RSNTNTCTHQKPKIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAIL 112

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +
Sbjct: 113 ISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLGSWI 172

Query: 889 NPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  N
Sbjct: 173 ETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWIN 232

Query: 947 RHGIDKN 953
           R     +
Sbjct: 233 RVDDSGD 239



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 66   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 124

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 125  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 178

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 179  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 236

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 237  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 275


>gi|260594109|gb|ACX46349.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGPNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|198279459|emb|CAP04764.1| RNA polymerase beta subunit [Pinus pinaster]
          Length = 267

 Score =  165 bits (418), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 150/246 (60%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 81/217 (37%), Gaps = 14/217 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
             GD+        V V+++ KR IQ GDK+AGRHGNKG
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKG 267


>gi|299849814|gb|ADJ57147.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
 gi|299849817|gb|ADJ57149.1| RNA polymerase II second largest subunit [Xylogone ganodermophthora]
          Length = 285

 Score =  165 bits (417), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 12   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 71

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 72   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRSDTLXLXHXXYDKLDDDGIIAPGARV 127

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 128  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 173  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 227

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 282



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 69/179 (38%), Gaps = 15/179 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 7   FDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 66

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D+ GII  GA 
Sbjct: 67  SIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRSDTLXLXHXXYDKLDDDGIIAPGAR 126

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           V+  DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 127 VSGEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 178


>gi|227826334|gb|ACP41894.1| RNA polymerase II [Petrocoptis pyrenaica]
          Length = 249

 Score =  165 bits (417), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 61/174 (35%), Gaps = 54/174 (31%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +GQ+ E  +G     +GK+                                  
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGD-------------------------------- 217

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                 +TP F     + I+  L+       G   +Y+G
Sbjct: 218  ---------------------ATP-FTDVTVDNISKALQKCGYQMRGFETMYNG 249



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|67942370|gb|AAY83385.1| DNA-dependent RNA polymerase II [Chorioactis geaster]
          Length = 529

 Score =  165 bits (417), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 83/641 (12%), Positives = 159/641 (24%), Gaps = 121/641 (18%)

Query: 601  PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
             Y    + +   +     +      ++      +  D       V        +      
Sbjct: 9    DYLAQHNMEFLEEYEPQRSPNATKVFVNGVWVGIHRDPMHLVRNVQEVRRKGIVGHEVSV 68

Query: 661  I-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVV 719
            I D  D   K          P    ++         +  Q   + + E          + 
Sbjct: 69   IRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEQDA------DLP 122

Query: 720  AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
                         GIVE VDA       +    +       + +              + 
Sbjct: 123  PDERWGWDGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAQQVRQGYVLDEETDQHKRVKA 182

Query: 780  PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            P+        +       PS  LG       +  + +P+  +N          M  + + 
Sbjct: 183  PI---NPNTHQYTHCEIHPSMILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG 232

Query: 840  TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
              + +  F                                 +  +             + 
Sbjct: 233  --VFLTNFSERM---------------------------DTMANILYYPQKPLATTRSME 263

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  +   +  +  I      +  D+ +   S +   +    +F R   D+ +R   +
Sbjct: 264  YLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRSYTDQEKRIGMM 322

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
              E+ E   R                   +  G           K+  ++ D        
Sbjct: 323  VVEEFEKPQRSNTLRLKHGTYEKLDDDGLVAPGVRVSGEDIIIGKTAPIAPD-------- 374

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    DE  QR     K    T     E+   +++             L+  KV + 
Sbjct: 375  -------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVLL-----TTNAEGLKFAKVRMR 422

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E 
Sbjct: 423  TTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTCEGIIPDLIINPHAIPSRMTIAHLIEC 482

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQ 1199
             L       G +                                                
Sbjct: 483  QLSKVSSLRGMEGD---------------------------------------------- 496

Query: 1200 WKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                   +TP F     ++++++LR       G  ++Y+G 
Sbjct: 497  -------ATP-FTDVTVDSVSNLLREEGYQSRGFEVMYNGH 529



 Score =  108 bits (270), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 77/487 (15%), Positives = 149/487 (30%), Gaps = 97/487 (19%)

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGG 548
           + +   ++   PQ   NA  V      F     +    + ++ +  +   RR   +G   
Sbjct: 13  QHNMEFLEEYEPQRSPNATKV------FVNGVWVGIHRDPMHLVRNVQEVRRKGIVG-HE 65

Query: 549 VARARAGVEMRDVHPTHYGRIC------PAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           V+  R   +      T  GR+C        +T+      LV       R+     +    
Sbjct: 66  VSVIRDIRDREFKIFTDAGRVCRPLFVVNNDTTSERRGQLVLQKEHIQRLEQDADLPPDE 125

Query: 603 RK-VCDGKVTNDVVYLSAMEEENRYIAQANSSLD-----EDGSFTEELVFCRCAGEEILV 656
           R           V Y+ A EEE   I      L+       G   +E        +  + 
Sbjct: 126 RWGWDGLLDEGIVEYVDAEEEETIMIVMTPEDLEIAQQVRQGYVLDEETDQHKRVKAPIN 185

Query: 657 PR-EKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM 715
           P   +    +  P  ++ I AS+IPF +++ S R      M +QA+ +            
Sbjct: 186 PNTHQYTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFS------ 239

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
                                              +   + + +  Y       +     
Sbjct: 240 -----------------------------------ERMDTMANILYYPQKPLATTRSMEY 264

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
           +  R                        +L  G+N +V  M + GYN EDS+++++  + 
Sbjct: 265 LKFR------------------------ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSID 300

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
             +F S+    +    +   +   E        +   +     + +D+ G++  G  V+ 
Sbjct: 301 RGLFRSLFYRSYTDQEKRIGMMVVEEFEKPQRSNTLRLKHGTYEKLDDDGLVAPGVRVSG 360

Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
            DI++GK  P         ++       +K    RD S  + S  +G V  V +      
Sbjct: 361 EDIIIGKTAPIAPDADEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVLLTTNAEG 413

Query: 951 DKNERSI 957
            K  +  
Sbjct: 414 LKFAKVR 420


>gi|91981508|gb|ABE68096.1| RNA polymerase subunit B [Pseudomonas sp. PGNL1]
          Length = 155

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 88/155 (56%), Positives = 115/155 (74%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           R   E  +   E +  +D SPKQVVS+AASLIPFL
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFL 155


>gi|198279441|emb|CAP04755.1| RNA polymerase beta subunit [Pinus strobus]
          Length = 270

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 99/243 (40%), Positives = 149/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 55/223 (24%), Positives = 87/223 (39%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S IL
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIIL 270


>gi|14971043|gb|AAK74086.1| RNA polymerase beta subunit [Bacillus anthracis]
          Length = 258

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDCRTLDRILPYLEKNI 188



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|219563987|gb|ACL28177.1| RNA polymerase II second largest subunit [Acrospermum compressum]
          Length = 284

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 54/287 (18%), Positives = 95/287 (33%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 9    YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 67

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   V    IE   +    E + L    Y +L E   +  G           
Sbjct: 68   RTYMDQEKR---VGFHTIESFEKPSRGETIRLKHGTYDKLDEDGVVAPGVRVSGEDIIIG 124

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R++                 +K    T     E+   +K+      
Sbjct: 125  KTAPIAPDAEELGQRTKL---------------HVKRDVSTPLRSTENGIVDKV-----M 164

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + +KV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 165  VTTNSEGNKFIKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLTPDLIIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 225  PHAIPSRMTIAHLIECLLSKVGSLRGNEGDATPFTDVTVESVSQLLR 271



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 19/178 (10%)

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                     Q+PL                      +L  G+N +VA   + GYN EDS+
Sbjct: 1   DTMMNVLYYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSV 50

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGII 882
           ++++  +   +F S+    +    +       E        +   +       +DE G++
Sbjct: 51  IMNQSSIDRGLFRSLFYRTYMDQEKRVGFHTIESFEKPSRGETIRLKHGTYDKLDEDGVV 110

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             G  V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 111 APGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHVKRDVSTPLRSTENGIVDKVM 164


>gi|219564117|gb|ACL28242.1| RNA polymerase II second largest subunit [Hymenoscyphus sp. Huhtinen
            06/23]
          Length = 263

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 55/271 (20%), Positives = 94/271 (34%), Gaps = 27/271 (9%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ +R   +   
Sbjct: 1    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMN 56

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E   +    + + L    Y +L E   +  G           K+  ++ D        
Sbjct: 57   VVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPD-------- 108

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                    +E  QR    +K    T     E+   +++             LR VKV + 
Sbjct: 109  -------AEELGQRTKAHVKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFVKVRMR 156

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF   G   D+++NP  +PSRM +  + E 
Sbjct: 157  TTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTVQGIVPDLIINPHAIPSRMTIAHLIEC 216

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             L       G +  +          +S L  
Sbjct: 217  QLSKVGTLRGLEGDATPFTEVTVDSVSKLLR 247



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 12/150 (8%)

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E 
Sbjct: 1   FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMNVVEQ 60

Query: 862 TR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                  D   +       +DE GI+  G  V+  DI++GK  P         ++     
Sbjct: 61  FEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT---- 116

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
              KA   RD S  + S  +G V  V I  
Sbjct: 117 ---KAHVKRDASTPLRSTENGIVDQVLITT 143


>gi|330785356|gb|AEC46484.1| RNA polymerase II second largest subunit [Roccellographa cretacea]
          Length = 307

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 57/380 (15%), Positives = 102/380 (26%), Gaps = 73/380 (19%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +       +             +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTXANILYYPQKPLATTRSLQFMNFRELPAGQNTIVAIACYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    +F R  I++ +       E+ E   +           +       +  G   
Sbjct: 61   DRGLF-RSLFYRSYIEQQQPVGFNALEEFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+    + +                E  QR  E  +          E    +
Sbjct: 120  SGEDVIIGKTAPFQAPMQDNA------------EGGQRTKEHTRRDVSCPLRSTEAGIID 167

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++              R VK+     +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 168  RVL------LTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEG 221

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          IS         
Sbjct: 222  VAPDLIINPHAIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS-------- 273

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
                             +L  A   + G  V                             
Sbjct: 274  -----------------ILESAGYQRRGFEV----------------------------- 287

Query: 1236 LYDGLTGEPFDRPVTVGYIY 1255
            +Y+G TG   +  + +G  Y
Sbjct: 288  MYNGHTGRKLNAQIFLGPTY 307



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 74/205 (36%), Gaps = 20/205 (9%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                   +  +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTXANILYYPQKPL----------ATTRSLQFMNFRELPAGQNTIVAIACYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGP-EEITRDIPNV----SEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       EE  + +  +           +DE G
Sbjct: 52  SVIMNQSSIDRGLFRSLFYRSYIEQQQPVGFNALEEFEKPVKQMTMRTRPGTYDKLDEDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  G  V+  D+++GK  P         E   R     K    RD S  + S  +G + 
Sbjct: 112 FVAPGVRVSGEDVIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIID 167

Query: 941 DVRIFNRHGIDKNE-RSISVEREQI 964
            V +    G    + R+ + +  QI
Sbjct: 168 RVLLTTTEGRRSVKIRTRTTKVPQI 192


>gi|194320162|gb|ACF48306.1| DNA-dependent RNA polymerase II second largest subunit [Candelariella
            terrigena]
          Length = 317

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 62/377 (16%), Positives = 107/377 (28%), Gaps = 75/377 (19%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 16   ILYYPQKPLATTRSMEYLKFRNLPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RS 74

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F+R   D+ +R      E  E   R           +       I  G           
Sbjct: 75   LFHRSYTDQEKRVGMNTVEHFEKPTRSDTLRLKHGTYDKIDEDGIIAPGVRVSGEDIIIG 134

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D                +E  QR    +K    T     E    +K+      
Sbjct: 135  KTAPIAPD---------------SEELGQRTKYHVKRDVSTPLRSAESGIVDKVMVTTNA 179

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
            D +     R VKV +   +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 180  DGL-----RFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGIVPDLIIN 234

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +  +          +S L      +   G H+ 
Sbjct: 235  PHAIPSRMTIAHLIECQLSKVSALQGFEGDATPFTDVTVDSVSRL------LYEQGYHSR 288

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                                           +G +       G+
Sbjct: 289  GFEVM-----------------------------------------YNGHT-------GK 300

Query: 1244 PFDRPVTVGYIYMLKLN 1260
                 + +G  Y  +L 
Sbjct: 301  KLMAQIFLGPTYYQRLR 317



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 66/191 (34%), Gaps = 22/191 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYEQRLDTMSNILYYPQKPL----------ATTRSMEYLKFRNLPAGQNAIVAIAVYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E        D   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFHRSYTDQEKRVGMNTVEHFEKPTRSDTLRLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           IDE GII  G  V+  DI++GK  P         ++    +        RD S  + S  
Sbjct: 114 IDEDGIIAPGVRVSGEDIIIGKTAPIAPDSEELGQRTKYHVK-------RDVSTPLRSAE 166

Query: 936 SGTVVDVRIFN 946
           SG V  V +  
Sbjct: 167 SGIVDKVMVTT 177


>gi|17225272|gb|AAL37329.1| RNA polymerase B-subunit [Staphylococcus kloosii]
          Length = 169

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLETNSITDQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNRE 169


>gi|283806285|dbj|BAI66382.1| RNA polymerase second largest subunit [Kalmusia brevispora]
          Length = 304

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 94/290 (32%), Gaps = 26/290 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 8    YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 66

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 67   RAYTEQEKR---IGVNVLEQFEKPTRMDTMRMKGGTYDKLDDDGIVAPGVRVSGDDIIIG 123

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + +D                 E  Q+     K    T     E+   +++      
Sbjct: 124  KTAPIPNDE--------------NKEMGQKLANHTKRDVSTPLRSTENGLVDQVLF---- 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF +DG   DIV+N
Sbjct: 166  -TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRDGLTPDIVIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            P  +PSRM +  + E  L        ++  +          +S L     
Sbjct: 225  PHAIPSRMTIAHLVECLLSKVGAINAQEGDATPFCGVTVDQVSDLLEGAN 274



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 62/176 (35%), Gaps = 18/176 (10%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 2   MMNVLYYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIM 51

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +D+ GI+  
Sbjct: 52  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRMDTMRMKGGTYDKLDDDGIVAP 111

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           G  V+  DI++GK  P          ++ + +      DV        +G+   V+
Sbjct: 112 GVRVSGDDIIIGKTAPIPNDENK---EMGQKLANHTKRDVSTPLRSTENGLVDQVL 164


>gi|17225274|gb|AAL37330.1| RNA polymerase B-subunit [Staphylococcus chromogenes]
          Length = 169

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 100/168 (59%), Positives = 128/168 (76%), Gaps = 2/168 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    + +E
Sbjct: 62  YRKVDLETNAITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
           K+D++D SPKQVVS A + IPFLENDDSNR LMG N+QRQAVPLL  E
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANIQRQAVPLLNPE 169


>gi|198279389|emb|CAP04729.1| RNA polymerase beta subunit [Pinus torreyana]
          Length = 264

 Score =  165 bits (417), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 150/246 (60%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQICQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 62.8 bits (151), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 50/214 (23%), Positives = 79/214 (36%), Gaps = 14/214 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            IC G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   ICQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             GD+        V V+++ KR IQ GDK+AGRHG
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHG 264


>gi|260593995|gb|ACX46292.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  165 bits (417), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT  RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITCKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEPDHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|152968516|gb|ABS50272.1| RNA polymerase II [Lychnis abyssinica]
          Length = 267

 Score =  165 bits (417), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 55/285 (19%), Positives = 88/285 (30%), Gaps = 23/285 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           N          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 265



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|14971023|gb|AAK74076.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971025|gb|AAK74077.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971027|gb|AAK74078.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971029|gb|AAK74079.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971033|gb|AAK74081.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971039|gb|AAK74084.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971041|gb|AAK74085.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971047|gb|AAK74088.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971049|gb|AAK74089.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971051|gb|AAK74090.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971053|gb|AAK74091.1| RNA polymerase beta subunit [Bacillus anthracis]
 gi|14971057|gb|AAK74093.1| RNA polymerase beta subunit [Bacillus cereus]
 gi|14971059|gb|AAK74094.1| RNA polymerase beta subunit [Bacillus cereus]
 gi|14971063|gb|AAK74096.1| RNA polymerase beta subunit [Bacillus cereus]
 gi|14971071|gb|AAK74100.1| RNA polymerase beta subunit [Bacillus thuringiensis]
 gi|14971073|gb|AAK74101.1| RNA polymerase beta subunit [Bacillus thuringiensis]
 gi|14971075|gb|AAK74102.1| RNA polymerase beta subunit [Bacillus thuringiensis]
 gi|14971077|gb|AAK74103.1| RNA polymerase beta subunit [Bacillus thuringiensis]
 gi|14971081|gb|AAK74105.1| RNA polymerase beta subunit [Bacillus sp. Ba813-9594/3]
 gi|14971085|gb|AAK74107.1| RNA polymerase beta subunit [Bacillus sp. Ba813-IB/A]
          Length = 258

 Score =  165 bits (417), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|14971037|gb|AAK74083.1| RNA polymerase beta subunit [Bacillus anthracis]
          Length = 258

 Score =  165 bits (417), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 87/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGSWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S          +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLXKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLXKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|290760052|gb|ADD54503.1| RNA polymerase II second largest subunit [Salsuginea ramicola]
          Length = 594

 Score =  165 bits (417), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 47/269 (17%), Positives = 88/269 (32%), Gaps = 27/269 (10%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D     +       +   +  + AI        +D+ +   S +   +    +F R   +
Sbjct: 350  DRYYSVMEYLKFRELPAGQNAIVAIACYSGNYQKDSVIMNQSSIDRGLF-RSLFYRAYTE 408

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVL 1008
            + +R   +    +E   +    + + L    Y +L +   +  G           K+  +
Sbjct: 409  QEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPI 465

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
             +D      ++           ++     +  Q                           
Sbjct: 466  PTDAKELGQKTAMHTKRDVSTPLRATENGIVDQ--------------------VLFTTNT 505

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +P
Sbjct: 506  EGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHAIP 565

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            SRM +  + E  L       G +  +   
Sbjct: 566  SRMTIAHLVECLLSKVGALRGCEGDATPF 594



 Score =  119 bits (297), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 79/455 (17%), Positives = 149/455 (32%), Gaps = 40/455 (8%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG   
Sbjct: 60  GVSQVLNRYTYASTLSHLRRTNT----PVGREGKLAKPRQLHNTHWGLVCPAETPEGQAC 115

Query: 581 GLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GLV +L+    V+        T +    +  +  +   +        ++      +    
Sbjct: 116 GLVKNLSLMCYVSVGSESTPITDFMSQRNMDLLEEYDPVVNPTATKVFVNGVWVGVHSQP 175

Query: 639 SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
           S    +V        +      I D  D   K        + P F+   D  +   G  +
Sbjct: 176 SQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVETDFKKPNRGSLI 235

Query: 697 QRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRS------- 747
             ++          + T G     A           + G+VE +DA              
Sbjct: 236 LDKSKIQKLQRDREIDTSGYSDEEAAQMKYGWRGLIQDGVVEYLDAEEEETAMIIMTPED 295

Query: 748 --VEGDLDPSTSGVDIYRLMKFQRSNQNT-------CVNQRPLVKVG--DEVRRNDIIAD 796
                +L      VD     + +R ++ +       C     ++  G     R +   + 
Sbjct: 296 LEDHQNLMSGVPVVDTASADRHKRISERSSVXTYTHCEIHPSMIXAGVLHYPRTDRYYSV 355

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA   + G   +DS+++++  +   +F S+    +    +   +
Sbjct: 356 MEYLKFRELPAGQNAIVAIACYSGNYQKDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGV 415

Query: 857 GPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        D   +       +D+ G++  G  V+  DI++GK  P         +K
Sbjct: 416 NVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPTDAKELGQK 475

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                        RD S  + +  +G V  V    
Sbjct: 476 T-------AMHTKRDVSTPLRATENGIVDQVLFTT 503


>gi|194320232|gb|ACF48351.1| DNA-dependent RNA polymerase II second largest subunit [Tephromela
            atra]
          Length = 317

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 58/385 (15%), Positives = 106/385 (27%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 71   LF-RSLFYRSYTDQEKR---IGMSVVEQFEKPMRSDTLKLKHGTYGKLDDDGIVAPGVRV 126

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S          
Sbjct: 127  SGEDIIIGKTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLS---------- 176

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 177  ----------TNADGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTGEG 226

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +          +S L    E  
Sbjct: 227  VVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSKLLR--EHG 284

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +                                                    +G + 
Sbjct: 285  YHSRGFEVM---------------------------------------------YNGHT- 298

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
               G         V +G  Y  +L 
Sbjct: 299  ---GR---KLVAQVFLGPTYYQRLR 317



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 67/172 (38%), Gaps = 15/172 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E     +  D   +       +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRSYTDQEKRIGMSVVEQFEKPMRSDTLKLKHGTYGKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           V+  DI++GK  P         ++        K    RDTS  + S  +G V
Sbjct: 126 VSGEDIIIGKTAPIAPDAEELGQRT-------KLHVKRDTSTPLRSTENGIV 170


>gi|198279463|emb|CAP04766.1| RNA polymerase beta subunit [Pinus echinata]
          Length = 264

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 151/246 (61%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IXGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 63.6 bits (153), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 49/214 (22%), Positives = 78/214 (36%), Gaps = 14/214 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             GD+        V V+++ KR IQ GDK+AGRHG
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHG 264


>gi|56406213|gb|AAV87490.1| RpoB [Pasteurella multocida subsp. septica]
          Length = 162

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 94/161 (58%), Positives = 120/161 (74%), Gaps = 1/161 (0%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 2   QFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+ 
Sbjct: 62  NSLSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDA 121

Query: 644 LVFCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            V CR   GE  L   ++I ++D S +QVVS+AA+LIPFLE
Sbjct: 122 FVTCRGEHGESGLYRPDEIHYMDVSTQQVVSVAAALIPFLE 162


>gi|194320138|gb|ACF48290.1| DNA-dependent RNA polymerase II second largest subunit [Candelaria
            concolor]
          Length = 324

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 60/385 (15%), Positives = 110/385 (28%), Gaps = 81/385 (21%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 18   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 77

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 78   LF-RSLFYRAYTDQGKR---IGVAVVEEFEKPMRSDTLKLKHGTYDKLDDDGIVAPGVRV 133

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q   S +        
Sbjct: 134  SGEDIIIGKTAPIAPDAEELGQRTKLHIKRDASTPLRSTENGIVDQVLLSNNQ------- 186

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR  KV +   +  Q GDK A RHG KG +      EDMPF +DG
Sbjct: 187  -------------DGLRFTKVRMRTTKVPQIGDKFASRHGQKGTIGITYRSEDMPFTRDG 233

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKV 1175
               D+++NP  +PSRM +  + E  L       G +  +         +IS L    E+ 
Sbjct: 234  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVQNISKLL--FEQG 291

Query: 1176 IGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
              +    E                                               +G + 
Sbjct: 292  YQSRGFEEM---------------------------------------------YNGHT- 305

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  G      V +G  Y  +L 
Sbjct: 306  ------GRKMVVQVFLGPTYYQRLR 324



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 65/184 (35%), Gaps = 22/184 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA   + G
Sbjct: 11  TNYGVRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 60

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +       
Sbjct: 61  YNQEDSVIMNQSSIDRGLFRSLFYRAYTDQGKRIGVAVVEEFEKPMRSDTLKLKHGTYDK 120

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GI+  G  V+  DI++GK  P         ++        K    RD S  + S  
Sbjct: 121 LDDDGIVAPGVRVSGEDIIIGKTAPIAPDAEELGQRT-------KLHIKRDASTPLRSTE 173

Query: 936 SGTV 939
           +G V
Sbjct: 174 NGIV 177


>gi|14971079|gb|AAK74104.1| RNA polymerase beta subunit [Bacillus thuringiensis]
          Length = 258

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 54/197 (27%), Positives = 90/197 (45%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K   +  +G           + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINXKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINXKLHIKNRLFNQRL 152


>gi|198279321|emb|CAP04778.1| RNA polymerase beta subunit [Pinus cembroides]
          Length = 272

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 98/238 (41%), Positives = 148/238 (62%), Gaps = 10/238 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE +TR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERVTREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           D+LVGK+TP+       TPE +LL+ IFG +    R++ L  P G  G V+DVR  NR
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINR 230



 Score = 67.4 bits (163), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 51/224 (22%), Positives = 80/224 (35%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERVTREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L         +++ R+ N++    
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINRV---- 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               B        V V+ + KR IQ G K+ GRHG KGI+S ILP
Sbjct: 232  ---BDSGXNAETVXVYXSQKRKIQVGXKVXGRHGXKGIISXILP 272


>gi|219564033|gb|ACL28200.1| RNA polymerase II second largest subunit [fungal sp. M145]
          Length = 287

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 99/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTQSMEFLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   I  G   
Sbjct: 61   LF-RSLFYRSYTDQEKR---IGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR     K    T+    E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELGQRTKSHSKRDASTALRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF ++G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYKQEDMPFTREG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVASLSGYEGDATPFTDVTVDSVSKLLR 271



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 66/177 (37%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTQSMEFLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GII  G  V+
Sbjct: 58  DRGLFRSLFYRSYTDQEKRIGMNVVEQFEKPFRSDTLKLKHGTYDKLDDDGIIAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        K+   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KSHSKRDASTALRSTENGIVDQVLITT 167


>gi|219564023|gb|ACL28195.1| RNA polymerase II second largest subunit [fungal sp. M132]
          Length = 285

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 55/293 (18%), Positives = 98/293 (33%), Gaps = 27/293 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G     
Sbjct: 62   -RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E+   +++
Sbjct: 118  EDIIIGKTAPIAPD---------------AEEMGQRTKAHIKRDASTPLRSTENGIVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 163  LI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRIEDMPFTSEGIV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 218  PDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSNLLR 270



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/158 (25%), Positives = 63/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA M + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 16  TRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 75

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +       +DE GI+  G  V+  DI++GK  P        
Sbjct: 76  IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIA---PDA 132

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           EE   R     KA   RD S  + S  +G V  V I  
Sbjct: 133 EEMGQRT----KAHIKRDASTPLRSTENGIVDQVLITT 166


>gi|260594113|gb|ACX46351.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  164 bits (416), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 87/158 (55%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGLGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++ +++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASAKMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|290760054|gb|ADD54504.1| RNA polymerase II second largest subunit [Salsuginea ramicola]
          Length = 594

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 47/269 (17%), Positives = 88/269 (32%), Gaps = 27/269 (10%)

Query: 892  DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
            D     +       +   +  + AI        +D+ +   S +   +    +F R   +
Sbjct: 350  DRYYSVMEYLKFRELPAGQNAIVAIACYSGNYQKDSVIMNQSSIDRGLF-RSLFYRAYTE 408

Query: 952  KNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVL 1008
            + +R   +    +E   +    + + L    Y +L +   +  G           K+  +
Sbjct: 409  QEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPI 465

Query: 1009 SSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPP 1068
             +D      ++           ++     +  Q                           
Sbjct: 466  PTDAKELGQKTAMHTKRDVSTPLRATENGIVDQ--------------------VLFTTNT 505

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +P
Sbjct: 506  EGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHAIP 565

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
            SRM +  + E  L       G +  +   
Sbjct: 566  SRMTIAHLVECLLSKVGALRGCEGDATPF 594



 Score =  118 bits (296), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 78/455 (17%), Positives = 144/455 (31%), Gaps = 40/455 (8%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
            +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG   
Sbjct: 60  GVSQVLNRYTYASTLSHLRRTNT----PVGREGKLAKPRQLHNTHWGLVCPAETPEGQAC 115

Query: 581 GLVSSLTSFARVNAYGF--IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           GLV +L+    V+        T +    +  +  +   +        ++      +    
Sbjct: 116 GLVKNLSLMCYVSVGSESTPITDFMSQRNMDLLEEYDPVVNPTATKVFVNGVWVGVHSQP 175

Query: 639 SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
           S    +V        +      I D  D   K        + P F+   D  +   G  +
Sbjct: 176 SQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVETDFKKPNRGSLI 235

Query: 697 QRQAVPLLKAEAPFVGT-GMESVVAKSSGAAIVA-KRAGIVEQVDAIRIVIRS------- 747
             ++          + T G     A           + G+VE +DA              
Sbjct: 236 LDKSKIQKLQRDREIDTSGYSDEEAAQMKYGWRGLIQDGVVEYLDAEEEETAMIIMTPED 295

Query: 748 --VEGDLDPSTSGVDIYRLMKFQR---------SNQNTCVNQRPLVKVGDEVRRNDIIAD 796
                +L      VD     + +R                      +V    R +   + 
Sbjct: 296 LEDHQNLMSGVPVVDTASADRHKRISERSSVXTYTHCEIHPSMIXARVLHYPRTDRYYSV 355

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
                  +L  G+N +VA   + G   +DS+++++  +   +F S+    +    +   +
Sbjct: 356 MEYLKFRELPAGQNAIVAIACYSGNYQKDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGV 415

Query: 857 GPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEK 911
              E        D   +       +D+ G++  G  V+  DI++GK  P         +K
Sbjct: 416 NVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPIPTDAKELGQK 475

Query: 912 LLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                        RD S  + +  +G V  V    
Sbjct: 476 T-------AMHTKRDVSTPLRATENGIVDQVLFTT 503


>gi|198279365|emb|CAP04717.1| RNA polymerase beta subunit [Pinus armandii]
          Length = 272

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 99/238 (41%), Positives = 148/238 (62%), Gaps = 10/238 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           D+LVGK+TP+       TPE +LL+ IFG +    R++ L  P G  G V+DVR  NR
Sbjct: 173 DVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINR 230



 Score = 73.6 bits (179), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 51/224 (22%), Positives = 81/224 (36%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L         +++ R+ N++    
Sbjct: 176  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLXAPIGGKGRVIDVRWINRV---- 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               B        V V+ + KR  Q GDK+ GRHGNKGI+S +LP
Sbjct: 232  ---BDSGXNAETVXVYXSQKRKXQVGDKVXGRHGNKGIISIVLP 272


>gi|319922011|gb|ADV78615.1| RNA polymerase beta subunit [Odontoglossum hybrid cultivar]
          Length = 300

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 81/268 (30%), Positives = 129/268 (48%), Gaps = 16/268 (5%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D +L     ++  +V 
Sbjct: 47   VQRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAAL-----INERLVY 100

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + +D    E  +L      R   ++ G    +G  
Sbjct: 101  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEARLLRN--LDRNGIVMLGSWIETGDI 158

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++   S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 159  LVGKLTPQTASEFSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK--- 215

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+
Sbjct: 216  ----GVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDM 271

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            V NPLGVPSRMNVGQIFE  LG A   L
Sbjct: 272  VFNPLGVPSRMNVGQIFECSLGLAGDLL 299



 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 96/234 (41%), Positives = 151/234 (64%), Gaps = 6/234 (2%)

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I+    +  +  S        L+ +QRSN+NTC++Q+  V+ G  +++  I+A G +T 
Sbjct: 7   KIIYTDTQKIIFSSNGDTLSIPLVMYQRSNKNTCMHQKTQVQRGKYIKKGQILAGGVATA 66

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+LVA+MPW GYNFED+ LI+ER+V ED++TS HI ++E+    T  GPE I
Sbjct: 67  GGELALGKNVLVAYMPWEGYNFEDAALINERLVYEDIYTSFHIRKYEIQTHVTSQGPERI 126

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP--MTPEEKLLRAIFGE 919
           T+DIP++    L+N+D  GI+ +G+ +  GDILVGK+TP+  S    TPE++LLRAI G 
Sbjct: 127 TKDIPHLEARLLRNLDRNGIVMLGSWIETGDILVGKLTPQTASEFSYTPEDRLLRAILGI 186

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID----KNERSISVEREQIELLAR 969
           +    ++TSLR+P G  G V+DVR  +R G+     +  R    ++ +I++  +
Sbjct: 187 QVSTSKETSLRLPIGGRGRVIDVRWIHRKGVSNSNPEKIRVYISQKREIKVGDK 240


>gi|312204336|gb|ADQ47485.1| RNA polymerase II second largest subunit [Gyalidea praetermissa]
          Length = 247

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 90/265 (33%), Gaps = 27/265 (10%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +++ +R  
Sbjct: 2    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRVYVEQEKRVG 60

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    E + L    Y +L +   I  G           K+  +  +   
Sbjct: 61   M---SMLEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIQQNSED 117

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +                  ++K+          L+ V
Sbjct: 118  PGQRTKIHTRRDASTPLRSTENGI------------------VDKVML--TTNAEGLKFV 157

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 158  KVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGITPDLIINPHAIPSRMTIA 217

Query: 1135 QIFETHLGWACVGLGKKIKSLINDY 1159
             + E  L       G +  +     
Sbjct: 218  HLIECQLSKVSSLRGFEGDATPFTE 242



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/162 (21%), Positives = 65/162 (40%), Gaps = 12/162 (7%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 1   SMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRVYVEQEKRVG 60

Query: 856 LGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +   E        +   +     + +D+ GII  G  V+  DI++GK  P  ++   P +
Sbjct: 61  MSMLEQFEKPLRSETLRLKHGTYEKLDDDGIIAPGVRVSGEDIIIGKTAPIQQNSEDPGQ 120

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +        K    RD S  + S  +G V  V +       K
Sbjct: 121 RT-------KIHTRRDASTPLRSTENGIVDKVMLTTNAEGLK 155


>gi|299013329|gb|ADJ00257.1| DNA-dependent RNA polymerase II subunit [Eutypa leptoplaca]
          Length = 254

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 52/271 (19%), Positives = 91/271 (33%), Gaps = 27/271 (9%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D  +R   +   
Sbjct: 2    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDCEKR---IGIN 57

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             IE   +    + + L +  Y +L +   I  G           K++ ++ +      R+
Sbjct: 58   TIETFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPINPENEEMGQRT 117

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
            +          ++     +                                LR VKV V 
Sbjct: 118  KVHVKRDASTPLRSTESGIIDS--------------------VVVTTNADGLRYVKVRVR 157

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E 
Sbjct: 158  TTKIPQIGDKFASRHGQKGTIGVTFRQEDMPFTREGIVPDIIINPHAIPSRMTIAHLIEC 217

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             L       G +  +          +S L  
Sbjct: 218  LLSKVSTLKGMEGDATPFTDVTVDSVSNLLR 248



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 35/151 (23%), Positives = 63/151 (41%), Gaps = 12/151 (7%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E
Sbjct: 1   KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDCEKRIGINTIE 60

Query: 861 ITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   D   + +     +D+ GII  G  V+  DI++GK +P       PE + +  
Sbjct: 61  TFEKPFRADTLRLKQGTYDKLDDDGIIAPGIRVSGEDIIIGKTSPIN-----PENEEMGQ 115

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                    RD S  + S  SG +  V +  
Sbjct: 116 RTKVHVK--RDASTPLRSTESGIIDSVVVTT 144


>gi|219564097|gb|ACL28232.1| RNA polymerase II second largest subunit [fungal sp. M293]
          Length = 287

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 55/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHIKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTSEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSNLLR 271



 Score = 85.5 bits (210), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/177 (22%), Positives = 66/177 (37%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA M + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 167


>gi|319922013|gb|ADV78616.1| RNA polymerase beta subunit [Odontoglossum hybrid cultivar]
 gi|319922015|gb|ADV78617.1| RNA polymerase beta subunit [Oncidium hybrid cultivar]
 gi|319922020|gb|ADV78619.1| RNA polymerase beta subunit [Oncidium hybrid cultivar]
 gi|319922022|gb|ADV78620.1| RNA polymerase beta subunit [Oncidium hybrid cultivar]
          Length = 300

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 82/267 (30%), Positives = 131/267 (49%), Gaps = 14/267 (5%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D  L     ++  +V 
Sbjct: 47   VQRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAVL-----INERLVY 100

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              I+    I K E    V  +  E + +D    +  L RN+  R   ++ G    +G   
Sbjct: 101  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEAHLLRNL-DRNGIVMLGSWIETGDIL 159

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  ++  +S  P  +  +  +  +       SL++       +++ R+ ++     
Sbjct: 160  VGKLTPQTASELSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK---- 215

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+V
Sbjct: 216  ---GVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMV 272

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGL 1148
             NPLGVPSRMNVGQIFE  LG A   L
Sbjct: 273  FNPLGVPSRMNVGQIFECSLGLAGDLL 299



 Score =  151 bits (382), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 96/234 (41%), Positives = 153/234 (65%), Gaps = 6/234 (2%)

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I+    +  +  S        L+ +QRSN+NTC++Q+  V+ G  +++  I+A G +T 
Sbjct: 7   KIIYTDTQKIIFSSNGDTLSIPLVMYQRSNKNTCMHQKTQVQRGKYIKKGQILAGGVATA 66

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+LVA+MPW GYNFED++LI+ER+V ED++TS HI ++E+    T  GPE I
Sbjct: 67  GGELALGKNVLVAYMPWEGYNFEDAVLINERLVYEDIYTSFHIRKYEIQTHVTSQGPERI 126

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM--TPEEKLLRAIFGE 919
           T+DIP++    L+N+D  GI+ +G+ +  GDILVGK+TP+  S +  TPE++LLRAI G 
Sbjct: 127 TKDIPHLEAHLLRNLDRNGIVMLGSWIETGDILVGKLTPQTASELSYTPEDRLLRAILGI 186

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID----KNERSISVEREQIELLAR 969
           +    ++TSLR+P G  G V+DVR  +R G+     +  R    ++ +I++  +
Sbjct: 187 QVSTSKETSLRLPIGGRGRVIDVRWIHRKGVSNSNPEKIRVYISQKREIKVGDK 240


>gi|224177813|gb|ACN38878.1| RNA polymerase II subunit [Dactylospora haliotrepha]
          Length = 586

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 94/616 (15%), Positives = 179/616 (29%), Gaps = 80/616 (12%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 40   GVSQVLNRFTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 95

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L     +     ++    + K    ++  +     +      ++      +  D 
Sbjct: 96   GLVKNLALMCYITVGTPMDPIVEFMKQRGMELLEEYEPYRSPNATKVFVNGVWVGVHRDP 155

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
            +    LV+       I      + D  D   K          P    ++  R      + 
Sbjct: 156  TRLVNLVYHLRRTNTISHEVGLVRDIRDREFKIYTDAGRVCRPLFVINNDPRSNNPGGLV 215

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGA-----AIVAKRAGIVEQVDAIRIVIRSVEGDL 752
                     +       + + +                + G+VE VDA       +    
Sbjct: 216  LTHD---HTDKLIRDRALPADMPPDERKKHVFGWEGLIKTGVVEYVDAEEEETVMIVMTP 272

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +       +    + Q  +    +N+R   KV   +         PS  LG       + 
Sbjct: 273  EDLEISRQVQAGYQ-QPEDXXEDLNKRVKAKVDKNLHTWTHCEIHPSMILG-------IC 324

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N                        ++       +G      D        
Sbjct: 325  ASIIPFPDHNQSPRN------------------TYQSAMGKQAMGVFLTNFDQRF----- 361

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +  + AI      +  D+ +   
Sbjct: 362  ------DTMSNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 415

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---I 989
            S +   +    +F R   D  +   SV    +E   +    E + +    Y +L E   +
Sbjct: 416  SSIDRGLF-RSLFYRAYTDAEKFMSSV---VVEAFEKPMRSETMRIKHGTYDKLDEDGLV 471

Query: 990  LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSIL 1049
              G           K+  +  +                  ++ +     K    T     
Sbjct: 472  CPGIRVSGDDIIIGKTAPIGGEA----------------SEIGQRKVHAKRDISTPLRST 515

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E    +++              R VKV +   +  Q GDK A RHG KG +      EDM
Sbjct: 516  ESGIVDRV-----MISTNSNGARFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDM 570

Query: 1110 PFLKDGTPVDIVLNPL 1125
            PF  +G   D+++NP 
Sbjct: 571  PFTVEGLTPDLIINPH 586



 Score =  107 bits (267), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 80/578 (13%), Positives = 166/578 (28%), Gaps = 71/578 (12%)

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILV 444
            T  +  S+    + D  K   +  G  ++  R    +      R          I    
Sbjct: 15  ITNGLKYSLATGNWGDQKKAMETKAGVSQVLNRFTFASTLSHLRRTNTPIGRDGKIAKPR 74

Query: 445 DLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLI 504
            L N    +         +      ++KN   +  + +   +   +  +    +   +  
Sbjct: 75  QLHNTHWGLVCPAETPEGQACG---LVKNLALMCYITVGTPMDPIVEFMKQRGMELLEEY 131

Query: 505 NAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL-GQGGVARARAGVEMRDVHP 563
                 +A   F     +    +    ++ + H RR + +  + G+ R     E +    
Sbjct: 132 EPYRSPNATKVFVNGVWVGVHRDPTRLVNLVYHLRRTNTISHEVGLVRDIRDREFK---- 187

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
                     T  G     +  + +  R N  G +      V     T+ +         
Sbjct: 188 --------IYTDAGRVCRPLFVINNDPRSNNPGGL------VLTHDHTDKL--------- 224

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEIL---VPREKIDFIDASPKQVVSIAASLIP 680
                     + +     +     R          +    ++++DA  ++ V I  +   
Sbjct: 225 ----------IRDRALPADMPPDERKKHVFGWEGLIKTGVVEYVDAEEEETVMIVMTPED 274

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
              +                    + +A            +   + I+   A I+   D 
Sbjct: 275 LEISRQVQ-AGYQQPEDXXEDLNKRVKAKVDKNLHTWTHCEIHPSMILGICASIIPFPDH 333

Query: 741 IRIVIRSVEGDLDPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
            +    + +  +     GV       +F   +      Q+PL                  
Sbjct: 334 NQSPRNTYQSAMGKQAMGVFLTNFDQRFDTMSNILYYPQKPL----------ATTRSMEF 383

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
               +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       
Sbjct: 384 LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDAEKFMSSVVV 443

Query: 860 E-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLR 914
           E     +  +   +       +DE G++C G  V+  DI++GK  P G            
Sbjct: 444 EAFEKPMRSETMRIKHGTYDKLDEDGLVCPGIRVSGDDIIIGKTAPIGGEAS-------- 495

Query: 915 AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            I   K    RD S  + S  SG V  V I       +
Sbjct: 496 EIGQRKVHAKRDISTPLRSTESGIVDRVMISTNSNGAR 533


>gi|152968496|gb|ABS50262.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968504|gb|ABS50266.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968508|gb|ABS50268.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968510|gb|ABS50269.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968512|gb|ABS50270.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968514|gb|ABS50271.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968526|gb|ABS50277.1| RNA polymerase II [Uebelinia kigesiensis subsp. kigesiensis]
 gi|152968528|gb|ABS50278.1| RNA polymerase II [Uebelinia kigesiensis subsp. ragazziana]
 gi|152968530|gb|ABS50279.1| RNA polymerase II [Uebelinia kigesiensis subsp. ragazziana]
          Length = 271

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 55/285 (19%), Positives = 88/285 (30%), Gaps = 23/285 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           N          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 265



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|152968502|gb|ABS50265.1| RNA polymerase II [Lychnis abyssinica]
          Length = 266

 Score =  164 bits (416), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 55/270 (20%), Positives = 86/270 (31%), Gaps = 23/270 (8%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +      + AI      +  D+ +   S +        +F R   D+ ++  ++ +
Sbjct: 14   HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLIK 72

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E      R           N          G           K+T L+ +          
Sbjct: 73   EDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTTPLAPEEAQGP----- 127

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                               +Y      +  R        Q         LR VKV V   
Sbjct: 128  -----------------AARYSRKDHSISLRHSESGIVDQVLLTTNADGLRFVKVRVRSV 170

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +
Sbjct: 171  RIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIM 230

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            G     +GK+  +         +IS     
Sbjct: 231  GKVAAHVGKEGDATPFTDVTVDNISKALQK 260



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 62/167 (37%), Gaps = 24/167 (14%)

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+PLV                      L  G N +VA   + GYN EDS+++++  +   
Sbjct: 1   QKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRG 50

Query: 838 VFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
            F S+    +    +      +E        +   +       +D+ G+   G  V+  D
Sbjct: 51  FFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGED 110

Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           +++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 111 VIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 148


>gi|198279519|emb|CAP04794.1| RNA polymerase beta subunit [Equisetum myriochaetum]
          Length = 259

 Score =  164 bits (416), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 107/238 (44%), Positives = 153/238 (64%), Gaps = 9/238 (3%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+E  +A  SG+ + ++R G V  +D  RI +   E              L+ ++
Sbjct: 1   CIVGTGLEGQIALDSGSCVTSEREGKVIYIDGQRITLFVDEETSINK-------NLLSYE 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW GYNFED+ L
Sbjct: 54  RSNNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPWEGYNFEDATL 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G++ +G+ V
Sbjct: 114 ISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDENGLVKLGSWV 173

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
             GD+LVGK+TP         PE KLL+AIFG +  + R+T L+VP G  G V+D++ 
Sbjct: 174 EAGDVLVGKLTPLDYLDTLGAPEGKLLQAIFGTELTNARETCLKVPVGFKGRVIDIKW 231


>gi|198279351|emb|CAP04710.1| RNA polymerase beta subunit [Pinus elliottii]
          Length = 273

 Score =  164 bits (416), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 101/245 (41%), Positives = 151/245 (61%), Gaps = 10/245 (4%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
            GTG+E   A  SG+  +A + G +E +DA+                       + +QRS
Sbjct: 1   AGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRS 52

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LIS
Sbjct: 53  NTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILIS 112

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  
Sbjct: 113 ERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIET 172

Query: 891 GDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR 
Sbjct: 173 GDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRV 232

Query: 949 GIDKN 953
               +
Sbjct: 233 DDSGD 237



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 64   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 122

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 123  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 176

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 177  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 234

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 235  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 273


>gi|219564027|gb|ACL28197.1| RNA polymerase II second largest subunit [fungal sp. M139]
          Length = 286

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 53/357 (14%), Positives = 98/357 (27%), Gaps = 75/357 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 5    ILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 63

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ ++      E  E   +           +       +  G           
Sbjct: 64   LFFRSYSDQEKKVGLNYTETFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIG 123

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+   Q       ++     +      + +                
Sbjct: 124  KTAPIDPENQDLGTRTAAHQKRDISTPLRSTENGIVDSVIMTVNA--------------- 168

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG V      EDMPF ++G   DI++N
Sbjct: 169  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTVGVTYRQEDMPFTREGITPDIIIN 223

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +                                
Sbjct: 224  PHAIPSRMTIAHLIECLLSKVSTLEGMEGD------------------------------ 253

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                   +TP F     + ++ +LR       G  ++Y+G 
Sbjct: 254  -----------------------ATP-FTDVTVDQVSDLLRKHGYQSRGFEVMYNGH 286



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 57/158 (36%), Gaps = 13/158 (8%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 16  TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 75

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E            +       +DE GI+  G  V+  DI++GK  P       P
Sbjct: 76  VGLNYTETFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID-----P 130

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           E + L             T LR        +VD  I  
Sbjct: 131 ENQDLGTRTAAHQKRDISTPLR---STENGIVDSVIMT 165


>gi|193201521|gb|ACF15968.1| RNA polymerase II subunit [Opegrapha rufescens]
          Length = 282

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 59/354 (16%), Positives = 101/354 (28%), Gaps = 79/354 (22%)

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     +  +     E
Sbjct: 4    THSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----E 59

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSD 1011
            +  SV    +E   R +  + +      Y +L +   +  G           K+    + 
Sbjct: 60   QQQSVGFNALEEFERPQRAQTMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAP 119

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
            +                E  QR  +  K          E    +++              
Sbjct: 120  M------------QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDRVL------LTTTEGK 161

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM
Sbjct: 162  RSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSRM 221

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +  + E  L       G +                                        
Sbjct: 222  TIAHLIECLLSKVSSITGHEGD-------------------------------------- 243

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                           +TP F       I+ +L+ A     G  ++Y+G  G   
Sbjct: 244  ---------------ATP-FTDITVSNISELLQFAGYQSRGFEMMYNGXXGRKL 281



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 67/177 (37%), Gaps = 10/177 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 4   THSMNYLRFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQS 63

Query: 854 TKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 EE  R              + +D+ G +  G  V+  DI++GK  P        
Sbjct: 64  VGFNALEEFERPQRAQTMRTRPGTYEKLDDDGFVPPGVRVSGEDIIIGKTAPFQAPMQEN 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQI 964
            E   R     K    RD S  + S  +G +  V +    G    + R+ + +  QI
Sbjct: 124 SEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRTTKVPQI 176


>gi|219564039|gb|ACL28203.1| RNA polymerase II second largest subunit [fungal sp. M160]
          Length = 286

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 56/295 (18%), Positives = 98/295 (33%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +    +E   + +    V +    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRSYVDQEKR---IGMAVVEQFEKPERRNTVRVKHGTYEKLDEDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ DL               +E  QR    +K    T     E    +
Sbjct: 117  SGEDIIIGKTAPMAPDL---------------EELGQRTTSHIKRDVSTPLRSTESGLVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLL-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTHQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTEVTVDSVSRLLR 271



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/171 (21%), Positives = 64/171 (37%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E       R+   V     + +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRSYVDQEKRIGMAVVEQFEKPERRNTVRVKHGTYEKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P         E+L +        DV        SG+   V+
Sbjct: 118 GEDIIIGKTAPMAPDL----EELGQRTTSHIKRDVSTPLRSTESGLVDQVL 164


>gi|193201493|gb|ACF15954.1| RNA polymerase II subunit [Lecanactis sp. Ertz 4780]
          Length = 255

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 54/273 (19%), Positives = 90/273 (32%), Gaps = 25/273 (9%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +     +  +     E+  SV   
Sbjct: 1    FRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----EQQQSVGFN 56

Query: 963  QIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRS 1019
             +E   + +  + +      Y +L +   +  G           K+    + +       
Sbjct: 57   ALEEFEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVSGEDIIIGKTAPFQAPM------- 109

Query: 1020 QWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVA 1079
                     E  QR  +  K          E    +K+              R VKV   
Sbjct: 110  -----QENSEGGQRTKDHTKRDVSAPLRSTEAGIIDKVL------LTTTEGKRSVKVRTR 158

Query: 1080 MKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFET 1139
              +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + E 
Sbjct: 159  TTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLIINPHAIPSRMTIAHLIEC 218

Query: 1140 HLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
             L       G++  +         DIS L  F 
Sbjct: 219  LLSKVSSITGREGDATPFTDITVSDISELLEFA 251



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 65/169 (38%), Gaps = 10/169 (5%)

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE- 860
             DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    +       E 
Sbjct: 1   FRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEE 60

Query: 861 ----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAI 916
                            + +D+ G +  G  V+  DI++GK  P         E   R  
Sbjct: 61  FEKPQKSQTMRTRPGTYEKLDDDGFVSPGVRVSGEDIIIGKTAPFQAPMQENSEGGQRT- 119

Query: 917 FGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQI 964
              K    RD S  + S  +G +  V +    G    + R+ + +  QI
Sbjct: 120 ---KDHTKRDVSAPLRSTEAGIIDKVLLTTTEGKRSVKVRTRTTKVPQI 165


>gi|260593997|gb|ACX46293.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594021|gb|ACX46305.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITYKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D   T+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALFTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|148628038|gb|ABQ97024.1| RNA polymerase II second largest subunit [Phialophora verrucosa]
          Length = 318

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 60/381 (15%), Positives = 104/381 (27%), Gaps = 75/381 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 13   MANILYYPQKPLARTMVMDYLKFRELPAGQNAIVAIACYSGYNQEDSVVMNQSSIDRGLF 72

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ +       EQ E   R+          +       +  G        
Sbjct: 73   -RSLFYRTYQDQEKVVGHAVLEQFEKPTRNDTLRLKHGTYDKIDEDGIVAPGVRVSGEDI 131

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D                +E  QR  + +K    T     E    +++   
Sbjct: 132  IMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGIVDQVML- 175

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G   D+
Sbjct: 176  ----STNSEGYRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGIVPDL 231

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +  +          IS L   +     +  
Sbjct: 232  IINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQISELLRRMG--YHSRG 289

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +G +    G 
Sbjct: 290  FEVM---------------------------------------------YNGHT----GR 300

Query: 1241 TGEPFDRPVTVGYIYMLKLNH 1261
                    V +G  Y  +L H
Sbjct: 301  ---KLVAQVFLGPTYYQRLRH 318



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/173 (21%), Positives = 64/173 (36%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A     D     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   FDQRMETMANILYYPQKPLARTMVMDYLKFRELPAGQNAIVAIACYSGYNQEDSVVMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    ++   +       E        D   +       IDE GI+  G  
Sbjct: 66  SIDRGLFRSLFYRTYQDQEKVVGHAVLEQFEKPTRNDTLRLKHGTYDKIDEDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++GK  P         E+L +        DV        SG+   V+
Sbjct: 126 VSGEDIIMGKTAPMAPDA----EELGQRQKQHIKRDVSTPLRSTESGIVDQVM 174


>gi|56694366|gb|AAW22923.1| RNA polymerase II second largest subunit [Trimenia moorei]
          Length = 531

 Score =  164 bits (415), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 68/436 (15%), Positives = 115/436 (26%), Gaps = 82/436 (18%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                        I   ++     + I   +     R+T             V+   L+  
Sbjct: 178  EEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 236

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 237  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSID 294

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   +F R   D+ ++  ++ +E      R+          +          G    
Sbjct: 295  RGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVS 353

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++ D                        E    +Y         R    
Sbjct: 354  GEDVIIGKTTPIAQD------------------------EGQPSRYTRRDHSTSLRHSES 389

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                Q         LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G 
Sbjct: 390  GMVDQVLLTTNADGLRFVKVRMRSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 449

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DI++NP  +PSRM +GQ+           +GK+                         
Sbjct: 450  TPDIIVNPHAIPSRMTIGQLXXXXXXXXXAHMGKEGD----------------------- 486

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                          +TP F     + I+  L        G   +
Sbjct: 487  ------------------------------ATP-FTDVTVDNISKALHKCGYQMRGFETM 515

Query: 1237 YDGLTGEPFDRPVTVG 1252
            Y+G TG      + +G
Sbjct: 516  YNGHTGRRLSAMIFLG 531



 Score =  101 bits (252), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 53/362 (14%), Positives = 106/362 (29%), Gaps = 33/362 (9%)

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
             F      G    P   V   +     V ++      R I      L  D       +F
Sbjct: 55  KIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLF 114

Query: 647 CRCAGEEILVPREKIDFI---DASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
                  ++  ++                 +A   I +++ ++    ++   +       
Sbjct: 115 IVEKQRLLIKKKDIRALQLRESVEEGWHDLVAKGFIEYVDTEEEETTMISMTISDLVSAR 174

Query: 704 LKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IY 762
              E  +  T       +   + I+   A I+   D  +    + +  +     G+    
Sbjct: 175 HNPEEAYSET---YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTN 231

Query: 763 RLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
             ++           Q+PLV                      L  G N +VA   + GYN
Sbjct: 232 YQLRMDTLAYVLYYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAISCYSGYN 281

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 282 QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLD 341

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +    P                RD S  +    SG
Sbjct: 342 DDGLAPPGTRVSGEDVIIGKTTPIAQDEGQP-----------SRYTRRDHSTSLRHSESG 390

Query: 938 TV 939
            V
Sbjct: 391 MV 392


>gi|152968520|gb|ABS50274.1| RNA polymerase II [Uebelinia kiwuensis subsp. erlangeriana]
 gi|152968524|gb|ABS50276.1| RNA polymerase II [Uebelinia kiwuensis subsp. erlangeriana]
 gi|152968534|gb|ABS50281.1| RNA polymerase II [Uebelinia kiwuensis]
          Length = 271

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/285 (18%), Positives = 88/285 (30%), Gaps = 23/285 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           +          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 265



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|319921999|gb|ADV78611.1| RNA polymerase beta subunit [x Beallara hybrid cultivar]
 gi|319922001|gb|ADV78612.1| RNA polymerase beta subunit [x Beallara hybrid cultivar]
          Length = 300

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 81/268 (30%), Positives = 128/268 (47%), Gaps = 16/268 (5%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  +  G IL G +   G   +   + +L A    +  +  D  L     ++  +V 
Sbjct: 47   VQRGKYIKKGQILAGGVATAG-GELALGKNVLVAYMPWEGYNFEDAVL-----INERLVY 100

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDK-DDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
              I+    I K E    V  +  E + +D    E  +L      R   ++ G    +G  
Sbjct: 101  EDIYTSFHIRKYEIQTHVTSQGPERITKDIPHLEARLLRN--LDRNGIVMLGSWIETGDI 158

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K T  ++   S  P  +  +  +  +       SL++       +++ R+ ++    
Sbjct: 159  LVGKLTPQTASEFSYTPEDRLLRAILGIQVSTSKETSLRLPIGGRGRVIDVRWIHRK--- 215

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                 +       ++V+++ KR I+ GDK+AGRHGNKGI+S+ILP +DMP+L+DGTPVD+
Sbjct: 216  ----GVSNSNPEKIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDM 271

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            V NPLGVPSRMNVGQIFE  LG A   L
Sbjct: 272  VFNPLGVPSRMNVGQIFECSLGLAGDLL 299



 Score =  151 bits (381), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 96/234 (41%), Positives = 152/234 (64%), Gaps = 6/234 (2%)

Query: 742 RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
           +I+    +  +  S        L+ +QRSN+NTC++Q+  V+ G  +++  I+A G +T 
Sbjct: 7   KIIYTDTQKIIFSSNGDTLSIPLVMYQRSNKNTCMHQKTQVQRGKYIKKGQILAGGVATA 66

Query: 802 LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
            G+LALG+N+LVA+MPW GYNFED++LI+ER+V ED++TS HI ++E+    T  GPE I
Sbjct: 67  GGELALGKNVLVAYMPWEGYNFEDAVLINERLVYEDIYTSFHIRKYEIQTHVTSQGPERI 126

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP--MTPEEKLLRAIFGE 919
           T+DIP++    L+N+D  GI+ +G+ +  GDILVGK+TP+  S    TPE++LLRAI G 
Sbjct: 127 TKDIPHLEARLLRNLDRNGIVMLGSWIETGDILVGKLTPQTASEFSYTPEDRLLRAILGI 186

Query: 920 KAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID----KNERSISVEREQIELLAR 969
           +    ++TSLR+P G  G V+DVR  +R G+     +  R    ++ +I++  +
Sbjct: 187 QVSTSKETSLRLPIGGRGRVIDVRWIHRKGVSNSNPEKIRVYISQKREIKVGDK 240


>gi|2662399|gb|AAB88270.1| RNA polymerase beta subunit [Plasmodium berghei]
          Length = 171

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/211 (27%), Positives = 86/211 (40%), Gaps = 41/211 (19%)

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG+KG++S I    DMP+L +    D+ ++ +G+PSR+N+GQI E   G   + L  + 
Sbjct: 2    RHGHKGVISYINDINDMPYLNNKIQPDLFVSAIGIPSRINIGQILEGIYGLNSLYLNNRY 61

Query: 1153 KSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFD 1212
                N      +         K     +       Y+ +                     
Sbjct: 62   IISNNLNTNYYNNYINNFNYYKYNYNNNFEFNKISYNYN--------------------- 100

Query: 1213 GADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARST 1272
                                +  L +  TG      + +  IY  KL HMV DK+  R  
Sbjct: 101  --------------------KYFLKNPFTGHLIQNSICLNNIYYYKLVHMVKDKLRYRFI 140

Query: 1273 GSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQ 1303
            G YS +TQQP+ G + +GGQR GEMEVW ++
Sbjct: 141  GLYSELTQQPVKGNTKQGGQRFGEMEVWALE 171


>gi|223585643|gb|ACM91692.1| ribosomal polymerase subunit beta [Staphylococcus sp. KS-SP_14]
          Length = 168

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 101/168 (60%), Positives = 129/168 (76%), Gaps = 2/168 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+
Sbjct: 61  KVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEAP 168


>gi|193201469|gb|ACF15942.1| RNA polymerase II subunit [Arthonia sp. Ertz 7775]
          Length = 290

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 52/359 (14%), Positives = 100/359 (27%), Gaps = 84/359 (23%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 7    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 66

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 67   LYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 126

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L +       R +          ++     +  Q                      
Sbjct: 127  KTAPLPAAAEERGVRLEQHTKRDVSTPLRSTEAGIIDQVL-------------------- 166

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 167  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLIPDLIIN 225

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 226  PHAIPSRMTIAHLIECLLPKVAATNAYEGD------------------------------ 255

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
                                   +TP F     E ++ +L  +   + G  ++Y+G TG
Sbjct: 256  -----------------------ATP-FTEITVEMVSEILEKSGYQKRGFEVMYNGHTG 290



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 67/196 (34%), Gaps = 19/196 (9%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S++   +    +   +   E            +       +D+ G
Sbjct: 51  SVIMNQSAIDRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  DI++GK  P   +      +L          DV        +G+   V+
Sbjct: 111 IVAPGVRVSGDDIIIGKTAPLPAAAEERGVRL----EQHTKRDVSTPLRSTEAGIIDQVL 166

Query: 941 DVRIFNRHGIDKNERS 956
              +  +  +    R+
Sbjct: 167 VTSVDGKKNVKIRTRT 182


>gi|194320153|gb|ACF48300.1| DNA-dependent RNA polymerase II second largest subunit [Catolechia
            wahlenbergii]
          Length = 317

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/382 (15%), Positives = 104/382 (27%), Gaps = 75/382 (19%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 11   DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 70

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ +R  +   EQ E   R    +              +  G      
Sbjct: 71   LF-RSLFYRAYTDQEKRVGNHIVEQFEKPMRSDTLKLKHGTYEKLDDDGIVAPGVRISGE 129

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+ +++ D      R++                 +K    T     E+   +++ 
Sbjct: 130  DIIIGKTALIAPDAEELGQRTKL---------------HIKRDVSTPLRSTENGIVDQVL 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                 D +     R VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 175  LTTNADGL-----RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVP 229

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
            D+V+NP  +PSRM +  + E  L       G +  +          +S L          
Sbjct: 230  DLVINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVDSVSKLLRESGYQSRG 289

Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
                                                                +G +    
Sbjct: 290  FEVM-----------------------------------------------YNGHT---- 298

Query: 1239 GLTGEPFDRPVTVGYIYMLKLN 1260
            G         V +G  Y  +L 
Sbjct: 299  GR---KLVAQVFLGPTYYQRLR 317



 Score = 81.7 bits (200), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 65/173 (37%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            +QR              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 6   YDQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 65

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +       E     +  D   +     + +D+ GI+  G  
Sbjct: 66  SIDRGLFRSLFYRAYTDQEKRVGNHIVEQFEKPMRSDTLKLKHGTYEKLDDDGIVAPGVR 125

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  DI++GK            E+L +        DV        +G+   V+
Sbjct: 126 ISGEDIIIGKTALIAPDA----EELGQRTKLHIKRDVSTPLRSTENGIVDQVL 174


>gi|260594101|gb|ACX46345.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 112/158 (70%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRGSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N  GF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQCGFLESPYRVVKDALVTDEIVFLSAIEEPDHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|186694355|gb|ACC86151.1| DNA-directed RNA polymerase beta subunit [Campylobacter sp. 24/06]
          Length = 173

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 93/173 (53%), Positives = 126/173 (72%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RRLSALG+GG+ + RAG+E+RDVH THYGRICP ET EG NIGL++
Sbjct: 1   FMDQTNPLSEVTHKRRLSALGEGGLVKERAGLEVRDVHSTHYGRICPVETPEGQNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           +L ++++VN  GF+E PYRKV + KV+++VVYL+A +EEN  IA A++ LD  G+  E+ 
Sbjct: 61  TLATYSKVNDLGFVEAPYRKVVNAKVSDEVVYLTATQEENLVIAAASTKLDSKGNIVEDF 120

Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           V  R  GE IL  ++++  ID     +V + ASLIPFLE+DD+NR LMG NMQ
Sbjct: 121 VEARKDGETILAKKDEVQLIDLCSGMIVGVTASLIPFLEHDDANRALMGPNMQ 173


>gi|46277300|gb|AAS86840.1| DNA-dependent RNA polymerase II [Ascobolus denudatus]
          Length = 520

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 52/292 (17%), Positives = 97/292 (33%), Gaps = 27/292 (9%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 242  ANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF- 300

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R        +E   +    E + L    Y +L E   +  G      
Sbjct: 301  RSLFYRAYLDQEKRVGM---SVVEEFEKPHRSETLRLKHGTYDKLDEDGLVAPGVRISGE 357

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D      R+++         ++     +                  ++
Sbjct: 358  DIIIGKTAPIAPDSEELGQRTKYHTKRDVSTPLRSTENGI------------------VD 399

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
            K+          L+ VKV +   +  Q GDK A RHG KG +     CEDMPF  +G   
Sbjct: 400  KVML--TTNASGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRCEDMPFTTEGVVP 457

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 458  DLIINPHAIPSRMTIAHLIECQLSKVASLRGFEGDATPFTEVTVDSVSSLLR 509



 Score = 86.3 bits (212), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 67/481 (13%), Positives = 124/481 (25%), Gaps = 87/481 (18%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +S +   RR   +
Sbjct: 5   EFMSQRNMEALEEYEPTRSPNATKI------FVNGVWVGVHRDPAQLVSTVQSLRRTGVI 58

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAETSE-------GHNIGLVSSLTSFARVNAYGF 597
                           +         P    E          + L          +    
Sbjct: 59  SPEISLVRDIRDREFKIFTDAGRVCRPLYVVETTDDNGRQGELALQKHHIEKLEDDKELP 118

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP 657
           +E  Y           V Y+ A EEE   I  +           E+L   R       V 
Sbjct: 119 LEERY-GWDGLLRDGVVEYIDAEEEETVMITMS----------PEDLEISRQVQAGYHVE 167

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMES 717
            E+                        D + R+    +M                     
Sbjct: 168 AEQ------------------------DLAKRIKASSSMNT----------------HTW 187

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CV 776
              +   + I+   A I+   D  +    +                         N    
Sbjct: 188 THCEIHPSMILGVCASIIPFPDHNQSPRNTXXXXXXXXXXXXXXXXXXXXXXXXANILYY 247

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
            Q+PL                      +L  G+N +VA   + GYN EDS+++++  +  
Sbjct: 248 PQKPL----------ATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDR 297

Query: 837 DVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPG 891
            +F S+    +    +   +   E        +   +       +DE G++  G  ++  
Sbjct: 298 GLFRSLFYRAYLDQEKRVGMSVVEEFEKPHRSETLRLKHGTYDKLDEDGLVAPGVRISGE 357

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           DI++GK  P         ++        K    RD S  + S  +G V  V +       
Sbjct: 358 DIIIGKTAPIAPDSEELGQRT-------KYHTKRDVSTPLRSTENGIVDKVMLTTNASGL 410

Query: 952 K 952
           K
Sbjct: 411 K 411


>gi|148767666|gb|ABR10825.1| RNA polymerase beta subunit [Bartonella silvicola]
          Length = 155

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 109/155 (70%), Positives = 126/155 (81%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL 
Sbjct: 1   QTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           +FARVN YGFIE+PYRK+ DGKVT +VVYLSAMEE   Y+AQANSSLD +G FTEE V C
Sbjct: 61  TFARVNKYGFIESPYRKIIDGKVTTEVVYLSAMEEAKHYVAQANSSLDSEGRFTEEFVVC 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           R AGE ++ PRE +D +D SPKQ+VS+AA+LIPFL
Sbjct: 121 RHAGEVLMAPREHVDLMDVSPKQLVSVAAALIPFL 155


>gi|198279405|emb|CAP04737.1| RNA polymerase beta subunit [Pinus pinea]
          Length = 272

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 101/244 (41%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 234  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 272


>gi|74099872|gb|AAZ99145.1| RpoB [Staphylococcus fleurettii]
 gi|74099894|gb|AAZ99156.1| RpoB [Staphylococcus sciuri subsp. carnaticus]
 gi|74099896|gb|AAZ99157.1| RpoB [Staphylococcus sciuri subsp. rodentium]
 gi|74099902|gb|AAZ99160.1| RpoB [Staphylococcus vitulinus]
          Length = 161

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 98/161 (60%), Positives = 124/161 (77%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV     +VT+ + YL+A EE++  +AQANS LDE G F ++ V CR  G+   
Sbjct: 61  IETPYRKVNIETNQVTDRIDYLTADEEDSYVVAQANSVLDETGKFVDDEVLCRFRGDNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            P+E++D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 KPKERMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|168809728|gb|ACA29583.1| RNA polymerase beta subunit [Streptococcus infantarius subsp.
            infantarius]
          Length = 134

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/138 (43%), Positives = 80/138 (57%), Gaps = 6/138 (4%)

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
            G     K T      +S   R     F  +  +V+     +    +     +      KI
Sbjct: 3    GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDV------KI 56

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD++  GV  +V+V++A KR I+ GDKMAGRHGNKG+VSR++P EDMP+L DGTP
Sbjct: 57   FTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRVVPVEDMPYLPDGTP 116

Query: 1118 VDIVLNPLGVPSRMNVGQ 1135
            VDI+LNPLGVPSRMN+GQ
Sbjct: 117  VDIMLNPLGVPSRMNIGQ 134



 Score = 54.7 bits (130), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/63 (61%), Positives = 47/63 (74%)

Query: 889 NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
             GDILVGK+TPKGE  ++ EE+LL AIFG+K+ +VRDTSLRVP G  G V DV+IF R 
Sbjct: 1   KEGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRA 60

Query: 949 GID 951
             D
Sbjct: 61  NGD 63


>gi|198279333|emb|CAP04701.1| RNA polymerase beta subunit [Pinus banksiana]
          Length = 274

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 101/246 (41%), Positives = 151/246 (61%), Gaps = 10/246 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPKIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINR 232

Query: 948 HGIDKN 953
                +
Sbjct: 233 VDDSGD 238



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 65   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 123

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 124  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 177

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 178  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRVD--D 235

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 236  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 274


>gi|198279391|emb|CAP04730.1| RNA polymerase beta subunit [Pinus brutia]
          Length = 271

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 101/244 (41%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 69.7 bits (169), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 53/223 (23%), Positives = 83/223 (37%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+ + KR IQ GDK+ GRHGNKG +S +L
Sbjct: 234  SGDNAE-----TVXVYXSQKRKIQVGDKVXGRHGNKGXISIVL 271


>gi|294721607|gb|ADF32950.1| RNA polymerase II second largest subunit [Sirodesmium olivaceum]
          Length = 274

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 48/287 (16%), Positives = 90/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RSLFY 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + L    Y +L +   +  G           
Sbjct: 62   RAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVSGDDIIIG 118

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + +D      ++           ++     +  Q                      
Sbjct: 119  KTAPIPTDAKELGQKTTLHTKRDVSTPLRSTENGIVDQ--------------------VL 158

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 159  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 219  PHAIPSRMTIAHLVECLLSKVGALKGAEGDATPFTDVTVDSVSKLLE 265



 Score = 79.0 bits (193), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 63/171 (36%), Gaps = 19/171 (11%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ G++  G  V+
Sbjct: 52  DRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             DI++GK  P      T  ++L +        DV        +G+   V+
Sbjct: 112 GDDIIIGKTAPI----PTDAKELGQKTTLHTKRDVSTPLRSTENGIVDQVL 158


>gi|225698431|gb|ACO07333.1| RpoB [Gallibacterium sp. TIS12317]
          Length = 160

 Score =  164 bits (415), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 94/160 (58%), Positives = 119/160 (74%), Gaps = 1/160 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V
Sbjct: 61  LSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTFV 120

Query: 646 FCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             R   GE  L   E I ++D S +QVVS+AA+LIPFLE+
Sbjct: 121 TARGEHGESGLYRPEDIHYMDISTQQVVSVAAALIPFLEH 160


>gi|74099898|gb|AAZ99158.1| RpoB [Staphylococcus succinus subsp. casei]
 gi|74099900|gb|AAZ99159.1| RpoB [Staphylococcus succinus subsp. succinus]
          Length = 161

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLETHSITDKIDYLTADEEDSYVVAQANSVLDENGRFVDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|14971061|gb|AAK74095.1| RNA polymerase beta subunit [Bacillus cereus]
          Length = 258

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYY---IGKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDDEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.5 bits (145), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + ++ Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDDEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|260593977|gb|ACX46283.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 85/157 (54%), Positives = 113/157 (71%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ     + LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NI
Sbjct: 2   QLSQFMGQESPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 61

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++    
Sbjct: 62  GLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVL 121

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 122 IDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|219564041|gb|ACL28204.1| RNA polymerase II second largest subunit [fungal sp. M168]
 gi|219564067|gb|ACL28217.1| RNA polymerase II second largest subunit [fungal sp. M193]
          Length = 287

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/295 (18%), Positives = 97/295 (32%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSVQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 271



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|283806288|dbj|BAI66384.1| RNA polymerase second largest subunit [Kalmusia brevispora]
          Length = 304

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 94/290 (32%), Gaps = 26/290 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 8    YPQKPLATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 66

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 67   RAYTEQEKR---IGVNVLEQFEKPTRMDTMRMKGGTYDKLDDDGIVAPGVRVSGDDIIIG 123

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  + +D                 E  Q+     K    T     E+   +++      
Sbjct: 124  KTAPIPNDE--------------NKEMGQKLANHTKRDVSTPLRSTENGLVDQVLF---- 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF +DG   DIV+N
Sbjct: 166  -TTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTRDGLTPDIVIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLE 1173
            P  +PSRM +  + E  L        ++  +          +S L     
Sbjct: 225  PHAIPSRMTIAHLVECLLSKVGAINAQEGDATPFCGVTVDQVSDLLEGAN 274



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 62/176 (35%), Gaps = 18/176 (10%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 2   MMNVLYYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIACYSGYNQEDSVIM 51

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +D+ GI+  
Sbjct: 52  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRMDTMRMKGGTYDKLDDDGIVAP 111

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           G  V+  DI++GK  P          ++ + +      DV        +G+   V+
Sbjct: 112 GVRVSGDDIIIGKTAPIPNDENK---EMGQKLANHTKRDVSTPLRSTENGLVDQVL 164


>gi|198279415|emb|CAP04742.1| RNA polymerase beta subunit [Pinus leiophylla]
          Length = 271

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 101/244 (41%), Positives = 151/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 76.3 bits (186), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 54/223 (24%), Positives = 85/223 (38%), Gaps = 14/223 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 176  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 233

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
             GD+        V V+++ KR IQ GDK+AGRHG KGI+S +L
Sbjct: 234  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGXKGIISIVL 271


>gi|151564512|gb|ABS17615.1| RpoB [Campylobacter canadensis]
          Length = 177

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 98/177 (55%), Positives = 132/177 (74%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIG
Sbjct: 1   LSQFMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT 641
           L++SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  
Sbjct: 61  LINSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNII 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
           ++L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG NMQ+
Sbjct: 121 DDLLEARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMGPNMQQ 177


>gi|74099870|gb|AAZ99144.1| RpoB [Staphylococcus equorum subsp. linens]
          Length = 161

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 97/161 (60%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V CR  G   +
Sbjct: 61  IETPYRKVDLETHSITDQIDYLTADEEDSYVVAQANSVLDENGRFVEDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|239909267|gb|ACS32292.1| RNA polymerase beta subunit [Corynebacterium sp. 1119]
          Length = 129

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 48/93 (51%), Positives = 62/93 (66%), Gaps = 8/93 (8%)

Query: 1207 STPVFDGADEEAINSMLRMADLDESG--------QSILYDGLTGEPFDRPVTVGYIYMLK 1258
            +TPVFDGA  E I  +L     D  G        ++ L+DG +GEPF  PV VG  YMLK
Sbjct: 37   ATPVFDGATNEEIEGLLGSTLPDRDGNRLVDKFGKAKLFDGRSGEPFKYPVCVGEKYMLK 96

Query: 1259 LNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGG 1291
            L+H+V +K++ARSTG YS++TQQPLGGK+  GG
Sbjct: 97   LHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 129


>gi|193201483|gb|ACF15949.1| RNA polymerase II subunit [Enterographa sp. Ertz 9770]
          Length = 277

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/352 (15%), Positives = 102/352 (28%), Gaps = 79/352 (22%)

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                S +   +  + AI      +  D+ +   S +   +    ++  +     E+  +V
Sbjct: 2    YLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFRSFLYRTYI----EQQKAV 57

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
                ++   +    + +      Y +L +   +  G           K+    + +    
Sbjct: 58   GFNALDEFEKPVRQQTLRTRPGTYEKLDDDGFVSPGIRVSGDDIIIGKTAPFQNAMQDNA 117

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
                        E  QR  +  +          E    +K+              R VK+
Sbjct: 118  ------------EGGQRTKQHTRRDVSAPLRSTEAGIVDKVL------VTTTEGRRSVKI 159

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
                 +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM V  +
Sbjct: 160  RTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDLIINPHAIPSRMTVAHL 219

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRV 1196
             E  L       G +                                             
Sbjct: 220  IECLLSKVSATQGLEGD------------------------------------------- 236

Query: 1197 AEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                      +TP F       I+++LR +     G  ++ +G TG      
Sbjct: 237  ----------ATP-FTDVTVSEISNLLRGSGYQSRGLELMRNGYTGRKLMAQ 277



 Score = 74.3 bits (181), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 29/164 (17%), Positives = 60/164 (36%), Gaps = 6/164 (3%)

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
              +  +L  G+N +VA   + GYN EDS+++++  +   +F S     +    +     
Sbjct: 1   EYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFRSFLYRTYIEQQKAVGFN 60

Query: 858 -----PEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
                 + + +          + +D+ G +  G  V+  DI++GK  P   +     E  
Sbjct: 61  ALDEFEKPVRQQTLRTRPGTYEKLDDDGFVSPGIRVSGDDIIIGKTAPFQNAMQDNAEGG 120

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            +        DV        +G+   V+      R  +    R+
Sbjct: 121 -QRTKQHTRRDVSAPLRSTEAGIVDKVLVTTTEGRRSVKIRTRA 163


>gi|330785402|gb|AEC46507.1| RNA polymerase II second largest subunit [Sclerophyton elegans]
          Length = 291

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 52/365 (14%), Positives = 98/365 (26%), Gaps = 79/365 (21%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +         +   +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLAVTRAMDYMQFKELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL---MEILCGQNAVSGPK 1000
             +  +     E+  +V    +E   +      +      Y +L     +  G        
Sbjct: 62   FYRTYI----EQQGTVGFNTLEEFEKPAKQNTMRTRPGTYEKLDIDGFVPPGVRVSGDDI 117

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +       Q  +   + +       +     +                 
Sbjct: 118  IIGKTAPFQAPMQENAEGGQRNKQHTRRDCSAPLRSTEAGIIDRVL-------------- 163

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+
Sbjct: 164  ----VTNTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYGQEDMPFTTDGLVPDL 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVAATKGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                      +TP         I+S+L+ +     G  ++++G 
Sbjct: 253  --------------------------ATPX-TNVTVSDISSLLKESGYQSRGFEMMHNGH 285

Query: 1241 TGEPF 1245
            TG   
Sbjct: 286  TGRKL 290



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 70/196 (35%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL           +          +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------AVTRAMDYMQFKELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +            E        +         + +D  G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQQGTVGFNTLEEFEKPAKQNTMRTRPGTYEKLDIDGFVPPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V + N  G
Sbjct: 114 GDDIIIGKTAPFQAPMQENAEGGQR----NKQHTRRDCSAPLRSTEAGIIDRVLVTNTEG 169

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 170 KRSVKVRTRTTKVPQI 185


>gi|82706465|gb|ABB89610.1| RNA polymerase II second largest subunit [Dermea acerina]
          Length = 594

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 103/613 (16%), Positives = 190/613 (30%), Gaps = 80/613 (13%)

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             ++ +SQ+         ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 50   STAGVSQVLNRYTFSXTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 105

Query: 578  HNIGLVSSLT--SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L    +  V         +    + +V  +   L +      ++      + 
Sbjct: 106  QACGLVKNLALMCYVTVGTPSDPIIEFMIQRNMEVLEEYEPLRSPNATKVFVNGVWVGVH 165

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMG 693
             D       V        I      I D  D   K          P F+ +++ +    G
Sbjct: 166  RDPGHLVANVQHLXRSHMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIDNNVDSANKG 225

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA--IVAKRAGIVEQVDAIRI---VIRSV 748
              +  +       E   +   M+     +SG         +G+VE VDA      +I   
Sbjct: 226  NLILNKEHIRRLEEDQMMPANMDQDQKAASGYFGFQGLINSGVVEYVDAEEEETIMIVMT 285

Query: 749  EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALG 808
              DLD S      Y++      +++  +N+R    +             PS  LG     
Sbjct: 286  PEDLDISRQLQAGYQIAP----DESGDLNKRVKAPMNPTAHIWTHCEIHPSMILG----- 336

Query: 809  RNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNV 868
              +  + +P+  +N                        ++       +G      D    
Sbjct: 337  --ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGVFLTNFDQRM- 375

Query: 869  SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                        +  +             +       +   +  + AI      +  D+ 
Sbjct: 376  ----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSV 425

Query: 929  LRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME 988
            +   S +   +    +F R   D+ +R   +    +E   +    + + L    Y +L +
Sbjct: 426  IMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRSDTLKLKHGTYDKLDD 481

Query: 989  ---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               +  G           K+  ++ D                +E  QR    +K    T 
Sbjct: 482  DGIVAPGVRVSGEDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTP 526

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                E+   +++             LR VKV +   +  Q GDK A RHG KG +     
Sbjct: 527  LRSTENGIVDQVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYR 581

Query: 1106 CEDMPFLKDGTPV 1118
             EDMPF ++G   
Sbjct: 582  HEDMPFTREGIVP 594


>gi|299115649|emb|CBN75850.1| conserved unknown protein (Partial) [Ectocarpus siliculosus]
          Length = 1050

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 45/189 (23%), Positives = 71/189 (37%), Gaps = 50/189 (26%)

Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
             +G + E+  G +    G    +    +     +                          
Sbjct: 834  TIGMLIESMAGKSGAMHGTYQDATPFAFHEEDRV-------------------------- 867

Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
                                     +     LR A     G   LY G+TG      + +
Sbjct: 868  ------------------------IDHFGEQLRSAGYAYHGSEPLYSGVTGTVMHADIFI 903

Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
            G +Y  +L HMVSDK   R+TG  + +T+QP+ G+ N+GG RLGEME   + ++GAA++L
Sbjct: 904  GLVYYQRLRHMVSDKSQVRATGPVNQLTRQPIKGRKNKGGVRLGEMERDALLSHGAAFLL 963

Query: 1312 QEMLTIKSD 1320
             + L   SD
Sbjct: 964  HDRLMNCSD 972



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/194 (19%), Positives = 56/194 (28%), Gaps = 72/194 (37%)

Query: 85  KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD--- 141
           K    +C  R LTY   L + L   V D D     K            GD P+M      
Sbjct: 80  KLTPRECRERGLTYHGALLVDLCYQVGDGDVVRTQKRA----------GDCPVMVGSRRC 129

Query: 142 ---------------------GTFVIKGIQRIVVSQLHR-------------SPGIHFDH 167
                                G F+++GI+R++     R             S G   D 
Sbjct: 130 HLRGHGPARLTRGREEAGEMGGYFIVRGIERVI-----RLLQVPKRNYAHAISRGTFKDR 184

Query: 168 DKGRASL------SGKLLYACRI----IPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            +G +        + K      +    I   G  +      ++ +         VPV   
Sbjct: 185 GQGYSEKGVMMRCARKDQSTLTVTLHYISTGGATLRFSVRKQEFL---------VPVVII 235

Query: 218 LMALGMDSE-EILS 230
           L AL   S+ EI  
Sbjct: 236 LKALRDTSDREIHE 249



 Score = 45.5 bits (106), Expect = 0.076,   Method: Composition-based stats.
 Identities = 45/262 (17%), Positives = 87/262 (33%), Gaps = 30/262 (11%)

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
           E   VP  K          + S  A +   + +  S R+     M +Q + +       V
Sbjct: 570 EVGWVPPMKGGAGPYPGLFLNSEGARMCRPVLHLQSGRMEWIGPMAQQFMEIACLADD-V 628

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
             G+ +         +++  A +    D  +      +  +   T G   + L   +  N
Sbjct: 629 RPGLTTHRELD-PTNMLSLVASLTPFSDYNQSPRNMYQCQMGKQTMGTPAHCLTPHRTDN 687

Query: 772 QNTC--VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           +       Q  +V+                  L D   G N +VA + + G++ ED+M++
Sbjct: 688 KMYKVLFPQAAIVQ----------TRRHGEYQLDDYPQGTNAVVAVISYTGFDMEDAMIL 737

Query: 830 SERMVSEDVFTSIHIEEFEVMARD---TKLGPEEITRDIPN-------------VSEEGL 873
           ++         +  ++ F V  RD      GP  + R                  + +  
Sbjct: 738 NKSSFERGFGHASVLKTFAVDLRDVAGKGAGPAAVARLKFCNVKPGSVGAGGAAAATKLH 797

Query: 874 KNIDECGIICVGAEVNPGDILV 895
           + +   G+  VG+ V PGD L 
Sbjct: 798 EGLGWDGLPMVGSWVQPGDALY 819


>gi|260594065|gb|ACX46327.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  164 bits (414), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 82/158 (51%), Positives = 111/158 (70%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N +S ITH RR+ ALG GG+ R RA  E+RDVH THYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNRVSEITHKRRVFALGPGGLTRERACFEVRDVHSTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           I L++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IVLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|330785192|gb|AEC46402.1| RNA polymerase II second largest subunit [Arthothelium galapagoense]
          Length = 291

 Score =  164 bits (414), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/366 (14%), Positives = 98/366 (26%), Gaps = 76/366 (20%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            ++ R  I++ +   S   E+ E   + +         +       +  G           
Sbjct: 61   LYYRTYIEQEQSVSSQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVSGEDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+++      R            ++     +  Q                      
Sbjct: 121  KTAPLAANAEERGARLSTHTKRDVSTPLRSTEAGIVDQVL-------------------- 160

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   DI++N
Sbjct: 161  -LTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGLIPDIIIN 219

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +  +         ++S L               
Sbjct: 220  PHAIPSRMTIAHLIECLLSKVAATSAYEGDATPFTDVTVENVSELL-------------- 265

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                            WKSG                            G  ++Y+G TG 
Sbjct: 266  ----------------WKSG------------------------YQSRGFEVMYNGHTGR 285

Query: 1244 PFDRPV 1249
                 V
Sbjct: 286  KLVAQV 291



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 69/187 (36%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      DL  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARD-TKLGPEEITRDI----PNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +  +    EE  + I      +       +D+ GI+  G  V+
Sbjct: 54  DRGLFRSLYYRTYIEQEQSVSSQVLEEFEKPIKSQTLRMRHGTYDKLDDDGIVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 114 GEDIIIGKTAPLAANAEERGARL----STHTKRDVSTPLRSTEAGIVDQVLLTSVDGKKN 169

Query: 950 IDKNERS 956
           +    R+
Sbjct: 170 VKIRTRT 176


>gi|198279507|emb|CAP04788.1| RNA polymerase beta subunit [Equisetum ramosissimum subsp. debile]
          Length = 240

 Score =  164 bits (414), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 106/236 (44%), Positives = 153/236 (64%), Gaps = 9/236 (3%)

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRS 770
           VGTG+E  +A  SG+ ++++R G +  +D  RI +   E              L+ ++RS
Sbjct: 2   VGTGLEGQIALDSGSCVISEREGKLIYIDGQRITLFVDEETSINK-------NLLSYERS 54

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
           N NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW GYNFED+ LIS
Sbjct: 55  NNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPWEGYNFEDATLIS 114

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNP 890
           ER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G++ +G+ V  
Sbjct: 115 ERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDENGLVKLGSWVEA 174

Query: 891 GDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           GD+LVGK+TP         PE KLL+AIFG    + R+T L+VP G  G V+D++ 
Sbjct: 175 GDVLVGKLTPLDYLDTLGAPEGKLLQAIFGTDVTNARETCLKVPVGFKGRVIDIKW 230


>gi|219563991|gb|ACL28179.1| RNA polymerase II second largest subunit [Bisporella citrina]
          Length = 272

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/276 (19%), Positives = 92/276 (33%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 7    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 63

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +    + + L    Y +L E   +  G           K+  L+ D   
Sbjct: 64   -IGMNIVETFEKPYRQDTLKLKHGTYDKLDEDGIVAPGVRISGEDIIIGKTAPLAPDNEE 122

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R++          ++     +  Q                             LR V
Sbjct: 123  LGQRTKVHVKRDASTPLRSTENGIVDQVLL--------------------TTNAEGLRFV 162

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM + 
Sbjct: 163  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRHEDMPFTREGIVPDIIINPHAIPSRMTIA 222

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 223  HLIECQLSKVSTLRGLEGDATPFTEVTVDSVSELLR 258



 Score = 79.7 bits (195), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 32/151 (21%), Positives = 59/151 (39%), Gaps = 12/151 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 4   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 63

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E       +D   +       +DE GI+  G  ++  DI++GK  P        
Sbjct: 64  IGMNIVETFEKPYRQDTLKLKHGTYDKLDEDGIVAPGVRISGEDIIIGKTAPLAPDNEEL 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            ++        K    RD S  + S  +G V
Sbjct: 124 GQRT-------KVHVKRDASTPLRSTENGIV 147


>gi|46277312|gb|AAS86846.1| DNA-dependent RNA polymerase II [Pachyphloeus carneus]
          Length = 546

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 48/273 (17%), Positives = 87/273 (31%), Gaps = 21/273 (7%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D S+ +  G     +   +F R  +D+ +R  
Sbjct: 279  MEFLKFRELPAGQNAIVAIMCYSGYNQED-SVIMNQGSIDRGLFRSLFFRTYMDQEKRVG 337

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   R           +       +  G           K+  ++ +      
Sbjct: 338  MDVVEEFEKPTRSNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQ 397

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+++         ++     +  Q                             L+ VKV 
Sbjct: 398  RTRFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFVKVR 437

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + 
Sbjct: 438  MRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGIVPDLIINPHAIPSRMTIAHLI 497

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            E  L       G +  +          +S L  
Sbjct: 498  ECLLSKVSSLRGFEGDATPFTDVTVDSVSKLLR 530



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 47/298 (15%), Positives = 96/298 (32%), Gaps = 26/298 (8%)

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVA 720
           +++IDA  ++ V I  +      +   +    G  +Q++  P  + +A            
Sbjct: 155 VEYIDAEEEETVMIVMTPEDLETSRQYH---AGYEIQQEVDPAQRVKASVSKFAHTWTHC 211

Query: 721 KSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT-CVNQR 779
           +   + I+   A I+   D  +                                      
Sbjct: 212 EIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLYYPXX 271

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           PL                      +L  G+N +VA M + GYN EDS+++++  +   +F
Sbjct: 272 PL----------GTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQGSIDRGLF 321

Query: 840 TSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            S+    +    +   +   E        +   +       +D+ G++  G  V+  DI+
Sbjct: 322 RSLFFRTYMDQEKRVGMDVVEEFEKPTRSNTLRLKHGTYDKLDDDGLVAPGVRVSGEDII 381

Query: 895 VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +GK  P   +     ++        +    RD S  + S  +G V  V +       K
Sbjct: 382 IGKTAPIAPNQEELGQRT-------RFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 432



 Score = 50.5 bits (119), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/215 (12%), Positives = 55/215 (25%), Gaps = 19/215 (8%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 25  DFMTQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L          +    
Sbjct: 79  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHIERLEDDRELD 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E+             V Y+ A EEE   I      L+    +       +E+   +   
Sbjct: 139 DESQRYGWAGLMSDGVVEYIDAEEEETVMIVMTPEDLETSRQYHAGYEIQQEVDPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +          +  P  ++ I AS+IPF +++ 
Sbjct: 199 ASVSKFAHTWTHCEIHPSMILGICASIIPFPDHNQ 233


>gi|260593949|gb|ACX46269.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET E  N
Sbjct: 1   SQLSQFMDQNNPLSEITYKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEVPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|238836446|gb|ACR61426.1| RNA polymerase beta subunit [Staphylococcus aureus]
 gi|238836448|gb|ACR61427.1| RNA polymerase beta subunit [Staphylococcus aureus]
 gi|238836450|gb|ACR61428.1| RNA polymerase beta subunit [Staphylococcus aureus]
 gi|238836452|gb|ACR61429.1| RNA polymerase beta subunit [Staphylococcus aureus]
          Length = 164

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 99/163 (60%), Positives = 126/163 (77%), Gaps = 2/163 (1%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETP
Sbjct: 2   SALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETP 61

Query: 602 YRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE 659
           YRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +E
Sbjct: 62  YRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKE 121

Query: 660 KIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           K+D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVP
Sbjct: 122 KMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVP 164


>gi|219564095|gb|ACL28231.1| RNA polymerase II second largest subunit [fungal sp. M292]
          Length = 287

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/293 (18%), Positives = 96/293 (32%), Gaps = 27/293 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   + +  E + L    Y ++ E   I  G     
Sbjct: 63   RSLFYRTYQDQE----KMIGHSVVEQFEKPQRSETLRLKHGTYDKIDEDGIIAPGIRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR  + +K    T     E    +++
Sbjct: 119  EDIIMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGVIDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MLTTTGD-----GTRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             DI++NP  +PSRM +  + E  L       G +  +          +S +  
Sbjct: 219  PDIIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQVSNILR 271



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/180 (21%), Positives = 66/180 (36%), Gaps = 23/180 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL +                    +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPLAR----------TMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    ++   +       E        +   +       IDE GII  G  V+
Sbjct: 58  DRGLFRSLFYRTYQDQEKMIGHSVVEQFEKPQRSETLRLKHGTYDKIDEDGIIAPGIRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P     M P+ + L     +       T LR        V+D  +    G
Sbjct: 118 GEDIIMGKTAP-----MAPDAEELGQRQKQHIKRDVSTPLR---STESGVIDQVMLTTTG 169


>gi|219564059|gb|ACL28213.1| RNA polymerase II second largest subunit [fungal sp. M187]
          Length = 287

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/294 (18%), Positives = 96/294 (32%), Gaps = 27/294 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   + +  E + L    Y ++ E   I  G     
Sbjct: 63   RSLFYRTYQDQE----KMIGHSVVEQFEKPQRSETLRLKHGTYDKIGEDGIIEPGIRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR  + +K    T     E    +++
Sbjct: 119  EDIIMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGVIDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MLTTTGD-----GTRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             DI++NP  +PSRM +  + E  L       G +  +          +S +   
Sbjct: 219  PDIIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQVSSILRK 272


>gi|125491401|gb|ABN43187.1| RpoB [Staphylococcus auricularis]
          Length = 161

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 97/161 (60%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      VT+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVNIETNAVTDQIDYLTADEEDSYVVAQANSRLDEEGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MNKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|219564019|gb|ACL28193.1| RNA polymerase II second largest subunit [fungal sp. M122]
          Length = 287

 Score =  163 bits (413), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 52/293 (17%), Positives = 96/293 (32%), Gaps = 27/293 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   + +  E + L    Y ++ +   I  G     
Sbjct: 63   RSLFYRTYQDQE----KMIGHSVVEQFEKPQRSETLRLKHGTYDKIGDDGIIEPGIRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR  + +K    T     E    +++
Sbjct: 119  EDIIMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGVIDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MLTTTGD-----GTRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             DI++NP  +PSRM +  + E  L       G +  +          +S +  
Sbjct: 219  PDIIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFTKVTVTQVSRILR 271


>gi|74099882|gb|AAZ99150.1| RpoB [Staphylococcus pasteuri]
          Length = 161

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLDTNAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|283132427|dbj|BAI63619.1| rpoB protein [Corynebacterium urealyticum]
          Length = 132

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 55/158 (34%), Positives = 80/158 (50%), Gaps = 34/158 (21%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G ++ +  +D K    +  L   L  V              
Sbjct: 1    RMNIGQVLEVHLGWLAKA-GWQVDTNSDDPKIKAMLETLPEDLYDVPADSLT-------- 51

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             STPVFDGA    ++ +LR +  D  G        ++ L DG T
Sbjct: 52   -----------------STPVFDGASNAELSGLLRSSRPDRDGIRLVDDFGKAQLIDGRT 94

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            GEP++ P++VGY+YMLKL+H+V +K++ARSTG YS++T
Sbjct: 95   GEPYEHPISVGYMYMLKLHHLVDEKIHARSTGPYSMIT 132


>gi|82706477|gb|ABB89616.1| RNA polymerase II second largest subunit [Xylaria acuta]
          Length = 549

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 94/612 (15%), Positives = 164/612 (26%), Gaps = 70/612 (11%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG   
Sbjct: 2    GVSQVLNRYTFASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPEGQAC 57

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L+    ++     E    Y    + +V  +   L        ++  +   + +D 
Sbjct: 58   GLVKNLSLMCSISVGTSTEPIIEYMISRNMEVLEEYEPLRYPHATKIFLNGSWIGIHQDP 117

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                  V       +I      I D  D   K        + P                 
Sbjct: 118  KALVRDVQQLRRTNQIPAEVSLIRDIRDREFKIFSHAGRVMRPLFVVXXXXXXXXXXXXX 177

Query: 698  RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                                                                        
Sbjct: 178  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEAF 237

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
             +     +     +     N+R   K+             PS  LG       +  + +P
Sbjct: 238  RMTKLGQLDPDAESNLNEPNKRLKTKMNPTTHTYTHCEIHPSMLLG-------ICASIIP 290

Query: 818  WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNID 877
            +  +N          M  + +     +  +                              
Sbjct: 291  FPDHNQSPRNTYQSAMGKQAMG--FFLTNYSRRM-------------------------- 322

Query: 878  ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
               +  +             +       +   +  + AI      +   + +   S +  
Sbjct: 323  -DTMANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAISCYSGYNQEXSVIMNQSSIDR 381

Query: 938  TVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQN 994
             +    +F R   D  +R        +E   +    + + L +  Y +L +   I  G  
Sbjct: 382  GLF-RSLFFRSYSDSEKRVGI---NTVEQFEKPFRADTLRLKQGTYDKLDDDGIIAPGIR 437

Query: 995  AVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFK 1054
                     K+  +S D                +E  QR    +K    T     E    
Sbjct: 438  VSGEDIIIGKTAPISPD---------------NEEMGQRQKIHVKRDASTPLRSTESGII 482

Query: 1055 NKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKD 1114
            + +      D +     R VKV V   +  Q GDK A RHG KG +      EDMPF ++
Sbjct: 483  DSVVLTTNADGL-----RFVKVRVRTTKIPQIGDKFASRHGQKGTIGVTFRNEDMPFSRE 537

Query: 1115 GTPVDIVLNPLG 1126
            G   DI++NP  
Sbjct: 538  GIVPDIIINPHA 549


>gi|91981498|gb|ABE68091.1| RNA polymerase subunit B [Pseudomonas sp. Q2-87]
          Length = 156

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 87/156 (55%), Positives = 115/156 (73%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +
Sbjct: 1   NNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R
Sbjct: 61  YARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
              E  +   E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 121 HLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEH 156


>gi|260594103|gb|ACX46346.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  I QA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIGQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKALEDVTLMDVSPKQVVSVAAS 158


>gi|74099862|gb|AAZ99140.1| RpoB [Staphylococcus cohnii subsp. urealyticus]
          Length = 161

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSKLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|194320186|gb|ACF48322.1| DNA-dependent RNA polymerase II second largest subunit [Amandinea
            punctata]
          Length = 317

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/383 (14%), Positives = 106/383 (27%), Gaps = 81/383 (21%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 13   MAHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 72

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+  R   +    +E   +      + L    Y +L +   I+ G     
Sbjct: 73   -RSLFYRSYHDQESR---IGMNIVECFEKPMRSNTMKLKHGTYDKLDDDGIIIPGYRVSG 128

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  +++D       +++         ++     L  Q                
Sbjct: 129  EDIIIGKTAPITADAEELGQGAKYQDKRDASTPLRSTESGLVDQVLL------------- 175

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 176  -------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVI 228

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIG 1177
             D+++NP  +PSRM +  + E  L       G +  +          +S L    ++   
Sbjct: 229  PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGLEGDATPFTDVTVDQVSRLLR--DEGYQ 286

Query: 1178 TGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILY 1237
            +                                                    +G +   
Sbjct: 287  SRGFEVM---------------------------------------------YNGHT--- 298

Query: 1238 DGLTGEPFDRPVTVGYIYMLKLN 1260
             G         V +G  Y  +L 
Sbjct: 299  -GR---KLVAQVFLGPTYYQRLR 317



 Score = 85.1 bits (209), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 38/184 (20%), Positives = 64/184 (34%), Gaps = 22/184 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                + +         Q+PL                      +L  G+N +VA   + G
Sbjct: 4   TNYDQRMETMAHILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +        +   E        +   +       
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSLFYRSYHDQESRIGMNIVECFEKPMRSNTMKLKHGTYDK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ GII  G  V+  DI++GK  P         +       G K  D RD S  + S  
Sbjct: 114 LDDDGIIIPGYRVSGEDIIIGKTAPITADAEELGQ-------GAKYQDKRDASTPLRSTE 166

Query: 936 SGTV 939
           SG V
Sbjct: 167 SGLV 170


>gi|198279431|emb|CAP04750.1| RNA polymerase beta subunit [Pinus nelsonii]
          Length = 270

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 98/242 (40%), Positives = 148/242 (61%), Gaps = 10/242 (4%)

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+E   A  SG+  +A + G +E +DA+                       + +QRSN N
Sbjct: 1   GLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGNTVRTESVIYQRSNTN 52

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+
Sbjct: 53  TCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERL 112

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+
Sbjct: 113 VYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDV 172

Query: 894 LVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR    
Sbjct: 173 LVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDS 232

Query: 952 KN 953
            +
Sbjct: 233 GD 234



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 61   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 119

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 120  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 173

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 174  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S ILP
Sbjct: 232  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISIILP 270


>gi|74099856|gb|AAZ99137.1| RpoB [Staphylococcus capitis subsp. urealyticus]
          Length = 161

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|219564101|gb|ACL28234.1| RNA polymerase II second largest subunit [fungal sp. M329]
          Length = 268

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 55/276 (19%), Positives = 96/276 (34%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 5    MEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 61

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    +E   +    + + L    Y +L E   +  G           K+  ++ D   
Sbjct: 62   -IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPD--- 117

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         +E  QR    +K    T     E+   +++             LR V
Sbjct: 118  ------------AEELGQRTKAHIKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFV 160

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 161  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTSEGIVPDLIINPHAIPSRMTIA 220

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 221  HLIECQLSKVSTLRGLEGDATPFTEVTVDSVSNLLR 256



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/158 (23%), Positives = 62/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA M + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 2   TRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 61

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +       +DE GI+  G  V+  DI++GK  P        
Sbjct: 62  IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEEL 121

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        KA   RD S  + S  +G V  V I  
Sbjct: 122 GQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 152


>gi|330785316|gb|AEC46464.1| RNA polymerase II second largest subunit [Roccellographa
            circumscripta]
          Length = 302

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/370 (15%), Positives = 102/370 (27%), Gaps = 81/370 (21%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + +    R +   +   V        +     +++    +R     
Sbjct: 5    NILYYPQKPLATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRS 64

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E++Q      +E   +      +      Y +L E   +  G           
Sbjct: 65   LFYRSYIEQQQPVGFNALETFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRVSGEDIIIG 124

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR  E  +          E    +++      
Sbjct: 125  KTAPFQAPMQDNA------------EGGQRTKEHTRRDVSCPLRSTEAGIIDRVL----- 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 168  -VTTTEGRRSVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTEGICPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L       G +  +          IS                 
Sbjct: 227  PHAIPSRMTIAHLIECLLSKVATTQGCEGDATPFTPVTVSSISS---------------- 270

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                     +L  A   + G  V                             +Y+G TG 
Sbjct: 271  ---------ILESAGYQRRGFEV-----------------------------MYNGHTGR 292

Query: 1244 PFDRPVTVGY 1253
              +  + +G 
Sbjct: 293  KLNAQIFLGP 302



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 69/196 (35%), Gaps = 20/196 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                   +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSLQFMNFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       E                    +DE G +  G  V+
Sbjct: 58  DRGLFRSLFYRSYIEQQQPVGFNALETFEKPVKQMTMRTRPGTYDKLDEDGFVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   R     K    RD S  + S  +G +  V +    G
Sbjct: 118 GEDIIIGKTAPFQAPMQDNAEGGQRT----KEHTRRDVSCPLRSTEAGIIDRVLVTTTEG 173

Query: 950 IDKNE-RSISVEREQI 964
               + R+ + +  QI
Sbjct: 174 RRSVKIRTRTTKVPQI 189


>gi|152968498|gb|ABS50263.1| RNA polymerase II [Lychnis abyssinica]
 gi|152968543|gb|ABS50286.1| RNA polymerase II [Uebelinia scottii]
          Length = 255

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/272 (19%), Positives = 85/272 (31%), Gaps = 23/272 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           N          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGDATPFT 252



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|198279469|emb|CAP04769.1| RNA polymerase beta subunit [Pinus heldreichii]
          Length = 271

 Score =  163 bits (412), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 100/243 (41%), Positives = 149/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 271


>gi|198279503|emb|CAP04786.1| RNA polymerase beta subunit [Equisetum hyemale]
          Length = 242

 Score =  163 bits (412), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 109/245 (44%), Positives = 153/245 (62%), Gaps = 9/245 (3%)

Query: 702 PLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
           PL K E   VG G+E  +A  SG  + ++R G V  +D  RI +   E            
Sbjct: 3   PLSKPEKCIVGXGLEGQIALDSGXCVXSEREGKVIYIDXQRITLFVDEETSINK------ 56

Query: 762 YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
             L+ ++RSN NTC+NQ PLV     +R+  IIADG ST  G+LALG+N+LVA+MPW GY
Sbjct: 57  -NLLSYERSNNNTCINQTPLVCKDKFLRQGQIIADGASTVGGELALGKNILVAYMPWEGY 115

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
           NFED+ LISER++ ED+FTS HIE  E+    T  GPE++TR+IP+++   L+++DE G+
Sbjct: 116 NFEDATLISERLIYEDIFTSFHIERHEINVSFTGEGPEKLTREIPHLNNHILRHLDENGL 175

Query: 882 ICVGAEVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           + +G+ V  GD+LVGK+ P         PE KLL+AIFG    + R+T L+VP G  G V
Sbjct: 176 VKLGSWVEXGDVLVGKLXPLDYLDTLGXPEGKLLQAIFGTDVTNARETCLKVPVGFKGRV 235

Query: 940 VDVRI 944
           +D++ 
Sbjct: 236 IDIKW 240


>gi|198279429|emb|CAP04749.1| RNA polymerase beta subunit [Pinus pseudostrobus]
 gi|198279437|emb|CAP04753.1| RNA polymerase beta subunit [Pinus greggii]
 gi|198279451|emb|CAP04760.1| RNA polymerase beta subunit [Pinus glabra]
          Length = 271

 Score =  163 bits (412), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 100/243 (41%), Positives = 150/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 271


>gi|166865104|gb|ABZ01811.1| RNA polymerase beta-subunit [Serratia ureilytica]
          Length = 152

 Score =  163 bits (412), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 95/152 (62%), Positives = 122/152 (80%)

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N
Sbjct: 1   EITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTN 60

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEE 653
            YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS+LD++G F E+LV CR  GE 
Sbjct: 61  EYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDDEGRFVEDLVTCRSKGES 120

Query: 654 ILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            L  R+++D++D S +QVVS+ ASLIPFLE+D
Sbjct: 121 SLFSRDQVDYMDVSTQQVVSVGASLIPFLEHD 152


>gi|260594055|gb|ACX46322.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET E  N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEVPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKALEDVTLMDVSPKQVVSVAAS 158


>gi|152968518|gb|ABS50273.1| RNA polymerase II [Uebelinia crassifolia]
 gi|152968522|gb|ABS50275.1| RNA polymerase II [Uebelinia kiwuensis subsp. erlangeriana]
 gi|152968536|gb|ABS50282.1| RNA polymerase II [Uebelinia kiwuensis]
 gi|152968538|gb|ABS50283.1| RNA polymerase II [Uebelinia kiwuensis]
          Length = 255

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 52/272 (19%), Positives = 85/272 (31%), Gaps = 23/272 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           +          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGDATPFT 252



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|74099890|gb|AAZ99154.1| RpoB [Staphylococcus saprophyticus subsp. bovis]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 97/161 (60%), Positives = 124/161 (77%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G FT + V CR  G   +
Sbjct: 61  IETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFTADEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|280985723|gb|ACZ99642.1| RNA polymerase II [Fusarium equiseti]
          Length = 284

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 54/359 (15%), Positives = 102/359 (28%), Gaps = 75/359 (20%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +                             
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGD--------------------------- 252

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDG 1239
                                      +TP F     ++++ +LR       G  ++Y+G
Sbjct: 253  --------------------------ATP-FTDVTVDSVSDLLRKHGYQSRGFEVMYNG 284



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|74099880|gb|AAZ99149.1| RpoB [Staphylococcus nepalensis]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 124/161 (77%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIETNSITDQIDYLTADEEDSYVVAQANSNLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|198279373|emb|CAP04721.1| RNA polymerase beta subunit [Pinus roxburghii]
          Length = 271

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 100/243 (41%), Positives = 149/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQIHQGEFVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 86/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   IHQGEFVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S  LP
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIXLP 271


>gi|74099878|gb|AAZ99148.1| RpoB [Staphylococcus nepalensis]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 124/161 (77%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRKRAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIETNSITDQIDYLTADEEDSYVVAQANSNLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|330785320|gb|AEC46466.1| RNA polymerase II second largest subunit [Reichlingia leopoldii]
          Length = 285

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 56/360 (15%), Positives = 106/360 (29%), Gaps = 84/360 (23%)

Query: 893  ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             ++        +  + E    R +   +   V        +     +++    +R     
Sbjct: 1    NILYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRS 60

Query: 953  NERSISVEREQ------IELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
                  +E+EQ      +E   +    + + +    Y +L +   +  G           
Sbjct: 61   LYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVSGDDIIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  L+               A  +E+  R  +  K    T     E    +++      
Sbjct: 121  KTAPLA---------------ATAEERGSRLSQHTKRDVSTPLRSTEAGIIDQVL----- 160

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + VK+     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 161  -VTSVDGKKNVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 219

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTE 1183
            P  +PSRM +  + E  L         +                                
Sbjct: 220  PHAIPSRMTIAHLIECLLSKVAATNAYEGD------------------------------ 249

Query: 1184 KISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGE 1243
                                   +TP F     E ++ +L  +   + G  ++Y+G TG 
Sbjct: 250  -----------------------ATP-FTEITVEMVSEILEKSXXQKRGFEVMYNGHTGR 285



 Score = 80.9 bits (198), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 66/187 (35%), Gaps = 19/187 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S++   +    +   +   E            +       +D+ GI+  G  V+
Sbjct: 54  DRGLFRSLYYRTYIEQEQTVGVQVLEEFEKPLKSQTLRMRHGTYDKLDDDGIVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P   +      +L          DV        +G+   V+   +  +  
Sbjct: 114 GDDIIIGKTAPLAATAEERGSRL----SQHTKRDVSTPLRSTEAGIIDQVLVTSVDGKKN 169

Query: 950 IDKNERS 956
           +    R+
Sbjct: 170 VKIRTRT 176


>gi|220961192|gb|ACL93062.1| RNA polymerase B subunit [Streptomyces macrosporus]
          Length = 180

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVHYLTADEEDRYVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFAEGRVLVRRRGGEVDYVPGDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL++AEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIRAEAPLVGTGMEYRSAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|159154266|gb|ABW93531.1| RNA polymerase B subunit [Microcystis aeruginosa PCC 7806]
          Length = 193

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 92/192 (47%), Positives = 129/192 (67%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  + + DE+G    E +  R   E      E++D++  SP Q+VS+A SLIPFLE+D
Sbjct: 2   RVAPGDVATDENGYILGETIPVRYRQEFSTTSPEQVDYVCVSPVQIVSVATSLIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G+V  VDA RI I
Sbjct: 62  DANRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTNGVVSHVDANRIRI 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           +  + D +        Y + K+QRSNQ+TC+NQRPLV  G++V    I+ADG +T+ G++
Sbjct: 122 KVADQDKEIFGKSEIEYEIQKYQRSNQDTCLNQRPLVYQGEQVVPGQILADGSATEGGEI 181

Query: 806 ALGRNMLVAFMP 817
           ALG+N+LVA+MP
Sbjct: 182 ALGQNILVAYMP 193


>gi|260594047|gb|ACX46318.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 84/158 (53%), Positives = 112/158 (70%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLS+     N LS  TH RR+SALG GG+ R RA  E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSRFMGQGNPLSETTHKRRVSALGPGGLTRERARFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|74099876|gb|AAZ99147.1| RpoB [Staphylococcus lutrae]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 94/161 (58%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQAN+ LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANARLDENGRFLDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|198279483|emb|CAP04776.1| RNA polymerase beta subunit [Pinus resinosa]
          Length = 265

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 100/243 (41%), Positives = 149/243 (61%), Gaps = 10/243 (4%)

Query: 713 TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQ 772
           TG+E   A  SG+  +A + G +E +DA+                       + +QRSN 
Sbjct: 1   TGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSNT 52

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           NTC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER
Sbjct: 53  NTCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISER 112

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGD 892
           +V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD
Sbjct: 113 LVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGD 172

Query: 893 ILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGI 950
           +LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR   
Sbjct: 173 VLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDD 232

Query: 951 DKN 953
             +
Sbjct: 233 SGD 235



 Score = 73.6 bits (179), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 53/218 (24%), Positives = 82/218 (37%), Gaps = 14/218 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 62   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 120

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 121  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 174

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 175  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 232

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGI 1099
             GD+        V V+++ KR IQ GDK+AGRHGNKGI
Sbjct: 233  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGI 265


>gi|74099888|gb|AAZ99153.1| RpoB [Staphylococcus piscifermentans]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 98/161 (60%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V CR  G   +
Sbjct: 61  IETPYRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFLSEEVVCRFRGNNTI 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + REK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MDREKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|74099864|gb|AAZ99141.1| RpoB [Staphylococcus condimenti]
 gi|74099866|gb|AAZ99142.1| RpoB [Staphylococcus condimenti]
          Length = 161

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 98/161 (60%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V CR  G   +
Sbjct: 61  IETPYRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFISEEVVCRFRGNNTM 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + REK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MDREKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|220961120|gb|ACL93026.1| RNA polymerase B subunit [Streptomyces niger]
          Length = 180

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 92/178 (51%), Positives = 124/178 (69%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL +FAR+NA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLAAFARINAFGFVETPYRKVVDGVVTDEVNYLTADEEDRFVIAQANAKLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DYRFAEARVLVRRRGGEIDYIPGSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+ AEAP VGTGME   A  +G  I A++ G++  V A  + I + +G   
Sbjct: 121 MMRQAVPLINAEAPLVGTGMEYRCATDAGDVIRAEQNGVISDVSADYVTIANDDGTHV 178


>gi|152968506|gb|ABS50267.1| RNA polymerase II [Lychnis abyssinica]
          Length = 240

 Score =  162 bits (411), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 83/257 (32%), Gaps = 23/257 (8%)

Query: 902  GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVER 961
                +      + AI      +  D+ +   S +        +F R   D+ ++  ++ +
Sbjct: 4    HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLIK 62

Query: 962  EQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQW 1021
            E      R           N          G           K+T L+ +          
Sbjct: 63   EDFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTTPLAPEEAQGP----- 117

Query: 1022 WQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK 1081
                               +Y      +  R        Q         LR VKV V   
Sbjct: 118  -----------------AARYSRKDHSISLRHSESGIVDQVLLTTNADGLRFVKVRVRSV 160

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +
Sbjct: 161  RIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIM 220

Query: 1142 GWACVGLGKKIKSLIND 1158
            G     +GK+  +    
Sbjct: 221  GKVAAHVGKEGDATPFT 237



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/144 (22%), Positives = 57/144 (39%), Gaps = 14/144 (9%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
               L  G N +VA   + GYN EDS+++++  +    F S+    +    +      +E
Sbjct: 4   HFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKE 63

Query: 861 IT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                   +   +       +D+ G+   G  V+  D+++GK TP     + PEE    A
Sbjct: 64  DFGRPDRSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----A 114

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTV 939
                    +D S+ +    SG V
Sbjct: 115 QGPAARYSRKDHSISLRHSESGIV 138


>gi|260594111|gb|ACX46350.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  162 bits (410), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 85/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNQLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++S+ ++AR N YGF+E+PY  V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSVAAYARTNHYGFLESPYCVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|164452778|gb|ABY57225.1| RpoB [Tortella fragilis]
          Length = 272

 Score =  162 bits (410), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 102/244 (41%), Positives = 158/244 (64%), Gaps = 9/244 (3%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E   VGTG+ES  A  SG+  +AK++G +   D  +I + +       +        L+ 
Sbjct: 1   EESIVGTGLESQAALDSGSVAIAKQSGKIVYTDGKKISLLN-------ANKKRTNXHLII 53

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSN +TC++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED+
Sbjct: 54  YQRSNNSTCMHQKTQVTQKTFLKKGQILADGAATLKGELALGKNILVAYMPWEGYNFEDA 113

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER++ ED++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+
Sbjct: 114 ILISERLIYEDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKNGLVLPGS 173

Query: 887 EVNPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            V  GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR 
Sbjct: 174 WVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRW 233

Query: 945 FNRH 948
             + 
Sbjct: 234 IXKK 237



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 70/184 (38%), Gaps = 16/184 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I ++  + I +ER +I+             E   L
Sbjct: 96   KNILVAYMPWEGYNFEDAILISERLIYEDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 155

Query: 979  DRNIY---SRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++     +   +L G    +G     K T   ++     P  +  Q     +      
Sbjct: 156  ENSVLRHLDKNGLVLPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 215

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E     +       + + V++A KR IQ GDK+AGRHG
Sbjct: 216  TCLKVPPGGKGRVIDVRWIXKKENSNXYE-------KTIHVYIAQKRKIQVGDKVAGRHG 268

Query: 1096 NKGI 1099
            NKGI
Sbjct: 269  NKGI 272


>gi|219564013|gb|ACL28190.1| RNA polymerase II second largest subunit [fungal sp. M33]
          Length = 287

 Score =  162 bits (410), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 54/295 (18%), Positives = 97/295 (32%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFSCQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 271



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|74099874|gb|AAZ99146.1| RpoB [Staphylococcus hominis subsp. novobiosepticus]
          Length = 161

 Score =  162 bits (410), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 96/161 (59%), Positives = 123/161 (76%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|56406215|gb|AAV87491.1| RpoB [Bisgaard Taxon 45]
          Length = 161

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 96/160 (60%), Positives = 123/160 (76%), Gaps = 1/160 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR 
Sbjct: 2   SEVTHNRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYART 61

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   G
Sbjct: 62  NDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAFVTCRGEHG 121

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           E  L   ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 122 ESGLYRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 161


>gi|225698405|gb|ACO07320.1| RpoB [Pasteurellaceae bacterium TIS17892]
          Length = 158

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 92/158 (58%), Positives = 118/158 (74%), Gaps = 1/158 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDE+  FT+  V
Sbjct: 61  LSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDENFRFTDAYV 120

Query: 646 FCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
             R   GE  L   E+I ++D S +QVVS+AA+LIPFL
Sbjct: 121 TARGEHGESGLYRPEEIQYMDVSTQQVVSVAAALIPFL 158


>gi|166865106|gb|ABZ01812.1| RNA polymerase beta-subunit [Serratia marcescens subsp. marcescens
           ATCC 13880]
          Length = 151

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 96/151 (63%), Positives = 122/151 (80%)

Query: 535 ITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNA 594
           ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N 
Sbjct: 1   ITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNE 60

Query: 595 YGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEI 654
           YGF+ETPYR+V DG VT+++ YLSA+EE N  IAQANS+LDE+G F E+LV CR  GE  
Sbjct: 61  YGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESS 120

Query: 655 LVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           L  R+++D++D S +QVVS+ ASLIPFLE+D
Sbjct: 121 LFSRDQVDYMDVSTQQVVSVGASLIPFLEHD 151


>gi|61969362|gb|AAX57439.1| DNA-dependent RNA polymerase II [Peziza subviolacea]
          Length = 256

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 46/277 (16%), Positives = 86/277 (31%), Gaps = 21/277 (7%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R  +D+ +R      E+ E   R           +       +  G         
Sbjct: 60   RSLFYRVYMDQEKRVGMNVVEEFEKPTRANTLRLKHGTYDKLDDDGLVAPGVRVSGEDII 119

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  ++ +L     R+++         ++     +  Q                    
Sbjct: 120  IGKTAPIAPNLDELGQRTKFHTKRDVSTPLRSTENGIVDQ-------------------- 159

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D++
Sbjct: 160  VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVPDLI 219

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            +NP  +PSRM +  + E  L       G +  +    
Sbjct: 220  INPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 256



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/164 (19%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA + + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 14  TRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSLFYRVYMDQEKR 73

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        +   +       +D+ G++  G  V+  DI++GK  P   +    
Sbjct: 74  VGMNVVEEFEKPTRANTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNLDEL 133

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
            ++        K    RD S  + S  +G V  V +       K
Sbjct: 134 GQRT-------KFHTKRDVSTPLRSTENGIVDQVMVTTNQEGLK 170


>gi|74099858|gb|AAZ99138.1| RpoB [Staphylococcus carnosus subsp. utilis]
 gi|74099860|gb|AAZ99139.1| RpoB [Staphylococcus carnosus subsp. utilis]
          Length = 161

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 97/161 (60%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V CR  G   +
Sbjct: 61  IETPYRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFISEEVVCRFRGNNTM 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + R+K+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MDRDKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|198279337|emb|CAP04703.1| RNA polymerase beta subunit [Pinus attenuata]
          Length = 272

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 100/244 (40%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           D+LVGK+TP+   ES  TPE +LL+ IFG +    R+  L  P G  G V+DVR  NR  
Sbjct: 173 DVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLXAPIGGRGRVIDVRWINRVB 232

Query: 950 IDKN 953
              +
Sbjct: 233 DSGD 236



 Score = 70.5 bits (171), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 80/224 (35%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L         +++ R+ N++    
Sbjct: 176  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLXAPIGGRGRVIDVRWINRV---- 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               B        V V+ + KR IQ G K+ GRHGNKGI+S +LP
Sbjct: 232  ---BDSGDNAETVXVYXSQKRKIQVGXKVXGRHGNKGIISIVLP 272


>gi|294721610|gb|ADF32952.1| RNA polymerase II second largest subunit [Sarcinomyces crustaceus]
          Length = 241

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 84/261 (32%), Gaps = 21/261 (8%)

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    +F R  +D+ +R      EQ E   
Sbjct: 2    GQNAIVAIACYGGYNQEDSVIMSQSSIDRGLF-RSLFYRAYMDQEKRVGMSVVEQFEKPT 60

Query: 969  RDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQD 1028
            R           +       I  G           K+  ++ D      R+Q        
Sbjct: 61   RADTLRMKHGTYDKLDDDGIIAPGTRVSGDDIIIGKTAPMAPDAEEMGQRTQLHVKRDTS 120

Query: 1029 EKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGD 1088
              ++     +  Q                             L+ VKV     +  Q GD
Sbjct: 121  TPLRSTESGIIDQVLL--------------------TTNVEGLKFVKVRTRTTKIPQIGD 160

Query: 1089 KMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGL 1148
            K A RHG KG +      EDMPF  DG   D+++NP  +PSRM +  + E  L       
Sbjct: 161  KFASRHGQKGTIGITYRQEDMPFTADGLTPDLIINPHAIPSRMTIAHLIECLLSKVGSLR 220

Query: 1149 GKKIKSLINDYKANGDISPLR 1169
            G++  +          IS L 
Sbjct: 221  GQEGDATPFTDVTVTQISTLL 241



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 37/150 (24%), Positives = 62/150 (41%), Gaps = 12/150 (8%)

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR---- 863
           G+N +VA   + GYN EDS+++S+  +   +F S+    +    +   +   E       
Sbjct: 2   GQNAIVAIACYGGYNQEDSVIMSQSSIDRGLFRSLFYRAYMDQEKRVGMSVVEQFEKPTR 61

Query: 864 -DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GII  G  V+  DI++GK  P     M P+ + +         
Sbjct: 62  ADTLRMKHGTYDKLDDDGIIAPGTRVSGDDIIIGKTAP-----MAPDAEEMGQRTQLHVK 116

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             RDTS  + S  SG +  V +       K
Sbjct: 117 --RDTSTPLRSTESGIIDQVLLTTNVEGLK 144


>gi|220961122|gb|ACL93027.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           hygroscopicus]
          Length = 180

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGIVTDEVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHFAENRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPLLKAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLLKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|161899557|ref|XP_001713004.1| second-largest subunit of DNA-directed RNA polymerase I [Bigelowiella
            natans]
 gi|75756499|gb|ABA27392.1| second-largest subunit of DNA-directed RNA polymerase I [Bigelowiella
            natans]
          Length = 1137

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 73/367 (19%), Positives = 125/367 (34%), Gaps = 77/367 (20%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
            Q  ++            G       K  K++  L      +   ++  +  +    + ++
Sbjct: 755  QNDMEDACVLNKFSSQNGLFHTIILKKVKQNNYLIEKDKEKIALTKNIRSLLNSLIINKS 814

Query: 1035 VESLKVQ--YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMK----------R 1082
            V +L       +S      + K K+++    D         VK     K          R
Sbjct: 815  VRNLCHNRFILSSIFNYTKKNKVKVQEYNNFDQFTYFGKEKVKSKTRFKFSLEITKNITR 874

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLK-DGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
             I  GDK+A  HG K +VS ++  ED+PF   DG   ++ LNP   PSRM +G + E  L
Sbjct: 875  NILVGDKLASLHGQKSVVSTLISREDLPFSFFDGIIPEVSLNPHSFPSRMTIGMLKEMAL 934

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
                +  GK +           +                                     
Sbjct: 935  LKNSIFTGKLLNLSDFTKHRKREYDWY--------------------------------- 961

Query: 1202 SGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV------GYIY 1255
                             I+   +        +S++ DG  G      +TV      G ++
Sbjct: 962  ---------------NDISVFFKEYGHTNINESLMIDGRLG------ITVKTFFYNGVVF 1000

Query: 1256 MLKLNHMVSDKVY--ARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQE 1313
              +L  MV+DK+    RS      +T+QP  G+   G  R GEME   + ++GA+ ++ +
Sbjct: 1001 YQRLPQMVNDKMQFSFRS--PTEPLTKQPRRGRKYGGAIRFGEMEKDALISHGASALVND 1058

Query: 1314 MLTIKSD 1320
             L+  SD
Sbjct: 1059 RLSKSSD 1065


>gi|91981526|gb|ABE68105.1| RNA polymerase subunit B [Pseudomonas sp. TM1B2]
 gi|91981530|gb|ABE68107.1| RNA polymerase subunit B [Pseudomonas sp. K93.3]
          Length = 154

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 86/154 (55%), Positives = 113/154 (73%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           R   E  +   E +  +D SPKQVVS+AASLIPF
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPF 154


>gi|307547641|gb|ADN44434.1| RNA polymerase II second largest subunit [Roccella montagnei]
          Length = 268

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 53/280 (18%), Positives = 89/280 (31%), Gaps = 23/280 (8%)

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     +  +     E
Sbjct: 5    THSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYI----E 60

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME--ILCGQNAVSGPKGFKKSTVLSSDL 1012
            +  SV    +E   + +  E +      Y +L +  ++     VSG       T      
Sbjct: 61   QQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDIIIGKTAPFQAP 120

Query: 1013 ISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLR 1072
            + E               V   + S +        +                       R
Sbjct: 121  LQENAEGGQRTKDHTKRDVSAPLRSTEAGIIDRVLL-----------------TTTEGKR 163

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
             VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++NP  +PSRM 
Sbjct: 164  SVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIINPHAIPSRMT 223

Query: 1133 VGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            +  + E  L       G++  +         +IS L  F 
Sbjct: 224  IAHLIECLLSKVSTVTGQEGDATPFTDVTVSNISELLRFA 263



 Score = 75.1 bits (183), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 68/177 (38%), Gaps = 10/177 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 5   THSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYIEQQQS 64

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 E        ++        + +D+ G++  G  V+  DI++GK  P        
Sbjct: 65  VGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDIIIGKTAPFQAPLQEN 124

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE-RSISVEREQI 964
            E   R     K    RD S  + S  +G +  V +    G    + R+ + +  QI
Sbjct: 125 AEGGQRT----KDHTKRDVSAPLRSTEAGIIDRVLLTTTEGKRSVKVRTRTTKVPQI 177


>gi|91981528|gb|ABE68106.1| RNA polymerase subunit B [Pseudomonas sp. P97.6]
          Length = 154

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 86/154 (55%), Positives = 113/154 (73%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           R   E  +   E +  +D SPKQVVS+AASLIPF
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPF 154


>gi|219564015|gb|ACL28191.1| RNA polymerase II second largest subunit [fungal sp. M35]
          Length = 287

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 54/295 (18%), Positives = 97/295 (32%), Gaps = 27/295 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFSCQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
               D+++NP  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 271



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|198279327|emb|CAP04698.1| RNA polymerase beta subunit [Pinus contorta]
          Length = 272

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 101/238 (42%), Positives = 150/238 (63%), Gaps = 10/238 (4%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+E   A  SG+  +A + G +E +DA+                       + +QRSN
Sbjct: 1   GTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSN 52

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISE
Sbjct: 53  TNTCTHQKPKIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISE 112

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  G
Sbjct: 113 RLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLGSWIETG 172

Query: 892 DILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           D+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR
Sbjct: 173 DVLVGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINR 230



 Score = 69.7 bits (169), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 81/224 (36%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 63   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 121

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 122  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 175

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N++    
Sbjct: 176  VGKLTPQTIEESLCTPEGRLLQTIFGIELSTARENCLRAPIGGRGRVIDVRWINRV---- 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
               B        V V+ + KR IQ G K+ GRHGNKGI+S +LP
Sbjct: 232  ---BDSGXNAETVXVYXSQKRKIQVGXKVXGRHGNKGIISIVLP 272


>gi|198279363|emb|CAP04716.1| RNA polymerase beta subunit [Pinus caribaea]
          Length = 237

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 99/239 (41%), Positives = 148/239 (61%), Gaps = 10/239 (4%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
             GTG+E   A  SG+  +A + G +E +DA+                       + +QR
Sbjct: 1   IAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQR 52

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LI
Sbjct: 53  SNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILI 112

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ + 
Sbjct: 113 SERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIE 172

Query: 890 PGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  L  P G  G V+DVR  N
Sbjct: 173 TGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLXAPIGGRGRVIDVRWIN 231


>gi|260594049|gb|ACX46319.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594051|gb|ACX46320.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 114/158 (72%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLS+     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSRSMGQSNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|151564524|gb|ABS17621.1| RpoB [Campylobacter canadensis]
          Length = 175

 Score =  162 bits (410), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 96/174 (55%), Positives = 129/174 (74%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIGL+
Sbjct: 2   QFMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  ++
Sbjct: 62  NSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNIIDD 121

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG NMQ
Sbjct: 122 LLEARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMGPNMQ 175


>gi|14971083|gb|AAK74106.1| RNA polymerase beta subunit [Bacillus sp. Ba813-S8553/2]
          Length = 258

 Score =  162 bits (409), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 85/197 (43%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S          +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLLKSNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    + E +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLXETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D  +L+ I     ++I
Sbjct: 172 LDRSTLDRILPYLEKNI 188



 Score = 58.5 bits (140), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL+       + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLLKSNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|11595846|emb|CAC18336.1| RNA polymerase beta subunit [Pseudomonas mendocina]
          Length = 148

 Score =  162 bits (409), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 86/148 (58%), Positives = 115/148 (77%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA+++L++ G   +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGQVTDEIVFLSAIEEADHVIAQASATLNDKGQLIDELVAVRHLNEFTVKAP 120

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 EDVTLMDVSPKQVVSVAASLIPFLEHDD 148


>gi|227826302|gb|ACP41878.1| RNA polymerase II [Heliosperma macranthum]
 gi|227826304|gb|ACP41879.1| RNA polymerase II [Heliosperma macranthum]
 gi|227826354|gb|ACP41904.1| RNA polymerase II [Silene zawadskii]
          Length = 243

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 235



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|227826292|gb|ACP41873.1| RNA polymerase II [Heliosperma alpestre]
          Length = 241

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 235



 Score = 75.1 bits (183), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|223585637|gb|ACM91689.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 162

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 98/162 (60%), Positives = 125/162 (77%), Gaps = 2/162 (1%)

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
           ALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPY
Sbjct: 1   ALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPY 60

Query: 603 RKVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREK 660
           RKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK
Sbjct: 61  RKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEK 120

Query: 661 IDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQAVP
Sbjct: 121 MDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVP 162


>gi|145307948|gb|ABP57268.1| RNA polymerase II second largest subunit [Schizangiella sp. ARSEF
            2237]
          Length = 266

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 49/278 (17%), Positives = 86/278 (30%), Gaps = 21/278 (7%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 10   YQLRMDTMANILYYPQKPLCTTRAMEYLRFRELPAGQNAIVAILCYSGYNQEDSLIMNQS 69

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    +F R  +D+ ++   +  E+ E   R+                  I  G 
Sbjct: 70   SIDRGLF-RSMFYRSYMDQEKKVGMMVMEEFEKPTRETTLRLKHGTYEKLEDDGLIAPGT 128

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  D      R++          ++     +  Q            
Sbjct: 129  RVSGDDIIIGKTAPIPPDSEELGQRTRTHSKRDASTPLRSTENGIVDQVML--------- 179

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VKV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 180  -----------TTNQEGLKFVKVRVRSTRIPQMGDKFASRHGQKGTIGVTYRQEDMPFNN 228

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            +G   D+++NP  +PSRM +G + E  L       G +
Sbjct: 229  EGIVPDLIINPHAIPSRMTIGHMVECLLSKVSTLSGNE 266



 Score = 79.7 bits (195), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/197 (17%), Positives = 68/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA + + G
Sbjct: 8   TNYQLRMDTMANILYYPQKPLC----------TTRAMEYLRFRELPAGQNAIVAILCYSG 57

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E            +     + 
Sbjct: 58  YNQEDSLIMNQSSIDRGLFRSMFYRSYMDQEKKVGMMVMEEFEKPTRETTLRLKHGTYEK 117

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         ++        +    RD S  + S  
Sbjct: 118 LEDDGLIAPGTRVSGDDIIIGKTAPIPPDSEELGQRT-------RTHSKRDASTPLRSTE 170

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 171 NGIVDQVMLTTNQEGLK 187


>gi|227826356|gb|ACP41905.1| RNA polymerase II [Viscaria vulgaris]
          Length = 244

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 235



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|227826298|gb|ACP41876.1| RNA polymerase II [Heliosperma insulare]
 gi|227826318|gb|ACP41886.1| RNA polymerase II [Heliosperma pusillum]
 gi|227826326|gb|ACP41890.1| RNA polymerase II [Heliosperma tommasinii]
 gi|227826328|gb|ACP41891.1| RNA polymerase II [Heliosperma veselskyi subsp. veselskyi]
 gi|227826338|gb|ACP41896.1| RNA polymerase II [Silene conica]
          Length = 243

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 235



 Score = 76.7 bits (187), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|82706453|gb|ABB89604.1| RNA polymerase II second largest subunit [Aleuria aurantia]
          Length = 619

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 100/692 (14%), Positives = 195/692 (28%), Gaps = 112/692 (16%)

Query: 474  QYRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
             +R    ++ + + + +               + +  + + +     +            
Sbjct: 1    LFRNLWKKLTKDVFKYLEKCVETGKEFSLPLAVKSNTISNGLKYSLATGNWGDQKKAMSA 60

Query: 522  ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
               +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61   KAGVSQVLNRYTFSSTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579  NIGLVSSLTS--FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
              GLV +L    +  V   G     +    + +   +     +      ++      +  
Sbjct: 117  ACGLVKNLALMSYITVGTPGHPLVNFMAEQNMEFLEEYEPQRSPNATKIFLNGVWIGIHR 176

Query: 637  DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMG 693
            D      LV        I      I D  D   K          P   ++ND ++     
Sbjct: 177  DPLHLVRLVQELRRRGSISHEVSVIRDIRDREFKIFTDAGRVCRPLFVIDNDPTHERRGQ 236

Query: 694  CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK-RAGIVEQVDAIRIVIRSVEGDL 752
              + ++ V  L+ +             + S          G VE VDA       +    
Sbjct: 237  LVLTKEHVMQLEEDHDL---------PEESRFGWKGLLECGAVEYVDAEEEETIMIVMTP 287

Query: 753  DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
            +       + +  +           + P+ K      +       PS  LG       + 
Sbjct: 288  EDLEVSRQVQQGYELAEETDPNKRVKTPINK---NTNQYTHCEIHPSMILG-------IC 337

Query: 813  VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG 872
             + +P+  +N          M  + +   + +  F                         
Sbjct: 338  ASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM--------------------- 374

Query: 873  LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
                    +  +             +       +   +  +  I      +  D+ +   
Sbjct: 375  ------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQ 428

Query: 933  SGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCG 992
            S +   +    +F R  +D+ +R      E+ E   R    +      +       +  G
Sbjct: 429  SSIDRGLF-RSLFYRAYMDQEKRIGMQVVEEFEKPTRGSTLKLKHGTYDKLDEDGLVAPG 487

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +++D                DE  QR     K    T     E+ 
Sbjct: 488  VRVSGEDIIIGKTAPITAD---------------ADEMGQRQKYHTKRDVSTPLRSTENG 532

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK--------------- 1097
              +++      D +     + VKV +   +  Q GDK A RHG K               
Sbjct: 533  IVDQVMLTTNADGL-----KFVKVRMRTTKIPQIGDKFASRHGQKVCFHIPPRECNVLIA 587

Query: 1098 ---GIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
               G +      EDMPF  +G   DI++NP  
Sbjct: 588  IVQGTIGITYRSEDMPFTCEGIVPDIIINPHA 619


>gi|74099892|gb|AAZ99155.1| RpoB [Staphylococcus schleiferi subsp. coagulans]
          Length = 161

 Score =  162 bits (409), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 95/161 (59%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDLETNTITDRIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|145307946|gb|ABP57267.1| RNA polymerase II second largest subunit [Schizangiella serpentis]
          Length = 263

 Score =  162 bits (409), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 49/278 (17%), Positives = 86/278 (30%), Gaps = 21/278 (7%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +             +       +   +  + AI      +  D+ +   S
Sbjct: 7    YQLRMDTMANILYYPQKPLCTTRAMEYLRFRELPAGQNAIVAILCYSGYNQEDSLIMNQS 66

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    +F R  +D+ ++   +  E+ E   R+                  I  G 
Sbjct: 67   SIDRGLF-RSMFYRSYMDQEKKVGMMVMEEFEKPTRETTLRLKHGTYEKLEDDGLIAPGT 125

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  D      R++          ++     +  Q            
Sbjct: 126  RVSGDDIIIGKTAPIPPDSEELGQRTRTHSKRDASTPLRSTENGIVDQVML--------- 176

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VKV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 177  -----------TTNQEGLKFVKVRVRSTRIPQMGDKFASRHGQKGTIGVTYRQEDMPFNN 225

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            +G   D+++NP  +PSRM +G + E  L       G +
Sbjct: 226  EGIVPDLIINPHAIPSRMTIGHMVECLLSKVSTLSGNE 263



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 34/197 (17%), Positives = 68/197 (34%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PL                      +L  G+N +VA + + G
Sbjct: 5   TNYQLRMDTMANILYYPQKPLC----------TTRAMEYLRFRELPAGQNAIVAILCYSG 54

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E            +     + 
Sbjct: 55  YNQEDSLIMNQSSIDRGLFRSMFYRSYMDQEKKVGMMVMEEFEKPTRETTLRLKHGTYEK 114

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         ++        +    RD S  + S  
Sbjct: 115 LEDDGLIAPGTRVSGDDIIIGKTAPIPPDSEELGQRT-------RTHSKRDASTPLRSTE 167

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 168 NGIVDQVMLTTNQEGLK 184


>gi|117667726|gb|ABK55909.1| RNA polymerase B subunit [Streptomyces graminofaciens]
 gi|157000413|gb|ABV00506.1| RNA polymerase subunit B [Streptomyces halstedii]
          Length = 180

 Score =  162 bits (409), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVTDGQVTDEVDYLTADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEARVLVRRRGGEVDYVPPTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G++++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCATDAGDVIKAEKDGVIQEVSADYVTVANDDG 175


>gi|307547555|gb|ADN44391.1| RNA polymerase II second largest subunit [Roccella applanata]
          Length = 289

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 91/289 (31%), Gaps = 25/289 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +     + 
Sbjct: 11   YPQKPLASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYR 70

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
             +     E+  SV    +E   + +  E +      Y +L +   +  G           
Sbjct: 71   TYI----EQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDGLVPPGVRVSGEDIIIG 126

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+    + +                E  QR  +  K          E    +++      
Sbjct: 127  KTAPFQAPMQENA------------EGGQRTKDHTKRDVSAPLRSTEAGIIDRVL----- 169

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D+++N
Sbjct: 170  -LTTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTTDGVVPDLIIN 228

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFL 1172
            P  +PSRM +  + E  L       G++  +         +IS L  F 
Sbjct: 229  PHAIPSRMTIAHLIECLLSKVSTVTGQEGDATPFTDVTVSNISELLKFA 277



 Score = 77.0 bits (188), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 74/205 (36%), Gaps = 20/205 (9%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +    +      Q+PL                      DL  G+N +VA   + GYN ED
Sbjct: 1   RMDTMSNXLYYPQKPL----------ASTHSMNYLKFRDLPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +       E        ++        + +D+ G
Sbjct: 51  SVIMNQSSIDRGLFRSLFYRTYIEQQQSVGFNALEEFEKPRRGEVMRTRPGTYEKLDDDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         E   R     K    RD S  + S  +G + 
Sbjct: 111 LVPPGVRVSGEDIIIGKTAPFQAPMQENAEGGQRT----KDHTKRDVSAPLRSTEAGIID 166

Query: 941 DVRIFNRHGIDKNE-RSISVEREQI 964
            V +    G    + R+ + +  QI
Sbjct: 167 RVLLTTTEGKRSVKVRTRTTKVPQI 191


>gi|293601676|gb|ADE48242.1| RNA polymerase II [Morchella punctipes]
          Length = 255

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 47/276 (17%), Positives = 87/276 (31%), Gaps = 21/276 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 61   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 119

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 120  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 165

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 166  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 219

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            D+++NP  +PSRM +  + E  L       G +  +
Sbjct: 220  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDA 255



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA + + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        +   +       +DE G++  G  V+
Sbjct: 58  DRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         ++       +K    RD S  + S  +G V  V +     
Sbjct: 118 GEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNAE 170

Query: 950 IDK 952
             K
Sbjct: 171 GLK 173


>gi|227826312|gb|ACP41883.1| RNA polymerase II [Heliosperma oliverae]
          Length = 248

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISKALQK 235



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGXPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|318085014|gb|ADV39397.1| RNA polymerase subunit B [Streptomyces gobitricini]
 gi|318085020|gb|ADV39400.1| RNA polymerase subunit B [Streptomyces lavendulocolor]
 gi|318085030|gb|ADV39405.1| RNA polymerase subunit B [Streptomyces luridus]
          Length = 180

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 90/175 (51%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGQVTDEVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFAEARVLVRRRGGEVDYVAPDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G++++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCATDAGDVIKAEKDGVIQEVSADYVTVANDDG 175


>gi|186694351|gb|ACC86149.1| DNA-directed RNA polymerase beta subunit [Campylobacter sp. 86/06]
          Length = 171

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 91/170 (53%), Positives = 124/170 (72%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG+GG+ + RAG+E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGEGGLVKERAGLEVRDVHSTHYGRICPVETPEGQNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           ++L ++++VN  GF+E PYRKV + KV+++VVYL+A +EEN  IA A++ LD  G+  E+
Sbjct: 61  NTLATYSKVNDLGFVEAPYRKVVNAKVSDEVVYLTATQEENLVIAAASTKLDSKGNIVED 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            V  R  GE IL  ++++  ID     +V + ASLIPFLE+DD+NR LMG
Sbjct: 121 FVEARKDGETILAKKDEVQLIDLCSGMIVGVTASLIPFLEHDDANRALMG 170


>gi|74099868|gb|AAZ99143.1| RpoB [Staphylococcus delphini]
          Length = 161

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 95/161 (59%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ + CR  G    
Sbjct: 61  IETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTT 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|50058759|gb|AAT69132.1| RNA polymerase II [Cuscuta europaea]
          Length = 191

 Score =  161 bits (408), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 94   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTAEGITPDIIVNPH 153

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 154  AIPSRMTIGQVIECIMGKVAAHMGKEGDATPFT 186



 Score = 40.8 bits (94), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 9/78 (11%)

Query: 862 TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
             +   +       +D+ G+   G  V+  D+++ K TP              A      
Sbjct: 19  RSNTMGMRHGSYNKLDDDGLAPPGTRVSGEDVIIRKTTPISPDD---------AQGQAAR 69

Query: 922 VDVRDTSLRVPSGVSGTV 939
              RD S  +P   +G V
Sbjct: 70  YTKRDHSTILPHSETGMV 87


>gi|151564508|gb|ABS17613.1| RpoB [Campylobacter canadensis]
          Length = 174

 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 96/173 (55%), Positives = 129/173 (74%)

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
           QLSQ  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NI
Sbjct: 1   QLSQFMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNI 60

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
           GL++SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+ 
Sbjct: 61  GLINSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNI 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            ++L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG
Sbjct: 121 IDDLLEARIDGETILAKREDIGLIDLTSCAIVGLAASLIPFLEHNDANRALMG 173


>gi|322709186|gb|EFZ00762.1| DNA-directed RNA polymerase I 135 kDa polypeptide [Metarhizium
            anisopliae ARSEF 23]
          Length = 1231

 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 102/304 (33%), Gaps = 62/304 (20%)

Query: 1021 WWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAM 1080
            W            N++ +           E  F  ++  I  G D     L+ V +   +
Sbjct: 864  WHTVTPDYNGNLVNLDGITHY--EKYKDGETGFVEEVRLI--GADTGGETLQTVSIKFRI 919

Query: 1081 KRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             R    GDK +                                     SR          
Sbjct: 920  PRSPIIGDKFS-------------------------------------SR---------- 932

Query: 1141 LGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS-DYDDDSVLRVAEQ 1199
                    G+K  +       +   S      + +I   +   +++     +S+   A  
Sbjct: 933  -------HGQKGVASQKWPAIDMPFSESGIQPDVIINPHAFPSRMTIGMFVESLAGKAGA 985

Query: 1200 WKSGVPVSTPV-FDGAD--EEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYM 1256
                   STP  FD  +   +     L  A     G   +Y G+TGE     + +G +Y 
Sbjct: 986  LHGLAQDSTPFKFDEENTAVDYFGHQLMKAGYSYHGNEPMYSGITGEELGADIYIGVVYY 1045

Query: 1257 LKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLT 1316
             +L HMV+DK   R+TG     T QP+ G+   GG R+GEME   + A+G A++LQ+ L 
Sbjct: 1046 QRLRHMVNDKFQVRTTGPVVPTTGQPIKGRKRGGGIRVGEMERDALLAHGTAFLLQDRLL 1105

Query: 1317 IKSD 1320
              SD
Sbjct: 1106 NCSD 1109



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 80/539 (14%), Positives = 176/539 (32%), Gaps = 73/539 (13%)

Query: 413 RVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVG---- 468
           R+ +    N++  ++    +   ++ +++ L  L  G+  +D+ D L N+ +   G    
Sbjct: 349 RIVLVHLGNVNVTEEQDLDKFRMLLFMVRKLYALAAGECAVDNPDALQNQEILLGGFLYG 408

Query: 469 ----EMLKNQYRLGLLRMERSIKERI-----SSVDIDSVMPQDLIN--AKPVVSAVCEFF 517
               E L     +G+    R    R      +S D     P  +     + + +A+  F 
Sbjct: 409 QILKERLDEFLSVGVRSSLRDFLRRHPEVPFTSEDFRKEFPGAIFKKANENLGNALEYFL 468

Query: 518 CSSQLS--------------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
            +  L                + E +N L  I+H R    + +G          +R + P
Sbjct: 469 STGNLQSPSGLDLQQTAGFTVVAEKLNFLRFISHFR---MVHRGAFFAQLRTTAVRKLLP 525

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY-RKVCDGKVTNDVVYLSAMEE 622
             +G +CP  T +G   GL++ L    ++       +     V +  V +    L++   
Sbjct: 526 ESWGFMCPVHTPDGSPCGLLNHLAHKCKIVTDHVDASKLPALVKELGVVDTSSALTSDN- 584

Query: 623 ENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPRE------KIDFIDAS-----PKQV 671
               +   +  +    +  E L    C     +          +I ++  S     P   
Sbjct: 585 ---VVVMMDGKILGWCTPKESLRIADCLRYWKVEGTHGVPLQLEIGYVPVSNGGSYPGVY 641

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAA--IVA 729
           ++   + +         +         Q    +      + +G+ + V         I+A
Sbjct: 642 ITSTPARMVRPVKYLPLQKEDFVGPYEQPYMSIAVLPQEIESGVSTHVEFDPTNMLSILA 701

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN--QRPLVKVGDE 787
                 +   + R + +   G     T G  I    +++  N++  +   Q P+V+    
Sbjct: 702 NMTPFSDFNQSPRNMYQCQMGKQTMGTPGAAI----RYRTDNKSYRIQTGQTPIVRA--- 754

Query: 788 VRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
                           +   G N +VA + + GY+ +D+M++++             +  
Sbjct: 755 -------PLHNDYGFDNFPNGMNAVVAVISYTGYDMDDAMILNKSAHERGFGHGTIYKTK 807

Query: 848 EVMARDTKLGPEEI-------TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           ++  +D                     VS      +D+ G+  VG  V  GD++    T
Sbjct: 808 KITLKDDSRTRAAKSVTKAFGFAPHSYVSASYQGMLDDDGLPHVGRLVQEGDVICAWHT 866



 Score = 63.6 bits (153), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 95/740 (12%), Positives = 206/740 (27%), Gaps = 123/740 (16%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS------GAAMLEFVSYEFDPP-- 84
              S++  +  N       + GL       F                +         P  
Sbjct: 43  HIESFNR-IFGNDGKKGLLDYGLTDIGTKTFLDGDERSGPEGKNRLRIRIKGVSLQKPQV 101

Query: 85  ----------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGD 134
                     +    +C  R ++Y   L  T    +   +     +           +G 
Sbjct: 102 PPTNKMARNREILPAECRERHVSYRGRLSATFEYSINGGEPIEFVRE----------LGQ 151

Query: 135 LPLMTKD------------------------GTFVIKGIQRIV----VSQLHRSPGIHFD 166
           +P+M K                         G F++ GI++I+    V+   R+  +  +
Sbjct: 152 VPIMIKSNRCHLENNSPAQLVQRKEESEELGGYFIVNGIEKIIRLLQVN--KRNFPMAIN 209

Query: 167 HDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVT 215
               ++  +G   Y   +   +      E    +++H         RI  R+    +PV 
Sbjct: 210 RPSFQSRGAGYTSYGVIVRSVRPD----ETSQTNVLHYLNDGNITFRISWRKNEYLIPVI 265

Query: 216 SFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVI 274
             L AL   ++ EI       +      + +        L+   K         T   + 
Sbjct: 266 MILKALVETNDREIFEGLIGPMGSKVTENTFLTD-RVELLLRTYKSYGLYSKSQTRAYLG 324

Query: 275 ESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETG----------EIYIEA 324
           E  + +  G+ +++ +  V    +    L  L         +            ++Y  A
Sbjct: 325 EKFRVVL-GVPETMSDYEVGTEFLRRIVLVHLGNVNVTEEQDLDKFRMLLFMVRKLYALA 383

Query: 325 GDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPG 384
                  + + + + EI     LY         ++  L    +   + +L D  R   P 
Sbjct: 384 AGECAVDNPDALQNQEILLGGFLY------GQILKERLDEFLSVGVRSSLRDFLRR-HPE 436

Query: 385 DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM-RLNLDTPDDVRHIRKEDIIAIIKIL 443
              T       F    F     +L       ++   L   +  D++      ++A     
Sbjct: 437 VPFTSEDFRKEFPGAIFKKANENLGNALEYFLSTGNLQSPSGLDLQQTAGFTVVAEKLNF 496

Query: 444 VDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDL 503
           +   +    +         R  +V ++L   +                      ++    
Sbjct: 497 LRFISHFRMVHRGAFFAQLRTTAVRKLLPESWGFMC-------PVHTPDGSPCGLLNHLA 549

Query: 504 INAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP 563
              K V   V        L +    V++ S +T    +  +    +        +R    
Sbjct: 550 HKCKIVTDHVDAS-KLPALVKELGVVDTSSALTSDNVVVMMDGKILGWCTPKESLRIADC 608

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
             Y ++      EG +   +     +  V+  G     Y      ++   V YL   +E+
Sbjct: 609 LRYWKV------EGTHGVPLQLEIGYVPVSNGGSYPGVYITSTPARMVRPVKYLPLQKED 662

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
             ++              +E            +       ++  P  ++SI A++ PF +
Sbjct: 663 --FVGPYEQPYMSIAVLPQE------------IESGVSTHVEFDPTNMLSILANMTPFSD 708

Query: 684 NDDSNRVLMGCNMQRQAVPL 703
            + S R +  C M +Q +  
Sbjct: 709 FNQSPRNMYQCQMGKQTMGT 728


>gi|318085068|gb|ADV39424.1| RNA polymerase subunit B [Streptomyces aurantiacus]
          Length = 180

 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 94/178 (52%), Positives = 127/178 (71%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGFVTDEVDYLTADEEDRFVIAQANAPLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EFRFEEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  + I + +G  +
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTIANDDGTYN 178


>gi|220961184|gb|ACL93058.1| RNA polymerase B subunit [Streptomyces luteoverticillatus]
          Length = 180

 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 93/178 (52%), Positives = 129/178 (72%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVNYLTADEEDRFVIAQANAALGE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEARVLVRRRGGEIDYIAPDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|220961194|gb|ACL93063.1| RNA polymerase B subunit [Streptomyces mashuensis]
          Length = 180

 Score =  161 bits (408), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 92/178 (51%), Positives = 128/178 (71%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVHYLTADEEDRFVIAQANAPLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFAEARVLVRRRGGEIDYIAPDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G  +
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDGTYN 178


>gi|227826286|gb|ACP41870.1| RNA polymerase II [Atocion rupestre]
 gi|227826336|gb|ACP41895.1| RNA polymerase II [Silene acaulis]
 gi|227826346|gb|ACP41900.1| RNA polymerase II [Silene menziesii]
 gi|227826348|gb|ACP41901.1| RNA polymerase II [Silene pseudoatocion]
          Length = 231

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 75.1 bits (183), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|117667782|gb|ABK55937.1| RNA polymerase B subunit [Streptomyces peucetius]
          Length = 180

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 130/175 (74%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVTDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEARVLVRRRGGEVDYVPPAEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G++++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCATDAGDVIKAEKDGVIQEVSADYVTVANDDG 175


>gi|227826278|gb|ACP41866.1| RNA polymerase II [Agrostemma githago]
          Length = 231

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS++++   +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNXSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKXTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|50058733|gb|AAT69119.1| RNA polymerase II [Porana velutina]
          Length = 223

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 89/245 (36%), Gaps = 23/245 (9%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R   
Sbjct: 2    IVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANT 60

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+T +S                  D+   
Sbjct: 61   MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DDAQG 103

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            +N    K  + TS    E    +++      D +     R VKV V   R  Q GDK + 
Sbjct: 104  QNARYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSS 158

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+ 
Sbjct: 159  RHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 218

Query: 1153 KSLIN 1157
             +   
Sbjct: 219  DATPF 223



 Score = 73.6 bits (179), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 50/134 (37%), Gaps = 14/134 (10%)

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DI 865
            +VA   + GYN EDS+++++  +    F S+    +    +      +E        + 
Sbjct: 1   AIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANT 60

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G+   G  V+  D+++GK TP  +           A         R
Sbjct: 61  MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQNARYTKR 111

Query: 926 DTSLRVPSGVSGTV 939
           D S  +    +G V
Sbjct: 112 DHSTSLRHSETGMV 125


>gi|224177815|gb|ACN38879.1| RNA polymerase II subunit [Sarcoscypha coccinea]
          Length = 569

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 95/606 (15%), Positives = 173/606 (28%), Gaps = 80/606 (13%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG   
Sbjct: 37   GVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQAC 92

Query: 581  GLVSSLTSFARVN--AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L   A ++    G     Y      +   +            +I      +  D 
Sbjct: 93   GLVKNLALMAYISVGTPGTPIVEYLAQRGMEFLEEYEPQRFPNATKVFINGVWVGVHRDP 152

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIP-FLENDDSNRVLMGCNM 696
                 +V        +      I D  D   K          P F  ++D      G  M
Sbjct: 153  IGLTRVVQDVRRKGIVSHEASVIRDIRDREFKIFTDAGRVCRPLFTIDNDPTSERRGQLM 212

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
             R+       E        E          + A   G ++ VDA       +    +   
Sbjct: 213  LRKEHIRRLQEDALAD---EDDQRFGWDGLLKA---GAIQYVDAEEEETIMIVMTPEDLE 266

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
               ++    + +         + P+      V +       PS  LG       +  + +
Sbjct: 267  LAREVQEGYEIEEDPDPMKRVKAPI---PPHVPQYTHCEIHPSMILG-------ICASII 316

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N       S R   +       +  +     +                       
Sbjct: 317  PFPDHNQ------SPRNTYQSAMGKQAMGVYLTNFAERM--------------------- 349

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  +  I      +  D+ +   S + 
Sbjct: 350  --DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSID 407

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQ 993
              +    +F R  +D+ +R   +  + +E   +      + L    Y +L +   +  G 
Sbjct: 408  RGLF-RSLFYRTYMDQEKR---IGMQVVEEFEKPMRGNTLRLKHGTYDKLDDDGLVAPGV 463

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +S D      R ++         ++     +  Q   S        
Sbjct: 464  RVTGEDIIIGKTAPISPDADEMGQRQKYHTKRDVSTPLRSTESGIVDQVMLS-------- 515

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             L+ VKV +   +  Q GDK A RHG KG +      EDMPF  
Sbjct: 516  ------------TNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTC 563

Query: 1114 DGTPVD 1119
            +G   D
Sbjct: 564  EGIVPD 569


>gi|220961138|gb|ACL93035.1| RNA polymerase B subunit [Streptomyces violaceusniger]
 gi|220961212|gb|ACL93072.1| RNA polymerase B subunit [Streptomyces javensis]
 gi|220961214|gb|ACL93073.1| RNA polymerase B subunit [Streptomyces yogyakartensis]
          Length = 180

 Score =  161 bits (407), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 125/175 (71%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG VT++V YL+A EE+   IAQAN+ L  
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGVVTDEVHYLTADEEDRFVIAQANAPLTN 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHFAENRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|286143014|gb|ADC41537.1| RNA polymerase beta subunit [Streptomyces mashuensis]
          Length = 185

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 107/192 (55%), Positives = 142/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + 
Sbjct: 1   ANRALMGSNMMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G         + YR+ KF RSNQ T  NQ+ +V  GD V    ++ADGPST+ G++A
Sbjct: 61  NDDGT-------YNTYRVAKFNRSNQGTSFNQKVVVDEGDRVVTGQVLADGPSTENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|260594115|gb|ACX46352.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 84/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS IT+ RR+SA G GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITYKRRVSAPGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++A  N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYASTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKALEDVTLMDVSPKQVVSVAAS 158


>gi|227826344|gb|ACP41899.1| RNA polymerase II [Silene latifolia]
          Length = 231

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 55/136 (40%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D  + +    SG V+
Sbjct: 112 KDHXISLRHSESGIVL 127


>gi|227826342|gb|ACP41898.1| RNA polymerase II [Silene integripetala]
          Length = 231

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|220961162|gb|ACL93047.1| RNA polymerase B subunit [Streptomyces ehimensis]
          Length = 180

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 92/178 (51%), Positives = 129/178 (72%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVNYLTADEEDRFVIAQANAALGD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEARVLVRRRGGEIDYIAPDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|4972803|gb|AAD34797.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            mustelae]
          Length = 178

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 46/104 (44%), Positives = 63/104 (60%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQ  GEMEVW ++AYGAAY L+EMLT+KSDDV GR   Y++I  G    E+  PE+F V
Sbjct: 1    GGQSFGEMEVWALEAYGAAYTLKEMLTVKSDDVKGRENAYKAITKGEAVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNS--------AKMEEIPDFNKCEL 1385
            L KE+Q+LGL +++       +         + +   DFN  +L
Sbjct: 61   LTKELQSLGLDVNIFGDDVDENGQPKPIVVEEEKRPKDFNTFQL 104


>gi|227826282|gb|ACP41868.1| RNA polymerase II [Atocion armeria]
          Length = 231

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 73.6 bits (179), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 55/136 (40%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN E S+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAISCYSGYNQEYSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|50058747|gb|AAT69126.1| RNA polymerase II [Maripa glabra]
          Length = 228

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 54/246 (21%), Positives = 88/246 (35%), Gaps = 23/246 (9%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R   
Sbjct: 2    IVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRANT 60

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+T +S                  D+   
Sbjct: 61   MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DDAQG 103

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            +     K  + TS    E    +++      D +     R VKV V   R  Q GDK + 
Sbjct: 104  QASRYTKRDHSTSLRHSETGIVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSS 158

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+ 
Sbjct: 159  RHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 218

Query: 1153 KSLIND 1158
             +    
Sbjct: 219  DATPFT 224



 Score = 73.6 bits (179), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 50/134 (37%), Gaps = 14/134 (10%)

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DI 865
            +VA   + GYN EDS+++++  +    F S+    +    +      +E        + 
Sbjct: 1   AIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANT 60

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G+   G  V+  D+++GK TP  +           A         R
Sbjct: 61  MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTKR 111

Query: 926 DTSLRVPSGVSGTV 939
           D S  +    +G V
Sbjct: 112 DHSTSLRHSETGIV 125


>gi|220961196|gb|ACL93064.1| RNA polymerase B subunit [Streptomyces griseoverticillatus]
 gi|220961204|gb|ACL93068.1| RNA polymerase B subunit [Streptomyces cinnamoneus]
          Length = 180

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 91/178 (51%), Positives = 129/178 (72%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGQVTDEVHYLTADEEDRFVIAQANAALGD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEARVLVRRRGGEIDYIAPDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|220961160|gb|ACL93046.1| RNA polymerase B subunit [Streptomyces abikoensis]
          Length = 180

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 93/178 (52%), Positives = 130/178 (73%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGQVTDEVHYLTADEEDRFVIAQANAALGE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTEARVLVRRRGGEIDYIAPDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|219564047|gb|ACL28207.1| RNA polymerase II second largest subunit [fungal sp. M174]
          Length = 255

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 51/277 (18%), Positives = 93/277 (33%), Gaps = 27/277 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   +    + + L    Y ++ E   I  G     
Sbjct: 63   RSLFYRTYQDQE----KMIGHSVLEQFEKPMRSDTLRLKHGTYDKIDEDGVIAPGVRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E+ QR  + +K    T     E    +++
Sbjct: 119  EDIIIGKTAPMAPD---------------SEEQGQRQKQHIKRDVSTPLRSTESGIVDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MLTTTGD-----GSRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
             DI++NP  +PSRM +  + E  L       G +  +
Sbjct: 219  PDIIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDA 255


>gi|220961128|gb|ACL93030.1| RNA polymerase B subunit [Streptomyces endus]
 gi|220961170|gb|ACL93051.1| RNA polymerase B subunit [Streptomyces sporocinereus]
 gi|220961222|gb|ACL93077.1| RNA polymerase B subunit [Streptomyces demainii]
 gi|325551438|gb|ADZ28560.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           hygroscopicus]
          Length = 180

 Score =  161 bits (407), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT+ V +L+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGVVTDQVDFLTADEEDRFVIAQANAPLAE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D ++ E  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DNTYAENRVLVRRRGGEVDYVPGSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|151564520|gb|ABS17619.1| RpoB [Campylobacter canadensis]
          Length = 175

 Score =  161 bits (407), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 96/174 (55%), Positives = 129/174 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            QLSQ  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG N
Sbjct: 1   GQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+
Sbjct: 61  IGLINSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGN 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             ++L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG
Sbjct: 121 IIDDLLEARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMG 174


>gi|219564031|gb|ACL28199.1| RNA polymerase II second largest subunit [fungal sp. M141]
          Length = 263

 Score =  161 bits (407), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 90/284 (31%), Gaps = 27/284 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLKHGTYEKLDEDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D      R++          ++     +  Q              
Sbjct: 117  SGEDIIIGKTAPMAPDAEEMGQRTKAHTKRDASTPLRSTENGIVDQVLI----------- 165

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 166  ---------TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTVEG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDY 1159
               D+++NP  +PSRM +  + E  L       G +  +     
Sbjct: 217  VVPDLIINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDATPFTE 260



 Score = 84.7 bits (208), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 67/177 (37%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +     + +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPYRSDTLKLKHGTYEKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P        EE   R     KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPMA---PDAEEMGQRT----KAHTKRDASTPLRSTENGIVDQVLITT 167


>gi|55650652|emb|CAF32197.1| RNA polymerase B subunit [Nostoc edaphicum X]
          Length = 187

 Score =  161 bits (407), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 92/192 (47%), Positives = 125/192 (65%), Gaps = 6/192 (3%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            IA  +  +DE G     LV  R   E      E++D++  SP Q+VS+A S+IPFLE+D
Sbjct: 2   RIAPGDIPVDETGHIIGPLVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +
Sbjct: 62  DANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRV 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R      +        Y L K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+L
Sbjct: 122 RPKPNTSE------IKYTLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGEL 175

Query: 806 ALGRNMLVAFMP 817
           ALG+N++VA+MP
Sbjct: 176 ALGQNIVVAYMP 187


>gi|227826284|gb|ACP41869.1| RNA polymerase II [Atocion lerchenfeldianum]
          Length = 231

 Score =  161 bits (407), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 38/102 (37%), Positives = 51/102 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 55/136 (40%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN E S+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIXCYSGYNQEYSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|151564510|gb|ABS17614.1| RpoB [Campylobacter canadensis]
          Length = 174

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 96/174 (55%), Positives = 129/174 (74%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
            QLSQ  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG N
Sbjct: 1   GQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+
Sbjct: 61  IGLINSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGN 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             ++L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG
Sbjct: 121 IIDDLLEARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMG 174


>gi|318085006|gb|ADV39393.1| RNA polymerase subunit B [Streptomyces cinereoruber subsp.
           fructofermentans]
          Length = 180

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANAVLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F+E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFSEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  + + + +G
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTVANDDG 175


>gi|194320296|gb|ACF48389.1| RNA polymerase II second largest subunit [Stictis urceolatum]
          Length = 318

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 62/396 (15%), Positives = 112/396 (28%), Gaps = 83/396 (20%)

Query: 870  EEGLKNIDE--CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
            E  L N DE    +  +             +       +   +  + AI      +  D+
Sbjct: 1    EFFLTNFDERIDTMSNILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDS 60

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R  +++ +R      E  E     + D    L    Y +L 
Sbjct: 61   VIMNQSSIDRGLF-RSLFYRAYVEQEKRVGMSLVEHFERPM--RSDTLR-LKHGTYEKLD 116

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K++ + +D      R++          ++     +      
Sbjct: 117  DDGLVAPGVRVSGEDIIIGKTSPIPADAEEMGQRTKLHTKRDASIPLRSTENGI------ 170

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                        ++K+          L+ VKV     +  Q GDK A RHG KG +    
Sbjct: 171  ------------VDKVLL--TTNAEGLKFVKVRTRATKIPQIGDKFASRHGQKGTIGITY 216

Query: 1105 PCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGD 1164
              EDMPF  +G   D+++NP  +PSRM +  + E  L       G +  +          
Sbjct: 217  RTEDMPFSAEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTVDS 276

Query: 1165 ISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLR 1224
            +S L    E    +                                              
Sbjct: 277  VSRLLR--EHGYQSRGFEVM---------------------------------------- 294

Query: 1225 MADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLN 1260
                  +G +    G         V +G  Y  +L 
Sbjct: 295  -----YNGHT----GR---KLVAQVFLGPTYYQRLK 318



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 71/197 (36%), Gaps = 22/197 (11%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                +    +      Q+PL                      +L  G+N +VA   + G
Sbjct: 5   TNFDERIDTMSNILYYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSG 54

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKN 875
           YN EDS+++++  +   +F S+    +    +   +   E     +  D   +     + 
Sbjct: 55  YNQEDSVIMNQSSIDRGLFRSLFYRAYVEQEKRVGMSLVEHFERPMRSDTLRLKHGTYEK 114

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G++  G  V+  DI++GK +P         ++        K    RD S+ + S  
Sbjct: 115 LDDDGLVAPGVRVSGEDIIIGKTSPIPADAEEMGQRT-------KLHTKRDASIPLRSTE 167

Query: 936 SGTVVDVRIFNRHGIDK 952
           +G V  V +       K
Sbjct: 168 NGIVDKVLLTTNAEGLK 184


>gi|50058727|gb|AAT69116.1| RNA polymerase II [Evolvulus glomeratus]
          Length = 228

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 54/246 (21%), Positives = 89/246 (36%), Gaps = 23/246 (9%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R   
Sbjct: 1    IVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGKPDRSNT 59

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+T +S                  D+   
Sbjct: 60   MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DDAQG 102

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            ++    K  + TS    E    +++      D +     R VKV V   R  Q GDK + 
Sbjct: 103  QSARYTKRDHSTSLRHSETGMVDQVLMTTNADGL-----RFVKVRVRSVRIPQIGDKFSS 157

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+ 
Sbjct: 158  RHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 217

Query: 1153 KSLIND 1158
             +    
Sbjct: 218  DATPFT 223



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 14/140 (10%)

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIP 866
           +VA   + GYN EDS+++++  +    F S+    +    +      +E        +  
Sbjct: 1   IVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGKPDRSNTM 60

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +       +D+ G+   G  V+  D+++GK TP  +           A         RD
Sbjct: 61  GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQSARYTKRD 111

Query: 927 TSLRVPSGVSGTVVDVRIFN 946
            S  +    +G V  V +  
Sbjct: 112 HSTSLRHSETGMVDQVLMTT 131


>gi|151573035|gb|ABS17688.1| RNA polymerase II [Fusarium sp. NRRL 43373]
 gi|151573041|gb|ABS17692.1| RNA polymerase II [Fusarium sp. NRRL 43378]
 gi|151573053|gb|ABS17700.1| RNA polymerase II [Fusarium sp. NRRL 43435]
 gi|151573062|gb|ABS17706.1| RNA polymerase II [Fusarium sp. NRRL 43439]
 gi|151573065|gb|ABS17708.1| RNA polymerase II [Fusarium sp. NRRL 43443]
 gi|151573068|gb|ABS17710.1| RNA polymerase II [Fusarium sp. NRRL 43444]
 gi|151573077|gb|ABS17716.1| RNA polymerase II [Fusarium sp. NRRL 43450]
 gi|151573083|gb|ABS17720.1| RNA polymerase II [Fusarium sp. NRRL 43452]
 gi|151573086|gb|ABS17722.1| RNA polymerase II [Fusarium sp. NRRL 43453]
 gi|151573095|gb|ABS17728.1| RNA polymerase II [Fusarium sp. FSSC_8a KOD-2010]
 gi|151573098|gb|ABS17730.1| RNA polymerase II [Fusarium sp. FSSC_5a KOD-2010]
 gi|151573110|gb|ABS17738.1| RNA polymerase II [Fusarium sp. NRRL 43474]
 gi|151573122|gb|ABS17746.1| RNA polymerase II [Fusarium sp. NRRL 43492]
 gi|151573125|gb|ABS17748.1| RNA polymerase II [Fusarium sp. NRRL 43493]
 gi|151573215|gb|ABS17808.1| RNA polymerase II [Fusarium sp. NRRL 43649]
 gi|151573221|gb|ABS17812.1| RNA polymerase II [Fusarium sp. NRRL 43651]
 gi|151573224|gb|ABS17814.1| RNA polymerase II [Fusarium sp. NRRL 43652]
 gi|151573245|gb|ABS17828.1| RNA polymerase II [Fusarium sp. NRRL 43659]
 gi|151573248|gb|ABS17830.1| RNA polymerase II [Fusarium sp. NRRL 43660]
 gi|151573251|gb|ABS17832.1| RNA polymerase II [Fusarium sp. NRRL 43661]
 gi|151573275|gb|ABS17848.1| RNA polymerase II [Fusarium sp. NRRL 43673]
 gi|151573299|gb|ABS17864.1| RNA polymerase II [Fusarium sp. NRRL 43681]
 gi|151573323|gb|ABS17880.1| RNA polymerase II [Fusarium sp. NRRL 43691]
 gi|151573354|gb|ABS17900.1| RNA polymerase II [Fusarium sp. NRRL 43702]
 gi|151573357|gb|ABS17902.1| RNA polymerase II [Fusarium sp. NRRL 43703]
 gi|151573360|gb|ABS17904.1| RNA polymerase II [Fusarium sp. NRRL 43704]
 gi|151573666|gb|ABS18107.1| RNA polymerase II [Fusarium sp. NRRL 43374]
 gi|151573669|gb|ABS18109.1| RNA polymerase II [Fusarium sp. NRRL 43458]
 gi|151573672|gb|ABS18111.1| RNA polymerase II [Fusarium sp. NRRL 43464]
          Length = 300

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 53/373 (14%), Positives = 98/373 (26%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +                              ++
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFT-------------------------DVT 256

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  +LR       G  +                        +G +    G       
Sbjct: 257  VDSVSELLRKHGYQSRGFEIM----------------------YNGHT----GR---KLR 287

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 288  AQVFFGPTYYQRL 300



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|4972807|gb|AAD34799.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            muridarum]
          Length = 179

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 45/106 (42%), Positives = 63/106 (59%), Gaps = 10/106 (9%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTIKSDDV GR   YE+I  G    ++  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDVNGRKEAYEAITKGFPVGDSAIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKN----------SAKMEEIPDFNKCEL 1385
            L KE+Q+L L +++   +               + +   DF+  +L
Sbjct: 61   LTKELQSLALDVNVYGDKVDEFGLIKPLVVGEDEKDRPRDFSAFQL 106


>gi|283806291|dbj|BAI66386.1| RNA polymerase second largest subunit [Roussoella hysterioides]
          Length = 308

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 48/287 (16%), Positives = 91/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 13   YPQKPLATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RSLFY 71

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 72   RAYTEQEKR---IGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDGVVSPGVRVSGDDIIIG 128

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D      ++           ++     +  Q                      
Sbjct: 129  KTAPIATDAKELGQKTSMHTKRDVSTPLRSTENGIVDQ--------------------VL 168

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 169  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGLTPDIIIN 228

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 229  PHAIPSRMTIAHLVECLLSKVGALKGAEGDATPFTDVTVDSVSKLLE 275



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           + +         Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 3   RMETMMNVLYYPQKPL----------ATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        D   +       +D+ G
Sbjct: 53  SVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         +K             RD S  + S  +G V 
Sbjct: 113 VVSPGVRVSGDDIIIGKTAPIATDAKELGQKT-------SMHTKRDVSTPLRSTENGIVD 165

Query: 941 DVRIFN 946
            V    
Sbjct: 166 QVLFTT 171


>gi|50058755|gb|AAT69130.1| RNA polymerase II [Dinetus truncatus]
          Length = 227

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 222



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 26/132 (19%), Positives = 48/132 (36%), Gaps = 14/132 (10%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA     GYN EDS+++++  +    F S+    +    +      +E        +   
Sbjct: 1   VAIAWXSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP  +           A         RD 
Sbjct: 61  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDH 111

Query: 928 SLRVPSGVSGTV 939
           S  +    +G V
Sbjct: 112 STSLRHSETGMV 123


>gi|283806300|dbj|BAI66392.1| RNA polymerase second largest subunit [Roussoellopsis tosaensis]
          Length = 306

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 47/287 (16%), Positives = 91/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 11   YPQKPLATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RSLFY 69

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 70   RAYTEQEKR---IGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDGVVSPGVRVSGDDIIIG 126

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D      ++           ++     +  Q                      
Sbjct: 127  KTAPIATDAKELGQKTSMHTKRDVSTPLRSTENGIVDQ--------------------VL 166

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 167  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGLTPDLIIN 226

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 227  PHAIPSRMTIAHLVECLLSKVGALKGAEGDATPFTDVTVDSVSKLLE 273



 Score = 79.0 bits (193), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 62/182 (34%), Gaps = 22/182 (12%)

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 5   MMNVLYYPQKPL----------ATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIM 54

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +D+ G++  
Sbjct: 55  NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDGVVSP 114

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  DI++GK  P         +K             RD S  + S  +G V  V  
Sbjct: 115 GVRVSGDDIIIGKTAPIATDAKELGQKT-------SMHTKRDVSTPLRSTENGIVDQVLF 167

Query: 945 FN 946
             
Sbjct: 168 TT 169


>gi|208609797|dbj|BAG72360.1| RNA polymerase II second largest subunit [Litsea ferruginea]
          Length = 170

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 45.1 bits (105), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|208609843|dbj|BAG72383.1| RNA polymerase II second largest subunit [Litsea resinosa]
          Length = 167

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 46.6 bits (109), Expect = 0.033,   Method: Composition-based stats.
 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+ GD+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGGDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|198279385|emb|CAP04727.1| RNA polymerase beta subunit [Pinus ponderosa]
          Length = 270

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 99/242 (40%), Positives = 149/242 (61%), Gaps = 10/242 (4%)

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+E   A  SG+  +A + G +E +DA+                       + +QRSN N
Sbjct: 1   GLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTN 52

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+
Sbjct: 53  TCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERL 112

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+
Sbjct: 113 VYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDV 172

Query: 894 LVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR    
Sbjct: 173 LVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDS 232

Query: 952 KN 953
            +
Sbjct: 233 GD 234



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 61   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 119

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 120  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 173

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 174  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 232  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 270


>gi|50058707|gb|AAT69106.1| RNA polymerase II [Lepistemon owariensis]
          Length = 225

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 222



 Score = 72.0 bits (175), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/132 (19%), Positives = 49/132 (37%), Gaps = 14/132 (10%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA   + GYN EDS+++++  +    F S+    +    +      +E        +   
Sbjct: 1   VAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP  +           A         RD 
Sbjct: 61  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDH 111

Query: 928 SLRVPSGVSGTV 939
           S  +    +G V
Sbjct: 112 STSLRHSETGMV 123


>gi|225698399|gb|ACO07317.1| RpoB [Pasteurellaceae bacterium TIS19658]
          Length = 156

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 91/156 (58%), Positives = 116/156 (74%), Gaps = 1/156 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDED  FT+  V
Sbjct: 61  LSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDEDFRFTDAYV 120

Query: 646 FCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             R   GE  L   E+I ++D S +QVVS+AA+LIP
Sbjct: 121 TARGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIP 156


>gi|227826300|gb|ACP41877.1| RNA polymerase II [Heliosperma intonsum]
 gi|227826310|gb|ACP41882.1| RNA polymerase II [Heliosperma monachorum]
 gi|227826314|gb|ACP41884.1| RNA polymerase II [Heliosperma pusillum]
 gi|227826316|gb|ACP41885.1| RNA polymerase II [Heliosperma pusillum]
 gi|227826320|gb|ACP41887.1| RNA polymerase II [Heliosperma pusillum]
 gi|227826322|gb|ACP41888.1| RNA polymerase II [Heliosperma pusillum]
 gi|227826324|gb|ACP41889.1| RNA polymerase II [Heliosperma retzdorffianum]
 gi|227826330|gb|ACP41892.1| RNA polymerase II [Heliosperma veselskyi subsp. widderi]
          Length = 229

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 37/100 (37%), Positives = 50/100 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             +PSRM +GQ+ E  +G     +GK+  +         +I
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNI 229



 Score = 76.3 bits (186), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|208609849|dbj|BAG72386.1| RNA polymerase II second largest subunit [Litsea rubicunda]
          Length = 167

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 41.6 bits (96), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G   +  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRASGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|208609695|dbj|BAG72309.1| RNA polymerase II second largest subunit [Actinodaphne macrophylla]
          Length = 167

 Score =  161 bits (406), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D ++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDAIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|151573624|gb|ABS18079.1| RNA polymerase II [Fusarium sp. NRRL 32173]
          Length = 300

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 53/373 (14%), Positives = 96/373 (25%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQESQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSNEGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +          +S L    +    +        
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLR--KHGYQSRGFENM-- 277

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                        +G +    G       
Sbjct: 278  -------------------------------------------YNGHT----GR---KLR 287

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 288  AQVFFGPTYYQRL 300



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQESQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|91981514|gb|ABE68099.1| RNA polymerase subunit B [Pseudomonas sp. Q7-87]
 gi|91981518|gb|ABE68101.1| RNA polymerase subunit B [Pseudomonas sp. Q12-87]
          Length = 153

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 85/153 (55%), Positives = 112/153 (73%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           R   E  +   E +  +D SPKQVVS+AASLIP
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIP 153


>gi|50058753|gb|AAT69129.1| RNA polymerase II [Poranopsis paniculata]
          Length = 221

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 129  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 188

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 189  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 221



 Score = 71.3 bits (173), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 48/131 (36%), Gaps = 14/131 (10%)

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
           A   + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 1   AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGM 60

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           A         RD S
Sbjct: 61  RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHS 111

Query: 929 LRVPSGVSGTV 939
             +    +G V
Sbjct: 112 TSLRHSETGMV 122


>gi|208609731|dbj|BAG72327.1| RNA polymerase II second largest subunit [Lindera erythrocarpa]
          Length = 167

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 45.1 bits (105), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDE--------AQQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|283806294|dbj|BAI66388.1| RNA polymerase second largest subunit [Roussoella hysterioides]
          Length = 309

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 48/287 (16%), Positives = 91/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 13   YPQKPLATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RSLFY 71

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 72   RAYTEQEKR---IGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDGVVSPGVRVSGDDIIIG 128

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D      ++           ++     +  Q                      
Sbjct: 129  KTAPIATDAKELGQKTSMHTKRDVSTPLRSTENGIVDQ--------------------VL 168

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 169  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGLTPDIIIN 228

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 229  PHAIPSRMTIAHLVECLLSKVGSLKGAEGDATPFTDVTVDSVSKLLE 275



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           + +         Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 3   RMETMMNVLYYPQKPL----------ATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        D   +       +D+ G
Sbjct: 53  SVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         +K             RD S  + S  +G V 
Sbjct: 113 VVSPGVRVSGDDIIIGKTAPIATDAKELGQKT-------SMHTKRDVSTPLRSTENGIVD 165

Query: 941 DVRIFN 946
            V    
Sbjct: 166 QVLFTT 171


>gi|220961144|gb|ACL93038.1| RNA polymerase B subunit [Streptomyces albulus]
          Length = 180

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LVP +++ ++D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFAEQRVLVRRRGGEVDLVPADEVHYMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKNGVVQEVSADYITVANDDG 175


>gi|208609729|dbj|BAG72326.1| RNA polymerase II second largest subunit [Lindera erythrocarpa]
          Length = 167

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +G++  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGREGDATPFT 164



 Score = 45.1 bits (105), Expect = 0.100,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDE--------AQQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|45331292|gb|AAS57917.1| DNA-dependent RNA polymerase beta [Enterococcus faecium]
          Length = 164

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 88/164 (53%), Positives = 122/164 (74%), Gaps = 2/164 (1%)

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
           PVV+++ EFF SSQLSQ  +  N L  +T+ RRLSALG GG+ R RAG E+RDVH +HYG
Sbjct: 1   PVVASIKEFFGSSQLSQFMDQTNPLGELTYKRRLSALGPGGLTRDRAGYEVRDVHYSHYG 60

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDG--KVTNDVVYLSAMEEENR 625
           R+CP ET EG NIGL++SL+S+A+VN +GFIETPYR+V     +VT+ + YL+A  E++ 
Sbjct: 61  RMCPIETPEGPNIGLINSLSSYAKVNKFGFIETPYRRVDRETGRVTDQIDYLTADIEDHY 120

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
            +AQANS L+EDG+F +++V  R   E + V  +K+D++D SPK
Sbjct: 121 IVAQANSPLNEDGTFAQDVVMARAQSENLEVSIDKVDYMDVSPK 164


>gi|283806297|dbj|BAI66390.1| RNA polymerase second largest subunit [Roussoella pustulans]
          Length = 307

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 48/287 (16%), Positives = 91/287 (31%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 12   YPQKPLATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQEDSVIMNQSSIDRGLF-RSLFY 70

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   ++ +R   +    +E   +    + + +    Y +L +   +  G           
Sbjct: 71   RAYTEQEKR---IGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDGVVSPGVRVSGDDIIIG 127

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D      ++           ++     +  Q                      
Sbjct: 128  KTAPIATDAKELGQKTSMHTKRDVSTPLRSTENGIVDQ--------------------VL 167

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV     +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 168  FTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRHEDMPFTREGLTPDIIIN 227

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 228  PHAIPSRMTIAHLVECLLSKVGALKGAEGDATPFTDVTVDSVSKLLE 274



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           + +         Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 2   RMETMMNVLYYPQKPL----------ATTRAMEYLKFRELPAGQNAIVAIAVYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        D   +       +D+ G
Sbjct: 52  SVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRGDTLRMKGGTYDKLDDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         +K             RD S  + S  +G V 
Sbjct: 112 VVSPGVRVSGDDIIIGKTAPIATDAKELGQKT-------SMHTKRDVSTPLRSTENGIVD 164

Query: 941 DVRIFN 946
            V    
Sbjct: 165 QVLFTT 170


>gi|227826308|gb|ACP41881.1| RNA polymerase II [Heliosperma macranthum]
          Length = 225

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFT 222



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|208609859|dbj|BAG72391.1| RNA polymerase II second largest subunit [Machilus rimosa]
          Length = 167

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|208609737|dbj|BAG72330.1| RNA polymerase II second largest subunit [Lindera glauca]
          Length = 167

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 42.8 bits (99), Expect = 0.50,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +++ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLNDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|227826306|gb|ACP41880.1| RNA polymerase II [Heliosperma macranthum]
          Length = 225

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFT 222



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMVMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|50058715|gb|AAT69110.1| RNA polymerase II [Convolvulus mauritanicus]
          Length = 219

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 122  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 181

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 182  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 214



 Score = 64.7 bits (156), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 44/124 (35%), Gaps = 14/124 (11%)

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 1   YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGCPDRANTMGMRHGSYDK 60

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D  G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 61  LDPDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHSTSLRHSE 111

Query: 936 SGTV 939
           +G V
Sbjct: 112 TGMV 115


>gi|219564049|gb|ACL28208.1| RNA polymerase II second largest subunit [fungal sp. M175]
          Length = 259

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 48/281 (17%), Positives = 91/281 (32%), Gaps = 27/281 (9%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   +    + + +    Y ++ +   I  G     
Sbjct: 63   RSLFYRTYQDQE----KQIGHSVLESFEKPSRTDTLRMKHGTYDKIDDDGIIAPGVRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E    +++
Sbjct: 119  EDIIMGKTAPMAPD---------------AEELGQRQKHHVKRDVSTPLRSTEAGVVDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MLTTTGD-----GTRFAKVRVRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGVV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 219  PDLIINPHAIPSRMTIAHLIECQLSKVATLRGDEGDATPFT 259



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 40/180 (22%), Positives = 65/180 (36%), Gaps = 23/180 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL +                    +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPLAR----------TMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    ++   +       E        D   +       ID+ GII  G  V+
Sbjct: 58  DRGLFRSLFYRTYQDQEKQIGHSVLESFEKPSRTDTLRMKHGTYDKIDDDGIIAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P     M P+ + L             T LR        VVD  +    G
Sbjct: 118 GEDIIMGKTAP-----MAPDAEELGQRQKHHVKRDVSTPLR---STEAGVVDQVMLTTTG 169


>gi|117667744|gb|ABK55918.1| RNA polymerase B subunit [Streptomyces kanamyceticus]
          Length = 180

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT+DV YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDDVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  + E  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHYAEPRVLIRRRGGEIDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  + + + +G
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTVTNDDG 175


>gi|219563989|gb|ACL28178.1| RNA polymerase II second largest subunit [Acrospermum gramineum]
          Length = 287

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 50/287 (17%), Positives = 95/287 (33%), Gaps = 27/287 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 9    YPQKPLATTRSMEYLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLF-RSLFY 67

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R  +D+ +R   +    IE   +    + + L    Y +L +   +  G           
Sbjct: 68   RTYMDQEKR---IGFHTIESFEKPSRGDTIRLKHGTYDKLDDDGVVAPGVRVSGEDIIIG 124

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D      R++                 +K    T     E+   +++      
Sbjct: 125  KTAPIAPDAEELGQRTKL---------------HIKRDVSTPLRSTENGIVDRV-----M 164

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    + +KV     +  Q GDK A RHG KG +      EDMPF ++G   D+++N
Sbjct: 165  VTTNSEGNKFIKVRTRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTREGLTPDLIIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM +  + E  L       G +  +          +S L  
Sbjct: 225  PHAIPSRMTIAHLIECLLSKVGSLRGSEGDATPFTDVTVESVSSLLR 271



 Score = 81.7 bits (200), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 19/178 (10%)

Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
                     Q+PL                      +L  G+N +VA   + GYN EDS+
Sbjct: 1   DTMMNVLYYPQKPL----------ATTRSMEYLRFRELPAGQNAIVAIATYSGYNQEDSV 50

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGII 882
           ++++  +   +F S+    +    +       E        D   +       +D+ G++
Sbjct: 51  IMNQSSIDRGLFRSLFYRTYMDQEKRIGFHTIESFEKPSRGDTIRLKHGTYDKLDDDGVV 110

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
             G  V+  DI++GK  P         E+L +        DV        +G+   V+
Sbjct: 111 APGVRVSGEDIIIGKTAPIAPDA----EELGQRTKLHIKRDVSTPLRSTENGIVDRVM 164


>gi|208609693|dbj|BAG72308.1| RNA polymerase II second largest subunit [Actinodaphne glomerata]
          Length = 167

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|325551436|gb|ADZ28559.1| RNA polymerase B subunit [Streptomyces cinnamoneus]
          Length = 180

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 92/178 (51%), Positives = 126/178 (70%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGVVTDEVDYLTADEEDRFVIAQANAPLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  + E  V  R  G E   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRYAEARVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|56406205|gb|AAV87486.1| RpoB [Pasteurella multocida subsp. multocida]
          Length = 156

 Score =  160 bits (405), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 94/156 (60%), Positives = 120/156 (76%), Gaps = 1/156 (0%)

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
           H RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N YG
Sbjct: 1   HKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTNDYG 60

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGEEIL 655
           F+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR   GE  L
Sbjct: 61  FLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAFVTCRGEHGESGL 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
              ++I ++D S +QVVS+AA+LIPFLE+DD+NR L
Sbjct: 121 YRPDEIHYMDVSTQQVVSVAAALIPFLEHDDANRAL 156


>gi|198279403|emb|CAP04736.1| RNA polymerase beta subunit [Pinus pinea]
          Length = 266

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 99/242 (40%), Positives = 148/242 (61%), Gaps = 10/242 (4%)

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           G+E   A  SG+  +A + G +E +DA+                       + +QRSN N
Sbjct: 1   GLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTN 52

Query: 774 TCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERM 833
           TC +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+
Sbjct: 53  TCTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERL 112

Query: 834 VSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDI 893
           V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+
Sbjct: 113 VYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDV 172

Query: 894 LVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGID 951
           LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR    
Sbjct: 173 LVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVDDS 232

Query: 952 KN 953
            +
Sbjct: 233 GD 234



 Score = 74.3 bits (181), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 83/220 (37%), Gaps = 14/220 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 61   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 119

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 120  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 173

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 174  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGKGRVIDVRWINRVD--D 231

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
             GD+        V V+++ KR IQ GDK+AGRHG KGI+S
Sbjct: 232  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGXKGIIS 266


>gi|74099884|gb|AAZ99151.1| RpoB [Staphylococcus pettenkoferi]
 gi|74099886|gb|AAZ99152.1| RpoB [Staphylococcus pettenkoferi]
 gi|144954324|gb|ABP04238.1| RpoB [Staphylococcus pettenkoferi]
          Length = 161

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 95/161 (59%), Positives = 122/161 (75%), Gaps = 2/161 (1%)

Query: 538 TRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGF 597
            RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GF
Sbjct: 1   KRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGF 60

Query: 598 IETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEIL 655
           IETPYRKV      +T+ + YL+A EE++  +AQANS  DE+G F ++ V CR  G   +
Sbjct: 61  IETPYRKVDIEKNAITDQIDYLTADEEDSYVVAQANSRTDEEGRFLDDEVVCRFRGNNTV 120

Query: 656 VPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           + +EK+D++D SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 MAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANM 161


>gi|220961206|gb|ACL93069.1| RNA polymerase B subunit [Streptomyces indonesiensis]
 gi|220961208|gb|ACL93070.1| RNA polymerase B subunit [Streptomyces rhizosphaericus]
 gi|220961210|gb|ACL93071.1| RNA polymerase B subunit [Streptomyces asiaticus]
 gi|220961216|gb|ACL93074.1| RNA polymerase B subunit [Streptomyces cangkringensis]
          Length = 180

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 125/175 (71%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV +G VT++V YL+A EE+   IAQAN+ L  
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVEGVVTDEVHYLTADEEDRFVIAQANAPLTN 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHFAENRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|112798781|gb|ABI22714.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798791|gb|ABI22719.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798793|gb|ABI22720.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798795|gb|ABI22721.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798797|gb|ABI22722.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798799|gb|ABI22723.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798829|gb|ABI22738.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798937|gb|ABI22792.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798939|gb|ABI22793.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798941|gb|ABI22794.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798943|gb|ABI22795.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799001|gb|ABI22824.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576833|gb|ADN53018.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 93/157 (59%), Positives = 116/157 (73%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG 
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT D+ YLSA+EE N  IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEDIEYLSAIEEGNYVIAQANSNLDENF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V CR   GE  L   E I ++D S +QVVS+
Sbjct: 121 RFTDTYVTCRGEHGESGLYKPEDIHYMDISTQQVVSV 157


>gi|208609841|dbj|BAG72382.1| RNA polymerase II second largest subunit [Litsea resinosa]
          Length = 167

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.3 bits (103), Expect = 0.14,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSSEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|46277334|gb|AAS86857.1| DNA-dependent RNA polymerase II [Ruhlandiella berolinensis]
          Length = 542

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 48/273 (17%), Positives = 86/273 (31%), Gaps = 21/273 (7%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R  +D+ +R  
Sbjct: 279  MEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFFRTYMDQEKRVG 337

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E+ E   R           +       +  G           K+  +  +      
Sbjct: 338  MSVFEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPIQPNQEELGQ 397

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+++         ++     +  Q                             L+ VKV 
Sbjct: 398  RTKFHTKRDVSTPLRSTENGIVDQ--------------------VMVTTNQEGLKFVKVR 437

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            +   +  Q GDK A RHG KG +      EDMPF  +G   D+V+NP  +PSRM +  + 
Sbjct: 438  MRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFXAEGVVPDLVINPHAIPSRMTIAHLI 497

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            E  L       G +  +          +S L  
Sbjct: 498  ECLLSKVSSLRGYEGDATPFTDVTVDSVSKLLR 530



 Score = 85.1 bits (209), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 61/440 (13%), Positives = 126/440 (28%), Gaps = 33/440 (7%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
           S  +       N    +       +     +      V    +H      +   +     
Sbjct: 20  SQPIVDFMMQRNM-EVLEEYEPSRSPNATKIFVNGVWV---GIHRDPGFIVRTIQKLRRQ 75

Query: 579 -NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            +IG   SL    R   +       R      V ++     A +     + Q +     +
Sbjct: 76  GHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDND---PASQRRGELVLQKSHISKLE 132

Query: 638 GSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                E    R   + +L     +++IDA  ++ V I  +      +   +    G  +Q
Sbjct: 133 DDRDIEDEAQRYGWQGLLTDG-VVEYIDAEEEETVMIVMTPEDLETSRQFH---AGYEIQ 188

Query: 698 RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
           ++  P  + +             +   + I+   A I+   D  +               
Sbjct: 189 QEVDPAQRVKGAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSPXXXXXXXXXXXXX 248

Query: 758 GVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMP 817
                                                         +L  G+N +VA M 
Sbjct: 249 XXXXXXXXXXXXXXXXXXXX---------XXXXXXXTRSMEFLKFRELPAGQNAIVAIMC 299

Query: 818 WHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEG 872
           + GYN EDS+++++  +   +F S+    +    +   +   E        +   +    
Sbjct: 300 YSGYNQEDSVIMNQSSIDRGLFRSLFFRTYMDQEKRVGMSVFEEFEKPTRGNTLRLKHGT 359

Query: 873 LKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVP 932
              +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S  + 
Sbjct: 360 YDKLDDDGLVAPGVRVSGEDIIIGKTAPIQPNQEELGQRT-------KFHTKRDVSTPLR 412

Query: 933 SGVSGTVVDVRIFNRHGIDK 952
           S  +G V  V +       K
Sbjct: 413 STENGIVDQVMVTTNQEGLK 432



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/217 (14%), Positives = 57/217 (26%), Gaps = 19/217 (8%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 25  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L  S  S    +    
Sbjct: 79  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASQRRGELVLQKSHISKLEDDRDIE 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            E              V Y+ A EEE   I      L+    F       +E+   +   
Sbjct: 139 DEAQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQEVDPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSN 688
             +          +  P  ++ I AS+IPF +++ S 
Sbjct: 199 GAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQSP 235


>gi|286142868|gb|ADC41464.1| RNA polymerase beta subunit [Streptomyces glaucescens]
          Length = 185

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 108/192 (56%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL++AEAP VGTGME   A  +G  + A++AG+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIQAEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD V    ++ADGP+T  G++A
Sbjct: 61  NDDGT-------YITYRLAKFARSNQGTSVNQKVIVNEGDRVIEGQVLADGPATQNGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|208609805|dbj|BAG72364.1| RNA polymerase II second largest subunit [Litsea garciae]
          Length = 167

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGIV 65


>gi|208609741|dbj|BAG72332.1| RNA polymerase II second largest subunit [Lindera glauca]
          Length = 167

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 45.1 bits (105), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLASPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|208609689|dbj|BAG72306.1| RNA polymerase II second largest subunit [Actinodaphne glomerata]
 gi|208609691|dbj|BAG72307.1| RNA polymerase II second largest subunit [Actinodaphne glomerata]
 gi|208609697|dbj|BAG72310.1| RNA polymerase II second largest subunit [Actinodaphne macrophylla]
 gi|208609701|dbj|BAG72312.1| RNA polymerase II second largest subunit [Actinodaphne macrophylla]
 gi|208609703|dbj|BAG72313.1| RNA polymerase II second largest subunit [Actinodaphne macrophylla]
 gi|208609705|dbj|BAG72314.1| RNA polymerase II second largest subunit [Actinodaphne maingayi]
 gi|208609707|dbj|BAG72315.1| RNA polymerase II second largest subunit [Actinodaphne maingayi]
 gi|208609709|dbj|BAG72316.1| RNA polymerase II second largest subunit [Actinodaphne malaccensis]
 gi|208609713|dbj|BAG72318.1| RNA polymerase II second largest subunit [Actinodaphne malaccensis]
 gi|208609717|dbj|BAG72320.1| RNA polymerase II second largest subunit [Actinodaphne malaccensis]
 gi|208609719|dbj|BAG72321.1| RNA polymerase II second largest subunit [Actinodaphne myriantha]
 gi|208609721|dbj|BAG72322.1| RNA polymerase II second largest subunit [Actinodaphne myriantha]
 gi|208609723|dbj|BAG72323.1| RNA polymerase II second largest subunit [Actinodaphne procera]
 gi|208609725|dbj|BAG72324.1| RNA polymerase II second largest subunit [Actinodaphne procera]
 gi|208609727|dbj|BAG72325.1| RNA polymerase II second largest subunit [Actinodaphne procera]
 gi|208609735|dbj|BAG72329.1| RNA polymerase II second largest subunit [Lindera glauca]
 gi|208609739|dbj|BAG72331.1| RNA polymerase II second largest subunit [Lindera glauca]
 gi|208609743|dbj|BAG72333.1| RNA polymerase II second largest subunit [Lindera lucida]
 gi|208609745|dbj|BAG72334.1| RNA polymerase II second largest subunit [Lindera lucida]
 gi|208609747|dbj|BAG72335.1| RNA polymerase II second largest subunit [Lindera obtusiloba]
 gi|208609749|dbj|BAG72336.1| RNA polymerase II second largest subunit [Lindera obtusiloba]
 gi|208609753|dbj|BAG72338.1| RNA polymerase II second largest subunit [Lindera polyantha]
 gi|208609755|dbj|BAG72339.1| RNA polymerase II second largest subunit [Lindera polyantha]
 gi|208609757|dbj|BAG72340.1| RNA polymerase II second largest subunit [Lindera aggregata]
 gi|208609759|dbj|BAG72341.1| RNA polymerase II second largest subunit [Lindera umbellata]
 gi|208609761|dbj|BAG72342.1| RNA polymerase II second largest subunit [Lindera umbellata]
 gi|208609763|dbj|BAG72343.1| RNA polymerase II second largest subunit [Litsea accedens]
 gi|208609765|dbj|BAG72344.1| RNA polymerase II second largest subunit [Litsea accedens]
 gi|208609769|dbj|BAG72346.1| RNA polymerase II second largest subunit [Litsea caulocarpa]
 gi|208609771|dbj|BAG72347.1| RNA polymerase II second largest subunit [Litsea caulocarpa]
 gi|208609773|dbj|BAG72348.1| RNA polymerase II second largest subunit [Litsea costalis]
 gi|208609775|dbj|BAG72349.1| RNA polymerase II second largest subunit [Litsea costalis]
 gi|208609777|dbj|BAG72350.1| RNA polymerase II second largest subunit [Litsea cubeba]
 gi|208609779|dbj|BAG72351.1| RNA polymerase II second largest subunit [Litsea cubeba]
 gi|208609781|dbj|BAG72352.1| RNA polymerase II second largest subunit [Litsea diversifolia]
 gi|208609783|dbj|BAG72353.1| RNA polymerase II second largest subunit [Litsea erectinervia]
 gi|208609785|dbj|BAG72354.1| RNA polymerase II second largest subunit [Litsea erectinervia]
 gi|208609787|dbj|BAG72355.1| RNA polymerase II second largest subunit [Litsea erectinervia]
 gi|208609789|dbj|BAG72356.1| RNA polymerase II second largest subunit [Litsea fenestrata]
 gi|208609791|dbj|BAG72357.1| RNA polymerase II second largest subunit [Litsea fenestrata]
 gi|208609793|dbj|BAG72358.1| RNA polymerase II second largest subunit [Litsea fenestrata]
 gi|208609795|dbj|BAG72359.1| RNA polymerase II second largest subunit [Litsea ferruginea]
 gi|208609799|dbj|BAG72361.1| RNA polymerase II second largest subunit [Litsea ferruginea]
 gi|208609801|dbj|BAG72362.1| RNA polymerase II second largest subunit [Litsea garciae]
 gi|208609809|dbj|BAG72366.1| RNA polymerase II second largest subunit [Litsea globularia]
 gi|208609813|dbj|BAG72368.1| RNA polymerase II second largest subunit [Litsea glutinosa]
 gi|208609815|dbj|BAG72369.1| RNA polymerase II second largest subunit [Litsea glutinosa]
 gi|208609817|dbj|BAG72370.1| RNA polymerase II second largest subunit [Litsea glutinosa]
 gi|208609823|dbj|BAG72373.1| RNA polymerase II second largest subunit [Litsea lancifolia]
 gi|208609825|dbj|BAG72374.1| RNA polymerase II second largest subunit [Litsea lancifolia]
 gi|208609827|dbj|BAG72375.1| RNA polymerase II second largest subunit [Litsea lancifolia]
 gi|208609829|dbj|BAG72376.1| RNA polymerase II second largest subunit [Litsea machilifolia]
 gi|208609831|dbj|BAG72377.1| RNA polymerase II second largest subunit [Litsea maingayi]
 gi|208609833|dbj|BAG72378.1| RNA polymerase II second largest subunit [Litsea maingayi]
 gi|208609835|dbj|BAG72379.1| RNA polymerase II second largest subunit [Litsea maingayi]
 gi|208609837|dbj|BAG72380.1| RNA polymerase II second largest subunit [Litsea noronhae]
 gi|208609839|dbj|BAG72381.1| RNA polymerase II second largest subunit [Litsea noronhae]
 gi|208609845|dbj|BAG72384.1| RNA polymerase II second largest subunit [Litsea resinosa]
 gi|208609847|dbj|BAG72385.1| RNA polymerase II second largest subunit [Litsea rubicunda]
 gi|208609851|dbj|BAG72387.1| RNA polymerase II second largest subunit [Litsea rubicunda]
 gi|208609853|dbj|BAG72388.1| RNA polymerase II second largest subunit [Litsea tomentosa]
 gi|208609855|dbj|BAG72389.1| RNA polymerase II second largest subunit [Machilus rimosa]
 gi|208609857|dbj|BAG72390.1| RNA polymerase II second largest subunit [Machilus rimosa]
 gi|208609861|dbj|BAG72392.1| RNA polymerase II second largest subunit [Neolitsea aciculata]
 gi|208609863|dbj|BAG72393.1| RNA polymerase II second largest subunit [Neolitsea aciculata]
 gi|208609865|dbj|BAG72394.1| RNA polymerase II second largest subunit [Neolitsea cassia]
 gi|208609867|dbj|BAG72395.1| RNA polymerase II second largest subunit [Neolitsea cassia]
 gi|208609871|dbj|BAG72397.1| RNA polymerase II second largest subunit [Neolitsea javanica]
 gi|208609875|dbj|BAG72399.1| RNA polymerase II second largest subunit [Neolitsea javanica]
 gi|208609877|dbj|BAG72400.1| RNA polymerase II second largest subunit [Neolitsea sericea]
 gi|208609879|dbj|BAG72401.1| RNA polymerase II second largest subunit [Neolitsea sericea]
 gi|208609881|dbj|BAG72402.1| RNA polymerase II second largest subunit [Neolitsea sericea]
 gi|208609883|dbj|BAG72403.1| RNA polymerase II second largest subunit [Phoebe excelsa]
 gi|208609885|dbj|BAG72404.1| RNA polymerase II second largest subunit [Phoebe excelsa]
 gi|208609887|dbj|BAG72405.1| RNA polymerase II second largest subunit [Phoebe excelsa]
          Length = 167

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|14971069|gb|AAK74099.1| RNA polymerase beta subunit [Bacillus thuringiensis]
          Length = 258

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 86/197 (43%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK      +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGVTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L ALG  S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALGFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +  ++L+ I     ++I
Sbjct: 172 LGRRTLDRILPYLEKNI 188



 Score = 60.9 bits (146), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|223585669|gb|ACM91705.1| ribosomal polymerase subunit beta [Staphylococcus sp. KS-SP_75]
          Length = 159

 Score =  160 bits (405), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 94/158 (59%), Positives = 122/158 (77%), Gaps = 2/158 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      VT+ + YL+A EE+   +AQAN+ LD++G F ++ V CR  G+  ++ RE++
Sbjct: 61  KVDIETNTVTSQIDYLTADEEDAYVVAQANARLDDNGKFLDDEVVCRFRGDNTVMARERM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 158


>gi|208609733|dbj|BAG72328.1| RNA polymerase II second largest subunit [Lindera glauca]
 gi|208609821|dbj|BAG72372.1| RNA polymerase II second largest subunit [Litsea grandis]
          Length = 167

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.3 bits (103), Expect = 0.14,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLALPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|318085022|gb|ADV39401.1| RNA polymerase subunit B [Streptomyces lavendofoliae]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGQVTDEVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFAEARVLVRRRGGEVDYVAPDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCATDAGDVIKAEKAGVVQEVSADYITTTNDDG 175


>gi|151564514|gb|ABS17616.1| RpoB [Campylobacter canadensis]
          Length = 175

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 96/174 (55%), Positives = 129/174 (74%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIGL+
Sbjct: 2   QXMDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  ++
Sbjct: 62  NSLSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNIIDD 121

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
           L+  R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG NMQ
Sbjct: 122 LLEARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMGPNMQ 175


>gi|50058729|gb|AAT69117.1| RNA polymerase II [Stylisma patens]
          Length = 223

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 129  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 188

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 189  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 221



 Score = 71.6 bits (174), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 47/131 (35%), Gaps = 14/131 (10%)

Query: 814 AFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNV 868
               + GYN EDS+++++  +    F S+    +    +      +E        +   +
Sbjct: 1   PIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGM 60

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTS 928
                  +D+ G+   G  V+  D+++GK TP  +           A         RD S
Sbjct: 61  RHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTKRDHS 111

Query: 929 LRVPSGVSGTV 939
             +    +G V
Sbjct: 112 TSLRHSETGIV 122


>gi|318085010|gb|ADV39395.1| RNA polymerase subunit B [Streptomyces diastatochromogenes]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F+E+ V  R  G E  LVP +++ ++D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFSEQRVLVRRRGGEVDLVPADEVHYMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKNGVVQEVSADYITVANDDG 175


>gi|193201527|gb|ACF15971.1| RNA polymerase II subunit [Opegrapha vermicellifera]
          Length = 279

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 50/292 (17%), Positives = 91/292 (31%), Gaps = 25/292 (8%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +     S +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFR 60

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              ++  +   +N  +     +Q+E   +      +      Y +L +   +  G      
Sbjct: 61   SFLYRTYIEQQNVSA----SQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVSGD 116

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+    + +                E  QR  +  +          E    +K+ 
Sbjct: 117  DIIIGKTAPFPAPMQDNA------------EGGQRTKQHTRRDVSAPLRSTEAGIVDKVL 164

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                         R VKV     +  Q GDK A RHG KG +      EDMP+  +G   
Sbjct: 165  ------VSNVDGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPYTAEGLVP 218

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            D+++NP  +PSRM V  + E  L       G +  +         +IS L  
Sbjct: 219  DLIINPHAIPSRMTVAHLIECLLSKVSATQGLEGDATPFTDVTVSEISSLLK 270



 Score = 75.5 bits (184), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 62/187 (33%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                   +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +      +     E                  + +D+ G +  G  V+
Sbjct: 55  DRGLFRSFLYRTYIEQQNVSASQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +        DV        +G+   V+   +  R  
Sbjct: 115 GDDIIIGKTAPFPAPMQDNAEGG-QRTKQHTRRDVSAPLRSTEAGIVDKVLVSNVDGRRT 173

Query: 950 IDKNERS 956
           +    R+
Sbjct: 174 VKVRTRA 180


>gi|208609699|dbj|BAG72311.1| RNA polymerase II second largest subunit [Actinodaphne macrophylla]
          Length = 167

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 42.8 bits (99), Expect = 0.43,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G    G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGQAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|117667818|gb|ABK55955.1| RNA polymerase B subunit [Streptomyces mauvecolor]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANAALSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFTEPRVLVRRRGGEVDYVPGTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ +EAP VGTGME   A  +G  I A++AG+V++V A  I + + +G
Sbjct: 121 MMRQAVPLITSEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYITVANDDG 175


>gi|280985749|gb|ACZ99655.1| RNA polymerase II [Fusarium redolens]
 gi|280985751|gb|ACZ99656.1| RNA polymerase II [Fusarium redolens]
 gi|280985753|gb|ACZ99657.1| RNA polymerase II [Fusarium redolens]
 gi|280985757|gb|ACZ99659.1| RNA polymerase II [Fusarium redolens]
          Length = 305

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/379 (14%), Positives = 98/379 (25%), Gaps = 75/379 (19%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
            ++NP  +PSRM +  + E  L       G +  +          +S L            
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRKHGYQSRGFE 279

Query: 1181 HTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGL 1240
                                                              +G +    G 
Sbjct: 280  VM-----------------------------------------------YNGHT----GR 288

Query: 1241 TGEPFDRPVTVGYIYMLKL 1259
                    V  G  Y  +L
Sbjct: 289  ---KLRAQVFFGPTYYQRL 304



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|82706461|gb|ABB89608.1| RNA polymerase II second largest subunit [Coccomyces dentatus]
          Length = 565

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 97/617 (15%), Positives = 177/617 (28%), Gaps = 82/617 (13%)

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             ++ +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG
Sbjct: 18   STAGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEG 73

Query: 578  HNIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L+    V      +    +       V  +   L        ++      + 
Sbjct: 74   QACGLVKNLSLMCYVTVGSPSDPIVEFMIQRGMDVLEEYEPLRNPNATKVFVNGVWVGVH 133

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD-------S 687
               +   E +        I      I D  D   K          P    D+        
Sbjct: 134  SFPARLVENIQQLRRTNLISHEVALIRDIRDREFKIFTDAGRVCRPVFAIDNKEGSPNKG 193

Query: 688  NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
            N  L   ++++               G  +      G        G+VE VDA       
Sbjct: 194  NLKLNKEHIKKLEDDQAMPLQWASMIGNLTATTDLXGLL----DDGVVEYVDAEEEETIM 249

Query: 748  VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +    +         +    Q  + +  +N+R    V             PS  LG    
Sbjct: 250  IVMTPEDLEISRQ-MQAGLAQLPDDSGDLNKRVKAPVNPTAHVWTHCEIHPSMILG---- 304

Query: 808  GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN 867
               +  + +P+  +N          M  + +   + +  ++                   
Sbjct: 305  ---ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VFLTNYQQRM---------------- 343

Query: 868  VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
                         +  +             +       +   +  + AI      +  D+
Sbjct: 344  -----------DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYTGYNQEDS 392

Query: 928  SLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLM 987
             +   S +   +    +F R   D+ +R        IE   +    + + L    Y +L 
Sbjct: 393  VIMNQSSIDRGLF-RSLFYRAYTDQEKRVGM---ATIESFEKPNRSDTIRLKMATYDKLD 448

Query: 988  E---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYET 1044
            +   +  G           K+  ++ D      R++          ++     +  Q   
Sbjct: 449  DDGIVSPGVRVSGEDIIIGKTAPIAPDAEELGQRTKAHTKRDASTPLRSTENGIVDQVLI 508

Query: 1045 SKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRIL 1104
                                      LR VKV +   +  Q GDK A RHG KG V    
Sbjct: 509  --------------------TTNADGLRFVKVRMRTTKIPQIGDKFASRHGQKGTVGITY 548

Query: 1105 PCEDMPFLKDGTPVDIV 1121
              EDMPF ++G   DI+
Sbjct: 549  RQEDMPFTREGIVPDII 565


>gi|220961168|gb|ACL93050.1| RNA polymerase B subunit [Streptomyces rimosus subsp.
           paromomycinus]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|220961118|gb|ACL93025.1| RNA polymerase B subunit [Streptomyces ochraceiscleroticus]
 gi|220961174|gb|ACL93053.1| RNA polymerase B subunit [Streptomyces violens]
 gi|220961180|gb|ACL93056.1| RNA polymerase B subunit [Streptomyces purpurogeneiscleroticus]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 97/175 (55%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +VVYL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVVYLTADEEDRFIIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LV  +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEADLVTVDEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|40643048|emb|CAD92466.1| RNA polymerase II [Cuscuta sp. Stefanovic s.n.]
          Length = 222

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 89/245 (36%), Gaps = 23/245 (9%)

Query: 913  LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKD 972
            + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R   
Sbjct: 1    IVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNT 59

Query: 973  DEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQ 1032
                    +          G           K+T +S                  D+   
Sbjct: 60   MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DDAQG 102

Query: 1033 RNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAG 1092
            +     K  + TS    E+   +++      D +     R VKV V   R  Q GDK + 
Sbjct: 103  QAARYTKRDHSTSLRHSENGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKFSS 157

Query: 1093 RHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +GK+ 
Sbjct: 158  RHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 217

Query: 1153 KSLIN 1157
             +   
Sbjct: 218  DATSF 222



 Score = 72.8 bits (177), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 26/133 (19%), Positives = 50/133 (37%), Gaps = 14/133 (10%)

Query: 812 LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIP 866
           +VA   + GYN EDS+++++  +    F S+    +    +      +E        +  
Sbjct: 1   IVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTM 60

Query: 867 NVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRD 926
            +       +D+ G+   G  V+  D+++GK TP  +           A         RD
Sbjct: 61  GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQAARYTKRD 111

Query: 927 TSLRVPSGVSGTV 939
            S  +    +G V
Sbjct: 112 HSTSLRHSENGMV 124


>gi|322510707|gb|ADX06021.1| putative DNA-directed RNA polymerase II [Organic Lake phycodnavirus
            1]
          Length = 995

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 126/836 (15%), Positives = 243/836 (29%), Gaps = 136/836 (16%)

Query: 357  YIRNTLVTDKNKDRKDALLDIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRV 414
             I +  +        D       ++RP   D  TF    +   ++       +++ V  +
Sbjct: 261  IISDKEICKCILSDLDHNETYLELLRPSINDAGTFYTQLTCLEYISCFLKLENINEVHNI 320

Query: 415  KMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQ 474
              N  L     +     +   +  ++   + +  G+  + D DN   +RV + G +LKN 
Sbjct: 321  LTN-YLLPHVGEMNYFSKALYLGYMVFETLKVIQGESQMTDRDNYMFKRVENTGTLLKNL 379

Query: 475  YRLGLLRMERSIK-------------ERISSVDIDSVMPQ----------DLINAKPVVS 511
            +      M + I                    D  +  P            + N   + +
Sbjct: 380  FTEYANIMYKEIHLVLEKDVYYNKDLYDDLDRDEQNFDPSKSNMVQLIKDSVFNETYIAN 439

Query: 512  AVCEFFCSSQLS----------QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDV 561
               + F     +          Q    ++  S ++H R+++      +  +   V    +
Sbjct: 440  GFKKAFKGDWGAHAHTKRLGALQDLNRLSYNSFLSHLRKVNI----EMDSSSKIVGPHLL 495

Query: 562  HPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAME 621
            H T YG + P +T +G N+GL   ++   ++      +  Y  +      + +   S   
Sbjct: 496  HGTQYGYLDPVDTPDGGNVGLHKHMSIMCKITDTIQYKPLYDFMHKYFNVHKLEECSYET 555

Query: 622  EENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
               ++    N          +E    +   + I+  R  I     S           I F
Sbjct: 556  IHKKFRLFINGRWVGMVDIHDEQDPLKFKNDFIMYRRLGILHYSISINIQFKDKMIFI-F 614

Query: 682  LENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAI 741
             +     R LM  + ++  +     +               S             Q D  
Sbjct: 615  SDEGRLLRPLMYFHNEKLMMAPYDRDFT-------WKRLIHSDIKQTPFVVPTDLQDDKS 667

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                       + +      Y  M + +S                   ++  +   PS  
Sbjct: 668  HYCYLEYIDPSETN----MCYIAMTYMKS-----------------TLQHTHLEIHPSLM 706

Query: 802  LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI 861
             G +          + +   N     L S     + V                       
Sbjct: 707  FGIMGNQ-------IIYPENNQLPRNLFSCGQSKQGVSL--------------------- 738

Query: 862  TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKA 921
                       +  ID+ GI+          +         E      E ++ AI    +
Sbjct: 739  ------YHSNFINRIDKMGIVL--NYGQKPIVRSRYFNYIHEEQHPYGENVIVAIMCHTS 790

Query: 922  VDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRN 981
             +V D  L   S V   +     +N +             E ++ + +   +E+ I   +
Sbjct: 791  YNVEDAILINESAVKRGLFKTTYYNMY-------------ETMDEITQAGKNEKRIDQVS 837

Query: 982  IYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
             Y    +   G N                + + E    +          V   V  +  +
Sbjct: 838  KYELARDTKPGYNY---------------NKLDERGLIEENTLMDDKTVVIGKVNMINNE 882

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
               S  + +      ++K    D+      ++ KV +   R    GDK   R G KG + 
Sbjct: 883  IYDSSILPKKGQLGYVDKTFIYDN---DGRKLAKVRIREDRAPTIGDKFCSRCGQKGTIG 939

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
             ++P E+MPF K G   DI++NP  +PSRM +GQ+ ET L   C   G    S   
Sbjct: 940  NLIPEENMPFTKSGLKPDIIVNPHALPSRMTIGQLIETILAKLCCVNGMSADSTRF 995



 Score =  104 bits (259), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 115/948 (12%), Positives = 259/948 (27%), Gaps = 172/948 (18%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSG-----AAMLEFVS 78
           L++ Q  S + F   +          ++  F+ + PI                  +    
Sbjct: 23  LVDHQIKSCNAFYKKD----------IKEIFRDLNPIKYSTNLDTDDQEDAYKINIYIGG 72

Query: 79  YEFDPPKFD-------------VDDCLWRDLTYAVPLK--ITLRLIVFDVDEFTGAKSIK 123
              +   F+              ++C  +++TYA  +   I +  ++++          K
Sbjct: 73  KNVEKLYFNSPMIVEDQKRHLFPNECRLKNITYATTIHYEIDVEFMIYNKALGKYVTFQK 132

Query: 124 DIKEQSIY-MGDLPLMTKD------------------------GTFVIKGIQRIVVSQLH 158
              E   Y +G  P+M K                         G F+I G +++++ Q  
Sbjct: 133 SFPENDKYELGSFPIMLKSDLCILKSLNKDIAYQLGECRHDYGGYFIIDGKEKVIIPQEK 192

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRII--------PDQGLWMDIEFDSKDII----HVRI 206
               + +     R     K  ++  I         P +   +  + +S + +    +VR+
Sbjct: 193 FGDNLIY----IRTLKDDKHDFSVEIRSVSEDNSKPKRTFAIRRDINSHNFVVDIPNVRM 248

Query: 207 DRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD 266
                +P+   + ALG+ S++ +                C  + +        +      
Sbjct: 249 P----IPLFIVMRALGIISDKEI----------------CKCILSDLDHNETYLELLRPS 288

Query: 267 IDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGD 326
           I+           L         E   +   I ++ L         +N  +  +Y+    
Sbjct: 289 INDAGTFYTQLTCLEYISCFLKLENINEVHNILTNYLLPHV---GEMNYFSKALYLGYMV 345

Query: 327 VIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDV 386
               K + +           ++    N    ++N      N   K+  L + + +     
Sbjct: 346 FETLKVI-QGESQMTDRDNYMFKRVENTGTLLKNLFTEYANIMYKEIHLVLEKDV----- 399

Query: 387 STFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDL 446
                        +++ D YD               D          +D +     + + 
Sbjct: 400 -------------YYNKDLYDDLDRDEQNF------DPSKSNMVQLIKDSVFNETYIANG 440

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
                  D   +   +R+ ++ ++ +  Y   L  + +   E  SS  I           
Sbjct: 441 FKKAFKGDWGAHAHTKRLGALQDLNRLSYNSFLSHLRKVNIEMDSSSKIVGPHLLHGTQY 500

Query: 507 KPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGV--------ARARAGVEM 558
             +         +  L +    +  ++     + L                +      + 
Sbjct: 501 GYLDPVDTPDGGNVGLHKHMSIMCKITDTIQYKPLYDFMHKYFNVHKLEECSYETIHKKF 560

Query: 559 RDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS 618
           R      +  +      +      +     F      G +   Y    + +  + ++++ 
Sbjct: 561 RLFINGRWVGMVDIHDEQDP----LKFKNDFIMYRRLGIL--HYSISINIQFKDKMIFIF 614

Query: 619 AMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASL 678
           + E            L    +    +           +    I          +    S 
Sbjct: 615 SDEGRLLR------PLMYFHNEKLMMAPYDRDFTWKRLIHSDIKQTPFVVPTDLQDDKSH 668

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
             +LE  D +   M           L+       T +E   +   G            Q+
Sbjct: 669 YCYLEYIDPSETNMCYIAMTYMKSTLQ------HTHLEIHPSLMFGIMGNQIIYPENNQL 722

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
                      G      S      + +  +        Q+P+V+               
Sbjct: 723 PRNLFSC----GQSKQGVSLYHSNFINRIDKMGIVLNYGQKPIVRS----------RYFN 768

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
                    G N++VA M    YN ED++LI+E  V   +F + +   +E M   T+ G 
Sbjct: 769 YIHEEQHPYGENVIVAIMCHTSYNVEDAILINESAVKRGLFKTTYYNMYETMDEITQAGK 828

Query: 859 EEITRDIPNVSE--------EGLKNIDECGIICVGAEVNPGDILVGKI 898
            E   D  +  E             +DE G+I     ++   +++GK+
Sbjct: 829 NEKRIDQVSKYELARDTKPGYNYNKLDERGLIEENTLMDDKTVVIGKV 876


>gi|50058713|gb|AAT69109.1| RNA polymerase II [Merremia peltata]
          Length = 223

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 128  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 187

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 188  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 220



 Score = 71.6 bits (174), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 47/130 (36%), Gaps = 14/130 (10%)

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVS 869
              + GYN EDS+++++  +    F S+    +    +      +E        +   + 
Sbjct: 1   IACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMR 60

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ G+   G  V+  D+++GK TP  +           A         RD S 
Sbjct: 61  HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQSSRYTKRDHST 111

Query: 930 RVPSGVSGTV 939
            +    +G V
Sbjct: 112 SLRHSETGMV 121


>gi|318085012|gb|ADV39396.1| RNA polymerase subunit B [Streptomyces umbrinus]
 gi|318085032|gb|ADV39406.1| RNA polymerase subunit B [Streptomyces ederensis]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+NA+GF+ETPYRKV +G+VT++V YL+A EE+   IAQAN+SL++
Sbjct: 1   GPNIGLIGSLASYGRINAFGFVETPYRKVVEGQVTDEVDYLTADEEDRFVIAQANASLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFDEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  I + + +G
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYITVANDDG 175


>gi|220961152|gb|ACL93042.1| RNA polymerase B subunit [Streptomyces albospinus]
          Length = 180

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 97/175 (55%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|294721633|gb|ADF32967.1| RNA polymerase II second largest subunit [Coniosporium uncinatum]
          Length = 267

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 51/276 (18%), Positives = 88/276 (31%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       M   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 8    MEYLRFRDMPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYSDQEKRVG 66

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
                  +E   +    + + L    Y +L +   +  G           K+  ++ D   
Sbjct: 67   M---ATVENFEKPMRADTIRLKHGTYDKLDDDGIVAPGVRVSGEDXIIGKTAPIAPDSEE 123

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+           ++     +  Q                             L+ V
Sbjct: 124  LGQRTXLHVKRDVSTPLRSTENGIIDQVLL--------------------TTNTEGLKYV 163

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV     +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 164  KVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGLXPDLIINPHAIPSRMTIA 223

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          IS L  
Sbjct: 224  HLIECLLSXVGALRGFEGDATPFLDITVTSISNLLR 259



 Score = 80.9 bits (198), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 30/152 (19%), Positives = 58/152 (38%), Gaps = 9/152 (5%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     D+  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 5   TRSMEYLRFRDMPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYSDQEKR 64

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E     +  D   +       +D+ GI+  G  V+  D ++GK  P        
Sbjct: 65  VGMATVENFEKPMRADTIRLKHGTYDKLDDDGIVAPGVRVSGEDXIIGKTAPIAPDS--- 121

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            E+L +        DV        +G+   V+
Sbjct: 122 -EELGQRTXLHVKRDVSTPLRSTENGIIDQVL 152


>gi|91981510|gb|ABE68097.1| RNA polymerase subunit B [Pseudomonas sp. K94.41]
 gi|91981512|gb|ABE68098.1| RNA polymerase subunit B [Pseudomonas sp. S8-62]
          Length = 151

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 83/150 (55%), Positives = 110/150 (73%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 150


>gi|297184767|gb|ADI20877.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [uncultured gamma proteobacterium EB080_L93H08]
          Length = 125

 Score =  160 bits (404), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 49/101 (48%), Positives = 69/101 (68%), Gaps = 5/101 (4%)

Query: 75  EFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKDIKEQ----S 129
           EFVSY  + P+F V +C  R L+YA  L++  +LI ++ D    + K +K+IK+      
Sbjct: 2   EFVSYRLEEPEFSVRECQLRGLSYASALRVKTKLITYNKDTNKESVKEVKNIKQTGDTTD 61

Query: 130 IYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKG 170
           +Y G++PLMT+ GTFVI G  R++VSQLHRSPG+ FDHDKG
Sbjct: 62  VYFGEVPLMTEHGTFVINGTDRVIVSQLHRSPGVFFDHDKG 102


>gi|208609715|dbj|BAG72319.1| RNA polymerase II second largest subunit [Actinodaphne malaccensis]
          Length = 167

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 43.1 bits (100), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +     G V
Sbjct: 54  STSLRHSEIGMV 65


>gi|112798905|gb|ABI22776.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 91/157 (57%), Positives = 114/157 (72%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDENF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V  R   GE  L   E+I ++D S +QVVS+
Sbjct: 121 RFTDAYVTARGEHGESGLYRPEEIHYMDVSTQQVVSV 157


>gi|193201513|gb|ACF15964.1| RNA polymerase II subunit [Opegrapha niveoatra]
          Length = 269

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 51/290 (17%), Positives = 91/290 (31%), Gaps = 25/290 (8%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +     S +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAIDRGLFRSF 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            ++  +   +N  +     +Q+E   +      +      Y +L +   +  G        
Sbjct: 61   LYRTYIEQQNVSA----SQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVSGDDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+    + +                E  QR  +  +          E    +K+   
Sbjct: 117  IIGKTAPFPAPMQDNA------------EGGQRTKQHTRRDVSAPLRSTEAGIVDKVL-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----VSNVEGRRTVKVRTRATKVPQIGDKFASRHGQKGTIGITYAQEDMPFTAEGLVPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            ++NP  +PSRM V  + E  L       G +  +         +IS L  
Sbjct: 219  IINPHAIPSRMTVAHLIECLLSKVSATQGLEGDATPFTDVTVSEISSLLK 268



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 62/187 (33%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                   +  +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEYLNFSELPAGQNAIVAIACYSGYNQEDSIIMNQSAI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S     +      +     E                  + +D+ G +  G  V+
Sbjct: 53  DRGLFRSFLYRTYIEQQNVSASQQLETFEKPVKQLTMRTRPGTYEKLDDDGFVSPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P         E   +        DV        +G+   V+   +  R  
Sbjct: 113 GDDIIIGKTAPFPAPMQDNAEGG-QRTKQHTRRDVSAPLRSTEAGIVDKVLVSNVEGRRT 171

Query: 950 IDKNERS 956
           +    R+
Sbjct: 172 VKVRTRA 178


>gi|117667814|gb|ABK55953.1| RNA polymerase B subunit [Streptomyces pulveraceus]
          Length = 180

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 125/175 (71%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+NA+GFIETPYRKV D +VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRINAFGFIETPYRKVVDDQVTDEVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFAESRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|169260878|gb|ACA52151.1| RpoB [Chelonobacter oris]
          Length = 158

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 95/158 (60%), Positives = 116/158 (73%), Gaps = 1/158 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS  TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEXTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +AR N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDED  FT+  V
Sbjct: 61  LSVYARTNDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDEDSRFTDAFV 120

Query: 646 FCR-CAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
            CR   GE  L   E I ++D S +QVVS+AA+LIPFL
Sbjct: 121 TCRGEHGESGLYRAEDIHYMDVSTQQVVSVAAALIPFL 158


>gi|50058763|gb|AAT69134.1| RNA polymerase II [Nicotiana tabacum]
          Length = 216

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 121  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 180

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 181  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 213



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 43/123 (34%), Gaps = 14/123 (11%)

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNI 876
           N EDS+++++  +    F S+    +    +      +E            +       +
Sbjct: 1   NQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRASTMGMRHGSYDKL 60

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D+ G+   G  V+  D+++GK TP  +           A         +D S  +    +
Sbjct: 61  DDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTRKDHSTSLRHSET 111

Query: 937 GTV 939
           G V
Sbjct: 112 GMV 114


>gi|11595844|emb|CAC18333.1| RNA polymerase beta subunit [Pseudomonas alcaligenes]
          Length = 148

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 86/148 (58%), Positives = 113/148 (76%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+ ALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVFALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +GKVT+++V+LSA+EE +  IAQA+++L+  G   +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGKVTDEIVFLSAIEEADHVIAQASATLNAKGELIDELVNVRHLNEFTVKAP 120

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 121 EDVTLMDVSPKQVVSVAASLIPFLEHDD 148


>gi|50058743|gb|AAT69124.1| RNA polymerase II [Jacquemontia blanchetii]
          Length = 208

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 114  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 173

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 174  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 206



 Score = 57.4 bits (137), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/116 (15%), Positives = 38/116 (32%), Gaps = 14/116 (12%)

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIIC 883
           +++  +    F S+    +    +      +E        +   +       +D+ G+  
Sbjct: 1   MNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAP 60

Query: 884 VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            G  V+  D+++GK TP  +           A         RD S  +    +G V
Sbjct: 61  PGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHSTSLRHSETGMV 107


>gi|219564057|gb|ACL28212.1| RNA polymerase II second largest subunit [fungal sp. M186]
          Length = 146

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 33/100 (33%), Positives = 44/100 (44%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP 
Sbjct: 47   TNADGLRYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTCEGITPDIIINPH 106

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             +PSRM +  + E  L       G +  +          +
Sbjct: 107  AIPSRMTIAHLIECLLSKVATLKGLEGDATPFTDVTVDSV 146


>gi|219564085|gb|ACL28226.1| RNA polymerase II second largest subunit [fungal sp. M229]
          Length = 244

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 92/262 (35%), Gaps = 27/262 (10%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 7    MEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 63

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +     E   +    + + L    Y +L E   +  G           K+  ++ D   
Sbjct: 64   -IXXXXXEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPD--- 119

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         +E  QR    +K    T     E+   +++             LR V
Sbjct: 120  ------------AEEMGQRTKAHIKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFV 162

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 163  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRIEDMPFTSEGIVPDLIINPHAIPSRMTIA 222

Query: 1135 QIFETHLGWACVGLGKKIKSLI 1156
             + E  L       G +  +  
Sbjct: 223  HLIECQLSKVSTLRGLEGDATP 244



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/158 (23%), Positives = 61/158 (38%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA M + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 4   TRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKR 63

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 E        D   +       +DE GI+  G  V+  DI++GK  P        
Sbjct: 64  IXXXXXEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEEM 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        KA   RD S  + S  +G V  V I  
Sbjct: 124 GQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 154


>gi|88697516|gb|ABD48452.1| RpoB [Morganella morganii]
 gi|88697518|gb|ABD48453.1| RpoB [Morganella morganii]
 gi|88697528|gb|ABD48458.1| RpoB [Morganella morganii]
 gi|88697530|gb|ABD48459.1| RpoB [Morganella morganii]
 gi|88697532|gb|ABD48460.1| RpoB [Morganella morganii subsp. morganii]
 gi|88697534|gb|ABD48461.1| RpoB [Morganella morganii subsp. sibonii]
 gi|88697552|gb|ABD48470.1| RpoB [Morganella morganii]
          Length = 151

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 88/151 (58%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V D  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVRDDVVTDEIHYLSAIEEGNFIIAQANTVLDDDGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +QVVS+ AS
Sbjct: 121 CRNKGESSLFSRDQVQYMDVSTQQVVSVGAS 151


>gi|253720405|gb|ACT33446.1| RNA polymerase II second largest subunit [Hyaloscypha vitreola]
          Length = 254

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 89/265 (33%), Gaps = 27/265 (10%)

Query: 909  EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLA 968
             +  + AI      +  D+ +   S +   +    +F R   D+ +R   +    +E   
Sbjct: 2    GQNAIVAIAWYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR---IGMNVVEQFE 57

Query: 969  RDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFA 1025
            +    + + L    Y +L +   +  G           K+  ++ D      R++     
Sbjct: 58   KPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDXEELGQRTKAHVKR 117

Query: 1026 VQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQ 1085
                 ++     +  Q                             LR VKV +   +  Q
Sbjct: 118  DASTPLRSTENGIVDQVXI--------------------TTNAEGLRFVKVRMRTTKIPQ 157

Query: 1086 SGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWAC 1145
             GDK A RHG KG +      EDMPF + G   D+++NP  +PSRM +  + E  L    
Sbjct: 158  IGDKFASRHGQKGTIGITYRQEDMPFTRQGIVPDLIINPHAIPSRMTIAHLIECQLSKVS 217

Query: 1146 VGLGKKIKSLINDYKANGDISPLRS 1170
               G +  +          +S L  
Sbjct: 218  TLRGLEGDATPFTEVTVDSVSKLLR 242



 Score = 72.4 bits (176), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/144 (23%), Positives = 59/144 (40%), Gaps = 12/144 (8%)

Query: 808 GRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR---- 863
           G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E       
Sbjct: 2   GQNAIVAIAWYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFR 61

Query: 864 -DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAV 922
            D   +       +D+ GI+  G  V+  DI++GK  P         ++        KA 
Sbjct: 62  QDTLKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDXEELGQRT-------KAH 114

Query: 923 DVRDTSLRVPSGVSGTVVDVRIFN 946
             RD S  + S  +G V  V I  
Sbjct: 115 VKRDASTPLRSTENGIVDQVXITT 138


>gi|220961140|gb|ACL93036.1| RNA polymerase B subunit [Streptomyces ramulosus]
 gi|325551442|gb|ADZ28562.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           angustmyceticus]
          Length = 180

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|50058703|gb|AAT69104.1| RNA polymerase II [Ipomoea batatas]
          Length = 211

 Score =  159 bits (403), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 36/92 (39%), Positives = 48/92 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 120  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 179

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
             +PSRM +GQ+ E  +G     +GK+  +   
Sbjct: 180  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 211



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 43/122 (35%), Gaps = 14/122 (11%)

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNID 877
            EDS+++++  +    F S+    +    +      +E        +   +       +D
Sbjct: 1   QEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLD 60

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G+   G  V+  D+++GK TP  +           A         RD S  +    +G
Sbjct: 61  DDGLAPPGTRVSGEDVIIGKTTPLSQED---------AQGQSARYTKRDHSTSLRHSETG 111

Query: 938 TV 939
            V
Sbjct: 112 MV 113


>gi|208609807|dbj|BAG72365.1| RNA polymerase II second largest subunit [Litsea garciae]
          Length = 167

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAPMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGIV 65


>gi|220961134|gb|ACL93033.1| RNA polymerase B subunit [Streptomyces tubercidicus]
 gi|220961136|gb|ACL93034.1| RNA polymerase B subunit [Streptomyces chattanoogensis]
          Length = 180

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|157000425|gb|ABV00512.1| RNA polymerase subunit B [Streptomyces tricolor]
          Length = 180

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 125/175 (71%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L  
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIDGQVTDEVDYLTADEEDRFVIAQANAPLTS 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFEENRVLVRRRGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL++AEAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIQAEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|260593935|gb|ACX46262.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260594043|gb|ACX46316.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 84/158 (53%), Positives = 113/158 (71%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS ITH R +SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMDQNNPLSEITHKRCVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR + YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTSQYGFLESPYRVVNDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +     +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPVDVTLMDVSPKQVVSVAAS 158


>gi|50058725|gb|AAT69115.1| RNA polymerase II [Seddera hirsuta]
          Length = 219

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 36/92 (39%), Positives = 48/92 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 128  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVNPH 187

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIN 1157
             +PSRM +GQ+ E  +G     +GK+  +   
Sbjct: 188  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 219



 Score = 70.9 bits (172), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 47/130 (36%), Gaps = 14/130 (10%)

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVS 869
              + GYN EDS+++++  +    F S+    +    +      +E        +   + 
Sbjct: 1   IACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMR 60

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ G+   G  V+  D+++GK TP  +           A         RD S 
Sbjct: 61  HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQSARYTKRDHST 111

Query: 930 RVPSGVSGTV 939
            +    +G V
Sbjct: 112 SLRHSETGMV 121


>gi|117667756|gb|ABK55924.1| RNA polymerase B subunit [Streptomyces cremeus]
 gi|117667776|gb|ABK55934.1| RNA polymerase B subunit [Streptomyces spiroverticillatus]
          Length = 180

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V +G VT++V YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTEGVVTDEVDYLTADEEDRFVIAQANATLGE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTESRVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ +EAP VGTGME   A  +G  I A++AG+V++V A  + + + +G
Sbjct: 121 MMRQAVPLITSEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTVANDDG 175


>gi|330785268|gb|AEC46440.1| RNA polymerase II second largest subunit [Paralecanographa grumulosa]
          Length = 281

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 48/287 (16%), Positives = 87/287 (30%), Gaps = 25/287 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +     + +   +  + AI      +  D+ +   S +   +     + 
Sbjct: 1    YPQKPLATTRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSFFYR 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
             +     E+  +V    +E   +      +      Y +L +   +  G           
Sbjct: 61   TYI----EQQKAVGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVSGDDIIIG 116

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+   ++ +       Q  +   + + V   + S +                        
Sbjct: 117  KTAPFANPMADNAEGGQRTKMHSKRD-VSAPLRSTEAGLVDRVL---------------- 159

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                    R VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++N
Sbjct: 160  -VTTNEGRRTVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTAEGLVPDLIIN 218

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            P  +PSRM V  + E  L       G +  +          IS L  
Sbjct: 219  PHAIPSRMTVAHLIECLLSKVSATQGLEGDATPFTDVTVSGISDLLK 265



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 31/168 (18%), Positives = 56/168 (33%), Gaps = 6/168 (3%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S     +    + 
Sbjct: 9   TRSMEYLQFAELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSFFYRTYIEQQKA 68

Query: 854 TKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 E                  + +D+ G +  G  V+  DI++GK  P        
Sbjct: 69  VGFNALEEFEKPNKSMTMRTRPGTYEKLDDDGFVAPGVRVSGDDIIIGKTAPFANPMADN 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            E   R        DV        +G+   V+      R  +    R+
Sbjct: 129 AEGGQRTKM-HSKRDVSAPLRSTEAGLVDRVLVTTNEGRRTVKVRTRT 175


>gi|151573032|gb|ABS17686.1| RNA polymerase II [Fusarium sp. NRRL 43372]
 gi|151573044|gb|ABS17694.1| RNA polymerase II [Fusarium sp. NRRL 43428]
 gi|151573050|gb|ABS17698.1| RNA polymerase II [Fusarium sp. NRRL 43434]
 gi|151573071|gb|ABS17712.1| RNA polymerase II [Fusarium sp. NRRL 43447]
 gi|151573080|gb|ABS17718.1| RNA polymerase II [Fusarium sp. NRRL 43451]
 gi|151573101|gb|ABS17732.1| RNA polymerase II [Fusarium sp. NRRL 43469]
 gi|151573116|gb|ABS17742.1| RNA polymerase II [Fusarium sp. NRRL 43487]
 gi|151573128|gb|ABS17750.1| RNA polymerase II [Fusarium sp. NRRL 43494]
 gi|151573131|gb|ABS17752.1| RNA polymerase II [Fusarium sp. NRRL 43495]
 gi|151573185|gb|ABS17788.1| RNA polymerase II [Fusarium sp. NRRL 43544]
 gi|151573194|gb|ABS17794.1| RNA polymerase II [Fusarium sp. NRRL 43642]
 gi|151573197|gb|ABS17796.1| RNA polymerase II [Fusarium sp. NRRL 43643]
 gi|151573200|gb|ABS17798.1| RNA polymerase II [Fusarium sp. NRRL 43644]
 gi|151573203|gb|ABS17800.1| RNA polymerase II [Fusarium sp. NRRL 43645]
 gi|151573218|gb|ABS17810.1| RNA polymerase II [Fusarium sp. NRRL 43650]
 gi|151573281|gb|ABS17852.1| RNA polymerase II [Fusarium sp. NRRL 43675]
 gi|151573284|gb|ABS17854.1| RNA polymerase II [Fusarium sp. NRRL 43676]
 gi|151573287|gb|ABS17856.1| RNA polymerase II [Fusarium sp. NRRL 43677]
 gi|151573305|gb|ABS17868.1| RNA polymerase II [Fusarium sp. NRRL 43683]
 gi|151573308|gb|ABS17870.1| RNA polymerase II [Fusarium sp. NRRL 43684]
 gi|151573311|gb|ABS17872.1| RNA polymerase II [Fusarium sp. NRRL 43685]
 gi|151573333|gb|ABS17886.1| RNA polymerase II [Fusarium sp. NRRL 43695]
 gi|151573345|gb|ABS17894.1| RNA polymerase II [Fusarium sp. NRRL 43699]
 gi|151573348|gb|ABS17896.1| RNA polymerase II [Fusarium sp. NRRL 43700]
 gi|151573351|gb|ABS17898.1| RNA polymerase II [Fusarium sp. NRRL 43701]
 gi|151573844|gb|ABS18225.1| RNA polymerase II [Fusarium sp. NRRL 43715]
 gi|151573847|gb|ABS18227.1| RNA polymerase II [Fusarium sp. NRRL 43716]
 gi|151573850|gb|ABS18229.1| RNA polymerase II [Fusarium sp. NRRL 43717]
          Length = 300

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 53/373 (14%), Positives = 98/373 (26%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +                              ++
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFT-------------------------DVT 256

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                  +LR       G  +                        +G +    G       
Sbjct: 257  VDSVSELLRKHGYQSRGFEIM----------------------YNGHT----GR---KLR 287

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 288  AQVFFGPTYYQRL 300



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|50058735|gb|AAT69120.1| RNA polymerase II [Bonamia media]
          Length = 195

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 36/93 (38%), Positives = 47/93 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 98   TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 157

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+       
Sbjct: 158  AIPSRMTIGQLIECIMGKVAAHMGKEGDVTPFT 190



 Score = 43.1 bits (100), Expect = 0.35,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 30/98 (30%), Gaps = 14/98 (14%)

Query: 847 FEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           +    +      +E        +   +       +D+ G+   G  V+  D++ GK TP 
Sbjct: 3   YRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIXGKTTPI 62

Query: 902 GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            +           A         RD S  +    +G V
Sbjct: 63  SQDD---------AQGQASRYTKRDHSTSLRHSETGIV 91


>gi|220961132|gb|ACL93032.1| RNA polymerase B subunit [Streptomyces lydicus]
 gi|220961146|gb|ACL93039.1| RNA polymerase B subunit [Streptomyces caniferus]
 gi|220961178|gb|ACL93055.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           decoyicus]
 gi|220961186|gb|ACL93059.1| RNA polymerase B subunit [Streptomyces platensis]
 gi|220961190|gb|ACL93061.1| RNA polymerase B subunit [Streptomyces libani subsp. rufus]
          Length = 180

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 97/175 (55%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F+E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFSEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|208609767|dbj|BAG72345.1| RNA polymerase II second largest subunit [Litsea caulocarpa]
          Length = 167

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQMGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 43.9 bits (102), Expect = 0.23,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 8/70 (11%)

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ G+   G  V+  D+++GK TP G+                     RD S 
Sbjct: 4   HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDHST 55

Query: 930 RVPSGVSGTV 939
            +    SG V
Sbjct: 56  SLRHSESGMV 65


>gi|151573513|gb|ABS18006.1| RNA polymerase II [Fusarium sp. NRRL 13713]
 gi|151573528|gb|ABS18016.1| RNA polymerase II [Fusarium sp. NRRL 25483]
 gi|151573603|gb|ABS18065.1| RNA polymerase II [Fusarium sp. NRRL 28505]
 gi|151573639|gb|ABS18089.1| RNA polymerase II [Fusarium sp. NRRL 32521]
          Length = 300

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 54/373 (14%), Positives = 96/373 (25%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +          +S L                  
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRKHGYQSRGFEVM---- 277

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                        +G +    G       
Sbjct: 278  -------------------------------------------YNGHT----GR---KLR 287

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 288  AQVFFGPTYYQRL 300



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|57864680|gb|AAW56959.1| RNA polymerase beta subunit [Silene latifolia]
          Length = 258

 Score =  159 bits (403), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 91/258 (35%), Positives = 149/258 (57%), Gaps = 2/258 (0%)

Query: 406 YDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465
            +L  +GR  MN RLNLD P     +   DI+A    L+ ++ G GT+DD+++L N+R+R
Sbjct: 1   CELGRIGRRNMNRRLNLDIPQXNTFLLPRDILAATDHLIGMKFGMGTLDDMNHLKNKRIR 60

Query: 466 SVGEMLKNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFCSSQLS 523
           SV ++L++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF    LS
Sbjct: 61  SVADLLQDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLS 120

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q+ +  N L++I H R+LS LG GG+    A   +RD+HP+HYGRICP +TSEG N+GL+
Sbjct: 121 QVLDRTNPLTQIVHGRKLSYLGPGGLTGRTASFRIRDIHPSHYGRICPIDTSEGINVGLI 180

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            SL   AR+   G +E+P+ K+ +      +++LS   +E   ++  NS     G   E+
Sbjct: 181 GSLAIHARIGLLGSLESPFYKISERSAMVQMLFLSPSIDEYYMVSTGNSLALNQGIQEEQ 240

Query: 644 LVFCRCAGEEILVPREKI 661
           +V  R   E + +  E++
Sbjct: 241 VVPARYRQEFLTIAWEQV 258


>gi|4972805|gb|AAD34798.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            cinaedi]
          Length = 178

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 45/104 (43%), Positives = 63/104 (60%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTIKSDD  GR   Y++I  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDTEGRRGAYKAITKGERVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNSAK-----MEEIP---DFNKCEL 1385
            L KE+Q+L L +++       +       ++E     DF+  +L
Sbjct: 61   LTKELQSLALDVNIYGEEVDENGMPVPITIKEDDRPKDFSSFQL 104


>gi|318085062|gb|ADV39421.1| RNA polymerase subunit B [Streptomyces puniciscabiei]
          Length = 180

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V YL+A EE+   IAQAN+ L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAPLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFAEARVLVRRRGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTANDDG 175


>gi|318085024|gb|ADV39402.1| RNA polymerase subunit B [Streptomyces alanosinicus]
          Length = 180

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 89/175 (50%), Positives = 122/175 (69%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV +  VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVDEHGVTDEVDYLTADEEDRFVIAQANAPLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFAEARVLVRRRGGEVDYVAPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTANDDG 175


>gi|220961220|gb|ACL93076.1| RNA polymerase B subunit [Streptomyces sclerotialus]
          Length = 179

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 92/174 (52%), Positives = 129/174 (74%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV DG+V+++V YL+A EE+   IAQAN+ LDE
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVVDGQVSDEVDYLTADEEDRFVIAQANAPLDE 60

Query: 637 DGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
           +  FTE ++  R  GE   VP +++ ++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM
Sbjct: 61  EMRFTERVLVRRRGGEVDYVPGDEVHYMDVSPRQMVSVATAMIPFLEHDDANRALMGANM 120

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 174


>gi|151573038|gb|ABS17690.1| RNA polymerase II [Fusarium sp. NRRL 43376]
 gi|151573047|gb|ABS17696.1| RNA polymerase II [Fusarium sp. NRRL 43429]
 gi|151573056|gb|ABS17702.1| RNA polymerase II [Fusarium sp. NRRL 43436]
 gi|151573059|gb|ABS17704.1| RNA polymerase II [Fusarium sp. NRRL 43437]
 gi|151573074|gb|ABS17714.1| RNA polymerase II [Fusarium sp. NRRL 43448]
 gi|151573089|gb|ABS17724.1| RNA polymerase II [Fusarium sp. NRRL 43454]
 gi|151573092|gb|ABS17726.1| RNA polymerase II [Fusarium sp. NRRL 43466]
 gi|151573104|gb|ABS17734.1| RNA polymerase II [Fusarium sp. NRRL 43472]
 gi|151573107|gb|ABS17736.1| RNA polymerase II [Fusarium sp. NRRL 43473]
 gi|151573119|gb|ABS17744.1| RNA polymerase II [Fusarium sp. NRRL 43491]
 gi|151573134|gb|ABS17754.1| RNA polymerase II [Fusarium sp. NRRL 43496]
 gi|151573137|gb|ABS17756.1| RNA polymerase II [Fusarium sp. NRRL 43497]
 gi|151573140|gb|ABS17758.1| RNA polymerase II [Fusarium sp. NRRL 43504]
 gi|151573143|gb|ABS17760.1| RNA polymerase II [Fusarium sp. NRRL 43506]
 gi|151573146|gb|ABS17762.1| RNA polymerase II [Fusarium sp. NRRL 43508]
 gi|151573188|gb|ABS17790.1| RNA polymerase II [Gibberella intermedia]
 gi|151573191|gb|ABS17792.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573206|gb|ABS17802.1| RNA polymerase II [Fusarium sp. NRRL 43646]
 gi|151573209|gb|ABS17804.1| RNA polymerase II [Fusarium sp. NRRL 43647]
 gi|151573212|gb|ABS17806.1| RNA polymerase II [Fusarium sp. NRRL 43648]
 gi|151573227|gb|ABS17816.1| RNA polymerase II [Fusarium sp. NRRL 43653]
 gi|151573230|gb|ABS17818.1| RNA polymerase II [Fusarium sp. NRRL 43654]
 gi|151573233|gb|ABS17820.1| RNA polymerase II [Fusarium sp. NRRL 43655]
 gi|151573236|gb|ABS17822.1| RNA polymerase II [Fusarium sp. NRRL 43656]
 gi|151573239|gb|ABS17824.1| RNA polymerase II [Fusarium sp. NRRL 43657]
 gi|151573242|gb|ABS17826.1| RNA polymerase II [Fusarium sp. NRRL 43658]
 gi|151573254|gb|ABS17834.1| RNA polymerase II [Fusarium sp. NRRL 43662]
 gi|151573257|gb|ABS17836.1| RNA polymerase II [Fusarium sp. NRRL 43663]
 gi|151573260|gb|ABS17838.1| RNA polymerase II [Fusarium sp. NRRL 43664]
 gi|151573263|gb|ABS17840.1| RNA polymerase II [Gibberella intermedia]
 gi|151573266|gb|ABS17842.1| RNA polymerase II [Gibberella intermedia]
 gi|151573269|gb|ABS17844.1| RNA polymerase II [Gibberella intermedia]
 gi|151573272|gb|ABS17846.1| RNA polymerase II [Fusarium sp. NRRL 43668]
 gi|151573278|gb|ABS17850.1| RNA polymerase II [Fusarium sp. NRRL 43674]
 gi|151573290|gb|ABS17858.1| RNA polymerase II [Fusarium sp. NRRL 43678]
 gi|151573293|gb|ABS17860.1| RNA polymerase II [Fusarium sp. NRRL 43679]
 gi|151573296|gb|ABS17862.1| RNA polymerase II [Fusarium sp. NRRL 43680]
 gi|151573302|gb|ABS17866.1| RNA polymerase II [Fusarium sp. NRRL 43682]
 gi|151573314|gb|ABS17874.1| RNA polymerase II [Fusarium sp. NRRL 43686]
 gi|151573317|gb|ABS17876.1| RNA polymerase II [Fusarium sp. NRRL 43687]
 gi|151573326|gb|ABS17882.1| RNA polymerase II [Fusarium sp. NRRL 43692]
 gi|151573330|gb|ABS17884.1| RNA polymerase II [Fusarium sp. FIESC_6a KOD-2010]
 gi|151573336|gb|ABS17888.1| RNA polymerase II [Fusarium sp. NRRL 43696]
 gi|151573339|gb|ABS17890.1| RNA polymerase II [Gibberella moniliformis]
 gi|151573342|gb|ABS17892.1| RNA polymerase II [Fusarium sp. NRRL 43698]
 gi|151573366|gb|ABS17908.1| RNA polymerase II [Fusarium sp. NRRL 43706]
 gi|151573369|gb|ABS17910.1| RNA polymerase II [Fusarium sp. NRRL 43707]
 gi|151573372|gb|ABS17912.1| RNA polymerase II [Fusarium sp. NRRL 43708]
 gi|151573375|gb|ABS17914.1| RNA polymerase II [Fusarium sp. NRRL 43709]
 gi|151573378|gb|ABS17916.1| RNA polymerase II [Fusarium sp. NRRL 43710]
 gi|151573486|gb|ABS17988.1| RNA polymerase II [Fusarium sp. NRRL 3211]
 gi|151573489|gb|ABS17990.1| RNA polymerase II [Fusarium sp. NRRL 5537]
 gi|151573492|gb|ABS17992.1| RNA polymerase II [Fusarium sp. NRRL 13335]
 gi|151573495|gb|ABS17994.1| RNA polymerase II [Fusarium sp. NRRL 13379]
 gi|151573498|gb|ABS17996.1| RNA polymerase II [Fusarium nygamai]
 gi|151573504|gb|ABS18000.1| RNA polymerase II [Gibberella fujikuroi]
 gi|151573510|gb|ABS18004.1| RNA polymerase II [Gibberella intermedia]
 gi|151573516|gb|ABS18008.1| RNA polymerase II [Fusarium sp. NRRL 20423]
 gi|151573519|gb|ABS18010.1| RNA polymerase II [Fusarium sp. NRRL 20425]
 gi|151573525|gb|ABS18014.1| RNA polymerase II [Gibberella thapsina]
 gi|151573531|gb|ABS18018.1| RNA polymerase II [Fusarium sp. NRRL 25489]
 gi|151573534|gb|ABS18020.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573589|gb|ABS18056.1| RNA polymerase II [Fusarium sp. FIESC_3b KOD-2010]
 gi|151573612|gb|ABS18071.1| RNA polymerase II [Fusarium sp. NRRL 31010]
 gi|151573615|gb|ABS18073.1| RNA polymerase II [Fusarium sp. NRRL 31011]
 gi|151573618|gb|ABS18075.1| RNA polymerase II [Fusarium sp. NRRL 31160]
 gi|151573621|gb|ABS18077.1| RNA polymerase II [Fusarium sp. NRRL 31167]
 gi|151573627|gb|ABS18081.1| RNA polymerase II [Gibberella intermedia]
 gi|151573630|gb|ABS18083.1| RNA polymerase II [Fusarium sp. NRRL 32175]
 gi|151573642|gb|ABS18091.1| RNA polymerase II [Fusarium sp. FIESC_25c KOD-2010]
 gi|151573645|gb|ABS18093.1| RNA polymerase II [Fusarium sp. FIESC_5a KOD-2010]
 gi|151573648|gb|ABS18095.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573779|gb|ABS18182.1| RNA polymerase II [Fusarium sp. NRRL 43622]
 gi|151573782|gb|ABS18184.1| RNA polymerase II [Fusarium sp. NRRL 43623]
 gi|151573835|gb|ABS18219.1| RNA polymerase II [Gibberella intermedia]
 gi|151573838|gb|ABS18221.1| RNA polymerase II [Fusarium oxysporum]
 gi|151573841|gb|ABS18223.1| RNA polymerase II [Gibberella moniliformis]
          Length = 300

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 54/373 (14%), Positives = 96/373 (25%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +          +S L                  
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRKHGYQSRGFEVM---- 277

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                        +G +    G       
Sbjct: 278  -------------------------------------------YNGHT----GR---KLR 287

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 288  AQVFFGPTYYQRL 300



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|294721636|gb|ADF32969.1| RNA polymerase II second largest subunit [Coniosporium uncinatum]
          Length = 257

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 51/274 (18%), Positives = 86/274 (31%), Gaps = 27/274 (9%)

Query: 900  PKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISV 959
                  M   +  + AI      +  D+ +   S +   +    +F R   D+ +R    
Sbjct: 2    YLRFRDMPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYSDQEKRVGM- 59

Query: 960  EREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEY 1016
                +E   +    + + L    Y +L +   +  G           K+  ++ D     
Sbjct: 60   --ATVENFEKPMRADTIRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDSEELG 117

Query: 1017 PRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKV 1076
             R+           ++     +  Q                             L  VKV
Sbjct: 118  QRTXLHVKRDVSTPLRSTENGIIDQVLL--------------------TTNTEGLXYVKV 157

Query: 1077 FVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQI 1136
                 +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  +
Sbjct: 158  RTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGLXPDLIINPHAIPSRMTIAHL 217

Query: 1137 FETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             E  L       G +  +          IS L  
Sbjct: 218  IECLLSKVGALRGFEGDATPFLDITVTSISNLLR 251



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 59/148 (39%), Gaps = 9/148 (6%)

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 D+  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   + 
Sbjct: 1   EYLRFRDMPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYSDQEKRVGMA 60

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E     +  D   +       +D+ GI+  G  V+  DI++GK  P         E+L
Sbjct: 61  TVENFEKPMRADTIRLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAPDS----EEL 116

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +        DV        +G+   V+
Sbjct: 117 GQRTXLHVKRDVSTPLRSTENGIIDQVL 144


>gi|260594093|gb|ACX46341.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 86/158 (54%), Positives = 112/158 (70%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGENNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT  +V+LSA+E+ +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTESIVFLSAIEQADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|193201519|gb|ACF15967.1| RNA polymerase II subunit [Opegrapha ochrocheila]
          Length = 280

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 50/290 (17%), Positives = 89/290 (30%), Gaps = 25/290 (8%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +N++ I       E   +      + +  N Y +L +   +  G        
Sbjct: 61   FYRTYNESENDKGI----NNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVSGDDV 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+  +                E   R     +          E    +K+   
Sbjct: 117  IIGKTEALAEPM------------RQGAEGGARLPTHERRDCSAPLRSTEAGIIDKVV-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----VTLSESKKSVKVRTRTTKVPQVGDKFASRHGQKGTIGITYRQEDMPFTSEGLTPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            ++NP  +PSRM +  + E  L       G +  +         DIS L  
Sbjct: 219  IINPHAIPSRMTIAHLIECLLSKVAAVDGMEGDATPFTPVTVQDISDLLQ 268



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 66/189 (34%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +     D  +   E           ++       +D+ G +  G  V+
Sbjct: 53  DRGLFRSLFYRTYNESENDKGINNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK     E      E   R        + RD S  + S     ++D  +     
Sbjct: 113 GDDVIIGKTEALAEPMRQGAEGGARLP----THERRDCSAPLRS-TEAGIIDKVVVTLSE 167

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 168 SKKSVKVRT 176


>gi|220961130|gb|ACL93031.1| RNA polymerase B subunit [Streptomyces nigrescens]
 gi|220961142|gb|ACL93037.1| RNA polymerase B subunit [Streptomyces rimosus subsp. rimosus]
 gi|220961198|gb|ACL93065.1| RNA polymerase B subunit [Streptomyces libani subsp. libani]
          Length = 180

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F+E+ V  R  G E  LVP +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFSEQRVLVRRRGGEVDLVPADEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|88697520|gb|ABD48454.1| RpoB [Morganella psychrotolerans]
 gi|88697522|gb|ABD48455.1| RpoB [Morganella psychrotolerans]
          Length = 151

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 87/151 (57%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVREDAVTDEIHYLSAIEEGNFIIAQANTVLDDDGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +QVVS+ AS
Sbjct: 121 CRNKGESSLFSRDQVQYMDVSTQQVVSVGAS 151


>gi|37956403|gb|AAP15373.1| RNA polymerase beta subunit [Desulfuromonas thiophila]
          Length = 177

 Score =  159 bits (402), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 86/146 (58%), Positives = 110/146 (75%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +SL+++AR+N +GF+ETPYR V DG+VT ++ Y SA+EEE   IAQAN+SLDE G F  E
Sbjct: 61  ASLSTYARINEHGFVETPYRLVKDGQVTEEIRYFSALEEEGHAIAQANASLDEQGCFVNE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPK 669
           +V  R  GE +++ RE+I  +D SP+
Sbjct: 121 VVNARLNGEFMMLRREEIKLMDVSPE 146


>gi|223585665|gb|ACM91703.1| ribosomal polymerase subunit beta [Macrococcus caseolyticus]
 gi|223585667|gb|ACM91704.1| ribosomal polymerase subunit beta [Staphylococcus sp. KS-SP_74]
          Length = 158

 Score =  159 bits (402), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 95/158 (60%), Positives = 122/158 (77%), Gaps = 2/158 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      VT+ + YL+A EE+   +AQANS LD++G F ++ V CR  G+  ++ RE++
Sbjct: 61  KVDIETNTVTSQIDYLTADEEDAYVVAQANSRLDDNGKFLDDEVVCRFRGDNTVMARERM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 158


>gi|4972793|gb|AAD34792.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter sp.
            CLO-3]
          Length = 178

 Score =  159 bits (402), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 48/104 (46%), Positives = 65/104 (62%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLT+KSDD++GR   Y SI  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTLKSDDIIGRENAYRSITKGEPVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDL------ENSRTKNSAKMEEIP--DFNKCEL 1385
            L KE+Q+L L +++      E+   K     E+    DFN  +L
Sbjct: 61   LTKELQSLALDVNVFDGSLDEDGNPKPLEIKEDNRPKDFNSFQL 104


>gi|193201517|gb|ACF15966.1| RNA polymerase II subunit [Opegrapha ochrocheila]
          Length = 281

 Score =  159 bits (402), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 50/290 (17%), Positives = 89/290 (30%), Gaps = 25/290 (8%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSL 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +N++ I       E   +      + +  N Y +L +   +  G        
Sbjct: 61   FYRTYNESENDKGI----NNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVSGDDV 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  L+  +                E   R     +          E    +K+   
Sbjct: 117  IIGKTEALAEPM------------RQGAEGGARLPTHERRDCSAPLRSTEAGIIDKVV-- 162

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                       + VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+
Sbjct: 163  ----VTLSESKKSVKVRTRTTKVPQVGDKFASRHGQKGTIGITYRQEDMPFTSEGLTPDL 218

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
            ++NP  +PSRM +  + E  L       G +  +         DIS L  
Sbjct: 219  IINPHAIPSRMTIAHLIECLLSKVAAVDGMEGDATPFTPVTVQDISDLLQ 268



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 66/189 (34%), Gaps = 20/189 (10%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRAMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSAI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +     D  +   E           ++       +D+ G +  G  V+
Sbjct: 53  DRGLFRSLFYRTYNESENDKGINNRERFEKPMRQTTMSMKHNAYDKLDDDGFVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK     E      E   R        + RD S  + S     ++D  +     
Sbjct: 113 GDDVIIGKTEALAEPMRQGAEGGARLP----THERRDCSAPLRS-TEAGIIDKVVVTLSE 167

Query: 950 IDKNERSIS 958
             K+ +  +
Sbjct: 168 SKKSVKVRT 176


>gi|151573609|gb|ABS18069.1| RNA polymerase II [Fusarium sp. NRRL 31005]
          Length = 299

 Score =  159 bits (402), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 54/373 (14%), Positives = 96/373 (25%), Gaps = 75/373 (20%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 61   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 120

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 121  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 163  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKIS 1186
            +PSRM +  + E  L       G +  +          +S L                  
Sbjct: 221  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRKHGYQSRGFEVM---- 276

Query: 1187 DYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFD 1246
                                                        +G +    G       
Sbjct: 277  -------------------------------------------YNGHT----GR---KLR 286

Query: 1247 RPVTVGYIYMLKL 1259
              V  G  Y  +L
Sbjct: 287  AQVFFGPTYYQRL 299



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 51  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 111 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 163

Query: 950 IDK 952
             K
Sbjct: 164 NVK 166


>gi|313494726|gb|ADR57500.1| RNA polymerase beta subunit [Cathaya argyrophylla]
          Length = 246

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 96/236 (40%), Positives = 145/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +DA+                     +L+ + RSN NTC +Q+
Sbjct: 2   ALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTKLVIYNRSNTNTCTHQK 53

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 54  PQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 113

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS+HI  + +    T  GPE ITR+IP++    L+++DE GI+ +G+ +  GD+LVGK+T
Sbjct: 114 TSLHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGIVMLGSWIETGDVLVGKLT 173

Query: 900 PKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 174 PQTTEESLCAPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 229


>gi|14971055|gb|AAK74092.1| RNA polymerase beta subunit [Bacillus cereus]
          Length = 258

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 87/197 (44%), Gaps = 19/197 (9%)

Query: 158 HRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSF 217
            RSP +++    G+   +GK  +   +IP++G W++ E D+KD+++VRIDR RK+PVT  
Sbjct: 1   VRSPSVYYS---GKVDKNGKRGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVL 57

Query: 218 LMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIE 275
           L AL   S+ EI          S   +      +   L+           +  GE   +E
Sbjct: 58  LRALRFGSDQEITELLGDNEYLSNTLEKDNTDSTEKALL------EIYERLRPGEPPTVE 111

Query: 276 SGKKLTSGLLKSLK--------EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDV 327
           + K L        K           +       + L    +AE +V+ ETGEI    G +
Sbjct: 112 NAKSLLVSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGXI 171

Query: 328 IDEKSLEEIFHSEIRDI 344
           +D ++L+ I     ++I
Sbjct: 172 LDRRTLDRILPYLEKNI 188



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 70  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 129

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 130 ANVGRYKINKKLHIKNRLFNQRL 152


>gi|325551444|gb|ADZ28563.1| RNA polymerase B subunit [Streptomyces kishiwadensis]
          Length = 180

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRYVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|126428502|gb|ABO13961.1| RNA polymerase II subunit 2 [Eupenicillium limosum]
          Length = 543

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 99/615 (16%), Positives = 182/615 (29%), Gaps = 86/615 (13%)

Query: 526  EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
                   S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +
Sbjct: 1    LSRYTFASSLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKN 56

Query: 586  LTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
            L     +      E    +    + +V  +            ++      +  D +    
Sbjct: 57   LALMCYITVGTPSEPIVDFMIQRNMEVLEEFEPQVTPNATKVFVNGVWVGIHRDPTHLVN 116

Query: 644  LVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ--RQA 700
             +        I      I D  D   K          P    D+  +     ++   ++ 
Sbjct: 117  TMQSLRRRNMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVVDNDPKSENAGSLVLNKEH 176

Query: 701  VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTS 757
            + LL+ +           + +         R+G+VE VDA      +I     DL+ S  
Sbjct: 177  IRLLELDKDLQRELPPEQLREQGFGWDGLVRSGVVEYVDAEEEETIMIVMTPEDLEISKH 236

Query: 758  GVDIYRLMKFQRSNQNTCVNQRPLVK-VGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                Y L +  +++ N        V+ V             PS  LG       +  + +
Sbjct: 237  LQAGYSLPEDDKNDPNK------RVRTVTQRAHTWTHCEIHPSMILG-------VCASII 283

Query: 817  PWHGYNFEDSMLISERMVSE--DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
            P+  +N          M  +   VF +   +  E                          
Sbjct: 284  PFPDHNQSPRNTYQSAMGKQAMGVFLTNFAQRMET------------------------- 318

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +             +       +   +  + AI      +  D+ +   S 
Sbjct: 319  ------MANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSS 372

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +     +  +     +   +V    +E   +    E + + +  Y +L E   +  
Sbjct: 373  IDRGLFRSLFYRTYT----DSEKTVGTSFVESFEKPLRTETLGMRKGTYDKLDEDGIVAP 428

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K   L+ D      R++          ++     +  Q   S      
Sbjct: 429  GVRVSGEDIIIGKVAPLAPDAEELGQRTKAHTKIDVSTPLRSTENGIVDQVVIS------ 482

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                               L+  KV +   +  Q GDK A RHG KG +      EDMPF
Sbjct: 483  --------------TANDGLKFAKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPF 528

Query: 1112 LKDGTPVDIVLNPLG 1126
             ++G   DI++NP  
Sbjct: 529  SREGXTPDIIINPHA 543



 Score =  102 bits (255), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 79/552 (14%), Positives = 149/552 (26%), Gaps = 95/552 (17%)

Query: 429 RHIRKEDIIAIIKILVDLRN-GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMER--S 485
           R          I     L N   G +   +    +    V  +    Y       E    
Sbjct: 15  RTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVD 74

Query: 486 IKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL- 544
              + +   ++   PQ   NA  V      F     +    +  + ++ +   RR + + 
Sbjct: 75  FMIQRNMEVLEEFEPQVTPNATKV------FVNGVWVGIHRDPTHLVNTMQSLRRRNMIS 128

Query: 545 GQGGVARARAGVEM-------RDVHPTHYGRICPAETSEGHNIGLVSSLTSFA------R 591
            +  + R     E        R   P       P   + G  +     +          R
Sbjct: 129 HEVSLIRDIRDREFKIFTDAGRVCRPLFVVDNDPKSENAGSLVLNKEHIRLLELDKDLQR 188

Query: 592 VNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAG 651
                 +            +  V Y+ A EEE   I      L+                
Sbjct: 189 ELPPEQLREQGFGWDGLVRSGVVEYVDAEEEETIMIVMTPEDLEISKHLQ---------- 238

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                                  A   +P  + +D N+ +                    
Sbjct: 239 -----------------------AGYSLPEDDKNDPNKRV----------------RTVT 259

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD-IYRLMKFQRS 770
                    +   + I+   A I+   D  +    + +  +     GV       + +  
Sbjct: 260 QRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFAQRMETM 319

Query: 771 NQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLIS 830
                  Q+PL                      +L  G+N +VA   + GYN EDS++++
Sbjct: 320 ANILYYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMN 369

Query: 831 ERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVG 885
           +  +   +F S+    +    +       E        +   + +     +DE GI+  G
Sbjct: 370 QSSIDRGLFRSLFYRTYTDSEKTVGTSFVESFEKPLRTETLGMRKGTYDKLDEDGIVAPG 429

Query: 886 AEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIF 945
             V+  DI++GK+ P         ++        KA    D S  + S  +G V  V I 
Sbjct: 430 VRVSGEDIIIGKVAPLAPDAEELGQRT-------KAHTKIDVSTPLRSTENGIVDQVVIS 482

Query: 946 NRHGIDKNERSI 957
             +   K  +  
Sbjct: 483 TANDGLKFAKVR 494


>gi|88697536|gb|ABD48462.1| RpoB [Morganella psychrotolerans]
 gi|88697538|gb|ABD48463.1| RpoB [Morganella psychrotolerans]
 gi|88697540|gb|ABD48464.1| RpoB [Morganella psychrotolerans]
 gi|88697542|gb|ABD48465.1| RpoB [Morganella psychrotolerans]
 gi|88697544|gb|ABD48466.1| RpoB [Morganella psychrotolerans]
 gi|88697546|gb|ABD48467.1| RpoB [Morganella psychrotolerans]
 gi|88697548|gb|ABD48468.1| RpoB [Morganella psychrotolerans]
 gi|88697550|gb|ABD48469.1| RpoB [Morganella psychrotolerans]
 gi|88697554|gb|ABD48471.1| RpoB [Morganella psychrotolerans]
          Length = 151

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVREDVVTDEIHYLSAIEEGNFIIAQANTVLDDDGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +Q+VS+ AS
Sbjct: 121 CRNRGESSLFSRDQVQYMDVSTQQIVSVGAS 151


>gi|219564087|gb|ACL28227.1| RNA polymerase II second largest subunit [fungal sp. M230]
          Length = 270

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/276 (19%), Positives = 96/276 (34%), Gaps = 27/276 (9%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ +R  
Sbjct: 3    MEFLKFRELPAGQNXIVAIACYXGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTDQEKR-- 59

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             +    IE   +    + + L    Y +L +   +  G           K+  ++ D   
Sbjct: 60   -IGINVIERFEKPYRSDTLKLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPMALD--- 115

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
                         +E  QR    +K    T     E+   +++             LR V
Sbjct: 116  ------------NEEMGQRTKAHIKRDASTPLRSTENGIVDQVLI-----TTNAEGLRFV 158

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV +   +  Q GDK A RHG KG +      EDMPF  +G   D+++NP  +PSRM + 
Sbjct: 159  KVRMRTTKIPQIGDKFASRHGQKGTIGITYRMEDMPFTVEGVVPDLIINPHAIPSRMTIA 218

Query: 1135 QIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             + E  L       G +  +          +S L  
Sbjct: 219  HLIECQLSKVSTLRGLEGDATPFTEVTVDSVSKLLR 254



 Score = 79.3 bits (194), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 35/156 (22%), Positives = 62/156 (39%), Gaps = 12/156 (7%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 2   SMEFLKFRELPAGQNXIVAIACYXGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIG 61

Query: 856 LGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           +   E        D   +     + +D+ GI+  G  V+  DI++GK  P         +
Sbjct: 62  INVIERFEKPYRSDTLKLKHGTYEKLDDDGIVAPGVRVSGEDIIIGKTAPMALDNEEMGQ 121

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           +        KA   RD S  + S  +G V  V I  
Sbjct: 122 RT-------KAHIKRDASTPLRSTENGIVDQVLITT 150


>gi|157000409|gb|ABV00504.1| RNA polymerase subunit B [Streptomyces globosus]
          Length = 180

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 125/175 (71%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L  
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIDGQVTDEVDYLTADEEDRFVIAQANAPLTS 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFEENRVLVRRRGGEVDYVGPEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|318085018|gb|ADV39399.1| RNA polymerase subunit B [Streptomyces neyagawaensis]
          Length = 180

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLTD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFAENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|318085036|gb|ADV39408.1| RNA polymerase subunit B [Streptomyces tauricus]
          Length = 180

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 91/174 (52%), Positives = 125/174 (71%), Gaps = 1/174 (0%)

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
            NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L++D
Sbjct: 2   PNIGLIGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANAVLNDD 61

Query: 638 GSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
             F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG NM
Sbjct: 62  MRFNEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANM 121

Query: 697 QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
            RQAVPL+ AEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 122 MRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKTGVVQEVSADYVTVANDDG 175


>gi|242060256|ref|XP_002451417.1| hypothetical protein SORBIDRAFT_04g001790 [Sorghum bicolor]
 gi|241931248|gb|EES04393.1| hypothetical protein SORBIDRAFT_04g001790 [Sorghum bicolor]
          Length = 192

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 41/106 (38%), Positives = 61/106 (57%), Gaps = 4/106 (3%)

Query: 1222 MLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQ 1281
            ML     +  G+ +LY G+ G   D  + +G +Y  +L HMVSDK   R+TG    +T+Q
Sbjct: 1    MLASYGFNYHGKEVLYSGVFGTEMDCEIFIGPVYYQRLRHMVSDKFQVRTTGRIDQITRQ 60

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVV 1323
            P+GG+ + GG R GEME   + A+G++Y+L + L   SD    DV 
Sbjct: 61   PIGGRKHGGGIRFGEMERDALLAHGSSYLLHDRLHSCSDYHIADVC 106


>gi|309753166|gb|ADO85606.1| DNA-dependent RNA polymerase II [Morchella elata]
 gi|309753168|gb|ADO85607.1| DNA-dependent RNA polymerase II [Morchella elata]
 gi|309753170|gb|ADO85608.1| DNA-dependent RNA polymerase II [Morchella elata]
          Length = 256

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 47/271 (17%), Positives = 85/271 (31%), Gaps = 21/271 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R  +D+ +R      E+ E   R    +      +       +  G      
Sbjct: 66   LF-RSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDGLVAPGVRVSGE 124

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ D+     R ++         ++     +  Q                 
Sbjct: 125  DIIIGKTAPIAPDVDEMGQRQKFHTKRDVSTPLRSTENGIVDQVML-------------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG V      EDMPF  +G   
Sbjct: 171  ------TTNAEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTVGITYRQEDMPFTCEGIVP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            D+++NP  +PSRM +  + E  L       G
Sbjct: 225  DLIINPHAIPSRMTIAHLIECQLSKVSSLRG 255



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 68/192 (35%), Gaps = 22/192 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA + + GYN ED
Sbjct: 4   RMDTMANILYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 53

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   +   E        +   +       +DE G
Sbjct: 54  SVIMNQSSIDRGLFRSLFYRSYMDQEKRIGMQVVEEFEKPTRANTLKLKHGTYDKLDEDG 113

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           ++  G  V+  DI++GK  P         ++       +K    RD S  + S  +G V 
Sbjct: 114 LVAPGVRVSGEDIIIGKTAPIAPDVDEMGQR-------QKFHTKRDVSTPLRSTENGIVD 166

Query: 941 DVRIFNRHGIDK 952
            V +       K
Sbjct: 167 QVMLTTNAEGLK 178


>gi|88697556|gb|ABD48472.1| RpoB [Morganella psychrotolerans]
          Length = 151

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVREDAVTDEIHYLSAIEEGNFIIAQANTVLDDDGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +Q+VS+ AS
Sbjct: 121 CRNKGESSLFSRDQVQYMDVSTQQIVSVGAS 151


>gi|220961188|gb|ACL93060.1| RNA polymerase B subunit [Streptomyces olivaceiscleroticus]
 gi|325551440|gb|ADZ28561.1| RNA polymerase B subunit [Streptomyces niger]
          Length = 180

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 97/175 (55%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVKYLTADEEDRFIIAQANAPLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E  LV  +++DF+D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEQRVLVRRRGGEADLVTVDEVDFMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|55650660|emb|CAF31387.1| RNA polymerase B subunit [Nostoc sp. 1tu14s8]
          Length = 187

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 90/192 (46%), Positives = 125/192 (65%), Gaps = 6/192 (3%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  +  +DE G     LV  R   E      E++D++  SP Q+VS+A S+IPFLE+D
Sbjct: 2   RVAPGDIPVDETGHIIGPLVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  +V++  G V  VDA  I +
Sbjct: 62  DANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVVVSRTDGDVTYVDATEIRV 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R      +        Y L K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+L
Sbjct: 122 RPKPNTSE------IRYTLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGEL 175

Query: 806 ALGRNMLVAFMP 817
           ALG+N++VA+MP
Sbjct: 176 ALGQNIVVAYMP 187


>gi|159154262|gb|ABW93529.1| RNA polymerase B subunit [Nostoc sp. IO-102-I]
          Length = 186

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 90/192 (46%), Positives = 125/192 (65%), Gaps = 6/192 (3%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  +  +DE G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+D
Sbjct: 1   RVAPGDIPVDETGHIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHD 60

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +
Sbjct: 61  DANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRV 120

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R      +        Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+L
Sbjct: 121 RPKPNTSE------IKYTLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGEL 174

Query: 806 ALGRNMLVAFMP 817
           ALG+N++VA+MP
Sbjct: 175 ALGQNIVVAYMP 186


>gi|55650698|emb|CAF31400.1| RNA polymerase B subunit [Nodularia spumigena HEM]
          Length = 187

 Score =  159 bits (401), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 91/190 (47%), Positives = 128/190 (67%), Gaps = 6/190 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDIPLDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRP 123

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
            +G+ +        YRL K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LAL
Sbjct: 124 KDGNSE------IRYRLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELAL 177

Query: 808 GRNMLVAFMP 817
           G+N+++A+MP
Sbjct: 178 GQNIVIAYMP 187


>gi|318085034|gb|ADV39407.1| RNA polymerase subunit B [Streptomyces ipomoeae]
          Length = 180

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAENRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL++AE+P VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIQAESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|157000421|gb|ABV00510.1| RNA polymerase subunit B [Streptomyces pluricolorescens]
 gi|220961114|gb|ACL93023.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           angustmyceticus]
 gi|220961116|gb|ACL93024.1| RNA polymerase B subunit [Streptomyces noursei]
          Length = 180

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 91/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV DG+VT++V YL+A EE+   IAQAN+ L++
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAPLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  +  R  G E   VP +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFVENRILVRRRGGEVDYVPGDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|145307890|gb|ABP57249.1| RNA polymerase II second largest subunit [Furia ithacensis]
          Length = 269

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 95/284 (33%), Gaps = 27/284 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 10   YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 69

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 70   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 125

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  D      R++          ++     +  +   + +   
Sbjct: 126  PGTRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 183

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 184  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 225

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            F  +G   D+V+NP  +PSRM +G + E  +G      G +  +
Sbjct: 226  FSAEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDGSEGDA 269



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 8   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 57

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 58  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 117

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 118 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGI 173

Query: 936 SGTVV 940
              V+
Sbjct: 174 VDRVM 178


>gi|112798753|gb|ABI22700.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798755|gb|ABI22701.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798763|gb|ABI22705.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798765|gb|ABI22706.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798767|gb|ABI22707.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798771|gb|ABI22709.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798773|gb|ABI22710.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798775|gb|ABI22711.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798777|gb|ABI22712.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798779|gb|ABI22713.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798785|gb|ABI22716.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798787|gb|ABI22717.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798789|gb|ABI22718.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798801|gb|ABI22724.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798803|gb|ABI22725.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798805|gb|ABI22726.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798807|gb|ABI22727.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798809|gb|ABI22728.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798811|gb|ABI22729.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798813|gb|ABI22730.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798819|gb|ABI22733.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798821|gb|ABI22734.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798823|gb|ABI22735.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798825|gb|ABI22736.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798827|gb|ABI22737.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798835|gb|ABI22741.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798839|gb|ABI22743.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798841|gb|ABI22744.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798843|gb|ABI22745.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798845|gb|ABI22746.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798847|gb|ABI22747.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798849|gb|ABI22748.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798851|gb|ABI22749.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798853|gb|ABI22750.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798857|gb|ABI22752.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798859|gb|ABI22753.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798861|gb|ABI22754.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798863|gb|ABI22755.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798873|gb|ABI22760.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798883|gb|ABI22765.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798885|gb|ABI22766.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798889|gb|ABI22768.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798891|gb|ABI22769.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798893|gb|ABI22770.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798895|gb|ABI22771.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798897|gb|ABI22772.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798899|gb|ABI22773.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798901|gb|ABI22774.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798903|gb|ABI22775.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798913|gb|ABI22780.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798915|gb|ABI22781.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798917|gb|ABI22782.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798919|gb|ABI22783.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798921|gb|ABI22784.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798925|gb|ABI22786.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798927|gb|ABI22787.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798929|gb|ABI22788.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798933|gb|ABI22790.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798935|gb|ABI22791.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798945|gb|ABI22796.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798947|gb|ABI22797.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798949|gb|ABI22798.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798951|gb|ABI22799.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798957|gb|ABI22802.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798959|gb|ABI22803.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798961|gb|ABI22804.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798963|gb|ABI22805.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798965|gb|ABI22806.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798967|gb|ABI22807.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798969|gb|ABI22808.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798971|gb|ABI22809.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798973|gb|ABI22810.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798975|gb|ABI22811.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798977|gb|ABI22812.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798979|gb|ABI22813.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798981|gb|ABI22814.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798985|gb|ABI22816.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798989|gb|ABI22818.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798991|gb|ABI22819.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798993|gb|ABI22820.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798997|gb|ABI22822.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799003|gb|ABI22825.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799005|gb|ABI22826.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799007|gb|ABI22827.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799009|gb|ABI22828.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799011|gb|ABI22829.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|148541622|gb|ABQ88287.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|148541624|gb|ABQ88288.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|148541626|gb|ABQ88289.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|148724117|gb|ABR08360.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|148724119|gb|ABR08361.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576831|gb|ADN53017.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576849|gb|ADN53026.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576857|gb|ADN53030.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576859|gb|ADN53031.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576865|gb|ADN53034.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576873|gb|ADN53038.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576877|gb|ADN53040.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 90/157 (57%), Positives = 115/157 (73%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V CR   GE  L   E+I ++D S +QVVS+
Sbjct: 121 RFTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSV 157


>gi|294721622|gb|ADF32960.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 275

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 49/283 (17%), Positives = 90/283 (31%), Gaps = 21/283 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 5    YPQKPLATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFY 63

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R  ID+ ++    + E+     R           +       I  G           K  
Sbjct: 64   RSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVSGDDVIIGKVA 123

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             ++ D      R++                    +Y    + L       ++ +      
Sbjct: 124  PIAPDADELGQRTK------------------AHEYRDVSTPLRSTENGIVDCVAL--TT 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                L+ VK+     +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  
Sbjct: 164  NAENLKFVKIRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTREGLTPDLIINPHA 223

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLR 1169
            +PSRM +  + E  L       G++  +         +IS L 
Sbjct: 224  IPSRMTIAHLIECLLSKVGAIKGQEGDATPFTDVTVQNISDLL 266



 Score = 82.0 bits (201), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEFLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E            +       +D+ G+I  G  V+
Sbjct: 54  DRGLFRSLFYRSYIDQEKKVGIHDVEKFLKPRRGTTLRMKHGTYDKLDDDGLIAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK+ P         ++        KA + RD S  + S  +G V  V +     
Sbjct: 114 GDDVIIGKVAPIAPDADELGQRT-------KAHEYRDVSTPLRSTENGIVDCVALTTNAE 166

Query: 950 IDK 952
             K
Sbjct: 167 NLK 169


>gi|219564009|gb|ACL28188.1| RNA polymerase II second largest subunit [fungal sp. M25]
          Length = 248

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 51/272 (18%), Positives = 91/272 (33%), Gaps = 27/272 (9%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + A       +  D+ +   S +   +    +F 
Sbjct: 1    YPQKPXXTTRXMEXXXFXELPAGQNAIVAXXCYSGYNQEDSVIMNQSSIDRGLF-RSLFY 59

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFK 1003
            R   D+ +R   +    +E   +    +   L    Y +L +   +  G           
Sbjct: 60   RAYXDQEKR---IGMNVVEQFEKPFRQDTXKLKHGTYDKLDDDGIVAPGVRVSGEDIIIG 116

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  ++ D                +E  QR    +K    T     E+   +++      
Sbjct: 117  KTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVDQVLI---- 157

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   LR VKV +   +  Q GDK A RHG KG +      EDMPF + G   D+++N
Sbjct: 158  -TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQGIVPDLIIN 216

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
            P  +PSRM +  + E  L       G +  + 
Sbjct: 217  PHAIPSRMTIAHLIECQLSKVSTLRGLEGDAT 248



 Score = 77.4 bits (189), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/163 (21%), Positives = 62/163 (38%), Gaps = 12/163 (7%)

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFE 848
           +              +L  G+N +VA   + GYN EDS+++++  +   +F S+    + 
Sbjct: 4   KPXXTTRXMEXXXFXELPAGQNAIVAXXCYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYX 63

Query: 849 VMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGE 903
              +   +   E        D   +       +D+ GI+  G  V+  DI++GK  P   
Sbjct: 64  DQEKRIGMNVVEQFEKPFRQDTXKLKHGTYDKLDDDGIVAPGVRVSGEDIIIGKTAPIAP 123

Query: 904 SPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                 ++        KA   RD S  + S  +G V  V I  
Sbjct: 124 DAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 159


>gi|164452767|gb|ABY57220.1| RpoB [Tortella arctica]
          Length = 270

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 98/242 (40%), Positives = 155/242 (64%), Gaps = 9/242 (3%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +Q
Sbjct: 1   CIVGTGLESQAALDSGSIAIAKQSGKIIYTDGKKISLLNANKKSTNTDLII-------YQ 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +T ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 54  RSNNSTYMHQKARVTQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAIL 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER++ +D++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V
Sbjct: 114 ISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWV 173

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR   
Sbjct: 174 ETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIY 233

Query: 947 RH 948
           + 
Sbjct: 234 KK 235



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 70/184 (38%), Gaps = 16/184 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + I +ER +I+             E   L
Sbjct: 94   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 153

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 154  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 213

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E             + + V++A KR IQ GDK+AGRHG
Sbjct: 214  TCLKVPPGGKGRVIDVRWIYKKE-------NSNHSEKTIHVYIAQKRKIQVGDKVAGRHG 266

Query: 1096 NKGI 1099
            NKGI
Sbjct: 267  NKGI 270


>gi|223585655|gb|ACM91698.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 158

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 94/158 (59%), Positives = 121/158 (76%), Gaps = 2/158 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+
Sbjct: 61  KVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 158


>gi|55650692|emb|CAF31397.1| RNA polymerase B subunit [Nostoc sp. 152]
          Length = 187

 Score =  159 bits (401), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 89/192 (46%), Positives = 128/192 (66%), Gaps = 6/192 (3%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  +  +D++G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+D
Sbjct: 2   RVAPGDIPVDDNGYIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  +V++  G V  VDA  I +
Sbjct: 62  DANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVVVSRTDGDVTYVDATEIRV 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R        +++    YRL K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+L
Sbjct: 122 RP------KTSTQEIKYRLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGEL 175

Query: 806 ALGRNMLVAFMP 817
           ALG+N++VA+MP
Sbjct: 176 ALGQNIVVAYMP 187


>gi|167043846|gb|ABZ08535.1| putative RNA polymerase Rpb2, domain 6 [uncultured marine
           crenarchaeote HF4000_APKG3E18]
          Length = 960

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 133/726 (18%), Positives = 259/726 (35%), Gaps = 85/726 (11%)

Query: 258 AKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317
            +V   L D+   + ++++ K     + K+               + G     ++V  E 
Sbjct: 158 ERVIVGLEDLSYNKIIVDADKIGGKKVFKAKVYS----------SIVGYRAKLELVLKED 207

Query: 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT----LVTDKNKDRKDA 373
           G I         +  +  +  +   +       +++ N  I+N         +    KDA
Sbjct: 208 GLIVARIPGSPVDIPIITLVRALGLESDKEIASAISLNDKIQNELEGSFEKTEIATPKDA 267

Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           +  I + + PG +  F +  +     +       L  +G+   N +  +    +      
Sbjct: 268 IEYISKRIAPGMLEEFQIKRAETLLDWGL-----LPHLGKQPENRKEKVQFLGEAAC--- 319

Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
                    L++L+ G    DD D+ GN+ V+  G+ML + +R     + R +K ++   
Sbjct: 320 --------KLLELKLGWIQPDDKDHYGNKVVKFAGQMLADLFRTAFRNLVRDMKYQLERS 371

Query: 494 -----------DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLS 542
                       I   +  D +N    ++          ++QL +  N LS ++H RR+ 
Sbjct: 372 GQKRGINAVSAAIRPGIISDKLN--NAIATGNWGRGRVGVTQLLDRTNYLSTLSHLRRV- 428

Query: 543 ALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPY 602
              Q  ++R +   E RD+H TH+GRICP+ET EG N GLV +L   A ++     E   
Sbjct: 429 ---QSPLSRTQPNFEARDLHSTHFGRICPSETPEGSNCGLVKNLALSAIISVSVPSEEIV 485

Query: 603 RKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKID 662
            K+ +           +++++   I   +  L       E+L                + 
Sbjct: 486 EKMYELGTDYFTDVKDSVKKDGTRI-FVDGKLIGYHKDGEKLASSLRELRRTNKIHRHVG 544

Query: 663 FIDASPKQ---------VVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGT 713
                P+Q           +    L   +   D    L    + + +  L+  E      
Sbjct: 545 ISIHIPEQEGATKRLYVNCNAGRVLRSLIIVKDGKSALTPDLLDKISKKLVSWEDLIRMG 604

Query: 714 GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI-------RSVEGDLDPSTSGVDIYRLMK 766
            +E + A       +      +++     I          S+    + + S  + Y    
Sbjct: 605 VIELIDANEEENCFITFDDKHIKKHTHTEIFPSAILGAGASIIPYPEHNQSPRNTYESAM 664

Query: 767 FQRS--NQNTCVNQRPLVKVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGY 821
            ++S       +N    V+    +     I    + +   L     G+N +VA +P+ GY
Sbjct: 665 AKQSLGFSTPMMNTSTYVRQHFMLYPQTSIVTTRAMELLGLEKRPAGQNCVVAVLPFDGY 724

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP--------NVSEEGL 873
           N ED++++S+  V   +  ++    +E  ++    G  +   +IP           E+  
Sbjct: 725 NIEDAIVLSKSSVERGLGRTLFYRIYEAESKQYPGGMRDNF-EIPNSDDNLRGYKGEKSY 783

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
           + ++E GII   + V  GDIL+GK +P        E               RDTS+ V  
Sbjct: 784 RLLEEDGIIASESRVTGGDILIGKTSPPRFMEEYRE-------LDSSGPYRRDTSIGVRP 836

Query: 934 GVSGTV 939
             +G V
Sbjct: 837 SETGVV 842



 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 31/104 (29%), Positives = 51/104 (49%)

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                 ++ KV +   R  + GDK A RHG KG+V  +   ED+P+  +G   D+++NP  
Sbjct: 850  SAEGGKMFKVRIRDFRSPEIGDKFASRHGQKGVVGLLAKAEDLPYTAEGVSPDVLINPHA 909

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRS 1170
             PSRM VG + E+  G A    G+K+       +   ++  +  
Sbjct: 910  FPSRMTVGMMMESITGKAAAMRGRKVDGSAFVGEKVDEVKGVLD 953



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 100/725 (13%), Positives = 205/725 (28%), Gaps = 130/725 (17%)

Query: 36  SYDHFLMMNIAPDERPNEGLQAAFKSV--FPITAFSGAAMLEFVSYEFDPPK-------- 85
           S+D FL           +GLQ     +    I        ++    +F  P+        
Sbjct: 28  SFDEFLT----------KGLQEIINEIDHIDIENAEYPYRIKLGRIQFKQPRMMELDGSV 77

Query: 86  --FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKD-- 141
                 +   R+++Y  PL +   +I       +            +++GD+P+M K   
Sbjct: 78  THITPAEARLRNVSYVAPLMMEASVIEDGKTLESRF----------LHIGDIPVMVKSDG 127

Query: 142 ----------------------GTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLL 179
                                 G F+I G +R++V     S   +         + GK +
Sbjct: 128 CILRSFTNQKLIDHAEDPEDPGGYFIINGSERVIVGLEDLS---YNKIIVDADKIGGKKV 184

Query: 180 YACRIIP----DQGLWMDIEFDSKDIIHVRIDRRR-KVPVTSFLMALGMDSEEIL----- 229
           +  ++       +   +++      +I  RI      +P+ + + ALG++S++ +     
Sbjct: 185 FKAKVYSSIVGYR-AKLELVLKEDGLIVARIPGSPVDIPIITLVRALGLESDKEIASAIS 243

Query: 230 --STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD--IDTGEQVIESGKKLTSGLL 285
                  ++  S        P  A + +        L +  I   E +++ G  L   L 
Sbjct: 244 LNDKIQNELEGSFEKTEIATPKDAIEYISKRIAPGMLEEFQIKRAETLLDWG--LLPHLG 301

Query: 286 KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIP 345
           K  + +  K   +          A  ++  + G I  +  D    K ++           
Sbjct: 302 KQPENRKEKVQFLGE-------AACKLLELKLGWIQPDDKDHYGNKVVKFAGQMLADLFR 354

Query: 346 ILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDK 405
             + + V +  Y        +  +   A       +RPG +S                  
Sbjct: 355 TAFRNLVRDMKYQLERSGQKRGINAVSAA------IRPGIISDKLNNAIATGNWGR---- 404

Query: 406 YDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGK-GTIDDIDNLGNR 462
                VG  ++  R N  +      R               DL +   G I   +     
Sbjct: 405 ---GRVGVTQLLDRTNYLSTLSHLRRVQSPLSRTQPNFEARDLHSTHFGRICPSETPEGS 461

Query: 463 RVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQL 522
               V  +  +      +  E  +++            +D +        V        +
Sbjct: 462 NCGLVKNLALSAIISVSVPSEEIVEKMYELGTDYFTDVKDSVKKDGTRIFVDGKL----I 517

Query: 523 SQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              ++     S +   RR + + +          E        Y   C A       I +
Sbjct: 518 GYHKDGEKLASSLRELRRTNKIHRHVGISIH-IPEQEGATKRLYV-NCNAGRVLRSLIIV 575

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
               ++    +    I        D      +  + A EEEN +I               
Sbjct: 576 KDGKSAL-TPDLLDKISKKLVSWEDLIRMGVIELIDANEEENCFIT-------------- 620

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
                           +K    +  P  ++   AS+IP+ E++ S R      M +Q++ 
Sbjct: 621 ----------FDDKHIKKHTHTEIFPSAILGAGASIIPYPEHNQSPRNTYESAMAKQSLG 670

Query: 703 LLKAE 707
                
Sbjct: 671 FSTPM 675


>gi|280985747|gb|ACZ99654.1| RNA polymerase II [Fusarium redolens]
          Length = 275

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 48/291 (16%), Positives = 89/291 (30%), Gaps = 21/291 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+Q  Q       ++     +  Q   + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            ++NP  +PSRM +  + E  L       G +  +          +S L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 270



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|151573663|gb|ABS18105.1| RNA polymerase II [Fusarium sp. NRRL 37071]
          Length = 274

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 47/285 (16%), Positives = 85/285 (29%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQESQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF  +G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSNEGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQESQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|198279453|emb|CAP04761.1| RNA polymerase beta subunit [Pinus halepensis]
          Length = 269

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 98/241 (40%), Positives = 147/241 (60%), Gaps = 10/241 (4%)

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A  SG+  +A + G +E +DA+                       + +QRSN NT
Sbjct: 1   LEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNT 52

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V
Sbjct: 53  CTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLV 112

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+L
Sbjct: 113 YEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVL 172

Query: 895 VGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     
Sbjct: 173 VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSG 232

Query: 953 N 953
           +
Sbjct: 233 D 233



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 60   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 118

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 119  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 172

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 173  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 230

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 231  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 269


>gi|286142830|gb|ADC41445.1| RNA polymerase beta subunit [Streptomyces tuirus]
          Length = 185

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 140/192 (72%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+E+P VGTGME   A  +G  + A++ G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKPGVVQEVSADYITTA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++A
Sbjct: 61  NDDGT-------YITYRLAKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATQNGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|220961156|gb|ACL93044.1| RNA polymerase B subunit [Streptomyces albofaciens]
 gi|220961158|gb|ACL93045.1| RNA polymerase B subunit [Streptomyces chrestomyceticus]
 gi|220961230|gb|ACL93081.1| RNA polymerase B subunit [Streptomyces coelicolor]
          Length = 180

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 98/175 (56%), Positives = 124/175 (70%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT  V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGRVTEQVDYLTADEEDRFLIAQANAPLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V CR  G E  L  RE +D++D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMQFAEGRVMCRRRGGEVDLAAREDVDYMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|56694288|gb|AAW22884.1| RNA polymerase II second largest subunit [Ophioglossum vulgatum]
          Length = 466

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 68/368 (18%), Positives = 110/368 (29%), Gaps = 32/368 (8%)

Query: 781  LVKVG--DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDV 838
            LV  G  + V   +      S  + DL   RN           +      I   M+    
Sbjct: 129  LVAKGFIEYVDTEEEETTMISMTISDLVNARNHP----EEAYSDTYTHCEIHPSMILGVC 184

Query: 839  FTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKI 898
             + I   +     R+T             V+   L+      +  V        +    +
Sbjct: 185  ASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM---DTLAYVLYYPQKPLVTTRAM 241

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
                   +      + AI      +  D+ +   S +        IF R   D+ ++  +
Sbjct: 242  EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSFIDRGFF-RSIFYRSYRDEEKKQGT 300

Query: 959  VEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPR 1018
            + +E+ E               +          G           K+T            
Sbjct: 301  LVKEEFERPNNMNTLNMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP----------- 349

Query: 1019 SQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFV 1078
                  A  D   Q    S + Q    +          +             LR VK+ V
Sbjct: 350  -----IAQDDSGTQAQRFSKRDQSTGLRHSETGMIDQVLL------TTNADGLRFVKIRV 398

Query: 1079 AMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFE 1138
               R  Q GDK + RHG KG V      EDMP+ ++G   DI++NP  +PSRM +GQ+ E
Sbjct: 399  RSVRVPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGITPDIIVNPHAIPSRMTIGQLIE 458

Query: 1139 THLGWACV 1146
              +G    
Sbjct: 459  CIMGKVAA 466



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 52/299 (17%), Positives = 93/299 (31%), Gaps = 36/299 (12%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARA 552
           +  S    + I+   +  A   F     +    +    +  +   RR   +  + GV R 
Sbjct: 20  EEWSTENFEEISPAVIPQATKIFVNGCWVGIHRDPELLVRTLRQLRRQVDVNTEVGVVRD 79

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + +  S      + A    E+      D     
Sbjct: 80  IRLKELR-LYTDYGRCSRPLFIVENQRLLIKKS-----DIRALQQKESTETGWYDLVAKG 133

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+              +LV  R   E      +     +  P  ++
Sbjct: 134 FIEYVDTEEEETTMISM----------TISDLVNARNHPE--EAYSDTYTHCEIHPSMIL 181

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GM 715
            + AS+IPF +++ S R      M +QA+                 L   + P V T  M
Sbjct: 182 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAM 241

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           E +  +   A I A  A            +   +  +D        YR  + +   Q T
Sbjct: 242 EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSFIDRGFFRSIFYRSYRDEEKKQGT 300


>gi|164452765|gb|ABY57219.1| RpoB [Pleurochaete squarrosa]
          Length = 281

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 99/242 (40%), Positives = 155/242 (64%), Gaps = 9/242 (3%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +Q
Sbjct: 1   CIVGTGLESQAALDSGSIAIAKQSGKIIYTDGKKISLLNANKKSTNTDLII-------YQ 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN NT ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 54  RSNNNTYMHQKARVTQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAIL 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER++ +D++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V
Sbjct: 114 ISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWV 173

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR   
Sbjct: 174 ETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIY 233

Query: 947 RH 948
           + 
Sbjct: 234 KK 235



 Score = 97.8 bits (242), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 47/195 (24%), Positives = 80/195 (41%), Gaps = 16/195 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + I +ER +I+             E   L
Sbjct: 94   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 153

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 154  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 213

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E             + + V++A KR IQ GDK+AGRHG
Sbjct: 214  TCLKVPPGGKGRVIDVRWIYKKE-------NSNHSEKTIHVYIAQKRKIQVGDKVAGRHG 266

Query: 1096 NKGIVSRILPCEDMP 1110
            NKGI+S+ILP +DMP
Sbjct: 267  NKGIISKILPRQDMP 281


>gi|88697558|gb|ABD48473.1| RpoB [Morganella psychrotolerans]
          Length = 151

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V +  VT+++ YLSA+EE N  IAQAN+ LD+DG F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVREDVVTDEIHYLSAIEEGNFIIAQANTILDDDGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +Q+VS+ AS
Sbjct: 121 CRNRGESSLFSRDQVQYMDVSTQQIVSVGAS 151


>gi|225698437|gb|ACO07336.1| RpoB [Volucribacter psittacicida]
          Length = 155

 Score =  158 bits (400), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 86/154 (55%), Positives = 113/154 (73%), Gaps = 1/154 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 2   FMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLIN 61

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  
Sbjct: 62  SLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAY 121

Query: 645 VFCR-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           V  R   GE  L   E+I ++D S +QVVS+AA+
Sbjct: 122 VTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAA 155


>gi|82706473|gb|ABB89614.1| RNA polymerase II second largest subunit [Pyronema domesticum]
          Length = 594

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 96/664 (14%), Positives = 184/664 (27%), Gaps = 88/664 (13%)

Query: 475  YRLGLLRMERSIKERISSVDI--DSVMPQDLINAKPVVSAVCEFFCSSQ----------- 521
            +R    ++ + + + +               + +  + + +     +             
Sbjct: 1    FRNLWKKLTKDVFKYLEKCVETGKEFSLPLAVKSNTISNGLKYSLATGNWGDQKKAMSSK 60

Query: 522  --LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
              +SQ+       S ++H RR +      + R     + R +H TH+G +CPAET EG  
Sbjct: 61   AGVSQVLNRYTFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 116

Query: 580  IGLVSSLTS--FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDED 637
             GLV +L    +  V   G     +    +     +     +      ++      +  D
Sbjct: 117  CGLVKNLALMSYITVGTPGHPLINFMAEQNMDFLXEYEPQRSPNATKIFLNGVWIGVHRD 176

Query: 638  GSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
                  LV        I      I D  D   K          P    D+          
Sbjct: 177  PLHLVRLVQELRRRGSISHEVSVIRDIRDREFKIFTDAGRVCRPLFVIDN------DPTH 230

Query: 697  QRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPST 756
            +R+   +L  E                         G VE VDA       +    +   
Sbjct: 231  ERRGQLVLTKEHVLSLEEDHEKPEDEKFGWKGLLXCGAVEYVDAEEEETIMIVMTPEDLE 290

Query: 757  SGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
                + +  +           + P+ K  ++          PS  LG       +  + +
Sbjct: 291  VARQVQQGYELAEETDTNKRVKTPINKNMNQY---THCEIHPSMILG-------ICASII 340

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
            P+  +N          M  + +   + +  F                             
Sbjct: 341  PFPDHNQSPRNTYQSAMGKQAMG--VFLTNFAERM------------------------- 373

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  +             +       +   +  +  I      +  D+ +   S + 
Sbjct: 374  --DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSID 431

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
              +    +F R  +D+ +R      E+ E   R    +      +       +  G    
Sbjct: 432  RGLF-RSLFYRAYMDQEKRIGMQVVEEFEKPTRGNTLKLKHGTYDKLDDDGLVAPGVRVS 490

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+  +++D                DE  QR     K    T     E+   ++
Sbjct: 491  GEDIIIGKTAPITAD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQ 535

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     + VKV +   +  Q GDK A RHG KG +      EDMPF  +G 
Sbjct: 536  VMLTTNADGL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTAEGI 590

Query: 1117 PVDI 1120
              D+
Sbjct: 591  VPDL 594


>gi|318085042|gb|ADV39411.1| RNA polymerase subunit B [Streptomyces turgidiscabies]
 gi|318085058|gb|ADV39419.1| RNA polymerase subunit B [Streptomyces reticuliscabiei]
          Length = 180

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANAILSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFEESRVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  + + + +G
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTVANDDG 175


>gi|4972797|gb|AAD34794.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            pylori]
          Length = 179

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 46/104 (44%), Positives = 62/104 (59%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTIKSDD+ GR   Y +I  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNSA-----KMEEIP---DFNKCEL 1385
            L KE+Q+L L I++               ++E     DF+  +L
Sbjct: 61   LTKELQSLALDINIFGDDVDEDGAPKPIVIKEDDRPKDFSSFQL 104


>gi|6449127|gb|AAF08837.1| RNA polymerase beta subunit [Streptococcus cristatus ATCC 51100]
          Length = 170

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 50/174 (28%), Positives = 79/174 (45%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EIL  F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEILDIFGDSDLVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             ES + L            +  +G           + L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKNRLLNQTLAEHLVDAETG 170



 Score = 55.5 bits (132), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEILDIFGDSDLVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+      + +
Sbjct: 120 SSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKNRLLNQTL 160


>gi|270000451|gb|ACZ58073.1| RNA polymerase II [Fusarium sp. NRRL 46604]
          Length = 281

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 46/291 (15%), Positives = 87/291 (29%), Gaps = 21/291 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E   +           +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            ++NP  +PSRM +  + E  L       G +  +          +S L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 270



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|164452771|gb|ABY57222.1| RpoB [Tortella bambergeri]
          Length = 270

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 98/242 (40%), Positives = 155/242 (64%), Gaps = 9/242 (3%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +Q
Sbjct: 1   CIVGTGLESQAALDSGSIAIAKQSGKILYTDGKKISLLNANKKSTNTDLII-------YQ 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +T ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 54  RSNNSTYMHQKARVIQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAIL 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER++ +D++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V
Sbjct: 114 ISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWV 173

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR   
Sbjct: 174 ETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIY 233

Query: 947 RH 948
           + 
Sbjct: 234 KK 235



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 70/184 (38%), Gaps = 16/184 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + I +ER +I+             E   L
Sbjct: 94   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 153

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 154  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 213

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E             + + V++A KR IQ GDK+AGRHG
Sbjct: 214  TCLKVPPGGKGRVIDVRWIYKKE-------NSNHSEKTIHVYIAQKRKIQVGDKVAGRHG 266

Query: 1096 NKGI 1099
            NKGI
Sbjct: 267  NKGI 270


>gi|286143016|gb|ADC41538.1| RNA polymerase beta subunit [Streptomyces galbus]
          Length = 185

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 140/192 (72%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++A
Sbjct: 61  NDDGT-------YITYRLAKFSRSNQGTSVNQKVIVNEGDRIITGQVLADGPATQNGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|198279427|emb|CAP04748.1| RNA polymerase beta subunit [Pinus patula]
          Length = 269

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 98/241 (40%), Positives = 148/241 (61%), Gaps = 10/241 (4%)

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A  SG+  +A + G +E +DA+                       + +QRSN NT
Sbjct: 1   LEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNT 52

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V
Sbjct: 53  CTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLV 112

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+L
Sbjct: 113 YEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVL 172

Query: 895 VGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     
Sbjct: 173 VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSG 232

Query: 953 N 953
           +
Sbjct: 233 D 233



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 60   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 118

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 119  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 172

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 173  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 230

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 231  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 269


>gi|117667742|gb|ABK55917.1| RNA polymerase B subunit [Streptomyces finlayi]
 gi|157000415|gb|ABV00507.1| RNA polymerase subunit B [Streptomyces nitrosporeus]
          Length = 180

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRFVIAQANATLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTEPRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYVTVTNDDG 175


>gi|313494596|gb|ADR57435.1| RNA polymerase beta subunit [Picea morrisonicola]
 gi|313494598|gb|ADR57436.1| RNA polymerase beta subunit [Picea wilsonii]
 gi|313494600|gb|ADR57437.1| RNA polymerase beta subunit [Picea farreri]
 gi|313494602|gb|ADR57438.1| RNA polymerase beta subunit [Picea glauca]
 gi|313494604|gb|ADR57439.1| RNA polymerase beta subunit [Picea rubens]
 gi|313494606|gb|ADR57440.1| RNA polymerase beta subunit [Picea sitchensis]
 gi|313494608|gb|ADR57441.1| RNA polymerase beta subunit [Picea mariana]
 gi|313494610|gb|ADR57442.1| RNA polymerase beta subunit [Picea likiangensis]
 gi|313494612|gb|ADR57443.1| RNA polymerase beta subunit [Picea likiangensis]
 gi|313494614|gb|ADR57444.1| RNA polymerase beta subunit [Picea schrenkiana]
 gi|313494616|gb|ADR57445.1| RNA polymerase beta subunit [Picea schrenkiana]
 gi|313494618|gb|ADR57446.1| RNA polymerase beta subunit [Picea obovata]
 gi|313494620|gb|ADR57447.1| RNA polymerase beta subunit [Picea obovata]
 gi|313494622|gb|ADR57448.1| RNA polymerase beta subunit [Picea obovata]
 gi|313494624|gb|ADR57449.1| RNA polymerase beta subunit [Picea koraiensis]
 gi|313494626|gb|ADR57450.1| RNA polymerase beta subunit [Picea asperata]
 gi|313494628|gb|ADR57451.1| RNA polymerase beta subunit [Picea asperata]
 gi|313494632|gb|ADR57453.1| RNA polymerase beta subunit [Picea brachytyla]
 gi|313494634|gb|ADR57454.1| RNA polymerase beta subunit [Picea retroflexa]
 gi|313494636|gb|ADR57455.1| RNA polymerase beta subunit [Picea likiangensis]
 gi|313494638|gb|ADR57456.1| RNA polymerase beta subunit [Picea likiangensis]
 gi|313494640|gb|ADR57457.1| RNA polymerase beta subunit [Picea purpurea]
 gi|313494642|gb|ADR57458.1| RNA polymerase beta subunit [Picea purpurea]
 gi|313494644|gb|ADR57459.1| RNA polymerase beta subunit [Picea purpurea]
 gi|313494646|gb|ADR57460.1| RNA polymerase beta subunit [Picea jezoensis]
 gi|313494648|gb|ADR57461.1| RNA polymerase beta subunit [Picea jezoensis]
 gi|313494650|gb|ADR57462.1| RNA polymerase beta subunit [Picea brachytyla]
 gi|313494652|gb|ADR57463.1| RNA polymerase beta subunit [Picea abies]
 gi|313494654|gb|ADR57464.1| RNA polymerase beta subunit [Picea abies]
 gi|313494656|gb|ADR57465.1| RNA polymerase beta subunit [Picea smithiana]
 gi|313494658|gb|ADR57466.1| RNA polymerase beta subunit [Picea orientalis]
 gi|313494660|gb|ADR57467.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494664|gb|ADR57469.1| RNA polymerase beta subunit [Picea engelmannii]
 gi|313494666|gb|ADR57470.1| RNA polymerase beta subunit [Picea torano]
 gi|313494668|gb|ADR57471.1| RNA polymerase beta subunit [Picea asperata]
 gi|313494670|gb|ADR57472.1| RNA polymerase beta subunit [Picea pungens]
 gi|313494672|gb|ADR57473.1| RNA polymerase beta subunit [Picea pungens]
 gi|313494674|gb|ADR57474.1| RNA polymerase beta subunit [Picea jezoensis]
 gi|313494676|gb|ADR57475.1| RNA polymerase beta subunit [Picea glehnii]
 gi|313494678|gb|ADR57476.1| RNA polymerase beta subunit [Picea neoveitchii]
 gi|313494680|gb|ADR57477.1| RNA polymerase beta subunit [Picea wilsonii]
 gi|313494682|gb|ADR57478.1| RNA polymerase beta subunit [Picea farreri]
 gi|313494684|gb|ADR57479.1| RNA polymerase beta subunit [Picea farreri]
 gi|313494686|gb|ADR57480.1| RNA polymerase beta subunit [Picea breweriana]
 gi|313494688|gb|ADR57481.1| RNA polymerase beta subunit [Picea omorika]
 gi|313494690|gb|ADR57482.1| RNA polymerase beta subunit [Picea chihuahuana]
 gi|313494692|gb|ADR57483.1| RNA polymerase beta subunit [Picea maximowiczii]
 gi|313494694|gb|ADR57484.1| RNA polymerase beta subunit [Picea spinulosa]
 gi|313494696|gb|ADR57485.1| RNA polymerase beta subunit [Picea breweriana]
 gi|313494698|gb|ADR57486.1| RNA polymerase beta subunit [Picea farreri]
 gi|313494700|gb|ADR57487.1| RNA polymerase beta subunit [Picea koyamae]
 gi|313494702|gb|ADR57488.1| RNA polymerase beta subunit [Picea morrisonicola]
 gi|313494704|gb|ADR57489.1| RNA polymerase beta subunit [Picea obovata]
 gi|313494706|gb|ADR57490.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494708|gb|ADR57491.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494710|gb|ADR57492.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494712|gb|ADR57493.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494714|gb|ADR57494.1| RNA polymerase beta subunit [Picea likiangensis]
 gi|313494716|gb|ADR57495.1| RNA polymerase beta subunit [Picea meyeri]
 gi|313494718|gb|ADR57496.1| RNA polymerase beta subunit [Picea crassifolia]
 gi|313494720|gb|ADR57497.1| RNA polymerase beta subunit [Picea smithiana]
 gi|313494722|gb|ADR57498.1| RNA polymerase beta subunit [Picea spinulosa]
          Length = 246

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 96/236 (40%), Positives = 144/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +DA+                      L+ +QRSN NTC +Q+
Sbjct: 2   ALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTELVIYQRSNTNTCTHQK 53

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 54  PQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 113

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+T
Sbjct: 114 TSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLT 173

Query: 900 PKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 174 PQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVDDSGD 229


>gi|286142904|gb|ADC41482.1| RNA polymerase beta subunit [Streptomyces acrimycini]
          Length = 185

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 140/192 (72%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+E+P VGTGME   A  +G  + A++ G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T  G++A
Sbjct: 61  NDDGT-------YITYRLAKFSRSNQGTSVNQKVIVNEGDRIITGQVLADGPATQNGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|88697524|gb|ABD48456.1| RpoB [Morganella morganii]
 gi|88697526|gb|ABD48457.1| RpoB [Morganella morganii]
          Length = 151

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 87/151 (57%), Positives = 114/151 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +A+ N YGF+ETPYR V D  VT+++ YLSA+EE N  IAQAN+ LD++G F +EL+ 
Sbjct: 61  SVYAQTNEYGFLETPYRLVRDDIVTDEIHYLSAIEEGNFIIAQANTVLDDEGHFVDELIT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           CR  GE  L  R+++ ++D S +QVVS+ AS
Sbjct: 121 CRNKGESSLFSRDQVQYMDVSTQQVVSVGAS 151


>gi|151573660|gb|ABS18103.1| RNA polymerase II [Fusarium sp. NRRL 37068]
          Length = 274

 Score =  158 bits (400), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 47/285 (16%), Positives = 86/285 (30%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDQVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDQVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|198279425|emb|CAP04747.1| RNA polymerase beta subunit [Pinus patula]
          Length = 269

 Score =  158 bits (399), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 98/241 (40%), Positives = 148/241 (61%), Gaps = 10/241 (4%)

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A  SG+  +A + G +E +DA+                       + +QRSN NT
Sbjct: 1   LEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNT 52

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V
Sbjct: 53  CTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLV 112

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+L
Sbjct: 113 YEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVL 172

Query: 895 VGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     
Sbjct: 173 VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSG 232

Query: 953 N 953
           +
Sbjct: 233 D 233



 Score = 77.4 bits (189), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 54/224 (24%), Positives = 85/224 (37%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 60   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 118

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 119  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 172

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 173  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 230

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+ GRHGNKG +S +LP
Sbjct: 231  SGDNAE-----TVHVYISQKRKIQVGDKVXGRHGNKGXISIVLP 269


>gi|157000405|gb|ABV00502.1| RNA polymerase subunit B [Streptomyces gelaticus]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+NA+GFIETPYRKV DG+VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRINAFGFIETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAPLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFAESRVLVRRRGGEVDYVPGADVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|220961164|gb|ACL93048.1| RNA polymerase B subunit [Streptomyces catenulae]
 gi|220961218|gb|ACL93075.1| RNA polymerase B subunit [Streptomyces monomycini]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 98/175 (56%), Positives = 124/175 (70%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT  V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGRVTEQVDYLTADEEDRFLIAQANAPLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V CR  G E  L  RE +D++D SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMEFAEGRVMCRRRGGEVDLAAREDVDYMDVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|145307876|gb|ABP57243.1| RNA polymerase II second largest subunit [Pandora dipterigena]
          Length = 263

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 49/277 (17%), Positives = 87/277 (31%), Gaps = 21/277 (7%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 8    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 67

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D+ ++S   E E  E   R                   I  G 
Sbjct: 68   SIDRGLF-RSIYYRTYLDQEKKSGLNEVESFEKPTRKTTLRLRHGTYEKLEDDGLIAPGT 126

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  +      R++          ++     +  +   + +      
Sbjct: 127  RVSGDDIIIGKTAPVPPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ----- 181

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             +R  KV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 182  ---------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFNA 226

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            +G   D+V+NP  +PSRM +G + E  +G      G 
Sbjct: 227  EGMVPDLVINPHAIPSRMTIGHMVECLVGKVGTLAGT 263



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 6   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 55

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 56  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEVESFEKPTRKTTLRLRHGTYEK 115

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 116 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHTKRDVSTPLKSTETGI 171

Query: 936 SGTVV 940
              V+
Sbjct: 172 VDRVM 176


>gi|151573584|gb|ABS18053.1| RNA polymerase II [Fusarium sp. NRRL 28019]
 gi|151573591|gb|ABS18057.1| RNA polymerase II [Fusarium sp. NRRL 28030]
 gi|151573597|gb|ABS18061.1| RNA polymerase II [Fusarium sp. NRRL 28033]
          Length = 274

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 46/285 (16%), Positives = 85/285 (29%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|219564061|gb|ACL28214.1| RNA polymerase II second largest subunit [fungal sp. M190]
          Length = 269

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 47/285 (16%), Positives = 86/285 (30%), Gaps = 21/285 (7%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 6    ILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 64

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ ++      E  E   +           +       +  G           
Sbjct: 65   LFFRSYSDQEKKVGLNYTETFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIG 124

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+   Q       ++     +      + +                
Sbjct: 125  KTAPIDPENQDLGTRTAAHQKRDISTPLRSTENGIVDSVIMTVNA--------------- 169

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG V      EDMPF ++G   DI++N
Sbjct: 170  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTVGVTYRQEDMPFTREGITPDIIIN 224

Query: 1124 PLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPL 1168
            P  +PSRM +  + E  L       G +  +          +S L
Sbjct: 225  PHAIPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDQVSDL 269



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 57/158 (36%), Gaps = 13/158 (8%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 17  TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 76

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E            +       +DE GI+  G  V+  DI++GK  P       P
Sbjct: 77  VGLNYTETFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID-----P 131

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
           E + L             T LR        +VD  I  
Sbjct: 132 ENQDLGTRTAAHQKRDISTPLR---STENGIVDSVIMT 166


>gi|55650650|emb|CAF32196.1| RNA polymerase B subunit [Nostoc calcicola VI]
          Length = 187

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 90/192 (46%), Positives = 124/192 (64%), Gaps = 6/192 (3%)

Query: 626 YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            +A  +  +DE G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+D
Sbjct: 2   RVAPKDIPIDETGHIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHD 61

Query: 686 DSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
           D+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +
Sbjct: 62  DANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRV 121

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
           R      +        Y L K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+L
Sbjct: 122 RPKPNTSE------IKYTLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGEL 175

Query: 806 ALGRNMLVAFMP 817
           ALG+N++VA+MP
Sbjct: 176 ALGQNIVVAYMP 187


>gi|286142832|gb|ADC41446.1| RNA polymerase beta subunit [Streptomyces griseoruber]
          Length = 185

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 142/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YITYRLAKFARSNQGTSVNQKVIVNEGDRIIEGQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|145307909|gb|ABP57258.1| RNA polymerase II second largest subunit [Erynia sciarae]
          Length = 261

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 51/280 (18%), Positives = 93/280 (33%), Gaps = 27/280 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 121

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  +      R++          ++     +  +   + +   
Sbjct: 122  PGTRVSGDDIIIGKTAPVPPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ-- 179

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 180  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 221

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            F  +G   D+V+NP  +PSRM +G + E  +G      G 
Sbjct: 222  FNAEGMVPDLVINPHAIPSRMTIGHMVECLVGKVGTLAGT 261



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHTKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|318085050|gb|ADV39415.1| RNA polymerase subunit B [Streptomyces scabiei]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFEEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|220961154|gb|ACL93043.1| RNA polymerase B subunit [Streptomyces aureoversilis]
 gi|220961172|gb|ACL93052.1| RNA polymerase B subunit [Streptomyces rectiverticillatus]
 gi|220961182|gb|ACL93057.1| RNA polymerase B subunit [Streptomyces hiroshimensis]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 93/178 (52%), Positives = 127/178 (71%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANAALTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEARVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           M RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + + +G  +
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDGTYN 178


>gi|46277322|gb|AAS86851.1| DNA-dependent RNA polymerase II [Peziza gerardii]
          Length = 487

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 47/280 (16%), Positives = 90/280 (32%), Gaps = 27/280 (9%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 232  ANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFR 291

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
               F  +   + +    +    +E   +      + L    Y +L +   +  G      
Sbjct: 292  SLFFRSYMDQEKK----IGNSTLEAFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRISGE 347

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++                 K    T     E+   +++ 
Sbjct: 348  DIIIGKTAPIAPNTEELGQRTKYHT---------------KRDVSTPLRSTENGIVDQVF 392

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                G       LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 393  ITMNG-----EGLRFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVP 447

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
            D+++NP  +PSRM +  + E  L       G +  +    
Sbjct: 448  DLIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFT 487



 Score = 89.0 bits (219), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 50/321 (15%), Positives = 103/321 (32%), Gaps = 28/321 (8%)

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           ED          R   + ++     +++IDA  ++ + I  +     +N        G  
Sbjct: 100 EDDKELSMNDPNRYGWKGLIADG-VVEYIDAEEEESIMIVMTPEDLEQNRQVA---AGYE 155

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           +Q+ A    + +A +          +   + I+   A I+   D  +             
Sbjct: 156 IQKSADTGQRVKAAYTQPAHTWTHCEIHPSMILGICASIIPFPDHNQXXXXXXXXXXXXX 215

Query: 756 TSGVDIYRLMKFQRSNQNT-CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                            N     Q+PL                      +L  G+N +VA
Sbjct: 216 XXXXXXXXXXXXXXXXANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVA 265

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVS 869
            + + GYN EDS+++++  +   +F S+    +    +       E        +   + 
Sbjct: 266 ILCYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYMDQEKKIGNSTLEAFEKPTRGNTLRLK 325

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ G++  G  ++  DI++GK  P   +     ++        K    RD S 
Sbjct: 326 HGTYDKLDDDGLVAPGVRISGEDIIIGKTAPIAPNTEELGQRT-------KYHTKRDVST 378

Query: 930 RVPSGVSGTVVDVRIFNRHGI 950
            + S     +VD      +G 
Sbjct: 379 PLRS-TENGIVDQVFITMNGE 398



 Score = 48.9 bits (115), Expect = 0.007,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 52/185 (28%), Gaps = 14/185 (7%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEM-------RDVHPTHYG 567
           F     +    + V  +  +   RR   +G +  +       E        R   P    
Sbjct: 18  FVNGVWVGVHRDPVALVRVVQQLRRSGVIGHELSLISDVRDREFKIFTDAGRICRPLFAI 77

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYI 627
              PA    G  I     +            +              V Y+ A EEE+  I
Sbjct: 78  DNDPASPGRGELILKREHIEKLEDDKELSMNDPNRYGWKGLIADGVVEYIDAEEEESIMI 137

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILV------PREKIDFIDASPKQVVSIAASLIPF 681
                 L+++          + A     V      P       +  P  ++ I AS+IPF
Sbjct: 138 VMTPEDLEQNRQVAAGYEIQKSADTGQRVKAAYTQPAHTWTHCEIHPSMILGICASIIPF 197

Query: 682 LENDD 686
            +++ 
Sbjct: 198 PDHNQ 202


>gi|208609819|dbj|BAG72371.1| RNA polymerase II second largest subunit [Litsea grandis]
          Length = 162

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 48/91 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
             +PSRM +GQ+ E  +G     +GK+  +  
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATP 162



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|157000411|gb|ABV00505.1| RNA polymerase subunit B [Streptomyces griseorubiginosus]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFEEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|157000389|gb|ABV00494.1| RNA polymerase subunit B [Streptomyces atratus]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRYVIAQANATLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFVEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|186694353|gb|ACC86150.1| DNA-directed RNA polymerase beta subunit [Campylobacter sp. 87/06]
          Length = 169

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 90/168 (53%), Positives = 123/168 (73%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RRLSALG+GG+ + RAG+E+RDVH THYGRICP ET EG NIGL+++
Sbjct: 1   MDQTNPLSEVTHKRRLSALGEGGLVKERAGLEVRDVHSTHYGRICPVETPEGQNIGLINT 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L ++++VN  GF+E PYRKV + KV+++VVYL+A +EEN  IA A++ LD  G+  E+ V
Sbjct: 61  LATYSKVNDLGFVEAPYRKVVNAKVSDEVVYLTATQEENLVIAAASTKLDSKGNIVEDFV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             R  GE IL  ++++  ID     +V + ASLIPFLE+DD+NR LMG
Sbjct: 121 EARKDGETILAKKDEVQLIDLCSGMIVGVTASLIPFLEHDDANRALMG 168


>gi|318085028|gb|ADV39404.1| RNA polymerase subunit B [Streptomyces torulosus]
          Length = 180

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFEESRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|152968532|gb|ABS50280.1| RNA polymerase II [Uebelinia kiwuensis]
          Length = 247

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 52/267 (19%), Positives = 84/267 (31%), Gaps = 23/267 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                  +    +       +      + AI      +  D+ +   S +        +F 
Sbjct: 4    YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFF 62

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++  ++ +E      R           +          G           K+T
Sbjct: 63   RSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTT 122

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             L+ +                             +Y      +  R        Q     
Sbjct: 123  PLAPEEAQGP----------------------AARYSRKDHSISLRHSESGIVDQVLLTT 160

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP  
Sbjct: 161  NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 220

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIK 1153
            +PSRM +GQ+ E  +G     +GK+  
Sbjct: 221  IPSRMTIGQLIECIMGKVAAHVGKEGD 247



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PLV                      L  G N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPLV----------TTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVN 889
               F S+    +    +      +E        +   +       +D+ G+   G  V+
Sbjct: 53  DRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             D+++GK TP     + PEE    A         +D S+ +    SG V
Sbjct: 113 GEDVIIGKTTP-----LAPEE----AQGPAARYSRKDHSISLRHSESGIV 153


>gi|151573805|gb|ABS18199.1| RNA polymerase II [Fusarium sp. NRRL 43632]
          Length = 273

 Score =  158 bits (399), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 48/285 (16%), Positives = 87/285 (30%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQTHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        +    RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QTHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|313494662|gb|ADR57468.1| RNA polymerase beta subunit [Picea alcoquiana]
          Length = 246

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 96/236 (40%), Positives = 144/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +DA+                      L+ +QRSN NTC +Q+
Sbjct: 2   ALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTELVIYQRSNTNTCTHQK 53

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 54  PQVRQGECVKKGQILADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 113

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+T
Sbjct: 114 TSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLT 173

Query: 900 PKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 174 PQTTEESLCVPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVDDSGD 229



 Score = 38.9 bits (89), Expect = 6.5,   Method: Composition-based stats.
 Identities = 39/205 (19%), Positives = 69/205 (33%), Gaps = 14/205 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL       G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 56   VRQGECVKKGQILADGAATVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 114

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 115  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 168

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 169  VGKLTPQTTEESLCVPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVD--D 226

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQS 1086
             GD+        V V+++ KR IQ 
Sbjct: 227  SGDNAE-----TVHVYISQKRKIQV 246


>gi|223585653|gb|ACM91697.1| ribosomal polymerase subunit beta [Staphylococcus sp. KS-SP_55]
          Length = 158

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 94/158 (59%), Positives = 121/158 (76%), Gaps = 2/158 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV     K+T+ + YL+A EE++  +AQAN+ LDE+G F ++ V CR  G    + +EK+
Sbjct: 61  KVDIASNKITDQIDYLTADEEDSYVVAQANARLDEEGRFLDDEVVCRFRGNNTTMAKEKM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           D++D SPKQVVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQ 158


>gi|91981506|gb|ABE68095.1| RNA polymerase subunit B [Pseudomonas sp. PGNR1]
          Length = 148

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 81/148 (54%), Positives = 108/148 (72%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++ G   +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKGQLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIA 675
           R   E  +   E +  +D SPKQVVS+A
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVA 148


>gi|15212093|emb|CAC51380.1| RNA polymerase beta subunit [Nicotiana tomentosiformis]
          Length = 220

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 57/205 (27%), Positives = 100/205 (48%), Gaps = 15/205 (7%)

Query: 52  NEGLQAAFKSVFPITAFSGAAMLE-FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLI 109
           ++GL         I         + FV  Y+   P     D ++  LTY+  L ++  LI
Sbjct: 4   DQGLTEELYKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVSAGLI 63

Query: 110 VFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDK 169
                     K+ +D++EQ+ ++G++PLM   GT ++ GI RIV++Q+ +SPGI++  + 
Sbjct: 64  W---------KNSRDMQEQTFFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYRSEL 114

Query: 170 GRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
               +S   +Y   II D G   ++E D K  I  R+ R++K+ +     A+G++  EIL
Sbjct: 115 DHNGIS---VYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGLNLREIL 171

Query: 230 STF-YPKIVYSQRGDFWCFPLSAAD 253
               YP+I  S   D     + + +
Sbjct: 172 ENVCYPEIFLSFLSDKERKKIGSKE 196


>gi|198279461|emb|CAP04765.1| RNA polymerase beta subunit [Pinus palustris]
          Length = 258

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 98/240 (40%), Positives = 147/240 (61%), Gaps = 10/240 (4%)

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG+  +A + G +E +DA+                       + +QRSN NTC
Sbjct: 1   EGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTC 52

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V 
Sbjct: 53  THQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVY 112

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LV
Sbjct: 113 EDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLV 172

Query: 896 GKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           GK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 173 GKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 232



 Score = 63.2 bits (152), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 49/214 (22%), Positives = 78/214 (36%), Gaps = 14/214 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 59   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 117

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 118  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 171

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 172  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 229

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
             GD+        V V+++ KR IQ GDK+AGRHG
Sbjct: 230  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHG 258


>gi|294345277|dbj|BAJ05044.1| DNA-directed RNA polymerase beta chain [Bartonella henselae]
          Length = 157

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 110/157 (70%), Positives = 133/157 (84%)

Query: 565 HYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEEN 624
           HYGRICP ET EG NIGL++SL +FARVN YGFIE+PYRK+ DGKVT +V+YLSAMEE  
Sbjct: 1   HYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKIIDGKVTTEVIYLSAMEESK 60

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            Y+AQANSSLD +G  +EE V CR AGE ++ PR+ +D +D SPKQ+VS+AA+LIPFLEN
Sbjct: 61  HYVAQANSSLDAEGRLSEEFVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLEN 120

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAK 721
            D+NR LMG NMQRQAVPL++AEAPFVGTGMES+VA+
Sbjct: 121 GDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVAR 157


>gi|283132429|dbj|BAI63620.1| rpoB protein [Corynebacterium auriscanis]
          Length = 130

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 55/156 (35%), Positives = 77/156 (49%), Gaps = 34/156 (21%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +   D K    +  L S L  V              
Sbjct: 1    RMNIGQVLEVHLGWLAKA-GWKVDTDSQDPKIQKMLETLPSELYDVPSDSLT-------- 51

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA    ++ +LR +  +  G        ++ L DG +
Sbjct: 52   -----------------ATPVFDGASNAELSGLLRSSRPNRDGIRLVDDFGKAQLMDGRS 94

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            GEPF  PV+VGY+YMLKL+H+V +K++ARSTG YS+
Sbjct: 95   GEPFPYPVSVGYMYMLKLHHLVDEKIHARSTGPYSM 130


>gi|318085026|gb|ADV39403.1| RNA polymerase subunit B [Streptomyces hygroscopicus subsp.
           ossamyceticus]
          Length = 180

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGVVTDEVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFTENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|289468047|gb|ADC95704.1| RpoB [Wautersiella falsenii]
          Length = 163

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 116/162 (71%), Gaps = 2/162 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 2   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRLCPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  FA+VN  GFIETPYRKV +GKV  +   +YL+A EEE++ IAQAN  + +DG+  
Sbjct: 62  SSLCVFAKVNNLGFIETPYRKVEEGKVDVESAPIYLTAEEEESKVIAQANIDMADDGTIA 121

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            E V  R  G+  +V   ++D ID +P Q+ SI+ASLIPFLE
Sbjct: 122 TERVTAREDGDFPVVTPSEVDLIDVAPNQIASISASLIPFLE 163


>gi|313494630|gb|ADR57452.1| RNA polymerase beta subunit [Picea likiangensis]
          Length = 246

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 96/236 (40%), Positives = 144/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +DA+                      L+ +QRSN NTC +Q+
Sbjct: 2   ALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTELVIYQRSNTNTCTHQK 53

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 54  PQVRQGECVKKGQIMADGAATVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 113

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+T
Sbjct: 114 TSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLT 173

Query: 900 PKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+        PE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 174 PQTTEESLCAPEGRLLQTIFGIEVSTARENCLRTPIGGRGRVIDVRWINRVDDSGD 229


>gi|193201523|gb|ACF15969.1| RNA polymerase II subunit [Opegrapha varia]
          Length = 273

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 56/184 (30%), Gaps = 53/184 (28%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                  + VKV     +    GDK A RHG KG +      EDMPF  +G   D+++NP 
Sbjct: 143  TTNDGRKNVKVRTRTTKVPNVGDKFASRHGQKGTIGITYRQEDMPFTSEGLTPDLIINPH 202

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKI 1185
             +PSRM +  + E  L      +G +  +         DIS L                 
Sbjct: 203  AIPSRMTIAHLIECLLSKVSACVGTEGDATPFTPVTVQDISYLLR--------------- 247

Query: 1186 SDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPF 1245
                                                        + G  I+++G TG+  
Sbjct: 248  --------------------------------------EQCGYQQRGFEIMHNGHTGQKL 269

Query: 1246 DRPV 1249
               +
Sbjct: 270  KAQI 273



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/159 (21%), Positives = 67/159 (42%), Gaps = 8/159 (5%)

Query: 804 DLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR 863
           DL  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   +   E   
Sbjct: 1   DLPAGQNAIVAIACYSGYNQEDSVIMNQSAIDRGLFRSLFYRTYIESEQTVGINNLEHFE 60

Query: 864 D-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP-KGESPMTPEEKLLRAIF 917
                    +S+   + +D+ G++  G  V+ GD+++GK  P +G      E      + 
Sbjct: 61  KPVRQVTMRMSQGTYEKLDDDGLVPPGMRVSGGDVIIGKTMPLQGPMQEGAEGGSRLXVH 120

Query: 918 GEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
            +K  DV        +G+   V+      R  +    R+
Sbjct: 121 EKK--DVSAALRSTEAGIIDRVLLTTNDGRKNVKVRTRT 157


>gi|151573600|gb|ABS18063.1| RNA polymerase II [Gibberella intermedia]
 gi|151573654|gb|ABS18099.1| RNA polymerase II [Fusarium nygamai]
 gi|151573657|gb|ABS18101.1| RNA polymerase II [Fusarium napiforme]
          Length = 274

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 48/285 (16%), Positives = 87/285 (30%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|4972810|gb|AAD34800.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter cf.
            canis 29176]
          Length = 177

 Score =  158 bits (399), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 46/104 (44%), Positives = 65/104 (62%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLT+KSDD+VGR   Y SI  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTLKSDDIVGRENAYRSITKGEPVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIP--------DFNKCEL 1385
            L+KE+QAL L  ++ ++    +   + +         DF+  +L
Sbjct: 61   LIKELQALALDANVFDNTLDENGNPKALEIKEDNRPKDFSSFQL 104


>gi|50058737|gb|AAT69121.1| RNA polymerase II [Neuropeltis acuminata]
          Length = 212

 Score =  157 bits (398), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 48/91 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG +      EDMP+  +G   DI++NP 
Sbjct: 122  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTIGMTYTQEDMPWTVEGITPDIIVNPH 181

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
             +PSRM +GQ+ E  +G     +GK+  +  
Sbjct: 182  AIPSRMTIGQLIECIMGKVAAHMGKEGDATP 212



 Score = 66.6 bits (161), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 24/124 (19%), Positives = 45/124 (36%), Gaps = 14/124 (11%)

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKN 875
           YN EDS+++++  V    F S+    +    +      +E        +   +       
Sbjct: 1   YNQEDSVIMNQSSVDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDK 60

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 61  LDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTKRDHSTSLRHSE 111

Query: 936 SGTV 939
           +G V
Sbjct: 112 TGIV 115


>gi|227826340|gb|ACP41897.1| RNA polymerase II [Silene fruticosa]
          Length = 239

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 51/106 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G     +GK+  +         +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKXXXXVGKEGDATPFTDVTVDNISKALQK 235



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|220961176|gb|ACL93054.1| RNA polymerase B subunit [Streptomyces hygroscopicus subsp.
           glebosus]
          Length = 180

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVN +GFIETPYRKV DG+VT +V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNVFGFIETPYRKVVDGQVTEEVDYLTADEEDRFLIAQANAKLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F+E+ V  R  G E  LVP +++DF++ SP+Q+VS A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFSEQRVLVRRRGGEVDLVPADEVDFMNVSPRQMVSAATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVANDDG 175


>gi|198279359|emb|CAP04714.1| RNA polymerase beta subunit [Pinus resinosa]
          Length = 269

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 98/241 (40%), Positives = 147/241 (60%), Gaps = 10/241 (4%)

Query: 715 MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNT 774
           +E   A  SG+  +A + G +E +DA+                       + +QRSN NT
Sbjct: 1   LEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGDTVRTESVIYQRSNTNT 52

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
           C +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V
Sbjct: 53  CTHQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLV 112

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDIL 894
            ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+L
Sbjct: 113 YEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVL 172

Query: 895 VGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           VGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     
Sbjct: 173 VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSG 232

Query: 953 N 953
           +
Sbjct: 233 D 233



 Score = 79.3 bits (194), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 86/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 60   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 118

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 119  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 172

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 173  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 230

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+ GRHGNKGI+S +LP
Sbjct: 231  SGDNAE-----TVHVYISQKRKIQVGDKVXGRHGNKGIISIVLP 269


>gi|159154258|gb|ABW93527.1| RNA polymerase B subunit [Hapalosiphon hibernicus BZ-3-1]
          Length = 195

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 90/195 (46%), Positives = 127/195 (65%), Gaps = 2/195 (1%)

Query: 625 RYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
             +A  ++ +DE+G      V  R   E      E++D+I  SP Q+VS+A S+IPFLE+
Sbjct: 1   FRVAAGDAPVDENGHLIGPEVPVRYRQEFSTTTPEQVDYIAVSPVQIVSVATSMIPFLEH 60

Query: 685 DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIV 744
           DD+NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA +I 
Sbjct: 61  DDANRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATKIR 120

Query: 745 IRS--VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDL 802
           +R     G+          Y + K+QRSNQ+TC+NQ+PLV++ + V    ++ADG ST+ 
Sbjct: 121 VRPRLRPGEESAKPPAEIEYIISKYQRSNQDTCLNQKPLVRMNERVVAGQVLADGSSTEG 180

Query: 803 GDLALGRNMLVAFMP 817
           G+LALG+N++VA+MP
Sbjct: 181 GELALGQNIVVAYMP 195


>gi|306413169|gb|ADM86685.1| RNA polymerase II beta subunit [Fusarium sacchari]
          Length = 276

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 48/285 (16%), Positives = 87/285 (30%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|117667784|gb|ABK55938.1| RNA polymerase B subunit [Streptomyces laceyi]
 gi|220961126|gb|ACL93029.1| RNA polymerase B subunit [Streptomyces caeruleus]
          Length = 180

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV  G VT+DV YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVSGVVTDDVDYLTADEEDRFVIAQANATLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFTEPRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ +EAP VGTGME   A  +G  I A++ G+V++V A  I I + +G
Sbjct: 121 MMRQAVPLITSEAPLVGTGMEYRCAVDAGDVIKAEKEGVVQEVSADYITIANDDG 175


>gi|330785376|gb|AEC46494.1| RNA polymerase II second largest subunit [Dendrographa decolorans]
          Length = 281

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 55/290 (18%), Positives = 89/290 (30%), Gaps = 23/290 (7%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 61

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--ILCGQNAVSGPKG 1001
             +  +     E+  SV    +E   R +  E +      Y +L +   +     VSG   
Sbjct: 62   FYRTYI----EQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVSGEDX 117

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
                T      + E           +   V   + S +        +             
Sbjct: 118  IXGKTAPFQAPMQENSEGGQRTKDHKKRDVSAPLRSTEAGIIDRVLL------------- 164

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                      R VKV     +  Q GDK A RHG KG +      EDMPF  DG   D++
Sbjct: 165  ----TTTEGKRSVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTSDGVVPDLI 220

Query: 1122 LNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +NP  +PSRM +  + E  L       G +  +          IS L SF
Sbjct: 221  INPHAIPSRMTIAHLIECLLSKVSTITGHEGDATPFTDITVSSISXLLSF 270



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 62/187 (33%), Gaps = 16/187 (8%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ASTHSMNYLRFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGP-EEITRD----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +       EE  R              + +D+ G +  G  V+
Sbjct: 54  DRGLFRSLFYRTYIEQQQSVGFNALEEFERPQRAETMRTRPGTYEKLDDDGFVPPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D + GK  P         E   +     K  DV        +G+   V+      +  
Sbjct: 114 GEDXIXGKTAPFQAPMQENSEGG-QRTKDHKKRDVSAPLRSTEAGIIDRVLLTTTEGKRS 172

Query: 950 IDKNERS 956
           +    R+
Sbjct: 173 VKVRTRT 179


>gi|289468065|gb|ADC95713.1| RpoB [Riemerella anatipestifer]
          Length = 166

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 95/166 (57%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
            E +  R  G+  +V  E++D ID +P Q+  I+ASLIPFLE+DD+
Sbjct: 121 TERIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPFLEHDDA 166


>gi|208609811|dbj|BAG72367.1| RNA polymerase II second largest subunit [Litsea globularia]
          Length = 167

 Score =  157 bits (398), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI+++P 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVSPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.10,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|117667718|gb|ABK55905.1| RNA polymerase B subunit [Streptomyces yanii]
 gi|157000429|gb|ABV00514.1| RNA polymerase subunit B [Streptomyces sanglieri]
          Length = 180

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRYVIAQANATLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFVEPRVLVRRRGGEVDYVPGADVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|164452775|gb|ABY57224.1| RpoB [Tortella densa]
          Length = 281

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 101/263 (38%), Positives = 165/263 (62%), Gaps = 10/263 (3%)

Query: 709 PFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQ 768
             VGTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +Q
Sbjct: 1   CIVGTGLESQAALDSGSIAIAKQSGKIIYTDGKKISLLNANKKSTNTDLII-------YQ 53

Query: 769 RSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSML 828
           RSN +T ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++L
Sbjct: 54  RSNNSTYMHQKAQVTQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAIL 113

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEV 888
           ISER++ +D++TS+HIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V
Sbjct: 114 ISERLIYKDIYTSVHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWV 173

Query: 889 NPGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI-F 945
             GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR  +
Sbjct: 174 ETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIY 233

Query: 946 NRHGIDKNERSISVEREQIELLA 968
            +   + +E++I V   Q   + 
Sbjct: 234 KKENYNHSEKTIHVYIAQKRKIQ 256



 Score = 97.5 bits (241), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 46/195 (23%), Positives = 81/195 (41%), Gaps = 16/195 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + + +ER +I+             E   L
Sbjct: 94   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSVHIERYEIKSRTTSQGPEKITKEIPHL 153

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 154  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 213

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E     +       + + V++A KR IQ GDK+AGRHG
Sbjct: 214  TCLKVPPGGKGRVIDVRWIYKKENYNHSE-------KTIHVYIAQKRKIQVGDKVAGRHG 266

Query: 1096 NKGIVSRILPCEDMP 1110
            NKGI+S+ILP +DMP
Sbjct: 267  NKGIISKILPRQDMP 281


>gi|50058739|gb|AAT69122.1| RNA polymerase II [Rapona tiliifolia]
          Length = 212

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 36/91 (39%), Positives = 48/91 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 122  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 181

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
             +PSRM +GQ+ E  +G     +GK+  +  
Sbjct: 182  AIPSRMTIGQLIECIMGKVAAHMGKEGDATP 212



 Score = 62.4 bits (150), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 43/123 (34%), Gaps = 14/123 (11%)

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNI 876
           N EDS++++   +    F S+    +    +      +E        +   +       +
Sbjct: 2   NQEDSVIMNHSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKL 61

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D+ G+   G  V+  D+++GK TP  +           A         RD S  +    +
Sbjct: 62  DDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQAARYTKRDHSTSLRHSET 112

Query: 937 GTV 939
           G V
Sbjct: 113 GMV 115


>gi|283132433|dbj|BAI63622.1| rpoB protein [Corynebacterium simulans]
          Length = 128

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 52/156 (33%), Positives = 78/156 (50%), Gaps = 36/156 (23%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+           +   L++  E++              
Sbjct: 1    RMNIGQVLEVHLGWLAHA-GWKVDV-----DDPANAELLKTLPEELYDVP---------- 44

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                        +G   +TPVFDGA  E I  +L  +  +  G        ++ L+DG +
Sbjct: 45   ------------AGSLTATPVFDGASNEEIGRLLASSRPNRDGDVMVDEHGKAQLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            GEP+  PV+VGY+YMLKL+H+V +K++ARSTG YS+
Sbjct: 93   GEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSM 128


>gi|151573483|gb|ABS17986.1| RNA polymerase II [Fusarium sp. NRRL 43878]
          Length = 277

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 46/285 (16%), Positives = 85/285 (29%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 122  PIDQENQDLGTRTTVHQRRDISTPLRSTENGIVDSVIVTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGVTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E+           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFQQSTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIVDSVIVTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|117667808|gb|ABK55950.1| RNA polymerase B subunit [Streptomyces nojiriensis]
 gi|117667812|gb|ABK55952.1| RNA polymerase B subunit [Streptomyces spororaveus]
          Length = 180

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIDGVVTDEVDYLTADEEDRFVIAQANAGLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G +I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDSIRAEKDGVVQEVSADYITVANDDG 175


>gi|91981520|gb|ABE68102.1| RNA polymerase subunit B [Pseudomonas sp. Q128-87]
          Length = 151

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 82/150 (54%), Positives = 109/150 (72%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLVDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 150


>gi|286142966|gb|ADC41513.1| RNA polymerase beta subunit [Streptomyces sp. CB169]
 gi|286142968|gb|ADC41514.1| RNA polymerase beta subunit [Streptomyces sp. CB170]
          Length = 185

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  + + 
Sbjct: 1   ANRALMGANMMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYVTVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V+ G  V    ++ADGP+T  G++A
Sbjct: 61  NDDGT-------YTTYRVAKFSRSNQGTSVNQKVVVEEGQRVIEGQVLADGPATQEGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|209553450|gb|ACI62294.1| RNA polymerase beta subunit [Helicobacter pullorum NCTC 12824]
 gi|307092496|gb|ADN28480.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092498|gb|ADN28481.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092500|gb|ADN28482.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092502|gb|ADN28483.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092504|gb|ADN28484.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092506|gb|ADN28485.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092508|gb|ADN28486.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092510|gb|ADN28487.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092512|gb|ADN28488.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092514|gb|ADN28489.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092516|gb|ADN28490.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092518|gb|ADN28491.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092520|gb|ADN28492.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092522|gb|ADN28493.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092524|gb|ADN28494.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092526|gb|ADN28495.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092528|gb|ADN28496.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092530|gb|ADN28497.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092532|gb|ADN28498.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092534|gb|ADN28499.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092536|gb|ADN28500.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092538|gb|ADN28501.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092540|gb|ADN28502.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092544|gb|ADN28504.1| RNA polymerase beta subunit [Helicobacter pullorum]
 gi|307092546|gb|ADN28505.1| RNA polymerase beta subunit [Helicobacter pullorum]
          Length = 162

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PYRKV D KVT+++VYL+A +EE   IA A++ L  D    E+++  R 
Sbjct: 61  AKVNELGFIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPASTVLTNDNVIKEDIIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL+   K++ ID SP+ VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGEIILMESSKVELIDLSPRMVVGVAASLIPFLEHDDANRAL 162


>gi|306413160|gb|ADM86679.1| RNA polymerase II beta subunit [Fusarium oxysporum]
          Length = 277

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 48/285 (16%), Positives = 87/285 (30%), Gaps = 21/285 (7%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 3    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 61

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E   +           +       +  G           K+ 
Sbjct: 62   RSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTA 121

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+Q  Q       ++     +  Q   + +                   
Sbjct: 122  PIDQENQDLGTRTQSHQRRDISTPLRSTENGIVDQVILTVNA------------------ 163

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 164  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFSREGLTPDIIINPHA 221

Query: 1127 VPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            +PSRM +  + E  L       G +  +          +S L   
Sbjct: 222  IPSRMTIAHLIECLLSKVSTLEGMEGDATPFTDVTVDSVSELLRK 266



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 2   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 51

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   EI           +       +DE GI+  G  V+
Sbjct: 52  DRGLFRSLFFRSYSDQEKKVGLNYTEIFEKPFQQTTLRMKHGTYDKLDEDGIVAPGVRVS 111

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +        ++   RD S  + S  +G V  V +     
Sbjct: 112 GEDIIIGKTAPIDQENQDLGTRT-------QSHQRRDISTPLRSTENGIVDQVILTVNAD 164

Query: 950 IDK 952
             K
Sbjct: 165 NVK 167


>gi|286143008|gb|ADC41534.1| RNA polymerase beta subunit [Streptomyces netropsis]
 gi|286143012|gb|ADC41536.1| RNA polymerase beta subunit [Streptomyces cinnamoneus]
          Length = 185

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 107/192 (55%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+KAEAP VGTGME   A  +G  I A++ G+V++V A  + + 
Sbjct: 1   ANRALMGSNMMRQAVPLIKAEAPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G         + YR+ KF RSNQ T  NQ+ +V  G  V    ++ADGPSTD G++A
Sbjct: 61  NDDGT-------YNTYRVAKFSRSNQGTSFNQKVVVDEGARVITGQVLADGPSTDEGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|157000397|gb|ABV00498.1| RNA polymerase subunit B [Streptomyces cinereorectus]
          Length = 180

 Score =  157 bits (398), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 123/175 (70%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG VT  V YL+A EE+   IAQAN+ L  
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGVVTEAVDYLTADEEDRYVIAQANAPLTN 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           + +F E  V  R  G E   +P  +ID++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELTFAEPRVLVRRRGGEIDYIPGTEIDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPLL++EAP VGTGME   A  +   I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLLRSEAPLVGTGMEYRCAVDAQDVITAEKPGVVQEVSADYVTVANDDG 175


>gi|198279399|emb|CAP04734.1| RNA polymerase beta subunit [Pinus brutia var. pityusa]
          Length = 268

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 98/240 (40%), Positives = 146/240 (60%), Gaps = 10/240 (4%)

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTC 775
           E   A  SG+  +A + G +E +DA+                       + +QRSN NTC
Sbjct: 1   EGQAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTC 52

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
            +Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V 
Sbjct: 53  THQKPQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVY 112

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LV
Sbjct: 113 EDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLGSWIETGDVLV 172

Query: 896 GKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           GK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 173 GKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 232



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 59   IHQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 117

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 118  SFHIVRYRIEICMTSQGPERITREIPHLDAHL-LRHLDEN-----GLVMLGSWIETGDVL 171

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 172  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 229

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 230  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISXVLP 268


>gi|55650594|emb|CAF31380.1| RNA polymerase B subunit [Anabaena flos-aquae 0tu33s15]
          Length = 199

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 89/196 (45%), Positives = 127/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q++S+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPSVPVRYRQDWTTTNPEQVDYVAVSPVQIISVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           +R LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  HRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVIYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQPIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|286142870|gb|ADC41465.1| RNA polymerase beta subunit [Streptomyces humidus]
          Length = 185

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+E+P VGTGME   A  +G  + A++ G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKDGVVQEVSADYITTT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YITYRLAKFSRSNQGTSVNQKVIVNEGDRIITGQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|117667790|gb|ABK55941.1| RNA polymerase B subunit [Streptomyces griseobrunneus]
 gi|157000393|gb|ABV00496.1| RNA polymerase subunit B [Streptomyces bacillaris]
          Length = 180

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|164452763|gb|ABY57218.1| RpoB [Pleurochaete luteola]
          Length = 278

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 99/241 (41%), Positives = 155/241 (64%), Gaps = 9/241 (3%)

Query: 710 FVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQR 769
            VGTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +QR
Sbjct: 1   IVGTGLESQAALDSGSIAIAKQSGKIIYTDGKKISLLNANKKSTNTDLII-------YQR 53

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
           SN NT ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LI
Sbjct: 54  SNNNTYMHQKARVTQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAILI 113

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVN 889
           SER++ +D++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V 
Sbjct: 114 SERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWVE 173

Query: 890 PGDILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
            GD+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR   +
Sbjct: 174 TGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIYK 233

Query: 948 H 948
            
Sbjct: 234 K 234



 Score = 90.1 bits (222), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/193 (23%), Positives = 78/193 (40%), Gaps = 16/193 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + I +ER +I+             E   L
Sbjct: 93   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 152

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 153  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 212

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E             + + V++A KR IQ GDK+AGRHG
Sbjct: 213  TCLKVPPGGKGRVIDVRWIYKKE-------NSNHSEKTIHVYIAQKRKIQVGDKVAGRHG 265

Query: 1096 NKGIVSRILPCED 1108
            NKGI+S+ILP +D
Sbjct: 266  NKGIISKILPRQD 278


>gi|117667716|gb|ABK55904.1| RNA polymerase B subunit [Streptomyces sindenensis]
 gi|117667732|gb|ABK55912.1| RNA polymerase B subunit [Streptomyces badius]
 gi|157000419|gb|ABV00509.1| RNA polymerase subunit B [Streptomyces parvus]
          Length = 180

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 130/175 (74%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPASEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|220961150|gb|ACL93041.1| RNA polymerase B subunit [Streptomyces coerulescens]
          Length = 180

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  E +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAEARVLVRRRGGEVDYVGGEDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|50058757|gb|AAT69131.1| RNA polymerase II [Porana commixta]
          Length = 212

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 36/91 (39%), Positives = 48/91 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 122  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 181

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
             +PSRM +GQ+ E  +G     +GK+  +  
Sbjct: 182  AIPSRMTIGQLIECIMGKVAAHMGKEGDATP 212



 Score = 65.5 bits (158), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 45/124 (36%), Gaps = 14/124 (11%)

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKN 875
           YN EDS+++++  +    F S+    +    +      +E        +   +       
Sbjct: 1   YNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDK 60

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +D+ G+   G  V+  D+++GK TP  +           A         RD S  +    
Sbjct: 61  LDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHSTSLRHSE 111

Query: 936 SGTV 939
           +G V
Sbjct: 112 TGMV 115


>gi|286142834|gb|ADC41447.1| RNA polymerase beta subunit [Streptomyces coelicolor]
 gi|286142836|gb|ADC41448.1| RNA polymerase beta subunit [Streptomyces coelescens]
 gi|286142838|gb|ADC41449.1| RNA polymerase beta subunit [Streptomyces violaceoruber]
 gi|286142840|gb|ADC41450.1| RNA polymerase beta subunit [Streptomyces sp. DSM 40419]
 gi|286142842|gb|ADC41451.1| RNA polymerase beta subunit [Streptomyces violaceolatus]
 gi|286142844|gb|ADC41452.1| RNA polymerase beta subunit [Streptomyces lividans]
 gi|286142846|gb|ADC41453.1| RNA polymerase beta subunit [Streptomyces sp. BTG 4-758]
 gi|286142848|gb|ADC41454.1| RNA polymerase beta subunit [Streptomyces sp. BTG 4-759]
 gi|286142850|gb|ADC41455.1| RNA polymerase beta subunit [Streptomyces sp. BTG 6-715]
 gi|286142852|gb|ADC41456.1| RNA polymerase beta subunit [Streptomyces sp. BTG 6-708]
 gi|286142854|gb|ADC41457.1| RNA polymerase beta subunit [Streptomyces sp. BTG 717 I]
 gi|286142856|gb|ADC41458.1| RNA polymerase beta subunit [Streptomyces coelicolor]
 gi|286142858|gb|ADC41459.1| RNA polymerase beta subunit [Streptomyces sp. BTG 723 I]
 gi|286142860|gb|ADC41460.1| RNA polymerase beta subunit [Streptomyces sp. BTG 4-723]
 gi|286142862|gb|ADC41461.1| RNA polymerase beta subunit [Streptomyces sp. BTG 4-738]
 gi|286142864|gb|ADC41462.1| RNA polymerase beta subunit [Streptomyces coelicolor]
 gi|286142866|gb|ADC41463.1| RNA polymerase beta subunit [Streptomyces violaceoruber]
          Length = 185

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 142/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAADAGDVVKAEKAGVVQEVSADYITTT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YITYRLAKFSRSNQGTSVNQKVIVAEGDRIIEGQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|221135678|ref|XP_002168548.1| PREDICTED: similar to RNA polymerase I polypeptide B, partial [Hydra
            magnipapillata]
          Length = 169

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 47/168 (27%), Positives = 75/168 (44%), Gaps = 35/168 (20%)

Query: 1227 DLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGK 1286
              +  G   +Y G+ G+  D  + +G +Y  +L HMV+DK   RSTG    +T QP+ G+
Sbjct: 1    GYNYYGNERMYSGINGKEMDVDIFIGIVYYQRLRHMVADKYQVRSTGPVDNLTHQPVQGR 60

Query: 1287 SNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD----DVVGRTR---VYESIVA----- 1334
              +GG R GEME   + A+G+ ++L + L   SD     V   T+   ++  IV      
Sbjct: 61   KRQGGIRFGEMERDALIAHGSGFLLHDRLFNCSDRCETHVC--TKCGSIFTPIVRKPVTH 118

Query: 1335 -------------------GNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                               G+D  +   P  F  L+ E+ A+  +I L
Sbjct: 119  HDSLIGFNDRKWFCRVCGHGDDIQKMLVPYVFKYLIAELTAM--NIRL 164


>gi|219564081|gb|ACL28224.1| RNA polymerase II second largest subunit [fungal sp. M223]
          Length = 248

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 90/259 (34%), Gaps = 27/259 (10%)

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +     +  +   +      +    +E   + +  E
Sbjct: 2    AIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQE----KMIGHSVVEQFEKPQRSE 57

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + L    Y ++ +   I  G           K+  ++ D                +E  
Sbjct: 58   TLRLKHGTYDKIGDDGIIEPGIRVSGEDIIMGKTAPMAPD---------------AEELG 102

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            QR  + +K    T     E    +++     GD       R  KV V   +  Q GDK A
Sbjct: 103  QRQKQHIKRDVSTPLRSTESGVIDQVMLTTTGD-----GTRFAKVRVRTTKIPQIGDKFA 157

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L       G +
Sbjct: 158  SRHGQKGTIGITYRQEDMPFSREGLVPDIIINPHAIPSRMTIAHLIECQLSKVATLRGDE 217

Query: 1152 IKSLINDYKANGDISPLRS 1170
              +          +S +  
Sbjct: 218  GDATPFTKVTVTQVSNILR 236


>gi|307092542|gb|ADN28503.1| RNA polymerase beta subunit [Helicobacter pullorum]
          Length = 162

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PYRKV D KVT+++VYL+A +EE   IA A++ L  D    E+++  R 
Sbjct: 61  AKVNELGFIEAPYRKVVDKKVTDEIVYLTATQEEGAVIAPASTVLTNDNVIKEDIIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL+   +++ ID SP+ VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGEIILMESSRVELIDLSPRMVVGVAASLIPFLEHDDANRAL 162


>gi|6449112|gb|AAF08831.1| RNA polymerase beta subunit [Granulicatella adiacens ATCC 49175]
          Length = 170

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 55/175 (31%), Positives = 80/175 (45%), Gaps = 16/175 (9%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG +F     R   +GK LY   +IP++G W++ E DSKDI +VRIDR RK+P+
Sbjct: 1   SQLVRSPGAYFH---DRPDKNGKQLYGSTLIPNRGAWLEYETDSKDISYVRIDRTRKIPL 57

Query: 215 TSFLMALGMDSEE-ILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVD-IDTGEQ 272
           T  + ALG  S+E I   F          D         D     +    + D +  GE 
Sbjct: 58  TVLVRALGFGSDELIQEIFGDSETLRLTLDKDVHKRM--DESRTEEALKDIYDRLRPGEP 115

Query: 273 -VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
              ES + L +      +   +  +G           + L    +AE++V+ ETG
Sbjct: 116 KTAESSRNLLTARFFDPRRYDLAAVGRYKVNKKLNLKNRLLHQTIAENLVDPETG 170



 Score = 54.3 bits (129), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/112 (26%), Positives = 48/112 (42%), Gaps = 10/112 (8%)

Query: 320 IYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYR 379
           + + A     ++ ++EIF         L  D                    ++AL DIY 
Sbjct: 59  VLVRALGFGSDELIQEIFGDSETLRLTLDKDV----------HKRMDESRTEEALKDIYD 108

Query: 380 VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            +RPG+  T   + ++    FFD  +YDL+ VGR K+N +LNL      + I
Sbjct: 109 RLRPGEPKTAESSRNLLTARFFDPRRYDLAAVGRYKVNKKLNLKNRLLHQTI 160


>gi|117667720|gb|ABK55906.1| RNA polymerase B subunit [Streptomyces vinaceus]
 gi|117667722|gb|ABK55907.1| RNA polymerase B subunit [Streptomyces galilaeus]
 gi|117667772|gb|ABK55932.1| RNA polymerase B subunit [Streptomyces argenteolus]
 gi|117667796|gb|ABK55944.1| RNA polymerase B subunit [Streptomyces albus]
 gi|157000407|gb|ABV00503.1| RNA polymerase subunit B [Streptomyces globisporus subsp.
           globisporus]
 gi|220961124|gb|ACL93028.1| RNA polymerase B subunit [Streptomyces sioyaensis]
 gi|220961226|gb|ACL93079.1| RNA polymerase B subunit [Streptomyces canescens]
 gi|220961228|gb|ACL93080.1| RNA polymerase B subunit [Streptomyces champavatii]
 gi|220961232|gb|ACL93082.1| RNA polymerase B subunit [Streptomyces felleus]
 gi|220961234|gb|ACL93083.1| RNA polymerase B subunit [Streptomyces globisporus subsp.
           caucasicus]
 gi|220961236|gb|ACL93084.1| RNA polymerase B subunit [Streptomyces limosus]
 gi|220961238|gb|ACL93085.1| RNA polymerase B subunit [Streptomyces odorifer]
 gi|220961240|gb|ACL93086.1| RNA polymerase B subunit [Streptomyces sampsonii]
 gi|220961242|gb|ACL93087.1| RNA polymerase B subunit [Streptomyces coelicolor]
 gi|220961244|gb|ACL93088.1| RNA polymerase B subunit [Streptomyces albidoflavus]
          Length = 180

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGIVTDEVDYLTADEEDRFVIAQANAGLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHFAEDRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITTTNDDG 175


>gi|256600052|gb|ACV04766.1| DNA-dependent RNA-polymerase beta-subunit [Pasteurellaceae
           bacterium B96/37]
          Length = 154

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 90/154 (58%), Positives = 115/154 (74%), Gaps = 1/154 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDE+  FT+  V  
Sbjct: 61  VYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDENLRFTDAYVTA 120

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           R   GE  L   E+I ++D S +QVVS+AA+LIP
Sbjct: 121 RGEHGESGLYRPEEIHYMDVSTQQVVSVAAALIP 154


>gi|76781325|gb|ABA54548.1| RpoB [Campylobacter lanienae]
          Length = 164

 Score =  157 bits (397), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/164 (57%), Positives = 123/164 (75%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLSEITHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A+VN  GF+E+PYRKV + KVTN++VYL+A +EE   IA A++ LDE+G   E+L+  
Sbjct: 61  TYAKVNDLGFVESPYRKVENSKVTNEIVYLTATQEEGHIIAPASTILDENGMIVEDLIEV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           R  GE IL  R+ +  ID     V+ +AASLIPFLE+DD+NR L
Sbjct: 121 RQDGEMILAKRDDVTLIDLCSGMVMGVAASLIPFLEHDDANRAL 164


>gi|112798757|gb|ABI22702.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798759|gb|ABI22703.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798761|gb|ABI22704.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798769|gb|ABI22708.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798783|gb|ABI22715.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798815|gb|ABI22731.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798817|gb|ABI22732.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798831|gb|ABI22739.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798833|gb|ABI22740.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798837|gb|ABI22742.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798855|gb|ABI22751.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798865|gb|ABI22756.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798867|gb|ABI22757.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798869|gb|ABI22758.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798871|gb|ABI22759.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798875|gb|ABI22761.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798879|gb|ABI22763.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798881|gb|ABI22764.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798887|gb|ABI22767.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798907|gb|ABI22777.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798909|gb|ABI22778.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798911|gb|ABI22779.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798923|gb|ABI22785.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798931|gb|ABI22789.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798953|gb|ABI22800.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798955|gb|ABI22801.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798983|gb|ABI22815.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798987|gb|ABI22817.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798995|gb|ABI22821.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112798999|gb|ABI22823.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|112799013|gb|ABI22830.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576835|gb|ADN53019.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576837|gb|ADN53020.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576841|gb|ADN53022.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576843|gb|ADN53023.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576845|gb|ADN53024.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576847|gb|ADN53025.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576851|gb|ADN53027.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576853|gb|ADN53028.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576855|gb|ADN53029.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576861|gb|ADN53032.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576871|gb|ADN53037.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576875|gb|ADN53039.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576879|gb|ADN53041.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576881|gb|ADN53042.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576883|gb|ADN53043.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576885|gb|ADN53044.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576887|gb|ADN53045.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576889|gb|ADN53046.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576891|gb|ADN53047.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 90/157 (57%), Positives = 115/157 (73%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGSGGLTRERAGFEVRDVHTTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V CR   GE  L   E+I ++D S +QVVS+
Sbjct: 121 RFTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSV 157


>gi|225698403|gb|ACO07319.1| RpoB [Pasteurellaceae bacterium TIS15908]
          Length = 154

 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 91/154 (59%), Positives = 116/154 (75%), Gaps = 1/154 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDE+  FT+  V  R
Sbjct: 61  YARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDENLRFTDAYVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
              GE  L   E+I ++D S +QVVS+AA+LIPF
Sbjct: 121 GEHGESGLYRPEEIHYMDVSTQQVVSVAAALIPF 154


>gi|318085008|gb|ADV39394.1| RNA polymerase subunit B [Streptomyces phaeochromogenes]
          Length = 180

 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+NA+GF+ETPYRKV +G+V++DV YL+A EE+   IAQAN+SL++
Sbjct: 1   GPNIGLIGSLASYGRINAFGFVETPYRKVVEGRVSDDVDYLTADEEDRFVIAQANASLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFDEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+ AEAP VGTGME   A  +G  I A++AG+V++V A  I + + +G
Sbjct: 121 MMRQAVPLITAEAPLVGTGMEYRCAVDAGDVIKAEKAGVVQEVSADYITVANDDG 175


>gi|117667730|gb|ABK55911.1| RNA polymerase B subunit [Streptomyces atroolivaceus]
 gi|117667774|gb|ABK55933.1| RNA polymerase B subunit [Streptomyces mutomycini]
 gi|157000417|gb|ABV00508.1| RNA polymerase subunit B [Streptomyces olivoviridis]
          Length = 180

 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV +G VT+DV YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANATLSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTEARVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A+++G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKSGVVQEVSADYITVTNDDG 175


>gi|82706455|gb|ABB89605.1| RNA polymerase II second largest subunit [Botryotinia fuckeliana]
          Length = 535

 Score =  157 bits (396), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 100/603 (16%), Positives = 186/603 (30%), Gaps = 80/603 (13%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT-- 587
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L   
Sbjct: 1    TFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALM 56

Query: 588  SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
             +  V         +    + +V  +   L A      ++      +  D +   + V  
Sbjct: 57   CYVTVGTPSDPIVEFMIQRNMEVLEEYEPLRAPNATKVFVNGVWVGIHRDPAHLVKCVQD 116

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLEN-DDSNRVLMGCNMQRQAVPLLK 705
                  I      I +  D   K          P L   +D +    G  +  +      
Sbjct: 117  LRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNDPDSANKGNLVLNKDHIRRL 176

Query: 706  AEAPFVGTGMESVVAKSSGA--AIVAKRAGIVEQVDAIRI---VIRSVEGDLDPSTSGVD 760
             +   +   M+      +G           +VE +DA      +I     DLD S     
Sbjct: 177  EDDQLLPANMDKDEKVRNGYYGFQGLINDXVVEYLDAEEEETVMITMTPEDLDISRQLQA 236

Query: 761  IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
             Y++    R +++  +N+R    +             PS  LG       +  + +P+  
Sbjct: 237  GYQI----RPDESGDLNKRVKAPINPTAHVWTHCEIHPSMILG-------ICASIIPFPD 285

Query: 821  YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
            +N                        ++       +G      D+               
Sbjct: 286  HNQSPRNC------------------YQSAMGKQAMGVFLTNFDVRM-----------DT 316

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 317  MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF 376

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L +  Y +L +   +  G     
Sbjct: 377  -RSLFYRAYTDQEKR---IGMNVVEQFEKPYRSDTLKLKQGTYDKLDDDGIVAPGVRVTG 432

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E    +++
Sbjct: 433  ADIIIGKTAPIAPD---------------SEEMGQRTKAHVKRDASTPLRSTESGLVDQV 477

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      +DMPF ++G  
Sbjct: 478  LI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYMQQDMPFTREGVV 532

Query: 1118 VDI 1120
             D+
Sbjct: 533  PDL 535


>gi|208609873|dbj|BAG72398.1| RNA polymerase II second largest subunit [Neolitsea javanica]
          Length = 167

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGNVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|6449142|gb|AAF08843.1| RNA polymerase beta subunit [Streptococcus parasanguinis ATCC
           15912]
          Length = 170

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 80/174 (45%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI+  F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIIDIFGDSELVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             ES + L        +   +  +G           + L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLVARFFDPRRYDLAPVGRYKINKKLNIKNRLLNQTIAEPLVDAETG 170



 Score = 53.9 bits (128), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIIDIFGDSELVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+      + I
Sbjct: 120 SSRSLLVARFFDPRRYDLAPVGRYKINKKLNIKNRLLNQTI 160


>gi|6449157|gb|AAF08849.1| RNA polymerase beta subunit [Streptococcus sanguinis SK1]
          Length = 170

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 50/174 (28%), Positives = 78/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EIL  F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEILDIFGDSDLVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             ES + L            +  +G             L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLDARFFDPHRYDLAAVGRYKINKKLSVKTRLLNQTIAEPLVDAETG 170



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 50/101 (49%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEILDIFGDSDLVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+ +  FFD  +YDL+ VGR K+N +L++ T    + I
Sbjct: 120 SSRSLLDARFFDPHRYDLAAVGRYKINKKLSVKTRLLNQTI 160


>gi|151564522|gb|ABS17620.1| RpoB [Campylobacter canadensis]
          Length = 172

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/172 (55%), Positives = 129/172 (75%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIGL++SL
Sbjct: 1   DQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  ++L+ 
Sbjct: 61  STYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNIIDDLLE 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
            R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG NMQ+
Sbjct: 121 ARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMGPNMQQ 172


>gi|117667800|gb|ABK55946.1| RNA polymerase B subunit [Streptomyces griseoplanus]
 gi|294963503|gb|ADF50236.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963505|gb|ADF50237.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963507|gb|ADF50238.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963509|gb|ADF50239.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963511|gb|ADF50240.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963513|gb|ADF50241.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963515|gb|ADF50242.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963517|gb|ADF50243.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963519|gb|ADF50244.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963521|gb|ADF50245.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963523|gb|ADF50246.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963525|gb|ADF50247.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963527|gb|ADF50248.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963529|gb|ADF50249.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963531|gb|ADF50250.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963533|gb|ADF50251.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963535|gb|ADF50252.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963537|gb|ADF50253.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963539|gb|ADF50254.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963541|gb|ADF50255.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963543|gb|ADF50256.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963545|gb|ADF50257.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963547|gb|ADF50258.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963549|gb|ADF50259.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963551|gb|ADF50260.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963553|gb|ADF50261.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963555|gb|ADF50262.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963557|gb|ADF50263.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963559|gb|ADF50264.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963561|gb|ADF50265.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963563|gb|ADF50266.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963565|gb|ADF50267.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963567|gb|ADF50268.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963569|gb|ADF50269.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963571|gb|ADF50270.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963573|gb|ADF50271.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|294963575|gb|ADF50272.1| RNA polymerase B subunit [Streptomyces flavogriseus]
          Length = 180

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV +G VT+DV YL+A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTEARVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKAGVVQEVSADYITVTNDDG 175


>gi|55650558|emb|CAF31379.1| RNA polymerase B subunit [Anabaena circinalis 1tu34s5]
          Length = 199

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 90/196 (45%), Positives = 127/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q++S+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPSVPVRYRQDWTTTNPEQVDYVAVSPVQIISVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVIYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQPIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|318085038|gb|ADV39409.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085044|gb|ADV39412.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085048|gb|ADV39414.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085052|gb|ADV39416.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085054|gb|ADV39417.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085060|gb|ADV39420.1| RNA polymerase subunit B [Streptomyces stelliscabiei]
 gi|318085064|gb|ADV39422.1| RNA polymerase subunit B [Streptomyces niveiscabiei]
          Length = 180

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTTNDDG 175


>gi|226427475|gb|ACO54931.1| RNA polymerase [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 165

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 92/164 (56%), Positives = 125/164 (76%), Gaps = 1/164 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 62  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR LM
Sbjct: 122 FNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRALM 165


>gi|145307906|gb|ABP57257.1| RNA polymerase II second largest subunit [Erynia rhizospora]
          Length = 261

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 50/276 (18%), Positives = 87/276 (31%), Gaps = 21/276 (7%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQ 993
             +   +    I+ R  +D+ ++S   E E  E   R                   I  G 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGMNEVESFEKPTRKTTLRLRHGTYEKLEDDGLIAPGT 124

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
                      K+  +  D      R++          ++     +  +   + +      
Sbjct: 125  RVSGDDIIIGKTAPVPPDSEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ----- 179

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
                             +R  KV V   R  Q GDK A RHG KG +      EDMPF  
Sbjct: 180  ---------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFNA 224

Query: 1114 DGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 225  EGIVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 260



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + +   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGMNEVESFEKPTRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHTKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|157000427|gb|ABV00513.1| RNA polymerase subunit B [Streptomyces rubiginosohelvolus]
          Length = 180

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGVVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+E+P VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|223585649|gb|ACM91695.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 161

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 97/161 (60%), Positives = 124/161 (77%), Gaps = 2/161 (1%)

Query: 551 RARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DG 608
           R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV     
Sbjct: 1   RERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTN 60

Query: 609 KVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASP 668
            +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SP
Sbjct: 61  SITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSP 120

Query: 669 KQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAP 709
           KQVVS A + IPFLENDDSNR LMG NMQRQAVPL+  EAP
Sbjct: 121 KQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNTEAP 161


>gi|145307874|gb|ABP57242.1| RNA polymerase II second largest subunit [Zoophthora anglica]
          Length = 263

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 51/281 (18%), Positives = 94/281 (33%), Gaps = 27/281 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 7    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 66

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 67   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 122

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  +      R++          ++     +  +   + +   
Sbjct: 123  PGTRVSGDDIIIGKTAPVPPESEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 180

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 181  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 222

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            F  +G   D+V+NP  +PSRM +G + E  +G      G +
Sbjct: 223  FSAEGIVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDGSE 263



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 5   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 54

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 55  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 114

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 115 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHSKRDVSTPLKSTETGI 170

Query: 936 SGTVV 940
              V+
Sbjct: 171 VDRVM 175


>gi|112798877|gb|ABI22762.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 89/157 (56%), Positives = 114/157 (72%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET E  
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHTTHYGRLCPIETPESP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE+ 
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDENF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V CR   GE  L   E+I ++D S +QVVS+
Sbjct: 121 RFTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSV 157


>gi|326533702|dbj|BAK05382.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 823

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 98/724 (13%), Positives = 215/724 (29%), Gaps = 110/724 (15%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+   I    R N  ++A                LE+ +     P    
Sbjct: 51  LVKEHIDSFNYFITKGIKNIVRANNRIEA---------RSDPGIYLEYKNIYIGEPSVQV 101

Query: 85  -----KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMT 139
                      C   D TY+ P+ + +   V          S          +G +P+M 
Sbjct: 102 DFRVETITPHFCRLTDRTYSAPVIVDVEYTVGKTHTQHRKPSFT--------IGYMPIML 153

Query: 140 ------------------------KDGTFVIKGIQRIVVSQLHRSPG-IHFDHD-KGR-- 171
                                     G F++KG +++++ Q   S   I  D D KGR  
Sbjct: 154 RSYACVLNGKDEAELARYGECPLDPGGYFIVKGAEKVILIQEQLSKNRIIIDTDNKGRVI 213

Query: 172 --ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEI 228
              + S   + +  +I             K+ I++++++  + +P+   + A+G+++++ 
Sbjct: 214 ASVTSSTHEVKSKTVIC----------MEKEKIYLQLNQFTKAIPIIVVMKAMGIETDQE 263

Query: 229 LSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
           +     +        +      A + +   + +   +D         +G          L
Sbjct: 264 VVQMVGRDPRYADLLYLSIQECATERIYTQQQALQYMDDKV--TYAGAGNIKDGRSKLIL 321

Query: 289 KEKGVKFLGITSDCLCGLYVA-----EDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
           ++  +  + + +       +        +++        +  D +  K LE         
Sbjct: 322 RDVFIAHVPVNNGNFQPKCIYTAVMLRRMLDAILNSDTFDDKDYVGNKRLELSGQLVSLL 381

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
              L+           N           D    I +     DV T  +  +  +   +D 
Sbjct: 382 FEDLFKTMNTYAVDRMNKNSDMARSSPLDFSQLIMQQ----DVITSGLERA-ISTGNWDI 436

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKI--LVDLRNGKGTIDDIDNLGN 461
            ++ +   G  ++  RL+                   K      L+  +  +    +   
Sbjct: 437 KRFKMHRKGVSQVLSRLSYMASLGYMTRITPQFEKTRKTSGPRALQPSQWGMLCPCDTPE 496

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ 521
                + + L     +   + E  ++    S+ ++ +            S +   F    
Sbjct: 497 GEACGLTKNLALMTHVTTDQEEGPLRNLCFSLGVEDLSLLSGEEIHAPGSFLV-MFNGLI 555

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHP-THYGRICPAETSEGHNI 580
           L +  +     + +   RR   +G+          +   +H  +  GR+C          
Sbjct: 556 LGKHRQPQKFANNMRTFRRSGKIGE--FVSVFVNEKQHCIHIASDGGRVCRPLIIADKGR 613

Query: 581 GLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSF 640
             V              +    R   D      + YL   EE N  IA            
Sbjct: 614 ARVKEHH-------MKELRDGIRSFDDFLRDGLIEYLDVNEENNALIA------------ 654

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQA 700
                      ++  V R  I  I+  P  ++ + A LIP+  ++ S R    C M +QA
Sbjct: 655 ------LYEHVDQDGVQRSSITHIEIEPMTLLGVVAGLIPYPHHNQSPRNTYQCAMGKQA 708

Query: 701 VPLL 704
           +  +
Sbjct: 709 MGNI 712


>gi|225698445|gb|ACO07340.1| RpoB [Volucribacter psittacicida]
          Length = 154

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 86/154 (55%), Positives = 113/154 (73%), Gaps = 1/154 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++
Sbjct: 1   FMDQKNQLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLIN 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
           SL+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  
Sbjct: 61  SLSVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAY 120

Query: 645 VFCR-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           V  R   GE  L   E+I ++D S +QVVS+AA+
Sbjct: 121 VTARGEHGESGLYRPEEIHYMDVSTQQVVSVAAA 154


>gi|55650686|emb|CAF31394.1| RNA polymerase B subunit [Anabaena lemmermannii 66A]
 gi|159154260|gb|ABW93528.1| RNA polymerase B subunit [Anabaena sp. 18B6]
          Length = 199

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 90/196 (45%), Positives = 127/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPHVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|318085016|gb|ADV39398.1| RNA polymerase subunit B [Streptomyces roseolilacinus]
          Length = 180

 Score =  157 bits (396), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 91/175 (52%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG+VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGQVTDEVDYLTADEEDRFVIAQANAGLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAENRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+E+P VGTGME   A  +G  + A++ G+V+++ A  I + + +G
Sbjct: 121 MMRQAVPLIKSESPLVGTGMEYRSAVDAGDVVKAEKDGVVQELSADYITVANDDG 175


>gi|318085066|gb|ADV39423.1| RNA polymerase subunit B [Streptomyces bottropensis]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGIVTDEVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTTNDDG 175


>gi|117667820|gb|ABK55956.1| RNA polymerase B subunit [Streptomyces fulvorobeus]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRYVIAQANALLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|50058767|gb|AAT69136.1| RNA polymerase II [Montinia caryophyllacea]
          Length = 222

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 36/90 (40%), Positives = 48/90 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 133  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTIEGVTPDIIVNPH 192

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             +PSRM +GQ+ E  +G     +GK+  + 
Sbjct: 193  AIPSRMTIGQLIECIMGKVAAHMGKEGDAT 222



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 51/135 (37%), Gaps = 14/135 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----D 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRTN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP  +           A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQED---------AQGAAARYSR 111

Query: 925 RDTSLRVPSGVSGTV 939
           RD S  +    +G V
Sbjct: 112 RDHSTSLRHSETGMV 126


>gi|117667804|gb|ABK55948.1| RNA polymerase B subunit [Streptomyces flavogriseus]
 gi|157000403|gb|ABV00501.1| RNA polymerase subunit B [Streptomyces flavovirens]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|117667748|gb|ABK55920.1| RNA polymerase B subunit [Streptomyces virginiae]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN++L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIDGVVTDEVDYLTADEEDRFVIAQANAALSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEIDYIAGGDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G +I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDSIRAEKDGVVQEVSADYITVANDDG 175


>gi|55650552|emb|CAF31378.1| RNA polymerase B subunit [Anabaena cf. cylindrica XP6B]
          Length = 199

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 91/196 (46%), Positives = 125/196 (63%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTHGDVIYVDATEIRVRV 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQISAASGSQVIEKGQEIRYTLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|145307884|gb|ABP57246.1| RNA polymerase II second largest subunit [Zoophthora lanceolata]
 gi|145307911|gb|ABP57259.1| RNA polymerase II second largest subunit [Zoophthora phalloides]
 gi|145307915|gb|ABP57261.1| RNA polymerase II second largest subunit [Zoophthora occidentalis]
          Length = 261

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 51/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 121

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  +      R++          ++     +  +   + +   
Sbjct: 122  PGTRVSGDDIIIGKTAPVPPESEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 179

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 180  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 221

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 222  FSAEGIVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 260



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHSKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|55650512|emb|CAF31375.1| RNA polymerase B subunit [Anabaena cf. circinalis macrospora
           1tu23s3]
 gi|55650538|emb|CAF31377.1| RNA polymerase B subunit [Anabaena cf. circinalis macrospora
           0tu25s6]
 gi|55650642|emb|CAF31385.1| RNA polymerase B subunit [Aphanizomenon gracile str. 'HEANEY
           1986/Camb140 1/1']
 gi|55650644|emb|CAF31386.1| RNA polymerase B subunit [Aphanizomenon gracile 1tu26s16]
 gi|55650672|emb|CAF31388.1| RNA polymerase B subunit [Anabaena sp. 123]
 gi|55650674|emb|CAF31389.1| RNA polymerase B subunit [Aphanizomenon sp. 202]
 gi|55650676|emb|CAF32206.1| RNA polymerase B subunit [Aphanizomenon flos-aquae PCC 7905]
 gi|55650680|emb|CAF31391.1| RNA polymerase B subunit [Aphanizomenon flos-aquae TR183]
          Length = 199

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 91/196 (46%), Positives = 127/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|198279471|emb|CAP04770.1| RNA polymerase beta subunit [Pinus cembra]
          Length = 264

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 95/236 (40%), Positives = 144/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +D +                       + +QRSN NTC +Q+
Sbjct: 1   ALDSGSVAIATQXGRIEYIDXV--------NITSSINGDTVRTESVIYQRSNTNTCTHQK 52

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 53  PQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 112

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+T
Sbjct: 113 TSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGKLT 172

Query: 900 PKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+       TPE +LL+ IFG +    R++ LR P G  G V+DVR  NR     +
Sbjct: 173 PQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVDDSGD 228



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 55   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 113

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 114  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 167

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 168  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 225

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKG +S ILP
Sbjct: 226  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGXISIILP 264


>gi|219564029|gb|ACL28198.1| RNA polymerase II second largest subunit [fungal sp. M140]
          Length = 265

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 48/274 (17%), Positives = 85/274 (31%), Gaps = 21/274 (7%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ ++  
Sbjct: 6    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVG 64

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E   +           +       +  G           K+  +  D      
Sbjct: 65   LNYTESFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDPDNQDLGT 124

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+   Q       ++     +      + +                       ++ VKV 
Sbjct: 125  RTAAHQKRDISTPLRSTENGIVDSVIMTVNA--------------------DNVKYVKVR 164

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   +  Q GDK A RHG KG V      EDMPF ++G   DI++NP  +PSRM +  + 
Sbjct: 165  VRTTKIPQIGDKFASRHGQKGTVGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLI 224

Query: 1138 ETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
            E  L       G +  +          +S L   
Sbjct: 225  ECLLSKVSTLEGMEGDATPFTDVTVDQVSDLLRK 258



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 59/164 (35%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 3   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 62

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E            +       +DE GI+  G  V+  DI++GK  P        
Sbjct: 63  VGLNYTESFEKPFQPSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDPDNQDL 122

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +         A   RD S  + S  +G V  V +       K
Sbjct: 123 GTRT-------AAHQKRDISTPLRSTENGIVDSVIMTVNADNVK 159


>gi|286142818|gb|ADC41439.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142828|gb|ADC41444.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142872|gb|ADC41466.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142874|gb|ADC41467.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142876|gb|ADC41468.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142884|gb|ADC41472.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142886|gb|ADC41473.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142888|gb|ADC41474.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142892|gb|ADC41476.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142896|gb|ADC41478.1| RNA polymerase beta subunit [Streptomyces californicus]
 gi|286142906|gb|ADC41483.1| RNA polymerase beta subunit [Streptomyces griseobrunneus]
 gi|286142910|gb|ADC41485.1| RNA polymerase beta subunit [Streptomyces bacillaris]
 gi|286142912|gb|ADC41486.1| RNA polymerase beta subunit [Streptomyces vinaceus]
 gi|286142922|gb|ADC41491.1| RNA polymerase beta subunit [Kitasatospora mediocidica]
 gi|286142926|gb|ADC41493.1| RNA polymerase beta subunit [Streptomyces floridae]
 gi|286142928|gb|ADC41494.1| RNA polymerase beta subunit [Streptomyces roseochromogenes]
 gi|286142958|gb|ADC41509.1| RNA polymerase beta subunit [Streptomyces sp. CB157]
 gi|286142962|gb|ADC41511.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142964|gb|ADC41512.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142974|gb|ADC41517.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142976|gb|ADC41518.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142982|gb|ADC41521.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142988|gb|ADC41524.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142990|gb|ADC41525.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142992|gb|ADC41526.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286143010|gb|ADC41535.1| RNA polymerase beta subunit [Streptomyces puniceus]
          Length = 185

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 143/192 (74%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + 
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YTTYRIAKFMRSNQGTSVNQKVVVSEGDRIVADQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|286142898|gb|ADC41479.1| RNA polymerase beta subunit [Streptomyces olivoviridis]
          Length = 185

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 144/192 (75%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A+++G+V++V A  I + 
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKSGVVQEVSADYITVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V  GD V  + ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YTTYRIAKFSRSNQGTSVNQKVVVSEGDRVIESQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|117667770|gb|ABK55931.1| RNA polymerase B subunit [Streptomyces cirratus]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT++V YL+A EE+   IAQAN+ L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVDGVVTDEVDYLTADEEDRFVIAQANAGLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFTENRVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G +I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDSIKAEKDGVVQEVSADYITVANDDG 175


>gi|208609711|dbj|BAG72317.1| RNA polymerase II second largest subunit [Actinodaphne malaccensis]
          Length = 167

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIERIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.13,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|91981516|gb|ABE68100.1| RNA polymerase subunit B [Pseudomonas sp. Q13-87]
          Length = 149

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 81/149 (54%), Positives = 108/149 (72%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL 
Sbjct: 1   QNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  
Sbjct: 61  AYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAA 676
           R   E  +   E +  +D SPKQVVS+AA
Sbjct: 121 RHLNEFTVKAPEDVTLMDVSPKQVVSVAA 149


>gi|50058709|gb|AAT69107.1| RNA polymerase II [Ipomoea pes-tigridis]
          Length = 215

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 36/89 (40%), Positives = 48/89 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 127  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 186

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
             +PSRM +GQ+ E  +G     +GK+  +
Sbjct: 187  AIPSRMTIGQLIECIMGKVAAHMGKEGDA 215



 Score = 69.7 bits (169), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 14/129 (10%)

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSE 870
             + GYN EDS+++++  +    F S+    +    +      +E        +   +  
Sbjct: 1   ACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRH 60

Query: 871 EGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLR 930
                +D+ G+   G  V+  D+++GK TP  +           A         RD S  
Sbjct: 61  GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHSTS 111

Query: 931 VPSGVSGTV 939
           +    +G V
Sbjct: 112 LRHSETGMV 120


>gi|286142908|gb|ADC41484.1| RNA polymerase beta subunit [Streptomyces microflavus]
 gi|286142914|gb|ADC41487.1| RNA polymerase beta subunit [Streptomyces microflavus]
 gi|286142916|gb|ADC41488.1| RNA polymerase beta subunit [Streptomyces alboviridis]
 gi|286142918|gb|ADC41489.1| RNA polymerase beta subunit [Streptomyces microflavus]
 gi|286142924|gb|ADC41492.1| RNA polymerase beta subunit [Streptomyces albidus]
          Length = 185

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 142/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + 
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V  GD V    ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YTTYRIAKFMRSNQGTSVNQKVVVSEGDRVIAEQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|225698427|gb|ACO07331.1| RpoB [Pasteurellaceae bacterium B96/4]
          Length = 160

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 92/160 (57%), Positives = 117/160 (73%), Gaps = 1/160 (0%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N+L+ +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIG
Sbjct: 1   LSQFMDQNNALAEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSF 640
           L+++L +FAR N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF
Sbjct: 61  LINTLATFARTNKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSF 120

Query: 641 TEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
             ELV  RC GE  + P E+I ++D S +Q+VS+AA+LIP
Sbjct: 121 ATELVPARCGGETGMFPPERISYMDVSAQQIVSVAAALIP 160


>gi|157000399|gb|ABV00499.1| RNA polymerase subunit B [Streptomyces clavifer]
          Length = 180

 Score =  156 bits (395), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 96/175 (54%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGIVTDDVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|286142806|gb|ADC41433.1| RNA polymerase beta subunit [Streptomyces platensis]
 gi|286142820|gb|ADC41440.1| RNA polymerase beta subunit [Streptomyces platensis]
          Length = 185

 Score =  156 bits (394), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 107/192 (55%), Positives = 140/192 (72%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  I + 
Sbjct: 1   ANRALMGSNMMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYITVA 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T  NQ+ +V  G  V    ++ADGPSTD G++A
Sbjct: 61  NDDGT-------YTTYRVAKFTRSNQGTSFNQKVVVDEGARVIEGQVLADGPSTDEGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLSDLDE 185


>gi|117667766|gb|ABK55929.1| RNA polymerase B subunit [Streptomyces cyaneus]
          Length = 180

 Score =  156 bits (394), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV  G VT++V YL+A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVTGGVVTDEVDYLTADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   V  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFAENRVLVRRRGGEVDYVAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTANDDG 175


>gi|117667798|gb|ABK55945.1| RNA polymerase B subunit [Streptomyces griseolus]
          Length = 180

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP  ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|318085040|gb|ADV39410.1| RNA polymerase subunit B [Streptomyces acidiscabies]
          Length = 180

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIEGIVTDDVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFTENRVLVRRRGGEVDYVPGDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKPGVVQEVSADYITTANDDG 175


>gi|13430397|gb|AAK25821.1| RNA polymerase beta subunit [Helicobacter cinaedi]
          Length = 162

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 90/162 (55%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
            RVN  GFIE PY+KV +G VT+++VYL+A +EE   IA A++++D+DG   E+L+  R 
Sbjct: 61  TRVNDLGFIEAPYKKVENGIVTDEIVYLTAAQEEGLVIAPASTAVDKDGRIIEDLIETRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  + ++  ID SP+ +V +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILLGEKSRVQLIDLSPRMLVGVAASLIPFLEHDDANRAL 162


>gi|307576839|gb|ADN53021.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576863|gb|ADN53033.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576867|gb|ADN53035.1| RNA polymerase beta subunit [Haemophilus parasuis]
 gi|307576869|gb|ADN53036.1| RNA polymerase beta subunit [Haemophilus parasuis]
          Length = 157

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 90/157 (57%), Positives = 114/157 (72%), Gaps = 1/157 (0%)

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
            SQLSQ  +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG 
Sbjct: 1   HSQLSQFMDQNNPLSEVTHKRRISALGSGGLTRERAGFEVRDVHTTHYGRLCPIETPEGP 60

Query: 579 NIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
           NIGL++SL+ +AR N YGF+ETP+RKV +G+VT ++ YLSA+EE    IAQANS+LDE  
Sbjct: 61  NIGLINSLSVYARTNNYGFLETPFRKVVNGQVTEEIEYLSAIEEGAYVIAQANSNLDESF 120

Query: 639 SFTEELVFCR-CAGEEILVPREKIDFIDASPKQVVSI 674
            FT+  V CR   GE  L   E+I ++D S +QVVS+
Sbjct: 121 RFTDTYVTCRGEHGESGLYRPEEIHYMDVSTQQVVSV 157


>gi|117667740|gb|ABK55916.1| RNA polymerase B subunit [Streptomyces microflavus]
 gi|117667760|gb|ABK55926.1| RNA polymerase B subunit [Streptomyces alboviridis]
 gi|117667792|gb|ABK55942.1| RNA polymerase B subunit [Streptomyces microflavus]
 gi|117667794|gb|ABK55943.1| RNA polymerase B subunit [Streptomyces microflavus]
          Length = 180

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 93/175 (53%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYITADEEDRFVIAQANAILSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|11595836|emb|CAC18346.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|11595838|emb|CAC18347.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
 gi|11595840|emb|CAC18348.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 147

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 86/148 (58%), Positives = 112/148 (75%), Gaps = 1/148 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V DG+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKDGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHDD 147


>gi|50058741|gb|AAT69123.1| RNA polymerase II [Jacquemontia tamnifolia]
          Length = 215

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 36/90 (40%), Positives = 48/90 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 126  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 185

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             +PSRM +GQ+ E  +G     +GK+  + 
Sbjct: 186  AIPSRMTIGQLIECIMGKVAAHMGKEGDAS 215



 Score = 68.6 bits (166), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 14/128 (10%)

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEE 871
              GYN EDS+++++  +    F S+    +    +      +E        +   +   
Sbjct: 1   CHSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHG 60

Query: 872 GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
               +D+ G+   G  V+  D+++GK TP  +           A         RD    +
Sbjct: 61  SYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQAARYTKRDHXTSL 111

Query: 932 PSGVSGTV 939
               +G V
Sbjct: 112 RHSETGMV 119


>gi|318085046|gb|ADV39413.1| RNA polymerase subunit B [Streptomyces scabiei]
 gi|318085056|gb|ADV39418.1| RNA polymerase subunit B [Streptomyces europaeiscabiei]
          Length = 180

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V +G VT++V YL+A EE+   IAQAN++LD+
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTEGVVTDEVDYLTADEEDRFVIAQANATLDD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++AG+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVKAEKAGVVQEVSADYITTTNDDG 175


>gi|50058711|gb|AAT69108.1| RNA polymerase II [Merremia vitifolia]
          Length = 213

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 37/90 (41%), Positives = 49/90 (54%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 124  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 183

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             +PSRM +GQ+ E  +G     +GK+  +L
Sbjct: 184  AIPSRMTIGQLIECIMGKVAAHMGKEGDAL 213



 Score = 68.2 bits (165), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 46/126 (36%), Gaps = 14/126 (11%)

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +    F S+    +    +      +E        +   +     
Sbjct: 1   SGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSY 60

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G+   G  V+  D+++GK TP  +           A         RD S  +  
Sbjct: 61  DKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTKRDHSTSLRH 111

Query: 934 GVSGTV 939
             +G V
Sbjct: 112 SETGMV 117


>gi|145307886|gb|ABP57247.1| RNA polymerase II second largest subunit [Pandora delphacis]
          Length = 260

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 51/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 121

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  +      R++          ++     +  +   + +   
Sbjct: 122  PGTRVSGDDIIIGKTAPVPPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ-- 179

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 180  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 221

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 222  FNGEGMVPDLVINPHAIPSRMTIGHMVECLVGKVGTLAG 260



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHTKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|283132431|dbj|BAI63621.1| rpoB protein [Corynebacterium accolens]
          Length = 128

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 49/156 (31%), Positives = 79/156 (50%), Gaps = 36/156 (23%)

Query: 1130 RMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYD 1189
            RMN+GQ+ E HLGW     G K+ +     +   +   L++  E++    + +       
Sbjct: 1    RMNIGQVLELHLGWLAHA-GWKVDT-----EDPANAELLKTLPEELYDVPADSLT----- 49

Query: 1190 DDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESG--------QSILYDGLT 1241
                             +TPVFDGA    I  +L  +  +  G        ++ L+DG +
Sbjct: 50   -----------------ATPVFDGATNHEIERLLASSRPNRDGDVLVNEHGKATLFDGRS 92

Query: 1242 GEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
            GEP+  P++VGY+YMLKL+H+V +K++ARSTG YS+
Sbjct: 93   GEPYKYPISVGYMYMLKLHHLVDEKIHARSTGPYSM 128


>gi|145307878|gb|ABP57244.1| RNA polymerase II second largest subunit [Erynia ovispora]
          Length = 252

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 50/271 (18%), Positives = 86/271 (31%), Gaps = 21/271 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    I+ R  +D+ ++S   E E  E   R                   I  G      
Sbjct: 62   LF-RSIYYRTYLDQEKKSGMNEVESFEKPTRKTTLRLRHGTYEKLEDDGLIAPGTRVSGD 120

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  D      R++          ++     +  +   + +           
Sbjct: 121  DIIIGKTAPVPPDSEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ---------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 171  ----------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFNAEGIVP 220

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            D+V+NP  +PSRM +G + E  +G      G
Sbjct: 221  DLVINPHAIPSRMTIGHMVECLVGKVSTLDG 251



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 66/179 (36%), Gaps = 19/179 (10%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PLV                     +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGI 881
           +++++  +   +F SI+   +    + + +   E            +     + +++ G+
Sbjct: 51  VIMNQSSIDRGLFRSIYYRTYLDQEKKSGMNEVESFEKPTRKTTLRLRHGTYEKLEDDGL 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 111 IAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHTKRDVSTPLKSTETGIVDRVM 165


>gi|151564516|gb|ABS17617.1| RpoB [Campylobacter canadensis]
          Length = 170

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 94/170 (55%), Positives = 127/170 (74%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIGL++SL
Sbjct: 1   DQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           +++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  ++L+ 
Sbjct: 61  STYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNIIDDLLE 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG NM
Sbjct: 121 ARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMGPNM 170


>gi|6449162|gb|AAF08851.1| RNA polymerase beta subunit [Streptococcus intermedius]
          Length = 170

 Score =  156 bits (394), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 79/174 (45%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSELVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             +S + L        +   +  +G           + L    +AE +V+ ETG
Sbjct: 117 TADSSRSLLIARFFDARRYDLAAVGRYKINKKLNIKNRLLNQTIAEPLVDPETG 170



 Score = 54.3 bits (129), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSELVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAD 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD+ +YDL+ VGR K+N +LN+      + I
Sbjct: 120 SSRSLLIARFFDARRYDLAAVGRYKINKKLNIKNRLLNQTI 160


>gi|286142812|gb|ADC41436.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142814|gb|ADC41437.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142816|gb|ADC41438.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142822|gb|ADC41441.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142824|gb|ADC41442.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142826|gb|ADC41443.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142878|gb|ADC41469.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142880|gb|ADC41470.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142882|gb|ADC41471.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142890|gb|ADC41475.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142894|gb|ADC41477.1| RNA polymerase beta subunit [Streptomyces sp. DSM 40932]
 gi|286142900|gb|ADC41480.1| RNA polymerase beta subunit [Streptomyces anulatus]
 gi|286142902|gb|ADC41481.1| RNA polymerase beta subunit [Streptomyces reticuli]
 gi|286142920|gb|ADC41490.1| RNA polymerase beta subunit [Streptomyces albovinaceus]
 gi|286142932|gb|ADC41496.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142938|gb|ADC41499.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142942|gb|ADC41501.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142954|gb|ADC41507.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142956|gb|ADC41508.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142960|gb|ADC41510.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142972|gb|ADC41516.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142984|gb|ADC41522.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142986|gb|ADC41523.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142996|gb|ADC41528.1| RNA polymerase beta subunit [Streptomyces griseus]
          Length = 185

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 143/192 (74%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + 
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V  GD +  + ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YTTYRIAKFMRSNQGTSVNQKVVVSEGDRIIADQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|115253023|emb|CAJ55537.1| DNA-directed RNA polymerase beta chain [Mycoplasma capricolum
           subsp. capricolum]
          Length = 163

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 91/163 (55%), Positives = 124/163 (76%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIASR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|117667752|gb|ABK55922.1| RNA polymerase B subunit [Nocardiopsis dassonvillei subsp.
           dassonvillei]
          Length = 180

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 92/178 (51%), Positives = 130/178 (73%), Gaps = 1/178 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL ++ RVN++GF+ETPYR++ DGKV++ V YL+A EE+   IAQAN+ ++ 
Sbjct: 1   GPNIGLIGSLAAYGRVNSFGFVETPYRRIIDGKVSDQVDYLTADEEDLHVIAQANTPMNP 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           DGSF E  V  R  G E   V  +++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DGSFAEAGVLVRRKGGEFEQVSTDEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
           MQRQAVPLL AE+PFVGTGME   A  +G  ++A++AG+VE V A  + + + +G   
Sbjct: 121 MQRQAVPLLMAESPFVGTGMEYRAATDAGEVVLAQKAGVVEDVTADYVTVMADDGTRK 178


>gi|219564017|gb|ACL28192.1| RNA polymerase II second largest subunit [fungal sp. M68]
          Length = 250

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 52/274 (18%), Positives = 93/274 (33%), Gaps = 27/274 (9%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 59

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
            +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G        
Sbjct: 60   LFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVSGEDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D                +E  QR    +K    T     E+   +++   
Sbjct: 117  IIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVDQVLI- 160

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      LR VKV +   +  Q GDK A RHG KG +      EDMPF   G   D+
Sbjct: 161  ----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFSCQGIVPDL 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKS 1154
            ++NP  +PSRM +  + E  L       G +  +
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVSTLRGLEGDA 250



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 3   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 52

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 53  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 112

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 113 GEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 162


>gi|302903611|ref|XP_003048895.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256729829|gb|EEU43182.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 1195

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 72/174 (41%), Gaps = 3/174 (1%)

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            + I +   +          R     +IG    +              A         STP
Sbjct: 899  RLIGAETGNEPLQTISVKFRVPRSPIIGDKFSSRHGQKGVASQKWPTAGALHGLAQDSTP 958

Query: 1210 V-FDGADE--EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
              FD  +   +     L  A  +  G   +Y G+TGE     + +G +Y  +L HMV+DK
Sbjct: 959  FKFDEENTAADYFGHQLMKAGYNYHGNEPMYSGITGEELAADIYIGVVYYQRLRHMVNDK 1018

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
               R+TG     T QP+ G+   GG R+GEME   + A+G A++LQ+ L   SD
Sbjct: 1019 YQVRTTGPVVPTTGQPIKGRKRGGGIRVGEMERDALLAHGTAFLLQDRLLNCSD 1072



 Score =  101 bits (251), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 121/946 (12%), Positives = 261/946 (27%), Gaps = 195/946 (20%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFS------GAAMLEFVSYEFDP 83
           I     S++     +  P      GL       F                + +       
Sbjct: 40  INPHIESFNGLFRDDGKPGL-LTHGLADIGTKTFLDGDERAGPQGKNRLTIRYKDVFLQK 98

Query: 84  PK------------FDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
           P+                +C  R +TY   L  TL   +   D     +           
Sbjct: 99  PQVPPSNKMARNRQIFPAECRERHVTYRGRLSATLEYRINGGDPIEFVRE---------- 148

Query: 132 MGDLPLMTKD------------------------GTFVIKGIQRIVVSQLHRSPGIHFDH 167
            G +P+M K                         G F++ GI++ ++  L  +       
Sbjct: 149 FGQVPIMIKSNRCHLEGNSPALLVERKEESEELGGYFIVNGIEK-IIRMLQLNKRNFPMA 207

Query: 168 DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIH--------VRIDRRRK---VPVTS 216
               +  +    Y    I  + +  D E    +++H         R   R+    +PV  
Sbjct: 208 INRPSFQNRGPGYTPYGIILRAVRPD-ETSQTNVLHYLNDGNMTFRFSWRKNEYLIPVMM 266

Query: 217 FLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIE 275
            L AL   ++ EI                           VG+K + +    D  E ++ 
Sbjct: 267 ILKALVETNDREI--------------------FEGLVGPVGSKSTENTFLTDRIELLLR 306

Query: 276 SGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEE 335
           + K          +    +   +    + G  V + + N + G  ++    ++   +++ 
Sbjct: 307 TYKSYNLYSKSETRAYLGEKFRV----VLG--VPDTMSNLDVGTEFLRRIVLVHLGNVDV 360

Query: 336 IFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESM 395
               +     +L        A +      D                 P  V    +    
Sbjct: 361 TEEQDNEKFKLLLFMIRKLYALVAGECAVD----------------NPDAVQNQEILLGG 404

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F +     ++ D                       +      ++   L            
Sbjct: 405 FLYGQILKERLD---------------------EFLSVNVRASLRDYL----------RR 433

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
              +         +   N +R     +  +++  +S+ ++ S    DL            
Sbjct: 434 NPTVPFTSEDFRKDFPNNIFRKANENLGNALEYFLSTGNMQSPSGLDLQQ---------- 483

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
              ++  + + E +N L  I+H R    + +G          +R + P  +G +CP  T 
Sbjct: 484 ---TAGFTVVAEKLNFLRFISHFR---MVHRGAFFAQLKTTAVRKLLPESWGFMCPVHTP 537

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
           +G   GL++ L    ++       +    +        V   SA  EEN  +        
Sbjct: 538 DGAPCGLLNHLAHKCKIMTDSVDVSHIAAL--AAELGIVDVSSASTEENVVV-------- 587

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSI--AASLIPFLENDDSNRVLMG 693
                 +  +   C  +E +   +   +        V +      +P         + M 
Sbjct: 588 ----MLDGKILGFCTPKESVRIADCFRYWKVEGTHGVPLQLEIGYVPPSHGGSYPGIYMT 643

Query: 694 C---NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIV-----AKRAGIVEQVDAIRIVI 745
                M R    L   +  +VG          S A +       K   +      +  ++
Sbjct: 644 STPARMVRPVKYLPLQKEDWVG---PYEQPYMSIAVVPQEVESGKSTHVEFDPTNMLSIL 700

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLV-KVGDEVRRNDII----ADGPST 800
            ++    D + S  ++Y+    +++      N R         ++             + 
Sbjct: 701 ANMTPFSDFNQSPRNMYQCQMGKQTMGTPSTNLRYRTDNKSYRIQTGQTPVVRAPLHNTY 760

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +   G N +VA + + GY+ +D+M++++             +  ++  +D       
Sbjct: 761 GFDNFPNGMNAVVAVISYTGYDMDDAMILNKSAHERGFGHGTIYKTKKISLKDDSRTKAT 820

Query: 861 I-------TRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
                         VS      +D+ G+  VG  +  GD++    T
Sbjct: 821 KSVTKAFGFAPHSYVSASYQGMLDDDGLPHVGRMIQEGDVICAWHT 866



 Score = 61.2 bits (147), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 75/235 (31%), Gaps = 30/235 (12%)

Query: 899  TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSIS 958
            +P+        ++ +            + S R+ +G +  V    + N +G D     ++
Sbjct: 712  SPRNMYQCQMGKQTMGTPSTNLRYRTDNKSYRIQTGQTPVVRAP-LHNTYGFDNFPNGMN 770

Query: 959  VEREQIELLARDKDDEQVILDRNIYSR---LMEILCGQNAVSGPKGFKKSTVLSSDLISE 1015
                 I     D DD  +IL+++ + R      I   +          K+T   +     
Sbjct: 771  AVVAVISYTGYDMDD-AMILNKSAHERGFGHGTIYKTKKISLKDDSRTKATKSVTKAFGF 829

Query: 1016 YPRSQW---WQFAVQDEKVQRNVESLKV------------QYETSKSILEDRFKNKIEKI 1060
             P S     +Q  + D+ +      ++              Y      L+     +  K 
Sbjct: 830  APHSYVSASYQGMLDDDGLPHVGRMIQEGDVICAWHTVTPDYNGKLVNLDGITHYEKYKD 889

Query: 1061 QW----------GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                        G +     L+ + V   + R    GDK + RHG KG+ S+  P
Sbjct: 890  GETGFVEEVRLIGAETGNEPLQTISVKFRVPRSPIIGDKFSSRHGQKGVASQKWP 944


>gi|115253005|emb|CAJ32587.1| DNA-directed RNA polymerase subunit B [Mycoplasma capricolum subsp.
           capripneumoniae]
 gi|115253025|emb|CAJ55538.1| DNA-directed RNA polymerase beta chain [Mycoplasma capricolum
           subsp. capripneumoniae]
 gi|115253027|emb|CAJ55539.1| DNA-directed RNA polymerase beta chain [Mycoplasma capricolum
           subsp. capripneumoniae]
          Length = 163

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 91/163 (55%), Positives = 123/163 (75%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E +  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDETIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|208609803|dbj|BAG72363.1| RNA polymerase II second largest subunit [Litsea garciae]
          Length = 167

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 48/93 (51%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMIIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 44.7 bits (104), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGIV 65


>gi|115253003|emb|CAJ32586.1| DNA-directed RNA polymerase subunit B [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|115253072|emb|CAK12512.1| DNA-directed RNA polymerase beta chain [Mycoplasma capricolum
           subsp. capricolum]
          Length = 163

 Score =  156 bits (393), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 91/163 (55%), Positives = 124/163 (76%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMAKVEEIHYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|225698433|gb|ACO07334.1| RpoB [Gallibacterium sp. TIS16289]
          Length = 153

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 88/153 (57%), Positives = 112/153 (73%), Gaps = 1/153 (0%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++S
Sbjct: 1   MDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+ +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V
Sbjct: 61  LSVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTFV 120

Query: 646 FCR-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
             R   GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 TARGEHGESGLYRPEDIHYMDISTQQVVSVAAA 153


>gi|208609869|dbj|BAG72396.1| RNA polymerase II second largest subunit [Neolitsea cassia]
          Length = 167

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 47/93 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDM +  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMSWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164



 Score = 46.6 bits (109), Expect = 0.033,   Method: Composition-based stats.
 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+ GD+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGGDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|117667738|gb|ABK55915.1| RNA polymerase B subunit [Streptomyces anulatus]
 gi|117667764|gb|ABK55928.1| RNA polymerase B subunit [Streptomyces albovinaceus]
 gi|117667778|gb|ABK55935.1| RNA polymerase B subunit [Streptomyces praecox]
 gi|117667802|gb|ABK55947.1| RNA polymerase B subunit [Streptomyces griseinus]
 gi|117667806|gb|ABK55949.1| RNA polymerase B subunit [Streptomyces mediolani]
          Length = 180

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|115252985|emb|CAJ32577.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri LC]
 gi|115252987|emb|CAJ32578.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri LC]
 gi|115252989|emb|CAJ32579.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri LC]
 gi|115252991|emb|CAJ32580.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri LC]
 gi|115252993|emb|CAJ32581.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri]
 gi|115252995|emb|CAJ32582.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri]
 gi|115252997|emb|CAJ32583.1| DNA-directed RNA polymerase subunit B [Mycoplasma mycoides subsp.
           capri]
 gi|115253009|emb|CAJ55530.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           mycoides SC]
 gi|115253011|emb|CAJ55531.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           mycoides SC]
 gi|115253013|emb|CAJ55532.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           mycoides SC]
 gi|115253058|emb|CAK12505.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri LC]
 gi|115253060|emb|CAK12506.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri LC]
 gi|115253062|emb|CAK12507.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri LC]
 gi|115253064|emb|CAK12508.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri LC]
 gi|115253066|emb|CAK12509.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri]
 gi|115253068|emb|CAK12510.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri]
 gi|115253070|emb|CAK12511.1| DNA-directed RNA polymerase beta chain [Mycoplasma mycoides subsp.
           capri]
          Length = 163

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 92/163 (56%), Positives = 125/163 (76%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|55650690|emb|CAF31396.1| RNA polymerase B subunit [Anabaena sp. PCC 7108]
          Length = 196

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 91/193 (47%), Positives = 126/193 (65%), Gaps = 3/193 (1%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDIPLDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDAAEIRVRV 123

Query: 748 VEGDLDPSTSGVDI---YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
            E   + +T        Y L K+QRSNQ+TC+NQ+PLV+ G++V    ++ADG  T+ G+
Sbjct: 124 REPLTETNTQHPPKEVRYVLSKYQRSNQDTCLNQKPLVRTGEKVVAGQVLADGSFTEGGE 183

Query: 805 LALGRNMLVAFMP 817
           LALG+N++VA+MP
Sbjct: 184 LALGQNIVVAYMP 196


>gi|117667754|gb|ABK55923.1| RNA polymerase B subunit [Streptomyces bobili]
          Length = 180

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 90/175 (51%), Positives = 123/175 (70%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ R+N +GFIETPYRKV  G VT++V YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRINPFGFIETPYRKVTGGVVTDEVDYLTADEEDRFVIAQANAPLSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F E  V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EFQFEEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRSAVDAGDVVRAEKDGVVQEVSADYITTANDDG 175


>gi|11595818|emb|CAC18337.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 147

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 86/148 (58%), Positives = 112/148 (75%), Gaps = 1/148 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHDD 147


>gi|269912634|emb|CAY86097.1| RNA polymerase beta subunit [Gluconobacter frateurii]
          Length = 150

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 60/144 (41%), Positives = 82/144 (56%), Gaps = 26/144 (18%)

Query: 173 SLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMAL----------- 221
             SGK L+A R+IP +G W+D EFD+KD+I+VRIDR+RK+PVT+ L AL           
Sbjct: 1   HSSGKYLFAARVIPYRGSWLDFEFDAKDLIYVRIDRKRKLPVTTLLYALEGANYIAQRDR 60

Query: 222 --------------GMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
                         GMD +EILS FY  + +++ GD W  P        G K+ S LVD 
Sbjct: 61  KIAEGGDVEGLDIRGMDQDEILSYFYDMVPFTRMGDGWARPFEPE-AFRGQKLLSPLVDA 119

Query: 268 DTGEQVIESGKKLTSGLLKSLKEK 291
           DTGE V E+  KLT+ +++ + EK
Sbjct: 120 DTGEVVAEADAKLTARMVRKIAEK 143


>gi|187372796|gb|ACD03135.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372798|gb|ACD03136.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372800|gb|ACD03137.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372802|gb|ACD03138.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372804|gb|ACD03139.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372806|gb|ACD03140.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372808|gb|ACD03141.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
 gi|187372810|gb|ACD03142.1| DNA-directed RNA polymerase subunit beta [Campylobacter
           cuniculorum]
          Length = 169

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 94/168 (55%), Positives = 126/168 (75%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++
Sbjct: 1   MDQTNPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINT 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+++A+VN  GF+E PY+KV +GK++N+VVYL+A +EE  +IA A++ +D  G+  EE V
Sbjct: 61  LSTYAKVNDLGFVEAPYKKVINGKISNEVVYLTATQEEGLFIAPASTKIDAKGNIIEEFV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             R  GE +LV RE++  ID     VV +AASLIPFLE+DD+NR LMG
Sbjct: 121 EARQDGETMLVKREEVQLIDLCSGMVVGVAASLIPFLEHDDANRALMG 168


>gi|145307923|gb|ABP57265.1| RNA polymerase II second largest subunit [Furia gastropachae]
          Length = 261

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 121

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  D      R++          ++     +  +   + +   
Sbjct: 122  PGTRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 179

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 180  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 221

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 222  FSAEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 260



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|260594053|gb|ACX46321.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 81/158 (51%), Positives = 112/158 (70%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           S+LS+ +   + L  ITH RR+SALG  G+ R RAG E+RDVHPTHYGR+C  ET EG N
Sbjct: 1   SRLSRFKGQDDPLFEITHKRRVSALGPSGLTRERAGFEVRDVHPTHYGRVCSIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKTV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|207721916|ref|YP_002252354.1| dna-directed rna polymerase beta chain (partial sequence c terminus)
            protein [Ralstonia solanacearum MolK2]
 gi|206587085|emb|CAQ17669.1| probable dna-directed rna polymerase beta chain (partial sequence c
            terminus) protein [Ralstonia solanacearum MolK2]
          Length = 70

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 47/70 (67%), Positives = 60/70 (85%)

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYE+IV G  + + G PESFNVLVKE+++
Sbjct: 1    MEVWALEAYGASYVLQEMLTVKSDDVNGRTKVYENIVKGEHSIDAGMPESFNVLVKEIRS 60

Query: 1357 LGLSIDLENS 1366
            LG+ IDLE +
Sbjct: 61   LGIDIDLERN 70


>gi|117667714|gb|ABK55903.1| RNA polymerase B subunit [Streptomyces californicus]
 gi|117667724|gb|ABK55908.1| RNA polymerase B subunit [Streptomyces ornatus]
 gi|117667728|gb|ABK55910.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|117667736|gb|ABK55914.1| RNA polymerase B subunit [Streptomyces griseus subsp. griseus]
 gi|117667758|gb|ABK55925.1| RNA polymerase B subunit [Streptomyces erumpens]
 gi|117667762|gb|ABK55927.1| RNA polymerase B subunit [Streptomyces fimicarius]
 gi|117667768|gb|ABK55930.1| RNA polymerase B subunit [Streptomyces acrimycini]
 gi|117667788|gb|ABK55940.1| RNA polymerase B subunit [Streptomyces caviscabies]
 gi|117667816|gb|ABK55954.1| RNA polymerase B subunit [Streptomyces floridae]
 gi|157000391|gb|ABV00495.1| RNA polymerase subunit B [Streptomyces baarnensis]
 gi|157000401|gb|ABV00500.1| RNA polymerase subunit B [Streptomyces flavofuscus]
 gi|157000423|gb|ABV00511.1| RNA polymerase subunit B [Streptomyces puniceus]
 gi|220961102|gb|ACL93017.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|220961104|gb|ACL93018.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|220961106|gb|ACL93019.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|220961108|gb|ACL93020.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|220961110|gb|ACL93021.1| RNA polymerase B subunit [Streptomyces griseus]
 gi|220961112|gb|ACL93022.1| RNA polymerase B subunit [Streptomyces griseus]
          Length = 180

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 129/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANATLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|115252999|emb|CAJ32584.1| DNA-directed RNA polymerase subunit B [Mycoplasma leachii PG50]
 gi|115253001|emb|CAJ32585.1| DNA-directed RNA polymerase subunit B [Mycoplasma sp. serogroup L]
 gi|115253019|emb|CAJ55535.1| DNA-directed RNA polymerase beta chain [Mycoplasma leachii]
          Length = 163

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 91/163 (55%), Positives = 124/163 (76%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMARVEEIHYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|198279413|emb|CAP04741.1| RNA polymerase beta subunit [Pinus jaliscana]
          Length = 266

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 97/238 (40%), Positives = 146/238 (61%), Gaps = 10/238 (4%)

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG+  +A + G +E +DA+                       + +QRSN NTC +
Sbjct: 1   QAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTH 52

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED
Sbjct: 53  QKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYED 112

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           ++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK
Sbjct: 113 IYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGK 172

Query: 898 ITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           +TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR  NR     +
Sbjct: 173 LTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVDDSGD 230



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 86/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 57   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 115

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 116  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 169

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 170  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 227

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+ GRHGNKGI+S +LP
Sbjct: 228  SGDNAE-----TVHVYISQKRKIQVGDKVXGRHGNKGIISIVLP 266


>gi|117667786|gb|ABK55939.1| RNA polymerase B subunit [Streptomyces aureus]
          Length = 180

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV +G VT+DV YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVVEGVVTDDVDYLTADEEDRFVIAQANAGLGE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  FTE  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DMRFTENRVLVRRRGGEIDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITTANDDG 175


>gi|117667750|gb|ABK55921.1| RNA polymerase B subunit [Streptomyces cyaneofuscatus]
 gi|157000395|gb|ABV00497.1| RNA polymerase subunit B [Streptomyces griseus]
          Length = 180

 Score =  156 bits (393), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 95/175 (54%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANAILSE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|117667746|gb|ABK55919.1| RNA polymerase B subunit [Streptomyces venezuelae]
          Length = 180

 Score =  155 bits (392), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 92/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++LDE
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANAALDE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  F+E  V  R  G E   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFSENRVLVRKRGGEVDYVEPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V+++ A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQELSADYITVANDDG 175


>gi|312204356|gb|ADQ47495.1| RNA polymerase II second largest subunit [Porina aenea]
          Length = 694

 Score =  155 bits (392), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 30/106 (28%), Positives = 43/106 (40%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 L  VKV +   +  Q GDK A RHG KG +      EDMPF   G   D+++NP 
Sbjct: 579  TNAEGLPFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSAQGITPDLIINPH 638

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +  + E  +       G +  +          +S     
Sbjct: 639  AIPSRMTIAHLIECQISKVASLSGFEGDATPFTDITVDQVSXXXRK 684



 Score = 73.2 bits (178), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/231 (14%), Positives = 71/231 (30%), Gaps = 22/231 (9%)

Query: 474 QYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---------- 521
            +R+   ++ + +   +               + +  + + +     +            
Sbjct: 1   LFRIQFQKLYKDVSXYLKKCVESGKEFNLTLGVKSTTLTNGLKYSLATGNWGEQKKASSA 60

Query: 522 ---LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGH 578
              +SQ+       + ++H RR +      + R     + R +H TH+G +CPAET EG 
Sbjct: 61  TAGVSQVLSRYTFAATLSHLRRTNT----PLGREGKIAKPRQLHNTHWGLVCPAETPEGQ 116

Query: 579 NIGLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
             GLV +L     +      E    +    + +V  +     A      ++      +  
Sbjct: 117 ACGLVKNLALMCYITVGSPSEPIVEFMIQRNMEVLEEFEPTRAPHSTKVFVNGVWVGVHR 176

Query: 637 DGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDD 686
           D +    ++        I      + D  D   K          P    D+
Sbjct: 177 DPTHLVRVMQQLRRSGTISPEVSLVRDIRDREFKIFTDGGRVCRPLFVIDN 227



 Score = 50.8 bits (120), Expect = 0.002,   Method: Composition-based stats.
 Identities = 44/358 (12%), Positives = 91/358 (25%), Gaps = 38/358 (10%)

Query: 362 LVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLN 421
                 K  KD    + + +  G    F++   + +    +  KY L   G      + +
Sbjct: 2   FRIQFQKLYKDVSXYLKKCVESG--KEFNLTLGVKSTTLTNGLKYSL-ATGNWGEQKKAS 58

Query: 422 LDTPDDVRHIRKEDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
             T    + + +    A +  L        R GK       +  +  +    E  + Q  
Sbjct: 59  SATAGVSQVLSRYTFAATLSHLRRTNTPLGREGKIAKPRQLHNTHWGLVCPAETPEGQAC 118

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPV--------VSAVCEFFCSSQLSQLEEH 528
             +  +       + S     V      N + +          +   F     +    + 
Sbjct: 119 GLVKNLALMCYITVGSPSEPIVEFMIQRNMEVLEEFEPTRAPHSTKVFVNGVWVGVHRDP 178

Query: 529 VNSLSRITHTRRLSALGQG-GVARARAGVEM-------RDVHPTHYGRICPAETSEGHNI 580
            + +  +   RR   +     + R     E        R   P       P    +G  +
Sbjct: 179 THLVRVMQQLRRSGTISPEVSLVRDIRDREFKIFTDGGRVCRPLFVIDNDPKSGKKGTLV 238

Query: 581 GLVSSLTSFARVNAYGFIE------TPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
                +                   + Y           V +L A EEE   IA     L
Sbjct: 239 LSKEHIKKLEEDGDLDDDMDPDEKASKYFGWNGLVKAGAVEFLDAEEEETVMIAMTPDDL 298

Query: 635 DEDGS--------FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
           +              +           +   ++     +  P  ++ I AS+ P  ++
Sbjct: 299 EISRQVQAGYELPELDPENPNARLKAPVRKSQQTWTHCEIHPSXILGICASIXPLPDH 356


>gi|50058723|gb|AAT69114.1| RNA polymerase II [Hildebrandtia valo]
          Length = 222

 Score =  155 bits (392), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 89/245 (36%), Gaps = 23/245 (9%)

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +        +F R   D+ ++  ++ +E      R 
Sbjct: 1    NAIVAIACYSGYNQEDSVIMNQSSIDRGFF-RSLFFRSYRDEEKKMGTLVKEDFGRPDRA 59

Query: 971  KDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEK 1030
                      +          G           K+T +S                  DE 
Sbjct: 60   NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ-----------------DEA 102

Query: 1031 VQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKM 1090
              ++    K  + TS    E    +++      D +     R VKV V   R  Q GDK 
Sbjct: 103  QGQSARYTKRDHSTSLRHSETGMVDQVLLTTNADGL-----RFVKVRVRSVRIPQIGDKF 157

Query: 1091 AGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGK 1150
            + RHG KG V      EDMP+  +G   DI+++P  +PSRM +GQ+ E  +G     +GK
Sbjct: 158  SSRHGQKGTVGMTYTQEDMPWTIEGITPDIIVSPHAIPSRMTIGQLIECIMGKVAAHMGK 217

Query: 1151 KIKSL 1155
            +  + 
Sbjct: 218  EGDAT 222



 Score = 75.5 bits (184), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 51/135 (37%), Gaps = 14/135 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----D 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRAN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP  +           A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDE---------AQGQSARYTK 111

Query: 925 RDTSLRVPSGVSGTV 939
           RD S  +    +G V
Sbjct: 112 RDHSTSLRHSETGMV 126


>gi|307147948|gb|ADN37850.1| DNA-directed RNA polymerase subunit beta [Mycobacterium triviale]
          Length = 101

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 41/76 (53%), Positives = 53/76 (69%)

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++
Sbjct: 1    AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEV 60

Query: 1364 ENSRTKNSAKMEEIPD 1379
             +S        E   D
Sbjct: 61   LSSDGAAIELREGEDD 76


>gi|170696797|ref|ZP_02887905.1| RNA polymerase Rpb2 domain 7 [Burkholderia graminis C4D1M]
 gi|257137637|ref|ZP_05585899.1| DNA-directed RNA polymerase subunit beta [Burkholderia thailandensis
            E264]
 gi|170138298|gb|EDT06518.1| RNA polymerase Rpb2 domain 7 [Burkholderia graminis C4D1M]
          Length = 70

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 45/70 (64%), Positives = 60/70 (85%)

Query: 1297 MEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQA 1356
            MEVW ++AYGA+YVLQEMLT+KSDDV GRT+VYE++V G+   + G PESFNVLVKE+++
Sbjct: 1    MEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRS 60

Query: 1357 LGLSIDLENS 1366
            LG+ IDL+ +
Sbjct: 61   LGIDIDLDRN 70


>gi|117667810|gb|ABK55951.1| RNA polymerase B subunit [Streptomyces tanashiensis]
          Length = 180

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 91/175 (52%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANAALND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   V    +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELQFTEARVLVRKRGGEVDYVEPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V+++ A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQELSADYITVANDDG 175


>gi|307147876|gb|ADN37802.1| DNA-directed RNA polymerase subunit beta [Mycobacterium asiaticum]
 gi|307147879|gb|ADN37804.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium subsp.
            avium ATCC 25291]
 gi|307147900|gb|ADN37818.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gordonae]
 gi|307147903|gb|ADN37820.1| DNA-directed RNA polymerase subunit beta [Mycobacterium haemophilum]
 gi|307147909|gb|ADN37824.1| DNA-directed RNA polymerase subunit beta [Mycobacterium interjectum]
 gi|307147912|gb|ADN37826.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            intracellulare ATCC 13950]
 gi|307147915|gb|ADN37828.1| DNA-directed RNA polymerase subunit beta [Mycobacterium kansasii ATCC
            12478]
 gi|307147918|gb|ADN37830.1| DNA-directed RNA polymerase subunit beta [Mycobacterium malmoense]
 gi|307147927|gb|ADN37836.1| DNA-directed RNA polymerase subunit beta [Mycobacterium scrofulaceum]
 gi|307147933|gb|ADN37840.1| DNA-directed RNA polymerase subunit beta [Mycobacterium simiae]
 gi|307147936|gb|ADN37842.1| DNA-directed RNA polymerase subunit beta [Mycobacterium simiae]
 gi|307147942|gb|ADN37846.1| DNA-directed RNA polymerase subunit beta [Mycobacterium szulgai]
 gi|307147957|gb|ADN37856.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium]
 gi|307147960|gb|ADN37858.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            intracellulare]
 gi|307147963|gb|ADN37860.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            intracellulare]
 gi|307147966|gb|ADN37862.1| DNA-directed RNA polymerase subunit beta [Mycobacterium kansasii]
 gi|307147969|gb|ADN37864.1| DNA-directed RNA polymerase subunit beta [Mycobacterium marinum]
 gi|307147978|gb|ADN37870.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium]
 gi|307147981|gb|ADN37872.1| DNA-directed RNA polymerase subunit beta [Mycobacterium avium]
 gi|307147990|gb|ADN37878.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gordonae]
 gi|307147993|gb|ADN37880.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gordonae]
 gi|307147996|gb|ADN37882.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            intracellulare]
 gi|307147999|gb|ADN37884.1| DNA-directed RNA polymerase subunit beta [Mycobacterium kansasii]
 gi|307148002|gb|ADN37886.1| DNA-directed RNA polymerase subunit beta [Mycobacterium kansasii]
 gi|307148005|gb|ADN37888.1| DNA-directed RNA polymerase subunit beta [Mycobacterium microti]
 gi|312166135|gb|ADQ39032.1| DNA-directed RNA polymerase subunit beta [Mycobacterium africanum]
 gi|312166145|gb|ADQ39038.1| DNA-directed RNA polymerase subunit beta [Mycobacterium gastri]
          Length = 101

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 42/81 (51%), Positives = 55/81 (67%), Gaps = 1/81 (1%)

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++
Sbjct: 1    AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEV 60

Query: 1364 ENSRTKNSAKME-EIPDFNKC 1383
             +S        E E  D  + 
Sbjct: 61   LSSDGAAIELREGEDEDLERA 81


>gi|55650684|emb|CAF31393.1| RNA polymerase B subunit [Anabaena sp. 202A1]
          Length = 199

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 89/196 (45%), Positives = 126/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPHVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ S   IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSRMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA+MP
Sbjct: 184 GGELALGQNIVVAYMP 199


>gi|117667734|gb|ABK55913.1| RNA polymerase B subunit [Streptomyces exfoliatus]
          Length = 180

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 89/175 (50%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT++V Y++A EE+   IAQAN++L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVIDGQVTDEVDYVTADEEDRFVIAQANAALND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +   TE  V  R  G E   V   ++D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRLTENRVLVRKRGGEVDYVLPSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V+++ A  + + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQELSADYVTVANDDG 175


>gi|117667780|gb|ABK55936.1| RNA polymerase B subunit [Streptomyces subrutilus]
 gi|220961224|gb|ACL93078.1| RNA polymerase B subunit [Streptomyces albidoflavus]
          Length = 180

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 128/175 (73%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYRKV DG VT+DV YL+A EE+   IAQAN+ L++
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRKVIDGVVTDDVDYLTADEEDRFVIAQANAGLND 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   +  + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  EMRFTENRVLVRRRGGEIDYIAGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAEAP VGTGME   A  +G +I A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKAEAPLVGTGMEYRCAVDAGDSIRAEKDGVVQEVSADYITVANDDG 175


>gi|117667712|gb|ABK55902.1| RNA polymerase B subunit [Streptomyces luridiscabiei]
          Length = 180

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 127/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG+VT+DV Y++A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDDVDYITADEEDRFVIAQANAILSD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           +  FTE  V  R  G E   VP   +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  ELRFTEPRVLVRRRGGEVDYVPGTDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + + +G
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVTNDDG 175


>gi|55650694|emb|CAF31398.1| RNA polymerase B subunit [Nodularia sphaerocarpa HKVV]
          Length = 187

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 88/190 (46%), Positives = 127/190 (66%), Gaps = 6/190 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  +DE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDIPVDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  +V++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVVVSRTDGDVTYVDATEIRVRP 123

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             G+ +        YRL K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG +T+ G+LAL
Sbjct: 124 KGGNSET------RYRLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSATEGGELAL 177

Query: 808 GRNMLVAFMP 817
           G+N+++A+MP
Sbjct: 178 GQNIVLAYMP 187


>gi|50058749|gb|AAT69127.1| RNA polymerase II [Erycibe hellwigii]
          Length = 210

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 37/90 (41%), Positives = 48/90 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 121  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 180

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             +PSRM +GQ+ E  +G     +GK+   L
Sbjct: 181  AIPSRMTIGQLIECIMGKVAAHMGKEGDVL 210



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 44/123 (35%), Gaps = 14/123 (11%)

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNI 876
           N EDS+++++  +    F S+    +    +      +E        +   +       +
Sbjct: 1   NQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKL 60

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D+ G+   G  V+  D+++GK TP  +           A         RD S  +    +
Sbjct: 61  DDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTKRDHSTSLRHSET 111

Query: 937 GTV 939
           G V
Sbjct: 112 GIV 114


>gi|55650696|emb|CAF31399.1| RNA polymerase B subunit [Nodularia sphaerocarpa PCC 7804]
          Length = 187

 Score =  155 bits (392), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 88/190 (46%), Positives = 127/190 (66%), Gaps = 6/190 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  +DE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDIPVDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  +V++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVVVSRTDGDVTYVDATEIRVRP 123

Query: 748 VEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             G+ +        YRL K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG +T+ G+LAL
Sbjct: 124 KGGNSE------IRYRLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSATEGGELAL 177

Query: 808 GRNMLVAFMP 817
           G+N+++A+MP
Sbjct: 178 GQNIVLAYMP 187


>gi|295682710|gb|ADG26784.1| RNA polymerase beta subunit [Sarcocystis neurona]
          Length = 303

 Score =  155 bits (391), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 114/304 (37%), Gaps = 42/304 (13%)

Query: 975  QVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRN 1034
              I  ++ Y++      G     G K  + + +++   + +   S      +      + 
Sbjct: 38   LEIPKQSSYNKKFLDFLGI-VKEGVKILQNNILITKIKVLKSSCSYLPLIKLIYSIFGQE 96

Query: 1035 VESLKVQ---YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            + +++      ++ KS    + +  +            V    ++F+  +R +  GDK+ 
Sbjct: 97   IRNIQDNSLYIQSGKSGKVSKIELFLLNKNSLGKQANTVYLKCRIFICRQRFLTIGDKLC 156

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
            GR+GNKGI+S I    D+P+L +    DI++  LG+PSRMN+GQ+ E+  G        +
Sbjct: 157  GRYGNKGILSYIAENVDLPYLPNSYYPDIIVGALGIPSRMNLGQLLESLFGKISFLSDIR 216

Query: 1152 IKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVF 1211
            I  + +       IS     +       +  +K                           
Sbjct: 217  I--MPSFSLHTNTISNYLKTIIYNYLINNKIKKSF------------------------- 249

Query: 1212 DGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARS 1271
                     + L    +   G+  L DG TG      V  G     KL HM+ DK++ R+
Sbjct: 250  ---------NWLYNPYIP--GKFCLRDGRTGSKLKLSVFCGVARYSKLIHMIKDKLHYRT 298

Query: 1272 TGSY 1275
            TG Y
Sbjct: 299  TGPY 302



 Score = 51.6 bits (122), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 38/115 (33%), Positives = 67/115 (58%), Gaps = 2/115 (1%)

Query: 827 MLISERMVSEDVFTSIHIEEFEVMA-RDTKLGPEEITRDIPNVSEEGLKNIDECGIICVG 885
           +++S++++ + +FTS+HI+ +E+    + K G E  T +IP  S    K +D  GI+  G
Sbjct: 1   LIVSKKVLYQQLFTSLHIDIYEINFSYNKKTGIEFSTLEIPKQSSYNKKFLDFLGIVKEG 60

Query: 886 AEVNPGDILVGKI-TPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
            ++   +IL+ KI   K      P  KL+ +IFG++  +++D SL + SG SG V
Sbjct: 61  VKILQNNILITKIKVLKSSCSYLPLIKLIYSIFGQEIRNIQDNSLYIQSGKSGKV 115


>gi|256600048|gb|ACV04764.1| DNA-dependent RNA-polymerase beta-subunit [Pasteurellaceae
           bacterium 69]
          Length = 153

 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 90/153 (58%), Positives = 115/153 (75%), Gaps = 1/153 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDE+  FT+  V  R
Sbjct: 61  YARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDENFRFTDAYVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
              GE  L   E+I ++D S +QVVS+AA+LIP
Sbjct: 121 GEHGESGLYRPEEIQYMDVSTQQVVSVAAALIP 153


>gi|164452769|gb|ABY57221.1| RpoB [Tortella arctica]
          Length = 267

 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 97/239 (40%), Positives = 154/239 (64%), Gaps = 9/239 (3%)

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
           GTG+ES  A  SG+  +AK++G +   D  +I + +       +   +       +QRSN
Sbjct: 1   GTGLESQAALDSGSIAIAKQSGKIIYTDGKKISLLNANKKSTNTDLII-------YQRSN 53

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
            +T ++Q+  V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISE
Sbjct: 54  NSTYMHQKARVTQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAILISE 113

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPG 891
           R++ +D++TSIHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V  G
Sbjct: 114 RLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWVETG 173

Query: 892 DILVGKITPKGESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
           D+LVGK+TP+        PE KLL+AIFG +    ++T L+VP G  G V+DVR   + 
Sbjct: 174 DVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIYKK 232



 Score = 75.1 bits (183), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 70/184 (38%), Gaps = 16/184 (8%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS-ISVEREQIE-----LLARDKDDEQVIL 978
            ++  +           D  + +   I K+  + I +ER +I+             E   L
Sbjct: 91   KNILVAYMPWEGYNFEDAILISERLIYKDIYTSIHIERYEIKSRTTSQGPEKITKEIPHL 150

Query: 979  DRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNV 1035
            + ++   L +   ++ G    +G     K T   ++     P  +  Q     +      
Sbjct: 151  ENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQETEESLRAPEGKLLQAIFGIQVATAKE 210

Query: 1036 ESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHG 1095
              LKV       +++ R+  K E             + + V++A KR IQ GDK+AGRHG
Sbjct: 211  TCLKVPPGGKGRVIDVRWIYKKE-------NSNHSEKTIHVYIAQKRKIQVGDKVAGRHG 263

Query: 1096 NKGI 1099
            NKGI
Sbjct: 264  NKGI 267


>gi|284799226|gb|ADB93969.1| RNA polymerase II second largest subunit [Floricola striata]
          Length = 610

 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 94/673 (13%), Positives = 190/673 (28%), Gaps = 91/673 (13%)

Query: 472  KNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQ-------- 521
             + +R+  L++ + +    +    +      Q  +    + + +     +          
Sbjct: 4    CHLFRILFLKLTKDVFKYLQKCVENNTEFNVQMAVKGSVLTNGLKYSLATGNWGDQKKAA 63

Query: 522  -----LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
                 +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET E
Sbjct: 64   SAKAGVSQVLNRYTYASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPE 119

Query: 577  GHNIGLVSSLTSFARVNAY--GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            G   GLV +L+    V+        T Y      ++  +   +        ++       
Sbjct: 120  GQACGLVKNLSLMCYVSVGTESTPITDYMGQRQMELLEEYDPVVNPNATKVFVNGVWVGT 179

Query: 635  DEDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRV--L 691
                S   E V        +      I D  D   K        + P    ++ +     
Sbjct: 180  HNSPSQLVENVQALRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENRHNASNR 239

Query: 692  MGCNMQRQAVPLLKAEAPFVGTGME-SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
                + +  +  L ++     +G      AK   +       G++E +DA       +  
Sbjct: 240  GQLALNKGHIQQLLSDKEVDTSGYNDEDTAKMKYSWRGLIHNGVIEYLDAEEEETAMIVM 299

Query: 751  DLDPSTSGVDIYRLMKFQRSNQNTCVNQ-RPLVKVGDEVRRNDIIADGPSTDLGDLALGR 809
              +      D+ + +            + +P  +    +R        PS  LG      
Sbjct: 300  SPEDLEEHRDLMQGIPAADVPDEDRHKRIKP--QPNPSIRMYTHCEIHPSMILG------ 351

Query: 810  NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVS 869
             +  +  P+  +N     L +  M  + +  ++                           
Sbjct: 352  -ICASIXPFPDHNQSPVTLTNXAMGKQAMGVALTKFTLXXXXXXXXF------------- 397

Query: 870  EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                                        +       +   +  + AI      +  D  +
Sbjct: 398  ----------------NYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQEDXLI 441

Query: 930  RVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME- 988
               S +   +    +F R   ++ +R   +    +E   +    + + L    Y +L + 
Sbjct: 442  MNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEKXEKPTRGDTLRLKGGTYDKLDDD 497

Query: 989  --ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSK 1046
              +  G           K+    +D      ++           ++     +  Q     
Sbjct: 498  GVVAPGVRVSGDDIIIGKTAPXPTDAKELGQKTTMHTKRDVSTPLRSTENGIVDQ----- 552

Query: 1047 SILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPC 1106
                                    LR VKV     +  Q GDK A RHG KG +      
Sbjct: 553  ---------------VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQ 597

Query: 1107 EDMPFLKDGTPVD 1119
            EDMPF ++G   D
Sbjct: 598  EDMPFTREGLTPD 610



 Score = 93.6 bits (231), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 79/617 (12%), Positives = 174/617 (28%), Gaps = 70/617 (11%)

Query: 339 SEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFN 397
           S      IL++  + +   Y++  +  +   + + A+         G V T  +  S+  
Sbjct: 2   SHCHLFRILFLKLTKDVFKYLQKCVENNTEFNVQMAV--------KGSVLTNGLKYSLAT 53

Query: 398 FLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRNGKGTIDD 455
             + D  K   +  G  ++  R    +      R          +     L N    +  
Sbjct: 54  GNWGDQKKAASAKAGVSQVLNRYTYASTLSHLRRTNTPVGRDGKLAKPRQLHNTHWGLVC 113

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
                  +   + + L     + +      I + +    ++ +   D +           
Sbjct: 114 PAETPEGQACGLVKNLSLMCYVSVGTESTPITDYMGQRQMELLEEYDPVVNPNATKVF-- 171

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
                 +         +  +   RR   L             +RD+    +     A   
Sbjct: 172 -VNGVWVGTHNSPSQLVENVQALRRNGTLSY-------EMSLIRDIRDREFKIFTDAGRV 223

Query: 576 EGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
                 + +   +    +  G +      +       +V      +E+   +  +   L 
Sbjct: 224 MRPLFVVENRHNA----SNRGQLALNKGHIQQLLSDKEVDTSGYNDEDTAKMKYSWRGLI 279

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
            +G                      I+++DA  ++   I  S     E+ D  + +   +
Sbjct: 280 HNG---------------------VIEYLDAEEEETAMIVMSPEDLEEHRDLMQGIPAAD 318

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           +  +         P     M     +   + I+   A I    D  +  +      +   
Sbjct: 319 VPDEDRHKRIKPQPNPSIRM-YTHCEIHPSMILGICASIXPFPDHNQSPVTLTNXAMGKQ 377

Query: 756 TSGVDIYRLM-KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
             GV + +               Q+PL                      +L  G+N +VA
Sbjct: 378 AMGVALTKFTLXXXXXXXXFNYPQKPL----------ATTRSMEYLKFRELPAGQNAIVA 427

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVS 869
              + GYN ED +++++  +   +F S+    +    +   +   E        D   + 
Sbjct: 428 IACYSGYNQEDXLIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEKXEKPTRGDTLRLK 487

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D+ G++  G  V+  DI++GK  P         +K             RD S 
Sbjct: 488 GGTYDKLDDDGVVAPGVRVSGDDIIIGKTAPXPTDAKELGQKT-------TMHTKRDVST 540

Query: 930 RVPSGVSGTVVDVRIFN 946
            + S  +G V  V    
Sbjct: 541 PLRSTENGIVDQVLFTT 557


>gi|225698401|gb|ACO07318.1| RpoB [Pasteurellaceae bacterium TIS2494]
          Length = 152

 Score =  155 bits (391), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 87/152 (57%), Positives = 113/152 (74%), Gaps = 1/152 (0%)

Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
           +  N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL
Sbjct: 1   DQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSL 60

Query: 587 TSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           + +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDED  FT+  V 
Sbjct: 61  SVYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDEDLRFTDAYVT 120

Query: 647 CR-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
            R   GE  L   E+I ++D S +QVVS+AA+
Sbjct: 121 ARGEHGESGLYRPEEIHYMDVSTQQVVSVAAA 152


>gi|6449137|gb|AAF08841.1| RNA polymerase beta subunit [Streptococcus oralis ATCC 35037]
          Length = 170

 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 78/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGITS--------DCLCGLYVAEDIVNGETG 318
             ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVTTRLLNQTIAEPLVDPETG 170



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSELVRNTVEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 120 SSRSLLVARFFDPRRYDLAAVGRYKINKKLNVTTRLLNQTI 160


>gi|13430391|gb|AAK25818.1| RNA polymerase beta subunit [Helicobacter cinaedi]
 gi|13430393|gb|AAK25819.1| RNA polymerase beta subunit [Helicobacter fennelliae]
 gi|13430395|gb|AAK25820.1| RNA polymerase beta subunit [Helicobacter fennelliae]
          Length = 162

 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS ITH RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL++++++F
Sbjct: 1   NPLSEITHKRRLSALGEGGLVKERVGFEARDVHPTHYGRICPIETPEGQNIGLINTISTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
             VN  GFIE PYRKV +GKVT+++VYL+A +E+ + IA A++ LD+D    + L+  RC
Sbjct: 61  TLVNDLGFIEAPYRKVVNGKVTDEIVYLTATQEDGKVIAPASTQLDKDNKIIDSLIETRC 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE  L   E ++ ID SP+ +V +AASLIPFLE+DD+NR L
Sbjct: 121 GGEITLRKTEDVELIDLSPRMLVGVAASLIPFLEHDDANRAL 162


>gi|50058719|gb|AAT69112.1| RNA polymerase II [Odonellia hirtiflora]
          Length = 202

 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 36/88 (40%), Positives = 47/88 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 115  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 174

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIK 1153
             +PSRM +GQ+ E  +G     +GK+  
Sbjct: 175  AIPSRMTIGQLIECIMGKVAAHMGKEGD 202



 Score = 58.2 bits (139), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/117 (15%), Positives = 39/117 (33%), Gaps = 14/117 (11%)

Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGII 882
           ++++  +    F S+    +    +      +E        +   +       +D+ G+ 
Sbjct: 1   IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMGMRHGSYDKLDDDGLA 60

Query: 883 CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
             G  V+  D+++GK TP  +           A         RD S  +    +G V
Sbjct: 61  PPGTRVSGEDVIIGKTTPISQDD---------AQGQSARYTKRDHSTSLRHSETGIV 108


>gi|4972795|gb|AAD34793.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            pametensis]
          Length = 178

 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 45/104 (43%), Positives = 61/104 (58%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTI SDD  GR R Y++I  G    E+  PE+F V
Sbjct: 1    GGQRFGEMEVWALEAYGAAHTLKEMLTITSDDTDGRVRAYKAITRGEPVGESEIPETFYV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIP--------DFNKCEL 1385
            L KE+Q+LG  +++           + +         DFN  +L
Sbjct: 61   LSKELQSLGSDVNVYGDEKDEDGNPQLLSIKEDGRPKDFNAFQL 104


>gi|55650678|emb|CAF31390.1| RNA polymerase B subunit [Anabaena flos-aquae 14]
          Length = 199

 Score =  155 bits (391), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 90/196 (45%), Positives = 127/196 (64%), Gaps = 6/196 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFMP 817
            G+LALG+N++VA++P
Sbjct: 184 GGELALGQNIVVAYLP 199


>gi|22208409|emb|CAC87033.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 212

 Score =  154 bits (390), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 98/209 (46%), Positives = 144/209 (68%), Gaps = 14/209 (6%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--PDDV 428
            +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L    P   
Sbjct: 4   DEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITS 63

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLKNQYR 476
             + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+++NQ R
Sbjct: 64  STLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIR 123

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N LS +T
Sbjct: 124 VGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLT 183

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTH 565
           H RR+ ALG GG++R RAG+E+RDVHP+H
Sbjct: 184 HKRRMFALGPGGLSRERAGLEVRDVHPSH 212


>gi|289468059|gb|ADC95710.1| RpoB [Riemerella anatipestifer]
          Length = 164

 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 94/164 (57%), Positives = 117/164 (71%), Gaps = 2/164 (1%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+S
Sbjct: 1   FMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLIS 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           SL  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F  
Sbjct: 61  SLGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFET 120

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  R  G+  +V  E++D ID +P Q+  I+ASLIPFLE+DD
Sbjct: 121 ERIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPFLEHDD 164


>gi|260780687|ref|YP_003227091.1| RNA polymerase beta subunit [Bryopsis hypnoides]
 gi|260176765|gb|ACX33774.1| RNA polymerase beta subunit [Bryopsis hypnoides]
          Length = 1310

 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 58/306 (18%), Positives = 114/306 (37%), Gaps = 26/306 (8%)

Query: 121 SIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGK--- 177
             K I+ Q +++G+LPLMTK G F+I G  R++V+Q+ R+ G+++     +    G+   
Sbjct: 120 KKKKIRFQWVFLGNLPLMTKRGHFIINGAPRVIVNQIIRAAGVYYQQQVNKVIKKGQKQI 179

Query: 178 -LLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL------- 229
              +   II  +G+W+  E D K  I V + +  K+P+  FL  +G   + IL       
Sbjct: 180 YRTFYVDIISYRGVWLRFELDKKRQIWVCMKKTPKMPIFVFLKFMGFSKKNILSNVRNIQ 239

Query: 230 -STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSL 288
            + F    ++++   F+       +       +          Q+ + G      L   L
Sbjct: 240 PNFFKNTKMHTRNFLFYLTQNFQLEKTFNHTFTY---RKFLNPQIYDLGIMGRKRLNSKL 296

Query: 289 KEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILY 348
             +  K +   SD L             T  +            ++ + +  IR +  L 
Sbjct: 297 GLRTKKTILTPSDFL-----------KITYRLLDLTNHQDVVDDIDNLGNRRIRTVGELL 345

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
                   +  N ++ +K K  +              +  F  +  +  FL   +   +L
Sbjct: 346 KIQFFQATFRLNKILEEKIKKTESMDSIFTTRPMNSVLREFFGSCQLSQFLDQTNPLSEL 405

Query: 409 STVGRV 414
           +   R+
Sbjct: 406 THKRRI 411



 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 106/394 (26%), Positives = 179/394 (45%), Gaps = 21/394 (5%)

Query: 230 STFYPKIVYSQRGDFWCFPLSAA-DLMVGAKVSSSLVDIDTG---EQVIESGKKLTSGLL 285
             F+  ++   +     F      +L +  K    +++        Q+I +        +
Sbjct: 109 QIFFSFLLIHNKKKKIRFQWVFLGNLPLMTKRGHFIINGAPRVIVNQIIRAAGVYYQQQV 168

Query: 286 KSLKEKGVKFLGITS--DCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRD 343
             + +KG K +  T   D +    V       +  +I++             +       
Sbjct: 169 NKVIKKGQKQIYRTFYVDIISYRGVWLRFELDKKRQIWVCMKKTPKMPIFVFLKFMGFSK 228

Query: 344 IPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDS 403
             IL         + +NT      ++    L   +++         +   +     F + 
Sbjct: 229 KNILSNVRNIQPNFFKNT--KMHTRNFLFYLTQNFQL-------EKTFNHTFTYRKFLNP 279

Query: 404 DKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRR 463
             YDL  +GR ++N +L L T      +   D + I   L+DL N +  +DDIDNLGNRR
Sbjct: 280 QIYDLGIMGRKRLNSKLGLRT--KKTILTPSDFLKITYRLLDLTNHQDVVDDIDNLGNRR 337

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
           +R+VGE+LK Q+     R+ + ++E+I   +        +   +P+ S + EFF S QLS
Sbjct: 338 IRTVGELLKIQFFQATFRLNKILEEKIKKTES----MDSIFTTRPMNSVLREFFGSCQLS 393

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RR+S LG  G+ R  AG+++R +H T++GRICP ET EG N GLV
Sbjct: 394 QFLDQTNPLSELTHKRRISCLGPNGIQRETAGMDIRGIHSTYFGRICPIETPEGQNAGLV 453

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYL 617
           +SLT F+  NA GF+E+ + K+  G++   +  L
Sbjct: 454 NSLTIFSTKNADGFLESIFYKIYKGQIQKQLEPL 487


>gi|76781327|gb|ABA54549.1| RpoB [Campylobacter hominis]
          Length = 162

 Score =  154 bits (390), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 97/162 (59%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS ITH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEITHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG+VT++VVYL+A +EE R IA A++ LDE+G   E+L+  R 
Sbjct: 61  AKVNNLGFIEAPYKKVVDGRVTDEVVYLTATQEEGRVIASASAKLDENGRIVEDLLEARK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE I+  RE I  ID     V  +AASLIPFLE+DD+NR L
Sbjct: 121 NGETIMTKREDITLIDLCSGMVAGVAASLIPFLEHDDANRAL 162


>gi|289468077|gb|ADC95719.1| RpoB [Riemerella anatipestifer]
          Length = 164

 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 94/164 (57%), Positives = 117/164 (71%), Gaps = 2/164 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
            E +  R  G+  +V  E++D ID +P Q+  I+ASLIPFLE+D
Sbjct: 121 TERIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPFLEHD 164


>gi|6449117|gb|AAF08833.1| RNA polymerase beta subunit [Streptococcus anginosus]
          Length = 170

 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 77/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSDLVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             +S + L            +  +G             L    +AE +V+ ETG
Sbjct: 117 TADSSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKTRLLNQTIAEPLVDPETG 170



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSDLVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAD 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 120 SSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKTRLLNQTI 160


>gi|313494724|gb|ADR57499.1| RNA polymerase beta subunit [Pinus thunbergii]
          Length = 246

 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 96/236 (40%), Positives = 144/236 (61%), Gaps = 10/236 (4%)

Query: 720 AKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
           A  SG+  +A + G +E +DA+                       + +QRSN NTC +Q+
Sbjct: 2   ALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTHQK 53

Query: 780 PLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
           P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED++
Sbjct: 54  PQIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIY 113

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKIT 899
           TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK+T
Sbjct: 114 TSFHIVRYRIEICMTSQGPERITREIPHLDAHLLRHLDENGLVMLGSWIETGDVLVGKLT 173

Query: 900 PK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           P+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR   R     +
Sbjct: 174 PQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWIIRVDDSGD 229


>gi|55650648|emb|CAF32195.1| RNA polymerase B subunit [Nostoc calcicola III]
          Length = 182

 Score =  154 bits (390), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 89/187 (47%), Positives = 122/187 (65%), Gaps = 6/187 (3%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           +  +DE G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR 
Sbjct: 2   DIPVDETGHIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRA 61

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R    
Sbjct: 62  LMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPN 121

Query: 751 DLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRN 810
             +        Y L K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N
Sbjct: 122 TSE------IKYTLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQN 175

Query: 811 MLVAFMP 817
           ++VA+MP
Sbjct: 176 IVVAYMP 182


>gi|145307921|gb|ABP57264.1| RNA polymerase II second largest subunit [Zoophthora radicans]
          Length = 258

 Score =  154 bits (389), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 50/277 (18%), Positives = 92/277 (33%), Gaps = 27/277 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 5    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 64

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 65   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 120

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  +      R++          ++     +  +   + +   
Sbjct: 121  PGTRVSGDDIIIGKTAPVPPESEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 178

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 179  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 220

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
            F  +G   D+V+NP  +PSRM +G + E  +G     
Sbjct: 221  FSAEGIVPDLVINPHAIPSRMTIGHMVECLVGKVSTL 257



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 3   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 52

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 53  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 112

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 113 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHSKRDVSTPLKSTETGI 168

Query: 936 SGTVV 940
              V+
Sbjct: 169 VDRVM 173


>gi|145307902|gb|ABP57255.1| RNA polymerase II second largest subunit [Furia neopyralidarum]
          Length = 262

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 7    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQXDSVIMNQS 66

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 67   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 122

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  D      R++          ++     +  +   + +   
Sbjct: 123  PGTRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 180

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 181  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 222

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 223  FSGEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 261



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 67/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 5   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 54

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN  DS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 55  YNQXDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 114

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 115 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGI 170

Query: 936 SGTVV 940
              V+
Sbjct: 171 VDRVM 175


>gi|6449132|gb|AAF08839.1| RNA polymerase beta subunit [Streptococcus mitis]
          Length = 170

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 78/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTIAEPLVDPETG 170



 Score = 55.1 bits (131), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSELVRNTVEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 120 SSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTI 160


>gi|286143002|gb|ADC41531.1| RNA polymerase beta subunit [Streptomyces sp. E1002]
          Length = 185

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 105/192 (54%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I + 
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITVT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YR+ KF RSNQ T VNQ+ +V  G  V    ++ADGP+T+ G++A
Sbjct: 61  NDDGT-------YTTYRIAKFMRSNQGTSVNQKVVVSEGARVIAEQVLADGPATENGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFMPW G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|224177811|gb|ACN38877.1| RNA polymerase II subunit [Mycosphaerella pneumatophorae]
          Length = 594

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 98/613 (15%), Positives = 172/613 (28%), Gaps = 78/613 (12%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG   
Sbjct: 45   GVSQVLNRYTFASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPEGQAC 100

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L+  + V   G  +    Y       V  +   +    +   ++      +  + 
Sbjct: 101  GLVKNLSLMSYVTVGGQSDPLVEYMMQRGMLVLEEYDPVMNPGDTKVFVNGVWVGVHSEP 160

Query: 639  SFTEELVFCRCAGEEILVPREKIDFIDA---SPKQVVSIAASLIPFLEN-------DDSN 688
            +     V     G  +    E     D      K          P           +  +
Sbjct: 161  ARLVTNVKGIRRGGIVPQASETSMVWDIRDREFKIFTDAGRVCRPLFVIDTDPTSINKGS 220

Query: 689  RVLMGCNMQRQAVPLLKA---EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
             VL   ++ R  +        E     TG         G   V  + G+VE +DA     
Sbjct: 221  LVLNKSHIDRLLLEKDFNGNIEEIANATGEPLDDRYGGGWQHVLLQKGVVEYLDADEEET 280

Query: 746  RSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDL 805
              +    D       +       + + +T  ++R   K    VR        PS  LG  
Sbjct: 281  XMIIMTPDDLEEHHKMVAGEP--QYDDDTDPHKRVKSKPNPSVREYTHCEIHPSMILG-- 336

Query: 806  ALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI 865
                 +  + +P+  +N          M  + +   +                       
Sbjct: 337  -----VCASIIPFPDHNQSPRNTYQSAMGKQAMGMVL----------------------- 368

Query: 866  PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
                     N+    +  V             +       +   +  + AI      +  
Sbjct: 369  ------TNYNLRMDTMANVLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIACYSGYNQE 422

Query: 926  DTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSR 985
            D+ +   S +   +    +F R   D+ ++      E+ E   R           +    
Sbjct: 423  DSVVMNQSSIDRGLF-RSLFYRAYTDQEKKVGMATVEEFEKPIRSDTLRMKHGTYDKLDA 481

Query: 986  LMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETS 1045
               I  G           K+  ++ D      R++          ++     +  Q    
Sbjct: 482  DGIIAPGVRVSGEDIIIGKTAPIAPDAEELGQRTKMHTKRDVSTPLRSTENGIVDQVLL- 540

Query: 1046 KSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
                                      + VKV     +  Q GDK A RHG KG +     
Sbjct: 541  -------------------TTNTEGNKFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYR 581

Query: 1106 CEDMPFLKDGTPV 1118
             EDMPF +DG   
Sbjct: 582  QEDMPFTRDGLTP 594


>gi|307147883|gb|ADN37807.1| DNA-directed RNA polymerase subunit beta [Mycobacterium celatum]
 gi|307147891|gb|ADN37812.1| DNA-directed RNA polymerase subunit beta [Mycobacterium fallax]
 gi|307147894|gb|ADN37814.1| DNA-directed RNA polymerase subunit beta [Mycobacterium flavescens]
 gi|307147897|gb|ADN37816.1| DNA-directed RNA polymerase subunit beta [Mycobacterium fortuitum]
 gi|307147921|gb|ADN37832.1| DNA-directed RNA polymerase subunit beta [Mycobacterium neoaurum]
 gi|307147930|gb|ADN37838.1| DNA-directed RNA polymerase subunit beta [Mycobacterium shimoidei]
 gi|307147939|gb|ADN37844.1| DNA-directed RNA polymerase subunit beta [Mycobacterium smegmatis]
 gi|307147945|gb|ADN37848.1| DNA-directed RNA polymerase subunit beta [Mycobacterium tokaiense]
 gi|307147951|gb|ADN37852.1| DNA-directed RNA polymerase subunit beta [Mycobacterium vaccae]
 gi|307147984|gb|ADN37874.1| DNA-directed RNA polymerase subunit beta [Mycobacterium sp.
            USFLOK0011]
 gi|307147987|gb|ADN37876.1| DNA-directed RNA polymerase subunit beta [Mycobacterium fortuitum]
 gi|312166140|gb|ADQ39035.1| DNA-directed RNA polymerase subunit beta [Mycobacterium fortuitum
            subsp. acetamidolyticum]
          Length = 101

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 42/83 (50%), Positives = 58/83 (69%), Gaps = 4/83 (4%)

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++
Sbjct: 1    AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEV 60

Query: 1364 ENSRTKNSAKMEEIPDFNKCELK 1386
             +S         E+ D +  +L+
Sbjct: 61   LSSDGAAI----EMRDGDDEDLE 79


>gi|297184764|gb|ADI20874.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit
           [uncultured gamma proteobacterium EB080_L93H08]
          Length = 185

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 100/180 (55%), Positives = 140/180 (77%)

Query: 414 VKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKN 473
           +K N R+   +      + KEDII+++K L+++RNG  ++DDID+LGNRR+R+VGEM +N
Sbjct: 1   MKFNRRIGRSSDKGDSVLSKEDIISVLKTLINIRNGSDSVDDIDHLGNRRIRTVGEMTEN 60

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
            +R+GL+R+ER++K+R+S V+ + +MP+DLIN+KPV +A+ EFF SSQLSQ  +  N LS
Sbjct: 61  AFRVGLVRVERAVKDRLSLVETEELMPRDLINSKPVSAAIKEFFGSSQLSQFMDQNNPLS 120

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            I H RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +ARVN
Sbjct: 121 EIAHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMAIYARVN 180


>gi|227826280|gb|ACP41867.1| RNA polymerase II [Agrostemma githago]
          Length = 231

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 36/102 (35%), Positives = 49/102 (48%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK +  HG KG V      EDMP+  +G   D ++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSXHGQKGTVGMTYTQEDMPWTVEGITPDXIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
             +PSRM +GQ+ E  +G     +GK+  +         +IS 
Sbjct: 190  AIPSRMTIGQLIECIMGKVAAHVGKEGDATPFTDVTVDNISK 231



 Score = 71.6 bits (174), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 53/136 (38%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +           +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEXKMGTLVKEDFGRPDRXN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++   TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIXXTTP-----LSPEE----AQGPAAXYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S  +    SG V+
Sbjct: 112 KDHSXSLRHSESGIVL 127


>gi|221112665|ref|XP_002157925.1| PREDICTED: similar to DNA-directed RNA polymerase III subunit RPC2,
            partial [Hydra magnipapillata]
          Length = 304

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 39/87 (44%), Positives = 54/87 (62%), Gaps = 4/87 (4%)

Query: 1241 TGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVW 1300
            T EP    + +G +Y  KL HMV DK++AR+ G  +++T+QP  G+S  GG RLGEME  
Sbjct: 18   TREPLSAYIYMGPVYYQKLKHMVLDKMHARAKGPRAVLTRQPTEGRSRDGGLRLGEMERD 77

Query: 1301 CIQAYGAAYVLQEMLTIKSD----DVV 1323
            C+  YGA+ ++ E L I SD    DV 
Sbjct: 78   CLIGYGASMLIVERLMISSDAFEIDVC 104


>gi|145307896|gb|ABP57252.1| RNA polymerase II second largest subunit [Pandora kondoiensis]
          Length = 262

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 7    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 66

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 67   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 122

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  D      R++          ++     +  +   + +   
Sbjct: 123  PGTRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 180

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 181  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 222

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 223  FSGEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 261



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 5   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 54

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 55  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 114

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 115 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGI 170

Query: 936 SGTVV 940
              V+
Sbjct: 171 VDRVM 175


>gi|11595832|emb|CAC18344.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 147

 Score =  154 bits (389), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 84/148 (56%), Positives = 112/148 (75%), Gaps = 1/148 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   +  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNQFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHDD 147


>gi|225698397|gb|ACO07316.1| RpoB [Pasteurellaceae bacterium TIS16433]
          Length = 151

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 88/151 (58%), Positives = 112/151 (74%), Gaps = 1/151 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QKNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQAN++LDED  FT+  V  
Sbjct: 61  VYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANANLDEDFRFTDAYVTA 120

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   GE  L   E+I ++D S +QVVS+AA+
Sbjct: 121 RGEHGESGLYRPEEIHYMDVSTQQVVSVAAA 151


>gi|297184757|gb|ADI20867.1| DNA-directed RNA polymerase, beta subunit/140 kD subunit [uncultured
            gamma proteobacterium EB080_L93H08]
          Length = 115

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 52/97 (53%), Positives = 66/97 (68%), Gaps = 9/97 (9%)

Query: 1206 VSTPVFDGADEEAINSMLRMADLDE--SGQSILYDGLTGEPFDRPVTV---GYIYMLKLN 1260
            ++TPVFDGADE  I S+L +       S Q+ L     GE  +  + +   GY+Y+LKLN
Sbjct: 1    MATPVFDGADEHEIKSLLTLXRFTREWSNQAXLM----GEVANFLIGLLQXGYMYILKLN 56

Query: 1261 HMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEM 1297
            H+V DK++ARSTG YSLVTQQPLGGK+  GGQR GEM
Sbjct: 57   HLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEM 93


>gi|15212086|emb|CAC51376.1| RNA polymerase beta subunit [Nicotiana sylvestris]
          Length = 329

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/191 (28%), Positives = 96/191 (50%), Gaps = 15/191 (7%)

Query: 66  TAFSGAAMLE-FVS-YEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIK 123
                    + FV  Y+   P     D ++  LTY+  L ++  LI          K+ +
Sbjct: 1   EDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVSAGLIW---------KNSR 51

Query: 124 DIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACR 183
           D++EQ+I++G++PLM   GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   
Sbjct: 52  DMQEQTIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYRSELDHNGIS---VYTGT 108

Query: 184 IIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRG 242
           II D G   ++E D K  I  R+ R++K+ +     A+G++  EIL    YP+I  S   
Sbjct: 109 IISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLS 168

Query: 243 DFWCFPLSAAD 253
           D     + + +
Sbjct: 169 DKERKKIGSKE 179



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 102/229 (44%), Gaps = 7/229 (3%)

Query: 296 LGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNN 355
           + + +  +   +     +  +             + S+  +  +   ++  +  +     
Sbjct: 102 ISVYTGTIISDWGGRSELEIDRKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPE 161

Query: 356 AYIRNTLVTDKNK--DRKDALLDIYRVMRP--GDVSTFSVAESMFNFLFFDSDKYDLSTV 411
            ++      ++ K   +++A+L+ Y+      GD              FF   + +L  +
Sbjct: 162 IFLSFLSDKERKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELGRI 220

Query: 412 GRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEML 471
           GR  MN RLNLD P +   +   DI+A    L+ L+ G G +DD+++L N+R+RSV ++L
Sbjct: 221 GRRNMNRRLNLDIPQNNTFLLPRDILAAADHLIGLKFGMGALDDMNHLKNKRIRSVADLL 280

Query: 472 KNQYRLGLLRMERSIKERISSVDIDSV--MPQDLINAKPVVSAVCEFFC 518
           ++Q+ L L+R+E  ++  I       +   PQ+L+ + P+ +    FF 
Sbjct: 281 QDQFGLALVRLENVVRGTICGAIRHKLIPTPQNLVTSTPLTTTYESFFG 329


>gi|91981472|gb|ABE68078.1| RNA polymerase subunit B [Pseudomonas sp. PITR2]
          Length = 147

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 80/147 (54%), Positives = 107/147 (72%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL +
Sbjct: 1   NNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++     +ELV  R
Sbjct: 61  YARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKVLIDELVAVR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIA 675
              E  +   E +  +D SPKQVVS+A
Sbjct: 121 HLNEFTVKAPEDVTLMDVSPKQVVSVA 147


>gi|289468045|gb|ADC95703.1| RpoB [Elizabethkingia meningoseptica]
          Length = 166

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 93/166 (56%), Positives = 117/166 (70%), Gaps = 2/166 (1%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIG
Sbjct: 1   LSQFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L+SSL  +A++N  GFIETPYRKV +GKV    D +YL+A +EE + IAQAN  L + G 
Sbjct: 61  LISSLGIYAKINNLGFIETPYRKVENGKVDLNADPIYLNAEDEEAKVIAQANVELSDSGD 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEND 685
           F  + +  R  G+  +V   ++D ID +P Q+  I+ASLIPFLE+D
Sbjct: 121 FETDRIIARLDGDYPVVEPGQVDLIDVAPNQISGISASLIPFLEHD 166


>gi|307147906|gb|ADN37822.1| DNA-directed RNA polymerase subunit beta [Mycobacterium hiberniae]
 gi|307147924|gb|ADN37834.1| DNA-directed RNA polymerase subunit beta [Mycobacterium
            nonchromogenicum]
          Length = 101

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 41/81 (50%), Positives = 53/81 (65%), Gaps = 1/81 (1%)

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++
Sbjct: 1    AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEV 60

Query: 1364 ENSRTKNSAKME-EIPDFNKC 1383
                       E E  D  + 
Sbjct: 61   LAKDGAAIELREGEDEDLERA 81


>gi|286143006|gb|ADC41533.1| RNA polymerase beta subunit [Streptomyces griseus]
          Length = 185

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 107/192 (55%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A+R G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAERDGVVQEVSADYITTT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+LG++A
Sbjct: 61  NDDGT-------YTTYRLAKFSRSNQGTSVNQKVVVDEGDRIIEGQVLADGPATELGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFM W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|145307900|gb|ABP57254.1| RNA polymerase II second largest subunit [Furia virescens]
          Length = 261

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 93/279 (33%), Gaps = 27/279 (9%)

Query: 874  KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
              +    +  +        +    +       +   +  + AI      +  D+ +   S
Sbjct: 6    YQLRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQS 65

Query: 934  GVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---IL 990
             +   +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I 
Sbjct: 66   SIDRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIA 121

Query: 991  CGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILE 1050
             G           K+  +  D      R++          ++     +  +   + +   
Sbjct: 122  PGTRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ-- 179

Query: 1051 DRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMP 1110
                                +R  KV V   R  Q GDK A RHG KG +      EDMP
Sbjct: 180  ------------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMP 221

Query: 1111 FLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
            F  +G   D+V+NP  +PSRM +G + E  +G      G
Sbjct: 222  FSGEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTLDG 260



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 68/185 (36%), Gaps = 19/185 (10%)

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
               ++           Q+PLV                     +L  G+N +VA   + G
Sbjct: 4   TNYQLRMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSG 53

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKN 875
           YN EDS+++++  +   +F SI+   +    + + L   E            +     + 
Sbjct: 54  YNQEDSVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEK 113

Query: 876 IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
           +++ G+I  G  V+  DI++GK  P         E+L +   G    DV        +G+
Sbjct: 114 LEDDGLIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGI 169

Query: 936 SGTVV 940
              V+
Sbjct: 170 VDRVM 174


>gi|55831377|gb|AAV66547.1| RNA polymerase II second largest subunit [Tilletiaria anomala]
          Length = 605

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 102/679 (15%), Positives = 201/679 (29%), Gaps = 96/679 (14%)

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L   +R+   ++ R I   +     +         + A  + + +     +
Sbjct: 2    KRLDMAGPLLAGLFRMLFRKLTRDIYRHLQKCVEEKKDFHISQAVKAATITNGLKYSIAT 61

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 62   GNWGDQKKFMQARAGVSQVLNRYTFASTLSHLRRCNT----PIGRDGKIAKPRQLHNTHW 117

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L+  + ++  G    P  +         +  +     +   
Sbjct: 118  GMVCPAETPEGQACGLVKNLSLMSTIS-VGSPSGPILEFLQSFNLESLEDMPIASNKATK 176

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLI----PFL 682
            +      L       +  VF R    +  +  E     D   K++     +       F+
Sbjct: 177  VFVNGVWLGTSDEPGQLAVFIRELRRKDDISAEVSMVHDIREKELRLYTDAGRVLRPLFI 236

Query: 683  ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKS-SGAAIVAKRAGIVEQVDAI 741
             ++D+  + M  +           +      G +   A+  S A I        E +DA 
Sbjct: 237  VDEDTMTLRMKRHHMDWLRNNSTPD------GQQWKWAEIVSNALI--------EYLDAE 282

Query: 742  RIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDE-VRRNDIIADGPST 800
                  +        +        K   +   +      LV       +        P+ 
Sbjct: 283  EEETVLICMSPQDLEASRAYNANPKSYAAQHASSDPSARLVSTAFFAPKTWTHCEIHPAM 342

Query: 801  DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             LG       +  + +P+  +N          M  + +   +++  +    R   +    
Sbjct: 343  ILG-------ICASIIPFPDHNQSPRNTYQSAMGKQAMG--VYLTNY--QMRMDTMSNIL 391

Query: 861  ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEK 920
                 P  +   ++++                             +   +  + AI    
Sbjct: 392  YYPQKPLATTRSMEHL-------------------------KFRELPAGQNAIVAILCYS 426

Query: 921  AVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDR 980
              +  D+ +   S +   +    ++ R   D  ++   +  E  E   RD          
Sbjct: 427  GYNQEDSVIMNQSSIDRGLF-RSLYYRTYTDMEKKLGVIHLESFEKPTRDTTLRMKHGTY 485

Query: 981  NIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKV 1040
            +       +  G           K+T L  D      R+                  +K 
Sbjct: 486  DKLDEDGLVAPGTRVSGEDIIIGKTTPLPPDSEELGLRNAM---------------HVKR 530

Query: 1041 QYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIV 1100
               T     E+   +++      D       R +KV V   R   +GDK A RHG KG +
Sbjct: 531  DVSTPLKSTENGIVDQVLVTVSHDHSQ----RFIKVRVHSTRVPHTGDKFASRHGQKGTI 586

Query: 1101 SRILPCEDMPFLKDGTPVD 1119
                  EDMPF  +G   D
Sbjct: 587  GITYRQEDMPFTTEGLTPD 605



 Score =  126 bits (316), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 84/594 (14%), Positives = 169/594 (28%), Gaps = 99/594 (16%)

Query: 376 DIYRVMRPG--DVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
           DIYR ++    +   F +++++      +  KY +   G      +         + + +
Sbjct: 25  DIYRHLQKCVEEKKDFHISQAVKAATITNGLKYSI-ATGNWGDQKKFMQARAGVSQVLNR 83

Query: 434 EDIIAIIKILVDL-----RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
               + +  L        R+GK       +  +  +    E  + Q    +  +      
Sbjct: 84  YTFASTLSHLRRCNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSTI 143

Query: 489 RISSVDIDSVMPQDLINAKPV-------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL 541
            + S     +      N + +         A   F     L   +E       I   RR 
Sbjct: 144 SVGSPSGPILEFLQSFNLESLEDMPIASNKATKVFVNGVWLGTSDEPGQLAVFIRELRRK 203

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
             +            +   ++      + P    +   + L         +      +  
Sbjct: 204 DDISAEVSMVHDIREKELRLYTDAGRVLRPLFIVDEDTMTLRMKRHHMDWLRNNSTPDGQ 263

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV----------FCRCAG 651
             K  +      + YL A EEE   I  +   L+   ++                     
Sbjct: 264 QWKWAEIVSNALIEYLDAEEEETVLICMSPQDLEASRAYNANPKSYAAQHASSDPSARLV 323

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFV 711
                  +     +  P  ++ I AS+IPF +++ S R      M +QA+ +        
Sbjct: 324 STAFFAPKTWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQM- 382

Query: 712 GTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSN 771
                                                      + S +  Y       + 
Sbjct: 383 ----------------------------------------RMDTMSNILYYPQKPLATTR 402

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
               +  R                        +L  G+N +VA + + GYN EDS+++++
Sbjct: 403 SMEHLKFR------------------------ELPAGQNAIVAILCYSGYNQEDSVIMNQ 438

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGA 886
             +   +F S++   +  M +   +   E            +       +DE G++  G 
Sbjct: 439 SSIDRGLFRSLYYRTYTDMEKKLGVIHLESFEKPTRDTTLRMKHGTYDKLDEDGLVAPGT 498

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            V+  DI++GK TP    P   EE  LR        DV        +G+   V+
Sbjct: 499 RVSGEDIIIGKTTP---LPPDSEELGLRNAM-HVKRDVSTPLKSTENGIVDQVL 548


>gi|55650588|emb|CAF32174.1| RNA polymerase B subunit [Anabaena flos-aquae 1tu31s11]
          Length = 193

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 89/193 (46%), Positives = 126/193 (65%), Gaps = 6/193 (3%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR 
Sbjct: 1   DVPLDENGYIKGPHVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRA 60

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-- 748
           LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+   
Sbjct: 61  LMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRASGQ 120

Query: 749 ----EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+
Sbjct: 121 LSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGE 180

Query: 805 LALGRNMLVAFMP 817
           LALG+N++VA+MP
Sbjct: 181 LALGQNIVVAYMP 193


>gi|11595820|emb|CAC18338.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 147

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 86/148 (58%), Positives = 111/148 (75%), Gaps = 1/148 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL +SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLFNSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHDD 147


>gi|208609751|dbj|BAG72337.1| RNA polymerase II second largest subunit [Lindera polyantha]
          Length = 167

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 47/93 (50%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV +   R  Q GDK + RHG KG V      EDM +  +G   DI++NP 
Sbjct: 72   TNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMLWTLEGITPDIIVNPH 131

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLIND 1158
             +PSRM +GQ+ E  +G     +GK+  +    
Sbjct: 132  AIPSRMTIGQLIECIMGKVAAHMGKEGDATSFT 164



 Score = 44.7 bits (104), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP G+                     RD 
Sbjct: 2   MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDET--------QQGQTSRYTRRDH 53

Query: 928 SLRVPSGVSGTV 939
           S  +    SG V
Sbjct: 54  STSLRHSESGMV 65


>gi|151564518|gb|ABS17618.1| RpoB [Campylobacter canadensis]
          Length = 168

 Score =  154 bits (388), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 92/168 (54%), Positives = 125/168 (74%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS +TH RRLSALG+GG+ + RA  E RDVH THYGRICP ET EG NIGL++S
Sbjct: 1   MDQTNPLSEVTHKRRLSALGEGGLVKERASFEARDVHTTHYGRICPVETPEGQNIGLINS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           L+++A+VN  GF+E PYRKV DGK+++++VYL+A +EE   IA A++ +DE+G+  ++L+
Sbjct: 61  LSTYAKVNDLGFVEAPYRKVVDGKISSEIVYLTATQEEGICIAPASTKVDENGNIIDDLL 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             R  GE IL  RE I  ID +   +V +AASLIPFLE++D+NR LMG
Sbjct: 121 EARIDGETILAKREDIGLIDLTSGAIVGLAASLIPFLEHNDANRALMG 168


>gi|115253015|emb|CAJ55533.1| DNA-directed RNA polymerase beta chain [Mycoplasma leachii]
 gi|115253017|emb|CAJ55534.1| DNA-directed RNA polymerase beta chain [Mycoplasma leachii]
 gi|115253021|emb|CAJ55536.1| DNA-directed RNA polymerase beta chain [Mycoplasma leachii]
          Length = 163

 Score =  154 bits (388), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 90/163 (55%), Positives = 123/163 (75%), Gaps = 1/163 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RD HP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDFHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 61  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             G++ +   E+I +ID SPKQ+VS+A S IPFLENDD+NR L
Sbjct: 121 FNGDDYMARVEEIHYIDVSPKQIVSVATSGIPFLENDDANRAL 163


>gi|46277360|gb|AAS86870.1| DNA-dependent RNA polymerase II [Peziza obtuspiculata]
          Length = 490

 Score =  154 bits (388), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 78/228 (34%), Gaps = 26/228 (11%)

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G       
Sbjct: 286  SLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGED 342

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  ++ +      R+++         ++     +  Q                  
Sbjct: 343  IIIGKTAPIAPNAEELGQRTKFHTKRDTSTPLRSTENGIVDQ------------------ 384

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   D
Sbjct: 385  --VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTSEGVVPD 442

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISP 1167
            I++NP  +PSRM +  + E  L       G +  +          +S 
Sbjct: 443  IIINPHAIPSRMTIAHLIECQLSKVSSLRGFEGDATPFTDVTVDSVSK 490



 Score = 53.2 bits (126), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 27/190 (14%), Positives = 48/190 (25%), Gaps = 13/190 (6%)

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE-- 573
           F     +    +    +  I   RR   +G               +         P    
Sbjct: 13  FVNGVWVGIHRDPGFIVRTIQKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVV 72

Query: 574 -----TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIA 628
                +     + L          +     E              V Y+ A EEE   I 
Sbjct: 73  DNDPASPRRGELVLQKHHIEKLEDDREIEDEGQRYGWQGLMTDGVVEYIDAEEEETVMIV 132

Query: 629 QANSSLDEDGSFT------EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
                L+    F       +E+   +     +          +  P  ++ I AS+IPF 
Sbjct: 133 MTPEDLETSRQFHAGYEIQQEIDPAQRVKAPLNKFAHTWTHCEIHPSMILGICASIIPFP 192

Query: 683 ENDDSNRVLM 692
           +++ S R   
Sbjct: 193 DHNQSPRNTY 202



 Score = 45.8 bits (107), Expect = 0.047,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 40/117 (34%), Gaps = 12/117 (10%)

Query: 841 SIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILV 895
           S+    +    +   +   E        +   +       +D+ G++  G  V+  DI++
Sbjct: 286 SLFFRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGEDIII 345

Query: 896 GKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           GK  P   +     ++        K    RDTS  + S  +G V  V +       K
Sbjct: 346 GKTAPIAPNAEELGQRT-------KFHTKRDTSTPLRSTENGIVDQVMVTTNQEGLK 395


>gi|76781271|gb|ABA54521.1| RpoB [Campylobacter sputorum]
          Length = 162

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 124/162 (76%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV DGKVTND+VYL+A++EE   IA A++ LD+ G+  +E++  R 
Sbjct: 61  AKVNDLGFVEAPYRKVVDGKVTNDIVYLTAIQEEGLVIAPASAKLDDKGNIVDEILEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILAKREEVSLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|145307870|gb|ABP57240.1| RNA polymerase II second largest subunit [Pandora blunckii]
 gi|145307892|gb|ABP57250.1| RNA polymerase II second largest subunit [Furia americana]
          Length = 252

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 51/275 (18%), Positives = 92/275 (33%), Gaps = 27/275 (9%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 2    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 61

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I  G
Sbjct: 62   DRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIAPG 117

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  D      R++          ++     +  +   + +     
Sbjct: 118  TRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ---- 173

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              +R  KV V   R  Q GDK A RHG KG +      EDMPF 
Sbjct: 174  ----------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFS 217

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
             +G   D+V+NP  +PSRM +G + E  +G     
Sbjct: 218  AEGMVPDLVINPHAIPSRMTIGHMVECLVGKVSTL 252



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 67/180 (37%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + + L   E            +     + +++ G
Sbjct: 53  SVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEKLEDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 113 LIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVM 168


>gi|20377913|gb|AAM20888.1| RopB [Campylobacter jejuni]
 gi|76781245|gb|ABA54508.1| RpoB [Campylobacter jejuni subsp. jejuni]
 gi|76781247|gb|ABA54509.1| RpoB [Campylobacter jejuni subsp. jejuni]
 gi|76781249|gb|ABA54510.1| RpoB [Campylobacter jejuni subsp. jejuni]
 gi|76781251|gb|ABA54511.1| RpoB [Campylobacter jejuni subsp. doylei]
 gi|307092470|gb|ADN28467.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092474|gb|ADN28469.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092476|gb|ADN28470.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092480|gb|ADN28472.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092482|gb|ADN28473.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092486|gb|ADN28475.1| RNA polymerase beta subunit [Campylobacter jejuni]
 gi|307092488|gb|ADN28476.1| RNA polymerase beta subunit [Campylobacter jejuni]
          Length = 162

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|11595830|emb|CAC18343.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 146

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 85/147 (57%), Positives = 111/147 (75%), Gaps = 1/147 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEND 685
           E +  +D SPKQVVS+AASLIPFLE+D
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHD 146


>gi|307092472|gb|ADN28468.1| RNA polymerase beta subunit [Campylobacter jejuni]
          Length = 162

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDTKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|225698443|gb|ACO07339.1| RpoB [Volucribacter psittacicida]
          Length = 151

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 112/151 (74%), Gaps = 1/151 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  V  
Sbjct: 61  VYARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAYVTA 120

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   GE  L   E+I ++D S +QVVS+AA+
Sbjct: 121 RGEHGESGLYRPEEIHYMDVSTQQVVSVAAA 151


>gi|55650682|emb|CAF31392.1| RNA polymerase B subunit [Anabaena circinalis 90]
          Length = 199

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 88/195 (45%), Positives = 126/195 (64%), Gaps = 6/195 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPHVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNMLVAFM 816
            G+LALG+N++VA++
Sbjct: 184 GGELALGQNIVVAYI 198


>gi|20377915|gb|AAM20889.1| RopB [Campylobacter coli]
 gi|76781233|gb|ABA54502.1| RpoB [Campylobacter coli]
 gi|76781239|gb|ABA54505.1| RpoB [Campylobacter coli]
 gi|76781241|gb|ABA54506.1| RpoB [Campylobacter coli]
 gi|76781243|gb|ABA54507.1| RpoB [Campylobacter coli]
 gi|307092490|gb|ADN28477.1| RNA polymerase beta subunit [Campylobacter coli]
 gi|307092492|gb|ADN28478.1| RNA polymerase beta subunit [Campylobacter coli]
 gi|307092494|gb|ADN28479.1| RNA polymerase beta subunit [Campylobacter coli]
          Length = 162

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHSTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVANGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|219563995|gb|ACL28181.1| RNA polymerase II second largest subunit [fungal sp. M1 (TL-2008)]
          Length = 243

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 50/267 (18%), Positives = 88/267 (32%), Gaps = 27/267 (10%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 1    ILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSL 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
             +  +   +      +    +E   + +  E + L    Y ++     I  G        
Sbjct: 61   FYRTYQDQE----KMIGHSVVEQFEKPQRSETLRLKHGTYDKIDNDGIIAPGIRVSGEDI 116

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  ++ D                +E  QR  + +K    T     E    +++   
Sbjct: 117  IMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGVIDQVMIT 161

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
              GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 162  TTGD-----GTRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLVPDI 216

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVG 1147
            ++NP  +PSRM +  + E  L      
Sbjct: 217  IINPHAIPSRMTIAHLIECQLSKVATL 243


>gi|197941954|gb|ACH78582.1| RNA polymerase subunit [Lycopodium obscurum]
          Length = 187

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 84/194 (43%), Positives = 135/194 (69%), Gaps = 7/194 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPLL+ E   VGTG+E  VA  SG+  +A ++G ++ +D+  I +    G+   +     
Sbjct: 1   VPLLEPERCIVGTGLEGQVASDSGSVAIAAQSGKIDYIDSKEITLLVDNGEAISTE---- 56

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+ +QRSN NTC++Q+P V +G+ +++  I+ADG +T+ G+ A G+N+LVA+MPW G
Sbjct: 57  ---LITYQRSNNNTCMHQKPRVNLGEYLKKGQILADGAATEGGEPASGKNVLVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LI+ER++ E+VFTSIHIE++E+ AR T  GPE +T +IP++ +  L+++DE G
Sbjct: 114 YNFEDAVLINERLIYENVFTSIHIEKYEIEARITLHGPEILTSEIPHLDDYFLRHLDENG 173

Query: 881 IICVGAEVNPGDIL 894
           ++  G+ V  GD+L
Sbjct: 174 LVLPGSWVETGDVL 187


>gi|76781261|gb|ABA54516.1| RpoB [Campylobacter sputorum]
 gi|76781267|gb|ABA54519.1| RpoB [Campylobacter sputorum]
 gi|76781269|gb|ABA54520.1| RpoB [Campylobacter sputorum]
          Length = 162

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV DGKVTND+VYL+A +EE   IA A++ LD+ G+  +E++  R 
Sbjct: 61  AKVNDLGFVEAPYRKVVDGKVTNDIVYLTATQEEGLVIAPASAKLDDKGNILDEILEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILAKREEVSLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|169260882|gb|ACA52153.1| RpoB [Pasteurella testudinis]
          Length = 153

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 90/153 (58%), Positives = 115/153 (75%), Gaps = 1/153 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR
Sbjct: 61  YARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDENSRFTDTFVTCR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
              GE  L   ++I ++D S +QVVS+AA+LIP
Sbjct: 121 GEHGESGLYKADEIHYMDISTQQVVSVAAALIP 153


>gi|6449147|gb|AAF08845.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
 gi|6449152|gb|AAF08847.1| RNA polymerase beta subunit [Streptococcus pneumoniae]
          Length = 170

 Score =  153 bits (387), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 78/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLVRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELESDSKDITYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSELVRNTVEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             ES + L        +   +  +G             L    +AE +V+ ETG
Sbjct: 117 TAESSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTIAEPLVDPETG 170



 Score = 55.1 bits (131), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSELVRNTVEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAE 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 120 SSRSLLVARFFDPRRYDLAAVGRYKINKKLNVKTRLLNQTI 160


>gi|307092478|gb|ADN28471.1| RNA polymerase beta subunit [Campylobacter jejuni]
          Length = 162

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVETRQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|76781263|gb|ABA54517.1| RpoB [Campylobacter sputorum]
 gi|76781265|gb|ABA54518.1| RpoB [Campylobacter sputorum]
          Length = 162

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV DGKVTND+VYL+A +EE   IA A++ LD+ G+  +E++  R 
Sbjct: 61  AKVNDLGFVEAPYRKVVDGKVTNDIVYLTATQEEGLVIAPASAKLDDKGNIVDEILEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILAKREEVSLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|289468061|gb|ADC95711.1| RpoB [Riemerella anatipestifer]
          Length = 163

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 93/163 (57%), Positives = 116/163 (71%), Gaps = 2/163 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            E +  R  G+  +V  E++D ID +P Q+  I+ASLIPFLE+
Sbjct: 121 TERIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPFLEH 163


>gi|307092484|gb|ADN28474.1| RNA polymerase beta subunit [Campylobacter jejuni]
          Length = 162

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVVNGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV ++ASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVSASLIPFLEHDDANRAL 162


>gi|50237515|gb|AAT71848.1| RNA polymerase beta subunit [Rock bream iridovirus]
          Length = 1053

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 38/103 (36%), Positives = 58/103 (56%), Gaps = 3/103 (2%)

Query: 1218 AINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSL 1277
             +   L         + ++Y G TG  F+  V +      KL H+V++KV+AR+TG    
Sbjct: 899  DLLKTLEELGYA---KQVMYCGRTGRRFESLVFMAPCPYQKLKHLVANKVHARTTGPVDP 955

Query: 1278 VTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +T+QP+ G+S  GG ++GEME WC  ++GAA  L E +T  SD
Sbjct: 956  LTRQPVAGRSRDGGIKIGEMEQWCKISHGAAAALHESMTTMSD 998



 Score =  123 bits (309), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 34/123 (27%), Positives = 48/123 (39%), Gaps = 9/123 (7%)

Query: 1050 EDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDM 1109
            E  F +K+              + VK+ +   R  + GDK A     KG    +    DM
Sbjct: 791  EGYFDDKLV------FNMADGCKCVKIKLRKIRIPEMGDKFASFTAQKGTCGMMYDQWDM 844

Query: 1110 PFLKDGTPVDIVLNPLGVPSRMNVGQIFETH--LGWACVGLGKKIKSLINDYKANGDISP 1167
            PF  DG   D+V+NP   PSRM V  + +    LG A  G GK   +   +      +  
Sbjct: 845  PFTADGVVPDLVINPHAFPSRMTVHYLLQMCFELG-AVAGGGKGYDATAFNSDGTDLLKT 903

Query: 1168 LRS 1170
            L  
Sbjct: 904  LEE 906



 Score = 90.1 bits (222), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 92/494 (18%), Positives = 166/494 (33%), Gaps = 60/494 (12%)

Query: 450 KGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLR--------MERSIKERISSVDIDSVMPQ 501
            G + D DNL  +RV + G ++   +R    +        ME+S    +  +   S    
Sbjct: 308 VGAVHDKDNLRWKRVDTSGALILFLFRNLFKQWVCTVKRVMEKSCVVGVPDLQGKSGSVN 367

Query: 502 DLINAKPVVSAVCEFFCSS----------------QLSQLEEHVNSLSRITHTRRLSALG 545
            + N    V  +     +                  +SQL    N  +RI++ RR++   
Sbjct: 368 AITNVITNVLHLAFATGNWLVRKNSGTSKNTYTPRGVSQLMCVQNYGARISNLRRMT--- 424

Query: 546 QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKV 605
              V      +++R +H +H G ICP ET EG  +G V  L   A V     +    R +
Sbjct: 425 -HAVGFKGKNIKVRQLHNSHNGYICPYETPEGDRVGNVVQLALSATVT----VPVCPRNI 479

Query: 606 CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
               ++   ++            Q N  +  +G     +      G  ++        + 
Sbjct: 480 HTLMMSALRLFADP---------QGNQPVLLNGEIVAWVRDRMLCGMAMMHVLWDYPHVT 530

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQ-AVPLLKAEAPFVGTGMESVVAKSSG 724
              +    +         + D +       M     V  L        T  E VV+  S 
Sbjct: 531 VVFRHGYGVHCVQRRAAVSCDLSLHRGQYRMVCPSLVQGLLVRPFPSPT--ERVVSMDSM 588

Query: 725 AAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL--V 782
            A      GIV   DA+  VI       + + S  + Y+    +++    C+N      V
Sbjct: 589 RAEFMDLPGIVVLTDAMSAVI----PFYNHTQSPRNAYQSNMGKQAVGLPCLNYMSRWDV 644

Query: 783 KVGDEVRRNDIIADGPSTD---LGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVF 839
            +   +     ++   + D      +  G   +VA + + GYN EDS++++   V   +F
Sbjct: 645 TLDVLMYPQVPLSRSKAMDALSFDTMPHGACPIVAVLTFDGYNQEDSIILNRSSVQRGMF 704

Query: 840 TSIHIEEFEVMARDTKLGPEEITRDIPNVSEEG---LKNIDECGIICV----GAEVNPGD 892
            S   +      +  K    E    +P            + + GI       G  V  G 
Sbjct: 705 VSTTYKTLCECEKHVKRCEFERIMCVPVDKRRPGLVYDYLGDDGIFDPALARGMFVTAGV 764

Query: 893 ILVGKITPKGESPM 906
           ++VGK++     P 
Sbjct: 765 VVVGKMSFDQSRPE 778


>gi|55650688|emb|CAF31395.1| RNA polymerase B subunit [Anabaena sp. 277]
          Length = 212

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 90/209 (43%), Positives = 125/209 (59%), Gaps = 19/209 (9%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR- 746
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGEVVYVDATEIRVRV 123

Query: 747 ------------------SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV 788
                             +              Y L K+QRSNQ+TC+NQ+PLV++G++V
Sbjct: 124 SSQWSIVSGQYSFTKQQTTDNEQQTTDKPQEIKYTLSKYQRSNQDTCLNQKPLVRIGEKV 183

Query: 789 RRNDIIADGPSTDLGDLALGRNMLVAFMP 817
               ++ADG ST+ G+LALG+N++VA+MP
Sbjct: 184 VAGQVLADGSSTEGGELALGQNIVVAYMP 212


>gi|4972799|gb|AAD34795.1| DNA-directed RNA polymerase beta and beta' subunits [Helicobacter
            fennelliae]
          Length = 178

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 47/104 (45%), Positives = 62/104 (59%), Gaps = 8/104 (7%)

Query: 1290 GGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNV 1349
            GGQR GEMEVW ++AYGAA+ L+EMLTIKSDD+VGR   Y SI       E+G PE+F V
Sbjct: 1    GGQRFGEMEVWPLEAYGAAHTLKEMLTIKSDDIVGRENAYRSITKSEPVGESGIPETFFV 60

Query: 1350 LVKEMQALGLSIDLENSRTKNSAKMEEIP--------DFNKCEL 1385
            L KE+Q+L L +++           + +         DFN  +L
Sbjct: 61   LTKELQSLTLDVNVFGDEVDEYGNPKALEIKEDNRPKDFNSLQL 104


>gi|55650654|emb|CAF32198.1| RNA polymerase B subunit [Nostoc ellipsosporum V]
          Length = 180

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 89/186 (47%), Positives = 122/186 (65%), Gaps = 6/186 (3%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR L
Sbjct: 1   VPLDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRAL 60

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           MG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R     
Sbjct: 61  MGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNA 120

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            +        Y L K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N+
Sbjct: 121 SE------LKYYLSKYQRSNQDTCLNQKPLVRIGERVVAGQVLADGSSTEGGELALGQNI 174

Query: 812 LVAFMP 817
           +VA+MP
Sbjct: 175 VVAYMP 180


>gi|50058751|gb|AAT69128.1| RNA polymerase II [Erycibe glomerata]
          Length = 211

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 35/84 (41%), Positives = 45/84 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 128  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 187

Query: 1126 GVPSRMNVGQIFETHLGWACVGLG 1149
             +PSRM +GQ+ E  +G     +G
Sbjct: 188  AIPSRMTIGQLIECIMGKVAAHMG 211



 Score = 71.6 bits (174), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 25/132 (18%), Positives = 48/132 (36%), Gaps = 16/132 (12%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA   + GYN EDS+++++  +    F S+    +    +      +E        +   
Sbjct: 1   VAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRANTMG 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ G+   G  V+  D+++GK TP  +                     RD 
Sbjct: 61  MRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIPQDD-----------AQASRYTKRDH 109

Query: 928 SLRVPSGVSGTV 939
           S  +    +G V
Sbjct: 110 STSLRHSETGIV 121


>gi|20377917|gb|AAM20890.1| RopB [Campylobacter coli]
 gi|20377919|gb|AAM20891.1| RopB [Campylobacter coli]
 gi|20377921|gb|AAM20892.1| RopB [Campylobacter coli]
 gi|20377923|gb|AAM20893.1| RopB [Campylobacter coli]
          Length = 162

 Score =  153 bits (386), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 95/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN+VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVANGKVTNEVVYLTATQEEGLFIAPASTKVDAKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|76781235|gb|ABA54503.1| RpoB [Campylobacter coli]
 gi|76781237|gb|ABA54504.1| RpoB [Campylobacter coli]
          Length = 162

 Score =  153 bits (386), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +G+VT+ VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVENGRVTDQVVYLTATQEEGLFIAPASTKVDAKGNIIEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|76781317|gb|ABA54544.1| RpoB [Campylobacter hyointestinalis subsp. hyointestinalis]
 gi|76781319|gb|ABA54545.1| RpoB [Campylobacter hyointestinalis subsp. hyointestinalis]
 gi|76781321|gb|ABA54546.1| RpoB [Campylobacter hyointestinalis subsp. hyointestinalis]
 gi|76781323|gb|ABA54547.1| RpoB [Campylobacter hyointestinalis subsp. hyointestinalis]
          Length = 162

 Score =  153 bits (386), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN++VYL+A +EE   IA A++ LDE+    E+L+  R 
Sbjct: 61  AKVNDLGFVEAPYRKVENGKVTNEIVYLTATQEEGHIIAPASTILDENDMIKEDLIEVRQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMLLAKREDVTLIDLCSGMVMGVAASLIPFLEHDDANRAL 162


>gi|289468055|gb|ADC95708.1| RpoB [Riemerella sp. IPDH 98/90]
          Length = 164

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 90/163 (55%), Positives = 118/163 (72%), Gaps = 2/163 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 2   QFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 61

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  +   ++L+A +EE++ IAQAN  L EDG+F 
Sbjct: 62  SSLGLYAKINNLGFIETPYRKVENGKVDLNAAPIFLNAEDEESKIIAQANVELAEDGTFE 121

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            + +  R  G+  +V  E++D ID +P Q+  I+ASLIPFLE+
Sbjct: 122 TDRIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPFLEH 164


>gi|169260874|gb|ACA52149.1| RpoB [Chelonobacter oris]
          Length = 151

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 93/151 (61%), Positives = 114/151 (75%), Gaps = 1/151 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR 
Sbjct: 1   SEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYART 60

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYRKV DG+VT ++ YLSA+EE    IAQANS+LDED  FT+  V CR   G
Sbjct: 61  NDYGFLETPYRKVVDGQVTEEIEYLSAIEEGKYVIAQANSNLDEDSRFTDAFVTCRGEHG 120

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E  L   E I ++D S +QVVS+AA+LIPFL
Sbjct: 121 ESGLYRAEDIHYMDVSTQQVVSVAAALIPFL 151


>gi|286142808|gb|ADC41434.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142810|gb|ADC41435.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142930|gb|ADC41495.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142934|gb|ADC41497.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142936|gb|ADC41498.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142940|gb|ADC41500.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142944|gb|ADC41502.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142946|gb|ADC41503.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142948|gb|ADC41504.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142950|gb|ADC41505.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142952|gb|ADC41506.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142970|gb|ADC41515.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142978|gb|ADC41519.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142980|gb|ADC41520.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286142994|gb|ADC41527.1| RNA polymerase beta subunit [Streptomyces griseus]
 gi|286142998|gb|ADC41529.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286143000|gb|ADC41530.1| RNA polymerase beta subunit [Streptomyces limosus]
 gi|286143004|gb|ADC41532.1| RNA polymerase beta subunit [Streptomyces limosus]
          Length = 185

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 106/192 (55%), Positives = 141/192 (73%), Gaps = 7/192 (3%)

Query: 687 SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
           +NR LMG NM RQAVPL+K+EAP VGTGME   A  +G  + A++ G+V++V A  I   
Sbjct: 1   ANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQEVSADYITTT 60

Query: 747 SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLA 806
           + +G           YRL KF RSNQ T VNQ+ +V  GD +    ++ADGP+T+LG++A
Sbjct: 61  NDDGT-------YTTYRLAKFSRSNQGTSVNQKVVVDEGDRIIEGQVLADGPATELGEMA 113

Query: 807 LGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIP 866
           LG+N+LVAFM W G+N+ED++++S+R+V +DV +SIHIEE EV ARDTKLGPEEITRDIP
Sbjct: 114 LGKNLLVAFMSWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIP 173

Query: 867 NVSEEGLKNIDE 878
           NVSEE L ++DE
Sbjct: 174 NVSEEVLADLDE 185


>gi|76781275|gb|ABA54523.1| RpoB [Campylobacter showae]
          Length = 162

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKDRAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DG+VT+++VYL+A +EEN  IA A+++LDE G   E+L+  R 
Sbjct: 61  AKVNNLGFVEAPYKKVVDGRVTDEIVYLTATQEENLVIAPASTALDESGYIVEDLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMILAKREDVKLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|225698429|gb|ACO07332.1| RpoB [Gallibacterium sp. TISWSGrun]
          Length = 151

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 88/151 (58%), Positives = 111/151 (73%), Gaps = 1/151 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V  
Sbjct: 61  VYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTFVTA 120

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 RGEHGESGLYRPEDIHYMDISTQQVVSVAAA 151


>gi|77632730|gb|ABB00327.1| RpoB [Campylobacter hyointestinalis subsp. lawsonii]
          Length = 162

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS ITH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEITHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKVTN++VYL+A +EE   IA A++ LDE+    E+L+  R 
Sbjct: 61  AKVNDLGFVEAPYRKVENGKVTNEIVYLTATQEEGHIIAPASTILDENDMIKEDLIEVRQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMLLAKREDVTLIDLCSGMVMGVAASLIPFLEHDDANRAL 162


>gi|145307894|gb|ABP57251.1| RNA polymerase II second largest subunit [Furia pieris]
          Length = 249

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 50/272 (18%), Positives = 91/272 (33%), Gaps = 27/272 (9%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +        +    +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I  G   
Sbjct: 62   LF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIAPGTRV 117

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  +      R++          ++     +  +   + +        
Sbjct: 118  SGDDIIIGKTAPVPPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ------- 170

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 171  -------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFNGEG 217

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETHLGWACVG 1147
               D+V+NP  +PSRM +G + E  +G     
Sbjct: 218  MVPDLVINPHAIPSRMTIGHMVECLVGKVGTL 249



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 66/179 (36%), Gaps = 19/179 (10%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PLV                     +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGI 881
           +++++  +   +F SI+   +    + + L   E            +     + +++ G+
Sbjct: 51  VIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEKLEDDGL 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 111 IAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVM 165


>gi|76781299|gb|ABA54535.1| RpoB [Campylobacter gracilis]
          Length = 162

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L ++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV +GKVT+++VYL+A +EE   IA A++ LDE+G+  EEL+  R 
Sbjct: 61  AKVNDLGFVEAPYKKVVNGKVTDEIVYLTATQEEGLVIAPASAKLDEEGNIVEELLEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE I+  RE I  ID     V  +AASLIPFLE+DD+NR L
Sbjct: 121 DGENIMARREDISLIDLCSGMVAGVAASLIPFLEHDDANRAL 162


>gi|76781273|gb|ABA54522.1| RpoB [Campylobacter showae]
          Length = 162

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKDRAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EEN  IA A+++LDE G   E+L+  R 
Sbjct: 61  AKVNNLGFVEAPYKKVVDGKVTDEIVYLTATQEENLVIAPASTALDESGYIVEDLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMILAKREDVKLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|55650662|emb|CAF32201.1| RNA polymerase B subunit [Trichormus azollae str. 'Kom BAI./1983']
          Length = 177

 Score =  152 bits (385), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 88/183 (48%), Positives = 121/183 (66%), Gaps = 6/183 (3%)

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DE+G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG 
Sbjct: 1   DENGYIIGPQVPVRYRLEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMGS 60

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
           NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R      + 
Sbjct: 61  NMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNSPE- 119

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y + K+QRSNQ+TC+NQ+PLV++G+ V    ++ADG ST+ G+LALG+N++VA
Sbjct: 120 -----IRYTVSKYQRSNQDTCLNQKPLVRMGERVVAGQVLADGSSTEGGELALGQNIVVA 174

Query: 815 FMP 817
           +MP
Sbjct: 175 YMP 177


>gi|11595826|emb|CAC18341.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 146

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 85/147 (57%), Positives = 111/147 (75%), Gaps = 1/147 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGLKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEND 685
           E +  +D SPKQVVS+AASLIPFLE+D
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHD 146


>gi|198279345|emb|CAP04707.1| RNA polymerase beta subunit [Pinus strobus]
          Length = 239

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 88/189 (46%), Positives = 130/189 (68%), Gaps = 2/189 (1%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED+
Sbjct: 23  YQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDA 82

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+
Sbjct: 83  ILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGS 142

Query: 887 EVNPGDILVGKITPKGESPM--TPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            +  GD+LVGK+TP+       TPE +LL+ IFG +    R++ LR P G  G V+DVR 
Sbjct: 143 WIETGDVLVGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRW 202

Query: 945 FNRHGIDKN 953
            NR     +
Sbjct: 203 INRVDDSGD 211



 Score = 65.5 bits (158), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 49/216 (22%), Positives = 80/216 (37%), Gaps = 14/216 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            +  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 38   VRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 96

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 97   SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 150

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  +++     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 151  VGKLTPQTTEESLCTPEGRLLQTIFGIEVSTARESCLRAPIGGKGRVIDVRWINRVD--D 208

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNK 1097
             GD+        V V+++ KR IQ GDK+AGRHG K
Sbjct: 209  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGXK 239


>gi|197941946|gb|ACH78578.1| RNA polymerase subunit [Diphasiastrum digitatum]
 gi|197941948|gb|ACH78579.1| RNA polymerase subunit [Diphasiastrum digitatum]
          Length = 187

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 83/194 (42%), Positives = 129/194 (66%), Gaps = 7/194 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           V L + E   VGTG+E  VA  SG+  +A + G +  +D+  I      G    +     
Sbjct: 1   VXLFEPERCIVGTGLEGQVALDSGSVAIAAQGGKINYIDSKEITSLVNNGKTISTE---- 56

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+ +QRSN NTC++Q+P V +G+ +++  I+ADG +T+ G+LA G+N LVA+MPW G
Sbjct: 57  ---LITYQRSNNNTCMHQKPRVNLGEYLKKGQILADGAATEGGELASGKNALVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LI+ER++ E+VFTSIHI+++EV AR T  GPE +T +IP++ +  L+++DE G
Sbjct: 114 YNFEDAVLINERLIYENVFTSIHIDKYEVEARVTLHGPEILTSEIPHLDDYFLRHLDENG 173

Query: 881 IICVGAEVNPGDIL 894
           ++  G+ V  GD+L
Sbjct: 174 LVLPGSWVETGDVL 187


>gi|281185449|gb|ADA54547.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus]
          Length = 103

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 37/75 (49%), Positives = 50/75 (66%)

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LG
Sbjct: 1    VWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLG 60

Query: 1359 LSIDLENSRTKNSAK 1373
            L + + + +      
Sbjct: 61   LDVKVMDEQDNEIEM 75


>gi|281185451|gb|ADA54548.1| DNA-directed RNA polymerase subunit beta [Staphylococcus aureus]
          Length = 103

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 37/75 (49%), Positives = 50/75 (66%)

Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
            VW ++AYGAAY LQE+LT KSDD VGR + YE+IV G +      PESF VL+KE+Q+LG
Sbjct: 1    VWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLG 60

Query: 1359 LSIDLENSRTKNSAK 1373
            L + + + +      
Sbjct: 61   LDVKVMDEQDNEIEM 75


>gi|55650658|emb|CAF32200.1| RNA polymerase B subunit [Nostoc muscorum II]
          Length = 179

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 89/185 (48%), Positives = 122/185 (65%), Gaps = 6/185 (3%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            +DE G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LM
Sbjct: 1   PVDETGHIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALM 60

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R      
Sbjct: 61  GSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNTS 120

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNML 812
           +        Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+LALG+N++
Sbjct: 121 E------IRYLLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGELALGQNIV 174

Query: 813 VAFMP 817
           VA+MP
Sbjct: 175 VAYMP 179


>gi|11595834|emb|CAC18345.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 145

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 84/146 (57%), Positives = 110/146 (75%), Gaps = 1/146 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V DG+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKDGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEN 684
           E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEH 145


>gi|260594033|gb|ACX46311.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 158

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 78/158 (49%), Positives = 110/158 (69%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLS+  +  N LS IT+ RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSEFMDQNNPLSEITYKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++S+ ++AR N  GF+E  Y  + +  VT+++ +LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSVAAYARTNQGGFVEIRYGVMKEALVTDEIAFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
             +ELV  R   E  +   E +  +D SPKQVVS+AAS
Sbjct: 121 LIDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAAS 158


>gi|226427477|gb|ACO54932.1| RNA polymerase [Mycoplasma mycoides subsp. mycoides]
          Length = 160

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 89/159 (55%), Positives = 122/159 (76%), Gaps = 1/159 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 2   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 61

Query: 590 ARVNAYGFIETPYRKVCD-GKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARVN YGFI TPYRKV +     + V YL+A +E+N  IAQ+N + DE+G   +E++  R
Sbjct: 62  ARVNEYGFITTPYRKVINGIIQNDQVEYLTADQEKNFIIAQSNVNQDENGKILDEIIVSR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
             G++ +   E+ID+ID SPKQ+VS+A S IPFLENDD+
Sbjct: 122 FNGDDYMAKVEEIDYIDVSPKQIVSVATSGIPFLENDDA 160


>gi|145307919|gb|ABP57263.1| RNA polymerase II second largest subunit [Pandora neoaphidis]
          Length = 249

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 51/272 (18%), Positives = 92/272 (33%), Gaps = 27/272 (9%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 2    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 61

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I  G
Sbjct: 62   DRGLF-RSIYYRTYLDQEKKSGMNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIAPG 117

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  D      R++          ++     +  +   + +     
Sbjct: 118  TRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTINQ---- 173

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              +R  KV V   R  Q GDK A RHG KG +      EDMPF 
Sbjct: 174  ----------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFS 217

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
             +G   D+V+NP  +PSRM +G + E  +G  
Sbjct: 218  AEGMVPDLVINPHAIPSRMTIGHMVECLVGKV 249



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 67/180 (37%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + + +   E            +     + +++ G
Sbjct: 53  SVIMNQSSIDRGLFRSIYYRTYLDQEKKSGMNEIESFEKPSRKTTLRLRHGTYEKLEDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 113 LIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVM 168


>gi|52694337|emb|CAG38008.1| RNA polymerase beta subunit [Pseudomonas mendocina]
          Length = 314

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 94/168 (55%), Positives = 121/168 (72%)

Query: 633 SLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
              ++G   +ELV  R   E  +   E +  +D SPKQVVS+AASLIPFLE+DD+NR LM
Sbjct: 147 PERQEGQLIDELVAVRHLNEFTVKAAEDVPLMDVSPKQVVSVAASLIPFLEHDDANRALM 206

Query: 693 GCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDL 752
           G NMQR AVP L+A+ P VGTGME  VA+ SG  +VA+R G+++ VDA RIV+R  + ++
Sbjct: 207 GSNMQRPAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRIVVRVNDDEV 266

Query: 753 DPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
           +   +GVDIY L K+ RSNQNTC+NQRPLV  GD+V R DI+ADGPST
Sbjct: 267 ETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDQVSRGDIMADGPST 314


>gi|76781277|gb|ABA54524.1| RpoB [Campylobacter upsaliensis]
 gi|76781279|gb|ABA54525.1| RpoB [Campylobacter upsaliensis]
 gi|76781283|gb|ABA54527.1| RpoB [Campylobacter upsaliensis]
          Length = 162

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKV+++VVYL+A +EE  +IA A++ +D  G+  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVENGKVSDEVVYLTATQEEGLFIAPASTKIDAKGNIIEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|25990083|gb|AAN75052.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 92/151 (60%), Positives = 125/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|307147885|gb|ADN37808.1| DNA-directed RNA polymerase subunit beta [Mycobacterium [chelonae]
            ATCC 14472]
 gi|307147889|gb|ADN37811.1| DNA-directed RNA polymerase subunit beta [Mycobacterium chelonae]
 gi|307147954|gb|ADN37854.1| DNA-directed RNA polymerase subunit beta [Mycobacterium abscessus]
 gi|307147972|gb|ADN37866.1| DNA-directed RNA polymerase subunit beta [Mycobacterium abscessus]
 gi|307147975|gb|ADN37868.1| DNA-directed RNA polymerase subunit beta [Mycobacterium abscessus]
          Length = 101

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 41/83 (49%), Positives = 57/83 (68%), Gaps = 4/83 (4%)

Query: 1304 AYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
            AYGAAY LQE+LTIKSDD VGR +VYE+IV G +  E G PESF VL+KE+Q+L L++++
Sbjct: 1    AYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEV 60

Query: 1364 ENSRTKNSAKMEEIPDFNKCELK 1386
             +          E+ D +  +L+
Sbjct: 61   LSKDGAAI----EMRDGDDEDLE 79


>gi|113473047|gb|ABI35955.1| DNA-directed RNA polymerase beta chain [Rickettsia bellii]
          Length = 152

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 94/152 (61%), Positives = 117/152 (76%), Gaps = 1/152 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ITH RRLSALG GG++R RAG E+RDVHPTHYGRICP ET EG NIGL++S+ ++A
Sbjct: 1   PLSEITHKRRLSALGPGGLSRDRAGFEVRDVHPTHYGRICPIETPEGQNIGLINSMATYA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R+N +GFIE+PYRKV DG VT++VVYLSA+EE    I QANS +D+DG    E + CR  
Sbjct: 61  RINKHGFIESPYRKVKDGHVTDEVVYLSAIEEGKYKIGQANSKVDKDGILQGEFINCRVE 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            G  ++V   ++DFID +P QVVS+AASLIPF
Sbjct: 121 GGNFVMVEPHEVDFIDVTPMQVVSVAASLIPF 152


>gi|76781303|gb|ABA54537.1| RpoB [Campylobacter rectus]
          Length = 162

 Score =  152 bits (384), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKDRAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EEN  IA A+++LDE G   E+L+  R 
Sbjct: 61  AKVNNLGFVEAPYKKVIDGKVTDEIVYLTATQEENLVIAPASTALDESGYIVEDLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMILAKREDVKLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|46277348|gb|AAS86864.1| DNA-dependent RNA polymerase II [Peziza subisabellina]
          Length = 497

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 80/568 (14%), Positives = 160/568 (28%), Gaps = 78/568 (13%)

Query: 586  LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
            L S+  V         +    + +V  +     +      ++      +  D  F    +
Sbjct: 1    LMSYVSVGTPSQPIVDFMMQRNMEVLEEYEPSRSPNATKIFVNGVWVGIHRDPGFIVRTI 60

Query: 646  FCRCAGEEILVPREKIDFIDASPKQVVSIA---ASLIPFLENDDSNRVLMGCNMQRQAVP 702
                    I      I  I     ++ + A      +  ++ND S+       +Q+Q + 
Sbjct: 61   QKLRRQGHIGSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPSSPRRGELALQKQHIE 120

Query: 703  LLKAEAPFVG-TGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDI 761
             L+ +      T         S   +        E +DA       +    +   +    
Sbjct: 121  KLEDDREIDDETQRYGWQGLLSDGVV--------EYIDAEEEETVMIVMTPEDLETSRQF 172

Query: 762  YRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGY 821
            +   + Q+        QR    V             PS  LG  A       + +P+  +
Sbjct: 173  HAGYEIQQELDPA---QRVKGAVNKFAHTWTHCEIHPSMILGIXA-------SIIPFPDH 222

Query: 822  NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGI 881
            N       S R   +       +  F    R+                           +
Sbjct: 223  NQ------SPRNTYQSAMGKQAMGVFLTNYRERM-----------------------DTM 253

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 254  ANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLF- 312

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSG 998
              +F R  +D+ +R   +    +E   +      + L    Y +L +   +  G      
Sbjct: 313  RSLFFRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYDKLDDDGLVAPGVRVSGE 369

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  ++ +      R+++         ++     +  Q                 
Sbjct: 370  DIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ----------------- 412

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G   
Sbjct: 413  ---VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRNEDMPFTAEGVVP 469

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACV 1146
            D+++NP  +PSR  +  + E  L     
Sbjct: 470  DLIINPHAIPSRXTIAHLXECLLSKVSS 497


>gi|256600050|gb|ACV04765.1| DNA-dependent RNA-polymerase beta-subunit [Pasteurellaceae
           bacterium CCUG 19808]
          Length = 150

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 87/149 (58%), Positives = 113/149 (75%), Gaps = 1/149 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR 
Sbjct: 2   SEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYART 61

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  V  R   G
Sbjct: 62  NNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENLRFTDAYVTARGEHG 121

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIP 680
           E  L   E+I ++D S +QVVS+AA+LIP
Sbjct: 122 ESGLYRPEEIHYMDVSTQQVVSVAAALIP 150


>gi|76781217|gb|ABA54494.1| RpoB [Campylobacter fetus subsp. fetus]
 gi|76781219|gb|ABA54495.1| RpoB [Campylobacter fetus subsp. fetus]
 gi|76781221|gb|ABA54496.1| RpoB [Campylobacter fetus subsp. fetus]
 gi|76781223|gb|ABA54497.1| RpoB [Campylobacter fetus subsp. fetus]
 gi|76781225|gb|ABA54498.1| RpoB [Campylobacter fetus subsp. venerealis NCTC 10354]
 gi|76781227|gb|ABA54499.1| RpoB [Campylobacter fetus subsp. venerealis]
 gi|76781229|gb|ABA54500.1| RpoB [Campylobacter fetus subsp. venerealis]
 gi|76781231|gb|ABA54501.1| RpoB [Campylobacter fetus subsp. venerealis]
          Length = 162

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E+PYR+V DGKVTN++VYL+A +EE   IA A++ LD +    E+L+  R 
Sbjct: 61  AKVNDLGFVESPYRRVIDGKVTNEIVYLTATQEEGHIIAPASTVLDANDIIKEDLIEVRR 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMLLAKREDVTLIDLCSGMVMGVAASLIPFLEHDDANRAL 162


>gi|197941950|gb|ACH78580.1| RNA polymerase subunit [Lycopodium obscurum]
 gi|197941952|gb|ACH78581.1| RNA polymerase subunit [Lycopodium obscurum]
          Length = 187

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 83/194 (42%), Positives = 134/194 (69%), Gaps = 7/194 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           V LL+ E   VGTG+E  VA  SG+  +A ++G ++ +D+  I +    G+   +     
Sbjct: 1   VXLLEPERCIVGTGLEGQVASDSGSVAIAAQSGKIDYIDSKEITLLVDNGEAISTE---- 56

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+ +QRSN NTC++Q+P V +G+ +++  I+ADG +T+ G+ A G+N+LVA+MPW G
Sbjct: 57  ---LITYQRSNNNTCMHQKPRVNLGEYLKKGQILADGAATEGGEPASGKNVLVAYMPWEG 113

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LI+ER++ E+VFTSIHIE++E+ AR T  GPE +T +IP++ +  L+++DE G
Sbjct: 114 YNFEDAVLINERLIYENVFTSIHIEKYEIEARITLHGPEILTSEIPHLDDYFLRHLDENG 173

Query: 881 IICVGAEVNPGDIL 894
           ++  G+ V  GD+L
Sbjct: 174 LVLPGSWVETGDVL 187


>gi|76781297|gb|ABA54534.1| RpoB [Campylobacter concisus]
          Length = 162

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EE   IA A++ LDE+G   E+L+  R 
Sbjct: 61  AKVNDLGFVEAPYKKVVDGKVTDEIVYLTATQEEGNVIAPASTKLDENGHIVEDLIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMMLARREDVTLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|76781301|gb|ABA54536.1| RpoB [Campylobacter rectus]
 gi|76781305|gb|ABA54538.1| RpoB [Campylobacter rectus]
          Length = 162

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 94/162 (58%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKDRAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EEN  IA A++ LDE G   E+L+  R 
Sbjct: 61  AKVNNLGFVEAPYKKVIDGKVTDEIVYLTATQEENLVIAPASTVLDESGYIVEDLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMILAKREDVKLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|37956397|gb|AAP15371.1| RNA polymerase beta subunit [Desulfuromusa bakii]
          Length = 145

 Score =  152 bits (383), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 115/145 (79%)

Query: 550 ARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGK 609
            R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+++AR+N YGF+ETPYR V DG+
Sbjct: 1   TRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIASLSTYARINEYGFVETPYRIVKDGQ 60

Query: 610 VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPK 669
           VT ++ Y SA+EEE   IAQAN+ +D++G F  ELV  R  GE +L+P ++ID +D SPK
Sbjct: 61  VTTEIKYFSALEEEGHAIAQANAPIDDNGVFVNELVNVRQTGEFLLLPPDQIDLMDVSPK 120

Query: 670 QVVSIAASLIPFLENDDSNRVLMGC 694
           Q+VS+AA+LIPFLENDD++R L+  
Sbjct: 121 QIVSVAAALIPFLENDDAHRALIRA 145


>gi|76781285|gb|ABA54528.1| RpoB [Campylobacter helveticus]
 gi|76781287|gb|ABA54529.1| RpoB [Campylobacter helveticus]
 gi|76781289|gb|ABA54530.1| RpoB [Campylobacter helveticus]
 gi|76781291|gb|ABA54531.1| RpoB [Campylobacter helveticus]
          Length = 164

 Score =  152 bits (383), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 92/164 (56%), Positives = 122/164 (74%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A+VN  GF+E PY+KV +GKV+++VVYL+A +EE  +IA A++ +D  G+  EE V  
Sbjct: 61  TYAKVNELGFVEAPYKKVVNGKVSDEVVYLTATQEEGLFIAPASTKIDAKGNIVEEFVEA 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           R  GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 RQDGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 164


>gi|145307882|gb|ABP57245.1| RNA polymerase II second largest subunit [Pandora delphacis]
          Length = 249

 Score =  152 bits (383), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 49/272 (18%), Positives = 92/272 (33%), Gaps = 27/272 (9%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 2    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 61

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I  G
Sbjct: 62   DRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKTTLRLRHGTYEKLEDDGLIAPG 117

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  +      R++          ++     +  +   + +     
Sbjct: 118  TRVSGDDIIIGKTAPVPPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVMLTINQ---- 173

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              +R  KV V   R  Q GDK A RHG KG +      EDMPF 
Sbjct: 174  ----------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFN 217

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
             +G   D+++NP  +PSRM +G + E  +G  
Sbjct: 218  GEGMVPDLIINPHAIPSRMTIGHMVECLVGKV 249



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 67/180 (37%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + + L   E            +     + +++ G
Sbjct: 53  SVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKTTLRLRHGTYEKLEDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 113 LIAPGTRVSGDDIIIGKTAPV----PPESEELGQRTRGHTKRDVSTPLKSTETGIVDRVM 168


>gi|223585645|gb|ACM91693.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 151

 Score =  152 bits (383), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 88/151 (58%), Positives = 115/151 (76%), Gaps = 2/151 (1%)

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC- 606
           G+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV  
Sbjct: 1   GLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDL 60

Query: 607 -DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
               +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D
Sbjct: 61  DTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMD 120

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNM 696
            SPKQVVS A + IPFLENDDSNR LMG NM
Sbjct: 121 VSPKQVVSAATACIPFLENDDSNRALMGANM 151


>gi|289468049|gb|ADC95705.1| RpoB [Pelistega europaea]
          Length = 148

 Score =  151 bits (382), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 91/147 (61%), Positives = 116/147 (78%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ITH RR+SALGQGG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++S+  +A
Sbjct: 1   PLSEITHKRRVSALGQGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSMALYA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           R+N YGF+ETPYRKV DGKVT  + YLSA+EE    IAQAN+ LDE+G F ++LV CR A
Sbjct: 61  RLNEYGFLETPYRKVADGKVTQIIEYLSAIEESKFVIAQANAHLDEEGRFMDDLVACREA 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAAS 677
           GE +L+  +K+ ++D +P Q+VS+AAS
Sbjct: 121 GETMLMSPDKVQYMDVAPSQIVSVAAS 147


>gi|225698439|gb|ACO07337.1| RpoB [Volucribacter psittacicida]
          Length = 150

 Score =  151 bits (382), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 86/150 (57%), Positives = 112/150 (74%), Gaps = 1/150 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  V  R
Sbjct: 61  YARTNNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAYVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAAS 677
              GE  L   E+I ++D S +QVVS+AA+
Sbjct: 121 GEHGESGLYRPEEIHYMDVSTQQVVSVAAA 150


>gi|310772097|emb|CBW46598.1| RNA polymerase subunit B [Arcobacter sp. CECT 7737]
          Length = 162

 Score =  151 bits (382), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 90/162 (55%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG VTN++ Y++A  EE   IA  ++ +D++G   E L+  R 
Sbjct: 61  AKVNDLGFIEAPYKKVKDGVVTNEITYMTATLEEGLVIAPGSTKVDDNGKIVEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R K+ +ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 NGEILLMERSKVSYIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|11595842|emb|CAC18349.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 145

 Score =  151 bits (382), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 83/146 (56%), Positives = 110/146 (75%), Gaps = 1/146 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L +     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-DGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEN 684
           E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEH 145


>gi|325301651|gb|ADZ05710.1| DNA-directed RNA polymerase beta subunit [Streptomyces
           albidoflavus]
          Length = 158

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 87/156 (55%), Positives = 115/156 (73%), Gaps = 1/156 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GF+ETPYR+V DG VT++V YL+A EE+   IAQAN+ L E
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFVETPYRRVTDGIVTDEVDYLTADEEDRFVIAQANAGLTE 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E+ V  R  G E   VP + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLHFAEDRVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGAN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           M RQAVPL+K+EAP VGTGME   A  +G  + A++
Sbjct: 121 MMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEK 156


>gi|225698407|gb|ACO07321.1| RpoB [Pasteurella multocida]
          Length = 151

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 111/151 (73%), Gaps = 1/151 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+
Sbjct: 1   QNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
            +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V  
Sbjct: 61  VYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEEFRFTDAFVTA 120

Query: 648 R-CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           R   GE  L   ++I ++D S +QVVS+AA+
Sbjct: 121 RGEHGESGLYRPDEIHYMDVSTQQVVSVAAA 151


>gi|76781295|gb|ABA54533.1| RpoB [Campylobacter concisus]
          Length = 162

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EE   IA A++ LDE+G   E+L+  R 
Sbjct: 61  AKVNDLGFVEAPYKKVIDGKVTDEIVYLTATQEEGNVIAPASTKLDENGHIVEDLIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 DGEMMLARREDVTLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|55650656|emb|CAF32199.1| RNA polymerase B subunit [Nostoc muscorum I]
          Length = 179

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 89/184 (48%), Positives = 122/184 (66%), Gaps = 6/184 (3%)

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           +DE G      V  R   E      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG
Sbjct: 2   VDETGHIIGPQVPVRYRQEFSTTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMG 61

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLD 753
            NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R      +
Sbjct: 62  SNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVTYVDATEIRVRPKPNTSE 121

Query: 754 PSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLV 813
                   Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+LALG+N++V
Sbjct: 122 ------IRYLLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGELALGQNIVV 175

Query: 814 AFMP 817
           A+MP
Sbjct: 176 AYMP 179


>gi|6449122|gb|AAF08835.1| RNA polymerase beta subunit [Streptococcus constellatus]
          Length = 170

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 77/174 (44%), Gaps = 14/174 (8%)

Query: 155 SQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPV 214
           SQL RSPG++F+    +   +GK+ Y   +IP++G W+++E DSKDI + RIDR RK+P 
Sbjct: 1   SQLDRSPGVYFN---DKVDKNGKVGYGSTVIPNRGAWLELETDSKDIAYTRIDRTRKIPF 57

Query: 215 TSFLMALGMD-SEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQ- 272
           T+ + ALG    +EI   F    +     +      +  D      +      +  GE  
Sbjct: 58  TTLVRALGFSGDDEIFDIFGDSDLVRNTIEKDI-HKNPMDSRTDEALKEIYERLRPGEPK 116

Query: 273 VIESGKKLTSGLLKSLKEKGVKFLGIT--------SDCLCGLYVAEDIVNGETG 318
             +S + L            +  +G             L    +AE +V+ ETG
Sbjct: 117 TADSSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKTRLLNQTIAEPLVDPETG 170



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 332 SLEEIFHSEIRDIPILYVD-SVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFS 390
            +  +  S   +I  ++ D  +  N   ++      +    +AL +IY  +RPG+  T  
Sbjct: 60  LVRALGFSGDDEIFDIFGDSDLVRNTIEKDIHKNPMDSRTDEALKEIYERLRPGEPKTAD 119

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHI 431
            + S+    FFD  +YDL+ VGR K+N +LN+ T    + I
Sbjct: 120 SSRSLLVARFFDPHRYDLAAVGRYKINKKLNIKTRLLNQTI 160


>gi|223585657|gb|ACM91699.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 152

 Score =  151 bits (382), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 89/152 (58%), Positives = 116/152 (76%), Gaps = 2/152 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+
Sbjct: 61  KVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           D++D SPKQVVS A + IPFLENDDSNR LMG
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRALMG 152


>gi|50058705|gb|AAT69105.1| RNA polymerase II [Astripomoea malvacea]
          Length = 210

 Score =  151 bits (381), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 35/90 (38%), Positives = 47/90 (52%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++ P 
Sbjct: 121  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVXPH 180

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSL 1155
             +PSRM +GQ+ E  +G     +GK+  + 
Sbjct: 181  AIPSRMTIGQLIECIMGKVAAHMGKEGDAT 210



 Score = 63.9 bits (154), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 44/123 (35%), Gaps = 14/123 (11%)

Query: 822 NFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNI 876
           N EDS+++++  +    F S+    +    +      +E        +   +       +
Sbjct: 1   NQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKL 60

Query: 877 DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
           D+ G+   G  V+  D+++GK TP  +           A         RD S  +    +
Sbjct: 61  DDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQNARYTKRDHSTSLRHSET 111

Query: 937 GTV 939
           G V
Sbjct: 112 GMV 114


>gi|309385726|gb|ADO66708.1| RNA polymerase beta subunit [Necropsobacter rosorum]
          Length = 151

 Score =  151 bits (381), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 90/151 (59%), Positives = 114/151 (75%), Gaps = 1/151 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR  
Sbjct: 61  RTNDYGFLETPYRKVINGQVTEEIEYLSAIEEGKYVIAQANSNLDENLRFTDAFVTCRGE 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            GE  L   E+I ++D S +QVVS+AA+LIP
Sbjct: 121 YGESGLYRPEEIHYMDVSTQQVVSVAAALIP 151


>gi|219563999|gb|ACL28183.1| RNA polymerase II second largest subunit [fungal sp. M10]
          Length = 237

 Score =  151 bits (381), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 87/253 (34%), Gaps = 27/253 (10%)

Query: 895  VGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNE 954
               +       +   +  + AI      +  D+ +   S +   +     +  +   +  
Sbjct: 9    TMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQE-- 66

Query: 955  RSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSD 1011
                +    +E   +   ++ + L    Y ++ +   +  G           K+  ++ D
Sbjct: 67   --KQIGHNVLEQFEKPSRNDTLRLKHGTYDKIDDDGIVAPGVRVSGEDIIMGKTAPMAPD 124

Query: 1012 LISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVL 1071
                            +E  QR    +K    T     E    +++     GD       
Sbjct: 125  ---------------AEELGQRQKHHIKRDVSTPLRSTESGVVDQVMLTTTGD-----GN 164

Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
            R  KV V   +  Q GDK A RHG KG +      EDMPF ++G   D+++NP  +PSRM
Sbjct: 165  RFAKVRVRTTKVPQIGDKFASRHGQKGTIGIXYRQEDMPFTREGVVPDLIINPHAIPSRM 224

Query: 1132 NVGQIFETHLGWA 1144
             +  + E  L   
Sbjct: 225  TIAHLIECQLSKV 237



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/161 (22%), Positives = 60/161 (37%), Gaps = 13/161 (8%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    ++   + 
Sbjct: 9   TMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYQDQEKQ 68

Query: 854 TKLGPEEIT-----RDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
                 E        D   +       ID+ GI+  G  V+  DI++GK  P     M P
Sbjct: 69  IGHNVLEQFEKPSRNDTLRLKHGTYDKIDDDGIVAPGVRVSGEDIIMGKTAP-----MAP 123

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           + + L             T LR        VVD  +    G
Sbjct: 124 DAEELGQRQKHHIKRDVSTPLR---STESGVVDQVMLTTTG 161


>gi|289468071|gb|ADC95716.1| RpoB [Riemerella columbina]
          Length = 162

 Score =  151 bits (381), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 90/162 (55%), Positives = 115/162 (70%), Gaps = 2/162 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV      VYL+A +EE++ IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDFKAAPVYLNAEDEESKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
            + +  R  G+  +V  +++D ID +P Q+  I+ASLIPFLE
Sbjct: 121 TDRIIARLDGDYPVVEPDQVDLIDIAPNQISGISASLIPFLE 162


>gi|25990093|gb|AAN75057.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  151 bits (381), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 91/151 (60%), Positives = 124/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRLSA G GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMDQNNPLSGLTHKRRLSAPGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|55650608|emb|CAF31382.1| RNA polymerase B subunit [Anabaena oscillarioides BECID32]
          Length = 194

 Score =  151 bits (381), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 87/191 (45%), Positives = 120/191 (62%), Gaps = 6/191 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTSPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTHGDVVYVDATEIRVRV 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQEIRYNLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRNML 812
            G+LALG+N++
Sbjct: 184 GGELALGQNIV 194


>gi|25990091|gb|AAN75056.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 91/151 (60%), Positives = 124/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMDQNNPLSGLTHKRRLWALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|301128437|gb|ADK61092.1| RNA polymerase subunit beta [Pasteurella multocida]
          Length = 151

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 89/151 (58%), Positives = 114/151 (75%), Gaps = 1/151 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +A
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R N YGF+ETPYRKV +G+VT ++ YLSA+EE    IAQANS+LDE+  FT+  V CR  
Sbjct: 61  RTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYVIAQANSNLDEELRFTDAFVTCRGE 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIP 680
            GE  L   ++I ++D S +QVVS+AA+LIP
Sbjct: 121 HGESGLYRPDEIHYMDVSTQQVVSVAAALIP 151


>gi|11595822|emb|CAC18339.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 145

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 84/146 (57%), Positives = 110/146 (75%), Gaps = 1/146 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGLKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEN 684
           E +  +D SPKQVVS+AASLIPFLE+
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEH 145


>gi|225698435|gb|ACO07335.1| RpoB [Gallibacterium sp. TIS16554]
          Length = 150

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 88/150 (58%), Positives = 111/150 (74%), Gaps = 1/150 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ 
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSV 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           +AR N YGF+ETPYRKV +G+VT ++ YLSA+EE N  IAQANS+LDE+  FT+  V  R
Sbjct: 61  YARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGNYVIAQANSNLDENFRFTDTFVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAAS 677
              GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 GEHGESGLYRPEDIHYMDISTQQVVSVAAA 150


>gi|22208419|emb|CAC87038.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 213

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 98/212 (46%), Positives = 143/212 (67%), Gaps = 14/212 (6%)

Query: 368 KDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--P 425
           +   +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L    P
Sbjct: 1   RRTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEP 60

Query: 426 DDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLKN 473
                + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+++N
Sbjct: 61  ITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQN 120

Query: 474 QYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLS 533
           Q R+G+ RMER ++ER+++ D++++ PQ LIN +P V+A+ EFF +SQLSQ     N LS
Sbjct: 121 QIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPAVAAIKEFFGTSQLSQFMVQNNPLS 180

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTH 565
            +T  RRLSALG GG++R RAG+E+RDVHP+H
Sbjct: 181 GLTQKRRLSALGPGGLSRERAGLEVRDVHPSH 212


>gi|50058745|gb|AAT69125.1| RNA polymerase II [Dicranostyles mildbraediana]
          Length = 215

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 34/83 (40%), Positives = 44/83 (53%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 133  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 192

Query: 1126 GVPSRMNVGQIFETHLGWACVGL 1148
             +PSRM +GQ+ E  +G     +
Sbjct: 193  AIPSRMTIGQLIECIMGKVAAXM 215



 Score = 75.5 bits (184), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 50/135 (37%), Gaps = 14/135 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----D 864
           N  VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAXVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRAN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP  +           A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDD---------AQGQASRYTK 111

Query: 925 RDTSLRVPSGVSGTV 939
           RD S  +    +G V
Sbjct: 112 RDHSTSLRHSETGIV 126


>gi|145307888|gb|ABP57248.1| RNA polymerase II second largest subunit [Eryniopsis caroliniana]
          Length = 245

 Score =  150 bits (380), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 53/265 (20%), Positives = 88/265 (33%), Gaps = 21/265 (7%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D+ ++S  VE E  E   +                   I  G   
Sbjct: 61   DRGLF-RSIYYRTYLDQEKKSGMVEMETFEKPTQKSTLRLRHGTYEKLEDDGLIAPGTRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D                +E  QR +   K    T     E    +
Sbjct: 120  SGDDIIIGKTAPVPPD---------------SEELGQRRLGQTKRDVSTPLKSTETGIVD 164

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++        +    +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 165  RVML-----TINQEGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFSAEG 219

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFETH 1140
               D+V+NP  +PSRM +G + E  
Sbjct: 220  IVPDLVINPHAIPSRMTIGHMVECL 244



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 2   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEI-----TRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + + +   E       +    +     + +++ G
Sbjct: 52  SVIMNQSSIDRGLFRSIYYRTYLDQEKKSGMVEMETFEKPTQKSTLRLRHGTYEKLEDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G+   DV        +G+   V+
Sbjct: 112 LIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRRLGQTKRDVSTPLKSTETGIVDRVM 167


>gi|310772070|emb|CBW43905.1| RNA polymerase subunit B [Arcobacter sp. CECT 7696]
 gi|310772072|emb|CBW43906.1| RNA polymerase subunit B [Arcobacter sp. F101-1]
 gi|310772074|emb|CBW43907.1| RNA polymerase subunit B [Arcobacter sp. F91]
          Length = 162

 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 124/162 (76%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG VTN+++Y++A  EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  AKVNDLGFIEAPYKKVKDGVVTNEIIYMTATLEEGLVIAPGSTKVDENGKIIEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ + K+D+ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILLIEKNKVDYIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|296278701|gb|ADH04305.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278703|gb|ADH04306.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278705|gb|ADH04307.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278723|gb|ADH04316.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278727|gb|ADH04318.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278729|gb|ADH04319.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278731|gb|ADH04320.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278733|gb|ADH04321.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
          Length = 151

 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 89/150 (59%), Positives = 112/150 (74%), Gaps = 1/150 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R
Sbjct: 61  FARTNDYGFLETPYRKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAAS 677
              GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 GERGESGLYKPEDIHYMDVSTQQVVSVAAA 150


>gi|227826288|gb|ACP41871.1| RNA polymerase II [Eudianthe laeta]
          Length = 241

 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 36/106 (33%), Positives = 46/106 (43%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSF 1171
             +PSRM +GQ+ E  +G                     +IS     
Sbjct: 190  AIPSRMTIGQLIECIMGKXXXXXXXXXXXTPFTDVTVDNISKALQK 235



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|115253007|emb|CAJ32588.1| DNA-directed RNA polymerase subunit B [Mycoplasma putrefaciens KS1]
          Length = 161

 Score =  150 bits (379), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 88/161 (54%), Positives = 124/161 (77%), Gaps = 1/161 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +T+ RRL+ALG GG++R RAG+E+RDVHP+HYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSELTNKRRLTALGPGGLSRDRAGLEVRDVHPSHYGRICPIETPEGPNIGLINNLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTND-VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           ARV+ YGFI TPYR+V +G + N+ + YL+A +E    IAQ+N   DE+G   +E+V  R
Sbjct: 61  ARVDEYGFITTPYRRVINGVIQNEQIEYLTADKERKFVIAQSNVKQDENGKILDEIVVSR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNR 689
             G++ +   ++I++ID SPKQ+VS+A S IPFLENDD+NR
Sbjct: 121 FNGDDYMARFDEIEYIDVSPKQIVSVATSAIPFLENDDANR 161


>gi|34451789|gb|AAQ72390.1| RpoB [Klebsiella variicola]
          Length = 153

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 99/153 (64%), Positives = 120/153 (78%)

Query: 670 QVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVA 729
           QVVS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VA
Sbjct: 1   QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVA 60

Query: 730 KRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVR 789
           KR G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + 
Sbjct: 61  KRGGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIE 120

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           R D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 121 RGDVLADGPSTDLGELALGQNMRVAFMPWNGYN 153


>gi|25990089|gb|AAN75055.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 92/151 (60%), Positives = 124/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ     N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMVQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|300193595|gb|ADJ68291.1| RNA polymerase B-subunit [Staphylococcus sciuri subsp. sciuri]
 gi|300193597|gb|ADJ68292.1| RNA polymerase B-subunit [Staphylococcus sciuri subsp. rodentium]
 gi|300193599|gb|ADJ68293.1| RNA polymerase B-subunit [Staphylococcus sciuri subsp. carnaticus]
          Length = 151

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 113/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RAG+E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV     +VT+ + YL+A EE++  +AQANS LDE G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVNIETNQVTDRIDYLTADEEDSYVVAQANSVLDETGKFVDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G+    P+E++D++D SPKQVVS A 
Sbjct: 121 LCRFRGDNTTKPKERMDYMDVSPKQVVSAAT 151


>gi|219564003|gb|ACL28185.1| RNA polymerase II second largest subunit [fungal sp. M20]
          Length = 240

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 50/264 (18%), Positives = 91/264 (34%), Gaps = 27/264 (10%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------AEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF + G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTRQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFET 1139
               D+++NP  +PSRM +  + E 
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIEC 240



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDAEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|25990085|gb|AAN75053.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 91/151 (60%), Positives = 124/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +TH RRL ALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMDQNNPLSGLTHKRRLLALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|226445707|gb|ACO58377.1| RNA polymerase [Mycoplasma iners]
          Length = 168

 Score =  150 bits (379), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 81/167 (48%), Positives = 112/167 (67%), Gaps = 1/167 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
           ++A+VN YGF++TPY KV +G V    V YL+A EE   YIAQ+   +DE+    ++ V 
Sbjct: 61  TYAKVNEYGFLQTPYYKVENGVVNYEKVEYLTATEEIGFYIAQSTVKVDENNRIIDKQVT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            R     +L    +ID+I+ +  Q+VS+AA  IPFLENDD+NR LMG
Sbjct: 121 MRHNYTYVLGEPTQIDYIEVASNQMVSVAAGCIPFLENDDANRALMG 167


>gi|76781281|gb|ABA54526.1| RpoB [Campylobacter upsaliensis]
          Length = 162

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PYRKV +GKV+++VVYL+A +EE  +IA A++ +D   +  EE V  R 
Sbjct: 61  AKVNELGFVEAPYRKVENGKVSDEVVYLTATQEEGLFIAPASTKIDAKDNIIEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     VV +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMVVGVAASLIPFLEHDDANRAL 162


>gi|289468041|gb|ADC95701.1| RpoB [Elizabethkingia meningoseptica]
          Length = 163

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 89/163 (54%), Positives = 114/163 (69%), Gaps = 2/163 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  +   +YL+A +EE + IAQAN  L + G F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDLNAAPIYLNAEDEEAKVIAQANVELSDSGDFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLEN 684
            + +  R  G+  +V   ++D ID +P Q+  I+ASLIPFLE+
Sbjct: 121 TDRIIARLDGDYPVVEPGQVDLIDVAPNQISGISASLIPFLEH 163


>gi|296278707|gb|ADH04308.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278709|gb|ADH04309.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278711|gb|ADH04310.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278713|gb|ADH04311.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278715|gb|ADH04312.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278717|gb|ADH04313.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278719|gb|ADH04314.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278721|gb|ADH04315.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|296278725|gb|ADH04317.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
          Length = 151

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 89/150 (59%), Positives = 112/150 (74%), Gaps = 1/150 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 1   NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R
Sbjct: 61  FARTNDYGFLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAAS 677
              GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 GERGESGLYKPEDIHYMDVSTQQVVSVAAA 150


>gi|300193575|gb|ADJ68281.1| RNA polymerase B-subunit [Staphylococcus equorum]
 gi|300193577|gb|ADJ68282.1| RNA polymerase B-subunit [Staphylococcus equorum]
          Length = 151

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 85/151 (56%), Positives = 112/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETHSITDQIDYLTADEEDSYVVAQANSVLDENGRFVEDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|76781253|gb|ABA54512.1| RpoB [Campylobacter lari subsp. lari]
 gi|76781255|gb|ABA54513.1| RpoB [Campylobacter lari]
          Length = 162

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV +GKV+N++VYL+A +EE   IA A++ +DE GS  EE V  R 
Sbjct: 61  AKVNDLGFVEAPYKKVENGKVSNEIVYLTATQEEGLVIAAASTKIDEKGSIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +V +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVHLIDLCSGMIVGVAASLIPFLEHDDANRAL 162


>gi|149067363|gb|EDM17096.1| similar to RNA polymerase III subunit RPC2 (predicted) [Rattus
            norvegicus]
          Length = 826

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 85/254 (33%), Gaps = 20/254 (7%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             + A      +    I       +   +    A+      D+ D  +   + +       
Sbjct: 590  YLLAYPQKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRC 649

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             ++        +R  +   +++     D    + I    I         G+   +     
Sbjct: 650  LVYKNAKCTL-KRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLV 708

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             KS                 Q  ++   V +       QY+      +    + IEK+  
Sbjct: 709  NKSMP------------TVTQIPLEGSNVPQQ-----PQYKDVPITYKGATDSYIEKVMI 751

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
              +       ++K+ +   R  + GDK + RHG KG+   I+P EDMPF   G   DI++
Sbjct: 752  SSNAEDAF--LIKMLLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIM 809

Query: 1123 NPLGVPSRMNVGQI 1136
            NP G PSRM V  +
Sbjct: 810  NPHGFPSRMTVSHL 823



 Score =  103 bits (257), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/312 (12%), Positives = 107/312 (34%), Gaps = 69/312 (22%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPP---- 84
           L++    S+++F+ + I    + NE          P+        L++++     P    
Sbjct: 28  LVKQHIDSFNYFINVEIKKIMKANE---KVTSDADPM------WYLKYLNIYVGLPDVEE 78

Query: 85  ------KFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
                      +C  RD+TY+ P+ + +             +  + I   ++ +G +P+M
Sbjct: 79  SFNVTRPVSPHECRLRDMTYSAPITVDIEYT----------RGSQRIIRNALPIGRMPIM 128

Query: 139 T------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASL 174
                                      G F++KG++++++ Q   S       +  R   
Sbjct: 129 LRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILIQEQLSKNRIIV-EADRKGA 187

Query: 175 SGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDSEEIL---- 229
            G  + +     ++    ++    +   ++R +     +P+     A+G++S++ +    
Sbjct: 188 VGASVTSST--HEKKSRTNMAV-KQGRFYLRHNTLSEDIPIVIIFKAMGVESDQEIVQMI 244

Query: 230 -------STFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTS 282
                  + F P +   Q+   +      + L        +       +QVI   +    
Sbjct: 245 GTEEHVMAAFGPSLEECQKAQIFTQMQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQF 304

Query: 283 GLLKSLKEKGVK 294
            ++K +++  + 
Sbjct: 305 DVVKHMRQDQIT 316



 Score = 90.9 bits (224), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 61/500 (12%), Positives = 144/500 (28%), Gaps = 43/500 (8%)

Query: 448 NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAK 507
            G    +        +++ +  + ++ ++     M++   + I             +   
Sbjct: 254 FGPSLEECQKAQIFTQMQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQD 313

Query: 508 PVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYG 567
            + + +     +   S     ++         RLS +   G+                  
Sbjct: 314 QITNGMVNAISTGNWSLKRFKMDRQGVTQVLSRLSYISALGM----------------MT 357

Query: 568 RICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENR-- 625
           RI           GLV +L     +      + P  K+       DV  L   EE +   
Sbjct: 358 RISSQFEKTRKACGLVKNLALMTHITTD-MEDGPIIKLAGNLGVEDVNLL-CGEELSYPN 415

Query: 626 -YIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS----LIP 680
            ++   N ++       ++LV             E +        + V I++       P
Sbjct: 416 VFLVFLNGNILGVIRDHKKLVSTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRP 475

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           ++        +   +M+  A      E     + +E +         +A     + +   
Sbjct: 476 YIIVKKQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTT 535

Query: 741 IRI--------VIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEV---- 788
                      V   +      + S  + Y+    +++      NQR  +     +    
Sbjct: 536 HLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYP 595

Query: 789 -RRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEF 847
            +           D   L  G+N  VA M + GY+ ED++++++  +       +  +  
Sbjct: 596 QKPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNA 655

Query: 848 EVMA-RDTKLGPEEITRDIPNVSEEGLKN----IDECGIICVGAEVNPGDILVGKITPKG 902
           +    R T    +++   + + +          +D  GI   G +V    +LV K  P  
Sbjct: 656 KCTLKRYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTV 715

Query: 903 ESPMTPEEKLLRAIFGEKAV 922
                    + +    +   
Sbjct: 716 TQIPLEGSNVPQQPQYKDVP 735


>gi|289468075|gb|ADC95718.1| RpoB [Riemerella anatipestifer DSM 15868]
          Length = 160

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 91/160 (56%), Positives = 113/160 (70%), Gaps = 2/160 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            E +  R  G+  +V  E++D ID +P Q+  I+ASLIPF
Sbjct: 121 TERIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPF 160


>gi|195424660|gb|ACF96948.1| RpoB [Arcobacter cryaerophilus]
 gi|310772095|emb|CBW46597.1| RNA polymerase subunit B [Arcobacter cryaerophilus]
          Length = 162

 Score =  150 bits (378), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG VTN++ Y +A +EE   IA  ++ LDE+G   E LV  R 
Sbjct: 61  SKVNELGFIEAPYKKVVDGVVTNEISYYTATQEEGLVIAPGSTKLDENGKIIEPLVEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL+ + K+D ID S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 NGEIILMDKNKVDLIDISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|223585647|gb|ACM91694.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 149

 Score =  149 bits (377), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 89/149 (59%), Positives = 115/149 (77%), Gaps = 2/149 (1%)

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKV 610
           RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +
Sbjct: 1   RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSI 60

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQ
Sbjct: 61  TDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 120

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQRQ 699
           VVS A + IPFLENDDSNR LMG NMQRQ
Sbjct: 121 VVSAATACIPFLENDDSNRALMGANMQRQ 149


>gi|76781309|gb|ABA54540.1| RpoB [Campylobacter mucosalis]
 gi|76781311|gb|ABA54541.1| RpoB [Campylobacter mucosalis]
 gi|76781313|gb|ABA54542.1| RpoB [Campylobacter mucosalis]
 gi|76781315|gb|ABA54543.1| RpoB [Campylobacter mucosalis]
          Length = 162

 Score =  149 bits (377), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPIETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV DGKVT+++VYL+A +EE   IA A++ LD+ G   E+L+  R 
Sbjct: 61  AKVNELGFVEAPYKKVVDGKVTDEIVYLTATQEEGNVIAPASTKLDDKGYIVEDLLEVRR 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 EGEMMLARREDVTLIDLCSGMIAGVAASLIPFLEHDDANRAL 162


>gi|55650670|emb|CAF32205.1| RNA polymerase B subunit [Anabaena augstumalis str. 'SCHMIDKE
           JAHNKE/4a']
          Length = 200

 Score =  149 bits (377), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 90/200 (45%), Positives = 125/200 (62%), Gaps = 14/200 (7%)

Query: 632 SSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
             +DE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR L
Sbjct: 1   IPVDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRAL 60

Query: 692 MGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGD 751
           MG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R  E  
Sbjct: 61  MGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDAAEIRVRVREQT 120

Query: 752 LDPS--------------TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADG 797
            D +                    Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG
Sbjct: 121 TDKTLTQSPASSKESPTGKPQEVTYYLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADG 180

Query: 798 PSTDLGDLALGRNMLVAFMP 817
            ST+ G+LALG+N++VA+MP
Sbjct: 181 SSTEGGELALGQNIVVAYMP 200


>gi|25990087|gb|AAN75054.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  149 bits (377), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 91/151 (60%), Positives = 124/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLSQ  +  N LS +T  RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSQFMDQNNPLSGLTCKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|55650610|emb|CAF31383.1| RNA polymerase B subunit [Anabaena oscillarioides str. 'BO HINDAK
           1984/43']
          Length = 210

 Score =  149 bits (377), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 90/207 (43%), Positives = 126/207 (60%), Gaps = 17/207 (8%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  +DE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDIPVDENGYIKGPQVPVRYRQDWATTTPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR- 746
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA +I +R 
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQGARDSGMVIVSRTDGDVVYVDAAQIRVRV 123

Query: 747 ----------------SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRR 790
                                    T     Y L K+QRSNQ+TC+NQ+PLV++G++V  
Sbjct: 124 RGDLSGVTGNLIAGKQHTNEQGQQVTDREIRYVLSKYQRSNQDTCLNQKPLVRIGEKVVA 183

Query: 791 NDIIADGPSTDLGDLALGRNMLVAFMP 817
             ++ADG ST+ G+LALG+N++VA+MP
Sbjct: 184 GQVLADGSSTEGGELALGQNIVVAYMP 210


>gi|25990095|gb|AAN75058.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 161

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 91/151 (60%), Positives = 125/151 (82%)

Query: 453 IDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSA 512
            DDID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A
Sbjct: 11  TDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAA 70

Query: 513 VCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPA 572
           + EFF +SQLS+  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP 
Sbjct: 71  IKEFFGTSQLSKFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI 130

Query: 573 ETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           ET EG NIGL+ SL+ +ARVN +GFIETPYR
Sbjct: 131 ETPEGPNIGLIGSLSVYARVNPFGFIETPYR 161


>gi|76781257|gb|ABA54514.1| RpoB [Campylobacter lari]
 gi|76781259|gb|ABA54515.1| RpoB [Campylobacter lari]
          Length = 162

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 92/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY+KV +GKV+N++VYL+A +EE   IA A++ +DE G+  EE V  R 
Sbjct: 61  AKVNDLGFVEAPYKKVENGKVSNEIVYLTATQEEGLVIAAASTKIDEKGNIVEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +V +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVHLIDLCSGMIVGVAASLIPFLEHDDANRAL 162


>gi|195424668|gb|ACF96952.1| RpoB [Arcobacter halophilus]
          Length = 162

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 93/162 (57%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG VTND+ Y++A  EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  AKVNELGFIEAPYKKVKDGVVTNDITYMTATLEEGLVIAPGSTKVDENGKIMEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R K+D+ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILLMERSKVDYIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|55650532|emb|CAF31376.1| RNA polymerase B subunit [Anabaena cf. circinalis macrospora
           1tu28s13]
          Length = 192

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 87/189 (46%), Positives = 120/189 (63%), Gaps = 6/189 (3%)

Query: 628 AQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDS 687
           A  +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+
Sbjct: 4   ATGDVPLDENGYIKGPQVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDA 63

Query: 688 NRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRS 747
           NR LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+
Sbjct: 64  NRALMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRA 123

Query: 748 V------EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTD 801
                   G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+
Sbjct: 124 SGQLSAASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTE 183

Query: 802 LGDLALGRN 810
            G+LALG+N
Sbjct: 184 GGELALGQN 192


>gi|83415449|gb|ABC17932.1| RNA polymerase II second largest subunit [Physoderma maydis]
          Length = 556

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 92/558 (16%), Positives = 170/558 (30%), Gaps = 90/558 (16%)

Query: 462 RRVRSVGEMLKNQYRLGLLRMERSI--KERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           +R+   G ++   +R+   ++ + +    + S            +++  + + +     +
Sbjct: 2   KRLDLAGPLMAGLFRMLFRKLVKDMGRHIQRSIDQRRDFNINLAVSSHTITNGLKYSLAT 61

Query: 520 -------------SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                        S +SQ+       S ++H RRL+      V R     + R +H TH+
Sbjct: 62  GNWGDQKKFMQTRSGVSQVLNRYTFASTLSHLRRLNT----PVGREGKLAKPRQLHNTHW 117

Query: 567 GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
           G +CPAE  EG   GLV +L   A V+  G +  P     D   T  +    + +     
Sbjct: 118 GMVCPAEVPEGQACGLVKNLALMAYVS-VGSVSDPIIDFLDEWTTEKLGEFESDQLSKCT 176

Query: 627 IAQANSSLDEDGSFTEELVFC----RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
               N          E+LV      R +G+         D  D   +    +     P  
Sbjct: 177 KIFVNGVWFGVHREPEDLVSTLKGLRRSGDITFEASIVHDIRDGELRIYTDVGRICRPLF 236

Query: 683 ENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGM--------------------------- 715
                 ++    +     V         V  G+                           
Sbjct: 237 IVSKDQQLECKKSHIDGIVNEQIYWRHLVSGGVIELLDTEEEETAMICMSPQDLFDEYPE 296

Query: 716 ------------------ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTS 757
                                  +   + I+   A I+   D  +    + +  +     
Sbjct: 297 VTDRTQRLRGRRAKEICNNWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAM 356

Query: 758 GVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFM 816
           G+       +           Q+PLV                  +  +L  G+N +VA  
Sbjct: 357 GIFLTNFQQRMDTLANILYYPQKPLV----------TTRAMEYLNFRELPAGQNAIVAIA 406

Query: 817 PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT--RDIPNVSEEGLK 874
            + GYN EDS+++++  +   +F S++   +      TK    E         +      
Sbjct: 407 CYSGYNQEDSVIMNQSSIDRGLFRSLYYRSYMDEQNSTKQELFEKPTRETTTRMRHGTYD 466

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            I++ G I  G  V+  DI++GK  P  E                 A   RD S+ + S 
Sbjct: 467 KIEDDGFIAPGTRVSGDDIIIGKTAPLPEGSNELGM--------RTAQTKRDCSISLKST 518

Query: 935 VSGTVVDVRIFNRHGIDK 952
            +G V  V +       K
Sbjct: 519 ENGIVDQVVVTTNADGFK 536


>gi|198279499|emb|CAP04784.1| RNA polymerase beta subunit [Equisetum telmateia]
          Length = 192

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 92/199 (46%), Positives = 133/199 (66%), Gaps = 7/199 (3%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQ QAVPL K E   VGTG+E   A  SG+ + ++R G +  +DA +I +   E      
Sbjct: 1   MQXQAVPLSKPEKCIVGTGLEGQTALDSGSCVTSEREGKLIYIDAEKITLFVDEETSINK 60

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                   L+ ++RSN NTC+NQ+PL+     +R+  IIADG ST  G+LALGRN+LVA+
Sbjct: 61  -------NLLSYERSNNNTCMNQKPLLCKNKFLRQGQIIADGASTVGGELALGRNILVAY 113

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER++ ED+FTS HIE +E+    T  GPE++TR+IP+++   L++
Sbjct: 114 MPWEGYNFEDAILISERLIYEDIFTSFHIERYEINVSFTSQGPEKLTREIPHLNNHILRH 173

Query: 876 IDECGIICVGAEVNPGDIL 894
           +DE G++ +G+ V  GD+L
Sbjct: 174 LDENGLVKLGSWVEAGDVL 192


>gi|195424664|gb|ACF96950.1| RpoB [Arcobacter mytili]
 gi|195424666|gb|ACF96951.1| RpoB [Arcobacter sp. F2076]
 gi|223959958|gb|ACN30291.1| RpoB [Arcobacter mytili]
          Length = 162

 Score =  149 bits (377), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 124/162 (76%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV +G VTN++VY++A  EE   IA  ++ +D++G   E L+  R 
Sbjct: 61  AKVNELGFIEAPYKKVKEGVVTNEIVYMTATLEEGLVIAPGSTKVDDNGKIIEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ + K+D+ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILLIEKNKVDYIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|289468053|gb|ADC95707.1| RpoB [Riemerella sp. IPDH 461/88]
          Length = 161

 Score =  149 bits (376), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 88/161 (54%), Positives = 116/161 (72%), Gaps = 2/161 (1%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIG
Sbjct: 1   LSQFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L+SSL  +A++N  GFIETPYRKV +G+V  +   ++L+A +EE++ IAQAN  L EDG+
Sbjct: 61  LISSLGLYAKINNLGFIETPYRKVKNGQVDLSAAPIFLNAEDEESKIIAQANVELAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           F  + +  R  G+  +V  E++D ID +P Q+  I+ASLIP
Sbjct: 121 FETDRIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIP 161


>gi|198279377|emb|CAP04723.1| RNA polymerase beta subunit [Pinus densata]
          Length = 236

 Score =  149 bits (376), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 92/238 (38%), Positives = 140/238 (58%), Gaps = 10/238 (4%)

Query: 718 VVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVN 777
             A  SG+  +A + G +E +DA+                       + +QRSN NTC +
Sbjct: 2   QAALDSGSVAIATQEGRIEYIDAV--------NITSSVNGDTVRTESVIYQRSNTNTCTH 53

Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
           Q+P +  G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED++LISER+V ED
Sbjct: 54  QKPKIHQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDAILISERLVYED 113

Query: 838 VFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGK 897
           ++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+ +  GD+LVGK
Sbjct: 114 IYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGSWIETGDVLVGK 173

Query: 898 ITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKN 953
           +TP+   ES  TP  +LL+ IFG +    R+  L  P    G V+  R  NR     +
Sbjct: 174 LTPQTIEESLCTPXGRLLQTIFGIEVSTARENCLXAPIXGRGRVIXXRWINRVDDSGD 231


>gi|225698447|gb|ACO07341.1| RpoB [Volucribacter psittacicida]
 gi|225698449|gb|ACO07342.1| RpoB [Volucribacter psittacicida]
          Length = 147

 Score =  149 bits (376), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 84/146 (57%), Positives = 110/146 (75%), Gaps = 1/146 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR 
Sbjct: 2   SEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYART 61

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAG 651
           N YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  V  R   G
Sbjct: 62  NNYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAYVTARGEHG 121

Query: 652 EEILVPREKIDFIDASPKQVVSIAAS 677
           E  L   E+I ++D S +QVVS+AA+
Sbjct: 122 ESGLYRPEEIHYMDVSTQQVVSVAAA 147


>gi|102620823|gb|ABF70980.1| RNA polymerase subunit B [Moraxella bovis]
          Length = 148

 Score =  149 bits (376), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 85/147 (57%), Positives = 111/147 (75%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FA
Sbjct: 1   PLSEITHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLAVFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           + N +GF+ETPYR+V DGKVT+D+ Y+SA+EE    +AQA+S ++E G  TEE+V  R  
Sbjct: 61  KTNNFGFLETPYRRVVDGKVTDDIEYMSAIEEVGTVVAQADSPMNEHGELTEEMVMVRYH 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAAS 677
           GE + +  +K+  +D SP+QVVS+AAS
Sbjct: 121 GESVRMSPDKVTHMDVSPRQVVSVAAS 147


>gi|198279347|emb|CAP04708.1| RNA polymerase beta subunit [Pinus muricata]
          Length = 253

 Score =  149 bits (376), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 89/189 (47%), Positives = 131/189 (69%), Gaps = 2/189 (1%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW GYNFED+
Sbjct: 29  YQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPWEGYNFEDA 88

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE G++ +G+
Sbjct: 89  ILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDENGLVMLGS 148

Query: 887 EVNPGDILVGKITPK--GESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
            +  GD+LVGK+TP+   ES  TPE +LL+ IFG +    R+  LR P G  G V+DVR 
Sbjct: 149 WIETGDVLVGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRW 208

Query: 945 FNRHGIDKN 953
            NR     +
Sbjct: 209 INRVDDSGD 217



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 87/224 (38%), Gaps = 14/224 (6%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
            I  G  V  G IL    T  G   ++  + +L A    +  +  D  L     V   +  
Sbjct: 44   IRQGECVKKGQILADGATTVG-GELSLGKNVLVAYMPWEGYNFEDAILISERLVYEDIYT 102

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
                 R+ I+    S   ER   E+   D       LD N       ++ G    +G   
Sbjct: 103  SFHIVRYRIEICMTSQGPERITREIPHLDAHS-LRHLDEN-----GLVMLGSWIETGDVL 156

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K T  + +     P  +  Q     E        L+        +++ R+ N+++   
Sbjct: 157  VGKLTPQTIEESLCTPEGRLLQTIFGIEVSTARENCLRAPIGGRGRVIDVRWINRVD--D 214

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILP 1105
             GD+        V V+++ KR IQ GDK+AGRHGNKGI+S +LP
Sbjct: 215  SGDNAE-----TVHVYISQKRKIQVGDKVAGRHGNKGIISIVLP 253


>gi|300193573|gb|ADJ68280.1| RNA polymerase B-subunit [Staphylococcus caprae]
          Length = 151

 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 84/151 (55%), Positives = 112/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|56694298|gb|AAW22889.1| RNA polymerase II second largest subunit [Adiantum tenerum]
          Length = 469

 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 60/321 (18%), Positives = 98/321 (30%), Gaps = 26/321 (8%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                 N      I   M+     + I   +     R+T             V+   L+  
Sbjct: 175  EEAYSNTYTHCXIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 233

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 234  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSID 291

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   IF R   D+ ++  S+ +E+ E   R+          +          G    
Sbjct: 292  RGFF-RSIFYRSYRDEEKKQGSLVKEEXERPIREHTQGMRHGSYDKLDDDGLAPPGTRVS 350

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K+T ++ D                         +L  +Y         R    
Sbjct: 351  GEDVIIGKTTPIAQDDTG----------------------TLAQRYSKRDQSTCLRHSES 388

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
                Q         LR VK+ V   R  Q GDK + RHG KG V      EDMP+ ++G 
Sbjct: 389  GMVDQVLLTTNADGLRFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGI 448

Query: 1117 PVDIVLNPLGVPSRMNVGQIF 1137
              DI++NP  +PSRM +GQ+ 
Sbjct: 449  SPDIIVNPHAIPSRMTIGQLI 469



 Score = 62.0 bits (149), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 54/328 (16%), Positives = 101/328 (30%), Gaps = 36/328 (10%)

Query: 464 VRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLS 523
                 ++KN   +  + +  +    +  ++  S    + I+   + +A   F     + 
Sbjct: 2   EGQACGLVKNLALMSYITVGSAANPILEFLEEWSTENFEEISPAVIPNATKIFVNGCWVG 61

Query: 524 QLEEHVNSLSRITHTRRLSALG-QGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGL 582
              +    +  +   RR   +  + GV R     E+R ++  +     P    E   + +
Sbjct: 62  IHRDPELLVRTLRQLRRQVDVNTEVGVVRDIHLKELR-LYTDYGRCSRPLFIVEKQRLLI 120

Query: 583 VSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
             S    A           Y  V  G     + Y+   EEE   I+             +
Sbjct: 121 KKS-DVRALQQKETTEPGWYDLVAKGY----IEYVDTEEEETTMISM----------TIQ 165

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVP 702
           +LV  R   E               P  ++ + AS+IPF +++ S R      M +QA+ 
Sbjct: 166 DLVNARLHPE--EAYSNTYTHCXIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 223

Query: 703 ----------------LLKAEAPFVGT-GMESVVAKSSGAAIVAKRAGIVEQVDAIRIVI 745
                           L   + P V T  ME +  +   A I A  A            +
Sbjct: 224 IYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSV 283

Query: 746 RSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
              +  +D        YR  + +   Q 
Sbjct: 284 IMNQSSIDRGFFRSIFYRSYRDEEKKQG 311


>gi|308191303|gb|ADO16230.1| RpoB [Arcobacter sp. FE2]
          Length = 162

 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 120/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ R RAG  +RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVRERAGXXVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG VTN++ Y +A +EE   IA  ++ LDE+G   E LV  R 
Sbjct: 61  SKVNELGFIEAPYKKVVDGIVTNEISYYTATQEEGLVIAPGSTKLDENGKIIEPLVEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L  + K+D ID S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 NGEILLXDKNKVDLIDISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|71727072|gb|AAZ39701.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 246

 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 4    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 63

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 64   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGDDV 122

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 123  IIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 170

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 171  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 222

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 223  IINPHAIPSRMTIAHLIECLLSKV 246



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 9   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 58

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 59  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 118

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 119 GDDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 171

Query: 950 IDK 952
             K
Sbjct: 172 NVK 174


>gi|71727086|gb|AAZ39708.1| RNA polymerase II [Aschersonia sp. BCC 1487]
          Length = 243

 Score =  149 bits (376), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 81/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            ++ +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MVHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDPESQDLGTRTNVHQRRDISTPLRSTENGIVDSVIVTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 40/186 (21%), Positives = 66/186 (35%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 3   HILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 52

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   L   E       +    +       +DE GI+  G 
Sbjct: 53  SSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGV 112

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  DI++GK  P       PE + L           RD S  + S  +G V  V +  
Sbjct: 113 RVSGEDIIIGKTAPID-----PESQDLGTRTNVHQR--RDISTPLRSTENGIVDSVIVTV 165

Query: 947 RHGIDK 952
                K
Sbjct: 166 NADNVK 171


>gi|300193581|gb|ADJ68284.1| RNA polymerase B-subunit [Staphylococcus saprophyticus subsp.
           saprophyticus]
          Length = 151

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 85/151 (56%), Positives = 113/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G FT + V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFTADEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|71727012|gb|AAZ39671.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 249

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 7    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 66

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 67   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 125

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 126  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 173

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 174  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 225

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 226  IINPHAIPSRMTIAHLIECLLSKV 249



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 12  YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 61

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 62  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 121

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 122 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 174

Query: 950 IDK 952
             K
Sbjct: 175 NVK 177


>gi|34451793|gb|AAQ72392.1| RpoB [Klebsiella sp. 910]
          Length = 152

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 97/151 (64%), Positives = 118/151 (78%)

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+ ASLIPFLE+DD+NR LMG NMQRQAVP L+A+ P VGTGME  VA  SG   VAKR
Sbjct: 2   VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR 61

Query: 732 AGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRN 791
            G V+ VDA RIVI+  E ++ P  +G+DIY L K+ RSNQNTC+NQ P V +G+ + R 
Sbjct: 62  GGTVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERG 121

Query: 792 DIIADGPSTDLGDLALGRNMLVAFMPWHGYN 822
           D++ADGPSTDLG+LALG+NM VAFMPW+GYN
Sbjct: 122 DVLADGPSTDLGELALGQNMRVAFMPWNGYN 152


>gi|300193585|gb|ADJ68286.1| RNA polymerase B-subunit [Staphylococcus piscifermentans]
          Length = 151

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 111/151 (73%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFLSEEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ REK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTIMDREKMDYMDVSPKQVVSAAT 151


>gi|209892875|ref|YP_002290848.1| rpoB [Babesia bovis T2Bo]
 gi|154795884|gb|EDO05068.1| rpoB [Babesia bovis]
          Length = 971

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 62/273 (22%), Positives = 105/273 (38%), Gaps = 55/273 (20%)

Query: 1044 TSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRI 1103
              K +++         ++ G ++     ++   F+     I  GDK+ GRHGNKG +S+I
Sbjct: 704  DIKKLVKYECTQYSNFVRIGSNLNYANFKL---FLVSINNINVGDKLCGRHGNKGTISKI 760

Query: 1104 LPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANG 1163
            +   + P+  +    +I+ +P+G  SRMNVGQ  E ++G                     
Sbjct: 761  IEIPESPYTSEDKLPNIITSPIGAASRMNVGQFIEGYIG------------------NTC 802

Query: 1164 DISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSML 1223
            DI  +R      + +      +      + +            +  VF         +  
Sbjct: 803  DIDNVRIKSPINLHSSDMYSSLYVKSVSNKINNRYVKLKSSQNAVSVF-----RDFKTGY 857

Query: 1224 RMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYAR--STGSYSLVTQQ 1281
            ++     +   IL                  Y  KL H    K   R  S+    LV  Q
Sbjct: 858  KLKGF--THHVIL------------------YFFKLMHTSKSKFRYRCSSS---KLV--Q 892

Query: 1282 PLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEM 1314
             + G+S    Q+ GEMEVW ++A+GA+Y L+EM
Sbjct: 893  YVHGESKE--QKFGEMEVWSLEAHGASYNLKEM 923



 Score =  100 bits (249), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 111/628 (17%), Positives = 227/628 (36%), Gaps = 31/628 (4%)

Query: 228 ILSTFYPKIVYSQRGDFWCFPLSAAD-LMVGAKVSSSLVDIDTGEQVIESGKKL----TS 282
           IL+  Y       +        +     +   K+  +L+ I + +++  +   L    T 
Sbjct: 18  ILNNIYTLFFDVVKYQKKLLKRNNYRVKVQNIKLYFNLLSIKSIDKINYNSYYLLSYSTM 77

Query: 283 GLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFH--SE 340
               ++  K +      S  +    +    V+  TGEI I   +      L+ I    S 
Sbjct: 78  YYSFNVPLKFIFNDQSKSININYNILNIPKVDA-TGEILINGFNRTPVLHLKSIIKHTST 136

Query: 341 IRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLF 400
           ++   ++    +N   +    +   +NK     L D+ ++     +   S+ ++      
Sbjct: 137 VQKKRLIKNYLINLTGFNYMHVSVSQNKYVYVKLNDLSKLDLSEVIKFNSIHKNFIKLTI 196

Query: 401 FDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLG 460
           F+  +           +  +N       ++    DII++I   ++  + K T  + D+  
Sbjct: 197 FEIIEAINDKFYNDYNDNVINSFFTAYNKNCSYADIISVINKFINAVHKKITFINSDSFI 256

Query: 461 NRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSS 520
           N+ V S+ + + N  +  L           +      +   D       +    E F  +
Sbjct: 257 NKNVNSICDNMFNLIKKSLS------TYHFTDPKKHILHVLDSKTKFSNIPLFRENFLLN 310

Query: 521 QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY---GRICPAETSEG 577
                   +N LS + +  +L+  G    + +      + +    Y     I    T +G
Sbjct: 311 PSLHYTNQLNLLSCVQNKFKLNIFGYSTSSTSTTFAIPKYLRQVQYFYLNFINILYTVDG 370

Query: 578 HNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLS--AMEEENRYIAQANSSLD 635
              G++S++      N     +     + + +   + +YL   +    +  I   N+ L 
Sbjct: 371 EKCGILSTI----TTNTIEQNKKLKTVIINKQKFLNNIYLDQFSKNLNSITINNYNNLLK 426

Query: 636 EDGSFTEELVFCRCAGEEILVPREKIDFID-ASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           +  +F    V     GE  +V  +K       +   + +I   LIPFL N+D  R LMG 
Sbjct: 427 KSYNFKINHVEVIENGEFKIVKLDKHSSNSSLTFYNIFNITELLIPFLLNNDMCRSLMGS 486

Query: 695 NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
            M  QAVPL+ +   +V T    +    S   I++  +GI+      +I I         
Sbjct: 487 KMHTQAVPLIHSNPQYVYTKYNQITNLISNKCIISSTSGIIVLSTNYKITILDDNNRYVS 546

Query: 755 STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
                  Y L  +   + N     RP+V  G++     I+A        +  LG N  V 
Sbjct: 547 -------YYLSPYNIHDYNYYTRYRPVVWEGEKSNIGTILAIPSDAANCEFTLGFNNFVN 599

Query: 815 FMPWHGYNFEDSMLISERMVSEDVFTSI 842
           +  ++GY  ED++++++ +   D+ TS+
Sbjct: 600 YSFYYGYEHEDAIVLNKNVAYNDMLTSL 627


>gi|71726996|gb|AAZ39663.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 247

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 5    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 64

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 65   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 123

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 124  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 171

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 172  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 223

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 224  IINPHAIPSRMTIAHLIECLLSKV 247



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 10  YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 59

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 60  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 119

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 120 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 172

Query: 950 IDK 952
             K
Sbjct: 173 NVK 175


>gi|219564011|gb|ACL28189.1| RNA polymerase II second largest subunit [fungal sp. M32]
          Length = 243

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 88/265 (33%), Gaps = 27/265 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+     S +   + 
Sbjct: 3    MANILYYPQKPLARTMSMEYLKFRELPAGQNAIVAIACYSGYNQEDSVXMNQSSIDRGLX 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
                +  +   +      +    +E   + +  E + L    Y ++     I  G     
Sbjct: 63   RSLFYRTYQDQE----KMIGHSVVEQFEKPQRSETLRLKHGTYDKIDNDGIIAPGIRVSG 118

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR  + +K    T     E    +++
Sbjct: 119  EDIIMGKTAPMAPD---------------AEELGQRQKQHIKRDVSTPLRSTESGVIDQV 163

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                 GD       R  KV V   +  Q GDK A RHG KG +      EDMPF ++G  
Sbjct: 164  MITTTGD-----GTRFAKVRVRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSREGLV 218

Query: 1118 VDIVLNPLGVPSRMNVGQIFETHLG 1142
             DI++NP  +PSRM +  + E  L 
Sbjct: 219  PDIIINPHAIPSRMTIAHLIECQLS 243


>gi|289468043|gb|ADC95702.1| RpoB [Coenonia anatina]
          Length = 159

 Score =  149 bits (375), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 88/159 (55%), Positives = 114/159 (71%), Gaps = 1/159 (0%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N L+ ITH RRLSALG GG++R RAG E+RDVH THYGR+CP ET EG NIGL+
Sbjct: 1   QFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKV-TNDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
           SSL  FA+VN  GFIETPYR+V +GKV  + +VYLSA EEE + IA AN  +D++G   E
Sbjct: 61  SSLAVFAKVNGMGFIETPYREVKEGKVNLDSMVYLSAEEEEGKKIAMANIPMDKEGKLEE 120

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
           E +  +  G+  +V   ++D+ D +P Q+ SI+ASLIPF
Sbjct: 121 ERLVVKEEGDFPVVEPTEVDYTDVAPNQIASISASLIPF 159


>gi|300193579|gb|ADJ68283.1| RNA polymerase B-subunit [Staphylococcus saprophyticus subsp.
           saprophyticus]
          Length = 151

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 84/151 (55%), Positives = 112/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS+LDE+G F  + V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNSITDQIDYLTADEEDSYVVAQANSTLDENGRFIADEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|71727074|gb|AAZ39702.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 243

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MAHILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 3   HILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 52

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   L   E       +    +       +DE GI+  G 
Sbjct: 53  SSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGV 112

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK  P  +       +             RD S  + S  +G V  V +  
Sbjct: 113 RVSGEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTV 165

Query: 947 RHGIDK 952
                K
Sbjct: 166 NADNVK 171


>gi|308191305|gb|ADO16231.1| RpoB [Arcobacter thereius]
          Length = 162

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 119/162 (73%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG  TN++ Y +A +EE   IA  ++ LDE+G   E LV  R 
Sbjct: 61  SKVNDLGFIEAPYKKVVDGVATNEITYFTATQEEGLVIAPGSTKLDENGKILEPLVEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R K+D ID S + V  +AASL PFLE++D+NR L
Sbjct: 121 NGEILLMERSKVDLIDISSQMVXGVAASLFPFLEHNDANRAL 162


>gi|145307904|gb|ABP57256.1| RNA polymerase II second largest subunit [Erynia conica]
          Length = 246

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 50/268 (18%), Positives = 90/268 (33%), Gaps = 27/268 (10%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 2    LRMDTLANILYYPQKPLVATRGMEFLRFRELPAGQNAIVAICCYSGYNQEDSVIMNQSSI 61

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCG 992
               +    I+ R  +D+ ++S   E   IE   +      + L    Y +L +   I  G
Sbjct: 62   DRGLF-RSIYYRTYLDQEKKSGLNE---IESFEKPSRKNTLRLRHGTYEKLEDDGLIAPG 117

Query: 993  QNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDR 1052
                       K+  +  D      R++          ++     +  +   + +     
Sbjct: 118  TRVSGDDIIIGKTAPVPPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVMLTVNQ---- 173

Query: 1053 FKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFL 1112
                              +R  KV V   R  Q GDK A RHG KG +      EDMPF 
Sbjct: 174  ----------------EGMRFAKVRVRSTRIPQIGDKFASRHGQKGTIGMTYRNEDMPFS 217

Query: 1113 KDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
             +G   D+V+NP  +PSRM +G + E  
Sbjct: 218  AEGMVPDLVINPHAIPSRMTIGHMVECL 245



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                     +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTLANILYYPQKPLVA----------TRGMEFLRFRELPAGQNAIVAICCYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RDIPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    + + L   E       ++   +     + +++ G
Sbjct: 53  SVIMNQSSIDRGLFRSIYYRTYLDQEKKSGLNEIESFEKPSRKNTLRLRHGTYEKLEDDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G    DV        +G+   V+
Sbjct: 113 LIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRTRGHSKRDVSTPLKSTETGIVDRVM 168


>gi|300193583|gb|ADJ68285.1| RNA polymerase B-subunit [Staphylococcus simiae]
          Length = 151

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 85/151 (56%), Positives = 112/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F E+ V
Sbjct: 61  SYARVNEFGFIETPYRKVDIDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFIEDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|227826352|gb|ACP41903.1| RNA polymerase II [Silene uniflora]
          Length = 229

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 35/100 (35%), Positives = 45/100 (45%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDI 1165
             +PSRM +GQ+ E  +G                     +I
Sbjct: 190  AIPSRMTIGQLIECIMGKXXXXXXXXXXXTPFXDVTVDNI 229



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|11595828|emb|CAC18342.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 147

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 83/148 (56%), Positives = 109/148 (73%), Gaps = 1/148 (0%)

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFI 598
           RR+SALG GG+ R RAG E+RDVHPTHYGR+CP    EG NIGL++SL ++A  N YGF+
Sbjct: 1   RRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIXXPEGPNIGLINSLAAYAGTNQYGFL 60

Query: 599 ETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           E+PYR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   
Sbjct: 61  ESPYRVVKEGEVTDEMVFLSAIEEADHVIAQASAKL-EGRKLVDELVAVRHLNEFTVKAP 119

Query: 659 EKIDFIDASPKQVVSIAASLIPFLENDD 686
           E +  +D SPKQVVS+AASLIPFLE+DD
Sbjct: 120 EDVTLMDVSPKQVVSVAASLIPFLEHDD 147


>gi|71726998|gb|AAZ39664.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 245

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 3    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 62

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 63   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 121

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 122  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 169

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 170  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 221

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 222  IINPHAIPSRMTIAHLIECLLSKV 245



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 58  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 118 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 170

Query: 950 IDK 952
             K
Sbjct: 171 NVK 173


>gi|71727016|gb|AAZ39673.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 249

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 80/266 (30%), Gaps = 21/266 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 65   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 123

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 124  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 173

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 174  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWA 1144
            DI++NP  +PSRM +  + E  L   
Sbjct: 224  DIIINPHAIPSRMTIAHLIECLLSKV 249



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 65/192 (33%), Gaps = 22/192 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   L   E       +    +       +DE G
Sbjct: 53  SVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  D+++GK  P  +       +             RD S  + S  +G V 
Sbjct: 113 IVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVD 165

Query: 941 DVRIFNRHGIDK 952
            V +       K
Sbjct: 166 SVILTVNADNVK 177


>gi|300193587|gb|ADJ68287.1| RNA polymerase B-subunit [Staphylococcus piscifermentans]
 gi|300193589|gb|ADJ68288.1| RNA polymerase B-subunit [Staphylococcus piscifermentans]
          Length = 151

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 86/151 (56%), Positives = 111/151 (73%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      VT+ + YL+A EE++  +AQANS LD++G F  E V
Sbjct: 61  SYARVNEFGFIETPYRKVDLDTNTVTDQIDYLTADEEDSYVVAQANSRLDDEGHFLSEEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ REK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTIMDREKMDYMDVSPKQVVSAAT 151


>gi|223585659|gb|ACM91700.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 148

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 88/148 (59%), Positives = 114/148 (77%), Gaps = 2/148 (1%)

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVC--DGKV 610
           RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYRKV      +
Sbjct: 1   RAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSI 60

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQ 670
           T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+D++D SPKQ
Sbjct: 61  TDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQ 120

Query: 671 VVSIAASLIPFLENDDSNRVLMGCNMQR 698
           VVS A + IPFLENDDSNR LMG NMQR
Sbjct: 121 VVSAATACIPFLENDDSNRALMGANMQR 148


>gi|224107471|ref|XP_002333507.1| predicted protein [Populus trichocarpa]
 gi|222837092|gb|EEE75471.1| predicted protein [Populus trichocarpa]
          Length = 259

 Score =  149 bits (375), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 55/186 (29%), Positives = 98/186 (52%), Gaps = 17/186 (9%)

Query: 73  MLEF----VSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQ 128
            +EF     +Y+   P     D ++  LTY+  L ++  LI          K+ +D++EQ
Sbjct: 6   EIEFQLFVETYQLVEPSIKERDAVYESLTYSSELYVSGGLIW---------KNSRDMQEQ 56

Query: 129 SIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQ 188
           +I++G++PLM   GT ++ GI RIV++Q+ +SPGI++  +     +S   +Y   II D 
Sbjct: 57  TIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYRSELNHNGIS---VYTGTIISDW 113

Query: 189 GLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTF-YPKIVYSQRGDFWCF 247
           G  +++E D K  I  R+ R++K+ +     A+G++  EIL    YP+I  S   D    
Sbjct: 114 GGRVELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLSDKEKK 173

Query: 248 PLSAAD 253
            + + +
Sbjct: 174 KIGSRE 179


>gi|289468057|gb|ADC95709.1| RpoB [Riemerella sp. IPDH 359/90]
 gi|289468079|gb|ADC95720.1| RpoB [Riemerella sp. IPDH 180/88]
          Length = 161

 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 89/161 (55%), Positives = 116/161 (72%), Gaps = 2/161 (1%)

Query: 522 LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIG 581
           LSQ  +  N LS +TH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIG
Sbjct: 1   LSQFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIG 60

Query: 582 LVSSLTSFARVNAYGFIETPYRKVCDGKV--TNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           L+SSL  +A++N  GFIETPYRKV +GKV  +   ++L+A +EE++ IAQAN  L EDG+
Sbjct: 61  LISSLGLYAKINNLGFIETPYRKVENGKVDLSAAPIFLNAEDEESKIIAQANVELAEDGT 120

Query: 640 FTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIP 680
           F  + +  R  G+  +V  E++D ID +P Q+  I+ASLIP
Sbjct: 121 FETDRIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIP 161


>gi|195424642|gb|ACF96939.1| RpoB [Arcobacter butzleri]
 gi|195424644|gb|ACF96940.1| RpoB [Arcobacter butzleri]
 gi|307092548|gb|ADN28506.1| RNA polymerase beta subunit [Arcobacter butzleri]
 gi|307092550|gb|ADN28507.1| RNA polymerase beta subunit [Arcobacter butzleri]
 gi|307092552|gb|ADN28508.1| RNA polymerase beta subunit [Arcobacter butzleri]
          Length = 162

 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  SKVNDLGFIEAPYKKVVDGVVTNEISYYTATQEEGLVIAPGSTKVDENGKIIEPLIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R  +D ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 NGEILLMERNSVDLIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|300193601|gb|ADJ68294.1| RNA polymerase B-subunit [Staphylococcus xylosus]
          Length = 151

 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 84/151 (55%), Positives = 111/151 (73%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T  + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|71726994|gb|AAZ39662.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 244

 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 2    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 62   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 120

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 121  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 168

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 169  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 220

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 221  IINPHAIPSRMTIAHLIECLLSKV 244



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 57  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 117 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 169

Query: 950 IDK 952
             K
Sbjct: 170 NVK 172


>gi|220961148|gb|ACL93040.1| RNA polymerase B subunit [Streptomyces antimycoticus]
 gi|220961166|gb|ACL93049.1| RNA polymerase B subunit [Streptomyces melanosporofaciens]
 gi|220961200|gb|ACL93066.1| RNA polymerase B subunit [Streptomyces castelarensis]
 gi|220961202|gb|ACL93067.1| RNA polymerase B subunit [Streptomyces sporoclivatus]
          Length = 180

 Score =  148 bits (374), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 94/175 (53%), Positives = 126/175 (72%), Gaps = 1/175 (0%)

Query: 577 GHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDE 636
           G NIGL+ SL S+ RVNA+GFIETPYRKV DG VT+DV YL+A EE+   IAQAN+ L +
Sbjct: 1   GPNIGLIGSLASYGRVNAFGFIETPYRKVVDGVVTDDVDYLTADEEDRFVIAQANAPLAD 60

Query: 637 DGSFTEELVFCRCAG-EEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCN 695
           D  F E  V  R  G E   +P + +D++D SP+Q+VS+A ++IPFLE+DD+NR LMG N
Sbjct: 61  DLRFAENRVLVRRRGGEVDYIPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGSN 120

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEG 750
           M RQAVPL+KAE+P VGTGME   A  +G  I A++ G+V++V A  + + + +G
Sbjct: 121 MMRQAVPLIKAESPLVGTGMEYRCAVDAGDVIKAEKDGVVQEVSADYVTVANDDG 175


>gi|71727000|gb|AAZ39665.1| RNA polymerase II [Aschersonia aleyrodis]
          Length = 243

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|195424662|gb|ACF96949.1| RpoB [Arcobacter cryaerophilus]
          Length = 162

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 90/162 (55%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  SKVNELGFIEAPYKKVVDGVVTNEISYYTATQEEGLVIAPGSTKVDENGKIIEPLIEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL+ + K+D ID S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 NGEIILMDKNKVDLIDISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|76781293|gb|ABA54532.1| RpoB [Campylobacter curvus]
          Length = 164

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 90/164 (54%), Positives = 121/164 (73%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L+
Sbjct: 1   QTNPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLS 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
           ++A+VN  GF+E PY+KV DGKV +++VYL++ +EE   IA A++ LDE+G   E+L+  
Sbjct: 61  TYAKVNDLGFVEAPYKKVVDGKVIDEIVYLTSTQEEGNVIAPASTKLDENGYIVEDLIEV 120

Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           R  GE +L  RE +  ID     +  +AASLIPFLE+DD+NR L
Sbjct: 121 RREGEMMLARREDVTLIDLCSGMIAGVAASLIPFLEHDDANRAL 164


>gi|161899345|ref|XP_001712899.1| second-largest subunit of RNA polymerase III [Bigelowiella natans]
 gi|75756393|gb|ABA27287.1| second-largest subunit of RNA polymerase III [Bigelowiella natans]
          Length = 1074

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 112/293 (38%), Gaps = 70/293 (23%)

Query: 1084 IQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGW 1143
             + GDK + RHG KG+V  +      PF          LN          GQI       
Sbjct: 838  PEIGDKYSSRHGQKGVVGLMGNKIHFPFN---------LN----------GQI------- 871

Query: 1144 ACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSG 1203
                                         + ++     T +++       L        G
Sbjct: 872  ----------------------------PDFIMNPAGFTSRMTMGQVLESLFTKVVLAKG 903

Query: 1204 VPVSTPVFDGADE--EAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNH 1261
             P  + +F+      +     L + D + SG+  + +   G  ++  +  G I+  KL H
Sbjct: 904  NPFKSSIFESNKLYLKDCTQSLILCDTEFSGKETMINPKKGSIYNSTIFTGPIFYHKLKH 963

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDD 1321
            +VS+K+ +RS+G   ++T+QP+ G+  +GG R+GEME  CI A+G   VL E +   SD 
Sbjct: 964  LVSNKIQSRSSGRKHILTKQPVKGRGKQGGLRIGEMEKDCIIAFGCTSVLVERMLENSDS 1023

Query: 1322 -----------VVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDL 1363
                       +    +        N  ++     +F +L +E+QA  +SI +
Sbjct: 1024 HKFILVKKSGIIDASNKKLS---TTNKIYKNRISYAFKLLFQELQATNISIRI 1073


>gi|296278699|gb|ADH04304.1| RNA polymerase beta subunit [Pasteurellaceae bacterium CR4]
          Length = 151

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 89/150 (59%), Positives = 112/150 (74%), Gaps = 1/150 (0%)

Query: 529 VNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS 588
            N LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++
Sbjct: 1   NNPLSEVTHKRRISALGSGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSA 60

Query: 589 FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           FAR N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R
Sbjct: 61  FARTNDYGFLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTAR 120

Query: 649 -CAGEEILVPREKIDFIDASPKQVVSIAAS 677
              GE  L   E I ++D S +QVVS+AA+
Sbjct: 121 GERGESGLYKPEDIHYMDVSTQQVVSVAAA 150


>gi|71067868|gb|AAZ22926.1| RNA polymerase II [Aschersonia placenta]
          Length = 243

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 79/262 (30%), Gaps = 21/262 (8%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 3    PNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 61

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R   D+ ++      E  E               +       +  G         
Sbjct: 62   RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVI 121

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  +      R+   Q       ++     +      + +              
Sbjct: 122  IGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------- 168

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI+
Sbjct: 169  -------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDII 221

Query: 1122 LNPLGVPSRMNVGQIFETHLGW 1143
            +NP  +PSRM +  + E  L  
Sbjct: 222  INPHAIPSRMTIAHLIECLLSK 243



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 7   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 56

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 57  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 116

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 117 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 169

Query: 950 IDK 952
             K
Sbjct: 170 NVK 172


>gi|195424646|gb|ACF96941.1| RpoB [Arcobacter cibarius]
 gi|195424648|gb|ACF96942.1| RpoB [Arcobacter cibarius]
          Length = 162

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 89/162 (54%), Positives = 121/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  SKVNDLGFIEAPYKKVVDGIVTNEITYYTATQEEGLVIAPGSTKVDENGKIVEPLIEVRK 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R  ++ ID S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 DGEILLMERSSVNLIDISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|225698441|gb|ACO07338.1| RpoB [Volucribacter psittacicida]
          Length = 145

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 83/145 (57%), Positives = 109/145 (75%), Gaps = 1/145 (0%)

Query: 534 RITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVN 593
            +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL+ +AR N
Sbjct: 1   EVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLSVYARTN 60

Query: 594 AYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-CAGE 652
            YGF+ETPYRKV +G+VT ++ YLSA+EE +  IAQAN++LDE+  FT+  V  R   GE
Sbjct: 61  NYGFLETPYRKVVNGQVTEEIEYLSAIEEGHYVIAQANANLDENFRFTDAYVTARGEHGE 120

Query: 653 EILVPREKIDFIDASPKQVVSIAAS 677
             L   E+I ++D S +QVVS+AA+
Sbjct: 121 SGLYRPEEIHYMDVSTQQVVSVAAA 145


>gi|71067879|gb|AAZ22931.1| RNA polymerase II [Moelleriella libera]
 gi|71727028|gb|AAZ39679.1| RNA polymerase II [Aschersonia aleyrodis]
 gi|71727046|gb|AAZ39688.1| RNA polymerase II [Aschersonia placenta]
          Length = 249

 Score =  148 bits (374), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 80/266 (30%), Gaps = 21/266 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 65   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 123

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 124  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 173

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 174  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWA 1144
            DI++NP  +PSRM +  + E  L   
Sbjct: 224  DIIINPHAIPSRMTIAHLIECLLSKV 249



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 22/193 (11%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 2   RRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 51

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +   L   E       +    +       +DE 
Sbjct: 52  DSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDED 111

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+  G  V+  D+++GK  P  +       +             RD S  + S  +G V
Sbjct: 112 GIVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIV 164

Query: 940 VDVRIFNRHGIDK 952
             V +       K
Sbjct: 165 DSVILTVNADNVK 177


>gi|293611888|gb|ADE48388.1| RNA polymerase beta chain [Bowenia serrulata]
          Length = 189

 Score =  148 bits (374), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 93/197 (47%), Positives = 134/197 (68%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAASDSGSATIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LI+ER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILINERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|71067886|gb|AAZ22934.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 243

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|323447742|gb|EGB03653.1| hypothetical protein AURANDRAFT_72696 [Aureococcus anophagefferens]
          Length = 902

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 134/997 (13%), Positives = 259/997 (25%), Gaps = 257/997 (25%)

Query: 29  LIEVQKASYDHFLMMNIA---PDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPK 85
           L++   AS+D F+   I      ER           V P         L +       P 
Sbjct: 43  LMKQHIASFDFFVETEIKNVVAAERDGAPNHTVRSEVDP------NFYLSYTDVYVGVPS 96

Query: 86  F----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDL 135
                         +C  RD TY+ P+ + +R            +  + +  + + +G +
Sbjct: 97  IEEDAFTSTAATPFECRLRDCTYSAPIYVDVRY----------RRGPQIVTTKRVPIGCI 146

Query: 136 PLMT------------------------KDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGR 171
           P+M                           G FV+KG++++++ Q   S           
Sbjct: 147 PIMLRSSKCVLHNQSWSQLEALKECPHDPGGYFVVKGVEKVILMQEQLSKN--------- 197

Query: 172 ASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRR---RK----------------- 211
                      R+I        IE D+K  +   I      RK                 
Sbjct: 198 -----------RMI--------IELDAKGFVCATITSSTHERKSRCSIVVKQTTHGHRVY 238

Query: 212 ---------VPVTSFLMALGMDSEE------------ILSTFYPKIVY----SQRGDFWC 246
                    +PV   L A+GM+S++            I + F   +        +     
Sbjct: 239 LKHNTLGDEIPVVIILKAMGMESDQEIAELVSSADLKIANIFVNSMEEPCAAHVKSQKQA 298

Query: 247 FPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGL 306
                  +    K  S+   +            +     + L    +  + +        
Sbjct: 299 LEYVGQAIRAKQKAQSAEGSLPQYFPRSRQPVSIEDEAREVLAHVVLSHVPVEDYDFVAK 358

Query: 307 -----YVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNT 361
                +V   ++        ++  D    K LE            L+     +     + 
Sbjct: 359 RTYIGHVTRRVLAASLDNSLLDDKDYYGNKRLELAGQLLSLLFEDLFKRFNADLKRSADL 418

Query: 362 LVTDKNKDRKDALLDIYR--VMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMR 419
           ++  +N+    A+ DI +  V R   +S   V             K D + V +V   + 
Sbjct: 419 VLQKQNRT---AVFDIVKSTVWRTDTISQGFVHAISTGNWVLKRFKMDRAGVTQVLSRLS 475

Query: 420 LNLDTPDDVRHIRKEDIIAIIKILVDLR-NGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
                    R   + +          L+ +  G +   D         V  +    +   
Sbjct: 476 YVSAIGMMTRVNSQFEKTRKTSGPRALQPSQWGMLCPADTPEGETCGLVKNLALLAHVTR 535

Query: 479 LLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHT 538
               ER                          + +        +            +   
Sbjct: 536 DADAERIRSSCFDLGVEQLGYLSGAELNSHPGAYLVFLNGLV-IGACRRPHKLAGALRCM 594

Query: 539 RRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS-----------LT 587
           RR   +G+              V     GR+C       H    +++           LT
Sbjct: 595 RRSKRIGEFVSVYTHTVHRAIYV-ACDGGRVCRPLIVAAHGHSRLTAARLATAFAKKCLT 653

Query: 588 SFARVNAYGFIETPYRKVC--------DGKVT-NDVVYLSAMEEENRYIAQANSSLDEDG 638
           S  R N          +V         D   T   + Y+   EE N +IA     L    
Sbjct: 654 SHDRSNLGELSNRMRSRVSVENSAGALDYLTTAGIIEYVDVNEENNCFIALDERELTP-- 711

Query: 639 SFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQR 698
                                +   ++  P  ++ + + L+ F  ++ S R    C M +
Sbjct: 712 ---------------------RHTHVEIDPVTILGVVSGLVAFPHHNQSPRNTYQCAMGK 750

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QA+         V T     +     + +                               
Sbjct: 751 QAMGS-------VSTNQYERMDSLLYSLVY------------------------------ 773

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                              Q+P+VK                     L  G N  +A M +
Sbjct: 774 ------------------PQKPMVKS----------RILDLVQFDALPGGCNATLAVMSY 805

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPN----------V 868
            GY+ ED++++++  +       + +++ +   R    G  + T   P            
Sbjct: 806 SGYDIEDAIVLNKASLDRGFMRCVVVKKHQASIRRYANGACDRTTGPPPATSFVQGTIDA 865

Query: 869 SEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESP 905
             +    +D+ GI  VG ++N   I++ +  P  +  
Sbjct: 866 RYKRYSALDDDGICRVGEKLNDQYIMINREIPVEDRD 902


>gi|186462236|gb|ACC78595.1| RNA polymerase subunit B [Serratia rubidaea]
          Length = 138

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 87/137 (63%), Positives = 112/137 (81%)

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
           RAG E+RDVHPTHYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYR+V DG VT+
Sbjct: 2   RAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTD 61

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
           ++ YLSA+EE N  IAQANS+LD+DG F E+LV CR  GE  L  R+++D++D S +QVV
Sbjct: 62  EINYLSAIEEGNFVIAQANSNLDDDGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVV 121

Query: 673 SIAASLIPFLENDDSNR 689
           S+ ASLIPFLE+DD+NR
Sbjct: 122 SVGASLIPFLEHDDANR 138


>gi|102620825|gb|ABF70981.1| RNA polymerase subunit B [Moraxella bovoculi 237]
 gi|102620827|gb|ABF70982.1| RNA polymerase subunit B [Moraxella bovoculi]
 gi|102620829|gb|ABF70983.1| RNA polymerase subunit B [Moraxella bovoculi]
 gi|102620831|gb|ABF70984.1| RNA polymerase subunit B [Moraxella ovis]
          Length = 148

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 86/147 (58%), Positives = 112/147 (76%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS ITH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL  FA
Sbjct: 1   PLSEITHKRRVSALGPGGLTRERAGFEVRDVHNTHYGRVCPIETPEGPNIGLINSLAVFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           + N +GF+ETPYR+V DGKVT+D+ Y+SA+EE    IAQA+S ++E+G  TEE+V  R  
Sbjct: 61  KTNNFGFLETPYRRVIDGKVTDDIEYMSAIEEVGSVIAQADSPMNENGELTEEMVMVRYQ 120

Query: 651 GEEILVPREKIDFIDASPKQVVSIAAS 677
           GE + +  +K+  +D SP+QVVS+AAS
Sbjct: 121 GESVRMGVDKVTHMDVSPRQVVSVAAS 147


>gi|300193571|gb|ADJ68279.1| RNA polymerase B-subunit [Staphylococcus cohnii subsp. cohnii]
          Length = 151

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 84/151 (55%), Positives = 112/151 (74%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNSITDHIDYLTADEEDSYVVAQANSKLDENGRFLDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G   ++ +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVVSAAT 151


>gi|63086898|gb|AAY30848.1| RNA polymerase II [Moelleriella zhongdongii]
          Length = 247

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 87/262 (33%), Gaps = 29/262 (11%)

Query: 890  PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH- 948
            P   ++        +  + E    R +   +   V        +     +++    +R  
Sbjct: 6    PWANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 65

Query: 949  GIDKNERSISVEREQI-----ELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPK 1000
                  RS S + +++     E+  +      + +    Y +L E   +  G        
Sbjct: 66   FRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 125

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 126  IIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 173

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 174  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 225

Query: 1121 VLNPLGVPSRMNVGQIFETHLG 1142
            ++NP  +PSRM +  + E  L 
Sbjct: 226  IINPHAIPSRMTIAHLIECLLS 247



 Score = 84.0 bits (206), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 12  YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 61

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 62  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 121

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 122 GEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 174

Query: 950 IDK 952
             K
Sbjct: 175 NVK 177


>gi|226445698|gb|ACO58371.1| RNA polymerase [Mycoplasma fermentans]
          Length = 165

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 79/165 (47%), Positives = 114/165 (69%), Gaps = 1/165 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNFATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY KV +G V  ++V YL+A EE    IAQ+   +DE+    ++ +  R
Sbjct: 61  AQVNKYGFLQTPYYKVENGVVDYSEVHYLTAAEEIGFNIAQSIVKVDENNKLVDKQLTMR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                I+   +++D+I+ +P Q+VS+AA  IPFLENDD+NR LMG
Sbjct: 121 HNYNYIIGKPKEVDYIEVAPNQMVSVAAGCIPFLENDDANRALMG 165


>gi|55650606|emb|CAF32179.1| RNA polymerase B subunit [Anabaena oscillarioides BECID22]
          Length = 193

 Score =  148 bits (373), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 86/188 (45%), Positives = 119/188 (63%), Gaps = 6/188 (3%)

Query: 631 NSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRV 690
           +  LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR 
Sbjct: 1   DVPLDENGYIKGPQVPVRYRQDWTTTSPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRA 60

Query: 691 LMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV-- 748
           LMG NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R    
Sbjct: 61  LMGSNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTHGDVVYVDATEIRVRVSGQ 120

Query: 749 ----EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGD 804
                G           Y L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+
Sbjct: 121 LSAASGSQVIEKGQEIRYNLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGE 180

Query: 805 LALGRNML 812
           LALG+N++
Sbjct: 181 LALGQNIV 188


>gi|71067876|gb|AAZ22930.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 243

 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 79/262 (30%), Gaps = 21/262 (8%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 3    HILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-R 61

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGF 1002
             +F R   D+ ++      E  E               +       +  G          
Sbjct: 62   SLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVII 121

Query: 1003 KKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQW 1062
             K+  +  +      R+   Q       ++     +      + +               
Sbjct: 122  GKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA-------------- 167

Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
                    ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++
Sbjct: 168  ------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIII 221

Query: 1123 NPLGVPSRMNVGQIFETHLGWA 1144
            NP  +PSRM +  + E  L   
Sbjct: 222  NPHAIPSRMTIAHLIECLLSKV 243



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 3   HILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 52

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   L   E       +    +       +DE GI+  G 
Sbjct: 53  SSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGV 112

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK  P  +       +             RD S  + S  +G V  V +  
Sbjct: 113 RVSGEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTV 165

Query: 947 RHGIDK 952
                K
Sbjct: 166 NADNVK 171


>gi|226445719|gb|ACO58385.1| RNA polymerase [Mycoplasma sualvi]
          Length = 166

 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 87/165 (52%), Positives = 114/165 (69%), Gaps = 1/165 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L  +
Sbjct: 2   NPLSEISNKRRITSLGPGGLNRETAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAVY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           AR+N YGF+ETPY +V  G V  ++ VYL A EE     AQ+  ++D++     E V  R
Sbjct: 62  ARINEYGFLETPYFRVNKGVVDYSEPVYLIASEEFGFTFAQSTVTIDDNNRIVNEEVTVR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
              + I+V  E++DFID S +Q+ SIAAS IPFLENDD+NR LMG
Sbjct: 122 KNHDFIIVKPEEVDFIDVSSRQMTSIAASAIPFLENDDANRALMG 166


>gi|71727082|gb|AAZ39706.1| RNA polymerase II [Aschersonia insperata]
          Length = 243

 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGARTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGART-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|326504892|dbj|BAK06737.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 978

 Score =  148 bits (373), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 58/305 (19%), Positives = 105/305 (34%), Gaps = 15/305 (4%)

Query: 856  LGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
               E     I +V        D         +       +G      +     +   L+ 
Sbjct: 678  THEEIHPTAILSVVANLTPWSDHNQSPRNMYQCQMAKQTMGFCGQALKFRTDVKAFHLQT 737

Query: 916  IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQ 975
                           +    SGT   V + +  G D  E ++ + +  ++          
Sbjct: 738  PQSPIVRTATYKKYHMDEFPSGTNAIVAVLSYTGYDM-EDAMILNKSAVDR--------- 787

Query: 976  VILDRNIYSRLMEILCGQNAVSGPKGFKKS--TVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
             +   +I+      L  +   + P+ F KS  +  + D+I      +  +  V  E+   
Sbjct: 788  GMFRGDIFQTECIDLSAKRTENVPEIFAKSPLSKGTGDVIDSDGLPRVGETVVPYEQYYS 847

Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
               +L       +  L+      I+ +        G L+ V + +  KR    GDK + R
Sbjct: 848  VYNTLTGAIRPVR--LKGTEPAAIDYVALNGTNSKGSLQKVNIRLRRKRNPIIGDKFSSR 905

Query: 1094 HGNKGIVSRILPCEDMPFLKD-GTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKI 1152
            HG KG+ S++ P  DMPF  + G   D+++NP   PSRM +  + E+    A    GK I
Sbjct: 906  HGQKGVCSQLWPDIDMPFSANTGMRPDLIINPHAFPSRMTIAMLLESIAAKAGSVHGKFI 965

Query: 1153 KSLIN 1157
             +   
Sbjct: 966  DATPF 970



 Score = 67.8 bits (164), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 94/749 (12%), Positives = 202/749 (26%), Gaps = 136/749 (18%)

Query: 33  QKASYDHFLMMNIAPDERPNEGLQAAFKSVFP--ITAFSGAAMLEF-----------VSY 79
              S+D+FL          +EGL     S+ P  IT  S    L                
Sbjct: 31  HIESFDYFL----------DEGLDKMLLSIRPMEITHPSSNTTLRMSLEKGHVLPPMKDG 80

Query: 80  EFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM- 138
               P +   +C    ++Y+   K+       D               Q+   G LP+M 
Sbjct: 81  RLGQPLY-PQECRQGRISYSGEFKVEAVFQFND----------GAPIRQTFNFGQLPIML 129

Query: 139 ----------------------TK-DGTFVIKGIQRIV---VSQ-------LHRSPGIHF 165
                                 T+  G F+  G++R++   + Q       + R  G   
Sbjct: 130 MSKLCHLRGADSRKLIYHGEEATEMGGYFISGGLERLIRILILQKRNYPMGMVR--GAFI 187

Query: 166 DHDKGRAS-------------LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKV 212
               G                     LY  +   +    +   F  ++I+         +
Sbjct: 188 KRGAGYTDKAVVMRCVHHDQSSVTVKLYYLQ---NGSARLGFWFGGREIL---------L 235

Query: 213 PVTSFLMALGMDSE-EILS--TFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDT 269
           PV   L AL   S+ EI +  T        +        L      +      +L     
Sbjct: 236 PVGIILKALIDTSDREIFASLTCCYSDKRERGKGVVSTQLIGERTQIILDEVRALSLFTR 295

Query: 270 GEQVIESGKKLTSGLL-KSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVI 328
            + ++  GK   S +      +       +  D +      ++  + +   +      + 
Sbjct: 296 TQCLVHIGKYFRSAMEGFEKDDYETVAEAVIKDYILVH--LQNDNHAKFNLLIFMLQKLY 353

Query: 329 DEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVST 388
                     +         +   +         + D  +  K  +++     +  ++++
Sbjct: 354 ALVDQTTSPDNPDALQFQEALLPGHLITVFLKDRIQDWLQKSKRLIMEEITKNKSFELNS 413

Query: 389 FSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRN 448
                   +       +   + +   + N +  LD P       + + +   + +   R+
Sbjct: 414 SLEIRKFLSKYTTSVGRAIEALIKVGRANSQSMLDLPQREGMTIQAERLNFHRYISHFRS 473

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +    +    R  +V ++L   +              +  V      P  L+N   
Sbjct: 474 ----VHRGSSFAKMRTTTVRKLLPESWG------------FLCPVHTPDGEPCGLLNHMT 517

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPT--HY 566
               +   + S    +          +    R   +            E+  VH      
Sbjct: 518 STCRISSCYNSEGAIKDF-QKIKDKLLVELVRGGMIPLLPKMEHTGPPEIMHVHLDGCIV 576

Query: 567 GRICPAETSEGHNIGLVSSL-----------TSFARVNAYGFIETPYRKVCDGKVTNDVV 615
           G I  A+  E  N      L             +  ++  G     Y      +    V 
Sbjct: 577 GSIASAKIEEVVNYLRRLKLLAHPATPEDLEVGYVPLSLGGAYPGLYLFTSPARFVRPVK 636

Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
            L ++ +   +I      L          + C   G+     +      +  P  ++S+ 
Sbjct: 637 NLVSLPDGEPHI-----ELIGPFEQAFMEIRCPDGGDGGRKEKFPATHEEIHPTAILSVV 691

Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
           A+L P+ +++ S R +  C M +Q +   
Sbjct: 692 ANLTPWSDHNQSPRNMYQCQMAKQTMGFC 720


>gi|71067883|gb|AAZ22933.1| RNA polymerase II [Aschersonia turbinata]
          Length = 242

 Score =  147 bits (372), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 79/263 (30%), Gaps = 21/263 (7%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R   D+ ++      E  E               +       +  G         
Sbjct: 60   RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDII 119

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  +      R+   Q       ++     +      + +              
Sbjct: 120  IGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------- 166

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI+
Sbjct: 167  -------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDII 219

Query: 1122 LNPLGVPSRMNVGQIFETHLGWA 1144
            +NP  +PSRM +  + E  L   
Sbjct: 220  INPHAIPSRMTIAHLIECLLSKV 242



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 55  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 115 GEDIIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 167

Query: 950 IDK 952
             K
Sbjct: 168 NVK 170


>gi|223585641|gb|ACM91691.1| ribosomal polymerase subunit beta [Staphylococcus devriesei]
          Length = 149

 Score =  147 bits (372), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 86/149 (57%), Positives = 113/149 (75%), Gaps = 2/149 (1%)

Query: 544 LGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYR 603
           LG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+S+ARVN +GFIETPYR
Sbjct: 1   LGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYR 60

Query: 604 KVC--DGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           KV      +T+ + YL+A EE++  +AQANS LDE+G F ++ V CR  G   ++ +EK+
Sbjct: 61  KVDLDTNSITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKM 120

Query: 662 DFIDASPKQVVSIAASLIPFLENDDSNRV 690
           D++D SPKQVVS A + IPFLENDDSNR 
Sbjct: 121 DYMDVSPKQVVSAATACIPFLENDDSNRA 149


>gi|71727062|gb|AAZ39696.1| RNA polymerase II [Epichloe elymi]
          Length = 243

 Score =  147 bits (372), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDI 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTTVHQRRDISTPLRSTENGIIDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETHLGWA 1144
            ++NP  +PSRM +  + E  L   
Sbjct: 220  IINPHAIPSRMTIAHLIECLLSKV 243



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             DI++GK  P  +       +             RD S  + S  +G +  V +     
Sbjct: 116 GEDIIIGKTAPIDQENQDLGTRT-------TVHQRRDISTPLRSTENGIIDSVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|293611872|gb|ADE48380.1| RNA polymerase beta chain [Cycas panzhihuaensis]
          Length = 189

 Score =  147 bits (372), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 133/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIATQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I                    L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKIT--------SSVDGDTVGTELVTYQRSNNNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS+HIE + ++   T  
Sbjct: 113 GAATVGGELSLGKNILVAHMPWEGYNFEDAILISERLVYEDIYTSLHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|71727032|gb|AAZ39681.1| RNA polymerase II [Aschersonia placenta]
          Length = 248

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/265 (16%), Positives = 80/265 (30%), Gaps = 21/265 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 65   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 123

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 124  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 173

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 174  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGW 1143
            DI++NP  +PSRM +  + E  L  
Sbjct: 224  DIIINPHAIPSRMTIAHLIECLLSK 248



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 65/192 (33%), Gaps = 22/192 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 3   RMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 52

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   L   E       +    +       +DE G
Sbjct: 53  SVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDG 112

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  D+++GK  P  +       +             RD S  + S  +G V 
Sbjct: 113 IVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVD 165

Query: 941 DVRIFNRHGIDK 952
            V +       K
Sbjct: 166 SVILTVNADNVK 177


>gi|283443702|gb|ADB19860.1| mutant required to maintain repression 7-3/RNA polymerase D second
           largest subunit 2-3 [Zea mays]
          Length = 1094

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 143/983 (14%), Positives = 286/983 (29%), Gaps = 251/983 (25%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKS-----VFPITAFSGA-------AMLEF 76
           LI  Q  SY+ F+            GLQ  F S     V P    S         A+++F
Sbjct: 104 LISHQINSYNEFVS----------HGLQELFDSLGEVIVEPGYDPSKKGSGGWKHAIIKF 153

Query: 77  VSYEFDPPKF-----------DVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKD- 124
              + + P F                  +++TYA  L + + + V+ +++   +K+  D 
Sbjct: 154 GRVKLEKPVFWTGKDEGSVDFKPWHARLQNMTYASRLIVEVTIQVYSLEKSDKSKTGNDG 213

Query: 125 --------IKEQSIYMGDLPLMTKD------------------GTFVIKGIQRIVVSQLH 158
                    +   I++G LP+M K                   G F++KG++++ ++Q  
Sbjct: 214 FVQKRNFMNETHWIFIGLLPVMVKSNLCLLHSLNESECLFDAGGYFLVKGMEKVFIAQEQ 273

Query: 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW-MDIEFDSK-DIIHVR-IDRRR----- 210
           R                 + L+    I D+  W +    + K   I+++ ++  R     
Sbjct: 274 RC---------------LRRLW----ISDRPCWTISFMSEIKRRRIYIKLVESTRSEDFS 314

Query: 211 --KV----------PVTSFLMALGMDSE----EILSTFYPKIVYSQRGDFWCFPLSAADL 254
             K+          PV     ALG+ S+    +++          Q  D       +A +
Sbjct: 315 ESKIITISFLYATMPVWLLFFALGISSDKEVFDMIDM--------QDCDASVINTISATI 366

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLY 307
               K+       D   Q ++   K +        +  +                  G  
Sbjct: 367 KESDKLCEDFRKSDKARQYVDELVKSSRFPPAESFDDYIARFLFPDISGNRNKALFLGYM 426

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI--PILYVDSVNNNAYIRNTLVTD 365
           V   ++   TG+   +  D    K L+       R++   +   +     A  R+     
Sbjct: 427 VKCLLM-AFTGKRKCDNKDDFRNKRLDLPGELLGRELRAQLRLAEKRMVKAIQRDLNSDR 485

Query: 366 KNKDRK---DALLDIYRVMRPGDVSTFSVAESMFNFLFFD------SDKYDLSTVGRVKM 416
           + +D +   DA +    + R     ++                   ++   + +  R   
Sbjct: 486 ELQDLERYIDASIVTNGLNRAFSTGSWCHPYKRAERCSGIVATLRRTNPLQMMSDLRKTR 545

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     D R+        +  +        G + ++        R +  ++++   
Sbjct: 546 QRVAYAGKAGDARYPNPSYWGKLCFMSTPDGENCGLVKNLAVTAIVSSRVMQPLIESFIS 605

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            G+ ++     E I  +D                     F   + +   E   + + R+ 
Sbjct: 606 CGMSKLNDIPTEHIQRMDK-------------------IFLNGNWVGSCENSASFVFRLR 646

Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
             RR S +      +         V       + P    E  N        SF+      
Sbjct: 647 CMRRSSLIDPQVEIKRDKHHNEVRVFTDAGRILRPLLVVENLNKIRKPKGRSFS------ 700

Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
                     +      + ++   EEE+   A     L E                    
Sbjct: 701 --------FHELMQQEIIEFIGVEEEEDIQCAWGIRHLFESEGAI--------------- 737

Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                   +  P  ++ ++  +IPF  ++ + RVL                         
Sbjct: 738 --SSYTHCELDPSFLLGLSCGIIPFANHNFARRVLYQSE--------------------- 774

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
               K S  AI         +VD                               +     
Sbjct: 775 ----KHSQQAIGYSTTNPHIRVD-----------------------------TLSHQLYY 801

Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLG--------DLALGRNMLVAFMPWHGYNFEDSML 828
            QRPL     +    D +        G        +   G+N +VA     G+N EDS++
Sbjct: 802 PQRPL----FKTVIADCLGRSDYASFGRKNDFARPEYFNGQNAIVAVNVHQGFNQEDSLV 857

Query: 829 ISERMVSEDVFTSIHIEEFEVMARDTKLG-----PEEITRDIPNVSEEGLKNIDECGIIC 883
           ++   +   +F + H+  ++    +          E+I           + N+D+ G+  
Sbjct: 858 MNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKEKIDFGKTESKRGRVDNLDDDGLPY 917

Query: 884 VGAEVNPGDILVGKITPKGESPM 906
           VGA +   DI++GK++  GE   
Sbjct: 918 VGASLQTNDIVIGKVSESGEDHS 940



 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 62/380 (16%), Positives = 96/380 (25%), Gaps = 72/380 (18%)

Query: 889  NPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                  +G  T      +      L          V    L      S    +      +
Sbjct: 775  KHSQQAIGYSTTNPHIRVDTLSHQLYYPQRPLFKTVIADCLGRSDYASFGRKNDFARPEY 834

Query: 949  GIDKNERSISVEREQIELLARDKDDEQVILDRNIY--SRLMEILCGQNAVSGPKGFKKST 1006
               +N        +            +  L+R ++    L           G K  K   
Sbjct: 835  FNGQNAIVAVNVHQGFNQEDS-LVMNRASLERGMFRTEHLRSYKADVENKDGTKRLKLKE 893

Query: 1007 VLS----------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
             +            D + +            ++ V   V      +       E     K
Sbjct: 894  KIDFGKTESKRGRVDNLDDDGLPYVGASLQTNDIVIGKVSESGEDHSIKLKHTEKGMVQK 953

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +           G    V V +   R    GDK +  HG KG+V  +   E+ PF  +G 
Sbjct: 954  VLL----SANDEGKNFAV-VTLRQVRTPCLGDKFSSMHGQKGVVGFLESQENFPFTHEGI 1008

Query: 1117 PVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVI 1176
              DIV+NP   P+R   GQ+ E     A +G G   K                       
Sbjct: 1009 VPDIVINPHAFPTRQTPGQLLE-----AALGKGIACKGT--------------------- 1042

Query: 1177 GTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSIL 1236
                                       +  +TP F  A  + I   L  A     G   +
Sbjct: 1043 ---------------------------MRYATP-FTTASVDVIAEQLHRAGYSRWGSENV 1074

Query: 1237 YDGLTGEPFDRPVTVGYIYM 1256
             +G TGE     V +G  + 
Sbjct: 1075 LNGRTGERVQSLVFMGPTFY 1094


>gi|300193591|gb|ADJ68289.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766932|gb|ADR80657.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766934|gb|ADR80658.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766936|gb|ADR80659.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766938|gb|ADR80660.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766940|gb|ADR80661.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766942|gb|ADR80662.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
 gi|313766944|gb|ADR80663.1| RNA polymerase B-subunit [Staphylococcus intermedius]
          Length = 151

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 83/151 (54%), Positives = 111/151 (73%), Gaps = 2/151 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ +
Sbjct: 61  SYARVNEFGFIETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAA 676
            CR  G    + +EK+D++D SPKQVVS A 
Sbjct: 121 VCRFRGNNTTMAKEKMDYMDVSPKQVVSAAT 151


>gi|71067881|gb|AAZ22932.1| RNA polymerase II [Aschersonia turbinata]
          Length = 250

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 80/266 (30%), Gaps = 21/266 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 66   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 124

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 125  DIIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 175  ----------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWA 1144
            DI++NP  +PSRM +  + E  L   
Sbjct: 225  DIIINPHAIPSRMTIAHLIECLLSKV 250



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/185 (20%), Positives = 67/185 (36%), Gaps = 15/185 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            ++R              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 1   YSRRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 60

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   L   E       +    +       +DE GI+  G  
Sbjct: 61  SIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVR 120

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+  DI++GK  P  +       +             RD S  + S  +G V  V +   
Sbjct: 121 VSGEDIIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVN 173

Query: 948 HGIDK 952
               K
Sbjct: 174 ADNVK 178


>gi|45120566|gb|AAO64652.2| RNA polymerase II subunit RPB2 [Chondrostereum purpureum]
          Length = 770

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 117/847 (13%), Positives = 244/847 (28%), Gaps = 133/847 (15%)

Query: 286  KSLKEKGVKFLGITSDCLCGLYVAEDI----VNGETGEIYIEAGDVIDEKSLEEIFHSEI 341
            K++ +  VK      +   G  +   I    V+     ++   G + D   LE I +   
Sbjct: 30   KTISQFQVKMFHRHQERSMGNIIKATIPYIKVDIPIWVVFRALGVISDRDILEHICYDMQ 89

Query: 342  RDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF 401
                +  +    ++ ++         +DR+ AL  I         +T    +    +   
Sbjct: 90   DTQMLEMLKPCIDDGFV--------IQDREVALDFIGNR----GTTTGLSRDRRIRYAQE 137

Query: 402  DSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGN 461
               K  L  V              +     +      +I  L+     +  +DD D+ G 
Sbjct: 138  ILQKEMLPHV-----------SMAEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGK 186

Query: 462  RRVRSVGEMLKNQYRLGLLRMERSIKE--RISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
            +R+   G +L N +R+   ++ + +    +              +  + + + +     +
Sbjct: 187  KRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLSLAVKHQTITNGLKYSLAT 246

Query: 520  SQ-------------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHY 566
                           +SQ+       S ++H RR +      + R     + R +H TH+
Sbjct: 247  GNWGDQKKSMASKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHW 302

Query: 567  GRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRY 626
            G +CPAET EG   GLV +L   + ++   F       + +  + +         EEN +
Sbjct: 303  GMVCPAETPEGQACGLVKNLALMSCISVGSFSAPVIEFLEEWGLESL--------EENAH 354

Query: 627  IAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +   + +  +G +       R     +   ++     D S +  V             D
Sbjct: 355  SSTPFTKVFVNGVWMG---VHRDPANLVKTIKKLRRRDDISHEVSVVRDIREKELRLYTD 411

Query: 687  SNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR 746
            + RV     +      +L+ +       +  + A   G     +       V +   +I 
Sbjct: 412  AGRVCRPLFIVENQQLVLQKK------HVNWIAA---GQDDTGEPFKWQNLVKS--GLIE 460

Query: 747  SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRP--------LVKVGDEVRRNDIIADGP 798
             ++ + + +         ++  R  Q+    Q P         +K G            P
Sbjct: 461  LLDAEEEETVMISMTPEDLESSRLQQSGISTQDPDAEFDPAARLKAGINAHTWTHCEIHP 520

Query: 799  STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
            S  LG       +  + +P+  +N                        ++       +G 
Sbjct: 521  SMILG-------ICASIIPFPDHNQSPRN------------------TYQSAMGKQAMGI 555

Query: 859  EEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFG 918
                  I               +  +             +       +   +  + AI  
Sbjct: 556  FLTNFLIRM-----------DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILC 604

Query: 919  EKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVIL 978
                +  D+ +   S +   +    I+ R  +D  ++S   + E+ E  +RD        
Sbjct: 605  YSGYNQEDSVIMNQSSIDRGLF-RSIYYRSYMDLEKKSGIQQLEEFEKPSRDNTLRMKHG 663

Query: 979  DRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESL 1038
                      I  G           K+  +  D      R++          ++     +
Sbjct: 664  TYAKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRRDVSTPLKSTESGM 723

Query: 1039 KVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKG 1098
              Q                              + VK+ V   R  Q GDK A RHG KG
Sbjct: 724  VDQVLI--------------------TTNHEGQKFVKIRVRSTRIPQIGDKFASRHGQKG 763

Query: 1099 IVSRILP 1105
             +     
Sbjct: 764  TIGITYR 770


>gi|71727084|gb|AAZ39707.1| RNA polymerase II [Aschersonia rhombispora]
          Length = 238

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/258 (16%), Positives = 78/258 (30%), Gaps = 21/258 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 2    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 60

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E               +       +  G           K+ 
Sbjct: 61   RSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTA 120

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 121  PIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------------ 162

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 163  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 220

Query: 1127 VPSRMNVGQIFETHLGWA 1144
            +PSRM +  + E  L   
Sbjct: 221  IPSRMTIAHLIECLLSKV 238



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 1   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 50

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 51  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 110

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 111 GEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 163

Query: 950 IDK 952
             K
Sbjct: 164 NVK 166


>gi|308191307|gb|ADO16232.1| RpoB [Arcobacter thereius]
          Length = 162

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 120/162 (74%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGXEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG  TN++ Y +A +EE   IA  ++ LDE+G   E LV  R 
Sbjct: 61  SKVNDLGFIEAPYKKVVDGVATNEITYFTATQEEGLVIAPGSTKLDENGKILEPLVEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE +L+ R K+D I  S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 NGEILLMERSKVDLIXISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|293611894|gb|ADE48391.1| RNA polymerase beta chain [Ceratozamia kuesteriana]
          Length = 189

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 134/197 (68%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAALDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|293611906|gb|ADE48397.1| RNA polymerase beta chain [Dioon spinulosum]
          Length = 189

 Score =  147 bits (372), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 133/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAMAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I        +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLVDGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|71067872|gb|AAZ22928.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 243

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 44/265 (16%), Positives = 85/265 (32%), Gaps = 27/265 (10%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 3    HILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-R 61

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R   D+ ++         E+  +      + +    Y +L +   +  G       
Sbjct: 62   SLFFRSYSDQEKKVGLNY---TEVFEKPFHQSTLRMKHGTYDKLDDDGIVAPGVRVSGED 118

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  +      R+   Q       ++     +      + +            
Sbjct: 119  VIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA----------- 167

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   D
Sbjct: 168  ---------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPD 218

Query: 1120 IVLNPLGVPSRMNVGQIFETHLGWA 1144
            I++NP  +PSRM +  + E  L   
Sbjct: 219  IIINPHAIPSRMTIAHLIECLLSKV 243



 Score = 82.0 bits (201), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 3   HILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 52

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   L   E       +    +       +D+ GI+  G 
Sbjct: 53  SSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDDDGIVAPGV 112

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK  P  +       +             RD S  + S  +G V  V +  
Sbjct: 113 RVSGEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTV 165

Query: 947 RHGIDK 952
                K
Sbjct: 166 NADNVK 171


>gi|293611874|gb|ADE48381.1| RNA polymerase beta chain [Cycas clivicola]
 gi|293611876|gb|ADE48382.1| RNA polymerase beta chain [Cycas guizhouensis]
 gi|293611878|gb|ADE48383.1| RNA polymerase beta chain [Cycas hainanensis]
 gi|293611880|gb|ADE48384.1| RNA polymerase beta chain [Cycas micronesica]
 gi|293611882|gb|ADE48385.1| RNA polymerase beta chain [Cycas simplicipinna]
 gi|293611884|gb|ADE48386.1| RNA polymerase beta chain [Cycas wadei]
          Length = 189

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 132/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIATQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I                    L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKIT--------SSVDGDTVGTELVTYQRSNNNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATVGGELSLGKNILVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|145307925|gb|ABP57266.1| RNA polymerase II second largest subunit [Entomophthora muscae]
          Length = 243

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 82/264 (31%), Gaps = 21/264 (7%)

Query: 876  IDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGV 935
            +    +  +        +    +       +   +  + AI      +  D+ +   S +
Sbjct: 1    LRMDTLANILYYPQKPLVATRGMEFLRFRXLPAGQNAIVAICCYSGYNQEDSVIMNQSSI 60

Query: 936  SGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNA 995
               +    I+ R  +D+ +++  VE E  E                       I  G   
Sbjct: 61   DRGLF-RSIYYRTYLDQEKKAGLVEMETFEKPTSATTLRLRHGTYEKLEDDGLIAPGTRV 119

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +  D      R            ++     +  +   + +        
Sbjct: 120  SGDDIIIGKTAPVPPDSEELGQRRHGQTKRDVSTPLKSTETGIVDRVMLTINQ------- 172

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           +R  KV V   R  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 173  -------------EGMRFAKVRVRSTRVPQIGDKFASRHGQKGTIGMTYRXEDMPFSAEG 219

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFET 1139
               D+V+NP  +PSRM +G + E 
Sbjct: 220  IVPDLVINPHAIPSRMTIGHMVEC 243



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 66/180 (36%), Gaps = 19/180 (10%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PLV                      L  G+N +VA   + GYN ED
Sbjct: 2   RMDTLANILYYPQKPLVA----------TRGMEFLRFRXLPAGQNAIVAICCYSGYNQED 51

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECG 880
           S+++++  +   +F SI+   +    +   L   E            +     + +++ G
Sbjct: 52  SVIMNQSSIDRGLFRSIYYRTYLDQEKKAGLVEMETFEKPTSATTLRLRHGTYEKLEDDG 111

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           +I  G  V+  DI++GK  P         E+L +   G+   DV        +G+   V+
Sbjct: 112 LIAPGTRVSGDDIIIGKTAPV----PPDSEELGQRRHGQTKRDVSTPLKSTETGIVDRVM 167


>gi|195424656|gb|ACF96946.1| RpoB [Arcobacter skirrowii]
 gi|195424658|gb|ACF96947.1| RpoB [Arcobacter skirrowii]
          Length = 162

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 91/162 (56%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           ++VN  GFIE PY+KV DG V+N++ Y +A +EE   IA  ++ +DE+G   E L+  R 
Sbjct: 61  SKVNDLGFIEAPYKKVVDGVVSNEITYYTATQEEGLVIAPGSTKVDENGKIVEPLIEVRL 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL+ R K+D ID S + V+ +AASLIPFLE++D+NR L
Sbjct: 121 NGEIILMERNKVDLIDISSQMVMGVAASLIPFLEHNDANRAL 162


>gi|225698417|gb|ACO07326.1| RpoB [Pasteurellaceae bacterium TIS15930]
          Length = 154

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 90/152 (59%), Positives = 113/152 (74%), Gaps = 1/152 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIGL+++L +FAR 
Sbjct: 3   AEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIGLINTLATFART 62

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSFTEELVFCRCAG 651
           N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF  ELV  RC G
Sbjct: 63  NKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSFATELVPARCGG 122

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           E  + P E+I ++D S +Q+VS+AA+LIPFLE
Sbjct: 123 ETGMFPPERISYMDVSAQQIVSVAAALIPFLE 154


>gi|218672631|ref|ZP_03522300.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli GR56]
          Length = 96

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/86 (70%), Positives = 71/86 (82%)

Query: 1  MAKGVVFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFK 60
          MA+ + FNG  RVRKFFGK PE+ ++P+LIEVQKASYD FLM+      RP+EGLQA FK
Sbjct: 1  MAQTLSFNGRRRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPKGGRPDEGLQAVFK 60

Query: 61 SVFPITAFSGAAMLEFVSYEFDPPKF 86
          SVFPIT FSGA+MLEFVSYEF+PPKF
Sbjct: 61 SVFPITDFSGASMLEFVSYEFEPPKF 86


>gi|227826332|gb|ACP41893.1| RNA polymerase II [Lychnis flos-cuculi]
          Length = 207

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 34/78 (43%), Positives = 43/78 (55%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGW 1143
             +PSRM +GQ+ E  +G 
Sbjct: 190  AIPSRMTIGQLIECIMGK 207



 Score = 74.7 bits (182), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 56/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     + PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LAPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|71067929|gb|AAZ22955.1| RNA polymerase II [Aschersonia turbinata]
          Length = 245

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/265 (16%), Positives = 80/265 (30%), Gaps = 21/265 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 2    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 61

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 62   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 120

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 121  DIIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 170

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 171  ----------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 220

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGW 1143
            DI++NP  +PSRM +  + E  L  
Sbjct: 221  DIIINPHAIPSRMTIAHLIECLLSK 245



 Score = 82.8 bits (203), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 64/191 (33%), Gaps = 22/191 (11%)

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
                      Q+PL                      +L  G+N +VA   + GYN EDS
Sbjct: 1   MDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDS 50

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGI 881
           +++++  +   +F S+    +    +   L   E       +    +       +DE GI
Sbjct: 51  VIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGI 110

Query: 882 ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
           +  G  V+  DI++GK  P  +       +             RD S  + S  +G V  
Sbjct: 111 VAPGVRVSGEDIIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDS 163

Query: 942 VRIFNRHGIDK 952
           V +       K
Sbjct: 164 VILTVNADNVK 174


>gi|197941988|gb|ACH78599.1| RNA polymerase subunit [Polytrichum juniperinum]
          Length = 186

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 89/194 (45%), Positives = 134/194 (69%), Gaps = 8/194 (4%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL+K E   VGTG+ES  A  SG+  +AK++G V   DA +I   + E  +        
Sbjct: 1   VPLIKPEKCIVGTGLESQAALDSGSVAIAKQSGKVSYTDAKKITFFNNEKRIST------ 54

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+K+QRSN +TC+NQ+P V     +++  I+ADG +T  G+LALG+N+LVA+MPW G
Sbjct: 55  --NLIKYQRSNNSTCMNQKPQVTQDVFIKKGQILADGAATLKGELALGKNILVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER++ ED++TSIHIE +E+ AR T  GPE+IT++IP++    L+++D+ G
Sbjct: 113 YNFEDAILISERLIYEDIYTSIHIERYEIEARTTSQGPEKITKEIPHLENNVLRHLDKSG 172

Query: 881 IICVGAEVNPGDIL 894
           ++ +G+ V  GD+L
Sbjct: 173 LVLIGSWVETGDVL 186


>gi|195424654|gb|ACF96945.1| RpoB [Arcobacter mytili]
          Length = 162

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 89/161 (55%), Positives = 122/161 (75%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++FA
Sbjct: 2   PLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTFA 61

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           +VN  GFIE PY+KV +G VTN++VY++A  EE   IA  ++ +D++G   E L+  R  
Sbjct: 62  KVNELGFIEAPYKKVKEGVVTNEIVYMTATLEEGLVIAPGSTKVDDNGKIIEPLIEARQD 121

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           GE +L+ + K+D+ID S + V+ +AASLIPFLE+DD+ R L
Sbjct: 122 GEILLIEKNKVDYIDISSQMVMGVAASLIPFLEHDDAXRAL 162


>gi|71727036|gb|AAZ39683.1| RNA polymerase II [Aschersonia placenta]
          Length = 240

 Score =  147 bits (371), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 79/260 (30%), Gaps = 21/260 (8%)

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  + AI      +  D+ +   S +   +    
Sbjct: 2    ILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RS 60

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R   D+ ++      E  E               +       +  G           
Sbjct: 61   LFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIG 120

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +  +      R+   Q       ++     +      + +                
Sbjct: 121  KTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA--------------- 165

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLN 1123
                   ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++N
Sbjct: 166  -----DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIIN 220

Query: 1124 PLGVPSRMNVGQIFETHLGW 1143
            P  +PSRM +  + E  L  
Sbjct: 221  PHAIPSRMTIAHLIECLLSK 240



 Score = 82.4 bits (202), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 4   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 53

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 54  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 113

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 114 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 166

Query: 950 IDK 952
             K
Sbjct: 167 NVK 169


>gi|227826350|gb|ACP41902.1| RNA polymerase II [Silene schafta]
          Length = 207

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 34/78 (43%), Positives = 43/78 (55%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 130  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 189

Query: 1126 GVPSRMNVGQIFETHLGW 1143
             +PSRM +GQ+ E  +G 
Sbjct: 190  AIPSRMTIGQLIECIMGK 207



 Score = 75.9 bits (185), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 810 NMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEIT-----RD 864
           N +VA   + GYN EDS+++++  +    F S+    +    +      +E        +
Sbjct: 1   NAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLIKEDFGRPDRSN 60

Query: 865 IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDV 924
              +       +D+ G+   G  V+  D+++GK TP     ++PEE    A         
Sbjct: 61  TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP-----LSPEE----AQGPAARYSR 111

Query: 925 RDTSLRVPSGVSGTVV 940
           +D S+ +    SG V+
Sbjct: 112 KDHSISLRHSESGIVL 127


>gi|195424650|gb|ACF96943.1| RpoB [Arcobacter nitrofigilis]
          Length = 162

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 89/162 (54%), Positives = 123/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG V+N+++Y++A +EE   IA  ++ +D++G   E L+  R 
Sbjct: 61  AKVNELGFIEAPYKKVQDGIVSNEIIYVTATQEEGLLIAPGSTKVDDNGKIVEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE ++V R K++ ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILIVERSKVNLIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|71067874|gb|AAZ22929.1| RNA polymerase II [Aschersonia basicystis]
          Length = 231

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 78/247 (31%), Gaps = 21/247 (8%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ ++  
Sbjct: 6    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVG 64

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E               +       +  G           K+  +  +      
Sbjct: 65   LNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGT 124

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+   Q       ++     +      + +                       ++ VKV 
Sbjct: 125  RTSVHQRRDISTPLRSTENGIVDSVILTVNA--------------------DNVKYVKVR 164

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + 
Sbjct: 165  VRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLI 224

Query: 1138 ETHLGWA 1144
            E  L   
Sbjct: 225  ECLLSKV 231



 Score = 81.7 bits (200), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 60/164 (36%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 3   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 62

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E       +    +       +DE GI+  G  V+  D+++GK  P  +     
Sbjct: 63  VGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDL 122

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +             RD S  + S  +G V  V +       K
Sbjct: 123 GTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNADNVK 159


>gi|77798195|gb|ABB03276.1| RNA polymerase beta subunit [Nocardia cerradoensis]
 gi|77798228|gb|ABB03292.1| RNA polymerase beta subunit [Nocardia veterana]
          Length = 145

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 86/145 (59%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +P+ +A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQLRVGLSRMERVVRERMTTQDVEAITPQTLINIRPITAAIREF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|28188320|gb|AAL78752.1| RpoB [Candidatus Baumannia cicadellinicola]
          Length = 67

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 41/67 (61%), Positives = 56/67 (83%)

Query: 1300 WCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGL 1359
            W ++AYGAAY LQEMLT+KSDDV GRT++Y++IV  N T E   PESFNVL+KE+++LG+
Sbjct: 1    WALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDCNHTMEPAMPESFNVLLKEIRSLGI 60

Query: 1360 SIDLENS 1366
            +I+LE +
Sbjct: 61   NIELEKN 67


>gi|293611904|gb|ADE48396.1| RNA polymerase beta chain [Dioon rzedowskii]
          Length = 189

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 133/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I        +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLVDGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|156361325|ref|XP_001625468.1| predicted protein [Nematostella vectensis]
 gi|156212303|gb|EDO33368.1| predicted protein [Nematostella vectensis]
          Length = 913

 Score =  147 bits (370), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 38/135 (28%), Positives = 57/135 (42%), Gaps = 1/135 (0%)

Query: 1082 RPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHL 1141
            R    GDK + RHG KGI S+  P E+MPF + G   DI+ NP G PSRM +G + E+  
Sbjct: 767  RNPIIGDKFSSRHGQKGICSQKWPVENMPFSESGMTPDIIFNPHGFPSRMTIGMMIESMA 826

Query: 1142 GWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWK 1201
            G +    G    +    +  +         L      G +   +           ++ +K
Sbjct: 827  GKSAALNGHVYDATPFTFSEDDSAIDYFGKLLVKWVEGINGLVLEVQGFRGWFNQSQGFK 886

Query: 1202 SGVPVSTPVFDGADE 1216
            S +   TPV+    E
Sbjct: 887  SYLRY-TPVYLPLTE 900



 Score = 82.4 bits (202), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 85/577 (14%), Positives = 172/577 (29%), Gaps = 69/577 (11%)

Query: 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDD 455
           F       D +    V +  +   + +    +    +   +I + + L  L   K   + 
Sbjct: 264 FRVKMRLPDWFSDEAVAQYLIQQCICIHLDTNAD--KFNLLILMTRKLYALALEKCCAES 321

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
            D+  N+ V   G +      L +L+ME  +            + Q              
Sbjct: 322 ADSPMNQEVLLGGHL-----YLMVLKMEYFLATGNLISKSGLALQQI------------- 363

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
               S  + + + +N    ++H R    + +G          +R + P  +G +CP  T 
Sbjct: 364 ----SGFTVVADRLNYFRFLSHFR---CIHRGAFFSQMRTTSVRKLLPEAWGFLCPVHTP 416

Query: 576 EGHNIGLVSSLTSFARV-NAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
           +G   GL++ L +  +V N    +    R +C   +      +    +    +      L
Sbjct: 417 DGAPCGLLNHLAAGCQVVNVVPLVAHMLRLLCTMGMIPVDAPVPGDYKNYYPVVMDGRVL 476

Query: 635 DEDGSFTEELVFCRCAG-------------EEILVPREKIDFIDASPKQVVSIAASLIPF 681
                     +  R                E  LVP  K+           S A  + P 
Sbjct: 477 GSVDRDLAPTLANRLRIMKVLGEERVPQFLEICLVPITKVASQYPGLFIFSSPARMMRPV 536

Query: 682 LENDDSNRVLMGCNMQRQAVPLLKAE--APFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           L    +   ++G   Q      +  E     V T ME         A+++  A +    D
Sbjct: 537 LNLAVNKIEMIGSFEQVYMDIAIVQEELHEGVTTHMELKP-----TAMLSAIASMTPYSD 591

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYR-LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
             +      +  +   T G  ++    +           Q PLV+           A   
Sbjct: 592 FNQSPRNMYQCQMGKQTMGTPVHAFQHRTDNKLYRIQTPQSPLVRP----------ASHD 641

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
              + +  LG N +VA + + GY+ ED+M++++           H   ++    + +   
Sbjct: 642 FYIMDEYPLGTNAIVAVISYTGYDMEDAMVLNKASYERGFA---HGSIYKAQFVNLEPKS 698

Query: 859 EEITRD------IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
           ++ T                   +D  G   +GA ++ GD     I       +  +   
Sbjct: 699 QDRTSSSNLQFGTLPDDPRIDGRLDADGFPPLGAHLSTGDPYYSYIDTNTGEAVVKKYSN 758

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
           L A   +    +         G    +   +    + 
Sbjct: 759 LEAGIIDDRNPIIGDKFSSRHGQK-GICSQKWPVENM 794



 Score = 55.9 bits (133), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 46/165 (27%), Gaps = 76/165 (46%)

Query: 15  KFFGKNPEII--DIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAA 72
           K +G+  +     I DL+     S++  L   +                           
Sbjct: 21  KNYGRLSDTQKQSIQDLVRPHIESFNFMLEEGLPLAA----------------------- 57

Query: 73  MLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYM 132
                             C  +  TY   L++TL+  + +V + +  K I          
Sbjct: 58  -----------------QCREKGSTYCSKLQVTLQWKIDNVPQGSVTKVIAA-------- 92

Query: 133 GDLPLMTKD------------------------GTFVIKGIQRIV 153
             +PLM K                         G F++ GI++I+
Sbjct: 93  --IPLMVKSNNCSLANLSPKELVRKNEESQEAGGYFIVNGIEKII 135


>gi|293611920|gb|ADE48404.1| RNA polymerase beta chain [Encephalartos ferox]
 gi|293611922|gb|ADE48405.1| RNA polymerase beta chain [Encephalartos gratus]
 gi|293611924|gb|ADE48406.1| RNA polymerase beta chain [Encephalartos manikensis]
 gi|293611928|gb|ADE48408.1| RNA polymerase beta chain [Encephalartos villosus]
          Length = 189

 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 134/197 (68%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNSNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|226427453|gb|ACO54920.1| RNA polymerase [Mycoplasma gallinarum]
          Length = 165

 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 80/164 (48%), Positives = 113/164 (68%), Gaps = 1/164 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLSEISNERRITSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNFATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN YGF++TPY +V +G V  + V YL+A++E   YIAQ+   +D+D   T+E +  R
Sbjct: 62  AKVNQYGFLQTPYYRVKNGVVQYDKVDYLTAVDEVGFYIAQSTVKVDKDNRITDEQITMR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                I+   E +D+I+ +  Q+VS+AA  IPFLENDD+NR LM
Sbjct: 122 HNYTFIMGGPEDVDYIEVASNQMVSVAAGCIPFLENDDANRALM 165


>gi|149992|gb|AAB59068.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 144

 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 88/144 (61%), Positives = 120/144 (83%)

Query: 460 GNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCS 519
           GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +
Sbjct: 1   GNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGT 60

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET EG N
Sbjct: 61  SQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPN 120

Query: 580 IGLVSSLTSFARVNAYGFIETPYR 603
           IGL+ SL+ +ARVN +GFIETPYR
Sbjct: 121 IGLIGSLSVYARVNPFGFIETPYR 144


>gi|226445686|gb|ACO58363.1| RNA polymerase [Mycoplasma canis]
          Length = 170

 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 79/170 (46%), Positives = 114/170 (67%), Gaps = 1/170 (0%)

Query: 525 LEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
             + +N L+ +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+ 
Sbjct: 1   FMDQINPLAEVSNKRRVTSLGPGGLSRDTAQFEVRDVHSTHYGRICPIETPEGLNIGLIL 60

Query: 585 SLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           +  ++A+V+  GF++TPY KV +G V   DV YL+A EE    IAQ++  +DE+    +E
Sbjct: 61  NFATYAKVDDKGFLKTPYYKVNNGVVDYEDVRYLTASEEFGYSIAQSSVRVDENNKIIDE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
            +  R          + +DFI+ S KQ+VS+AA+ IPFLENDD+NR LMG
Sbjct: 121 FLTIRRNYTYENGRSDDVDFIEVSSKQIVSVAAAGIPFLENDDANRALMG 170


>gi|11595824|emb|CAC18340.1| RNA polymerase beta subunit [Pseudomonas stutzeri]
          Length = 145

 Score =  146 bits (369), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 82/143 (57%), Positives = 107/143 (74%), Gaps = 1/143 (0%)

Query: 542 SALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETP 601
           SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG NIGL++SL ++AR N YGF+E+P
Sbjct: 4   SALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLAAYARTNQYGFLESP 63

Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
           YR V +G+VT+++V+LSA+EE +  IAQA++ L E     +ELV  R   E  +   E +
Sbjct: 64  YRVVKEGEVTDEIVFLSAIEEADHVIAQASAKL-EGLKLVDELVAVRHLNEFTVKAPEDV 122

Query: 662 DFIDASPKQVVSIAASLIPFLEN 684
             +D SPKQVVS+AASLIPFLE+
Sbjct: 123 TLMDVSPKQVVSVAASLIPFLEH 145


>gi|293611892|gb|ADE48390.1| RNA polymerase beta chain [Ceratozamia hildae]
          Length = 183

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 93/191 (48%), Positives = 132/191 (69%), Gaps = 8/191 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAALDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPN 867
           GPE IT++IP+
Sbjct: 173 GPERITKEIPH 183


>gi|225698411|gb|ACO07323.1| RpoB [Pasteurellaceae bacterium Kleiz10257]
          Length = 154

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 90/154 (58%), Positives = 115/154 (74%), Gaps = 1/154 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           ++L+ +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIGL+++L +F
Sbjct: 1   HALAEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIGLINTLATF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSFTEELVFCR 648
           AR N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF  ELV  R
Sbjct: 61  ARTNKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSFATELVPAR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           C GE  + P E+I ++D S +Q+VS+AA+LIPFL
Sbjct: 121 CGGETGMFPPERISYMDVSAQQIVSVAAALIPFL 154


>gi|289468067|gb|ADC95714.1| RpoB [Riemerella anatipestifer]
          Length = 158

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 90/158 (56%), Positives = 112/158 (70%), Gaps = 2/158 (1%)

Query: 526 EEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSS 585
            +  N LS ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+SS
Sbjct: 1   MDQTNPLSEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLISS 60

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEE 643
           L  +A++N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F  E
Sbjct: 61  LGIYAKINNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFETE 120

Query: 644 LVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPF 681
            +  R  G+  +V  E++D ID +P Q+  I+ASLIPF
Sbjct: 121 RIIARLDGDYPVVEPEQVDLIDVAPNQISGISASLIPF 158


>gi|329132751|gb|AEB78306.1| RNA polymerase B [Mycobacterium timonense]
          Length = 147

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 120/145 (82%)

Query: 456 IDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCE 515
           ID+ GNRR+R+VGE+++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ E
Sbjct: 1   IDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKE 60

Query: 516 FFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETS 575
           FF +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET 
Sbjct: 61  FFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETP 120

Query: 576 EGHNIGLVSSLTSFARVNAYGFIET 600
           EG NIGL+ SL+ +ARVN +GFIET
Sbjct: 121 EGPNIGLIGSLSVYARVNPFGFIET 145


>gi|294886743|ref|XP_002771831.1| DNA-directed RNA polymerase II subunit, putative [Perkinsus marinus
           ATCC 50983]
 gi|239875631|gb|EER03647.1| DNA-directed RNA polymerase II subunit, putative [Perkinsus marinus
           ATCC 50983]
          Length = 993

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 91/568 (16%), Positives = 178/568 (31%), Gaps = 69/568 (12%)

Query: 432 RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERIS 491
           +   I  ++  L+  + G+   DD D+ G +R+   G ++   +     ++ +  K  + 
Sbjct: 386 KAYFIGYMVHRLLLGQLGRIAEDDRDHFGKKRMDMAGPLMAASFAQLFRKLVQDSKRILQ 445

Query: 492 SVDIDSVMP---QDLINAKPVVSAVCEFFCSSQ-------------LSQLEEHVNSLSRI 535
                         + +A  +   +     +               +SQ+   +  +S +
Sbjct: 446 RQVDSGRHFDLNSAIRSASSITDGLRYQLATGNWGIDKSGKSVRTGVSQVLNRLTFMSTM 505

Query: 536 THTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAY 595
           +H RR++      + R+    + R +H TH+G ICPAET EG  +GLV ++     +   
Sbjct: 506 SHLRRMNT----PLERSGKLAKPRQLHNTHWGMICPAETPEGQAVGLVKNIALMCTITVG 561

Query: 596 GFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG----SFTEELVFCRCAG 651
                 Y  + +     ++  ++  + ++      N              E L   R   
Sbjct: 562 SLPNVVYDFL-NEWGLENLDEINPSQIKHMTKVFLNGQWVGMHADATMLCETLRDLRRKR 620

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLEND--DSNRVLMGCNMQRQAVPLLKA--- 706
           +         D      +       +  P        S ++ +          +L     
Sbjct: 621 DIDPEVSIIRDLQANELRIFTDGGRACRPLYVVQPPPSQKLCIKREHVEALRRMLLNNEH 680

Query: 707 --EAPFVGTGM-ESVVAKSSGAAIVAKRAGIVEQV------------DAIRIVIRSVEGD 751
                 V  G+ E + A+     +VA     +                     I      
Sbjct: 681 GGWDMLVEEGLVEYIDAEEEETCMVAMFVDDLRNAQRRKSKASSYCHTYTHCEIHPSLIL 740

Query: 752 LDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD--------------G 797
              ++           + + Q+    Q   V   +   R D +A                
Sbjct: 741 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYATNFNMRIDTMAHVLNYPQKPLVGTRAM 800

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G N +VA M + GYN EDS++++   +      S+H + +    +     
Sbjct: 801 EYLRFRELPAGNNAIVAIMTYSGYNQEDSLIMNASSIDRGFMRSVHFKSYMADEKRQGAQ 860

Query: 858 PEEITRDIPN-----VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E  R         +       +D  G+I  G  V+  DIL+GK++P      T EE  
Sbjct: 861 VVEEFRAPSWSKTYAMKRGDYSKLDNDGLINPGTRVHGDDILIGKVSPIP--NQTDEE-- 916

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
              I      D         +GV   V+
Sbjct: 917 -GRIQKYTERDCSVALKGADNGVVDQVM 943



 Score = 94.4 bits (233), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 56/181 (30%), Gaps = 64/181 (35%)

Query: 29  LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA----------------A 72
           L+  Q  S+D F+   +          Q       PIT                      
Sbjct: 127 LVSQQVGSFDDFVTYKM----------QEIVDECPPITIIPQNQVGWESEGARVYMDSSF 176

Query: 73  MLEFVSYEFDPPK----------FDVDDCLWRDLTYAVPLKITLRLIVF---DVDEFTGA 119
           ++EF     + P              +    R+LTY+ P+ + +    +   D D+    
Sbjct: 177 LVEFGQLSLNKPTVEEVDGAMTSLTPNQARLRNLTYSSPVYVNVTQTTYALADPDDPNSE 236

Query: 120 KS-IKDIKEQSIYMGDLPLMTKD------------------------GTFVIKGIQRIVV 154
           K  I +     I +G +P+M K                         G F+I G +++++
Sbjct: 237 KQLISEDSYSKILIGRIPMMLKSEYCWLKNQTERGLVEMGECVFDQGGYFIINGSEKVLI 296

Query: 155 S 155
           +
Sbjct: 297 A 297


>gi|109649510|gb|ABG36706.1| RNA polymerase beta subunit [Bartonella australis]
          Length = 187

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 110/180 (61%), Positives = 135/180 (75%)

Query: 552 ARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
            R   ++RDV PT+YGRIC  ET EG NIGL++ L +FARV  YGFI+  YR++ DGK+ 
Sbjct: 4   RRRRFQVRDVRPTNYGRICQFETPEGPNIGLINFLATFARVTKYGFIQVQYREIIDGKLP 63

Query: 612 NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQV 671
             V+YLSAME+  RY+AQANSSLD +G FTEE V CR AGE +  PR+ +D +D SPKQ+
Sbjct: 64  KQVIYLSAMEQAKRYVAQANSSLDSEGRFTEEFVVCRQAGEVLTAPRDHVDLMDVSPKQL 123

Query: 672 VSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKR 731
           VS+AA+LIPFLEN    R  MG NMQRQAVPL++AEAPFVGT ME VVA+ SG A+ A R
Sbjct: 124 VSVAAALIPFLENPPPPRAKMGSNMQRQAVPLVRAEAPFVGTAMEPVVARDSGPAVSANR 183


>gi|164452773|gb|ABY57223.1| RpoB [Tortella bambergeri]
          Length = 240

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 91/229 (39%), Positives = 147/229 (64%), Gaps = 9/229 (3%)

Query: 722 SSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPL 781
            SG+  +AK++G +   D  +I + +       +   +       +QRSN +T ++Q+  
Sbjct: 3   DSGSIAIAKQSGKILYTDGKKISLLNANKKSTNTDLII-------YQRSNNSTYMHQKAR 55

Query: 782 VKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTS 841
           V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED++LISER++ +D++TS
Sbjct: 56  VIQKTFLKKGQILADGAATIKGELALGKNILVAYMPWEGYNFEDAILISERLIYKDIYTS 115

Query: 842 IHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPK 901
           IHIE +E+ +R T  GPE+IT++IP++    L+++D+ G++  G+ V  GD+LVGK+TP+
Sbjct: 116 IHIERYEIKSRTTSQGPEKITKEIPHLENSVLRHLDKSGLVIPGSWVETGDVLVGKLTPQ 175

Query: 902 GESPMT--PEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH 948
                   PE KLL+AIFG +    ++T L+VP G  G V+DVR   + 
Sbjct: 176 ETEESLRAPEGKLLQAIFGIQVATAKETCLKVPPGGKGRVIDVRWIYKK 224


>gi|226445680|gb|ACO58359.1| RNA polymerase [Mycoplasma bovis]
          Length = 165

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 79/164 (48%), Positives = 113/164 (68%), Gaps = 1/164 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N+L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++
Sbjct: 2   NALAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY KV +  V  ++VVYL+A +E    IAQ+ +++D++    +E +  R
Sbjct: 62  ASVNEYGFLQTPYFKVENSVVDYDNVVYLTAADEFGYNIAQSTATVDDNNRLIDETLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                IL     +D I+ S +Q+VS+AA  IPFLENDD+NR LM
Sbjct: 122 KNYTYILGKPSDVDLIEVSSRQMVSVAAGCIPFLENDDANRALM 165


>gi|225698419|gb|ACO07327.1| RpoB [Pasteurellaceae bacterium TIS16932]
          Length = 153

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 89/151 (58%), Positives = 112/151 (74%), Gaps = 1/151 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIGL+++L +FAR 
Sbjct: 3   AEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIGLINTLATFART 62

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSFTEELVFCRCAG 651
           N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF  ELV  RC G
Sbjct: 63  NKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSFATELVPARCGG 122

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFL 682
           E  + P E+I ++D S +Q+VS+AA+LIPFL
Sbjct: 123 ETGMFPPERISYMDVSAQQIVSVAAALIPFL 153


>gi|71067889|gb|AAZ22935.1| RNA polymerase II [Aschersonia turbinata]
          Length = 222

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 77/242 (31%), Gaps = 21/242 (8%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 2    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 60

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E               +       +  G           K+  +  +      R+   
Sbjct: 61   VFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQESQDLGTRTSVH 120

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +      + +                       ++ VKV V   +
Sbjct: 121  QRRDISTPLRSTENGIVDSVILTVNA--------------------DNVKYVKVRVRTTK 160

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 161  VPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLS 220

Query: 1143 WA 1144
              
Sbjct: 221  KV 222



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 60/157 (38%), Gaps = 12/157 (7%)

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
              +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L   E
Sbjct: 1   KFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTE 60

Query: 861 -----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRA 915
                  +    +       +DE GI+  G  V+  DI++GK  P  +       +    
Sbjct: 61  VFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDQESQDLGTRT--- 117

Query: 916 IFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    RD S  + S  +G V  V +       K
Sbjct: 118 ----SVHQRRDISTPLRSTENGIVDSVILTVNADNVK 150


>gi|50058717|gb|AAT69111.1| RNA polymerase II [Iseia luxurians]
          Length = 208

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 35/77 (45%), Positives = 44/77 (57%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV V   R  Q GDK + RHG KG V      EDMP+  +G   DI++NP 
Sbjct: 132  TNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPH 191

Query: 1126 GVPSRMNVGQIFETHLG 1142
            G+PSRM +GQ+ E  +G
Sbjct: 192  GIPSRMTIGQVIECIMG 208



 Score = 69.7 bits (169), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 48/134 (35%), Gaps = 14/134 (10%)

Query: 811 MLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DI 865
            +VA   + GYN EDS++++   +    F S+         +      +E        + 
Sbjct: 1   AIVAIACYSGYNQEDSVIMNHSSIDRGFFRSLFFRSHRDEEKKMGTLVKEDFGRPDRANT 60

Query: 866 PNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVR 925
             +       +D+ G+   G  V+  D+++GK TP  +           A         R
Sbjct: 61  MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQED---------AQGQSARYTKR 111

Query: 926 DTSLRVPSGVSGTV 939
           D S  +    +G V
Sbjct: 112 DHSTSLRHSETGIV 125


>gi|63086889|gb|AAY30844.1| RNA polymerase II [Aschersonia aleyrodis]
 gi|63086908|gb|AAY30853.1| RNA polymerase II [Moelleriella libera]
          Length = 240

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 79/261 (30%), Gaps = 21/261 (8%)

Query: 882  ICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVD 941
              +             +       +   +  + AI      +  D+ +   S +   +  
Sbjct: 1    ANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF- 59

Query: 942  VRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKG 1001
              +F R   D+ ++      E  E               +       +  G         
Sbjct: 60   RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVI 119

Query: 1002 FKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQ 1061
              K+  +  +      R+   Q       ++     +      + +              
Sbjct: 120  IGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------- 166

Query: 1062 WGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIV 1121
                     ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI+
Sbjct: 167  -------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDII 219

Query: 1122 LNPLGVPSRMNVGQIFETHLG 1142
            +NP  +PSRM +  + E  L 
Sbjct: 220  INPHAIPSRMTIAHLIECLLS 240



 Score = 82.8 bits (203), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 5   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 54

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 55  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 114

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 115 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 167

Query: 950 IDK 952
             K
Sbjct: 168 NVK 170


>gi|293611890|gb|ADE48389.1| RNA polymerase beta chain [Bowenia spectabilis]
          Length = 188

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 92/195 (47%), Positives = 132/195 (67%), Gaps = 8/195 (4%)

Query: 679 IPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQV 738
           IPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +
Sbjct: 2   IPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAASDSGSATIAAQGGRITYI 61

Query: 739 DAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGP 798
           DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG 
Sbjct: 62  DAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILADGA 113

Query: 799 STDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGP 858
           +T  G+L+LG+N+LVA MPW GYNFED++LI+ER+V ED++TS HIE F ++   T  GP
Sbjct: 114 ATLGGELSLGKNVLVAHMPWEGYNFEDAILINERLVYEDIYTSFHIERFGIVTCMTSQGP 173

Query: 859 EEITRDIPNVSEEGL 873
           E IT++IP++    L
Sbjct: 174 ERITKEIPHLDAHLL 188


>gi|71727034|gb|AAZ39682.1| RNA polymerase II [Aschersonia placenta]
          Length = 247

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 65   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 123

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 124  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 173

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 174  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLG 1142
            DI++NP  +PSRM +  + E  L 
Sbjct: 224  DIIINPHAIPSRMTIAHLIECLLS 247



 Score = 83.6 bits (205), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 22/193 (11%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 2   RRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 51

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +   L   E       +    +       +DE 
Sbjct: 52  DSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDED 111

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+  G  V+  D+++GK  P  +       +             RD S  + S  +G V
Sbjct: 112 GIVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIV 164

Query: 940 VDVRIFNRHGIDK 952
             V +       K
Sbjct: 165 DSVILTVNADNVK 177


>gi|300193603|gb|ADJ68295.1| RNA polymerase B-subunit [Staphylococcus xylosus]
          Length = 147

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 82/147 (55%), Positives = 109/147 (74%), Gaps = 2/147 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T  + YL+A EE++  +AQANS LDE+G F ++ V
Sbjct: 61  SYARVNEFGFIETPYRKVDLETNSITEQIDYLTADEEDSYVVAQANSKLDENGRFLDDEV 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVV 672
            CR  G   ++ +EK+D++D SPKQVV
Sbjct: 121 VCRFRGNNTVMAKEKMDYMDVSPKQVV 147


>gi|197941990|gb|ACH78600.1| RNA polymerase subunit [Polytrichum juniperinum]
          Length = 186

 Score =  146 bits (368), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 89/194 (45%), Positives = 134/194 (69%), Gaps = 8/194 (4%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VPL+K E   VGTG+ES  A  SG+  +AK++G V   DA +I   + E  +        
Sbjct: 1   VPLIKPEKXIVGTGLESQAALDSGSVAIAKQSGKVSYTDAKKITFFNNEKRIST------ 54

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+K+QRSN +TC+NQ+P V     +++  I+ADG +T  G+LALG+N+LVA+MPW G
Sbjct: 55  --NLIKYQRSNNSTCMNQKPQVTQDVFIKKGQILADGAATLKGELALGKNILVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER++ ED++TSIHIE +E+ AR T  GPE+IT++IP++    L+++D+ G
Sbjct: 113 YNFEDAILISERLIYEDIYTSIHIERYEIEARTTSQGPEKITKEIPHLENNVLRHLDKSG 172

Query: 881 IICVGAEVNPGDIL 894
           ++ +G+ V  GD+L
Sbjct: 173 LVLIGSWVETGDVL 186


>gi|71727042|gb|AAZ39686.1| RNA polymerase II [Aschersonia placenta]
 gi|71727050|gb|AAZ39690.1| RNA polymerase II [Aschersonia placenta]
          Length = 246

 Score =  145 bits (367), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 4    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 63

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 64   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 122

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 123  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 172

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 173  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 222

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLG 1142
            DI++NP  +PSRM +  + E  L 
Sbjct: 223  DIIINPHAIPSRMTIAHLIECLLS 246



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 22/193 (11%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 1   RRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 50

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +   L   E       +    +       +DE 
Sbjct: 51  DSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDED 110

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+  G  V+  D+++GK  P  +       +             RD S  + S  +G V
Sbjct: 111 GIVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIV 163

Query: 940 VDVRIFNRHGIDK 952
             V +       K
Sbjct: 164 DSVILTVNADNVK 176


>gi|293611926|gb|ADE48407.1| RNA polymerase beta chain [Encephalartos umbeluziensis]
          Length = 186

 Score =  145 bits (367), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 93/193 (48%), Positives = 133/193 (68%), Gaps = 8/193 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNSNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVS 869
           GPE IT++IP++ 
Sbjct: 173 GPERITKEIPHLD 185


>gi|293611918|gb|ADE48403.1| RNA polymerase beta chain [Encephalartos bubalinus]
          Length = 184

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 93/192 (48%), Positives = 133/192 (69%), Gaps = 8/192 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNSNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNV 868
           GPE IT++IP++
Sbjct: 173 GPERITKEIPHL 184


>gi|63086906|gb|AAY30852.1| RNA polymerase II [Aschersonia sp. ARSEF 7511]
          Length = 240

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 78/256 (30%), Gaps = 21/256 (8%)

Query: 887  EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
                       +       +   +  + AI      +  D+ +   S +   +    +F 
Sbjct: 6    YPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFF 64

Query: 947  RHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKST 1006
            R   D+ ++      E  E               +       +  G           K+ 
Sbjct: 65   RSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTA 124

Query: 1007 VLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDM 1066
             +  +      R+   Q       ++     +      + +                   
Sbjct: 125  PIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------------ 166

Query: 1067 PPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLG 1126
                ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  
Sbjct: 167  --DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHA 224

Query: 1127 VPSRMNVGQIFETHLG 1142
            +PSRM +  + E  L 
Sbjct: 225  IPSRMTIAHLIECLLS 240



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 66/185 (35%), Gaps = 22/185 (11%)

Query: 773 NTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISER 832
           ++   Q+PL                      +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 3   SSYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 52

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   L   E       +    +       +DE GI+  G  
Sbjct: 53  SIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVR 112

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+  D+++GK  P  +       +             RD S  + S  +G V  V +   
Sbjct: 113 VSGEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVN 165

Query: 948 HGIDK 952
               K
Sbjct: 166 ADNVK 170


>gi|76781329|gb|ABA54550.1| RpoB [Campylobacter insulaenigrae]
          Length = 162

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 90/162 (55%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH RRLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L+++
Sbjct: 1   NPLSEVTHKRRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GF+E PY++V +GK++N++VYL+A +EE   IA A++ +DE G+  EE V  R 
Sbjct: 61  AKVNDLGFVEAPYKQVENGKISNEIVYLTATQEEGLIIAAASTKIDEKGNILEEFVEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE IL  RE++  ID     +V +AASLIPFLE+DD+NR L
Sbjct: 121 DGETILARREEVQLIDLCSGMIVGVAASLIPFLEHDDANRAL 162


>gi|219564063|gb|ACL28215.1| RNA polymerase II second largest subunit [fungal sp. M191]
          Length = 239

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 90/263 (34%), Gaps = 27/263 (10%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 1    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 60

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R   D+ +R   +    +E   +    + + L    Y +L +   +  G   
Sbjct: 61   LF-RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRV 116

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  ++ D                +E  QR    +K    T     E+   +
Sbjct: 117  SGEDIIIGKTAPIAPD---------------SEELGQRTKAHVKRDASTPLRSTENGIVD 161

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            ++             LR VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 162  QVLI-----TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFSVQG 216

Query: 1116 TPVDIVLNPLGVPSRMNVGQIFE 1138
               D+++NP  +PSRM +  + E
Sbjct: 217  IVPDLIINPHAIPSRMTIAHLIE 239



 Score = 82.0 bits (201), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 65/177 (36%), Gaps = 22/177 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 8   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 57

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   +   E        D   +       +D+ GI+  G  V+
Sbjct: 58  DRGLFRSLFYRAYTDQEKRIGMNVVEQFEKPFRQDTLKLKHGTYDKLDDDGIVAPGVRVS 117

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
             DI++GK  P         ++        KA   RD S  + S  +G V  V I  
Sbjct: 118 GEDIIIGKTAPIAPDSEELGQRT-------KAHVKRDASTPLRSTENGIVDQVLITT 167


>gi|291170438|gb|ADD82428.1| RNA polymerase II second largest subunit [Capnodiales sp. A73]
          Length = 325

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 41/198 (20%), Positives = 54/198 (27%), Gaps = 54/198 (27%)

Query: 1069 GVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVP 1128
              L  VKV     +  Q GD  A RHG KG +      EDMP   DG   DI++NP  +P
Sbjct: 182  EGLXFVKVRTRTTKVPQIGDXFASRHGXKGTIGITYRQEDMPXTADGLXPDIIINPHAIP 241

Query: 1129 SRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDY 1188
            SRM      E  L       G++  +          IS +                    
Sbjct: 242  SRMTXAHXIECLLSKVASLTGQEGXATPFTDVTITSISXILKQQGFQHRGFEVM------ 295

Query: 1189 DDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRP 1248
                                                      +G +    G         
Sbjct: 296  -----------------------------------------YNGHT----GR---KLAAQ 307

Query: 1249 VTVGYIYMLKLNHMVSDK 1266
            V +G     +L  MV DK
Sbjct: 308  VFLGPTXYQRLXXMVDDK 325



 Score = 61.6 bits (148), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 55/173 (31%), Gaps = 12/173 (6%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            N R              +A   S +      L  G   +VA     GY  EDS+ +++ 
Sbjct: 8   YNVRMDTMANVLYYPQKPLATTRSMEXLXXRXLPAGXXAIVAIACXSGYXQEDSVXMNQS 67

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   +   E        D   +       +D  GII  GA 
Sbjct: 68  SIDRGLFRSLXXXAYMDXEKXVGMSVVEAFEKPXXXDTLKMKXGTYXKLDXDGIIMPGAR 127

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           V+  DI++G   P         +     +      DV        +G+   V+
Sbjct: 128 VSGEDIIIGXTAPIAPDAEXXGQXTKXHVK----RDVSTPLRSTXNGIIXQVL 176


>gi|289468063|gb|ADC95712.1| RpoB [Riemerella anatipestifer]
          Length = 157

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 92/156 (58%), Positives = 114/156 (73%), Gaps = 2/156 (1%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           S ITH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+SSL  +A++
Sbjct: 2   SEITHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLISSLGIYAKI 61

Query: 593 NAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           N  GFIETPYRKV +GKV  D   +YL+A +EE + IAQAN  L +DG F  E +  R  
Sbjct: 62  NNLGFIETPYRKVENGKVDLDAAPIYLNAEDEEAKIIAQANVELADDGKFETERIIARLD 121

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
           G+  +V  E++D ID +P Q+  I+ASLIPFLE+DD
Sbjct: 122 GDYPVVEPEQVDLIDVAPNQISGISASLIPFLEHDD 157


>gi|238592160|ref|XP_002392825.1| hypothetical protein MPER_07551 [Moniliophthora perniciosa FA553]
 gi|215459407|gb|EEB93755.1| hypothetical protein MPER_07551 [Moniliophthora perniciosa FA553]
          Length = 401

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 41/168 (24%), Positives = 64/168 (38%), Gaps = 5/168 (2%)

Query: 980  RNIYSRLMEI---LCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVE 1036
               Y RL +      G+                 + +         Q  +         +
Sbjct: 96   NGTYDRLADAPLDENGKITKKFDIIQPDGLAGVGERVDPGDVYINKQTPMNANDNTFTGQ 155

Query: 1037 SLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGN 1096
            +  V Y+ S    +      I+K+   +        ++KV +   R  + GDK + RHG 
Sbjct: 156  AATVPYKNSPMTYKSPVAGNIDKVMISETEND--QTLIKVLIRQTRRPELGDKFSSRHGQ 213

Query: 1097 KGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            KG+   I+  EDMPF   G   D ++NP G PSRM VG++    LG A
Sbjct: 214  KGVCGLIVNQEDMPFNDQGIVPDTIMNPHGFPSRMTVGKMINCSLGNA 261



 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 38/101 (37%), Positives = 53/101 (52%), Gaps = 12/101 (11%)

Query: 1220 NSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVT 1279
            + +L       SG+ +L  G+TG            Y     HMV DK++AR+ G  + +T
Sbjct: 283  SRLLIENGFSYSGKDMLTSGITGNL--------VSY----KHMVMDKMHARARGPRATLT 330

Query: 1280 QQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
            +QP  G+S  GG RLGEME  C+  YGA  +L E L + SD
Sbjct: 331  RQPTEGRSREGGLRLGEMERDCLIGYGATQLLLERLMLSSD 371



 Score = 62.0 bits (149), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 31/156 (19%), Positives = 57/156 (36%), Gaps = 14/156 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
             Q+P+VK                     L  G+N  VA M + GY+ ED++++++  + 
Sbjct: 26  YPQQPMVK----------TKTIELIGYDRLPAGQNATVAVMSYSGYDIEDALILNKASLD 75

Query: 836 EDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGL-KNID---ECGIICVGAEVNPG 891
                   + +   + R    G  +   D P      + K  D     G+  VG  V+PG
Sbjct: 76  RGYGRCQVLRKNTTLIRKYPNGTYDRLADAPLDENGKITKKFDIIQPDGLAGVGERVDPG 135

Query: 892 DILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           D+ + K TP   +  T   +     +    +  +  
Sbjct: 136 DVYINKQTPMNANDNTFTGQAATVPYKNSPMTYKSP 171


>gi|71727040|gb|AAZ39685.1| RNA polymerase II [Aschersonia placenta]
 gi|71727054|gb|AAZ39692.1| RNA polymerase II [Hypocrella raciborskii]
          Length = 246

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 80/263 (30%), Gaps = 21/263 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 5    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 64

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 65   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 123

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 124  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 173

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 174  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 223

Query: 1119 DIVLNPLGVPSRMNVGQIFETHL 1141
            DI++NP  +PSRM +  + E  L
Sbjct: 224  DIIINPHAIPSRMTIAHLIECLL 246



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 65/193 (33%), Gaps = 22/193 (11%)

Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
            +           Q+PL                      +L  G+N +VA   + GYN E
Sbjct: 2   RRMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQE 51

Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDEC 879
           DS+++++  +   +F S+    +    +   L   E       +    +       +DE 
Sbjct: 52  DSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDED 111

Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
           GI+  G  V+  D+++GK  P  +       +             RD S  + S  +G V
Sbjct: 112 GIVAPGVRVSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIV 164

Query: 940 VDVRIFNRHGIDK 952
             V +       K
Sbjct: 165 DSVILTVNADNVK 177


>gi|213494447|gb|ACJ48962.1| RNA polymerase subunit beta [Propionibacterium acidifaciens]
 gi|224925944|gb|ACN69996.1| RNA polymerase subunit beta [Propionibacterium acidifaciens]
          Length = 263

 Score =  145 bits (367), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 90/265 (33%), Positives = 147/265 (55%), Gaps = 14/265 (5%)

Query: 287 SLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
              +K V    +      G ++  +I   +T  + ++     +   L  +      +  I
Sbjct: 5   KTSDKDVFTCKVIPSR--GAWLELEIDKRDTVGVRLDRKRKQNVTVL--LKALGWTEEQI 60

Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
           L  +       IR T+  D    + +ALLDIYR +RPG+  +   A+++    +F+  +Y
Sbjct: 61  L--EEFGQYESIRMTMDKDHVTTQGEALLDIYRKLRPGEPPSRDAAQTLLENFYFNPKRY 118

Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTID--------DIDN 458
           D + VGR K+N +L L+ P D + +  +DI A I  +  L  G+  +D        DID+
Sbjct: 119 DTAKVGRYKINKKLGLNLPFDQQVLTIDDIKAAIHYICALHEGRTELDGGLPVEADDIDH 178

Query: 459 LGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFC 518
            GNRR+R+VGE+++NQ R GL RMER +++R+++ DI+++ PQ LIN +PV +A+ EFF 
Sbjct: 179 FGNRRLRTVGELIQNQLRTGLGRMERVVRDRMTTQDIEAITPQTLINVRPVTAALKEFFG 238

Query: 519 SSQLSQLEEHVNSLSRITHTRRLSA 543
           +SQLSQ  +  N L+ +TH RRLSA
Sbjct: 239 TSQLSQFMDQNNPLAEMTHKRRLSA 263



 Score =  109 bits (271), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 45/215 (20%), Positives = 81/215 (37%), Gaps = 13/215 (6%)

Query: 168 DKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEE 227
           D  +   S K ++ C++IP +G W+++E D +D + VR+DR+RK  VT  L ALG   E+
Sbjct: 2   DPDKT--SDKDVFTCKVIPSRGAWLELEIDKRDTVGVRLDRKRKQNVTVLLKALGWTEEQ 59

Query: 228 ILSTF--YPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL- 284
           IL  F  Y  I  +   D       A   +            D  + ++E+         
Sbjct: 60  ILEEFGQYESIRMTMDKDHVTTQGEALLDIYRKLRPGEPPSRDAAQTLLENFYFNPKRYD 119

Query: 285 -LKSLKEKGVKFLGITSDCLCG-------LYVAEDIVNGETGEIYIEAGDVIDEKSLEEI 336
             K  + K  K LG+                    I     G   ++ G  ++   ++  
Sbjct: 120 TAKVGRYKINKKLGLNLPFDQQVLTIDDIKAAIHYICALHEGRTELDGGLPVEADDIDHF 179

Query: 337 FHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRK 371
            +  +R +  L  + +         +V D+   + 
Sbjct: 180 GNRRLRTVGELIQNQLRTGLGRMERVVRDRMTTQD 214


>gi|238800327|gb|ACR56029.1| At4g21710-like protein [Solanum hirtum]
 gi|238800329|gb|ACR56030.1| At4g21710-like protein [Solanum hirtum]
 gi|238800331|gb|ACR56031.1| At4g21710-like protein [Solanum quitoense]
 gi|238800333|gb|ACR56032.1| At4g21710-like protein [Solanum quitoense]
          Length = 125

 Score =  145 bits (366), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 55/176 (31%), Gaps = 54/176 (30%)

Query: 1090 MAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLG 1149
             + RHG KG V      EDMP+  +G   DI++NP  +PSRM +GQ+ E  +G     +G
Sbjct: 4    FSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMG 63

Query: 1150 KKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDDSVLRVAEQWKSGVPVSTP 1209
            K+  +         +IS         +                                 
Sbjct: 64   KEGDATPFTDVTVDNISKALHKCGYQMRGFETM--------------------------- 96

Query: 1210 VFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSD 1265
                                 +G +    G         + +G  Y  +L HMV D
Sbjct: 97   --------------------YNGHT----GR---RLTAMIFLGPTYYQRLKHMVDD 125


>gi|71067897|gb|AAZ22939.1| RNA polymerase II [Aschersonia turbinata]
          Length = 245

 Score =  145 bits (366), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 21/264 (7%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 3    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 62

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 63   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 121

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 122  DIIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 171

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 172  ----------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 221

Query: 1119 DIVLNPLGVPSRMNVGQIFETHLG 1142
            DI++NP  +PSRM +  + E  L 
Sbjct: 222  DIIINPHAIPSRMTIAHLIECLLS 245



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/192 (19%), Positives = 65/192 (33%), Gaps = 22/192 (11%)

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFED 825
           +           Q+PL                      +L  G+N +VA   + GYN ED
Sbjct: 1   RMDTMANILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQED 50

Query: 826 SMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECG 880
           S+++++  +   +F S+    +    +   L   E       +    +       +DE G
Sbjct: 51  SVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDG 110

Query: 881 IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
           I+  G  V+  DI++GK  P  +       +             RD S  + S  +G V 
Sbjct: 111 IVAPGVRVSGEDIIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVD 163

Query: 941 DVRIFNRHGIDK 952
            V +       K
Sbjct: 164 SVILTVNADNVK 175


>gi|77798197|gb|ABB03277.1| RNA polymerase beta subunit [Nocardia crassostreae]
          Length = 145

 Score =  145 bits (366), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 88/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRTRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|67942352|gb|AAY83376.1| DNA-dependent RNA polymerase II [Pseudopithyella minuscula]
          Length = 461

 Score =  145 bits (366), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 86/262 (32%), Gaps = 27/262 (10%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  +  I      +  D+ +   S +   
Sbjct: 224  DTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRG 283

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNA 995
            +    +F R  +D+ +R   +  + +E   +      + L    Y +L +   +  G   
Sbjct: 284  LF-RSLFYRTYMDQEKR---IGMQVVEEFEKPMRGNTLRLKHGTYDKLDDDGLVAPGVRV 339

Query: 996  VSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKN 1055
                    K+  +S D      R ++         ++     +  Q   S          
Sbjct: 340  TGEDIIIGKTAPISPDADEMGQRQKYHTKRDVSTPLRSTESGIVDQVMLS---------- 389

Query: 1056 KIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
                           L+ VKV +   +  Q GDK A RHG KG +      EDMPF  +G
Sbjct: 390  ----------TNSEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEG 439

Query: 1116 TPVDIVLNPLGVPSRMNVGQIF 1137
               DI++NP  +PSRM +  + 
Sbjct: 440  IVPDIIINPHAIPSRMTIAHLI 461



 Score = 84.4 bits (207), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/375 (14%), Positives = 103/375 (27%), Gaps = 34/375 (9%)

Query: 603 RKVCDGKVTNDVVY----LSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPR 658
           R V D +    V +    +  + +    I      +       +        G+ +L   
Sbjct: 31  RVVQDVRRKGIVSHEASVIRDIRDREFKIFTDAGRVCRPLFTIDNDPTSERRGQLVLRKE 90

Query: 659 EKIDFIDASPKQVVSIAASLIPFLEN--DDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
                 + +              L+              +     P     A  V  G E
Sbjct: 91  HIRKLQEDALADEDDQRFGWDGLLKAGAIQYVDAEEEETIMIVMTPEDLELAREVQEGYE 150

Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
                     + A     V Q       I                          Q+   
Sbjct: 151 IEEDPDPMKRVKAPIPQHVPQ--YTHCEIHPSMILGXXXXXXXXXXXXXXXXXXYQSAMG 208

Query: 777 NQRPLVKVGDEVRRNDIIA--------------DGPSTDLGDLALGRNMLVAFMPWHGYN 822
            Q   V + +   R D +A                      +L  G+N +V  M + GYN
Sbjct: 209 KQAMGVYLTNFAERMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYN 268

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNID 877
            EDS+++++  +   +F S+    +    +   +   E     +  +   +       +D
Sbjct: 269 QEDSVIMNQSSIDRGLFRSLFYRTYMDQEKRIGMQVVEEFEKPMRGNTLRLKHGTYDKLD 328

Query: 878 ECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSG 937
           + G++  G  V   DI++GK  P         ++       +K    RD S  + S  SG
Sbjct: 329 DDGLVAPGVRVTGEDIIIGKTAPISPDADEMGQR-------QKYHTKRDVSTPLRSTESG 381

Query: 938 TVVDVRIFNRHGIDK 952
            V  V +       K
Sbjct: 382 IVDQVMLSTNSEGLK 396


>gi|77798252|gb|ABB03304.1| RNA polymerase beta subunit [Nocardia higoensis]
          Length = 145

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 88/145 (60%), Positives = 120/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|77798191|gb|ABB03274.1| RNA polymerase beta subunit [Nocardia brevicatena]
          Length = 145

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 88/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL  +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLAVYARVNPFGFIETP 145


>gi|55650598|emb|CAF32176.1| RNA polymerase B subunit [Anabaena flos-aquae 1tu30s4]
 gi|55650602|emb|CAF31381.1| RNA polymerase B subunit [Anabaena lemmermannii 1tu32s11]
          Length = 186

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 86/186 (46%), Positives = 121/186 (65%), Gaps = 6/186 (3%)

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           LDE+G      V  R   +      E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG
Sbjct: 1   LDENGYIKGPHVPVRYRQDWTTTGPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMG 60

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSV----- 748
            NMQRQAVPLL+ E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R+      
Sbjct: 61  SNMQRQAVPLLRPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRASGQLSA 120

Query: 749 -EGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLAL 807
             G           Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG ST+ G+LAL
Sbjct: 121 ASGSQVIEKGQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSSTEGGELAL 180

Query: 808 GRNMLV 813
           G+N++V
Sbjct: 181 GQNIVV 186


>gi|44894157|gb|AAS48628.1| RpoB [Nocardia abscessus]
 gi|58531766|gb|AAW78643.1| RNA polymerase B-subunit [Nocardia ignorata]
 gi|58531770|gb|AAW78645.1| RNA polymerase B-subunit [Nocardia ignorata]
 gi|58531772|gb|AAW78646.1| RNA polymerase B-subunit [Nocardia ignorata]
 gi|58531774|gb|AAW78647.1| RNA polymerase B-subunit [Nocardia ignorata]
 gi|62464841|gb|AAX83133.1| RpoB [Nocardia ignorata]
 gi|77798183|gb|ABB03270.1| RNA polymerase beta subunit [Nocardia asteroides]
 gi|77798187|gb|ABB03272.1| RNA polymerase beta subunit [Nocardia beijingensis]
 gi|77798199|gb|ABB03278.1| RNA polymerase beta subunit [Nocardia cummidelens]
 gi|77798207|gb|ABB03282.1| RNA polymerase beta subunit [Nocardia fluminea]
 gi|77798210|gb|ABB03283.1| RNA polymerase beta subunit [Nocardia paucivorans]
 gi|77798216|gb|ABB03286.1| RNA polymerase beta subunit [Nocardia salmonicida]
 gi|77798218|gb|ABB03287.1| RNA polymerase beta subunit [Nocardia seriolae]
 gi|77798220|gb|ABB03288.1| RNA polymerase beta subunit [Nocardia soli]
 gi|77798226|gb|ABB03291.1| RNA polymerase beta subunit [Nocardia vaccinii]
 gi|77798234|gb|ABB03295.1| RNA polymerase beta subunit [Nocardia inohanensis]
 gi|77798236|gb|ABB03296.1| RNA polymerase beta subunit [Nocardia testacea]
 gi|77798240|gb|ABB03298.1| RNA polymerase beta subunit [Nocardia neocaledoniensis]
 gi|77798244|gb|ABB03300.1| RNA polymerase beta subunit [Nocardia yamanashiensis]
 gi|77798248|gb|ABB03302.1| RNA polymerase beta subunit [Nocardia puris]
 gi|77798254|gb|ABB03305.1| RNA polymerase beta subunit [Nocardia shimofusensis]
 gi|77798256|gb|ABB03306.1| RNA polymerase beta subunit [Nocardia pneumoniae]
 gi|77798258|gb|ABB03307.1| RNA polymerase beta subunit [Nocardia araoensis]
          Length = 145

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 88/145 (60%), Positives = 120/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|63086892|gb|AAY30845.1| RNA polymerase II [Aschersonia andropogonis]
          Length = 241

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 44/263 (16%), Positives = 85/263 (32%), Gaps = 27/263 (10%)

Query: 883  CVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDV 942
             +             +       +   +  + AI      +  D+ +   S +   +   
Sbjct: 3    HILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-R 61

Query: 943  RIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGP 999
             +F R   D+ ++         E+  +      + +    Y +L +   +  G       
Sbjct: 62   SLFFRSYSDQEKKVGLNY---TEVFEKPFHQSTLRMKHGTYDKLDDDGIVAPGVRVSGED 118

Query: 1000 KGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEK 1059
                K+  +  +      R+   Q       ++     +      + +            
Sbjct: 119  VIIGKTAPIDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA----------- 167

Query: 1060 IQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVD 1119
                       ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   D
Sbjct: 168  ---------DNVKYVKVRVRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPD 218

Query: 1120 IVLNPLGVPSRMNVGQIFETHLG 1142
            I++NP  +PSRM +  + E  L 
Sbjct: 219  IIINPHAIPSRMTIAHLIECLLS 241



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 772 QNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISE 831
                 Q+PL                      +L  G+N +VA   + GYN EDS+++++
Sbjct: 3   HILYYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQ 52

Query: 832 RMVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGA 886
             +   +F S+    +    +   L   E       +    +       +D+ GI+  G 
Sbjct: 53  SSIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDDDGIVAPGV 112

Query: 887 EVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            V+  D+++GK  P  +       +             RD S  + S  +G V  V +  
Sbjct: 113 RVSGEDVIIGKTAPIDQESQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTV 165

Query: 947 RHGIDK 952
                K
Sbjct: 166 NADNVK 171


>gi|300193593|gb|ADJ68290.1| RNA polymerase B-subunit [Staphylococcus pseudintermedius]
          Length = 148

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 81/147 (55%), Positives = 109/147 (74%), Gaps = 2/147 (1%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
             N L+ +TH RRLSALG GG+ R RA +E+RDVH +HYGR+CP ET EG NIGL++SL+
Sbjct: 1   QANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLS 60

Query: 588 SFARVNAYGFIETPYRKV--CDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
           S+ARVN +GFIETPYRKV      +T+ + YL+A EE++  +AQANS LDE+G F ++ +
Sbjct: 61  SYARVNEFGFIETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEI 120

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVV 672
            CR  G    + +EK+D++D SPKQVV
Sbjct: 121 VCRFRGNNTTMAKEKMDYMDVSPKQVV 147


>gi|242048684|ref|XP_002462088.1| hypothetical protein SORBIDRAFT_02g017766 [Sorghum bicolor]
 gi|241925465|gb|EER98609.1| hypothetical protein SORBIDRAFT_02g017766 [Sorghum bicolor]
          Length = 89

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 49/73 (67%), Positives = 62/73 (84%)

Query: 1073 VVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMN 1132
            +V+V++  KR I+ GDK+AGRHGNKGI+S+ LP +DMP+L+DGTP D+V NPLGVPSRMN
Sbjct: 10   MVRVYILQKREIKVGDKVAGRHGNKGIISKNLPRQDMPYLQDGTPADMVFNPLGVPSRMN 69

Query: 1133 VGQIFETHLGWAC 1145
            VGQIFE+ LG A 
Sbjct: 70   VGQIFESSLGLAG 82


>gi|198279371|emb|CAP04720.1| RNA polymerase beta subunit [Pinus arizonica]
          Length = 190

 Score =  145 bits (366), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 82/197 (41%), Positives = 124/197 (62%), Gaps = 8/197 (4%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVPL + E    GTG+E   A  SG+  +A + G +E +DA+              
Sbjct: 1   MQRQAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSV 52

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    + +QRSN NTC +Q+P ++ G+ V++  I+ADG +T  G+L+LG+N+LVA+
Sbjct: 53  NGDTVRTESVIYQRSNTNTCTHQKPQIRQGECVKKGQILADGATTVGGELSLGKNVLVAY 112

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L++
Sbjct: 113 MPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRH 172

Query: 876 IDECGIICVGAEVNPGD 892
           +DE G++ +G+ +  GD
Sbjct: 173 LDENGLVMLGSWIETGD 189


>gi|71067893|gb|AAZ22937.1| RNA polymerase II [Aschersonia rhombispora]
          Length = 228

 Score =  145 bits (366), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 82/250 (32%), Gaps = 27/250 (10%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +     F  +   + +   
Sbjct: 3    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLXFRSYSDQEXK--- 59

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLIS 1014
             V     E+  +      + +    Y +L E   +  G           K+  +  +   
Sbjct: 60   -VGXNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQD 118

Query: 1015 EYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVV 1074
               R+   Q       ++     +      + +                       ++ V
Sbjct: 119  LGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA--------------------DNVKYV 158

Query: 1075 KVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVG 1134
            KV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM + 
Sbjct: 159  KVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIA 218

Query: 1135 QIFETHLGWA 1144
             + E  L   
Sbjct: 219  HLIECLLSKV 228



 Score = 77.8 bits (190), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 58/162 (35%), Gaps = 12/162 (7%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +        
Sbjct: 2   SMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLXFRSYSDQEXKVG 61

Query: 856 LGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
               E       +    +       +DE GI+  G  V+  D+++GK  P  +       
Sbjct: 62  XNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGT 121

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +             RD S  + S  +G V  V +       K
Sbjct: 122 RT-------SVHQRRDISTPLRSTENGIVDSVILTVNADNVK 156


>gi|22208411|emb|CAC87034.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 206

 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 96/205 (46%), Positives = 139/205 (67%), Gaps = 14/205 (6%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--PDDV 428
            +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L    P   
Sbjct: 2   DEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITS 61

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLKNQYR 476
             + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+++NQ R
Sbjct: 62  STLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIR 121

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQ SQ     N LS +T
Sbjct: 122 VGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQPSQFMGQNNPLSGLT 181

Query: 537 HTRRLSALGQGGVARARAGVEMRDV 561
           H RRLSALG GG++R RAG+E+RDV
Sbjct: 182 HKRRLSALGPGGLSRERAGLEVRDV 206


>gi|77798201|gb|ABB03279.1| RNA polymerase beta subunit [Nocardia cyriacigeorgica]
          Length = 145

 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRARTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|197941986|gb|ACH78598.1| RNA polymerase subunit [Polytrichum commune]
          Length = 186

 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 86/194 (44%), Positives = 131/194 (67%), Gaps = 8/194 (4%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           VP +  E   VGTG+ES  A  SG+   A++ G V   DA +I + + E  +        
Sbjct: 1   VPXIXPEKXIVGTGLESQAALDSGSVAXARQNGKVSYTDAKKITLFNSEKTIST------ 54

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
              L+K+QRSN +TC+NQ+P V     +++  I+ADG +T  G+LALG+N+LVA+MPW G
Sbjct: 55  --NLIKYQRSNNSTCMNQKPQVTQDVFIKKGQILADGAATLKGELALGKNILVAYMPWEG 112

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER++ ED++TSIHIE +E+ AR T  GPE+IT++IP++    L+++D+ G
Sbjct: 113 YNFEDAILISERLIYEDIYTSIHIERYEIEARTTSQGPEKITKEIPHLENNVLRHLDKSG 172

Query: 881 IICVGAEVNPGDIL 894
           ++ +G+ V  GD+L
Sbjct: 173 LVLIGSWVETGDVL 186


>gi|219564051|gb|ACL28209.1| RNA polymerase II second largest subunit [fungal sp. M178]
          Length = 238

 Score =  145 bits (365), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 50/261 (19%), Positives = 90/261 (34%), Gaps = 27/261 (10%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +     +   + 
Sbjct: 2    MANILYYPQKPLGTTRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQXSIDRGLF 61

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILCGQNAVS 997
               +F R   D+ +R   +    +E   +    + + L    Y +L E   +  G     
Sbjct: 62   -RSLFYRAYTDQEKR---IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSG 117

Query: 998  GPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKI 1057
                  K+  ++ D                +E  QR    +K    T     E+   +++
Sbjct: 118  EDIIIGKTAPIAPD---------------AEEMGQRTKAHIKRDASTPLRSTENGIVDQV 162

Query: 1058 EKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTP 1117
                         LR VKV +   +  Q GDK A RHG KG +      EDMPF  +G  
Sbjct: 163  LITT-----NAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRIEDMPFTSEGIV 217

Query: 1118 VDIVLNPLGVPSRMNVGQIFE 1138
             D+++NP  +PSRM +  + E
Sbjct: 218  PDLIINPHAIPSRMTIAHLIE 238



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/158 (23%), Positives = 62/158 (39%), Gaps = 12/158 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA M + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 16  TRSMEFLKFRELPAGQNAIVAIMCYSGYNQEDSVIMNQXSIDRGLFRSLFYRAYTDQEKR 75

Query: 854 TKLGPEEITR-----DIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             +   E        D   +       +DE GI+  G  V+  DI++GK  P        
Sbjct: 76  IGMNVVEQFEKPFRQDTLKLKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIAPDAEEM 135

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            ++        KA   RD S  + S  +G V  V I  
Sbjct: 136 GQRT-------KAHIKRDASTPLRSTENGIVDQVLITT 166


>gi|32745095|gb|AAP87113.1| Hypothetical RPB2 protein [Trypanosoma rangeli]
          Length = 252

 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 52/246 (21%), Positives = 79/246 (32%), Gaps = 29/246 (11%)

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S V         + R      ER     ++    L  + D  
Sbjct: 2    AIACYSGYNQEDSIIMSXSAVERGFFRSAFW-RSYKASEER-----KKDGRELFENPDRN 55

Query: 975  QVILDRNIYSRL---MEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
               + R  Y++L     I  G   + G     K+  +    +                  
Sbjct: 56   ICRVKRADYTKLDADGLIKPGMPVMGGDILVGKTIPIPEAALENAVVGNT---------- 105

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
                  LK     +    E    +K+              R  KV V   +    GDK  
Sbjct: 106  ----RLLKRDCSIASRTTEKGVVDKVM------LTENSGNRFTKVKVRSIKIPNIGDKFC 155

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG        EDMPF +DG   D+++NP  +PSRM V  + ET  G      G +
Sbjct: 156  SRHGQKGTNGIQFRQEDMPFNRDGIVPDLIINPHAIPSRMTVAHLIETLAGKVACYKGSE 215

Query: 1152 IKSLIN 1157
            + +   
Sbjct: 216  VYATPF 221



 Score = 74.0 bits (180), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/142 (30%), Positives = 57/142 (40%), Gaps = 9/142 (6%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE---EITRDIPNVS 869
           VA   + GYN EDS+++S   V    F S     ++      K G E      R+I  V 
Sbjct: 1   VAIACYSGYNQEDSIIMSXSAVERGFFRSAFWRSYKASEERKKDGRELFENPDRNICRVK 60

Query: 870 EEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSL 929
                 +D  G+I  G  V  GDILVGK  P       PE  L  A+ G   +  RD S+
Sbjct: 61  RADYTKLDADGLIKPGMPVMGGDILVGKTIPI------PEAALENAVVGNTRLLKRDCSI 114

Query: 930 RVPSGVSGTVVDVRIFNRHGID 951
              +   G V  V +    G  
Sbjct: 115 ASRTTEKGVVDKVMLTENSGNR 136


>gi|289468073|gb|ADC95717.1| RpoB [Riemerella columbina]
          Length = 156

 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 84/156 (53%), Positives = 109/156 (69%), Gaps = 2/156 (1%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  +  N LS +TH RRLSALG GG++R RAG E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQTNPLSEVTHKRRLSALGPGGLSRERAGFEVRDVHHTHYGRICPIETPEGPNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVTND--VVYLSAMEEENRYIAQANSSLDEDGSFT 641
           SSL  +A++N  GFIETPYRKV +GKV      VYL+A +EE++ IAQAN  L +DG F 
Sbjct: 61  SSLGIYAKINNLGFIETPYRKVENGKVDFKAAPVYLNAEDEESKIIAQANVELADDGKFE 120

Query: 642 EELVFCRCAGEEILVPREKIDFIDASPKQVVSIAAS 677
            + +  R  G+  +V  +++D ID +P Q+  I+AS
Sbjct: 121 TDRIIARLDGDYPVVEPDQVDLIDIAPNQISGISAS 156


>gi|63086912|gb|AAY30855.1| RNA polymerase II [Aschersonia basicystis]
          Length = 239

 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 78/245 (31%), Gaps = 21/245 (8%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ ++  
Sbjct: 16   MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVG 74

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E               +       +  G           K+  +  +      
Sbjct: 75   LNYTEVFEKPFHQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGT 134

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+   Q       ++     +      + +                       ++ VKV 
Sbjct: 135  RTTVHQRRDISTPLRSTENGIVDSVILTVNA--------------------DNVKYVKVR 174

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + 
Sbjct: 175  VRTTKVPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLI 234

Query: 1138 ETHLG 1142
            E  L 
Sbjct: 235  ECLLS 239



 Score = 81.3 bits (199), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/162 (20%), Positives = 60/162 (37%), Gaps = 12/162 (7%)

Query: 796 DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTK 855
                   +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   
Sbjct: 15  SMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVG 74

Query: 856 LGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEE 910
           L   E+           +       +DE GI+  G  V+  D+++GK  P  +       
Sbjct: 75  LNYTEVFEKPFHQTTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGT 134

Query: 911 KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           +             RD S  + S  +G V  V +       K
Sbjct: 135 RT-------TVHQRRDISTPLRSTENGIVDSVILTVNADNVK 169


>gi|226445710|gb|ACO58379.1| RNA polymerase [Mycoplasma moatsii]
          Length = 165

 Score =  145 bits (365), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 85/164 (51%), Positives = 113/164 (68%), Gaps = 1/164 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS I++ RR+++LG GG+ R  A  E+RDVHPTHYGRICP ET EG NIGL+ +L  +A
Sbjct: 2   PLSEISNKRRITSLGPGGLNRDTAQFEVRDVHPTHYGRICPIETPEGPNIGLILNLAVYA 61

Query: 591 RVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           R+N YGF+ETPY +V  G V  +  +YL A EE     AQ+  +++E    T +LV  R 
Sbjct: 62  RINEYGFLETPYYRVNKGVVDYSKPIYLIASEEYGFTFAQSTVTVNEKNKITNKLVTVRK 121

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
             + I+V  E++DFID + +Q+ SIAAS IPFLENDD+NR LMG
Sbjct: 122 NHDFIIVKPEEVDFIDVASRQMTSIAASCIPFLENDDANRALMG 165


>gi|293611898|gb|ADE48393.1| RNA polymerase beta chain [Dioon edule]
          Length = 189

 Score =  144 bits (364), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 93/197 (47%), Positives = 131/197 (66%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I                    L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLV--------GGDTVGTELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+L A MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLXAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|22208407|emb|CAC87032.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 206

 Score =  144 bits (364), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 95/205 (46%), Positives = 140/205 (68%), Gaps = 14/205 (6%)

Query: 371 KDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--PDDV 428
            +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L    P   
Sbjct: 2   DEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITS 61

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLKNQYR 476
             + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+++NQ R
Sbjct: 62  STLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIR 121

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
           +G+ RMER ++ER+++ D++++ P+ LIN +PVV+A+ EFF +SQLSQ  +  N LS +T
Sbjct: 122 VGMSRMERVVRERMTTQDVEAITPRTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLT 181

Query: 537 HTRRLSALGQGGVARARAGVEMRDV 561
           H RRL ALG GG++R RAG+E+RDV
Sbjct: 182 HKRRLLALGPGGLSRERAGLEVRDV 206


>gi|293611912|gb|ADE48400.1| RNA polymerase beta chain [Lepidozamia peroffskyana]
          Length = 182

 Score =  144 bits (364), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 94/190 (49%), Positives = 132/190 (69%), Gaps = 8/190 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E  VA  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQVAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRRGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIP 866
           GPE IT++IP
Sbjct: 173 GPERITKEIP 182


>gi|293611902|gb|ADE48395.1| RNA polymerase beta chain [Dioon mejiae]
          Length = 189

 Score =  144 bits (364), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 92/197 (46%), Positives = 133/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I        +           L+ +QRSN NTC++Q+P V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLVDGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+L+A MPW GYNFED++LI+ER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLLAHMPWEGYNFEDAILITERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|77798203|gb|ABB03280.1| RNA polymerase beta subunit [Nocardia farcinica]
          Length = 145

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 86/145 (59%), Positives = 118/145 (81%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+  E+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTSAELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|109289915|gb|ABG29321.1| DNA-directed RNA polymerase, putative [Solanum bulbocastanum]
          Length = 1018

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 120/981 (12%), Positives = 259/981 (26%), Gaps = 228/981 (23%)

Query: 30  IEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPIT-----AFSGA-------AMLEFV 77
           I  Q  SY+ F+            G+Q  F SV  I        S         A ++F 
Sbjct: 86  ISHQIDSYNDFIR----------YGIQRVFDSVGEIHVEPGYDPSKKGEGDWKHASVKFG 135

Query: 78  SYEFDPPKFD-----------------VDDCLWRDLTYAVPLKI-----TLRLIVFDVDE 115
               D PKF                        +++TY+  + +     T +L+  D  +
Sbjct: 136 KVTLDRPKFWAGEKFSAYNGEEYLNLWPRHARLQNMTYSARIIVETHVFTKKLVRSDKFK 195

Query: 116 FTGAKSIKD--IKEQ--SIYMGDLPLMTKD------------------GTFVIKGIQRIV 153
               + +    + E    +++G +P+M                     G F++KG ++I 
Sbjct: 196 TGVEQFVDKECVMEDKRDVFIGRIPVMVNSELCWMSGADRPDCEFDHGGYFIVKGAEKIF 255

Query: 154 VSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRK-- 211
           ++Q      I           +  + Y        G       + ++ +++++    K  
Sbjct: 256 IAQEQ----ICLKRLWVSNHSTWMVAYRS------G-------EKRNRVYLKLTETLKHE 298

Query: 212 ----------------VPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLSAADL 254
                           +P+     ALG+ S+ E++      I      D     +  A +
Sbjct: 299 HIKGEAKALSVYFFAEMPIWVLFFALGVSSDREVVDLIDVDI-----KDTNIINILVASI 353

Query: 255 MVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGIT-------SDCLCGLY 307
               K              ++   K      +   E+ +K                 G  
Sbjct: 354 HDADKNCEDFRKGKKALAYVDRLVKSCKFPPQESVEECIKEYLFPNLSGLKQKARFLGYM 413

Query: 308 VAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAY-----IRNTL 362
           V   +++   G   ++  D    K L+       R++ +    +           +    
Sbjct: 414 VKCLLLSYI-GRRKVDNRDDFRNKRLDLAGELLERELRVHVKHAERRMVKALQRDLCGDR 472

Query: 363 VTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFF------DSDKYDLSTVGRVKM 416
                +   DA +    + R      +         +         ++   ++   R   
Sbjct: 473 QVQPIEHYLDASIITNGLSRAFSTGHWCHPYKRMERVSGVVATLRRTNPLQMTADLRKTR 532

Query: 417 NMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYR 476
                     D R+        +  +        G + ++ ++G      +  +L+  +R
Sbjct: 533 QQVTYTGKVGDARYPHPSHWGKVCFLSTPDGENCGLVKNLASMGLVSTTVLKPLLETLFR 592

Query: 477 LGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
            G+ ++               ++  D +      +                     + + 
Sbjct: 593 CGMQKLVDD-SATSLHGKQKVLLDGDWVGVCEDSALFVSK---------LRRQRRRNEVP 642

Query: 537 HTRRLSALGQGGVARARAGVEM-----------RDVHPTHYGRICPAETSEGHNIGLVSS 585
           H    +     G+                    RD           A       + + + 
Sbjct: 643 HQLAHTLAIPPGICYLLPTHVPVTLTEAQVEVKRDEQQDEVRIFSDAGRIMRPLLVVSNL 702

Query: 586 LTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELV 645
               A  +     +  ++ + D      +  +   EEE+   A     L +         
Sbjct: 703 KNIKALKDGMKGGDYGFQTLLD---KGIIELIGPEEEEDCRTAWGVEYLLKADKEN---- 755

Query: 646 FCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLK 705
                      P       +     ++ ++  LIPF  +D + RVL              
Sbjct: 756 -----------PPVNYTHCELDMSFLLGLSCGLIPFANHDHARRVLYQSE---------- 794

Query: 706 AEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLM 765
                          K S  AI         +VD                          
Sbjct: 795 ---------------KHSQQAIGFSTVNPNARVDTNT----------------------- 816

Query: 766 KFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWH---GYN 822
                       QRPL                    +       N   A +  +   GYN
Sbjct: 817 ------HQLYYPQRPLFGTMLSDSLGKPKCARHQKGMLSRPEYYNGQCAIVAVNVHLGYN 870

Query: 823 FEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDI------PNVSEEGLKNI 876
            EDS++++   +   +F S H+  ++    + +   ++   +              + ++
Sbjct: 871 QEDSVVMNRASLERGMFRSEHVRSYKAEVDNKEAMGKKSKVEDSVNFGKTQSKIGRVDSL 930

Query: 877 DECGIICVGAEVNPGDILVGK 897
           D+ G   +GA +  GDI++GK
Sbjct: 931 DDDGFPFIGANLQSGDIIIGK 951


>gi|293611914|gb|ADE48401.1| RNA polymerase beta chain [Encephalartos hildebrandtii]
          Length = 186

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 91/194 (46%), Positives = 131/194 (67%), Gaps = 8/194 (4%)

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +D
Sbjct: 1   PFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRITYID 60

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG +
Sbjct: 61  AGKITSLADGDTVGT--------ELVIYQRSNSNTCMHQKPRVRRGEYVKKGQILADGAA 112

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  GPE
Sbjct: 113 TLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGPE 172

Query: 860 EITRDIPNVSEEGL 873
            IT++IP++    L
Sbjct: 173 RITKEIPHLDAHLL 186


>gi|77798181|gb|ABB03269.1| RNA polymerase beta subunit [Nocardia africana]
          Length = 145

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 86/145 (59%), Positives = 117/145 (80%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRRVR+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +P+ +A+ EF
Sbjct: 1   DHFGNRRVRTVGELIQNQMRVGLSRMERVVRERMTTQDVEAITPQTLINIRPITAAIREF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQHNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPCHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+  L+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGYLSVYARVNPFGFIETP 145


>gi|82706463|gb|ABB89609.1| RNA polymerase II second largest subunit [Cochliobolus
            heterostrophus]
          Length = 547

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 90/611 (14%), Positives = 180/611 (29%), Gaps = 76/611 (12%)

Query: 521  QLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNI 580
             +SQ+       S ++H RR +      V R     + R +H +H+G +CPAET EG   
Sbjct: 1    GVSQVLXRYTYASTLSHLRRTNT----PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQAC 56

Query: 581  GLVSSLTSFARVNAYGFIET--PYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDG 638
            GLV +L+    V+          +    + ++  +       +    ++      +  + 
Sbjct: 57   GLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQNPDATKVFVNGVWVGVHSNA 116

Query: 639  SFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQ 697
                 +V        +      I D  D   K        + P    ++  R     ++ 
Sbjct: 117  QQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVENDIRKPNRNHLI 176

Query: 698  --RQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAK---RAGIVEQVDAIRIVIRSVEGDL 752
              ++    LKAE     T       +   A    +   + G+VE +DA       +    
Sbjct: 177  FTKEISNKLKAEQQETSTRQGWSQEEVEQATYGWRGLIQDGVVEYLDAEEEETAMITFSP 236

Query: 753  DPSTSGVD-IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNM 811
            +      +    L   +RS +     +R   +    +         P+  LG       +
Sbjct: 237  EDLEEWREMKMGLPAAERSTEGKDRLRRLKPQPDPRIHAYTHCEIHPAMILG-------I 289

Query: 812  LVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEE 871
              + +P+  +N          M  + +  ++      +                      
Sbjct: 290  CASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNFALRMETMMN----------------- 332

Query: 872  GLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRV 931
                        V             +       +   +  + AI      +  D+ +  
Sbjct: 333  ------------VLYYPQKPLATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIMN 380

Query: 932  PSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME--- 988
             S +   +    +F R   ++ +R   +    +E   +    + + L    Y +L +   
Sbjct: 381  QSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGV 436

Query: 989  ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSI 1048
            +  G           K+  +++D      ++           ++     +  Q       
Sbjct: 437  VAPGVRVSGDDIIIGKTAPIAADAQELGQKTTLHTKRDVSTPLRSTENGIVDQ------- 489

Query: 1049 LEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCED 1108
                                  LR VKV     +  Q GDK A RHG KG +      ED
Sbjct: 490  -------------VLFTTNTEGLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQED 536

Query: 1109 MPFLKDGTPVD 1119
            MPF ++G   D
Sbjct: 537  MPFTREGVTPD 547



 Score = 99.0 bits (245), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 75/542 (13%), Positives = 141/542 (26%), Gaps = 91/542 (16%)

Query: 429 RHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
           R          +     L N    +         +   + + L     + +      I +
Sbjct: 20  RTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIID 79

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QG 547
            ++  ++  +   D                   +         ++ +   RR   L  + 
Sbjct: 80  FMTQRNMQLLEEYDQNQNPDATKVF---VNGVWVGVHSNAQQLVTVVQELRRNGTLSYEM 136

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFAR-------------VNA 594
            + R     E + +       + P    E        +   F +                
Sbjct: 137 SLIRDIRDREFK-IFTDAGRVMRPLFVVENDIRKPNRNHLIFTKEISNKLKAEQQETSTR 195

Query: 595 YGF----IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
            G+    +E              V YL A EEE   I  +   L+E       L      
Sbjct: 196 QGWSQEEVEQATYGWRGLIQDGVVEYLDAEEEETAMITFSPEDLEEWREMKMGLPA---- 251

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPF 710
                                               + R   G +  R+  P        
Sbjct: 252 ------------------------------------AERSTEGKDRLRRLKPQPDPRIH- 274

Query: 711 VGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGV-DIYRLMKFQR 769
             T  E   A   G       A I+   D  +    + +  +     GV      ++ + 
Sbjct: 275 AYTHCEIHPAMILGIC-----ASIIPFPDHNQSPRNTYQSAMGKQAMGVALTNFALRMET 329

Query: 770 SNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLI 829
                   Q+PL                      +L  G+N +VA   + GYN EDS+++
Sbjct: 330 MMNVLYYPQKPL----------ATTRSMEYLKFRELPAGQNAIVAIATYGGYNQEDSVIM 379

Query: 830 SERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGLKNIDECGIICV 884
           ++  +   +F S+    +    +   +   E        D   +       +D+ G++  
Sbjct: 380 NQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRADTLRLKGGTYDKLDDDGVVAP 439

Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
           G  V+  DI++GK  P         +K             RD S  + S  +G V  V  
Sbjct: 440 GVRVSGDDIIIGKTAPIAADAQELGQKT-------TLHTKRDVSTPLRSTENGIVDQVLF 492

Query: 945 FN 946
             
Sbjct: 493 TT 494


>gi|312204292|gb|ADQ47463.1| RNA polymerase II second largest subunit [Absconditella lignicola]
          Length = 225

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 85/237 (35%), Gaps = 27/237 (11%)

Query: 911  KLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARD 970
              + AI      +  D+ +   S +   +    +F R  I++ +R        +E   + 
Sbjct: 13   NAIVAIACYSGYNXEDSVIMXQSSIDRGLF-RSLFYRAYIEQEKRVGM---SVVESFEKP 68

Query: 971  KDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQ 1027
               + + L    Y +L +   I  G           K+  ++ D      R++       
Sbjct: 69   MRSDTLRLKHGTYXKLDDDGIIAPGVRVSGEDIIIGKTAPIAPDAEEMGQRTKLHXKRDT 128

Query: 1028 DEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSG 1087
               ++     +                  ++K+          LR VKV +   +  Q G
Sbjct: 129  STPLRSTESGI------------------VDKVXL--TTNSEGLRFVKVRMRTTKVPQVG 168

Query: 1088 DKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWA 1144
            DK A RHG KG +      EDMPF  +G   D+++NP  +PSRM +  + E  L   
Sbjct: 169  DKFASRHGQKGTIGITYRQEDMPFSTEGITPDLIINPHAIPSRMTIAHLVECXLSKV 225



 Score = 72.4 bits (176), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/154 (24%), Positives = 60/154 (38%), Gaps = 12/154 (7%)

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                  +A   N +VA   + GYN EDS+++ +  +   +F S+    +    +   + 
Sbjct: 1   EFLKFRRVAXWXNAIVAIACYSGYNXEDSVIMXQSSIDRGLFRSLFYRAYIEQEKRVGMS 60

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E     +  D   +       +D+ GII  G  V+  DI++GK  P        EE  
Sbjct: 61  VVESFEKPMRSDTLRLKHGTYXKLDDDGIIAPGVRVSGEDIIIGKTAPIA---PDAEEMG 117

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFN 946
            R     K    RDTS  + S  SG V  V +  
Sbjct: 118 QRT----KLHXKRDTSTPLRSTESGIVDKVXLTT 147


>gi|258590768|emb|CBB97105.1| RNA polymerase beta subunit [Enterobacter radicincitans]
 gi|258590770|emb|CBB97108.1| RNA polymerase beta subunit [Enterobacter radicincitans]
 gi|258590772|emb|CBB97110.1| RNA polymerase beta subunit [Enterobacter radicincitans]
          Length = 132

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 79/132 (59%), Positives = 104/132 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++L E+G F ++LV CR  GE  L   +++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLTEEGRFVDDLVTCRSKGESSLFSADQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCN 695
           +DD+NR LMG N
Sbjct: 121 HDDANRALMGAN 132


>gi|77798193|gb|ABB03275.1| RNA polymerase beta subunit [Nocardia carnea]
 gi|77798205|gb|ABB03281.1| RNA polymerase beta subunit [Nocardia flavorosea]
 gi|77798224|gb|ABB03290.1| RNA polymerase beta subunit [Nocardia uniformis]
          Length = 145

 Score =  144 bits (364), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRIRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRL+ALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL  +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLAVYARVNPFGFIETP 145


>gi|310770188|gb|ADP21592.1| RpoB [Arcobacter defluvii]
          Length = 162

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 89/161 (55%), Positives = 119/161 (73%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F+
Sbjct: 2   PLSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTFS 61

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           +VN  GFIE PY+ V DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R  
Sbjct: 62  KVNELGFIEAPYKTVVDGVVTNEIKYYTATQEEGLVIAPGSTKVDENGKIVESLIEARKD 121

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           GE +L+ R  +D ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 122 GEILLMERSSVDLIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|22208405|emb|CAC87031.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 211

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 97/211 (45%), Positives = 142/211 (67%), Gaps = 14/211 (6%)

Query: 365 DKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT 424
           D      +ALLDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L  
Sbjct: 1   DNTVGTDEALLDIYRKLRPGESPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHV 60

Query: 425 --PDDVRHIRKEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEM 470
             P     + +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+
Sbjct: 61  GEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGEL 120

Query: 471 LKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVN 530
           ++NQ R+G+ RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQLSQ  +  N
Sbjct: 121 IQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNN 180

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDV 561
            LS +T+ RRLSALG GG++R RAG+E+RDV
Sbjct: 181 PLSGLTYKRRLSALGPGGLSRERAGLEVRDV 211


>gi|293611910|gb|ADE48399.1| RNA polymerase beta chain [Macrozamia moorei]
          Length = 186

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 90/194 (46%), Positives = 130/194 (67%), Gaps = 8/194 (4%)

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +D
Sbjct: 1   PFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRITYID 60

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG +
Sbjct: 61  AGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRRGEYVKKGQILADGAA 112

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  G E
Sbjct: 113 TLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGLE 172

Query: 860 EITRDIPNVSEEGL 873
            IT++IP++    L
Sbjct: 173 RITKEIPHLDAHLL 186


>gi|258590774|emb|CBB97112.1| RNA polymerase beta subunit [Enterobacter radicincitans]
          Length = 132

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 78/132 (59%), Positives = 103/132 (78%)

Query: 564 THYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE 623
           THYGR+CP ET EG NIGL++SL+ +A+ N YGF+ETPYRKV DG VT+++ YLSA+EE 
Sbjct: 1   THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEG 60

Query: 624 NRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLE 683
           N  IAQAN++L ++G F  +LV CR  GE  L   +++D++D S +QVVS+ ASLIPFLE
Sbjct: 61  NYVIAQANTNLTDEGRFVNDLVTCRSKGESSLFSADQVDYMDVSTQQVVSVGASLIPFLE 120

Query: 684 NDDSNRVLMGCN 695
           +DD+NR LMG N
Sbjct: 121 HDDANRALMGAN 132


>gi|293611896|gb|ADE48392.1| RNA polymerase beta chain [Ceratozamia microstrobila]
          Length = 180

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 90/188 (47%), Positives = 129/188 (68%), Gaps = 8/188 (4%)

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +D
Sbjct: 1   PFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAALDSGSAAIAAQGGRITYID 60

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG +
Sbjct: 61  AGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILADGAA 112

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  GPE
Sbjct: 113 TLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGPE 172

Query: 860 EITRDIPN 867
            IT++IP+
Sbjct: 173 RITKEIPH 180


>gi|63086894|gb|AAY30846.1| RNA polymerase II [Aschersonia incrassata]
          Length = 223

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 77/240 (32%), Gaps = 21/240 (8%)

Query: 903  ESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVERE 962
               +   +  + AI      +  D+ +   S +   +    +F R   D+ ++      E
Sbjct: 5    FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVGLNYTE 63

Query: 963  QIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWW 1022
              E               +       +  G           K+  +  +      R+   
Sbjct: 64   VFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGTRTSVH 123

Query: 1023 QFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKR 1082
            Q       ++     +      + +                       ++ VKV V   +
Sbjct: 124  QRRDISTPLRSTENGIVDSVILTVNA--------------------DNVKYVKVRVRTTK 163

Query: 1083 PIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLG 1142
              Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + E  L 
Sbjct: 164  VPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDIIINPHAIPSRMTIAHLIECLLS 223



 Score = 80.5 bits (197), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/160 (20%), Positives = 60/160 (37%), Gaps = 12/160 (7%)

Query: 798 PSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLG 857
                 +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    +   L 
Sbjct: 1   EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKKVGLN 60

Query: 858 PEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKL 912
             E       +    +       +DE GI+  G  V+  D+++GK  P  +       + 
Sbjct: 61  YTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDLGTRT 120

Query: 913 LRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                       RD S  + S  +G V  V +       K
Sbjct: 121 -------SVHQRRDISTPLRSTENGIVDSVILTVNADNVK 153


>gi|310770190|gb|ADP21593.1| RpoB [Arcobacter defluvii]
 gi|310770192|gb|ADP21594.1| RpoB [Arcobacter defluvii]
          Length = 162

 Score =  144 bits (363), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 88/161 (54%), Positives = 118/161 (73%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
             S +TH RRLSALG+GG+ + RAG E+RDVHPTHYGRICP ET EG NIGL+++L++F+
Sbjct: 2   PXSEVTHKRRLSALGEGGLVKERAGFEVRDVHPTHYGRICPVETPEGQNIGLINTLSTFS 61

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCA 650
           +VN  GFIE PY+ V DG VTN++ Y +A +EE   IA  ++ +DE+G   E L+  R  
Sbjct: 62  KVNELGFIEAPYKTVVDGVVTNEIKYYTATQEEGLVIAPGSTKVDENGKIVESLIEARKD 121

Query: 651 GEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
           GE +L+ R  +D ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 122 GEILLMERSSVDLIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|225698415|gb|ACO07325.1| RpoB [Pasteurellaceae bacterium TIS12640]
          Length = 151

 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 87/149 (58%), Positives = 110/149 (73%), Gaps = 1/149 (0%)

Query: 533 SRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
           + +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIGL+++L +FAR 
Sbjct: 3   AEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIGLINTLATFART 62

Query: 593 NAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSFTEELVFCRCAG 651
           N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF  ELV  RC G
Sbjct: 63  NKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSFATELVPARCGG 122

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIP 680
           E  + P E+I ++D S +Q+VS+AA+LIP
Sbjct: 123 ETGMFPPERISYMDVSAQQIVSVAAALIP 151


>gi|294721616|gb|ADF32956.1| RNA polymerase II second largest subunit [Coniosporium apollinis]
          Length = 215

 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 31/91 (34%), Positives = 42/91 (46%)

Query: 1066 MPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPL 1125
                 LR VKV     +  Q GDK A RHG KG +      EDMPF  +G   D+++NP 
Sbjct: 125  TNAENLRFVKVRTRTTKVPQIGDKFASRHGQKGTIGITYRQEDMPFTCEGLTPDLIINPX 184

Query: 1126 GVPSRMNVGQIFETHLGWACVGLGKKIKSLI 1156
             +PSRM +  + E  L       G +  +  
Sbjct: 185  AIPSRMTIAHLIECLLSKVGAIKGSEGDATP 215



 Score = 62.8 bits (151), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 26/125 (20%), Positives = 51/125 (40%), Gaps = 12/125 (9%)

Query: 820 GYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRD-----IPNVSEEGLK 874
           GYN EDS+++++  +   +F S+    +    +   +   E            +      
Sbjct: 1   GYNQEDSVIMNQSSIDRGLFRSLFYRSYIDQEKKVGIHDVEKFMKPRRGTTLRMKHGTYD 60

Query: 875 NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
            I++ G+I  G  V+  D+++GK+ P         ++        KA + RD S  + S 
Sbjct: 61  KIEDDGLIAPGTRVSGDDVIIGKVAPIAPDADELGQRT-------KAHEFRDVSTPLRST 113

Query: 935 VSGTV 939
            +G V
Sbjct: 114 ENGIV 118


>gi|226427441|gb|ACO54914.1| RNA polymerase [Mycoplasma bovirhinis]
          Length = 173

 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 76/171 (44%), Positives = 116/171 (67%), Gaps = 1/171 (0%)

Query: 524 QLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLV 583
           Q  + +N LS +++ RR+++LG GG++R  A  E+RDVH THYGRICP ET EG NIGL+
Sbjct: 1   QFMDQINPLSEVSNKRRVTSLGPGGLSRDTAQFEVRDVHATHYGRICPIETPEGLNIGLI 60

Query: 584 SSLTSFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTE 642
            +  ++A+++  GF++TPY KV +G +  +DV YL+A +E    IAQ++  +DE+    +
Sbjct: 61  LNFATYAQIDDKGFLKTPYYKVNNGVIDYSDVRYLNATQELGYSIAQSSVKVDENNKIID 120

Query: 643 ELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           + +  R           +IDF++ S KQ++S+AA+ IPFLENDD+NR LMG
Sbjct: 121 DNLTIRRNYTYTNGTSSEIDFVEVSSKQILSVAAAGIPFLENDDANRALMG 171


>gi|71727060|gb|AAZ39695.1| RNA polymerase II [Aschersonia placenta]
          Length = 239

 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 79/260 (30%), Gaps = 21/260 (8%)

Query: 881  IICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVV 940
            +  +             +       +   +  + AI      +  D+ +   S +   + 
Sbjct: 1    MANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF 60

Query: 941  DVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPK 1000
               +F R   D+ ++      E  E               +       +  G        
Sbjct: 61   -RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDV 119

Query: 1001 GFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
               K+  +  +      R+   Q       ++     +      + +             
Sbjct: 120  IIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------ 167

Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
                      ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI
Sbjct: 168  --------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTPDI 219

Query: 1121 VLNPLGVPSRMNVGQIFETH 1140
            ++NP  +PSRM +  + E  
Sbjct: 220  IINPHAIPSRMTIAHLIECL 239



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 64/183 (34%), Gaps = 22/183 (12%)

Query: 775 CVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMV 834
              Q+PL                      +L  G+N +VA   + GYN EDS+++++  +
Sbjct: 6   YYPQKPL----------ATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSI 55

Query: 835 SEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVN 889
              +F S+    +    +   L   E       +    +       +DE GI+  G  V+
Sbjct: 56  DRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVS 115

Query: 890 PGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHG 949
             D+++GK  P  +       +             RD S  + S  +G V  V +     
Sbjct: 116 GEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNAD 168

Query: 950 IDK 952
             K
Sbjct: 169 NVK 171


>gi|226445716|gb|ACO58383.1| RNA polymerase [Mycoplasma pullorum]
          Length = 166

 Score =  144 bits (362), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 78/166 (46%), Positives = 112/166 (67%), Gaps = 1/166 (0%)

Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
            +N L+ +++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  
Sbjct: 1   QINPLAEVSNKRRVTSLGPGGLNRDTAQFEVRDVHSTHYGRICPIETPEGPNIGLILNYA 60

Query: 588 SFARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVF 646
            +++VN  GF++TPY KV +G V  NDV YL+A EE     AQ++  +DE+    +E + 
Sbjct: 61  IYSKVNKMGFLQTPYYKVNNGVVDYNDVHYLTASEEIGHKFAQSSVHVDENNRIIDETLT 120

Query: 647 CRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
            R   + ++   E +DF++ S KQ+VS+AA  IPFLENDD+NR LM
Sbjct: 121 IRHNYQYLIARPEDVDFLEVSSKQMVSVAAGAIPFLENDDANRALM 166


>gi|77798214|gb|ABB03285.1| RNA polymerase beta subunit [Nocardia pseudovaccinii]
 gi|77798230|gb|ABB03293.1| RNA polymerase beta subunit [Nocardia vinacea]
          Length = 145

 Score =  144 bits (362), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+++NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHTSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|71727052|gb|AAZ39691.1| RNA polymerase II [Aschersonia placenta]
          Length = 246

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 79/262 (30%), Gaps = 21/262 (8%)

Query: 879  CGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGT 938
              +  +             +       +   +  + AI      +  D+ +   S +   
Sbjct: 6    DTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 65

Query: 939  VVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSG 998
            +    +F R   D+ ++      E  E               +       +  G      
Sbjct: 66   LF-RSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGE 124

Query: 999  PKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIE 1058
                 K+  +  +      R+   Q       ++     +      + +           
Sbjct: 125  DVIIGKTAPIDQENQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA---------- 174

Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
                        ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   
Sbjct: 175  ----------DNVKYVKVRVRTTKIPQIGDKFASRHGQKGTIGVTYRQEDMPFTREGVTP 224

Query: 1119 DIVLNPLGVPSRMNVGQIFETH 1140
            DI++NP  +PSRM +  + E  
Sbjct: 225  DIIINPHAIPSRMTIAHLIECL 246



 Score = 83.2 bits (204), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 67/185 (36%), Gaps = 15/185 (8%)

Query: 776 VNQRPLVKVGDEVRRNDIIADGPSTDL---GDLALGRNMLVAFMPWHGYNFEDSMLISER 832
            ++R              +A   S +     +L  G+N +VA   + GYN EDS+++++ 
Sbjct: 1   YSRRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQS 60

Query: 833 MVSEDVFTSIHIEEFEVMARDTKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAE 887
            +   +F S+    +    +   L   E       +    +       +DE GI+  G  
Sbjct: 61  SIDRGLFRSLFFRSYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVR 120

Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
           V+  D+++GK  P  +       +             RD S  + S  +G V  V +   
Sbjct: 121 VSGEDVIIGKTAPIDQENQDLGTRT-------SVHQRRDISTPLRSTENGIVDSVILTVN 173

Query: 948 HGIDK 952
               K
Sbjct: 174 ADNVK 178


>gi|293611936|gb|ADE48412.1| RNA polymerase beta chain [Zamia picta]
          Length = 189

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 132/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIM 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            VDA +I   +    +           L+ +QRSN NTC++Q+  V+ G+ V++  I+AD
Sbjct: 61  YVDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKLRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GTATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP +    L
Sbjct: 173 GPERITKEIPYLDAHLL 189


>gi|94537350|gb|ABF29777.1| RNA polymerase B subunit [Bacillus cereus biovar anthracis str. CI]
          Length = 225

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 77/175 (44%), Gaps = 16/175 (9%)

Query: 180 YACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIVY 238
           +   +IP++G W++ E D+KD+++VRIDR RK+PVT  L ALG  S+ EI          
Sbjct: 3   FTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEITELLGDNEYL 62

Query: 239 SQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGE-QVIESGKKLTSGLLKSLK-------- 289
           S   +      +   L+           +  GE   +E+ K L        K        
Sbjct: 63  SNTLEKDNTDSTEKALL------EIYERLRPGEPPTVENAKSLLVSRFFDPKRYDLANVG 116

Query: 290 EKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI 344
              +       + L    +AE +V+ ETGEI    G ++D ++L+ I     ++I
Sbjct: 117 RYKINKKLHIKNRLFNQRLAETLVDPETGEILAAEGTILDRRTLDRILPYLEKNI 171



 Score = 60.9 bits (146), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 47/83 (56%)

Query: 349 VDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDL 408
            + + +N Y+ NTL  D     + ALL+IY  +RPG+  T   A+S+    FFD  +YDL
Sbjct: 53  TELLGDNEYLSNTLEKDNTDSTEKALLEIYERLRPGEPPTVENAKSLLVSRFFDPKRYDL 112

Query: 409 STVGRVKMNMRLNLDTPDDVRHI 431
           + VGR K+N +L++      + +
Sbjct: 113 ANVGRYKINKKLHIKNRLFNQRL 135


>gi|22208413|emb|CAC87035.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
 gi|22208415|emb|CAC87036.1| RNA polymerase beta subunit [Mycobacterium tuberculosis]
          Length = 203

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 96/203 (47%), Positives = 138/203 (67%), Gaps = 14/203 (6%)

Query: 375 LDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDT--PDDVRHIR 432
           LDIYR +RPG+  T   A+++   LFF   +YDL+ VGR K+N +L L    P     + 
Sbjct: 1   LDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLT 60

Query: 433 KEDIIAIIKILVDLRNGKGTI------------DDIDNLGNRRVRSVGEMLKNQYRLGLL 480
           +ED++A I+ LV L  G+ T+            DDID+ GNRR+R+VGE+++NQ R+G+ 
Sbjct: 61  EEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMS 120

Query: 481 RMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRR 540
           RMER ++ER+++ D++++ PQ LIN +PVV+A+ EFF +SQ SQ     N LS +TH RR
Sbjct: 121 RMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQPSQFMGQNNPLSGLTHKRR 180

Query: 541 LSALGQGGVARARAGVEMRDVHP 563
           LSALG GG++R RAG+E+RDVHP
Sbjct: 181 LSALGPGGLSRERAGLEVRDVHP 203


>gi|50657993|gb|AAT79831.1| RNA polymerase beta subunit [Legionella pneumophila]
          Length = 139

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 83/139 (59%), Positives = 108/139 (77%)

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL+ +AR N YGFIETP RKV +G+VT++V YLSA+EE ++YIAQ+N  L
Sbjct: 1   PEGPNIGLINSLSVYARTNEYGFIETPCRKVVNGRVTDEVEYLSAIEEVDQYIAQSNVEL 60

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           D  G+   +LV CR   E  L   +KI+++D SPKQ+VS+AASLIPFLE+DD++R LMG 
Sbjct: 61  DAQGNILADLVPCRHQNEFSLTTPDKINYMDVSPKQIVSVAASLIPFLEHDDAHRALMGS 120

Query: 695 NMQRQAVPLLKAEAPFVGT 713
           NMQRQAVP L++E P VGT
Sbjct: 121 NMQRQAVPTLRSEKPLVGT 139


>gi|293611908|gb|ADE48398.1| RNA polymerase beta chain [Macrozamia lucida]
          Length = 183

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 89/190 (46%), Positives = 129/190 (67%), Gaps = 8/190 (4%)

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +D
Sbjct: 1   PFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRITYID 60

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG +
Sbjct: 61  AGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKPRVRRGEYVKKGQILADGAA 112

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  G E
Sbjct: 113 TLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGLE 172

Query: 860 EITRDIPNVS 869
            IT++IP++ 
Sbjct: 173 RITKEIPHLD 182


>gi|50657991|gb|AAT79830.1| RNA polymerase beta subunit [Legionella pneumophila]
          Length = 139

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 85/139 (61%), Positives = 109/139 (78%)

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL+ +AR N YGFIETP RKV +G+VT++V YLSA+EE ++YIAQ+N  L
Sbjct: 1   PEGPNIGLINSLSVYARTNEYGFIETPCRKVVNGRVTDEVEYLSAIEEVDQYIAQSNVEL 60

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DE G+   +LV CR   E  L   +KI+++D SPKQ+VS+AASLIPFLE+DD+NR LMG 
Sbjct: 61  DEQGNILADLVPCRHQNEFSLTTPDKINYMDVSPKQIVSVAASLIPFLEHDDANRALMGS 120

Query: 695 NMQRQAVPLLKAEAPFVGT 713
           NMQRQAVP L++E P VGT
Sbjct: 121 NMQRQAVPTLRSEKPLVGT 139


>gi|226427467|gb|ACO54927.1| RNA polymerase [Mycoplasma primatum]
          Length = 165

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 80/165 (48%), Positives = 113/165 (68%), Gaps = 1/165 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I++ RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +L ++
Sbjct: 1   NPLAEISNERRITSLGPGGLNRDTAQFEVRDVHATHYGRICPIETPEGPNIGLILNLATY 60

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A VN YGF++TPY +V +  V  NDVVYL+A +E    IAQ+  ++DE+    ++ +  R
Sbjct: 61  ANVNEYGFLQTPYFRVNNAVVDYNDVVYLTAADEFGFNIAQSTITVDENNRIVDDTLTIR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
                I+     +DFI+ + +Q+VS+AA  IPFLENDD+NR LMG
Sbjct: 121 KNYSYIIGKASDVDFIEVASRQMVSVAAGCIPFLENDDANRALMG 165


>gi|327133541|gb|AEA29775.1| RNA polymerase subunit B [Acinetobacter sp. 18N3]
          Length = 125

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 48/125 (38%), Positives = 72/125 (57%)

Query: 994  NAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRF 1053
               +G    K+   L+ D +S+       +    DE +   +  ++   +   + ++++F
Sbjct: 1    QMSNGGGTTKRGDQLTEDKLSQLEMVDLLEIPPSDEGIAERLTQIQTYLKEKSAEIDEKF 60

Query: 1054 KNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLK 1113
              K  K   GD++  GVL+VVKV++A+KR IQ GDKMAGRHGNKG+VS ILP EDMP   
Sbjct: 61   AEKKRKFSTGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDA 120

Query: 1114 DGTPV 1118
            +G PV
Sbjct: 121  NGVPV 125


>gi|197941910|gb|ACH78560.1| RNA polymerase subunit [Juniperus virginiana]
 gi|197941912|gb|ACH78561.1| RNA polymerase subunit [Juniperus virginiana]
 gi|197941914|gb|ACH78562.1| RNA polymerase subunit [Juniperus virginiana]
 gi|197941916|gb|ACH78563.1| RNA polymerase subunit [Juniperus virginiana]
          Length = 188

 Score =  143 bits (361), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 87/194 (44%), Positives = 131/194 (67%), Gaps = 6/194 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +PL++ E   VGTG+E  VA  SG+  +AK+ G ++ +D   I+I S     +  T  + 
Sbjct: 1   LPLVQPEKCIVGTGLEGQVALDSGSVAIAKQGGKIKYIDGENIIITSSIARDNIETELIL 60

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                 +QRSN +TC++Q+P V+ G+ V+R  IIAD  +T  G+L+LG+N+LVA+MPW G
Sbjct: 61  ------YQRSNSDTCMHQKPRVRQGEYVKRGQIIADSAATAGGELSLGKNILVAYMPWEG 114

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED+FTS  I  +++ A  T  GPE ITR+IP+++   L+++DE G
Sbjct: 115 YNFEDAILISERLVYEDIFTSFQIVRYKIGAYFTDQGPEVITREIPHLNAYLLRHLDENG 174

Query: 881 IICVGAEVNPGDIL 894
           I+ +G+ V  GDIL
Sbjct: 175 IVMIGSWVETGDIL 188


>gi|198279369|emb|CAP04719.1| RNA polymerase beta subunit [Pinus longaeva]
          Length = 187

 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 80/194 (41%), Positives = 121/194 (62%), Gaps = 8/194 (4%)

Query: 699 QAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSG 758
           QAVPL + E    GTG+E   A  SG+  +A + G +E +DA+                 
Sbjct: 1   QAVPLFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSINGD 52

Query: 759 VDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPW 818
                 + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+MPW
Sbjct: 53  TVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAYMPW 112

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDE 878
            GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L+++DE
Sbjct: 113 EGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRHLDE 172

Query: 879 CGIICVGAEVNPGD 892
            G++ +G+ +  GD
Sbjct: 173 NGLVMLGSWIETGD 186


>gi|195424652|gb|ACF96944.1| RpoB [Arcobacter nitrofigilis]
          Length = 162

 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 88/162 (54%), Positives = 122/162 (75%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N LS +TH  RLSALG+GG+ + RAG E+RDVH THYGRICP ET EG NIGL+++L++F
Sbjct: 1   NPLSEVTHKXRLSALGEGGLVKERAGFEVRDVHATHYGRICPVETPEGQNIGLINTLSTF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRC 649
           A+VN  GFIE PY+KV DG V+N+++Y++A +EE   IA  ++ +D++G   E L+  R 
Sbjct: 61  AKVNELGFIEAPYKKVNDGIVSNEIIYVTATQEEGLLIAPGSTKVDDNGKIVEPLIEARQ 120

Query: 650 AGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVL 691
            GE ++V R K++ ID S + V+ +AASLIPFLE+DD+NR L
Sbjct: 121 DGEILIVERGKVNLIDISSQMVMGVAASLIPFLEHDDANRAL 162


>gi|122936034|gb|ABM68536.1| RNA polymerase II subunit 2 [Juncigena adarca]
          Length = 615

 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 92/609 (15%), Positives = 177/609 (29%), Gaps = 65/609 (10%)

Query: 518  CSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEG 577
             ++ +SQ+       S ++H RR +      V R     + R +H TH+G +CPAET EG
Sbjct: 64   STAGVSQVLNRYTFASTLSHLRRTNT----PVGRDGKLAKPRQLHNTHWGLVCPAETPEG 119

Query: 578  HNIGLVSSLTSFARVNAYGFIETP--YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLD 635
               GLV +L+    V+          +      +V  +   L        ++      + 
Sbjct: 120  QACGLVKNLSLMCYVSMGSPASPTVTFMISTGMEVLEEYEPLRYPNATKVFVNGVWVGVH 179

Query: 636  EDGSFTEELVFCRCAGEEILVPREKI-DFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
             D S   + +        +      + D  +   K        + P       +    G 
Sbjct: 180  HDPSHLAKYMQGLRTKGLVSYEASLVRDIREREFKIFSDPGRVMRPVFAVQQEDDYEAG- 238

Query: 695  NMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDP 754
               R    LL  +        E     + G         +  Q    R V+  ++ + + 
Sbjct: 239  ---RSKGQLLLTKDMIRRLQYEHDALDADGKLPEDDPDFLGWQGLVSRGVVEYLDAEEEE 295

Query: 755  STSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVA 814
            +         ++                   +  +R+         D  +LA G N  + 
Sbjct: 296  TAMICMTPEDLE-------------------EYRKRSLNPGSAAEKDDDELADGPNARLK 336

Query: 815  FMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLK 874
                   +      I   M+     + I   +    A   +     +T     +      
Sbjct: 337  LALKDTTHMYTHCEIHPSMILGICASIIPFPDHNQSAMGKQAMGFFLTNYSRRM------ 390

Query: 875  NIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSG 934
                  +  +         +   +       +   +  + AI      +  D+ +   S 
Sbjct: 391  ----DTMANILYYPQKPLAITRSMEFLKFRELPAGQNAIVAISCYSGYNQEDSVIMNQSS 446

Query: 935  VSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLME---ILC 991
            +   +     F  +     +    V   ++E   +      + L    Y +L +   +  
Sbjct: 447  IDRGLFRSLFFRCYT----DFEKQVGINKVESFEKPFKSNTLRLKHGTYDKLDDDGIVAP 502

Query: 992  GQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILED 1051
            G           K+  ++    +        QF  +D      + S +     S  +   
Sbjct: 503  GVRVSGEDIIIGKTAPINPGADNREMGLLTNQFQKRDASTP--LRSTENGIVDSVVL--- 557

Query: 1052 RFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPF 1111
                          +    L+ VKV V   +  Q GDK A RHG KG +      EDMPF
Sbjct: 558  -------------TVNHENLKYVKVRVRTTKIPQIGDKFASRHGQKGTIGLTYRQEDMPF 604

Query: 1112 LKDGTPVDI 1120
             ++G   DI
Sbjct: 605  TREGITPDI 613



 Score = 50.1 bits (118), Expect = 0.003,   Method: Composition-based stats.
 Identities = 48/390 (12%), Positives = 96/390 (24%), Gaps = 46/390 (11%)

Query: 391 VAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDV--RHIRKEDIIAIIKILVDLRN 448
           +  S+    + D  K   ST G  ++  R    +      R          +     L N
Sbjct: 46  LKYSLATGNWGDQKKAMSSTAGVSQVLNRYTFASTLSHLRRTNTPVGRDGKLAKPRQLHN 105

Query: 449 GKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKP 508
               +         +   + + L     + +          + S  ++ +   + +    
Sbjct: 106 THWGLVCPAETPEGQACGLVKNLSLMCYVSMGSPASPTVTFMISTGMEVLEEYEPLRYPN 165

Query: 509 VVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGR 568
                        +    +  +    +   R    +                +       
Sbjct: 166 ATKVF---VNGVWVGVHHDPSHLAKYMQGLRTKGLVSYEASLVRDIREREFKIFSDPGRV 222

Query: 569 ICPA-------ETSEGHNIGLVSSLTSFAR--------VNAYGFI---ETPYRKVCDGKV 610
           + P        +   G + G +       R        ++A G +   +  +        
Sbjct: 223 MRPVFAVQQEDDYEAGRSKGQLLLTKDMIRRLQYEHDALDADGKLPEDDPDFLGWQGLVS 282

Query: 611 TNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVP------------- 657
              V YL A EEE   I      L+E    +          ++ L               
Sbjct: 283 RGVVEYLDAEEEETAMICMTPEDLEEYRKRSLNPGSAAEKDDDELADGPNARLKLALKDT 342

Query: 658 REKIDFIDASPKQVVSIAASLIPFLENDDS---------NRVLMGCNMQRQAVPLLKAEA 708
                  +  P  ++ I AS+IPF +++ S                 M   A  L   + 
Sbjct: 343 THMYTHCEIHPSMILGICASIIPFPDHNQSAMGKQAMGFFLTNYSRRMDTMANILYYPQK 402

Query: 709 PFVGT-GMESVVAKSSGAAIVAKRAGIVEQ 737
           P   T  ME +  +   A   A  A     
Sbjct: 403 PLAITRSMEFLKFRELPAGQNAIVAISCYS 432


>gi|294462738|gb|ADE76913.1| unknown [Picea sitchensis]
          Length = 135

 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 38/131 (29%), Positives = 61/131 (46%), Gaps = 18/131 (13%)

Query: 1262 MVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD- 1320
            MV DK+++R  G   ++T+QP  G+S  GG R GEME  C+ A+GAA+ L+E L  +SD 
Sbjct: 1    MVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDA 60

Query: 1321 ---DVVGRTRVYESIV---------AG----NDTFETGTPESFNVLVKEMQALGLSIDLE 1364
                V  R     +I           G     D  +   P +  +L +E+ A+ ++  + 
Sbjct: 61   YRVHVCERCG-LIAIANLKKNSFDCRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMF 119

Query: 1365 NSRTKNSAKME 1375
                K     +
Sbjct: 120  TKEVKELKDQK 130


>gi|218507180|ref|ZP_03505058.1| DNA-directed RNA polymerase subunit beta [Rhizobium etli Brasil 5]
          Length = 129

 Score =  143 bits (360), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 112/129 (86%), Positives = 123/129 (95%)

Query: 790 RNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEV 849
           R DI+ADGPSTDLGDLALGRN LVAFMPW+GYN+EDS+L+SER+V++DVFTSIHIEEFEV
Sbjct: 1   RGDILADGPSTDLGDLALGRNALVAFMPWNGYNYEDSILLSERIVADDVFTSIHIEEFEV 60

Query: 850 MARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPE 909
           MARDTKLGPEEITRDIPNVSEE LKN+DE GI+ +GAEV PGDILVGKITPKGESPMTPE
Sbjct: 61  MARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVQPGDILVGKITPKGESPMTPE 120

Query: 910 EKLLRAIFG 918
           EKLLRAIFG
Sbjct: 121 EKLLRAIFG 129


>gi|224077110|ref|XP_002305136.1| predicted protein [Populus trichocarpa]
 gi|222848100|gb|EEE85647.1| predicted protein [Populus trichocarpa]
          Length = 690

 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 86/687 (12%), Positives = 198/687 (28%), Gaps = 113/687 (16%)

Query: 29  LIEVQKASYDHFLMM------------NIAPDERPNEGLQAAFKSVFPITAFSGA-AMLE 75
           L+  Q  S+D F+               I P+ + N G Q         + F+     + 
Sbjct: 30  LVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGHQ---------SDFAETIYKIS 80

Query: 76  FVSYEFDPPKFDVDD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGA-KSIKD 124
           F       P     D             R+LTY+ PL + +   V             +D
Sbjct: 81  FGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQD 140

Query: 125 IKEQSIYMGD--------LPLMTKD------------------------GTFVIKGIQRI 152
             +  +++G         +P+M +                         G F+I G +++
Sbjct: 141 FTK--VFIGKASIMNYLFVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKV 198

Query: 153 VVSQLHRSPG-IHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRI-DR-- 208
           +++Q   S   ++      +     K  Y   +        + +      + VR+  R  
Sbjct: 199 LIAQEKMSTNHVY----VFKKRQPNKYAYVGEVR----SMAESQNRPPSTMFVRMLSRTS 250

Query: 209 -----------------RRKVPVTSFLMALGMDSE-EILSTFYPKIVYSQRGDFWCFPLS 250
                            R ++P+     ALG  ++ +IL         +Q  +     L 
Sbjct: 251 AKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFADTQMMELLRPSLE 310

Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
            A ++   +V+   +        +   K++     + L+++ +  +G+   C        
Sbjct: 311 EAFVIQNQQVALDYIGKRGATVGVTREKRIKYAK-EILQKEMLPHVGVGEYCETKKAYYF 369

Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDI-PILYVDSVNNNAYIRNTLVTDKNKD 369
             +      + + A     E   +   +  +    P+L          +   + +   K 
Sbjct: 370 GYIIH---RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRSYVQKC 426

Query: 370 RKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVR 429
             +      +        T  +  S+    +  ++           +N      T   +R
Sbjct: 427 VDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLR 486

Query: 430 HI-RKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKE 488
            +         +     L N +  +         +      ++KN   +  + +  +   
Sbjct: 487 RLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACG---LVKNLALMVYITVGSAAYP 543

Query: 489 RISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALG-QG 547
            +  ++       + I+   +  A   F     +    +    +  +   RR   +  + 
Sbjct: 544 ILEFLEEWGTENFEEISPAVIPQATKIFVNGGWVGIHRDPDMLVKTLRRLRRRVDVNTEV 603

Query: 548 GVARARAGVEMRDVHPTHYGRICPAETSEGHN--IGLVSSLTSFARVNAYGFIETPYRK- 604
           GV R     E+R ++  +     P    E     I          RV+   + +  ++  
Sbjct: 604 GVVRDIRLKELR-IYTDYGRCSRPLFIVEKQKLLIRKKDIHALQQRVSHLIYNDHLFKYE 662

Query: 605 --VCDGKVTNDVVYLSAMEEENRYIAQ 629
               D      + Y+   EEE   I+ 
Sbjct: 663 GGWHDLVSKGFIEYIDTEEEETTMISM 689



 Score = 83.6 bits (205), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 52/328 (15%), Positives = 109/328 (33%), Gaps = 25/328 (7%)

Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
            +       +    ++       ++A +   + +    +       +          KY 
Sbjct: 287 DILEHICYDFADTQMMELLRPSLEEAFVIQNQQVA---LDYIGKRGATVGVTREKRIKYA 343

Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
              + +  +      +  +  +         II  L+    G+   DD D+ GN+R+   
Sbjct: 344 KEILQKEMLPHVGVGEYCETKK---AYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 400

Query: 468 GEMLKNQYRLGLLRMERSIKERISSV--DIDSVMPQDLINAKPVVSAVCEFFCSSQ---- 521
           G +L   +R+   ++ R ++  +     +   V  Q  I AK + S +     +      
Sbjct: 401 GPLLGGLFRMLFRKLTRDVRSYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 460

Query: 522 --------LSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAE 573
                   +SQ+   +   S ++H RRL++     + R     + R +H + +G +CPAE
Sbjct: 461 NAAGTRAGVSQVLNRLTYASTLSHLRRLNS----PIGREGKLAKPRQLHNSQWGMMCPAE 516

Query: 574 TSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSS 633
           T EG   GLV +L     +   G    P  +  +   T +   +S            N  
Sbjct: 517 TPEGQACGLVKNLALMVYIT-VGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGG 575

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKI 661
                   + LV         +    ++
Sbjct: 576 WVGIHRDPDMLVKTLRRLRRRVDVNTEV 603


>gi|50657969|gb|AAT79819.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657971|gb|AAT79820.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657973|gb|AAT79821.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657975|gb|AAT79822.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657977|gb|AAT79823.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657979|gb|AAT79824.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657985|gb|AAT79827.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657987|gb|AAT79828.1| RNA polymerase beta subunit [Legionella pneumophila]
 gi|50657995|gb|AAT79832.1| RNA polymerase beta subunit [Legionella pneumophila]
          Length = 139

 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 84/139 (60%), Positives = 108/139 (77%)

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL+ +AR N YGFIETP RKV +G+VT++V YLSA+EE ++YIAQ+N  L
Sbjct: 1   PEGPNIGLINSLSVYARTNEYGFIETPCRKVVNGRVTDEVEYLSAIEEVDQYIAQSNVEL 60

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           D  G+   +LV CR   E  L   +KI+++D SPKQ+VS+AASLIPFLE+DD+NR LMG 
Sbjct: 61  DAQGNILADLVPCRHQNEFSLTTPDKINYMDVSPKQIVSVAASLIPFLEHDDANRALMGS 120

Query: 695 NMQRQAVPLLKAEAPFVGT 713
           NMQRQAVP L++E P VGT
Sbjct: 121 NMQRQAVPTLRSEKPLVGT 139


>gi|226445713|gb|ACO58381.1| RNA polymerase [Mycoplasma opalescens]
          Length = 165

 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 77/164 (46%), Positives = 112/164 (68%), Gaps = 1/164 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N L+ I + RR+++LG GG+ R  A  E+RDVH THYGRICP ET EG NIGL+ +  ++
Sbjct: 2   NPLAEIANKRRITSLGPGGLNRETAQFEVRDVHATHYGRICPIETPEGPNIGLILNYATY 61

Query: 590 ARVNAYGFIETPYRKVCDGKVT-NDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR 648
           A+VN +GF++TPY +V +G V  ++VVYL+A +E    IAQ+ + +DE+    +E +  R
Sbjct: 62  AKVNDHGFLQTPYYRVENGIVDYSEVVYLTAADEIGYRIAQSIAHIDENNKIVDERLTIR 121

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLM 692
                ++    +IDFI+ +  Q+VS+AA  IPFLENDD+NR LM
Sbjct: 122 YNYNYVVGTPAEIDFIEVASNQMVSVAAGCIPFLENDDANRALM 165


>gi|77798222|gb|ABB03289.1| RNA polymerase beta subunit [Nocardia transvalensis]
          Length = 145

 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 87/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRR+R+VGE+ +NQ R+GL RMER ++ER+++ D++++ PQ LIN +PVV+A+ EF
Sbjct: 1   DHFGNRRLRTVGELDQNQIRVGLSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVHP+HYGR+CP ET E
Sbjct: 61  FGTSQLSQFLDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ +L+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGTLSVYARVNPFGFIETP 145


>gi|198279375|emb|CAP04722.1| RNA polymerase beta subunit [Pinus balfouriana]
          Length = 185

 Score =  143 bits (360), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 80/193 (41%), Positives = 121/193 (62%), Gaps = 8/193 (4%)

Query: 696 MQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPS 755
           MQRQAVP  + E    GTG+E   A  SG+  +A + G +E +DA+              
Sbjct: 1   MQRQAVPXFRPEKCIAGTGLEGQAALDSGSVAIATQEGRIEYIDAV--------NITSSI 52

Query: 756 TSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAF 815
                    + +QRSN NTC +Q+P V+ G+ V++  I+ADG +T  G+L+LG+N+LVA+
Sbjct: 53  NGDTVRTESVIYQRSNTNTCTHQKPQVRQGECVKKGQILADGATTVGGELSLGKNVLVAY 112

Query: 816 MPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKN 875
           MPW GYNFED++LISER+V ED++TS HI  + +    T  GPE ITR+IP++    L++
Sbjct: 113 MPWEGYNFEDAILISERLVYEDIYTSFHIVRYRIEICMTSQGPERITREIPHLDAHSLRH 172

Query: 876 IDECGIICVGAEV 888
           +DE G++ +G+ +
Sbjct: 173 LDENGLVMLGSWI 185


>gi|77798238|gb|ABB03297.1| RNA polymerase beta subunit [Nocardia tenerifensis]
          Length = 145

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 88/145 (60%), Positives = 119/145 (82%)

Query: 457 DNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEF 516
           D+ GNRRVR+VGE+++NQ R+GL RMER ++ER+++ DI+++ PQ LIN +PVV+++ EF
Sbjct: 1   DHFGNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDIEAITPQTLINIRPVVASIKEF 60

Query: 517 FCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSE 576
           F +SQLSQ  +  N LS +TH RRLSALG GG++R RAG+E+RDVH +HYGR+CP ET E
Sbjct: 61  FGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHFSHYGRMCPIETPE 120

Query: 577 GHNIGLVSSLTSFARVNAYGFIETP 601
           G NIGL+ SL+ +ARVN +GFIETP
Sbjct: 121 GPNIGLIGSLSVYARVNPFGFIETP 145


>gi|225698409|gb|ACO07322.1| RpoB [Pasteurellaceae bacterium Kleiz1967]
          Length = 150

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 86/149 (57%), Positives = 110/149 (73%), Gaps = 1/149 (0%)

Query: 530 NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSF 589
           N+L+ +TH RR+SALG GGV R RA  E+RDVH THYGRICP ET EG NIGL+++L +F
Sbjct: 1   NALAEVTHKRRISALGAGGVTRERADFEIRDVHVTHYGRICPIETPEGQNIGLINTLATF 60

Query: 590 ARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEE-NRYIAQANSSLDEDGSFTEELVFCR 648
           AR N YGF+ETPYRKV +G VT +  YLS +EE  +  IAQAN+ L+ D SF  ELV  R
Sbjct: 61  ARTNKYGFLETPYRKVVNGIVTEEFEYLSPLEENTDVVIAQANAKLNPDNSFATELVPAR 120

Query: 649 CAGEEILVPREKIDFIDASPKQVVSIAAS 677
           C GE  + P E+I ++D S +Q+VS+AA+
Sbjct: 121 CGGETGMFPPERISYMDVSAQQIVSVAAA 149


>gi|56694306|gb|AAW22893.1| RNA polymerase II second largest subunit [Dryopteris filix-mas]
          Length = 459

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/321 (17%), Positives = 101/321 (31%), Gaps = 26/321 (8%)

Query: 817  PWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNI 876
                 +      I   M+     + I   +     R+T             V+   L+  
Sbjct: 165  EEAYSDTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRM- 223

Query: 877  DECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVS 936
                +  V        +    +       +      + AI      +  D+ +   S + 
Sbjct: 224  --DTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSID 281

Query: 937  GTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAV 996
                   IF R   D+ ++  S+ +E+ E   R+          +          G    
Sbjct: 282  RGFF-RSIFYRSYRDEEKKQGSLVKEEFERPIRENTQGMRHGSYDKLDDDGLAPPGTRVS 340

Query: 997  SGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNK 1056
                   K++ +                  QD+   +     K    T     E    ++
Sbjct: 341  GEDVIIGKTSPI-----------------PQDDTGTQAQRYSKRDQSTCLRHSESGMVDQ 383

Query: 1057 IEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGT 1116
            +      D +     R VK+ V   R  Q GDK + RHG KG V      EDMP+ ++G 
Sbjct: 384  VLLTTNADGL-----RFVKIRVRSIRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTQEGI 438

Query: 1117 PVDIVLNPLGVPSRMNVGQIF 1137
              DI+++P  +PSRM +GQ+ 
Sbjct: 439  TPDIIVSPHAIPSRMTIGQLI 459



 Score = 58.2 bits (139), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 50/298 (16%), Positives = 91/298 (30%), Gaps = 36/298 (12%)

Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL-SALGQGGVARA 552
           +       + I+   ++     F     +    +    +  +   RR  +   + GV R 
Sbjct: 22  EEWGTENFEEISPTVILQVTKIFVNGCWVGFHTQPELLVQTLRQLRRHDNMNTEVGVVRD 81

Query: 553 RAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTN 612
               E+R ++  +     P    E   + L+      A           Y  V  G    
Sbjct: 82  IRLKELR-LYTDYGRCSRPLFIVEKQRL-LIKKTDIRALQQKESTEPGWYELVTKGF--- 136

Query: 613 DVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVV 672
            + Y+   EEE   I+             ++LV  R   E      +     +  P  ++
Sbjct: 137 -IEYVDTEEEETTMISM----------TIQDLVNARLHPE--EAYSDTYTHCEIHPSMIL 183

Query: 673 SIAASLIPFLENDDSNRVLMGCNMQRQAVP----------------LLKAEAPFVGT-GM 715
            + AS+IPF +++ S R      M +QA+                 L   + P V T  M
Sbjct: 184 GVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAM 243

Query: 716 ESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQN 773
           E +  +   A I A  A            +   +  +D        YR  + +   Q 
Sbjct: 244 EHLHFRQLPAGINAVVAIACYSGYNQEDSVIMNQSSIDRGFFRSIFYRSYRDEEKKQG 301


>gi|70938731|ref|XP_740002.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56517408|emb|CAH79249.1| hypothetical protein PC000182.03.0 [Plasmodium chabaudi chabaudi]
          Length = 203

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 38/114 (33%), Positives = 55/114 (48%)

Query: 1207 STPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHMVSDK 1266
            +T +      +    +L     D  G  +LY G+ G P    +  G IY  +L HM  DK
Sbjct: 5    ATEISYDEKIDFFAKLLLNKGYDYYGTELLYSGIYGVPLQAHIFFGVIYYQRLRHMAYDK 64

Query: 1267 VYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSD 1320
               R TG    +T QPL GK   GG RLGEME   + ++G ++++ E   + SD
Sbjct: 65   AQVRRTGPVCHLTHQPLKGKKRHGGIRLGEMERDGLISHGCSFIINERFLMNSD 118


>gi|197941902|gb|ACH78556.1| RNA polymerase subunit [Juniperus communis]
 gi|197941906|gb|ACH78558.1| RNA polymerase subunit [Juniperus communis]
 gi|197941908|gb|ACH78559.1| RNA polymerase subunit [Juniperus communis]
          Length = 188

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 86/194 (44%), Positives = 130/194 (67%), Gaps = 6/194 (3%)

Query: 701 VPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVD 760
           +PL++ E   VGTG+E  VA  SG+  +AK+ G ++ +D   I+I S     +  T  + 
Sbjct: 1   LPLVQPEKCIVGTGLEGQVALDSGSVAIAKQGGKIKYIDGENIIITSSVARDNIETELIL 60

Query: 761 IYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHG 820
                 +QRSN +TC++Q+P V+ G+ V+R  IIAD  +T  G+L+LG+N+LVA+MPW G
Sbjct: 61  ------YQRSNSDTCMHQKPRVRQGEYVKRGQIIADSAATAGGELSLGKNILVAYMPWEG 114

Query: 821 YNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECG 880
           YNFED++LISER+V ED+FTS  I  +++    T  GPE ITR+IP+++   L+++DE G
Sbjct: 115 YNFEDAILISERLVYEDIFTSFQIVRYKIGVYFTDQGPEVITREIPHLNAYLLRHLDENG 174

Query: 881 IICVGAEVNPGDIL 894
           I+ +G+ V  GDIL
Sbjct: 175 IVMIGSWVETGDIL 188


>gi|48473888|dbj|BAD22702.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473894|dbj|BAD22706.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473897|dbj|BAD22708.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473906|dbj|BAD22714.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473912|dbj|BAD22718.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473915|dbj|BAD22720.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473924|dbj|BAD22726.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
 gi|48473927|dbj|BAD22728.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
          Length = 77

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 38/77 (49%), Positives = 51/77 (66%)

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA  VL+EMLT KSDDV GRT+ Y +I  G +   +G PE+F VL KE++
Sbjct: 1    EMEVWALEAYGATNVLKEMLTTKSDDVEGRTKAYRAIANGENVPNSGVPETFFVLTKELK 60

Query: 1356 ALGLSIDLENSRTKNSA 1372
            AL L +++      N  
Sbjct: 61   ALALDVEIFGEVENNEQ 77


>gi|293611900|gb|ADE48394.1| RNA polymerase beta chain [Dioon merolae]
          Length = 189

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 93/197 (47%), Positives = 132/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIT 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I                    L+ +QRSN NTC++Q+P V+ G+ V++  I+A+
Sbjct: 61  HIDAGKITSLV--------GGDTVGTELVIYQRSNNNTCMHQKPRVRQGEYVKKGQILAN 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GAATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP++    L
Sbjct: 173 GPERITKEIPHLDAHLL 189


>gi|118152119|gb|ABK63802.1| RNA polymerase II second largest subunit [Cheilymenia stercorea]
          Length = 521

 Score =  142 bits (359), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 93/592 (15%), Positives = 169/592 (28%), Gaps = 79/592 (13%)

Query: 530  NSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTS- 588
               S ++H RR +      + R     + R +H TH+G +CPAET EG   GLV +L   
Sbjct: 1    TFASTLSHLRRTNT----PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALM 56

Query: 589  -FARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
             +  V   G     +    + +   +     +      ++      +  D      LV  
Sbjct: 57   SYITVGTPGHPLVNFMAEQNMEFLEEYEPQRSPNATKIFLNGVWIGIHRDPLHLVRLVQE 116

Query: 648  RCAGEEILVPREKI-DFIDASPKQVVSIAASLIPF--LENDDSNRVLMGCNMQRQAVPLL 704
                  I      I D  D   K          P   ++ND ++       + ++ V  L
Sbjct: 117  LRRRGSISHEVSVIRDIRDREXKIFTDAGRVCRPLFVIDNDPTHERRGQLVLTKEHVMQL 176

Query: 705  KAEAPFVGTG-MESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYR 763
            + +     T           GA          E VDA       +    +       + +
Sbjct: 177  EEDHELQETERFGWKGLLECGAV---------EYVDAEEEETIMIVMTPEDLEVSRQVQQ 227

Query: 764  LMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNF 823
              +           + P+ K      +       PS  LG       +  + +P+  +N 
Sbjct: 228  GYELAEETDPNKRVKTPINK---NTNQYTHCEIHPSMILG-------ICASIIPFPDHNQ 277

Query: 824  EDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIIC 883
                     M  + +   + +  F                                 +  
Sbjct: 278  SPRNTYQSAMGKQAMG--VFLTNFAERM---------------------------DTMAN 308

Query: 884  VGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVR 943
            +             +       +   +  +  I      +  D+ +   S +   +    
Sbjct: 309  ILYYPQKPLATTRSMEYLKFRELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLF-RS 367

Query: 944  IFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFK 1003
            +F R  +D+ +R      E+ E   R    +      +       +  G           
Sbjct: 368  LFYRAYMDQEKRIGMQVVEEFEKPTRGSTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIG 427

Query: 1004 KSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWG 1063
            K+  +++D                DE  QR     K    T     E+   +++      
Sbjct: 428  KTAPITAD---------------ADEMGQRQKFHTKRDVSTPLRSTENGIVDQVMLTTNA 472

Query: 1064 DDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDG 1115
            D +     + VKV +   +  Q GDK A RHG KG +      EDMPF   G
Sbjct: 473  DGL-----KFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRSEDMPFTSRG 519



 Score = 79.7 bits (195), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 68/532 (12%), Positives = 143/532 (26%), Gaps = 99/532 (18%)

Query: 447 RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINA 506
           R+GK       +  +  +    E  + Q    +  +       + +     V      N 
Sbjct: 18  RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYITVGTPGHPLVNFMAEQNM 77

Query: 507 KPV--------VSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEM 558
           + +         +A   F     +    + ++ +  +   RR  ++    V+  R   + 
Sbjct: 78  EFLEEYEPQRSPNATKIFLNGVWIGIHRDPLHLVRLVQELRRRGSI-SHEVSVIRDIRDR 136

Query: 559 RDVHPTHYGRIC-------PAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVT 611
                T  GR+C          T E     +++          +   ET           
Sbjct: 137 EXKIFTDAGRVCRPLFVIDNDPTHERRGQLVLTKEHVMQLEEDHELQETERFGWKGLLEC 196

Query: 612 NDVVYLSAMEEENRYIAQ------ANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFID 665
             V Y+ A EEE   I         +  + +     EE    +     I     +    +
Sbjct: 197 GAVEYVDAEEEETIMIVMTPEDLEVSRQVQQGYELAEETDPNKRVKTPINKNTNQYTHCE 256

Query: 666 ASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGA 725
             P  ++ I AS+IPF +++ S R      M +QA+ +                      
Sbjct: 257 IHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFA---------------- 300

Query: 726 AIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVG 785
                                    +   + + +  Y       +     +  R      
Sbjct: 301 -------------------------ERMDTMANILYYPQKPLATTRSMEYLKFR------ 329

Query: 786 DEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIE 845
                   +  G +  +G +          +  +  + +  +  S           +   
Sbjct: 330 -------ELPAGQNAIVGIMCYSGYNQEDSVIMNQSSIDRGLFRS-----------LFYR 371

Query: 846 EFEVMARDTKLGPEEITRD-----IPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITP 900
            +    +   +   E            +       +DE G++  G  V+  DI++GK  P
Sbjct: 372 AYMDQEKRIGMQVVEEFEKPTRGSTLKLKHGTYDKLDEDGLVAPGVRVSGEDIIIGKTAP 431

Query: 901 KGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
                    ++       +K    RD S  + S  +G V  V +       K
Sbjct: 432 ITADADEMGQR-------QKFHTKRDVSTPLRSTENGIVDQVMLTTNADGLK 476


>gi|293611916|gb|ADE48402.1| RNA polymerase beta chain [Encephalartos whitelockii]
          Length = 185

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 90/193 (46%), Positives = 130/193 (67%), Gaps = 8/193 (4%)

Query: 681 FLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDA 740
           FLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  +DA
Sbjct: 1   FLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRITYIDA 60

Query: 741 IRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPST 800
            +I   +    +           L+ +QRSN NTC++Q+P V+ G+ V++  I+ADG +T
Sbjct: 61  GKITSLADGDTVGT--------ELVIYQRSNSNTCMHQKPRVRRGEYVKKGQILADGAAT 112

Query: 801 DLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEE 860
             G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  GPE 
Sbjct: 113 LGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGPER 172

Query: 861 ITRDIPNVSEEGL 873
           IT++IP++    L
Sbjct: 173 ITKEIPHLDAHLL 185


>gi|222427591|dbj|BAH20756.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
          Length = 142

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 83/141 (58%), Positives = 104/141 (73%), Gaps = 1/141 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R  
Sbjct: 61  RTNDYGFLETPYRKVVDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGE 120

Query: 650 AGEEILVPREKIDFIDASPKQ 670
            GE  L   E I ++D S +Q
Sbjct: 121 RGESGLYKPEDIHYMDVSTQQ 141


>gi|48473891|dbj|BAD22704.1| DNA-directed RNA polymerase beta subunit [Arcobacter butzleri]
          Length = 77

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 38/77 (49%), Positives = 51/77 (66%)

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA  VL+EMLT KSDDV GRT+ Y +I  G +   +G PE+F VL KE++
Sbjct: 1    EMEVWALEAYGATNVLKEMLTTKSDDVDGRTKAYRAIANGENVPSSGVPETFFVLTKELK 60

Query: 1356 ALGLSIDLENSRTKNSA 1372
            AL L +++      N  
Sbjct: 61   ALALDVEIFEEVENNEQ 77


>gi|283806270|dbj|BAI66372.1| RNA polymerase second largest subunit [Kalmusia scabrispora]
          Length = 269

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 88/257 (34%), Gaps = 26/257 (10%)

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   +    +
Sbjct: 2    AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRMD 57

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + +    Y +L +   +  G           K+  + +D                 E  
Sbjct: 58   TMRMKGGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPIPNDE--------------NKEMG 103

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q+     K    T     E+   +++             LR VKV     +  Q GDK A
Sbjct: 104  QKLANHTKRDVSTPLRSTENGLVDQVLF-----TTNTEGLRFVKVRTRTTKVPQIGDKFA 158

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF +DG  VD+V++P  + SRM +    E  L        ++
Sbjct: 159  SRHGQKGTIGITYRQEDMPFTRDGLGVDLVVDPHAIASRMTIAHEVECLLSKVGAINAQE 218

Query: 1152 IKSLINDYKANGDISPL 1168
              +          I  L
Sbjct: 219  GDATPFCGVTVHQICDL 235



 Score = 72.0 bits (175), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/133 (19%), Positives = 52/133 (39%), Gaps = 8/133 (6%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D   
Sbjct: 1   VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRMDTMR 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ GI+  G  V+  DI++GK  P          ++ + +      DV   
Sbjct: 61  MKGGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPIPNDENK---EMGQKLANHTKRDVSTP 117

Query: 928 SLRVPSGVSGTVV 940
                +G+   V+
Sbjct: 118 LRSTENGLVDQVL 130


>gi|307111255|gb|EFN59490.1| hypothetical protein CHLNCDRAFT_19065 [Chlorella variabilis]
          Length = 92

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 36/79 (45%), Positives = 51/79 (64%)

Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
            +  G+TGEPF   + +G +Y  +L HMVSDK   RSTG  + +T+QP+ G+   GG R G
Sbjct: 1    MVSGVTGEPFPVDIYIGVVYYQRLRHMVSDKFQVRSTGPINPLTRQPIKGRKFGGGIRFG 60

Query: 1296 EMEVWCIQAYGAAYVLQEM 1314
            EME   + A+GAAY+L + 
Sbjct: 61   EMERDSLLAHGAAYLLHDR 79


>gi|222427607|dbj|BAH20764.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427621|dbj|BAH20771.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427653|dbj|BAH20787.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427655|dbj|BAH20788.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427661|dbj|BAH20791.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
          Length = 142

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 82/141 (58%), Positives = 104/141 (73%), Gaps = 1/141 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R N YGF+ETPYRKV +G+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R  
Sbjct: 61  RTNDYGFLETPYRKVINGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGE 120

Query: 650 AGEEILVPREKIDFIDASPKQ 670
            GE  L   E I ++D S +Q
Sbjct: 121 RGESGLYKPEDIHYMDVSTQQ 141


>gi|293611934|gb|ADE48411.1| RNA polymerase beta chain [Zamia katzeriana]
 gi|293611938|gb|ADE48413.1| RNA polymerase beta chain [Zamia acuminata]
 gi|293611940|gb|ADE48414.1| RNA polymerase beta chain [Zamia furfuracea]
 gi|293611942|gb|ADE48415.1| RNA polymerase beta chain [Zamia inermis]
 gi|293611944|gb|ADE48416.1| RNA polymerase beta chain [Zamia lacandona]
 gi|293611946|gb|ADE48417.1| RNA polymerase beta chain [Zamia loddigesii]
 gi|293611952|gb|ADE48420.1| RNA polymerase beta chain [Zamia standleyi]
          Length = 189

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 93/197 (47%), Positives = 132/197 (67%), Gaps = 8/197 (4%)

Query: 677 SLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVE 736
           SLIPFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G + 
Sbjct: 1   SLIPFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIM 60

Query: 737 QVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIAD 796
            +DA +I   +    +           L+ +QRSN NTC++Q+  V+ G+ V++  I+AD
Sbjct: 61  YIDAGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKLRVRQGEYVKKGQILAD 112

Query: 797 GPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKL 856
           G +T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  
Sbjct: 113 GTATLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQ 172

Query: 857 GPEEITRDIPNVSEEGL 873
           GPE IT++IP +    L
Sbjct: 173 GPERITKEIPYLDAHLL 189


>gi|46277384|gb|AAS86882.1| DNA-dependent RNA polymerase II [Tirmania pinoyi]
          Length = 500

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 78/219 (35%), Gaps = 26/219 (11%)

Query: 925  RDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDEQVILDRNIYS 984
            ++ S+ +        +   +F R  +D+ +R   +    +E   +      + L    Y 
Sbjct: 305  QEDSVIMNQSSIDRGLFRSLFYRTYMDQEKR---IGMSVVEEFEKPTRGNTLRLKHGTYD 361

Query: 985  RLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQ 1041
            +L +   +  G           K+  ++ +      R+++         ++     +  Q
Sbjct: 362  KLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRTKFHTKRDVSTPLRSTENGIVDQ 421

Query: 1042 YETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVS 1101
                                         L+ VKV +   +  Q GDK A RHG KG + 
Sbjct: 422  --------------------VMVTTNQEGLKFVKVRMRTTKIPQIGDKFASRHGQKGTIG 461

Query: 1102 RILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETH 1140
                 EDMPF  +G   D+++NP  +PSRM +  + E  
Sbjct: 462  ITYRNEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECL 500



 Score = 68.2 bits (165), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/139 (19%), Positives = 53/139 (38%), Gaps = 12/139 (8%)

Query: 819 HGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPNVSEEGL 873
            GYN EDS+++++  +   +F S+    +    +   +   E        +   +     
Sbjct: 301 SGYNQEDSVIMNQSSIDRGLFRSLFYRTYMDQEKRIGMSVVEEFEKPTRGNTLRLKHGTY 360

Query: 874 KNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPS 933
             +D+ G++  G  V+  DI++GK  P   +     ++        K    RD S  + S
Sbjct: 361 DKLDDDGLVAPGVRVSGEDIIIGKTAPIAPNQEELGQRT-------KFHTKRDVSTPLRS 413

Query: 934 GVSGTVVDVRIFNRHGIDK 952
             +G V  V +       K
Sbjct: 414 TENGIVDQVMVTTNQEGLK 432



 Score = 51.2 bits (121), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/215 (13%), Positives = 55/215 (25%), Gaps = 19/215 (8%)

Query: 485 SIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSAL 544
               + +   ++   P    NA  +      F     +    +    +  I   RR   +
Sbjct: 25  DFMMQRNMEVLEEYEPSRSPNATKI------FVNGVWVGIHRDPGFIVRTIQKLRRQGHI 78

Query: 545 GQGGVARARAGVEMRDVHPTHYGRICPAE-------TSEGHNIGLVSSLTSFARVNAYGF 597
           G               +         P         +     + L     +    +    
Sbjct: 79  GSEVSLIQDIRNREFKIFTDAGRICRPLFVVDNDPASPRRGELVLQKHHITKLEDDREAD 138

Query: 598 IETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFT------EELVFCRCAG 651
            ET             V Y+ A EEE   I      L+    F       + L   +   
Sbjct: 139 DETQRYGWQGLLTDGVVEYIDAEEEETVMIVMTPEDLETSRQFHAGYEIQQTLDPAQRVK 198

Query: 652 EEILVPREKIDFIDASPKQVVSIAASLIPFLENDD 686
             +          +  P  ++ I AS+IPF +++ 
Sbjct: 199 GAVNKFAHTWTHCEIHPSMILGICASIIPFPDHNQ 233


>gi|283806267|dbj|BAI66370.1| RNA polymerase second largest subunit [Kalmusia scabrispora]
          Length = 269

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 87/257 (33%), Gaps = 26/257 (10%)

Query: 915  AIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDDE 974
            AI      +  D+ +   S +   +    +F R   ++ +R   +    +E   +    +
Sbjct: 2    AIACYSGYNQEDSVIMNQSSIDRGLF-RSLFYRAYTEQEKR---IGVNVLEQFEKPTRMD 57

Query: 975  QVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKV 1031
             + +    Y +L +   +  G           K+  + +D                 E  
Sbjct: 58   TMRMKGGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPIPNDE--------------NKEMG 103

Query: 1032 QRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMA 1091
            Q      K    T     E+   +++             LR VKV     +  Q GDK A
Sbjct: 104  QILANHTKRDVSTPLRSTENGLVDQVLF-----TTNTEGLRFVKVRTRTTKVPQIGDKFA 158

Query: 1092 GRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKK 1151
             RHG KG +      EDMPF +DG  VD+V++P  + SRM +    E  L        ++
Sbjct: 159  SRHGQKGTIGITYRQEDMPFTRDGLGVDLVVDPHAIASRMTIAHEVECLLSKVGAINAQE 218

Query: 1152 IKSLINDYKANGDISPL 1168
              +          I  L
Sbjct: 219  GDATPFWGVTVHQICDL 235



 Score = 72.4 bits (176), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 27/133 (20%), Positives = 51/133 (38%), Gaps = 8/133 (6%)

Query: 813 VAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITR-----DIPN 867
           VA   + GYN EDS+++++  +   +F S+    +    +   +   E        D   
Sbjct: 1   VAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTEQEKRIGVNVLEQFEKPTRMDTMR 60

Query: 868 VSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
           +       +D+ GI+  G  V+  DI++GK  P          ++L         DV   
Sbjct: 61  MKGGTYDKLDDDGIVAPGVRVSGDDIIIGKTAPIPNDENKEMGQIL---ANHTKRDVSTP 117

Query: 928 SLRVPSGVSGTVV 940
                +G+   V+
Sbjct: 118 LRSTENGLVDQVL 130


>gi|48473933|dbj|BAD22732.1| DNA-directed RNA polymerase beta subunit [Arcobacter cryaerophilus]
          Length = 76

 Score =  142 bits (358), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 39/76 (51%), Positives = 51/76 (67%)

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA  VL+EMLT KSDDV GRTR Y +I  G +   +G PE+F VL KE++
Sbjct: 1    EMEVWALEAYGATAVLKEMLTTKSDDVEGRTRAYRAIANGENVPPSGVPETFFVLTKELK 60

Query: 1356 ALGLSIDLENSRTKNS 1371
            AL L +++      N 
Sbjct: 61   ALALDVEIFEEVENNE 76


>gi|63086883|gb|AAY30841.1| RNA polymerase II [Cordyceps militaris]
          Length = 229

 Score =  142 bits (358), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 79/245 (32%), Gaps = 21/245 (8%)

Query: 898  ITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSI 957
            +       +   +  + AI      +  D+ +   S +   +    +F R   D+ ++  
Sbjct: 6    MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLF-RSLFFRSYSDQEKKVG 64

Query: 958  SVEREQIELLARDKDDEQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYP 1017
                E  E               +       +  G           K+  +  +      
Sbjct: 65   LNYTEIFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPIDPETQDLGT 124

Query: 1018 RSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVF 1077
            R+   Q       ++     +  Q   + +                       ++ VKV 
Sbjct: 125  RTTAHQRRDISTPLRSTENGIVDQVIVTVNA--------------------DNVKYVKVR 164

Query: 1078 VAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIF 1137
            V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +PSRM +  + 
Sbjct: 165  VRTTKIPQIGDKFASRHGQKGTIGVTYRXEDMPFTREGVTPDIIINPHAIPSRMTIAHLI 224

Query: 1138 ETHLG 1142
            E  L 
Sbjct: 225  ECLLS 229



 Score = 82.4 bits (202), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/164 (23%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N +VA   + GYN EDS+++++  +   +F S+    +    + 
Sbjct: 3   TRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFFRSYSDQEKK 62

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E       +    +       +DE GI+  G  V+  DI++GK  P       P
Sbjct: 63  VGLNYTEIFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPID-----P 117

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
           E + L       A   RD S  + S  +G V  V +       K
Sbjct: 118 ETQDLGTR--TTAHQRRDISTPLRSTENGIVDQVIVTVNADNVK 159


>gi|63086896|gb|AAY30847.1| RNA polymerase II [Aschersonia incrassata]
          Length = 235

 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 84/255 (32%), Gaps = 29/255 (11%)

Query: 897  KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRH-GIDKNER 955
                   +  + E    R +   +   V        +     +++    +R        R
Sbjct: 1    YXQKPLATTRSMEFLKFRELPAGQNAXVAIACYSGYNQEXSVIMNQSSIDRGLFRSLFXR 60

Query: 956  SISVEREQI-----ELLARDKDDEQVILDRNIYSRLME---ILCGQNAVSGPKGFKKSTV 1007
            S S + +++     E+  +      + +    Y +L E   +  G           K+  
Sbjct: 61   SYSDQEKKVGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAP 120

Query: 1008 LSSDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKIQWGDDMP 1067
            +  +      R+   Q       ++     +      + +                    
Sbjct: 121  IDQESQDLGTRTSVHQRRDISTPLRSTENGIVDSVILTVNA------------------- 161

Query: 1068 PGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGV 1127
               ++ VKV V   +  Q GDK A RHG KG +      EDMPF ++G   DI++NP  +
Sbjct: 162  -DNVKYVKVRVRTTKVPQIGDKFASRHGQKGXIGVTYRQEDMPFTREGVTPDIIINPHAI 220

Query: 1128 PSRMNVGQIFETHLG 1142
            PSRM +  + E  L 
Sbjct: 221  PSRMTIAHLIECLLS 235



 Score = 80.1 bits (196), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/164 (19%), Positives = 58/164 (35%), Gaps = 12/164 (7%)

Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
                     +L  G+N  VA   + GYN E S+++++  +   +F S+    +    + 
Sbjct: 9   TRSMEFLKFRELPAGQNAXVAIACYSGYNQEXSVIMNQSSIDRGLFRSLFXRSYSDQEKK 68

Query: 854 TKLGPEE-----ITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTP 908
             L   E       +    +       +DE GI+  G  V+  D+++GK  P  +     
Sbjct: 69  VGLNYTEVFEKPFHQSTLRMKHGTYDKLDEDGIVAPGVRVSGEDVIIGKTAPIDQESQDL 128

Query: 909 EEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDK 952
             +             RD S  + S  +G V  V +       K
Sbjct: 129 GTRT-------SVHQRRDISTPLRSTENGIVDSVILTVNADNVK 165


>gi|208973034|dbj|BAG74360.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|208973036|dbj|BAG74361.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|208973038|dbj|BAG74362.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427565|dbj|BAH20753.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427567|dbj|BAH20754.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427589|dbj|BAH20755.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427593|dbj|BAH20757.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427595|dbj|BAH20758.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427597|dbj|BAH20759.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427599|dbj|BAH20760.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427601|dbj|BAH20761.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427603|dbj|BAH20762.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427605|dbj|BAH20763.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427609|dbj|BAH20765.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427613|dbj|BAH20767.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427615|dbj|BAH20768.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427617|dbj|BAH20769.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427619|dbj|BAH20770.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427623|dbj|BAH20772.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427625|dbj|BAH20773.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427627|dbj|BAH20774.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427629|dbj|BAH20775.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427631|dbj|BAH20776.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427633|dbj|BAH20777.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427639|dbj|BAH20780.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427641|dbj|BAH20781.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427643|dbj|BAH20782.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427645|dbj|BAH20783.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427647|dbj|BAH20784.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427649|dbj|BAH20785.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427651|dbj|BAH20786.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427657|dbj|BAH20789.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427659|dbj|BAH20790.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
 gi|222427663|dbj|BAH20792.1| RNA polymerase beta subunit [Pasteurella pneumotropica]
          Length = 142

 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 83/141 (58%), Positives = 104/141 (73%), Gaps = 1/141 (0%)

Query: 531 SLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFA 590
            LS +TH RR+SALG GG+ R RAG E+RDVH THYGR+CP ET EG NIGL++SL++FA
Sbjct: 1   PLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFA 60

Query: 591 RVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCR-C 649
           R N YGF+ETPYRKV DG+VT ++ YLSA++E N  IAQANS+LDE+  FT+  V  R  
Sbjct: 61  RTNDYGFLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGE 120

Query: 650 AGEEILVPREKIDFIDASPKQ 670
            GE  L   E I ++D S +Q
Sbjct: 121 RGESGLYKPEDIHYMDVSTQQ 141


>gi|50657983|gb|AAT79826.1| RNA polymerase beta subunit [Legionella pneumophila]
          Length = 139

 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 85/139 (61%), Positives = 109/139 (78%)

Query: 575 SEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSL 634
            EG NIGL++SL+ +AR N YGFIETP RKV +G+VT++V YLSA+EE ++YIAQ+N  L
Sbjct: 1   PEGLNIGLINSLSVYARTNEYGFIETPCRKVVNGRVTDEVEYLSAIEEVDQYIAQSNVEL 60

Query: 635 DEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGC 694
           DE G+   +LV CR   E  L   +KI+++D SPKQ+VS+AASLIPFLE+DD+NR LMG 
Sbjct: 61  DEQGNILADLVPCRHQNEFSLTTPDKINYMDVSPKQIVSVAASLIPFLEHDDANRALMGS 120

Query: 695 NMQRQAVPLLKAEAPFVGT 713
           NMQRQAVP L++E P VGT
Sbjct: 121 NMQRQAVPTLRSEKPLVGT 139


>gi|197941992|gb|ACH78601.1| RNA polymerase subunit [Polytrichum juniperinum]
          Length = 186

 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 84/188 (44%), Positives = 129/188 (68%), Gaps = 8/188 (4%)

Query: 707 EAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMK 766
           E   VGTG+ES  A  SG+  +A+++G V   DA +I   + E  +           L+K
Sbjct: 7   EKXIVGTGLESQAALDSGSVAIARQSGRVSYTDAKKITFFNNEKRIST--------NLIK 58

Query: 767 FQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDS 826
           +QRSN +TC+NQ+P V     +++  I+ADG +T  G+LALG+N+LVA+MPW GYNFED+
Sbjct: 59  YQRSNNSTCMNQKPQVTQDVFIKKGQILADGAATLKGELALGKNILVAYMPWEGYNFEDA 118

Query: 827 MLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGA 886
           +LISER++ ED++TSIHIE +E+ AR T  GPE+IT++IP++    L+++D+ G++ +G+
Sbjct: 119 ILISERLIYEDIYTSIHIERYEIEARTTSQGPEKITKEIPHLENNVLRHLDKSGLVLIGS 178

Query: 887 EVNPGDIL 894
            V  GD+L
Sbjct: 179 WVETGDVL 186


>gi|48473936|dbj|BAD22734.1| DNA-directed RNA polymerase beta subunit [Arcobacter cryaerophilus]
          Length = 76

 Score =  142 bits (357), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 39/76 (51%), Positives = 51/76 (67%)

Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
            EMEVW ++AYGA  VL+EMLT KSDDV GRTR Y +I  G +   +G PE+F VL KE++
Sbjct: 1    EMEVWALEAYGATAVLKEMLTTKSDDVDGRTRAYRAIANGENVPSSGVPETFFVLTKELK 60

Query: 1356 ALGLSIDLENSRTKNS 1371
            AL L +++      N 
Sbjct: 61   ALALDVEIFEEVENNE 76


>gi|293611930|gb|ADE48409.1| RNA polymerase beta chain [Microcycas calocoma]
          Length = 186

 Score =  142 bits (357), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 91/194 (46%), Positives = 130/194 (67%), Gaps = 8/194 (4%)

Query: 680 PFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVD 739
           PFLE++D+NR LMG NMQRQAVPL + E   VGTG+E   A  SG+A +A + G +  VD
Sbjct: 1   PFLEHNDANRALMGSNMQRQAVPLFQPEKCIVGTGLEGQAAPDSGSAAIAAQGGRIMYVD 60

Query: 740 AIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
           A +I   +    +           L+ +QRSN NTC++Q+  V+ G+ V++  I+ADG +
Sbjct: 61  AGKITSLADGDTVGT--------ELVIYQRSNNNTCMHQKLRVRQGEYVKKGQILADGAA 112

Query: 800 TDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPE 859
           T  G+L+LG+N+LVA MPW GYNFED++LISER+V ED++TS HIE + ++   T  GPE
Sbjct: 113 TLGGELSLGKNVLVAHMPWEGYNFEDAILISERLVYEDIYTSFHIERYGIVTCMTSQGPE 172

Query: 860 EITRDIPNVSEEGL 873
            IT++IP++    L
Sbjct: 173 RITKEIPHLDAHLL 186


>gi|55650638|emb|CAF31384.1| RNA polymerase B subunit [Aphanizomenon flos-aquae 1tu37s13]
          Length = 194

 Score =  142 bits (357), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 88/194 (45%), Positives = 120/194 (61%), Gaps = 14/194 (7%)

Query: 634 LDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMG 693
           LDE G      V  R   +    P E++D++  SP Q+VS+A S+IPFLE+DD+NR LMG
Sbjct: 1   LDEYGFIKGPNVPVRYRQDWTTTPPEQVDYVAVSPVQIVSVATSMIPFLEHDDANRALMG 60

Query: 694 CNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIR------- 746
            NMQRQAVPLLK E P VGTG+E+  A+ SG  IV++  G V  VDA  I +R       
Sbjct: 61  SNMQRQAVPLLKPERPLVGTGLEAQAARDSGMVIVSRTDGDVVYVDATEIRVRVGGQRLV 120

Query: 747 -------SVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPS 799
                       L         Y+L K+QRSNQ+TC+NQ+PLV++G++V    ++ADG S
Sbjct: 121 VGDEEKTGDREQLRTDKPQELKYKLSKYQRSNQDTCLNQKPLVRIGEKVVAGQVLADGSS 180

Query: 800 TDLGDLALGRNMLV 813
           T+ G+LALG+N++V
Sbjct: 181 TEGGELALGQNIVV 194


>gi|260593971|gb|ACX46280.1| RpoB [Pseudomonas fluorescens SBW25]
 gi|260593983|gb|ACX46286.1| RpoB [Pseudomonas fluorescens SBW25]
          Length = 126

 Score =  142 bits (357), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 73/126 (57%), Positives = 96/126 (76%)

Query: 520 SQLSQLEEHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHN 579
           SQLSQ     N LS ITH RR+SALG GG+ R RAG E+RDVHPTHYGR+CP ET EG N
Sbjct: 1   SQLSQFMGQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 60

Query: 580 IGLVSSLTSFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGS 639
           IGL++SL ++AR N YGF+E+PYR V D  VT+++V+LSA+EE +  IAQA++++++   
Sbjct: 61  IGLINSLAAYARTNQYGFLESPYRVVKDALVTDEIVFLSAIEEADHVIAQASATMNDKKV 120

Query: 640 FTEELV 645
             +ELV
Sbjct: 121 LIDELV 126


  Database: nr
    Posted date:  May 13, 2011  4:10 AM
  Number of letters in database: 999,999,932
  Number of sequences in database:  2,987,209
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 13, 2011  4:17 AM
  Number of letters in database: 999,998,956
  Number of sequences in database:  2,896,973
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 13, 2011  4:23 AM
  Number of letters in database: 999,999,979
  Number of sequences in database:  2,907,862
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 13, 2011  4:29 AM
  Number of letters in database: 999,999,513
  Number of sequences in database:  2,932,190
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 13, 2011  4:33 AM
  Number of letters in database: 792,586,372
  Number of sequences in database:  2,260,650
  
Lambda     K      H
   0.314    0.133    0.431 

Lambda     K      H
   0.267   0.0406    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,827,515,655
Number of Sequences: 13984884
Number of extensions: 740928124
Number of successful extensions: 1457979
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 16151
Number of HSP's successfully gapped in prelim test: 2732
Number of HSP's that attempted gapping in prelim test: 1376793
Number of HSP's gapped (non-prelim): 41781
length of query: 1386
length of database: 4,792,584,752
effective HSP length: 152
effective length of query: 1234
effective length of database: 2,666,882,384
effective search space: 3290932861856
effective search space used: 3290932861856
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 88 (38.5 bits)